@article {pmid40576334, year = {2025}, author = {Lee, EM and Srinivasan, S and Purvine, SO and Fiedler, TL and Leiser, OP and Proll, SC and Minot, SS and Djukovic, D and Raftery, D and Johnston, C and Fredricks, DN and Deatherage Kaiser, BL}, title = {Syntrophic bacterial and host-microbe interactions in bacterial vaginosis.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf055}, pmid = {40576334}, issn = {1751-7370}, abstract = {Bacterial vaginosis (BV) is a common, polymicrobial condition of the vaginal microbiota that is associated with symptoms such as malodor and excessive discharge, along with increased risk of various adverse sequelae. Host-bacteria and bacteria-bacteria interactions are thought to contribute to the condition, but many of these functions have yet to be elucidated. Using untargeted metaproteomics, we identified 1068 host and 1418 bacterial proteins in a set of cervicovaginal lavage samples collected from 20 participants with BV and 9 who were negative for the condition. We identified Dialister micraerophilus as a major producer of malodorous polyamines and identified a syntrophic interaction between this organism and Fannyhessea vaginae that leads to increased production of putrescine, a metabolite characteristic of BV. Although formate synthesis has not previously been noted in BV, we discovered diverse bacteria associated with the condition express pyruvate formate-lyase enzymes in vivo and confirm these organisms secrete formic acid in vitro. Sodium hypophosphite efficiently inhibited this function in multiple taxa. We also found that the fastidious organism Coriobacteriales bacterium DNF00809 can metabolize formic acid secreted by Gardnerella vaginalis, representing another syntrophic interaction. We noted an increased abundance of the host epithelial repair protein transglutaminase 3 in the metaproteomic data, which we confirmed by enzyme-linked immunosorbent assay. Other proteins identified in our samples implicate Finegoldia magna and Parvimonas micra in the production of malodorous trimethylamine. Some bacterial proteins identified represent novel targets for future therapeutics to disrupt BV communities and promote vaginal colonization by commensal lactobacilli.}, }
@article {pmid40573780, year = {2025}, author = {Zhang, S and Luo, Z and Peng, J and Wu, X and Meng, X and Qin, Y and Zhu, F}, title = {Analysis of Cadmium Accumulation Characteristics Affected by Rhizosphere Bacterial Community of Two High-Quality Rice Varieties.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {12}, pages = {}, doi = {10.3390/plants14121790}, pmid = {40573780}, issn = {2223-7747}, support = {2024YFD2301400//the National Key Research and Development Program of China/ ; 2024CX09//the Agricultural Science and Technology Innovation Project of Hunan Province, China/ ; }, abstract = {Cadmium-contaminated rice poses serious health risks through the bioaccumulation of Cd (cadmium) from soil to edible grains. Cd contamination disrupts soil microbial ecology and alters microbial diversity. However, the role of cultivar-specific rhizosphere microbial communities in modulating Cd uptake remains unclear. In this study, we aimed to elucidate the mechanism underlying variety-dependent rhizosphere microecological remodeling and Cd accumulation in two independently selected late rice varieties, Yuzhenxiang (YZX) and Xiangwanxian 12 (XWX12). Combining physiological and metagenomic analyses, we revealed variety-specific correlations between root Cd accumulation and dynamic changes in soil pH, soil available phosphorus, and rhizosphere bacteria. The key bacterial genera (Variibacter, Nitrospira) showed differential enrichment patterns under Cd stress. In contrast, Galella and Anaeromyxobacter likely reduce Cd bioavailability by modulating phosphorus availability. Overall, this study elucidates that rice cultivars indirectly shape Cd accumulation patterns via rhizosphere microbial remodeling, providing novel insights for microbial remediation strategies in Cd-contaminated farmland.}, }
@article {pmid40572127, year = {2025}, author = {Mohammadi, T and Ely, B}, title = {Dolichocephalovirinae Phages Exist as Episomal Pseudolysogens Across Diverse Soil Bacteria.}, journal = {Microorganisms}, volume = {13}, number = {6}, pages = {}, pmid = {40572127}, issn = {2076-2607}, abstract = {Interactions between bacteria and bacteriophages are important for the maintenance of soil communities. In this study, we characterized the giant bacteriophages found within diverse soil bacteria and 14 additional phages isolated directly from soil samples. Based on their genome sizes and genetic composition, we concluded that these phages belong to the Dolichocephalovirinae subfamily. In addition, we used pulsed-field gel electrophoresis to show that the genomes of these phages were present as episomal pseudolysogens in the cytoplasm of their host cells. These findings suggest that episomal phages are important components of soil microbial ecosystems. Understanding the interactions between bacteriophages and bacteria is essential for microbial ecology, as they influence nutrient cycling, community composition, and host evolution. Furthermore, these phage-bacteria dynamics offer potential applications in plant disease control, as bacteriophages could serve as biocontrol agents against soilborne pathogens, promoting sustainable agricultural practices.}, }
@article {pmid40569388, year = {2025}, author = {Dellicour, S and Gámbaro, F and Jacquot, M and Lequime, S and Baele, G and Gilbert, M and Pybus, OG and Suchard, MA and Lemey, P}, title = {Comparative performance of viral landscape phylogeography approaches.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {26}, pages = {e2506743122}, doi = {10.1073/pnas.2506743122}, pmid = {40569388}, issn = {1091-6490}, mesh = {Phylogeography/methods ; *RNA Viruses/genetics ; Phylogeny ; Genome, Viral ; Computer Simulation ; }, abstract = {The rapid evolution of RNA viruses implies that their evolutionary and ecological processes occur on the same time scale. Genome sequences of these pathogens therefore can contain information about the processes that govern their transmission and dispersal. Landscape phylogeographic approaches use phylogeographic reconstructions to investigate the impact of environmental factors and variables on the spatial spread of viruses. Here, we extend and improve existing approaches and develop three novel landscape phylogeographic methods that can test the impact of continuous environmental factors on the diffusion velocity of viral lineages. In order to evaluate the different methods, we also implemented two simulation frameworks to test and compare their statistical performance. The results enable us to formulate clear guidelines for the use of three complementary landscape phylogeographic approaches that have sufficient statistical power and low rates of false positives. Our open-source methods are available to the cientific community and can be used to investigate the drivers of viral spread, with potential benefits for understanding virus epidemiology and designing tailored intervention strategies.}, }
@article {pmid40569073, year = {2025}, author = {Kobiałka, M and Świerczewski, D and Walczak, M and Urbańczyk, W}, title = {Extremely distinct microbial communities in closely related leafhopper subfamilies: Typhlocybinae and Eurymelinae (Cicadellidae, Hemiptera).}, journal = {mSystems}, volume = {}, number = {}, pages = {e0060325}, doi = {10.1128/msystems.00603-25}, pmid = {40569073}, issn = {2379-5077}, abstract = {UNLABELLED: Among the Hemiptera insects, a widespread way of feeding is sucking sap from host plants. Due to their nutrient-poor diet, these insects enter into obligate symbiosis with their microorganisms involved in the synthesis of components essential for host survival. However, within the Cicadellidae family, there is a relatively large group of mesophyll feeders-Typhlocybinae-that is considered to be devoid of obligate symbiotic companions. In this work, we examine the composition of microorganisms in this subfamily and compare the results with their close relatives-the Eurymelinae subfamily. To study the microbiome, we used high-throughput next-generation sequencing (NGS, Illumina) and advanced microscopic techniques, such as transmission electron microscopy (TEM) and fluorescence in situ hybridization (FISH), in a confocal microscope. In the bodies of Typhlocybinae insects, we did not detect the presence of microorganisms deemed to be obligate symbionts. Their microbial communities consist of facultative symbionts, mainly alphaproteobacteria such as Wolbachia or Rickettsia as well as others that can be considered as facultative, including Spiroplasma, Acidocella, Arsenophonus, Sodalis, Lariskella, Serratia, Cardinium, and Asaia. On the other hand, the Eurymelinae group is characterized by a high diversity of microbial communities, both obligate and facultative, similar to other Cicadomorpha. We find co-symbionts involved in the synthesis of essential amino acids such as Karelsulcia, betaproteobacteria Nasuia, or gammaproteobacteria Sodalis. In other representatives, we observed symbiotic yeast-like fungi from the family Ophiocordycipitaceae or Arsenophonus bacteria inhabiting the interior of Karelsulcia bacteria. Additionally, we investigated some aspects of symbiont transmission and the phylogeny of symbiotic organisms and their hosts.<br><br>IMPORTANCE: The Typhlocybinae and Eurymelinae leafhoppers differ significantly in their symbiotic communities. They have different diets, as Typhlocybinae insects feed on parenchyma, which is richer in nutrients, while Eurymelinae, like most representatives of Auchenorrhyncha, consume sap from the phloem fibers of plants. Our work presents comprehensive studies of 42 species belonging to the two above-mentioned, and so far poorly known, Cicadomorpha subfamilies. Phylogenetic studies indicate that the insects from the studied groups have a common ancestor. The diet shift in the Typhlocybinae leafhoppers contributed to major changes in the composition of microorganisms inhabiting the body of these insects. Research on the impact of diet on the microbiome and the subsequent consequences on the evolution and adaptation of organisms plays an important role in the era of climate change.}, }
@article {pmid40568985, year = {2025}, author = {Zhao, J and Brandt, G and Gronniger, JL and Wang, Z and Li, J and Hunt, DE and Rodriguez-R, LM and Hatt, JK and Konstantinidis, KT}, title = {Quantifying the contribution of the rare biosphere to natural disturbances.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf129}, pmid = {40568985}, issn = {1751-7370}, abstract = {Understanding how populations respond to disturbances represents a major goal for microbial ecology. While several hypotheses have been advanced to explain microbial community compositional changes in response to disturbance, appropriate data to test these hypotheses is scarce, due to the challenges in delineating rare vs. abundant taxa and generalists vs. specialists, a prerequisite for testing the theories. Here, we operationally define these two key concepts by employing the patterns of coverage of a (target) genome by a metagenome to identify rare populations, and by borrowing the proportional similarity index (PS index) from macroecology to identify generalists. We applied these concepts to time-series (field) metagenomes from the Piver's Island Coastal Observatory (PICO) to establish that coastal microbial communities are resilient to major perturbations such as tropical cyclones and (uncommon) cold or warm temperature events, in part due to the response of rare populations. Therefore, these results provide support for the insurance hypothesis [i.e., the rare biosphere has the buffering capacity to mitigate the effects of disturbance]. Additionally, generalists appear to contribute proportionally more than specialists to community adaptation to perturbations like warming, supporting the disturbance-specialization hypothesis [i.e., disturbance favors generalists]. Several of these findings were also observed in replicated laboratory mesocosms that aimed to simulate disturbances such as a rain-driven washout of microbial cells and a labile organic matter release from a phytoplankton bloom. Taken together, our results advance understanding of the mechanisms governing microbial population dynamics under changing environmental conditions and have implications for ecosystem modeling.}, }
@article {pmid40567269, year = {2025}, author = {Mohamadi Nasrabadi, A and Eckstein, D and Mettke, P and Ghanem, N and Kallies, R and Schmidt, M and Mothes, F and Schaefer, T and Graefe, R and Bandara, CD and Maier, M and Liebert, UG and Richnow, H and Herrmann, H}, title = {A Virus Aerosol Chamber Study: The Impact of UVA, UVC, and H2O2 on Airborne Viral Transmission.}, journal = {Environment &amp; health (Washington, D.C.)}, volume = {3}, number = {6}, pages = {648-658}, pmid = {40567269}, issn = {2833-8278}, abstract = {The COVID-19 pandemic highlighted the urgent need to control airborne virus transmission, particularly in indoor environments with limited ventilation. This study evaluates the effectiveness of UVA and UVC irradiation, along with hydrogen peroxide (H2O2), in inactivating aerosolized viruses. A 19 m[3] virus aerosol simulation chamber, replicating indoor conditions, was used to simulate human respiratory emissions by aerosolizing Escherichia phage T4 (T4 phages) embedded in a pig mucin medium that mimics respiratory aerosols. Results showed a clear, dose-dependent reduction in viral genome copies with UVC exposure, where a dose of 129.9 mJ/cm[2] reduced over 99% of the viral genome copies. Although less efficient, UVA still contributed to virus inactivation, reducing detectable phages to 20% at 513.30 J/cm[2]. Mucin provided a protective effect, making virus removal more challenging. Hydrogen peroxide enhanced disinfection, with 1.6 ppm reducing viral genome copies by 78%, and higher concentrations (up to 16 ppm) achieving over 99% reduction in the dark condition. The combination of UVA/UVC with H2O2 further enhanced disinfection, eliminating detectable virus genome copies entirely. These findings underscore the potential for using combined UV light and chemical treatments to effectively mitigate airborne viral transmission in enclosed spaces.}, }
@article {pmid40566942, year = {2025}, author = {Kara, K and Yilmaz Öztaş, S and Baytok, E}, title = {In Vitro Ruminal Metagenomic Profiles and Ruminal Fermentation Variables of Aromatic Plant Pulps.}, journal = {Veterinary medicine and science}, volume = {11}, number = {4}, pages = {e70447}, doi = {10.1002/vms3.70447}, pmid = {40566942}, issn = {2053-1095}, support = {TSA-2023-13007//Erciyes University Scientific Research Projects Unit/ ; }, mesh = {*Fermentation ; *Rumen/microbiology/metabolism/physiology ; Animals ; Cattle ; Metagenomics ; Animal Feed/analysis ; *Metagenome ; Gastrointestinal Microbiome ; Digestion ; }, abstract = {BACKGROUND: Aromatic plant residues remaining after aromatic oil extraction represent a promising alternative feed source due to their rich bioactive compound content and fibrous structure. However, their fermentative behaviour and microbial degradability in the rumen require evaluation.<br><br>OBJECTIVE: This study aimed to determine the nutrient composition, in vitro ruminal gas production, digestibility characteristics and fermentation end-products of aromatic plant pulps (sage, thyme, lavender and yarrow) obtained via hydrodistillation.<br><br>METHODS: Dried pulps were analysed for nutrient contents and subjected to in vitro ruminal fermentation for 24&#xa0;h. Gas production estimated metabolizable energy (ME), net energy for lactation (NEL), organic matter digestibility (OMd), ammonia nitrogen (NH3-N) and short-chain fatty acid (SCFA) profiles were evaluated. Microbial community composition was assessed via 16S rRNA-based metagenomics.<br><br>RESULTS: Yarrow pulp had the highest gas production, ME, NEL, OMd and SCFA concentrations (AA, BA, IVA, T-SCFA) (p&#xa0;<&#xa0;0.05). Thyme pulp exhibited the highest NH3-N levels (75.14&#xa0;mg/L), suggesting high rumen-degradable protein content. Sage pulp had the lowest NH3-N levels (60.93&#xa0;mg/L). Microbial composition shifted with fibre content; higher lignin (in lavender) was associated with lower Bacteroidota and higher Firmicutes abundance. Methanogenic archaea (Methanobrevibacter) were least abundant in thyme pulp (p&#xa0;<&#xa0;0.05).<br><br>CONCLUSION: Due to their fermentability and favourable microbial responses, aromatic plant pulps, particularly yarrow, show promise as functional ruminant feed ingredients. These byproducts may enhance ruminal fibre utilization while modulating microbial ecology and reducing methane-associated archaea.}, }
@article {pmid40564363, year = {2025}, author = {Luo, G and Cheng, Y and Xu, Y and Liu, J and Yang, W and Liu, J and Guo, B and Zhu, H}, title = {Monochromatic Light Impacts the Growth Performance, Intestinal Morphology, Barrier Function, Antioxidant Status, and Microflora of Yangzhou Geese.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/ani15121815}, pmid = {40564363}, issn = {2076-2615}, support = {32202622//National Natural Science Foundation of China/ ; 32102542//National Natural Science Foundation of China/ ; CX(24)1012//Jiangsu Agricultural Science and Technology Innovation Fund/ ; 2025SKLAB6-17//Open project of State Key Laboratory of Animal Biotech Breeding/ ; }, abstract = {This study investigates the effect of monochromatic light on the body weight (BW), melatonin concentration and its receptors expression levels, intestinal health, and gut microorganisms of Yangzhou geese. Green light (GL) significantly increased BW, melatonin and its receptor expression levels, villus height (VH) and villus height/crypt depth (VH/CD) ratio, superoxide dismutase (SOD), catalase (CAT), and total antioxidant capacity (T-AOC) activities, as well as the abundance of Synergistota and Prevotellaceae_UCG-001, compared with white light (WL). Blue light (BL) significantly increased the mRNA expression of melatonin membrane receptor 1a (Mel1a) and nuclear receptor 1α (RORα), VH and VH/CD ratio, CAT activity, cecal microbes diversity, and decreased malondialdehyde (MDA) levels. Red light (RL) significantly decreased average daily feed intake, reduced the abundances of Synergistota and Prevotellaceae_UCG-001, and increased Mel1a and RORα mRNA expression levels, MDA content, and cecum microbial diversity. Moreover, melatonin levels were significantly higher in the GL and BL groups compared to RL. Furthermore, the mRNA expression levels of Claudin-10, Occludin, and occludens-1 (ZO-1) were significantly upregulated under GL or BL exposures compared to the WL group, whereas RL only enhanced the expression levels of ZO-1. Spearman's correlation analysis revealed that the relative abundance of Prevotellaceae_UCG-001 exhibited positive correlations with BW, melatonin and its receptors expression, gut health, and antioxidant capacity. Overall, these findings suggested that GL exposure enhanced melatonin synthesis and its receptors expression, modulated intestinal homeostasis and microbial ecology, and ultimately increased goose BW.}, }
@article {pmid40562244, year = {2025}, author = {Costa, BF and Sawaya, C and Buren, JV and Smith, AL}, title = {Investigating anaerobic digestion microbiome resilience to high PFOA and PFOS mixtures during cometabolism.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132877}, doi = {10.1016/j.biortech.2025.132877}, pmid = {40562244}, issn = {1873-2976}, abstract = {Anaerobic digestion (AD) is a reducing environment with high microbial diversity and potential for biotransformation of PFAS. Yet, their fate and impact on the microbial community remains poorly understood. This study evaluated the long-term impact (100 d) of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) spiked at10 mg/L (low) and 100 mg/L (high), respectively. Although resilient to complete system failure, high PFAS concentrations disrupted AD, evidenced by 25-50 % reduction in methane content, 45 %-48 % reduction in cumulative biogas production, and accumulation of butyric acid. No significant decrease in PFAS concentration was observed in the liquid fraction after 100 d relative to the kill controls, indicating PFAS adsorption behavior. However, PFAS concentrations were temporally variable. Microbial community analysis revealed enrichment of notable AD groups, such as Firmicutes, Synergistetes, and Methanomassillicoccus phyla in high PFAS reactors, which underscores the potential for the microbiome adaptation and informs future strategies for PFAS-contaminated sludge treatment.}, }
@article {pmid40561955, year = {2025}, author = {Yasin, MU and Muhammad, S and Chen, N and Hannan, F and Afzal, M and Haider, Z and Ali, B and Ahmad, I and Rehman, M and Gan, Y}, title = {Nano-engineered biochar enhances soil microbial interactions and maize transcriptomic pathways for cadmium detoxification.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {139029}, doi = {10.1016/j.jhazmat.2025.139029}, pmid = {40561955}, issn = {1873-3336}, abstract = {Cadmium (Cd) contamination threatens agroecosystems and food security by degrading soil health, inducing plant oxidative stress, and reducing crop yields. Sustainable strategies integrating biochar (BC) with nanoparticles (NPs) for Cd immobilization and soil-plant-microbe restoration remain underexplored. Here, we demonstrate the efficacy of BC, nano-silicon (nSi), and nano-iron (nFe) to immobilize Cd, improve soil health and reprogram maize stress responses in Cd-contaminated soil. Soil Cd bioavailability, microbial networks, and maize transcriptomes were analyzed under varying BC-nSi-nFe formulations. Among these formulations, the BC + 25 % nSi + 75 % nFe + Cd (T6) composite reduced bioavailable Cd by 21 %, raised soil pH from 6.21 to 6.98, and enhanced soil enzyme activities (118-139 %). T6 improved maize biomass (115-119 %), reduced shoot Cd accumulation (78 %), and suppressed oxidative stress (67-75 % ROS reduction). This study presents transcriptomic evidence showing that BC-NPs composites mitigate Cd stress and modulate maize antioxidant defense and phytohormone signaling pathways, offering new insights into the molecular mechanisms underlying improved plant resilience. Soil microbial networks shifted toward metal-resistant taxa, with enriched glutathione metabolism and nitrogen fixation. BC-NPs composites offer a multidimensional remediation strategy, integrating nanomaterial science, microbial ecology, and plant molecular biology to mitigate Cd toxicity. This approach enhances soil-plant resilience, supporting sustainable agriculture in contaminated ecosystems.}, }
@article {pmid40561631, year = {2025}, author = {Ma, X and Li, Y and Niu, L and Grossart, HP and Shang, J and Zheng, J and Wu, J}, title = {Salinity regulates nutrient cycling via top-down and bottom-up forces in artificial cut-off tidal channels: Insights from multitrophic microbiota.}, journal = {Water research}, volume = {285}, number = {}, pages = {124037}, doi = {10.1016/j.watres.2025.124037}, pmid = {40561631}, issn = {1879-2448}, abstract = {Artificial cut-off of natural tidal meanders for flood control has substantially altered microbial communities and their role in nutrient cycling, yet the lack of comprehensive investigations into these specific anthropogenic impacts introduces greater uncertainty regarding the resultant water quality of nutrient-enriched estuaries. Here, we investigated how planktonic multitrophic microbiota and their mediated nutrient cycling respond to artificial meander cut-off using the environmental DNA (eDNA) approach. Results showed that despite the decline in α diversity of multitrophic microbiota, the nutrient cycling potential of the water column was enhanced 2.91-fold in the straight tidal channel. The artificial cut-off restructured the microbial food web, with trophic transfer efficiency from basal species to protozoa increasing. Salinity was identified to be the key environmental driver, mitigating the negative impact of decreased biodiversity on estuarine nutrient cycling potential by intensifying protozoan predation on heterotrophic bacteria (top-down forces). Additionally, salinity further enhanced environmental selection (bottom-up forces), reducing heterotrophic bacterial diversity while promoting the proliferation of functional microbial taxa, such as Comamonadaceae, Chitinophagaceae, and Rhodocyclaceae. This study offers novel insights into nutrient cycling in artificial straight tidal channels and provides critical foundations for optimizing restoration and management strategies in anthropogenically modified tidal river.}, }
@article {pmid40560449, year = {2025}, author = {de Meireles, DA and Souza, T and de A A Carneiro, K and da S Fraga, V and de O Dias, B and da S Batista, D and Martins, EL and de Lima, AFL and Dos Santos Nascimento, G and Campos, MCC}, title = {Treated Wastewater Irrigation Enhances Plant Biomass, Soil Fertility, and Rhizosphere Microbial Activity in C4 and CAM species Grown on a Degraded Planosol.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {7}, pages = {804}, pmid = {40560449}, issn = {1573-2959}, mesh = {*Wastewater/chemistry ; *Agricultural Irrigation/methods ; *Soil Microbiology ; *Soil/chemistry ; *Rhizosphere ; Biomass ; *Waste Disposal, Fluid/methods ; Brazil ; }, abstract = {The Brazilian semi-arid region, marked by erratic rainfall and severely degraded soils, presents critical challenges for sustainable agriculture. In this context, the reuse of treated domestic wastewater-collected from a septic tank and anaerobic filter system-offers a promising strategy to enhance plant productivity and rehabilitate soil conditions, particularly within the Caatinga biome. This study evaluated the long-term (four-year) effects of irrigation with pure water versus treated domestic wastewater on plant dry biomass, soil fertility, and rhizospheric microbial activity in a degraded Planosol. Two plant types were assessed: a C4 species (Mimosa caesalpiniifolia) and a CAM species (Opuntia atropes). Results demonstrated that treated wastewater irrigation significantly increased dry biomass, with a 12.18% increase in the C4 species and a 29.33% increase in the CAM species. Soil chemical fertility improved notably, with wastewater application raising soil pH by 5.0%, increasing soil organic carbon by 87.9%, and enhancing nutrient availability, including nitrogen, potassium, magnesium, and sodium. A 37.5% reduction in exchangeable aluminum further indicated mitigation of soil acidity. Microbial responses varied between species: while soil respiration increased in both rhizospheres-more prominently in CAM species-microbial biomass carbon rose significantly in the C4 rhizosphere but declined in CAM, suggesting species-specific microbial interactions. These findings support the potential of treated domestic wastewater as a nutrient-rich, low-cost irrigation alternative for improving plant performance and soil quality in semi-arid degraded lands. Nevertheless, potential risks-including salinity build-up and pathogen persistence-necessitate long-term monitoring and further environmental safety assessments. By integrating plant physiology, soil chemistry, and microbial ecology, this study offers a comprehensive approach to evaluating wastewater reuse as a sustainable agricultural and ecological restoration practice in the Caatinga biome.}, }
@article {pmid28732554, year = {2017}, author = {De Vuyst, L and Van Kerrebroeck, S and Leroy, F}, title = {Microbial Ecology and Process Technology of Sourdough Fermentation.}, journal = {Advances in applied microbiology}, volume = {100}, number = {}, pages = {49-160}, doi = {10.1016/bs.aambs.2017.02.003}, pmid = {28732554}, issn = {0065-2164}, mesh = {Bread/analysis/*microbiology ; Fermentation ; Food Handling ; Lactobacillus/genetics/*metabolism ; *Microbiota ; Triticum/*metabolism/microbiology ; Yeasts/genetics/*metabolism ; }, abstract = {From a microbiological perspective, sourdough is to be considered as a specific and stressful ecosystem, harboring yeasts and lactic acid bacteria (LAB), that is used for the production of baked goods. With respect to the metabolic impact of the sourdough microbiota, acidification (LAB), flavor formation (LAB and yeasts), and leavening (yeasts and heterofermentative LAB species) are most noticeable. Three distinct types of sourdough fermentation processes can be discerned based on the inocula applied, namely backslopped ones (type 1), those initiated with starter cultures (type 2), and those initiated with a starter culture followed by backslopping (type 3). A sourdough-characteristic LAB species is Lactobacillus sanfranciscensis. A sourdough-characteristic yeast species is Candida humilis. Although it has been suggested that the microbiota of a specific sourdough may be influenced by its geographical origin, region specificity often seems to be an artefact resulting from interpretation of the research data, as those are dependent on sampling, isolation, and identification procedures. It is however clear that sourdough-adapted microorganisms are able to withstand stress conditions encountered during their growth. Based on the technological setup, type 0 (predoughs), type I (artisan bakery firm sourdoughs), type II (industrial liquid sourdoughs), and type III sourdoughs (industrial dried sourdoughs) can be distinguished. The production of all sourdoughs, independent of their classification, depends on several intrinsic and extrinsic factors. Both the flour (type, quality status, etc.) and the process parameters (fermentation temperature, pH and pH evolution, dough yield, water activity, oxygen tension, backslopping procedure and fermentation duration, etc.) determine the dynamics and outcome of (backslopped) sourdough fermentation processes.}, }
@article {pmid40559796, year = {2025}, author = {Popov, IV and Peshkova, DA and Lukbanova, EA and Tsurkova, IS and Emelyantsev, SA and Krikunova, AA and Malinovkin, AV and Chikindas, ML and Ermakov, AM and Popov, IV}, title = {Gut Microbiota Dynamics in Hibernating and Active Nyctalus noctula: Hibernation-Associated Loss of Diversity and Anaerobe Enrichment.}, journal = {Veterinary sciences}, volume = {12}, number = {6}, pages = {}, doi = {10.3390/vetsci12060559}, pmid = {40559796}, issn = {2306-7381}, support = {23-14-00316//Russian Science Foundation/ ; 075-10-2025-017//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Hibernation in mammals entails profound physiological changes that are known to impact host-associated microbial communities, yet its effects on the gut microbiota of synanthropic bats remain underexplored. In this study, we investigated the gut bacterial composition and diversity of Nyctalus noctula before and during hibernation using high-throughput 16S rRNA amplicon sequencing. Fecal samples from individually banded bats were collected under controlled conditions at a rehabilitation center and analyzed for alpha and beta diversity, as well as differential taxonomic abundance. Hibernation was associated with a marked reduction in microbial diversity according to the Shannon and Simpson indices and a distinct restructuring of gut communities based on the Bray-Curtis dissimilarity index. Active bats exhibited a diverse microbiota enriched in facultative anaerobes, including Lactococcus, Enterococcus, and Escherichia-Shigella, while hibernating individuals were dominated by obligate anaerobes, such as Romboutsia and Paeniclostridium. These findings suggest a contraction and functional specialization of the gut microbiota during torpor, potentially reflecting adaptations to fasting, hypothermia, and reduced gut motility. Our results demonstrate that the bat's gut microbiome is highly responsive to physiological status and underscore the importance of microbial ecology for understanding the host's energy balance and health under seasonal contexts.}, }
@article {pmid40559651, year = {2025}, author = {Wimmer, BC and Dwan, C and De Medts, J and Duysburgh, C and Rotsaert, C and Marzorati, M}, title = {Undaria pinnatifida Fucoidan Enhances Gut Microbiome, Butyrate Production, and Exerts Anti-Inflammatory Effects in an In Vitro Short-Term SHIME[®] Coupled to a Caco-2/THP-1 Co-Culture Model.}, journal = {Marine drugs}, volume = {23}, number = {6}, pages = {}, doi = {10.3390/md23060242}, pmid = {40559651}, issn = {1660-3397}, support = {n.a.//Marinova Pty Ltd., 249 Kennedy Drive, Cambridge, TAS 7170, Australia/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Polysaccharides/pharmacology/isolation &amp; purification ; *Undaria/chemistry ; *Anti-Inflammatory Agents/pharmacology ; Caco-2 Cells ; Coculture Techniques ; *Butyrates/metabolism ; THP-1 Cells ; Colon/microbiology/drug effects ; Feces/microbiology ; Cytokines/metabolism ; Adult ; Fatty Acids, Volatile/metabolism ; Edible Seaweeds ; }, abstract = {Fucoidans have demonstrated a wide range of bioactivities including immune modulation and benefits in gut health. To gain a deeper understanding on the effects of fucoidan from Undaria pinnatifida (UPF) on the colonic microbiome, the short-term Simulator of the Human Intestinal Microbial Ecosystem[®], a validated in vitro gut model, was applied. Following a three-week intervention period on adult faecal samples from three healthy donors, microbial community activity of the colonic microbiota was assessed by quantifying short-chain fatty acids while composition was analysed utilising 16S-targeted Illumina sequencing. Metagenomic data were used to describe changes in community structure. To assess the secretion of cytokines, co-culture experiments using Caco-2 and THP1-Blue™ cells were performed. UPF supplementation over a three-week period had a profound butyrogenic effect while also enriching colonic microbial diversity, consistently stimulating saccharolytic genera, and reducing genera linked with potentially negative health effects in both regions of the colon. Mild immune modulatory effects of UPF were also observed. Colonic fermentation of UPF showed anti-inflammatory properties by inducing the secretion of the anti-inflammatory cytokines IL-6 and IL-10 in two out of three donors in the proximal and distal colon. In conclusion, UPF supplementation may provide significant gut health benefits.}, }
@article {pmid40558970, year = {2025}, author = {Vieira, RIM and Peixoto, ADS and Monclaro, AV and Ricart, CAO and Filho, EXF and Miller, RNG and Gomes, TG}, title = {Fungal Coculture: Unlocking the Potential for Efficient Bioconversion of Lignocellulosic Biomass.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {6}, pages = {}, doi = {10.3390/jof11060458}, pmid = {40558970}, issn = {2309-608X}, support = {00193-00002388/2023-21//Foundation for Research Support of the Federal District/ ; }, abstract = {Microbial decomposition of persistent natural compounds such as phenolic lignin and polysaccharides in plant cell walls plays a crucial role in the global carbon cycle and underpins diverse biotechnological applications. Among microbial decomposers, fungi from the Ascomycota and Basidiomycota phyla have evolved specialized mechanisms for efficient lignocellulosic biomass degradation, employing extracellular enzymes and synergistic fungal consortia. Fungal coculture, defined as the controlled, axenic cultivation of multiple fungal species or strains in a single culture medium, is a promising strategy for industrial processes. This approach to biomass conversion offers potential for enhancing production of enzymes, biofuels, and other high-value bioproducts, while enabling investigation of ecological dynamics and metabolic pathways relevant to biorefinery operations. Lignocellulosic biomass conversion into fuels, energy, and biochemicals is central to the bioeconomy, integrating advanced biotechnology with sustainable resource use. Recent advancements in -omics technologies, including genomics, transcriptomics, and proteomics, have facilitated detailed analysis of fungal metabolism, uncovering novel secondary metabolites and enzymatic pathways activated under specific growth conditions. This review highlights the potential of fungal coculture systems to advance sustainable biomass conversion in alignment with circular bioeconomy goals.}, }
@article {pmid40557448, year = {2025}, author = {Lingua, MS and Sabatino, ME and Cuatrin, A and Salvucci, E and Blajman, JE and Páez, RB and Wunderlin, DA and Baroni, MV}, title = {From waste to worth: stability, bioaccessibility, and cellular antioxidant activity of microencapsulated red grape pomace phenolics.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.70010}, pmid = {40557448}, issn = {1097-0010}, support = {//This work was supported by the National Institute of Agricultural Technology (INTA, Argentina) (Projects 2019-PD-I152-A537 and 2019-PE-I150-A5) and the National Agency of Scientific and Technological Promotion (FONCyT, Argentina), and Argentine Wine Corporation (COVIAR) (Project PICTO-COVIAR-2017-0123)./ ; }, abstract = {BACKGROUND: Red grape pomace (RGP) is a recognized winery by-product due to its phenolic profile with valuable antioxidant power and beneficial health properties. Following the latest trends in food science and technology, this study valorizes the use of RGP to obtain a food ingredient rich in antioxidant phenolics. An integrated approach was proposed, investigating the production by spray drying of easy-to-handle microparticles, rich in stable compounds with antioxidant properties demonstrated after simulated digestion using in vitro assays and Caco-2 cells. The changes in microbiota composition after fermentation were also studied.<br><br>RESULTS: Among investigated wall materials, maltodextrin/skimmed milk powder (1:1) 300&#x2009;g&#x2009;L[-1] offered the highest drying yield, appropriate moisture, solubility, and adequate microparticle morphology, as well as the best stability of polyphenols. Encapsulation improved the protection of phenolic compounds and the in vitro antioxidant capacity during 120&#x2009;days of storage at 4 and 25&#x2009;&#xb0;C, as compared to those unencapsulated. Microencapsulated polyphenols bioaccessibility was evident in 15 out of 22 compounds initially quantified, with 6.6% potentially absorbed. The polyphenols from microcapsules modulated positively the microbial ecology after colonic fermentation. Those derived from intestinal digestion demonstrated the highest capacity to reduce the reactive oxygen species under oxidative stress conditions in Caco-2 cells.<br><br>CONCLUSION: RGP could be used in the development of new food ingredients as a potential candidate for health promotion. This represents the first report on the benefits of RGP microcapsules as a food ingredient, validating its final biological effects in a cellular model considering the processing and digestion effects. &#xa9; 2025 Society of Chemical Industry.}, }
@article {pmid40556886, year = {2025}, author = {Klein, ML and Erikson, CB and McCabe, CJ and Huang, L and Rodrigues, JLM and Mitloehner, FM}, title = {Limited effects of tannin supplementation on the dairy cattle fecal microbiome with modulation of metabolites.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1570127}, doi = {10.3389/fmicb.2025.1570127}, pmid = {40556886}, issn = {1664-302X}, abstract = {Tannins are plant secondary metabolites that bind organic carbon (C) and nitrogen (N), potentially altering substrate bioavailability for enteric fermentation in ruminants. This interaction may reduce greenhouse gas (GHG) emissions and influence nitrogen partitioning. Given tannins' resistance to ruminal degradation and persistence through the gastrointestinal tract, this study investigated the effects of a tannin-based feed additive on fecal microbial diversity, fecal chemical composition, and GHG emissions. Twenty-four early- to mid-lactation dairy cows were randomized to receive either a tannin-based feed additive (TRT; containing condensed and hydrolyzable tannins from Schinopsis quebracho-colorado [Schltdl.]) or a control diet (CON) for 64 days. Cows were blocked by parity, dry matter intake, milk yield, body weight, and days in milk. Fecal samples were collected on days 0, 16, 32, and 64 and analyzed using 16S rRNA gene amplicon sequencing. Fecal C, N, and indole-3-lactate were measured, and GHG emissions (N2O, CH4, CO2) were assessed via 14-day laboratory incubation. A total of 1,538 amplicon sequence variants were identified, with Firmicutes as the dominant phylum. Fecal phylogenetic diversity showed a significant treatment × day interaction (p < 0.01), with TRT cows exhibiting reduced microbial diversity from day 16 to 64. Fecal C and N concentrations were significantly lower (p < 0.01) in TRT cows on day 16, while indole-3-lactate levels were higher on day 64 (p = 0.02). GHG emissions did not differ significantly between treatments. The tannin-based feed additive influenced fecal microbial community structure and select chemical parameters but did not significantly affect GHG emissions from feces. These findings suggest that dietary tannins may modulate gut microbial ecology with minimal impact on downstream manure-related emissions.}, }
@article {pmid40556136, year = {2025}, author = {Long, Y and Li, Y and Zhang, J and Liu, J and Han, Q and Cao, Y and Jiang, Y and Liu, C and Hu, Y and Wang, G and Zhang, X and Jin, J and Semenov, M and Han, G and Liu, X and Yu, Z}, title = {Unconventional Nitrogen Fixation and Adaptive Genomics of a New Neorhizobium glycines sp. nov., A Promising Soybean Symbiont.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70046}, pmid = {40556136}, issn = {1365-3040}, support = {//This study was funded by the National Key R &amp; D Program of China (2021YFD1500400), Strategic Priority Research Program of Chinese Academy of Sciences (XDA28020201), National Natural Science Foundation of China (32172123, 42207399)./ ; }, }
@article {pmid40555367, year = {2025}, author = {McGrath, AH and Steinberg, PD and Egan, S and Kjelleberg, S and Marzinelli, EM}, title = {Disruption of host-associated and benthic microbiota affects reproductive output and settlement of a habitat-forming macroalga.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2049}, pages = {20250729}, doi = {10.1098/rspb.2025.0729}, pmid = {40555367}, issn = {1471-2954}, support = {//University of Sydney/ ; //Australian Research Council/ ; //Ecological Society of Australia/ ; }, mesh = {*Microbiota/drug effects ; Reproduction ; Ecosystem ; *Rhodophyta/microbiology/physiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The reproduction and establishment of habitat-forming species are key processes affecting their persistence and associated biodiversity. In marine systems, microbial communities associated with habitat-forming macroalgae can influence various aspects of host performance; however, the role of these microorganisms in influencing macroalgal reproduction and settlement is poorly understood. Using a dominant habitat-forming macroalga on Australian rocky shores, Hormosira banksii, we manipulated host- and benthic-associated microbiota to determine the relative importance of microorganisms to reproductive output (number of viable eggs released) and settlement (settlement and morphogenesis of algal zygotes). Disruption of the host microbiota using antibiotics decreased reproductive output after 2 weeks, with the effect dependent on the type of antibiotic used. Disruption of host- and benthic-associated microbiota, in combination, caused a significant decrease in settlement of H. banksii zygotes, with the combined disruption having the greatest impact on settlement success. Our results demonstrate the importance of host-associated microbiota in macroalgal reproduction and an interactive effect of host- and benthic-associated microbiota on settlement-a key ecological process with important implications for host fitness and potentially ecosystem persistence.}, }
@article {pmid40553410, year = {2025}, author = {Bota, JL and Baum, C and Gawronski, S and Grafe, TU and Kerth, G and Schöner, MG and Schöner, CR}, title = {UV treatment of the digestive fluid of Nepenthes hemsleyana pitcher plants affects their digestive process, possibly via reducing microbial inquilines.}, journal = {Oecologia}, volume = {207}, number = {7}, pages = {108}, pmid = {40553410}, issn = {1432-1939}, support = {SCHO1740/1-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Ultraviolet Rays ; Animals ; Digestion/radiation effects ; }, abstract = {Interactions with microbes are ubiquitous, and many of them are essential for the survival and success of plants. In Nepenthes pitcher plants, they occur as part of a diverse community of organisms, so-called inquilines, that live inside the digestive fluid of the pitcher traps. However, evidence is ambiguous regarding the role of microbial inquilines: they may complement the plants' prey digestion, fix atmospheric N, act as competitors that reduce plant-available nutrients or affect the plants in other ways unrelated to the breakdown of prey. In a field experiment on Borneo, we investigated the effect of UV disinfection of the digestive fluid on prey digestion of N. hemsleyana that captures and digests insects as well as bat faeces in its pitchers. We show that in the short term, the photosynthetic performance of plants with UV-treated digestive fluids decreases compared to untreated plants, likely due to lower abundances of microbial inquilines. However, at the end of 2 months, responses of pitcher plants with UV-treated and untreated digestive fluids tend to equalise. Nutrient source, whether from insects or bat faeces, does not influence prey digestion. We expect our findings to be a starting point for unveiling the ecological role of microbial inquilines in pitcher plants and how they interact with other inquiline groups of higher trophic levels. Ultimately, this will also help to improve understanding of the functioning and evolution of convergent interactions in other carnivorous plants.}, }
@article {pmid40553254, year = {2025}, author = {Wu, BX and Ma, JY and Huang, XC and Liang, XS and Ning, BL and Wu, Q and Wang, SZ and Zhou, JH and Fu, WB}, title = {Acupuncture as A Potential Therapeutic Approach for Tourette Syndrome: Modulation of Neurotransmitter Levels and Gut Microbiota.}, journal = {Chinese journal of integrative medicine}, volume = {}, number = {}, pages = {}, pmid = {40553254}, issn = {1993-0402}, abstract = {OBJECTIVE: To investigate the effects of acupuncture on the neurotransmitter levels and gut microbiota in a mouse model of Tourette syndrome (TS).<br><br>METHODS: Thirty-six male C57/BL6 mice were randomly divided into 4 groups using a random number table method: 3,3'-iminodipropionitrile (IDPN) group, control group, acupuncture group, and tiapride group, with 9 mice in each group. In the IDPN group, acupuncture group, and tiapride group, mice received daily intraperitoneal injections of IDPN (300 mg/kg body weight) for 7 consecutive days to induce stereotyped behaviors. Subsequently, in the acupuncture intervention group, standardized acupuncture treatment was administered for 14 consecutive days to IDPN-induced TS model mice. The selected acupoints included Baihui (DU 20), Yintang (DU 29), Waiguan (SJ 5), and Zulinqi (GB 41). In the tiapride group, mice were administered tiapride (50 mg/kg body weight) via oral gavage daily for 14 consecutive days. The control group, IDPN group, and acupuncture group received the same volume of saline orally for 14 consecutive days. Stereotypic behaviors were quantified through behavioral assessments. Neurotransmitter levels, including dopamine (DA), glutamate (Glu), and aspartate (ASP) in striatal tissue were measured using enzyme-linked immunosorbent assay. Dopamine transporter (DAT) expression levels were additionally quantified through quantitative polymerase chain reaction (qPCR). Gut microbial composition was analyzed through 16S ribosomal RNA gene sequencing, while metabolic profiling was conducted using liquid chromatography-mass spectrometry (LC-MS).<br><br>RESULTS: Acupuncture administration significantly attenuated stereotypic behaviors, concurrently reducing striatal levels of DA, Glu and ASP concentrations while upregulating DAT expression compared with untreated TS controls (P<0.05 or P<0.01). Comparative analysis identified significant differences in Muribaculaceae (P=0.001), Oscillospiraceae (P=0.049), Desulfovibrionaceae (P=0.001), and Marinifilaceae (P=0.014) following acupuncture intervention. Metabolomic profiling revealed alterations in 7 metabolites and 18 metabolic pathways when compared to the TS mice, which involved various amino acid metabolisms associated with DA, Glu, and ASP.<br><br>CONCLUSIONS: Acupuncture demonstrates significant modulatory effects on both central neurotransmitter systems and gut microbial ecology, thereby highlighting its dual therapeutic potential for TS management through gut-brain axis regulation.}, }
@article {pmid40548738, year = {2025}, author = {Mattelin, V and Van Landuyt, J and Kerkhof, F-M and Minnebo, Y and Boon, N}, title = {Integrating taxonomic and phenotypic information through FISH-enhanced flow cytometry for microbial community dynamics analysis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0197324}, doi = {10.1128/spectrum.01973-24}, pmid = {40548738}, issn = {2165-0497}, abstract = {UNLABELLED: Flow cytometry is a powerful tool to monitor microbial communities, as it allows tracking both changes in the subpopulations and cell numbers at high throughput and a low sample cost. This information can be combined in a phenotypic fingerprint that can be leveraged for diversity analysis. However, as isogenic individuals can manifest phenotypic diversity, for example, due to differing physiological state and phenotypic plasticity, combining the phenotypic information with taxonomic information adds an extra dimension for describing the dynamics of a microbial community. In this research, taxonomic information was incorporated in the microbial fingerprint through fluorescent in situ hybridization (FISH) at a single-cell level. To validate this concept and explore its versatility, two ecosystems with different micro-biodiversity were considered. In the first environment, marine bacteria were monitored for plastic biodegradation in a trickling filter, and in the second, an in vitro simulated human gut microbiome was followed over time. Samples were prepared using different (staining) methods, including FISH, and beta diversity analysis was used to evaluate the level of distinction between differently treated groups in both environments. As a reference to correlate increased distinction with the incorporation of taxonomic information, 16S rRNA gene sequencing was used. Finally, a predictive algorithm was trained to correctly classify samples in the differently treated groups. The results showed that the implementation of FISH in flow cytometry provides more information on a single-cell level to answer specific scientific questions, like distinguishing between phenotypically similar communities or following a specific taxonomic group over time.<br><br>IMPORTANCE: Understanding microbial communities is crucial for elucidating their role in maintaining ecosystem health and stability. Researchers are increasingly interested in studying microbial communities by looking at not just their genetic makeup but also their physical traits and functions. In our study, we used common techniques like fluorescence in situ hybridization and flow cytometry, along with advanced data analysis, to better understand these communities. This combination allowed us to gather and use data more effectively, demonstrating that these easy-to-use methods, when paired with proper analysis, can enhance our understanding of changing microbial ecosystems.}, }
@article {pmid40545777, year = {2025}, author = {VanWallendael, A and Wijewardana, C and Bonnette, J and Vormwald, L and Fritschi, FB and Boe, A and Chambers, S and Mitchell, RB and Rouquette, FM and Wu, Y and Fay, PA and Jastrow, JD and Lovell, JT and Juenger, TE and Lowry, DB}, title = {Local adaptation of both plant and pathogen: an arms-race compromise in switchgrass rust.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70313}, pmid = {40545777}, issn = {1469-8137}, support = {DE-AC02-06CH11357//Biological and Environmental Research/ ; DE-SC0014156//Biological and Environmental Research/ ; DE-SC0017883//Biological and Environmental Research/ ; DE-SC0018409//Biological and Environmental Research/ ; 1832042//Division of Environmental Biology/ ; DE-AC02-05CH11231//Joint Genome Institute/ ; }, abstract = {In coevolving species, parasites locally adapt to host populations as hosts locally adapt to resist parasites. Parasites often outpace host local adaptation since they have rapid life cycles, but host diversity, the strength of selection, and external environmental influence can result in complex outcomes. To better understand local adaptation in host-parasite systems, we examined locally adapted switchgrass (Panicum virgatum), and its leaf rust pathogen (Puccinia novopanici) across a latitudinal range in North America. We grew switchgrass genotypes in 10 replicated multiyear common gardens, measuring rust severity from natural infection in a 'host reciprocal transplant' framework for testing local adaptation. We conducted genome-wide association mapping to identify genetic loci associated with rust severity. Genetically differentiated rust populations were locally adapted to northern and southern switchgrass, despite host local adaptation to environmental conditions in the same regions. Rust resistance was polygenic, and distinct loci were associated with rust severity in the north and south. We narrowed a previously identified large-effect quantitative trait locus for rust severity to a candidate YELLOW STRIPE-LIKE gene and linked numerous other loci to defense-related genes. Overall, our results suggest that both hosts and parasites can be simultaneously locally adapted, especially when parasites impose less selection than other environmental factors.}, }
@article {pmid40542918, year = {2025}, author = {Zhang, W and Li, XJ and Liu, F and Zhang, J and Tian, J and Gao, Y}, title = {Fungen: clustering and correcting long-read metatranscriptomic data for exploring eukaryotic microorganisms.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {40542918}, issn = {1869-1889}, abstract = {Long-read metatranscriptomics is a powerful and cost-effective technology for elucidating the genetic diversity and expression dynamics of active eukaryotic microorganisms by characterizing full-length transcripts. However, its potential has been limited by the lack of high-quality reference genomes and high sequencing error rates. We present Fungen, a reference-free tool that constructs accurate transcripts from long-read metatranscriptomic data through read clustering and error correction. Fungen achieves superior accuracy in transcript determination while significantly reducing memory usage and offering a 22 to 56-fold speed improvement over existing methods. This novel approach overcomes the challenges posed by sequence similarity among closely related species, enabling the analysis of deeply sequenced metatranscriptomes by generating reliable gene clusters and accurate sequences. Two applications showcase Fungen's capabilities to perform high-resolution taxonomic assignments and gene profiling in marine direct RNA datasets, as well as resolving reliable annotation identities in full-length rRNA targeted sequencing datasets. When applied to soil metatranscriptomic data, Fungen offers valuable insights into the in situ fungal composition and gene expression dynamics, revealing specialized life strategies of plant-pathogenic fungi in soil environments. Overall, Fungen provides a fast, scalable, and accurate solution for analyzing complex metatranscriptomic datasets, paving the way for a comprehensive understanding of eukaryotic diversity and function from long-read sequencing data.}, }
@article {pmid40542710, year = {2025}, author = {Susukida, S and Miyazawa, K and Ichikawa, H and Muto, K and Yoshimi, A and Kumagai, T and Kato, Y and Abe, K}, title = {Improved Mixing Properties of Stirred Fermentation of an Aspergillus oryzae Hyphal Dispersion Mutant.}, journal = {Biotechnology and bioengineering}, volume = {}, number = {}, pages = {}, doi = {10.1002/bit.70004}, pmid = {40542710}, issn = {1097-0290}, support = {//This study was supported by the Institute for Fermentation, Grant/Award Number: L-2018-2-014; Japan Science and Technology Agency-Adaptable and Seamless Technology Transfer Program through target-driven R&amp;D, Grant/Award Number: JPMJTM19Y4; JSPS KAKENHI, Grant/Award Number: JP20H02895; and New Energy and Industrial Technology Development Organization, Grant/Award Number: JPNP20011./ ; }, abstract = {The complexity of mechanical and biological processes in filamentous fungal fermentation remains a major obstacle to improving product yield. We previously demonstrated that the AGΔ-GAGΔ strain of Aspergillus oryzae, lacking both α-1,3-glucan (AG) and galactosaminogalactan (GAG), had improved hyphal dispersion, reduced culture viscosity, and increased recombinant protein production. Here, we applied computational fluid dynamics (CFD) and multi-omics analysis to characterize the AGΔ-GAGΔ strain during fermentation in a stirred-tank bioreactor. CFD simulations revealed large gas cavities behind the impeller blades and severe compartmentalization in both wild-type and AGΔ-GAGΔ cultures. However, shear stress distribution was broader and gas cavity formation was lower in the AGΔ-GAGΔ strain than in the wild type. The simulation results were consistent with measurements of volumetric oxygen mass transfer coefficients (KLa) and mixing times. Transcriptome analysis revealed upregulation of TCA-cycle genes in AGΔ-GAGΔ relative to the wild type. Analysis of intracellular and extracellular metabolites indicated distinct metabolic profiles associated with oxygen availability. Our findings highlight the critical role of hydrodynamics in fungal fermentation and demonstrate the potential of strain engineering for improving mixing characteristics.}, }
@article {pmid40540980, year = {2025}, author = {Noviello, D and Amoroso, C and Vecchi, M and Facciotti, F and Caprioli, F}, title = {Curing inflammatory bowel diseases: breaking the barriers of current therapies- emerging strategies for a definitive treatment.}, journal = {Current opinion in immunology}, volume = {95}, number = {}, pages = {102593}, doi = {10.1016/j.coi.2025.102593}, pmid = {40540980}, issn = {1879-0372}, abstract = {Chronic intestinal inflammation in inflammatory bowel diseases (IBD) reflects the interplay of genetic predisposition, immune dysregulation, microbial imbalance, and epithelial barrier defects. Current therapies for IBD primarily focus on controlling inflammation necessitating lifelong treatment and face a 'therapeutic ceiling' due to primary and secondary loss of efficacy over time. Immune-mediated approaches do not address additional pathogenic mechanisms, such as impairment of epithelial barrier and gut microbial ecology. Thus, innovative strategies are required to foster the field closer to a definitive cure. This review discusses novel strategies to overcome current therapeutic limitations, including immune reset via hematopoietic stem cell transplantation and B cell-targeted therapies, antigen-specific interventions such as chimeric antigen receptor T cells and tolerogenic vaccines, and intestinal epithelial barrier restoration. We also explore microbiota-based strategies - ranging from fecal microbiota transplantation to engineered consortia and bacteriophages - and discuss the adjunctive role of diet. Together, we outline a potential research roadmap toward a potential cure for IBD.}, }
@article {pmid40540566, year = {2025}, author = {Woods, PH and Speth, DR and Laso-Pérez, R and Utter, DR and Ruff, SE and Orphan, VJ}, title = {Identification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaea.}, journal = {Science advances}, volume = {11}, number = {25}, pages = {eadq5232}, pmid = {40540566}, issn = {2375-2548}, mesh = {*Methane/metabolism ; Anaerobiosis ; Phylogeny ; *Evolution, Molecular ; Genome, Archaeal ; *Archaea/genetics/metabolism ; Metagenomics ; Gene Transfer, Horizontal ; }, abstract = {Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recently evolved but understudied ANME group, "Candidatus Methanovorans" (ANME-3), to identify evolutionary processes and innovations at work in ANME, which may be obscured in earlier evolved lineages. We identified horizontal transfer of hdrA homologs and convergent evolution in carbon and energy metabolic genes as potential early steps in Methanovorans evolution. We also identified the erosion of genes required for methylotrophic methanogenesis along with horizontal acquisition of multiheme cytochromes and other loci uniquely associated with ANME. The assembly and comparative analysis of multiple Methanovorans genomes offers important functional context for understanding the niche-defining metabolic differences between methane-oxidizing ANME and their methanogen relatives. Furthermore, this work illustrates the multiple evolutionary modes at play in the transition to a globally important metabolic niche.}, }
@article {pmid40539105, year = {2025}, author = {Zhang, Z and Shi, Z and Zheng, L and Zhang, H}, title = {Remediation of acetochlor-contaminated maize field soil using Serratia odorifera AC-1 fertilizer: effects on soil microbial communities.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1510157}, pmid = {40539105}, issn = {1664-302X}, abstract = {Acetochlor is a chloroacetamide herbicide that is widely applied in corn fields. Nevertheless, the long-term usage of acetochlor in the soil leads to residues, which severely affect the germination of corn seeds and the growth of seedlings, and even exert an influence on the soil microbial community. Microbial degradation of acetochlor is the principal approach for restoring the soil microbial ecology. In this study, the Serratia odorifera AC-1 strain was isolated and identified from the soil for the degradation of residual acetochlor in the soil. To enhance the degradation efficiency, a solid microbial agent was prepared by using activated carbon as a carrier and the AC-1 strain at a 1:1 ratio and applied to the soil for degradation and remediation experiments. The content of the microbial cells in the solid microbial agent was 1.49 × 106 CFU/g after 120 days of preparation. The application of the AC-1 solid microbial agent significantly influenced the relative abundance of soil microbial communities (Actinobacteria, Firmicutes, and Proteobacteria), increasing the diversity of bacterial populations in the soil. The experimental results indicated that after the application of the AC-1 solid microbial agent, the plant height, stem diameter, and photosynthetic efficiency of corn seedlings under acetochlor stress were significantly elevated. When the application rate of the AC-1 solid microbial agent was 5.00 mg/kg, the stem diameter of corn increased by 56.4% compared with the control group. When the acetochlor concentration in the soil was 6.65 mg/kg, the DT50 value of the AC-1 solid microbial agent was 2.28 days. This study clarified the degradation mechanism and remediation capacity of the Serratia odorifera AC-1 strain in acetochlor-contaminated soil and proposed a new strategy to improve the stability and degradation efficiency of the microbial strain by optimizing the immobilization technology of the strain on activated carbon. This research provides a scientific basis and technical guidance for the future application of bioremediation technology in the field environment to remove pesticide residues, restore soil health, and enhance crop productivity.}, }
@article {pmid40537563, year = {2025}, author = {Embury, EL and Romero-Olivares, AL}, title = {Fungi Follow Flora, Bacteria Track the Seasons: A Tale of a Changing Landscape.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {68}, pmid = {40537563}, issn = {1432-184X}, support = {R16 GM146585/GM/NIGMS NIH HHS/United States ; 1R16GM146585//National Institute of General Medical Sciences of the National Institutes of Health/ ; 2312226//National Science Foundation Building Research Capacity in Biology/ ; }, mesh = {Seasons ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; Desert Climate ; *Microbiota ; Ecosystem ; Grassland ; Soil/chemistry ; Biomass ; Biodiversity ; }, abstract = {Microbes play critical roles in dryland ecosystems, driving nutrient cycling, soil stability, and plant interactions. Despite their ecological importance, few studies have examined how microbial communities respond to vegetation changes in arid landscapes. In the northern extent of the Chihuahuan Desert, the encroachment of woody shrubs into grasslands has been occurring since the 1800s, largely driven by extensive livestock grazing and increased drought levels. In this study, we investigated how microbial communities respond to both biotic (i.e., vegetation) and abiotic (i.e., seasonality) factors, how they assemble in a changing landscape, and which taxa may be particularly responsive to shrub encroachment or even facilitating this transformation. We assessed microbial communities using soil surface samples across five distinct seasonal periods in a grassland-to-shrubland gradient in the Jornada Experimental Range in the Chihuahuan Desert through the use of phospholipid fatty-acid analysis and DNA metabarcoding techniques. Our findings reveal that bacterial and fungal biomass are significantly influenced by seasonal changes, with strong correlations to humidity and temperature fluctuations. We also found that fungal community assembly and diversity were highly impacted by vegetation whereas seasons were more impactful on bacteria. Our results support the idea that microbes may be playing a crucial role in facilitating the grassland-to-shrubland transition. Overall, our study highlights the complex interactions between microbial communities and biotic and abiotic factors in dryland systems. These findings are essential for understanding the future of dryland ecosystems undergoing shrub encroachment and provide a critical foundation for guiding restoration efforts, particularly those looking to incorporate microbial-mediated solutions.}, }
@article {pmid40536564, year = {2025}, author = {Parret, L and Simoens, K and Horemans, B and De Vrieze, J and Smets, I}, title = {Establishing a co-culture aggregate of N-cycle bacteria to elucidate flocculation in biological wastewater treatment.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {149}, pmid = {40536564}, issn = {1432-0614}, support = {C24/18/043//KU Leuven/ ; FWO-G032321N//Fonds Wetenschappelijk Onderzoek/ ; FWO- 1191022N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {Flocculation ; *Wastewater/microbiology ; Coculture Techniques/methods ; Sewage/microbiology ; *Bacteria/metabolism/growth &amp; development ; Bioreactors/microbiology ; Alginates ; *Water Purification/methods ; *Nitrogen/metabolism ; Nitrification ; Microbial Consortia ; }, abstract = {Biological flocculation is a complex phenomenon that is often treated as a black box. As a result, flocculation problems are usually remediated without knowledge of the exact causes. We show that it is feasible to exploit a model (N-cycle) consortium with reduced complexity to fundamentally study bioflocculation. Strong nitrifier microcolonies were formed during oxic/anoxic cycles in sequencing batch reactors, using alginate entrapment as a cell retention system. After the release of these aggregates into suspension, macroclusters with flocs of the denitrifier were observed. These results suggest that a living model of a full-scale activated sludge floc can be built through the use of this bottom-up approach. By eliminating shifts in the microbial community, the applied experimental conditions have a more direct effect on the observations. Key Points ∙ Studying flocculation with a model consortium is feasible ∙ Alginate entrapment leads to strong microcolony formation of nitrifiers ∙ FISH by itself is not suitable to study aggregation of a coculture.}, }
@article {pmid40536143, year = {2025}, author = {Timmis, K and Williams, P and Karahan, ZC and López-García, P and Rainey, P and Chavarria, M and Greening, C and Steward, K and Hallsworth, JE and Pereira, CS and Giraldo, R and Verstraete, W and Jonjić, S and Ramos, JL and Nunes, O and Ventosa, A and Armstrong, R and Sessitsch, A and Ron, E and Wang, H}, title = {Journals Operating Predatory Practices Are Systematically Eroding the Science Ethos: A Gate and Code Strategy to Minimise Their Operating Space and Restore Research Best Practice.}, journal = {Microbial biotechnology}, volume = {18}, number = {6}, pages = {e70180}, pmid = {40536143}, issn = {1751-7915}, mesh = {*Periodicals as Topic/standards ; Peer Review, Research/standards ; Humans ; }, abstract = {Scientific research seeks to extend knowledge and understanding, an activity that perhaps more than any other advances society and humanity. In essence, it is the search for truth. But, because it seeks new knowledge, there is little or no benchmark for appraisal of the plausibility or validity of the immediate conclusions drawn from new information gained, no instant confirmation. For this and other reasons, the science ethos requires the highest level of rigour to ensure the highest level of probability that new findings are true, or at least the most plausible under the prevailing circumstances and state of knowledge. Research is only as good as its degree of rigour. Rigour comes through intensive and comprehensive scientific training and mentoring that teaches critical and agnostic evaluation of new results, self-scrutiny and self-criticism. Additional rigour comes via independent scrutiny and validation: peer review of results and interpretations submitted as publications, and peer repetition of key experiments. However, the current proliferation of publication vehicles whose business model is based on maximisation of papers published, and the revenue stream of article processing charges (APCs) they generate, is promoting an insidious degradation of rigour and quality standards of reviewing-editing practices. Such predatory practices result in the systematic degradation of research quality and its "truthfulness". Moreover, they undermine the science ethos and threaten to create a new generation of scientists that lack this ethos. These trends will inevitably progressively erode public trust in scientists and the research ecosystem. This Editorial is a call for action to all actors, in particular leaders, in scientific research to oppose predatory practices in science dissemination-to restrict the operational space of those responsible for such practices-in order to restore and maintain research rigour and the science ethos and to prevent a downward spiral of research quality. It proposes two linked actionable solutions to the problem, one for the "pull" element of predatory practices and one for the "push" element of research ecosystem management practices, especially those promoting the publish or perish mentality, that drive authors to publish in journals with predatory practices. To counter the "pull", we propose a solution based on the principle of prevention, rather than cure, and list a number of essential policy decisions and actions that should be taken at all levels of the science chain/cloud to achieve this. A central plank of the concept is journal accreditation, without which a journal would be ineligible for payment of APCs from public funds. For accreditation, a journal would need to convincingly demonstrate adoption of a prescribed journal code of conduct. Ideally, accreditation would also be required for inclusion in journal indexing and ranking services and bibliographic databases. To counter the "push", we propose a top-down imposition of a cultural change in science management that ensures merit-based success of scientists and their careers, research best practice, improved education and mentoring of younger scientists in the science ethos and greater support of them in their careers. This must include explicit recognition of the crucial role of peer reviewing for the good health of the research enterprise, its incentivisation and appropriate appreciation of the time and effort involved. To orchestrate this change, we propose the creation of a multi-stakeholder alliance whose brief is to develop the framework and implementation strategy for changes in the research ecosystem. This Editorial also exhorts all actors to embrace the principle of publish less, publish better and to use public funding provided by tax revenues more effectively to perpetually raise the bar of science quality, dissemination and potential to advance humanity.}, }
@article {pmid40534981, year = {2025}, author = {Hodgson, RJ and Cando-Dumancela, C and Liddicoat, C and Ramesh, SA and Edwards, RA and Breed, MF}, title = {Strong Host Modulation of Rhizosphere-to-Endosphere Microbial Colonisation in Natural Populations of the Pan-Palaeotropical Keystone Grass Species, Themeda triandra.}, journal = {Ecology and evolution}, volume = {15}, number = {6}, pages = {e71595}, pmid = {40534981}, issn = {2045-7758}, abstract = {Soil microbiota can colonise plant roots through a two-step selection process, involving recruitment of microbiota first from bulk soil into plant rhizospheres, then into root endospheres. This process is poorly understood in all but a few model species (e.g., Arabidopsis), which is surprising given its fundamental role in plant and soil ecology. Here, we examined the microbial community assembly processes across the rhizospheres and root endospheres in eight natural populations of the pan-palaeotropical C4 grass, Themeda triandra, in southern Australia. Using a space-for-time substitution approach, we assessed whether bacterial root colonisation patterns conformed to the two-step model and tested whether community assembly was driven more by deterministic or stochastic processes. Our results show that the two-step selection process shaped bacterial recruitment dynamics across these natural T. triandra populations, and we provide clear evidence that host plants influence microbial assembly via deterministic pressures that produce strong community convergence within endospheres. These findings highlight the central role of host filtering in shaping a conserved 'core' endosphere microbiome. However, limited understanding of these endosphere communities constrains efforts to harness these important relationships to, for example, improve plant propagation and revegetation practices.}, }
@article {pmid40533683, year = {2025}, author = {Rios-Reyes, A and Gonzalez-Lozano, KJ and Cabral-Miramontes, JP and Hernandez-Gonzalez, JJ and Rios-Sosa, A and Alvarez-Gutierrez, PE and Mireles-Torres, SP and Batista-García, RA and Arechiga-Carvajal, ET}, title = {Exploration of Plant and Microbial Life at "El Chichonal" Volcano with a Sustainable Agriculture Prospection.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {67}, pmid = {40533683}, issn = {1432-184X}, support = {700634//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 2055419//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 1081508//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 315114//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 252373/SEP-CONACYT//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; CBF2023-2024-3120//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; }, mesh = {*Soil Microbiology ; *Bacteria/classification/isolation &amp; purification/genetics/metabolism ; *Fungi/isolation &amp; purification/classification/genetics ; Agriculture ; Soil/chemistry ; *Volcanic Eruptions ; Bacillus cereus/isolation &amp; purification/genetics ; Plant Roots/microbiology ; Microbiota ; }, abstract = {Active volcanic environments represent extreme habitats with underexplored potential for microbial bioprospecting. This study aimed to characterize pioneer vegetation and associated microbial diversity in the crater of "El Chichonal" volcano, with an emphasis on their potential applications in sustainable agriculture. A physicochemical analysis of the soil was performed, identifying acidic and nutrient-poor conditions. Three pioneer plant species were described: Tibouchina longifolia (dominant) and Poaceae spp. (co-dominant), and Palhinhaea cernua (non-dominant). A total of 311 microorganisms were predominantly bacteria, were isolated from soil, root, stem, and water samples. Bacillus cereus and Priestia megaterium were molecularly identified, and in vitro assays demonstrated their ability to fix nitrogen, produce auxins, and antagonize fungal pathogens (Alternaria solani, Botrytis cinerea, and Colletotrichum gloeosporioides). These results suggest that microorganisms adapted to extreme volcanic environments could be promising sources of plant growth-promoting bacteria (PGPB) with application in biological control.}, }
@article {pmid40533475, year = {2025}, author = {Wollrab, S and Schmidt, SR and Woodhouse, J and Kasprzak, P and Berger, SA and Beyer, U and Bodenlos, M and Dalchow, J and Degebrodt, M and Ganzert, L and Gonsiorczyk, T and Huth, E and Kiel, C and Küchler, L and Krienitz, L and Lentz, M and Mach, E and Mallok, U and Nejstgaard, JC and Papke, M and Penske, A and Pinnow, S and Roßberg, R and Ronneberger, D and Sachtleben, M and Scheffler, A and Grossart, HP and Casper, P and Gessner, MO and Koschel, R}, title = {Fifty years of limnological data on Lake Stechlin, a temperate clearwater lake.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1028}, pmid = {40533475}, issn = {2052-4463}, abstract = {We present 50 years of monitoring data on water quality of Lake Stechlin, a deep, dimictic hardwater lake in northeastern Germany known for its exceptionally clear water. Although located in a forested catchment, the lake has undergone major changes in recent decades, including a period of massive heating of surface water when receiving cooling water from a nearby nuclear power plant (1966-1990), accompanied by a greatly shortened water residence time from more than 40 years to less than 300 days. These changes are superimposed by a long-term trend of surface water warming and a concomitant decrease in winter ice cover. Total phosphorus concentrations have quadrupled since 2010 and zones of deep-water oxygen depletion have greatly expanded. The presented dataset covers basic water-chemical and physical records taken at monthly to fortnightly intervals from 1970 to 2020, documenting limnological changes during that period. Furthermore, it serves as a valuable basis to assess and project potential consequences of climate change and other types of environmental change on deep clearwater lakes in temperate climates.}, }
@article {pmid40531665, year = {2025}, author = {Phithakrotchanakoon, C and Kitikhun, S and Siriarchawatana, P and Charoenyingcharoen, P and Jeennor, S and Nilsakha, T and Chanpet, A and Vorajinda, T and Mayteeworakoon, S and Yukphan, P and Ingsriswang, S}, title = {Flavobacterium mekongense sp. nov., isolated from the Mekong River in Thailand.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {75}, number = {6}, pages = {}, doi = {10.1099/ijsem.0.006815}, pmid = {40531665}, issn = {1466-5034}, mesh = {Thailand ; *Flavobacterium/classification/genetics/isolation &amp; purification ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Rivers/microbiology ; Fatty Acids/chemistry/analysis ; DNA, Bacterial/genetics ; Base Composition ; Bacterial Typing Techniques ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry/analysis ; Nucleic Acid Hybridization ; Genome, Bacterial ; Phospholipids/analysis/chemistry ; *Water Microbiology ; }, abstract = {Two Gram-stain-negative, aerobic, non-motile, non-gliding, rod-shaped bacterial strains, designated as TBRC 19031[T] and TBRC 19032, were isolated from water samples collected from the Mekong River, Thailand. Strain TBRC 19031[T] was obtained from Chiang Saen in the upstream section near the borders with China and Myanmar, while TBRC 19032 originated from Khong Chiam, in the downstream section where the river exits Thailand. Colonies of both strains were circular, smooth and deep yellow on Reasoner's 2A agar and did not produce flexirubin-type pigments. Phylogenetic analysis with 16S rRNA gene sequences placed both strains within the genus Flavobacterium, showing the highest sequence similarity to Flavobacterium cheonhonense ARSA-15[T] (98.29% for TBRC 19031[T] and 98.22% for TBRC 19032). However, whole-genome comparisons between the strains and F. cheonhonense ARSA-15[T] revealed average nt identity (89.39% and 89.29%), average aa identity (92.84% and 92.95%) and digital DNA-DNA hybridization (35.00% and 34.70%). The predominant fatty acids were iso-C15:1, iso-C15:0 and iso-C15:0 3-OH, and menaquinone MK-6 was the major respiratory quinone. The major polar lipids of both strains included phosphatidylethanolamine, steryl ester and diacylglycerol. The genome sizes were 3.02 and 3.04 Mbp, with G+C contents of 38.3% and 38.2% for TBRC 19031[T] and TBRC 19032, respectively. Comparative genomic analyses revealed the absence of genes involved in sulphate reduction and denitrification pathways and the presence of a gene encoding phosphatidylinositol synthase, distinguishing them from other Flavobacterium within the clade. Ecological profiling using public metagenomic datasets showed that both strains were associated with lotic freshwater environments. This study not only introduces Flavobacterium mekongense sp. nov. as a new species but also provides broader insights into the ecology, metabolism and environmental distribution of freshwater Flavobacterium. The genomic features identified here offer promising leads for future studies in microbial ecology, comparative genomics and functional gene mining in aquatic ecosystems. The type strain is TBRC 19031[T] (TBRC 19031[T]=NBRC 117006[T]).}, }
@article {pmid40531656, year = {2025}, author = {Bou Orm, E and Mukherjee, S and Rifa, E and Créach, A and Grec, S and Bayle, S and Benezet, JC and Bergeret, A and Malhautier, L}, title = {Enhancing Biodiversity-Function Relationships in Field Retting: Towards Key Microbial Indicators for Retting Control.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70102}, pmid = {40531656}, issn = {1758-2229}, mesh = {*Biodiversity ; *Fungi/classification/genetics/enzymology/isolation &amp; purification/metabolism ; *Bacteria/classification/genetics/enzymology/isolation &amp; purification/metabolism ; *Cannabis/microbiology/metabolism ; Pectins/metabolism ; Glycoside Hydrolases/metabolism ; Microbiota ; }, abstract = {Hemp field retting is a bioprocess that facilitates fibre extraction by degrading pectin and other matrix components surrounding fibre bundles. However, traditional methods rely on empirical practices, often resulting in inconsistent fibre quality. This study investigates the biodiversity-function relationship in the hemp retting ecosystem to identify microbial and enzymatic indicators for improved process control. Over six weeks of field retting, we monitored bacterial and fungal community dynamics using high-throughput sequencing and assessed enzymatic activity profiles. Our results revealed a sequential enzymatic pattern: pectinases (e.g., polygalacturonase) dominated early stages, followed by hemicellulases (β-xylosidase, β-galactosidase), and later cellulases. These enzymatic shifts were reflected in the changes in microbial community composition, with pectinolytic bacteria (e.g., Proteobacteria) dominating the initial phases and cellulolytic fungi (e.g., Ascomycota) becoming more prevalent later. Our results identified specific microbial taxa correlated with optimal retting, suggesting their potential as bioindicators for monitoring retting. Specifically, key bacterial genera such as Pseudomonas and Sphingomonas, and fungal genera like Cladosporium, were associated with distinct enzymatic profiles. Our findings offer new insights into the microbial ecology of retting, providing both microbial and enzymatic indicators that could inform the development of monitoring strategies for process control, ultimately contributing to more consistent hemp fibre production.}, }
@article {pmid40530365, year = {2025}, author = {Akdur Öztürk, E and Guadano-Procesi, I and Figueiredo, AM and Godfrey, A and Gentekaki, E and Tsaousis, AD and Carmena, D and Dogruman-Al, F}, title = {A protocol for mapping Blastocystis epidemiology and diagnostics from One Health perspective.}, journal = {Open research Europe}, volume = {5}, number = {}, pages = {133}, pmid = {40530365}, issn = {2732-5121}, abstract = {Blastocystis is a globally prevalent gut protist colonising over a billion people worldwide, yet its epidemiology, transmission dynamics, and clinical significance remain underexplored. This protocol represents the first step of a large-scale effort to map Blastocystis epidemiology and diagnostic practices across Europe through the COST Action CA21105: Blastocystis under One Health. By assessing diagnostic methodologies across clinical, veterinary, and environmental sectors, this work sets the foundation for future research and standardisation. Here, we highlight key findings, challenges, and a roadmap for improving Blastocystis detection, ultimately influencing global health policies and microbial ecology studies.}, }
@article {pmid40530126, year = {2025}, author = {Wu, WJ and Wang, K and Yang, YV and Yang, X}, title = {Identification of neuronal synapse-related signatures and potential therapeutic drugs in colorectal cancer based on machine learning algorithms and molecular docking.}, journal = {Translational cancer research}, volume = {14}, number = {5}, pages = {2737-2757}, pmid = {40530126}, issn = {2219-6803}, abstract = {BACKGROUND: Nervous system-cancer interactions can regulate tumorigenesis, invasion, and metastasis. However, specific biomarkers for targeting neuron synapse in colorectal cancer (CRC) remain unexplored. This study aims to develop a neuronal synapse-related signature (NSRS) to predict survival in CRC patients, identify potential therapeutic drugs, and explore its clinical applications.<br><br>METHODS: We collected neuronal synapse genes (NSGs) from the Molecular Signatures Database (MSigDB) and published mass spectrometry data. Using weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator Cox regression (LASSO-Cox), we identified prognostic NSGs and constructed a NSRS through multivariate Cox regression. Functional enrichment analysis revealed the molecular characteristics of NSRS subgroups. Additionally, xCell and ESTIMATE algorithms quantified the abundance of 54 cell subtypes and assessed the tumor immune microenvironment (TIME) of the two NSRS subgroups. Finally, drug prediction and molecular docking identified candidate drugs with therapeutic potential.<br><br>RESULTS: Seven key prognostic NSGs were identified, and an independent, stable NSRS model was constructed. Kaplan-Meier survival curves indicated that the high NSRS group had poorer outcomes (log-rank test, P<0.05). Functional enrichment analysis revealed significant enrichment of epithelial-mesenchymal transition, hypoxia, and inflammation features in the high NSRS group. xCell and ESTIMATE analyses showed a more complex TIME and lower tumor purity in the high NSRS group, highlighting the role of neuro-tumor interactions in CRC. Drug prediction and molecular docking suggested alprostadil, dihydroergocristine, and nocodazole as candidate drugs for CRC treatment.<br><br>CONCLUSIONS: This is the first study to develop neuron synapse-related biomarkers from the perspective of neuron-cancer interactions using machine learning. We constructed a robust NSRS model and identified candidate drugs targeting prognostic NSGs, providing new insights into CRC prognosis and treatment.}, }
@article {pmid40529576, year = {2025}, author = {Sanz-López, C and Amato, M and Torrent, D and Borrego, M and Anza, M and Bibiso, M and Grijalva-Vallejos, N and Vilanova, C and Porcar, M and Pascual, J}, title = {Microbial ecology of selected traditional Ethiopian fermented products.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1570914}, pmid = {40529576}, issn = {1664-302X}, abstract = {The consumption of traditional fermented foods and beverages plays an important role in the diet of Ethiopia, providing significant nutritional and health benefits to the local population. The present study aimed to investigate the microbial ecology and diversity of nine types of fermented products. These include two foods (Kotcho and Injera), one food condiment (Datta), and six beverages (Tej, Tella, Cheka, Kinito, Borde, and Shamita). A combination of metataxonomic and culturomic approaches was used to achieve a comprehensive characterization of the bacterial communities, together with a thorough physicochemical characterization of the fermented products. This study provides one of the most comprehensive microbial characterizations of a wide selection of Ethiopian fermented products, highlighting that some bacterial species involved in the fermentation processes could contribute to the safety and nutritional quality of fermented foods and, based on previous studies, could also play a key role in enhancing their potential probiotic properties.}, }
@article {pmid40529573, year = {2025}, author = {Ma, R and Zhang, Z and Wang, J and Han, Y and Li, K and Hou, M and Lei, Y and Xiong, S and Yang, B and Zhi, X and Jiao, Y and Lin, T and Zhang, S and Li, Y}, title = {Mitigating gaseous nitrogen emissions in cotton fields through green manure and reduced nitrogen fertilization.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1615142}, pmid = {40529573}, issn = {1664-302X}, abstract = {Integrating green manure with reduced nitrogen (N) fertilization is a promising strategy to mitigate N emissions in intensive cotton cultivation, however, the underlying mechanisms remain poorly understood. This study investigated the effects of three green manure incorporation patterns-no green manure (NG), Orychophragmus violaceus (OVG), and Vicia villosa (VVG)-combined with four N reduction levels (100, 50, 25%, and conventional) on gaseous N emissions (NH3 and N2O), soil physicochemical properties, and bacterial community characteristics using a cotton field experiment in the Yellow River Basin. Results showed that OVG incorporation with 25% N reduction (N2 treatment) significantly reduced total gaseous N emissions by 36.07% on average during the cotton growth period, reducing NH3 and N2O emissions by 13.31-54.11% and 32.25-68.77%, respectively, compared with N2 application without OVG. OVG application also increased the relative abundance of Proteobacteria (28.10%), enhanced heterogeneous selection in bacterial community assembly (200%), and increased the complexity of co-occurrence networks, compared with NG. Compared with conventional N fertilization (N3 treatment), ≥50% N reduction significantly lowered NH3 (>25.51%) and N2O (>32.76%) emissions, reduced the relative abundance of Acidobacteria (-20.23%), simplified co-occurrence networks, and increased homogeneous selection in bacterial assembly (50.00%). Integrating green manure with 25% N reduction substantially reduced gaseous N emissions, which was associated with the enhanced microbial biomass carbon (MBC) and facilitated recruitment of key bacterial taxa (e.g., Sphingosinicella, Azohydromonas, Phototrophicus) within the microbial co-occurrence network. These findings provide insight into how green manure application coupled with N reduction can mitigate gaseous N losses and reshape soil microbial ecology, offering a theoretical basis for sustainable nutrient management during cotton production.}, }
@article {pmid40528722, year = {2025}, author = {Gao, D and Guo, X and Yang, Z and Li, H and Chen, Y and Yang, X and Song, L and Yang, X and Yang, J and Zhou, C}, title = {Effects of Sibiraea laevigate maxim polysaccharides on intestinal flora in immunosuppressed mice.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.14433}, pmid = {40528722}, issn = {1097-0010}, support = {//The program of Science and Technology Department of Gansu Province (2024ZDPC001, 24YFFA026, 23CXGP0002)/ ; //The innovation Drive assistance project of Gansu for Science and Technology Association (GXH20240328-3)/ ; 2023QB-001//The Young Doctor Fund of Gansu Province/ ; //The youth science and technology talent innovation project of Lanzhou (2023-QN-69)./ ; //The Fundamental Research Funds for the Central Universities of Northwest Minzu University (31920240125-01)./ ; 2024RCXM45//The key talent project of Gansu Province (2024)/ ; }, abstract = {BACKGROUND: The intestinal microbial ecology plays a significant role in maintaining normal physiological function processes and significantly influences the immune system. However, research regarding its effects on gut flora and in vivo immunomodulation is insufficient.<br><br>RESULTS: In this study, cyclophosphamide was administered to mice to establish an immunosuppressed mouse model. The regulatory effects of Sibiraea laevigata maxim polysaccharides (SLMPs) on immunity and intestinal microbiota in the immunosuppressed mouse model were investigated. The results indicated that SLMPs could mitigate spleen and thymus damage, protect immune organs, increase the levels of leukocytes, lymphocytes, neutrophils and monocytes in mouse blood and upregulate the levels of IL-2, IFN-&#x3b3;, TNF-&#x3b1; and IgA in mouse serum. Furthermore, SLMPs can restore intestinal microbial imbalance and enhance the diversity of gut microorganisms in immunosuppressed mice.<br><br>CONCLUSION: The findings from this study indicated that SLMPs could enhance immunity and improve the structure and abundance of intestinal flora in mice. These results provide a theoretical basis for the further development and utilization of SLMPs in immunomodulatory adjuvants and functional foods, thereby promoting their application in these fields. &#xa9; 2025 Society of Chemical Industry.}, }
@article {pmid40528265, year = {2025}, author = {Selak, L and Meier, DV and Marinović, M and Čačković, A and Kajan, K and Pjevac, P and Orlić, S}, title = {Salinization alters microbial methane cycling in freshwater sediments.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {73}, pmid = {40528265}, issn = {2524-6372}, support = {DOK-2018-09-1550//Hrvatska Zaklada za Znanost/ ; IP-2020-02-9021//Hrvatska Zaklada za Znanost/ ; }, abstract = {Climate change-induced salinization poses a global threat to freshwater ecosystems and challenges microbial communities driving crucial biogeochemical processes, particularly methane cycling. This study examined the impact of salinization and the accompanying sulfate concentration increases on microbial community dynamics and methane cycling in coastal freshwater lake sediments. We show that sulfate enrichment in sediment profiles enables the proliferation of distinct sulfate-reducing bacteria (SRB) that reshape microbial niches by competing with methanogens and promoting sulfate-dependent anaerobic oxidation of methane (AOM). Freshwater SRB clusters, which compete with some methanogens for substrates but also degrade organic compounds into methanogenesis precursors, are replaced by the SEEP-SRB groups that form syntrophic relationships with ANME-1 in salinized sediments. As seawater intrudes and reshapes microbial communities, a methane pocket forms that escapes both aerobic and anaerobic oxidation. Underneath this methane pocket, SRB play a key role in enabling sulfate-dependent AOM, facilitating methane consumption at higher sediment depths. While all microorganisms demonstrated some physiological adaptability potential to elevated osmotic stress, SRB exhibited the highest resilience to increased salinity. These findings highlight how salinization-induced geochemical shifts, particularly sulfate enrichment, directly affect microbial community assembly and impact methane cycling in coastal freshwater ecosystems.}, }
@article {pmid40528093, year = {2025}, author = {Goswami, R and Sarkar, A and Bandyopadhyay, B and Sadhukhan, S}, title = {Exploring microbial diversity in the Kharasinpur hot spring of West Bengal, India.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {608}, pmid = {40528093}, issn = {1573-4978}, mesh = {*Hot Springs/microbiology ; India ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/isolation &amp; purification/classification ; Phylogeny ; Biodiversity ; Water Microbiology ; Microbiota/genetics ; Hydrogen-Ion Concentration ; Iron/analysis ; }, abstract = {BACKGROUND: Hot springs are natural geothermal environments that harbour thermophilic microorganisms with significant biotechnological potential. Despite extensive studies on many Indian hot springs, Kharasinpur Hot Spring in West Bengal remains totally unexplored in terms of microbial diversity and physicochemical properties.<br><br>METHODS: A total of seven bacterial isolates were obtained from water samples collected at the Kharasinpur Hot Spring. These isolates underwent morphological, physiological, biochemical, and molecular characterization through 16S rRNA gene sequencing. Water samples were analyzed for physicochemical parameters such as temperature, pH, total hardness, iron concentration, salt content, and total dissolved solids (TDS).<br><br>RESULTS: The water temperature was recorded at 65&#xa0;&#xb0;C with a slightly alkaline pH (7.24). The 16S rRNA analysis identified isolates belonging to the phyla Pseudomonadota (e.g., Pseudomonas sp., Hydrogenophaga sp.) and Bacillota (e.g., Staphylococcus sp., Neobacillus sp.). The high iron content in the hot spring water was notable and rendered it unsafe for direct human consumption.<br><br>CONCLUSION: This study provides novel insights into the microbial diversity and physicochemical characteristics of a relatively unstudied Indian hot spring. The findings contribute to broader research efforts on hot spring ecosystems in India, enhancing our understanding of their microbial ecology and potential health implications.}, }
@article {pmid40528049, year = {2025}, author = {Blair, EM and Margalith, NJ and O'Malley, MA}, title = {Microbial Enrichments Contribute to Characterization Of Desert Tortoise Gut Microbiota.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {66}, pmid = {40528049}, issn = {1432-184X}, support = {DE-SC0020420//U.S. Department of Energy/ ; DE-SC0020420//U.S. Department of Energy/ ; DE-SC0020420//U.S. Department of Energy/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Turtles/microbiology ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Desert Climate ; Fatty Acids, Volatile/metabolism ; Lignin/metabolism ; DNA, Bacterial/genetics ; Biomass ; }, abstract = {Desert tortoises play ecologically significant roles, including plant seed dispersal and mineral cycling, and yet little is known about microbial members that are critical to their gut and overall health. Tortoises consume recalcitrant plant material, which their gut microbiota degrades and converts into usable metabolites and nutrients for the tortoise. Findings from tortoise gut microbiomes may translate well into biotechnological applications as these microbes have evolved to efficiently degrade recalcitrant substrates and generate useful products. In this study, we cultivated microbial communities from desert tortoise fecal samples following a targeted anaerobic enrichment for microbes involved in deconstruction and utilization of plant biomass. We employed 16S rRNA amplicon sequencing to compare cultivated communities to initial fecal source material and found high abundances of Firmicutes and Bacteroidota typically associated with biomass deconstruction in all cultivated samples. Significantly decreased microbial diversity was observed in the cultivated microbial communities, yet several key taxa thrived in lignocellulose enrichments, including Lachnospiraceae and Enterococcus. Additionally, cultivated communities produced short-chain fatty acids under anaerobic conditions, and their growth and metabolic output provide evidence of their viability in the initial fecal communities. Overall, this study adds to the limited understanding of reptilian herbivore microbiota, and offers a path towards biotechnological translation based on the ability of the cultivated communities to convert lignocellulose directly to acetate, propionate, and butyrate.}, }
@article {pmid40527958, year = {2025}, author = {Jendrusch, MA and Yang, ALJ and Cacace, E and Bobonis, J and Voogdt, CGP and Kaspar, S and Schweimer, K and Perez-Borrajero, C and Lapouge, K and Scheurich, J and Remans, K and Hennig, J and Typas, A and Korbel, JO and Sadiq, SK}, title = {AlphaDesign: a de novo protein design framework based on AlphaFold.}, journal = {Molecular systems biology}, volume = {}, number = {}, pages = {}, pmid = {40527958}, issn = {1744-4292}, support = {de.NBI project: 031A537B//Bundesministerium f&#xfc;r Bildung und Forschung (BMBF)/ ; contract 95826//Volkswagen Foundation (VolkswagenStiftung)/ ; 93874-1//Volkswagen Foundation (VolkswagenStiftung)/ ; COFUND grant nr. 847543//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, abstract = {De novo protein design is of fundamental interest to synthetic biology, with a plethora of computational methods of various degrees of generality developed in recent years. Here, we introduce AlphaDesign, a hallucination-based computational framework for de novo protein design developed with maximum generality and usability in mind, which combines AlphaFold with autoregressive diffusion models to enable rapid generation and computational validation of proteins with controllable interactions, conformations and oligomeric state without the requirement for class-dependent model re-training or fine-tuning. We apply our framework to design and systematically validate in vivo active inhibitors of a family of bacterial phage defense systems with toxic effectors called retrons, paving the way towards efficient, rational design of novel proteins as biologics.}, }
@article {pmid40525968, year = {2025}, author = {Lopez-Echartea, E and Dusek, N and Misialek, M and Mahmud-Un-Nabi, MA and Williamson, R and Marathe, K and Geddes, BA}, title = {Culturomics from field-grown crop plants using dilution to extinction, two-step library preparation and amplicon sequencing.}, journal = {Microbiology (Reading, England)}, volume = {171}, number = {6}, pages = {}, pmid = {40525968}, issn = {1465-2080}, mesh = {RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/growth &amp; development ; *Zea mays/microbiology ; *Microbiota/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Plant Roots/microbiology ; *Pisum sativum/microbiology ; *Crops, Agricultural/microbiology ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Gene Library ; Soil Microbiology ; }, abstract = {Culturomics approaches have advanced microbial research by enabling the high-throughput isolation and characterization of a broader range of bacterial taxa, including some previously considered unculturable. Here, we present the testing and optimization of a protocol for isolating and identifying hundreds of cultivable microbes from field-grown plants. This protocol was tested and optimized using the root microbiomes of field-grown corn and pea plants under varying environmental conditions in ND, USA. By employing dilution-to-extinction culturing and a two-step barcoding PCR strategy targeting the V4 region of the 16S rRNA gene, we identified over 200 unique bacterial isolates. The optimized bioinformatic pipeline, built around the DADA2 package, ensured accurate amplicon sequence variant detection and taxonomy assignment. The resulting bacterial isolates span diverse phylogenetic groups, including plant-associated taxa known for promoting plant growth and mitigating stress. Our findings highlight the value of culturomics in generating microbial collections for synthetic community design and advancing plant-microbe interaction research. The protocol's scalability, cost-effectiveness and robust performance demonstrate its potential for widespread application in agricultural microbiome studies.}, }
@article {pmid40525847, year = {2025}, author = {Kroos, L and Wall, D and Islam, ST and Whitworth, DE and Muñoz-Dorado, J and Higgs, PI and Singer, M and Mauriello, EM and Treuner-Lange, A and Søgaard-Andersen, L and Kaimer, C and Elías-Arnanz, M and Stojković, EA and Müller, R and Volz, C and Velicer, GJ and Nan, B}, title = {Milestones in the development of Myxococcus xanthus as a model multicellular bacterium.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0007125}, doi = {10.1128/jb.00071-25}, pmid = {40525847}, issn = {1098-5530}, abstract = {From the humblest of beginnings (i.e. a pile of dry cow dung) over 80 years ago, the Gram-negative bacterium Myxococcus xanthus has emerged as a premier model system for studying diverse fields of bacteriology, including multicellular development, sporulation, motility, cell-envelope biogenesis, spatiotemporal regulation, signaling, photoreception, kin recognition, social evolution, and predation. As the flagship representative of myxobacteria found in varied terrestrial and aquatic environments, M. xanthus research has evolved into a collaborative global effort, as reflected by the contributions to this article. In celebration of the upcoming 50th anniversary of the International Conference on the Biology of Myxobacteria, this review highlights the historical and ongoing contributions of M. xanthus as a multifaceted model bacterium.}, }
@article {pmid40524759, year = {2025}, author = {Lacerda, AL and Proietti, MC and Kessler, F and Mendes, CR and Secchi, ER and Taylor, JD}, title = {Oceanic regions shape the composition of the Antarctic plastisphere.}, journal = {Communications earth &amp; environment}, volume = {6}, number = {1}, pages = {462}, pmid = {40524759}, issn = {2662-4435}, abstract = {Antarctica, once considered pristine, is increasingly threatened by plastic pollution, with debris found in its waters, sediments, sea ice, and biota. Here, we provide a comprehensive molecular survey of both prokaryotic and eukaryotic diversity on plastics around the Antarctic Peninsula, addressing a gap in existing research. Using eDNA metabarcoding, we identified diverse communities, with Pseudomonadota and Bacteroidota dominating prokaryotic communities, while Gyrista (mostly diatoms), Fungi and Arthropods were prevalent among eukaryotes. Geographic location significantly influenced community composition, with differences between the Bransfield Strait and the Gerlache Strait/Bellingshausen Sea. Polymer type and plastic shape did not impact species richness or community structure. These findings offer new insights into the complexity of the Antarctic plastisphere, highlighting potential impacts on biodiversity, ecosystem functions, and the broader implications of marine plastic pollution.}, }
@article {pmid40524188, year = {2025}, author = {Perillo, VL and Nute, M and Sapoval, N and Curry, KD and Golia, L and Yin, Y and Ogilvie, HA and Nakhleh, L and Segarra, S and Bhaya, D and Cuadrado, DG and Treangen, TJ}, title = {A survey of computational approaches for characterizing microbial interactions in microbial mats.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {168}, pmid = {40524188}, issn = {1474-760X}, support = {EF-2126387//National Science Foundation/ ; BBSRC-NSF/BIO #1921429//National Science Foundation/ ; NSF#2125965//National Science Foundation/ ; PICT 2020-302//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; Pampa Azul A8 Programa "Investigaci&#xf3;n//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; Desarrollo e Innovaci&#xf3;n en Ciencias del Mar"//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; Proposal 503441//Joint Genome Institute/ ; proposal: 10.46936/10.25585/60001132//Joint Genome Institute/ ; }, mesh = {*Microbial Interactions ; *Computational Biology/methods ; *Microbiota ; Ecosystem ; Bacteria/genetics/metabolism ; }, abstract = {In this review, we use microbial mat communities as a general model system to highlight the strengths and limitations of current computational methods for analyzing interactions between members of microbial ecosystems. We describe the factors that make this environment have such a high degree of interaction, and we explore different categories of both laboratory and computational tools for studying these interactions. For each tool, we describe efforts to apply them to microbial mats in the past and, in the process, argue that genome-scale metabolic models have breakthrough potential for modeling microbial interactions in microbial mats.}, }
@article {pmid40523669, year = {2025}, author = {Prakash, O and Chauhan, A and Green, SJ}, title = {The Study of Microbial Physiology Under Microoxic Conditions Is Critical but Neglected.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70108}, pmid = {40523669}, issn = {1758-2229}, support = {2200615//BioXFEL Science and Technology Center/ ; DE-FE0032198//DOE's University Training &amp; Research Program University Coal Research (UCR)/ ; 0000602538//The Department of Energy/ ; //Major Research Project (MJRP) intramural grant from Symbiosis International (Deemed University)/ ; 1901371//National Science Foundation/ ; 2200615//National Science Foundation/ ; W911NF2210145//Department of Defence contract/ ; }, mesh = {Anaerobiosis ; Aerobiosis ; *Oxygen/metabolism ; *Bacteria/metabolism/genetics/growth &amp; development ; Ecosystem ; *Bacterial Physiological Phenomena ; Humans ; }, abstract = {During the early evolution of life on Earth, the environment was largely free of molecular oxygen, and only anaerobic life existed. With the subsequent oxidation of oceans and the atmosphere, a wide range of environmental niches, ranging from anoxic to microoxic/hypoxic and oxic, developed. Despite this broad range of natural environments, microbiology as a field has focused on the physiology, metabolism, and genetics of aerobic microorganisms, with less attention paid to anaerobes and much less attention paid to microaerophiles. The disparity in studies between aerobic and anaerobic conditions is rampant in host-associated systems, particularly in human health, and studies of microorganisms in intermediate oxygen conditions between fully aerobic and fully anoxic conditions are exceedingly rare. Studies on the physiological behaviour, metabolism, growth response, and drug susceptibility patterns of commensal and pathogenic organisms are almost totally neglected in microoxic conditions. Furthermore, microorganisms from microaerobic and microoxic ecosystems have been less robustly explored in terms of physiology, growth, and metabolism. In this work, we highlight the importance of understanding the physiological and metabolic behaviours of microorganisms under hypoxic or microoxic conditions.}, }
@article {pmid40522148, year = {2025}, author = {Fejes, R and Séneca, J and Pjevac, P and Lutnik, M and Weisshaar, S and Pilat, N and Steiner, R and Wagner, KH and Woodman, RJ and Bondonno, CP and Hodgson, JM and Berry, D and Wolzt, M and Neubauer, O}, title = {Increased Nitrate Intake From Beetroot Juice Over 4 Weeks Changes the Composition of the Oral, But Not the Intestinal Microbiome.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e70156}, doi = {10.1002/mnfr.70156}, pmid = {40522148}, issn = {1613-4133}, support = {//Austrian Science Fund (FWF)/ ; KLI 858//Clinical Research (KLIF) program/ ; }, abstract = {Inorganic dietary nitrate, metabolized through an endogenous pathway involving nitrate reducing bacteria, improves cardiovascular health, but its effects on the oral and intestinal microbiomes of older adults with treated hypertension are unknown. Our study investigated the effects of nitrate from beetroot juice on the oral and intestinal microbiomes of this population. A randomized, double-blind, placebo-controlled crossover trial was conducted with 15 participants (age range: 56-71 years), who consumed nitrate-rich or nitrate-depleted (placebo) beetroot juice for 4 weeks. The oral microbiome analysis revealed an increase in Neisseria and a decrease in Veillonella relative abundance (for both, PERMANOVA p < 0.001), with no significant changes in the intestinal microbiome composition. Our findings suggest that an increased dietary nitrate intake from a vegetable source may selectively modulate the oral microbiome and promote an increased abundance of nitrate-reducing species, which was previously associated with improved cardiovascular health outcomes.}, }
@article {pmid40521244, year = {2025}, author = {Addo, M and Apaame, S and Ghanney, MA and Adu, HK and DeWitt, ME and Addo, SO}, title = {Hepatitis B Infection in Outpatients and Pregnant Women Visiting a Mission Hospital in Ghana.}, journal = {Public health challenges..}, volume = {4}, number = {2}, pages = {e70071}, pmid = {40521244}, issn = {2769-2450}, abstract = {Millions of individuals worldwide suffer from hepatitis B, a serious, potentially fatal liver infection brought on by the hepatitis B virus (HBV). Although vaccines are available for HBV, infections continue to persist in Ghana. This study reports the prevalence of HBV infections in outpatients and pregnant women attending antenatal care at the Seventh-day Adventist (SDA) Hospital in Gbawe, Ghana. This retrospective cohort study involved the review of de-identified medical records of outpatients and pregnant women who visited the hospital between 2022 and 2024. Data on their HBV infection status, sex and age were analysed using R version 4.4.1. A total of 531 outpatients and 768 pregnant women visited the hospital during the study period. The prevalence of HBV infection was 7.5% in outpatients and 3.9% in pregnant women. It was observed that outpatients were more likely to be hepatitis B surface antigen (HBsAg) positive (OR = 2.0, 95%CI = 1.24-3.28, p = 0.005). It was also seen that HBV prevalence increased from 2022 to 2023 and decreased in 2024. There is a need for more educational campaigns to raise awareness of HBV infections, especially in pregnant women due to the risk of mother-to-child transmission. Furthermore, vaccinations need to be made affordable and easily accessible to the general population to ensure maximum coverage within the country.}, }
@article {pmid40518732, year = {2025}, author = {Mota de Almeida, FJ and Rakhimova, O and Romani Vestman, N and Lee, NM and Brundin, M}, title = {In situ imaging and microbiome analysis of calculus-like deposits at the root apex: A case report of refractory apical periodontitis.}, journal = {International endodontic journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/iej.14268}, pmid = {40518732}, issn = {1365-2591}, support = {7003589//Region of V&#xe4;sterbotten (Sweden)/ ; 977100//Region of V&#xe4;sterbotten (Sweden)/ ; RV-967705//Region of V&#xe4;sterbotten (Sweden)/ ; }, abstract = {AIM: This case report explored the application of next-generation sequencing (NGS) and fluorescence in situ hybridization (FISH) to visualize and characterize microbial populations in a refractory endodontic infection with apical calculus-like deposits, a rarely reported phenomenon.<br><br>SUMMARY: Histopathologic analysis revealed bacterial biofilms and calcifications on the root surface, with Gram-positive bacteria predominant in both hard and soft tissues. Microbial sequencing showed Pseudomonadota dominated hard tissues, whereas Bacillota were prevalent in soft tissues, with distinct genera like Lactibacterium and Streptococcus identified. FISH imaging confirmed spatially distributed bacterial taxa, including Actinomycetota and Chloroflexota, within the biofilm, aligning with NGS findings. Notably, Bacteroidota was exclusive to soft tissues, whereas Chloroflexota was detected only in hard tissues. The presence of extensive calculus-like deposits on the root surface provided new insights into the microbial complexity of persistent endodontic infections and their management.<br><br>KEY LEARNING POINTS: The combination of NGS and FISH provided unprecedented insights into the microbial composition of refractory endodontic infections, revealing a diverse and spatially organized ecosystem. Distinct microbial compositions in hard and soft tissues emphasize the importance of targeted therapeutic strategies for endodontic infections. The presence of unique bacterial taxa and biofilms in calculus-like deposits offers new avenues for research into the pathogenesis and persistence of endodontic infections.}, }
@article {pmid40511921, year = {2025}, author = {Mayer, L and Nikolov, G and Kunert, M and Horn, M and Willemsen, A}, title = {Mimivirus transcription and translation occur at well-defined locations within amoeba host cells.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {e0055425}, doi = {10.1128/jvi.00554-25}, pmid = {40511921}, issn = {1098-5514}, abstract = {Many giant viruses replicate in the cytoplasm in viral factories. How exactly these viral factories are established and where the different steps of the replication cycle occur remain largely obscure. We have developed a single-molecule messenger RNA fluorescence in situ hybridization (smFISH) protocol for giant viruses in an Acanthamoeba host. Combined with other labeling techniques (FUNCAT, DiD, rRNA FISH, and DAPI), we show the Mimivirus transcription and translation sites during an infection cycle in the amoeba host cell. Although viral mRNA localization changes depend on the infection stage, transcription occurs at well-defined spots within the viral factory. The original viral cores released within the cytoplasm most likely define these spots. When transported outside of the viral factory, the translation of viral mRNA takes place in a well-defined ring surrounding it. With this study, we obtained novel insights into giant virus replication, of which the methods are widely applicable to other viruses for the visualization and quantification of RNA molecules.IMPORTANCEGiant viruses have massive particle and genome sizes, which are known to infect unicellular eukaryotes. Although most viruses replicate in the host cell's nucleus, the giant Mimivirus replicates in viral factories established in the host cell's cytoplasm. Before this study, the location of the various steps in the Mimivirus replication cycle was largely unknown. By developing new protocols to label giant virus mRNA, protein synthesis, host cell membranes and rRNA, we demonstrate that Mimivirus transcription occurs at well-defined sites within the viral factory. In contrast, translation takes place directly outside of it. This is different from other viruses known to have a cytoplasmic life cycle. These results bring us a step closer to understanding how the genome complexity of viruses influences the virus-host interactions and viral replication strategies.}, }
@article {pmid40510670, year = {2025}, author = {Barnhart, EP and Douterelo, I and Morgan, MJ and Puzon, GJ}, title = {Editorial: Microbial ecology supporting growth of free-living amoebae in natural and engineered water systems.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1620877}, doi = {10.3389/fmicb.2025.1620877}, pmid = {40510670}, issn = {1664-302X}, }
@article {pmid40509663, year = {2025}, author = {van Dijk, JR and Geelhoed, JS and Geerlings, N and Choyikutty, JA and Boschker, HTS and Verbruggen, E and Meysman, FJR}, title = {Inactive "Ghost" Cells Do Not Affect Motility and Long-Range Electron Transport in Filamentous Cable Bacteria.}, journal = {Environmental microbiology}, volume = {27}, number = {6}, pages = {e70117}, pmid = {40509663}, issn = {1462-2920}, support = {G038819N//Fonds Wetenschappelijk Onderzoek/ ; S004523N//Fonds Wetenschappelijk Onderzoek/ ; //Universiteit Antwerpen/ ; PRINGLE 101046719//HORIZON EUROPE European Innovation Council/ ; EMBO ALTF 102-2023//European Molecular Biology Organization/ ; }, mesh = {Electron Transport ; *Bacteria/metabolism/cytology ; Oxidation-Reduction ; Sulfur/metabolism ; *Bacterial Physiological Phenomena ; }, abstract = {Cable bacteria are multicellular filamentous microorganisms that perform electrogenic sulphur oxidation over centimetre-long distances. These filaments contain so-called "ghost cells", which display a highly reduced cytoplasmic content and a lack of metabolic activity. However, the origin and abundance of these ghost cells are not well understood, raising questions about their formation and potential impact on the functioning of the entire filaments. Here, we quantified the abundance of ghost cells in cable bacteria via a targeted propidium iodide staining technique and investigated their morphology and possible origin. Microscopy revealed that ghost cells are present in filaments under in situ conditions, and hence, they are not an artefact from filament sampling. Interestingly, filaments containing ghost cells retained gliding motility, as well as the capacity for long-distance electron transport, thus suggesting that the functionality of the filament as a whole remains largely unaffected by the presence of these ghost cells. Noteworthy is the higher frequency of ghost cells near the ends of filaments, and within filament fragments retrieved from oxic environments. Our findings provide new insights into the adaptive strategies of filamentous bacteria, highlighting their ability to maintain functionality at the organism level despite the fact that some individual cells are no longer metabolically active.}, }
@article {pmid40509476, year = {2025}, author = {Bemis, DH and Camphausen, CE and Liu, E and Dantus, JJ and Navarro, JA and Dykstra, KL and Paltrowitz, LA and Dzhelmach, M and Joerg, M and Tamelessio, P and Belenky, P}, title = {Nutrient Availability and Pathogen Clearance Impact Microbiome Composition in a Gnotobiotic Kimchi Model.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {11}, pages = {}, pmid = {40509476}, issn = {2304-8158}, abstract = {Kimchi is a fermented Korean food typically made with napa cabbage, garlic, radish, ginger, and chili pepper. It is becoming increasingly popular due to its flavor, high fiber content, and purported probiotic benefits. The microbial ecology of the fermentation community has been extensively studied, though what's less understood is how its microbial community changes when nutrients or pathogens are introduced. To study this, we used gnotobiotic cabbage media inoculated with a kimchi starter culture as a model system. These inoculated samples were exposed to E. coli or Bacillus cereus, with or without added nutrients in the form of tryptic soy broth (TSB). We tracked pH, colony-forming units (CFUs), and community composition over time. We also used Oxford Nanopore sequencing to analyze the 16S rRNA gene (V4-V9), followed by use of the Emu algorithm for taxonomic assignments. As expected, LABs suppressed pathogens, but this effect was weaker early on in the nutrient-rich condition. Pathogen exposure changed the overall community-Lactobacillus species became more common, and Leuconostoc mesenteroides less so. Interestingly, adding nutrients alone caused similar microbial shifts to those seen with pathogen exposure. This could suggest that nutrient levels have a larger impact on the final microbiome structure than direct microbial competition. Together, these findings suggest that monitoring total microbial composition, and not just the presence of pathogens, may be important for ensuring kimchi fermentation reproducibility.}, }
@article {pmid40507003, year = {2025}, author = {Karkala, A and Kotoulas, SC and Tzinas, A and Massa, E and Mouloudi, E and Gkakou, F and Pataka, A}, title = {The Lung Microbiome and Its Impact on Obstructive Sleep Apnea: A Diagnostic Frontier.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, pmid = {40507003}, issn = {2075-4418}, abstract = {Obstructive sleep apnea (OSA), a prevalent disorder characterized by recurrent upper airway collapse, is increasingly recognized as a systemic inflammatory condition influenced by microbial dysregulation. Emerging evidence underscores the lung microbiome as a mediator in OSA pathophysiology, where dysbiotic shifts driven by intermittent hypoxia, oxidative stress and mechanical airway trauma amplify inflammatory cascades and perpetuate respiratory instability. This review synthesizes current knowledge on the bidirectional interplay between OSA and lung microbial communities. It aims to highlight how hypoxia-induced alterations in microbial ecology disrupt immune homeostasis, while inflammation-driven mucosal injury fosters pathogenic colonization. Clinical correlations between specific taxa like Streptococcus and Prevotella, and disease severity, suggest microbial signatures as novel biomarkers for OSA progression and treatment response. Furthermore, oxidative stress markers and pro-inflammatory cytokines emerge as potential diagnostic tools that bridge microbial dysbiosis with sleep-related outcomes. However, challenges persist in sampling standardization of the low-biomass lower airways, as well as in causative mechanisms linking microbial dysbiosis to OSA pathophysiology. By integrating microbial ecology with precision sleep medicine, this paradigm shift promises to transform OSA management from mechanical stabilization to holistic ecosystem restoration.}, }
@article {pmid40504771, year = {2025}, author = {Augustijn, HE and Reitz, ZL and Zhang, L and Boot, JA and Elsayed, SS and Challis, GL and Medema, MH and van Wezel, GP}, title = {Genome mining based on transcriptional regulatory networks uncovers a novel locus involved in desferrioxamine biosynthesis.}, journal = {PLoS biology}, volume = {23}, number = {6}, pages = {e3003183}, pmid = {40504771}, issn = {1545-7885}, mesh = {*Deferoxamine ; *Gene Regulatory Networks ; Gene Expression Regulation, Bacterial ; *Streptomyces coelicolor/genetics/metabolism ; *Genome, Bacterial ; Multigene Family ; Bacterial Proteins/genetics/metabolism ; Operon ; Computational Biology ; Iron/metabolism ; Data Mining ; }, abstract = {Bacteria produce a plethora of natural products that are in clinical, agricultural and biotechnological use. Genome mining has uncovered millions of biosynthetic gene clusters (BGCs) that encode their biosynthesis, the vast majority of them lacking a clear product or function. Thus, a major challenge is to predict the bioactivities of the molecules these BGCs specify, and how to elicit their expression. Here, we present an innovative strategy whereby we harness the power of regulatory networks combined with global gene expression patterns to predict BGC functions. Bioinformatic analysis of all genes predicted to be controlled by the iron master regulator DmdR1 combined with co-expression data, led to identification of the novel operon desJGH that plays a key role in the biosynthesis of the iron overload drug desferrioxamine (DFO) B in Streptomyces coelicolor. Deletion of either desG or desH strongly reduces the biosynthesis of DFO B, while that of DFO E is enhanced. DesJGH most likely act by changing the balance between the DFO precursors. Our work shows the power of harnessing regulation-based genome mining to functionally prioritize BGCs, accelerating the discovery of novel bioactive molecules.}, }
@article {pmid40504377, year = {2025}, author = {Zhang, J and Zhao, Z and Zhu, C and Wang, E and Brunel, B and Li, S and Zheng, Q and Feng, Z and Zhang, H}, title = {Diverse Peanut Bradyrhizobial Communities in Chinese Soils: Insights from Eastern, Central, and Northern Henan Province.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {65}, pmid = {40504377}, issn = {1432-184X}, support = {2024M761756//China Postdoctoral Science Foundation/ ; Yuzutong[2023]No.11//Central Plains Youth Top Talent Project/ ; Sabbatical Year SIP20200726//IPN, Mexico/ ; }, mesh = {*Arachis/microbiology ; China ; *Bradyrhizobium/genetics/classification/isolation &amp; purification ; Phylogeny ; *Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Polymorphism, Restriction Fragment Length ; Symbiosis ; Soil/chemistry ; Root Nodules, Plant/microbiology ; Bacterial Proteins/genetics ; }, abstract = {Henan province is a major peanut-producing area in China, but research on rhizobia nodulating peanut have been limited to southern Henan, which accounts for only less than half of the province. A collection of 212 strains of peanut rhizobia was obtained from six field sites in eastern, central, and northern Henan, Central China, by using peanut as a trap host under glasshouse conditions. PCR-RFLP analysis of ribosomal IGS sequences classified the 212 strains into 28 distinct types. Phylogenetic analyses of the 16S rRNA, atpD, gyrB, dnaK, and rpoB genes from 30 representative strains of the 28 IGS types identified revealed the presence of Bradyrhizobium. liaoningense, B. yuanmingense, B. zhengyangense, and two novel Bradyrhizobium genospecies. This composition differs from the peanut rhizobia community found in southern Henan. B. liaoningense was the dominant species, covering 49% of the total isolates across the field sites, while B. zhengyangense accounting for 27%, B. yuanmingense for 7% and the two novel Bradyrhizobium genospecies for 17%. Phylogenetic analysis showed that the symbiosis-related nodC and nifH gene sequences clustered into six groups: three associated exclusively with the peanut host (symbiovar arachidis and two unnamed group), three originating from other legume hosts (sv. glycinearum, cajani and retamae). Through the principal component analysis (PCA) between IGS types or species and soil physicochemical properties and environmental factors, it showed that IGS types 1, 3, 5, 8, 9, 12, 14, 15, 18, and 21 positively correlated with AveTmax, AveTmin, AN and AP. IGS types 4, 11, 16, 17, 20, 25, and 26 were positively associated with Alt, AvePrecp, and pH. IGS types 2, 7, 10, 22, 24, and 27 correlated with AP, while remaining types exhibited correlations with OM. In addition, B. yuanmingense, B. liaoningense, and Bradyrhizobium genosp. I positively affected by AveTmax, AP, AN, and AK. Bradyrhizobium genosp. II positively correlated with AK, AN, and OM while B. zhengyangense mainly affected by AvePrecp and pH. The alkaline soil pH in this study differs greatly from the acid soils in southern Henan, explaining the inconsistency between the species of peanut rhizobia detected in southern Henan and the rest of the province. The symbiotic effect assay demonstrated that all representative strains successfully formed nodules and exhibited a significant increase in symbiotic efficiency. Representative strains revealed diverse abiotic stress tolerance to NaCl, acidity, alkalinity, temperature and drought. It conducted a comprehensive collection of peanut rhizobia in eastern, central, and northern Henan province, identifying two putative novel Bradyrhizobium species and isolating rhizobial strains with high symbiotic efficiency and robust stress tolerance. This study is a necessary basic for the producing and application of peanut rhizobial inoculant in this main agricultural province.}, }
@article {pmid40504009, year = {2025}, author = {Schroer, HW and Markland, K and Ling, F and Just, CL}, title = {Hydraulic Connectivity and Hydrochemistry Influence Microbial Community Structure in Agriculturally Affected Alluvial Aquifers in the Midwestern United States.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {24}, pages = {12279-12291}, doi = {10.1021/acs.est.5c03155}, pmid = {40504009}, issn = {1520-5851}, mesh = {*Groundwater/microbiology ; *Microbiota ; Midwestern United States ; Drinking Water ; }, abstract = {Alluvial aquifers can provide ecosystem services and drinking water, but much remains unknown about human effects on aquifer microbiomes. Therefore, we used amplicon sequencing and hydrochemical characterization to pair microbial communities with environmental conditions across 37 alluvial aquifer wells. The study region spanned eastern Iowa and southern Minnesota (USA) and contained a combination of drinking water and monitoring wells. In terms of microbial ecology, dominant phyla across the wells included Proteobacteria, Bacteroidota, Patescibacteria, Planctomycetota, and Nitrospirota. Tritium, an indicator of infiltration and surface water influence, was the highest correlated variable with the Shannon index (α-diversity) by the Spearman rank sum (ρ = 0.60) and one of only four significant environmental variables in the constrained correspondence analysis. We built random forest regression models to predict tritium concentrations from microbial family relative abundance (held-out testing coefficient of determination (R[2]) = 0.77 and mean absolute percentage error = 7%) and interpreted the models with Shapley additive explanation values. The most important families for predicting tritium concentrations were Nitrosopumilaceae and Methylomirabilaceae. Upwelling methane could contribute to the unusual coupling of ammonia oxidation by Nitrosopumilaceae with simultaneous nitrite-dependent methane oxidation by Methylomirabilaceae. Taken together, we illuminate the relationship among hydrochemistry, hydraulic connectivity, and alluvial aquifer microbiomes.}, }
@article {pmid40502102, year = {2025}, author = {Baty, JJ and Drozdick, AK and Pfeiffer, JK}, title = {P. aeruginosa rhamnolipids stabilize human rhinovirus 14 virions.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40502102}, issn = {2692-8205}, abstract = {Many mammalian viruses encounter bacteria and bacterial molecules over the course of infection. Previous work has shown that the microbial ecology of the gut plays an integral role in poliovirus and coxsackievirus infection, where bacterial glycans can facilitate virus-receptor interactions, enhance viral replication, and stabilize viral particles. However, how airway bacteria alter respiratory viral infection is less understood. Therefore, we investigated whether a panel of airway bacteria affect rhinovirus stability. We found that Pseudomonas aeruginosa, an opportunistic airway pathogen, protects human rhinovirus 14 from acid or heat inactivation. Further investigation revealed that P. aeruginosa rhamnolipids, glycolipids with surfactant properties, are necessary and sufficient for stabilization of rhinovirus virions. Taken together, this work demonstrates that specific molecules produced by an opportunistic airway pathogen can influence a respiratory virus.}, }
@article {pmid40500964, year = {2025}, author = {Li, S and Wang, T and Liu, M and Ma, T and Li, Y and Liu, J and Liu, Y and Shen, W and Ma, J and Wang, X and Han, X and Wang, H and Zhang, X}, title = {α-Linolenic Acid-Rich Flaxseed Oil Improves Polycystic Ovary Syndrome via Regulating Lipid Metabolism by GPR120-cAMP Pathway and Restoring Gut Microecology.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e70136}, doi = {10.1002/mnfr.70136}, pmid = {40500964}, issn = {1613-4133}, support = {82460793//National Natural Science Foundation of China/ ; 82160691//National Natural Science Foundation of China/ ; 2023AAC03216//Ningxia Natural Science Foundation, China/ ; 2023BEG02011//Key Research and Development Program of Ningxia/ ; 2022BSB03112//Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; XZ2021003//Key Laboratory of Fertility Preservation and Maintainance of Ministry of Education of Ningxia Medical University/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; }, abstract = {Polycystic ovary syndrome (PCOS) is a common endocrine disorder that affects metabolic and reproductive health in women. α-Linolenic acid (ALA)-rich flaxseed oil as a dietary food has been suggested to offer potential therapeutic benefits in managing metabolic disturbances associated with PCOS. This study investigates the effects of ALA-rich flaxseed oil on lipid metabolism and gut microecology in a PCOS rat model. The PCOS model was induced in rats using letrozole, and the animals were then administered ALA-rich flaxseed oil. Metabolomics, transcriptomics, 16S rRNA sequencing, hormonal levels, and markers of metabolic health were assessed. Results showed that ALA-rich flaxseed oil significantly improved lipid metabolism by reducing serum cholesterol and triglycerides. In addition, we found that the improvement in lipid metabolism may be associated with the activation of the GPR120-cAMP pathway. Furthermore, gut microbiota analysis revealed a restoration of gut microbial ecology, with a shift toward a more balanced and healthy microbial composition. ALA-rich flaxseed oil shows promising potential as a dietary intervention for managing metabolic disturbances in PCOS. Its effects on lipid metabolism and gut microecology highlight its nutritional relevance, offering new insights into the dietary management of PCOS and its associated metabolic disorders.}, }
@article {pmid40500753, year = {2025}, author = {Bograd, A and Oppenheimer-Shaanan, Y and Levy, A}, title = {Plasmids, prophages, and defense systems are depleted from plant microbiota genomes.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {163}, pmid = {40500753}, issn = {1474-760X}, support = {1535/20//Israeli Science Foundation/ ; 1535/20//Israeli Science Foundation/ ; 1535/20//Israeli Science Foundation/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 81259//Israel Innovation Authority/ ; 81259//Israel Innovation Authority/ ; 81259//Israel Innovation Authority/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; ZN4041//Volkswagen Stiftung/ ; ZN4041//Volkswagen Stiftung/ ; ZN4041//Volkswagen Stiftung/ ; }, mesh = {*Prophages/genetics ; *Plasmids/genetics ; *Plants/microbiology ; *Genome, Bacterial ; *Microbiota/genetics ; Metagenome ; *Bacteria/genetics/virology ; }, abstract = {Plant-associated bacteria significantly impact plant growth and health. Understanding how bacterial genomes adapt to plants can provide insights into their growth promotion and virulence functions. Here, we compare 38,912 bacterial genomes and 6073 metagenomes to explore the distribution of mobile genetic elements and defense systems in plant-associated bacteria. We reveal a consistent taxon-independent depletion of prophages, plasmids, and defense systems in plant-associated bacteria, particularly in the phyllosphere, compared to other ecosystems. The mobilome depletion suggests the presence of unique ecological constraints or molecular mechanisms exerted by plants to control the bacterial mobilomes independently of bacterial immunity.}, }
@article {pmid40500405, year = {2025}, author = {Chen, TK and Shiau, YJ}, title = {Effects of Soil Properties and Seasonal Variations on Microbial Communities in Constructed Wetlands.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {64}, pmid = {40500405}, issn = {1432-184X}, support = {110-2313-B-002-033-MY3//National Science and Technology Council/ ; }, mesh = {*Wetlands ; Seasons ; *Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Soil/chemistry ; Denitrification ; *Microbiota ; Biodiversity ; Nitrates/analysis ; Sulfates/analysis ; Nitrification ; }, abstract = {Constructed wetlands (CWs) are important ecosystems with numerous benefits such as wastewater treatment, wildlife habitat protection, and stormwater remediation. However, the development of soil microbial communities in CWs over time remains understudied. This study comprehensively investigates microbial diversity and community composition in three constructed wetlands, focusing on the influence of wetland age, soil depth, and environmental factors. The results indicate that both soil depth and seasonal variations significantly affect alpha diversity, particularly in surface soils. The predominant microbial communities, including nitrifying and denitrifying communities, were identified across the studied wetlands. Moreover, sulfate-rich conditions may promote sulfur autotrophic denitrification. Redundancy analysis and multiple linear regression highlighted the distinction between autotrophic and heterotrophic denitrifiers. Soluble organic carbon was identified as a major factor influencing heterotrophic denitrifying bacteria, while sulfate and nitrate levels were more closely associated with autotrophic denitrifying bacteria. Overall, these findings provide valuable insights into microbial community dynamics in CWs and can help optimize wetland management strategies for improved nutrient removal efficiency.}, }
@article {pmid40499249, year = {2025}, author = {McDonagh, F and Murray, EK and Hallahan, B and Miliotis, G}, title = {Systematic examination of off-target effects of antipsychotic medications associated with microbiome disruption and heightened bacterial infection risks.}, journal = {Journal of psychiatric research}, volume = {189}, number = {}, pages = {171-183}, doi = {10.1016/j.jpsychires.2025.05.046}, pmid = {40499249}, issn = {1879-1379}, abstract = {OBJECTIVE: This systematic review aims to critically evaluate the link between antipsychotic drugs and bacterial infection risk, emphasising antimicrobial properties of antipsychotics, and microbiome changes that might heighten susceptibility to bacterial infections.<br><br>METHODS: A systematic literature search was conducted across PubMed, Scopus, and Google Scholar, up to March 2024. Peer-reviewed articles that investigated the relationship between antipsychotics, their antimicrobial effects, microbiome alterations, and bacterial infection risk were included. Data extracted included antipsychotic type, infection risks, patient demographics, and study methodologies. Risk-of-bias assessments were performed using tools such as the Newcastle-Ottawa Scale and the SYRCLE risk-of-bias tool.<br><br>RESULTS: The review analysed twenty-six studies detailing antimicrobial properties of antipsychotics, four studies on antipsychotic-induced microbiome alterations, and thirty-one studies assessing bacterial infection risk associated with antipsychotics. First-generation antipsychotics were observed to have broad antimicrobial properties, whereas second-generation antipsychotics primarily affected commensal bacteria. At least four antipsychotics were observed to disrupt the gut microbiota. A heightened risk of infection was observed among psychiatric cohorts as well as off-label antipsychotics use, with clozapine linked to a substantial increase in respiratory infection risk.<br><br>DISCUSSION: Although antipsychotics remain indispensable in psychiatric care, their association with an increased risk of bacterial infections underscores the need for judicious prescribing and vigilant monitoring. The review identifies significant knowledge gaps attributable to inconsistent research methodologies, small study cohorts, lack of controls, and focus on a limited range of antipsychotics. Further standardised research is essential to deepen our understanding of these associations and to inform improved prescribing practices and risk mitigation strategies.}, }
@article {pmid40498465, year = {2025}, author = {Samimi, A and Hengoju, S and Martin, K and Rosenbaum, MA}, title = {Advancing droplet-based microbiological assays: optofluidic detection meets multiplexed droplet generation.}, journal = {The Analyst}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5an00130g}, pmid = {40498465}, issn = {1364-5528}, abstract = {Microbiological assays are crucial in understanding microbial ecology and developing new bioproducts. Given the significance of these assays, there is a growing interest in developing high throughput experimentation methods capable of assay multiplexing to enhance the accuracy and efficiency. In this study, we integrate a multiplexed droplet generation set-up into an optofluidic detection chip to facilitate rapid and high throughput analysis of microbiological assays. The optofluidic detection set-up at the same time enables fast and sensitive assessment of droplet condition and content, providing analysis scalability in a high throughput manner. Employing the integration, we produced unique fluorescence barcoded droplets containing defined concentrations of various carbon sources, allowing the simultaneous investigation of microbial growth and metabolic capacity under different experimental conditions. We successfully validated the robustness of the established setup in analyzing and distinguishing different fluorescence barcodes. Our findings highlight the potential of the integrated platform for a broader range of applications in high throughput drug screening, environmental monitoring, and microbiology research.}, }
@article {pmid40498364, year = {2025}, author = {Castledine, M and Esom, C and Van Nieuwenhuyse, B and Djebara, S and Merabishvili, M and Pirnay, JP and Buckling, A}, title = {Predicting clinical phage therapy outcomes in vitro: results using mixed versus single isolates from an MRSA case study.}, journal = {Journal of applied microbiology}, volume = {136}, number = {6}, pages = {}, doi = {10.1093/jambio/lxaf144}, pmid = {40498364}, issn = {1365-2672}, support = {NE/V012347/1//NERC/ ; NE/S000771/1//NERC/ ; }, mesh = {*Methicillin-Resistant Staphylococcus aureus/virology/isolation &amp; purification ; *Phage Therapy/methods ; Humans ; *Staphylococcal Infections/therapy/microbiology ; Anti-Bacterial Agents/therapeutic use ; Treatment Outcome ; Bacteriophages ; Male ; *Staphylococcus Phages/physiology ; }, abstract = {AIMS: In phage therapy case studies, 1-3 bacteria isolates are typically tested against phages (phagogram). However, as bacteria populations differ in their susceptibility to phages and antibiotics, the strains selected may not represent how the infecting population will respond to treatment. Our aim was to assess whether the effects of phage on single or a mix of isolates in vitro show more comparable results to that observed during a clinical case study.<br><br>METHODS AND RESULTS: The patient presented with a methicillin resistant Staphylococcus aureus infection (MRSA). In this previously published case study, phage therapy alongside antibiotics rapidly cleared blood cultures of bacteria while localized regions, including the lungs, took longer to clear of bacteria. In this follow-up study, mixed isolates were more likely to persist than single isolates in vitro, more closely representing the lung, but not blood, infections. These results may reflect the different degrees of genetic diversity of the infecting bacteria in these sites.<br><br>CONCLUSIONS: For this patient, phage therapy predictions were significantly affected by whether we used mixed versus single isolates, but the predictive precision depended on the site of in vivo infection.}, }
@article {pmid40495815, year = {2025}, author = {Abiriga, D and Odong, R and Bakyayita, GK and Semyalo, R and Okello, W and Grossart, HP}, title = {The microbiology of Uganda's large freshwater lakes experiencing anthropogenic and climatic perturbations: why it matters-a review.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2048}, pages = {20243072}, pmid = {40495815}, issn = {1471-2954}, mesh = {Uganda ; *Lakes/microbiology ; *Climate Change ; *Anthropogenic Effects ; *Water Microbiology ; Biodiversity ; Bacteria ; }, abstract = {Intensification of pollution of African water resources due to human activities together with climate change has serious implications for Africa's blue economy, biodiversity and human health. Despite these overwhelming threats, there is limited research as evidenced by the underrepresentation of Africa-based data in global ecological and biochemical models. This review, therefore, aims to highlight key challenges and existing research gaps, particularly in Ugandan freshwater ecosystems. We focus on lake microbiology as this scientific field has been greatly underrepresented. Aquatic microorganisms are situated at the base of lake food webs and thus play crucial roles in the evolution and maintenance of water quality, attenuation of pollutants, and control of biogeochemical cycling through the microbial loop. Until now, the microbiology of Ugandan lakes has not been systematically studied. Thus, many open fundamental microbial ecology questions need to be urgently addressed to generate valuable information to advance future research, education, management and policy in Uganda and beyond. These include, but are not limited to: identification of microbial taxa and functional genes in relation to anthropogenic and climatic influence; seasonal and spatial variation in species diversity and functions; diversity and functions of planktonic, sediment, biofilm and mat communities; antimicrobial resistance burden; plastisphere communities; and geomicrobiology.}, }
@article {pmid40493213, year = {2025}, author = {Vila Duplá, M}, title = {Advancements in Algal Microbiome Research: A Game-Changer for Climate Resilience and Invasion Success?.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {63}, pmid = {40493213}, issn = {1432-184X}, mesh = {*Microbiota ; *Climate Change ; *Seaweed/microbiology ; *Introduced Species ; }, abstract = {While marine microbiomes have been getting more attention in recent years, they remain understudied compared to those of terrestrial systems. With the refinement of molecular methods, microbiome research has extended to other key marine organisms such as macroalgae. The microbiome plays a key role in macroalgal health, adaptation to environmental conditions, and resilience to climate stressors. The main factors affecting the algal microbiome are host specificity (genetics, functional profile, phylum and species identity), life stage, morphology, thallus region, and tissue age. Other significant drivers of microbiome community structure include spatiotemporal distribution and environmental conditions, especially as global stressors intensify with climate change. The mechanisms through which the microbiome of invasive seaweeds might enhance their competitiveness over native species are still unclear. However, there is evidence that, like climate resilience, invasive potential is linked to the functional flexibility of associated microbiota, allowing the host to adapt to the new environmental conditions. The main objective of this review was to synthesize the current understanding of the macroalgal microbiome and propose future directions in microbiome research based on identified shortcomings. Based on the knowledge gaps detected, there is an urgent need for multi-factorial experimental studies that link host and microbiome gene expression through chemical signals under future climate change scenarios, standardization of analytical methods, and a focus on underrepresented geographical regions and species. While algal microbiome research holds great promise for predicting and mitigating the effects of climate change and invasive species, embracing new tools and tackling ecologically relevant mechanistic and applied questions will be essential to advancing this field.}, }
@article {pmid40492114, year = {2025}, author = {Zhang, Y and Fan, J and Zhao, J and Zhu, H and Xia, Y and Xu, H}, title = {A telomere-associated molecular landscape reveals immunological, microbial, and therapeutic heterogeneity in colorectal cancer.}, journal = {Frontiers in molecular biosciences}, volume = {12}, number = {}, pages = {1615533}, pmid = {40492114}, issn = {2296-889X}, abstract = {BACKGROUND: Colorectal cancer (CRC) ranks among the most prevalent malignancies of the gastrointestinal tract and remains a leading cause of cancer-related mortality worldwide. Although telomere biology has been increasingly implicated in immune modulation and tumor progression, its clinical significance in CRC remains poorly understood.<br><br>METHODS: We developed a telomere score, termed TELscore, by integrating transcriptomic and intratumoral microbiome profiles from publicly available colorectal cancer (CRC) cohorts. To comprehensively characterize TELscore subgroups, we performed pathway enrichment analysis, tumor immune microenvironment (TIME) profiling, and microbiome niche assessment. Whole-slide histopathological images (WSIs) and immunohistochemical (IHC) staining were utilized to visualize immune features, including tertiary lymphoid structures (TLSs), across subgroups. Patients were stratified into high and low TELscore categories, and the predictive robustness was validated across multiple independent training and validation cohorts. Chemotherapeutic drug sensitivity was evaluated using pharmacogenomic data from the Genomics of Drug Sensitivity in Cancer (GDSC) database. Furthermore, the predictive capacity of TELscore for immunotherapy response was independently assessed in an external cohort. Finally, single-cell RNA sequencing (scRNA-seq) analysis was conducted to further dissect the cellular landscape and immunological heterogeneity within the TME.<br><br>RESULTS: TELscore stratified patients into two biologically and clinically distinct subgroups. The high TELscore group, which exhibited significantly shorter DFS, showed marked enrichment of tumorigenic pathways such as EMT, along with a distinctly immunosuppressive TME. This was reflected by elevated ESTIMATE/TIDE scores and corroborated by CIBERSORT, which revealed increased infiltration of M0 macrophages and upregulation of immunosuppressive signatures. In contrast, the low TELscore group was enriched for cell cycle related pathways, including E2F targets and the G2/M checkpoint, and demonstrated higher infiltration of pro-inflammatory M1 macrophages. 16S rRNA sequencing further revealed a divergent intratumoral microbiome between subgroups, the high TELscore group harbored significantly greater relative abundance of Selenomonas and Lachnoclostridium, two pathogenic genera previously associated with colorectal tumorigenesis. Complementary histopathological assessment via WSI demonstrated a marked absence of intraTLSs in high TELscore tumors. From a therapeutic standpoint, high TELscore tumors exhibited reduced sensitivity to standard chemotherapeutic agents-including Fluorouracil, Irinotecan, Oxaliplatin, and Docetaxel-as reflected by elevated IC50 values. Conversely, these tumors demonstrated increased susceptibility to MAPK pathway inhibitors, such as Selumetinib and Trametinib. Notably, TELscore also served as a robust predictor of immunotherapy response, which was validated in the IMvigor210 cohort. Finally, scRNA analysis highlighted profound cellular and functional divergence between TELscore subgroups. We identified intensified intercellular communication between inflammatory macrophages and fibroblasts, reinforcing the presence of an immunosuppressive niche.<br><br>CONCLUSION: TELscore is a robust stratification tool that captures the interplay between tumor biology, immune characteristics, and microbial ecology in colorectal cancer. By identifying clinically relevant subtypes with distinct therapeutic vulnerabilities, TELscore offers a powerful framework to advance personalized treatment and precision oncology.}, }
@article {pmid40488407, year = {2025}, author = {Grossman, AS and Lei, L and Botting, JM and Liu, J and Nahar, N and Liu, J and McLean, JS and He, X and Bor, B}, title = {Saccharibacteria deploy two distinct type IV pili, driving episymbiosis, host competition, and twitching motility.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf119}, pmid = {40488407}, issn = {1751-7370}, abstract = {All cultivated Patescibacteria, also known as the candidate phyla radiation, are obligate episymbionts residing on other microbes. Despite being ubiquitous in many diverse environments, including mammalian microbiomes, molecular mechanisms of host identification and binding amongst ultrasmall bacterial episymbionts remain largely unknown. Type 4 pili are well conserved in this group and could potentially facilitate these symbiotic interactions. To test this hypothesis, we genetically targeted pili genes in Saccharibacteria Nanosynbacter lyticus strain TM7x to assess their essentiality and roles in symbiosis. Our results revealed that Nanosynbacter lyticus assembles two distinct type 4 pili: a non-essential thin pilus that has the smallest diameter of any type 4 pili and contributes to host-binding and episymbiont growth; and an essential thick pilus involved in twitching motility. To understand the role of these pili in vivo we developed Saccharibacteria competition assays and species specific Fluorescence in situ hybridization probes. Competition between different Saccharibacteria within mock communities demonstrated consistent competitive outcomes that were not driven by priority effects but were dependent on the thin pilus. Collectively our findings demonstrate that Saccharibacteria encode unique extracellular pili that enable their underexplored episymbiotic lifestyle and competitive fitness within a community.}, }
@article {pmid40487916, year = {2025}, author = {Okazaki, Y and Nishikawa, Y and Wagatsuma, R and Takeyama, H and Nakano, SI}, title = {Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus-host pairing of freshwater bacteria.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf086}, pmid = {40487916}, issn = {2730-6151}, abstract = {Characterizing virus-host pairs and the infection state of individual cells is the major technical challenge in microbial ecology. We addressed these challenges using state-of-the-art single-cell genome technology (SAG-gel) combined with extensive metagenomic datasets targeting the bacterial and viral communities in Lake Biwa. From two water layers and two seasons, we obtained 862 single-cell amplified genomes (SAGs), including 176 viral (double-stranded DNA phage) contigs, which identified novel virus-host pairs involving dominant freshwater lineages. The viral infection rate, estimated by mapping the individual SAG's raw reads to viral contigs, showed little variation among samples (12.1%-18.1%) but significant variation in host taxonomy (4.2%-65.3%), with copiotrophs showing higher values than oligotrophs. The high infection rates of copiotrophs were attributed to collective infection by diverse viruses, suggesting weak density-dependent virus-host selection, presumably due to their nonpersistent interactions with viruses resulting from fluctuating abundance. In contrast, the low infection rates of oligotrophs supported the idea that their codominance with viruses is achieved by genomic microdiversification, which diversifies the virus-host specificity, sustained by their large population size and persistent density-dependent fluctuating selection. Notably, we discovered viruses infecting CL500-11, the dominant bacterioplankton lineage in deep freshwater lakes worldwide. These viruses showed extremely high read coverages in cellular and virion metagenomes but were detected in <1% of host cells, suggesting a low infection rate and high burst size. Overall, we revealed highly diverse virus-host interactions within and between host lineages that were overlooked at the metagenomic resolution.}, }
@article {pmid40487326, year = {2025}, author = {Bornbusch, SL and Dami, KA}, title = {Connecting microbial ecology to human fertility and reproduction: perspectives from the reproductive microbiomes of animals.}, journal = {F&amp;S reports}, volume = {6}, number = {Suppl 1}, pages = {45-49}, pmid = {40487326}, issn = {2666-3341}, abstract = {In all vertebrates, reproduction occurs in the context of host-associated microbiomes, which are increasingly recognized for their contributions to reproductive success. Although host-associated microbiomes are species specific, synthesizing patterns in microbial ecology across human and animal taxa provides perspectives for understanding the factors that shape microbial communities and their contributions to reproduction. Additionally, the fertility and reproductive physiology of animals under human care-particularly endangered species-is often meticulously monitored to maximize reproductive opportunities. In this mini-review, we examine current knowledge on reproductive microbiomes in animals, focusing, when available, on the sparse literature for wildlife species. We suggest ways in which studying animal microbial ecology may advance human fertility and reproduction by focusing on 3 microbial communities-vaginal, milk, and seminal microbiomes-which represent a large portion of literature and have clear implications for reproductive health. We identify avenues of future research that will further strengthen the linkages between reproductive research in wildlife species and humans and provide potential guidelines for practical applications of microbiome science to human reproductive health.}, }
@article {pmid40483289, year = {2025}, author = {Swain, PP and Subudhi, E and Sahoo, RK}, title = {Heavy Metals and Carbapenem-Resistant Klebsiella pneumoniae in a River System of Odisha, India: Correlation and Integrated Risk Assessment.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {62}, pmid = {40483289}, issn = {1432-184X}, support = {523/2020(BSR)//University Grants Commission/ ; }, mesh = {*Metals, Heavy/analysis ; *Rivers/microbiology/chemistry ; India ; *Klebsiella pneumoniae/drug effects/genetics/isolation &amp; purification ; Risk Assessment ; *Water Pollutants, Chemical/analysis ; *Carbapenems/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Wastewater/microbiology ; Environmental Monitoring ; Humans ; Microbial Sensitivity Tests ; }, abstract = {The unregulated release of heavy metals and antibiotics into rivers has the potential to significantly impact human health. Infections caused by healthcare-associated pathogen, carbapenem-resistant Klebsiella pneumoniae (CRKP), present a critical challenge to clinical practitioners due to its resistance to last-line antibiotics. In this study, we investigated co-contamination of heavy metals (As, Cd, Cr, Mn, and Pb) and CRKP isolates in water samples from multiple sites along the river receiving wastewater discharge from urban areas of twin-city, Odisha. We used a composite risk scoring framework integrating chemical risks (based on hazard indices (HI) of heavy metals) and biological risks (based on the proportion of CRKP isolates exhibiting multidrug-resistant phenotypes and their multiple antibiotic resistance (MAR) index. Furthermore, Spearman's correlations and redundancy analysis (RDA) were employed to assess the association between heavy metals and antibiotic resistance genes (ARGs). From the total CRKP isolates identified (n = 91), 90.1% and 9.89% exhibited multidrug resistant (MDR) and extensively drug-resistant (XDR) phenotypes, respectively. Sites D2 and C2 were flagged as high-risk sites based on their composite risk scores of 0.735 and 0.699, respectively. Positive correlations were observed between heavy metals and ARGs (blaOXA-48, blaTEM, and blaSHV). The findings raise concern regarding the potential threat of CRKP and heavy metal pollution in river water while also emphasizing the need for integrated assessment to control their release into the environment.}, }
@article {pmid40482721, year = {2025}, author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW}, title = {Root architecture and the rhizosphere microbiome: Shaping sustainable agriculture.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {359}, number = {}, pages = {112599}, doi = {10.1016/j.plantsci.2025.112599}, pmid = {40482721}, issn = {1873-2259}, abstract = {Understanding root architecture and exudation is fundamental for enhancing crop productivity and promoting sustainable agriculture. Historically, plant researchers have focused on above-ground traits to increase yield and reduce input dependence. However, below-ground traits, especially those related to the root system, are equally critical yet often overlooked due to phenotyping challenges. Root architecture, including some root traits, i.e., lateral root density, root hair abundance, and root tip number, plays central roles in plant establishment, stress tolerance, and the recruitment of beneficial microbes in the rhizosphere. Root exudates, a complex array of chemical compounds released by roots, vary with plant species, developmental stage, and environmental conditions. These compounds act as signals and nutrients, shaping the composition and function of rhizosphere microbial communities. In turn, the microbiome of rhizosphere contributes to plant health by facilitating nutrient uptake, enhancing stress resilience, and providing defense against pathogens. Integrating root traits into breeding programs offers promising opportunities to select for genotypes that are more efficient in recruiting beneficial microbes. Heritable root traits, such as increased branching, finer roots, and higher exudation capacity, can enhance microbiome assembly and stability. The assessment of genes can also regulate of these traits and represent targets for genomics-assisted selection. Some strategies, such as microbiome engineering, particularly through the design of synthetic microbial communities (SynComs), can be used to modulate root architecture and optimize plant-microbe interactions. Despite these promising outcomes, challenges remain in translating SynCom applications to the field due to environmental variability, native microbial competition, and limited understanding of host genetic controls. This review discusses how root architecture shapes the rhizosphere microbiome and explores strategies, such as trait-based breeding and microbiome engineering, for advancing sustainable crop production.}, }
@article {pmid40481550, year = {2025}, author = {Zhu, F and Ying, H and Siadat, SD and Fateh, A}, title = {The gut-lung axis and microbiome dysbiosis in non-tuberculous mycobacterial infections: immune mechanisms, clinical implications, and therapeutic frontiers.}, journal = {Gut pathogens}, volume = {17}, number = {1}, pages = {40}, pmid = {40481550}, issn = {1757-4749}, abstract = {Non-tuberculous mycobacteria (NTM) are emerging pathogens of global concern, particularly in regions with declining tuberculosis rates. This review synthesizes current evidence on the epidemiology, immune pathogenesis, and microbiome interactions underlying NTM infections. The rising incidence of NTM is driven by environmental factors, immunocompromised populations, and advanced diagnostics. Clinically, NTM manifests as pulmonary, lymphatic, skin/soft tissue, or disseminated disease, with Mycobacterium avium complex (MAC) and M. abscessus being predominant pathogens. Host immunity, particularly Th1 responses mediated by IL-12/IFN-γ and TLR2 signaling, is critical for controlling NTM, while dysregulated immunity (e.g., elevated Th2 cytokines, PD-1/IL-10 pathways) exacerbates susceptibility. Emerging research highlights the gut-lung axis as a pivotal mediator of disease, where microbiome dysbiosis-marked by reduced Prevotella and Bifidobacterium-impairs systemic immunity and promotes NTM progression. Short-chain fatty acids (SCFAs) and microbial metabolites like inosine modulate macrophage and T-cell responses, offering therapeutic potential. Studies reveal distinct airway microbiome signatures in NTM patients, characterized by enriched Streptococcus and Prevotella, and reduced diversity linked to worse outcomes. Despite advances, treatment remains challenging due to biofilm formation, antibiotic resistance, and relapse rates. This review underscores the need for microbiome-targeted therapies, personalized medicine, and longitudinal studies to unravel causal relationships between microbial ecology and NTM pathogenesis.}, }
@article {pmid40481438, year = {2025}, author = {Babalola, OO and Osuji, IE and Akanmu, AO}, title = {Amplicon-based metagenomic survey of microbes associated with the organic and inorganic rhizosphere soil of Glycine max L.}, journal = {BMC genomic data}, volume = {26}, number = {1}, pages = {40}, pmid = {40481438}, issn = {2730-6844}, abstract = {OBJECTIVES: The metagenomic dataset of 16S rRNA and ITS gene amplicons of DNA were obtained from the cultivated soybean rhizosphere of organic and inorganic treatments. The organic treatments consisted of poultry waste, and cow dung treatments while the inorganic consisted of samples from untreated soybean plots and the bulk. Amplicon sequencing was performed on the Illumina platform, and the raw sequence data were processed and analyzed using Quantitative Insights Into Microbial Ecology (QIIME 2 version 2019.1.).<br><br>DATA DESCRIPTION: The analysis revealed a metagenomic library from soybean rhizospheric soils, providing insights into diversity and distribution of the bacterial and fungal community diversities. The most predominant bacteria phylum taxa across the treatments were Proteobacteria, Firmicutes, Actinobacteriota and Bacteriodota, while those for fungi were Ascomycota, Basidiomycota and Glomeromycota. The dataset provides insights into how different organic fertilization sources affect the structure, composition, and diversity of the microbiome in the soybean rhizosphere. The sequences have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) with assigned bioproject accession numbers; 16S rRNA (SRP540791) and ITS (SRP541849).}, }
@article {pmid40480043, year = {2025}, author = {Keating, C and Trego, A and O'Flaherty, V and Ijaz, UZ}, title = {Microbiomes of high-rate anaerobic digestors reveal 'Study'-specific factors and limitations of synthetic wastewater.}, journal = {Water research}, volume = {282}, number = {}, pages = {123931}, doi = {10.1016/j.watres.2025.123931}, pmid = {40480043}, issn = {1879-2448}, mesh = {*Wastewater/microbiology ; *Microbiota ; *Bioreactors/microbiology ; Anaerobiosis ; Archaea/genetics ; Bacteria/genetics ; Waste Disposal, Fluid ; }, abstract = {Anaerobic digestion (AD) is a key technology for the treatment of organic wastes and the production of renewable energy. The stability of the process hinges on the underlying microbial populations. Amplicon sequencing is increasingly used to characterise AD microbiomes, yet sequencing efforts have not translated to process engineering of the microbiome or prediction of failure using microbial tools. Using high-rate biofilm wastewater bioreactors as a study system, we aimed to i) discern trends in archaeal and bacterial diversity, ii) identify a core AD microbiome, iii) determine the functional stability of AD microbiomes, and iv) correlate taxa to experimental conditions. We analysed amplicon sequencing data from 32 high-rate anaerobic digestor studies (> 1258 samples) at various operational conditions and applied a suite of statistical microbiome tools. We found that taxonomic archaeal diversity was highly study dependent, while functional diversity was highly shared across studies. A core AD microbiome was identified with > 100 bacterial genera and 6 archaeal genera which were present at > 1 % relative abundance in at least 50 % of samples. Interestingly, we observed that microbiome stability was significantly impacted by the choice of real or synthetic wastewater, with synthetic wastewaters yielding a more stable and less complex microbiome. This was correlated to the abundances of 37 taxa in the synthetic wastewater, including 3 key methanogens (Methanothrix, Methanobacterium, and Methanosphaerula). This suggests that when synthetic wastewater is used in experimental studies, it may not result in an AD microbiome representative of real wastewater treatment systems.}, }
@article {pmid40476717, year = {2025}, author = {Baer, J and Little, M and Aquino, J and van der Geer, A and Sánchez-Quinto, A and Ballard, A and Lawrence, C and Carilli, J and Hartmann, A and Rohwer, F}, title = {Viralization as a microbial approach for enhancing coral reef restoration.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf110}, pmid = {40476717}, issn = {1751-7370}, support = {2022717//National Science Foundation/ ; 2209377//National Science Foundation/ ; 9207//Gordon and Betty Moore Foundation/ ; CR20-5175//United States Department of Defense Environmental Security Technology Certification Program/ ; }, mesh = {*Coral Reefs ; Animals ; *Anthozoa/virology/growth &amp; development/microbiology ; *Viruses/isolation &amp; purification ; Seawater/chemistry/virology ; *Environmental Restoration and Remediation/methods ; }, abstract = {Coral reef ecosystems rely on microorganisms to carry out biogeochemical processes essential to the survival of corals and the reef food web. However, widespread shifts from coral to algal dominance as a result of anthropogenic pressures have promoted microbial communities that compromise reef health through deoxygenation and disease. These degraded reefs become locked in a "microbialized" state characterized by high microbial biomass, low oxygen, and heightened pathogenic activity that stymie efforts to outplant corals onto the reef, a common approach applied to restore these ecosystems. Over 18 months, we compared viral and microbial dynamics alongside physical and chemical parameters ("water quality") between two coral outplanting sites and two midwater reef mesocosms called Coral Arks. Seafloor sites exhibited microbialization, whereas Arks maintained conditions with higher viral abundances and virus-to-microbe ratios, smaller and less abundant microorganisms, and consistently higher dissolved oxygen, water flow, and light availability. These conditions, which we term "viralized", supported enhanced coral growth and survival, greater benthic diversity, increased coral recruitment, reduced turf and macroalgae, and higher fish abundance compared to outplanting sites. Despite these benefits, analysis of microbial carbon metabolism genes revealed an underlying trend towards microbialization at both sites, reflecting larger-scale regional decline. These findings emphasize that microbial and physicochemical conditions are drivers of reef restoration outcomes; to be successful, restoration strategies must target the underlying environmental factors that support coral survival and resilience. We identify key microbial and physical variables-such as oxygen levels, flow, and viral activity-associated with viralized reef states, which should serve as focal points for developing new interventions and technologies aimed at creating conditions conducive to reef recovery.}, }
@article {pmid40474779, year = {2025}, author = {Green, N and Norwood, A and Sidhe, C and Mutlow, A and Aymen, J and Stiles, R and Bushell, J and Lim, T and Culver, E and Reeder, N and Timmer, M and Connelly, F and Charbonneau, J and McCall, W and Koenig, L and Stein, M and Geist, N and Lambert, MR and Hernández-Gómez, O}, title = {Shell Lesion Prevalence and Bacteriome Associations in Threatened Western Pond Turtles (Actinemys marmorata and Actinemys pallida) in California, USA.}, journal = {Journal of wildlife diseases}, volume = {}, number = {}, pages = {}, pmid = {40474779}, issn = {1943-3700}, abstract = {Bacteriome characterization studies can provide insights into the microbial ecology associated with disease. We collected western pond turtles (Actinemys marmorata and Actinemys pallida) from six San Francisco Bay Area, California, US, ponds; assessed their shells for lesions; and collected shell swabs and keratin scrape samples to evaluate bacteriome differences between the whole shell (swabs) and the affected tissues (scrapes). We quantified shell lesion type and prevalence by using visual inspections of photographs collected of the plastron and carapace and then applied 16S rRNA amplicon sequencing to characterize the associated bacteriomes of shells that observed pits, ulcerations, or no lesions. We observed shell lesions at high frequencies throughout our sites, with larger individuals (>100-mm plastron length) more likely to possess injuries. We saw no differences in alpha diversities between shells presenting with lesions and those on which we did not observe lesions; however, swab samples showed higher bacterial richness than keratin scrapes. The bacterial composition within the scrapes was influenced by pond location and then lesion presence. We observed a higher relative abundance of Actinobacteriota, Bacteroidota, Cyanobacteria, and Deinococcota in the shell keratin microflora of turtles with shell lesions. Because western pond turtles are under consideration for listing under the Endangered Species Act of 1973 in the US, understanding patterns of shell disease pathologies and the bacteria associated with disease is imperative for the management of current populations.}, }
@article {pmid40474000, year = {2025}, author = {Cottam, DE and Cosgrove, DW and Megía-Palma, R and Žagar, A and Blázquez-Castro, S and Faria, JF and Turner, AE and Silva, DO and Pie, MR}, title = {Does the Gut Microbiome of the Insular Lizard Gallotia galloti Reflect Variation in Sex, Environment, and Population Genetic Differentiation?.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {61}, pmid = {40474000}, issn = {1432-184X}, mesh = {Animals ; *Lizards/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Female ; Spain ; *Bacteria/classification/genetics/isolation &amp; purification ; Environment ; Genetic Variation ; Genetics, Population ; Sex Factors ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Despite their critical role in maintaining organismal health, the factors driving intraspecific variation in gut microbiotas in the wild are poorly understood. Gallotia galloti is a lizard endemic to the Canary Islands characterized by substantial phenotypic and genetic differentiation across populations, as well as by its ability to occur across considerably different environmental conditions. However, the extent to which such diversity is reflected in their gut microbiota is still unknown. Here, we use metabarcoding of fecal samples to explore how the gut microbiome of G. galloti reflects variation in sex, environment, human footprint, and subspecies identity. Fecal samples of 47 individuals were obtained across 13 locations to reflect the extent of intraspecific variation in the species. We found no evidence for consistent differences in microbiota richness across the studied groups, regardless of whether analyses were carried out at the genus, family, or phylum levels. Moreover, neither the richness nor composition of the microbiota was associated with variation in mean annual temperature, annual precipitation, and human footprint. Our results suggest that the generalist diet of G. galloti exposes them to a broad range of food items that provide a common template across the island, despite ecological and historical differences between populations.}, }
@article {pmid40473091, year = {2025}, author = {Santos, FSA and Corgosinho, PHC and de Abreu, FVS and Vaca-Sánchez, MS and Cuevas-Reyes, P and de Faria, ML and Valério, HM and Borges, MAZ}, title = {Assessing the impact of different scale removal methods on the geometric morphometrics of Aedes aegypti wings.}, journal = {Acta tropica}, volume = {268}, number = {}, pages = {107686}, doi = {10.1016/j.actatropica.2025.107686}, pmid = {40473091}, issn = {1873-6254}, abstract = {This work aimed to test different treatments for removing wing scales from Aedes aegypti, and evaluate through geometric morphometrics, if these treatments can modify the wing venation morphometric pattern. The treatments were wing agitation in mineral water and NaOH (sodium hydroxide) saline solution using a mini-ultrasound, and manual wing scales removal using a size zero (0) tip brush. We propose an alternative method for mounting wings on slides using glycerin. We conclude that glycerin use for slide mounting provides better optics and translucency, and that treatments with NaOH saline solution and water can impair morphometric analysis of wings. The size zero (0) tip brush treatment efficiently removed wing scales, improving wing structure visualization without causing significant modifications to the specimens.}, }
@article {pmid40471139, year = {2025}, author = {Gawish, R and Varada, R and Deckert, F and Hladik, A and Steinbichl, L and Cimatti, L and Milanovic, K and Jain, M and Torgasheva, N and Tanzer, A and De Paepe, K and Van de Wiele, T and Hausmann, B and Lang, M and Pechhacker, M and Ibrahim, N and De Vries, I and Brostjan, C and Sixt, M and Gasche, C and Boon, L and Berry, D and Jantsch, MF and Pereira, FC and Vesely, C}, title = {Filamin A editing in myeloid cells reduces intestinal inflammation and protects from colitis.}, journal = {The Journal of experimental medicine}, volume = {222}, number = {9}, pages = {}, pmid = {40471139}, issn = {1540-9538}, support = {57-B28//Austrian Science Fund/ ; V 1025-B//Austrian Science Fund/ ; DOC32-B28//Austrian Science Fund/ ; F8007//Austrian Science Fund/ ; P32678//Austrian Science Fund/ ; //Medical University of Vienna/ ; }, mesh = {*Filamins/genetics/metabolism ; Animals ; *Myeloid Cells/metabolism/pathology ; Humans ; *Colitis/genetics/pathology/prevention &amp; control ; *Inflammation/pathology/genetics ; Mice ; Mice, Inbred C57BL ; Neutrophils/metabolism ; *RNA Editing ; Macrophages/metabolism ; Male ; }, abstract = {Patho-mechanistic origins of ulcerative colitis are still poorly understood. The actin cross-linker filamin A (FLNA) impacts cellular responses through interaction with cytosolic proteins. Posttranscriptional A-to-I editing generates two forms of FLNA: genome-encoded FLNAQ and FLNAR. FLNA is edited in colon fibroblasts, smooth muscle cells, and endothelial cells. We found that the FLNA editing status determines colitis severity. Editing was highest in healthy colons and reduced during murine and human colitis. Mice that exclusively express FLNAR were highly resistant to DSS-induced colitis, whereas fully FLNAQ animals developed severe inflammation. While the genetic induction of FLNA editing influenced transcriptional states of structural cells and microbiome composition, we found that FLNAR exerts protection specifically via myeloid cells, which are physiologically unedited. Introducing fixed FLNAR did not hamper cell migration but reduced macrophage inflammation and rendered neutrophils less prone to NETosis. Thus, loss of FLNA editing correlates with colitis severity, and targeted editing of myeloid cells serves as a novel therapeutic approach in intestinal inflammation.}, }
@article {pmid40469738, year = {2025}, author = {Amen, R and Ganzert, L and Friedl, T and Rybalka, N and Wagner, D}, title = {From single pioneers to complex pro- and eukaryotic microbial networks in soils along a glacier forefield chronosequence in continental Antarctica.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1576898}, pmid = {40469738}, issn = {1664-302X}, abstract = {INTRODUCTION: In the extremely dry and oligotrophic soils of East Antarctica, where low temperatures and humidity result in minimal biological turnover rates, extracellular DNA (eDNA) can persist over extended timescales. Differentiating between sequences from living, potentially active cells (intracellular DNA, or iDNA) and those from ancient, non-living organisms (eDNA) is crucial for accurately assessing the current microbial community and understanding historical microbial dynamics.<br><br>METHODS: This study was conducted along a chronosequence in the Larsemann Hills, East Antarctica, where soil samples were collected from sites at varying distances from the glacier. By employing DNA separation methods, we distinguished iDNA, which represents living cells, from eDNA derived from dead organisms. High-throughput sequencing was used to characterize bacterial and eukaryotic communities across different successional stages.<br><br>RESULTS: The DNA separation approach revealed distinct bacterial and eukaryotic community structures along the glacier transect. Actinobacteria were consistently abundant across all sites, while other phyla such as Chloroflexi, Gemmatimonadetes, and Proteobacteria thrived in extreme, nutrient-poor environments. Early successional stages were characterized by the simultaneous colonization of green algae Trebouxiophyceae and cryophilic fungi, alongside nitrogen-fixing bacteria, which contributed to initial soil development. The study also identified three distinct modes of microbial distribution, reflecting varying degrees of activity and adaptability.<br><br>DISCUSSION: Our findings provide new insights into microbial dynamics in extreme habitats and propose new hypotheses for microbial colonization in newly exposed soils. Moreover, they contribute to the ongoing debate in microbial ecology regarding the viability of dormant or dead cells and emphasize the need for refining DNA-based methods and exploring functional pathways to deepen our understanding of microbial succession in polar regions.}, }
@article {pmid40469504, year = {2025}, author = {Van Den Bossche, T and Armengaud, J and Benndorf, D and Blakeley-Ruiz, JA and Brauer, M and Cheng, K and Creskey, M and Figeys, D and Grenga, L and Griffin, TJ and Henry, C and Hettich, RL and Holstein, T and Jagtap, PD and Jehmlich, N and Kim, J and Kleiner, M and Kunath, BJ and Malliet, X and Martens, L and Mehta, S and Mesuere, B and Ning, Z and Tanca, A and Uzzau, S and Verschaffelt, P and Wang, J and Wilmes, P and Zhang, X and Zhang, X and Li, L and , }, title = {The microbiologist's guide to metaproteomics.}, journal = {iMeta}, volume = {4}, number = {3}, pages = {e70031}, pmid = {40469504}, issn = {2770-596X}, abstract = {Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding of microbial ecology, interactions, and functional dynamics. This review, developed by the Metaproteomics Initiative (www.metaproteomics.org), serves as a practical guide for both microbiome and proteomics researchers, presenting key principles, state-of-the-art methodologies, and analytical workflows essential to metaproteomics. Topics covered include experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches.}, }
@article {pmid40468430, year = {2025}, author = {Khoiri, AN and Costa, NR and Crusciol, CAC and Pariz, CM and Costa, C and Calonego, JC and de Castilhos, AM and de Souza, DM and de Lima Meirelles, PR and Cru, IV and Moretti, LG and Bossolani, JW and Kuramae, EE}, title = {Pigeon pea-mediated soil microbial shifts improve agroecosystem multifunctionality in long-term maize-palisade grass intercropping.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {60}, pmid = {40468430}, issn = {2524-6372}, support = {#2014/21772-4 and #2014/14935-4//S&#xe3;o Paulo Research Foundation (FAPESP)/ ; #458225/2014-2//National Council for Scientific and Technological Development (CNPq)/ ; 1378/14//Funda&#xe7;&#xe3;o Agrisus/ ; }, abstract = {BACKGROUND: Intercropping systems enhance agricultural sustainability by promoting ecosystem multifunctionality (EMF). This study examined the impact of adding pigeon pea (M + PG + PP) into a maize-palisade grass (M + PG) intercropping system under a no-till system (NTS) on soil microbial communities and ecosystem services. After five consecutive growing seasons, bulk soil samples from a soybean-based crop-livestock system were analyzed using metagenomics.<br><br>RESULTS: The inclusion of pigeon pea significantly improved the EMF index, with higher plant productivity and slightly enhanced outcomes in soil health, lamb meat productivity, and climate protection. The M&#x2009;+&#x2009;PG&#x2009;+&#x2009;PP treatment enriched Bradyrhizobium spp., which were positively correlated with soil health, plant productivity, and EMF index. Functional analysis indicated that M&#x2009;+&#x2009;PG&#x2009;+&#x2009;PP treatment enhanced nitrogen metabolism, biofilm formation, and exopolysaccharide (EPS) biosynthesis, improving soil fertility and microbial activity. Similarly, functional analysis of microbial plant growth-promoting traits revealed that the M&#x2009;+&#x2009;PG&#x2009;+&#x2009;PP treatment promoted microbial functions related to nitrogen and iron acquisition, sulfur assimilation, and plant colonization, all essential for plant growth and nutrient cycling. In contrast, the M&#x2009;+&#x2009;PG treatment primarily enhanced pathways related to competitive exclusion and phytohormone production.<br><br>CONCLUSIONS: These findings highlight the importance of incorporating legumes such as pigeon pea into intercropping systems to optimize ecosystem services, enhance soil health, and promote long-term agricultural productivity and sustainability.}, }
@article {pmid40467851, year = {2025}, author = {Rakotonindrina, V and Andriamananjara, A and Razafimbelo, T and Okamoto, T and Sarr, PS}, title = {Land Cover and Seasonal Variations Shape Soil Microbial Communities and Nutrient Cycling in Madagascar Tropical Forests.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {60}, pmid = {40467851}, issn = {1432-184X}, mesh = {*Soil Microbiology ; Seasons ; Madagascar ; *Forests ; Soil/chemistry ; Tropical Climate ; Nitrogen/analysis/metabolism ; Carbon/analysis ; *Microbiota ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Fungi/genetics/classification/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Phosphorus/analysis/metabolism ; Trees ; Ecosystem ; }, abstract = {Understanding how land cover and seasonal variations influence soil microbial communities and nutrient cycling is crucial for sustainable land management in tropical forests. However, such investigations are limited in Madagascar's tropical ecosystems. This study investigated the impacts of land cover types and seasonal variations on soil properties and microbial communities in the tropical forest region of Andasibe, Madagascar. Soil samples were collected from four land cover types-tree fallow (TSA), shrub fallow (SSA), eucalyptus forest (EUC), and degraded land (TM)-across three seasonal periods: the dry season, the start of the rainy season, and the end of the rainy season. Both land cover and sampling season affected soil pH and available P, whereas total nitrogen, soil organic carbon, and the C/N ratio were affected only by land cover. The soil organic carbon and total nitrogen concentrations were greater in TM. NextSeq sequencing of the 16S rRNA gene and ITS regions of the nuclear rRNA operon revealed distinct microbial community compositions across land covers, with greater diversity in the TSA and SSA. Bacteria are more sensitive to seasonal changes than are fungi, with phosphate-solubilizing (gcd) and phosphate-mineralizing (phoD) genes being more abundant in the rainy season, emphasizing the role of microbes in nutrient availability under different climatic conditions. Principal component analysis highlighted SSA as a hotspot for microbial activity, reinforcing the potential of shrub ecosystems in soil restoration. These findings reveal strong land cover and seasonal effects on soil microbial functions, with implications for nutrient cycling, ecosystem resilience, and sustainable land management in tropical forest landscapes.}, }
@article {pmid40467767, year = {2025}, author = {Yan, Z and Yao, Y and Xu, Q and He, X and Zhou, X and Wang, H}, title = {Dietary microbiota-mediated shifts in gut microbial ecology and pathogen interactions in giant pandas (Ailuropoda melanoleuca).}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {864}, pmid = {40467767}, issn = {2399-3642}, mesh = {Animals ; *Ursidae/microbiology ; *Gastrointestinal Microbiome ; *Diet/veterinary ; Feces/microbiology ; *Bacteria/genetics/classification ; }, abstract = {The impact of dietary microorganisms on host microbiota is recognized, but the underlying mechanisms remain unclear. This study examined the effects of bamboo surface microbiota, including virulence factors, antibiotic resistance genes (ARGs), and mobile genetic elements from different bamboo parts (leaves, shoots, and culms), on giant panda gut microbiota using three pairs of twins. Results showed that bamboo and fecal samples shared 1670 microbial species, with shoot surface microbiota contributing the highest proportion (21%, Bayesian source tracking) of contemporaneous gut microbiota, primarily by increasing abundances of Escherichia coli and ARGs. Klebsiella pneumoniae and Salmonella enterica also showed high co-occurrence in both bamboo and fecal samples, indicating potential colonization. Additionally, Streptococcus suis, Acinetobacter, and Mycobacterium progressively declined in fecal samples as bamboo shoot intake increased, suggesting these microbes are likely transient. The findings emphasize the impact of foodborne microorganisms on the host and the importance of conservation management.}, }
@article {pmid40467587, year = {2025}, author = {Xiong, S and Xie, B and Yin, N and Zhu, H and Gao, H and Xu, X and Xiao, K and Cai, X and Sun, G and Sun, X and Cui, Y and Van de Wiele, T and Zhu, Y}, title = {Prenatal exposure to trace elements impacts mother-infant gut microbiome, metabolome and resistome during the first year of life.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {5186}, pmid = {40467587}, issn = {2041-1723}, support = {No. L232076//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; Pregnancy ; Infant ; *Trace Elements/adverse effects ; *Metabolome/drug effects ; Feces/microbiology ; *Prenatal Exposure Delayed Effects/microbiology/metabolism ; Adult ; Male ; Metagenomics ; Hair/chemistry ; *Maternal Exposure/adverse effects ; Infant, Newborn ; Bacteria/genetics/classification/drug effects ; Copper ; }, abstract = {Infancy is a critical window for the colonization of gut microbiome. However, xenobiotic impacts on gut microbiome development in early life remain poorly understood. Here, we recruit 146 mother-infant pairs and collect stool samples at 3, 6, and 12 months after delivery for amplicon sequencing (N = 353), metagenomics (N = 65), and metabolomics (N = 198). Trace elements in maternal hair samples (N = 119) affect diversity and composition of the infant gut microbiome. Shannon diversity in 3 month-old infants is correlated positively with selenium and negatively with copper, and relative abundance of Bifidobacterium increases under high exposure to aluminum and manganese. During the first year of life, infants and their paired mothers have distinct microbial diversity and composition, and their bacterial community structures gradually approach. here are 56 differential metabolites between the first and second visit and 515 differential metabolites between the second and third visit. The typical profile of antibiotic resistance genes (ARGs) significantly differs between infants and their mothers. High levels of copper and arsenic exposure may induce the enrichment of ARGs in the infant gut. Our findings highlight the dynamics of the gut microbiome, metabolites, and ARG profiles of mother-infant pairs after delivery, associated with prenatal exposure to trace elements.}, }
@article {pmid40467261, year = {2025}, author = {Cabezas-Terán, K and Grootaert, C and Van Camp, J and Ortiz, J and Ruales, J and Donoso, S and Van de Wiele, T}, title = {Bioaccessibility of β-carotene during in vitro co-digestion of encapsulated mango peel carotenoids with milk.}, journal = {Food research international (Ottawa, Ont.)}, volume = {214}, number = {}, pages = {116576}, doi = {10.1016/j.foodres.2025.116576}, pmid = {40467261}, issn = {1873-7145}, mesh = {*Mangifera/chemistry ; *beta Carotene/pharmacokinetics/metabolism ; *Milk/chemistry/metabolism ; *Digestion ; Animals ; Biological Availability ; *Fruit/chemistry ; *Carotenoids ; Particle Size ; }, abstract = {β-carotene is a carotenoid with provitamin A activity whose digestive stability and bioaccessibility prior to intestinal absorption are important to fully exploit its health benefits. Microencapsulation protects carotenoids, but there is a lack of information on the extent to which its characteristics and interactions with complex food matrices could impact the carotenoid micellization during digestion. We evaluated the effect of milk fat content on the in vitro bioaccessibility of β-carotene from microparticles containing carotenoids from mango peel. The microparticles tested contained solvent-extracted carotenoids and supercritical fluid-extracted carotenoids, and were separately co-digested with whole, semi-skimmed and skimmed milks. Bioaccessibility was assessed using an in vitro digestion method adapted to carotenoids. β-carotene recoveries after in vitro digestions ranged from 79.6 to 102.2 %, with the highest values corresponding mainly to microparticles with the lowest initial β-carotene concentration. β-carotene bioaccessibilities ranged from 8.8 to 75.5 %, the highest values being obtained mainly when the microparticles were co-digested with whole milk, especially when those containing supercritical fluid-extracted carotenoids were used. The bioaccessibility-enhancing effect of the milk fat was explained by the higher concentration of free fatty acids in the micellar phase, while the better results in the microparticles containing supercritical-fluid-extract was attributed to the lower initial concentration of β-carotene. In conclusion, increasing the milk fat content increased the bioaccessibility of encapsulated β-carotene from mango peel, further determining that, a lower initial concentration of β-carotene in the microparticles resulted in higher bioaccessibility.}, }
@article {pmid40467013, year = {2025}, author = {Valmas, MI and Kormas, K and Karpouzas, DG and Konstantinidis, KT and Rozman, SD and Udiković-Kolić, N and Remus-Emsermann, MNP and Vasileiadis, S}, title = {Targeted analysis of metagenomes: divide and conquer.}, journal = {Biotechnology advances}, volume = {83}, number = {}, pages = {108619}, doi = {10.1016/j.biotechadv.2025.108619}, pmid = {40467013}, issn = {1873-1899}, abstract = {The rapidly developing field of targeted analysis of metagenomes focuses on retrieving information about specific genes and/or genome(s) from environmental DNA. The traditional shotgun sequencing methods overemphasise dominant microorganisms and often fail to confidently assign the entirety of the analysed genetic material to specific species, genomovars, or strains. The ultimate goal of the targeted methods is to overcome this limitation of throughput and precision of current shotgun metagenomics when analysing complex microbial communities in the quest of refined information. Here, we discuss recent technological advances that are designed to focus the analytical power of diagnostic tools like sequencing, towards phylogenetically or functionally distinct and rare microbial groups and enhance e.g. the confidence in the assignment of genetic elements to their respective owning organisms. We specifically showcase the capabilities of these technological advances for targeted analysis of metagenomes, identify suitable related applications, discuss methodological limitations, and propose solutions for addressing these limitations. This review aspires to inspire highly relevant experimental designs in the future that will unlock unknown and important aspects of microbial ecology, and the yet-uncultivated microbial majority.}, }
@article {pmid40465274, year = {2025}, author = {Hassen, B and Hammami, S}, title = {Environmental phages: ecosystem dynamics, biotechnological applications and their limits, and future directions.}, journal = {Journal of applied microbiology}, volume = {136}, number = {6}, pages = {}, doi = {10.1093/jambio/lxaf136}, pmid = {40465274}, issn = {1365-2672}, support = {//IRESA/ ; }, mesh = {*Bacteriophages/physiology/genetics ; *Ecosystem ; *Biotechnology/methods/trends ; Gene Transfer, Horizontal ; Bacteria/virology ; *Environmental Microbiology ; }, abstract = {Phages, the most abundant biological entities on Earth, play a crucial role in various microbial ecosystems, significantly impacting biogeochemical cycles and bacterial evolution. They inhabit diverse environments, including soil, water, and extreme conditions, where they contribute to the contribute to regulating microbial populations, facilitate genetic exchange, and aid in nutrient cycling. Recent research has highlighted their potential in addressing antibiotic resistance, enhancing wastewater treatment, promoting agricultural sustainability, and tackling environmental issues. However, their ability to disseminate antibiotic resistance genes through horizontal gene transfer raises important concerns, warranting a thorough assessment of their ecological and biotechnological applications. This review synthesizes current knowledge on the diversity, ecological roles, and practical uses of environmental phages, emphasizing both their benefits and limitations. By analyzing recent findings and real-world applications, it provides insights into the challenges encountered and future directions for leveraging phages in environmental management, biotechnology, and healthcare.}, }
@article {pmid40464990, year = {2025}, author = {Peng, Z and Kang, C and Xu, Y and Zhang, C and Zhang, Y and Yan, B and Wang, S and Guo, X and Wan, X and Lv, C and Huang, L and Guo, L and Wang, H}, title = {Effects of Wild and Domesticated Seeds on the Colonization of Rhizosphere Microorganisms in Atractylodes lancea.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {59}, pmid = {40464990}, issn = {1432-184X}, support = {2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; }, mesh = {*Rhizosphere ; *Seeds/microbiology/growth &amp; development ; *Soil Microbiology ; *Atractylodes/microbiology/growth &amp; development ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Seedlings/microbiology/growth &amp; development ; Plant Roots/microbiology ; Domestication ; Endophytes/classification/isolation &amp; purification/genetics ; Plant Leaves/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The domestication of plant species has played a pivotal role in shaping human civilization, yet it has also contributed to a significant reduction in the genetic diversity of crop varieties. This reduction may have profound implications for the formation and establishment of rhizosphere microbial communities in plants. This study systematically investigates microbiome dynamics during seed development in wild and domesticated Atractylodes lancea. The seeds from both wild and domesticated A. lancea exhibited shared microbial genera, while their communities were changed significantly. However, when A. lancea seeds from wild and domesticated germinated into seedlings under identical microbiological conditions, the leaves and root endophytic microbial and rhizosphere microbiome displayed similar genus. Remarkably, the rhizosphere microbial communities of the seedlings consistently enriched Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Paenibacillus, Variovorax, Conexibacter, and norank_f__Micropepsaceae. And this convergence likely arises from the shared chemotype of A. lancea and exposure to identical environmental microbiomes. In summary, this study delineates the transmission processes of A. lancea seed endophytes and identifies the dynamic patterns of microbial shifts during its development from seed to seedling. These findings contribute to a broader understanding of plant-microbe interactions and the role of microbial ecology in crop improvement.}, }
@article {pmid40463892, year = {2025}, author = {Shepherd, RM and Oliverio, AM}, title = {The Biogeography of Apicomplexan Parasites in Tropical Soils.}, journal = {Ecology and evolution}, volume = {15}, number = {6}, pages = {e71478}, pmid = {40463892}, issn = {2045-7758}, abstract = {Parasitic protists such as Apicomplexa, an abundant group of soil protists, contribute to ecosystem processes and nutrient cycling in belowground soil systems through their obligate symbioses with soil Metazoa. Yet despite the importance of soil parasites, the biodiversity and biogeography of Apicomplexa in belowground systems remain poorly characterized. Leveraging 205 soils collected across a rainfall gradient spanning the isthmus of Panama, we sought to understand the distribution of soil Apicomplexa lineages and how abiotic (e.g., soil and climatic) and biotic (e.g., soil Metazoa) factors relate to their diversity and structure. Apicomplexa were highly heterogeneous across the samples and comprised 30% of the soil protist community on average. Soil pH, along with phosphorus and magnesium, best explained the overall distribution of Apicomplexa. Soil Metazoa distributions also corresponded to Apicomplexa distributions, and many Metazoan taxa co-occurred with particular Apicomplexa, which may reflect ecological interactions (such as parasitism) or shared habitat preferences. These results highlight the potential roles of both soil and climatic variables and putative hosts in structuring parasite distributions in belowground tropical systems. Our work builds a broader understanding of Apicomplexa biodiversity in tropical soils and sheds light on environmental factors that may contribute to shaping their distribution in belowground systems. These results help inform our understanding of the importance of parasites in tropical forest soils.}, }
@article {pmid40463148, year = {2025}, author = {Usman, H and Molaei, M and House, S and Haase, MF and Dennis, CL and Niepa, THR}, title = {Magnetically Responsive Nanocultures for Direct Microbial Assessment in Soil Environments.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.05.17.654660}, pmid = {40463148}, issn = {2692-8205}, abstract = {UNLABELLED: Cultivating microorganisms in native-like conditions is vital for bioprospecting and accessing currently unculturable species. However, there remains a gap in scalable tools that can both mimic native microenvironments and enable targeted recovery of microbes from complex settings. Such approaches are essential to advance our understanding of microbial ecology, predict community functions, and discover novel biotherapeutics. We present magnetic nanocultures-a high-throughput microsystem for isolating and growing environmental microbes under near-native conditions. These nanoliter-scale bioreactors are encapsulated in semi-permeable membranes that form magnetic polymeric microcapsules using iron oxide nanoparticles within polydimethylsiloxane-based shells. This design offers mechanical stability and magnetic actuation, enabling efficient retrieval from soil-like environments. The nanocultures are optimized for optical and biological properties to support microbial encapsulation, growth, and sorting. Our study demonstrates the feasibility of using magnetically responsive microenvironments to cultivate elusive microbes, offering a promising platform for discovering previously uncultured or unknown microbial species.<br><br>TEASER: Engineered magnetic nanocultures support microbial growth and magnetic separation from complex environments.}, }
@article {pmid40462960, year = {2025}, author = {Wheeler, KM and Oh, MW and Fusco, J and Mershon, A and Kim, E and De Oliveira, A and Rahme, LG}, title = {MvfR shapes Pseudomonas aeruginosa Interactions in Polymicrobial Contexts: Implications for Targeted Quorum Sensing Inhibition.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40462960}, issn = {2692-8205}, support = {R01 AI177555/AI/NIAID NIH HHS/United States ; }, abstract = {Infections often occur in complex niches consisting of multiple bacteria. Despite the in-creasing awareness, there is a fundamental gap in understanding which interactions govern mi-crobial community composition. Pseudomonas aeruginosa is frequently isolated from monomicrobi-al and polymicrobial human infections. This pathogen forms polymicrobial infections with other ESKAPEE pathogens and defies eradication by conventional therapies. By analyzing the competi-tion within cocultures of P. aeruginosa and representative secondary pathogens that commonly co-infect patients, we demonstrate the antagonism of P. aeruginosa against other ESKAPEE pathogens and the contribution of this pathogen's multiple quorum sensing (QS) systems in these interac-tions. QS is a highly conserved bacterial cell-to-cell communication mechanism that coordinates collective gene expressions at the population level, and it is also involved in P. aeruginosa virulence. Using a collection of P. aeruginosa QS mutants of the three major systems, LasR/LasI, MvfR/PqsABCDE, and RhlR/RhlI and mutants of several QS-regulated functions, we reveal that MvfR and, to a lesser extent, LasR and RhlR control competition between P. aeruginosa and other microbes, possibly through their positive impact on pyoverdine, pyochelin, and phenazine genes. We show that MvfR inhibition alters competitive interspecies interactions and preserves the coexistence of P. aeruginosa with ESKAPEE pathogens tested while disarming the pathogens' ability to form biofilm and adhere to lung epithelial cells. Our results highlight the role of MvfR inhibition in modulating microbial competitive interactions across multiple species, while simultaneously atten-uating virulence traits. These findings reveal the complexity and importance of QS in interspecies interactions and underscore the impact of the anti-virulence approach in microbial ecology and its importance for treating polymicrobial infections.}, }
@article {pmid40462143, year = {2025}, author = {Kindtler, NL and Sheikh, S and Zervas, A and Ellegaard-Jensen, L and Feld, L and Scheel, M and Jiménez, FC and da Fonseca, RR and Laursen, KH and Jacobsen, CS and Ekelund, F}, title = {Small sample amounts from rhizosphere of barley maintain microbial community structure and diversity revealed by total RNA sequencing.}, journal = {Plant methods}, volume = {21}, number = {1}, pages = {79}, pmid = {40462143}, issn = {1746-4811}, abstract = {Total RNA sequencing is a crucial technique in microbial ecology for profiling active microbial communities in various environments, including the rhizosphere. Since total RNA sequencing yields both 16 S and 18 S ribosomal RNA (rRNA), it is effective for taxonomic profiling of the full microbial community in a sample. However, the effectiveness of this approach with limited initial sample amounts remains unclear. In this study, we grew barley in a growth system designed for highly controlled plant experiments using an inert growth medium inoculated with a soil microbiome. Our objectives were two-fold: firstly, to test the feasibility of extracting total RNA from the rhizosphere of barley grown in an inert growth medium consisting of sand and perlite. Secondly, we aimed to address the challenge of extracting comprehensive taxonomic information from minimal amounts of rhizosphere samples from barley plants, using three different amounts of freeze-dried rhizosphere material: 10, 40, and 200 mg. We showed that although smaller sample amounts yielded lower concentrations of extracted RNA, this did not significantly influence the diversity or composition of the rhizosphere microbiome as indicated by SSU rRNA. Our results demonstrate that total RNA sequencing, focusing on SSU rRNA, robustly captures the taxonomic diversity of active rhizosphere microbial communities, even in small initial sample amounts. Effective use of smaller samples opens new possibilities for detailed studies in environments where sample quantity is limited. We also conclude that the growth system applied in this experiment is suitable for highly controlled plant experiments focusing on total RNA extraction from the rhizosphere.}, }
@article {pmid40461733, year = {2025}, author = {Ruiz-Blas, F and Friese, A and Bartholomäus, A and Henny, C and Russell, JM and Kallmeyer, J and Vuillemin, A}, title = {The Deep Subsurface Biosphere and its Substrates Along a One-Million-Year Ferruginous Lake Archive.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {58}, pmid = {40461733}, issn = {1432-184X}, support = {KA 2293/8-1//Deutsche Forschungsgemeinschaft/ ; VU 94/1-1//Deutsche Forschungsgemeinschaft/ ; P2GEP2_148621//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Indonesia ; *Archaea/genetics/classification/isolation &amp; purification ; Phylogeny ; Iron/analysis/metabolism ; Biodiversity ; }, abstract = {Lake Towuti, Indonesia, is an ancient stratified lake with ferruginous (iron-rich, sulfate-poor) anoxic bottom water conditions and a long depositional record affected by redox changes in the water column and sediments. As modern analogue of Earth's early ferruginous oceans, it enables the study of an active microbial subsurface biosphere and its role in organic matter and iron mineralization. Combining 16S rRNA genes, cell counts, pore water geochemistry, and bulk sediment profiles from a 100-m-long core, we present the first comprehensive characterization of the deep subsurface biosphere along a one-million-year lacustrine archive. Electron acceptors in the pore water became depleted at shallow depths, resulting in a drastic decrease in cell densities in the fermentative zone, where Bathyarchaeia dominate the microbial community composition. Although alpha and beta diversity reflected initial depletion of substrates during burial, they also varied across successive lithologies, indicating that sediment composition subsequent to deposition also affects diversity. The upper sediments (0-20 mblf) sheltered a dense and diverse microbial community involved in organic matter remineralization, actively producing and converting volatile fatty acids into carbon dioxide and methane. Deeper sediments (20-70 mblf) contained low-diversity microbial communities adapted to nutrient scarcity. In contrast, deepest lacustrine sediments (70-100 mblf) contained an increased microbial diversity reflecting greater availability of organic matter of terrestrial origin. Despite Bathyarchaeia being prime constituents of the deep subsurface biosphere, increased diversity in 16S rRNA gene composition was observed in discrete sediment layers (tephra, diatom ooze, peat). This demonstrated that depositional conditions remained traceable, while stratified microbial communities drove reductive diagenesis.}, }
@article {pmid40461630, year = {2025}, author = {Koch, M and Lado, S and Bodner-Adler, B and Carlin, G and Pacífico, C and Bauer, C and Cartwright, R and Seki, D and Steininger, C and Makristathis, A and Umek, W}, title = {Women suffering from overactive bladder syndrome exhibit a higher urethral viral abundance compared to healthy controls: a pilot study.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {19484}, pmid = {40461630}, issn = {2045-2322}, support = {1815//OeNB Jubil&#xe4;umsfonds/ ; }, mesh = {Humans ; Female ; *Urinary Bladder, Overactive/virology/microbiology ; Pilot Projects ; Middle Aged ; *Urethra/virology/microbiology ; Microbiota ; Case-Control Studies ; Prospective Studies ; Adult ; Phylogeny ; Aged ; Bacteria/genetics ; Virome ; *Viruses/genetics/isolation &amp; purification/classification ; High-Throughput Nucleotide Sequencing ; }, abstract = {The interactions between the human bacterial microbiome and essential bodily functions are well established for organ systems such as the oral cavity, gut, and female reproductive tract. However, the urinary microbiome, particularly its viral component, remains largely unexplored. Emerging evidence suggests that the urinary microbiome may play a significant role in the development of overactive bladder syndrome (OAB). This study aims to fill this knowledge gap by investigating the potential link between the urethral virome and female overactive bladder syndrome, and by aligning these findings with the bacterial microbiome. Prospective pilot study including 15 patients with overactive bladder syndrome and five controls. Current urinary tract infection and antibiotic therapy within the last two months were ruled out and controls were matched to cases by age and body mass index. Urethral swabs (Copan eSwab[®] urethra) were taken from each participant at one single time point. Subsequent viral isolation, purification, and enrichment were conducted using the ViPEP method. Next-generation sequencing was performed on pooled samples, followed by bioinformatic analysis to identify and classify viral contigs. Phylogenetic analysis was conducted to assess genetic relationships among identified viral sequences. The bacterial microbiome was analyzed by sequencing of the variable V3-4 region of the eubacterial 16 S rDNA gene on the Illumina MiSeq platform. We identified twenty-one viruses and bacteriophages only in pooled urethral swab samples of the OAB group, but no valid detections were retained in the control group after analysis. The most abundant human virus in urethral swab samples was human papilloma virus, whereas the most abundant bacteriophages belong to the family of Siphoviridae. In the bacterial microbiome analysis, we identified statistically higher levels of Veillonella and Bacteroides in OAB samples. Results of this pilot study suggest a difference in the urethral virome between women with OAB and healthy controls. When looking deeper into the detected virus families and species, we might postulate a unique microbial pattern of OAB patients. This pattern suggests an interplay of immunosuppression, autoimmune processes and a larger diversity of bacterial and viral microbes. Current evidence strongly suggests a disturbance of the healthy microbiome of the urogenital tract in patients with OAB, leading to subclinical chronic inflammation and thus typical OAB symptoms. Further research should focus on interventions aimed at restoring a healthy microbiome in OAB patients to mitigate inflammation and improve symptom control.}, }
@article {pmid40459550, year = {2025}, author = {Wu, Y and Zhang, F and Zhang, S and Zhang, J and Zhao, S and Qiu, Z and Zhu 朱, M&#x58a8;}, title = {Curvularia spicifera causing black rot on Ipomoea batatas in China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-03-25-0477-PDN}, pmid = {40459550}, issn = {0191-2917}, abstract = {Ipomoea batatas (sweet potato) is an annual herb originating from South America and the large and small Antilles. It is widely cultivated in tropical and subtropical regions around the world and is widely grown in most parts of China. As an edible plant with rich nutrition, I. batatas has high economic and medicinal value (Suhendy et al. 2023). In September 2023, black rot-like disease signs and symptoms were observed on the roots of I. batatas in a farmland (about 6667 m2) located in Kaifeng city, Henan Province, China. The roots showed irregular brown or dark spots on the surface, extending to the internal center, and brown to black necrosis. Additionally, above-ground parts of infected plants showed symptoms such as yellowing and wilting of leaves, brown spots on stems, and stunted growth. Around 80 % of monitored plant roots (n = 200) exhibited the symptoms. Infected roots were cut into pieces and then placed on potato dextrose agar (PDA) (light/dark, 16 h/8 h; temperature, 18°C). After a period of 3-10 days, single hyphal tips of each fungal colony were placed on PDA and incubated for another 5-10 days (Paul et al. 2021). Colonies of the fungal pathogen on PDA reached 50 mm in diameter within 7 days, dark gray on the inner side, dark brown extending to the edge, irregular round edge, with abundant aerial mycelium, cotton-like, irregularly convex upward, undulating. The conidia were brown, ellipsoid to oval, 8 to 19 × 3 to 6 μm (n = 50). Morphologically similar isolates with characteristics consistent with those of Curvularia spicifera (Cui et al. 2020) were recovered from 87% of symptomatic root tissues (n=100). The internal transcribed spacer (ITS) region and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene from three independent isolates (CSZM202101, CSZM202102, and CSZM202103) of the fungus were amplified and sequenced with primers ITS1/ITS4 (Seliger et al. 1990) and GAPDH1/GAPDH3R (Bradshaw et al. 2022) according to a previously reported method (Zhu et al. 2022). The resulting sequences were deposited in GenBank (Accession No. OR885691, PV056889, PV056568, PQ839726, PV072835 and PV02836). BLASTn analysis showed that the ITS and GAPDH sequences had 100% (ITS, 516/516; GAPDH, 508/508) identity with C. spicifera (OQ845826 and CBS 274.52 JN192387) from maize (Ram et al. 2024) and pearl millet (S. et al. 2024), respectively. The phylogenetic analysis clearly illustrated that these isolates clustered with the sequences of a representative reference strain of C. spicifera(CBS 274.52, GenBank accession number JN192387). Therefore, the morphological, molecular and phylogenetic analysis indicated that the pathogen was C. spicifera. To complete Koch's postulates, pathogenicity experiments were carried out by inoculating spore suspension (106 spores mL-1) into the wounded roots (n=10) of I. batatas plants. Sterile distilled water treated wounded roots (n=10) served as control. One to two days after inoculation, visible mycelia were produced at the inoculation sites of I. batatas. Inoculated roots showed black rot signs 21 days post-inoculation; controls were unaffected. This was confirmed in three repeated pathogenicity tests. To our knowledge, this is the first report of black rot caused by C. spicifera on I. batatas in China. The emergence of the black rot pathogen could harm valuable food crops and reduce agricultural productivity in China. Accurate identification of the black rot fungus is essential for devising effective disease management strategies and supporting future control of C. spicifera in China.}, }
@article {pmid40459301, year = {2025}, author = {Zhang, J and Guo, Z and Liu, J and Pan, X and Huang, Y and Cui, X and Wang, Y and Jin, Y and Sheng, J}, title = {Capabilities and Limitations of Air-Dried Soils in Microbial Biogeography: A Regional-Scale Comparative Analysis.}, journal = {Environmental microbiology}, volume = {27}, number = {6}, pages = {e70111}, doi = {10.1111/1462-2920.70111}, pmid = {40459301}, issn = {1462-2920}, support = {KFJ-SW-YW043-2//Field Station Basic Research Project of the Chinese Academy of Sciences/ ; 42107145//National Natural Science Foundation of China/ ; 42407410//National Natural Science Foundation of China/ ; 0270756100ZX//Jiangsu Agricultural Biodiversity Cultivation and Utilization Research Center/ ; CX (22) 2002//Jiangsu Agricultural Science and Technology Innovation Fund/ ; CX (23) 3105//Jiangsu Agricultural Science and Technology Innovation Fund/ ; 3220220039//Pilot Project for Mineral-Land Integration of Jiangsu Province/ ; //Jiangsu Provincial Territorial Ecological Monitoring/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; China ; *Bacteria/classification/genetics/isolation &amp; purification ; *Desiccation ; Biodiversity ; *Microbiota ; }, abstract = {Air-dried soil archives offer valuable potential for studying long-term microbial dynamics, yet systematic evaluations across large spatial scales with paired fresh-soil comparisons remain limited. Here, we systematically evaluated the effects of 1-month air-drying on microbial biogeography across 244 paddy fields in eastern China. Results showed that air-drying significantly altered communities by reducing diversity through the elimination of rare taxa while enriching desiccation-resistant phyla like Firmicutes, Chloroflexi and Actinobacteria. These compositional shifts further triggered functional bias, enhancing fermentation/methanogenesis pathways while suppressing nitrogen cycling processes. Despite these alterations, air-dried samples maintained remarkable fidelity to key ecological patterns observed in fresh soils. Multivariate analyses demonstrated strong structural concordance between paired samples, with soil pH consistently emerging as the primary environmental driver in both data sets. This preservation of biogeographical relationships occurred despite significant changes in underlying ecological mechanisms. Air-dried soil communities exhibited increased stochastic assembly, reduced niche breadth and simplified co-occurrence networks with altered keystone taxa, indicative of a two-phase process: deterministic filtering of drought-sensitive taxa followed by stochastic reorganisation among survivors. Overall, our findings provide a framework for utilising soil archives in microbial ecology, showing that while air-drying introduces predictable distortions, samples retain essential ecological information for reconstructing historical microbial-environmental relationships at large scales.}, }
@article {pmid40456365, year = {2025}, author = {Zhao, X and Van Overbeek, L and Burgess, CM and Holden, N and Brennan, F and Johannessen, GS and Allende, A and Höfte, M and Cottyn, B and Pothier, JF and Schikora, A and Uyttendaele, M}, title = {Human Pathogenic Microorganisms in Fresh Produce Production: Lessons Learned When Plant Science Meets Food Safety.}, journal = {Journal of food protection}, volume = {88}, number = {7}, pages = {100551}, doi = {10.1016/j.jfp.2025.100551}, pmid = {40456365}, issn = {1944-9097}, mesh = {Humans ; *Food Safety ; Food Microbiology ; Food Contamination/prevention &amp; control ; }, abstract = {To enhance control of human pathogenic microorganisms in plant production systems, an EU COST Action (HUPLANTcontrol CA16110) was initiated, bringing together microbiologists in food, environmental, and plant microbial ecology. This article summarizes the outcomes of multiple workshops and the four main lessons learned: (i) many terminologies need further explanation to facilitate multidisciplinary communication on the behavior of human pathogens from preharvest plant production to postharvest food storage, (ii) the complexity of bacterial taxonomy pushes microbial hazard identification for greater resolution of characterization (to subspecies, or even strain level) needing a multimethod approach, (iii) hazard characterization should consider a range of factors to evaluate the weight of evidence for adverse health effects in humans, including strain pathogenicity, host susceptibility, and the impact of the plant, food, or human gut microbiome, (iv) a wide diversity of microorganisms in varying numbers and behaviors coexist in the plant microbiome, including good (beneficial for plant or human health), bad (established human or plant pathogens), or ugly (causing spoilage or opportunistic disease). In conclusion, active listening in communication and a multiperspective approach are the foundation for every successful conversation when plant science meets food safety.}, }
@article {pmid40456197, year = {2025}, author = {Song, W and Lin, L and Oh, S and Grossart, HP and Yang, Y}, title = {Tire wear particles in aquatic environments: From biota to ecosystem impacts.}, journal = {Journal of environmental management}, volume = {388}, number = {}, pages = {126059}, doi = {10.1016/j.jenvman.2025.126059}, pmid = {40456197}, issn = {1095-8630}, mesh = {*Ecosystem ; Biota ; Microplastics ; *Water Pollutants, Chemical ; Animals ; }, abstract = {Tire wear particles (TWPs), mainly generated through friction between tires and road surfaces, represent a major source of traffic-related microplastic pollution, posing threats to biota and ecosystem functions. These particles are a complex mixture of toxic compounds, including heavy metals (e.g., zinc) and organic compounds (e.g., 6-PPD), and their diverse leachates exacerbate their ecological impacts. This review collates current knowledge on the occurrence of TWPs and their leachates in aquatic systems, emphasizing their toxicological effects on species and cascading ecological consequences at the community and ecosystem levels. TWP concentrations in aquatic environments span several orders of magnitude, ranging from 10[-5] to 10[4] mg/L in water via pyrolysis-GC/MS. TWPs and their leachates induce oxidative stress, DNA damage, and alter immune responses of aquatic biota, while disrupting feeding behavior, reproduction, and survival. At the ecosystem level, TWPs and their leachates cause shifts in species composition, reduce biodiversity, and alter trophic interactions, destabilizing natural food web dynamics through selective pressure that promotes tolerant taxa and triggers cascading ecological effects. Their presence significantly influences carbon and nitrogen cycling, with environmentally relevant concentrations could promote primary producers, while higher concentrations inhibit photosynthetic nitrogen-fixing biota, disrupt microbial communities, and impair processes such as denitrification and carbon mineralization. Their toxicological and ecological impacts are likely to be intensified by global environmental change, highlighting the need for long-term studies under realistic environmental conditions to better understand underlying mechanisms and develop effective mitigation strategies.}, }
@article {pmid40453667, year = {2025}, author = {Yang, H and Shao, C and Liu, Z and Zhang, X and Liu, Y and Xiao, J and Tang, L}, title = {Cold- and hot-classified botanical drugs differentially modulate gut microbiota: linking TCM emic classification to microbial ecology.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1545619}, pmid = {40453667}, issn = {1663-9812}, abstract = {INTRODUCTION: Traditional Chinese Medicine (TCM) classifies botanical drugs based on their thermal properties (an emic classification system), categorizing them as "cold" (e.g., "clearing heat" for anti-inflammatory effects) or "hot" (e.g., "warming the middle" for metabolic enhancement). However, the specific roles of these botanical drugs in restoring gut microbiota dysbiosis remain unclear. This study aimed to explore whether TCM-classified cold and hot botanical drugs differentially restore gut microbiota dysbiosis and host physiology in antibiotic-treated mice.<br><br>METHODS: Mice with antibiotic-induced dysbiosis were treated with eight TCM-classified botanical drugs (four cold: Rheum palmatum L., Scutellaria baicalensis Georgi, Senna alexandrina Mill., Coptis chinensis Franch.; four hot: Codonopsis pilosula (Franch.) Nannf., Astragalus membranaceus (Fisch.) Bunge, Angelica sinensis (Oliv.) Diels, Panax ginseng C.A.Mey.) for 20&#xa0;days. Gut microbiota were analyzed via 16S rRNA sequencing on days 5, 10, 15, and 20, alongside physiological parameters including blood glucose, serum lipids, TNF-&#x3b1;, adiponectin, and intestinal histomorphology.<br><br>RESULTS: By day 20, all botanical drugs restored the diversity and ranking of dominant genera (those with >10% abundance, such as Lactobacillus and unclassified Muribaculaceae). However, cold-classified drugs, traditionally associated with anti-inflammatory effects, selectively enriched anti-inflammatory taxa, including Akkermansia and Bifidobacterium. In contrast, hot-classified drugs, linked to metabolic enhancement, promoted metabolic-modulating genera such as Clostridia and Eubacterium coprostanoligenes. These differential enrichments corresponded with the therapeutic principles defined by TCM: cold-classified drugs reduced serum TNF-&#x3b1; levels (P < 0.01), demonstrating anti-inflammatory effects, whereas hot-classified drugs improved lipid profiles (TG: P < 0.001), thereby promoting metabolic modulation.<br><br>DISCUSSION: TCM-classified cold and hot botanical drugs universally stabilize dominant microbiota while differentially modulating low-abundance taxa. The enrichment of Akkermansia (cold) and Clostridia (hot) offers a microbiota-driven validation of TCM's empirical classification framework. These findings connect traditional knowledge with microbial ecology, underscoring the potential of TCM-guided microbiota modulation for precision therapies.}, }
@article {pmid40450024, year = {2025}, author = {Masigol, H and Solbach, MD and Pourmoghaddam, MJ and Ahadi, R and Mostowfizadeh-Ghalamfarsa, R and Taheri, SR and Tobias-Hünefeldt, SP and Bonkowski, M and Grossart, HP}, title = {A glimpse into Oomycota diversity in freshwater lakes and adjacent forests using a metabarcoding approach.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {19124}, pmid = {40450024}, issn = {2045-2322}, mesh = {*Lakes/microbiology ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *Forests ; *Oomycetes/genetics/classification/isolation &amp; purification ; Ecosystem ; Germany ; Phylogeny ; Fresh Water/microbiology ; }, abstract = {Oomycota, a diverse group of fungus-like protists, play key ecological roles in aquatic and terrestrial ecosystems, yet their habitat-specific diversity and distribution remain poorly understood. This study investigates the diversity of two major Oomycota classes, Saprolegniomycetes and Peronosporomycetes, in two freshwater lakes and their adjacent forests in northeastern Germany. Using a combination of targeted metabarcoding and traditional isolation techniques, we analyzed samples from six habitats, including soil (forest), rotten leaves (forest and shoreline), sediments (shoreline), and surface waters (littoral and pelagic zones). Metabarcoding revealed 401 Oomycota OTUs, with Pythium, Globisporangium, and Saprolegnia as dominant genera. Culture-based methods identified 110 strains, predominantly from surface water and sediment, with Pythium sensu lato and Saprolegnia as the most frequent taxa. Alpha and beta diversity analyses highlighted distinct community structures influenced by lake and habitat type, with significant co-occurrence of Saprolegniomycetes and Peronosporomycetes across habitats. This study provides the first comprehensive metabarcoding-based exploration of Oomycota biodiversity in interconnected freshwater and terrestrial ecotones, uncovering previously unrecognized patterns of habitat-specific diversity.}, }
@article {pmid40448709, year = {2025}, author = {Samaniego, T and La Torre, R and Orjeda, G and Ramirez, JL}, title = {Lima Megacity's Influence on Aquatic Microbial Communities in the Rímac River: Dominance Over Spatial and Seasonal Variations.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {57}, pmid = {40448709}, issn = {1432-184X}, support = {B2110006i//Universidad Nacional Mayor de San Marcos/ ; B2110006i//Universidad Nacional Mayor de San Marcos/ ; B2110006i//Universidad Nacional Mayor de San Marcos/ ; }, mesh = {*Rivers/microbiology ; Seasons ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Peru ; *Microbiota ; *Water Microbiology ; Environmental Monitoring ; DNA, Bacterial/genetics ; Biodiversity ; }, abstract = {The Rímac River, a vital watershed on the Peruvian coast, is confronted with substantial environmental challenges stemming from intensive exploitation and widespread contamination. As the primary source of water for Lima, supplying approximately 80% of the city's needs, the river is heavily impacted by pollutants from domestic, hospital, industrial, and mining effluents. These contaminants introduce microbiota that pose significant public health risks. This study utilizes 16S rRNA gene metabarcoding to characterize the bacterial communities along the Rímac River, examining both spatial (upper, middle, and lower basins) and temporal (dry and rainy seasons) variations. Over a year-long sampling period, DNA sequencing revealed pronounced microbiological differences between the Metropolitan and Regional zones, primarily driven by anthropogenic activities. Key findings include a significant reduction in microbial diversity and an increase in pathogenic bacteria within the Metropolitan zone, while the influence of seasonal variations and altitudinal gradients was comparatively minor. Betaproteobacteria emerged as the most abundant class across most samples. Notably, Aliarcobacter cryaerophilus, an indicator of fecal contamination and a potential public health hazard, was predominantly detected in the Metropolitan zone. These results underscore the necessity for comprehensive monitoring of the Rímac River's microbiota, incorporating advanced molecular techniques to effectively track and mitigate pollution. The study emphasizes the urgent need for robust water quality management strategies to protect this critical resource, ensuring the health and sustainability of Lima and its surrounding regions.}, }
@article {pmid40446899, year = {2025}, author = {Fang, P and Ye, S and Luo, Z and Guo, R and Jiang, Y and Liu, L and Li, S and Xiao, F}, title = {Nanoplastics under the charge effects: Unveiling the potential threats to amphibian (Rana nigromaculata) growth, intestinal damage and microbial ecology.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {381}, number = {}, pages = {126566}, doi = {10.1016/j.envpol.2025.126566}, pmid = {40446899}, issn = {1873-6424}, mesh = {Animals ; *Microplastics/toxicity ; Larva/drug effects/growth &amp; development ; *Intestines/drug effects ; *Ranidae/growth &amp; development ; *Water Pollutants, Chemical/toxicity ; Gastrointestinal Microbiome/drug effects ; Oxidative Stress ; }, abstract = {Nanoplastics (NPs) are contaminants that may be found in charged forms in the environment, capable of accumulating in aquatic organisms and affecting their health. This study compared the effects of positively charged Polystyrene-NPs (PS-NH2, 30 nm) and negatively charged Polystyrene-NPs (PS-COOH, 30 nm) at 6 and 60 mg/L on the growth and development of black-spotted frog tadpoles (Rana nigromaculata), as well as on intestinal damage and microbial ecology. The results demonstrated that exposure to both types of NPs significantly reduced the survival rate of tadpoles, while significantly increased their body weight and body length. Compared to PS-COOH, PS-NH2 exposure resulted in more adverse intestinal tissue damage, manifested by more severe intestinal oxidative stress. Furthermore, exposure to PS-NH2 significantly reduced the abundance and diversity of the microbiome associated with gut function and nutrient absorption, thereby indirectly causing more severe intestinal damage and growth changes. In addition, functional prediction and gene transcription analysis showed that exposure to charged PS-NPs caused changes in genes associated with glycolysis and lipid metabolism, indicating that the glucose-lipid metabolism of tadpoles is impacted. This study revealed the effects of different charged NPs exposure on the growth of tadpoles and their intestinal toxicity, clarified the potential connections between gut microbiota and glucose-lipid metabolism, and provided a new perspectives on the health risks of NPs in amphibians.}, }
@article {pmid40446767, year = {2025}, author = {Adyari, B and Liao, X and Yan, X and Qiu, Y and Grossart, HP and Li, L and Yu, T and Mao, G and Liu, K and Su, J and Liu, Y and Hu, A}, title = {Anthropogenic gene dissemination in Tibetan Plateau rivers: sewage-driven spread, environmental selection, and microeukaryotic inter-trophic driving factors.}, journal = {Water research}, volume = {284}, number = {}, pages = {123887}, doi = {10.1016/j.watres.2025.123887}, pmid = {40446767}, issn = {1879-2448}, abstract = {The spread of anthropogenic genes, such as antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), virulence factor genes (VFGs), and antibiotic-resistant bacteria (ARBs), is a growing public health concern. However, the role of anthropogenic activities in the dissemination of these genes and bacteria in Tibetan Plateau rivers is still unclear. In this study, we analyzed 138 metagenomic samples from water and sediment across nine Tibetan rivers, along with sewage samples from 21 wastewater treatment plants (WWTPs), at both the gene and contig levels, to investigate the spread of the sewage-enriched genes and their bacterial hosts (contigs) in Tibetan rivers. Overall, sewage input was positively correlated with increased the abundance of an average 56 % and 17 % of detected genes in water and sediment, respectively. However, FEAST source tracking analysis revealed that the overall contribution of sewage across all rivers was significantly lower than that of water and sediment. Additionally, sewage's impact varied across rivers, with the Yarlung Zangbo, the largest river, exhibiting limited influence despite receiving inputs from smaller rivers and WWTPs. Neutral community model (NCM) suggested that neutral processes and negative selection predominantly governed the spread of majority of highly abundant sewage-enriched genes and contigs, suggesting restricted environmental spread. In contrast, a subset of genes over-represented relative to neutral expectations (above-neutral prediction) showed lower overall abundance but higher richness, potentially reflecting selection that favor their retention in certain downstream environments. Furthermore, sewage-enriched genes and contigs in water, regardless of their community assembly processes, were linked to microbial interaction modules dominated by microeukaryotic groups associated with sewage, including consumer protists (ciliate), human parasites (e.g., Naegleria), algae, and fungi. These interactions may facilitate the dissemination of antimicrobial resistance in aquatic environments, though this pattern was less pronounced in sediment.}, }
@article {pmid40446743, year = {2025}, author = {Jansriphibul, K and Krohn, C and Ball, AS}, title = {Sources of variability for viability PCR using propidium monoazide.}, journal = {Microbiological research}, volume = {298}, number = {}, pages = {128224}, doi = {10.1016/j.micres.2025.128224}, pmid = {40446743}, issn = {1618-0623}, mesh = {*Propidium/analogs &amp; derivatives/chemistry ; *Azides/chemistry ; *Microbial Viability ; *Polymerase Chain Reaction/methods/standards ; DNA, Bacterial/isolation &amp; purification/genetics ; *Bacteria/genetics/isolation &amp; purification ; Environmental Microbiology ; }, abstract = {The molecular detection of microorganisms in environmental samples relies on PCR-associated molecular workflows that typically cannot differentiate live from dead microbes. Understanding the microbial functions of complex communities can be significantly hindered by presence of the dead microbes. Using propidium monoazide (PMA), PMA-based viability PCR, is arguably the most convenient method to differentiate viability status apart. Errors from variabilities of non-standardized practices and a lack of understanding of the PMA mechanism deter the viability PCR approach. This review discusses the sources of variability in each of four key sequential steps: pre-analysis, PMA activation, DNA extraction and PCR. An analysis of previous literature on optimization of PMA-based viability PCR indicates that often only one source of variability is considered. However, all steps are interrelated and should be considered together when understanding and mitigating unwanted variability, especially in the PMA activation and PCR steps. Research gaps in PMA are addressed, such as the chemical mechanisms of PMA and possible by-products interferences, internal standard spiking and recommendations for future research.}, }
@article {pmid40446651, year = {2025}, author = {O'Connor, L and Minogue, E and Carolan, S and Darcy, G and Chueiri, A and Faherty, M and Morton, J and Mc Donagh, F and Singh, NK and Venkateswaran, K and Miliotis, G and Smith, TJ}, title = {Rapid detection of the novel human pathogen Pantoea piersonii: advancements in methodology.}, journal = {Diagnostic microbiology and infectious disease}, volume = {113}, number = {2}, pages = {116905}, doi = {10.1016/j.diagmicrobio.2025.116905}, pmid = {40446651}, issn = {1879-0070}, abstract = {Pantoea piersonii a novel bacterium isolated from the International Space Station (ISS) presents a unique challenge for microbial monitoring in spaceflight and more recently in clinical environments. Identification of the organism currently involves culture, followed by whole genome sequencing and analysis of generated sequences. Since the MALDI-TOF profile of this pathogen is absent from the database and 16S rRNA sequencing fails to resolve its identity to the nearest neighbour, a definitive genetic marker is required for unambiguous identification of the organism. Given the increase in the number of reported clinical cases, there exists a need for a rapid method for identification of the organism which could be utilised in a range of environments including the clinical setting. This study describes the design, development and validation of a specific and sensitive real-time PCR assay for the specific detection of P. piersonii. The assay targets a unique region of the malate dehydrogenase gene, confirmed through comparative genomic analysis. We demonstrate the performance of the assay in terms of analytical specificity, sensitivity, and robustness, ensuring its suitability for both space microbiology applications and clinical use.}, }
@article {pmid40445193, year = {2025}, author = {Cisneros, M and Blanco-Fuertes, M and Lluansí, A and Brotons, P and Henares, D and Pérez-Argüello, A and González-Comino, G and Ciruela, P and Mira, A and Muñoz-Almagro, C}, title = {Synergistic inhibition of pneumococcal growth by Dolosigranulum pigrum and Corynebacterium pseudodiphtheriticum: insights into nasopharyngeal microbial interactions.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0013825}, doi = {10.1128/spectrum.00138-25}, pmid = {40445193}, issn = {2165-0497}, abstract = {Streptococcus pneumoniae is a nasopharynx colonizer that can invade sterile tissues, causing invasive pneumococcal disease (IPD). Dolosigranulum pigrum and Corynebacterium pseudodiphtheriticum are commensal bacteria commonly isolated from the nasopharynx of healthy children, potentially playing a protective role. This study aims to analyze the effects of D. pigrum and C. pseudodiphtheriticum on S. pneumoniae in vitro growth. Pneumococcal strains were collected from IPD patients and healthy carriers in Catalonia (2016-2023). D. pigrum and C. pseudodiphtheriticum strains were isolated from a healthy child's nasopharynx. S. pneumoniae was co-cultured with each commensal bacterium in triplicate experiments. Pneumococcal growth was quantified using a real-time PCR assay targeting the lytA gene. The effect of commensal bacteria on pneumococcal growth was evaluated using a linear mixed-effect regression model. Twenty-eight pneumococcal strains expressing 24 different serotypes and 27 clonal types were analyzed (18 isolated in blood and 10 in nasopharyngeal aspirate). Pneumococcal growth was decreased by D. pigrum (β = -0.763, 95% confidence interval [CI]: -0.94 to -0.59, P < 0.0001) and C. pseudodiphtheriticum (β = -0.583, 95% CI: -0.76 to -0.41, P < 0.0001). The combined presence of both had a stronger inhibitory effect (β = -0.971, 95% CI: -1.15 to -0.79, P < 0.0001). No association was found between isolation site or serotype with pneumococcal growth. D. pigrum and C. pseudodiphtheriticum significantly reduced pneumococcal growth, with a synergistic effect when combined. This antagonistic effect supports the potential protective factor of healthy nasopharyngeal microbiota against IPD and the development of these microorganisms as probiotics.IMPORTANCEInvasive pneumococcal disease (IPD) is a significant worldwide health challenge. The present study highlights the significant inhibitory effect of two commensal bacteria, Dolosigranulum pigrum and Corynebacterium pseudodiphtheriticum, on pneumococcal growth, with a stronger effect observed when both bacteria are present together. Through testing different strains of S. pneumoniae and the implementation of a robust statistical model, this research advances in the knowledge of microbial ecology and provides evidence to support the development of the use of these commensal bacteria as probiotics. These results emphasize the possibility of using the nasopharyngeal microbiota's natural interactions to mitigate the risk of IPD.}, }
@article {pmid40444437, year = {2025}, author = {Pan, Y and Tao, Y and Yang, X and Du, S and Ding, H and Li, J and Jia, H and Chen, H}, title = {Underlying mechanisms of spatial distribution of prokaryotic community in surface seawater from Arctic Ocean to the Sea of Japan.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0051725}, doi = {10.1128/spectrum.00517-25}, pmid = {40444437}, issn = {2165-0497}, abstract = {Microorganisms play critical roles in marine ecosystems, so understanding the factors shaping microbial communities across various oceanic regions is essential for predicting ecosystem resilience and biogeochemical cycles. This study investigated the marine prokaryotic communities across 22 stations spanning the Arctic Ocean, the Chukchi Sea, the Bering Sea, and the Sea of Japan, with an emphasis on how environmental factors shape these communities. Results showed that the microbial alpha diversity generally declines with increasing latitude, though Arctic Ocean stations exhibited higher Chao 1 indices compared to the Bering Sea. Beta diversity analyses revealed that temperature and salinity were key factors associated with community composition variation across latitudes. Proteobacteria and Cyanobacteria were the dominant phyla showing opposite distribution trends across sampling stations. Cold-adapted oligotrophs such as Planktomarina and the SAR11 clade thrived in Arctic waters, while Sphingomonas, known for pollutant degradation, was more abundant in the Sea of Japan. Temperature was positively correlated to the relative abundance of Sphingomonas. At broad spatial scales, stochastic processes dominated community assembly of microbial phylogenetic diversity, while in specific regions like the Arctic Ocean, deterministic homogeneous selection appeared to shape microbial communities; and temperature showed a pronounced influence on phylogenetic turnover across all samples. Co-occurrence networks identified several key taxa, such as Polaribacter_1, Candidatus_Aquiluna, and NS5_marine_group. Overall, the study underscores temperature's role in shaping microbial community diversity, composition, and assembly processes across latitudinal gradients, highlighting unique community adaptations to extreme environments.IMPORTANCEMicrobes are the invisible engines of ocean health, recycling nutrients and sustaining marine life. This research helps us understand how climate factors like temperature shape these microscopic communities, which differ starkly between icy Arctic waters and warmer seas. As oceans warm due to climate change, microbial populations and their critical roles in cleaning pollutants or supporting food webs could shift dramatically. The study suggests Arctic microbes are uniquely adapted to cold, low-nutrient conditions, making them vulnerable to warming. By linking temperature to microbial diversity, this work provides clues to predict how marine ecosystems might respond to climate shifts, informing efforts to protect ocean biodiversity and processes vital to Earth's carbon and nutrient cycles.}, }
@article {pmid40442489, year = {2025}, author = {Ostap-Chec, M and Antoł, W and Bajorek, D and Berbeć, E and Moroń, D and Rapacz, M and Miler, K}, title = {Meta-Analysis and Experimental Evidence Reveal No Impact of Nosema ceranae Infection on Honeybee Carbohydrate Consumption.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {56}, pmid = {40442489}, issn = {1432-184X}, support = {Preludium 2021/41/N/NZ8/02917//Narodowe Centrum Nauki/ ; }, mesh = {Animals ; Bees/microbiology/physiology/metabolism ; *Nosema/physiology ; Hemolymph/chemistry/metabolism ; Feeding Behavior ; Trehalose/metabolism/analysis ; *Carbohydrate Metabolism ; }, abstract = {Honeybees (Apis mellifera) are indispensable pollinators for ecosystem stability and agricultural productivity. However, they face numerous challenges, including pathogens threatening their survival and ecosystem services. Among these pathogens, Nosema ceranae, a microsporidian parasite, causes significant damage to the intestinal tract and induces energetic imbalances in the organism, posing a major threat to both individual bees and entire colonies. In response to infections, bees often engage in behavioral defenses, such as self-medicating with antimicrobial substances available in their environment. We hypothesized that bees infected with N. ceranae might compensate behaviorally by increasing their carbohydrate consumption. To test this hypothesis, we conducted a meta-analysis of existing studies comparing sugar consumption in healthy and infected bees, complemented by an experimental study. In our experiment, we measured sugar intake and quantified trehalose levels in the hemolymph, a key indicator of energy reserves. Both the meta-analysis and experimental results consistently showed no significant differences in sugar consumption between healthy and infected bees. Similarly, trehalose levels in the hemolymph remained comparable between the two groups. Our findings suggest that the infection caused by N. ceranae does not elicit compensatory feeding behavior in honeybees. Moreover, the meta-analysis revealed significant gaps in current research, particularly a lack of studies focusing on forager bees, which face the highest energetic demands among colony members. Our findings call for future studies on the energetic effects of nosemosis and studies conducted under natural or semi-natural conditions.}, }
@article {pmid40440849, year = {2025}, author = {Ramadoss, R and Nishad, AK and Moovarkumudalvan, B and Shomar, B}, title = {Bacterial composition of dust deposited in Qatar: A seasonal study.}, journal = {The Science of the total environment}, volume = {985}, number = {}, pages = {179766}, doi = {10.1016/j.scitotenv.2025.179766}, pmid = {40440849}, issn = {1879-1026}, mesh = {Qatar ; *Dust/analysis ; Seasons ; *Bacteria/classification ; *Air Microbiology ; *Environmental Monitoring ; RNA, Ribosomal, 16S/analysis ; *Microbiota ; *Air Pollutants/analysis ; }, abstract = {Dust storms in the Middle East threaten public health by deteriorating air quality and transporting microorganisms over vast distances. This study analyzes seasonal variations in dust-borne bacterial diversity on photovoltaic (PV) panels using 16S rRNA gene sequencing and bioinformatics to assess community composition and metabolic potential. Our findings suggest that seasonal ecological factors have potential effects on the composition of the airborne bacterial community. In Qatar, the high atmospheric CO2 levels associated with hydrocarbon refining had promoted the growth of hydrocarbon-degrading bacteria belonging to the phyla Campilobacterota, Proteobacteria, and Bacteroidota. High temperatures and photothermal reactions of summer conditions have favored sulfur-metabolizing bacteria. Conversely, milder temperatures, increased humidity, reduced wind speed, and a decline in summer-favoring bacteria had contributed to the increased abundance of the phyla Patescibacteria, Firmicutes, and Actinobacteriota during other seasons. This study had also identified dust borne pathogenic bacteria associated with human and plant diseases, highlighting the need for environmental surveillance to monitor microbial diversity and its shifts driven by ecological factors. This knowledge is crucial for public health, environmental protection, sustainable farming and advancing our understanding of microbial ecology.}, }
@article {pmid40439420, year = {2025}, author = {Park, J and Kohn, E and Schenk, S and Davis, KM and Clark, JS and Parfrey, LW}, title = {An experimental test of the influence of microbial manipulation on sugar kelp (Saccharina latissima) supports the core influences host function hypothesis.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {6}, pages = {e0030125}, pmid = {40439420}, issn = {1098-5336}, mesh = {*Kelp/microbiology/growth &amp; development ; *Bacteria/isolation &amp; purification/classification/genetics ; *Microbiota ; Edible Seaweeds ; Laminaria ; }, abstract = {UNLABELLED: Kelp are valued for a wide range of commercial products and their role in kelp forest ecosystems, making kelp cultivation a rapidly expanding economic sector. Microbes associated with kelp and other macroalgae play a critical role in processes such as nutrient exchange, chemical signaling, and defense against pathogens. Thus, manipulating the microbiome to enhance macroalgal growth and resilience is a promising yet underexplored approach for sustainable kelp cultivation. The core microbiome hypothesis suggests that the bacteria that are consistently found on a host (the core microbes) are likely to have a disproportionate impact on host biology, making them an attractive target for microbiome manipulation. In this study, we surveyed wild Saccharina latissima and their surrounding environment to identify core bacterial taxa, compared them to cultivated kelp, and experimentally tested how cultured bacterial isolates affect kelp development. We found that core bacteria are nearly absent in cultivated juvenile sporophytes in nurseries, but eventually colonize them after outplanting to ocean farm sites. Bacterial inoculants had both positive and negative effects on kelp development. Notably, the strength of association of a bacterial genus with kelp in the wild positively correlated with its impact on gametophyte settlement and sporophyte development in kelp co-culture experiments, aligning with predictions from the core microbiome influences host function hypothesis. These findings affirm the feasibility of using microbial manipulations to improve current kelp aquaculture practices and provide a framework for developing these techniques.<br><br>IMPORTANCE: Microorganisms consistently associated with hosts are widely thought to be more likely to impact host biology and health. However, this intuitive concept has not been experimentally evaluated. This study formalizes this concept as the Core Microbiome Influences Host Function hypothesis and experimentally tests this hypothesis in sugar kelp (Saccharina). The distribution of bacteria on wild kelp and core microbes was first identified by compiling a broad dataset of the kelp microbiome sampled across space and time. Bacterial cultures were isolated from the surface of sugar kelp and individually grown in laboratory co-culture with sugar kelp spores to assess the ability of bacterial isolates to influence kelp growth and development. In support of the core influences host function hypothesis, isolates belonging to bacterial genera that are more strongly associated with wild sugar kelp are more likely to influence development in laboratory experiments.}, }
@article {pmid40437905, year = {2025}, author = {Ni, J and Yang, Z and Sun, X and Cui, Q and Zhang, R and Lu, H and Wu, Z and Zhu, J and Mao, H and Liu, K and Tang, C and Wang, C and Xing, C and Zhu, J}, title = {Probiotic Akkermansia muciniphila alleviates acute kidney injury by protecting the intestinal barrier and modulating gut microbiota and metabolites.}, journal = {Journal of biomedical research}, volume = {}, number = {}, pages = {1-12}, doi = {10.7555/JBR.39.20250162}, pmid = {40437905}, issn = {1674-8301}, abstract = {Acute kidney injury (AKI) is a critical condition with limited effective therapies. Akkermansia muciniphila (A. muciniphila) is a probiotic with multiple beneficial effects, including epithelial cell tight junctions regulation. Since renal pathophysiology is associated with gut barrier integrity, we hypothesized that A. muciniphila may have potential preventive effects on AKI. We established a lipopolysaccharide (LPS)-induced AKI mouse model to evaluate the effects of A. muciniphila. Our findings showed that pretreatment with A. muciniphila significantly attenuated kidney injury, as evidenced by reduced serum creatinine and urea nitrogen levels, alongside diminished tubular necrosis and apoptosis. A. muciniphila preserved the intestinal barrier integrity and induced marked shifts in gut microbial ecology and the metabolome. A. muciniphila induced notably an increase in the relative abundance of phylum Proteobacteria while a decrease of Bacteroidetes. At the genus level, Prevotella, Faecalibaculum, Moraxella and Lactobacillus were more abundant in A. muciniphila-pretreated mice. Metabolomic analysis revealed that A. muciniphila altered the gut metabolome affecting modulation of pathways, including tyrosine metabolism, alanine/aspartate/glutamate homeostasis, cancer-related carbon flux, and GABAergic synaptic signaling. In conclusion, our findings demonstrate A. muciniphila's renoprotective effects through gut-kidney axis modulation, laying the foundation for subsequent studies to verify the connection between gut microbiota and AKI.}, }
@article {pmid40436193, year = {2025}, author = {Lacerda, AL and Casotti, R and Briand, JF and Lenoble, V and Muniategui-Lorenzo, S and Kessler, F and Barre, A and Moscoso-Pérez, CM and Fernández-González, V and Andrade-Garda, JM and Murano, C and Donnarumma, V and Oreste, E and Joyce, H and Hannon, C and Nash, R and Orange, F and Frias, J and Pedrotti, ML}, title = {The plastisphere: a comprehensive description of geographic and temporal community patterns across the Mediterranean Sea and the Atlantic Ocean.}, journal = {Environmental research}, volume = {282}, number = {}, pages = {121929}, doi = {10.1016/j.envres.2025.121929}, pmid = {40436193}, issn = {1096-0953}, abstract = {Plastic pollution is a global ecological threat, not only as physical debris but also as a novel substrate hosting microbial communities, known as "plastisphere". Polymer type (virgin vs. recycled), combined with environmental variations, may influence both early and mature colonization stages. While biogeography has been identified as a key driver of the plastisphere community structure, prior research often relied on isolated studies with no methodological standardization or on opportunistic sampling. Here, this study stands out by conducting a simultaneous and harmonized investigation across environmentally distinct sites in the Mediterranean Sea and the Atlantic Ocean. Three polymers (LDPE, PP-PC, PLA) were incubated in situ, across six locations. Using standardized protocols and eDNA metabarcoding (16S and 18S rRNA), we assessed how biogeography, environmental variables, polymer type, and exposure time shape the diversity and composition of prokaryotic and eukaryotic communities colonizing plastics. Incubations lasted up to one year, with sampling at 7, 30 and 90 days, covering all four seasons. Microbial colonization in all plastics occurred within 7 days, but community richness and maturity fluctuated across sites and seasons. Proteobacteria, Bacteroidia and Planctomycetes were the dominant prokaryotes, while Ciliophora, Cercozoa and Dinoflagellata dominated eukaryotes. Taxa with potential for plastic biodegradation (e.g., Oleibacter, Alcanivorax) and pathogenicity (e.g., Pseudomonas, Candida) were identified, highlighting the plastisphere's ecological role. This dataset represents the most comprehensive assessment of marine plastisphere diversity to date, allowing the understanding of species occurrence and their interactions, influence on ecological processes and the emerging health risks of the plastisphere, which should be considered when developing global strategies to mitigate ocean plastic pollution.}, }
@article {pmid40435560, year = {2025}, author = {Fazio, NA and Albertin, W and Masneuf-Pomarede, I and Randazzo, CL and Caggia, C}, title = {Structure of culturable indigenous yeast population and genetic diversity of Saccharomyces cerevisiae and non-Saccharomyces yeasts during spontaneous fermentation of Etna vineyards grapes.}, journal = {International journal of food microbiology}, volume = {440}, number = {}, pages = {111282}, doi = {10.1016/j.ijfoodmicro.2025.111282}, pmid = {40435560}, issn = {1879-3460}, mesh = {*Vitis/microbiology ; Fermentation ; *Genetic Variation ; *Wine/microbiology ; *Saccharomyces cerevisiae/genetics/isolation &amp; purification/metabolism/classification ; *Yeasts/genetics/isolation &amp; purification/classification/metabolism/growth &amp; development ; Italy ; Microsatellite Repeats ; Farms ; }, abstract = {The microbial diversity of indigenous yeasts plays a fundamental role in the spontaneous fermentation of wines, contributing to the concept of microbial terroir and potentially influencing the sensory profile of the final product. This study explores the yeast ecology and genetic diversity of Saccharomyces cerevisiae and non-Saccharomyces yeasts in four wineries located on two different sides of Mount Etna, a region of unique viticultural significance due to its volcanic soils and diverse microclimatic conditions. A total of 454 yeast isolates were obtained from spontaneous fermentations of different grape varieties, and identified as belonging to 18 distinct species. The spontaneous fermentation was characterized by an initial dominance of non-Saccharomyces yeasts, especially Hanseniaspora uvarum and Metschnikowia pulcherrima, followed by a gradual dominance of S. cerevisiae at later stages. Microsatellite genotyping revealed significant genetic diversity among S. cerevisiae strains, with some distinct genetic patterns associated with Italian winery environments. Additionally, H. uvarum exhibited significant genetic variation but lacked clear geographic clustering, suggesting complex ecological and enological interactions. Statistical analyses of microbial diversity indices indicated that vineyard-specific factors, including altitude, soil composition, and agronomic practices, may influence yeast community structure among the four wineries. These findings provide new insights into the microbial ecology of Etna wines and highlight the potential of indigenous yeast populations for maintaining and enhancing regional wine identity.}, }
@article {pmid40432969, year = {2025}, author = {Wang, JQ and Yu, T and Qiu, HY and Ji, SW and Xu, ZQ and Cui, QC and Li, HF and Liang, WF and Feng, S and Fu, CT and Gao, X and Han, ZZ and Tian, WN and Li, JX and Xue, SJ}, title = {Differential impact of spotted fever group rickettsia and anaplasmosis on tick microbial ecology: evidence from multi-species comparative microbiome analysis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1589263}, pmid = {40432969}, issn = {1664-302X}, abstract = {Tick-borne diseases (TBDs) pose a significant public health challenge, as their incidence is increasing due to the effects of climate change and ecological shifts. The interplay between tick-borne pathogens and the host microbiome is an emerging area of research that may elucidate the mechanisms underlying disease susceptibility and severity. To investigate the diversity of microbial communities in ticks infected with vertebrate pathogens, we analyzed the microbiomes of 142 tick specimens. The presence of Rickettsia and Anaplasma pathogens in individual samples was detected through PCR. Our study aimed to elucidate the composition and variation of microbial communities associated with three tick species, which are known vectors for various pathogens affecting both wildlife and humans. We employed high-throughput sequencing techniques to characterize the microbial diversity and conducted statistical analyses to assess the correlation between the presence of specific pathogens and the overall microbial community structure. Pathogen screening revealed an overall positivity rate of 51.9% for Anaplasma and 44.6% for spotted fever group rickettsia (SFGR). Among the three tick species (Dermacentor silvarum, Haemaphysalis concinna, and Haemaphysalis japonica) analyzed, D. silvarum (the predominant species) exhibited the highest pathogen prevalence. The results indicate significant variation in microbial diversity between tick samples, with the presence of Anaplasma and SFGR associated with distinct changes in the microbial community composition. These findings underscore the complex interactions between ticks and their microbial inhabitants, enriching our understanding of tick-borne diseases.}, }
@article {pmid40431577, year = {2025}, author = {Jia, J and Bao, P and Yu, Q and Li, N and Ren, H and Chen, Q and Yan, P}, title = {Lactobacillus Re-Engineers Gut Microbiota to Overcome E. coli Colonization Resistance in Mice.}, journal = {Veterinary sciences}, volume = {12}, number = {5}, pages = {}, pmid = {40431577}, issn = {2306-7381}, support = {KCXF20201221173205015//the Shenzhen Science and Technology Program/ ; TCYC-TP2023//Xinjiang Tianchi introduction of talent research Program/ ; }, abstract = {The intestinal health and functionality of animals play pivotal roles in nutrient digestion and absorption, as well as in maintaining defense against pathogenic invasions. These biological processes are modulated by various determinants, including husbandry conditions, dietary composition, and gut microbial ecology. The excessive use of anthropogenic antibiotics may disrupt intestinal microbiota composition, potentially leading to dysbiosis that directly compromises host homeostasis. While Lactobacillus species are recognized for their immunomodulatory properties, their precise mechanisms in regulating host anti-inflammatory gene expression and influencing mucosal layer maturation, particularly regarding E. coli colonization resistance, require further elucidation. To investigate the regulatory mechanisms of Lactobacillus in relation to intestinal architecture and function during E. coli infection, we established a colonic infection model using Bal b/c mice, conducting systematic analyses of intestinal morphology, inflammatory mediator profiles, and microbial community dynamics. Our results demonstrate that Lactobacillus supplementation (Pediococcus acidilactici) effectively mitigated E. coli O78-induced enteritis, with co-administration during infection facilitating the restoration of physiological parameters, including body mass, intestinal histoarchitecture, and microbial metabolic functions. Microbiome profiling revealed that the Lactobacillus intervention significantly elevated Lactococcus abundance while reducing Weissella populations (p < 0.05), concurrently enhancing metabolic pathways related to nutrient assimilation and environmental signal processing (including translation mechanisms, ribosomal biogenesis, amino acid transport metabolism, and energy transduction systems; p < 0.05). Mechanistically, Lactobacillus administration attenuated E. coli-induced intestinal pathology through multiple pathways: downregulating pro-inflammatory cytokine expression (IL-1β, IL-1α, and TNF-α), upregulating epithelial junctional complexes (Occludin, Claudin-1, and ZO-1), and stimulating mucin biosynthesis (MUC1 and MUC2; p < 0.05). These modifications collectively enhanced mucosal barrier integrity and promoted epithelial maturation. This investigation advances our comprehension of microbiota-host crosstalk during enteropathogenic infections under probiotic intervention, offering valuable insights for developing novel nutritional strategies and microbial management protocols in animal husbandry.}, }
@article {pmid40431542, year = {2025}, author = {Karukayil Gopalakrishnan, N and Pappuswamy, M and Meganathan, G and Shanmugam, S and Pushparaj, K and Balasubramanian, B and Kim, IH}, title = {Influence of Probiotic Administration in Canine Feed: A Comprehensive Review.}, journal = {Veterinary sciences}, volume = {12}, number = {5}, pages = {}, pmid = {40431542}, issn = {2306-7381}, abstract = {Dogs are cherished companions, and in today's world, pets are increasingly regarded as family members. Pet owners are placing growing emphasis on their animals' health, particularly for dogs. Probiotics, which are living bacteria that benefit the host when given in sufficient quantities, have drawn a lot of interest in the veterinary nutrition community due to their beneficial effects on companion animals, including dogs. This study emphasizes the advantages of adding probiotics to canine diets in order to enhance the health of the gut flora and the technologies used to incorporate probiotics into canine feed. It looks at the best ways to deal with common dog health problems, highlighting probiotics as a helpful substitute for antibiotics, which can have serious adverse effects, encourage bacterial resistance, and disturb the gut's microbial ecology, which is necessary for digesting. Such disruptions are linked to chronic inflammatory enteropathy and obesity in dogs. This paper also examines biotechnological advancements in probiotic incorporation methods in dog feed, aiming to optimize their health benefits. Probiotic feed supplements may thus represent a promising approach to advancing canine health care, providing a natural adjunct to conventional treatments and preventive measures.}, }
@article {pmid40431287, year = {2025}, author = {Zhong, J and Ran, Q and Han, Y and Gan, L and Dong, C}, title = {Biosynthetic Mechanisms of Plant Chlorogenic Acid from a Microbiological Perspective.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, pmid = {40431287}, issn = {2076-2607}, support = {32360029//the National Science Foundation of China/ ; 32400111//the National Science Foundation of China/ ; Qiankehe Foundation-ZK (2024) General 091//he Guizhou Provincial Basic Research Program (Natural Science)/ ; }, abstract = {Chlorogenic acid (CGA), a phenolic compound with diverse bioactivities, plays a crucial role in plant defense mechanisms and has significant therapeutic potential in human inflammatory and cardiovascular diseases. The biosynthesis and accumulation of CGA in plants result from a complex interplay between internal factors (e.g., hormones, enzymes, and genes) and external factors (e.g., microbial interactions, drought, and temperature fluctuations). This review systematically investigates the influence of microbes on internal regulatory factors governing CGA biosynthesis in plants. CGA is synthesized through four distinct metabolic pathways, with hormones, enzymes, and genes as key regulators. Notably, microbes enhance CGA biosynthesis by improving plant nutrient uptake, supplying essential hormones, regulating the expression of related enzymes and genes, and the interaction between bacteria and fungi. In addition, our review summarizes the challenges currently present in the research and proposes a series of innovative strategies. These include in-depth investigations into the molecular mechanisms of microbial regulation of plant gene expression, gene editing, development of microbial inoculants, construction of synthetic microbial communities, and exogenous application of plant hormones.}, }
@article {pmid40431158, year = {2025}, author = {Mirete, S and Sánchez-Costa, M and Díaz-Rullo, J and González de Figueras, C and Martínez-Rodríguez, P and González-Pastor, JE}, title = {Metagenome-Assembled Genomes (MAGs): Advances, Challenges, and Ecological Insights.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, pmid = {40431158}, issn = {2076-2607}, support = {PID2021-126114NB-C43//Spanish Ministry of Science and Innovation which also included European Regional Development Fund (FEDER)/ ; }, abstract = {Metagenome-assembled genomes (MAGs) have revolutionized microbial ecology by enabling the genome-resolved study of uncultured microorganisms directly from environmental samples. By leveraging high-throughput sequencing, advanced assembly algorithms, and genome binning techniques, researchers can reconstruct microbial genomes without the need for cultivation. These methodological advances have expanded the known microbial diversity, revealing novel taxa and metabolic pathways involved in key biogeochemical cycles, including carbon, nitrogen, and sulfur transformations. MAG-based studies have identified microbial lineages form Archaea and Bacteria responsible for methane oxidation, carbon sequestration in marine sediments, ammonia oxidation, and sulfur metabolism, highlighting their critical roles in ecosystem stability. From a sustainability perspective, MAGs provide essential insights for climate change mitigation, sustainable agriculture, and bioremediation. The ability to characterize microbial communities in diverse environments, including soil, aquatic ecosystems, and extreme habitats, enhances biodiversity conservation and supports the development of microbial-based environmental management strategies. Despite these advancements, challenges such as assembly biases, incomplete metabolic reconstructions, and taxonomic uncertainties persist. Continued improvements in sequencing technologies, hybrid assembly approaches, and multi-omics integration will further refine MAG-based analyses. As methodologies advance, MAGs will remain a cornerstone for understanding microbial contributions to global biogeochemical processes and developing sustainable interventions for environmental resilience.}, }
@article {pmid40427685, year = {2025}, author = {Chen, Z and Zhong, Y and Chen, L and Liu, W and Lin, C and Chen, Y and Wang, X}, title = {HGF Aggravated Periodontitis-Associated Gut Barrier and Microbial Dysfunction: Implications for Oral-Gut Axis Regulation.}, journal = {Biology}, volume = {14}, number = {5}, pages = {}, pmid = {40427685}, issn = {2079-7737}, support = {81700985//National Natural Science Foundation of China/ ; 2024A03J0138//Guangzhou Municipal Science and Technology Bureau/ ; 02-408-2304-05037XM and 02-408-240603131063//Plan on Enhancing Scientific Research in Guangzhou Medical University/ ; 202201020203//Guangzhou Science and Technology Program/ ; }, abstract = {While periodontitis is increasingly linked to systemic disorders through the oral-gut axis, the molecular mediators driving gut microbiota dysbiosis and barrier disruption remain elusive. Hepatocyte growth factor (HGF), a novel regulator of inflammatory bone loss in periodontitis, may serve as a critical communicator between oral infection and distal intestinal pathology. This study investigates how HGF overexpression modulates the gut microbial ecosystem and intestinal barrier integrity in a transgenic periodontitis model. In this study, we combined 16S rRNA sequencing of fecal microbiota with comprehensive gut barrier assessments, including systemic markers (D-lactate, LPS, and DAO ELISA), structural integrity (villous morphology), and molecular analysis (ZO-1, occludin, and NOD2 immunohistochemistry), using HGF-overexpressing transgenic (HGF-Tg) mice with periodontitis. The results demonstrated that HGF increased gut permeability in the context of periodontitis, as evidenced by elevated serum levels of D-lactate and LPS compared to wild type (WT) mice. In addition, gut villous morphology disorder was observed in HGF-Tg mice with periodontitis. HGF also diminished the protein level of occludin and upregulated NOD2 expression in mice with periodontitis. Moreover, HGF-Tg mice with periodontitis exhibited significant dysbiosis of gut microbiota, with reduced levels of probiotics (e.g., Faecalibaculum). Notably, HGF also increased the enrichment of the periodontitis-associated pathogens (e.g., Desulfovibrio and Streptococcus) in the gut. Microbial functions, particularly metabolic pathways, were significantly altered by HGF when periodontitis occurred. Some microorganisms like g_Desulfovibrio may play a role in gut barrier disorder in HGF-Tg mice with periodontitis. Overall, our findings position HGF as a novel orchestrator of oral-gut crosstalk, where its overexpression reshapes gut microbial ecology toward a "leaky gut" phenotype to compromise intestinal barrier integrity, further deepening our understanding of the oral-gut axis.}, }
@article {pmid40427319, year = {2025}, author = {Xu, C and Guo, X and Li, L}, title = {Metagenomic Comparison of Gut Microbes of Lemur catta in Captive and Semi-Free-Range Environments.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {10}, pages = {}, pmid = {40427319}, issn = {2076-2615}, abstract = {In order to protect endangered species, many zoos adopt diverse rearing models to achieve optimal conservation outcomes. This study employed metagenomic approaches to assess differences in the fecal microbiome of captive and semi-free-ranging ring-tailed lemurs (Lemur catta). The results show that captivity significantly altered the microbial community structure. The inter-individual variability in the microbial community within the captive-bred (CB) group was lower than that in the semi-free-ranging (FR) group, yet these individuals harbored a higher abundance of potential pathogens (Treponema_D). In contrast, microbial genera associated with fiber degradation and short-chain fatty acid production in the FR group were significantly elevated (Faecalibacterium, Roseburia, and Megamonas) as compared to the CB group. Environmental variations between the two rearing systems led to distinct profiles in microbial functions and carbohydrate-active enzyme gene composition. Notably, the FR group of lemurs exhibited an increased abundance of enzyme genes associated with the degradation of complex polysaccharides (cellulose, hemicellulose, and pectin), suggesting that their diet, rich in natural plant fibers, enhances the capacity of their gut microbiota to extract essential energy and nutrients. Conversely, the CB group displayed a more homogeneous microbial community with a higher prevalence of potential pathogens, implying that a captive lifestyle may negatively impact gastrointestinal health. These findings offer valuable insights into the influence of rearing conditions on gut microbial ecology and its potential implications for the health management of ring-tailed lemurs.}, }
@article {pmid40426572, year = {2025}, author = {Touati, A and Ibrahim, NA and Mairi, A and Kirat, H and Basher, NS and Idres, T}, title = {One Health at Risk: Plasmid-Mediated Spread of mcr-1 Across Clinical, Agricultural, and Environmental Ecosystems.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, pmid = {40426572}, issn = {2079-6382}, support = {IMSIU-DDRSP2501//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; }, abstract = {The global dissemination of plasmid-mediated mcr genes, which confer resistance to the last-resort antibiotic colistin, represents a critical public health challenge driven by the interplay of clinical, agricultural, and environmental factors. This review examines the genetic and ecological dynamics of mcr-bearing plasmids, focusing on their role in disseminating colistin resistance across diverse bacterial hosts and ecosystems. Key plasmid families demonstrate distinct evolutionary strategies, including IncI2, IncHI2, and IncX4. IncI2 plasmids favor stability in livestock and clinical settings. IncHI2 plasmids, on the other hand, leverage transposons to co-select for multidrug resistance, while IncX4 plasmids achieve global dissemination through streamlined, conjugation-efficient architectures. The pervasive spread of mcr genes is exacerbated by their integration into chromosomes via mobile genetic elements and co-selection with resistance to other antibiotic classes, amplifying multidrug-resistant phenotypes. Environmental reservoirs, food chains, and anthropogenic practices further facilitate cross-niche transmission, underscoring the interconnectedness of resistance under the One Health framework. Addressing this crisis requires coordinated strategies, including reducing colistin misuse in agriculture, enhancing surveillance of high-risk plasmid types, and fostering international collaboration to preserve antimicrobial efficacy and mitigate the threat of untreatable infections.}, }
@article {pmid40423845, year = {2025}, author = {Pérez-Gómez, O and Domínguez-Maqueda, M and García-Márquez, J and Moriñigo, M&#xc1; and Tapia-Paniagua, ST}, title = {Metabolite-Driven Modulation of Biofilm Formation in Shewanella: Insights from Shewanella sp. Pdp11 Extracellular Products.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {55}, pmid = {40423845}, issn = {1432-184X}, support = {PID2020-113637RB-C21//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-113637RB-C21//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-113637RB-C21//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-113637RB-C21//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-113637RB-C21//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {*Shewanella/metabolism/physiology/genetics ; *Biofilms/growth &amp; development/drug effects ; Glycogen/metabolism ; }, abstract = {Biofilm formation is a survival strategy for bacteria, contributing to their persistence in natural and industrial environments. In this study, we investigated the ability of extracellular products (ECPs) produced by the probiotic strain Shewanella sp. Pdp11 under different culture conditions to inhibit biofilm formation in pathogenic and environmental Shewanella strains. ECPs from specific culture conditions altered biofilm formation in several Shewanella strains, with Shewanella hafniensis P14 displaying the highest sensitivity. Metabolomic analysis of the ECPs identified glycogen as a key metabolite associated with biofilm inhibition. Further genomic analysis of S. hafniensis P14 revealed an interruption in its glycogen synthesis pathway, suggesting a dependency on external glycogen-related metabolites for biofilm development. These findings demonstrate that Shewanella sp. Pdp11 ECPs can modify biofilm formation across multiple Shewanella strains, particularly in S. hafniensis P14 through glycogen-associated mechanisms.}, }
@article {pmid40423805, year = {2025}, author = {Meehan, DE and O'Toole, PW}, title = {A Review of Diet and Foraged Pollen Interactions with the Honeybee Gut Microbiome.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {54}, pmid = {40423805}, issn = {1432-184X}, support = {GOIPG/2024/5035//Taighde &#xc9;ireann/ ; 12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Bees/microbiology/physiology ; Animals ; *Gastrointestinal Microbiome ; *Pollen/metabolism ; *Diet ; }, abstract = {The honeybee Apis mellifera is a globally vital pollinator for flowering plants and crops, but it is currently facing mounting threats to survival due to habitat anthropization, emerging pathogens, and climate change. Over the past decade, increasing research efforts to understand and combat these challenges have led to an exploration of the honeybee gut microbiome-a relatively simple and highly conserved community of commensals which has a range of effects on the host. Researchers have now unravelled the main functional roles of this microbiome which include innate immune system stimulation, metabolism of dietary compounds, and mediation of host development and behaviour. Key amongst these is its role in aiding nutrition through the metabolism of complex carbohydrates and by degradation of otherwise indigestible pollen compounds. Increasingly, research is indicating that a diverse and high-quality pollen diet is key to maintaining healthy colonies and a stable microbiome. However, colonies can struggle to meet these dietary needs, particularly if they are located in anthropized ecosystems. Disruptions to honeybee diets or a reduction in the availability of diverse foraging options can significantly alter the composition of the microbiome, shifting it towards an abnormal state that leaves the honeybee more vulnerable to infection. Seasonal changes, primarily the overwintering period, also induce shifts in microbiome composition and are periods of time when a colony is particularly vulnerable to pathogenic infection. A comprehensive understanding of the effect these variables have on both microbiome composition and colony health is key to tackling the unprecedented environmental challenges that honeybees now face. This review summarises recent research which has elucidated the functional role of the gut microbiome in metabolism and how the composition of this bacterial community can alter due to seasonal change, anthropized landscapes, and dietary shifts. Finally, we also discuss recent studies investigating the effect that dietary supplementation has on the gut microbiome and the application of probiotic candidates for improving colony resilience and strength.}, }
@article {pmid40423261, year = {2025}, author = {Rotsaert, C and Minnebo, Y and Duysburgh, C and Liu, LS and Mahalak, KK and Firman, J and Mattei, LM and Moustafa, AM and Bittinger, K and Hu, W and Marzorati, M and Michiels, J and Van de Wiele, T}, title = {Digestive parameters and gut microbiota load and composition along the in vivo piglet gastrointestinal tract.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skaf107}, pmid = {40423261}, issn = {1525-3163}, abstract = {The increased attention towards the role of the gut microbiome in health and disease for both animals and humans has fuelled the demand for more relevant and accurate research models. In this study, we present an overview of biochemical and microbial parameters measured throughout the digestive tract of ten TopigsNorsvin x German Piétrain piglets to better understand the in vivo dynamics of digestive and fermentative processes in different gastrointestinal segments, as pigs are suggested to be a representative animal model for the human gastrointestinal tract. Our key findings include region-specific and significantly differing (P < 0.001) pH profiles, with the stomach having the lowest pH (3.36 ± 0.72) and the ileum the highest (7.24 ± 0.18). Dry matter content also varied significantly (P < 0.001), with the stomach having the highest (27.8 ± 2.4%) and the duodenum the lowest (10.6 ± 0.7%). The average total transit time was 12 hours and 45 minutes ± 1 hour and 42 minutes. Enzyme activities (pepsin, trypsin, amylase) showed interindividual differences. Amino acid levels varied among piglets, with total concentrations averaging 7.04 x 102 ± 2.29 x 102 µg mL-1 in the duodenum, 1.19 x 103 ± 2.69 x 102 µg mL-1 in the jejunum and 9.39 x 102 ± 2.54 x 102 µg mL-1 in the ileum. Bile acid concentrations varied strongly between piglets, with high levels in the gall bladder and varying levels throughout the digestive tract. Short-chain fatty acid concentrations increased significantly (P < 0.001) along the digestive tract, with the highest levels in the large intestine. The microbial load increased consistently (P < 0.001) along the digestive tract, with the highest loads in the rectum (6.82 x 1010 ± 2.88 x 1010 cells mL-1). The highest microbial diversity was observed in the lower intestine (i.e. caecum, colon and rectum), with significant shifts in microbial community composition, especially from the ileum to the caecum. This study provides valuable insights into the digestive and microbiological parameters of the porcine gut, confirming the pig's relevance as a model for gastrointestinal research. The findings can inform the development of in vitro or ex vivo models, reducing ethical constraints of animal studies and aiding in the assessment of dietary interventions on gut health.}, }
@article {pmid40422247, year = {2025}, author = {Wheeler, KM and Oh, MW and Fusco, J and Mershon, A and Kim, E and De Oliveira, A and Rahme, LG}, title = {MvfR Shapes Pseudomonas aeruginosa Interactions in Polymicrobial Contexts: Implications for Targeted Quorum-Sensing Inhibition.}, journal = {Cells}, volume = {14}, number = {10}, pages = {}, pmid = {40422247}, issn = {2073-4409}, support = {R01 AI177555/AI/NIAID NIH HHS/United States ; 5R01AI177555-02/GF/NIH HHS/United States ; N/A//Massachusetts General Hospital Research Scholar Award/ ; }, mesh = {*Quorum Sensing/genetics ; *Pseudomonas aeruginosa/pathogenicity/physiology/genetics/metabolism ; Humans ; *Bacterial Proteins/metabolism/genetics ; Biofilms/growth &amp; development ; Virulence ; Gene Expression Regulation, Bacterial ; Microbial Interactions ; Pseudomonas Infections/microbiology ; }, abstract = {Infections often occur in complex niches consisting of multiple bacteria. Despite the increasing awareness, there is a fundamental gap in understanding which interactions govern microbial community composition. Pseudomonas aeruginosa is frequently isolated from monomicrobial and polymicrobial human infections. This pathogen forms polymicrobial infections with other ESKAPEE pathogens and defies eradication by conventional therapies. By analyzing the competition within co-cultures of P. aeruginosa and representative secondary pathogens that commonly co-infect patients, we demonstrate the antagonism of P. aeruginosa against other ESKAPEE pathogens and the contribution of this pathogen's multiple quorum-sensing (QS) systems in these interactions. QS is a highly conserved bacterial cell-to-cell communication mechanism that coordinates collective gene expressions at the population level, and it is also involved in P. aeruginosa virulence. Using a collection of P. aeruginosa QS mutants of the three major systems, LasR/LasI, MvfR/PqsABCDE, and RhlR/RhlI, and mutants of several QS-regulated functions, we reveal that MvfR and, to a lesser extent, LasR and RhlR, control competition between P. aeruginosa and other microbes, possibly through their positive impact on pyoverdine, pyochelin, and phenazine genes. We show that MvfR inhibition alters competitive interspecies interactions and preserves the coexistence of P. aeruginosa with the ESKAPEE pathogens tested while disarming the pathogens' ability to form biofilm and adhere to lung epithelial cells. Our results highlight the role of MvfR inhibition in modulating microbial competitive interactions across multiple species, while simultaneously attenuating virulence traits. These findings reveal the complexity and importance of QS in interspecies interactions and underscore the impact of the anti-virulence approach in microbial ecology and its importance for treating polymicrobial infections.}, }
@article {pmid40421462, year = {2025}, author = {Liu, RZ and Zhao, XY and Feng, B and Zhao, WS and Li, MY and Yu, XF and Hu, SP and Li, RP and Gao, JL and Borjigin, Q}, title = {Research on soil bacterial community assembly and function under different straw returning practices in arid and semi-arid agricultural ecosystems over multiple years.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1590686}, pmid = {40421462}, issn = {1664-302X}, abstract = {INTRODUCTION: Straw return has gained attention for its potential to improve soil quality and crop yields, particularly in semi-arid regions like the Tumu Chuan Plain Irrigation Area. Soil bacteria play a crucial role in regulating soil biological processes, and understanding how straw return affects bacterial populations can guide better agricultural management practices.<br><br>METHODS: We investigated the impact of continuous straw return on soil bacterial communities using 16S rRNA gene sequencing. Four treatments were applied: Farmers' shallow rotation (CK), straw incorporated with deep tillage (DPR), straw incorporated with subsoiling (SSR), and no-tillage mulching straw return (NTR). Bacterial community structure, metabolic pathways, and assembly mechanisms were analyzed using Bugbase and PICRUSt2 for phenotypic and metabolic pathway predictions.<br><br>RESULTS: The study found that straw return practices significantly altered the relative abundance and life history strategies of bacterial phyla, mainly influenced by soil organic matter (SOM) and enzyme activity. The K-strategist to r-strategist ratio was highest in CK (2.06) and lowest in SSR (1.89). DPR and NTR treatments significantly changed bacterial community structure compared to CK (p < 0.05), resembling SSR. Predictions showed that DPR and NTR enhanced carbohydrate and amino acid metabolism and promoted more stable bacterial networks, with homogenous selection and drift effects. Bacterial aggregation in all treatments was driven by random processes, with varying aggregation levels: CK (20%), DPR (38.6%), SSR (16.5%), and NTR (30.7%).<br><br>DISCUSSION: The study demonstrates that continuous straw return practices significantly impact soil bacterial communities. DPR and NTR notably improved microbial diversity, bacterial cooperation, and ecosystem stability. These findings provide valuable insights for sustainable agricultural practices in semi-arid regions, enhancing soil microbial ecology and soil health through strategic straw return.}, }
@article {pmid40419814, year = {2025}, author = {Srivastava, AK and Riaz, A and Jiang, J and Li, X and Uzair, M and Mishra, P and Zeb, A and Zhang, J and Singh, RP and Luo, L and Chen, S and Yang, S and Zhao, Y and Xie, X}, title = {Advancing Climate-Resilient Sorghum: the Synergistic Role of Plant Biotechnology and Microbial Interactions.}, journal = {Rice (New York, N.Y.)}, volume = {18}, number = {1}, pages = {41}, pmid = {40419814}, issn = {1939-8425}, support = {[2022]091//Guizhou Provincial Youth Science and Technology Talents Growth Project/ ; }, abstract = {Climate-related problems such as drought stress, extreme temperature, erratic rainfall patterns, soil degradation, heatwaves, flooding, water logging, pests and diseases afflict the production and sustainability of sorghum. These challenges may be addressed by adopting climate-resilient practices and using advanced agronomic techniques. These challenges are being addressed through innovative applications of plant biotechnology and microbiology, which offer targeted solutions to enhance sorghum's resilience. For instance, biotechnological tools like CRISPR/Cas9 enable precise genetic modifications to improve drought and heat tolerance, while microbial inoculants, such as plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF), enhance nutrient uptake and stress tolerance through symbiotic interactions. However, biotechnological tools lead to the development of sorghum varieties with heat, drought and salinity tolerance, while marker-assisted selection significantly accelerates breeding for stress-resilient traits. When genetic engineering is introduced, genes encoding heat shock proteins, Osmo protectants and antioxidant pathways are introduced to increase plant resistance to abiotic stress. These compounds stabilise cellular structures, protect enzymes, and maintain osmotic balance, enhancing the plant's ability to survive and function in adverse environmental conditions. At the same time, it is reported that microbiology offers beneficial microbes, nitrogen-fixing bacteria, phosphate-solubilizing microorganisms, and arbuscular mycorrhizal fungi that help enhance nutrient availability, soil health and water uptake. Combinations of endophytes and microbial inoculants enhance plant immunity to pests and diseases while increasing tolerance to stress. Biocontrol agents such as Bacillus and Trichoderma contain suppression of pathogens and need less dependence on the use of chemical pesticides. On top of that, genetic modification increases the nutritional quality of sorghum biofortified. This is where biotechnology and microbiology work together to deliver sustainable farming systems reducing environmental impacts, boosting yields and securing food supply under environmental stresses. This review aims to examine the synergistic integration of plant biotechnology and microbial interactions as a strategy to enhance sorghum's resilience to climate-induced stresses, including drought, elevated temperatures, and nutrient-deficient soils. It highlights recent advancements in biotechnological tools such as gene editing, marker-assisted selection, and tissue culture, alongside the emerging role of plant-beneficial microbes in promoting stress tolerance and improving soil health. By synthesizing current knowledge across these disciplines, this review seeks to outline a framework for future research that harnesses the intersection of biotechnology and microbial ecology to support the sustainable improvement of sorghum resilience.}, }
@article {pmid40419768, year = {2025}, author = {Keegstra, JM and Landry, ZC and Zweifel, ST and Roller, BRK and Baumgartner, DA and Carrara, F and Martínez-Pérez, C and Clerc, EE and Ackermann, M and Stocker, R}, title = {Risk-reward trade-off during carbon starvation generates dichotomy in motility endurance among marine bacteria.}, journal = {Nature microbiology}, volume = {10}, number = {6}, pages = {1393-1403}, pmid = {40419768}, issn = {2058-5276}, support = {542395FY22//Simons Foundation/ ; 542379FY22//Simons Foundation/ ; GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 205321 207488//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 51NF40 225148//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {*Carbon/metabolism ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Seawater/microbiology ; *Aquatic Organisms/physiology/metabolism ; Biomass ; Carbon Cycle ; *Bacterial Physiological Phenomena ; }, abstract = {Copiotrophic marine bacteria contribute to the control of carbon storage in the ocean by remineralizing organic matter. Motility presents copiotrophs with a risk-reward trade-off: it is highly beneficial in seeking out sparse nutrient hotspots, but energetically costly. Here we studied the motility endurance of 26 marine isolates, representing 18 species, using video microscopy and cell tracking over 2 days of carbon starvation. We found that the trade-off results in a dichotomy among marine bacteria, in which risk-averse copiotrophs ceased motility within hours ('limostatic'), whereas risk-prone copiotrophs converted ~9% of their biomass per day into energy to retain motility for the 2 days of observation ('limokinetic'). Using machine learning classifiers, we identified a genomic component associated with both strategies, sufficiently robust to predict the response of additional species with 86% accuracy. This dichotomy can help predict the prevalence of foraging strategies in marine microbes and inform models of ocean carbon cycles.}, }
@article {pmid40417422, year = {2025}, author = {Roothans, N and Pabst, M and van Diemen, M and Herrera Mexicano, C and Zandvoort, M and Abeel, T and van Loosdrecht, MCM and Laureni, M}, title = {Long-term multi-meta-omics resolves the ecophysiological controls of seasonal N2O emissions during wastewater treatment.}, journal = {Nature water}, volume = {3}, number = {5}, pages = {590-604}, pmid = {40417422}, issn = {2731-6084}, abstract = {Nitrous oxide (N2O) is the third most important greenhouse gas and originates primarily from natural and engineered microbiomes. Effective emission mitigations are currently hindered by the largely unresolved ecophysiological controls of coexisting N2O-converting metabolisms in complex communities. To address this, we used biological wastewater treatment as a model ecosystem and combined long-term metagenome-resolved metaproteomics with ex situ kinetic and full-scale operational characterization over nearly 2 years. By leveraging the evidence independently obtained at multiple ecophysiological levels, from individual genetic potential to actual metabolism and emergent community phenotype, the cascade of environmental and operational triggers driving seasonal N2O emissions has ultimately been resolved. We identified nitrifier denitrification as the dominant N2O-producing pathway and dissolved O2 as the prime operational parameter, paving the way to the design and fostering of robust emission control strategies. This work exemplifies the untapped potential of multi-meta-omics in the mechanistic understanding and ecological engineering of microbiomes towards reducing anthropogenic impacts and advancing sustainable biotechnological developments.}, }
@article {pmid40413948, year = {2025}, author = {Pholtaisong, J and Kongsinkaew, C and On-Mee, T and Chittapun, S and Pornpukdeewattana, S and Todhanakasem, T and Kunyanee, K and Panya, A and Phonsatta, N and Yingcharoen, P and Charoenrat, T}, title = {Natural versus Saccharomyces boulardii self-induced anaerobic coffee fermentation: Effects on physicochemical properties and microbial ecology, and their influence on volatile profiles and sensory attributes across roast levels.}, journal = {Food chemistry}, volume = {488}, number = {}, pages = {144871}, doi = {10.1016/j.foodchem.2025.144871}, pmid = {40413948}, issn = {1873-7072}, mesh = {Fermentation ; *Volatile Organic Compounds/metabolism/chemistry/analysis ; Taste ; *Coffee/microbiology/chemistry/metabolism ; Humans ; *Saccharomyces boulardii/metabolism ; Anaerobiosis ; *Coffea/microbiology/chemistry/metabolism ; Bacteria/metabolism/isolation &amp; purification/classification/genetics ; Flavoring Agents/metabolism/chemistry ; }, abstract = {This study investigates the effects of natural self-induced anaerobic fermentation (NSIAF) and Saccharomyces boulardii self-induced anaerobic fermentation (SSIAF) on Arabica coffee during wet processing. Over 24 h of fermentation, NSIAF exhibited greater microbial diversity, higher titratable acidity, and increased reducing sugar consumption, while SSIAF provided a more controlled microbial environment dominated by S. boulardii. Volatile compound analysis identified 207 compounds, with lighter roasts showing the greatest number of significantly different compounds between NSIAF and SSIAF treatments. Sensory evaluation revealed a higher cupping score for NSIAF at a light roast (82.08 ± 0.14) compared to SSIAF (81.58 ± 0.14), reflecting distinct flavor characteristics imparted by each fermentation process. Both methods achieved specialty coffee standards (≥80 points), highlighting the potential of NSIAF for complex and diverse profiles and the suitability of SSIAF for consistency and controlled fermentation.}, }
@article {pmid40413198, year = {2025}, author = {Brandão Gontijo, J and Huang, L and Levintal, E and Prieto García, C and Erikson, CB and Coyotl, A and Horwath, WR and Dahlke, HE and Mazza Rodrigues, JL}, title = {Depth-dependent Metagenome-Assembled Genomes of Agricultural Soils under Managed Aquifer Recharge.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {858}, pmid = {40413198}, issn = {2052-4463}, support = {7975//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 2021-38420-34070//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; }, mesh = {*Soil Microbiology ; *Groundwater ; Agriculture ; *Metagenome ; Microbiota ; Bacteria/genetics/classification ; Metagenomics ; California ; Archaea/genetics ; Soil ; }, abstract = {Managed Aquifer Recharge (MAR) systems, which intentionally replenish groundwater aquifers with excess water, are critical for addressing water scarcity exacerbated by demographic shifts and climate variability. To date, little is known about the functional diversity of the soil microbiome at different soil depth inhabiting agricultural soils used for MAR. Knowing the functional diversity is pivotal in regulating nutrient cycling and maintaining soil health. Metagenomics, particularly Metagenome-Assembled Genomes (MAGs), provide a powerful tool to explore the diversity of uncultivated soil microbes, facilitating in-depth investigations into microbial functions. In a field experiment conducted in a California vineyard, we sequenced soil DNA before and after water application of MAR. Through this process, we assembled 146 medium and 14 high-quality MAGs, uncovering a wide array of archaeal and bacterial taxa across different soil depths. These findings advance our understanding of the microbial ecology and functional diversity of soils used for MAR, contributing to the development of more informed and sustainable land management strategies.}, }
@article {pmid40412969, year = {2025}, author = {Yan, W and Gu, L and Yue, X and Zhong, H and Wang, D}, title = {Vertical distribution of intracellular protoporphyrin IX in coastal sediment cores: Implications for sedimentology and microbial community composition.}, journal = {Journal of environmental sciences (China)}, volume = {156}, number = {}, pages = {712-724}, doi = {10.1016/j.jes.2024.11.014}, pmid = {40412969}, issn = {1001-0742}, mesh = {*Geologic Sediments/chemistry/microbiology ; *Protoporphyrins/analysis ; *Microbiota ; RNA, Ribosomal, 16S ; *Environmental Monitoring ; }, abstract = {Protoporphyrin IX (PPIX), a basic porphyrin system found in nature, all "porphyrin-type" tetrapyrroles with a biological function are biosynthetically derived thereof. PPIX is a metalloprosthetic group of numerous proteins involved in diverse metabolic and respiratory processes across all domains of life, and is thus considered essential for respiring organisms. Determining the biotic and abiotic factors that influence marine microbial growth and community structure is critical for understanding global biogeochemical cycles. Here, we present vertical profiles of intracellular PPIX and four derivative products (Chlorophyll-a/b and Pheophytin-a/b) from two coastal sediment cores, alongside ancillary geochemical and 16S rRNA microbial community data. Our findings indicated that PPIX is present in the natural sediment environment and displays a decreasing trend with depth, revealing a significant positive correlation with both organic matter and microbial abundance. Co-occurrence networks revealed that the environmental distribution of PPIX was positively correlated with the microbial porphyrin producer (high genetic completeness), but negatively correlated with auxotrophs (absence or low genetic completeness). It emphasized the critical role of PPIX as a biological molecule involved in key physiological processes. These results suggest that PPIX is a prominent component of the shared extracellular metabolite pool, especially in anoxic marine sediments where it exists at physiologically relevant concentrations for microbial metabolism. This study highlighted the significance of PPIX in microbial ecology and its potential impact on biogeochemical cycles in marine sedimentary environments.}, }
@article {pmid40412391, year = {2025}, author = {Breyer, E and Stix, C and Kilker, S and Roller, BRK and Panagou, F and Doebke, C and Amano, C and Saavedra, DEM and Coll-García, G and Steger-Mähnert, B and Dachs, J and Berrojalbiz, N and Vila-Costa, M and Sobrino, C and Fuentes-Lema, A and Berthiller, F and Polz, MF and Baltar, F}, title = {The contribution of pelagic fungi to ocean biomass.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2025.05.004}, pmid = {40412391}, issn = {1097-4172}, abstract = {Metagenomic analysis has recently unveiled the widespread presence of pelagic fungi in the global ocean, yet their quantitative contribution to carbon stocks remains elusive, hindering their incorporation into biogeochemical models. Here, we revealed the biomass of pelagic fungi in the open-ocean water column by combining ergosterol extraction, Calcofluor-White staining, catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), and microfluidic mass sensor techniques. We compared fungal biomass with the biomass of other more studied microbial groups in the ocean such as archaea and bacteria. Globally, fungi contributed 0.32 Gt C (CI: 0.19-0.46), refining previous uncertainty estimates from two orders of magnitude to less than one. While fungal biomass was lower than that of bacteria, it exceeded that of the archaea (archaea:fungi:bacteria biomass ratio of 1:9:44). Collectively, our findings reveal the important contribution of fungi to open-ocean biomass and, consequently, the marine carbon cycle, emphasizing the need for their inclusion in biogeochemical models.}, }
@article {pmid40411587, year = {2025}, author = {Kelleher, LA and Anderson, Z and Stratford, JA and Fortunato, CS}, title = {Deciphering Soil Microbial Dynamics in Northeastern American Grasslands with Goldenrods (Solidago sp.).}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {53}, pmid = {40411587}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Grassland ; Rhizosphere ; *Bacteria/classification/genetics/isolation &amp; purification ; Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Pennsylvania ; *Solidago/microbiology ; Plant Roots/microbiology ; Biodiversity ; Hydrogen-Ion Concentration ; }, abstract = {Grasslands are important centers of biodiversity; however, these ecosystems have been in decline. Although many methods for grassland restoration have been developed, the abundant microbial communities in these regions are understudied and could be used to assist in these efforts. In this study, we aimed to understand how microbial communities varied by soil type, grassland site, and environmental conditions. Samples were taken from rhizosphere soil (attached to plant roots), proximal soil (close to the plant roots), and from bulk cores at Ricketts Glen State Park and Nescopeck State Park in northeastern Pennsylvania, USA, during June and August of 2021 and 2022. Rhizosphere soil samples were taken from the native common grassland plant, Solidago rugosa. 16S rRNA gene sequencing revealed that pH as well as soil type (bulk, proximal, or rhizosphere) significantly influenced the microbial community composition of each soil. Each soil type had its own distinct microbial communities, and proximal soil was identified as a transition zone between rhizosphere and bulk microbial communities. We also observed that the rhizosphere communities were dependent upon geography, as these communities were significantly different between grasslands even though the plant species remained the same. Our results highlight the complex nature of soil microbial communities and how many factors, including pH, soil type, and geography, can be overlayed to impact soil microbes. Results suggest future avenues of conservation research through modification and regulation of specific soil microbial communities in order to aid in the rehabilitation of these diminished regions.}, }
@article {pmid40410028, year = {2025}, author = {Vareschi, S and Jaut, V and Vijay, S and Allen, RJ and Schreiber, F}, title = {Antimicrobial efflux and biofilms: an interplay leading to emergent resistance evolution.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.04.012}, pmid = {40410028}, issn = {1878-4380}, abstract = {The biofilm mode of growth and drug efflux are both important factors that impede the treatment of bacterial infections with antimicrobials. Decades of work have uncovered the mechanisms involved in both efflux and biofilm-mediated antimicrobial tolerance, but links between these phenomena have only recently been discovered. Novel findings show how efflux impacts global cellular physiology and antibiotic tolerance, underpinned by phenotypic heterogeneity. In addition efflux can mediate cell-to-cell interactions, relevant in biofilms, via mechanisms including efflux of signaling molecules and metabolites, signaling using pump components and the establishment of local antibiotic gradients via pumping. These recent findings suggest that biofilm antibiotic tolerance and efflux are closely coupled, with synergistic effects leading to the evolution of antimicrobial resistance in the biofilm environment.}, }
@article {pmid40408931, year = {2025}, author = {Conall Holohan, B and Trego, A and Keating, C and Bressani-Ribeiro, T and Chernicharo, CL and Daigger, G and Galdi, SM and Knörle, U and Paissoni, E and Robles, A and Rogalla, F and Shin, C and Soares, A and Smith, AL and Szczuka, A and Hughes, D and O'Flaherty, V}, title = {Anaerobic microbial core for municipal wastewater treatment - the sustainable platform for resource recovery.}, journal = {Current opinion in biotechnology}, volume = {94}, number = {}, pages = {103317}, doi = {10.1016/j.copbio.2025.103317}, pmid = {40408931}, issn = {1879-0429}, abstract = {The requirement for carbon neutrality and bioresource recovery has shifted our views on water treatment from health and pollution avoidance to one of sustainability with water and nutrient circularity. Despite progress, the current process of wastewater treatment is linear, based on core aerobic microbiology, which is unlikely to be carbon neutral due to its large use of energy and production of waste sludge. Here, we outline a shift from aerobic to anaerobic microbiology at the core of wastewater treatment and resource recovery, illustrating the state-of-the-art technologies available for this paradigm shift. Anaerobic metabolism primarily offers the benefit of minimal energy input (up to 50% reduction) and minimal biomass production, resulting in up to 95% less waste sludge compared with aerobic treatment, which is increasingly attractive, given dialogue surrounding emerging contaminants in biosolids. Recent innovative research solutions have made ambient (mainstream) anaerobic treatment a ready substitute for the aerobic processes for municipal wastewater in temperate regions. Moreover, utilising anaerobic treatment as the core carbon removal step allows for more biological downstream resource recovery with several opportunities to couple the process with (anaerobic) nitrogen and phosphorus recovery, namely, potential mainstream anaerobic ammonium oxidation (anammox) and methane oxidation (N-DAMO). Furthermore, these technologies can be mixed and matched with membranes and ion-exchange systems, high-value biochemical production, and/or water reuse installations. As such, we propose the reconfiguration of the wastewater treatment plant of the futurewith anaerobic microbiology. Mainstream anaerobic treatment at the core of a truly sustainable platform for modern municipal wastewater treatment, facilitating circular economy and net-zero carbon goals.}, }
@article {pmid40408805, year = {2025}, author = {Bi, W and Butardo, V and Sha, G and Zhang, H and Wu, X and Wang, L}, title = {Microbial degradation and pollutant control in aerobic composting and anaerobic digestion of organic wastes: A review.}, journal = {Waste management (New York, N.Y.)}, volume = {204}, number = {}, pages = {114894}, doi = {10.1016/j.wasman.2025.114894}, pmid = {40408805}, issn = {1879-2456}, abstract = {Aerobic composting (AC) and anaerobic digestion (AD) are promising technologies for organic waste treatment, but their efficiency and safety are influenced by complex waste composition and persistent contaminants. This review identifies the advances in understanding microbial community dynamics, enzymatic degradation pathways, and the fate of contaminants during AC and AD processes. The findings indicate that substrate composition shapes dominant microbial populations and their degradative enzymes, with this correlation potentially useful for predicting functional microbial communities. Additionally, AC shows advantages in antibiotic elimination while AD excels in heavy metal immobilization, with both contributing to removing certain antibiotic resistance genes (ARGs). The strategic manipulation of environmental conditions, particularly temperature and oxygen levels, can drive microbial succession to optimize organic matter decomposition while minimizing ARG proliferation. Economic analyses reveal that AC offers lower operational costs and AD generates valuable by-products with potential energy recovery from organic waste. Case studies indicate that integrating both technologies can overcome individual limitations and enhance degradation efficiency compared to conventional single-technology approaches. This work proposes a comprehensive framework for developing coupled AC-AD systems to achieve more efficient and safer organic waste valorization than conventional single-technology approaches. This review has important implications for advancing sustainable waste management practices and mitigating the spread of antibiotic resistance in the environment.}, }
@article {pmid40408146, year = {2025}, author = {Fontanarrosa, P and Clare, C and Fedorec, AJH and Barnes, CP}, title = {MIMIC: a Python package for simulating, inferring, and predicting microbial community interactions and dynamics.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {5}, pages = {}, pmid = {40408146}, issn = {1367-4811}, support = {BB/W013770/1//Bioengineered Cells &amp; Systems/ ; BB/T008709/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Software ; *Microbiota ; Bayes Theorem ; *Computational Biology/methods ; *Microbial Interactions ; Machine Learning ; Computer Simulation ; }, abstract = {SUMMARY: The study of microbial communities is vital for understanding their impact on environmental, health, and technological domains. The Modelling and Inference of MICrobiomes Project (MIMIC) introduces a Python package designed to advance the simulation, inference, and prediction of microbial community interactions and dynamics. Addressing the complex nature of microbial ecosystems, MIMIC integrates a suite of mathematical models, including previously used approaches such as Generalized Lotka-Volterra (gLV), Gaussian Processes (GP), and Vector Autoregression (VAR) plus newly developed models for integrating multi-omic data, to offer a versatile framework for analyzing microbial dynamics. By leveraging Bayesian inference and machine learning techniques, MIMIC provides the ability to infer the dynamics of microbial communities from empirical data, facilitating a deeper understanding of their complex biological processes, unveiling possible unknown ecological interactions, and enabling the design of microbial communities. Such insights could help to advance microbial ecology research, optimizing biotechnological applications, and contribute to environmental sustainability and public health strategies. MIMIC is designed for flexibility and ease of use, aiming to support researchers and practitioners in microbial ecology and microbiome research.<br><br>MIMIC is freely available under the MIT License at https://github.com/ucl-cssb/MIMIC. It is implemented in Python (version 3.7 or higher) and is compatible with Windows, macOS, and Linux operating systems. MIMIC depends on standard Python libraries including NumPy, SciPy, and PyMC. Comprehensive examples and tutorials (including the main text demonstrations) are provided as Jupyter notebooks in the examples/directory and at the MIMIC Docs website, along with detailed installation instructions and real-world data use cases. The software will remain freely available for at least two years following publication. A code snapshot for this publication is also available at Zenodo: https://doi.org/10.5281/zenodo.15149003.}, }
@article {pmid40407874, year = {2025}, author = {Velthuis, M and Zoccarato, L and Veraart, AJ and Monaghan, MT and Funke, E and Verdonschot, P and Grossart, HP and Hilt, S}, title = {Light-Driven Changes in Macrophyte Tissue Quality Affect the Composition of Associated Microbial Communities.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {52}, pmid = {40407874}, issn = {1432-184X}, support = {Veni.202.053//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, mesh = {Biofilms/growth &amp; development/radiation effects ; *Fungi/classification/genetics/radiation effects/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Microbiota/radiation effects ; *Light ; *Hydrocharitaceae/microbiology/radiation effects/chemistry/metabolism ; Nitrogen/metabolism/analysis ; Carbon/metabolism/analysis ; Phosphorus/metabolism/analysis ; Biodiversity ; Plant Leaves/microbiology ; Phenols/analysis/metabolism ; }, abstract = {Microbial biofilms are important components in macrophyte decomposition, and their composition depends on the decomposition stage and host plant quality. Here, we investigated how macrophyte tissue quality (i.e., C:N:P stoichiometry and phenolic contents) influences epiphytic microbial biofilms during litter decomposition. Consecutive experiments were conducted to (1) modify the C:N:P stoichiometry and phenolic content of the freshwater macrophyte Elodea nuttallii by manipulating light and nutrient availability and (2) test how the modified tissue quality affected epiphytic microbial biofilm diversity and community composition before and during macrophyte decomposition. Our results showed that shading led to lower C:N ratios (28.6 to 12.6) and higher phenolic content (10.8 to 19.2 µg/mg dry weight). Simultaneously, shading affected the epiphytic bacterial and fungal community composition, and these shifts correlated with the macrophyte C:N ratio. While no effects of macrophyte tissue quality on decomposition rates were observed, the epiphytic bacterial community composition on the litter was significantly affected by light treatment, time, and their interaction. Bacterial community composition shifted from a high abundance of Comamonadaceae to a more diverse community over time. Overall bacterial diversity was lower on the litter grown in the shaded mesocosms. Fungal diversity and community composition during litter decomposition were not affected by litter quality. Overall, our results reveal a structuring role of macrophyte tissue quality on its associated microbial biofilm and uniquely show a continuation of light-driven changes in epiphytic bacterial community composition after exposure. We conclude that light-driven changes in C:N stoichiometry are a crucial factor in shaping epiphytic microbial communities during macrophyte decomposition.}, }
@article {pmid40407873, year = {2025}, author = {Van Heurck, B and Cardenas, DV and Hylén, A and Jankowska, E and Cole, DB and Montserrat, F and Kreuzburg, M and Romaniello, SJ and Meysman, FJR}, title = {Microbial Community Structure in Contrasting Hawaiian Coastal Sediments.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {51}, pmid = {40407873}, issn = {1432-184X}, mesh = {*Geologic Sediments/microbiology/chemistry ; Hawaii ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Seawater/microbiology/chemistry ; Bays/microbiology/chemistry ; Biodiversity ; }, abstract = {Microbe-mineral interactions play a fundamental role in marine sediments and global biogeochemical cycles. Here, we investigated the sediment microbial communities in two contrasting field sites on Big Island, Hawaii (USA), that differ in their bay morphology and sediment grain size distributions: Papakōlea Beach (exposed, finer sediment) and Richardson Ocean Park (sheltered, coarser sediment). We selected three stations within each bay and characterized the mineral and chemical composition of the sediment and porewater, and used 16S rRNA amplicon sequencing of the V4V5 hypervariable region to investigate the naturally occurring microbial communities. Microbial community structure differed significantly between the two bays, rather than within each bay, whereby microbial diversity was markedly lower at Papakōlea compared to Richardson. We correlated environmental variables to microbial community structure in order to identify the key drivers of community differences between and within the two bays. Our study suggests that differing physico-chemical properties of the sediment and porewater, resulting from the contrasting bay morphologies and geophysical drivers, are the main factors influencing microbial community structure in these two bays. Papakōlea Beach is a naturally occurring "green sand" beach, due to its high olivine content. This site was selected in the broader context of a field campaign investigating olivine as a source mineral for ocean alkalinity enhancement (OAE), a carbon dioxide removal technology. Our results highlight the complexity of marine sediment environments, with implications for the monitoring, reporting and verification of future field trials involving olivine addition for ocean alkalinity enhancement.}, }
@article {pmid40406230, year = {2025}, author = {Li, M and Meng, Z and Li, J and Zhang, X and Wang, Y and Li, X and Yang, Y and Li, Y and Yang, X and Chen, X and Fan, Y}, title = {Stochastic processes dominate the community assembly of ectomycorrhizal fungi associated with Betula platyphylla in Inner Mongolia, China.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19364}, pmid = {40406230}, issn = {2167-8359}, mesh = {*Mycorrhizae/genetics/classification/isolation &amp; purification ; China ; *Soil Microbiology ; *Betula/microbiology ; Stochastic Processes ; Biodiversity ; Rhizosphere ; DNA, Fungal/genetics ; Mycobiome ; }, abstract = {The maintenance and driving mechanisms of microbial community structure have become important research focuses in microbial ecology. Therefore, clarifying the assembly of ectomycorrhizal (EM) fungal communities can provide a relevant basis for studying forest diversity, ecological diversity, and ecological evolution. Betula platyphylla is a typical EM dependent tree species with characteristics such as renewal ability and strong competitive adaptability, and it plays a crucial ecological function in Inner Mongolia. However, the research on EM fungi's diversity and community assembly is very limited. We investigated EM fungal communities associated with B. platyphylla from 15 rhizosphere soil samples across five sites in Inner Mongolia. The fungal rDNA ITS2 region was sequenced using Illumina Miseq sequencing. A total of 295 EM fungal OTUs belonging to two phyla, three classes, nine orders, 20 families, and 31 genera were identified, of which Russula, Cortinarius, and Sebacina were the most dominant taxa. Significant differences existed in the composition of dominant genera of EM fungi across the five sites, and the relative abundances of dominant genera also showed significant differences among the sites. The β NTI and NCM fitting analyses suggest that stochastic processes mainly determine the EM fungal community assembly. Our study indicates that B. platyphylla harbors a high EM fungal diversity and highlights the important role of the stochastic process in driving community assembly of mutualistic fungi associated with B. platyphylla in north China.}, }
@article {pmid40405772, year = {2025}, author = {Onghena, L and Heldens, A and De Paepe, K and Antwi, M and Van Vlierberghe, H and Raevens, S and Verhelst, X and Hoorens, A and Devisscher, L and van Nieuwenhove, Y and Van de Wiele, T and Geerts, A and Lefere, S}, title = {The double-edged sword of metabolic and bariatric surgery: extending the biliary limb can trigger bacterial translocation, sepsis, and liver inflammation - an experimental study.}, journal = {International journal of surgery (London, England)}, volume = {}, number = {}, pages = {}, doi = {10.1097/JS9.0000000000002502}, pmid = {40405772}, issn = {1743-9159}, abstract = {BACKGROUND: Metabolic and bariatric surgery (MBS) procedures with extended biliary limb length are gaining popularity to expedite weight loss but can induce liver failure. We aimed to investigate the underlying pathophysiology for this potentially fatal complication.<br><br>MATERIALS AND METHODS: We compared mouse models of vertical sleeve plication, sleeve gastrectomy, Roux-en-Y gastric bypass (RYGB), and one-anastomosis gastric bypass with three biliary limb lengths (25%&#xa0;=&#xa0;&#x3a9;1, 50%&#xa0;=&#xa0;&#x3a9;2, 75%&#xa0;=&#xa0;&#x3a9;3) by analyzing mortality, weight loss, metabolic and liver health, bacterial translocation, inflammation, and biliary and fecal microbiome. Gut decontamination with oral antibiotics (amoxicillin, vancomycin, neomycin, and metronidazole) was performed in a subset of &#x3a9;3 mice. Liver histology from mice with different biliary limb lengths was compared to samples from human patients who developed liver failure following biliopancreatic diversion or RYGB.<br><br>RESULTS: RYGB and &#x3a9;1&amp;2 significantly improved glucose intolerance and liver steatosis compared to sham surgery. However, extending the biliary limb (&#x3a9;3) resulted in 100% mortality. The &#x3a9;3 procedure induced bacterial translocation of enterococcus genus to the spleen and biliary fluid, consistent with increased serum lipopolysaccharide levels and terminal ileum, biliary limb, and hepatic inflammation. Liver histology in &#x3a9;3 mice was characterized by mediovesicular steatosis, closely resembling the histological picture observed in patients with liver failure after MBS. Oral gut decontamination significantly improved &#x3a9;3 one-week-survival from 31.3% to 80.0%, prevented bacterial overgrowth in biliary fluid and spleen, and decreased liver damage.<br><br>CONCLUSION: Mortality in longer biliary limb MBS surgery is caused by bacterial overgrowth, translocation, and gut-liver axis inflammation, which were reversed by oral gut decontamination with antibiotics.}, }
@article {pmid40405300, year = {2025}, author = {He, T and Moukarzel, R and Fu, M and Yang, M and Du, R and Zhao, J and Liu, J and Wu, J and Deng, W and Zhu, Y and Yang, M and Zhu, S and Du, F}, title = {Rain-shelter cultivation promotes grapevine health by altering phyllosphere microecology in rainy areas.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {56}, pmid = {40405300}, issn = {2524-6372}, support = {32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 2018HA009//Yunnan Provincial Academician Exploration Funding Project/ ; }, abstract = {Grapes are a globally significant fruit crop, but their cultivation is often challenged by leaf diseases, which limit industrial productivity. Rain-shelter cultivation has emerged as a sustainable agricultural strategy to mitigate these challenges. This study examines the effects of rain-shelter cultivation, compared to open-air cultivation, on the microclimate within the grape canopy and the microbial ecology of the grape phyllosphere. The research focused on two cultivation methods: rain-shelter and open-air cultivation. Key environmental factors such as temperature, relative humidity, and light intensity within the grape canopy were measured during the growing season. The study also explored how these conditions influence the biodiversity, stability, and functional roles of phyllosphere microbiota, particularly focusing on the community assembly processes of bacteria and oomycetes, and the efficacy of culturable microorganisms in combating grape leaf diseases. The results showed that rain-shelter cultivation signifcantly reduced leaf humidity, increased canopy temperature, and decreased light intensity, regardless of weather conditions. This approach led to a significant decrease in the incidence of grape downy mildew without affecting the overall Shannon diversity index of phyllosphere microbes. At the Class level, there was a reduction in Cystobasidiomycetes, Bacteroidia, Brocadiae, and Phycisphaerae, while Oligoflexia levels are significantly increased under rain-shelter conditions. Genus-level analysis revealed significant reductions in plant pathogens such as Erysiphe, Alternaria, and Cercospora. The study found that rain-shelter cultivation shifts fungal community assembly from stochastic to deterministic processes, while bacterial networks showed increased stability. Additionally, the beneficial microorganism Pseudomonas aeruginosa exhibited a preventive effect against grape leaf diseases, enhancing grape berry quality by increasing puncture resistance and leaf internode length. These findings provide understanding of the complex relationship between grape canopy microclimate, disease management, and microbial dynamics suggesting rain-shelter cultivation as a viable strategy for sustainable grape production, it offers insights into the research and development of future biological control agents.}, }
@article {pmid40404904, year = {2025}, author = {Scheelings, TF and Kodikara, S and Beale, DJ and Van, TTH and Moore, RJ and Skerratt, LF}, title = {Pondering Ponds: Exploring Correlations Between Cloacal Microbiota and Blood Metabolome in Freshwater Turtles.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {50}, pmid = {40404904}, issn = {1432-184X}, mesh = {Animals ; *Turtles/microbiology/blood ; *Metabolome ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; *Cloaca/microbiology ; *Ponds/microbiology ; *Microbiota ; Gastrointestinal Microbiome ; Fresh Water ; }, abstract = {The gut microbiota of vertebrates significantly influences host physiology, yet little is known about how habitat factors shape microbiotas in non-human species, especially freshwater turtles. This study explores the relationship between cloacal microbiota and serum metabolome in eastern longneck turtles (Chelodina longicollis), marking the first such investigation in chelonians. By comparing microbiotas from two distinct pond environments, we applied a multi-omics approach combining 16S rRNA sequencing and metabolomic profiling. Results showed that location influenced microbial composition and metabolic profiles, with dominant bacterial phyla Pseudomonadota, Actinomycetota, and Bacillota, and distinct families linked to differences in microbial diversity. Notably, turtles from one pond displayed an unusually high proportion of Actinomycetota. We also found a clear connection between microbiota diversity and metabolome, suggesting certain bacterial combinations impact host physiology. These findings offer important insights into the complex interaction between microbial communities and metabolism in freshwater turtles, a highly threatened group. This research emphasises the value of integrating microbiota and metabolomic data in conservation strategies and highlights the need for further longitudinal studies to explore the dynamic host-microbiota relationship in these understudied species.}, }
@article {pmid40403739, year = {2025}, author = {Kramer, SJ and Jones, EL and Estapa, ML and Paul, NL and Rynearson, TA and Santoro, AE and Sudek, S and Durkin, CA}, title = {Sinking particles exporting diatoms and Hacrobia predict the magnitude of oceanic POC flux.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40403739}, issn = {1751-7370}, support = {#986836//Simons Foundation Postdoctoral Fellowship in Marine Microbial Ecology/ ; 80NSSC21K0015//NASA Ocean Biology and Biogeochemistry/ ; 80NSSC18K1431//NASA Ocean Biology and Biogeochemistry/ ; 80NSSC17K0716//NASA Ocean Biology and Biogeochemistry/ ; }, mesh = {*Seawater/microbiology/chemistry ; *Phytoplankton/genetics/metabolism/classification ; *Diatoms/metabolism/genetics/classification ; RNA, Ribosomal, 18S/genetics ; Pacific Ocean ; Atlantic Ocean ; *Carbon/metabolism/analysis ; Ecosystem ; Sequence Analysis, DNA ; }, abstract = {Carbon flux to the deep sea can be dictated by surface ocean phytoplankton community composition, but translating surface ocean observations into quantitative predictions of carbon export requires additional consideration of the underlying ecosystem drivers. Here, we used genetic tracers of phytoplankton detected in surface seawater and within sinking particles collected in the mesopelagic ocean to identify mechanistic links between surface communities and carbon export in the North Pacific and North Atlantic Oceans. Phytoplankton 18S rRNA gene sequences were sampled over a 1-month period in surface seawater and within bulk-collected and individually isolated sinking particles using mesopelagic sediment traps (100-500 m). Nearly all phytoplankton amplicon sequence variants exported from the surface were packaged in large (>300 μm) particles. Individually, each of these particles contained only a few distinct phytoplankton amplicon sequence variants, but collectively, large particles transported about half of the surface taxonomic diversity into the mesopelagic. The relative sequence abundances of the surface community detected within particles were quantitatively related to measured carbon fluxes: a linear model based on the relative sequence abundance of just two pigment-based phytoplankton taxa, diatoms and photosynthetic Hacrobia, was predictive of carbon flux magnitude. These two taxa were also enriched in the ecologically distinct particle classes that had the greatest influence on carbon export magnitude. As global, hyperspectral ocean color satellites begin to quantify these taxonomic groups in the surface ocean, the relationship of these taxa to carbon fluxes demonstrated here may help in developing more accurate algorithms to estimate global carbon export in the ocean.}, }
@article {pmid40402470, year = {2025}, author = {Moukarzel, R and Waller, LP and Jones, EE and Ridgway, HJ}, title = {Arbuscular mycorrhizal fungal symbiosis in New Zealand ecosystems: challenges and opportunities.}, journal = {Letters in applied microbiology}, volume = {78}, number = {5}, pages = {}, doi = {10.1093/lambio/ovaf070}, pmid = {40402470}, issn = {1472-765X}, mesh = {*Mycorrhizae/physiology/genetics/classification ; New Zealand ; *Symbiosis ; *Ecosystem ; *Plants/microbiology ; Soil Microbiology ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) are obligate biotrophs that form a symbiotic and mutualistic relationship with most terrestrial plants, playing an important role in plant growth, nutrient acquisition, and ecosystem stability. This review synthesizes current knowledge on AMF colonization in plants within New Zealand ecosystems, including the challenges and opportunities of molecular identification techniques used in characterizing AMF communities in natural and managed systems. The ecosystem services provided by AMF, such as improved growth parameters, enhanced nutrition, and disease control, are discussed in detail, highlighting their significance in sustainable agriculture and natural ecosystems. Additionally, the role of AMF in invasion ecology was examined, revealing their dual potential to either facilitate or hinder invasive plant species. Despite significant advances in understanding AMF biology, future research is needed to explore the underlying mechanisms of AMF-plant interactions and to address the challenges caused by changing environmental conditions. This review focused on the importance of AMF in promoting ecosystem resilience and suggests avenues for future research to harness their full potential in agricultural and ecological contexts.}, }
@article {pmid40402324, year = {2025}, author = {Mizeriene, G and Lygis, V and Prospero, S}, title = {Oomycete Diversity and Ecology in Declining Alder Stands in Switzerland.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {49}, pmid = {40402324}, issn = {1432-184X}, support = {Project Code 14.035//Sciex-NMSch Fellowship/ ; }, mesh = {Switzerland ; *Alnus/microbiology/parasitology ; *Oomycetes/classification/isolation &amp; purification/genetics ; *Biodiversity ; *Soil Microbiology ; Plant Diseases/microbiology ; Rhizosphere ; Phytophthora/isolation &amp; purification/classification/genetics ; Phylogeny ; Pythium/isolation &amp; purification/genetics/classification ; }, abstract = {In this study, we assessed the occurrence and diversity of four oomycete genera (Phytophthora, Phytopythium, Pythium, and Globisporangium) in 13 declining alder (Alnus glutinosa and A. incana) stands in Switzerland. For this, we sampled and analyzed soil from tree rhizosphere, water from streams and rivers along which the stands were located, and symptomatic alder bark. The overall isolation rate was 47.2%, with a total of 400 oomycete isolates recovered at all 13 sites. The highest incidence of oomycete isolates was in soil samples (baiting, 82.5% isolation rate), followed by water (baiting, 14.7%), and bark (direct isolation, 2.7%). Of all recovered oomycete isolates, 90.3% could be successfully assigned to a known species, for a total of 23 species identified, including both preferential saprotrophs and pathogens. Among all genera, Phytophthora was the most abundant with 273 isolates (75.6%), followed by Phytopythium, Pythium, and Globisporangium. Oomycete species diversity showed a significant variation among substrates. Only one species-Phytophthora lacustris-was abundant in all substrates, while 16 species were restricted to a specific substrate, mainly soil. The rhizosphere of symptomatic alder trees harbored the most diverse oomycete community, highlighting once again the importance of soil as a reservoir for these microorganisms. Only two Phytophthora species were isolated from alder bark lesions, namely, P. × alni, the known causal agent of alder decline, and P. lacustris. The low recovery rate of P. × alni might be due to attempts to isolate it from old, inactive lesions, but may also suggest that alder decline might be caused by other oomycetes infecting the root system of the trees.}, }
@article {pmid40402315, year = {2025}, author = {Mitchell, JK and Matthee, S and Ndhlovu, A and Miller, M and Buss, P and Matthee, CA}, title = {The Microbiome and Coxiella Diversity Found in Amblyomma hebraeum and Dermacentor rhinocerinus Ticks Sampled from White Rhinoceros.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {48}, pmid = {40402315}, issn = {1432-184X}, mesh = {Animals ; *Microbiota ; *Perissodactyla/parasitology/microbiology ; *Amblyomma/microbiology ; *Coxiella/genetics/classification/isolation &amp; purification ; *Dermacentor/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; South Africa ; Coxiella burnetii/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Female ; Male ; }, abstract = {The microbiome and the prevalence of the pathogenic bacterium Coxiella burnetii in ticks associated with white rhinoceros, Ceratotherium simum, is unknown. Targeted Illumina 16S rRNA amplicon sequencing was used to characterize the bacterial microbiome diversity found within 40 Amblyomma hebraeum and 40 Dermacentor rhinocerinus ticks collected from 40 white rhinoceros individuals in the Kruger National Park, South Africa. Specific emphasis was also given to further investigate the prevalence of the pathogenic C. burnetti in these tick species. At the phylum level, Proteobacteria dominated both tick microbiomes, followed by Actinobacteria and Firmicutes; Coxiella was the most abundant genus within A. hebraeum and Rickettsia within D. rhinocerinus. While alpha diversity did not differ significantly between the two tick species, beta diversity revealed significant species-specific differences in bacterial community composition. Additionally, there was no correlation between sampling region and microbiome diversity or composition for either tick species. Twenty-five Coxiella amplicon sequence variants (ASVs) were identified, forming three distinct monophyletic Coxiella clades and a fourth single ASV lineage. The Coxiella clades showed a correlation to tick species identity with D. rhinocerinus harboring significantly greater Coxiella diversity than A. hebraeum-potentially indicative of different coevolutionary pathways between the bacteria and their respective hosts. PCR of the IS1111 transposase gene for 238 ticks detected a 66.1% (56.7-74.4%) prevalence for C. burnetii in D. rhinocerinus compared to 55.8% in A. hebraeum (46.5-64.8%). These findings support a notion that each tick species is characterized by its own microbiome community composition and that both A. hebraeum and D. rhinocerinus may act as reservoirs and potential vectors of C. burnetii to white rhinoceros.}, }
@article {pmid40402178, year = {2025}, author = {Salazar, J and González, J and Riofrío, R and Siavichay, F and Carrera, M and Mogrovejo, A and Barrera-Galicia, G and Valdez-Tenezaca, A}, title = {MALDI-TOF Mass Spectrometry Characterization of Culturable Microbiota Associated with the Skin of Amphibians from the Southern Andes Mountains of Ecuador.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {47}, pmid = {40402178}, issn = {1432-184X}, support = {PICCIITT19-11//Universidad Cat&#xf3;lica de Cuenca/ ; PICCIITT19-11//Universidad Cat&#xf3;lica de Cuenca/ ; PICCIITT19-11//Universidad Cat&#xf3;lica de Cuenca/ ; }, mesh = {Ecuador ; Animals ; *Skin/microbiology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Microbiota ; *Bacteria/classification/isolation &amp; purification/genetics ; *Fungi/classification/isolation &amp; purification/genetics ; *Anura/microbiology ; Biodiversity ; }, abstract = {Ecuador is recognized for having a high diversity of anuran species, which are distributed mainly south of the Andes mountains. However, due to their geographic location and accessibility, there are few studies related to the culturable microbiota of these amphibians in this region. The objective of this study was to explore the bacterial and fungal biodiversity present on the skin of wild anuran species in the southern Andes of Ecuador and to observe whether geographical barriers in the region could increase the variability of the culturable microbiota through MALDI-TOF mass spectrometry. This analysis revealed the presence of 29 bacterial taxa and 9 fungal taxa, consisting mainly of: Pseudomonas chlororaphis (28%), Acinetobacter iwoffii (14%), Pseudomonas fluorescens (14%), and Hortaea werneckii (26.4%), Fusarium solani (20.5%), Syncephalastrum spp. (20.5%), respectively. Diversity varied across the five sampling locations, with geographic location proving to be a significant driver of diversity. Some of the most abundant bacterial and fungal genera have important associations with skin diseases in wildlife and humans. This work represents a glimpse into the complex biodiversity of bacteria and fungi that inhabit the skin substrate, and further studies will be needed to better understand bacterial and fungal biodiversity with potential implications for establishing conservation strategies, along with the development of necessary animal protection measures.}, }
@article {pmid40401940, year = {2025}, author = {Nieves-Morales, R and Paez-Diaz, JA and Rivera-Lopez, EO and Pérez-Santos, N and Borrero-Villabol, SJ and Rodríguez-Ramos, J and Nieves-Rivera, AM and Rios-Velazquez, C}, title = {Characterization of fungal communities in Puerto Rican caves using internal transcribed spacer sequencing.}, journal = {Microbiology resource announcements}, volume = {14}, number = {6}, pages = {e0002225}, pmid = {40401940}, issn = {2576-098X}, abstract = {Cave ecosystems harbor unique and diverse microbial ecology, with fungal communities playing important roles. This study utilizes internal transcribed spacer across seven caves in the northern limestone karst belt area of Puerto Rico to investigate fungal composition. This enhances scientific understanding of subterranean microbial dynamics and supports conservation efforts.}, }
@article {pmid40401939, year = {2025}, author = {Darden, B and Johnson, G and Busch, G and Sharma, I}, title = {Draft genome sequence of Vreelandella neptunia strain 04GJ23 isolated from the underwater Hawaii seamounts.}, journal = {Microbiology resource announcements}, volume = {14}, number = {6}, pages = {e0088224}, pmid = {40401939}, issn = {2576-098X}, support = {2205569//National Science Foundation/ ; }, abstract = {We report a draft genome sequence for Vreelandella neptunia strain 04GJ23 isolated from the underwater Hawaii seamounts. The whole-genome sequence will help understand the ecology and evolution of various ecotypes that are physiologically distinct from the surrounding environments.}, }
@article {pmid40401933, year = {2025}, author = {Das, J and Pal, S and Negi, A and Sundharam, SS and Yadav, A and Subramanian, S and Sinha, SK and Samanta, J and Krishnamurthi, S}, title = {Genomic insights into novel predatory myxobacteria isolated from human feces.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0214724}, doi = {10.1128/spectrum.02147-24}, pmid = {40401933}, issn = {2165-0497}, abstract = {Myxobacteria are Gram-negative, spore-forming predatory bacteria isolated from diverse environmental samples that feed on other microbes for their survival and growth. However, no reports of cultured representatives from the human gut have been published to date, although previous investigations have revealed the presence of myxobacterial operational taxonomic units (OTUs) in skin and fecal samples. In this study, three myxobacterial strains designated as O35, O15, and Y35 were isolated and purified from fecal samples of two inflammatory bowel disease (IBD) patients. The 16S rRNA gene sequence analysis and phylogeny identified the strains as Myxococcus spp. belonging to two different clades. Genome-based phylogeny and overall genome-related indices, i.e., average amino acid identity and percentage of conserved proteins, confirmed the heterogeneity within the genus and placed the three strains within two different clades separated at the level of different genera. Digital DNA-DNA hybridization and average nucleotide identity values indicated that they belonged to two novel Myxococcus spp. The analysis of meta-barcoding data from IBD and control cohorts detected OTU lineages closely affiliated to the three novel strains. Based on evidence from detailed structural and functional genomics, we propose the novel species Myxococcus faecalis sp. nov. O35[T] and a new genus Pseudomyxococcus gen. nov. to accommodate the novel species Pseudomyxococcus flavus sp. nov. Y35[T]. Overall, these findings provide new information about the occurrence of myxobacteria in the human gut and lay the foundations for a new classification scheme for myxobacterial taxa.IMPORTANCEMyxobacteria have been described from a variety of niches ranging from terrestrial to marine habitats and are known to harbor a diverse portfolio of bioactive molecules. However, to date, there has been no report of isolating culturable representatives from the human gut. This study describes novel myxobacteria from the human gut based on phylogenomics and phenotypic description. The findings are complemented by sequence-based data, wherein operational taxonomic unit (OTU) lineages closely affiliated with the isolated strains have been identified, thus opening a Pandora's box of opportunities for research into the microbial ecology and functional potential of these taxa in the gut ecosystem. Additionally, the study also seeks to establish a new systematic framework, expanding our understanding of myxobacterial taxonomy.}, }
@article {pmid40400674, year = {2025}, author = {Kokociński, M and Graco-Roza, C and Jasser, I and Karosienė, J and Kasperovičienė, J and Kobos, J and Koreivienė, J and Mankiewicz-Boczek, J and Soininen, J and Szczurowska, A}, title = {Environmental factors determining the distribution patterns of invasive Raphidiopsis raciborskii and R. mediterranea in central east Europe.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1533716}, pmid = {40400674}, issn = {1664-302X}, abstract = {OBJECTIVE: In recent decades, the invasive cyanobacteria Raphidiopsis raciborskii and Raphidiopsis mediterranea have expanded their distribution globally, particularly in temperate regions. Understanding the ecological drivers of Raphidiopsis distribution is imperative to addressing the challenges associated with these species. Here, we aimed to characterize the distribution and biomass of R. raciborskii and R. mediterranea across 112 lakes in Poland and Lithuania in relation to local and regional factors.<br><br>RESEARCH DESIGN AND METHODS: Integrated water samples were collected from 102 Polish and 10 Lithuanian lakes from different regions for phytoplankton and chemical analyses. The lakes varied in surface area, and exhibited diverse mixing regimes, trophic states, and morphometries. Phytoplankton was identified and quantified using a Fuchs-Rosenthal or Nageotte chamber. Additionally, we characterized the degree of human pressures the climatic constraints experienced by each lake.<br><br>RESULTS: R. raciborskii occurrence has increased in eastern regions of Poland but biomass is relatively low compared to western Poland, likely due to lower air temperatures and nutrient concentrations, especially phosphorus. In contrast, R. mediterranea only occurred in a small number of lakes in Poland, and in a single lake in Lithuania, with no relation to measured local and regional variables.<br><br>CONCLUSIONS: Our study shows contrasting patterns in the distribution of two invasive cyanobacteria species in Europe, highlighting the importance of climate and nutrients to the distribution of R. raciborskii, the most widespread species, and providing relevant information for decision making and conservation strategies.}, }
@article {pmid40399330, year = {2025}, author = {Liang, X and Yang, S and Radosevich, M and Wang, Y and Duan, N and Jia, Y}, title = {Bacteriophage-driven microbial phenotypic heterogeneity: ecological and biogeochemical importance.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {82}, pmid = {40399330}, issn = {2055-5008}, support = {42377306//National Natural Science Foundation of China/ ; 2023JH3/10200009//Natural Science Foundation of Liaoning Province/ ; No.KLFES-2027//CAS Key Laboratory of Forest Ecology and Silviculture, Institute of Applied Ecology, Chinese Academy of Sciences/ ; No.KLFES-2027//CAS Key Laboratory of Forest Ecology and Silviculture, Institute of Applied Ecology, Chinese Academy of Sciences/ ; }, mesh = {*Bacteriophages/physiology ; Phenotype ; *Bacteria/virology/metabolism/genetics ; Ecosystem ; *Host Microbial Interactions ; *Microbiota ; }, abstract = {Bacteriophages (phages) reprogram host metabolism and generate phenotypic heterogeneity, yet the mechanisms and ecological implications remain poorly understood representing a major knowledge gap in microbial ecology. This review explores how phage infection alters microbial physiology, contributes to single-cell variation, and influences population dynamics. We highlight the potential consequences of phage-driven heterogeneity for microbial community structure and biogeochemical cycling, underscoring the importance of integrating phage-host interactions into ecological and ecosystem models.}, }
@article {pmid40398824, year = {2025}, author = {Massaro, A and Peruzzo, A and Zacometti, C and Zancato, M and Piro, R and Losasso, C and Tata, A and Peron, G}, title = {Exploring the crosstalk between gut microbiota and stool metabolome in omnivorous, vegetarian, and vegan diets: A pilot study.}, journal = {The Journal of nutritional biochemistry}, volume = {144}, number = {}, pages = {109965}, doi = {10.1016/j.jnutbio.2025.109965}, pmid = {40398824}, issn = {1873-4847}, abstract = {Gut microbiota (GM) and fecal metabolome are shaped by different dietary regimens. Nevertheless, outlining generalized patterns is challenging, due to the intrinsic heterogeneity of individual dietary choices. In this work, the fecal metabolome of adult volunteers consuming omnivorous (n=44), vegetarian (n=29), and vegan diets (n=25) for at least 12 months was characterized. The crosstalk among diet, GM and fecal metabolome was also investigated correlating metabolomics and metataxonomics data. Untargeted metabolomic profiles were correlated with metataxonomics data previously acquired on the same stool samples. The sphingomyelin SM(d18:2/18:1-2OH) and phosphoethanolamines from animal-based food were associated to the omnivorous diet and were negatively correlated to beneficial Bacteroides ovatus and Odoribacter genus. Plant glycerides, sterols, triterpenes, and oleic-linoleic acid were associated with the vegan diet. Oleic-linoleic acid was positively correlated with Alistipes putredinis. Chenodeoxycholic acid, a primary bile acid, was identified as a marker of vegan diet, while ketolithocholic acid, a secondary bile acid, was associated to the omnivorous diet. This latter was also negatively correlated to B.ovatus. Overall, results confirm that assessing markers of dietary regimens instead of specific food categories is challenging, especially if volunteers' diet is not strictly monitored. However, the integration of metabolomics and metataxonomic data allows to better understand the effects of specific food components on the GM and represents a suitable approach for further molecular investigation in nutrition.}, }
@article {pmid40394467, year = {2025}, author = {Van Hee, S and Segurado Luchsinger, AE and Cusumano, A and Masschelein, J and Jacquemyn, H and Lievens, B}, title = {Correction: The plant-beneficial fungus Trichoderma harzianum T22 modulates plant metabolism and negatively affects Nezara viridula.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {671}, pmid = {40394467}, issn = {1471-2229}, }
@article {pmid40394206, year = {2025}, author = {Khurshid, H and Jamshaid, MB and Salahuudin, Z and Sibtain, K and Fayyaz, I and Ameer, A and Kerbiriou, C and Mckirdy, S and Malik, SN and Gerasimidis, K and Noreen, Z and Javed, S and Tariq, A and Ijaz, UZ and Tariq, A}, title = {Gut microbial ecology and function of a Pakistani cohort with Iron deficiency Anemia.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {17532}, pmid = {40394206}, issn = {2045-2322}, support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; MR/Z50628X/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Anemia, Iron-Deficiency/microbiology/epidemiology ; *Gastrointestinal Microbiome ; Humans ; Pakistan/epidemiology ; Female ; Adult ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; Iron/metabolism ; Bacteria/genetics/classification ; Diet ; }, abstract = {Iron deficiency anemia (IDA) is a major public health concern among women of reproductive age leading to high maternal mortality. Pakistan being one of the Lower -Middle income countries (LMIC) is facing this challenge tremendously. The objective of this study is to determine the impact of IDA on gut microbial diversity as well as its relationship with microbial metabolites.16 S rRNA gene profiling of healthy and IDA affected meconium samples was performed with additional meta-data collected through questionnaire. The anemia was linked to different dietary parameters through chi-square test of independence and Generalized Linear Latent Variable Model (GLLVM). Anaerobic bacterial genera such as Coprococcus, Anaerovoracaceae, strongly associated with anemia and negatively correlated with red meat and fish consumption. Moreover, these microbes positively correlated with branched short chain fatty acids (BSCFAs) production. BSCFAs have strong implications in metabolic disorders. This study provides a snapshot of how anemia modulates gut microbial diversity and microbial metabolites production which may have an impact on iron metabolism.}, }
@article {pmid40393817, year = {2025}, author = {Pantigoso, HA and Ossowicki, A and Stringlis, IA and Carrión, VJ}, title = {Hub metabolites at the root-microbiome interface: unlocking plant drought resilience.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.04.007}, pmid = {40393817}, issn = {1878-4372}, abstract = {Drought is one of the most devastating environmental challenges, severely affecting agriculture, ecosystems, and global food security. Effective strategies to predict and mitigate drought are limited. The root-soil-microbiome interface is pivotal in mediating plant resilience to drought. Recent studies highlight dynamics between plant root exudates and microbial communities, influencing stress tolerance through chemical signaling under drought. By integrating plant molecular biology, root chemistry, and microbiome research, we discuss insights into how these mechanisms can be harnessed to enhance crop resilience. Here, we focus on the interplay between plants and their microbiomes with metabolites as a central point of interactions. We synthesize recent developments, identify critical knowledge gaps, and propose future directions to leverage plant-microbe interactions to improve plant drought tolerance.}, }
@article {pmid40393246, year = {2025}, author = {Liu, X and Li, Y and Yuan, C and Zhao, Y and Zhou, L and Yan, Y and Ren, J and Liu, Q}, title = {Sophocarpine suppresses MAPK-mediated inflammation by restoring gut microbiota in colorectal cancer.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {143}, number = {}, pages = {156833}, doi = {10.1016/j.phymed.2025.156833}, pmid = {40393246}, issn = {1618-095X}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/drug therapy/microbiology ; Animals ; Humans ; Mice ; *Alkaloids/pharmacology ; Fecal Microbiota Transplantation ; Inflammation/drug therapy ; Cell Line, Tumor ; Male ; Mice, Inbred BALB C ; *Antineoplastic Agents, Phytogenic/pharmacology ; MAP Kinase Signaling System/drug effects ; Dysbiosis/drug therapy ; Xenograft Model Antitumor Assays ; Mice, Nude ; p38 Mitogen-Activated Protein Kinases/metabolism ; Matrines ; }, abstract = {BACKGROUND: Colorectal cancer (CRC), as one of the most common cancers globally, poses a significant challenge to public health due to its high incidence and mortality rates. This underscores the need for continuous exploration of new therapeutic targets and effective drugs. Sophocarpine (SC), a natural compound derived from traditional Chinese medicine, holds considerable therapeutic potential in the treatment of CRC, however, the relevant mechanisms remains unclear.<br><br>PURPOSE: This study aims to explore the anti-tumor effects of SC against CRC by modulating gut microbiota, and uncover potential mechanisms linking SC's therapeutic effects to gut microbiota regulation by analyzing the impact of SC on microbiota composition and CRC progression.<br><br>MATERIAL: This study explores the impact of SC on the gut microbiota in CRC by constructing subcutaneous xenograft tumors of CRC and integrating 16S rRNA sequencing and RNA transcriptomic sequencing. The fecal microbiota transplantation (FMT) mouse model was used to validate the biological function of SC in correcting gut microbiota dysbiosis to treat CRC. Subsequently, we conducted in vitro studies on the molecular mechanisms by which SC regulates the gut microbiota as an effective hallmark of CRC treatment, using lipopolysaccharide (LPS) to simulate an inflammatory gut microbiota environment and P38 MAPK knockdown cell line.<br><br>RESULTS: SC significantly inhibited CRC cell proliferation with IC50 values of 2.547&#xb1;0.256 &#x3bc;M for HCT116 and 2.851&#xb1;0.332 &#x3bc;M for LoVo cells. In vivo experiments demonstrated that SC effectively suppressed tumor growth in xenograft models. 16S rRNA sequencing revealed that SC modulated gut microbiota composition, particularly affecting Bacteroides and Alistipes populations. SC significantly reduced the levels of inflammatory factors and inhibited the MAPK signaling pathway, as evidenced by decreased p-JNK, p-p38 MAPK, and p-NF-&#x3ba;B p65 expression.<br><br>CONCLUSIONS: Current clinical practice still lacks effective therapeutic agents targeting CRC through gut microbiota modulation. This study presents the first evidence that SC, a natural compound, exhibits dual-action therapeutic efficacy against CRC progression by simultaneously modulating gut microbial composition and suppressing MAPK pathway-mediated inflammatory responses. These findings highlight SC's novel therapeutic potential as a promising microbiota-regulating candidate for CRC intervention, offering an innovative approach that bridges microbial ecology with cancer signaling pathways.}, }
@article {pmid40387954, year = {2025}, author = {Warren, ML and Tsuji, K and Decker, LE and Kishi, M and Yang, J and Howe, AC and Fukami, T}, title = {Bacteria in Honeybee Crops Are Decoupled from Those in Floral Nectar and Bee Mouths.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {46}, pmid = {40387954}, issn = {1432-184X}, support = {1656518//National Science Foundation Graduate Research Fellowship Program/ ; }, mesh = {Bees/microbiology ; Animals ; *Plant Nectar ; *Bacteria/classification/isolation &amp; purification/genetics ; *Flowers/microbiology ; Japan ; *Mouth/microbiology ; Seasons ; Gastrointestinal Microbiome ; }, abstract = {Bacteria in the honeybee gut are a well-recognized factor affecting bee health. However, the primary focus of this research has been the hindgut, while the crop, or honey stomach, is assumed to be dominated by environmentally acquired transient taxa that matter little to the bees. To evaluate this assumption, we examined bacterial taxa in the crop and mouth of Apis mellifera and A. cerana japonica foragers and in the nectar of Prunus mume flowers visited by the bees in the Minabe-Tanabe region of Japan. We found that in bacterial composition, the crop was distinct from both the mouth and the nectar, whereas mouth and nectar samples were indistinguishable. Furthermore, the crop remained similar in bacterial composition and diversity, while the mouth showed a sharp drop in alpha diversity and a large increase in beta diversity, from summer to winter. These results refute the conventional assumption, suggesting instead that the crop contains a conserved bacterial community largely distinct from environmental taxa. We also found that strains of a crop-associated species, Apilactobacillus kunkeei, could be season- and host species-specific. Together, these findings suggest that crop-associated bacterial communities should be studied further to better understand the relationship between honeybees and their gut bacteria.}, }
@article {pmid40387916, year = {2025}, author = {González-Villalobos, E and de Almeida Kumlien, ACM and Sànchez-Melsió, A and Balcázar, JL}, title = {Bacteriophages as Vehicles for Antibiotic Resistance Genes in the Onyar River, Spain.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {41}, pmid = {40387916}, issn = {1432-184X}, support = {CVU: 441304//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 792686//European Union's Horizon 2020 Research and Innovation Programme under the Marie Sk&#x142;odowska-Curie/ ; SGR 01282//Generalitat de Catalunya/ ; }, mesh = {Spain ; *Rivers/microbiology/virology ; *Bacteriophages/genetics ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/virology/isolation &amp; purification ; *Drug Resistance, Bacterial/genetics ; Geologic Sediments/microbiology/virology ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; DNA, Viral/genetics ; }, abstract = {This study aimed to investigate the presence and abundance of antibiotic resistance genes (ARGs) in bacterial and phage DNA fractions from sediment samples collected from the Onyar River, both before and after its passage through the urban area of Girona (northeast Spain). Genes conferring resistance to β-lactams, fluoroquinolones, macrolides, sulfonamides, and tetracyclines were quantified using quantitative PCR. Our findings showed that ARGs are present in both bacterial and phage DNA fractions, with a higher abundance in the bacterial fraction. Notably, our analysis revealed an increased abundance of the sulfonamide resistance gene sulI in the phage DNA fraction when comparing samples collected before and after the river's passage through the city. Although similar trends were observed for other ARGs (e.g., qnrS and sulII), these differences were not statistically significant (p > 0.05). These findings emphasize the importance of phages as potential reservoirs or vehicles for ARGs in environmental settings. Further research is needed to elucidate the factors that influence gene transfer dynamics and the persistence of ARGs within phages.}, }
@article {pmid40385475, year = {2025}, author = {Li, J and Zhou, L and Xiao, Z}, title = {Advances in the study of Ophiopogon japonicus polysaccharides: structural characterization, bioactivity and gut microbiota modulation regulation.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1583711}, pmid = {40385475}, issn = {1663-9812}, abstract = {Ophiopogon japonicus polysaccharides (OJPS), the principal bioactive constituents isolated from Ophiopogon japonicus, demonstrate substantial physiological efficacy. OJPS is characterized by a high molecular weight, typically ranging from 2.48 to 324.7 kDa. Emerging evidence indicates that OJPS modulates the composition and structural organization of the gut microbiota, thereby maintaining intestinal barrier integrity and enhancing both gastrointestinal and systemic homeostasis. Moreover, OJPS and its metabolic derivatives engage in dynamic interactions with microbial communities, mediating cellular signaling cascades and endocrine regulation to elicit hypoglycemic effects. Despite these findings, comprehensive analyses of OJPS extraction and purification methodologies, structural elucidation, biological functionalities, and mechanistic insights into its crosstalk with the gut microbiota remain scarce. This review systematically synthesizes contemporary knowledge pertaining to the preparation, structural attributes, bioactivity, and mechanistic underpinnings of OJPS, with particular emphasis on its dual regulatory role in host physiology and gut microbial ecology.}, }
@article {pmid40384051, year = {2025}, author = {Khafagy, ES and Saqr, AA and Almutairy, BK and Aldawsari, MF and Lila, ASA and Ibrahim, TS and Hegazy, WAH and Salem, IM}, title = {Repurposing Nitroimidazoles: A New Frontier in Combatting Bacterial Virulence and Quorum Sensing via In Silico, In Vitro, and In Vivo Insights.}, journal = {Drug development research}, volume = {86}, number = {3}, pages = {e70101}, doi = {10.1002/ddr.70101}, pmid = {40384051}, issn = {1098-2299}, support = {//The authors extend their appreciation to Prince Sattam bin Abdulaziz University for funding this research work through the project number (PSAU/2024/03/29653)./ ; }, mesh = {*Quorum Sensing/drug effects ; Animals ; Biofilms/drug effects ; *Drug Repositioning ; Humans ; Molecular Docking Simulation ; Virulence/drug effects ; *Nitroimidazoles/pharmacology ; Mice ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; HeLa Cells ; Chromobacterium/drug effects ; Molecular Dynamics Simulation ; Pseudomonas aeruginosa/drug effects ; Female ; Indoles/metabolism ; }, abstract = {The global antibiotic resistance crisis demands innovative strategies targeting bacterial virulence rather than survival. Quorum sensing (QS), a key regulator of virulence and biofilm formation, offers a promising avenue to mitigate resistance by disarming pathogens without bactericidal pressure. This study investigates the repurposing of nitroimidazoles as anti-QS and anti-virulence agents at subminimum inhibitory concentrations (sub-MICs). In Silico analyses, including molecular docking and molecular dynamics (MD) simulations, were performed to investigate ligand-receptor interactions with structurally distinct Lux-type QS receptors and assess binding stability and conformational dynamics over time. In Vitro assays evaluated the effects of representative nitroimidazoles, metronidazole (MET) and secnidazole (SEC), on QS-controlled phenotypes, including violacein production in Chromobacterium violaceum and biofilm formation and protease activity in Pseudomonas aeruginosa, Acinetobacter baumannii, Salmonella enterica, and Proteus mirabilis. In Vivo efficacy was assessed using a murine infection model and HeLa cell invasion assays. Molecular docking revealed high-affinity binding to QS receptors, corroborating their mechanistic interference. Sub-MIC MET/SEC significantly suppressed violacein synthesis, biofilm biomass, and protease secretion in Gram-negative pathogens. Both compounds reduced bacterial invasiveness in HeLa cells and In Vivo protected mice from lethal P. aeruginosa infections. Crucially, nitroimidazoles attenuated virulence without affecting bacterial viability, preserving microbial ecology. These findings position nitroimidazoles as dual-function agents; antimicrobial at bactericidal doses and anti-virulence at sub-MICs. Their validated efficacy across In Silico, In Vitro, and In Vivo models underscores their potential as adjunctive therapies, bridging the gap between drug repurposing and next-generation anti-infective development.}, }
@article {pmid40383311, year = {2025}, author = {Zhu, L and Huang, K and Bai, T and Xia, H}, title = {Bacteriophages enhance the transformation of dissolved organic matter during vermicomposting of sludge.}, journal = {Bioresource technology}, volume = {432}, number = {}, pages = {132694}, doi = {10.1016/j.biortech.2025.132694}, pmid = {40383311}, issn = {1873-2976}, mesh = {*Sewage/microbiology/chemistry ; *Bacteriophages/physiology/metabolism ; *Composting/methods ; *Organic Chemicals/metabolism ; Biodegradation, Environmental ; Carbon ; Solubility ; }, abstract = {Vermicomposting is an eco-friendly technology for treating sewage sludge, however its efficiency in transforming biological material is often constrained. This study investigates the potential of bacteriophages to enhance the transformation of dissolved organic matter (DOM) during sludge vermicomposting. Fresh dewatered sludge treated with bacteriophages (VP) were compared to untreated controls (CK) over a 30 days' vermicomposting. The results showed that bacteriophage inoculation led to a 58.17 % reduction in dissolved organic carbon (DOC), significantly higher than the 10.67 % reduction in the CK group (P < 0.05). Additionally, the DOM stability indices in the VP treatment were significantly decreased by 30.95 % (P < 0.05), alongside an increased humification rate. Partial least squares path modeling (PLS-PM) revealed that bacteriophages played a pivotal role in accelerating DOM degradation by selectively lysing specific bacterial populations and altering DOM transformation pathways.}, }
@article {pmid40382531, year = {2025}, author = {Hasegawa, R and Poulin, R and Salloum, PM}, title = {Testing for Consistency in Co-occurrence Patterns Among Bacterial Taxa Across the Microbiomes of Four Different Trematode Parasites.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {45}, pmid = {40382531}, issn = {1432-184X}, support = {202460294//Japan Society for the Promotion of Science/ ; UOO2113//Marsden Fund/ ; UOO2113//Marsden Fund/ ; }, mesh = {Animals ; *Trematoda/microbiology/classification ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Snails/parasitology/microbiology ; Phylogeny ; }, abstract = {Elucidating the specific processes and drivers of community assembly in the host microbiome is essential to fully understand host biology. Toward this goal, an important first step is to describe co-occurrence patterns among different microbial taxa, which can be driven by numerous factors, such as host identity. While host identity can be an important influential factor on co-occurrence patterns, a limited number of studies have explored the relative importance of host identity after controlling for other environmental factors. Here, we examined microbial co-occurrence patterns in four phylogenetically distinct trematode species living within the same snail species, collected concomitantly from the same habitat. Our previous study determined that all these trematodes shared some bacterial taxa, and the relative abundance of microbial taxa differed among trematodes, possibly due to differences in their eco-physiological traits. Here, we specifically predict that pairwise microbial co-occurrence patterns also vary among trematode host species. Our results showed that co-occurrence patterns among eight microbial families varied greatly among the four trematode hosts, with some microbial families co-occurring in some trematode species, whereas no such patterns were observed in other trematodes. Our study suggests that the habitat identity (trematode species) and its associated biotic characteristics, such as physiological and ecological traits, can determine co-occurrence patterns among microbial taxa, with substantial effects on local community composition.}, }
@article {pmid40382475, year = {2025}, author = {Yang, Q and Downey, R and Stark, JS and Johnstone, GJ and Mitchell, JG}, title = {The Microbial Ecology of Antarctic Sponges.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {44}, pmid = {40382475}, issn = {1432-184X}, mesh = {*Porifera/microbiology ; Animals ; Antarctic Regions ; *Microbiota ; Symbiosis ; *Bacteria/classification/genetics/isolation &amp; purification ; Archaea/classification/genetics/isolation &amp; purification ; Ecosystem ; Fungi/classification/genetics/isolation &amp; purification ; }, abstract = {Microbial communities in Antarctic marine sponges have distinct taxonomic and functional profiles due to low temperatures, seasonal days and nights, and geographic isolation. These sponge holobionts contribute to nutrient cycling, structural habitat formation, and benthic ecosystem resilience. We review Antarctic sponge holobiont knowledge, integrating culture-based and molecular data across environmental and taxonomic gradients. Although microbiome data exist for only a fraction of the region's 593 known sponge species, these hosts support diverse symbionts spanning at least 63 bacterial, 5 archaeal, and 6 fungal phyla, highlighting the complexity and ecological significance of these understudied polar microbiomes. A conserved core microbiome, dominated by Proteobacteria, Bacteroidetes, Nitrospinae, and Planctomycetes, occurs across Antarctic sponges, alongside taxa shaped by host identity, depth, and environment. Metagenomic data indicate microbial nitrogen cycling, chemoautotrophic carbon fixation, and stress tolerance. Despite these advances, major knowledge gaps remain, particularly in deep-sea and sub-Antarctic regions, along with challenges in taxonomy, methodological biases, and limited functional insights. We identify key research priorities, including developing standardised methodologies, expanded sampling across ecological and depth gradients, and integrating multi-omics with environmental and host metadata. Antarctic sponge holobionts provide a tractable model for investigating microbial symbiosis, functional adaptation, and ecosystem processes in one of Earth's most rapidly changing marine environments.}, }
@article {pmid40380820, year = {2025}, author = {Lakamp, AD and Neujahr, AC and Fernando, SC and Snelling, WM and Spangler, ML}, title = {Short communication: imputation accuracy of host genomic data from metagenomic sequence information.}, journal = {Journal of animal science}, volume = {103}, number = {}, pages = {}, doi = {10.1093/jas/skaf175}, pmid = {40380820}, issn = {1525-3163}, mesh = {Animals ; Cattle/genetics ; *Metagenomics/methods ; Genotype ; Sequence Analysis, DNA/veterinary ; }, abstract = {Metagenomic sequencing is the process of extracting all the genomic information from a given sample. Most metagenomic studies remove any host reads as a matter of course. However, host reads can be used as the basis for genotype imputation to obtain whole genomic sequences. The accuracy of these imputed genotypic calls from a bovine ocular sample was determined by comparing results to those from a commercial array. Overall, imputed genotype calls proved to have a high concordance with array genotype calls (average concordance of 83% and correlation of 0.81 with no filtering). Accuracy increased as filters for host read depth and imputed call confidence were implemented. With filters in place, the average percent concordance was 98% (88% to 99%) while the mean correlation was 0.98 (0.89 to 0.99). Further, identity verification of the metagenomic samples can be carried out if the host is genotyped on another platform.}, }
@article {pmid40379949, year = {2025}, author = {Onaka, H}, title = {Unlocking hidden bioactive compounds: from indolocarbazole and RiPP biosynthesis to the activation of cryptic secondary metabolism via microbial interactions.}, journal = {The Journal of antibiotics}, volume = {}, number = {}, pages = {}, pmid = {40379949}, issn = {1881-1469}, abstract = {Actinomycetes, particularly Streptomyces, are soil microorganisms that produce diverse secondary metabolites with pharmaceutical applications, such as antibiotics and anticancer drugs. These metabolites play important roles in microbial competition and survival. This review highlights three major aspects of actinomycete secondary metabolism: (1) the biosynthesis of indolocarbazoles, (2) the biosynthesis of RiPPs (ribosomally synthesized and post-translationally modified peptides), and (3) the activation of secondary metabolism through microbial interactions. Indolocarbazoles, including staurosporine and rebeccamycin, are potent inhibitors of kinases and DNA topoisomerase I, with potential as anticancer agents. Their biosynthetic pathways involve multiple enzymatic steps, notably carbon-carbon bond formation catalyzed by cytochrome P450 enzymes. RiPPs such as goadsporin and lactazole are highly modular peptide natural products; structural gene modification enables the generation of diverse analogs. A cell-free one-pot synthesis platform has been developed for efficient analog production. To activate cryptic biosynthetic pathways, we employed a combined-culture strategy using actinomycetes and mycolic acid-containing bacteria, resulting in the discovery of 42 novel compounds. Genetic and physiological data indicate that physical contact, rather than diffusible signaling, is essential for induction. These insights emphasize the importance of microbial interactions in natural product biosynthesis and offer new directions for drug discovery through synthetic biology and microbial ecology.}, }
@article {pmid40376461, year = {2025}, author = {Davis, RA and Mafune, KK and Winkler, MKH}, title = {Biodegradable hydrogels and microbial consortia as a treatment for soil dysbiosis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1565940}, pmid = {40376461}, issn = {1664-302X}, abstract = {Terrestrial microbial communities drive many soil processes and can be pushed into a state of dysbiosis upon disturbance. This dysregulation negatively impacts soil biogeochemical cycles, which threatens plant and soil health. Effective treatment of soil dysbiosis requires simultaneous restoration of multiple system components, addressing both the physical structure of soil and its microbial communities. Hydrogels with microbial consortia simultaneously remedy soil hydrodynamics while promoting microbial reestablishment. The purpose of this review is to shed light on soil management practices through the lens of soil dysbiosis. This is important to address not only for soil health and crop productivity, but also to mitigate climate change through improved soil carbon sequestration and reduced greenhouse gas emissions. This review positions hydrogels and microbes as tools for the treatment of soil dysbiosis, contributing to agricultural and climate resilience.}, }
@article {pmid40373669, year = {2025}, author = {Rescan, M and Gros, M and Borrego, CM}, title = {Multidimensional tolerance landscapes reveal antibiotic-environment interactions affecting population dynamics of wastewater bacteria.}, journal = {Water research}, volume = {282}, number = {}, pages = {123720}, doi = {10.1016/j.watres.2025.123720}, pmid = {40373669}, issn = {1879-2448}, mesh = {*Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology ; Escherichia coli/drug effects ; Temperature ; Salinity ; Sewage/microbiology ; *Bacteria/drug effects ; Population Dynamics ; }, abstract = {City sewers harbor diverse bacterial communities that are continuously exposed to a myriad of antibiotic residues resulting from human consumption and excretion. Despite their sub-inhibitory concentrations in sewage, these pharmaceutical residues affect the growth rate and the yield of susceptible wastewater-associated bacteria. Moreover, environmental conditions in sewers are complex, including variations in temperature and, in many coastal city sewers, salinity. These variables can modulate antibiotic tolerance and therefore affect the dynamics of microbial populations. To explore such interactions between antibiotics and abiotic environmental factors, we built continuous multivariate tolerance landscapes for three bacterial species commonly detected in sewage: Escherichia coli, the emerging pathogen Streptococcus suis, and a typical sewer dweller, Arcobacter cryaerophilus. We projected their intrinsic growth rate and carrying capacity onto a complex environment including temperature, salinity, and a range of concentrations of two antibiotics frequently measured in urban wastewater (ciprofloxacin and azithromycin). We revealed that antibiotic tolerance was maximal at salinities close to seawater for both E. coli and S. suis, and that the direction of the interaction between antibiotics and temperature is species dependent. In E. coli, we additionally observed a third-order interaction among salinity, temperature and antibiotics, highlighting the limits of predicting field dynamics of bacterial populations using standard laboratory measures. We projected these tolerance curves onto time series data of temperature and conductivity measured in the sewers of Barcelona. Our model highlights that low concentrations of antibiotics could exclude the most sensitive species, while interactions between antibiotics, temperature, and salinity substantially affected the dynamics of the more tolerant ones.}, }
@article {pmid40373649, year = {2025}, author = {Rosa-Masegosa, A and Vilchez-Vargas, R and Gorrasi, S and Monteoliva-García, A and Gonzalez-Martinez, A and Gonzalez-Lopez, J and Muñoz-Palazon, B}, title = {Unraveling the composition and succession of the microbial community in aerobic granular sludge treating urban wastewater with high load from hospital effluent.}, journal = {Chemosphere}, volume = {381}, number = {}, pages = {144483}, doi = {10.1016/j.chemosphere.2025.144483}, pmid = {40373649}, issn = {1879-1298}, mesh = {*Wastewater/microbiology/chemistry ; *Sewage/microbiology ; *Waste Disposal, Fluid/methods ; *Water Pollutants, Chemical/analysis/metabolism ; Bioreactors/microbiology ; Hospitals ; Bacteria/classification/genetics ; Fungi/classification ; *Microbiota ; Cities ; Aerobiosis ; Pharmaceutical Preparations/analysis ; }, abstract = {The treatment of wastewater containing high concentrations of pharmaceutical compounds is a challenge that has not yet been fully resolved. In this study, the occurrence of pharmaceutical and the bacterial and fungal communities were investigated during the treatment of urban wastewater including the hospital effluents using aerobic granular sludge technology. The physic-chemical results pointed out the capability of this technology to remove high rates of organic matter (97 %), total suspended solids (90 %), and nitrogen (85 %) without compromising the granular integrity and properties. The obtained data of pharmaceuticals remarked that the influent concentration had a strong effect on the removal ratio. The better average pharmaceutical removal performances were for carbamazepine (60-85 %), ketoprofen(50-60 %), cyclophosphamide(∼70 %), and trimethoprim(70 %), while the most recalcitrant compound was diclofenac. The molecular analysis exposed the relevance of endogenous microbial loads in the raw wastewater, especially in the start-up period. The mature granules demonstrated the strong selection of granules-forming bacteria, whereas the fungal populations took a longer period to be stable in granular biomass. Once the reactor was stable, the system was able to compete successfully with the influent microorganisms and avoid the spreading of pathogen microorganisms in the effluent, achieving excellent macro-pollutant and micro-pollutant removal ratios.}, }
@article {pmid40373419, year = {2025}, author = {Orsi, AS and Lemos Junior, WJF and Alegbeleye, OO and Muniz, DC and Horita, CN and Sant'Ana, AS}, title = {Sodium chloride reduction in meat processing: Microbial shifts, spoilage risks, and metagenomic insights.}, journal = {Meat science}, volume = {226}, number = {}, pages = {109848}, doi = {10.1016/j.meatsci.2025.109848}, pmid = {40373419}, issn = {1873-4138}, mesh = {*Meat Products/microbiology/analysis ; *Food Microbiology ; *Sodium Chloride/analysis ; *Food Handling/methods ; Animals ; Metagenomics ; Microbiota ; Bacteria ; Food Preservation/methods ; }, abstract = {This review evaluated the impact of sodium chloride (NaCl) reduction or substitution on the microbial ecology of meat products, with a focus on how these changes affect shelf life and safety. Reducing NaCl in fresh meat products promotes the growth of psychrotrophic spoilage bacteria, such as Pseudomonas sp., which thrive at low temperatures, and mesophilic pathogens like Escherichia coli and Staphylococcus aureus, particularly under inadequate storage conditions. In cured and fermented meats, such as salami, lowering NaCl levels disrupts the balance of salt-tolerant microorganisms, notably lactic acid bacteria (LAB) and coagulase-negative staphylococci, potentially leading to increased spoilage and pathogen proliferation. In smoked meats, the combination of reduced NaCl and altered microbial ecology, including a shift toward LAB dominance, may weaken the inhibitory effects on spore-forming bacteria like Clostridium botulinum. Additionally, using metagenomics, we explore the shifts in microbial communities observed in studies involving meat, revealing critical insights into the composition and diversity of bacteria in meat products, as well as the gaps in research on the impact of NaCl reduction and/or substitution on the microbiota. This review provides a comprehensive understanding of these microbial shifts, highlighting the distinct responses of psychrotrophic, mesophilic, and LAB groups to NaCl modification and the need to understand the effects of these alternatives on the meat product microbiome, as well as the neglected microorganisms that can affect the quality and safety of these products.}, }
@article {pmid40372110, year = {2025}, author = {Rohrhofer, J and Wolflehner, V and Schweighardt, J and Koidl, L and Stingl, M and Zehetmayer, S and Séneca, J and Pjevac, P and Untersmayr, E}, title = {Gastrointestinal Barrier Disruption in Post-COVID Syndrome Fatigue Patients.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.16593}, pmid = {40372110}, issn = {1398-9995}, support = {//WE&amp;ME Foundation/ ; //Medizinisch-Wissenschaftlicher Fond des Buergermeisters der Bundeshauptstadt Wien/ ; }, abstract = {BACKGROUND: Post-COVID Syndrome (PCS) is the term for a condition with persistent symptoms in a proportion of COVID-19 patients after asymptomatic, mild, or severe disease courses. Numbers vary, but the current estimate is that after COVID-19 approximately 10% develop PCS. The aim of our study was to evaluate the impact of SARS-CoV-2 infection on the gastrointestinal (GI) tract and associations with the development of PCS with fatigue, post-exertional malaise (PEM), orthostatic dysregulation, autonomous dysregulation, and/or neurocognitive dysregulation.<br><br>METHODS: By combining medical record data from a prospective observational study with symptom analysis before, during, and after SARS-CoV-2 infection, we aimed to identify potential risk factors and predictive markers for PCS. Additionally, we analyzed blood, saliva, and stool samples from this well-characterized PCS patient cohort to biologically validate our findings.<br><br>RESULTS: We identified significant associations between pre-existing GI complaints and the development of PCS Fatigue. PCS patients showed higher LBP/sCD14 ratios, lower IL-33 levels, and higher IL-6 levels compared to control groups. Our results highlight the critical role of the GI tract in PCS development of post-viral Fatigue.<br><br>CONCLUSION: We propose that the viral infection disrupts pathways related to the innate immune response and GI barrier function, evidenced by intestinal low-grade inflammation and GI barrier leakage. Monitoring GI symptoms and markers before, during, and after SARS-CoV-2 infection is crucial for identifying predictive clinical phenotypes in PCS. Understanding the interaction between viral infections, immune responses, and gut integrity could lead to more effective diagnostic and treatment strategies, ultimately reducing the burden on PCS patients.}, }
@article {pmid40367785, year = {2025}, author = {Wang, Y and Huang, S and He, J and Feng, Z and Wu, W and Guo, C and He, J}, title = {Unveiling the dynamic viral landscape across developmental stages of cold seep ecosystems: Implications for global marine biogeochemistry.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138594}, doi = {10.1016/j.jhazmat.2025.138594}, pmid = {40367785}, issn = {1873-3336}, abstract = {Cold seeps are methane-rich ecosystems playing pivotal roles in global biogeochemical cycling, yet their viral communities remain underexplored. We present the first comprehensive viral metagenomic analysis across developmental stages of the Haima Cold Seep. Characterizing viral assemblages from chemoautotrophic, mature, and extinct seep sediments revealed 4272 viral operational taxonomic units, with 77 % representing novel lineages, highlighting cold seeps' unique viral diversity. Viral community structure and diversity varied significantly by seep stage, with highest diversity in the chemoautotrophic stage. While Siphoviridae and Microviridae dominated, their relative abundances shifted with maturity. Gammaproteobacteria emerged as predominant viral hosts, exhibiting distinct interaction patterns across stages. Notably, the chemoautotrophic stage harbored the highest abundance and diversity of virus-encoded auxiliary metabolic genes (AMGs; ∼450 AMGs), with significantly enriched carbohydrate metabolism and central carbon pathway genes (2.2-fold and 1.8-fold higher respectively, p < 0.005), amino acid metabolism (1.9-fold, p = 0.003), and sulfur relay system genes (2.0-fold, p = 0.002). In contrast, the mature stage exhibited distinct enrichment in energy metabolism genes (up to 3.9-fold difference between sites, p < 0.001) and xenobiotics degradation pathways, suggesting stage-specific viral impacts on biogeochemical cycling. Lytic lifestyles prevailed across stages, indicating dynamic virus-host interactions during seep development. These findings unveil complex viral ecology in cold seeps, with potential influences on microbial community structure and biogeochemical processes. Providing a foundation for understanding viral roles in cold seep ecosystem functioning and biogeochemical cycles, this study has implications for marine microbial ecology and environmental biotechnology.}, }
@article {pmid40366158, year = {2025}, author = {Geonczy, SE and Hillary, LS and Santos-Medellín, C and Sorensen, JW and Emerson, JB}, title = {Patchy burn severity explains heterogeneous soil viral and prokaryotic responses to fire in a mixed conifer forest.}, journal = {mSystems}, volume = {10}, number = {6}, pages = {e0174924}, pmid = {40366158}, issn = {2379-5077}, mesh = {*Soil Microbiology ; Forests ; *Fires ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Soil/chemistry ; *Tracheophyta ; *Viruses/genetics/classification/isolation &amp; purification ; Microbiota ; Metagenome ; Virome ; }, abstract = {UNLABELLED: Effects of fire on soil viruses and virus-host dynamics are largely unexplored, despite known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we assessed how viral and prokaryotic communities responded to a prescribed burn in a mixed conifer forest. We sequenced 91 viral-size fraction metagenomes (viromes) and 115 16S rRNA gene amplicon libraries from 120 samples: four samples at five timepoints (two before fire and three after fire) at six sites (four treatment, two control). We hypothesized that compositional differences would be most significant between burned and unburned soils, but instead, plot location best distinguished viral communities, more than treatment (burned or not), depth (0-3 or 3-6 cm), or timepoint. For both viruses and prokaryotes, some burned communities resembled unburned controls, while others were significantly different, revealing heterogeneous responses to fire. These patterns were explained by burn severity, here defined by soil chemistry. Viral but not prokaryotic richness decreased significantly with burn severity, and low viromic DNA yields indicated substantial loss of viral biomass at higher severity. The relative abundances of Firmicutes, Actinobacteriota, and the viruses predicted to infect them increased significantly with burn severity, suggesting survival and viral infection of these fire-responsive and potentially spore-forming taxa. The degree of burn severity experienced by each patch of soil, rather than burn status alone, differed over mere meters in the same fire. Therefore, our analyses highlight the importance of high-resolution, paired biogeochemical data to explain soil community responses to fire.<br><br>IMPORTANCE: The impact of fire on the soil microbiome, particularly on understudied soil viral communities, warrants investigation, given known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we collected 120 soil samples before and after a prescribed burn in a mixed conifer forest to assess the impacts of this disturbance on soil viral and prokaryotic communities. We show that simple categorical comparisons of burned and unburned areas were insufficient to reveal the underlying community response patterns. The patchy nature of the fire (indicated by soil chemistry data) led to significant changes in viral and prokaryotic community composition in areas of high burn severity, while communities that experienced lower burn severity were indistinguishable from those in unburned controls. Our results highlight the importance of considering highly resolved burn severity and biogeochemical measurements, even in nearby soils after the same fire, in order to understand soil microbial responses to prescribed burns.}, }
@article {pmid40366134, year = {2025}, author = {Gilbert, NE and Kimbrel, JA and Samo, TJ and Siccardi, AJ and Stuart, RK and Mayali, X}, title = {A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse.}, journal = {mSystems}, volume = {10}, number = {6}, pages = {e0037525}, pmid = {40366134}, issn = {2379-5077}, support = {SCW1039//U.S. Department of Energy/ ; 1939//Joint Genome Institute/ ; 50220//Facilities Integrating collaborations for User Science/ ; }, mesh = {*Diatoms/growth &amp; development/microbiology ; *Microbiota ; *Eutrophication ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Flavobacteriaceae/genetics/metabolism ; Metagenomics ; }, abstract = {Algae-dominated ecosystems are fundamentally influenced by their microbiome. We lack information on the identity and function of bacteria that specialize in consuming algal-derived dissolved organic matter in high algal density ecosystems such as outdoor algal ponds used for biofuel production. Here, we describe the metagenomic and metaproteomic signatures of a single bacterial strain that bloomed during a population-wide crash of the diatom, Phaeodactylum tricornutum, grown in outdoor ponds. 16S rRNA gene data indicated that a single Kordia sp. strain (family Flavobacteriaceae) contributed up to 93% of the bacterial community during P. tricornutum demise. Kordia sp. expressed proteins linked to microbial antagonism and biopolymer breakdown, which likely contributed to its dominance over other microbial taxa during diatom demise. Analysis of accompanying downstream microbiota (primarily of the Rhodobacteraceae family) provided evidence that cross-feeding may be a pathway supporting microbial diversity during diatom demise. In situ and laboratory data with a different strain suggested that Kordia was a primary degrader of biopolymers during algal demise, and co-occurring Rhodobacteraceae exploited degradation molecules for carbon. An analysis of 30 Rhodobacteraceae metagenome assembled genomes suggested that algal pond Rhodobacteraceae commonly harbored pathways to use diverse carbon and energy sources, including carbon monoxide, which may have contributed to the prevalence of this taxonomic group within the ponds. These observations further constrain the roles of functionally distinct heterotrophic bacteria in algal microbiomes, demonstrating how a single dominant bacterium, specialized in processing senescing or dead algal biomass, shapes the microbial community of outdoor algal biofuel ponds.IMPORTANCEAquatic biogeochemical cycles are dictated by the activity of diverse microbes inhabiting the algal microbiome. Outdoor biofuel ponds provide a setting analogous to aquatic algal blooms, where monocultures of fast-growing algae reach high cellular densities. Information on the microbial ecology of this setting is lacking, and so we employed metagenomics and metaproteomics to understand the metabolic roles of bacteria present within four replicated outdoor ponds inoculated with the diatom Phaeodactylum tricornutum. Unexpectedly, after 29 days of cultivation, all four ponds crashed concurrently with a "bloom" of a single taxon assigned to the Kordia bacterial genus. We assessed how this dominant taxon influenced the chemical and microbial fate of the ponds following the crash, with the hypothesis that it was primarily responsible for processing senescent/dead algal biomass and providing the surrounding microbiota with carbon. Overall, these findings provide insight into the roles of microbes specialized in processing algal organic matter and enhance our understanding of biofuel pond microbial ecology.}, }
@article {pmid40366070, year = {2025}, author = {Herz, CT and Kulterer, OC and Prager, M and Marculescu, R and Prager, G and Kautzky-Willer, A and Hacker, M and Trajanoski, S and Köfeler, HC and Gallé, B and Haug, AR and Berry, D and Kiefer, FW}, title = {Bariatric surgery promotes recruitment of brown fat linked to alterations in the gut microbiota.}, journal = {European journal of endocrinology}, volume = {192}, number = {5}, pages = {603-611}, doi = {10.1093/ejendo/lvaf081}, pmid = {40366070}, issn = {1479-683X}, support = {P 27391//Austrian Science Fund/ ; 17094//Medical Scientific Fund of the Mayor of the City of Vienna/ ; //Austrian Diabetes Association Research Fund/ ; }, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Adipose Tissue, Brown/metabolism/diagnostic imaging ; *Bariatric Surgery ; Energy Metabolism/physiology ; Fatty Acids, Volatile/metabolism/blood ; *Gastrointestinal Microbiome/physiology ; *Obesity, Morbid/surgery/metabolism/microbiology ; Positron Emission Tomography Computed Tomography ; Weight Loss/physiology ; }, abstract = {OBJECTIVE: The mechanisms of bariatric surgery-induced weight loss and metabolic improvements are still incompletely understood and reach beyond malabsorption or calorie restriction. We sought to investigate the effect of bariatric surgery on brown adipose tissue (BAT) activity and a potential connection with changes in energy metabolism, the gut microbiota, and short-chain fatty acid (SCFA) composition.<br><br>METHODS: We included 32 subjects (25 females) with morbid obesity and analyzed their metabolic profile, gut microbiota composition, circulating SCFAs, energy expenditure, and cold-induced BAT activity using [18F]Fluorodeoxyglucose-positron emission tomography-computed tomography before and up to 1 year after bariatric surgery.<br><br>RESULTS: Twelve months after surgery, the percentage of individuals with active BAT had increased from 28% to 53%. The BAT-negative (BATneg) individuals who had an adverse metabolic profile at baseline compared with subjects with active BAT (BATpos) showed a greater metabolic benefit after surgery. While no changes in overall gut bacterial diversity were observed between BATpos and BATneg, the abundance of 3 specific bacterial families, including Akkermansiaceae, Pasteurellaceae, and Carnobacteriaceae, was distinctly regulated between BAT groups. The bacterial genera most strongly increased in BATpos vs BATneg subjects were all positively correlated with BAT volume and BAT activity. Finally, circulating concentrations of the SCFAs acetate, butyrate, and propionate rose after bariatric surgery and were related to bacterial genera such as Akkermansia, Dialister, and Lachnospiraceae FCS020 group, all known SCFA producers.<br><br>CONCLUSIONS: Bariatric surgery helps recruit active BAT in individuals with obesity and is linked to distinct alterations in the gut microbiome and SCFA composition.<br><br>TRIAL REGISTRATION NUMBER: ClinicalTrials.gov (NCT03168009).}, }
@article {pmid40361280, year = {2025}, author = {Wan, SH and Xu, Y and Xu, W and Leung, SKK and Yu, EYN and Yung, CCM}, title = {Environmental Heterogeneity Drives Ecological Differentiation in Vibrio Populations Across Subtropical Marine Habitats.}, journal = {Environmental microbiology}, volume = {27}, number = {5}, pages = {e70107}, pmid = {40361280}, issn = {1462-2920}, support = {AoE/P-601/23-N//Research Grants Council of Hong Kong/ ; }, mesh = {*Vibrio/genetics/classification/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; *Ecosystem ; Hong Kong ; Temperature ; Salinity ; Chaperonin 60/genetics ; Bays/microbiology ; }, abstract = {Elucidating how environmental gradients structure bacterial communities remains fundamental to microbial ecology. We investigated Vibrio population dynamics across contrasting subtropical marine environments in Hong Kong over a year period. Using an integrated approach combining cultivation techniques with molecular analyses of Hsp60 and 16S rRNA genes, we characterised the population structure between a coastal site (Clear Water Bay) and an estuarine site (Deep Bay). The estuarine environment consistently harboured higher Vibrio abundances (10[4]-10[7] copies/mL) compared to coastal waters (10[2]-10[4] copies/mL), with significantly greater phylogenetic diversity. Multivariate analyses revealed salinity as the primary driver of community differentiation between sites, while temperature governed seasonal succession patterns. Phylogenetic analysis of 1521 Vibrio isolates identified three distinct ecological groups corresponding to specific temperature-salinity niches, with evidence of habitat-specific thermal adaptations among closely related strains. Experimental characterisation of thermal performance curves confirmed physiological differentiation between warm- and cool-temperature adapted strains despite high genetic similarity (> 97% Hsp60 gene sequence identity). Several abundant species detected via amplicon sequencing (including V. navarrensis and V. mimicus) displayed site-specific ecotypes but remained uncultivated, highlighting methodological constraints in community characterisation. Our findings demonstrate how environmental heterogeneity drives fine-scale ecological differentiation in Vibrio populations, providing insights into mechanisms of bacterial adaptation in dynamic marine environments.}, }
@article {pmid40359204, year = {2025}, author = {Ghyselinck, J and Verstrepen, L and Rakebrandt, M and Marynissen, S and Daminet, S and Marzorati, M}, title = {In vitro fermentation of yeast cell walls (mannan-oligosaccharide) and purified β-glucans modulates the colonic microbiota of dogs with inflammatory bowel disease and demonstrates protective effects on barrier integrity and anti-inflammatory properties.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0322877}, pmid = {40359204}, issn = {1932-6203}, mesh = {Animals ; Dogs ; *Inflammatory Bowel Diseases/microbiology/veterinary ; *Gastrointestinal Microbiome/drug effects ; *Mannans/metabolism/pharmacology ; *beta-Glucans/pharmacology/metabolism ; Prebiotics ; *Saccharomyces cerevisiae/metabolism/chemistry ; *Cell Wall/metabolism/chemistry ; Humans ; Fermentation ; *Colon/microbiology ; Caco-2 Cells ; *Anti-Inflammatory Agents/pharmacology ; *Oligosaccharides/metabolism ; RNA, Ribosomal, 16S/genetics ; Intestinal Mucosa ; }, abstract = {Inflammatory bowel disease (IBD) is characterized by a disruption of intestinal homeostasis, chronic inflammation, and dysbiosis. Prebiotic supplementation may be useful for managing IBD in dogs. The aim of the study is to investigate the effects of two prebiotics, Biolex MB40 or Leiber Beta-S, on the gut microbiota isolated from three dogs with IBD, using the Colon-on-a-plate technology. Biolex MB40 and Leiber Beta-S contain concentrated 1,3-1,6- β-D-glucan isolated from the Saccharomyces cerevisiae cell walls. Biolex MB40 also contains mannan-oligosaccharide (MOS). Wells of the Colon-on-a-plate set up were inoculated with fecal suspensions and supplemented with either Biolex MB40 and Leiber Beta-S, or no test product (blank). Following 48h incubation, bacterial metabolites were measured and 16S rRNA targeted gene sequencing was performed. Colonic supernatants were added to a Caco-2/THP1 co-culture model to evaluate their effects on barrier integrity upon inflammation-induced barrier disruption and interleukin (IL)-10 production. Acetate and propionate concentrations were significantly increased versus blank with Biolex MB40, and biologically relevant numerical increases were observed with Leiber Beta-S supplementation. A donor-dependent, biologically relevant increase in butyrate was observed with both test products versus blank. Alpha diversity and microbiota biomass were increased, as well as the abundance of the five predominant phyla with both test products relative to blank. The greatest increases in abundance were observed for the Bacteroidetes and Firmicutes phyla. Fermentation of both test products had a protective effect on the gut epithelial barrier (measured by transepithelial electrical resistance) that was donor dependent. IL-10 production was significantly increased with Biolex MB40 supplementation for all donors, and with Leiber Beta-S supplementation for one donor. These in vitro findings confirm a prebiotic effect for both products and suggest that supplementation with either Biolex MB40 or Leiber Beta-S may have beneficial effects on the gut microbiota of dogs with IBD.}, }
@article {pmid40358239, year = {2025}, author = {Waegenaar, F and Pluym, T and Vermeulen, E and De Gusseme, B and Boon, N}, title = {Impact of flushing procedures on drinking water biostability and invasion susceptibility in distribution systems.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {6}, pages = {e0068625}, pmid = {40358239}, issn = {1098-5336}, support = {1S02022N//Fonds Wetenschappelijk Onderzoek/ ; 1S26823N//Fonds Wetenschappelijk Onderzoek/ ; S006221N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {*Drinking Water/microbiology ; Belgium ; *Water Purification/methods ; *Bacteria/drug effects/growth &amp; development ; *Water Microbiology ; Water Supply ; Halogenation ; Sodium Hypochlorite/pharmacology ; Chlorine ; }, abstract = {UNLABELLED: Ensuring high-quality drinking water remains challenging, as complaints about odors, discoloration, or contamination persist. In Belgium and beyond, traditional flushing is a common curative strategy that involves discharging large water volumes through hydrants while the network remains in use. In some cases, free chlorine (0.5 mg/L) is added, and consumers are advised not to drink the water. However, flushing can alter water biostability, potentially increasing susceptibility to microbial invasion. This study used a pilot-scale drinking water distribution system with three identical 100 m polyvinyl chloride(PVC) loops (DN 80 mm) to assess the impact of flushing with and without chlorination as practiced in chlorinated networks. Loop 1 was flushed with tap water and sodium hypochlorite (NaOCl), followed by two non-chlorinated flushes, loop 2 was unflushed, and loop 3 underwent three flushes. Biostability was assessed using online flow cytometry, and susceptibility to bacterial invasion (Aeromonas media, Pseudomonas putida, and Serratia fonticola) was evaluated in the days following flushing. The water had a 7-day residence time. Results showed that chlorinated flushing promoted microbial regrowth (3.8 × 10[5] vs 2.0 × 10[5] and 1.6 × 10[5] cells/mL for loops 1, 2, and 3, respectively), primarily of resident Sphingopyxis spp. Biofilm cell densities (~4 × 10[6] cells/cm[2]) remained stable across conditions. Bacterial indicators declined over time, with P. pudita and S. fonticola surviving longer (>100 hours) than A. media (13 hours). Decay rates were highest in chlorinated loops, likely due to increased microbial competition. For example, the decay constant of S. fonticola at 20°C was -0.082 h[-1], -0.042 h[-1], and -0.027 h[-1] for loops 1, 2, and 3, respectively.<br><br>IMPORTANCE: Traditional flushing is used as a curative strategy to solve unwanted quality issues during distribution, yet its impact on microbial biostability remains poorly understood. This study provides critical insights into how traditional flushing, both with and without chlorination, influences microbial regrowth and susceptibility to invasion. Findings reveal that chlorinated flushing promotes the regrowth of resident drinking water bacteria while accelerating the decay of introduced unwanted bacterial indicators, emphasizing the complex trade-off between microbial control and system stability. Understanding these dynamics is essential for optimizing flushing procedures, minimizing unintended consequences, and improving distribution system resilience.}, }
@article {pmid40358205, year = {2025}, author = {An, Y and Garcia, SL and Hambäck, PA}, title = {Microbial transfer through fecal strings on eggs affects leaf beetle microbiome dynamics.}, journal = {mSystems}, volume = {10}, number = {6}, pages = {e0172324}, pmid = {40358205}, issn = {2379-5077}, support = {#2019-4980//Vetenskapsr&#xe5;det/ ; }, mesh = {Animals ; *Coleoptera/microbiology ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Female ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Ovum/microbiology ; Larva/microbiology ; }, abstract = {UNLABELLED: Gut microbiomes of holometabolous insects can be strongly affected by metamorphosis. Previous studies suggest that microbiome colonization and community development often rely on specialized transmission routes between host life stages. However, there is a lack of comparative studies of microbial community dynamics from different transmission mechanisms. We compared the gut microbial community dynamics across life stages in five Galerucella species that differ in their potential microbial transfer mechanism by sequencing amplicons of the 16S rRNA gene. Females of three of the studied species place a fecal string on top of the egg, which may enhance the transfer of gut microbes, whereas females of the two other species do not. We found that the α-diversity was more stable between life stages in fecal string-placer species compared with the non-fecal string-placer species. Moreover, there were consistent microbiome differences between species, with multiple taxa in each species consistently appearing in all life stages. Fecal strings placed on eggs seem to play an important role in the diversity and dynamics of gut bacteria in Galerucella species, facilitating the vertical transfer of gut bacteria between host insect generations. Alternative, but less efficient, transmission routes appear to occur in non-fecal string-placer species.<br><br>IMPORTANCE: We explore the consequences of having different mechanisms for transferring and establishing the gut microbiome between generations on gut microbial community dynamics. This process is often problematic in holometabolous insects, which have a complete metamorphosis between larval and adult stages. In our previous research, we found that females of some species within the genus Galerucella (Chrysomelidae) place a fecal string on the eggs, which is later consumed by the hatching larvae, whereas other species in the same genus do not have this behavior. In this paper, we therefore quantify the microbial community dynamics across all life stages in five Galerucella beetles (three with and two without fecal strings). Our results also indicate that the dynamics are much more stable in the species with fecal strings, particularly in the early life stages.}, }
@article {pmid40356667, year = {2025}, author = {Martínez-Mota, R and Vásquez-Aguilar, AA and Hernández-Rodríguez, D and Suárez-Domínguez, EA and Krömer, T}, title = {Close neighbors, not intruders: investigating the role of tank bromeliads in shaping faunal microbiomes.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19376}, pmid = {40356667}, issn = {2167-8359}, mesh = {Animals ; *Diptera/microbiology ; Larva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Mexico ; *Bromeliaceae/microbiology ; *Bacteria/genetics/classification ; Ecosystem ; }, abstract = {BACKGROUND: Tropical montane cloud forests contain high levels of epiphyte diversity. Epiphytic tank bromeliads play an important role in the functioning of these ecosystems and provide a microhabitat for many species of invertebrates. Microbial ecology theory suggests that the environment serves as a source of microbes for animals, but the contribution of this factor to the composition of an animal microbiome varies. In this study, we examined the extent to which tank bromeliads (Tillandsia multicaulis) serve as a source of microbes for two species of fly larvae in a cloud forest fragment in central Veracruz, Mexico.<br><br>METHODS: We used 16S rRNA sequencing to characterize the bacterial communities in the organic matter within bromeliad tanks and in the whole bodies (surface and gut) of larvae from two fly taxa (Austrophorocera sp., Tachinidae, and Copestylum sp., Syrphidae) that inhabit these bromeliads. To assess the contribution of bromeliads to the microbiome of the fly larvae, we conducted fast expectation-maximization microbial source tracking (FEAST) analysis.<br><br>RESULTS: The bacterial communities in bromeliad tanks were primarily composed of Pseudomonadota, Acidobacteriota, Bacteroidota, Verrucomicrobiota, and Spirochaetota. Similarly, communities of the fly larvae contained Pseudomonadota, Bacteroidota, Bacillota, and Actinomycetota. Bromeliad tanks exhibited the highest bacterial richness, followed by Copestylum and Austrophorocera larvae. Beta diversity analyses indicated that bacterial communities clustered by species. We found a modest contribution of bromeliads to the fly microbiome, with nearly 30% of the larvae microbiome traced to the organic matter deposited in the tanks.<br><br>CONCLUSIONS: Our data suggest that the microbiome of flies, which inhabit tank bromeliads during their larval stage, is nourished to some extent by the bacterial communities present in the organic matter within the tank.}, }
@article {pmid40356640, year = {2025}, author = {Sun, Z and Hu, Y and Yang, YX and Lei, MY and Han, ZM and Cheng, L and Wang, W and Han, M and Lyu, ZL and Yang, LM}, title = {Changes in the diversity of ginseng endophyte flora driven by Fusarium solani.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1554706}, pmid = {40356640}, issn = {1664-302X}, abstract = {Endophytic flora serves a crucial function as a secondary line of defense against pathogen invasion in plants. To investigate the mechanisms underlying the relationship between changes in endophytic flora and ginseng root rot, exhumate beneficial endophytic bacteria, and explore biological management approaches for ginseng root rot. In this study, we used Illumina high-throughput sequencing and bioinformatics analysis to investigate the characteristics and differences in endophytic microbial community structure between healthy ginseng (HG) and diseased ginseng (BLS) after Fusarium solani infection. The findings revealed that as ginseng root rot increased, the diversity and richness of endophytic bacterial communities increased before decreasing, but the diversity and richness of endophytic fungal communities decreased. The dominating bacterial phylum in ginseng roots was Proteobacteria, which declined in quantity as the disease progressed. Ascomycota was the dominating fungal phylum among endophytes, and its prevalence grew as the disease progressed. At the genus level, the relative abundance of Rhodococcus, Stenotrophomonas, Variovorax, and Achromobacter species increased with the occurrence of ginseng root rot, in contrast, Pantoea and Pseudomonas species decreased in relative abundance as the prevalence of ginseng root rot increased. The relative abundance of the pathogenic fungi Gibberella, Nectria, Ilyonectria, and Alternaria in ginseng roots increased as the disease progressed. Endophytic fungal LEfSe research revealed that Neonectria was the particular biomarker discovered in the highly susceptible group. Additionally, commensal nutrient-type fungi appeared to be absent in moderately susceptible ginseng, but pathognomic nutrient-type fungi grew, coupled with potentially pathogenic fungi, exacerbating the condition. These results suggest that there is a pattern of response of ginseng endophytic microbial diversity to disease infestation. In this work, we investigated the impact of varying degrees of root rot on ginseng's endophytic flora structure. The study's findings give a theoretical framework for understanding the microecological processes of ginseng root rot via the lens of microbial ecology and applying biological control tools.}, }
@article {pmid40356172, year = {2025}, author = {Cardinali, F and Rampanti, G and Harasym, J and Lucci, P and Ferrocino, I and Pacetti, D and Fanesi, B and Milanović, V and Garofalo, C and Petruzzelli, A and Savelli, D and Gabucci, C and Aquilanti, L and Osimani, A}, title = {Comprehensive profiling of smoked cheese from raw goat's milk handcrafted in Lower Silesia (Poland).}, journal = {Food research international (Ottawa, Ont.)}, volume = {211}, number = {}, pages = {116398}, doi = {10.1016/j.foodres.2025.116398}, pmid = {40356172}, issn = {1873-7145}, mesh = {*Cheese/microbiology/analysis ; Animals ; Goats ; Fatty Acids/analysis ; Volatile Organic Compounds/analysis ; Poland ; *Milk/microbiology/chemistry ; *Food Microbiology ; *Food Handling/methods ; Consumer Behavior ; Humans ; *Smoke ; Colony Count, Microbial ; }, abstract = {This study aimed to explore the distinctive characteristics of smoked cheese made from raw goat's milk, labelled "Produkt polski" and crafted in the Lower Silesia region of Poland. A comprehensive range of analyses was performed, including physico-chemical and morpho-textural evaluations, microbial counts, and a metataxonomic investigation to uncover the microbial diversity occurring in the cheese. The volatile organic compounds (VOCs) and the total fatty acid composition were also determined. Additionally, a consumer test based on a hedonic scale was conducted to capture the subjective experience of the product's appeal. The cheese samples revealed water activity (aw) ranging between 0.901 ± 0.003 and 0.926 ± 0.001, with pH levels between 5.08 ± 0.15 and 5.44 ± 0.01. Regarding fatty acid composition, all of the smoked cheeses displayed a similar profile, with saturated fatty acids dominating (SFA, ∼75 %), followed by monounsaturated (MUFA, ∼22 %) and polyunsaturated fatty acids (PUFA, ∼3 %). Microbial analysis revealed thriving populations, including lactococci (up to 8.63 ± 0.07 log colony-forming units g[-1]), thermophilic cocci (up to 6.85 ± 0.08 log cfu g[-1]), lactobacilli (up to 9.50 ± 0.04 log cfu g[-1]), enterococci (up to 5.93 ± 0.00 log cfu g[-1]), and eumycetes (up to 2.68 ± 0.48 log cfu g[-1]). Metataxonomic analysis identified dominant bacterial taxa such as Lactobacillus, Lactococcus, and Leuconostoc, as well as Carnobacterium and Lacticaseibacillus. Among the 24 lactic acid bacteria cultures isolated, the closest relatives to Enterococcus, Lacticaseibacillus, Lactococcus, and Leuconostoc were identified. Some isolates demonstrated promising pro-technological traits, positioning them as potential adjunct cultures for improving fermented dairy products. The volatile profile of the smoked cheese was particularly intriguing, with a total of 87 VOCs detected, categorized as esters (18), ketones (14), hydrocarbons (11), acids (10), phenols (11), alcohols (8), furans (5), lactones (4), aldehydes (3), and other compounds (3). Sensory evaluation revealed a moderate appreciation for the cheese's appearance, whereas the smoked flavor elicited the most varied scores, highlighting its strong impact on consumer preference.}, }
@article {pmid40356145, year = {2025}, author = {Wang, S and Zheng, C and Bu, C and Guo, D and Zhang, C and Xie, Q and Pan, J and Sun, J and Chen, W and Jiang, S and Zhai, Q}, title = {Role of sn-2 palmitate on the development of the infant gut microbiome: A metagenomic insight.}, journal = {Food research international (Ottawa, Ont.)}, volume = {211}, number = {}, pages = {116488}, doi = {10.1016/j.foodres.2025.116488}, pmid = {40356145}, issn = {1873-7145}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Infant Formula/chemistry ; Infant ; Feces/microbiology ; *Metagenomics/methods ; Milk, Human/chemistry ; Female ; Male ; Breast Feeding ; *Palmitates/pharmacology ; Infant, Newborn ; Phylogeny ; }, abstract = {The infant gut microbiome, which develops from birth, has profound and lasting effects on human health. Its establishment in early life is influenced by events such as delivery mode and feeding type. This study examined the effects of formula milk enriched with sn-2 palmitate on the gut microbiota of healthy term infants. We conducted a 16-week comparative analysis of three feeding groups: infants receiving high sn-2 palmitate formula (n = 30), regular vegetable oil formula (n = 32), and breast milk (n = 30). Using shotgun metagenomic sequencing of fecal samples, we performed a comprehensive assessment of the gut microbiota. While overall microbial composition and diversity were comparable across groups, the functional profile of the microbiome in infants receiving sn-2 palmitate-enriched formula more closely resembled that of breastfed infants compared to the control formula group. This similarity extended to microbial species interactions, virulence gene abundance, and metabolic pathway expression patterns. In addition, sn-2 palmitate promoted the proliferation of Bifidobacterium breve and enhanced the robustness of the gut microbial ecology. Notably, the phylogenetic analysis of B. breve strains in the sn-2 palmitate group showed closer alignment with the breastfed group compared to the control group. These findings suggest that sn-2 palmitate-enriched formula may confer gut microbiota functional benefits that more closely resemble those of breast milk compared to control formula milk. This study provides scientific evidence for the development of future functional infant formulas.}, }
@article {pmid40354775, year = {2025}, author = {Frazier, CF and Harris, TD and DelSontro, T and Grossart, HP and Sturm, BSM and Murry, JM and Ising, A}, title = {Phytoplankton abundance and methane emissions are minimally impacted by environmentally-relevant glyphosate concentrations in small-scale outdoor mesocosms.}, journal = {Water research}, volume = {283}, number = {}, pages = {123764}, doi = {10.1016/j.watres.2025.123764}, pmid = {40354775}, issn = {1879-2448}, abstract = {Glyphosate is one of the most widely applied agrochemicals in North America and can be directly transported via runoff into non-target aquatic habitats. Yet, our understanding of how this herbicide affects aquatic ecosystems is limited; past studies have often focused on single species effects and/or used herbicide concentrations several orders of magnitude higher than what has been reported in contaminated aquatic systems. Further, glyphosate in aquatic systems has the potential to alter greenhouse gas emissions (methane) if it is broken down for phosphate utilization by bacteria under specific environmental conditions (i.e., oxygen, nutrient concentrations). In this study, we assessed the temporal changes in nutrients, phytoplankton, copy number of genes associated with breakdown of glyphosate or production of methane (phnJ, mcrA), and methane concentrations in 12-day mesocosms with amendments of glyphosate, nitrogen, and/or phosphorus. We found glyphosate at environmentally-relevant concentrations (∼4 ug/L) did not confer changes in overall ratios and total concentrations of nutrients, or abundance of any major phytoplankton group (cyanobacteria, diatoms, green algae), methane concentration or flux, or gene copy numbers of phnJ and mcrA. Our results suggest that the relatively low concentrations of glyphosate we used (relative to levels used in toxicological studies) did not cause major changes over short time periods in mesocosms, and that the potential for glyphosate to increase greenhouse gas emissions in aquatic systems requires specific conditions to occur and may not be universal in contaminated systems.}, }
@article {pmid40354740, year = {2025}, author = {Rodrigo, MA and Puche, E and Muñoz-Colmenares, M and Sánchez-Carrillo, S}, title = {Vascular macrophytes versus charophytes: how the macrophyte type and warming affect the sediment microbial community and the production of greenhouse gases.}, journal = {Journal of environmental management}, volume = {386}, number = {}, pages = {125654}, doi = {10.1016/j.jenvman.2025.125654}, pmid = {40354740}, issn = {1095-8630}, mesh = {*Greenhouse Gases ; *Geologic Sediments/microbiology ; Global Warming ; Carbon Dioxide ; Ecosystem ; Microbiota ; }, abstract = {In the global warming context, adaptive management strategies involve the conservation and restoration of inland waters by planning the reintroduction of macrophytes to substantially mitigate greenhouse gas emissions (GHG). The selection of appropriate species is crucial. We studied the influence of two submerged macrophyte species on GHG production, sediment-oxygen microprofiles, and microbial community composition under two thermal regimes by means of a microcosm experiment. We chose the phanerogam Myriophyllum spicatum, more typical of meso-eutrophic habitats, and the charophyte Chara hispida, more frequent in oligotrophic waters and belonging to a much less studied macrophyte group, which, moreover, exhibit contrasting functional traits (i.e., roots versus rhizoids). The presence of both macrophyte types considerably reduced the diurnal diffusive CO2 emissions due to their photosynthetic activity compared to bare-sediment situations. The radial oxygen loss of M. spicatum roots provided aerobic-microaerobic conditions beyond the first sediment centimeter, in contrast to more anoxic sediments created by C. hispida. As a result of this, each type of macrophyte determined a particular sediment microbiome. Despite dissolved CH4 being greater in the presence of plants, no statistical differences in CH4 diffusive flux caused by the presence or absence of plants was found. We demonstrated how the presence, or not, of macrophytes is more important than warming (in our case with a temperature difference of 3 °C) in relation to GHG emissions. Both species, being perennial, provide ecosystem services year-round and are strong candidates for management strategies aimed at transforming new or restored aquatic ecosystems into carbon sinks.}, }
@article {pmid40353721, year = {2025}, author = {Pellitier, PT and Kling, MM and Qin, C and Van Nuland, ME and Zhu, K and Peay, KG}, title = {Wind Patterns Influence the Dispersal and Assembly of North American Soil Fungal Communities.}, journal = {Ecology letters}, volume = {28}, number = {5}, pages = {e70130}, doi = {10.1111/ele.70130}, pmid = {40353721}, issn = {1461-0248}, support = {1845544//Directorate for Biological Sciences/ ; 1926335//Directorate for Biological Sciences/ ; 2010897//Directorate for Biological Sciences/ ; 2244711//Directorate for Biological Sciences/ ; }, mesh = {*Wind ; *Soil Microbiology ; *Fungi/physiology/genetics ; North America ; *Mycobiome ; Spores, Fungal/physiology ; Climate Change ; Models, Biological ; }, abstract = {Wind is the primary dispersal mechanism of most fungal spores but is rarely considered in studies of fungal communities, limiting inference of assembly mechanisms and forecasting responses to climate change. We compiled wind-connectivity models-'windscapes'-to model potential dispersal of fungal spores at the continental scale and linked them with a molecular dataset of North American soil fungi. Our analyses demonstrate that prevailing windflow patterns exhibit a significantly stronger signal on fungal community structure than do geographic distances amongst sites. Notably, the signature of wind was detectable for mushrooms and fungi producing primarily wind-dispersed spores. Contrastingly, fungi primarily reliant on animal dispersal exhibited a strong signature of geographic distance but not wind-connectivity. Additionally, we show that directionally 'downwind' sites are more diverse than comparatively 'upwind' sites. Altogether, our findings suggest that future wind patterns will shape the adaptation potential of fungal communities dispersing into suitable climatic niches.}, }
@article {pmid40353658, year = {2025}, author = {Laso-Pérez, R and Rivas-Santisteban, J and Fernandez-Gonzalez, N and Mundy, CJ and Tamames, J and Pedrós-Alió, C}, title = {Nitrogen cycling during an Arctic bloom: from chemolithotrophy to nitrogen assimilation.}, journal = {mBio}, volume = {16}, number = {6}, pages = {e0074925}, pmid = {40353658}, issn = {2150-7511}, support = {FJC2019-041362-I, RyC2021-031775-I//Ministerio de Ciencia e Innovaci&#xf3;n (MCIN)/ ; PID2019-110011RB-C33, PID2023-146919NB-C21//MEC | Agencia Estatal de Investigaci&#xf3;n (AEI)/ ; }, mesh = {Arctic Regions ; *Nitrogen/metabolism ; *Bacteria/metabolism/genetics/classification ; *Nitrogen Cycle ; *Archaea/metabolism/genetics/classification ; Phytoplankton/growth &amp; development/metabolism ; Metagenomics ; Canada ; *Chemoautotrophic Growth ; Seasons ; Metagenome ; }, abstract = {In the Arctic, phytoplankton blooms are recurring phenomena occurring during the spring-summer seasons and influenced by the strong polar seasonality. Bloom dynamics are affected by nutrient availability, especially nitrogen, which is the main limiting nutrient in the Arctic. This study aimed to investigate the changes in an Arctic microbial community using omics approaches during a phytoplankton bloom focusing on the nitrogen cycle. Using metagenomic and metatranscriptomic samples from the Dease Strait (Canada) from March to July (2014), we reconstructed 176 metagenome-assembled genomes. Bacteria dominated the microbial community, although archaea reached up to 25% of metagenomic abundance in early spring, when Nitrososphaeria archaea actively expressed genes associated with ammonia oxidation to nitrite (amt, amo, nirK). The resulting nitrite was presumably further oxidized to nitrate by a Nitrospinota bacterium that highly expressed a nitrite oxidoreductase gene (nxr). Since May, the constant increase in chlorophyll a indicated the occurrence of a phytoplankton bloom, promoting the successive proliferation of different groups of chemoorganotrophic bacteria (Bacteroidota, Alphaproteobacteria, Gammaproteobacteria). These bacteria showed different strategies to obtain nitrogen, whether it be from organic or inorganic sources, according to the expression patterns of genes encoding transporters for nitrogen compounds. In contrast, during summer, the chemolithotrophic organisms thriving during winter reduced their relative abundance and the expression of their catabolic genes. Based on our functional analysis, we see a transition from a community where nitrogen-based chemolitotrophy plays a relevant role to a chemoorganotrophic community based on the carbohydrates released during the phytoplankton bloom, where different groups seem to specialize in different nitrogen sources.IMPORTANCEThe Arctic is one of the environments most affected by anthropogenic climate change. It is expected that the rise in temperature and change in ice cover will impact the marine microbial communities and the associated biogeochemical cycles. In this regard, nitrogen is the main nutrient limiting Arctic phytoplankton blooms. In this study, we combine genetic and expression data to study the nitrogen cycle at the community level over a time series covering from March to July. Our results indicate the importance of different taxa (from archaea to bacteria) and processes (from chemolithoautotrophy to incorporation of different nitrogen sources) in the cycling of nitrogen during this period. This study provides a baseline for future research that should include additional methodologies like biogeochemical analysis to fully understand the changes occurring on these communities due to global change.}, }
@article {pmid40352645, year = {2025}, author = {Quinn, LK and Sharma, K and Faber, KT and Orphan, VJ}, title = {Clear as mud redefined: Tunable transparent mineral scaffolds for visualizing microbial processes below ground.}, journal = {PNAS nexus}, volume = {4}, number = {5}, pages = {pgaf118}, pmid = {40352645}, issn = {2752-6542}, abstract = {Microbes inhabiting complex porous microenvironments in sediments and aquifers catalyze reactions that are critical to global biogeochemical cycles and ecosystem health. However, the opacity and complexity of porous sediment and rock matrices have considerably hindered the study of microbial processes occurring within these habitats. Here, we generated microbially compatible, optically transparent mineral scaffolds to visualize and investigate microbial colonization and activities occurring in these environments, in laboratory settings and in situ. Using inexpensive synthetic cryolite mineral, we produced optically transparent scaffolds mimicking the complex 3D structure of sediments and rocks by adapting a suspension-based, freeze-casting technique commonly used in materials science. Fine-tuning of parameters, such as freezing rate and choice of solvent, provided full control of pore size and architecture. The combined effects of scaffold porosity and structure on the movement of microbe-sized particles, tested using velocity tracking of fluorescent beads, showed diverse yet reproducible behaviors. The scaffolds we produced are compatible with epifluorescence microscopy, allowing the fluorescence-based identification of colonizing microbes by DNA-based staining and fluorescence in situ hybridization (FISH) to depths of 100 µm. Additionally, Raman spectroscopy analysis indicates minimal background signal in regions used for measuring deuterium and [13]C enrichment in microorganisms, highlighting the potential to directly couple D2O or [13]C stable isotope probing and Raman-FISH for quantifying microbial activity at the single-cell level. To demonstrate the relevance of cryolite scaffolds for environmental field studies, we visualized their colonization by diverse microorganisms within rhizosphere sediments of a coastal seagrass plant using epifluorescence microscopy. The tool presented here enables highly resolved, spatially explicit, and multimodal investigations into the distribution, activities, and interactions of underground microbes typically obscured within opaque geological materials until now.}, }
@article {pmid40352477, year = {2025}, author = {Coltman, BL and Motheramgari, K and Tatto, N and Gasser, B}, title = {Identification and functional analysis of growth rate associated long non-coding RNAs in Komagataella phaffii.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {1693-1705}, pmid = {40352477}, issn = {2001-0370}, abstract = {Long non-coding RNAs (lncRNAs) are a regulatory feature that have been reported to operate on both transcriptional and translational levels. With DNA-based prediction still limited, lncRNAs are most reliably identified through genome-guided mapping of RNA-Seq data. Reports of lncRNAs in yeast have been increasing in recent years and changes in their expression levels have often been associated with stressful conditions. As the transition to near zero-growth conditions likely imposes stress, we used RNA-Seq data from the non-conventional, biotechnologically established yeast Komagataella phaffii, cultivated in glucose-limited retentostats, to identify the expression of lncRNAs. Using an adapted bioinformatics pipeline, we identified 168 mostly novel lncRNAs from the K. phaffii retentostat RNA-Seq data, 36 of which demonstrate likely growth-associated expression changes. lncRNA expression levels were associated to that of possible interaction partners, in both cis and trans, suggesting potential roles in regulatory adaptations. Our analysis indicates that lncRNAs likely contribute to how K. phaffii responds to changing environmental conditions, as exemplified here by the adaptation to extremely slow growth.}, }
@article {pmid40349898, year = {2025}, author = {Moghaddam, ZS and Dehghan, A and Halimi, S and Najafi, F and Nokhostin, A and Naeini, AE and Akbarzadeh, I and Ren, Q}, title = {Bacterial Extracellular Vesicles: Bridging Pathogen Biology and Therapeutic Innovation.}, journal = {Acta biomaterialia}, volume = {200}, number = {}, pages = {1-20}, doi = {10.1016/j.actbio.2025.05.028}, pmid = {40349898}, issn = {1878-7568}, mesh = {*Extracellular Vesicles/metabolism ; Humans ; *Bacteria/metabolism ; Animals ; Drug Delivery Systems ; *Host-Pathogen Interactions ; }, abstract = {The main role of bacterial extracellular vesicles (BEVs) has been associated with various processes such as intercellular communication and host-pathogen interactions. This comprehensive review explores the multifaceted functions of BEVs across different biological domains, emphasizing their dual nature as contributors to disease and potential vehicles for therapeutic intervention. We examine the intricate interactions of BEVs within bacterial communities and between bacteria and hosts, their involvement in disease development through cargo delivery mechanisms, and their beneficial impact on microbial ecology. The review also highlights BEVs' applications in biomedical field, where they are revolutionizing vaccine development, targeted drug delivery, and cancer therapy. By utilizing the inherent properties of BEVs for controlled drug release, targeted antigen delivery, and immune modulation, they offer a promising frontier in precision medicine. In addition, the diagnostic potential of BEVs is explored through their utility as biomarkers, providing valuable insights into disease states and treatment efficacy. Looking forward, this review underscores the challenges and opportunities in translating BEV research to clinical practice, promoting the need of standardized methods in BEV characterization and scaling up production. The diverse abilities of BEVs, ranging from contributing to pathogen virulence to driving therapeutic innovation, highlight their potential as a cornerstone in the future of biomedical advancements. STATEMENT OF SIGNIFICANCE: Bacterial extracellular vesicles (BEVs) are emerging as pivotal players in both pathogenesis and therapeutic innovation. This review explores their dual nature as agents of disease and as promising biomaterials for biomedical applications, and provides a comprehensive survey on their involvement in disease mechanisms and microbial ecology, and their potential in biomedical applications such as vaccine development, targeted drug delivery, cancer therapy, and diagnosis. It highlights the complex interactions of BEVs within bacterial communities and between bacteria and hosts. This review also addresses current advancements, challenges, and opportunities in translating BEV research into clinical practice. The insights presented here position BEVs as a cornerstone in the future of biomedical advancements, advocating for standardized methods in BEV characterization and scalable production techniques.}, }
@article {pmid40348966, year = {2025}, author = {Van Hee, S and Segurado Luchsinger, AE and Cusumano, A and Masschelein, J and Jacquemyn, H and Lievens, B}, title = {The plant-beneficial fungus Trichoderma harzianum T22 modulates plant metabolism and negatively affects Nezara viridula.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {615}, pmid = {40348966}, issn = {1471-2229}, support = {C24E/19/052//KU Leuven/ ; }, mesh = {*Hypocreales/physiology ; Animals ; Plant Leaves/metabolism/microbiology ; Herbivory ; Metabolome ; *Capsicum/microbiology/metabolism ; Plant Roots/microbiology/metabolism ; Plant Defense Against Herbivory ; }, abstract = {BACKGROUND: Plant-beneficial fungi play an important role in enhancing plant health and resistance against biotic and abiotic stresses. Although extensive research has focused on their role in eliciting plant defences against pathogens, their contribution to induced resistance against herbivorous insects and the underlying mechanisms remain poorly understood. In this study, we used insect bioassays and untargeted metabolomics to investigate the impact of root inoculation of sweet pepper with the plant-beneficial fungus Trichoderma harzianum T22 on direct defence responses against the insect herbivore Nezara viridula.<br><br>RESULTS: We observed reduced relative growth rate of N. viridula on leaves of fungus-inoculated plants, with no change in mortality. Untargeted metabolomic analyses revealed that inoculation with T. harzianum did not affect the leaf metabolome in the absence of herbivory five weeks after inoculation. However, compared to non-inoculated plants, inoculated plants exhibited significant metabolic alterations in herbivore-damaged leaves following N. viridula feeding, while changes in the metabolic profile of distant leaves were less pronounced. Notably, metabolites involved in the shikimate-phenylpropanoid pathway, known to be involved in plant defence responses, displayed higher accumulation in damaged leaves of inoculated plants compared to non-inoculated plants.<br><br>CONCLUSION: Our results indicate that root inoculation with T. harzianum T22 affects plant defences against N. viridula, leading to reduced insect performance. Metabolite-level effects were primarily observed in damaged leaves, suggesting that the priming effect mainly results in localized metabolite accumulation at the site of attack. Future research should focus on identifying the detected compounds and determining their role in impairing N. viridula performance.}, }
@article {pmid40347612, year = {2025}, author = {Rodríguez-Seijo, A and Pérez-Rodríguez, P and Arias-Estévez, M and Gómez-Armesto, A and Conde-Cid, M and Santás-Miguel, V and Campillo-Cora, C and Ollio, I and Lloret, E and Martínez-Martínez, S and Zornoza, R and Waeyenberge, L and Schrader, S and Brandt, KK and Loit, K and Põldmets, M and Shanskiy, M and Peltoniemi, K and Hagner, M and Calviño, DF}, title = {Occurrence, persistence and risk assessment of pesticide residues in European wheat fields: A continental scale approach.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138291}, doi = {10.1016/j.jhazmat.2025.138291}, pmid = {40347612}, issn = {1873-3336}, abstract = {Pesticide residues in agricultural soils represent an environmental concern that requires special attention due to their potential ecological and public health risks. We analyzed 614 pesticides in 188 wheat fields across Europe subjected to both conventional and organic farming systems. At least one pesticide residue was detected in 141 soils. Seventy-eight pesticides or their metabolites were detected. The presence of pesticides was significantly higher in both number and concentration in conventional fileds (up to 0.98 mg kg[-1]) compared to organically managed sites (up to 0.40 mg kg[-1]). A total of 88 % of conventional fields and 63 % of organic fields contained two or more pesticides. Conversion from conventional to organic farming does not guarantee that soils will be pesticide-free in the short term. Fenbutatin oxide was the most frequently detected pesticide in both farming systems, followed by AMPA. Other substances, such as boscalid, epoxiconazole, diflufenican, tebuconazole, dinoterb, bixafen, and DEET, were found in ≥ 10 % of samples. Some Persistent Organic Pollutants, including dieldrin, endosulfan sulphate, and chlorpyrifos, were also detected. Ecological risks were higher in conventionally managed fields, with 46 % exhibiting high-risk levels, compared to just 1 % in organic fields. Epoxiconazole and boscalid were the substances with the highest risk levels.}, }
@article {pmid40347236, year = {2025}, author = {Qi, W and Song, W and Qi, R and Li, Y and Yang, H and Li, Y and Chang, Z}, title = {Land Use Types Drive the Distinct Patterns of Bacterial and Fungal Communities in Soils from the Semi-arid Area.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {43}, pmid = {40347236}, issn = {1432-184X}, support = {2021-XBQNXZ-001//The West Light Foundation of Chinese Academy of Science/ ; DD20242544//The Ecological Protection and Restoration Support Survey Project of China Geological Survey/ ; }, mesh = {*Soil Microbiology ; China ; *Bacteria/classification/isolation &amp; purification/genetics ; *Fungi/classification/isolation &amp; purification/genetics ; Soil/chemistry ; Biodiversity ; Grassland ; Ecosystem ; Desert Climate ; Agriculture ; *Microbiota ; Farms ; Mycobiome ; }, abstract = {Land types and ways of utilization significantly influence soil microbial communities in arid and semi-arid regions, which are vital for nutrient cycling and ecosystem functionality. In this study, the soil bacterial and fungal communities of five land types, including natural grasslands, farmlands, artificial grasslands, uncultivated lands, and riverbeds in the semi-arid lower reaches of the Heihe River, China, were investigated. Farmlands exhibited the highest bacterial Chao1 richness and Shannon diversity, while uncultivated soils had the lowest bacterial Chao1 richness. Fungal diversity was highest in uncultivated soils compared to farmlands. Principal coordinate analysis (PCoA) showed distinct microbial community structures across land types, with Actinobacteria, Proteobacteria, Firmicutes, and Chloroflexi dominating bacterial communities, and Ascomycota and Basidiomycota dominating fungal communities. Life history strategies revealed distinct patterns between bacterial and fungal communities within farmland soils and artificial grassland soils. Microbial community assembly in natural grasslands was primarily deterministic, with limited stochastic influence, while farmlands exhibited mixed assembly processes. Co-occurrence network analysis showed more stable and cooperative microbial networks in natural grasslands, while farmland networks were more competitive and reliant on key species. These findings provide important insights into the role of land use in shaping microbial diversity and ecosystem function, offering guidance for sustainable land management in semi-arid oasis regions.}, }
@article {pmid40347194, year = {2025}, author = {Su, QY and Zhang, JT and Gao, HJ and Zhang, Y and Luo, J and Cao, TY and Yang, MY and Zhang, SX}, title = {Mechanism and clinical utility of abatacept in the treatment of rheumatoid arthritis.}, journal = {Expert opinion on drug safety}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/14740338.2025.2505542}, pmid = {40347194}, issn = {1744-764X}, abstract = {INTRODUCTION: Abatacept, a biological disease-modifying antirheumatic drug(bDMARD), has demonstrated unique and effective therapeutic properties for rheumatoid arthritis (RA).<br><br>AREAS COVERED: This review offers an in-depth examination of the mechanism by which abatacept exerts its effects in RA treatment and assesses its efficacy and safety based on a range of studies. We conducted a comprehensive search of PubMed, Embase databases, Web of Science, the Cochrane Library, MEDLINE, Wanfang Data, and CNKI from the time the databases were created until 30 July 2024.<br><br>EXPERT OPINION: By modulating the CD28 and CD80/CD86 costimulatory signaling pathways, abatacept is instrumental in regulating immune cells and cytokines implicated in the pathogenesis RA. Longitudinal studies have highlighted its capacity to mitigate disease advancement and maintain joint functionality. The most frequently reported adverse effects associated with abatacept are headache, nausea, and upper respiratory tract infections, which are typically self-resolving. The incidence of serious infections was not high, mainly various types of bacterial pneumonia. Comparative safety analyses of abatacept with other DMARDs yield encouraging results. As our understanding of the mechanism of action of abatacept improves, we may be able to better identify appropriate biologic therapies and advanced combination therapies for RA patients and ultimately improve patient outcomes.}, }
@article {pmid40346393, year = {2025}, author = {Leiter, N and Wohlschläger, M and Versen, M and Harter, SD and Kießlich, T and Lederer, F and Clauß, S and Schlosser, D and Armanu, EG and Eberlein, C and Heipieper, HJ and Löder, MGJ and Laforsch, C}, title = {Effects of defined organic layers on the fluorescence lifetime of plastic materials.}, journal = {Analytical and bioanalytical chemistry}, volume = {}, number = {}, pages = {}, pmid = {40346393}, issn = {1618-2650}, support = {FKZ 031B0828A//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 391977956 - SFB 1357//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Plastics have become an integral part of modern life, and linked to that fact, the demand for and global production of plastics are still increasing. However, the environmental pollution caused by plastics has reached unprecedented levels. The accumulation of small plastic fragments-microplastics and nanoplastics-potentially threatens organisms, ecosystems, and human health. Researchers commonly employ non-destructive analytical methods to assess the presence and characteristics of microplastic particles in environmental samples. However, these techniques require extensive sample preparation, which represents a significant limitation and hinders a direct on-site analysis. In this context, previous investigations showed the potential of fluorescence lifetime imaging microscopy (FLIM) for fast and reliable identification of microplastics in an environmental matrix. However, since microplastics receive an environmental coating after entering nature, a challenge arises from organic contamination on the surface of microplastic particles. How this influences the fluorescence signal and the possibility of microplastic detection are unknown. To address this research gap, we exposed acrylonitrile butadiene styrene (ABS) and polyethylene terephthalate (PET) plastic samples to peptides, proteins, bacteria, and a filamentous fungus to induce organic contamination and mimic environmental conditions. We analyzed the fluorescence spectra and lifetimes of the samples using fluorescence spectroscopy and frequency-domain fluorescence lifetime imaging microscopy (FD-FLIM), respectively. Our results demonstrate that reliably identifying and differentiating ABS and PET was possible via FD-FLIM, even in the presence of these biological contaminations. These findings highlight the potential of this technique as a valuable tool for environmental monitoring and plastic characterization, offering a rapid and efficient alternative to currently used analytical methods.}, }
@article {pmid40345255, year = {2025}, author = {Feng, J and Zhang, C and Bao, J and Xu, Q and Gan, Y and Hu, Y}, title = {A modified variable flip angle release device for endoscopic titanium clips.}, journal = {Endoscopy}, volume = {57}, number = {S 01}, pages = {E396-E397}, pmid = {40345255}, issn = {1438-8812}, support = {2024GZL-CX58//Xiamen High-quality Development Medical Innovation Fund/ ; }, }
@article {pmid40343125, year = {2025}, author = {Tóth, VR}, title = {The impact of epiphytic algae on the foliar traits of Potamogeton perfoliatus.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1561709}, pmid = {40343125}, issn = {1664-462X}, abstract = {This study investigated the effect of epiphyton on foliar traits of a submerged rooted macrophyte, Potamogeton perfoliatus, in a shallow freshwater lake, highlighting its influence on the ecological dynamics of littoral zones in aquatic ecosystems. It was shown that the limnological characteristics of the sampling sites (water chlorophyll-a, total suspended matter and coloured dissolved organic matter content) had no significant effect on the average values of epiphytic algal content found on pondweed leaves, while influencing the plasticity of these data. The responses of morphological and physiological traits of submerged macrophytes to accumulated epiphyton demonstrate the complexity of their relationship: epiphyton colonisation had no relevant effect on leaf morphology (except leaf length) and leaf pigment content (except Chl-a/Chl-b ratio), however, this study highlights the significant influence of epiphytic algal biomass on photophysiological traits of submerged macrophyte leaves, as 5 out of 6 photophysiological traits were affected. The results highlight the importance of considering epiphyte colonisation when seeking to understand the ecological functioning of littoral aquatic ecosystems. Furthermore, the complex interactions between epiphytes and submerged rooted macrophytes should be considered in integrated lake management and environmental protection policies. These interactions play an important, though ambiguous role in shaping habitat variability and overall ecosystem health in littoral zones.}, }
@article {pmid40341906, year = {2025}, author = {Shoemaker, WR and Sánchez, &#xc1; and Grilli, J}, title = {Macroecological patterns in experimental microbial communities.}, journal = {PLoS computational biology}, volume = {21}, number = {5}, pages = {e1013044}, pmid = {40341906}, issn = {1553-7358}, mesh = {*Models, Biological ; *Ecology/methods ; Biodiversity ; Ecosystem ; *Microbiota/physiology ; Computational Biology ; }, abstract = {Ecology has historically benefited from the characterization of statistical patterns of biodiversity within and across communities, an approach known as macroecology. Within microbial ecology, macroecological approaches have identified universal patterns of diversity and abundance that can be captured by effective models. Experimentation has simultaneously played a crucial role, as the advent of high-replication community time-series has allowed researchers to investigate underlying ecological forces. However, there remains a gap between experiments performed in the laboratory and macroecological patterns documented in natural systems, as we do not know whether these patterns can be recapitulated in the lab and whether experimental manipulations produce macroecological effects. This work aims at bridging the gap between experimental ecology and macroecology. Using high-replication time-series, we demonstrate that microbial macroecological patterns observed in nature exist in a laboratory setting, despite controlled conditions, and can be unified under the Stochastic Logistic Model of growth (SLM). We found that demographic manipulations (e.g., migration) impact observed macroecological patterns. By modifying the SLM to incorporate said manipulations alongside experimental details (e.g., sampling), we obtain predictions that are consistent with macroecological outcomes. By combining high-replication experiments with ecological models, microbial macroecology can be viewed as a predictive discipline.}, }
@article {pmid40338317, year = {2025}, author = {Graziosi, S and Deloche, L and Januario, M and Selosse, MA and Deveau, A and Bach, C and Chen, Z and Murat, C and Iotti, M and Rech, P and Zambonelli, A}, title = {Newly Designed Fluorescence In Situ Hybridization Probes Reveal Previously Unknown Endophytic Abilities of Tuber magnatum in Herbaceous Plants.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {42}, pmid = {40338317}, issn = {1432-184X}, support = {K272X8 - CUP J53D23010090006//European Union - NextGenerationEU under the National Recovery and Resilience Plan (PNRR) - Mission 4 Education and research - Component 2 From research to business - Investment 1.1 Notice Prin 2022 - DD N. 104 del 2/2/2022, from title "Interactions of the white truffle Tuber magnatum with soil microbiome and plants"/ ; K272X8 - CUP J53D23010090006//European Union - NextGenerationEU under the National Recovery and Resilience Plan (PNRR) - Mission 4 Education and research - Component 2 From research to business - Investment 1.1 Notice Prin 2022 - DD N. 104 del 2/2/2022, from title "Interactions of the white truffle Tuber magnatum with soil microbiome and plants"/ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; }, mesh = {*Endophytes/genetics/isolation &amp; purification/physiology ; *In Situ Hybridization, Fluorescence/methods ; Plant Roots/microbiology ; *Mycorrhizae/genetics/isolation &amp; purification/physiology ; *Ascomycota/genetics/isolation &amp; purification/physiology ; Symbiosis ; Italy ; Polymerase Chain Reaction ; Hyphae/genetics ; }, abstract = {Tuber magnatum Picco (the Italian white truffle) is the most valuable and widely appreciated truffle. It is an ectomycorrhizal fungus known to associate with many broadleaf tree species. However, its mycorrhizae are rarely observed in the field, suggesting possible alternative symbiotic strategies, such as endophytism with non-ectomycorrhizal plants. In order to test potential endophytic interactions of T. magnatum with wild plants, a combination of polymerase chain reaction (PCR) and Fluorescence In Situ Hybridization (FISH) approaches were used. Specific FISH probes for T. magnatum were designed, tested in vitro on hyphae and/or ectomycorrhizae, and selected for their specificity. These probes were then used on a wide variety root samples of wild plants collected from three T. magnatum production areas in Italy and previously tested for the presence of T. magnatum mycelium using PCR-specific primers. Molecular analyses detected the presence of T. magnatum in 21 of 100 plant samples analyzed. FISH analysis confirmed the extracellular presence of active T. magnatum hyphae inside the root system of Carex pendula Huds plant. This study provides the first evidence of T. magnatum acting as an endophyte in an herbaceous plant. The newly designed, highly specific T. magnatum FISH probes can be used for further investigations to confirm the endophytic tendencies of T. magnatum and to understand their influence on the life cycle and biology of this fungus.}, }
@article {pmid40336837, year = {2025}, author = {Couch, CE and Xavier, R and Beechler, BR}, title = {Editorial: Parasite, host, and microbiome interactions in natural host systems.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1589627}, doi = {10.3389/fmicb.2025.1589627}, pmid = {40336837}, issn = {1664-302X}, }
@article {pmid40335733, year = {2025}, author = {Guo, Y and Tian, L and Zhu, X and Liu, S and Wang, L and Li, W}, title = {Antagonism of Bacillus velezensis ZGE166 Against the Pathogenic Fungi Causing Corm Rot Disease in Saffron (Crocus sativus L.).}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {40}, pmid = {40335733}, issn = {1432-184X}, mesh = {*Bacillus/physiology/genetics/isolation &amp; purification ; *Crocus/microbiology/growth &amp; development ; Rhizosphere ; *Plant Diseases/microbiology/prevention &amp; control ; Soil Microbiology ; *Antibiosis ; *Fungi/physiology ; Genome, Bacterial ; Phylogeny ; }, abstract = {Saffron can be infected with pathogenic fungi that cause corm rot as it grows and multiplies, which can reduce the quality and yield of saffron. Corm rot has become one of the most serious diseases of saffron. In this study, rhizosphere bacteria were isolated from saffron rhizosphere soil, and bacteria exhibiting antagonistic effects against corm rot pathogenic fungi were screened using in vitro plate co-culture assays and dual-compartment agar plate systems. Selected strains were further evaluated for hydrolase activity determination and PGP potential assessment. Among them, Bacillus velezensis showed the best disease resistance activity. The degradative enzyme production and some beneficial characteristics of Bacillus velezensis for plant growth promotion were evaluated. It was found that Bacillus velezensis possesses nitrogen fixing, NH3-producing, IAA production, and ACC-deaminating enzymes. The whole genome sequence of this strain was annotated and analyzed. The genome of Bacillus velezensis consists of a circular chromosome of 3,908,025 bp base pairs, with a guanine and cytosine content of 46.64%. There are 3737 protein-coding genes, including 86 tRNA genes, 27 rRNA genes, and 85 sRNA genes. The genome also contains four genomic islands, two pre-phages, and one transposon. The prediction of the secondary metabolic accumulation gene cluster demonstrated that the genome sequence of ZGE166 encodes 12 gene clusters involved in the synthesis of secondary metabolites, including macrolactin H, bacillaene, fengycin, difficidin, and bacillibactin. In summary, strain ZGE166 Bacillus velezensis has the potential to be developed as a biological agent.}, }
@article {pmid40335388, year = {2025}, author = {Dwivedi, SL and Vetukuri, RR and Kelbessa, BG and Gepts, P and Heslop-Harrison, P and Araujo, ASF and Sharma, S and Ortiz, R}, title = {Exploitation of rhizosphere microbiome biodiversity in plant breeding.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.04.004}, pmid = {40335388}, issn = {1878-4372}, abstract = {Climate change-induced stresses are perceived by plants at the root-soil interface, where they are alleviated through interactions between the host plant and the rhizosphere microbiome. The recruitment of specific microbiomes helps mitigate stress, increases resistance to pathogens, and promotes plant growth, development, and reproduction. The structure of the rhizosphere microbiome is shaped by crop domestication and variations in ploidy levels. Here we list key genes that regulate rhizosphere microbiomes and host genetic traits. We also discuss the prospects for rigorous analysis of symbiotic interactions, research needs, and strategies for systematically utilizing microbe-crop interactions to improve crop performance. Finally, we highlight challenges of maintaining live rhizosphere microbiome collections and mining heritable variability to enhance interactions between host plants and their rhizosphere microbiomes.}, }
@article {pmid40334664, year = {2025}, author = {Sandin, MM and Renaudie, J and Suzuki, N and Not, F}, title = {Extant diversity, biogeography, and evolutionary history of Radiolaria.}, journal = {Current biology : CB}, volume = {35}, number = {11}, pages = {2524-2538.e6}, doi = {10.1016/j.cub.2025.04.032}, pmid = {40334664}, issn = {1879-0445}, mesh = {*Biological Evolution ; *Biodiversity ; *Fossils ; Phylogeny ; *Plankton/classification/physiology/genetics ; Phylogeography ; }, abstract = {Since Ernst Haeckel and the Challenger expedition (1872-1876), Radiolaria have been known as ubiquitous and abundant star-shaped oceanic plankton. Their exquisite biomineralized skeletons left an extensive fossil record extremely valuable for biostratigraphic and paleo-environmental research. In contemporary oceans, there is growing evidence that Radiolaria are significant contributors to marine food webs and global biogeochemical cycles. Here we provide a comprehensive morpho-molecular framework to assess the extant diversity, biogeography, and evolutionary history of Radiolaria. Our analyses reveal that half of radiolarian diversity is morphologically undescribed, with a large part forming three hyper-diverse environmental clades, named Rad-A, Rad-B, and Rad-C. We suggest that most of this undescribed diversity comprises skeleton-less life forms or endosymbionts, explaining their elusive, yet abundant, nature. Phylogenetic analyses highlight the need for a major revision of high-level Radiolaria taxonomy, including placement of Collodaria within the order Nassellaria. Global metabarcoding surveys show that Radiolaria contributes more than 12% to the total eukaryotic community, displaying distinct biogeographic patterns with the skeleton-less lineages at depth and photosymbiont-bearing lineages in the surface. Fossil calibration of a molecular clock revealed the first appearance of Radiolaria ∼760 million years ago (mya), the development of the skeleton in the early Paleozoic (∼500 mya), and the onset of photosymbiotic relationships during the mid to late Mesozoic (∼140 mya), related to geological periods of oligotrophy and anoxia. The results presented here provide a robust framework for developing new perspectives on early eukaryotic diversification, paleo-environmental impacts on plankton evolution, and marine microbial ecology in rapidly evolving ecosystems.}, }
@article {pmid40333193, year = {2025}, author = {Hodžić, A and Kunert, M and Berry, D}, title = {Protocol for the visualization of bacteria in the tick gut using whole-mount fluorescence in situ hybridization.}, journal = {STAR protocols}, volume = {6}, number = {2}, pages = {103814}, pmid = {40333193}, issn = {2666-1667}, mesh = {*In Situ Hybridization, Fluorescence/methods ; Animals ; *Bacteria/isolation &amp; purification/genetics ; *Ticks/microbiology ; *Gastrointestinal Tract/microbiology ; }, abstract = {The tick gut harbors a relatively diverse microbial community that includes commensal, beneficial, and pathogenic bacterial species. Here, we present a protocol for the visualization of bacteria in the tick gut using whole-mount fluorescence in situ hybridization. We describe steps for tick dissection, tissue fixation, hybridization, washing, and mounting. We then detail procedures for microscopy imaging of the whole-mounted samples. Although the procedure is designed for gut tissue samples, it can be readily modified for use with other tissue types. For complete details on the use and execution of this protocol, please refer to Hodžić et al.[1].}, }
@article {pmid40333163, year = {2025}, author = {Touati, A and Ibrahim, NA and Idres, T}, title = {Disarming Staphylococcus aureus: Review of Strategies Combating This Resilient Pathogen by Targeting Its Virulence.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {40333163}, issn = {2076-0817}, support = {IMSIU-DDRSP2501//The Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; }, mesh = {Humans ; *Staphylococcal Infections/microbiology/drug therapy ; Virulence/drug effects ; *Staphylococcus aureus/drug effects/pathogenicity/physiology ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Biofilms/drug effects/growth &amp; development ; *Virulence Factors/antagonists &amp; inhibitors/metabolism ; Quorum Sensing/drug effects ; Methicillin-Resistant Staphylococcus aureus/drug effects/pathogenicity ; Animals ; }, abstract = {Staphylococcus aureus is a formidable pathogen notorious for its antibiotic resistance and diverse virulence mechanisms, including toxin production, biofilm formation, and immune evasion. This article explores innovative anti-virulence strategies to disarm S. aureus by targeting critical virulence factors without exerting bactericidal pressure. Key approaches include inhibiting adhesion and biofilm formation, neutralizing toxins, disrupting quorum sensing (e.g., Agr system inhibitors), and blocking iron acquisition pathways. Additionally, interventions targeting two-component regulatory systems are highlighted. While promising, challenges such as strain variability, biofilm resilience, pharmacokinetic limitations, and resistance evolution underscore the need for combination therapies and advanced formulations. Integrating anti-virulence strategies with traditional antibiotics and host-directed therapies offers a sustainable solution to combat multidrug-resistant S. aureus, particularly methicillin-resistant strains (MRSA), and mitigate the global public health crisis.}, }
@article {pmid40333144, year = {2025}, author = {Plewa-Tutaj, K and Chmielewska, Z and Twarużek, M and Kosicki, R and Soszczyńska, E}, title = {An Analysis of the Mycotoxins, Cytotoxicity, and Biodiversity of Airborne Molds Belonging to Aspergillus Genera Isolated from the Zoological Garden.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {40333144}, issn = {2076-0817}, support = {"MINIATURA 6," grant 2022/06/X/NZ8/00430//National Science Centre, Poland/ ; }, mesh = {*Mycotoxins/toxicity/analysis ; *Aspergillus/isolation &amp; purification/classification/genetics/metabolism ; *Air Microbiology ; *Biodiversity ; Animals ; Humans ; }, abstract = {The present study aimed to identify airborne molds of the Aspergillus genus and to determine the secondary metabolite profiles and toxicity of dominant fungal species isolated from various locations in the Wroclaw Zoological Garden. Air samples were collected using a MAS-100 air sampler and analyzed for fungal colony-forming units (CFU). Morphological and molecular methods, including ITS sequencing, were employed for dominant mold identification. The most frequently encountered species were A. fumigatus and A. niger, while A. pseudoglaucus and A. nomius were the least common. The high prevalence of species from sections Nigri, Flavi, and Fumigati suggests their adaptability to the zoo environment. A total of 17 Aspergillus isolates were analyzed for both their capacity to induce cellular toxicity and their production of mycotoxins. The results indicated that all isolates exhibited cellular toxicity, with 70.6% displaying levels of toxicity that were medium to high. Furthermore, the mycotoxicological analysis revealed that only A. fumigatus strains were capable of producing mycotoxins, specifically gliotoxin. The study underscores the discrepancy between the levels of toxicity and the production of mycotoxins, thereby suggesting the presence of additional cytotoxic metabolites. These findings emphasize the need for a comprehensive understanding of the complex interplay between fungal metabolites and their consequences for human health.}, }
@article {pmid40333133, year = {2025}, author = {Niculescu, AG and Mitache, MM and Grumezescu, AM and Chifiriuc, MC and Mihai, MM and Tantu, MM and Tantu, AC and Popa, LG and Grigore, GA and Cristian, RE and Popa, MI and Vrancianu, CO}, title = {From Microbial Ecology to Clinical Challenges: The Respiratory Microbiome's Role in Antibiotic Resistance.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {40333133}, issn = {2076-0817}, support = {CNFIS-FDI-2024-F-0484 INOVEX//University of Bucharest/ ; Pillar III, Component C9/Investment no. 8 (I8) - contract CF 68//; Ministry of Research, Innovation and Digitalization through the National Recovery and Resilience Plan (PNRR) of Romania/ ; project no. 23020101, Contract no. 7N from 3 January 2023//The core program within the National Research Development and Innovation Plan, 2022-2027', carried out with the support of the Ministry of Research, Innovation and Digitalization (MCID)/ ; }, mesh = {Humans ; *Microbiota/drug effects ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Respiratory Tract Infections/microbiology/drug therapy ; *Drug Resistance, Microbial ; Probiotics ; *Drug Resistance, Bacterial ; *Respiratory System/microbiology ; }, abstract = {Antibiotic resistance represents a growing public health threat, with airborne drug-resistant strains being especially alarming due to their ease of transmission and association with severe respiratory infections. The respiratory microbiome plays a pivotal role in maintaining respiratory health, influencing the dynamics of antibiotic resistance among airborne pathogenic microorganisms. In this context, this review proposes the exploration of the complex interplay between the respiratory microbiota and antimicrobial resistance, highlighting the implications of microbiome diversity in health and disease. Moreover, strategies to mitigate antibiotic resistance, including stewardship programs, alternatives to traditional antibiotics, probiotics, microbiota restoration techniques, and nanotechnology-based therapeutic interventions, are critically presented, setting an updated framework of current management options. Therefore, through a better understanding of respiratory microbiome roles in antibiotic resistance, alongside emerging therapeutic strategies, this paper aims to shed light on how the global health challenges posed by multi-drug-resistant pathogens can be addressed.}, }
@article {pmid40332344, year = {2025}, author = {Figueiredo, JEF and Marins, MS and Silva, FC and Ribeiro, VP and Diniz, GdFD and Rodrigues, VA and Oliveira-Paiva, CA and Lana, UGdP and Ferreira, LVS and Sousa Tinoco, SMd and Cruz-Magalhães, V}, title = {Draft genome of the endophytic Bacillus velezensis CNPMS-22 isolated from maize leaves.}, journal = {Microbiology resource announcements}, volume = {14}, number = {6}, pages = {e0127924}, pmid = {40332344}, issn = {2576-098X}, abstract = {Bacillus velezensis has been widely used as a biocontrol agent and plant growth promoter in agricultural bio-inputs. The genome of the endophytic bacterial strain CNPMS-22 isolated from maize leaves was sequenced, and the results showed that the strain is a Bacillus velezensis species.}, }
@article {pmid40329925, year = {2025}, author = {Razzaq Meo, S and Van de Wiele, T and Defoirdt, T}, title = {Indole signaling in Escherichia coli: a target for antivirulence therapy?.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2499573}, pmid = {40329925}, issn = {1949-0984}, mesh = {*Indoles/metabolism/pharmacology ; *Escherichia coli/drug effects/metabolism/pathogenicity/genetics ; Humans ; *Signal Transduction/drug effects ; *Escherichia coli Infections/microbiology/drug therapy ; Virulence/drug effects ; Quorum Sensing/drug effects ; *Anti-Bacterial Agents/pharmacology ; Virulence Factors/metabolism/genetics/antagonists &amp; inhibitors ; Animals ; Escherichia coli Proteins/metabolism/genetics ; Biofilms/drug effects/growth &amp; development ; }, abstract = {Pathogenic Escherichia coli are a major cause of infections in both humans and animals, leading to conditions such as severe diarrheal diseases, urinary tract infections, enteritis, and septicemia. To combat bacterial infections, antibiotics are widely utilized. However, the extensive and inappropriate use of antibiotics has fueled the development and spread of antibiotic resistance, posing a significant challenge to the effective treatment of E. coli. There is consequently an urgent need to explore alternative therapies to control such infections. This review provides an overview of the recent findings concerning indole signaling in E. coli. E. coli uses indole as a quorum sensing molecule, and indole signaling has been reported to decrease various virulence factors in pathogenic E. coli, including motility, biofilm formation, adherence to host cells, expression of the LEE pathogenicity island, and formation of attaching and effacing lesions. This makes indole signaling an interesting target for the development of new therapeutics in the framework of antivirulence therapy. Both natural and synthetic indole analogues have been explored as potential virulence inhibitors. This alternative approach could be advantageous, as it will exert less selective pressure for resistance development than conventional antibiotics.}, }
@article {pmid40329550, year = {2025}, author = {Jenkins, GB and Boyd, ES and Danchin, A and Hervé, V and Huggett, MJ and Sánchez, &#xc1; and Trevorrow, P}, title = {Environmental Microbiology and Environmental Microbiology Reports: Two Journals, One Goal.}, journal = {Environmental microbiology}, volume = {27}, number = {5}, pages = {e70078}, doi = {10.1111/1462-2920.70078}, pmid = {40329550}, issn = {1462-2920}, }
@article {pmid40329526, year = {2025}, author = {Ory, F and Dainat, B and Würgler, O and Wenger, F and Roetschi, A and Braillard, L and Charrière, JD and Dietemann, V}, title = {Ecology and Pathogenicity for Honey Bee Brood of Recently Described Paenibacillus melissococcoides and Comparison With Paenibacillus dendritiformis, Paenibacillus thiaminolyticus.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70089}, pmid = {40329526}, issn = {1758-2229}, mesh = {Bees/microbiology ; Animals ; *Paenibacillus/pathogenicity/genetics/isolation &amp; purification/classification ; Virulence ; Spores, Bacterial ; Paenibacillus larvae ; Phylogeny ; Larva/microbiology ; }, abstract = {Honey bee colonies contain thousands of individuals living in close proximity in a thermally homeostatic nest, creating ideal conditions for the thriving of numerous pathogens. Among the bacterial pathogens, Paenibacillus larvae infects larvae via the nutritive jelly that adult workers feed them, causing the highly contagious American foulbrood disease. Further Paenibacillus species were anecdotally found in association with honey bees, including when affected by another disease, European foulbrood (EFB). However, their pathogenicity remains largely unknown. Our results indicate that Paenibacillus dendritiformis, Paenibacillus thiaminolyticus and newly described Paenibacillus melissococcoides are pathogenic towards honey bee brood and that their virulence correlates with their sporulation ability, which confers them resistance to the bactericidal properties of the nutritive jelly. Our survey occasionally but increasingly detected P. melissococcoides in confirmed and idiopathic cases of EFB but never in healthy colonies, suggesting that this bacterium is an emerging pathogen of honey bee brood. Overall, our results suggest that virulence traits allowing a pathogenic or opportunistically pathogenic habit towards honey bee brood are frequent in Paenibacillus spp., but that their degree of adaptation to this host varies. Our study clarifies the ecology of this ubiquitous genus, especially when infecting honey bees.}, }
@article {pmid40327698, year = {2025}, author = {Clegg, T and Gross, T}, title = {Cross-feeding creates tipping points in microbiome diversity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {19}, pages = {e2425603122}, pmid = {40327698}, issn = {1091-6490}, mesh = {*Microbiota/physiology ; *Biodiversity ; *Models, Biological ; }, abstract = {A key unresolved question in microbial ecology is how the extraordinary diversity of microbiomes emerges from the interactions among their many functionally distinct populations. This process is driven in part by the cross-feeding networks that help to structure these systems, in which consumers use resources to fuel their metabolism, creating by-products which can be used by others in the community. Understanding the effects of cross-feeding presents a major challenge, as it creates complex interdependencies between populations which can be hard to untangle. We address this problem using the tools of network science to develop a structural microbial community model. Using methods from percolation theory, we identify feasible community states for cross-feeding network structures in which the needs of consumers are met by metabolite production across the community. We identify tipping points at which small changes in structure can cause the catastrophic collapse of cross-feeding networks and abrupt declines in microbial community diversity. Our results are an example of a well-defined tipping point in a complex ecological system and provide insight into the fundamental processes shaping microbiomes and their robustness. We further demonstrate this by considering how network attacks affect community diversity and apply our results to show how the apparent difficulty in culturing the microbial diversity emerges as an inherent property of their cross-feeding networks.}, }
@article {pmid40327084, year = {2025}, author = {Zhang, M and Hu, Y and Ma, Y and Hou, T and Wang, J and Che, Q and Chen, B and Wang, Q and Feng, G}, title = {Soil Bacterial Diversity and Community Structure of Cotton Rhizosphere under Mulched Drip-Irrigation in Arid and Semi-arid Regions of Northwest China.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {39}, pmid = {40327084}, issn = {1432-184X}, mesh = {*Gossypium/microbiology/growth &amp; development ; *Rhizosphere ; *Soil Microbiology ; China ; *Bacteria/classification/genetics/isolation &amp; purification ; Soil/chemistry ; *Agricultural Irrigation/methods ; Biodiversity ; Desert Climate ; Microbiota ; Alkaline Phosphatase/genetics ; }, abstract = {Xinjiang is situated in an arid and semi-arid region, where abundant heat and sunlight create highly favorable conditions for cotton cultivation. Xinjiang's cotton output accounts for nearly one-quarter of global production. Moreover, the implementation of advanced planting techniques, such as 'dwarfing, high-density, early-maturing' strategies combined with mulched drip irrigation, ensures stable and high yields in this region. Despite these advancements, limited research has focused on the microbial mechanisms in cotton fields employing these advanced planting methods. In this study, high-throughput sequencing technology was utilized to investigate the diversity and composition of bacterial and phoD (Alkaline phosphatases encoding gene) communities in the rhizosphere of cotton grown under different yield levels in Xinjiang Province, China. The Mantel test, redundancy analysis (RDA) and partial least squares path modeling (PLS-PM) were employed to explore the interactions between soil bacterial and phoD communities, their network structures, and environmental factors. The bacterial and phoD communities in the cotton rhizosphere were predominantly composed of nine bacterial phyla (i.e., Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, Bacteroidetes, Rokubacteria, Firmicutes, and Nitrospirae) and five phoD phyla (i.e., Proteobacteria, Actinobacteria, Planctomycetes, Acidobacteria, and Firmicutes), respectively. Alpha diversity analysis indicated that the medium yield cotton field (MYF) exhibited higher bacterial richness and diversity indices compared to low yield (LYF) and high yield (HYF) fields. The symbiotic network analysis of LYF revealed greater values of average degree, number of edges, and modularity, suggesting a more complex network structure in both bacterial and phoD communities. The Mantel test, RDA, and PLS-PM model identified soil pH, electrical conductivity (EC), organic phosphorus (OP), available phosphorus (AP), total nitrogen (TN), microbial biomass carbon (MBC), and clay content as the main driving factors influencing changes in the rhizosphere bacterial community diversity and network structure. These findings provide a theoretical basis for future research aimed at improving soil quality and cotton yield.}, }
@article {pmid40324073, year = {2025}, author = {Hoffman, PF}, title = {Ecosystem relocation on Snowball Earth: Polar-alpine ancestry of the extant surface biosphere?.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {20}, pages = {e2414059122}, pmid = {40324073}, issn = {1091-6490}, support = {EAR-0417422//NSF (NSF)/ ; }, mesh = {*Ecosystem ; Earth, Planet ; Oceans and Seas ; Ice Cover ; Fossils ; Biological Evolution ; }, abstract = {Geological observations informed by climate dynamics imply that the oceans were 99.9% covered by light-blocking ice shelves during two discrete, self-reversing Snowball Earth epochs spanning a combined 60 to 70 Myr of the Cryogenian Period (720 to 635 Ma). The timescale for initial ice advances across the tropical oceans is ~300 y in an ice-atmosphere-ocean general circulation model in Cryogenian paleogeography. Areas of optically thin oceanic ice are usually invoked to account for fossil marine phototrophs, including macroscopic multicellular eukaryotes, before and after each Snowball, but different taxa. Ecosystem relocation is a scenario that does not require thin marine ice. Assume that long before Cryogenian Snowballs, diverse supra- and periglacial biomes were established in polar-alpine regions. When the Snowball onsets occurred, those biomes migrated in step with their ice margins to the equatorial zone of net sublimation. There, they prospered and evolved, their habitat areas expanded, and the cruelty of winter reduced. Nutrients were supplied by dust (loess) derived from cozonal ablative lands where surface winds were strong. When each Snowball finally ended, those biomes were mostly inundated by the meltwater-dominated and rapidly warming lid of a nutrient-rich but depauperate ocean. Some taxa returned to the mountaintops while others restocked the oceans. This ecosystem relocation scenario makes testable predictions. The lineages required for post-Cryogenian biotic radiations should be present in modern polar-alpine biomes. Legacies of polar-alpine ancestry should be found in the genomes of living organisms. Examples of such tests are highlighted herein.}, }
@article {pmid40323108, year = {2025}, author = {Oz, A and Mairesse, O and Raikin, S and Hanani, H and Mor, H and Dafny Yelin, M and Sharon, I}, title = {Pear flower and leaf microbiome dynamics during the naturally occurring spread of Erwinia amylovora.}, journal = {mSphere}, volume = {10}, number = {5}, pages = {e0001125}, pmid = {40323108}, issn = {2379-5042}, support = {Accelerator project//The JCA Foundation/ ; }, mesh = {*Erwinia amylovora/genetics ; *Pyrus/microbiology ; *Flowers/microbiology ; *Microbiota ; *Plant Diseases/microbiology ; *Plant Leaves/microbiology ; Bacteria/classification/genetics ; }, abstract = {Erwinia amylovora is the causal pathogen of fire blight, a contagious disease that affects apple and pear trees and other members of the family Rosaceae. In this study, we investigated the community dynamics of the pear flower microbiome in an agricultural setting during the naturally occurring infection of E. amylovora. Five potential factors were considered: collection date, the flower's phenological stage, location on the tree, location within the orchard, and pear cultivar. The phenological stage and the collection date were identified as the most important factors associated with pear flower microbiome composition, while the location of the tree in the orchard and the flower's location on the tree had a marginal effect. The leaf microbiome reflected that of the abundant phenological stage on each date. The flower microbiome shifted toward E. amylovora dominating the community as time and phenological stages progressed, leading to a decreased community diversity. The E. amylovora population was represented almost exclusively by six amplicon sequence variants (ASVs) with similar proportions throughout the entire collection period. Other taxa, including Pseudomonas, Pantoea, Lactobacillus, and Sphingomonas, were represented by dozens of ASVs, and different succession patterns in their populations were observed. Some of the taxa identified include known antagonists to E. amylovora. Overall, our results suggest that flower physiology and the interaction with the environment are strongly associated with the pear flower microbiome and should be considered separately. Taxon-specific succession patterns under E. amylovora spread should be considered when choosing candidates for antagonist-based treatments for fire blight.IMPORTANCEThe spread of pathogens in plants is an important ecological phenomenon and has a significant economic impact on agriculture. Flowers serve as the entry point for E. amylovora, but members of the flower microbiome can inhibit or slow down the proliferation and penetration of the pathogen. Knowledge about leaf and flower microbiome response to the naturally occurring spread of E. amylovora is still lacking. The current study is the first to describe the Rosaceae flower microbiome dynamics during the naturally occurring infection of E. amylovora. Unlike previous studies, the study design enabled us to evaluate the contribution of five important environmental parameters to community composition. We identified different ASV succession patterns across different taxa in the flower consortia throughout the season. These results contribute to our understanding of plant microbial ecology during pathogen spread and can help improve biological treatments for fire blight.}, }
@article {pmid40322584, year = {2025}, author = {Zschaubitz, E and Schröder, H and Glackin, CC and Vogel, L and Labrenz, M and Sperlea, T}, title = {A benchmark analysis of feature selection and machine learning methods for environmental metabarcoding datasets.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {1636-1647}, pmid = {40322584}, issn = {2001-0370}, abstract = {Next-Generation Sequencing methods like DNA metabarcoding enable the generation of large community composition datasets and have grown instrumental in many branches of ecology in recent years. However, the sparsity, compositionality, and high dimensionality of metabarcoding datasets pose challenges in data analysis. In theory, feature selection methods improve the analyzability of eDNA metabarcoding datasets by identifying a subset of informative taxa that are relevant for a certain task and discarding those that are redundant or irrelevant. However, general guidelines on selecting a feature selection method for application to a given setting are lacking. Here, we report a comparison of feature selection methods in a supervised machine learning setup across 13 environmental metabarcoding datasets with differing characteristics. We evaluate workflows that consist of data preprocessing, feature selection and a machine learning model by their ability to capture the ecological relationship between the microbial community composition and environmental parameters. Our results demonstrate that, while the optimal feature selection approach depends on dataset characteristics, feature selection is more likely to impair model performance than to improve it for tree ensemble models like Random Forests. Furthermore, our results show that calculating relative counts impairs model performance, which suggests that novel methods to combat the compositionality of metabarcoding data are required.}, }
@article {pmid40322503, year = {2025}, author = {Mandal, A and Ghosh, A and Kumar, G and Bhadury, P}, title = {Dataset of benthic foraminiferal community structure from sediment eDNA of Sundarbans mangrove ecosystem.}, journal = {Data in brief}, volume = {60}, number = {}, pages = {111554}, pmid = {40322503}, issn = {2352-3409}, abstract = {Sundarbans, the world's largest contiguous mangrove wetland, a UNESCO World Heritage Site and a RAMSAR site formed on the delta of Ganga-Brahmaputra-Meghna (GBM) and influenced by coastal water entering from the Bay of Bengal contribute immensely to biodiversity and blue economy. To track the changes driven by natural and anthropogenic stressors, sediment based environmental DNA (eDNA) biomonitoring of benthic foraminifera communities, an important biological group sensitive to changes, has been initiated along with estimation of dissolved nutrients from estuarine surface water of Sundarbans. In pre-monsoon of 2022 (June), sediment cores and surface water were collected as well as in situ environmental parameters were measured from two pre-designated sampling points of Sundarbans to elucidate the benthic foraminifera community based on sediment eDNA approach. Based on Oxford Nanopore Technologies (ONT) sequencing in MinION platform, high abundance of Sorites sp., Elphidium excavatum, Textularia gramen, Quinqueloculina sp. and Trochammina hadai were detected. The increasing nutrient concentrations and elucidated benthic foraminiferal signals can contribute towards tracking the state of ecological health of Sundarbans. This study is aimed at generating baseline information on mangrove benthic foraminifera communities using sediment eDNA based high-throughput sequencing.}, }
@article {pmid40319780, year = {2025}, author = {Attiani, V and Smidt, H and van der Wielen, PWJJ}, title = {Investigating spatial and temporal dynamics in microbial community composition of multiple full-scale slow sand filters in drinking water treatment.}, journal = {Water research}, volume = {282}, number = {}, pages = {123751}, doi = {10.1016/j.watres.2025.123751}, pmid = {40319780}, issn = {1879-2448}, mesh = {*Water Purification ; *Drinking Water/microbiology ; Filtration ; *Sand ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Netherlands ; Bacteria ; }, abstract = {Slow sand filters (SSFs) are essential for producing high-quality and sustainable drinking water, relying on chemical, physical, and microbial processes to remove nutrients, organic matter, and pathogens. Despite numerous studies on the physical and chemical mechanisms in SSFs, the microbial processes and dynamics remain poorly understood. This study bridges this knowledge gap by investigating the spatial and temporal dynamics of prokaryotic communities within SSFs, by analysing different depths and the top layer, the Schmutzdecke (SCM), over time in full-scale SSFs from different drinking water treatment plants in The Netherlands. Utilising 16S ribosomal RNA gene-targeted amplicon sequencing and quantitative PCR, we observed a horizontally uniform prokaryotic community at each depth at all analysed SSFs, suggesting effective influent water and nutrient distribution, regardless of filter size or influent inlet design. Vertically, however, the prokaryotic composition varied significantly, with the SCM showing higher biomass and diversity compared to the deeper layers. This study identified a core prokaryotic community, including the families Nitrospiraceae, Pirellulaceae, Nitrosomonadaceae, Gemmataceae, and Vicinamibacteriaceae, consistent across various depths and SSFs, and in the SCMs of different ages. Their presence suggests a central role in supporting key biological processes in SSFs such as organic matter degradation and nitrification. Additionally, the relative abundance of archaea increased with sand depth in all SSFs, suggesting their adaptation to lower-nutrient conditions found in deeper layers. Analysis of the SCM over time showed that after scraping, the prokaryotic community gradually adapted, with minimal biomass increase during the first 3.6 years, eventually evolving into a mature, diverse, and even prokaryotic community. Our findings highlight the presence of spatially distinct microbial communities at various depths of SSFs, suggesting the removal of specific compounds in distinct sand layers. Moreover, the persistence of a core prokaryotic community across different SSFs, SCM maturation stages, and even after disturbances like scraping, demonstrates that the biology in SSFs is resilient and likely ensures reliable SSF performance. It also implies possibilities for earlier SSF operational restart after cleaning than is conventionally done, but with continuous monitoring of water quality parameters to ensure microbial safety. These findings lay the groundwork for future research to focus on these microorganisms and their functional potential.}, }
@article {pmid40319213, year = {2025}, author = {Liu, Y and Hu, Y and Ma, B and Wang, Z and Wei, B}, title = {Gut Microbiota and Exercise: Probiotics to Modify the Composition and Roles of the Gut Microbiota in the Context of 3P Medicine.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {38}, pmid = {40319213}, issn = {1432-184X}, mesh = {*Probiotics/administration &amp; dosage/pharmacology ; Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Exercise/physiology ; Athletic Performance/physiology ; Precision Medicine ; Animals ; }, abstract = {Prolonged and intense physical activity can trigger stress response mechanisms across various physiological systems-including the cardiovascular, respiratory, gastrointestinal, musculoskeletal, and neuroendocrine systems-disrupting energy metabolism, immune function, redox balance, and hormonal regulation. Critically, when not accompanied by adequate recovery, such exertion may impair rather than enhance athletic performance. In parallel, there has been growing interest in probiotics as natural, safe, and accessible dietary supplements with the potential to support performance and recovery. Emerging evidence highlights the pivotal role of the gut microbiome in mediating communication along the gut-brain and gut-muscle axes, thereby influencing not only metabolic and immune functions but also neuromuscular adaptation and fatigue resistance. This review explores the mechanisms through which probiotics may enhance exercise performance, mitigate exercise-induced fatigue, and improve physiological adaptation via modulation of inflammation, oxidative stress, and metabolic signaling pathways. Framed within the context of predictive, preventive, and personalized medicine (3P medicine), this paper emphasizes the diagnostic and therapeutic potential of personalized probiotic strategies in optimizing athletic performance through the qualitative and quantitative assessment of microbiota and host responses.}, }
@article {pmid40316823, year = {2025}, author = {Ben Ammar, FE and Hkiri, AE and Zaafouri, K and Saidane Bchir, F and Hamdi, M}, title = {Enhanced growth of Chlorella sorokiniana on ash-enriched treated wastewater for large-scale lipid and chlorophyll a production using a hybrid raceway photobioreactor.}, journal = {Environmental science and pollution research international}, volume = {32}, number = {21}, pages = {12610-12629}, pmid = {40316823}, issn = {1614-7499}, mesh = {*Chlorella ; *Wastewater ; *Photobioreactors ; Lipids ; Chlorophyll A ; Microalgae ; Biomass ; }, abstract = {Nutrient concentration in microalgal cultivation media greatly influences microalgal growth and macromolecules production. In the present study, treated urban wastewater was used as a medium for Chlorella sorokiniana, incorporating mineral components and ashes in batch culture. The aim was to assess the combined effect of nutrients on microalgal growth, Chlorophyll a content, and lipid production using customized experimental design and response surface methodology. Another objective was to evaluate response improvement after using hybrid raceway photobioreactor HRPBR. The results showed that the highest microalgal biomass growth as well as the highest Chlorophyll a and lipid concentrations was obtained using 2015 mg. L[-1]of NaNO3 and 2086.76 mg. L[-1] of NaHCO3 with a mineral solution concentration of 120 mg. L[-1]. After the HRPBR cultivation, Chlorophyll a content increased from 40.26 to 65.04 mg. L[-1] and the lipid content rose from 37 to 40% and then to 68% under starvation conditions. In these circumstances, the FA profile of Chlorella sorokiniana became in line with the requirements of the European biodiesel standard. Thus, the low-cost nutrient sources for culture medium formulation can be used to culture C. sorokiniana as an efficient strain for sustainable and cost-effective biofuel production.}, }
@article {pmid40312782, year = {2025}, author = {Kynast, D and Reverey, F and Ganzert, L and Grossart, HP and Lischeid, G and Kolb, S}, title = {Detectable land use impact on methanotrophs and methanogens in kettle hole sediments but not on net methane production potentials.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {6}, pages = {}, pmid = {40312782}, issn = {1574-6941}, support = {465808595//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Archaea/metabolism/classification/genetics/isolation &amp; purification ; Microbiota ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Soil Microbiology ; Soil/chemistry ; Agriculture ; Biodiversity ; Forests ; }, abstract = {Kettle holes (KHs) are dynamic freshwater systems and potential sources of the greenhouse gas methane. Due to their small size (<1 hectare), KHs are subject to inorganic and organic matter input from their terrestrial surroundings, governed by land use. Matter inputs include inorganic solutes that are alternative electron acceptors and impact on methanotrophs and methanogens. Thus, they might affect methane net production. We sampled 10 kettle hole sediments embedded in landscapes with either agricultural or forest land use and determined their (i) potential net methane production rates, (ii) the composition of their microbial communities, and (iii) physicochemical soil parameters. Potential net methane production did not significantly differ by land use type but between single KHs. However, land use type had a strong impact on methanotroph and methanogen and on total bacterial and archaeal microbiota structure. Relative abundances of methanotrophs and methanogens were significantly higher in agricultural KHs, and their relative abundances were among the most influential variables projecting net methane production potentials along with nutrient status and water content. Land use type was thus identified as a major factor that impacts the structure and biodiversity of general and methane-cycling microbiota, but it did not affect net methane production potentials.}, }
@article {pmid40312547, year = {2025}, author = {Hu, L and Zhang, K and Xu, Y and Zheng, X and Waterman, JM and Ouyang, X and Wu, Z and Shen, Z and He, Y and Ma, B and Robert, CAM and Raaijmakers, JM and Ye, M and Erb, M and Xu, J}, title = {Herbivory-induced green leaf volatiles increase plant performance through jasmonate-dependent plant-soil feedbacks.}, journal = {Nature plants}, volume = {11}, number = {5}, pages = {1001-1017}, pmid = {40312547}, issn = {2055-0278}, support = {32372775//National Natural Science Foundation of China (National Science Foundation of China)/ ; 200355//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {*Oxylipins/metabolism ; *Cyclopentanes/metabolism ; *Herbivory ; *Volatile Organic Compounds/metabolism ; *Plant Leaves/metabolism ; *Zea mays/physiology/metabolism/growth &amp; development ; Soil Microbiology ; Soil/chemistry ; Animals ; Rhizosphere ; }, abstract = {Plants influence each other chemically by releasing leaf volatiles and root exudates, but whether and how these two phenomena interact remains unknown. Here we demonstrate that volatiles that are released by herbivore-attacked leaves trigger plant-soil feedbacks, resulting in increased performance of different plant species. We show that this phenomenon is due to green leaf volatiles that induce jasmonate-dependent systemic defence signalling in receiver plants, which results in the accumulation of beneficial soil bacteria in the rhizosphere. These soil bacteria then increase plant growth and enhance plant defences. In maize, a cysteine-rich receptor-like protein kinase, ZmCRK25, is required for this effect. In four successive year-field experiments, we demonstrate that this phenomenon can suppress leaf herbivore abundance and enhance maize growth and yield. Thus, volatile-mediated plant-plant interactions trigger plant-soil feedbacks that shape plant performance across different plant species through broadly conserved defence signalling mechanisms and changes in soil microbiota. This phenomenon expands the repertoire of biologically relevant plant-plant interactions in space and time and holds promise for the sustainable intensification of agriculture.}, }
@article {pmid40310547, year = {2025}, author = {Calcagnile, M and Quarta, E and Sicuro, A and Pecoraro, L and Schiavone, R and Tredici, SM and Talà, A and Corallo, A and Verri, T and Stabili, L and Alifano, P}, title = {Effect of Bacillus velezensis MT9 on Nile Tilapia (Oreochromis Niloticus) Intestinal Microbiota.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {37}, pmid = {40310547}, issn = {1432-184X}, support = {ARS01_01053//Ministero dell'Istruzione e del Merito/ ; ARS01_01053//Ministero dell'Istruzione e del Merito/ ; CUP B83C22002930006//European Union Next Generation EU (PNRR)/ ; }, mesh = {Animals ; *Bacillus/physiology/genetics ; *Cichlids/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/administration &amp; dosage/pharmacology ; RNA, Ribosomal, 16S/genetics ; Aquaculture ; Bacteria/classification/genetics/isolation &amp; purification ; Animal Feed/analysis ; }, abstract = {In recent years, there has been a growing interest in the use of probiotics in aquaculture, due to their effectiveness on production, safety, and environmental friendliness. Probiotics, used as feed additives and as an alternative to antibiotics for disease prevention, have been shown to be active as growth promoters, improving survival and health of farmed fish. In this study, we have investigated the ability of the strain Bacillus velezensis MT9, as potential probiotic, to modulate the intestinal microbiota of the Nile tilapia (Oreochromis niloticus) fed with the Bacillus velezensis-supplemented feed in an experimental aquaculture plant. The analysis of the microbial community of the Nile tilapia by culture-based and 16S rRNA gene metabarcoding approaches demonstrated that B. velezensis MT9 reshapes the fish intestinal microbiota by reducing the amounts of opportunistic Gram-negative bacterial pathogens belonging to the phylum of Proteobacterium (Pseudomonadota) and increasing the amounts of beneficial bacteria belonging to the phyla Firmicutes (Bacillota) and Actinobacteria (Actinomycetota). Specifically, dietary supplementation of Nile tilapia with B. velezensis MT9 resulted in an increase in the relative abundance of bacteria of the genus Romboutsia, which has a well-documented probiotic activity, and a decrease in the relative abundance of Gammaproteobacteria of the genera Aeromonas and Vibrio, which include opportunistic pathogens for fish, and Escherichia/Shigella, which may pose a risk to consumers. The whole genome sequence of B. velezensis MT9 was then determined. Genome analysis revealed several peculiarities of B. velezensis MT9 compared to other B. velezensis reference strains including specific metabolic traits, differences in two-component and quorum sensing systems as well as the potential ability to produce a distinct array of secondary metabolites, which could explain the strong ability of this strain to modulate the intestinal microbiota of the Nile tilapia.}, }
@article {pmid40309103, year = {2025}, author = {Cong, X and Liu, X and Zhou, D and Xu, Y and Liu, J and Tong, F}, title = {Characterization and comparison of the fecal bacterial microbiota in Red Back Pine Root Snake (Oligodon formosanus) and Chinese Slug-Eating Snake (Pareas chinensis).}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1575405}, pmid = {40309103}, issn = {1664-302X}, abstract = {INTRODUCTION: The gastrointestinal tracts and oral cavities of animals harbor complex microbial communities that assist hosts in nutrient absorption and immune responses, thereby influencing behavior, development, reproduction, and overall health.<br><br>METHODS: We utilized metagenomic sequencing technology to conduct a detailed analysis of the fecal bacterial communities of six Red Back Pine Root Snakes (Oligodon formosanus, XT) and three Chinese Slug-Eating Snakes (Pareas chinensis, Z) individuals. The microbial composition was assessed through taxonomic profiling, alpha diversity analysis, and functional annotation using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.<br><br>RESULTS: The results indicated that Proteobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, Actinobacteria, and Fusobacteria were the dominant phyla in XT samples, while Z samples additionally contained Patescibacteria. Alpha diversity analysis revealed significant differences in species abundance at the family level, with Z samples exhibiting higher microbial richness than XT. Furthermore, KEGG analysis showed that XT had higher functional gene abundance in pathways related to transcription, translation, environmental adaptation, membrane transport, cellular communities (prokaryotes), motility, and replication/repair compared to Z.<br><br>DISCUSSION: This study provides a comparative analysis of their gut microbiomes, offering valuable insights for future research on zoonotic diseases, host-microbe interactions, and ecological, evolutionary, behavioral, and seasonal influences on snake microbiota. These findings contribute to a broader understanding of microbial ecology in reptiles and its implications for conservation and disease dynamics.}, }
@article {pmid40307095, year = {2025}, author = {Zhang, D and Gao, JT and Zhou, SG}, title = {Microbial electrotaxis: rewiring environmental microbiomes.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.04.005}, pmid = {40307095}, issn = {1878-4380}, abstract = {Electric fields in sediments and soils are critical yet overlooked drivers of microbial ecology. This review examines the importance of electrotaxis in shaping microbial community dynamics and ecology models, surpassing traditional frameworks centered on chemotaxis. We analyze evidence that electric field gradients influence microbial community structure, function, and biogeochemical cycles in natural environments. Current mechanistic models, primarily based on eukaryotic systems, insufficiently explain bacterial electrotactic responses, necessitating new conceptual frameworks that integrate electrochemical and biological perspectives. We also evaluate its applications in environmental and microbiome engineering, with future research recommendations and methodologies in electrotaxis research. This synthesis aims to establish electrotaxis as an essential consideration in microbial ecology, presenting both challenges and opportunities for advancing our understanding of microbial ecosystems.}, }
@article {pmid40305681, year = {2025}, author = {Bennett, BD and Meier, DAO and Lanclos, VC and Asrari, H and Coates, JD and Thrash, JC}, title = {Polyhydroxybutyrate production by freshwater SAR11 (LD12).}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40305681}, issn = {1751-7370}, mesh = {Phylogeny ; *Fresh Water/microbiology ; *Hydroxybutyrates/metabolism ; *Polyhydroxyalkanoates/metabolism/biosynthesis ; Escherichia coli/genetics/metabolism ; *Alphaproteobacteria/metabolism/genetics/classification ; Bacterial Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Polyhydroxybutyrates ; }, abstract = {SAR11 bacteria (order Pelagibacterales) are oligotrophs and often the most abundant bacterioplankton in aquatic environments. A subset of sequenced SAR11 genomes, predominantly in the brackish and freshwater SAR11 subclades, contain homologs of pha genes, which in other organisms confer the ability to store carbon and energy via polyhydroxyalkanoate (PHA) polymers. Here, we investigated the relevance of PHA production to SAR11 biology. Phylogenetics showed that Pha proteins occurred on a long branch and provided evidence for origin at the common ancestor of the brackish IIIa and freshwater LD12 subclades, followed by horizontal transfer within SAR11. Using the LD12 representative "Candidatus Fonsibacter ubiquis" strain LSUCC0530, we found that many LSUCC0530 cells contained a single Nile red-staining granule, confirmed that the cells produced polyhydroxybutyrate, a common form of PHA, and estimated the total polyhydroxybutyrate content in the cells. We heterologously expressed the LSUCC0530 phaCAB locus in Escherichia coli, finding it to be functional and the likely origin of the polyhydroxybutyrate. We also determined that, irrespective of changes to carbon, nitrogen, and phosphorus concentrations, a similar fraction of LSUCC0530 cells generated polyhydroxybutyrate granules and expression of the phaCAB locus remained constant. We suggest that polyhydroxybutyrate synthesis in LSUCC0530 may be constitutively active due to the slow growth dynamics and minimal regulation that characterize SAR11 bacteria. This work characterizes polymer storage in SAR11, providing new insights into the likely fitness advantage for cells harboring this metabolism.}, }
@article {pmid40304437, year = {2025}, author = {Kardish, MR and Stachowicz, JJ}, title = {More Than a Stick in the Mud: Eelgrass Leaf and Root Bacterial Communities Are Distinct From Those on Physical Mimics.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70086}, pmid = {40304437}, issn = {1758-2229}, support = {//UC Davis Center for Population Biology/ ; OCE 1829992//National Science Foundation/ ; //National Science Foundation GRFP/ ; TG-DEB160008//Extreme Science and Engineering Discovery Environment (XSEDE)/ ; //Gordon and Betty Moore Foundation/ ; }, mesh = {*Zosteraceae/microbiology ; *Plant Roots/microbiology ; *Plant Leaves/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {We examine the role of physical structure versus biotic interactions in structuring host-associated microbial communities on a marine angiosperm, Zostera marina, eelgrass. Across several months and sites, we compared microbiomes on physical mimics of eelgrass roots and leaves to those on intact plants. We find large, consistent differences in the microbiome of mimics and plants, especially on roots, but also on leaves. Key taxa that are more abundant on leaves have been associated with microalgal and macroalgal disease and merit further investigation to determine their role in mediating plant-microalgal-pathogen interactions. Root associated taxa were associated with sulphur and nitrogen cycling, potentially ameliorating environmental stresses for the plant. Our work identifies targets for future work on the functional role of the seagrass microbiome in promoting the success of these angiosperms in the sea through identifying components of microbial communities that are specific to seagrasses.}, }
@article {pmid40303429, year = {2025}, author = {Zhao, C and Zhang, J and Chen, Y and Yang, L and Chen, H and Liang, Y and Wang, W and He, S and Luo, Y and Zhang, J and Zhang, H and Yang, S and Guo, G and Dai, W and Yang, Z and Chen, J and Zhou, Y and Khan, WU and Liu, G and Jiang, Y and Zhu, T and Xu, Y and García-Caparros, P and Van de Peer, Y and Xue, JY and Chen, C and Zhang, L and Chen, F}, title = {Water lily pond: a multiomics database for water lilies.}, journal = {Horticulture research}, volume = {12}, number = {6}, pages = {uhaf076}, pmid = {40303429}, issn = {2662-6810}, }
@article {pmid40302853, year = {2025}, author = {Gharbi, D and Neumann, FH and Podile, K and McDonald, M and Linde, JH and Frampton, M and Liebenberg, JL and Cilliers, S and Mmatladi, T and Nkosi, P and Paledi, K and Piketh, S and Staats, J and Burger, RP and Havenga, H and Garland, RM and Bester, P and Lebre, PH and Ricci, C}, title = {Exposure to outdoor aerospora and associated respiratory health risks among adults in Potchefstroom, North-West province, South Africa.}, journal = {Frontiers in allergy}, volume = {6}, number = {}, pages = {1568669}, pmid = {40302853}, issn = {2673-6101}, abstract = {BACKGROUND: Data on allergic rhinitis and respiratory health metrics are limited for South Africa, with grass pollen as a key outdoor aeroallergen. Exotic trees such as plane trees and ragweed produce highly allergenic pollen, dominating indigenous trees and weeds. Pollen allergy prevalence data is lacking in cities of North-West province such as Potchefstroom.<br><br>OBJECTIVES: This study aimed to (i) assess the prevalence of allergies to major aeroallergens, including Poaceae (grasses), Cupressus/Hesperocyparis (cypresses), Platanus (plane tree), Ulmus (elm), Quercus (oak), Betula (birch), Olea (olive), Artemisia (sagebrush), Amaranthus (amaranth), Plantago (plantain), Morus (mulberry), and Ambrosia (ragweed), along with fungal spores such as Alternaria, Cladosporium, and Penicillium/Aspergillus, and (ii) investigate the monthly incidence of major aeroallergens and reactivity levels in sensitized adults in Potchefstroom.<br><br>METHODS: Skin prick tests (SPTs) were performed on 202 adults aged 18-64 years with confirmed allergic symptoms during a field campaign at North-West University (NWU)'s Potchefstroom campus. A test panel of grass, weed, tree, and fungal spore extracts previously identified via aerobiological monitoring was used. Symptom scores were recorded using ISAAC questionnaires; Spearman's statistical correlation between symptom frequency and monthly aeroallergen concentrations were analyzed.<br><br>RESULTS: Among the participants, 184 (91%) exhibited positive SPT reactions: 104 (57%) are monosensitized to pollen, 45 (24%) to fungal spores, and 35 (19%) are polysensitized. Aeroallergen prevalence was higher in females (73%) than in males (27%). The most common pollen allergens were Cynodon dactylon (Bermuda grass) (85%), Zea mays (maize) (46%), Platanus spp. (plane tree) (35%), and Ulmus campestris (field elm) (33%). Among fungal spores, Alternaria was the most common (93%), followed by Cladosporium (27%). A significant and positive statistical correlation was found between allergic rhinitis symptoms and monthly pollen concentrations of Betula, Morus, Platanus, and Quercus.<br><br>DISCUSSION &amp; CONCLUSION: This pilot study linked aeroallergens detected in Potchefstroom with allergy profiles of local residents. The findings highlight the need for more comprehensive regional studies that integrate allergen testing with aerobiological data. Raising awareness and implementing health strategies are essential for managing allergic rhinitis in South Africa. More affordable and available SPTs kits, adapted to allergy prevalence in South Africa, are strongly suggested.}, }
@article {pmid40301344, year = {2025}, author = {Zhu, C and Wu, L and Ning, D and Tian, R and Gao, S and Zhang, B and Zhao, J and Zhang, Y and Xiao, N and Wang, Y and Brown, MR and Tu, Q and ,  and Ju, F and Wells, GF and Guo, J and He, Z and Nielsen, PH and Wang, A and Zhang, Y and Chen, T and He, Q and Criddle, CS and Wagner, M and Tiedje, JM and Curtis, TP and Wen, X and Yang, Y and Alvarez-Cohen, L and Stahl, DA and Alvarez, PJJ and Rittmann, BE and Zhou, J}, title = {Global diversity and distribution of antibiotic resistance genes in human wastewater treatment systems.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4006}, pmid = {40301344}, issn = {2041-1723}, support = {EF-2025558//National Science Foundation (NSF)/ ; 32371724//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82202299//National Natural Science Foundation of China (National Science Foundation of China)/ ; 61872218//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Wastewater/microbiology ; Humans ; Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Water Purification ; *Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences/genetics ; }, abstract = {Antibiotic resistance poses a significant threat to human health, and wastewater treatment plants (WWTPs) are important reservoirs of antibiotic resistance genes (ARGs). Here, we analyze the antibiotic resistomes of 226 activated sludge samples from 142 WWTPs across six continents, using a consistent pipeline for sample collection, DNA sequencing and analysis. We find that ARGs are diverse and similarly abundant, with a core set of 20 ARGs present in all WWTPs. ARG composition differs across continents and is distinct from that of the human gut and the oceans. ARG composition strongly correlates with bacterial taxonomic composition, with Chloroflexi, Acidobacteria and Deltaproteobacteria being the major carriers. ARG abundance positively correlates with the presence of mobile genetic elements, and 57% of the 1112 recovered high-quality genomes possess putatively mobile ARGs. Resistome variations appear to be driven by a complex combination of stochastic processes and deterministic abiotic factors.}, }
@article {pmid40301151, year = {2025}, author = {Kaufmann, H and Salvador, C and Salazar, VW and Cruz, N and Dias, GM and Tschoeke, D and Campos, L and Sawabe, T and Miyazaki, M and Maruyama, F and Thompson, F and Thompson, C}, title = {Genomic Repertoire of Twenty-Two Novel Vibrionaceae Species Isolated from Marine Sediments.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {36}, pmid = {40301151}, issn = {1432-184X}, mesh = {*Geologic Sediments/microbiology ; *Vibrionaceae/genetics/classification/isolation &amp; purification ; *Genome, Bacterial ; Phylogeny ; Japan ; *Seawater/microbiology ; Genetic Variation ; }, abstract = {The genomic repertoire of vibrios has been extensively studied, particularly regarding their metabolic plasticity, symbiotic interactions, and resistance mechanisms to environmental stressors. However, little is known about the genomic diversity and adaptations of vibrios inhabiting deep-sea marine sediments. In this study, we investigated the genomic diversity of vibrios isolated from deep-sea core sediments collected using a manned submersible off Japan. A total of 50 vibrio isolates were obtained and characterized phenotypically, and by genome sequencing. From this total, we disclosed 22 novel species examining genome-to-genome distance, average amino acid identity, and phenotypes (Alivibrio: 1; Enterovibrio: 1; Photobacterium: 8; Vibrio: 12). The novel species have fallen within known clades (e.g., Fisheri, Enterovibrio, Profundum, and Splendidus) and novel clades (JAMM0721, JAMM0388, JAMM0395). The 28 remainder isolates were identified as known species: Aliivibrio sifiae (2), A. salmonicida (1), Enterovibrio baiacu (1), E. norvegicus (1), Photobacterium profundum (3), P. angustum (1), P. chitiniliticum (1), P. frigidiphilum (1), Photobacterium indicum (1), P. sanguinicancri (1). P. swingsii (2), Vibrio alginolyticus (3), V. anguillarum (1), V. campbellii (1), V. fluvialis (1), V. gigantis (1), V. lentus (1), V. splendidus (4), and V. tasmaniensis (1). Genomic analyses revealed that all 50 vibrios harbored genes associated with high-pressure adaptation, including sensor kinases, chaperones, autoinducer-2 (AI-2) signaling, oxidative damage repair, polyunsaturated fatty acid biosynthesis, and stress response mechanisms related to periplasmic and outer membrane protein misfolding under heat shock and osmotic stress. Additionally, alternative sigma factors, trimethylamine oxide (TMAO) respiration, and osmoprotectant acquisition pathways were identified, further supporting their ability to thrive in deep-sea environments. Notably, the genomes exhibited a high prevalence of antibiotic resistance genes, with antibiotic efflux pumps being the most abundant group. The ugd gene expanded in number in some novel species (Photobacterium satsumensis sp. nov. JAMM1754: 4 copies; Vibrio makurazakiensis sp. nov. JAMM1826: 3 copies). This gene may confer antibiotic (polymyxin) resistance to these vibrios.}, }
@article {pmid40301143, year = {2025}, author = {Weitzman, CL and Day, K and Brown, GP and Gibb, K and Christian, K}, title = {Differential Temporal Shifts in Skin Bacteria on Wild and Captive Toads.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {35}, pmid = {40301143}, issn = {1432-184X}, support = {DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; }, mesh = {Animals ; *Skin/microbiology ; Seasons ; *Bacteria/classification/isolation &amp; purification/genetics ; *Bufo marinus/microbiology ; *Microbiota ; Ecosystem ; Australia ; Animals, Wild/microbiology ; Animals, Zoo/microbiology ; }, abstract = {Skin bacteria on amphibian hosts play an important role in host health, but those communities are also constantly shifting based on environmental and host-related feedback. On some hosts, stability of skin communities depends on relatively abundant taxa, with less abundant taxa more readily entering and exiting the system. Cane toads (Rhinella marina) have invaded widespread, diverse tropical ecosystems, with varying ecology, physiology, and behaviour in different environments. In this study, we described temporal patterns of skin bacterial communities on cane toads at a site in northern Australia through the wet and dry seasons over two years. Toads in the wild population were paired with a captive-held population, housed in a semi-natural environment, to detect effects of time and season on wild toads, explore bacterial transience and volatility in skin taxa, and determine the extent to which skin communities on captive toads represent those on the wild population. We found community differences by captivity status, sampling timepoint, and season, with increased richness in the wet season on wild toads. Bacterial communities also became more similar among individuals (lower dispersion) in the wet season. Captive toads harboured more stable communities over time, likely owing to the reduced bacterial reservoirs experienced while in captivity. We propose that cane toads, with varied movement patterns among their diverse invaded habitats, provide an interesting direction for future work understanding the influences of habitat and movement on skin microbes, and the flexibility of microbial symbiotic interactions in invasive hosts.}, }
@article {pmid40300605, year = {2025}, author = {Lopez, JA and McKeithen-Mead, S and Shi, H and Nguyen, TH and Huang, KC and Good, BH}, title = {Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome.}, journal = {Current biology : CB}, volume = {35}, number = {10}, pages = {2282-2294.e11}, doi = {10.1016/j.cub.2025.03.073}, pmid = {40300605}, issn = {1879-0445}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Bacteriophages/physiology/genetics ; *Lysogeny ; Mice ; Animals ; *Bacteria/virology/genetics ; *Virome ; }, abstract = {The human gut contains diverse communities of bacteriophage, whose interactions with the broader microbiome and potential roles in human health are only beginning to be uncovered. Here, we combine multiple types of data to quantitatively estimate gut phage population dynamics and lifestyle characteristics in human subjects. Unifying results from previous studies, we show that an average human gut contains a low ratio of phage particles to bacterial cells (∼1:100) but a much larger ratio of phage genomes to bacterial genomes (∼4:1), implying that most gut phage are effectively temperate (e.g., integrated prophage and phage-plasmids). By integrating imaging and sequencing data with a generalized model of temperate phage dynamics, we estimate that phage induction and lysis occur at a low average rate (∼0.001-0.01 per bacterium per day), imposing only a modest fitness burden on their bacterial hosts. Consistent with these estimates, we find that the phage composition of a diverse synthetic community in gnotobiotic mice can be quantitatively predicted from bacterial abundances alone while still exhibiting phage diversity comparable to native human microbiomes. These results provide a foundation for interpreting existing and future studies on links between the gut virome and human health.}, }
@article {pmid40299544, year = {2025}, author = {Veenhof, RJ and McGrath, AH and Champion, C and Dworjanyn, SA and Marzinelli, EM and Coleman, MA}, title = {The role of microbiota in kelp gametophyte development and resilience to thermal stress.}, journal = {Journal of phycology}, volume = {61}, number = {3}, pages = {633-649}, pmid = {40299544}, issn = {1529-8817}, support = {//The University of Sydney/ ; DP200100201//Australian Research Council/ ; //NSW Climate Change Fund/ ; //Holsworth Wildlife Research Endowment/ ; }, mesh = {*Microbiota ; *Kelp/microbiology/growth &amp; development/physiology ; *Germ Cells, Plant/growth &amp; development/microbiology ; Hot Temperature ; Stress, Physiological ; }, abstract = {Ocean warming is driving profound changes in the ecology of marine habitat formers such as kelps, with negative implications for the biodiversity and ecosystem services they support. Thermal stress can disturb associated microbiota that are essential to the healthy functioning of kelp, but little is known about how this process influences early-life stages. Because kelps have a biphasic life cycle, thermal stress dynamics of adult sporophyte microbiota may not reflect those of the free-living haploid gametophyte. We investigated the role of microbial disruption under thermal stress on gametophytes of the kelp Ecklonia radiata and compared sporophyte and gametophyte microbiota. The microbiota of gametophytes changed significantly when the microbiome was disrupted and under increased temperature (26°C), in which putative generalist bacterial taxa proliferated and bacterial families associated with nitrogen fixation decreased. Concurrently, the survival of gametophytes decreased to <10%, and surviving gametophytes did not become fertile when the microbiome was disrupted. The length of gametophytes decreased under both microbial disruption and thermal stress. Taken together, this suggests that the associated microbiota of Ecklonia gametophytes is important for their survival, fertility, and response to warming. Gametophyte and parental sporophyte microbiota were also distinct from the water column but not each other, suggesting vertical transmission of microbiota from one life stage to the next. This study furthers our understanding of the role of microbiota in gametophyte stress tolerance as well as the acquisition of microbiota, which may prove vital in protecting and increasing the stress resilience of these foundation species.}, }
@article {pmid40298441, year = {2025}, author = {Peng, S-X and Gao, S-M and Lin, Z-L and Luo, Z-H and Zhang, S-Y and Shu, W-S and Meng, F and Huang, L-N}, title = {Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sediments.}, journal = {mBio}, volume = {16}, number = {6}, pages = {e0070525}, pmid = {40298441}, issn = {2150-7511}, support = {no. 31870111//National Natural Science Foundation of China/ ; no. 41830318//National Natural Science Foundation of China/ ; no. 32300001//National Natural Science Foundation of China/ ; no. 2022A1515010625//Natural Science Foundation of Guangdong Province/ ; no. 2021A1515012468//Natural Science Foundation of Guangdong Province/ ; }, mesh = {*Bacteria/classification/genetics/isolation &amp; purification/metabolism ; China ; *Archaea/genetics/classification/isolation &amp; purification/metabolism ; *Geologic Sediments/microbiology ; Metagenomics ; Metagenome ; Mining ; Phylogeny ; Acids ; Phylogeography ; }, abstract = {Recent genomic surveys have uncovered candidate phyla radiation (CPR) bacteria and DPANN archaea as major microbial dark matter lineages in various anoxic habitats. Despite their extraordinary diversity, the biogeographic patterns and ecological implications of these ultra-small and putatively symbiotic microorganisms have remained elusive. Here, we performed metagenomic sequencing on 90 geochemically diverse acid mine drainage sediments sampled across southeast China and recovered 282 CPR and 189 DPANN nonredundant metagenome-assembled genomes, which collectively account for up to 28.6% and 31.2% of the indigenous prokaryotic communities, respectively. We found that, remarkably, geographic distance represents the primary factor driving the large-scale ecological distribution of both CPR and DPANN organisms, followed by pH and Fe. Although both groups might be capable of iron reduction through a flavin-based extracellular electron transfer mechanism, significant differences are found in their metabolic capabilities (with complex carbon degradation and chitin degradation being more prevalent in CPR whereas fermentation and acetate production being enriched in DPANN), indicating potential niche differentiation. Predicted hosts are mainly Acidobacteriota, Bacteroidota, and Proteobacteria for CPR and Thermoplasmatota for DPANN, and extensive, unbalanced metabolic exchanges between these symbionts and putative hosts are displayed. Together, our results provide initial insights into the complex interplays between the two lineages and their physicochemical environments and host populations at a large geographic scale.IMPORTANCECandidate phyla radiation (CPR) bacteria and DPANN archaea constitute a significant fraction of Earth's prokaryotic diversity. Despite their ubiquity and abundance, especially in anoxic habitats, we know little about the community patterns and ecological drivers of these ultra-small, putatively episymbiotic microorganisms across geographic ranges. This study is facilitated by a large collection of CPR and DPANN metagenome-assembled genomes recovered from the metagenomes of 90 sediments sampled from geochemically diverse acid mine drainage (AMD) environments across southeast China. Our comprehensive analyses have allowed first insights into the biogeographic patterns and functional differentiation of these major enigmatic prokaryotic groups in the AMD model system.}, }
@article {pmid40297467, year = {2025}, author = {Deep, A and Sieber, G and Boden, L and David, GM and Baikova, D and Buchner, D and Starke, J and Stach, TL and Reinders, T and Hadžiomerović, U and Beszteri, S and Probst, AJ and Boenigk, J and Beisser, D}, title = {A metatranscriptomic exploration of fungal and bacterial contributions to allochthonous leaf litter decomposition in the streambed.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19120}, pmid = {40297467}, issn = {2167-8359}, mesh = {*Plant Leaves/metabolism/microbiology ; *Bacteria/genetics/metabolism ; *Fungi/genetics/metabolism ; *Rivers/microbiology ; Ecosystem ; Alnus ; Transcriptome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The decomposition of organic matter is essential for sustaining the health of freshwater ecosystems by enabling nutrient recycling, sustaining food webs, and shaping habitat conditions, which collectively enhance ecosystem resilience and productivity. Bacteria and fungi play a crucial role in this process by breaking down coarse particulate organic matter (CPOM), such as leaf litter, into nutrients available for other organisms. However, the specific contribution of bacteria and their functional interactions with fungi in freshwater sediments have yet to be thoroughly explored. In the following study, we enriched organic matter through the addition of alder (Alnus glutinosa) leaves into artificial stream channels (AquaFlow mesocosms). We then investigated enzyme expression, metabolic pathways, and community composition of fungi and bacteria involved in the degradation of CPOM through metatranscriptomics and amplicon sequencing. Enzymes involved in the degradation of lignin, cellulose, and hemicellulose were selectively upregulated with increased organic matter. Analysis of ITS and 16S rRNA gene sequences revealed that during decomposition, fungal communities were predominantly composed of Basidiomycota and Ascomycota, while bacterial communities were largely dominated by Pseudomonadota and Bacteroidota. The similar gene expression patterns of CPOM degradation related enzymes observed between bacteria and fungi indicate potential functional interaction between these microbial groups. This correlation in enzyme expression may indicate that bacteria and fungi are jointly involved in the breakdown of coarse particulate organic matter, potentially through mutualistic interaction. This study uncovers the specific enzymatic activities of bacteria and fungi and the importance of microbial interactions in organic matter decomposition, revealing their central role in facilitating nutrient cycling and maintaining the ecological health and stability of freshwater ecosystems.}, }
@article {pmid40294427, year = {2025}, author = {Ran, X and Wang, T and Zhou, M and Li, Z and Wang, H and Tsybekmitova, GT and Guo, J and Wang, Y}, title = {A Novel Perspective on the Instability of Mainstream Partial Nitrification: The Niche Differentiation of Nitrifying Guilds.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {18}, pages = {8922-8938}, doi = {10.1021/acs.est.5c01214}, pmid = {40294427}, issn = {1520-5851}, mesh = {*Nitrification ; Bacteria/metabolism ; Nitrogen ; Wastewater ; Nitrites/metabolism ; Ammonia/metabolism ; }, abstract = {Short-cut biological nitrogen removal (sBNR) favors the paradigm shift toward energy-positive and carbon-neutral wastewater treatment processes. Partial nitrification (PN) is a key approach to provide nitrite for anammox or denitritation during sBNR, and its stability is the precondition for achieving robust nitrogen removal performance. However, maintaining a stable mainstream PN process has been a long-standing challenge. This review analyzes the mainstream PN process from a microbial ecology perspective, focusing on the niche differentiation among nitrifiers. First, we propose that mainstream PN systems are ecologically unstable, and the failure of the mainstream PN process due to the reactivation of nitrite-oxidizing bacteria (NOB) can be regarded as a behavior to restore system stabilization. Thus, maintaining mainstream PN systems primarily relies on enhancing the niche differentiation between ammonia-oxidizing bacteria (AOB) and NOB. We then summarize the realized niches of indigenous nitrifiers within nitrification systems and discuss their ecophysiological characteristics (e.g., cell structure and substrate affinity) that define their specific ecological niches. By comparing the niche breadths of AOB and NOB on various niche axes, we further discuss their niche differentiation and identify the different responses of AOB (resistance) and NOB (resilience) to exogenous perturbations. Finally, we propose outlook for achieving a stable mainstream PN process through an ecological lens. This review provides ecological insights into the instability of the mainstream PN process, which is intended to guide the derivation of optimized strategies from a single-factor approach to integrated solutions.}, }
@article {pmid40294268, year = {2025}, author = {Sun, W and Wang, J and Wang, G and Jiang, L and Feng, W and Dang, S and Li, M and Jiao, S and Wei, G and Gu, J and Tiedje, JM and Qian, X}, title = {Exposure and health risks of livestock air resistomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {18}, pages = {e2403866122}, pmid = {40294268}, issn = {1091-6490}, support = {42277412 and 42207463//NSF of China/ ; 2024RS-CXTD-68//Shaanxi Innovation Support Program/ ; }, mesh = {Animals ; *Livestock/microbiology ; Humans ; *Air Microbiology ; Anti-Bacterial Agents/pharmacology ; Farms ; Swine ; China ; Chickens ; *Drug Resistance, Microbial/genetics ; *Occupational Exposure ; *Drug Resistance, Bacterial/genetics ; Europe ; }, abstract = {Most of the global antibiotic consumption is by the livestock industry, making livestock farms a hotspot of antibiotic resistance genes (ARGs). Farm air poses direct ARG exposure to workers, but the health risks of air resistomes remain unclear. We evaluated the human exposure and health risks of air resistomes in pig and chicken farms and compared air resistomes in Chinese farms to those in European farms given their long-term restrictions on use of antibiotics in livestock. We found that livestock air was highly enriched in ARGs, with each cell harboring seven times more ARGs than urban air. The daily ARG inhalation of farm workers was equivalent to several years of ARG inhalation by urban residents. ARGs encoding resistance to last-resort antibiotics such as mcr-1 and tetX were detected in farm air, and tetX variants were prevalent in both Chinese and European farms. ARGs in livestock air were highly associated with mobile genetic elements, and conjugation experiments confirmed their cross-phyla transferability. The projected resistome risk of farm air was significantly higher than well-recognized ARG hotspots like air from hospitals, sewage treatment plants, and from animal manures. The diversity, abundance, and risk score of air resistomes in Chinese farms were significantly higher than those in European farms, suggesting that long-term restriction of antibiotic use mitigates antibiotic resistance in the livestock environment. Our results underscore the high exposure of farm workers to ARGs via farm air and highlight its role in ARG dissemination, supporting the importance of antibiotic stewardship practices in combating antibiotic resistance.}, }
@article {pmid40293502, year = {2025}, author = {Cao, X and Liu, H and Zhang, R and Wen, Y and Ma, L and Xu, Z and Wen, L and Zhuo, Y and Liu, D and Wang, L}, title = {Composition, Predicted Functions, and Co-occurrence Networks of Bacteria and Fungi in Hummock Wetlands of Northeastern Inner Mongolia, China.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {34}, pmid = {40293502}, issn = {1432-184X}, support = {YSS2021007//the Funds of Yinshanbeilu Grassland Eco-hydrology National Observation and Research Station/ ; 32160279, 32161143025, 31960249//the National Natural Science Funds, P.R. China/ ; 2022YFHH0017//Science and Technology Major Project of Inner Mongolia/ ; 2022EEDSKJZDZX010, 2022EEDSKJXM005//Ordos Science and Technology Plan/ ; }, mesh = {China ; *Wetlands ; *Soil Microbiology ; Soil/chemistry ; Ecosystem ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; }, abstract = {Wetland microhabitats, varying in water table position, pH, and biochemical properties, have been understudied in terms of their influence on soil microbial community structure. This study employed amplicon-based gene sequencing to investigate the responses of both fungal and bacterial communities to habitat changes in northeastern Inner Mongolia, China. The results showed that while α-diversity indices (Shannon and Chao1) did not significantly differ between hummocks and hollows, β-diversity analyses revealed distinct microbial community structures in these habitats. Bacterial communities were primarily influenced by soil pH, EC, and AP, whereas fungal communities were affected by pH, AKP, MBC, MBN, and AP. Bacterial interactions were predominant in hollows, whereas fungal interactions were predominant in hummocks. Hummocks significantly enhanced amino acid metabolism function, whereas hollows significantly increased the abundance of endophyte-litter saprotroph-soil saprotroph-undefined saprotroph. This study underscores the importance of habitats in regulating microbial networks and functions, thereby enhancing our understanding of the influence of microhabitats, such as hummocks, on wetland ecosystem structure and function.}, }
@article {pmid40287826, year = {2025}, author = {Gerhardt, K and Ruiz-Perez, CA and Rodriguez-R, LM and Jain, C and Tiedje, JM and Cole, JR and Konstantinidis, KT}, title = {FastAAI: efficient estimation of genome average amino acid identity and phylum-level relationships using tetramers of universal proteins.}, journal = {Nucleic acids research}, volume = {53}, number = {8}, pages = {}, pmid = {40287826}, issn = {1362-4962}, support = {DBI1356288NSF//NSF/ ; }, mesh = {Phylogeny ; *Genome, Bacterial ; *Software ; *Bacteria/genetics/classification ; *Amino Acids/genetics ; *Computational Biology/methods ; }, abstract = {Estimation of whole-genome relatedness and taxonomic identification are two important bioinformatics tasks in describing environmental or clinical microbiomes. The genome-aggregate Average Nucleotide Identity is routinely used to derive the relatedness of closely related (species level) microbial and viral genomes, but it is not appropriate for more divergent genomes. Average Amino-acid Identity (AAI) can be used in the latter cases, but no current AAI implementation can efficiently compare thousands of genomes. Here we present FastAAI, a tool that estimates whole-genome pairwise relatedness using shared tetramers of universal proteins in a matter of microseconds, providing a speedup of up to 5 orders of magnitude when compared with current methods for calculating AAI or alternative whole-genome metrics. Further, FastAAI resolves distantly related genomes related at the phylum level with comparable accuracy to the phylogeny of ribosomal RNA genes, substantially improving on a known limitation of current AAI implementations. Our analysis of the resulting AAI matrices also indicated that bacterial lineages predominantly evolve gradually, rather than showing bursts of diversification, and that AAI thresholds to define classes, orders, and families are generally elusive. Therefore, FastAAI uniquely expands the toolbox for microbiome analysis and allows it to scale to millions of genomes.}, }
@article {pmid40287775, year = {2025}, author = {Ren, H and Hong, H and Zha, B and Lamlom, SF and Qiu, H and Cao, Y and Sun, R and Wang, H and Ma, J and Zhang, H and Sun, L and Yang, Q and Zhou, C and Liu, X and Wang, X and Zhang, C and Zhang, F and Zhao, K and Yuan, R and Abdelghany, AM and Zhang, B and Zheng, Y and Wang, J and Lu, W}, title = {Soybean productivity can be enhanced by understanding rhizosphere microbiota: evidence from metagenomics analysis from diverse agroecosystems.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {105}, pmid = {40287775}, issn = {2049-2618}, mesh = {*Rhizosphere ; *Metagenomics/methods ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Glycine max/microbiology/growth &amp; development ; *Microbiota/genetics ; China ; Fungi/classification/genetics/isolation &amp; purification ; Plant Roots/microbiology ; Archaea/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Microbial communities associated with roots play a crucial role in the growth and health of plants and are constantly influenced by plant development and alterations in the soil environment. Despite extensive rhizosphere microbiome research, studies examining multi-kingdom microbial variation across large-scale agricultural gradients remain limited.<br><br>RESULTS: This study investigates the rhizosphere microbial communities associated with soybean across 13 diverse geographical locations in China. Using high-throughput shotgun metagenomic sequencing on the BGISEQ T7 platform with 10 GB per sample, we identified a total of 43,337 microbial species encompassing bacteria, archaea, fungi, and viruses. Our analysis revealed significant site-specific variations in microbial diversity and community composition, underscoring the influence of local environmental factors on microbial ecology. Principal coordinate analysis (PCoA) indicated distinct clustering patterns of microbial communities, reflecting the unique environmental conditions and agricultural practices of each location. Network analysis identified 556 hub microbial taxa significantly correlated with soybean yield traits, with bacteria showing the strongest associations. These key microorganisms were found to be involved in critical nutrient cycling pathways, particularly in carbon oxidation, nitrogen fixation, phosphorus solubilization, and sulfur metabolism. Our findings demonstrate the pivotal roles of specific microbial taxa in enhancing nutrient cycling, promoting plant health, and improving soybean yield, with significant positive correlations (r&#x2009;= 0.5, p&#x2009;= 0.039) between microbial diversity and seed yield.<br><br>CONCLUSION: This study provides a comprehensive understanding of the diversity and functional potential of rhizosphere microbiota in enhancing soybean productivity. The findings underscore the importance of integrating microbial community dynamics into crop management strategies to optimize nutrient cycling, plant health, and yield. While this study identifies key microbial taxa with potential functional roles, future research should focus on isolating and validating these microorganisms for their bioremediation and biofertilization activities under field conditions. This will provide actionable insights for developing microbial-based agricultural interventions to improve crop resilience and sustainability. Video Abstract.}, }
@article {pmid40287657, year = {2025}, author = {De Maayer, P and Green, T and Jordan, S and Smits, THM and Coutinho, TA}, title = {Pan-genome analysis of the Enterobacter hormaechei complex highlights its genomic flexibility and pertinence as a multidrug resistant pathogen.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {408}, pmid = {40287657}, issn = {1471-2164}, support = {310030L_204333//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Enterobacter/genetics/classification/drug effects/pathogenicity ; *Genome, Bacterial ; Phylogeny ; *Drug Resistance, Multiple, Bacterial/genetics ; *Genomics/methods ; Anti-Bacterial Agents/pharmacology ; DNA Transposable Elements ; Plasmids/genetics ; }, abstract = {BACKGROUND: Enterobacter hormaechei is of increasing concern as both an opportunistic and nosocomial pathogen, exacerbated by its evolving multidrug resistance. However, its taxonomy remains contentious, and little is known about its pathogenesis and the broader context of its resistome. In this study, a comprehensive comparative genomic analysis was undertaken to address these issues.<br><br>RESULTS: Phylogenomic analysis revealed that E. hormaechei represents a complex, comprising three predicted species, E. hormaechei, E. hoffmannii and E. xiangfangensis, with the latter putatively comprising three distinct subspecies, namely oharae, steigerwaltii and xiangfangensis. The species and subspecies all display open and distinct pan-genomes, with diversification driven by an array of mobile genetic elements including numerous plasmid replicons and prophages, integrative conjugative elements (ICE) and transposable elements. These elements have given rise to a broad, relatively conserved set of pathogenicity determinants, but also a variable set of secretion systems. The E. hormaechei complex displays a highly mutable resistome, with most taxa being multidrug resistant.<br><br>CONCLUSIONS: This study addressed key issues pertaining to the taxonomy of the E. hormaechei complex, which may contribute towards more accurate identification of strains belonging to this species complex in the clinical setting. The pathogenicity determinants identified in this study could serve as a basis for a deeper understanding of E. hormaechei complex pathogenesis and virulence. The extensive nature of multidrug resistance among E. hormaechei complex strains highlights the need for responsible antibiotic stewardship to ensure effective treatment of these emerging pathogens.}, }
@article {pmid40287646, year = {2025}, author = {He, L and Zou, Q and Wang, Y}, title = {metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {111}, pmid = {40287646}, issn = {1471-2105}, support = {62102269//National Natural Science Foundation of China/ ; }, mesh = {*Metagenomics/methods ; Computational Biology/methods ; *Software ; *Gene Expression Profiling/methods ; *Microbiota ; Data Collection ; Quality Control ; Workflow ; RNA, Untranslated ; Molecular Sequence Annotation ; Rhizosphere ; Automation ; }, abstract = {BACKGROUND: The accessibility of sequencing technologies has enabled meta-transcriptomic studies to provide a deeper understanding of microbial ecology at the transcriptional level. Analyzing omics data involves multiple steps that require the use of various bioinformatics tools. With the increasing availability of public microbiome datasets, conducting meta-analyses can reveal new insights into microbiome activity. However, the reproducibility of data is often compromised due to variations in processing methods for sample omics data. Therefore, it is essential to develop efficient analytical workflows that ensure repeatability, reproducibility, and the traceability of results in microbiome research.<br><br>RESULTS: We developed metaTP, a pipeline that integrates bioinformatics tools for analyzing meta-transcriptomic data comprehensively. The pipeline includes quality control, non-coding RNA removal, transcript expression quantification, differential gene expression analysis, functional annotation, and co-expression network analysis. To quantify mRNA expression, we rely on reference indexes built using protein-coding sequences, which help overcome the limitations of database analysis. Additionally, metaTP provides a function for calculating the topological properties of gene co-expression networks, offering an intuitive explanation for correlated gene sets in high-dimensional datasets. The use of metaTP is anticipated to support researchers in addressing microbiota-related biological inquiries and improving the accessibility and interpretation of microbiota RNA-Seq data.<br><br>CONCLUSIONS: We have created a conda package to integrate the tools into our pipeline, making it a flexible and versatile tool for handling meta-transcriptomic sequencing data. The metaTP pipeline is freely available at: https://github.com/nanbei45/metaTP .}, }
@article {pmid40287414, year = {2025}, author = {Bull, F and Tavaddod, S and Bommer, N and Perry, M and Brackley, CA and Allen, RJ}, title = {Different factors control long-term versus short-term outcomes for bacterial colonisation of a urinary catheter.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3940}, pmid = {40287414}, issn = {2041-1723}, support = {682237 EVOSTRUC//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council(H2020 Excellent Science - European Research Council)/ ; EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft(German Research Foundation)/ ; EP/L015110/1//RCUK | Engineering and Physical Sciences Research Council(EPSRC)/ ; }, mesh = {*Urinary Catheters/microbiology/adverse effects ; Humans ; *Urinary Tract Infections/microbiology/prevention &amp; control/etiology ; *Catheter-Related Infections/microbiology/prevention &amp; control ; *Urinary Catheterization/adverse effects ; Computer Simulation ; *Bacteria/growth &amp; development ; Urinary Bladder/microbiology ; Models, Theoretical ; Models, Biological ; Time Factors ; }, abstract = {Urinary catheters are used extensively in hospitals and long-term care and they are highly prone to infection. Understanding the pathways by which bacteria colonise a urinary catheter could guide strategies to mitigate infection, but quantitative models for this colonisation process are lacking. Here we present a mathematical model for bacterial colonisation of a urinary catheter that integrates population dynamics and fluid dynamics. The model describes bacteria migrating up the outside surface of the catheter, spreading into the bladder and being swept through the catheter lumen. Computer simulations of the model reveal that clinical outcomes for long-term versus short-term catheterisation are controlled by different factors: the rate of urine production by the kidneys as opposed to urethral length, catheter surface properties and bacterial motility. Our work may help explain variable susceptibility to catheter-associated urinary tract infection (CAUTI) among individuals and the mixed success of antimicrobial surface coatings. Our model suggests that for long-term catheterised patients, increasing fluid intake or reducing residual urine volume in the bladder may help prevent infection, while antimicrobial surface coatings are predicted to be effective only for short-term catheterised patients. Therefore, different catheter management strategies could be rationally targeted to long-term vs short-term catheterised patients.}, }
@article {pmid40286617, year = {2025}, author = {Kang, S and Lee, JY and Natsagdorj, A and Matsuki, A and Cho, KS}, title = {Functional adaptation of PM2.5 microbiomes to varying environmental conditions in Northeast Asia: Ulaanbaatar, Seoul, and Noto.}, journal = {The Science of the total environment}, volume = {979}, number = {}, pages = {179495}, doi = {10.1016/j.scitotenv.2025.179495}, pmid = {40286617}, issn = {1879-1026}, mesh = {*Particulate Matter/analysis ; *Microbiota ; *Environmental Monitoring ; *Air Pollutants/analysis ; Fungi ; Bacteria ; *Air Microbiology ; Seoul ; }, abstract = {This study examined the bacterial and fungal communities associated with PM2.5 collected from three geographically distinct locations in Northeast Asia-Ulaanbaatar (high pollution), Seoul (moderate pollution), and Noto (low pollution)-which collectively represent a gradient of urbanization and environmental conditions during the spring sampling period from March 15 to April 7, 2022. Ulaanbaatar exhibited the highest abundance of both bacteria and fungi, yet exhibited the lowest fungal diversity. In contrast, Noto exhibited the lowest microbial abundance but the highest fungal diversity, while Seoul displayed intermediate values. Dominant bacterial genera, including Caldalkalibacillus, Halomonas, and Nesterenkonia, demonstrated notable resilience across all three locations, highlighting their adaptability to diverse environmental conditions. The dominant fungal genera were Cladosporium and Candida. Analyses revealed significant correlations between microbial community structures and environmental factors. In Ulaanbaatar, microbial communities were strongly associated with meteorological parameters such as temperature, humidity, and wind speed. In Seoul, stronger correlations were observed with polycyclic aromatic hydrocarbons (PAHs). Noto exhibited weaker correlations with both meteorological factors and organic compounds. Across all sites, bacteria consistently showed broader niche breadths compared to fungi, reflecting their greater metabolic versatility and resource utilization capacity. Both bacterial and fungal niche breadths generally increased at intermediate concentrations of alkanes and DCAs but declined at extreme concentrations, suggesting optimal survival ranges. These findings highlight the complex interplay of environmental factors and pollutants in shaping microbial community structures and functional diversity across diverse geographical settings during the spring season.}, }
@article {pmid40285533, year = {2025}, author = {Liao, X and Wang, H and Wu, D and Grossart, HP and Yang, X and Li, L and Wang, Y and Li, S and Li, J and Cao, M and Chen, N and Hu, A}, title = {Geographical and Environmental Factors Differentially Shape Planktonic Microbial Community Assembly and Resistomes Composition in Urban Rivers.}, journal = {Global change biology}, volume = {31}, number = {4}, pages = {e70211}, doi = {10.1111/gcb.70211}, pmid = {40285533}, issn = {1365-2486}, support = {//the Ocean Negative Carbon Emissions (ONCE) Program/ ; 2021QZKK0103//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2023YFC3804904//National Key Research and Development Program/ ; }, mesh = {*Microbiota ; *Plankton ; China ; *Rivers/microbiology ; Bacteria/genetics/drug effects ; Urbanization ; }, abstract = {Global urbanization accelerates pollution challenges in urban rivers, including increased transmission of bacterial antibiotic resistance genes (ARGs), severely threatening the health of aquatic ecosystems and human health. Yet, systematic knowledge of differences in distribution and community assembly patterns of bacterial resistance across urban rivers at a continental scale is still insufficient. In this study, we conducted extensive sampling in nine representative urban rivers across China. We used amplicon and shotgun metagenomic sequencing, state-of-the-art bioinformatics, and multivariate statistics to investigate distribution patterns and community assembly mechanisms of planktonic microbiomes (i.e., bacterioplankton and planktonic microeukaryotes), including their resistomes, i.e., ARGs and metal resistance genes (MRGs). Geographical and environmental factors played a pivotal role in shaping distribution patterns of planktonic microbiomes vs. resistomes in the studied urban rivers. Phylogenetic-bin-based null model analysis (iCAMP) indicated that planktonic microbiomes, dominated by dispersal limitation and drift, tend toward spatial heterogeneity. In contrast, planktonic resistomes, driven by deterministic processes, display more similar distribution patterns. Cross-validated Mantel tests revealed that geographical factors (i.e., geographic distance) were the primary regulators of planktonic microbial community assembly, while environmental factors (i.e., temperature) control assembly processes of planktonic resistomes. Our findings provide crucial insights into the mechanisms driving the biogeographical distribution and community assembly of planktonic microbial entities in urban rivers at a continental scale, offering valuable implications for mitigating and managing the spread of ARGs from the environment to humans.}, }
@article {pmid40284744, year = {2025}, author = {Yahya, R and Albaqami, A and Alzahrani, A and Althubaiti, SM and Alhariri, M and Alrashidi, ET and Alhazmi, N and Al-Matary, MA and Alharbi, N}, title = {Comprehensive Genomic Analysis of Klebsiella pneumoniae and Its Temperate N-15-like Phage: From Isolation to Functional Annotation.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, pmid = {40284744}, issn = {2076-2607}, support = {NRC21R/053/02//King Abdullah International Medical Research Center/ ; }, abstract = {Antibiotic resistance to Klebsiella pneumoniae poses a major public health threat, particularly in intensive care unit (ICU) settings. The emergence of extensively drug-resistant (XDR) strains complicates treatment options, requiring a deeper understanding of their genetic makeup and potential therapeutic targets. This research delineated an extensively drug-resistant (XDR) Klebsiella pneumoniae strain obtained from an ICU patient and telomeric temperate phage derived from hospital effluent. The bacteria showed strong resistance to multiple antibiotics, including penicillin (≥16 μg/mL), ceftriaxone (≥32 μg/mL), and meropenem (≥8 μg/mL), which was caused by SHV-11 beta-lactamase, NDM-1 carbapenemase, and porin mutations (OmpK37, MdtQ). The strain was categorized as K46 and O2a types and carried virulence genes involved in iron acquisition, adhesion, and immune evasion, as well as plasmids (IncHI1B_1_pNDM-MAR, IncFIB) and eleven prophage regions, reflecting its genetic adaptability and resistance dissemination. The 172,025 bp linear genome and 46.3% GC content of the N-15-like phage showed strong genomic similarities to phages of the Sugarlandvirus genus, especially those that infect K. pneumoniae. There were structural proteins (11.8%), DNA replication and repair enzymes (9.3%), and a toxin-antitoxin system (0.4%) encoded by the phage genome. A protelomerase and ParA/B partitioning proteins indicate that the phage is replicating and maintaining itself in a manner similar to the N15 phage, which is renowned for maintaining a linear plasmid prophage throughout lysogeny. Understanding the dynamics of antibiotic resistance and pathogen development requires knowledge of phages like this one, which are known for their temperate nature and their function in altering bacterial virulence and resistance profiles. The regulatory and structural proteins of the phage also provide a model for research into the biology of temperate phages and their effects on microbial communities. The importance of temperate phages in bacterial genomes and their function in the larger framework of microbial ecology and evolution is emphasized in this research.}, }
@article {pmid40284675, year = {2025}, author = {Li, M and Liu, X and Chen, W and Xu, H and Huang, F and Yao, Q and Jia, X and Huang, Y}, title = {Alleviating Effect of Lactiplantibacillus plantarum HYY-S10 on Colitis in Mice Based on an Analysis of the Immune Axis in the Intestine.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, pmid = {40284675}, issn = {2076-2607}, support = {32302242//the National Natural Science Foundation of China/ ; 2022A1515110426//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023B0202040002//Guangdong Provincial Key Research and Development Program/ ; 2022B1212010015//Key Laboratory Project of Guangdong Province/ ; }, abstract = {The pathogenesis of ulcerative colitis (UC) has been fundamentally associated with intestinal microbiota dysbiosis and disruption of immune homeostasis. This study systematically investigates the therapeutic potential of Lactiplantibacillus plantarum HYY-S10 (HYY-S10), a novel strain isolated from De'ang sour tea in Yun an, China, with a focus on its mechanisms for alleviating colitis through the modulation of gut microbiota. Using a dextran sulfate sodium (DSS)-induced colitis model in C57BL/6J mice, our findings demonstrated that seven days of oral supplementation with HYY-S10 (1 × 10[8] CFU/mL, 0.2 mL/10 g body weight) significantly improved Disease Activity Index (DAI) scores and attenuated characteristic colitis symptoms, including progressive weight loss, rectal bleeding, and abnormal stool consistency. Administration of HYY-S10 exhibited significant immunomodulatory effects characterized by the downregulation of pro-inflammatory mediators (such as IL-1β, IL-6, IFN-γ, and LPS) while concomitantly upregulating anti-inflammatory IL-10 expression. Additionally, the strain enhanced intestinal antioxidant capacity by increasing GSH-Px activity, which collectively contributed to the reduction in intestinal inflammation. Furthermore, HYY-S10 demonstrated multifaceted protective effects by ameliorating oxidative stress through the restoration of redox homeostasis and modulation of gut microbial ecology. Probiotic intervention significantly increased short-chain fatty acids (SCFAs) production and notably enhanced the relative abundance of beneficial taxa, including Akkermansia and Ruminococcus_B, while restoring microbial diversity and ecological stability. Collectively, our results demonstrate that HYY-S10 alleviates experimental colitis by modulating the intestinal immune axis and microbiota composition, providing mechanistic insights to support its potential as a probiotic-based therapeutic strategy for UC.}, }
@article {pmid40284595, year = {2025}, author = {Frazier, AN and Willis, W and Robbe, H and Ortiz, A and Koziel, JA}, title = {Characterization and Assembly Dynamics of the Microbiome Associated with Swine Anaerobic Lagoon Manure Treated with Biochar.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, pmid = {40284595}, issn = {2076-2607}, support = {3090-31630-006//USDA-ARS CRIS/ ; }, abstract = {Biochar has significant potential for livestock microbiomes and crop agriculture regarding greenhouse gas emissions reduction. Therefore, a pilot study was designed to investigate the effect of biochar application on the surface of swine manure from an open lagoon and the associated microbial communities. Samples were collected from four different treatment groups: control (n = 4), coarse biochar (n = 4), fine biochar (n = 4), and ultra-fine biochar (n = 4). Additionally, aged manure in bulk was collected (n = 4) to assess alterations from the control group. The method of 16S rRNA amplicon sequencing along with microbial analyses was performed. Diversity was significantly different between aged manure in bulk samples and all treatment groups (Kruskal-Wallis; p < 0.05). Additionally, distinct community compositions were seen using both weighted and unweighted UniFrac distance matrices (PERMANOVA; p < 0.01). Differential abundance analysis revealed four distinct features within all treatment groups that were enriched (q < 0.001): Idiomarina spp., Geovibrio thiophilus, Parapusillimonas granuli, and an uncultured Gammaproteobacteria species. Similarly, Comamonas spp. and Brumimicrobium aurantiacum (q-value < 0.001) were significantly depleted by all the treatments. Stochastic and functional analyses revealed that biochar treatments were not deterministically altering assembly patterns, and functional redundancy was evident regardless of compositional shifts.}, }
@article {pmid40280843, year = {2025}, author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW}, title = {Plant-microbe interactions: plants modulating their defenses.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.04.001}, pmid = {40280843}, issn = {1878-4372}, abstract = {Plant immunity is mediated by multiple factors, including microbial interactions and gene expression. Keppler et al. identified a set of microbe-responsive genes (general non-self response genes) whose expression or products affect bacterial strain abundance and enhance immunity. We explore how these genes shape alternative plant defense strategies for sustainable agriculture.}, }
@article {pmid40280003, year = {2025}, author = {Cholet, F and Vignola, M and Quinn, D and Ijaz, UZ and Sloan, WT and Smith, CJ}, title = {Microbial ecology of drinking water biofiltration based on 16S rRNA sequencing: A meta-analysis.}, journal = {Water research}, volume = {281}, number = {}, pages = {123684}, doi = {10.1016/j.watres.2025.123684}, pmid = {40280003}, issn = {1879-2448}, mesh = {*Filtration ; *RNA, Ribosomal, 16S/genetics ; *Water Purification/methods ; *Drinking Water/microbiology ; Microbiota ; }, abstract = {Biofiltration, a sustainable water treatment technology relying on microbial processes to remove contaminants, offers a promising approach to achieving the United Nations Sustainable Goal 6 of universal access to clean water and sanitation by 2030. However, a key barrier to optimising biofiltration is the incomplete understanding of the biological mechanisms governing its performance. Despite numerous studies examining how engineering decisions impact biofilter performance and the associated microbiome, the significant influence of geographical location on microbial communities raises the question of whether these findings are universally applicable or location-specific. To address this, we conducted a meta-analysis of 15 biofilter microbiomes using 16S rRNA high-throughput sequencing (HTS) data, mainly originating from rapid gravity and/or granular activated carbon (GAC) filters. Despite different types and scales, results highlight geographical location as the major contributor to microbiome dissimilarity in biofilter samples (Top and Bottom) (R[2]∼ 0.5; p-value<0.001). The same was observed for influent waters (PERMANOVA R[2]= 0.76; p-value<0.001), indicating location-specific microbiomes as opposed to differences driven by different biofilter operating parameters. Irrespective of location, the higher percentage of the microbiome was assembled through deterministic processes (∼55 %) compared to stochastic processes (∼45 %). Finally, our findings suggest that the depth stratification of biofilter microbiomes may be associated with the enrichment of taxa capable of metabolising more complex organic carbon in deeper filter layers (10 enriched pathways in biofilter Bottom layers compared to 3 at the Top). These insights provide a broader understanding of biofiltration microbiomes and offer possible research avenues for targeted and effective biofilter design strategies.}, }
@article {pmid40279085, year = {2025}, author = {Zheng, F and Zhao, J and Yuan, Z and Gao, Y and Li, Y and Li, Y and Geng, Y and Qiang, Y}, title = {Interpretable drug-target affinity prediction based on pre-trained models' output as embeddings and based on structure-aware cross-attention for feature fusion.}, journal = {Molecular diversity}, volume = {}, number = {}, pages = {}, pmid = {40279085}, issn = {1573-501X}, support = {U21A20469//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 62376183//National Natural Science Foundation of China/ ; 202304051001009//the special fund for Science and Technology Innovation Teams of Shanxi Province/ ; 2020-PT320-005//National Health Commission Key Laboratory of Pneumoconiosis/ ; }, abstract = {The characteristics of protein pockets can better capture the interaction information between proteins and small molecules, thereby improving the performance of drug-target interaction (DTI) prediction tasks. However, pocket data typically need to be predicted using software such as AlphaFold, which would entail a massive workload for datasets ranging from tens of thousands to hundreds of thousands of samples. Moreover, feature representation networks for 3D pocket data are computationally intensive. To address this, we propose simulating 3D pocket data using sequence data through feature fusion of two different objects based on structure cross-attention (CASD). Additionally, precise feature representation is a prerequisite for accurately identifying pocket information. We introduce a method that leverages the output of the last layer of a pre-trained model as an embedding layer for training a new model from scratch. This approach not only incorporates prior knowledge from the pre-trained model but also expands model capacity, enabling more accurate feature representation. Furthermore, we enhance the multimodal representation of small molecule compounds using feature fusion based on structure cross-attention for the same object (CASS), further improving feature representation capabilities. Our cross-attention mechanisms operate at the token-level or node-level, allowing fine-grained capture of interactions between amino acids and atoms. This enables the identification of the contribution score of each atom or amino acid to the task, making our model interpretable for drug-target prediction. Experimental validation demonstrates that our model achieves state-of-the-art predictive performance.}, }
@article {pmid40277367, year = {2025}, author = {Thapa, BS and Flynn, TM and Jensvold, ZD and Kemner, KM and Sladek, MF and O'Loughlin, EJ and Marshall, CW}, title = {Effects of soluble electron shuttles on microbial iron reduction and methanogenesis.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {5}, pages = {e0222224}, pmid = {40277367}, issn = {1098-5336}, support = {DE-AC02-06CH11357//U.S. Department of Energy (DOE)/ ; }, mesh = {Oxidation-Reduction ; *Iron/metabolism ; *Methane/metabolism ; *Bacteria/metabolism/classification/genetics ; Electron Transport ; Electrons ; Quinones/metabolism ; Acetates/metabolism ; Riboflavin/metabolism ; Archaea/metabolism ; Microbiota ; }, abstract = {In many aquatic and terrestrial ecosystems, iron (Fe) reduction by microorganisms is a key part of biogeochemical cycling and energy flux. The presence of redox-active electron shuttles in the environment potentially enables a phylogenetically diverse group of microbes to use insoluble iron as a terminal electron acceptor. We investigated the impact that different electron shuttles had on respiration, microbial physiology, and microbial ecology. We tested eight different electron shuttles, seven quinones and riboflavin, with redox potentials between 0.217 and -0.340 V. Fe(III) reduction coupled with acetate oxidation was observed with all shuttles. Once Fe(III) reduction began to plateau, a rapid increase in acetate consumption was observed and coincided with the onset of methane production, except in the incubations with the shuttle 9,10-anthraquinone-2-carboxylic acid (AQC). The rates of iron reduction, acetate consumption, methanogenesis, and the microbial communities varied significantly across the different shuttles independent of redox potential. In general, shuttles appeared to reduce the overall diversity of the community compared to no shuttle controls, but certain shuttles were exceptions to this trend. Geobacteraceae were the predominant taxonomic family in all enrichments except in the presence of AQC or 1,2-dihydroxyanthraquinone (AQZ), but each shuttle enriched a unique community significantly different from the no shuttle control conditions. This suggests that the presence of different redox-active electron shuttles can have a large influence on the microbial ecology and total carbon flux in the environment.IMPORTANCEIron is the fourth most abundant element in the Earth's crust, and the reduction of iron by microbes is an important component of global biogeochemical cycles. A phylogenetically diverse group of microbes is capable of conserving energy with oxidized iron as a terminal electron acceptor, but the environmental conditions favoring certain taxonomic clades in iron-reducing environments are unclear. One complicating factor often overlooked in small-scale enrichments is the influence of soluble, redox-active electron shuttles on the rate and microbial ecology of iron reduction. We tested the effects of eight different electron shuttles on microbial physiology and ecology in iron-reducing enrichments derived from a local wetland. Each electron shuttle varied the microbial activity and enriched for a microbial community distinct from the no shuttle control condition. Therefore, in complex subsurface environments with many redox-active compounds present, we propose electron shuttles as a reason for the coexistence of multiple clades of iron-reducing bacteria.}, }
@article {pmid40277363, year = {2025}, author = {Wang, Y and Yang, L and Wu, W and Feng, Z and He, J and Guo, C and He, J}, title = {Bacillus haimaensis sp. nov.: a novel cold seep-adapted bacterium with unique biosynthetic potential.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {5}, pages = {e0245624}, pmid = {40277363}, issn = {1098-5336}, support = {No. 2022B1111030001//Guangdong key Research and Developement program/ ; No. CARS-46//China Agricultural Research System/ ; No. 32473201//National Natural Science Foundation of China/ ; No. 2022YFE0203900//National Key Research and Development Program of China/ ; No. 2023A1515110395//Guangdong Province Basic and Applied Basic Research Found project/ ; No. 2024B1212040007//Science and Technology Plan Project of Guangdong Province/ ; }, mesh = {*Bacillus/genetics/classification/isolation &amp; purification/physiology/metabolism ; Phylogeny ; *Geologic Sediments/microbiology ; China ; Genome, Bacterial ; *Seawater/microbiology ; Cold Temperature ; Multigene Family ; RNA, Ribosomal, 16S/genetics ; Adaptation, Physiological ; }, abstract = {Deep-sea cold seeps harbor unique microbial communities that play crucial roles in biogeochemical cycles and possess potential biotechnological applications. Herein, we report the isolation, characterization, and genomic analysis of a novel Bacillus species, Bacillus haimaensis sp. nov. (type strain CSS-39[T], CCTCC M20241382), obtained from sediments collected at a depth of 1,350 m in the Haima cold seep, South China Sea. Phylogenomic analysis, revealing an average nucleotide identity of 87.78% and a digital DNA-DNA hybridization value of 34.0% with its closest relative B. tianshenii DSM 25879[T], confirms the taxonomic novelty of the genus Bacillus. The complete 4.54 Mb genome of B. haimaensis reveals adaptations to the cold seep environment, including enhanced nutrient acquisition capabilities and stress response mechanisms. Comparative genomic analysis identifies 27 unique gene clusters related to spore germination and sulfate assimilation, suggesting specialized metabolic strategies for this extreme habitat. Furthermore, six biosynthetic gene clusters, including a novel lassopeptide cluster, indicate a potential for secondary metabolite production. Phenotypic characterization demonstrates the strain's ability to utilize diverse carbon sources and tolerate a wide range of environmental conditions. Our findings provide insights into microbial adaptations to deep-sea cold seeps and highlight the potential of B. haimaensis for biotechnological applications in bioremediation and natural product discovery. This study expands our understanding of microbial diversity in extreme marine environments and offers a new model bacterium for investigating bacterial adaptations to deep-sea ecosystems.IMPORTANCEThe discovery of Bacillus haimaensis sp. nov. in the Haima cold seep of the South China Sea represents a significant advancement in our understanding of microbial adaptations to extreme marine environments. This novel species exhibits remarkable metabolic versatility and unique genomic features, providing insights into bacterial survival strategies in nutrient-variable, high-pressure deep-sea ecosystems. Comprehensive genomic analysis reveals distinctive biosynthetic gene clusters, suggesting untapped potential for discovering novel natural product. Furthermore, B. haimaensis exhibits promising capabilities for aromatic compound degradation, indicating potential applications in marine bioremediation. This work not only expands our knowledge of microbial diversity in understudied deep-sea habitats but also highlights the biotechnological promise of extremophiles. The adaptive mechanisms elucidated in B. haimaensis, particularly those related to sporulation and sulfate assimilation, contribute to our broader understanding of microbial ecology in cold seeps and may inform future research on climate change impacts on deep-sea ecosystems.}, }
@article {pmid40276016, year = {2025}, author = {Papazlatani, C and Wagner, A and Chen, Z and Zweers, H and de Boer, W and Garbeva, P}, title = {Enhancement of production of pathogen-suppressing volatiles using amino acids.}, journal = {Current research in microbial sciences}, volume = {8}, number = {}, pages = {100385}, pmid = {40276016}, issn = {2666-5174}, abstract = {Bacterial volatile organic compounds can play a significant role in antagonistic interactions. Enhancing the production of bacterial volatiles that suppress the growth of soil-borne phytopathogenic fungi, has perspective as a sustainable disease control strategy. In the present study, we explored the potential of stimulating Burkholderia AD24 and Paenibacillus AD87 to produce volatiles that suppress the growth of the plant pathogenic fungi Fusarium culmorum PV and Rhizoctonia solani AG2.2IIIb. We provided the bacterial strains with a mixture of amino acids that can serve as precursor molecules in metabolic routes leading to emission of suppressive bacterial volatiles. Only Burkholderia AD24 was stimulated to produce a volatile blend that led to higher suppression of both pathogens. Subsequent analysis of the volatile composition emitted by Burkholderia AD24 in the presence of amino acids, showed higher abundance of antifungal compounds, including sulfur compounds (DMDS), pyrazines (2,5-dimethyl pyrazine) and carbohydrates (3-methyl-1-butanol). Follow-up trials with single amino acids revealed a pathogen specific response effect. When Burkholderia AD24 was cultivated in the presence of glutamine and asparagine, the emitted volatile blend suppressed the growth of F. culmorum, whereas when cultivated in the presence of glycine, glutamine, arginine and lysine the volatile blend suppressed the growth of R. solani. Analysis of the volatile blend composition showed differences between the amino acid treatments. Our findings show that amino acid precursor molecules can stimulate the production of fungistatic volatiles but the sensitivity of the fungal pathogens to these bacterial volatiles varies. This should be considered in future application strategies.}, }
@article {pmid40275504, year = {2025}, author = {Ekemezie, SC and Davis, CC and Russo, MV and Carpenter, LP and Russell, AL}, title = {Pollen-microbe interactions in nectar weakly influence bee foraging behavior.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icaf017}, pmid = {40275504}, issn = {1557-7023}, abstract = {Plant-pollinator interactions are frequently affected by microbes that grow on flowers. Bacteria and yeast commonly grow within floral nectar, which is a sugar-rich floral reward often sought out by pollinators. Nectar is also commonly contaminated with protein-rich pollen. Microbes can induce this pollen to germinate or burst within the nectar, which potentially results in pollen nutrients being made available to nectar foraging pollinators. Yet whether pollen-microbe interactions in nectar impact pollinator behavior remains unknown. We therefore investigated how a common nectar yeast (Metschnikowia reukaufii) and bacteria (Acinetobacter nectaris) affected pollen germination and bursting within artificial nectar and effects on bumble bee (Bombus impatiens) foraging behavior. We found that both bacteria and yeast reduced the proportion of intact pollen in nectar, with bacteria inducing the most germination and bursting. Although microbes may thus potentially increase the quality of the nectar reward via increased access to pollen nutrients, we did not observe effects on bee flower preference. Similarly, bees did not show increased constancy (i.e., fidelity to one flower type across flower visits) to nectar contaminated with pollen and microbes. In contrast, bees were much more likely to reject flowers with nectar contaminated with pollen and yeast alone or together, relative to flowers that offered uncontaminated nectar. Altogether, our work suggests pollen-microbe interactions within nectar may have relatively minor influences on pollinator foraging behavior. We discuss possible explanations and implications of these results for plant and pollinator ecology.}, }
@article {pmid40273553, year = {2025}, author = {Ballan, D and Picot, A and Rolland, N and Bovo, C and Prévost, C and Coton, E and Mounier, J}, title = {Diversity of spoilage microorganisms associated with fresh fruits and vegetables in French households.}, journal = {International journal of food microbiology}, volume = {437}, number = {}, pages = {111204}, doi = {10.1016/j.ijfoodmicro.2025.111204}, pmid = {40273553}, issn = {1879-3460}, mesh = {*Vegetables/microbiology ; France ; *Fruit/microbiology ; *Bacteria/isolation &amp; purification/classification/genetics ; *Fungi/isolation &amp; purification/classification/genetics ; *Food Microbiology ; Family Characteristics ; Seasons ; Biodiversity ; Food Contamination/analysis ; }, abstract = {Food loss and waste generated throughout the food chain are major concerns in today's society. A high level of food waste occurs at the household's level and fresh fruit and vegetable (FFV) spoilage caused by microbial growth accounts for a large part of these losses. While numerous studies focused on spoilage microorganism diversity from primary production to distribution, little is known about those involved at the household level. In this context, this study aimed at investigating which FFV are usually wasted depending on the season and storage conditions at households, and identifying the microorganisms associated with spoiled FFV. During two periods (summer and autumn), 346 spoiled FFV samples were collected using a citizen science approach in 49 households in the Brest area (Finistère, Brittany, France). About three quarters of spoiled FFV collected originated from room temperature storage and 75 % were collected during summer. Among the studied samples, 75 % showed microbial growth after plating onto agar-based medium, and therefore, were likely spoiled because of microbial spoilage. Overall, 183 molds, 31 yeasts and 96 bacteria were isolated and identified using MALDI-TOF MS and sequencing. Among the 42 different mold species identified, Penicillium spp. were the most common representing more than 50 % of mold isolates followed by Botrytis (12.4 %), Mucor (8.6 %) and Cladosporium (7.6 %) spp. Hanseniaspora uvarum and Aureobasidium pullulans were the most prevalent yeast species while bacterial isolates showed the highest diversity of all identified organisms (49 species) with Pseudomonas spp., enterobacteria and lactic acid bacteria representing the most frequently isolated taxa. This study shows for the first time the microbial diversity associated with spoiled FFV of which a large proportion were stored at room temperature, suggesting that a better usage of FFV refrigeration could help reduce FFV waste in households.}, }
@article {pmid40270585, year = {2025}, author = {Zheng, Z and Gong, Z and Zhang, R and Lin, X and Hong, W and Song, L}, title = {Potential pathogens drive ARGs enrichment during biofilms formation on environmental surfaces.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf057}, pmid = {40270585}, issn = {2730-6151}, abstract = {The enrichment of antibiotic resistance genes (ARGs) on environmental surfaces is a fundamental question in microbial ecology. Understanding the processes driving ARG variations can provide clues into their transfer mechanisms between phases and offer insights for public health management. In this study, we examined microbiota, potential pathogen, and ARG dynamics on two common environment surfaces-polyvinyl chloride (PVC) and carbon steel (CS)-under environmental stress (induced by landfill leachate flow) in a Center for Disease Control and Prevention Biofilm Reactor using metagenomics and quantitative polymerase chain reaction-Chip techniques. Contrary to the expected changes in biofilms morphology and physiochemical properties, microbiota, potential pathogens, and ARGs exhibited a divergence-convergence pattern, primarily shaped by attachment surface properties and, subsequently, biofilm maturity during biofilms formation. During this process, ARG levels in biofilms gradually increased to and exceeded the levels in the surrounding environment, but with a distinct structure (P < .05). Furthermore, 1.93- and 3.05-fold increases in the concentrations of mobile genetic elements intI-1 in PVC and CS biofilms, respectively, suggested their important role in the transfer and spread of ARGs within the biofilm matrix. Although potential pathogens were less abundant (3.48%-5.63%) in the biofilms microbiota, they accounted for 18.28%-45.16% of the ARG hosts and harbored multiple ARGs. Pathogens significantly impacted ARG enrichment (Procrustes analysis: P = .0136, M[2] = 0.34) although microbiota development also influenced this process (P = .0385, M[2] = 0.67). These results suggest that pathogens are key in shaping ARG enrichment in biofilms. Our findings provide dynamic insights into resistome enrichment on environmental surfaces.}, }
@article {pmid40270532, year = {2025}, author = {Ma, J and Wang, M and Sun, Y and Zheng, Y and Lai, S and Zhang, Y and Wu, Y and Jiang, C and Shen, F}, title = {Cockroach Microbiome Disrupts Indoor Environmental Microbial Ecology with Potential Public Health Implications.}, journal = {Environment &amp; health (Washington, D.C.)}, volume = {3}, number = {4}, pages = {380-391}, pmid = {40270532}, issn = {2833-8278}, abstract = {Cockroaches pose a significant global public health concern. However, besides the well-recognized cockroach-induced allergy, the potential impact of the cockroach microbiome on human health through various means is not yet fully elucidated. This study aimed to clarify the health impacts of cockroaches by investigating the microbial interactions among cockroaches, the indoor environment, and humans. We simultaneously collected cockroach, indoor environment (indoor air and floor dust), and human (exhaled breath condensate and skin) samples from residential areas in five cities representing distinct climate zones in China. The 16S rDNA sequencing results revealed that cockroaches harbor diverse bacterial populations that vary across different cities. The prevalence of potential pathogenic bacteria (PPB) in cockroaches ranged from 1.1% to 58.9%, with dominant resistance genes conferring resistance to tetracycline, macrolide, and beta-lactam. The relationships between the cockroach microbiome and the associated environmental and human microbiomes were explored by using fast expectation-maximization microbial source tracking (FEAST). The potential contribution of cockroach bacteria to the floor dust-borne microbiome and indoor airborne microbiome was estimated to be 5.6% and 1.3%, respectively. Similarly, the potential contribution of cockroach PPB to the floor dust-borne microbiome and indoor airborne microbiome was calculated to be 4.0% and 1.2%, respectively. In residences with cockroach infestations, the contribution of other sources to the indoor environment was slightly increased. Collectively, the role of cockroaches in the transmission of microorganisms, particularly pathogenic bacteria and antibiotic resistance genes, cannot be overlooked.}, }
@article {pmid40268300, year = {2025}, author = {Goyal, A and Chure, G}, title = {Paradox of the Sub-Plankton: Plausible Mechanisms and Open Problems Underlying Strain-Level Diversity in Microbial Communities.}, journal = {Environmental microbiology}, volume = {27}, number = {4}, pages = {e70094}, pmid = {40268300}, issn = {1462-2920}, mesh = {*Biodiversity ; *Microbiota ; *Bacteria/genetics/classification ; Gene Transfer, Horizontal ; Genetic Variation ; Ecosystem ; Biological Evolution ; }, abstract = {Microbial communities are often complex and highly diverse, typically with dozens of species sharing spatially-restricted environments. Within these species, genetic and ecological variation often exists at a much finer scale, with closely related strains coexisting and competing. While the coexistence of strains in communities has been heavily explored over the past two decades, we have no self-consistent theory of how this diversity is maintained. This question challenges our conventional understanding of ecological coexistence, typically framed around species with clear phenotypic and ecological differences. In this review, we synthesise plausible mechanisms underlying strain-level diversity (termed microdiversity), focusing on niche-based mechanisms such as nutrient competition, neutral mechanisms such as migration, and evolutionary mechanisms such as horizontal gene transfer. We critically assess the strengths and caveats of these mechanisms, acknowledging key gaps that persist in linking genetic similarity to ecological divergence. Finally, we highlight how the origin and maintenance of microdiversity could pose a major challenge to conventional ecological thinking. We articulate a call-to-arms for a dialogue between well-designed experiments and new theoretical frameworks to address this grand conceptual challenge in understanding microbial biodiversity.}, }
@article {pmid40267173, year = {2025}, author = {Bull, CT and Salgado-Salazar, C and Romberg, MK and Allen, C and Kantor, M and Handoo, Z and Aboughanem-Sabanadzovic, N and Sabanadzovic, S and Coutinho, T}, title = {Plant Pathogen Name Game: Cross Kingdom Review for the Naming of Biotic Agents Associated with Plants.}, journal = {Annual review of phytopathology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-phyto-111424-090412}, pmid = {40267173}, issn = {1545-2107}, abstract = {To communicate across scientific disciplines, regulatory bodies, and the agricultural community, the naming of plant pathogens assigned to specific taxa is critical. Here, we provide an overview of the nomenclatural systems governing the naming of plant-pathogenic nematodes, fungi, oomycetes, prokaryotes, and viruses. Although we focus on the nature of the nomenclatural codes, we briefly discuss fundamental principles of taxonomy, including classification and identification. Key elements of the codes of nomenclature that ensure stability and clarity when naming species of pathogens are defined. When comparing the practice of nomenclature across different kingdoms, the classification and nomenclatural systems differ, and thus unique challenges are faced. We provide guidance from the codes and current practice for naming novel species. When there are nomenclatural conflicts, international committees play a critical role in their resolution. They also play a role in updating the codes to reflect new advancements in science. With this review, we aim to assist plant pathologists, journal editors, and those in related fields by providing an entrée to the legalistic requirements of the codes. Authors must consult and follow the rules of the appropriate code for any proposal of new or new combinations of names. To those interested in naming new species (or renaming the current ones), we recommend collaborations with experts in the field of taxonomy to ensure that rules for accurate and consistent naming practices and procedures are followed and to increase the likelihood that the proposed nomenclature is correct and acceptable.}, }
@article {pmid40266732, year = {2025}, author = {Duque-Granda, D and Vivero-Gómez, RJ and González Ceballos, LA and Junca, H and Duque, SR and Aroca Aguilera, MC and Castañeda-Espinosa, A and Cadavid-Restrepo, G and Gómez, GF and Moreno-Herrera, CX}, title = {Exploring the Diversity of Microbial Communities Associated with Two Anopheles Species During Dry Season in an Indigenous Community from the Colombian Amazon.}, journal = {Insects}, volume = {16}, number = {3}, pages = {}, pmid = {40266732}, issn = {2075-4450}, support = {Hermes 57545//Universidad Nacional de Colombia/ ; }, abstract = {Malaria disease affects millions of people annually, making the Amazon Basin a major hotspot in the Americas. While traditional control strategies rely on physical and chemical methods, the Anopheles microbiome offers a promising avenue for biological control, as certain bacteria can inhibit parasite development and alter vector immune and reproductive systems, disrupting the transmission cycle. For this reason, this study aimed to explore the bacterial communities in An. darlingi and An. triannulatus s.l., including breeding sites, immature stages, and adults from San Pedro de los Lagos (Leticia, Amazonas) through next-generation sequencing of the 16S rRNA gene. The results revealed a higher bacterial genus richness in the L1-L2 larvae of An. triannulatus s.l. Aeromonas and Enterobacter were prevalent in most samples, with abundances of 52.51% in L3-L4 larvae and 48.88% in pupae of An. triannulatus s.l., respectively. In breeding site water, Verrucomicrobiota bacteria were the most dominant (52.39%). We also identified Delftia (15.46%) in An. triannulatus s.l. pupae and Asaia (98.22%) in An. triannulatus, linked to Plasmodium inhibition, and Elizabethkingia, in low abundances, along with Klebsiella and Serratia, known for paratransgenesis potential. Considering the high bacterial diversity observed across the different mosquito life stages, identifying bacterial composition is the first step towards developing new strategies for malaria control. However, the specific roles of these bacteria in anophelines and the malaria transmission cycle remain to be elucidated.}, }
@article {pmid40266381, year = {2025}, author = {Cuny, MAC and Gloder, G and Bourne, ME and Kalisvaart, SN and Verreth, C and Crauwels, S and Cusumano, A and Lievens, B and Poelman, EH}, title = {Parasitoid Calyx Fluid and Venom Affect Bacterial Communities in Their Lepidopteran Host Labial Salivary Glands.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {33}, pmid = {40266381}, issn = {1432-184X}, support = {ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; }, mesh = {Animals ; *Salivary Glands/microbiology ; *Wasps/physiology ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects ; *Microbiota ; Larva/parasitology/microbiology ; Host-Parasite Interactions ; *Butterflies/microbiology/parasitology ; Hemolymph/microbiology ; Polydnaviridae/physiology ; *Wasp Venoms/pharmacology ; *Moths/microbiology/parasitology ; }, abstract = {The influence of gut and gonad bacterial communities on insect physiology, behaviour, and ecology is increasingly recognised. Parasitism by parasitoid wasps alters many physiological processes in their hosts, including gut bacterial communities. However, it remains unclear whether these changes are restricted to the gut or also occur in other tissues and fluids, and the mechanisms underlying such changes are unknown. We hypothesise that host microbiome changes result from the injection of calyx fluid (that contain symbiotic viruses known as polydnaviruses) and venom during parasitoid oviposition and that these effects vary by host tissue. To test this, we microinjected Pieris brassicae caterpillars with calyx fluid and venom from Cotesia glomerata, using saline solution and natural parasitism by C. glomerata as controls. We analysed changes in the bacterial community composition in the gut, regurgitate, haemolymph, and labial salivary glands of the host insects. Multivariate analysis revealed distinct bacterial communities across tissues and fluids, with high diversity in the salivary glands and haemolymph. Parasitism and injection of calyx fluid and venom significantly altered bacterial communities in the salivary glands. Differential abundance analysis showed that parasitism affected bacterial relative abundance in the haemolymph, and that Wolbachia was only found in the haemolymph of parasitized caterpillars. Altogether, our findings reveal that parasitism influences the host haemolymph microbiome, and both parasitism and injection of calyx fluid and venom drive changes in the bacterial community composition within the host salivary glands. Given that the composition of salivary glands can influence plant response to herbivory, we discuss these results in the broader context of plant-parasitoid interactions.}, }
@article {pmid40262702, year = {2025}, author = {Zhang, S and Sun, C}, title = {Ecological divergence of marine bacteria Alteromonas mediterranea.}, journal = {Molecular phylogenetics and evolution}, volume = {208}, number = {}, pages = {108359}, doi = {10.1016/j.ympev.2025.108359}, pmid = {40262702}, issn = {1095-9513}, mesh = {*Phylogeny ; *Alteromonas/genetics/classification ; Ecosystem ; Evolution, Molecular ; Seawater/microbiology ; Sequence Analysis, DNA ; Gene Transfer, Horizontal ; Ecotype ; Phylogeography ; }, abstract = {Alteromonas mediterranea, originally designated as A. macleodii, is a deep-sea ecotype that plays an important ecological role in the ocean. However, a comprehensive understanding of their biogeographic distribution and evolutionary histories remains limited. In this study, our analysis indicated that A. mediterranea members could adapt contrasting marine ecosystems and flourish in nutrient-rich habitats such as feces and coral reefs. No significant correlations between the relative abundance of A. mediterranea members and the environmental variables were identified. Phylogenetic analysis and geographic patterns of A. mediterranea strains suggested that they could be clustered into two clades (clade Ⅰ and clade Ⅱ). In contrast, many distinct genomic traits exist between these clades, such as the complete genes encoding cytochrome o ubiquinol oxidase only involved in clade Ⅱ. Genes were more likely to be lost in the evolutionary history of A. mediterranea relatives. Gene loss might be a major force in all phylogenetic groups driving the distinct clades. Adaptation to different biotopes resulted in the functional differentiation of A. mediterranea members, with the loss of genes encoding carbohydrate-active enzymes. Genes acquired horizontally from unclassified bacteria, and Proteobacteria represented by Gammaproteobacteria played key roles in the functional diversification of A. mediterranea in marine habitats. Given these data, these results are useful for information supplementation of A. mediterranea strains, particularly for making significant advances in understanding marine microbial ecology within different clonal frames using genome-wide recruitments.}, }
@article {pmid40262432, year = {2025}, author = {Wu, G and Zhang, H and Huang, T and Song, Y and Liu, X and Liu, X and Wang, X and Pei, T and Xu, G and Wang, Z}, title = {Hydraulic and thermal performance trigger the deterministic assembly of water microbiomes: From biogeographical homogenization to machine learning model.}, journal = {Water research}, volume = {282}, number = {}, pages = {123626}, doi = {10.1016/j.watres.2025.123626}, pmid = {40262432}, issn = {1879-2448}, mesh = {*Machine Learning ; *Microbiota ; *Water Microbiology ; Temperature ; Drinking Water/microbiology ; Seasons ; }, abstract = {Water quality at the point of consumption has long been a health issue because of the potential for microbial ecology. However, research on water hydraulic performance remains in its infancy, and in particular, little is known about the effects of thermal performance during winter. This study explored the effects of stagnation and municipal heating on microbial communities in tap water, focusing on spatial and temporal variations in microbial community composition. The results revealed that stagnation significantly alters the microbial community, especially in heating areas, where the temperature exacerbates microbial growth. Furthermore, hydraulic and thermal performance drive deterministic assembly processes in microbial communities, as evidenced by the reductions in β-diversity, normalized stochasticity ratio (NST), and neutral community model (NCM) fit. Machine learning models revealed that stagnation time greater than 8 h results in increased community abundance because of longer exposure to organic matter and nutrients. The study finding illustrate the importance of environmental influences on microbial community dynamics, and provide valuable insights into the water microbial community, particularly in areas with prolonged stagnation.}, }
@article {pmid40261360, year = {2025}, author = {Cho, KH and Kwon, Y and Kasani, PH and Lee, SG and Jeong, SJ}, title = {Influence of Maternal Weight Dynamics Prior to and Throughout Gestation on Early Infant Gut Microbiome Colonization.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {32}, pmid = {40261360}, issn = {1432-184X}, support = {HR22C1605//Korea Health Technology R&amp;D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health &amp; Welfare, Republic of Korea/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Pregnancy ; *Bacteria/classification/genetics/isolation &amp; purification ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; Adult ; Body Mass Index ; Feces/microbiology ; *Gestational Weight Gain ; Male ; Meconium/microbiology ; Infant ; *Body Weight ; }, abstract = {This study is aimed at exploring the relationship between maternal weight categories, including pre-pregnancy body mass index (P-BMI) and gestational weight gain (GWG), and the composition of the infant gut microbiome in the early days of life. We recruited 71 mother-infant pairs from Kangwon National University Hospital and Bundang CHA Hospital, collecting meconium samples from the infants within the first 5 days postpartum. Using 16S ribosomal RNA gene sequencing (V3-V4 region), this study assessed microbial diversity and the relative abundance of specific bacterial taxa in these initial stool samples. Participants were categorized into groups based on maternal P-BMI and GWG, enabling a comprehensive comparison of the microbiota composition in the infants' meconium across different maternal weight metrics. Our analysis identified significant variations in the infant gut microbiome correlated with maternal weight categories. Key findings include a differential abundance of genera such as Sphingobacteriaceae, Bacillaceae, Cytophagaceae, and Alteromonadaceae across maternal P-BMI groups, whereas Moraxellaceae and Rhodospirillaceae varied across GWG groups. In the P-BMI category, infants born to overweight mothers demonstrated a higher abundance of Pseudopedobacter, and a lower abundance of Citrobacter and Lachnospira, while infants in the underweight group showed a higher abundance of Lachnospira and Weissella. In the normal weight group, Citrobacter and Pseudopedobacter were more abundant. Within the GWG category, infants in the inadequate group showed a higher abundance of Klebsiella, whereas the normal group showed a higher abundance of Holdemania. The composition of the infant gut microbiome in the early postnatal period is significantly influenced by maternal weight categories. Understanding the role of maternal weight in shaping early microbial colonization may provide insights into developing strategies to optimize infant health outcomes through targeted interventions before and during pregnancy.}, }
@article {pmid40261136, year = {2025}, author = {Elias Masiques, N and De Vrieze, J and Hemeryck, LY and Vanhaecke, L and De Smet, S and Van Hecke, T}, title = {Dietary fiber mitigates the differential impact of beef and chicken meat consumption on rat intestinal health.}, journal = {Food &amp; function}, volume = {16}, number = {10}, pages = {3949-3962}, doi = {10.1039/d5fo00900f}, pmid = {40261136}, issn = {2042-650X}, mesh = {Animals ; Rats ; *Dietary Fiber/metabolism ; Male ; Chickens ; Gastrointestinal Microbiome ; Cattle ; *Red Meat/analysis ; Oxidative Stress ; Colon/metabolism/microbiology ; Rats, Wistar ; Oligosaccharides/metabolism ; *Meat/analysis ; Fermentation ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; }, abstract = {In this rat feeding study, it was hypothesized that the impact of red (vs. white) meat consumption on gut health is more pronounced in fiber-deprived diets, whereas fiber-rich diets may attenuate meat-related differences. For this purpose, rats were fed a red (beef) or white (chicken) meat diet with and without fructo-oligosaccharides (FOS) for three weeks. Gut health was assessed through colonic microbiota, fermentation metabolites, oxidative stress, inflammation, DNA adducts and histology. In rats on the fiber-deprived diets, beef consumption resulted in higher abundance of mucin-degrading bacteria Akkermansia and lower blood glutathione levels compared to chicken-fed rats. Adding FOS to the meat diets modulated the gut microbiota and fermentation metabolites, affected oxidative stress and inflammation markers in tissues and blood, increased colon length, and reduced fat deposition and liver weight. Thus, results showed that the dietary context should be considered when evaluating the impact of red meat consumption on gut health.}, }
@article {pmid40260087, year = {2025}, author = {Matsumura, E and Kato, H and Hara, S and Ohbayashi, T and Ito, K and Shingubara, R and Kawakami, T and Mitsunobu, S and Saeki, T and Tsuda, S and Minamisawa, K and Wagai, R}, title = {Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1557188}, pmid = {40260087}, issn = {1664-302X}, abstract = {Soil particles in plant rooting zones are largely clustered to form porous structural units called aggregates where highly diverse microorganisms inhabit and drive biogeochemical cycling. The complete extraction of microbial cells and DNA from soil is a substantial task as certain microorganisms exhibit strong adhesion to soil surfaces and/or inhabit deep within aggregates. However, the degree of aggregate dispersion and the efficacy of extraction have rarely been examined, and thus, adequate cell extraction methods from soil remain unclear. We aimed to develop an optimal method of cell extraction for single-cell genomics (SCG) analysis of single soil aggregates by focusing on water-stable macroaggregates (diameter: 5.6-8.2 mm) from the topsoil of cultivated Acrisol. We postulated that the extraction of microorganisms with distinct taxonomy and functions could be achieved depending on the degree of soil aggregate dispersion. To test this idea, we used six individual aggregates and performed both SCG sequencing and amplicon analysis. While both bead-vortexing and sonication dispersion techniques improved the extractability of bacterial cells compared to previous ones, the sonication technique led to more efficient dispersion and yielded a higher number and more diverse microorganisms than the bead technique. Furthermore, the analyses of nitrogen cycling and exopolysaccharides-related genes suggested that the sonication-assisted extraction led to the greater recovery of microorganisms strongly attached to soil particles and/or inhabited the aggregate subunits that were more physically stable (e.g., aggregate core). Further SCG analysis revealed that all six aggregates held intact microorganisms holding the genes (potentials) to convert nitrate into all possible nitrogen forms while some low-abundance genes showed inter-aggregate heterogeneity. Overall, all six aggregates studied showed similarities in pore characteristics, phylum-level composition, and microbial functional redundancy. Together, these results suggest that water-stable macroaggregates may act as a functional unit in soil and show potential as a useful experimental unit in soil microbial ecology. Our study also suggests that conventional methods employed for the extraction of cells and DNA may not be optimal. The findings of this study emphasize the necessity of advancing extraction methodologies to facilitate a more comprehensive understanding of microbial diversity and function in soil environments.}, }
@article {pmid40259028, year = {2025}, author = {Hsieh, YE and Yang, SY and Liu, SL and Wang, SW and Wang, WL and Tang, SL and Yang, SH}, title = {Microbial Community Shifts and Nitrogen Utilization in Peritidal Microbialites: The Role of Salinity and pH in Microbially Induced Carbonate Precipitation.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {31}, pmid = {40259028}, issn = {1432-184X}, support = {MOST 111-2621-B-029 -002 -MY3//National Science and Technology Council, Taiwan/ ; MOST 110-2611-M-002-024//National Science and Technology Council/ ; }, mesh = {*Carbonates/metabolism/chemistry ; Hydrogen-Ion Concentration ; Salinity ; *Nitrogen/metabolism ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Microbiota ; *Seawater/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; Chemical Precipitation ; }, abstract = {Microbialites have the potential to record environmental changes and act as biosignatures of past geochemical conditions. As such, they could be used as indicators to decipher ancient rock records. Modern microbialites are primarily found in environments where competitors and destructors are absent or where biogeochemical conditions favor their continuous formation. Many previous studies have essentially focused on the role of photosynthetic microbes in controlling pH and carbonate speciation and potentially overlooked alternative non-photosynthetic pathways of carbonate precipitation. Given that microbial activity induces subtle geochemical changes, microbially induced carbonate precipitation (MICP) can involve several mechanisms, from extracellular polymeric substances (EPS), sulfate reduction, anaerobic oxidation of methane, to nitrogen cycling processes, such as ammonification, ureolysis, and denitrification. Moreover, the peritidal zone where temperate microbialites are mostly found today, is under the influence of both freshwater and seawater, arguing for successive biogeochemical processes leading to mineral saturation, and questioning interpretations of fossil records. This study investigates microbialites in three tide pools from the peritidal zone of Fongchueisha, Hengchun, Taiwan, to address the influence of salinity on microbial community composition and carbonate precipitation mechanisms. Microbial samples were collected across varying salinity gradients at multiple time points and analyzed using next-generation sequencing (NGS) of bacterial 16S and eukaryotic 18S rRNA genes. Our results indicate that dominant bacterial groups, including Cyanobacteria and Alphaproteobacteria, were largely influenced by salinity variations, albeit pH exhibited stronger correlation with community composition. Combining our results on geochemistry and taxonomic diversity over time, we inferred a shift in the trophic mode under high salinity conditions, during which the use of urea and amino acids as a nitrogen source outcompetes diazotrophy, ureolysis and ammonification of amino acids reinforcing carbonate precipitation dynamics by triggering an increase in both pH and dissolved inorganic carbon.}, }
@article {pmid40258091, year = {2025}, author = {Hashem, I and Wang, J and Van Impe, JFM}, title = {A Discretized Overlap Resolution Algorithm (DORA) for resolving spatial overlaps in individual-based models of microbes.}, journal = {PLoS computational biology}, volume = {21}, number = {4}, pages = {e1012974}, pmid = {40258091}, issn = {1553-7358}, mesh = {*Algorithms ; *Models, Biological ; Computational Biology/methods ; Computer Simulation ; Biofilms/growth &amp; development ; }, abstract = {Individual-based modeling (IbM) is an instrumental tool for simulating spatial microbial growth, with applications in both microbial ecology and biochemical engineering. Unlike Cellular Automata (CA), which use a fixed grid of cells with predefined rules for interactions, IbMs model the individual behaviors of cells, allowing complex population dynamics to emerge. IbMs require more detailed modeling of individual interactions, which introduces significant computational challenges, particularly in resolving spatial overlaps between cells. Traditionally, this is managed using arrays or kd-trees, which require numerous pairwise comparisons and become inefficient as population size increases. To address this bottleneck, we introduce the Discretized Overlap Resolution Algorithm (DORA), which employs a grid-based framework to efficiently manage overlaps. By discretizing the simulation space further and assigning circular cells to specific grid units, DORA transforms the computationally intensive pairwise comparison process into a more efficient grid-based operation. This approach significantly reduces the computational load, particularly in simulations with large cell populations. Our evaluation of DORA, through simulations of microbial colonies and biofilms under varied nutrient conditions, demonstrates its superior computational efficiency and ability to accurately capture microbial growth dynamics compared to conventional methods. DORA's grid-based strategy enables the modeling of densely populated microbial communities within practical computational timeframes, thereby expanding the scope and applicability of individual-based modeling.}, }
@article {pmid40257249, year = {2025}, author = {Maggiori, C and John, Z and Bower, DM and Millan, M and Hahn, AS and McAdam, A and Johnson, SS}, title = {Draft genome sequence of a member of a putatively novel Rubrobacteraceae genus from lava tubes in Lava Beds National Monument.}, journal = {Microbiology resource announcements}, volume = {14}, number = {5}, pages = {e0133524}, pmid = {40257249}, issn = {2576-098X}, support = {/NASA/NASA/United States ; }, abstract = {We report the draft genome sequence of a member of a potentially novel genus of Rubrobacteraceae isolated from Golden Dome Cave in Lava Beds National Monument. Members of this family are known to inhabit thermophilic environments. The metagenome-assembled genome presented here helps illuminate the genetic capacity of basaltic lava tube environments.}, }
@article {pmid40253969, year = {2025}, author = {Achouri, H and Derguini, A and Idres, T and Selamoglu, Z and Hamadi, NB and Jalouli, M and Elfalleh, W and Bendif, H and Badraoui, R and Boufahja, F and Dellali, M}, title = {Impact of climate change on the toxicity of bisphenol A in Mytilus galloprovincialis and assessment of phycoremediation using Nannochloropsis salina via a multi-biomarker strategy and modeling.}, journal = {Marine pollution bulletin}, volume = {216}, number = {}, pages = {118010}, doi = {10.1016/j.marpolbul.2025.118010}, pmid = {40253969}, issn = {1879-3363}, mesh = {Animals ; *Mytilus/drug effects ; *Benzhydryl Compounds/toxicity ; *Phenols/toxicity ; *Water Pollutants, Chemical/toxicity ; Biomarkers/metabolism ; *Climate Change ; *Stramenopiles ; Oxidative Stress ; Lipid Peroxidation ; Bisphenol A Compounds ; }, abstract = {In the current study, the mussels Mytilus galloprovincialis, exposed to four varying temperatures (17, 20, 23, and 26 °C), were contaminated with 50 μg/L of bisphenol A both with and without Nannochloropsis salina. The toxicity evaluation is determined by quantifying various biomarkers related to oxidative stress, neurotoxicity, and cellular damage. The key findings indicate that the toxicity of bisphenol A is heightened by rising temperature. The impact of bisphenol A is most evident at 26 °C, leading to excessive production of reactive oxygen species, depletion of non-enzymatic antioxidants, and activation of antioxidant enzymes (catalase and glutathione-S-transferase). The rise in malondialdehyde levels confirms lipid peroxidation caused by bisphenol A and intensified by thermal stress. These findings have been supported by strong molecular interactions between bisphenol A and lectin mytilec apo-form and proximal thread matrix protein 1 from M. galloprovincialis following the computational modeling assay. The incorporation of N. salina as a food additive helped, firstly, to mitigate the stress effects and, secondly, resulted in a noticeable enhancement of oxidative balance and filtration ability, along with decreased lipid peroxidation.}, }
@article {pmid40252751, year = {2025}, author = {Tuts, L and Heyndrickx, M and Becue, I and Boon, N and De Maesschalck, P and Rasschaert, G}, title = {Tracking antibiotics and antibiotic-resistant E. coli in the aquatic environment linked to agriculture.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {374}, number = {}, pages = {126265}, doi = {10.1016/j.envpol.2025.126265}, pmid = {40252751}, issn = {1873-6424}, mesh = {*Escherichia coli/drug effects ; *Anti-Bacterial Agents/analysis ; *Environmental Monitoring ; *Agriculture ; *Water Pollutants, Chemical/analysis ; *Drug Resistance, Bacterial ; Groundwater/microbiology/chemistry ; Water Microbiology ; }, abstract = {The application of manure to fertilize agricultural land is associated with the introduction of antibiotic residues and bacteria, including antibiotic-resistant bacteria, which can reach surface water through runoff and drainage and groundwater through leaching from the soil. This was investigated by sampling 50 surface water locations (before and after fertilization) and 50 groundwater wells for the presence of antibiotic residues and the presence of antibiotic-resistant bacteria. For the latter, Escherichia coli and extended-spectrum β-lactamase (ESBL) producing E. coli were used as indicators and profiled for antibiotic resistance. The presence of a wide range of antibiotic residues, though at low concentrations (0.01-10 μg/L), in freshwater ecosystems highlights the extensive spread of these substances. Only 16 % of the samples were consistently free of antibiotic residues throughout both sampling periods. Notably, the frequent occurrence of sulfonamides and lincomycin in surface waters raises concerns as their concentrations occasionally exceed the predicted no-effect levels for antimicrobial resistance selection. Maximum concentrations were reported at 8.83 μg/L and 1.60 μg/L for sulfamethoxazole and lincomycin, respectively. Additionally, resistance patterns in E. coli indicate increased resistance to sulfamethoxazole following the fertilization period, suggesting that the application of manure on fields contributes to a rise in antibiotic resistance from 20 % to 48 %. Although antibiotic contamination in groundwater is less prevalent, antibiotic resistance remains widespread. In particular, ESBL-producing E. coli exhibit heightened resistance levels, not limited to β-lactam antibiotics. The detection of resistance to critical last-resort antibiotics such as carbapenems and colistin further emphasizes the urgency of addressing antibiotic resistance in environmental contexts. This study highlights the need for continued monitoring and the implementation of legislation to reduce antibiotic pollution and tackle resistance in aquatic ecosystems.}, }
@article {pmid40251008, year = {2025}, author = {Rizaludin, MS and Díaz, ASL and Zweers, H and Raaijmakers, JM and Garbeva, P}, title = {Foliar infections by Botrytis cinerea modulate the tomato root volatilome and microbiome.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {5}, pages = {}, pmid = {40251008}, issn = {1574-6941}, support = {024.004.014/NWO_/Dutch Research Council/Netherlands ; }, mesh = {*Plant Roots/microbiology/chemistry/metabolism ; *Botrytis/physiology ; *Solanum lycopersicum/microbiology/genetics/chemistry ; *Microbiota ; *Volatile Organic Compounds/metabolism/analysis ; *Plant Diseases/microbiology ; Rhizosphere ; Bacteria/classification/genetics/isolation &amp; purification ; Plant Leaves/microbiology ; Soil Microbiology ; }, abstract = {The fungal pathogen Botrytis cinerea causes significant damage to aboveground plant parts, but its impact on root chemistry and microbiome composition is less understood. This study investigated how B. cinerea foliar infection influences the root volatilome and microbiome of two tomato genotypes: wild Solanum pimpinellifolium and domesticated Solanum lycopersicum var. Moneymaker. In the absence of infection, wild tomato roots emitted higher levels of monoterpenes such as α-pinene and terpinene compared to domesticated tomato roots. The fungal infection induced elevated levels of benzyl alcohol and benzofuran in the root headspace and/or rhizosphere of both genotypes, alongside genotype-specific changes. Multivariate analyses revealed that B. cinerea significantly altered bacterial and fungal community compositions in the rhizosphere and rhizoplane, with stronger bacterial community shifts in the rhizoplane. Taxa depletion and enrichment were observed, particularly among Proteobacteria and Ascomycota. Mantel tests showed significant correlations between rhizoplane bacterial community compositions and root-associated volatilome. Notably, enriched bacterial taxa such as Pelomonas and Comamonadaceae positively correlated with benzyl alcohol and benzofuran levels in the root volatilome. These findings demonstrate that B. cinerea foliar infection might induce profound changes in root-associated volatilome and microbiome composition, highlighting its systemic effects on plant root chemistry and microbiome composition.}, }
@article {pmid40250533, year = {2025}, author = {Rosario Rodero, MD and Steyer, JP and Pérez-Bernal, MF and Verstraete, W and Escudié, R and Capson-Tojo, G}, title = {Dinitrogen fixation by open purple non-sulfur bacteria cultures for protein production: Diazotrophy boosts photoheterotrophic uptake rates.}, journal = {Bioresource technology}, volume = {430}, number = {}, pages = {132554}, doi = {10.1016/j.biortech.2025.132554}, pmid = {40250533}, issn = {1873-2976}, mesh = {*Nitrogen Fixation/physiology ; Biomass ; Rhodopseudomonas/metabolism ; Nitrogen/metabolism ; Heterotrophic Processes ; Light ; *Bacterial Proteins/biosynthesis ; }, abstract = {Purple non-sulfur bacteria (PNSB) offer a sustainable alternative to current inefficient protein production systems thanks to their high yields. This study explored the potential of specialized diazotrophic PNSB open cultures for protein production, benchmarking their performance against ammonium-grown PNSB and other diazotrophs. While diazotrophic yields (0.85-0.93 gCODbiomass·gCODsubstrate[-1]; COD being chemical oxygen demand) were slightly lower than non-diazotrophic (∼1.0), they were over double those of heterotrophic-diazotrophic rhizobacteria, with full N recovery as biomass (∼1.0 gNbiomass·gNfixed[-1]). Photoheterotrophic-diazotrophic uptake rates were the fastest ever reported for PNSB and any other diazotroph (e.g., 5.20 ± 0.83 vs. 2.64 ± 0.34 gCODsubstrate·gCODbiomass[-1]·d[-1] for PNSB on NH4[+]). Optimal rates required high light intensities, aligning with diazotrophic energy demands. Photoheterotrophic-diazotrophic conditions were highly selective, enriching a specialized Rhodopseudomonas palustris strain. Biomass protein contents and essential amino acid metrics confirmed nutritional suitability for humans. This work lays the background for exploiting PNSB's potential to address global protein demands through sustainable nitrogen fixation.}, }
@article {pmid40248914, year = {2025}, author = {Zhang, RG and Shang, HY and Milne, RI and Almeida-Silva, F and Chen, H and Zhou, MJ and Shu, H and Jia, KH and Van de Peer, Y and Ma, YP}, title = {SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics.}, journal = {Nucleic acids research}, volume = {53}, number = {7}, pages = {}, pmid = {40248914}, issn = {1362-4962}, support = {2022YFF1301700//National Key Research and Development Program/ ; KIBXD202401//Kunming Institute of Botany, Chinese Academy of Sciences/ ; //Light of West China/ ; 202101BC070003//Key Basic Research Programs of Yunnan Province/ ; 2022SJ07X-03//PSESP/ ; }, mesh = {*Synteny/genetics ; *Genomics/methods ; *Evolution, Molecular ; *Genome, Plant ; Phylogeny ; Polyploidy ; Algorithms ; Plants/genetics ; }, abstract = {With the explosive growth of whole-genome datasets, accurate detection of orthologous synteny has become crucial for reconstructing evolutionary history. However, current methods for identifying orthologous synteny face great limitations, particularly in scaling with varied polyploidy histories and accurately removing out-paralogous synteny. In this study, we developed a scalable and robust approach, based on the Orthology Index (OI), to effectively identify orthologous synteny. Our evaluation across a large-scale empirical dataset with diverse polyploidization events demonstrated the high reliability and robustness of the OI method. Simulation-based benchmarks further validated the accuracy of our method, showing its superior performance against existing methods across a wide range of scenarios. Additionally, we explored its broad applications in reconstructing the evolutionary histories of plant genomes, including the inference of polyploidy, identification of reticulation, and phylogenomics. In conclusion, OI offers a robust, interpretable, and scalable approach for identifying orthologous synteny, facilitating more accurate and efficient analyses in plant evolutionary genomics.}, }
@article {pmid40248762, year = {2025}, author = {Flores, C and Millard, S and Seekatz, AM}, title = {Bridging Ecology and Microbiomes: Applying Ecological Theories in Host-associated Microbial Ecosystems.}, journal = {Current clinical microbiology reports}, volume = {12}, number = {1}, pages = {9}, pmid = {40248762}, issn = {2196-5471}, abstract = {PURPOSE OF REVIEW: This review explores the application of classical ecological theory to host-associated microbiomes during initial colonization, maintenance, and recovery. We discuss unique challenges of applying these theories to host-associated microbiomes and host factors to consider going forward.<br><br>RECENT FINDINGS: Recent studies applying community ecology principles to host microbiomes continue to demonstrate a role for both selective and stochastic processes in shaping host-associated microbiomes. However, ecological frameworks developed to describe dynamics during homeostasis do not necessarily apply during diseased or highly perturbed states, where large variations can potentially lead to alternate stable states.<br><br>SUMMARY: Despite providing valuable insights, the application of ecological theories to host-associated microbiomes has some unique challenges. The integration of host-specific factors, such as genotype or immune dynamics in ecological models or frameworks is crucial for understanding host microbiome assembly and stability, which could improve our ability to predict microbiome outcomes and improve host health.}, }
@article {pmid40247944, year = {2025}, author = {Sun, Y and Sun, S and Zahid, MS and Qiu, Q and Wang, L and Wang, S}, title = {Root-applied brassinosteroid and salicylic acid enhance thermotolerance and fruit quality in heat-stressed 'Kyoho' grapevines.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1563270}, pmid = {40247944}, issn = {1664-462X}, abstract = {INTRODUCTION: The increasingly severe global greenhouse effect has become an irreversible trend, significantly impacting viticulture regions through heat stress during various grape growth stages, especially under protected cultivation conditions where high temperatures frequently occur. Therefore, studying the impact of heat stress on grapevine growth and fruit quality across the entire growth and development period, along with effective mitigation measures, is crucial.<br><br>METHODS: In this study, three-year-old 'Kyoho' grapevines were used as experimental materials, with four treatment groups: a control group, a hightemperature group (heat stress, HT), a high-temperature + brassinolide group (BR), and a high-temperature + salicylic acid group (SA). During the flowering, young berry swelling, and veraison stages, BR and SA were applied via nutrient solutions every seven days.<br><br>RESULTS: The results demonstrated that BR restored the maximum photosynthetic rate (Amax) to 96.14% of CK by the 18th day of flowering, significantly outperforming SA's recovery rate of 86.64%. Both treatments maintained light saturation points (1200 &#x3bc;mol&#x2022;m[&#x207b;&#xb2;]&#x2022;s[&#x207b;&#xb9;]) and CO2 saturation thresholds equivalent to CK. The decline in PSII photochemical efficiency (Fv/Fm) was reduced from 18% in HT to 5-8% in BR/SA-treated groups, with BR showing minimal deviation (2.3%) from CK during veraison, effectively mitigating PSII photoinhibition caused by heat stress. Furthermore, both treatments reduced leaf malondialdehyde (MDA) content, minimizing membrane lipid peroxidation, while increasing soluble protein (SP) content to protect leaves. Under heat stress, BR notably improved the fruit set rate by 22.67% compared to HT (SA: 13%), promoted berry expansion, and enhanced the accumulation of sugars and anthocyanins in the fruit skin, with SA showing similar, though slightly less pronounced, effects.<br><br>DISCUSSION: These findings provide valuable theoretical insights into the use of exogenous hormones in root nutrient solutions as a strategy to mitigate the adverse effects of heat stress in grape production.}, }
@article {pmid40247820, year = {2025}, author = {Liu, M and Yao, X and Wang, H and Xu, X and Kong, J and Wang, Y and Chen, W and Bai, H and Wang, Z and Setati, ME and Crauwels, S and Blancquaert, E and Fan, P and Liang, Z and Dai, Z}, title = {Carposphere microbiota alters grape volatiles and shapes the wine grape typicality.}, journal = {The New phytologist}, volume = {246}, number = {5}, pages = {2280-2294}, doi = {10.1111/nph.70152}, pmid = {40247820}, issn = {1469-8137}, support = {NXNYYZ202101//Agricultural Breeding Project of Ningxia Hui Autonomous Region/ ; U20A2041//National Natural Science Foundation of China/ ; JCTD-2022-06//CAS Youth Interdisciplinary Team/ ; 2021YFE0109500//National Key Research and Development Program of China/ ; YSBR-093//CAS Project for Young Scientists in Basic Research/ ; }, mesh = {*Vitis/microbiology/genetics/metabolism ; *Volatile Organic Compounds/metabolism ; *Microbiota ; Fruit/microbiology/genetics/metabolism ; *Wine/microbiology ; Sphingomonas/physiology ; Transcriptome/genetics ; Metabolome ; Gene Expression Regulation, Plant ; }, abstract = {While specific environments are known to shape plant metabolomes and the makeup of their associated microbiome, it is as yet unclear whether carposphere microbiota contribute to the characteristics of grape fruit flavor of a particular wine region. Here, carposphere microbiomes and berry transcriptomes and metabolomes of three grape cultivars growing at six geographic sites were analyzed. The composition of the carposphere microbiome was determined mainly by environmental conditions, rather than grape genotype. Bacterial microbiota likely contributed to grape volatile profiles. Particularly, candidate operational taxonomic units (OTUs) in genus Sphingomonas were highly correlated with grape C6 aldehyde volatiles (also called green leaf volatiles, GLVs), which contribute to a fresh taste. Furthermore, a core set of expressed genes was enriched in lipid metabolism, which is responsible for bacterial colonization and C6 aldehyde volatile synthesis activation. Finally, a similar grape volatile profile was observed after inoculating the berry skin of two grape cultivars with Sphingomonas sp., thus providing evidence for the hypothetical microbe-metabolite relationship. These results provide novel insight into how the environment-microbiome-plant quality (E × Mi × Q) interaction may shape berry flavor and thereby typicality, serving as a foundation for decision-making in vineyard microbial management.}, }
@article {pmid40247656, year = {2025}, author = {Bonazzi, E and De Barba, C and Lorenzon, G and Maniero, D and Bertin, L and Barberio, B and Facciotti, F and Caprioli, F and Scaldaferri, F and Zingone, F and Savarino, EV}, title = {Recent developments in managing luminal microbial ecology in patients with inflammatory bowel disease: from evidence to microbiome-based diagnostic and personalized therapy.}, journal = {Expert review of gastroenterology &amp; hepatology}, volume = {19}, number = {5}, pages = {563-576}, doi = {10.1080/17474124.2025.2495087}, pmid = {40247656}, issn = {1747-4132}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Precision Medicine ; Animals ; Fecal Microbiota Transplantation ; *Colitis, Ulcerative/therapy/microbiology/diagnosis ; *Inflammatory Bowel Diseases/therapy/microbiology/diagnosis ; *Crohn Disease/therapy/microbiology/diagnosis ; }, abstract = {INTRODUCTION: Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is a chronic condition characterized by abnormal immune responses and intestinal inflammation. Emerging evidence highlights the vital role of gut microbiota in IBD's onset and progression. Recent advances have shaped diagnostic and therapeutic strategies, increasingly focusing on microbiome-based personalized care. Methodology: this review covers studies from 2004 to 2024, reflecting the surge in research on luminal microbial ecology in IBD. Human studies were prioritized, with select animal studies included for mechanistic insights. Only English-language, peer-reviewed articles - clinical trials, systematic reviews, and meta-analyses - were considered. Studies without clinical validation were excluded unless offering essential insights. Searches were conducted using PubMed, Scopus, and Web of Science.<br><br>AREAS COVERED: we explore mechanisms for managing IBD-related microbiota, including microbial markers for diagnosis and novel therapies such as fecal microbiota transplantation, metabolite-based treatments, and precision microbiome modulation. Additionally, we review technologies and diagnostic tools used to analyze gut microbiota composition and function in clinical settings. Emerging data supporting personalized therapeutic strategies based on individual microbial profiles are discussed.<br><br>EXPERT OPINION: Standardized microbiome research integration into clinical practice will enhance precision in IBD care, signaling a shift toward microbiota-based personalized medicine.}, }
@article {pmid40246153, year = {2025}, author = {Bharathan, A and Arafath, Y and Fathima, A and Hassan, S and Singh, P and Kiran, GS and Selvin, J}, title = {Implication of environmental factors on the pathogenicity of Vibrio vulnificus: Insights into gene activation and disease outbreak.}, journal = {Microbial pathogenesis}, volume = {204}, number = {}, pages = {107591}, doi = {10.1016/j.micpath.2025.107591}, pmid = {40246153}, issn = {1096-1208}, mesh = {*Vibrio vulnificus/pathogenicity/genetics/drug effects ; Humans ; *Vibrio Infections/epidemiology/microbiology ; *Disease Outbreaks ; Virulence Factors/genetics ; Climate Change ; Virulence/genetics ; Gene Expression Regulation, Bacterial ; Temperature ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Animals ; Biofilms/growth &amp; development ; }, abstract = {Climate change, particularly rising sea surface temperatures and altered salinity levels has contributed to the increased prevalence of Vibrio vulnificus infections in humans and marine life. This opportunistic pathogen thrives in warm, estuarine environments, and its virulence is influenced by temperature-dependent gene expression, such as the activation of pVvBt2. Elevated temperatures and iron availability enhance pathogenicity by upregulating key virulence factors, including hemolysin, exotoxins, and biofilm-associated genes. Climate-driven shifts in microbial ecology have also facilitated the global expansion of V. vulnificus, leading to more frequent outbreaks and an increasing threat to public health. The unregulated use of antibiotics has also contributed to the emergence of resistant strains, complicating treatment strategies. This review explores the complex interplay between climate change and the molecular mechanisms driving V. vulnificus pathogenicity, global gene expression responses, and the implications for disease outbreaks. We also discuss current and emerging therapeutic approaches, including antibiotic stewardship and vaccine development, to mitigate the rising health risks posed by this climate-sensitive pathogen.}, }
@article {pmid40244660, year = {2025}, author = {Narla, AV and Hwa, T and Murugan, A}, title = {Dynamic coexistence driven by physiological transitions in microbial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {16}, pages = {e2405527122}, pmid = {40244660}, issn = {1091-6490}, support = {R35 GM151211/GM/NIGMS NIH HHS/United States ; R35GM151211//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 542387//Simons Foundation (SF)/ ; 2029480//NSF | BIO | Division of Molecular and Cellular Biosciences (MCB)/ ; 2317138//NSF | MPS | Division of Physics (PHY)/ ; }, mesh = {*Ecosystem ; *Models, Biological ; Biomass ; *Microbiota/physiology ; *Microbial Interactions/physiology ; Bacteria/growth &amp; development ; }, abstract = {Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes in exponential growth often modify their environments so strongly that they are forced out of the growth state into stressed, nongrowing states. Such dynamics are typical of ecological succession in nature and serial-dilution cycles in the laboratory. Here, we introduce a phenomenological model, the Community State Model, to gain insight into the dynamic coexistence of microbes due to changes in their physiological states during cyclic succession. Our model specifies the growth preference of each species along a global ecological coordinate, taken to be the biomass density of the community, but is otherwise agnostic to specific interactions (e.g., nutrient starvation, stress, aggregation), in order to focus on self-consistency conditions on combinations of physiological states, "community states," in a stable ecosystem. We identify three key features of such dynamical communities that contrast starkly with steady-state communities: enhanced community stability through staggered dominance of different species in different community states, increased tolerance of community diversity to fast growing species dominating distinct community states, and increased requirement of growth dominance by late-growing species. These features, derived explicitly for simplified models, are proposed here as principles aiding the understanding of complex dynamical communities. Our model shifts the focus of ecosystem dynamics from bottom-up studies based on fixed, idealized interspecies interaction to top-down studies based on accessible macroscopic observables such as growth rates and total biomass density, enabling quantitative examination of community-wide characteristics.}, }
@article {pmid40243315, year = {2025}, author = {Weng, L and Cui, Y and Jian, W and Zhang, Y and Pang, L and Cao, Y and Zhou, Y and Liu, W and Lin, H and Tao, Y}, title = {Inter-kingdom interactions and environmental influences on the oral microbiome in severe early childhood caries.}, journal = {Microbiology spectrum}, volume = {13}, number = {6}, pages = {e0251824}, pmid = {40243315}, issn = {2165-0497}, support = {31901116//National Natural Science Foundation of China/ ; 2022A1515012345//Basic and Applied Basic Research Foundation of Guangdong Province/ ; }, mesh = {Humans ; *Dental Caries/microbiology ; *Microbiota/genetics ; Child, Preschool ; Saliva/microbiology/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Female ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Dental Plaque/microbiology ; Fungi/classification/genetics/isolation &amp; purification ; Hydrogen-Ion Concentration ; Candida albicans/isolation &amp; purification ; }, abstract = {UNLABELLED: Dental caries arise from intricate interactions among oral microorganisms, impacting ecological stability and disease progression. In this study, we aimed to investigate the microbial diversity and inter-kingdom interactions in severe early childhood caries (S-ECC) and assess the influence of environmental factors such as salivary pH and trace elements. We analyzed 61 children aged 3-4 years with complete deciduous dentition, evaluating salivary pH, buffering capacity, and trace elements (iron, fluoride). We examined the performance of 16S rRNA V1-V9 regions gene and internal transcribed spacer (ITS) primers for bacteria and fungi from plaque and saliva to characterize community compositions and diversity. Findings revealed significant shifts in bacterial diversity in S-ECC saliva samples, marked by decreased diversity and elevated abundance of cariogenic species, particularly Streptococcus mutans. Candida albicans was notably more prevalent in the S-ECC group, implicating its potential role in pathogenesis. Iron and fluoride concentrations showed no significant correlation with microbial community structure. Network analyses uncovered complex intra- and inter-kingdom interactions, underscoring cooperative and competitive dynamics. S-ECC children exhibited higher abundances of bacteria (Streptococcus mutans, Granulicatella, Actinomyces) and fungi (Candida albicans), with specific microbial taxa associated with reduced salivary pH.<br><br>IMPORTANCE: This study illuminates the intricate relationship between bacteria and fungi within the oral microbial community of children, specifically highlighting differences between those with S-ECC and those without caries. Through an extensive analysis of the microbial composition in both saliva and dental plaque, we identified a significant increase in the abundance of specific bacterial taxa (e.g., S. mutans, Granulicatella, Actinomyces) and fungal species (e.g., C. albicans) in the oral cavities of children with S-ECC. This finding underscores the potential role of these microorganisms in the development of caries. Contrary to previous studies that emphasize the importance of iron and fluoride in oral health, our research found no significant correlation between the concentrations of these elements and the composition of oral microbial communities. This result challenges conventional understanding and opens new avenues for future research. Additionally, our findings revealed an association between Veillonella sp., Propionibacterium sp., and Candida sp. and reduced salivary pH. This provides novel insights into the relationship between the oral microenvironment and caries development. The implications of our findings are substantial for the development of prevention and intervention strategies targeting childhood caries. They also underscore the critical need for a deeper exploration of oral microbial interactions and their environmental influences.}, }
@article {pmid40241747, year = {2025}, author = {Takahashi, M and Hiraoka, S and Matsumoto, Y and Shibagaki, R and Ujihara, T and Maeda, H and Seo, S and Nagasaki, K and Takeuchi, H and Matsuzaki, S}, title = {Host-encoded DNA methyltransferases modify the epigenome and host tropism of invading phages.}, journal = {iScience}, volume = {28}, number = {4}, pages = {112264}, pmid = {40241747}, issn = {2589-0042}, abstract = {Restriction modification (RM) systems are ubiquitous bacterial defense systems; however, some phages evade RM system and adapt to their bacterial hosts. In such cases, phages are thought to stochastically acquire DNA methylation from host-encoded DNA methyltransferases (MTases), facilitating host adaptation. However, no studies have directly compared the methylomes of host bacteria and their infecting phages. Here, we demonstrate the epigenetic landscape of adapted phages with diverse infection histories, focusing on the broad host-range phage KHP30T as its adapts to three Helicobacter pylori strains. Using a multistage infection system, we observed that the adapted phages displayed significantly high titers against the last infected H. pylori strain, suggesting an attendant change in host tropism. Single-molecule real-time sequencing revealed that methylated motifs were predominantly shared between the adapted phages and their most recent host. Our findings enhance our understanding of epigenetic phage-host interactions, which have significant implications for microbial ecology.}, }
@article {pmid40240613, year = {2025}, author = {Dhungana, I and Nguyen, NH}, title = {Legacy of Repeated Cultivation Drives Cyclical Microbial Community Development in a Tropical Oxisol Soil.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {30}, pmid = {40240613}, issn = {1432-184X}, support = {HAW08042-H//U.S. Department of Agriculture/ ; }, mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/growth &amp; development ; *Fungi/classification/growth &amp; development/genetics/isolation &amp; purification ; Soil/chemistry ; Agriculture/methods ; Zea mays/growth &amp; development/microbiology ; *Archaea/classification/growth &amp; development/genetics/isolation &amp; purification ; *Microbiota ; Tropical Climate ; Crops, Agricultural/growth &amp; development/microbiology ; Lactuca/growth &amp; development/microbiology ; Mustard Plant/growth &amp; development/microbiology ; }, abstract = {Agricultural practices and the crop being actively cultivated are some of the most important contributors to soil microbial community assembly processes in agroecosystems. However, it is not well-understood how the cultivation of diverse crop species can directionally shift complex soil microbial communities, especially under continuous monoculture systems. Here, we conducted a field experiment to assess how three crop species (Lactuca sativa, Brassica juncea, and Zea mays) may shift soil microbial (bacteria/archaea and fungi) communities when planted in a monoculture and repeatedly grown for three cycles in a tropical Oxisol soil. We found that while plant species made limited contributions to microbial community differentiation, repeated cultivation was a strong driver of community development over time. The bacterial/archaeal communities exhibited a cyclical community development pattern, initially with strong differentiation that attenuated to a steady state at the end of the three cycles. In contrast, fungal communities generally developed more linearly and may have only started to stabilize after three cropping cycles. These developments may speak to the stronger legacy effects on fungal communities. Together, these results highlight the differences between how bacteria/archaea and fungal communities develop, especially in tropical, underdeveloped, intensively degraded, or marginal soils.}, }
@article {pmid40239902, year = {2025}, author = {Ma, H and Chen, S and Lv, L and Ye, Z and Yang, J and Wang, B and Zou, J and Li, J and Ganigué, R}, title = {Large-sized aerobic granular biofilm: stable biotechnology to improve nitrogen removal and reduce sludge yield.}, journal = {Bioresource technology}, volume = {429}, number = {}, pages = {132543}, doi = {10.1016/j.biortech.2025.132543}, pmid = {40239902}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Biofilms/growth &amp; development ; *Nitrogen/isolation &amp; purification/metabolism ; Aerobiosis ; Bioreactors/microbiology ; *Biotechnology/methods ; Biomass ; }, abstract = {Three parallel sequencing batch reactors (control, small-sized polyurethane sponge (PUS) (3.0 mm), and large-sized PUS (10.0 mm)) were used to investigate aerobic granular biofilm (AGB) characteristics. Results show that 10.0 mm PUS facilitated rapid formation of large-sized AGB (AGBL), which exhibited higher biomass concentration (8.5 g/L) and faster settling velocity (69.2-159.3 m/h) than aerobic granular sludge (AGS) (3.2 g/L and 38.6-80.0 m/h). The AGBL system also maintained long-term structural stability with a lower instability coefficient (0.004-0.018 min[-1]) than AGS (0.053-0.090 min[-1]). Additionally, during long-term operation, the AGBL system achieved excellent removal efficiencies for NH4[+]-N (99.6 ± 0.4 %) and total nitrogen (92.3 ± 2.6 %), and exhibited a lower sludge yield (0.05 gVSS/gCOD) than AGS (0.14 gVSS/gCOD). The larger size and compact structure of AGBL increased anoxic/anaerobic zones, enriching denitrifying and hydrolytic/fermentative bacteria. These findings highlight AGBL with large PUS as a more promising biotechnology for practical applications than conventional AGS.}, }
@article {pmid40238873, year = {2025}, author = {Bukhdruker, S and Gushchin, I and Shevchenko, V and Kovalev, K and Polovinkin, V and Tsybrov, F and Astashkin, R and Alekseev, A and Mikhaylov, A and Bukhalovich, S and Bratanov, D and Ryzhykau, Y and Kuklina, D and Caramello, N and Rokitskaya, T and Antonenko, Y and Rulev, M and Stoev, C and Zabelskii, D and Round, E and Rogachev, A and Borshchevskiy, V and Ghai, R and Bourenkov, G and Zeghouf, M and Cherfils, J and Engelhard, M and Chizhov, I and Rodriguez-Valera, F and Bamberg, E and Gordeliy, V}, title = {Proteorhodopsin insights into the molecular mechanism of vectorial proton transport.}, journal = {Science advances}, volume = {11}, number = {16}, pages = {eadu5303}, pmid = {40238873}, issn = {2375-2548}, mesh = {*Protons ; *Rhodopsins, Microbial/chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Proton Pumps/chemistry/metabolism ; Protein Conformation ; }, abstract = {Bacterial proton pumps, proteorhodopsins (PRs), are a major group of light-driven membrane proteins found in marine bacteria. They are functionally and structurally distinct from archaeal and eukaryotic proton pumps. To elucidate the proton transfer mechanism by PRs and understand the differences to nonbacterial pumps on a molecular level, high-resolution structures of PRs' functional states are needed. In this work, we have determined atomic-resolution structures of MAR, a PR from marine actinobacteria, in various functional states, notably the challenging late O intermediate state. These data and information from recent atomic-resolution structures on an archaeal outward proton pump bacteriorhodopsin and bacterial inward proton pump xenorhodopsin allow for deducing key universal elements for light-driven proton pumping. First, long hydrogen-bonded chains characterize proton pathways. Second, short hydrogen bonds allow proton storage and inhibit their backflow. Last, the retinal Schiff base is the active proton donor and acceptor to and from hydrogen-bonded chains.}, }
@article {pmid40238292, year = {2025}, author = {Zhang, Y and Lin, H and Xiong, Y and Zhang, Z and Zeng, L and Liu, Z}, title = {Fu Brick Tea Protects the Intestinal Barrier and Ameliorates Colitis in Mice by Regulating Gut Microbiota.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, pmid = {40238292}, issn = {2304-8158}, support = {2024HX118//Horizontal project of Shaoyang University/ ; 2024JJ7497//Foundation regional joint fund of Hunan Province natural Science/ ; 202401001313//The teaching reform research project of Hunan Province in 2024/ ; 2022YFE0111200//Innovation and transformation of key technologies for efficient preparation of catechin oxidation polymerization products/ ; }, abstract = {Ulcerative colitis (UC) pathogenesis is strongly linked to gut microbiota dysbiosis and compromised intestinal barrier integrity. Emerging evidence suggests that targeted dietary interventions may restore microbial homeostasis and ameliorate colitis progression. In this study, we evaluated the therapeutic potential of Fu Brick tea (FBT) using a dextran sulfate sodium (DSS)-induced murine colitis model. The results indicated that oral administration of FBT extract significantly improved the disease index, reduced inflammatory response, protected intestinal barrier protein (e.g., ZO-1), and maintained intestinal structure integrity. Furthermore, FBT intake increased the diversity of gut microbiota, promoted the growth of beneficial bacteria (e.g., Akkermansia), inhibited the proliferation of harmful bacteria (e.g., Desulfovibrioceae, Escherichia, and Helicobacter), restored intestinal homeostasis, and alleviated colitis symptoms including diarrhea. These findings position FBT as a promising nutraceutical candidate for UC management via multi-target modulation of mucosal immunity and microbial ecology.}, }
@article {pmid40238218, year = {2025}, author = {Zhadyra, S and Tao, F and Xu, P}, title = {Exploring the Microbiome and Functional Metabolism of Fermented Camel Milk (Shubat) Using Metagenomics.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, pmid = {40238218}, issn = {2304-8158}, abstract = {Shubat is a traditional fermented camel milk drink that originated in Central Asia, with especially deep cultural roots in Kazakhstan. However, systematic studies on the microbial ecology and functional genes of Shubat remain scarce. As a distinctive fer-mented food, its microbial diversity and functional properties have not been fully ex-plored. This study investigates the microbial diversity and functional potential of Shubat by using advanced metagenomic techniques. Its microbial community is mainly composed of bacteria (96.6%), with Lactobacillus, Lactococcus, and Streptococcus being the dominant genera. Functional annotations through EggNOG, KEGG, and CAZy databases highlighted the metabolic versatility of Shubat's microbiota. Key pathways included amino acid and carbohydrate metabolism, vitamin biosynthesis, and central carbon metabolism, emphasizing their roles in fermentation and nutritional enhancement. The identification of various enzymes related to chemical synthesis further emphasizes the contribution of the microbiota to Shubat's unique flavor and texture. This study not only provides an important basis for the scientific understanding of Shubat but also expands the application possibilities of fermented food in the field of health and nutrition and confers modern value and significance to traditional food. This integration of science and tradition has not only facilitated the development of food microbiology but also paved new pathways for the global dissemination of traditional foods and the development of functional foods.}, }
@article {pmid40237447, year = {2025}, author = {Choudoir, MJ and Ishaq, SL and Beiko, RG and Silva, DS and Allen-Vercoe, E and O'Doherty, KC}, title = {The case for microbiome stewardship: what it is and how to get there.}, journal = {mSystems}, volume = {10}, number = {5}, pages = {e0006225}, pmid = {40237447}, issn = {2379-5077}, support = {//University of Guelph Institute of Environmental Research/ ; R15 DK133826/DK/NIDDK NIH HHS/United States ; 191753/CAPMC/CIHR/Canada ; //Canada Research Chairs/ ; 7004439, ME022329//U.S. Department of Agriculture's National Institute of Food and Agriculture/ ; //Natural Sciences and Engineering Research Council of Canada/ ; NIH/NIDDK 1R15DK133826-01/NH/NIH HHS/United States ; }, mesh = {Animals ; Humans ; Agriculture ; Anti-Bacterial Agents ; Ecosystem ; *Microbiota ; Public Health ; }, abstract = {Microbiomes are essential for human, animal, plant, and ecosystem health. Despite widespread recognition of the importance of microbiomes, there is little attention paid to monitoring and safeguarding microbial ecologies on policy levels. We observe that microbiomes are deteriorating owing to practices at societal levels such as pesticide use in agriculture, air and water pollution, and overuse of antibiotics. Potential policy on these issues would cross multiple domains such as public health, environmental protection, and agriculture. We propose microbiome stewardship as a foundational concept that can act across policy domains to facilitate healthy microbiomes for human and ecosystem health. We examine challenges to be addressed and steps to take toward developing meaningful microbiome stewardship.}, }
@article {pmid40235320, year = {2025}, author = {Bahram Wlia, A and Majedi, S}, title = {Optimizing hygiene and microbial aspect of paper recycling: a sustainable approach for environmental conservation.}, journal = {Cellular and molecular biology (Noisy-le-Grand, France)}, volume = {71}, number = {3}, pages = {151-157}, doi = {10.14715/cmb/2025.71.3.18}, pmid = {40235320}, issn = {1165-158X}, mesh = {*Recycling/methods ; *Paper ; *Hygiene ; *Bacteria/isolation &amp; purification/classification/genetics ; *Conservation of Natural Resources/methods ; Iraq ; Waste Management/methods ; }, abstract = {This study explores microbial dynamics in paper recycling, emphasizing the significance of sustainable practices for environmental preservation. Samples were collected from various urban waste sources in Erbil city, Kurdistan Region, Iraq, including materials such as pizza boxes, cigarette packets, and coffee cups. Pure bacterial colonies were isolated using standard methods, and their morphological and physiological traits were characterized through biochemical tests. Identification of bacterial species followed established protocols. The study identified diverse bacterial species associated with paper waste, highlighting potential hygiene concerns in the recycling process. The findings of this study contribute to understanding the microbial ecology associated with paper waste and recycling processes. By optimizing hygiene measures and gaining insights into the microbial communities present, this research underscores the importance of sustainable practices in paper recycling to mitigate environmental impacts and promote a healthier ecosystem. Policies for future waste management and reduction of environmental risks have been proposed.}, }
@article {pmid40234253, year = {2025}, author = {Yao, B and Mou, X and Li, Y and Lian, J and Niu, Y and Liu, J and Lu, J and Li, Y and Li, Y and Wang, X}, title = {Distinct Assembly Patterns of Soil Bacterial and Fungal Communities along Altitudinal Gradients in the Loess Plateau's Highest Mountain.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {29}, pmid = {40234253}, issn = {1432-184X}, support = {23JRRA672//Youth Science and Technology Fund Program of Gansu Province/ ; 2023449//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 22JR5RA076//Gansu Province Natural Science Foundation Program/ ; }, mesh = {*Soil Microbiology ; *Altitude ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Ecosystem ; *Microbiota ; Biodiversity ; *Mycobiome ; China ; High-Throughput Nucleotide Sequencing ; }, abstract = {A critical issue in microbial ecology is quantifying the relative contributions of deterministic and stochastic processes to microbial community assembly, and predicting ecosystem function by understanding the ecological processes of community composition is an integral part. However, the mechanisms driving microbial community assembly along altitudinal gradients in mountain ecosystems remain largely unexplored. Here, we used high-throughput sequencing to examine the structural characteristics and diversity maintenance mechanisms of soil bacterial and fungal communities along an altitudinal gradient (2632-3661 m) in Mahan Mountain, the highest peak of the Loess Plateau. Proteobacteria, Acidobacteriota and Actinobacteriota dominated the bacterial communities, while Ascomycota, Basidiomycota and Mortierellomycota were the predominant fungal groups. Although elevation did not significantly affect bacterial and fungal alpha diversity, notable shifts in community structure were observed along the altitudinal gradients. Bacterial communities were predominantly shaped by deterministic processes, leading to pronounced structural and compositional differentiation across altitudes. In contrast, fungal community assembly was primarily determined by a combination of deterministic and stochastic processes, leading to small pronounced structural divergence. The interplay of topography, climate, and soil conditions influenced the altitudinal distribution and community structure of soil bacteria in this mountain ecosystem.}, }
@article {pmid40230839, year = {2025}, author = {Zhao, T and Wang, C and Liu, Y and Li, B and Shao, M and Zhao, W and Zhou, C}, title = {The role of polysaccharides in immune regulation through gut microbiota: mechanisms and implications.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1555414}, pmid = {40230839}, issn = {1664-3224}, mesh = {*Gastrointestinal Microbiome/immunology ; Humans ; *Polysaccharides/immunology/metabolism ; Animals ; Fatty Acids, Volatile/metabolism ; *Immunomodulation ; Cytokines/metabolism ; }, abstract = {Polysaccharides, as complex carbohydrates, play a pivotal role in immune modulation and interactions with the gut microbiota. The diverse array of dietary polysaccharides influences gut microbial ecology, impacting immune responses, metabolism, and overall well-being. Despite their recognized benefits, there is limited understanding of the precise mechanisms by which polysaccharides modulate the immune system through the gut microbiota. A comprehensive search of Web of Science, PubMed, Google Scholar, and Embase up to May 2024 was conducted to identify relevant studies. This study employs a systematic approach to explore the interplay between polysaccharides and the gut microbiota, focusing on cytokine-mediated and short-chain fatty acid (SCFA)-mediated pathways. The findings underscore the significant role of polysaccharides in shaping the composition and function of the gut microbiota, thereby influencing immune regulation and metabolic processes. However, further research is necessary to elucidate the detailed molecular mechanisms and translate these findings into clinical applications.}, }
@article {pmid40229524, year = {2025}, author = {Sakae, K and Kitagami, Y and Matsuda, Y}, title = {Rhizosphere Bacterial Communities Alter in Process to Mycorrhizal Developments of a Mixotrophic Pyrola japonica.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {28}, pmid = {40229524}, issn = {1432-184X}, support = {2023-4099//Japan Science Society/ ; JRMJSP2137//Japan Science and Technology Agency/ ; 24K01796//Japan Society for the Promotion of Science/ ; }, mesh = {*Mycorrhizae/growth &amp; development/physiology ; *Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology ; *Ericaceae/microbiology/growth &amp; development ; *Microbiota ; Biodiversity ; DNA, Bacterial/genetics ; }, abstract = {Rhizosphere bacteria work in synergy with mycorrhizal fungi to promote plant growth. The community structure of rhizosphere bacteria may be influenced by continuous changes in fungal associations with host plants. Asiatic herbaceous plant Pyrola japonica (Ericaceae) forms arbutoid mycorrhizas without fungal mantles, with its mycorrhizal development being visually distinguishable at the cellular level. This study aimed to investigate roles of rhizosphere bacteria and their community shifts along with mycorrhizal developments. We examined bacterial communities at three different developmental stages of mycorrhizal roots-limited, full, and digested-via a partial 16S rRNA amplicon sequencing. Both α- and β-diversities in the full condition were significantly lower than those in the limited and digested conditions. Significant clusters of bacterial compositions were found among all treatments. In terms of ecological processes of community assembly, communities in limited conditions and bulk soil were influenced by both deterministic and stochastic processes, whereas those in full and digested conditions were regulated only by stochastic ways. Furthermore, the order Rhizobiales and Actinomycetales known as mycorrhizal helper bacteria were characterized in the full and digested conditions through phylogenetic analysis and detection of indicator taxa. These results suggest that mycorrhizal fungi may play ecologically important roles not only as temporal drivers initiating the formation rhizosphere bacterial communities but also as key founders exerting continuous influences to establish priority effects. Moreover, the rhizosphere bacterial community remains after mycorrhizal degeneration and their historical continuity may contribute to maintaining plant-mycorrhizal fungi-bacterial associations.}, }
@article {pmid40228732, year = {2025}, author = {Zhang, R and Gong, C and Gao, Y and Chen, Y and Zhou, L and Lou, Q and Zhao, Y and Zhuang, H and Zhang, J and Shan, S and Wang, X and Qian, X and Lei, L and Wong, MH}, title = {Reducing antibiotic resistance genes in soil: The role of organic materials in reductive soil disinfestation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {374}, number = {}, pages = {126245}, doi = {10.1016/j.envpol.2025.126245}, pmid = {40228732}, issn = {1873-6424}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Genes, Bacterial ; }, abstract = {Increasing attention has been given to the role of reductive soil disinfestation (RSD) on antibiotic resistance genes (ARGs) in soil. The selection of organic materials in RSD is crucial to the effectiveness of the RSD method. However, the effects of distinct organic materials on ARGs remains unclear. In this study, we selected straw and rapeseed meal as the organic materials in RSD and explored their effects on ARGs. The results showed that using straw significantly reduced the abundance of ARGs, high-risk ARGs, and mobile genetic elements (MGEs) by 31.5 %-65.8 %, while using rapeseed meal led to ARGs enrichment. Structural equation modeling (SEM) analysis identified MGEs and microbial communities as the primary drivers of ARGS changes under different organic materials. The abundance of MGEs was effectively controlled in straw treatments, reducing the potential for horizontal gene transfer of ARGs. Bacterial diversity was significantly lower in the straw treatments compared to the rapeseed meal treatments, potentially leading to a reduced abundance of ARGs host bacteria. Network co-occurrence analysis further revealed that Symbiobacteraceae and Bacillus were potential bacterial hosts of ARGs. In straw treatments, these genera' abundance decreased by 12 %-100 % compared to the control (CK) and rapeseed meal groups, further inhibiting the spread of ARGs. These findings demonstrate that RSD with straw as the organic material is more effective in mitigating ARGs compared to rapeseed meal, providing insights into controlling soil antibiotic resistance risks and utilizing agricultural waste resources.}, }
@article {pmid40227232, year = {2025}, author = {Prochera, A and Muppirala, AN and Kuziel, GA and Soualhi, S and Shepherd, A and Sun, L and Issac, B and Rosenberg, HJ and Karim, F and Perez, K and Smith, KH and Archibald, TH and Rakoff-Nahoum, S and Hagen, SJ and Rao, M}, title = {Enteric glia regulate Paneth cell secretion and intestinal microbial ecology.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {40227232}, issn = {2050-084X}, support = {Fellowship//Schmidt Family Foundation/ ; K08 DK110532/DK/NIDDK NIH HHS/United States ; R01DK135707/NH/NIH HHS/United States ; Fellowship//National Defense Science and Engineering Graduate/ ; P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 DK135707/DK/NIDDK NIH HHS/United States ; Graduate Research Fellowship Program//National Science Foundation/ ; K08DK110532/NH/NIH HHS/United States ; R01 DK130836/DK/NIDDK NIH HHS/United States ; Odyssey Award//Smith Family Foundation/ ; R01DK130836/NH/NIH HHS/United States ; }, mesh = {Animals ; *Paneth Cells/metabolism/physiology ; Mice ; *Neuroglia/physiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Humans ; Myelin Proteolipid Protein/metabolism/genetics ; *Intestinal Mucosa/metabolism/microbiology ; *Enteric Nervous System/physiology ; Mice, Inbred C57BL ; Male ; Female ; }, abstract = {Glial cells of the enteric nervous system (ENS) interact closely with the intestinal epithelium and secrete signals that influence epithelial cell proliferation and barrier formation in vitro. Whether these interactions are important in vivo, however, is unclear because previous studies reached conflicting conclusions (Prochera and Rao, 2023). To better define the roles of enteric glia in steady state regulation of the intestinal epithelium, we characterized the glia in closest proximity to epithelial cells and found that the majority express the gene Proteolipid protein 1 (PLP1) in both mice and humans. To test their functions using an unbiased approach, we genetically depleted PLP1[+] cells in mice and transcriptionally profiled the small and large intestines. Surprisingly, glial loss had minimal effects on transcriptional programs and the few identified changes varied along the gastrointestinal tract. In the ileum, where enteric glia had been considered most essential for epithelial integrity, glial depletion did not drastically alter epithelial gene expression but caused a modest enrichment in signatures of Paneth cells, a secretory cell type important for innate immunity. In the absence of PLP1[+] glia, Paneth cell number was intact, but a subset appeared abnormal with irregular and heterogenous cytoplasmic granules, suggesting a secretory deficit. Consistent with this possibility, ileal explants from glial-depleted mice secreted less functional lysozyme than controls with corresponding effects on fecal microbial composition. Collectively, these data suggest that enteric glia do not exert broad effects on the intestinal epithelium but have an essential role in regulating Paneth cell function and gut microbial ecology.}, }
@article {pmid40223273, year = {2025}, author = {Yang, SY and Han, SM and Lee, JY and Kim, KS and Lee, JE and Lee, DW}, title = {Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2412001}, pmid = {40223273}, issn = {1738-8872}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Metagenomics/trends ; Multiomics/trends ; *Host Microbial Interactions/physiology ; *Translational Research, Biomedical/methods/trends ; Precision Medicine/methods/trends ; }, abstract = {The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.}, }
@article {pmid40222749, year = {2025}, author = {Belda, I and Izquierdo-Gea, S and Benitez-Dominguez, B and Ruiz, J and Vila, JCC}, title = {Wine Fermentation as a Model System for Microbial Ecology and Evolution.}, journal = {Environmental microbiology}, volume = {27}, number = {4}, pages = {e70092}, pmid = {40222749}, issn = {1462-2920}, support = {//Center for Computational, Evolutionary and Human Genomics, Stanford University. Postdoc Fellowship to Jean CC VIla/ ; FPU21/06830//Spanish Ministry of Science, Innovation and Universities/ ; PID2019-105834GA-I00//Agencia Estatal de Investigaci&#xf3;n/ ; PID2022-138343NB-I00//Agencia Estatal de Investigaci&#xf3;n/ ; PRE2022-103063//Agencia Estatal de Investigaci&#xf3;n/ ; }, mesh = {*Wine/microbiology ; *Fermentation ; *Biological Evolution ; Microbiota ; *Bacteria/metabolism/genetics ; Ecosystem ; Models, Biological ; Ecology ; }, abstract = {In vitro microbial communities have proven to be invaluable model systems for studying ecological and evolutionary processes experimentally. However, it remains unclear whether quantitative insights obtained from these laboratory systems can be applied to complex communities assembling and evolving in their natural ecological context. To bridge the gap between the lab and the 'real-world', there is a need for laboratory model systems that better approximate natural and semi-natural ecosystems. Wine fermentation presents an ideal system for this purpose, balancing experimental tractability with rich ecological and evolutionary dynamics. In this perspective piece we outline the key features that make wine fermentation a fruitful model system for ecologists and evolutionary biologists. We highlight the diversity of environmentally mediated interactions that shape community dynamics during fermentation, the complex evolutionary history of wine microbial populations, and the opportunity to study the impact of complex ecologies on evolutionary dynamics. By integrating knowledge from both wine research and microbial ecology and evolution we aim to enhance understanding and foster collaboration between these fields.}, }
@article {pmid40220383, year = {2025}, author = {Li, C and Zhu, L and Axe, L and Li, M}, title = {Acclimation of sludge-derived biofilms for effective removal of emerging contaminants: Impacts of inoculum source and carbon supplementation.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138235}, doi = {10.1016/j.jhazmat.2025.138235}, pmid = {40220383}, issn = {1873-3336}, mesh = {*Biofilms ; *Sewage/microbiology ; *Carbon ; *Water Pollutants, Chemical/metabolism ; Biodegradation, Environmental ; Sulfamethoxazole/metabolism ; Carbamazepine/metabolism ; Waste Disposal, Fluid/methods ; Acclimatization ; }, abstract = {Contaminants of emerging concern (CECs) have gathered significant public attention due to their widespread occurrence, high persistence, and increasing exposure potential. In this study, we used polyethylene biocarriers for acclimating biofilms from singular or combined activated sludges collected from three wastewater treatment plants (R, P, and L) over 5 month-long cycles. The acclimated biofilms achieved an average removal rate at 0.333, 0.313, and 0.185 week[-1] for N, N-diethyl-meta-toluamide (DEET), sulfamethoxazole (SMX), and carbamazepine (CBZ), respectively, when external carbon was supplemented, which were significantly higher (p < 0.05) than biofilms that did not receive external carbons. Metabolite screening revealed SMX transformation through ipso-hydroxylation and acetyl conjugation, while CBZ degradation could be initiated by epoxidation. Significant but slower degradation rates (0.024∼0.031 week[-1]) were observed for aminotriazole (AMT), lidocaine (LDC), and trimethoprim (TMP), whereas atrazine (ATZ) exhibited minimal removal, highlighting its high recalcitrance. Biofilms acclimated from individual R and P sludges, with external carbon supplementation, attained the greatest removal efficiencies for 7 CECs. Multivariate statistical correlations (p < 0.05) identified potential degraders, including Sphingomonas and Zoogolea for AMT, Labrys and Koazkia for CBZ, and Asprobacter, unclassified Cyclobacteriaceae (ELB16-189) and Bryobacteraceae (Fen-178) for LDC. Abundance distribution of potential degraders among biofilms revealed that Sludge R favored the enrichment of key degraders for AMT, CBZ and LDC, while Sludge P was more conducive to acclimating CBZ degraders. This study advances our understanding of strategies in biofilm acclimation to improve CEC removal and provides insights into degradation pathways and associated microbial communities for future research.}, }
@article {pmid40220189, year = {2025}, author = {Knoppersen, RS and Bose, T and Coutinho, TA and Hammerbacher, A}, title = {Inside the Belly of the Beast: Exploring the Gut Bacterial Diversity of Gonipterus sp. n. 2.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {27}, pmid = {40220189}, issn = {1432-184X}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Eucalyptus/parasitology/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Diet ; South Africa ; *Coleoptera/microbiology/physiology ; Gas Chromatography-Mass Spectrometry ; Introduced Species ; Biodiversity ; }, abstract = {The Eucalyptus snout beetle (Gonipterus sp. n. 2) is a destructive invasive pest of Eucalyptus plantations, responsible for significant defoliation and wood yield losses globally. Native to Australia, this beetle has adapted to thrive on diverse Eucalyptus hosts, overcoming their chemical defences. However, the mechanisms by which Gonipterus tolerates or utilises these plant defence metabolites remain poorly understood. In South Africa, Gonipterus sp. n. 2 poses a significant threat to Eucalyptus plantations by causing extensive defoliation and leading to substantial reductions in growth and wood production. This study investigates the relationship between diet, host Eucalyptus species, and the gut microbiome of Gonipterus sp. n. 2. Using controlled feeding experiments, beetles were reared on artificial, semi-artificial, and natural diets, as well as two Eucalyptus genotypes with distinct secondary metabolite profiles. High-throughput 16S rDNA sequencing and gas chromatography-mass spectrometry (GC-MS) revealed significant shifts in gut bacterial diversity and composition across diets. Natural diets supported the most diverse microbial communities, while artificial diets fostered a homogenised microbiome dominated by opportunistic taxa like Serratia. Host-specific effects were observed in frass microbiota, with substantial biotransformation of monoterpenes into less toxic derivatives. The results highlight the plasticity of Gonipterus gut microbiota, which enables metabolic adaptability and resilience in diverse environments. This microbial flexibility underpins the invasiveness of Gonipterus, emphasising the role of gut symbionts in overcoming host chemical defences. Understanding these interactions offers novel insights for microbiome-targeted pest management strategies, providing a sustainable approach to mitigate the impact of Gonipterus on global Eucalyptus forestry.}, }
@article {pmid40216640, year = {2025}, author = {Huttunen, KL and Malazarte, J and Jyväsjärvi, J and Lehosmaa, K and Muotka, T}, title = {Temporal Beta Diversity of Bacteria in Streams: Network Position Matters But Differently for Bacterioplankton and Biofilm Communities.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {26}, pmid = {40216640}, issn = {1432-184X}, support = {356403//Research Council of Finland/ ; 318230//Research Council of Finland/ ; 318230//Research Council of Finland/ ; }, mesh = {*Biofilms/growth &amp; development ; *Rivers/microbiology/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; *Biodiversity ; *Plankton/classification/genetics ; Soil Microbiology ; Ecosystem ; Seasons ; }, abstract = {Concern about biodiversity loss has yielded a surge of studies on temporal change in α-diversity, whereas temporal β-diversity has gained less interest. We sampled bacterioplankton, biofilm, and riparian soil bacteria repeatedly across the open-water season in a pristine stream network to determine the level of temporal β-diversity in relation to stream network position and environmental variability. We tested the hypothesis that aquatic bacterial communities in isolated and environmentally heterogenous headwaters exhibit high temporal β-diversity while the better-connected and environmentally more stable mainstem sections support more stable communities, and soil communities bear no relationship to network position. As expected, temporal β-diversity decreased from headwaters toward mainstems for bacterioplankton. Against expectations, an opposite pattern was observed for biofilm. For bacterioplankton, temporal β-diversity was positively related to temporal variability in water chemistry. For biofilm bacteria, temporal variability was negatively related to variability in temperature. Temporal β-diversity of soil communities did not show any response to stream network position, but was strongly related to variability in the soil environment. The two aquatic habitats and riparian soils supported distinctly different bacterial communities. The number of ASVs shared between the soil and the aquatic communities decreased along the network, and more so for bacterioplankton. The higher temporal variability of bacterial communities in the headwaters likely results from temporally variable input of propagules from riparian soil, emphasizing the role of land-water connection and network position to bacterioplankton community composition. Overall, bacterial communities exhibited high temporal variability, highlighting the importance of temporal replication to fully capture their network-scale biodiversity.}, }
@article {pmid40214404, year = {2025}, author = {Nilsen, T and Pettersen, R and Keeley, NB and Ray, JL and Majaneva, S and Stokkan, M and Hervik, A and Angell, IL and Snipen, LG and Sundt, M&#xd8; and Rudi, K}, title = {Association of Microbial Networks with the Coastal Seafloor Macrofauna Ecological State.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {15}, pages = {7517-7529}, pmid = {40214404}, issn = {1520-5851}, mesh = {Animals ; Aquaculture ; Archaea ; Ecosystem ; Iceland ; *Microbiota ; Norway ; *Aquatic Organisms/microbiology ; }, abstract = {Recent evidence suggests that there is a major switch in coastal seafloor microbial ecology already at a mildly deteriorated macrofaunal state. This knowledge is of critical value in the management and conservation of the coastal seafloor. We therefore aimed to determine the relationships between seafloor microbiota and macrofauna on a regional scale. We compared prokaryote, macrofauna, chemical, and geographical data from 1546 seafloor samples, which varied in their exposure to aquaculture activities along the Norwegian and Icelandic coasts. We found that the seafloor samples contained either a network centralized by a sulfur oxidizer (42.4% of samples, n = 656) or a network centralized by an archaeal ammonium oxidizer (44.0% of samples, n = 681). Very few samples contained neither network (9.8% of samples, n = 151) or both (3.8% of samples, n = 58). Samples with a sulfur oxidizer network had a 10-fold higher risk of macrofauna loss (odds ratios, 95% CI: 9.5 to 15.6), while those with an ammonium oxidizer network had a 10-fold lower risk (95% CI: 0.068 to 0.11). The sulfur oxidizer network was negatively correlated to distance from Norwegian aquaculture sites (Spearman rho = -0.42, p < 0.01) and was present in all Icelandic samples (n = 274). The ammonium oxidizer network was absent from Icelandic samples and positively correlated to distance from Norwegian aquaculture sites (Spearman rho = 0.67, p < 0.01). Based on 356 high-quality metagenome-assembled genomes (MAGs), we found that bicarbonate-dependent carbon fixation and low-affinity oxygen respiration were associated with the ammonium oxidizer network, while the sulfur oxidizer network was associated with ammonium retention, sulfur metabolism, and high-affinity oxygen respiration. In conclusion, our findings highlight the critical roles of microbial networks centralized by sulfur and ammonium oxidizers in mild macrofauna deterioration, which should be included as an essential part of seafloor surveillance.}, }
@article {pmid40209676, year = {2025}, author = {Schell, LD and Carmody, RN}, title = {An energetic framework for gut microbiome-mediated obesity induced by early-life exposure to antibiotics.}, journal = {Cell host &amp; microbe}, volume = {33}, number = {4}, pages = {470-483}, doi = {10.1016/j.chom.2025.03.009}, pmid = {40209676}, issn = {1934-6069}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/adverse effects/pharmacology ; *Obesity/chemically induced/microbiology/etiology/metabolism ; Animals ; Humans ; *Energy Metabolism/drug effects ; Female ; Mice ; Male ; }, abstract = {Early-life antibiotic (ELA) exposure has garnered attention for its potential role in modulating obesity risk, although outcomes from mouse experiments and human epidemiological studies often vary based on dosage and sex. Low-dose (subtherapeutic) antibiotics can enhance energy availability through moderate alterations in gut microbiome profile, while high-dose (therapeutic) antibiotics substantially deplete the gut microbiota, thereby contributing to short-term negative energy balance. In this perspective, we propose a framework to understand how these distinct impacts of antibiotics on the gut microbiome during critical developmental windows shape long-term obesity risk through their influence on host energy balance. Using this framework, we then propose several hypotheses to explain variation in ELA-induced obesity outcomes across males and females. We conclude by discussing the evolutionary implications of ELAs, positing that the response of the gut microbiome to ELAs may signal energy availability and environmental volatility, influencing metabolic programming and adaptive traits across generations.}, }
@article {pmid40208324, year = {2025}, author = {Mazzella, V and Zahn, G and Dell'Anno, A and Pons, LN}, title = {Marine Mycobiomes Colonize Mediterranean Sponge Hosts in a Random Fashion.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {25}, pmid = {40208324}, issn = {1432-184X}, support = {C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; }, mesh = {Animals ; *Porifera/microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; Mediterranean Sea ; *Mycobiome ; *Seawater/microbiology ; Phylogeny ; Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; Ecosystem ; }, abstract = {Marine sponges are widespread, sessile, filter-feeding animals, known for living in association with complex prokaryotic communities structured by host species. Though marine fungi are ubiquitous across marine environments, little is known about sponge-associated fungal communities (mycobiome). Indeed, aside from a few studies based on the isolation of fungal strains for biotechnological purposes, little information is available to understand the diversity and structure of sponge mycobiome. Here, a metabarcoding approach based on the ITS1 marker was applied to examine the structure and composition of fungal communities associated with four Mediterranean sponges. The species: Petrosia ficiformis, Chondrosia reniformis, Crambe crambe, and Chondrilla nucula were analyzed along with the surrounding seawater, revealing Aspergillus (1-56%), Cladosporium (1-75%), Malassezia (1-38.5%), and Pennicillium (1.5-36%) as the most represented fungal genera. Our data showed high intra-specific variability and no clear core mycobiome within each of the sponge species host, suggesting stochastic and perhaps transient community membership. This study sheds light on one of the most abundant yet least understood components of the marine ecosystem. Unraveling the dynamics of fungal interactions within sponge holobionts is essential to advance our understanding of their ecological roles and functions. By addressing the enigmatic nature of sponge-associated fungi, this research opens new avenues for exploring their contributions to marine ecosystems and resolving the many unanswered questions in this field.}, }
@article {pmid40208265, year = {2025}, author = {DiPietri, VT and Grady, ZS and Frost, AN and Stitzel, SE and Sivey, JD}, title = {Toilet Bowl Cleaning Tablets as Sources of Chlorine, Bromine, and Disinfection Byproducts in Wastewater.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {15}, pages = {7646-7655}, doi = {10.1021/acs.est.4c12026}, pmid = {40208265}, issn = {1520-5851}, mesh = {*Chlorine/analysis ; *Wastewater/chemistry ; *Bromine/analysis ; Disinfection ; *Water Pollutants, Chemical/analysis ; Tablets ; *Disinfectants/analysis ; }, abstract = {Commercial toilet bowl cleaning tablets were examined in laboratory systems to characterize their release of active halogens and their potential to form trihalomethanes (THMs) when combined with synthetic sewage. Active halogens (e.g., HOCl, HOBr, and reactive halamines) were quantified via derivatization with 1,3,5-trimethoxybenzene prior to analysis by liquid chromatography. The effects of several variables on halogen release profiles were examined, including pH, ionic strength, temperature, tank solution volume, flushing frequency, and tablet brand. Changes in pH resulted in modest or no appreciable changes in halogen release profiles. Release of active halogens increased as ionic strength decreased and as temperature increased. Tank volume, flushing frequency, and tablet brand had pronounced impacts on halogen release profiles. Maximum measured active chlorine and bromine concentrations in toilet tank water were 189 mg/L as Cl2 and 164 mg/L as Cl2, respectively. Active halogens persisted in toilet bowl water for >24 h. When toilet-tablet-treated water was combined with synthetic sewage, THMs formed at up to 219 ppb with bromine incorporation factors up to 2.86. Active halogens and highly brominated THMs released into wastewater from toilet tablets could have implications for downstream microbial ecology, septic system performance, and overall water quality.}, }
@article {pmid40206699, year = {2025}, author = {Connors, E and Gallagher, KL and Dutta, A and Oliver, M and Bowman, JS}, title = {Suspended detrital particles support a distinct microbial ecosystem in Palmer Canyon, Antarctica, a coastal biological hotspot.}, journal = {Polar biology}, volume = {48}, number = {2}, pages = {62}, pmid = {40206699}, issn = {0722-4060}, support = {S10 OD026929/OD/NIH HHS/United States ; }, abstract = {UNLABELLED: The coastal region of the Western Antarctic Peninsula is considered a biological hotspot with high levels of phytoplankton productivity and krill biomass. Recent in situ observations and particle modeling studies of Palmer Canyon, a deep bathymetric feature in the region, demonstrated the presence of a recirculating eddy that traps particles, retaining a distinct particle layer over the summer season. We applied metagenomic sequencing and Imaging Flow Cytobot (IFCB) analysis to characterize the microbial community in the particle layer. We sampled across the upper water column (< 200 m) along a transect to identify the locations of increased particle density, categorizing particles into either living cells or cellular detritus via IFCB. An indicator species analysis of community composition demonstrated the diatom Corethron and the bacteria Sulfitobacter were significantly highly abundant in samples with high levels of living cells, while the mixotrophic dinoflagellate Prorocentrum texanum and prokaryotes Methanomassiliicoccales and Fluviicola taffensis were significantly more abundant in samples with high detritus within the particle layer. From our metagenomic analysis, the significantly differentially abundant metabolic pathway genes in the particle layer of Palmer Canyon included pathways for anaerobic metabolism, such as methanogenesis and sulfate reduction. Overall, our results indicate that distinct microbial species and metabolic pathway genes are present in the retained particle layer of Palmer Canyon.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00300-025-03380-y.}, }
@article {pmid40205489, year = {2025}, author = {Soares, A and Rassner, SME and Edwards, A and Farr, G and Blackwell, N and Sass, H and Persiani, G and Schofield, D and Mitchell, AC}, title = {Hydrogeological and geological partitioning of iron and sulfur cycling bacterial consortia in subsurface coal-based mine waters.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {5}, pages = {}, pmid = {40205489}, issn = {1574-6941}, support = {//S&#xea;r Cymru/ ; NE/V012991/1//Natural Environment Research Council/ ; }, mesh = {*Sulfur/metabolism ; *Iron/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Coal/microbiology ; *Groundwater/microbiology/chemistry ; *Microbial Consortia ; Oxidation-Reduction ; Seasons ; Phylogeny ; Sulfides/metabolism ; Wales ; Coal Mining ; Mining ; }, abstract = {Pyrite oxidation drives iron and sulfur availability across Earth's subsurface and is partly microbially mediated. Subsurface microbial communities accelerate this process at circumneutral pH directly by weathering pyritic surfaces and indirectly by causing changes to the surrounding microenvironment, thereby further accelerating pyrite weathering. However, our understanding of community structure dynamics and associated biogeochemistry in Fe- and S-rich lithologies, e.g. pyritic coal, is limited. Here, we present the first comprehensive regional and seasonal genus-level survey of bacterial groundwater communities in a pyritic coal-based aquifer in the South Wales Coalfield (SWC), using 16S rRNA gene amplicon sequencing. Seasonal changes in community structure were limited, suggesting limited influence of surface processes on subsurface communities. Instead, hydrogeologically distinct mine water blocks (MWB) and coal rank largely explained bacterial community structure variation across sites. Fe(II)-oxidizing Betaproteobacteriales genera Gallionella and Sideroxydans dominated the bacterial communities across nine sites and seven MWBs, while three sites within a single MWB, were dominated by S-oxidizing Epsilonbacteraeota genera Sulfuricurvum and Sulfurovum. The cooccurrence of pairs of Fe(II)- and S-oxidizing bacterial genera suggests functional redundancy, which coupled with genus-specific morphologies and life strategies, indicates the importance of distinct environmental and ecological niches within the SWC groundwater at seasonal and regional scales.}, }
@article {pmid40205473, year = {2025}, author = {Rodriguez-Cruz, UE and Ochoa-Sánchez, M and Eguiarte, LE and Souza, V}, title = {Running against the clock: exploring microbial diversity in an extremely endangered microbial oasis in the Chihuahuan Desert.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {5}, pages = {}, pmid = {40205473}, issn = {1574-6941}, support = {//DGAPA/ ; IG200319//UNAM/ ; //Instituto de Ecolog&#xed;a, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Biodiversity ; *Bacteria/classification/genetics/isolation &amp; purification ; Desert Climate ; *Microbiota/genetics ; Phylogeny ; Ecosystem ; Groundwater/microbiology ; }, abstract = {The Cuatro Ciénegas Basin is a biodiversity hotspot known for its unique biodiversity. However, this ecosystem is facing severe anthropogenic threats that are drying its aquatic systems. We investigated microbial communities at three sites with different physicochemical and environmental characteristics (Pozas Rojas, Archean Domes, and the Churince system) within the basin to explore potential connections to deep aquifers and determine if the sites shared microorganisms. Utilizing 16S rRNA gene data, we identified a core microbiota between Pozas Rojas (PR) and Archean Domes (AD). Sulfur reduction appears to shape the microbial connectivity among sites, since sulfur-reducing bacteria has the highest prevalence between samples from PR and AD: Halanaerobium sp. (88.46%) and Desulfovermiculus halophilus (65%); and between the Churince system and AD: Halanaerobium sp. (63%) and D. halophilus (60%). Furthermore, metagenome-assembled genomes from Ectothiorhodospira genus were found in both AD and Churince, suggesting microbial dispersal. An important finding is that microbial diversity in the AD system declined, from 2016 to 2023 the ecosystem lost 29 microbial phyla. If this trend continues, the basin will lose most of its water, resulting in the loss of various prokaryotic lineages and potential biotechnological solutions, such as enzymes or novel antibiotics. Our findings highlighting the need for water extraction regulations to preserve the basin's biodiversity.}, }
@article {pmid40205253, year = {2025}, author = {Dasgupta, M and Paul, R and Chowdhury, P and Mondal, S and Ahmed, J and Mukherjee, C and Das, S and Tribedi, P}, title = {Management of Enterococcus faecalis biofilms: a combinatorial approach with phytochemical.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {56}, number = {2}, pages = {1131-1143}, pmid = {40205253}, issn = {1678-4405}, support = {TNU/R&amp;D/MP/2021/010//The Neotia University/ ; }, mesh = {*Biofilms/drug effects/growth &amp; development ; *Enterococcus faecalis/drug effects/physiology ; Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; *Phytochemicals/pharmacology ; *Benzoquinones/pharmacology ; *Benzaldehydes/pharmacology ; Humans ; }, abstract = {The rapid emergence of antimicrobial resistance in Enterococcus faecalis infections was primarily due to their robust biofilm formation, highlighting the urgent need for meaningful strategies. Since combinatorial application of natural phytochemical often offer promising outcomes in dealing with microbial infections, present study indicated the pharmacological, antimicrobial and antibiofilm potential of combinatorial strategies of natural phytochemical involving cuminaldehyde and thymoquinone against E. faecalis. Towards this direction, in silico analysis suggested that both compounds could show favourable oral bioavailability and high GI absorption, with a considerable solubility and drug-likeness profiles. Furthermore, in vitro antimicrobial assay indicated that the minimum inhibitory concentrations (MIC) of cuminaldehyde and thymoquinone were found to be 500 µg/mL and 30 µg/mL, respectively against E. faecalis. Thereafter, the fractional inhibitory concentration (FIC) index score of 0.73 indicated an additive effect prevailed between cuminaldehyde and thymoquinone, enhancing their antimicrobial potential. Thereafter, sub-MIC doses of cuminaldehyde (40 µg/mL) and thymoquinone (8 µg/mL) were selected to assess their antibiofilm potential. Though the compounds were able to show antibiofilm activity separately, their combination was significantly more effective, reduced biofilm formation by approximately 80%, and decreased production of extracellular polymeric substance (EPS) and protein content by ~ 76% and ~ 70%, respectively. Further studies revealed that the antibiofilm activity of the test compounds could likely to be attributed to the accumulation of reactive oxygen species (ROS) and enhancement of membrane permeability. Taken together, all this experimental observation revealed that combination of these natural compounds could potentially improve the treatment outcomes of biofilm-borne infections of E. faecalis.}, }
@article {pmid40203032, year = {2025}, author = {Timilsina, S and Iruegas-Bocardo, F and Jibrin, MO and Sharma, A and Subedi, A and Kaur, A and Minsavage, GV and Huguet-Tapia, JC and Klein-Gordon, J and Adhikari, P and Adhikari, TB and Cirvilleri, G and de la Barrera, LBT and Bernal, E and Creswell, TC and Doan, TTK and Coutinho, TA and Egel, DS and Félix-Gastélum, R and Francis, DM and Kebede, M and Ivey, ML and Louws, FJ and Luo, L and Maynard, ET and Miller, SA and Nguyen, NTT and Osdaghi, E and Quezado-Duval, AM and Roach, R and Rotondo, F and Ruhl, GE and Shutt, VM and Thummabenjapone, P and Trueman, C and Roberts, PD and Jones, JB and Vallad, GE and Goss, EM}, title = {Diversification of an emerging bacterial plant pathogen; insights into the global spread of Xanthomonas euvesicatoria pv. perforans.}, journal = {PLoS pathogens}, volume = {21}, number = {4}, pages = {e1013036}, pmid = {40203032}, issn = {1553-7374}, mesh = {*Xanthomonas/genetics/pathogenicity/classification ; *Plant Diseases/microbiology ; *Solanum lycopersicum/microbiology ; *Genetic Variation ; Phylogeny ; }, abstract = {Emerging and re-emerging plant diseases continue to present multifarious threats to global food security. Considerable recent efforts are therefore being channeled towards understanding the nature of pathogen emergence, their spread and evolution. Xanthomonas euvesicatoria pv. perforans (Xep), one of the causal agents of bacterial spot of tomato, rapidly emerged and displaced other bacterial spot xanthomonads in many tomato production regions around the world. In less than three decades, it has become a dominant xanthomonad pathogen in tomato production systems across the world and presents a compelling example for understanding diversification of recently emerged bacterial plant pathogens. Although Xep has been continuously monitored in Florida since its discovery, the global population structure and evolution at the genome-scale is yet to be fully explored. The objectives of this work were to determine genetic diversity globally to ascertain if different tomato production regions contain genetically distinct Xep populations, to examine genetic relatedness of strains collected in tomato seed production areas in East Asia and other production regions, and to evaluate variation in type III secretion effectors, which are critical pathogenicity and virulence factors, in relationship to population structure. We used genome data from 270 strains from 13 countries for phylogenetic analysis and characterization of type III effector gene diversity among strains. Our results showed notable genetic diversity in the pathogen. We found genetically similar strains in distant tomato production regions, including seed production regions, and diversification over the past 100 years, which is consistent with intercontinental dissemination of the pathogen in hybrid tomato production chains. Evolution of the Xep pangenome, including the acquisition and loss of type III secreted effectors, is apparent within and among phylogenetic lineages. The apparent long-distance movement of the pathogen, together with variants that may not yet be widely distributed, poses risks of emergence of new variants in tomato production.}, }
@article {pmid40202691, year = {2025}, author = {Pimentel, AC and Cesar, CS and Martins, AHB and Martins, M and Cogni, R}, title = {Wolbachia Offers Protection Against Two Common Natural Viruses of Drosophila.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {24}, pmid = {40202691}, issn = {1432-184X}, mesh = {Animals ; *Wolbachia/physiology ; *Drosophila melanogaster/virology/microbiology ; *Drosophila/virology/microbiology ; Symbiosis ; Female ; }, abstract = {Wolbachia pipientis is a maternally transmitted endosymbiont infecting more than half of terrestrial arthropod species. Wolbachia can express parasitic phenotypes such as manipulation of host reproduction and mutualist phenotypes such as protection against RNA virus infections. Because Wolbachia can invade populations by reproductive manipulation and block virus infection, it is used to modify natural insect populations. However, the ecological importance of virus protection is not yet clear, especially due to scarce information on Wolbachia protection against viruses that are common in nature. We used systemic infection to investigate whether Wolbachia protects its host by suppressing the titer of DMELDAV and DMelNora virus, two viruses that commonly infect Drosophila melanogaster flies in natural populations. Antiviral protection was tested in three systems to assess the impact of Wolbachia strains across species: (1) a panel of Wolbachia strains transfected into Drosophila simulans, (2) two Wolbachia strains introgressed into the natural host D. melanogaster, and (3) two native Wolbachia strains in their natural hosts Drosophila baimaii and Drosophila tropicalis. We showed that certain Wolbachia strains provide protection against DMelNora virus and DMELDAV, and this protection is correlated with Wolbachia density, which is consistent with what has been observed in protection against other RNA viruses. Additionally, we found that Wolbachia does not protect its original host, D. melanogaster, from DMELDAV infection. While native Wolbachia can reduce DMELDAV titers in D. baimaii, this effect was not detected in D. tropicalis. Although the Wolbachia protection-induced phenotype seems to depend on the virus, the specific Wolbachia strain, and the host species, our findings suggest that antiviral protection may be one of the mutualistic effects that helps explain why Wolbachia is so widespread in arthropod populations.}, }
@article {pmid40201423, year = {2025}, author = {Boden, L and Bludau, D and Sieber, G and Deep, A and Baikova, D and David, GM and Hadžiomerović, U and Stach, TL and Boenigk, J}, title = {The impact of elevated temperature and salinity on microbial communities and food selectivity in heterotrophic nanoflagellates in the Boye River.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf049}, pmid = {40201423}, issn = {2730-6151}, abstract = {Microbial predator-prey interactions play a crucial role in aquatic food webs. Bacterivorous protists not only regulate the quantity and biomass of bacterial populations but also profoundly influence the structure of bacterial communities. Consequently, alterations in both the quantity and quality of protist bacterivory can influence the overall structure of aquatic food webs. While it is well-documented that changes in environmental conditions or the occurrence of abiotic stressors can lead to shifts in microbial community compositions, the impact of such disturbances on food selection remains unknown. Here, we investigated the effects of elevated temperature and salinization on food selectivity of heterotrophic nanoflagellates by monitoring the uptake of preselected target bacteria via catalyzed reporter deposition fluorescence in situ hybridization and fluorescence microscopy. Our results indicate that salinization, but not increased temperature, significantly increased the flagellates' selection against Microbacterium lacusdiani (Actinomycetota). However, the effect of the reduced grazing pressure was counterbalanced by the negative effect of increased salinity on the growth of Actinomycetota. Our results suggest that the effect of stressors on the feeding behavior of protistan predators may strongly affect the composition of their prey community, when bacterial taxa are concerned that are less sensitive to the particular stressor.}, }
@article {pmid40200306, year = {2025}, author = {Bindels, LB and Watts, JEM and Theis, KR and Carrion, VJ and Ossowicki, A and Seifert, J and Oh, J and Shao, Y and Hilty, M and Kumar, P and Hildebrand, F and Lovejoy, C and Wigley, P and Yu, K and Zhang, M and Zhang, T and Walter, J and Desai, MS and Huws, SA and Schriml, LM and Ravel, J and Fricke, WF and Eloe-Fadrosh, EA and Lee, CK and Clavel, T}, title = {A blueprint for contemporary studies of microbiomes.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {95}, pmid = {40200306}, issn = {2049-2618}, mesh = {*Microbiota ; *Publishing/standards ; }, abstract = {This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opportunity to clarify our expectations for the articles submitted to the journal. At Microbiome, we are seeking studies that provide either new mechanistic insights into the role of microbiomes in health and environmental systems or substantial conceptual or technical advances. Manuscripts need to meet high standards of language accuracy, quality of microbiome analyses, and data and protocol availability, including detailed reporting of wet-lab and in silico protocols, all of which can critically enhance transparency and reproducibility. We think that such efforts are essential to push the boundaries of our knowledge on microbiomes in a concerted, international effort.}, }
@article {pmid40197060, year = {2025}, author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Spatial ecology of the Neisseriaceae family in the human oral cavity.}, journal = {Microbiology spectrum}, volume = {13}, number = {5}, pages = {e0327524}, pmid = {40197060}, issn = {2165-0497}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; }, abstract = {The human oral microbiome is a diverse ecosystem in which bacterial species have evolved to occupy specific niches within the oral cavity. The Neisseriaceae family, which includes human oral species in the genera Neisseria, Eikenella, Kingella, and Simonsiella, plays a significant role in both commensal and pathogenic relationships. In this study, we investigate the distribution and functional adaptations of Neisseriaceae species across oral habitats, focusing on their site tropisms and ecological roles. We employed a metapangenomic approach in which a curated set of reference genomes representing Neisseriaceae diversity was used for competitive mapping of metagenomic reads. Our analysis revealed distinct habitat preferences among Neisseriaceae species, with Kingella oralis, Neisseria elongata, and Neisseria mucosa primarily found in dental plaque; Neisseria subflava on the tongue dorsum; and Neisseria cinerea in the keratinized gingiva. Functional enrichment analyses identified genes and pathways underpinning habitat-specific adaptations. Plaque specialists showed metabolic versatility, with adaptations in nitrogen metabolism, including nitrate reduction and denitrification, lysine degradation, and galactose metabolism. Tongue dorsum specialists exhibited adaptations including enhanced capabilities for amino acid biosynthesis, short-chain fatty acid and glycerol transport, as well as lipopolysaccharide glycosylation, which may aid in resisting antimicrobial peptides and maintaining membrane integrity. These findings provide insights into the ecological roles and adaptive strategies of Neisseriaceae species within the human oral microbiome and establish a foundation for exploring functional specialization and microbial interactions in these niches.IMPORTANCEUnraveling the distribution and functional adaptations of Neisseriaceae within the human oral microbiome is essential for understanding the roles of these abundant and prevalent commensals in both health and disease. Through a metapangenomic approach, we uncovered distinct habitat preferences of various Neisseriaceae taxa across the oral cavity and identified key genetic traits that may drive their habitat specialization and role in host-microbe interactions. These insights enhance our understanding of the microbial dynamics that shape oral microbial ecology, offering potential pathways for advancing oral health research.}, }
@article {pmid40197052, year = {2025}, author = {Liu, S and Ru, J and Guo, X and Gao, Q and Deng, S and Lei, J and Song, J and Zhai, C and Wan, S and Yang, Y}, title = {Altered precipitation and nighttime warming reshape the vertical distribution of soil microbial communities.}, journal = {mSystems}, volume = {10}, number = {5}, pages = {e0124824}, pmid = {40197052}, issn = {2379-5077}, support = {32161123002//MOST | National Natural Science Foundation of China (NSFC)/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; 20223BBG74S02//the Key Technology R&amp;D Program of JiangXi Province grant/ ; KY-23ZK01//the Hainan Institute of National Park grant/ ; }, mesh = {*Soil Microbiology ; *Microbiota ; Bacteria/genetics/classification ; *Rain ; China ; Fungi/genetics/classification ; Climate Change ; Soil/chemistry ; Grassland ; Biodiversity ; }, abstract = {Soil depth determines microbial community composition. Yet, it remains largely unexplored how climate changes affect the vertical distribution of soil microbial communities. Here, we investigated the effects of altered precipitation and nighttime warming on microbial communities in the topsoils (0-20 cm) and subsoils (20-50 cm) of a temperate grassland in Inner Mongolia, China. As commonly observed under nutrient scarcity conditions, bacterial and fungal α-diversity and network complexity decreased with soil depth. However, protistan α-diversity and network complexity increased, which was attributed to less niche overlap and smaller body size. Strikingly, the slopes of linear regressions of microbial α-diversity/network complexity and soil depth were all reduced by altered precipitation. Microbial community composition was significantly influenced by both depth and reduced precipitation, and to a lesser extent by nighttime warming and elevated precipitation. The ribosomal RNA gene operon (rrn) copy number, a genomic proxy of bacterial nutrient demand, decreased with soil depth, and the percentages of positive network links were higher in the subsoil, supporting the "hunger game" hypothesis. Both reduced precipitation and nighttime warming decreased the rrn copy number in the subsoils while increasing the percentages of positive links, enhancing potential niche sharing among bacterial species. The stochasticity level of bacterial and fungal community assemblies decreased with soil depth, showing that depth acted as a selection force. Altered precipitation increased stochasticity, attenuating the depth's filtering effect and diminishing its linear relationship with microbial diversity. Collectively, we unveiled the predominant influence of altered precipitation in affecting the vertical distribution of soil microbial communities.IMPORTANCEUnderstanding how climate change impacts the vertical distribution of soil microbial communities is critical for predicting ecosystem responses to global environmental shifts. Soil microbial communities exhibit strong depth-related stratification, yet the effects of climate change variables, such as altered precipitation and nighttime warming, on these vertical patterns have been inadequately studied. Our research uncovers that altered precipitation disrupts the previously observed relationships between soil depth and microbial diversity, a finding that challenges traditional models of soil microbial ecology. Furthermore, our study provides experimental support for the hunger game hypothesis, highlighting that oligotrophic microbes, characterized by lower ribosomal RNA gene operon (rrn) copy numbers, are selectively favored in nutrient-poor subsoils, fostering increased microbial cooperation for resource exchange. By unraveling these complexities in soil microbial communities, our findings offer crucial insights for predicting ecosystem responses to climate change and for developing strategies to mitigate its adverse impacts.}, }
@article {pmid40196585, year = {2025}, author = {Dellicour, S and Gámbaro, F and Jacquot, M and Lequime, S and Baele, G and Gilbert, M and Pybus, OG and Suchard, MA and Lemey, P}, title = {Comparative performance of novel viral landscape phylogeography approaches.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40196585}, issn = {2692-8205}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI153044/AI/NIAID NIH HHS/United States ; R01 AI162611/AI/NIAID NIH HHS/United States ; U19 AI135995/AI/NIAID NIH HHS/United States ; }, abstract = {The fast rate of evolution in RNA viruses implies that their evolutionary and ecological processes occur on the same time scale. Genome sequences of these pathogens can therefore contain information about the processes that govern their transmission and dispersal. In particular, landscape phylogeographic approaches use phylogeographic reconstructions to investigate the impact of environmental factors and variables on the spatial spread of viruses. Here, we extend and improve existing approaches and develop three novel landscape phylogeographic methods that can test the impact of continuous environmental factors on the diffusion velocity of viral lineages. In order to evaluate the different methods, we also implemented two simulation frameworks to test and compare their statistical performance. The results enable us to formulate clear guidelines for the use of three complementary landscape phylogeographic approaches that have sufficient statistical power and low rates of false positives. Our open-source methods are available to the scientific community and can be used to investigate the drivers of viral spread, with potential benefits for understanding virus epidemiology and designing tailored intervention strategies.}, }
@article {pmid40195174, year = {2025}, author = {Burazerović, J and Jovanović, M and Savković, &#x17d; and Breka, K and Stupar, M}, title = {Finding the Right Host in the Darkness of the Cave-New Insights into the Ecology and Spatio-temporal Dynamics of Hyperparasitic Fungi (Arthrorhynchus nycteribiae, Laboulbeniales).}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {23}, pmid = {40195174}, issn = {1432-184X}, support = {451- 03- 66/2024- 03/200178; 451- 03- 65/2024- 03/ 200178//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; 451- 03- 66/2024- 03/200178; 451- 03- 65/2024- 03/ 200178//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; 451- 03- 66/2024- 03/200178; 451- 03- 65/2024- 03/ 200178//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; 451- 03- 66/2024- 03/200178; 451- 03- 65/2024- 03/ 200178//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; }, mesh = {Animals ; *Chiroptera/parasitology/microbiology ; *Caves/microbiology ; *Ascomycota/genetics/isolation &amp; purification/physiology/classification ; *Diptera/microbiology ; Serbia ; Male ; Female ; Phylogeny ; }, abstract = {The aim of this study was to determine the presence of the hyperparasitic fungus Arthrorhynchus nycteribiae and to analyze its spatio-temporal pattern in the two bat flies (Penicillidia conspicua and P. dufourii) parasitizing on bats. We collected 612 samples of bat flies from 400 bats in 20 caves in the Central Balkans. Hyperparasite was identified based on morphological and molecular analyses of rDNA genes (LSU and SSU). A. nycteribiae was reported for the first time in Bosnia and Herzegovina and Montenegro, and confirmed in Serbia. Of the 20 sites examined, we found A. nycteribiae at 11 sites. The prevalence of A. nycteribiae infection in the bats examined was approximately 17%. Miniopterus schreibersii harbored the highest number of bat flies and was the only bat species hosting the infected bat flies of the species P. conspicua. Our results showed significant differences in infection patterns during the different seasons: the highest prevalence of bat flies with hyperparasitic fungi was found in the summer season (23%) and the lowest in spring (2%). Female bat fly hosts showed a significantly higher prevalence of infection than male bat flies. This study makes an important contribution to the knowledge of the distribution of A. nycteribiae and to the understanding of complex parasite-host relationships in the poorly studied areas of the Central Balkans.}, }
@article {pmid40194740, year = {2025}, author = {Nieman, DC and Sakaguchi, CA and Williams, JC and Lawson, J and Lambirth, KC and Omar, AM and Mulani, FA and Zhang, Q}, title = {Gut Prevotella copri abundance linked to elevated post-exercise inflammation.}, journal = {Journal of sport and health science}, volume = {14}, number = {}, pages = {101039}, pmid = {40194740}, issn = {2213-2961}, abstract = {PURPOSE: This study aimed to examine the linkage between gut microbiome taxa and exercise-induced inflammation.<br><br>METHODS: Twenty-five cyclists provided 4 stool samples during a 10-week period and cycled vigorously for 2.25 h at 67% maximal oxygen uptake (VO2max) in a laboratory setting. Blood samples were collected pre- and post-exercise, with additional samples collected at 1.5-h, 3-h, and 24-h post exercise. Primary outcomes included stool microbiome composition and alpha diversity via whole genome shotgun (WGS) sequencing (averaged from 4 stool samples) and a targeted panel of 75 plasma oxylipins. A total of 5719 taxa were identified, and the 339 that were present in more than 20% of stool samples were used in the analysis. Alpha diversity was calculated by evenness, and the Analysis of Composition of Microbiomes (ANCOM) differential abundance analysis was performed using Quantitative Insights Into Microbial Ecology-2 (QIIME2). A composite variable was calculated from 8 pro-inflammatory oxylipins generated from arachidonic acid (ARA) and cytochrome P-450 (CYP).<br><br>RESULTS: ARA-CYP oxylipins were significantly elevated for at least 3-h post-exercise (p < 0.001); they were strongly and positively related to Prevotella copri (P. copri) abundance (R[2]&#x202f;=&#x202f;0.676, p < 0.001) and negatively related to gut microbiome alpha diversity (R[2]&#x202f;=&#x202f;0.771, p < 0.001).<br><br>CONCLUSION: This analysis revealed for the first time a novel, positive relationship between gut microbiome P. copri abundance in cyclists and post-exercise pro-inflammatory oxylipins. These data demonstrate that about two-thirds of the wide variance in inflammation following prolonged and intensive exercise is largely explained by the abundance of a single gut bacterial species: P. copri.}, }
@article {pmid40186763, year = {2025}, author = {Huang, YD and Zhao, XL and Lin, Y and Ouyang, XM and Cheng, XS and Liang, LY and Huo, YN and Xie, GJ and Lin, JH and Jazag, A and Guleng, B}, title = {Mindin orchestrates the macrophage-mediated resolution of liver fibrosis in mice.}, journal = {Hepatology international}, volume = {}, number = {}, pages = {}, pmid = {40186763}, issn = {1936-0541}, support = {No. 81970460//National Natural Science Foundation of China/ ; No. 2023J011598//Natural Science Foundation of Fujian Province/ ; }, abstract = {BACKGROUND &amp; AIMS: Liver disease that progresses to cirrhosis is an enormous health problem worldwide. The extracellular matrix protein Mindin is known to have immune functions, but its role in liver homeostasis remains largely unexplored. We aimed to characterize the role of Mindin in the regulation of liver fibrosis.<br><br>APPROACH &amp; RESULTS: Mindin was upregulated in mice with carbon tetrachloride (CCl4) or thioacetamide (TAA)-induced liver fibrosis, and was primarily expressed in hepatocytes. Global Mindin knockout mice were generated, which were susceptible to liver fibrosis. Notably, Mindin failed to activate hepatic stellate cells directly; however, it played a role in promoting the recruitment and phagocytosis of macrophages, and caused a phenotypic switch toward restorative macrophages during liver fibrosis. Furthermore, Mindin was found to bind to the &#x3b1;M-I domain of CD11b/CD18 heterodimeric receptors. To further explore this mechanism, we created Mindin and CD11b double-knockout (DKO) mice. In DKO mice, phagocytosis was further reduced, and liver fibrosis was markedly exacerbated.<br><br>CONCLUSIONS: Mindin promotes the resolution of liver fibrosis and the Mindin/CD11b axis might represent a novel target for the macrophage-mediated regression of liver fibrosis.}, }
@article {pmid40186595, year = {2025}, author = {Pérez, J and Boyero, L and Pearson, RG and Gessner, MO and Tonin, A and López-Rojo, N and Rubio-Ríos, J and Correa-Araneda, F and Alonso, A and Cornejo, A and Albariño, RJ and Anbalagan, S and Barmuta, LA and Boulton, AJ and Burdon, FJ and Caliman, A and Callisto, M and Campbell, IC and Cardinale, BJ and Carneiro, LS and Casas, JJ and Chará-Serna, AM and Chauvet, E and Colón-Gaud, C and Davis, AM and de Eyto, E and Degebrodt, M and Díaz, ME and Douglas, MM and Encalada, AC and Figueroa, R and Flecker, AS and Fleituch, T and Frainer, A and García, EA and García, G and García, PE and Giller, PS and Gómez, JE and Gonçalves, JF and Graça, MAS and Hall, RO and Hamada, N and Hepp, LU and Hui, C and Imazawa, D and Iwata, T and Junior, ESA and Landeira-Dabarca, A and Leal, M and Lehosmaa, K and M'Erimba, CM and Marchant, R and Martins, RT and Masese, FO and Maul, M and McKie, BG and Medeiros, AO and Middleton, JA and Muotka, T and Negishi, JN and Ramírez, A and Rezende, RS and Richardson, JS and Rincón, J and Serrano, C and Shaffer, AR and Sheldon, F and Swan, CM and Tenkiano, NSD and Tiegs, SD and Tolod, JR and Vernasky, M and Wanderi, EW and Watson, A and Yule, CM}, title = {Positive Feedback on Climate Warming by Stream Microbial Decomposers Indicated by a Global Space-For-Time Substitution Study.}, journal = {Global change biology}, volume = {31}, number = {4}, pages = {e70171}, doi = {10.1111/gcb.70171}, pmid = {40186595}, issn = {1365-2486}, support = {UAL18-RNM-B006-B//2014-2020 Operational Programme FEDER Andalusia/ ; IT951-16//Eusko Jaurlaritza/ ; IT1471-22//Eusko Jaurlaritza/ ; UIDB/04292/2020//Funda &#xe7; &#xe3;o para a Ci &#xea;ncia e a Tecnologia, Portugal/ ; //UAL-HIPATIA/ ; }, mesh = {*Rivers/microbiology ; *Climate Change ; Temperature ; *Global Warming ; Plants/metabolism ; Carbon Cycle ; }, abstract = {Decomposition of plant litter is a key ecological process in streams, whose contribution to the global carbon cycle is large relative to their extent on Earth. We examined the mechanisms underlying the temperature sensitivity (TS) of instream decomposition and forecast effects of climate warming on this process. Comparing data from 41 globally distributed sites, we assessed the TS of microbial and total decomposition using litter of nine plant species combined in six mixtures. Microbial decomposition conformed to the metabolic theory of ecology and its TS was consistently higher than that of total decomposition, which was higher than found previously. Litter quality influenced the difference between microbial and total decomposition, with total decomposition of more recalcitrant litter being more sensitive to temperature. Our projections suggest that (i) warming will enhance the microbial contribution to decomposition, increasing CO2 outgassing and intensifying the warming trend, especially in colder regions; and (ii) riparian species composition will have a major influence on this process.}, }
@article {pmid40185870, year = {2025}, author = {Ripoll, J and Stenger, PL and Nuñez, NF and Demenois, J and Stokes, A and Gourmelon, V and Dinh, K and Robert, N and Drouin, J and Mournet, P and Léopold, A and Read, J and Gardes, M and Maggia, L and Carriconde, F}, title = {Unexpected microbial diversity in new Caledonia's ultramafic ecosystems with conservation implications in a biodiversity hotspot.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {11564}, pmid = {40185870}, issn = {2045-2322}, support = {IAC-SLN Research Collaboration N&#xb0;DE2013-041//Soci&#xe9;t&#xe9; Le Nickel (SLN-Eramet Group)/ ; agreement CSF N&#xb0;1PS2013-CNRT.IAC/BIOINDIC//CNRT "Nickel &amp; son Environnement"/ ; }, mesh = {New Caledonia ; *Biodiversity ; *Soil Microbiology ; *Ecosystem ; Mycorrhizae/genetics/classification ; Conservation of Natural Resources ; Fungi/genetics/classification ; *Bacteria/genetics/classification ; }, abstract = {Soils harbour an incredible diversity of microorganisms that play crucial roles in ecosystem functioning. However, this biodiversity remains largely overlooked, with a poor understanding of how patterns form across landscapes. An eDNA metabarcoding approach was used to identify potential overarching patterns in fungal and bacterial communities from ultramafic ecosystems in New Caledonia, a renowned biodiversity hotspot. Our comprehensive analysis revealed several key findings, notably an important microbial diversity in the extreme environments of iron crust soils. Clear tendencies in phyla composition were also observed, with the fungal groups Ascomycota and Mucoromycota acting as potential indicators of land degradation (only in lateritic soils for Mucoromycota). For bacteria, Chloroflexi was characteristic of open vegetation, while Proteobacteria and Cyanobacteria were observed in higher relative abundances in the closed vegetation. The ectomycorrhizal fungal functional group was also found to be rich and unique, with a hypothetical endemism rate of 87%, and over-represented by the Cortinarius genus in rainforests and maquis (shrublands) dominated by ectomycorrhizal plants. Finally, each ultramafic Massif demonstrated a unique microbial community. Thus, our findings provide valuable insights into microbial ecology and emphasize the need for tailored conservation strategies for this biodiversity hotspot.}, }
@article {pmid40184706, year = {2025}, author = {He, L and Li, J and Tang, L and Wang, Y and Zhao, X and Ding, K and Xu, L and Gu, L and Cheng, S and Wei, YY}, title = {Applying side-stream gas recirculation to promote anaerobic digestion of food waste under ammonia stress: Overlooked impact of gaseous atmospheres on microorganisms.}, journal = {Water research}, volume = {281}, number = {}, pages = {123571}, doi = {10.1016/j.watres.2025.123571}, pmid = {40184706}, issn = {1879-2448}, mesh = {*Ammonia ; Anaerobiosis ; Bioreactors/microbiology ; Hydrogen ; Gases ; Food Loss and Waste ; }, abstract = {High ammonia concentrations can be toxic to microorganisms, leading to the accumulation of hydrogen (H2) and acids in anaerobic digestion (AD) system. In this study, a side gas recycling strategy (SGR), coupled with a primary reactor and a small side-stream reactor, which recirculates biogas between primary reactor and side reactor was employed to mitigate ammonia inhibition. This approach enabled the mesophilic side-stream gas recirculation system (SMGR) and the thermophilic side-stream gas recirculation system (STGR) to ultimately withstand ammonia stress levels of 2.5 g/L and 3.5 g/L, respectively, while maintaining lower hydrogen partial pressures. In contrast, the control group experienced system failure at an ammonia concentration of 2 g/L. Enzyme activity, microbial community, and metaproteomic analysis indicated that the side reactor enriched microorganisms with strong hydrogen-utilizing capacity, while the primary reactor was enriched with Methanosaeta. Furthermore, key pathways related to propionate metabolism, ABC transporters, and methane production were enhanced in the primary reactor, along with increased ATPase activity. The activity of key enzymes involved in AD was also significantly enhanced. This study enhances the understanding of the impact of gas atmosphere control on the microbial ecology and metabolic characteristics of AD system, providing valuable insights and practical guidance for the development of Engineering applications in this field.}, }
@article {pmid40184705, year = {2025}, author = {Barrantes-Jiménez, K and Lejzerowicz, F and Tran, T and Calderón-Osorno, M and Rivera-Montero, L and Rodríguez-Sánchez, C and Wikmark, OG and Eiler, A and Grossart, HP and Arias-Andrés, M and Rojas-Jiménez, K}, title = {Anthropogenic imprint on riverine plasmidome diversity and proliferation of antibiotic resistance genes following pollution and urbanization.}, journal = {Water research}, volume = {281}, number = {}, pages = {123553}, doi = {10.1016/j.watres.2025.123553}, pmid = {40184705}, issn = {1879-2448}, mesh = {*Plasmids/genetics ; *Rivers/microbiology ; *Urbanization ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; }, abstract = {Plasmids are key determinants in microbial ecology and evolution, facilitating the dissemination of adaptive traits and antibiotic resistance genes (ARGs). Although the molecular mechanisms governing plasmid replication, maintenance, and transfer have been extensively studied, the specific impacts of urbanization-induced pollution on plasmid ecology, diversity, and associated ARGs in tropical regions remain underexplored. This study investigates these dynamics in a tropical aquatic ecosystem, providing novel insights into how pollution shapes plasmid composition and function. In contrast to the observed decrease in chromosomal diversity, we demonstrate that pollution associated with urbanization increases the diversity and taxonomic composition of plasmids within a bacterial community (plasmidome). We analyzed eighteen water and sediment metagenomes, capturing a gradient of pollution and ARG contamination along a tropical urban river. Plasmid and chromosomal diversity profiles were found to be anti-correlated. Plasmid species enrichment along the pollution gradient led to significant compositional differences in water samples, where differentially abundant species suggest plasmid maintenance within specific taxonomic classes. Additionally, the diversity and abundance of ARGs related to the plasmidome increased concomitantly with the intensity of fecal and chemical pollution. These findings highlight the critical need for targeted plasmidome studies to better understand plasmids' environmental spread, as their dynamics are independent of chromosomal patterns. This research is crucial for understanding the consequences of bacterial evolution, particularly in the context of environmental and public health.}, }
@article {pmid40184632, year = {2025}, author = {Huang, Y and Mao, X and Zheng, X and Zhao, Y and Wang, D and Wang, M and Chen, Y and Liu, L and Wang, Y and Polz, MF and Zhang, T}, title = {Longitudinal dynamics and cross-domain interactions of eukaryotic populations in wastewater treatment plants.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40184632}, issn = {1751-7370}, support = {17212124//Hong Kong GRF/ ; }, mesh = {*Eukaryota/classification/genetics/isolation &amp; purification ; *Sewage/microbiology/virology/parasitology ; *Wastewater/microbiology ; Hong Kong ; Metagenomics ; Animals ; Biodiversity ; Phylogeny ; }, abstract = {Activated sludge is a large reservoir of novel microorganisms and microbial genetic diversity. While much attention has been given to the profile and functions of prokaryotes, the eukaryotic diversity remains largely unexplored. In this study, we analysed longitudinal activated sludge samples spanning 13 years from the largest secondary wastewater treatment plants in Hong Kong, unveiling a wealth of eukaryotic taxa and 681 856 non-redundant protein-coding genes, the majority (416 044) of which appeared novel. Ciliophora was the most dominant phylum with a significant increase after a transient intervention (bleaching event). Our metagenomic analysis reveals close linkage and covariation of eukaryotes, prokaryotes, and prokaryotic viruses (phages), indicating common responses to environmental changes such as transient intervention and intermittent fluctuations. Furthermore, high-resolution cross-domain relationships were interpreted by S-map, demonstrating a predatory role of Arthropoda, Ascomycota, Mucoromycota, and Rotifera. This high-resolution profile of microbial dynamics expands our knowledge on yet-to-be-cultured populations and their cross-domain interactions and highlights the ecological importance of eukaryotes in the activated sludge ecosystem.}, }
@article {pmid40183581, year = {2025}, author = {Aminian-Dehkordi, J and Dickson, A and Valiei, A and Mofrad, MRK}, title = {MetaBiome: a multiscale model integrating agent-based and metabolic networks to reveal spatial regulation in gut mucosal microbial communities.}, journal = {mSystems}, volume = {10}, number = {5}, pages = {e0165224}, pmid = {40183581}, issn = {2379-5077}, mesh = {*Gastrointestinal Microbiome/physiology ; *Metabolic Networks and Pathways ; *Intestinal Mucosa/microbiology/metabolism ; *Metabolomics/methods ; Models, Biological ; Humans ; Computer Simulation ; }, abstract = {Mucosal microbial communities (MMCs) are complex ecosystems near the mucosal layers of the gut essential for maintaining health and modulating disease states. Despite advances in high-throughput omics technologies, current methodologies struggle to capture the dynamic metabolic interactions and spatiotemporal variations within MMCs. In this work, we present MetaBiome, a multiscale model integrating agent-based modeling (ABM), finite volume methods, and constraint-based models to explore the metabolic interactions within these communities. Integrating ABM allows for the detailed representation of individual microbial agents each governed by rules that dictate cell growth, division, and interactions with their surroundings. Through a layered approach-encompassing microenvironmental conditions, agent information, and metabolic pathways-we simulated different communities to showcase the potential of the model. Using our in-silico platform, we explored the dynamics and spatiotemporal patterns of MMCs in the proximal small intestine and the cecum, simulating the physiological conditions of the two gut regions. Our findings revealed how specific microbes adapt their metabolic processes based on substrate availability and local environmental conditions, shedding light on spatial metabolite regulation and informing targeted therapies for localized gut diseases. MetaBiome provides a detailed representation of microbial agents and their interactions, surpassing the limitations of traditional grid-based systems. This work marks a significant advancement in microbial ecology, as it offers new insights into predicting and analyzing microbial communities.IMPORTANCEOur study presents a novel multiscale model that combines agent-based modeling, finite volume methods, and genome-scale metabolic models to simulate the complex dynamics of mucosal microbial communities in the gut. This integrated approach allows us to capture spatial and temporal variations in microbial interactions and metabolism that are difficult to study experimentally. Key findings from our model include the following: (i) prediction of metabolic cross-feeding and spatial organization in multi-species communities, (ii) insights into how oxygen gradients and nutrient availability shape community composition in different gut regions, and (iii) identification of spatiallyregulated metabolic pathways and enzymes in E. coli. We believe this work represents a significant advance in computational modeling of microbial communities and provides new insights into the spatial regulation of gut microbiome metabolism. The multiscale modeling approach we have developed could be broadly applicable for studying other complex microbial ecosystems.}, }
@article {pmid40179787, year = {2025}, author = {Wang, Z and Tu, S and Shehzad, K and Hou, J and Xiong, S and Cao, M}, title = {Comparative study of organosilicon and inorganic silicon in reducing cadmium accumulation in wheat: Insights into rhizosphere microbial communities and molecular regulation mechanisms.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138061}, doi = {10.1016/j.jhazmat.2025.138061}, pmid = {40179787}, issn = {1873-3336}, mesh = {*Triticum/metabolism/growth &amp; development/drug effects ; *Cadmium/metabolism ; *Silicon/pharmacology/chemistry ; Rhizosphere ; *Soil Pollutants/metabolism ; Microbiota/drug effects ; Soil Microbiology ; }, abstract = {Silicon is widely used as a "quality element" and "stress resistance element" in crop production and the remediation of heavy metal-contamination soils. Compared to inorganic silicon, organosilicon has unique properties such as amphiphilicity, low surface energy and high biocompatibility. Our previous research has confirmed the effectiveness of organosilicon-modified fertilizers in inhibiting Cadmium (Cd) absorption in wheat. Therefore, it is of great importance to further explore the potential mechanisms and comprehensive benefits of organosilicon. In this study, the microbiological and molecular mechanisms by which organosilicon reduces Cd concentration in wheat compared to inorganic silicon were investigated in depth. The findings indicated that, in comparison with inorganic silicon, organosilicon exhibited a more remarkable efficacy. Specifically, it was more effective in reducing the Cd concentration in wheat grains, achieving a reduction range of 35-39 % as opposed to the 23-28 % reduction achieved by inorganic silicon. Moreover, it manifested a greater ability to mitigate health risks, with a reduction range of 33-42 % compared to the 25-30 % reduction of inorganic silicon. Furthermore, organosilicon contributed to a significant increase in wheat yield, with a growth range of 11-14 % in contrast to the 8-11 % increase from inorganic silicon. Additionally, it enhanced the quality of the grains, substantially improving the protein content and amino acid content. The comparative advantages of organosilicon over inorganic silicon would be firstly due to the reduction of the bioavailability of soil Cd by increasing the available silicon content in the soil and improving the soil microbial ecology (increasing the abundance of Bacillus, Pseudomonas, Massilia and Talaromyces and reducing the enrichment of Fusarium). Secondly, organosilicon achieved vacuolar compartmentalization of Cd by upregulating the expression of the ABC transporter gene (TaABCB7), thereby alleviating Cd toxicity and restricting Cd transport from leaves to grains. Meanwhile, organosilicon increased the wheat yield by optimizing the availability of soil nutrients and enhancing photosynthesis. These results demonstrate the immense potential of organosilicon in mitigating heavy metal contamination in crops.}, }
@article {pmid40179176, year = {2025}, author = {Lentsch, V and Woller, A and Rocker, A and Aslani, S and Moresi, C and Ruoho, N and Larsson, L and Fattinger, SA and Wenner, N and Barazzone, EC and Hardt, WD and Loverdo, C and Diard, M and Slack, E}, title = {Vaccine-enhanced competition permits rational bacterial strain replacement in the gut.}, journal = {Science (New York, N.Y.)}, volume = {388}, number = {6742}, pages = {74-81}, pmid = {40179176}, issn = {1095-9203}, support = {176954/SNSF_/Swiss National Science Foundation/Switzerland ; 180953/SNSF_/Swiss National Science Foundation/Switzerland ; 865730/ERC_/European Research Council/International ; }, mesh = {Animals ; Female ; Mice ; Adaptive Immunity ; Administration, Oral ; *Antibiosis ; Antibodies, Bacterial/immunology ; *Escherichia coli/immunology/growth &amp; development/physiology ; Escherichia coli Infections/prevention &amp; control/immunology/microbiology ; Gastrointestinal Microbiome ; Immunity, Mucosal ; Mice, Inbred C57BL ; *Salmonella typhimurium/immunology/growth &amp; development/physiology ; *Salmonella Vaccines/immunology/administration &amp; dosage ; Vaccination ; }, abstract = {Colonization of the intestinal lumen precedes invasive infection for a wide range of enteropathogenic and opportunistic pathogenic bacteria. We show that combining oral vaccination with engineered or selected niche-competitor strains permits pathogen exclusion and strain replacement in the mouse gut lumen. This approach can be applied either prophylactically to prevent invasion of nontyphoidal Salmonella strains, or therapeutically to displace an established Escherichia coli. Both intact adaptive immunity and metabolic niche competition are necessary for efficient vaccine-enhanced competition. Our findings imply that mucosal antibodies have evolved to work in the context of gut microbial ecology by influencing the outcome of competition. This has broad implications for the elimination of pathogenic and antibiotic-resistant bacterial reservoirs and for rational microbiota engineering.}, }
@article {pmid40177466, year = {2025}, author = {Hwang, J and Hayward, A and Sofen, LE and Pitz, KJ and Chavez, FP and Edwards, BR}, title = {Daily microbial rhythms of the surface ocean interrupted by the new moon-a lipidomic study.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf044}, pmid = {40177466}, issn = {2730-6151}, abstract = {Lipids are essential biomolecules for cell physiology and are commonly used as biomarkers to elucidate biogeochemical processes over a large range of environments and timescales. Here, we use high-temporal-resolution lipidomic analysis to characterize the surface ocean community in the productive upwelling region overlying the Monterey Bay Canyon. We observed a strong diel signal with a drawdown of lipids at night and an increase during the day that seemed to correspond to wholesale removal of lipids from the surface ocean as opposed to internal metabolism. Individual lipid species were organized into coregulated groups that were interpreted as representing different phytoplankton guilds. Concentrations of long-chained triacylglycerols (TAGs) showed unique patterns over the course of five days. TAGs were used to estimate the amount of energy cycled through the surface ocean. These calculations revealed diurnal carbon cycling that was on scales comparable to net primary production. The diel pattern dissipated from most lipid modules on Day 3 as tidal forcing increased at our site with the advent of the new moon. Pigment analysis indicated that the community shifted from a diatom-dominated community to a more diverse assemblage, including more haptophytes, chlorophytes, and Synechococcus during the new moon. The shift in community appears to promote higher nutritional quality of biomass, with more essential fatty acids in the surface ocean during the spring tide. This analysis showcases the utility of lipidomics in characterizing community dynamics and underscores the importance of considering both diel and tidal timescales when sampling in productive coastal regions.}, }
@article {pmid40177465, year = {2025}, author = {Krause, SMB and van den Berg, NI and Brenzinger, K and Zweers, H and Bodelier, PLE}, title = {Beyond methane consumption: exploring the potential of methanotrophic bacteria to produce secondary metabolites.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf030}, pmid = {40177465}, issn = {2730-6151}, abstract = {Microbial methane-consuming communities significantly impact biogeochemical processes and greenhouse gas emissions. In this study, we explored secondary metabolites produced by methane-oxidizing bacteria (MOB) and their ecological roles. We analyzed the volatile profiles of four MOB strains under controlled conditions and conducted a meta-analysis using high-quality genomes from 62 cultured MOB strains and 289 metagenome-assembled genomes to investigate their potential for producing secondary metabolites. Results show species-specific volatile production, such as germacrene by Methylobacter luteus, which may play a role in the regulation of environmental methane consumption. The meta-analysis revealed that biosynthetic gene clusters (BGCs) for terpenes and β-lactones were more prevalent in the Methylocystaceae and/or Beijerinckiaceae families, while aryl polyene BGCs were dominant in the Methylococcaceae family, reflecting habitat-specific adaptations. These findings advance our understanding of the metabolic capabilities of MOB and underscore the importance of integrating experimental data with genomic and metabolomic analyses to elucidate their ecology, environmental interactions, and contributions to methane cycling.}, }
@article {pmid40177402, year = {2025}, author = {Pellengahr, F and Corella-Puertas, E and Mattelin, V and Saadi, N and Bertella, F and Boulay, AM and van der Meer, Y}, title = {Modeling marine microplastic emissions in Life Cycle Assessment: characterization factors for biodegradable polymers and their application in a textile case study.}, journal = {Frontiers in toxicology}, volume = {7}, number = {}, pages = {1494220}, pmid = {40177402}, issn = {2673-3080}, abstract = {INTRODUCTION: With the continuous increase of plastics production, it is imperative to carefully examine their environmental profile through Life Cycle Assessment (LCA). However, current LCA modeling is not considering the potential impacts of plastic emissions on the biosphere. To integrate plastic emissions into LCA, characterization factors are needed that commonly consist of three elements: a fate factor, an exposure factor, and an effect factor. In this context, fate factors quantify the distribution and longevity of plastics in the environment. Research on these fate factors is still limited, especially for biodegradable polymers. Hence, the main objective of this research was to determine the fate factors of biodegradable polymers [poly (lactic acid), poly (butylene succinate), and poly (ε-caprolactam)] based on primary experimental data for the marine environment.<br><br>METHODS: The validity of former research is tested by comparing the degradation evolution of i. macro- and microplastic particles, ii. two different grades of the polymer, and iii. different temperature levels. The degradation data are obtained by monitoring the oxygen consumption over a period of six months in natural seawater. The determined degradation rates are combined with sedimentation, resuspension, and deep burial rates to obtain fate factors. These fate factors are used to develop polymer-specific characterization factors. The resulting characterization factors are tested in an LCA case study of a synthetic sports shirt made from biodegradable polymer fibers. It allows to assess the relative importance of microplastic impacts compared to other life cycle impacts.<br><br>RESULTS AND DISCUSSION: Comparing the resulting specific surface degradation rates indicates that microplastic degradation rates could be overestimated when using macroplastic degradation data. Pertaining to the case study, the results show that the impact on ecosystem quality by microplastic emissions could account for up to 30% of the total endpoint category. Overall, this work aims to foster interdisciplinary collaboration to leverage the accuracy of LCA studies and thus provide guidance for novel material development.}, }
@article {pmid40175811, year = {2025}, author = {Alexander, NR and Brown, RS and Duwadi, S and Womble, SG and Ludwig, DW and Moe, KC and Murdock, JN and Phillips, JL and Veach, AM and Walker, DM}, title = {Leveraging Fine-Scale Variation and Heterogeneity of the Wetland Soil Microbiome to Predict Nutrient Flux on the Landscape.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {22}, pmid = {40175811}, issn = {1432-184X}, support = {DEB 1933925//National Science Foundation/ ; EF-2125065//National Science Foundation/ ; sub-award 220858//Natural Resource Conservation Services/ ; Molecular Biosciences Program//Middle Tennessee State University/ ; }, mesh = {*Wetlands ; *Soil Microbiology ; *Microbiota ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Soil/chemistry ; Nitrogen/metabolism ; *Nutrients/metabolism ; Nitrogen Cycle ; Phosphorus/metabolism ; Ecosystem ; Agriculture ; }, abstract = {Shifts in agricultural land use over the past 200 years have led to a loss of nearly 50% of existing wetlands in the USA, and agricultural activities contribute up to 65% of the nutrients that reach the Mississippi River Basin, directly contributing to biological disasters such as the hypoxic Gulf of Mexico "Dead" Zone. Federal efforts to construct and restore wetland habitats have been employed to mitigate the detrimental effects of eutrophication, with an emphasis on the restoration of ecosystem services such as nutrient cycling and retention. Soil microbial assemblages drive biogeochemical cycles and offer a unique and sensitive framework for the accurate evaluation, restoration, and management of ecosystem services. The purpose of this study was to elucidate patterns of soil bacteria within and among wetlands by developing diversity profiles from high-throughput sequencing data, link functional gene copy number of nitrogen cycling genes to measured nutrient flux rates collected from flow-through incubation cores, and predict nutrient flux using microbial assemblage composition. Soil microbial assemblages showed fine-scale turnover in soil cores collected across the topsoil horizon (0-5 cm; top vs bottom partitions) and were structured by restoration practices on the easements (tree planting, shallow water, remnant forest). Connections between soil assemblage composition, functional gene copy number, and nutrient flux rates show the potential for soil bacterial assemblages to be used as bioindicators for nutrient cycling on the landscape. In addition, the predictive accuracy of flux rates was improved when implementing deep learning models that paired connected samples across time.}, }
@article {pmid40175529, year = {2025}, author = {Pascoal, F and Branco, P and Torgo, L and Costa, R and Magalhães, C}, title = {Definition of the microbial rare biosphere through unsupervised machine learning.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {544}, pmid = {40175529}, issn = {2399-3642}, mesh = {*Unsupervised Machine Learning ; *Microbiota ; Machine Learning ; }, abstract = {The microbial rare biosphere, composed of low-abundance microorganisms in a community, lacks a standardized delineation method for its definition. Currently, most studies rely on arbitrary thresholds to define the microbial rare biosphere (e.g., 0.1% relative abundance per sample), hampering comparisons across studies. To address this challenge, we present ulrb (Unsupervised Learning based Definition of the Rare Biosphere), available as an R package. ulrb uses unsupervised machine learning to optimally classify taxa into abundance categories (e.g., rare, intermediate, or abundant) within microbial communities. We show that ulrb is more consistent than threshold-based approaches and can be applied to data derived from common microbial ecology protocols and non-microbial studies. ulrb can be used to identify different types of rarity and is statistically valid for the analysis of various dataset sizes. In conclusion, ulrb discerns rare from abundant organisms in a user-independent manner, finding applicability in selected ecological datasets.}, }
@article {pmid40174026, year = {2024}, author = {Shimano, S and Hiruta, SF and Sánchez-Chávez, DI and Pfingstl, T}, title = {Coastal mites (Oribatida, Ameronothridae) found far from the coast in moss growing on the Cathédrale Notre-Dame de Paris, France, fifty years after their first discovery in this historic site.}, journal = {Zootaxa}, volume = {5556}, number = {1}, pages = {62-71}, doi = {10.11646/zootaxa.5556.1.6}, pmid = {40174026}, issn = {1175-5334}, mesh = {Animals ; *Mites/classification/genetics/anatomy &amp; histology/growth &amp; development/ultrastructure ; Male ; Animal Distribution ; Female ; Ecosystem ; France ; Phylogeny ; Body Size ; Animal Structures/growth &amp; development/anatomy &amp; histology ; Organ Size ; *Bryophyta/parasitology ; }, abstract = {A species of oribatid mite, Ameronothrus maculatus (Michael, 1882), was collected from moss growing on the building of the Cathédrale Notre-Dame de Paris. This species of Ameronothridae is usually found in coastal Holarctic environments. The specimens were studied by Scanning Electron Microscope and could be clearly assigned to this taxon. This population was first discovered by F. Grandjean approximately 50 years ago, and the present record demonstrates that it has persisted despite its habitat being a tourist destination visited by over 14 million people annually. The record of this species far upstream and on anthropogenic structures is rare but not out of the ordinary in Northern Europe where its distribution can reach far beyond the edges of the estuaries. For further confirmation, we obtained DNA sequences for the COI gene (1554 bp, LC848687), and they were almost identical to those of an earlier found and sequenced specimen of A. maculatus from Germany, differing by only a single base. As supplemental information on A. maculatus from Paris, the region includes whole nucleic ribosomal RNA genes (18S, 5.8S, and 28S, LC848688), partial elongation factor 1 alpha (LC848689), and the complete nucleotide sequence of mitochondrion were also determined.}, }
@article {pmid40172536, year = {2025}, author = {Madison, JD and Osborne, OG and Ellison, A and Garvey Griffith, CN and Gentry, L and Gross, H and Gratwicke, B and Grayfer, L and Muletz-Wolz, CR}, title = {Probiotic colonization of Xenopus laevis skin causes short-term changes in skin microbiomes and gene expression.}, journal = {Infection and immunity}, volume = {93}, number = {5}, pages = {e0056924}, pmid = {40172536}, issn = {1098-5522}, support = {IOS-2131060//National Science Foundation/ ; IOS-2131061//National Science Foundation/ ; BB/W013517/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {Animals ; *Probiotics/pharmacology/administration &amp; dosage ; *Skin/microbiology/immunology ; *Xenopus laevis/microbiology/immunology/genetics ; *Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; Batrachochytrium ; Transcriptome ; }, abstract = {Probiotic therapies have been suggested for amelioration efforts of wildlife disease such as chytridiomycosis caused by Batrachochytrium spp. in amphibians. However, there is a lack of information on how probiotic application affects resident microbial communities and immune responses. To better understand these interactions, we hypothesized that probiotic application would alter microbial community composition and host immune expression in Xenopus laevis. Accordingly, we applied three amphibian-derived and anti-Batrachochytrium bacteria strains (two Pseudomonas spp. and one Stenotrophomonas sp.) to X. laevis in monoculture and also as a cocktail. We quantified microbial community structure using 16S rRNA gene sequencing. We also quantified genes involved in X. laevis immune responses using quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) and skin transcriptomics over 1 and 3-week periods. All probiotic treatments successfully colonized X. laevis skin for 3 weeks, but with differential amplicon sequence variant (ASV) sequence counts over time. Bacterial community and immune gene effects were most pronounced at week 1 post-probiotic exposure and decreased thereafter. All probiotic treatments caused initial changes to bacterial community alpha and beta diversity, including reduction in diversity from pre-exposure anti-Batrachochytrium bacterial ASV relative abundance. Probiotic colonization by Pseudomonas probiotic strain RSB5.4 reduced expression of regulatory T cell marker (FOXP3, measured with RT-qPCR) and caused the greatest gene expression changes detected by transcriptomics. Single bacterial strains and mixed cultures, therefore, altered amphibian microbiome-immune interactions. This work will help to improve our understanding of the role of the microbiome-immune interface underlying both disease dynamics and emergent eco-evolutionary processes.IMPORTANCEAmphibian skin microbial communities have an important role in determining disease outcomes, in part through complex yet poorly understood interactions with host immune systems. Here we report that probiotic-induced changes to the Xenopus laevis frog skin microbial communities also result in significant alterations to these animals' immune gene expression. These findings underscore the interdependence of amphibian skin immune-microbiome interactions.}, }
@article {pmid40170918, year = {2025}, author = {Hager, K and Luo, ZH and Montserrat-Diez, M and Ponce-Toledo, RI and Baur, P and Dahlke, S and Andrei, AS and Bulzu, PA and Ghai, R and Urich, T and Glatzel, S and Schleper, C and Rodrigues-Oliveira, T}, title = {Diversity and environmental distribution of Asgard archaea in shallow saline sediments.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1549128}, pmid = {40170918}, issn = {1664-302X}, abstract = {In recent years, our understanding of archaeal diversity has greatly expanded, especially with the discovery of new groups like the Asgard archaea. These archaea show diverse phylogenetic and genomic traits, enabling them to thrive in various environments. Due to their close relationship to eukaryotes, a large number of metagenomic studies have been performed on Asgard archaea. Research on the fine scale distribution, diversity and quantification in saline aquatic sediments where they mostly occur, has, however, remained scarce. In this study, we investigated depths of shallow saline sediment cores from three distinct European environments: the Baltic Sea near Hiddensee, the coastal Lake Techirghiol in Romania, and an estuarine canal in Piran, Slovenia. Based on 16S rDNA amplicon sequencing, we observe variation in the relative abundance and occurrence of at least seven different Asgard groups that are distinct between the three environments and in their depth distribution. Lokiarchaeia and Thorarchaeia emerge as dominant Asgard groups across all sites, reaching maximal relative abundances of 2.28 and 2.68% of the total microbial communities respectively, with a maximal abundance of all Asgard reaching approx. 5.21% in Hiddensee. Quantitative PCR assays provide insights into the absolute abundance of Lokiarchaeia, supporting distinct patterns of distribution across depths in different sediments. Co-occurrence network analysis indicates distinct potential microbial partners across different Asgard groups. Overall, our study shows that Asgard archaea are found as a stable component in shallow sediment layers and have considerably diversified on macro- and microscales.}, }
@article {pmid40168336, year = {2025}, author = {Brangsch, H and Marcordes, S and Busch, A and Weber, M and Wolf, SA and Semmler, T and Höper, D and Calvelage, S and Linde, J and Barth, SA}, title = {Comparative genomics of Mycobacterium avium subsp. hominissuis strains within a group of captive lowland tapirs.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0320499}, pmid = {40168336}, issn = {1932-6203}, mesh = {Animals ; *Mycobacterium avium/genetics/isolation &amp; purification/classification ; *Perissodactyla/microbiology ; Polymorphism, Single Nucleotide ; *Genome, Bacterial ; *Genomics ; Phylogeny ; Multilocus Sequence Typing ; Whole Genome Sequencing ; }, abstract = {Within a group of three captive lowland tapirs (Tapirus terrestris) suffering from clinically apparent mycobacteriosis, non-tuberculous Mycobacterium avium subsp. hominissuis (MAH) strains were isolated from the animals and the tapir's enclosure. Based on MIRU-VNTR findings, which identified two closely related INMV profiles (124 and 246), a micro-evolutionary event was assumed, and four available MAH strains were submitted to whole genome sequencing (short- and long-read technologies). Surprisingly, the differences based on single nucleotide polymorphisms (SNPs) were exceptionally high between the four strains, i.e., between 841 and 11,166 bases, due to a strong impact of homologous recombination. Thus, an ad hoc core genome multilocus sequence typing (cgMLST) scheme was created and pangenome analysis was conducted for determining the genomic similarity between the strains. The INMV246 isolate obtained from sputum on the enclosure floor and one INMV124 isolate of tapir #2 showed the highest congruence, suggesting that both originated from a shared source. The other two INMV124 isolates were genomically distinct from these strains. Nevertheless, in all four strains two plasmids were detected, which were highly conserved between the strains. The study showed that the genomic variability between MAH strains isolated from the same site within a short period of time can be exceptionally high and the influence of homologous recombination needs to be considered when determining MAH strain relationships, particularly via SNP analyses.}, }
@article {pmid40167801, year = {2025}, author = {Banu, S and Valero, KCW and Rivero, F}, title = {Simulated Heat Waves Affect Cell Fate and Fitness in the Social Amoeba Dictyostelium discoideum.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {21}, pmid = {40167801}, issn = {1432-184X}, support = {#101044202/ERC_/European Research Council/International ; }, mesh = {*Dictyostelium/genetics/growth &amp; development/physiology/cytology ; *Hot Temperature ; Protozoan Proteins/genetics/metabolism ; Spores, Protozoan/growth &amp; development/genetics ; }, abstract = {The effects of heatwaves at organism and population levels have been widely investigated; however, little is known about how they affect the development of cell populations and the fitness of the resulting organism. Disruptions caused by heatwaves are especially critical during early developmental stages in organisms lacking parental developmental protection or care. Here we use the social amoeba Dictyostelium discoideum, a soil microbe with a life cycle that transitions between single-cell and multicellular stages. D. discoideum thrives optimally at 22 °C and elevated temperatures impair (27 °C) or completely arrest (30 °C) growth, development, and spore yield. We established a simulated heatwave model in which vegetative cells were exposed to 27 °C for 3 days and studied the effects on the expression of early and cell type specific developmental genes using real-time quantitative PCR. A single heatwave severely impaired the expression of cyclic AMP-dependent early developmental gene markers (carA, acaA, pkaR, gtaC, tgrC1, and csaA) as well as that of prespore markers (cotB and spiA), while the expression of the prestalk marker ecmA was less affected. When mixed with heat-stressed cells, reporter cells expressing β-galactosidase grown at 22 °C preferentially occupy the spore mass of the fruiting body. Chimera assays of wild-type and reporter cells grown at optimal temperature or subjected to a heatwave confirmed a decreased fitness (contribution to chimeric fruiting bodies). We conclude that exposure of unprotected organisms at the single cell stage to a single heatwave has the potential to negatively impact their ability to cope with environmental extremes.}, }
@article {pmid40167318, year = {2025}, author = {Détain, A and Suzuki, H and Wijffels, RH and Leborgne-Castel, N and Hulatt, CJ}, title = {Snow algae exhibit diverse motile behaviors and thermal responses.}, journal = {mBio}, volume = {16}, number = {5}, pages = {e0295424}, pmid = {40167318}, issn = {2150-7511}, support = {No. 319352//Norwegian Research Council/ ; No. 349485//Norwegian Research Council/ ; }, mesh = {*Snow/microbiology ; Temperature ; Microbiota ; Eutrophication ; Phototaxis ; }, abstract = {Snow algal blooms influence snow and glacier melt dynamics, yet the mechanisms involved in community assemblage, development, and dispersal are not well understood. While microbial swimming behavior contributes significantly to the productivity and organization of aquatic and terrestrial microbiomes, the potential impact of algal cell motility in melting snow on the formation of visible, large-scale surface bloom patterns is largely unknown. Here, using video tracking and phototaxis experiments of unique isolates, we evaluated the motility of diverse snow algal taxa from green, red, and golden colored snow blooms in response to light and thermal gradients. We show that many species are efficient cryophilic microswimmers with speed thermal optima below 10°C although taxa with cryotolerant swimming traits were also identified. The significant motility of snow algae at low temperatures, a result of specialized adaptations, supports the importance of active movement in the life histories of algae inhabiting snow meltwater. However, diversity in swimming performance and behavior reveal a range of evolutionary outcomes and sensitivity of motile life stages to dynamic environments.IMPORTANCESwimming motility is a fundamental mechanism that controls the assembly, structure, and productivity of microbiomes across diverse environments and is highly sensitive to temperature. Especially, the role of cell swimming activity in algal bloom formation at the very low temperatures of snowmelt has been hypothesized, but not studied. By examining the movement patterns of snow algae and modeling the thermal response curves of swimming speed, the data reveal the key role of active cell movement that may have further important impacts on the microbial ecology and melt rates of snow and ice in polar and alpine regions.}, }
@article {pmid40162837, year = {2025}, author = {Major, SR and Polinski, JM and Penn, K and Rodrigue, M and Harke, MJ}, title = {Novel and diverse features identified in the genomes of bacteria isolated from a hydrothermal vent plume.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {4}, pages = {e0259324}, pmid = {40162837}, issn = {1098-5336}, support = {22-08846//Dalio Foundation/ ; }, mesh = {*Hydrothermal Vents/microbiology ; *Genome, Bacterial ; *Bacteria/genetics/isolation &amp; purification/classification ; Phylogeny ; Multigene Family ; Seawater/microbiology ; Gene Transfer, Horizontal ; }, abstract = {Hydrothermal vent plumes (HVPs), formed by high-temperature vent emissions, are rich in compounds that support chemosynthesis and serve as reservoirs of microbial diversity and genetic innovation. Through turbulence, mixing, and interaction with subsea currents, vent communities are thought to disperse across ocean basins. In this study, we focused on the plume of the Moytirra hydrothermal vent field, a relatively unexplored site, to investigate its microbial inhabitants. We cultured bacteria from the Moytirra HVP using 11 different media types and performed complete genome sequencing on 12 isolates. Our analyses revealed four putatively novel species from the Thalassobaculum, Sulfitobacter, Idiomarina, and Christiangramia genera. Comparative genomics identified unique genomic islands containing biosynthetic gene clusters, including a novel Non-Ribosomal Peptide Synthetase/Polyketide Synthase cluster, toxin-antitoxin systems, and evidence of horizontal gene transfer facilitated by prophages. These findings underscore the potential of HVPs as a source of novel microbial species and biotechnologically relevant genes, contributing to our understanding of the biodiversity and genetic complexity of these extreme environments.IMPORTANCEHydrothermal vents are dynamic environments that offer unique nutrients for chemosynthetic organisms to drive biology in the deep-sea. The dynamics of these ecosystems are thought to drive genomic innovation in resident populations. Hydrothermal vent plumes (HVPs) mix with surrounding water, carrying local microbiota with them and dispersing for hundreds of kilometers. This study isolated bacteria from a HVP to capture a genomic snapshot of the microbial community, revealing four putatively novel species of bacteria within three taxonomic classes. The addition of these genomes to public databases provides valuable insights into the genomic function, architecture, and novel biosynthetic gene clusters of bacteria found in these extreme environments.}, }
@article {pmid40162703, year = {2025}, author = {Souza Beraldo, C}, title = {An interactive art activity to promote student reflection and learning about host-microbe interactions.}, journal = {Journal of microbiology &amp; biology education}, volume = {26}, number = {1}, pages = {e0006325}, pmid = {40162703}, issn = {1935-7877}, abstract = {The use of art in science teaching can effectively help students understand complex and abstract concepts, particularly in the fields of Microbiology and Microbial Ecology, where the study objects-the microbes-are invisible to human eyes. To explore how different factors shape host-microbe interactions, I developed the activity MicrobiART, which uses mixed art materials to create analogies that illustrate the dynamic relationships between hosts, microbes, and their environments. MicrobiART was presented as an alternative session at a PhD students' conference in Espoo, Finland. Participants were invited to combine papers, balls, and paint-representing hosts, microbes, and environmental factors, respectively-to create paintings that depict the outcomes of these interactions. The completed artworks were then displayed in a mini exhibition. Following this session, participants were invited to engage in discussion to identify patterns in the paintings and reflect on the analogies' meanings and limitations. The activity is adaptable to various age groups and to both non-specialist and specialist audiences. Anecdotal evidence suggests that participants understood how interaction outcomes depend on the specific combination of players (host, microbes, and environment), while also recognizing emergent patterns. For instance, interactions within the same environment often share similar colors, contrasting with those from a different environment. Moreover, participants found the experience enjoyable, particularly due to its interactive and aesthetic appeal. These findings highlight the value of integrating science and art in science communication, especially in conference spaces: such integration fosters connections, inspires new ideas and teaching approaches, and provides a relaxed setting for discussion.}, }
@article {pmid40161817, year = {2025}, author = {Band, VI and Gribonika, I and Stacy, A and Bouladoux, N and Mistry, S and Burns, A and Perez-Chaparro, PJ and Chau, J and Enamorado, M and Nagai, M and Bhushan, V and Golec, DP and Schwartzberg, PL and Hourigan, SK and Nita-Lazar, A and Belkaid, Y}, title = {Sulfide is a keystone metabolite for gut homeostasis and immunity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40161817}, issn = {2692-8205}, support = {ZIA AI001115/ImNIH/Intramural NIH HHS/United States ; ZIA AI001132/ImNIH/Intramural NIH HHS/United States ; }, abstract = {Hydrogen sulfide is a gaseous, reactive molecule specifically enriched in the gastrointestinal tract. Here, we uncover a non-redundant role for sulfide in the control of both microbial and immune homeostasis of the gut. Notably, depletion of sulfide via both pharmaceutical and dietary interventions led to a profound collapse of CD4 T cells in the ileum of the small intestine lamina propria and significant impact on microbial ecology. As a result, mice with reduced sulfide within the gut were deficient in their ability to mount T cell dependent antibody responses to oral vaccine. Mechanistically, our results support the idea that sulfide could act directly on CD4 T cells via enhanced AP-1 activation, leading to heightened proliferation and cytokine production. This study uncovers sulfides as keystone components in gut ecology and provides mechanistic insight between diet, gut sulfide production and mucosal immunity.}, }
@article {pmid40160925, year = {2025}, author = {Amirmijani, A and Pordel, A and Dehghani, K and Pourmoghaddam, MJ and Masigol, H and Grossart, HP}, title = {Two new pestalotioid fungi from tropical fruits in Iran.}, journal = {MycoKeys}, volume = {115}, number = {}, pages = {221-240}, pmid = {40160925}, issn = {1314-4049}, abstract = {In a survey of tropical plant diseases in southern and southeastern Iran, samples of diseased Mangiferaindica and Psidiumguava leaves with necrotic symptoms were collected between 2021 and 2022. Six representative isolates of Neopestalotiopsis and Robillarda (three isolates for each) were studied using morphological characteristics as well as multi-locus phylogenetic analysis based on (i) the internal transcribed spacer (ITS) region of the nuclear rDNA, (ii) part of the translation elongation factor 1-alpha (tef1), and (iii) the β-tubulin (tub2). After morphological investigation, our phylogenetic analysis revealed that the Neopestalotiopsis and Robillarda isolates under study differed from all previously described species within these genera. Based on our polyphasic approach, two new species, including Neopestalotiopsisguava sp. nov. from necrotic Mangiferaindica and Robillardakhodaparastii sp. nov. from Psidiumguava are described and illustrated from Iran.}, }
@article {pmid40157674, year = {2025}, author = {Wu, X and Yu, D and Ma, Y and Fang, X and Sun, P}, title = {Function and therapeutic potential of Amuc_1100, an outer membrane protein of Akkermansia muciniphila: A review.}, journal = {International journal of biological macromolecules}, volume = {308}, number = {Pt 4}, pages = {142442}, doi = {10.1016/j.ijbiomac.2025.142442}, pmid = {40157674}, issn = {1879-0003}, mesh = {Humans ; Animals ; Gastrointestinal Microbiome/drug effects ; *Bacterial Outer Membrane Proteins/pharmacology/therapeutic use/chemistry ; Akkermansia ; Probiotics/therapeutic use ; }, abstract = {The gut microbiota-derived protein Amuc_1100, a key outer membrane component of Akkermansia muciniphila, has emerged as a groundbreaking therapeutic agent with unique structural and functional properties. Amuc_1100 exerts multifaceted immune-metabolic effects through novel mechanisms, including modulation of TLR2/4 and JAK/STAT pathways. This review highlights its unique multi-component structure that enables synergistic biological activity, and its pharmacological properties, which underlies its ability to enhance intestinal barrier integrity, restore microbiota balance, and suppress systemic inflammation. Crucially, Amuc_1100 demonstrates unprecedented therapeutic versatility across both intestinal disorders (e.g., inflammatory bowel disease, antibiotic-associated diarrhea) and extraintestinal conditions-notably improving neuropsychiatric symptoms via gut-serotonin axis regulation, combating cancer through CD8+ T cell activation, and mitigating cardiotoxicity via gut-heart immune crosstalk. Emerging innovations in targeted delivery systems, including gut-retentive nano-formulations and engineered probiotic vectors, further amplify its clinical potential. We critically evaluate recent advances distinguishing Amuc_1100's mechanisms from live bacterial interventions. By synthesizing evidence from preclinical models, this work positions Amuc_1100 as a prototype for next-generation microbiome-derived therapeutics, bridging microbial ecology with precision medicine.}, }
@article {pmid40152585, year = {2025}, author = {Wang, F and Luo, J and Zhang, Z and Liu, Y and Sheng, Dh and Zhuo, L and Li, Y-z}, title = {Differential crosstalk between toxin-immunity protein homologs divides Myxococcus nonself siblings into close and distant social relatives.}, journal = {mBio}, volume = {16}, number = {5}, pages = {e0390224}, pmid = {40152585}, issn = {2150-7511}, support = {2022FY101100//Science &amp; Technology Fundamental Resources Investigation Program/ ; 32070030//MOST | National Natural Science Foundation of China (NSFC)/ ; 32270073//MOST | National Natural Science Foundation of China (NSFC)/ ; ZR2022QC001//Natural Science Foundation of Shandong Province ()/ ; BK20230248//JST | Natural Science Foundation of Jiangsu Province(Jiangsu Natural Science Foundation)/ ; }, mesh = {*Myxococcus xanthus/genetics/physiology/immunology ; *Bacterial Toxins/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism ; *Toxin-Antitoxin Systems ; Microbial Interactions ; }, abstract = {Many bacteria discriminate self and nonself using toxins and their corresponding immunity proteins. The toxin-immunity systems often include homologs, potentially creating crosstalk with unknown influences on kin discrimination. In this study, we investigated the kinship controlled by four homologous toxin-immunity systems in the social bacterium Myxococcus xanthus. We determined that the four homologous systems each play an independent role in the discrimination of self and nonself. However, the immunity proteins inactivate not only the corresponding nuclease toxin proteins but also some non-corresponding toxin proteins, depending on their sequence and structural similarities. The nonself relatives controlled by toxin-immunity proteins with or without crosstalk exhibit differential co-growth and collaborative behaviors. We concluded that differential crosstalk between toxin-immunity protein homologs can divide bacterial nonself lineages into close and distant relatives displaying differential collaboration and antagonistic behaviors.IMPORTANCEThis study significantly contributes to our knowledge of kin selection and social behavior in bacteria. The interactions between four homologous toxin-immunity protein systems of Myxococcus xanthus were investigated, and evidence was obtained that these systems can distinguish between self and nonself cells within a species. Importantly, this study revealed that nonself lineages, which display varying degrees of genetic relatedness, can co-grow and collaborate in distinct patterns. This discovery implies that the differential crosstalk between homologous toxin-immunity proteins can mimic the degree of kinship; through this activity, bacteria can differentiate close and distant relatives. This novel insight into bacterial social dynamics and kin discrimination supports kin selection theory and enriches our knowledge on microbial interactions and evolutionary strategies. These findings have broad implications for microbial ecology, evolution, and the development of cooperation strategies.}, }
@article {pmid40151948, year = {2025}, author = {Šulčius, S and Alzbutas, G and Lukashevich, V}, title = {Cyanophage Lysis of the Cyanobacterium Nodularia spumigena Affects the Variability and Fitness of the Host-Associated Microbiome.}, journal = {Environmental microbiology}, volume = {27}, number = {4}, pages = {e70042}, doi = {10.1111/1462-2920.70042}, pmid = {40151948}, issn = {1462-2920}, support = {S-LL-21-10//Lietuvos Mokslo Taryba/ ; }, mesh = {*Microbiota ; *Bacteriophages/physiology ; *Cyanobacteria/virology/metabolism/genetics/physiology ; *Bacteriolysis ; }, abstract = {Cyanobacteria are intricately linked with its microbiome through multiple metabolic interactions. We assessed how these interactions might be affected by cyanophage infection and lysis in cyanobacterium Nodularia spumigena. The genome-scale metabolic models and analysis of putative metabolic interactions revealed a bidirectional cross-feeding potential within the N. spumigena microbiome, with heterotrophic bacteria exhibiting a greater level of trophic dependency on the cyanobacterium. Our results indicate that microbes associated with N. spumigena rely on the supply of various amino acids, reduced carbon compounds and protein synthesis cofactors released by the cyanobacterial host. We observed that compositional changes in the N. spumigena microbiome were associated with the multiplicity of infection and increased with increasing initial viral load. Higher mortality of N. spumigena led to decreased variability in the relative abundances of bacteria, suggesting an indirect restriction of their niche space. Lysis of N. spumigena resulted in a substantial decline in the estimated absolute abundances of heterotrophic bacteria, indicating reduced fitness of co-occurring bacteria in the absence of N. spumigena. Altogether, we demonstrate how a gradual increase in viral pressure on the photosynthetic host propagates through the co-occurring microbial community, disrupting cooperative nature and microbial connectivity within the N. spumigena microbiome.}, }
@article {pmid40149089, year = {2025}, author = {Nussbaumer-Pröll, A and Hausmann, B and Weber, M and Pjevac, P and Berry, D and Zeitlinger, M}, title = {A Pilot Study on the Impact of Cranberry and Ascorbic Acid Supplementation on the Urinary Microbiome of Healthy Women: A Randomized Controlled Trial.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, pmid = {40149089}, issn = {2079-6382}, abstract = {Background: The collection of microorganisms that colonize the human genital and urinary tract is referred to as the genitourinary microbiome. Urinary tract infections (UTIs), which predominantly affect women, are linked to alterations in the genitourinary microbiome. Cranberries (Vaccinium oxycoccos), rich in proanthocyanidins, and ascorbic acid (vitamin C), known for their urinary acidification properties, are commonly used for UTI prevention. However, their effects on the genitourinary microbiome remain inadequately characterized. This pilot study assesses the genitourinary microbiome composition in healthy women and evaluates the influence of cranberry and ascorbic acid supplementation. Methods: In a randomized, controlled, and open-label trial, 27 healthy women in their reproductive age (18-40 years) were assigned to three groups: cranberry (n = 8), ascorbic acid (n = 10), and control (n = 9). Urine samples were collected at three time points and processed for 16S rRNA gene amplicon-based microbial community composition analysis. Microbiome composition was compared within and between groups, and between study visits. Results: Sufficient microbial DNA was extracted from all midstream urine samples. The genitourinary microbiome was predominantly composed of Lactobacillus spp., as reported previously. No significant shifts in microbial composition were observed in response to cranberry or ascorbic acid supplementation, and no statistically significant differences were detected between the intervention and control groups or between study visits. Conclusion: The genitourinary microbiome of healthy women remained stable during cranberry or ascorbic acid supplementation. Further studies in patients with recurrent UTIs are needed to explore the potential impacts of these supplements on the genitourinary microbiome in disease states.}, }
@article {pmid40149015, year = {2025}, author = {Fournier, P and Pellan, L and Jaswa, A and Cambon, MC and Chataigner, A and Bonnard, O and Raynal, M and Debord, C and Poeydebat, C and Labarthe, S and Delmotte, F and This, P and Vacher, C}, title = {Revealing microbial consortia that interfere with grapevine downy mildew through microbiome epidemiology.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {37}, pmid = {40149015}, issn = {2524-6372}, support = {20-PCPA-0010//Agence Nationale de la Recherche/ ; }, abstract = {BACKGROUND: Plant and soil microbiomes can interfere with pathogen life cycles, but their influence on disease epidemiology remains understudied. Here, we analyzed the relationships between plant and soil microbiomes and long-term epidemiological records of grapevine downy mildew, a major disease caused by the oomycete Plasmopara viticola.<br><br>RESULTS: We found that certain microbial taxa were consistently more abundant in plots with lower disease incidence and severity and that the microbial community composition could predict disease incidence and severity. Microbial diversity was not strongly linked to epidemiological records, suggesting that disease incidence and severity is more related to the abundance of specific microbial taxa. These key taxa were identified in the topsoil, where the pathogen's oospores overwinter, and in the phyllosphere, where zoospores infect leaves. By contrast, the leaf endosphere, where the pathogen's mycelium develops, contained few taxa of interest. Surprisingly, the soil microbiota was a better predictor of disease incidence and severity than the leaf microbiota, suggesting that the soil microbiome could be a key indicator of the dynamics&#xa0;of this primarily aerial disease.<br><br>CONCLUSION: Our study integrates long-term epidemiological data with microbiome profiles of healthy plants to reveal fungi and bacteria relevant for the biocontrol of grapevine downy mildew. The resulting database provides a valuable resource for designing microbial consortia with potential biocontrol activity. The framework can be applied to other crop systems to guide the development of biocontrol strategies and reduce pesticide use in agriculture.}, }
@article {pmid40148178, year = {2025}, author = {Hodžić, A and Duscher, GG and Alić, A and Beck, R and Berry, D}, title = {Peritrophic matrix: an important determinant of vector competence in hematophagous arthropods.}, journal = {Trends in parasitology}, volume = {41}, number = {5}, pages = {374-386}, doi = {10.1016/j.pt.2025.03.005}, pmid = {40148178}, issn = {1471-5007}, mesh = {Animals ; *Arthropod Vectors/immunology/physiology ; *Arthropods/immunology/physiology/parasitology ; Immunity, Innate ; }, abstract = {The peritrophic matrix (PM) is a non-cellular, glycan-rich structure that lines the gut epithelium of most invertebrates, including arthropod vectors that transmit diseases of public health and veterinary concern. This semipermeable barrier, functionally analogous to the vertebrate mucosal layer, separates the gut lumen from epithelial cells and provides protection against invading pathogens and their toxins. Beyond its mechanical protective role in the gut, the PM plays a crucial part in arthropod innate immunity. Here, we summarize the most recent advances in understanding the molecular mechanisms of vector-pathogen interactions in blood-feeding arthropods and discuss the significance of the PM in modulating vector competence. This knowledge could contribute to the development of novel strategies to control vector-borne infections.}, }
@article {pmid40147302, year = {2025}, author = {Keneally, C and Chilton, D and Dornan, TN and Kidd, SP and Gaget, V and Toomes, A and Lassaline, C and Petrovski, R and Wood, L and Brookes, JD}, title = {Multi-omics reveal microbial succession and metabolomic adaptations to flood in a hypersaline coastal lagoon.}, journal = {Water research}, volume = {280}, number = {}, pages = {123511}, doi = {10.1016/j.watres.2025.123511}, pmid = {40147302}, issn = {1879-2448}, mesh = {*Floods ; Salinity ; RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology ; Metabolomics ; Microbiota ; Multiomics ; }, abstract = {Microorganisms drive essential biogeochemical processes in aquatic ecosystems and are sensitive to both salinity and hydrological changes. As climate change and anthropogenic activities alter hydrology and salinity worldwide, understanding microbial ecology and metabolism becomes increasingly important for managing aquatic ecosystems. Biogeochemical processes were investigated on sediment microbial communities during a significant flood event in the hypersaline Coorong lagoon, South Australia (the largest in the Murray-Darling Basin since 1956). Samples from six sites across a salinity gradient were collected before and during flooding in 2022. To assess changes in microbial taxonomy and metabolic function, 16S rRNA amplicon sequencing was employed alongside untargeted liquid chromatography-mass spectrometry (LC-MS) to assess changes in microbial taxonomy and metabolic function. Results showed a decrease in microbial richness and diversity during flooding, especially in hypersaline conditions. Pre-flood communities were enriched with osmolyte-degrading and methanogenic taxa, alongside osmoprotectant metabolites, such as glycine betaine and choline. Flood conditions favored taxa such as Halanaerobiaceae and Beggiatoaceae, inducing inferred metagenomic shifts indicative of sulfur cycling and nitrogen reduction pathways, while also enriching a greater diversity of metabolites including Gly-Phe dipeptides and guanine. This study demonstrates that integrating metabolomics with microbial community analysis enhances understanding of ecosystem responses to disturbance. These findings suggest microbial communities rapidly change in response to salinity reductions while maintaining key biogeochemical functions. Such insights are valuable for ecosystem management and predictive modelling under environmental stressors such as flooding.}, }
@article {pmid40146382, year = {2025}, author = {Nain, D and Rana, A and Raychoudhury, R and Sen, R}, title = {Parasite-Induced Replacement of Host Microbiota: Impact of Xenos gadagkari Parasitization on the Microbiota of Polistes wattii.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {20}, pmid = {40146382}, issn = {1432-184X}, support = {DST/INSPIRE/03/2021/000175, IF200146//Department of Science and Technology, Ministry of Science and Technology, India/ ; 1061830779//Council of Scientific and Industrial Research, India/ ; CRG-2021/007010//Science and Engineering Research Board/ ; }, mesh = {Animals ; *Wasps/microbiology/physiology/parasitology ; *Microbiota ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Seasons ; *Host-Parasite Interactions ; }, abstract = {The study of microbiota of social insects under different ecological conditions can provide important insights into the role of microbes in their biology and behavior. Polistes is one of the most widely distributed and extensively studied genera of social wasps, yet a comprehensive study on the microbiota of any species of Polistes or any primitively eusocial wasp is missing. Polistes wattii is an Asian wasp, which hibernates in winter and exhibits a biannual nest founding strategy. It is often parasitized by the strepsipteran endoparasite/parasitoid Xenos gadagkari, which changes the morpho-physiology and behavior of their hosts. In this study, we employ 16S rRNA amplicon sequencing, using the Oxford Nanopore platform, to study the microbial community of P. wattii and investigate the effects of seasonality, sex, and Xenos parasitism. We show that the microbiota differs in females from solitary foundress spring nests and multiple foundress summer nests. The microbiota also differs in males and females. Finally, we show that X. gadagkari parasitism replaces and homogenizes the microbiota of P. wattii. Unlike the unparasitized wasps, the microbiota of X. gadagkari parasitoids and parasitized wasps are dominated by Wolbachia and Providencia. Although the normal microbiota of P. wattii resembles that of highly eusocial vespid wasps, we show that the microbiota of parasitized P. wattii becomes more like the microbiota of strepsipterans. Therefore, it appears that X. gadagkari and other such strepsipteran parasitoids may have a bigger impact on the biology of their hosts than previously thought.}, }
@article {pmid40146077, year = {2025}, author = {Savchenko, V and Yu, XA and Polz, MF and Böttcher, T}, title = {Chitinivorax: The New Kid on the Block of Bacterial 2-Alkyl-4(1H)-quinolone Producers.}, journal = {ACS chemical biology}, volume = {20}, number = {4}, pages = {960-966}, pmid = {40146077}, issn = {1554-8937}, mesh = {*Quinolones/metabolism/chemistry ; Multigene Family ; Phylogeny ; *Comamonadaceae/metabolism/genetics ; }, abstract = {2-Alkyl-4(1H)-quinolones play a key role in bacterial communication, regulating biofilm formation, and virulence. Their antimicrobial properties also support bacterial survival and interspecies competition in microbial communities. In addition to the human pathogen Pseudomonas aeruginosa various species of Burkholderia and Pseudoalteromonas are known to produce 2-alkyl-4(1H)-quinolones. However, the evolutionary relationships of their biosynthetic gene clusters remain largely unexplored. To address this, we investigated the phylogeny of 2-alkyl-4(1H)-quinolone biosynthetic gene clusters, leading to the discovery of Chitinivorax as a fourth genus capable of producing 2-alkyl-4(1H)-quinolones, expanding our knowledge of the diversity of bacteria involved in quinolone-biosynthesis.}, }
@article {pmid40143451, year = {2025}, author = {Jenkins, G and Boyd, ES and Danchin, A and Hervé, V}, title = {Microbiome Notes-Building a Library of Descriptive Microbial Ecology.}, journal = {Environmental microbiology reports}, volume = {17}, number = {2}, pages = {e70085}, pmid = {40143451}, issn = {1758-2229}, }
@article {pmid40142506, year = {2025}, author = {Govaert, M and Duysburgh, C and Kesler, B and Marzorati, M}, title = {Effects of NatureKnit™, a Blend of Fruit and Vegetable Fibers Rich in Naturally Occurring Bound Polyphenols, on the Metabolic Activity and Community Composition of the Human Gut Microbiome Using the M-SHIME[®] Gastrointestinal Model.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, pmid = {40142506}, issn = {2076-2607}, support = {Not applicable//VDF FutureCeuticals, Inc./ ; }, abstract = {This study evaluated the impact of a proprietary blend of fruit and vegetable fibers rich in naturally occurring bound polyphenols (commercially marketed as NatureKnit[TM]), compared to purified fibers (inulin and psyllium), on the human gut microbiome using the validated M-SHIME[®] gastrointestinal model. A short-term single-stage colonic M-SHIME[®] experiment (with fecal inoculum from three healthy human donors) was used to evaluate the test products compared to a negative control. Samples were assessed for pH, gas pressure, short-chain fatty acid (SCFA) production, lactate, and ammonium from 0 h to 48 h. Microbial community composition was assessed at 0 h (negative control only), 24 h, and 48 h (lumen) or 48 h (mucosal). All test products were fermented well in the colon as demonstrated by decreases in pH and increases in gas pressure over time; these changes occurred faster with the purified fibers, whereas NatureKnit™ demonstrated slow, steady changes, potentially indicating a gentler fermentation process. SCFA production significantly increased over the course of the 48 h experiment with all test products versus negative control. SCFA production was significantly greater with NatureKnit™ versus the purified fibers. Shifts in the microbial community composition were observed with all test products versus negative control. At the conclusion of the 48 h experiment, the absolute bacterial abundance and the richness of observed bacterial taxa in the lumen compartment was significantly greater with NatureKnit™ compared with inulin, psyllium, and negative control. Overall, NatureKnit™ demonstrated greater or similar prebiotic effects on study measures compared with established prebiotic fibers.}, }
@article {pmid40142410, year = {2025}, author = {Hassen, AI and Muema, EK and Diale, MO and Mpai, T and Bopape, FL}, title = {Non-Rhizobial Endophytes (NREs) of the Nodule Microbiome Have Synergistic Roles in Beneficial Tripartite Plant-Microbe Interactions.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, pmid = {40142410}, issn = {2076-2607}, support = {A-089//Department of Agriculture Land Reform and Rural Development/ ; }, abstract = {Microbial symbioses deal with the symbiotic interactions between a given microorganism and another host. The most widely known and investigated microbial symbiosis is the association between leguminous plants and nitrogen-fixing rhizobia. It is one of the best-studied plant-microbe interactions that occur in the soil rhizosphere and one of the oldest plant-microbe interactions extensively studied for the past several decades globally. Until recently, it used to be a common understanding among scientists in the field of rhizobia and microbial ecology that the root nodules of thousands of leguminous species only contain nitrogen-fixing symbiotic rhizobia. With the advancement of molecular microbiology and the coming into being of state-of-the-art biotechnology innovations, including next-generation sequencing, it has now been revealed that rhizobia living in the root nodules of legumes are not alone. Microbiome studies such as metagenomics of the root nodule microbial community showed that, in addition to symbiotic rhizobia, other bacteria referred to as non-rhizobial endophytes (NREs) exist in the nodules. This review provides an insight into the occurrence of non-rhizobial endophytes in the root nodules of several legume species and the beneficial roles of the tripartite interactions between the legumes, the rhizobia and the non-rhizobial endophytes (NREs).}, }
@article {pmid40141768, year = {2025}, author = {Ghobashy, MOI and Al-Otaibi, AS and Alharbi, BM and Alshehri, D and Ghabban, H and Albalawi, DA and Alenzi, AM and Alatawy, M and Alatawi, FA and Algammal, AM and Mir, R and Mahrous, YM}, title = {Metagenomic Characterization of Microbiome Taxa Associated with Coral Reef Communities in North Area of Tabuk Region, Saudia Arabia.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {40141768}, issn = {2075-1729}, support = {Research no.0144-1444-S//Deanship of Research and Graduate Studies at University of Tabuk/ ; }, abstract = {The coral microbiome is highly related to the overall health and the survival and proliferation of coral reefs. The Red Sea's unique physiochemical characteristics, such a significant north-south temperature and salinity gradient, make it a very intriguing research system. However, the Red Sea is rather isolated, with a very diversified ecosystem rich in coral communities, and the makeup of the coral-associated microbiome remains little understood. Therefore, comprehending the makeup and dispersion of the endogenous microbiome associated with coral is crucial for understanding how the coral microbiome coexists and interacts, as well as its contribution to temperature tolerance and resistance against possible pathogens. Here, we investigate metagenomic sequencing targeting 16S rRNA using DNAs from the sediment samples to identify the coral microbiome and to understand the dynamics of microbial taxa and genes in the surface mucous layer (SML) microbiome of the coral communities in three distinct areas close to and far from coral communities in the Red Sea. These findings highlight the genomic array of the microbiome in three areas around and beneath the coral communities and revealed distinct bacterial communities in each group, where Pseudoalteromonas agarivorans (30%), Vibrio owensii (11%), and Pseudoalteromonas sp. Xi13 (10%) were the most predominant species in samples closer to coral (a coral-associated microbiome), with the domination of Pseudoalteromonas_agarivorans and Vibrio_owensii in Alshreah samples distant from coral, while Pseudoalteromonas_sp._Xi13 was more abundant in closer samples. Moreover, Proteobacteria such as Pseudoalteromonas, Pseudomonas and Cyanobacteria were the most prevalent phyla of the coral microbiome. Further, Saweehal showed the highest diversity far from corals (52.8%) and in Alshreah (7.35%) compared to Marwan (1.75%). The microbial community was less diversified in the samples from Alshreah Far (5.99%) and Marwan Far (1.75%), which had comparatively lower values for all indices. Also, Vibrio species were the most prevalent microorganisms in the coral mucus, and the prevalence of these bacteria is significantly higher than those found in the surrounding saltwater. These findings reveal that there is a notable difference in microbial diversity across the various settings and locales, revealing that geographic variables and coral closeness affect the diversity of microbial communities. There were significant differences in microbial community composition regarding the proximity to coral. In addition, there were strong positive correlations between genera Pseudoalteromonas and Vibrio in close-to-coral environments, suggesting that these bacteria may play a synergistic role in Immunizing coral, raising its tolerance towards environmental stress and overall coral health.}, }
@article {pmid40138093, year = {2025}, author = {Demeulenaere, &#xc9;}, title = {In search of the microbial path to Terroir: a place-based history of the ecologization of French cheese microbiology, 1990-2000s.}, journal = {History and philosophy of the life sciences}, volume = {47}, number = {2}, pages = {22}, pmid = {40138093}, issn = {1742-6316}, support = {EXORIGINS//Emergence(s) Ville de Paris/ ; }, mesh = {*Cheese/microbiology/history ; France ; History, 20th Century ; *Food Microbiology/history ; Animals ; Milk/microbiology ; Laboratories/history ; }, abstract = {At the crossroads between food studies and science and technology studies, this paper analyzes the role of laboratories located within traditional cheese territories in the ecologization of cheese microbiology in France at the turn of the twentieth century. The paper argues that their connectedness with Protected Designation of Origin raw-milk cheese organizations advocating for a strong understanding of terroir played a key role in challenging the modern strain-by-strain approach and fostering a shift towards a new research object: microbial communities in their ecologies. Modernization and standardization in cheese production from the 1950s onwards laid indeed on the improvement of hygiene to get "cleaner" milks, and on lab research on microbial strains to develop selected starter cultures. This led to a dramatic loss of microbial abundance within raw milks, which progressively provoked milk processing issues, as well as a loss of cheese typicality, an issue for place-based cheeses. To face it, the modernist approach promoted more laboratorial research on microbial strains to develop new starter cultures and the diversification of microbial collections, within an ex-situ conservation framework. In contrast, microbiologists conducting applied research for raw-milk terroir cheeses investigated environmental microbial reservoirs, microbial fluxes, as well as farming practices that favor "natural seeding" and enrich milk native microflora. A new approach emerged, namely "practice-driven microbial ecology" (écologie microbienne dirigée), which enacts the dynamic and ubiquitous properties of microbial life. The paper offers a situated account on the "microbial (ecology) turn" described by other authors, highlighting the ecological approach developed in the 1990s-2000s by French microbiologists in search of "the microbial path to terroir".}, }
@article {pmid40137691, year = {2025}, author = {Maitre, A and Mateos-Hernandez, L and Kratou, M and Egri, N and Maye, J and Juan, M and Hodžić, A and Obregón, D and Abuin-Denis, L and Piloto-Sardinas, E and Fogaça, AC and Cabezas-Cruz, A}, title = {Effects of Live and Peptide-Based Antimicrobiota Vaccines on Ixodes ricinus Fitness, Microbiota, and Acquisition of Tick-Borne Pathogens.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, pmid = {40137691}, issn = {2076-0817}, mesh = {Animals ; *Ixodes/microbiology/immunology ; *Microbiota/immunology ; Mice ; *Bacterial Vaccines/immunology/administration &amp; dosage ; Vaccines, Subunit/immunology/administration &amp; dosage ; Staphylococcus epidermidis/immunology ; *Lyme Disease/prevention &amp; control/immunology/microbiology ; Borrelia burgdorferi Group/immunology ; Vaccines, Attenuated/immunology/administration &amp; dosage ; Female ; *Tick-Borne Diseases/prevention &amp; control/microbiology/immunology ; }, abstract = {This study explored the effects of antimicrobiota vaccines on the acquisition of Borrelia and Rickettsia, and on the microbiota composition of Ixodes ricinus ticks. Using a murine model, we investigated the immunological responses to live Staphylococcus epidermidis and multi-antigenic peptide (MAP) vaccines. Immunized mice were infected with either Borrelia afzelii or Rickettsia helvetica, and subsequently infested with pathogen-free I. ricinus nymphs. We monitored the tick feeding behavior, survival rates, and infection levels. Additionally, we employed comprehensive microbiota analyses, including the alpha and beta diversity assessments and microbial co-occurrence network construction. Our results indicate that both live S. epidermidis and MAP vaccines elicited significant antibody responses in mice, with notable bactericidal effects against S. epidermidis. The vaccination altered the feeding patterns and fitness of the ticks, with the Live vaccine group showing a higher weight and faster feeding time. Microbiota analysis revealed significant shifts in the beta diversity between vaccine groups, with distinct microbial networks and taxa abundances observed. Notably, the MAP vaccine group exhibited a more robust and complex network structure, while the Live vaccine group demonstrated resilience to microbial perturbations. However, the effects of antimicrobiota vaccination on Borrelia acquisition appeared taxon-dependent, as inferred from our results and previous findings on microbiota-driven pathogen refractoriness. Staphylococcus-based vaccines altered the microbiota composition but had no effect on B. afzelii infection, and yielded inconclusive results for R. helvetica. In contrast, previous studies suggest that E. coli-based microbiota modulation can induce a pathogen-refractory state, highlighting the importance of both bacterial species and peptide selection in shaping microbiota-driven pathogen susceptibility. However, a direct comparison under identical experimental conditions across multiple taxa is required to confirm this taxon-specific effect. These findings suggest that antimicrobiota vaccination influences tick fitness and microbiota assembly, but its effects on pathogen transmission depend on the bacterial taxon targeted and the selected peptide epitopes. This research provides insights into the need for strategic bacterial taxon selection to enhance vaccine efficacy in controlling tick-borne diseases.}, }
@article {pmid40134242, year = {2025}, author = {Trombley, J and Celenza, JL and Frey, SD and Anthony, MA}, title = {Arbuscular Mycorrhizal Fungi Boost Development of an Invasive Brassicaceae.}, journal = {Plant, cell &amp; environment}, volume = {48}, number = {7}, pages = {4928-4937}, pmid = {40134242}, issn = {1365-3040}, support = {//This study was supported by the Dick George Invasives Fund awarded to S.D.F. and M.A.A. M.A.A. was supported by a Vienna Science and Technology Fund (WWTF) Vienna Research Groups for Young Investigators grant awarded to MAA (VRG22-007)./ ; }, mesh = {*Mycorrhizae/physiology ; *Introduced Species ; *Brassicaceae/growth &amp; development/microbiology ; Symbiosis ; Plant Roots/microbiology/growth &amp; development ; Glucosinolates/metabolism ; Nitrogen/metabolism ; }, abstract = {Invasive plant growth is affected by interactions with arbuscular mycorrhizal fungi (AMF). AMF are mutualists of most land plants but suppress the growth of many plants within the Brassicaceae, a large plant family including many invasive species. Alliaria petiolata (garlic mustard) is a nonnative, nonmycorrhizal Brassicaceae distributed throughout North America in forest understories where native species rely on AMF. If AMF suppress growth of garlic mustard, it may be possible to inoculate AMF to manage invasions. Here, we show that in contrast to expectation, garlic mustard growth nearly doubled in response to AMF inoculation under both laboratory and field conditions. This effect was negatively linked to investments in glucosinolates, a class of defensive compounds. In contrast to typical symbiosis, AMF did not produce arbuscules where nutrient exchange occurs in roots, but AMF inoculation increased plant and soil nitrogen availability. Our findings reveal an adjacent pathway by which AMF promote invasive plant growth without classic symbiotic exchanges. Prior assumptions that garlic mustard suppresses AMF are inadequate to explain invasion success since it benefits from interactions with AMF. This study is the first to demonstrate extensive growth promotion following AMF inoculation in mustard plants, with important implications for invasion biology and agriculture.}, }
@article {pmid40131450, year = {2025}, author = {Sun, L and Guan, W and Tai, X and Qi, W and Zhang, Y and Ma, Y and Sun, X and Lu, Y and Lin, D}, title = {Research Progress on Microbial Nitrogen Conservation Technology and Mechanism of Microorganisms in Aerobic Composting.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {19}, pmid = {40131450}, issn = {1432-184X}, support = {32160756//National Natural Science Foundation of China/ ; GAUfx-04J03//Fuxi Foundation of Gansu Agricultural University/ ; 23CXNN0007//Gansu Province Science and Technology Plan Project Technology Innovation Guidance Program - LuGan Science and Technology Collaboration topic/ ; 2023-3-66//Science and Technology Plan Project of Lanzhou city/ ; GNKJ-2024-46//Research and Application of Supporting Technologies for Gansu Pig Industry/ ; GAU-XKTD-2022-24//The Discipline Team Project of Gansu Agricultural University/ ; }, mesh = {*Composting/methods ; *Nitrogen/metabolism ; *Soil Microbiology ; Aerobiosis ; *Bacteria/metabolism/genetics ; Manure/microbiology ; Soil/chemistry ; Animals ; }, abstract = {With economic development and improvements in living standards, the demand for livestock products has steadily increased, resulting in the generation of large amounts of livestock manure, which seriously pollutes the ecological environment and poses a threat to human health. High-temperature aerobic composting is an effective method for treating livestock manure; however, traditional composting processes often lead to considerable nitrogen loss, reduced efficiency of soil conditioners, and increased emissions of harmful gases. The incorporation of physical, chemical, and biological additives can effectively retain nitrogen within the compost. Among these, microbial agents are particularly noteworthy as they precisely regulate the microbial community structure associated with nitrogen transformation during aerobic composting, altering the abundance of functional genes and enzyme activities involved in nitrogen transformation. This approach significantly reduces nitrogen loss and harmful gas emissions. This paper reviews the application effects of microbial agents on nitrogen retention during aerobic composting and explores the underlying regulatory mechanisms, aiming to provide theoretical guidance and new research directions for the application of microbial agents in enhancing nitrogen retention during aerobic composting.}, }
@article {pmid40129674, year = {2025}, author = {Hussain, N and Ibrahim Al Haddad, AH and Abbass, S and Alfahl, Z}, title = {The potential impact of habitual sleep quality on glycaemic control and inflammation: A study on geriatric patients recently diagnosed with type 2 diabetes mellitus (T2DM).}, journal = {Sleep medicine: X}, volume = {9}, number = {}, pages = {100139}, pmid = {40129674}, issn = {2590-1427}, abstract = {Sleep quality and its relationship with glycaemic control is of particular interest in the context of geriatric diabetes. We aimed to investigate the potential impact of habitual sleep quality on glycaemic control status among geriatric patients recently diagnosed with type 2 diabetes mellitus (T2DM). A total of 193 geriatric patients recently diagnosed with T2DM in a tertiary-care hospital were selected. A developed questionnaire was used to assess various aspects of sleep quality. Glycaemic control was evaluated through fasting blood glucose levels, HbA1c measurements and number of admissions to the hospital for hypoglycaemic or hyperglycaemic episodes. Patients were divided into Poor Sleep Quality (PSQ, n = 132) and Adequate Sleep Quality (ASQ, n = 61) groups. The PSQ group exhibited significantly worse sleep outcomes, including longer sleep latency (35 ± 9.2 min vs. 15 ± 6.4 min), shorter sleep duration (5 h 42 min vs. 7 h 18 min) and greater use of sleep medications (72 % vs. 22 %). Glycaemic control, measured by HbA1c, was worse in the PSQ group (8.7 ± 1.9 vs. 7.2 ± 1.2; p < 0.01), which also had more frequent severe hypoglycaemic (35 ± 1.4 vs. 8 ± 2.1; p = 0.02) and ketoacidotic episodes (72 ± 1.0 vs. 5 ± 1.1; p = 0.01). These findings suggest an association between poor sleep quality and poorer glycaemic control, with more frequent diabetes-related complications, highlighting the need for further research to explore potential causal relationships and targeted interventions in this population.}, }
@article {pmid40127879, year = {2025}, author = {Mirsalami, SM and Mirsalami, M}, title = {Assessing microbial ecology and antibiotic resistance genes in river sediments.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {130}, number = {}, pages = {105738}, doi = {10.1016/j.meegid.2025.105738}, pmid = {40127879}, issn = {1567-7257}, mesh = {*Geologic Sediments/microbiology ; *Rivers/microbiology ; Phylogeny ; *Bacteria/genetics/classification/drug effects ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Anthropogenic activities greatly affect the Karon River leading to deterioration of water quality. This investigation utilizes environmental genomic techniques to delineate microbial populations, examine functional genomics, and evaluate the occurrence of virulence determinants and antibiotic resistance genes (ARGs) in fluvial sediment. Taxonomic assessment identified that Firmicutes were the predominant phyla, with Bacillus being the most abundant genus across samples. Functional analysis revealed the metabolic capabilities of sediment-associated bacteria, linking them to biogeochemical processes and potential health impacts. The S2 samples exhibited the highest virulence factor genes, while the S3 samples had the most ARGs (30), highlighting concerns about pathogenicity. Analyzing ARGs provides critical insights into environmental data collected, such as water quality parameters (e.g., nutrient concentrations, pH) or pollution levels, prevalence, and distribution of these resistance factors within the sediment samples, helping to identify potential hotspots of antibiotic resistance in the Karon River ecosystem. The study identified similar operational taxonomic units (OTUs) across sampling sites at the phylogenetic level, indicating a consistent presence of certain microbial taxa. However, the lack of variation in functional classification suggests that while these taxa may be present, they are not exhibiting significant differences in metabolic capabilities or functional roles. These findings emphasize the significance of metagenomic methods in understanding microbial ecology and antibiotic resistance in aquatic environments, suggesting a need for further research into the restoration of microbial functions related to ARGs and virulence factors.}, }
@article {pmid40121181, year = {2025}, author = {Eaton, WD and McGee, KM and Glahn, A and Lemenze, A and Soteropoulos, P}, title = {Use of a logging road in a Costa Rican forest changes the composition and stability of soil microbial decomposer communities, and the conversion of organic carbon into biomass.}, journal = {Journal of applied microbiology}, volume = {136}, number = {4}, pages = {}, doi = {10.1093/jambio/lxaf075}, pmid = {40121181}, issn = {1365-2672}, support = {//Pace University Dyson College Office of the Dean/ ; }, mesh = {*Soil Microbiology ; Costa Rica ; *Forests ; Biomass ; *Carbon/metabolism/analysis ; *Fungi/metabolism/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Actinobacteria/metabolism/genetics/isolation &amp; purification ; Nitrogen/analysis/metabolism ; Acidobacteria/metabolism/genetics/isolation &amp; purification ; *Forestry ; Trees ; }, abstract = {AIMS: The effects of a tropical forest logging road on soil C and N, and the compositions of Actinobacteria, Acidobacteria, and wood rot/lignin-degrading fungal (WRT/LD) decomposer communities were evaluated.<br><br>METHODS AND RESULTS: Soils from a healthy Costa Rican old growth forest before Hurricane Otto and from an adjacent, recently formed logging road built after Hurricane Otto were collected over 4 years and assessed for C and N metrics, and characteristics of the three decomposer communities determined by Illumina amplicon sequencing methods. The Logging Road negatively impacted the soil total organic C, respiration, biomass C, qCO2, and total N, while the Actinobacterial and Acidobacterial communities changed from stable compositions of copiotrophic taxa in the rich forest soil to stable compositions of oligotrophic taxa in the poor logging road soil, and the WRT/LD community changed from stable compositions of copiotrophic taxa in the forest soils to an unstable community of oligotrophic taxa with almost no overlap in genera between logging road soils.<br><br>CONCLUSIONS: The logging road negatively influenced 3 decomposer communities and associated C and N metrics, with the two bacterial communities taxonomically stabilizing, but the fungal community taxonomically diverging into an unstable composition over time. Monitoring efforts are on-going to provide local forest land managers with potential indicators of soil ecosystem damage and recovery.}, }
@article {pmid40120670, year = {2025}, author = {San-Blas, E and Cornejo, MJ and Guerra, M and Olivares, M and Faundez, S and Bastidas, B and Morales-Montero, P and Pizarro, L and Aponte, H and Castaneda-Alvarez, C and Lankin, G}, title = {Where are my nematodes? labelling and visualising entomopathogenic nematodes in vivo using carbon quantum dots.}, journal = {Journal of invertebrate pathology}, volume = {211}, number = {}, pages = {108317}, doi = {10.1016/j.jip.2025.108317}, pmid = {40120670}, issn = {1096-0805}, mesh = {Animals ; *Quantum Dots ; *Nematoda ; Carbon ; *Staining and Labeling/methods ; }, abstract = {Identifying single or groups of animals has significantly advanced our understanding of animal biology and ecology. However, labelling is extremely difficult in small animals, like soil invertebrates. Due to the complexity of current methods, the dynamics and interactions of these populations are often studied indirectly. Labelling nematodes or microarthropods such as collembolans or soil acari has been challenging due to the high cost, potential toxicity, genetic modification requirements, cellular processes interference, and photobleaching. In this scenario, no methods can be applied to large numbers of microorganisms at once due to their mentioned practical and biological limitations and cost. In this work we show that quantum carbon dots (Cdots) are effective for labelling infective juveniles (IJs) of entomopathogenic nematodes (EPNs). In in vitro assays the IJs gradually acquired fluorescence, as Cdots accumulated in the lysosome-related organelles from their intestine cells, peaking at day 14, and with no lethal or sub-lethal effects on IJs. Fluorescence was clearly distinguishable from the natural auto-fluorescence of non-labelled IJs and persisted for months in IJs transferred to water. We and non-experts easily differentiated between similar species of EPNs and between two strains of S. feltiae placed in the same matrix (soil or water). We demonstrated for the first time the feasibility of labelling large numbers of IJs (hundreds of thousands/millions) with Cdots at minimal cost without any adverse effects for over a year. Our findings could be the starting point for detailed and large-scale field investigations on nematodes and other small organisms, allowing deeper understanding of their roles in soil ecosystems. This method provides a cost-effective and reliable tool for advancing research in the ecology of soil invertebrates, such as the interactions occurring in communities or between specific organisms, movement and dispersal, population dynamics or ecosystem services in a cryptic environment difficult to study.}, }
@article {pmid40119062, year = {2025}, author = {Acharya, P and Yegon, MJ and Haferkemper, L and Misteli, B and Griebler, C and Vitecek, S and Attermeyer, K}, title = {Leaf Conditioning and Shredder Activity Shape Microbial Dynamics on Fine Particulate Organic Matter Produced During Decomposition of Different Leaf Litter in Streams.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {18}, pmid = {40119062}, issn = {1432-184X}, mesh = {*Plant Leaves/metabolism/chemistry/microbiology ; Acer/metabolism/chemistry ; Animals ; *Rivers/microbiology/chemistry ; Fatty Acids/analysis ; Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Fagus/metabolism ; *Microbiota ; *Particulate Matter/metabolism ; Larva/microbiology ; Alnus/metabolism ; Feces/microbiology/chemistry ; Ecosystem ; Carbon/analysis ; }, abstract = {Leaf litter decomposition (LLD) is a key ecosystem function where invertebrate shredders produce large amounts of fine particulate organic matter (FPOM) that serves as a substrate for microbial assemblages. Here, we explore the shredder-produced FPOM composition and activity of FPOM-associated microbial communities in response to different leaf species and their conditioning. In a laboratory experiment, we fed leaves of different elemental compositions (alder, beech and maple), conditioned under oxic or anoxic conditions, to caddisfly larvae (Sericostoma sp.). We hypothesized differences in FPOM elemental and fatty acid composition and FPOM-associated microbial activity among the leaf species, conditioning, and two types of shredder-produced FPOM, i.e. shredded leaves and faecal pellets. Our results suggest that leaf conditioning and shredder activity play pivotal roles in shaping FPOM composition and FPOM-associated microbial activity. We observed lower C/N ratios with high-C/N litter (beech and maple leaves) after conditioning and no change in the elemental composition of the faecal pellets compared to the leaves. However, we observed differences in microbial fatty acid proportions and composition on leaves and faecal pellets with significantly higher fractions of bacterial fatty acids on faecal pellets than on leaves. We also noted a significant impact of leaf conditioning on the microbial activity of shredded leaves and faecal pellets, with a higher microbial growth efficiency observed on faecal pellets compared to ingested leaves. These findings highlight the crucial influence of leaf species and conditioning on the activity of shredder-produced FPOM, emphasizing the complex interplay between leaf properties and fate and microbial processes in streams.}, }
@article {pmid40118512, year = {2025}, author = {Gomes, IB}, title = {The overlooked interaction of emerging contaminants and microbial communities: a threat to ecosystems and public health.}, journal = {Journal of applied microbiology}, volume = {136}, number = {4}, pages = {}, doi = {10.1093/jambio/lxaf064}, pmid = {40118512}, issn = {1365-2672}, support = {//FCT/ ; UIDB/00511/2020//MCTES/ ; }, mesh = {*Public Health ; Humans ; *Ecosystem ; *Microbiota ; Animals ; *Microbial Interactions ; One Health ; *Environmental Pollutants ; Bacteria ; Biodegradation, Environmental ; }, abstract = {CONTEXT AND AIMS: Emerging contaminants (ECs) and microbial communities should not be viewed in isolation, but through the One Health perspective. Both ECs and microorganisms lie at the core of this interconnected framework, as they directly influence the health of humans, animals, and the environment.The interactions between ECs and microbial communities can have profound implications for public health, affecting all three domains. However, these ECs-microorganism interactions remain underexplored, potentially leaving significant public health and ecological risks unrecognized. Therefore, this article seeks to alert the scientific community to the overlooked interactions between ECs and microbial communities, emphasizing the pivotal role these interactions may play in the management of 'One Health.'<br><br>RESULTS: The most extensively studied interaction between ECs and microbial communities is biodegradation. However, other more complex and concerning interactions demand attention, such as the impact of ECs on microbial ecology (disruptions in ecosystem balance affecting nutrient and energy cycles) and the rise and spread of antimicrobial resistance (a growing global health crisis). Although these ECs-microbial interactions had not been extensively studied, there are scientific evidence that ECs impact on microbial communities may be concerning for public health and ecosystem balance.<br><br>CONCLUSIONS: So, this perspective summarizes the impact of ECs through a One Health lens and underscores the urgent need to understand their influence on microbial communities, while highlighting the key challenges researchers must overcome. Tackling these challenges is vital to mitigate potential long-term consequences for both ecosystems and public health.}, }
@article {pmid40118002, year = {2025}, author = {Wan, W and Grossart, HP and Wu, QL and Xiong, X and Yuan, W and Zhang, W and Zhang, Q and Liu, W and Yang, Y}, title = {Global meta-analysis deciphering ecological restoration performance of dredging: Divergent variabilities of pollutants and hydrobiontes.}, journal = {Water research}, volume = {280}, number = {}, pages = {123506}, doi = {10.1016/j.watres.2025.123506}, pmid = {40118002}, issn = {1879-2448}, mesh = {Ecosystem ; *Environmental Restoration and Remediation ; Water Pollutants, Chemical ; Geologic Sediments ; }, abstract = {Global "Sustainable Development Goals" propose ambitious targets to protect water resource and provide clean water, whereas comprehensive understanding of restoration performance and ecological mechanisms are lacking for dredging adopted for purifying polluted waterbodies and maintaining navigation channels. Here, we conducted a global meta-analysis to estimate ecological restoration consequence of dredging as pollution mitigation and navigation channel maintenance measures using a dataset compiled from 191 articles covering 696 studies and 84 environmental and ecological parameters (e.g., pollutants and hydrobiontes). We confirm that dredging shows negative influences on 77.50% pollutants in the BA model (before dredging vs. after dredging) and 84.21% pollutants in the CI model (control vs. impact) as well as on sediment nutrient fluxes. Additionally, 57.14% attributes (i.e., richness, diversity, biomass, and density) of hydrobiontes in the BA model and 89.47% attributes of hydrobiontes in the CI model responded negatively to dredging. As a result, 76.32% of the pollutants and 61.11% of the hydrobiont attributes responded uniformly to dredging in the BA and CI models. Our findings emphasize that dredging generally decreases pollutants and mitigates algal blooms, controlling phosphorus is easier than controlling nitrogen by dredging, and attributes (i.e., richness, diversity, and biomass) of hydrobiontes (i.e., zooplankton, phytoplankton, and zoobenthos) are density-dependent in dredging-disturbed environments. Our findings broaden our knowledge on ecological restoration performance of dredging as a mitigation measure in global aquatic ecosystems, and these findings might be helpful to use and optimize dredging to efficiently and sustainably purify polluted aquatic ecosystems.}, }
@article {pmid40116066, year = {2025}, author = {Cusenza, BS and Scelfo, G and Licata, G and Capri, FC and Vicari, F and Alduina, R and Villanova, V}, title = {First Insights Into the Biological and Physical-Chemical Diversity of Various Salt Ponds of Trapani, Sicily.}, journal = {Environmental microbiology reports}, volume = {17}, number = {2}, pages = {e70075}, pmid = {40116066}, issn = {1758-2229}, support = {MSCA_0000011//Next Generation EU/ ; }, mesh = {*Ponds/microbiology/chemistry ; Sicily ; *Archaea/genetics/classification/isolation &amp; purification ; *Bacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Salinity ; Biodiversity ; *Microbiota ; Phylogeny ; DNA, Archaeal/genetics ; Sodium Chloride/analysis ; DNA, Bacterial/genetics ; Ecosystem ; }, abstract = {The salt ponds of Trapani, Sicily, represent an extreme and under-explored ecosystem characterised by varying salinity gradients and environmental conditions. These ponds, integral to traditional salt extraction, include cold, driving, hot and crystallizer ponds, each hosting diverse microbial communities. This study aimed to explore the biological and physical-chemical diversity of 11 ponds during the salt production season in Trapani. We conducted comprehensive physical-chemical characterizations, including measurements of pH, conductivity, viscosity, density, organic carbon and ion concentration. Microbial DNA was extracted from salt pond waters and subjected to metabarcoding of 16S rRNA genes to determine the diversity of archaea and bacteria. High-throughput sequencing revealed significant variations in microbial communities across different pond types and seasons. Cold ponds showed a higher diversity of moderately halophilic organisms, while crystallizer and feeding ponds were dominated by extreme halophiles, particularly archaeal genus Halorubrum and Haloquadratum and bacterial genus Salinibacter. Statistical analyses indicated that environmental parameters, especially salinity and temperature, significantly influenced microbial community composition. Our findings enhance the understanding of microbial ecology in saline environments and highlight the potential of halophilic microorganisms. This study provides a foundation for future research into the functional roles of these microorganisms and their industrial applications.}, }
@article {pmid40113629, year = {2025}, author = {Moldovan, OT and Levei, E and Ferreira, RL and Silva, MS and Mirea, IC}, title = {Exploring the Bacteriome Diversity and Use as a Proxy for Climate Change and Human Impacts on Groundwater in Temperate and Tropical Countries.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {17}, pmid = {40113629}, issn = {1432-184X}, support = {PN-III-P4-ID-PCCF-2016-0016 (DARKFOOD)//Ministry of Research and Innovation, CNCS - UEFISCDI/ ; GA N&#xb0;101052342//Biodiversa+, the European Biodiversity Partnership/ ; CNPq n. 302925/2022-8//National Council for Scientific and Technological Development/ ; }, mesh = {*Groundwater/microbiology ; *Climate Change ; *Bacteria/classification/genetics/isolation &amp; purification ; Brazil ; *Caves/microbiology ; Romania ; Humans ; Tropical Climate ; Biodiversity ; Seasons ; *Microbiota ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Environmental Monitoring ; }, abstract = {This research investigates bacterial communities in various cave pool water and substrates from Brazil and Romania for their use as indicators of environmental impacts on groundwater. Regional and seasonal differences were observed even if, at the phylum level, common bacteria for both countries were found. Distinct patterns emerged at the genus level due to the different climates (tropical vs. temperate) and ecosystems. Chemoautotrophic conditions define an utterly different groundwater bacteriome than oligotrophic conditions independent of the temperature. Bacteria as a proxy for climate change were explored using seasonal changes in Romanian caves; specific genera become dominant in summer months, such as Acinetobacter, Paeniglutamicibacter, Polaromonas, and Saccharimonadales, indicating processes that occur during the low-water season. Climate change, particularly dryness, is expected to exacerbate these variations, threatening the stability of groundwater ecosystems. The research also identified anthropic pollution indicators (Vogesella, Cutibacterium) and potential decontaminants (Bacillus) in Brazilian cave waters. Anthropic pollution indicators, like Pseudoarthrobacter. were also found in Romanian caves. Other key bacteria genera, such as Flavobacterium, Pseudomonas, and Acinetobacter, are chemolithotrophs or involved in the nitrogen cycle, which is critical in supplying nutrients for the cave food web. Marked differences between water and substrate microbiomes within the same pools suggested that substrates may play a crucial, underexplored role in groundwater ecosystem processes. Our study found unassigned taxa, 3 phyla, 2 families, and 832 genera (> 40%) in the studied pools. The results underscore the need to further explore groundwater microbiomes as potentially crucial yet fragile ecosystems in the face of climate change and human impacts.}, }
@article {pmid40112476, year = {2025}, author = {Xu, RZ and Cao, JS and Cheng, S and Luo, JY and Ni, BJ and Fang, F and Liu, W and Wang, P}, title = {Heterotrophic nitrification-aerobic denitrification strains: An overlooked microbial interaction nexus in the anaerobic-swing-anoxic-oxic (ASAO) plug-flow system.}, journal = {Journal of environmental management}, volume = {380}, number = {}, pages = {125030}, doi = {10.1016/j.jenvman.2025.125030}, pmid = {40112476}, issn = {1095-8630}, mesh = {*Denitrification ; *Nitrification ; Nitrogen/metabolism ; Anaerobiosis ; Aerobiosis ; Heterotrophic Processes ; Bioreactors/microbiology ; Bacteria/metabolism ; Oxygen ; Phosphorus/metabolism ; }, abstract = {This study aims to clarify the overlooked functions of heterotrophic nitrification-aerobic denitrification (HNAD) bacteria in a novel anaerobic-swing-anoxic-oxic (ASAO) continuous plug-flow system. The dissolved oxygen (DO) levels and aerated hydraulic retention time (HRT) varied in the swing zones, providing a more diverse redox environment. High nitrogen (85.0 %) and phosphorus (80.0 %) removal were achieved by enriched HNAD bacteria (e.g., Thauera and Malikia) and phosphate accumulating organisms (PAO, e.g., Rhodocyclus and Azonexus) under middle DO level (1.0-2.0 mg/L) and longer aerated HRT (5.0 h). More importantly, microbial network revealed that HNAD bacteria became a connection point for other functional microorganisms associated with pollutant metabolism, and promoted the cooperation and functional evolution of microbial communities. The microbial ecology analysis captured the high importance of homogeneous selection, diffusion restriction, and drift for microbial community assembly in the ASAO system. Among them, HNAD bacteria contributed to both deterministic and stochastic processes, whereas the community assembly of PAO was mainly affected by the deterministic processes. The upregulation of denitrification genes (i.e., napA, napB, nirS, norB and norC) further confirmed the nitrogen removal contribution of aerobic denitrification by HNAD bacteria. Through this study, a comprehensive analysis of microbial interactions in the ASAO system was achieved, providing valuable insights into the targeted regulation of functional microorganisms in wastewater biological treatment processes.}, }
@article {pmid40112457, year = {2025}, author = {Liu, J and Xu, G and Zhao, S and He, J}, title = {Microbiomes of coastal sediments and plastispheres shaped by microplastics and decabrominated diphenyl ether.}, journal = {Water research}, volume = {280}, number = {}, pages = {123417}, doi = {10.1016/j.watres.2025.123417}, pmid = {40112457}, issn = {1879-2448}, mesh = {*Geologic Sediments/microbiology ; *Microplastics ; *Microbiota/drug effects ; *Halogenated Diphenyl Ethers ; Water Pollutants, Chemical ; }, abstract = {Deciphering the impact of microplastic and persistent organic pollutants (POPs) co-contamination on coastal sediment is critical for developing effective remediation strategies for polluted sites yet remains underexplored. This study investigated the interactions between microplastics, decabrominated diphenyl ether (deca-BDE), and their co-contamination effects on the evolvement of coastal sediment and plastisphere microbiomes for over 2 years. Results showed that deca-BDE was naturally debrominated in sediments via diverse pathways, with microplastic polystyrene stimulating the debromination rate by up to 78.7 ± 10.0 %. The putative OHRB Dehalobacter and uncultured Dehalococcoidia populations were identified responsible for the complete debromination. Co-exposure to microplastics and deca-BDE induced significant shifts in community composition, diversity, and function in the sediment microbiomes, while plastisphere microbiomes exhibited distinct compositions and functional profiles, specializing in pathogenicity, pollutant degradation, and biogeochemical cycling. The type of plastics and the presence of deca-BDE influenced the plastisphere composition. Changes in sediment properties and debromination activity profoundly shaped microbial communities, with deterministic assembly dominating the plastisphere. Co-contamination increased the complexity, modularity, and stability of the plastisphere networks, creating unique niches for OHRB. These findings highlight the intricate interplay between microplastics, deca-BDE, and microbiomes, with significant implications for ecosystem health and remediation efforts.}, }
@article {pmid40109964, year = {2025}, author = {Figueiredo, JEF and Diniz, GFD and Marins, MS and Silva, FC and Ribeiro, VP and Lanza, FE and de Oliveira-Paiva, CA and Cruz-Magalhães, V}, title = {Bacillus velezensis CNPMS-22 as biocontrol agent of pathogenic fungi and plant growth promoter.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1522136}, pmid = {40109964}, issn = {1664-302X}, abstract = {INTRODUCTION: Bacillus velezensis is a ubiquitous bacterium with potent antifungal activity and a plant growth promoter. This study investigated the potential of B. velezensis CNPMS-22 as a biocontrol agent against phytopathogenic fungi under diverse experimental conditions and its potential as a plant growth promoter. Genome sequencing and analysis revealed putative genes involved in these traits.<br><br>METHODS: This research performed in vitro experiments to evaluate the CNPMS-22 antagonistic activity against 10 phytopathogenic fungi using dual culture in plate (DCP) and inverted sealed plate assay (ISP). Greenhouse and field tests evaluated the ability of CNPMS-22 to control Fusarium verticillioides in maize plants in vivo. The CNPMS-22 genome was sequenced using the Illumina HiSeq 4,000 platform, and genomic analysis also included manual procedures to identify genes of interest accurately.<br><br>RESULTS: CNPMS-22 showed antifungal activity in vitro against all fungi tested, with notable reductions in mycelial growth in both DCP and ISP experiments. In the ISP, volatile organic compounds (VOCs) produced by CNPMS-22 also altered the mycelium coloration of some fungi. Scanning electron microscopy revealed morphological alterations in the hyphae of F. verticillioides in contact with CNPMS-22, including twisted, wrinkled, and ruptured hyphae. Eight cluster candidates for synthesizing non-ribosomal lipopeptides and ribosomal genes for extracellular lytic enzymes, biofilm, VOCs, and other secondary metabolites with antifungal activity and plant growth promoters were identified by genomic analysis. The greenhouse and field experiments showed that seed treatment with CNPMS-22 reduced Fusarium symptoms in plants and increased maize productivity.<br><br>CONCLUSION: Our findings highlight the CNPMS-22's potential as bioinoculant for fungal disease control and plant growth with valuable implications for a sustainable crop productivity.}, }
@article {pmid40109356, year = {2025}, author = {Kantor, RS and Kennedy, LC and Miller, SE and Favere, J and Nelson, KL}, title = {Reverse Osmosis in an Advanced Water Treatment Train Produces a Simple, Consistent Microbial Community.}, journal = {ACS ES&amp;T engineering}, volume = {5}, number = {3}, pages = {772-781}, pmid = {40109356}, issn = {2690-0645}, abstract = {Potable water reuse has become a key component of water sustainability planning in arid regions. Many advanced water purification facilities use reverse osmosis (RO) as part of treatment, including as a barrier for microorganisms; however, regrowth after RO treatment has been observed. Questions remain about the identity, source, and survival mechanisms of microorganisms in RO permeate, but the extremely low biomass of this water is a limitation for common microbiological methods. Here, we performed high-throughput sequencing on samples collected throughout a potable reuse train, including samples collected by filtering large volumes of RO permeate and biomass collected from RO membranes during an autopsy. We observed a stable, consistent microbial community across three months and in two parallel RO trains. RO permeate samples contained Burkholderiaceae at high relative abundance, including one Aquabacterium sp. that accounted for 29% of the community, on average. Like most other RO permeate microorganisms, this sequence was not seen in upstream samples and we suggest that biofilm growing on unit process infrastructure, rather than active treatment breakthrough, was the primary source. A metagenome-assembled genome corresponding to Aquabacterium sp. from RO permeate was found to lack most sugar-utilization pathways and to be able to consume low molecular weight organic molecules, potentially those that pass through RO.}, }
@article {pmid40107140, year = {2025}, author = {Quattrocelli, P and Piccirillo, C and Kuramae, EE and Pullar, RC and Ercoli, L and Pellegrino, E}, title = {Synergistic interaction of phosphate nanoparticles from fish by-products and phosphate-solubilizing bacterial consortium on maize growth and phosphorus cycling.}, journal = {The Science of the total environment}, volume = {973}, number = {}, pages = {179082}, doi = {10.1016/j.scitotenv.2025.179082}, pmid = {40107140}, issn = {1879-1026}, mesh = {*Zea mays/growth &amp; development ; *Phosphorus/metabolism ; *Phosphates/metabolism ; *Nanoparticles/chemistry ; *Fish Products ; Bacteria/metabolism ; Microbial Consortia ; Animals ; }, abstract = {Phosphate nanomaterials, such as hydroxyapatite/β-tricalcium nanoparticles (nHAs) derived from food industry by-products, offer a sustainable alternative to enhance P-use efficiency in agriculture. However, their limited solubility remains a challenge. This study first investigated the mechanisms of P solubilization of salmon and tuna bones (SnHAs and TnHAs) in fifteen strains of phosphate-solubilizing bacteria (PSB) by an in vitro system. Then, best-performing strains were assembled in a consortium and tested in vivo on maize. We hypothesized that combining nHAs and the PSB consortium inoculated as seed coating (SC) outperforms single treatments alone in promoting plant growth and P cycling, and ensures the establishment in plant-soil system without a bacterial reinforcement (BR) by an additional inoculum suspension. The synergistic effect of nHAs and PSB was proved, improving maize root (+22 %) and total plant biomass (+29 %), as well as P (+32 %) and K (66 %) uptake compared to single treatments. With nHAs and SC, P-use efficiency and recovery increased by 25 % and three-fold, respectively, compared to nHAs alone or with bacterial reinforcement. Consistently, root and substrate bacterial biomass were associated with nHAs plus SC, while nHAs alone or with PSB upregulated PHT1;1 and PHT1;2 transporter genes in maize. Finally, linking the in vitro and in vivo system, we demonstrated that propionic acid production and P-solubilization efficiency of PSB co-applied with nHAs are key drivers of maize growth and P uptake. Our findings indicated that co-applying nHAs and PSB through SC offers a sustainable strategy to improve maize P-use efficiency.}, }
@article {pmid40106821, year = {2025}, author = {Yang, CC and Washio, J and Lin, YC and Hsu, ML and Wang, DH and Tsai, FT and Lin, YM and Tu, HF and Chang, HC and Takahashi, N}, title = {Microbiome Signatures and Dysbiotic Patterns in Oral Cancer and Precancerous Lesions.}, journal = {Oral diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/odi.15317}, pmid = {40106821}, issn = {1601-0825}, support = {112-2314-B-A49-027//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-028-MY2//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-026-MY3//the National Science and Technology Council, Taiwan/ ; 112-2314-B-A49-058//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-087-MY3//the National Science and Technology Council, Taiwan/ ; 21H03151//the Japan Society for the Promotion of Science/ ; 20K10241//the Japan Society for the Promotion of Science/ ; 23K18349//the Japan Society for the Promotion of Science/ ; 23K21499//the Japan Society for the Promotion of Science/ ; //the National Yang Ming Chiao Tung University and Ministry of Education (MOE), Taiwan/ ; }, abstract = {BACKGROUND: The oral microbiome has been shown to be associated with the development of oral squamous cell carcinoma (OSCC). Research has primarily focused on elucidating the oncogenic mechanisms of specific pathogens by comparing the microbiomes of OSCC and normal tissues. However, the characteristics of the microbiome in the precancerous state remain less understood, as does the influence of metabolic and environmental factors on OSCC-associated microbiomes.<br><br>METHODS: In this study, we analyzed mucosa-associated microbiomes in normal, precancerous, and OSCC lesions from a cohort of 51 patients using 16S rRNA amplicon sequencing. We investigated compositional changes in the microbiome, including the specific abundances and co-occurrences of OSCC-associated bacteria.<br><br>RESULTS: Our findings indicate that the microbiome associated with precancerous lesions is indistinguishable from that of the normal mucosa, whereas the OSCC microbiome significantly differs from both normal and precancerous conditions. Specifically, the OSCC microbiome harbors less Streptococcus, coupled with an increase in amino-acid-degrading anaerobes such as Fusobacterium and Prevotella. The metabolic properties of individual microbes reported suggest that the overrepresentation of OSCC-specific bacteria is a result of metabolic adaptation to tumor microenvironments, although this possibility needs to be experimentally confirmed.<br><br>CONCLUSIONS: Our results demonstrate oral microbiome patterns across OSCC progression, offering insights into microbial ecological perspectives.}, }
@article {pmid40106330, year = {2025}, author = {Maguire, M and DeLappe, N and Clarke, C and Touhy, A and Carlino-MacDonald, U and Hutson, A and Cormican, M and Brennan, W and Devane, G and Morris, D and Coughlan, SC and Miliotis, G and Russo, TA and Burke, LP}, title = {Genomic and phylogenetic analysis of hypervirulent Klebsiella pneumoniae ST23 in Ireland.}, journal = {Microbial genomics}, volume = {11}, number = {3}, pages = {}, doi = {10.1099/mgen.0.001373}, pmid = {40106330}, issn = {2057-5858}, mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/classification/isolation &amp; purification/drug effects ; Animals ; *Klebsiella Infections/microbiology/epidemiology ; Humans ; Virulence/genetics ; Ireland/epidemiology ; Mice ; *Phylogeny ; beta-Lactamases/genetics ; Retrospective Studies ; Bacterial Proteins/genetics ; Microbial Sensitivity Tests ; Female ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Genomics ; Male ; Genotype ; Aged ; }, abstract = {Hypervirulent Klebsiella pneumoniae (hvKp) has emerged as a pathogen of global concern associated with invasive community-acquired infections. The combination of hypervirulence and carbapenem resistance can result in severe and difficult-to-treat infections. This retrospective study aimed to investigate the spread of hvKp sequence type 23 (ST23) in Ireland and the convergence of hypervirulent (hv) and antimicrobial resistance genotypes. Short-read sequences (PE300) for 90 K. pneumoniae ST23 isolates were generated by the Galway Reference Laboratory Services (GRLS). Isolates were from screening swabs (n=59), invasive infections (n=18), non-invasive sites (n=12) and the hospital environment (n=1). The virulence and resistance content were assessed genomically using Kleborate (v2.2.0), ABRicate (v1.0.1) and Platon (v1.6). The in vivo virulence of the isolates was assessed using a murine model. All isolates were genotypically hv with 88/90 isolates having a maximal Kleborate virulence score of 5 including carriage of key genes. Eighty-two per cent of isolates (74/90) carried a carbapenemase gene (bla OXA-48/bla OXA-181/bla NDM-1), and 42% carried resistance genes to 3 or more antimicrobial classes. Core genomic delineation revealed the isolates to be clonal with similar resistance and virulence profiles. Two distinct clusters of Irish isolates were detected consisting of 82/90 of the isolates. Isolates associated with carriage and infection demonstrated similar in vivo virulence. An established clone of hvKp ST23 is circulating within Ireland and causing both colonization and infection of patients. The lack of reliable screening methods for hvKp makes its detection and control in the healthcare setting challenging.}, }
@article {pmid40100630, year = {2025}, author = {Feng, W and Wan, X and Zhang, Y and Quensen, J and Williams, TA and Thompson, M and Streeter, M and Zhang, Y and Jiao, S and Wei, G and Zhu, Y and Gu, J and Tiedje, JM and Qian, X}, title = {Diversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {12}, pages = {e2424463122}, pmid = {40100630}, issn = {1091-6490}, mesh = {Phylogeny ; *Soil Microbiology ; *Bacteria/genetics/classification/metabolism ; *Adaptation, Physiological ; *Microbiota/genetics ; *Biological Evolution ; Genome, Bacterial ; Energy Metabolism ; Evolution, Molecular ; }, abstract = {The deep subsurface soil microbiome encompasses a vast amount of understudied phylogenetic diversity and metabolic novelty, and the metabolic capabilities and ecological roles of these communities remain largely unknown. We observed a widespread and relatively abundant bacterial phylum (CSP1-3) in deep soils and evaluated its phylogeny, ecology, metabolism, and evolutionary history. Genome analysis indicated that members of CSP1-3 were actively replicating in situ and were widely involved in the carbon, nitrogen, and sulfur cycles. We identified potential adaptive traits of CSP1-3 members for the oligotrophic deep soil environments, including a mixotrophic lifestyle, flexible energy metabolisms, and conservation pathways. The ancestor of CSP1-3 likely originated in an aquatic environment, subsequently colonizing topsoil and, later, deep soil environments, with major CSP1-3 clades adapted to each of these distinct niches. The transition into the terrestrial environment was associated with genome expansion, including the horizontal acquisition of a range of genes for carbohydrate and energy metabolism and, in one lineage, high-affinity terminal oxidases to support a microaerophilic lifestyle. Our results highlight the ecology and genome evolution of microbes in the deep Critical Zone.}, }
@article {pmid40099901, year = {2025}, author = {Lysenko, V and Machushynets, NV and van Dam, JL and Sterk, FAC and Speer, A and Ram, AFJ and Slingerland, CJ and Van Wezel, GP and Martin, NI}, title = {Total Synthesis, Structure Elucidation, and Bioactivity Evaluation of the Cyclic Lipopeptide Natural Product Paenilipoheptin A.}, journal = {Organic letters}, volume = {27}, number = {12}, pages = {2826-2831}, pmid = {40099901}, issn = {1523-7052}, mesh = {*Lipopeptides/chemistry/pharmacology/chemical synthesis ; Molecular Structure ; *Biological Products/chemistry/pharmacology/chemical synthesis ; *Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology/chemistry/chemical synthesis ; Peptides, Cyclic/chemistry/chemical synthesis/pharmacology ; Antifungal Agents/pharmacology/chemistry/chemical synthesis ; Gram-Positive Bacteria/drug effects ; Stereoisomerism ; }, abstract = {In this study, we further investigated the structure of the recently reported cyclic lipopeptide natural product paenilipoheptin A. Here, we disclose the first total synthesis of the compound, allowing for its complete structural assignment. The route developed employs automated SPPS, providing access to the compound in quantities suitable for antibacterial and antifungal testing. These studies unequivocally establish the stereochemical framework of paenilipoheptin A and further reveal that the compound possesses moderate activity against Gram-positive bacteria.}, }
@article {pmid40099871, year = {2025}, author = {Bittleston, L and Gilbert, J and Klassen, J and Mackelprang, R and Mandel, MJ and Newton, RJ and Paudel, A and Rodriguez-Verdugo, A and Shade, A and Wilhelm, RC and Zhang, Y}, title = {Embracing the systems complexity of microbial ecology and evolution: call for papers.}, journal = {mSystems}, volume = {10}, number = {3}, pages = {e0009125}, doi = {10.1128/msystems.00091-25}, pmid = {40099871}, issn = {2379-5077}, }
@article {pmid40099188, year = {2025}, author = {Silverio, MP and Schultz, J and Parise, MTD and Parise, D and Viana, MVC and Nogueira, W and Ramos, RTJ and Góes-Neto, A and Azevedo, VAC and Brenig, B and Bonelli, RR and Rosado, AS}, title = {Genomic and phenotypic insight into antimicrobial resistance of Pseudomonas fluorescens from King George Island, Antarctica.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1535420}, pmid = {40099188}, issn = {1664-302X}, abstract = {The genus Pseudomonas includes metabolically versatile microorganisms occupying diverse niches, from environmental habitats to plant pathogens, and has clinically significant strains. For this reason, Pseudomonas spp. might act as a reservoir of antimicrobial resistance genes, which have been detected even in isolated environments. The aim of this study was to report the antimicrobial susceptibility profile of 25 Pseudomonas fluorescens isolates from soil samples collected on King George Island (Antarctic Peninsula), and to select non-clonal isolates with unusual phenotypes for whole genome sequencing (WGS). Six classes of antimicrobials were assessed with disk diffusion and colistin with minimum inhibitory concentration (MIC) by broth microdilution. In order to confirm the discrepant phenotypes, MIC by agar dilution was performed for the beta-lactams aztreonam, ceftazidime, cefepime and the aminoglycoside neomycin. The genus Pseudomonas was confirmed by matrix-assisted laser desorption/ionization - time of flight (MALDI-TOF) and the clonal relationships were examined using repetitive extragenic palindromic polymerase chain reaction (BOX-PCR), from which 14 strains were selected for WGS. Antimicrobial susceptibility testing revealed that all strains were susceptible to neomycin and exhibited varying degrees of intermediate or full resistance to aztreonam and colistin. Additionally, 11 strains demonstrated intermediate resistance to ceftazidime, and six were resistant to cefepime. The genomic analysis identified various efflux pumps, predominantly from the ABC transporter and resistance-nodulation-division families. Resistance genes were detected against eight classes of antimicrobials, listed by prevalence: beta-lactams, tetracyclines, polymyxins, aminoglycosides, fosmidomycin, fosfomycin, quinolones, and chloramphenicol. Genes associated with heavy-metal resistance, prophages, and adaptations to extreme environments were also investigated. One notable isolate exhibited not only the highest number of pathogenicity and resistance islands, but also presented a carbapenemase-encoding gene (bla PFM-2) in its genome. Overall, one plasmid was identified in a distinct isolate, which did not exhibit antimicrobial resistance determinants. The genotypic and phenotypic findings are consistent, suggesting that efflux pumps play a critical role in antimicrobial extrusion. This study offers valuable insight into the evolution of antimicrobial resistance in P. fluorescens, particularly in extreme environments, such as Antarctica. By exploring the antimicrobial resistance mechanisms in P. fluorescens, the study sheds light on how isolated ecosystems drive the natural evolution of resistance genes.}, }
@article {pmid40098226, year = {2025}, author = {Frühe, L and Klein, SG and Angulo-Preckler, C and Martynova, A and Alamoudi, T and García, JVA and Arossa, S and Breavington, J and Frappi, S and Laiolo, E and Lim, KK and Parry, AJ and Re, E and Rosas, DER and Rodrigue, M and Steckbauer, A and Pieribone, VA and Qurban, MA and Duarte, CM}, title = {Particle-Associated Bacterioplankton Communities Across the Red Sea.}, journal = {Environmental microbiology}, volume = {27}, number = {3}, pages = {e70075}, pmid = {40098226}, issn = {1462-2920}, support = {//National Center of Wildlife/ ; //King Abdullah University of Science and Technology/ ; }, mesh = {Indian Ocean ; *Bacteria/classification/genetics/isolation &amp; purification ; *Seawater/microbiology ; *Plankton/classification/genetics/isolation &amp; purification ; Biodiversity ; Ecosystem ; Saudi Arabia ; Phylogeny ; DNA Barcoding, Taxonomic ; }, abstract = {Pelagic particle-associated bacterioplankton play crucial roles in marine ecosystems, influencing biogeochemical cycling and ecosystem functioning. However, their diversity, composition, and dynamics remain poorly understood, particularly in unique environments such as the Red Sea. In this study, we employed eDNA metabarcoding to comprehensively characterise bacterioplankton communities associated with pelagic particles in a three-dimensional assessment spanning depths from the surface to a depth of 2300 m along the full length of the eastern Red Sea within the exclusive economic zone of the Kingdom of Saudi Arabia. Our results reveal a diverse assemblage of taxa, with Pseudomonadota, Cyanobacteriota, and Planctomycetota being the dominant phyla. We identified pronounced spatial variability in community composition among five major Red Sea geographical regions, with a third of all amplicon sequence variants being unique to the Southern Red Sea in contrast to a relatively homogenous distribution along the water column depth gradient. Our findings contribute to a deeper understanding of microbial ecology in the Red Sea and provide valuable insights into the factors governing pelagic particle-associated bacterioplankton communities in this basin.}, }
@article {pmid40097839, year = {2025}, author = {Blanco, S and Viso, R and Borrego-Ramos, M and López-Flores, R and Mota-Echeandía, D and Tierra, M and Herrero, J and C Castañeda, }, title = {The Ecology of Benthic Diatom Assemblages in Saline Wetlands of the Ebro Basin, NE Spain.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {16}, pmid = {40097839}, issn = {1432-184X}, support = {TED2021-130303B-I00//MCIN/AEI/ ; }, mesh = {*Diatoms/classification/physiology ; *Wetlands ; Spain ; Biodiversity ; Ecosystem ; Salinity ; Electric Conductivity ; }, abstract = {Benthic diatoms play a crucial role in aquatic ecosystems as indicators of environmental conditions and contributors to primary productivity. This study explores the ecology of benthic diatom assemblages in saline wetlands in NE Spain, focusing on the relationships between community parameters, species distributions, and environmental factors, particularly conductivity. Samples were collected from several wetlands representing a range of conductivity and trophic state. A total of 25 diatom taxa were identified, with assemblages dominated by halophilous species. Non-metric multidimensional scaling analysis revealed electrical conductivity (EC) as a primary factor shaping diatom communities, with nutrient levels as a secondary influence. Species exhibited varying responses to the EC gradient, with some showing overlapping niches and others clearly separated. The study found strong correlations between species abundance, occupancy, and their contribution to dissimilarity between sampling sites. More abundant and widespread species were key drivers of community structure and differentiation. Additionally, a significant relationship was observed between taxa occurrence and niche breadth, measured as EC tolerance. Species with broader tolerances tended to have higher occupancy rates, supporting ecological theories about generalist strategies in variable environments. Contrary to some previous research, rare taxa (3-5% in relative abundance) had a negligible effect on assemblage segregation among habitats. The findings suggest that both environmental filtering based on EC tolerance and species' inherent characteristics play important roles in shaping diatom community composition across these saline wetlands. This study contributes to our understanding of diatom ecology in saline habitats and highlights the importance of considering both local abundance and environmental tolerance in ecological studies of these communities. The insights gained can inform more accurate ecological models and improve our understanding of species distribution and community dynamics in saline aquatic ecosystems.}, }
@article {pmid40097820, year = {2025}, author = {Blanchette, RA and Rajtar, NN and Lochridge, AG and Held, BW}, title = {Intercontinental movement of exotic fungi on decorative wood used in aquatic and terrestrial aquariums.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9142}, pmid = {40097820}, issn = {2045-2322}, support = {no number//Minnesota Invasive Terrestrial Plants and Pests Center, University of Minnesota/ ; }, mesh = {*Wood/microbiology ; *Fungi/isolation &amp; purification/genetics/classification ; Plant Diseases/microbiology ; United States ; Introduced Species ; }, abstract = {The intercontinental movement of fungi or fungus-like organisms brings nonnative species into areas where they may become invasive pathogens of trees and other plants. In the past century, many examples such as Dutch elm disease, sudden oak death, laurel wilt, and others have resulted in large economic losses and ecological disasters. Although various safeguards to prevent the transport of potential pathogens have been in effect, new avenues of introduction have occurred causing new disease outbreaks. This study examined fungi in wood shipped from Asia that is used for decorative purposes in aquatic and terrestrial aquariums. From 44 imported wood samples, 202 cultures representing 123 different fungal taxa were obtained and identified using molecular methods. These included 31 species not previously reported in the United States, 21 potential plant pathogens, 37 species of wood decay fungi and 24 taxa with a 97% sequence match or less to known isolates suggesting these are unknown species. The results demonstrate that wood used for decorative purposes in aquariums harbor large numbers of diverse fungi that remain viable during shipping and storage. These fungi are currently being imported into areas where they are not native, and they may pose serious biosecurity threats to the United States and other countries around the world.}, }
@article {pmid40097298, year = {2025}, author = {Morin, C and Alfahl, Z}, title = {A systematic review on the utility of wastewater surveillance for monitoring yellow fever virus and other arboviruses.}, journal = {Journal of applied microbiology}, volume = {136}, number = {3}, pages = {}, doi = {10.1093/jambio/lxaf066}, pmid = {40097298}, issn = {1365-2672}, support = {02-303952//Applied Microbiology International Summer Studentship/ ; }, mesh = {*Wastewater/virology ; *Yellow fever virus/isolation &amp; purification/genetics ; *Arboviruses/isolation &amp; purification/genetics ; Humans ; *Environmental Monitoring/methods ; Yellow Fever/virology ; }, abstract = {AIMS: This review aims to examine wastewater surveillance for the detection of yellow fever virus (YFV) and related arboviruses, focusing on concentration and extraction methodology, viral decay kinetics, and quantification techniques.<br><br>METHODS: A literature search was conducted across 5 databases: PubMed, Science Direct, Web of Science, Embase, and Google Scholar following the PRISMA guidelines. Studies included were original scientific articles published between April 2014 and April 2024. Human research studies investigating wastewater surveillance and YFV or other arboviruses/flaviviruses were assessed.<br><br>RESULTS: A total of 17 studies were included in this review. YFV was not detected in population-based wastewater samples; however, successful detection of similar viruses suggests potential for YFV monitoring with wastewater surveillance. YFV-spiked wastewater studies reveal similar concentration efficiency and decay rates between arboviruses. Effective concentration methods for YFV likely include centrifugation ultrafiltration and solid pellet extraction. YFV and arboviruses decay faster at higher temperatures, though YFV remains detectable for several days at these temperatures.<br><br>CONCLUSIONS: Wastewater surveillance presents a promising approach for monitoring YFV and other arboviruses. However, further research is needed to overcome existing limitations and enhance its effectiveness.}, }
@article {pmid40092580, year = {2025}, author = {Li, G and Wang, Z and Wu, C and Wang, D and Han, I and Lee, J and Kaeli, DR and Dy, JG and Weinberger, KQ and Gu, AZ}, title = {Towards high-accuracy bacterial taxonomy identification using phenotypic single-cell Raman spectroscopy data.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf015}, pmid = {40092580}, issn = {2730-6151}, abstract = {Single-cell Raman Spectroscopy (SCRS) emerges as a promising tool for single-cell phenotyping in environmental ecological studies, offering non-intrusive, high-resolution, and high-throughput capabilities. In this study, we obtained a large and the first comprehensive SCRS dataset that captured phenotypic variations with cell growth status for 36 microbial strains, and we compared and optimized analysis techniques and classifiers for SCRS-based taxonomy identification. First, we benchmarked five dimensionality reduction (DR) methods, 10 classifiers, and the impact of cell growth variances using a SCRS dataset with both taxonomy and cellular growth stage labels. Unsupervised DR methods and non-neural network classifiers are recommended for at a balance between accuracy and time efficiency, achieved up to 96.1% taxonomy classification accuracy. Second, accuracy variances caused by cellular growth variance (<2.9% difference) was found less than the influence from model selection (up to 41.4% difference). Remarkably, simultaneous high accuracy in growth stage classification (93.3%) and taxonomy classification (94%) were achievable using an innovative two-step classifier model. Third, this study is the first to successfully apply models trained on pure culture SCRS data to achieve taxonomic identification of microbes in environmental samples at an accuracy of 79%, and with validation via Raman-FISH (fluorescence in situ hybridization). This study paves the groundwork for standardizing SCRS-based biotechnologies in single-cell phenotyping and taxonomic classification beyond laboratory pure culture to real environmental microorganisms and promises advances in SCRS applications for elucidating organismal functions, ecological adaptability, and environmental interactions.}, }
@article {pmid40090302, year = {2025}, author = {Wang, J and Hu, Y and An, L and Wang, J and Wu, F and Gu, J and Wang, X and Tiedje, JM}, title = {An efficient strategy for BDD electrode drive electro-catalysis triggering active species on lincomycin and antibiotic resistance genes removal: Electron transfer based on calculation modeling.}, journal = {Journal of hazardous materials}, volume = {491}, number = {}, pages = {137915}, doi = {10.1016/j.jhazmat.2025.137915}, pmid = {40090302}, issn = {1873-3336}, mesh = {Electrodes ; *Anti-Bacterial Agents/chemistry ; Electron Transport ; *Water Pollutants, Chemical/chemistry ; Genes, Bacterial ; Electrochemical Techniques ; Catalysis ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; }, abstract = {Identifying the degradation pathway and the final by-products is essential, as their ecological risks are pertinent to the advancement of this technology and its potential application in practical environmental pollution treatment. Elucidating the reaction mechanisms of the degradation system represents the most effective strategy for controlling this process. This study thoroughly revealed that indirect oxidation predominates throughout the electrochemical system, while direct oxidation serves a significant auxiliary role under the synergistic influence. It elucidates the critical importance of electron transfer behavior at the electrode surface for pollutant degradation and unveil potential mechanisms underlying primary degradation reactions via integrating charge density differences and Bader atomic charge analysis. In situ electrochemical infrared spectroscopy (In situ EC-FTIR) and density functional calculation (DFT) were used to analyze the final by-product generation path. It further elucidated the correlation between antibiotic resistance gene (ARGs) and binding strength among base pairs. The oxidative stress process of antibiotic resistance bacteria (ARB) was explained in detail. To comprehensively assess the impact of electrochemical treatment on environmental microbial communities, combined horizontal gene transfer (HGT) experiments were conducted to confirm that electrolytically treated wastewater does not induce ecological stress effects on microorganisms. Finally, a small cyclic electrochemical system was employed to evaluate both ecological impacts and economic benefits associated with wastewater treatment, thereby providing a novel theoretical framework for this domain.}, }
@article {pmid40087979, year = {2025}, author = {Van den Wyngaert, S and Cerbin, S and Garzoli, L and Grossart, HP and Gsell, AS and Kraberg, A and Lepère, C and Neuhauser, S and Stupar, M and Tarallo, A and Cunliffe, M and Gachon, C and Gavrilović, A and Masigol, H and Rasconi, S and Selmeczy, GB and Schmeller, DS and Scholz, B and Timoneda, N and Trbojević, I and Wilk-Woźniak, E and Reñé, A}, title = {ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14099}, doi = {10.1111/1755-0998.14099}, pmid = {40087979}, issn = {1755-0998}, support = {PID2020-112978GB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; CA20125//European Cooperation in Science and Technology/ ; 451-03-66/2024-03/200178//Ministarstvo Prosvete, Nauke i Tehnolo&#x161;kog Razvoja/ ; 239548-051//RANNIS Icelandic Research Fund/ ; 340659//Research Council of Finland/ ; 346387//Research Council of Finland/ ; 101086521//European Commission/ ; IR0000005//European Commission/ ; NKFIH KKP 144068//National Laboratory for Water Science and Water Security/ ; RRF-2.3.1-21-2022-00008//National Laboratory for Water Science and Water Security/ ; Y0801-B16//Austrian Science Fund/ ; //AXA Research Fund/ ; ANR-21-BIRE-0002-01//Agence Nationale de la Recherche/ ; 101052342//Biodiversa+/ ; CIR-01_00028//Italian Ministry of University and Research/ ; GR1540/33-1//Deutsche Forschungsgemeinschaft/ ; GR1540/47-1//Deutsche Forschungsgemeinschaft/ ; GR1540/48-1//Deutsche Forschungsgemeinschaft/ ; GR1540/51-1//Deutsche Forschungsgemeinschaft/ ; CEX2019-000928-S//AEI/ ; }, abstract = {Amplicon sequencing tools such as metabarcoding are commonly used for thorough characterisation of microbial diversity in natural samples. They mostly rely on the amplification of conserved universal markers, mainly ribosomal genes, allowing the taxonomic assignment of barcodes. However, linking taxonomic classification with functional traits is not straightforward and requires knowledge of each taxonomic group to confidently assign taxa to a given functional trait. Zoosporic parasites are highly diverse and yet understudied, with many undescribed species and host associations. However, they can have important impacts on host populations in natural ecosystems (e.g., controlling harmful algal blooms), as well as on industrial-scale algae production, e.g. aquaculture, causing their collapse or economic losses. Here, we present ParAquaSeq, a curated database of available molecular ribosomal sequences belonging to zoosporic parasites infecting aquatic vascular plants, macroalgae and photosynthetic microorganisms, i.e. microalgae and cyanobacteria. These sequences are aligned with ancillary data and other information currently available, including details on their hosts, occurrence, culture availability and associated bibliography. The database includes 1131 curated sequences from marine, freshwater and industrial or artificial environments, and belonging to 13 different taxonomic groups, including Chytridiomycota, Oomycota, Phytomyxea, and Syndiniophyceae. The curated database will allow a comprehensive analysis of zoosporic parasites in molecular datasets to answer questions related to their occurrence and distribution in natural communities. Especially through meta-analysis, the database serves as a valuable tool for developing effective mitigation and sustainable management strategies in the algae biomass industry, but it will also help to identify knowledge gaps for future research.}, }
@article {pmid40086056, year = {2025}, author = {Liang, L and Dang, B and Ouyang, X and Zhao, X and Huang, Y and Lin, Y and Cheng, X and Xie, G and Lin, J and Mi, P and Ye, Z and Guleng, B and Cheng, SC}, title = {Dietary succinate supplementation alleviates DSS-induced colitis via the IL-4Rα/Hif-1α Axis.}, journal = {International immunopharmacology}, volume = {152}, number = {}, pages = {114408}, doi = {10.1016/j.intimp.2025.114408}, pmid = {40086056}, issn = {1878-1705}, mesh = {Animals ; *Succinic Acid/therapeutic use/pharmacology ; *Colitis/chemically induced/immunology/drug therapy ; Dextran Sulfate ; Mice ; *Hypoxia-Inducible Factor 1, alpha Subunit/metabolism/genetics ; Mice, Inbred C57BL ; Dietary Supplements ; Mice, Knockout ; Monocytes/immunology ; Colon/immunology/drug effects/pathology ; Male ; Disease Models, Animal ; Humans ; Signal Transduction ; Cytokines/metabolism ; Interleukin-4 Receptor alpha Subunit ; }, abstract = {Inflammatory bowel disease (IBD) remains a pressing global health challenge, necessitating novel therapeutic strategies. Succinate, a metabolite known for its role in type 2 immunity and tuft cell activation in the small intestine, presents its potential in IBD management. However, its impact on colonic inflammation has not been explored. Here, we demonstrate that succinate administration induces a type 2 immune response, significantly alleviating dextran sulfate sodium (DSS)-induced colonic inflammation. Succinate enhances antibacterial capacity, reduces intestinal permeability, and reshapes the colonic cytokine milieu. Mechanistically, succinate promotes myeloid cell expansion in peripheral blood, mesenteric lymph nodes, and the colonic lamina propria. The protective effects of succinate were abolished in Ccr2[-/-] mice, confirming the role of monocyte recruitment, but persisted in Rag1[-/-] mice, indicating independence from adaptive immunity. Adoptive transfer of monocytes from succinate-treated donors mitigated intestinal inflammation in recipient mice. Transcriptomic analysis revealed heightened expression of Il1b and Il6, and higher lactate production in monocytes upon lipopolysaccharide (LPS) stimulation, highlighting a reprogrammed pro-inflammatory trained immunity phenotype. Finally, we identify the IL-4Rα/Hif-1α axis is critical for succinate-mediated protection. These findings reveal the ability of succinate to reprogram monocytes into protective intestinal macrophages via induction of type 2 response, restoring homeostasis through enhanced barrier function and immune modulation. Our study positions thus uncover succinate as a promising therapeutic candidate for IBD.}, }
@article {pmid40085655, year = {2025}, author = {Muratore, D and Gilbert, NE and LeCleir, GR and Wilhelm, SW and Weitz, JS}, title = {Diel partitioning in microbial phosphorus acquisition in the Sargasso Sea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {11}, pages = {e2410268122}, pmid = {40085655}, issn = {1091-6490}, support = {OCE-1829641//National Science Foundation (NSF)/ ; OCE-1829636//National Science Foundation (NSF)/ ; 721231//Simons Foundation (SF)/ ; }, mesh = {*Phosphorus/metabolism ; *Phytoplankton/metabolism/genetics ; *Seawater/microbiology ; *Cyanobacteria/metabolism/genetics ; Nitrogen/metabolism ; Ecosystem ; *Bacteria/metabolism/genetics ; Oceans and Seas ; Pacific Ocean ; }, abstract = {The daily cycle of photosynthetic primary production at the base of marine food webs is often limited by the availability of scarce nutrients. Microbial competition for these scarce resources can be alleviated insofar as the intensity of nutrient uptake and assimilation activities are distributed heterogeneously across organisms over periodic input cycles. Recent analysis of community transcriptional dynamics in the nitrogen-limited subtropical North Pacific gyre revealed evidence of temporal partitioning of nitrogen uptake and assimilation between eukaryotic phytoplankton, cyanobacteria, and heterotrophic bacteria over day-night cycles. Here, we present results from a Lagrangian metatranscriptomic time series survey in the Sargasso Sea and demonstrate temporally partitioned phosphorus uptake in this phosphorus-limited environment. In the Sargasso, heterotrophic bacteria, eukaryotic phytoplankton, and cyanobacteria express genes for phosphorus assimilation during the morning, day, and dusk, respectively. These results support the generality of temporal niche partitioning as an emergent mechanism that can structure uptake of limiting nutrients and facilitate coexistence of diverse microbes in open ocean ecosystems.}, }
@article {pmid40085287, year = {2025}, author = {Micciulla, JL and Baubin, C and Fierer, N}, title = {Effects of Geosmin on the Behavior of Soil Protists.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {14}, pmid = {40085287}, issn = {1432-184X}, support = {2126106//National Science Foundation/ ; }, mesh = {*Soil/parasitology/chemistry ; *Soil Microbiology ; *Naphthols/metabolism/pharmacology ; *Acanthamoeba castellanii/physiology/drug effects ; *Ciliophora/physiology/drug effects ; Bacteria/metabolism ; Cercozoa/physiology/drug effects ; }, abstract = {Geosmin is a volatile organic compound (VOC) produced by a range of different soil microorganisms, and is most commonly recognized for its characteristic "earthy" scent evident after rainfall. Though it remains unclear why microorganisms produce geosmin, we know that exposure to geosmin can influence behaviors across a wide range of organisms, serving as both an attractant and a repellant, but geosmin effects on soil protists remain largely unstudied. We investigated how soil protists respond to geosmin exposures, focusing on representatives of three morphological groups of protists, Colpoda sp. (ciliate), Cercomonas sp. (flagellate), and Acanthamoeba castellanii (naked amoeba), testing the hypothesis that geosmin production by bacteria influences soil protist behavior. We conducted experiments to evaluate protist excystment (waking up) and predation responses to geosmin-producing (Streptomyces coelicolor M145) and non-producing (S. coelicolor J3003) bacteria, as well as synthetic geosmin. All three protists excysted at higher rates when exposed to geosmin-producing bacteria or synthetic geosmin, while no significant excystment occurred with the non-producing strains or in the absence of synthetic geosmin. Protist feeding preferences were also affected, with two of the three protists (Cercomonas sp. and A. castellanii) less likely to predate geosmin-producing versus non-producing bacterial strains. Our findings suggest that soil protists can detect geosmin as a signal indicating favorable soil conditions and geosmin production by bacteria may serve as a deterrent to predation by protists. More generally, our results highlight the ecological significance of geosmin in the soil food web and its role in mediating bacteria-protist interactions.}, }
@article {pmid40085262, year = {2025}, author = {Castelli, M and Petroni, G}, title = {An Evolutionary-Focused Review of the Holosporales (Alphaproteobacteria): Diversity, Host Interactions, and Taxonomic Re-ranking as Holosporineae Subord. Nov.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {15}, pmid = {40085262}, issn = {1432-184X}, mesh = {Phylogeny ; *Biological Evolution ; Animals ; *Alphaproteobacteria/classification/genetics/physiology ; *Biodiversity ; *Host Microbial Interactions ; }, abstract = {The order Holosporales is a broad and ancient lineage of bacteria obligatorily associated with eukaryotic hosts, mostly protists. Significantly, this is similar to other evolutionary distinct bacterial lineages (e.g. Rickettsiales and Chlamydiae). Here, we provide a detailed and comprehensive account on the current knowledge on the Holosporales. First, acknowledging the up-to-date phylogenetic reconstructions and recent nomenclatural proposals, we reevaluate their taxonomy, thus re-ranking them as a suborder, i.e. Holosporineae, within the order Rhodospirillales. Then, we examine the phylogenetic diversity of the Holosporineae, presenting the 20 described genera and many yet undescribed sub-lineages, as well as the variety of the respective environments of provenance and hosts, which belong to several different eukaryotic supergroups. Noteworthy representatives of the Holosporineae are the infectious intranuclear Holospora, the host manipulator 'Caedimonas', and the farmed shrimp pathogen 'Candidatus Hepatobacter'. Next, we put these bacteria in the broad context of the whole Holosporineae, by comparing with the available data on the least studied representatives, including genome sequences. Accordingly, we reason on the most probable evolutionary trajectories for host interactions, host specificity, and emergence of potential pathogens in aquaculture and possibly humans, as well as on future research directions to investigate those many open points on the Holosporineae.}, }
@article {pmid40084873, year = {2025}, author = {Soh, M and Er, S and Low, A and Jaafar, Z and de Boucher, R and Seedorf, H}, title = {Spatial and temporal changes in gut microbiota composition of farmed Asian seabass (Lates calcarifer) in different aquaculture settings.}, journal = {Microbiology spectrum}, volume = {13}, number = {5}, pages = {e0198924}, pmid = {40084873}, issn = {2165-0497}, abstract = {UNLABELLED: The microbiota composition of healthy farmed fishes remains poorly characterized for many species. This study explores the influence of the external environment and innate factors that may shape the gut microbiota of farmed Asian seabass, Lates calcarifer. The α-diversity based on Shannon, Simpson, and Chao1 indices was lower for fishes reared in sea cages and tanks than for fishes that experienced a transfer from sea cages to tanks. Longitudinal analyses of gut segments revealed no significant differences in alpha diversity between segments within the same containment type, except for the Chao1 index between the stomach and pyloric cecum of sea-caged fishes. β-diversity analysis using weighted UniFrac distance and Bray-Curtis dissimilarity demonstrated that fish reared in the same containment type shared similar microbial communities. PERMANOVA tests confirmed that containment type, farm, and batch significantly influenced these distances. Containment type accounted for 10.4% of the observed diversity, farm for 29.8%, and batch for 10.7%. Genera comprising potential pathogens such as Aeromonas, Flavobacterium, and Vibrio were differentially abundant along the guts of fish from different containment types and particularly increased in tanks. Microbiota changes were observed with host age and gut segment, with differentially abundant microbial genera identified along the gut and as the seabass grew. Comparing the hindgut microbiota of Asian seabass to other species of farmed fishes revealed host-specific clustering as indicated by PERMANOVA. Overall, these findings underscore the significance of containment conditions on the gut microbiota of Asian seabass, with broad implications for aquaculture practices.<br><br>IMPORTANCE: Understanding the microbiota composition of healthy farmed fishes is crucial for optimizing aquaculture practices. This study highlights the significant influence of containment conditions on the gut microbiota of farmed Asian seabass (Lates calcarifer). By demonstrating that gut microbiota diversity and community composition are shaped by containment type, farm location, and batch, the research provides valuable insights into how external environmental factors and innate host factors interact to influence fish health. The findings, particularly the differential abundance of potential pathogens in various containment types, underscore the need for tailored management strategies in aquaculture. This research not only advances our knowledge of fish microbiota but also has broad implications for improving the sustainability and productivity of aquaculture practices.}, }
@article {pmid40084850, year = {2025}, author = {Machushynets, NV and Lysenko, V and Du, C and Slingerland, CJ and Elsayed, SS and Liles, MR and Martin, NI and van Wezel, GP}, title = {Exploring the Chemical Space of Paenibacillus NRPs and Discovery of Paenilipoheptin B.}, journal = {Organic letters}, volume = {27}, number = {12}, pages = {2821-2825}, pmid = {40084850}, issn = {1523-7052}, mesh = {*Paenibacillus/chemistry/metabolism ; Molecular Structure ; *Lipopeptides/chemistry ; Peptide Synthases/metabolism/chemistry ; Nuclear Magnetic Resonance, Biomolecular ; }, abstract = {A combination of genomic and metabolomic analyses paired with molecular networking was applied to a collection of Paenibacillus spp. to identify the producers of a little-studied class of lipopeptides known as paenilipoheptins. Mass spectrometry and NMR spectroscopy allowed revision of the structure of previously reported paenilipoheptin A and elucidation of the structure of novel paenilipoheptin B.}, }
@article {pmid40083115, year = {2025}, author = {Dodds, IL and Watts, EC and Schuster, M and Buscaill, P and Tumas, Y and Holton, NJ and Song, S and Stuttmann, J and Joosten, MHAJ and Bozkurt, T and van der Hoorn, RAL}, title = {Immunity gene silencing increases transient protein expression in Nicotiana benthamiana.}, journal = {Plant biotechnology journal}, volume = {23}, number = {5}, pages = {1768-1770}, pmid = {40083115}, issn = {1467-7652}, support = {BB/R017913/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S003193/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DDT00060/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DDT00230/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 101019324/ERC_/European Research Council/International ; }, }
@article {pmid40082592, year = {2025}, author = {Thomas, PW and Kothamasi, D}, title = {Hunting dog behaviour is a key driver impacting harvest quantity and quality of truffles.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8662}, pmid = {40082592}, issn = {2045-2322}, mesh = {Animals ; Humans ; Dogs ; *Ascomycota/physiology/growth &amp; development ; *Hunting ; *Behavior, Animal ; Seasons ; }, abstract = {Truffles are an iconic food that have long held high regard. Here we explore the seasonality and eco-physiological interactions affecting truffle quality and quantity across time and space. Collaborating with professional truffle hunters working eight different locations, detailed metrics of 3180 recovered truffles from 236 hunt events and spanning a full fruiting period, were recorded. Contrary to expectations, truffle weight showed no correlation with climate variables, suggesting a limited influence of environmental factors such as temperature and precipitation on truffle size. We also found that truffle maturity and damage from mycophagy were strongly linked, with deeper truffles being more mature but also more susceptible to damage. Finally, we observe that scent-dog behaviour significantly impacts the quantity and quality of recovered truffles, and we address the necessity of considering this in truffle ecophysiology studies. Alongside advances in our biological understanding, we make recommendations of how training methods can be improved to lead to greater detection and quality targeting with immediate socioeconomic impact. These findings highlight the complex interplay between truffle physiology, environmental factors, and human and animal behaviours, emphasizing the need for further considered research to enhance our understanding of truffle biology and to improve truffle cultivation practices.}, }
@article {pmid40080573, year = {2025}, author = {Shumilova, O and Sukhodolov, A and Osadcha, N and Oreshchenko, A and Constantinescu, G and Afanasyev, S and Koken, M and Osadchyi, V and Rhoads, B and Tockner, K and Monaghan, MT and Schröder, B and Nabyvanets, J and Wolter, C and Lietytska, O and van de Koppel, J and Magas, N and Jähnig, SC and Lakisova, V and Trokhymenko, G and Venohr, M and Komorin, V and Stepanenko, S and Khilchevskyi, V and Domisch, S and Blettler, M and Gleick, P and De Meester, L and Grossart, HP}, title = {Environmental effects of the Kakhovka Dam destruction by warfare in Ukraine.}, journal = {Science (New York, N.Y.)}, volume = {387}, number = {6739}, pages = {1181-1186}, doi = {10.1126/science.adn8655}, pmid = {40080573}, issn = {1095-9203}, mesh = {Humans ; *Ecosystem ; Geologic Sediments/chemistry ; Ukraine ; *Warfare ; *Disasters ; }, abstract = {The use of water as a weapon in highly industrialized areas in the Russo-Ukrainian war has resulted in catastrophic economic and environmental damages. We analyze environmental effects caused by the military destruction of the Kakhovka Dam. We link field, remote sensing, and modeling data to demarcate the disaster's spatial-temporal scales and outline trends in reestablishment of damaged ecosystems. Although media attention has focused on the immediate impacts of flooding on society, politics, and the economy, our results show that toxic contamination within newly exposed sediments of the former reservoir bed poses a largely overlooked long-term threat to freshwater, estuarine, and marine ecosystems. The continued use of water as a weapon may lead to even greater risks for people and the environment.}, }
@article {pmid40080167, year = {2025}, author = {Kouakou, AK and Collart, P and Perron, T and Kolo, Y and Gay, F and Brauman, A and Brunel, C}, title = {Soil Microbial Recovery to the Rubber Tree Replanting Process in Ivory Coast.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {13}, pmid = {40080167}, issn = {1432-184X}, support = {(PFI : 7250A1, Centre de co&#xfb;t : 210F2CVNB)//Institut Fran&#xe7;ais du Caoutchouc/ ; ARTS, 2019//IRD PhD Grant Program/ ; }, mesh = {*Soil Microbiology ; *Hevea/growth &amp; development ; Cote d'Ivoire ; Soil/chemistry ; Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Agriculture/methods ; RNA, Ribosomal, 18S/genetics ; Trees ; }, abstract = {The resistance and resilience of soil microbial communities to an environmental disturbance are poorly documented, due to the lack on onfield diachronic experiments, limiting our ability to design adapted agroecological practices. This is especially true in rubber plantations, one of the most planted tree in tropical areas. We aimed to understand (1) how soil disturbances occurring during the rubber replanting phase affect the soil microbiome, (2) how agricultural practices combining legumes cover crops and tree logging residues shape community resilience and (3) how microbial responses vary across different edaphic contexts. In two plantations with distinct soil properties in Ivory Coast, soil microbial communities were surveyed every 6 months for 24 months after soil perturbation. Community structure, functioning and networks were described based on a 16S/18S rRNA gene investigation. Prokaryotes were generally more resistant to soil perturbation than microeukaryote communities. Prokaryotic resilience dynamics were faster than those of microeukaryotes, the latter being deeply modulated by cover treatments. These specific dynamics were exacerbated in the sandy site. Co-occurrence network modelling provided useful insights into microbial resilience trajectories. We argue that this tool should be more widely used to describe microbial community dynamics. Practices involving a combination of logging residues and legume cover crops have shown beneficial effects on the community resilience in the sandy site and appears as promising agroecological practices. However, the major influence of soil texture warns of the need to consider pedological context when designing pertinent agroecological practices.}, }
@article {pmid40078544, year = {2025}, author = {Acciardo, AS and Arnet, M and Gholizadeh Doonechaly, N and Ceccato, A and Rodriguez, P and Tran, HNH and Wenning, Q and Zimmerman, E and Hertrich, M and Brixel, B and Magnabosco, C}, title = {Spatial and temporal groundwater biogeochemical variability help inform subsurface connectivity within a high-altitude Alpine catchment (Riale di Ronco, Switzerland).}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1522714}, pmid = {40078544}, issn = {1664-302X}, abstract = {Accessing the deep terrestrial subsurface (greater than 1 km below the surface) presents significant practical challenges, leaving these ecosystems largely uncharacterized despite their extensive presence beneath Earth's landmasses. In this study, we introduce the BedrettoLab Deep Life Observatory (DELOS), a new underground laboratory to study the biogeochemical diversity of groundwater in a high-altitude Alpine catchment tens of meters to 1.6 km underground. Biogeochemical monitoring of DELOS over spatial and temporal scales highlight three dominant ecotypes throughout DELOS: (1) Shallow groundwater with low electrical conductivity enriched in Leptospirillia; (2) High-inflow fault zones enriched in ultra-small bacteria and archaea; (3) Bicarbonate-enriched waters that are enriched in Candidatus Kryptonia and Spirochaetota. Despite a consistent lithology throughout DELOS, groundwater from fractures that are spatially near each other are not always represented by the same ecotype and can be more similar to groundwater emitted from fractures thousands of meters away. Despite this heterogeneity, the biological and hydrochemical compositions of the groundwater of individual fractures remained relatively stable throughout the course of a 1-year monitoring period. An exception to this trend occurred after a series of seismic events near one groundwater-bearing fracture. Here, the microbial community and hydrochemical composition of the groundwater changed after the seismic events but returned to the site's "baseline" composition within 3 weeks. Taken together, these findings provide new insights into the spatial and temporal heterogeneity of deep subsurface ecosystems and the subsurface connectivity of an Alpine subsurface environment.}, }
@article {pmid40077554, year = {2025}, author = {Smirani, N and Bouazizi, S and Bettaieb, E and Torkhani, R and Hamdi, M}, title = {Effect of Environmentally Friendly Betalain Extraction Methods on Antioxidant Compounds of Tunisian Opuntia stricta Fruit.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, pmid = {40077554}, issn = {2304-8158}, abstract = {This study focuses on the extraction of betalain compounds from Opuntia stricta as a natural alternative to synthetic colorants and sustainable environmentally friendly technology solutions. Non-conventional extraction technologies including microwave (MW) and ultrasound (US) were used alone or in combination. The extraction process was conducted for both undried Opuntia stricta (OS) and dried Opuntia stricta (DOS) plant material at two distinct drying temperatures, 40 °C and 60 °C, to assess the stability of betalain molecules. The colorant's potential was evaluated by determining the betalain content, total phenolic content, and antioxidant activity. The MW (2 min) and MW (2 min) + US (10 min) extraction processes yielded the greatest betalain content in OS fresh weight (FW), with 48.54 ± 0.29 mg/100 g FW and 51.01 ± 0.16 mg/100 g FW, respectively. Furthermore, the results showed a considerable drop in betalain content when the plant material was dried at 40 °C and 60 °C, with reduction rates of 53.75% and 24.82%, respectively, compared to the betalain content before the drying process. The LC-DAD-ESI-MS analysis supported this result, revealing the presence of 17-decarboxy betanin, 17-decarboxy neobetanin, and Cyclo-dopa5-O-βglucoside in DOS at 40 °C. This study highlights the potential future in the sustainable green extraction of betalain compounds with less heat degradation to offer a stable natural colorant.}, }
@article {pmid40072629, year = {2025}, author = {Dyczko, D and Szymański, DM and Szymański, D and Kupczak, M and Kolenda, K}, title = {First European record of Rickettsia bellii in Amblyomma rotundatum from Rhinella marina imported to Poland.}, journal = {Experimental &amp; applied acarology}, volume = {94}, number = {3}, pages = {43}, pmid = {40072629}, issn = {1572-9702}, mesh = {Animals ; Poland ; *Amblyomma/microbiology ; *Rickettsia/isolation &amp; purification/genetics ; Female ; *Tick Infestations/veterinary/parasitology ; }, abstract = {This study reports on the first documented case of Amblyomma rotundatum ticks, a species typically found in the Americas, parasitising an imported toad in Poland. A total of 12 ticks were collected from a single Rhinella marina toad. These ticks were identified as female specimens of A. rotundatum using an examination of morphological characteristics and a molecular analysis. Polymerase chain reaction testing revealed that 75.0% (9/12) of these females were positive for Rickettsia spp. Sequencing of positive samples confirmed the presence of R. bellii. However, no DNA evidence of Borrelia spp. and Anaplasma spp. was detected in the tested ticks. Nevertheless, given the limited number of tick specimens collected from a single host, further research is required to elucidate the pathogen profile of a tick species. This finding represents the second European report of A. rotundatum associated with exported animals, underscoring the importance of vigilance in monitoring the potential spread of ticks and tick-borne pathogens through the global wildlife trade.}, }
@article {pmid40072582, year = {2025}, author = {Barjau-Aguilar, M and Reyes-Hernández, AMJ and Merino-Ibarra, M and Vilaclara, G and Ramírez-Zierold, JA and Alcántara-Hernández, RJ}, title = {Diversity and Structure of the Prokaryotic Community in Tropical Monomictic Reservoir.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {12}, pmid = {40072582}, issn = {1432-184X}, support = {CVU: 747276//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; CVU: 1249011//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; CF-2023-G-155//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; CVU: 41120//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; UNAM, PAPIIT-IN207702//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; UNAM-PAPIIT IN217622//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, mesh = {*Archaea/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; *Biodiversity ; Nitrogen/analysis ; Phosphorus/analysis ; *Fresh Water/microbiology/chemistry ; Tropical Climate ; Oxygen/analysis ; Phylogeny ; *Microbiota ; Water Microbiology ; Eutrophication ; }, abstract = {Bacteria and Archaea are microorganisms that play key roles in the biogeochemical transformations that control water quality in freshwater ecosystems, such as in reservoirs. In this study, we characterize the prokaryotic community of a high-relevance tropical eutrophic reservoir using a 16S rRNA gene survey during a low-water level fluctuation period mainly used for storage, associating the distribution of these microorganisms with the hydrogeochemical conditions of the water column. Our findings revealed that diversity and structure of the prokaryotic community exhibited spatio-temporal variations driven by the annual circulation-stratification hydrodynamic cycle and are significantly correlated with the concentrations of dissolved oxygen (DO), soluble reactive phosphorus (SRP), and dissolved inorganic nitrogen (DIN). During the heterotrophic circulation, the breakdown of thermal gradient leads to a homogeneous distribution of the nutrients, where the presence of DO promotes the dominance of aerobic and facultative heterotrophic bacteria such as Bacteroidota, Actinobacteriota, and Verrucomicrobiota. Also, the autotrophic circulation was characterized by an increase of DO and NO3[-] concentrations, with abundant Cyanobacteria. Finally, during the stratification, the presence of prokaryotes associated with the metabolism of CH4 was detected, mainly in the hypolimnion, as well as others related to sulfate reduction and nitrification. This study shows the diversity of the prokaryotic community in tropical eutrophic reservoirs, and how the continuous monitoring with metabarcoding techniques can provide critical insights for a deeper understanding of the biogeochemical dynamics and improve the water resource management in the future.}, }
@article {pmid40070274, year = {2025}, author = {Cidan, Y and Wang, J and Wang, H and Xu, C and Zhu, Y and Khan, MK and Basang, W and Li, K}, title = {Composition and diversity of rumen mycobiota in Jiani yaks (Bos grunniens jiani): insights into microbial ecology and functions.}, journal = {Animal biotechnology}, volume = {36}, number = {1}, pages = {2476539}, doi = {10.1080/10495398.2025.2476539}, pmid = {40070274}, issn = {1532-2378}, mesh = {Animals ; *Rumen/microbiology ; Cattle/microbiology ; *Fungi/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Mycobiome ; *Gastrointestinal Microbiome ; }, abstract = {This study aimed to explore the diversity and functions of rumen mycobiota in 14‑ (PLf) and 15‑rib (DLf) Jiani yaks using ITS sequencing. A total of 1,079,105 and 1,086,799 filtered sequences were obtained for the PLf and DLf groups, respectively, with 491 ASVs common to both. No significant difference regarding the α‑diversity of mycobiota within the two groups was observed. While β‑diversity analysis indicated that the abundance of fifteen (15) genera in the PLf group and two (2) genera in the DLf group was found to be significantly different (p < 0.05). 16S rRNA sequencing results indicated that at the phylum level, in 14 ribs yaks Ascomycota, Basidiomycota, and Olpidiomycota, while in 15 rib yaks, Neocallimastigomycota, Mortierellomycota, and Rozellomycota were found to be significantly different (p < 0.05). At the genus level, Rhodotorula, Kluyveromyces, Comoclathris, Arthrinium, Cladophialophora, Seimatosporium, Lambertella, and Sphacelotheca in 14 rib yaks, and Orpinomyces, Ustilago, Fusarium, Aspergillus, Caecomyces, Alternaria, Trichoderma and Acremonium in 15 rib yaks were found to be significantly (p < 0.05) different. Predictive functional analysis based on ruminal fungal DNA sequences from 15‑rib yaks (DLf) demonstrated that genes involved in energy metabolism were upregulated. This study sheds novel insights into how genetic variations influence gut mycobiota in Jiani yak.}, }
@article {pmid40068413, year = {2025}, author = {Yang, H and Cappitelli, F and Li, X}, title = {Pollution gradients shape structure and functions of stone heritage bacterial communities at global scale.}, journal = {The Science of the total environment}, volume = {971}, number = {}, pages = {179087}, doi = {10.1016/j.scitotenv.2025.179087}, pmid = {40068413}, issn = {1879-1026}, mesh = {*Bacteria/classification ; *Microbiota/drug effects ; *Environmental Monitoring ; Particulate Matter/analysis ; Biodiversity ; }, abstract = {Previous studies mainly focused on the impact of climatic conditions on stone heritage microbial communities, while ignoring a global ecological perspective of pollution on heritage microorganisms. In particular, there is a lack of detailed analysis of the impact of pollution levels on microbial metabolic function. In this study, >6000 bacterial OTUs from 17 world cultural heritage sites were considered. The microbial diversity indexes and potential functions under different pollution levels were analyzed. The results show that particulate matter pollution, such as PM2.5, has an effect on the microbial community in heritage sites comparable to that of temperature and precipitation. High concentrations of particulate matter increased bacterial richness and facilitated the introduction of unique species. Among them, phototrophic bacteria (e.g., Cyanobacteria) and some heterotrophic bacteria (e.g., Actinobacteria and Proteobacteria) formed the core of the microbial community. However, high concentrations of particulate matter reduced the complexity and stability of microbial ecological networks, favoring pollution-tolerant species. Furthermore, elevated particulate concentrations partially suppressed the expression of certain metabolic pathways, particularly genes related to denitrification (e.g., nosZ and nirS). This study reveals the long-term impact of polluted environments on the diversity and potential functions of microbial communities, providing a theoretical basis for developing sustainable strategies for cultural heritage conservation.}, }
@article {pmid40066860, year = {2025}, author = {Defoirdt, T}, title = {Resistance to quorum sensing inhibition spreads more slowly during host infection than antibiotic resistance.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2476582}, pmid = {40066860}, issn = {1949-0984}, mesh = {*Quorum Sensing/drug effects ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Drug Resistance, Bacterial ; *Bacteria/drug effects ; *Bacterial Infections/microbiology/drug therapy ; Animals ; }, abstract = {Antibiotic resistance is a rising problem and new and sustainable strategies to combat bacterial (intestinal) infections are therefore urgently needed. One promising strategy under intense investigation is the inhibition of quorum sensing, bacterial cell-to-cell communication with small molecules. A key question with respect to the application of quorum sensing inhibition is whether it will impose selective pressure for the spread of resistance. It was recently shown that resistance to quorum sensing inhibition will spread more slowly during infection of a host than resistance to traditional antibiotics.}, }
@article {pmid40065660, year = {2025}, author = {Guislain, ALN and Nejstgaard, JC and Köhler, J and Sperfeld, E and Mischke, U and Skjelbred, B and Grossart, HP and Lyche Solheim, A and Gessner, MO and Berger, SA}, title = {Cell size explains shift in phytoplankton community structure following storm-induced changes in light and nutrients.}, journal = {Ecology}, volume = {106}, number = {3}, pages = {e70043}, pmid = {40065660}, issn = {1939-9170}, support = {731065//European Commission/ ; 871081//European Commission/ ; 01LC1501//German Federal Ministry of Education and Research (BMBF)/ ; GE 1775/2-1//German Research Foundation (DFG)/ ; 603378//the European Commission under its 7th Framework Programme/ ; SAW-2015-IGB-1//Leibniz Association/ ; K45/2017//Leibniz Association/ ; 033L041B//BMBF Infrastructure/ ; }, mesh = {*Phytoplankton/physiology/cytology ; *Light ; *Ecosystem ; Nutrients ; }, abstract = {Understanding the mechanisms driving community structure and dynamics is crucial in the face of escalating climate change, including increasing incidences of extreme weather. Cell size is a master trait of small organisms that is subject to a trade-off between resistance to grazing and competition for resources, and thus holds potential to explain and predict community dynamics in response to disturbances. Here, we aimed at determining whether cell size can explain shifts in phytoplankton communities following changes in nutrient and light conditions resulting from storm-induced inputs of nutrients and colored dissolved organic matter (cDOM) to deep clearwater lakes. To ensure realistic environmental conditions, we used a crossed gradient design to conduct a large-scale enclosure experiment over 6 weeks. Cell size explained phytoplankton community structure when light availability declined as a result of cDOM supply. Initially unimodal, with small-celled species accounting for up to 60% of the total community biovolume, the cell-size distribution gradually shifted toward large-celled species as light levels declined following cDOM addition. Neither nutrients nor mesozooplankton affected the shift in cell-size distribution. These results suggest a distinct competitive advantage of larger over smaller species at reduced light levels following cDOM inputs during storm events. Importantly, the clustering of species in two distinct size classes implies that interspecific size differences matter as much as cell size per se to understand community dynamics. Given that shifts in cell-size distribution have strong implications for food-web structure and biogeochemical cycles, our results point to the importance of analyzing cell-size distributions of small organisms as an essential element to forecast community and ecosystem dynamics in response to environmental change.}, }
@article {pmid40064943, year = {2025}, author = {Roegiers, I and Gheysens, T and Minsart, M and De Clercq, P and Vanbeversluys, K and Rać, N and Stroka, G and de Croock, J and Van de Wiele, T and Dubruel, P and Arroyo, MC}, title = {GelMA as scaffold material for epithelial cells to emulate the small intestinal microenvironment.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8214}, pmid = {40064943}, issn = {2045-2322}, support = {3G062519//Fonds Wetenschappelijk Onderzoek/ ; 1S51925N//Fonds Wetenschappelijk Onderzoek/ ; 40007505//Excellence Of Science (F.W.O.-F.R.S.-FNRS.)/ ; }, mesh = {Humans ; *Tissue Scaffolds/chemistry ; Caco-2 Cells ; *Epithelial Cells/cytology/metabolism ; Hydrogels/chemistry ; *Intestine, Small/cytology ; *Gelatin/chemistry ; Cell Survival/drug effects ; Permeability ; *Cellular Microenvironment ; Biocompatible Materials/chemistry ; Intestinal Mucosa ; Cell Adhesion ; Coculture Techniques ; }, abstract = {Host-microbe interactions in the intestine play a significant role in health and disease. Novel scaffolds for host cells, capable of potentially supporting these intricate interactions, are necessary to improve our current systems for mimicking host-microbiota interplay in vitro/ex vivo. In this research paper, we study the application of gelatin methacrylamide (GelMA) as scaffold material for intestinal epithelial cells in terms of permeability, mechanical strength, and biocompatibility. We investigated whether the degree of substitution (DS) of GelMA influences the permeability and found that both high and low DS GelMA show sufficient permeability of biorelevant transport markers. Additionally, we researched epithelial cell adherence and viability, as well as mechanical characteristics of different concentrations of GelMA. All concentrations of hydrogel show long-term biocompatibility for the mono- and co-cultures, despite the goblet-like cells (LS174T) showing lower performance than enterocyte-like cells (Caco-2). The mechanical strength of all hydrogel concentrations was in a physiologically relevant range to be used as scaffold material for intestinal cells. Lastly, we examined the effect of the two sterilization methods, ethylene oxide (EO) and 70% ethanol followed by UVC (EtOH/UVC). We found that the impact of the two methods on the mechanical characteristics was minimal, and we did not find a significant effect between the two methods on cell viability and confluency of Caco-2 cells seeded on the GelMA hydrogels. Based on these results, we conclude that GelMA is a suitable material as a scaffold for intestinal cell types in terms of permeability, mechanical strength and biocompatibility. These findings contribute to the growing field of in vitro modeling of the gut and moves the field further to ensuring more translatable research on host-microbe interactions.}, }
@article {pmid40062895, year = {2025}, author = {McDonald, MD and Lewis, KL and Gentry, TJ}, title = {No-tillage systems promote bacterial photosynthetic gene expression in low carbon, semi-arid surface soils.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {4}, pages = {e0018425}, pmid = {40062895}, issn = {1098-5336}, support = {//Texas A&amp;M AgriLife Research Air Quality Initiative/ ; }, mesh = {*Soil Microbiology ; *Carbon/metabolism/analysis ; *Photosynthesis/genetics ; *Soil/chemistry ; *Agriculture/methods ; *Bacteria/genetics/metabolism ; Triticum/growth &amp; development ; Crops, Agricultural/growth &amp; development ; }, abstract = {Managing soils in semi-arid agricultural croplands generally focuses on reducing wind erosion, increasing fertility, and storing carbon. Thus, converting conventionally tilled systems to no-tillage and cover-cropped systems are often the first steps towards a conservation management approach across the growing area of semi-arid croplands. From a soil biological perspective, introducing cover crops to semi-arid soils has been shown to alter microbial community structure, which may lead to changes in the biogeochemical pathways expressed in these soils. In this study, we examined the impact of single-species wheat cover cropping and no-tillage on microbial gene expression after 4 and 5 years of implementation. We sequenced the metatranscriptomes of three production systems with varying levels of conservation management: conventional tillage winter fallow, no-tillage winter fallow, and no-tillage with a winter wheat cover crop. Removing tillage was the biggest factor altering microbial gene expression in this study, specifically resulting in upregulation of several photosystem-associated functions. These functions were taxonomically linked to organisms that make up the early stages of biological soil crusts, which may introduce additional benefits to these semi-arid agricultural systems beyond a reduction in wind erosion. Implementing a cover crop did not clearly alter gene expression beyond the effect of tillage removal; however, it did indicate a potential to reduce fungal disease incidence in 1 year of the study. These alterations of microbial activities and selection for potentially beneficial functions should be considered and further studied to aid in maintaining sustainable croplands for our changing climate.IMPORTANCEEliminating tillage from semi-arid agricultural soils has the potential to significantly alter the activities of the soil bacterial community compared with conventionally tilled soils. A major driver of this change was the activities of biological soil crust forming organisms that can provide several environmental benefits to the soil ecosystem beyond the typically associated benefits of conservation management. Furthermore, this study revealed that the implementation of a cover crop regime on no-tillage soils does not confer a major change in the function of the organisms present. Overall, the study reported here reveals that soil management practices aimed at reducing wind erosion and improving sustainability will positively impact the function of the microbial community and suggests that future investigations into the consequences of these functional changes may provide valuable services to these agricultural ecosystems.}, }
@article {pmid40062772, year = {2025}, author = {Connolly, JP and Kelly, L}, title = {The physical biogeography of Fusobacterium nucleatum in health and disease.}, journal = {mBio}, volume = {16}, number = {4}, pages = {e0298924}, pmid = {40062772}, issn = {2150-7511}, support = {T32 GM007491/GM/NIGMS NIH HHS/United States ; 5T32GM007491-46//HHS | National Institutes of Health (NIH)/ ; //Elsa U. Pardee Foundation (EUPF)/ ; }, mesh = {*Fusobacterium nucleatum/genetics/isolation &amp; purification/classification/physiology ; Humans ; *Colorectal Neoplasms/microbiology ; Female ; Male ; *Fusobacterium Infections/microbiology ; Crohn Disease/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Metagenome ; Gingiva/microbiology ; Genome, Bacterial ; }, abstract = {UNLABELLED: Fusobacterium nucleatum (Fn) is an oral commensal inhabiting the human gingival plaque that is rarely found in the gut. However, in colorectal cancer (CRC), Fn can be isolated from stool samples and detected in metagenomes. We hypothesized that ecological characteristics of the gut are altered by disease, enabling Fn to colonize. Multiple genomically distinct populations of Fn exist, but their ecological preferences are unstudied. We identified six well-separated populations in 133 Fn genomes and used simulated metagenomes to demonstrate sensitive detection of populations in human oral and gut metagenomes. In 9,560 samples from 11 studies, Fn population C2 animalis is elevated in gut metagenomes from CRC and Crohn's disease patients and is observed more frequently in CRC stool samples than in the gingiva. Polymorphum, the most prevalent gingival Fn population, is significantly increased in Crohn's stool samples; this effect was significantly stronger in male hosts than in female. We find polymorphum genomes are enriched for biosynthetic gene clusters and fluoride exporters, while C2 animalis are high in iron transporters. Fn populations thus associate with specific clinical and demographic phenotypes and harbor distinct functional features. Ecological differences in closely related groups of bacteria inform microbiome impacts on human health.<br><br>IMPORTANCE: Fusobacterium nucleatum is a bacterium normally found in the gingiva. F. nucleatum generally does not colonize the healthy gut, but is observed in approximately a third of colorectal cancer (CRC) patient guts. F. nucleatum's presence in the gut during CRC has been linked to worse prognosis and increased tumor proliferation. Here, we describe the population structure of F. nucleatum in oral and gut microbiomes. We report substantial diversity in gene carriage among six distinct populations of F. nucleatum and identify population disease and body-site preferences. We find the C2 animalis population is more common in the CRC gut than in the gingiva and is enriched for iron transporters, which support gut colonization in known pathogens. We find that C2 animalis is also enriched in Crohn's disease and type 2 diabetes, suggesting ecological commonalities between the three diseases. Our work shows that closely related bacteria can have different associations with human physiology.}, }
@article {pmid40062764, year = {2025}, author = {Watkins, E and Lin, J and Lingohr-Smith, M and Yong, C and Tangirala, K and Collins, K}, title = {Biological, Clinical, and Sociobehavioral Factors Associated with Disproportionate Burden of Bacterial Vaginosis in the United States: A Comprehensive Literature Review.}, journal = {Journal of women's health (2002)}, volume = {34}, number = {5}, pages = {644-652}, doi = {10.1089/jwh.2024.0583}, pmid = {40062764}, issn = {1931-843X}, mesh = {Humans ; *Vaginosis, Bacterial/epidemiology/microbiology/ethnology ; Female ; United States/epidemiology ; Prevalence ; Vagina/microbiology ; Risk Factors ; Microbiota ; Black or African American/statistics &amp; numerical data ; White ; }, abstract = {Background: Bacterial vaginosis (BV), a common gynecological infection characterized by reduced lactic acid-producing bacteria and increased anerobic bacteria in the vaginal microbiome, is associated with adverse health outcomes. Methods: A PubMed search for English-language articles about BV in the USA and factors contributing to disparities in BV risk, with an emphasis on the role of the vaginal microbiome, published from August 2012 to August 2022, identified 760 articles. Results: Among the 52 articles meeting the prespecified criteria, BV prevalence varied among different populations and disproportionately impacted Black women (49-51%), Hispanic ethnicity (32-43%), and women of reproductive age (30%). Differences in microbial ecology and host genetics were important factors underlying these disparities. Colonization of BV-associated bacteria was more common in women of color than in non-Hispanic White women. Other factors linked with disproportionate burden included multiple/same-sex partners, obesity, immunosuppression, and C-section birth. Conclusions: BV prevalence was multifactorial, with some populations having higher prevalence rates and distinctive microbiome profiles that may predispose them to the condition. BV treatment and recurrence prevention were challenging due to the complex interplay of biological, clinical, and sociobehavioral factors. Understanding these disparate risk factors is critical to reducing BV burden.}, }
@article {pmid40062709, year = {2025}, author = {Jeong, IJ and Hong, JK and Bae, YJ and Lee, TK}, title = {Enhancing Bacterial Phenotype Classification Through the Integration of Autogating and Automated Machine Learning in Flow Cytometric Analysis.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {107}, number = {3}, pages = {203-213}, doi = {10.1002/cyto.a.24923}, pmid = {40062709}, issn = {1552-4930}, support = {2020R1C1C100624912//National Research Foundation of Korea/ ; }, mesh = {*Flow Cytometry/methods ; *Machine Learning ; *Bacteria/classification/isolation &amp; purification ; Phenotype ; Escherichia coli ; }, abstract = {Although flow cytometry produces reliable results, the data processing from gating to fingerprinting is prone to subjective bias. Here, we integrated autogating with Automated Machine Learning in flow cytometry to enhance the classification of bacterial phenotypes. We analyzed six bacterial strains prevalent in the soil and groundwater- Bacillus subtilis , Burkholderia thailandensis , Corynebacterium glutamicum , Escherichia coli , Pseudomonas putida , and Pseudomonas stutzeri . Using the H2O-AutoML framework, we applied gradient-boosting machine (GBM) models to classify bacteria across different metabolic phases. Our results demonstrated an overall classification accuracy of 82.34% for GBM. Notably, accuracy varied across metabolic phases, with the highest observed during the late log (88.06%), lag (88.43%), and early log phases (89.37%), whereas the stationary phase showed a slightly lower accuracy of 80.73%. P. stutzeri exhibited consistently high sensitivity and specificity across all the phases, which indicated that it was the most distinctly identifiable strain. In contrast, E. coli showed low sensitivity, particularly in the stationary phase, which indicated challenges in its classification. Overall, this study with incorporating autogating and the AutoML framework, substantially reduces subjective biases and enhances the reproducibility and accuracy of microbial classification. Our methodology offers a robust framework for microbial classification in flow cytometric analysis, paving the way for more precise and comprehensive analyses of microbial ecology.}, }
@article {pmid40060716, year = {2025}, author = {Zhao, Y and Yuan, X and Ran, W and Zhao, Z and Su, D and Song, Y}, title = {The Ecological Restoration Strategies in Terrestrial Ecosystems Were Reviewed: A New Trend Based on Soil Microbiomics.}, journal = {Ecology and evolution}, volume = {15}, number = {3}, pages = {e70994}, pmid = {40060716}, issn = {2045-7758}, abstract = {Soil microorganisms play a pivotal role in the biogeochemical cycle and serve as crucial indicators of ecological restoration in terrestrial ecosystems. The soil microbial community is regarded as a pivotal participant in environmental processes, offering both positive and negative feedback to diverse media within the ecosystem. This community can serve as a potential indicator in ecological monitoring and restoration processes. Consequently, an increasing number of scholars are directing their research towards the field of soil microbial ecology in diverse ecosystems and fragile areas, with the aim of elucidating the intricate interactions between microbes and vegetation. However, the implementation of soil microbiome in ecological restoration remains in the experimental stage due to the interference of extreme events and the complexity of governance measures. Consequently, a comprehensive evaluation of existing research is imperative. This review aims to address the ecological crises currently experienced by diverse terrestrial ecosystems and to provide a comprehensive overview of the specific practices of soil microorganisms in the context of ecological restoration. We also incorporate them into fragile habitats and identify urgent issues that need to be addressed in the ecological restoration process of fragile areas.}, }
@article {pmid40060289, year = {2025}, author = {Sarkar, A and Bhattacharjee, S}, title = {Biofilm-mediated bioremediation of xenobiotics and heavy metals: a comprehensive review of microbial ecology, molecular mechanisms, and emerging biotechnological applications.}, journal = {3 Biotech}, volume = {15}, number = {4}, pages = {78}, pmid = {40060289}, issn = {2190-572X}, abstract = {Environmental pollution, driven by rapid industrialization and urbanization, has emerged as a critical global challenge in the twenty-first century. This comprehensive review explores the potential of bacterial biofilms in bioremediation, focusing on their ability to degrade and transform a wide array of pollutants, including heavy metals, persistent organic pollutants (POPs), oil spills, pesticides, and emerging contaminants, such as pharmaceuticals and microplastics. The unique structural and functional characteristics of biofilms, including their extracellular polymeric substance (EPS) matrix, enhanced genetic exchange, and metabolic cooperation, contribute to their superior pollutant degradation capabilities compared to planktonic bacteria. Recent advancements in biofilm-mediated bioremediation include the application of genetically engineered microorganisms, nanoparticle-biofilm interactions, and innovative biofilm reactor designs. The CRISPR-Cas9 system has shown promise in enhancing the degradative capabilities of biofilm-forming bacteria while integrating nanoparticles with bacterial biofilms demonstrates significant improvements in pollutant degradation efficiency. As global pollution rises, biofilm-based bioremediation emerges as a cost-effective and environmentally friendly approach to address diverse contaminants. This review signifies the need for further research to optimize these techniques and harness their full potential in addressing pressing environmental challenges.}, }
@article {pmid40060287, year = {2025}, author = {Maity, A and Das, A and Roy, R and Malik, M and Das, S and Paul, P and Sarker, RK and Sarkar, S and Dasgupta, A and Chakraborty, P and Tribedi, P}, title = {Development of novel strategies against the threats of drug-resistant Escherichia coli: an in silico and in vitro investigation.}, journal = {3 Biotech}, volume = {15}, number = {4}, pages = {77}, pmid = {40060287}, issn = {2190-572X}, abstract = {UNLABELLED: Escherichia coli (E. coli) biofilms pose alarming threats in healthcare due to their invulnerability to drug therapy. Stand-alone therapies of antimicrobial compounds/antibiotics are not particularly effective against those resistant strains. However, combination therapy of compounds could be used to deal with such threats. Towards this direction, the natural compound cuminaldehyde was employed in combination with the aminoglycoside antibiotic tobramycin to target the biofilm-forming multidrug-resistant (MDR) clinical strains of E. coli, which were isolated from urine samples of patient's at Suraksha Diagnostic Private Limited (Kolkata, India). At first, an integrated in silico approach (PASS online, Swiss ADME, PROTOX 3.0, and OSIRIS) was explored to predict the potential biological activities, and other relevant pharmacokinetic parameters of cuminaldehyde and tobramycin. The in silico analysis suggested that tobramycin might not be bioavailable orally due to its molecular size, polarity, and poor GI absorption. However, cuminaldehyde was well absorbed in the GI but could cause irritation if swallowed in LD50 amounts. Further, in vitro assessments were performed to analyse the antimicrobial and antibiofilm activity of both compounds, alone and in combination, against clinical strains of E. coli. The results suggested that cuminaldehyde and tobramycin together could show an additive effect against the clinical strains of E. coli. The combination of the compounds showed a substantial decrease in minimum inhibitory concentration (MIC) and biofilm formation compared to individual application. The present study indicates that combinatorial application involving cuminaldehyde and tobramycin could inhibit the formation of biofilms in E. coli, potentially aiding in the management of microbial infections.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04246-0.}, }
@article {pmid40058043, year = {2025}, author = {Zhong, Q and Santás-Miguel, V and Cruz-Paredes, C and Rousk, J}, title = {Does the land-use impact the risk of inducing antibiotic tolerance by heavy metal pollution?.}, journal = {Journal of environmental management}, volume = {379}, number = {}, pages = {124883}, doi = {10.1016/j.jenvman.2025.124883}, pmid = {40058043}, issn = {1095-8630}, mesh = {*Metals, Heavy ; *Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; *Soil Pollutants ; Soil/chemistry ; Agriculture ; Forests ; Tetracycline ; Copper ; Bacteria/drug effects ; }, abstract = {The rise of antibiotic-resistant soil microbial communities is a critical global issue. Evidence suggests that heavy metals can select or co-select for tolerance to metals and antibiotics in soil bacteria, but it is unclear if this tolerance varies with land use. We tested the potential of bacterial communities to develop resistance to copper (Cu) or tetracycline (Tet) after amending soils from pristine forests, contaminated forests, and agricultural lands with 3000 mg kg[-1] Cu and 6000 mg kg[-1] tetracycline, separately. Results showed that bacterial communities of unamended contaminated forest soils had the highest initial tolerance to Cu, while unamended agricultural soils exhibited the highest initial tolerance to tetracycline. The inducibility of bacterial resistance to antibiotics after Cu amendment varied by land use. In pristine forests, Cu amendment significantly increased microbial tetracycline resistance, as indicated by bacterial community tolerance, likely due to higher biodiversity. In contaminated forests, Cu amendment did not induce tetracycline-resistance, as indicated by unchanged bacterial community tolerance, possibly because of existing metal pollution and compromised bacterial communities by metal pollution. In agricultural soils, microbial tetracycline resistance as indicated by bacterial community tolerance developed slowly, becoming evident only after 42 days. These findings reveal significant differences in environmental risks related to soil metal pollution across different land uses, highlighting the need for systematic studies on the mechanisms of bacterial resistance to antibiotics in metal-contaminated soils due to their human health implications.}, }
@article {pmid40052378, year = {2025}, author = {Mise, K and Masuda, Y and Senoo, K and Itoh, H}, title = {Betaproteobacterial clade II nosZ activated under high N2O concentrations in paddy soil microcosms.}, journal = {Journal of applied microbiology}, volume = {136}, number = {3}, pages = {}, doi = {10.1093/jambio/lxaf055}, pmid = {40052378}, issn = {1365-2672}, support = {JPNP18016//New Energy and Industrial Technology Development Organization/ ; JPMJMI20E5//JST-Mirai Program/ ; }, mesh = {*Soil Microbiology ; *Nitrous Oxide/metabolism ; RNA, Ribosomal, 16S/genetics ; *Oxidoreductases/genetics/metabolism ; *Betaproteobacteria/genetics/metabolism/classification/enzymology ; Soil/chemistry ; Phylogeny ; Oryza ; }, abstract = {AIMS: Microbial communities in paddy soils act as potential sinks of nitrous oxide (N2O), a notorious greenhouse gas, but their potential to reduce external N2O is unclear. The direct observation of N2O reduction in submerged field soils is technically difficult. Here, we aimed to identify soil microbial clades that underpin the strong N2O mitigation capacity.<br><br>METHODS AND RESULTS: We constructed paddy soil microcosms with external N2O amendment that enabled the simultaneous evaluation of N2O reductase gene (nosZ) transcripts and N2O consumption. Although the amount of N2O amended was large, it was mostly consumed after 6-8 days of microcosm incubation. Metatranscriptomic sequencing revealed that betaproteobacterial nosZ, especially those classified as clade II nosZ belonging to the orders Rhodocyclales or Nitrosomonadales, occupied&#xa0;>50% of the nosZ transcripts in three of the five paddy soils used. On the other hand, publicly available shotgun metagenomic sequences of 46 paddy soils were not dominated by betaproteobacterial clade II nosZ sequences, although they were ubiquitous. The same applied to the 16S rRNA sequences of Rhodocyclales or Nitrosomonadales.<br><br>CONCLUSIONS: The results indicated that betaproteobacterial N2O reducers potentially serve as powerful N2O sinks. Betaproteobacteria holding clade II nosZ can be targets of biostimulation, although further studies are required to understand their ecophysiology.}, }
@article {pmid40049093, year = {2025}, author = {Fonvielle, J and Thuile Bistarelli, L and Tao, Y and Woodhouse, JN and Shatwell, T and Villalba, LA and Berger, SA and Kyba, CCM and Nejstgaard, JC and Jechow, A and Kupprat, F and Stephan, S and Walles, TJW and Wollrab, S and Hölker, F and Dittmar, T and Gessner, MO and Singer, GA and Grossart, HP}, title = {Skyglow increases cyanobacteria abundance and organic matter cycling in lakes.}, journal = {Water research}, volume = {278}, number = {}, pages = {123315}, doi = {10.1016/j.watres.2025.123315}, pmid = {40049093}, issn = {1879-2448}, mesh = {*Lakes/microbiology ; *Cyanobacteria ; Ecosystem ; Light ; Carbon Cycle ; }, abstract = {Artificial light propagating towards the night sky can be scattered back to Earth and reach ecosystems tens of kilometres away from the original light source. This phenomenon is known as artificial skyglow. Its consequences on freshwaters are largely unknown. In a large-scale lake enclosure experiment, we found that skyglow at levels of 0.06 and 6 lux increased the abundance of anoxygenic aerobic phototrophs and cyanobacteria by 32 (±22) times. An ecosystem metabolome analysis revealed that skyglow increased the production of algal-derived metabolites, which appeared to stimulate heterotrophic activities as well. Furthermore, we found evidence that skyglow decreased the number of bacteria-bacteria interactions. Effects of skyglow were more pronounced at night, suggesting that responses to skyglow can occur on short time scales. Overall, our results call for considering skyglow as a reality of increasing importance for microbial communities and carbon cycling in lake ecosystems.}, }
@article {pmid40048904, year = {2025}, author = {Chen, L and Zhao, B and Zhang, M and Yan, Y and Nie, C and Yu, K and Tu, Z and Xia, Y}, title = {Micron-scale heterogeneity reduction leads to increased interspecies competition in thermophilic digestion microbiome.}, journal = {Water research}, volume = {279}, number = {}, pages = {123419}, doi = {10.1016/j.watres.2025.123419}, pmid = {40048904}, issn = {1879-2448}, mesh = {*Microbiota ; Anaerobiosis ; Bioreactors/microbiology ; }, abstract = {Microbial spatial heterogeneity is an important determinant of larger-scale community properties, whereas most studies neglect it and therefore only provide average information, potentially obscuring the signal of microbial interactions. Our study takes a step toward addressing this problem by characterizing the spatial heterogeneity of a microbiome with micron-scale resolution. Micron-scale single clusters (40-70 μm) were randomly collected from lab-scale anaerobic digestion (AD) biosystems, and a comparative analysis was performed to evaluate differences between mesophilic and thermophilic systems. Here we reveal a cascading effect from high-temperature selection to global microbial interactions. We observed that thermophilic communities exhibited less spatial heterogeneity than mesophilic communities, which we attribute to the considerable extinction of low-abundant species by high-temperature selection. Then, the low spatial heterogeneity and the high-temperature selection acting in conjunction resulted in a high proportion of competitive interactions in thermophilic communities. Unexpectedly, however, the thermophilic AD, characterized by lower micron-scale spatial heterogeneity, showed more efficient synergistic and syntrophic cooperations involving around Clostridiales, which significantly enhanced hydrolysis performance under thermophilic conditions. In addition, the fact that high temperatures favor slower growers, along with functional redundancy-related competitive advantage, led to the selection of more proficient methanogens in more competitive environments, which are also potentially associated with enhanced methanogenic performance. In summary, our findings underscore the significance of micron-scale resolution for revealing the microbial ecology in spatially structured environments.}, }
@article {pmid40047954, year = {2025}, author = {Sobhy, IS and Goelen, T and Wäckers, F and Verstrepen, KJ and Wenseleers, T and Jacquemyn, H and Lievens, B}, title = {Impact of Nectar Composition and Nectar Yeasts on Volatile Emissions and Parasitoid Behavior.}, journal = {Journal of chemical ecology}, volume = {51}, number = {2}, pages = {29}, pmid = {40047954}, issn = {1573-1561}, support = {C3 grant (IOF-C32/15/020)//KU Leuven/ ; }, mesh = {Animals ; *Volatile Organic Compounds/metabolism/analysis/chemistry ; *Plant Nectar/chemistry/metabolism ; Female ; *Wasps/physiology ; *Metschnikowia/metabolism/physiology ; Fermentation ; *Aphids/parasitology/physiology ; Amino Acids/analysis/metabolism ; Gas Chromatography-Mass Spectrometry ; *Yeasts ; }, abstract = {Nectar yeasts can significantly influence the scent of floral nectar and therefore the foraging behavior of flower-visiting insects. While these effects likely depend on nectar chemistry and yeast species, their joint impact on nectar volatile profiles and associated insect responses remain poorly understood. Here, we used four synthetic nectar types varying in sugar and amino acid concentration and two specialist nectar yeasts (Metschnikowia gruessii and Metschnikowia reukaufii) to investigate how nectar composition and yeast species affect volatile profiles and the olfactory responses of the generalist aphid parasitoid Aphidius ervi. Olfactometer assays showed that A. ervi females significantly preferred fermented nectars with high amino acid-low sugar content (HL) and low amino acid-high sugar (LH) content, regardless being fermented by M. gruessii or M. reukaufii, over non-inoculated nectars. This effect was not observed for nectars with low amino acid-low sugar (LL) and high amino acid-high sugar (HH) content. Moreover, LL nectar fermented with M. gruessii became even repellent to the parasitoids. GC-MS analysis of volatile organic compounds (VOCs) revealed that VOC profiles of fermented nectars depended significantly on nectar type (i.e., chemical composition), yeast species, and their interaction. Whereas propyl acetate, isobutyl acetate, styrene, α-guaiene and pentyl-octanoate were associated with the LH fermented nectars, ethyl acetate and E-methyl isoeugenol were mainly associated with the HL fermented nectars, suggesting possible involvement in A. ervi attraction to these nectars. In contrast, isopropyl-hexadecanoate was associated with the non-attractive or repellent LL fermented nectars. Altogether, our results indicate that nectar composition has a strong impact on nectar scent when fermented by specialist nectar yeasts and subsequently on insect foraging behavior.}, }
@article {pmid40046987, year = {2025}, author = {Scott, WT and Rockx, S and Mariën, Q and Regueira, A and Candry, P and Ganigué, R and Koehorst, JJ and Schaap, PJ}, title = {Implementation of a Clostridium luticellarii genome-scale model for upgrading syngas fermentations.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {649-660}, pmid = {40046987}, issn = {2001-0370}, abstract = {Syngas fermentation is a powerful platform for converting waste streams into sustainable carboxylic acid precursors for value-added biochemicals. Steel mills produce significant syngas, yet industrial microbial syngas valorization remains unrealized. The most promising syngas-converting biocatalysts consist of Clostridia species, such as Clostridium kluyveri, Clostridium autoethanogenum, and Clostridium ljungdahlii. Clostridium luticellarii, a recently discovered species, shares close phylogenetic ties with these organisms. Preliminary metabolic studies suggest its potential for syngas acetogenesis as well as chain elongation. In this study, we create iSJ444, a constraint-based metabolic model of C. luticellarii using iHN637 of a close relative C. ljungdahlii as a starting point. Model predictions support hypothesized methanol and syngas pathways from the metabolic characterization studies; however, the use of propionate could not be accurately predicted. Thermodynamic Flux Analysis (TFA) reveals that C. luticellarii maintains stable energy dissipation across most reactions when exposed to varying pH, with significant increases observed in reactions associated with the Wood-Ljungdahl pathway (WLP), such as the HACD1 reaction, at higher pH (6.5), suggesting an adaptive role in energy management under neutral conditions. Flux sampling simulations exploring metabolic flux distributions show that C. luticellarii might fit into syngas fermenting platforms. In both cases, high hydrogen-to-carbon source ratios result in better production of (iso)butyrate and caproate. We present a minimal genome-scale metabolic model of C. luticellarii as a foundation for further exploration and optimization. Although our predictions of its metabolic behavior await experimental validation, they underscore the potential of C. luticellarii to enhance syngas fermentation platforms.}, }
@article {pmid40045231, year = {2025}, author = {Agyapong, D and Propster, JR and Marks, J and Hocking, TD}, title = {Cross-validation for training and testing co-occurrence network inference algorithms.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {74}, pmid = {40045231}, issn = {1471-2105}, support = {2125088//National Science Foundation/ ; }, mesh = {*Algorithms ; *Microbiota ; *Computational Biology/methods ; }, abstract = {BACKGROUND: Microorganisms are found in almost every environment, including soil, water, air and inside other organisms, such as animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as decomposition, fermentation and nutrient cycling. Much research has been conducted on the study of microbial communities in various environments and how their interactions and relationships can provide insight into various diseases. Co-occurrence network inference algorithms help us understand the complex associations of micro-organisms, especially bacteria. Existing network inference algorithms employ techniques such as correlation, regularized linear regression, and conditional dependence, which have different hyper-parameters that determine the sparsity of the network. These complex microbial communities form intricate ecological networks that are fundamental to ecosystem functioning and host health. Understanding these networks is crucial for developing targeted interventions in both environmental and clinical settings. The emergence of high-throughput sequencing technologies has generated unprecedented amounts of microbiome data, necessitating robust computational methods for network inference and validation.<br><br>RESULTS: Previous methods for evaluating the quality of the inferred network include using external data, and network consistency across sub-samples, both of which have several drawbacks that limit their applicability in real microbiome composition data sets. We propose a novel cross-validation method to evaluate co-occurrence network inference algorithms, and new methods for applying existing algorithms to predict on test data. Our method demonstrates superior performance in handling compositional data and addressing the challenges of high dimensionality and sparsity inherent in real microbiome datasets. The proposed framework also provides robust estimates of network stability.<br><br>CONCLUSIONS: Our empirical study shows that the proposed cross-validation method is useful for hyper-parameter selection (training) and comparing the quality of inferred networks between different algorithms (testing). This advancement represents a significant step forward in microbiome network analysis, providing researchers with a reliable tool for understanding complex microbial interactions. The method's applicability extends beyond microbiome studies to other fields where network inference from high-dimensional compositional data is crucial, such as gene regulatory networks and ecological food webs. Our framework establishes a new standard for validation in network inference, potentially accelerating discoveries in microbial ecology and human health.}, }
@article {pmid40044467, year = {2025}, author = {Sharma, P and Reitz, T and Singh, SP and Worrich, A and Muehe, EM}, title = {Going beyond improving soil health: cover plants as contaminant removers in agriculture.}, journal = {Trends in plant science}, volume = {30}, number = {5}, pages = {539-552}, doi = {10.1016/j.tplants.2025.01.009}, pmid = {40044467}, issn = {1878-4372}, mesh = {*Agriculture/methods ; *Soil/chemistry ; *Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Plants/metabolism ; }, abstract = {Agriculture faces the increasing demands of a growing global population amid simultaneous challenges to soils from climate change and human-induced contamination. Cover plants are vital in sustainable agriculture, contributing to soil health improvement, erosion prevention, and enhanced climate resilience, but their role in contaminant management is underexplored. Herein we review the utilization of cover plants for remediating contaminants such as metals, organic pollutants, nitrate, antibiotics, antimicrobial resistance genes, plastics, and salts. We explore phytoremediation strategies - including phytoextraction, phytodegradation, and phytostabilization - in cover plant management. We highlight the challenges of selecting effective cover plants and the need for biomass removal of non-biodegradable contaminants, and we advocate incorporating phytoremediation concepts into sustainable agricultural management practices beyond nutrient cycling and climate resilience.}, }
@article {pmid40042720, year = {2025}, author = {Zhang, H and Zhang, H and Du, H and Zhang, Y and Zhang, M and Yu, X and Xu, Y}, title = {Unraveling the multiple interactions between phages, microbes and flavor in the fermentation of strong-flavor Baijiu.}, journal = {Bioresources and bioprocessing}, volume = {12}, number = {1}, pages = {14}, pmid = {40042720}, issn = {2197-4365}, abstract = {The fermentation process of strong-flavor Baijiu represents a complex and unique ecosystem, characterized by the involvement of various microorganisms that drive intricate biochemical reactions, ultimately contributing to the distinct flavor profile of the Baijiu. Viruses may affect the succession of microorganisms and thus affect the style and quality of the product. However, the interaction between viruses and microorganisms during the fermentation of Baijiu is still unclear. Here we combined viral metagenomics and amplicon sequencing, physicochemical analysis, and GC-MS detection with temporal sampling to study the dynamics of viral and microbial communities, physicochemical properties, and flavor compounds during strong-flavor Baijiu fermentation. Viral metagenomic analysis revealed 513 viral operational taxonomic units (vOTUs), encompassing 34 viral families. Principal coordinates analysis (PCoA) demonstrated significant differences in vOTUs at different fermentation stages. Notably, the microbial community exhibited distinct succession patterns at various fermentation stages; it changed rapidly during the initial five days, with similarities observed between days 10 and 20. Volatile profile analysis identified 38 flavor components in fermented grains, comprising 16 ester compounds, 11 alcohols, and 8 acids, with the majority formed between days 10 and 30. The Spearman's rank correlation analysis revealed that Peduoviridae exhibited a negative correlation with Gluconobacter. Genomoviridae showed a negative correlation with Issatchenkia, Penicillium, and Monascus. These findings highlight the potential for complex interactions between viruses and microbial communities during Baijiu fermentation, underscoring the importance of considering viral communities in studies of the microbial ecology of fermented foods.}, }
@article {pmid40042690, year = {2025}, author = {Zhang, T and Wang, XL and Zhou, J and Zhou, W and Zhou, SQ}, title = {Construction of Phosphate-Solubilizing Microbial Consortium and Its Effect on the Remediation of Saline-Alkali Soil.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {11}, pmid = {40042690}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Phosphates/metabolism ; Phosphorus/metabolism ; *Microbial Consortia ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Arachis/growth &amp; development ; Alkalies/metabolism ; Calcium Sulfate/metabolism ; Salinity ; Nitrogen/analysis/metabolism ; Hydrogen-Ion Concentration ; }, abstract = {In this study, phosphate solubilizing bacteria (PSB) with good phosphate-solubilizing capability were isolated from phosphogypsum (PG) storage yard, and phosphate-solubilizing bacteria without antagonistic effect were selected to construct phosphate solubilizing microbial consortium (PSMC), and the synergistic effect of PSMC and PG on the physical and chemical properties of saline-alkali soil, soil enzyme activity, soil bacterial diversity, and the growth index and biomass of peanut plants were explored. The results showed that the effect of phosphorus containing soil amendment on saline-alkali soil was better than that of single PSMC or PG. In the T6 group (untreated saline-alkali soil (1.5 kg) + PSMC stock solution (15 mL) + PG (6.0 g)), the pH of saline-alkali soil decreased from 8.54 to 7.03, the content of organic matter increased by 6.64%, the content of alkali hydrolyzable nitrogen, available phosphorus and available potassium increased by 81.68%, 60.31%, and 42.03%, respectively, and the activity of alkaline phosphatase increased by 94.95%. In addition, the electrical conductivity value in T4 group (untreated saline-alkali soil (1.5 kg) + PSMC stock solution (15 mL) + PG (3.0g)) decreased significantly by 20.21%. The diversity and richness of bacterial community in T4 group were the highest, and the growth of peanut plants was the best. The fresh weight of roots and stems increased by 73.34% and 116.6%, respectively. In conclusion, the phosphorus containing soil conditioner prepared by PSMC and PG can effectively improve the soil environment of saline-alkali soil and promote the resource utilization of saline alkali soil.}, }
@article {pmid40042528, year = {2025}, author = {Zaki, H and Hussein, MA and El-Dawy, EGAM}, title = {Diversity and Symbiotic Associations of Endophytic Fungi in Calotropis procera (Aiton) W.T. Aiton (Asclepiadaceae) Across Three Egyptian Regions: Phenotypic Characterization and Mitotic Activity.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {10}, pmid = {40042528}, issn = {1432-184X}, mesh = {*Endophytes/physiology/classification/isolation &amp; purification/genetics ; Egypt ; *Fungi/classification/physiology/isolation &amp; purification/genetics ; *Symbiosis ; *Biodiversity ; Soil Microbiology ; *Calotropis/microbiology/physiology ; Mitosis ; Phenotype ; }, abstract = {Endophytic fungi are essential contributors to fungal biodiversity, playing key roles in plant defense against pathogens, alleviation of abiotic stress, and promotion of growth. This study conducted a comprehensive survey of the phenotypic characterization of Calotropis procera and its associated endophytic fungi across three regions in Egypt: Qena-Safaga, Qena, and Qena-Kosseir. Positive and significant Pearson correlations among plant morphological traits suggest intrinsic connections. Fungal species diversity exhibited significant variation across the three regions examined. Particularly, the Qena-Kosseir region demonstrated the highest fungal species richness both in soil samples and endophytic fungi. Unique to this region, Allocanariomyces tritici, Aspergillus terreus, Chaetomium globosum, C. murorum, Cladosporium cladosporioides, C. sphaerospermum, Fusarium proliferatum, Penicillium crustosum, P. granulatum, P. spinuloseum, and Roussoella intermedia were identified as endophytes. Additionally, compared to other regions, the Qena-Kosseir area exhibited the presence of Aspergillus fumigatus, A. ochraceus, A. ornatus, A. sclerotiocabonarus, Drechslera halodes, Emericella echinulata, Fusarium oxysporum, and Macrophomina phaseolina in soil samples, underscoring its distinct fungal community composition. Furthermore, antimitotic assays using the Allium cepa test revealed distinct effects of endophytic extracts on various mitotic stages. Of the 33 treatments, 11 showed an increase in the mitotic index (MI), indicating a potential positive effect on plant growth and cell division. This study offers valuable insights into the diversity and functional roles of endophytic fungi associated with C. procera, highlighting their promising applications in sustainable agriculture and plant health management.}, }
@article {pmid40042412, year = {2025}, author = {Hicks, LC and Leizeaga, A and Cruz Paredes, C and Brangarí, AC and Tájmel, D and Wondie, M and Sandén, H and Rousk, J}, title = {Simulated Climate Change Enhances Microbial Drought Resilience in Ethiopian Croplands but Not Forests.}, journal = {Global change biology}, volume = {31}, number = {3}, pages = {e70065}, pmid = {40042412}, issn = {1365-2486}, support = {2016-06327//Vetenskapsr&#xe5;det/ ; 2020-03858//Vetenskapsr&#xe5;det/ ; CTS 22:2131//Carl Tryggers Stiftelse f&#xf6;r Vetenskaplig Forskning/ ; 2022-00672//Svenska Forskningsr&#xe5;det Formas/ ; 2023-02438//Svenska Forskningsr&#xe5;det Formas/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; KAW 2023.0384//Knut och Alice Wallenbergs Stiftelse/ ; }, mesh = {*Climate Change ; *Droughts ; Ethiopia ; *Forests ; *Soil Microbiology ; Fungi/growth &amp; development ; *Microbiota ; Soil/chemistry ; Bacteria/growth &amp; development ; Crops, Agricultural ; }, abstract = {Climate change and land-use change represent a dual threat to terrestrial ecosystem functioning. In the tropics, forest conversion to agriculture is occurring alongside warming and more pronounced periods of drought. Rainfall after drought induces enormous dynamics in microbial growth (potential soil carbon storage) and respiration (determining carbon loss), affecting the ecosystem carbon budget. We investigated how legacies of drought and warming affected microbial functional (growth and respiration) and structural (16S and ITS amplicon) responses after drought. Rain shelters and open-top chambers (OTCs) were used to simulate drought and warming in tropical cropland and forest sites in Ethiopia. Rain shelters reduced soil moisture by up to 25 vol%, with a bigger effect in the forest, while OTCs increased soil temperature by up to 6°C in the cropland and also reduced soil moisture but had no clear effect in the forest. Soils from these field treatments were then exposed to a standardized drought cycle to test how microbial community traits had been shaped by the different climate legacies. Microbial growth started increasing immediately after rewetting in all soils, reflecting a resilient response and indicating that microbial communities perceived the perturbation as relatively mild. Fungi recovered faster than bacteria, and the recovery of fungal growth was generally accelerated in soils with a legacy of drought. Microbial community functions and structures were both more responsive in the cropland than in forest soils, and a legacy of drought particularly enhanced microbial growth and respiration responses in the cropland but not the forest. Microbial communities in cropland soils also used carbon with a higher efficiency after rewetting. Together, these results suggest contrasting feedbacks to climate change determined by land use, where croplands will be associated with mitigated losses of soil carbon by microorganisms in response to future cycles of drought, compared to forests where soil carbon reservoirs remain more sensitive.}, }
@article {pmid40042334, year = {2025}, author = {Venturini, AM and Gontijo, JB and Berrios, L and Rodrigues, JLM and Peay, KG and Tsai, SM}, title = {Linking soil microbial genomic features to forest-to-pasture conversion in the Amazon.}, journal = {Microbiology spectrum}, volume = {13}, number = {4}, pages = {e0156124}, pmid = {40042334}, issn = {2165-0497}, support = {2014/50320-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; DEB 1952687//National Science Foundation (NSF)/ ; 2015/13546-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; 2018/14974-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; 140032/2015-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 133769/2015-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 311008/2016-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 314806/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; Finance Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; DEB 1442214//National Science Foundation (NSF)/ ; //Canadian Institute for Advanced Research (CIFAR)/ ; 2109481//National Science Foundation (NSF)/ ; //Stanford Doerr School of Sustainability Discovery grant/ ; }, mesh = {*Soil Microbiology ; Brazil ; Forests ; *Bacteria/genetics/classification/isolation &amp; purification ; *Archaea/genetics/classification/isolation &amp; purification ; Metagenome ; Genome, Bacterial ; Phylogeny ; Soil/chemistry ; Base Composition ; Genome, Archaeal ; Genomics ; }, abstract = {Amazonian soil microbial communities are known to be altered by land-use change. However, attempts to understand these impacts have focused on broader community alterations or the response of specific microbial groups. Here, we recovered and characterized 69 soil bacterial and archaeal metagenome-assembled genomes (MAGs) from three forests and three pastures of the Eastern Brazilian Amazon and evaluated the impacts of land conversion on their genomic features. Pasture MAGs had significantly higher GC content (64.9% vs 60.2%), genome size (4.0 vs 3.1 Mbp), and number of coding sequences (4,058 vs 3,306) compared to forest genomes. Taxonomically, MAGs belonged to eight phyla; however, most (90%) had low similarity to previously known species, indicating potentially novel taxa at multiple levels. We also observed that the functional profiles associated with biogeochemical cycling and carbohydrate-active enzyme genes were impacted by forest conversion, with pasture MAGs exhibiting a notably higher number of both gene groups. Together, these data constitute the largest single-sourced genomic data set from upland soils of the Brazilian Amazon to date and increase the known MAG richness in these soils by 78%. Our data, therefore, not only add to a neglected yet emerging field but, importantly, highlight that land-use change has drastic impacts on the genomic characteristics and functional traits of dominant soil microbes.IMPORTANCEThe Brazilian Amazon is facing unprecedented threats, including increasing deforestation and degradation, which together impact half of the original forest area. Soil microorganisms are sensitive indicators of land-use change, linked to a rise in microbial methane emissions and antibiotic-resistance genes in the Amazon. However, most Amazonian soil microbes remain unknown, and little attention has been given to their genomes. Using sequencing and bioinformatics, we recovered and characterized 69 soil bacterial and archaeal genomes (metagenome-assembled genomes). These abundant members of the microbial communities diverged across forests and pastures in terms of taxonomic and functional traits. Forest conversion favors organisms with specific genomic features - increased GC content, genome size, and gene number - selecting for microorganisms that can thrive under altered conditions. Our paper helps us understand the intricate relationships between microbes and the environment, which are crucial pieces of information for comprehensive soil health assessments and future policy formulation.}, }
@article {pmid40041707, year = {2025}, author = {Liu, X and Gong, X and Ma, K and Song, W and Zhou, J and Wang, M and Li, Y and Ji, M and Li, Y and Han, H and Wang, Y and Tu, Q}, title = {Resolving ecological drivers of temporal variations of β-diversity across intertidal microbiomes.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf025}, pmid = {40041707}, issn = {2730-6151}, abstract = {Resolving the ecological drivers mediating the diversity patterns of microbial communities across space and through time is a central issue in microbial ecology. Both regional species pools and local community assembly contribute to the spatial turnover of biodiversity. In this study, we extended the concept of regional species pool to temporal, and investigated the seasonal dynamics of intertidal microbiomes across four microbial domains/kingdoms (bacteria, archaea, fungi, and protists). The results showed that the seasonal variations of microbial β-diversity were primarily governed by community assembly processes rather than temporal species pools. Different microbial domains/kingdoms were structured by different ecological processes, with homogeneous selection as the major process for all of them. Additionally, bacteria and fungi were critically shaped by drift, and protists by drift and homogeneous dispersal. Among various factors, temperature was important in shaping the temporal patterns of microbial β-diversity. The fluctuation in temperature was strongly associated with fungi and protists, resulting in high drift of community composition. This study demonstrated that community assembly processes governed the dynamic seasonal β-variations of intertidal microbiomes, expanding our understanding from spatial ecology.}, }
@article {pmid40041702, year = {2025}, author = {Xu, Z and Chen, J and Liang, W and Chen, ZL and Wu, W and Xia, X and Chen, B and He, D and Liu, H}, title = {Contrasting diversity patterns between microeukaryotic and prokaryotic communities in cold-seep sediments.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf002}, pmid = {40041702}, issn = {2730-6151}, abstract = {Cold seeps are hotspots of biodiversity. However, the quantification of the microbial diversity, particularly that of microeukaryotes, remains scarce and little is known about the active groups. In this study we investigated the diversity and activity of prokaryotes and microeukaryotes in the Haima cold seep sediments in the northern South China Sea using both DNA (whole community) and RNA (active community) signatures. We found that, in general, prokaryotes had lower diversity in the seep sediment than in non-seep regions while microeukaryotes showed the opposite pattern. This finding could be explained by the dominance of homogeneous selection in the prokaryotic community while microeukaryotic communities were less affected by environmental selection, harboring high richness of abundant groups in the seep regions. The compositional difference between DNA and RNA communities was much larger in microeukaryotes than prokaryotes, which could be reflected by the large number of inactive microeukaryotic taxa. Compared to the whole community, the seep-active groups, e.g. among microeukaryotes, Breviatea, Labyrinthulomycetes, and Apicomplexa were more sensitive to and directly influenced by environmental factors, suggesting their pivotal roles in ecosystem biodiversity and functions. This study provides insight into the distinct diversity patterns and regulating mechanisms that occur between prokaryotic and microeukaryotic communities in cold-seep sediments, deepening our understanding of microbial ecology in deep-sea extreme habitats.}, }
@article {pmid40041671, year = {2025}, author = {Zernadji, W and Rahmani, F and Jebri, S and Hamdi, M and Khammassi, M and Dhib, S and Hmaied, F}, title = {Distribution of Microbial Contaminants of Minimally Processed Salads Produced in Tunisia: Need to Strengthen Good Hygiene Practices.}, journal = {International journal of food science}, volume = {2025}, number = {}, pages = {9570620}, pmid = {40041671}, issn = {2314-5765}, abstract = {The microbiological safety of ready-to-eat (RTE) salads is considered as a major concern due to the absence of lethal treatments during processing. In this study, we aimed to investigate the microbiological quality of RTE salads commercialized in Tunisia and to determine the antibiotic resistance of isolated pathogens, in particular Staphylococcus aureus (S. aureus). A total of 100 samples were analyzed for total aerobic bacteria, total coliforms, Escherichia coli (E. coli), yeasts and molds, Salmonella spp., Listeria monocytogenes (L. monocytogenes), and S. aureus as well as norovirus (NoV) GI and GII using specific standard methods described by the International Organization for Standardization (ISO). All samples presented unacceptable microbiological quality due to high concentrations of total aerobic bacteria and yeasts (> 10[6] CFU/g) and total coliforms (> 10[4] CFU/g). E. coli and molds were detected at unsatisfactory levels in 4% and 12% of samples, respectively. The pathogens Salmonella spp. and L. monocytogenes were not detected. S. aureus were detected at unsatisfactory levels in 6% of samples. S. aureus isolates were resistant to more than five antibiotic classes. Thus, RTE salads could be a vehicle of multiresistant S. aureus. The total prevalence of NoV GII was 2% (mean 3.81 ± 0.30 Log GC/25 g), and no NoV GI-positive samples were identified. This study showed that the microbiological quality of RTE salads commercialized in Tunisia was unacceptable, highlighting the need to ensure good agricultural and hygiene practices from farm to fork to improve the quality and safety of these products.}, }
@article {pmid40037241, year = {2025}, author = {Lu, Z and Zeng, J and Wang, L and Zhu, D and Cheng, X and Huang, D and Zhang, J and Yuan, L}, title = {The influence of turbulence caused by hydraulic structures on the community assembly of epilithic biofilms in rivers.}, journal = {Journal of environmental management}, volume = {378}, number = {}, pages = {124645}, doi = {10.1016/j.jenvman.2025.124645}, pmid = {40037241}, issn = {1095-8630}, mesh = {*Biofilms ; *Rivers/microbiology ; Ecosystem ; Hydrodynamics ; }, abstract = {The assembly mechanisms of riverine biofilm communities in river systems represent a central question in aquatic microbial ecology. However, the influence of turbulence on the assembly of generalists and specialists within biofilms remains poorly understood. This study aimed to address this gap by examining a river with multiple spur dikes, using high-throughput sequencing, ecological network analysis, and partial least squares path modeling to explore the assembly process and community structure of biofilms. The results revealed that turbulence intensity (0.029 m/s) and kinetic energy (0.0018 m[2]/s[2]) were significantly higher at the heads of spur dikes compared to the tails. Notably, hydrodynamic parameters explained 6.50% of biofilm community variance, highlighting their underappreciated role as deterministic drivers of microbial assembly. Habitat specialists exhibited heightened sensitivity to hydrodynamic fluctuations, occupying central positions in co-occurrence networks. Additionally, turbulence intensity and kinetic energy emerged as the primary drivers of community assembly, influencing critical ecological processes such as homogeneous selection, drift and dispersal limitation. At the head of spur dikes, a high turbulence region, the weakened impact of homogeneous selection, combined with an increase in dispersal limitation, created conditions that particularly favored habitat generalists. Conversely, low turbulence dike tails supported specialist proliferation via strengthened deterministic selection and nutrient-driven niche partitioning. Furthermore, the partial least squares path modeling confirmed that turbulence dominates the assembly process of microbial specialists and generalists. This study revealed the pivotal role of turbulence in shaping biofilm assembly and driving the spatial differentiation of generalists and specialists, offering fresh insights into the complex interplay between hydrodynamics and microbial ecology in rivers impacted by hydraulic structures. These findings significantly enhance the understanding of biofilm assembly mechanisms and their broader implications for effective river ecosystem management.}, }
@article {pmid40036370, year = {2025}, author = {Duysburgh, C and Nicolas, C and Van den Broeck, M and Lloret, F and Monginoux, P and Rème, C and Marzorati, M}, title = {A specific blend of prebiotics and postbiotics improved the gut microbiome of dogs with soft stools in the in vitro Simulator of the Canine Intestinal Microbial Ecosystem.}, journal = {Journal of animal science}, volume = {103}, number = {}, pages = {}, pmid = {40036370}, issn = {1525-3163}, mesh = {Animals ; Dogs/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Feces/microbiology ; *Prebiotics/administration &amp; dosage ; Animal Feed/analysis ; Diet/veterinary ; Bacteria/classification ; Male ; }, abstract = {The Simulator of the Canine Intestinal Microbial Ecosystem (SCIME) allows for the study of the long-term effects of food, supplements, or ingredients on the canine gut microbiome in a simulated proximal and distal colon. This model has been used to evaluate the impact of repeated administration of a test product blend composed of a mixture of baobab fruit pulp, acacia gum, heat-killed Lactobacillus helveticus HA-122, and specific fractions of selected inactivated yeast strains (including Saccharomyces cerevisiae AQP 12260 and AQP 12988 and Cyberlindnera jadinii AQP 12549), on the activity and composition of the gut microbiome of canine donors with soft stools. The SCIME colonic reactors were inoculated with fecal material from 3 different canine donors. After 2 d of stabilization, the 8-d parallel control/treatment period was initiated; reactors were fed with SCIME nutritional medium with or without test product. Changes in microbial metabolic activity were assessed by measuring levels of acetate, propionate, butyrate, lactate, branched short-chain fatty acids, and ammonium. Changes in microbial community composition were assessed using 16S-targeted Illumina sequencing. Overall, test product supplementation resulted in increased saccharolytic fermentation, as evidenced by increases in the health-promoting bacterial metabolites such as propionate (donor-dependent), acetate, and butyrate (donor-dependent) as well as increased abundances of several saccharolytic fermenting microbes, including Bifidobacterium. Conversely, proteolytic bacteria like Proteobacteria were reduced with the test product compared to control. Repeated supplementation with the test product was therefore able to induce-in vitro-a positive modulation of the microbiome originated from dogs with soft stools.}, }
@article {pmid40035794, year = {2025}, author = {Vieira, AR and Camacho, F and Sousa, ML and Luelmo, S and Santarém, N and Cordeiro-da-Silva, A and Leão, PN}, title = {The Cyanobacterial Oxadiazine Nocuolin A Shows Broad-Spectrum Toxicity Against Protozoans and the Nematode C. elegans.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {9}, pmid = {40035794}, issn = {1432-184X}, support = {2022.04572.PTDC//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2021.04285.CEECIND/CP1663/CT0004//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 952374//Horizon 2020/ ; }, mesh = {Animals ; *Cyanobacteria/chemistry/metabolism ; *Caenorhabditis elegans/drug effects ; *Dictyostelium/drug effects ; }, abstract = {Cyanobacteria, known to be rich sources of valuable natural products (NPs) with relevant biological properties, are a unique subject to study the interplay between chemistry and ecology. Cultivation of cyanobacteria as isolated strains may only reveal a small fraction of their NPs. In contrast, investigating microbial interactions from an ecological perspective is a particularly fruitful approach to unveil both new chemistry and bioactivity. Cyanobacteria and amoebae are known to co-exist in diverse environments, but the interaction between these organisms has been poorly investigated. Defense strategies against grazer organisms may rely on morphological changes including biofilm formation or increased motility; however, secretion of toxic metabolites seems to be more effective on this regard. Among the most structurally unique cyanobacterial secondary metabolites is nocuolin A, an 1,2,3-oxadiazine metabolite isolated from the cyanobacterial strain Nodularia sp. LEGE 06071 that exhibits potent anti-proliferative activity against several human cancer lines, associated with impairment of mitochondrial oxidative phosphorylation. In this work, we show that nocuolin A is toxic against two well-known model amoebae, Acanthamoeba and Dictyostelium, leading to amoebae encystation and decrease in viability. In addition, in lawn grazing assays, we observed that Nodularia sp. LEGE 06071, the producer strain of nocuolin A, was not grazed by amoeba, while a related strain, which does not produce detectable levels of nocuolin A, was. These results support the possible involvement of nocuolin A as a chemical mediator during the interaction between these organisms. Furthermore, we show that this cyanobacterial metabolite also exhibits potent toxicity against other protozoan organisms and a free-living nematode, making it an interesting broad-spectrum scaffold for the development of antiprotozoal or anti-helminthic drugs.}, }
@article {pmid40034844, year = {2024}, author = {Thompson, MA and Valentine, DL and Peng, X}, title = {Size fractionation informs microbial community composition and interactions in the eastern tropical North Pacific Ocean.}, journal = {FEMS microbes}, volume = {5}, number = {}, pages = {xtae028}, pmid = {40034844}, issn = {2633-6685}, abstract = {Marine microorganisms are drivers of biogeochemical cycles in the world's oceans, including oxygen minimum zones (OMZs). Using a metabarcoding survey of the 16S rRNA gene, we investigated prokaryotic communities, as well as their potential interactions with fungi, at the coastal, offshore, and peripheral OMZ of the eastern tropical North Pacific. Water samples were collected along a vertical oxygen gradient, and large volumes were filtered through three size fractions, 0.22, 2, and 22 µm. The changes in community composition along the oxygen gradient were driven by Planctomycetota, Bacteroidota, Verrucomicrobiota, and Gammaproteobacteria; most are known degraders of marine polysaccharides and usually associated with the large particle-associated (LPA) community. The relative abundance of Nitrososphaerota, Alphaproteobacteria, Actinomycetota, and Nitrospinota was high in free-living and small particle-associated (SPA) communities. Network analyses identified putative interactions between fungi and prokaryotes in the particle-associated fractions, which have been largely overlooked in the ocean. In the SPAnetwork analysis, fungal amplicon sequence variants (ASVs) had exclusively negative connections with SAR11 nodes. In the LPA network analysis, fungal ASVs displayed both negative and positive connections with Pseudomonadota, SAR324, and Thermoplasmatota. Our findings demonstrate the utility of three-stage size-fractioned filtration in providing novel insights into marine microbial ecology.}, }
@article {pmid40033656, year = {2025}, author = {Orr, JA and Armitage, DW and Letten, AD}, title = {Coexistence Theory for Microbial Ecology, and Vice Versa.}, journal = {Environmental microbiology}, volume = {27}, number = {3}, pages = {e70072}, pmid = {40033656}, issn = {1462-2920}, support = {DE230100373//Australian Research Council/ ; DP220103350//Australian Research Council/ ; DE250100656//Australian Research Council/ ; }, mesh = {*Ecology/methods ; *Microbiota ; Ecosystem ; Models, Biological ; Bacteria ; }, abstract = {Classical models from theoretical ecology are seeing increasing uptake in microbial ecology, but there remains rich potential for closer cross-pollination. Here we explore opportunities for stronger integration of ecological theory into microbial research (and vice versa) through the lens of so-called "modern" coexistence theory. Coexistence theory can be used to disentangle the contributions different mechanisms (e.g., resource partitioning, environmental variability) make to species coexistence. We begin with a short primer on the fundamental concepts of coexistence theory, with an emphasis on the relevance to microbial communities. We next present a systematic review, which highlights the paucity of empirical applications of coexistence theory in microbial systems. In light of this gap, we then identify and discuss ways in which: (i) coexistence theory can help to answer fundamental and applied questions in microbial ecology, particularly in spatio-temporally heterogeneous environments, and (ii) experimental microbial systems can be leveraged to validate and advance coexistence theory. Finally, we address several unique but often surmountable empirical challenges posed by microbial systems, as well as some conceptual limitations. Nevertheless, thoughtful integration of coexistence theory into microbial ecology presents a wealth of opportunities for the advancement of both theoretical and microbial ecology.}, }
@article {pmid40028056, year = {2025}, author = {Vignolle, A and Zehl, M and Kirkegaard, RH and Vignolle, GA and Zotchev, SB}, title = {Secondary Metabolite Biosynthesis Potential of Streptomyces Spp. from the Rhizosphere of Leontopodium nivale Subsp. alpinum.}, journal = {ACS omega}, volume = {10}, number = {7}, pages = {7163-7171}, pmid = {40028056}, issn = {2470-1343}, abstract = {Bacteria of the phylum Actinomycetota, particularly those of the genus Streptomyces, are prolific producers of secondary metabolites (SMs), many of which have been developed into antibiotics, immunosuppressants, and cancer therapeutics. With high rediscovery rates, the attention has shifted to Streptomyces from unique ecological niches for the discovery of new SMs. The plant rhizosphere is one such niche, characterized by complex chemical interactions between the plant and its rhizobiome, which can elicit the production of SMs in Streptomyces. In the present study, 18 Streptomyces strains were previously isolated from the rhizosphere of the rare alpine medicinal plant Leontopodium nivale subsp. alpinum were investigated for their capacity to produce secondary metabolites. Genomes of these strains were analyzed for the presence of SM biosynthetic gene clusters (BGCs). In total, 551 BGCs were detected, of which 217 could not be linked to known SMs. These isolates were cultivated in different media known to support the production of SMs, and 15 out of the 54 methanolic extracts from these cultures exhibited antimicrobial activities. Subsequent liquid chromatography-mass spectrometry analyses of the bioactive extracts led to a putative identification of 69 known SMs as well as 16 potentially new molecules. The results of this study may provide a basis for the discovery of unique molecules with the potential to be developed as drugs against a variety of human diseases.}, }
@article {pmid40025674, year = {2025}, author = {Abdolahpur Monikh, F and Quik, JTK and Wiesner, MR and Tapparo, A and Pastore, P and Grossart, HP and Akkanen, J and Kortet, R and Kukkonen, JVK}, title = {Importance of Attachment Efficiency in Determining the Fate of PS and PVC Nanoplastic Heteroaggregation with Natural Colloids Using a Multimedia Model.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {9}, pages = {4674-4683}, pmid = {40025674}, issn = {1520-5851}, mesh = {*Polyvinyl Chloride/chemistry ; Colloids/chemistry ; *Polystyrenes/chemistry ; Silicon Dioxide/chemistry ; Calcium Chloride/chemistry ; Models, Chemical ; Nanoparticles ; }, abstract = {Here, we assessed the heteroaggregation of polystyrene (PS) and poly(vinyl chloride) (PVC) nanoplastics with SiO2 as a model of natural colloids. Homoaggregation and heteroaggregation were evaluated as a function of CaCl2 (0-100 mM) and natural organic matter (NOM) (50 mg L[-1]) at a designated concentration of nanoplastics (200 μg L[-1]). Critical coagulation concentrations (CCC) of nanoplastics were determined in homoaggregation and heteroaggregation experiments with SiO2 and CaCl2. The attachment efficiency (α) was calculated by quantifying the number of nanoplastics in the presence of CaCl2, NOM, and SiO2 using single-particle inductively coupled plasma mass spectrometry (spICP-MS) and pseudo-first-order kinetics. The calculated α was fed into the SimpleBox4Plastics model to predict the fate of nanoplastics across air, water, soil, and sediment compartments. Nanoplastics exhibited high stability against homoaggregation, while significant heteroaggregation with SiO2 occurred at CaCl2 concentrations above 100 mM. The influence of NOM was also evaluated, showing a reduction in heteroaggregation with SiO2 for both nanoplastic types. Sensitivity analysis indicated that the degradation half-life of the tested nanoplastics had a more significant impact on persistence than did α. The results emphasize the environmental stability of nanoplastics, particularly in freshwater and soil compartments, and the critical role of NOM and emission pathways in determining their fate.}, }
@article {pmid40024538, year = {2025}, author = {Sliti, A and Kim, RH and Lee, D and Shin, JH}, title = {Whole genome sequencing and In silico analysis of the safety and probiotic features of Lacticaseibacillus paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules.}, journal = {Microbial pathogenesis}, volume = {202}, number = {}, pages = {107405}, doi = {10.1016/j.micpath.2025.107405}, pmid = {40024538}, issn = {1096-1208}, mesh = {*Probiotics/adverse effects ; *Whole Genome Sequencing ; Genome, Bacterial ; *Fecal Microbiota Transplantation ; Humans ; *Lacticaseibacillus paracasei/genetics/isolation &amp; purification/classification ; Phylogeny ; Computer Simulation ; Virulence Factors/genetics ; Feces/microbiology ; Capsules ; Plasmids/genetics ; Prophages/genetics ; Multigene Family ; Gastrointestinal Microbiome ; Clustered Regularly Interspaced Short Palindromic Repeats ; }, abstract = {Lacticaseibacillus paracasei is widely used as a probiotic supplement and food additive in the medicinal and food industries. However, its application requires careful evaluation of safety traits associated with probiotic pathogenesis, including the transfer of antibiotic-resistance genes, the presence of virulence and pathogenicity factors, and the potential disruptions of the gut microbiome and immune system. In this study, we conducted whole genome sequencing (WGS) of L. paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules and performed genome annotation to assess its probiotic and safety attributes. Our comparative genomic analysis assessed this novel strain's genetic attributes and functional diversity and unraveled its evolutionary relationships with other L. paracasei strains. The assembly yielded three contigs: one corresponding to the chromosome and two corresponding to plasmids. Genome annotation revealed the presence of 2838 DNA-coding sequences (CDS), 78 ribosomal RNAs (rRNAs), 60 transfer RNAs (tRNAs), three non-coding RNAs (ncRNAs), and 126 pseudogenes. The strain lacked antibiotic resistance genes and pathogenicity factors. Two intact prophages, one Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, and three antimicrobial peptide gene clusters were identified, highlighting the genomic stability and antimicrobial potential of the strain. Furthermore, genes linked to probiotic functions, such as mucosal colonization, stress resistance, and biofilm formation, were characterized. The pan-genome analysis identified 3358 orthologous clusters, including 1775 single-copy clusters, across all L. paracasei strains. Notably, L. paracasei FMT2 contained many unique singleton genes, potentially contributing to its distinctive probiotic properties. Our findings confirm the potential of L. paracasei FMT2 for food and therapeutic applications based on its probiotic profile and safety.}, }
@article {pmid40022977, year = {2025}, author = {Noiset, P and Héger, M and Salmon, C and Kwapong, P and Combey, R and Thevan, K and Warrit, N and Rojas-Oropeza, M and Cabirol, N and Zaragoza-Trello, C and Rasmussen, C and Nkoba, K and Vereecken, NJ}, title = {Ecological and evolutionary drivers of stingless bee honey variation at the global scale.}, journal = {The Science of the total environment}, volume = {969}, number = {}, pages = {178945}, doi = {10.1016/j.scitotenv.2025.178945}, pmid = {40022977}, issn = {1879-1026}, mesh = {*Honey/analysis ; Bees ; Animals ; Biological Evolution ; }, abstract = {Stingless bee honey (SBH) is a prime natural product consumed and used for diverse medicinal and traditional purposes by local communities across the (sub-)tropics. Despite its ecological and cultural significance, the drivers of its compositional variation within and among species remain poorly understood, particularly throughout Asia and sub-Saharan Africa. Addressing this issue at the global scale has the potential to inform broader and less explored eco-evolutionary and how variation in SBH across the (sub-)tropics has led human communities to develop diverse and sometimes specific patterns of practices that are now integral to their cultural and economic life. In this study, we aimed to disentangle the roles of evolutionary and environmental drivers of SBH compositional variation using a sampling design that combines honey profiling by H1-NMR spectroscopy with the collection of honeys from honey bees and stingless bees at the global scale. The results show a clear differentiation between the chemical composition and functional diversity of honey bee and stingless bee honeys, mainly due to the production of a range of bioproducts during sugar fermentation. The study of compositional variation of stingless bee honey showed that the role of ecological and evolutionary drivers and their joint effects varied within each tropical region, preventing the identification of a clear continental, phylogenetic or ecological pattern. We provide the first global and comprehensive characterization of SBH composition, a prerequisite for defining and accepting SBH in the different Codex Alimentarius. We also highlight the need for more interdisciplinary and trans-sectoral research adopting a holistic approach to investigate stingless bee honey characteristics.}, }
@article {pmid40022770, year = {2025}, author = {Attiani, V and Smidt, H and van der Wielen, PWJJ}, title = {Impact of environmental and process conditions on the microbial ecology and performance of full-scale slow sand filters in drinking water treatment.}, journal = {Water research}, volume = {277}, number = {}, pages = {123328}, doi = {10.1016/j.watres.2025.123328}, pmid = {40022770}, issn = {1879-2448}, mesh = {*Drinking Water/microbiology ; *Water Purification/methods ; *Filtration/methods ; *Sand/chemistry ; Netherlands ; Water Microbiology ; }, abstract = {Slow sand filters (SSFs) are commonly used for treating drinking water, effectively removing contaminants such as particles, organic matter, and microorganisms. However, the ecological dynamics of prokaryotic communities within SSFs remain poorly understood. This study investigated the top sand layer, the Schmutzdecke (SCM), along with the influent and effluent water of full-scale SSFs at four drinking water treatment plants (DWTPs) in the Netherlands. These plants use SSFs as the final step in their treatment to produce unchlorinated drinking water. Two DWTPs treat surface water after dune infiltration and do not apply advanced oxidation processes prior the SSF. In contrast, the other two DWTPs treat reservoir-stored surface water and incorporate ozonation or UV and activated carbon filtration as part of their treatment train. All SSFs consistently reduced biomass in the effluent compared to the influent, confirming their role in biomass load reduction. Key biological and chemical parameters showed that pretreatment with dune infiltration produced more biologically stable drinking water compared to reservoir storage. Moreover, while SSFs act as polishing filters when treating dune-infiltrated surface water, they significantly alter the prokaryotic community and biological stability of the water when treating reservoir-stored surface water. Prokaryotic communities in the SCM and water samples showed distinct compositions rather than merely the accumulation of microorganisms in the SCM from the influent water, demonstrating that SSF are active ecosystems different from water. The SCM exhibited a higher relative abundance of the genera SWB02, Gemmata, Pedomicrobium, Nitrospira, and mle1-7, while in the water samples the genus Candidatus Omnitrophus was relatively more abundant. Moreover, each DWTP hosts a unique prokaryotic profiles in both the SCM and water samples. Source water, upstream treatment and/or the biological stability of the influent water are identified as potential causes affecting the prokaryotic communities in SSFs that affect the microbial water quality of the effluent water.}, }
@article {pmid40016229, year = {2025}, author = {Chang, J and Costa, OYA and Sun, Y and Wang, J and Tian, L and Shi, S and Wang, E and Ji, L and Wang, C and Pang, Y and Yao, Z and Ye, L and Zhang, J and Chen, H and Cai, Y and Chen, D and Song, Z and Rong, J and Raaijmakers, JM and Tian, C and Kuramae, EE}, title = {Domesticated rice alters the rhizosphere microbiome, reducing nitrogen fixation and increasing nitrous oxide emissions.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2038}, pmid = {40016229}, issn = {2041-1723}, mesh = {*Oryza/microbiology/metabolism/genetics ; *Nitrous Oxide/metabolism ; *Rhizosphere ; *Microbiota/genetics ; *Nitrogen Fixation/genetics ; Soil Microbiology ; Plant Roots/microbiology/metabolism ; Domestication ; Metagenomics ; Soil/chemistry ; Nitrogenase/metabolism/genetics ; Bacteria/genetics/metabolism ; Nitrogen/metabolism ; }, abstract = {Crop domestication has revolutionized food production but increased agriculture's reliance on fertilizers and pesticides. We investigate differences in the rhizosphere microbiome functions of wild and domesticated rice, focusing on nitrogen (N) cycling genes. Shotgun metagenomics and real-time PCR reveal a higher abundance of N-fixing genes in the wild rice rhizosphere microbiomes. Validation through transplanting rhizosphere microbiome suspensions shows the highest nitrogenase activity in soils with wild rice suspensions, regardless of planted rice type. Domesticated rice, however, exhibits an increased number of genes associated with nitrous oxide (N2O) production. Measurements of N2O emissions in soils with wild and domesticated rice are significantly higher in soil with domesticated rice compared to wild rice. Comparative root metabolomics between wild and domesticated rice further show that wild rice root exudates positively correlate with the frequency and abundance of microbial N-fixing genes, as indicated by metagenomic and qPCR, respectively. To confirm, we add wild and domesticated rice root metabolites to black soil, and qPCR shows that wild rice exudates maximize microbial N-fixing gene abundances and nitrogenase activity. Collectively, these findings suggest that rice domestication negatively impacts N-fixing bacteria and enriches bacteria that produce the greenhouse gas N2O, highlighting the environmental trade-offs associated with crop domestication.}, }
@article {pmid40012773, year = {2025}, author = {Sun, P and Wu, Y and Zhu, P and Wang, J and Yu, X and Guo, W}, title = {Spartina alterniflora invasion significantly alters the assembly and structure of soil bacterial communities in the Yellow River Delta.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1525632}, pmid = {40012773}, issn = {1664-302X}, abstract = {Soil microbial communities are integral to almost all terrestrial biogeochemical cycles, which are essential to coastal wetland functioning. However, how soil bacterial community assembly, composition, and structure respond to native and non-native plant invasions in coastal wetlands remains unclear. In this study of the coastal wetlands of the Yellow River Delta in China, the assembly, community composition, and diversity of soil bacterial communities associated with four wetland plant species (Phragmites australis, Spartina alterniflora, Suaeda salsa, and Tamarix chinensis) and four soil depths (0-10 cm, 10-20 cm, 20-30 cm, and 30-40 cm) were characterized using high-throughput sequencing. Plant species identity, as well as environmental factors, rather than soil depth, was found to play predominant roles in shaping the diversity and structure of wetland soil bacterial communities. S. alterniflora invasion altered bacterial community structure and increased bacterial diversity. Phragmites australis-associated bacterial communities were enriched with sulfate-reducing bacteria such as Desulfurivibrio and Desulfuromonas. In comparison, S. alterniflora-associated bacterial communities were enriched with both sulfate-reducing bacteria (SEEP-SRB1) and sulfate-oxidizing bacteria (Sulfurimonas), which maintained a dynamic balance in the local sulfur-cycle, and thereby enhanced S. alterniflora growth. In addition, stochastic processes dominated the assembly of soil bacterial communities associated with all four plant species, but were most important for the S. alterniflora community. The S. alterniflora-associated bacterial community also showed stronger interactions and more extensive connections among bacterial taxa; a co-occurrence network for this community had the greatest average clustering coefficient, average degree, modularity, and number of links and nodes, but the lowest average path length. Altogether, individual plant species had distinct effects on soil bacterial community assembly and structure, with the invasive species having the strongest impact. These results provide insights into microbial ecology and inform management strategies for coastal wetland restoration.}, }
@article {pmid40008244, year = {2025}, author = {Xu, LL and McIlroy, SE and Ni, Y and Guibert, I and Chen, J and Rocha, U and Baker, DM and Panagiotou, G}, title = {Chemical pollution drives taxonomic and functional shifts in marine sediment microbiome, influencing benthic metazoans.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycae141}, pmid = {40008244}, issn = {2730-6151}, abstract = {Microbial communities in marine sediments contribute significantly to the overall health and resiliency of marine ecosystems. However, increased human disturbance undermines biodiversity and, hence, natural functionality provided by marine sediments. Here, through a deep shotgun metagenomics sequencing of the sediment microbiome and COI metabarcoding of benthic metazoans, we demonstrate that >50% of the microorganisms' and metazoan's taxonomic variation can be explained by specific chemical pollution indices. Interestingly, there was a significant correlation between the similarity in microbiome communities' taxonomical and functional attributes and the similarity of benthic metazoans community composition. Furthermore, mediation analysis was conducted to evaluate the microbiome-mediated indirect effect, suggesting that microbial species and functions accounted for 36% and 26%, respectively, of the total effect of pollution on the benthic metazoans. Our study introduces a multi-level perspective for future studies in urbanized coastal areas to explore marine ecosystems, revealing the impact of pollution stress on microbiome communities and their critical biogeochemical functions, which in turn may influence macrofaunal composition.}, }
@article {pmid40005728, year = {2025}, author = {Yi, S and Wu, H and Lin, Y and Cha, X and Shang, Y}, title = {Antibiotic Resistance Profiles and Genomic Analysis of Endophytic Bacteria Isolates from Wild Edible Fungi in Yunnan.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, pmid = {40005728}, issn = {2076-2607}, support = {R21 AG050009/AG/NIA NIH HHS/United States ; 32260624//the National Natural Science Foundation of China/ ; 202202AG050009//Yunnan Major Scientific and Technological Projects/ ; }, abstract = {The use of antibiotics has led to the emergence of antibiotic resistance, posing significant challenges in the prevention, control, and treatment of microbial diseases, while threatening public health, the environment, and food safety. In this study, the antibiotic resistance phenotypes and genotypes of 56 endophytic bacteria isolates from three species of wild edible fungi in Yunnan were analyzed using the Kirby-Bauer disk diffusion method and PCR amplification. The results revealed that all isolates were sensitive to ofloxacin, but resistance was observed against 17 other antibiotics. Specifically, 55, 53, and 51 isolates exhibited resistance to amoxicillin, penicillin, and vancomycin, respectively. Antibiotic resistance gene (ARG) detection indicated that the sulfonamide sul1 gene had the highest detection rate (53.57%). Excluding the ARG that was not detected, the lowest detection rates were the sulfonamide sul2 and sul3 genes, both at 1.79%. Among six tetracycline resistance genes, only tetK and tetM were detected. For β-lactam antibiotics, blaTEM, blaVIM, and blaSHV genes were present, while blaOXA was absent. In aminoglycoside resistance genes, aadB was not detected, while detection rates for aac(3')-IIa, acrB, and aadA1 were 3.57%, 1.79%, and 37.5%, respectively. The chloramphenicol Cat gene was detected at a rate of 14.29%, whereas floR was absent. For polypeptide resistance, VanC was detected at 3.57%, with EmgrB not detected. All three quinolone genes were detected, with detection rates of 8.92% for GyrA, 39.29% for GyrB, and 37.5% for ParC. Through phylogenetic analysis, 12 isolates that are closely related to ten common foodborne pathogenic bacteria were further selected for whole-genome sequencing and assembly. Gene annotations revealed that each isolate contained more than 15 ARGs and over 30 virulence factors. Notably, the detection rate of antibiotic resistance phenotypes was higher than that of genotypes, highlighting the importance of studying phenotypic antibiotic resistance that lacks identifiable ARGs. This study enriches the research on endophytes in wild edible fungi and provides new data for microbial ecology and antibiotic resistance research. It also offers critical insights for monitoring microbial antibiotic resistance in wild edible fungi and potentially other food sources, contributing to more effective strategies for ecological protection, sustainable agricultural development, and public health security.}, }
@article {pmid40005607, year = {2025}, author = {Li, S and Zhuang, W and Feng, X and Warren, A and Gong, J}, title = {Morphology and Molecular Phylogeny of Four Anaerobic Ciliates (Protista, Ciliophora, Armophorea), with Report of a New Species and a Unique Arrangement Pattern of Dikinetids in Family Metopidae.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, pmid = {40005607}, issn = {2076-2607}, support = {41976086, 42276094//National Natural Science Foundation of China/ ; }, abstract = {The diversity of anaerobic ciliates is greatly underestimated owing to the limitation in sampling and cultivation when compared with their aerobic counterparts. In this study, four anaerobic ciliates, viz. Brachonella abnormalis sp. nov., Brachonella contorta (Levander, 1894) Jankowski, 1964, Metopus contortus (Quennerstedt, 1867) Kahl, 1932, and Metopus major Kahl, 1932, were investigated by live observation, protargol staining and 18S rRNA gene sequencing. B. abnormalis sp. nov. can be separated from its congeners by a combination of the following features: bullet-shaped cell with a life size of about 130-190 × 90-120 μm, dikinetids distributed along dorsal dome kineties, highly developed adoral zone comprised of 87-107 polykinetids, making about 450° spiralization around the long axis. The present work demonstrates that two known species, M. contortus and M. major, have a special trait never previously reported, viz. short, regularly arranged preoral dome dikinetids. Species with short, regularly arranged dome dikinetids appear in divergent clades in SSU rRNA gene trees, which may infer that this trait evolved several times. Phylogenetic analyses based on SSU rRNA gene sequence data also support the monophyly of the genus Brachonella and the paraphyly of the order Metopida, respectively.}, }
@article {pmid40005589, year = {2025}, author = {Warkhade, Y and Schaerer, LG and Bigcraft, I and Hazen, TC and Techtmann, SM}, title = {Diversity and Distribution of Hydrocarbon-Degrading Genes in the Cold Seeps from the Mediterranean and Caspian Seas.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, pmid = {40005589}, issn = {2076-2607}, support = {Merck Future Insight Prize//Merck KGaA/ ; }, abstract = {Marine cold seeps are unique ecological niches characterized by the emergence of hydrocarbons, including methane, which fosters diverse microbial communities. This study investigates the diversity and distribution of hydrocarbon-degrading genes and organisms in sediments from the Caspian and Mediterranean Seas, utilizing 16S rRNA and metagenomic sequencing to elucidate microbial community structure and functional potential. Our findings reveal distinct differences in hydrocarbon degrading gene profiles between the two seas, with pathways for aerobic and anaerobic hydrocarbon degradation co-existing in sediments from both basins. Aerobic pathways predominate in the surface sediments of the Mediterranean Sea, while anaerobic pathways are favored in the surface sediments of the anoxic Caspian Sea. Additionally, sediment depths significantly influence microbial diversity, with variations in gene abundance and community composition observed at different depths. Aerobic hydrocarbon-degrading genes decrease in diversity with depth in the Mediterranean Sea, whereas the diversity of aerobic hydrocarbon-degrading genes increases with depth in the Caspian Sea. These results enhance our understanding of microbial ecology in cold seep environments and have implications for bioremediation practices targeting hydrocarbon pollutants in marine ecosystems.}, }
@article {pmid40003826, year = {2025}, author = {Castañeda-Espinosa, A and Duque-Granda, D and Cadavid-Restrepo, G and Murcia, LM and Junca, H and Moreno-Herrera, CX and Vivero-Gómez, RJ}, title = {Study of Bacterial Communities in Water and Different Developmental Stages of Aedes aegypti from Aquatic Breeding Sites in Leticia City, Colombian Amazon Biome.}, journal = {Insects}, volume = {16}, number = {2}, pages = {}, pmid = {40003826}, issn = {2075-4450}, support = {57545//Universidad Nacional de Colombia/ ; }, abstract = {Aedes aegypti is a key vector in the transmission of arboviral diseases in the Colombian Amazon. This study aimed to characterize microbiota composition using DNA extracted from water in artificial breeding sites, immature stages, and adults of Ae. aegypti in Leticia, Amazonas. Additionally, the physicochemical water variables were correlated with the bacterial communities present. Eight artificial breeding sites were identified, with bucket, plant pot, and tire being the most frequent. The breeding sites exhibited similar physicochemical profiles, with significant temperature and salinity differences (p-value < 0.03). The most representative bacterial genera included Ottowia (82%), Xanthobacter (70.59%), and Rhodocyclaceae (92.78%) in breeding site water; Aquabacterium (61.07%), Dechloromonas (82.85%), and Flectobacillus (58.94%) in immature stages; and Elizabethkingia (70.89%) and Cedecea (39.19%) in males and females of Ae. aegypti. Beta diversity analysis revealed distinct clustering between adults and the water and immature communities (p-value < 0.001). Multivariate analysis showed strong correlations among bacterial communities, breeding sites, and physicochemical variables such as tire and drum cover which exhibited high levels of total dissolved solids, conductivity, and salinity associated with Flectobacillus, Leifsonia, Novosphingobium, Ottowia, and Rhodobacter. Bacterial genera such as Mycobacterium, Escherichia, Salmonella, and Clostridium, present in artificial breeding sites, are associated with public health relevance. This study provides insights into bacterial community dynamics across Ae. aegypti's life cycle and underscores the importance of water physicochemical and biological characteristics for developing new vector control strategies.}, }
@article {pmid40003751, year = {2025}, author = {Rampanti, G and Cardinali, F and Ferrocino, I and Milanović, V and Garofalo, C and Osimani, A and Aquilanti, L}, title = {Deciphering the Microbiota of Edible Insects Sold by Street Vendors in Thailand Using Metataxonomic Analysis.}, journal = {Insects}, volume = {16}, number = {2}, pages = {}, pmid = {40003751}, issn = {2075-4450}, abstract = {The aim of the present study was to investigate the microbiota of processed ready-to-eat (fried or boiled) edible insects sold by street vendors at local green markets in Thailand (Bangkok and Koh Samui). To this end, samples of 4 insect species (rhino beetle adults, silkworm pupae, giant waterbugs adults, and black scorpions) were collected and analyzed through viable counting and metataxonomic analysis. Enterobacteriaceae showed counts below 1 log cfu g[-1] in all samples, except for black scorpions, which showed elevated counts reaching up to 4 log cfu g[-1]. Total mesophilic aerobes counts were up to 8 log cfu g[-1] in all the analyzed samples. Counts below 1 log cfu g[-1] were observed for Escherichia coli, Staphylococcus aureus, sulfite-reducing clostridia viable cells and spores, and Bacillus cereus. All the samples showed the absence of Listeria monocytogenes and Salmonella spp. According to metataxonomic analysis, 14 taxa were consistently present across all insect samples, including Dellaglioa algida, Latilactobacillus curvatus, Latilactobacillus sakei, Acetobacteraceae, Apilactobacillus kunkeei, Bombilactobacillus spp., Enterobacteriaceae, Gilliamella spp., Lactobacillus spp., Lactobacillus apis, Streptococcus thermophilus, Lacticaseibacillus rhamnosus, Lactiplantibacillus plantarum, and Weissella spp. Minority taxa included Alcaligenes spp., Brochothrix thermosphacta, Psychrobacter spp., Staphylococcus saprophyticus, Lactobacillus melliventris, Pediococcus spp., Levilactobacillus brevis, and Snodgrassella alvi.}, }
@article {pmid39998093, year = {2025}, author = {Varini, C and Manganelli, M and Scardala, S and Antonelli, P and Losasso, C and Testai, E}, title = {An Update of Tetrodotoxins Toxicity and Risk Assessment Associated to Contaminated Seafood Consumption in Europe: A Systematic Review.}, journal = {Toxins}, volume = {17}, number = {2}, pages = {}, pmid = {39998093}, issn = {2072-6651}, support = {project n. RF-2021-12373885//Ministry of Health of Italy/ ; }, mesh = {Risk Assessment ; Europe ; *Food Contamination/analysis ; *Seafood/analysis ; Humans ; Animals ; *Tetrodotoxin/toxicity/analysis ; }, abstract = {Following the occurrence of Tetrodotoxins (TTXs) in Europe-a group of neurotoxins identified in Asia, where fatalities occurred after the ingestion of contaminated pufferfish-the EFSA proposed a limit of 44 µg of TTX/kg of shellfish meat in mollusks in 2017, to protect heavy consumers. The limit was based on an acute reference dose (ARfD) derived from the few available data on TTX toxicity. TTX is expected to increase with sea-surface warming; indeed, it has been found in spring/summer in mollusks in Europe, with concentrations often exceeding this limit. Due to the numerous uncertainties of the EFSA's ARfD, we conducted a systematic review to provide an update on TTX toxicity. Out of 12,741 articles retrieved from PubMed, Science Direct, and Scopus since 2017, only 17 were eligible for data extraction. Our results show that they are not sufficient to modify the EFSA's conclusions. Furthermore, our analysis of occurrence data in European seafood, to assess the current risk of exposure to TTX, reveals several gaps, such as different LODs/LOQs and seasonal monitoring not allowing comparisons between areas and too few analyzed sites. However, the presence of positive samples exceeding the EFSA limit indicates a potential risk even for general consumers, highlighting the urgency to address these knowledge gaps.}, }
@article {pmid39996333, year = {2025}, author = {Medeiros, W and Kralova, S and Oliveira, V and Ziemert, N and Sehnal, L}, title = {Antarctic bacterial natural products: from genomic insights to drug discovery.}, journal = {Natural product reports}, volume = {42}, number = {5}, pages = {774-787}, doi = {10.1039/d4np00045e}, pmid = {39996333}, issn = {1460-4752}, mesh = {*Biological Products/chemistry/pharmacology/metabolism ; Antarctic Regions ; *Drug Discovery ; *Bacteria/genetics/chemistry/metabolism ; Genomics ; Molecular Structure ; }, abstract = {Covering: up to the end of 2024Microbial life dominates the extreme continent Antarctica, playing a pivotal role in ecosystem functioning and serving as a reservoir of specialized metabolites known as natural products (NPs). NPs not only contribute to microbial adaptation to harsh conditions but also modulate microbial community structure. Long-term isolation and environmental pressures have shaped the genomes of Antarctic bacteria, suggesting that they also encode unique NPs. Since NPs are also an important source of drugs, we argue that investigating Antarctic bacterial NPs is essential not only for understanding their ecological role and evolution, but also for discovering new chemical structures, biosynthetic mechanisms, and potential new drugs. Yet, despite advances in omics technologies and increased scientific activities in Antarctica, relatively few new bacterial NPs have been discovered. The lack of systematic research activities focused on the exploration of Antarctic bacteria and their NPs constitutes a big problem considering the climate change issue, to which ecosystems in polar regions are the most sensitive areas on the Earth. Here, we highlight the currently available data on Antarctic bacteria, their biosynthetic potential, and the successful NP discoveries, while addressing the challenges in NP research and advocating for systematic, collaborative efforts aligned with the Antarctic Treaty System and the Antarctic Conservation Biogeographic Regions.}, }
@article {pmid39992142, year = {2025}, author = {Sun, L and Wang, Q and Huang, J and Wang, H and Yu, Z}, title = {Disrupting the balance: how acne duration impacts skin microbiota assembly processes.}, journal = {Microbiology spectrum}, volume = {13}, number = {4}, pages = {e0260324}, pmid = {39992142}, issn = {2165-0497}, support = {32000054, 32170071//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Humans ; *Acne Vulgaris/microbiology ; *Skin/microbiology ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Female ; Male ; Adult ; Young Adult ; Skin Microbiome ; }, abstract = {Growing interest in the impact of microbial balance on health has driven studies on the ecological processes shaping the skin microbiota. Skin diseases, which alter the skin's local environment, can disrupt the microbial structure and interact with the disease itself. However, research on microbial assembly in diseased skin remains limited. In this study, we applied ecological models to characterize the processes shaping the skin microbiota in acne patients, considering the impact of disease duration on both skin pores and surfaces using bacterial amplicon sequencing. Our results revealed a significant shift in microbial diversity on the skin surface of patients with long-term acne. Further microbial community analyses showed a transition in ecological processes from healthy to diseased skin. Microbial communities on the skin surfaces of healthy controls and individuals with short-duration acne were primarily driven by heterogeneous selection, whereas microbial drift dominated the assembly process in the long-duration groups. Using the Sloan neutral model, we classified amplicon sequence variants (ASVs) into high-effect and low-effect groups based on relative abundance and sample occurrence. High-effect ASVs, likely exerting a greater ecological influence, were predominantly represented by Cutibacterium across all acne-affected skin groups, while Staphylococcus became enriched among high-effect ASVs in patients with long-term acne. Functional profiling further demonstrated that high-effect ASVs were significantly enriched in motility-related pathways. Additionally, we observed a reduction in microbial network complexity on skin surfaces as disease duration increased. Overall, the ecological dynamics of skin microbial communities may offer valuable insights into the mechanisms underlying disease onset and persistence.IMPORTANCEThe skin microbiota plays a critical role in acne development, yet the processes governing microbial assembly during acne progression remain poorly understood. Previous studies predominantly focused on factors such as acne severity, location, and duration in relation to skin microbial structure, with little attention given to the ecological mechanisms shaping the communities. In this study, we applied ecological models to investigate the processes influencing microbial assembly of skin microbiota in acne patients with varying disease durations and examined functions of ecologically important non-neutral amplicon sequence variants (ASVs). Our findings reveal a transition in ecological processes from deterministic to neutral processes as acne duration increased, with non-neutral ASVs potentially contributing to acne pathogenicity and persistence. These insights contribute to a deeper understanding of the ecological dynamics underlying acne and indicate that targeting these non-neutral ASVs or their associated functions may serve as the basis for future therapeutic strategies.}, }
@article {pmid39992122, year = {2025}, author = {Li, X and Wang, H and Zang, Y and Xue, S and Xin, J and Liu, L and Tang, X and Chen, J}, title = {Exploring the structure and assembly of seagrass microbial communities in rhizosphere and phyllosphere.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {3}, pages = {e0243724}, pmid = {39992122}, issn = {1098-5336}, support = {42176154,42206117//MOST | National Natural Science Foundation of China (NSFC)/ ; U1806213//MOST | NSFC | National Natural Science Foundation of China-Shandong Joint Fund (-)/ ; 2019YFD0901204//MOST | National Key Research and Development Program of China (NKPs)/ ; ZR2024QD017//| Natural Science Foundation of Shandong Province ()/ ; }, mesh = {*Rhizosphere ; *Zosteraceae/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Plant Leaves/microbiology ; *Soil Microbiology ; Ecosystem ; }, abstract = {Microbial community assembly and interactions are pivotal research areas within microbial ecology, yet relevant studies in seagrass rhizospheres and phyllosphere remain relatively scarce. In this study, we utilized high-throughput sequencing technology to investigate the microbial communities in different periods and microhabitats (rhizosphere and phyllosphere) of two seagrass species (Zostera marina and Phyllospadix iwatensis). Our findings suggest that microhabitats have a more pronounced impact on the composition of seagrass-associated microbial communities compared to periods and species. Further investigations reveal that the phyllosphere microbial community exhibits a more intricate co-occurrence network and interactions than the rhizosphere microbial community. Keystone taxa show distinct functional roles in different microhabitats of seagrasses. Additionally, we observed that differences in seagrass microhabitats influence community assembly, with the rhizosphere microbial community being more influenced by deterministic processes (heterogeneous selection) compared to the phyllosphere. These findings contribute to our understanding of the intricate interactions between seagrasses and their associated microbial communities, providing valuable insights into their distribution patterns and microhabitat preferences.IMPORTANCEStudying the community structure and assembly of different microhabitats in seagrass beds contributes to revealing the complexity and dynamic processes of seagrass ecosystems. In the rhizosphere microhabitat of seagrasses, microbial communities may assist in disease resistance or enhance nutrient uptake efficiency in seagrasses. On the other hand, in the microhabitat on the surface of seagrass blades, microorganisms may be closely associated with the physiological functions and nutrient cycling of seagrass blades. Therefore, understanding the structure and assembly mechanisms of rhizosphere and phyllosphere microbial communities is crucial for exploring the interactions between seagrass and microbial communities, as well as for enhancing our comprehension of the stability and resilience of seagrass bed ecosystems.}, }
@article {pmid39991271, year = {2025}, author = {Morales, SE and Tobias-Hünefeldt, SP and Armstrong, E and Pearman, WS and Bogdanov, K}, title = {Marine phytoplankton impose strong selective pressures on in vitro microbiome assembly, but drift is the dominant process.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf001}, pmid = {39991271}, issn = {2730-6151}, abstract = {Phytoplankton are known ecosystem engineers that modulate ocean community assembly processes, but the universality and extent of their microbiome control remains unclear. We used in vitro incubations and 16S ribosomal RNA gene amplicon sequencing to test the influence of Southern and South Pacific oceans dominant phytoplankton on assembly processes and community successions in response to phytoplankton blooms. Phytoplankton grown with reduced-diversity cultures or supplemented with exogenously added microbiomes showed reduced diversity, suggesting environmental filtering. Community profiles were distinct under all culture conditions, further confirming strong selection for specific microbiomes based on phytoplankton. Analysis of core, abundant, and rare organisms in each culture condition showed a conserved response in which core organisms were enriched under conditions of exogenously added phytoplankton. Progression through phytoplankton growth phases selected first for rare and abundant organisms, with increased selection for core members during the exponential phase and relaxing of selection during the death phase, as seen throughout incubations for microbiome-only controls. Surprisingly, selection process quantification identified drift as the dominant process across all conditions and growth phases, with homogenous selection and dispersal limitation accounting for the remainder. Altogether, using Southern Ocean-derived model organisms we confirmed the role phytoplankton play in community assembly but also demonstrated that stochastic processes still predominately drive community selection.}, }
@article {pmid39988434, year = {2025}, author = {Howells, G and Sezmis, AL and Blake, C and McDonald, MJ}, title = {Co-Existence Slows Diversification in Experimental Populations of E. coli and P. fluorescens.}, journal = {Environmental microbiology}, volume = {27}, number = {2}, pages = {e70061}, pmid = {39988434}, issn = {1462-2920}, support = {APP1186140//National Health and Medical Research Council/ ; DP220103548//Australian Research Council/ ; }, mesh = {*Pseudomonas fluorescens/genetics/growth &amp; development/physiology ; *Escherichia coli/genetics/growth &amp; development/physiology ; Coculture Techniques ; Adaptation, Physiological ; Genome, Bacterial ; Whole Genome Sequencing ; }, abstract = {Microbes grown in heterogeneous laboratory environments can rapidly diversify into multiple, coexisting variants. While the genetic and evolutionary mechanisms of laboratory adaptive radiations are well studied, how the presence of other species alters the outcomes of diversification is less well understood. To test the effect of co-culture growth on the Pseudomonas fluorescens SBW25 adaptive radiation, Escherichia coli and P. fluorescens were cultured in monoculture and co-culture for 8 weeks. In P. fluorescens monoculture, Wrinkly and Smooth Spreader types rapidly evolved and were maintained over 8 weeks, while E. coli monocultures evolved two colony types, a big and a small colony variant. In contrast, we found that in co-culture, E. coli did not evolve small colony variants. Whole genome sequencing revealed the genetic basis of possible co-culture specific adaptations in both E. coli and P. fluorescens. Altogether, our data support that the presence of multiple species changed the outcome of adaptive radiation.}, }
@article {pmid39987915, year = {2025}, author = {De Luca, G and Barakat, M and Verméglio, A and Achouak, W and Heulin, T}, title = {The Bacterial Genus Ramlibacter: Betaproteobacteria Capable of Surviving in Oligotrophic Environments Thanks to Several Shared Genetic Adaptation Traits.}, journal = {Environmental microbiology}, volume = {27}, number = {2}, pages = {e70059}, pmid = {39987915}, issn = {1462-2920}, mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Adaptation, Physiological/genetics ; Genome, Bacterial ; Soil Microbiology ; *Burkholderiaceae/genetics/physiology/classification ; }, abstract = {Ramlibacter tataouinensis, the type species of the genus Ramlibacter, is renowned for its ability to thrive in hot, arid and nutrient-poor desert soils. To investigate whether its adaptive properties are shared across all 20 currently described Ramlibacter species found in diverse terrestrial and aquatic habitats worldwide, we conducted a comprehensive analysis of 16S rRNA sequences and genomic information available from the literature. Our study encompassed approximately 40 deposited genomes, allowing us to propose a genomic phylogeny that aligns with the 16S rRNA phylogeny. Our findings reveal several conserved features across the genus Ramlibacter. This includes the presence of light sensors, environmental sensing networks, organic carbon and phosphate acquisition systems and the ability to store carbon and energy in the form of polyhydroxyalkanoate or polyphosphate granules. These shared traits rationalise the widespread distribution of Ramlibacter in oligotrophic terrestrial and aquatic environments. They also explain the genus' ability to withstand desiccation, endure extended periods of starvation, and survive in nutrient-depleted conditions. Notably, certain adaptive features are further enhanced in several species by their pleiomorphism and ability to form cysts. Overall, our study not only highlights the ecological adaptations of Ramlibacter species but also extends our understanding of microbial ecology in oligotrophic environments.}, }
@article {pmid39987257, year = {2025}, author = {Zhang, X and Ta, N and Yi, S and Xiong, H}, title = {Intolerance of uncertainty and mental health in patients with IBD: the mediating role of maladaptive coping.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {6464}, pmid = {39987257}, issn = {2045-2322}, mesh = {Humans ; *Adaptation, Psychological ; Female ; Male ; *Inflammatory Bowel Diseases/psychology ; Uncertainty ; Adult ; *Mental Health ; Middle Aged ; Anxiety/psychology ; Surveys and Questionnaires ; Depression/psychology ; Young Adult ; }, abstract = {The aim of this study was to investigate the relationship between intolerance of uncertainty (IU) and mental health in patients with Inflammatory Bowel Disease (IBD), and to explore the mediating role of coping styles. A questionnaire was administered to adult patients with IBD, which included general demographic information, the Intolerance of Uncertainty Scale, the Generalized Anxiety Disorder-7, and the Patient Health Questionnaire-9. The study ultimately included validated questionnaires from 163 IBD patients. Intolerance of uncertainty was significantly and positively correlated with anxiety (r = 0.738, p < 0.01) and depression (r = 0.683, p < 0.01). The mediating effect of adaptive coping style was not significant. The maladaptive coping style partially mediated the relationship between IU and anxiety, as well as between IU and depression, with the mediating effect size of 25.5% and 34.2%, respectively. Our findings emphasize the impact of the inability to tolerate uncertainty on the mental health of patients with IBD. It suggests that interventions can be implemented to enhance IBD patients' tolerance of uncertainty and to modify their maladaptive coping styles to promote mental health. This offers a valuable framework for psychological interventions for IBD patients.}, }
@article {pmid39985718, year = {2025}, author = {Gufwan, LA and Peng, L and Gufwan, NM and Lan, S and Wu, L}, title = {Enhancing Soil Health Through Biocrusts: A Microbial Ecosystem Approach for Degradation Control and Restoration.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {8}, pmid = {39985718}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Ecosystem ; Fungi/metabolism ; *Environmental Restoration and Remediation/methods ; Biodiversity ; Lichens ; Cyanobacteria ; Microbiota ; Bryophyta ; Biodegradation, Environmental ; }, abstract = {Escalating global concerns about soil degradation, driven by erosion, salinization, compaction, pollution, and organic matter loss, highlights the critical need for sustainable remediation. Biocrusts-complex communities of cyanobacteria, algae, lichens, bryophytes, and fungi-play a pivotal role in soil stabilization, erosion prevention, and nutrient cycling. This study presents recent advancements in biocrust application for soil management and restoration, focusing on artificial biocrusts as a nature-based solution biotechnology. It emphasizes their effectiveness in enhancing soil quality, biodiversity, and ecosystem functionality. Researchers are leveraging these microbial communities to develop strategies that improve soil health and rehabilitate degraded landscapes. The review concludes that biocrusts are a viable strategy for boosting soil resilience and enhancing soil health against environmental stressors. It recommends future research on their long-term ecological impacts and methods to enhance their functionality.}, }
@article {pmid39978646, year = {2025}, author = {Kij, A and Kieronska-Rudek, A and Bar, A and Czyzynska-Cichon, I and Strus, M and Kozien, L and Wiecek, G and Zeber-Lubecka, N and Kulecka, M and Kwiatkowski, G and Przyborowski, K and Mohaissen, T and Sternak, M and Buczek, E and Zakrzewska, A and Proniewski, B and Kus, K and Franczyk-Zarow, M and Kostogrys, RB and Pieterman, EJ and Princen, HMG and Chlopicki, S}, title = {Low phylloquinone intake deteriorates endothelial function in normolipidemic and dyslipidaemic mice.}, journal = {The Journal of nutritional biochemistry}, volume = {140}, number = {}, pages = {109867}, doi = {10.1016/j.jnutbio.2025.109867}, pmid = {39978646}, issn = {1873-4847}, mesh = {Animals ; Male ; Mice, Inbred C57BL ; *Endothelium, Vascular/physiopathology/drug effects/metabolism ; *Vitamin K 1/administration &amp; dosage/blood ; *Dyslipidemias/physiopathology/metabolism ; Mice ; Vitamin K 2/analogs &amp; derivatives/metabolism ; Liver/metabolism ; Vasodilation/drug effects ; Aorta/metabolism ; Gastrointestinal Microbiome ; Dietary Supplements ; }, abstract = {While the plasma phylloquinone (PK) concentration is inversely correlated with cardiovascular risk, the involvement of PK in regulating endothelial function has not been directly investigated. Therefore, in this study we assessed the effects of short-term treatment with PK-deficient diets (5-10 weeks) on endothelial function in normolipidemic 14-week-old male C57BL/6JCmd mice and age-matched dyslipidaemic male E3L.CETP mice. Our results show that in normolipidemic mice dietary PK deficiency was associated with a marked reduction of PK levels in the plasma and liver (liquid chromatography-mass spectrometry measurements) and with impaired endothelium-dependent vasodilation assessed in vivo by magnetic resonance imaging (MRI). Dietary PK deficiency-induced endothelial dysfunction was fully reversed by PK supplementation. In dyslipidaemic E3L.CETP mice, dietary PK deficiency exacerbated preexisting endothelial dysfunction. Furthermore, dietary PK deficiency decreased menaquinone-4 (MK-4) levels in the aorta but did not affect blood coagulation (calibrated automated thrombography), microbiota composition (culturing and next-generation sequencing), and gut menaquinone production. In conclusion, our study demonstrated for the first time that sufficient dietary PK intake supports endothelial function in normolipidemic and dyslipidaemic mice indicating nutritional significance of dietary PK in the maintenance of endothelial function in humans.}, }
@article {pmid39976768, year = {2025}, author = {Kauserud, H and Martin-Sanchez, PM and Estensmo, EL and Botnen, S and Morgado, L and Maurice, S and Høiland, K and Skrede, I}, title = {Yeasts Prefer Daycares and Molds Prefer Private Homes.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {7}, pmid = {39976768}, issn = {1432-184X}, support = {741332//Horizon 2020/ ; PID2021-123184OA-I00//MICIN/AEI, Spain/ ; }, mesh = {*Fungi/classification/isolation &amp; purification/genetics ; *Yeasts/isolation &amp; purification/classification/genetics ; Humans ; Dust/analysis ; *Air Pollution, Indoor/analysis ; *Child Day Care Centers ; *Mycobiome ; Norway ; *Air Microbiology ; *Housing ; DNA, Fungal/genetics ; Child ; Child, Preschool ; }, abstract = {Worldwide, people spend most of their time indoors; in their homes, workplaces, schools, and daycares. Indoor fungi can cause negative health effects due to the production of toxins or volatiles that trigger the immune system of the occupants. To what degree indoor fungi (mycobiomes) differ between buildings with different usage is poorly known. Here, we compare the indoor mycobiomes in 123 children's daycare centers and 214 private homes throughout Norway, as revealed by metabarcoding of DNA extracted from dust samples collected by community scientists. Although the fungal richness per se was similar in dust samples from daycares and homes, the fungal community composition differed. Yeast fungi, distributed mainly across the orders Saccharomycetales, Filobasidiales, and Tremellales, were proportionally more abundant in the daycares, while filamentous fungi, including spore-producing molds such as Aspergillus, Penicillum, and Cladosporium, were relatively more abundant in homes. Number of occupants, which is considerably higher in daycares, correlated significantly with the fungal community shift. We hypothesize that the density of occupants and their age distribution drive the systematic difference of yeasts and filamentous fungi in the two building types.}, }
@article {pmid39972634, year = {2025}, author = {de Sousa, T and Silva, C and Igrejas, G and Hébraud, M and Poeta, P}, title = {The Interactive Dynamics of Pseudomonas aeruginosa in Global Ecology.}, journal = {Journal of basic microbiology}, volume = {65}, number = {4}, pages = {e70004}, doi = {10.1002/jobm.70004}, pmid = {39972634}, issn = {1521-4028}, support = {//This work was supported by grant 2020.05332.BD, and the projects UI/00772 and LA/P/0059/2020 funded by the Portuguese Foundation for Science and Technology (FCT)./ ; }, mesh = {*Pseudomonas aeruginosa/genetics/drug effects/physiology ; Humans ; Ecosystem ; *Pseudomonas Infections/microbiology ; Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Biodiversity ; Ecology ; }, abstract = {Pseudomonas aeruginosa is an opportunistic bacterium widely distributed in both natural and urban environments, playing a crucial role in global microbial ecology. This article reviews the interactive dynamics of P. aeruginosa across different ecosystems, highlighting its capacity for adaptation and resistance in response to environmental and therapeutic pressures. We analyze the mechanisms of antibiotic resistance, including the presence of resistance genes and efflux systems, which contribute to its persistence in both clinical and nonclinical settings. The interconnection between human, animal, and environmental health, within the context of the One Health concept, is discussed, emphasizing the importance of monitoring and sustainable management practices to mitigate the spread of resistance. Through a holistic approach, this work offers insights into the influence of P. aeruginosa on public health and biodiversity.}, }
@article {pmid39971349, year = {2025}, author = {Russo, CJ and Husain, K and Murugan, A}, title = {Soft Modes as a Predictive Framework for Low-Dimensional Biological Systems Across Scales.}, journal = {Annual review of biophysics}, volume = {54}, number = {1}, pages = {401-426}, pmid = {39971349}, issn = {1936-1238}, support = {R35 GM151211/GM/NIGMS NIH HHS/United States ; }, mesh = {*Models, Biological ; Animals ; Humans ; }, abstract = {All biological systems are subject to perturbations arising from thermal fluctuations, external environments, or mutations. Yet, while biological systems consist of thousands of interacting components, recent high-throughput experiments have shown that their response to perturbations is surprisingly low dimensional: confined to only a few stereotyped changes out of the many possible. In this review, we explore a unifying dynamical systems framework-soft modes-to explain and analyze low dimensionality in biology, from molecules to ecosystems. We argue that this soft mode framework makes nontrivial predictions that generalize classic ideas from developmental biology to disparate systems, namely phenocopying, dual buffering, and global epistasis. While some of these predictions have been borne out in experiments, we discuss how soft modes allow for a surprisingly far-reaching and unifying framework in which to analyze data from protein biophysics to microbial ecology.}, }
@article {pmid39970705, year = {2025}, author = {Yuan, K and Xu, H and Li, S and Coker, OO and Liu, W and Wang, L and Zhang, X and Yu, J}, title = {Intraneoplastic fungal dysbiosis is associated with colorectal cancer progression and host gene mutation.}, journal = {EBioMedicine}, volume = {113}, number = {}, pages = {105608}, pmid = {39970705}, issn = {2352-3964}, mesh = {Humans ; *Colorectal Neoplasms/pathology/genetics/microbiology/etiology ; *Dysbiosis/microbiology ; *Mutation ; Disease Progression ; Female ; Male ; Middle Aged ; *Fungi/genetics/classification ; Microsatellite Instability ; Aged ; Adenoma/microbiology/genetics/pathology ; Proto-Oncogene Proteins p21(ras)/genetics ; }, abstract = {BACKGROUND: The relationship between intraneoplastic fungi and colorectal cancer (CRC) progression remains largely unclear. Here, we investigated fungal community changes in adenoma and CRC and their correlation with host genetic mutations.<br><br>METHODS: We obtained 261 tissue biopsies from two geographically distinct cohorts of CRC and adenoma patients, with each individual contributing 2-5 biopsies from lesions and 2 from adjacent normal tissues. 18S ribosomal RNA gene sequencing was used for microbial profiling. Host genetic alterations including KRAS mutations and microsatellite instability (MSI) were detected concurrently.<br><br>FINDINGS: Intra-neoplastic fungal composition significantly differed between CRC and adenoma in two independent cohorts, with enrichment of highly variable fungi (HVF) in CRC. Six HVFs exhibited higher abundances in adenoma and CRC compared to adjacent normal tissues with Malassezia showing a progressive increase from adenoma to CRC. Fungi intratumoral heterogeneity index also increased from adenoma through stages I to IV of CRC. Intra-tumoral fungi-fungi co-abundance analysis indicated stronger positive interactions in CRC than in adenoma, with increasingly robust links among intra-tumoral fungi along adenoma-CRC progression, primarily driven by Malassezia and Aspergillus. Furthermore, fungal heterogeneity was significantly correlated with host genetic mutations, with higher risk indices in CRC tissues harboring KRAS and MSI mutations. Thirteen fungi stratified CRC samples with KRAS mutations, achieving an area under the curve (AUC) of 0.86, while those associated with MSI status showed an AUC of 0.89.<br><br>INTERPRETATION: This study demonstrates that intraneoplastic fungal community alterations occur between adenoma and CRC, with increasing heterogeneity associated with host genetic mutations, emphasizing the role of fungal dysbiosis in CRC.<br><br>FUNDING: This work was supported by RGC Research Impact Fund Hong Kong (R4032-21F); RGC-CRF (C4008-23W); Strategic Seed Funding Collaboration Research Scheme CUHK (3133344); Strategic Impact Enhancement Fund CUHK (3135509); Impact case for RAE CUHK (3134277).}, }
@article {pmid39970561, year = {2025}, author = {Gullì, M and Cangioli, L and Frusciante, S and Graziano, S and Caldara, M and Fiore, A and Klonowski, AM and Maestri, E and Brunori, A and Mengoni, A and Pihlanto, A and Diretto, G and Marmiroli, N and Bevivino, A}, title = {The relevance of biochar and co-applied SynComs on maize quality and sustainability: Evidence from field experiments.}, journal = {The Science of the total environment}, volume = {968}, number = {}, pages = {178872}, doi = {10.1016/j.scitotenv.2025.178872}, pmid = {39970561}, issn = {1879-1026}, mesh = {*Zea mays/growth &amp; development/physiology ; *Charcoal ; Fertilizers ; *Agriculture/methods ; *Soil Microbiology ; Soil/chemistry ; Mycorrhizae ; Microbiota ; }, abstract = {Adoption of sustainable maize cropping practices is urgently needed. Synthetic microbial communities (SynComs) made of plant growth-promoting microorganisms (PGPMs), coupled with biochar from residual biomass, offer an environmentally compatible alternative to inorganic fertilizers and may improve soil fertility. This article extends in a two-year field trial with preliminary results obtained in previous pot experiments, monitoring plant physiology, soil biology and chemistry, and kernel metabolomics. Here, we report the synergistic effect of the co-application of biochar, SynComs, and arbuscular mycorrhizal fungi on the soil microbiome, maize growth, and kernel metabolomic profile. SynComs application did not affect the diversity and richness of soil microbial communities; therefore, it posed a low risk of long-term effects on soil microbial ecology. With SynComs and biochar co-application to the soil, the physiology of maize plants was characterized by higher chlorophyll content, ear weight, and kernel weight. The combination of SynComs and biochar also affected the kernel metabolome, resulting in enriched health-beneficial and anti-stress metabolites. Since the preliminary evidence on the environmental and economic impact of these new associations was more favorable than that of conventional fertilizers, it seems reasonable that their large-scale implementation can eventually favor the transition to more sustainable agriculture.}, }
@article {pmid39970001, year = {2025}, author = {Vo, L and Avgidis, F and Mattingly, HH and Edmonds, K and Burger, I and Balasubramanian, R and Shimizu, TS and Kazmierczak, BI and Emonet, T}, title = {Nongenetic adaptation by collective migration.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {8}, pages = {e2423774122}, pmid = {39970001}, issn = {1091-6490}, support = {R01 GM138533/GM/NIGMS NIH HHS/United States ; R01 GM106189/GM/NIGMS NIH HHS/United States ; R01GM138533//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01GM106189//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; F31 GM149174/GM/NIGMS NIH HHS/United States ; F31GM149174-01//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {*Escherichia coli/physiology/genetics ; *Adaptation, Physiological ; *Chemotaxis/physiology ; Phenotype ; Escherichia coli Proteins/metabolism/genetics ; }, abstract = {Cell populations must adjust their phenotypic composition to adapt to changing environments. One adaptation strategy is to maintain distinct phenotypic subsets within the population and to modulate their relative abundances via gene regulation. Another strategy involves genetic mutations, which can be augmented by stress-response pathways. Here, we studied how a migrating bacterial population regulates its phenotypic distribution to traverse diverse environments. We generated isogenic Escherichia coli populations with varying distributions of swimming behaviors and observed their phenotype distributions during migration in liquid and porous environments. We found that the migrating populations became enriched with high-performing swimming phenotypes in each environment, allowing the populations to adapt without requiring mutations or gene regulation. This adaptation is dynamic and rapid, reversing in a few doubling times when migration ceases. By measuring the chemoreceptor abundance distributions during migration toward different attractants, we demonstrated that adaptation acts on multiple chemotaxis-related traits simultaneously. These measurements are consistent with a general mechanism in which adaptation results from a balance between cell growth generating diversity and collective migration eliminating underperforming phenotypes. Thus, collective migration enables cell populations with continuous, multidimensional phenotypes to flexibly and rapidly adapt their phenotypic composition to diverse environmental conditions.}, }
@article {pmid39963424, year = {2024}, author = {Höner Zu Siederdissen, C and Spangenberg, J and Bisdorf, K and Krautwurst, S and Srivastava, A and Marz, M and Taubert, M}, title = {Nanopore sequencing enables novel detection of deuterium incorporation in DNA.}, journal = {Computational and structural biotechnology journal}, volume = {23}, number = {}, pages = {3584-3594}, pmid = {39963424}, issn = {2001-0370}, abstract = {Identifying active microbes is crucial to understand their role in ecosystem functions. Metabolic labeling with heavy, non-radioactive isotopes, i.e., stable isotope probing (SIP), can track active microbes by detecting heavy isotope incorporation in biomolecules such as DNA. However, the detection of heavy isotope-labeled nucleotides directly during sequencing has, to date, not been achieved. In this study, Oxford nanopore sequencing was utilized to detect heavy isotopes incorporation in DNA molecules. Two isotopes widely used in SIP experiments were employed to label a bacterial isolate: deuterium (D, as D2O) and carbon-13 ([13]C, as glucose). We hypothesize that labeled DNA is distinguishable from unlabeled DNA by changes in the nanopore signal. To verify this distinction, we employed a Bayesian classifier trained on signal distributions of short oligonucleotides (k-mers) from labeled and unlabeled sequencing reads. Our results show a clear distinction between D-labeled and unlabeled reads, based on changes in median and median absolute deviation (MAD) of the nanopore signals for different k-mers. In contrast, [13]C-labeled DNA cannot be distinguished from unlabeled DNA. For D, the model employed correctly predicted more than 85% of the reads. Even when metabolic labeling was conducted with only 30% D2O, 80% of the obtained reads were correctly classified with a 5% false discovery rate. Our work demonstrates the feasibility of direct detection of deuterium incorporation in DNA molecules during Oxford nanopore sequencing. This finding represents a first step in establishing the combined use of nanopore sequencing and SIP for tracking active organisms in microbial ecology.}, }
@article {pmid39962695, year = {2025}, author = {Peng, SW and Zhang, GY and Jiao, YY}, title = {[Microbial Ecology in the Mask-derived Plastisphere in a Water Environment].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {2}, pages = {1193-1202}, doi = {10.13227/j.hjkx.202402057}, pmid = {39962695}, issn = {0250-3301}, mesh = {*Masks/microbiology ; *Microplastics/analysis ; *Water Microbiology ; COVID-19/prevention &amp; control ; *Microbiota ; *Ecosystem ; }, abstract = {As a result of the impact of COVID-19 and other respiratory diseases, the regular use of medical masks and the associated risk that the mask waste enters the water environment have increased, and the mask-derived microplastics are finally posing a potential impact on the aquatic ecological environment. This study explored the microbial diversity, function, assembly mechanism, and ecological network in the plastisphere derived from different layers of masks. The results indicated that the plastisphere in each layer had a unique microbial community, and the community richness gradually increased over time. The functions of microbial communities in the plastisphere, including pathogenicity, phototrophy, compound degradation, and the functions related to the cycling of carbon, nitrogen, and sulfur, changed significantly over time. As to the microbial assembly mechanism in the plastisphere, stochastic processes were more dominant （NST>0.5）, but the influence of deterministic processes gradually grew. The ecological network results indicated that all the plastispheres exhibited a high number of modules and high modularity, and the complexity of the microbial community gradually decreased with colonization time. This study indicates that the mask-derived plastisphere has a unique ecological process, which strengthens our understanding of the ecological effects and microbial colonization processes of the mask-derived plastisphere.}, }
@article {pmid39961999, year = {2025}, author = {Popov, IV and Popov, IV and Chebotareva, IP and Tikhmeneva, IA and Peshkova, DA and Krikunova, AA and Tkacheva, EV and Algburi, AR and Abdulhameed, AM and Jargalsaikhan, A and Ganbold, O and Chikindas, ML and Venema, K and Ermakov, AM}, title = {Differences in gut microbiota composition, diversity, and predicted functional activity between wild and captive zoo Carollia perspicillata in a One Health perspective.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {56}, number = {2}, pages = {1291-1302}, pmid = {39961999}, issn = {1678-4405}, support = {075-10-2021-093//Ministry of Science and Higher Education of the Russian Federation/ ; 23-14-00316//Russian Science Foundation/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Animals, Zoo/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Animals, Wild/microbiology ; *Chiroptera/microbiology ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Russia ; Panama ; }, abstract = {Bats play an important role in global microbial ecology, as they are the host of various microbes. Carollia perspicillata is one of the most popular bat species in zoos. The influence of the captive environment on the gut microbiota of this species is underinvestigated. In this study, we compared gut microbiota composition, diversity, and the potential functional activity of wild and captive C. perspicillata from Panama and Russia (Moscow Zoo), respectively, based on high-throughput 16S rRNA sequencing data. The abundance of 13 bacterial phyla and 35 bacterial genera significantly differed. Environment- and farm animal health-related bacteria (Mannheimia, unclassified Pasteurellaceae, Staphylococcus, and Mycoplasma) dominated wild bats, while bacteria important for public health (Bacteroides, Clostridium sensu stricto 1, and Acinetobacter) were higher in zoo bats. We also observed significantly greater alpha diversity in zoo bats, while there were no significant differences in beta diversity. These findings were accompanied by significant differences in the abundance of 32 functional pathways of gut bacteria, which are probably associated with the different diets of wild and zoo bats. This study shows that the rearing environment significantly affects the gut microbiota of C. perspicillata and highlights that the outcomes of microbiome research of captive bats need to be interpreted with care. Such differences in gut bacterial communities should be the basis for the development of new handling and veterinary care protocols, and also be the justification for further studies of the impact of microbiota of wild and zoo bats on One Health.}, }
@article {pmid39961275, year = {2025}, author = {Wang, A and Bong, CW and Tao, S and Ye, X and Liu, B and Liang, H and Zheng, X and Wong, YY and Loh, KH and Li, H and Chen, K and Lim, SH and Lee, CW}, title = {Evaluation of heavy metal pollution and ecological risk of surface sediments in a tropical mountainous River-Estuary-Shelf Continuum system: A case study of the Selangor River, Malaysia.}, journal = {Marine environmental research}, volume = {205}, number = {}, pages = {107017}, doi = {10.1016/j.marenvres.2025.107017}, pmid = {39961275}, issn = {1879-0291}, mesh = {*Metals, Heavy/analysis ; *Water Pollutants, Chemical/analysis ; *Geologic Sediments/chemistry ; *Rivers/chemistry ; *Environmental Monitoring ; Malaysia ; *Estuaries ; Risk Assessment ; }, abstract = {As human activities continue to increase, the global production of pollutants has increased significantly, with the majority of pollutants being transported to the ocean via rivers, resulting in intensified pollution in estuaries and coastal areas. To maintain a healthy marine ecological environment, it is necessary to consider rivers, estuaries, and coastal seas as integrated systems and implement pollution management based on the concept of land-ocean integration. In this study, heavy metal elements in the surface sediments of Selangor River-Estuary-Coastal Shelf Continuum were collected and analysed to assess their pollution levels and potential ecological risks. The results show that the heavy metal content is high in the downstream and estuarine regions, with a general decreasing trend observed from nearshore to offshore in the coastal shelf area. The heavy metal pollution assessment indicates that the surface sediments of the Selangor River-Estuary-Coastal Shelf continuum were contaminated, with the most severe pollution occurring downstream and within the estuary. The pollution levels gradually decrease after exiting the estuary. The ecological risk associated with heavy metal pollution in rivers, estuaries, and southeastern coastal areas was classified as moderate to serious, whereas other areas exhibited only slight ecological risks. Specifically, As causes serious pollution in the river and estuary, with moderate-to-serious pollution in the coastal shelf area and moderate-to-serious ecological risks, mainly originating from mining within the river basin. Pb causes moderate pollution in the river, estuary, and coastal areas, with slight ecological risks due to mining within the river basin and inputs from nearby rivers, ports, and industrial activities. Other heavy metals cause minor pollution and pose minimal ecological risks.}, }
@article {pmid39961017, year = {2025}, author = {Colman, DR and Templeton, AS and Spear, JR and Boyd, ES}, title = {Microbial ecology of serpentinite-hosted ecosystems.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39961017}, issn = {1751-7370}, support = {80NSSC21K0489//NASA Exobiology and Evolutionary Biology program/ ; }, mesh = {*Ecosystem ; *Microbiota ; Bacteria/genetics/classification ; }, abstract = {Serpentinization, the collective set of geochemical reactions initiated by the hydration of ultramafic rock, has occurred throughout Earth history and is inferred to occur on several planets and moons in our solar system. These reactions generate highly reducing conditions that can drive organic synthesis reactions potentially conducive to the emergence of life, while concomitantly generating fluids that challenge life owing to hyperalkalinity and limited inorganic carbon (and oxidant) availability. Consequently, the serpentinite-hosted biosphere offers insights into the earliest life, the habitable limits for life, and the potential for life on other planets. However, the support of abundant microbial communities by serpentinites was only recognized ~20 years ago with the discovery of deep-sea hydrothermal vents emanating serpentinized fluids. Here, we review the microbial ecology of both marine and continental serpentinization-influenced ecosystems in conjunction with a comparison of publicly available metagenomic sequence data from these communities to provide a global perspective of serpentinite microbial ecology. Synthesis of observations across global systems reveal consistent themes in the diversity, ecology, and functioning of communities. Nevertheless, individual systems exhibit nuances due to local geology, hydrology, and input of oxidized, near-surface/seawater fluids. Further, several new (and old) questions remain including the provenance of carbon to support biomass synthesis, the physical and chemical limits of life in serpentinites, the mode and tempo of in situ evolution, and the extent that modern serpentinites serve as analogs for those on early Earth. These topics are explored from a microbial perspective to outline key knowledge-gaps for future research.}, }
@article {pmid39960660, year = {2025}, author = {Gomi, R and Adachi, F}, title = {Quinolone Resistance Genes qnr, aac(6')-Ib-cr, oqxAB, and qepA in Environmental Escherichia coli: Insights into Their Genetic Contexts from Comparative Genomics.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {6}, pmid = {39960660}, issn = {1432-184X}, support = {JP22K18038//JSPS KAKENHI/ ; 22B006//Kurita Water and Environment Foundation, Japan/ ; 2230113//Sumitomo Foundation, Japan/ ; JPMEERF20235R01//Environment Research and Technology Development Fund/ ; }, mesh = {*Escherichia coli/genetics/drug effects/isolation &amp; purification ; *Quinolones/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli Proteins/genetics ; *Drug Resistance, Bacterial/genetics ; Genome, Bacterial ; Genomics ; Plasmids/genetics ; }, abstract = {Previous studies have reported the occurrence of transferable quinolone resistance determinants in environmental Escherichia coli. However, little is known about their vectors and genetic contexts. To gain insights into these genetic characteristics, we analyzed the complete genomes of 53 environmental E. coli isolates containing one or more transferable quinolone resistance determinants, including 20 sequenced in this study and 33 sourced from RefSeq. The studied genomes carried the following transferable quinolone resistance determinants alone or in combination: aac(6')-Ib-cr, oqxAB, qepA1, qnrA1, qnrB4, qnrB7, qnrB19, qnrD1, qnrS1, and qnrS2, with qnrS1 being predominant. These resistance genes were detected on plasmids of diverse replicon types; however, aac(6')-Ib-cr, qnrS1, and qnrS2 were also detected on the chromosome. The genetic contexts surrounding these genes included not only those found in clinical isolates but also novel contexts, such as qnrD1 embedded within a composite transposon-like structure bounded by Tn3-derived inverted-repeat miniature elements (TIMEs). This study provides deep insights into mobile genetic elements associated with transferable quinolone resistance determinants, highlighting the importance of genomic surveillance of antimicrobial-resistant bacteria in the environment.}, }
@article {pmid39954521, year = {2025}, author = {Hernández-Villamor, D and Li, P and Aydogan, M and Verhelst, M and Van de Wiele, T and Rabaey, K and Prévoteau, A}, title = {Low electrode potentials enhance current generation by Geobacter sulfurreducens biofilms: A high-throughput study.}, journal = {Biosensors &amp; bioelectronics}, volume = {276}, number = {}, pages = {117232}, doi = {10.1016/j.bios.2025.117232}, pmid = {39954521}, issn = {1873-4235}, mesh = {*Geobacter/physiology/growth &amp; development/metabolism ; *Biofilms/growth &amp; development ; Electrodes ; *Bioelectric Energy Sources/microbiology ; Electron Transport ; *Biosensing Techniques ; Oxidation-Reduction ; }, abstract = {The microbial species Geobacter sulfurreducens uses different extracellular electron transfer (EET) pathways depending on the potential of the final electron acceptor, yet a complete understanding of EET mechanisms and the impact of thermodynamically limiting potentials remains elusive. Here, we employ a custom-designed high-throughput system that enables the simultaneous and continuous execution of 128 parallel experiments to investigate the complete spectrum of potentials ([-0.25 to 0] V vs. SHE) impacting the metabolic energy generation in axenic G. sulfurreducens electroactive biofilms (EABs). These were grown for 500 h in three consecutive stages and characterized electrochemically. The EABs grown on electrodes poised below the apparent midpoint potential ([-0.18 to -0.16] V) grew slower than those grown at conventional, non-limiting potential (0 V), developing 50% smaller biofilms and 2.4-fold higher anodic plateau currents on average ([0.1 vs. 0.04] mA cm[-2]). These also exhibited enhanced charge transport coupled to higher average concentrations of charge carriers ([1.6 vs. 0.4] mMe[-]), the latter impacting linearly the anodic plateau current. Low- and high-potential redox pools were discriminated with the former comprising 50%-70% of storable charge. Overall, these findings strongly suggest an overexpression of charge carriers in G. sulfurreducens EABs cultivated at lower potentials and highlight the useful contribution of high-throughput tools for boosting research in electromicrobiology.}, }
@article {pmid39954444, year = {2025}, author = {He, M and Tang, R and Guan, F and Peng, W and Lu, J and Li, K and Zhou, L and Wang, Y and Yuan, Y}, title = {Methanogenic response of paddy soils exposed to zinc oxide nanoparticles and sulfurized products.}, journal = {Journal of hazardous materials}, volume = {489}, number = {}, pages = {137608}, doi = {10.1016/j.jhazmat.2025.137608}, pmid = {39954444}, issn = {1873-3336}, mesh = {*Zinc Oxide/toxicity/chemistry ; *Soil Microbiology ; *Methane/biosynthesis ; Soil/chemistry ; *Soil Pollutants/toxicity ; *Metal Nanoparticles/toxicity ; RNA, Ribosomal, 16S/genetics ; Oryza ; *Sulfides/toxicity ; *Nanoparticles/toxicity ; }, abstract = {The use of zinc oxide nanoparticles (ZnO NPs) in agriculture is expanding, yet their effects on microbial ecology in flooded paddy soils remain unclear. This study examined the influence of ZnO NPs and their sulfide derivatives (S-ZnO NPs) on methane production in paddy soils. Results showed that ZnO NPs at a concentration of 1000 mg/kg significantly inhibited methane production by 28.97 % in an acid soil and by 26.83 % in an alkaline soil. S-ZnO NPs at the same concentration did not significantly affect methane production in the alkaline soil and increased it by 15.33 % in the acid soil. High-throughput sequencing revealed that ZnO NPs significantly altered the microbial community structure, affecting the prevalence of methanogenic organisms like Methanosarcina in the acid soil and Methanobacterium in the alkaline soil. Quantitative PCR analysis showed a reduction in the expression of methanogenic gene (mcrA) and total bacterial 16S rRNA genes with ZnO NPs exposure, but S-ZnO NPs had a lesser impact on these genes. This research highlights the more toxic impact of ZnO NPs compared to S-ZnO NPs on methane production and microbial communities in paddy soils, emphasizing the necessity for careful evaluation of nanoparticles in agricultural use to avoid ecological disturbances.}, }
@article {pmid39954056, year = {2025}, author = {Ren, Z and Gao, H and Martyniuk, N and Ren, H and Xiong, X and Luo, W}, title = {Dual-Domain Primary Succession of Bacteria in Glacier Forefield Streams and Soils of a Maritime and Continental Glacier.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {5}, pmid = {39954056}, issn = {1432-184X}, support = {2023YFF1303700//National Key Research and Development Program of China/ ; }, mesh = {*Soil Microbiology ; *Ice Cover/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Rivers/microbiology ; China ; Ecosystem ; Biodiversity ; Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; Microbiota ; }, abstract = {Glaciers retreat rapidly and create newly exposed terrestrial and aquatic habitats in glacier forefields, where primary succession proceeds synchronously in glacier forefields. Here, we introduced the "Dual-Domain Primary Succession" concept to examine the parallel yet distinct primary succession processes in soil and stream ecosystems within glacier forefields, by focusing on Hailuogou Glacier and Urumqi Glacier No.1 in China. Findings showed that soil bacterial communities exhibited higher α-diversity with a decreasing pattern in Hailuogou Glacier, in contrast to Urumqi Glacier No.1, which displayed lower and unimodally distributed α-diversity along the glacier forefield chronosequence (GFC). A similar pattern emerged in streams, except for an increasing α-diversity trend in Urumqi Glacier No.1 stream along the GFC. Additionally, α-diversity in streams changed more rapidly than in soils for Hailuogou Glacier, but more slowly for Urumqi Glacier No.1. Along GFC, both soil and stream bacterial communities experienced spatial variations, primarily due to species turnover. The succession of community composition was evident at the OTU level, with each module in the co-occurrence network consisting of OTUs enriched at specific successional stages. A substantial number of OTUs shared between paired soil and stream samples showed a decreasing trend along the GFC, while β-diversity increased. The results suggested that bacterial communities have a similar succession pattern but in different pace between soil and stream while having distinct successional trajectories between the studied glaciers. This study highlighted the "Dual-Domain Primary Succession" in glacier forefields, but further studies with more glaciers are necessary to make broader generalizations.}, }
@article {pmid39953673, year = {2025}, author = {Kotsakis, GA and Ganesan, SM}, title = {Microbial Dysbiosis, Titanium Release, and Peri-implantitis.}, journal = {Journal of dental research}, volume = {104}, number = {5}, pages = {473-480}, doi = {10.1177/00220345241307939}, pmid = {39953673}, issn = {1544-0591}, mesh = {Humans ; *Peri-Implantitis/microbiology/immunology/etiology ; *Dysbiosis/microbiology/immunology ; *Titanium/adverse effects ; *Dental Implants/adverse effects/microbiology ; Microbiota ; }, abstract = {The peri-implant mucosal barrier is a unique microenvironment where host-microbiome interactions take place on the surface of an implanted biomaterial. Therefore, peri-implant immunity not only is quintessential to oral health but also contributes to the maintenance of the biomaterial-tissue equilibrium in health. This review delves into the intricate interplay between host factors, biomaterial properties, and the microbiome with a focus on the mechanisms underlying peri-implant dysbiosis. Investigations into this complex milieu have led to the emerging understanding of titanium particles released from the implant as significant exposomes. When biomaterial breakdown occurs, implant degradation products form particles that are released in the peri-implant crevice, exerting profound effects on the local immune surveillance. Comparative analyses with natural dentition highlight the distinct immune responses elicited by titanium particles, thereby implicating them as a key modulator of peri-implant dysbiosis that differentiates peri-implant from periodontal inflammation. Nonetheless, disruptions in the homeostatic balance of host-biomaterial interactions are linked to pathogenic shifts of the peri-implant microbiome that are correlated with titanium particles in humans. Collectively, it is now well established that to elucidate the mechanisms governing peri-implant dysbiosis, this triangle of host-microbiome-biomaterial has to be conjointly investigated. This review highlights findings from studies that have underscored the multifaceted nature of peri-implant dysbiosis, emphasizing the intricate crosstalk between host immunity, biomaterial characteristics, and microbial ecology. These findings suggest that the titanium particle exposome may alter key inflammatory cascades in the peri-implant tissues including toll-like receptor activation and inflammasome and complement signaling, which lead to nonresolving destructive inflammation. The presence of abiotic danger signals in the form of implant degradation products in peri-implant tissues may make antimicrobial monotherapies largely ineffective for managing peri-implantitis. In turn, the future of peri-implantitis therapy seems to lie in the development of targeted host modulatory interventions against titanium-mediated inflammatory pathways.}, }
@article {pmid39952886, year = {2025}, author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW}, title = {Restoring unbalanced rhizosphere: microbiome transplants combatting leaf diseases.}, journal = {Trends in plant science}, volume = {30}, number = {5}, pages = {451-453}, doi = {10.1016/j.tplants.2025.01.011}, pmid = {39952886}, issn = {1878-4372}, mesh = {*Microbiota ; *Plant Diseases/microbiology/prevention &amp; control ; *Plant Leaves/microbiology ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Similar to humans, plants experience microbiome imbalance, which increases their vulnerability to pathogens. In a recent study, Ketehouli et al. applied a soil microbiome transplant (SMT) to restore the microbiome balance, which potentially reduced the severity of leaf diseases. Here, we examine this approach, highlighting its limitation and offering perspectives on its use for controlling leaf diseases in plants.}, }
@article {pmid39952771, year = {2025}, author = {Cantuti Gendre, J and Le Marrec, C and Chaillou, S and Omhover-Fougy, L and Landaud, S and Dugat-Bony, E}, title = {Exploring viral diversity in fermented vegetables through viral metagenomics.}, journal = {Food microbiology}, volume = {128}, number = {}, pages = {104733}, doi = {10.1016/j.fm.2025.104733}, pmid = {39952771}, issn = {1095-9998}, mesh = {*Vegetables/virology/microbiology ; Metagenomics ; Fermentation ; *Fermented Foods/virology/microbiology ; *Bacteriophages/genetics/classification/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Brassica/virology/microbiology ; Microbiota ; *Viruses/classification/genetics/isolation &amp; purification ; Food Microbiology ; Biodiversity ; RNA Viruses/genetics/classification/isolation &amp; purification ; Virome ; DNA Viruses/genetics/classification/isolation &amp; purification ; Daucus carota/virology/microbiology ; }, abstract = {Fermented vegetables are traditionally produced using the endogenous microorganisms present in raw ingredients. While the diversity of bacteria and fungi in fermented vegetables has been relatively well studied, phage communities remain largely unexplored. In this study, we collected twelve samples of fermented cabbage, carrot, and turnip after fermentation and analyzed the microbial and viral communities using shotgun and viral metagenomic approaches. Assessment of the viral diversity also benefited from epifluorescence microscopy to estimate viral load. The viral metagenomics approach targeted dsDNA, ssDNA, and RNA viruses. The microbiome of fermented vegetables was dominated by lactic acid bacteria and varied according to the type of vegetable used as raw material. The analysis of metagenome-assembled-genomes allowed the detection of 22 prophages of which 8 were present as free particles and therefore detected in the metaviromes. The viral community, estimated to range from 5.28 to 7.57 log virus-like particles per gram of fermented vegetables depending on the sample, was mainly composed of dsDNA viruses, although ssDNA and non-bacterial RNA viruses, possibly originating from the phyllosphere, were also detected. The dsDNA viral community, primarily comprising bacteriophages, varied depending on the type of vegetable used for fermentation. The bacterial hosts predicted for these phages mainly belonged to Lactobacillaceae and Enterobacteriaceae families. These results highlighted the complex microbial and viral composition of fermented vegetables, which varied depending on the three types of vegetables used as raw material. Further research is needed to deepen our understanding of the impact of these viruses on the microbial ecology of fermented vegetables and on the quality of the final products.}, }
@article {pmid39952743, year = {2025}, author = {Wu, Y and Ma, F and Tan, S and Niu, A and Chen, Y and Liu, Y and Qiu, W and Wang, G}, title = {The aprD-mutated strain modulates the development of Pseudomonas fragi population but has limited effects on the spoilage profiles of native residents.}, journal = {Food microbiology}, volume = {128}, number = {}, pages = {104708}, doi = {10.1016/j.fm.2024.104708}, pmid = {39952743}, issn = {1095-9998}, mesh = {*Bacterial Proteins/genetics/metabolism ; Chickens/microbiology ; Animals ; *Pseudomonas fragi/genetics/growth &amp; development/metabolism ; *Meat/microbiology ; Biofilms/growth &amp; development ; Mutation ; Food Microbiology ; Pseudomonas/genetics ; }, abstract = {Extracellular enzymes produced by predominant bacteria exert important roles in inducing and accelerating spoilage, with their secretion regulated by specific genes. In Pseudomonas fragi, the aprD gene is a recognized regulator for secreting an alkaline extracellular protease. However, limited studies have focused on this gene in P. fragi population and its impact on meat microbial community structure and function. This study addressed this gap by monitoring the changes in biological properties of P. fragi populations and analyzing the discrepancies in spoilage phenotypes and microbial community structures of chilled chicken among groups differentiated by the initial prevalence of aprD-positive strains. The results showed that aprD-positive strains were disseminated in P. fragi populations, and its prevalence was associated with significant increases in swimming motility and biofilm formation capacities in specific groups. In situ contamination experiments revealed varying spoilage characteristics and community compositions among groups by day 3 of storage. Correlation analysis demonstrated a strong association between spoilage phenotypes and certain bacterial genera, such as Pseudomonadaceae_Pseudomonas and Carnobacterium. However, the microbial community structure and spoilage characteristics of samples from each group were not significantly different on the 5th day of storage. These findings suggest that even a small number of aprD mutants can significantly affect the assembly of the chilled meat microbial community. Nonetheless, the regulatory effect of aprD on spoilage at the strain and population levels of P. fragi is negligible in the context of complex natural microbiota. This work underscores the complex interactions between specific bacterial genes and the broader microbial ecology in refrigerated meat environments, providing deeper insights into the meat spoilage mechanisms.}, }
@article {pmid39951503, year = {2025}, author = {Bauermann, J and Benzi, R and Nelson, DR and Shankar, S and Toschi, F}, title = {Turbulent mixing controls fixation of growing antagonistic populations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {7}, pages = {e2417075122}, pmid = {39951503}, issn = {1091-6490}, mesh = {*Models, Biological ; *Saccharomyces cerevisiae/growth &amp; development/physiology ; Population Dynamics ; *Antibiosis/physiology ; Computer Simulation ; *Bacteria/growth &amp; development ; }, abstract = {Unlike coffee and cream that homogenize when stirred, growing micro-organisms (e.g., bacteria, baker's yeast) can actively kill each other and avoid mixing. How do such antagonistic interactions impact the growth and survival of competing strains, while being spatially advected by turbulent flows? By using numerical simulations of a continuum model, we study the dynamics of two antagonistic strains that are dispersed by incompressible turbulent flows in two spatial dimensions. A key parameter is the ratio of the fluid transport time to that of biological reproduction, which determines the winning organism that ultimately takes over the whole population from an initial heterogeneous state, a process known as fixation. By quantifying the probability and mean time for fixation along with the spatial structure of concentration fluctuations, we demonstrate how turbulence raises the threshold for biological nucleation and antagonism suppresses flow-induced mixing by depleting the population at interfaces. Our work highlights the unusual biological consequences of the interplay of turbulent fluid flows with antagonistic population dynamics, with potential implications for marine microbial ecology and origins of biological chirality.}, }
@article {pmid39950593, year = {2025}, author = {Kiesewetter, KN and Rawstern, AH and Cline, E and Ortiz, GR and Santamaria, F and Coronado-Molina, C and Sklar, FH and Afkhami, ME}, title = {Microbes in reconstructive restoration: Divergence in constructed and natural tree island soil fungi affects tree growth.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {35}, number = {1}, pages = {e70007}, pmid = {39950593}, issn = {1939-5582}, support = {//South Florida Water Management District/ ; 1922521//Division of Environmental Biology/ ; 2030060//Division of Environmental Biology/ ; //National Science Foundation Graduate Research Fellowship Program/ ; //University of Miami Dissertation Year Fellowship/ ; //USDA NIFA Predoctoral Fellowship/ ; }, mesh = {*Soil Microbiology ; *Trees/growth &amp; development/microbiology ; *Fungi/physiology/classification ; *Microbiota ; *Conservation of Natural Resources ; *Environmental Restoration and Remediation ; }, abstract = {As ecosystems face unprecedented change and habitat loss, pursuing comprehensive and resilient habitat restoration will be integral to protecting and maintaining natural areas and the services they provide. Microbiomes offer an important avenue for improving restoration efforts as they are integral to ecosystem health and functioning. Despite microbiomes' importance, unresolved knowledge gaps hinder their inclusion in restoration efforts. Here, we address two critical gaps in understanding microbial roles in restoration-fungal microbiomes' importance in "reconstructive" restoration efforts and how management and restoration decisions interactively impact fungal communities and their cascading effects on trees. We combined field surveys, microbiome sequencing, and greenhouse experiments to determine how reconstructing an iconic landscape feature-tree islands-in the highly imperiled Everglades impacts fungal microbiomes and fungal effects on native tree species compared with their natural counterparts under different proposed hydrological management regimes. Constructed islands used in this research were built from peat soil and limestone collected from deep sloughs and levees nearby the restoration sites in 2003, providing 18 years for microbiome assembly on constructed islands. We found that while fungal microbiomes from natural and constructed tree islands exhibited similar diversity and richness, they differed significantly in community composition. These compositional differences arose mainly from changes to which fungal taxa were present on the islands rather than changes in relative abundances. Surprisingly, ~50% of fungal hub taxa (putative keystone fungi) from natural islands were missing on constructed islands, suggesting that differences in community composition of constructed island could be important for microbiome stability and function. The differences in fungal composition between natural and constructed islands had important consequences for tree growth. Specifically, these compositional differences interacted with hydrological regime (treatments simulating management strategies) to affect woody growth across the four tree species in our experiment. Taken together, our results demonstrate that reconstructing a landscape feature without consideration of microbiomes can result in diverging fungal communities that are likely to interact with management decisions leading to meaningful consequences for foundational primary producers. Our results recommend cooperation between restoration practitioners and ecologists to evaluate opportunities for active management and restoration of microbiomes during future reconstructive restoration.}, }
@article {pmid39945937, year = {2025}, author = {Gharbi, D and Neumann, FH and Staats, J and McDonald, M and Linde, JH and Mmatladi, T and Podile, K and Piketh, S and Burger, R and Garland, RM and Bester, P and Lebre, PH and Ricci, C}, title = {Prevalence of aeroallergen sensitization in a polluted and industrialized area: a pilot study in South Africa's Vaal Triangle.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {3}, pages = {287}, pmid = {39945937}, issn = {1573-2959}, support = {ST-POC-2312-61906//Grand Challenges Canada/ ; ST-POC-2312-61906//South African Medical Research Council/ ; }, mesh = {South Africa/epidemiology ; Humans ; *Allergens/analysis/immunology ; Male ; Adult ; Female ; Pilot Projects ; Adolescent ; Prevalence ; Middle Aged ; Young Adult ; *Air Pollutants/analysis ; *Hypersensitivity/epidemiology ; *Air Pollution/statistics &amp; numerical data ; Pollen ; *Environmental Exposure/statistics &amp; numerical data ; Skin Tests ; }, abstract = {This pioneering study evaluates the prevalence of aeroallergens reactivity among atopic populations living in the Vaal Triangle Airshed Priority Area (VTAPA), South Africa. A total of 138 volunteers (51 males and 87 females), of African, colored, white, and Asian ethnicity, and with a mean (range) age of 22 (18-56) years were participating in the study. The study was conducted on the North-West University (NWU) campus in Vanderbijlpark/VTAPA. The International Study of Asthma and Allergies in Childhood questionnaire was utilized for pre-screening to identify individuals with probable allergic dispositions. Subsequently, skin prick testing was conducted using commercial aeroallergen extracts for all confirmed participants with allergy symptoms. One hundred six participants were clinically diagnosed with pollen and fungal spore allergies. The highest allergy prevalence was attributed to Cynodon dactylon ((L.) Pers) (Bermuda grass) (41.5%), followed by Lolium perenne (L.) (ryegrass), grass mix, and Zea mays (L.) (maize) (31.1%), respectively. Moreover, among the tree allergens, Olea (L.) (olive tree) was the most prevalent allergen (20; 18.8%), followed by Platanus (L.) (plane tree) (18; 16.9%). Among the weeds, 16 (15.1%) participants were allergic to the weed mix (Artemisia (L.) (wormwood), Chenopodium (Link) (goosefoot), Salsola (L.) (saltwort), Plantago (L.) (plantain), and 11 (10.3%) to Ambrosia (L.) (ragweed)). Regarding the fungal spores, Alternaria (Fr.) (9; 8.5%) followed by Cladosporium (Link) (5; 4.7%) had the highest skin sensitivity. In this pilot study, our findings provide insights into the prevalence of allergic responses in the study population-underlining the strong impact of allergens of exotic plants-and contribute to the existing aerobiological data in South Africa.}, }
@article {pmid39945839, year = {2025}, author = {Márquez-Sanz, R and Garrido-Benavent, I and Durán, J and de Los Ríos, A}, title = {The Establishment of a Terrestrial Macroalga Canopy Impacts Microbial Soil Communities in Antarctica.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {4}, pmid = {39945839}, issn = {1432-184X}, support = {PID2019-105469RB-C22//AEI, MICINN/ ; TED2021-130908A-C43//Agencia Estatal de Investigaci&#xf3;n/ ; CNS2023-145367//EU Next Generation PRTR program/ ; PCI2023-143393//EIG EU-CELAC 2022/ ; 20224AT022//Consejo Superior de Investigaciones Cient&#xed;ficas/ ; RYC2020-029331-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; Soil/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; Phylogeny ; *Chlorophyta/growth &amp; development/physiology/classification ; *Microbiota ; Nitrogen/analysis ; Ecosystem ; }, abstract = {Prasiola is a genus of foliose green algae that forms extensive cryptogamic canopies that contribute to the greening of ice-free areas in the Antarctic tundra. To better understand the impact of Prasiola canopy establishment on colonization in these areas, this study compared the taxonomic and functional structures of bacterial and fungal communities in adjacent soils with and without extensive Prasiola colonization. DNA metabarcoding was employed to analyze the microbial community structure in these soils and in the canopy. Additionally, a phylogenetic study of Prasiola samples was conducted to characterize the taxonomic composition of the analyzed canopies, revealing the presence of Prasiola crispa (Lightfoot) Kützing and P. antarctica Kützing. Key soil attributes were assessed to examine the canopy's influence. Higher pH and carbon, nitrogen, and organic matter contents were found in Prasiola-covered soils than in bare soils. Furthermore, Prasiola canopy establishment not only influenced abiotic soil properties but also shaped soil microbial community structure and its functions. For instance, while Actinobacteriota predominated in bacterial communities both within the Prasiola canopy and beneath it, Bacteroidota dominated in the bare soil. Despite significant variability across soil types, fungal communities showed a trend of higher abundances in certain Ascomycetes, such as Helotiales, Hypocreales, or Xylariales, in soils beneath Prasiola compared to bare soils. Regarding functional diversity, covered soils exhibited a statistically significant lower potential for bacterial methanogenesis and autotrophic CO2 fixation compared to bare soils. Finally, lichenized fungi, plant pathogens, and fungal wood saprotrophs tended to be more abundant in covered soils.}, }
@article {pmid39943131, year = {2025}, author = {Frazier, AN and Ferree, L and Belk, AD and Al-Lakhen, K and Cramer, MC and Metcalf, JL}, title = {Stochasticity Highlights the Development of Both the Gastrointestinal and Upper-Respiratory-Tract Microbiomes of Neonatal Dairy Calves in Early Life.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {3}, pages = {}, pmid = {39943131}, issn = {2076-2615}, abstract = {The microbiome of dairy calves undergoes extensive change due to various forces during the first weeks of life. Importantly, diseases such as bovine respiratory disease (BRD) and calf diarrhea can have profound impacts on the early-life microbiome. Therefore, a longitudinal, repeated-measures pilot study was designed to characterize the establishment of nasal and fecal microbiomes of dairy calves, assess the governing forces of microbial assembly, and evaluate how disease states impact these microbial ecologies. Dairy calves (n = 19) were clinically evaluated for gastrointestinal and respiratory disease across three weeks beginning at age ≤ seven days old. Fecal (n = 57) and nasal (n = 57) microbial samples were taken for paired-end 16S rRNA gene amplicon sequencing. Taxonomy and diversity analyses were used to characterize early-life nasal and fecal microbiomes. Stochasticity and determinism were measured using normalized stochasticity testing (NST) and Dirichlet multinomial model (DMM). All analyses were tested for statistical significance. Clinical diarrhea was observed in 11 of the 19 calves. Clinical BRD was not independently observed among the cohort; however, two calves presented clinical signs of both BRD and diarrhea. Taxonomic analysis revealed that fecal samples were highlighted by Bacteroidaceae (40%; relative abundance), Ruminococcaceae (13%), and Lachnospiraceae (10%), with changes in diversity (Kruskal-Wallis; p < 0.05) and composition (PERMANOVA; p < 0.05). Clinical diarrhea reduced diversity in the fecal microbiome but did not impact composition. Nasal samples featured Moraxellaceae (49%), Mycoplasmataceae (16%), and Pasteurellaceae (3%). While no diversity changes were seen in nasal samples, compositional changes were observed (p < 0.05). NST metrics (Kruskal-Wallis; p > 0.01) and DMM (PERMANOVA; p < 0.01) revealed that stochastic, neutral theory-based assembly dynamics govern early-life microbial composition and that distinct microbial populations drive community composition in healthy and diarrheic calves.}, }
@article {pmid39942291, year = {2025}, author = {Santás-Miguel, V and Lalín-Pousa, V and Conde-Cid, M and Rodríguez-Seijo, A and Pérez-Rodríguez, P}, title = {Use of Biopowders as Adsorbents of Potentially Toxic Elements Present in Aqueous Solutions.}, journal = {Materials (Basel, Switzerland)}, volume = {18}, number = {3}, pages = {}, pmid = {39942291}, issn = {1996-1944}, support = {ED481D-2021/016//Conseller&#xed;a de Cultura, Educaci&#xf3;n e Universidade (Xunta de Galicia)/ ; IJC2020-044197-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; IJC2020-044426-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; 101112754//MRV4SOC project/ ; ED481B-2022-081//Xunta de Galicia/ ; }, abstract = {This study examines the adsorption and desorption behaviors of phosphorus (P), arsenic (As), fluoride (F), and chromium (Cr) in aqueous solutions on green materials such as cork bark (CB) and pine bark (PB). These materials are characterized by active functional groups and net negative charges on their surfaces and porous structures. The evaluation considers variations in contaminant concentrations (0.01-10 mM) and pH (3.5-12). Cork bark exhibited higher adsorption capacity for As and F, while PB was more effective for P and Cr. Adsorption isotherms followed the Freundlich and Langmuir models, indicating surface heterogeneity and multilayer adsorption for most potentially toxic elements (PTEs). Desorption tests demonstrated low rates, with CB retaining up to 99% of F and 85% of As, and PB achieving up to 86% retention for Cr and 70% for P. The influence of pH was minimal for As, P, and F, but acidic conditions significantly enhanced Cr adsorption, showing similar behavior for both biopowders. These findings suggest that CB and PB biopowders are promising, environmentally friendly biosorbents for the removal of PTEs from aqueous solutions. Their effectiveness varies depending on the specific contaminant. This study highlights the potential of these natural materials for sustainable applications in water treatment and soil remediation.}, }
@article {pmid39942061, year = {2025}, author = {Di Biase, M and Scicchitano, D and Valerio, F and Lonigro, SL and Cifarelli, V and Ostante, G and D'Antuono, I and Candela, M and Ferrara, M}, title = {Microbial Ecology and Nutritional Features in Liquid Sourdough Containing Hemp Flour Fermented by Lactic Acid Bacterial Strains.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, pmid = {39942061}, issn = {2304-8158}, support = {MicroBHE Project//IBISBA - IT/ ; DAB.AD005.225//FOE - 2021/ ; }, abstract = {Hemp seed flour (Cannabis sativa) is a non-traditional matrix alternative to wheat for baked goods production. The aim of this study was to investigate the microbiota of two liquid sourdoughs (SLs) based on hemp or a wheat-hemp mixture, before and after spontaneous or piloted fermentation (Lactiplantibacillus plantarum ITM21B or Weissella cibaria C43-11 used as starters). Culture-dependent and -independent (high-throughput sequencing of bacterial phylogenetic V3-V4 regions of the 16S rRNA gene) methods, were used to evaluate the microbial community. The effect of fermentation on the content of bioactive molecules (polyphenols, organic acids, proteins, and amino acids) was also investigated. Results indicated that the microbial community of all SLs was mainly (99.7 ÷ 100%) composed of Firmicutes and Proteobacteria, and the latter was the unique phylum before fermentation in formulations produced exclusively with hemp flour. Two PCoA plots (Test adonis with pseudo-F ratio, p > 0.05) showed no significance difference between the microbial communities of the formulations. However, the relative abundance variation at the family level in the wheat-hemp-based mixture SLs showed a significant enrichment of the Lactobacillaceae family (Kruskal-Wallis test, p = 0.04). Moreover, results confirmed hemp seed flour as a suitable fermentation substrate to obtain microbial consortia allowing for an increase in organic acids, especially lactic acid (9.12 ± 1.22 and 7.45 ± 0.75 mmol/kg with Lpb. plantarum and W. cibaria, respectively), in both piloted fermentations, and in polyphenols by 21% and amino acids by 158% in SL fermented by the C43-11 strain.}, }
@article {pmid39937305, year = {2025}, author = {Argentino, ICV and Godoy, MG and Seldin, L and Jurelevicius, D}, title = {Distribution of Bacillota in Water and Sediments from Aquatic Environments.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {3}, pmid = {39937305}, issn = {1432-184X}, mesh = {*Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Brazil ; Microbiota ; Phylogeny ; *Water Microbiology ; *Seawater/microbiology ; *Fresh Water/microbiology ; DNA, Bacterial/genetics ; Biodiversity ; }, abstract = {The phylum Bacillota comprises metabolically diverse bacteria with potential relevance in several fields. Although some genera, such as Bacillus and others, have been extensively studied, the distribution of Bacillota in the environment is still poorly understood. This study aimed to analyze the distribution of Bacillota present in water and sediment samples from different environments. For this purpose, water (W) and sediment (S) samples were collected from different marine environments (Dois Rios Beach - DR, Abraão Beach - AB, Massambaba Beach - MB, and Guanabara Bay - GB), freshwater lagoons (Jacarepiá Lagoon- JL) and hypersaline lagoons (Vermelha Lagoon - VL), all of which are located in Rio de Janeiro, Brazil. The microbial communities present in each sample were determined by sequencing 16S rRNA-encoding genes. The distribution and diversity of Bacillota were analyzed via QIIME2. The results revealed that Bacillota represented an average of 1% of the microbial community of aquatic microbiomes and were unevenly distributed in aquatic water and sediment. The highest abundances of Bacillota were detected in JL_S and VL_S, and the lowest abundances were observed in MB_W and AB_W. Only sequences related to the Bacilli and Clostridia classes were identified. The main Bacillota genera identified were Bacillus and an unidentified Clostridiales order genus. The VL_S and JL_S samples had the highest numbers of exclusive Bacillota genera. On the other hand, 15 Bacillota genera, which are generally observed in the human and animal guts, were found only in anthropogenically impacted GB_W and AB_W. The obtained results revealed how Bacillota are distributed in different aquatic environments.}, }
@article {pmid39936183, year = {2025}, author = {Brait, N and Hackl, T and Lequime, S}, title = {detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data.}, journal = {Molecular ecology resources}, volume = {25}, number = {4}, pages = {e14083}, pmid = {39936183}, issn = {1755-0998}, mesh = {*Computational Biology/methods ; *Genomics/methods ; *Software ; Genome, Viral ; *Viruses/genetics ; Sensitivity and Specificity ; }, abstract = {Endogenous viral elements (EVEs) are fragments of viral genomic material embedded within the host genome. Retroviruses contribute to the majority of EVEs because of their genomic integration during their life cycle; however, the latter can also arise from non-retroviral RNA or DNA viruses, then collectively known as non-retroviral (nr) EVEs. Detecting nrEVEs poses challenges because of their sequence and genomic structural diversity, contributing to the scarcity of specific tools designed for nrEVEs detection. Here, we introduce detectEVE, a user-friendly and open-source tool designed for the accurate identification of nrEVEs in genomic assemblies. detectEVE deviates from other nrEVE detection pipelines, which usually classify sequences in a more rigid manner as either virus-associated or not. Instead, we implemented a scaling system assigning confidence scores to hits in protein sequence similarity searches, using bit score distributions and search hints related to various viral characteristics, allowing for higher sensitivity and specificity. Our benchmarking shows that detectEVE is computationally efficient and accurate, as well as considerably faster than existing approaches, because of its resource-efficient parallel execution. Our tool can help to fill current gaps in both host-associated fields and virus-related studies. This includes (i) enhancing genome annotations with metadata for EVE loci, (ii) conducting large-scale paleo-virological studies to explore deep viral evolutionary histories, and (iii) aiding in the identification of actively expressed EVEs in transcriptomic data, reducing the risk of misinterpretations between exogenous viruses and EVEs.}, }
@article {pmid39935057, year = {2025}, author = {Ruiz-Ruiz, P and Mohedano-Caballero, P and De Vrieze, J}, title = {Ectoine production through a marine methanotroph-microalgae culture allows complete biogas valorization.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124223}, doi = {10.1016/j.jenvman.2025.124223}, pmid = {39935057}, issn = {1095-8630}, mesh = {*Biofuels ; *Microalgae/metabolism ; Methane/metabolism ; *Amino Acids, Diamino/metabolism ; Carbon Dioxide/metabolism ; }, abstract = {Methanotrophs have recently emerged as a promising platform for producing bio-based chemicals, like ectoine, from biogas, offering an economical alternative to glucose. However, most studies have focused solely on CH4 consumption, often overlooking the CO2, which is both produced by methanotrophs and present in biogas, despite its potential as a carbon source for microorganisms, such as microalgae. In this study, marine methanotrophic-microalgal cultures were enriched from environmental samples collected at the North Sea coast to explore ectoine production from both CH4 and CO2 in biogas. The sediment-derived culture exhibited the highest CH4 removal efficiency and CO2 uptake, and was selected for further experiments. The culture was primarily composed of Methylobacter marinus, Methylophaga marina, and the microalga Picochlorum oklahomensis. Gas consumption, growth, and ectoine production were evaluated under varying salinity levels and osmotic stress. The NaCl concentrations above 6% negatively impacted CH4 oxidation and inhibited ectoine synthesis, while osmotic shocks enhanced ectoine accumulation, with a maximum ectoine content of 51.3 mgectoine gVSS[-1] at 4.5% NaCl. This study is the first to report ectoine production from methanotroph-microalgal cultures, showing its potential for biogas valorization into high-value bio-based chemicals, like ectoine, marking a significant step toward sustainable biogas utilization.}, }
@article {pmid39934529, year = {2025}, author = {Roy, R and Das, A and Ganguly, D and Chakraborty, P and Paul, P and Das, S and Maity, A and Malik, M and Tribedi, P}, title = {Cuminaldehyde synergistically enhances the antimicrobial and antibiofilm potential of gentamicin: A direction towards an effective combination for the control of biofilm-linked threats of Staphylococcus aureus.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {56}, number = {2}, pages = {1033-1048}, pmid = {39934529}, issn = {1678-4405}, support = {TNU/R&amp;D/M/11//The Neotia University/ ; }, mesh = {*Biofilms/drug effects ; *Gentamicins/pharmacology ; *Staphylococcus aureus/drug effects/physiology ; *Anti-Bacterial Agents/pharmacology ; Drug Synergism ; Microbial Sensitivity Tests ; Humans ; Staphylococcal Infections/microbiology/drug therapy ; *Benzaldehydes/pharmacology ; Reactive Oxygen Species/metabolism ; }, abstract = {Staphylococcus aureus, a Gram-positive, coccus-shaped bacterium often causes several infections on human hosts by exploiting biofilm. This current work investigates a potential strategy to manage the threats of biofilm-linked infections by embracing a combinatorial approach involving cuminaldehyde (phytochemical) and gentamicin (antibiotic). Despite showing antimicrobial properties individually, cuminaldehyde and gentamicin could exhibit enhanced antimicrobial potential when used together against S. aureus. The fractional inhibitory concentration index (FICI = 0.36) suggested that the selected compounds (cuminaldehyde and gentamicin) offered synergistic interaction while showing antimicrobial potential against the same organism. A series of experiments indicated that the selected compounds (cuminaldehyde and gentamicin) showed substantial antibiofilm potential against S. aureus when combined. The increased antibiofilm potential was linked to the accumulation of reactive oxygen species (ROS) and increased cell membrane permeability. Additionally, the combination of the selected compounds (cuminaldehyde and gentamicin) also impeded the cell surface hydrophobicity of S. aureus, aiding in the prevention of biofilm formation. The present study also showed that combining the mentioned compounds (cuminaldehyde and gentamicin) notably reduced the secretion of several virulence factors from S. aureus. Furthermore, the current research showed that these compounds (cuminaldehyde and gentamicin) could also exhibit antibiofilm potential against the clinical strains of Methicillin-Resistant S. aureus (MRSA). Taken together, this innovative approach not only enhances the potential of existing standard antibiotics but also opens up new therapeutic possibilities for combating biofilm-related infections.}, }
@article {pmid39933594, year = {2025}, author = {Verdon, N and Popescu, O and Titmuss, S and Allen, RJ}, title = {Habitat fragmentation enhances microbial collective defence.}, journal = {Journal of the Royal Society, Interface}, volume = {22}, number = {223}, pages = {20240611}, pmid = {39933594}, issn = {1742-5662}, support = {//Deutsche Forschungsgemeinschaft/ ; //H2020 European Research Council/ ; //Engineering and Physical Sciences Research Council/ ; }, mesh = {*Ecosystem ; *Models, Biological ; *Bacteria ; }, abstract = {Microbes often inhabit complex, spatially partitioned environments such as host tissue or soil, but the effects of habitat fragmentation on microbial ecology and infection dynamics are poorly understood. Here, we investigate how habitat fragmentation impacts a prevalent microbial collective defence mechanism: enzymatic degradation of an environmental toxin. Using a theoretical model, we predict that habitat fragmentation can strongly enhance the collective benefits of enzymatic toxin degradation. For the example of [Formula: see text]-lactamase-producing bacteria that mount a collective defence by degrading a [Formula: see text]-lactam antibiotic, we find that realistic levels of habitat fragmentation can allow a population to survive antibiotic doses that greatly exceed those required to kill a non-fragmented population. This 'habitat-fragmentation rescue' is a stochastic effect that originates from variation in bacterial density among different subpopulations and demographic noise. We also study the contrasting case of collective enzymatic foraging, where enzyme activity releases nutrients from the environment; here we find that increasing habitat fragmentation decreases the lag time for population growth but does not change the ecological outcome. Taken together, this work predicts that stochastic effects arising from habitat fragmentation can greatly enhance the effectiveness of microbial collective defence via enzymatic toxin degradation.}, }
@article {pmid39928396, year = {2025}, author = {Nakajima, M and Nakai, R and Hirakata, Y and Kubota, K and Satoh, H and Nobu, MK and Narihiro, T and Kuroda, K}, title = {Minisyncoccus archaeiphilus gen. nov., sp. nov., a mesophilic, obligate parasitic bacterium and proposal of Minisyncoccaceae fam. nov., Minisyncoccales ord. nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. formerly referred to as Candidatus Patescibacteria or candidate phyla radiation.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {75}, number = {2}, pages = {}, doi = {10.1099/ijsem.0.006668}, pmid = {39928396}, issn = {1466-5034}, mesh = {*Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Base Composition ; Methanospirillum/growth &amp; development ; Symbiosis ; DNA, Archaeal/genetics ; Fatty Acids/chemistry/analysis ; }, abstract = {In the domain Bacteria, one of the largest, most diverse and environmentally ubiquitous phylogenetic groups, Candidatus Patescibacteria (also known as candidate phyla radiation/CPR), remains poorly characterized, leaving a major knowledge gap in microbial ecology. We recently discovered a novel cross-domain symbiosis between Ca. Patescibacteria and Archaea in highly purified enrichment cultures and proposed Candidatus taxa for the characterized species, including Ca. Minisyncoccus archaeophilus and the corresponding family Ca. Minisyncoccaceae. In this study, we report the isolation of this bacterium, designated strain PMX.108[T], in a two-strain co-culture with a host archaeon, Methanospirillum hungatei strain DSM 864[T] (JF-1[T]), and hereby describe it as the first representative species of Ca. Patescibacteria. Strain PMX.108[T] was isolated from mesophilic methanogenic sludge in an anaerobic laboratory-scale bioreactor treating synthetic purified terephthalate- and dimethyl terephthalate-manufacturing wastewater. The strain could not grow axenically and is obligately anaerobic and parasitic, strictly depending on M. hungatei as a host. The genome was comparatively large (1.54 Mbp) compared to other members of the clade, lacked some genes involved in the biosynthesis pathway and encoded type IV pili-related genes associated with the parasitic lifestyle of ultrasmall microbes. The G+C content of the genomic DNA was 36.6 mol%. Here, we report the phenotypic and genomic properties of strain PMX.108[T]; we propose Minisyncoccus archaeiphilus gen. nov., sp. nov. to accommodate this strain. The type strain of the species is PMX.108[T] (=JCM 39522[T]). We also propose the associated family, order, class and phylum as Minisyncoccaceae fam. nov. Minisyncoccales nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. within the bacterial kingdom Bacillati.}, }
@article {pmid39924526, year = {2025}, author = {Díez López, C and Van Herreweghen, F and De Pessemier, B and Minnebo, Y and Taelman, S and Judge, K and Ransley, K and Hammond, C and Batson, M and Stock, M and Van Criekinge, W and Van de Wiele, T and Macmaster, A and Callewaert, C}, title = {Unravelling the hidden side of laundry: malodour, microbiome and pathogenome.}, journal = {BMC biology}, volume = {23}, number = {1}, pages = {40}, pmid = {39924526}, issn = {1741-7007}, support = {HBC.2020.2292//Agentschap Innoveren en Ondernemen/ ; FWO19/PSD/084//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {*Microbiota ; *Odorants/analysis ; Volatile Organic Compounds/analysis ; Humans ; *Clothing ; *Laundering ; Skin/microbiology ; Bacteria/genetics ; }, abstract = {BACKGROUND: Recent trends towards lower washing temperatures and a reduction in the use of bleaching agents in laundry undoubtedly benefit our environment. However, these conditions impair microbial removal on clothes, leading to malodour generation and negative impacts on consumer well-being. Clothing undergoes cycles of wearing, washing and drying, with variable exposure to microorganisms and volatilomes originating from the skin, washing machine, water and laundry products. Laundry malodour is therefore a complex problem that reflects its dynamic ecosystem. To date, comprehensive investigations that encompass the evaluation of both microbial community and malodorous volatile organic compounds throughout all stages of the wash-wear-dry cycle are scarce. Furthermore, the microbial and malodour profiles associated with extended humid-drying conditions are poorly defined.<br><br>RESULTS: Here we present olfaction-directed chemical and microbiological studies of synthetic T-shirts after wearing, washing and drying. Results show that although washing reduces the occurrence of known malodour volatile organic compounds, membrane-intact bacterial load on clothing is increased. Skin commensals are displaced by washing machine microbiomes, and for the first time, we show that this shift is accompanied by an altered pathogenomic profile, with many genes involved in biofilm build-up. We additionally highlight that humid-drying conditions are associated with characteristic malodours and favour the growth of specific Gram-negative bacteria.<br><br>CONCLUSIONS: These findings have important implications for the development of next-generation laundry products that enhance consumer well-being, while supporting environmentally friendly laundry practices.}, }
@article {pmid39915510, year = {2025}, author = {Rabbani, G and Afiq-Rosli, L and Lee, JN and Waheed, Z and Wainwright, BJ}, title = {Effects of life history strategy on the diversity and composition of the coral holobiont communities of Sabah, Malaysia.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {4459}, pmid = {39915510}, issn = {2045-2322}, mesh = {Animals ; *Anthozoa/microbiology/physiology ; Malaysia ; *Microbiota ; Biodiversity ; Symbiosis ; Coral Reefs ; Bacteria/genetics/classification ; Climate Change ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Coral-associated microbes have essential roles in promoting and regulating host function and health. As climate change advances and other environmental perturbations increasingly impact corals, it is becoming ever more important that we understand the composition of the microbial communities hosted. Without this baseline it is impossible to assess the magnitude and direction of any future changes in microbial community structure. Here, we characterised both the bacterial and Symbiodiniaceae communities in four coral species (Diploastrea heliopora, Porites lutea, Pachyseris speciosa, and Pocillopora acuta) collected from Sabah, Malaysia. Our findings reveal distinct microbial communities associated with different coral species tending to reflect the varied life history strategies of their hosts. Microbial communities could be differentiated by collection site, with shifts in Symbiodiniaceae communities towards more stress tolerant types seen in samples collected on the shallow Sunda Shelf. Additionally, we identified a core microbiome within species and a more discrete core between all species. We show bacterial and Symbiodiniaceae communities are structured by host species and appear to be influenced by host life history characteristics. Furthermore, we identified a core microbiome for each species finding that several amplicon sequence variants were shared between hosts, this suggests a key role in coral health regardless of species identity. Given the paucity of work performed in megadiverse regions such as the Coral Triangle, this research takes on increased importance in our efforts to understand how the coral holobiont functions and how it could be altered as climate change advances.}, }
@article {pmid39914458, year = {2025}, author = {Wenger, A and Bakkeren, E and Granato, E and Tecon, R and Mitri, S and Möbius, W}, title = {MEEhubs2024: A hub-based conference on microbial ecology and evolution fostering sustainability.}, journal = {FEMS microbiology letters}, volume = {372}, number = {}, pages = {}, pmid = {39914458}, issn = {1574-6968}, support = {51NF40_180575/SNSF_/Swiss National Science Foundation/Switzerland ; BB/V004328/1//BBSRC/ ; 51NF40_180575//NCCR Microbiomes/ ; }, mesh = {*Congresses as Topic ; Humans ; *Ecology ; *Biological Evolution ; *Microbiology ; Europe ; }, abstract = {Scientific conferences are essential to academic exchange. However, related air travel contributes to greenhouse gas emissions, while expensive registration and travel costs limit the participation of early career researchers and those from low-income countries. Virtual conferences offer promising solutions for reducing emissions and enhancing accessibility and inclusivity but often limit networking and personal interaction. Hybrid multi-hub conferences, which combine virtually connected in-person venues with individual virtual participation, combine the benefits of both conference formats. Thus, we present and discuss MEEhubs2024, a multi-hub conference on microbial ecology and evolution held in January 2024. During this 3-day conference, attendees participated virtually or at one of six hubs in Europe and North America. We analyzed the participants' and organizers' feedback to create a template and provide insights into the scientific community's adoption of this new conference format, which was positively evaluated by most participants. Because technical, logistical, and structural challenges remain, including limited opportunities to interact and network across hubs and participation modes, we provide recommendations for improvement, such as hiring technical hosts and offering virtual-only social activities. Finally, we used the participants' feedback to reflect on conference expectations, highlighting research gaps and the need for organizers to define and communicate goals when organizing conferences.}, }
@article {pmid39914213, year = {2025}, author = {Ma, R and Huang, Z and Jiang, Y and Zhao, A and Yu, G and Lin, C and Zhu, L and Zhang, X and Li, X and Wang, C}, title = {Regulation of ethanol production from anaerobic fermentation of food waste using aromatic alcohol-based quorum-sensing molecules.}, journal = {Journal of environmental management}, volume = {376}, number = {}, pages = {124382}, doi = {10.1016/j.jenvman.2025.124382}, pmid = {39914213}, issn = {1095-8630}, mesh = {Fermentation ; *Quorum Sensing ; *Ethanol/metabolism ; Anaerobiosis ; Phenylethyl Alcohol/analogs &amp; derivatives ; Food Loss and Waste ; }, abstract = {Quorum-sensing molecules (QSMs) are used to regulate microbial metabolites to effectively improve food waste anaerobic fermentation to produce high-value products of ethanol and lactic acid. In this study, low concentrations (25 and 50 μmol/L) of aromatic alcohol favored the synthesis of ethanol and lactic products. Among the aromatic alcohol QSMs, 50 μmol/L of tyrosol enhanced the yield of products. The correlations between substrate composition indicators confirmed that tyrosol was conducive to the anaerobic fermentation of food waste. The regulation mechanism of tyrosol, such as microbial diversity in anaerobic fermentation, was analyzed from the perspective of microbial ecology. The result revealed that tyrosol increased the microbial diversity in the system. Limosilactobacillus, Weissella, and Pediococcus were the dominant bacterial species in the early stages of fermentation, whereas Clostridiaceae and Bacillus were dominant in the later stages. Meanwhile, the main dominant fungal species were Saccharomyces, Aspergillus, and Pichia. The results of this study show that using QSMs, including tyrosol, to regulate the physiological characteristics of anaerobic fermentation microorganisms, promote the synthesis of cell metabolites, and regulate the diversity and succession of microbial communities is a feasible measure. This approach improves the resource utilization efficiency of anaerobic fermentation technology for food waste, which is significant for promoting sustainable development.}, }
@article {pmid39913585, year = {2025}, author = {Pertierra, LR and Convey, P and Barbosa, A and Biersma, EM and Cowan, D and Diniz-Filho, JAF and de Los Ríos, A and Escribano-Álvarez, P and Fraser, CI and Fontaneto, D and Greve, M and Griffiths, HJ and Harris, M and Hughes, KA and Lynch, HJ and Ladle, RJ and Liu, XP and le Roux, PC and Majewska, R and Molina-Montenegro, MA and Peck, LS and Quesada, A and Ronquillo, C and Ropert-Coudert, Y and Sancho, LG and Terauds, A and Varliero, G and Vianna, JA and Wilmotte, A and Chown, SL and Olalla-Tárraga, M&#xc1; and Hortal, J}, title = {Advances and shortfalls in knowledge of Antarctic terrestrial and freshwater biodiversity.}, journal = {Science (New York, N.Y.)}, volume = {387}, number = {6734}, pages = {609-615}, doi = {10.1126/science.adk2118}, pmid = {39913585}, issn = {1095-9203}, mesh = {Antarctic Regions ; *Biodiversity ; Animals ; *Fresh Water ; Invertebrates/physiology ; Vertebrates ; }, abstract = {Antarctica harbors many distinctive features of life, yet much about the diversity and functioning of Antarctica's life remains unknown. Evolutionary histories and functional ecology are well understood only for vertebrates, whereas research on invertebrates is largely limited to species descriptions and some studies on environmental tolerances. Knowledge on Antarctic vegetation cover showcases the challenges of characterizing population trends for most groups. Recent community-level microbial studies have provided insights into the functioning of life at its limits. Overall, biotic interactions remain largely unknown across all groups, restricted to basic information on trophic level placement. Insufficient knowledge of many groups limits the understanding of ecological processes on the continent. Remedies for the current situation rely on identifying the caveats of each ecological discipline and finding targeted solutions. Such precise delimitation of knowledge gaps will enable a more aware, representative, and strategic systematic conservation planning of Antarctica.}, }
@article {pmid39912641, year = {2025}, author = {Hamovit, N and RoyChowdhury, T and Akob, DM and Zhang, X and McCarty, G and Yarwood, S}, title = {Comparative assessment of a restored and natural wetland using [13]C-DNA SIP reveals a higher potential for methane production in the restored wetland.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {3}, pages = {e0216124}, pmid = {39912641}, issn = {1098-5336}, support = {2017-67003-26484//U.S. Department of Agriculture (USDA)/ ; }, mesh = {*Wetlands ; *Methane/metabolism ; *Soil Microbiology ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics/analysis ; Carbon Isotopes/analysis ; *Archaea/metabolism/genetics/classification ; Oxidation-Reduction ; Maryland ; Microbiota ; }, abstract = {Wetlands are the largest natural source of methane (CH4), a potent greenhouse gas produced by methanogens. Methanogenesis rates are controlled by environmental factors such as redox potential, temperature, and carbon and electron acceptor availability and are presumably dependent on the composition of the active methanogen community. We collected intact soil cores from a restored and natural freshwater depressional wetland on Maryland's Delmarva Peninsula (USA) to assess the effects of wetland restoration and redox shifts on microbial processes. Intact soil cores were incubated under either saturated (anoxic) or unsaturated (oxic) conditions and amended with [13]C-acetate for quantitative stable isotope probing (qSIP) of the 16S rRNA gene. Restored wetland cores supported a distinct community of methanogens compared to natural cores, and acetoclastic methanogens putatively identified in the genus Methanosarcina were among the most abundant taxa in restored anoxic and oxic cores. The active microbial communities in the restored wetland cores were also distinguished by the unique presence of facultatively anaerobic bacteria belonging to the orders Firmicutes and Bacteroidetes. In natural wetland incubations, methanogen populations were not among the most abundant taxa, and these communities were instead distinguished by the unique presence of aerobic bacteria in the phyla Acidobacteria, Actinobacteria, and class Alphaproteobacteria. Iron-reducing bacteria, in the genus Geobacter, were active across all redox conditions in both the restored and the natural cores, except the natural oxic-anoxic condition. These findings suggest an overall higher potential for methanogenesis in the restored wetland site compared to the natural wetland site, even when there is evidence of Fe reduction.IMPORTANCEMethane (CH4) is a potent greenhouse gas with an atmospheric half-life of ~10 years. Wetlands are the largest natural emitters of CH4, but CH4 dynamics are difficult to constrain due to high spatial and temporal variability. In the past, wetlands were drained for agriculture. Now, restoration is an important strategy to increase these ecosystems' potential for sequestering carbon. However, the consequences of wetland restoration on carbon biogeochemistry are under-evaluated, and a thorough assessment of the active microbial community as a driver of biogeochemical changes is needed. Particularly, the effects of seasonal flooding/drying cycles in geographically isolated wetlands might have implications for CH4 emissions in both natural and restored wetlands. Here, we found that active microbial communities in natural and restored wetlands responded differently to flooding and drying regimes, resulting in differences in CH4 production potentials. Restored wetlands had a higher potential for CH4 production compared to natural wetlands. Our results show that controls on CH4 production in a restored wetland are complex, and dynamics of active microbial communities are linked to seasonal dry-wet cycles.}, }
@article {pmid39912591, year = {2025}, author = {Porras-Socias, P and Mattiussi, R and Silveira, KA and O'Flaherty, V}, title = {Methan-o-poly: a giant collaborative game to "digest" the microbiology of green biogas production.}, journal = {Journal of microbiology &amp; biology education}, volume = {26}, number = {1}, pages = {e0011624}, pmid = {39912591}, issn = {1935-7877}, abstract = {In an era of rapid change and global challenges, impactful educational experiences about sustainability become imperative. Especially in organic waste conversion bioprocess such as anaerobic digestion (AD). Here proposed, is a gamified approach to learn AD and hidden microbial interactions, bringing to real-life size an invisible phenomenon. In Methan-o-poly, participants roleplay cooperating microbes within a bioreactor engaged in four sequential mini-games to mimic organic waste degradation and methane production. Perturbations in the activity simulate real challenges, enhancing adaptability and problem-solving skills. Overall, this cooperative game promotes motivation, collaboration, and experiential learning. Its initial implementation received positive feedback across various age groups, enhancing green education initiatives.}, }
@article {pmid39911734, year = {2025}, author = {Jia, C and Li, J and Li, Z and Zhang, L}, title = {Influence of high-load shocks on achieving mainstream partial nitrification: Microbial community succession.}, journal = {Water research X}, volume = {27}, number = {}, pages = {100304}, pmid = {39911734}, issn = {2589-9147}, abstract = {Driving microbial community succession through the regulation of operational strategies is crucial for achieving partial nitrification (PN) in municipal wastewater. However, at present, there is a decoupling between the strategic regulation of PN systems and the succession characteristics of the microbial community. This study examined the correlation between microbial community succession and PN performance under two high-load shocks (HLS1 and HLS2) treating actual sewage. During HLS1, the influent organic loading rate (OLR) and nitrogen loading rate (NLR) increased from 116.7 ± 37.7 to 219.7 ± 24.7 mg COD/(g VSS·d) and 0.21±0.02 to 0.33±0.02 kg N/m[3]/d respectively, with the nitrite concentration and nitrite accumulation ratio only reaching 11.7 ± 2.7 mg/L and 49.3 ± 13.9 %, respectively. During HLS2, the influent OLR and NLR increased from 123.5 ± 17.2 to 300.3 ± 49.2 mg COD/(g VSS·d) and 0.19±0.03 to 0.32±0.03 kg N/m[3]/d respectively, resulting in a nitrite accumulation ratio of 89.4 ± 10.7 %. The system achieved efficient PN performance and sustained for 124 days. High-throughput sequencing results showed that community diversity remained consistently high, and the community composition returned to its initial state following a minor succession during HLS1. During HLS2, the high-load shock reduced the richness and evenness of the microbial community. The community underwent succession in a new direction, leading to community composition and function changes. The results indicate that the realization, stabilization, and disruption of PN are influenced not only by operational parameters but also by microbial community structure.}, }
@article {pmid39911603, year = {2025}, author = {Sikombe, TW and Linnemann, AR and Moonga, HB and Quilitz, S and Schoustra, SE and Smid, EJ and Alekseeva, A}, title = {Odor-active aroma compounds in traditional fermented dairy products: The case of mabisi in supporting food and nutrition security in Zambia.}, journal = {Current research in food science}, volume = {10}, number = {}, pages = {100976}, pmid = {39911603}, issn = {2665-9271}, abstract = {Aroma is a key sensory attribute that determines consumer preference and acceptability of foods. The aroma of fermented dairy products comprises the volatile organic compounds (VOCs) produced by the activity of fermenting microbes and the compounds originally present in unfermented raw milk. A unique combination of specific compounds detectable by human olfactory senses creates the distinct odor profile of fermented products. This study investigated the influence of different production methods on the VOCs responsible for the odor-active compounds, and the microbial communities present in mabisi, a traditional Zambian fermented dairy product. The VOCs and microbial community composition of four mabisi variants were investigated using GC-O-MS and PTR-QiTOF-MS techniques, and 16S rRNA amplicon sequencing, respectively. A panel of three assessors identified the odor-active compounds from the GC-O-MS, and the compound's quantitative aspects were obtained by the PTR-QiTOF-MS. Twelve volatile compounds were identified as odor-active compounds during the GC-O-MS analysis. The most prominent were ketones and esters, which imparted a buttery and fruity aroma, respectively. The PTR-QiTOF-MS run identified and quantified a total of 390 m/z peaks, 55 of which were tentatively identified. 16S rRNA amplicon sequencing revealed a diverse microbial community, with Lactococcus species dominating. While the VOC profiles showed significant variation in functionality among the variants, minor differences were observed in microbial composition. The study confirms that high compound concentration does not necessarily correlate with compound odor activity. Our findings offer insights into the significance of aromas and microbial ecology to support optimization strategies for upscaling traditional fermented products.}, }
@article {pmid39911488, year = {2024}, author = {Vaselek, S and Alten, B}, title = {Microbial ecology of sandflies-the correlation between nutrition, Phlebotomus papatasi sandfly development and microbiome.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1522917}, pmid = {39911488}, issn = {2297-1769}, abstract = {The role and the impact of the microbial component on the biology, ecology, and development of sandflies is largely unknown. We evaluated the impact of larval nutrition on laboratory-reared sandflies in correlation to the abundance of food, light starvation, and food with/without live microbiome, by monitoring the survival and development of immature stages, and the longevity of adult sandflies. Within this study we examined 360 larvae, 116 pupae, and 120 adult flies of Phlebotomus papatasi for the microbial gut content. The data showed that the presence of a live and diverse microbiome plays a role in the development and survival of larvae. The mortality rate of the larvae was higher, and larval development was longer for sandflies maintained on microbiome-depleted medium, in comparison to the larvae fed with medium containing alive and complex microbiome. Actively feeding larvae reduce microbial abundance and diversity of the medium. The microbial content of the larval gut depends on the composition of the rearing medium, indicating a potential attraction to certain bacteria. The microbial content of the pupa gut was severely diminished, with overall survival of two bacterial species in adult insects - Ochrobactrum intermedium (found in 95% of dissected adults) and Bacillus subtilis (16%). Further microbial studies may aid in developing biological control methods for sandfly larval or adult stages.}, }
@article {pmid39909903, year = {2025}, author = {Panico, SC and Alberti, G and Foscari, A and Sciabbarrasi, GL and Tomao, A and Incerti, G}, title = {Bacterial and Fungal Communities Respond Differently to Changing Soil Properties Along Afforestation Dynamic.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {2}, pmid = {39909903}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Soil/chemistry ; *Fungi/classification/genetics/isolation &amp; purification ; Italy ; Biodiversity ; Grassland ; Nitrogen/analysis ; Forests ; Carbon/analysis ; Phosphorus/analysis ; Microbiota ; *Mycobiome ; }, abstract = {Spontaneous afforestation following land abandonment has been increasingly recognized as a nature-based solution to mitigate climate change and provide measurable benefits to biodiversity. However, afforestation effects on biodiversity, particularly on soil microbial communities, are still poorly characterized, with most previous studies focusing on artificial plantations rather than forest rewilding dynamics. Here, we assessed changes in topsoil physical-chemical properties and related dynamics of bacterial and fungal community composition and structure following spontaneous afforestation of abandoned grasslands in Northeast Italy over the last 70 years. With a space-for-time approach, we selected four chronosequences representing different successional stages: grassland, early (2000-2020), intermediate (1978-2000), and late (1954-1978). Results showed that spontaneous afforestation progressively reduced topsoil pH and total phosphorus (P), while soil organic carbon (SOC), nitrogen (N), and C:N ratio increased. Correspondingly, the overall α-diversity of the fungal community, assessed by ITS DNA metabarcoding, progressively decreased after an initial increase from grassland conditions, following substrate acidification and trophic specialization. Bacterial diversity, assessed by 16S DNA metabarcoding, was highest at the initial stages, then progressively decreased at later stages, likely limited by lower organic matter quality. Shifts of fungal community composition included an increase of ectomycorrhizal Basidiomycota linked to topsoil's higher SOC, N, and C:N ratio. Differently, bacterial community composition responded substantially to pH, with topsoil acidity favoring Proteobacteria (Pseudomonadota) and Acidobacteria (Acidobacteriota) at the late afforestation stages. Our findings provide a first contribution to clarify how fungi and bacteria respond to spontaneous afforestation. This is particularly relevant in the context of climate change mitigation, considering the fundamental role of microorganisms in shaping soil carbon storage dynamics.}, }
@article {pmid39907926, year = {2025}, author = {Breedt, G and Korsten, L and Gokul, JK}, title = {Enhancing multi-season wheat yield through plant growth-promoting rhizobacteria using consortium and individual isolate applications.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {39907926}, issn = {1874-9356}, abstract = {In recent decades, there has been a growing interest in harnessing plant growth-promoting rhizobacteria (PGPR) as a possible mechanism to mitigate the environmental impact of conventional agricultural practices and promote sustainable agricultural production. This study investigated the transferability of promising PGPR research from maize to another Poaceae cereal crop, wheat. This multi-seasonal study evaluated the wheat grain yield effect of Lysinibacillus sphaericus (T19), Paenibacillus alvei (T29) when applied i. individually, ii. as a consortium with Bacillus safensis (S7), and iii. at a 75% reduced fertilizer rate. Whole genome sequencing allowed annotation of genes linked to plant growth promotion, providing potential genomic explanations for the observed in-field findings. Application of the consortium compared to a commercial PGPR showed significantly increased wheat yield by 30.71%, and 25.03%, respectively, in season one, and 63.92% and 58.45%, respectively, under reduced fertilizer rates in season two. Individual application of T19 and T29 showed varying results, with T19 increasing wheat yield by 9.33% and 16.22% during seasons three and four but a substantial reduction (33.39%) during season five. T29 exhibited yield increases during season three (9.31%) and five (5.61%) but led to a significant reduction (21.15%) in season four. Genomic analysis unveiled a spectrum of plant growth-promoting genes including those associated with ammonification, phosphate solubilization, ethylene, siderophore, catalase, and superoxide dismutase production. These findings offer valuable insights into the mechanisms behind observed field results, with potential implications for advancing sustainable agriculture and crop productivity in evolving agricultural landscapes.}, }
@article {pmid39905550, year = {2025}, author = {Martínez Rendón, C and Braun, C and Kappelsberger, M and Boy, J and Casanova-Katny, A and Glaser, K and Dumack, K}, title = {Enhancing microbial predator-prey detection with network and trait-based analyses.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {37}, pmid = {39905550}, issn = {2049-2618}, mesh = {*Food Chain ; Antarctic Regions ; *Microbiota ; Animals ; Predatory Behavior ; Bacteria/classification/genetics ; Eukaryota ; }, abstract = {BACKGROUND: Network analyses are often applied to microbial communities using sequencing survey datasets. However, associations in such networks do not necessarily indicate actual biotic interactions, and even if they do, the nature of the interactions commonly remains unclear. While network analyses are valuable for generating hypotheses, the inferred hypotheses are rarely experimentally confirmed.<br><br>RESULTS: We employed cross-kingdom network analyses, applied trait-based functions to the microorganisms, and subsequently experimentally investigated the found putative predator-prey interactions to evaluate whether, and to what extent, correlations indicate actual predator-prey relationships. For this, we investigated algae and their protistan predators in biocrusts of three distinct polar regions, i.e., Svalbard, the Antarctic Peninsula, and Continental Antarctica. Network analyses using FlashWeave indicated that 89, 138, and 51 correlations occurred between predatory protists and algae, respectively. However, trait assignment revealed that only 4.7-9.3% of said correlations link predators to actually suitable prey. We further confirmed these results with HMSC modeling, which resulted in similar numbers of 7.5% and 4.8% linking predators to suitable prey for full co-occurrence and abundance models, respectively. The combination of network analyses and trait assignment increased confidence in the prediction of predator-prey interactions, as we show that 82% of all experimentally investigated correlations could be verified. Furthermore, we found that more vicious predators, i.e., predators with the highest growth rate in co-culture with their prey, exhibit higher stress and betweenness centrality - giving rise to the future possibility of determining important predators from their network statistics.<br><br>CONCLUSIONS: Our results support the idea of using network analyses for inferring predator-prey interactions, but at the same time call for cautionary consideration of the results, by combining them with trait-based approaches to increase confidence in the prediction of biological interactions. Video Abstract.}, }
@article {pmid39903999, year = {2025}, author = {Mondal, A and Parvez, SS and Majumder, A and Sharma, K and Das, B and Bakshi, U and Alam, M and Banik, A}, title = {Co-inoculation of Trichoderma and tea root-associated bacteria enhance flavonoid production and abundance of mycorrhizal colonization in tea (Camellia sinensis).}, journal = {Microbiological research}, volume = {293}, number = {}, pages = {128084}, doi = {10.1016/j.micres.2025.128084}, pmid = {39903999}, issn = {1618-0623}, mesh = {*Camellia sinensis/microbiology/metabolism ; *Flavonoids/biosynthesis ; *Plant Roots/microbiology ; *Mycorrhizae/growth &amp; development ; Soil Microbiology ; Rhizosphere ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Microbiota ; *Trichoderma/physiology/growth &amp; development ; India ; Symbiosis ; Plant Leaves/microbiology/metabolism ; Tea/microbiology ; Phylogeny ; }, abstract = {Tea is one of the most popular nonalcoholic beverages, that contains several medicinally important flavonoids. Due to seasonal variation and various environmental stresses, the overall consistency of tea flavonoids affects the tea quality. To combat stress, plants stimulate symbiotic relationships with root-associated beneficial microbiomes that sustain nutrient allocation. Therefore, a study has been designed to understand the role of the tea root microbiome in sustaining tea leaf flavonoid production. To enumerate the microbiome, tea root and rhizoplane soil were collected from 3 years of healthy plants from Jalpaiguri district, West Bengal, India. A culture-independent approach was adopted to identify root and rhizosphere microbial diversity (BioSample: SAMN31404869; SRA: SRS15503027 [rhizosphere soil metagenome] BioSample: SAMN31404868;SRA:SRS15503030 [root metagenome]. In addition to diverse microbes, four mycorrhiza fungi, i.e., Glomus intraradices, Glomus irregulare, Paraglomus occultum and Scutellospora heterogama were predominant in collected root samples. A culture-dependent approach was also adopted to isolate several plant growth-promoting bacteria [Bacillus sp. D56, Bacillus sp. D42, Bacillus sp. DR15, Rhizobium sp. DR23 (NCBI Accession: OR821747-OR821750)] and one fungal [Trichoderma sp. AM6 (NCBI Accession:OM915414)] strain. A pot experiment was designed to assess the impact of that isolated microbiome on tea seedlings. After six months of microbiome inoculation, tea plants' physicochemical and transcriptional parameters were evaluated. The results confer that the microbiome-treated treatments [(T1-without any microbial inoculation; NCBI Accession: SAMN33591153), Trichoderma sp. AM6 (T2; NCBI Accession: SAMN33591155) and Trichoderma sp. AM6 +VAM containing tea root+synthetic microbial consortia (T5; NCBI Accession: SAMN33591154)] could enhance the total flavonoid content in tea seedlings by upregulating certain transcripts associated with the flavonoid biosynthesis pathway of tea.}, }
@article {pmid39902955, year = {2025}, author = {Li, Q and Marietou, A and Andersen, FF and Hosek, J and Scavenius, C and Zhang, J and Schwab, C}, title = {In vitro investigations on the impact of fermented dairy constituents on fecal microbiota composition and fermentation activity.}, journal = {Microbiology spectrum}, volume = {13}, number = {3}, pages = {e0219324}, pmid = {39902955}, issn = {2165-0497}, support = {00//M&#xe6;lkeafgiftsfonden (Milk Tax Fund)/ ; 00//Brodrene Hartmann Fonden/ ; }, mesh = {*Feces/microbiology ; Fermentation ; Lactose/metabolism ; *Gastrointestinal Microbiome ; Humans ; beta-Galactosidase/genetics/metabolism ; Streptococcus thermophilus/metabolism/genetics ; RNA, Ribosomal, 16S/genetics ; *Cultured Milk Products/microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Butyrates/metabolism ; *Dairy Products/microbiology ; }, abstract = {UNLABELLED: Fermented dairy constitutes a major dietary source and contains lactose as the main carbohydrate and living starter cultures, which can encounter the intestinal microbiota after ingestion. To investigate whether dairy-related nutritional and microbial modulation impacted intestinal microbiota composition and activity, we employed static fecal microbiota fermentations and a dairy model system consisting of lactose and Streptococcus thermophilus wild type and β-galactosidase deletion mutant. In addition, we conducted single-culture validation studies. 16S rRNA gene-based microbial community analysis showed that lactose increased the abundance of Bifidobacteriaceae and Anaerobutyricum and Faecalibacterium spp. The supplied lactose was hydrolyzed within 24 h of fermentation and led to higher expression of community-indigenous β-galactosidases. Targeted protein analysis confirmed that bifidobacteria contributed most β-galactosidases together with other taxa, including Escherichia coli and Anaerobutyricum hallii. Lactose addition led to higher (P < 0.05) levels of butyrate compared to controls, likely due to lactate-based cross-feeding and direct lactose metabolism by butyrate-producing Anaerobutyricum and Faecalibacterium spp. Representatives of both genera used lactose to produce butyrate in single cultures. When supplemented at around 5.5 log cells mL[-1], S. thermophilus or its β-galactosidase-negative mutant outnumbered the indigenous Streptococcaceae population at the beginning of fermentation but had no impact on lactose utilization and final short-chain fatty acid profiles.<br><br>IMPORTANCE: The consumption of fermented food has been linked to positive health outcomes, possibly due to interactions of food components with the intestinal microbiota. This study brings forward new insights into how major constituents of fermented dairy affect intestinal microbial ecology and activity when supplied together or alone. We provide evidence that lactose availability increased the production of butyrate by fecal microbiota through cross-feeding and did not observe a contribution of starter cultures to lactose metabolism, possibly due to a lack of competitiveness. The methodological setup used in this study can be implemented in future investigations to determine the impact of other fermented foods and their major components on intestinal microbiota composition and activity.}, }
@article {pmid39897492, year = {2025}, author = {Keleher, JG and Strope, TA and Estrada, NE and Griggs Mathis, AM and Easson, CG and Fiore, C}, title = {Freshwater sponges in the southeastern U.S. harbor unique microbiomes that are influenced by host and environmental factors.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18807}, pmid = {39897492}, issn = {2167-8359}, mesh = {*Porifera/microbiology ; Animals ; *Microbiota ; *Fresh Water/microbiology ; North Carolina ; *Bacteria/classification/genetics/isolation &amp; purification ; Symbiosis ; }, abstract = {Marine, and more recently, freshwater sponges are known to harbor unique microbial symbiotic communities relative to the surrounding water; however, our understanding of the microbial ecology and diversity of freshwater sponges is vastly limited compared to those of marine sponges. Here we analyzed the microbiomes of three freshwater sponge species: Radiospongilla crateriformis, Eunapius fragilis, and Trochospongilla horrida, across four sites in western North Carolina, U.S.A. Our results support recent work indicating that freshwater sponges indeed harbor a distinct microbiome composition compared to the surrounding water and that these varied across sampling site indicating both environmental and host factors in shaping this distinct community. We also sampled sponges at one site over 3 months and observed that divergence in the microbial community between sponge and water occurs at least several weeks after sponges emerge for the growing season and that sponges maintain a distinct community from the water as the sponge tissue degrades. Bacterial taxa within the Gammproteobacteria, Alphproteobacteria, Bacteroidota (Flavobacteriia in particular), and Verrucomicrobia, were notable as enriched in the sponge relative to the surrounding water across sponge individuals with diverging microbial communities from the water. These results add novel information on the assembly and maintenance of microbial communities in an ancient metazoan host and is one of few published studies on freshwater sponge microbial symbiont communities.}, }
@article {pmid39890664, year = {2025}, author = {Zhou, Y and Jiang, P and Ding, Y and Zhang, Y and Yang, S and Liu, X and Cao, C and Luo, G and Ou, L}, title = {Deciphering the Distinct Associations of Rhizospheric and Endospheric Microbiomes with Capsicum Plant Pathological Status.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {1}, pmid = {39890664}, issn = {1432-184X}, support = {2023YFD1201502//National Key Research and Development Program of China/ ; 42107262//National Natural Science Foundation of China/ ; CARS-24-A05//China Agriculture Research System of MOF and MARA/ ; }, mesh = {*Capsicum/microbiology ; *Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Plant Diseases/microbiology ; Fungi/classification/isolation &amp; purification/genetics ; Endophytes/classification/genetics/physiology/isolation &amp; purification ; Plant Roots/microbiology ; Biodiversity ; }, abstract = {Exploring endospheric and rhizospheric microbiomes and their associations can help us to understand the pathological status of capsicum (Capsicum annuum L.) for implementing appropriate management strategies. To elucidate the differences among plants with distinct pathological status in the communities and functions of the endospheric and rhizospheric microbiomes, the samples of healthy and diseased capsicum plants, along with their rhizosphere soils, were collected from a long-term cultivation field. The results indicated a higher bacterial richness in the healthy rhizosphere than in the diseased rhizosphere (P < 0.05), with rhizospheric bacterial diversity surpassing endospheric bacterial diversity. The community assemblies of both the endospheric and rhizospheric microbiomes were driven by a combination of stochastic and deterministic processes, with the stochastic processes playing a primary role. The majority of co-enriched taxa in the healthy endophyte and rhizosphere mainly belonged to bacterial Proteobacteria, Actinobacteria, and Firmicutes, as well as fungal Ascomycota. Most of the bacterial indicators, primarily Alphaproteobacteria and Actinobacteria, were enriched in the healthy rhizosphere, but not in the diseased rhizosphere. In addition, most of the fungal indicators were enriched in both the healthy and diseased endosphere. The diseased endophyte constituted a less complex and stable microbial community than the healthy endophyte, and meanwhile, the diseased rhizosphere exhibited a higher complexity but lower stability than the healthy rhizosphere. Notably, only a microbial function, namely biosynthesis of other secondary metabolites, was higher in the healthy endophytes than in the diseased endophyte. These findings indicated the distinct responses of rhizospheric and endospheric microbiomes to capsicum pathological status, and in particular, provided a new insight into leveraging soil and plant microbial resources to enhance agriculture production.}, }
@article {pmid39890294, year = {2025}, author = {Baker, JM and Dickson, RP}, title = {The Microbiome and Pulmonary Immune Function.}, journal = {Clinics in chest medicine}, volume = {46}, number = {1}, pages = {77-91}, doi = {10.1016/j.ccm.2024.10.006}, pmid = {39890294}, issn = {1557-8216}, mesh = {Humans ; *Microbiota/immunology ; *Lung/immunology/microbiology ; *Lung Diseases/immunology/microbiology ; }, abstract = {In the last decade, the lung microbiome field has matured into a promising area of translational and clinical research due to emerging evidence indicating a role for respiratory microbiota in lung immunity and pathogenesis. Here, we review recent insights pertaining to the lung microbiome's relationship with pulmonary immune function. We discuss areas of future investigation that will be essential to the development of immunomodulatory therapies targeting the respiratory microbiome.}, }
@article {pmid39889603, year = {2025}, author = {Fu, P and Zhai, J and Yang, X and Gao, J and Ren, Z and Guo, B and Qi, P}, title = {Distribution and influencing factors of antibiotic resistance genes in two mussel species along the coasts of the East China Sea and the Yellow Sea.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137399}, doi = {10.1016/j.jhazmat.2025.137399}, pmid = {39889603}, issn = {1873-3336}, mesh = {Animals ; China ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; *Mytilus/microbiology ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Oceans and Seas ; Microbiota ; Aquaculture ; }, abstract = {Antibiotic resistance genes (ARGs) raise a global public health concern. The ARGs profile in marine aquaculture environments was well reported, yet it is poorly revealed in marine bivalves. This study investigated the microbiota, resistome, and environmental factors within the digestive glands of two mussel species (Mytilus coruscus and Mytilus galloprovincialis) cultivated in the East China Sea and Yellow Sea. The microbial communities in the digestive glands of mussels exhibit significant variations across different sampling sites and between the two seas. The three bacterial phyla that predominated in all samples were Firmicutes, Bacteroidota, and Proteobacteria. A total of 88 ARGs were detected, with aminoglycoside resistance genes and multidrug resistance genes being the dominant categories. Analysis revealed that the quinolone resistance gene qnrB, associated with clinically relevant human pathogens, was ubiquitous in all samples. Members of the Enterobacteriaceae family may serve as a reservoir for qnrB within the investigated environment. The distribution of ARGs shows potential associations with the composition of microbial communities in the digestive glands, environmental factors, and mobile genetic elements (MGEs). These findings enhance the elucidation of microbial ecology and antibiotic resistance in marine aquaculture.}, }
@article {pmid39885242, year = {2025}, author = {Grafmüller, J and Möllmer, J and Muehe, EM and Kammann, CI and Kray, D and Schmidt, HP and Hagemann, N}, title = {Publisher Correction: Granulation compared to co-application of biochar plus mineral fertilizer and its impacts on crop growth and nutrient leaching.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {3796}, doi = {10.1038/s41598-025-87051-2}, pmid = {39885242}, issn = {2045-2322}, }
@article {pmid39884152, year = {2025}, author = {Maphosa, S and Steyn, M and Lebre, PH and Gokul, JK and Convey, P and Marais, E and Maggs-Kölling, G and Cowan, DA}, title = {Rhizosphere bacterial communities of Namib Desert plant species: Evidence of specialised plant-microbe associations.}, journal = {Microbiological research}, volume = {293}, number = {}, pages = {128076}, doi = {10.1016/j.micres.2025.128076}, pmid = {39884152}, issn = {1618-0623}, mesh = {*Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Desert Climate ; Phylogeny ; Plant Roots/microbiology ; *Microbiota ; *Plants/microbiology ; Namibia ; DNA, Bacterial/genetics ; Soil/chemistry ; Biodiversity ; }, abstract = {Rhizosphere microbial communities are intimately associated with plant root surfaces. The rhizosphere microbiome is recruited from the surrounding soil and is known to impact positively on the plant host via enhanced resistance to pathogens, increased nutrient availability, growth stimulation and increased resistance to desiccation. Desert ecosystems harbour a diversity of perennial and annual plant species, generally exhibiting considerable physiological adaptation to the low-water environment. In this study, we explored the rhizosphere bacterial microbiomes associated with selected desert plant species. The rhizosphere bacterial communities of 11 plant species from the central Namib Desert were assessed using 16S rRNA gene-dependent phylogenetic analyses. The rhizosphere microbial community of each host plant species was compared with control soils collected from their immediate vicinity, and with those of all other host plants. Rhizosphere and control soil bacterial communities differed significantly and were influenced by both location and plant species. Rhizosphere-associated genera included 67 known plant growth-promoting taxa, including Rhizobium, Bacillus, Microvirga, Kocuria and Paenibacillus. Other than Kocuria, these genera constituted the 'core' rhizosphere bacterial microbiome, defined as being present in > 90 % of the rhizosphere communities. Nine of the 11 desert plant species harboured varying numbers and proportions of species-specific microbial taxa. Predictive analyses of functional pathways linked to rhizosphere microbial taxa showed that these were significantly enriched in the biosynthesis or degradation of a variety of substances such as sugars, secondary metabolites, phenolic compounds and antimicrobials. Overall, our data suggest that plant species in the Namib Desert recruit unique taxa to their rhizosphere bacterial microbiomes that may contribute to their resilience in this extreme environment.}, }
@article {pmid39883228, year = {2024}, author = {Han, JR and Li, S and Li, WJ and Dong, L}, title = {Mining microbial and metabolic dark matter in extreme environments: a roadmap for harnessing the power of multi-omics data.}, journal = {Advanced biotechnology}, volume = {2}, number = {3}, pages = {26}, pmid = {39883228}, issn = {2948-2801}, support = {32270076//National Natural Science Foundation of China/ ; 2022xjkk1200//The Third Xinjiang Scientific Expedition Program/ ; 2022B0202110001//The Key-Area Research and Development Program of Guangdong Province/ ; }, abstract = {Extreme environments such as hyperarid, hypersaline, hyperthermal environments, and the deep sea harbor diverse microbial communities, which are specially adapted to extreme conditions and are known as extremophiles. These extremophilic organisms have developed unique survival strategies, making them ideal models for studying microbial diversity, evolution, and adaptation to adversity. They also play critical roles in biogeochemical cycles. Additionally, extremophiles often produce novel bioactive compounds in response to corresponding challenging environments. Recent advances in technologies, including genomic sequencing and untargeted metabolomic analysis, have significantly enhanced our understanding of microbial diversity, ecology, evolution, and the genetic and physiological characteristics in extremophiles. The integration of advanced multi-omics technologies into culture-dependent research has notably improved the efficiency, providing valuable insights into the physiological functions and biosynthetic capacities of extremophiles. The vast untapped microbial resources in extreme environments present substantial opportunities for discovering novel natural products and advancing our knowledge of microbial ecology and evolution. This review highlights the current research status on extremophilic microbiomes, focusing on microbial diversity, ecological roles, isolation and cultivation strategies, and the exploration of their biosynthetic potential. Moreover, we emphasize the importance and potential of discovering more strain resources and metabolites, which would be boosted greatly by harnessing the power of multi-omics data.}, }
@article {pmid39883081, year = {2025}, author = {Shin, GY and Asselin, JA and Smith, A and Aegerter, B and Coutinho, T and Zhao, M and Dutta, B and Mazzone, J and Neupane, R and Gugino, B and Hoepting, C and Khanal, M and Malla, S and Nischwitz, C and Sidhu, J and Burke, AM and Davey, J and Uchanski, M and Derie, ML and du Toit, LJ and Stresow-Cortez, S and Bonasera, JM and Stodghill, P and Kvitko, B}, title = {Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39883081}, issn = {1751-7370}, support = {2019-51181-30013//Specialty Crops Research Initiative Award/ ; //National Institute of Food and Agriculture/ ; //U.S. Department of Agriculture/ ; }, mesh = {*Onions/microbiology ; *Pantoea/genetics/pathogenicity ; *Plasmids/genetics ; *Plant Diseases/microbiology ; Phylogeny ; Genome, Bacterial ; Virulence ; Multigene Family ; Virulence Factors/genetics ; }, abstract = {Pantoea agglomerans is one of four Pantoea species reported in the USA to cause bacterial rot of onion bulbs. However, not all P. agglomerans strains are pathogenic to onion. We characterized onion-associated strains of P. agglomerans to elucidate the genetic and genomic signatures of onion-pathogenic P. agglomerans. We collected >300 P. agglomerans strains associated with symptomatic onion plants and bulbs from public culture collections, research laboratories, and a multi-year survey in 11 states in the USA. Combining the 87 genome assemblies with 100 high-quality, public P. agglomerans genome assemblies we identified two well-supported P. agglomerans phylogroups. Strains causing severe symptoms on onion were only identified in Phylogroup II and encoded the HiVir pantaphos biosynthetic cluster, supporting the role of HiVir as a pathogenicity factor. The P. agglomerans HiVir cluster was encoded in two distinct plasmid contexts: (i) as an accessory gene cluster on a conserved P. agglomerans plasmid (pAggl), or (ii) on a mosaic cluster of plasmids common among onion strains (pOnion). Analysis of closed genomes revealed that the pOnion plasmids harbored alt genes conferring tolerance to Allium thiosulfinate defensive chemistry and many harbored cop genes conferring resistance to copper. We demonstrated that the pOnion plasmid pCB1C can act as a natively mobilizable pathogenicity plasmid that transforms P. agglomerans Phylogroup I strains, including environmental strains, into virulent pathogens of onion. This work indicates a central role for plasmids and plasmid ecology in mediating P. agglomerans interactions with onion plants, with potential implications for onion bacterial disease management.}, }
@article {pmid39882875, year = {2025}, author = {Cross, K and Beckman, N and Jahnes, B and Sabree, ZL}, title = {Microbiome metabolic capacity is buffered against phylotype losses by functional redundancy.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {2}, pages = {e0236824}, pmid = {39882875}, issn = {1098-5336}, support = {IOS 2312818//National Science Foundation (NSF)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics/analysis ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Phylogeny ; Diet ; }, abstract = {UNLABELLED: Many animals contain a species-rich and diverse gut microbiota that likely contributes to several host-supportive services that include diet processing and nutrient provisioning. Loss of microbiome taxa and their associated metabolic functions as result of perturbations may result in loss of microbiome-level services and reduction of metabolic capacity. If metabolic functions are shared by multiple taxa (i.e., functional redundancy), including deeply divergent lineages, then the impact of taxon/function losses may be dampened. We examined to what degree alterations in phylotype diversity impact microbiome-level metabolic capacity. Feeding two nutritionally imbalanced diets to omnivorous Periplaneta americana over 8 weeks reduced the diversity of their phylotype-rich gut microbiomes by ~25% based on 16S rRNA gene amplicon sequencing, yet PICRUSt2-inferred metabolic pathway richness was largely unaffected due to their being polyphyletic. We concluded that the nonlinearity between taxon and metabolic functional losses is due to microbiome members sharing many well-characterized metabolic functions, with lineages remaining after perturbation potentially being capable of preventing microbiome "service outages" due to functional redundancy.<br><br>IMPORTANCE: Diet can affect gut microbiome taxonomic composition and diversity, but its impacts on community-level functional capabilities are less clear. Host health and fitness are increasingly being linked to microbiome composition and further modeling of the relationship between microbiome taxonomic and metabolic functional capability is needed to inform these linkages. Invertebrate animal models like the omnivorous American cockroach are ideal for this inquiry because they are amenable to various diets and provide high replicates per treatment at low costs and thus enabling rigorous statistical analyses and hypothesis testing. Microbiome taxonomic composition is diet-labile and diversity was reduced after feeding on unbalanced diets (i.e., post-treatment), but the predicted functional capacities of the post-treatment microbiomes were less affected likely due to the resilience of several abundant taxa surviving the perturbation as well as many metabolic functions being shared by several taxa. These results suggest that both taxonomic and functional profiles should be considered when attempting to infer how perturbations are altering gut microbiome services and possible host outcomes.}, }
@article {pmid39882867, year = {2025}, author = {Asmus, AE and Gaire, TN and Schweisthal, KJ and Staben, SM and Noyes, NR}, title = {Microbiome characterization of two fresh pork cuts during production in a pork fabrication facility.}, journal = {Microbiology spectrum}, volume = {13}, number = {3}, pages = {e0220924}, pmid = {39882867}, issn = {2165-0497}, mesh = {Animals ; *Microbiota/genetics ; Swine ; RNA, Ribosomal, 16S/genetics ; Food Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Red Meat/microbiology ; *Pork Meat/microbiology ; Salmonella/isolation &amp; purification/genetics/classification ; *Meat/microbiology ; Food Handling ; }, abstract = {The goal of this study was to characterize the microbial profile of two different fresh pork cuts, bootjack (BJ) trim and tenderloin (TL), through a 16S rRNA sequencing workflow developed specifically for investigating low-biomass fresh meat within a commercial production schedule. Additionally, this study aimed to determine a baseline Salmonella prevalence and enumeration profile across these two fresh pork cuts. Results showed that microbiome diversity was different between the BJ and TL, and also differed significantly by processing date. The relative abundance of key bacterial genera associated with food safety and spoilage was also different between the two meat types. However, over the course of the production shift, changes in the meat microbiome were limited in both the BJ and TL. The crude prevalence and enumerated burden of Salmonella were lower than what has been previously reported in similar fresh pork cuts, and all of the Salmonella-positive samples occurred on just two processing windows of 1-2 days each. Taken together, the results of this study suggest that the microbial profile of two fresh pork cuts is significantly different even within the same plant at the same time points, and that day-to-day variability within the production process likely influences both the fresh pork microbiome and Salmonella profile of these two meat types.IMPORTANCEModern pork processing involves a series of processes that begin with the handling and transport of the live animals, proceed through harvest and fabrication, and end with the packaging and distribution of fresh pork to the consumer. Each step in this process can alter the microbial community of fresh pork and influence the meat's safety and shelf life. However, little is known about the microbial ecology of individual, unprocessed pork cuts and if the diversity of the meat microbiome remains consistent throughout a production schedule. Additionally, the crude prevalence and enumeration of Salmonella have not been well established for individual fresh pork cuts throughout a production schedule. A more thorough understanding of the microbial profile at different stages of pork production will help processors determine processing steps that impact the microbial characteristics of fresh pork. This insight will help processors implement targeted intervention strategies to enhance food safety and quality.}, }
@article {pmid39880965, year = {2025}, author = {Contreras-Negrete, G and Valiente-Banuet, A and Molina-Freaner, F and Partida-Martínez, LP and Hernández-López, A}, title = {Agricultural Practices and Environmental Factors Drive Microbial Communities in the Mezcal-Producing Agave angustifolia Haw.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {181}, pmid = {39880965}, issn = {1432-184X}, support = {CV549242//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 319061//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; }, mesh = {*Agave/microbiology/growth &amp; development ; *Soil Microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Agriculture/methods ; RNA, Ribosomal, 16S/genetics ; *Alcoholic Beverages/microbiology ; Mexico ; Rhizosphere ; Biodiversity ; }, abstract = {Mezcal, a traditional Mexican alcoholic beverage, has been a vital source of livelihood for indigenous and rural communities for centuries. However, increasing international demand is exerting pressure on natural resources and encouraging intensive agricultural practices. This study investigates the impact of management practices (wild, traditional, and conventional) and environmental factors on the microbial communities associated with Agave angustifolia, a key species in mezcal production. High-throughput sequencing of the 16S rRNA and ITS2 gene regions revealed distinct prokaryotic and fungal community structures across different plant compartments (endosphere, episphere, and soil), identifying 8214 prokaryotic and 7459 fungal ASVs. Core microbial communities were dominated by Proteobacteria, Actinobacteria, Ascomycota, and Basidiomycota. Alpha diversity analyses showed significant increases in prokaryotic diversity from the endosphere to soil, while fungal diversity remained stable. Notably, conventional management practices were associated with reductions in beneficial microbial taxa. Environmental factors such as precipitation and temperature significantly influenced microbial diversity and composition, especially in the rhizosphere. Beta diversity patterns underscored the strong impact of plant compartment, with management practices and aridity further shaping microbial communities. These results reveal the intricate interactions between management practices, environmental conditions, and microbial diversity, providing valuable insights for the sustainable cultivation of A. angustifolia.}, }
@article {pmid39880083, year = {2025}, author = {Vande Moortele, T and Verschaffelt, P and Huang, Q and Doncheva, NT and Holstein, T and Jachmann, C and Dawyndt, P and Martens, L and Mesuere, B and Van Den Bossche, T}, title = {PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways.}, journal = {Molecular &amp; cellular proteomics : MCP}, volume = {24}, number = {3}, pages = {100918}, pmid = {39880083}, issn = {1535-9484}, mesh = {*Software ; *Metabolic Networks and Pathways ; Humans ; *Proteomics/methods ; Gastrointestinal Microbiome ; User-Computer Interface ; Proteome/metabolism ; *Computational Biology/methods ; Caloric Restriction ; }, abstract = {Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health. Pathway analysis offers structured insights into the biochemical processes within these communities. However, no existing tool effectively combines pathway analysis with peptide- or protein-level data. We here introduce PathwayPilot, a web-based application designed to improve metaproteomic data analysis by integrating pathway analysis with peptide- and protein-level data, filling a critical gap in current metaproteomics bioinformatics tools. By allowing users to compare functional annotations across different samples or multiple organisms within a sample, PathwayPilot provides valuable insights into microbial functions. In the re-analysis of a study examining the effects of caloric restriction on gut microbiota, the tool successfully identified shifts in enzyme expressions linked to short-chain fatty acid biosynthesis, aligning with its original findings. PathwayPilot's user-friendly interface and robust capabilities make it a significant advancement in metaproteomics, with the potential for widespread application in microbial ecology and health sciences. All code is open source under the Apache2 license and is available at https://pathwaypilot.ugent.be.}, }
@article {pmid39878512, year = {2025}, author = {Flanagan, K and Gassner, K and Lang, M and Ozelyte, J and Hausmann, B and Crepaz, D and Pjevac, P and Gasche, C and Berry, D and Vesely, C and Pereira, FC}, title = {Human-derived microRNA 21 regulates indole and L-tryptophan biosynthesis transcripts in the gut commensal Bacteroides thetaiotaomicron.}, journal = {mBio}, volume = {16}, number = {3}, pages = {e0392824}, pmid = {39878512}, issn = {2150-7511}, support = {ZK-57//Austrian Science Fund (FWF)/ ; }, mesh = {*MicroRNAs/genetics/metabolism ; Humans ; *Tryptophan/biosynthesis ; *Gastrointestinal Microbiome/genetics ; *Bacteroides thetaiotaomicron/metabolism/genetics ; Feces/microbiology ; Irritable Bowel Syndrome/microbiology ; Gene Expression Regulation, Bacterial ; Indoles ; }, abstract = {UNLABELLED: In the gut, microRNAs (miRNAs) produced by intestinal epithelial cells are secreted into the lumen and can shape the composition and function of the gut microbiome. Crosstalk between gut microbes and the host plays a key role in irritable bowel syndrome (IBS) and inflammatory bowel diseases, yet little is known about how the miRNA-gut microbiome axis contributes to the pathogenesis of these conditions. Here, we investigate the ability of miR-21, a miRNA that we found decreased in fecal samples from IBS patients, to associate with and regulate gut microbiome function. When incubated with the human fecal microbiota, miR-21 revealed a rapid internalization or binding to microbial cells, which varied in extent across different donor samples. Fluorescence-activated cell sorting and sequencing of microbial cells incubated with fluorescently labeled miR-21 identified organisms belonging to the genera Bacteroides, Limosilactobacillus, Ruminococcus, or Coprococcus, which predominantly interacted with miR-21. Surprisingly, these and other genera also interacted with a miRNA scramble control, suggesting that physical interaction and/or uptake of these miRNAs by gut microbiota is not sequence-dependent. Nevertheless, transcriptomic analysis of the gut commensal Bacteroides thetaiotaomicron revealed a miRNA sequence-specific effect on bacterial transcript levels. Supplementation of miR-21, but not of small RNA controls, resulted in significantly altered levels of many cellular transcripts and increased transcription of a biosynthetic operon for indole and L-tryptophan, metabolites known to regulate host inflammation and colonic motility. Our study identifies a novel putative miR-21-dependent pathway of regulation of intestinal function through the gut microbiome with implications for gastrointestinal conditions.<br><br>IMPORTANCE: The mammalian gut represents one of the largest and most dynamic host-microbe interfaces. Host-derived microRNAs (miRNAs), released from the gut epithelium into the lumen, have emerged as important contributors to host-microbe crosstalk. Levels of several miRNAs are altered in the stool of patients with irritable bowel syndrome or inflammatory bowel disease. Understanding how miRNAs interact with and shape gut microbiota function is crucial as it may enable the development of new targeted treatments for intestinal diseases. This study provides evidence that the miRNA miR-21 can rapidly associate with diverse microbial cells form the gut and increase levels of transcripts involved in tryptophan synthesis in a ubiquitous gut microbe. Tryptophan catabolites regulate key functions, such as gut immune response or permeability. Therefore, this mechanism represents an unexpected host-microbe interaction and suggests that host-derived miR-21 may help regulate gut function via the gut microbiota.}, }
@article {pmid39878482, year = {2025}, author = {Rodriguez-Garcia, C and Wall, H and Ottesen, E and Grainy, J}, title = {Characterization of extended-spectrum beta-lactamase-producing Enterobacteriaceae from recreational water in Athens, GA, using an undergraduate laboratory module.}, journal = {Journal of microbiology &amp; biology education}, volume = {26}, number = {1}, pages = {e0005624}, pmid = {39878482}, issn = {1935-7877}, abstract = {We present a laboratory module that uses isolation of antibiotic-resistant bacteria from locally collected stream water samples to introduce undergraduate students to basic microbiological culture-based and molecular techniques. This module also educates them on the global public health threat of antibiotic-resistant organisms. Through eight laboratory sessions, students are involved in quality testing of water sources from their neighborhoods, followed by isolation of extended-spectrum beta-lactamase-producing Enterobacteriaceae. By the end of the module, students should be able to isolate Enterobacteriaceae from the environment using selective and differential media, identify isolates using biochemical tests, characterize antibiotic resistance phenotypes using Kirby Bauer and MIC tests, and evaluate the presence of select beta-lactamase genes of interest using PCR. To complement laboratory sessions, students participated in a weekly flipped classroom session with collaborative peer discussions and activities to reinforce concepts applied in the laboratory. Learning outcomes were measured over four semesters with concept checks, in-lecture activities, exams, and laboratory reports. We hypothesized that more than 50% of the student population would achieve each learning objective through the implementation of this authentic research laboratory module. Here, we highlight specific questions used to assess learning objective comprehension and demonstrate that each learning objective was achieved by 65%-100% of the student population. We present a ready-to-adapt module with flexible resources that can be implemented in courses across disciplines in biology, microbiology, environmental sciences, and public health.}, }
@article {pmid39876091, year = {2025}, author = {Tocarruncho, OI and Neuta, Y and Lesmes, Y and Castillo, DM and Leal, S and Chambrone, L and Lafaurie, GI}, title = {Submucosal Microbiome Profiles in Paired and Unpaired Samples From Healthy and Peri-Implantitis Dental Implants.}, journal = {Clinical implant dentistry and related research}, volume = {27}, number = {1}, pages = {e13423}, doi = {10.1111/cid.13423}, pmid = {39876091}, issn = {1708-8208}, support = {490-21//Research Vice Rectory of Universidad El Bosque/ ; }, mesh = {Humans ; *Peri-Implantitis/microbiology ; *Microbiota ; Cross-Sectional Studies ; Male ; Middle Aged ; Female ; *Dental Implants/microbiology ; RNA, Ribosomal, 16S ; Adult ; Aged ; }, abstract = {BACKGROUND: This cross-sectional study aimed to compare the composition of the submucosal microbiome of peri-implantitis with paired and unpaired healthy implant samples.<br><br>METHODS: We evaluated submucosal plaque samples obtained in 39 cases, including 13 cases of peri-implantitis, 13 cases involving healthy implants from the same patient (paired samples), and 13 cases involving healthy implants from different individuals (unpaired samples). The patients were evaluated using next-generation genomic sequencing (Illumina) based on 16S rRNA gene amplification. The sequences were grouped according to the amplicon sequence variant (ASV) to define the taxonomic categories. Alpha diversity was analyzed using Shannon's and Simpson's indices, while beta diversity was evaluated using principal coordinate analysis, analysis of similarities, and permutational multivariate variance analysis. Additionally, UniFrac distances were evaluated using Quantitative Insights into Microbial Ecology 2. Finally, we evaluated between-group differences in the taxonomic components.<br><br>RESULTS: There were no significant between-group differences in alpha diversity. The average bacterial ratios of Filifactor alocis, Porphyromona endodontalis, Tannerella forsythia, Treponema denticola, Peptostreptococcaceae [Eubacterium nodatum], Desulfobulbus sp. HTM 041, and Mogibacterium timidum significantly differed between peri-implantitis samples and unpaired samples from the healthy implants (p&#x2009;<&#x2009;0.05). However, there were few differences in the microbiota between peri-implantitis samples and those paired with healthy implants in the same patient.<br><br>CONCLUSIONS: Future studies comparing the microbiome compositions using sequencing techniques between healthy implants and implants with peri-implantitis should focus on retrieving samples from the same patient, especially in individuals with a history of periodontitis.}, }
@article {pmid39874167, year = {2025}, author = {Zhang, F and Zhang, S and Wu, Y and Liu, J and Zhao, S and Qiu, Z and Zhu 朱, M&#x58a8;}, title = {Powdery Mildew of Echinacea purpurea Caused by Podosphaera xanthii in China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-12-24-2632-PDN}, pmid = {39874167}, issn = {0191-2917}, abstract = {Echinacea purpurea (Eastern Purple Coneflower) is a perennial herbaceous plant belonging to the Asteraceae. It originated from North America and is cultivated all over the world. Extracts of E. purpurea are widely used for the treatments of colds and sore throats (Jiao et al. 2020). In October 2024, powdery mildew-like signs and symptoms were observed on leaves of E. purpurea plants (n=100) cultivated in a garden (20 m2) in Xinxiang city, Henan Province, China (35.32° N, 113.92° E). A specimen (PX-ZM20241024) was stored in Xinxiang Key Laboratory of Plant Stress Biology. The infected leaves were covered with white and thin masses and showed senescence symptoms. More than 80% of plants (n=100) exhibited these signs and symptoms. White colonies were on both sides surfaces of the leaves, covering about 80% of the leaf area. The slightly curved or straight Conidia chain (n = 50) were 70 to 156 × 8 to 12 μm in size and consisted of foot cells, shorter cells, and conidia. Foot cells were straight, 30 to 60 μm long. Conidia were ellipsoid to oval, 20 to 35 × 12 to 17 μm (n = 50), with a length/width ratio of 1.8 to 2.2, containing fibrosin bodies. These morphological characteristics were similar to Podosphaera xanthii (Braun and Cook 2012). Following a previously reported method (Zhu et al. 2022), the internal transcribed spacer (ITS) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) regions of a selected specimen of the fungus were amplified and sequenced with primers ITS1/ITS4 (White et al. 1990) and GAPDH1/GAPDH3R (Bradshaw et al. 2022). The resulting sequences were deposited in GenBank (Accession No. PQ508348 and PQ734986). BLASTn analysis indicated that the ITS and GAPDH sequences had 99.82 % (564/565 bp) and 100% (238/238 bp) identity with reported P. xanthii (MW300956 and ON075660) on Xanthium strumarium and Cucurbita moschata, respectively (Zhu et al. 2024; Bradshaw et al. 2022). By phylogenetic analysis, the isolated fungus clustered with previously reported P. xanthii (Zhu et al. 2024; Bradshaw et al. 2022). Therefore, the morphology and phylogenetic analysis indicated that the pathogen was P. xanthii. To complete Koch's postulates, mature leaves of three healthy E. purpurea (30 cm high) were inoculated with fungal conidia by gently pressing surfaces of infested leaves onto leaves of healthy plants. Three untreated plants served as controls. Both the control and inoculated plants were separately placed in greenhouses (humidity, 60%; light/dark, 16 h/8 h; temperature, 18°C). 10 to 12 days post inoculation, the leaves of the inoculated plants exhibited signs of powdery mildew, whereas the control group remained unaffected. The experiments were repeated three times and the same results were obtained. Therefore, the pathogenicity of this fungal pathogen was confirmed. Previously, P. xanthii was reported on E. purpurea in Korea (Choi et al. 2020). To the best of our knowledge, this is the first report of P. xanthii on E. purpurea in China. The sudden presence of powdery mildew caused by P. xanthii may adversely affect plant health and thus reduce the medicinal value of E. purpurea. Therefore, the identification and confirmation of P. xanthii infecting E. purpurea enhances our comprehension of hosts of this pathogen and provides fundamental information for forthcoming disease control studies.}, }
@article {pmid39873755, year = {2025}, author = {Mwaheb, MA and El-Aziz, BMA and Abd-Elhalim, BT and El-Kassim, NA and Radwan, TEE}, title = {Correction to: Study of Different Cultivated Plants Rhizosphere Soil Fungi-Mediated Pectinase: Insights into Production, Optimization, Purification, Biocompatibility, and Application.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {180}, doi = {10.1007/s00248-025-02498-0}, pmid = {39873755}, issn = {1432-184X}, }
@article {pmid39871445, year = {2025}, author = {Zahir, Z and Khan, F and Hall, BD}, title = {Sulfate and Dissolved Organic Carbon Concentrations Drive Distinct Microbial Community Patterns in Prairie Wetland Ponds.}, journal = {Environmental microbiology reports}, volume = {17}, number = {1}, pages = {e70069}, pmid = {39871445}, issn = {1758-2229}, support = {//Agricultural Development Fund/ ; //Natural Sciences and Engineering Research Council of Canada/ ; //Faculty of Graduate Studies and Research, University of Regina/ ; //Government of Canada/ ; }, mesh = {*Wetlands ; *Sulfates/analysis ; *Ponds/microbiology/chemistry ; *Carbon/analysis/metabolism ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Phylogeny ; *Microbiota ; Geologic Sediments/microbiology/chemistry ; }, abstract = {Prairie wetland ponds on the Great Plains of North America offer a diverse array of geochemical scenarios that can be informative about their impact on microbial communities. These ecosystems offer invaluable ecological services while experiencing significant stressors, primarily through drainage and climate change. In this first study systematically combining environmental conditions with microbial community composition to identify various niches in prairie wetland ponds, sediments had higher microbial abundance but lower phylogenetic diversity in ponds with lower concentrations of dissolved organic carbon ([DOC]; 10-18 mg/L) and sulfate ([SO4 [2-]]; 37-58 mg/L) in water. As [DOC] and [SO4 [2-]] increased, there was an initial decline in abundance but not phylogenetic diversity. Maximum values of both abundance and phylogenetic diversity occurred between 56 and 115 mg/L [DOC] and 5,000-6,000 mg/L [SO4 [2-]] and decreased thereafter in ponds with 150-180 mg/L and 8,000-14,000 mg/L [DOC] and [SO4 [2-]], respectively. These findings confirm that environmental variables shape the microbial communities and that key microbial taxa involved in sulfur and carbon cycling dominated these ponds potentially impacting vital biogeochemical processes such as bioavailability of heavy metals, carbon sequestration, and methane emissions.}, }
@article {pmid39871406, year = {2025}, author = {Noell, SE and Abbaszadeh, J and Richards, H and Labat Saint Vincent, M and Lee, CK and Herbold, CW and Stott, MB and Cary, SC and McDonald, IR}, title = {Antarctic Geothermal Soils Exhibit an Absence of Regional Habitat Generalist Microorganisms.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70032}, pmid = {39871406}, issn = {1462-2920}, support = {18-UOW-028//Marsden Fund/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Ecosystem ; *Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Hot Springs/microbiology ; }, abstract = {Active geothermal systems are relatively rare in Antarctica and represent metaphorical islands ideal to study microbial dispersal. In this study, we tested the macro-ecological concept that high dispersal rates result in communities being dominated by either habitat generalists or specialists by investigating the microbial communities on four geographically separated geothermal sites on three Antarctic volcanoes (Mts. Erebus, Melbourne, and Rittman). We found that the microbial communities at higher temperature (max 65°C) sites (Tramway Ridge on Erebus and Rittmann) were unique from each other and were dominated by a variety of novel Archaea from class Nitrososphaeria, while lower temperature (max 50°C) sites (Western Crater on Erebus and Melbourne) had characteristically mesophilic communities (Planctomycetes, Acidobacteriota, etc.) that were highly similar. We found that 97% of the detected microbial taxa were regional habitat specialists, with no generalists, with community assembly driven by high dispersal rates and drift (25% and 30% of community assembly, respectively), not environmental selection. Our results indicate that for microbial communities experiencing high dispersal rates between isolated communities, habitat specialists may tend to out-compete habitat generalists.}, }
@article {pmid39871020, year = {2025}, author = {Zhang, Z and Zhang, Q and Guo, X and Zeng, Z and Wang, Y and Zhang, P and Gao, D and Deng, G and Sun, G and Yang, Y and Wang, J}, title = {Forest Soil pH and Dissolved Organic Matter Aromaticity Are Distinct Drivers for Soil Microbial Community and Carbon Metabolism Potential.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {177}, pmid = {39871020}, issn = {1432-184X}, support = {2023A1515110368//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B1212060002//Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control/ ; }, mesh = {*Soil Microbiology ; *Forests ; *Carbon/metabolism ; *Soil/chemistry ; Hydrogen-Ion Concentration ; China ; *Microbiota ; Carbon Cycle ; Bacteria/metabolism/classification ; Ecosystem ; Microbial Interactions ; }, abstract = {The ecological niche separation of microbial interactions in forest ecosystems is critical to maintaining ecological balance and biodiversity and has yet to be comprehensively explored in microbial ecology. This study investigated the impacts of soil properties on microbial interactions and carbon metabolism potential in forest soils across 67 sites in China. Using redundancy analysis and random forest models, we identified soil pH and dissolved organic matter (DOM) aromaticity as the primary drivers of microbial interactions, representing abiotic conditions and resource niches, respectively. Our network comparison results highlighted significant differences in microbial interactions between acidic and non-acidic soils, suggesting the critical influences of abiotic conditions on microbial interactions. Conversely, abiotic resource niches played a more pivotal role in shaping the carbon metabolism of soil microbes, supporting the concept that resource niche-based processes drive microbial carbon cycling. Additionally, we demonstrated that microbial interactions contributed significantly to ecosystem function stability and served as potential ecological indicators of microbial functional resilience under environmental stress. These insights emphasize the critical need to preserve microbial interactions for effective forest ecosystem management and projection of ecological outcomes in response to future environmental changes.}, }
@article {pmid39870904, year = {2025}, author = {Stenger, PL and Tribollet, A and Guilhaumon, F and Cuet, P and Pennober, G and Jourand, P}, title = {A Multimarker Approach to Identify Microbial Bioindicators for Coral Reef Health Monitoring-Case Study in La Réunion Island.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {179}, pmid = {39870904}, issn = {1432-184X}, mesh = {*Coral Reefs ; *Microbiota ; *Anthozoa/microbiology ; Animals ; *Bacteria/classification/genetics/isolation &amp; purification ; Reunion ; Fungi/classification/isolation &amp; purification/genetics ; *Seawater/microbiology ; *Environmental Monitoring/methods ; Geologic Sediments/microbiology ; Biodiversity ; Seasons ; Microalgae/classification/isolation &amp; purification/genetics ; Biomarkers/analysis ; }, abstract = {The marine microbiome arouses an increasing interest, aimed at better understanding coral reef biodiversity, coral resilience, and identifying bioindicators of ecosystem health. The present study is a microbiome mining of three environmentally contrasted sites along the Hermitage fringing reef of La Réunion Island (Western Indian Ocean). This mining aims to identify bioindicators of reef health to assist managers in preserving the fringing reefs of La Réunion. The watersheds of the fringing reefs are small, steeply sloped, and are impacted by human activities with significant land use changes and hydrological modifications along the coast and up to mid-altitudes. Sediment, seawater, and coral rubble were sampled in austral summer and winter at each site. For each compartment, bacterial, fungal, microalgal, and protist communities were characterized by high throughput DNA sequencing methodology. Results show that the reef microbiome composition varied greatly with seasons and reef compartments, but variations were different among targeted markers. No significant variation among sites was observed. Relevant bioindicators were highlighted per taxonomic groups such as the Firmicutes:Bacteroidota ratio (8.4%:7.0%), the genera Vibrio (25.2%) and Photobacterium (12.5%) dominating bacteria; the Ascomycota:Basidiomycota ratio (63.1%:36.1%), the genera Aspergillus (40.9%) and Cladosporium (16.2%) dominating fungi; the genus Ostreobium (81.5%) in Chlorophyta taxon for microalgae; and the groups of Dinoflagellata (63.3%) and Diatomea (22.6%) within the protista comprising two dominant genera: Symbiodinium (41.7%) and Pelagodinium (27.8%). This study highlights that the identified bioindicators, mainly in seawater and sediment reef compartments, could be targeted by reef conservation stakeholders to better monitor La Réunion Island's reef state of health and to improve management plans.}, }
@article {pmid39870843, year = {2025}, author = {Li, Q and Shao, H}, title = {The Role of Pathogens in Plant Invasion: Accumulation of Local Pathogens Hypothesis.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {178}, pmid = {39870843}, issn = {1432-184X}, support = {No.2023E01012//Ministry of Science and Technology of the People's Republic of China/ ; 2022D01D02//Science and Technology Department of Xinjiang Uygur Autonomous Region/ ; }, mesh = {*Introduced Species ; *Plants/microbiology ; *Plant Diseases/microbiology ; Soil Microbiology ; Host-Pathogen Interactions ; }, abstract = {In the past decades, dozens of invasion hypotheses have been proposed to elucidate the invasion mechanisms of exotic species. Among them, the accumulation of local pathogens hypothesis (ALPH) posits that invasive plants can accumulate local generalist pathogens that have more negative effect on native species than on themselves; as a result, invasive plants might gain competitive advantages that eventually lead to their invasion success. However, research on this topic is still quite insufficient. In this context, we performed a comprehensive literature survey in order to provide a detailed description of the origin and theoretical framework of ALPH; in addition, challenges in contemporary research such as limitations in technical methods and the complexity of interactions between plants and soil microorganisms, as well as future directions of ALPH research, are also discussed in this review. So far, there are less than ten case studies supporting ALPH; therefore, more work is needed to demonstrate whether ALPH is a suitable hypothesis to elucidate the invasion success of certain plant species.}, }
@article {pmid39868213, year = {2025}, author = {Schechter, MS and Trigodet, F and Veseli, IA and Miller, SE and Klein, ML and Sever, M and Maignien, L and Delmont, TO and Light, SH and Eren, AM}, title = {Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39868213}, issn = {2692-8205}, support = {T32 GM007197/GM/NIGMS NIH HHS/United States ; }, abstract = {The increasing availability of microbial genomes is essential to gain insights into microbial ecology and evolution that can propel biotechnological and biomedical advances. Recent advances in genome recovery have significantly expanded the catalogue of microbial genomes from diverse habitats. However, the ability to explain how well a set of genomes account for the diversity in a given environment remains challenging for individual studies or biome-specific databases. Here we present EcoPhylo, a computational workflow to characterize the phylogeography of any gene family through integrated analyses of genomes and metagenomes, and our application of this approach to ribosomal proteins to quantify phylogeny-aware genome recovery rates across three biomes. Our findings show that genome recovery rates vary widely across taxa and biomes, and that single amplified genomes, metagenome-assembled genomes, and isolate genomes have non-uniform yet quantifiable representation of environmental microbes. EcoPhylo reveals highly resolved, reference-free, multi-domain phylogenies in conjunction with distribution patterns of individual clades across environments, providing a means to assess genome recovery in individual studies and benchmark biome-level genome collections.}, }
@article {pmid39868180, year = {2025}, author = {Peters, DI and Shin, IJ and Deever, AN and Kaspar, JR}, title = {Design, Development and Validation of New Fluorescent Strains for Studying Oral Streptococci.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39868180}, issn = {2692-8205}, support = {P30 CA016058/CA/NCI NIH HHS/United States ; R03 DE031766/DE/NIDCR NIH HHS/United States ; }, abstract = {Bacterial strains that are genetically engineered to constitutively produce fluorescent proteins have aided our study of bacterial physiology, biofilm formation, and interspecies interactions. Here, we report on the construction and utilization of new strains that produce the blue fluorescent protein mTagBFP2, the green fluorescent protein sfGFP, and the red fluorescent protein mScarlet-I3 in species Streptococcus gordonii, Streptococcus mutans, and Streptococcus sanguinis. Gene fragments, developed to contain the constitutive promoter Pveg, the fluorescent gene of interest as well as aad9, providing resistance to the antibiotic spectinomycin, were inserted into selected open reading frames on the chromosome that were both transcriptionally silent and whose loss caused no measurable changes in fitness. All strains, except for sfGFP in S. sanguinis, were validated to produce a detectable and specific fluorescent signal. Individual stains, along with extracellular polymeric substances (EPS) within biofilms, were visualized and quantified through either widefield or super-resolution confocal microscopy approaches. Finally, to validate the ability to perform single cell-level analysis using the strains, we imaged and analyzed a triculture mixed-species biofilm of S. gordonii, S. mutans, and S. sanguinis grown with and without addition of human saliva. Quantification of the loss in membrane integrity using a SYTOX dye revealed that all strains had increased loss of membrane integrity with water or human saliva added to the growth media, but the proportion of the population stained by the SYTOX dye varied by species. In all, these fluorescent strains will be a valuable resource for the continued study of oral microbial ecology.}, }
@article {pmid39862387, year = {2025}, author = {Almeida-Silva, F and Van de Peer, Y}, title = {doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {2}, pages = {}, pmid = {39862387}, issn = {1367-4811}, support = {/ERC_/European Research Council/International ; 833522//European Union's Horizon 2020 research and innovation program/ ; }, mesh = {*Software ; *Gene Duplication ; *Genome ; *Genomics/methods ; }, abstract = {SUMMARY: Gene and genome duplications are major evolutionary forces that shape the diversity and complexity of life. However, different duplication modes have distinct impacts on gene function, expression, and regulation. Existing tools for identifying and classifying duplicated genes are either outdated or not user-friendly. Here, we present doubletrouble, an R/Bioconductor package that provides a comprehensive and robust framework for analyzing duplicated genes from genomic data. doubletrouble can detect and classify gene pairs as derived from six duplication modes (segmental, tandem, proximal, retrotransposon-derived, DNA transposon-derived, and dispersed duplications), calculate substitution rates, detect signatures of putative whole-genome duplication events, and visualize results as publication-ready figures. We applied doubletrouble to classify the duplicated gene repertoire in 822 eukaryotic genomes, and results were made available through a user-friendly web interface.<br><br>doubletrouble is available on Bioconductor (https://bioconductor.org/packages/doubletrouble), and the source code is available in a GitHub repository (https://github.com/almeidasilvaf/doubletrouble). doubletroubledb is available online at https://almeidasilvaf.github.io/doubletroubledb/.}, }
@article {pmid39861970, year = {2025}, author = {Saati-Santamaría, Z and Navarro-Gómez, P and Martínez-Mancebo, JA and Juárez-Mugarza, M and Flores, A and Canosa, I}, title = {Genetic and species rearrangements in microbial consortia impact biodegradation potential.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39861970}, issn = {1751-7370}, support = {//University of Seville from the Ministry of Universities/ ; CLU-2018-04//Regional Government of Castilla y Le&#xf3;n/ ; //European NextGenerationEU program/ ; //University of Salamanca/ ; 101090267//EU Horizon Europe program/ ; ProyExcel_00358//Programa de Excelencia de la Junta de Andaluc&#xed;a/ ; //V Plan Propio de investigaci&#xf3;n of the University Pablo de Olavide/ ; }, mesh = {*Microbial Consortia/genetics ; Biodegradation, Environmental ; Plasmids/genetics ; *Ibuprofen/metabolism ; *Bacteria/genetics/metabolism/classification ; Gene Transfer, Horizontal ; Wastewater/microbiology ; Phylogeny ; }, abstract = {Genomic reorganisation between species and horizontal gene transfer have been considered the most important mechanism of biological adaptation under selective pressure. Still, the impact of mobile genes in microbial ecology is far from being completely understood. Here we present the collection and characterisation of microbial consortia enriched from environments contaminated with emerging pollutants, such as non-steroidal anti-inflammatory drugs. We have obtained and further enriched two ibuprofen-degrading microbial consortia from two unrelated wastewater treatment plants. We have also studied their ability to degrade the drug and the dynamics of the re-organisations of the genetic information responsible for its biodegradation among the species within the consortium. Our results show that genomic reorganisation within microorganisms and species rearrangements occur rapidly and efficiently during the selection process, which may be facilitated by plasmids and/or transposable elements located within the sequences. We show the evolution of at least two different plasmid backbones on samples from different locations, showing rearrangements of genomic information, including genes encoding activities for IBU degradation. As a result, we found variations in the expression pattern of the consortia after evolution under selective pressure, as an adaptation process to the new conditions. This work provides evidence for changes in the metagenomes of microbial communities that allow adaptation under a selective constraint -ibuprofen as a sole carbon source- and represents a step forward in knowledge that can inspire future biotechnological developments for drug bioremediation.}, }
@article {pmid39857259, year = {2025}, author = {Chung, CC and Gong, GC and Tseng, HC and Chou, WC and Ho, CH}, title = {Dominance of Sulfur-Oxidizing Bacteria, Thiomicrorhabdus, in the Waters Affected by a Shallow-Sea Hydrothermal Plume.}, journal = {Biology}, volume = {14}, number = {1}, pages = {}, pmid = {39857259}, issn = {2079-7737}, support = {NSTC 113-2611-M-019-006//National Science and Technology Council of Taiwan/ ; }, abstract = {The shallow-sea hydrothermal vent at Guishan Islet, located off the coast of Taiwan, serves as a remarkable natural site for studying microbial ecology in extreme environments. In April 2019, we investigated the composition of prokaryotic picoplankton communities, their gene expression profiles, and the dissolved inorganic carbon uptake efficiency. Our results revealed that the chemolithotrophs Thiomicrorhabdus spp. contributed to the majority of primary production in the waters affected by the hydrothermal vent plume. The metatranscriptomic analysis aligned with the primary productivity measurements, indicating the significant gene upregulations associated with carboxysome-mediated carbon fixation in Thiomicrorhabdus. Synechococcus and Prochlorococcus served as the prokaryotic photoautotrophs for primary productivity in the waters with lower influence from hydrothermal vent emissions. Thiomicrorhabdus and picocyanobacteria jointly provided organic carbon for sustaining the shallow-sea hydrothermal vent ecosystem. In addition to the carbon fixation, the upregulation of genes involved in the SOX (sulfur-oxidizing) pathway, and the dissimilatory sulfate reduction indicated that energy generation and detoxification co-occurred in Thiomicrorhabdus. This study improved our understanding of the impacts of shallow-sea hydrothermal vents on the operation of marine ecosystems and biogeochemical cycles.}, }
@article {pmid39856188, year = {2025}, author = {Tokodi, N and Łobodzińska, A and Klimczak, B and Antosiak, A and Młynarska, S and Šulčius, S and Avrani, S and Yoshida, T and Dziga, D}, title = {Proliferative and viability effects of two cyanophages on freshwater bloom-forming species Microcystis aeruginosa and Raphidiopsis raciborskii vary between strains.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {3152}, pmid = {39856188}, issn = {2045-2322}, support = {PPN/ULM/2019/1/00219//Narodowa Agencja Wymiany Akademickiej/ ; 2021/41/N/NZ9/02957//Narodowym Centrum Nauki/ ; 2020/38/L/NZ9/00135//Narodowym Centrum Nauki/ ; S-LL-21-10//Research Council of Lithuania/ ; 1386/20//Israel Science Foundation/ ; }, mesh = {*Microcystis/virology/growth &amp; development ; *Bacteriophages/physiology ; Fresh Water/microbiology ; *Cyanobacteria/virology ; Photosynthesis ; Eutrophication ; }, abstract = {Viruses that infect cyanobacteria are an integral part of aquatic food webs, influencing nutrient cycling and ecosystem health. However, the significance of virus host range, replication efficiency, and host compatibility on cyanobacterial dynamics, growth, and toxicity remains poorly understood. In this study, we examined the effects of cyanophage additions on the dynamics and activity of optimal, sub-optimal, and non-permissive cyanobacterial hosts in cultures of Microcystis aeruginosa and Raphidiopsis raciborskii. Our findings reveal that cross-infectivity can substantially reduce the proliferative success of the cyanophage under conditions of high-density of sub-optimal hosts which suggests phage dispersal limitation as a result of shared infections, in turn impairing their top-down control over the host community. Furthermore, we found that cyanophage addition triggers host strain-specific responses in photosynthetic performance, population size and toxin production, even among non-permissive hosts. These non-lytic effects suggest indirect impacts on co-existing cyanobacteria, increasing the overall complexity and variance in many ecologically relevant cyanobacterial traits. The high variability in responses observed with a limited subset of cyanophage-cyanobacteria combinations not only highlights the intricate role of viral infections in microbial ecosystems but also underscores the significant challenges in predicting the composition, toxicity, and dynamics of cyanobacterial blooms.}, }
@article {pmid39855017, year = {2025}, author = {Savadova-Ratkus, K and Grendaitė, D and Karosienė, J and Stonevičius, E and Kasperovičienė, J and Koreivienė, J}, title = {Modelling harmful algal blooms in a mono- and a polydominant eutrophic lake under temperature and nutrient changes.}, journal = {Water research}, volume = {275}, number = {}, pages = {123138}, doi = {10.1016/j.watres.2025.123138}, pmid = {39855017}, issn = {1879-2448}, mesh = {*Lakes/microbiology ; *Harmful Algal Bloom ; Temperature ; Cyanobacteria ; Climate Change ; Nutrients ; Eutrophication ; Phosphorus ; }, abstract = {Cyanobacterial blooms, driven by nutrient loading and temperature, pose significant ecological and economic challenges. This study employs a combined data-driven and trait-based modelling approach to predict changes in cyanobacterial communities in a mono- and a polydominant shallow temperate lakes under varying temperature and nutrient scenarios. Results of the AQUATOX simulation model for two aquatic systems suggest that a 2 °C temperature increase, consistent with Intergovernmental Panel on Climate Change's predictions, may influence cyanobacteria species composition and dominance, with trends indicating a possible shift favouring Nostocales over Oscillatoriales and Chroococcales. Temperature increases by 4 °C clearly promoted the dominance of Nostocales. Nutrient dynamics appear to influence community structure. In a nutrient-rich monodominant lake, temperature was the primary driver, while in a nutrient-limited polydominant lake, phosphorus availability influenced cyanobacteria species dominance. Combined warming and phosphorus alterations significantly affected cyanobacteria bloom intensity and duration, particularly enhancing Nostocales growth. The study highlights the complexity of cyanobacterial responses to climate change, emphasizing the need for more analysis and comprehensive models to predict harmful algal blooms (HABs) in freshwater ecosystems. While the findings suggest that temperature and nutrient availability may be critical drivers of cyanobacterial dominance, additional research across a broader range of systems is necessary.}, }
@article {pmid39854900, year = {2025}, author = {Reid, CJ and Farrell, M and Kirby, JK}, title = {Microbial communities in biosolids-amended soils: A critical review of high-throughput sequencing approaches.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124203}, doi = {10.1016/j.jenvman.2025.124203}, pmid = {39854900}, issn = {1095-8630}, mesh = {*Soil Microbiology ; Soil/chemistry ; High-Throughput Nucleotide Sequencing ; *Sewage/microbiology ; Microbiota ; }, abstract = {Sustainable reuse of treated wastewater sludge or biosolids in agricultural production requires comprehensive understanding of their risks and benefits. Microbes are central mediators of many biosolids-associated risks and benefits, however understanding of their responses to biosolids remains minimal. Application of biosolids to soils amounts to a coalescence of two distinct microbial communities adapted to vastly different matrices. High-throughput DNA and RNA sequencing (HTS) approaches are required to accurately describe the compositional and functional outcomes of this process as they currently provide the highest possible resolution to deal with complex community-scale phenomena. Furthermore, linkage of HTS data to physicochemical and functional data can reveal biotic and abiotic drivers of coalescence, impacts of biosolids-borne contaminants and the collective downstream implications for soil and plant health. Here we review the current body of literature examining microbial communities in biosolids-amended soils using HTS of total community DNA and RNA. We provide a critical synthesis of soil microbial community composition and functional responses, the physical, chemical and biological drivers of these responses, and the influence of three major biosolids-borne anthropogenic contaminants of concern; antimicrobials and antimicrobial resistance genes, plastics, and per- and polyfluoroalkyl substances (PFAS). Finally, we identify methodological limitations and outstanding research questions precluding a holistic understanding of microbial responses in biosolids-amended soils and envision future research whereby sequence-based microbial ecology is integrated with soil, plant, and contaminant data to preserve soil health, support plant productivity, and remediate contaminants.}, }
@article {pmid39853499, year = {2025}, author = {Lucia, Z and Giulio, G and Matteo, G and Stefano, C and Irene, LP and Paolo, P and Giorgio, B and Hauffe, HC}, title = {More Than Meets the Eye: Unraveling the Interactions Between Skin Microbiota and Habitat in an Opportunistic Amphibian.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {176}, pmid = {39853499}, issn = {1432-184X}, mesh = {Animals ; *Skin/microbiology ; *Microbiota ; *Ecosystem ; *Anura/microbiology ; *Bacteria/classification/isolation &amp; purification/genetics ; Italy ; Batrachochytrium/isolation &amp; purification/genetics ; *Fungi/classification/isolation &amp; purification/genetics ; Wetlands ; Temperature ; Biodiversity ; Hydrogen-Ion Concentration ; Skin Microbiome ; }, abstract = {With amphibians still holding the record as the most threatened class of terrestrial vertebrates, their skin microbiota has been shown to play a relevant role in their survival in a fast-changing world. Yet little is known about how abiotic factors associated with different aquatic habitats impact these skin microorganisms. Here we chose the yellow-bellied toad (Bombina variegata), a small anuran that colonizes a wide range of wetland habitats, to investigate how the diversity and composition of both its bacterial and fungal skin communities vary across different habitats and with water characteristics (temperature, pH, and dissolved oxygen) of these habitats. Skin microbiota was sampled from 14 sites in the Province of Trento (Italy), including natural pools, ephemeral ponds, irrigation tanks, and farm ponds. Interestingly, the diversity of the two microbial components was also highly correlated. Close associations between both the diversity and composition of water and skin communities were noted for each habitat and sampling site, suggesting that water bodies actively contribute to the skin microbiota assemblage. In addition, water pH, temperature, and dissolved oxygen affected both bacterial and fungal diversity of skin. We confirmed the presence of Batrachochytrium dendrobatidis in skin samples of animals collected from eight waterbodies, as well as more than 60 microbial taxa previously associated with resistance to this pathogen. We concluded that both skin bacterial and fungal communities appear to be influenced by each other as well as by environmental communities and conditions, and these relationships connecting the whole ecosystem should be considered in future research concerning amphibian conservation.}, }
@article {pmid39849986, year = {2025}, author = {Liu, Y and Geng, Y and Jiang, Y and Li, P and Li, YZ and Zhang, Z}, title = {Global microbial community biodiversity increases with antimicrobial toxin abundance of rare taxa.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39849986}, issn = {1751-7370}, support = {SDCX-ZG-202203032//Postdoctoral Innovation Project of Shandong Province/ ; BK20230248//Natural Science Foundation of Jiangsu Province/ ; ZR2022QC001//Science Foundation for Youths of Shandong Province/ ; 32070030//National Natural Science Foundation of China/ ; }, mesh = {*Biodiversity ; *Bacteria/classification/metabolism/drug effects/genetics ; *Anti-Infective Agents/metabolism ; *Toxins, Biological ; *Microbiota ; }, abstract = {One of the central questions in microbial ecology is how to explain the high biodiversity of communities. A large number of rare taxa in the community have not been excluded by abundant taxa with competitive advantages, a contradiction known as the biodiversity paradox. Recently, increasing evidence has revealed the central importance of antimicrobial toxins as crucial weapons of antagonism in microbial survival. The powerful effects of antimicrobial toxins result in simple combinations of microorganisms failing to coexist under laboratory conditions, but it is unclear whether they also have a negative impact on the biodiversity of natural communities. Here, we revealed that microbial communities worldwide universally possess functional potential for antimicrobial toxin production. Counterintuitively, the biodiversity of global microbial communities increases, rather than decreases, as the abundance of antimicrobial toxins in rare taxa rises. Rare taxa may encode more antimicrobial toxins than abundant taxa, which is associated with the maintenance of the high biodiversity of microbial communities amid complex interactions. Our findings suggest that the antagonistic interaction caused by antimicrobial toxins may play a positive role in microbial community biodiversity at the global scale.}, }
@article {pmid39849009, year = {2025}, author = {Calderón-Osorno, M and Rojas-Villalta, D and Lejzerowicz, F and Cortés, J and Arias-Andres, M and Rojas-Jimenez, K}, title = {The influence of depth on the global deep-sea plasmidome.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2959}, pmid = {39849009}, issn = {2045-2322}, support = {SIA 0483-21//Universidad Nacional de Costa Rica/ ; C1455//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; C2650//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; C3509//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; }, mesh = {*Plasmids/genetics ; *Metagenome ; *Seawater/microbiology ; Ecosystem ; Gammaproteobacteria/genetics ; Alphaproteobacteria/genetics ; Oceans and Seas ; Bacteria/genetics ; Computational Biology/methods ; Indian Ocean ; }, abstract = {Plasmids play a crucial role in facilitating genetic exchange and enhancing the adaptability of microbial communities. Despite their importance, environmental plasmids remain understudied, particularly those in fragile and underexplored ecosystems such as the deep-sea. In this paper we implemented a bioinformatics pipeline to study the composition, diversity, and functional attributes of plasmid communities (plasmidome) in 81 deep-sea metagenomes from the Tara and Malaspina expeditions, sampled from the Pacific, Atlantic, and Indian Oceans at depths ranging from 270 to 4005 m. We observed an association between depth and plasmid traits, with the 270-1000 m range (mesopelagic samples) exhibiting the highest number of plasmids and the largest plasmid sizes. Plasmids of Alphaproteobacteria and Gammaproteobacteria were predominant across the oceans, particularly in this depth range, which also showed the highest species diversity and abundance of metabolic pathways, including aromatic compound degradation. Surprisingly, relatively few antibiotic resistance genes were found in the deep-sea ecosystem, with most being found in the mesopelagic layer. These included classes such as beta-lactamase, biocide resistance, and aminoglycosides. Our study also identified the MOBP and MOBQ relaxase families as prevalent across various taxonomic classes. This research underscores the importance of studying the plasmidome independently from the chromosomal context. Our limited understanding of the deep-sea's microbial ecology, especially its plasmidome, necessitates caution in human activities like mining. Such activities could have unforeseen impacts on this largely unexplored ecosystem.}, }
@article {pmid39848193, year = {2025}, author = {Odales-Bernal, L and González, LML and Ghysels, S and Lobanov, V and De Vrieze, J and Barrera, EL and Ronsse, F}, title = {Optimized hydrothermal carbonization of chicken manure and anaerobic digestion of its process water for better energy management.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124191}, doi = {10.1016/j.jenvman.2025.124191}, pmid = {39848193}, issn = {1095-8630}, mesh = {*Manure ; Chickens ; Animals ; Anaerobiosis ; Water ; Carbon/chemistry ; Methane ; }, abstract = {Modern poultry production is faced with the challenge of properly managing its associated wastes, in particular chicken manure (CM). There is a need to improve the management of CM through conversion processes that allow the production of value-added products, particularly for energy purposes, such as hydrothermal carbonization (HTC) and anaerobic digestion (AD). The objectives of this study were: i) to optimize the CM-HTC, using response surface methodology with simultaneous optimization of mass yield and higher heating value (HHV), and ii) to evaluate the biomethane potential of the process water generated from hydrochar production under the optimized condition. An analysis of the overall energy potential was also performed. The optimal condition for HTC was 234 °C for 30 min, resulting in hydrochar with an HHV of 14.88 ± 0.22 MJ/kg and a mass yield of 50.00 ± 3.13 wt%. The cumulative methane yield was 179.2 ± 13.1 NmL CH4/g VSadded and 255.5 ± 14.5 NmL CH4/g VSadded for process water at 180 °C and 234 °C, respectively. The addition of hydrochar improved the methane yield by 49.6 ± 10.8%, indicating that this is a valuable option for energy recovery from CM. Overall, the HTC-AD integration approach achieved an energy recovery potential of more than 79%, offering an efficient strategy for CM valorization.}, }
@article {pmid39847340, year = {2025}, author = {Ganley, JG and Seyedsayamdost, MR}, title = {Iron limitation triggers roseoceramide biosynthesis and membrane remodeling in marine roseobacter.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {4}, pages = {e2414434122}, pmid = {39847340}, issn = {1091-6490}, support = {R35 GM152049/GM/NIGMS NIH HHS/United States ; Postdoctoral Fellowship in Marine Microbial Ecology//Simons Foundation (SF)/ ; }, mesh = {*Roseobacter/metabolism ; *Iron/metabolism ; Symbiosis ; *Cell Membrane/metabolism ; Metabolome ; }, abstract = {Chemical communication between marine bacteria and their algal hosts drives population dynamics and ultimately determines the fate of major biogeochemical cycles in the ocean. To gain deeper insights into this small molecule exchange, we screened niche-specific metabolites as potential modulators of the secondary metabolome of the roseobacter, Roseovarius tolerans. Metabolomic analysis led to the identification of a group of cryptic lipids that we have termed roseoceramides. The roseoceramides are elicited by iron-binding algal flavonoids, which are produced by macroalgae that Roseovarius species associate with. Investigations into the mechanism of elicitation show that iron limitation in R. tolerans initiates a stress response that results in lowered oxidative phosphorylation, increased import and catabolism of algal exudates, and reconfiguration of lipid ynthesis to prioritize production of roseoceramides over phospholipids, likely to fortify membrane integrity as well as promote a sessile and symbiotic lifestyle. Our findings add new small molecule words and their "meanings" to the algal-bacterial lexicon and have implications for the initiation of these interactions.}, }
@article {pmid39845484, year = {2024}, author = {Tóth, VR}, title = {Photosynthetic traits of Phragmites australis along an ecological gradient and developmental stages.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1476142}, pmid = {39845484}, issn = {1664-462X}, abstract = {Common reed (Phragmites australis) is a cosmopolitan species, though its dieback is a worldwide phenomenon. In order to assess the evolutionary role of phenotypic plasticity in a successful plant, the values and plasticity of photophysiological traits of Phragmites australis were investigated in the Lake Fertő wetlands at 5 sites with different degrees of reed degradation and along a seasonal sequence. On the one hand, along the established ecological degradation gradient, photophysiological traits of Phragmites changed significantly, affecting plant productivity, although no consistent gradient-type trends were observed. Gradual changes within a season in the values of photosynthetic traits were observed that were recorded in both degraded and stable stands, suggesting a universal response to seasonally changing environmental conditions that could not be overridden by the ecological gradient. On the other hand, reed plants exposed to different levels of degradation showed comparable physiological plasticity; there was no difference in trait variability between stable and degraded stands. This relatively uniform plasticity is likely to contribute to the resilience of reed plants by providing a wider range of adaptive traits under different conditions. In contrast, the 150-200% gradual change in photophysiological trait plasticity with senescence in Phragmites was also demonstrated, reflecting a more dynamic response of the photosynthetic apparatus to seasonal changes. Senescence affected the plasticity of plant traits independently of their degradation status, suggesting a more universal nature of seasonal changes. This research shows that under conditions of conservative resource use determined by stressful habitats, trait values respond to conditions, while trait plasticity shows minimal changes. Furthermore, phenological sequence significantly influenced both the values and the plasticity of the photosynthetic traits studied. Our results underline the impact of ecological degradation on reed physiology and highlight the importance of understanding both trait values and plasticity in plant responses to environmental and seasonal change.}, }
@article {pmid39844349, year = {2025}, author = {Fonseca de Souza, L and Oliveira, HG and Pellegrinetti, TA and Mendes, LW and Bonatelli, ML and Dumaresq, ASR and Sinatti, VVC and Pinheiro, JB and Azevedo, JL and Quecine, MC}, title = {Co-inoculation with Bacillus thuringiensis RZ2MS9 and rhizobia improves the soybean development and modulates soil functional diversity.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {2}, pages = {}, pmid = {39844349}, issn = {1574-6941}, support = {2021/12378-4//FAPESP/ ; 166644/2020-0//National Council for Scientific and Technological Development/ ; 69242/2018-8//H.G.O./ ; 22.1.08498.01.0//T.A.P./ ; }, mesh = {*Glycine max/growth &amp; development/microbiology ; *Soil Microbiology ; *Bacillus thuringiensis/physiology ; Soil/chemistry ; *Rhizobium/physiology ; Biodiversity ; }, abstract = {Despite the beneficial effects of plant growth-promoting rhizobacteria on agriculture, understanding the consequences of introducing foreign microbes into soil taxonomic and functional diversity is necessary. This study evaluated the effects co-inoculation of soybean with Bacillus thuringiensis (Bt) RZ2MS9 and commercial rhizobia on the natural microbial community structure and functional potential. Our results indicated that soybean development was positively influenced by co-inoculation, plants exhibited greater height and a higher number of pods, and no reductions in productivity estimates. Soil prokaryotic diversity and community structure remained unchanged by Bt RZMS9 inoculation or co-inoculation with rhizobia 147 days after sowing. However, functional diversity was influenced by sole Bt inoculation, potentially due to community quorum sensing disruption by N-acyl homoserine lactone hydrolases. The genes enriched by co-inoculation were mostly related to soil phosphorus cycling, with gcd showing the most pronounced increase. The nifA genes increased when rhizobia alone were inoculated, suggesting that this pathway could be affected by Bt RZ2MS9 inoculation. This study demonstrates the synergistic activity of rhizobia and Bt RZ2MS9 on soybean development, without significantly interfering with natural microbial community, presenting a promising approach for sustainable crop management.}, }
@article {pmid39844346, year = {2025}, author = {Melville, DW and Meyer, M and Kümmerle, C and Alvarado-Barrantes, KA and Wilhelm, K and Sommer, S and Tschapka, M and Risely, A}, title = {Delayed feeding disrupts diurnal oscillations in the gut microbiome of a neotropical bat in captivity.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {2}, pages = {}, pmid = {39844346}, issn = {1574-6941}, support = {DFG SO 428/17-1//German Research Foundation/ ; //Ulm University/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Chiroptera/microbiology/physiology ; *Circadian Rhythm ; Feces/microbiology ; *Feeding Behavior ; Hydrogen-Ion Concentration ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Diurnal rhythms of the gut microbiota are emerging as an important yet often overlooked facet of microbial ecology. Feeding is thought to stimulate gut microbial rhythmicity, but this has not been explicitly tested. Moreover, the role of the gut environment is entirely unexplored, with rhythmic changes to gut pH rather than feeding per se possibly affecting gut microbial fluctuations. In this study, we experimentally manipulated the feeding schedule of captive lesser long-nosed bats, Leptonycteris yerbabuenae, to dissociate photic and feeding cues, and measured the faecal microbiota and gut pH every 2 h. We detected strong diurnal rhythms in both microbial alpha diversity and beta diversity as well as in pH within the control group. However, a delay in feeding disrupted oscillations of gut microbial diversity and composition, but did not affect rhythms in gut pH. The oscillations of some genera, such as Streptococcus, which aid in metabolizing nutrients, shifted in accordance with the delayed-feeding cue and were correlated with pH. For other bacterial genera, oscillations were disturbed and no connection to pH was found. Our findings suggest that the rhythmic proliferation of bacteria matches peak feeding times, providing evidence that diurnal rhythms of the gut microbiota likely evolved to optimize their metabolic support to the host's circadian phenotype.}, }
@article {pmid39843903, year = {2025}, author = {Tóth, AB and Terauds, A and Chown, SL and Hughes, KA and Convey, P and Hodgson, DA and Cowan, DA and Gibson, J and Leihy, RI and Murray, NJ and Robinson, SA and Shaw, JD and Stark, JS and Stevens, MI and van den Hoff, J and Wasley, J and Keith, DA}, title = {A dataset of Antarctic ecosystems in ice-free lands: classification, descriptions, and maps.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {133}, pmid = {39843903}, issn = {2052-4463}, support = {LP170101143//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; LP170101143//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005 Securing Antarctica's Environmental Future//Department of Education and Training | Australian Research Council (ARC)/ ; LP170101143//Department of Education and Training | Australian Research Council (ARC)/ ; }, abstract = {Antarctica, Earth's least understood and most remote continent, is threatened by human disturbances and climate-related changes, underscoring the imperative for biodiversity inventories to inform conservation. Antarctic ecosystems support unique species and genetic diversity, deliver essential ecosystem services and contribute to planetary stability. We present Antarctica's first comprehensive ecosystem classification and map of ice-free lands, which host most of the continent's biodiversity. We used latent variables in factor analyses to partition continental-scale abiotic variation, then biotic variation represented in spatial models, and finally recognised regional-scale variation among biogeographic units. This produced a spatially explicit hierarchical classification with nine Major Environment Units (Tier 1), 33 Habitat Complexes (Tier 2) and 269 Bioregional Ecosystem Types (Tier 3) mapped at 100 m resolution and aligned with 'level 4' of the IUCN Global Ecosystem Typology. This comprehensive ecosystem inventory provides foundational data to inform protected area designation under the Antarctic Treaty's Environmental Protocol and track risks to Antarctic ecosystems. Its tiered structure and workflow accommodate data scarcity and facilitate updates, promoting robustness as knowledge builds.}, }
@article {pmid39840338, year = {2024}, author = {Salerno, B and Cornaggia, M and Sabatino, R and Di Cesare, A and Mantovani, C and Barco, L and Cordioli, B and Bano, L and Losasso, C}, title = {The "best practices for farming" successfully contributed to decrease the antibiotic resistance gene abundances within dairy farms.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1420282}, pmid = {39840338}, issn = {2297-1769}, abstract = {INTRODUCTION: Farms are significant hotspots for the dissemination of antibiotic-resistant bacteria and genes (ARGs) into the environment and directly to humans. The prevalence of ARGs on farms underscores the need for effective strategies to reduce their spread. This study aimed to evaluate the impact of a guideline on "best practices for farming" aimed at reducing the dissemination of antibiotic resistance.<br><br>METHODS: A guideline focused on prudent antibiotic use, selective therapy, and hygienic and immune-prophylactic practices was developed and provided to the owners of 10 selected dairy farms and their veterinarians. Fecal samples were collected from lactating cows, dry cows, and calves both before and after the implementation of the guideline. ARGs (bla TEM, ermB, sul2, and tetA) were initially screened by end-point PCR, followed by quantification using digital droplet PCR. ARG abundance was expressed in relative terms by dividing the copy number of ARGs by the copy number of the 16S rRNA gene.<br><br>RESULTS: The ARG abundances were higher in lactating cows compared to other categories. Despite similar levels of antibiotic administration (based on veterinary prescription data from the sampled farms) in both sampling campaigns, the total abundance of selected ARGs, particularly bla TEM and tetA, significantly decreased after the adoption of the farming guidelines.<br><br>DISCUSSION: This study highlights the positive impact of prudent antibiotic use and the implementation of farming best practices in reducing the abundance of ARGs. The lactating cow category emerged as a crucial point of intervention for reducing the spread of antibiotic resistance. These findings contribute to ongoing efforts to address antibiotic resistance in farm environments and strengthen the evidence supporting the adoption of good farming practices.}, }
@article {pmid39838963, year = {2024}, author = {Guan, J and Ji, Y and Peng, C and Zou, W and Tang, X and Shang, J and Sun, Y}, title = {GOPhage: protein function annotation for bacteriophages by integrating the genomic context.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39838963}, issn = {1477-4054}, support = {11209823//City University of Hong Kong/ ; }, mesh = {*Bacteriophages/genetics ; *Genome, Viral ; *Viral Proteins/genetics/metabolism/chemistry ; *Molecular Sequence Annotation/methods ; Genomics/methods ; Computational Biology/methods ; }, abstract = {Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new phages have been identified via metagenomic sequencing, many of them have limited protein function annotation. Accurate function annotation of phage proteins presents several challenges, including their inherent diversity and the scarcity of annotated ones. Existing tools have yet to fully leverage the unique properties of phages in annotating protein functions. In this work, we propose a new protein function annotation tool for phages by leveraging the modular genomic structure of phage genomes. By employing embeddings from the latest protein foundation models and Transformer to capture contextual information between proteins in phage genomes, GOPhage surpasses state-of-the-art methods in annotating diverged proteins and proteins with uncommon functions by 6.78% and 13.05% improvement, respectively. GOPhage can annotate proteins lacking homology search results, which is critical for characterizing the rapidly accumulating phage genomes. We demonstrate the utility of GOPhage by identifying 688 potential holins in phages, which exhibit high structural conservation with known holins. The results show the potential of GOPhage to extend our understanding of newly discovered phages.}, }
@article {pmid39838210, year = {2025}, author = {Ouyang, XM and Lin, JH and Lin, Y and Zhao, XL and Huo, YN and Liang, LY and Huang, YD and Xie, GJ and Mi, P and Ye, ZY and Guleng, B}, title = {The SERPINB4 gene mutation identified in twin patients with Crohn's disease impaires the intestinal epithelial cell functions.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2638}, pmid = {39838210}, issn = {2045-2322}, support = {81970460//National Natural Science Foundation of China/ ; 2023J011598//Natural Science Foundation Program, Fujian Province, China/ ; }, mesh = {Humans ; *Crohn Disease/genetics/pathology ; Male ; Female ; *Mutation ; *Epithelial Cells/metabolism/pathology ; Apoptosis/genetics ; Adult ; Exome Sequencing ; *Intestinal Mucosa/metabolism/pathology ; Genetic Predisposition to Disease ; Cell Proliferation/genetics ; *Serpins/genetics ; Cell Movement/genetics ; }, abstract = {Crohn's disease (CD) is a chronic inflammatory autoimmune disease of unknown etiology. To identify new targets related to the initiation of CD, we screened a pair of twins with CD, which is a rare phenomenon in the Chinese population, for genetic susceptibility factors. Whole-exome sequencing (WES) of these patients revealed a mutation in their SERPINB4 gene. Therefore, we studied a wider clinical cohort of patients with CD or ulcerous colitis (UC), healthy individuals, and those with a family history of CD for this mutation by Sanger sequencing. The single-nucleotide difference in the SERPINB4 gene, which was unique to the twin patients with CD, led to the substitution of lysine by a glutamic acid residue. Functional analysis indicated that this mutation of SERPINB4 inhibited the proliferation, colony formation, wound healing, and migration of intestinal epithelial cells (IECs). Furthermore, mutation of SERPINB4 induced apoptosis and activated apoptosis-related proteins in IECs, and a caspase inhibitor significantly reduced these effects. Transcriptome sequencing revealed that the expression of genes encoding proinflammatory proteins (IL1B, IL6, IL17, IL24, CCL2, and CXCR2) and key proteins in the immune response (S100A9, MMP3, and MYC) was significantly upregulated during SERPINB4 mutant-induced apoptosis. Thus, the heterozygous SERPINB4 gene mutation causes the dysfunction of IECs, which would disrupt the intestinal epithelial barrier and contribute to the development of intestinal inflammation. The activation of SERPINB4 might represent a novel therapeutic target for inflammatory bowel disease.}, }
@article {pmid39838107, year = {2025}, author = {Teso-Pérez, C and López-Gazcón, A and Peralta-Sánchez, JM and Martínez-Bueno, M and Valdivia, E and Fárez-Vidal, ME and Martín-Platero, AM}, title = {Bacteriocin-Producing Enterococci Modulate Cheese Microbial Diversity.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {175}, pmid = {39838107}, issn = {1432-184X}, support = {PEJ2018-003019-A//Plan Estatal de Garant&#xed;a Juvenil (Fondo Social Europeo, Gobierno de Espa&#xf1;a/ ; Group BIO 309//PAIDI Program/ ; A-BIO-083-UGR18//Programa Operativo FEDER Andaluc&#xed;a 2014-2020/ ; }, mesh = {*Cheese/microbiology ; *Bacteriocins/biosynthesis/metabolism ; *Enterococcus/metabolism/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Food Microbiology ; Biodiversity ; Microbiota ; Animals ; Milk/microbiology ; }, abstract = {Cheese production involves various lactic acid bacteria (LAB) that break down lactose, milk proteins, and fats, producing key nutrients and influencing the cheese's flavor. They form communities that play a crucial role in determining the cheese's organoleptic properties. The composition of cheeses' microbial communities is shaped by physicochemical factors (e.g., temperature, pH, and salinity) and biological factors (i.e. microbial interactions). While starter cultures are introduced to control these communities, non-starter LAB represent a significant portion of the final microbial assemblage, but their interactions remain unclear. LAB often produce bacteriocins, antimicrobial peptides that antagonize other bacteria, but their role within LAB communities is not fully understood. This study aimed to assess the impact of bacteriocin production on LAB diversity in cheese, using Enterococcus as a model organism, a common bacteriocin producer. We analyzed enterocin production of enterococcal isolates by antimicrobial assays and microbial diversity differences in raw milk cheeses by two approaches: 16S RNA gene amplicon metagenomic sequencing for the whole microbial community and multi-locus sequence analysis (MLSA) for the enterococcal diversity. Our results revealed that LAB communities were dominated by lactococci, lactobacilli, and streptococci, with enterococci present in lower numbers. However, cheeses containing bacteriocin-producing enterococci exhibited higher microbial diversity. Interestingly, the highest diversity occurred at low levels of bacteriocin producers, but this effect was not observed within enterococcal populations. These findings suggest that bacteriocin production plays a key role in shaping LAB communities during cheese ripening, although further research is needed to understand its broader implications in other microbial ecosystems.}, }
@article {pmid39836327, year = {2025}, author = {Flores Clavo, R and Suclupe-Campos, DO and Castillo Rivadeneira, L and Velez Chicoma, RLJ and Sánchez-Purihuamán, M and Quispe Choque, KG and Casado Peña, FL and Binatti Ferreira, M and Fantinatti Garboggini, F and Carreño-Farfan, C}, title = {Harnessing PGPRs from Asparagus officinalis to Increase the Growth and Yield of Zea mays L.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {174}, pmid = {39836327}, issn = {1432-184X}, mesh = {*Zea mays/growth &amp; development/microbiology ; *Soil Microbiology ; *Asparagus Plant/microbiology/growth &amp; development ; Plant Roots/microbiology/growth &amp; development ; Rhizosphere ; Peru ; *Bacteria/isolation &amp; purification/genetics/classification/metabolism ; RNA, Ribosomal, 16S/genetics ; Indoleacetic Acids/metabolism ; Salt Tolerance ; Soil/chemistry ; }, abstract = {Microbial biotechnology employs techniques that rely on the natural interactions that occur in ecosystems. Bacteria, including rhizobacteria, play an important role in plant growth, providing crops with an alternative that can mitigate the negative effects of abiotic stress, such as those caused by saline environments, and increase the excessive use of chemical fertilizers. The present study examined the promoting potential of bacterial isolates obtained from the rhizospheric soil and roots of the Asparagus officinalis cultivar UF-157 F2 in Viru, la Libertad, Peru. This region has high soil salinity levels. Seventeen strains were isolated, four of which are major potential plant growth-promoting traits, and were characterized based on their morphological and molecular characteristics. These salt-tolerant bacteria were screened for phosphate solubilization, indole acetic acid, deaminase activity, and molecular characterization by 16S rDNA sequencing. Fifteen samples were from saline soils of A. officinalis plants in the northern coastal desert of San Jose, Lambayeque, Peru. The bacterial isolates were screened in a range of salt tolerances from 3 to 6%. Isolates 05, 08, 09, and 11 presented maximum salt tolerance, ammonium quantification, phosphate solubilization, and IAA production. The four isolates were identified by sequencing the amplified 16S rRNA gene and were found to be Enterobacter sp. 05 (OQ885483), Enterobacter sp. 08 (OQ885484), Pseudomonas sp. 09 (OR398704) and Klebsiella sp. 11 (OR398705). These microorganisms promoted the germination of Zea mays L. plants, increased the germination rates in the treatments with chemical fertilizers at 100% and 50%, and the PGPRs increased the height and length of the roots 40 days after planting. The beneficial effects of salt-tolerant PGPR isolates isolated from saline environments may lead to new species that can be used to overcome the detrimental effects of salt stress on plants. The biochemical response and inoculation of the three isolates prove the potential of these strains as sources of products to develop new compounds, confirming their potential as biofertilizers for saline environments.}, }
@article {pmid39833680, year = {2025}, author = {Sbissi, I and Chouikhi, F and Ghodhbane-Gtari, F and Gtari, M}, title = {Ecogenomic insights into the resilience of keystone Blastococcus Species in extreme environments: a comprehensive analysis.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {51}, pmid = {39833680}, issn = {1471-2164}, mesh = {*Extreme Environments ; Phylogeny ; Genome, Bacterial ; Soil Microbiology ; Genomics ; Stress, Physiological ; Metals, Heavy ; }, abstract = {BACKGROUND: The stone-dwelling genus Blastococcus plays a key role in ecosystems facing extreme conditions such as drought, salinity, alkalinity, and heavy metal contamination. Despite its ecological significance, little is known about the genomic factors underpinning its adaptability and resilience in such harsh environments. This study investigates the genomic basis of Blastococcus's adaptability within its specific microniches, offering insights into its potential for biotechnological applications.<br><br>RESULTS: Comprehensive pangenome analysis revealed that Blastococcus possesses a highly dynamic genetic composition, characterized by a small core genome and a large accessory genome, indicating significant genomic plasticity. Ecogenomic assessments highlighted the genus's capabilities in substrate degradation, nutrient transport, and stress tolerance, particularly on stone surfaces and archaeological sites. The strains also exhibited plant growth-promoting traits, enhanced heavy metal resistance, and the ability to degrade environmental pollutants, positioning Blastococcus as a candidate for sustainable agriculture and bioremediation. Interestingly, no correlation was found between the ecological or plant growth-promoting traits (PGPR) of the strains and their isolation source, suggesting that these traits are not linked to their specific environments.<br><br>CONCLUSIONS: This research highlights the ecological and biotechnological potential of Blastococcus species in ecosystem health, soil fertility improvement, and stress mitigation strategies. It calls for further studies on the adaptation mechanisms of the genus, emphasizing the need to validate these findings through wet lab experiments. This study enhances our understanding of microbial ecology in extreme environments and supports the use of Blastococcus in environmental management, particularly in soil remediation and sustainable agricultural practices.}, }
@article {pmid39830292, year = {2024}, author = {Crous, PW and Wingfield, MJ and Jurjević, &#x17d; and Balashov, S and Osieck, ER and Marin-Felix, Y and Luangsa-Ard, JJ and Mejía, LC and Cappelli, A and Parra, LA and Lucchini, G and Chen, J and Moreno, G and Faraoni, M and Zhao, RL and Weholt, &#xd8; and Borovička, J and Jansen, GM and Shivas, RG and Tan, YP and Akulov, A and Alfenas, AC and Alfenas, RF and Altés, A and Avchar, R and Barreto, RW and Catcheside, DEA and Chi, TY and Esteve-Raventós, F and Fryar, SC and Hanh, LTM and Larsbrink, J and Oberlies, NH and Olsson, L and Pancorbo, F and Raja, HA and Thanh, VN and Thuy, NT and Ajithkumar, K and Akram, W and Alvarado, P and Angeletti, B and Arumugam, E and Khalilabad, AA and Bandini, D and Baroni, TJ and Barreto, GG and Boertmann, D and Bose, T and Castañeda Ruiz, RF and Couceiro, A and Cykowska-Marzencka, B and Dai, YC and Darmostuk, V and da Silva, SBG and Dearnaley, JDW and de Azevedo Santiago, ALCM and Declercq, B and de Freitas, LWS and De la Peña-Lastra, S and Delgado, G and de Lima, CLF and Dhotre, D and Dirks, AC and Eisvand, P and Erhard, A and Ferro, LO and García, D and García-Martín, A and Garrido-Benavent, I and Gené, J and Ghobad-Nejhad, M and Gore, G and Gunaseelan, S and Gusmão, LFP and Hammerbacher, A and Hernández-Perez, AT and Hernández-Restrepo, M and Hofmann, TA and Hubka, V and Jiya, N and Kaliyaperumal, M and Keerthana, KS and Ketabchi, M and Kezo, K and Knoppersen, R and Kolarczyková, D and Kumar, TKA and Læssøe, T and Langer, E and Larsson, E and Lodge, DJ and Lynch, MJ and Maciá-Vicente, JG and Mahadevakumar, S and Mateos, A and Mehrabi-Koushki, M and Miglio, BV and Noor, A and Oliveira, JA and Pereira, OL and Piątek, M and Pinto, A and Ramírez, GH and Raphael, B and Rawat, G and Renuka, M and Reschke, K and Mateo, AR and Saar, I and Saba, M and Safi, A and Sánchez, RM and Sandoval-Denis, M and Savitha, AS and Sharma, A and Shelke, D and Sonawane, H and Souza, MGAP and Stryjak-Bogacka, M and Thines, M and Thomas, A and Torres-Garcia, D and Traba, JM and Vauras, J and Vermaas, M and Villarreal, M and Vu, D and Whiteside, EJ and Zafari, D and Starink-Willemse, M and Groenewald, JZ}, title = {Fungal Planet description sheets: 1697-1780.}, journal = {Fungal systematics and evolution}, volume = {14}, number = {}, pages = {325-577}, pmid = {39830292}, issn = {2589-3831}, support = {P01 CA125066/CA/NCI NIH HHS/United States ; }, abstract = {Novel species of fungi described in this study include those from various countries as follows: Antarctica, Leuconeurospora bharatiensis from accumulated snow sediment sample. Argentina, Pseudocercospora quetri on leaf spots of Luma apiculata. Australia, Polychaetomyces verrucosus on submerged decaying wood in sea water, Ustilaginoidea cookiorum on Scleria levis, Xylaria guardiae as endophyte from healthy leaves of Macaranga tanarius. Belgium, Iodophanus taxi on leaf of Taxus baccata. Belize, Hygrocybe mirabilis on soil. Brazil, Gongronella irregularis from soil, Linodochium splendidum on decaying sheath of Euterpe oleracea, Nothophysalospora agapanthi (incl. Nothophysalospora gen. nov.) on flower stalks of Agapanthus praecox, Phaeosphaeria tabebuiae on leaf of Tabebuia sp., Verrucohypha endophytica (incl. Verrucohypha gen. nov.) from healthy roots of Acrocomia aculeata. Estonia, Inosperma apricum on soil under Quercus robur. Greece, Monosporascus solitarius isolated from surface-sterilised, asymptomatic roots of Microthlaspi perfoliatum. India, Diaporthe neocapsici on young seedling stems of Capsicum annuum, Fuscoporia naditirana on dead wood, Sebacina spongicarpa on soil, Torula kanvae from the gut of a Copris signatus beetle. Iran, Sarcinomyces pruni from twig and petiole tissues of Prunus persica and Prunus armeniaca, Xenodidymella quercicola from leaf spots of Quercus brantii. Italy, Agaricus aereiceps on grass, Agaricus bellui in meadows, Agaricus fabrianensis in urban grasslands, Beaucarneamyces muscorum on moss growing in forest, Xenoanthostomella quercus on leaf litter of Quercus ilex. Netherlands, Alfaria neerlandica on stem lesions of Cortaderia selloana, Neodictyosporium juncicola on culms of Juncus maritimus, Penicillium geertdesnooi from soil under Papaver rhoeas, Russula abscondita on rich calcareous soil with Quercus, Russula multiseptata on rich clay soil with Quercus, Russula purpureopallescens on soil with Populus, Sarocladium caricicola on leaves of Carex riparia. Pakistan, Circinaria shimlaensis on limestone rocks. Panama, Acrocalymma philodendri on leaf spots of Philodendron sp., Caligospora panamaensis on leaf litter, Chlamydocillium simulans associated with a Xylaria sp., Corynesporina panamaensis on leaf litter, Cylindromonium panamaense on twig litter of angiosperm, Cyphellophora panamaensis on twig litter of angiosperm, Microcera panamensis on leaf litter of fern, Pseudotricholoma pusillum in tropical montane forest dominated by Quercus spp., Striaticonidium panamaense on leaf litter, Yunnanomyces panamaensis on leaf litter. Poland, Albocremella abscondita (incl. Albocremella gen. nov.) from rhizoids of liverwort Conocephalum salebrosum. Portugal, Agaricus occidualis in meadows. South Africa, Alternaria elsarustiae on culms of unidentified Poaceae, Capronia capensis on dead twig of unidentified angiosperm, Codinaeella bulbinicola on dead leaves of Bulbine frutescens, Cytospora carpobroticola on leaf of Carpobrotus quadrifidus, Neophaeomoniella watsoniae on leaf of Watsonia sp., Neoplatysporoides aloigena on leaf of Aloe khamiesensis, Nothodactylaria comitabilis on living leaf of Itea rhamnoides, Nothopenidiella beaucarneae (incl. Nothopenidiella gen. nov.) on dead leaves of Beaucarnea stricta, Orbilia kirstenboschensis on dead flower stalks of Agapanthus praecox, Phragmocephala agapanthi on dead flower stalks of Agapanthus praecox, Podocarpigena hagahagaensis (incl. Podocarpigena gen. nov.) on leaf spots of Podocarpus falcatus, Sporisorium enterogonipteri from the gut of Gonipterus sp., Synnemapestaloides searsiae on leaf of Searsia populifolia, Xenophragmocapnias diospyri (incl. Xenophragmocapnias gen. nov.) on leaf spots of Diospyros sp., Yunnanomyces hagahagaensis on leaf spots of Sideroxylon inerme. Spain, Agaricus basicinctus in meadows, Agaricus quercetorum among leaf litter in oak forests, Coprinopsis palaciosii on degraded woody debris, Inocybe complutensis in calcareous loamy soil, Inocybe tanitiae in calcareous sandy soil, Mycena subfragosa on dead leaves of Salix atrocinerea, Pseudobaeospora cortegadensis in laurel forests, Trichoderma sedimenticola from fluvial sediments. Sweden, Inocybe badjelanndana on calcareous soil. Ukraine, Beaucarneamyces lupini on overwintered stems of Lupinus polyphyllus, Protocreopsis globulosa on thallus and apothecia of Lecania cyrtella on bark of Populus sp., Thyridium tiliae on dead twigs of Tilia sp. USA, Cladosporium louisianense, Cyphellophora americana from a bedroom vent, Extremus massachusettsianus from lyse buffer, Myxotrichum tapetae on carpet in basement, Neospissiomyces floridanus (incl. Neospissiomyces gen. nov.) on swab from hospital, Polychaetomyces marinus (incl. Polychaetomyces gen. nov.) on submerged driftwood in sea water, Steccherinum fragrans on hardwood fallen on the beach, Steinbeckomyces carnegieae (incl. Steinbeckomyces gen. nov.) on Carnegiea gigantea, Tolypocladium pennsylvanicum from air sampled in basement. Vietnam, Acidomyces ducanhii from Aglaia flowers, Acidomyces paludis from dead bark of Acacia sp., Phakopsora sageretiae on Sageretia theezans, Puccinia stixis on Stixis scandens. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Wingfield MJ, Jurjević Ž, et al. (2024). Fungal Planet description sheets: 1697-1780. Fungal Systematics and Evolution 14: 325-577. doi: 10.3114/fuse.2024.14.19.}, }
@article {pmid39828718, year = {2025}, author = {Wang, Z and Fuad, MTI and Liu, J and Lin, K and Liu, L and Gao, C and Wang, W and Liu, X}, title = {Spatial Patterns of Microbial Communities in Intertidal Sediments of the Yellow River Estuary, China.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {173}, pmid = {39828718}, issn = {1432-184X}, support = {41976131//National Natural Science Foundation of China/ ; }, mesh = {*Geologic Sediments/microbiology ; China ; *Archaea/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; *Estuaries ; *Rivers/microbiology ; *Microbiota ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Ecosystem ; Metals, Heavy/analysis ; }, abstract = {Estuarine ecosystems are among the most important natural ecosystems on Earth and contribute substantially to human survival and development. The Yellow River Estuary (YRE) is the second largest estuary in China. Microbial communities play an essential role in the material cycle and energy flow in estuarine ecosystems. To date, our knowledge of the spatial patterns of bacterial and archaeal communities is limited. In this study, we investigated the spatial profile of bacterial and archaeal communities and their co-occurrence patterns, functional roles, and environmental driving factors in the intertidal sediments of the YRE from June to July, 2019. The results showed that Proteobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes were the dominant bacterial phyla, whereas Nanoarchaeaeota, Euryarchaeota and Thaumarchaeota were the dominant archaeal phyla in the intertidal sediments of the YRE. Diversity indices and differential abundance analyses revealed significant (p < 0.05) differences in the bacterial and archaeal communities in the intertidal sediments of the YRE. Bacterial communities demonstrated distinct correlations with heavy metals and pollutants. Six archaeal genera exhibited co-occurrence patterns with bacterial genera. Functions associated with sulfur cycles, disease, and pollution were specific to bacterial communities. This study presents a detailed outline of the spatial patterns of microbial communities in the YRE, enriching our understanding of microbial ecology, especially of bacteria and archaea.}, }
@article {pmid39826456, year = {2025}, author = {Wang, Y and Zhang, F and Yang, L and Zhang, G and Wang, H and Zhu, S and Zhang, H and Guo, T}, title = {Synergy of plastics and heavy metals weakened soil bacterial diversity by regulating microbial functions in the Qinghai-Tibet Plateau.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137241}, doi = {10.1016/j.jhazmat.2025.137241}, pmid = {39826456}, issn = {1873-3336}, mesh = {*Soil Microbiology ; *Metals, Heavy/toxicity/analysis ; *Soil Pollutants/toxicity/analysis ; *Bacteria/drug effects/genetics ; *Plastics/toxicity ; Tibet ; Biodiversity ; Soil/chemistry ; China ; *Microplastics/toxicity ; }, abstract = {How plastics coupled with metals regulate microbial functions-diversity relationships remain unknown in plateau soil environment. Three representative catchments in the Qinghai-Tibet Plateau, focusing on microplastics, their plasticisers, and metals in soils, were investigated. This research explores responses of bacterial diversity and functions to the co-existence of target pollutants, and pathways by which target pollutants regulate the diversity. Soil bacterial beta diversity and functional genes exhibited negative correlations with phthalate esters across three catchments (p < 0.05). Dibutyl phthalate emerged as a primary factor affecting beta diversity, rather than the quantity of microplastics. Additionally, the synergy of cadmium and fiber-shaped microplastics exacerbated the impact on diversity. Structural equation modeling further elucidated that plastics, copper, and iron influenced nirK/nirS genes and phoD gene, subsequently affected cbbL/cbbM genes, and ultimately the diversity. In this context, microplastics, phthalate esters and copper, iron exerted antagonistic effects on one another. Consequently, the co-existence of plastics and cadmium weakened soil bacterial diversity in the Qinghai-Tibet Plateau by disrupting microbial functions, but micronutrients alleviated these negative impacts. This research reveals that the co-existence of plastics and metals regulates soil bacterial diversity in the Qinghai-Tibet Plateau, providing a valuable reference for the protection of microbial ecology in plateau regions.}, }
@article {pmid39826104, year = {2025}, author = {Lin, A and Jiang, A and Huang, L and Li, Y and Zhang, C and Zhu, L and Mou, W and Liu, Z and Zhang, J and Cheng, Q and Wei, T and Luo, P}, title = {From chaos to order: optimizing fecal microbiota transplantation for enhanced immune checkpoint inhibitors efficacy.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2452277}, doi = {10.1080/19490976.2025.2452277}, pmid = {39826104}, issn = {1949-0984}, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Immune Checkpoint Inhibitors/therapeutic use ; *Gastrointestinal Microbiome ; *Neoplasms/therapy/immunology/microbiology ; Animals ; Tumor Microenvironment ; Immunotherapy/methods ; Treatment Outcome ; }, abstract = {The integration of fecal microbiota transplantation (FMT) with immune checkpoint inhibitors (ICIs) presents a promising approach for enhancing cancer treatment efficacy and overcoming therapeutic resistance. This review critically examines the controversial effects of FMT on ICIs outcomes and elucidates the underlying mechanisms. We investigate how FMT modulates gut microbiota composition, microbial metabolite profiles, and the tumor microenvironment, thereby influencing ICIs effectiveness. Key factors influencing FMT efficacy, including donor selection criteria, recipient characteristics, and administration protocols, are comprehensively discussed. The review delineates strategies for optimizing FMT formulations and systematically monitoring post-transplant microbiome dynamics. Through a comprehensive synthesis of evidence from clinical trials and preclinical studies, we elucidate the potential benefits and challenges of combining FMT with ICIs across diverse cancer types. While some studies report improved outcomes, others indicate no benefit or potential adverse effects, emphasizing the complexity of host-microbiome interactions in cancer immunotherapy. We outline critical research directions, encompassing the need for large-scale, multi-center randomized controlled trials, in-depth microbial ecology studies, and the integration of multi-omics approaches with artificial intelligence. Regulatory and ethical challenges are critically addressed, underscoring the imperative for standardized protocols and rigorous long-term safety assessments. This comprehensive review seeks to guide future research endeavors and clinical applications of FMT-ICIs combination therapy, with the potential to improve cancer patient outcomes while ensuring both safety and efficacy. As this rapidly evolving field advances, maintaining a judicious balance between openness to innovation and cautious scrutiny is crucial for realizing the full potential of microbiome modulation in cancer immunotherapy.}, }
@article {pmid39825576, year = {2025}, author = {Fouché, J and Lebre, PH and Melville, HA and Cowan, DA}, title = {The Functional and Structural Succession of Mesic-Grassland Soil Microbiomes Beneath Decomposing Large Herbivore Carcasses.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70022}, pmid = {39825576}, issn = {1462-2920}, mesh = {Animals ; *Soil Microbiology ; *Microbiota ; *Herbivory ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Grassland ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; }, abstract = {Plant detritus is abundant in grasslands but decomposes slowly and is relatively nutrient-poor, whereas animal carcasses are labile and nutrient-rich. Recent studies have demonstrated that labile nutrients from carcasses can significantly alter the long-term soil microbial function at an ecosystem scale. However, there is a paucity of knowledge on the functional and structural response and temporal scale of soil microbiomes beneath large herbivore carcasses. This study compared microbiome functions and structures of soil beneath Connochaetes taurinus (hereafter 'wildebeest') carcasses at various postmortem intervals of decomposition to matched control samples over 18 months. Microbial functions were compared by their community-level physiological profiles determined by sole-carbon substrate utilisation and structures by metagenomic sequences using 16S rRNA gene markers. Overall metabolism and metabolic diversity remained increased and functionally dissimilar to control soils throughout the experimental period, with successive sole-carbon substrate utilisation observed. Conversely, diversity was initially reduced and structurally dissimilar from the control soil but recovered within the experimental period. The study contributes to the knowledge of carcass decomposition by investigating the long-term soil microbiome dynamics resulting from large herbivore carcasses decomposing in a mesic grassland. Microbial functional succession and ecologically relevant bacterial biomarkers of soil beneath the decomposing carcasses were identified for various postmortem intervals.}, }
@article {pmid39825218, year = {2025}, author = {de Freitas, AS and Zagatto, LFG and Rocha, GS and Muchalak, F and Martins, GL and Silva-Zagatto, SDS and Hanada, RE and Muniz, AW and Tsai, SM}, title = {Harnessing the synergy of Urochloa brizantha and Amazonian Dark Earth microbiomes for enhanced pasture recovery.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {27}, pmid = {39825218}, issn = {1471-2180}, support = {2021/10626-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2022/05561-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 01.02.016301.00293/2021//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Amazonas/ ; }, mesh = {*Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Plant Roots/microbiology ; Brazil ; *Poaceae/microbiology/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Rainforest ; Biodiversity ; DNA, Bacterial/genetics ; }, abstract = {Amazonian Dark Earths (ADEs) are fertile soils from the Amazon rainforest that harbor microorganisms with biotechnological potential. This study aimed to investigate the individual and potential synergistic effects of a 2% portion of ADEs and Urochloa brizantha cv. Marandu roots (Brazil's most common grass species used for pastures) on soil prokaryotic communities and overall soil attributes in degraded soil. We conducted a comprehensive plant succession experiment in the greenhouse, utilizing vase soil samples for next-generation sequencing of 16 S rDNA, enzymatic activity assays, and soil chemical properties analysis. Univariate and multivariate analyses were performed to understand better the prokaryotic interactions within soil environments influenced by ADEs and U. brizantha roots, including differential abundance, diversity, and network analyses. Our findings reveal a complementary relationship between U. brizantha and ADEs, each contributing to distinct positive aspects of soil bacterial communities and quality. The combined influence of U. brizantha roots and ADEs exhibited synergies that enhanced prokaryotic diversity and enzyme activity. This balance supported plant growth and increased the general availability of beneficial bacteria in the soil, such as Chujaibacter and Curtobacterium while reducing the presence of potentially pathogenic taxa. This research provided valuable insights into the intricate dynamics of plant-soil feedback, emphasizing the potential for complementary interactions between specific plant species and unique soil environments like ADEs. The findings highlight the potential for pasture ecological rehabilitation and underscore the benefits of integrating plant and soil management strategies to optimize soil characteristics.}, }
@article {pmid39821365, year = {2025}, author = {Zhang, D and Cai, Y and Sun, Y and Zeng, P and Wang, W and Wang, W and Jiang, X and Lian, Y}, title = {A Real-World Disproportionality Analysis of Histamine H2-Receptors Antagonists (Famotidine): A Pharmacovigilance Study Based on Spontaneous Reports in the FDA Adverse Event Reporting System.}, journal = {Drug development research}, volume = {86}, number = {1}, pages = {e70045}, doi = {10.1002/ddr.70045}, pmid = {39821365}, issn = {1098-2299}, support = {//This study was funded by the National Natural Science Foundation of China (Grant No: 82303109), the Natural Science Foundation of Fujian Province, China (Grant No: 2022J05299), Cross-Strait Postdoctoral Exchange Funding Program of Fujian Province, China (Grant No: 2021B002)./ ; }, mesh = {Humans ; *Pharmacovigilance ; *Adverse Drug Reaction Reporting Systems/statistics &amp; numerical data ; *Histamine H2 Antagonists/adverse effects/administration &amp; dosage ; United States ; United States Food and Drug Administration ; *Famotidine/adverse effects/administration &amp; dosage ; Female ; Male ; Middle Aged ; Adult ; Aged ; Young Adult ; Adolescent ; Databases, Factual ; Child ; }, abstract = {Famotidine is an H2 receptor antagonist and is currently used on a large scale in gastroenterology. However, Famotidine may also cause severe toxicity to organ systems, including the blood system, digestive system, and urinary system. The objective of this study was to scientifically and systematically investigate the adverse events (AEs) of Famotidine in the real world through the FDA Adverse Event Reporting System (FAERS) database. A disproportionality analysis was used to quantify the signals of AEs associated with Famotidine in FAERS data from the first quarter of 2004 to the first quarter of 2023. The clinical features, onset time, oral and intravenous administration and severe consequences of Famotidine induced AEs were further analyzed. Among the four tests, we found several AEs that were not mentioned in the drug label. For example, abdominal pain upper, abdominal discomfort, dyspepsia, liver disorder, gastrooesophageal reflux disease, and rhabdomyolysis. These AEs are consistent with the drug instructions. Interestingly, we found several unreported AEs, such as: cerebral infarction, hypocalcaemia, hallucination, visual, hypomagnesaemia, hypoparathyroidism, diabetes insipidus, vulvovaginal candidiasis, retro-orbital neoplasm, neuroblastoma recurrent, and malignant cranial nerve neoplasm. Most of our findings are consistent with clinical observations and drug labels, and we also found possible new and unexpected AEs signals, which suggest the need for prospective clinical studies to confirm these results and explain their relationships. Our findings provide valuable evidence for further safety studies.}, }
@article {pmid39820572, year = {2025}, author = {Azpiazu-Muniozguren, M and García-Martínez, M and Zabaleta, A and Antiguedad, I and Garaizar, J and Laorden, L and Martinez-Malaxetxebarria, I and Martinez-Ballesteros, I}, title = {Prokaryotic Diversity and Community Distribution in the Complex Hydrogeological System of the Añana Continental Saltern.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {171}, pmid = {39820572}, issn = {1432-184X}, support = {US19/01//Euskal Herriko Unibertsitatea/ ; GIU21/021//Euskal Herriko Unibertsitatea/ ; IT1678-22//Eusko Jaurlaritza/ ; }, mesh = {Spain ; *Archaea/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Salinity ; *Biodiversity ; Phylogeny ; *Natural Springs/microbiology ; *Saline Waters ; DNA, Bacterial/genetics ; Rivers/microbiology ; Water Microbiology ; DNA, Archaeal/genetics ; }, abstract = {The Añana Salt Valley (northern Spain) is a continental saltern consisting of a series of natural springs that have been used for salt production for at least 7000 years. This habitat has been relatively understudied; therefore, prokaryotic diversity was investigated through Illumina-based 16S rRNA gene sequencing to determine if the waters within the valley exhibit distinctive microbiological characteristics. Two main types of water were found in the valley: salty (approximately 200 g/L salinity) from the diapiric structure and brackish (≤ 20 g/L salinity) from shallow streams. The beta diversity indices showed that salinity was the primary factor influencing the prokaryotic distribution. However, a niche-specific influence was observed between waters of the same origin, with significant differences in the relative abundance of the ASVs. The microbiome of the saltern revealed that the archaeal domain was mainly restricted to salty waters, while the bacterial domain was ubiquitous throughout the saltern, with a notable prevalence in brackish waters. The main bacterial and archaeal phyla identified were Pseudomonadota and Halobacterota, respectively. The genus Halorubrum was abundant and widespread in salty waters, while Pseudomonas was a significant part of the prokaryote community, mainly in brackish waters. The relative abundance of the genera Haloplanus and Salinibacter increased in the salt ponds used for salt production. The taxa involved in chemoheterotrophy and fermentation were widespread, sharing the same niche. Overall, the location of this saltern on a diapiric structure favors the occurrence of waters with different origins that affect the prokaryotic distribution beyond the niche location in the valley.}, }
@article {pmid39820498, year = {2025}, author = {Luo, H and Xie, K and Dong, P and Zhang, Y and Ren, T and Sui, C and Ma, C and Zhao, C and Dewangan, NK and Gong, Z}, title = {Assessing the Risks of Potential Pathogens and Antibiotic Resistance Genes Among Heterogeneous Habitats in a Temperate Estuary Wetland: a Meta-analysis.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {172}, pmid = {39820498}, issn = {1432-184X}, support = {H2022011//Horizontal scientific research project (microbial-enhanced treatment of petroleum hydrocarbon pollutants: technical and engineering demonstration)/ ; 32303039//National Natural Science Foundation of China/ ; 2021DG700024-KF202425//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality, Safety of Agro-products/ ; 30501466//Top-Notch Talents Program of Henan Agricultural University/ ; 242102111013//Henan Province Science and Technology Key Project/ ; 2023HNUAHEDF009//Initial Scientific Research Fund of Young Teachers in Henan University of Animal Husbandry and Economy/ ; }, mesh = {*Wetlands ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Estuaries ; Soil Microbiology ; Geologic Sediments/microbiology ; Ecosystem ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Water Microbiology ; *Drug Resistance, Microbial/genetics ; Microbiota ; }, abstract = {Temperate estuary wetlands act as natural filters for microbiological contamination and have a profound impact on "One Health." However, knowledge of microbiological ecology security across the different habitats in temperate estuarine wetlands remains limited. This study employed meta-analysis to explore the characteristics of bacterial communities, potential pathogens, and antibiotic resistance genes (ARGs) across three heterogeneous habitats (water, soil, and sediment) within the Liaohe Estuary landscape. The diversity and composition of the three bacterial communities differed with biogeography, temperature, and pH, with the highest α-diversity showing a significantly negative correlation along latitude in soil. Furthermore, aminoglycosides were significantly enriched in water and soil, while dihydrofolate was more likely to be enriched in soil. The potential pathogens, Pseudoalteromonas and Planococcus, were dominant in water and sediment, while Stenotrophomonas was the dominant bacterium in soil. The network topology parameter revealed interspecific interactions within the community. PLS-PM highlights the main direct factors affecting the abundance of potential pathogens and the spread of ARGs, while temperature and pH indirectly influence these potential pathogens. This study advances our understanding of bacterial communities in estuarine wetlands, while highlighting the need for effective monitoring to mitigate the risks associated with potential pathogens and ARGs in these ecosystems.}, }
@article {pmid39820407, year = {2025}, author = {Hahn, MW and Kisand, V}, title = {Editorial: FEMS EC Thematic Issue "Aquatic Microbial Ecology".}, journal = {FEMS microbiology ecology}, volume = {101}, number = {2}, pages = {}, pmid = {39820407}, issn = {1574-6941}, abstract = {High relative abundance of yeast (Vishniacozyma, Papiliotrema, and Filobasidium) and bacterial (Massilia) genera found in spinach seeds correlates with suppression of Globisporangium ultimum damping-off infection.}, }
@article {pmid39817738, year = {2025}, author = {Wittlinger, J-P and Castejón, N and Hausmann, B and Berry, D and Schnorr, SL}, title = {Shewanella is a putative producer of polyunsaturated fatty acids in the gut soil of the composting earthworm Eisenia fetida.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {2}, pages = {e0206924}, pmid = {39817738}, issn = {1098-5336}, support = {847693//EC | H2020 | PRIORITY 'Excellent science' | H2020 Marie Sk&#x142;odowska-Curie Actions (MSCA)/ ; }, mesh = {*Oligochaeta/microbiology ; Animals ; *Gastrointestinal Microbiome ; *Fatty Acids, Unsaturated/metabolism/biosynthesis ; Composting ; *Soil Microbiology ; *Shewanella/metabolism/genetics ; RNA, Ribosomal, 16S/analysis/genetics ; Soil/chemistry ; Phylogeny ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; }, abstract = {Polyunsaturated fatty acids (PUFAs) play a crucial role in aiding bacteria to adapt to extreme and stressful environments. While there is a well-established understanding of their production, accrual, and transfer within marine ecosystems, knowledge about terrestrial environments remains limited. Investigation of the intestinal microbiome of earthworms has illuminated the presence of PUFAs presumably of microbial origin, which contrasts with the surrounding soil. To comprehensively study this phenomenon, a multi-faceted approach was employed, combining fatty acid analysis with amplicon sequencing of the PfaA-KS domain of the anaerobic fatty acid synthase gene (pfa), as well as the 16S rRNA and 18S rRNA genes. This methodology was applied to scrutinize the gut microbiome of Eisenia fetida, its compost-based dietary source, and the resultant castings. This study unveiled a distinct gut soil ecosystem from input compost and output castings in fatty acid profile as well as type and abundance of organisms. 16S sequencing provided insights into the microbial composition, showing increased relative abundance of certain Pseudomonadota, including Shewanellaceae, and Planctomycetota, including Gemmataceae within the gut microbiome compared to input bulk soil compost, while Actinomycetota and Bacillota were relatively enriched compared to the casted feces. Sequencing of the PfaA-KS domain revealed amplicon sequence variants (ASVs) belonging primarily to Shewanella. Intriguingly, the 20C PUFAs were identified only in gut soil samples, though PfaA-KS sequence abundance was highest in output castings, indicating a unique metabolism occurring only in the gut. Overall, the results indicate that Shewanella can explain PUFA enrichment in the gut environment because of the pfa gene presence detected via PfaA-KS sequence data.IMPORTANCEPrior research has demonstrated that earthworm microbiomes can potentially harbor polyunsaturated fatty acids (PUFAs) that are not found within their residing soil environment. Moreover, distinct indicator species have been pinpointed for various microbial genera in earthworm microbiomes. Nevertheless, none of these studies have integrated metataxonomic and fatty acid analyses to explore the origin of PUFA synthesis in any earthworm species, with the objective of identifying the specific organisms and locations responsible for this production. This study suggests that earthworms accumulate PUFAs produced from bacteria, especially Shewanella, activated through the gut ecosystem.}, }
@article {pmid39813101, year = {2025}, author = {Shan, Y and Hao, H and He, J and Hu, N and Liu, P and Zhan, M and Jiao, W and Yin, Y}, title = {Thermal Enhanced Electrokinetic Bacterial Transport in Porous Media.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {3}, pages = {1683-1692}, doi = {10.1021/acs.est.4c07954}, pmid = {39813101}, issn = {1520-5851}, mesh = {Bacteria ; Kinetics ; Porosity ; Soil ; *Soil Microbiology ; }, abstract = {Soil bacterial communities are crucial to various ecosystem services, with significant implications for environmental processes and human health. Delivering functional bacterial strains to target locations enhances the preferred ecological features. However, the delivery process is often constrained by limited bacterial transport through low-permeability soil. Although electrokinetics breaks the bottleneck of bacterial transport in thin porous media, its efficiency remains limited. Here, we tested the hypothesis that thermal effects enhance electrokinetic transport by shifting the net force acting on the bacterium. We found that heating significantly increased electrokinetic transport by 2.75-fold at 1 V cm[-1] through porous media. Thermal enhancement mechanisms were interpreted by the heating shift of net force integrating matrix attractive and electrokinetic forces and verified by the Quartz Crystal Microbalance with Dissipation Monitoring (QCMD) observed adhesion rigidity shift. Thermal-dependent parameters liquid viscosity and dielectric constant were the primary contributors to the net force shift. Their variations reduce the attractive force and augment the electrokinetic forces, resulting in lower adhesion rigidity and enhanced bacterial transport. A mechanism-based approach interlinking electric field strength, thermal effect, and collision efficiency was established to facilitate the application of thermally enhanced electrokinetic bacterial transport. These findings provide new prospects for improving bacterial transport, hence optimizing soil ecosystem functions.}, }
@article {pmid39811355, year = {2025}, author = {Paredes Contreras, BV and Vermelho, AB and Casanova, L and de Alencar Santos Lage, C and Spindola Vilela, CL and da Silva Cardoso, V and Pacheco Arge, LW and Cardoso-Rurr, JS and Correa, SS and Passos De Mansoldo, FR and Pinheiro Pereira Reis-Mansur, MC and Alves da Silva, E and Schultz, J and Rosado, AS}, title = {Enhanced UV-B photoprotection activity of carotenoids from the novel Arthrobacter sp. strain LAPM80 isolated from King George Island, Antarctica.}, journal = {Heliyon}, volume = {11}, number = {1}, pages = {e41400}, pmid = {39811355}, issn = {2405-8440}, abstract = {Antarctica's harsh environmental conditions, characterized by high levels of ultraviolet (UV) radiation, pose challenges for microorganisms. To survive in these extreme cold regions with heightened UV exposure, microorganisms employ various adaptive strategies, including photoprotective carotenoid synthesis. Carotenoids are garnering attention in the skin health industry because of their UV photoprotection potential, given the direct relationship between UV exposure and skin burns, and cancer. Also, there is a growing demand for natural and environmentally friendly photoprotectors, such as microbial-based products, in opposition to synthetic photoprotective agents with known adverse effects. In this study, we assessed the carotenoid-producing abilities of Actinomycetota strains from Antarctic Peninsula soils and the photoprotective carotenoid action on UV irradiation resistance. Among 20 evaluated strains, one exhibited significant carotenoid production and it was identified through genomic analysis as a likely novel Arthrobacter sp. strain, LAPM80. This strain's genome revealed the presence of genes coding for the biosynthesis of decaprenoxanthin C50 carotenoid. The LAPM80 strain exhibited enhanced resistance against UV-B irradiation, correlating with increased total carotenoid production in its stationary growth phase. Chemical characterization of the carotenoid extract identified major components as C50 carotenoids, probably decaprenoxanthin and/or sarcinaxanthin. Scanning electron microscopy revealed minimal surface changes in bacteria during carotenoid-rich phase after UV-B irradiation exposure. These findings highlight the likely ability of LAPM80 strain's C50 carotenoids to improve UV-B iiradiation resistance, indicating their potential for developing natural photoprotective compounds for the dermo-cosmetic industry.}, }
@article {pmid39808188, year = {2025}, author = {Nguyen, MP and Lehosmaa, K and Martz, F and Koskimäki, JJ and Toth, K and Ahonen, SHK and Häggman, H and Pirttilä, AM}, title = {Dynamics of fungal endophytic communities in bilberry (Vaccinium myrtillus L.) fruits through development is shaped by host phenolic compounds.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {1}, pages = {}, pmid = {39808188}, issn = {1574-6941}, support = {//Finnish Cultural Foundation/ ; //European Regional Development Fund/ ; 240208//Alfred Kordelin Foundation/ ; }, mesh = {*Vaccinium myrtillus/microbiology/growth &amp; development/chemistry ; *Phenols/metabolism/analysis ; *Fruit/microbiology/growth &amp; development/chemistry ; *Endophytes/genetics/classification/physiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Mycobiome ; }, abstract = {The physical and chemical properties of wild berry fruits change dramatically during development, and the ripe berries host species-specific endophytic communities. However, the development of fungal endophytic communities during berry ripening is unknown. We studied bilberries (Vaccinium myrtillus L.), valuable natural resources in northern Europe and richest sources of phenolic compounds, to characterize dynamics of the fungal communities over fruit developmental stages (raw, veraison, and ripe). Our focus was to examine the changes in the fruit phenolic compounds associated with the fungal community structure using liquid chromatography-mass spectrometry for phenolic compounds and high-throughput sequencing technology targeting the internal transcribed spacer 2 ribosomal DNA region for endophytic fungi. We found that the fungal diversity increased with the ripening stages. The fungal profile changed dramatically through fruit development, and the veraison stage was a transition stage, where the core mycobiome of fruits changed. The fungal community structure and abundance of the most dominant genera in raw and ripe stages, Monilinia and Cladosporium, respectively, were driven by the bilberry phenolic profile. We conclude that sampling time, tissue age, and phenolic compounds play important roles in the development of fruit fungal community. Moreover, phenolic compounds could be the host's strategy to recruit beneficial microbes.}, }
@article {pmid39807875, year = {2025}, author = {Schloss, PD}, title = {phylotypr: an R package for classifying DNA sequences.}, journal = {Microbiology resource announcements}, volume = {14}, number = {2}, pages = {e0114424}, pmid = {39807875}, issn = {2576-098X}, abstract = {The phylotypr R package implements the popular naive Bayesian classification algorithm that is frequently used to classify 16S rRNA and other gene sequences to taxonomic lineages. A companion data package, phylotyprrefdata, also provides numerous versions of taxonomic databases from the Ribosomal Database Project, SILVA, and greengenes.}, }
@article {pmid39806487, year = {2025}, author = {Dieppa-Colón, E and Martin, C and Kosmopoulos, JC and Anantharaman, K}, title = {Prophage-DB: a comprehensive database to explore diversity, distribution, and ecology of prophages.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {5}, pmid = {39806487}, issn = {2524-6372}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; T32 GM135066/GM/NIGMS NIH HHS/United States ; R35GM143024/GM/NIGMS NIH HHS/United States ; T32GM135066/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are extremely underexplored. Phages are classified as virulent or temperate based on their life cycles. Temperate phages adopt the lysogenic mode of infection, where the genome integrates into the host cell genome forming a prophage. Prophages enable viral genome replication without host cell lysis, and often contribute novel and beneficial traits to the host genome. Current phage research predominantly focuses on lytic phages, leaving a significant gap in knowledge regarding prophages, including their biology, diversity, and ecological roles.<br><br>RESULTS: Here we develop and describe Prophage-DB, a database of prophages, their proteins, and associated metadata that will serve as a resource for viral genomics and microbial ecology. To create the database, we identified and characterized prophages from genomes in three of the largest publicly available databases. We applied several state-of-the-art tools in our pipeline to annotate these viruses, cluster them, taxonomically classify them, and detect their respective auxiliary metabolic genes. In total, we identify and characterize over 350,000 prophages and 35,000 auxiliary metabolic genes. Our prophage database is highly representative based on statistical results and contains prophages from a diverse set of archaeal and bacterial hosts which show a wide environmental distribution.<br><br>CONCLUSION: Given that prophages are particularly overlooked and merit increased attention due to their vital implications for microbiomes and their hosts, we created Prophage-DB to advance our understanding of prophages in microbiomes through a comprehensive characterization of prophages in publicly available genomes. We propose that Prophage-DB will serve as a valuable resource for advancing phage research, offering insights into viral taxonomy, host relationships, auxiliary metabolic genes, and environmental distribution.}, }
@article {pmid39805038, year = {2025}, author = {Wei, L and Van Beeck, W and Hanlon, M and DiCaprio, E and Marco, ML}, title = {Lacto-Fermented Fruits and Vegetables: Bioactive Components and Effects on Human Health.}, journal = {Annual review of food science and technology}, volume = {16}, number = {1}, pages = {289-314}, doi = {10.1146/annurev-food-052924-070656}, pmid = {39805038}, issn = {1941-1421}, mesh = {Humans ; *Fruit/chemistry/microbiology ; *Vegetables/chemistry/microbiology ; Fermentation ; *Fermented Foods/microbiology/analysis ; Food Microbiology ; }, abstract = {Lacto-fermented fruits and vegetables (FVs) such as kimchi, sauerkraut, and fermented olives and nonalcoholic juices have a long history as dietary staples. Herein, the production steps and microbial ecology of lacto-fermented FVs are discussed alongside findings from human and laboratory studies investigating the health benefits of these foods. Lacto-fermented FVs are enriched in beneficial live microbes and bioactive compounds, including lactic and acetic acids, phenolic compounds, bacteriocins, and amino acid derivatives such as indole-3-lactic acid, phenyl-lactic acid, and γ-aminobutyric acid. At least 11 human studies have been performed on kimchi, whereas others have been investigated in only one or two trials. Besides exploring the health benefits, it is imperative to ensure that these foods made either commercially or at home have minimal risk for foodborne illness and exposure to undesired compounds like biogenic amines. Development of starter-culture strains and production protocols can lead to lacto-fermented FVs designed for specific health benefits.}, }
@article {pmid39804671, year = {2025}, author = {Broderick, CM and Benucci, GMN and Bachega, LR and Miller, GD and Evans, SE and Hawkes, CV}, title = {Long-term climate establishes functional legacies by altering microbial traits.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39804671}, issn = {1751-7370}, mesh = {*Soil Microbiology ; Metagenomics ; *Climate ; Carbon Cycle ; Soil/chemistry ; Droughts ; *Bacteria/genetics/classification/metabolism ; }, abstract = {Long-term climate history can influence rates of soil carbon cycling but the microbial traits underlying these legacy effects are not well understood. Legacies may result if historical climate differences alter the traits of soil microbial communities, particularly those associated with carbon cycling and stress tolerance. However, it is also possible that contemporary conditions can overcome the influence of historical climate, particularly under extreme conditions. Using shotgun metagenomics, we assessed the composition of soil microbial functional genes across a mean annual precipitation gradient that previously showed evidence of strong climate legacies in soil carbon flux and extracellular enzyme activity. Sampling coincided with recovery from a regional, multi-year severe drought, allowing us to document how the strength of climate legacies varied with contemporary conditions. We found increased investment in genes associated with resource cycling with historically higher precipitation across the gradient, particularly in traits related to resource transport and complex carbon degradation. This legacy effect was strongest in seasons with the lowest soil moisture, suggesting that contemporary conditions-particularly, resource stress under water limitation-influences the strength of legacy effects. In contrast, investment in stress tolerance did not vary with historical precipitation, likely due to frequent periodic drought throughout the gradient. Differences in the relative abundance of functional genes explained over half of variation in microbial functional capacity-potential enzyme activity-more so than historical precipitation or current moisture conditions. Together, these results suggest that long-term climate can alter the functional potential of soil microbial communities, leading to legacies in carbon cycling.}, }
@article {pmid39799671, year = {2025}, author = {Mo, Y and Abdolahpur Monikh, F and Jaffer, YD and Mugani, R and Ionescu, D and Chen, G and Yang, J and Grossart, HP}, title = {Effects of tire wear particles on freshwater bacterial-fungal community dynamics and subsequent elemental cycles using microcosms.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137062}, doi = {10.1016/j.jhazmat.2024.137062}, pmid = {39799671}, issn = {1873-3336}, mesh = {*Bacteria/drug effects ; *Fungi/drug effects ; *Fresh Water/microbiology ; Lakes/microbiology ; Geologic Sediments/microbiology ; *Water Microbiology ; }, abstract = {Ecological impacts of tire wear particles (TWPs) on microbial communities and biogeochemical cycles in freshwater remain largely unknown. Here, we conducted a microcosm experiment to investigate interactions between the overlying water and sediment without and with TWPs addition in a rural vs. urban lake system. Our results revealed the degree of change in microbial community diversity in water is higher than that in sediment following TWPs addition. For bacterial communities, TWPs addition changed their composition in the water, but only little in the sediment. For fungal communities, TWPs addition changed their composition both in water and sediments. Furthermore, in water, TWPs addition increased network complexity between bacteria-bacteria, fungi-fungi and bacteria-fungi in the urban system but reduced it in the rural one. In contrast, TWPs presence did not significantly change network complexity among microbial communities in the sediment of both lakes. Isotope labeling analysis uncovered that based on a short-term (6 hours) incubation experiment, TWPs addition did not significantly change carbon nor nitrogen cycling in the water. Yet, certain changes could be observed, especially in the long-term experiment (1 month), indicating that TWPs pollution has the potential to impact elemental cycling and thus ecosystem functions by altering microbial communities. Our results provide new insights into TWPs-induced ecological effects on microorganisms and potential biogeochemical consequences in a rural vs. urban lakes.}, }
@article {pmid39798462, year = {2025}, author = {Kovarova, A and Prole, G and Farrell, ML and Maguire, M and Murphy, LC and Chueiri, A and O'Connor, L and Miliotis, G and Morris, D and Burke, LP}, title = {Antimicrobial resistant Enterobacterales of clinical importance in mute swans.}, journal = {The Science of the total environment}, volume = {961}, number = {}, pages = {178400}, doi = {10.1016/j.scitotenv.2025.178400}, pmid = {39798462}, issn = {1879-1026}, mesh = {*Enterobacteriaceae/drug effects ; Animals ; *Drug Resistance, Bacterial/genetics ; Ireland ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Feces/microbiology ; Clinical Relevance ; }, abstract = {Urban water environments, including canals, harbours and estuaries are susceptible to contamination with antimicrobials and drug-resistant bacteria through domestic and industrial wastewater discharges and storm water overflows. There is potential for wildlife using these waters to acquire and transmit drug-resistant bacteria and antimicrobial resistance genes (ARGs) of clinical importance. This study aimed to assess clinically important drug-resistant bacteria in urban waterfowl, particularly mute swans. Faecal samples were collected from 17 mute swans in the Greater Dublin Area, Ireland during July, August, October, and November of 2022. Samples were swabbed directly onto agars to select for carbapenem resistant, Extended-spectrum Beta-lactamase (ESBL)-producing, ciprofloxacin resistant and colistin resistant bacteria. Isolates identified by MALDI-TOF as Enterobacterales were tested for susceptibility to a panel of 16 antimicrobials and real-time PCR was employed to detect cefotaximase and carbapenemase genes (CRGs). Drug-resistant isolates were characterised by Whole Genome Sequencing (WGS), including long read sequencing for carbapenemase and mobile colistin resistance (mcr) gene-producing Enterobacterales isolates. Eleven of seventeen (65 %) swan samples were positive for the resistant organism(s) (n = 35), comprising Escherichia coli (n = 32; 82 %) and other Enterobacterales (n = 3). Twenty E. coli (63 %) produced ESBL, with 16/20 (80 %) identified as positive for blaCTX-M-group 1 enzymes, comprising CTX-M-15 (n = 13), CTX-M-55 (n = 2) and CTX-M-1 (n = 1) and 4/20 (20 %) positive for blaCTX-M-group 9 enzymes CTX-M-27 (n = 2) and CTX-M-9 (n = 2). Three E. coli isolates were phenotypically ertapenem resistant, one of which was an ST4450 isolate which carried plasmid encoded blaOXA-181 and blaCMY-141 with blaCTX-M-15 identified chromosomally. One colistin resistant E. coli bore the mcr-1 gene chromosomally. Bioinformatic analysis revealed high-risk pathogenic ESBL E. coli clones including ST38 (n = 3), ST69 (n = 3), and ST131 (n = 2). The study indicates mute swans are a reservoir for drug-resistant Enterobacterales and ARGs of clinical importance and may be a useful sentinel species for antimicrobial resistance (AMR) surveillance in wildlife.}, }
@article {pmid39798088, year = {2025}, author = {Stefanic, P and Stare, E and Floccari, VA and Kovac, J and Hertel, R and Rocha, U and Kovács, &#xc1;T and Mandić-Mulec, I and Strube, ML and Dragoš, A}, title = {Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scales.}, journal = {Cell reports}, volume = {44}, number = {1}, pages = {115197}, doi = {10.1016/j.celrep.2024.115197}, pmid = {39798088}, issn = {2211-1247}, mesh = {*Bacillus subtilis/virology/genetics ; *Prophages/genetics ; Phylogeny ; Genome, Bacterial/genetics ; }, abstract = {Prophages constitute a substantial portion of bacterial genomes, yet their effects on hosts remain poorly understood. We examine the abundance, distribution, and activity of prophages in Bacillus subtilis using computational and laboratory analyses. Genome sequences from the NCBI database and riverbank soil isolates reveal prophages primarily related to mobile genetic elements in laboratory strains. Distinct and previously unknown prophages in local isolates prompt an investigation into factors shaping prophage presence, with phylogenetic relatedness predicting the prophage repertoire slightly better than geographical origin. Data also show that prophages exhibit strong co-occurrence and exclusion patterns within genomes. Laboratory experiments indicate that most predicted prophages are cryptic, as they are not induced under DNA-damaging conditions. Importantly, stress responses increase with the number of predicted prophages, suggesting their influence on host physiology. This study highlights the diversity, integration patterns, and potential roles of prophages in B. subtilis, shedding light on bacterial genome evolution and phage-host dynamics.}, }
@article {pmid39797436, year = {2025}, author = {Shopen Gochev, C and Demory, D and Lopes Dos Santos, A and Carlson, MCG and Gutiérrez-Rodríguez, A and Weitz, JS and Lindell, D}, title = {Cold Surface Waters of the Sub-Antarctic Pacific Ocean Support High Cyanophage Abundances and Infection Levels.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70031}, pmid = {39797436}, issn = {1462-2920}, support = {2679/20//Israel Science Foundation/ ; 639682//Simons Foundation/ ; 721231//Simons Foundation/ ; 721254//Simons Foundation/ ; }, mesh = {*Cyanobacteria/classification/virology ; Pacific Ocean ; *Seawater/chemistry/microbiology/virology ; Bacteriophages ; Cold Temperature ; Iron/analysis ; }, abstract = {Cyanobacterial distributions are shaped by abiotic factors including temperature, light and nutrient availability as well as biotic factors such as grazing and viral infection. In this study, we investigated the abundances of T4-like and T7-like cyanophages and the extent of picocyanobacterial infection in the cold, high-nutrient-low-chlorophyll, sub-Antarctic waters of the southwest Pacific Ocean during austral spring. Synechococcus was the dominant picocyanobacterium, ranging from 4.7 × 10[3] to 1.2 × 10[5] cells∙mL[-1], while Prochlorococcus abundances were relatively low overall, ranging from 1.0 × 10[3] to 3.9 × 10[4] cells∙mL[-1]. Using taxon-specific, single-virus and single-cell polony methods, we found that cyanophages were on average 15-fold, and up to 50-fold, more abundant than cyanobacteria in these waters. T4-like cyanophages (ranging from 1.7 × 10[5] to 6.5 × 10[5] phage·mL[-1]) were 2.7-fold more abundant than T7-like cyanophages (ranging from 3.1 × 10[4] to 2.8 × 10[5] phage·mL[-1]). Picocyanobacteria were primarily infected by T4-like cyanophages with more Synechococcus (4.8%-12.1%) infected than Prochlorococcus (2.5%-6.2%), whereas T7-like cyanophages infected less than 1% of both genera. These infection levels translated to daily mortality in the range of 5.7%-26.2% and 2.9%-14.3% of the standing stock of Synechococcus and Prochlorococcus, respectively. Our findings suggest that T4-like cyanophages are significant agents of cyanobacterial mortality in the cold, low-iron, sub-Antarctic waters of the South Pacific Ocean.}, }
@article {pmid39794865, year = {2025}, author = {Passarelli-Araujo, H and Venancio, TM and Hanage, WP}, title = {Relating ecological diversity to genetic discontinuity across bacterial species.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {8}, pmid = {39794865}, issn = {1474-760X}, mesh = {*Genome, Bacterial ; *Bacteria/genetics/classification ; *Genetic Variation ; Phylogeny ; Mycobacterium tuberculosis/genetics ; Biodiversity ; }, abstract = {BACKGROUND: Genetic discontinuity represents abrupt breaks in genomic identity among species. Advances in genome sequencing have enhanced our ability to track and characterize genetic discontinuity in bacterial populations. However, exploring the degree to which bacterial diversity exists as a continuum or sorted into discrete and readily defined species remains a challenge in microbial ecology. Here, we aim to quantify the genetic discontinuity (δ) and investigate how this metric is related to ecology.<br><br>RESULTS: We harness a dataset comprising 210,129 genomes to systematically explore genetic discontinuity patterns across several distantly related species, finding clear breakpoints which vary depending on the taxa in question. By delving into pangenome characteristics, we uncover a significant association between pangenome saturation and genetic discontinuity. Closed pangenomes are associated with more pronounced breaks, exemplified by Mycobacterium tuberculosis. Additionally, through a machine learning approach, we detect key features such as gene conservation patterns and functional annotations that significantly impact genetic discontinuity prediction.<br><br>CONCLUSIONS: Our study clarifies bacterial genetic patterns and their ecological impacts, enhancing the delineation of species boundaries and deepening our understanding of microbial diversity.}, }
@article {pmid39794276, year = {2025}, author = {Tang, L and Manefield, M}, title = {Aeration promotes Proteobacteria over Firmicutes in macerated food waste, resulting in superior anaerobic digestion efficiency.}, journal = {FEMS microbiology letters}, volume = {372}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf001}, pmid = {39794276}, issn = {1574-6968}, support = {//Department of Planning, Industry and Environment/ ; }, mesh = {Anaerobiosis ; *Proteobacteria/metabolism/genetics ; *Firmicutes/metabolism ; Biofuels ; Food ; Aerobiosis ; Food Loss and Waste ; }, abstract = {Aeration is a common pretreatment method to enhance biogas production via anaerobic digestion of waste organic feedstocks such as unused food. While impacts on downstream anaerobic digestion have been intensively investigated, the consequence of aeration on the microbial community in food waste has not been characterized. Food waste has a low pH resulting from the dominance of lactic acid bacteria within the Firmicutes phylum. This excludes other phylotypes with a higher potential to hydrolyse complex biopolymers in food waste. In this study, we reveal that aeration of macerated food waste results in a dramatic shift away from Firmicutes towards dominance of Proteobacteria that are better known for extracellular enzyme production. Given that hydrolysis is the rate limiting step in anaerobic digestion, this explains why aeration improves the efficiency of biogas production from food waste. The discovery that Proteobacteria dominate microbial communities in aerated food waste opens up opportunities to manipulate extracellular enzyme production through gene expression mechanisms common among Proteobacteria such as quorum sensing.}, }
@article {pmid39792461, year = {2025}, author = {Tan, G and LeCates, CN and Simpson, A and Holtzen, S and Parris, DJ and Stewart, FJ and Stockton, A and , }, title = {Amplicon Sequencing Reveals Diversity in Spatially Separated Microbial Communities in the Icelandic Mars Analog Environment Mælifellssandur.}, journal = {Astrobiology}, volume = {25}, number = {1}, pages = {72-81}, doi = {10.1089/ast.2023.0124}, pmid = {39792461}, issn = {1557-8070}, mesh = {*Mars ; Iceland ; *Extraterrestrial Environment ; *Microbiota/genetics ; Phylogeny ; Exobiology ; RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology ; Bacteria/genetics/classification ; Biodiversity ; Sequence Analysis, DNA ; }, abstract = {Exploration missions to Mars rely on landers or rovers to perform multiple analyses over geographically small sampling regions, while landing site selection is done using large-scale but low-resolution remote-sensing data. Utilizing Earth analog environments to estimate small-scale spatial and temporal variation in key geochemical signatures and biosignatures will help mission designers ensure future sampling strategies meet mission science goals. Icelandic lava fields can serve as Mars analog sites due to conditions that include low nutrient availability, temperature extremes, desiccation, and isolation from anthropogenic contamination. This work reports analysis of samples collected using methods analogous to those of planetary missions to characterize microbial communities at different spatial scales in Mælifellssandur, Iceland, an environment with homogeneity at "remote imaging" resolution (overall temperature, apparent moisture content, and regolith grain size). Although microbial richness did not vary significantly among samples, the phylogenetic composition of the sediment microbiome differed significantly among sites separated by 100 m, which suggests distinct microbial signatures despite apparent homogeneity from remote observations. This work highlights the importance of considering microenvironments in future life-detection missions to extraterrestrial planetary bodies.}, }
@article {pmid39792290, year = {2025}, author = {Foffi, R and Brumley, DR and Peaudecerf, FJ and Stocker, R and Słomka, J}, title = {Slower swimming promotes chemotactic encounters between bacteria and small phytoplankton.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {2}, pages = {e2411074122}, pmid = {39792290}, issn = {1091-6490}, support = {PZ00P2_202188//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; ANR-22-CPJ2-0015-01//Agence Nationale de la Recherche (ANR)/ ; GBMF9197//Gordon and Betty Moore Foundation (GBMF)/ ; 542395FY22//Simons Foundation (SF)/ ; 205321_207488//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; CRSII5-186422//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; 51NF40_180575//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; 955910//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, mesh = {*Phytoplankton/physiology ; *Chemotaxis/physiology ; Bacteria/metabolism ; Bacterial Physiological Phenomena ; Models, Biological ; }, abstract = {Chemotaxis enables marine bacteria to increase encounters with phytoplankton cells by reducing their search times, provided that bacteria detect noisy chemical gradients around phytoplankton. Gradient detection depends on bacterial phenotypes and phytoplankton size: large phytoplankton produce spatially extended but shallow gradients, whereas small phytoplankton produce steeper but spatially more confined gradients. To date, it has remained unclear how phytoplankton size and bacterial swimming speed affect bacteria's gradient detection ability and search times for phytoplankton. Here, we compute an upper bound on the increase in bacterial encounter rate with phytoplankton due to chemotaxis over random motility alone. We find that chemotaxis can substantially decrease search times for small phytoplankton, but this advantage is highly sensitive to variations in bacterial phenotypes or phytoplankton leakage rates. By contrast, chemotaxis toward large phytoplankton cells reduces the search time more modestly, but this benefit is more robust to variations in search or environmental parameters. Applying our findings to marine phytoplankton communities, we find that, in productive waters, chemotaxis toward phytoplankton smaller than 2 μm provides little to no benefit, but can decrease average search times for large phytoplankton (∼20 μm) from 2 wk to 2 d, an advantage that is robust to variations and favors bacteria with higher swimming speeds. By contrast, in oligotrophic waters, chemotaxis can reduce search times for picophytoplankton (∼1 μm) up to 10-fold, from a week to half a day, but only for bacteria with low swimming speeds and long sensory timescales. This asymmetry may promote the coexistence of diverse search phenotypes in marine bacterial populations.}, }
@article {pmid39789151, year = {2025}, author = {Frasca, S and Alabiso, A and D'Andrea, MM and Migliore, L}, title = {Uncovering the Fungal Community Composition of Alive and Dead Posidonia oceanica Matte.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {170}, pmid = {39789151}, issn = {1432-184X}, mesh = {*Alismatales/microbiology ; Ascomycota/genetics/classification/metabolism/growth &amp; development ; Mycobiome ; Fungi/genetics/classification/metabolism/isolation &amp; purification ; DNA, Fungal/genetics ; Seawater/microbiology ; Biodegradation, Environmental ; Geologic Sediments/microbiology ; Phylogeny ; }, abstract = {Posidonia oceanica retains a large amount of carbon within its belowground recalcitrant structure, the 'matte,' which is characterized by low oxygen availability and biodegradation. Fungi may play a pivotal role in carbon sequestration within the matte, even if little/no information is available. To fill this gap, we profiled fungal communities from the upper and lower layers of alive and dead matte, by using an ITS2-5.8S rDNA metabarcoding approach. The study was conducted in a shallow coastal stretch of the Aegean Sea (Crete). Then, 184 operational taxonomic units were identified, predominantly belonging to Ascomycota, in alive and dead matte. Nevertheless, their composition significantly differed: the host-specific Posidoniomyces atricolor was dominant in alive but not in dead matte, while fast-growing saprotrophs, potentially accelerating the decomposition rate, increased in dead matte. These findings lay the groundwork for future investigations on the possible increase of biodegradation under the changing environmental conditions.}, }
@article {pmid39788196, year = {2025}, author = {Kim, YT and Huang, YP and Ozturk, G and Hahn, J and Taha, AY and Wang, A and Barile, D and Mills, DA}, title = {Characterization of Bifidobacterium bifidum growth and metabolism on whey protein phospholipid concentrate.}, journal = {Journal of dairy science}, volume = {108}, number = {4}, pages = {3366-3381}, doi = {10.3168/jds.2024-25885}, pmid = {39788196}, issn = {1525-3198}, mesh = {*Bifidobacterium bifidum/metabolism/growth &amp; development ; *Whey Proteins ; Humans ; *Phospholipids/metabolism ; Milk, Human/chemistry ; Animals ; Oligosaccharides/metabolism ; }, abstract = {Whey protein phospholipid concentrate (WPPC) is a co-product generated during the manufacture of whey protein isolate. Whey protein phospholipid concentrate is depleted of simple sugars but contains numerous glycoconjugates embedded in the milk fat globule membrane, suggesting this fraction may serve as a carbon source for growth of bifidobacteria commonly enriched in breastfed infants. In this work, we demonstrate that WPPC can serve as a sole carbon source for the growth of Bifidobacterium bifidum, a species common to the breastfed infant and routinely used as a probiotic. Growth on WPPC fractions resulted in expression of key extracellular glycosyl hydrolases in B. bifidum associated with the catabolism of glycoproteins. Interestingly, this included induction of fucosidase genes in B. bifidum linked to catabolism of fucosylated human milk oligosaccharides even though the WPPC glycan possesses little fucose. Additional growth studies revealed that WPPC-glycan components N-acetylglucosamine or N-acetylgalactosamine were required for pre-activation of B. bifidum toward rapid growth on fucosylated human milk oligosaccharides. Growth on WPPC fractions also resulted in expression of extracellular sialidases in B. bifidum which promoted a consistent release of sialic acid, a well-known component of bovine milk oligosaccharides and glycoconjugates with potential effects on gut microbial ecology and host cognition. These studies suggest WPPC may serve as a promising bioactive component to facilitate probiotic activity for use in infant formulas and other synbiotic applications.}, }
@article {pmid39787750, year = {2025}, author = {Zhang, S and Wang, J and Liu, Z and Xia, X and Wu, X and Li, X and Liu, Y and Xu, Z and Marzadri, A and McDowell, WH and Cai, Y and Yang, Z}, title = {Temperature has an enhanced role in sediment N2O and N2 fluxes in wider rivers.}, journal = {Water research}, volume = {273}, number = {}, pages = {123095}, doi = {10.1016/j.watres.2025.123095}, pmid = {39787750}, issn = {1879-2448}, mesh = {*Rivers/chemistry ; *Geologic Sediments/chemistry ; *Nitrogen ; *Temperature ; *Nitrous Oxide ; China ; Denitrification ; Nitrates ; Bacteria/metabolism ; }, abstract = {Riverine N2O and N2 fluxes, key components of the global nitrogen budget, are known to be influenced by river size (often represented by average river width), yet the specific mechanisms behind these effects remain unclear. This study examined how environmental and microbial factors influenced sediment N2O and N2 fluxes across rivers with varying widths (2.8 to 2,000 m) in China. Sediment acted as sources of both N2O and N2 emissions, with both N2 (0.2 to 20.8 mmol m[-2] d[-1]) and N2O fluxes (0.7-54.2 μmol m[-2] d[-1]) decreasing significantly as river width increased. N2 fluxes were positively correlated with denitrifying bacterial abundance, whereas N2O fluxes, when normalized by the abundance of denitrifying bacteria, were negatively correlated with the abundance of N2O-reducing microbes. Water physicochemical factors, particularly temperature and nitrate, were more important drivers of these fluxes than sediment factors. Nitrate significantly increased denitrifying bacterial abundance, whereas higher temperatures enhanced cell-specific activity. Lower N2O and N2 emissions in wider rivers were attributed to decreased denitrifying microbial abundance and lower denitrification rates, in addition to the commonly assumed reduction in exogenous N2O and N2 inputs. Rolling regression analysis showed that nitrate concentration had a stronger effect on sediment N2O and N2 fluxes in narrower rivers, whereas temperature was more influential in wider rivers. This difference is attributed to more stable nitrate concentrations and decreased nitrogen removal efficiency in wider rivers, while temperature variation remained consistent across all river widths. Beyond sediments, temperature had a greater effect on excess N2O concentrations than nitrate in the overlying water of wider rivers (>165 m), highlighting its broader impact. This study provides new biogeochemical insights into how river width influences sediment N2O and N2 fluxes and highlights the importance of incorporating temperature into flux predictions, particularly for wider rivers.}, }
@article {pmid39786593, year = {2025}, author = {Xu, Y and Liang, J and Qin, L and Niu, T and Liang, Z and Li, Z and Chen, B and Zhou, J and Yu, K}, title = {The Dynamics of Symbiodiniaceae and Photosynthetic Bacteria Under High-Temperature Conditions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {169}, pmid = {39786593}, issn = {1432-184X}, support = {42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; 2018GXNSFAA281328//Guangxi scientific projects/ ; }, mesh = {*Photosynthesis ; *Symbiosis ; *Anthozoa/microbiology/physiology ; China ; *Hot Temperature ; *Dinoflagellida/physiology ; Animals ; *Seasons ; Bacteria/classification/metabolism/genetics ; Cyanobacteria/physiology ; Chlorophyll A/metabolism ; }, abstract = {Coral thermal tolerance is intimately linked to their symbiotic relationships with photosynthetic microorganisms. However, the potential compensatory role of symbiotic photosynthetic bacteria in supporting Symbiodiniaceae photosynthesis under extreme summer temperatures remains largely unexplored. Here, we examined the seasonal variations in Symbiodiniaceae and photosynthetic bacterial community structures in Pavona decussata corals from Weizhou Island, Beibu Gulf, China, with particular emphasis on the role of photosynthetic bacteria under elevated temperature conditions. Our results revealed that Symbiodiniaceae density and Chlorophyll a concentration were lowest during the summer and highest in the winter. Notably, the summer bacterial community was predominately composed of the proteorhodopsin bacterium BD 1-7 _clade, alongside a significant increase in Cyanobacteria, particularly Synechococcus_CC9902 and Cyanobium_PCC-6307, which represented 61.85% and 31.48% of the total Cyanobacterial community, respectively. In vitro experiments demonstrated that Cyanobacteria significantly enhanced Symbiodiniaceae photosynthetic efficiency under high-temperature conditions. These findings suggest that the increased abundance of photosynthetic bacteria during summer may mitigate the adverse physiological effects of reduced Symbiodiniaceae density, thereby contributing to coral stability. Our study highlights a potential synergistic interaction between Symbiodiniaceae and photosynthetic bacteria, emphasizing the importance of understanding these dynamic interactions in sustaining coral resilience against environmental stress, although further research is necessary to establish their role in preventing coral bleaching.}, }
@article {pmid39786575, year = {2025}, author = {McNeal, R and Wells, JD and Tomberlin, JK}, title = {Bernard Greenberg: a legacy in medical, veterinary, and forensic entomology.}, journal = {Journal of medical entomology}, volume = {62}, number = {2}, pages = {231-235}, doi = {10.1093/jme/tjae158}, pmid = {39786575}, issn = {1938-2928}, mesh = {Animals ; History, 20th Century ; *Entomology/history ; *Forensic Entomology/history ; *Diptera/microbiology ; History, 21st Century ; Humans ; United States ; Veterinary Medicine/history ; }, abstract = {Bernard Greenberg was a ground-breaking scientist in the worlds of medical-veterinary and forensic entomology, studying the ability of flies to serve as a vector of human and other vertebrate pathogens. His work also extended beyond these topics, creating key studies on flies and their associated microbial ecology. These efforts led to numerous research publications and two books on flies and their associated microorganisms. Greenberg served a pioneering role in establishing the field of forensic entomology in the USA later in his career, publishing key papers and a book that are highly cited to this day. We present a review of Dr Greenberg's scientific contributions concerning flies and disease, insect/microbe interactions, and insects as forensic indicators.}, }
@article {pmid39779689, year = {2025}, author = {Cottin, A and Dequiedt, S and Djemiel, C and Prévost-Bouré, NC and Tripied, J and Lelièvre, M and Terreau, L and Régnier, T and Karimi, B and Jolivet, C and Bispo, A and Saby, N and Maron, PA and Ranjard, L and Terrat, S}, title = {Harmonized Datasets of microbiological parameters from a French national-scale soil monitoring survey.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {34}, pmid = {39779689}, issn = {2052-4463}, support = {2021PRE00370//Conseil r&#xe9;gional de Bourgogne-Franche-Comt&#xe9; (Regional Council of Burgundy)/ ; }, mesh = {*Soil Microbiology ; France ; *Fungi/genetics ; *Archaea/genetics ; *Bacteria/genetics/classification ; Environmental Monitoring ; Soil ; Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbiological datasets and associated environmental parameters from the French soil quality monitoring network (RMQS) offer an opportunity for long-term and large-scale soil quality monitoring. Soils supply important ecosystem services e.g. carbon dynamics/storage or mineral element recycling, supported by the soil microbial diversity (bacteria, archaea and fungi). Based on the 2,240 sites of the 2000-2015 RMQS, molecular tools were applied to characterize soil microbiota. Soil DNA analysis yielded molecular microbial biomass for 2,168 sites, bacterial and fungal qPCR for 2,073 sites, and high-throughput amplicon sequencing of targeted 16S rDNA bacterial and archaeal genes for 1,842 sites. All these datasets were partially or completely unavailable, so raw results files from RMQS microbiological studies were harmonized and published in a Dataverse repository to facilitate their reusability. Altogether, these datasets allow for in-depth studies of soil microbial ecology and biogeography, and will be updated with fungal datasets and the second currently ongoing monitoring campaign (2016-2027).}, }
@article {pmid39779584, year = {2025}, author = {Roy, A and Ray, S}, title = {Molecular Evolution of Paralogous Cold Shock Proteins in E. coli: A Study of Asymmetric Divergence and Protein Functional Networks.}, journal = {Molecular biotechnology}, volume = {}, number = {}, pages = {}, pmid = {39779584}, issn = {1559-0305}, abstract = {Nine homologous Cold Shock Proteins (Csps) have been recognized in the E.coli Cold Shock Domain gene family. These Csps function as RNA chaperones. This study aims to establish the evolutionary relationships among these genes by identifying and classifying their paralogous counterparts. It focuses on the physicochemical, structural, and functional analysis of the genes to explore the phylogeny of the Csp gene family. Computational tools were employed for protein molecular modeling, conformational analysis, functional studies, and duplication-divergence assessments. The research also examined amino acid conservation, protein mutations, domain-motif patterns, and evolutionary residue communities to better understand residual interactions, evolutionary coupling, and co-evolution. H33, M5, W11 and F53 residues were highly conserved within the protein family. It was further seen that residues M5, G17, G58, G61, P62, A64, V67 were intolerant to any kind of mutation whereas G3, D40, G41, Y42, S44, T54, T68, S69 were most tolerable towards substitutions. The study of residue communities displayed that the strongest residue coupling was observed in N13, F18, S27, F31, and W11. It was observed that all the gene pairs except CspF/CspH had new motifs generated over time. It was ascertained that all the gene pairs underwent asymmetric expression divergence after duplication. The Ka/ Ks ratio also revealed that all residues undertook neutral and purifying selection pressure. New functions were seen to develop in gene pairs evident from generation of new motifs. The discovery of new motifs and functions in Csps highlights their adaptive versatility, crucial for E. coli's resilience to environmental stressors and valuable for understanding bacterial stress response mechanisms. These findings will pave the way for future investigations into Csp evolution, with potential applications in microbial ecology and antimicrobial strategy development.}, }
@article {pmid39779304, year = {2025}, author = {Diakaki, M and Andreo Jimenez, B and de Lange, E and Butterbach, P and van der Heijden, L and Köhl, J and de Boer, W and Postma, J}, title = {Spinach seed microbiome characteristics linked to suppressiveness against Globisporangium ultimum damping-off.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {2}, pages = {}, pmid = {39779304}, issn = {1574-6941}, support = {//Ministry of Agriculture/ ; }, mesh = {*Spinacia oleracea/microbiology ; *Seeds/microbiology ; *Microbiota ; *Plant Diseases/microbiology/prevention &amp; control ; *Pythium/physiology ; Bacteria/classification/genetics/isolation &amp; purification ; Fungi/genetics/classification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recently we demonstrated that the seed microbiome of certain spinach (Spinacia oleracea) seed lots can confer disease suppression against Globisporangium ultimum damping-off (previously known as Pythium ultimum). We hypothesized that differences in the microbial community composition of spinach seed lots correlate with the levels of damping-off suppressiveness of each seed lot. Here, we show that a large proportion of variance in seed-associated bacterial (16S) and fungal (Internal Transcribed Spacer 1) amplicon sequences was explained by seed lot identity, while 9.8% of bacterial and 7.1% of fungal community variance correlated with disease suppression. More specifically, a higher relative abundance of basidiomycetous dimorphic yeasts such as Vishniacozyma, Filobasidium, and Papiliotrema and of the bacterial genus Massilia was a key feature of suppressive seed microbiomes. We suggest that the abundance of these genera is indicative of seed lot suppressive potential. Seed processing and treatment can become more targeted with indicator taxa being used to evaluate the presence of beneficial seed-associated microbial functions. This process, in turn, could contribute to the sustainable management of seedling diseases. Finally, this study highlights the ubiquity of yeasts in spinach seed microbiota and their potential beneficial roles for seed health.}, }
@article {pmid39777550, year = {2025}, author = {Byers, AK and Wakelin, SA and Condron, L and Black, A}, title = {Land Use Change Disrupts the Network Complexity and Stability of Soil Microbial Carbon Cycling Genes Across an Agricultural Mosaic Landscape.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {167}, pmid = {39777550}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Carbon Cycle ; New Zealand ; *Agriculture ; *Soil/chemistry ; *Microbiota ; *Bacteria/genetics/classification/metabolism ; Carbon/metabolism ; Gene Regulatory Networks ; Forests ; Ecosystem ; }, abstract = {To understand the effects of agricultural land use change and management on soil carbon (C) cycling, it is crucial to examine how these changes can influence microbial soil C cycling. Network analysis can offer insights into the structure, complexity, and stability of the soil microbiome in response to environmental disturbances, including land use change. Using SparCC-based co-occurrence networks, we studied how land use change impacts the connectivity, complexity, and stability of microbial C-cycling gene networks across an agricultural mosaic landscape in Canterbury, New Zealand. The most densely connected networks were found in land uses that were under the most intensive agricultural management, or under naturally regenerating vegetation. The microbial C-cycling gene networks from both land uses presented high network connectivity, low modularity, and a low proportion of negative gene interactions. In contrast, microbial C-cycling genes from native forests, which had the most stable and undisturbed plant cover, had the lowest network connectivity, highest modularity, and a greater proportion of negative gene interactions. Although the differences in total soil C content between land uses were small, the large effects of land use on the network structure of microbial C-cycling genes may have important implications for long-term microbial soil C cycling. Furthermore, this research highlights the value of using microbial network analysis to study the metabolic gene interactions shaping the functional structure of soil microbial communities in a manner not typically captured by more traditional forms of microbial diversity analysis.}, }
@article {pmid39777152, year = {2024}, author = {Liao, H and Wang, X and Wang, X and Zhang, M and Zhang, Y and Huang, S and Wang, H and Jin, H and Wang, J and Li, X and Yan, J and Schubert, T and Löffler, FE and Yang, Y}, title = {Organohalide respiration: retrospective and perspective through bibliometrics.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1490849}, pmid = {39777152}, issn = {1664-302X}, abstract = {Organohalide-respiring bacteria (OHRB) play a pivotal role in the transformation of organohalogens in diverse environments. This bibliometric analysis provides a timely overview of OHRB research trends and identifies knowledge gaps. Publication numbers have steadily increased since the process was discovered in 1982, with fluctuations in total citations and average citations per publication. The past decade witnessed a peak in publications, underscoring heightened research activity and extensive collaboration. Thematic analysis identified two primary research foci: mechanistic exploration of OHRB and their interplay with environmental factors. Future research should prioritize elucidating the roles OHRB's play in biogeochemical cycling, utilizing synthetic biology tools for enhanced biotransformation, deciphering OHRB's ecological interactions, unraveling their evolutionary pathways, and investigating dehalogenation capabilities in other microorganisms, including archaea. These research directions promise to advance our understanding of microbially-driven organohalide transformations, microbial ecology, and genetic engineering potential, ultimately informing natural organohalide cycling and environmental management strategies.}, }
@article {pmid39775407, year = {2025}, author = {Sun, X and Armstrong, M and Moradi, A and Bhattacharya, R and Antão-Geraldes, AM and Munthali, E and Grossart, HP and Matsuzaki, SS and Kangur, K and Dunalska, JA and Stockwell, JD and Borre, L}, title = {Impacts of climate-induced drought on lake and reservoir biodiversity and ecosystem services: A review.}, journal = {Ambio}, volume = {54}, number = {3}, pages = {488-504}, pmid = {39775407}, issn = {1654-7209}, support = {RGPIN-2019-04315//Natural Sciences and Engineering Research Council of Canada/ ; 1638679//U.S. National Science Foundation (NSF) Macrosystems Biology Program/ ; 722518//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; LA/P/0007/2020//SusTEC/ ; PRG 1266//Estonian Research Council/ ; JPMEERF20232002//Environmental Restoration and Conservation Agency/ ; 1702991//National Science Foundation/ ; UIDB/00690/2020//CIMO/ ; UIDP/00690/2020//CIMO/ ; PIDDAC//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {*Droughts ; *Biodiversity ; *Lakes ; *Ecosystem ; *Climate Change ; Conservation of Natural Resources ; }, abstract = {Intensifying extreme droughts are altering lentic ecosystems and disrupting services provisioning. Unfortunately, drought research often lacks a holistic and intersectoral consideration of drought impacts, which can limit relevance of the insights for adaptive management. This literature review evaluated the current state of lake and reservoir extreme drought research in relation to biodiversity and three ecosystem services. The study findings demonstrated that few articles linked or discussed drought implications with one or more ecosystem services, instead focusing primarily on biodiversity. Drought effects on biodiversity varied among species and taxonomic groups. In the limited literature that included ecosystem service provisioning, droughts had a general negative effect. Drinking water supply can decrease and become more costly. Decreasing water flow and volume can reduce hydropower generation. Degraded water quality can also impact recreation. Future intersectoral collaborations and research on intensifying droughts should support adaptive management efforts in mitigating drought impacts.}, }
@article {pmid39774713, year = {2025}, author = {Dobrzyński, J and Kulkova, I and Jakubowska, Z and Wróbel, B}, title = {Non-native PGPB Consortium Altered the Rhizobacterial Community and Slightly Stimulated the Growth of Winter Oilseed Rape (Brassica napus L.) Under Field Conditions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {168}, pmid = {39774713}, issn = {1432-184X}, support = {DDD.6509.00267.2022.15.//The research was funded by the European Agricultural Fund under the Rural Development Programme for 2014-2020/ ; DDD.6509.00267.2022.15.//The research was funded by the European Agricultural Fund under the Rural Development Programme for 2014-2020/ ; DDD.6509.00267.2022.15.//The research was funded by the European Agricultural Fund under the Rural Development Programme for 2014-2020/ ; DDD.6509.00267.2022.15.//The research was funded by the European Agricultural Fund under the Rural Development Programme for 2014-2020/ ; }, mesh = {*Brassica napus/microbiology/growth &amp; development ; *Soil Microbiology ; Pseudomonas/growth &amp; development/metabolism ; Plant Roots/microbiology/growth &amp; development ; Phosphorus/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/growth &amp; development ; Nitrogen/metabolism ; Rhizosphere ; Microbial Consortia ; Indoleacetic Acids/metabolism ; Microbiota ; Azotobacter/growth &amp; development/metabolism ; }, abstract = {Plant growth-promoting bacteria (PGPB) are among the most promising alternatives to mineral fertilizers. However, little is known about the effects of applied bacteria on the native microbiota, including the rhizobacterial community, which plays a crucial role in bacteria-plant interactions. Therefore, this study is aimed at assessing the effects of PGPB not only on plants but also, importantly, on the native rhizobacterial community of winter oilseed rape. The bacterial consortium, consisting of Pseudomonas sp. KR227 and Azotobacter PBC1 (P2A), slightly promoted plant growth, increasing the root weight by 21.95% and seed yield by 18.94%. This likely results from its ability to produce indole-3-acetic acid (IAA), solubilize phosphorus, and fix nitrogen, as indicated by a 35.76% increase in N-NH4 and a 35.05% increase in available phosphorus (AP). The introduced PGPB altered the rhizobacterial community of rapeseed, increasing the relative abundance of the phylum Proteobacteria and the genus Pseudomonas while decreasing the relative abundance of phylum Verrucomicrobiota (3 weeks after inoculation). Moreover, Proteobacteria were positively correlated with AP, while Verrucomicrobiota were correlated with N-NH4. At the genus level, Flavobacterium and Pseudomonas were positively correlated with AP, whereas Candidatus Udaeobacter showed a positive correlation with N-NH4 and a negative correlation with pH. Importantly, the P2A consortium did not significantly affect the diversity of native rapeseed rhizobacteria. These findings suggest that the tested P2A consortium has potential as a biostimulant in rapeseed cultivation.}, }
@article {pmid39774673, year = {2025}, author = {Chen, SC and Chen, S and Musat, N and Kümmel, S and Ji, J and Lund, MB and Gilbert, A and Lechtenfeld, OJ and Richnow, HH and Musat, F}, title = {Author Correction: Back flux during anaerobic oxidation of butane support archaea-mediated alkanogenesis.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {453}, doi = {10.1038/s41467-024-55458-6}, pmid = {39774673}, issn = {2041-1723}, }
@article {pmid39772705, year = {2025}, author = {Zhou, J and Liu, Z and Wang, S and Li, J and Zhang, L and Liao, Z}, title = {A novel framework unveiling the importance of heterogeneous selection and drift on the community structure of symbiotic microbial indicator taxa across altitudinal gradients in amphibians.}, journal = {Microbiology spectrum}, volume = {13}, number = {2}, pages = {e0419223}, pmid = {39772705}, issn = {2165-0497}, support = {20190ZKK0303//The Second Tibetan Plateau Scientific Expedition and Research Program/ ; 32201424//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Symbiosis ; *Microbiota/genetics ; *Amphibians/microbiology ; Altitude ; China ; *Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {UNLABELLED: Existing analytical frameworks for community assembly have a noticeable knowledge gap, lacking a comprehensive assessment of the relative contributions of individual or grouped microbial distinct sampling units (DSUs) and distinct taxonomic units (DTUs) to each mechanism. Here, we propose a comprehensive framework for identifying DTUs/DSUs that remarkably contribute to the various mechanisms sustaining microbial community structure. Amphibian symbiotic microbes along an altitudinal gradient from Sichuan Province, China, were employed to examine the proposed statistical framework. In different altitude groups, we found that heterogeneous selection governed the community structure of symbiotic microbes across DSUs, while stochastic processes tended to increase with altitude. For DTUs at phylum and family levels, drift emerged as the dominant mechanism driving the community structure in the most symbiotic microbial taxa, while heterogeneous selection governs the most dominant or indicator taxa. Notably, the relative contribution of heterogeneous selection was significantly positively correlated with the relative abundance and niche breadth of taxa, and negatively correlated with drift. We also detected that community assembly processes remarkably regulate the structure of symbiotic microbial communities and their correlation with environmental variables. Altogether, our modeling framework is a robust and valuable tool that further enlarges our insight into microbiota community assembly.<br><br>IMPORTANCE: Distinguishing the drivers regulating microbial community assembly is essential in microbial ecology. We propose a novel modeling framework to partition the relative contributions of each individual or group of microbial DSUs and DTUs into different underpinning mechanisms. An empirical study on amphibian symbiotic microbes notably enlarges insight into community assembly patterns in the herpetological symbiotic ecosystem and demonstrates that the proposed statistical framework is an informative and sturdy tool to quantify microbial assembly processes at both levels of DSUs and DTUs. More importantly, our proposed modeling framework can provide in-depth insights into microbiota community assembly within the intricate tripartite host-environment-microbe relationship.}, }
@article {pmid39772204, year = {2024}, author = {Obong'o, BO and Ogutu, FO and Hurley, SK and Okiko, GM and Mahony, J}, title = {Exploring the Microbial Ecology of Water in Sub-Saharan Africa and the Potential of Bacteriophages in Water Quality Monitoring and Treatment to Improve Its Safety.}, journal = {Viruses}, volume = {16}, number = {12}, pages = {}, pmid = {39772204}, issn = {1999-4915}, mesh = {Africa South of the Sahara ; *Bacteriophages/physiology ; *Water Quality ; *Water Microbiology ; *Water Purification/methods ; Bacteria/virology ; Humans ; Food Safety/methods ; Biodegradation, Environmental ; }, abstract = {Access to safe water and food is a critical issue in sub-Saharan Africa, where microbial contamination poses significant health risks. Conventional water treatment and food preservation methods have limitations in addressing water safety, particularly for antibiotic-resistant bacteria and other pathogenic microorganisms. This review explores the potential application of bacteriophages as an innovative solution for water treatment and food safety in the region. Bacteriophages specifically infect bacteria and offer a targeted approach to reducing bacterial load, including multidrug-resistant strains, without the drawbacks of chemical disinfectants. This review also highlights the advantages of phage bioremediation, including its specificity, adaptability, and minimal environmental impact. It also discusses various case studies demonstrating its efficacy in different water systems. Additionally, we underscore the need for further research and the development of region-specific phage applications to improve water quality and public health outcomes in sub-Saharan Africa. By integrating bacteriophage strategies into water treatment and food production, the region can address critical microbial threats, mitigate the spread of antimicrobial resistance, and advance global efforts toward ensuring safe water for all.}, }
@article {pmid39771075, year = {2024}, author = {Tapia, Y and Salazar, O and Seguel, O and Suazo-Hernández, J and Urdiales-Flores, D and Aponte, H and Urdiales, C}, title = {Optimizing Heavy Metal Uptake in Carpobrotus aequilaterus Through Electrokinetic Treatment: A Comprehensive Study on Phytoremediation from Mine Tailings.}, journal = {Toxics}, volume = {12}, number = {12}, pages = {}, pmid = {39771075}, issn = {2305-6304}, support = {3220201//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; }, abstract = {Copper mining drives economic growth, with the global demand expected to reach 120 million metric tons annually by 2050. However, mining produces tailings containing heavy metals (HMs), which poses environmental risks. This study investigated the efficacy of phytoremediation (Phy) combined with electrokinetic treatment (EKT) to increase metal uptake in Carpobrotus aequilaterus grown in tailings from the Metropolitan Region of Chile. The plants were exposed to varying voltages and treatment durations. In the control (no EKT), the root metal contents were Fe (1008.41 mg/kg) > Cu (176.38 mg/kg) > Mn (103.73 mg/kg) > Zn (30.26 mg/kg), whereas in the shoots, the order was Mn (48.69 mg/kg) > Cu (21.14 mg/kg) > Zn (17.67 mg/kg) > Fe (27.32 mg/kg). The optimal EKT (15 V for 8 h) significantly increased metal uptake, with roots accumulating Fe (5997.24 mg kg[-1]) > Mn (672 mg kg[-1]) > Cu (547.68 mg kg[-1]) > Zn (90.99 mg kg[-1]), whereas shoots contained Fe (1717.95 mg kg[-1]) > Mn (930 mg kg[-1]) > Cu (219.47 mg kg[-1]) > Zn (58.48 mg kg[-1]). Although EKT enhanced plant growth and biomass, higher voltages stressed the plants. Longer treatments were more effective, suggesting that EK-Phy is a promising method for remediating metal-contaminated tailings.}, }
@article {pmid39770685, year = {2024}, author = {Han, Y and He, J and Li, M and Peng, Y and Jiang, H and Zhao, J and Li, Y and Deng, F}, title = {Unlocking the Potential of Metagenomics with the PacBio High-Fidelity Sequencing Technology.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770685}, issn = {2076-2607}, support = {SQ2023YFE0102739//National Key Research and Development Program of China/ ; 2022A1515110819//Youth project of Guangdong Foshan joint fund of the Guangdong Natural Science Foundation/ ; 32170430//National Natural Science Foundation of China/ ; }, abstract = {Traditional methods for studying microbial communities have been limited due to difficulties in culturing and sequencing all microbial species. Recent advances in third-generation sequencing technologies, particularly PacBio's high-fidelity (HiFi) sequencing, have significantly advanced metagenomics by providing accurate long-read sequences. This review explores the role of HiFi sequencing in overcoming the limitations of previous sequencing methods, including high error rates and fragmented assemblies. We discuss the benefits and applications of HiFi sequencing across various environments, such as the human gut and soil, which provides broader context for further exploration. Key studies are discussed to highlight HiFi sequencing's ability to recover complete and coherent microbial genomes from complex microbiomes, showcasing its superior accuracy and continuity compared to other sequencing technologies. Additionally, we explore the potential applications of HiFi sequencing in quantitative microbial analysis, as well as the detection of single nucleotide variations (SNVs) and structural variations (SVs). PacBio HiFi sequencing is establishing a new benchmark in metagenomics, with the potential to significantly enhance our understanding of microbial ecology and drive forward advancements in both environmental and clinical applications.}, }
@article {pmid39770645, year = {2024}, author = {Neviani, E}, title = {The Natural Whey Starter Used in the Production of Grana Padano and Parmigiano Reggiano PDO Cheeses: A Complex Microbial Community.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770645}, issn = {2076-2607}, abstract = {Natural whey starter (NWS) is an undefined complex culture used in the production of Grana Padano and Parmigiano Reggiano PDO cheeses. The aim of this review is to discuss, in light of the latest research results, the role of NWS as a primary player in the cheese-making process, considering the microbial community scenario. NWS is traditionally produced by fermenting part of the whey collected at the end of a previous cheese-making process. The method used to produce NWS, based on the back-slopping principle, favors the selection of a microbiota composed mainly of thermophilic lactic acid bacteria. This method of preparation induces the survival of several different species and biotypes. The presence of such a mixture of strains facilitates the development of a natural starter characterized by a remarkable ability to adapt to non-standardized cheese-making parameters. NWS is a microbial community whose activity is not simply the result of the sum of the activities of individual microorganisms, but rather the activity of the community as a whole, in which each individual bacterial cell responds to the presence of the others. According to this traditional protocol, the NWS becomes the 'microbiological bond' between cheeses over time.}, }
@article {pmid39770585, year = {2024}, author = {Heczko, PB and Giemza, M and Ponikiewska, W and Strus, M}, title = {Importance of Lactobacilli for Human Health.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770585}, issn = {2076-2607}, support = {RPMP.01.02.01-12-0413/17.//The National Centre for Research and Development/ ; }, abstract = {As an extraordinarily diverse group of bacteria, lactobacilli are now classified into several genera, many of which still include "Lactobacillus" in their names. Despite their names, this group of lactic acid bacteria comprises microorganisms that are crucial for human health, especially during the early development of the human microbiota and immune system. The interactions between lactobacilli and components of the mucosal immunity lead to its shaping and development, which is possibly considered a prime mover in the advancement of the human immune system. Although much of the evidence backing the pivotal role of lactobacilli in maintaining human health comes from studies on probiotics aiming to elucidate the mechanisms of their functional activities and studies on mucosal immunity in germ-free mice, it is justifiable to extend observations on the properties of the individual probiotic Lactobacillus that are related to health benefits onto other strains sharing common characteristics of the species. In this review, we will discuss the acquisition, presence, and functions of lactobacilli in different human microbiota throughout their whole life, including those arising in the amnion and their interactions with mucosal and immune cells. Examples of immune system modulation by probiotic lactobacilli include their colonic competition for available nutrients, interference with colonization sites, competition for binding sites on gut epithelial cells, bacteriocin production, reduction of colonic pH, and nonspecific stimulation of the immune system.}, }
@article {pmid39770454, year = {2024}, author = {Atazhanova, GA and Levaya, YK and Badekova, KZ and Ishmuratova, MY and Smagulov, MK and Ospanova, ZO and Smagulova, EM}, title = {Inhibition of the Biofilm Formation of Plant Streptococcus mutans.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {17}, number = {12}, pages = {}, pmid = {39770454}, issn = {1424-8247}, support = {&#x410;&#x420;23488250//MINISTRY OF SCIENCE AND HIGHER EDUCATION OF REPUBLIC OF KAZAKHSTAN/ ; }, abstract = {This review is devoted to a systematic analysis of studies aimed at investigating plant extracts, essential oils and phytochemical compounds capable of inhibiting Streptococcus mutans biofilm formation. This paper investigates the effect of extracts, essential oils and individual plant compounds on inhibiting the biofilm formation of Streptococcus mutans, one of the major pathogens responsible for the development of dental caries. Using cultural microbiology and molecular biology techniques, the authors describe the mechanisms by which plant samples reduce Streptococcus mutans adhesion and growth. The results show that several plant components have antibacterial properties, contributing to the reduction of Streptococcus mutans colony numbers and inhibiting the synthesis of extract-exopolysaccharide matrices required for biofilm formation. This work highlights the potential of botanicals in inhibiting Streptococcus mutans biofilm formation, which can be applied as natural antimicrobial agents in the prevention and treatment of dental diseases. Views on the use of these plant extracts and their components in dental preparations such as toothpastes, rinses and gels aimed at preventing dental caries are evaluated. The review shows the relevance of the research to optimizing the use of plant extracts, essential oils, individual compounds and their active actions in the control of Streptococcus mutans biofilms.}, }
@article {pmid39769364, year = {2024}, author = {Grzyb, T and Szulc, J}, title = {Deciphering Molecular Mechanisms and Diversity of Plant Holobiont Bacteria: Microhabitats, Community Ecology, and Nutrient Acquisition.}, journal = {International journal of molecular sciences}, volume = {25}, number = {24}, pages = {}, pmid = {39769364}, issn = {1422-0067}, mesh = {*Microbiota ; *Bacteria/genetics/classification/metabolism ; *Plants/microbiology ; Biodiversity ; Ecosystem ; Phosphorus/metabolism ; Nitrogen/metabolism ; Symbiosis ; Nutrients/metabolism ; }, abstract = {While gaining increasing attention, plant-microbiome-environment interactions remain insufficiently understood, with many aspects still underexplored. This article explores bacterial biodiversity across plant compartments, including underexplored niches such as seeds and flowers. Furthermore, this study provides a systematic dataset on the taxonomic structure of the anthosphere microbiome, one of the most underexplored plant niches. This review examines ecological processes driving microbial community assembly and interactions, along with the discussion on mechanisms and diversity aspects of processes concerning the acquisition of nitrogen, phosphorus, potassium, and iron-elements essential in both molecular and ecological contexts. These insights are crucial for advancing molecular biology, microbial ecology, environmental studies, biogeochemistry, and applied studies. Moreover, the authors present the compilation of molecular markers for discussed processes, which will find application in (phylo)genetics, various (meta)omic approaches, strain screening, and monitoring. Such a review can be a valuable source of information for specialists in the fields concerned and for applied researchers, contributing to developments in sustainable agriculture, environmental protection, and conservation biology.}, }
@article {pmid39768235, year = {2024}, author = {Riekeles, M and Santos, B and Youssef, SA and Schulze-Makuch, D}, title = {Viability and Motility of Escherichia coli Under Elevated Martian Salt Stresses.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {12}, pages = {}, pmid = {39768235}, issn = {2075-1729}, support = {Scholarship for Max Riekeles//Friedrich-Ebert-Stiftung e.V./ ; }, abstract = {This study investigates the effects of three Martian-relevant salts-sodium chlorate, sodium perchlorate, and sodium chloride-on the viability and motility of Escherichia coli, a model organism for understanding microbial responses to environmental stress. These salts are abundant on Mars and play a crucial role in forming brines, one of the few sources of stable liquid water on the planet. We analyze the survivability under different salt concentrations using colony plating. Additionally, we perform a semi-automated motility analysis, analyzing microbial speeds and motility patterns. Our results show that sodium perchlorate is the most toxic, followed by sodium chlorate, with sodium chloride being the least harmful. Both survivability and motility are affected by salt concentration and exposure time. Notably, we observe a short-lived increase in motility at certain concentrations, particularly under sodium chlorate and sodium perchlorate stress, despite rapid declines in cell viability, suggesting a stress response mechanism. Given that motility might enhance an organism's ability to navigate harsh and variable environments, it holds promise as a key biosignature in the search for life on Mars.}, }
@article {pmid39764393, year = {2024}, author = {Russo, CJ and Husain, K and Murugan, A}, title = {Soft Modes as a Predictive Framework for Low Dimensional Biological Systems across Scales.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {39764393}, issn = {2331-8422}, support = {R35 GM151211/GM/NIGMS NIH HHS/United States ; }, abstract = {All biological systems are subject to perturbations: due to thermal fluctuations, external environments, or mutations. Yet, while biological systems are composed of thousands of interacting components, recent high-throughput experiments show that their response to perturbations is surprisingly low-dimensional: confined to only a few stereotyped changes out of the many possible. Here, we explore a unifying dynamical systems framework - soft modes - to explain and analyze low-dimensionality in biology, from molecules to eco-systems. We argue that this one framework of soft modes makes non-trivial predictions that generalize classic ideas from developmental biology to disparate systems, namely: phenocopying, dual buffering, and global epistasis. While some of these predictions have been borne out in experiments, we discuss how soft modes allow for a surprisingly far-reaching and unifying framework in which to analyze data from protein biophysics to microbial ecology.}, }
@article {pmid39762141, year = {2025}, author = {Nguyen, PN and Rehan, SM}, title = {Supporting wild bee development with a bacterial symbiont.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxae317}, pmid = {39762141}, issn = {1365-2672}, abstract = {AIMS: Wild bees foster diverse microbiota that may determine survival success of developing larvae. Here, we compare survivorship and microbial communities of Ceratina calcarata small carpenter bees reared from eggs across three treatments: maternally collected control provisions with diverse microbiota, sterile provisions, and probiotic provisions supplemented with a beneficial symbiont, Apilactobacillus kunkeei.<br><br>METHODS AND RESULTS: Survival probability and adult masses differed across treatments, with the probiotic treatment resulting in highest survivorship and masses. By comparing the bacterial (16S rRNA), fungal (ITS), and plant (rbcL) communities of adults reared across treatments, we characterized distinct microbial communities across each that suggest the microbiome may be sensitive to microbial succession and competition.<br><br>CONCLUSIONS: We describe positive implications for the usage of probiotics on wild bees. Furthermore, the sensitivity of bee microbiota's relationships to their host, floral resources, and the environment suggests that holistic approaches best encapsulate the complex network of interactions between bees and their microbes.}, }
@article {pmid39760916, year = {2025}, author = {García-Bodelón, &#xc1; and Baković, N and Cano, E and Useros, F and Lara, E and González-Miguéns, R}, title = {Predators in the Dark: Metabarcoding Reveals Arcellinida Communities Associated with Bat Guano, Endemic to Dinaric Karst in Croatia.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {166}, pmid = {39760916}, issn = {1432-184X}, support = {PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-128499NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; Garant&#xed;a Juvenil CM 2021//Comunidad de Madrid (Spain)/ ; Garant&#xed;a Juvenil CM 2021//Comunidad de Madrid (Spain)/ ; Class: UP/I-612-07/21-48/170, Ref. No.: 517-10-1-1-21-3, 16.07.2021//Croatian Ministry of Economy and Sustainable Development/ ; }, mesh = {Croatia ; Animals ; *Chiroptera/microbiology ; *Caves/microbiology ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Ecosystem ; Chironomidae/genetics ; Feces/microbiology ; Electron Transport Complex IV/genetics/analysis ; Geologic Sediments/microbiology ; Phylogeny ; }, abstract = {Karst caves, formed from the dissolution of soluble rocks, are characterized by the absence of photosynthetic activity and low levels of organic matter. Organisms evolve under these particular conditions, which causes high levels of endemic biodiversity in both macroorganism and microbes. Recent research has highlighted the presence of testate amoebae (Arcellinida) group in cave environments. This study investigates the diversity of Arcellinida in Dinaric karstic caves in Croatia, a global diversity hotspot, focusing on the influence of bat guano on community structure. Sediment samples were collected from two independent hydrosystems, and a metabarcoding approach was used to assess Arcellinida diversity at specific and intraspecific levels, using Arcellinid-specific primers to amplify the mitochondrial cytochrome oxidase subunit I (COI) region. Results reveal a significant impact of guano on both specific and intraspecific diversity of Arcellinida. Communities in guano-rich sites displayed higher diversity, abundance, and the presence of unique OTUs and genetic variants not observed in other habitats, highlighting the crucial role of bats as ecosystem engineers. In contrast, sites without guano hosted communities with low abundance and reduced biodiversity. These differences suggest the existence of guano-associated Arcellinida communities. This study provides new insights into the biodiversity of subterranean ecosystems and the ecological roles of Arcellinida in karstic environments.}, }
@article {pmid39760871, year = {2025}, author = {Mwaheb, MA and El-Aziz, BMA and Abd-Elhalim, BT and El-Kassim, NA and Radwan, TEE}, title = {Study of Different Cultivated Plants Rhizosphere Soil Fungi-Mediated Pectinase: Insights into Production, Optimization, Purification, Biocompatibility, and Application.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {165}, pmid = {39760871}, issn = {1432-184X}, mesh = {*Polygalacturonase/metabolism ; *Soil Microbiology ; *Rhizosphere ; Fungi/enzymology/metabolism/isolation &amp; purification/classification/genetics ; Aspergillus/metabolism/enzymology/isolation &amp; purification ; Egypt ; Fungal Proteins/metabolism ; }, abstract = {Microorganisms are preferred as an enzyme source due to their short lifespan, high production rate, affordability, and absence of harmful chemicals in enzymes generated from plant and animal sources. Fungi communities are biological factories for many bioactive compounds such as the important industrial enzyme pectinase. The current study dealt with production, optimization, purification, biocompatibility, and application of fungal pectinase obtained from five plant rhizospheres (banana, jarawa, lemon, tomato, and wheat) at Fayoum Governorate, Egypt. The highest pectinase degrading index (PDI) was scored for FB5, FJ2, and FW1 isolates. Pectinase production was also examined quantitively and the highest output of 1603.67, 1311.22, and 1264.83 U/ml was gained by FB5, FJ1, and FW1 fungal isolates, respectively. The most active pectinase-producing fungi were identified as Aspergillus niveus strain AUMC1624, A. niger strain AUMC16245, and A. brasiliensis strain AUMC16244, respectively. For pectinase production optimization, one factor at a time (OFAT) protocol was applied and revealed that A. niger, A. niveus, and A. brasiliensis reached maximum pectinase levels at 1% pectin after 5, 7, and 7 days, at 40, 45, and 45 °C, respectively. Obtained pectinases were partially purified using ammonium sulfate precipitation (ASP) and organic solvent precipitation (OSP) methods. The highest activity using the ASP method scored at 40-60% saturation with A. niger. The thermostability characterization of A. niger pectinase was reached with relative activities of 61.7, 69.0, 99.9, 91.3, and 90.6% at temperatures ranging between 30 and 70 °C. pH optimized at pH 5-7. The enzyme's molecular weight was approximately 30 kDa. The GC-mass analysis of pectinase end products included acetic acid ethyl ester, hexadecane carbonsaure methylase, and hexadecenoic acid. The biocompatibility was examined using a human skin cell line (HFb-4) for the first time, with a minimal half concentration (IC50) of 151.86 ± 0.76 U/ml. The biocompatible pectinase was applied as a clothes bioscouring agent with different concentrations of 1893.52 U/ml achieving the highest bioscouring with 20.0%.}, }
@article {pmid39760805, year = {2025}, author = {Willemsen, A and Manzano-Marín, A and Horn, M}, title = {Novel High-Quality Amoeba Genomes Reveal Widespread Codon Usage Mismatch Between Giant Viruses and Their Hosts.}, journal = {Genome biology and evolution}, volume = {17}, number = {1}, pages = {}, pmid = {39760805}, issn = {1759-6653}, support = {//European Union's Horizon 2020 research and innovation programme/ ; 891572//Marie Sklodowska-Curie/ ; 101039843//European Union/ ; //European Research Council Executive Agency/ ; //Austrian Science Fund/ ; }, mesh = {*Giant Viruses/genetics ; *Codon Usage ; *Amoeba/virology/genetics ; Genome, Protozoan ; Host Specificity ; Phylogeny ; Acanthamoeba/virology/genetics ; }, abstract = {The need for high-quality protist genomes has prevented in-depth computational and experimental studies of giant virus-host interactions. In addition, our current knowledge of host range is highly biased due to the few hosts used to isolate novel giant viruses. This study presents 6 high-quality amoeba genomes from known and potential giant virus hosts belonging to 2 distinct eukaryotic clades: Amoebozoa and Discoba. We employ their genomic data to investigate the predictability of giant virus host range. Using a combination of long- and short-read sequencing, we obtained highly contiguous and complete genomes of Acanthamoeba castellanii, Acanthamoeba griffini, Acanthamoeba terricola, Naegleria clarki, Vermamoeba vermiformis, and Willaertia magna, contributing to the collection of sequences for the eukaryotic tree of life. We found that the 6 amoebae have distinct codon usage patterns and that, contrary to other virus groups, giant viruses often have different and even opposite codon usage with their known hosts. Conversely, giant viruses with matching codon usage are frequently not known to infect or replicate in these hosts. Interestingly, analyses of integrated viral sequences in the amoeba host genomes reveal potential novel virus-host associations. Matching of codon usage preferences is often used to predict virus-host pairs. However, with the broad-scale analyses performed in this study, we demonstrate that codon usage alone appears to be a poor predictor of host range for giant viruses infecting amoeba. We discuss the potential strategies that giant viruses employ to ensure high viral fitness in nonmatching hosts. Moreover, this study emphasizes the need for more high-quality protist genomes. Finally, the amoeba genomes presented in this study set the stage for future experimental studies to better understand how giant viruses interact with different host species.}, }
@article {pmid39753761, year = {2025}, author = {Peng, Z and van der Heijden, MGA and Liu, Y and Li, X and Pan, H and An, Y and Gao, H and Qi, J and Gao, J and Qian, X and Tiedje, JM and Wei, G and Jiao, S}, title = {Agricultural subsoil microbiomes and functions exhibit lower resistance to global change than topsoils in Chinese agroecosystems.}, journal = {Nature food}, volume = {6}, number = {4}, pages = {375-388}, pmid = {39753761}, issn = {2662-1355}, mesh = {Agriculture ; Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; China ; *Climate Change ; Crops, Agricultural/growth &amp; development ; *Ecosystem ; *Microbiota ; *Soil/chemistry ; *Soil Microbiology ; }, abstract = {Soils play a critical role in supporting agricultural production. Subsoils, below 20 cm, underpin fundamental agroecosystem sustainability traits including soil carbon storage, climate regulation and water provision. However, little is known about the ecological stability of subsoils in response to global change. Here we conducted a microcosm experiment to determine whether subsoils were more sensitive to global changes across 40 agricultural ecosystems in China, in combination with a multiple global change factor experiment and an in situ field study. We found that subsoils exhibited greater fluctuation in species diversity, community composition, and complexity of microbial networks and ecosystem functions than topsoils, indicating lower resistance to global changes. Soil biodiversity was a major driver of ecosystem resistance, surpassing climate and soil parameters. A reciprocal microorganism transplant experiment showed that microorganisms isolated from the topsoil are more resistant to global changes than those from subsoil. Our study emphasizes that subsoil ecosystems are sensitive to global changes, underscoring the importance of including subsoils in predictions of agricultural sustainability and crop productivity under changing environmental conditions.}, }
@article {pmid39752189, year = {2025}, author = {Bloomfield, SJ and Hildebrand, F and Zomer, AL and Palau, R and Mather, AE}, title = {Ecological insights into the microbiology of food using metagenomics and its potential surveillance applications.}, journal = {Microbial genomics}, volume = {11}, number = {1}, pages = {}, pmid = {39752189}, issn = {2057-5858}, mesh = {*Metagenomics/methods ; *Food Microbiology ; Metagenome ; Bacteria/genetics/classification/isolation &amp; purification ; Salmonella/genetics/isolation &amp; purification/classification ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics/isolation &amp; purification/classification ; }, abstract = {A diverse array of micro-organisms can be found on food, including those that are pathogenic or resistant to antimicrobial drugs. Metagenomics involves extracting and sequencing the DNA of all micro-organisms on a sample, and here, we used a combination of culture and culture-independent approaches to investigate the microbial ecology of food to assess the potential application of metagenomics for the microbial surveillance of food. We cultured common foodborne pathogens and other organisms including Escherichia coli, Klebsiella/Raoultella spp., Salmonella spp. and Vibrio spp. from five different food commodities and compared their genomes to the microbial communities obtained by metagenomic sequencing following host (food) DNA depletion. The microbial populations of retail food were found to be predominated by psychrotrophic bacteria, driven by the cool temperatures in which the food products are stored. Pathogens accounted for a small percentage of the food metagenome compared to the psychrotrophic bacteria, and cultured pathogens were inconsistently identified in the metagenome data. The microbial composition of food varied amongst different commodities, and metagenomics was able to classify the taxonomic origin of 59% of antimicrobial resistance genes (ARGs) found on food to the genus level, but it was unclear what percentage of ARGs were associated with mobile genetic elements and thus transferable to other bacteria. Metagenomics may be used to survey the ARG burden, composition and carriage on foods to which consumers are exposed. However, food metagenomics, even after depleting host DNA, inconsistently identifies pathogens without enrichment or further bait capture.}, }
@article {pmid39745433, year = {2025}, author = {Grüterich, L and Woodhouse, JN and Mueller, P and Tiemann, A and Ruscheweyh, H-J and Sunagawa, S and Grossart, H-P and Streit, WR}, title = {Assessing environmental gradients in relation to dark CO2 fixation in estuarine wetland microbiomes.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0217724}, pmid = {39745433}, issn = {1098-5336}, support = {407270017//Deutsche Forschungsgemeinschaft (DFG)/ ; 502681570//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {*Wetlands ; *Microbiota ; *Carbon Dioxide/metabolism ; *Bacteria/metabolism/genetics/classification ; *Carbon Cycle ; Estuaries ; Soil Microbiology ; }, abstract = {UNLABELLED: The rising atmospheric concentration of CO2 is a major concern to society due to its global warming potential. In soils, CO2-fixing microorganisms are preventing some of the CO2 from entering the atmosphere. Yet, the controls of dark CO2 fixation are rarely studied in situ. Here, we examined the gene and transcript abundance of key genes involved in microbial CO2 fixation along major environmental gradients within estuarine wetlands. A combined multi-omics approach incorporating metabarcoding, deep metagenomic, and metatranscriptomic analyses confirmed that wetland microbiota harbor four out of seven known CO2 fixation pathways, namely, the Calvin cycle, reverse tricarboxylic acid cycle, Wood-Ljungdahl pathway, and reverse glycine pathway. These pathways are transcribed at high frequencies along several environmental gradients, albeit at different levels depending on the environmental niche. Notably, the transcription of the key genes for the reverse tricarboxylic acid cycle was associated with high nitrate concentration, while the transcription of key genes for the Wood-Ljungdahl pathway was favored by reducing, O2-poor conditions. The transcript abundance of the Calvin cycle was favored by niches high in organic matter. Taxonomic assignment of transcripts implied that dark CO2 fixation was mainly linked to a few bacterial phyla, namely, Desulfobacterota, Methylomirabilota, Nitrospirota, Chloroflexota, and Pseudomonadota.<br><br>IMPORTANCE: The increasing concentration of atmospheric CO2 has been identified as the primary driver of climate change and poses a major threat to human society. This work explores the mostly overlooked potential of light-independent CO2 fixation by soil microbes (a.k.a. dark CO2 fixation) in climate change mitigation efforts. Applying a combination of molecular microbial tools, our research provides new insights into the ecological niches where CO2-fixing pathways are most active. By identifying how environmental factors, like oxygen, salinity and organic matter availability, influence these pathways in an estuarine wetland environment, potential strategies for enhancing natural carbon sinks can be developed. The importance of our research is in advancing the understanding of microbial CO2 fixation and its potential role in the global climate system.}, }
@article {pmid39745058, year = {2025}, author = {Doyle, RT and Grieves, LA and Gerstein, AC}, title = {Microbial ecology and evolution.}, journal = {Canadian journal of microbiology}, volume = {71}, number = {}, pages = {1-3}, doi = {10.1139/cjm-2024-0192}, pmid = {39745058}, issn = {1480-3275}, }
@article {pmid39744675, year = {2024}, author = {Mathers, AJ and Li, TJX and He, Q and Narendra, S and Stoesser, N and Eyre, DW and Walker, AS and Barry, KE and Castañeda-Barba, S and Huang, FW and Parikh, H and Kotay, S and Crook, DW and Reidys, C}, title = {Developing a framework for tracking antimicrobial resistance gene movement in a persistent environmental reservoir.}, journal = {npj antimicrobials and resistance}, volume = {2}, number = {1}, pages = {50}, pmid = {39744675}, issn = {2731-8745}, abstract = {Mobile genetic elements are key to the global emergence of antibiotic resistance. We successfully reconstructed the complete bacterial genome and plasmid assemblies of isolates sharing the same bla KPC carbapenemase gene to understand evolution over time in six confined hospital drains over five years. From 82 isolates we identified 14 unique strains from 10 species with 113 bla KPC-carrying plasmids across 16 distinct replicon types. To assess dynamic gene movement, we introduced the 'Composite-Sample Complex', a novel mathematical approach to using probability to capture the directional movement of antimicrobial resistance genes. The Composite Sample Complex accounts for the co-occurrence of both plasmids and chromosomes within an isolate, and highlights likely gene donors and recipients. From the validated model, we demonstrate frequent transposition events of bla KPC from plasmids to other plasmids, as well as integration into the bacterial chromosome within specific drains. We present a novel approach to estimate the directional movement of antimicrobial resistance via gene mobilization.}, }
@article {pmid39744400, year = {2024}, author = {Bradbury, ES and Holland-Moritz, H and Gill, A and Havrilla, CA}, title = {Plant and soil microbial composition legacies following indaziflam herbicide treatment.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1450633}, pmid = {39744400}, issn = {1664-302X}, abstract = {Land stewards in dryland ecosystems across the western U.S. face challenges to manage the exotic grass Bromus tectorum (cheatgrass), which is a poor forage, is difficult to remove, and increases risk of catastrophic fire. Managers may consider using indaziflam (Rejuvra™), a relatively new pre-emergent herbicide, which may reduce cheatgrass cover within drylands. However, few studies have explored the effects of indaziflam on non-target organisms. We tested how indaziflam application impacted cover and biomass of native and exotics within the plant community and composition and diversity of the soil microbiome by comparing untreated and treated arid shrubland sites in Boulder County, Colorado, USA. We found that indaziflam application decreased cheatgrass cover by as much as 80% and increased native plant cover by the same amount. Indaziflam application also was associated with increased soil nitrate (NO3 [-]), decreased soil organic matter, and had a significant effect on the composition of the soil microbiome. Microbial community composition was significantly related to soil NO3 [-], soil organic matter, soil pH, and native species and cheatgrass biomass. An indicator species analysis suggested that indaziflam application shifted microbial communities. In untreated sites, ammonia-oxidizing bacteria Nitrosomonadaceae and nitrogen-digesting Opitutaceae and the fungi Articulospora proliferata were found. While in treated sites, ammonia-oxidizing archaea which are associated with intact drylands, Nitrososphaeraceae and toxin digesters and acidic-soil species Sphingomonas and Acidimicrobiia were significantly associated. Overall, these results demonstrate that indaziflam application can increase native plant recruitment, while also affecting soil properties and the soil microbiome. The findings from this study can be used to inform decision-making during dryland restoration planning process as indaziflam use may have benefits and unknown long-term consequences for the biogeochemistry and microbial ecology of the system.}, }
@article {pmid39742975, year = {2025}, author = {Dougherty, PE and Pedersen, MS and Forero-Junco, LM and Carstens, AB and Raaijmakers, JM and Riber, L and Hansen, LH}, title = {Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks.}, journal = {Virus research}, volume = {352}, number = {}, pages = {199524}, pmid = {39742975}, issn = {1872-7492}, mesh = {*Triticum/microbiology/virology ; Phylogeny ; *Bacteriophages/genetics/classification/isolation &amp; purification ; *Erwinia/virology ; Genome, Viral ; *Pseudomonas/virology ; DNA, Viral/genetics ; Microbiota ; Plant Leaves/microbiology ; Metagenome ; }, abstract = {The phyllosphere microbiome can positively or negatively impact plant health and growth, but we currently lack the tools to control microbiome composition. Contributing to a growing collection of bacteriophages (phages) targeting bacteria living in the wheat phyllosphere, we here isolate and sequence eight novel phages targeting common phyllosphere Erwinia and Pseudomonas strains, including two jumbo phages. We characterize genomic, phylogenetic, and morphological traits from these phages and argue for establishing four novel viral genera. We also search the genomes for anti-defense systems and investigate DNA modifications using Nanopore sequencing. In Pseudomonas phage Rembedalsseter we find evidence of 13 motif-associated single-stranded DNA breaks. A bioinformatics search revealed that 60 related Pseudomonas phages are enriched in the same motif, suggesting these single-stranded nicks may be widely distributed in this family of phages. Finally, we also search the Sequence Read Archive for similar phages in public metagenomes. We find close hits to the Erwinia jumbo-phage Kaldavass in a wide variety of plant, food, and wastewater metagenomes including a near-perfect hit from a Spanish spinach sample, illustrating how interconnected geographically distant phages can be.}, }
@article {pmid39742000, year = {2024}, author = {Ford, SE and Slater, GF and Engel, K and Warr, O and Lollar, GS and Brady, A and Neufeld, JD and Lollar, BS}, title = {Deep terrestrial indigenous microbial community dominated by Candidatus Frackibacter.}, journal = {Communications earth &amp; environment}, volume = {5}, number = {1}, pages = {795}, pmid = {39742000}, issn = {2662-4435}, abstract = {Characterizing deep subsurface microbial communities informs our understanding of Earth's biogeochemistry as well as the search for life beyond the Earth. Here we characterized microbial communities within the Kidd Creek Observatory subsurface fracture water system with mean residence times of hundreds of millions to over one billion years. 16S rRNA analysis revealed that biosamplers well isolated from the mine environment were dominated by a putatively anaerobic and halophilic bacterial species from the Halobacteroidaceae family, Candidatus Frackibacter. Contrastingly, biosamplers and biofilms exposed to the mine environment contained aerobic Sphingomonas taxa. δ[13]C values of phospholipid fatty acids and putative functional predictions derived from 16S rRNA gene profiles, imply Candidatus Frackibacter may use carbon derived from ancient carbon-rich layers common in these systems. These results indicate that Candidatus Frackibacter is not unique to hydraulically fracked sedimentary basins but rather may be indigenous to a wide range of deep, saline groundwaters hosted in carbon-rich rocks.}, }
@article {pmid39741633, year = {2024}, author = {Zhang, D and Cai, Y and Sun, Y and Zeng, P and Wang, W and Wang, W and Jiang, X and Lian, Y}, title = {A real-world pharmacovigilance study of Sorafenib based on the FDA Adverse Event Reporting System.}, journal = {Frontiers in pharmacology}, volume = {15}, number = {}, pages = {1442765}, pmid = {39741633}, issn = {1663-9812}, abstract = {AIMS: The primary objective of this study was to closely monitor and identify adverse events (AEs) associated with Sorafenib, a pharmacological therapeutic agent used to treat hepatocellular carcinoma, renal cell carcinoma, and thyroid cancer. The ultimate goal was to optimize patient safety and provide evidence-based guidance for the appropriate use of this drug.<br><br>METHODS: Reports from the FDA Adverse Event Reporting System (FAERS) database were comprehensively collected and analyzed, covering the first quarter of 2004 to the first quarter of 2024. Disproportionality analysis was performed using robust algorithms for effective data mining to quantify the signals associated with Sorafenib-related AEs.<br><br>RESULTS: In total, we identifued 18,624 patients (82,857 AEs in the Sorafenib population) from the collected reports and examined, the occurrence of Sorafenib-induced AEs in 26 organ systems. The study results revealed the presence of the expected AEs, including Diarrhoea, Palmar-plantar erythrodysaesthesia syndrome, Hepatocellular carcinoma, Fatigue, and Rash, which was consistent with the information provided in the drug insert. In addition, unexpected significant AEs, such as Gait inability, Palmoplantar keratoderma and Hyperkeratosis were observed at the preferred term (PT) level. These findings suggest the potential occurrence of adverse reactions not currently documented in drug descriptions.<br><br>CONCLUSION: This study successfully detected new and unforeseen signals associated with Sorafenib-related AEs related to Sorafenib administration, providing important insights into the complex correlations between AEs and Sorafenib use. The results of this study emphasize the critical importance of continuous and vigilant surveillance for the timely identification and effective management of AEs to improve the overall patient safety and wellbeing in the context of Sorafenib therapy.}, }
@article {pmid39739109, year = {2024}, author = {Rovira-Alsina, L and Romans-Casas, M and Perona-Vico, E and Ceballos-Escalera, A and Balaguer, MD and Bañeras, L and Puig, S}, title = {Microbial Electrochemical Technologies: Sustainable Solutions for Addressing Environmental Challenges.}, journal = {Advances in biochemical engineering/biotechnology}, volume = {}, number = {}, pages = {}, pmid = {39739109}, issn = {0724-6145}, abstract = {Addressing global challenges of waste management demands innovative approaches to turn biowaste into valuable resources. This chapter explores the potential of microbial electrochemical technologies (METs) as an alternative opportunity for biowaste valorisation and resource recovery due to their potential to address limitations associated with traditional methods. METs leverage microbial-driven oxidation and reduction reactions, enabling the conversion of different feedstocks into energy or value-added products. Their versatility spans across gas, food, water and soil streams, offering multiple solutions at different technological readiness levels to advance several sustainable development goals (SDGs) set out in the 2030 Agenda. By critically examining recent studies, this chapter uncovers challenges, optimisation strategies, and future research directions for real-world MET implementations. The integration of economic perspectives with technological developments provides a comprehensive understanding of the opportunities and demands associated with METs in advancing the circular economy agenda, emphasising their pivotal role in waste minimisation, resource efficiency promotion, and closed-loop system renovation.}, }
@article {pmid39738334, year = {2024}, author = {Ahadi, R and Bouket, AC and Alizadeh, A and Masigol, H and Grossart, HP}, title = {Globisporangium tabrizense sp. nov., Globisporangium mahabadense sp. nov., and Pythium bostanabadense sp. nov. (Oomycota), three new species from Iranian aquatic environments.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31701}, pmid = {39738334}, issn = {2045-2322}, mesh = {Iran ; *Phylogeny ; *Pythium/genetics/isolation &amp; purification ; Oomycetes/genetics/classification/isolation &amp; purification ; Cucumis sativus/microbiology ; }, abstract = {During a survey on the biodiversity of oomycetes in aquatic environments in northwest Iran (East Azarbaijan and West Azarbaijan provinces), three Pythium and four Globisporangium isolates were recovered from agricultural water pools and irrigation canals, respectively. Through a polyphasic approach combining morphology and phylogenetic analysis using the nuclear rDNA ITS1-5.8 S-ITS2 (ITS) and partial sequences of the cytochrome c oxidase subunit I and II (COX1 and COX2), three novel species were identified namely Globisporangium tabrizense sp. nov., G. mahabadense sp. nov., and Pythium bostanabadense sp. nov. Furthermore, experiments confirmed the pathogenicity of all identified species on cucumber seedlings, suggesting a pathogenic lifestyle also in aquatic systems. Our research contributes to a better understanding of the diversity, host range and distribution of oomycetes genera Globisporangium and Pythium in northwestern Iran. Detailed morphological descriptions and illustrations are provided for all species.}, }
@article {pmid39737770, year = {2025}, author = {Rawstern, AH and Hernandez, DJ and Afkhami, ME}, title = {Central Taxa Are Keystone Microbes During Early Succession.}, journal = {Ecology letters}, volume = {28}, number = {1}, pages = {e70031}, pmid = {39737770}, issn = {1461-0248}, support = {DEB-1922521//National Science Foundation/ ; DEB-2030060//National Science Foundation/ ; }, mesh = {*Soil Microbiology ; *Microbiota ; Biodiversity ; Bacteria/classification/genetics ; Ecosystem ; }, abstract = {Microorganisms underpin numerous ecosystem processes and support biodiversity globally. Yet, we understand surprisingly little about what structures environmental microbiomes, including how to efficiently identify key players. Microbiome network theory predicts that highly connected hubs act as keystones, but this has never been empirically tested in nature. Combining culturing, sequencing, networks and field experiments, we isolated 'central' (highly connected, hub taxa), 'intermediate' (moderately connected), and 'peripheral' (weakly/unconnected) microbes and experimentally evaluated their effects on soil microbiome assembly during early succession in nature. Central early colonisers significantly (1) enhanced biodiversity (35%-40% richer communities), (2) reshaped trajectories of microbiome assembly and (3) increased recruitment of additional influential microbes by > 60%. In contrast, peripheral microbes did not increase diversity and were transient taxa, minimally affected by the presence of other microbes. This work elucidates fundamental principles of network theory in microbial ecology and demonstrates for the first time in nature that central microbes act as keystone taxa.}, }
@article {pmid39736538, year = {2024}, author = {Radjasa, OK and Steven, R and Natanael, Y and Nugrahapraja, H and Radjasa, SK and Kristianti, T and Moeis, MR and Trinugroho, JP and Suharya, HB and Rachmatsyah, AO and Dwijayanti, A and Putri, MR and de Fretes, CE and Siallagan, ZL and Fadli, M and Opier, RDA and Farahyah, JD and Rahmawati, V and Rizanti, M and Humaira, Z and Prihatmanto, AS and Hananto, ND and Susanto, RD and Chahyadi, A and Elfahmi,  and Priharto, N and Kamarisima,  and Dwivany, FM}, title = {From the depths of the Java Trench: genomic analysis of Priestia flexa JT4 reveals bioprospecting and lycopene production potential.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1259}, pmid = {39736538}, issn = {1471-2164}, mesh = {*Lycopene/metabolism ; Indonesia ; *Genome, Bacterial ; Bioprospecting ; Genomics/methods ; Phylogeny ; Multigene Family ; Peptide Synthases/genetics/metabolism ; Whole Genome Sequencing ; Carotenoids/metabolism ; Actinobacteria/genetics/metabolism ; }, abstract = {BACKGROUND: The marine environment boasts distinctive physical, chemical, and biological characteristics. While numerous studies have delved into the microbial ecology and biological potential of the marine environment, exploration of genetically encoded, deep-sea sourced secondary metabolites remains scarce. This study endeavors to investigate marine bioproducts derived from deep-sea water samples at a depth of 1,000 m in the Java Trench, Indonesia, utilizing both culture-dependent and whole-genome sequencing methods.<br><br>RESULTS: Our efforts led to the successful isolation and cultivation of a bacterium Priestia flexa JT4 from the water samples, followed by comprehensive genome sequencing. The resultant high-quality draft genome, approximately 4&#xa0;Mb, harbored 5185 coding sequences (CDSs). Notably, 61.97% of these CDSs were inadequately characterized, presenting potential novel CDSs. This study is the first to identify the "open-type" (&#x3b1;&#x2009;<&#x2009;1) pangenome within the genus Priestia. Moreover, our analysis uncovered eight biosynthetic gene clusters (BGCs) using the common genome mining pipeline, antiSMASH. Two non-ribosomal peptide synthetase (NRPS) BGCs within these clusters exhibited the potential to generate novel biological compounds. Noteworthy is the confirmation that the terpene BGC in P. flexa JT4 can produce lycopene, a compound in substantial industrial demand. The presence of lycopene in the P. flexa JT4 cells was verified using Ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS) in multiple reaction modes.<br><br>CONCLUSIONS: This study highlights the bioprospecting opportunity to explore novel bioproducts and lycopene compounds from P. flexa JT4. It marks the pioneering exploration of deep-sea bacterium bioprospecting in Indonesia, seeking to unveil novel bioproducts and lycopene compounds through a genome mining approach.}, }
@article {pmid39736196, year = {2025}, author = {Wong, JWH and Balskus, EP}, title = {Small molecules as modulators of phage-bacteria interactions.}, journal = {Current opinion in chemical biology}, volume = {84}, number = {}, pages = {102566}, doi = {10.1016/j.cbpa.2024.102566}, pmid = {39736196}, issn = {1879-0402}, mesh = {*Bacteriophages/physiology/drug effects ; *Bacteria/virology/metabolism/drug effects ; *Small Molecule Libraries/pharmacology/chemistry ; Lysogeny/drug effects ; }, abstract = {Bacteriophages (phages) play a critical role in microbial ecology and evolution. Their interactions with bacteria are influenced by a complex network of chemical signals derived from a wide range of sources including both endogenous bacterial metabolites and exogenous environmental compounds. In this review, we highlight two areas where small molecules play a pivotal role in modulating phage behaviors. First, we discuss how temperate phages respond to various chemical cues that influence the lysis-lysogeny decision, describing recent advances in our understanding of noncanonical cues. Second, we examine the diverse array of small molecules that disrupt phage infection, potentially serving as bacterial defense strategies against their long-standing competitors. Collectively, this growing body of research highlights the intricate molecular mechanisms governing phage-bacteria dynamics, offering new perspectives on the chemical language shaping microbial communities.}, }
@article {pmid39732620, year = {2025}, author = {Berrios, L and Ansell, TB and Dahlberg, PD and Peay, KG}, title = {Standardizing experimental approaches to investigate interactions between bacteria and ectomycorrhizal fungi.}, journal = {FEMS microbiology reviews}, volume = {49}, number = {}, pages = {}, pmid = {39732620}, issn = {1574-6976}, support = {2109481//National Science Foundation/ ; //Canadian Institute for Advanced Research/ ; 1845544//DEB/ ; }, mesh = {*Mycorrhizae/physiology ; *Bacteria ; Soil Microbiology ; Plant Roots/microbiology ; *Microbial Interactions ; }, abstract = {Bacteria and ectomycorrhizal fungi (EcMF) represent two of the most dominant plant root-associated microbial groups on Earth, and their interactions continue to gain recognition as significant factors that shape forest health and resilience. Yet, we currently lack a focused review that explains the state of bacteria-EcMF interaction research in the context of experimental approaches and technological advancements. To these ends, we illustrate the utility of studying bacteria-EcMF interactions, detail outstanding questions, outline research priorities in the field, and provide a suite of approaches that can be used to promote experimental reproducibility, field advancement, and collaboration. Though this review centers on the ecology of bacteria, EcMF, and trees, it by default offers experimental and conceptual insights that can be adapted to various subfields of microbiology and microbial ecology.}, }
@article {pmid39732444, year = {2025}, author = {Correa, SS and Schultz, J and Zahodnik-Huntington, B and Naschberger, A and Rosado, AS}, title = {Carboxysomes: The next frontier in biotechnology and sustainable solutions.}, journal = {Biotechnology advances}, volume = {79}, number = {}, pages = {108511}, doi = {10.1016/j.biotechadv.2024.108511}, pmid = {39732444}, issn = {1873-1899}, mesh = {*Biotechnology/methods ; *Organelles/metabolism ; Carbon Cycle ; Ribulose-Bisphosphate Carboxylase/metabolism ; *Bacteria/metabolism ; Carbonic Anhydrases/metabolism ; Cyanobacteria/metabolism ; Carbon Dioxide/metabolism ; }, abstract = {Some bacteria possess microcompartments that function as protein-based organelles. Bacterial microcompartments (BMCs) sequester enzymes to optimize metabolic reactions. Several BMCs have been characterized to date, including carboxysomes and metabolosomes. Genomic analysis has identified novel BMCs and their loci, often including genes for signature enzymes critical to their function, but further characterization is needed to confirm their roles. Among the various BMCs, carboxysomes, which are found in cyanobacteria and some chemoautotrophic bacteria, and are most extensively investigated. These self-assembling polyhedral proteinaceous BMCs are essential for carbon fixation. Carboxysomes encapsulate the enzymes RuBisCo and carbonic anhydrase, which increase the carbon fixation rate in the cell and decrease the oxygenation rate by RuBisCo. The ability of carboxysomes to concentrate carbon dioxide in crops and industrially relevant microorganisms renders them attractive targets for carbon assimilation bioengineering. Thus, carboxysome characterization is the first step toward developing carboxysome-based applications. Therefore, this review comprehensively explores carboxysome morphology, physiology, and biochemistry. It also discusses recent advances in microscopy and complementary techniques for isolating and characterizing this versatile class of prokaryotic organelles.}, }
@article {pmid39731630, year = {2024}, author = {Fluch, M and Corretto, E and Feldhaar, H and Schuler, H}, title = {Seasonal Changes in the Gut Microbiota of Halyomorpha halys.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {164}, pmid = {39731630}, issn = {1432-184X}, mesh = {Animals ; *Seasons ; *Gastrointestinal Microbiome ; *Heteroptera/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Symbiosis ; Pantoea/isolation &amp; purification/physiology/genetics/classification ; Phylogeny ; }, abstract = {The gut microbiome plays an important role in insect evolution and ecology. Bacteria support the host's nutrition and defense and therefore play an important role in the fitness of the host. Halyomorpha halys is one of the most important invasive pest species in the world. Native to North-Eastern Asia, this Pentatomid bug has recently invaded North America and Europe, causing significant damage to agricultural production. Although an increasing number of studies investigated the biology of this pest species, little is known about the composition of its gut microbiota. Like many other Pentatomid species, H. halys harbors a primary symbiont called "Candidatus Pantoea carbekii," which produces vitamins and essential amino acids for the host. However, information about the presence of other bacteria is currently lacking. Therefore, we investigated the gut microbiota of H. halys individuals, which were collected in the field across the year using a high-throughput 16S rRNA gene metabarcoding approach. Our results revealed 3309 different ASVs associated with H. halys, with Pantoea being the most abundant symbiont, present in almost all individuals. Additionally, many individuals harbor Commensalibacter, a genus of acetic acid bacterial symbionts. Besides these two predominant taxa, we show a high diversity of microorganisms associated with H. halys with seasonal fluctuations, highlighting a dynamic microbiota that might influence the biology of this species.}, }
@article {pmid39730790, year = {2024}, author = {Struniawski, K and Kozera, R and Trzciński, P and Marasek-Ciołakowska, A and Sas-Paszt, L}, title = {Extreme learning machine for identifying soil-dwelling microorganisms cultivated on agar media.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31034}, pmid = {39730790}, issn = {2045-2322}, support = {BIOSTRATEG3/344433/16/NCBR/2018//Narodowe Centrum Bada&#x144; i Rozwoju/ ; }, mesh = {*Soil Microbiology ; *Machine Learning ; Agar/chemistry ; Soil/chemistry ; Image Processing, Computer-Assisted/methods ; Culture Media ; }, abstract = {The aim of this research is to create an automated system for identifying soil microorganisms at the genera level based on raw microscopic images of monocultural colonies grown in laboratory environment. The examined genera are: Fusarium, Trichoderma, Verticillium, Purpureolicillium and Phytophthora. The proposed pipeline deals with unprocessed microscopic images, avoiding additional sample marking or coloration. The methodology includes several stages: image preprocessing, segmenting images to isolate microorganisms from the background, calculating features related to image color and texture for classification. Using an extensive dataset of 2866 images from the National Institute of Horticultural Research in Skierniewice the Extreme Learning Machine model was trained and validated. The model showcases high accuracy and computational efficiency compared to other Machine Learning state-of-the art methods e.g. CatBoost, Random Forest or Convolutional Neural Networks. Statistical techniques, including Multivariate Analysis of Variance were employed to confirm significant differences among the datasets, enhancing the model's robustness. Nevertheless, Shapley Additive Explanations values provided transparency into the model's decision-making process. This approach has the potential to improve early detection and management of soil pathogens, promoting sustainable agriculture and demonstrating machine learning's potential in environmental monitoring, microbial ecology or industrial microbiology.}, }
@article {pmid39730187, year = {2025}, author = {Yan, M and Andersen, TO and Pope, PB and Yu, Z}, title = {Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.}, journal = {Genome research}, volume = {35}, number = {2}, pages = {368-378}, pmid = {39730187}, issn = {1549-5469}, mesh = {Animals ; *Ruminants/microbiology/parasitology/genetics ; *Metagenomics/methods ; Metagenome ; *Deep Learning ; *Databases, Protein ; Rumen/microbiology ; Fungi/genetics/classification ; Computational Biology/methods ; *Eukaryota/genetics/classification ; *Gastrointestinal Microbiome/genetics ; }, abstract = {Metagenomics, particularly genome-resolved metagenomics, have significantly deepened our understanding of microbes, illuminating their taxonomic and functional diversity and roles in ecology, physiology, and evolution. However, eukaryotic populations within various microbiomes, including those in the mammalian gastrointestinal (GI) tract, remain relatively underexplored in metagenomic studies owing to the lack of comprehensive reference genome databases and robust bioinformatic tools. The GI tract of ruminants, particularly the rumen, contains a high eukaryotic biomass but a relatively low diversity of ciliates and fungi, which significantly impacts feed digestion, methane emissions, and rumen microbial ecology. In the present study, we developed GutEuk, a bioinformatics tool that improves upon the currently available Tiara and EukRep in accurately identifying eukaryotic sequences from metagenomes. GutEuk is optimized for high precision across different sequence lengths. It can also distinguish fungal and protozoal sequences, further elucidating their unique ecological, physiological, and nutritional impacts. GutEuk was shown to facilitate comprehensive analyses of protozoa and fungi within more than 1000 rumen metagenomes, revealing a greater genomic diversity among protozoa than previously documented. We further curated several ruminant eukaryotic protein databases, significantly enhancing our ability to distinguish the functional roles of ruminant fungi and protozoa from those of prokaryotes. Overall, the newly developed package GutEuk and its associated databases create new opportunities for the in-depth study of GI tract eukaryotes.}, }
@article {pmid39730090, year = {2025}, author = {Nguyen, TV and Kim, NK and Lee, SH and Trinh, HP and Park, HD}, title = {Gene abundance and microbial syntrophy as key drivers of anaerobic digestion revealed through 16S rRNA gene and metagenomic analysis.}, journal = {Chemosphere}, volume = {370}, number = {}, pages = {144028}, doi = {10.1016/j.chemosphere.2024.144028}, pmid = {39730090}, issn = {1879-1298}, mesh = {Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; Metagenomics ; Wastewater/microbiology ; *Bacteria/genetics/metabolism ; Bioreactors/microbiology ; }, abstract = {Genes in microorganisms influence the biological processes in anaerobic digestion (AD). However, key genes involved in the four metabolic steps (hydrolysis, acidogenesis, acetogenesis, and methanogenesis) remain largely unexplored. This study investigated the abundance and distribution of key functional genes in full-scale anaerobic digesters processing food waste (FWDs) and municipal wastewater (MWDs) through 16S rRNA gene and shotgun metagenomic analysis. Our results revealed that FWDs exhibited a higher abundance of key genes in the metabolic steps, despite having significantly lower microbial diversity compared to MWDs. Pathways and genes associated with syntrophic oxidation of acetate (SAO) and butyrate (SBO) were more present in FWDs. SAO potentially used both the conventional reversed Wood-Ljungdahl pathway and its integration with the glycine cleavage system in FWDs, which complements pathways for acetate oxidation under ammonia stress conditions. Similarly, genes associated with SBO (atoB and croR) were notably more prevalent in FWDs compared to MWDs with an 8.4-fold and 108-fold increase, respectively, indicating the adaptation of SBO bacteria to convert butyrate into acetate. The higher abundance of key genes in FWDs was driven by microbes adapting to the feedstock compositions with higher levels of substrate content, volatile fatty acids, and ammonia. This study quantified the genes central to AD metabolism and uncovered the contributions of microbial diversity, gene abundance, syntrophy, and feedstock characteristics to the functionality of AD processes. These findings enhance understanding of the microbial ecology in AD and provide a foundation for developing innovative strategies to enhance biogas production and waste management.}, }
@article {pmid39726151, year = {2024}, author = {Nieland, MA and Lacy, P and Allison, SD and Bhatnagar, JM and Doroski, DA and Frey, SD and Greaney, K and Hobbie, SE and Kuebbing, SE and Lewis, DB and McDaniel, MD and Perakis, SS and Raciti, SM and Shaw, AN and Sprunger, CD and Strickland, MS and Templer, PH and Vietorisz, C and Ward, EB and Keiser, AD}, title = {Nitrogen Deposition Weakens Soil Carbon Control of Nitrogen Dynamics Across the Contiguous United States.}, journal = {Global change biology}, volume = {30}, number = {12}, pages = {e70016}, doi = {10.1111/gcb.70016}, pmid = {39726151}, issn = {1365-2486}, support = {1831944//Division of Environmental Biology/ ; SC0020382//Biological and Environmental Research/ ; 1845417//National Science Foundation/ ; 2045135//Division of Earth Sciences/ ; //University of Massachusetts Amherst/ ; }, mesh = {*Soil/chemistry ; United States ; *Carbon/metabolism/analysis ; *Nitrogen/metabolism/analysis ; *Soil Microbiology ; *Nitrification ; Forests ; Biomass ; }, abstract = {Anthropogenic nitrogen (N) deposition is unequally distributed across space and time, with inputs to terrestrial ecosystems impacted by industry regulations and variations in human activity. Soil carbon (C) content normally controls the fraction of mineralized N that is nitrified (ƒnitrified), affecting N bioavailability for plants and microbes. However, it is unknown whether N deposition has modified the relationships among soil C, net N mineralization, and net nitrification. To test whether N deposition alters the relationship between soil C and net N transformations, we collected soils from coniferous and deciduous forests, grasslands, and residential yards in 14 regions across the contiguous United States that vary in N deposition rates. We quantified rates of net nitrification and N mineralization, soil chemistry (soil C, N, and pH), and microbial biomass and function (as beta-glucosidase (BG) and N-acetylglucosaminidase (NAG) activity) across these regions. Following expectations, soil C was a driver of ƒnitrified across regions, whereby increasing soil C resulted in a decline in net nitrification and ƒnitrified. The ƒnitrified value increased with lower microbial enzymatic investment in N acquisition (increasing BG:NAG ratio) and lower active microbial biomass, providing some evidence that heterotrophic microbial N demand controls the ammonium pool for nitrifiers. However, higher total N deposition increased ƒnitrified, including for high soil C sites predicted to have low ƒnitrified, which decreased the role of soil C as a predictor of ƒnitrified. Notably, the drop in contemporary atmospheric N deposition rates during the 2020 COVID-19 pandemic did not weaken the effect of N deposition on relationships between soil C and ƒnitrified. Our results suggest that N deposition can disrupt the relationship between soil C and net N transformations, with this change potentially explained by weaker microbial competition for N. Therefore, past N inputs and soil C should be used together to predict N dynamics across terrestrial ecosystems.}, }
@article {pmid39725503, year = {2025}, author = {Belanche, A and Bannink, A and Dijkstra, J and Durmic, Z and Garcia, F and Santos, FG and Huws, S and Jeyanathan, J and Lund, P and Mackie, RI and McAllister, TA and Morgavi, DP and Muetzel, S and Pitta, DW and Yáñez-Ruiz, DR and Ungerfeld, EM}, title = {Feed additives for methane mitigation: A guideline to uncover the mode of action of antimethanogenic feed additives for ruminants.}, journal = {Journal of dairy science}, volume = {108}, number = {1}, pages = {375-394}, doi = {10.3168/jds.2024-25046}, pmid = {39725503}, issn = {1525-3198}, mesh = {*Methane ; Animals ; *Animal Feed ; *Ruminants ; *Rumen/metabolism ; Diet/veterinary ; }, abstract = {This publication aims to provide guidelines of the knowledge required and the potential research to be conducted in order to understand the mode of action of antimethanogenic feed additives (AMFA). In the first part of the paper, we classify AMFA into 4 categories according to their mode of action: (1) lowering dihydrogen (H2) production; (2) inhibiting methanogens; (3) promoting alternative H2-incorporating pathways; and (4) oxidizing methane (CH4). The second part of the paper presents questions that guide the research to identify the mode of action of an AMFA on the rumen CH4 production from 5 different perspectives: (1) microbiology; (2) cell and molecular biochemistry; (3) microbial ecology; (4) animal metabolism; and (5) cross-cutting aspects. Recommendations are provided to address various research questions within each perspective, along with examples of how aspects of the mode of action of AMFA have been elucidated before. In summary, this paper offers timely and comprehensive guidelines to better understand and reveal the mode of action of current and emerging AMFA.}, }
@article {pmid39725195, year = {2025}, author = {Xu, W and Lam, C and Wang, Y and Wan, SH and Ho, PH and Myung, J and Yung, CCM}, title = {Temporal succession of marine microbes drives plastisphere community convergence in subtropical coastal waters.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {367}, number = {}, pages = {125572}, doi = {10.1016/j.envpol.2024.125572}, pmid = {39725195}, issn = {1873-6424}, mesh = {*Plastics/analysis ; *Seawater/microbiology ; Hong Kong ; *Microbiota ; *Water Pollutants, Chemical/analysis ; Ecosystem ; Environmental Monitoring ; Bacteria/classification ; *Water Microbiology ; }, abstract = {Marine plastic pollution is a pervasive environmental issue, with microplastics serving as novel substrates for microbial colonization in aquatic ecosystems. This study investigates the succession of plastisphere communities on four common plastic types (polyethylene, polypropylene, polyethylene terephthalate, and polystyrene) in subtropical coastal waters of Hong Kong SAR. Over a 42-day period, we analysed the temporal development of microbial communities using a three-domain universal metabarcoding method. Our results reveal that temporal succession is a stronger driver of community structure than plastic type, with prokaryotic communities converging across different plastics as biofilms mature. Despite this convergence, plastisphere communities remain distinct from planktonic communities throughout the experiment, suggesting that plastics create unique ecological niches in marine environments. We observed differences in diversity patterns and community composition among prokaryotic, eukaryotic, and chloroplastic communities, highlighting the importance of multi-domain analyses in plastisphere research. Functional predictions suggest potential roles of prokaryotic communities in biogeochemical cycling and possible pathogenicity, highlighting the ecological and public health implications of plastisphere formation. This study provides valuable insights into the dynamics of microbial colonization across domains on marine plastics and enhances our understanding of how these anthropogenic substrates influence microbial ecology in marine ecosystems.}, }
@article {pmid39724890, year = {2024}, author = {Kusradze, I and Rcheulishvili, O and Karumidze, N and Rigvava, S and Rcheulishvili, A and Goliadze, R and Kamashidze, L and Chipurupalli, A and Metreveli, N and Goderdzishvili, M}, title = {PHAGE-BACTERIA INTERACTIONS UNDER METAL STRESS: A STUDY OF THE NOVEL STENOTROPHOMONAS MALTOPHILIA PHAGE VB_STM18.}, journal = {Georgian medical news}, volume = {}, number = {355}, pages = {117-122}, pmid = {39724890}, issn = {1512-0112}, mesh = {*Stenotrophomonas maltophilia/virology/drug effects ; *Cadmium/toxicity ; *Bacteriophages ; Biodegradation, Environmental ; Stress, Physiological/drug effects ; }, abstract = {Stenotrophomonas maltophilia is a highly adaptable gram-negative bacteria, demonstrating resilience in metal-contaminated environment, which makes it a key subject for understanding microbial survival under heavy metal stress. This study investigates the effects of cadmium ions (Cd[2+]) on the growth dynamics, cadmium uptake, and bacteriophage vB_Stm18-host interactions, with implications for environmental microbiology and applied biotechnology. Growth analysis revealed that S. maltophilia tolerates Cd[2+] at 0.01 g/L, although exposure prolonged the lag phase by 3 hours. Despite the initial growth inhibition, the bacterium adapted and achieved control-like growth levels by 18 hours. Bioaccumulation assays showed progressive cadmium uptake, reaching 1876 µg/g at 24 hours, highlighting its potential for bioremediation. The influence of Cd[2+] on phage vB_Stm18's life cycle was assessed through adsorption efficiency and burst size measurements. Short-term exposure to Cd[2+] caused minimal reductions in adsorption efficiency (97% vs. 98% in control) but significantly decreased the burst size to 17 particles per infected cell. Prolonged exposure exacerbated these effects, with adsorption efficiency decreasing to 58% and burst size dropping to 6 particles per infected cell, after 18 hours of pre-incubation. These findings suggest that cadmium alters bacterial surface structures, intracellular processes and disrupts phage replication and release. Therefore, this study sheds light on the molecular interplay between environmental pollutants and microbial systems providing valuable insights into microbial ecology in metal-contaminated habitats as well as informing strategies for optimizing phage therapy and bioremediation under heavy metal stress.}, }
@article {pmid39724159, year = {2024}, author = {Ulbrich, J and Jobe, NE and Jones, DS and Kieft, TL}, title = {Cave Pools in Carlsbad Caverns National Park Contain Diverse Bacteriophage Communities and Novel Viral Sequences.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {163}, pmid = {39724159}, issn = {1432-184X}, support = {NCKRI-NMT Internal Seed Grant Program//National Cave and Karst Research Institute/ ; }, mesh = {*Caves ; *Parks, Recreational ; *Bacteriophages/genetics/isolation &amp; purification/classification ; *Bacteria/genetics/classification/isolation &amp; purification/virology ; *RNA, Ribosomal, 16S/genetics ; California ; Metagenome ; Phylogeny ; Virome ; Biodiversity ; }, abstract = {Viruses are the most abundant biological entities on Earth, and they play a critical role in the environment and biosphere where they regulate microbial populations and contribute to nutrient cycling. Environmental viruses have been the most studied in the ocean, but viral investigations have now spread to other environments. Here, viral communities were characterized in four cave pools in Carlsbad Caverns National Park to test the hypotheses that (i) viral abundance is ten-fold higher than prokaryotic cell abundance in cavern pools, (ii) cavern pools contain novel viral sequences, and (iii) viral communities in pools from developed portions of the cave are distinct from those of pools in undeveloped parts of the same cave. The relationship between viral and microbial abundance was determined through direct epifluorescence microscopy counts. Viral metagenomes were constructed to examine viral diversity among pools, identify novel viruses, and characterize auxiliary metabolic genes (AMGs). Bacterial communities were characterized by 16S rRNA gene amplicon sequencing. Epifluorescence microscopy showed that the ratio of viral-like particles (VLPs) to microorganisms was approximately 22:1 across all sites. Viral communities from pools with higher tourist traffic were more similar to each other than to those from less visited pools, although surprisingly, viruses did not follow the same pattern as bacterial communities, which reflected pool geochemistry. Bacterial hosts predicted from viral sequences using iPHoP showed overlap with both rare and abundant genera and families in the 16S rRNA gene dataset. Gene-sharing network analysis revealed high viral diversity compared to a reference viral database as well as to other aquatic environments. AMG presence showed variation in metabolic potential among the four pools. Overall, Carlsbad Cavern harbors novel viruses with substantial diversity among pools within the same system, indicating that caves are likely an important repository for unexplored viromes.}, }
@article {pmid39723821, year = {2025}, author = {Sanchez, VA and Renner, T and Baker, LJ and Hendry, TA}, title = {Genome evolution following an ecological shift in nectar-dwelling Acinetobacter.}, journal = {mSphere}, volume = {10}, number = {1}, pages = {e0101024}, pmid = {39723821}, issn = {2379-5042}, mesh = {*Acinetobacter/genetics/classification ; *Genome, Bacterial ; *Plant Nectar/metabolism ; Phylogeny ; *Evolution, Molecular ; Ecosystem ; Gene Transfer, Horizontal ; }, abstract = {UNLABELLED: The bacterial genus Acinetobacter includes species found in environmental habitats like soil and water, as well as taxa adapted to be host-associated or pathogenic. High genetic diversity may allow for this habitat flexibility, but the specific genes underlying switches between habitats are poorly understood. One lineage of Acinetobacter has undergone a substantial habitat change by evolving from a presumed soil-dwelling ancestral state to thrive in floral nectar. Here, we compared the genomes of floral-dwelling and pollinator-associated Acinetobacter, including newly described species, with genomes from relatives found in other environments to determine the genomic changes associated with this ecological shift. Following one evolutionary origin of floral nectar adaptation, nectar-dwelling Acinetobacter taxa have undergone reduction in genome size compared with relatives and have experienced dynamic gene gains and losses as they diversified. Gene content changes suggest a shift to metabolism of monosaccharides rather than diverse carbohydrates, and scavenging of nitrogen sources, which we predict to be beneficial in nectar environments. Gene gains appear to result from duplication events, evolutionary divergence, and horizontal gene transfer. Most notably, nectar-dwelling Acinetobacter acquired the ability to degrade pectin from plant pathogens, and the genes underlying this ability have duplicated and are under selection within the clade. We hypothesize that this ability was a key trait for adaptation to floral nectar, as it could improve access to nutrients in the nutritionally unbalanced habitat of nectar. These results identify the genomic changes and traits coinciding with a dramatic habitat switch from soil to floral nectar.<br><br>IMPORTANCE: Many bacteria, including the genus Acinetobacter, commonly evolve to exploit new habitats. However, the genetic changes that underlie habitat switches are often unknown. Floral nectar is home to specialized microbes that can grow in this nutritionally unbalanced habitat. Several specialized Acinetobacter species evolved from soil-dwelling relatives to become common and abundant in floral nectar. Here, we investigate the genomic adaptations required to successfully colonize a novel habitat like floral nectar. We performed comparative genomics analyses between nectar-dwelling Acinetobacter and Acinetobacter species from other environments, like soil and water. We find that although gene loss coincided with the switch to living in nectar, gains of specific genes from other bacteria may have been particularly important for this ecological change. Acinetobacter living in nectar gained genes for degrading pectin, a plant polysaccharide, which may improve access to nutrients in their environment. These findings shed light on how evolutionary novelty evolves in bacteria.}, }
@article {pmid39723138, year = {2024}, author = {Xie, S and Ma, J and Lu, Z}, title = {Bacteroides thetaiotaomicron enhances oxidative stress tolerance through rhamnose-dependent mechanisms.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1505218}, pmid = {39723138}, issn = {1664-302X}, abstract = {This study probes into the unique metabolic responses of Bacteroides thetaiotaomicron (B. thetaiotaomicron), a key player in the gut microbiota, when it metabolizes rhamnose rather than typical carbohydrates. Known for its predominant role in the Bacteroidetes phylum, B. thetaiotaomicron efficiently breaks down poly- and mono-saccharides into beneficial short-chain fatty acids (SCFAs), crucial for both host health and microbial ecology balance. Our research focused on how this bacterium's SCFA production differ when utilizing various monosaccharides, with an emphasis on the oxidative stress responses triggered by rhamnose consumption. Notably, rhamnose use results in unique metabolic byproducts, including substantial quantities of 1,2-propanediol, which differs significantly from those produced during glucose metabolism. Our research reveals that rhamnose consumption is associated with a reduction in reactive oxygen species (ROS), signifying improved resistance to oxidative stress compared to other sugars. This effect is attributed to specific gene expressions within the rhamnose metabolic pathway. Notably, overexpression of the rhamnose metabolism regulator RhaR in B. thetaiotaomicron enhances its survival in oxygen-rich conditions by reducing hydrogen peroxide production. This reduction is linked to decreased expression of pyruvate:ferredoxin oxidoreductase (PFOR). In contrast, experiments with a rhaR-deficient strain demonstrated that the absence of RhaR causes B. thetaiotaomicron cells growing on rhamnose to produce ROS at rates comparable to cells grown on glucose, therefore, losing their advantage in oxidative resistance. Concurrently, the expression of PFOR is no longer suppressed. These results indicate that when B. thetaiotaomicron is cultured in a rhamnose-based medium, RhaR can restrain the expression of PFOR. Although PFOR is not a primary contributor to intracellular ROS production, its sufficient inhibition does reduce ROS levels to certain extent, consequently improving the bacterium's resistance to oxidative stress. It highlights the metabolic flexibility and robustness of microbes in handling diverse metabolic challenges and oxidative stress in gut niches through the consumption of alternative carbohydrates.}, }
@article {pmid39721552, year = {2025}, author = {IJdema, F and Lievens, S and Smets, R and Poma, G and Van Der Borght, M and Lievens, B and De Smet, J}, title = {Modulating the fatty acid composition of black soldier fly larvae via substrate fermentation.}, journal = {Animal : an international journal of animal bioscience}, volume = {19}, number = {1}, pages = {101383}, doi = {10.1016/j.animal.2024.101383}, pmid = {39721552}, issn = {1751-732X}, mesh = {Animals ; Larva/growth &amp; development/metabolism/chemistry ; Fermentation ; *Animal Feed/analysis ; *Simuliidae/growth &amp; development/metabolism ; *Mortierella/metabolism ; *Fatty Acids/metabolism ; Dietary Fiber/metabolism ; Fatty Acids, Omega-6/metabolism ; Fatty Acids, Omega-3/metabolism ; Aquaculture/methods ; }, abstract = {Black soldier fly larvae (BSFL, Hermetia illucens) contain high amounts of proteins and essential amino acids and are therefore an appropriate feed source. However, they lack essential fatty acids (FAs), specifically ω-3 and ω-6, making them a less desirable feed choice for aquaculture. The aim of this study was to increase the ω-3 and ω-6 FA concentrations in BSFL by manipulating the FA composition in their rearing substrate. Specifically, the potential of substrate fermentation using the ω-3 and ω-6 FA-producing fungus Mortierella alpina was assessed. Fermentation of two agricultural side streams (wheat bran (WB) and WB with distiller's dried grains with solubles (DDGS)) increased substrate total crude fat concentration by 2.1 - 4.6%, as well as the concentration of several essential FAs, including the ω-6 FAs arachidonic acid (from less than 0.2 mg/g fat to a maximum of 44.2 mg/g fat) and gamma-linolenic acid (from less than 1.2 mg/g fat to a maximum of 45.8 mg/g fat and the ω-3 FA eicosapentaenoic acid (EPA) (from less than 0.7 mg/g fat to a maximum of 49.9 mg/g fat). Rearing BSFL on feeds from such fermented substrates resulted in similar changes in larval FA composition, specifically a higher concentration of EPA (from less than 0.2 mg/g fat to a maximum of 26.6 mg/g fat in the larvae fed on fermented diets), however, larval growth was reduced. Feeds made from fermented substrates were prone to stickiness and dehydration, possibly limiting larval movement and feeding, thereby affecting larval growth. Furthermore, proximate analysis of the substrates revealed sugar depletion after fermentation, which could be detrimental for larval growth and illustrate important attention points going forward. This study shows that fermentation of agricultural side streams WB and a mixture of WB with DDGS with Mortierella alpina alters their FA profile, increasing their ω-3 and ω-6 FA concentrations and that of BSFL fed with those substrates. Therefore, these results suggest that BSFL with tailor-made FA profiles for a specific application could be successfully produced.}, }
@article {pmid39716780, year = {2025}, author = {Quevedo-Caraballo, S and de Vega, C and Lievens, B and Fukami, T and Álvarez-Pérez, S}, title = {Tiny but mighty? Overview of a decade of research on nectar bacteria.}, journal = {The New phytologist}, volume = {245}, number = {5}, pages = {1897-1910}, pmid = {39716780}, issn = {1469-8137}, support = {//Agentschap Innoveren en Ondernemen/ ; //Fonds Wetenschappelijk Onderzoek/ ; //KU Leuven/ ; PIPF-2023/ECO-29442//Consejer&#xed;a de Educaci&#xf3;n, Ciencia y Universidades, Comunidad de Madrid/ ; CNS2022-135237//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; PID2022-136719NB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; RYC2018-023847-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; //Complutense University of Madrid, Spain/ ; DEB 1737758//Directorate for Biological Sciences/ ; //ESF Investing in your future/ ; }, mesh = {*Plant Nectar/chemistry/metabolism ; *Bacteria/metabolism/genetics ; Microbiota ; *Research ; Animals ; Flowers/microbiology ; }, abstract = {An emerging focus of research at the intersection of botany, zoology, and microbiology is the study of floral nectar as a microbial habitat, referred to as the nectar microbiome, which can alter plant-pollinator interactions. Studies on these microbial communities have primarily focused on yeasts, and it was only about a decade ago that bacteria began to be studied as widespread inhabitants of floral nectar. This review aims to give an overview of the current knowledge on nectar bacteria, with emphasis on evolutionary origin, dispersal mode, effects on nectar chemistry and plant-animal interactions, community assembly, agricultural applications, and their use as model systems in ecological research. We further outline gaps in our understanding of the ecological significance of these microorganisms, their response to environmental changes, and the potential cascading effects.}, }
@article {pmid39716385, year = {2025}, author = {Lu, Z and Entwistle, E and Kuhl, MD and Durrant, AR and Barreto Filho, MM and Goswami, A and Morris, JJ}, title = {Coevolution of marine phytoplankton and Alteromonas bacteria in response to pCO2 and coculture.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39716385}, issn = {1751-7370}, mesh = {*Phytoplankton/growth &amp; development/genetics/metabolism ; *Carbon Dioxide/metabolism ; *Alteromonas/growth &amp; development/genetics/metabolism ; *Seawater/microbiology/chemistry ; *Biological Evolution ; Diatoms/growth &amp; development/genetics ; Coculture Techniques ; Prochlorococcus/growth &amp; development/genetics ; }, abstract = {As a result of human activity, Earth's atmosphere and climate are changing at an unprecedented pace. Models based on short-term experiments predict major changes will occur in marine phytoplankton communities in the future ocean, but rarely consider how evolution or interactions with other microbes may influence these changes. Here, we experimentally evolved several phytoplankton in coculture with a heterotrophic bacterium, Alteromonas sp. EZ55, under either present-day or predicted future pCO2 conditions. Growth rates of phytoplankton generally increased over time under both conditions, but only Thalassiosira oceanica had evidence of a growth rate tradeoff in the ancestral environment after evolution at elevated pCO2. The growth defects observed in ancestral Prochlorococcus cultures at elevated pCO2 and in axenic culture were diminished after evolution, possibly due to regulatory mutations in antioxidant genes. Except for Prochlorococcus, mutational profiles suggested phytoplankton experienced primarily purifying selection, but most Alteromonas lineages showed evidence of directional selection, where evolution appeared to favor a metabolic switch between growth on small organic acids with cyanobacteria versus catabolism of more complex carbon substrates with eukaryotic phytoplankton. Evolved Alteromonas were also poorer "helpers" for Prochlorococcus, consistent with that interaction being a competitive Black Queen process rather than a true mutualism. This work provides new insights on how phytoplankton will respond to increased pCO2 and on the evolutionary mechanisms governing phytoplankton:bacteria interactions. It also clearly demonstrates that both evolution and interspecies interactions must be considered to predict future marine biogeochemistry.}, }
@article {pmid39715919, year = {2024}, author = {Jiang, ZB and Zhang, H and Tian, JJ and Guo, HH and Zhou, LR and Ma, XL}, title = {The Microbial Diversity of Biological Moss Crust: Application in Saline-Alkali Soil Management.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {162}, pmid = {39715919}, issn = {1432-184X}, support = {82160672//the National Natural Science Foundation of China/ ; 2022AAC05041 and 2023AAC05048//Outstanding Youth Program of Ningxia Natural Science Foundation/ ; 2021BEB04019//the Key R&amp;D Projects in Ningxia/ ; 2021AAC03210 and 2019AAC03113//the Ningxia Natural Science Foundation/ ; }, mesh = {*Soil/chemistry ; *Soil Microbiology ; *Bryophyta/microbiology ; China ; Biodiversity ; Alkalies/analysis ; Salinity ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Chlorophyll/analysis ; }, abstract = {Soil salinization poses a substantial threat to global food security, particularly under the influence of climate change, and is recognized as one of the most urgent challenges in land degradation. This study aims to elucidate the challenges associated with managing arid and semi-arid saline-alkali lands in China's Ningxia province and propose feasible solutions. To assess moss crust colonization, we measured changes in organic matter and chlorophyll levels. Additionally, we investigated the impact of an interlayer composed of Goji berry root bark using liquid chromatography-mass spectrometry analysis, biological enzyme activity analysis, and metagenomic sequencing. A total of 45 endophytes were isolated from the moss crust. The most significant colonization of moss crusts was observed when the Goji berry root bark was used as the interlayer, resulting in a significant increase in chlorophyll content. Several responses were identified as pivotal factors facilitating moss crust growth when the Goji berry root bark was used as the interlayer. In saline-alkali soil, the Goji berry root bark interlayer increased the activities of sucrase, urease, and alkaline phosphatase. Metagenomic data analysis revealed variations in the relative abundance of microorganisms at the phylum level, although these differences were not statistically significant. Evaluation of the impact of physical isolation and moss crust transplantation on the ecological restoration of saline-alkali soil using liquid chromatography-tandem mass spectrometry and metagenomic sequencing indicated that the Goji berry root bark as a physical isolation method promotes moss crust colonization in saline-alkali soil and increases soil organic matter and nutrient elements, offering valuable insights for the ecological management of saline-alkali land and serving as a reference for future research in this field.}, }
@article {pmid39714209, year = {2025}, author = {Payne, PE and Knobbe, LN and Chanton, P and Zaugg, J and Mortazavi, B and Mason, OU}, title = {Uncovering novel functions of the enigmatic, abundant, and active Anaerolineae in a salt marsh ecosystem.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0116224}, pmid = {39714209}, issn = {2379-5077}, support = {2342607//National Science Foundation (NSF)/ ; 1643486//National Science Foundation (NSF)/ ; 1438092//National Science Foundation (NSF)/ ; 503678//Joint Genome Institute (JGI)/ ; }, mesh = {*Wetlands ; Rhizosphere ; Metagenome ; Soil Microbiology ; Ecosystem ; Genome, Bacterial ; }, abstract = {Anaerolineae, particularly uncultured representatives, are one of the most abundant microbial groups in coastal salt marshes, dominating the belowground rhizosphere, where over half of plant biomass production occurs. However, this class generally remains poorly understood, particularly in a salt marsh context. Here, novel Anaerolineae metagenome-assembled genomes (MAGs) were generated from the salt marsh rhizosphere representing Anaerolineales, Promineifilales, JAAYZQ01, B4-G1, JAFGEY01, UCB3, and Caldilineales orders. Metagenome and metatranscriptome reads were mapped to annotated MAGs, revealing nearly all Anaerolineae encoded and transcribed genes required for oxidation of carbon compounds ranging from simple sugars to complex polysaccharides, fermentation, and carbon fixation. Furthermore, the majority of Anaerolineae expressed genes involved in anaerobic and aerobic respiration and secondary metabolite production. The data revealed that the belowground salt marsh Anaerolineae in the rhizosphere are important players in carbon cycling, including degradation of simple carbon compounds and more recalcitrant plant material, such as cellulose, using a diversity of electron acceptors and represent an unexplored reservoir of novel secondary metabolites.IMPORTANCEGiven that coastal salt marshes are recognized as biogeochemical hotspots, it is fundamentally important to understand the functional role of the microbiome in this ecosystem. In particular, Anaerolineae are abundant members of the salt marsh rhizosphere and have been identified as core microbes, suggesting they play an important functional role. Yet, little is known about the metabolic pathways encoded and expressed in this abundant salt marsh clade. Using an 'omics-based approach, we determined that Anaerolineae are capable of oxidizing a range of carbon compounds, including simple sugars to complex carbon compounds, while also encoding fermentation and carbon fixation. Surprisingly, Anaerolineae encoded and transcribed genes involved in aerobic respiration, which was unexpected given the reduced nature of the salt marsh rhizosphere. Finally, the majority of Anaerolineae appear to be involved in secondary metabolite production, suggesting that this group represents an unexplored reservoir of novel and important secondary metabolites.}, }
@article {pmid39714150, year = {2025}, author = {Beizman-Magen, Y and Orevi, T and Kashtan, N}, title = {Hydration conditions as a critical factor in antibiotic-mediated bacterial competition outcomes.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0200424}, pmid = {39714150}, issn = {1098-5336}, support = {220020475//James S. McDonnell Foundation (JSMF)/ ; 12-02-0046//The minisitry of Agriculture and rural development, Israel/ ; }, mesh = {*Bacillus/physiology/metabolism/drug effects ; *Pseudomonas syringae/physiology/drug effects ; *Xanthomonas/physiology/drug effects ; *Anti-Bacterial Agents/pharmacology/metabolism ; *Microbial Interactions ; *Water ; *Antibiosis ; }, abstract = {Antibiotic secretion plays a pivotal role in bacterial interference competition; yet, the impact of environmental hydration conditions on such competition is not well understood. Here, we investigate how hydration conditions affect interference competition among bacteria, studying the interactions between the antibiotic-producing Bacillus velezensis FZB42 and two bacterial strains susceptible to its antibiotics: Xanthomonas euvesicatoria 85-10 and Pseudomonas syringae DC3000. Our results show that wet-dry cycles significantly modify the response of the susceptible bacteria to both the supernatant and cells of the antibiotic-producing bacteria, compared to constantly wet conditions. Notably, X. euvesicatoria shows increased protection against both the cells and supernatants of B. velezensis under wet-dry cycles, while P. syringae cells become more susceptible under wet-dry cycles. In addition, we observed a reciprocal interaction between P. syringae and B. velezensis, where P. syringae inhibits B. velezensis under wet conditions. Our findings highlight the important role of hydration conditions in shaping bacterial interference competition, providing valuable insights into the microbial ecology of water-unsaturated surfaces, with implications for applications such as biological control of plant pathogens and mitigating antibiotic resistance.IMPORTANCEOur study reveals that hydration conditions, particularly wet-dry cycles, significantly influence antibiotic-mediated competition between bacterial species. We revealed that the effectiveness of antibiotics produced by Bacillus velezensis against two susceptible bacterial species: Xanthomonas and Pseudomonas varies based on these hydration conditions. Unlike traditional laboratory environments, many real-world habitats, such as soil, plant surfaces, and even animal skin, undergo frequent wet-dry cycles. These conditions affect bacterial competition dynamics and outcomes, with wet-dry cycles providing increased protection for some bacteria while making others more susceptible. Our findings highlight the importance of considering environmental hydration when studying microbial interactions and developing biological control strategies. This research has important implications for improving agricultural practices and understanding natural microbial ecosystems.}, }
@article {pmid39711055, year = {2025}, author = {Mant, D and Orevi, T and Kashtan, N}, title = {Impact of micro-habitat fragmentation on microbial population growth dynamics.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39711055}, issn = {1751-7370}, support = {//Interdisciplinary Data Science Research/ ; 220020475//James S. McDonnell Foundation/ ; 1322/23//Israel Science Foundation/ ; }, mesh = {*Ecosystem ; *Escherichia coli/growth &amp; development ; Population Dynamics ; }, abstract = {Microbial communities thrive in virtually every habitat on Earth and are essential to the function of diverse ecosystems. Most microbial habitats are not spatially continuous and well-mixed, but rather composed, at the microscale, of many isolated or semi-isolated local patches of different sizes, resulting in partitioning of microbial populations into discrete local populations. The impact of this spatial fragmentation on population dynamics is not well-understood. Here, we study how such variably sized micro-habitat patches affect the growth dynamics of clonal microbial populations and how dynamics in individual patches dictate those of the metapopulation. To investigate this, we developed the μ-SPLASH, an ecology-on-a-chip platform, enabling the culture of microbes in microscopic landscapes comprised of thousands of microdroplets, with a wide range of sizes. Using the μ-SPLASH, we cultured the model bacteria Escherichia coli and based on time-lapse microscopy, analyzed the population dynamics within thousands of individual droplets. Our results reveal that growth curves substantially vary with droplet size. Although growth rates generally increase with drop size, reproductive success and the time to approach carrying capacity, display non-monotonic patterns. Combining μ-SPLASH experiments with computational modeling, we show that these patterns result from both stochastic and deterministic processes, and demonstrate the roles of initial population density, patchiness, and patch size distribution in dictating the local and metapopulation dynamics. This study reveals basic principles that elucidate the effects of habitat fragmentation and population partitioning on microbial population dynamics. These insights deepen our understanding of natural microbial communities and have significant implications for microbiome engineering.}, }
@article {pmid39710833, year = {2024}, author = {Bullington, JA and Langenfeld, K and Phaneuf, JR and Boehm, AB and Francis, CA}, title = {Microbial Community of a Sandy Beach Subterranean Estuary is Spatially Heterogeneous and Impacted by Winter Waves.}, journal = {Environmental microbiology}, volume = {26}, number = {12}, pages = {e70009}, doi = {10.1111/1462-2920.70009}, pmid = {39710833}, issn = {1462-2920}, support = {2024504//National Science Foundation, Understanding the Rules of Life: Microbiome Theory and Mechanisms (URoL:MTM)/ ; //Stanford McGee and Levorsen Research Grant/ ; //ARCO Stanford Graduate Fellowship/ ; }, mesh = {*Microbiota/genetics ; *Estuaries ; *Seasons ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Bathing Beaches ; California ; *Seawater/microbiology ; Archaea/genetics/classification ; Phylogeny ; }, abstract = {Subterranean estuaries (STEs) are critical ecosystems at the interface of meteoric groundwater and subsurface seawater that are threatened by sea level rise. To characterize the influence of tides and waves on the STE microbial community, we collected porewater samples from a high-energy beach STE at Stinson Beach, California, USA, over the two-week neap-spring tidal transition during both a wet and dry season. The microbial community, analyzed by 16S rRNA gene (V4) amplicon sequencing, clustered according to consistent physicochemical features found within STEs. The porewater community harbored relatively abundant Proteobacteria, Verrucomicrobiota, and Bacteroidota, as well as members of the archaeal DPANN superphylum and bacterial Candidate Phyla Radiation (CPR). Tidal conditions were not associated with microbial community composition; however, a wave overtopping event significantly impacted the beach microbiome. As a baseline for environmental change, our results elucidate the unique dynamics of a STE microbiome with unprecedented temporal resolution, highlighting the transport of cellular material through beach porewater due to waves.}, }
@article {pmid39710772, year = {2025}, author = {Ali, A and Zhong, X and Wang, Q and Xu, H}, title = {Use of a broad β-diversity for bioassessment of salinity stress on community homogeneity in marine environments.}, journal = {Environmental science and pollution research international}, volume = {32}, number = {3}, pages = {1167-1175}, pmid = {39710772}, issn = {1614-7499}, support = {31672308//The Natural Science Foundation of China/ ; 41076089//The Natural Science Foundation of China/ ; ZR2022QD065//Youth Project of the Natural Science Foundation of Shandong Province, China/ ; }, mesh = {*Salinity ; China ; *Salt Stress ; *Biodiversity ; Ecosystem ; Seawater/chemistry ; }, abstract = {To determine the feasibility of β-diversity measures to evaluate the impact of salinity stress on community homogeneity in marine environments, a 1-month bioassay was conducted using the protozoan assemblage as the test community. The test samples were collected using the slide method in coastal waters of the Yellow Sea, northern China. Five treatments were designed according to a salinity gradient of 9, 19, 29, 39, and 49 PSU. The homogeneity of the test community showed significant variability in both composition and abundance patterns among five treatments. The multivariate dispersion measure on compositional data was linearly associated with the salinity stress compared to those on abundance alone or in combination with occurrence. The traditional β-diversity index represented a different behavior from that of the multivariate dispersion measures. These findings suggest that the composition-based multivariate dispersion may be a useful tool to evaluate the global salinity stress on community homogeneity in marine ecosystems.}, }
@article {pmid39710259, year = {2025}, author = {Callaway, T and Perez, HG and Corcionivoschi, N and Bu, D and Fluharty, FL}, title = {International Symposium on Ruminant Physiology: The holobiont concept in ruminant physiology-More of the same, or something new and meaningful to food quality, food security, and animal health?.}, journal = {Journal of dairy science}, volume = {108}, number = {7}, pages = {7567-7575}, doi = {10.3168/jds.2024-25847}, pmid = {39710259}, issn = {1525-3198}, mesh = {Animals ; *Ruminants/physiology/microbiology ; Gastrointestinal Microbiome ; Humans ; *Food Security ; *Food Quality ; Food Supply ; }, abstract = {The holobiont concept has emerged as an attempt to recognize and describe the myriad interactions and physiological signatures inherent to a host organism, as affected by the microbial communities that colonize and co-inhabit the environment within which the host resides. The field acknowledges and draws upon principles from evolution, ecology, genetics, and biology, and in many respects has been pushed by the advent of high throughput DNA sequencing and, to a lesser extent, other omics-based technologies. Despite the explosion in data generation and analyses, much of our current understanding of the human and ruminant holobiont is based on compositional forms of data and thereby, restricted to describing host phenotypes via associative or correlative studies. So, where to from here? We will discuss some past findings arising from ruminant and human gut microbiota research and seek to evaluate the rationale, progress, and opportunities that might arise from the holobiont approach to the ruminant and human host. In particular, we will consider what is a "good" or "bad" host gastrointestinal microbiome in different scenarios, as well as potential avenues to sustain or alter the holobiont. Although the holobiont approach might improve food quality, food security, and animal health, these benefits will most likely be achieved via a judicious and pragmatic compromise in data generation, both in terms of its scale as well as its generation, in context with the forgotten knowledge of ruminant and human physiology.}, }
@article {pmid39709274, year = {2025}, author = {Kerkar, AU and Sutherland, KR and Thompson, AW}, title = {Non-viral predators of marine picocyanobacteria.}, journal = {Trends in microbiology}, volume = {33}, number = {5}, pages = {558-568}, doi = {10.1016/j.tim.2024.11.010}, pmid = {39709274}, issn = {1878-4380}, mesh = {*Prochlorococcus/physiology/growth &amp; development ; *Synechococcus/physiology/growth &amp; development ; Ecosystem ; *Seawater/microbiology ; Aquatic Organisms ; Food Chain ; }, abstract = {The Earth's most abundant photosynthetic cells, the picocyanobacteria - Prochlorococcus and Synechococcus - play a fundamental global role in aquatic ecosystems. The success of these picocyanobacteria is interpreted through a cross-scale systems framework that integrates bottom-up controls on growth (e.g., nutrients and light), diversity, and the selective pressures and response to predation. While viral predators are well studied and experimentally tractable, the diverse non-viral predators of picocyanobacteria are disconnected from this framework and experimentally challenging, leaving a major gap in understanding the picocyanobacteria. This review presents existing research on non-viral picocyanobacterial predators and promising research frontiers that will expand knowledge of the ecology and evolution of these crucial microorganisms.}, }
@article {pmid39708482, year = {2025}, author = {Zhao, H and Hu, X and Guan, S and Cai, J and Li, W and Zhang, D and Feng, Y and Zhu, W and Marzorati, M and Li, B and Zhang, X and Tian, J}, title = {Capilliposide A alleviates DSS-induced colitis by regulating the intestinal flora and its metabolites of origin.}, journal = {International immunopharmacology}, volume = {146}, number = {}, pages = {113858}, doi = {10.1016/j.intimp.2024.113858}, pmid = {39708482}, issn = {1878-1705}, mesh = {Animals ; Dextran Sulfate ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Saponins/therapeutic use/pharmacology ; Disease Models, Animal ; Colon/pathology/drug effects/microbiology ; *Anti-Inflammatory Agents/therapeutic use/pharmacology ; *Colitis/drug therapy/chemically induced ; Male ; *Triterpenes/therapeutic use/pharmacology ; Mice, Inbred C57BL ; *Colitis, Ulcerative/drug therapy/chemically induced ; Cytokines/metabolism ; Intestinal Mucosa/drug effects ; Humans ; }, abstract = {Ulcerative colitis is a chronic idiopathic inflammatory disease that impacts the mucous membrane of the colon. Lately, the incidence and prevalence of UC has been increasing globally. However, there are significant side effects of existing drugs for UC intervention. Accordingly, there is a pressing demand to explore novel bioactive substances for addressing UC. Natural product saponins have attracted great attention due to their obvious anti-colitis potential. Capilliposide A is a triterpenoid saponin, which is derived from Lysimachia capillipes Hemsl., exhibits good anti-inflammatory activity. Nonetheless, the impact and mechanism of CPS-A on ulcerative colitis remains obscure. This study aimed to investigate the therapeutic effects of CPS-A on the dextran sulphate sodium induced colitis mouse model and explore its mechanism. The efficacy and safety of CPS-A were evaluated in a well-established dextran sodium sulfate (DSS)-induced colitis mice model. Disease progression was monitored via clinical symptoms, histopathological examination, quantification of inflammatory cytokines, and epithelial barrier function evaluation. Plasma samples and intestinal contents were collected for non-targeted metabolomics and 16sRNA sequencing, respectively, to jointly evaluate the mechanism of action. CPS-A alleviated colitis by improving weight, Disease activity index score, histopathology, goblet cell, colon length, and expression of inflammatory factors. Moreover, CPS-A effectively preserved the integrity of the intestinal barrier by enhancing the expression of tight junction proteins and mucin in the colonic tissue of mice. Furthermore, CPS-A exerted a regulatory effect on the composition of the gut microbiota, promoting bacterial richness and diversity. It not only suppressed the abundance of detrimental bacteria while enhancing the abundance of advantageous bacteria, but also modulated the metabolites derived from the intestinal flora. Importantly, correlation analysis shows that these indicators are highly correlated. This study revealed that CPS-A exhibits a favorable therapeutic efficacy against colitis, primarily attributed to its ability to modulate the gut microbiota their associated metabolites as the key mechanisms of action.}, }
@article {pmid39708146, year = {2024}, author = {Zhao, L and Zhang, S and Li, J and Zhang, C and Xiao, R and Bai, X and Xu, H and Zhang, F}, title = {Unveiling Diversity and Function: Venom-Associated Microbes in Two Spiders, Heteropoda venatoria and Chilobrachys guangxiensis.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {156}, pmid = {39708146}, issn = {1432-184X}, mesh = {Animals ; *Spiders/microbiology/physiology ; *Spider Venoms ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Apoptosis ; Symbiosis ; Humans ; Cell Line, Tumor ; High-Throughput Nucleotide Sequencing ; Anti-Inflammatory Agents/pharmacology ; }, abstract = {Spiders are natural predators of agricultural pests, primarily due to the potent venom in their venom glands. Spider venom is compositionally complex and holds research value. This study analyzes the diversity of symbiotic bacteria in spider venom glands and venom, as well as the biological activity of culturable symbiotic bacteria. Focusing on the venom glands and venom of Heteropoda venatoria and Chilobrachys guangxiensis, we identified a diverse array of microorganisms. High-throughput sequencing detected 2151 amplicon sequence variants (ASVs), spanning 31 phyla, 75 classes, and 617 genera. A total of 125 strains of cultivable bacteria were isolated. Using the Oxford cup method, crude extracts from 46 of these strains exhibited inhibitory effects against at least one indicator bacterium. MTT (Thiazolyl blue) assays revealed that the crude extracts from 43 strains had inhibitory effects on tumor cell line MGC-803 growth. Additionally, DAPI (4',6-diamidino-2'-phenylindole) staining and flow cytometry were employed to detect cell apoptosis. The anti-inflammatory activity of nine bacterial strains was assessed using a NO assay kit and enzyme-linked immunosorbent assay (ELISA). This study further investigated the biological activity of venom, exploring the relationship between the venom and the functional activity of venom-associated bacteria.}, }
@article {pmid39708144, year = {2024}, author = {Quevedo-Caraballo, S and Roldán, A and Álvarez-Pérez, S}, title = {Demethylation Inhibitor Fungicides Have a Significantly Detrimental Impact on Population Growth and Composition of Nectar Microbial Communities.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {160}, pmid = {39708144}, issn = {1432-184X}, support = {PIPF-2023/ECO-29442//Consejer&#xed;a de Educaci&#xf3;n, Ciencia y Universidades, Comunidad de Madrid/ ; RYC2018-023847-I, CNS2022-135237//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {*Fungicides, Industrial/pharmacology ; *Plant Nectar ; *Microbiota/drug effects ; Bacteria/classification/drug effects/isolation &amp; purification/genetics ; Demethylation ; Fungi/drug effects/classification/isolation &amp; purification ; Metschnikowia/drug effects ; Flowers/microbiology/growth &amp; development ; }, abstract = {Demethylation inhibitor (DMI) fungicides are a mainstay of modern agriculture due to their widespread use for crop protection against plant-pathogenic fungi. However, DMI residues can disperse and persist in the environment, potentially affecting non-target fungi. Previous research has demonstrated that DMIs and other fungicides inhibit yeast growth in floral nectar microbial communities and decrease fungal richness and diversity of exposed flowers with no apparent effect on bacteria. Nevertheless, the effect of DMIs on the population growth of different species of nectar inhabitants and the dynamics of these microbial communities remains understudied. To address these issues, in this study we created synthetic microbial communities including yeasts (Metschnikowia reukaufii and Metschnikowia pulcherrima) and bacteria (Rosenbergiella epipactidis and Comamonas sp.) and propagated them in culture media containing different DMIs (imazalil, propiconazole, and prothioconazole) at different doses or no fungicide. Our results showed that DMIs have a significant impact on some of the most common microbial inhabitants of floral nectar by favoring the growth of bacteria over yeasts. Furthermore, habitat generalists such as M. pulcherrima and Comamonas sp. were more impacted by the presence of fungicides than the nectar specialists M. reukaufii and R. epipactidis, especially upon dispersal across habitat patches. Future research should determine if the patterns observed in the present study hold true for other species of nectar microbes and explore the interaction between growth limitation due to fungicide presence, dispersal limitation, and other mechanisms involved in community assembly in floral nectar.}, }
@article {pmid39708139, year = {2024}, author = {Zhao, Z and Liu, S and Jiang, S and Zhang, D and Sha, Z}, title = {Diversity and Potential Metabolic Characteristics of Culturable Copiotrophic Bacteria That Can Grow on Low-Nutrient Medium in Zhenbei Seamount in the South China Sea.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {157}, pmid = {39708139}, issn = {1432-184X}, support = {LSKJ202203102//the Science and Technology Innovation Project of Laoshan Laboratory/ ; XDB42000000//the Strategic Priority Research Program of Chinese Academy of Sciences/ ; 42221005//the NSFC Innovative Group Grant/ ; 42376143//the National Natural Science Foundation of China/ ; }, mesh = {*Seawater/microbiology ; China ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification/growth &amp; development ; Gammaproteobacteria/metabolism/genetics/isolation &amp; purification/classification/growth &amp; development ; Phylogeny ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Nitrates/metabolism ; Culture Media/chemistry ; Nutrients/metabolism ; Alphaproteobacteria/metabolism/genetics/isolation &amp; purification/classification/growth &amp; development ; Vibrio/metabolism/genetics/isolation &amp; purification/growth &amp; development/classification ; }, abstract = {Oligotrophs are predominant in nutrient-poor environments, but copiotrophic bacteria may tolerate conditions of low energy and can also survive and thrive in these nutrient-limited conditions. In the present study, we isolated 648 strains using a dilution plating method after enrichment for low-nutrient conditions. We collected 150 seawater samples at 21 stations in different parts of the water column at the Zhenbei Seamount in the South China Sea. The 648 isolated copiotrophic strains that could grow on low-nutrient medium were in 21 genera and 42 species. A total of 99.4% (644/648) of the bacteria were in the phylum Pseudomonadota, with 73.3% (472/644) in the class Gammaproteobacteria and 26.7% (172/644) in the class Alphaproteobacteria. Among the 42 representative isolates, Pseudoalteromonas arabiensis, Roseibium aggregatum, and Vibrio neocaledonicus were present in all layers of seawater and at almost all of the stations. Almost half of these species (20/42) contained genes that performed nitrate reduction, with confirmation by nitrate reduction testing. These isolates also contained genes that functioned in sulfur metabolism, including sulfate reduction, thiosulfate oxidation, thiosulfate disproportionation, and dimethylsulfoniopropionate degradation. GH23, CBM50, GT4, GT2, and GT51 were the main carbohydrate-active enzymes (CAZymes), and these five enzymes were present in all or almost all of the isolated strains. The most abundant classes of CAZymes were those associated with the degradation of chitin, starch, and cellulose. Collectively, our study of marine copiotrophic bacteria capable of growing on low-nutrient medium demonstrated the diversity of these species and their potential metabolic characteristics.}, }
@article {pmid39708121, year = {2024}, author = {Grisnik, M and Walker, DM}, title = {Bat Cutaneous Microbial Assemblage Functional Redundancy Across a Host-Mediated Disturbance.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {161}, pmid = {39708121}, issn = {1432-184X}, support = {32801-00803//Tennessee Wildlife Resources Agency,United States/ ; }, mesh = {*Chiroptera/microbiology ; Animals ; *Seasons ; *Bacteria/genetics/classification/isolation &amp; purification ; *Skin/microbiology ; *Microbiota ; Ascomycota/genetics/physiology ; Ecosystem ; }, abstract = {Understanding the processes and factors that influence the structure of host-associated microbial assemblages has been a major area of research as these assemblages play a role in host defense against pathogens. Previous work has found that bacterial taxa within bat cutaneous microbial assemblages have antifungal capabilities against the emerging fungal pathogen, Pseudogymnoascus destructans. However, our understanding of natural fluctuations in these cutaneous microbial assemblages over time due to shifts in host habitat is lacking. The objective of this work was to understand how the taxonomic and functional bat cutaneous microbial assemblage responds to seasonal shifts in host habitat. We hypothesized that at the community level, there will be turnover in taxonomic structure but functional redundancy across seasons. On a finer scale, we hypothesized that there will be differences in the relative abundance of functional genes that code for select pathways across seasons. Results showed that, on a broad scale, the bat cutaneous microbial assemblage is seasonally taxonomically dynamic but functionally redundant. Additionally, although there was almost complete taxonomic turnover between winter and summer bat microbial assemblages, there was no difference in assemblage structure across winters. This functional redundancy was also observed at finer scales, with no differences in the abundance of genes within pathways of hypothesized importance across seasons or winters. Taken together, results suggest species sorting mechanisms correlated with shifts in host habitat use, drive taxonomic but not functional host-associated cutaneous microbial community assembly.}, }
@article {pmid39708106, year = {2024}, author = {Singh, S and Singh, AK and Pradhan, B and Tripathi, S and Kumar, KS and Chand, S and Rout, PR and Shahid, MK}, title = {Harnessing Trichoderma Mycoparasitism as a Tool in the Management of Soil Dwelling Plant Pathogens.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {158}, pmid = {39708106}, issn = {1432-184X}, mesh = {*Trichoderma/physiology ; *Soil Microbiology ; *Plant Diseases/microbiology/prevention &amp; control ; Pest Control, Biological/methods ; Agriculture/methods ; Plants/microbiology ; Biological Control Agents ; Soil/chemistry ; }, abstract = {Maintaining and enhancing agricultural productivity for food security while preserving the ecology and environment from the harmful effects of toxicants is the main challenge in modern monoculture farming systems. Microbial biological agents can be a promising substitute for traditional synthetic pesticides to manage plant diseases. Trichoderma spp. are soil-dwelling ascomycete fungi and are common biocontrol agents against diverse phytopathogens. Trichoderma-based biocontrol techniques can regulate and control soil-borne plant diseases through mechanisms such as mycoparasitism, the production of antibiotics and hydrolytic enzymes, rhizo-sphere competence, the effective competition for available resources, induction of plant resistance and facilitation of plant growth. Numerous secondary metabolites produced by Trichoderma spp. are reported to prevent the development of soil-borne plant disease. Thus, Trichoderma spp. may have direct and indirect biological impacts on the targeted plant pathogens. Furthermore, this review discusses the convenient implications and challenges of applying Trichoderma-based strategies in agricultural settings. Overall, the assessment underscores the potential of Trichoderma as a sustainable and effective tool for mitigating soil-borne pathogens, highlighting avenues for future research and applications.}, }
@article {pmid39708073, year = {2024}, author = {Han, GH and Yu, J and Kang, MJ and Park, MJ and Noh, CH and Kim, YJ and Kwon, KK}, title = {Correction to: Phylosymbiosis in Seven Wild Fish Species Collected Off the Southern Coast of Korea: Skin Microbiome Most Strongly Reflects Evolutionary Pressures.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {159}, doi = {10.1007/s00248-024-02478-w}, pmid = {39708073}, issn = {1432-184X}, }
@article {pmid39708062, year = {2024}, author = {Nonthijun, P and Tanunchai, B and Schroeter, SA and Wahdan, SFM and Alves, EG and Hilke, I and Buscot, F and Schulze, ED and Disayathanoowat, T and Purahong, W and Noll, M}, title = {Feels Like Home: A Biobased and Biodegradable Plastic Offers a Novel Habitat for Diverse Plant Pathogenic Fungi in Temperate Forest Ecosystems.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {155}, pmid = {39708062}, issn = {1432-184X}, mesh = {*Forests ; *Fungi/genetics/metabolism/classification ; *Biodegradable Plastics/metabolism ; *Trees/microbiology ; Soil Microbiology ; Plant Diseases/microbiology ; Biodegradation, Environmental ; Ecosystem ; Soil/chemistry ; Plant Leaves/microbiology ; }, abstract = {Poly(butylene succinate-co-adipate) (PBSA), a biodegradable plastic, is significantly colonized and degraded by soil microbes under natural field conditions, especially by fungal plant pathogens, raising concerns about potential economic losses. This study hypothesizes that the degradation of biodegradable plastics may increase the presence and abundance of plant pathogens by serving as an additional carbon source, ultimately posing a risk to forest ecosystems. We investigated (i) fungal plant pathogens during the exposure of PBSA in European broadleaved and coniferous forests (two forest types), with a specific focus on potential risk to tree health, and (ii) the response of such fungi to environmental factors, including tree species, soil pH, nutrient availability, moisture content, and the physicochemical properties of leaf litter layer. Next-generation sequencing (NGS) revealed that PBSA harbored a total of 318 fungal plant pathogenic amplicon sequence variants (ASVs) belonging to 108 genera. Among the identified genera (Alternaria, Nectria, Phoma, Lophodermium, and Phacidium), some species have been reported as causative agents of tree diseases. Plenodomus was present in high relative abundances on PBSA, which have not previously been associated with disease in broadleaved and coniferous forests. Furthermore, the highest number of fungal plant pathogens were detected at 200 days of PBSA exposure (112 and 99 fungal plant pathogenic ASV on PBSA degraded under Q. robur and F. sylvatic-dominated forest, respectively), which was double compared mature leaves and needles from the same forest sites. These findings suggest that PBSA attracts fungal plant pathogens in forests as an additional carbon source, potentially leading to increased disease outbreaks and disrupting the stability of forest ecosystems. The fungal plant pathogenic community compositions were mainly shaped by forest type, PBSA exposure time, site locations, leaf litter layer water content, and N:P ratio from leaf litter layer in both forest types. This study provides valuable insights into the potential risks posed by biodegradable plastic degradation in forests after 200 and 400 days of exposure, respectively. Further comprehensive evaluations of their effects on tree health and ecosystems, ideally on a long-term basis, are needed. These evaluations should include integrating microbial investigation, soil health monitoring, and ecosystem interaction assessments. Nevertheless, it should be noted that our interpretation of plant pathogens is solely based on high-throughput sequencing, bioinformatics, and annotation tools.}, }
@article {pmid39703713, year = {2024}, author = {Sheng, Y and Zeng, X and Zhao, L and Li, Y}, title = {Editorial: Microbial involvement in biogeochemical cycling and contaminant transformations at land-water ecotones.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1525521}, pmid = {39703713}, issn = {1664-302X}, }
@article {pmid39701829, year = {2025}, author = {McAlister, JS and Blum, MJ and Bromberg, Y and Fefferman, NH and He, Q and Lofgren, E and Miller, DL and Schreiner, C and Candan, KS and Szabo-Rogers, H and Reed, JM}, title = {An interdisciplinary perspective of the built-environment microbiome.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {1}, pages = {}, pmid = {39701829}, issn = {1574-6941}, support = {CCF 2200140//U.S. National Science Foundation/ ; }, mesh = {*Microbiota ; *Built Environment ; Humans ; Interdisciplinary Research ; }, abstract = {The built environment provides an excellent setting for interdisciplinary research on the dynamics of microbial communities. The system is simplified compared to many natural settings, and to some extent the entire environment can be manipulated, from architectural design to materials use, air flow, human traffic, and capacity to disrupt microbial communities through cleaning. Here, we provide an overview of the ecology of the microbiome in the built environment. We address niche space and refugia, population, and community (metagenomic) dynamics, spatial ecology within a building, including the major microbial transmission mechanisms, as well as evolution. We also address landscape ecology, connecting microbiomes between physically separated buildings. At each stage, we pay particular attention to the actual and potential interface between disciplines, such as ecology, epidemiology, materials science, and human social behavior. We end by identifying some opportunities for future interdisciplinary research on the microbiome of the built environment.}, }
@article {pmid39701529, year = {2025}, author = {Firkins, JL and Henderson, EL and Duan, H and Pope, PB}, title = {International Symposium on Ruminant Physiology: Current perspective on rumen microbial ecology to improve fiber digestibility.}, journal = {Journal of dairy science}, volume = {108}, number = {7}, pages = {7511-7529}, doi = {10.3168/jds.2024-25863}, pmid = {39701529}, issn = {1525-3198}, mesh = {Animals ; *Rumen/microbiology/metabolism/physiology ; *Dietary Fiber/metabolism ; *Ruminants/microbiology/physiology ; *Digestion/physiology ; Animal Feed ; Fermentation ; Diet/veterinary ; Bacteria/metabolism ; }, abstract = {Although cellulose has received the most attention, further research is needed for a complete comprehension of other fiber components in forage and nonforage fiber sources corresponding to the array of enzymes needed for depolymerization and resulting fermentation of sugars. Carbohydrate-active enzymes (CAZymes) have been described in detail herein, although new information will no doubt accumulate in the future. Known CAZymes are attributed to taxa that are easily detected via 16S rRNA gene profiling techniques, but such approaches have limitations. We describe how closely related species or strains expand into different niches depending on diet and the dynamic availability of remaining fibrous substrates. Moreover, expression of CAZymes and other enzymes such as in fermentation pathways can shift among strains and even within strains over time of incubation. We describe unique fibrolytic components of bacteria, protozoa, and fungi and emphasize the development of consortia that efficiently increase neutral detergent fiber degradability (NDFD). For example, more powerful genome-centric functional omics approaches combined with expanded bioinformatics and network analyses are needed to expand our current understanding of ruminal function and the bottlenecks that lead to among-study variation in NDFD. Specific examples highlighted include our lack of fundamental understanding why starch limits NDFD, whereas moderate inclusion of rumen-degraded protein, certain supplemental fatty acids (especially palmitic acid), and supplemental sugars sometimes stimulates NDFD. Current and future research must uncover deeper complexity in the rumen microbiome through a combination of approaches described herein to be followed by validation using novel cultivation studies and, ultimately, NDFD measured in vivo for integration with ruminant productivity traits.}, }
@article {pmid39699229, year = {2025}, author = {Anuforo, PC and Würz, B and Wick, LY and Kallies, R}, title = {Draft genome sequences of Pseudomonas chengduensis strain BW1 and Sphingobium sp. strain MK2 isolated from oil sands process-affected water.}, journal = {Microbiology resource announcements}, volume = {14}, number = {2}, pages = {e0067724}, pmid = {39699229}, issn = {2576-098X}, support = {57610608//Deutscher Akademischer Austauschdienst (DAAD)/ ; 57610608//MPR | Petroleum Technology Development Fund (PTDF)/ ; }, abstract = {Draft genomes of two phenanthrene-degrading bacterial isolates from oil sands process-affected water (OSPW) in Alberta, Canada were sequenced. Both isolates grew in close association on agar plates and were difficult to obtain axenically. They represent novel Pseudomonas chengduensis and Sphingobium sp. strains with genomes of 5.5 and 4.1 Mbases length, respectively.}, }
@article {pmid39699221, year = {2025}, author = {Lustermans, JJM and Sereika, M and Burdorf, LDW and Albertsen, M and Schramm, A and Marshall, IPG}, title = {Extracellular electron transfer genes expressed by candidate flocking bacteria in cable bacteria sediment.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0125924}, pmid = {39699221}, issn = {2379-5077}, support = {DNRF136//Danmarks Grundforskningsfond (DNRF)/ ; S004523N//Flanders Research FWO/ ; TopBOF//University Antwerp TopBOF program/ ; Microflora Danica//Poul Due Jensens Fond (Poul Due Jensen Foundation)/ ; HORIZON-MSCA-2023-PF-01: 101152850//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, mesh = {*Geologic Sediments/microbiology ; Electron Transport/genetics ; *Bacteria/genetics/metabolism/classification ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Oxidation-Reduction ; Phylogeny ; }, abstract = {UNLABELLED: Cable bacteria, filamentous sulfide oxidizers that live in sulfidic sediments, are at times associated with large flocks of swimming bacteria. It has been proposed that these flocks of bacteria transport electrons extracellularly to cable bacteria via an electron shuttle intermediate, but the identity and activity of these bacteria in freshwater sediment remain mostly uninvestigated. Here, we elucidate the electron exchange capabilities of the bacterial community by coupling metagenomics and metatranscriptomics to 16S rRNA amplicon-based correlations with cable bacteria over 155 days. We identified candidate flocking bacteria as bacteria containing genes for motility and extracellular electron transfer including synthesis genes for potential extracellular electron shuttles: phenazines and flavins. Based on these criteria, 22 MAGs were from candidate flockers, which constituted 21.4% of all 103 MAGs. Of the candidate flocking bacteria, 42.1% expressed extracellular electron transfer genes. The proposed flockers belonged to a large variety of metabolically versatile taxonomic groups: 18 genera spread across nine phyla. Our data suggest that cable bacteria in freshwater sediments engage in electric relationships with diverse exoelectrogenic microbes. This community, found in deeper anoxic sediment layers, is involved in sulfur, carbon, and metal (in particular Fe) cycling and indirectly utilizes oxygen here by extracellularly transferring electrons to cable bacteria.<br><br>IMPORTANCE: Cable bacteria are ubiquitous, filamentous bacteria that couple sulfide oxidation to the reduction of oxygen at up to centimeter distances in sediment. Cable bacterial impact extends beyond sulfide oxidation via interactions with other bacteria that flock around cable bacteria and use them as electron acceptor "shortcut" to oxygen. The exact nature of this interspecies electric interaction remained unknown. With metagenomics and metatranscriptomics, we determined what extracellular electron transport processes co-occur with cable bacteria, demonstrating the identity and metabolic capabilities of these potential flockers. In sediments, microbial activities are sharply divided into anaerobic and aerobic processes, with oxygen reaching only millimeters deep. Cable bacteria extend the influence of oxygen to several centimeters, revealing a new class of anaerobic microbial metabolism with cable bacteria as electron acceptors. This fundamentally changes our understanding of sediment microbial ecology with wide-reaching consequences for sulfur, metal (in particular Fe), and carbon cycling in freshwater and marine sediments.}, }
@article {pmid39698295, year = {2024}, author = {Bovio-Winkler, P and Cabezas, A and Etchebehere, C}, title = {Unveiling the hidden diversity and functional role of Chloroflexota in full-scale wastewater treatment plants through genome-centric analyses.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae050}, pmid = {39698295}, issn = {2730-6151}, abstract = {The phylum Chloroflexota has been found to exhibit high abundance in the microbial communities from wastewater treatment plants (WWTPs) in both aerobic and anaerobic systems. However, its metabolic role has not been fully explored due to the lack of cultured isolates. To address this gap, we use publicly available metagenome datasets from both activated sludge (AS) and methanogenic (MET) full-scale wastewater treatment reactors to assembled genomes. Using this strategy, 264 dereplicated, medium- and high-quality metagenome-assembled genomes (MAGs) classified within Chloroflexota were obtained. Taxonomic classification revealed that AS and MET reactors harbored distinct Chloroflexota families. Nonetheless, the majority of the annotated MAGs (166 MAGs with >85% completeness and < 5% contamination) shared most of the metabolic potential features, including the ability to degrade simple sugars and complex polysaccharides, fatty acids and amino acids, as well as perform fermentation of different products. While Chloroflexota MAGs from MET reactors showed the potential for strict fermentation, MAGs from AS harbored the potential for facultatively aerobic metabolism. Metabolic reconstruction of Chloroflexota members from AS unveiled their versatile metabolism and suggested a primary role in hydrolysis, carbon removal and involvement in nitrogen cycling, thus establishing them as fundamental components of the ecosystem. Microbial reference genomes are essential resources for understanding the potential functional role of uncultured organisms in WWTPs. Our study provides a comprehensive genome catalog of Chloroflexota for future analyses aimed at elucidating their role in these ecosystems.}, }
@article {pmid39697668, year = {2024}, author = {Roy, A and Ghosh, A and Bhadury, P}, title = {Delving deep into the draft genome of Mangrovibacter sp. SLW1, isolated from Sundarbans mangrove.}, journal = {Access microbiology}, volume = {6}, number = {8}, pages = {}, pmid = {39697668}, issn = {2516-8290}, abstract = {Mangrovibacter sp. SLW1, a Gram-negative, aerobic, motile bacterium, was isolated from mangrove litterfall in Sundarbans mangrove. The draft genome is 5.5 Mbp in size with 49.45 mol% guanine-cytosine (GC) content. The linear chromosome of the bacterium consists of 27 contigs with 7339 coding sequences. The detailed in silico analyses of the genome of Mangrovibacter sp. SLW1 provide information on ecological adaptation. The genome is a reservoir for multiple heavy metals and metalloid resistance gene clusters as well as exhibit metabolic capabilities for utilization of a wide range of carbohydrates. It also encodes for tris-catecholate siderophore and can regulate uptake of iron thereby may influence plant growth such as mangrove vegetation.}, }
@article {pmid39695543, year = {2024}, author = {Qin, K and Qing, J and Wang, Q and Li, Y}, title = {Epidemiological shifts in chronic kidney disease: a 30-year global and regional assessment.}, journal = {BMC public health}, volume = {24}, number = {1}, pages = {3519}, pmid = {39695543}, issn = {1471-2458}, support = {82170716//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; }, mesh = {Humans ; *Renal Insufficiency, Chronic/epidemiology/mortality ; Male ; Incidence ; *Global Health/statistics &amp; numerical data ; Female ; Middle Aged ; Adult ; Prevalence ; Aged ; *Global Burden of Disease ; Risk Factors ; Disability-Adjusted Life Years ; Adolescent ; Young Adult ; Quality-Adjusted Life Years ; }, abstract = {BACKGROUND: Chronic kidney disease (CKD) presents a growing global health challenge, with significant variability in disease burden across different regions and countries. This study aimed to analyze the trends in incidence, prevalence, mortality, and disability-adjusted life years (DALYs) for CKD from 1990 to 2019, utilizing data from the Global Burden of Disease Study.<br><br>METHODS: We conducted an in-depth study on the global and age-standardized incidence, prevalence, mortality, and DALYs of CKD, and assessed trends over a 30-year period. Additionally, we explored the associations between healthcare access and quality (HAQ), the Socio-Demographic Index (SDI), and CKD. Furthermore, we conducted a detailed analysis of six risk factors closely related to CKD, and based on these findings, provided strong evidence for enhancing the management of CKD.<br><br>RESULTS: In 2019, there were 18,986,903 cases of CKD, with an average annual percent change (AAPC) of 1.82 (95% CI&#x2009;=&#x2009;1.8 to 1.82) in incidence since 1990. The age-standardized incidence rate increased from 192.45 per 100,000 in 1990 to 233.65 per 100,000 in 2019. Prevalence also rose, with a total of 69,729,430 cases in 2019 and an AAPC of 1.19 (95% CI&#x2009;=&#x2009;1.19 to 1.2). Mortality and DALYs have increased correspondingly, with the mortality rate reaching 18.29 per 100,000 and total DALYs at 41,538,592 in 2019. The analysis showed that higher HAQ levels are associated with better outcomes in terms of lower mortality and DALY rates, whereas lower HAQ levels correlate with poorer outcomes. In addition, high fasting plasma glucose and high systolic blood pressure are the main contributors to CKD-related deaths, with their population attributable fraction&#xa0;(PAF) significantly decreasing as the SDI decreases.<br><br>CONCLUSION: The burden of CKD has significantly increased over the past three decades, influenced by demographic changes and variations in healthcare quality and access. Effective public health strategies and improvements in healthcare delivery are needed to address the disparities in CKD outcomes globally.}, }
@article {pmid39695352, year = {2025}, author = {Moore, M and Whittington, HD and Knickmeyer, R and Azcarate-Peril, MA and Bruno-Bárcena, JM}, title = {Non-stochastic reassembly of a metabolically cohesive gut consortium shaped by N-acetyl-lactosamine-enriched fibers.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2440120}, pmid = {39695352}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Bacteria/metabolism/classification/isolation &amp; purification/genetics ; Feces/microbiology ; Lactose/metabolism ; Dietary Fiber/metabolism ; Oligosaccharides/metabolism ; Amino Sugars ; }, abstract = {Diet is one of the main factors shaping the human microbiome, yet our understanding of how specific dietary components influence microbial consortia assembly and subsequent stability in response to press disturbances - such as increasing resource availability (feeding rate) - is still incomplete. This study explores the reproducible re-assembly, metabolic interplay, and compositional stability within microbial consortia derived from pooled stool samples of three healthy infants. Using a single-step packed-bed reactor (PBR) system, we assessed the reassembly and metabolic output of consortia exposed to lactose, glucose, galacto-oligosaccharides (GOS), and humanized GOS (hGOS). Our findings reveal that complex carbohydrates, especially those containing low inclusion (~1.25 gL[-1]) components present in human milk, such as N-acetyl-lactosamine (LacNAc), promote taxonomic, and metabolic stability under varying feeding rates, as shown by diversity metrics and network analysis. Targeted metabolomics highlighted distinct metabolic responses to different carbohydrates: GOS was linked to increased lactate, lactose to propionate, sucrose to butyrate, and CO2, and the introduction of bile salts with GOS or hGOS resulted in butyrate reduction and increased hydrogen production. This study validates the use of single-step PBRs for reliably studying microbial consortium stability and functionality in response to nutritional press disturbances, offering insights into the dietary modulation of microbial consortia and their ecological dynamics.}, }
@article {pmid39694113, year = {2025}, author = {Van Peteghem, L and Matassa, S and Sakarika, M}, title = {Fueling the protein transition: Can waste-derived ethanol enable efficient and high-quality microbial protein production?.}, journal = {Bioresource technology}, volume = {418}, number = {}, pages = {131990}, doi = {10.1016/j.biortech.2024.131990}, pmid = {39694113}, issn = {1873-2976}, mesh = {*Bacterial Proteins/biosynthesis ; Biomass ; *Ethanol/isolation &amp; purification/metabolism ; Fermentation ; *Waste Products ; }, abstract = {Meeting the protein needs of a growing population will require significant resources. In this context, microbial protein (MP) offers a nutritious and versatile protein source from recovered resources. This meta-analysis of over 100 studies examines the efficiency and nutritional quality of MP production using ethanol. Ethanol, a feedstock derived from CO2 and biological waste, is used by various microorganisms, and has an established role in the food sector. Results show that ethanol-based MP production is technically feasible for food applications, reaching biomass concentrations of 14-230 g/L and productivities of 11-13 g/L/h. The protein content of MP correlates with productivity, and the nutritional quality of ethanol-grown MP matches common sources like pork and tofu. Lastly, operational choices affect the techno-economic feasibility of using waste-derived ethanol and other recovered resources. This meta-analysis highlights the potential of ethanol-grown MP, though further research is needed to close existing knowledge gaps.}, }
@article {pmid39693383, year = {2024}, author = {Arrington, EC and Tarn, J and Kivenson, V and Nunn, BL and Liu, RM and Paul, BG and Valentine, DL}, title = {Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae247}, pmid = {39693383}, issn = {1751-7370}, abstract = {Aqueous-soluble hydrocarbons dissolve into the ocean's interior and structure deep-sea microbial populations influenced by natural oil seeps and spills. n-Pentane is a seawater-soluble, volatile compound abundant in petroleum products and reservoirs and will partially partition to the deep-water column following release from the seafloor. In this study, we explore the ecology and niche partitioning of two free-living Cycloclasticus strains recovered from seawater incubations with n-pentane and distinguish them as an open ocean variant and a seep-proximal variant, each with distinct capabilities for hydrocarbon catabolism. Comparative metagenomic analysis indicates the variant more frequently observed further from natural seeps encodes more general pathways for hydrocarbon consumption, including short-chain alkanes, aromatics, and long-chain alkanes, and also possesses redox versatility in the form of respiratory nitrate reduction and thiosulfate oxidation; in contrast, the seep variant specializes in short-chain alkanes and relies strictly on oxygen as the terminal electron acceptor. Both variants observed in our work were dominant ecotypes of Cycloclasticus observed during the Deepwater Horizon disaster, a conclusion supported by 16S rRNA gene analysis and read-recruitment of sequences collected from the submerged oil plume during active flow. A comparative genomic analysis of Cycloclasticus across various ecosystems suggests distinct strategies for hydrocarbon transformations among each clade. Our findings suggest Cycloclasticus is a versatile and opportunistic consumer of hydrocarbons and may have a greater role in the cycling of sulfur and nitrogen, thus contributing broad ecological impact to various ecosystems globally.}, }
@article {pmid39693347, year = {2024}, author = {Sun, X and Buchanan, PJ and Zhang, IH and San Roman, M and Babbin, AR and Zakem, EJ}, title = {Ecological dynamics explain modular denitrification in the ocean.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {52}, pages = {e2417421121}, pmid = {39693347}, issn = {1091-6490}, support = {LS-FMME-00871981//Simons Foundation (SF)/ ; OCE-2138890 and OCE-2142998//NSF (NSF)/ ; N/A//MIT School of Science MathWorks Science Fellowship/ ; 2125142//NSF (NSF)/ ; }, mesh = {*Denitrification/physiology ; *Oceans and Seas ; *Ecosystem ; Seawater/microbiology/chemistry ; Nitrogen/metabolism ; Nitrous Oxide/metabolism ; Oxygen/metabolism ; Bacteria/metabolism ; }, abstract = {Microorganisms in marine oxygen minimum zones (OMZs) drive globally impactful biogeochemical processes. One such process is multistep denitrification (NO3[-]→NO2[-]→NO→N2O→N2), which dominates OMZ bioavailable nitrogen (N) loss and nitrous oxide (N2O) production. Denitrification-derived N loss is typically measured and modeled as a single step, but observations reveal that most denitrifiers in OMZs contain subsets ("modules") of the complete pathway. Here, we identify the ecological mechanisms sustaining diverse denitrifiers, explain the prevalence of certain modules, and examine the implications for N loss. We describe microbial functional types carrying out diverse denitrification modules by their underlying redox chemistry, constraining their traits with thermodynamics and pathway length penalties, in an idealized OMZ ecosystem model. Biomass yields of single-step modules increase along the denitrification pathway when organic matter (OM) limits growth, which explains the viability of populations respiring NO2[-] and N2O in a NO3[-]-filled ocean. Results predict denitrifier community succession along environmental gradients: Pathway length increases as the limiting substrate shifts from OM to N, suggesting a niche for the short NO3[-]→NO2[-] module in free-living, OM-limited communities, and for the complete pathway in organic particle-associated communities, consistent with observations. The model captures and mechanistically explains the observed dominance and higher oxygen tolerance of the NO3[-]→NO2[-] module. Results also capture observations that NO3[-] is the dominant source of N2O. Our framework advances the mechanistic understanding of the relationship between microbial ecology and N loss in the ocean and can be extended to other processes and environments.}, }
@article {pmid39692747, year = {2025}, author = {Wallace, EJ and O'Dwyer, J and Dolan, EB and Burke, LP and Wylie, R and Bellavia, G and Straino, S and Cianfarani, F and Ciotti, G and Serini, S and Calviello, G and Roche, ET and Mitra, T and Duffy, GP}, title = {Actuation-Mediated Compression of a Mechanoresponsive Hydrogel by Soft Robotics to Control Release of Therapeutic Proteins.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {12}, number = {7}, pages = {e2401744}, pmid = {39692747}, issn = {2198-3844}, support = {713690//Horizon 2020/ ; 812865//Horizon 2020/ ; GOIPD/2020/157//Irish Research Council/ ; 13/RC/2073/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Animals ; Rats ; *Vascular Endothelial Growth Factor A/administration &amp; dosage ; *Hydrogels/chemistry ; *Robotics/methods ; *Drug Delivery Systems/methods ; Diabetes Mellitus, Experimental/drug therapy ; Male ; Rats, Sprague-Dawley ; }, abstract = {Therapeutic proteins, the fastest growing class of pharmaceuticals, are subject to rapid proteolytic degradation in vivo, rendering them inactive. Sophisticated drug delivery systems that maintain protein stability, prolong therapeutic effects, and reduce administration frequency are urgently required. Herein, a mechanoresponsive hydrogel is developed contained within a soft robotic drug delivery (SRDD) device. In a step-change from previously reported systems, pneumatic actuation of this system releases the cationic therapeutic protein Vascular Endothelial Growth Factor (VEGF) in a bioactive form which is required for therapeutic angiogenesis, the growth of new blood vessels, in numerous clinical conditions. The ability of the SRDD device to release bioactive VEGF in a spatiotemporal manner from the hydrogel is tested in diabetic rats - a model in which angiogenesis is difficult to stimulate. Daily actuation of the SRDD device in the diabetic rat model significantly increased cluster of differentiation 31+ (CD31+) blood vessel number (p = 0.0335) and the diameter of alpha-smooth muscle actin+ (α-SMA+) blood vessels (p = 0.0025) compared to passive release of VEGF from non-actuated devices. The SRDD device combined with the mechanoresponsive hydrogel offers the potential to deliver an array of bioactive therapeutics in a spatiotemporal manner to mimic their natural release in vivo.}, }
@article {pmid39691821, year = {2024}, author = {Ghosh, A and Bhambra, SK and Chandrasekaran, R and Bhadury, P}, title = {Genome description of a potentially new species of Streptomyces isolated from the Indian Sundarbans mangrove.}, journal = {Access microbiology}, volume = {6}, number = {12}, pages = {}, pmid = {39691821}, issn = {2516-8290}, abstract = {A potentially new species of Streptomyces was isolated from station 177 of the Sundarbans Seasonal Time Series in the Indian Sundarbans mangrove. The isolate was cultured from a sediment sample on TYS medium of salinity 15. Sequencing and annotation of the 16S rRNA showed 100% identity against S. laurentii NPS17 against GenBank/ENA/DDBJ. Annotation of the whole genome against the GTDB database showed closest identity with S. terrae SKN60 and belongs to the same clade as S. roseicoloratus TRM44457T and S. laurentii ATCC 31255. The genome is ~7.2 Mb and has a G+C% of 73%. The average amino acid identity was 85.01% with S. roseicoloratus and 80.34% with S. roseolus. The assembly reflected the presence of all essential genes and had 19 biosynthetic gene clusters predicted.}, }
@article {pmid39689568, year = {2025}, author = {Sumerta, IN and Ruan, X and Howell, K}, title = {The forgotten wine: Understanding palm wine fermentation and composition.}, journal = {International journal of food microbiology}, volume = {429}, number = {}, pages = {111022}, doi = {10.1016/j.ijfoodmicro.2024.111022}, pmid = {39689568}, issn = {1879-3460}, mesh = {*Arecaceae/microbiology/chemistry ; Bacteria/metabolism/classification/isolation &amp; purification ; *Fermentation ; Microbiota ; *Wine/microbiology/analysis ; }, abstract = {Palm wine is an alcoholic beverage that has existed for centuries and has important economic and socio-culture values in many tropical and sub-tropical countries. Lesser known than other types of wines, palm wine is made by spontaneous fermentation of palm sap by naturally occurring microbial communities. The palm sap ecosystem has unique microbial composition and diversity, which determines the composition of the eventual wine and is likely affected by geographical distinctiveness. While these features are well understood in grape and rice wine, these features have not been understood in palm wine. Here, we gather information of microbial communities and metabolite profiles from published studies, covering a wide range of methodologies and regions to better understand the causal links between the principal microbial species and major metabolites of palm wine. We assessed palm wine quality across production regions and local practices to provide general characteristics of palm wine and identify specific regional information. These will provide better understandings to the function of microbial communities and metabolite diversity, the contribution of regional variations and to ensure product quality in this unique, yet overlooked, fermented beverage.}, }
@article {pmid39689238, year = {2024}, author = {Yang, Q and Defoirdt, T}, title = {Weak selection for resistance to quorum sensing inhibition during multiple host infection cycles.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39689238}, issn = {1751-7370}, support = {//Special Research Fund of Ghent University/ ; G016823N//Scientific Research Fund of Flanders/ ; }, mesh = {*Quorum Sensing/drug effects ; *Vibrio/drug effects/physiology/genetics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Animals ; Vibrio Infections/microbiology ; Selection, Genetic ; }, abstract = {Quorum sensing (QS) inhibition is a promising novel approach to control bacterial infections. However, it is not clear whether QS inhibition will impose selective pressure for the spread of resistance against QS inhibition in pathogen populations. Previous research tried to answer this question by using synthetic growth media, and this revealed that whether or not resistance will spread completely depends on the environment in which it is studied. Therefore, the spread of resistance should be studied in the environment where it ultimately matters: in vivo during infection of a host. Here, using QS inhibitor-susceptible and -resistant mimics, we show that resistance to QS inhibition does not spread in host-associated populations of Vibrio campbellii during up to 35 cycles of infection and transmission if the initial frequency of the resistance is low in the pathogen population, whereas it further increases to 100% if it is already prevalent. However, even in the latter case, the resistance spreads at a slower pace than resistance to antibiotics spreads under the same conditions.}, }
@article {pmid39689178, year = {2024}, author = {Li, G and Liu, T and Xie, W and Liu, Z and Li, H and Whalen, JK and Jousset, A and Wei, Z}, title = {Metabolites limiting predator growth wane with prey biodiversity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {52}, pages = {e2410210121}, pmid = {39689178}, issn = {1091-6490}, support = {32201399//MOST | National Natural Science Foundation of China (NSFC)/ ; 32171640//MOST | National Natural Science Foundation of China (NSFC)/ ; KYQN2023048//MOE | Fundamental Research Funds for the Central Universities (Fundamental Research Fund for the Central Universities)/ ; 2022YFD1500302//MOST | National Key Research and Development Program of China (NKPs)/ ; }, mesh = {Animals ; *Biodiversity ; *Nematoda/physiology ; *Food Chain ; *Predatory Behavior/physiology ; Microbiota/physiology ; Bacteria/metabolism/classification ; Soil Microbiology ; }, abstract = {Predator-prey interactions are a major driver of microbiome dynamics, but remain difficult to predict. While several prey traits potentially impact resistance to predation, their effects in a multispecies context remain unclear. Here, we leverage synthetic bacterial communities of varying complexity to identify traits driving palatability for nematodes, a main consumer of bacteria in soil. We assessed trophic interactions between four nematode species and 122 bacterial isolates, across a gradient of prey biodiversity ranging from single species to 50 species. Nematode size, a proxy for prey palatability, varied strongly with prey community composition and could be predicted by metabolic and morphological properties of the prey. However, the influence of prey traits on predators depended on biodiversity. Secondary metabolites drove palatability in monoculture, but this effect vanished under increasing prey biodiversity, where prey size became the dominant predictors of nematode size. Although idiosyncratic properties are often emphasized in the literatures, our results suggest that in biodiverse assemblages, the composition of available prey and their traits are more reliable predictors of predator-prey interactions. This study offers valuable insights into microbial ecology in the context of predator-prey interactions, as cryptic microbial responses can be guided by deductions based on generalizable biological traits.}, }
@article {pmid39687379, year = {2024}, author = {Lee, D and Oliveira, FCC and Conant, RT and Kim, M}, title = {Microbial community assembly across agricultural soil mineral mesocosms revealed by 16S rRNA gene amplicon sequencing data.}, journal = {Data in brief}, volume = {57}, number = {}, pages = {111125}, pmid = {39687379}, issn = {2352-3409}, abstract = {Increasing atmospheric carbon dioxide (CO2) concentrations are impacting the global climate, resulting in significant interest in soil carbon sequestration as a mitigation strategy. While recognized that mineral-associated organic matter (MAOM) in soils is mainly formed through microbial activity, our understanding of microbial-derived MAOM formation processes remains limited due to the complexity of the soil environment. To gain insights into this issue, we incubated fresh soil samples for 45 days with one of three mineral additions: Sand, Kaolinite+Sand, or Illite+Sand. 16S rRNA V3/V4 gene amplicon sequencing was then conducted on samples using an Illumina NextSeq 2000 flow cell. The reads were analyzed and taxonomically assigned with QIIME2 v2023.5.1 and SILVA 138. The dataset has been made publicly available through NCBI GenBank under BioProject ID PRJNA1124235. This dataset is important and useful as it provides valuable insights into the interactions between soil minerals and microbial communities, which can inform strategies for enhancing soil carbon sequestration and mitigating climate change. Moreover, it serves as a crucial reference for future studies, offering a foundational understanding of microbial dynamics in soil systems and guiding further research in microbial ecology and carbon cycling.}, }
@article {pmid39683937, year = {2024}, author = {Liu, S and Teng, L and Ping, J}, title = {Graphitic Carbon Nitride Confers Bacterial Tolerance to Antibiotics in Wastewater Relating to ATP Depletion.}, journal = {Molecules (Basel, Switzerland)}, volume = {29}, number = {23}, pages = {}, pmid = {39683937}, issn = {1420-3049}, support = {62105175//National Natural Science Foundation of China/ ; ZR2021QF058//Natural Science Foundation of Shandong Province/ ; 2022PY036//The Education and Industry Integration Pilot Project of Qilu University of Technology/ ; 432413/01090//Start-up fund of Tianjin Renai College/ ; }, mesh = {*Graphite/chemistry ; *Wastewater/microbiology/chemistry ; *Anti-Bacterial Agents/pharmacology ; *Adenosine Triphosphate/metabolism ; Nitrogen Compounds/chemistry ; Staphylococcus aureus/drug effects ; Ofloxacin/pharmacology ; Drug Resistance, Bacterial/drug effects ; Reactive Oxygen Species/metabolism ; Microbial Sensitivity Tests ; Water Purification/methods ; }, abstract = {Graphitic carbon nitride (C3N4) is a kind of visible light-responsive photocatalyst that has been of great interest in wastewater treatment. However, its environmental impact and biological effect remains to be elucidated. This study investigated the effect of C3N4 nanosheets on bacterial abundance and antibiotic tolerance in wastewater. Interestingly, as compared to the wastewater containing the antibiotic ofloxacin alone, the wastewater containing both ofloxacin and C3N4 had much higher numbers of total living bacteria, but lower levels of the ofloxacin-resistant bacteria and the ofloxacin-resistant gene qnrS. The model bacterium Staphylococcus aureus was then used to explore the mechanism of C3N4-induced antibiotic tolerance. The nanosheets neither adsorbed the antibiotic nor promoted drug efflux, uncovering that drug adsorption and efflux were not involved in antibiotic tolerance. Further investigations revealed that the nanosheets, like arsenate and menadione, drastically reduced ATP levels and induced the production of reactive oxygen species for enhanced antibiotic tolerance. This study revealed an antibiotic-tolerating mechanism associated with C3N4-induced ATP depletion, and shed a light on the effect of photocatalysts on microbial ecology during their application in wastewater treatment.}, }
@article {pmid39682491, year = {2024}, author = {Suriyasathaporn, W and Kongkaew, A and Intanon, M and Srithanasuwan, A and Saipinta, D and Pangprasit, N and Thongtharb, A and Chuasakhonwilai, A and Chaisri, W}, title = {Non-aureus Staphylococci Cause the Spontaneous Cure or Persistent Infection of Major Bovine Mastitis Pathogens in the Murine Mammary Glands.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {23}, pages = {}, pmid = {39682491}, issn = {2076-2615}, support = {FF66/017//The Fundamental Fund, Chiang Mai University/ ; }, abstract = {The microbial ecology in mastitis involves the interactions between bacteria and the mammary gland environment. Poor mastitis control, for which understanding these microbial relationships is crucial, increases the risk of mastitis and co-infections. The aim of this study was to determine the pathogenesis and bacterial ecology of murine mammary glands following intramammary infection (IMI) with S. aureus (AU), S. agalactiae (SA), and four isolates of selected non-aureus staphylococci (NAS), as well as co-infections of AU or SA with NAS. Selected NAS demonstrated resistance to growth inhibition after co-culture with AU and SA and were proven to be protective in vitro against AU and SA. Both single infections and co-infections of AU, SA, two selected isolates of S. hominis (NAS1 and NAS2), and two selected isolates of S. chromogens (NAS3 and NAS4) were injected into the murine mammary glands at 10[5] CFU/mL. After 72 h of inoculation, the results showed that AU, AU-NAS2, and AU-NAS3 expressed severe inflammation with clinical signs of mastitis. The persistence of AU was found for AU, NAS3, and AU-NAS3, whereas the persistence of SA was found for SA-NAS1, SA-NAS3, and SA-NAS, although single SA could not persist. Interestingly, NAS2 in both the single- and co-IMIs with AU or SA resulted in a spontaneous cure 72 h after the IMI. In conclusion, some NAS have beneficial results because they can eliminate S. aureus and S. agalactiae, but some NAS have negative effects because they can support persistent S. agalactiae infection. These results may be used to explain both the advantages and disadvantages of NAS on farms with poor mastitis control. In addition, the beneficial S. hominis may initiate natural live antibiotics and reduce antibiotic resistance problems.}, }
@article {pmid39681734, year = {2024}, author = {Rajendran, D and Vinayagam, S and Sekar, K and Bhowmick, IP and Sattu, K}, title = {Symbiotic Bacteria: Wolbachia, Midgut Microbiota in Mosquitoes and Their Importance for Vector Prevention Strategies.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {154}, pmid = {39681734}, issn = {1432-184X}, mesh = {Animals ; Culicidae/microbiology ; Gastrointestinal Microbiome ; *Mosquito Control/methods ; *Mosquito Vectors/microbiology ; Symbiosis ; *Wolbachia/physiology ; }, abstract = {Mosquito-borne illnesses pose a significant threat to eradication under existing vector management measures. Chemo-based vector control strategies (use of insecticides) raise a complication of resistance and environmental pollution. Biological control methods are an alternative approach to overcoming this complication arising from insecticides. The mosquito gut microbiome is essential to supporting the factors that involve metabolic regulation and metamorphic development (from juvenile to adult), as well as the induction of an immune response. The induced immune response includes the JAK-STAT, IMD, and Toll pathways due to the microbial interaction with the midgut cells (MG cells) that prevent disease transmission to humans. The aforementioned sequel to the review provides information about endosymbiont Wolbachia, which contaminates insect cells, including germline and somatic cytoplasm, and inhibits disease-causing pathogen development and transmission by competing for resources within the cell. Moreover, it reduces the host population via cytoplasmic incompatibility (CI), feminization, male killing, and parthenogenesis. Furthermore, the Cif factor in Wolbachia is responsible for CI induction that produces inviable cells with the translocating systems and the embryonic defect-causing protein factor, WalE1 (WD0830), which manipulates the host actin. This potential of Wolbachia can be used to design a paratransgenic system to control vectors in the field. An extracellular symbiotic bacterium such as Asaia, which is grown in the growth medium, is used to transfer lethal genes within itself. Besides, the genetically transferred symbiotic bacteria infect the wild mosquito population and are easily manifold. So, it might be suitable for vector control strategies in the future.}, }
@article {pmid39681034, year = {2025}, author = {Fu, Y and Hu, F and Wang, F and Xu, M and Jia, Z and Amelung, W and Mei, Z and Han, X and Virta, M and Jiang, X and Tiedje, JM}, title = {Field-based evidence for the prevalence of soil antibiotic resistomes under long-term antibiotic-free fertilization.}, journal = {Environment international}, volume = {195}, number = {}, pages = {109202}, doi = {10.1016/j.envint.2024.109202}, pmid = {39681034}, issn = {1873-6750}, mesh = {*Fertilizers/analysis ; *Soil Microbiology ; Anti-Bacterial Agents ; Manure ; Soil/chemistry ; *Drug Resistance, Microbial/genetics ; Agriculture ; }, abstract = {Growing evidence suggests that the use of manure containing residual antibiotics universally leads to an increase in soil antibiotic resistance genes (ARGs). However, there is limited understanding of the influence of long-term antibiotic-free fertilization and the differences between antibiotic-free manure and chemical fertilizer on soil ARGs. This study aimed to quantify the assembly patterns of the antibiotic resistome by in situ probing bacterial community and environmental variations in field soils that have been subjected to long-term exposure to chemical fertilizer and/or manure from animals without antibiotic amendments. Long-term fertilization slightly impacts the diversity of antibiotic resistomes, with 85.5 % of total ARGs and mobile genetic elements (MGEs) being common across all treatment types, while significantly increasing their abundances from 0.68 to a maximum of 0.90 copies/16S rRNA. The rise in ARG abundances was less pronounced when using antibiotic-free manure compared to chemical fertilizer, particularly for Rank Ⅱ ARGs. However, when antibiotic-free manure and chemical fertilizer were combined, a significant increase in nutrients (such as available nitrogen and organic matter) and MGEs occurred, leading to the enrichment of soil microbial populations, especially in certain resistant species, and Rank Ⅰ and Ⅱ ARGs. Despite the influence of various factors like bacterial communities, soil properties, heavy metals, and MGEs, the MGEs had the most significant standardized effects on shaping ARGs through both direct and indirect pathways. Our findings indicates that while of antibiotic-free manure can lower the risk of antibiotic residues and promote sustainable farming practices, it may not fully eliminate the prevalence of ARGs, highlighting the need for more comprehensive strategies to address antibiotic resistance in agriculture rather than simply prohibiting the use of antibiotics.}, }
@article {pmid39680930, year = {2024}, author = {Li, XY and Zhu, CW and Chen, S and Xiang, Q and Lu, C and Lin, XY and Chen, QL}, title = {Elevated CO2 Increased Antibiotic Resistomes in Seed Endophytes: Evidence from a Free-Air CO2 Enrichment (FACE) Experiment.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {52}, pages = {23190-23200}, doi = {10.1021/acs.est.4c09625}, pmid = {39680930}, issn = {1520-5851}, mesh = {*Carbon Dioxide ; Seeds/microbiology ; *Endophytes ; Bacteria ; Fungi ; Anti-Bacterial Agents ; *Drug Resistance, Microbial/genetics ; Microbiota ; Soil Microbiology ; }, abstract = {Climate warming affects antibiotic resistance genes (ARGs) in soil and the plant microbiome, including seed endophytes. Seeds act as vectors for ARG dissemination in the soil-plant system, but the impact of elevated CO2 on seed resistomes remains poorly understood. Here, a free-air CO2 enrichment system was used to examine the impact of elevated CO2 on seed-associated ARGs and seed endophytic bacteria and fungi. Results indicated that elevated CO2 levels significantly increased the relative abundance of seed ARGs and mobile genetic elements (MGEs), especially those related to beta-lactam resistance and MGEs. Increased CO2 levels also influenced the composition of seed bacterial and fungal communities and the complexity of bacteria-fungi interactions. Fungi were more sensitive to changes in the CO2 level than bacteria, with deterministic processes playing a greater role in fungal community assembly. Co-occurrence network analysis revealed a stronger correlation between fungi and ARGs compared to bacteria. The structure equation model (SEM) showed that elevated CO2 directly influenced seed resistomes by altering bacterial composition and indirectly through bacteria-fungi interactions. Together, our work offers new insights into the effects of elevated CO2 on antibiotic resistomes in the seed endosphere, highlighting their increased dissemination potential within soil-plant systems and the associated health risks in a changing environment.}, }
@article {pmid39680691, year = {2025}, author = {Yang, JC and Lagishetty, V and Aja, E and Arias-Jayo, N and Chang, C and Hauer, M and Katzka, W and Zhou, Y and Sedighian, F and Koletic, C and Liang, F and Dong, TS and Situ, J and Troutman, R and Buri, H and Bhute, S and Simpson, CA and Braun, J and Jacob, N and Jacobs, JP}, title = {Biogeographical distribution of gut microbiome composition and function is partially recapitulated by fecal transplantation into germ-free mice.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39680691}, issn = {1751-7370}, support = {CDA2 IK2CX001717//Crohn's and Colitis Foundation Career Development/ ; //Vatche and Tamar Manoukian Division of Digestive Diseases/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Fecal Microbiota Transplantation ; Germ-Free Life ; RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Mice, Inbred C57BL ; Colon/microbiology ; Specific Pathogen-Free Organisms ; Male ; }, abstract = {Fecal microbiota transplantation has been vital for establishing whether host phenotypes can be conferred through the microbiome. However, whether the existing microbial ecology along the mouse gastrointestinal tract can be recapitulated in germ-free mice colonized with stool remains unknown. We first identified microbes and their predicted functions specific to each of six intestinal regions in three cohorts of specific pathogen-free mice spanning two facilities. Of these region-specific microbes, the health-linked genus Akkermansia was consistently enriched in the lumen of the small intestine compared to the colon. Predictive functional modeling on 16S rRNA gene amplicon sequencing data recapitulated in shotgun sequencing data revealed increased microbial central metabolism, lipolytic fermentation, and cross-feeding in the small intestine, whereas butyrate synthesis was colon-enriched. Neuroactive compound metabolism also demonstrated regional specificity, including small intestine-enriched gamma-aminobutyric acid degradation and colon-enriched tryptophan degradation. Specifically, the jejunum and ileum stood out as sites with high predicted metabolic and neuromodulation activity. Differences between luminal and mucosal microbiomes within each site of the gastrointestinal tract were largely facility-specific, though there were a few consistent patterns in microbial metabolism in specific pathogen-free mice. These included luminal enrichment of central metabolism and cross-feeding within both the small intestine and the colon, and mucosal enrichment of butyrate synthesis within the colon. Across three cohorts of germ-free mice colonized with mice or human stool, compositional and functional region specificity were inconsistently reproduced. These results underscore the importance of investigating the spatial variation of the gut microbiome to better understand its impact on host physiology.}, }
@article {pmid39679708, year = {2025}, author = {Liu, Z and Jiang, C and Yin, Z and Ibrahim, IA and Zhang, T and Wen, J and Zhou, L and Jiang, G and Li, L and Yang, Z and Huang, Y and Yang, Z and Gu, Y and Meng, D and Yin, H}, title = {Ecological features of microbial community linked to stochastic and deterministic assembly processes in acid mine drainage.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0102824}, pmid = {39679708}, issn = {1098-5336}, support = {2023YFE0114500//MOST | National Key Research and Development Program of China (NKPs)/ ; 92351303//MOST | National Natural Science Foundation of China (NSFC)/ ; BX20230437//Postdoctoral Fellowship Program of CPSF/ ; }, mesh = {*Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; *Mining ; Phylogeny ; Acids ; Stochastic Processes ; }, abstract = {UNLABELLED: Ecological processes greatly shape microbial community assembly, but the driving factors remain unclear. Here, we compiled a metagenomic data set of microbial communities from global acid mine drainage (AMD) and explored the ecological features of microbial community linked to stochastic and deterministic processes from the perspective of species niche position, interaction patterns, gene functions, and viral infection. Our results showed that dispersal limitation (DL) (48.5%~93.5%) dominated the assembly of phylogenetic bin in AMD microbial community, followed by homogeneous selection (HoS) (3.1%~39.2%), heterogeneous selection (HeS) (1.4%~22.2%), and drift (DR) (0.2%~2.7%). The dominant process of dispersal limitation was significantly influenced by niche position in temperature (r = -0.518, P = 0.007) and dissolved oxygen (r = 0.471, P = 0.015). Network stability had a significantly negative correlation with the relative importance of dispersal limitation, while it had a positive correlation with selection processes, implying changes in network properties could be mediated by ecological processes. Furthermore, we found that ecological processes were mostly related to the gene functions of energy production and conversion (C), and amino acid transport and metabolism (E). Meanwhile, our results showed that the number of proviruses and viral genes involved in arsenic (As) resistance is negatively associated with the relative importance of ecological drift in phylogenetic bin assembly, implying viral infection might weaken ecological drift. Taken together, these results highlight that ecological processes are associated with ecological features at multiple levels, providing a novel insight into microbial community assembly in extremely acidic environments.<br><br>IMPORTANCE: Unraveling the forces driving community assemblage is a core issue in microbial ecology, but how ecological constraints impose stochasticity and determinism remains unknown. This study presents a comprehensive investigation to uncover the association of ecological processes with species niche position, interaction patterns, microbial metabolisms, and viral infections, which provides novel insights into community assembly in extreme environments.}, }
@article {pmid39679616, year = {2024}, author = {Seki, D and Kirkegaard, R and Osvatic, J and Hausmann, B and Séneca, J and Pjevac, P and Berger, A and J Hall, L and Wisgrill, L and Berry, D}, title = {Gut microbiota genome features associated with brain injury in extremely premature infants.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2410479}, pmid = {39679616}, issn = {1949-0984}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *Infant, Extremely Premature ; *Brain Injuries/microbiology/genetics ; *Feces/microbiology ; Female ; Male ; Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Genome, Bacterial ; Cohort Studies ; }, abstract = {Severe brain damage is common among premature infants, and the gut microbiota has been implicated in its pathology. Although the order of colonizing bacteria is well described, the mechanisms underlying aberrant assembly of the gut microbiota remain elusive. Here, we employed long-read nanopore sequencing to assess abundances of microbial species and their functional genomic potential in stool samples from a cohort of 30 extremely premature infants. We identify several key microbial traits significantly associated with severe brain damage, such as the genomic potential for nitrate respiration and iron scavenging. Members of the Enterobacteriaceae were prevalent across the cohort and displayed a versatile metabolic potential, including pathogenic and nonpathogenic traits. Predominance of Enterobacter hormaechei and Klebsiella pneumoniae were associated with an overall loss of genomic functional redundancy as well as poor neurophysiological outcome. These findings reveal microbial traits that may be involved in exacerbating brain injury in extremely premature infants and provide suitable targets for therapeutic interventions.}, }
@article {pmid39675658, year = {2025}, author = {Yan, R and Xu, X and Niu, Y and Ying, S and Cai, J and Chen, R and Gu, Y and Kan, H}, title = {Microbial diversity and environmental determinants at Shanghai Hongqiao railway station: A comprehensive microbial assessment.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {366}, number = {}, pages = {125534}, doi = {10.1016/j.envpol.2024.125534}, pmid = {39675658}, issn = {1873-6424}, mesh = {China ; *Railroads ; *Environmental Monitoring ; *Air Microbiology ; *Microbiota ; Seasons ; RNA, Ribosomal, 16S/analysis ; *Air Pollution, Indoor/analysis ; Humans ; SARS-CoV-2 ; }, abstract = {The COVID-19 pandemic has underscored the importance of indoor environmental management in transportation hubs, which are critical for pathogen transmission due to high foot traffic. However, research has primarily focused on subways, with limited studies on train stations. In this study, samples were collected at the Shanghai Hongqiao Railway Station in winter, spring, and summer. Microbial DNA was extracted from collected indoor surfaces and ambient air samples and then analyzed through high-throughput 16S rRNA gene sequencing. Alongside sample collection, environmental data were recorded. Alpha diversity was greatest in winter, followed by summer, and least in spring within the train station environment. Surface samples exhibited higher alpha diversity compared to air samples, with no notable difference between indoor and outdoor air. Beta diversity showed significant variation across seasons and locations, with seasonal changes more pronounced than spatial ones, primarily due to differences between air and surface samples rather than indoor and outdoor environments. Key determinants of microbial community structure included CO2, temperature, illuminance, and passenger volume. The microbial community in train stations originates from various sources, with contributions from both natural elements (like wastewater/sludge, soil, and plants) and human sources (such as gastrointestinal, oral, and dermal flora). This study highlights the microbial ecology of train stations, emphasizing the need for microbial surveillance and management in transportation settings.}, }
@article {pmid39673336, year = {2024}, author = {Liu, J and He, Y and Qiu, Z and Fahad, S and Zhao, S and Zhu 朱, M&#x58a8;}, title = {Erysiphe russellii Causing Powdery Mildew on Oxalis corniculata L. in Central China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-10-24-2249-PDN}, pmid = {39673336}, issn = {0191-2917}, abstract = {Oxalis corniculata L. (Creeping woodsorrel) is a perennial plant of the genus Oxalis in Oxalidaceae family, which has the high ornamental and medicinal value. Extracts of creeping woodsorrel are used as antioxidants and cholinesterase inhibitors and for anti-inflammatory, antiseptic, analgesic, antirheumatic ache, and antimicrobial purposes (Leporatti et al. 2003). In June 2024, powdery mildew was found on the leaves of Creeping woodsorrel in Xinxiang City, Henan Province, China (113.925°E, 35.294°N). About 100 plants were examined and 80 % were infected with disease symptoms, i.e. curling and senescence. The white masses were on the both sides of plant leaves covering up to 90% of the leaves area. The slightly or straight curved conidiophores (n = 50) were 68 to 99× 6 to 12 μm in size and consisted of foot cells, shorter cells and singly conidia. The ellipsoidal to oval conidia (n =50), were 26 to 10 ×11 to 5 μm in size and had a length/width ratio of 1.6 to 2.2. These morphological characteristics were similar to the previously reported Creeping woodsorrel powdery mildew fungus, Erysiphe russellii (Thuong et al. 2017; Takamatsu et al. 2015). Following previously described methods (White et al. 1990; Bradshaw et al. 2022; Zhu et al. 2022), the ITS (ribosomal transcribed spacer), GAPDH (glyceraldehyde-3-phosphate dehydrogenase), RPB2 (RNA polymerase II), GS (glutamine synthetase) and CAM (calmodulin) gene regions of three isolates were amplified with specific primers ITS1/ITS4 (ITS1 5'-TCCGTAGGTGAACCTGCGG-3'; ITS4 5'-TCCTCCGCTTATTGATATGC-3'), PMGAPDH1/PMGAPDH3R (PMGAPDH1 5'-GGAATGGCTATGCGTGTACC-3'; PMGAPDH3R 5'-CCCCATTCGTTGTCGTACCATG-3'), CAM1/CAM4R (CAM1 5'-CTTTGCATCATGAGTTGGAC-3'; CAM4R 5'-GGCTCGAAAAATGAAAGATACCG-3'), Rpb2_4/Rpb2_6R (Rpb2_4 5'-GCAAGCTCAACTGCTGGTG-3'; Rpb2_6R 5'-TCCAGCGATGTGCTGTTGG-3'), GSPM2/GSPM3R (GSPM2 5'-CCAATCAGTTACTGTTTGTTCCC-3'; GSPM3R 5'-GGACTTCCTGATATTATGCC3'). Sanger sequencing results showed that each sequence of the three isolates were the same. Then sequences of one isolate were uploaded in GenBank (Accession No. PQ044579, PQ149219, PQ149220, PQ149221and PQ149222, respectively). The sequences were 100% identical to those of a previously reported E russellii on O. corniculata (Thuong et al. 2017; Takamatsu et al. 2015). The pathogen and the previously reported E russellii are clustered in the same branch in the phylogenetic tree (Thuong et al. 2017; Takamatsu et al. 2015). The pathogenicity was tested according to the method previously described (Zhu et al. 2021). By blowing conidia on infected leaves with pressurized air, the fungus was inoculated onto the leaves of three healthy plants (three-month-old), with three uninoculated plants (three-month-old) treated as controls. The infected plants and the control plants were placed in the culture room with the temperature 23 °C, humidity 50% and light/Dark 16/8 h, respectively. 10-12 days post inoculation, the leaves of the inoculated plants showed signs and symptoms of powdery mildew, while the control group was unaffected. The pathogen of the infected plant disease was re-examined by morphological characteristics and was similar to the original fungus. The pathogenicity tests were repeated three times and same results were obtained. Therefore, the pathogen was identified and confirmed as E russellii (isolate ER-ZM2024). Previously, E russellii was reported on Oxalis corniculata L. in Japan and Korea (Thuong et al. 2017; Takamatsu et al. 2015). To the best our knowledge, this is the first report of powdery mildew caused by E russellii on O. corniculata L. in central China. This identification of E russellii on O. corniculata L. provides a new perspective for the study of the disease. The results of this study provide the sequences of E russellii for further phylogenetic analysis.}, }
@article {pmid39670887, year = {2025}, author = {Vlasselaer, L and Moons, J and De Clercq, T and Lievens, B and De Coninck, B}, title = {Development of a Toolbox to Study Phytophthora cryptogea-Lettuce Interactions: Characterization and Detection of P. cryptogea in Hydroponic Lettuce.}, journal = {Plant disease}, volume = {}, number = {}, pages = {PDIS09242018RE}, doi = {10.1094/PDIS-09-24-2018-RE}, pmid = {39670887}, issn = {0191-2917}, abstract = {Climate change poses a major threat to crop production, resulting in the emergence of new pests and diseases. Phytophthora cryptogea has recently emerged as a major concern in hydroponic lettuce cultivation, causing substantial yield and economic losses. This oomycete pathogen thrives in elevated water temperatures induced by warmer weather conditions (e.g., heatwaves), facilitating rapid pathogen propagation. Although the disease is already present for several decades in chicory cultivation, where it originates from the field, its origin in lettuce cultivation remains unclear. To get a better understanding of its origin, we conducted a multilocus sequence analysis using five reference genes (ITS, β-tub, COI, EF1α, and HSP90) and 33 P. cryptogea isolates from various hosts, including chicory and lettuce. Results revealed a clear separation between lettuce and chicory isolates. Furthermore, we developed and implemented a robust disease bioassay and qPCR assay to investigate the interaction between P. cryptogea strains and lettuce. Our findings revealed that while lettuce isolates exhibited the highest virulence, some chicory isolates also caused disease in lettuce, suggesting a potential evolutionary link between P. cryptogea in lettuce and chicory. Our experiments also revealed that even a low concentration of zoospores (100 zoospores/liter) can elicit severe symptoms, underscoring the pathogen's high virulence. Therefore, effective disease management strategies are needed for controlling (the spread of) the disease. Together, this research provides several tools that can be used to enhance our understanding of the interaction between P. cryptogea and its host plants, including the development of proper disease management strategies.}, }
@article {pmid39665561, year = {2025}, author = {Unzueta-Martínez, A and Girguis, PR}, title = {Taxonomic diversity and functional potential of microbial communities in oyster calcifying fluid.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0109424}, pmid = {39665561}, issn = {1098-5336}, support = {2109473//National Science Foundation (NSF)/ ; 9208//Gordon and Betty Moore Foundation (GBMF)/ ; }, mesh = {Animals ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Ostreidae/microbiology ; *Archaea/classification/genetics/isolation &amp; purification/metabolism ; Biomineralization ; Viruses/classification/genetics/isolation &amp; purification ; Calcification, Physiologic ; Metagenomics ; Biodiversity ; Phylogeny ; }, abstract = {UNLABELLED: Creating and maintaining an appropriate chemical environment is essential for biomineralization, the process by which organisms precipitate minerals to form their shells or skeletons, yet the mechanisms involved in maintaining calcifying fluid chemistry are not fully defined. In particular, the role of microorganisms in facilitating or hindering animal biomineralization is poorly understood. Here, we investigated the taxonomic diversity and functional potential of microbial communities inhabiting oyster calcifying fluid. We used shotgun metagenomics to survey calcifying fluid microbial communities from three different oyster harvesting sites. There was a striking consistency in taxonomic composition across the three collection sites. We also observed archaea and viruses that had not been previously identified in oyster calcifying fluid. Furthermore, we identified microbial energy-conserving metabolisms that could influence the host's calcification, including genes involved in sulfate reduction and denitrification that are thought to play pivotal roles in inorganic carbon chemistry and calcification in microbial biofilms. These findings provide new insights into the taxonomy and functional capacity of oyster calcifying fluid microbiomes, highlighting their potential contributions to shell biomineralization, and contribute to a deeper understanding of the interplay between microbial ecology and biogeochemistry that could potentially bolster oyster calcification.<br><br>IMPORTANCE: Previous research has underscored the influence of microbial metabolisms in carbonate deposition throughout the geological record. Despite the ecological importance of microbes to animals and inorganic carbon transformations, there have been limited studies characterizing the potential role of microbiomes in calcification by animals such as bivalves. Here, we use metagenomics to investigate the taxonomic diversity and functional potential of microbial communities in calcifying fluids from oysters collected at three different locations. We show a diverse microbial community that includes bacteria, archaea, and viruses, and we discuss their functional potential to influence calcifying fluid chemistry via reactions like sulfate reduction and denitrification. We also report the presence of carbonic anhydrase and urease, both of which are critical in microbial biofilm calcification. Our findings have broader implications in understanding what regulates calcifying fluid chemistry and consequentially the resilience of calcifying organisms to 21st century acidifying oceans.}, }
@article {pmid39660837, year = {2025}, author = {Lewin, GR}, title = {mSphere of Influence: How the single cell contributes to the collective.}, journal = {mSphere}, volume = {10}, number = {1}, pages = {e0043124}, pmid = {39660837}, issn = {2379-5042}, support = {DP2 AI184733/AI/NIAID NIH HHS/United States ; R00 DE031018/DE/NIDCR NIH HHS/United States ; }, mesh = {*Single-Cell Analysis ; Humans ; *Bacteria/genetics/classification ; *Microbiota/genetics ; RNA-Seq ; }, abstract = {Gina Lewin works in the field of microbial ecology, with a focus on the human microbiota. In this mSphere of Influence article, she reflects on how two papers describing bacterial single-cell RNA-seq-"Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing" by S. B. Blattman, W. Jiang, P. Oikonomou, and S. Tavazoie (Nat Microbiol 5:1192-1201, 2020, https://doi.org/10.1038/s41564-020-0729-6) and "Microbial single-cell RNA sequencing by split-pool barcoding" by A. Kuchina, L. M. Brettner, L. Paleologu, C. M. Roco, et al. (Science 371:eaba5257, 2021, https://doi.org/10.1126/science.aba5257)-impacted her work by developing a new approach to study how single cells of bacteria contribute to ecosystem-level processes.}, }
@article {pmid39659497, year = {2024}, author = {Ritsch, M and Brait, N and Harvey, E and Marz, M and Lequime, S}, title = {Endogenous viral elements: insights into data availability and accessibility.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {veae099}, pmid = {39659497}, issn = {2057-1577}, abstract = {Endogenous viral elements (EVEs) are remnants of viral genetic material endogenized into the host genome. They have, in the last decades, attracted attention for their role as potential contributors to pathogenesis, drivers of selective advantage for the host, and genomic remnants of ancient viruses. EVEs have a nuanced and complex influence on both host health and evolution, and can offer insights on the deep evolutionary history of viruses. As an emerging field of research, several factors limit a comprehensive understanding of EVEs: they are currently underestimated and periodically overlooked in studies of the host genome, transcriptome, and virome. The absence of standardized guidelines for ensuring EVE-related data availability and accessibility following the FAIR ('findable, accessible, interoperable, and reusable') principles obstructs our ability to gather and connect information. Here, we discuss challenges to the availability and accessibility of EVE-related data and propose potential solutions. We identified the biological and research focus imbalance between different types of EVEs, and their overall biological complexity as genomic loci with viral ancestry, as potential challenges that can be addressed with the development of a user-oriented identification tool. In addition, reports of EVE identification are scattered between different subfields under different keywords, and EVE sequences and associated data are not properly gathered in databases. While developing an open and dedicated database might be ideal, targeted improvements of generalist databases might provide a pragmatic solution to EVE data and metadata accessibility. The implementation of these solutions, as well as the collective effort by the EVE scientific community in discussing and setting guidelines, is now drastically needed to lead the development of EVE research and offer insights into host-virus interactions and their evolutionary history.}, }
@article {pmid39657855, year = {2025}, author = {Gu, Z and He, L and Liu, T and Xing, M and Feng, L and Luo, G}, title = {Exploring strategies for kitchen waste treatment and remediation from the perspectives of microbial ecology and genomics.}, journal = {Chemosphere}, volume = {370}, number = {}, pages = {143925}, doi = {10.1016/j.chemosphere.2024.143925}, pmid = {39657855}, issn = {1879-1298}, mesh = {Animals ; Oligochaeta/growth &amp; development ; *Composting ; Sewage/microbiology ; Biodegradation, Environmental ; Metagenomics ; Genomics ; *Soil Microbiology ; *Refuse Disposal/methods ; Bacteria/genetics ; Lignin ; }, abstract = {Nowadays, the rapid growth of population has led to a substantial increase in kitchen waste and wasted sludge. Kitchen waste is rich in organic matter, including lignocellulose. Synergistic treatment involving kitchen waste and wasted sludge can enhance treatment process. Vermicomposting can facilitate microbial activities on organic matter. Nevertheless, the underlying mechanisms remain unclear. In this study, metagenomics was used to analyze microbial functional genes in vermicomposting. Redundancy analysis found that TOC, TN and DTN adversely affect earthworm growth and reproduction. The relative abundance of Bacteroidetes and Firmicutes increased with earthworms, thereby potentially augmenting lignocellulose degradation. The predominant functional genes included amino acid, carbohydrate, and inorganic ion conversion and metabolism. Metagenomics analysis demonstrated that GH1, GH3, GH5, GH6, GH9, GH12, GH44, GH48 and GH74, GT41, GT4, GT2, and GT51 were dominant. Furthermore, there was higher abundance of carbohydrate-active enzymes in the vermicomposting, particularly during the later phases (30-45 days). Co-occurrence network revealed that Cellvibrio in the vermicomposting exhibited a relatively dense positive correlation with other microbial groups. The findings elucidated the mechanism of vermicomposting as a promising approach for managing kitchen waste and wasted sludge.}, }
@article {pmid39657789, year = {2025}, author = {Zdouc, MM and Blin, K and Louwen, NLL and Navarro, J and Loureiro, C and Bader, CD and Bailey, CB and Barra, L and Booth, TJ and Bozhüyük, KAJ and Cediel-Becerra, JDD and Charlop-Powers, Z and Chevrette, MG and Chooi, YH and D'Agostino, PM and de Rond, T and Del Pup, E and Duncan, KR and Gu, W and Hanif, N and Helfrich, EJN and Jenner, M and Katsuyama, Y and Korenskaia, A and Krug, D and Libis, V and Lund, GA and Mantri, S and Morgan, KD and Owen, C and Phan, CS and Philmus, B and Reitz, ZL and Robinson, SL and Singh, KS and Teufel, R and Tong, Y and Tugizimana, F and Ulanova, D and Winter, JM and Aguilar, C and Akiyama, DY and Al-Salihi, SAA and Alanjary, M and Alberti, F and Aleti, G and Alharthi, SA and Rojo, MYA and Arishi, AA and Augustijn, HE and Avalon, NE and Avelar-Rivas, JA and Axt, KK and Barbieri, HB and Barbosa, JCJ and Barboza Segato, LG and Barrett, SE and Baunach, M and Beemelmanns, C and Beqaj, D and Berger, T and Bernaldo-Agüero, J and Bettenbühl, SM and Bielinski, VA and Biermann, F and Borges, RM and Borriss, R and Breitenbach, M and Bretscher, KM and Brigham, MW and Buedenbender, L and Bulcock, BW and Cano-Prieto, C and Capela, J and Carrion, VJ and Carter, RS and Castelo-Branco, R and Castro-Falcón, G and Chagas, FO and Charria-Girón, E and Chaudhri, AA and Chaudhry, V and Choi, H and Choi, Y and Choupannejad, R and Chromy, J and Donahey, MSC and Collemare, J and Connolly, JA and Creamer, KE and Crüsemann, M and Cruz, AA and Cumsille, A and Dallery, JF and Damas-Ramos, LC and Damiani, T and de Kruijff, M and Martín, BD and Sala, GD and Dillen, J and Doering, DT and Dommaraju, SR and Durusu, S and Egbert, S and Ellerhorst, M and Faussurier, B and Fetter, A and Feuermann, M and Fewer, DP and Foldi, J and Frediansyah, A and Garza, EA and Gavriilidou, A and Gentile, A and Gerke, J and Gerstmans, H and Gomez-Escribano, JP and González-Salazar, LA and Grayson, NE and Greco, C and Gomez, JEG and Guerra, S and Flores, SG and Gurevich, A and Gutiérrez-García, K and Hart, L and Haslinger, K and He, B and Hebra, T and Hemmann, JL and Hindra, H and Höing, L and Holland, DC and Holme, JE and Horch, T and Hrab, P and Hu, J and Huynh, TH and Hwang, JY and Iacovelli, R and Iftime, D and Iorio, M and Jayachandran, S and Jeong, E and Jing, J and Jung, JJ and Kakumu, Y and Kalkreuter, E and Kang, KB and Kang, S and Kim, W and Kim, GJ and Kim, H and Kim, HU and Klapper, M and Koetsier, RA and Kollten, C and Kovács, &#xc1;T and Kriukova, Y and Kubach, N and Kunjapur, AM and Kushnareva, AK and Kust, A and Lamber, J and Larralde, M and Larsen, NJ and Launay, AP and Le, NT and Lebeer, S and Lee, BT and Lee, K and Lev, KL and Li, SM and Li, YX and Licona-Cassani, C and Lien, A and Liu, J and Lopez, JAV and Machushynets, NV and Macias, MI and Mahmud, T and Maleckis, M and Martinez-Martinez, AM and Mast, Y and Maximo, MF and McBride, CM and McLellan, RM and Bhatt, KM and Melkonian, C and Merrild, A and Metsä-Ketelä, M and Mitchell, DA and Müller, AV and Nguyen, GS and Nguyen, HT and Niedermeyer, THJ and O'Hare, JH and Ossowicki, A and Ostash, BO and Otani, H and Padva, L and Paliyal, S and Pan, X and Panghal, M and Parade, DS and Park, J and Parra, J and Rubio, MP and Pham, HT and Pidot, SJ and Piel, J and Pourmohsenin, B and Rakhmanov, M and Ramesh, S and Rasmussen, MH and Rego, A and Reher, R and Rice, AJ and Rigolet, A and Romero-Otero, A and Rosas-Becerra, LR and Rosiles, PY and Rutz, A and Ryu, B and Sahadeo, LA and Saldanha, M and Salvi, L and Sánchez-Carvajal, E and Santos-Medellin, C and Sbaraini, N and Schoellhorn, SM and Schumm, C and Sehnal, L and Selem, N and Shah, AD and Shishido, TK and Sieber, S and Silviani, V and Singh, G and Singh, H and Sokolova, N and Sonnenschein, EC and Sosio, M and Sowa, ST and Steffen, K and Stegmann, E and Streiff, AB and Strüder, A and Surup, F and Svenningsen, T and Sweeney, D and Szenei, J and Tagirdzhanov, A and Tan, B and Tarnowski, MJ and Terlouw, BR and Rey, T and Thome, NU and Torres Ortega, LR and Tørring, T and Trindade, M and Truman, AW and Tvilum, M and Udwary, DW and Ulbricht, C and Vader, L and van Wezel, GP and Walmsley, M and Warnasinghe, R and Weddeling, HG and Weir, ANM and Williams, K and Williams, SE and Witte, TE and Rocca, SMW and Yamada, K and Yang, D and Yang, D and Yu, J and Zhou, Z and Ziemert, N and Zimmer, L and Zimmermann, A and Zimmermann, C and van der Hooft, JJJ and Linington, RG and Weber, T and Medema, MH}, title = {MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D678-D690}, pmid = {39657789}, issn = {1362-4962}, support = {//Conahcyt Mexico International PhD Studentship/ ; 32170080//National Natural Science Foundation of China/ ; 547394769//German Research Foundation/ ; 101066127//European Union/ ; NNF19SA0059360//Novo Nordisk Foundation INTERACT/ ; //Swedish Pharmaceutical Society PostDoc/ ; F32AT011475/AT/NCCIH NIH HHS/United States ; //Werner Siemens Foundation/ ; 027/E5/PG.02.00.PL/2024//Ministry of Education/ ; ANR-17-EUR-0007//EUR Saclay Plant Sciences-SPS/ ; PROYEXCEL_00012//Spanish "Junta de Andaluc&#xed;a"/ ; 1347411//CONAHCYT/ ; IM230100154//Australian Research Council Industry Fellowship/ ; 1229222N//Research Foundation-Flanders (FWO)/ ; R01 GM146224/GM/NIGMS NIH HHS/United States ; //Swiss Federal Government/ ; OSF.23.1.044//NWO Open Science Project 'BiG-CODEC'/ ; //NWO Merian/ ; R01 GM097142/GM/NIGMS NIH HHS/United States ; 024.004.014//MiCRop Consortium/ ; CZIF2022-007203//Chan Zuckerberg Initiative Foundation/ ; BB/T007222/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DP230102668//Australian Research Council Discovery Project/ ; 57/0009//Ministry of Education and Science of Ukraine/ ; //Delta Stewardship Council Delta Science Program/ ; T32 GM136629/GM/NIGMS NIH HHS/United States ; //Basic Science Research Program/ ; R01-GM146224/GM/NIGMS NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; AUFF-E-2022-9-42//AUFF/ ; 10062709//UK Innovation Funding Agency (UKRI)/ ; CBET-2032243//U.S. National Science Foundation/ ; //University of Illinois/ ; //HZI POF IV Cooperativity and Creativity Project Call/ ; //Horizon Europe Marie Sk&#x142;odowska-Curie Actions Postdoctoral Fellowship/ ; NE/T010959/1//Signals in the Soil/ ; ANR-24-CE20-7299-01//Agence Nationale de la Recherche/ ; DNRF137//Danish National Research Foundation/ ; OCENW.GROOT.2019.063//NWO-XL/ ; BB/V005723/2//BBSRC/ ; 101087181//EU/ ; 101000392//Horizon 2020/ ; 101072485//European Union's Horizon/ ; 10.55776/P 34036//Austrian Science Fund/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; 23/01956-2//S&#xe3;o Paulo Research Foundation/ ; //Department of Biotechnology/ ; 222676//USDA Evans-Allen Research/ ; //Saarland University/ ; 102022750//SINTEF/ ; //Hans Fischer Society/ ; 21K06336//KAKENHI/ ; CF22-1239//Carlsberg Foundation/ ; ANR-22-CE44-0011-01 UMISYN//Agence Nationale de la Recherche/ ; 495740318//German Research Foundation/ ; 802736//European Union Horizon 2020/ ; //Strathclyde University Global Research Scholarship/ ; NNF22OC0079021//Novo Nordisk Foundation Postdoctoral Fellowship/ ; 101055020-COMMUNITY//ERC Advanced/ ; 101099528//European Innovation Council/ ; GNT2021638//National Health and Medical Research Council/ ; 757173//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; NA22NOS4200050//NERRS/ ; 865738/ERC_/European Research Council/International ; DGE 2241144//NSF GRFP/ ; //National Research Fund of Ukraine/ ; RYC2020-029240-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; MR/V022334/1//UKRI Future Leaders Fellowship/ ; 102029187//SEP AGREE/ ; NNF22OC0078997//Novo Nodisk Foundation/ ; F31 ES036421/ES/NIEHS NIH HHS/United States ; KICH1.LWV04.21.013//NWO/ ; DM60066//Italian Ministry of Research/ ; 101117891-MeDiSyn//ERC Starting/ ; //European Union's Horizon 2020 Research/ ; R01 GM123998/GM/NIGMS NIH HHS/United States ; NRF 2018R1A5A2023127//Korea Government (MSIT)/ ; PS00349981//Fulbright/ ; NRF-2020R1A6A1A03044512//Korean Government (MSIT)/ ; 735867//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 3141-00013A//Innovation Fund Denmark/ ; CFB 2.0//Novo Nordisk Foundation/ ; 21/07038-0//S&#xe3;o Paulo Research Foundation/ ; 2021YFA0909500//National Key Research and Development Program of China/ ; 101072485//European Union's Horizon Europe/ ; OCENW.XL21.XL21.088//NWO-XL/ ; //University Grants Commission/ ; //Natural Science and Research Council of Canada/ ; TTU 09.826//German Center for Infection Research/ ; //European Regional Development Fund/ ; 101072485//Horizon Europe Marie Sk&#x142;odowska-Curie/ ; DNRF137//Danish National Research Foundation CeMiSt/ ; BB/X010953/1//Growing Health Institute Strategic Programme/ ; BB/X01097X/1//BBSRC Institute Strategic Program/ ; 802736//European Union's Horizon 2020/ ; //Alexander von Humboldt-Stiftung/ ; //UK Government Department for Environment, Food &amp; Rural Affairs (DEFRA) Global Centre on Biodiversity for the Climate/ ; //Shanghai Pilot Program for Basic Research - Shanghai Jiao Tong University/ ; 102024676-14//POS BIOINFO 2024/ ; MR/W011247/1//UKRI Future Leaders Fellowship/ ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; 101106349//Marie Sklodowska-Curie/ ; T32-GM136629//Chemical-Biology Interface Training/ ; //University of Sydney/ ; 101000794//SECRETed EU Project Horizon 2020/ ; 2022R1C1C2004118//National Research Foundation of Korea/ ; //Indonesia Endowment Fund for Education Agency (LPDP)/ ; 101130799//European Union's Horizon/ ; 852600//Innovation Program ERC St/ ; //National Agri-Food Biotechnology Institute/ ; //German Academic Scholarship Foundation/ ; 205320_219638/SNSF_/Swiss National Science Foundation/Switzerland ; EXC-2124/1-09.029_0//Cluster of Excellence: Controlling Microbes to Fight Infection/ ; F32 AT011475/AT/NCCIH NIH HHS/United States ; 398967434-TRR 261//Deutsche Forschungsgemeinschaft/ ; 212747/SNSF_/Swiss National Science Foundation/Switzerland ; K445/2022//Leibniz Association/ ; NRF-RS-2024-00352229//Ministry of Science and ICT/ ; //Natural Sciences and Engineering Research Council of Canada Discovery/ ; VI.Veni.202.130//NWO Talent/ ; 106/IV/KS/11/2023//National Research and Innovation Agency/ ; T32GM136583/NH/NIH HHS/United States ; DE-AC02-05CH11231//U.S. Department of Energy/ ; }, mesh = {*Multigene Family ; *Databases, Genetic ; Biosynthetic Pathways/genetics ; Molecular Sequence Annotation ; Biological Products/metabolism/chemistry ; Data Curation ; }, abstract = {Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.}, }
@article {pmid39651958, year = {2024}, author = {Werlang, CA and Sahoo, JK and Cárcarmo-Oyarce, G and Stevens, C and Uzun, D and Putnik, R and Hasturk, O and Choi, J and Kaplan, DL and Ribbeck, K}, title = {Selective Biofilm Inhibition through Mucin-Inspired Engineering of Silk Glycopolymers.}, journal = {Journal of the American Chemical Society}, volume = {146}, number = {50}, pages = {34661-34668}, pmid = {39651958}, issn = {1520-5126}, support = {P41 EB027062/EB/NIBIB NIH HHS/United States ; }, mesh = {*Biofilms/drug effects ; *Mucins/chemistry/metabolism ; *Streptococcus mutans/drug effects ; *Silk/chemistry ; Humans ; Streptococcus sanguis/drug effects ; Streptococcus/drug effects/chemistry ; }, abstract = {Mucins are key components of innate immune defense and possess remarkable abilities to manage pathogenic microbes while supporting beneficial ones and maintaining microbial homeostasis at mucosal surfaces. Their unique properties have garnered significant interest in developing mucin-inspired materials as novel therapeutic strategies for selectively controlling pathogens without disrupting the overall microbial ecology. However, natural mucin production is challenging to scale, driving the need for simpler materials that reproduce mucin's bioactivity. In this work, we generated silk-based glycopolymers with different monosaccharides (GalNAc, GlcNAc, NeuNAc, GlcN, and GalN) and different grafting densities. Using the oral cavity as a model system, we treated in vitro cultures of pathogenic Streptococcus mutans and commensal Streptococcus sanguinis with our glycopolymers, finding that silk-tethered GalNAc uniquely prevented biofilm formation without affecting overall bacterial growth of either species. This relatively simple material reproduced mucin's virulence-neutralizing effects while maintaining biocompatibility. These mucin-inspired materials represent a valuable tool for preventing infection-related harm and offer a strategy for the domestication of pathogens in other environments.}, }
@article {pmid39651889, year = {2025}, author = {Wang, J and Schamp, CN and Hudson, LK and Chaggar, HK and Bryan, DW and Garman, KN and Radosevich, M and Denes, TG}, title = {Whole-genome sequencing and metagenomics reveal diversity and prevalence of Listeria spp. from soil in the Nantahala National Forest.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0171224}, pmid = {39651889}, issn = {2165-0497}, mesh = {*Soil Microbiology ; *Listeria/genetics/classification/isolation &amp; purification ; *Metagenomics ; *Whole Genome Sequencing ; North Carolina ; *Forests ; *Genome, Bacterial ; *Phylogeny ; Humans ; Listeriosis/microbiology/epidemiology/transmission ; Listeria monocytogenes/genetics/classification/isolation &amp; purification ; Metagenome ; Prevalence ; Soil/chemistry ; }, abstract = {UNLABELLED: Listeria spp. are widely distributed environmental bacteria associated with human foodborne illness. The ability to detect and characterize Listeria strains in the natural environment will contribute to improved understanding of transmission routes of contamination. The current standard for surveillance and outbreak source attribution is whole-genome sequencing (WGS) of Listeria monocytogenes clinical isolates. Recently, metagenomic sequencing has also been explored as a tool for the detection of Listeria spp. in environmental samples. This study evaluated soil samples from four locations across altitudes ranging from 1,500 to 4,500 ft in the Nantahala National Forest in North Carolina, USA. Forty-two Listeria isolates were cultured and sequenced, and 12 metagenomes of soil bacterial communities were generated. These isolates comprised 14 distinct strains from five species, including Listeria cossartiae subsp. cayugensis (n = 8; n represents the number of distinct strains), L. monocytogenes (n = 3), "Listeria swaminathanii" (Lsw) (n = 1), Listeria marthii (n = 1), and Listeria booriae (n = 1). Most strains (n = 13) were isolated from lower altitudes (1,500 or 2,500 ft), while the L. swaminathanii strain was isolated from both higher (4,500 ft) and lower (1,500 ft) altitudes. Metagenomic analysis of soil described a reduction in both bacterial community diversity and relative abundance of Listeria spp. as the altitude increased. Soil pH and cation exchange capacity were positively correlated (P < 0.05) with the abundance of Listeria spp. as detected by metagenomics. By integrating culture-independent metagenomics with culture-based WGS, this study advances current knowledge regarding distribution of Listeria spp. in the natural environment and suggests the potential for future use of culture-independent methods in tracking the transmission of foodborne pathogens.<br><br>IMPORTANCE: As a foodborne pathogen, Listeria continues to cause numerous illnesses in humans and animals. Studying the diversity and distribution of Listeria in soil is crucial for understanding potential sources of contamination and developing effective strategies to prevent foodborne outbreaks of listeriosis. Additionally, examining the ecological niches and survival mechanisms of Listeria in natural habitats provides insights into its persistence and adaptability, informing risk assessments and public health interventions. This research contributes to a broader understanding of microbial ecology and the factors influencing foodborne pathogen emergence, ultimately enhancing food safety and protecting public health. Moreover, using a metagenomic approach provides a detailed understanding of the soil microbial ecosystems, leading to more effective monitoring and control of foodborne pathogens. This study also highlights the potential for integrating metagenomics into routine surveillance systems for food safety in the near future.}, }
@article {pmid39644970, year = {2025}, author = {Tumeo, A and McDonagh, F and Kovarova, A and Ryan, K and Clarke, C and Miliotis, G}, title = {Draft genome sequence of a co-harbouring blaNDM-5 and mcr-1.1 Escherichia coli phylogroup A isolate associated with patient colonisation in Ireland.}, journal = {Journal of global antimicrobial resistance}, volume = {40}, number = {}, pages = {62-65}, doi = {10.1016/j.jgar.2024.11.018}, pmid = {39644970}, issn = {2213-7173}, mesh = {*Escherichia coli/genetics/isolation &amp; purification/drug effects/classification ; Humans ; Ireland ; *beta-Lactamases/genetics ; *Genome, Bacterial ; *Escherichia coli Infections/microbiology ; Whole Genome Sequencing ; *Escherichia coli Proteins/genetics ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Colistin/pharmacology ; Virulence Factors/genetics ; Multilocus Sequence Typing ; Plasmids ; }, abstract = {OBJECTIVES: While Escherichia coli phylogroup-A is typically associated with commensal strains, some isolates can harbour virulence and exhibit multidrug-resistant (MDR) phenotypes. We report the draft genome of a rare instance of carbapenem, fosfomycin and colistin resistant E. coli phylogroup-A, isolated as part of routine screening of a human patient in a clinical setting in Ireland.<br><br>METHODS: E. coli E230738 was identified using MALDI-ToF/MS. Antibiotic susceptibility testing was performed using the Sensititre-EUMDRXXF plate. Whole-genome-sequencing was conducted with NextSeq1000, and genomic analysis identified antibiotic-resistance-genes (ARGs) and virulence-factors (VFs). Phylogenetic analysis was performed using whole-genome-multilocus-sequence-typing (wgMLST).<br><br>RESULTS: E. coli E230738 genome was identified to belong to phylogroup-A/ST10 complex and to harbour 63 ARGs, 17 of which acquired. Resistance to beta-lactams, including carbapenems and cephalosporins was likely due to chromosomally identified blaNDM-5. Colistin resistance appeared associated with acquired mcr-1.1. Despite lacking fosfomycin-inactivating-enzymes, fosfomycin resistance was observed, possibly due to efflux pumps. Forty-seven chromosomal VFs were identified, involved in adhesion and iron acquisition amongst other properties. Plasmid replicons associated with the spread of MDR genes such as IncHI2/HI2A were detected. wgMLST analysis showed the closest relative being a strain from the UK, exhibiting differences in the sequences of 851 genes.<br><br>CONCLUSION: This is a first detected instance of a blaNDM-5 and mcr-1.1 co-occurring in E. coli in Ireland. The MDR profile of E. coli E230738 highlights the growing public health concern posed by the dissemination of MDR E. coli lineages with limited treatment options and underscores the need for clinical screening coupled with genomic surveillance to better understand evolving MDR patterns in E. coli.}, }
@article {pmid39642168, year = {2024}, author = {Champion, C and Momal, R and Le Chatelier, E and Sola, M and Mariadassou, M and Berland, M}, title = {OneNet-One network to rule them all: Consensus network inference from microbiome data.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1012627}, pmid = {39642168}, issn = {1553-7358}, mesh = {*Computational Biology/methods ; Humans ; *Microbiota/physiology ; *Algorithms ; *Gastrointestinal Microbiome/physiology ; Microbial Interactions/physiology ; }, abstract = {Modeling microbial interactions as sparse and reproducible networks is a major challenge in microbial ecology. Direct interactions between the microbial species of a biome can help to understand the mechanisms through which microbial communities influence the system. Most state-of-the art methods reconstruct networks from abundance data using Gaussian Graphical Models, for which several statistically grounded and computationnally efficient inference approaches are available. However, the multiplicity of existing methods, when applied to the same dataset, generates very different networks. In this article, we present OneNet, a consensus network inference method that combines seven methods based on stability selection. This resampling procedure is used to tune a regularization parameter by computing how often edges are selected in the networks. We modified the stability selection framework to use edge selection frequencies directly and combine them in the inferred network to ensure that only reproducible edges are included in the consensus. We demonstrated on synthetic data that our method generally led to slightly sparser networks while achieving much higher precision than any single method. We further applied the method to gut microbiome data from liver-cirrothic patients and demonstrated that the resulting network exhibited a microbial guild that was meaningful in terms of human health.}, }
@article {pmid39641603, year = {2025}, author = {Grimm, H and Lorenz, J and Straub, D and Joshi, P and Shuster, J and Zarfl, C and Muehe, EM and Kappler, A}, title = {Nitrous oxide is the main product during nitrate reduction by a novel lithoautotrophic iron(II)-oxidizing culture from an organic-rich paddy soil.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0126224}, pmid = {39641603}, issn = {1098-5336}, support = {project ID 431072007//Deutsche Forschungsgemeinschaft (DFG)/ ; project ID 390838134//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {*Nitrous Oxide/metabolism ; Oxidation-Reduction ; *Nitrates/metabolism ; *Soil Microbiology ; *Ferrous Compounds/metabolism ; China ; *Iron/metabolism ; Soil/chemistry ; *Gallionellaceae/metabolism/isolation &amp; purification ; }, abstract = {Microbial nitrate reduction coupled to iron(II) oxidation (NRFeOx) occurs in paddy soils due to high levels of dissolved iron(II) and regular application of nitrogen fertilizer. However, to date, there is no lithoautotrophic NRFeOx isolate or enrichment culture available from this soil environment. Thus, resulting impacts on greenhouse gas emissions during nitrate reduction (i.e., nitrous oxide [N2O]) and on toxic metalloid (i.e., arsenic) mobility can hardly be investigated. We enriched a lithoautotrophic NRFeOx culture, culture HP (Huilongpu paddy, named after its origin), from a paddy soil (Huilongpu Town, China), which was dominated by Gallionella (71%). The culture reduced 0.45 to 0.63 mM nitrate and oxidized 1.76 to 2.31 mM iron(II) within 4 days leading to N2O as the main N-product (62%-88% N2O-N of total reduced NO3[-]-N). Nitrite was present as an intermediate at a maximum of 0.16 ± 0.1 mM. Cells were associated with, but mostly not encrusted by, poorly crystalline iron(III) minerals (ferrihydrite). Culture HP performed best below an iron(II) threshold of 2.5-3.5 mM and in a pH range of 6.50-7.05. In the presence of 100 µM arsenite, only 0%-18% of iron(II) was oxidized. Due to low iron(II) oxidation, arsenite was not immobilized. However, the proportion of N2O-N of total reduced NO3[-]-N decreased from 77% to 30%. Our results indicate that lithoautotrophic NRFeOx occurs even in organic-rich paddy soils, resulting in denitrification and subsequent N2O emissions. The obtained novel enrichment culture allows us to study the impact of lithoautotrophic NRFeOx on arsenic mobility and N2O emissions in paddy soils.IMPORTANCEPaddy soils are naturally rich in iron(II) and regularly experience nitrogen inputs due to fertilization. Nitrogen fertilization increases nitrous oxide emissions as it is an intermediate product during nitrate reduction. Microorganisms can live using nitrate and iron(II) as electron acceptor and donor, respectively, but mostly require an organic co-substrate. By contrast, microorganisms that only rely on nitrate, iron(II), and CO2 could inhabit carbon-limited ecological niches. So far, no isolate or consortium of lithoautotrophic iron(II)-oxidizing, nitrate-reducing microorganisms has been obtained from paddy soil. Here, we describe a lithoautotrophic enrichment culture, dominated by a typical iron(II)-oxidizer (Gallionella), that oxidized iron(II) and reduced nitrate to nitrous oxide, negatively impacting greenhouse gas dynamics. High arsenic concentrations were toxic to the culture but decreased the proportion of nitrous oxide of the total reduced nitrate. Our results suggest that autotrophic nitrate reduction coupled with iron(II) oxidation is a relevant, previously overlooked process in paddy soils.}, }
@article {pmid39637856, year = {2025}, author = {Caty, SN and Alvarez-Buylla, A and Vasek, C and Tapia, EE and Martin, NA and McLaughlin, T and Golde, CL and Weber, PK and Mayali, X and Coloma, LA and Morris, MM and O'Connell, LA}, title = {Alkaloids are associated with increased microbial diversity and metabolic function in poison frogs.}, journal = {Current biology : CB}, volume = {35}, number = {1}, pages = {187-197.e8}, doi = {10.1016/j.cub.2024.10.069}, pmid = {39637856}, issn = {1879-0445}, mesh = {Animals ; *Alkaloids/metabolism ; *Microbiota ; *Anura/microbiology/metabolism ; Skin/microbiology/metabolism ; Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Poison Frogs ; }, abstract = {Shifts in host-associated microbiomes can impact both host and microbes.[1][,][2][,][3][,][4][,][5][,][6] It is of interest to understand how perturbations, like the introduction of exogenous chemicals,[7][,][8][,][9][,][10][,][11][,][12][,][13] impact microbiomes. In poison frogs (family Dendrobatidae), the skin microbiome is exposed to alkaloids that the frogs sequester for defense.[14][,][15][,][16][,][17][,][18][,][19] These alkaloids are antimicrobial[20][,][21][,][22]; however, their effect on the frogs' skin microbiome is unknown. To test this, we characterized microbial communities from field-collected dendrobatid frogs. Then, we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of two frog species with contrasting alkaloid loads in nature. In both datasets, we found that alkaloid-exposed microbiomes were more phylogenetically diverse, with an increase in diversity among rare taxa. To better understand the isolate-specific response to alkaloids, we cultured microbial isolates from poison frog skin and found that many isolates exhibited enhanced growth or were not impacted by the addition of DHQ. To further explore the microbial response to alkaloids, we sequenced the metagenomes from high- and low-alkaloid frogs and observed a greater diversity of genes associated with nitrogen and carbon metabolism in high-alkaloid frogs. From these data, we hypothesized that some strains may metabolize the alkaloids. We used stable isotope tracing coupled to nanoSIMS (nanoscale secondary ion mass spectrometry), which supported the idea that some of these isolates are able to metabolize DHQ. Together, these data suggest that poison frog alkaloids open new niches for skin-associated microbes with specific adaptations, such as alkaloid metabolism, that enable survival in this environment.}, }
@article {pmid39637512, year = {2025}, author = {Wilkie, I and Orellana, LH}, title = {Elusive marine Verrucomicrobiota: Seasonally abundant members of the novel genera Seribacter and Chordibacter specialize in degrading sulfated glycans.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {1}, pages = {126562}, doi = {10.1016/j.syapm.2024.126562}, pmid = {39637512}, issn = {1618-0984}, mesh = {Phylogeny ; *Polysaccharides/metabolism ; *Sulfates/metabolism ; RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; Seasons ; North Sea ; *Seawater/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Metagenome ; }, abstract = {Members of the phylum Verrucomicrobiota play a significant role in various ecosystems, yet they are underrepresented in databases due to their comparatively lower abundance and isolation challenges. The use of cultivation-independent approaches has unveiled their hidden diversity and specialized metabolic capabilities, yet many of these populations remain uncharacterized. In this study, we focus on members of the family MB11C04 associated with North Sea spring blooms. Our analyses revealed recurrent MB11C04 populations with increased abundance in the late stages of spring blooms over ten-years. By examining their genomic content, we identified specialized genetic features for the degradation of complex polysaccharides, particularly sulfated and fucose-rich compounds, suggesting their role in utilizing organic matter during the collapse of the bloom. Furthermore, we describe two novel genera each with a novel species (Seribacter gen. Nov., Chordibacter gen. Nov.) in accordance with the SeqCode initiative based on high quality metagenome-assembled genomes. We also propose a new name for the family MB11C04, Seribacteraceae. Our findings shed light on the ecological significance and metabolic potential of Verrucomicrobiota populations in spring bloom events.}, }
@article {pmid39633812, year = {2024}, author = {Bauchinger, F and Seki, D and Berry, D}, title = {Characteristics of putative keystones in the healthy adult human gut microbiota as determined by correlation network analysis.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1454634}, pmid = {39633812}, issn = {1664-302X}, abstract = {Keystone species are thought to play a critical role in determining the structure and function of microbial communities. As they are important candidates for microbiome-targeted interventions, the identification and characterization of keystones is a pressing research goal. Both empirical as well as computational approaches to identify keystones have been proposed, and in particular correlation network analysis is frequently utilized to interrogate sequencing-based microbiome data. Here, we apply an established method for identifying putative keystone taxa in correlation networks. We develop a robust workflow for network construction and systematically evaluate the effects of taxonomic resolution on network properties and the identification of keystone taxa. We are able to identify correlation network keystone species and genera, but could not detect taxa with high keystone potential at lower taxonomic resolution. Based on the correlation patterns observed, we hypothesize that the identified putative keystone taxa have a stabilizing effect that is exerted on correlated taxa. Correlation network analysis further revealed subcommunities present in the dataset that are remarkably similar to previously described patterns. The interrogation of available metatranscriptomes also revealed distinct transcriptional states present in all putative keystone taxa. These results suggest that keystone taxa may have stabilizing properties in a subset of community members rather than global effects. The work presented here contributes to the understanding of correlation network keystone taxa and sheds light on their potential ecological significance.}, }
@article {pmid39633134, year = {2024}, author = {Han, GH and Yu, J and Kang, MJ and Park, MJ and Noh, CH and Kim, YJ and Kwon, KK}, title = {Phylosymbiosis in Seven Wild Fish Species Collected Off the Southern Coast of Korea: Skin Microbiome Most Strongly Reflects Evolutionary Pressures.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {153}, pmid = {39633134}, issn = {1432-184X}, support = {20210469//Ministry of Oceans and Fisheries/ ; }, mesh = {Animals ; Republic of Korea ; *Microbiota ; *Skin/microbiology ; *Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Fishes/microbiology ; *Symbiosis ; *Bacteria/classification/genetics/isolation &amp; purification ; Gills/microbiology ; Biological Evolution ; Species Specificity ; }, abstract = {Phylosymbiosis is defined as the relationship in which the microbiome recapitulates the phylogeny of the host and has been demonstrated in a variety of terrestrial organisms, although it has been understudied in fish, the most phylogenetically diverse vertebrate. Given that the species-specificity of fish microbiomes was detected in multiple body parts and differed by body parts, we assumed that the phylogenetic reflection of the microbiome would differ across body parts. Thus, we analyze the difference of phylosymbiotic relationships in the microbial communities found in three body parts (skin, gills, and intestine) of seven wild fish species from four families (Labridae, Sebastidae, Sparidae, and Rajidae) via 16S rRNA gene amplicon sequencing. Fishes were purchased at Docheon port market in Tongyeong City, Korea and were transported to nearby research institutes for aliveness. Mantel tests using dissimilarity values of microbiomes and hosts' divergence times showed that the differences in microbial communities in all three body parts were related to the hosts' divergence time. This pattern was the most pronounced in the skin. Furthermore, fishes from the same family showed similar bacterial compositions on their skins and gills, with clear differences depending on the family, with the exception of Labridae. These results suggest that the skin microbiome is particularly vulnerable to evolutionary pressures. We hypothesized that the evolution of the fish immune system and the difference in feeding habits induced the stronger phylosymbiotic signal in the skin. Collectively, this dataset will be useful for understanding the fish microbiome and give insights into phylosymbiosis of aquatic animals across body parts.}, }
@article {pmid39633061, year = {2024}, author = {Paduano, S and Marchesi, I and Valeriani, F and Frezza, G and Facchini, MC and Romano Spica, V and Bargellini, A}, title = {Characterization by 16S Amplicon Sequencing of Bacterial Communities Overall and During the Maturation Process of Peloids in Two Spas of an Italian Thermal Complex.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {152}, pmid = {39633061}, issn = {1432-184X}, mesh = {*Bacteria/genetics/classification/isolation &amp; purification ; Italy ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Clay/chemistry ; Biodiversity ; High-Throughput Nucleotide Sequencing ; DNA, Bacterial/genetics ; Mineral Waters/microbiology ; Phylogeny ; }, abstract = {Peloids are made by mixing clay materials with thermo-mineral waters, enriched with organic substances from microorganisms during maturation. Their beneficial properties may depend on clay minerals, water characteristics, and microbial components, although strong evidence is lacking. Next Generation Sequencing (NGS) allows a comprehensive approach to studying the entire microbial community, including cultivable and uncultivable bacteria. Our study aims to characterize, by NGS, the bacterial community overall and during the maturation process of thermal muds in two spas (A-B) of an Italian thermal complex. Peloids were produced from sulfurous-bromine-iodine thermal water and clay material: natural mud for spa A and sterile clay for spa B. Thermal waters and peloids at different maturation stages (2/4/6 months) were analyzed for microbiome characterization by 16S amplicon sequencing. Biodiversity profiles showed a low level of similarity between peloids and water used for their maturation. Peloids from spa A showed greater microbial richness than those from spa B, suggesting that natural mud with an existing bacterial community leads to greater biodiversity than sterile clay. Genera involved in sulfur metabolism were prevalent in both spas, as expected considering peloids matured in sulfide-rich water. For all three maturation stages, the prevalent genera were Thiobacillus and Pelobacter in spa A and Thiobacillus, Thauera, Pelobacter, and Desulfuromonas in spa B. Richness and diversity indices showed that the community seemed to stabilize after 2-4 months. The 16S amplicon sequencing to study bacterial communities enables the identification of a biological signature that characterizes a specific thermal matrix, defining its therapeutic and cosmetic properties. The bacterial composition of peloids is affected by the thermal water and the type of clay material used in their formulation and maturation.}, }
@article {pmid39632307, year = {2025}, author = {Delmoitié, B and Sakarika, M and Rabaey, K and De Wever, H and Regueira, A}, title = {Tailoring non-axenic lactic acid fermentation from cheese whey permeate targeting a flexible lactic acid platform.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123529}, doi = {10.1016/j.jenvman.2024.123529}, pmid = {39632307}, issn = {1095-8630}, mesh = {*Cheese ; Fermentation ; *Whey/metabolism ; *Lactic Acid/metabolism ; Hydrogen-Ion Concentration ; Temperature ; }, abstract = {Lactic acid (LA) is an important biobased platform chemical, with potential applications in synthetising a wide range of chemical products or serving as feedstock for various bioprocesses. Industrial LA production via pure culture fermentation is characterized by high operational costs and utilizes food-grade sugars, thereby reducing the feasibility of LA applications. In this context, our research focussed on valorising the largest dairy side stream, cheese whey permeate, through the use of mixed microbial communities. We evaluated the effect of different operational parameters (temperature, pH and hydraulic retention time) in non-axenic fermentations on productivity, yield, concentration, optical purity, and community. Our findings revealed that operating at mildly thermophilic conditions (45 °C) resulted in highly selective LA production, and significantly augmented the LA yield, and productivity, compared to higher temperatures (50-55 °C). In addition, operating at circumneutral pH conditions (6.0-6.5) led to significantly increased the LA fermentation performance compared to the conventional acid pH conditions (≤5.5). This led to an unprecedented LA productivity of 27.4 g/L/h with a LA yield of 70.0% which is 2.5 times higher compared to previous reported maximum. Additionally, varying pH levels influenced the optical purity of LA: we achieved an optical L-LA purity of 98.3% at pH 6.0-6.5, and an optical D-LA purity of 91.3% at a pH of 5.5. A short hydraulic retention time of less than 12 h was crucial for selective LA production. This process also yielded a microbial biomass composed of 90.3-98.6% Lactobacillus delbrueckii, which could be potentially valorised as probiotic or protein ingredient in food or feed products. Our work shows that by careful selection of operational conditions, the overall performance can be significantly increased compared to the state-of-the-art. These results highlight the potential of non-sterile LA fermentation and show that careful selection of simple reactor operation parameters can maximize process performance. A preliminary assessment suggests that valorising EU cheese whey permeate could increase LA and poly-LA production by 40 and 125 times, respectively. This could also lead to the production of 4,000 kton protein-rich biomass, potentially reducing CO2 emissions linked to EU food and feed production by 4.87% or 2.77% respectively.}, }
@article {pmid39629059, year = {2024}, author = {Pecsi, EL and Forbes, S and Guillemette, F}, title = {Organic Matter Composition as a Driver of Soil Bacterial Responses to Pig Carcass Decomposition in a Canadian Continental Climate.}, journal = {Journal of geophysical research. Biogeosciences}, volume = {129}, number = {12}, pages = {e2024JG008355}, pmid = {39629059}, issn = {2169-8953}, abstract = {Organic by-products are released into the surrounding soil during the terrestrial decomposition of animal remains. The affected area, known as the Cadaver Decomposition Island (CDI), can undergo biochemical changes that contribute to landscape heterogeneity. Soil bacteria are highly sensitive to labile inputs, but it is unknown how they respond to shifts in dissolved organic matter (DOM) quantity and quality resulting from animal decomposition. We aimed to evaluate the relationship between soil DOM composition and bacterial activity/function in CDIs under a Canadian temperate continental climate. This was studied in soils surrounding adult pig carcasses (n = 3) that were surface deposited within a mixed forested environment (Trois-Rivières, Québec) in June 2019. Using fluorescence spectroscopy and dissolved organic carbon analyses, we detected a pulse of labile protein-like DOM during the summer season (day 55). This was found to be an important driver of heightened soil bacterial respiration, cell abundance and potential carbohydrate metabolism. These bacterial disturbances persisted into the cooler autumn season (day 156) and led to the gradual transformation of labile DOM inputs into microbially sourced humic-like compounds. By the spring (day 324), DOM quantities and bacterial measures almost recovered, but DOM quality remained distinct from surrounding vegetal humic signals. All observed effects were spatially constrained to the topsoil (A-horizon) and within 20 cm laterally from the carcasses. These findings provide valuable insight into CDI organic matter cycling within a cold-climate ecosystem. Repeated CDI studies will however be required to capture the changing dynamics resulting from increasing global temperatures.}, }
@article {pmid39628456, year = {2024}, author = {Sinclair, JS and Buchner, D and Gessner, MO and Müller, J and Pauls, SU and Stoll, S and Welti, EAR and Bässler, C and Buse, J and Dziock, F and Enss, J and Hörren, T and Künast, R and Li, Y and Marten, A and Morkel, C and Richter, R and Seibold, S and Sorg, M and Twietmeyer, S and Weis, D and Weisser, W and Wiggering, B and Wilmking, M and Zotz, G and Frenzel, M and Leese, F and Haase, P}, title = {Effects of land cover and protected areas on flying insect diversity.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {}, number = {}, pages = {e14425}, doi = {10.1111/cobi.14425}, pmid = {39628456}, issn = {1523-1739}, support = {//Hessisches Landesamt f&#xfc;r Umwelt und Geologie/ ; //LOEWE Centre for Translational Biodiversity Genomics/ ; 871128//EU Horizon project eLTER PLUS/ ; }, abstract = {Widespread insect losses are a critical global problem. Mitigating this problem requires identifying the principal drivers across different taxa and determining which insects are covered by protected areas. However, doing so is hindered by missing information on most species owing to extremely high insect diversity and difficulties in morphological identification. To address this knowledge gap, we used one of the most comprehensive insect DNA metabarcoding data sets assembled (encompassing 31,846 flying insect species) in which data were collected from a network of 75 Malaise traps distributed across Germany. Collection sites encompass gradients of land cover, weather, and climate, along with differences in site protection status, which allowed us to gain broader insights into how insects respond to these factors. We examined changes in total insect biomass, species richness, temporal turnover, and shifts in the composition of taxa, key functional groups (pollinators, threatened species, and invasive species), and feeding traits. Lower insect biomass generally equated to lower richness of all insects and higher temporal turnover, suggesting that biomass loss translates to biodiversity loss and less stable communities. Spatial variability in insect biomass and composition was primarily driven by land cover, rather than weather or climate change. As vegetation and land-cover heterogeneity increased, insect biomass increased by 50% in 2019 and 56% in 2020 and total species richness by 58% and 33%, respectively. Similarly, areas with low-vegetation habitats exhibited the highest richness of key taxa, including pollinators and threatened species, and the widest variety of feeding traits. However, these habitats tended to be less protected despite their higher diversity. Our results highlight the value of heterogeneous low vegetation for promoting overall insect biomass and diversity and that better protection of insects requires improved protection and management of unforested areas, where many biodiversity hotspots and key taxa occur.}, }
@article {pmid39624182, year = {2024}, author = {Wirth, JS and Katz, LS and Williams, GM and Chen, JC}, title = {primerForge: a Python program for identifying primer pairs capable of distinguishing groups of genomes from each other.}, journal = {Journal of open source software}, volume = {9}, number = {101}, pages = {}, pmid = {39624182}, issn = {2475-9066}, support = {CC999999/ImCDC/Intramural CDC HHS/United States ; }, abstract = {In both molecular epidemiology and microbial ecology, it is useful to be able to categorize specific strains of microorganisms in either an ingroup or an outgroup in a given population, e.g. to distinguish a pathogenic strain of interest from its non-virulent relatives. An "ingroup" refers to a group of microbes that are the primary focus of study or interest. Conversely, an "outgroup" consists of microbes that are closely-related to, but have evolved separately from, the ingroup. While whole genome sequencing and downstream phylogenetic analyses can be employed to do this, these techniques are often slow and can be resource intensive. Additionally, the laboratory would have to sequence the whole genome to use these tools to determine whether or not a new sample is part of the ingroup or outgroup. Alternatively, polymerase chain reaction (PCR) can be used to amplify regions of genetic material that are specific to the strain(s) of interest. PCR is faster, less expensive, and more accessible than whole genome sequencing, so having a PCR-based approach can accelerate the detection of specific strain(s) of microbes and facilitate diagnoses and/or population studies.}, }
@article {pmid39621250, year = {2024}, author = {Lin, X and Lin, C and Li, X and Yao, F and Guo, X and Wang, M and Zeng, M and Yuan, Y and Xie, Q and Huang, X and Jiao, X}, title = {Gut Microbiota Dysbiosis Facilitates Susceptibility to Bloodstream Infection.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {62}, number = {12}, pages = {1113-1124}, pmid = {39621250}, issn = {1976-3794}, support = {201224106490150//Shantou Science and Technology Project/ ; }, mesh = {Humans ; *Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Adult ; Bacteremia/microbiology ; Disease Susceptibility ; DNA, Bacterial/genetics ; }, abstract = {To study the role of intestinal flora in the development of bloodstream infections (BSIs). 42 patients and 19 healthy controls (HCs) were screened into the study and their intestinal flora was measured by 16S rRNA gene sequencing. The bacterial diversity was significantly lower in the BSI group compared with that in the HCs (P < 0.001), and beta diversity was significantly differentiated between the two groups (PERMANOVA, P = 0.001). The four keystone species [Roseburia, Faecalibacterium, Prevotella, and Enterococcus (LDA > 4)] differed significantly between the two groups. Dysbiosis of fecal microbial ecology is a common condition present in patients with BSI. The proliferation of certain pathogens or reduction of SCFA-producing bacteria would cause susceptibility to BSI.}, }
@article {pmid39619625, year = {2024}, author = {Sakarika, M and Matassa, S and Carvajal-Arroyo, JM and Ganigué, R}, title = {Editorial: Microbial biorefineries for a more sustainable, circular economy.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {12}, number = {}, pages = {1512756}, doi = {10.3389/fbioe.2024.1512756}, pmid = {39619625}, issn = {2296-4185}, }
@article {pmid39612478, year = {2025}, author = {Zhao, Y and Ran, W and Xu, W and Song, Y}, title = {ITS amplicon sequencing revealed that rare taxa of tea rhizosphere fungi are closely related to the environment and provide feedback on tea tree diseases.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0188924}, pmid = {39612478}, issn = {2165-0497}, support = {32260120//MOST | National Natural Science Foundation of China (NSFC)/ ; Qiankehejichu-ZK [2023] General 257//Guizhou Natural Science Foundation/ ; Qiankehepingtairencai-GCC [2023]032//Training Program for High-level Innovative Talents of Guizhou Province/ ; Qiankehepingtairencai-CXTD [2023]010//Science and Techonlogy Innovation Talent Team Building Project of Guizhou Province/ ; }, mesh = {*Rhizosphere ; *Soil Microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Camellia sinensis/microbiology ; *Plant Diseases/microbiology ; China ; Symbiosis ; Tea/microbiology ; High-Throughput Nucleotide Sequencing ; Phylogeny ; }, abstract = {The rhizospheres of plants and soil microorganisms are intricately interconnected. Tea trees are cultivated extensively on the karst plateau of Guizhou Province, China; however, the understanding of the interactions among fungal communities, community taxa, and diseases impacting tea tree in the soil rhizosphere is limited. Our aim is to offer insights for the advancement of modern agriculture in ecologically fragile karst tea gardens, as well as microbiomics concepts for green and sustainable environmental development. This study utilized the internal transcribed spacer high-throughput sequencing technology to explore the symbiotic relationship between rhizosphere fungi and plant disease feedback in multiple tea estates across the Guizhou Plateau. The ecological preferences and environmental thresholds of fungi were investigated via environmental variables. Furthermore, a correlation was established between different taxa and individual soil functions. Research has indicated that tea leaf blight disrupts symbiotic connections among fungal groups. For various taxa, we found that numerous taxa consistently maintained core positions within the community, whereas rare taxa were able to stabilize due to a high proportion of positive effects. Additionally, abundant taxa presented a wider range of environmental feedback, whereas the rare taxon diversity presented a stronger positive association with the soil Z score. This study contributes to our understanding of the importance of rare taxa in plant rhizosphere soil processes. Emphasis should be placed on the role of rare taxa in pest and disease control within green agriculture while also strengthening systematic development and biogeographical research related to rare taxa in this region.IMPORTANCEIn this study, based on internal transcribed spacer high-throughput sequencing, fungal communities in the rhizosphere soil of tea trees and their interactions with the environment in karst areas were reported, and the symbiotic relationships of different fungal taxa and their feedback to the environment were described in detail by using the knowledge of microbial ecology. On this basis, it was found that tea tree diseases affect the symbiotic relationships of fungal taxa. At the same time, we found that rare taxa have stronger cooperative relationships in response to environmental changes and explored their participation in soil processes based on fungal trait sets. This study will provide basic data for the development of modern agriculture in tea gardens and theoretical basis for the sustainable prevention and control of tea tree diseases.}, }
@article {pmid39611982, year = {2024}, author = {Kou, Z and Liu, J and Tohti, G and Zhu, X and Zheng, B and Zhu, Y and Zhang, W}, title = {Distinct Bacterial Communities Within the Nonrhizosphere, Rhizosphere, and Endosphere of Ammodendron bifolium Under Winter Condition in the Takeermohuer Desert.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {151}, pmid = {39611982}, issn = {1432-184X}, support = {2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; }, mesh = {*Rhizosphere ; *Bacteria/classification/genetics/isolation &amp; purification ; *Soil Microbiology ; *Desert Climate ; *Seasons ; Plant Roots/microbiology ; Soil/chemistry ; Microbiota ; }, abstract = {Due to human activities and severe climatic conditions, the population of Ammodendron bifolium, an excellent sand-fixing plant, has gradually decreased in the Takeermohuer Desert. The plant-associated bacteria community can enhance its survival in harsh environments. However, the understanding of A. bifolium-associated bacterial community is still unclear during the harsh winter. We investigated the bacterial community structure from the A. bifolium rhizosphere and nonrhizosphere at different depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) and from endosphere (i.e., root endosphere and stem endosphere) in winter. At the same time, we analyzed the impact of different compartments and soil factors on the bacterial community structure. Studies have shown that the A. bifolium rhizosphere exhibits higher levels of SOM (soil organic matter), SOC (soil organic carbon), SAN (soil alkaline nitrogen), and SAK (soil available potassium) compared with the nonrhizosphere. The dominant bacterial phyla were Proteobacteria (19.6%), Cyanobacteria (15.9%), Actinobacteria (13.6%), Acidobacteria (9.0%), and Planctomycetota (5.7%) in the desert. Proteobacteria (24.0-30.2%) had the highest relative abundance in rhizosphere, Actinobacteria (18.3-22.6%) had the highest relative abundance in nonrhizosphere, and Cyanobacteria had the highest relative abundance in endosphere. At the genus level, the relative abundance of Pseudomonas (1.2%) in the root endosphere was the highest and the other genera were mostly unclassified. The Chao1 and PD_whole_tree indices showed that the diversity of the bacterial communities decreased from nonrhizosphere, rhizosphere, root endosphere to stem endosphere. Co-occurrence network analyses identified Proteobacteria and Actinobacteria as key species across the three compartments. Additionally, unique keystone species like Cyanobacteria, Verrucomicrobiota, and Desulfobacterota were found only in the endosphere. The bacterial community in the rhizosphere was influenced by factors such as EC (electrical conductivity), STC (soil total carbon), SOM, SOC, STN (soil total nitrogen), SAN, STP (soil total phosphorus), and SAK, while that of the nonrhizosphere was mainly influenced by pH, C/N (STC/STN), SAP, and distance. The study highlighted differences in bacterial community composition, diversity, and influencing factors across the three compartments, which can provide a better understanding of the association/interactions between A. bifolium and bacterial communities and lay a foundation for revealing its adaptability in winter.}, }
@article {pmid39611949, year = {2024}, author = {Makumbi, JP and Leareng, SK and Pierneef, RE and Makhalanyane, TP}, title = {Synergizing Ecotoxicology and Microbiome Data Is Key for Developing Global Indicators of Environmental Antimicrobial Resistance.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {150}, pmid = {39611949}, issn = {1432-184X}, support = {UID 110717//National Research Foundation of South Africa/ ; UID 110717//National Research Foundation of South Africa/ ; }, mesh = {*Microbiota/drug effects ; Humans ; *Ecotoxicology ; Animals ; Risk Assessment ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Public Health ; Drug Resistance, Microbial ; }, abstract = {The One Health concept recognises the interconnectedness of humans, plants, animals and the environment. Recent research strongly supports the idea that the environment serves as a significant reservoir for antimicrobial resistance (AMR). However, the complexity of natural environments makes efforts at AMR public health risk assessment difficult. We lack sufficient data on key ecological parameters that influence AMR, as well as the primary proxies necessary for evaluating risks to human health. Developing environmental AMR 'early warning systems' requires models with well-defined parameters. This is necessary to support the implementation of clear and targeted interventions. In this review, we provide a comprehensive overview of the current tools used globally for environmental AMR human health risk assessment and the underlying knowledge gaps. We highlight the urgent need for standardised, cost-effective risk assessment frameworks that are adaptable across different environments and regions to enhance comparability and reliability. These frameworks must also account for previously understudied AMR sources, such as horticulture, and emerging threats like climate change. In addition, integrating traditional ecotoxicology with modern 'omics' approaches will be essential for developing more comprehensive risk models and informing targeted AMR mitigation strategies.}, }
@article {pmid39611829, year = {2025}, author = {Hameed, A and McDonagh, F and Sengupta, P and Miliotis, G and Sivabalan, SKM and Szydlowski, L and Simpson, A and Singh, NK and Rekha, PD and Raman, K and Venkateswaran, K}, title = {Neobacillus driksii sp. nov. isolated from a Mars 2020 spacecraft assembly facility and genomic potential for lasso peptide production in Neobacillus.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0137624}, pmid = {39611829}, issn = {2165-0497}, support = {Mars Program Office//NASA | Jet Propulsion Laboratory (JPL)/ ; IBSE//Indian Institute of Technology Madras (IITM)/ ; WSAI//Indian Institute of Technology Madras (IITM)/ ; }, mesh = {*Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Spacecraft ; *Mars ; Genome, Bacterial ; Fatty Acids/metabolism/analysis ; DNA, Bacterial/genetics ; Genomics ; Base Composition ; Bacillales/genetics/classification/isolation &amp; purification/metabolism ; Soil Microbiology ; Peptides/metabolism ; Whole Genome Sequencing ; }, abstract = {UNLABELLED: During microbial surveillance of the Mars 2020 spacecraft assembly facility, two novel bacterial strains, potentially capable of producing lasso peptides, were identified. Characterization using a polyphasic taxonomic approach, whole-genome sequencing and phylogenomic analyses revealed a close genetic relationship among two strains from Mars 2020 cleanroom floors (179-C4-2-HS, 179-J1A1-HS), one strain from the Agave plant (AT2.8), and another strain from wheat-associated soil (V4I25). All four strains exhibited high 16S rRNA gene sequence similarity (>99.2%) and low average nucleotide identity (ANI) with Neobacillus niacini NBRC 15566[T], delineating new phylogenetic branches within the genus. Detailed molecular analyses, including gyrB (90.2%), ANI (86.4%), average amino acid identity (87.8%) phylogenies, digital DNA-DNA hybridization (32.6%), and percentage of conserved proteins (77.7%) indicated significant divergence from N. niacini NBRC 15566[T]. Consequently, these strains have been designated Neobacillus driksii sp. nov., with the type strain 179-C4-2-HS[T] (DSM 115941[T] = NRRL B-65665[T]). N. driksii grew at 4°C to 45°C, pH range of 6.0 to 9.5, and 0.5% to 5% NaCl. The major cellular fatty acids are iso-C15:0 and anteiso-C15:0. The dominant polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminolipid. Metagenomic analysis within NASA cleanrooms revealed that N. driksii is scarce (17 out of 236 samples). Genes encoding the biosynthesis pathway for lasso peptides were identified in all N. driksii strains and are not commonly found in other Neobacillus species, except in 7 out of 26 recognized species. This study highlights the unique metabolic capabilities of N. driksii, underscoring their potential in antimicrobial research and biotechnology.<br><br>IMPORTANCE: The microbial surveillance of the Mars 2020 assembly cleanroom led to the isolation of novel N. driksii with potential applications in cleanroom environments, such as hospitals, pharmaceuticals, semiconductors, and aeronautical industries. N. driksii genomes were found to possess genes responsible for producing lasso peptides, which are crucial for antimicrobial defense, communication, and enzyme inhibition. Isolation of N. driksii from cleanrooms, Agave plants, and dryland wheat soils, suggested niche-specific ecology and resilience under various environmentally challenging conditions. The discovery of potent antimicrobial agents from novel N. driksii underscores the importance of genome mining and the isolation of rare microorganisms. Bioactive gene clusters potentially producing nicotianamine-like siderophores were found in N. driksii genomes. These siderophores can be used for bioremediation to remove heavy metals from contaminated environments, promote plant growth by aiding iron uptake in agriculture, and treat iron overload conditions in medical applications.}, }
@article {pmid39611809, year = {2025}, author = {Mermans, F and Chatzigiannidou, I and Teughels, W and Boon, N}, title = {Quantifying synthetic bacterial community composition with flow cytometry: efficacy in mock communities and challenges in co-cultures.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0100924}, pmid = {39611809}, issn = {2379-5077}, mesh = {*Flow Cytometry/methods ; RNA, Ribosomal, 16S/genetics ; Coculture Techniques/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota/genetics ; Humans ; DNA, Bacterial/genetics ; }, abstract = {Determination of bacterial community composition in synthetic communities is critical for understanding microbial systems. The community composition is typically determined through bacterial plating or through PCR-based methods, which can be labor-intensive, expensive, or prone to bias. Simultaneously, flow cytometry has been suggested as a cheap and fast alternative. However, since the technique captures the phenotypic state of bacterial cells, accurate determination of community composition could be affected when bacteria are co-cultured. We investigated the performance of flow cytometry for quantifying oral synthetic communities and compared it to the performance of strain specific qPCR and 16S rRNA gene amplicon sequencing. Therefore, axenic cultures, mock communities and co-cultures of oral bacteria were prepared. Random forest classifiers trained on flow cytometry data of axenic cultures were used to determine the composition of the synthetic communities, as well as strain specific qPCR and 16S rRNA gene amplicon sequencing. Flow cytometry was shown to have a lower average root mean squared error and outperformed the PCR-based methods in even mock communities (flow cytometry: 0.11 ± 0.04; qPCR: 0.26 ± 0.09; amplicon sequencing: 0.15 ± 0.01). When bacteria were co-cultured, neither flow cytometry, strain-specific qPCR, nor 16S rRNA gene amplicon sequencing resulted in similar community composition. Performance of flow cytometry was decreased compared with mock communities due to changing phenotypes. Finally, discrepancies between flow cytometry and strain-specific qPCR were found. These findings highlight the challenges ahead for quantifying community composition in co-cultures by flow cytometry.IMPORTANCEQuantification of bacterial composition in synthetic communities is crucial for understanding and steering microbial interactions. Traditional approaches like plating, strain-specific qPCR, and amplicon sequencing are often labor-intensive and expensive and limit high-throughput experiments. Recently, flow cytometry has been suggested as a swift and cheap alternative for quantifying communities and has been successfully demonstrated on simple bacterial mock communities. However, since flow cytometry measures the phenotypic state of cells, measurements can be affected by differing phenotypes. Especially, changing phenotypes resulting from co-culturing bacteria can have a profound effect on the applicability of the technique in this context. This research illustrates the feasibility and challenges of flow cytometry for the determination of community structure in synthetic mock communities and co-cultures.}, }
@article {pmid39609949, year = {2024}, author = {Almela, P and Elser, JJ and Giersch, JJ and Hotaling, S and Rebbeck, V and Hamilton, TL}, title = {Laboratory Experiments Suggest a Limited Impact of Increased Nitrogen Deposition on Snow Algae Blooms.}, journal = {Environmental microbiology reports}, volume = {16}, number = {6}, pages = {e70052}, pmid = {39609949}, issn = {1758-2229}, support = {2113783//National Science Foundation/ ; 2113784//National Science Foundation/ ; }, mesh = {*Nitrogen/metabolism/analysis ; *Snow/chemistry ; *Phosphorus/metabolism/analysis ; *Eutrophication ; *Biomass ; }, abstract = {Snow algal blooms decrease snow albedo and increase local melt rates. However, the causes behind the size and frequency of these blooms are still not well understood. One factor likely contributing is nutrient availability, specifically nitrogen and phosphorus. The nutrient requirements of the taxa responsible for these blooms are not known. Here, we assessed the growth of three commercial strains of snow algae under 24 different nutrient treatments that varied in both absolute and relative concentrations of nitrogen and phosphorus. After 38 days of incubation, we measured total biomass and cell size and estimated their effective albedo reduction surface. Snow algal strains tended to respond similarly and achieved bloom-like cell densities over a wide range of nutrient conditions. However, the molar ratio of nitrogen to phosphorus at which maximum biomass was achieved was between 4 and 7. Our data indicate a high requirement for phosphorus for snow algae and highlights phosphorus availability as a critical factor influencing the frequency and extent of snow algae blooms and their potential contribution to snow melt through altered albedo. Snow algae can thrive across a range of nitrogen (N) and phosphorus (P) conditions, with a higher P requirement for optimal growth. Our study suggests that increased N deposition may have a limited impact on snow algae bloom occurrence and size, emphasising P as a key factor influencing these blooms and their potential to accelerate snow melt by lowering albedo.}, }
@article {pmid39609930, year = {2024}, author = {Paquette, AJ and Bhatnagar, S and Vadlamani, A and Gillis, T and Khot, V and Novotnik, B and De la Hoz Siegler, H and Strous, M and Rattray, JE}, title = {Ecology and biogeochemistry of the microbial underworld in two sister soda lakes.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {98}, pmid = {39609930}, issn = {2524-6372}, abstract = {BACKGROUND: Approximately 3.7 billion years ago, microbial life may have emerged in phosphate-rich salty ponds. Surprisingly, analogs of these environments are present in alkaline lake systems, recognized as highly productive biological ecosystems. In this study, we investigate the microbial ecology of two Canadian soda lake sediment systems characterized by naturally high phosphate levels.<br><br>RESULTS: Using a comprehensive approach involving geochemistry, metagenomics, and amplicon sequencing, we discovered that groundwater infiltration into Lake Goodenough sediments supported stratified layers of microbial metabolisms fueled by decaying mats. Effective degradation of microbial mats resulted in unexpectedly low net productivity. Evaporation of water from Last Chance Lake and its sediments led to saturation of brines and a habitat dominated by inorganic precipitation reactions, with low productivity, low organic matter turnover and little biological uptake of phosphorus, leading to high phosphate concentrations. Highly alkaline brines were found to be dominated by potentially dormant spore-forming bacteria. These saturated brines also hosted potential symbioses between Halobacteria and Nanoarchaeaota, as well as Lokiarchaea and bacterial sulfate reducers. Metagenome-assembled genomes of Nanoarchaeaota lacked strategies for coping with salty brines and were minimal for Lokiarchaea.<br><br>CONCLUSIONS: Our research highlights that modern analogs for origin-of-life conditions might be better represented by soda lakes with low phosphate concentrations. Thus, highly alkaline brine environments could be too extreme to support origin of life scenarios. These findings shed light on the complex interplay of microbial life in extreme environments and contribute to our understanding of early Earth environments.}, }
@article {pmid39608606, year = {2025}, author = {Lee, JY and Jo, YH and Kim, TH and Lee, SE and Hong, ES and Kang, TS}, title = {Microbial and Sensory Characteristics of Traditional Watery Kimchi (Dongchimi) Fortified with Probiotics.}, journal = {Journal of food protection}, volume = {88}, number = {1}, pages = {100422}, doi = {10.1016/j.jfp.2024.100422}, pmid = {39608606}, issn = {1944-9097}, mesh = {*Probiotics ; *Food Microbiology ; *Fermentation ; *Fermented Foods/microbiology ; Humans ; }, abstract = {Dongchimi, a traditional Korean watery kimchi, relies on complex interactions among diverse lactic acid bacteria (LAB) to maintain its freshness and quality. Recently, dongchimi has gained attention as a health-promoting food due to its content of probiotics and prebiotics. In this study, six probiotic strains were employed into dongchimi fermentation, and its sensory and microbial characteristics were evaluated. The LAB-enriched dongchimi demonstrated improved sensory preference (63%) and significantly higher LAB counts (average 5.2 × 10[7] CFU/ml) compared to traditional dongchimi. Furthermore, microbial diversity between the LAB-enriched and traditional dongchimi was analyzed during the fermentation process using both culture-dependent Sanger sequencing and culture-independent metabarcoding techniques, employing 16S ribosomal RNA gene sequences. Lactiplantibacillus plantarum was identified as the dominant probiotic strain in both types of dongchimi, while other probiotics, including Bifidobacterium bifidum, B. animalis, Limosilactobacillus fermentum, and Heyndrickxia coagulans, were exclusively detected in the LAB-enriched dongchimi. In conclusion, Lactiplanti. plantarum and Limosi. fermentum were identified as the most effective probiotics for dongchimi fermentation. These results offer critical insights into the microbial ecology and probiotic strains essential for optimizing synbiotic dongchimi, thereby reinforcing health claims related to probiotics and prebiotics.}, }
@article {pmid39605469, year = {2024}, author = {Woodruff, GC and Moser, KA and Wang, J}, title = {The Bacteria of a Fig Microcommunity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.22.624729}, pmid = {39605469}, issn = {2692-8205}, abstract = {UNLABELLED: Understanding the biotic drivers of diversity is a major goal of microbial ecology. One approach towards tackling this issue is to interrogate relatively simple communities that are easy to observe and perturb. Figs (syconia) of the genus Ficus represent such a system. Here, we describe the microbial communities of Ficus septica figs, which are associated with the nematode Caenorhabditis inopinata (the sister species of the C. elegans genetic model system). In 2019, 38 Ficus septica figs (across 12 plants in Taiwan) were dissected, and metadata such as foundress wasp number and nematode occupancy were collected for each fig. Suspensions derived from interior fig material and fig surface washes were prepared for 16S microbial metabarcoding. Over 3,000 OTUs were detected, and microbial communities were dominated by members of Proteobacteria , Bacteroidota , and Actinobacteriota . Although microbial communities of fig exteriors and interiors can be distinguished, levels of microbial alpha diversity were comparable across these areas of the fig. Nematodes likewise had no detectable impact on microbial alpha diversity, although nematodes were associated with a modest change in microbial community composition. A handful of OTUs (associated with the genera Kosokonia , Ochobactrum , and Stenotrophomonas) revealed potential differential abundance among figs varying in nematode occupancy. Additionally, foundress wasp number was negatively correlated with microbial alpha diversity. These findings set the stage for future studies that directly test the role of nematode and wasp occupancy on microbial communities, as well as investigations that probe nematode-microbe interactions through laboratory experiments. Taken together, these results constitute a fundamental step in characterizing the natural microbial communities of figs and Caenorhabditis nematodes.<br><br>IMPORTANCE: Unraveling why different species live in different places is a longstanding open question in ecology, and it is clear that interspecific interactions among species are a major contributor to species distributions. Ficus figs are a useful system for ecological studies because they are relatively simple microcosms where characterizing animal community composition of multiple samples is straightforward. Additionally, Caenorhabditis inopinata , a close relative of the C. elegans genetic model system, thrives in Ficus septica figs. Here, we tie 16S microbial metabarcoding to nematode and wasp occupancy data to understand the causes of bacterial community composition in F. septica figs. We found that microbial composition, but not total diversity, varies among fig surface and interiors. Likewise, we found that nematode occupancy impacts microbial composition but not alpha diversity. Moreover, we show that as the number of foundress wasps increases, the microbial alpha diversity decreases. Finally, we identified OTUs that are potentially associated with nematode occupancy. Taken together, these results represent a key step in describing a microcommunity wherein ecological genetic hypotheses can be tested, as well as one that can potentially reveal the roles of uncharacterized genes in established model systems.}, }
@article {pmid39605409, year = {2024}, author = {Alexander, AM and Loo, HQ and Askew, L and Raghuram, V and Read, TD and Goldberg, JB}, title = {Intraspecific Diversity of Staphylococcus aureus Populations Isolated from Cystic Fibrosis Respiratory Infections.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39605409}, issn = {2692-8205}, support = {R21 AI148847/AI/NIAID NIH HHS/United States ; T32 AI138952/AI/NIAID NIH HHS/United States ; }, abstract = {Chronic bacterial infections are often polymicrobial, comprising multiple bacterial species or variants of the same species. Because chronic infections may last for decades, they have the potential to generate high levels of intraspecific variation through within-host diversification over time, and the potential for superinfections to occur through the introduction of multiple pathogen populations to the ongoing infection. Traditional methods for identifying infective agents generally involve isolating one single colony from a given sample, usually after selecting for a specific pathogen or antibiotic resistance profile. Isolating a recognized virulent or difficult to treat pathogen is an important part of informing clinical treatment and correlative research; however, these reductive methods alone, do not provide researchers or healthcare providers with the potentially important perspective on the true pathogen population structure and dynamics over time. To begin to address this limitation, in this study, we compare findings on Staphylococcus aureus single colonies versus and pools of colonies taken from fresh sputum samples from three patients with cystic fibrosis to isolates collected from the same sputum samples and processed by the clinical microbiology laboratory. Phenotypic and genotypic analysis of isolated S. aureus populations revealed coexisting lineages in two of three sputum samples as well as population structures that were not reflected in the single colony isolates. Altogether, our observations presented here demonstrate that clinically relevant diversity can be missed with standard sampling methods when assessing chronic infections. More broadly, this work outlines the potential impact that comprehensive population-level sampling may have for both research efforts and more effective treatment practices.}, }
@article {pmid39604741, year = {2024}, author = {de Freitas, AS and Carlos, FS and Martins, GL and Monteiro, GGTN and Roesch, LFW}, title = {Bacterial Resilience and Community Shifts Under 11 Draining-Flooding Cycles in Rice Soils.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {149}, pmid = {39604741}, issn = {1432-184X}, mesh = {*Oryza/microbiology ; *Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Floods ; *Soil/chemistry ; Brazil ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Hydrogen-Ion Concentration ; Ecosystem ; }, abstract = {Flooded rice cultivation, accounting for 75% of global rice production, significantly influences soil redox potential, element speciation, pH, and nutrient availability, presenting challenges such as extensive water usage and altered soil properties. This study investigates bacterial community dynamics in rice soils subjected to repeated draining and flooding in Rio Grande do Sul, Brazil. We demonstrate that bacterial communities exhibit remarkable resilience (the capacity to recover after being altered by a disturbance) but cannot remain stable after long-term exposure to environmental changes. The beta diversity analysis revealed four distinct community states after 11 draining/flooding cycles, indicating resilience over successive environment changes. However, the consistent environmental disturbance reduced microbial resilience, causing the bacterial community structure to shift over time. Those differences were driven by substitutions of taxa and functions and not by the loss of diversity. Notable shifts included a decline in Acidobacteria and an increase in Proteobacteria and Chloroflexi. Increased Verrucomicrobia abundance corresponded with lower pH levels. Functional predictions suggested dynamic metabolic responses, with increased nitrification during drained cycles and a surge in fermenters after the sixth cycle. Despite cyclic disturbances, bacterial communities exhibit resilience, contributing to stable ecosystem functioning in flooded rice soils. These findings enhance our understanding of microbial adaptation, providing insights into sustainable rice cultivation and soil management practices.}, }
@article {pmid39603473, year = {2025}, author = {Li, Y and Tao, C and Li, S and Chen, W and Fu, D and Jafvert, CT and Zhu, T}, title = {Feasibility study of machine learning to explore relationships between antimicrobial resistance and microbial community structure in global wastewater treatment plant sludges.}, journal = {Bioresource technology}, volume = {417}, number = {}, pages = {131878}, doi = {10.1016/j.biortech.2024.131878}, pmid = {39603473}, issn = {1873-2976}, mesh = {*Machine Learning ; *Sewage/microbiology ; *Wastewater/microbiology ; Water Purification/methods ; Feasibility Studies ; Bacteria/drug effects/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/drug effects ; China ; Drug Resistance, Bacterial/genetics ; }, abstract = {Wastewater sludges (WSs) are major reservoirs and emission sources of antibiotic resistance genes (ARGs) in cities. Identifying antimicrobial resistance (AMR) host bacteria in WSs is crucial for understanding AMR formation and mitigating biological and ecological risks. Here 24 sludge data from wastewater treatment plants in Jiangsu Province, China, and 1559 sludge data from genetic databases were analyzed to explore the relationship between 7 AMRs and bacterial distribution. The results of the Procrustes and Spearman correlation analysis were unsatisfactory, with p-value exceeding the threshold of 0.05 and no strong correlation (r > 0.8). In contrast, explainable machine learning (EML) using SHapley Additive exPlanation (SHAP) revealed Pseudomonadota as a major contributor (39.3 %-74.2 %) to sludge AMR. Overall, the application of ML is promising in analyzing AMR-bacteria relationships. Given the different applicable occasions and advantages of various analysis methods, using ML as one of the correlation analysis tools is strongly recommended.}, }
@article {pmid39601575, year = {2025}, author = {Maguire, M and Serna, C and Montero Serra, N and Kovarova, A and O'Connor, L and Cahill, N and Hooban, B and DeLappe, N and Brennan, W and Devane, G and Cormican, M and Morris, D and Coughlan, SC and Miliotis, G and Gonzalez-Zorn, B and Burke, LP}, title = {Spatiotemporal and genomic analysis of carbapenem resistance elements in Enterobacterales from hospital inpatients and natural water ecosystems of an Irish city.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0090424}, pmid = {39601575}, issn = {2165-0497}, support = {773830//EC | Horizon 2020 Framework Programme (H2020)/ ; 18/CRT/6214//Science Foundation Ireland (SFI)/ ; 2017-HW-LS-1//Environmental Protection Agency (EPA)/ ; 2017-HW-LS-1//Health Service Executive (HSE)/ ; }, mesh = {Humans ; *beta-Lactamases/genetics ; Ireland ; *Plasmids/genetics ; *Bacterial Proteins/genetics ; *Carbapenems/pharmacology ; Anti-Bacterial Agents/pharmacology ; Enterobacteriaceae/genetics/drug effects/isolation &amp; purification ; Inpatients ; Enterobacteriaceae Infections/microbiology/epidemiology ; Whole Genome Sequencing ; Wastewater/microbiology ; Genomics ; Ecosystem ; Klebsiella pneumoniae/genetics/drug effects/isolation &amp; purification ; Microbial Sensitivity Tests ; Genome, Bacterial ; Carbapenem-Resistant Enterobacteriaceae/genetics/isolation &amp; purification/drug effects ; Cities ; Spatio-Temporal Analysis ; }, abstract = {Carbapenemase-producing Enterobacterales (CPE) is a diverse group of often multidrug-resistant organisms. Surveillance and control of infections are complicated due to the inter-species spread of carbapenemase-encoding genes (CEGs) on mobile genetic elements (MGEs), including plasmids and transposons. Due to wastewater discharges, urban water ecosystems represent a known reservoir of CPE. However, the dynamics of carbapenemase-bearing MGE dissemination between Enterobacterales in humans and environmental waters are poorly understood. We carried out whole-genome sequencing, combining short- and long-sequencing reads to enable complete characterization of CPE isolated from patients, wastewaters, and natural waters between 2018 and 2020 in Galway, Ireland. Isolates were selected based on their carriage of Class A blaKPC-2 (n = 6), Class B blaNDM-5 (n = 12), and Class D blaOXA-48 (n = 21) CEGs. CEGs were plasmid-borne in all but two isolates. OXA-48 dissemination was associated with a 64 kb IncL plasmid (62%), in a broad range of Enterobacterales isolates from both niches. Conversely, blaKPC-2 and blaNDM-5 genes were usually carried on larger and more variable multireplicon IncF plasmids in Klebsiella pneumoniae and Escherichia coli, respectively. In every isolate, each CEG was surrounded by a gene-specific common genetic environment which constituted part, or all, of a transposable element that was present in both plasmids and the bacterial chromosome. Transposons Tn1999 and Tn4401 were associated with blaOXA-48 and blaKPC-2, respectively, while blaNDM-5 was associated with variable IS26 bound composite transposons, usually containing a class 1 integron.IMPORTANCESince 2018, the Irish National Carbapenemase-Producing Enterobacterales (CPE) Reference Laboratory Service at University Hospital Galway has performed whole-genome sequencing on suspected and confirmed CPE from clinical specimens as well as patient and environmental screening isolates. Understanding the dynamics of CPE and carbapenemase-encoding gene encoding mobile genetic element (MGE) flux between human and environmental reservoirs is important for One Health surveillance of these priority organisms. We employed hybrid assembly approaches for improved resolution of CPE genomic surveillance, typing, and plasmid characterization. We analyzed a diverse collection of human (n = 17) and environmental isolates (n = 22) and found common MGE across multiple species and in different ecological niches. The conjugation ability and frequency of a subset of these plasmids were demonstrated to be affected by the presence or absence of necessary conjugation genes and by plasmid size. We characterize several MGE at play in the local dissemination of carbapenemase genes. This may facilitate their future detection in the clinical laboratory.}, }
@article {pmid39601521, year = {2025}, author = {Atkinson, CGF and Kerns, KA and Hendrickson, EL and He, X and Bor, B and McLean, JS}, title = {Complete genome of Nanosynbacter sp. strain BB002, isolated and cultivated from a site of periodontal disease.}, journal = {Microbiology resource announcements}, volume = {14}, number = {1}, pages = {e0063724}, pmid = {39601521}, issn = {2576-098X}, support = {R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 DE031470/DE/NIDCR NIH HHS/United States ; R01 DE031274/DE/NIDCR NIH HHS/United States ; T90 DE021984/DE/NIDCR NIH HHS/United States ; T90DE021984, R01DE031470, R01DE023810, R01DE031274//HHS | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; }, abstract = {Nanosynbacter sp. strain BB002, was isolated from the human oral cavity on its basibiont bacterial host Actinomyces sp. oral taxon 171 strain F0337, related to Actinomyces oris. As a member of the Saccharibacteria within the candidate phylum radiation group (CPR), its reduced genome facilitates the survival as an ultrasmall (<0.2 μm) epibiont.}, }
@article {pmid39597739, year = {2024}, author = {Sun, X and Liu, Y and He, L and Kuang, Z and Dai, S and Hua, L and Jiang, Q and Wei, T and Ye, P and Zeng, H}, title = {Response of Yields, Soil Physiochemical Characteristics, and the Rhizosphere Microbiome to the Occurrence of Root Rot Caused by Fusarium solani in Ligusticum chuanxiong Hort.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597739}, issn = {2076-2607}, support = {2023NSFSC1262//the Natural Science Foundation of Sichuan Province of China/ ; SCCXTD-2024-19//Sichuan Innovation Team of the Chinese National Modern Agriculture Industry Technology System/ ; CARS-21-21//National Chinese Medicinal Materials Technology System/ ; 2022ZZCX078//Sichuan Provincial Finance Independent Innovation Project/ ; }, abstract = {Ligusticum chuanxiong Hort. is considered an important medicinal herb with extremely high economic value and medicinal value due to its various effects, including anti-oxidation, sedative action, hepatoprotection, and invigorating blood circulation. However, L. chuanxiong cultivation is hampered by various plant diseases, especially the root rot caused by Fusarium solani, hindering the sustainable development of the L. chuanxiong industry. The occurrence of soil-borne diseases is closely linked to imbalances in the microbial community structure. Here, we studied the yields, rhizosphere microbiota, and soil physiochemical characteristics of healthy and diseased L. chuanxiong plants affected by root rot with high-throughput sequencing and microbial network analysis, aiming to explore the relationships between soil environmental factors, microbiomes, and plant health of L. chuanxiong. According to the results, L. chuanxiong root rot significantly decreased the yields, altered microbial community diversity and composition, enriched more pathogenic fungi, recruited some beneficial bacteria, and reduced microbial interaction network stability. The Mantel test showed that soil organic matter and pH were the major environmental factors modulating plant microbiome assembly. The root rot severity was significantly affected by soil physiochemical properties, including organic matter, cation exchange capacity, available nitrogen, phosphorus, potassium, and pH. Furthermore, two differential microbes that have great potential in the biocontrol of L. chuanxiong root rot were dug out in the obtained results, which were the genera Trichoderma and Bacillus. This study provided a theoretical basis for further studies revealing the microecological mechanism of L. chuanxiong root rot and the ecological prevention and control of L. chuanxiong root rot from a microbial ecology perspective.}, }
@article {pmid39597685, year = {2024}, author = {Zhang, K and Chen, X and Shi, X and Yang, Z and Yang, L and Liu, D and Yu, F}, title = {Endophytic Bacterial Community, Core Taxa, and Functional Variations Within the Fruiting Bodies of Laccaria.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597685}, issn = {2076-2607}, support = {202205AD160036//the Yunnan Technology Innovation/ ; 42077072//the National Natural Science Foundation of Management Practices China/ ; }, abstract = {Macrofungi do not exist in isolation but establish symbiotic relationships with microorganisms, particularly bacteria, within their fruiting bodies. Herein, we examined the fruiting bodies' bacteriome of seven species of the genus Laccaria collected from four locations in Yunnan, China. By analyzing bacterial diversity, community structure, and function through 16S rRNA sequencing, we observed the following: (1) In total, 4,840,291 high-quality bacterial sequences obtained from the fruiting bodies were grouped into 16,577 amplicon sequence variants (ASVs), and all samples comprised 23 shared bacterial ASVs. (2) The Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium complex was found to be the most abundant and presumably coexisting bacterium. (3) A network analysis revealed that endophytic bacteria formed functional groups, which were dominated by the genera Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Novosphingobium, and Variovorax. (4) The diversity, community structure, and dominance of ecological functions (chemoheterotrophy and nitrogen cycling) among endophytic bacteria were significantly shaped by geographic location, habitat, and fungal genotype, rather than fruiting body type. (5) A large number of the endophytic bacteria within Laccaria are bacteria that promote plant growth; however, some pathogenic bacteria that pose a threat to human health might also be present. This research advances our understanding of the microbial ecology of Laccaria and the factors shaping its endophytic bacterial communities.}, }
@article {pmid39597671, year = {2024}, author = {Skliros, D and Kostakou, M and Kokkari, C and Tsertou, MI and Pavloudi, C and Zafeiropoulos, H and Katharios, P and Flemetakis, E}, title = {Unveiling Emerging Opportunistic Fish Pathogens in Aquaculture: A Comprehensive Seasonal Study of Microbial Composition in Mediterranean Fish Hatcheries.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597671}, issn = {2076-2607}, support = {5010932//Operational Program Fisheries and Maritime 2014-2020/ ; }, abstract = {The importance of microbial communities in fish hatcheries for fish health and welfare has been recognized, with several studies mapping these communities during healthy rearing conditions and disease outbreaks. In this study, we analyzed the bacteriome of the live feeds, such as microalgae, rotifers, and Artemia, used in fish hatcheries that produce Mediterranean species. Our goal was to provide baseline information about their structure, emphasizing in environmental putative fish pathogenic bacteria. We conducted 16S rRNA amplicon Novaseq sequencing for our analysis, and we inferred 46,745 taxonomically annotated ASVs. Results showed that incoming environmental water plays a significant role in the presence of important taxa that constitute presumptive pathogens. Bio-statistical analyses revealed a relatively stable bacteriome among seasonal samplings for every hatchery but a diverse bacteriome between sampling stations and a distinct core bacteriome for each hatchery. Analysis of putative opportunistic fish pathogenic genera revealed some co-occurrence correlation events and a high average relative abundance of Vibrio, Tenacibaculum, and Photobacterium genera in live feeds, reaching a grand mean average of up to 7.3% for the hatchery of the Hellenic Center of Marine Research (HCMR), 12% for Hatchery A, and 11.5% for Hatchery B. Mapping the bacteriome in live feeds is pivotal for understanding the marine environment and distinct aquaculture practices and can guide improvements in hatchery management, enhancing fish health and sustainability in the Mediterranean region.}, }
@article {pmid39597543, year = {2024}, author = {Wu, D and He, X and Lu, Y and Gao, Z and Chong, Y and Hong, J and Wu, J and Deng, W and Xi, D}, title = {Effects of Different Dietary Combinations on Blood Biochemical Indicators and Rumen Microbial Ecology in Wenshan Cattle.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597543}, issn = {2076-2607}, abstract = {With the continuous optimization of feed ingredients in livestock production, barley has garnered significant attention as a potential substitute for corn in feed. This study aims to investigate the effects of replacing part of the corn and soybean meal with barley, wheat bran, and rapeseed meal on Wenshan cattle, focusing on the rumen microbial community, blood physiological and biochemical indicators, and growth traits. Through an intensive feeding experiment with two different dietary ratios, we found that adding barley to the diet significantly reduced the host's blood lipid concentration and significantly increased the height, body length, heart girth, and average daily weight gain of Wenshan cattle. Analysis of the rumen microbial community structure showed that the addition of barley significantly affected the relative abundance of Firmicutes, Proteobacteria, and Bacteroidetes, with the relative abundance of Spirochaetes being significantly lower than that of the control group (p < 0.05). The dominant bacterial groups mainly included Acinetobacter, Solibacillus, and Lysinibacillus. In summary, this study reveals the potential of different feed ingredient ratios involving barley, wheat bran, and rapeseed meal in the production performance of Wenshan cattle. By regulating blood physiology and improving the rumen micro-ecological structure, it provides new scientific evidence for optimizing livestock and poultry feeding management strategies. Future research will further explore the optimal application ratio of barley under different feeding conditions and its long-term impact on animal health and production performance.}, }
@article {pmid39597512, year = {2024}, author = {Banerji, A and Brinkman, NE and Davis, B and Franklin, A and Jahne, M and Keely, SP}, title = {Food Webs and Feedbacks: The Untold Ecological Relevance of Antimicrobial Resistance as Seen in Harmful Algal Blooms.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597512}, issn = {2076-2607}, abstract = {Antimicrobial resistance (AMR) has long been framed as an epidemiological and public health concern. Its impacts on the environment are unclear. Yet, the basis for AMR is altered cell physiology. Just as this affects how microbes interact with antimicrobials, it can also affect how they interact with their own species, other species, and their non-living environment. Moreover, if the microbes are globally notorious for causing landscape-level environmental issues, then these effects could alter biodiversity and ecosystem function on a grand scale. To investigate these possibilities, we compiled peer-reviewed literature from the past 20 years regarding AMR in toxic freshwater cyanobacterial harmful algal blooms (HABs). We examined it for evidence of AMR affecting HAB frequency, severity, or persistence. Although no study within our scope was explicitly designed to address the question, multiple studies reported AMR-associated changes in HAB-forming cyanobacteria (and co-occurring microbes) that pertained directly to HAB timing, toxicity, and phase, as well as to the dynamics of HAB-afflicted aquatic food webs. These findings highlight the potential for AMR to have far-reaching environmental impacts (including the loss of biodiversity and ecosystem function) and bring into focus the importance of confronting complex interrelated issues such as AMR and HABs in concert, with interdisciplinary tools and perspectives.}, }
@article {pmid39596705, year = {2024}, author = {Moraes, BDGC and Martins, RCR and Fonseca, JVDS and Franco, LAM and Pereira, GCO and Bartelli, TF and Cortes, MF and Scaccia, N and Santos, CF and Musqueira, PT and Otuyama, LJ and Pylro, VS and Mariano, L and Rocha, V and Witkin, SS and Sabino, E and Guimaraes, T and Costa, SF}, title = {Impact of Exogenous Lactiplantibacillus plantarum on the Gut Microbiome of Hematopoietic Stem Cell Transplantation Patients Colonized by Multidrug-Resistant Bacteria: An Observational Study.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, pmid = {39596705}, issn = {2079-6382}, support = {FAPESP//001/ ; }, abstract = {Background:Lactiplantibacillus plantarum can inhibit the growth of multidrug-resistant organisms (MDROs) and modulate the gut microbiome. However, data on hematopoietic stem cell transplantation (HSCT) are scarce. Aim: In an observational study, we assessed the impact of L. plantarum on the modulation of the gut microbiome in HSCT patients colonized by MDROs. Methods: Participants were allocated to an intervention group (IG = 22) who received capsules of L. plantarum (5 × 10[9] CFU) twice per day until the onset of neutropenia or a control group (CG = 20). The V4 region of the 16S bacterial rRNA gene was sequenced in 87 stool samples from a subset of 33 patients (IG = 20 and CG = 13). The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) program was used to predict metagenome functions. Results:L. plantarum demonstrated an average 86% (±11%) drug-target engagement at 43 (±29) days of consumption and was deemed safe, well-tolerated, and associated with an increase in the abundance of the Lactobacillales (p < 0.05). A significant increase in Lactococcus and a reduction in Turicibacter (p < 0.05) were identified on the second week of L. plantarum use. Although Enterococcus abundance had a greater rise in the CG (p = 0.07), there were no significant differences concerning the Gram-negative MDROs. No serious adverse effects were reported in the IG. We observed a greater, non-significant pyruvate fermentation to propanoate I (p = 0.193) relative abundance in the IG compared with the CG. L. plantarum use was safe and tolerable by HSCT patients. Conclusions: While L. plantarum is safe and may impact Enterococcus and Turicibacter abundance, it showed no impact on Gram-negative MDRO abundance in HSCT patients.}, }
@article {pmid39592542, year = {2025}, author = {Kaur, T and Devi, R and Negi, R and Kour, H and Singh, S and Khan, SS and Kumari, C and Kour, D and Chowdhury, S and Kapoor, M and Rai, AK and Rustagi, S and Shreaz, S and Yadav, AN}, title = {Macronutrients-availing microbiomes: biodiversity, mechanisms, and biotechnological applications for agricultural sustainability.}, journal = {Folia microbiologica}, volume = {70}, number = {2}, pages = {293-319}, pmid = {39592542}, issn = {1874-9356}, mesh = {*Microbiota ; Phosphorus/metabolism ; Agriculture ; Soil Microbiology ; *Biodiversity ; Potassium/metabolism ; Nitrogen/metabolism ; *Biotechnology ; *Nutrients/metabolism ; *Bacteria/metabolism/genetics/classification ; Soil/chemistry ; Crops, Agricultural ; }, abstract = {Nitrogen, phosphorus, and potassium are the three most essential micronutrients which play major roles in plant survivability by being a structural or non-structural component of the cell. Plants acquire these nutrients from soil in the fixed (NO3[¯], NH4[+]) and solubilized forms (K[+], H2PO4[-] and HPO4[2-]). In soil, the fixed and solubilized forms of nutrients are unavailable or available in bare minimum amounts; therefore, agrochemicals were introduced. Agrochemicals, mined from the deposits or chemically prepared, have been widely used in the agricultural farms over the decades for the sake of higher production of the crops. The excessive use of agrochemicals has been found to be deleterious for humans, as well as the environment. In the environment, agrochemical usage resulted in soil acidification, disturbance of microbial ecology, and eutrophication of aquatic and terrestrial ecosystems. A solution to such devastating agro-input was found to be substituted by macronutrients-availing microbiomes. Macronutrients-availing microbiomes solubilize and fix the insoluble form of nutrients and convert them into soluble forms without causing any significant harm to the environment. Microbes convert the insoluble form to the soluble form of macronutrients (nitrogen, phosphorus, and potassium) through different mechanisms such as fixation, solubilization, and chelation. The microbiomes having capability of fixing and solubilizing nutrients contain some specific genes which have been reported in diverse microbial species surviving in different niches. In the present review, the biodiversity, mechanism of action, and genomics of different macronutrients-availing microbiomes are presented.}, }
@article {pmid39587684, year = {2025}, author = {DuBose, JG and Crook, TB and Matzkin, LM and Haselkorn, TS}, title = {The relative importance of host phylogeny and dietary convergence in shaping the bacterial communities hosted by several Sonoran Desert Drosophila species.}, journal = {Journal of evolutionary biology}, volume = {38}, number = {2}, pages = {180-189}, doi = {10.1093/jeb/voae143}, pmid = {39587684}, issn = {1420-9101}, support = {//University of Central Arkansas Southwest Energy Research Fellowship program/ ; }, mesh = {Animals ; *Drosophila/microbiology/genetics/classification/physiology ; *Phylogeny ; *Diet ; *Microbiota ; Symbiosis ; Desert Climate ; *Bacteria/classification ; }, abstract = {Complex eukaryotes vary greatly in the mode and extent that their evolutionary histories have been shaped by the microbial communities that they host. A general understanding of the evolutionary consequences of host-microbe symbioses requires that we understand the relative importance of host phylogenetic divergence and other ecological processes in shaping variation in host-associated microbial communities. To contribute to this understanding, we described the bacterial communities hosted by several Drosophila species native to the Sonoran Desert of North America. Our sampling consisted of four species that span multiple dietary shifts to cactophily, as well as the dietary generalist D. melanogaster, allowing us to partition the influences of host phylogeny and extant ecology. We found that bacterial communities were compositionally indistinguishable when considering incidence only but varied when considering the relative abundances of bacterial taxa. Variation in community composition was not explained by host phylogenetic divergence but could be partially explained by dietary variation. In support of the important role of diet as a source of ecological selection, we found that specialist cactophilic Drosophila deviated more from neutral predictions than dietary generalists. Overall, our findings provide insight into the evolutionary and ecological factors that shape host-associated microbial communities in a natural context.}, }
@article {pmid39587399, year = {2024}, author = {Trevathan-Tackett, SM and Kepfer-Rojas, S and Malerba, M and Macreadie, PI and Djukic, I and Zhao, J and Young, EB and York, PH and Yeh, SC and Xiong, Y and Winters, G and Whitlock, D and Weaver, CA and Watson, A and Visby, I and Tylkowski, J and Trethowan, A and Tiegs, S and Taylor, B and Szpikowski, J and Szpikowska, G and Strickland, VL and Stivrins, N and Sousa, AI and Sinutok, S and Scheffel, WA and Santos, R and Sanderman, J and Sánchez-Carrillo, S and Sanchez-Cabeza, JA and Rymer, KG and Ruiz-Fernandez, AC and Robroek, BJM and Roberts, T and Ricart, AM and Reynolds, LK and Rachlewicz, G and Prathep, A and Pinsonneault, AJ and Pendall, E and Payne, R and Ozola, I and Onufrock, C and Ola, A and Oberbauer, SF and Numbere, AO and Novak, AB and Norkko, J and Norkko, A and Mozdzer, TJ and Morgan, P and Montemayor, DI and Martin, CW and Malone, SL and Major, M and Majewski, M and Lundquist, CJ and Lovelock, CE and Liu, S and Lin, HJ and Lillebo, A and Li, J and Kominoski, JS and Khuroo, AA and Kelleway, JJ and Jinks, KI and Jerónimo, D and Janousek, C and Jackson, EL and Iribarne, O and Hanley, T and Hamid, M and Gupta, A and Guariento, RD and Grudzinska, I and da Rocha Gripp, A and González Sagrario, MA and Garrison, LM and Gagnon, K and Gacia, E and Fusi, M and Farrington, L and Farmer, J and de Assis Esteves, F and Escapa, M and Domańska, M and Dias, ATC and de Los Santos, CB and Daffonchio, D and Czyryca, PM and Connolly, RM and Cobb, A and Chudzińska, M and Christiaen, B and Chifflard, P and Castelar, S and Carneiro, LS and Cardoso-Mohedano, JG and Camden, M and Caliman, A and Bulmer, RH and Bowen, J and Boström, C and Bernal, S and Berges, JA and Benavides, JC and Barry, SC and Alatalo, JM and Al-Haj, AN and Adame, MF}, title = {Climate Effects on Belowground Tea Litter Decomposition Depend on Ecosystem and Organic Matter Types in Global Wetlands.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {49}, pages = {21589-21603}, pmid = {39587399}, issn = {1520-5851}, mesh = {*Wetlands ; Tea ; Climate ; Ecosystem ; Carbon ; Temperature ; }, abstract = {Patchy global data on belowground litter decomposition dynamics limit our capacity to discern the drivers of carbon preservation and storage across inland and coastal wetlands. We performed a global, multiyear study in over 180 wetlands across 28 countries and 8 macroclimates using standardized litter as measures of "recalcitrant" (rooibos tea) and "labile" (green tea) organic matter (OM) decomposition. Freshwater wetlands and tidal marshes had the highest tea mass remaining, indicating a greater potential for carbon preservation in these ecosystems. Recalcitrant OM decomposition increased with elevated temperatures throughout the decay period, e.g., increase from 10 to 20 °C corresponded to a 1.46-fold increase in the recalcitrant OM decay rate constant. The effect of elevated temperature on labile OM breakdown was ecosystem-dependent, with tidally influenced wetlands showing limited effects of temperature compared with freshwater wetlands. Based on climatic projections, by 2050 wetland decay constants will increase by 1.8% for labile and 3.1% for recalcitrant OM. Our study highlights the potential for reduction in belowground OM in coastal and inland wetlands under increased warming, but the extent and direction of this effect at a large scale is dependent on ecosystem and OM characteristics. Understanding local versus global drivers is necessary to resolve ecosystem influences on carbon preservation in wetlands.}, }
@article {pmid39587087, year = {2024}, author = {Whalen, ED and Grandy, AS and Geyer, KM and Morrison, EW and Frey, SD}, title = {Microbial trait multifunctionality drives soil organic matter formation potential.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {10209}, pmid = {39587087}, issn = {2041-1723}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Fungi/metabolism ; *Carbon/metabolism ; Biomass ; Organic Chemicals/metabolism ; }, abstract = {Soil microbes are a major source of organic residues that accumulate as soil organic matter, the largest terrestrial reservoir of carbon on Earth. As such, there is growing interest in determining the microbial traits that drive soil organic matter formation and stabilization; however, whether certain microbial traits consistently predict soil organic matter accumulation across different functional pools (e.g., total vs. stable soil organic matter) is unresolved. To address these uncertainties, we incubated individual species of fungi in soil organic matter-free model soils, allowing us to directly relate the physiological, morphological, and biochemical traits of fungi to their soil organic matter formation potentials. We find that the formation of different soil organic matter functional pools is associated with distinct fungal traits, and that 'multifunctional' species with intermediate investment across this key grouping of traits (namely, carbon use efficiency, growth rate, turnover rate, and biomass protein and phenol contents) promote soil organic matter formation, functional complexity, and stability. Our results highlight the limitations of categorical trait-based frameworks that describe binary trade-offs between microbial traits, instead emphasizing the importance of synergies among microbial traits for the formation of functionally complex soil organic matter.}, }
@article {pmid39586934, year = {2024}, author = {Rong, X and Liu, X and Du, F and Aanderud, ZT and Zhang, Y}, title = {Biocrusts Mediate the Niche Distribution and Diversity of Ammonia-Oxidizing Microorganisms in the Gurbantunggut Desert, Northwestern China.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {148}, pmid = {39586934}, issn = {1432-184X}, support = {2022TSYCCX0007//the Xinjiang Tianshan Youth Talent Top Project/ ; 2022D01D083//the Key Fund Projects of the Natural Science Foundation of Xinjiang/ ; U2003214//the National Natural Science Foundation of China/ ; }, mesh = {*Archaea/genetics/metabolism/classification ; *Desert Climate ; *Ammonia/metabolism ; *Soil Microbiology ; China ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Oxidation-Reduction ; Soil/chemistry ; Biodiversity ; Ecosystem ; Seasons ; Microbiota ; Nitrification ; }, abstract = {Biological soil crusts (biocrusts) play pivotal ecological roles in regulating nitrogen cycling within desert ecosystems. While acknowledging the essential role played by ammonia-oxidizing microorganisms in nitrogen transformation, there remains a paucity of understanding concerning how disturbances to biocrusts impact the diversity and spatial distribution patterns among ammonia oxidizer communities within temperate deserts. This investigation delved into assessing how 4 years' worth of removing biocrust influenced niche differentiation between nitrifying archaea and bacteria while also examining its effects on shaping community structures of predominant ammonia-oxidizing archaea (AOA) within the Gurbantunggut Desert soils. Despite notable variations in abundance of ammonia-oxidizing microbes across distinct soil depths throughout different seasons, it became apparent that removing biocrust significantly altered both the abundance and niche pattern for AOA alongside their bacterial counterparts during winter and summer periods. Notably dominating over their bacterial counterparts within desert soils, AOA displayed their highest archaeal to bacterial amoA gene copy ratio (6549-fold higher) at a soil depth of 5-10 cm during summer. Moreover, substantial impacts were observed upon AOA diversity along with compositional changes following such perturbation events. The aftermath saw an emergence of more diffuse yet dynamic AOA communities, especially noticeable amidst winter when nitrogen and water limitations were relatively alleviated. In summary, our findings underscore how interactions between biocrust coverages alongside factors like soil temperature, total carbon content, or NO3[-]_N concentrations govern niches occupied by ammoxidation communities whilst influencing assemblage processes too. The sensitivity shown by dominant AOAs towards biocrust removal further underscores how biocrust coverage influences nitrogen transformation processes while potentially involving other communities and functions in desert ecosystems.}, }
@article {pmid39585925, year = {2024}, author = {Richards, TA and Eme, L and Archibald, JM and Leonard, G and Coelho, SM and de Mendoza, A and Dessimoz, C and Dolezal, P and Fritz-Laylin, LK and Gabaldón, T and Hampl, V and Kops, GJPL and Leger, MM and Lopez-Garcia, P and McInerney, JO and Moreira, D and Muñoz-Gómez, SA and Richter, DJ and Ruiz-Trillo, I and Santoro, AE and Sebé-Pedrós, A and Snel, B and Stairs, CW and Tromer, EC and van Hooff, JJE and Wickstead, B and Williams, TA and Roger, AJ and Dacks, JB and Wideman, JG}, title = {Reconstructing the last common ancestor of all eukaryotes.}, journal = {PLoS biology}, volume = {22}, number = {11}, pages = {e3002917}, pmid = {39585925}, issn = {1545-7885}, support = {R35 GM143039/GM/NIGMS NIH HHS/United States ; }, mesh = {*Eukaryota/genetics ; *Phylogeny ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; Genomics/methods ; Biological Evolution ; }, abstract = {Understanding the origin of eukaryotic cells is one of the most difficult problems in all of biology. A key challenge relevant to the question of eukaryogenesis is reconstructing the gene repertoire of the last eukaryotic common ancestor (LECA). As data sets grow, sketching an accurate genomics-informed picture of early eukaryotic cellular complexity requires provision of analytical resources and a commitment to data sharing. Here, we summarise progress towards understanding the biology of LECA and outline a community approach to inferring its wider gene repertoire. Once assembled, a robust LECA gene set will be a useful tool for evaluating alternative hypotheses about the origin of eukaryotes and understanding the evolution of traits in all descendant lineages, with relevance in diverse fields such as cell biology, microbial ecology, biotechnology, agriculture, and medicine. In this Consensus View, we put forth the status quo and an agreed path forward to reconstruct LECA's gene content.}, }
@article {pmid39583547, year = {2024}, author = {Yang, X and Gänzle, M and Wang, R}, title = {Editorial: How the application of antimicrobial hurdles in meat processing facilities shapes microbial ecology.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1501925}, pmid = {39583547}, issn = {1664-302X}, }
@article {pmid39578630, year = {2024}, author = {Barber, DG and Child, HT and Joslin, GR and Wierzbicki, L and Tennant, RK}, title = {Statistical design approach enables optimised mechanical lysis for enhanced long-read soil metagenomics.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {28934}, pmid = {39578630}, issn = {2045-2322}, support = {CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; }, mesh = {*Metagenomics/methods ; *Soil Microbiology ; Soil/chemistry ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; }, abstract = {Metagenomic analysis has enabled insights into soil community structure and dynamics. Long-read sequencing for metagenomics can enhance microbial ecology by improving taxonomic classification, genome assembly, and functional annotation. However, protocols for purifying high-molecular weight DNA from soil are not yet optimised. We used a statistical design of experiments approach to enhance mechanical lysis of soil samples, increasing the length of purified DNA fragments. Low energy input into mechanical lysis improved DNA integrity, resulting in longer sequenced reads. Our optimized settings of 4 m s[-1] for 10 s increased fragment length by 70% compared to the manufacturer's recommendations. Longer reads from low intensity lysis produced longer contiguous sequences after assembly, potentially improving a range of down-stream analyses. Importantly, there was minimal bias exhibited in the microbial community composition due to lysis efficiency variations. We therefore propose a framework for improving the fragment lengths of DNA purified from diverse soil types, improving soil science research with long-read sequencing.}, }
@article {pmid39572704, year = {2024}, author = {Li, J and Göbel, F and Hsu, HY and Koch, JN and Hager, N and Flegler, WA and Tanabe, TS and Dahl, C}, title = {YeeE-like bacterial SoxT proteins mediate sulfur import for oxidation and signal transduction.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1548}, pmid = {39572704}, issn = {2399-3642}, support = {Da 351/8-2//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Da 351/13-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Da 351/14-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Sulfur/metabolism ; *Oxidation-Reduction ; *Signal Transduction ; *Bacterial Proteins/metabolism/genetics ; *Gene Expression Regulation, Bacterial ; Biological Transport ; }, abstract = {Many sulfur-oxidizing prokaryotes oxidize sulfur compounds through a combination of initial extracytoplasmic and downstream cytoplasmic reactions. Facultative sulfur oxidizers adjust transcription to sulfur availability. While sulfur-oxidizing enzymes and transcriptional repressors have been extensively studied, sulfur import into the cytoplasm and how regulators sense external sulfur are poorly understood. Addressing this gap, we show that SoxT1A and SoxT1B, which resemble YeeE/YedE-family thiosulfate transporters and are encoded alongside sulfur oxidation and transcriptional regulation genes, fulfill these roles in the Alphaproteobacterium Hyphomicrobium denitrificans. SoxT1A mutants are sulfur oxidation-negative despite high transcription levels of sulfur oxidation genes, showing that SoxT1A delivers sulfur to the cytoplasm for its further oxidation. SoxT1B serves as a signal transduction unit for the transcriptional repressor SoxR, as SoxT1B mutants are sulfur oxidation-negative due to low transcription unless SoxR is also absent. Thus, SoxT1A and SoxT1B play essential but distinct roles in oxidative sulfur metabolism and its regulation.}, }
@article {pmid39572621, year = {2024}, author = {Rabenhorst, SHB and Ferrasi, AC and Barboza, MMO and Melo, VMM}, title = {Microbial composition of gastric lesions: differences based on Helicobacter pylori virulence profile.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {28890}, pmid = {39572621}, issn = {2045-2322}, support = {07939716/2020//Funda&#xe7;&#xe3;o Cearense de Apoio ao Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Humans ; *Helicobacter pylori/pathogenicity/genetics ; *Helicobacter Infections/microbiology/pathology ; *Stomach Neoplasms/microbiology/pathology ; *Gastritis/microbiology/pathology ; Virulence ; *Gastric Mucosa/microbiology/pathology ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Aged ; Metaplasia/microbiology ; Adult ; Gastrointestinal Microbiome ; }, abstract = {Helicobacter pylori infection is a major risk factor for gastric adenocarcinomas. In the case of the intestinal subtype, chronic gastritis and intestinal metaplasia are well-known sequential steps in carcinogenesis. H. pylori has high genetic diversity that can modulate virulence and pathogenicity in the human host as a cag Pathogenicity Island (cagPAI). However, bacterial gene combinations do not always explain the clinical presentation of the disease, indicating that other factors associated with H. pylori may play a role in the development of gastric disease. In this context, we characterized the microbial composition of patients with chronic gastritis (inactive and active), intestinal metaplasia, and gastric cancer as well as their potential association with H. pylori. To this end, 16 S rRNA metagenomic analysis was performed on gastric mucosa samples from patients with different types of lesions and normal gastric tissues. Our main finding was that H. pylori virulence status can contribute to significant differences in the constitution of the gastric microbiota between the sequential steps of the carcinogenesis cascade. Differential microbiota was observed in inactive and active gastritis dependent of the H. pylori presence and status (p = 0.000575). Pseudomonades, the most abundant order in the gastritis, was associated the presence of non-virulent H. pylori in the active gastritis. Notably, there are indicator genera according to H. pylori status that are poorly associated with diseases and provide additional evidence that the microbiota, in addition to H. pylori, is relevant to gastric carcinogenesis.}, }
@article {pmid39572453, year = {2024}, author = {Méndez, A and Sanmartín, P and Balboa, S and Trueba-Santiso, A}, title = {Environmental Proteomics Elucidates Phototrophic Biofilm Responses to Ornamental Lighting on Stone-built Heritage.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {147}, pmid = {39572453}, issn = {1432-184X}, support = {04_IN606D_2021_2598528//Programa de Doutoramento Industrial - Xunta de Galicia/ ; ED431F 2022/14//FONTES project - Xunta de Galicia/ ; ED431F 2022/14//FONTES project - Xunta de Galicia/ ; ED431C 2022/09//Competitive Reference Group (GRC) grant - GEMAP/ ; ED431C 2022/09//Competitive Reference Group (GRC) grant - GEMAP/ ; RYC2020-029987-I//Ram&#xf3;n y Cajal contract - Spanish State Research Agency (AEI)/ ; ED431C-2021/37//Competitive Reference Group (GRC) - Biogroup/ ; ED431C-2021/37//Competitive Reference Group (GRC) - Biogroup/ ; }, mesh = {*Biofilms/radiation effects/growth &amp; development ; *Proteomics ; Light ; Phototrophic Processes ; Cyanobacteria/metabolism/radiation effects/physiology ; Chlorophyta/radiation effects/metabolism/physiology ; Proteome ; Lighting ; }, abstract = {Recent studies are showing that some lights suitable for illuminating the urban fabric (i.e. that do not include the red, green and blue sets of primary colours) may halt biological colonisation on monuments, mainly that caused by phototrophic subaerial biofilms (SABs), which may exacerbate the biodeterioration of substrates. However, the light-triggered mechanisms that cause changes in the growth of the phototrophs remain unknown. Environmental proteomics could be used to provide information about the changes in the SAB metabolism under stress inflicted by nocturnal lighting. Here, laboratory-produced SABs, composed of Chlorophyta, Streptophyta and Cyanobacteriota, were subjected to three types of lighting used for monuments: cool white, warm white and amber + green (potentially with a biostatic effect). A control without light (i.e. darkness) was also included for comparison. The nocturnal lighting impaired the capacity of the SABs to decompose superoxide radicals and thus protect themselves from oxidative stress. Cool white and warm white light both strongly affected the proteomes of the SABs and reduced the total peptide content, with the extent of the reduction depending on the genera of the organisms involved. Analysis of the photo-damaging effect of amber + green light on the biofilm metabolism revealed a negative impact on photosystems I and II and production of photosystem antenna protein-like, as well as a triggering effect on protein metabolism (synthesis, folding and degradation). This research provides, for the first-time, a description of the proteomic changes induced by lighting on SABs colonising illuminated monuments in urban areas.}, }
@article {pmid39571806, year = {2025}, author = {Graham, A and Thorn, C and McDonagh, M and O'Donnell, C and Nolan, S and Kirwan, SF and O'Connor, S and Nzeteu, CO and Montoya, ACV and Bartle, A and Hall, A and Abberton, C and Friel, R and Waters, SM and O'Flaherty, V}, title = {Development and in-vitro assessment of novel oxygen-releasing feed additives to reduce enteric ruminant methane emissions.}, journal = {The Science of the total environment}, volume = {963}, number = {}, pages = {177598}, doi = {10.1016/j.scitotenv.2024.177598}, pmid = {39571806}, issn = {1879-1026}, mesh = {*Methane/metabolism/analysis ; Animals ; *Animal Feed/analysis ; Ruminants ; Rumen/metabolism ; Oxygen ; Oxidation-Reduction ; Fatty Acids, Volatile ; }, abstract = {Ruminant livestock contribute significantly to global methane production and mitigation of which is of utmost importance. Feed additives represent a cost-effective means of achieving this. A potential target for such additives is rumen Oxidative Reduction Potential (ORP), a parameter which influences CH4 production rates, with methanogenesis occurring optimally at ORPs below -300 mV. Thus, a controlled elevation of rumen ORP represents a potentially benign means of methanogen suppression. This research involved assessing a range of oxygen-releasing compounds for their ability to increase rumen ORP and inhibit methanogenesis, using the in-vitro rumen simulation technique (RUSITEC). Seven potential CH4 inhibitors were tested in a 21-day trial monitoring biogas volume, CH4 content, ORP, digestibility, ammonia, and volatile fatty acids concentration. The additives evaluated included: liquid peroxide (H2O2) and urea hydrogen peroxide (UHP), as well as slower reacting species (calcium and magnesium peroxide), in addition to encapsulated liquid H2O2 for controlled, slow release. Consistent CH4 reductions of >50 % were observed from all additives. Reduced neutral detergent fibre (NDF) digestibility and a reduction in total volatile fatty acids (VFAs) was observed for some treatments, but MgO2 and encapsulated H2O2 reduced CH4 volume by 62 % and 58 %, respectively, and had no detrimental effects on digestibility (p > 0.05) or on VFA production. Ex-situ ORP measurements demonstrated significant increases in ORP upon addition of the additives, with MgO2 and encapsulated H2O2 inducing a more moderate effect suggesting a controlled additive release was achieved with the slow-release format of encapsulated liquid H2O2. Thus, potential slow-release forms deemed suitable to progress to bolus or pellet format in-vivo were identified and could enable a longer-lasting suppression of methanogens within the rumen, facilitating application in both intensive and pasture-based production systems.}, }
@article {pmid39571521, year = {2025}, author = {Zuo, J and Yang, S and Grossart, HP and Xiao, P and Zhang, H and Sun, R and Li, G and Jiang, H and Zhao, Q and Jiao, M and Cheng, Y and Wang, Z and Geng, R and Ma, Z and Li, R}, title = {Sequential decline in cyanobacterial, total prokaryotic, and eukaryotic responses to backward flow in a river connected to Lake Taihu.}, journal = {Water research}, volume = {269}, number = {}, pages = {122784}, doi = {10.1016/j.watres.2024.122784}, pmid = {39571521}, issn = {1879-2448}, mesh = {*Cyanobacteria/physiology ; *Rivers/microbiology ; *Lakes/microbiology ; China ; Ecosystem ; Eukaryota ; }, abstract = {River ecosystems face escalating challenges due to altered flow regimes from human activities, such as urbanization with hydrological modifications. Understanding the role of microbial communities for ecosystems with changing flow regimes is still incomplete and remains at the frontier of aquatic microbial ecology. In particular, influences of riverine backward flow on the aquatic biota remain largely unknown. Therefore, we examined the impact of backward flow on the cyanobacterial, total prokaryotic, and eukaryotic communities in the Changdougang River, which naturally flows into Lake Taihu, through environmental DNA metabarcoding. We analyzed the differences in community diversity, assembly, and ecological network stability among groups under backward, weak, and forward flow direction conditions. Non-metric multidimensional scaling showed higher variations in communities of groups across flow direction conditions than seasonal groups. Variations in alpha and beta diversity showed that cyanobacterial and total prokaryotic communities experienced strong homogenization under backward flow conditions, whereas the ecological uniqueness of the eukaryotic community decreased. Assembly of the three flow-related communities was primarily governed by drift and dispersal limitation in stochastic processes. However, in the cyanobacterial community, homogeneous selection in deterministic processes increased from 22.79 % to 42.86 % under backward flow, aligning with trends observed in the checkerboard score (C-score). More importantly, the topological properties of ecological networks and the degree of average variation revealed higher stability in the cyanobacterial community compared to total prokaryotic and eukaryotic communities. Considering the variations in cohesion, the network stability in the cyanobacterial community decreased under backward flow. Our findings emphasize the distinct and sequentially diminishing responses of cyanobacterial, total prokaryotic, and eukaryotic communities to backward flowing rivers. This knowledge is crucial for maintaining ecological health of rivers, assessing the complex ecological impacts on hydrological engineering, and formulating sustainable water management strategies.}, }
@article {pmid39570409, year = {2024}, author = {Xu, H and Zhang, Y and Fan, D and Meng, S and Fan, L and Song, C and Qiu, L and Li, D and Fang, L and Liu, Z and Bing, X}, title = {Influences of Community Coalescence on the Assembly of Bacterial Communities of the Small-Scale Complex Aquatic System from the Perspective of Bacterial Transmission, Core Taxa, and Co-occurrence Patterns.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {145}, pmid = {39570409}, issn = {1432-184X}, support = {2023JBFR01//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; CARS-46//the earmarked fund for CARS/ ; 2023TD18//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; }, mesh = {*Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Aquaculture ; *Rhizosphere ; *Feces/microbiology ; Animals ; Biofilms ; Fishes/microbiology ; Water Microbiology ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recirculating aquaculture and aquaponics are considered sustainable aquaculture models playing important roles in animal-derived protein supply. In these aquaculture systems, microorganisms are crucial for the system stability. The community coalescence by mixing substances and microorganisms from various microhabitats under hydraulic forces is important for shaping the bacterial communities in these small-scale complex systems. However, the influences of community coalescence on bacterial communities remain rarely revealed in these systems. In this study, aquaponics (APS) and recirculating aquaculture (RAS) systems were set up to explore the bacterial community coalescence across different microhabitats, including water, fish feces, biofilter biofilms, and plant rhizosphere environment. Our results showed that diversity and compositions varied across different microhabitats in both systems. However, bacterial transmissions across these microhabitats differed between systems. The core microbiome of the RAS and APS were formed under community coalescence with the highest contribution of bacterial taxa derived from the fish feces. Nevertheless, the plant rhizosphere bacterial community also contributed to the core microbiome of the APS. Furthermore, the core taxa showed a higher average degree than the other nodes in the bacterial community networks in all microhabitats except for the plant rhizosphere environment, implying the important roles of core taxa in maintaining these bacterial community networks. Our results provide new insights into the assembly of bacterial communities under community coalescence in the artificial aquatic ecosystems comprising complex microhabitats, which is vital for developing microbial solutions for regulating the microbial communities to improve system performance in the future.}, }
@article {pmid39570377, year = {2024}, author = {Jensen, IC and Schramm, A and Offenberg, J}, title = {Fungus Fighters: Wood Ants (Formica polyctena) and Their Associated Microbes Inhibit Plant Pathogenic Fungi.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {146}, pmid = {39570377}, issn = {1432-184X}, support = {NNF21OC0071665//Novo Nordisk Fonden/ ; NNF21OC0071665//Novo Nordisk Fonden/ ; 34009-19-1562//Internationalt Center for Forskning i &#xd8;kologisk Jordbrug og F&#xf8;devaresystemer/ ; }, mesh = {*Ants/microbiology/physiology ; Animals ; *Plant Diseases/microbiology/prevention &amp; control ; Malus/microbiology ; Fungi/physiology/classification ; Antibiosis ; Bacteria/classification/drug effects/isolation &amp; purification ; Ascomycota/physiology/drug effects ; }, abstract = {Plant diseases cost the global economy billions of US dollars every year. The problem has mainly been addressed by using chemical pesticides, but recently, the use of ants has shown promising effects against plant pathogens. However, the mechanisms accounting for these effects have not yet been determined. One possible explanation is antimicrobial microorganisms associated with ants. Through controlled laboratory experiments, we investigated the inhibitory effects of wood ants (Formica polyctena) and their associated microorganisms against economically important plant pathogenic fungi. All live ants, extracts from crushed ants, and extracts from washed ants significantly inhibited the apple brown rot (Monilinia fructigena) while yielding the growth of other microbes. Furthermore, all investigated wood ants transferred microorganisms to their surroundings within 10 s when walking across a surface. We isolated the most dominant microorganisms deposited by walking ants and from washed ant extracts (i.e., strains likely found on the surface of ants), resulting in four bacterial cultures and one yeast. Two of these isolates, strain I3 (most closely related to Pseudomonas sichuanensis and P. entomophila) and strain I1b (most closely related to Bacillus mycoides), showed inhibitory effects against apple brown rot and apple scab (Venturia inaequalis), while strain I3 also inhibited gray mold (Botrytis cinerea) and Fusarium head blight (Fusarium graminearum). These results suggest that wood ants have potential as biological control agents against commercially relevant plant pathogens, and that their inhibitory effect might be at least partially caused by antibiotic compounds produced by their associated microorganisms.}, }
@article {pmid39568064, year = {2024}, author = {Sauma-Sánchez, T and Alcorta, J and Tamayo-Leiva, J and Díez, B and Bezuidenhout, H and Cowan, DA and Ramond, JB}, title = {Functional redundancy buffers the effect of poly-extreme environmental conditions on southern African dryland soil microbial communities.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {12}, pages = {}, pmid = {39568064}, issn = {1574-6941}, support = {FBIS160422162807//National Research Foundation/ ; 1210912//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; }, mesh = {*Soil Microbiology ; *Bacteria/genetics/classification ; *Archaea/genetics/classification ; *Microbiota ; *Salinity ; *Fungi/genetics/classification ; Climate Change ; Desert Climate ; Soil/chemistry ; Extreme Environments ; Africa, Southern ; Biodiversity ; }, abstract = {Drylands' poly-extreme conditions limit edaphic microbial diversity and functionality. Furthermore, climate change exacerbates soil desiccation and salinity in most drylands. To better understand the potential effects of these changes on dryland microbial communities, we evaluated their taxonomic and functional diversities in two Southern African dryland soils with contrasting aridity and salinity. Fungal community structure was significantly influenced by aridity and salinity, while Bacteria and Archaea only by salinity. Deterministic homogeneous selection was significantly more important for bacterial and archaeal communities' assembly in hyperarid and saline soils when compared to those from arid soils. This suggests that niche partitioning drives bacterial and archaeal communities' assembly under the most extreme conditions. Conversely, stochastic dispersal limitations drove the assembly of fungal communities. Hyperarid and saline soil communities exhibited similar potential functional capacities, demonstrating a disconnect between microbial structure and function. Structure variations could be functionally compensated by different taxa with similar functions, as implied by the high levels of functional redundancy. Consequently, while environmental selective pressures shape the dryland microbial community assembly and structures, they do not influence their potential functionality. This suggests that they are functionally stable and that they could be functional even under harsher conditions, such as those expected with climate change.}, }
@article {pmid39567391, year = {2024}, author = {Vezina, B and Cooper, HB and Wisniewski, JA and Parker, MH and Jenney, AWJ and Holt, KE and Wyres, KL}, title = {Wild-Type Domestication: Loss of Intrinsic Metabolic Traits Concealed by Culture in Rich Media.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {144}, pmid = {39567391}, issn = {1432-184X}, support = {DP200103364//Australian Research Council/ ; DP200103364//Australian Research Council/ ; APP1176192//National Health and Medical Research Council/ ; }, mesh = {*Klebsiella pneumoniae/genetics/metabolism/growth &amp; development ; *Culture Media/chemistry ; *Genome, Bacterial ; Histidine/metabolism ; Mutation ; Whole Genome Sequencing ; }, abstract = {Bacteria are typically isolated on rich media to maximise isolation success, removing them from their native evolutionary context. This eliminates selection pressures, enabling otherwise deleterious genomic events to accumulate. Here, we present a cautionary tale of these 'quiet mutations' which can persist unnoticed in bacterial culture lines. We used a combination of microbiological culture (standard and minimal media conditions), whole genome sequencing and metabolic modelling to investigate putative Klebsiella pneumoniae L-histidine auxotrophs. Additionally, we used genome-scale metabolic modelling to predict auxotrophies among completed public genomes (n = 2637). Two sub-populations were identified within a K. pneumoniae frozen stock, differing in their ability to grow in the absence of L-histidine. These sub-populations were the same 'strain', separated by eight single nucleotide variants and an insertion sequence-mediated deletion of the L-histidine biosynthetic operon. The His[-] sub-population remained undetected for > 10 years despite its inclusion in independent laboratory experiments. Genome-scale metabolic models predicted 0.8% public genomes contained ≥ 1 auxotrophy, with purine/pyrimidine biosynthesis and amino acid metabolism most frequently implicated. We provide a definitive example of the role of standard rich media culture conditions in obscuring biologically relevant mutations (i.e. nutrient auxotrophies) and estimate the prevalence of such auxotrophies using public genome collections. While the prevalence is low, it is not insignificant given the thousands of K. pneumoniae that are isolated for global surveillance and research studies each year. Our data serve as a pertinent reminder that rich-media culturing can cause unnoticed wild-type domestication.}, }
@article {pmid39567372, year = {2024}, author = {Issifu, S and Acharya, P and Kaur-Bhambra, J and Gubry-Rangin, C and Rasche, F}, title = {Biological Nitrification Inhibitors with Antagonistic and Synergistic Effects on Growth of Ammonia Oxidisers and Soil Nitrification.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {143}, pmid = {39567372}, issn = {1432-184X}, support = {RA 1717/8-1//2019-2020 Bio-divERsA joint call for research proposals, under the BiodivClim ERA-Net COFUND programme, and with the funding organisations German Research Foundation/ ; RA 1717/8-1//2019-2020 Bio-divERsA joint call for research proposals, under the BiodivClim ERA-Net COFUND programme, and with the funding organisations German Research Foundation/ ; URF150571//Royal Society University Research Fellowship/ ; }, mesh = {*Nitrification ; *Soil Microbiology ; *Ammonia/metabolism ; *Soil/chemistry ; Archaea/metabolism/drug effects/growth &amp; development ; Oxidation-Reduction ; Rhizosphere ; Bacteria/metabolism/drug effects/growth &amp; development ; }, abstract = {Biological nitrification inhibition (BNI) refers to the plant-mediated process in which nitrification is inhibited through rhizospheric release of diverse metabolites. While it has been assumed that interactive effects of these metabolites shape rhizosphere processes, including BNI, there is scant evidence supporting this claim. Hence, it was a primary objective to assess the interactive effects of selected metabolites, including caffeic acid (CA), vanillic acid (VA), vanillin (VAN), syringic acid (SA), and phenylalanine (PHE), applied as single and combined compounds, against pure cultures of various ammonia-oxidising bacteria (AOB, Nitrosomonas europaea, Nitrosospira multiformis, Nitrosospira tenuis, Nitrosospira briensis) and archaea (AOA, Nitrososphaera viennensis), as well as soil nitrification. Additionally, benzoic acid (BA) was examined as a novel biological nitrification inhibitor. All metabolites, except SA, tested as single compounds, achieved varied levels of inhibition of microbial growth, with CA exhibiting the highest inhibitory potential. Similarly, all metabolites applied as single compounds, except PHE, inhibited soil nitrification by up to 62%, with BA being the most potent. Inhibition of tested nitrifying microbes was also observed when compounds were assessed in combination. The combinations VA + PH, VA + CA, and VA + VAN exhibited synergism against N. tenuis and N. briensis, while others showed antagonism against N. europaea, N. multiformis, and N. viennensis. Although all combinations suppressed soil nitrification, their interactions against soil nitrification revealed antagonism. Our findings indicate that both antagonism and synergism are possible in rhizospheric interactions involving BNI metabolites, resulting in growth inhibition of nitrifiers and suppression of soil nitrification.}, }
@article {pmid39565130, year = {2025}, author = {Yu, C and Yu, M and Ma, R and Wei, S and Jin, M and Jiao, N and Zheng, Q and Zhang, R and Feng, X}, title = {A novel Alteromonas phage with tail fiber containing six potential iron-binding domains.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0093424}, pmid = {39565130}, issn = {2165-0497}, mesh = {*Bacteriophages/genetics/metabolism/isolation &amp; purification ; *Iron/metabolism ; *Phylogeny ; *Alteromonas/virology/metabolism/genetics ; Host Specificity ; Viral Tail Proteins/metabolism/genetics ; Genome, Viral/genetics ; Protein Domains ; }, abstract = {Viruses play a vital role in regulating microbial communities, contributing to biogeochemical cycles of carbon, nitrogen, and essential metals. Alteromonas is widespread and plays an essential role in marine microbial ecology. However, there is limited knowledge about the interactions of Alteromonas and its viruses (alterophages). This study isolated a novel podovirus, vB_AmeP-R22Y (R22Y), which infects Alteromonas marina SW-47 (T). Phylogenetic analysis suggested that R22Y represented a novel viral genus within the Schitoviridae family. R22Y exhibited a broad host range and a relatively large burst size, exerting an important impact on the adaptability and dynamics of host populations. Two auxiliary metabolic genes, encoding Acyl carrier protein and AAA domain-containing protein, were predicted in R22Y, which may potentially assist in host fatty acid metabolism and VB12 biosynthesis, respectively. Remarkably, the prediction of the R22Y tail fiber structure revealed six conserved histidine residues (HxH motifs) that could potentially bind iron ions, suggesting that alterophages may function as organic iron-binding ligands in the marine environment. Our isolation and characterization of R22Y complements the Trojan Horse hypothesis, proposes the possible role of alterophages for marine iron biogeochemical cycling, and provides new insights into phage-host interactions in the iron-limited ocean.IMPORTANCEIron (Fe), as an essential micronutrient, is often a limiting factor for microbial growth in marine ecosystems. The Trojan Horse hypothesis suggests that iron in the phage tail fibers is recognized by the host's siderophore-bound iron receptor, enabling the phage to attach and initiate infection. The potential role of phages as iron-binding ligands has significant implications for oceanic trace metal biogeochemistry. In this study, we isolated a new phage R22Y with the potential to bind iron ions, using Alteromonas, a major siderophore producer, as the host. The tail fiber structure of R22Y exhibits six conserved HxH motifs, suggesting that each phage could potentially bind up to 36 iron ions. R22Y may contribute to colloidal organically complexed dissolved iron in the marine environment. This finding provides further insights into the Trojan Horse hypothesis, suggesting that alterophages may act as natural iron-binding ligands in the marine environment.}, }
@article {pmid39563404, year = {2024}, author = {Chari, NR and Muratore, TJ and Frey, SD and Winters, CL and Martinez, G and Taylor, BN}, title = {Long-Term Soil Warming Drives Different Belowground Responses in Arbuscular Mycorrhizal and Ectomycorrhizal Trees.}, journal = {Global change biology}, volume = {30}, number = {11}, pages = {e17550}, doi = {10.1111/gcb.17550}, pmid = {39563404}, issn = {1365-2486}, support = {DEB-1456610//National Science Foundation/ ; DEB-1832110//National Science Foundation/ ; }, mesh = {*Mycorrhizae/physiology ; *Trees/microbiology/physiology/growth &amp; development ; *Soil/chemistry ; *Plant Roots/microbiology ; *Global Warming ; Biomass ; Soil Microbiology ; Carbon/metabolism/analysis ; Nitrogen/metabolism/analysis ; Climate Change ; Temperature ; }, abstract = {The ability of trees to acquire soil nutrients under future climate conditions will influence forest composition and function in a warmer world. Rarely are multiple belowground carbon allocation pathways measured simultaneously in large global change experiments, restricting our understanding of how trees may shift their allocation of resources to different nutrient acquisition mechanisms under future climates. Leveraging a 20-year soil warming experiment, we show that ectomycorrhizal (EM) trees reduce mycorrhizal colonization and root exudation while increasing fine root biomass, while arbuscular mycorrhizal (AM) trees largely maintained their belowground carbon allocation patterns in warmer soils. We suggest that AM trees may be better adapted to thrive under global warming due to higher rates of nitrogen mineralization in warmer soils and the ability of their mycorrhizal symbiont to acquire mineralized inorganic nutrients, whereas EM trees may need to alter their belowground carbon allocation patterns to remain competitive as global temperatures rise.}, }
@article {pmid39561700, year = {2024}, author = {Partida-Martínez, LP}, title = {Laila P. Partida-Martínez.}, journal = {Current biology : CB}, volume = {34}, number = {22}, pages = {R1121-R1122}, doi = {10.1016/j.cub.2024.09.085}, pmid = {39561700}, issn = {1879-0445}, mesh = {*Symbiosis ; Fungi/physiology ; Plants/microbiology ; History, 21st Century ; History, 20th Century ; }, abstract = {Interview with Laila Partida-Martínez, who studies microbial ecology, fungal-bacterial symbioses and plant-microbe interactions at the Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav).}, }
@article {pmid39561304, year = {2024}, author = {Vargas Ribera, PR and Kim, N and Venbrux, M and Álvarez-Pérez, S and Rediers, H}, title = {Evaluation of sequence-based tools to gather more insight into the positioning of rhizogenic agrobacteria within the Agrobacterium tumefaciens species complex.}, journal = {PloS one}, volume = {19}, number = {11}, pages = {e0302954}, pmid = {39561304}, issn = {1932-6203}, mesh = {*Agrobacterium tumefaciens/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Agrobacterium/genetics ; Genome, Bacterial ; DNA, Bacterial/genetics ; }, abstract = {Rhizogenic Agrobacterium, the causative agent of hairy root disease (HRD), is known for its high phenotypic and genetic diversity. The taxonomy of rhizogenic agrobacteria has undergone several changes in the past and is still somewhat controversial. While the classification of Agrobacterium strains was initially mainly based on phenotypic properties and the symptoms they induced on plants, more and more genetic information has been used along the years to infer Agrobacterium taxonomy. This has led to the definition of the so-called Agrobacterium tumefaciens species complex (Atsc), which comprises several genomospecies. Interestingly, the rhizogenic Agrobacterium strains are found in several of these genomospecies. Nevertheless, even up until today Agrobacterium strains, and in particular rhizogenic agrobacteria, are prone to misclassification and considerable confusion in literature. In this study, we evaluated different phylogenetic analysis approaches for their use to improve Agrobacterium taxonomy and tried to gain more insight in the classification of strains into this complex genus, with a particular focus on rhizogenic agrobacteria. The genome sequence analysis of 580 assemblies, comprising Agrobacterium, Allorhizobium and Rhizobium strains demonstrated that phylogenies based on single marker genes, such as the commonly used 16S rRNA and recA gene, do not provide sufficient resolution for proper delineation of the different genomospecies within the Atsc. Our results revealed that (in silico) multi-locus sequences analysis (MLSA) in combination with average nucleotide identity (ANIb) at a 94.0% threshold delineates genomospecies accurately and efficiently. Additionally, this latter approach permitted the identification of two new candidate genomospecies.}, }
@article {pmid39560406, year = {2024}, author = {Ye, Y-Q and Ye, M-Q and Zhang, X-Y and Huang, Y-Z and Zhou, Z-Y and Feng, Y-J and Du, Z-J}, title = {Description of the first marine-isolated member of the under-represented phylum Gemmatimonadota, and the environmental distribution and ecogenomics of Gaopeijiales ord. nov.}, journal = {mSystems}, volume = {9}, number = {12}, pages = {e0053524}, pmid = {39560406}, issn = {2379-5077}, support = {92351301//MOST | National Natural Science Foundation of China (NSFC)/ ; 32070002//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022FY101100//National Science and Technology Fundamental Resources Investigation Program of China/ ; }, mesh = {*Phylogeny ; *Geologic Sediments/microbiology ; China ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/metabolism ; DNA, Bacterial/genetics ; }, abstract = {The phylum Gemmatimonadota is widespread but rarely cultured and, in fact, there are only six described species isolated from soil, freshwater, and wastewater treatment. However, no isolates of Gemmatimonadota from marine environment have been described; thus, little is known about the physiology and metabolism of members of the marine lineages. In this study, four novel facultatively anaerobic bacterial strains belonging to Gemmatimonadota were isolated from marine sediments collected from Xiaoshi Island in Weihai, China, using an aerobic enrichment method. The integrated results of phylogenetic and phenotypic characteristics supported that these four strains represent one novel species in a novel genus, for which the name Gaopeijia maritima gen. nov., sp. nov. is proposed, as the first representative of novel taxa, Gaopeijiales ord. nov., Gaopeijiaceae fam. nov. in the class Longimicrobiia. Gaopeijiales was detected in 22,884 out of 95,549 amplicon data sets, mainly from soil. However, the highest mean relative abundances were in sponge (0.7%) and marine sediment (0.35%), showing salt-related character. Most of the Gaopeijiales subgroups potentially belong to the rare bacterial biosphere. The aerobic enrichment in this study could significantly increase the relative abundance of Gaopeijiales (from 0.37% to 2.6%). Furthermore, the metabolic capabilities inferred from high-quality representative Gaopeijiales genomes/MAGs suggest that this group primarily performs chemoorganoheterotrophic metabolism with facultatively anaerobic characteristics and possesses various secondary metabolite biosynthesis gene clusters (BGCs), mirroring those observed in the four novel strains.IMPORTANCEDespite rapid advances in molecular and sequencing technologies, obtaining pure cultures remains a crucial research goal in microbiology, as it is essential for a deeper understanding of microbial metabolism. Gemmatimonadota is a widespread but rarely cultured bacterial phylum. Currently, there are only six cultured strains of this interesting group, all isolated from non-marine environments. Little is known about the physiology and metabolism of members of the marine lineages. Here we isolated and characterized four novel marine strains, and proposed a new order Gaopeijiales within Gemmatimonadota. Furthermore, the global distribution, environmental preference, and metabolic potential of Gaopeijiales are analyzed using public data. Our work enriches the resources available for the under-represented phylum Gemmatimonadota and provides insights into the physiological and metabolic characteristics of the marine lineage (Gaopeijiales) through culturology and omics.}, }
@article {pmid39558480, year = {2024}, author = {Zechner, EL and Kienesberger, S}, title = {Microbiota-derived small molecule genotoxins: host interactions and ecological impact in the gut ecosystem.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2430423}, pmid = {39558480}, issn = {1949-0984}, mesh = {Animals ; Humans ; *Bacteria/drug effects/genetics/metabolism ; Enterotoxins/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Host Microbial Interactions ; Mutagens/metabolism/toxicity ; Polyketides/metabolism/toxicity ; }, abstract = {The human intestinal tract is densely colonized by a microbial community that is subject to intense competition. Bacteria in this complex habitat seek to outcompete their neighbors for nutrients and eliminate competitors with antibacterial toxins. Antagonism can be mediated by diverse effectors including toxic proteins and small molecule inhibitors that are released extracellularly or delivered by specialized secretion systems to targeted cells. Two prototypical microbiota-derived enterotoxins, colibactin and tilimycin, and the newly discovered family of indolimines represent an expanding group of non-proteinaceous small molecules which specifically target DNA. In addition to cell killing, they generate mutations and genome instability in intoxicated microbes and host cells alike. They have been studied in detail because of their direct toxicity to human cells and important etiological roles in intestinal pathologies. Increasing evidence, however, reveals that these commensal genotoxins are also mediators of interbacterial antagonism, which impacts gut microbial ecology. In this review, we illustrate the functional versatility of commensal genotoxins in the gut ecosystem.}, }
@article {pmid39557685, year = {2024}, author = {Mai, N and Foysal, MJ and Timms, VJ and Pearson, LA and Romanis, CS and Mills, TJT and Powell, JR and Neilan, BA}, title = {Seasonal and Spatial Dynamics of Fungal Leaf Endophytes in Eucalyptus crebra (Narrow-Leaved Ironbark).}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {142}, pmid = {39557685}, issn = {1432-184X}, support = {CE200100029//Australian Research Council/ ; CE200100029//Australian Research Council/ ; CE200100029//Australian Research Council/ ; CE200100029//Australian Research Council/ ; FF0883440//Australian Research Council/ ; }, mesh = {*Eucalyptus/microbiology ; *Seasons ; *Endophytes/isolation &amp; purification/classification/genetics ; *Plant Leaves/microbiology ; *Fungi/classification/isolation &amp; purification/genetics ; Biodiversity ; Ascomycota/genetics/isolation &amp; purification ; Basidiomycota/isolation &amp; purification/genetics/classification ; }, abstract = {Fungal endophytes play an important role in improving the health and productivity of native and cultivated plant species. Despite their ecological and industrial importance, few eucalypt species have been studied in terms of their endophyte communities. We examined the seasonal and spatial dynamics of fungal leaf endophytes in the model species, Eucalyptus crebra (narrow-leaved ironbark), using ITS-based amplicon sequencing. Alpha and beta diversity analyses revealed significantly higher species richness in summer compared to autumn and spring. Similarly, two-way ANOVA analysis showed significantly higher species diversity in summer compared to autumn (observed p < 0.001, Chao1 p < 0.005) and spring (observed p < 0.005, Chao1 p < 0.005). No difference in Shannon index was observed among different canopy levels across the season. Beta-diversity showed differences in fungal composition across the seasons and at various canopy levels based on unweighted UniFrac distance metric (PERMANOVA season p < 0.001, canopy p < 0.05), signifying distinct separation of fungi based on presence-absence. Ascomycota was the most abundant and diverse phylum and was present throughout the year. In contrast, Basidiomycota was only observed during cooler and drier seasons. Neofusicoccum was the most abundant genus, but distribution fluctuated significantly across the seasons. Pestalotiopsis and Neopestalotiopsis were most abundant in the low leaf canopy, whereas Pseudosydowia was most abundant in the high canopy. This study indicates that the diversity and abundance of endophytic fungi in the leaves of healthy E. crebra trees fluctuate seasonally and across canopy levels. The data generated can be used as a baseline for assessing and potentially modulating the health of E. crebra and other important Eucalyptus spp.}, }
@article {pmid39551884, year = {2024}, author = {Mamo, Z and Abera, S and Tafesse, M}, title = {Taxonomic and functional profiling of microbial community in municipal solid waste dumpsite.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {40}, number = {12}, pages = {384}, pmid = {39551884}, issn = {1573-0972}, support = {EN-1/17-1/18//Addis Ababa Science and Technology University/ ; }, mesh = {*Solid Waste ; *Bacteria/classification/genetics/metabolism ; *Waste Disposal Facilities ; *Microbiota ; *Metagenomics ; Phylogeny ; Refuse Disposal ; Biodegradation, Environmental ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; }, abstract = {Understanding the microbial ecology of landfills is crucial for improving waste management strategies and utilizing the potential of these microbial communities for biotechnological applications. This study aimed to conduct a comprehensive taxonomic and functional profiling of the microbial community present in the Addis Ababa municipal solid waste dumpsite using a shotgun metagenomics sequencing approach. The taxonomic analysis of the sample revealed the significant presence of bacteria, with the Actinomycetota (56%), Pseudomonadota (23%), Bacillota (3%), and Chloroflexota (3%) phyla being particularly abundant. The most abundant KEGG categories were carbohydrates metabolism, membrane transport, signal transduction, and amino acid metabolism. The biodegradation and metabolism of xenobiotics, as well as terpenoids and polyketides, were also prevalent. Moreover, the Comprehensive Antibiotic Resistance Database (CARD) identified 52 antibiotic resistance gene (ARG) subtypes belonging to 14 different drug classes, with the highest abundances observed for glycopeptide, phosphonic acid, and multidrug resistance genes. Actinomycetota was the dominant phylum harboring ARGs, followed by Pseudomonadota and Chloroflexota. This study offers valuable insights into the taxonomic and functional diversity of the microbial community in the Addis Ababa municipal solid waste dumpsite. It sheds light on the widespread presence of metabolically versatile microbes, antibiotic resistance genes, mobile genetic elements, and pathogenic bacteria. This understanding can contribute to the creation of efficient waste management strategies and the investigation of possible biotechnological uses for these microbial communities.}, }
@article {pmid39551202, year = {2024}, author = {Duran, C and Bouchard, A and Agogué, H and Dupuy, C and Duran, R and Cravo-Laureau, C}, title = {Importance of eukaryotes in shaping microbial benthic communities in Charente-maritime marshes, France.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177523}, doi = {10.1016/j.scitotenv.2024.177523}, pmid = {39551202}, issn = {1879-1026}, mesh = {*Eukaryota ; France ; *Microbiota ; *Wetlands ; Animals ; Bacteria/classification ; Salinity ; Archaea ; Seasons ; Environmental Monitoring ; }, abstract = {Marshes are wetlands known for providing major ecosystem services in terms of water quality and human activities. These ecosystem services are mainly provided by marshes' benthic community, composed of prokaryotes (bacteria and archaea) but also of eukaryotes (micro-eukaryotes and meiofauna). The aim of this study is to (1) assess the environmental parameters affecting benthic community composition in marshes, (2) highlight the associations between organisms from the three domains of life, and (3) determine the parameters controlling these associations. Hence, benthic communities of eight different marshes from three typologies (salted, brackish and freshwater) and four seasons (autumn 2020, spring 2021, summer 2021 and autumn 2021) were assessed. This study revealed three main drivers of community composition. First, salinity drives the community composition illustrated by the differences observed between the three typologies of marshes. Relative abundance of Nitrososphaeria, Halobacteria, Bacillariophyceae, Conoidasida and nematodes increased with salinity while methanogenic archaea, Chlorophyceae and copepod's relative abundance decreased. The second driver is the physical-chemistry of the site, particularly nutrients. The season is the last driver of community composition, seasonal pattern varying for each site within a typology. LEfSe analyses defined biomarkers of typology and season, among which many prokaryotes involved in the nitrogen cycle and photosynthetic micro-eukaryotes where present in different co-occurrence networks, highlighting the importance of nitrogen cycle in marshes. Co-occurrence networks revealed several connections between organisms of the three domains of life, particularly between prokaryotes and photosynthetic eukaryotes. This study illustrates thus the importance of holistic approaches in microbial ecology for revealing a comprehensive view of the whole microbial interactions occurring in complex ecosystems.}, }
@article {pmid39549623, year = {2025}, author = {White, CA and Antell, EH and Schwartz, SL and Lawrence, JE and Keren, R and Zhou, L and Yu, K and Zhuang, WQ and Alvarez-Cohen, L}, title = {Life history strategies determine response to SRT driven crash in anammox bioreactors.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122727}, doi = {10.1016/j.watres.2024.122727}, pmid = {39549623}, issn = {1879-2448}, mesh = {*Bioreactors/microbiology ; Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; Oxidation-Reduction ; Ammonium Compounds/metabolism ; Waste Disposal, Fluid/methods ; Bacteria/metabolism/genetics ; }, abstract = {Anaerobic ammonium oxidation (anammox) is a biological process often applied in wastewater treatment plants for nitrogen removal from highly concentrated side-stream effluents from anaerobic digesters. However, they are vulnerable to process instability prompted by operational shocks and microbial community imbalances, resulting in lengthy recovery times. These issues are further compounded by a lack of understanding of how sustained press disturbances influence the microbial ecology of the system. Here we investigate the response and recovery of an anammox membrane bioreactor to a solids retention time (SRT)-induced reactor crash using 16S rRNA gene and shotgun metagenomic sequencing. We observed a strong selection of bacterial groups based on reproduction strategies, with the Orders Rhodospirillales and Sphingobacteriales increasing from 1.0 % and 11.9 % prior to the crash to 31.9 % and 18.1 % during the crash respectively. The Orders Brocadiales and Anaerolineales decreased from 17.3 % and 28.3 % to 7.3 % and 1.4 % over the same time period, respectively. Metagenomic and metatranscriptomic analyses revealed differential crash responses in metabolically distinct groups of bacteria, with increased expression of genes for extracellular carbohydrate active enzymes, peptidases and membrane transporters. Following the crash, the reactor recovered to its prior state of nitrogen removal performance and pathway analysis demonstrated increased expression of genes related to exopolysaccharide biosynthesis and quorum sensing during the reactor recovery period. This study highlights the effects of reactor perturbations on microbial community dynamics in anammox bioreactors and provides insight into potential recovery mechanisms from severe disturbance.}, }
@article {pmid39549075, year = {2024}, author = {de la Sovera, V and Bovio-Winkler, P and Zinola, G and Etchebehere, C}, title = {Microbial community evolution in a lab-scale reactor operated to obtain biomass for biochemical methane potential assays.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {519}, pmid = {39549075}, issn = {1432-0614}, support = {SNI//ANII/ ; SNI//ANII/ ; SNI//ANII/ ; (II/FVF/2019/121).//Carlos Vaz Ferreira/ ; }, mesh = {*Methane/metabolism ; *Biomass ; *Bioreactors/microbiology ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Archaea/genetics/metabolism/classification ; Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; *Sewage/microbiology ; Microbiota ; Biodegradation, Environmental ; }, abstract = {Biochemical methane potential (BMP) test is an important tool to evaluate the methane production biodegradability and toxicity of different wastes or wastewaters. This is a key parameter for assessing design and feasibility issues in the full-scale implementation of anaerobic digestion processes. A standardized and storable inoculum is the key to obtain reproducible results. In Uruguay, a local enterprise dedicated to design and install anaerobic digesters operated a lab-scale bioreactor as a source of biomass for BMP tests, using a protocol previously described. This reactor was controlled and fed with a mixture of varied organic compounds (lipids, cellulolytic wastes, proteins). Biomass was reintroduced into the reactor after BMP assays to maintain a constant volume and biomass concentration. The aim of this work was to evaluate how the microbial community evolved during this operation and the effect of storing biomass in the refrigerator. The composition of the microbial communities was analyzed by 16S rRNA amplicon sequencing using primers for Bacteria and Archaea. The methanogenic activity was determined, and the methanogens were quantified by mcrA qPCR. One sample was stored for a 5-month period in the refrigerator (4 °C); the activity and the microbial community composition were analyzed before and after storage. Results showed that applying the reported methodology, a reliable methanogenic sludge with an acceptable SMA was obtained even though the reactor suffered biomass alterations along the evaluated period. Refrigerating the acclimatized biomass for 5 months did not affect its activity nor its microbial composition according to the 16S rRNA gene sequence analysis, even though changes in the mcrA abundance were observed. KEY POINTS: • The applied methodology was successful to obtain biomass suitable to perform BMP assays. • The microbial community was resilient to external biomass addition. • Biomass storage at 4 °C for 5 months did not alter the methanogenic activity.}, }
@article {pmid39546027, year = {2024}, author = {Khamespanah, E and Asad, S and Vanak, Z and Mehrshad, M}, title = {Niche-Aware Metagenomic Screening for Enzyme Methioninase Illuminates Its Contribution to Metabolic Syntrophy.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {141}, pmid = {39546027}, issn = {1432-184X}, mesh = {*Carbon-Sulfur Lyases/genetics/metabolism ; *Metagenomics ; *Phylogeny ; *Bacteria/genetics/classification/enzymology/isolation &amp; purification/metabolism ; Archaea/genetics/enzymology/classification ; Groundwater/microbiology ; Metagenome ; Seawater/microbiology ; }, abstract = {The single-step methioninase-mediated degradation of methionine (as a sulfur containing amino acid) is a reaction at the interface of carbon, nitrogen, sulfur, and methane metabolism in microbes. This enzyme also has therapeutic application due to its role in starving auxotrophic cancer cells. Applying our refined in silico screening pipeline on 33,469 publicly available genome assemblies and 1878 metagenome assembled genomes/single-cell amplified genomes from brackish waters of the Caspian Sea and the Fennoscandian Shield deep groundwater resulted in recovering 1845 methioninases. The majority of recovered methioninases belong to representatives of phyla Proteobacteria (50%), Firmicutes (29%), and Firmicutes_A (13%). Prevalence of methioninase among anaerobic microbes and in the anoxic deep groundwater together with the relevance of its products for energy conservation in anaerobic metabolism highlights such environments as desirable targets for screening novel methioninases and resolving its contribution to microbial metabolism and interactions. Among archaea, majority of detected methioninases are from representatives of Methanosarcina that are able to use methanethiol, the sulfur containing product from methionine degradation, as a precursor for methanogenesis. Branching just outside these archaeal methioninases in the phylogenetic tree, we recovered three methioninases belonging to representatives of Patescibacteria reconstructed from deep groundwater metagenomes. We hypothesize that methioninase in Patescibacteria could contribute to their syntrophic interactions where their methanogenic partners/hosts benefit from the produced 2-oxobutyrate and methanethiol. Our results underscore the significance of accounting for specific ecological niche in screening for enzyme variates with desired characteristics. Finally, complementing of our findings with experimental validation of methioninase activity confirms the potential of our in silico screening in clarifying the peculiar ecological role of methioninase in anoxic environments.}, }
@article {pmid39545996, year = {2024}, author = {Scheelings, TF and Van, TTH and Moore, RJ and Skerratt, LF}, title = {Location Matters: Variations in Cloacal Microbiota Composition of Spatially Separated Freshwater Turtles.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {140}, pmid = {39545996}, issn = {1432-184X}, mesh = {Animals ; *Turtles/microbiology ; *Cloaca/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Fresh Water/microbiology ; Australia ; Gastrointestinal Microbiome ; Biodiversity ; }, abstract = {The gut microbiota of vertebrates is malleable and may be shaped by both intrinsic and extrinsic factors. Here, the effect that geography has on the cloacal microbiota of two species of Australian freshwater chelonians, eastern longneck turtle (Chelodina longicollis) and Macquarie River turtle (Emydura macquarii), captured from waterbodies with different levels of anthropogenic pressure was investigated. We analysed the microbiota composition, structure and diversity through 16S rRNA gene amplicon sequencing. It was hypothesised that animals from less disturbed environments would harbour a more diverse cloacal microbial population. The cloacal microbiotas from 93 turtles (C. longicollis n = 78; E. macquarii n = 15), from five locations, were analysed. For both species, the most predominant phylum was Proteobacteria. Cloacal microbiota alpha diversity varied significantly between the C. longicollis from all locations, but no differences were found for E. macquarii. In C. longicollis, turtles from wetlands within the centre of Melbourne had the lowest alpha diversity metrics, while the highest alpha diversity values were seen in turtles captured from an undisturbed rural waterbody. Beta diversity, obtained by weighted UniFrac distance, showed significant differences between locations of capture for both species of turtles in this investigation. For C. longicollis, 87 biomarkers were identified responsible for explaining differences between locations, and in E. macquarii, 42 biomarkers were found. This is the first study to explore the cloacal microbiota composition of the eastern longneck turtle and gives greater insight into microbial community structures in Macquarie River turtles. Our study demonstrated that cloacal microbiota composition of freshwater turtles was significantly influenced by locality and that disrupted environments may reduce microbial diversity in C. longicollis. Interestingly, we discovered that the effects of location contrasted significantly between species for alpha diversity with differences discovered for C. longicollis but not E. macquarii. However, for both species, beta diversity was notably influenced by habitat type. These results highlight the need to interpret chelonian microbiota data in the context of geography and human disturbance of the environment.}, }
@article {pmid39545729, year = {2024}, author = {Beaudry, MS and Bhuiyan, MIU and Glenn, TC}, title = {Enriching the future of public health microbiology with hybridization bait capture.}, journal = {Clinical microbiology reviews}, volume = {37}, number = {4}, pages = {e0006822}, pmid = {39545729}, issn = {1098-6618}, support = {R01 AI148667/AI/NIAID NIH HHS/United States ; 75D30118C02889, 75D30120R67837//HHS | Centers for Disease Control and Prevention (CDC)/ ; 1R01AI148667-01A1//HHS | National Institutes of Health (NIH)/ ; }, mesh = {Humans ; Bacteria/genetics/classification/isolation &amp; purification ; Fungi/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; *Microbiological Techniques/methods/trends ; Nucleic Acid Hybridization/methods ; *Public Health ; }, abstract = {SUMMARYPublic health microbiology focuses on microorganisms and infectious agents that impact human health. For years, this field has relied on culture or molecular methods to investigate complex samples of public health importance. However, with the increase in accuracy and decrease in sequencing cost over the last decade, there has been a transition to the use of next-generation sequencing in public health microbiology. Nevertheless, many available sequencing methods (e.g., shotgun metagenomics and amplicon sequencing) do not work well in complex sample types, require deep sequencing, or have inherent biases associated with them. Hybridization bait capture, also known as target enrichment, brings in solutions for such limitations. It is an increasingly popular technique to simultaneously characterize many thousands of genetic elements while reducing the amount of sequencing needed (thereby reducing the sequencing costs). Here, we summarize the concept of hybridization bait capture for public health, reviewing a total of 35 bait sets designed in six key topic areas for public health microbiology [i.e., antimicrobial resistance (AMR), bacteria, fungi, parasites, vectors, and viruses], and compare hybridization bait capture to previously relied upon methods. Furthermore, we provide an in-depth comparison of the three most popular bait sets designed for AMR by evaluating each of them against three major AMR databases: Comprehensive Antibiotic Resistance Database, Microbial Ecology Group Antimicrobial Resistance Database, and Pathogenicity Island Database. Thus, this article provides a review of hybridization bait capture for public health microbiologists.}, }
@article {pmid39544963, year = {2024}, author = {Wong, HL and Bulzu, PA and Ghai, R and Chiriac, MC and Salcher, MM}, title = {Ubiquitous genome streamlined Acidobacteriota in freshwater environments.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae124}, pmid = {39544963}, issn = {2730-6151}, abstract = {Acidobacteriota are abundant in soil, peatlands, and sediments, but their ecology in freshwater environments remains understudied. UBA12189, an Acidobacteriota genus, is an uncultivated, genome-streamlined lineage with a small genome size found in aquatic environments where detailed genomic analyses are lacking. Here, we analyzed 66 MAGs of UBA12189 (including one complete genome) from freshwater lakes and rivers in Europe, North America, and Asia. UBA12189 has small genome sizes (<1.4 Mbp), low GC content, and a highly diverse pangenome. In freshwater lakes, this bacterial lineage is abundant from the surface waters (epilimnion) down to a 300-m depth (hypolimnion). UBA12189 appears to be free-living from CARD-FISH analysis. When compared to other genome-streamlined bacteria such as Nanopelagicales and Methylopumilus, genome reduction has caused UBA12189 to have a more limited metabolic repertoire in carbon, sulfur, and nitrogen metabolisms, limited numbers of membrane transporters, as well as a higher degree of auxotrophy for various amino acids, vitamins, and reduced sulfur. Despite having reduced genomes, UBA12189 encodes proteorhodopsin, complete biosynthesis pathways for heme and vitamin K2, cbb3-type cytochrome c oxidases, and heme-requiring enzymes. These genes may give a selective advantage during the genome streamlining process. We propose the new genus Acidiparvus, with two new species named "A. lacustris" and "A. fluvialis". Acidiparvus is the first described genome-streamlined lineage under the phylum Acidobacteriota, which is a free-living, slow-growing scavenger in freshwater environments.}, }
@article {pmid39543974, year = {2024}, author = {Gonsiorczyk, T and Hupfer, M and Hilt, S and Gessner, MO}, title = {Rapid Eutrophication of a Clearwater Lake: Trends and Potential Causes Inferred From Phosphorus Mass Balance Analyses.}, journal = {Global change biology}, volume = {30}, number = {11}, pages = {e17575}, doi = {10.1111/gcb.17575}, pmid = {39543974}, issn = {1365-2486}, mesh = {*Eutrophication ; *Lakes/chemistry ; *Phosphorus/analysis ; *Geologic Sediments/analysis/chemistry ; *Seasons ; Environmental Monitoring/methods ; }, abstract = {Many clearwater lakes increasingly show symptoms of eutrophication, but the underlying causes are largely unknown. We combined long-term water chemistry data, multi-year sediment trap measurements, sediment analyses and simple mass balance models to elucidate potential causes of eutrophication of a deep temperate clearwater lake, where total phosphorus (TP) concentrations quadrupled within a decade, accompanied by expanding hypolimnetic anoxia. Discrepancies between modeled and empirically determined P inputs suggest that the observed sharp rise in TP was driven by internal processes. The magnitude of seasonal variation in TP greatly increased at the same time, both in surface and deep water, partly decoupled from deep water oxygen conditions. A positive correlation between annual P loss from the upper water column and hypolimnetic P accumulation could hint at a short-circuited P cycle involving lateral TP transport from shallow-water zones and deposition and release from sediments in deep water. This hypothesis is also supported by P budgets for the upper 20 m during stable summer stratification, suggesting that sediments in shallow lake areas acted as a P net source until 2018. These changes are potentially related to shifts in submerged macrophytes from wintergreen charophyte meadows (Nitellopsis obtusa) to annual free-floating hornwort (Ceratophyllum demersum) and to increased sulfide formation, promoting iron fixation in the sediments. Iron bound to sulfur is unavailable for binding P, resulting in a positive feedback between P release in shallow lake areas, primary productivity, macrophyte community structure and redox-dependent sediment biogeochemistry. Overall, our results suggest that relationships more complex than the commonly invoked increase in internal P release under increasingly anoxic conditions can drive rapid lake eutrophication. Since the proportion of littoral areas is typically large even in deep stratified lakes, littoral processes may contribute more frequently to the rapid lake eutrophication trends observed around the world than is currently recognized.}, }
@article {pmid39541983, year = {2024}, author = {Urtecho, G and Moody, T and Huang, Y and Sheth, RU and Richardson, M and Descamps, HC and Kaufman, A and Lekan, O and Zhang, Z and Velez-Cortes, F and Qu, Y and Cohen, L and Ricaurte, D and Gibson, TE and Gerber, GK and Thaiss, CA and Wang, HH}, title = {Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut.}, journal = {Cell systems}, volume = {15}, number = {11}, pages = {1002-1017.e4}, pmid = {39541983}, issn = {2405-4720}, support = {R35 GM143056/GM/NIGMS NIH HHS/United States ; T32 GM007367/GM/NIGMS NIH HHS/United States ; R01 GM130777/GM/NIGMS NIH HHS/United States ; P30 DK132710/DK/NIDDK NIH HHS/United States ; R21 AI146817/AI/NIAID NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; R01 AI132403/AI/NIAID NIH HHS/United States ; R01 EB031935/EB/NIBIB NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Fecal Microbiota Transplantation/methods ; Mice, Inbred C57BL ; Gastrointestinal Tract/microbiology ; Dysbiosis/microbiology ; Mammals/microbiology ; Feces/microbiology ; }, abstract = {While fecal microbiota transplantation (FMT) has been shown to be effective in reversing gut dysbiosis, we lack an understanding of the fundamental processes underlying microbial engraftment in the mammalian gut. Here, we explored a murine gut colonization model leveraging natural inter-individual variations in gut microbiomes to elucidate the spatiotemporal dynamics of FMT. We identified a natural "super-donor" consortium that robustly engrafts into diverse recipients and resists reciprocal colonization. Temporal profiling of the gut microbiome showed an ordered succession of rapid engraftment by early colonizers within 72 h, followed by a slower emergence of late colonizers over 15-30 days. Moreover, engraftment was localized to distinct compartments of the gastrointestinal tract in a species-specific manner. Spatial metagenomic characterization suggested engraftment was mediated by simultaneous transfer of spatially co-localizing species from the super-donor consortia. These results offer a mechanism of super-donor colonization by which nutritional niches are expanded in a spatiotemporally dependent manner. A record of this paper's transparent peer review process is included in the supplemental information.}, }
@article {pmid39541852, year = {2025}, author = {Wang, Q and Wang, M and Yang, Q and Feng, L and Zhang, H and Wang, R and Wang, R}, title = {The role of bacteriophages in facilitating the horizontal transfer of antibiotic resistance genes in municipal wastewater treatment plants.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122776}, doi = {10.1016/j.watres.2024.122776}, pmid = {39541852}, issn = {1879-2448}, mesh = {*Bacteriophages/genetics ; *Gene Transfer, Horizontal ; *Wastewater ; Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid ; Plasmids/genetics ; Bacteria/virology/genetics ; }, abstract = {Bacteriophages play integral roles in the ecosystem; however, their precise involvement in horizontal gene transfer and the spread of antibiotic resistance genes (ARGs) are not fully understood. In this study, a coculture system involving consortia of bacteriophages and multidrug-resistant bacteria from an aerobic tank in a municipal wastewater treatment plant (WWTP) was established to investigate the functions of bacteriophages in ARG transfer and spread. The results of the cocultivation of the MRB and bacteriophage consortia indicated that the bacterial community remained stable throughout the whole process, but the addition of bacteriophages significantly increased ARG abundance, especially in bacteriophage DNA. Nine out of the 11 identified ARGs significantly increased, indicating that more bacteriophage particles carried ARGs in the system after cocultivation. In addition, 686 plasmids were detected during cocultivation, of which only 3.36 % were identified as conjugative plasmids, which is significantly lower than the proportion found among previously published plasmids (25.2 %, totaling 14,029 plasmids). Our findings revealed that bacteriophages may play important roles in the horizontal transfer of ARGs through both bacteriophage-mediated conduction and an increase in extracellular ARGs; however, conjugative transfer may not be the main mechanism by which multidrug-resistant bacteria acquire and spread ARGs. Unlike in most previous reports, a coculture system of diverse bacteria and bacteriophages was established in this study to assess bacteriophage functions in ARG transfer and dissemination in the environment, overcoming the limitations associated with the isolation of bacteria and bacteriophages, as well as the specificity of bacteriophage hosts.}, }
@article {pmid39540979, year = {2024}, author = {Frew, A and Aguilar-Trigueros, CA}, title = {Increasing Phylogenetic Clustering of Arbuscular Mycorrhizal Fungal Communities in Roots Explains Enhanced Plant Growth and Phosphorus Uptake.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {139}, pmid = {39540979}, issn = {1432-184X}, support = {DE220100479//Australian Research Council/ ; }, mesh = {*Mycorrhizae/genetics/physiology ; *Phosphorus/metabolism ; *Plant Roots/microbiology/growth &amp; development ; *Phylogeny ; *Symbiosis ; *Sorghum/microbiology/growth &amp; development ; Soil Microbiology ; Mycobiome ; Biomass ; Plant Development ; }, abstract = {Temporal variation during the assembly of arbuscular mycorrhizal (AM) fungal communities within plant roots have been posited as critical drivers of the plant-fungal symbiotic outcomes. However, functional implications of these dynamics for the host plant remain poorly understood. We conducted a controlled pot experiment with Sorghum bicolor to investigate how temporal shifts in AM fungal community composition and phylogenetic diversity influence plant growth and phosphorus responses to the symbiosis. We characterised the root-colonising AM fungal communities across three time points and explored their community assembly processes by analysing their phylogenetic diversity and employing joint species distribution modelling with the Hierarchical Modelling of Species Communities (HMSC) framework. We found strong AM fungal turnover through time with a high phylogenetic signal, indicating recruitment of phylogenetically clustered AM fungal species in the host. This temporal phylogenetic clustering of communities coincided with marked increases in plant biomass and phosphorus responses to the AM fungal symbiosis, suggesting that host selection for specific fungi may be a key determinant of these benefits.}, }
@article {pmid39537004, year = {2025}, author = {Bernetti, A and Barili, S and Sannino, C and Mugnai, G and Borruso, L and Pinchuk, I and Pezzolla, D and Turchetti, B and Gigliotti, G and Buzzini, P}, title = {Selective response of soil bacterial and fungal taxa to biodegradable polymers.}, journal = {Environmental research}, volume = {264}, number = {Pt 1}, pages = {120344}, doi = {10.1016/j.envres.2024.120344}, pmid = {39537004}, issn = {1096-0953}, mesh = {*Fungi/metabolism/classification ; *Soil Microbiology ; *Bacteria/classification/metabolism/drug effects ; *Biodegradation, Environmental ; Polymers ; Soil/chemistry ; }, abstract = {Biodegradable mulching films offer an eco-friendly alternative to petroleum-based plastics in agriculture, but their effects on soil parameters are not well understood. A microcosm experiment (20 °C, 75% field capacity) investigated the impact of two doses (0.021% and 1% w/w) of a biodegradable polymer on soil chemical and microbiological properties over a year. The 1% dose significantly (p < 0.05) increased CO2 emissions, water-extractable organic C, and hydrolytic activity. A significant (p < 0.05) effect on microbial alpha- and beta-diversity was noted only during short- and medium-term incubations. In contrast, a taxon-related response was found for both bacterial and fungal taxa affecting the abundance of the genera Aquicella, Cellvibrio, Bacillus, Ramlibacter, and Saccharibacteria genera incertae sedis among bacteria, and Malassezia, Orbilia, and Rhodotorula among fungi (including both yeast and filamentous lifestyles). Microbial functions revealed a greater impact on fungal communities compared to bacterial ones. However, after one year of exposition, only a marginal effect on the abundance of both bacterial and fungal functional groups was found in the microcosms. A significantly higher concentration of tightly bound exopolysaccharides in the presence of 1% biodegradable polymer at the start of the experiment suggested their key role in microbial degradation of bioplastics via biofilm formation.}, }
@article {pmid39536049, year = {2024}, author = {Zhao, Y and Cordero, OX and Tikhonov, M}, title = {Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function.}, journal = {PLoS computational biology}, volume = {20}, number = {11}, pages = {e1012590}, pmid = {39536049}, issn = {1553-7358}, mesh = {*Algorithms ; Linear Models ; *Ecosystem ; *Computational Biology/methods ; Models, Biological ; Microbiota/physiology ; Nonlinear Dynamics ; }, abstract = {Microbial communities play key roles across diverse environments. Predicting their function and dynamics is a key goal of microbial ecology, but detailed microscopic descriptions of these systems can be prohibitively complex. One approach to deal with this complexity is to resort to coarser representations. Several approaches have sought to identify useful groupings of microbial species in a data-driven way. Of these, recent work has claimed some empirical success at de novo discovery of coarse representations predictive of a given function using methods as simple as a linear regression, against multiple groups of species or even a single such group (the ensemble quotient optimization (EQO) approach). Modeling community function as a linear combination of individual species' contributions appears simplistic. However, the task of identifying a predictive coarsening of an ecosystem is distinct from the task of predicting the function well, and it is conceivable that the former could be accomplished by a simpler methodology than the latter. Here, we use the resource competition framework to design a model where the "correct" grouping to be discovered is well-defined, and use synthetic data to evaluate and compare three regression-based methods, namely, two proposed previously and one we introduce. We find that regression-based methods can recover the groupings even when the function is manifestly nonlinear; that multi-group methods offer an advantage over a single-group EQO; and crucially, that simpler (linear) methods can outperform more complex ones.}, }
@article {pmid39524341, year = {2024}, author = {Dzialo, MC and Arumugam, S and Piampongsant, S and Cool, L and Vanderaa, C and Herrera-Malaver, B and Opsomer, T and Dehaen, W and Wenseleers, T and Roncoroni, M and Alawamleh, A and Wäckers, F and Lievens, B and Hansson, BS and Voordeckers, K and Sachse, S and Verstrepen, KJ}, title = {Drosophila suzukii and Drosophila melanogaster prefer distinct microbial and plant aroma compounds in a complex fermented matrix.}, journal = {iScience}, volume = {27}, number = {11}, pages = {111141}, pmid = {39524341}, issn = {2589-0042}, abstract = {Volatile aroma compounds are important chemical cues for insects. Behavioral responses to specific odors differ strongly between insect species, and the exact causative molecules are often unknown. Beer is frequently used in insect traps because it combines hundreds of plant and microbial aromas that attract many insects. Here, we analyzed responses of the pest fruit fly Drosophila suzukii and benign Drosophila melanogaster to beers with different chemical compositions. Using extensive chemical and behavioral assays, we identified ecologically relevant chemicals that influence drosophilid behavior and that induce different odor-evoked activity patterns in the antennal lobe of the two species obtained by functional imaging. Specific mixes of compounds increased the species-specificity and sex-specificity of lures in both laboratory and greenhouse settings. Together, our study shows how examining insect responses to highly complex natural mixtures of aroma compounds provides insight into insect-specific behavioral responses and also opens avenues for improved pest control.}, }
@article {pmid39535358, year = {2024}, author = {Tidimalo, C and Maximiliano, O and Karen, J and Lebre, PH and Bernard, O and Michelle, G and Oagile, D and Cowan, DA}, title = {Microbial diversity in the arid and semi-arid soils of Botswana.}, journal = {Environmental microbiology reports}, volume = {16}, number = {6}, pages = {e70044}, pmid = {39535358}, issn = {1758-2229}, support = {//PhD bursary for Tidimalo Coetzee from the University of Botswana/ ; //Oppenheimer Foundation/ ; 674-AA-2010-A1//United States Agency for International Development/ ; //University of Pretoria for postdoctoral support/ ; }, mesh = {*Soil Microbiology ; Botswana ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Soil/chemistry ; *Biodiversity ; Microbiota/genetics ; Phylogeny ; Hydrogen-Ion Concentration ; DNA, Bacterial/genetics ; }, abstract = {To date, little research has been conducted on the landscape-scale distribution of soil microbial communities and the factors driving their community structures in the drylands of Africa. We investigated the influence of landscape-scale variables on microbial community structure and diversity across different ecological zones in Botswana. We used amplicon sequencing of bacterial 16S rRNA gene and fungal internal transcribed spacers (ITS) and a suite of environmental parameters to determine drivers of microbial community structure. Bacterial communities were dominated by Actinomycetota (21.1%), Pseudomonadota (15.9%), and Acidobacteriota (10.9%). The dominant fungal communities were Ascomycota (57.3%) and Basidiomycota (7.5%). Soil pH, mean annual precipitation, total organic carbon, and soil ions (calcium and magnesium) were the major predictors of microbial community diversity and structure. The co-occurrence patterns of bacterial and fungal communities were influenced by soil pH, with network-specific fungi-bacteria interactions observed. Potential keystone taxa were identified for communities in the different networks. Most of these interactions were between microbial families potentially involved in carbon cycling, suggesting functional redundancy in these soils. Our findings highlight the significance of soil pH in determining the landscape-scale structure of microbial communities in Botswana's dryland soils.}, }
@article {pmid39532738, year = {2024}, author = {Fu, M and Liu, Y and Li, S and Yan, D and Liu, P and Liu, Y and Ji, M}, title = {The Spatial Dynamics of Diazotrophs in the Forefield of Three Tibetan Glaciers.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {138}, pmid = {39532738}, issn = {1432-184X}, support = {42171138//National Natural Science Foundation of China/ ; 32161123004//National Natural Science Foundation of China/ ; 32161123004//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 32161123004//National Natural Science Foundation of China/ ; }, mesh = {*Ice Cover/microbiology ; Tibet ; *Soil Microbiology ; *Nitrogen Fixation ; Soil/chemistry ; Nitrogen/metabolism ; Ecosystem ; Bacteria/classification/metabolism/genetics/isolation &amp; purification/enzymology ; Nitrogen-Fixing Bacteria/metabolism/classification/isolation &amp; purification/genetics ; Phylogeny ; Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Nitrogen is often a limiting nutrient for microbial communities and plants in glacier forefields. Nitrogen-fixing microorganisms (diazotrophs) play an important role in providing bioavailable nitrogen, with their composition determining the nitrogen-fixating capacities. This study investigates the spatial and temporal dynamics of diazotrophs in the forefields of three Tibetan glaciers: Qiangyong, Kuoqionggangri, and Longxiazailongba. We collected soil samples from recently deglaciated barren grounds, and also along an ecosystem succession transect at Kuoqionggangri glacier, encompassing barren ground, herb steppe, legume steppe, and alpine meadow ecosystems. Our finding revealed abundant and diverse diazotrophs in the recently deglaciated barren ground. They are taxonomically affiliated with anaerobic Bradyrhizobium, Desulfobulbus, and Pelobacter, which may be relics from subglacial sediments. The vegetated soils (herb steppe, legume steppe, and alpine meadow) were dominated by phototrophic Nostoc and Anabaena, as well as symbiotic Sinorhizobium. Soil physicochemical parameters, such as soil organic carbon, pH, and nitrate ion, significantly influenced diazotroph community structure. This study highlights the critical role of diazotrophs in mitigating nitrogen limitation during early ecosystem development in glacier forefields. Understanding the distribution and ecological drivers of diazotrophs in these rapidly changing environments provides insights into biogeochemical cycling and ecosystem resilience under climate change.}, }
@article {pmid39528791, year = {2025}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {Nature reviews. Microbiology}, volume = {23}, number = {1}, pages = {1-2}, pmid = {39528791}, issn = {1740-1534}, support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, }
@article {pmid39528727, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {Nature microbiology}, volume = {9}, number = {12}, pages = {3084-3085}, pmid = {39528727}, issn = {2058-5276}, support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, }
@article {pmid39528652, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {npj biodiversity}, volume = {3}, number = {1}, pages = {34}, pmid = {39528652}, issn = {2731-4243}, support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, abstract = {This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.}, }
@article {pmid39528617, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1466}, pmid = {39528617}, issn = {2399-3642}, support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, abstract = {This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.}, }
@article {pmid39528577, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {122}, pmid = {39528577}, issn = {2055-5008}, support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, abstract = {This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.}, }
@article {pmid39528441, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9637}, pmid = {39528441}, issn = {2041-1723}, support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, abstract = {This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.}, }
@article {pmid39528211, year = {2024}, author = {Jang, J and Park, J and Hwang, CY and Gim, Y and Park, KT and Yoon, YJ and Seo, M and Lee, BY}, title = {Selective transmission of airborne bacterial communities from the ocean to the atmosphere over the Northern Pacific Ocean.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177462}, doi = {10.1016/j.scitotenv.2024.177462}, pmid = {39528211}, issn = {1879-1026}, mesh = {Pacific Ocean ; *Air Microbiology ; *Seawater/microbiology ; *Bacteria/classification ; Environmental Monitoring ; Atmosphere/chemistry ; Aerosols/analysis ; }, abstract = {This study simultaneously measured the taxonomic diversity of bacterial communities in both seawater and PM2.5 aerosol samples collected from the Northern Pacific Ocean during a cruise covering 7724 km between 37°N 126°E and 58°N 179°E. The relative abundance of Proteobacteria, Cyanobacteria, and Firmicutes were found to be more prevalent in aerosol samples (39 ± 16 %, 5.1 ± 1.9 %, and 3.2 ± 1.7 %, respectively) than in seawater samples (26 ± 9 %, 3.8 ± 1.7 %, and 0.02 ± 0.09 %, respectively). The preferential aerosolization of bacterial communities such as Proteobacteria and Firmicutes was likely to be accompanied by a terrestrial origin and high hydrophobicity. Cyanobacteria could undergo increased aerosolization, possibly because of their smaller size in the significantly higher salinity open ocean (32.8 ± 0.14 PSU) compared to those in lower salinity coastal areas (31.3 ± 1.4 PSU). The results of this study indicated that bacterial properties substantially affect their transfer from the ocean to the atmosphere, possibly influencing climate change and public health.}, }
@article {pmid39527614, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39527614}, issn = {1751-7370}, }
@article {pmid39527081, year = {2024}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Falcao Salles, J and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Adoukè Agbodjato, N and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {11}, pages = {}, pmid = {39527081}, issn = {1574-6941}, abstract = {Injecting H2 in deep underground to store this energy carrier will produce artificial subsurface lithoautotrophic microbial ecosystems that modify the taxonomic diversity of indigenous microbial communities and their metabolic activities.}, }
@article {pmid39526991, year = {2025}, author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Falcao Salles, J and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA}, title = {Microbial solutions must be deployed against climate catastrophe.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0141624}, pmid = {39526991}, issn = {2379-5077}, }
@article {pmid39526896, year = {2024}, author = {Wei, F and Jiang, H and Zhu, C and Zhong, L and Lin, Z and Wu, Y and Song, L}, title = {The co-fermentation of whole-grain black barley and quinoa improves murine cognitive impairment induced by a high-fat diet via altering gut microbial ecology and suppressing neuroinflammation.}, journal = {Food &amp; function}, volume = {15}, number = {23}, pages = {11667-11685}, doi = {10.1039/d4fo02704c}, pmid = {39526896}, issn = {2042-650X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Diet, High-Fat/adverse effects ; *Cognitive Dysfunction ; *Mice, Inbred C57BL ; *Chenopodium quinoa/chemistry ; Male ; *Hordeum/chemistry ; *Fermentation ; Neuroinflammatory Diseases/metabolism ; Lactobacillus ; Hippocampus/metabolism ; Brain-Gut Axis ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {A high-fat diet (HFD) is associated with various adverse health outcomes, including cognitive impairment and an elevated risk of neurodegenerative conditions. This relationship is partially attributed to the influence of an HFD on the gut microbiota. The objective of this research was to evaluate the neuroprotective benefits of co-fermented black barley and quinoa with Lactobacillus (FG) against cognitive impairments triggered by an HFD and to investigate the microbiota-gut-brain axis mechanisms involved. C57BL/6J mice were randomized into four groups: the normal control group (NC, n = 10), the high-fat diet group (HFD, n = 10), the high-fat diet group supplemented with FG (HFG, 10 mL per kg BW, n = 10), and the high-fat diet group supplemented with Lactobacillus (HFL, 10 mL per kg BW, n = 10). Our results showed that the FG intervention enhanced the behavioral and locomotor skills of the mice, elevated the levels of dopamine (DA) and norepinephrine (NPI) in brain tissues, and alleviated synaptic ultrastructural damage in the hippocampus. Furthermore, FG intervention was observed to exert a protective effect on both the blood-brain barrier and the colonic barrier, as evidenced by an increase in the mRNA levels of Zona occludens-1 (ZO-1), Claudin-4, and Occludin in the hippocampus and colon. These beneficial effects may be attributed to FG's regulation of gut microbiota dysbiosis, which involves the restoration of intestinal flora diversity, reduction of the Firmicutes/Bacteroidetes (F/B) ratio, and a decrease in the levels of pro-inflammatory bacteria such as s_Escherichia coli E and g_Escherichia; moreover, there was an increase in the abundances of anti-inflammatory bacteria, such as s_Bacteroides thetaiotaomicron and s_Parabacteroides goldsteinii. Metagenomic analysis revealed that the FG treatment downregulated the lipopolysaccharide (LPS) pathway and upregulated neurotransmitter biosynthetic pathways. These probiotic effects of FG resulted in reduced production and "leakage" of LPS and decreased mRNA expression of Toll-like receptor 4 (Tlr4), cluster of differentiation 14 (CD14), and myeloid differentiation factor 88 (Myd88) in hippocampal and colon tissues. Consequently, a reduction was observed in the levels of inflammatory cytokines in the serum, hippocampus, and colon, along with suppression of the immunoreactivity of microglia and astrocytes. Our results suggest that FG may serve as an intervention strategy for preventing cognitive impairments caused by an HFD.}, }
@article {pmid39526802, year = {2024}, author = {Schiml, VC and Walter, JM and Hagen, LH and Varnai, A and Bergaust, LL and De Leon, AVP and Elsgaard, L and Bakken, LR and Arntzen, M&#xd8;}, title = {Microbial consortia driving (ligno)cellulose transformation in agricultural woodchip bioreactors.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {12}, pages = {e0174224}, pmid = {39526802}, issn = {1098-5336}, support = {295910//Norges Forskningsr&#xe5;d (Forskningsr&#xe5;det)/ ; NNF20OC0061313//Novo Nordisk Fonden (NNF)/ ; }, mesh = {*Bioreactors/microbiology ; *Lignin/metabolism ; *Microbial Consortia ; Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Denitrification ; Agriculture ; RNA, Ribosomal, 16S/genetics ; Cellulose/metabolism ; Wood/metabolism/microbiology ; }, abstract = {UNLABELLED: Freshwater ecosystems can be largely affected by neighboring agriculture fields where potential fertilizer nitrate run-off may leach into surrounding water bodies. To counteract this eutrophic driver, farmers in certain areas are utilizing denitrifying woodchip bioreactors (WBRs) in which a consortium of microorganisms convert the nitrate into nitrogen gases in anoxia, fueled by the degradation of lignocellulose. Polysaccharide-degrading strategies have been well described for various aerobic and anaerobic systems, including the use of carbohydrate-active enzymes, utilization of lytic polysaccharide monooxygenases (LPMOs) and other redox enzymes, as well as the use of cellulosomes and polysaccharide utilization loci (PULs). However, for denitrifying microorganisms, the lignocellulose-degrading strategies remain largely unknown. Here, we have applied a combination of enrichment techniques, gas measurements, multi-omics approaches, and amplicon sequencing of fungal ITS and procaryotic 16S rRNA genes to identify microbial drivers for lignocellulose transformation in woodchip bioreactors and their active enzymes. Our findings highlight a microbial community enriched for (ligno)cellulose-degrading denitrifiers with key players from the taxa Giesbergeria, Cellulomonas, Azonexus, and UBA5070 (Fibrobacterota). A wide substrate specificity is observed among the many expressed carbohydrate-active enzymes (CAZymes) including PULs from Bacteroidetes. This suggests a broad degradation of lignocellulose subfractions, including enzymes with auxiliary activities whose functionality is still puzzling under strict anaerobic conditions.<br><br>IMPORTANCE: Freshwater ecosystems face significant threats from agricultural runoff, which can lead to eutrophication and subsequent degradation of water quality. One solution to mitigate this issue is using denitrifying woodchip bioreactors (WBRs), where microorganisms convert nitrate into nitrogen gases utilizing lignocellulose as a carbon source. Despite the well-documented polysaccharide-degrading strategies in various systems, the mechanisms employed by denitrifying microorganisms in WBRs remain largely unexplored. This study fills a critical knowledge gap by revealing the degrading strategies of denitrifying microbial communities in WBRs. By integrating state-of-the-art techniques, we have identified key microbial drivers including Giesbergeria, Cellulomonas, Azonexus, and UBA5070 (Fibrobacterota) playing significant roles in lignocellulose transformation and showcasing a broad substrate specificity and complex metabolic capability. Our findings advance the understanding of microbial ecology in WBRs and by revealing the enzymatic activities, this research may inform efforts to improve water quality, protect aquatic ecosystems, and reduce greenhouse gas emissions from WBRs.}, }
@article {pmid39520764, year = {2025}, author = {Rodriguez-Caturla, MY and Margalho, LP and Graça, JS and Pia, AKR and Xavier, VL and Noronha, MF and Cabral, L and Lemos-Junior, WJF and Castillo, CJC and SantˈAna, AS}, title = {Bacterial dynamics and volatile metabolome changes of vacuum-packaged beef with different pH during chilled storage.}, journal = {International journal of food microbiology}, volume = {427}, number = {}, pages = {110955}, doi = {10.1016/j.ijfoodmicro.2024.110955}, pmid = {39520764}, issn = {1879-3460}, mesh = {*Volatile Organic Compounds/analysis/metabolism ; Hydrogen-Ion Concentration ; Vacuum ; Cattle ; Animals ; *Red Meat/microbiology ; *Food Packaging/methods ; *Food Microbiology ; *Food Storage ; Bacteria/metabolism/growth &amp; development/classification/genetics/isolation &amp; purification ; Metabolome ; Brazil ; RNA, Ribosomal, 16S/genetics ; }, abstract = {This study aimed to assess the growth of spoilage bacteria in Brazilian vacuum-packed beef across different pH ranges (5.4-5.8, 5.8-6.1, ≥6.1) stored at temperatures of 0 °C, 4 °C, and 7 °C. Additionally, the research sought to identify predominant spoilage bacteria at the genus level using 16S rDNA gene sequencing and analyze the principal volatile organic compounds (VOCs) produced by this microbiota through HS-SPME/GC-MS. Lactic acid bacteria (LAB) consistently exhibited counts exceeding 6.0 Log CFU/g, regardless of temperature and pH conditions. The bacterial diversity in the meat samples reflected the influence of slaughterhouse environments, with Pseudomonas and Serratia remaining dominant across different cuts and pH levels. Post-storage, variations in pH and temperature modulated the initial bacterial diversity, leading to a reduction in diversity and an increase in LAB such as Lactobacillus, Lactococcus, Leuconostoc, and Carnobacterium. Notably, these changes were observed within pH ranges of 5.4-5.8 and 5.8-6.1, irrespective of beef cuts and storage temperatures. Based on high throughput sequencing and VOCS, correlation analysis revealed a relationship between the growth of specific spoilage microorganisms under vacuum conditions and the presence of VOCs such as alcohols (e.g., 1-propanol, 2-methyl-) and ketones (e.g., 2-nonanone, 2-octanone, 2-heptanone), identifying them as potential indicators of spoilage bacteria growth.}, }
@article {pmid39520558, year = {2024}, author = {Boadella, J and Butturini, A and Doménech-Pascual, A and Freixinos, Z and Perujo, N and Urmeneta, J and Vidal, A and Romaní, AM}, title = {Microbial Life in Playa-Lake Sediments: Adapted Structure, Plastic Function to Extreme Water Activity Variations.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {137}, pmid = {39520558}, issn = {1432-184X}, support = {PID2021-123735OB-C21//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-123735OB-C21//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-123735OB-C21//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-123735OB-C21//Spanish Ministry of Science, Innovation and Universities/ ; 2020 FISDU 00465//Catalan Government Ministry of Business and Knowledge, Area of Universities and Research/ ; }, mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; *Biofilms/growth &amp; development ; *Salinity ; *Bacteria/classification/genetics/metabolism ; Biomass ; Droughts ; Water ; }, abstract = {Saline shallow lakes in arid and semi-arid regions frequently undergo drying episodes, leading to significant variations in salinity and water availability. Research on the impacts of salinity and drought on the structure and function of biofilms in hypersaline shallow lakes is limited. This study aimed to understand the potential changes of biofilms in playa-lake sediments during the drying process. Sediments were sampled at different depths (surface, subsurface) and hydrological periods (wet, retraction, and dry), which included a decrease in water activity (aw, the availability of water for microbial use) from 0.99 to 0.72. aw reduction caused a greater effect on functional variables compared to structural variables, indicating the high resistance of the studied biofilms to changes in salinity and water availability. Respiration and hydrolytic extracellular enzyme activities exhibited higher values under high aw, while phenol oxidase activity and prokaryote biomass increased at lower aw. This shift occurred at both depths but was more pronounced at the surface, possibly due to the more extreme conditions (up to 0.7 aw). The increased levels of extracellular polymeric substances and carotenoids developed at low aw may help protect microorganisms in high salinity and drought environments. However, these harsh conditions may interfere with the activity of hydrolytic enzymes and their producers, while promoting the growth of resistant prokaryotes and their capacity to obtain C and N sources from recalcitrant compounds. The resilience of biofilms in hypersaline lakes under extreme conditions is given by their resistant biochemichal structure and the adaptability of their microbial functioning.}, }
@article {pmid39516195, year = {2024}, author = {Speth, DR and Zeller, LM and Graf, JS and Overholt, WA and Küsel, K and Milucka, J}, title = {Genetic potential for aerobic respiration and denitrification in globally distributed respiratory endosymbionts.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9682}, pmid = {39516195}, issn = {2041-1723}, mesh = {*Symbiosis ; *Phylogeny ; *Denitrification ; Metagenome ; Aerobiosis ; Ciliophora/genetics/metabolism ; Groundwater/microbiology ; Gammaproteobacteria/genetics/metabolism ; Germany ; Electron Transport Complex IV/genetics/metabolism ; California ; Genome, Bacterial ; }, abstract = {The endosymbiont Candidatus Azoamicus ciliaticola was proposed to generate ATP for its eukaryotic host, an anaerobic ciliate of the Plagiopylea class, fulfilling a function analogous to mitochondria in other eukaryotic cells. The discovery of this respiratory endosymbiosis has major implications for both evolutionary history and ecology of microbial eukaryotes. However, with only a single species described, knowledge of its environmental distribution and diversity is limited. Here we report four complete, circular metagenome assembled genomes (cMAGs) representing respiratory endosymbionts inhabiting groundwater in California, Ohio, and Germany. These cMAGs form two lineages comprising a monophyletic clade within the uncharacterized gammaproteobacterial order UBA6186, enabling evolutionary analysis of their key protein complexes. Strikingly, all four cMAGs encode a cytochrome cbb3 oxidase, which indicates that these endosymbionts have the capacity for aerobic respiration. Accordingly, we detect these respiratory endosymbionts in diverse habitats worldwide, thus further expanding the ecological scope of this respiratory symbiosis.}, }
@article {pmid39513042, year = {2024}, author = {Park, KJ and Gao, Y}, title = {Gut-brain axis and neurodegeneration: mechanisms and therapeutic potentials.}, journal = {Frontiers in neuroscience}, volume = {18}, number = {}, pages = {1481390}, pmid = {39513042}, issn = {1662-4548}, abstract = {This paper reviews the effects of gut microbiota in regulating neurodegenerative diseases through controlling gut-brain axis. Specific microbial populations and their metabolites (short-chain fatty acids and tryptophan derivatives) regulate neuroinflammation, neurogenesis and neural barrier integrity. We then discuss ways by which these insights lead to possible interventions - probiotics, prebiotics, dietary modification, and fecal microbiota transplantation (FMT). We also describe what epidemiological and clinical studies have related certain microbiota profiles with the courses of neurodegenerative diseases and how these impact the establishment of microbiome-based diagnostics and individualized treatment options. We aim to guide microbial ecology research on this key link to neurodegenerative disorders and also to highlight collaborative approaches to manage neurological health by targeting microbiome-related factors.}, }
@article {pmid39511174, year = {2024}, author = {Chen, SC and Chen, S and Musat, N and Kümmel, S and Ji, J and Lund, MB and Gilbert, A and Lechtenfeld, OJ and Richnow, HH and Musat, F}, title = {Back flux during anaerobic oxidation of butane support archaea-mediated alkanogenesis.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9628}, pmid = {39511174}, issn = {2041-1723}, support = {NNF22OC0071609//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; ERC-RA-0020//Helmholtz Association/ ; 101059607//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; 12471341//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Oxidation-Reduction ; Anaerobiosis ; *Archaea/metabolism/genetics ; *Butanes/metabolism ; *Carbon Dioxide/metabolism ; Oxidoreductases/metabolism/genetics ; Kinetics ; Alkanes/metabolism ; Thermodynamics ; }, abstract = {Microbial formation and oxidation of volatile alkanes in anoxic environments significantly impacts biogeochemical cycles on Earth. The discovery of archaea oxidizing volatile alkanes via deeply branching methyl-coenzyme M reductase variants, dubbed alkyl-CoM reductases (ACR), prompted the hypothesis of archaea-catalysed alkane formation in nature (alkanogenesis). A combination of metabolic modelling, anaerobic physiology assays, and isotope labeling of Candidatus Syntrophoarchaeum archaea catalyzing the anaerobic oxidation of butane (AOB) show a back flux of CO2 to butane, demonstrating reversibility of the entire AOB pathway. Back fluxes correlate with thermodynamics and kinetics of the archaeal catabolic system. AOB reversibility supports a biological formation of butane, and generally of higher volatile alkanes, helping to explain the presence of isotopically light alkanes and deeply branching ACR genes in sedimentary basins isolated from gas reservoirs.}, }
@article {pmid39509969, year = {2024}, author = {Aparicio, S and Ríos-Mejía, A and Gallardo-Mejías, JP and Robles, &#xc1; and Borrás, L}, title = {Microalgae-bacteria consortia dynamics in a long term operated membrane-coupled high-rate algal pond (MHRAP).}, journal = {Journal of environmental management}, volume = {371}, number = {}, pages = {123186}, doi = {10.1016/j.jenvman.2024.123186}, pmid = {39509969}, issn = {1095-8630}, mesh = {*Microalgae ; *Wastewater/microbiology ; *Bacteria/metabolism/classification ; Ponds/microbiology ; Waste Disposal, Fluid/methods ; Biomass ; }, abstract = {Traditional activated sludge-based technologies have significant drawbacks, including high energy requirements and greenhouse gas emissions. Microalgae-based processes offer a promising, low-cost, and environmentally friendly alternative. However, the knowledge of treatment systems based on microalgae-bacteria consortia is limited, and even more so is their microbial composition and its relationship with operational parameters. Thus, this study explores the dynamics of microalgae-bacteria consortia in a long-term operated membrane-coupled high-rate algal pond (MHRAP) for wastewater treatment. For this, a pilot-scale MHRAP plant, located in a wastewater treatment plant in Valencia (Spain), was monitored under various hydraulic retention times (HRT) and wastewater influents: i) effluent from a primary settler and ii) effluent form pre-treatment. The biomass retention time was kept constant at 6 days. The composition of the bacterial community was studied through 16S rDNA sequencing, while 18S rDNA sequencing was used to study the microalgae. The results indicate that shorter HRTs significantly increased bacterial diversity, but not eukarya. Principal Co-ordinates Analysis (PCoA) revealed that the HRT and the incoming wastewater quality control the type of the bacterial populations. However, this effect was not observed in eukaryotic organisms. The dominant microalgae genera identified were Desmodesmus and Coelastrella, with Coelastrella becoming more prevalent at shorter HRTs. For bacteria, Verrumicrobiota dominated (18-56%) at high HRT while Proteobacteria was dominant (28-44%) at HRTs below 6 days. The changes observed in the bacterial composition, including the ammonia oxidizing bacteria (AOB) community (mainly Nitrosomonas), suggest that photo-inhibition could be taking place. The nitrite oxidizing bacteria (NOB) community was dominated by Nitrospira and Candidatus Nitrotoga. Operational parameters such as light intensity, pH, and nitrite concentration were found to significantly influence the microbial community structure. Higher light intensity and alkaline pH favored the growth of Desmodesmus, while Coelastrella thrived under lower HRTs. Bacterial diversity plays a crucial role in the treatment process, while microalgae primarily support aerobic bacterial processes by providing oxygen. These findings contribute to a deeper understanding of the complex biological processes in microalgae-bacteria consortia and offer insights into improving wastewater treatment technologies.}, }
@article {pmid39508609, year = {2024}, author = {Xue, S-J and Liu, J and Zhao, F-Y and Zhang, X-T and Zhu, Z-Q and Zhang, J-Y}, title = {Spatio-temporal distribution and biotechnological potential of culturable yeasts in the intertidal sediments and seawater of Aoshan Bay, China.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {12}, pages = {e0157024}, pmid = {39508609}, issn = {1098-5336}, support = {1120015//the Advanced Talents Foundation of Qingdao Agricultural University/ ; tsqn201909133//the Young experts of Taishan Scholars in Shandong Province/ ; 1120011//the Initiative grant for high-level personnel recruitment in Qingdao Agricultural University/ ; CARS-47//the earmarked fund/ ; }, mesh = {*Geologic Sediments/microbiology ; China ; *Seawater/microbiology ; *Yeasts/genetics/classification/isolation &amp; purification/metabolism ; *Bays/microbiology ; Biodiversity ; Biotechnology ; Spatio-Temporal Analysis ; Ecosystem ; Microbiota ; }, abstract = {Marine yeasts play a crucial role in marine microbial ecology, facilitating the biogeochemical cycling of carbon and nitrogen in marine ecosystems, while also serving as important reservoirs of bioactive compounds with extensive applications in pharmaceuticals, agriculture, and various industries. Intertidal flats, characterized by their complex ecological dynamics, are postulated to harbor a wealth of yeast resources. This study employed a culture-dependent approach to assess the diversity, spatio-temporal distribution, and biotechnological potential of yeast communities residing within the intertidal sediments and seawater of Aoshan Bay. A total of 392 yeast strains were identified from 20 distinct genera, encompassing 43 recognized species and four candidate novel species. Notably, 17 of these species were identified as novel occurrences in marine environments, underscoring the rich yeast biodiversity of the Aoshan Bay ecosystem, with Candida emerging as the dominant genus in both sedimentary and aqueous habitats. Yeast community composition exhibited significant spatial and temporal variation, with peak diversity and abundance observed in autumn, the subtidal zone, and the surface soil layer. No clear pattern, however, emerged linking these shifts to specific changes in community composition, highlighting the complex interactions between microbial communities, environmental variables, and anthropogenic disturbance. Although several yeast species isolated here have been previously recognized for their biotechnological potential, their diverse and abundant extracellular enzyme profiles were characterized, further highlighting their crucial role in organic matter decomposition and nutrient cycling within the tidal ecosystem, as well as their potential applicability in the food, fine chemical, textile, and pharmaceutical industries.IMPORTANCEThis study presents groundbreaking insights into the yeast diversity of Aoshan Bay, offering invaluable information on their spatial and temporal distribution patterns, as well as their biotechnological potential in the tidal environment. The findings reveal that the eutrophic intertidal flat is a rich repository of yeasts with abundant extracellular enzymatic activity and an important role in nutrient cycling and decomposition processes. Also, these yeasts serve as crucial indicators of ecosystem health and function and are excellent candidates for biotechnological and industrial applications. Collectively, this study not only expands our knowledge of the diversity and distribution of intertidal yeasts but also highlights their promising potential for biotechnological applications.}, }
@article {pmid39505133, year = {2025}, author = {Hu, Y and Song, Y and Cai, J and Chao, J and Gong, Y and Jiang, X and Shao, K and Tang, X and Gao, G}, title = {Stronger biogeographical pattern of bacterioplankton communities than biofilm communities along a riverine ecosystem: A local scale study of the Kaidu river in the arid and semi-arid northwest of China.}, journal = {Environmental research}, volume = {264}, number = {Pt 1}, pages = {120294}, doi = {10.1016/j.envres.2024.120294}, pmid = {39505133}, issn = {1096-0953}, mesh = {China ; *Biofilms/growth &amp; development ; *Rivers/microbiology ; *Plankton ; *Bacteria/classification/genetics ; Ecosystem ; }, abstract = {Although the biogeographical pattern and mechanisms underlying microbial assembly have been well-explored in lentic ecosystems, the relevant scenarios in lotic ecosystems remain poorly understood. By sequencing the bacterial communities in bacterioplankton and biofilm, our study detected their distance-decay relationship (DDR), and the balance between deterministic and stochastic processes, along the Kaidu river in an arid and semi-arid region of northwest China. Our results revealed that bacterioplankton and biofilm had significantly contrasting community structures. The bacterioplankton communities showed a gradually decreasing trend in alpha-diversity from the headwater to the river mouth, contrasting with the alpha-diversity of biofilm communities which was constant along the river length. Both bacterioplankton and biofilm showed significant DDRs along the 500-km river corridor with the slope of the bacterioplankton DDR being steeper than that of the biofilm DDR, which implies a stronger biogeography of bacterioplankton than biofilm. Relative to biofilm communities, the species interactions formed a denser and more complex network in the bacterioplankton communities than in the biofilm communities. Our results also revealed that there was a transition of community assembly from deterministic to stochastic processes upstream to downstream, although both the bacterioplankton and biofilm communities were mainly regulated by deterministic processes within the entire river. All these empirical results expand our knowledge of microbial ecology in an arid and semi-arid lotic ecosystem.}, }
@article {pmid39503489, year = {2024}, author = {Teixeira, GM and Cordeiro Montanari, GC and Nicoletto, MLA and da Silva, DV and Noriler, SA and de Oliveira, JP and da Silva Rodrigues, MV and Sipoli Sanches, D and de Padua Pereira, U and Nunes da Rocha, U and Oliveira, AGd}, title = {Draft genome of Bacillus velezensis CMRP6330, a suitable biocontrol agent for disease management in crops.}, journal = {Microbiology resource announcements}, volume = {13}, number = {12}, pages = {e0065724}, pmid = {39503489}, issn = {2576-098X}, support = {305899/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 465133/2014-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 460129525//Deutsche Forschungsgemeinschaft (DFG)/ ; }, abstract = {As a biological alternative to managing diseases in crop production, we highlight the Bacillus velezensis strain LABIM41 (CMRP6330). Its genome, composed of 3,970,959 bp, possesses a rich metabolic machinery and a wide range of molecules with different biological activities and roles in its symbiotic relationship with its plant hosts.}, }
@article {pmid39502209, year = {2024}, author = {Kipkoech, R and Takase, M and Ahogle, AMA and Ocholla, G}, title = {Analysis of properties of biodiesel and its development and promotion in Ghana.}, journal = {Heliyon}, volume = {10}, number = {20}, pages = {e39078}, pmid = {39502209}, issn = {2405-8440}, abstract = {The increasing global population and the challenges associated with fossil fuel has led to a surge in energy demand, necessitating research on renewable and environmentally friendly energy sources. Biodiesel, is produced from biomass materials like vegetable oil and fats, is a promising alternative. Transesterification is a principal method used in biodiesel production, as it is simple, versatile, and efficient. Biodiesel offers several advantages, including emissions, lubricity, and safety, making it a sustainable fuel option and its properties conforms to the international standards. However, it has lower energy content, cold weather performance issues, and slightly reduced engine power compared to petroleum diesel. The choice of biodiesel feedstock depends on its properties, with jatropha oil and other feedstocks being potential in Ghana. Research on biodiesel in Ghana is still in early stages and the Ghanaian government's policy aims to replace 10 % of petroleum fuel with biofuel by 2020 and 20 % by 2030, but these goals have not been achieved due to barriers. Despite these challenges, the government and stakeholders in the biofuel industry are working to optimize the biodiesel sector for sustainability, efficiency, and scalability. Innovative cultivation techniques and low-cost oil extraction methods are required, necessitating interdisciplinary research collaborations. By capitalizing on these opportunities and implementing targeted interventions, Ghana can become a regional leader in sustainable biodiesel production.}, }
@article {pmid39501667, year = {2025}, author = {You, Z and Zhang, X and Huang, S and Chen, D and Zhu, Y and Li, G and Chen, X}, title = {The influence of skin microbial ecology on γδ T-cell immune pathways in allergic dermatitis models in mice.}, journal = {Journal of leukocyte biology}, volume = {117}, number = {5}, pages = {}, doi = {10.1093/jleuko/qiae244}, pmid = {39501667}, issn = {1938-3673}, mesh = {Animals ; *Dermatitis, Atopic/immunology/microbiology/pathology ; *Skin/microbiology/immunology/pathology ; *Microbiota/immunology ; Disease Models, Animal ; Mice ; *Receptors, Antigen, T-Cell, gamma-delta/immunology/metabolism ; RNA, Ribosomal, 16S/genetics ; Cytokines/metabolism ; Immunoglobulin E/blood ; Female ; *Intraepithelial Lymphocytes/immunology ; }, abstract = {Atopic dermatitis is a complex disease influenced by alterations in the skin microbiome and immune dysregulation. Despite the recognized role of these factors, the specific pathways by which distinct microbial populations affect skin immunity remain insufficiently understood. On a molecular level, the pathogenesis of atopic dermatitis involves critical cytokines such as IL-4, IL-17, interferon-γ, and IL-10, which contribute to the imbalance in T helper cell responses. Importantly, gamma-delta (γδ) T cells, which produce these cytokines and infiltrate affected epithelial cells in atopic dermatitis, have been underexplored. This study seeks to alleviate atopic dermatitis symptoms in mice by adjusting both peripheral and local immune environments through the transplantation of skin microbiota. By employing 16S rRNA sequencing, we characterized the skin microbiome of the mouse model. Our results demonstrate that microbiota intervention significantly reduces skin thickening and serum IgE levels in DNCB-induced atopic dermatitis mice. Additionally, changes in skin microbiota modulated immune cell dynamics, restoring the T helper 1 / T helper 2 balance and leading to clinical improvement. These findings highlight the critical role of skin microbiota in shaping immune responses, positioning microbiota-based therapies as a potential treatment for atopic dermatitis.}, }
@article {pmid39501615, year = {2025}, author = {Prost-Boxoen, L and Bafort, Q and Van de Vloet, A and Almeida-Silva, F and Paing, YT and Casteleyn, G and D'hondt, S and De Clerck, O and Van de Peer, Y}, title = {Asymmetric genome merging leads to gene expression novelty through nucleo-cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids.}, journal = {The New phytologist}, volume = {245}, number = {2}, pages = {869-884}, pmid = {39501615}, issn = {1469-8137}, support = {833522//H2020 European Research Council/ ; I001621N//European Marine Biological Resource Centre Belgium/ ; 11H0426N//Fonds Wetenschappelijk Onderzoek/ ; G0C0116N//Fonds Wetenschappelijk Onderzoek/ ; 833522/ERC_/European Research Council/International ; BOF.MET.2021.0005.01//Bijzonder Onderzoeksfonds UGent/ ; 1168420N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {*Genome, Plant ; *Transcriptome/genetics ; *Chlamydomonas reinhardtii/genetics ; *Cell Nucleus/metabolism/genetics ; *Cytoplasm/metabolism/genetics ; Triploidy ; Gene Expression Regulation, Plant ; Genetic Fitness ; }, abstract = {Genome merging is a common phenomenon causing a wide range of consequences on phenotype, adaptation, and gene expression, yet its broader implications are not well-understood. Two consequences of genome merging on gene expression remain particularly poorly understood: dosage effects and evolution of expression. We employed Chlamydomonas reinhardtii as a model to investigate the effects of asymmetric genome merging by crossing a diploid with a haploid strain to create a novel triploid line. Five independent clonal lineages derived from this triploid line were evolved for 425 asexual generations in a laboratory natural selection experiment. Utilizing fitness assays, flow cytometry, and RNA-Seq, we assessed the immediate consequences of genome merging and subsequent evolution. Our findings reveal substantial alterations in genome size, gene expression, protein homeostasis, and cytonuclear stoichiometry. Gene expression exhibited expression-level dominance and transgressivity (i.e. expression level higher or lower than either parent). Ongoing expression-level dominance and a pattern of 'functional dominance' from the haploid parent was observed. Despite major genomic and nucleo-cytoplasmic disruptions, enhanced fitness was detected in the triploid strain. By comparing gene expression across generations, our results indicate that proteostasis restoration is a critical component of rapid adaptation following genome merging in Chlamydomonas reinhardtii and possibly other systems.}, }
@article {pmid39500284, year = {2024}, author = {Arrigan, D and Kothe, CI and Oliverio, A and Evans, JD and Wolfe, BE}, title = {Novel fermentations integrate traditional practice and rational design of fermented-food microbiomes.}, journal = {Current biology : CB}, volume = {34}, number = {21}, pages = {R1094-R1108}, doi = {10.1016/j.cub.2024.09.047}, pmid = {39500284}, issn = {1879-0445}, mesh = {*Fermented Foods/microbiology ; *Fermentation ; *Microbiota ; *Food Microbiology/methods ; Humans ; }, abstract = {Fermented foods and beverages have been produced around the world for millennia, providing humans with a range of gastronomic, cultural, health, and scientific benefits. Building on these traditional forms, a convergence of factors, including culinary innovation, globalization, shifts in consumer preferences, and advances in microbiome sciences, has led to the emergence of so-called 'novel fermentations'. In this review, we define novel fermentation as the confluence of traditional food practices and rational microbiome design. Using principles of microbial ecology and evolution, we develop a microbiological framework that outlines several strategies for producing and characterizing novel fermentations, including switching substrates, engrafting target species, assembling whole-community chimeras, and generating novel phenotypes. A subsequent analysis of existing traditional ferments points to gaps in 'fermentation space' where novel ferments could potentially be produced using new combinations of microbes and food substrates. We highlight some important safety and sociocultural issues presented by the repurposing and modification of microbes from traditional ferments that fermented-food producers and microbiologists need to address.}, }
@article {pmid39499580, year = {2024}, author = {Zhang, X and Zhang, XX and Ma, L}, title = {New Horizons in Micro/Nanoplastic-Induced Oxidative Stress: Overlooked Free Radical Contributions and Microbial Metabolic Dysregulations in Anaerobic Digestion.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {48}, pages = {21251-21264}, doi = {10.1021/acs.est.4c08865}, pmid = {39499580}, issn = {1520-5851}, mesh = {*Oxidative Stress ; Anaerobiosis ; Free Radicals/metabolism ; *Reactive Oxygen Species/metabolism ; }, abstract = {Excessive production of reactive oxygen species (ROS) induced by micro/nanoplastics (MPs/NPs) is highly toxic to microbes. However, the mechanisms underlying ROS generation and metabolic regulation within anaerobic guilds remain poorly understood. In this study, we investigated the effects of environmentally relevant levels of polypropylene (PP)-MPs/NPs on oxidative stress and microbial ecology during anaerobic digestion (AD). Electron paramagnetic resonance spectroscopy revealed that PP-MPs/NPs elevated the concentrations of environmentally persistent free radicals (EPFRs) and derived hydroxyl radicals ([•]OH). EPFRs were identified as the primary contributors to [•]OH generation, as evidenced by a high Spearman correlation coefficient (r = 0.884, p < 0.001) and free radical-quenching studies. The formation of [•]OH enhanced ROS production by 86.2-100.9%, resulting in decreased cellular viability and methane production (by 37.5-50.5%) at 100 mg/g TS PP-MPs/NPs. Genome-centric metagenomic and metatranscriptomic analyses suggested that PP-MPs/NPs induced the reassembly of community structures, re-evolution of functional traits, and remodeling of interspecies interactions. Specifically, PP-MPs/NPs induced a shift in methanogen consortia from hydrogenotrophic Methanofollis sp. to acetoclastic and hydrogenotrophic Methanothrix soehngenii, primarily because of the latter's diverse ingestion patterns, electron bifurcation complexes, and ROS-scavenging abilities. Downregulation of genes associated with antioxidative defense systems (i.e., sodN, katA, and osmC) and ROS-driven redox signal transduction pathways (c-di-AMP and phosphorylation signaling pathways) provided insights into the mechanisms underlying ROS-induced microbial metabolic dysregulation. Our findings enhance the understanding of microbial ecological and metabolic traits under MPs/NPs stressors, facilitating the control of MPs/NPs toxicity and the stabilization of AD processes.}, }
@article {pmid39498487, year = {2024}, author = {Dooley, KD and Henry, LP and Bergelson, J}, title = {Impact of timing on the invasion of synthetic bacterial communities.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39498487}, issn = {1751-7370}, support = {//Hutchinson Fund at The University of Chicago/ ; //The Simons Foundation/ ; 951444//ERC Synergy/ ; }, mesh = {*Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; Biodiversity ; Introduced Species ; Time Factors ; }, abstract = {Microbial communities regularly experience ecological invasions that can lead to changes in composition and function. Factors thought to impact susceptibility to invasions, such as diversity and resource use, vary over the course of community assembly. We used synthetic bacterial communities to evaluate the success and impact of invasions occurring at different times during the community assembly process. Fifteen distinct communities were subjected to each of three bacterial invaders at the initial assembly of the community ("initial invasion"), 24 h into community assembly ("early invasion"), when the community was still undergoing transient dynamics, and 7 days into community assembly ("late invasion"), once the community had settled into its final composition. Communities were passaged daily and characterized through sequencing after reaching a stable composition. Invasions often failed to persist over time, particularly in higher richness communities. However, invasions had their largest effect on composition when they occurred before a community had settled into a stable composition. We found instances where an invader was ultimately excluded yet had profound and long-lasting effects on invaded communities. Invasion outcome was positively associated with lower community richness and resource use efficiency by the community, which varied throughout assembly. Our results demonstrate that microbial communities experiencing transient community dynamics are more affected by, and in some instances prone to, invasion, a finding relevant to efforts to modify the composition of microbial communities.}, }
@article {pmid39498135, year = {2024}, author = {Gu, Y and Meng, D and Liu, Z and Zhang, M and Yang, Z and Yin, H and Liang, Y and Xiao, N}, title = {Biotic and abiotic properties mediating sediment microbial diversity and function in a river-lake continuum.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1479670}, pmid = {39498135}, issn = {1664-302X}, abstract = {A river-lake system plays an important role in water management by providing long-term and frequent water diversions. However, hydrological connectivity in the system can have a profound effect on sediment microbial communities through pH, nutrient concentrations, and benthos invertebrates. Consequently, identifying the key environmental factors and their driving mechanisms is vital for microbial adaptation strategies to extreme environments. In this study, we analyzed the significant difference in sediment bacterial and fungal community structures and diversity indices among Dongting Lake and its tributary rivers, which worked as a typical river-connected lake ecosystem. There were significant differences in biotic and abiotic environments in the sediment habitats of Dongting Lake and its tributary rivers. Random forest analysis revealed that pH and Mollusca were found to be the most important abiotic and biotic variables for predicting both bacterial and fungal community structures, respectively. The beta diversity decomposition analyses showed that the bacterial and fungal community compositional dissimilarities among different sections were dominated by species replacement processes, with more than half of the OTUs in each section being unique. Notably, both biotic and abiotic factors affected the number and the relative abundance of these bacterial and fungal unique OTUs, leading to changes in community composition. Mollusca, pH, TP, NO3-N, and NH4-N were negatively related to the relative abundance of Actinobacteria, Acidobacteria, Gemmatimonadetes, Planctomycetes, and Ascomycota, while Annelida and ORP were positively related to the relative abundance of Actinobacteria and Gemmatimonadetes. Additionally, PICRUSt analysis revealed that the functional dissimilarity among lakes and rivers was strengthened in unique species compared to all species in bacterial and fungal communities, and the changes of functional types helped to improve the habitat environment in the main Dongting Lake and promote the process of microbial growth. From our results, the role of macrozoobenthos and physicochemical characteristics in driving the sediment microbial community spatial variations became clear, which contributed to further understanding of the river-lake ecosystem.}, }
@article {pmid39497067, year = {2024}, author = {Moeller, AH and Dillard, BA and Goldman, SL and Real, MVF and Sprockett, DD}, title = {Removal of sequencing adapter contamination improves microbial genome databases.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1033}, pmid = {39497067}, issn = {1471-2164}, support = {R01 DK139214/DK/NIDDK NIH HHS/United States ; R35 GM138284/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Databases, Genetic ; DNA Contamination ; Genome, Microbial ; Humans ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Cattle ; Mice ; Swine ; }, abstract = {Advances in assembling microbial genomes have led to growth of reference genome databases, which have been transformative for applied and basic microbiome research. Here we show that published microbial genome databases from humans, mice, cows, pigs, fish, honeybees, and marine environments contain significant sequencing-adapter contamination that systematically reduces assembly accuracy and contiguousness. By removing the adapter-contaminated ends of contiguous sequences and reassembling MGnify reference genomes, we improve the quality of assemblies in these databases.}, }
@article {pmid39496952, year = {2024}, author = {Djotan, AKG and Matsushita, N and Fukuda, K}, title = {Within-Site Variations in Soil Physicochemical Properties Explained the Spatiality and Cohabitation of Arbuscular Mycorrhizal Fungi in the Roots of Cryptomeria Japonica.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {136}, pmid = {39496952}, issn = {1432-184X}, support = {JP22H02382//Japan Society for the Promotion of Science/ ; }, mesh = {*Mycorrhizae/classification ; *Soil/chemistry ; *Soil Microbiology ; *Cryptomeria/microbiology ; *Plant Roots/microbiology ; Japan ; Phosphorus/analysis ; Forests ; Hydrogen-Ion Concentration ; Nitrogen/analysis/metabolism ; Carbon/analysis/metabolism ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) live in a community in the roots of host plants. Still, the patterns and factors that drive their spatiality and cohabitation remain uncovered, particularly that of trees in planted forests, which we aimed to clarify in Cryptomeria japonica, a major plantation tree in Japan. We analyzed 65 paired root and soil samples of Cryptomeria japonica trees collected from 11 microsite (MS) plots at two environmentally different forest sites in central Japan and measured soil pH, total phosphorus (TP), C, N, and the carbon-to-nitrogen ratio. Root AMF communities were recovered using Illumina's next-generation amplicon sequencing targeting the small subunit of ribosomal DNA. We detected more than 500 AMF OTUs at each site but only three belonging to Dominikia, Rhizophagus, and Sclerocystis were dominant in the roots of C. japonica, detected each at an average relative abundance higher than 20%. Two showed negatively correlated spatial distributions and different associations with soil pH. Similarly, the physicochemical properties at MSs significantly determined the AMF assemblages in the roots of C. japonica. Dominikia, Rhizophagus, and Sclerocystis coexist in the roots of C. japonica where soil physicochemical properties, particularly pH, determine their spatial dynamic, turnovers, and cohabitation patterns. These findings highlight the importance of simultaneous colonization of plants by multiple AMF.}, }
@article {pmid39496518, year = {2024}, author = {Khaleque, HN and Fathollahzadeh, H and Kaksonen, AH and Valdés, J and Vergara, E and Holmes, DS and Watkin, ELJ}, title = {Genomic insights into key mechanisms for carbon, nitrogen, and phosphate assimilation by the acidophilic, halotolerant genus Acidihalobacter members.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {12}, pages = {}, pmid = {39496518}, issn = {1574-6941}, support = {//Curtin University/ ; //CSIRO/ ; }, mesh = {*Phosphates/metabolism ; *Carbon/metabolism ; *Nitrogen/metabolism ; *Genome, Bacterial ; Citric Acid Cycle/genetics ; Genomics ; Phylogeny ; Bacterial Proteins/genetics/metabolism ; }, abstract = {In-depth comparative genomic analysis was conducted to predict carbon, nitrogen, and phosphate assimilation pathways in the halotolerant, acidophilic genus Acidihalobacter. The study primarily aimed to understand how the metabolic capabilities of each species can determine their roles and effects on the microbial ecology of their unique saline and acidic environments, as well as in their potential application to saline water bioleaching systems. All four genomes encoded the genes for the complete tricarboxylic acid cycle, including 2-oxoglutarate dehydrogenase, a key enzyme absent in obligate chemolithotrophic acidophiles. Genes for a unique carboxysome shell protein, csoS1D, typically found in halotolerant bacteria but not in acidophiles, were identified. All genomes contained lactate and malate utilization genes, but only A. ferrooxydans DSM 14175T contained genes for the metabolism of propionate. Genes for phosphate assimilation were present, though organized differently across species. Only A. prosperus DSM 5130T and A. aeolianus DSM 14174T genomes contained nitrogen fixation genes, while A. ferrooxydans DSM 14175T and A. yilgarnensis DSM 105917T possessed genes for urease transporters and respiratory nitrate reductases, respectively. The findings suggest that all species can fix carbon dioxide but can also potentially utilize exogenous carbon sources and that the non-nitrogen-fixing species rely on alternative nitrogen assimilation mechanisms.}, }
@article {pmid39494810, year = {2024}, author = {Malik, M and Das, S and Paul, P and Chakraborty, P and Roy, R and Maity, A and Das, A and Dasgupta, M and Trivedi, S and Tribedi, P}, title = {Cuminaldehyde in combination with tetracycline shows promising antibiofilm activity against drug-resistant Pseudomonas aeruginosa.}, journal = {Biofouling}, volume = {40}, number = {10}, pages = {862-881}, doi = {10.1080/08927014.2024.2422874}, pmid = {39494810}, issn = {1029-2454}, mesh = {*Biofilms/drug effects ; *Pseudomonas aeruginosa/drug effects/physiology ; *Anti-Bacterial Agents/pharmacology ; *Tetracycline/pharmacology ; *Microbial Sensitivity Tests ; *Benzaldehydes/pharmacology ; *Cymenes/pharmacology ; Drug Synergism ; Reactive Oxygen Species/metabolism ; Drug Resistance, Bacterial/drug effects ; Virulence Factors ; }, abstract = {Pseudomonas aeruginosa, an opportunistic pathogen often causes biofilm-linked infections. A combinatorial approach involving tetracycline (antibiotic) and cuminaldehyde (phytochemical) was explored to combat this infectious pathogen. The results showed that both tetracycline and cuminaldehyde individually demonstrated antibacterial effects. However, when the compounds were applied together, there was a significant increase in their antimicrobial potential. The determined fractional inhibitory concentration index of 0.43 indicated a synergistic interaction between the two compounds. Furthermore, a series of experiments demonstrated that the combined application of cuminaldehyde and tetracycline could lead to a significant enhancement of their antibiofilm potential. This enhanced antibiofilm potential was attributed to the accumulation of reactive oxygen species and increased cell membrane permeability. Besides, this combinatorial application reduced the secretion of various virulence factors from P. aeruginosa. Therefore, this combined approach holds promise for effectively treating P. aeruginosa biofilms.}, }
@article {pmid39493671, year = {2024}, author = {Kleikamp, HBC and van der Zwaan, R and van Valderen, R and van Ede, JM and Pronk, M and Schaasberg, P and Allaart, MT and van Loosdrecht, MCM and Pabst, M}, title = {NovoLign: metaproteomics by sequence alignment.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae121}, pmid = {39493671}, issn = {2730-6151}, abstract = {Tremendous advances in mass spectrometric and bioinformatic approaches have expanded proteomics into the field of microbial ecology. The commonly used spectral annotation method for metaproteomics data relies on database searching, which requires sample-specific databases obtained from whole metagenome sequencing experiments. However, creating these databases is complex, time-consuming, and prone to errors, potentially biasing experimental outcomes and conclusions. This asks for alternative approaches that can provide rapid and orthogonal insights into metaproteomics data. Here, we present NovoLign, a de novo metaproteomics pipeline that performs sequence alignment of de novo sequences from complete metaproteomics experiments. The pipeline enables rapid taxonomic profiling of complex communities and evaluates the taxonomic coverage of metaproteomics outcomes obtained from database searches. Furthermore, the NovoLign pipeline supports the creation of reference sequence databases for database searching to ensure comprehensive coverage. We assessed the NovoLign pipeline for taxonomic coverage and false positive annotations using a wide range of in silico and experimental data, including pure reference strains, laboratory enrichment cultures, synthetic communities, and environmental microbial communities. In summary, we present NovoLign, a de novo metaproteomics pipeline that employs large-scale sequence alignment to enable rapid taxonomic profiling, evaluation of database searching outcomes, and the creation of reference sequence databases. The NovoLign pipeline is publicly available via: https://github.com/hbckleikamp/NovoLign.}, }
@article {pmid39491387, year = {2023}, author = {González-Alonso, V and Pradal, I and Wardhana, YR and Cnockaert, M and Wieme, AD and Vandamme, P and De Vuyst, L}, title = {Microbial ecology and metabolite dynamics of backslopped triticale sourdough productions and the impact of scale.}, journal = {International journal of food microbiology}, volume = {408}, number = {}, pages = {110445}, doi = {10.1016/j.ijfoodmicro.2023.110445}, pmid = {39491387}, issn = {1879-3460}, abstract = {Triticale (X Triticosecale Wittmack) is a hybrid of wheat (Triticum aestivum L.) and rye (Secale cereale L.), combining the positive attributes of both cereals. However, it has not been exploited for sourdough production yet. Further, the effect of scale on sourdough production has not been investigated systematically up to now. The aims of the present study were to assess the microbial ecology and metabolomic output of eleven spontaneously fermented, backslopped sourdough productions made with triticale flour on a scale of 100, 200, 500, and 1000 g. The acidification profile [pH and total titratable acidity (TTA)], microbial diversity (culture-dependent and culture-independent), metabolite dynamics, and appropriate correlations were determined. After ten fermentation steps, different species of Lactobacillaceae were prevalent in the mature sourdoughs, in particular Latilactobacillus curvatus, Limosilactobacillus fermentum, and Pediococcus pentosaceus. The microbial diversity could be traced back to the grains and was also present in the milling fractions (flour, bran, and shorts). Furthermore, thanks to the use of Illumina-based high-throughput sequencing and an amplicon sequence variant (ASV) approach, the presence of undesirable bacterial groups (bacilli, clostridia, and enterobacteria) during the initial steps of the backslopping cycle was revealed, as well as a finetuned taxonomic diversity of the LAB genera involved. Small sourdough productions (100 and 200 g) selected for a lower species diversity and reached a stable consortium faster than large ones (500 and 1000 g). Although a comparable final pH of 3.6-4.0 was obtained, the TTA of small sourdoughs was lower than that of large ones. Regarding the metabolic output, the simultaneous production of mannitol and erythritol, beyond ethanol and glycerol, could be linked to sourdoughs in which Liml. fermentum was the sole LAB species present. Further, the use of the arginine deiminase pathway by P. pentosaceus and Liml. fermentum was obvious. An appropriate extraction method followed by liquid injection gas chromatography coupled to triple quadrupole tandem mass spectrometry allowed the quantification of interesting volatile organic compounds, such as ethyl lactate. These findings support the inclusion of triticale as a viable alternative to wheat or rye for the production of sourdoughs that can be integrated into bread-making production schemes.}, }
@article {pmid39482450, year = {2024}, author = {Gao, L and Rao, MPN and Liu, YH and Wang, PD and Lian, ZH and Abdugheni, R and Jiang, HC and Jiao, JY and Shurigin, V and Fang, BZ and Li, WJ}, title = {SALINITY-Induced Changes in Diversity, Stability, and Functional Profiles of Microbial Communities in Different Saline Lakes in Arid Areas.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {135}, pmid = {39482450}, issn = {1432-184X}, support = {2021FY100900//National Science and Technology Fundamental Resources Investigation Program of China/ ; 2022D01A154//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022B0202110001//Key-Area Research and Development Programof Guangdong Province/ ; }, mesh = {*Lakes/microbiology/chemistry ; *Salinity ; *Archaea/genetics/classification/isolation &amp; purification ; *Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Biodiversity ; Geologic Sediments/microbiology ; Phylogeny ; Desert Climate ; Ecosystem ; }, abstract = {Saline lakes, characterized by high salinity and limited nutrient availability, provide an ideal environment for studying extreme halophiles and their biogeochemical processes. The present study examined prokaryotic microbial communities and their ecological functions in lentic sediments (with the salinity gradient and time series) using 16S rRNA amplicon sequencing and a metagenomic approach. Our findings revealed a negative correlation between microbial diversity and salinity. The notable predominance of Archaea in high-salinity lakes signified a considerable alteration in the composition of the microbial community. The results indicate that elevated salinity promotes homogeneous selection pressures, causing substantial alterations in microbial diversity and community structure, and simultaneously hindering interactions among microorganisms. This results in a notable decrease in the complexity of microbial ecological networks, ultimately influencing the overall ecological functional responses of microbial communities such as carbon fixation, sulfur, and nitrogen metabolism. Overall, our findings reveal salinity drives a notable predominance of Archaea, selects for species adapted to extreme conditions, and decreases microbial community complexity within saline lake ecosystems.}, }
@article {pmid39480531, year = {2024}, author = {Dobrzyński, J and Naziębło, A}, title = {Paenibacillus as a Biocontrol Agent for Fungal Phytopathogens: Is P. polymyxa the Only One Worth Attention?.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {134}, pmid = {39480531}, issn = {1432-184X}, mesh = {*Plant Diseases/microbiology/prevention &amp; control ; *Paenibacillus/physiology/metabolism ; *Paenibacillus polymyxa/physiology ; Biological Control Agents ; Fusarium/physiology ; Colletotrichum/physiology/growth &amp; development ; Pest Control, Biological ; Rhizoctonia/physiology/growth &amp; development ; Botrytis/growth &amp; development/physiology ; Fungi/physiology ; }, abstract = {Control of fungal phytopathogens is a significant challenge in modern agriculture. The widespread use of chemical fungicides to control these pathogens often leads to environmental and food contamination. An eco-friendly alternative that can help reduce reliance on these chemicals is plant growth-promoting bacteria (PGPB), particularly those of the genus Paenibacillus, which appear to be highly effective. The review aims to summarize the existing knowledge on the potential of Paenibacillus spp. as fungal biocontrol agents, identify knowledge gaps, and answer whether other species of the genus Paenibacillus, in addition to Paenibacillus polymyxa, can also be effective biocontrol agents. Paenibacillus spp. can combat plant phytopathogens through various mechanisms, including the production of lipopeptides (such as fusaricidin, paenimyxin, and pelgipeptin), the induction of systemic resistance (ISR), hydrolytic enzymes (chitinase, cellulase, and glucanase), and volatile organic compounds. These properties enable Paenibacillus strains to suppress the growth of fungi such as Fusarium oxysporum, F. solani, Rhizoctonia solani, Botrytis cinerea, or Colletotrichum gloeosporioides. Notably, several strains of Paenibacillus, including P. polymyxa, P. illinoisensis KJA-424, P. lentimorbus B-30488, and P. elgii JCK1400, have demonstrated efficacy in controlling fungal diseases in plants. Importantly, many formulations with Paenibacillus strains have already been patented, and some are commercially available, but most of them contain only P. polymyxa. Nevertheless, considering the data presented in this review, we believe that other strains from the Paenibacillus genus (besides P. polymyxa) will also be commercialized and used in plant protection in the future. Importantly, there is still limited information regarding their impact on the native microbiota, particularly from the metataxonomic and metagenomic perspectives. Expanding knowledge in this area could enhance the effectiveness of biocontrol agents containing Paenibacillus spp., ensuring safe and sustainable use of biological fungicides.}, }
@article {pmid39488271, year = {2024}, author = {Allen, J and Sire, M and Belouard, N and Gorzerino, C and Coutellec, MA and Mony, C and Pannard, A and Piscart, C}, title = {Could landscape ecology principles apply at the microscale? A metabarcoding approach on Trichoptera larvae-associated microbial diversity.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {177304}, doi = {10.1016/j.scitotenv.2024.177304}, pmid = {39488271}, issn = {1879-1026}, mesh = {Animals ; *Larva ; *Microbiota ; *Insecta ; *DNA Barcoding, Taxonomic ; *Bacteria/classification/genetics ; Fungi ; Biodiversity ; Ecology ; Diatoms ; Ecosystem ; Environmental Monitoring/methods ; }, abstract = {Landscape heterogeneity is known as a major factor of community structure and composition. Whether this effect of the landscape extends at different scales and particularly at the relevant scale for microorganisms remained to be determined. We used the cases produced by aquatic larvae of Trichoptera, which assemble organic or mineral particles, as naturally replicated experimental systems representing structured substrates to determine the effect of landscape structuration on microbial communities. A metabarcoding approach was used to characterise fungal, bacterial and diatom communities on cases produced by six Trichoptera species and related unstructured organic and mineral substrates. The structuration of the particles constituting the cases was also determined as a measure of microscale landscape. Structured substrates harboured communities of diatoms, fungi and bacteria that differed from those found on unstructured substrates. Microbial communities also differed between organic and mineral substrates. We found a higher microbial diversity on structured substrates than on unstructured substrates. The heterogeneity of the microscale landscape also affected bacterial and fungal communities within cases. These results highlight the importance of microscale landscape structuration for microbial diversity and demonstrate that approaches of landscape ecology could be downscaled to the microscale.}, }
@article {pmid39488149, year = {2024}, author = {Németh, Z and Svigruha, R and Ács, A and Farkas, A and Tapolczai, K and Elekes, K and Fodor, I and Pirger, Z}, title = {Developmental, behavioral, and biochemical effects of chronic exposure to sublethal concentrations of organic UV-filter compounds on a freshwater model species.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {277}, number = {}, pages = {107134}, doi = {10.1016/j.aquatox.2024.107134}, pmid = {39488149}, issn = {1879-1514}, mesh = {Animals ; *Water Pollutants, Chemical/toxicity ; *Sunscreening Agents/toxicity ; *Daphnia/drug effects ; Reproduction/drug effects ; Ultraviolet Rays ; Heart Rate/drug effects ; Fresh Water/chemistry ; Catalase/metabolism ; Swimming ; Behavior, Animal/drug effects/radiation effects ; Superoxide Dismutase/metabolism ; Glutathione Transferase/metabolism ; Acrylates ; }, abstract = {The prevalence of organic/chemical UV-filter compounds in aquatic ecosystems represents a growing environmental issue. The long-term toxicity risks of many UV-filters at environmentally relevant concentrations to aquatic biota are still less studied, especially in the case of invertebrates. This study was designed to evaluate the chronic toxicity of avobenzone (AVO), octocrylene (OCTO), and octinoxate (OCTI), three UV-filters which frequently occur in the aquatic environment, to the water flea (Daphnia magna) at an environmentally relevant concentration of 200 ng l[-1] in a 21-day exposure. Potential alterations in the growth, reproduction, and heart rate were continuously monitored during the treatments. Filtration rate, swimming, and the state of the antioxidant- and metabolic functions were evaluated at the end of exposures. Avobenzone significantly increased the reproductive output, heart rate, and filtration rate, while evoked a significant decrease of swimming behavior, and inhibited the activity of catalase (CAT) and glutathione S-transferase (GST) enzymes. The body size, reproduction, heart rate, and superoxide dismutase (SOD) activity were significantly increased whereas the activity of GST and CAT was significantly reduced by OCTO. OCTI significantly increased reproduction, heart rate, CAT and SOD activity but significantly decreased the swimming behavior. Our results confirmed that chronic exposure to organic UV-filters even at environmentally relevant concentrations affect basic physiological traits and cellular defense pathways in D. magna. Highlighting, our observations revealed previously unknown physiological changes (e.g., altered heart rate, filtration rate, SOD activity) caused by the investigated UV-filter compounds. Future research is to be aimed at investigating the mixture effects of these compounds and at the understanding of the potential cellular and molecular mechanisms underlying the changes induced.}, }
@article {pmid39485000, year = {2024}, author = {Kortekaas Krohn, I and Callewaert, C and Belasri, H and De Pessemier, B and Diez Lopez, C and Mortz, CG and O'Mahony, L and Pérez-Gordo, M and Sokolowska, M and Unger, Z and Untersmayr, E and Homey, B and Gomez-Casado, C}, title = {The influence of lifestyle and environmental factors on host resilience through a homeostatic skin microbiota: An EAACI Task Force Report.}, journal = {Allergy}, volume = {79}, number = {12}, pages = {3269-3284}, pmid = {39485000}, issn = {1398-9995}, support = {//European Academy of Allergy and Clinical Immunology/ ; }, mesh = {Humans ; *Microbiota/immunology ; *Skin/microbiology/immunology ; *Homeostasis ; *Life Style ; Skin Diseases/etiology/immunology/microbiology ; Environment ; }, abstract = {Human skin is colonized with skin microbiota that includes commensal bacteria, fungi, arthropods, archaea and viruses. The composition of the microbiota varies at different anatomical locations according to changes in body temperature, pH, humidity/hydration or sebum content. A homeostatic skin microbiota is crucial to maintain epithelial barrier functions, to protect from invading pathogens and to interact with the immune system. Therefore, maintaining homeostasis holds promise to be an achievable goal for microbiome-directed treatment strategies as well as a prophylactic strategy to prevent the development of skin diseases, as dysbiosis or disruption of homeostatic skin microbiota is associated with skin inflammation. A healthy skin microbiome is likely modulated by genetic as well as environmental and lifestyle factors. In this review, we aim to provide a complete overview of the lifestyle and environmental factors that can contribute to maintaining the skin microbiome healthy. Awareness of these factors could be the basis for a prophylactic strategy to prevent the development of skin diseases or to be used as a therapeutic approach.}, }
@article {pmid39482383, year = {2024}, author = {Gaborieau, B and Vaysset, H and Tesson, F and Charachon, I and Dib, N and Bernier, J and Dequidt, T and Georjon, H and Clermont, O and Hersen, P and Debarbieux, L and Ricard, JD and Denamur, E and Bernheim, A}, title = {Prediction of strain level phage-host interactions across the Escherichia genus using only genomic information.}, journal = {Nature microbiology}, volume = {9}, number = {11}, pages = {2847-2861}, pmid = {39482383}, issn = {2058-5276}, support = {R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; R21042KS/RSE22002KSA//Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (National Institute of Health and Medical Research)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PECAN 101040529//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; ANR-19-AMRB-0002//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-AMRB-0002//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-20-CE92-0048//Agence Nationale de la Recherche (French National Research Agency)/ ; DEQ20161136698//Fondation pour la Recherche M&#xe9;dicale (Foundation for Medical Research in France)/ ; }, mesh = {*Host Specificity ; *Bacteriophages/genetics/physiology/classification ; *Genomics/methods ; Algorithms ; Escherichia coli/virology/genetics ; Phage Therapy ; Escherichia/genetics/virology ; Genome, Bacterial/genetics ; Genome, Viral/genetics ; Host-Pathogen Interactions ; ROC Curve ; Host Microbial Interactions ; }, abstract = {Predicting bacteriophage infection of specific bacterial strains promises advancements in phage therapy and microbial ecology. Whether the dynamics of well-established phage-host model systems generalize to the wide diversity of microbes is currently unknown. Here we show that we could accurately predict the outcomes of phage-bacteria interactions at the strain level in natural isolates from the genus Escherichia using only genomic data (area under the receiver operating characteristic curve (AUROC) of 86%). We experimentally established a dataset of interactions between 403 diverse Escherichia strains and 96 phages. Most interactions are explained by adsorption factors as opposed to antiphage systems which play a marginal role. We trained predictive algorithms and pinpoint poorly predicted interactions to direct future research efforts. Finally, we established a pipeline to recommend tailored phage cocktails, demonstrating efficiency on 100 pathogenic E. coli isolates. This work provides quantitative insights into phage-host specificity and supports the use of predictive algorithms in phage therapy.}, }
@article {pmid39481794, year = {2024}, author = {Li, X and Li, Y and Wang, Y and Liu, Y and Riaz, L and Wang, Q and Zeng, X and Qin, Z and Irfan, M and Yang, Q}, title = {Methodology comparison of environmental sediment fungal community analysis.}, journal = {Environmental research}, volume = {263}, number = {Pt 3}, pages = {120260}, doi = {10.1016/j.envres.2024.120260}, pmid = {39481794}, issn = {1096-0953}, mesh = {*Geologic Sediments/microbiology ; *Fungi/genetics/isolation &amp; purification/classification ; *RNA, Ribosomal, 18S/genetics ; *High-Throughput Nucleotide Sequencing ; DNA, Fungal/analysis ; DNA, Ribosomal Spacer/genetics ; Mycobiome ; Rivers/microbiology ; }, abstract = {Fungi play important roles in ecosystems. Analyzing fungal communities in environments has long been a challenge due to the large difference in compositions retrieved using different methods or sequencing regions, obscuring the true abundance and species information. Our study aimed to compare and determine more accurate approach for evaluating fungal populations in river sediment. To achieve this, different primer sets in the internal transcribed spacer (ITS) (ITS5/ITS1R, ITS1F/ITS2), 18S rRNA gene (0817F/1196R) for High-throughput sequencing (HTS), metagenomic shotgun sequencing (MS) directly from environmental samples, and HTS using ITS primers for the fungal samples collected from plate cultivation were used to characterize the fungal communities. We calculated diversity index and used FungalTraits to analyze methods preferences for fungal species. The study revealed that when analyzing the fungal species directly from environmental samples, amplification and sequencing of ITS region demonstrated more accuracy than MS and 18S rRNA gene sequencing methods, but displayed significant primer preference. Over 30 % fungal species from HTS after plate cultivation were not present in HTS from the environmental samples. NMDS analysis demonstrated significant disparities in species diversity among different methods, suggesting potential complementarity between them. Over 85% species identified by HTS using ITS primers belonged to filamentous fungi, while the MS mostly identified yeast (62%). Therefore, to get more accurate fungal community information in sediment, multiple methods were recommended by using cultivation, molecular biological methods dependent on PCR techniques like ITS1F/ITS2 primer for HTS and PCR independent method such as metagenomic shotgun sequencing techniques.}, }
@article {pmid39476778, year = {2025}, author = {Li, J and Sun, Y and Zhang, Q and Liu, S and Liu, P and Zhang, XX}, title = {Unveiling the potential role of virus-encoded polyphosphate kinases in enhancing phosphorus removal in activated sludge systems.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122678}, doi = {10.1016/j.watres.2024.122678}, pmid = {39476778}, issn = {1879-2448}, mesh = {*Viral Proteins/genetics/metabolism ; Phylogeny ; *Viruses/classification/enzymology/genetics ; Bacteria/classification/enzymology/genetics ; Water Purification ; Genetic Variation ; *Phosphotransferases (Phosphate Group Acceptor)/chemistry/genetics/metabolism ; Models, Molecular ; Protein Structure, Tertiary ; Sequence Analysis, Protein ; Sewage/virology ; }, abstract = {While microbial phosphate removal in activated sludge (AS) systems has been extensively studied, the role of viruses in this process remains largely unexplored. In this study, we identified 149 viral auxiliary metabolic genes associated with phosphorus cycling from 2,510 viral contigs (VCs) derived from AS systems. Notably, polyphosphate kinase 1 (ppk1) and polyphosphate kinase 2 (ppk2) genes, which are primarily responsible for phosphate removal, were found in five unclassified VCs. These genes exhibited conserved protein structures and active catalytic sites, indicating a pivotal role of viruses in enhancing phosphorus removal. Phylogenetic analysis demonstrated a close relationship between viral ppk genes and their bacterial counterparts, suggesting the occurrence of horizontal gene transfer. Furthermore, experimental assays validated that viral ppk genes enhanced host phosphate removal capabilities. VCs carrying ppk genes were observed across diverse ecological and geographical contexts, suggesting their potential to bolster host functions in varied environmental and nutrient settings, spanning natural and engineered systems. These findings uncover a previously underappreciated mechanism by which viruses enhance phosphate removal in wastewater treatment plants. Overall, our study highlights the potential for leveraging virus-encoded genes to improve the efficiency of biological phosphorus removal processes, offering new insights into the microbial ecology of AS systems and the role of viruses in biogeochemical cycling.}, }
@article {pmid39472801, year = {2024}, author = {Valiei, A and Dickson, AM and Aminian-Dehkordi, J and Mofrad, MRK}, title = {Bacterial community dynamics as a result of growth-yield trade-off and multispecies metabolic interactions toward understanding the gut biofilm niche.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {441}, pmid = {39472801}, issn = {1471-2180}, mesh = {*Bacteria/metabolism/classification/growth &amp; development/genetics ; *Biofilms/growth &amp; development ; Humans ; *Gastrointestinal Microbiome ; Microbial Interactions ; Bacterial Physiological Phenomena ; Models, Biological ; Kinetics ; Symbiosis ; Ecosystem ; Nutrients/metabolism ; }, abstract = {Bacterial communities are ubiquitous, found in natural ecosystems, such as soil, and within living organisms, like the human microbiome. The dynamics of these communities in diverse environments depend on factors such as spatial features of the microbial niche, biochemical kinetics, and interactions among bacteria. Moreover, in many systems, bacterial communities are influenced by multiple physical mechanisms, such as mass transport and detachment forces. One example is gut mucosal communities, where dense, closely packed communities develop under the concurrent influence of nutrient transport from the lumen and fluid-mediated detachment of bacteria. In this study, we model a mucosal niche through a coupled agent-based and finite-volume modeling approach. This methodology enables us to model bacterial interactions affected by nutrient release from various sources while adjusting individual bacterial kinetics. We explored how the dispersion and abundance of bacteria are influenced by biochemical kinetics in different types of metabolic interactions, with a particular focus on the trade-off between growth rate and yield. Our findings demonstrate that in competitive scenarios, higher growth rates result in a larger share of the niche space. In contrast, growth yield plays a critical role in neutralism, commensalism, and mutualism interactions. When bacteria are introduced sequentially, they cause distinct spatiotemporal effects, such as deeper niche colonization in commensalism and mutualism scenarios driven by species intermixing effects, which are enhanced by high growth yields. Moreover, sub-ecosystem interactions dictate the dynamics of three-species communities, sometimes yielding unexpected outcomes. Competitive, fast-growing bacteria demonstrate robust colonization abilities, yet they face challenges in displacing established mutualistic systems. Bacteria that develop a cooperative relationship with existing species typically obtain niche residence, regardless of their growth rates, although higher growth yields significantly enhance their abundance. Our results underscore the importance of bacterial niche dynamics in shaping community properties and succession, highlighting a new approach to manipulating microbial systems.}, }
@article {pmid39470240, year = {2024}, author = {Dumann, G and Rohland, O and Abdel-Glil, MY and Allen, RJ and Bauer, M and Busch, A}, title = {Draft genomes of the bile duct microbiome strains Klebsiella pneumoniae and Enterococcus lactis isolated from bilioenteric drainages with biofilm-forming abilities.}, journal = {Microbiology resource announcements}, volume = {13}, number = {12}, pages = {e0020224}, pmid = {39470240}, issn = {2576-098X}, support = {EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft (DFG)/ ; }, abstract = {We describe the genetic properties of two strains isolated from the elusive bile duct microbiome from solid organ transplant patients. Bacterial strains Enterococcus lactis (MS-STENT-08-E-001) and Klebsiella pneumoniae (MS-STENT-01-M-001) were isolated from the biofilms of bile duct catheters.}, }
@article {pmid39468827, year = {2024}, author = {Flores, JN and Lubin, JB and Silverman, MA}, title = {The case for microbial intervention at weaning.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2414798}, pmid = {39468827}, issn = {1949-0984}, support = {R01 DK133453/DK/NIDDK NIH HHS/United States ; T32 GM008562/GM/NIGMS NIH HHS/United States ; }, mesh = {*Weaning ; *Gastrointestinal Microbiome ; Humans ; Animals ; *Probiotics/administration &amp; dosage ; Host Microbial Interactions ; Diet ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Intestines/microbiology/immunology ; }, abstract = {Weaning, the transition from a milk-based diet to solid food, coincides with the most significant shift in gut microbiome composition in the lifetime of most mammals. Notably, this period also marks a "window of opportunity" where key components of the immune system develop, and host-microbe interactions shape long-term immune homeostasis thereby influencing the risk of autoimmune and inflammatory diseases. This review provides a comprehensive analysis of the changes in nutrition, microbiota, and host physiology that occur during weaning. We explore how these weaning-associated processes differ across species, lifestyles, and regions of the intestine. Using prinicples of microbial ecology, we propose that the weaning transition is an optimal period for microbiome-targeted therapeutic interventions. Additionally, we suggest that replicating features of the weaning microbiome in adults could promote the successful engraftment of probiotics. Finally, we highlight key research areas that could deepen our understanding of the complex relationships between diet, commensal microbes, and the host, informing the development of more effective microbial therapies.}, }
@article {pmid39468208, year = {2024}, author = {Ilicic, D and Woodhouse, J and Karsten, U and Schimani, K and Zimmermann, J and Grossart, HP}, title = {Chytrid fungi infecting Arctic microphytobenthic communities under varying salinity conditions.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {25821}, pmid = {39468208}, issn = {2045-2322}, mesh = {Arctic Regions ; *Salinity ; *Chytridiomycota/genetics/isolation &amp; purification ; Diatoms/microbiology/genetics ; Mycobiome ; Ecosystem ; Biodiversity ; Food Chain ; }, abstract = {This study aimed to investigate the presence and diversity of fungal parasites in Arctic coastal microphytobenthic communities. These communities represent a key component in the functioning of Arctic trophic food webs. Fungal parasites, particularly Chytridiomycota (chytrids), play significant roles by controlling microalgal bloom events, impacting genetic diversity, modifying microbial interactions, and accelerating nutrient and energy transfer to higher trophic levels. In the context of rapid Arctic warming and increased glacier meltwater, which significantly affects these communities, we used high-throughput sequencing to explore fungal community composition. Our results show that chytrids dominate fungal communities in Arctic benthic habitats and that the overall fungal diversity is primarily influenced by the salinity gradient. Chytrid representation is positively correlated with the presence of potential benthic diatom (Surirella, Nitzschia, Navicula) and green algae (Ulvophyceae) hosts, while microscopic observations provide further evidence for the presence of active chytrid infections.}, }
@article {pmid39467902, year = {2024}, author = {Awais, M and Xiang, Y and Shah, N and Bilal, H and Yang, D and Hu, H and Li, T and Ji, X and Li, H}, title = {Unraveling the Role of Contaminants Reshaping the Microflora in Zea mays Seeds from Heavy Metal-Contaminated and Pristine Environment.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {133}, pmid = {39467902}, issn = {1432-184X}, support = {KUST-AN2023006Y//Kunming University of Science and Technology Plan Project/ ; KUST-AN2023006Y//Kunming University of Science and Technology Plan Project/ ; 42267059//National Natural Science Foundation of China/ ; SKLEG2023216//State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences/ ; }, mesh = {*Zea mays/microbiology ; *Metals, Heavy/analysis ; *Seeds/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; China ; *Soil Pollutants/analysis ; *Fungi/genetics/classification/isolation &amp; purification/drug effects ; *Microbiota/drug effects ; Soil Microbiology ; High-Throughput Nucleotide Sequencing ; }, abstract = {Heavy metal (HM) contaminants are the emerging driving force for reshaping the microflora of plants by eradicating the non-tolerance and non-resistant microbes via their lethal effects. Seeds served as a prime source of ancestral microbial diversity hereditary transfer from generation to generation. However, the problem arises when they got exposed to metal contamination, does metal pollutant disrupt the delicate balance of microbial communities within seeds and lead to shifts in their microflora across generations. In this study, the endophytic community within Zea mays seeds was compared across three distinct regions in Yunnan province, China: a HM-contaminated site Ayika (AK), less-contaminated site Sanduoduo (SD), and a non-contaminated Site Dali (DL). High-throughput sequencing techniques were employed to analyze the microbial communities. A total of 492,177 high-quality reads for bacterial communities and 1,001,229 optimized sequences for fungal communities were obtained. These sequences were assigned to 502 and 239 operational taxonomic units (OTUs) for bacteria and fungi, respectively. A higher diversity was recorded in AK samples than in SD and DL. Microbial community structure analysis showed higher diversity and significant fluctuation in specific taxa abundance in the metal-polluted samples exhibiting higher response of microbial flora to HM. In AK samples, bacterial genera such as Gordonia and Burkholderia-Caballeronia-Paraburkholderia were dominant, while in SD Pseudomonas and Streptomyces were dominant. Among the fungal taxa, Fusarium, Saccharomycopsis, and Lecanicillium were prevalent in HM-contaminated sites. Our finding revealed the influential effect of HM contaminants on reshaping the seed microbiome of the Zea mays, showing both the resilience of certain important microbial taxa as well the shifts in the diversity in the contaminated and pristine conditions. The knowledge will benefit to develop effective soil remediation, reclamation, and crop management techniques, and eventually assisting in the extenuation of metal pollution's adverse effects on plant health and agricultural productivity.}, }
@article {pmid39460615, year = {2024}, author = {Wen, J and Zhang, H and Chu, D and Chen, X and Feng, J and Wang, Y and Liu, G and Zhang, Y and Li, Y and Ning, K}, title = {Deep learning revealed the distribution and evolution patterns for invertible promoters across bacterial lineages.}, journal = {Nucleic acids research}, volume = {52}, number = {21}, pages = {12817-12830}, pmid = {39460615}, issn = {1362-4962}, support = {32071465//National Natural Science Foundation of China/ ; 2023YFA1800900//National Key Research and Development Program of China/ ; }, mesh = {*Promoter Regions, Genetic ; *Deep Learning ; *Bacteria/genetics/classification ; *Genome, Bacterial ; *Phylogeny ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Metagenome/genetics ; Biofilms ; }, abstract = {Invertible promoters (invertons) are crucial regulatory elements in bacteria, facilitating gene expression changes under stress. Despite their importance, their prevalence and the range of regulated gene functions are largely unknown. We introduced DeepInverton, a deep learning model that identifies invertons across a broad phylogenetic spectrum without using sequencing reads. By analyzing 68 733 bacterial genomes and 9382 metagenomes, we have uncovered over 200 000 nonredundant invertons and have also highlighted their abundance in pathogens. Additionally, we identified a post-Cambrian Explosion increase of invertons, paralleling species diversification. Furthermore, we revealed that invertons regulate diverse functions, including antimicrobial resistance and biofilm formation, underscoring their role in environmental adaptation. Notably, the majority of inverton identifications by DeepInverton have been confirmed by the in vitro experiments. The comprehensive inverton profiles have deepened our understanding of invertons at pan-genome and pan-metagenome scales, enabling a broad spectrum of applications in microbial ecology and synthetic biology.}, }
@article {pmid39454273, year = {2025}, author = {Xun, F and Feng, M and Zhao, C and Luo, W and Han, X and Ci, Z and Yin, Y and Wang, R and Wu, QL and Grossart, HP and Xing, P}, title = {Epilimnetic oligotrophication increases contribution of oxic methane production to atmospheric methane flux from stratified lakes.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122602}, doi = {10.1016/j.watres.2024.122602}, pmid = {39454273}, issn = {1879-2448}, mesh = {*Methane/metabolism ; *Lakes/microbiology ; Atmosphere ; Phosphorus/metabolism ; }, abstract = {Although considerable attention has been paid to the effects of eutrophication on aquatic methane (CH4) emissions to the atmosphere, the ecosystem-level effects of oligotrophication/re-oligotrophication on aquatic CH4 production and subsequent ecological responses remain to be elucidated. It has been hypothesized that dissolved inorganic phosphorus (DIP)-deficient conditions drive the ecosystem to utilize poorly bioavailable organic phosphorus for biomass formation, thereby generating CH4 as a by-product. To test this hypothesis, a mass balance approach was used to estimate in situ oxic methane production (OMP) in an oligotrophic, deep Lake Fuxian. The isotopic signature of dissolved [13]C-CH4, the potential substrates for OMP, and the phnJ/phnD genes associated with microbial demethylation of organic phosphorus compounds were analyzed. Our results indicate that CH4 accumulation was maximal in the surface mixed layer (SML, i.e., Epilimnion) during lake stratification, and ∼ 86 % of the total CH4 flux to the atmosphere was due to OMP. Decomposition of methylphosphonate (MPn) by Alphaproteobacteria (genera Sphingomonas and Mesorhizobium) contributed significantly to OMP. Furthermore, water temperature (Temp), chlorophyll a (Chla), and DIP were the most critical predictors of water OMP potential. Meta-analysis of currently available global data showed that OMP had a negative exponential distribution with DIP (OMP = 2.0 e[-0.71DIP], R[2] = 0.57, p < 0.05). DIP concentrations below a threshold of 3.40 ∼ 9.35 μg P L[-1] triggered OMP processes and increased the atmospheric CH4 emissions. Under future warming scenarios, stratification and catchment management induced oligotrophication or re-oligotrophication may systematically affect the biogeochemical cycling of phosphorus and the OMP contribution to CH4 emission in stratified lakes.}, }
@article {pmid39452361, year = {2024}, author = {Kiewra, D and Dyczko, D and Žákovská, A and Nejezchlebova, H}, title = {Prevalence of Borrelia and Rickettsia in Ixodes ricinus from Chosen Urban and Protected Areas in Poland and the Czech Republic.}, journal = {Insects}, volume = {15}, number = {10}, pages = {}, pmid = {39452361}, issn = {2075-4450}, abstract = {(1) Background: Ixodes ricinus is responsible for the spreading of medically important pathogens. Monitoring the level of tick infection in various areas is essential for determining the potential tick-born risk. This study aimed to detect Borrelia spp. and Rickettsia spp. in I. ricinus ticks collected in urban and protected areas both in Poland and the Czech Republic. (2) Methods: Ticks were collected by flagging in the years 2016-2017. Borrelia spp. was detected using nested PCR targeting the flaB gene and Rickettsia spp. using nested PCR targeting gltA. (3) Results: In total, DNA of Borrelia spp. was detected in 25.9% of samples. Ticks collected in Poland were more infected compared to the Czech Republic and ticks collected in protected areas were more infected with Borrelia spp. than ticks collected in urban areas. The RFLP analysis showed the occurrence of B. afzelii and B. garinii in both countries, and additionally B. valaisiana, B. burgdorferi s.s., and B. miyamotoi in Poland. Rickettsia spp. was detected in 17.4% of I. ricinus, with comparable infection level in both countries; however, regional differences were observed. (4) Conclusion: The regional differences in Borrelia spp. and Rickettsia spp. prevalence in I. ricinus indicate the complexity of factors influencing the level of infection and underline the need for adaptation public health surveillance strategies in each region.}, }
@article {pmid39450335, year = {2024}, author = {Hodžić, A and Veinović, G and Alić, A and Seki, D and Kunert, M and Nikolov, G and Sukara, R and Šupić, J and Tomanović, S and Berry, D}, title = {A metalloprotease secreted by an environmentally acquired gut bacterium hinders Borrelia afzelii colonization in Ixodes ricinus.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1476266}, pmid = {39450335}, issn = {2235-2988}, mesh = {*Ixodes/microbiology ; Animals ; *Borrelia burgdorferi Group/genetics/metabolism ; *Gastrointestinal Microbiome ; *Metalloproteases/metabolism ; Bacillus cereus/enzymology/metabolism/genetics ; Lyme Disease/microbiology ; Bacterial Proteins/metabolism/genetics ; }, abstract = {Although the importance of the microbiome in the context of tick biology and vector competence has recently come into a broader research focus, the field is still in its infancy and the complex ecological interactions between the tick residential bacteria and pathogens are obscure. Here, we show that an environmentally acquired gut bacterium has the potential to impair Borrelia afzelii colonization within the tick vector through a secreted metalloprotease. Oral introduction of either Bacillus cereus LTG-1 isolate or its purified enhancin (BcEnhancin) protein significantly reduces B. afzelii burden in the guts of Ixodes ricinus ticks. This effect is attributed to the ability of BcEnhancin to degrade a glycan-rich peritrophic matrix (PM), which is a gut protective barrier essential for Borrelia survival. Our study highlights the importance of the gut microbiome in determining tick vector competence and provides a deeper mechanistic insight into the complex network of interactions between Borrelia, the tick, and the tick microbiome.}, }
@article {pmid39450162, year = {2024}, author = {Nenciarini, S and Rivero, D and Ciccione, A and Amoriello, R and Cerasuolo, B and Pallecchi, M and Bartolucci, GL and Ballerini, C and Cavalieri, D}, title = {Impact of cooperative or competitive dynamics between the yeast Saccharomyces cerevisiae and lactobacilli on the immune response of the host.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1399842}, pmid = {39450162}, issn = {1664-3224}, mesh = {Humans ; *Saccharomyces cerevisiae/immunology ; *Gastrointestinal Microbiome/immunology ; *Lactobacillus/immunology ; Probiotics ; Animals ; Microbial Interactions/immunology ; Dysbiosis/immunology ; }, abstract = {Fungi and bacteria can be found coexisting in a wide variety of environments. The combination of their physical and molecular interactions can result in a broad range of outcomes for each partner, from competition to cooperative relationships. Most of these interactions can also be found in the human gastrointestinal tract. The gut microbiota is essential for humans, helping the assimilation of food components as well as the prevention of pathogen invasions through host immune system modulation and the production of beneficial metabolites such as short-chain fatty acids (SCFAs). Several factors, including changes in diet habits due to the progressive Westernization of the lifestyle, are linked to the onset of dysbiosis statuses that impair the correct balance of the gut environment. It is therefore crucial to explore the interactions between commensal and diet-derived microorganisms and their influence on host health. Investigating these interactions through co-cultures between human- and fermented food-derived lactobacilli and yeasts led us to understand how the strains' growth yield and their metabolic products rely on the nature and concentration of the species involved, producing either cooperative or competitive dynamics. Moreover, single cultures of yeasts and lactobacilli proved to be ideal candidates for developing immune-enhancing products, given their ability to induce trained immunity in blood-derived human monocytes in vitro. Conversely, co-cultures as well as mixtures of yeasts and lactobacilli have been shown to induce an anti-inflammatory response on the same immune cells in terms of cytokine profiles and activation surface markers, opening new possibilities in the design of probiotic and dietary therapies.}, }
@article {pmid39449043, year = {2024}, author = {Zhai, X and Gobbi, A and Kot, W and Krych, L and Nielsen, DS and Deng, L}, title = {A single-stranded based library preparation method for virome characterization.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {219}, pmid = {39449043}, issn = {2049-2618}, mesh = {*Virome/genetics ; *Genome, Viral/genetics ; *Gastrointestinal Microbiome/genetics ; *Gene Library ; Humans ; DNA, Viral/genetics ; DNA, Single-Stranded/genetics ; High-Throughput Nucleotide Sequencing/methods ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: The gut virome is an integral component of the gut microbiome, playing a crucial role in maintaining gut health. However, accurately depicting the entire gut virome is challenging due to the inherent diversity of genome types (dsDNA, ssDNA, dsRNA, and ssRNA) and topologies (linear, circular, or fragments), with subsequently biases associated with current sequencing library preparation methods. To overcome these problems and improve reproducibility and comparability across studies, universal or standardized virome sequencing library construction methods are highly needed in the gut virome study.<br><br>RESULTS: We repurposed the ligation-based single-stranded library (SSLR) preparation method for virome studies. We demonstrate that the SSLR method exhibits exceptional efficiency in quantifying viral DNA genomes (both dsDNA and ssDNA) and outperforms existing double-stranded (Nextera) and single-stranded (xGen, MDA&#x2009;+&#x2009;Nextera) library preparation approaches in terms of minimal amplification bias, evenness of coverage, and integrity of assembling viral genomes. The SSLR method can be utilized for the simultaneous library preparation of both DNA and RNA viral genomes. Furthermore, the SSLR method showed its ability to capture highly modified phage genomes, which were often lost using other library preparation approaches.<br><br>CONCLUSION: We introduce and improve a fast, simple, and efficient ligation-based single-stranded DNA library preparation for gut virome study. This method is compatible with Illumina sequencing platforms and only requires ligation reagents within 3-h library preparation, which is similar or even better than the advanced library preparation method (xGen). We hope this method can be further optimized, validated, and widely used to make gut virome study more comparable and reproducible. Video Abstract.}, }
@article {pmid39448159, year = {2025}, author = {Diaz, M and Aird, H and Le Viet, T and Gutiérrez, AV and Larke-Mejia, N and Omelchenko, O and Moragues-Solanas, L and Fritscher, J and Som, N and McLauchlin, J and Hildebrand, F and Jørgensen, F and Gilmour, M}, title = {Microbial composition and dynamics in environmental samples from a ready-to-eat food production facility with a long-term colonization of Listeria monocytogenes.}, journal = {Food microbiology}, volume = {125}, number = {}, pages = {104649}, doi = {10.1016/j.fm.2024.104649}, pmid = {39448159}, issn = {1095-9998}, mesh = {*Listeria monocytogenes/genetics/isolation &amp; purification/growth &amp; development/classification ; *Fast Foods/microbiology ; Food Microbiology ; Microbiota ; Bacteria/genetics/classification/isolation &amp; purification/growth &amp; development ; Environmental Microbiology ; Metagenomics ; Pseudomonas fluorescens/genetics/isolation &amp; purification/growth &amp; development/classification ; Food Contamination/analysis ; }, abstract = {Listeria monocytogenes is a foodborne pathogen of significant concern for the food industry due to its remarkable ability to persist through safety control efforts, posing a subsequent health threat to consumers. Understanding the microbial communities coexisting with L. monocytogenes in food processing environments provides insights into its persistence mechanisms. We investigated the microbial communities on non-food contact surfaces in a facility producing ready-to-eat foods, known to harbour a ST121 L. monocytogenes strain over multiple years. A 10-week sampling period was coordinated with the company and public health authorities. Metagenomic analysis revealed a stable microbial composition dominated by Pseudomonas fluorescens. While highly related populations were present in high-care production zones, distinctive taxa characteristic of specific areas were observed (e.g., Sphingomonas aerolata). Although Listeria spp. were not detected in metagenomes, they were detected in cultured samples, suggesting low relative abundance in factory settings. The findings suggest that a stable resident microbiota, with distinct adaptations to different areas within the factory, was selected for by their collective ability to survive control efforts in this environment. Listeria spp. was a member of this microbial community, albeit at low abundance, and may likewise benefit from the mutualism of the overall microbial community.}, }
@article {pmid39446706, year = {2024}, author = {Shinfuku, MS and Domeignoz-Horta, LA and Choudoir, MJ and Frey, SD and Mitchell, MF and Ranjan, R and DeAngelis, KM}, title = {Seasonal effects of long-term warming on ecosystem function and bacterial diversity.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0311364}, pmid = {39446706}, issn = {1932-6203}, mesh = {*Seasons ; *Soil Microbiology ; *Biodiversity ; *Bacteria/classification/genetics ; *Ecosystem ; *Climate Change ; Soil/chemistry ; Global Warming ; }, abstract = {Across biomes, soil biodiversity promotes ecosystem functions. However, whether this relationship will be maintained within ecosystems under climate change is uncertain. Here, using two long-term soil warming experiments, we investigated how warming affects the relationship between ecosystem functions and bacterial diversity across seasons, soil horizons, and warming duration. Soils were sampled from these warming experiments located at the Harvard Forest Long-Term Ecological Research (LTER) site, where soils had been heated +5°C above ambient for 13 or 28 years at the time of sampling. We assessed seven measurements representative of different ecosystem functions and nutrient pools. We also surveyed bacterial community diversity. We found that ecosystem function was significantly affected by season, with autumn samples having a higher intercept than summer samples in our model, suggesting a higher overall baseline of ecosystem function in the fall. The effect of warming on bacterial diversity was similarly affected by season, where warming in the summer was associated with decreased bacterial evenness in the organic horizon. Despite the decreased bacterial evenness in the warmed plots, we found that the relationship between ecosystem function and bacterial diversity was unaffected by warming or warming duration. Our findings highlight that season is a consistent driver of ecosystem function as well as a modulator of climate change effects on bacterial community evenness.}, }
@article {pmid39445507, year = {2024}, author = {Liu, L and Zhang, X and Schorn, S and Doda, T and Kang, M and Bouffard, D and Kirillin, G and Milucka, J and Shi, X and Grossart, HP}, title = {Strong Subseasonal Variability of Oxic Methane Production Challenges Methane Budgeting in Freshwater Lakes.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {44}, pages = {19690-19701}, doi = {10.1021/acs.est.4c07413}, pmid = {39445507}, issn = {1520-5851}, mesh = {*Methane ; *Lakes ; Seasons ; Environmental Monitoring ; Fresh Water ; }, abstract = {Methane (CH4) accumulation in the well-oxygenated lake epilimnion enhances the diffusive atmospheric CH4 emission. Both lateral transport and in situ oxic methane production (OMP) have been suggested as potential sources. While the latter has been recently supported by increasing evidence, quantifying the exact contribution of OMP to atmospheric emissions remains challenging. Based on a large high-resolution field data set collected during 2019-2020 in the deep stratified Lake Stechlin and on three-dimensional hydrodynamic modeling, we improved existing CH4 budgets by resolving each component of the mass balance model at a seasonal scale and therefore better constrained the residual OMP. All terms in our model showed a large temporal variability at scales from intraday to seasonal, and the modeled OMP was most sensitive to the surface CH4 flux estimates. Future efforts are needed to reduce the uncertainties in estimating OMP rates using the mass balance approach by increasing the frequency of atmospheric CH4 flux measurements.}, }
@article {pmid39442306, year = {2024}, author = {Wen, X and Xiang, L and Harindintwali, JD and Wang, Y and He, C and Fu, Y and Wei, S and Hashsham, SA and Jiang, J and Jiang, X and Wang, F}, title = {Mitigating risks from atrazine drift to soybeans through foliar pre-spraying with a degrading bacterium.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136224}, doi = {10.1016/j.jhazmat.2024.136224}, pmid = {39442306}, issn = {1873-3336}, mesh = {*Atrazine/toxicity/metabolism ; *Glycine max/metabolism/drug effects/growth &amp; development/microbiology ; *Herbicides/toxicity/metabolism ; *Plant Leaves/metabolism/drug effects ; *Biodegradation, Environmental ; Soil Pollutants/toxicity/metabolism ; Chlorophyll/metabolism ; }, abstract = {Herbicides play a crucial role in managing weeds in agriculture, ensuring the productivity and quality of crops. However, herbicide drift poses a significant threat to sensitive plants, necessitating the consideration of ecosystem-based solutions to address this issue. In this study, foliar pre-spraying of atrazine-degrading Paenarthrobacter sp. AT5 was proposed as a new approach to mitigate the risks associated with atrazine drift on soybeans. Exposure to atrazine reduced chlorophyll levels and disturbed the antioxidant system and metabolic processes in soybean leaves, ultimately causing leaves to turn yellow. However, by pre-spraying, strain AT5 successfully colonized the surface of soybean leaves and mitigated the harmful effects of atrazine. This was achieved by slowing down atrazine absorption, expediting its reduction (half-life decreased from 2.22 d to 0.86 d), altering its degradation pathway (enhancing hydroxylation while weakening alkylation), and enhancing the interaction within phyllosphere bacteria communities. This study introduces a new approach that is both eco-friendly and user-friendly for reducing the risks of herbicide drift to sensitive crops, hence promoting the development of mixed cropping.}, }
@article {pmid39440978, year = {2024}, author = {Soto Ocaña, J and Friedman, ES and Keenan, O and Bayard, NU and Ford, E and Tanes, C and Munneke, MJ and Beavers, WN and Skaar, EP and Bittinger, K and Zemel, BS and Wu, GD and Zackular, JP}, title = {Metal availability shapes early life microbial ecology and community succession.}, journal = {mBio}, volume = {15}, number = {11}, pages = {e0153424}, pmid = {39440978}, issn = {2150-7511}, support = {R01DK107565, P30DK050306//HHS | National Institutes of Health (NIH)/ ; R35GM138369//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; UL1 TR001878/TR/NCATS NIH HHS/United States ; R01DK107565//HHS | National Institutes of Health (NIH)/ ; P30 DK050306/DK/NIDDK NIH HHS/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; R01 DK107565/DK/NIDDK NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Metals/metabolism ; *Leukocyte L1 Antigen Complex/metabolism/analysis ; Bacteria/metabolism/classification/genetics ; Breast Feeding ; Feces/microbiology ; Gastrointestinal Tract/microbiology ; Infant, Newborn ; Microbiota ; Infant Formula ; }, abstract = {The gut microbiota plays a critical role in human health and disease. Microbial community assembly and succession early in life are influenced by numerous factors. In turn, assembly of this microbial community is known to influence the host, including immune system development, and has been linked to outcomes later in life. To date, the role of host-mediated nutritional immunity and metal availability in shaping microbial community assembly and succession early in life has not been explored in depth. Using a human infant cohort, we show that the metal-chelating protein calprotectin is highly abundant in infants. Taxa previously shown to be successful early colonizers of the infant gut, such as Enterococcus, Enterobacteriaceae, and Bacteroides, are highly resistant to experimental metal starvation in culture. Lactobacillus, meanwhile, is highly susceptible to metal restriction, pointing to a possible mechanism by which host-mediated metal limitation shapes the fitness of early colonizing taxa in the infant gut. We further demonstrate that formula-fed infants harbor markedly higher levels of metals in their gastrointestinal tract compared to breastfed infants. Formula-fed infants with high levels of metals harbor distinct microbial communities compared to breastfed infants, with higher levels of Enterococcus, Enterobacter, and Klebsiella, taxa which show increased resistance to the toxic effects of high metal concentrations. These data highlight a new paradigm in microbial community assembly and suggest an unappreciated role for nutritional immunity and dietary metals in shaping the earliest colonization events of the microbiota.IMPORTANCEEarly life represents a critical window for microbial colonization of the human gastrointestinal tract. Surprisingly, we still know little about the rules that govern the successful colonization of infants and the factors that shape the success of early life microbial colonizers. In this study, we report that metal availability is an important factor in the assembly and succession of the early life microbiota. We show that the host-derived metal-chelating protein, calprotectin, is highly abundant in infants and successful early life colonizers can overcome metal restriction. We further demonstrate that feeding modality (breastmilk vs formula) markedly impacts metal levels in the gut, potentially influencing microbial community succession. Our work suggests that metals, a previously unexplored aspect of early life ecology, may play a critical role in shaping the early events of microbiota assembly in infants.}, }
@article {pmid39440963, year = {2024}, author = {Wang, Y and Sun, Y and Huang, K and Gao, Y and Lin, Y and Yuan, B and Wang, X and Xu, G and Nussio, LG and Yang, F and Ni, K}, title = {Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0068224}, pmid = {39440963}, issn = {2379-5077}, support = {32171686//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Medicago sativa/microbiology/metabolism ; *Silage/microbiology ; *Fermentation ; *Microbiota/genetics ; Animals ; Biomarkers/metabolism ; Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Cattle ; Multiomics ; }, abstract = {UNLABELLED: Alfalfa (Medicago sativa L.) is one of the most extensively cultivated forage crops globally, and its nutritional quality critically influences the productivity of dairy cows. Silage fermentation is recognized as a crucial technique for the preservation of fresh forage, ensuring the retention of its vital nutrients. However, the detailed microbial components and their functions in silage fermentation are not fully understood. This study integrated large-scale microbial culturing with high-throughput sequencing to thoroughly examine the microbial community structure in alfalfa silage and explored the potential pathways of nutritional degradation via metagenomic analysis. The findings revealed an enriched microbial diversity in silage, indicated by the identification of amplicon sequence variants. Significantly, the large-scale culturing approach recovered a considerable number of unique microbes undetectable by high-throughput sequencing. Predominant genera, such as Lactiplantibacillus, Leuconostoc, Lentilactobacillus, Weissella, and Liquorilactobacillus, were identified based on their abundance and prevalence. Additionally, genes associated with Enterobacteriaceae were discovered, which might be involved in pathways leading to the production of ammonia-N and butyric acid. Overall, this study offers a comprehensive insight into the microbial ecology of silage fermentation and provides valuable information for leveraging microbial consortia to enhance fermentation quality.<br><br>IMPORTANCE: Silage fermentation is a microbial-driven anaerobic process that efficiently converts various substrates into nutrients readily absorbable and metabolizable by ruminant animals. This study, integrating culturomics and metagenomics, has successfully identified core microorganisms involved in silage fermentation, including those at low abundance. This discovery is crucial for the targeted cultivation of specific microorganisms to optimize fermentation processes. Furthermore, our research has uncovered signature microorganisms that play pivotal roles in nutrient metabolism, significantly advancing our understanding of the intricate relationships between microbial communities and nutrient degradation during silage fermentation.}, }
@article {pmid39437908, year = {2024}, author = {Yang, X and Chen, N and Yu, H and Liu, X and Feng, Y and Xing, D and Tian, Y}, title = {Applying machine learning and genetic algorithms accelerated for optimizing ethanol production.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {177027}, doi = {10.1016/j.scitotenv.2024.177027}, pmid = {39437908}, issn = {1879-1026}, mesh = {*Ethanol/metabolism ; *Machine Learning ; *Algorithms ; Zea mays ; Fermentation ; Neural Networks, Computer ; Biofuels ; }, abstract = {Corn straws can produce bioethanol via simultaneous saccharification and co-fermentation (SSCF). However, identifying optimal combinations of operating parameters from numerous possibilities through a cost-effective strategy to improve SSCF efficiency and yield remains challenging. The eXtreme Gradient Boost (XGB) and deep neural network (DNN) models were constructed to accurately predict ethanol yield from only five input variables, achieving >83 % accuracy. Subsequently, the XGB and the DNN models were merged with the genetic algorithm (GA) as the new optimization strategies. Experimental validation showed that the new strategy optimize the efficiency and yield of the SSCF ethanol production system quickly and accurately. Moreover, the potential optimization mechanism was investigated through the comprehensive interpretability analysis for XGB and the microbial ecology analysis. Enzyme Solution Volume (61.7 %) dominated, followed by time (12.9 %), substrate concentration (10.4 %), temperature (7.7 %), and inoculum volume (7.3 %). This efficient and accurate algorithm design strategy can significantly reduce the time required to optimize biochemical systems.}, }
@article {pmid39436938, year = {2024}, author = {Rocha, U and Kasmanas, JC and Toscan, R and Sanches, DS and Magnusdottir, S and Saraiva, JP}, title = {Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery.}, journal = {PLoS computational biology}, volume = {20}, number = {10}, pages = {e1012530}, pmid = {39436938}, issn = {1553-7358}, mesh = {*Metagenome/genetics ; *Microbiota/genetics ; *Computer Simulation ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Bacteria/genetics/classification ; Genome, Bacterial/genetics ; }, abstract = {We hypothesize that sample species abundance, sequencing depth, and taxonomic relatedness influence the recovery of metagenome-assembled genomes (MAGs). To test this hypothesis, we assessed MAG recovery in three in silico microbial communities composed of 42 species with the same richness but different sample species abundance, sequencing depth, and taxonomic distribution profiles using three different pipelines for MAG recovery. The pipeline developed by Parks and colleagues (8K) generated the highest number of MAGs and the lowest number of true positives per community profile. The pipeline by Karst and colleagues (DT) showed the most accurate results (~ 92%), outperforming the 8K and Multi-Metagenome pipeline (MM) developed by Albertsen and collaborators. Sequencing depth influenced the accurate recovery of genomes when using the 8K and MM, even with contrasting patterns: the MM pipeline recovered more MAGs found in the original communities when employing sequencing depths up to 60 million reads, while the 8K recovered more true positives in communities sequenced above 60 million reads. DT showed the best species recovery from the same genus, even though close-related species have a low recovery rate in all pipelines. Our results highlight that more bins do not translate to the actual community composition and that sequencing depth plays a role in MAG recovery and increased community resolution. Even low MAG recovery error rates can significantly impact biological inferences. Our data indicates that the scientific community should curate their findings from MAG recovery, especially when asserting novel species or metabolic traits.}, }
@article {pmid39436933, year = {2024}, author = {Di Nezio, F and Ong, ILH and Riedel, R and Goshal, A and Dhar, J and Roman, S and Storelli, N and Sengupta, A}, title = {Synergistic phenotypic adaptations of motile purple sulphur bacteria Chromatium okenii during lake-to-laboratory domestication.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0310265}, pmid = {39436933}, issn = {1932-6203}, mesh = {*Lakes/microbiology ; *Phenotype ; *Adaptation, Physiological ; Chromatiaceae/physiology ; Microscopy, Atomic Force ; }, abstract = {Isolating microorganisms from natural environments for cultivation under optimized laboratory settings has markedly improved our understanding of microbial ecology. Artificial growth conditions often diverge from those in natural ecosystems, forcing wild isolates into distinct selective pressures, resulting in diverse eco-physiological adaptations mediated by modification of key phenotypic traits. For motile microorganisms we still lack a biophysical understanding of the relevant traits emerging during domestication and their mechanistic interplay driving short-to-long-term microbial adaptation under laboratory conditions. Using microfluidics, atomic force microscopy, quantitative imaging, and mathematical modeling, we study phenotypic adaptation of Chromatium okenii, a motile phototrophic purple sulfur bacterium from meromictic Lake Cadagno, grown under laboratory conditions over multiple generations. Our results indicate that naturally planktonic C. okenii leverage shifts in cell-surface adhesive interactions, synergistically with changes in cell morphology, mass density, and distribution of intracellular sulfur globules, to suppress their swimming traits, ultimately switching to a sessile lifeform. A computational model of cell mechanics confirms the role of such phenotypic shifts in suppressing the planktonic lifeform. By investigating key phenotypic traits across different physiological stages of lab-grown C. okenii, we uncover a progressive loss of motility during the early stages of domestication, followed by concomitant deflagellation and enhanced surface attachment, ultimately driving the transition of motile sulfur bacteria to a sessile state. Our results establish a mechanistic link between suppression of motility and surface attachment via phenotypic changes, underscoring the emergence of adaptive fitness under laboratory conditions at the expense of traits tailored for natural environments.}, }
@article {pmid39436423, year = {2024}, author = {Hirota, A and Kouduka, M and Fukuda, A and Miyakawa, K and Sakuma, K and Ozaki, Y and Ishii, E and Suzuki, Y}, title = {Biofilm Formation on Excavation Damaged Zone Fractures in Deep Neogene Sedimentary Rock.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {132}, pmid = {39436423}, issn = {1432-184X}, mesh = {*Biofilms/growth &amp; development ; *RNA, Ribosomal, 16S/genetics ; *Geologic Sediments/microbiology ; Phylogeny ; Groundwater/microbiology ; Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Gammaproteobacteria/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; }, abstract = {Deep underground galleries are used to access the deep biosphere in addition to mining and other engineering applications, such as geological disposal of radioactive waste. Fracture networks developed in the excavation damaged zone (EDZ) are concerned with accelerating mass transport, where microbial colonization might be possible due to the availability of space and nutrients. In this study, microbial biofilms at EDZ fractures were investigated by drilling from a 350-m-deep gallery and subsequent borehole logging at the Horonobe Underground Research Laboratory (URL). By using microscopic and spectroscopic techniques, the dense colonization of microbial cells was demonstrated at the surfaces of the EDZ fractures with high hydraulic conductivity. 16S rRNA gene sequence analysis revealed the dominance of gammaproteobacterial lineages, the cultivated members of which are aerobic methanotrophs. The near-complete genomes from Horonobe groundwater, affiliated with the methanotrophic lineages, were fully equipped with genes involved in aerobic methanotrophy. Although the mediation of aerobic methanotrophy remains to be demonstrated, microbial O2 production was supported by the presence of genes in the near-complete genomes, such as catalase and superoxide dismutase that produce O2 from reactive oxygen species and a nitric oxide reductase gene with the substitutions of amino acids in motifs. It is concluded that the EDZ fractures provide energetically favorable subsurface habitats for microorganisms.}, }
@article {pmid39435521, year = {2024}, author = {Muratore, TJ and Knorr, MA and Simpson, MJ and Stephens, RB and Phillips, RP and Frey, SD}, title = {Response of Root Respiration to Warming and Nitrogen Addition Depends on Tree Species.}, journal = {Global change biology}, volume = {30}, number = {10}, pages = {e17530}, doi = {10.1111/gcb.17530}, pmid = {39435521}, issn = {1365-2486}, support = {DEB-1456610//National Science Foundation/ ; DEB-1832110//National Science Foundation/ ; 2106096//National Science Foundation/ ; Hatch NH-00701//New Hampshire Agricultural Experiment Station/ ; //Natural Sciences and Engineering Research Council (NSERC) of Canada/ ; }, mesh = {*Plant Roots/metabolism/growth &amp; development ; *Nitrogen/metabolism ; *Acer/physiology/metabolism/growth &amp; development ; *Quercus/physiology/metabolism ; Soil/chemistry ; Global Warming ; Biomass ; Carbon Dioxide/metabolism ; Trees/growth &amp; development/metabolism/physiology ; }, abstract = {Roots contribute a large fraction of CO2 efflux from soils, yet the extent to which global change factors affect root-derived fluxes is poorly understood. We investigated how red maple (Acer rubrum) and red oak (Quercus rubra) root biomass and respiration respond to long-term (15 years) soil warming, nitrogen addition, or their combination in a temperate forest. We found that ecosystem root respiration was decreased by 40% under both single-factor treatments (nitrogen addition or warming) but not under their combination (heated × nitrogen). This response was driven by the reduction of mass-specific root respiration under warming and a reduction in maple root biomass in both single-factor treatments. Mass-specific root respiration rates for both species acclimated to soil warming, resulting in a 43% reduction, but were not affected by N addition or the combined heated × N treatment. Notably, the addition of nitrogen to warmed soils alleviated thermal acclimation and returned mass-specific respiration rates to control levels. Oak roots contributed disproportionately to ecosystem root respiration despite the decrease in respiration rates as their biomass was maintained or enhanced under warming and nitrogen addition. In contrast, maple root respiration rates were consistently higher than oak, and this difference became critical in the heated × nitrogen treatment, where maple root biomass increased, contributing significantly more CO2 relative to single-factor treatments. Our findings highlight the importance of accounting for the root component of respiration when assessing soil carbon loss in response to global change and demonstrate that combining warming and N addition produces effects that cannot be predicted by studying these factors in isolation.}, }
@article {pmid39435438, year = {2024}, author = {Michalska-Smith, M and Schlatter, DC and Pombubpa, N and Castle, SC and Grandy, AS and Borer, ET and Seabloom, EW and Kinkel, LL}, title = {Plant community richness and foliar fungicides impact soil Streptomyces inhibition, resistance, and resource use phenotypes.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1452534}, pmid = {39435438}, issn = {1664-302X}, abstract = {Plants serve as critical links between above- and below-ground microbial communitites, both influencing and being influenced by microbes in these two realms. Below-ground microbial communities are expected to respond to soil resource environments, which are mediated by the roots of plants that can, in turn, be influenced by the above-ground community of foliar endophytes. For instance, diverse plant communities deposit more, and more diverse, nutrients into the soil, and this deposition is often increased when foliar pathogens are removed. Differences in soil resources can alter soil microbial composition and phenotypes, including inhibitory capacity, resource use, and antibiotic resistance. In this work, we consider plots differing in plant richness and application of foliar fungicide, evaluating consequences on soil resource levels and root-associated Streptomyces phenotypes. Soil carbon, nitrogen, phosphorus, potassium, and organic matter were greater in samples from polyculture than monoculture, yet this increase was surprisingly offset when foliar fungal communities were disrupted. We find that Streptomyces phenotypes varied more between richness plots-with the Streptomyces from polyculture showing lower inhibitory capacity, altered resource-use profiles, and greater antibiotic resistance-than between subplots with/without foliar fungicide. Where foliar fungicide affected phenotypes, it did so differently in polyculture than in monoculture, for instance decreasing niche width and overlap in monoculture while increasing them in polyculture. No differences in phenotype were correlated with soil nutrient levels, suggesting the need for further research looking more closely at soil resource diversity and particular compounds that were found to differ between treatments.}, }
@article {pmid39435044, year = {2024}, author = {Gruseck, R and Palatinszky, M and Wagner, M and Hofmann, T and Zumstein, M}, title = {Quantification of guanidine in environmental samples using benzoin derivatization and LC-MS analysis.}, journal = {MethodsX}, volume = {13}, number = {}, pages = {102972}, pmid = {39435044}, issn = {2215-0161}, abstract = {The recent discovery of guanidine-dependent riboswitches in many microbes raised interest in the biological function and metabolism of this nitrogen-rich compound. However, very little is known about the concentrations of guanidine in the environment. Several methods have been published for quantifying guanidine and guanidino compounds in human urine and blood, often relying on derivatization followed by fluorescence detection. We adapted this analytical approach using benzoin as the derivatization agent to sensitively and selectively quantify guanidine in environmental samples, thereby facilitating future research on the biological and environmental roles of guanidine. This adapted method was applied to human urine, raw wastewater, and biological growth media as relevant matrices. Our liquid chromatography-tandem mass spectrometry analyses of the derivatized solutions identified a different major derivatization product than previously reported. This product was consistently observed across various substrates (guanidine, methylguanidine, and arginine) and derivatization agents (benzoin and anisoin). We observed a constant background signal, restricting our analyses to a lower limit of quantification of 50 nM. Despite this limitation, our method allowed for the quantification of guanidine concentrations significantly lower than those reported in previous derivatization-based studies.•Selective and sensitive detection of guanidine by LC-MS.•Method development and validation for robust detection of guanidine in environmental samples.•Reduction of sample preparation steps and reduced usage of toxic chemicals compared to previous methods.}, }
@article {pmid39432984, year = {2024}, author = {Sun, Y and Wang, N and Zhong, X and Xu, G}, title = {Can microplastics variability drive the colonization dynamics of periphytic protozoan fauna in marine environments?.}, journal = {Marine pollution bulletin}, volume = {209}, number = {Pt A}, pages = {117148}, doi = {10.1016/j.marpolbul.2024.117148}, pmid = {39432984}, issn = {1879-3363}, mesh = {*Microplastics ; *Water Pollutants, Chemical/analysis ; *Environmental Monitoring ; Biodiversity ; Animals ; Aquatic Organisms ; }, abstract = {In recent years, microplastics have become a global environmental hot topic of concern. To explore the effects of different concentrations of microplastics on colonization dynamics of periphytic protozoan fauna, a 21-day study was conducted in temperature-controlled circulation systems. Periphytic protozoan communities were used as test organisms and exposed to five concentrations of MPs: 0, 1, 5, 25, and 125 mg l[-1], identification and enumeration were conducted on days 3, 5, 7, 10, 14 and 21. The results showed that the colonization dynamics were driven by MPs and significantly shifted at concentrations over 5 mg l[-1]. However, a notable decline in maximum species richness and abundance was observed in the high concentrations of microplastic, along with significant deviations in colonization patterns from the control group (0 mg l[-1]). Therefore, it is suggested that the colonization dynamics of periphytic protozoa can serve as a bioindicator for assessing microplastic concentrations in marine environments.}, }
@article {pmid39432094, year = {2024}, author = {Shafana Farveen, M and Narayanan, R}, title = {Omic-driven strategies to unveil microbiome potential for biodegradation of plastics: a review.}, journal = {Archives of microbiology}, volume = {206}, number = {11}, pages = {441}, pmid = {39432094}, issn = {1432-072X}, mesh = {*Biodegradation, Environmental ; *Plastics/metabolism ; *Microbiota ; Bacteria/metabolism/genetics/classification ; Proteomics ; Genomics ; Microbial Consortia ; }, abstract = {Plastic waste accumulation has lately been identified as the leading and pervasive environmental concern, harming all living beings, natural habitats, and the global market. Given this issue, developing ecologically friendly solutions, such as biodegradation instead of standard disposal, is critical. To effectively address and develop better strategies, it is critical to understand the inter-relationship between microorganisms and plastic, the role of genes and enzymes involved in this process. However, the complex nature of microbial communities and the diverse mechanisms involved in plastic biodegradation have hindered the development of efficient plastic waste degradation strategies. Omics-driven approaches, encompassing genomics, transcriptomics and proteomics have revolutionized our understanding of microbial ecology and biotechnology. Therefore, this review explores the application of omics technologies in plastic degradation studies and discusses the key findings, challenges, and future prospects of omics-based approaches in identifying novel plastic-degrading microorganisms, enzymes, and metabolic pathways. The integration of omics technologies with advanced molecular technologies such as the recombinant DNA technology and synthetic biology would guide in the optimization of microbial consortia and engineering the microbial systems for enhanced plastic biodegradation under various environmental conditions.}, }
@article {pmid39431865, year = {2024}, author = {Daly, SE and Feng, J and Daeschel, D and Kovac, J and Snyder, AB}, title = {The choice of 16S rRNA gene sequence analysis impacted characterization of highly variable surface microbiota in dairy processing environments.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0062024}, pmid = {39431865}, issn = {2379-5077}, support = {2022-67017-36289//U.S. Department of Agriculture (USDA)/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics/classification ; Food Microbiology ; Food Handling ; Dairying ; Dairy Products/microbiology ; }, abstract = {Accurate knowledge of the microbiota collected from surfaces in food processing environments is important for food quality and safety. This study assessed discrepancies in taxonomic composition and alpha and beta diversity values generated from eight different bioinformatic workflows for the analysis of 16S rRNA gene sequences extracted from the microbiota collected from surfaces in dairy processing environments. We found that the microbiota collected from environmental surfaces varied widely in density (0-9.09 log10 CFU/cm[2]) and Shannon alpha diversity (0.01-3.40). Consequently, depending on the sequence analysis method used, characterization of low-abundance genera (i.e., below 1% relative abundance) and the number of genera identified (114-173 genera) varied considerably. Some low-abundance genera, including Listeria, varied between the amplicon sequence variant (ASV) and operational taxonomic unit (OTU) methods. Centered log-ratio transformation inflated alpha and beta diversity values compared to rarefaction. Furthermore, the ASV method also inflated alpha and beta diversity values compared to the OTU method (P < 0.05). Therefore, for sparse, uneven, low-density data sets, the OTU method and rarefaction are better for taxonomic and ecological characterization of surface microbiota.IMPORTANCECulture-dependent environmental monitoring programs are used by the food industry to identify foodborne pathogens and spoilage biota on surfaces in food processing environments. The use of culture-independent 16S rRNA amplicon sequencing to characterize this surface microbiota has been proposed as a tool to enhance environmental monitoring. However, there is no consensus on the most suitable bioinformatic analyses to accurately capture the diverse levels and types of bacteria on surfaces in food processing environments. Here, we quantify the impact of different bioinformatic analyses on the results and interpretation of 16S rRNA amplicon sequences collected from three cultured dairy facilities in New York State. This study provides guidance for the selection of appropriate 16S rRNA analysis procedures for studying environmental microbiota in dairy processing environments.}, }
@article {pmid39430784, year = {2024}, author = {Li, X and Wang, Q and Wu, F and Ye, Z and Li, Y}, title = {Association between advanced lung cancer inflammation index and chronic kidney disease: a cross-sectional study.}, journal = {Frontiers in nutrition}, volume = {11}, number = {}, pages = {1430471}, pmid = {39430784}, issn = {2296-861X}, abstract = {BACKGROUND: Chronic kidney disease (CKD) is one of the common chronic diseases, and malnutrition and inflammation play a key role in the development of CKD. The advanced lung cancer inflammation index (ALI) is a novel index of nutrition and inflammation, and its association with CKD has not yet been clarified. The aim of this study was to explore the potential association between ALI and CKD.<br><br>METHODS: We conducted a cross-sectional survey using data extracted from the National Health and Nutrition Examination Survey (NHANES, 2003-2018). Weighted multivariate logistic regression was used to assess the association between ALI and CKD, and smoothed curve fitting and threshold effect analyses were used to describe the nonlinear association between ALI and CKD. Subgroup analyses were performed to further assess the influence of other covariates on the relationship between ALI and CKD.<br><br>RESULTS: A total of 39,469 adult participants were included in the study, of whom 7,204 (18.25%) were diagnosed with CKD. After adjusting for multiple confounders, we found a significant negative correlation between ALI and CKD (OR&#x2009;=&#x2009;0.93; 95%CI, 0.91-0.95; p&#x2009;<&#x2009;0.0001). The risk of CKD tended to decrease with increasing quartiles of ALI. Smoothed curve fitting showed an L-shaped negative correlation between ALI and CKD. Threshold analysis showed a saturation effect of ALI at the inflection point of 55.09. Subgroup analyses and interaction tests showed that this negative association was maintained across age, sex, race, BMI, diabetes, hypertension, cardiovascular disease, and cancer subgroups (P for interaction >0.05).<br><br>CONCLUSION: Our findings suggest a significant correlation between ALI and CKD in the US adult population. However, more large-scale prospective studies are still needed to further confirm our findings.}, }
@article {pmid39430052, year = {2025}, author = {Qin, K and Wang, Q and Qing, J and Li, Y and Gong, H and Zha, Z and Zhou, B and Li, Y}, title = {Analysis of mutations in Chinese patients with polycystic kidney disease by targeted exome sequencing.}, journal = {Genes &amp; diseases}, volume = {12}, number = {1}, pages = {101246}, pmid = {39430052}, issn = {2352-3042}, }
@article {pmid39425011, year = {2024}, author = {Sánchez, V and Baumann, A and Kromm, F and Yergaliyev, T and Brandt, A and Scholda, J and Kopp, F and Camarinha-Silva, A and Bergheim, I}, title = {Oral supplementation of choline attenuates the development of alcohol-related liver disease (ALD).}, journal = {Molecular medicine (Cambridge, Mass.)}, volume = {30}, number = {1}, pages = {181}, pmid = {39425011}, issn = {1528-3658}, mesh = {Animals ; *Choline/administration &amp; dosage/metabolism ; *Liver Diseases, Alcoholic/metabolism/etiology/prevention &amp; control/pathology/drug therapy ; *Dietary Supplements ; Mice ; Female ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Liver/metabolism/drug effects/pathology ; Administration, Oral ; Permeability ; Ethanol/adverse effects ; Disease Models, Animal ; }, abstract = {BACKGROUND: Chronic alcohol intake is associated with alterations of choline metabolism in various tissues. Here, we assessed if an oral choline supplementation attenuated the development of alcohol-related liver disease (ALD) in mice.<br><br>METHODS: Female C57BL/6&#xa0;J mice (n&#x2009;=&#x2009;8/group) were either pair-fed a liquid control diet, or a Lieber DeCarli liquid diet (5% ethanol)&#x2009;&#xb1;&#x2009;2.7&#xa0;g choline/kg diet for 29&#xa0;days. Liver damage, markers of intestinal permeability and intestinal microbiota composition were determined. Moreover, the effects of choline on ethanol-induced intestinal permeability were assessed in an ex vivo model.<br><br>RESULTS: ALD development as determined by liver histology and assessing markers of inflammation (e.g., nitric oxide, interleukin 6 and 4-hydroxynonenal protein adducts) was attenuated by the supplementation of choline. Intestinal permeability in small intestine being significantly higher in ethanol-fed mice was at the level of controls in ethanol-fed mice receiving choline. In contrast, no effects of the choline supplementation were found on intestinal microbiota composition. Choline also significantly attenuated the ethanol-induced intestinal barrier dysfunction in small intestinal tissue ex vivo, an effect almost entirely abolished by the choline oxidase inhibitor dimbunol.<br><br>CONCLUSION: Our results suggest that an oral choline supplementation attenuates the development of ALD in mice and is related to a protection from intestinal barrier dysfunction.}, }
@article {pmid39423562, year = {2024}, author = {Dal Bello, M and Abreu, CI}, title = {Temperature structuring of microbial communities on a global scale.}, journal = {Current opinion in microbiology}, volume = {82}, number = {}, pages = {102558}, pmid = {39423562}, issn = {1879-0364}, support = {F32 GM145148/GM/NIGMS NIH HHS/United States ; }, mesh = {*Temperature ; *Microbiota ; *Bacteria/metabolism/genetics/classification/growth &amp; development ; Bacterial Physiological Phenomena ; Ecosystem ; }, abstract = {Temperature is a fundamental physical constraint regulating key aspects of microbial life. Protein binding, membrane fluidity, central dogma processes, and metabolism are all tightly controlled by temperature, such that growth rate profiles across taxa and environments follow the same general curve. An open question in microbial ecology is how the effects of temperature on individual traits scale up to determine community structure and function at planetary scales. Here, we review recent theoretical and experimental efforts to connect physiological responses to the outcome of species interactions, the assembly of microbial communities, and their function as temperature changes. We identify open questions in the field and define a roadmap for future studies.}, }
@article {pmid39423289, year = {2024}, author = {Steensen, K and Séneca, J and Bartlau, N and Yu, XA and Hussain, FA and Polz, MF}, title = {Tailless and filamentous prophages are predominant in marine Vibrio.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39423289}, issn = {1751-7370}, support = {//Life Science Compute Cluster of the University of Vienna/ ; 572792//Simons Foundation/ ; //Austrian Science Fund/ ; }, mesh = {*Prophages/genetics/isolation &amp; purification ; *Vibrio/virology/genetics ; *Genome, Viral ; Phylogeny ; Genomics ; }, abstract = {Although tailed bacteriophages (phages) of the class Caudoviricetes are thought to constitute the most abundant and ecologically relevant group of phages that can integrate their genome into the host chromosome, it is becoming increasingly clear that other prophages are widespread. Here, we show that prophages derived from filamentous and tailless phages with genome sizes below 16 kb make up the majority of prophages in marine bacteria of the genus Vibrio. To estimate prophage prevalence unaffected by database biases, we combined comparative genomics and chemical induction of 58 diverse Vibrio cyclitrophicus isolates, resulting in 107 well-curated prophages. Complemented with computationally predicted prophages, we obtained 1158 prophages from 931 naturally co-existing strains of the family Vibrionaceae. Prophages resembling tailless and filamentous phages predominated, accounting for 80% of all prophages in V. cyclitrophicus and 60% across the Vibrionaceae. In our experimental model, prophages of all three viral realms actively replicated upon induction indicating their ability to transfer to new hosts. Indeed, prophages were rapidly gained and lost, as suggested by variable prophage content between closely related V. cyclitrophicus. Prophages related to filamentous and tailless phages were integrated into only three genomic locations and restored the function of their integration site. Despite their small size, they contained highly diverse accessory genes that may contribute to host fitness, such as phage defense systems. We propose that, like their well-studied tailed equivalent, tailless and filamentous temperate phages are active and highly abundant drivers of host ecology and evolution in marine Vibrio, which have been largely overlooked.}, }
@article {pmid39419992, year = {2024}, author = {Mei, S and Wang, M and Salles, JF and Hackl, T}, title = {Diverse rhizosphere-associated Pseudomonas genomes from along a Wadden Island salt marsh transition zone.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1140}, pmid = {39419992}, issn = {2052-4463}, support = {[2020]596//China Scholarship Council (CSC)/ ; }, mesh = {*Rhizosphere ; *Pseudomonas/genetics ; *Soil Microbiology ; *Wetlands ; *Genome, Bacterial ; Artemisia/genetics/microbiology ; Biodiversity ; }, abstract = {Soil microbes are key drivers of ecosystem processes promoting nutrient cycling, system productivity, and resilience. While much is known about the roles of microbes in established systems, their impact on soil development and the successional transformation over time remains poorly understood. Here, we provide 67 diverse, rhizosphere-associated Pseudomonas draft genomes from an undisturbed salt march primary succession spanning >100 years of soil development. Pseudomonas are cosmopolitan bacteria with a significant role in plant establishment and growth. We obtained isolates associated with Limonium vulgare and Artemisia maritima, two typical salt marsh perennial plants with roles in soil stabilization, salinity regulation, and biodiversity support. We anticipate that our data, in combination with the provided physiochemical measurements, will help identify genomic signatures associated with the different selective regimes along the successional stages, such as varying soil complexity, texture, and nutrient availability. Such findings would advance our understanding of Pseudomonas' role in natural soil ecosystems and provide the basis for a better understanding of the roles of microbes throughout ecosystem transformations.}, }
@article {pmid39419884, year = {2024}, author = {Mohammed, FA and Abu-Hussien, SH and Dougdoug, NKE and Koutb, N and Korayem, AS}, title = {Streptomyces fradiae Mitigates the Impact of Potato Virus Y by Inducing Systemic Resistance in Two Egyptian Potato (Solanum tuberosum L.) Cultivars.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {131}, pmid = {39419884}, issn = {1432-184X}, mesh = {*Solanum tuberosum/virology/microbiology ; *Streptomyces/isolation &amp; purification/physiology/genetics ; *Potyvirus/physiology ; *Plant Diseases/virology/microbiology ; *Disease Resistance ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In this study, the impact of culture media filtrate of QD3 actinobacterial isolate on two potato cultivars, Spunta and Diamond, infected with potato virus Y (PVY) was investigated. Various parameters, including infection percentage, PVY virus infectivity, disease severity scoring, PVY optical density, photosynthetic and defense-related biochemical markers, enzymatic profiling, phenolic compounds, proline content, salicylic acid levels, and growth and yield parameters, were assessed to elucidate the potential of the QD3 actinobacterial isolate culture filtrate in mitigating PVY-induced damage. The physiological and biochemical characteristics of the QD3 actinobacterial isolate, including its salinity tolerance, pH preferences, and metabolic traits, were investigated. Molecular identification via 16S rRNA gene sequencing confirmed its classification as Streptomyces fradiae QD3, and it was deposited in GenBank with the gene accession number MN160630. Distinct responses between Spunta and Diamond cultivars, with Spunta displaying greater resistance to PVY infection. Notably, pre-infection foliar application of the QD3 filtrate significantly reduced disease symptoms and virus infection in both cultivars. For post-PVY infection, the QD3 filtrate effectively mitigated disease severity and the PVY optical density. Furthermore, the QD3 filtrate positively influenced photosynthetic pigments, enzymatic antioxidant activities, and key biochemical components associated with plant defense mechanisms. Gas chromatography‒mass spectrometry (GC‒MS) analysis revealed palmitic acid (hexadecanoic acid, methyl ester) and oleic acid (9-octadecanoic acid, methyl ester) as the most prominent compounds, with retention times of 23.23 min and 26.41 min, representing 53.27% and 23.25%, respectively, of the total peak area as primary unsaturated fatty acids and demonstrating antiviral effects against plant viruses. Cytotoxicity assays on normal human skin fibroblasts (HSFs) revealed the safety of QD3 metabolites, with low discernible toxicity at high concentrations, reinforcing their potential as safe and effective interventions. The phytotoxicity results indicate that all the seeds presented high germination rates of approximately 95-98%, suggesting that the treatment conditions had no phytotoxic effect on the Brassica oleracea (broccoli) seeds, Lactuca sativa (lettuce) seeds, and Eruca sativa (arugula or rocket) seeds. Overall, the results of this study suggest that the S. fradiae filtrate has promising anti-PVY properties, influencing various physiological, biochemical, and molecular aspects in potato cultivars. These findings provide valuable insights into potential strategies for managing PVY infections in potato crops, emphasizing the importance of Streptomyces-derived interventions in enhancing plant health and crop protection.}, }
@article {pmid39419230, year = {2024}, author = {Siebert, C and Ionescu, D and Mallast, U and Merchel, S and Merkel, B and Möller, P and Pavetich, S and Pohl, T and Rödiger, T and Yechieli, Y}, title = {A new type of submarine chimneys built of halite.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {176752}, doi = {10.1016/j.scitotenv.2024.176752}, pmid = {39419230}, issn = {1879-1026}, abstract = {In contrast to the subaquatic sulphide and carbonate chimneys, which are known from Mid Ocean Ridges and abyssal submarine volcanoes, chimneys built of salts have not been described yet. Here we present such halite chimneys as a new form of cold-water smokers in hypersaline environments. The here described structures rise up from the bottom of the Dead Sea and result from the submarine discharge of saturated halite-dissolution brines into the salt lake, which is at halite saturation and holds remarkable chloride excess. At the interface with the lake brine, halite precipitates instantaneously, forming chimneys up to several meters in height. The brines leading to the formation of these chimneys vary in composition, while their generation processes are similar. Fresh groundwater from surrounding aquifers enters the saline lake sediments and considerably leaches halite in the adjacencies of the lake. Simultaneously, it mixes with ancient brines before it emerges from the lake floor. The distinct differences in composition between the Dead Sea and the emerging chimney brines lead to the instantaneous crystallisation of halite and few other mineral phases. The chimney structure result from the buoyancy flow of the chimney brines, which are less dense then the ambient Dead Sea. The chimneys indicate intense cavitation of massive halite bodies in the subsurface of the Dead Sea environment, a process that leads to increasing formation of hazardous sinkholes. Since chimneys are proven in shallow water but may be expected in deeper parts too, they are comfortably mappable by echo-sounding or aerial imaging. They thus provide in the Dead Sea as in any likewise setting a potent predictive tool to locate dangerous subsurface cavitation and hence areas that are at risk of collapse in the near future.}, }
@article {pmid39419211, year = {2024}, author = {Santos-Silva, L and Roque, WF and de Moura, JM and Mello, IS and de Carvalho, LAL and Pinheiro, DG and Bouzan, RS and Brescovit, AD and de Andrade, RLT and da Silva, GF and Battirola, LD and Soares, MA}, title = {Toxic metals in Amazonian soil modify the bacterial community associated with Diplopoda.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {176915}, doi = {10.1016/j.scitotenv.2024.176915}, pmid = {39419211}, issn = {1879-1026}, mesh = {*Soil Pollutants/toxicity ; Animals ; *Bacteria/drug effects/classification ; *Microbiota/drug effects ; Arthropods/drug effects ; Soil Microbiology ; Cadmium/toxicity ; Brazil ; Mercury/toxicity/metabolism ; Soil/chemistry ; Environmental Monitoring ; Rainforest ; }, abstract = {Toxic metal pollution in the Amazon is a serious problem that reduces the quality of water, soil, air, and consequently alters communities of fauna, flora, and microbiota, harming human health and well-being. Our aim was to determine the impact of toxic metals on the structure of the bacterial community associated with Diplopoda in the Amazon rainforest. Animals were kept in microcosms contaminated with cadmium (50 mg.kg[-1]), mercury (35 mg.kg[-1]) and no toxic metal (control). The intestinal and molting chamber microbiota were accessed by culture-dependent and culture-independent methods (16S metabarcoding). The cultivated strains were identified, and their functional traits evaluated: secretion of enzymes, growth at different pH, resistance to metals and antibiotics, and ability to reduce toxic effects of metals on plants. Our research described Brachyurodesmus albus, a new species of Diplopoda. We obtained 177 isolates distributed in 35 genera and 61 species of bacteria (Pseudomonadota, Bacillota, Bacteroidota and Actinomycetota) associated with the gut and molting chamber of B. albus. Metabarcoding data provided a more robust access to the bacterial community, resulting in 24 phyla, 561 genera and 6792 ASVs. The presence of metal Cd and Hg alters the composition and abundance of bacteria associated with B. albus (PERMANOVA p < 0.05). The microhabitat (gut and molting chamber) harbours bacterial communities that differ in composition and abundance (PERMANOVA p < 0.05). The presence of Cd and Hg alters important metabolic pathways related to the prokaryotic defense system; antimicrobial resistance genes, endocytosis and secretion system, estimated by PICRUSt. Bacteria selected with high resistance to Cd and Hg buffer the toxic effect of metals on tomato seedlings. This work describes B. albus and concludes that its diverse bacterial microbiota is altered by soil contamination by toxic metals, as well as being an important repository for prospecting strains to be applied in bioremediation programs.}, }
@article {pmid39419002, year = {2024}, author = {Meroz, N and Livny, T and Toledano, G and Sorokin, Y and Tovi, N and Friedman, J}, title = {Evolution in microbial microcosms is highly parallel, regardless of the presence of interacting species.}, journal = {Cell systems}, volume = {15}, number = {10}, pages = {930-940.e5}, doi = {10.1016/j.cels.2024.09.007}, pmid = {39419002}, issn = {2405-4720}, mesh = {*Biological Evolution ; Microbial Interactions/physiology ; Adaptation, Physiological ; Mutation ; Bacteria/genetics/metabolism ; Evolution, Molecular ; }, abstract = {Evolution often follows similar trajectories in replicate populations, suggesting that it may be predictable. However, populations are naturally embedded in multispecies communities, and the extent to which evolution is contingent on the specific species interacting with the focal population is still largely unexplored. Here, we study adaptations in strains of 11 different species, experimentally evolved both in isolation and in various pairwise co-cultures. Although partner-specific effects are detectable, evolution was mostly shared between strains evolved with different partners; similar changes occurred in strains' growth abilities, in community properties, and in about half of the repeatedly mutated genes. This pattern persisted even in species pre-adapted to the abiotic conditions. These findings indicate that evolution may not always depend strongly on the biotic environment, making predictions regarding coevolutionary dynamics less challenging than previously thought. A record of this paper's transparent peer review process is included in the supplemental information.}, }
@article {pmid39418776, year = {2024}, author = {Xie, Q and Sun, J and Sun, M and Wang, Q and Wang, M}, title = {Perturbed microbial ecology in neuromyelitis optica spectrum disorder: Evidence from the gut microbiome and fecal metabolome.}, journal = {Multiple sclerosis and related disorders}, volume = {92}, number = {}, pages = {105936}, doi = {10.1016/j.msard.2024.105936}, pmid = {39418776}, issn = {2211-0356}, mesh = {*Neuromyelitis Optica/microbiology/immunology ; Humans ; *Gastrointestinal Microbiome/physiology ; *Feces/microbiology ; Animals ; Female ; Adult ; *Fecal Microbiota Transplantation ; Mice ; Male ; Metabolome/physiology ; Middle Aged ; }, abstract = {BACKGROUND: Neuromyelitis optica spectrum disorder (NMOSD) is a central nervous system inflammatory demyelinating immune-mediated ailment, which is influenced by genetic, epigenetic, and environmental elements. The escalating incidence of NMOSD in recent years implies alterations in environmental risk factors. Recent research has established a correlation between gut microbiomes and the development of NMOSD.<br><br>METHODS: Metagenomic shotgun sequencing and gas chromatography-mass spectrometry (GC-MS) were employed to assess alterations of the structure and function in the fecal microbiome, as well as levels of short-chain fatty acids (SCFAs) in fecal and blood samples, among individuals with neuromyelitis optica spectrum disorder (NMOSD) during the acute phase (n = 25), the remission phase (n = 11), and a group of healthy controls (HCs) (n = 24). We further explored the correlation between gut microbiota and the pathogenesis of NMOSD through fecal microbiota transplantation (FMT). The gut microbiome from human donors diagnosed with NMOSD or HCs was transplanted into germ-free mice, followed by an analysis of the alterations in the structure and functionality of the transplanted mice's gut microbiome. Additionally, the impact of microbiome transfer on the immunity and spinal cord of germ-free mice was assessed through various techniques, including ELISA, flow cytometry, western blot, histopathology, and transcriptome sequencing.<br><br>RESULTS: (1) At the taxonomic levels of genus and species, there were significant differences in the &#x3b1;-diversity of the microbiome between HCs and NMOSD patients in the acute phase, with NMOSD patients having higher species diversity. (2) In the acute phase, the gut microbiota of NMOSD patients was characterized by Ruminococcaceae_unclassified, Campylobacter, Parabacteroides, Lactobacillus, Akkermansia, Streptococcus oralis, Clostridium leptum, Clostridium asparagiforme, Firmicutes bacterium CAG 238, and Lactobacillus fermentum. (3) The relative abundances of Coprobacter, Turicimonas, Gemmiger, Enterobacter, Roseburia sp.CAG 471, Veillonella tobetsuensis, Proteobacteria bacterium CAG 139, Ruminococcus bicirculans, Lactococcus lactis, Flavonifractor plautii, and Streptococcus cristatus were notably lower in patients experiencing remission compared to NMOSD patients in the acute phase, On the other hand, the relative abundances of Flavonifractor (P = 0.049) and Clostridium aldenense (P = 0.049) were significantly higher. Following medication, the gut microbiome distribution in NMOSD patients during remission closely resembled that of healthy controls (HCs). (4) Compared with HCs, acetate levels in the feces of patients with NMOSD in the acute phase were significantly lower. (5) In addition, we transplanted feces from NMOSD patients into germ-free mice and revealed a significant increase in the levels of IL-6, IL-17A, and IL-23 in the blood of mice belonging to the NMOSD fecal transplantation (NFMT) group. Additionally, the IL-10 level exhibited a significant reduction. Moreover, the proportion of Th17 cells displayed a significant increase, while the proportion of Treg cells exhibited a significant decrease in the spleens of NFMT mice.<br><br>CONCLUSION: Patients in the acute phase of neuromyelitis optica spectrum disorder (NMOSD) exhibited imbalances in their gut microbiota and a deficiency in short-chain fatty acids (SCFAs). Following drug treatment, the composition of intestinal microbes in NMOSD patients during the remission phase closely resembled that of the healthy control population. The FMT experiment provided evidence of the significant association between intestinal flora and the pathogenesis of NMOSD. Consequently, investigating gut microbiota and identifying novel microbial markers hold promise for the diagnosis and treatment of NMOSD patients.}, }
@article {pmid39418385, year = {2024}, author = {Lien, YW and Amendola, D and Lee, KS and Bartlau, N and Xu, J and Furusawa, G and Polz, MF and Stocker, R and Weiss, GL and Pilhofer, M}, title = {Mechanism of bacterial predation via ixotrophy.}, journal = {Science (New York, N.Y.)}, volume = {386}, number = {6719}, pages = {eadp0614}, doi = {10.1126/science.adp0614}, pmid = {39418385}, issn = {1095-9203}, mesh = {*Bacterial Adhesion ; *Bacteroidetes/physiology/ultrastructure ; Cryoelectron Microscopy ; Single-Cell Analysis ; *Type VI Secretion Systems/metabolism/ultrastructure ; *Vibrio/physiology/ultrastructure ; *Flagella/ultrastructure ; }, abstract = {Ixotrophy is a contact-dependent predatory strategy of filamentous bacteria in aquatic environments for which the molecular mechanism remains unknown. We show that predator-prey contact can be established by gliding motility or extracellular assemblages we call "grappling hooks." Cryo-electron microscopy identified the grappling hooks as heptamers of a type IX secretion system substrate. After close predator-prey contact is established, cryo-electron tomography and functional assays showed that puncturing by a type VI secretion system mediated killing. Single-cell analyses with stable isotope-labeled prey revealed that prey components are taken up by the attacker. Depending on nutrient availability, insertion sequence elements toggle the activity of ixotrophy. A marine metagenomic time series shows coupled dynamics of ixotrophic bacteria and prey. We found that the mechanism of ixotrophy involves multiple cellular machineries, is conserved, and may shape microbial populations in the environment.}, }
@article {pmid39417884, year = {2024}, author = {Mircea, C and Rusu, I and Levei, EA and Cristea, A and Gridan, IM and Zety, AV and Banciu, HL}, title = {The Fungal Side of the Story: Saprotrophic- vs. Symbiotrophic-Predicted Ecological Roles of Fungal Communities in Two Meromictic Hypersaline Lakes from Romania.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {130}, pmid = {39417884}, issn = {1432-184X}, support = {PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P1-1.1-PD-2021-0634//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; }, mesh = {*Lakes/microbiology ; Romania ; *Fungi/genetics/classification/isolation &amp; purification/physiology ; *Salinity ; *Mycobiome ; RNA, Ribosomal, 18S/genetics ; Biodiversity ; Geologic Sediments/microbiology ; Soil Microbiology ; DNA, Fungal/genetics ; Phylogeny ; }, abstract = {Over three-quarters of Earth's surface exhibits extreme environments where life thrives under harsh physicochemical conditions. While prokaryotes have often been investigated in these environments, only recent studies have revealed the remarkable adaptability of eukaryotes, in particular fungi. This study explored the mycobiota of two meromictic hypersaline lakes, Ursu and Fără Fund, in Transylvania (Romania). The intrinsic and extrinsic fungal diversity was assessed using amplicon sequencing of environmental DNA samples from sediments, water columns, surrounding soils, and an associated rivulet. The fungal communities, illustrated by the 18S rRNA gene and ITS2 region, exhibited contrasting patterns between the lakes. The ITS2 region assessed better than the 18S rRNA gene the fungal diversity. The ITS2 data showed that Ascomycota was the most abundant fungal group identified in both lakes, followed by Aphelidiomycota, Chytridiomycota, and Basidiomycota. Despite similar α-diversity levels, significant differences in fungal community structure were observed between the lakes, correlated with salinity, total organic carbon, total nitrogen, and ammonium. Taxonomic profiling revealed depth-specific variations, with Saccharomycetes prevalent in Ursu Lake's deeper layers and Lecanoromycetes prevalent in the Fără Fund Lake. The functional annotation using FungalTraits revealed diverse ecological roles within the fungal communities. Lichenized fungi were dominant in Fără Fund Lake, while saprotrophs were abundant in Ursu Lake. Additionally, wood and soil saprotrophs, along with plant pathogens, were more prevalent in the surrounding soils, rivulet, and surface water layers. A global overview of the trophic relations in each studied niche was impossible to establish due to the unconnected graphs corresponding to the trophic interactions of the analyzed fungi. Plotting the unweighted connected subgraphs at the genus level suggests that salinity made the studied niches similar for the identified taxa. This study shed light on the understudied fungal diversity, distribution, and ecological functions in hypersaline environments.}, }
@article {pmid39415203, year = {2024}, author = {Tong, X and Luo, D and Leung, MHY and Lee, JYY and Shen, Z and Jiang, W and Mason, CE and Lee, PKH}, title = {Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {198}, pmid = {39415203}, issn = {2049-2618}, support = {BK20230230//Jiangsu Science and Technology Programme/ ; 11214721//Hong Kong Research Grants Council, General Research Fund/ ; R1016-20F//Hong Kong Research Grants Council, Research Impact Fund/ ; }, mesh = {Humans ; Hong Kong ; *Microbiota ; *Built Environment ; *Metagenome ; *Phylogeny ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Skin/microbiology ; Micrococcus luteus/genetics/metabolism ; Genome, Bacterial ; }, abstract = {BACKGROUND: Built environments (BEs) are typically considered to be oligotrophic and harsh environments for microbial communities under normal, non-damp conditions. However, the metabolic functions of microbial inhabitants in BEs remain poorly understood. This study aimed to shed light on the functional capabilities of microbes in BEs by analyzing 860 representative metagenome-assembled genomes (rMAGs) reconstructed from 738 samples collected from BEs across the city of Hong Kong and from the skin surfaces of human occupants. The study specifically focused on the metabolic functions of rMAGs that are either phylogenetically novel or prevalent in BEs.<br><br>RESULTS: The diversity and composition of BE microbiomes were primarily shaped by the sample type, with Micrococcus luteus and Cutibacterium acnes being prevalent. The metabolic functions of rMAGs varied significantly based on taxonomy, even at the strain level. A novel strain affiliated with the Candidatus class Xenobia in the Candidatus phylum Eremiobacterota and two novel strains affiliated with the superphylum Patescibacteria exhibited unique functions compared with their close relatives, potentially aiding their survival in BEs and on human skins. The novel strains in the class Xenobia possessed genes for transporting nitrate and nitrite as nitrogen sources and nitrosative stress mitigation induced by nitric oxide during denitrification. The two novel Patescibacteria strains both possessed a broad array of genes for amino acid and trace element transport, while one of them carried genes for carotenoid and ubiquinone biosynthesis. The globally prevalent M. luteus in BEs displayed a large and open pangenome, with high infraspecific genomic diversity contributed by 11 conspecific strains recovered from BEs in a single geographic region. The versatile metabolic functions encoded in the large accessory genomes of M. luteus may contribute to its global ubiquity and specialization in BEs.<br><br>CONCLUSIONS: This study illustrates that the microbial inhabitants of BEs possess metabolic potentials that enable them to tolerate and counter different biotic and abiotic conditions. Additionally, these microbes can efficiently utilize various limited residual resources from occupant activities, potentially enhancing their survival and persistence within BEs. A better understanding of the metabolic functions of BE microbes will ultimately facilitate the development of strategies to create a healthy indoor microbiome. Video Abstract.}, }
@article {pmid39414684, year = {2024}, author = {Siqueira, JS and de Carvalho, LAL and Santos, CHB and Frezarin, ET and Pinheiro, DG and Nicodemo, D and Desoignies, N and Rigobelo, EC}, title = {Influence of Growth Support on the Diversity, Composition, and Functionality of Microbial Communities Associated with Tillandsia recurvata.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {129}, pmid = {39414684}, issn = {1432-184X}, mesh = {*Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Plant Roots/microbiology ; *Plant Leaves/microbiology ; Fungi/classification/genetics/isolation &amp; purification/physiology ; Biodiversity ; Trees/microbiology ; Soil Microbiology ; }, abstract = {Tillandsia recurvata is an epiphytic plant commonly found in tropical regions and colonizes tree trunks, fences, and power wires. This plant plays an important role in interacting with trees, sharing microorganisms, and performing specific functions in the process of tree colonization. The objective of this study was to evaluate and compare the microbiomes of T. recurvata collected from two different locations (trees and fences) and two plant tissues (leaves and roots). The hypothesis of this study was that the microbiome of T. recurvata is composed of microorganisms that would provide nutritional support to compensate for the lack of nutrients in a particular growth support. The results showed significant differences in microbial diversity between trees and fences, with trees exhibiting higher richness and more complex microbial networks. Proteobacteria was the most prevalent bacterial phylum, with Actinobacteria and Sphingomonas also playing key roles in nitrogen fixation and plant growth. Fungal communities were similar across locations, with Ascomycota and Basidiomycota being predominant, but Paraconiothyrium and Nigrospora showed significant differences in abundance between trees and fences. Functional analysis indicated similar metabolic profiles across leaf and root samples, with key functions for T. recurvata including carbohydrate and amino acid metabolism, stress control, and biofertilization.}, }
@article {pmid39411441, year = {2024}, author = {Pardo-Esté, C and Cortés, J and Castro-Severyn, J and Pérez, V and Henriquez-Aedo, K and Cuadros, F and Yañez, C and Cuadros-Orellana, S and Dorador, C and Molina, V and Eissler, Y and Paquis, P and Jeffrey, WH and Pozo, P and Pérez, PA and Hengst, MB}, title = {Secondary metabolites with antimicrobial activity produced by thermophilic bacteria from a high-altitude hydrothermal system.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1477458}, pmid = {39411441}, issn = {1664-302X}, abstract = {Thermophilic microorganisms possess several adaptations to thrive in high temperature, which is reflected as biosynthesis of proteins and thermostable molecules, isolation and culture represent a great methodological challenge, therefore High throughput sequencing enables screening of the whole bacterial genome for functional potential, providing rapid and cost-effective information to guide targeted cultures for the identification and characterization of novel natural products. In this study, we isolated two thermophilic bacterial strains corresponding to Bacillus LB7 and Streptomyces LB8, from the microbial mats in the Atacama Desert. By combining genome mining, targeted cultures and biochemical characterization, we aimed to identify their capacity to synthesize bioactive compounds with antimicrobial properties. Additionally, we determined the capability to produce bioactive compounds under controlled in vitro assays and detected by determining their masses by Thin-Layer Chromatography/Mass Spectrometry (TLC/MS). Overall, both isolates can produce antimicrobial (e.g., Myxalamide C by-product) and antioxidants (e.g. Dihydroxymandelic Acid, Amide biotine and Flavone by-products) compounds. Bacillus LB7 strain possesses a more diverse repertoire with 51.95% of total metabolites unmatched, while Streptomyces LB8 favors mainly antioxidants, but has over 70% of unclassified compounds, highlighting the necessity to study and elucidate the structure of novel compounds. Based on these results, we postulate that the uncultured or rare cultured thermophiles inhabiting high-altitude hydrothermal ecosystems in the Atacama Desert offer a promising opportunity to the study of novel microbial bioactive compounds.}, }
@article {pmid39411429, year = {2024}, author = {Xiao, P and Wu, Y and Zuo, J and Grossart, HP and Sun, R and Li, G and Jiang, H and Cheng, Y and Wang, Z and Geng, R and Zhang, H and Ma, Z and Yan, A and Li, R}, title = {Differential microbiome features in lake-river systems of Taihu basin in response to water flow disturbance.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1479158}, pmid = {39411429}, issn = {1664-302X}, abstract = {INTRODUCTION: In riverine ecosystems, dynamic interplay between hydrological conditions, such as flow rate, water level, and rainfall, significantly shape the structure and function of bacterial and microeukaryotic communities, with consequences for biogeochemical cycles and ecological stability. Lake Taihu, one of China's largest freshwater lakes, frequently experiences cyanobacterial blooms primarily driven by nutrient over-enrichment and hydrological changes, posing severe threats to water quality, aquatic life, and surrounding human populations. This study explored how varying water flow disturbances influence microbial diversity and community assembly within the interconnected river-lake systems of the East and South of Lake Taihu (ET&amp;ST). The Taipu River in the ET region accounts for nearly one-third of Lake Taihu's outflow, while the ST region includes the Changdougang and Xiaomeigang rivers, which act as inflow rivers. These two rivers not only channel water into Lake Taihu but can also cause the backflow of lake water into the rivers, creating distinct river-lake systems subjected to different intensities of water flow disturbances.<br><br>METHODS: Utilizing high-throughput sequencing, we selected 22 sampling sites in the ET and ST interconnected river-lake systems and conducted seasonally assessments of bacterial and microeukaryotic community dynamics. We then compared differences in microbial diversity, community assembly, and co-occurrence networks between the two regions under varying hydrological regimes.<br><br>RESULTS AND DISCUSSION: This study demonstrated that water flow intensity and temperature disturbances significantly influenced diversity, community structure, community assembly, ecological niches, and coexistence networks of bacterial and eukaryotic microbes. In the ET region, where water flow disturbances were stronger, microbial richness significantly increased, and phylogenetic relationships were closer, yet variations in community structure were greater than in the ST region, which experienced milder water flow disturbances. Additionally, migration and dispersal rates of microbes in the ET region, along with the impact of dispersal limitations, were significantly higher than in the ST region. High flow disturbances notably reduced microbial niche width and overlap, decreasing the complexity and stability of microbial coexistence networks. Moreover, path analysis indicated that microeukaryotic communities exhibited a stronger response to water flow disturbances than bacterial communities. Our findings underscore the critical need to consider the effects of hydrological disturbance on microbial diversity, community assembly, and coexistence networks when developing strategies to manage and protect river-lake ecosystems, particularly in efforts to control cyanobacterial blooms in Lake Taihu.}, }
@article {pmid39409485, year = {2024}, author = {Jechow, A and Bumberger, J and Palm, B and Remmler, P and Schreck, G and Ogashawara, I and Kiel, C and Kohnert, K and Grossart, HP and Singer, GA and Nejstgaard, JC and Wollrab, S and Berger, SA and Hölker, F}, title = {Characterizing and Implementing the Hamamatsu C12880MA Mini-Spectrometer for Near-Surface Reflectance Measurements of Inland Waters.}, journal = {Sensors (Basel, Switzerland)}, volume = {24}, number = {19}, pages = {}, pmid = {39409485}, issn = {1424-8220}, support = {Leibniz Competition No. K45/2017 (CONNECT-Connectivity and synchronization of lake ecosystems in space and time)//Leibniz Association/ ; IGB Frontiers project (2017)//Leibniz Institute of Freshwater Ecology and Inland Fisheries/ ; }, abstract = {In recent decades, inland water remote sensing has seen growing interest and very strong development. This includes improved spatial resolution, increased revisiting times, advanced multispectral sensors and recently even hyperspectral sensors. However, inland waters are more challenging than oceanic waters due to their higher complexity of optically active constituents and stronger adjacency effects due to their small size and nearby vegetation and built structures. Thus, bio-optical modeling of inland waters requires higher ground-truthing efforts. Large-scale ground-based sensor networks that are robust, self-sufficient, non-maintenance-intensive and low-cost could assist this otherwise labor-intensive task. Furthermore, most existing sensor systems are rather expensive, precluding their employability. Recently, low-cost mini-spectrometers have become widely available, which could potentially solve this issue. In this study, we analyze the characteristics of such a mini-spectrometer, the Hamamatsu C12880MA, and test it regarding its application in measuring water-leaving radiance near the surface. Overall, the measurements performed in the laboratory and in the field show that the system is very suitable for the targeted application.}, }
@article {pmid39406893, year = {2025}, author = {Ioannou, A and Berkhout, MD and Geerlings, SY and Belzer, C}, title = {Akkermansia muciniphila: biology, microbial ecology, host interactions and therapeutic potential.}, journal = {Nature reviews. Microbiology}, volume = {23}, number = {3}, pages = {162-177}, pmid = {39406893}, issn = {1740-1534}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Akkermansia/physiology/genetics/classification ; Probiotics/therapeutic use ; *Host Microbial Interactions ; *Verrucomicrobia/physiology/genetics/classification ; Animals ; Intestinal Mucosa/microbiology ; Phylogeny ; Mucins/metabolism ; }, abstract = {Akkermansia muciniphila is a gut bacterium that colonizes the gut mucosa, has a role in maintaining gut health and shows promise for potential therapeutic applications. The discovery of A. muciniphila as an important member of our gut microbiome, occupying an extraordinary niche in the human gut, has led to new hypotheses on gut health, beneficial microorganisms and host-microbiota interactions. This microorganism has established a unique position in human microbiome research, similar to its role in the gut ecosystem. Its unique traits in using mucin sugars and mechanisms of action that can modify host health have made A. muciniphila a subject of enormous attention from multiple research fields. A. muciniphila is becoming a model organism studied for its ability to modulate human health and gut microbiome structure, leading to commercial products, a genetic model and possible probiotic formulations. This Review provides an overview of A. muciniphila and Akkermansia genus phylogeny, ecophysiology and diversity. Furthermore, the Review discusses perspectives on ecology, strategies for harnessing beneficial effects of A. muciniphila for human mucosal metabolic and gut health, and its potential as a biomarker for diagnostics and prognostics.}, }
@article {pmid39406702, year = {2024}, author = {Wegner, H and Roitman, S and Kupczok, A and Braun, V and Woodhouse, JN and Grossart, HP and Zehner, S and Béjà, O and Frankenberg-Dinkel, N}, title = {Identification of Shemin pathway genes for tetrapyrrole biosynthesis in bacteriophage sequences from aquatic environments.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8783}, pmid = {39406702}, issn = {2041-1723}, support = {FR1487/16-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 143/18//Israel Science Foundation (ISF)/ ; }, mesh = {*Tetrapyrroles/biosynthesis/metabolism ; *Bacteriophages/genetics/metabolism ; Escherichia coli/genetics/virology/metabolism ; 5-Aminolevulinate Synthetase/genetics/metabolism ; Amino Acid Sequence ; Heme/metabolism/biosynthesis ; Aminolevulinic Acid/metabolism ; Phylogeny ; Fresh Water/virology ; Biosynthetic Pathways/genetics ; }, abstract = {Tetrapyrroles such as heme, chlorophyll, and vitamin B12 are essential for various metabolic pathways. They derive from 5-aminolevulinic acid (5-ALA), which can be synthesized by a single enzyme (5-ALA synthase or AlaS, Shemin pathway) or by a two-enzyme pathway. The genomes of some bacteriophages from aquatic environments carry various tetrapyrrole biosynthesis genes. Here, we analyze available metagenomic datasets and identify alaS homologs (viral alaS, or valaS) in sequences corresponding to marine and freshwater phages. The genes are found individually or as part of complete or truncated three-gene loci encoding heme-catabolizing enzymes. Amino-acid sequence alignments and three-dimensional structure prediction support that the valaS sequences likely encode functional enzymes. Indeed, we demonstrate that is the case for a freshwater phage valaS sequence, as it can complement an Escherichia coli 5-ALA auxotroph, and an E. coli strain overexpressing the gene converts the typical AlaS substrates glycine and succinyl-CoA into 5-ALA. Thus, our work identifies valaS as an auxiliary metabolic gene in phage sequences from aquatic environments, further supporting the importance of tetrapyrrole metabolism in bacteriophage biology.}, }
@article {pmid39404095, year = {2024}, author = {Leleiwi, I and Kokkinias, K and Kim, Y and Baniasad, M and Shaffer, M and Sabag-Daigle, A and Daly, RA and Flynn, RM and Wysocki, VH and Ahmer, BMM and Borton, MA and Wrighton, KC}, title = {Gut microbiota carbon and sulfur metabolisms support Salmonella infections.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39404095}, issn = {1751-7370}, support = {T32GM132057//NIH Predoctoral Training/ ; DE-SC0021350//DOE/ ; R01AI143288//NIH NIAID/ ; R01 AI143288/AI/NIAID NIH HHS/United States ; T32 GM132057/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Sulfur/metabolism ; *Carbon/metabolism ; *Salmonella typhimurium/genetics ; Feces/microbiology ; Mice, Inbred C57BL ; Salmonella Infections/microbiology ; Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Salmonella Infections, Animal/microbiology ; Female ; }, abstract = {Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome, we performed multi-omics on fecal microbial communities from untreated and Salmonella-infected mice. Reconstructed genomes recruited metatranscriptomic and metabolomic data providing a strain-resolved view of the expressed metabolisms of the microbiome during Salmonella infection. These data informed possible Salmonella interactions with members of the gut microbiome that were previously uncharacterized. Salmonella-induced inflammation significantly reduced the diversity of genomes that recruited transcripts in the gut microbiome, yet increased transcript mapping was observed for seven members, among which Luxibacter and Ligilactobacillus transcript read recruitment was most prevalent. Metatranscriptomic insights from Salmonella and other persistent taxa in the inflamed microbiome further expounded the necessity for oxidative tolerance mechanisms to endure the host inflammatory responses to infection. In the inflamed gut lactate was a key metabolite, with microbiota production and consumption reported amongst members with detected transcript recruitment. We also showed that organic sulfur sources could be converted by gut microbiota to yield inorganic sulfur pools that become oxidized in the inflamed gut, resulting in thiosulfate and tetrathionate that support Salmonella respiration. This research advances physiological microbiome insights beyond prior amplicon-based approaches, with the transcriptionally active organismal and metabolic pathways outlined here offering intriguing intervention targets in the Salmonella-infected intestine.}, }
@article {pmid39404077, year = {2024}, author = {Ellington, AJ and Walters, K and Christner, BC and Fox, S and Bonfantine, K and Walker, C and Lampman, P and Vuono, DC and Strickland, M and Lambert, K and Kobziar, LN}, title = {Dispersal of microbes from grassland fire smoke to soils.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39404077}, issn = {1751-7370}, support = {P20 GM103408/GM/NIGMS NIH HHS/United States ; 2039531//National Science Foundation/ ; P20GM103408//National Institute of General Medical Sciences of the National Institutes of Health/ ; }, mesh = {*Soil Microbiology ; *Smoke ; *Grassland ; *Soil/chemistry ; Bacteria/classification/isolation &amp; purification/radiation effects ; Microbiota ; Wildfires ; Fires ; Biomass ; Poaceae/microbiology ; Carbon/analysis/metabolism ; }, abstract = {Wildland fire is increasingly recognized as a driver of bioaerosol emissions, but the effects that smoke-emitted microbes have on the diversity and community assembly patterns of the habitats where they are deposited remain unknown. In this study, we examined whether microbes aerosolized by biomass burning smoke detectably impact the composition and function of soil sinks using lab-based mesocosm experiments. Soils either containing the native microbial community or presterilized by γ-irradiation were inundated with various doses of smoke from native tallgrass prairie grasses. Smoke-inundated, γ-irradiated soils exhibited significantly higher respiration rates than both smoke-inundated, native soils and γ-irradiated soils exposed to ambient air only. Microbial communities in γ-irradiated soils were significantly different between smoke-treated and control soils, which supports the hypothesis that wildland fire smoke can act as a dispersal agent. Community compositions differed based on smoke dose, incubation time, and soil type. Concentrations of phosphate and microbial biomass carbon and nitrogen together with pH were significant predictors of community composition. Source tracking analysis attributed smoke as contributing nearly 30% of the taxa found in smoke-inundated, γ-irradiated soils, suggesting smoke may play a role in the recovery of microbial communities in similar damaged soils. Our findings demonstrate that short-distance microbial dispersal by biomass burning smoke can influence the assembly processes of microbial communities in soils and has implications for a broad range of subjects including agriculture, restoration, plant disease, and biodiversity.}, }
@article {pmid39402079, year = {2024}, author = {Ashraf, H and Dikarlo, P and Masia, A and Zarbo, IR and Solla, P and Ijaz, UZ and Sechi, LA}, title = {Mycobacterium avium subspecies paratuberculosis (MAP) infection, and its impact on gut microbiome of individuals with multiple sclerosis.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {24027}, pmid = {39402079}, issn = {2045-2322}, support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Mycobacterium avium subsp. paratuberculosis/isolation &amp; purification ; *Paratuberculosis/microbiology ; *Multiple Sclerosis/microbiology ; Female ; Male ; *RNA, Ribosomal, 16S/genetics ; Adult ; Feces/microbiology ; Middle Aged ; }, abstract = {The microbial ecology of Mycobacterium avium subspecies paratuberculosis infections (MAP) within the context of Multiple Sclerosis (MS) is largely an unexplored topic in the literature. Thus, we have characterized the compositional and predicted functional differences of the gut microbiome between MS patients with MAP (MAP+) and without (MAP-) infection. This was done in the context of exposome differences (through self-reported filled questionnaires), principally in anthropometric and sociodemographic patterns to gain an understanding of the gut microbiome dynamics. 16S rRNA microbiome profiling of faecal samples (n = 69) was performed for four groups, which differed by disease and MAP infection: healthy cohort (HC) MAP-; HC MAP+ ; MS MAP-; and MS MAP+ . Using a dynamic strategy, with MAP infection and time of sampling as occupancy models, we have recovered the core microbiome for both HC and MS individuals. Additional application of neutral modeling suggests key genera that are under selection pressure by the hosts. These include members of the phyla Actinobacteriota, Bacteroidota, and Firmicutes. As several subjects provided multiple samples, a Quasi Conditional Association Test that incorporates paired-nature of samples found major differences in Archaea. To consolidate treatment groups, confounders, microbiome, and the disease outcome parameters, a mediation analysis is performed for MS cohort. This highlighted certain genera i.e., Sutterella, Akkermansia, Bacteriodes, Gastranaerophilales, Alistipes, Balutia, Faecalibacterium, Lachnospiraceae, Anaerostipes, Ruminococcaceae, Eggerthellaceae and Clostridia-UCG-014 having mediatory effect using disease duration as an outcome and MAP infection as a treatment group. Our analyses indicate that the gut microbiome may be an important target for dietary and lifestyle intervention in MS patients with and without MAP infection.}, }
@article {pmid39401449, year = {2024}, author = {Ahmerkamp, S and Pacherres, CO and Mosshammer, M and Godefroid, M and Wind-Hansen, M and Kuypers, M and Behrendt, L and Koren, K and Kühl, M}, title = {Novel Approach for Lifetime-Proportional Luminescence Imaging Using Frame Straddling.}, journal = {ACS sensors}, volume = {9}, number = {10}, pages = {5531-5540}, pmid = {39401449}, issn = {2379-3694}, mesh = {*Luminescent Measurements/methods ; Luminescence ; Oxygen/chemistry ; }, abstract = {Optode-based chemical imaging is a rapidly evolving field that has substantially enhanced our understanding of the role of microenvironments and chemical gradients in biogeochemistry, microbial ecology, and biomedical sciences. Progress in sensor chemistry has resulted in a broadened spectrum of analytes, alongside enhancements in sensor performance (e.g., sensitivity, brightness, and photostability). However, existing imaging techniques are often costly, challenging to implement, and limited in their recording speed. Here we use the "frame-straddling" technique, originally developed for particle image velocimetry for imaging the O2-dependent, integrated luminescence decay of optical O2 sensor materials. The method synchronizes short excitation pulses and camera exposures to capture two frames at varying brightness, where the first excitation pulse occurs at the end of the exposure of the first frame and the second excitation pulse at the beginning of the second frame. Here the first frame truncates the luminescence decay, whereas the second frame fully captures it. The difference between the frames quantifies the integral of the luminescence decay curve, which is proportional to the luminescence lifetime, at time scales below one millisecond. Short excitation pulses avoid depopulation of the ground state of luminophores, resulting in a linear Stern-Volmer response with increasing concentrations of the quencher (O2), which can be predicted through a simple model. This methodology is compatible with a wide range of camera systems, making it a versatile tool for various optode based chemical imaging applications. We showcase the utility of frame straddling in measuring O2 dynamics around algae and by observing O2 scavenging sodium dithionite particles sinking through oxygenated water.}, }
@article {pmid39399973, year = {2024}, author = {Simpson, A and Wood-Charlson, EM and Smith, M and Koch, BJ and Beilsmith, K and Kimbrel, JA and Kellom, M and Hunter, CI and Walls, RL and Schriml, LM and Wilhelm, RC}, title = {MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment.}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {39399973}, issn = {2047-217X}, support = {IND90024429//USDA/ ; //Purdue University/ ; //Lawrence Berkeley National Laboratory/ ; }, mesh = {*Isotope Labeling/methods ; Reproducibility of Results ; Microbiota/genetics ; Metadata ; Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; }, abstract = {DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields-isotope, isotopolog, isotopolog label, labeling approach, and gradient position-and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.}, }
@article {pmid39398475, year = {2024}, author = {Kumar, G and Bhadury, P}, title = {Dataset of metagenomic profiles of human gut microbiome from frozen fecal samples sequenced using Illumina and ONT chemistries.}, journal = {Data in brief}, volume = {57}, number = {}, pages = {110961}, pmid = {39398475}, issn = {2352-3409}, abstract = {The data presented in this study are metagenomic profiles of human gut microbiome deduced from frozen fecal samples using two different sequencing chemistries namely, Illumina and Oxford Nanopore Technologies (ONT). The generated data is obtained from genomic DNA extracted from frozen fecal samples collected from a healthy individual on Day 3, Day 5, Day 9, Day 12, and Day 30, in addition to Day 1 (unfrozen). The metagenomic sequence data have been deposited at NCBI SRA as BioProject PRJNA827663. The taxonomic annotation undertaken using MG-RAST showed relative abundance of bacteria represented by different taxonomic levels varied significantly based on two sequencing chemistries. There was distinct temporal variation in the relative abundance of bacteria at different taxonomic levels based on the day of extraction of genomic DNA. This dataset can be used to study differences in functional profiles of human gut microbiome using different sequencing technologies. Moreover, generated data can aid in selection of most appropriate sequencing chemistry to study future human gut microbiome studies based on the appropriate preservation method of fecal samples.}, }
@article {pmid39397203, year = {2024}, author = {Liu, K and Yan, Q and Guo, X and Wang, W and Zhang, Z and Ji, M and Wang, F and Liu, Y}, title = {Glacier Retreat Induces Contrasting Shifts in Bacterial Biodiversity Patterns in Glacial Lake Water and Sediment : Bacterial Communities in Glacial Lakes.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {128}, pmid = {39397203}, issn = {1432-184X}, support = {ANSO-CR-KP-2021-04//the Key Collaborative Research Program of the Alliance of International Science Organizations/ ; 42330410//National Natural Science Foundation of China/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program (STEP)/ ; }, mesh = {*Lakes/microbiology ; *Geologic Sediments/microbiology ; *Ice Cover/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Biodiversity ; Microbiota ; Ecosystem ; Tibet ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; }, abstract = {Glacial lake ecosystems are experiencing rapid changes due to accelerated glacier retreat. As glaciers recede, their influence on downstream habitats diminishes, potentially affecting the biodiversity of glacial lake microbial communities. However, there remains a knowledge gap regarding how bacterial biodiversity patterns in glacial lakes are altered by diminishing glacial influence. Here, we investigated shifts in bacterial communities in paired water and sediment samples collected from seven glacial lakes on the Tibetan Plateau, using a space-for-time substitution approach to understand the consequences of glacier retreat. Our findings reveal that bacterial diversity in lake water increases significantly with a higher glacier index (GI), whereas sediment bacterial diversity exhibits a negative correlation with GI. Both the water and sediment bacterial communities display significant structural shifts along the GI gradient. Notably, reduced glacial influence decreases the complexity of bacterial co-occurrence networks in lake water but enhances the network complexity in sediment. This divergence in diversity and co-occurrence patterns highlights that water and sediment bacterial communities respond differently to changes in glacial influence in these lake ecosystems. This study provides insights into how diminishing glacial influence impacts the bacterial biodiversity in glacial lake water and sediments, revealing contrasting patterns between the two habitats. These findings emphasize the need for comprehensive monitoring to understand the implications of glacier retreat on these fragile ecosystems.}, }
@article {pmid39388223, year = {2024}, author = {Alcaraz, CM and Séneca, J and Kunert, M and Pree, C and Sudo, M and Petersen, JM}, title = {Sulfur-oxidizing symbionts colonize the digestive tract of their lucinid hosts.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39388223}, issn = {1751-7370}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; *Symbiosis ; *Bivalvia/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Tract/microbiology ; *Gills/microbiology ; *Sulfur/metabolism ; *In Situ Hybridization, Fluorescence ; Oxidation-Reduction ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Phylogeny ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; }, abstract = {Like many marine invertebrates, marine lucinid clams have an intimate relationship with beneficial sulfur-oxidizing bacteria located within specialized gill cells known as bacteriocytes. Most previous research has focused on the symbionts in the gills of these (and other) symbiotic bivalves, often assuming that the symbionts only persistently colonize the gills, at least in the adult stage. We used 16S rRNA gene sequencing and digital polymerase chain reaction with symbiont-specific primers targeting the soxB gene on the foot, mantle, visceral mass, and gills of the lucinid clam Loripes orbiculatus. We also used fluorescence in situ hybridization with symbiont-specific probes to examine symbiont distribution at the level of the whole holobiont. Despite 40 years of research on these symbioses, we detected previously unknown populations of symbiont cells in several organs, including the digestive tract. As in the well-studied gills, symbionts in the digestive tract may be housed within host cells. A 14-month starvation experiment without hydrogen sulfide to power symbiont metabolism caused a larger reduction in symbiont numbers in the gills compared to the visceral mass, raising the possibility that symbionts in the digestive tract are persistent and may have a distinct physiology and role in the symbiosis compared with the gill symbionts. Our results highlight the unexpectedly complex relationships between marine lucinid clams and their symbionts and challenge the view that chemosynthetic symbionts are restricted to the gills of these hosts.}, }
@article {pmid39387587, year = {2024}, author = {Akob, DM and Oates, AE and Girguis, PR and Badgley, BD and Cooper, VS and Poretsky, RS and Tierney, BT and Litchman, E and Whitaker, RJ and Whiteson, KL and Metcalf, CJE and , }, title = {Perspectives on the future of ecology, evolution, and biodiversity from the Council on Microbial Sciences of the American Society for Microbiology.}, journal = {mSphere}, volume = {9}, number = {11}, pages = {e0030724}, pmid = {39387587}, issn = {2379-5042}, mesh = {*Biodiversity ; *Ecology ; *Microbiology ; *Societies, Scientific ; United States ; Biological Evolution ; Humans ; Microbiota ; }, abstract = {The field of microbial ecology, evolution, and biodiversity (EEB) is at the leading edge of understanding how microbes shape our biosphere and influence the well-being of humankind and Earth. To that end, EEB is developing new transdisciplinary tools to analyze these ecologically critical, complex microbial communities. The American Society for Microbiology's Council on Microbial Sciences hosted a virtual retreat in 2023 to discuss the trajectory of EEB both within the Society and microbiology writ large. The retreat emphasized the interconnectedness of microbes and their outsized global influence on environmental and host health. The maximal potential impact of EEB will not be achieved without contributions from disparate fields that unite diverse technologies and data sets. In turn, this level of transdisciplinary efforts requires actively encouraging "broad" research, spanning inclusive global collaborations that incorporate both scientists and the public. Together, the American Society for Microbiology and EEB are poised to lead a paradigm shift that will result in a new era of collaboration, innovation, and societal relevance for microbiology.}, }
@article {pmid39387577, year = {2024}, author = {Beck, KL and Haiminen, N and Agarwal, A and Carrieri, AP and Madgwick, M and Kelly, J and Pylro, V and Kawas, B and Wiedmann, M and Ganda, E}, title = {Development and evaluation of statistical and artificial intelligence approaches with microbial shotgun metagenomics data as an untargeted screening tool for use in food production.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0084024}, pmid = {39387577}, issn = {2379-5077}, support = {#PEN04752, #PEN04731//U.S. Department of Agriculture (USDA)/ ; }, mesh = {*Metagenomics/methods ; *Artificial Intelligence ; *Milk/microbiology/chemistry ; Animals ; Food Microbiology/methods ; Microbiota/genetics ; Algorithms ; Principal Component Analysis ; Machine Learning ; }, abstract = {UNLABELLED: The increasing knowledge of microbial ecology in food products relating to quality and safety and the established usefulness of machine learning algorithms for anomaly detection in multiple scenarios suggests that the application of microbiome data in food production systems for anomaly detection could be a valuable approach to be used in food systems. These methods could be used to identify ingredients that deviate from their typical microbial composition, which could indicate food fraud or safety issues. The objective of this study was to assess the feasibility of using shotgun sequencing data as input into anomaly detection algorithms using fluid milk as a model system. Contrastive principal component analysis (PCA), cluster-based methods, and explainable artificial intelligence (AI) were evaluated for the detection of two anomalous sample classes using longitudinal metagenomic profiling of fluid milk compared to baseline (BL) samples collected under comparable circumstances. Traditional methods (alpha and beta diversity, clustering-based contrastive PCA, multidimensional scaling, and dendrograms) failed to differentiate anomalous sample classes; however, explainable AI was able to classify anomalous vs baseline samples and indicate microbial drivers in association with antibiotic use. We validated the potential for explainable AI to classify different milk sources using larger publicly available fluid milk 16S rDNA sequencing data sets and demonstrated that explainable AI is able to differentiate between milk storage methods, processing stages, and seasons. Our results indicate that the application of artificial intelligence continues to hold promise in the realm of microbiome data analysis and could present further opportunities for downstream analytic automation to aid in food safety and quality.<br><br>IMPORTANCE: We evaluated the feasibility of using untargeted metagenomic sequencing of raw milk for detecting anomalous food ingredient content with artificial intelligence methods in a study specifically designed to test this hypothesis. We also show through analysis of publicly available fluid milk microbial data that our artificial intelligence approach is able to successfully predict milk in different stages of processing. The approach could potentially be applied in the food industry for safety and quality control.}, }
@article {pmid39387551, year = {2024}, author = {Halbrook, S and Wilber, W and Barrow, ME and Farrer, EC}, title = {Bacterial community response to novel and repeated disturbances.}, journal = {Environmental microbiology reports}, volume = {16}, number = {5}, pages = {e70022}, pmid = {39387551}, issn = {1758-2229}, support = {LEQSF(2017-20)-RD-A-14//Louisiana Board of Regents/ ; //Tulane University/ ; DEB-2141922//National Science Foundation/ ; }, mesh = {*Bacteria/genetics/classification/isolation &amp; purification ; Salinity ; Microbiota ; Ecosystem ; Biodiversity ; }, abstract = {Disturbance response and recovery are increasingly important in microbial ecology, as microbes may recover from disturbances differently than macro communities. Past disturbances can alter microbial community structure and their response to subsequent disturbance events, but it remains unclear if the same recovery patterns persist after long-term exposure to stress. Here, we compare bacterial community composition in a community that experienced 2 years of monthly salinity addition disturbances with a community that has not experienced salinity additions. We then track the response and recovery to an additional salinity addition based on past disturbance exposure. We tested the following hypotheses: first, communities with a repeated disturbance history will have a different community composition than communities without a disturbance history; second, communities exposed to repeated disturbances will undergo a different recovery trajectory than communities experiencing a novel disturbance. We find that repeated disturbances alter community composition and affect community response and recovery to a subsequent disturbance after 2 years, primarily through increased resistance. This work enhances our understanding of microbial temporal dynamics and suggests that novel disturbances may pose a threat to microbial community structure and function.}, }
@article {pmid39392836, year = {2024}, author = {Daisley, BA and Allen-Vercoe, E}, title = {Microbes as medicine.}, journal = {Annals of the New York Academy of Sciences}, volume = {1541}, number = {1}, pages = {63-82}, pmid = {39392836}, issn = {1749-6632}, support = {950-232131//Canada Research Chairs/ ; PDF-402947//Natural Sciences and Engineering Research Council of Canada/ ; //Natural Sciences and Engineering Research Council of Canada/ ; 2023//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Humans ; *Probiotics/therapeutic use ; *Microbiota/drug effects/physiology ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Precision Medicine/methods ; Animals ; }, abstract = {Over the last two decades, advancements in sequencing technologies have significantly deepened our understanding of the human microbiome's complexity, leading to increased concerns about the detrimental effects of antibiotics on these intricate microbial ecosystems. Concurrently, the rise in antimicrobial resistance has intensified the focus on how beneficial microbes can be harnessed to treat diseases and improve health and offer potentially promising alternatives to traditional antibiotic treatments. Here, we provide a comprehensive overview of both established and emerging microbe-centric therapies, from probiotics to advanced microbial ecosystem therapeutics, examine the sophisticated ways in which microbes are used medicinally, and consider their impacts on microbiome homeostasis and health outcomes through a microbial ecology lens. In addition, we explore the concept of rewilding the human microbiome by reintroducing "missing microbes" from nonindustrialized societies and personalizing microbiome modulation to fit individual microbial profiles-highlighting several promising directions for future research. Ultimately, the advancements in sequencing technologies combined with innovative microbial therapies and personalized approaches herald a new era in medicine poised to address antibiotic resistance and improve health outcomes through targeted microbiome management.}, }
@article {pmid39392487, year = {2024}, author = {Legeay, J and Basiru, S and Ziami, A and Errafii, K and Hijri, M}, title = {Response of Alternaria and Fusarium Species to Low Precipitation in a Drought-Tolerant Plant in Morocco.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {127}, pmid = {39392487}, issn = {1432-184X}, support = {Project AS-85//OPC Africa and OCP Innovation/ ; }, mesh = {Morocco ; *Fusarium/physiology/isolation &amp; purification/classification ; *Droughts ; *Alternaria/physiology/classification ; *Plant Roots/microbiology ; *Rain ; Soil Microbiology ; Mycobiome ; Rhizosphere ; }, abstract = {The plant mycobiome plays a crucial role in the host life cycle, influencing both healthy and diseased states, and is essential for plant tolerance to drought. In this study, we used ITS metabarcoding to investigate the fungal community of the drought-resistant plant Malva sylvestris L. in Morocco along a gradient of precipitation, encompassing subhumid and semi-arid environments. We sampled three biotopes: rhizosphere, bulk soil, and root endosphere. Our findings revealed an absence of beta-diversity differences between bulk soil and rhizosphere, indicating that the plant does not selectively influence its rhizosphere mycobiome. Additionally, ASVs belonging to the genus Alternaria represented up to 30% of reads in the plant's roots and correlated with drought (p = 0.006), indicating a potential role for this fungal genus in mitigating drought, possibly as part of the dark septate endophyte group. Root staining and microscopic observation revealed extensive colonization by fungal hyphae and microsclerotia-like structures. Furthermore, ASVs identified as Fusarium equiseti were also correlated with low precipitation and recognized as a hub taxon in the roots. However, it remains uncertain whether this species is pathogenic or beneficial to the plant. These insights contribute to our understanding of the plant mycobiome's role in drought tolerance and highlight the importance of specific fungal taxa in supporting plant health under varying environmental conditions. Future research should focus on characterizing these taxa's functional roles and their interactions with the host plant to further elucidate their contributions to drought resistance.}, }
@article {pmid39390291, year = {2025}, author = {Delzenne, NM and Bindels, LB and Neyrinck, AM and Walter, J}, title = {The gut microbiome and dietary fibres: implications in obesity, cardiometabolic diseases and cancer.}, journal = {Nature reviews. Microbiology}, volume = {23}, number = {4}, pages = {225-238}, pmid = {39390291}, issn = {1740-1534}, mesh = {*Dietary Fiber/metabolism ; Humans ; *Gastrointestinal Microbiome/physiology ; *Obesity/microbiology ; *Neoplasms/microbiology/prevention &amp; control ; *Cardiovascular Diseases/microbiology/prevention &amp; control ; *Metabolic Diseases/microbiology ; Animals ; Bacteria/classification/metabolism/genetics ; }, abstract = {Dietary fibres constitute a heterogeneous class of nutrients that are key in the prevention of various chronic diseases. Most dietary fibres are fermented by the gut microbiome and may, thereby, modulate the gut microbial ecology and metabolism, impacting human health. Dietary fibres may influence the occurrence of specific bacterial taxa, with this effect varying between individuals. The effect of dietary fibres on microbial diversity is a matter of debate. Most intervention studies with dietary fibres in the context of obesity and related metabolic disorders reveal the need for an accurate assessment of the microbiome to better understand the variable response to dietary fibres. Epidemiological studies confirm that a high dietary fibre intake is strongly associated with a reduced occurrence of many types of cancer. However, there is a need to determine the impact of intervention with specific dietary fibres on cancer risk, therapy efficacy and toxicity, as well as in cancer cachexia. In this Review, we summarize the mechanisms by which the gut microbiome can mediate the physiological benefits of dietary fibres in the contexts of obesity, cardiometabolic diseases and cancer, their incidence being clearly linked to low dietary fibre intake.}, }
@article {pmid39389280, year = {2024}, author = {Lima, M and Muddana, C and Xiao, Z and Bandyopadhyay, A and Wangikar, PP and Pakrasi, HB and Tang, YJ}, title = {The new chassis in the flask: Advances in Vibrio natriegens biotechnology research.}, journal = {Biotechnology advances}, volume = {77}, number = {}, pages = {108464}, doi = {10.1016/j.biotechadv.2024.108464}, pmid = {39389280}, issn = {1873-1899}, mesh = {*Vibrio/genetics ; *Biotechnology/methods ; *Metabolic Engineering/methods ; *Synthetic Biology/methods ; Systems Biology/trends ; }, abstract = {Biotechnology has been built on the foundation of a small handful of well characterized and well-engineered organisms. Recent years have seen a breakout performer gain attention as a new entrant into the bioengineering toolbox: Vibrio natriegens. This review covers recent research efforts into making V. natriegens a biotechnology platform, using a large language model (LLM) and knowledge graph to expedite the literature survey process. Scientists have made advancements in research pertaining to the fundamental metabolic characteristics of V. natriegens, development and characterization of synthetic biology tools, systems biology analysis and metabolic modeling, bioproduction and metabolic engineering, and microbial ecology. Each of these subcategories has relevance to the future of V. natriegens for bioengineering applications. In this review, we cover these recent advancements and offer context for the impact they may have on the field, highlighting benefits and drawbacks of using this organism. From examining the recent bioengineering research, it appears that V. natriegens is on the precipice of becoming a platform bacterium for the future of biotechnology.}, }
@article {pmid39386005, year = {2024}, author = {Lin, X and Waring, K and Ghezzi, H and Tropini, C and Tyson, J and Ziels, RM}, title = {High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform.}, journal = {PNAS nexus}, volume = {3}, number = {10}, pages = {pgae411}, pmid = {39386005}, issn = {2752-6542}, abstract = {Small subunit (SSU) ribosomal RNA (rRNA) gene amplicon sequencing is a foundational method in microbial ecology. Currently, short-read platforms are commonly employed for high-throughput applications of SSU rRNA amplicon sequencing, but at the cost of poor taxonomic classification due to limited fragment lengths. The Oxford Nanopore Technologies (ONT) platform can sequence full-length SSU rRNA genes, but its lower raw-read accuracy has so-far limited accurate taxonomic classification and de novo feature generation. Here, we present a sequencing workflow, termed ssUMI, that combines unique molecular identifier (UMI)-based error correction with newer (R10.4+) ONT chemistry and sample barcoding to enable high throughput near full-length SSU rRNA (e.g. 16S rRNA) amplicon sequencing. The ssUMI workflow generated near full-length 16S rRNA consensus sequences with 99.99% mean accuracy using a minimum subread coverage of 3×, surpassing the accuracy of Illumina short reads. The consensus sequences generated with ssUMI were used to produce error-free de novo sequence features with no false positives with two microbial community standards. In contrast, Nanopore raw reads produced erroneous de novo sequence features, indicating that UMI-based error correction is currently necessary for high-accuracy microbial profiling with R10.4+ ONT sequencing chemistries. We showcase the cost-competitive scalability of the ssUMI workflow by sequencing 87 time-series wastewater samples and 27 human gut samples, obtaining quantitative ecological insights that were missed by short-read amplicon sequencing. ssUMI, therefore, enables accurate and low-cost full-length 16S rRNA amplicon sequencing on Nanopore, improving accessibility to high-resolution microbiome science.}, }
@article {pmid39383960, year = {2024}, author = {Goswami, V and Deepika, S and Sharma, P and Kothamasi, D}, title = {Recycling steel slag as fertiliser proxy in agriculture is good circular economy but disrupts plant microbial symbioses in the soil.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176750}, doi = {10.1016/j.scitotenv.2024.176750}, pmid = {39383960}, issn = {1879-1026}, mesh = {*Agriculture/methods ; *Fertilizers ; *Mycorrhizae/physiology ; *Soil Microbiology ; *Symbiosis ; Steel ; Hordeum/microbiology ; Recycling ; Soil/chemistry ; }, abstract = {Modern agriculture depends on synthetic fertilisers to ensure food security but their manufacture and use accounts for ~5 % of the global greenhouse gas emissions. Achieving climate change targets therefore requires alternatives, that while maintaining crop productivity, reduce emissions across the lifecycle of fertiliser utilisation. Steel slag, a nutrient-rich by-product of steel manufacture, offers a viable alternative. Being substantially cheaper than fertilisers, it is economically attractive for farmers, particularly in low-middle income countries of the Global South. However, slag application in agriculture poses risk of pollutant transfer to the human food chain and disruption of key plant-microbe symbioses like the arbuscular mycorrhizal fungi (AMF). Here, using barley as a model crop, we tested the suitability of slag as a fertiliser proxy. Mycorrhizal and non-mycorrhizal barley were grown in soils ameliorated with slag in concentrations of 0, 2, 5 and 10 t ha[-1]. We analysed slag-mycorrhiza interaction and their combined effects on crop yield and risks to human nourishment. Slag increased grain yield by respective 32 and 21 % in mycorrhizal and non-mycorrhizal barley. Grain concentration of metal pollutants in mycorrhizal and non-mycorrhizal barley fertilised with slag were within the WHO recommended limits. But slag reduced mycorrhizal colonisation in barley roots and extraradical hyphal spread in the soil. The consequent decline in symbiont function lowered AMF-mediated plant nutrient uptake and increased mineral losses in leachates. AMF are keystone species of the soil microbiome. Loss of AMF function presents long-term ecological consequences for agriculture and necessitates a careful evaluation of slag application to soil.}, }
@article {pmid39382725, year = {2024}, author = {Wang, L and Liu, Z and Bres, C and Jin, G and Fanin, N}, title = {Coniferous Tree Species Identity and Leaf Aging Alter the Composition of Phyllosphere Communities Through Changes in Leaf Traits.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {126}, pmid = {39382725}, issn = {1432-184X}, support = {2572021AW30//Fundamental Research Funds for the Central Universities/ ; 2022YFD2201100//National Key R &amp; D Program of China/ ; 2572022DS13//the Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Plant Leaves/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Trees/microbiology/growth &amp; development ; Fungi/classification/genetics/physiology/isolation &amp; purification ; Pinus/microbiology/growth &amp; development ; Abies/microbiology ; Picea/microbiology/growth &amp; development ; Biodiversity ; Tracheophyta/microbiology ; }, abstract = {Phyllosphere microorganisms are essential for plant growth and health. Although there are an increasing number of studies showing that the composition of phyllosphere communities varies among different plant species, it remains unclear whether and how their bacterial and fungal community composition predictably varies with plant traits and leaf age. In this study, we used high-throughput sequencing to explore the diversity and composition of phyllosphere communities in needles of different ages (originating from different cohorts) for three evergreen coniferous species (Pinus koraiensis, Picea koraiensis, and Abies nephrolepis). Our results indicated that Gammaproteobacteria (bacteria) and Dothideomycetes (fungi) were dominant in newly formed needles, whereas Actinobacteria (bacteria) and Eurotiomycetes (fungi) were dominant in perennial needles. Tree species identity and needle age were the main factors explaining the variations of the α diversity (species richness of phyllosphere communities) and β diversity (dissimilarity among phyllosphere communities). In particular, we found that leaf dry matter content, leaf mass per area, and total phosphorus content emerged as key predictors of composition and diversity of phyllosphere microbial communities, underscoring the major influence of tree species identity and needle age on phyllosphere communities through changes in plant functional traits. Finally, we found that the interaction between tree species identity and needle age also contributed significantly to explaining the diversity and composition of phyllosphere communities, probably because differences in plant functional traits or environmental conditions between new and perennial needles depend on tree growth rates and resource acquisition strategies. These findings provide new insights into the mechanisms of community assembly among different evergreen tree species and offer a better understanding of the interactions between plant traits and phyllosphere microorganisms during needle aging.}, }
@article {pmid39382674, year = {2024}, author = {Murray, MLH and Dopheide, A and Leonard, J and Padamsee, M and Schwendenmann, L}, title = {Phyllosphere of Agathis australis Leaves and the Impact of the Soil-Borne Pathogen Phytophthora agathidicida.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {125}, pmid = {39382674}, issn = {1432-184X}, mesh = {*Plant Leaves/microbiology ; *Phytophthora/isolation &amp; purification/genetics ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Microbiota ; New Zealand ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Combretaceae/microbiology ; }, abstract = {Leaf surface microbial communities play an important role in forest ecosystems and are known to be affected by environmental and host conditions, including diseases impacting the host. Phytophthora agathidicida is a soil-borne pathogen that causes severe disease (kauri dieback) in one of New Zealand's endemic trees, Agathis australis (kauri). This research characterised the microbial communities of the A. australis phyllosphere (i.e. leaf surface) using modern molecular techniques and explored the effects of P. agathidicida on those communities. Fresh leaves were collected from trees where P. agathidicida was and was not detected in the soil and characterisation of the leaf surface microbial community was carried out via high-throughput amplicon sequencing of the internal transcribed spacer (ITS) and 16S ribosomal RNA regions. Nutrients in leaf leachates were also measured to identify other possible drivers of microbial diversity. The dominant phyllosphere microbial phylum was Proteobacteria followed by Acidobacteria. The phyllosphere microbial richness of A. agathis associated with P. agathidicida-infected soils was found to be generally lower than where the pathogen was not detected for both prokaryote (bacterial) and fungal phyla. Leaf leachate pH as well as boron and silicon had significant associations with bacterial and fungal community structure. These findings contribute to the development of a comprehensive understanding of A. australis leaf surface microbial communities and the effects of the soil pathogen P. agathidicida on those communities.}, }
@article {pmid39382297, year = {2024}, author = {Eigemann, F and Hoffmann, J and Schampera, C and Liu, S and Bolaños, LM and Heemeyer, M and Carlson, CA and Giovannoni, S and Hellweger, FL}, title = {Emergent ecology in a microscale model of the surface ocean.}, journal = {mBio}, volume = {15}, number = {11}, pages = {e0237224}, pmid = {39382297}, issn = {2150-7511}, support = {BIOS-SCOPE//Simons Foundation (SF)/ ; //North-German Supercomputing Alliance/ ; }, mesh = {*Phytoplankton/metabolism/physiology ; *Oceans and Seas ; *Ecosystem ; *Seawater/microbiology/chemistry ; Bacteria/metabolism/genetics ; Models, Biological ; Chemotaxis ; Bacterial Physiological Phenomena ; Carbon/metabolism ; Cyanobacteria/metabolism/physiology/growth &amp; development ; Ecology ; }, abstract = {Microbial processes operate at the microscale, which is not resolved by existing ecosystem models. Here, we present a novel model that simulates a 1 mL three-dimensional cube using a hybrid Lagrangian-Eulerian approach, at ecologically relevant timescales. The model simulates individual microbes, including three phytoplankton size classes with healthy, senescent, and dead lifecycle stages; copiotrophic and oligotrophic heterotrophic bacteria; and dissolved organic matter at 50 µm resolution. Diffusion, shear, sedimentation, chemotaxis, and attachment processes are explicitly resolved. The emerging quantitative representation of the ecosystem shows that (1) copiotrophs grow mostly attached to eukaryotic phytoplankters and get almost all of their carbon from them vs. oligotrophs that grow on exudates and lysates of cyanobacteria; (2) contrasting diel patterns in substrate appearance in the phycosphere vs. ambient water and growth of particle-associated copiotrophs vs. free-living oligotrophs; (3) attached bacteria reduce carbon flux from the phycosphere, lowering chemotactic efficiency toward eukaryotes below that toward cyanobacteria; (4) shear reduces chemotactic efficiency and fitness of the copiotroph; and (5) the main benefit of chemotaxis is to locate attachment partners. These patterns are consistent with available observations. Our study provides insights into the microscale ecology of marine bacteria, and the open-source code is a tool for further research in this area.IMPORTANCEA large amount of global CO2 fixation is performed by marine phytoplankton, and a substantial fraction of that is released as dissolved organic carbon and further processed by heterotrophic bacteria. The interaction between phytoplankton and bacteria, i.e., the carbon flux between them, is therefore an important process in the global carbon and climate system. Some bacteria have developed specialized behavioral traits, like swimming and attachment, to increase their carbon acquisition. These interactions occur at the micrometer scale, for example, the immediate vicinity of phytoplankters (the phycosphere), but existing biogeochemical models typically only simulate down to the 1 meter vertical or ~100 kilometer horizontal scale. We present a new microscale model and use it to predict fluxes and other features in the surface ocean. The model makes important predictions about the fluxes between various types of phytoplankton and bacteria and the role of behavioral traits, and it provides a basis and tool for further research in this area.}, }
@article {pmid39381885, year = {2024}, author = {Witzgall, K and Hesse, BD and Pacay-Barrientos, NL and Jansa, J and Seguel, O and Oses, R and Buegger, F and Guigue, J and Rojas, C and Rousk, K and Grams, TEE and Pietrasiak, N and Mueller, CW}, title = {Soil carbon and nitrogen cycling at the atmosphere-soil interface: Quantifying the responses of biocrust-soil interactions to global change.}, journal = {Global change biology}, volume = {30}, number = {10}, pages = {e17519}, doi = {10.1111/gcb.17519}, pmid = {39381885}, issn = {1365-2486}, support = {MU3021/6-2//Deutsche Forschungsgemeinschaft/ ; EAR-2012475//National Science Foundation (NSF)/ ; }, mesh = {*Soil/chemistry ; *Climate Change ; *Nitrogen Cycle ; *Soil Microbiology ; *Carbon Cycle ; *Droughts ; *Atmosphere/chemistry ; Carbon/metabolism/analysis ; Carbon Dioxide/metabolism/analysis ; Nitrogen/metabolism/analysis ; Ecosystem ; }, abstract = {In drylands, where water scarcity limits vascular plant growth, much of the primary production occurs at the soil surface. This is where complex macro- and microbial communities, in an intricate bond with soil particles, form biological soil crusts (biocrusts). Despite their critical role in regulating C and N cycling in dryland ecosystems, there is limited understanding of the fate of biologically fixed C and N from biocrusts into the mineral soil, or how climate change will affect C and N fluxes between the atmosphere, biocrusts, and subsurface soils. To address these gaps, we subjected biocrust-soil systems to experimental warming and drought under controlled laboratory conditions, monitored CO2 fluxes, and applied dual isotopic labeling pulses ([13]CO2 and [15]N2). This allowed detailed quantification of elemental pathways into specific organic matter (OM) pools and microbial biomass via density fractionation and phospholipid fatty acid analyses. While biocrusts modulated CO2 fluxes regardless of the temperature regime, drought severely limited their photosynthetic C uptake to the extent that the systems no longer sustained net C uptake. Furthermore, the effect of biocrusts extended into the underlying 1 cm of mineral soil, where C and N accumulated as mineral-associated OM (MAOM<63μm). This was strongly associated with increased relative dominance of fungi, suggesting that fungal hyphae facilitate the downward C and N translocation and subsequent MAOM formation. Most strikingly, however, these pathways were disrupted in systems exposed to warming, where no effects of biocrusts on the elemental composition of the underlying soil nor on MAOM were determined. This was further associated with reduced net biological N fixation under combined warming and drought, highlighting how changing climatic conditions diminish some of the most fundamental ecosystem functions of biocrusts, with detrimental repercussions for C and N cycling and the persistence of soil organic matter pools in dryland ecosystems.}, }
@article {pmid39380680, year = {2024}, author = {Karavaeva, V and Sousa, FL}, title = {Navigating the archaeal frontier: insights and projections from bioinformatic pipelines.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1433224}, pmid = {39380680}, issn = {1664-302X}, abstract = {Archaea continues to be one of the least investigated domains of life, and in recent years, the advent of metagenomics has led to the discovery of many new lineages at the phylum level. For the majority, only automatic genomic annotations can provide information regarding their metabolic potential and role in the environment. Here, genomic data from 2,978 archaeal genomes was used to perform automatic annotations using bioinformatics tools, alongside synteny analysis. These automatic classifications were done to assess how good these different tools perform in relation to archaeal data. Our study revealed that even with lowered cutoffs, several functional models do not capture the recently discovered archaeal diversity. Moreover, our investigation revealed that a significant portion of archaeal genomes, approximately 42%, remain uncharacterized. In comparison, within 3,235 bacterial genomes, a diverse range of unclassified proteins is obtained, with well-studied organisms like Escherichia coli having a substantially lower proportion of uncharacterized regions, ranging from <5 to 25%, and less studied lineages being comparable to archaea with the range of 35-40% of unclassified regions. Leveraging this analysis, we were able to identify metabolic protein markers, thereby providing insights into the metabolism of the archaea in our dataset. Our findings underscore a substantial gap between automatic classification tools and the comprehensive mapping of archaeal metabolism. Despite advances in computational approaches, a significant portion of archaeal genomes remains unexplored, highlighting the need for extensive experimental validation in this domain, as well as more refined annotation methods. This study contributes to a better understanding of archaeal metabolism and underscores the importance of further research in elucidating the functional potential of archaeal genomes.}, }
@article {pmid39379763, year = {2024}, author = {Peng, Z and Xu, Z and Tong, H and Xing, Y and Luo, Z and Wu, Y and Yu, Z}, title = {Leaf Rust Pathogens on Hypericum pseudohenryi: Describing Melampsora danbaensis sp. nov. and M. hyperici-pseudohenryi sp. nov. from China.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {122}, pmid = {39379763}, issn = {1432-184X}, support = {2023YFC2604800-03//National Key Research and Development Program of China/ ; }, mesh = {China ; *Hypericum/microbiology/classification ; *Phylogeny ; *Plant Diseases/microbiology ; *Plant Leaves/microbiology ; *Basidiomycota/classification/genetics/isolation &amp; purification ; DNA, Fungal/genetics ; Spores, Fungal ; }, abstract = {Based on morphological and phylogenetic evidence, two novel species of Melampsora were discovered on Hypericum pseudohenryi in China and have been thoroughly characterized. One of these species, designated as M. danbaensis, exhibits distinct features such as aecia of Uredo-type, typically appearing in gregarious or grouped arrangements, and presenting a shallowly pulvinate structure. Aeciospores exhibit tremendous variations in size, ranging in shape from globose to ellipsoidal and bearing pronounced verrucose texture. Telia resemble crusts one-spore deep, covering nearly the entire abaxial leaf surface, with sessile teliospores reaching sizes of up to 65.8 µm, and exhibiting a clavate to cylindrical shape. Another species, designated as M. hyperici-pseudohenryi, is distinguished by Uredo-type uredinia, which are hypophyllous, scattered or grouped, and interspersed with numerous paraphyses. Its urediniospores tend to be globose, ellipsoidal or obovoid, echinulate, and are accompanied by clavate to capitate paraphyses reaching lengths up to 77.6 µm. Phylogenetically, both species form a novel monophyletic clade within the Melampsora genus, with robust support demonstrated by a high Maximum likelihood bootstrap support (MLBS) value of 100% and a Bayesian posterior probability (BPP) of 1. This study enriches our understanding of the diversity and geographical distribution of Melampsora species that infect Hypericum plants in China.}, }
@article {pmid39379709, year = {2024}, author = {Larrouy, JL and Ridgway, HJ and Dhami, MK and Jones, EE}, title = {Improvement in Microbiota Recovery Using Cas-9 Digestion of Mānuka Plastid and Mitochondrial DNA.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {124}, pmid = {39379709}, issn = {1432-184X}, support = {C11X1803//Ministry of Business, Innovation and Employment/ ; C11X1803//Ministry of Business, Innovation and Employment/ ; C11X1803//Ministry of Business, Innovation and Employment/ ; C11X1803//Ministry of Business, Innovation and Employment/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Plastids/genetics ; *DNA, Mitochondrial/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Lamiales/microbiology/genetics ; CRISPR-Cas Systems ; DNA, Bacterial/genetics ; RNA, Guide, CRISPR-Cas Systems/genetics ; Sequence Analysis, DNA ; }, abstract = {Understanding host-microbe interactions in planta is an expanding area of research. Amplicon sequencing of the 16S rRNA gene is a powerful and common method to study bacterial communities associated with plants. However, the co-amplification of mitochondrial and plastid 16S rRNA genes by universal primers impairs the sensitivity and performance of 16S rRNA sequencing. In 2020, a new method, Cas-16S-seq, was reported in the literature to remove host contamination for profiling the microbiota in rice, a well-studied domestic plant, by engineering RNA-programmable Cas9 nuclease in 16S rRNA sequencing. For the first time, we tested the efficiency and applicability of the Cas-16S-seq method on foliage, flowers, and seed of a non-domesticated wild plant for which there is limited genomic information, Leptospermum scoparium (mānuka). Our study demonstrated the efficiency of the Cas-16S-seq method for L. scoparium in removing host contamination in V4-16S amplicons. An increase of 46% in bacterial sequences was found using six guide RNAs (gRNAs), three gRNAs targeting the mitochondrial sequence, and three gRNAs targeting the chloroplast sequence of L. scoparium in the same reaction. An increase of 72% in bacterial sequences was obtained by targeting the mitochondrial and chloroplast sequences of L. scoparium in the same sample at two different steps of the library preparation (DNA and 1st step PCR). The number of OTUs (operational taxonomic units) retrieved from soil samples was consistent when using the different methods (Cas-16S-seq and 16S-seq) indicating that the Cas-16S-seq implemented for L. scoparium did not introduce bias to microbiota profiling. Our findings provide a valuable tool for future studies investigating the bacterial microbiota of L. scoparium in addition to evaluating an important tool in the plant microbiota research on other non-domesticated wild species.}, }
@article {pmid39379544, year = {2024}, author = {Bastidas Navarro, M and Balseiro, E and Modenutti, B}, title = {Lake Bacterial Communities in North Patagonian Andes: The Effect of the Nothofagus pumilio Treeline.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {123}, pmid = {39379544}, issn = {1432-184X}, support = {PICT 2015-2138//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICT 2017-1940//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICT 2018-1563//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; }, mesh = {*Lakes/microbiology/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; *Phylogeny ; Cyanobacteria/genetics/classification ; Microbiota ; Nitrogen/analysis ; Carbon/analysis/metabolism ; Phosphorus/analysis ; Biodiversity ; Altitude ; Trees/microbiology ; Argentina ; }, abstract = {One of the most noticeable environmental discontinuities in mountains is the transition that exists in vegetation below and above the treeline. In the North Patagonian Andean lakes (between 900 and 1950 m a.s.l.), we analyzed the bacterial community composition of lakes in relation to surrounding vegetation (erected trees, krummholz belt, and bare rocks), dissolved organic carbon (DOC), and total dissolved nutrients (nitrogen, TDN and phosphorus, TDP). We observed a decrease in DOC, TDP, and TDN concentrations with altitude, reflecting shifts in the source inputs entering the lakes by runoff. Cluster analysis based on bacterial community composition showed a segregation of the lakes below treeline, from those located above. This first cluster was characterized by the cyanobacteria Cyanobium PCC-6307, while in the krummholz belt and bare rocks, bacterial communities were dominated by Actinobacteria hgcl-clade and Proteobacteria (Sandarakinorhabdus and Rhodovarius), with the presence of pigments such as actinorhodopsin, carotenoids, and bacteriochlorophyll a. The net relatedness index (NRI), which considers the community phylogenetic dispersion, showed that lakes located on bare rocks were structured by environmental filtering, while communities of lakes below treeline were structured by species interactions such as competition. Beta-diversity was higher among lakes below than among lakes located above the treeline. The contribution of species turnover was more important than nestedness. Our study brings light on how bacterial communities may respond to changes in the surrounding vegetation, highlighting the importance of evaluating different aspects of community structure to understand metacommunity organization.}, }
@article {pmid39378744, year = {2025}, author = {Zhu, T and Li, S and Tao, C and Chen, W and Chen, M and Zong, Z and Wang, Y and Li, Y and Yan, B}, title = {Understanding the mechanism of microplastic-associated antibiotic resistance genes in aquatic ecosystems: Insights from metagenomic analyses and machine learning.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122570}, doi = {10.1016/j.watres.2024.122570}, pmid = {39378744}, issn = {1879-2448}, mesh = {*Machine Learning ; *Microplastics/toxicity ; *Drug Resistance, Microbial/genetics ; *Metagenomics ; *Ecosystem ; Water Pollutants, Chemical/toxicity ; }, abstract = {The pervasive presence of microplastics (MPs) in aquatic systems facilitates the transmission of antibiotic resistance genes (ARGs), thereby posing risks to ecosystems and human well-being. However, owing to variations in environmental backgrounds and the limited scope of research subjects, studies on ARGs in MPs lack unified conclusions, particularly regarding whether different types of MPs selectively promote ARG enrichment. Analysing large-scale datasets can better encompass broad spatiotemporal scales and diverse samples, facilitating a more extensive exploration of the complex ecological relationships between MPs and ARGs. The present study integrated existing metagenomic datasets to conduct a comprehensive risk assessment and comparative analysis of resistance groups across various MPs. In addition, we endeavoured to elucidate potential associations between ARGs and bacterial taxa, as well as MP structural features, using machine learning (ML) methods. The findings of our research highlight the pivotal role of MP type in shaping plastispheres, accounting for 9.56 % of the biotic variation (Adonis index) and explaining 18.59 % of the ARG variance. Compared to conventional MPs, biodegradable MPs, such as polyhydroxyalkanoates (PHA) and polylactic acid (PLA), exhibit lower species uniformity and diversity but pose a higher risk of ARG occurrence. These ML approaches effectively forecasted ARG abundance by using the bacterial taxa and molecular structure descriptors (MDs) of MPs (average R[2]tra = 0.882, R[2]test = 0.759). Feature analysis showed that MDs associated with lipophilicity, solubility, toxicity, and surface potential significantly influenced the relative abundance of ARGs in the plastispheres. The interpretable multiple linear regression (MLR) model, particularly notable, elucidated a linear relationship between bacterial genera and ARGs, offering promise for identifying potential ARG hosts. This study offers novel insights into ARG dynamics and ecological risks within aquatic plastispheres, highlighting the importance of comprehensive MP monitoring initiatives.}, }
@article {pmid39377576, year = {2024}, author = {Woldetsadik, YA and Lazinski, DW and Camilli, A}, title = {A Vibrio cholerae anti-phage system depletes nicotinamide adenine dinucleotide to restrict virulent bacteriophages.}, journal = {mBio}, volume = {15}, number = {11}, pages = {e0245724}, pmid = {39377576}, issn = {2150-7511}, support = {AI055058//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; GM139772//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R37 AI055058/AI/NIAID NIH HHS/United States ; R01 AI055058/AI/NIAID NIH HHS/United States ; R21 AI147658/AI/NIAID NIH HHS/United States ; T32 GM139772/GM/NIGMS NIH HHS/United States ; AI147658//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {*NAD/metabolism ; *Bacteriophages/genetics/physiology ; *Vibrio cholerae/virology/genetics ; Virulence ; Bacterial Proteins/genetics/metabolism ; Genomic Islands ; Virus Replication ; }, abstract = {Bacteria and their predatory viruses (bacteriophages or phages) are in a perpetual molecular arms race. This has led to the evolution of numerous phage defensive systems in bacteria that are still being discovered, as well as numerous ways of interference or circumvention on the part of phages. Here, we identify a unique molecular battle between the classical biotype of Vibrio cholerae and virulent phages ICP1, ICP2, and ICP3. We show that classical biotype strains resist almost all isolates of these phages due to a 25-kb genomic island harboring several putative anti-phage systems. We observed that one of these systems, Nezha, encoding SIR2-like and helicase proteins, inhibited the replication of all three phages. Bacterial SIR2-like enzymes degrade the essential metabolic coenzyme nicotinamide adenine dinucleotide (NAD[+]), thereby preventing replication of the invading phage. In support of this mechanism, we identified one phage isolate, ICP1_2001, which circumvents Nezha by encoding two putative NAD[+] regeneration enzymes. By restoring the NAD[+] pool, we hypothesize that this system antagonizes Nezha without directly interacting with its proteins and should be able to antagonize other anti-phage systems that deplete NAD[+].IMPORTANCEBacteria and phages are in a perpetual molecular arms race, with bacteria evolving an extensive arsenal of anti-phage systems and phages evolving mechanisms to overcome these systems. This study identifies a previously uncharacterized facet of the arms race between Vibrio cholerae and its phages. We identify an NAD[+]-depleting anti-phage defensive system called Nezha, potent against three virulent phages. Remarkably, one phage encodes proteins that regenerate NAD[+] to counter the effects of Nezha. Without Nezha, the NAD[+] regeneration genes are detrimental to the phage. Our study provides new insight into the co-evolutionary dynamics between bacteria and phages and informs the microbial ecology and phage therapy fields.}, }
@article {pmid39376571, year = {2024}, author = {Qian, C and Hui, J and Peng, Z and Sun, X and Zhang, J}, title = {Mucosal microbiota characterization in gastric cancer identifies immune-activated-related transcripts relevant gastric microbiome signatures.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1435334}, pmid = {39376571}, issn = {1664-3224}, mesh = {Humans ; *Stomach Neoplasms/immunology/microbiology/genetics/mortality ; *Gastric Mucosa/microbiology/immunology/metabolism ; Female ; *Tumor Microenvironment/immunology ; Male ; Middle Aged ; *Gastrointestinal Microbiome/immunology/genetics ; Aged ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/immunology/genetics ; Adult ; }, abstract = {Tumor microenvironment (TME) immune cells and gastric mucosal microbiome constitute two vital elements of tumor tissue. Increasing evidence has elucidated their clinicopathological significance in predicting outcomes and therapeutic efficacy. However, comprehensive characterization of immune cell-associated microbiome signatures in the TME is still in the early stages of development. Here, we characterized the gastric mucosa microbiome and its associations with immune-activated related transcripts (IATs) in 170 GC tumor tissues and matched non-tumor tissues using 16s rRNA gene sequencing and quantitative reverse transcription-PCR. Microbial diversity and richness were significantly higher in GC tumor tissues than in non-tumor tissues. Differences in microbial composition between the groups were evident, with Firmicutes, Proteobacteria, Bacteroidota, Campilobacterota, Actinobacteria, Fusobacteriota, Verrucomicrobiota, Acidobacteriota, and Cyanobacteria being the dominant phyla in the gastric mucosal microbiota. Microbial interaction network analysis revealed distinctive centralities of oral bacteria (such as Fusobacterium, Porphyromonas, Prevotella, etc.) in both tumor and normal mucosae networks, suggesting their significant influence on GC microbial ecology. Furthermore, we analyzed the expression of IATs (CXCL9, CXCL10, GZMA, GZMB, PRF1, CD8A, IFNG, TBX2, and TNF) and characterized IAT-relevant gastric microbiome signatures in GC patients. Our results showed that the expression of CXCL9, CXCL10, GZMA, GZMB, PRF1 and IFNG was significantly higher in tumor tissues than in adjacent normal tissues in GC patients. Notably, high expression of IATs in tumor tissues was associated with improved survival in GC patients and could serve as a powerful predictor for disease-free survival. Additionally, analysis of IAT levels and mucosal microbiota diversity revealed a correlation between higher IAT expression and increased microbiota richness and evenness in the IATs [high] group, suggesting potential interactions between mucosal microbiota and tumor immunopathology. Spearman correlation analysis showed positive associations between IAT expression and specific mucosal bacterial species. Notably, Akkermansia muciniphila demonstrated potential involvement in modulating GZMB expression in the GC mucosal microenvironment. These findings underscore the importance of mucosal microbiota alterations in GC and suggest potential therapeutic targets focusing on modulating the tumor microbiota for improved clinical outcomes. The detailed characterization of these elements has profound implications for both treatment and survival prediction in GC. We observed that microbial diversity and richness were significantly higher in GC tumor tissues compared to non-tumor tissues. These differences highlight the unique microbial landscape of GC tumors and suggest that the microbiome could influence tumor development and progression. Importantly, our study demonstrated that high expression levels of IATs in GC tumor tissues were associated with improved patient survival. This suggests that IATs not only reflect immune activation but also serve as valuable biomarkers for predicting disease-free survival. The potential of IATs as predictive markers underscores their utility in guiding therapeutic strategies and personalizing treatment approaches. Moreover, the correlation between higher IAT expression and increased microbiota richness and evenness suggests that a diverse and balanced microbiome may enhance immune responses and contribute to better clinical outcomes. These findings highlight the critical need to consider mucosal microbiota alterations in GC management. Targeting the tumor microbiota could emerge as a promising therapeutic strategy, potentially leading to more effective treatments and improved patient outcomes. Understanding and modulating the microbiome's role in GC opens new avenues for innovative therapeutic interventions and personalized medicine.}, }
@article {pmid39375832, year = {2024}, author = {Obiol, A and Del Campo, J and de Vargas, C and Mahé, F and Massana, R}, title = {How marine are Marine Stramenopiles (MAST)? A cross-system evaluation.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {11}, pages = {}, pmid = {39375832}, issn = {1574-6941}, support = {PID2019-108457RB-I00//Spanish Ministry of Science and Innovation/ ; EUR2022-134047//GENEXLAB/ ; PID2022-137508NB-I00//EPIC/ ; CEX2019-000928-S//Severo Ochoa Centre of Excellence/ ; }, mesh = {*Phylogeny ; *Seawater/microbiology ; *Stramenopiles/genetics/classification ; Aquatic Organisms/genetics ; Biodiversity ; Ecosystem ; Sequence Analysis, DNA ; Genes, rRNA ; }, abstract = {Marine Stramenopiles (MAST) were first described two decades ago through ribosomal RNA gene (rRNA gene) sequences from marine surveys of microbial eukaryotes. MAST comprise several independent lineages at the base of the Stramenopiles. Despite their prevalence in the ocean, the majority of MAST diversity remains uncultured. Previous studies, mainly in marine environments, have explored MAST's cell morphology, distribution, trophic strategies, and genomics using culturing-independent methods. In comparison, less is known about their presence outside marine habitats. Here, we analyse the extensive EukBank dataset to assess the extent to which MAST can be considered marine protists. Additionally, by incorporating newly available rRNA gene sequences, we update Stramenopiles phylogeny, identifying three novel MAST lineages. Our results indicate that MAST are primarily marine with notable exceptions within MAST-2 and MAST-12, where certain subclades are prevalent in freshwater and soil habitats. In the marine water column, only a few MAST species, particularly within clades -1, -3, -4, and -7, dominate and exhibit clear latitudinal distribution patterns. Overall, the massive sequencing dataset analysed in our study confirms and partially expands the previously described diversity of MASTs groups and underscores the predominantly marine nature of most of these uncultured lineages.}, }
@article {pmid39366327, year = {2024}, author = {Xu, J and Li, X and Xi, C and Weir, MH}, title = {Development of a machine learning model to support low cost real-time Legionella monitoring in premise plumbing systems.}, journal = {Water research}, volume = {267}, number = {}, pages = {122510}, doi = {10.1016/j.watres.2024.122510}, pmid = {39366327}, issn = {1879-2448}, mesh = {*Machine Learning ; *Water Microbiology ; *Legionella pneumophila ; Legionella ; Water Quality ; Environmental Monitoring/methods ; Water Supply ; Amoeba ; }, abstract = {Legionella pneumophila (L. pneumophila) is a pathogenic bacterium primarily known for causing Legionnaires' Disease which is known for high mortality rates, particularly in the elderly. With caseloads continuing to increase, further research is needed to improve our understanding of optimized sampling schema and safe limits of L. pneumophila, in part to target improved treatment options and realistic population-level risk modeling. Particularly in healthcare and other high-risk locations these become crucial and time sensitive needs. Therefore, we conceptualized this research as a means of incorporating easily measured physiochemical water quality parameters and generalization of the unique ecology of building water systems to build a computational model that can allow for more rapid and accurate decision making. This research uses the specific machine learning (ML) method called statistical learning theory to incorporate concentration of host cells, such as native amoeba, and physiochemical water quality parameters to estimate the probability of observing ranges of Legionella gene copy concentrations. Using data from previously published research on Legionella prevalence in a large building, our ML method trains the model on the relative impacts of physiochemical parameters on likely amoeba host cell occurrences. The model is expanded to estimate host cell concentrations using correlations and regressions operated through LASSO algorithms. After categorization variables from these results are then used to inform a logistic regression to provide an estimate of the probability of Legionella gene copy concentration ranges. In summary, conventional results generated by logistic regression and multiple linear regression quantified the associations among ecological conditions in the water and ability to predict a likely range of Legionella concentration in a management focused way. Further, two ML methods, PCA and LASSO, demonstrated feasibility in accurate real-time monitoring of Legionella through physiochemical indicators as evidenced with good accuracy of predictions based for validation results. Furthermore results demonstrate the vital need to account for the impact of water quality on building on host cells, and via their quantified water microbial ecology, not just Legionella concentrations.}, }
@article {pmid39365014, year = {2024}, author = {Arnold, ND and Paper, M and Fuchs, T and Ahmad, N and Jung, P and Lakatos, M and Rodewald, K and Rieger, B and Qoura, F and Kandawa-Schulz, M and Mehlmer, N and Brück, TB}, title = {High-quality genome of a novel Thermosynechococcaceae species from Namibia and characterization of its protein expression patterns at elevated temperatures.}, journal = {MicrobiologyOpen}, volume = {13}, number = {5}, pages = {e70000}, pmid = {39365014}, issn = {2045-8827}, support = {031B0838B//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031A305A//Bundesministerium f&#xfc;r Wirtschaft und Energie/ ; //Bayerisches Staatsministerium f&#xfc;r Umwelt und Verbraucherschutz/ ; }, mesh = {Namibia ; *Cyanobacteria/genetics/classification/metabolism ; *Genome, Bacterial ; *Phylogeny ; *Hot Springs/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacterial Proteins/genetics/metabolism ; Hot Temperature ; Sequence Analysis, DNA ; Proteome/analysis ; DNA, Bacterial/genetics ; }, abstract = {Thermophilic cyanobacteria thrive in extreme environments, making their thermoresistant enzymes valuable for industrial applications. Common habitats include hot springs, which act as evolutionary accelerators for speciation due to geographical isolation. The family Thermosynechococcaceae comprises thermophilic cyanobacteria known for their ability to thrive in high-temperature environments. These bacteria are notable for their photosynthetic capabilities, significantly contributing to primary production in extreme habitats. Members of Thermosynechococcaceae exhibit unique adaptations that allow them to perform photosynthesis efficiently at elevated temperatures, making them subjects of interest for studies on microbial ecology, evolution, and potential biotechnological applications. In this study, the genome of a thermophilic cyanobacterium, isolated from a hot spring near Okahandja in Namibia, was sequenced using a PacBio Sequel IIe long-read platform. Cultivations were performed at elevated temperatures of 40, 50, and 55°C, followed by proteome analyses based on the annotated genome. Phylogenetic investigations, informed by the 16S rRNA gene and aligned nucleotide identity (ANI), suggest that the novel cyanobacterium is a member of the family Thermosynechococcaceae. Furthermore, the new species was assigned to a separate branch, potentially representing a novel genus. Whole-genome alignments supported this finding, revealing few conserved regions and multiple genetic rearrangement events. Additionally, 129 proteins were identified as differentially expressed in a temperature-dependent manner. The results of this study broaden our understanding of cyanobacterial adaptation to extreme environments, providing a novel high-quality genome of Thermosynechococcaceae cyanobacterium sp. Okahandja and several promising candidate proteins for expression and characterization studies.}, }
@article {pmid39364584, year = {2025}, author = {Buchner, D and Sinclair, JS and Ayasse, M and Beermann, AJ and Buse, J and Dziock, F and Enss, J and Frenzel, M and Hörren, T and Li, Y and Monaghan, MT and Morkel, C and Müller, J and Pauls, SU and Richter, R and Scharnweber, T and Sorg, M and Stoll, S and Twietmeyer, S and Weisser, WW and Wiggering, B and Wilmking, M and Zotz, G and Gessner, MO and Haase, P and Leese, F}, title = {Upscaling biodiversity monitoring: Metabarcoding estimates 31,846 insect species from Malaise traps across Germany.}, journal = {Molecular ecology resources}, volume = {25}, number = {1}, pages = {e14023}, pmid = {39364584}, issn = {1755-0998}, support = {//Hessisches Landesamt f&#xfc;r Naturschutz, Umwelt und Geologie/ ; 871128//EU Horizon 2020 project eLTER PLUS/ ; //Landes-Offensive zur Entwicklung Wissenschaftlich-&#xf6;konomischer Exzellenz of the German federal State of Hesse/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Germany ; *Biodiversity ; *Insecta/classification/genetics/physiology ; }, abstract = {Mitigating ongoing losses of insects and their key functions (e.g. pollination) requires tracking large-scale and long-term community changes. However, doing so has been hindered by the high diversity of insect species that requires prohibitively high investments of time, funding and taxonomic expertise when addressed with conventional tools. Here, we show that these concerns can be addressed through a comprehensive, scalable and cost-efficient DNA metabarcoding workflow. We use 1815 samples from 75 Malaise traps across Germany from 2019 and 2020 to demonstrate how metabarcoding can be incorporated into large-scale insect monitoring networks for less than 50 € per sample, including supplies, labour and maintenance. We validated the detected species using two publicly available databases (GBOL and GBIF) and the judgement of taxonomic experts. With an average of 1.4 M sequence reads per sample we uncovered 10,803 validated insect species, of which 83.9% were represented by a single Operational Taxonomic Unit (OTU). We estimated another 21,043 plausible species, which we argue either lack a reference barcode or are undescribed. The total of 31,846 species is similar to the number of insect species known for Germany (~35,500). Because Malaise traps capture only a subset of insects, our approach identified many species likely unknown from Germany or new to science. Our reproducible workflow (~80% OTU-similarity among years) provides a blueprint for large-scale biodiversity monitoring of insects and other biodiversity components in near real time.}, }
@article {pmid39361898, year = {2024}, author = {Ramoneda, J and Hoffert, M and Stallard-Olivera, E and Casamayor, EO and Fierer, N}, title = {Leveraging genomic information to predict environmental preferences of bacteria.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39361898}, issn = {1751-7370}, support = {OPP 2133684//US National Science Foundation/ ; AEROSMIC PID2021-127701NB-I00//European Regional Development Fund/ ; //Spanish Agency of Research/ ; PID2023-151209NA-I00//Spanish Agency of Research/ ; 2022-BP-00050//Generalitat de Catalunya/ ; P2EZP3_199849/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Bacteria/genetics/classification ; Genome, Bacterial ; Genomics ; Environment ; Bacterial Physiological Phenomena ; }, abstract = {Genomic information is now available for a broad diversity of bacteria, including uncultivated taxa. However, we have corresponding knowledge on environmental preferences (i.e. bacterial growth responses across gradients in oxygen, pH, temperature, salinity, and other environmental conditions) for a relatively narrow swath of bacterial diversity. These limits to our understanding of bacterial ecologies constrain our ability to predict how assemblages will shift in response to global change factors, design effective probiotics, or guide cultivation efforts. We need innovative approaches that take advantage of expanding genome databases to accurately infer the environmental preferences of bacteria and validate the accuracy of these inferences. By doing so, we can broaden our quantitative understanding of the environmental preferences of the majority of bacterial taxa that remain uncharacterized. With this perspective, we highlight why it is important to infer environmental preferences from genomic information and discuss the range of potential strategies for doing so. In particular, we highlight concrete examples of how both cultivation-independent and cultivation-dependent approaches can be integrated with genomic data to develop predictive models. We also emphasize the limitations and pitfalls of these approaches and the specific knowledge gaps that need to be addressed to successfully expand our understanding of the environmental preferences of bacteria.}, }
@article {pmid39360821, year = {2024}, author = {Han, S and Kim, S and Sedlacek, CJ and Farooq, A and Song, C and Lee, S and Liu, S and Brüggemann, N and Rohe, L and Kwon, M and Rhee, S-K and Jung, M-Y}, title = {Adaptive traits of Nitrosocosmicus clade ammonia-oxidizing archaea.}, journal = {mBio}, volume = {15}, number = {11}, pages = {e0216924}, pmid = {39360821}, issn = {2150-7511}, support = {2019R1A6A1A10072987//National Research Foundation of Korea (NRF)/ ; 2021R1C1C1008303//National Research Foundation of Korea (NRF)/ ; 2022R1A4A503144711//National Research Foundation of Korea (NRF)/ ; ZK74//Austrian Science Fund (FWF)/ ; 2023RIS-009//Regional Innovation Strategy (RIS)/ ; }, mesh = {*Ammonia/metabolism ; *Oxidation-Reduction ; *Archaea/genetics/metabolism/classification ; *Nitrification ; *Phylogeny ; Genome, Archaeal ; Adaptation, Physiological ; Genomics ; }, abstract = {UNLABELLED: Nitrification is a core process in the global nitrogen (N) cycle mediated by ammonia-oxidizing microorganisms, including ammonia-oxidizing archaea (AOA) as a key player. Although much is known about AOA abundance and diversity across environments, the genetic drivers of the ecophysiological adaptations of the AOA are often less clearly defined. This is especially true for AOA within the genus Nitrosocosmicus, which have several unique physiological traits (e.g., high substrate tolerance, low substrate affinity, and large cell size). To better understand what separates the physiology of Nitrosocosmicus AOA, we performed comparative genomics with genomes from 39 cultured AOA, including five Nitrosocosmicus AOA. The absence of a canonical high-affinity type ammonium transporter and typical S-layer structural genes was found to be conserved across all Nitrosocosmicus AOA. In agreement, cryo-electron tomography confirmed the absence of a visible outermost S-layer structure, which has been observed in other AOA. In contrast to other AOA, the cryo-electron tomography highlighted the possibility that Nitrosocosmicus AOA may possess a glycoprotein or glycolipid-based glycocalyx cell covering outer layer. Together, the genomic, physiological, and metabolic properties revealed in this study provide insight into niche adaptation mechanisms and the overall ecophysiology of members of the Nitrosocosmicus clade in various terrestrial ecosystems.<br><br>IMPORTANCE: Nitrification is a vital process within the global biogeochemical nitrogen cycle but plays a significant role in the eutrophication of aquatic ecosystems and the production of the greenhouse gas nitrous oxide (N2O) from industrial agriculture ecosystems. While various types of ammonia-oxidizing microorganisms play a critical role in the N cycle, ammonia-oxidizing archaea (AOA) are often the most abundant nitrifiers in natural environments. Members of the genus Nitrosocosmicus are one of the prevalent AOA groups detected in undisturbed terrestrial ecosystems and have previously been reported to possess a range of physiological characteristics that set their physiology apart from other AOA species. This study provides significant progress in understanding these unique physiological traits and their genetic drivers. Our results highlight how physiological studies based on comparative genomics-driven hypotheses can contribute to understanding the unique niche of Nitrosocosmicus AOA.}, }
@article {pmid39360459, year = {2024}, author = {Li, X and Leizeaga, A and Rousk, J and Zhou, S and Hugelius, G and Manzoni, S}, title = {Recovery of Soil Microbial Metabolism After Rewetting Depends on Interacting Environmental Conditions and Changes in Functional Groups and Life History Strategies.}, journal = {Global change biology}, volume = {30}, number = {10}, pages = {e17522}, doi = {10.1111/gcb.17522}, pmid = {39360459}, issn = {1365-2486}, support = {101001608//H2020 European Research Council/ ; KAW 2017.0171//Knut och Alice Wallenbergs Stiftelse/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; //Schmidt Sciences, LLC/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism ; *Fungi/physiology/metabolism ; *Climate Change ; Bacteria/metabolism/growth &amp; development ; Microbiota ; Hydrogen-Ion Concentration ; }, abstract = {Climate change is causing an intensification of soil drying and rewetting events, altering microbial functioning and potentially destabilizing soil organic carbon. After rewetting, changes in microbial community carbon use efficiency (CUE), investment in life history strategies, and fungal to bacterial dominance co-occur. Still, we have yet to generalize what drives these dynamic responses. Here, we collated 123 time series of microbial community growth (G, sum of fungal and bacterial growth, evaluated by leucine and acetate incorporation, respectively) and respiration (R) after rewetting and calculated CUE = G/(G + R). First, we characterized CUE recovery by two metrics: maximum CUE and time to maximum CUE. Second, we translated microbial growth and respiration data into microbial investments in life history strategies (high yield (Y), resource acquisition (A), and stress tolerance (S)). Third, we characterized the temporal change in fungal to bacterial dominance. Finally, the metrics describing the CUE recovery, investment in life history strategies, and fungal to bacterial dominance after rewetting were explained by environmental factors and microbial properties. CUE increased after rewetting as fungal dominance declined, but the maximum CUE was explained by the CUE under moist conditions, rather than specific environmental factors. In contrast, higher soil pH and carbon availability accelerated the decline of microbial investment in stress tolerance and fungal dominance. We conclude that microbial CUE recovery is mostly driven by the shifting microbial community composition and the metabolic capacity of the community, whereas changes in microbial investment in life history strategies and fungal versus bacterial dominance depend on soil pH and carbon availability.}, }
@article {pmid39360321, year = {2024}, author = {MacGregor, H and Fukai, I and Ash, K and Arkin, AP and Hazen, TC}, title = {Potential applications of microbial genomics in nuclear non-proliferation.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1410820}, pmid = {39360321}, issn = {1664-302X}, abstract = {As nuclear technology evolves in response to increased demand for diversification and decarbonization of the energy sector, new and innovative approaches are needed to effectively identify and deter the proliferation of nuclear arms, while ensuring safe development of global nuclear energy resources. Preventing the use of nuclear material and technology for unsanctioned development of nuclear weapons has been a long-standing challenge for the International Atomic Energy Agency and signatories of the Treaty on the Non-Proliferation of Nuclear Weapons. Environmental swipe sampling has proven to be an effective technique for characterizing clandestine proliferation activities within and around known locations of nuclear facilities and sites. However, limited tools and techniques exist for detecting nuclear proliferation in unknown locations beyond the boundaries of declared nuclear fuel cycle facilities, representing a critical gap in non-proliferation safeguards. Microbiomes, defined as "characteristic communities of microorganisms" found in specific habitats with distinct physical and chemical properties, can provide valuable information about the conditions and activities occurring in the surrounding environment. Microorganisms are known to inhabit radionuclide-contaminated sites, spent nuclear fuel storage pools, and cooling systems of water-cooled nuclear reactors, where they can cause radionuclide migration and corrosion of critical structures. Microbial transformation of radionuclides is a well-established process that has been documented in numerous field and laboratory studies. These studies helped to identify key bacterial taxa and microbially-mediated processes that directly and indirectly control the transformation, mobility, and fate of radionuclides in the environment. Expanding on this work, other studies have used microbial genomics integrated with machine learning models to successfully monitor and predict the occurrence of heavy metals, radionuclides, and other process wastes in the environment, indicating the potential role of nuclear activities in shaping microbial community structure and function. Results of this previous body of work suggest fundamental geochemical-microbial interactions occurring at nuclear fuel cycle facilities could give rise to microbiomes that are characteristic of nuclear activities. These microbiomes could provide valuable information for monitoring nuclear fuel cycle facilities, planning environmental sampling campaigns, and developing biosensor technology for the detection of undisclosed fuel cycle activities and proliferation concerns.}, }
@article {pmid39359935, year = {2024}, author = {Li, Y and Li, Z and Zheng, S and Xu, X}, title = {Probiotics in the management of radiation-induced oral mucositis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1477143}, pmid = {39359935}, issn = {2235-2988}, mesh = {*Probiotics/therapeutic use ; Humans ; *Stomatitis/etiology/microbiology/therapy/prevention &amp; control ; *Radiation Injuries/therapy ; *Dysbiosis ; Microbiota ; Head and Neck Neoplasms/radiotherapy ; Radiotherapy/adverse effects ; Mouth/microbiology ; Quality of Life ; }, abstract = {Oral mucositis is a common and debilitating oral complication in head and neck cancer patients undergoing radiotherapy, resulting in diminished quality of life and potential treatment disruptions. Oral microbiota has long been recognized as a contributing factor in the initiation and progression of radiation-induced oral mucositis (RIOM). Numerous studies have indicated that the radiation-induced oral microbial dysbiosis promotes the occurrence and severity of oral mucositis. Therefore, approaches that modulate oral microbial ecology are promising for the management of RIOM. Probiotics as a relatively predicable and safe measure that modulates microecology have garnered significant interest. In this review, we discussed the correlation between RIOM and oral microbiota, with a particular focus on the efficacy of probiotics in the control of RIOM, in order to provide novel paradigm for the management of this disease.}, }
@article {pmid39358950, year = {2024}, author = {Zhang, J and Qin, L and Chang, Y and He, Y and Zhao, W and Zhao, Y and Ding, Y and Gao, J and Zhao, X}, title = {One-Pot Assay for Rapid Detection of Stenotrophomonas maltophilia by RPA-CRISPR/Cas12a.}, journal = {ACS synthetic biology}, volume = {13}, number = {10}, pages = {3400-3412}, doi = {10.1021/acssynbio.4c00481}, pmid = {39358950}, issn = {2161-5063}, mesh = {*Stenotrophomonas maltophilia/genetics ; *CRISPR-Cas Systems/genetics ; Nucleic Acid Amplification Techniques/methods ; Recombinases/metabolism/genetics ; DNA, Bacterial/genetics ; CRISPR-Associated Proteins/genetics ; Endodeoxyribonucleases/genetics ; Bacterial Proteins ; }, abstract = {Stenotrophomonas maltophilia (S. maltophilia, SMA) is a common opportunistic pathogen that poses a serious threat to the food industry and human health. Traditional detection methods for SMA are time-consuming, have low detection rates, require complex and expensive equipment and professional technical personnel for operation, and are unsuitable for on-site detection. Therefore, establishing an efficient on-site detection method has great significance in formulating appropriate treatment strategies and ensuring food safety. In the present study, a rapid one-pot detection method was established for SMA using a combination of Recombinase Polymerase Amplification (RPA) and CRISPR/Cas12a, referred to as ORCas12a-SMA (one-pot RPA-CRISPR/Cas12a platform). In the ORCas12a-SMA detection method, all components were added into a single tube simultaneously to achieve one-pot detection and address the problems of nucleic acid cross-contamination and reduced sensitivity caused by frequent cap opening during stepwise detection. The ORCas12a-SMA method could detect at least 3 × 10° copies·μL[-1] of SMA genomic DNA within 30 min at 37 °C. Additionally, this method exhibited sensitivity compared to the typical two-step RPA-CRISPR/Cas12a method. Overall, the ORCas12a-SMA detection offered the advantages of rapidity, simplicity, high sensitivity and specificity, and decreased need for complex large-scale instrumentation. This assay is the first application of the one-pot platform based on the combination of RPA and CRISPR/Cas12a in SMA detection and is highly suitable for point-of-care testing. It helps reduce losses in the food industry and provides assistance in formulating timely and appropriate antimicrobial treatment plans.}, }
@article {pmid39358586, year = {2025}, author = {de Lorenzo, V and Baquero, F and Aguilar, A}, title = {Carlos Asensio and the dawn of molecular microbial ecology.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {28}, number = {5}, pages = {897-908}, pmid = {39358586}, issn = {1618-1905}, support = {CL6-2021-UE 101060625//Horizon 2020 Framework Programme/ ; Y2020/TCS- 6555//Comunidad de Madrid/ ; }, mesh = {History, 20th Century ; Spain ; Humans ; Gastrointestinal Microbiome ; *Microbiology/history ; }, abstract = {At near 50 years of the discovery of microcins, this article highlights the pivotal-but under-recognised-influence of Spanish biochemist Carlos Asensio (1925-1982) in contemporary microbiology, featuring the epistemological, sociological, and cultural impact of his scientific achievements. At a time when the intestinal microbiome is central to current biomedical research, it is due to emphasise his role in the establishment of new scientific fields that are now considered fundamental. Despite his premature death at the peak of his conceptual and experimental creativity, many of his ideas about microbial communication in complex communities inspired a generation of researchers and opened new topics reach to this day. Asensio was also a trailblazer in Spain, advocating for fundamental research within the socio-economic context of his time. He foresaw the shift towards what is now termed the knowledge-based bioeconomy, recognised the need for multidisciplinary research teams, and advocated integration science into societal and political agendas. These facets became evident during his research on microcins, low molecular weight bioactive compounds produced by enterobacteria. These molecules were hypothesised as mediators of microbial interactions in the human gut and were considered potential new antibiotics and even antitumoral agents. His research mobilised young talent and attracted unprecedented resources in Spain during the late 1970s-early 1980s. It underscored the medical value of microbial ecology and exemplified the benefits of collaboration between academia and industry. Asensio played a pivotal role in the emergence of molecular microbial ecology as a research discipline and its foundational and applied significance in biotechnology.}, }
@article {pmid39358432, year = {2024}, author = {Zhi, W and Li, A and Wang, Q and Yuan, X and Qing, J and Zhang, C and Wang, Y and Li, Y}, title = {Safety and efficacy assessment of fecal microbiota transplantation as an adjunctive treatment for IgA nephropathy: an exploratory clinical trial.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {22935}, pmid = {39358432}, issn = {2045-2322}, support = {82170716//National Science Foundation of China/ ; }, mesh = {Humans ; *Glomerulonephritis, IGA/therapy ; Male ; Female ; Adult ; *Fecal Microbiota Transplantation/methods/adverse effects ; *Gastrointestinal Microbiome ; Middle Aged ; Treatment Outcome ; Cytokines/blood/metabolism ; }, abstract = {To assess the safety and efficacy of fecal microbiota transplantation (FMT) as an adjunctive therapeutic intervention for IgA nephropathy (IgAN). Fifteen patients with IgA nephropathy were recruited based on inclusion and exclusion criteria and underwent FMT using enteric microbial capsules. Clinical indicators, intestinal microbiota and metabolomic profiles, as well as changes in serum immune cells and cytokines, were monitored before and after FMT. No severe adverse reactions were observed in the subjects. After FMT, there was a reduction in the 24-h urinary protein quantification in subjects. The relative abundances of Phocaeicola_vulgatus, Bacteroides_uniformis, Prevotella_copri, Phocaeicola_dorei, Bacteroides_ovatus, Bacteroides_xylanisolvens, Parabacteroides _distasonis, Bifidobacterium_pseudocatenulatum, Bacteroides_sp._HF-162, and Bifidobacterium_longum changed after FMT. In terms of intestinal metabolites, the levels of acylcarnitine18:0 (ACar.18:0), cotinine, N-arachidonoyl-L-serine, phosphatidylcholine (PC. (18:3e/22:6)), serotonin, and fumagillin showed significant changes. Flow cytometry analysis showed the absolute count of plasma B cells decreased in subjects, and this change correlated with alterations in the intestinal microbiota and metabolites. This study preliminarily evaluates the safety and efficacy of FMT in patients with IgAN. No significant adverse reactions were observed, and the administration of FMT alongside ACEI/ARB therapy was effective in reducing urinary protein levels in patients with IgAN, a process that may be associated with B-cell immunity.}, }
@article {pmid39357457, year = {2024}, author = {Olavarria, K and Sousa, DZ}, title = {Thermodynamic tools for more efficient biotechnological processes: an example in poly-(3-hydroxybutyrate) production from carbon monoxide.}, journal = {Current opinion in biotechnology}, volume = {90}, number = {}, pages = {103212}, doi = {10.1016/j.copbio.2024.103212}, pmid = {39357457}, issn = {1879-0429}, mesh = {*Carbon Monoxide/metabolism ; *Hydroxybutyrates/metabolism ; *Thermodynamics ; *Polyesters/metabolism/chemistry ; *Biotechnology/methods ; Metabolic Engineering/methods ; Polyhydroxybutyrates ; }, abstract = {Modern biotechnology requires the integration of several disciplines, with thermodynamics being a crucial one. Experimental approaches frequently used in biotechnology, such as rewiring of metabolic networks or culturing of micro-organisms in engineered environments, can benefit from the application of thermodynamic tools. In this paper, we provide an overview of several thermodynamic tools that are useful for the design and optimization of biotechnological processes, and we demonstrate their potential application in the production of poly-(3-hydroxybutyrate) (PHB) from carbon monoxide (CO). We discuss how these tools can aid in the design of metabolic engineering strategies, the calculation of expected yields, the assessment of the thermodynamic feasibility of the targeted conversions, the identification of potential thermodynamic bottlenecks, and the selection of genetic engineering targets. Although we illustrate these tools using the specific example of PHB production from CO, they can be applied to other substrates and products.}, }
@article {pmid39357161, year = {2024}, author = {Wan, W and Grossart, HP and Zhang, W and Xiong, X and Yuan, W and Liu, W and Yang, Y}, title = {Lake ecological restoration of vegetation removal mitigates algal blooms and alters landscape patterns of water and sediment bacteria.}, journal = {Water research}, volume = {267}, number = {}, pages = {122516}, doi = {10.1016/j.watres.2024.122516}, pmid = {39357161}, issn = {1879-2448}, mesh = {*Lakes/microbiology ; *Geologic Sediments/microbiology ; *Bacteria ; *Eutrophication ; Nitrogen ; Phosphorus ; Ecosystem ; Phylogeny ; }, abstract = {Elucidating the influences of ecological restoration measure of lakeshore vegetation removal on water quality and biological community is an important but underestimated subject. We adopted molecular and statistical tools to estimate ecological restoration performance in a plateau lake receiving vegetation removal and simultaneously investigated variabilities of bacterial communities in water and sediment. Significant decreases in lake trophic level and algal bloom degree followed notable decreases in water total nitrogen and total phosphorus after vegetation removal. Non-significant changes in sediment nutrients accompanied remarkable variabilities of abundance and composition of nutrient-cycling functional genes (NCFGs) of sediment bacteria. Taxonomic and phylogenetic α-diversities, functional redundancies, and dispersal potentials of bacteria in water and sediment decreased after vegetation removal, and community successions of water and sediment bacteria were separately significant and non-significant. There were opposite changes in ecological attributes of bacteria in water and sediment in response to vegetation removal, including niche breadth, species replacement, richness difference, community complexity, and community stability. Species replacement rather than richness difference affected more on taxonomic β-diversities of bacteria in water and sediment before and after vegetation removal, and determinism rather than stochasticity dominated bacterial community assemblage. Our results highlighted vegetation removal mitigated algal bloom and affected differently on landscapes of water and sediment bacteria. These findings point to dominant ecological mechanisms underlying landscape shifts in water and sediment bacteria in a disturbed lake receiving vegetation removal and have the potential to guide lake ecological restoration.}, }
@article {pmid39353102, year = {2024}, author = {He, J and Castilla-Alcantara, JC and Ortega-Calvo, JJ and Harms, H and Wick, LY}, title = {DC Electric Fields Promote Biodegradation of Waterborne Naphthalene in Biofilter Systems.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {41}, pages = {18234-18243}, pmid = {39353102}, issn = {1520-5851}, mesh = {*Biodegradation, Environmental ; Filtration ; Electricity ; Water Pollutants, Chemical/metabolism ; Naphthalenes/metabolism ; }, abstract = {Biofiltration is a simple and low-cost method for the cleanup of contaminated water. However, the reduced availability of dissolved chemicals to surface-attached degrader bacteria may limit its efficient use at certain hydraulic loadings. When a direct current (DC) electric field is applied to an immersed packed bed, it invokes electrokinetic processes, such as electroosmotic water flow (EOF). EOF is a surface-charge-induced plug-flow-shaped movement of pore fluids. It acts at a nanometer distance above surfaces and allows the change of microscale pressure-driven flow profiles and, hence, the availability of dissolved contaminants to microbial degraders. In laboratory percolation columns, we assessed the effects of a weak DC electric field (E = 0.5 V·cm[-1]) on the biodegradation of waterborne naphthalene (NAH) by surface-attached Pseudomonas fluorescens LP6a. To vary NAH bioavailability, we used different NAH concentrations (C0 = 2.7, 5.1, or 7.8 × 10[-5] mol·L[-1]) and Darcy velocities typical for biofiltration (U¯ = 0.2-1.2 × 10[-4] m·s[-1]). In DC-free controls, we observed higher specific degradation rates (qc) at higher NAH concentrations. The qc depended on U¯, suggesting bioavailability restrictions depending on the hydraulic residence times. DC fields consistently increased qc and resulted in linearly increasing benefits up to 55% with rising hydraulic loadings relative to controls. We explain these biodegradation benefits by EOF-altered microscale flow profiles allowing for better NAH provision to bacteria attached to the collectors even though the EOF was calculated to be 100-800 times smaller than bulk water flow. Our data suggest that electrokinetic approaches may give rise to future technical applications that allow regulating biodegradation, for example, in response to fluctuating hydraulic loadings.}, }
@article {pmid39354222, year = {2024}, author = {Suzuki, Y and Webb, SJ and Kouduka, M and Kobayashi, H and Castillo, J and Kallmeyer, J and Moganedi, K and Allwright, AJ and Klemd, R and Roelofse, F and Mapiloko, M and Hill, SJ and Ashwal, LD and Trumbull, RB}, title = {Subsurface Microbial Colonization at Mineral-Filled Veins in 2-Billion-Year-Old Mafic Rock from the Bushveld Igneous Complex, South Africa.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {116}, pmid = {39354222}, issn = {1432-184X}, support = {AB0502//Astrobiology Center Program of National Institutes of Natural Sciences (NINS)/ ; }, mesh = {South Africa ; *Bacteria/isolation &amp; purification/classification ; Geologic Sediments/microbiology ; Minerals/analysis/metabolism ; Clay/chemistry ; Soil Microbiology ; }, abstract = {Recent advances in subsurface microbiology have demonstrated the habitability of multi-million-year-old igneous rocks, despite the scarce energy supply from rock-water interactions. Given the minimal evolution coupled with exceedingly slow metabolic rates in subsurface ecosystems, spatiotemporally stable igneous rocks can sustain microbes over geological time scales. This study investigated a 2-billion-year-old mafic rock in the Bushveld Igneous Complex, South Africa, where ultradeep drilling is being executed by the International Continental Scientific Drilling Program (ICDP). New procedures were successfully developed to simultaneously detect indigenous and contaminant microbial cells in a drill core sample. Precision rock sectioning coupled with infrared, fluorescence, and electron microscopy imaging of the rock section with submicron resolution revealed microbial colonization in veins filled with clay minerals. The entry and exit of microbial cells in the veins are severely limited by tight packing with clay minerals, the formation of which supplies energy sources for long-term habitability. Further microbiological characterization of drilled rock cores from the Bushveld Igneous Complex will expand the understanding of microbial evolution in deep igneous rocks over 2 billion years.}, }
@article {pmid39354152, year = {2024}, author = {Freire-Zapata, V and Holland-Moritz, H and Cronin, DR and Aroney, S and Smith, DA and Wilson, RM and Ernakovich, JG and Woodcroft, BJ and Bagby, SC and ,  and ,  and Rich, VI and Sullivan, MB and Stegen, JC and Tfaily, MM}, title = {Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient.}, journal = {Nature microbiology}, volume = {9}, number = {11}, pages = {2892-2908}, pmid = {39354152}, issn = {2058-5276}, support = {DE-SC0021349//DOE | SC | Biological and Environmental Research (BER)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; }, mesh = {*Permafrost/microbiology ; *Greenhouse Gases/metabolism/analysis ; *Microbiota ; *Methane/metabolism ; *Metagenomics ; *Carbon Dioxide/metabolism ; *Bacteria/metabolism/genetics/classification ; Sweden ; Ecosystem ; Soil Microbiology ; }, abstract = {Interactions between microbiomes and metabolites play crucial roles in the environment, yet how these interactions drive greenhouse gas emissions during ecosystem changes remains unclear. Here we analysed microbial and metabolite composition across a permafrost thaw gradient in Stordalen Mire, Sweden, using paired genome-resolved metagenomics and high-resolution Fourier transform ion cyclotron resonance mass spectrometry guided by principles from community assembly theory to test whether microorganisms and metabolites show concordant responses to changing drivers. Our analysis revealed divergence between the inferred microbial versus metabolite assembly processes, suggesting distinct responses to the same selective pressures. This contradicts common assumptions in trait-based microbial models and highlights the limitations of measuring microbial community-level data alone. Furthermore, feature-scale analysis revealed connections between microbial taxa, metabolites and observed CO2 and CH4 porewater variations. Our study showcases insights gained by using feature-level data and microorganism-metabolite interactions to better understand metabolic processes that drive greenhouse gas emissions during ecosystem changes.}, }
@article {pmid39350412, year = {2024}, author = {Khan, A and Abass, S and Nizami, SAI and Shariq, M and Zahiruddin, S and Parveen, B and Parveen, R}, title = {The Gut Health Revolution: Herbs and Dietary Phytochemicals in Balancing Gut Microbiota for Optimal Human Health.}, journal = {Current pharmaceutical biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113892010313921240923125946}, pmid = {39350412}, issn = {1873-4316}, abstract = {The gut microbiota is a varied population of microorganisms that live in the human gastrointestinal system. Emerging research emphasizes the importance of this microbial ecology in general health and its influence on a variety of disorders. The review explores the synergy between herbal treatment and traditional medicine, emphasizing their cultural significance and therapeutic benefits. It delves into the intricate relationship between herbal remedies, traditional healing practices, and their sustained usage over centuries. The review highlights the pivotal role of the gut microbiota in herbal medicine, elucidating how treatments influence the gastrointestinal microorganisms, impacting overall health. Dietary phytochemicals are underscored for their significance in herbal medicine and nutritional well-being, along with the interdependence of plant extracts and botanicals. The investigation explores the molecular connections between phytoconstituents and gut microbiota, aiming to deepen the understanding of herbal medicine's tailored approach to specific health challenges. The summary concludes by emphasizing herbal treatments' unique ability to regulate gut flora, contributing to overall gastrointestinal wellbeing. In closing, the review provides a concise overview, serving as a valuable resource for integrative medicine research, with recommendations for future exploration of herbal medicine's potential in healthcare.}, }
@article {pmid39349736, year = {2024}, author = {Karačić, S and Suarez, C and Hagelia, P and Persson, F and Modin, O and Martins, PD and Wilén, BM}, title = {Microbial acidification by N, S, Fe and Mn oxidation as a key mechanism for deterioration of subsea tunnel sprayed concrete.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {22742}, pmid = {39349736}, issn = {2045-2322}, mesh = {*Oxidation-Reduction ; *Manganese/metabolism ; *Iron/metabolism ; *Construction Materials/microbiology ; Corrosion ; *Biofilms/growth &amp; development ; Nitrogen/metabolism ; Sulfur/metabolism ; Steel/chemistry ; Bacteria/metabolism/genetics ; Hydrogen-Ion Concentration ; }, abstract = {The deterioration of fibre-reinforced sprayed concrete was studied in the Oslofjord subsea tunnel (Norway). At sites with intrusion of saline groundwater resulting in biofilm growth, the concrete exhibited significant concrete deterioration and steel fibre corrosion. Using amplicon sequencing and shotgun metagenomics, the microbial taxa and surveyed potential microbial mechanisms of concrete degradation at two sites over five years were identified. The concrete beneath the biofilm was investigated with polarised light microscopy, scanning electron microscopy and X-ray diffraction. The oxic environment in the tunnel favoured aerobic oxidation processes in nitrogen, sulfur and metal biogeochemical cycling as evidenced by large abundances of metagenome-assembled genomes (MAGs) with potential for oxidation of nitrogen, sulfur, manganese and iron, observed mild acidification of the concrete, and the presence of manganese- and iron oxides. These results suggest that autotrophic microbial populations involved in the cycling of several elements contributed to the corrosion of steel fibres and acidification causing concrete deterioration.}, }
@article {pmid39349195, year = {2024}, author = {Cheng, X and Zhao, R and Bodelier, PLE and Song, Y and Yang, K and Tuovinen, OH and Wang, H}, title = {Differential response of subterranean microbiome to exogenous organic matter input in a cave ecosystem.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176584}, doi = {10.1016/j.scitotenv.2024.176584}, pmid = {39349195}, issn = {1879-1026}, mesh = {*Microbiota ; *Caves/microbiology ; Soil Microbiology ; Bacteria/metabolism ; Fungi ; Ecosystem ; Climate Change ; }, abstract = {As a recurrent climatic phenomenon in the context of climate change, extreme rainstorms induce vertical translocation of organic matter and increase moisture content in terrestrial ecosystems. However, it remains unclear whether heavy rainstorms can impact microbial communities in the deep biosphere by modulating organic matter input. In this study, we present findings on the different responses of bacterial and fungal communities in a subsurface cave to rainstorms and moisture variations through field surveys and microcosm experiments. During periods of rainstorms, the influx of dissolved organic matter (DOM) from soil overlying the cave into cave sediments significantly enhanced the correlation between core bacteria and environmental factors, particularly fluorescence spectral indices. The resource utilization of core bacteria was diminished, while the functional diversity of core fungi remained relatively unaltered. We also performed simulated experiments with restricted external DOM inputs, in which DOM content was observed to decrease and microbial diversity increase in response to artificially increased moisture content (MC). The niche breadth of core bacteria decreased and became more closely associated with DOM as the MC increased, while the niche breadth of core fungi remained predominantly unchanged. Compared to fungi, cave bacteria exhibited higher sensitivity towards variations in DOM. The core microbiome can efficiently utilize the available organic matter and participate in nitrogen- and sulfur-related metabolic processes. The study systematically revealed distinct microbial responses to rainstorm events, thereby providing valuable insights for future investigations into energy utilization within deep biospheres.}, }
@article {pmid39349071, year = {2024}, author = {Toporowska, M and Żebracki, K and Mazur, A and Mazur-Marzec, H and Šulčius, S and Alzbutas, G and Lukashevich, V and Dziga, D and Mieczan, T}, title = {Biodegradation of microcystins by microbiota of duckweed Spirodelapolyrhiza.}, journal = {Chemosphere}, volume = {366}, number = {}, pages = {143436}, doi = {10.1016/j.chemosphere.2024.143436}, pmid = {39349071}, issn = {1879-1298}, mesh = {*Microcystins/metabolism ; *Biodegradation, Environmental ; *Microbiota ; *Araceae/metabolism ; Tandem Mass Spectrometry ; Cyanobacteria/metabolism/genetics ; Bacteria/metabolism/genetics/classification ; }, abstract = {Cyanobacteria-produced allelochemicals, including hepatotoxic microcystins (MCs), exert an inhibitory effect on macrophyte growth. However, the role of macrophyte-associated bacteria and algae (macrophyte microbiota) in mitigating these immediate negative effects of cyanotoxins remains poorly understood. In this paper, we analyzed the biodegradation of microcystin-RR, MC-LR, and MC-LF by microbiota of the macrophyte Spirodela polyrhiza. The biodegradation of two MC variants was observed and LC-MS/MS analysis allowed identifying the degradation products of MC-RR (m/z 1011, 984, 969, 877, 862, 820, and 615) and MC-LR (m/z 968 and 953), including eight previously unreported products. No degradation products of MC-LF were detected, suggesting its stability and resistance under experimental conditions. NGS-based profiling of microbial consortia revealed no major differences in bacterial community composition across experimental treatments. Taxa previously reported as capable of MC degradation have been found in S. polyrhiza microbiota. Furthermore, the presence of genes encoding putative microcystinase homologues and the formation of new linear intermediates suggest a biochemical pathway that is similar, but not identical to previously reported. The ability of aquatic plant microbiota to biodegrade MCs holds environmental significance, and further studies in this field are required.}, }
@article {pmid39348267, year = {2024}, author = {Clegg, T and Pawar, S}, title = {Variation in thermal physiology can drive the temperature-dependence of microbial community richness.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39348267}, issn = {2050-084X}, support = {NERC QMEE Centre for Doctoral Training NE/P012345/1//Natural Environment Research Council/ ; RF-2020-653\2//Leverhulme Trust/ ; NE/M020843/1//NERC Natural Environment Research Council/ ; NE/S000348/1//NERC Natural Environment Research Council/ ; }, mesh = {*Temperature ; *Microbiota/physiology ; Bacteria/classification/genetics/metabolism ; Biodiversity ; Bacterial Physiological Phenomena ; }, abstract = {Predicting how species diversity changes along environmental gradients is an enduring problem in ecology. In microbes, current theories tend to invoke energy availability and enzyme kinetics as the main drivers of temperature-richness relationships. Here, we derive a general empirically-grounded theory that can explain this phenomenon by linking microbial species richness in competitive communities to variation in the temperature-dependence of their interaction and growth rates. Specifically, the shape of the microbial community temperature-richness relationship depends on how rapidly the strength of effective competition between species pairs changes with temperature relative to the variance of their growth rates. Furthermore, it predicts that a thermal specialist-generalist tradeoff in growth rates alters coexistence by shifting this balance, causing richness to peak at relatively higher temperatures. Finally, we show that the observed patterns of variation in thermal performance curves of metabolic traits across extant bacterial taxa is indeed sufficient to generate the variety of community-level temperature-richness responses observed in the real world. Our results provide a new and general mechanism that can help explain temperature-diversity gradients in microbial communities, and provide a quantitative framework for interlinking variation in the thermal physiology of microbial species to their community-level diversity.}, }
@article {pmid39346682, year = {2024}, author = {Child, HT and Wierzbicki, L and Joslin, GR and Tennant, RK}, title = {Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing.}, journal = {Access microbiology}, volume = {6}, number = {9}, pages = {}, pmid = {39346682}, issn = {2516-8290}, abstract = {Metagenomics has been transformative in our understanding of the diversity and function of soil microbial communities. Applying long read sequencing to whole genome shotgun metagenomics has the potential to revolutionise soil microbial ecology through improved taxonomic classification, functional characterisation and metagenome assembly. However, optimisation of robust methods for long read metagenomics of environmental samples remains undeveloped. In this study, Oxford Nanopore sequencing using samples from five commercially available soil DNA extraction kits was compared across four soil types, in order to optimise read length and reproducibility for comparative long read soil metagenomics. Average extracted DNA lengths varied considerably between kits, but longer DNA fragments did not translate consistently into read lengths. Highly variable decreases in the length of resulting reads from some kits were associated with poor classification rate and low reproducibility in microbial communities identified between technical repeats. Replicate samples from other kits showed more consistent conversion of extracted DNA fragment size into read length and resulted in more congruous microbial community representation. Furthermore, extraction kits showed significant differences in the community representation and structure they identified across all soil types. Overall, the QIAGEN DNeasy PowerSoil Pro Kit displayed the best suitability for reproducible long-read WGS metagenomic sequencing, although further optimisation of DNA purification and library preparation may enable translation of higher molecular weight DNA from other kits into longer read lengths. These findings provide a novel insight into the importance of optimising DNA extraction for achieving replicable results from long read metagenomic sequencing of environmental samples.}, }
@article {pmid39346007, year = {2024}, author = {Eisenhofer, R and Alberdi, A and Woodcroft, BJ}, title = {Quantifying microbial DNA in metagenomes improves microbial trait estimation.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae111}, pmid = {39346007}, issn = {2730-6151}, abstract = {Shotgun metagenomics is a powerful tool for studying the genomic traits of microbial community members, such as genome size, gene content, etc. While such traits can be used to better understand the ecology and evolution of microbial communities, the accuracy of their estimations can be critically influenced by both known and unknown factors. One factor that can bias trait estimations is the proportion of eukaryotic and viral DNA in a metagenome, as some bioinformatic tools assume that all DNA reads in a metagenome are bacterial or archaeal. Here, we add to a recent debate about the influence of eukaryotic DNA in the estimation of average genome size from a global soil sample dataset using a new bioinformatic tool. Contrary to what was assumed, our reanalysis of this dataset revealed that soil samples can contain a substantial proportion of non-microbial DNA, which severely inflated the original estimates of average genome size. Correcting for this bias significantly improves the statistical support for the negative relationship between average bacterial genome size and soil pH. These results highlight that metagenomes can contain large quantities of non-microbial DNA and that new methods that correct for this can improve microbial trait estimation.}, }
@article {pmid39340684, year = {2024}, author = {Vinothini, K and Nakkeeran, S and Saranya, N and Jothi, P and Richard, JI and Perveen, K and Bukhari, NA and Glick, BR and Sayyed, RZ and Mastinu, A}, title = {Rhizosphere Engineering of Biocontrol Agents Enriches Soil Microbial Diversity and Effectively Controls Root-Knot Nematodes.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {120}, pmid = {39340684}, issn = {1432-184X}, mesh = {Animals ; *Solanum lycopersicum/microbiology/parasitology ; *Soil Microbiology ; *Rhizosphere ; *Bacillus/genetics/physiology ; *Plant Roots/microbiology/parasitology ; *Pest Control, Biological ; Plant Diseases/parasitology/prevention &amp; control/microbiology ; Trichoderma/physiology/genetics ; Tylenchoidea/physiology ; Microbiota ; Antinematodal Agents/pharmacology ; Biological Control Agents/pharmacology ; Bacteria/genetics/classification ; }, abstract = {The root-knot nematode (RKN) causes significant yield loss in tomatoes. Understanding the interaction of biocontrol agents (BCAs)-nematicides-soil microbiomes and RKNs is essential for enhancing the efficacy of biocontrol agents and nematicides to curb RKN damage to crops. The present study aimed to evaluate the in vitro effectiveness of BACa and nematicide against RKN and to apply the amplicon sequencing to assess the interaction of Bacillus velezensis (VB7) and Trichoderma koningiopsis (TK) against RKNs. Metagenomic analysis revealed the relative abundance of three phyla such as Proteobacteria (42.16%), Firmicutes (19.57%), and Actinobacteria (17.69%) in tomato rhizospheres. Those tomato rhizospheres treated with the combined application of B. velezensis VB7 + T. koningiopsis TK and RKN had a greater frequency of diversity and richness than the control. RKN-infested tomato rhizosphere drenched with bacterial and fungal antagonists had the maximum diversity index of bacterial communities. A strong correlation with a maximum number of interconnection edges in the phyla Proteobacteria, Firmicutes, and Actinobacteria was evident in soils treated with both B. velezensis VB7 and T. koningiopsis TK challenged against RKN in infected soil. The present study determined a much greater diversity of bacterial taxa observed in tomato rhizosphere soils treated with B. velezensis VB7 and T. koningiopsis TK than in untreated soil. It is suggested that the increased diversity and abundance of bacterial communities might be responsible for increased nematicidal properties in tomato plants. Hence, the combined applications of B. velezensis VB7 and T. koningiopsis TK can enhance the nematicidal action to curb RKN infecting tomatoes.}, }
@article {pmid39340560, year = {2024}, author = {Charalampous, G and Kormas, KA and Antoniou, E and Kalogerakis, N and Gontikaki, E}, title = {Distinct Communities of Bacteria and Unicellular Eukaryotes in the Different Water Masses of Cretan Passage Water Column (Eastern Mediterranean Sea).}, journal = {Current microbiology}, volume = {81}, number = {11}, pages = {381}, pmid = {39340560}, issn = {1432-0991}, support = {1874//Hellenic Foundation for Research and Innovation/ ; 1510//Hellenic Foundation for Research and Innovation/ ; }, mesh = {Mediterranean Sea ; *Bacteria/classification/genetics/isolation &amp; purification ; *Eukaryota/classification/genetics/isolation &amp; purification ; *Seawater/microbiology ; *Microbiota ; *RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Phylogeny ; Ecosystem ; }, abstract = {Elucidating marine microbiota diversity and dynamics holds significant importance due to their role in maintaining vital ecosystem functions and services including climate regulation. This work aims to contribute in the understanding of microbial ecology and networking in one of the world's most understudied marine regions, the Eastern Mediterranean Sea. High-throughput 16S and 18S rRNA gene sequencing analysis was applied to study the diversity of bacteria and unicellular eukaryotes in the different water masses of the Cretan Passage during two seasonally-different sampling expeditions. We assumed that microbial associations differ between the surface and deepwater masses and created co-occurrence networks to evaluate this hypothesis. Our results unveiled vertical variations in both bacterial and unicellular eukaryotic diversity with species fluctuations indicative of seasonality being recorded in the surface water mass. Heterotrophic taxa and grazers related to organic matter degradation and nutrient cycling were enriched in the deepest water layers. Moreover, surface waters presented a higher number of microbial associations indicating abundant ecological niches compared to the deepest layer, possibly related to the lack of bottom-up resources in the oligotrophic deep ocean. Overall, our data provide insight in a heavily stressed, yet underexplored, marine area that requires further research to unravel the ecological roles of marine microbes. To our knowledge, this is the first study that combines molecular biology tools to provide data on both planktic prokaryotes and unicellular eukaryotes across the different water masses in this marine region of the Eastern Mediterranean basin.}, }
@article {pmid39340556, year = {2024}, author = {Fernandez de Landa, G and Alberoni, D and Braglia, C and Baffoni, L and Fernandez de Landa, M and Revainera, PD and Quintana, S and Zumpano, F and Maggi, MD and Di Gioia, D}, title = {The Gut Microbiome of Two Wild Bumble Bee Species Native of South America: Bombus pauloensis and Bombus bellicosus.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {121}, pmid = {39340556}, issn = {1432-184X}, support = {777760//European Commission/ ; 777760//European Commission/ ; 777760//European Commission/ ; 777760//European Commission/ ; }, mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome ; *Nosema/physiology/isolation &amp; purification/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; South America ; }, abstract = {South America is populated by a wide range of bumble bee species that represent an important source of biodiversity, supporting pollination services in natural and agricultural ecosystems. These pollinators provide unique specific microbial niches, populated by a wide number of microorganisms such as symbionts, environmental opportunistic bacteria, and pathogens. Recently, it was demonstrated how microbial populations are shaped by trophic resources and environmental conditions but also by anthropogenic pressure, which strongly affects microbes' functionality. This study is focused on the impact of different land uses (natural reserve, agroecosystem, and suburban) on the gut microbiome composition of two South American bumble bees, Bombus pauloensis and Bombus bellicosus. Gut microbial DNA extracted from collected bumble bees was sequenced on the Illumina MiSeq platform and correlated with land use. Nosema ceranae load was analyzed with qPCR and correlated with microbiome data. Significant differences in gut microbiome composition between the two wild bumble bee species were highlighted, with notable variations in α- and β-diversity across study sites. Bombus bellicosus showed a high abundance of Pseudomonas, a genus that includes environmental saprobes, and was found to be the second major taxa populating the gut microbiome, probably indicating the vulnerability of this host to environmental pollution. Pathogen analysis unveils a high prevalence of N. ceranae, with B. bellicosus showing higher susceptibility. Finally, Gilliamella exhibited a negative correlation with N. ceranae, suggesting a potential protective role of this commensal taxon. Our findings underscore the importance of considering microbial dynamics in pollinator conservation strategies, highlighting potential interactions between gut bacteria and pathogens in shaping bumble bee health.}, }
@article {pmid39340548, year = {2024}, author = {Radouane, N and Errafii, K and Mouhib, S and Mhand, KA and Legeay, J and Hijri, M}, title = {Potential Plant-To-Plant Transmission: Shared Endophytic Bacterial Community Between Ziziphus lotus and Its Parasite Cuscuta epithymum.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {119}, pmid = {39340548}, issn = {1432-184X}, support = {Projects AS-77 and AS-85//OCP Group/ ; }, mesh = {*Cuscuta/physiology/microbiology/genetics ; *Ziziphus/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Endophytes/genetics/physiology/classification/isolation &amp; purification ; *Bacteria/genetics/classification/isolation &amp; purification ; Host-Parasite Interactions ; DNA, Bacterial/genetics ; }, abstract = {Microbiota associated with host-parasite relationships offer an opportunity to explore interactions among plants, parasites, and microbes, thereby contributing to the overall complexity of community structures. The dynamics of ecological interactions between parasitic plants and their hosts in arid environments remain largely understudied, especially in Africa. This study aimed to examine the bacterial communities of Cuscuta epithymum L. (clover dodder), an epiphytic parasitic plant, and its host, Ziziphus lotus L. (jujuba), in an arid environment. Our goal was to uncover the ecological complexities of microbial communities within the framework of plant-plant interactions. We conducted a comprehensive analysis of the bacterial composition and diversity within populations of the C. epithymum parasite, the infected- and non-infected jujuba host, and their interface at the shoots of the host. This involved amplicon sequencing, targeting the V5-V6 regions of the 16S rRNA gene. A total of 5680 amplicon sequence variants (ASVs) were identified, with Pseudomonadota, Bacillota, and Actinobacteriota being prevalent phyla. Among the bacterial communities, three genera were dominant: Cutibacterium, Staphylococcus, and Acinetobacter. Interestingly, analyses of alpha-diversity (p = 0.3 for Shannon index and p = 0.5 for Simplon index) and beta-diversity (PERMANOVA, with p-values of 0.6 and 0.3) revealed no significant differences between Cuscuta-infected and non-infected jujube shrubs, suggesting a shared shoot endophytic bacteriome. This finding advances our comprehension of microbial communities linked to plant-parasite interactions in the arid environments of Africa. Further research on various hosts is required to confirm plant-to-plant bacterial transmission through Cuscuta infection. Additionally, studies on functional diversity, cytology, ecophysiology and the mechanisms by which bacterial communities transferred between host and parasite are necessary.}, }
@article {pmid39338505, year = {2024}, author = {Shah, H and Trivedi, M and Gurjar, T and Sahoo, DK and Jergens, AE and Yadav, VK and Patel, A and Pandya, P}, title = {Decoding the Gut Microbiome in Companion Animals: Impacts and Innovations.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338505}, issn = {2076-2607}, abstract = {The changing notion of "companion animals" and their increasing global status as family members underscores the dynamic interaction between gut microbiota and host health. This review provides a comprehensive understanding of the intricate microbial ecology within companion animals required to maintain overall health and prevent disease. Exploration of specific diseases and syndromes linked to gut microbiome alterations (dysbiosis), such as inflammatory bowel disease, obesity, and neurological conditions like epilepsy, are highlighted. In addition, this review provides an analysis of the various factors that impact the abundance of the gut microbiome like age, breed, habitual diet, and microbe-targeted interventions, such as probiotics. Detection methods including PCR-based algorithms, fluorescence in situ hybridisation, and 16S rRNA gene sequencing are reviewed, along with their limitations and the need for future advancements. Prospects for longitudinal investigations, functional dynamics exploration, and accurate identification of microbial signatures associated with specific health problems offer promising directions for future research. In summary, it is an attempt to provide a deeper insight into the orchestration of multiple microbial species shaping the health of companion animals and possible species-specific differences.}, }
@article {pmid39338496, year = {2024}, author = {Denux, M and Armenteros, M and Weber, L and Miller, CA and Sántha, K and Apprill, A}, title = {Coral Reef Water Microbial Communities of Jardines de la Reina, Cuba.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338496}, issn = {2076-2607}, abstract = {Globally, coral reef ecosystems are undergoing significant change related to climate change and anthropogenic activities. Yet, the Cuban archipelago of Jardines de la Reina (JR) has experienced fewer stressors due to its geographical remoteness and high level of conservation. This study examines the surface and benthic reef water microbial communities associated with 32 reef sites along the JR archipelago and explores the relationship between the community composition of reef microorganisms examined using bacterial and archaeal small subunit ribosomal RNA gene (16S rRNA gene) sequencing compared to geographic, conservation/protection level, environmental, physicochemical, and reef benthic and pelagic community features. Reef nutrient concentrations were low and microbial communities dominated by picocyanobacteria and SAR11 and SAR86 clade bacteria, characteristic of an oligotrophic system. Reef water microbial community alpha and beta diversity both varied throughout the archipelago and were strongly related to geography. Three sites in the western archipelago showed unique microbial communities, which may be related to the hydrogeography and influences of the channels linking the Ana Maria gulf with the Caribbean Sea. Overall, this work provides the first extensive description of the reef microbial ecology of the Caribbean's 'Crown Jewel' reef system and a framework to evaluate the influence of ongoing stressors on the reef microorganisms.}, }
@article {pmid39338466, year = {2024}, author = {Lauzon, J and Caron, D and Lazar, CS}, title = {The Saint-Leonard Urban Glaciotectonic Cave Harbors Rich and Diverse Planktonic and Sedimentary Microbial Communities.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338466}, issn = {2076-2607}, support = {RGPIN-2019-06670//Natural Sciences and Engineering Research Council/ ; }, abstract = {The terrestrial subsurface harbors unique microbial communities that play important biogeochemical roles and allow for studying a yet unknown fraction of the Earth's biodiversity. The Saint-Leonard cave in Montreal City (Canada) is of glaciotectonic origin. Its speleogenesis traces back to the withdrawal of the Laurentide Ice Sheet 13,000 years ago, during which the moving glacier dislocated the sedimentary rock layers. Our study is the first to investigate the microbial communities of the Saint-Leonard cave. By using amplicon sequencing, we analyzed the taxonomic diversity and composition of bacterial, archaeal and eukaryote communities living in the groundwater (0.1 µm- and 0.2 µm-filtered water), in the sediments and in surface soils. We identified a microbial biodiversity typical of cave ecosystems. Communities were mainly shaped by habitat type and harbored taxa associated with a wide variety of lifestyles and metabolic capacities. Although we found evidence of a geochemical connection between the above soils and the cave's galleries, our results suggest that the community assembly dynamics are driven by habitat selection rather than dispersal. Furthermore, we found that the cave's groundwater, in addition to being generally richer in microbial taxa than sediments, contained a considerable diversity of ultra-small bacteria and archaea.}, }
@article {pmid39338465, year = {2024}, author = {Cruz, LG and Shen, FT and Chen, CP and Chen, WC}, title = {Dose Effect of Polyethylene Microplastics Derived from Commercial Resins on Soil Properties, Bacterial Communities, and Enzymatic Activity.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338465}, issn = {2076-2607}, support = {MOST 110-2313-B-005-015-//National Science and Technology Council/ ; }, abstract = {Soils are the largest reservoir of microplastics (MPs) on earth. Since MPs can remain in soils for a very long time, their effects are magnified. In this study, different concentrations of polyethylene (PE) MPs derived from commercial resins (0%, 1%, 7%, and 14%, represented as MP_0, MP_1, MP_7, and MP_14) were added to soils to assess the changes in the soils' chemical properties, enzyme activities, and bacterial communities during a 70-day incubation period. The results show that PE MP treatments with low concentrations differed from other treatments in terms of exchangeable Ca and Mg, whereas at high concentrations, the pH and availability of phosphate ions differed. Fluorescein diacetate (FDA), acid phosphatase (ACP), and N-acetyl-β-d-glucosaminidase (NAG) enzyme activities exhibited a dose-related trend with the addition of the PE MPs; however, the average FDA and ACP activities were significantly affected only by MP_14. Changes in the microbial communities were observed at both the phylum and family levels with all PE MP treatments. It was revealed that even a low dosage of PE MPs in soils can affect the functional microbes, and a greater impact is observed on those that can survive in polluted environments with limited resources.}, }
@article {pmid39338425, year = {2024}, author = {Lyu, G and Hu, J and Ma, J}, title = {Variation in Bacterial and Fungal Communities in Soils from Three Major Apple Pear (Pyrus bretschneideri Rehd.) Orchards.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338425}, issn = {2076-2607}, support = {41571304//National Natural Science Foundation of China/ ; }, abstract = {Microbial communities are closely related to the overall health and quality of soil, but studies on microbial ecology in apple pear orchard soils are limited. In the current study, 28 soil samples were collected from three apple pear orchards, and the composition and structure of fungal and bacterial communities were investigated by high-throughput sequencing. The molecular ecological network showed that the keystone taxa of bacterial communities were Actinobacteria, Proteobacteria, Gemmatimonadetes, Acidobacteria, Nitrospirae, and Chloroflexi, and the keystone taxon of fungal communities was Ascomycota. Mantel tests showed that soil texture and pH were important factors shaping soil bacterial and fungal communities, and soil water soluble organic carbon (WSOC) and nitrate nitrogen (NO3[-]-N) were also closely related to soil bacterial communities. Canonical correspondence analysis (CCA) and variation partition analysis (VPA) revealed that geographic distance, soil texture, pH, and other soil properties could explain 10.55%, 13.5%, and 19.03% of the overall variation in bacterial communities, and 11.61%, 13.03%, and 20.26% of the overall variation in fungal communities, respectively. The keystone taxa of bacterial and fungal communities in apple pear orchard soils and their strong correlation with soil properties could provide useful clues toward sustainable management of orchards.}, }
@article {pmid39338386, year = {2024}, author = {Galinytė, D and Bernatoniene, J and Žilius, M and Rysevaitė-Kyguolienė, K and Savickas, A and Karosienė, J and Briedis, V and Pauža, DH and Savickienė, N}, title = {In Vitro Study of Cyano-Phycocyanin Release from Hydrogels and Ex Vivo Study of Skin Penetration.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {17}, number = {9}, pages = {}, pmid = {39338386}, issn = {1424-8247}, abstract = {BACKGROUND: This study explored the most suitable materials for incorporating cyano-phycocyanin (C-PC) into hydrogels, focusing on maintaining the C-PC's long-term structural integrity and stabilityNext, the release of C-PC from the hydrogels and its skin penetration were investigated.<br><br>METHODS: A series of 1% (w/w) C-PC hydrogels was prepared using various gelling agents and preservatives. Spectrophotometric measurements compared the amount of C-PC in the hydrogels to the initially added amount. After selecting the most suitable gelling agent and preservative, two C-PC hydrogels, with and without propylene glycol (PG) (Sigma-Aldrich, St. Louis, MO, USA), were produced for further testing. In vitro release studies utilized modified Franz-type diffusion cells, while ex vivo skin-permeation studies employed Bronaugh-type cells and human skin. Confocal laser scanning microscopy analyzed C-PC accumulation in the skin.<br><br>RESULTS: The findings demonstrated that sodium alginate (Sigma-Aldrich, St. Louis, MO, USA), hydroxyethyl cellulose (HEC) (Sigma-Aldrich, St. Louis, MO, USA), and Soligel[TM] (Givaudan, Vernier, Switzerland) are effective biopolymers for formulating hydrogels while maintaining C-PC stability. After 6 h, C-PC release from the hydrogel containing PG was approximately 10% or 728.07 (&#xb1;19.35) &#x3bc;g/cm[2], significantly higher than the nearly 7% or 531.44 (&#xb1;26.81) &#x3bc;g/cm[2] release from the hydrogel without PG (p < 0.05). The ex vivo qualitative skin-permeation study indicated that PG enhances C-PC penetration into the outermost skin layer.<br><br>CONCLUSION: PG's ability to enhance the release of C-PC from the hydrogel, coupled with its capacity to modify the skin barrier ex vivo, facilitates the penetration of C-PC into the stratum corneum.}, }
@article {pmid39335049, year = {2024}, author = {Afonso, L and Grzegorczyk, KG and Salomão, JM and Basso, KR and Alves, LC and Silva, MCD and Chryssafidis, AL and Gionco-Cano, B and Yamada-Ogatta, SF and Andrade, G}, title = {Fluopsin C Promotes Biofilm Removal of XDR Acinetobacter baumannii and Presents an Additive Effect with Polymyxin B on Planktonic Cells.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {9}, pages = {}, pmid = {39335049}, issn = {2079-6382}, support = {439754/2018-6//National Council for Scientific and Technological Development/ ; 406016/2022-4//National Council for Scientific and Technological Development/ ; }, abstract = {Acinetobacter baumannii emerged as one of the most important pathogens for the development of new antimicrobials due to the worldwide detection of isolates resistant to all commercial antibiotics, especially in nosocomial infections. Biofilm formation enhances A. baumannii survival by impairing antimicrobial action, being an important target for new antimicrobials. Fluopsin C (FlpC) is an organocupric secondary metabolite with broad-spectrum antimicrobial activity. This study aimed to evaluate the antibiofilm activity of FlpC in established biofilms of extensively drug-resistant A. baumannii (XDRAb) and the effects of its combination with polymyxin B (PolB) on planktonic cells. XDRAb susceptibility profiles were determined by Vitek 2 Compact, disk diffusion, and broth microdilution. FlpC and PolB interaction was assessed using the microdilution checkerboard method and time-kill kinetics. Biofilms of XDRAb characterization and removal by FlpC exposure were assessed by biomass staining with crystal violet. Confocal Laser Scanning Microscopy was used to determine the temporal removal of the biofilms using DAPI, and cell viability using live/dead staining. The minimum inhibitory concentration (MIC) of FlpC on XDRAb was 3.5 µg mL[-1]. Combining FlpC + PolB culminated in an additive effect, increasing bacterial susceptibility to both antibiotics. FlpC-treated 24 h biofilms reached a major biomass removal of 92.40 ± 3.38% (isolate 230) using 7.0 µg mL[-1] FlpC. Biomass removal occurred significantly over time through the dispersion of the extracellular matrix and decreasing cell number and viability. This is the first report of FlpC's activity on XDRAb and the compound showed a promissory response on planktonic and sessile cells, making it a candidate for the development of a new antimicrobial product.}, }
@article {pmid39332295, year = {2024}, author = {Tapia, N and Gallardo-Bustos, C and Rojas, C and Vargas, IT}, title = {Long-term evaluation of soil-based bioelectrochemical green roof systems for greywater treatment.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122643}, doi = {10.1016/j.jenvman.2024.122643}, pmid = {39332295}, issn = {1095-8630}, mesh = {*Soil/chemistry ; *Bioelectric Energy Sources ; Water Purification/methods ; Waste Disposal, Fluid/methods ; Biological Oxygen Demand Analysis ; }, abstract = {Water scarcity has generated the need to identify new sources. Due to its low organic contaminant load, greywater reuse has emerged as a potential alternative. Moreover, the search for decentralized treatment systems in urban areas has prompted research on using green roofs for greywater treatment. However, the performance of organic matter removal is limited by the type of substrate and height of the growing media. Bioelectrochemical systems (BESs) improve treatment performance by providing an additional electron acceptor (the electrode). In this study, nine reactors under three different conditions, i.e., open circuit (OC), microbial fuel cell (MFC), and microbial electrolysis cell (MEC), were built to evaluate the treatment of synthetic greywater in a substrate-growing medium composed of perlite and coconut fiber and operated in batch-cycle mode for 397 days. The results suggested that using BESs enables greywater treatment and the removal of pollutants to levels that allow their reuse for irrigation. Furthermore, electrical conductivity was reduced from 732.4 ± 41.2 μS/cm[2] in OC to 637.32 ± 22.73 μS/cm[2] and 543.15 ± 19.69 μS/cm[2] in MEC and MFC, respectively. The soluble chemical oxygen demand in the latter treatments reached 76% removal, compared to levels above the OC, which only reached approximately 67%. Microbial community analysis revealed differences, mainly in the cathodes, showing a higher development of Flavobacterium, Azospirillum, and Zoogloea in MFCs, which could explain the higher levels of organic matter removal in the other conditions, suggesting that the BES could produce an enrichment of beneficial bacterial groups for treatment. Therefore, implementing BESs in green roofs enables sustainable long-term greywater treatment.}, }
@article {pmid39331293, year = {2024}, author = {Bianchelli, J and Sagua, MI and Quiroga, MP and Nuozzi, G and Fernández, J and Schiaffino, MR}, title = {Temporal dynamics of Legionella (Proteobacteria, Legionellaceae) in two Pampean shallow lakes from Argentina.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {49}, pages = {59058-59070}, pmid = {39331293}, issn = {1614-7499}, support = {PICT 0891-2017//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICTO 00006-2019//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; SIB 2053-2022//Universidad Nacional del Noroeste de la Provincia de Buenos Aires/ ; }, mesh = {Argentina ; *Lakes/microbiology ; *Legionella/genetics ; Water Microbiology ; Real-Time Polymerase Chain Reaction ; }, abstract = {Aquatic systems have traditionally played a key role in the development of human life, providing multiple ecosystem services to society and being a reservoir for a wide biodiversity of organisms. Among them, bacteria belonging to Legionella stand out, mainly because they are of great interest both in the field of microbial ecology and public health, since some of them turn out to be pathogenic for humans. The aim of this work was to study the monthly temporal dynamics of Legionella spp. and its relationship with the environmental variables measured in two Pampean shallow lakes (Gómez and Carpincho, Buenos Aires Province, Argentina). The analysis was carried out using a quantitative approach by real-time polymerase chain reaction (qPCR) and a non-quantitative approach using bacterial diversity data obtained by next-generation sequencing (NGS), using the Illumina MiSeq platform. Our results showed that the overall Legionella abundance was very high in the studied Pampean shallow lakes. Notably, fluctuations in dissolved organic carbon and temperature influenced the dynamics shifts in Legionella abundances. Correlation analyses between Legionella reads from NGS and copy numbers obtained through qPCR revealed positive relationships, unveiling distinctions attributable to the diverse sequence processing algorithms employed in the analysis of NGS data.}, }
@article {pmid39330355, year = {2024}, author = {Abbà, S and Valentini, B and Stefanini, I}, title = {Fungal Identifier (FId): An Updated Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Approach to Ease Ascomycetous Yeast Isolates' Identification in Ecological Studies.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {10}, number = {9}, pages = {}, pmid = {39330355}, issn = {2309-608X}, support = {RGP0060/2021//HFSP/ ; 20225SXSHY//PRIN 2022/ ; }, abstract = {Culturomics has been temporarily exceeded by the advent of omics approaches such as metabarcoding and metagenomics. However, despite improving our knowledge of microbial population composition, both metabarcoding and metagenomics are not suitable for investigating and experimental testing inferences about microbial ecological roles and evolution. This leads to a recent revival of culturomics approaches, which should be supported by improvements in the available tools for high-throughput microbial identification. This study aimed to update the classical PCR-RFLP approach in light of the currently available knowledge on yeast genomics. We generated and analyzed a database including more than 1400 ascomycetous yeast species, each characterized by PCR-RFLP profiles obtained with 143 different endonucleases. The results allowed for the in silico evaluation of the performance of the tested endonucleases in the yeast species' identification and the generation of FId (Fungal Identifier), an online freely accessible tool for the identification of yeast species according to experimentally obtained PCR-RFLP profiles.}, }
@article {pmid39328926, year = {2024}, author = {Duque-Granda, D and Vivero-Gómez, RJ and Junca, H and Cadavid-Restrepo, G and Moreno-Herrera, CX}, title = {Interaction and effects of temperature preference under a controlled environment on the diversity and abundance of the microbiome in Lutzomyia longipalpis (Diptera: Psychodidae).}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {44}, number = {}, pages = {e00857}, pmid = {39328926}, issn = {2215-017X}, abstract = {Characterization of the temperature effects on the abundance and richness of the microbiota of Lutzomyia longipalpis, insect vector of Leishmania infantum in America, is an aspect of pivotal importance to understand the interactions between temperature, bacteria, and Leishmania infection. We developed and used a customized device with a temperature gradient (21-34 °C) to assess the temperature preferences of wild females of Lu. longipalpis collected in a rural area (Ricaurte, Cundinamarca, Colombia). Each replicate consisted of 50 females exposed to the gradient for an hour. At the end of the exposure time, insects were collected and separated by the temperature ranges selected varying from 21 °C to 34 °C. They were organized in 17 pools from which total DNA extracts were obtained, and samples were subjected to 16S rRNA amplicon sequencing analyzes. The most abundant phyla across the different temperature ranges were Proteobacteria (17.22-90.73 %), Firmicutes (5.99-77.21 %) and Actinobacteria (1.56-59.85 %). Results also showed an abundance (30 % to 57.36 %) of Pseudomonas (mainly at temperatures of 21-29 °C and 34 °C) that decreased to 6.55 %-13.20 % at temperatures of 31-33 °C, while Bacillus increase its abundance to 67.24 % at 29-33 °C. Serratia also had a greater representation (49.79 %), specifically in sand flies recovered at 25-27 °C. No significant differences were found at α-diversity level when comparing richness using the Shannon-Wiener, Simpson, and Chao1 indices, while β-diversity differences were found using the Bray-Curtis index (F-value of 3.5073, p-value < 0.013, R-squared of 0,4889), especially in the groups of Lu. longipalpis associated at higher temperatures (29-33 °C). It was also possible to detect the presence of endosymbionts such as Spiroplasma and Arsenophonus in the range of 29-33 °C. Rickettsia was only detected in Lu. longipalpis sand flies recovered between 25-27 °C. It was possible to characterize Lu. longipalpis microbiota in response to intraspecific temperature preferences and observe changes in bacterial communities and endosymbionts at different ranges of said environmental variable, which may be important in its vector competence and environmental plasticity to adapt to new climate change scenarios.}, }
@article {pmid39327479, year = {2024}, author = {Tavaddod, S and Dawson, A and Allen, RJ}, title = {Bacterial aggregation triggered by low-level antibiotic-mediated lysis.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {90}, pmid = {39327479}, issn = {2055-5008}, support = {682237//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; BB/R012415/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 682237//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Euratom (H2020 Euratom Research and Training Programme 2014-2018)/ ; 682237//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Euratom (H2020 Euratom Research and Training Programme 2014-2018)/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; *Escherichia coli/drug effects/genetics ; *Bacteriolysis/drug effects ; Biofilms/drug effects/growth &amp; development ; Microbial Sensitivity Tests ; }, abstract = {Suspended bacterial aggregates play a central role in ocean biogeochemistry, industrial processes and probably many clinical infections - yet the factors that trigger aggregation remain poorly understood, as does the relationship between suspended aggregates and surface-attached biofilms. Here we show that very low doses of cell-wall targeting antibiotic, far below the minimal inhibitory concentration, can trigger aggregation of Escherichia coli cells. This occurs when a few cells lyse, releasing extracellular DNA - thus, cell-to-cell variability in antibiotic response leads to population-level aggregation. Although lysis-triggered aggregation echoes known trigger mechanisms for surface-attached biofilms, these aggregates may have different ecological implications since they do not show increased biofilm-forming potential or increased antibiotic resistance. Our work contributes to understanding the nature of bacterial aggregates and the factors that trigger their formation, and the possible consequences of widespread low-dose antibiotic exposure in the environment and in the body.}, }
@article {pmid39327101, year = {2024}, author = {Goldman, AD and Fournier, GP}, title = {The very early evolution of biological complexity.}, journal = {Trends in genetics : TIG}, volume = {40}, number = {11}, pages = {912-913}, doi = {10.1016/j.tig.2024.09.001}, pmid = {39327101}, issn = {0168-9525}, mesh = {*Biological Evolution ; Phylogeny ; Evolution, Molecular ; }, abstract = {All extant life is descended from a common ancestor, which, despite being very ancient, appears to have been a complex cellular organism. A new study by Moody et al. shows that this ancestor was not only a complex cell, but also lived within a microbial ecology likely inhabited by other complex cells.}, }
@article {pmid39326062, year = {2024}, author = {Sun, X and Favier, A and Folmar, J and Pyenson, NC and Sanchez, A and Rebolleda-Gómez, M}, title = {Metabolic Plasticity Shapes Microbial Communities across a Temperature Gradient.}, journal = {The American naturalist}, volume = {204}, number = {4}, pages = {381-399}, doi = {10.1086/731997}, pmid = {39326062}, issn = {1537-5323}, mesh = {*Temperature ; *Microbiota ; Bacteria/metabolism ; Fermentation ; Carbon/metabolism ; Ecosystem ; }, abstract = {AbstractA central challenge in community ecology is understanding and predicting the effects of abiotic factors on community assembly. In particular, microbial communities play a central role in the ecosystem, but we do not understand how changing factors like temperature are going to affect community composition or function. In this article, we studied the self-assembly of multiple communities in synthetic environments to understand changes in microbial community composition based on metabolic responses of different functional groups along a temperature gradient. In many microbial communities, different microbial functional groups coexist through the partitioning of carbon sources in an emergent trophic structure (cross-feeding). In this system, respirofermentative bacteria display a preference for the sugars supplied as the only carbon source but secrete secondary carbon sources (organic acids) that are more efficiently consumed by obligate respirators. As a consequence of this trophic structure, the metabolic plasticity of the respirofermenters has downstream consequences for the relative abundance of respirators across temperatures. We found that the effects of different temperatures on microbial composition can largely be described by an increase in fermentation by-products with increasing temperatures from the respirofermentative bacteria. This research highlights the importance of metabolic plasticity and metabolic trade-offs in predicting species interactions and community dynamics across abiotic gradients.}, }
@article {pmid39321934, year = {2024}, author = {Liu, YC and Ramiro-Garcia, J and O'Connor, S and Paulo, LM and Maria Braguglia, C and Cristina Gagliano, M and O'Flaherty, V}, title = {Microbial community response to temperature reduction during anaerobic treatment of long chain fatty acids-containing wastewater.}, journal = {Bioresource technology}, volume = {413}, number = {}, pages = {131529}, doi = {10.1016/j.biortech.2024.131529}, pmid = {39321934}, issn = {1873-2976}, mesh = {*Wastewater/microbiology/chemistry ; Anaerobiosis ; *Fatty Acids/metabolism ; *Bioreactors ; *Temperature ; Bacteria/metabolism ; Water Purification/methods ; Biomass ; Microbiota/physiology ; }, abstract = {Acclimating mesophilic biomass to low temperatures have been used to start-up psychrophilic anaerobic reactors, but limited microbial information is available during the acclimation. To investigate microbial responses to temperature reductions, duplicate lab-scale anaerobic digestion (AD) reactors were operated for 166 days, with the temperature being reduced from 37°C to 15°C, using synthetic long chain fatty acid (LCFA)-containing wastewater as the feedstock. The acclimated biomass at 15°C exhibited efficient removal of organic matter (total COD>75%, soluble COD>88%, and LCFA>99%). Temperature reductions lead to significant reductions in microbiome diversity. Fermentative bacteria were highly dynamic and functional redundant during temperature reductions. Smithella was the dominant syntrophic bacteria involved in LCFA degradation coupled with Methanothrix and Methanocorpusculum at 15°C. Membrane modifications and compatible cellular solutes production were triggered by temperature reductions as microbial response to cold stress. This study provided molecular insights in microbial acclimation to low temperatures for psychrophilic AD.}, }
@article {pmid39319483, year = {2024}, author = {Rasmussen, KL and Thieringer, PH and Nevadomski, S and Martinez, AM and Dawson, KS and Corsetti, FA and Zheng, XY and Lv, Y and Chen, X and Celestian, AJ and Berelson, WM and Rollins, NE and Spear, JR}, title = {Living to Lithified: Construction and Preservation of Silicified Biomarkers.}, journal = {Geobiology}, volume = {22}, number = {5}, pages = {1-30}, doi = {10.1111/gbi.12620}, pmid = {39319483}, issn = {1472-4669}, support = {/NASA/NASA/United States ; //Geological Society of America/ ; }, mesh = {*Biomarkers/analysis ; Cyanobacteria/metabolism ; Geologic Sediments/microbiology/chemistry ; Bacteria/metabolism ; Hot Springs/microbiology/chemistry ; }, abstract = {Whole microorganisms are rarely preserved in the fossil record but actively silicifying environments like hot springs provide an opportunity for microbial preservation, making silicifying environments critical for the study of microbial life through time on Earth and possibly other planetary bodies. Yet, the changes that biosignatures may undergo through lithification and burial remain unconstrained. At Steep Cone Geyser in Yellowstone National Park, we collected microbial material from (1) the living system across the active outflows, (2) the silicified areas adjacent to flows, and (3) lithified and buried material to assess the preservation of biosignatures and their changes across the lithification transect. Five biofabrics, built predominantly by Cyanobacteria Geitlerinema, Pseudanabaenaceae, and Leptolyngbya with some filamentous anoxygenic phototrophs contributions, were identified and tracked from the living system through the process of silicification/lithification. In the living systems, δ[30]Si values decrease from +0.13‰ in surficial waters to -2‰ in biomat samples, indicating a kinetic isotope effect potentially induced by increased association with actively growing biofabrics. The fatty acids C16:1 and iso-C14:0 and the hydrocarbon C17:0 were disentangled from confounding signals and determined to be reliable lipid biosignatures for living biofabric builders and tenant microorganisms. Builder and tenant microbial biosignatures were linked to specific Cyanobacteria, anoxygenic phototrophs, and heterotrophs, which are prominent members of the living communities. Upon lithification and burial, silicon isotopes of silicified biomass began to re-equilibrate, increasing from δ[30]Si -2‰ in living biomats to -0.55‰ in lithified samples. Active endolithic microbial communities were identified in lithified samples and were dominated by Cyanobacteria, heterotrophic bacteria, and fungi. Results indicate that distinct microbial communities build and inhabit silicified biofabrics through time and that microbial biosignatures shift over the course of lithification. These findings improve our understanding of how microbial communities silicify, the biomarkers they retain, and transitionary impacts that may occur through lithification and burial.}, }
@article {pmid39317790, year = {2024}, author = {Knorr, MA and Contosta, AR and Morrison, EW and Muratore, TJ and Anthony, MA and Stoica, I and Geyer, KM and Simpson, MJ and Frey, SD}, title = {Unexpected sustained soil carbon flux in response to simultaneous warming and nitrogen enrichment compared with single factors alone.}, journal = {Nature ecology &amp; evolution}, volume = {8}, number = {12}, pages = {2277-2285}, pmid = {39317790}, issn = {2397-334X}, mesh = {*Soil/chemistry ; *Nitrogen/analysis/metabolism ; *Carbon Cycle ; *Carbon/analysis/metabolism ; Global Warming ; Forests ; Climate Change ; }, abstract = {Recent observations document that long-term soil warming in a temperate deciduous forest leads to significant soil carbon loss, whereas chronic soil nitrogen enrichment leads to significant soil carbon gain. Most global change experiments like these are single factor, investigating the impacts of one stressor in isolation of others. Because warming and ecosystem nitrogen enrichment are happening concurrently in many parts of the world, we designed a field experiment to test how these two factors, alone and in combination, impact soil carbon cycling. Here, we show that long-term continuous soil warming or nitrogen enrichment when applied alone followed the predicted response, with warming resulting in significant soil carbon loss and nitrogen fertilization tending towards soil carbon gain. The combination treatment showed an unanticipated response, whereby soil respiratory carbon loss was significantly higher than either single factor alone, but without a concomitant decline in soil carbon storage. Observations suggest that when soils are exposed to both factors simultaneously, plant carbon inputs to the soil are enhanced, counterbalancing soil carbon loss and helping maintain soil carbon stocks near control levels. This has implications for both atmospheric CO2 emissions and soil fertility and shows that coupling two important global change drivers results in a distinctive response that was not predicted by the behaviour of the single factors in isolation.}, }
@article {pmid39311575, year = {2024}, author = {Han, C-J and Huang, J-P and Chiang, M-R and Jean, OSM and Nand, N and Etebari, K and Shelomi, M}, title = {The hindgut microbiota of coconut rhinoceros beetles (Oryctes rhinoceros) in relation to their geographical populations.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {10}, pages = {e0098724}, pmid = {39311575}, issn = {1098-5336}, support = {MOST-109-2311-B-002-016-MY3//National Science and Technology Council (NSTC)/ ; 111L7822,112L7814,113L7801//Ministry of Education, Taiwan/ ; }, mesh = {Animals ; *Coleoptera/microbiology ; *Gastrointestinal Microbiome ; *Symbiosis ; Bacteria/classification/genetics/isolation &amp; purification ; Cocos/microbiology ; Genetic Variation ; }, abstract = {The coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is a palm tree pest capable of rapidly expanding its population in new territories. Previous studies identified a digestive symbiosis between CRB and its gut microbes. However, no research compared the genetic variation of CRBs with their hindgut microbiota on a global scale. This study aims to investigate the genetic divergence of CRB and the compositional variation of CRB's microbiota across different geographical locations, and explore the association between them and their predicted functional profiles and environmental data. The research reveals a distinct and consistent microbial community within local populations, but it varies across different geographical populations. The microbial functional profiles linked to the production of digestive enzymes, including cellulases and ligninases, are nonetheless globally conserved. This suggests that CRBs employ specific mechanisms to select and maintain microbes with functional benefits, contributing to host adaptability, stress tolerance, and fitness. The CRB microbial communities did not appear to recapitulate the genetic variation of their hosts. Rather than depend on obligate symbionts, CRBs seem to establish similar digestive associations with whatever environmentally acquired microbes are available wherever they are, aiding them in successfully establishing after invading a new location.IMPORTANCECoconut rhinoceros beetles (CRBs) are notorious pests on Arecaceae plants, posing destructive threats to countries highly reliant on coconut, oil palm, and date palm as economic crops. In the last century, CRBs have rapidly expanded their presence to territories that were once free of these beetles. The United States, for instance, has officially designated CRBs as invasive and alien pests. Given their remarkable ability to swiftly adapt to new environments, their gut microbes may play a crucial role in this process. While the microbiota of CRBs vary depending on geographical location, these beetles consistently exhibit a functionally identical digestive association with locally acquired microbes. This underscores the significance of CRB-microbe association in shaping the adaptive strategies of this agricultural pest.}, }
@article {pmid39311333, year = {2025}, author = {Deo, R and Lakra, U and Ojha, M and Nigam, VK and Sharma, SR}, title = {Exopolysaccharides in microbial interactions: signalling, quorum sensing, and community dynamics.}, journal = {Natural product research}, volume = {39}, number = {11}, pages = {3224-3239}, doi = {10.1080/14786419.2024.2405867}, pmid = {39311333}, issn = {1478-6427}, mesh = {*Quorum Sensing/physiology ; *Microbial Interactions ; *Polysaccharides, Bacterial/metabolism ; Ecosystem ; Signal Transduction ; }, abstract = {Microbial interactions within diverse ecosystems are intricately governed by the dynamic interplay of exopolysaccharides (EPSs) produced by microorganisms. This review delves into the multifaceted roles of EPS in microbial signalling, quorum sensing (QS), and community dynamics, highlighting their significance in orchestrating cooperative behaviours and shaping community structures. EPSs serve as pivotal signalling molecules, influencing chemical communication and promoting intricate interactions among microorganisms. The integration of EPS into QS mechanisms adds an additional layer of complexity, allowing microorganisms to assess population density and synchronise communal responses. Furthermore, EPSs actively contribute to community dynamics by influencing spatial organisation, adhesion, and resistance to environmental stressors. By providing comprehensive knowledge of EPS dynamics, this review offers valuable insights into microbial ecology, serving as a foundational resource for future research. It will benefit the research community by advancing our understanding of microbial ecosystems, with broad applications in biotechnology, environmental science, and beyond.}, }
@article {pmid39297874, year = {2024}, author = {Castledine, M and Pennycook, J and Newbury, A and Lear, L and Erdos, Z and Lewis, R and Kay, S and Sanders, D and Sünderhauf, D and Buckling, A and Hesse, E and Padfield, D}, title = {Characterizing a stable five-species microbial community for use in experimental evolution and ecology.}, journal = {Microbiology (Reading, England)}, volume = {170}, number = {9}, pages = {}, pmid = {39297874}, issn = {1465-2080}, mesh = {*Soil Microbiology ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; Ecology ; Biological Evolution ; Microbial Interactions ; }, abstract = {Model microbial communities are regularly used to test ecological and evolutionary theory as they are easy to manipulate and have fast generation times, allowing for large-scale, high-throughput experiments. A key assumption for most model microbial communities is that they stably coexist, but this is rarely tested experimentally. Here we report the (dis)assembly of a five-species microbial community from a metacommunity of soil microbes that can be used for future experiments. Using reciprocal invasion-from-rare experiments we show that all species can coexist and we demonstrate that the community is stable for a long time (~600 generations). Crucially for future work, we show that each species can be identified by their plate morphologies, even after >1 year in co-culture. We characterise pairwise species interactions and produce high-quality reference genomes for each species. This stable five-species community can be used to test key questions in microbial ecology and evolution.}, }
@article {pmid39303870, year = {2024}, author = {McDonagh, F and Tumeo, A and Murray, EK and Hallahan, B and Miliotis, G}, title = {Complete genome of Escherichia coli sequence type 73 with acquired blaTEM-1 and high genotypic virulence load identified in human saliva.}, journal = {Journal of global antimicrobial resistance}, volume = {39}, number = {}, pages = {149-152}, doi = {10.1016/j.jgar.2024.08.011}, pmid = {39303870}, issn = {2213-7173}, mesh = {Humans ; *Escherichia coli/genetics/drug effects/pathogenicity/isolation &amp; purification ; *Genome, Bacterial ; *Virulence Factors/genetics ; *Phylogeny ; *Escherichia coli Infections/microbiology ; *Saliva/microbiology ; Virulence/genetics ; Genotype ; beta-Lactamases/genetics ; Whole Genome Sequencing ; Schizophrenia/genetics/microbiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {OBJECTIVES: Escherichia coli sequence type (ST) 73 is a pandemic lineage of the ExPEC (Extraintestinal Pathogenic E. coli) family associated with conserved virulence. We report the complete genome of a genomically hypervirulent E. coli ST73 strain isolated from the oral cavity of a patient with a diagnosis of treatment resistant schizophrenia and receiving clozapine treatment.<br><br>METHODS: E. coli strain GABEEC132 underwent second and third generation sequencing with Illumina and Oxford-Nanopore-Technologies (ONT) platforms. Antibiotic resistance genes (ARGs) and virulence factors (VFs) were bioinformatically identified using the NCBI-AMR-Finder-Plus database and Virulence-Factors-database (VFDB), respectively. To contextualize the genome within a broader epidemiological framework, phylogenetic analysis was conducted using representative genomes of E. coli ST73 O6:H1 (n = 55).<br><br>RESULTS: E. coli strain GABEEC132 was identified as possessing the O6:H1 serotype and classified within the B2 phylogroup. The strain exhibited a high genomic virulence load, encoding for 194 VFs. Additionally, it encoded three ARGs, including an acquired blaTEM-1 located on a rep_cluster_2350 8 237 Kb mobilisable plasmid, presenting phenotypic resistance to ampicillin and piperacillin.<br><br>CONCLUSION: This report provides novel insights into the oral prevalence of genotypically hypervirulent and drug-resistant E. coli ST73, a pandemic lineage.}, }
@article {pmid39301056, year = {2024}, author = {Smith, L and Fullerton, H and Moyer, CL}, title = {Complex hydrothermal vent microbial mat communities used to assess primer selection for targeted amplicon surveys from Kama'ehuakanaloa Seamount.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18099}, pmid = {39301056}, issn = {2167-8359}, mesh = {*Hydrothermal Vents/microbiology ; *Archaea/genetics/isolation &amp; purification ; *Microbiota/genetics ; *Bacteria/genetics/isolation &amp; purification/classification ; DNA Primers/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The microbiota of hydrothermal vents has been widely implicated in the dynamics of oceanic biogeochemical cycling. Lithotrophic organisms utilize reduced chemicals in the vent effluent for energy, which fuels carbon fixation, and their metabolic byproducts can then support higher trophic levels and high-biomass ecosystems. However, despite the important role these microorganisms play in our oceans, they are difficult to study. Most are resistant to culturing in a lab setting, so culture-independent methods are necessary to examine community composition. Targeted amplicon surveying has become the standard practice for assessing the structure and diversity of hydrothermal vent microbial communities. Here, the performance of primer pairs targeting the V3V4 and V4V5 variable regions of the SSU rRNA gene was assessed for use on environmental samples from microbial mats surrounding Kama'ehuakanaloa Seamount, an iron-dominated hydrothermal vent system. Using the amplicon sequence variant (ASV) approach to taxonomic identification, the structure and diversity of microbial communities were elucidated, and both primer pairs generated robust data and comparable alpha diversity profiles. However, several distinct differences in community composition were identified between primer sets, including differential relative abundances of both bacterial and archaeal phyla. The primer choice was determined to be a significant driver of variation among the taxonomic profiles generated. Based on the higher quality of the raw sequences generated and on the breadth of abundant taxa found using the V4V5 primer set, it is determined as the most efficacious primer pair for whole-community surveys of microbial mats at Kama'ehuakanaloa Seamount.}, }
@article {pmid39303138, year = {2024}, author = {Boukheloua, R and Mukherjee, I and Park, H and Šimek, K and Kasalický, V and Ngochera, M and Grossart, HP and Picazo-Mozo, A and Camacho, A and Cabello-Yeves, PJ and Rodriguez-Valera, F and Callieri, C and Andrei, AS and Pernthaler, J and Posch, T and Alfreider, A and Sommaruga, R and Hahn, MW and Sonntag, B and López-García, P and Moreira, D and Jardillier, L and Lepère, C and Biderre-Petit, C and Bednarska, A and Ślusarczyk, M and Tóth, VR and Banciu, HL and Kormas, K and Orlić, S and Šantić, D and Muyzer, G and Herlemann, DPR and Tammert, H and Bertilsson, S and Langenheder, S and Zechmeister, T and Salmaso, N and Storelli, N and Capelli, C and Lepori, F and Lanta, V and Vieira, HH and Kostanjšek, F and Kabeláčová, K and Chiriac, MC and Haber, M and Shabarova, T and Fernandes, C and Rychtecký, P and Znachor, P and Szőke-Nagy, T and Layoun, P and Wong, HL and Kavagutti, VS and Bulzu, PA and Salcher, MM and Piwosz, K and Ghai, R}, title = {Global freshwater distribution of Telonemia protists.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39303138}, issn = {1751-7370}, support = {20-12496X//Grant Agency of the Czech Republic/ ; 017/2022/P//GAJU/ ; 2021/03/Y/NZ8/00076//National Science Centre/ ; }, mesh = {*Fresh Water/microbiology/parasitology ; *Phylogeny ; *RNA, Ribosomal, 18S/genetics ; *In Situ Hybridization, Fluorescence ; Metagenome ; Lakes/microbiology/parasitology ; Biodiversity ; Metagenomics ; }, abstract = {Telonemia are one of the oldest identified marine protists that for most part of their history have been recognized as a distinct incertae sedis lineage. Today, their evolutionary proximity to the SAR supergroup (Stramenopiles, Alveolates, and Rhizaria) is firmly established. However, their ecological distribution and importance as a natural predatory flagellate, especially in freshwater food webs, still remain unclear. To unravel the distribution and diversity of the phylum Telonemia in freshwater habitats, we examined over a thousand freshwater metagenomes from all over the world. In addition, to directly quantify absolute abundances, we analyzed 407 samples from 97 lakes and reservoirs using Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). We recovered Telonemia 18S rRNA gene sequences from hundreds of metagenomic samples from a wide variety of habitats, indicating a global distribution of this phylum. However, even after this extensive sampling, our phylogenetic analysis did not reveal any new major clades, suggesting current molecular surveys are near to capturing the full diversity within this group. We observed excellent concordance between CARD-FISH analyses and estimates of abundances from metagenomes. Both approaches suggest that Telonemia are largely absent from shallow lakes and prefer to inhabit the colder hypolimnion of lakes and reservoirs in the Northern Hemisphere, where they frequently bloom, reaching 10%-20% of the total heterotrophic flagellate population, making them important predatory flagellates in the freshwater food web.}, }
@article {pmid39302483, year = {2024}, author = {Nelson, K and Schloter, M}, title = {Special Collection on Pollution, Bioremediation, and the Environment.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {118}, pmid = {39302483}, issn = {1432-184X}, mesh = {*Biodegradation, Environmental ; *Environmental Pollution ; }, }
@article {pmid39299325, year = {2024}, author = {Ren, W and Ren, G and Kuramae, EE and Bodelier, PLE and Chen, S and Teng, Y and Luo, Y}, title = {Mode of application of sulfonated graphene modulated bioavailable heavy metal contents and microbial community composition in long-term heavy metal contaminated soil.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176295}, doi = {10.1016/j.scitotenv.2024.176295}, pmid = {39299325}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Soil Pollutants/metabolism/analysis ; *Graphite ; *Metals, Heavy/analysis/metabolism ; *Microbiota/drug effects ; *Biodegradation, Environmental ; Soil/chemistry ; Bacteria/metabolism ; Cadmium/metabolism/analysis ; }, abstract = {Nanomaterials are increasingly recognized for their potential in soil remediation. However, their impact on soil microbial communities in contaminated soil remains poorly understood. In this study, we investigated the dynamic effects of sulfonated graphene (SG) following one-time or repeated applications on heavy metal availability and soil microbial communities in long-term heavy metal-contaminated soil over 180 days. Our findings revealed that one-time SG application at 30 mg kg[-1] significantly increased the bioavailable cadmium (Cd) and copper (Cu) contents by approximately 30 %-40 % after 2 and 180 days. Repeated SG applications, however, displayed no significant influence on heavy metal availability. One-time SG application, coupled with the increased available Cd, induced significant enrichment of some specific functional bacterial genera involved in glycan biosynthesis metabolism and biosynthesis of other secondary metabolites, thereby decreasing the available contents of heavy metals after 90 days. However, the shifts in bacterial community structure and function were subsequently partially recovered after 180 days. Conversely, repeated SG treatments led to minimal alterations after 90 days while leading to similar shifts in the bacterial community at 60 mg kg[-1] after 180 days. The fungal community structure remained largely unaltered across all SG treatments. Intriguingly, SG treatments substantially stimulated fungal biomass, with the stimulation degree dependent on SG dosage. These results provide valuable insights for developing phytoremediation strategies, suggesting tailored SG applications during specific growth phases to optimize remediation efficiency.}, }
@article {pmid39298326, year = {2024}, author = {Gordon, JI and Barratt, MJ and Hibberd, MC and Rahman, M and Ahmed, T}, title = {Establishing human microbial observatory programs in low- and middle-income countries.}, journal = {Annals of the New York Academy of Sciences}, volume = {1540}, number = {1}, pages = {13-20}, doi = {10.1111/nyas.15224}, pmid = {39298326}, issn = {1749-6632}, support = {//Fondazione Internazionale Premio Balzan/ ; //Bill and Melinda Gates Foundation/ ; /NH/NIH HHS/United States ; /NH/NIH HHS/United States ; }, mesh = {Humans ; *Developing Countries ; Global Health ; *Microbiota ; }, abstract = {Studies of the human microbiome are progressing rapidly but have largely focused on populations living in high-income countries. With increasing evidence that the microbiome contributes to the pathogenesis of diseases that affect infants, children, and adults in low- and middle-income countries (LMICs), and with profound and rapid ongoing changes occurring in our lifestyles and biosphere, understanding the origins of and developing microbiome-directed therapeutics for treating a number of global health challenges requires the development of programs for studying human microbial ecology in LMICs. Here, we discuss how the establishment of long-term human microbial observatory programs in selected LMICs could provide one timely approach.}, }
@article {pmid39296299, year = {2024}, author = {Wang, X and Li, H and Yang, Y and Wu, Z and Wang, Z and Li, D and Xia, W and Zou, S and Liu, Y and Wang, F}, title = {Geographic and environmental impacts on gut microbiome in Himalayan langurs (Semnopithecus schistaceus) and Xizang macaques (Macaca mulatta vestita).}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1452101}, pmid = {39296299}, issn = {1664-302X}, abstract = {INTRODUCTION: Gut microbiome plays a crucial role in the health of wild animals. Their structural and functional properties not only reflect the host's dietary habits and habitat conditions but also provide essential support for ecological adaptation in various environments.<br><br>METHODS: This study investigated the gut microbiome of Himalayan langurs (Semnopithecus schistaceus) and Xizang macaques (Macaca mulatta vestita) across different geographic regions using 16S rRNA gene and metagenomic sequencing.<br><br>RESULTS: Results showed distinct clustering patterns in gut microbiota based on geographic location. Soil had an insignificant impact on host gut microbiome. Himalayan langurs from mid-altitude regions exhibited higher levels of antibiotic resistance genes associated with multidrug resistance, while Xizang macaques from high-altitude regions showed a broader range of resistance genes. Variations in carbohydrate-active enzymes and KEGG pathways indicated unique metabolic adaptations to different environments.<br><br>DISCUSSION: These findings provide valuable insights into the health and conservation of these primates and the broader implications of microbial ecology and functional adaptations in extreme conditions.}, }
@article {pmid39296290, year = {2024}, author = {Wang, Z and Gao, Z and Yu, Y and Li, H and Luo, W and Ji, Z and Ding, H}, title = {New insights into the structure and function of microbial communities in Maxwell Bay, Antarctica.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1463144}, pmid = {39296290}, issn = {1664-302X}, abstract = {The microbial communities inhabiting polar ecosystems, particularly in Maxwell Bay, Antarctica, play a pivotal role in nutrient cycling and ecosystem dynamics. However, the diversity of these microbial communities remains underexplored. In this study, we aim to address this gap by investigating the distribution, environmental drivers, and metabolic potential of microorganisms in Maxwell Bay. We analyzed the prokaryotic and eukaryotic microbiota at 11 stations, revealing distinctive community structures and diverse phylum dominance by using high-throughput sequencing. Spatial analysis revealed a significant impact of longitude on microbial communities, with microeukaryotes exhibiting greater sensitivity to spatial factors than microprokaryotes. We constructed co-occurrence networks to explore the stability of microbial communities, indicating the complexity and stability of microprokaryotic communities compared with those of microeukaryotes. Our findings suggest that the microeukaryotic communities in Maxwell Bay are more susceptible to disturbances. Additionally, this study revealed the spatial correlations between microbial communities, diversity, and environmental variables. Redundancy analysis highlighted the significance of pH and dissolved oxygen in shaping microprokaryotic and microeukaryotic communities, indicating the anthropogenic influence near the scientific research stations. Functional predictions using Tax4Fun2 and FUNGuild revealed the metabolic potential and trophic modes of the microprokaryotic and microeukaryotic communities, respectively. Finally, this study provides novel insights into the microbial ecology of Maxwell Bay, expanding the understanding of polar microbiomes and their responses to environmental factors.}, }
@article {pmid39294302, year = {2024}, author = {Sousa, LGV and Novak, J and França, A and Muzny, CA and Cerca, N}, title = {Gardnerella vaginalis, Fannyhessea vaginae, and Prevotella bivia Strongly Influence Each Other's Transcriptome in Triple-Species Biofilms.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {117}, pmid = {39294302}, issn = {1432-184X}, support = {R01AI146065-01A1//National Institute of Allergy and Infectious Diseases/ ; UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2020.04912.BD//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; DL57/2016/CP1377/CT0032//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; R01 AI146065/AI/NIAID NIH HHS/United States ; }, mesh = {*Biofilms/growth &amp; development ; *Gardnerella vaginalis/genetics ; *Transcriptome ; *Prevotella/genetics/physiology ; Female ; Humans ; Vaginosis, Bacterial/microbiology ; Vagina/microbiology ; }, abstract = {Bacterial vaginosis (BV), the most common vaginal infection worldwide, is characterized by the development of a polymicrobial biofilm on the vaginal epithelium. While Gardnerella spp. have been shown to have a prominent role in BV, little is known regarding how other species can influence BV development. Thus, we aimed to study the transcriptome of Gardnerella vaginalis, Fannyhessea vaginae, and Prevotella bivia, when growing in triple-species biofilms. Single and triple-species biofilms were formed in vitro, and RNA was extracted and sent for sequencing. cDNA libraries were prepared and sequenced. Quantitative PCR analysis (qPCR) was performed on the triple-species biofilms to evaluate the biofilm composition. The qPCR results revealed that the triple-species biofilms were mainly composed by G. vaginalis and P. bivia was the species with the lowest percentage. The RNA-sequencing analysis revealed a total of 432, 126, and 39 differentially expressed genes for G. vaginalis, F. vaginae, and P. bivia, respectively, when growing together. Gene ontology enrichment of G. vaginalis downregulated genes revealed several functions associated with metabolism, indicating a low metabolic activity of G. vaginalis when growing in polymicrobial biofilms. This work highlighted that the presence of 3 different BV-associated bacteria in the biofilm influenced each other's transcriptome and provided insight into the molecular mechanisms that enhanced the virulence potential of polymicrobial consortia. These findings will contribute to understand the development of incident BV and the interactions occurring within the biofilm.}, }
@article {pmid39290267, year = {2024}, author = {Zhang, K and Zhang, Q and Qiu, H and Ma, Y and Hou, N and Zhang, J and Kan, C and Han, F and Sun, X and Shi, J}, title = {The complex link between the gut microbiome and obesity-associated metabolic disorders: Mechanisms and therapeutic opportunities.}, journal = {Heliyon}, volume = {10}, number = {17}, pages = {e37609}, pmid = {39290267}, issn = {2405-8440}, abstract = {Microbial interactions are widespread and important processes that support the link between disease and microbial ecology. The gut microbiota is a major source of microbial stimuli that can have detrimental or beneficial effects on human health. It is also an endocrine organ that maintains energy homeostasis and host immunity. Obesity is a highly and increasingly prevalent metabolic disease and the leading cause of preventable death worldwide. An imbalance in the gut microbiome is associated with several diseases including obesity-related metabolic disorders. This review summarizes the complex association between the gut microbiome and obesity-associated metabolic diseases and validates the role and mechanisms of ecological dysregulation in the gut in obesity-associated metabolic disorders. Therapies that could potentially alleviate obesity-associated metabolic diseases by modulating the gut microbiota are discussed.}, }
@article {pmid39288091, year = {2024}, author = {Liu, X and Salles, JF}, title = {Drivers and consequences of microbial community coalescence.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39288091}, issn = {1751-7370}, support = {//China Scholarship Council and the European Research Council/ ; }, mesh = {*Microbiota ; *Ecosystem ; Bacteria/genetics/classification/isolation &amp; purification ; }, abstract = {Microbial communities are undergoing unprecedented dispersion and amalgamation across diverse ecosystems, thereby exerting profound and pervasive influences on microbial assemblages and ecosystem dynamics. This review delves into the phenomenon of community coalescence, offering an ecological overview that outlines its four-step process and elucidates the intrinsic interconnections in the context of community assembly. We examine pivotal mechanisms driving community coalescence, with a particular emphasis on elucidating the fates of both source and resident microbial communities and the consequential impacts on the ecosystem. Finally, we proffer recommendations to guide researchers in this rapidly evolving domain, facilitating deeper insights into the ecological ramifications of microbial community coalescence.}, }
@article {pmid39287748, year = {2024}, author = {Kujawska, M and Neuhaus, K and Huptas, C and Jiménez, E and Arboleya, S and Schaubeck, M and Hall, LJ}, title = {Exploring the Potential Probiotic Properties of Bifidobacterium breve DSM 32583-A Novel Strain Isolated from Human Milk.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {39287748}, issn = {1867-1314}, abstract = {Human milk is the best nutrition for infants, providing optimal support for the developing immune system and gut microbiota. Hence, it has been used as source for probiotic strain isolation, including members of the genus Bifidobacterium, in an effort to provide beneficial effects to infants who cannot be exclusively breastfed. However, not all supplemented bifidobacteria can effectively colonise the infant gut, nor confer health benefits to the individual infant host; therefore, new isolates are needed to develop a range of dietary products for this specific age group. Here, we investigated the beneficial potential of Bifidobacterium breve DSM 32583 isolated from human milk. We show that in vitro B. breve DSM 32583 exhibited several characteristics considered fundamental for beneficial bacteria, including survival in conditions simulating those present in the digestive tract, adherence to human epithelial cell lines, and inhibition of growth of potentially pathogenic microorganisms. Its antibiotic resistance patterns were comparable to those of known beneficial bifidobacterial strains, and its genome did not contain plasmids nor virulence-associated genes. These results suggest that B. breve DSM 32583 is a potential probiotic candidate.}, }
@article {pmid39287688, year = {2024}, author = {Demin, K and Prazdnova, E and Kulikov, M and Mazanko, M and Gorovtsov, A}, title = {Alternative agar substitutes for culturing unculturable microorganisms.}, journal = {Archives of microbiology}, volume = {206}, number = {10}, pages = {405}, pmid = {39287688}, issn = {1432-072X}, support = {SP-12-23-04//Strategic Academic Leadership Program of the Southern Federal University "Priority 2030"/ ; SP-12-23-04//Strategic Academic Leadership Program of the Southern Federal University "Priority 2030"/ ; SP-12-23-04//Strategic Academic Leadership Program of the Southern Federal University "Priority 2030"/ ; }, mesh = {*Agar/chemistry ; *Culture Media/chemistry ; *Polysaccharides, Bacterial/metabolism ; *Bacteria/growth &amp; development/metabolism/drug effects ; Gels/chemistry ; }, abstract = {Gelling agents are necessary for the preparation of solid or semisolid media. For more than a hundred years, agar has been the primary gelling agent. However, a substantial body of evidence has accumulated suggesting that agar-based media inhibit the growth of many microbial species through the generation of reactive oxygen species (ROS), toxic organic contaminants, or competitive exclusion effects. In this review we have compiled the largest amount of data to date on the use of various gelling agents in microbial isolation and cultivation, with the particular emphasis on rare microbe isolation cases. Our analysis suggested that microbial-derived compounds (especially gellan gum), as gelling agents, are superior to agar in their ability to isolate and maintain either new or known microbial species. We analyzed the reasons behind this success and concluded that there are phylum-level differences in microbial responses to the changes in conditions from natural to the laboratory conditions (with respect to gelling agent usage). Consequently, we hypothesize that at least partial success of microbial-derived gelling agents lies in the recreation of the natural microenvironment conditions (which we address as the "familiarity of conditions" hypothesis). Finally, we present a list of recommendations and suggestions for further microbial ecology studies.}, }
@article {pmid39287374, year = {2024}, author = {Vinogradova, E and Mukhanbetzhanov, N and Nurgaziyev, M and Jarmukhanov, Z and Aipova, R and Sailybayeva, A and Bekbossynova, M and Kozhakhmetov, S and Kushugulova, A}, title = {Impact of urbanization on gut microbiome mosaics across geographic and dietary contexts.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0058524}, pmid = {39287374}, issn = {2379-5077}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Urbanization ; Male ; Female ; Kazakhstan/epidemiology ; *Diet ; Adult ; Rural Population/statistics &amp; numerical data ; Middle Aged ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Urban Population/statistics &amp; numerical data ; Bacteria/genetics/classification/isolation &amp; purification ; Feces/microbiology ; Young Adult ; }, abstract = {UNLABELLED: This study provides a comprehensive assessment of how urban-rural divides influence gut microbial diversity and composition across the distinct geographical landscapes of Kazakhstan, elucidating the intricate interplay between lifestyle, environment, and gut microbiome. In this prospective cohort study, we enrolled 651 participants from urban centers and rural settlements across Kazakhstan, following ethical approval and informed consent. Comprehensive demographic, dietary, and stool sample data were collected. 16S rRNA gene sequencing and shotgun metagenomics techniques were employed to delineate the intricate patterns of the gut microbiome. A rigorous statistical framework dissected the interplay between urbanization gradients, geography, dietary lifestyles, and microbial dynamics. Our findings demonstrate a stark microbial divide between urban and rural gut ecosystems. The study found significant differences in gut microbiome diversity and composition between urban and rural populations in Kazakhstan. Urban microbiomes exhibited reduced diversity, higher Firmicutes/Bacteroidetes ratios, and increased prevalence of genera Coprococcus and Parasutterella. In contrast, rural populations had greater microbial diversity and abundance of Ligilactobacillus, Sutterella, and Paraprevotella. Urbanization also influenced dietary patterns, with urban areas consuming more salt, cholesterol, and protein, while rural areas had diets richer in carbohydrates and fiber. The study also identified distinct patterns in the prevalence of antibiotic resistance genes and virulence factors between urban and rural gut microbiomes. This study sheds light on how urbanization may be deeply involved in shaping the intricate mosaic of the gut microbiome across Kazakhstan's diverse geographical and dietary landscapes, underscoring the complex interplay between environmental exposures, dietary lifestyles, and the microbial residents inhabiting our intestines.<br><br>IMPORTANCE: The study examined gut microbiome composition across diverse geographical locations in Kazakhstan, spanning urban centers and rural settlements. This allows for thoroughly investigating how urbanization gradients and geographic factors shape the gut microbiome. The study's examination of the gut resistome and prevalence of virulence-associated genes provide essential insights into the public health implications of urbanization-driven microbiome alterations. Collecting comprehensive demographic, dietary, and stool sample data enables the researchers to better understand the relationships between urbanization, nutritional patterns, and gut microbiome composition. The findings have important implications for understanding how urbanization-driven microbiome changes may impact human health and well-being, paving the way for tailored interventions to restore a balanced gut microbial ecology.}, }
@article {pmid39283121, year = {2024}, author = {Machado, DT and Dias, BdC and Cayô, R and Gales, AC and Marques de Carvalho, F and Vasconcelos, ATR}, title = {Uncovering new Firmicutes species in vertebrate hosts through metagenome-assembled genomes with potential for sporulation.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0211324}, pmid = {39283121}, issn = {2165-0497}, support = {E-26/210.012/2020//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; 88887.677436/2022-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; 402659/2018-0,443805/2018-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; OPP1193112//Bill and Melinda Gates Foundation (GF)/ ; 88887.508687/2020-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; 302023/2024-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 307915/2022-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 312066/2019-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; E-26/201.046/2022//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; }, mesh = {Animals ; *Spores, Bacterial/genetics/growth &amp; development ; *Phylogeny ; *Metagenome ; *Genome, Bacterial/genetics ; *Firmicutes/genetics/classification ; Humans ; Cattle ; Swine ; Gastrointestinal Microbiome/genetics ; Vertebrates/microbiology ; Poultry/microbiology ; }, abstract = {Metagenome-assembled genomes (MAGs) have contributed to identifying non-culturable microorganisms and understanding their ecological functions. MAGs offer an advantage in investigating sporulation-associated genes, especially given the difficulty of isolating many species residing in the gut microbiota of multiple hosts. Bacterial sporulation is a key survival mechanism with implications for pathogenicity and biotechnology. Here, we investigate MAGs from vertebrate hosts, emphasizing taxonomic identification and identifying sporulation-associated genes in potential novel species within the Firmicutes phylum. We identified potential new species in the classes Clostridia (Borkfalkiaceae, Lachnospiraceae, Monoglobaceae, and Oscillospiraceae families) and Bacilli (Bacillaceae and Erysipelotrichaceae families) through phylogenetic and functional pathway analyses, highlighting their sporulation potential. Our study covers 146 MAGs, 124 of them without refined taxonomic assignments at the family level. We found that Clostridia and Bacilli have unique sporulation gene profiles in the refined family MAGs for cattle, swine, poultry, and human hosts. The presence of genes related to Spo0A regulon, engulfment, and spore cortex in MAGs underscores fundamental mechanisms in sporulation processes in currently uncharacterized species with sporulation potential from metagenomic dark matter. Furthermore, genomic analyses predict sporulation potential based on gene presence, genome size, and metabolic pathways involved in spore formation. We emphasize MAGs covering families not yet characterized through the phylogenetic analysis, and with extensive potential for spore-forming bacteria within Clostridia, Bacilli, UBA4882, and UBA994 classes. These findings contribute to exploring spore-forming bacteria, which provides evidence for novel species diversity in multiple hosts, their adaptive strategies, and potential applications in biotechnology and host health.IMPORTANCESpores are essential for bacterial survival in harsh environments, facilitating their persistence and adaptation. Exploring sporulation-associated genes in metagenome-assembled genomes (MAGs) from different hosts contributes to clinical and biotechnological domains. Our study investigated the extent of genes associated with bacterial sporulation in MAGs from poultry, swine, cattle, and humans, revealing these genes in uncultivated bacteria. We identified potential novel Firmicutes species with sporulation capabilities through phylogenetic and functional analyses. Notably, MAGs belonging to Clostridia, Bacilli, and unknown classes, namely UBA4882 and UBA994, remained uncharacterized at the family level, which raises the hypothesis that sporulation would also be present in these genomes. These findings contribute to our understanding of microbial adaptation and have implications for microbial ecology, underlining the importance of sporulation in Firmicutes across different hosts. Further studies into novel species and their sporulation capability can contribute to bacterial maintenance mechanisms in various organisms and their applications in biotechnology studies.}, }
@article {pmid39282566, year = {2024}, author = {Abdelshafy Mohamad, OA and Liu, YH and Huang, Y and Kuchkarova, N and Dong, L and Jiao, JY and Fang, BZ and Ma, JB and Hatab, S and Li, WJ}, title = {Metabonomic analysis to identify exometabolome changes underlying antifungal and growth promotion mechanisms of endophytic Actinobacterium Streptomyces albidoflavus for sustainable agriculture practice.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1439798}, pmid = {39282566}, issn = {1664-302X}, abstract = {In recent years, there has been an increasing focus on microbial ecology and its possible impact on agricultural production, owing to its eco-friendly nature and sustainable use. The current study employs metabolomics technologies and bioinformatics approaches to identify changes in the exometabolome of Streptomyces albidoflavus B24. This research aims to shed light on the mechanisms and metabolites responsible for the antifungal and growth promotion strategies, with potential applications in sustainable agriculture. Metabolomic analysis was conducted using Q Exactive UPLC-MS/MS. Our findings indicate that a total of 3,840 metabolites were identified, with 137 metabolites exhibiting significant differences divided into 61 up and 75 downregulated metabolites based on VIP >1, |FC| >1, and p < 0.01. The interaction of S. albidoflavus B24 monoculture with the co-culture demonstrated a stronger correlation coefficient. The Principal Component Analysis (PCA) demonstrates that PCA1 accounted for 23.36%, while PCA2 accounted for 20.28% distinction. OPLS-DA score plots indicate significant separation among different groups representing (t1) 24% as the predicted component (to1) depicts 14% as the orthogonal component. According to the findings of this comprehensive study, crude extracts from S. albidoflavus demonstrated varying abilities to impede phytopathogen growth and enhance root and shoot length in tested plants. Through untargeted metabolomics, we discovered numerous potential molecules with antagonistic activity against fungal phytopathogens among the top 10 significant metabolites with the highest absolute log2FC values. These include Tetrangulol, 4-Hydroxybenzaldehyde, and Cyclohexane. Additionally, we identified plant growth-regulating metabolites such as N-Succinyl-L-glutamate, Nicotinic acid, L-Aspartate, and Indole-3-acetamide. The KEGG pathway analysis has highlighted these compounds as potential sources of antimicrobial properties. The inhibitory effect of S. albidoflavus crude extracts on pathogen growth is primarily attributed to the presence of specific gene clusters responsible for producing cyclic peptides such as ansamycins, porphyrin, alkaloid derivatives, and neomycin. Overall, it is apparent that crude extracts from S. albidoflavus exhibited varying abilities to inhibit the growth of three phytopathogens and enhancement in both root and shoot length of tested plants. This research enhances our understanding of how secondary metabolites contribute to growth promotion and biocontrol, supporting ecosystem sustainability and resilience while boosting productivity in sustainable agriculture.}, }
@article {pmid39282232, year = {2024}, author = {Taylor, T and Daksa, J and Shimels, MZ and Etalo, DW and Thiombiano, B and Walmsey, A and Chen, AJ and Bouwmeester, HJ and Raaijmakers, JM and Brady, SM and Kawa, D}, title = {Evaluating Mechanisms of Soil Microbiome Suppression of Striga Infection in Sorghum.}, journal = {Bio-protocol}, volume = {14}, number = {17}, pages = {e5058}, pmid = {39282232}, issn = {2331-8325}, abstract = {The root parasitic weed Striga hermonthica has a devastating effect on sorghum and other cereal crops in Sub-Saharan Africa. Available Striga management strategies are rarely sufficient or not widely accessible or affordable. Identification of soil- or plant-associated microorganisms that interfere in the Striga infection cycle holds potential for development of complementary biological control measures. Such inoculants should be preferably based on microbes native to the regions of their application. We developed a method to assess microbiome-based soil suppressiveness to Striga with a minimal amount of field-collected soil. We previously used this method to identify the mechanisms of microbe-mediated suppression of Striga infection and to test individual microbial strains. Here, we present protocols to assess the functional potential of the soil microbiome and individual bacterial taxa that adversely affect Striga parasitism in sorghum via three major known suppression mechanisms. These methods can be further extended to other Striga hosts and other root parasitic weeds. Key features • This protocol provides a detailed description of the methods used in Kawa et al. [1]. • This protocol is optimized to assess soil suppressiveness to Striga infection by using natural field-collected soil and the same soil sterilized by gamma-radiation. • This protocol is optimized to test bacterial (and not fungal) isolates. • This protocol can be easily extended to other host-parasite-microbiome systems.}, }
@article {pmid39277779, year = {2024}, author = {Boltz, JP and Rittmann, BE}, title = {Microbial ecology of nitrate-, selenate-, selenite-, and sulfate-reducing bacteria in a H2-driven bioprocess.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {11}, pages = {}, pmid = {39277779}, issn = {1574-6941}, mesh = {*Nitrates/metabolism ; *Sulfates/metabolism ; *Bioreactors/microbiology ; *Selenic Acid/metabolism ; *Hydrogen/metabolism ; *Bacteria/metabolism/genetics/growth &amp; development/classification ; *Selenious Acid/metabolism ; *Oxidation-Reduction ; Wastewater/microbiology ; Selenium Compounds/metabolism ; Biofilms/growth &amp; development ; Autotrophic Processes ; }, abstract = {A hydrogen (H2)-based membrane biofilm reactor (H2-MBfR) can reduce electron acceptors nitrate (NO3-), selenate (SeO42-), selenite (HSeO3-), and sulfate (SO42-), which are in wastewaters from coal mining and combustion. This work presents a model to describe a H2-driven microbial community comprised of hydrogenotrophic and heterotrophic bacteria that respire NO3-, SeO42-, HSeO3-, and SO42-. The model provides mechanistic insights into the interactions between autotrophic and heterotrophic bacteria in a microbial community that is founded on H2-based autotrophy. Simulations were carried out for a range of relevant solids retention times (SRT; 0.1-20 days) and with adequate H2-delivery capacity to reduce all electron acceptors. Bacterial activity began at an ∼0.6-day SRT, when hydrogenotrophic denitrifiers began to accumulate. Selenate-reducing and selenite-reducing hydrogenotrophs became established next, at SRTs of ∼1.2 and 2 days, respectively. Full NO3-, SeO42-, and HSeO3- reductions were complete by an SRT of ∼5 days. SO42- reduction began at an SRT of ∼10 days and was complete by ∼15 days. The desired goal of reducing NO3-, SeO42-, and HSeO3-, but not SO42-, was achievable within an SRT window of 5-10 days. Autotrophic hydrogenotrophs dominated the active biomass, but nonactive solids were a major portion of the solids, especially for an SRT ≥ 5 days.}, }
@article {pmid39267336, year = {2024}, author = {Du, X and Guo, Y and Zhao, X and Zhang, L and Fan, R and Li, Y}, title = {METTL3-mediated TIM1 promotes macrophage M1 polarization and inflammation through IGF2BP2-dependent manner.}, journal = {Journal of biochemical and molecular toxicology}, volume = {38}, number = {10}, pages = {e23845}, doi = {10.1002/jbt.23845}, pmid = {39267336}, issn = {1099-0461}, support = {20210302124578//This study was supported by the Shanxi Province Basic Research Program Project/ ; }, mesh = {Humans ; *Macrophages/metabolism ; *Inflammation/metabolism/pathology/genetics ; *Hepatitis A Virus Cellular Receptor 1/metabolism/genetics ; *Methyltransferases/metabolism/genetics ; *RNA-Binding Proteins/metabolism/genetics ; THP-1 Cells ; Lipopolysaccharides/pharmacology ; }, abstract = {Macrophage polarization and inflammation may play an important role in the development of sepsis. T-cell immunoglobulin mucin 1 (TIM1) has been demonstrated to promote macrophage inflammatory responses. However, whether TIM1 regulates macrophage polarization and inflammation to affect sepsis development remains unclear. Human monocytic leukemia cell line was induced into macrophages, followed by stimulated with LPS and IL-4 to induce M1 polarization and M2 polarization. The expression levels of TIM1, methyltransferase 3 (METTL3), and insulin like growth factor 2 mRNA binding protein 2 (IGF2BP2) were examined by qRT-PCR and western blot. IL-6, IL-1β, and TNF-α levels were tested by ELISA. CD86[+]cell rate was analyzed by flow cytometry. The m[6]A methylation level of TIM1 was assessed by MeRIP assay. The interaction of between TIM1 and METTL3 or IGF2BP2 was assessed by dual-luciferase reporter assay and RIP assay. TIM1 knockdown repressed LPS-induced macrophage M1 polarization and inflammation. In terms of mechanism, METTL3 promoted TIM1 expression through m[6]A modification, and this modification could be recognized by IGF2BP2. Besides, knockdown of METTL3/IGF2BP2 suppressed LPS-induced macrophage M1 polarization and inflammation, while this effect could be eliminated by TIM1 overexpression. METTL3/IGF2BP2/TIM1 axis promoted macrophage M1 polarization and inflammation, which might provide potential target for sepsis treatment.}, }
@article {pmid39273112, year = {2024}, author = {Druker, S and Sicsic, R and Ravid, S and Scheinin, S and Raz, T}, title = {Reproductive Tract Microbial Transitions from Late Gestation to Early Postpartum Using 16S rRNA Metagenetic Profiling in First-Pregnancy Heifers.}, journal = {International journal of molecular sciences}, volume = {25}, number = {17}, pages = {}, pmid = {39273112}, issn = {1422-0067}, mesh = {Female ; Animals ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; Cattle ; *Postpartum Period ; *Vagina/microbiology ; *Microbiota/genetics ; *Uterus/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; Metagenome ; }, abstract = {Studies in recent years indicate that reproductive tract microbial communities are crucial for shaping mammals' health and reproductive outcomes. Following parturition, uterine bacterial contamination often occurs due to the open cervix, which may lead to postpartum uterine inflammatory diseases, especially in primiparous individuals. However, investigations into spatio-temporal microbial transitions in the reproductive tract of primigravid females remain limited. Our objective was to describe and compare the microbial community compositions in the vagina at late gestation and in the vagina and uterus at early postpartum in first-pregnancy heifers. Three swab samples were collected from 33 first-pregnancy Holstein Friesian heifers: one vaginal sample at gestation day 258 ± 4, and vaginal and uterine samples at postpartum day 7 ± 2. Each sample underwent 16S rRNA V4 region metagenetic analysis via Illumina MiSeq, with bioinformatics following Mothur MiSeq SOP. The reproductive tract bacterial communities were assigned to 1255 genus-level OTUs across 30 phyla. Dominant phyla, accounting for approximately 90% of the communities, included Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Fusobacteria. However, the results revealed distinct shifts in microbial composition between the prepartum vagina (Vag-pre), postpartum vagina (Vag-post), and postpartum uterus (Utr-post). The Vag-pre and Utr-post microbial profiles were the most distinct. The Utr-post group had lower relative abundances of Proteobacteria but higher abundances of Bacteroidetes, Fusobacteria, and Tenericutes compared to Vag-pre, while Vag-post displayed intermediate values for these phyla, suggesting a transitional profile. Additionally, the Utr-post group exhibited lower bacterial richness and diversity compared to both Vag-pre and Vag-post. The unsupervised probabilistic Dirichlet Multinomial Mixtures model identified two distinct community types: most Vag-pre samples clustered into one type and Utr-post samples into another, while Vag-post samples were distributed evenly between the two. LEfSe analysis revealed distinct microbial profiles at the genus level. Overall, specific microbial markers were associated with anatomical and temporal transitions, revealing a dynamic microbial landscape during the first pregnancy and parturition. These differences highlight the complexity of these ecosystems and open new avenues for research in reproductive biology and microbial ecology.}, }
@article {pmid39272492, year = {2024}, author = {Nerini, M and Russo, A and Decorosi, F and Meriggi, N and Viti, C and Cavalieri, D and Marvasi, M}, title = {A Microbial Phenomics Approach to Determine Metabolic Signatures to Enhance Seabream Sparus aurata Traceability, Differentiating between Wild-Caught and Farmed.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {17}, pages = {}, pmid = {39272492}, issn = {2304-8158}, support = {2/SSL/16/TO-1/ICR/21/TO//Regione Toscana with the project PO FEAMP 2014-2020 - Misura 1.39 SSL FLAG Costa degli Etrusch/ ; }, abstract = {BACKGROUND: The need for efficient and simplified techniques for seafood traceability is growing. This study proposes the Biolog EcoPlate assay as an innovative method for assessing wild and farmed Sparus aurata traceability, offering advantages over other molecular techniques in terms of technical simplicity.<br><br>METHODS: The Biolog EcoPlate assay, known for its high-throughput capabilities in microbial ecology, was utilized to evaluate the functional diversity of microbial communities from various organs of S. aurata (seabream) from the Mediterranean area. Samples were taken from the anterior and posterior gut, cloaca swabs and gills to distinguish between farmed and wild-caught individuals. The analysis focused on color development in OmniLog Units for specific carbon sources at 48 h.<br><br>RESULTS: Gills provided the most accurate clusterization of sample origin. The assay monitored the development of color for carbon sources such as &#x3b1;-cyclodextrin, D-cellobiose, glycogen, &#x3b1;-D-lactose, L-threonine and L-phenylalanine. A mock experiment using principal component analysis (PCA) successfully identified the origin of a blind sample. Shannon and Simpson indexes were used to statistically assess the diversity, reflecting the clusterization of different organ samples; Conclusions: The Biolog EcoPlate assay proves to be a quick, cost-effective method for discriminate S. aurata traceability (wild vs. farmed), demonstrating reliable reproducibility and effective differentiation between farmed and wild-caught seabream.}, }
@article {pmid39268533, year = {2024}, author = {Wilson, T and Siddiqi, M and Xi, Y and LaPointe, G}, title = {Tracking the microbial communities from the farm to the processing facility of a washed-rind cheese operation.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1404795}, pmid = {39268533}, issn = {1664-302X}, abstract = {Milk residue and the accompanying biofilm accumulation in milking systems can compromise the microbial quality of milk and the downstream processes of cheese production. Over a six-month study, the microbial ecosystems of milk (n = 24), tap water (n = 24) and environmental swabs (n = 384) were cultured by plating decimal dilutions to obtain viable counts of total aerobic mesophilic lactose-utilizing bacteria (lactose-M17), lactic acid bacteria (MRS), yeasts and molds (Yeast, Glucose, Chloramphenicol (YGC) medium). Viable aerobic lactose-M17 plate counts of milk remained well below 4.7 log CFU/ml over five of the months, except for 1 week in November where milk at the facility exceeded 5 log CFU/ml. Swab samples of the farm milking equipment showed consistent viable counts after sanitation, while the bulk tank swabs contained the lowest counts. Viable counts from swabs of the facility were generally below the detection limit in the majority of samples with occasional residual contamination on some food contact surfaces. Extracted DNA was amplified using primers targeting the V3-V4 region of the 16S rRNA gene, and the amplicons were sequenced by MiSeq to determine the shared microbiota between the farm and the processing facility (8 genera). Culture independent analysis of bacterial taxa in milk, water and residual contamination after sanitation with swab samples revealed the shared and distinct microbiota between the sample types of both facilities. Amplicon sequence variants (ASVs) of the V3-V4 region of the 16S rRNA gene revealed that the microbiota of milk samples had lower diversity than water or environmental swabs (279 ASVs compared to 3,444 in water and 8,747 in environmental swabs). Brevibacterium and Yaniella (both Actinomycetota) were observed in all sampling types. Further studies will include whole genome sequencing of Brevibacterium spp. isolates to determine their functionality and diversity within the system.}, }
@article {pmid39266780, year = {2024}, author = {Cao, X and Li, M and Wu, X and Fan, S and Lin, L and Xu, L and Zhang, X and Zhou, F}, title = {Gut fungal diversity across different life stages of the onion fly Delia antiqua.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {115}, pmid = {39266780}, issn = {1432-184X}, mesh = {Animals ; *Diptera/microbiology/growth &amp; development ; *Fungi/classification/isolation &amp; purification/genetics ; *Gastrointestinal Microbiome ; *Larva/microbiology/growth &amp; development ; Male ; Female ; Pupa/microbiology/growth &amp; development ; Biodiversity ; Life Cycle Stages ; Mycobiome ; }, abstract = {A significant number of microorganisms inhabit the intestinal tract or the body surface of insects. While the majority of research on insect microbiome interaction has mainly focused on bacteria, of late multiple studies have been acknowledging the importance of fungi and have started reporting the fungal communities as well. In this study, high-throughput sequencing was used to compare the diversity of intestinal fungi in Delia antiqua (Diptera: Anthomyiidae) at different growth stages, and effect of differential fungi between adjacent life stages on the growth and development of D. antiqua was investigated. The results showed that there were significant differences in the α and β diversity of gut fungal communities between two adjacent growth stages. Among the dominant fungi, genera Penicillium and Meyerozyma and family Cordycipitaceae had higher abundances. Cordycipitaceae was mainly enriched in the pupal and adult (male and female) stages, Penicillium was mainly enriched in the pupal, 2nd instar and 3rd instar larval stages, and Meyerozyma was enriched in the pupal stage. Only three fungal species were found to differ between two adjacent growth stages. These three fungal species including Fusarium oxysporum, Meyerozyma guilliermondii and Penicillium roqueforti generally inhibited the growth and development of D. antiqua, with only P. roqueforti promoting the growth and development of female insects. This study will provide theoretical support for the search for new pathogenic microorganisms for other fly pests control and the development of new biological control strategies for fly pests.}, }
@article {pmid39264951, year = {2024}, author = {Pfennig, T and Kullmann, E and Zavřel, T and Nakielski, A and Ebenhöh, O and Červený, J and Bernát, G and Matuszyńska, AB}, title = {Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012445}, pmid = {39264951}, issn = {1553-7358}, mesh = {*Photosynthesis/physiology ; *Synechocystis/metabolism/physiology ; *Light ; *Models, Biological ; Computational Biology ; Carbon Dioxide/metabolism ; Carbon Cycle/physiology ; Phycobilisomes/metabolism ; Computer Simulation ; }, abstract = {Cyanobacteria hold great potential to revolutionize conventional industries and farming practices with their light-driven chemical production. To fully exploit their photosynthetic capacity and enhance product yield, it is crucial to investigate their intricate interplay with the environment including the light intensity and spectrum. Mathematical models provide valuable insights for optimizing strategies in this pursuit. In this study, we present an ordinary differential equation-based model for the cyanobacterium Synechocystis sp. PCC 6803 to assess its performance under various light sources, including monochromatic light. Our model can reproduce a variety of physiologically measured quantities, e.g. experimentally reported partitioning of electrons through four main pathways, O2 evolution, and the rate of carbon fixation for ambient and saturated CO2. By capturing the interactions between different components of a photosynthetic system, our model helps in understanding the underlying mechanisms driving system behavior. Our model qualitatively reproduces fluorescence emitted under various light regimes, replicating Pulse-amplitude modulation (PAM) fluorometry experiments with saturating pulses. Using our model, we test four hypothesized mechanisms of cyanobacterial state transitions for ensemble of parameter sets and found no physiological benefit of a model assuming phycobilisome detachment. Moreover, we evaluate metabolic control for biotechnological production under diverse light colors and irradiances. We suggest gene targets for overexpression under different illuminations to increase the yield. By offering a comprehensive computational model of cyanobacterial photosynthesis, our work enhances the basic understanding of light-dependent cyanobacterial behavior and sets the first wavelength-dependent framework to systematically test their producing capacity for biocatalysis.}, }
@article {pmid39264809, year = {2024}, author = {Boverhoff, D and Kool, J and Pijnacker, R and Ducarmon, QR and Zeller, G and Shetty, S and Sie, S and Mulder, AC and van der Klis, F and Franz, E and Mughini-Gras, L and van Baarle, D and Fuentes, S}, title = {Profiling the fecal microbiome and its modulators across the lifespan in the Netherlands.}, journal = {Cell reports}, volume = {43}, number = {9}, pages = {114729}, doi = {10.1016/j.celrep.2024.114729}, pmid = {39264809}, issn = {2211-1247}, mesh = {Netherlands ; Humans ; *Feces/microbiology ; Adult ; Aged ; Middle Aged ; Adolescent ; Child, Preschool ; Aged, 80 and over ; Child ; Infant ; Male ; Female ; Young Adult ; Infant, Newborn ; Longevity ; Gastrointestinal Microbiome/genetics ; Microbiota ; }, abstract = {Defining what constitutes a healthy microbiome throughout our lives remains an ongoing challenge. Understanding to what extent host and environmental factors can influence it has been the primary motivation for large population studies worldwide. Here, we describe the fecal microbiome of 3,746 individuals (0-87 years of age) in a nationwide study in the Netherlands, in association with extensive questionnaires. We validate previous findings, such as infant-adult trajectories, and explore the collective impact of our variables, which explain over 40% of the variation in microbiome composition. We identify associations with less explored factors, particularly those ethnic related, which show the largest impact on the adult microbiome composition, diversity, metabolic profiles, and CAZy (carbohydrate-active enzyme) repertoires. Understanding the sources of microbiome variability is crucial, given its potential as a modifiable target with therapeutic possibilities. With this work, we aim to serve as a foundational element for the design of health interventions and fundamental research.}, }
@article {pmid39264366, year = {2024}, author = {Yüksel, E and Voragen, AGJ and Kort, R}, title = {The pectin metabolizing capacity of the human gut microbiota.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-23}, doi = {10.1080/10408398.2024.2400235}, pmid = {39264366}, issn = {1549-7852}, abstract = {The human gastrointestinal microbiota, densely populated with a diverse array of microorganisms primarily from the bacterial phyla Bacteroidota, Bacillota, and Actinomycetota, is crucial for maintaining health and physiological functions. Dietary fibers, particularly pectin, significantly influence the composition and metabolic activity of the gut microbiome. Pectin is fermented by gut bacteria using carbohydrate-active enzymes (CAZymes), resulting in the production of short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate, which provide various health benefits. The gastrointestinal microbiota has evolved to produce CAZymes that target different pectin components, facilitating cross-feeding within the microbial community. This review explores the fermentation of pectin by various gut bacteria, focusing on the involved transport systems, CAZyme families, SCFA synthesis capacity, and effects on microbial ecology in the gut. It addresses the complexities of the gut microbiome's response to pectin and highlights the importance of microbial cross-feeding in maintaining a balanced and diverse gut ecosystem. Through a systematic analysis of pectinolytic CAZyme production, this review provides insights into the enzymatic mechanisms underlying pectin degradation and their broader implications for human health, paving the way for more targeted and personalized dietary strategies.}, }
@article {pmid39264291, year = {2024}, author = {Jones, BS and DeWitt, ME and Wenner, JJ and Sanders, JW}, title = {Lyme Disease Under-Ascertainment During the COVID-19 Pandemic in the United States: Retrospective Study.}, journal = {JMIR public health and surveillance}, volume = {10}, number = {}, pages = {e56571}, pmid = {39264291}, issn = {2369-2960}, mesh = {Humans ; *Lyme Disease/epidemiology ; *COVID-19/epidemiology ; United States/epidemiology ; North Carolina/epidemiology ; Retrospective Studies ; Pandemics ; Bayes Theorem ; }, abstract = {BACKGROUND: The COVID-19 pandemic resulted in a massive disruption in access to care and thus passive, hospital- and clinic-based surveillance programs. In 2020, the reported cases of Lyme disease were the lowest both across the United States and North Carolina in recent years. During this period, human contact patterns began to shift with higher rates of greenspace utilization and outdoor activities, putting more people into contact with potential vectors and associated vector-borne diseases. Lyme disease reporting relies on passive surveillance systems, which were likely disrupted by changes in health care-seeking behavior during the pandemic.<br><br>OBJECTIVE: This study aimed to quantify the likely under-ascertainment of cases of Lyme disease during the COVID-19 pandemic in the United States and North Carolina.<br><br>METHODS: We fitted publicly available, reported Lyme disease cases for both the United States and North Carolina prior to the year 2020 to predict the number of anticipated Lyme disease cases in the absence of the pandemic using a Bayesian modeling approach. We then compared the ratio of reported cases divided by the predicted cases to quantify the number of likely under-ascertained cases. We then fitted geospatial models to further quantify the spatial distribution of the likely under-ascertained cases and characterize spatial dynamics at local scales.<br><br>RESULTS: Reported cases of Lyme Disease were lower in 2020 in both the United States and North Carolina than prior years. Our findings suggest that roughly 14,200 cases may have gone undetected given historical trends prior to the pandemic. Furthermore, we estimate that only 40% to 80% of Lyme diseases cases were detected in North Carolina between August 2020 and February 2021, the peak months of the COVID-19 pandemic in both the United States and North Carolina, with prior ascertainment rates returning to normal levels after this period. Our models suggest both strong temporal effects with higher numbers of cases reported in the summer months as well as strong geographic effects.<br><br>CONCLUSIONS: Ascertainment rates of Lyme disease were highly variable during the pandemic period both at national and subnational scales. Our findings suggest that there may have been a substantial number of unreported Lyme disease cases despite an apparent increase in greenspace utilization. The use of counterfactual modeling using spatial and historical trends can provide insight into the likely numbers of missed cases. Variable ascertainment of cases has implications for passive surveillance programs, especially in the trending of disease morbidity and outbreak detection, suggesting that other methods may be appropriate for outbreak detection during disturbances to these passive surveillance systems.}, }
@article {pmid39260494, year = {2024}, author = {Ejaz, MR and Badr, K and Hassan, ZU and Al-Thani, R and Jaoua, S}, title = {Metagenomic approaches and opportunities in arid soil research.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {176173}, doi = {10.1016/j.scitotenv.2024.176173}, pmid = {39260494}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Metagenomics ; *Soil/chemistry ; Desert Climate ; Microbiota ; }, abstract = {Arid soils present unique challenges and opportunities for studying microbial diversity and bioactive potential due to the extreme environmental conditions they bear. This review article investigates soil metagenomics as an emerging tool to explore complex microbial dynamics and unexplored bioactive potential in harsh environments. Utilizing advanced metagenomic techniques, diverse microbial populations that grow under extreme conditions such as high temperatures, salinity, high pH levels, and exposure to metals and radiation can be studied. The use of extremophiles to discover novel natural products and biocatalysts emphasizes the role of functional metagenomics in identifying enzymes and secondary metabolites for industrial and pharmaceutical purposes. Metagenomic sequencing uncovers a complex network of microbial diversity, offering significant potential for discovering new bioactive compounds. Functional metagenomics, connecting taxonomic diversity to genetic capabilities, provides a pathway to identify microbes' mechanisms to synthesize valuable secondary metabolites and other bioactive substances. Contrary to the common perception of desert soil as barren land, the metagenomic analysis reveals a rich diversity of life forms adept at extreme survival. It provides valuable findings into their resilience and potential applications in biotechnology. Moreover, the challenges associated with metagenomics in arid soils, such as low microbial biomass, high DNA degradation rates, and DNA extraction inhibitors and strategies to overcome these issues, outline the latest advancements in extraction methods, high-throughput sequencing, and bioinformatics. The importance of metagenomics for investigating diverse environments opens the way for future research to develop sustainable solutions in agriculture, industry, and medicine. Extensive studies are necessary to utilize the full potential of these powerful microbial communities. This research will significantly improve our understanding of microbial ecology and biotechnology in arid environments.}, }
@article {pmid39259499, year = {2024}, author = {Schwab, ST and Bühler, LY and Schleheck, D and Nelson, TF and Mecking, S}, title = {Correlation of Enzymatic Depolymerization Rates with the Structure of Polyethylene-Like Long-Chain Aliphatic Polyesters.}, journal = {ACS macro letters}, volume = {13}, number = {10}, pages = {1245-1250}, pmid = {39259499}, issn = {2161-1653}, abstract = {Long-chain aliphatic polyesters are emerging sustainable materials that exhibit polyethylene-like properties while being amenable to chemical recycling and biodegradation. However, varying polyester chemical structures results in markedly different degradation rates, which cannot be predicted from commonly correlated bulk polyester properties, such as polymer melting temperature. To elucidate these structure-degradability relationships, long-chain polyesters varying in their monomer composition and crystallinity were subjected to enzymatic hydrolysis, the rates of which were quantified via detection of formed monomers. Copolymers with poorly water-soluble, long-chain diol monomers (e.g., 1,18-octadecanediol) demonstrated strongly reduced depolymerization rates compared to copolymers with shorter chain length diol monomers. This was illustrated by, e.g., the 20× faster hydrolysis of PE-4,18, consisting of 1,4-butanediol and 1,18-octadecanedicarboxylic acid monomers, relative to PE-18,4. The insoluble long-chain diol monomer released upon hydrolysis was proposed to remain attached to the bulk polymer surface, decreasing the accessibility of the remaining ester bonds to enzymes for further hydrolysis. Tuning of polyester crystallinity via the introduction of branched monomers led to variable hydrolysis rates, which increased by an order of magnitude when crystallinity decreased from 72% to 45%. The results reported enables the informed design of polyester structures with balanced material properties and amenability to depolymerization.}, }
@article {pmid39259393, year = {2024}, author = {Berlow, M and Mesa, M and Creek, M and Duarte, JG and Carpenter, E and Phinizy, B and Andonian, K and Dlugosch, KM}, title = {Plant G × Microbial E: Plant Genotype Interaction with Soil Bacterial Community Shapes Rhizosphere Composition During Invasion.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {113}, pmid = {39259393}, issn = {1432-184X}, support = {1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 1750280//NSF/ ; 2023-67012-40306//USDA/ ; 2023-67013-40169//USDA/ ; 2023-67013-40169//USDA/ ; }, mesh = {*Soil Microbiology ; *Rhizosphere ; *Introduced Species ; *Genotype ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; Centaurea/microbiology/genetics ; Plant Roots/microbiology ; California ; Soil/chemistry ; }, abstract = {It is increasingly recognized that different genetic variants of hosts can uniquely shape their microbiomes. Invasive species often evolve in their introduced ranges, but little is known about the potential for their microbial associations to change during invasion as a result. We asked whether host genotype (G), microbial environment (E), or their interaction (G × E) affected the composition and diversity of host-associated microbiomes in Centaurea solstitialis (yellow starthistle), a Eurasian plant that is known to have evolved novel genotypes and phenotypes and to have altered microbial interactions, in its severe invasion of CA, USA. We conducted an experiment in which native and invading plant genotypes were inoculated with native and invaded range soil microbial communities. We used amplicon sequencing to characterize rhizosphere bacteria in both the experiment and the field soils from which they were derived. We found that native and invading plant genotypes accumulated different microbial associations at the family level in each soil community, often counter to differences in family abundance between soil communities. Root associations with potentially beneficial Streptomycetaceae were particularly interesting, as these were more abundant in the invaded range field soil and accumulated on invading genotypes. We also found that bacterial diversity is higher in invaded soils, but that invading genotypes accumulated a lower diversity of bacteria and unique microbial composition in experimental inoculations, relative to native genotypes. Thus variation in microbial associations of invaders was driven by the interaction of plant G and microbial E, and rhizosphere microbial communities appear to change in composition in response to host evolution during invasion.}, }
@article {pmid39259373, year = {2024}, author = {Zhang, K and Tan, X and Zhang, Q}, title = {Nutritional Quality of Basal Resource in Stream Food Webs Increased with Light Reduction-Implications for Riparian Revegetation.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {114}, pmid = {39259373}, issn = {1432-184X}, support = {Nos. 32271665, 32030069//National Natural Science Foundation of China/ ; Nos. 32271665, 32030069//National Natural Science Foundation of China/ ; Nos. 32271665, 32030069//National Natural Science Foundation of China/ ; }, mesh = {*Rivers/microbiology/chemistry ; *Food Chain ; *Fatty Acids, Unsaturated/analysis/metabolism ; *Light ; Cyanobacteria/metabolism/growth &amp; development ; Chlorophyta/metabolism/growth &amp; development ; Diatoms/metabolism/growth &amp; development ; Nutritive Value ; }, abstract = {Biofilms are considered a basal resource with high nutritional quality in stream food webs, as periphytic algae are abundant of polyunsaturated fatty acids (PUFAs). PUFAs are essential for growth and reproduction of consumers who cannot or have very limited capacity to biosynthesize. Yet, how the nutritional quality based on PUFA of basal food sources changes with light intensity remains unclear. We conducted a manipulative experiment in mesocosms to explore the response and mechanisms of nutritional quality to shading, simulating riparian restoration. We found a significant increase in PUFA% (including arachidonic acid, ARA) under shading conditions. The increased PUFA is caused by the algal community succession from Cyanobacteria and Chlorophyta to Bacillariophyta which is abundant of PUFA (especially eicosapentaenoic acid, EPA; docosahexaenoic acid, DHA). On the other hand, shading increased PUFA via upregulating enzymes such as Δ12 desaturase (FAD2, EC:1.14.19.6) and 3-ketoacyl-CoA synthase (KCS, EC:2.3.1.199) in the biosynthesis of unsaturated fatty acid elongation pathways. Our findings imply that riparian reforestation by decreasing light intensity increases the nutritional quality of basal resources in streams, which may enhance transfer of good quality carbon to consumers in higher trophic levels through bottom-up effects.}, }
@article {pmid39258201, year = {2024}, author = {Iliopoulou, S and Kourteli, M and Damialis, A and Kapsanaki-Gotsi, E and Pyrri, I}, title = {Air mycobiome in the National Library of Greece following relocation to novel premises.}, journal = {Heliyon}, volume = {10}, number = {16}, pages = {e36362}, pmid = {39258201}, issn = {2405-8440}, abstract = {The aim of this work was to study the diversity and spatiotemporal fluctuations of airborne fungi in the National Library of Greece after its relocation from the Vallianeio historic building in the center of Athens to entirely new premises at the Stavros Niarchos Foundation Cultural Center, and also to compare the fungal aerosol in between the two sites. The air mycobiota were studied by a volumetric culture-based method, during the year 2019 in order to assess their diversity and abundance and to compare with those previously reported in the historic building. Twenty-eight genera of filamentous fungi were recovered indoors and 17 outdoors, in addition to yeasts registered as a group. The number of fungal genera recovered was almost similar in both premises, whereas seventeen genera indoors were identical, dominated by Penicillium, Cladosporium and Aspergillus. The mean daily fungal concentration was found to be 66 CFU m[-3] indoors and 927 CFU m[-3] outdoors in the new location vs 293 and 428 CFU m[-] [3] indoors and 707 and 648 CFU m[-] [3] outdoors in the previous one. The mean daily concentration indoors was consistently and significantly lower (P < 0.05) in the new building than in the historic one, although it was higher outdoors. The indoor/outdoor ratio for the total fungi was 0.07 in the new vs 0.41 and 0.66 in the previous one and reveals a superior indoor air quality in the new site. Air temperature and occupancy had a statistically significant impact on the concentration of indoor fungi. The remarkably reduced concentration of the mycobiota in the new premises indicated a considerable decline in fungal burden, mainly due to technological excellency of the facility and continuous preventive measures to ensure an enhanced indoor air quality in the National Library of Greece. This case study provides a paradigm about upgrading of indoor air after re-establishment of a facility in another setting.}, }
@article {pmid39256405, year = {2024}, author = {Gan, L and Zheng, J and Xu, WH and Lin, J and Liu, J and Zhang, Y and Wu, Z and Lv, Z and Jia, Y and Guo, Q and Chen, S and Liu, C and Defoirdt, T and Qin, Q and Liu, Y}, title = {Author Correction: Deciphering the virulent Vibrio harveyi causing spoilage in muscle of aquatic crustacean Litopenaeus vannamei.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21131}, doi = {10.1038/s41598-024-71652-4}, pmid = {39256405}, issn = {2045-2322}, }
@article {pmid39256399, year = {2024}, author = {Huang, WRH and Braam, C and Kretschmer, C and Villanueva, SL and Liu, H and Ferik, F and van der Burgh, AM and Boeren, S and Wu, J and Zhang, L and Nürnberger, T and Wang, Y and Seidl, MF and Evangelisti, E and Stuttmann, J and Joosten, MHAJ}, title = {Author Correction: Receptor-like cytoplasmic kinases of different subfamilies differentially regulate SOBIR1/BAK1-mediated immune responses in Nicotiana benthamiana.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7910}, doi = {10.1038/s41467-024-52322-5}, pmid = {39256399}, issn = {2041-1723}, }
@article {pmid39255667, year = {2024}, author = {Mei, Z and Wang, F and Fu, Y and Liu, Y and Hashsham, SA and Wang, Y and Harindintwali, JD and Dou, Q and Virta, M and Jiang, X and Deng, Y and Zhang, T and Tiedje, JM}, title = {Biofilm enhanced the mitigations of antibiotics and resistome in sulfadiazine and trimethoprim co-contaminated soils.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135721}, pmid = {39255667}, issn = {1873-3336}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, mesh = {*Sulfadiazine/pharmacology ; *Biofilms/drug effects ; *Trimethoprim/pharmacology ; *Soil Pollutants/toxicity ; *Anti-Bacterial Agents/pharmacology ; *Soil Microbiology ; *Manure/microbiology ; Arthrobacter/genetics/drug effects/metabolism ; Charcoal ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; }, abstract = {Reducing antibiotic levels in soil ecosystems is vital to curb the dissemination of antimicrobial resistance genes (ARGs) and mitigate global health threats. However, gaps persist in understanding how antibiotic resistome can be suppressed during antibiotic degradation. Herein, we investigate the efficacy of a biochar biofilm incorporating antibiotics-degrading bacterial strain (Arthrobacter sp. D2) to mitigate antibiotic resistome in non-manured and manure-amended soils with sulfadiazine (SDZ) and trimethoprim (TMP) contamination. Results show that biofilm enhanced SDZ degradation by 83.0% within three days and increased TMP attenuation by 55.4% over 60 days in non-manured soils. In the non-manured black soil, the relative abundance of ARGs increased initially after biofilm inoculation. However, by day 30, it decreased by 20.5% compared to the controls. Moreover, after 7 days, biofilm reduced TMP by 38.5% in manured soils and decreased the total ARG abundance by 19.0%. Thus, while SDZ degradation did not increase sulfonamide resistance genes, TMP dissipation led to a proliferation of insertion sequences and related TMP resistance genes. This study underscores the importance of antibiotic degradation in reducing related ARGs while cautioning against the potential proliferation and various ARGs transfer by resistant microorganisms.}, }
@article {pmid39254334, year = {2024}, author = {Lyng, M and Þórisdóttir, B and Sveinsdóttir, SH and Hansen, ML and Jelsbak, L and Maróti, G and Kovács, &#xc1;T}, title = {Taxonomy of Pseudomonas spp. determines interactions with Bacillus subtilis.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0021224}, pmid = {39254334}, issn = {2379-5077}, support = {DNRF137//Danmarks Grundforskningsfond (DNRF)/ ; NNF19SA0059360//Novo Nordisk Fonden (NNF)/ ; NNF19OC0055625//Novo Nordisk Fonden (NNF)/ ; PhD fellowship//Technical University of Denmark/ ; }, mesh = {*Pseudomonas/physiology ; *Bacillus subtilis/physiology ; *Soil Microbiology ; *Microbial Interactions/physiology ; Rhizosphere ; }, abstract = {UNLABELLED: Bacilli and pseudomonads are among the most well-studied microorganisms commonly found in soil and frequently co-isolated. Isolates from these two genera are frequently used as plant beneficial microorganisms; therefore, their interaction in the plant rhizosphere is relevant for agricultural applications. Despite this, no systematic approach has been employed to assess the coexistence of members from these genera. Here, we screened 720 fluorescent soil isolates for their effects on Bacillus subtilis pellicle formation in two types of media and found a predictor for interaction outcome in Pseudomonas taxonomy. Interactions were context-dependent, and both medium composition and culture conditions strongly influenced interactions. Negative interactions were associated with Pseudomonas capeferrum, Pseudomonas entomophila, and Pseudomonas protegens, and 2,4-diacetylphloroglucinol was confirmed as a strong (but not exclusive) inhibitor of B. subtilis. Non-inhibiting strains were closely related to Pseudomonas trivialis and Pseudomonas lini. Using such a non-inhibiting isolate, Pseudomonas P9_31, which increased B. subtilis pellicle formation demonstrated that the two species were spatially segregated in cocultures. Our study is the first one to propose an overall negative outcome from pairwise interactions between B. subtilis and fluorescent pseudomonads; hence, cocultures comprising members from these groups are likely to require additional microorganisms for coexistence.<br><br>IMPORTANCE: There is a strong interest in the microbial ecology field to predict interaction among microorganisms, whether two microbial isolates will promote each other's growth or compete for resources. Numerous studies have been performed based on surveying the available literature or testing phylogenetically diverse sets of species in synthetic communities. Here, a high throughput screening has been performed using 720 Pseudomonas isolates, and their impact on the biofilm formation of Bacillus subtilis was tested. The aim was to determine whether a majority of Pseudomonas will promote or inhibit the biofilms of B. subtilis in the co-cultures. This study reports that Pseudomonas taxonomy is a good predictor of interaction outcome, and only a minority of Pseudomonas isolates promote Bacillus biofilm establishment.}, }
@article {pmid39252061, year = {2024}, author = {Trego, A and O'Sullivan, S and O'Flaherty, V and Collins, G and Ijaz, UZ}, title = {Individual methanogenic granules are whole-ecosystem replicates with reproducible responses to environmental cues.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {68}, pmid = {39252061}, issn = {2524-6372}, support = {3C-BIOTECH 261330/ERC_/European Research Council/International ; 3C-BIOTECH 261330/ERC_/European Research Council/International ; 3C-BIOTECH 261330/ERC_/European Research Council/International ; TC/2014/0016//Enterprise Ireland/ ; 14/IA/2371/SFI_/Science Foundation Ireland/Ireland ; 17/CDA/4658/SFI_/Science Foundation Ireland/Ireland ; NE/L011956/1//Natural Environment Research Council/ ; }, abstract = {BACKGROUND: In this study, individual methanogenic (anaerobic), granular biofilms were used as true community replicates to assess whole-microbial-community responses to environmental cues. The aggregates were sourced from a lab-scale, engineered, biological wastewater treatment system, were size-separated, and the largest granules were individually subjected to controlled environmental cues in micro-batch reactors (μBRs).<br><br>RESULTS: Individual granules were identical with respect to the structure of the active community based on cDNA analysis. Additionally, it was observed that the active microbial community of individual granules, at the depth of 16S rRNA gene sequencing, produced reproducible responses to environmental changes in pH, temperature, substrate, and trace-metal supplementation. We identified resilient and susceptible taxa associated with each environmental condition tested, as well as selected specialists, whose niche preferences span the entire trophic chain required for the complete anaerobic degradation of organic matter.<br><br>CONCLUSIONS: We found that single anaerobic granules can be considered highly-replicated whole-ecosystems with potential usefulness for the field of microbial ecology. Additionally, they act as the smallest whole-community unit within the meta-community of an engineered bioreactor. When subjected to various environmental cues, anaerobic granules responded reproducibly allowing for rare or unique opportunities for high-throughput studies testing whole-community responses to a wide range of environmental conditions.}, }
@article {pmid39250422, year = {2024}, author = {Vijay, S and Bao, NLH and Vinh, DN and Nhat, LTH and Thu, DDA and Quang, NL and Trieu, LPT and Nhung, HN and Ha, VTN and Thai, PVK and Ha, DTM and Lan, NH and Caws, M and Thwaites, GE and Javid, B and Thuong, NT}, title = {Rifampicin tolerance and growth fitness among isoniazid-resistant clinical Mycobacterium tuberculosis isolates from a longitudinal study.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39250422}, issn = {2050-084X}, support = {10.35802/207487/WT_/Wellcome Trust/United Kingdom ; R21 AI169005/AI/NIAID NIH HHS/United States ; R21AI169005//National Institute of Allergy and Infectious Diseases/ ; 10.35802/106680/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 10.35802/206724/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Rifampin/pharmacology ; *Mycobacterium tuberculosis/drug effects/genetics ; *Isoniazid/pharmacology ; Longitudinal Studies ; *Microbial Sensitivity Tests ; Humans ; *Antitubercular Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Tuberculosis, Multidrug-Resistant/microbiology/drug therapy ; Tuberculosis/microbiology/drug therapy ; }, abstract = {Antibiotic tolerance in Mycobacterium tuberculosis reduces bacterial killing, worsens treatment outcomes, and contributes to resistance. We studied rifampicin tolerance in isolates with or without isoniazid resistance (IR). Using a minimum duration of killing assay, we measured rifampicin survival in isoniazid-susceptible (IS, n=119) and resistant (IR, n=84) isolates, correlating tolerance with bacterial growth, rifampicin minimum inhibitory concentrations (MICs), and isoniazid-resistant mutations. Longitudinal IR isolates were analyzed for changes in rifampicin tolerance and genetic variant emergence. The median time for rifampicin to reduce the bacterial population by 90% (MDK90) increased from 1.23 days (IS) and 1.31 days (IR) to 2.55 days (IS) and 1.98 days (IR) over 15-60 days of incubation, indicating fast and slow-growing tolerant sub-populations. A 6 log10-fold survival fraction classified tolerance as low, medium, or high, showing that IR is linked to increased tolerance and faster growth (OR = 2.68 for low vs. medium, OR = 4.42 for low vs. high, p-trend = 0.0003). High tolerance in IR isolates was associated with rifampicin treatment in patients and genetic microvariants. These findings suggest that IR tuberculosis should be assessed for high rifampicin tolerance to optimize treatment and prevent the development of multi-drug-resistant tuberculosis.}, }
@article {pmid39249553, year = {2024}, author = {Morimura, H and Ishigami, K and Sato, T and Sone, T and Kikuchi, Y}, title = {Geographical, Seasonal, and Growth-Related Dynamics of Gut Microbiota in a Grapevine Pest, Apolygus spinolae (Heteroptera: Miridae).}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {112}, pmid = {39249553}, issn = {1432-184X}, support = {22KJ0057//Japan Society for the Promotion of Science/ ; 21K20579//Japan Society for the Promotion of Science/ ; S-3-7//Northern Advancement Center for Science and Technology/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Vitis/microbiology ; *Heteroptera/microbiology/growth &amp; development ; *Seasons ; *Bacteria/classification/genetics/isolation &amp; purification ; *Symbiosis ; Japan ; Nymph/microbiology/growth &amp; development ; }, abstract = {A number of insects are associated with gut symbiotic microorganisms, wherein symbiotic partners play pivotal metabolic roles for each other such as nutrient supplementation, diet degradation, and pesticide detoxification. Despite the ecological and evolutionary importance of gut microbial communities in insects, their diversity and dynamics remain unclear in many species. The green plant bug Apolygus spinolae, a notorious grapevine pest in Japan, damages grape shoots and severely reduces grape berry yield and quality. The plant bug possesses a simple tubular gut housing ~ 10[4] bacteria. Here, we investigated geographic, seasonal, and growth-related dynamics of gut microbiota by high-throughput sequencing in 82 individuals (11 nymphs and 71 adults) from five locations in Hokkaido, Japan. In plant bugs, gut microbiota changed dynamically depending on region, season, and developmental stage. Among the gut bacteria, Serratia was consistently and abundantly detected and was significantly affected by seasonal changes. In addition, Caballeronia, known as a specific symbiont in some stinkbug species, was abundantly detected, especially in insects collected in late summer despite A. spinolae complete lack of midgut crypts known as symbiotic organ harboring Caballeronia in other stinkbug species. Considering their prevalence among host bug populations, it is possible these gut microorganisms play a pivotal role in the adaptation of the green plant bug to grapevine fields, although further confirmation through rearing experiments is needed.}, }
@article {pmid39248572, year = {2024}, author = {Sivaloganathan, DM and Wan, X and Leon, G and Brynildsen, MP}, title = {Loss of Gre factors leads to phenotypic heterogeneity and cheating in Escherichia coli populations under nitric oxide stress.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0222924}, pmid = {39248572}, issn = {2150-7511}, support = {CBET-1453325//National Science Foundation (NSF)/ ; PGSD3 - 516782 - 2018//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; Focused Research Team award on Precision Antibiotics//Princeton University (PU)/ ; }, mesh = {*Escherichia coli/genetics/metabolism/drug effects ; *Escherichia coli Proteins/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Hydrogen Peroxide/pharmacology/metabolism/toxicity ; *Nitric Oxide/metabolism ; Phenotype ; Stress, Physiological ; Transcription Factors/genetics/metabolism ; Transcriptional Elongation Factors/metabolism/genetics ; }, abstract = {Nitric oxide (·NO) is one of the toxic metabolites that bacteria can be exposed to within phagosomes. Gre factors, which are also known as transcript cleavage factors or transcription elongation factors, relieve back-tracked transcription elongation complexes by cleaving nascent RNAs, which allows transcription to resume after stalling. Here we discovered that loss of both Gre factors in Escherichia coli, GreA and GreB, significantly compromised ·NO detoxification due to ·NO-induced phenotypic heterogeneity in ΔgreAΔgreB populations, which did not occur in wild-type cultures. Under normal culturing conditions, both wild-type and ΔgreAΔgreB synthesized transcripts uniformly, whereas treatment with ·NO led to bimodal transcript levels in ΔgreAΔgreB that were unimodal in wild-type. Interestingly, exposure to another toxic metabolite of phagosomes, hydrogen peroxide (H2O2), produced analogous results. Furthermore, we showed that loss of Gre factors led to cheating under ·NO stress where transcriptionally deficient cells benefited from the detoxification activities of the transcriptionally proficient subpopulation. Collectively, these results show that loss of Gre factor activities produces phenotypic heterogeneity under ·NO and H2O2 stress that can yield cheating between subpopulations.IMPORTANCEToxic metabolite stress occurs in a broad range of contexts that are important to human health, microbial ecology, and biotechnology, whereas Gre factors are highly conserved throughout the bacterial kingdom. Here we discovered that loss of Gre factors in E. coli leads to phenotypic heterogeneity under ·NO and H2O2 stress, which we further show with ·NO results in cheating between subpopulations. Collectively, these data suggest that Gre factors play a role in coping with toxic metabolite stress, and that loss of Gre factors can produce cheating between neighbors.}, }
@article {pmid39248476, year = {2024}, author = {Maitra, P and Hrynkiewicz, K and Szuba, A and Niestrawska, A and Mucha, J}, title = {The effects of Pinus sylvestris L. geographical origin on the community and co-occurrence of fungal and bacterial endophytes in a common garden experiment.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0080724}, pmid = {39248476}, issn = {2165-0497}, mesh = {*Pinus sylvestris/microbiology ; *Endophytes/classification/isolation &amp; purification/genetics/physiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/isolation &amp; purification/genetics/physiology ; *Plant Roots/microbiology ; *Microbiota ; Seasons ; Phylogeny ; Biodiversity ; }, abstract = {UNLABELLED: Below-ground microorganisms, particularly endophytes, are pivotal for plant establishment and functioning through nutrient acquisition and enhancing resistance to abiotic and biotic stresses. The impact of host plant origin within a species on the composition and interaction networks of root endophytic fungi and bacteria has been less explored compared with plant phylogeny and biological distance. This study investigates the effect of geographic origin on the fungal and bacterial microbiomes of Pinus sylvestris L. root endophytes. Roots from plants grown in a common garden, originating from six locations, were harvested in two distinct seasons. Fungal and bacterial microbiomes were analyzed using Illumina MiSeq sequencing. The operational taxonomic unit (OTU) richness of endophytic fungi and bacteria showed no significant variation due to tree origin or season. However, the Shannon diversity index for endophytic fungi was seasonally influenced. The composition of endophytic fungal and bacterial communities was affected by both tree origin and season, correlating with host root biochemical parameters, such as starch, total non-structural carbohydrates, carbon, nitrogen, and climatic factors, such as mean annual precipitation and temperature. Moreover, the abundance of specific endophytic fungi and bacteria varied across different P. sylvestris origins, depending on the season. The complexity of the co-occurrence networks of fungal and bacterial endophytes within P. sylvestris also differed by geographical origin and season. This study highlights the significant role of biochemical and climatic factors associated with tree origin in shaping interactions with endophytic communities, potentially affecting plant health and adaptability across diverse environments.<br><br>IMPORTANCE: This study advances our understanding of how plant ecotype and seasonal changes influence root endophytic communities in Scots pine (Pinus sylvestris). By examining trees from various origins grown in a common garden, it highlights the role of tree origin and season in shaping fungal and bacterial community and co-occurrence networks. Importantly, this research demonstrates that tree origin impacts the composition and interaction networks of root endophytes and depends on the season. The study's findings suggest that root biochemical traits and climatic conditions (e.g., temperature, precipitation) associated with tree origin are crucial in determining the assembly of endophytic communities. This understanding could lead to innovative strategies for enhancing plant health and adaptability across different environments, contributing to forestry and conservation efforts. The research underscores the complexity of plant-microbe interactions and the need for a comprehensive approach to studying them, highlighting the interplay between tree origin and microbial ecology in forest ecosystems.}, }
@article {pmid39248406, year = {2024}, author = {Yuan, X and Qing, J and Zhi, W and Wu, F and Yan, Y and Li, Y}, title = {Gut and respiratory microbiota landscapes in IgA nephropathy: a cross-sectional study.}, journal = {Renal failure}, volume = {46}, number = {2}, pages = {2399749}, pmid = {39248406}, issn = {1525-6049}, mesh = {Humans ; *Glomerulonephritis, IGA/microbiology ; Cross-Sectional Studies ; Male ; Female ; Adult ; *Gastrointestinal Microbiome ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Machine Learning ; Case-Control Studies ; Bacteria/isolation &amp; purification/classification/genetics ; Microbiota ; Young Adult ; }, abstract = {BACKGROUND: IgA nephropathy (IgAN) is intimately linked to mucosal immune responses, with nasopharyngeal and intestinal lymphoid tissues being crucial for its abnormal mucosal immunity. The specific pathogenic bacteria in these sites associated with IgAN, however, remain elusive. Our study employs 16S rRNA sequencing and machine learning (ML) approaches to identify specific pathogenic bacteria in these locations and to investigate common pathogens that may exacerbate IgAN.<br><br>METHODS: In this cross-sectional analysis, we collected pharyngeal swabs and stool specimens from IgAN patients and healthy controls. We applied 16SrRNA sequencing to identify differential microbial populations. ML algorithms were then used to classify IgAN based on these microbial differences. Spearman correlation analysis was employed to link key bacteria with clinical parameters.<br><br>RESULTS: We observed a reduced microbial diversity in IgAN patients compared to healthy controls. In the gut microbiota of IgAN patients, increases in Bacteroides, Escherichia-Shigella, and Parabacteroides, and decreases in Parasutterella, Dialister, Faecalibacterium, and Subdoligranulum were notable. In the respiratory microbiota, increases in Neisseria, Streptococcus, Fusobacterium, Porphyromonas, and Ralstonia, and decreases in Prevotella, Leptotrichia, and Veillonella were observed. Post-immunosuppressive therapy, Oxalobacter and Butyricoccus levels were significantly reduced in the gut, while Neisseria and Actinobacillus levels decreased in the respiratory tract. Veillonella and Fusobacterium appeared to influence IgAN through dual immune loci, with Fusobacterium abundance correlating with IgAN severity.<br><br>CONCLUSIONS: This study revealing that changes in flora structure could provide important pathological insights for identifying therapeutic targets, and ML could facilitate noninvasive diagnostic methods for IgAN.}, }
@article {pmid39247694, year = {2024}, author = {Nasher, F and Wren, BW}, title = {Unravelling mechanisms of bacterial recognition by Acanthamoeba: insights into microbial ecology and immune responses.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1405133}, pmid = {39247694}, issn = {1664-302X}, abstract = {Acanthamoeba, are ubiquitous eukaryotic microorganisms, that play a pivotal role in recognizing and engulfing various microbes during predation, offering insights into microbial dynamics and immune responses. An intriguing observation lies in the apparent preference of Acanthamoeba for Gram-negative over Gram-positive bacteria, suggesting potential differences in the recognition and response mechanisms to bacterial prey. Here, we comprehensively review pattern recognition receptors (PRRs) and microbe associated molecular patterns (MAMPs) that influence Acanthamoeba interactions with bacteria. We analyze the molecular mechanisms underlying these interactions, and the key finding of this review is that Acanthamoeba exhibits an affinity for bacterial cell surface appendages that are decorated with carbohydrates. Notably, this parallels warm-blooded immune cells, underscoring a conserved evolutionary strategy in microbial recognition. This review aims to serve as a foundation for exploring PRRs and MAMPs. These insights enhance our understanding of ecological and evolutionary dynamics in microbial interactions and shed light on fundamental principles governing immune responses. Leveraging Acanthamoeba as a model organism, provides a bridge between ecological interactions and immunology, offering valuable perspectives for future research.}, }
@article {pmid39247294, year = {2024}, author = {Grimm, H and Drabesch, S and Nicol, A and Straub, D and Joshi, P and Zarfl, C and Planer-Friedrich, B and Muehe, EM and Kappler, A}, title = {Arsenic immobilization and greenhouse gas emission depend on quantity and frequency of nitrogen fertilization in paddy soil.}, journal = {Heliyon}, volume = {10}, number = {16}, pages = {e35706}, pmid = {39247294}, issn = {2405-8440}, abstract = {Nitrogen (N) fertilization in paddy soils decreases arsenic mobility and methane emissions. However, it is unknown how quantity and frequency of N fertilization affects the interlinked redox reactions of iron(II)-driven denitrification, iron mineral (trans-)formation with subsequent arsenic (im-)mobilization, methane and nitrous oxide emissions, and how this links to microbiome composition. Thus, we incubated paddy soil from Vercelli, Italy, over 129 days and applied nitrate fertilizer at different concentrations (control: 0, low: ∼35, medium: ∼100, high: ∼200 mg N kg[-1] soil[-1]) once at the beginning and after 49 days. In the high N treatment, nitrate reduction was coupled to oxidation of dissolved and solid-phase iron(II), while naturally occurring arsenic was retained on iron minerals due to suppression of reductive iron(III) mineral dissolution. In the low N treatment, 40 μg L[-1] of arsenic was mobilized into solution after nitrate depletion, with 69 % being immobilized after a second nitrate application. In the non-fertilized control, concentrations of dissolved arsenic were as high as 76 μg L[-1], driven by mobilization of 36 % of the initial mineral-bound arsenic. Generally, N fertilization led to 1.5-fold higher total GHG emissions (sum of CO2, CH4 and N2O as CO2 equivalents), 158-fold higher N2O, and 7.5-fold lower CH4 emissions compared to non-fertilization. On day 37, Gallionellaceae, Comamonadaceae and Rhodospirillales were more abundant in the high N treatment compared to the non-fertilized control, indicating their potential role as key players in nitrate reduction coupled to iron(II) oxidation. The findings underscore the dual effect of N fertilization, immobilizing arsenic in the short-term (low/medium N) or long-term (high N), while simultaneously increasing N2O and lowering CH4 emissions. This highlights the significance of both the quantity and frequency of N fertilizer application in paddy soils.}, }
@article {pmid39244747, year = {2024}, author = {Bayer, B and Liu, S and Louie, K and Northen, TR and Wagner, M and Daims, H and Carlson, CA and Santoro, AE}, title = {Metabolite release by nitrifiers facilitates metabolic interactions in the ocean.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39244747}, issn = {1751-7370}, support = {J 4426/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Seawater/microbiology ; *Nitrification ; Oceans and Seas ; Nitrites/metabolism ; Heterotrophic Processes ; Microbial Interactions ; Metabolome ; Coculture Techniques ; Ammonia/metabolism ; }, abstract = {Microbial chemoautotroph-heterotroph interactions may play a pivotal role in the cycling of carbon in the deep ocean, reminiscent of phytoplankton-heterotroph associations in surface waters. Nitrifiers are the most abundant chemoautotrophs in the global ocean, yet very little is known about nitrifier metabolite production, release, and transfer to heterotrophic microbial communities. To elucidate which organic compounds are released by nitrifiers and potentially available to heterotrophs, we characterized the exo- and endometabolomes of the ammonia-oxidizing archaeon Nitrosopumilus adriaticus CCS1 and the nitrite-oxidizing bacterium Nitrospina gracilis Nb-211. Nitrifier endometabolome composition was not a good predictor of exometabolite availability, indicating that metabolites were predominately released by mechanisms other than cell death/lysis. Although both nitrifiers released labile organic compounds, N. adriaticus preferentially released amino acids, particularly glycine, suggesting that its cell membranes might be more permeable to small, hydrophobic amino acids. We further initiated co-culture systems between each nitrifier and a heterotrophic alphaproteobacterium, and compared exometabolite and transcript patterns of nitrifiers grown axenically to those in co-culture. In particular, B vitamins exhibited dynamic production and consumption patterns in nitrifier-heterotroph co-cultures. We observed an increased production of vitamin B2 and the vitamin B12 lower ligand dimethylbenzimidazole by N. adriaticus and N. gracilis, respectively. In contrast, the heterotroph likely produced vitamin B5 in co-culture with both nitrifiers and consumed the vitamin B7 precursor dethiobiotin when grown with N. gracilis. Our results indicate that B vitamins and their precursors could play a particularly important role in governing specific metabolic interactions between nitrifiers and heterotrophic microbes in the ocean.}, }
@article {pmid39244369, year = {2024}, author = {Baptista, RC and Ferrocino, I and Pavani, M and Guerreiro, TM and Câmara, AA and Lang, &#xc9; and Dos Santos, JLP and Catharino, RR and Alves Filho, EG and Rodrigues, S and de Brito, ES and Caturla, MYR and Sant'Ana, AS and Cocolin, L}, title = {Microbiota diversity of three Brazilian native fishes during ice and frozen storage.}, journal = {Food microbiology}, volume = {124}, number = {}, pages = {104617}, doi = {10.1016/j.fm.2024.104617}, pmid = {39244369}, issn = {1095-9998}, mesh = {Animals ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Volatile Organic Compounds/analysis/metabolism ; *Food Storage ; *Fishes/microbiology ; Brazil ; *Seafood/microbiology/analysis ; *RNA, Ribosomal, 16S/genetics ; *Freezing ; Ice ; Food Microbiology ; Biodiversity ; Female ; }, abstract = {This study aimed to assess the bacterial microbiota involved in the spoilage of pacu (Piaractus mesopotamics), patinga (female Piaractus mesopotamics x male Piaractus brachypomus), and tambacu (female Colossoma macropomum × male Piaractus mesopotamics) during ice and frozen storage. Changes in the microbiota of three fish species (N = 22) during storage were studied through 16S rRNA amplicon-based sequencing and correlated with volatile organic compounds (VOCs) and metabolites assessed by nuclear magnetic resonance (NMR). Storage conditions (time and temperature) affected the microbiota diversity in all fish samples. Fish microbiota comprised mainly of Pseudomonas sp., Brochothrix sp., Acinetobacter sp., Bacillus sp., Lactiplantibacillus sp., Kocuria sp., and Enterococcus sp. The relative abundance of Kocuria, P. fragi, L. plantarum, Enterococcus, and Acinetobacter was positively correlated with the metabolic pathways of ether lipid metabolism while B. thermosphacta and P. fragi were correlated with metabolic pathways involved in amino acid metabolism. P. fragi was the most prevalent spoilage bacteria in both storage conditions (ice and frozen), followed by B. thermosphacta. Moreover, the relative abundance of identified Bacillus strains in fish samples stored in ice was positively correlated with the production of VOCs (1-hexanol, nonanal, octenol, and 2-ethyl-1-hexanol) associated with off-flavors. [1]H NMR analysis confirmed that amino acids, acetic acid, and ATP degradation products increase over (ice) storage, and therefore considered chemical spoilage index of fish fillets.}, }
@article {pmid39243903, year = {2024}, author = {Macedo Silva, JR and Petra de Oliveira Barros, V and Terceiro, PS and Nunes de Oliveira, &#xcd; and Francisco da Silva Moura, O and Duarte de Freitas, J and Crispim, AC and Maciel Melo, VM and Thompson, FL and Maraschin, M and Landell, MF}, title = {Brazilian mangrove sediments as a source of biosurfactant-producing yeast Pichia pseudolambica for bioremediation.}, journal = {Chemosphere}, volume = {365}, number = {}, pages = {143285}, doi = {10.1016/j.chemosphere.2024.143285}, pmid = {39243903}, issn = {1879-1298}, mesh = {*Surface-Active Agents/metabolism ; *Biodegradation, Environmental ; Brazil ; *Pichia/metabolism ; *Geologic Sediments/microbiology/chemistry ; Surface Tension ; Wetlands ; Hydrocarbons/metabolism ; }, abstract = {This work highlights the biosurfactant production potential of yeasts from mangroves in northeastern Brazil. The biosurfactants were evaluated by their emulsifying capacity (EI24), with 6 isolates showing values between 50% and 62%. Surfactant properties from crude extract were measured using drop collapse, oil displacement, Parafilm® M, surface tension and critical micellar concentration tests. The effects of temperature, salinity, pH, and the ability to emulsify different hydrocarbons were analyzed, showing a promising potential of the yeast species investigated to tolerance to high temperatures and acidic pH, in addition to emulsifying different sources of hydrocarbons with environmental impact. It is important to note that the Pichia pseudolambica isolates showed a remarkable ability to reduce the surface tension of water, from 70.82 mN/m to 36.47 mN/m. In addition, the critical micellar concentration (CMC) values ranged from 7 to 16 mg/mL, highlighting the promising surfactant activity of these isolates for future applications. It was identified that the biosurfactant adhered to the yeast cell wall, and FTIR and 1H NMR spectroscopy analysis was carried out on the yeast biomass and its post-sonication supernatant. The results indicate the presence of characteristic functional groups and peaks found in biosurfactants of a glycolipid nature. Taking together the results reveals the promising potential of biosurfactant biosynthesis of P. pseudolambica yeast, a trait not reported in the literature so far for this species. P. pseudolambica presents a relevant metabolic potential for alternative substrate use and resilience to adverse conditions that could enable it to produce biosurfactants for the biotechnological remediation of areas contaminated by oil derivatives. The metabolic properties herein investigated, together with their presence in Brazilian mangroves, make P. pseudolambica an emerging candidate for developing industrial processes and sustainable strategies for the recovery of ecosystems impacted by oil spills, being positioned as a sustainable alternative to conventional surfactants.}, }
@article {pmid39243542, year = {2024}, author = {Song, Y and Zhang, Z and Liu, Y and Peng, F and Feng, Y}, title = {Enhancement of anaerobic treatment of antibiotic pharmaceutical wastewater through the development of iron-based and carbon-based materials: A critical review.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135514}, doi = {10.1016/j.jhazmat.2024.135514}, pmid = {39243542}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/chemistry ; *Wastewater/chemistry ; Anaerobiosis ; *Iron/chemistry ; *Water Pollutants, Chemical/chemistry ; Carbon/chemistry ; Waste Disposal, Fluid/methods ; Biodegradation, Environmental ; Water Purification/methods ; }, abstract = {The extensive use of antibiotics has created an urgent need to address antibiotic wastewater treatment, posing significant challenges for environmental protection and public health. Recent advances in the efficacy and mechanisms of conductive materials (CMs) for enhancing the anaerobic biological treatment of antibiotic pharmaceutical wastewater are reviewed. For the first time, the focus is on the various application forms of iron-based and carbon-based CMs in strengthening the anaerobic methanogenic system. This includes the use of single CMs such as zero-valent iron (ZVI), magnetite, biochar (BC), activated carbon (AC), and graphene (GP), as well as iron-based and carbon-based composite CMs with diverse structures. These structures include mixed, surface-loaded, and core-shell combinations, reflecting the development of CMs. Iron-based and carbon-based CMs promote the rapid removal of antibiotics through adsorption and enhanced biodegradation. They also mitigate the inhibitory effects of toxic pollutants on microbial activity and reduce the expression of antibiotic resistance genes (ARGs). Additionally, as effective electron carriers, these CMs enrich microorganisms with direct interspecies electron transfer (DIET) functions, accelerate interspecies electron transfer, and facilitate the conversion of organic matter into methane. Finally, this review proposes the use of advanced molecular detection technologies to clarify microbial ecology and metabolic mechanisms, along with microscopic characterization techniques for the modification of CMs. These methods can provide more direct evidence to analyze the mechanisms underlying the cooperative anaerobic treatment of refractory organic wastewater by CMs and microorganisms.}, }
@article {pmid39239791, year = {2024}, author = {Fouad, AM and Abo-Al-Ela, HG and Negm, EA and Abdelhaseib, M and Alian, A and Abdelsater, N and Said, REM and Anwar, FAS and Assar, DH and Mohamed, SA}, title = {Impact of Polyonchobothrium magnum on health and gut microbial ecology of African catfish (Clarias gariepinus): Insights from morphological, molecular, and microbiological analyses.}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {e14013}, doi = {10.1111/jfd.14013}, pmid = {39239791}, issn = {1365-2761}, abstract = {Parasites pose significant challenges to aquaculture and fisheries industries. Our study focuses on the Polyonchobothrium magnum and African catfish to address a potential health issue in aquaculture, explore host-parasite interactions that can help develop effective management practices to ensure fish health and industry sustainability. P. magnum was isolated from the stomach of African catfish (Clarias gariepinus) as the primary site of infection, with a prevalence of 10%. Most affected fish were heavily infected (8 out of 10). Infection was confirmed by sequencing the PCR-targeted region of the nicotinamide adenine dinucleotide dehydrogenase subunit 1 (ND1) gene, along with light and scanning electron microscopes. The parasite had an elongated scolex with deep bothria, a prominent apical disc wider than the scolex itself, and a four-lobed appearance. The scolex contained a central rostellum divided into two semicircles, bearing 26-30 hooks, with an average of 28. The apical disc had large hooks arranged in four quadrants, with 6-8 hooks each, averaging 7 per quadrant. No neck was observed. Phylogenetic analysis of our sequence showed a 100% match with isolates from Guangzhou, China. In infected fish, the anterior kidney showed increased expression levels of nuclear factor kappa B and lysozyme, but decreased levels of in major histocompatibility complex antigen II. Plasma analysis revealed a significant drop in superoxide dismutase, a rise in interleukin-1 beta, and lower IgM levels compared to non-infected controls. Non-infected fish displayed greater gut microbiota diversity, with dominant families including Moraxellaceae, Enterobacteriaceae, Fusobacteriaceae, and Caulobacteraceae, and prevalent genera such as Acinetobacter, Cetobacterium, and Brevundimonas. In contrast, infected fish exhibited very low diversity, with significantly higher proportions of Enterobacteriaceae (45.99%) and Aeromonadaceae (41.79%) compared to non-infected fish, which had 13.76% and 3.64% respectively. Cetobacterium somerae was prevalent in non-infected fish, while infected fish harboured Aeromonas fluvialis, Plesiomonas shigelloides, and Gallaecimonas xiamenensis. Overall, P. magnum disrupted the immune status and gut microbiota of the host, thereby impacting its health.}, }
@article {pmid39236824, year = {2024}, author = {Guo, Q and Xiao, Y and Zhu, Y and Korpelainen, H and Li, C}, title = {Selenium availability in tea: Unraveling the role of microbiota assembly and functions.}, journal = {The Science of the total environment}, volume = {952}, number = {}, pages = {175995}, doi = {10.1016/j.scitotenv.2024.175995}, pmid = {39236824}, issn = {1879-1026}, mesh = {*Selenium/metabolism/analysis ; *Microbiota ; *Camellia sinensis/metabolism ; *Soil Microbiology ; Tea ; Soil/chemistry ; Soil Pollutants/metabolism/analysis ; Bacteria/metabolism ; }, abstract = {Tea (Camellia sinensis (L.) O. Kuntze) plants have a strong ability to accumulate selenium (Se). However, the question of how tea plants affect Se availability has received little attention. In this study, five tea cultivars, including Soubei (SB), Aolǜ (AL), Longjing43 (LJ), Zhaori (ZR) and Fenglǜ (FL), were chosen for the study. Quantitative Microbial Ecology Chip and high-throughput sequencing were used to explore the effects of five tea cultivars on soil functions, microbial community structures and Se availability. The results showed that the total soil Se content in the FL garden was lower compared to LJ and SB gardens, whereas available Se was highest in the FL garden. Based on the Bray-Curtis distances, tea cultivar was the main factor affecting bacterial and fungal community structures. The abundance of functional genes concerning carbon, nitrogen, phosphorus and sulfur cycling processes varied among tea gardens. The higher soil NH4[+] and NO3[-] contents, and higher abundance of functional genes like nifH, amoA1 and narG, whereas lower total nitrogen in the FL garden than in the AL and LJ tea gardens demonstrated that the FL tea plants induced microbes to accelerate soil nitrogen cycling processes. Dominant microbes that positively related with functional genes like nifH, narG, and amoA1 were also positively related with the available Se content. In conclusion, tea cultivars could regulate soil functions through affecting microbial community structures and then affecting the soil Se availability. The soil nitrogen cycle processes are suggested to be closely related with Se transformation in tea gardens.}, }
@article {pmid39236233, year = {2024}, author = {Richards, L and Cremin, K and Coates, M and Vigor, F and Schäfer, P and Soyer, OS}, title = {Ammonia leakage can underpin nitrogen-sharing among soil microorganisms.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39236233}, issn = {1751-7370}, support = {//Gordon and Betty Moore Foundation/ ; //Midlands Integrative Biosciences Training Partnership/ ; P3141153//Baden-W&#xfc;rttemberg Stiftung/ ; }, mesh = {*Ammonia/metabolism ; *Soil Microbiology ; *Nitrogen/metabolism ; *Nitrates/metabolism ; *Bacillus subtilis/metabolism/growth &amp; development/genetics ; Soil/chemistry ; Microbial Interactions ; Hydrogen-Ion Concentration ; Ammonium Compounds/metabolism ; }, abstract = {Soil microbial communities host a large number of microbial species that support important ecological functions such as biogeochemical cycling and plant nutrition. The extent and stability of these functions are affected by inter-species interactions among soil microorganisms, yet the different mechanisms underpinning microbial interactions in the soil are not fully understood. Here, we study the extent of nutrient-based interactions among two model, plant-supporting soil microorganisms, the fungi Serendipita indica, and the bacteria Bacillus subtilis. We found that S. indica is unable to grow with nitrate - a common nitrogen source in the soil - but this inability could be rescued, and growth restored in the presence of B. subtilis. We demonstrate that this effect is due to B. subtilis utilising nitrate and releasing ammonia, which can be used by S. indica. We refer to this type of mechanism as ammonia mediated nitrogen sharing (N-sharing). Using a mathematical model, we demonstrated that the pH dependent equilibrium between ammonia (NH3) and ammonium (NH+4) results in an inherent cellular leakiness, and that reduced amonnium uptake or assimilation rates could result in higher levels of leaked ammonia. In line with this model, a mutant B. subtilis - devoid of ammonia uptake - showed higher S. indica growth support in nitrate media. These findings highlight that ammonia based N-sharing can be a previously under-appreciated mechanism underpinning interaction among soil microorganisms and could be influenced by microbial or abiotic alteration of pH in microenvironments.}, }
@article {pmid39235751, year = {2025}, author = {Lemée, P and Bridier, A}, title = {Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2852}, number = {}, pages = {289-309}, pmid = {39235751}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Food Microbiology/methods ; *Bacteria/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Microbiota/genetics ; }, abstract = {Next-generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize, and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.}, }
@article {pmid39235736, year = {2025}, author = {Islam, DT and Mobasser, S and Kotaru, S and Telli, AE and Telli, N and Cupples, AM and Hashsham, SA}, title = {Electrochemical Detection of Nucleic Acids Using Three-Dimensional Graphene Screen-Printed Electrodes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2852}, number = {}, pages = {47-64}, pmid = {39235736}, issn = {1940-6029}, mesh = {*Graphite/chemistry ; *Electrodes ; *Electrochemical Techniques/methods/instrumentation ; *Biosensing Techniques/methods/instrumentation ; Nucleic Acids/analysis ; Humans ; DNA/analysis ; }, abstract = {Electrochemical approaches, along with miniaturization of electrodes, are increasingly being employed to detect and quantify nucleic acid biomarkers. Miniaturization of the electrodes is achieved through the use of screen-printed electrodes (SPEs), which consist of one to a few dozen sets of electrodes, or by utilizing printed circuit boards. Electrode materials used in SPEs include glassy carbon (Chiang H-C, Wang Y, Zhang Q, Levon K, Biosensors (Basel) 9:2-11, 2019), platinum, carbon, and graphene (Cheng FF, He TT, Miao HT, Shi JJ, Jiang LP, Zhu JJ, ACS Appl Mater Interfaces 7:2979-2985, 2015). There are numerous modifications to the electrode surfaces as well (Cheng FF, He TT, Miao HT, Shi JJ, Jiang LP, Zhu JJ, ACS Appl Mater Interfaces 7:2979-2985, 2015). These approaches offer distinct advantages, primarily due to their demonstrated superior limit of detection without amplification. Using the SPEs and potentiostats, we can detect cells, proteins, DNA, and RNA concentrations in the nanomolar (nM) to attomolar (aM) range. The focus of this chapter is to describe the basic approach adopted for the use of SPEs for nucleic acid measurement.}, }
@article {pmid39235733, year = {2025}, author = {Williams, MR and Telli, AE and Telli, N and Islam, DT and Hashsham, SA}, title = {Direct or DNA Extraction-Free Amplification and Quantification of Foodborne Pathogens.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2852}, number = {}, pages = {3-17}, pmid = {39235733}, issn = {1940-6029}, mesh = {*Nucleic Acid Amplification Techniques/methods ; *Food Microbiology/methods ; Animals ; *Milk/microbiology ; *Salmonella/genetics/isolation &amp; purification ; *DNA, Bacterial/genetics/isolation &amp; purification ; *Polymerase Chain Reaction/methods ; Foodborne Diseases/microbiology ; Escherichia coli/genetics/isolation &amp; purification ; Molecular Diagnostic Techniques/methods ; Swine ; }, abstract = {The use of direct nucleic acid amplification of pathogens from food matrices has the potential to reduce time to results over DNA extraction-based approaches as well as traditional culture-based approaches. Here we describe protocols for assay design and experiments for direct amplification of foodborne pathogens in food sample matrices using loop-mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR). The examples provided include the detection of Escherichia coli in milk samples and Salmonella in pork meat samples. This protocol includes relevant reagents and methods including obtaining target sequences, assay design, sample processing, and amplification. These methods, though used for specific example matrices, could be applied to many other foodborne pathogens and sample types.}, }
@article {pmid39234658, year = {2024}, author = {King, WL and Hayward, RJ and Goebel, M and Fleishman, SM and Bauerle, TL and Bell, TH}, title = {Getting to the root of root-microbe interactions.}, journal = {Science progress}, volume = {107}, number = {3}, pages = {368504241278783}, pmid = {39234658}, issn = {2047-7163}, mesh = {Ecosystem ; Microbiota/physiology ; *Plant Roots/microbiology/metabolism ; Plants/microbiology/metabolism ; *Soil Microbiology ; }, abstract = {Microbial relationships with roots influence many ecosystem functions and nutrient fluxes, including their sometimes-profound effects on plant health and productivity. Fine roots were often classified with a diameter less than 2 mm, but fine roots under that size perform distinct functional roles in the environment. Importantly, two broad functional categories of fine roots are absorptive and transportive, with absorptive fine roots acting as metabolic hotspots for root activity. In two of our recent studies, we have shown that several microbial community characteristics differ between absorptive and transportive fine roots, including composition, abundance, and function, as well as the root metabolome. This highlights a growing recognition within microbial ecology that we must consider fine-scale environmental variability, such as root physiology and morphology, when interpreting microbial patterns. In this commentary, we summarize the findings of our latest article, further speculate on some of these patterns, and suggest future studies for examining decomposition and applying cutting-edge single-cell sequencing techniques.}, }
@article {pmid39234547, year = {2024}, author = {Marshall, IPG}, title = {Electromicrobiological concentration cells are an overlooked potential energy conservation mechanism for subsurface microorganisms.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1407868}, pmid = {39234547}, issn = {1664-302X}, abstract = {Thermodynamics has predicted many different kinds of microbial metabolism by determining which pairs of electron acceptors and donors will react to produce an exergonic reaction (a negative net change in Gibbs free energy). In energy-limited environments, such as the deep subsurface, such an approach can reveal the potential for unexpected or counter-intuitive energy sources for microbial metabolism. Up until recently, these thermodynamic calculations have been carried out with the assumption that chemical species appearing on the reactant and product side of a reaction formula have a constant concentration, and thus do not count towards net concentration changes and the overall direction of the reaction. This assumption is reasonable considering microorganisms are too small (~1 μm) for any significant differences in concentration to overcome diffusion. However, recent discoveries have demonstrated that the reductive and oxidative halves of reactions can be separated by much larger distances, from millimetres to centimetres via conductive filamentous bacteria, mineral conductivity, and biofilm conductivity. This means that the concentrations of reactants and products can indeed be different, and that concentration differences can contribute to the net negative change in Gibbs free energy. It even means that the same redox reaction, simultaneously running in forward and reverse, can drive energy conservation, in an ElectroMicrobiological Concentration Cell (EMCC). This paper presents a model to investigate this phenomenon and predict under which circumstances such concentration-driven metabolism might take place. The specific cases of oxygen concentration cells, sulfide concentration cells, and hydrogen concentration cells are examined in more detail.}, }
@article {pmid39233440, year = {2024}, author = {Hosseiniyan Khatibi, SM and Dimaano, NG and Veliz, E and Sundaresan, V and Ali, J}, title = {Exploring and exploiting the rice phytobiome to tackle climate change challenges.}, journal = {Plant communications}, volume = {5}, number = {12}, pages = {101078}, pmid = {39233440}, issn = {2590-3462}, mesh = {*Climate Change ; *Oryza/microbiology/growth &amp; development ; *Microbiota ; Crops, Agricultural/growth &amp; development/genetics ; Agriculture/methods ; }, abstract = {The future of agriculture is uncertain under the current climate change scenario. Climate change directly and indirectly affects the biotic and abiotic elements that control agroecosystems, jeopardizing the safety of the world's food supply. A new area that focuses on characterizing the phytobiome is emerging. The phytobiome comprises plants and their immediate surroundings, involving numerous interdependent microscopic and macroscopic organisms that affect the health and productivity of plants. Phytobiome studies primarily focus on the microbial communities associated with plants, which are referred to as the plant microbiome. The development of high-throughput sequencing technologies over the past 10 years has dramatically advanced our understanding of the structure, functionality, and dynamics of the phytobiome; however, comprehensive methods for using this knowledge are lacking, particularly for major crops such as rice. Considering the impact of rice production on world food security, gaining fresh perspectives on the interdependent and interrelated components of the rice phytobiome could enhance rice production and crop health, sustain rice ecosystem function, and combat the effects of climate change. Our review re-conceptualizes the complex dynamics of the microscopic and macroscopic components in the rice phytobiome as influenced by human interventions and changing environmental conditions driven by climate change. We also discuss interdisciplinary and systematic approaches to decipher and reprogram the sophisticated interactions in the rice phytobiome using novel strategies and cutting-edge technology. Merging the gigantic datasets and complex information on the rice phytobiome and their application in the context of regenerative agriculture could lead to sustainable rice farming practices that are resilient to the impacts of climate change.}, }
@article {pmid39233079, year = {2024}, author = {Zhang, G and Guo, Z and Ke, Y and Li, H and Xiao, X and Lin, D and Lin, L and Wang, Y and Liu, J and Lu, H and Hong, H and Yan, C}, title = {Comparative analysis of size-fractional eukaryotic microbes in subtropical riverine systems inferred from 18S rRNA gene V4 and V9 regions.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {175972}, doi = {10.1016/j.scitotenv.2024.175972}, pmid = {39233079}, issn = {1879-1026}, mesh = {*RNA, Ribosomal, 18S/genetics ; *Rivers/microbiology ; *Eukaryota/genetics ; Microbiota/genetics ; Ecosystem ; Environmental Monitoring/methods ; }, abstract = {Eukaryotic microbes play key ecological roles in riverine ecosystems. Amplicon sequencing has greatly facilitated the identification and characterization of eukaryotic microbial communities. Currently, 18S rRNA gene V4 and V9 hypervariable regions are widely used for sequencing eukaryotic microbes. Identifying optimal regions for the profiling of size-fractional eukaryotic microbial communities is critical for microbial ecological studies. In this study, we spanned three rivers with typical natural-human influenced transition gradients to evaluate the performance of the 18S rRNA gene V4 and V9 hypervariable regions for sequencing size-fractional eukaryotic microbes (>180 μm, 20-180 μm, 5-20 μm, 3-5 μm, 0.8-3 μm). Our comparative analysis revealed that amplicon results depend on the specific species and microbial size. The V9 region was most effective for detecting a broad taxonomic range of species. The V4 region was superior to the V9 region for the identification of microbes in the minor 3 μm and at the family and genus levels, especially for specific microbial groups, such as Labyrinthulomycetes. However, the V9 region was more effective for studies of diverse eukaryotic groups, including Archamoebae, Heterolobosea, and Microsporidia, and various algae, such as Haptophyta, Florideophycidae, and Bangiales. Our results highlight the importance of accounting for potential misclassifications when employing both V4 and V9 regions for the identification of microbial sequences. The use of optimal regions for amplification could enhance the utility of amplicon sequencing in environmental studies. The insights gained from this work will aid future studies that employ amplicon-based identification approaches for the characterization of eukaryotic microbial communities and contribute to our understanding of microbial ecology within aquatic systems.}, }
@article {pmid39231820, year = {2024}, author = {Song, X and Li, J and Xiong, Z and Sha, H and Wang, G and Liu, Q and Zeng, T}, title = {Effects of Detoxifying Substances on Uranium Removal by Bacteria Isolated from Mine Soils: Performance, Mechanisms, and Bacterial Communities.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {111}, pmid = {39231820}, issn = {1432-184X}, support = {52170164//National Natural Science Foundation of China/ ; 2022RC1184//Science and Technology Innovation Program of Hunan Province of China/ ; }, mesh = {*Uranium/metabolism ; *Soil Microbiology ; *Bacteria/metabolism/genetics/isolation &amp; purification/classification ; *Mining ; *Biodegradation, Environmental ; Acyl-Butyrolactones/metabolism ; Glutathione/metabolism ; Soil Pollutants, Radioactive/metabolism ; }, abstract = {In this study, we investigated the effect of detoxifying substances on U(VI) removal by bacteria isolated from mine soil. The results demonstrated that the highest U(VI) removal efficiency (85.6%) was achieved at pH 6.0 and a temperature of 35 °C, with an initial U(VI) concentration of 10 mg/L. For detoxifying substances, signaling molecules acyl homoserine lactone (AHLs, 0.1 µmol/L), anthraquinone-2, 6-disulfonic acid (AQDS, 1 mmol/L), reduced glutathione (GSH, 0.1 mmol/L), selenium (Se, 1 mg/L), montmorillonite (MT, 1 g/L), and ethylenediaminetetraacetic acid (EDTA, 0.1 mmol/L) substantially enhanced the bacterial U(VI) removal by 34.9%, 37.4%, 54.5%, 35.1%, 32.8%, and 47.8% after 12 h, respectively. This was due to the alleviation of U(VI) toxicity in bacteria through detoxifying substances, as evidenced by lower malondialdehyde (MDA) content and higher superoxide dismutase (SOD) and catalase (CAT) activities for bacteria exposed to U(VI) and detoxifying substances, compared to those exposed to U(VI) alone. FTIR results showed that hydroxyl, carboxyl, phosphorus, and amide groups participated in the U(VI) removal. After exposure to U(VI), the relative abundances of Chryseobacterium and Stenotrophomonas increased by 48.5% and 12.5%, respectively, suggesting their tolerance ability to U(VI). Gene function prediction further demonstrated that the detoxifying substances AHLs alleviate U(VI) toxicity by influencing bacterial metabolism. This study suggests the potential application of detoxifying substances in the U(VI)-containing wastewater treatment through bioremediation.}, }
@article {pmid39230264, year = {2024}, author = {Rodriguez-Gonzalez, RA and Balacheff, Q and Debarbieux, L and Marchi, J and Weitz, JS}, title = {Metapopulation model of phage therapy of an acute Pseudomonas aeruginosa lung infection.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0017124}, pmid = {39230264}, issn = {2379-5077}, support = {R01 AI146592/AI/NIAID NIH HHS/United States ; //Consejo Nacional de Ciencia y Tecnolog&#xed;a (CONACYT)/ ; }, mesh = {*Pseudomonas aeruginosa/virology ; *Phage Therapy/methods ; *Pseudomonas Infections/therapy/immunology ; Animals ; Mice ; Bacteriophages/physiology ; Lung/microbiology/immunology/virology ; Models, Biological ; Mice, Inbred C57BL ; Humans ; Drug Resistance, Multiple, Bacterial ; }, abstract = {UNLABELLED: Infections caused by multidrug resistant (MDR) pathogenic bacteria are a global health threat. Bacteriophages ("phage") are increasingly used as alternative or last-resort therapeutics to treat patients infected by MDR bacteria. However, the therapeutic outcomes of phage therapy may be limited by the emergence of phage resistance during treatment and/or by physical constraints that impede phage-bacteria interactions in vivo. In this work, we evaluate the role of lung spatial structure on the efficacy of phage therapy for Pseudomonas aeruginosa infections. To do so, we developed a spatially structured metapopulation network model based on the geometry of the bronchial tree, including host innate immune responses and the emergence of phage-resistant bacterial mutants. We model the ecological interactions between bacteria, phage, and the host innate immune system at the airway (node) level. The model predicts the synergistic elimination of a P. aeruginosa infection due to the combined effects of phage and neutrophils, given the sufficient innate immune activity and efficient phage-induced lysis. The metapopulation model simulations also predict that MDR bacteria are cleared faster at distal nodes of the bronchial tree. Notably, image analysis of lung tissue time series from wild-type and lymphocyte-depleted mice revealed a concordant, statistically significant pattern: infection intensity cleared in the bottom before the top of the lungs. Overall, the combined use of simulations and image analysis of in vivo experiments further supports the use of phage therapy for treating acute lung infections caused by P. aeruginosa, while highlighting potential limits to therapy in a spatially structured environment given impaired innate immune responses and/or inefficient phage-induced lysis.<br><br>IMPORTANCE: Phage therapy is increasingly employed as a compassionate treatment for severe infections caused by multidrug-resistant (MDR) bacteria. However, the mixed outcomes observed in larger clinical studies highlight a gap in understanding when phage therapy succeeds or fails. Previous research from our team, using in vivo experiments and single-compartment mathematical models, demonstrated the synergistic clearance of acute P. aeruginosa pneumonia by phage and neutrophils despite the emergence of phage-resistant bacteria. In fact, the lung environment is highly structured, prompting the question of whether immunophage synergy explains the curative treatment of P. aeruginosa when incorporating realistic physical connectivity. To address this, we developed a metapopulation network model mimicking the lung branching structure to assess phage therapy efficacy for MDR P. aeruginosa pneumonia. The model predicts the synergistic elimination of P. aeruginosa by phage and neutrophils but emphasizes potential challenges in spatially structured environments, suggesting that higher innate immune levels may be required for successful bacterial clearance. Model simulations reveal a spatial pattern in pathogen clearance where P. aeruginosa are cleared faster at distal nodes of the bronchial tree than in primary nodes. Interestingly, image analysis of infected mice reveals a concordant and statistically significant pattern: infection intensity clears in the bottom before the top of the lungs. The combined use of modeling and image analysis supports the application of phage therapy for acute P. aeruginosa pneumonia while emphasizing potential challenges to curative success in spatially structured in vivo environments, including impaired innate immune responses and reduced phage efficacy.}, }
@article {pmid39229495, year = {2024}, author = {Li, L and Chen, S and Xue, X and Chen, J and Tian, J and Huo, L and Zhang, T and Zeng, X and Su, S}, title = {Purifying selection drives distinctive arsenic metabolism pathways in prokaryotic and eukaryotic microbes.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae106}, pmid = {39229495}, issn = {2730-6151}, abstract = {Microbes play a crucial role in the arsenic biogeochemical cycle through specific metabolic pathways to adapt to arsenic toxicity. However, the different arsenic-detoxification strategies between prokaryotic and eukaryotic microbes are poorly understood. This hampers our comprehension of how microbe-arsenic interactions drive the arsenic cycle and the development of microbial methods for remediation. In this study, we utilized conserved protein domains from 16 arsenic biotransformation genes (ABGs) to search for homologous proteins in 670 microbial genomes. Prokaryotes exhibited a wider species distribution of arsenic reduction- and arsenic efflux-related genes than fungi, whereas arsenic oxidation-related genes were more prevalent in fungi than in prokaryotes. This was supported by significantly higher acr3 (arsenite efflux permease) expression in bacteria (upregulated 3.72-fold) than in fungi (upregulated 1.54-fold) and higher aoxA (arsenite oxidase) expression in fungi (upregulated 5.11-fold) than in bacteria (upregulated 2.05-fold) under arsenite stress. The average values of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site (dN/dS) of homologous ABGs were higher in archaea (0.098) and bacteria (0.124) than in fungi (0.051). Significant negative correlations between the dN/dS of ABGs and species distribution breadth and gene expression levels in archaea, bacteria, and fungi indicated that microbes establish the distinct strength of purifying selection for homologous ABGs. These differences contribute to the distinct arsenic metabolism pathways in prokaryotic and eukaryotic microbes. These observations facilitate a significant shift from studying individual or several ABGs to characterizing the comprehensive microbial strategies of arsenic detoxification.}, }
@article {pmid39226184, year = {2024}, author = {Zhai, Z and Yang, Y and Chen, S and Wu, Z}, title = {Long-Term Exposure to Polystyrene Microspheres and High-Fat Diet-Induced Obesity in Mice: Evaluating a Role for Microbiota Dysbiosis.}, journal = {Environmental health perspectives}, volume = {132}, number = {9}, pages = {97002}, pmid = {39226184}, issn = {1552-9924}, mesh = {Animals ; *Dysbiosis/microbiology ; Mice ; *Obesity/microbiology ; *Diet, High-Fat ; *Mice, Inbred C57BL ; *Microspheres ; *Polystyrenes/toxicity ; *Gastrointestinal Microbiome/drug effects ; Male ; Microplastics/toxicity ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Microplastics (MPs) have become a global environmental problem, emerging as contaminants with potentially alarming consequences. However, long-term exposure to polystyrene microspheres (PS-MS) and its effects on diet-induced obesity are not yet fully understood.<br><br>OBJECTIVES: We aimed to investigate the effect of PS-MS exposure on high-fat diet (HFD)-induced obesity and underlying mechanisms.<br><br>METHODS: In the present study, C57BL/6J mice were fed a normal diet (ND) or a HFD in the absence or presence of PS-MS via oral administration for 8 wk. Antibiotic depletion of the microbiota and fecal microbiota transplantation (FMT) were performed to assess the influence of PS-MS on intestinal microbial ecology. We performed 16S rRNA sequencing to dissect microbial discrepancies and investigated the dysbiosis-associated intestinal integrity and inflammation in serum.<br><br>RESULTS: Compared with HFD mice, mice fed the HFD with PS-MS exhibited higher body weight, liver weight, metabolic dysfunction-associated steatotic liver disease (MASLD) activity scores, and mass of white adipose tissue, as well as higher blood glucose and serum lipid concentrations. Furthermore, 16S rRNA sequencing of the fecal microbiota revealed that mice fed the HFD with PS-MS had greater &#x3b1;-diversity and greater relative abundances of Lachnospiraceae, Oscillospiraceae, Bacteroidaceae, Akkermansiaceae, Marinifilaceae, Deferribacteres, and Desulfovibrio, but lower relative abundances of Atopobiaceae, Bifidobacterium, and Parabacteroides. Mice fed the HFD with PS-MS exhibited lower expression of MUC2 mucin and higher levels of lipopolysaccharide and inflammatory cytokines [tumor necrosis factor-&#x3b1; (TNF-&#x3b1;), interleukin-6 (IL-6), IL-1&#x3b2;, and IL-17A] in serum. Correlation analyses revealed that differences in the microbial flora of mice exposed to PS-MS were associated with obesity. Interestingly, microbiota-depleted mice did not show the same PS-MS-associated differences in Muc2 and Tjp1 expression in the distal colon, expression of inflammatory cytokines in serum, or obesity outcomes between HFD and HFD + PS-MS. Importantly, transplantation of feces from HFD + PS-MS mice to microbiota-depleted HFD-fed mice resulted in a lower expression of mucus proteins, higher expression of inflammatory cytokines, and obesity outcomes, similar to the findings in HFD + PS-MS mice.<br><br>CONCLUSIONS: Our findings provide a new gut microbiota-driven mechanism for PS-MS-induced obesity in HFD-fed mice, suggesting the need to reevaluate the adverse health effects of MPs commonly found in daily life, particularly in susceptible populations. https://doi.org/10.1289/EHP13913.}, }
@article {pmid39224076, year = {2024}, author = {McMillan, AS and Theriot, CM}, title = {Bile acids impact the microbiota, host, and C. difficile dynamics providing insight into mechanisms of efficacy of FMTs and microbiota-focused therapeutics.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2393766}, pmid = {39224076}, issn = {1949-0984}, support = {R35 GM149222/GM/NIGMS NIH HHS/United States ; T32 GM133366/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bile Acids and Salts/metabolism ; Humans ; *Fecal Microbiota Transplantation ; *Clostridioides difficile/physiology ; *Gastrointestinal Microbiome ; *Clostridium Infections/therapy/microbiology ; Animals ; }, abstract = {Clostridioides difficile is a major nosocomial pathogen, causing significant morbidity and mortality worldwide. Antibiotic usage, a major risk factor for Clostridioides difficile infection (CDI), disrupts the gut microbiota, allowing C. difficile to proliferate and cause infection, and can often lead to recurrent CDI (rCDI). Fecal microbiota transplantation (FMT) and live biotherapeutic products (LBPs) have emerged as effective treatments for rCDI and aim to restore colonization resistance provided by a healthy gut microbiota. However, much is still unknown about the mechanisms mediating their success. Bile acids, extensively modified by gut microbes, affect C. difficile's germination, growth, and toxin production while also shaping the gut microbiota and influencing host immune responses. Additionally, microbial interactions, such as nutrient competition and cross-feeding, contribute to colonization resistance against C. difficile and may contribute to the success of microbiota-focused therapeutics. Bile acids as well as other microbial mediated interactions could have implications for other diseases being treated with microbiota-focused therapeutics. This review focuses on the intricate interplay between bile acid modifications, microbial ecology, and host responses with a focus on C. difficile, hoping to shed light on how to move forward with the development of new microbiota mediated therapeutic strategies to combat rCDI and other intestinal diseases.}, }
@article {pmid39222062, year = {2024}, author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Kurilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I}, title = {CAIM: coverage-based analysis for identification of microbiome.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {5}, pages = {}, pmid = {39222062}, issn = {1477-4054}, support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 CA143130/CA/NCI NIH HHS/United States ; P20GM125503//National Institute of General Medical Sciences of the National Institutes of Health/ ; R01CA143130/NH/NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Software ; Algorithms ; Sequence Analysis, DNA/methods ; }, abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic approach. In this study, we developed a new bioinformatics tool, coverage-based analysis for identification of microbiome (CAIM), for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count-based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consistently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similarity of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and 44 primary liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.}, }
@article {pmid39221110, year = {2024}, author = {Mohr, AE and Jasbi, P and van Woerden, I and Chi, J and Gu, H and Bruening, M and Whisner, CM}, title = {Microbial Ecology and Metabolism of Emerging Adulthood: Gut Microbiome Insights from a College Freshman Cohort.}, journal = {Gut microbes reports}, volume = {1}, number = {1}, pages = {1-23}, pmid = {39221110}, issn = {2993-3935}, support = {DP5 OD017910/OD/NIH HHS/United States ; T32 DK137525/DK/NIDDK NIH HHS/United States ; }, abstract = {The human gut microbiome (GM) undergoes dynamic changes throughout life, transitioning from infancy to adulthood. Despite improved understanding over the past years about how genetics, lifestyle, and the external environment impact the GM, limited research has explored the GM's evolution during late-stage adolescence, especially among college students. This study addresses this gap by investigating the longitudinal dynamics of fecal microbial, functional, and metabolomic signatures in a diverse group of first-year, dormitory-housed college students. A total of 485 stool samples from 246 participants were analyzed, identifying four primary GM community types, predominantly led by Bacteroides (66.8% of samples), as well as Blautia and Prevotella. The Prevotella/Bacteroides (P/B) ratio emerged as a robust GM composition indicator, predictively associated with 15 metabolites. Notably, higher P/B ratios correlated negatively with p-cresol sulfate and cholesterol sulfate, implying potential health implications, while positively correlating with kynurenic acid. Distinct GM transition and stability patterns were found from a detailed longitudinal subset of 93 participants over an academic year. Parasutterella and the Ruminococcus gnavus group exhibited positive associations with compositional variability, whereas Faecalibacterium and Eubacterium ventriosum group displayed negative associations, the latter suggesting stabilizing roles in the GM. Most notably, nearly half of the longitudinal cohort experienced GM community shifts, emphasizing long-term GM adaptability. Comparing individuals with stable community types to those undergoing transitions, we observed significant differences in microbial composition and diversity, signifying substantial shifts in the microbiota during transitions. Although diet-related variables contributed to some observed variance, diet did not independently predict the probability of switching between community types within the study's timeframe via multi-state Markov modeling. Furthermore, exploration of stability within dynamic microbiomes among the longitudinal cohort experiencing shifts in community types revealed that microbiome taxa at the genus level exhibited significantly higher total variance than estimated functional and fecal metabolomic features. This suggests tight control of function and metabolism, despite community shifting. Overall, this study highlights the dynamic nature of the late-stage adolescent GM, the role of core taxa, metabolic pathways, the fecal metabolome, and lifestyle and dietary factors, contributing to our understanding of GM assembly and potential health implications during this life phase.}, }
@article {pmid39218095, year = {2024}, author = {Anedda, E and Alexa, EA and Farrell, ML and Croffie, M and Madigan, G and Morris, D and Burgess, CM}, title = {Comparison of antimicrobial resistant Enterobacterales isolates from the dairy production environment in low and high zinc containing regions.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {175905}, doi = {10.1016/j.scitotenv.2024.175905}, pmid = {39218095}, issn = {1879-1026}, mesh = {*Zinc/analysis ; *Enterobacteriaceae/drug effects ; *Soil Microbiology ; Anti-Bacterial Agents/pharmacology ; Dairying ; Drug Resistance, Bacterial/genetics ; Ireland ; Animals ; Milk/microbiology ; Cattle ; Soil Pollutants/analysis ; }, abstract = {Heavy metals occur naturally in the environment, and their concentration varies in soil across different regions. However, the presence of heavy metals may influence the antimicrobial resistance (AMR) in bacterial populations. Therefore, the objective of this study was to investigate and characterise the antimicrobial resistance profiles of Enterobacterales in soil and bovine milk filters from high and low zinc-containing regions in Ireland. In total, 50 soil samples and 29 milk filters were collected from two geographic locations with varying soil zinc concentrations. Samples were cultured for the enumeration and detection of Enterobacterales. Specifically, extended-spectrum beta-lactamase-producing Enterobacterales, carbapenem-resistant Enterobacterales and ciprofloxacin-resistant Enterobacterales were isolated using selective media. Species identification was performed using MALDI-TOF. The phenotypic resistance profiles of selected Enterobacterales were determined by disk diffusion testing, following EUCAST and CLSI criteria; while, the genotypic resistance profiles of the same isolates were determined by whole genome sequencing (WGS). Heavy metal concentrations were also measured for all soil samples. A total of 40 antimicrobial resistant Enterobacterales were identified in soil (n = 31) and milk filters (n = 9). The predominant species detected in the high zinc-containing region was Escherichia coli in both sample types (soil n = 10, milk filters n = 2), while in the low zinc-containing region Serratia fonticola was predominant in soil samples (n = 8) and E. coli in milk filters (n = 4). Ten E. coli isolates identified from soil samples in the high zinc-containing region were multidrug resistant, showing resistance to all the antimicrobials tested, except for carbapenems. The WGS findings confirmed the phenotypic resistance results. Moreover, zinc resistance-associated genes and genes encoding for efflux pumps were identified. The current study revealed distinct phenotypic resistance profiles of Enterobacterales in low and high zinc-containing regions, and highlighted the benefit of utilising milk filters for AMR surveillance in dairy production.}, }
@article {pmid39216241, year = {2024}, author = {Liao, X and Hou, L and Zhang, L and Grossart, HP and Liu, K and Liu, J and Chen, Y and Liu, Y and Hu, A}, title = {Distinct influences of altitude on microbiome and antibiotic resistome assembly in a glacial river ecosystem of Mount Everest.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135675}, doi = {10.1016/j.jhazmat.2024.135675}, pmid = {39216241}, issn = {1873-3336}, mesh = {*Rivers/microbiology ; *Altitude ; *Microbiota/drug effects ; *Drug Resistance, Microbial/genetics ; Ecosystem ; Bacteria/genetics/drug effects/classification ; Geologic Sediments/microbiology ; Viruses/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Ice Cover/microbiology ; China ; }, abstract = {The profound influences of altitude on aquatic microbiome were well documented. However, differences in the responses of different life domains (bacteria, microeukaryotes, viruses) and antibiotics resistance genes (ARGs) in glacier river ecosystems to altitude remain unknown. Here, we employed shotgun metagenomic and amplicon sequencing to characterize the altitudinal variations of microbiome and ARGs in the Rongbu River, Mount Everest. Our results indicated the relative influences of stochastic processes on microbiome and ARGs assembly in water and sediment were in the following order: microeukaryotes < ARGs < viruses < bacteria. Moreover, distinct assembly patterns of the microbiome and ARGs were found in response to differences in altitude, the latter of which shift from deterministic to stochastic processes with increasing differences in altitude. Partial least squares path modeling revealed that mobile genetic elements (MGEs) and viral β-diversity were the major factors influencing the ARG abundances. Taken together, our work revealed that altitude-caused environmental changes led to significant changes in the composition and assembly processes of the microbiome and ARGs, while ARGs had a unique response pattern to altitude. Our findings provide novel insights into the impacts of altitude on the biogeographic distribution of microbiome and ARGs, and the associated driving forces in glacier river ecosystems.}, }
@article {pmid39215820, year = {2024}, author = {Thompson, C and Silva, R and Gibran, FZ and Bacha, L and de Freitas, MAM and Thompson, M and Landuci, F and Tschoeke, D and Zhang, XH and Wang, X and Zhao, W and Gatts, PV and de Almeida, MG and de Rezende, CE and Thompson, F}, title = {The Abrolhos Nominally Herbivorous Coral Reef Fish Acanthurus chirurgus, Kyphosus sp., Scarus trispinosus, and Sparisoma axillare Have Similarities in Feeding But Species-Specific Microbiomes.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {110}, pmid = {39215820}, issn = {1432-184X}, mesh = {Animals ; *Coral Reefs ; *RNA, Ribosomal, 16S/genetics ; *Fishes/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; Herbivory ; Species Specificity ; Carbon Isotopes/analysis ; Nitrogen Isotopes/analysis ; Perciformes/microbiology ; Diet/veterinary ; }, abstract = {Coral reefs rely heavily on reef fish for their health, yet overfishing has resulted in their decline, leading to an increase in fast-growing algae and changes in reef ecosystems, a phenomenon described as the phase-shift. A clearer understanding of the intricate interplay between herbivorous, their food, and their gut microbiomes could enhance reef health. This study examines the gut microbiome and isotopic markers (δ[13]C and δ[15]N) of four key nominally herbivorous reef fish species (Acanthurus chirurgus, Kyphosus sp., Scarus trispinosus, and Sparisoma axillare) in the Southwestern Atlantic's Abrolhos Reef systems. Approximately 16.8 million 16S rRNA sequences were produced for the four fish species, with an average of 317,047 ± 57,007 per species. Bacteria such as Proteobacteria, Firmicutes, and Cyanobacteria were prevalent in their microbiomes. These fish show unique microbiomes that result from co-diversification, diet, and restricted movement. Coral-associated bacteria (Endozoicomonas, Rhizobia, and Ruegeria) were found in abundance in the gut contents of the parrotfish species Sc. trispinosus and Sp. axillare. These parrotfishes could aid coral health by disseminating such beneficial bacteria across the reef. Meanwhile, Kyphosus sp. predominantly had Pirellulaceae and Rhodobacteraceae. Four fish species had a diet composed of turf components (filamentous Cyanobacteria) and brown algae (Dictyopteris). They also had similar isotopic niches, suggesting they shared food sources. A significant difference was observed between the isotopic signature of fish muscular gut tissue and gut contents, pointing to the role that host genetics and gut microbes play in differentiating fish tissues.}, }
@article {pmid39215735, year = {2024}, author = {Paulo, LM and Liu, YC and Castilla-Archilla, J and Ramiro-Garcia, J and Hughes, D and Mahony, T and Holohan, BC and Wilmes, P and O'Flaherty, V}, title = {Full-scale study on high-rate low-temperature anaerobic digestion of agro-food wastewater: process performances and microbial community.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {90}, number = {4}, pages = {1239-1249}, pmid = {39215735}, issn = {0273-1223}, support = {14/IA/2371/SFI_/Science Foundation Ireland/Ireland ; TC/2014/0016//Enterprise Ireland/ ; }, mesh = {*Bioreactors ; Anaerobiosis ; *Wastewater ; *Waste Disposal, Fluid/methods ; Temperature ; Biological Oxygen Demand Analysis ; Bacteria/metabolism/classification ; Biofuels ; Industrial Waste ; }, abstract = {The fast-growing global population has led to a substantial increase in food production, which generates large volumes of wastewater during the process. Despite most industrial wastewater being discharged at lower ambient temperatures (<20 °C), majority of the high-rate anaerobic reactors are operated at mesophilic temperatures (>30 °C). High-rate low-temperature anaerobic digestion (LtAD) has proven successful in treating industrial wastewater both at laboratory and pilot scales, boasting efficient organic removal and biogas production. In this study, we demonstrated the feasibility of two full-scale high-rate LtAD bioreactors treating meat processing and dairy wastewater, and the microbial communities in both reactors were examined. Both reactors exhibited rapid start-up, achieving considerable chemical oxygen demand (COD) removal efficiencies (total COD removal >80%) and generating high-quality biogas (CH4% in biogas >75%). Long-term operations (6-12 months) underscored the robustness of LtAD bioreactors even during winter periods (average temperature <12 °C), as evidenced by sustained high COD removal rates (total COD removal >80%). The stable performance was underpinned by a resilient microbial community comprising active acetoclastic methanogens, hydrolytic, and fermentative bacteria. These findings underscore the feasibility of high-rate low-temperature anaerobic wastewater treatment, offering promising solutions to the zero-emission wastewater treatment challenge.}, }
@article {pmid39212186, year = {2024}, author = {Junker Mentzel, CM and Hui, Y and Hammerich, TMS and Klug-Dambmann, M and Liu, Y and Zachariassen, LF and Hansen, LH and Aslampaloglou, A and Kiersgaard, M and Nielsen, DS and Hansen, AK and Krych, L}, title = {Low-gainer diet-induced obese microbiota transplanted mice exhibit increased fighting.}, journal = {Clinical and translational science}, volume = {17}, number = {9}, pages = {e13906}, pmid = {39212186}, issn = {1752-8062}, support = {//LIFEPHARM/ ; //Novo Nordisk A/S/ ; //Center for Applied Laboratory Animal Research/ ; }, mesh = {Animals ; Male ; *Obesity/microbiology/etiology ; *Gastrointestinal Microbiome/physiology ; *Fecal Microbiota Transplantation ; *Mice, Inbred C57BL ; *Diet, High-Fat/adverse effects ; *Weight Gain ; Mice ; Disease Models, Animal ; Leptin/blood/metabolism ; Feces/microbiology ; }, abstract = {Weight gain variation is a great challenge in diet-induced obesity studies since low-gainer animals are of limited experimental value. The inbred C57BL/6 (B6) mice are frequently used models due to their genetic homogeneity and susceptibility to diet-induced obesity (DIO). The aim of this study is to investigate if the gut microbiota (GM) influences the fraction of low weight gainers in DIO studies. A total of 100 male B6 mice (donor population) were fed a high-fat diet for 14 weeks and divided into the study groups high gainer (HG) and low gainer (LG) based on their weight gain. Subsequently, fecal matter transplantation (FMT) was done on germ-free B6 mice with GM from HG and LG donors (FMT population). LG (13.35 ± 2.5 g) and HG (25.52 ± 2.0 g) animals were identified by the weight gain from week 1 to week 12. Interestingly, the start weight of the LG (20.36 ± 1.4 g) and HG (21.59 ± 0.7 g) groups differed significantly. Transplanting LG or HG fecal matter to germ-free mice resulted in significant differences in weight gain between HG and LG, as well as differences in serum leptin levels and epididymal fat pad weight. A clear LG-specific GM composition could not be distinguished by 16S rRNA gene amplicon sequencing. Surprisingly, significantly more fighting was recorded in LG groups of both donor populations and when transplanted to germ-free mice. The HG and LG phenotypes could be transferred to germ-free mice. The increased fighting in the LG group in both studies suggests not only that the tendency to fight can be transferred by FMT in these mice, but also that fighting should be prevented in DIO studies to minimize the number of LG animals.}, }
@article {pmid39214074, year = {2024}, author = {Letourneau, J and Carrion, VM and Zeng, J and Jiang, S and Osborne, OW and Holmes, ZC and Fox, A and Epstein, P and Tan, CY and Kirtley, M and Surana, NK and David, LA}, title = {Interplay between particle size and microbial ecology in the gut microbiome.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39214074}, issn = {1751-7370}, support = {R01 DK116187/DK/NIDDK NIH HHS/United States ; 2016-IDG-1013//North Carolina Biotechnology Center/ ; N00014-18-1-2616//Office of Naval Research/ ; 1R01DK116187/NH/NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; Animals ; *Feces/microbiology ; Mice ; *Particle Size ; Adult ; Male ; Female ; Bacteria/classification/genetics/isolation &amp; purification ; Diet ; Young Adult ; Mice, Inbred C57BL ; Mastication ; Middle Aged ; }, abstract = {Physical particles can serve as critical abiotic factors that structure the ecology of microbial communities. For non-human vertebrate gut microbiomes, fecal particle size (FPS) has been known to be shaped by chewing efficiency and diet. However, little is known about what drives FPS in the human gut. Here, we analyzed FPS by laser diffraction across a total of 76 individuals and found FPS to be strongly individualized. Contrary to our initial hypothesis, a behavioral intervention with 41 volunteers designed to increase chewing efficiency did not impact FPS. Dietary patterns could also not be associated with FPS. Instead, we found evidence that human and mouse gut microbiomes shaped FPS. Fecal samples from germ-free and antibiotic-treated mice exhibited increased FPS relative to colonized mice. In humans, markers of longer transit time were correlated with smaller FPS. Gut microbiota diversity and composition were also associated with FPS. Finally, ex vivo culture experiments using human fecal microbiota from distinct donors showed that differences in microbiota community composition can drive variation in particle size. Together, our results support an ecological model in which the human gut microbiome plays a key role in reducing the size of food particles during digestion. This finding has important implications for our understanding of energy extraction and subsequent uptake in gastrointestinal tract. FPS may therefore be viewed as an informative functional readout, providing new insights into the metabolic state of the gut microbiome.}, }
@article {pmid39211880, year = {2024}, author = {Schluter, J and Matheis, F and Ebina, W and Jogia, W and Sullivan, AP and Gordon, K and Fanega de la Cruz, E and Victory-Hays, ME and Heinly, MJ and Diefenbach, CS and Peled, JU and Foster, KR and Levitt, A and McLaughlin, E}, title = {A randomized controlled trial of postbiotic administration during antibiotic treatment increases microbiome diversity and enriches health associated taxa.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.07.25.24311015}, pmid = {39211880}, abstract = {Antibiotic-induced microbiome injury, defined as a reduction of ecological diversity and obligate anaerobe taxa, is associated with negative health outcomes in hospitalized patients, and healthy individuals who received antibiotics in the past are at higher risk for autoimmune diseases. No interventions are currently available that effectively target the microbial ecosystem in the gut to prevent this negative collateral damage of antibiotics. Here, we present the results from a single-center, randomized placebo-controlled trial involving 32 patients who received an oral, fermentation-derived postbiotic alongside oral antibiotic therapy for gastrointestinal (GI)-unrelated infections. Postbiotics comprise complex mixtures of metabolites produced by bacteria during fermentation and other processes, which can mediate microbial ecology. Bacterial ecosystem alpha diversity, quantified by the inverse Simpson index, during the end of the antibiotic course was significantly higher (+40%) across the 16 postbiotic-treated patients compared with the 16 patients who received a placebo, and the postbiotic was well-tolerated. Secondary analyses of 157 stool samples collected longitudinally revealed that the increased diversity was driven by enrichment in health-associated microbial genera: obligate anaerobe Firmicutes, in particular taxa belonging to the Lachnospiraceae family, were higher in treated patients; conversely, Escherichia/Shigella abundances, which comprise pathobionts and antimicrobial-resistant strains, were reduced in postbiotic-treated patients at the end of their antibiotic course and up to 10 days later. Taken together, these results indicate that postbiotic co-administration during antibiotic therapy could support a health-associated gut microbiome community and may reduce antibiotic-induced microbiome injury.}, }
@article {pmid39204682, year = {2024}, author = {Andreata, MFL and Afonso, L and Niekawa, ETG and Salomão, JM and Basso, KR and Silva, MCD and Alves, LC and Alarcon, SF and Parra, MEA and Grzegorczyk, KG and Chryssafidis, AL and Andrade, G}, title = {Microbial Fertilizers: A Study on the Current Scenario of Brazilian Inoculants and Future Perspectives.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {16}, pages = {}, pmid = {39204682}, issn = {2223-7747}, abstract = {The increasing need for sustainable agricultural practices, combined with the demand for enhanced crop productivity, has led to a growing interest in utilizing microorganisms for biocontrol of diseases and pests, as well as for growth promotion. In Brazilian agriculture, the use of plant growth-promoting rhizobacteria (PGPR) and plant growth-promoting fungi (PGPF) has become increasingly prevalent, with a corresponding rise in the number of registered microbial inoculants each year. PGPR and PGPF occupy diverse niches within the rhizosphere, playing a crucial role in soil nutrient cycling and influencing a wide range of plant physiological processes. This review examines the primary mechanisms employed by these microbial agents to promote growth, as well as the strategy of co-inoculation to enhance product efficacy. Furthermore, we provide a comprehensive analysis of the microbial inoculants currently available in Brazil, detailing the microorganisms accessible for major crops, and discuss the market's prospects for the research and development of novel products in light of current challenges faced in the coming years.}, }
@article {pmid39203927, year = {2024}, author = {Govaert, M and Rotsaert, C and Vannieuwenhuyse, C and Duysburgh, C and Medlin, S and Marzorati, M and Jarrett, H}, title = {Survival of Probiotic Bacterial Cells in the Upper Gastrointestinal Tract and the Effect of the Surviving Population on the Colonic Microbial Community Activity and Composition.}, journal = {Nutrients}, volume = {16}, number = {16}, pages = {}, pmid = {39203927}, issn = {2072-6643}, support = {Not applicable//Heights/ ; }, mesh = {*Probiotics ; Humans ; *Gastrointestinal Microbiome ; *Colon/microbiology ; *Upper Gastrointestinal Tract/microbiology ; Microbial Viability ; Bacteria/growth &amp; development ; Fatty Acids, Volatile/metabolism ; }, abstract = {Many health-promoting effects have been attributed to the intake of probiotic cells. However, it is important that probiotic cells arrive at the site of their activity in a viable state in order to exert their beneficial effects. Careful selection of the appropriate probiotic formulation is therefore required as mainly the type of probiotic species/strain and the administration strategy may affect survival of the probiotic cells during the upper gastrointestinal (GIT) passage. Therefore, the current study implemented Simulator of the Human Microbial Ecosystem (SHIME[®]) technology to investigate the efficacy of different commercially available probiotic formulations on the survival and culturability of probiotic bacteria during upper GIT passage. Moreover, Colon-on-a-Plate (CoaP™) technology was applied to assess the effect of the surviving probiotic bacteria on the gut microbial community (activity and composition) of three human donors. Significantly greater survival and culturability rates were reported for the delayed-release capsule formulation (>50%) as compared to the powder, liquid, and standard capsule formulations (<1%) (p < 0.05), indicating that the delayed-release capsule was most efficacious in delivering live bacteria cells. Indeed, administration of the delayed-release capsule probiotic digest resulted in enhanced production of SCFAs and shifted gut microbial community composition towards beneficial bacterial species. These results thus indicate that careful selection of the appropriate probiotic formulation and administration strategy is crucial to deliver probiotic cells in a viable state at the site of their activity (distal ileum and colon).}, }
@article {pmid39203578, year = {2024}, author = {Yan, Y and Shi, Z and Wang, C and Jin, Z and Yin, J and Zhu, G}, title = {Viral Diversity and Ecological Impact of DNA Viruses in Dominant Tick Species in China.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203578}, issn = {2076-2607}, support = {RCYJ2012//Basic Scientific Research Funds of Hangzhou Medical College/ ; }, abstract = {Ticks are blood-feeding ectoparasites that also transmit various pathogens, posing severe risks to human and animal health. DNA viruses play a crucial role in the microbial ecology of ticks, but their distribution and ecological significance remain largely undetermined. Here, we assembled an extensive catalog encompassing 4320 viral operational taxonomic units (vOTUs) from six main dominant tick species in China, of which 94.8% have not been found in any other environment. To bridge the knowledge gap in tick DNA virus research and provide a crucial resource platform, we developed the Tick DNA Virus Database. This database includes the vOTUs that are known to cause diseases. Most of the predicted vOTUs are associated with dominant bacterial and archaeal phyla. We identified 105 virus-encoded putative auxiliary metabolic genes (AMGs) that are involved in host metabolism and environmental adaptation, potentially influencing ticks through both top-down and bottom-up mechanisms. The identification of microbial communities and antibiotic resistance in wild tick species suggests that wild ticks are reservoirs of antibiotic resistance and potential spreaders of antibiotic resistance. These findings reveal the potential role of tick viruses in ecosystems, highlighting the importance of monitoring tick microbiomes to address global public health challenges.}, }
@article {pmid39203418, year = {2024}, author = {Barazetti, AR and Dealis, ML and Basso, KR and Silva, MCD and Alves, LDC and Parra, MEA and Simionato, AS and Cely, MVT and Macedo, AL and Silva, DB and Andrade, G}, title = {Evaluation of Resistance Induction Promoted by Bioactive Compounds of Pseudomonas aeruginosa LV Strain against Asian Soybean Rust.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203418}, issn = {2076-2607}, abstract = {Pseudomonas are known as higher producers of secondary metabolites with antimicrobial properties and plant growth promoters, including resistance induction. These mechanisms should be an alternative to pesticide use in crop production. Phakopsora pachyrhizi causes Asian soybean rust, representing a high loss of yield around the world. The objective of this paper was to evaluate the application of secondary metabolites produced by Pseudomonas aeruginosa LV strain from the semi-purified fraction F4A in soybean plants to induce plant resistance against P. pachyrhizi in field conditions. The experimental design was performed in randomized blocks with three replicates using two F4A doses (1 and 10 μg mL[-1]) combined or not with fungicides (Unizeb Gold[®] or Sphere Max[®]). The control treatment, with Uni + Sph, saponins, flavonoids, and sphingolipids, showed higher intensities in the plants. In contrast, plants treated with the F4A fraction mainly exhibited fatty acid derivatives and some non-identified compounds with nitrogen. Plants treated with Sphere Max[®], with or without F4A10, showed higher intensities of glycosylated flavonoids, such as kaempferol, luteolin, narigenin, and apigenin. Plants treated with F4A showed higher intensities of genistein and fatty acid derivatives. These increases in flavonoid compound biosynthesis and antioxidant properties probably contribute to the protection against reactive oxygen species (ROS).}, }
@article {pmid39203403, year = {2024}, author = {Al-Tarshi, M and Dobretsov, S and Al-Belushi, M}, title = {Bacterial Communities across Multiple Ecological Niches (Water, Sediment, Plastic, and Snail Gut) in Mangrove Habitats.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203403}, issn = {2076-2607}, support = {RC/GRG-AGR/FISH/22/01//Ministry of Higher Education, Research and Innovation/ ; RC/GRG-AGR/FISH/22/01//Sultan Qaboos University/ ; }, abstract = {Microbial composition across substrates in mangroves, particularly in the Middle East, remains unclear. This study characterized bacterial communities in sediment, water, Terebralia palustris snail guts, and plastic associated with Avicennia marina mangrove forests in two coastal lagoons in the Sea of Oman using 16S rDNA gene MiSeq sequencing. The genus Vibrio dominated all substrates except water. In the gut of snails, Vibrio is composed of 80-99% of all bacterial genera. The water samples showed a different pattern, with the genus Sunxiuqinia being dominant in both Sawadi (50.80%) and Qurum (49.29%) lagoons. There were significant differences in bacterial communities on different substrata, in particular plastic. Snail guts harbored the highest number of unique Operational Taxonomic Units (OTUs) in both lagoons, accounting for 30.97% OTUs in Sawadi and 28.91% OTUs in Qurum, compared to other substrates. Plastic in the polluted Sawadi lagoon with low salinity harbored distinct genera such as Vibrio, Aestuariibacter, Zunongwangia, and Jeotgalibacillus, which were absent in the Qurum lagoon with higher salinity and lower pollution. Sawadi lagoon exhibited higher species diversity in sediment and plastic substrates, while Qurum lagoon demonstrated lower species diversity. The principal component analysis (PCA) indicates that environmental factors such as salinity, pH, and nutrient levels significantly influence bacterial community composition across substrates. Variations in organic matter and potential anthropogenic influences, particularly from plastics, further shape bacterial communities. This study highlights the complex microbial communities in mangrove ecosystems, emphasizing the importance of considering multiple substrates in mangrove microbial ecology studies. The understanding of microbial dynamics and anthropogenic impacts is crucial for shaping effective conservation and management strategies in mangrove ecosystems, particularly in the face of environmental changes.}, }
@article {pmid39200461, year = {2024}, author = {Han, D and Yang, Y and Guo, Z and Dai, S and Jiang, M and Zhu, Y and Wang, Y and Yu, Z and Wang, K and Rong, C and Yu, Y}, title = {A Review on the Interaction of Acetic Acid Bacteria and Microbes in Food Fermentation: A Microbial Ecology Perspective.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {16}, pages = {}, pmid = {39200461}, issn = {2304-8158}, support = {32200012//National Natural Science Foundation of China/ ; 22KJB180016//Basic Science Research Program for Higher Education Institutions in Jiangsu Province (Natural Science)/ ; }, abstract = {In fermented foods, acetic acid bacteria (AAB), kinds of bacteria with a long history of utilization, contribute to safety, nutritional, and sensory properties primarily through acetic acid fermentation. AAB are commonly found in various fermented foods such as vinegar, sour beer, fermented cocoa and coffee beans, kefir beverages, kombucha, and sourdough. They interact and cooperate with a variety of microorganisms, resulting in the formation of diverse metabolites and the production of fermented foods with distinct flavors. Understanding the interactions between AAB and other microbes is crucial for effectively controlling and utilizing AAB in fermentation processes. However, these microbial interactions are influenced by factors such as strain type, nutritional conditions, ecological niches, and fermentation duration. In this review, we examine the relationships and research methodologies of microbial interactions and interaction studies between AAB and yeasts, lactic acid bacteria (LAB), and bacilli in different food fermentation processes involving these microorganisms. The objective of this review is to identify key interaction models involving AAB and other microorganisms. The insights gained will provide scientific guidance for the effective utilization of AAB as functional microorganisms in food fermentation processes.}, }
@article {pmid39198281, year = {2024}, author = {He, Z and Smets, BF and Dechesne, A}, title = {Mating Assay: Plating Below a Cell Density Threshold is Required for Unbiased Estimation of Plasmid Conjugation Frequency of RP4 Transfer Between E. coli Strains.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {109}, pmid = {39198281}, issn = {1432-184X}, support = {0236-00022B//Innovationsfonden/ ; 0236-00022B//Innovationsfonden/ ; 0236-00022B//Innovationsfonden/ ; PhD Scholarship//Sino-Danish Center/ ; PhD Scholarship//Sino-Danish Center/ ; }, mesh = {*Escherichia coli/genetics ; *Conjugation, Genetic ; *Plasmids/genetics ; Gene Transfer, Horizontal ; }, abstract = {Mating assays are common laboratory experiments for measuring the conjugation frequency, i.e. efficiency at which a plasmid transfers from a population of donor cells to a population of recipient cells. Selective plating remains a widely used quantification method to enumerate transconjugants at the end of such assays. However, conjugation frequencies may be inaccurately estimated because plasmid transfer can occur on transconjugant-selective plates rather than only during the intended mating duration. We investigated the influence of cell density on this phenomenon. We conducted mating experiments with IncPα plasmid RP4 harbored in Escherichia coli at a fixed cell density and mating conditions, inoculated a serial dilution of the mating mixture on transconjugant-selective plates or in transconjugant-selective broth, and compared the results to a model of cell-to-cell distance distribution. Our findings suggest that irrespective of the mating mode (liquid vs solid), the enumeration of transconjugants becomes significantly biased if the plated cell density exceeds 28 Colony Forming Unit (CFU)/mm[2] (or 1.68•10[5] CFU/standard 9 cm Petri dish). This threshold is determined with a 95% confidence interval of ± 4 CFU/mm[2] (± 2.46•10[4] CFU/standard 9 cm Petri dish). Liquid mating assays were more sensitive to this bias because the conjugation frequency of RP4 is several orders of magnitude lower in suspension compared to surface mating. Therefore, if selective plating is used, we recommend to plate at this density threshold and that negative controls are performed where donors and recipients are briefly mixed before plating at the same dilutions as for the actual mating assay. As an alternative, a liquid enumeration method can be utilized to increase the signal-to-noise ratio and allow for more accurate enumeration of transconjugants.}, }
@article {pmid39197278, year = {2024}, author = {Peng, C and Wang, Y and Sha, X and Li, M and Wang, X and Wang, J and Wang, Y and Liu, C and Wang, L}, title = {Adverse effect of TWPs on soil fungi and the contribution of benzothiazole rubber additives.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135574}, doi = {10.1016/j.jhazmat.2024.135574}, pmid = {39197278}, issn = {1873-3336}, mesh = {*Benzothiazoles ; *Soil Microbiology ; *Fungi/drug effects ; *Rubber ; *Soil Pollutants/toxicity/analysis ; Biomass ; }, abstract = {Tire wear particles (TWPs) pollution is widely present in soil, especially in areas severely affected by traffic. Herein, regular variation of fungal biomass with TWPs was found in soils with different distances from the highway. In addition, the concentrations of benzothiazole compounds (BTHs), an important class of rubber vulcanization accelerators, were found to be positively correlated to the TWPs abundance. Sixty days' soil microcosm experiments were conducted to further confirm the adverse effect of TWPs and BTHs on soil fungi. TWPs spiking at 1000 mg/kg, a detectable level in the roadside, resulted in significant reduction of biomass and significant changes of soil fungal community structure, with Eurotium and Polyporales being the sensitive species. BTH+ 2-hydroxybenzothiazole (OHBT) (the dominant BTHs in soil) spiking at 200 ng/kg, the dose equivalent to 1000 mg/kg TWPs pollution, also caused a similar magnitude of soil fungal biomass reduction. Adonis demonstrated no significant difference of fungal community structure between TWPs and BTH+OHBT spiked soil, suggesting the adverse effect of TWPs on soil fungi may be explained by the act of BTHs. Pure culture using the representative soil fungi Eurotium and Polyporales also confirmed that BTHs were the main contributors to the adverse effect of TWPs on soil fungi.}, }
@article {pmid39196435, year = {2024}, author = {Tenore, A and Russo, F and Jacob, J and Grattepanche, JD and Buttaro, B and Klapper, I}, title = {A Mathematical Model of Diel Activity and Long Time Survival in Phototrophic Mixed-Species Subaerial Biofilms.}, journal = {Bulletin of mathematical biology}, volume = {86}, number = {10}, pages = {123}, pmid = {39196435}, issn = {1522-9602}, support = {1951532//National Science Foundation/ ; 2325170//National Science Foundation/ ; }, mesh = {*Biofilms/growth &amp; development ; *Models, Biological ; *Mathematical Concepts ; *Phototrophic Processes/physiology ; *Cyanobacteria/physiology/metabolism ; *Computer Simulation ; Biomass ; Heterotrophic Processes/physiology ; Microbial Interactions/physiology ; Bacterial Physiological Phenomena ; }, abstract = {Subaerial biofilms (SAB) are intricate microbial communities living on terrestrial surfaces, of interest in a variety of contexts including cultural heritage preservation, microbial ecology, biogeochemical cycling, and biotechnology. Here we propose a mathematical model aimed at better understanding the interplay between cyanobacteria and heterotrophic bacteria, common microbial SAB constituents, and their mutual dependence on local environmental conditions. SABs are modeled as thin mixed biofilm-liquid water layers sitting on stone. A system of ordinary differential equations regulates the dynamics of key SAB components: cyanobacteria, heterotrophs, polysaccharides and decayed biomass, as well as cellular levels of organic carbon, nitrogen and energy. These components are interconnected through a network of energetically dominant metabolic pathways, modeled with limitation terms reflecting the impact of biotic and abiotic factors. Daily cylces of temperature, humidity, and light intensity are considered as input model variables that regulate microbial activity by influencing water availability and metabolic kinetics. Relevant physico-chemical processes, including pH regulation, further contribute to a description of the SAB ecology. Numerical simulations explore the dynamics of SABs in a real-world context, revealing distinct daily activity periods shaped by water activity and light availability, as well as longer time scale survivability conditions. Results also suggest that heterotrophs could play a substantial role in decomposing non-volatile carbon compounds and regulating pH, thus influencing the overall composition and stability of the biofilm.}, }
@article {pmid39196422, year = {2024}, author = {Toloza-Moreno, DL and Yockteng, R and Pérez-Zuñiga, JI and Salinas-Castillo, C and Caro-Quintero, A}, title = {Implications of Domestication in Theobroma cacao L. Seed-Borne Microbial Endophytes Diversity.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {108}, pmid = {39196422}, issn = {1432-184X}, mesh = {*Cacao/microbiology ; *Endophytes/genetics/classification/isolation &amp; purification/physiology ; *Seeds/microbiology/growth &amp; development ; *Bacteria/classification/genetics/isolation &amp; purification ; *Domestication ; Microbiota ; Fungi/genetics/classification/isolation &amp; purification ; Genotype ; Biodiversity ; }, abstract = {The study of plant-microbe interactions is a rapidly growing research field, with increasing attention to the role of seed-borne microbial endophytes in protecting the plant during its development from abiotic and biotic stresses. Recent evidence suggests that seed microbiota is crucial in establishing the plant microbial community, affecting its composition and structure, and influencing plant physiology and ecology. For Theobroma cacao L., the diversity and composition of vertically transmitted microbes have yet to be addressed in detail. We explored the composition and diversity of seed-borne endophytes in cacao pods of commercial genotypes (ICS95, IMC67), recently liberated genotypes from AGROSAVIA (TCS01, TCS19), and landraces from Tumaco (Colombia) (AC9, ROS1, ROS2), to evaluate microbial vertical transmission and establishment in various tissues during plant development. We observed a higher abundance of Pseudomonas and Pantoea genera in the landraces and AGROSAVIA genotypes, while the commercial genotypes presented a higher number of bacteria species but in low abundance. In addition, all the genotypes and plant tissues showed a high percentage of fungi of the genus Penicillium. These results indicate that domestication in cacao has increased bacterial endophyte diversity but has reduced their abundance. We isolated some of these seed-borne endophytes to evaluate their potential as growth promoters and found that Bacillus, Pantoea, and Pseudomonas strains presented high production of indole acetic acid and ACC deaminase activity. Our results suggest that cacao domestication could lead to the loss of essential bacteria for seedling establishment and development. This study improves our understanding of the relationship and interaction between perennial plants and seed-borne microbiota.}, }
@article {pmid39295780, year = {2022}, author = {Mesnage, R and Calatayud, M and Duysburgh, C and Marzorati, M and Antoniou, MN}, title = {Alterations in infant gut microbiome composition and metabolism after exposure to glyphosate and Roundup and/or a spore-based formulation using the SHIME technology.}, journal = {Gut microbiome (Cambridge, England)}, volume = {3}, number = {}, pages = {e6}, pmid = {39295780}, issn = {2632-2897}, abstract = {Despite extensive research into the toxicology of the herbicide glyphosate, there are still major unknowns regarding its effects on the human gut microbiome. We describe the effects of glyphosate and a Roundup glyphosate-based herbicide on infant gut microbiota using SHIME technology. SHIME microbiota culture was undertaken in the presence of a concentration of 100-mg/L glyphosate and the same glyphosate equivalent concentration of Roundup. Roundup and to a lesser extent glyphosate caused an increase in fermentation activity, resulting in acidification of the microbial environment. This was also reflected by an increase in lactate and acetate production concomitant to a decrease in the levels of propionate, valerate, caproate and butyrate. Ammonium production reflecting proteolytic activities was increased by Roundup exposure. Global metabolomics revealed large-scale disturbances, including an increased abundance of long-chain polyunsaturated fatty acids. Changes in bacterial composition measured by qPCR and 16S rRNA suggested that lactobacilli had their growth stimulated as a result of microenvironment acidification. Co-treatment with the spore-based probiotic formulation MegaSporeBiotic reverted some of the changes in short-chain fatty acid levels. Altogether, our results suggest that glyphosate can exert effects on human gut microbiota.}, }
@article {pmid39193431, year = {2024}, author = {Ding, J and Cui, X and Wang, X and Zhai, F and Wang, L and Zhu, L}, title = {Multi-omics analysis of gut microbiota and metabolites reveals contrasting profiles in domestic pigs and wild boars across urban environments.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1450306}, pmid = {39193431}, issn = {1664-302X}, abstract = {The gut microbiota plays a crucial role in host health and metabolism. This study explores the differences in gut microbiota and metabolites between domestic pigs (DP) and wild boars (WB) in urban environments. We analyzed gut microbial composition, metabolic profiles, virome composition, antibiotic resistance genes (ARGs), and human pathogenic bacteria (HPB) in both DP and WB. Our results revealed that DP exhibited a higher Firmicutes/Bacteroidetes ratio and were enriched in bacterial genera associated with domestication and modern feeding practices. Metabolomic analysis showed distinct profiles, with WB significantly enriched in the Pantothenate and CoA biosynthesis pathway, highlighting dietary and environmental influences on host metabolism. Additionally, DP had a distinct gut virome composition, particularly enriched in lytic phages of the Chaseviridae family. ARG analysis indicated a higher abundance of tetracycline resistance genes in DP, likely due to antibiotic use in pig farms. Furthermore, variations in HPB composition underscored potential health risks associated with contact with pig feces. These findings provide valuable insights into the microbial ecology of domestic pigs and wild boars, emphasizing the importance of these comparisons in identifying zoonotic pathogen transmission pathways and managing antibiotic resistance. Continued research in this area is essential for developing effective strategies to mitigate public health risks and promote sustainable livestock management practices.}, }
@article {pmid39191402, year = {2024}, author = {Aoun, N and Georgoulis, SJ and Avalos, JK and Grulla, KJ and Miqueo, K and Tom, C and Lowe-Power, TM}, title = {A pangenomic atlas reveals eco-evolutionary dynamics that shape type VI secretion systems in plant-pathogenic Ralstonia.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0032324}, pmid = {39191402}, issn = {2150-7511}, support = {Hatch #1023861,Award# 1030618//USDA | National Institute of Food and Agriculture (NIFA)/ ; //Hellman Foundation (The Hellman Foundation)/ ; }, mesh = {*Type VI Secretion Systems/genetics/metabolism ; *Phylogeny ; *Genome, Bacterial ; *Ralstonia solanacearum/genetics/metabolism ; *Evolution, Molecular ; Plant Diseases/microbiology ; Bacterial Toxins/genetics/metabolism ; Burkholderiaceae/genetics/metabolism/classification ; Multigene Family ; Ralstonia/genetics/metabolism ; Genomics ; Gene Transfer, Horizontal ; }, abstract = {Soilborne Ralstonia solanacearum species complex (RSSC) pathogens disrupt microbial communities as they invade roots and fatally wilt plants. RSSC pathogens secrete antimicrobial toxins using a type VI secretion system (T6SS). To investigate how evolution and ecology have shaped the T6SS of these bacterial pathogens, we analyzed the T6SS gene content and architecture across the RSSC and their evolutionary relatives. Our analysis reveals that two ecologically similar Burkholderiaceae taxa, xylem-pathogenic RSSC and Paracidovorax, have convergently evolved to wield large arsenals of T6SS toxins. To understand the mechanisms underlying genomic enrichment of T6SS toxins, we compiled an atlas of 1,066 auxiliary T6SS toxin clusters ("aux" clusters) across 99 high-quality RSSC genomes. We classified 25 types of aux clusters with toxins that predominantly target lipids, nucleic acids, or unknown cellular substrates. The aux clusters were located in diverse genetic neighborhoods and had complex phylogenetic distributions, suggesting frequent horizontal gene flow. Phages and other mobile genetic elements account for most of the aux cluster acquisition on the chromosome but very little on the megaplasmid. Nevertheless, RSSC genomes were more enriched in aux clusters on the megaplasmid. Although the single, ancestral T6SS was broadly conserved in the RSSC, the T6SS has been convergently lost in atypical, non-soilborne lineages. Overall, our data suggest dynamic interplay between the lifestyle of RSSC lineages and the evolution of T6SSes with robust arsenals of toxins. This pangenomic atlas poises the RSSC as an emerging, tractable model to understand the role of the T6SS in shaping pathogen populations.IMPORTANCEWe explored the eco-evolutionary dynamics that shape the inter-microbial warfare mechanisms of a globally significant plant pathogen, the Ralstonia solanacearum species complex. We discovered that most Ralstonia wilt pathogens have evolved extensive and diverse repertoires of type VI secretion system-associated antimicrobial toxins. These expansive toxin arsenals potentially enhance the ability of Ralstonia pathogens to invade plant microbiomes, enabling them to rapidly colonize and kill their host plants. We devised a classification system to categorize the Ralstonia toxins. Interestingly, many of the toxin gene clusters are encoded on mobile genetic elements, including prophages, which may be mutualistic symbionts that enhance the inter-microbial competitiveness of Ralstonia wilt pathogens. Moreover, our findings suggest that the convergent loss of this multi-gene trait contributes to genome reduction in two vector-transmitted lineages of Ralstonia pathogens. Our findings demonstrate that the interplay between microbial ecology and pathogen lifestyle shapes the evolution of a genetically complex antimicrobial weapon.}, }
@article {pmid39190978, year = {2024}, author = {Xu, M and Wang, F and Stedtfeld, RD and Fu, Y and Xiang, L and Sheng, H and Li, Z and Hashsham, SA and Jiang, X and Tiedje, JM}, title = {Transfer of antibiotic resistance genes from soil to rice in paddy field.}, journal = {Environment international}, volume = {191}, number = {}, pages = {108956}, doi = {10.1016/j.envint.2024.108956}, pmid = {39190978}, issn = {1873-6750}, mesh = {*Oryza/genetics ; *Soil Microbiology ; *Fertilizers ; *Soil/chemistry ; *Drug Resistance, Microbial/genetics ; Animals ; Agriculture ; Swine ; Composting ; Genes, Bacterial ; }, abstract = {The global spread and distribution of antibiotic resistance genes (ARGs) has received much attention whereas knowledge about the transmission of ARGs from one matrix to another is still insufficient. In this study, the paddy fields fertilized with chemical fertilizer, swine compost, and no fertilizer were investigated to assess the transfer of ARGs from soil to rice. Soil and plant samples were collected at day 0, 7, 30 and 79 representing various stages of paddy growth. High throughput qPCR was applied to quantify ARGs using a set of 144 primers. Gene copy number of ARGs measured in soil initially decreased and then increased in soil with no fertilizer and chemical fertilizer, indicating that crop planting and flooding conditions did influence the ARGs profiles in soil. Application of swine compost significantly enhanced the relative abundance and gene copy number of ARGs in paddy soil. Rice seedlings contained substantial amount of ARGs and their relative abundance continually decreased after transplant. Compared with initial stage, detection frequencies of ARGs increased in soil without swine compost at harvest time (day 79), indicating the transmission of ARGs from irrigation water to soil. Detection frequencies of ARGs increased in soil and rice root with swine compost at harvest time, indicating the transfer of ARGs from swine compost to soil and rice root. There was no significant difference in abundance and diversity of ARGs in rice grains with these three different fertilizations. The source of the ARGs in rice grain still needs further exploration.}, }
@article {pmid39189736, year = {2024}, author = {Wang, L and Ducoste, JJ and de Los Reyes, FL}, title = {Perturbations to common gardens of anaerobic co-digesters reveal relationships between functional resilience and microbial community composition.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {9}, pages = {e0029824}, pmid = {39189736}, issn = {1098-5336}, support = {15-05-U//North Carolina Water Resources Research Institute/ ; CBET 1805666//National Science Foundation (NSF)/ ; }, mesh = {*Microbiota/physiology ; *Bioreactors/microbiology ; Anaerobiosis ; *Methane/metabolism ; Bacteria/metabolism/classification/genetics ; }, abstract = {We report the relationship between enrichment of adapted populations and enhancement of community functional resilience in methanogenic bioreactors. Although previous studies have shown the positive effects of acclimation, this work directly investigated the relationships between microbiome dynamics and performance of anaerobic co-digesting reactors in response to different levels of an environmental perturbation (loading of grease interceptor waste [GIW]). Using the methanogenic microbiome from a full-scale digester, we developed eight sets of microbial communities in triplicate using different feed sources. These substrate-specific microbiomes were then exposed to three independent disturbance events of low-, mid- and high-GIW loading rates. This approach allowed us to directly attribute differences in community responses to differences in community composition. Despite identical inocula, environment (digester operation, substrate loading rate, and feeding patterns) and general whole-community function (methane production and effluent quality) during the cultivation period, different substrates led to different microbial community assemblies. Lipid pre-acclimation led to enrichment of a pool of specialized populations, along with thriving of sub-dominant communities. The enrichment of these populations improved functional resilience and process performance when exposed to a low level of lipid-rich perturbation compared with less-acclimated communities. At higher levels of perturbation, the communities were not able to recover methanogenesis, indicating a loading limit to the resilience response. This study extends our current understanding of environmental perturbations, feed-specific adaptation, and functional resilience in methanogenic bioreactors.IMPORTANCEThis study demonstrates, for the first time for GIW co-digestion, how applying similar perturbations to different microbial communities was used to directly identify the causal relationships between microbial community, function, and environment in triplicate anaerobic microbiomes. We evaluated the impact of feed-specific adaptation on methanogenic microbiomes and demonstrated how microbiomes can be influenced to improve their functional (methanogenic) resilience to GIW inhibition. These findings demonstrate how an ecological framework can help improve a biological engineering application, and more specifically, increase the potential of anaerobic co-digestion for converting wastes to energy.}, }
@article {pmid39188310, year = {2024}, author = {Berrios, L and Venturini, AM and Ansell, TB and Tok, E and Johnson, W and Willing, CE and Peay, KG}, title = {Co-inoculations of bacteria and mycorrhizal fungi often drive additive plant growth responses.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae104}, pmid = {39188310}, issn = {2730-6151}, abstract = {Controlled greenhouse studies have shown the numerous ways that soil microbes can impact plant growth and development. However, natural soil communities are highly complex, and plants interact with many bacterial and fungal taxa simultaneously. Due to logistical challenges associated with manipulating more complex microbiome communities, how microbial communities impact emergent patterns of plant growth therefore remains poorly understood. For instance, do the interactions between bacteria and fungi generally yield additive (i.e. sum of their parts) or nonadditive, higher order plant growth responses? Without this information, our ability to accurately predict plant responses to microbial inoculants is weakened. To address these issues, we conducted a meta-analysis to determine the type (additive or higher-order, nonadditive interactions), frequency, direction (positive or negative), and strength that bacteria and mycorrhizal fungi (arbuscular and ectomycorrhizal) have on six phenotypic plant growth responses. Our results demonstrate that co-inoculations of bacteria and mycorrhizal fungi tend to have positive additive effects on many commonly reported plant responses. However, ectomycorrhizal plant shoot height responds positively and nonadditively to co-inoculations of bacteria and ectomycorrhizal fungi, and the strength of additive effects also differs between mycorrhizae type. These findings suggest that inferences from greenhouse studies likely scale to more complex field settings and that inoculating plants with diverse, beneficial microbes is a sound strategy to support plant growth.}, }
@article {pmid39187952, year = {2024}, author = {Stryker, J and White, E and Díaz-Almeyda, E and Sidoti, B and Oberle, B}, title = {Tank formation transforms nitrogen metabolism of an epiphytic bromeliad and its phyllosphere bacteria.}, journal = {American journal of botany}, volume = {111}, number = {12}, pages = {e16396}, doi = {10.1002/ajb2.16396}, pmid = {39187952}, issn = {1537-2197}, mesh = {*Nitrogen/metabolism ; *Plant Leaves/microbiology/metabolism ; *Bacteria/metabolism/classification ; Tillandsia/metabolism/physiology ; Microbiota ; Bromeliaceae/metabolism/microbiology/physiology ; }, abstract = {PREMISE: Up to half of tropical forest plant species grow on other plants. Lacking access to soils, vascular epiphytes have unique adaptations for mineral nutrition. Among the most distinctive is the tank growth form of certain large bromeliads, which absorb nutrients that are cycled by complex microbial communities in water trapped among their overlapping leaf bases. However, tanks form only after years of growth by juvenile plants, which must acquire nutrients differently. Understanding how nutrient dynamics change during tank bromeliad development can provide key insights into the role of microorganisms in the maintenance of tropical forest biodiversity.<br><br>METHODS: We evaluated variations in plant morphology, growth, foliar nitrogen physiology, and phyllosphere bacterial communities along a size gradient spanning the transition to tank formation in the threatened species Tillandsia utriculata.<br><br>RESULTS: Sequential morphological and growth phases coincided with the transition to tank formation when the longest leaf on plants was between 14 and 19&#x2009;cm. Before this point, foliar ammonium concentrations were very high, but after, leaf segments absorbed significantly more nitrate. Leaf-surface bacterial communities tracked ontogenetic changes in plant morphology and nitrogen metabolism, with less-diverse communities in tankless plants distinguished by a high proportion of taxa implicated in ureolysis, nitrogen fixation, and methanotrophy, whereas nitrate reduction characterized communities on individuals that could form a tank.<br><br>CONCLUSIONS: Coupled changes in plant morphology, physiology, and microbiome function facilitate the transition between alternative nutritional modes in tank bromeliads. Comparing bromeliads across life stages and habitats may illuminate how nitrogen-use varies across scales.}, }
@article {pmid39182301, year = {2024}, author = {Peruzzo, A and Petrin, S and Boscolo Anzoletti, A and Mancin, M and Di Cesare, A and Sabatino, R and Lavagnolo, MC and Beggio, G and Baggio, G and Danesi, P and Barco, L and Losasso, C}, title = {The integration of omics and cultivation-dependent methods could effectively determine the biological risks associated with the utilization of soil conditioners in agriculture.}, journal = {Journal of hazardous materials}, volume = {478}, number = {}, pages = {135567}, doi = {10.1016/j.jhazmat.2024.135567}, pmid = {39182301}, issn = {1873-3336}, mesh = {*Agriculture ; *Soil Microbiology ; *Sewage/microbiology ; *Bacteria/genetics ; Soil/chemistry ; Composting ; Metagenomics ; Fertilizers ; }, abstract = {In the circular economy, reusing agricultural residues, treated biowaste, and sewage sludges-commonly referred to as soil conditioners-in agriculture is essential for converting waste into valuable resources. However, these materials can also contribute to the spread of antimicrobial-resistant pathogens in treated soils. In this study, we analyzed different soil conditioners categorized into five groups: compost from source-separated biowaste and green waste, agro-industrial digestate, digestate from anaerobic digestion of source-separated biowaste, compost from biowaste digestate, and sludges from wastewater treatment plants. Under Italian law, only the first two categories are approved for agricultural use, despite Regulation 1009/2019/EU allowing the use of digestate from anaerobic digestion of source-separated biowaste in CE-marked fertilizers. We examined the bacterial community and associated resistome of each sample using metagenomic approaches. Additionally, we detected and isolated various pathogens to provide a comprehensive understanding of the potential risks associated with sludge application in agriculture. The compost samples exhibited higher bacterial diversity and a greater abundance of potentially pathogenic bacteria compared to other samples, except for wastewater treatment plant sludges, which had the highest frequency of Salmonella isolation and resistome diversity. Our findings suggest integrating omics and cultivation-dependent methods to accurately assess the biological risks of using sludge in agriculture.}, }
@article {pmid39180136, year = {2024}, author = {Khadem, S and Berry, D and Al-Khlifeh, E}, title = {Climate influences the gut eukaryome of wild rodents in the Great Rift Valley of Jordan.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {358}, pmid = {39180136}, issn = {1756-3305}, mesh = {Jordan ; Animals ; Mice ; Rats ; *Eukaryota/classification/genetics/growth &amp; development ; *Climate ; *Gastrointestinal Microbiome/genetics ; *Rodentia/parasitology ; *Animals, Wild/parasitology ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 18S ; Feces/parasitology ; }, abstract = {BACKGROUND: The mammalian gut microbiome includes a community of eukaryotes with significant taxonomic and functional diversity termed the eukaryome. The molecular analysis of eukaryotic diversity in microbiomes of wild mammals is still in its early stages due to the recent emergence of interest in this field. This study aimed to fill this knowledge gap by collecting data on eukaryotic species found in the intestines of wild rodents. Because little is known about the influence of climate on the gut eukaryome, we compared the composition of the gut eukaryotes in two rodent species, Mus musculus domesticus and Acomys cahirinus, which inhabit a transect crossing a temperate and tropical zone on the Jordanian side of the Great Rift Valley (GRV).<br><br>METHODS: We used high-throughput amplicon sequencing targeting the 18S rRNA gene in fecal samples from rodents to identify eukaryotic organisms, their relative abundance, and their potential for pathogenicity.<br><br>RESULTS: Nematodes and protozoa were the most prevalent species in the eukaryome communities, whereas fungi made up 6.5% of the total. Sixty percent of the eukaryotic ASVs belonged to taxa that included known pathogens. Eighty percent of the rodents were infected with pinworms, specifically Syphacia obvelata. Eukaryotic species diversity differed significantly between bioclimatic zones (p&#x2009;=&#x2009;0.001). Nippostrongylus brasiliensis and Aspiculuris tetraptera were found to be present exclusively in the Sudanian zone rodents. This area has not reported any cases of Trichuris infections. Yet, Capillaria infestations were unique to the Mediterranean region, while Trichuris vulpis infestations were also prevalent in the Mediterranean and Irano-Turanian regions.<br><br>CONCLUSIONS: This study highlights the importance of considering host species diversity and environmental factors when studying eukaryome composition in wild mammals. These data will be valuable as a reference to eukaryome study.}, }
@article {pmid39178936, year = {2024}, author = {Anedda, E and Ekhlas, D and Alexa, E and Farrell, ML and Gaffney, MT and Madigan, G and Morris, D and Burgess, CM}, title = {Characterization of antimicrobial resistant Enterobacterales isolated from spinach and soil following zinc amendment.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {361}, number = {}, pages = {124774}, doi = {10.1016/j.envpol.2024.124774}, pmid = {39178936}, issn = {1873-6424}, mesh = {*Spinacia oleracea/microbiology ; *Soil Microbiology ; *Zinc/pharmacology ; *Enterobacteriaceae/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; *Soil Pollutants ; Soil/chemistry ; Microbial Sensitivity Tests ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antimicrobial resistant bacteria can occur in the primary food production environment. The emergence and dissemination of antimicrobial resistance (AMR) in the environment can be influenced by several factors, including the presence of heavy metals. The aim of this study was to examine the presence and characteristics of antimicrobial resistant Enterobacterales in soils and spinach grown in soils with and without zinc amendment. A total of 160 samples (92 soil and 68 spinach) were collected from two locations, in which some plots had been amended with zinc. Samples were cultured on selective agars for detection of extended-spectrum beta-lactamase-producing Enterobacterales (ESBL), carbapenem-resistant Enterobacterales and ciprofloxacin-resistant Enterobacterales. Samples were also cultured for enumeration of total Enterobacterales. Isolates were identified by MALDI-TOF. Antimicrobial susceptibility testing was carried out in accordance with EUCAST and CLSI criteria. The whole genome sequence (WGS) of selected isolates was determined. Inductively coupled plasma atomic emission spectrometry was also performed on soil samples in order to measure the concentration of zinc. In total 20 antimicrobial resistant Enterobacterales were isolated from the soil (n = 8) and spinach samples (n = 12). In both sample types, Serratia fonticola (n = 16) was the dominant species, followed by Escherichia coli (n = 1), Citrobacter freundii (n = 1) and Morganella morganii (n = 1) detected in spinach samples, and Enterobacter cloacae (n = 1) detected in a soil sample. The WGS identified genes conferring resistance to different antimicrobials in agreement with the phenotypic results; 14 S. fonticola isolates were confirmed as ESBL producers and harboured the blaFONA gene. Genes that encoded for zinc resistance and multidrug efflux pumps, transporters that can target both antimicrobials and heavy metals, were also identified. Overall, the findings of this study suggest the presence of zinc did not influence the AMR Enterobacterales in soil or spinach samples.}, }
@article {pmid39178591, year = {2024}, author = {Gao, FZ and Hu, LX and Liu, YS and Qiao, LK and Chen, ZY and Su, JQ and He, LY and Bai, H and Zhu, YG and Ying, GG}, title = {Unveiling the overlooked small-sized microbiome in river ecosystems.}, journal = {Water research}, volume = {265}, number = {}, pages = {122302}, doi = {10.1016/j.watres.2024.122302}, pmid = {39178591}, issn = {1879-2448}, mesh = {*Rivers/microbiology ; *Microbiota ; *Ecosystem ; Metagenomics ; Bacteria/genetics ; }, abstract = {Enriching microorganisms using a 0.22-μm pore size is a general pretreatment procedure in river microbiome research. However, it remains unclear the extent to which this method loses microbiome information. Here, we conducted a comparative metagenomics-based study on microbiomes with sizes over 0.22 μm (large-sized) and between 0.22 μm and 0.1 μm (small-sized) in a subtropical river. Although the absolute concentration of small-sized microbiome was about two orders of magnitude lower than that of large-sized microbiome, sequencing only large-sized microbiome resulted in a significant loss of microbiome diversity. Specifically, the microbial community was different between two sizes, and 347 genera were only detected in small-sized microbiome. Small-sized microbiome had much more diverse viral community than large-sized fraction. The viruses had abundant ecological functions and were hosted by 825 species of 169 families, including pathogen-related families. Small-sized microbiome had distinct antimicrobial resistance risks from large-sized microbiome, showing an enrichment of eight antibiotic resistance gene (ARG) types as well as the detection of 140 unique ARG subtypes and five enriched risk rank I ARGs. Draft genomes of five major resistant pathogens having diverse ecological and pollutant-degrading functions were only assembled in small-sized microbiome. These findings provide novel insights into river ecosystems, and highlight the overlooked small-sized microbiome in the environment.}, }
@article {pmid39175749, year = {2024}, author = {Peña-Salinas, ME and Speth, DR and Utter, DR and Spelz, RM and Lim, S and Zierenberg, R and Caress, DW and Núñez, PG and Vázquez, R and Orphan, VJ}, title = {Thermotogota diversity and distribution patterns revealed in Auka and JaichMaa 'ja 'ag hydrothermal vent fields in the Pescadero Basin, Gulf of California.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17724}, pmid = {39175749}, issn = {2167-8359}, mesh = {*Hydrothermal Vents/microbiology ; *Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Seawater/microbiology/chemistry ; California ; Bacteria/genetics/classification ; }, abstract = {Discovering new deep hydrothermal vent systems is one of the biggest challenges in ocean exploration. They are a unique window to elucidate the physical, geochemical, and biological processes that occur on the seafloor and are involved in the evolution of life on Earth. In this study, we present a molecular analysis of the microbial composition within the newly discovered hydrothermal vent field, JaichMaa 'ja 'ag, situated in the Southern Pescadero Basin within the Gulf of California. During the cruise expedition FK181031 in 2018, 33 sediment cores were collected from various sites within the Pescadero vent fields and processed for 16S rRNA amplicon sequence variants (ASVs) and geochemical analysis. Correlative analysis of the chemical composition of hydrothermal pore fluids and microbial abundances identified several sediment-associated phyla, including Thermotogota, that appear to be enriched in sediment horizons impacted by hydrothermal fluid flow. Comparative analysis of Thermotogota with the previously explored Auka hydrothermal vent field situated 2 km away displayed broad similarity between the two locations, although at finer scales (e.g., ASV level), there were notable differences that point to core-to-core and site-level factors revealing distinct patterns of distribution and abundance within these two sediment-hosted hydrothermal vent fields. These patterns are intricately linked to the specific physical and geochemical conditions defining each vent, illuminating the complexity of this unique deep ocean chemosynthetic ecosystem.}, }
@article {pmid39175056, year = {2024}, author = {Sbardellati, DL and Vannette, RL}, title = {Targeted viromes and total metagenomes capture distinct components of bee gut phage communities.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {155}, pmid = {39175056}, issn = {2049-2618}, support = {2023-67011-40501//U.S. Department of Agriculture/ ; 1929516//National Science Foundation/ ; }, mesh = {Bees/virology/microbiology ; Animals ; *Bacteriophages/genetics/isolation &amp; purification/classification ; *Virome ; *Metagenome ; Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Gastrointestinal Tract/microbiology/virology ; }, abstract = {BACKGROUND: Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey bee Apis mellifera and the eastern bumble bee Bombus impatiens.<br><br>RESULTS: We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low occupancy phage, while total metagenomes were biased towards sampling temperate phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments.<br><br>CONCLUSIONS: Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage. Video Abstract.}, }
@article {pmid39174521, year = {2024}, author = {Foulquier, A and Datry, T and Corti, R and von Schiller, D and Tockner, K and Stubbington, R and Gessner, MO and Boyer, F and Ohlmann, M and Thuiller, W and Rioux, D and Miquel, C and Albariño, R and Allen, DC and Altermatt, F and Arce, MI and Arnon, S and Banas, D and Banegas-Medina, A and Beller, E and Blanchette, ML and Blessing, J and Boëchat, IG and Boersma, K and Bogan, M and Bonada, N and Bond, N and Brintrup, K and Bruder, A and Burrows, R and Cancellario, T and Canhoto, C and Carlson, S and Cid, N and Cornut, J and Danger, M and de Freitas Terra, B and De Girolamo, AM and Del Campo, R and Díaz Villanueva, V and Dyer, F and Elosegi, A and Febria, C and Figueroa Jara, R and Four, B and Gafny, S and Gómez, R and Gómez-Gener, L and Guareschi, S and Gücker, B and Hwan, J and Jones, JI and Kubheka, PS and Laini, A and Langhans, SD and Launay, B and Le Goff, G and Leigh, C and Little, C and Lorenz, S and Marshall, J and Martin Sanz, EJ and McIntosh, A and Mendoza-Lera, C and Meyer, EI and Miliša, M and Mlambo, MC and Morais, M and Moya, N and Negus, P and Niyogi, D and Pagán, I and Papatheodoulou, A and Pappagallo, G and Pardo, I and Pařil, P and Pauls, SU and Polášek, M and Rodríguez-Lozano, P and Rolls, RJ and Sánchez-Montoya, MM and Savić, A and Shumilova, O and Sridhar, KR and Steward, A and Taleb, A and Uzan, A and Valladares, Y and Vander Vorste, R and Waltham, NJ and Zak, DH and Zoppini, A}, title = {Unravelling large-scale patterns and drivers of biodiversity in dry rivers.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7233}, pmid = {39174521}, issn = {2041-1723}, support = {869226 (DRYvER)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 European Institute of Innovation and Technology (H2020 The European Institute of Innovation and Technology)/ ; }, mesh = {*Biodiversity ; *Rivers/microbiology ; Animals ; Fungi/classification/genetics ; Geologic Sediments/microbiology ; Bacteria/classification/genetics ; Invertebrates/classification ; DNA Barcoding, Taxonomic ; Plants/classification ; Archaea/classification/genetics ; }, abstract = {More than half of the world's rivers dry up periodically, but our understanding of the biological communities in dry riverbeds remains limited. Specifically, the roles of dispersal, environmental filtering and biotic interactions in driving biodiversity in dry rivers are poorly understood. Here, we conduct a large-scale coordinated survey of patterns and drivers of biodiversity in dry riverbeds. We focus on eight major taxa, including microorganisms, invertebrates and plants: Algae, Archaea, Bacteria, Fungi, Protozoa, Arthropods, Nematodes and Streptophyta. We use environmental DNA metabarcoding to assess biodiversity in dry sediments collected over a 1-year period from 84 non-perennial rivers across 19 countries on four continents. Both direct factors, such as nutrient and carbon availability, and indirect factors such as climate influence the local biodiversity of most taxa. Limited resource availability and prolonged dry phases favor oligotrophic microbial taxa. Co-variation among taxa, particularly Bacteria, Fungi, Algae and Protozoa, explain more spatial variation in community composition than dispersal or environmental gradients. This finding suggests that biotic interactions or unmeasured ecological and evolutionary factors may strongly influence communities during dry phases, altering biodiversity responses to global changes.}, }
@article {pmid39172818, year = {2024}, author = {Frazier, AN and Belk, AD and Beck, MR and Koziel, JA}, title = {Impact of methane mitigation strategies on the native ruminant microbiome: A protocol for a systematic review and meta-analysis.}, journal = {PloS one}, volume = {19}, number = {8}, pages = {e0308914}, pmid = {39172818}, issn = {1932-6203}, mesh = {*Methane/metabolism ; *Ruminants/microbiology ; Animals ; *Microbiota ; *Systematic Reviews as Topic ; *RNA, Ribosomal, 16S/genetics ; *Meta-Analysis as Topic ; }, abstract = {Recently, research has investigated the role of the ruminant native microbiome, and the role microbes play in methane (CH4) production and mitigation. However, the variation across microbiome studies makes implementing impactful strategies difficult. The first objective of this study is to identify, summarize, compile, and discuss the current literature on CH4 mitigation strategies and how they interact with the native ruminant microbiome. The second objective is to perform a meta-analysis on the identified16S rRNA sequencing data. A literature search using Web of Science, Scopus, AGRIS, and Google Scholar will be implemented. Eligible criteria will be defined using PICO (population, intervention, comparator, and outcomes) elements. Two independent reviewers will be utilized for both the literature search and data compilation. Risk of bias will be assessed using the Cochrane Risk Bias 2.0 tool. Publicly available 16S rRNA amplicon gene sequencing data will be downloaded from NCBI Sequence Read Archive, European Nucleotide Archive or similar database using appropriate extraction methods. Data processing will be performed using QIIME2 following a standardized protocol. Meta-analyses will be performed on both alpha and beta diversity as well as taxonomic analyses. Alpha diversity metrics will be tested using a Kruskal-Wallis test with a Benjamini-Hochberg multiple testing correction. Beta diversity will be statistically tested using PERMANOVA testing with multiple test corrections. Hedge's g standardized mean difference statistic will be used to calculate fixed and random effects model estimates using a 95% confidence interval. Heterogeneity between studies will be assessed using the I2 statistic. Potential publication bias will be further assessed using Begg's correlation test and Egger's regression test. The GRADE approach will be used to assess the certainty of evidence. The following protocol will be used to guide future research and meta-analyses for investigating CH4 mitigation strategies and ruminant microbial ecology. The future work could be used to enhance livestock management techniques for GHG control. This protocol is registered in Open Science Framework (https://osf.io/vt56c) and available in the Systematic Reviews for Animals and Food (https://www.syreaf.org/contact).}, }
@article {pmid39171106, year = {2024}, author = {Pi, X and Du, Z and Teng, W and Fu, H and Hu, L and Li, J and Ding, J and Yang, X and Zhang, Y}, title = {Characteristics of stachyose-induced effects on gut microbiota and microbial metabolites in vitro associated with obesity in children.}, journal = {Frontiers in nutrition}, volume = {11}, number = {}, pages = {1411374}, pmid = {39171106}, issn = {2296-861X}, abstract = {Childhood obesity presents a serious health concern associated with gut microbiota alterations. Dietary interventions targeting the gut microbiota have emerged as promising strategies for managing obesity in children. This study aimed to elucidate the impact of stachyose (STS) supplementation on the gut microbiota composition and metabolic processes in obese children. Fecal samples were collected from 40 obese children (20 boys and 20 girls) aged between 6 and 15 and in vitro fermentation was conducted with or without the addition of STS, respectively, followed by 16S rRNA amplicon sequencing and analysis of short-chain fatty acids (SCFAs) and gases. Notably, our results revealed that STS supplementation led to significant alterations in gut microbiota composition, including an increase in the abundance of beneficial bacteria such as Bifidobacterium and Faecalibacterium, and a decrease in harmful bacteria including Escherichia-Shigella, Parabacteroides, Eggerthella, and Flavonifractor. Moreover, STS supplementation resulted in changes in SCFAs production, with significant increases in acetate levels and reductions in propionate and propionate, while simultaneously reducing the generation of gases such as H2S, H2, and NH3. The Area Under the Curve (AUC)-Random Forest algorithm and PICRUSt 2 were employed to identify valuable biomarkers and predict associations between the gut microbiota, metabolites, and metabolic pathways. The results not only contribute to the elucidation of STS's modulatory effects on gut microbiota but also underscore its potential in shaping metabolic activities within the gastrointestinal environment. Furthermore, our study underscores the significance of personalized nutrition interventions, particularly utilizing STS supplementation, in the management of childhood obesity through targeted modulation of gut microbial ecology and metabolic function.}, }
@article {pmid39168311, year = {2024}, author = {MacGibeny, MA and Adjei, S and Pyle, H and Bunick, CG and Ghannoum, M and Grada, A and Harris-Tryon, T and Tyring, SK and Kong, HH}, title = {The Human Skin Microbiome in Health: CME Part 1.}, journal = {Journal of the American Academy of Dermatology}, volume = {}, number = {}, pages = {}, pmid = {39168311}, issn = {1097-6787}, support = {Z99 AR999999/ImNIH/Intramural NIH HHS/United States ; ZIA AR041217/ImNIH/Intramural NIH HHS/United States ; }, abstract = {Human skin is home to a myriad of microorganisms, including bacteria, viruses, fungi, and mites, many of which are considered commensal microbes that aid in maintaining the overall homeostasis or steady-state condition of the skin and contribute to skin health. Our understanding of the complexities of the skin's interaction with its microorganisms is evolving. This knowledge is based primarily on in vitro and animal studies, and more work is needed to understand how this knowledge relates to humans. Here, we introduce the concept of the skin microbiome and discuss skin microbial ecology, some intrinsic factors with potential influence on the human skin microbiome, and possible microbiome-host interactions. The second article of this two-part CME series describes how microbiome alterations may be associated with skin disease, how medications can affect the microbiome, and what microbiome-based therapies are under investigation.}, }
@article {pmid39165397, year = {2024}, author = {Jacob, M and Thomas, PK and Giebel, HA and Billerbeck, S and Simon, M and Striebel, M and Dlugosch, L}, title = {Cross-domain diversity effects: linking diatom species richness, intraspecific richness, and biomass production to host-associated bacterial diversity.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae046}, pmid = {39165397}, issn = {2730-6151}, abstract = {Interactions between bacteria and microalgae are important for the functioning of aquatic ecosystems, yet interactions based on the biodiversity of these two taxonomic domains have been scarcely studied. Specifically, it is unclear whether a positive biodiversity-productivity relationship in phytoplankton is largely facilitated by niche partitioning among the phytoplankton organisms themselves or whether associated bacterial communities play an additional role in modifying these diversity effects. Moreover, the effects of intraspecific diversity in phytoplankton communities on bacterial community diversity have not been tested. To address these points, we factorially manipulated both species and intraspecific richness of three diatoms to test the effects of diatom species/strain diversity on biomass production and bacterial diversity in algae-bacteria communities. The results show that diatom intraspecific diversity has significant positive effects on culture biomass and the diversity of the associated free-living bacterial community (0.2-3 μm size fraction), which are comparable in magnitude to species diversity effects. However, there were little to no effects of diatom diversity on host-associated bacterial diversity (>3 μm size fraction), or of bacterial diversity on biomass production. These results suggest a decoupling of bacterial diversity from the diatom diversity-productivity relationship and provide early insights regarding the relations between diversity across domains in aquatic ecosystems.}, }
@article {pmid39165109, year = {2024}, author = {Gloder, G and Bourne, ME and Cuny, MAC and Verreth, C and Crauwels, S and Dicke, M and Poelman, EH and Jacquemyn, H and Lievens, B}, title = {Caterpillar-parasitoid interactions: species-specific influences on host microbiome composition.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {10}, pages = {}, pmid = {39165109}, issn = {1574-6941}, support = {G.0961.19//Flemish Fund for Scientific Research/ ; }, mesh = {Animals ; *Larva/microbiology ; *Microbiota ; *Butterflies/microbiology/parasitology ; *Host-Parasite Interactions ; Wolbachia/genetics ; Species Specificity ; Nosema/pathogenicity ; Wasps/microbiology ; Bacteria/classification/genetics/growth &amp; development ; }, abstract = {There is increasing evidence that host-parasitoid interactions can have a pronounced impact on the microbiome of host insects, but it is unclear to what extent this is caused by the host and/or parasitoid. Here, we compared the internal and external microbiome of caterpillars of Pieris brassicae and Pieris rapae parasitized by Cotesia glomerata or Cotesia rubecula with nonparasitized caterpillars. Additionally, we investigated the internal and external microbiome of the parasitoid larvae. Both internal and external bacterial densities were significantly higher for P. brassicae than P. rapae, while no differences were found between parasitized and nonparasitized caterpillars. In contrast, parasitism significantly affected the composition of the internal and external microbiome of the caterpillars and the parasitoid larvae, but the effects were dependent on the host and parasitoid species. Irrespective of host species, a Wolbachia species was exclusively found inside caterpillars parasitized by C. glomerata, as well as in the corresponding developing parasitoid larvae. Similarly, a Nosema species was abundantly present inside parasitized caterpillars and the parasitoid larvae, but this was independent of the host and the parasitoid species. We conclude that parasitism has pronounced effects on host microbiomes, but the effects depend on both the host and parasitoid species.}, }
@article {pmid39163484, year = {2024}, author = {Dede, B and Reeves, EP and Walter, M and Bach, W and Amann, R and Meyerdierks, A}, title = {Bacterial chemolithoautotrophy in ultramafic plumes along the Mid-Atlantic Ridge.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39163484}, issn = {1751-7370}, support = {EXC-309-49926684//Deutsche Forschungsgemeinschaft/ ; //Norwegian Research Council/ ; 179560//University of Bergen Centre for Geobiology/ ; //Max Planck Society/ ; }, mesh = {*Hydrothermal Vents/microbiology ; Atlantic Ocean ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Chemoautotrophic Growth ; *Seawater/microbiology ; Microbiota ; Hydrogen/metabolism ; Phylogeny ; Sulfur/metabolism ; Oxidation-Reduction ; In Situ Hybridization, Fluorescence ; Carbon Dioxide/metabolism ; }, abstract = {Hydrothermal vent systems release reduced chemical compounds that act as an important energy source in the deep sea. Chemolithoautotrophic microbes inhabiting hydrothermal plumes oxidize these compounds, in particular, hydrogen and reduced sulfur, to obtain the energy required for CO2 fixation. Here, we analysed the planktonic communities of four hydrothermal systems located along the Mid-Atlantic Ridge: Irinovskoe, Semenov-2, Logatchev-1, and Ashadze-2, by combining long-read 16S rRNA gene analysis, fluorescence in situ hybridization, meta-omics, and thermodynamic calculations. Sulfurimonas and SUP05 dominated the microbial communities in these hydrothermal plumes. Investigation of Sulfurimonas and SUP05 MAGs, and their gene transcription in plumes indicated a niche partitioning driven by hydrogen and sulfur. In addition to sulfur and hydrogen oxidation, a novel SAR202 clade inhabiting the plume, here referred to as genus Carboxydicoccus, harbours the capability for CO oxidation and CO2 fixation via reverse TCA cycle. Both pathways were also highly transcribed in other hydrogen-rich plumes, including the Von Damm vent field. Carboxydicoccus profundi reached up to 4% relative abundance (1.0 x 103 cell ml- 1) in Irinovskoe non-buoyant plume and was also abundant in non-hydrothermally influenced deep-sea metagenomes (up to 5 RPKM). Therefore, CO, which is probably not sourced from the hydrothermal fluids (1.9-5.8 μM), but rather from biological activities within the rising fluid, may serve as a significant energy source in hydrothermal plumes. Taken together, this study sheds light on the chemolithoautotrophic potential of the bacterial community in Mid-Atlantic Ridge plumes.}, }
@article {pmid39162854, year = {2024}, author = {Joshi, S and Pham, K and Moe, L and McNees, R}, title = {Exploring the Microbial Diversity and Composition of Three Cigar Product Categories.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {107}, pmid = {39162854}, issn = {1432-184X}, mesh = {*Tobacco Products ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Biodiversity ; Phylogeny ; High-Throughput Nucleotide Sequencing ; DNA, Bacterial/genetics ; }, abstract = {Cigars and cigarillos are emerging as popular tobacco alternatives to cigarettes. However, these products may be equally harmful to human health than cigarettes and are associated with similar adverse health effects. We used 16S rRNA gene amplicon sequencing to extensively characterize the microbial diversity and investigate differences in microbial composition across 23 different products representing three different cigar product categories: filtered cigar, cigarillo, and large cigar. High throughput sequencing of the V4 hypervariable region of the 16 s rRNA gene revealed 2124 Operational Taxonomic Units (OTUs). Our findings showed that the three categories of cigars differed significantly in observed richness and Shannon diversity, with filtered cigars exhibiting lower diversity compared to large cigars and cigarillos. We also found a shared and unique microbiota among different product types. Firmicutes was the most abundant phylum in all product categories, followed by Actinobacteria. Among the 16 genera shared across all product types were Bacillus, Staphylococcus, Pseudomonas, and Pantoea. Nine genera were exclusively shared by large cigars and cigarillos and an additional thirteen genera were exclusive to filtered cigars. Analysis of individual cigar products showed consistent microbial composition across replicates for most large cigars and cigarillos while filtered cigars showed more inter-product variability. These findings provide important insights into the microbial diversity of the different cigar product types.}, }
@article {pmid39162497, year = {2024}, author = {Chatzigiannidou, I and Heyse, J and Props, R and Rubbens, P and Mermans, F and Teughels, W and Van de Wiele, T and Boon, N}, title = {Real-time flow cytometry to assess qualitative and quantitative responses of oral pathobionts during exposure to antiseptics.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0095524}, pmid = {39162497}, issn = {2165-0497}, support = {G0B2719N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 1221020N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 3G020119//Fonds Wetenschappelijk Onderzoek (FWO)/ ; }, mesh = {*Flow Cytometry/methods ; *Anti-Infective Agents, Local/pharmacology ; *Chlorhexidine/pharmacology ; Humans ; *Bacteria/drug effects ; *Triclosan/pharmacology ; Cetylpyridinium/pharmacology ; Microbial Sensitivity Tests/methods ; Mouth/microbiology ; Periodontitis/microbiology ; }, abstract = {UNLABELLED: Antiseptics are widely used in oral healthcare to prevent or treat oral diseases, such as gingivitis and periodontitis. However, the incidence of bacteria being tolerant to standard antiseptics has sharply increased over the last few years. This stresses the urgency for surveillance against tolerant organisms, as well as the discovery of novel antimicrobials. Traditionally, susceptibility to antimicrobials is assessed by broth micro-dilution or disk diffusion assays, both of which are time-consuming, labor-intensive, and provide limited information on the mode of action of the antimicrobials. The abovementioned limitations highlight the need for the development of new methods to monitor and further understand antimicrobial susceptibility. In this study, we used real-time flow cytometry, combined with membrane permeability staining, as a quick and sensitive technology to study the quantitative and qualitative responses of two oral pathobionts to different concentrations of chlorhexidine (CHX), cetylpyridinium chloride (CPC), or triclosan. Apart from the real-time monitoring of cell damage, we further applied a phenotypic fingerprinting method to differentiate between the bacterial subpopulations that arose due to treatment. We quantified the pathobiont damage rate of different antiseptics at different concentrations within 15 minutes of exposure and identified the conditions under which the bacteria were most susceptible. Moreover, we detected species-specific and treatment-specific phenotypic subpopulations. This proves that real-time flow cytometry can provide information on the susceptibility of different microorganisms in a short time frame while differentiating between antiseptics and thus could be a valuable tool in the discovery of novel antimicrobial compound, while at the same time deciphering their mode of action.<br><br>IMPORTANCE: With increasing evidence that microorganisms are becoming more tolerant to standard antimicrobials, faster and more accessible antimicrobial susceptibility testing methods are needed. However, traditional susceptibility assays are laborious and time-consuming. To overcome the abovementioned limitations, we introduce a novel approach to define antimicrobial susceptibility in a much shorter time frame with the use of real-time flow cytometry. Furthermore, phenotypic fingerprinting analysis can be applied on the data to study the way antiseptics affect the bacterial cell morphology over time and, thus, gain information on the mode of action of a certain compound.}, }
@article {pmid39162262, year = {2024}, author = {Liu, M and Li, Q and Xu, W and Wang, L and Wu, F and Tan, L and Li, L and Zhang, G}, title = {Characterization of water microbiota and their relationship with resident oysters during an oyster mortality event.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0288123}, pmid = {39162262}, issn = {2165-0497}, support = {2022YFD2400304//National Key R&amp;D Program of China/ ; 2022LZGC015//Key Research and Development Program of Shandong/ ; ZFJH202309//Key Research and Development Program of Shandong/ ; CARS-49//Earmarked Fund for CARS/ ; }, mesh = {Animals ; *Microbiota/physiology ; *Ostreidae/microbiology ; *Water Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Seawater/microbiology ; Cyanobacteria/genetics/physiology/growth &amp; development ; Temperature ; }, abstract = {Microorganisms are vital for the health of marine invertebrates, and their assembly is driven by both deterministic and stochastic factors that regulate residents (innate to the host) and transients (from ambient water). However, the role of water microbiota and the significance of deterministic and stochastic processes in aquatic hosts facing mortality threats are largely unknown. This study examines the shifts in water microbiota during an oyster mortality event using amplicon sequencing and compared with those of resident oysters to disentangle the balance of the deterministic and stochastic factors involved. Water temperature and dissolved oxygen significantly shape the microbial community with a distinct monthly pattern, and Cyanobacteria blooms might exacerbate oyster mortality. The comparative analysis of microbial communities in oysters and water revealed that ≤ 21% of the genera were shared between oysters and water, implying that water microbiota cannot easily transfer into oysters. Furthermore, these shared genera had different functions, with oysters more involved in promoting host digestion and nutrient acquisition and water bacteria enriched more in functions promoting their own growth and survival. These findings illustrate that oysters may possess specific selection or barrier mechanisms that permit a small percentage of transients, controlled by stochastic factors and having a minimal effect on oyster mortality, to enter, whereas the majority of oyster microbiota are residents governed by deterministic factors. Consequently, oysters exhibit some plasticity in their symbiotic microbiota, enabling them to maintain microbial homeostasis and adapt to complex microbial surroundings. This may be a shared mechanism among marine invertebrates for survival in complex marine environments.IMPORTANCEPacific oysters are widely cultured and play vital ecological roles. However, the summer mortality hinders sustainable oyster farming. Untangling causative mechanisms of oyster mortality is a complex task due to the intricate "interactome" involving environmental factors, hosts, and pathogens. Interactions between hosts and microorganisms offer an ideal avenue for investigating the truth. We systematically investigated the microbial community in water and resident oysters during a summer mortality event and proposed that the assembly of oyster microbiota is primarily governed by deterministic processes independent of mortality. Pathogens mainly originate from resident members of the oyster microbiota, with a limited influence from the microbial community in the water. Additionally, environmental degraders, such as Cyanobacteria blooms, cannot be overlooked as a contributing factor of oyster mortality. This study evaluated the weight of deterministic and stochastic factors in microbial assembly during an oyster mortality event and greatly broadened our understanding of the "interactome" through the interaction between oysters and water in microbiota.}, }
@article {pmid39161630, year = {2024}, author = {Blázquez, M and Pérez-Vargas, I and Garrido-Benavent, I and Villar-dePablo, M and Turégano, Y and Frías-López, C and Sánchez-Gracia, A and de Los Ríos, A and Gasulla, F and Pérez-Ortega, S}, title = {Endless forms most frustrating: disentangling species boundaries in the Ramalina decipiens group (Lecanoromycetes, Ascomycota), with the description of six new species and a key to the group.}, journal = {Persoonia}, volume = {52}, number = {}, pages = {44-93}, pmid = {39161630}, issn = {0031-5850}, abstract = {Oceanic islands have been recognized as natural laboratories in which to study a great variety of evolutionary processes. One such process is evolutionary radiations, the diversification of a single ancestor into a number of species that inhabit different environments and differ in the traits that allow them to exploit those environments. The factors that drive evolutionary radiations have been studied for decades in charismatic organisms such as birds or lizards, but are lacking in lichen-forming fungi, despite recent reports of some lineages showing diversification patterns congruent with radiation. Here we propose the Ramalina decipiens group as a model system in which to carry out such studies. This group is currently thought to be comprised of five saxicolous species, all of them endemic to the Macaronesian region (the Azores, Madeira, Selvagens, Canary and Cape Verde islands). Three species are single-island endemics (a rare geographic distribution pattern in lichens), whereas two are widespread and show extreme morphological variation. The latter are suspected to harbor unrecognized species-level lineages. In order to use the Ramalina decipiens group as a model system it is necessary to resolve the group's phylogeny and to clarify its species boundaries. In this study we attempt to do so following an integrative taxonomy approach. We constructed a phylogenetic tree based on six molecular markers, four of which are newly developed and generated competing species hypotheses based on molecular (species discovery strategies based on both single locus and multilocus datasets) and phenotypic data (unsupervised clustering algorithms based on morphology, secondary chemistry and geographic origin). We found that taxonomic diversity in the Ramalina decipiens group has been highly underestimated in previous studies. In consequence, we describe six new species, most of them single-island endemics and provide a key to the group. Phylogenetic relationships among species have been reconstructed with almost full support which, coupled with the endemic character of the group, makes it an excellent system for the study of island radiations in lichen-forming fungi. Citation: Blázquez M, Pérez-Vargas I, Garrido-Benavent I, et al. 2024. Endless forms most frustrating: disentangling species boundaries in the Ramalina decipiens group (Lecanoromycetes, Ascomycota), with the description of six new species and a key to the group. Persoonia 52: 44-93. https://doi.org/10.3767/persoonia.2024.52.03 .}, }
@article {pmid39160591, year = {2024}, author = {Lee, H and Hwang, K and Cho, A and Kim, S and Kim, M and Morgan-Kiss, R and Priscu, JC and Kim, KM and Kim, OS}, title = {Microbial assemblages and associated biogeochemical processes in Lake Bonney, a permanently ice-covered lake in the McMurdo Dry Valleys, Antarctica.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {60}, pmid = {39160591}, issn = {2524-6372}, support = {PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; OPP 1637708//National Science Foundation/ ; OPP 1637708//National Science Foundation/ ; }, abstract = {BACKGROUND: Lake Bonney, which is divided into a west lobe (WLB) and an east lobe (ELB), is a perennially ice-covered lake located in the McMurdo Dry Valleys of Antarctica. Despite previous reports on the microbial community dynamics of ice-covered lakes in this region, there is a paucity of information on the relationship between microbial genomic diversity and associated nutrient cycling. Here, we applied gene- and genome-centric approaches to investigate the microbial ecology and reconstruct microbial metabolic potential along the depth gradient in Lake Bonney.<br><br>RESULTS: Lake Bonney is strongly chemically stratified with three distinct redox zones, yielding different microbial niches. Our genome enabled approach revealed that in the sunlit and relatively freshwater epilimnion, oxygenic photosynthetic production by the cyanobacterium Pseudanabaena and a diversity of protists and microalgae may provide new organic carbon to the environment. CO-oxidizing bacteria, such as Acidimicrobiales, Nanopelagicales, and Burkholderiaceae were also prominent in the epilimnion and their ability to oxidize carbon monoxide to carbon dioxide may serve as a supplementary energy conservation strategy. In the more saline metalimnion of ELB, an accumulation of inorganic nitrogen and phosphorus supports photosynthesis despite relatively low light levels. Conversely, in WLB the release of organic rich subglacial discharge from Taylor Glacier into WLB would be implicated in the possible high abundance of heterotrophs supported by increased potential for glycolysis, beta-oxidation, and glycoside hydrolase and may contribute to the growth of iron reducers in the dark and extremely saline hypolimnion of WLB. The suboxic and subzero temperature zones beneath the metalimnia in both lobes supported microorganisms capable of utilizing reduced nitrogens and sulfurs as electron donors. Heterotrophs, including nitrate reducing sulfur oxidizing bacteria, such as Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), and denitrifying bacteria, such as Gracilimonas (MAG7), Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), dominated the hypolimnion of WLB, whereas the environmental harshness of the hypolimnion of ELB was supported by the relatively low in metabolic potential, as well as the abundance of halophile Halomonas and endospore-forming Virgibacillus.<br><br>CONCLUSIONS: The vertical distribution of microbially driven C, N and S cycling genes/pathways in Lake Bonney reveals the importance of geochemical gradients to microbial diversity and biogeochemical cycles with the vertical water column.}, }
@article {pmid39159439, year = {2024}, author = {Dos Santos, A and Schultz, J and Almeida Trapp, M and Modolon, F and Romanenko, A and Kumar Jaiswal, A and Gomes, L and Rodrigues-Filho, E and Rosado, AS}, title = {Investigating Polyextremophilic Bacteria in Al Wahbah Crater, Saudi Arabia: A Terrestrial Model for Life on Saturn's Moon Enceladus.}, journal = {Astrobiology}, volume = {24}, number = {8}, pages = {824-838}, doi = {10.1089/ast.2024.0017}, pmid = {39159439}, issn = {1557-8070}, mesh = {Saudi Arabia ; *Exobiology/methods ; *Extraterrestrial Environment ; Genome, Bacterial/genetics ; Mars ; Bacteria/genetics/isolation &amp; purification ; Phylogeny ; }, abstract = {The study of extremophilic microorganisms has sparked interest in understanding extraterrestrial microbial life. Such organisms are fundamental for investigating life forms on Saturn's icy moons, such as Enceladus, which is characterized by potentially habitable saline and alkaline niches. Our study focused on the salt-alkaline soil of the Al Wahbah crater in Saudi Arabia, where we identified microorganisms that could be used as biological models to understand potential life on Enceladus. The search involved isolating 48 bacterial strains, sequencing the genomes of two thermo-haloalkaliphilic strains, and characterizing them for astrobiological application. A deeper understanding of the genetic composition and functional capabilities of the two novel strains of Halalkalibacterium halodurans provided valuable insights into their survival strategies and the presence of coding genes and pathways related to adaptations to environmental stressors. We also used mass spectrometry with a molecular network approach, highlighting various classes of molecules, such as phospholipids and nonproteinogenic amino acids, as potential biosignatures. These are essential features for understanding life's adaptability under extreme conditions and could be used as targets for biosignatures in upcoming missions exploring Enceladus' orbit. Furthermore, our study reinforces the need to look at new extreme environments on Earth that might contribute to the astrobiology field.}, }
@article {pmid39158314, year = {2024}, author = {Guéneau, V and Jiménez, G and Castex, M and Briandet, R}, title = {Insights into the genomic and phenotypic characteristics of Bacillus spp. strains isolated from biofilms in broiler farms.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {9}, pages = {e0066324}, pmid = {39158314}, issn = {1098-5336}, support = {2020/0548//Association Nationale de la Recherche et de la Technologie (ANRT)/ ; }, mesh = {*Genome, Bacterial ; *Phenotype ; *Bacillus/genetics/isolation &amp; purification ; *Biofilms ; *Chickens/microbiology ; Animals ; *Farms ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Biosynthetic Pathways/genetics ; Multigene Family ; Phylogeny ; Livestock/microbiology ; DNA, Bacterial/genetics ; Deoxyribonuclease I/metabolism ; }, abstract = {The characterization of surface microbiota living in biofilms within livestock buildings has been relatively unexplored, despite its potential impact on animal health. To enhance our understanding of these microbial communities, we characterized 11 spore-forming strains isolated from two commercial broiler chicken farms. Sequencing of the strains revealed them to belong to three species Bacillus velezensis, Bacillus subtilis, and Bacillus licheniformis. Genomic analysis revealed the presence of antimicrobial resistance genes and genes associated with antimicrobial secretion specific to each species. We conducted a comprehensive characterization of the biofilm formed by these strains under various conditions, and we revealed significant structural heterogeneity across the different strains. A macro-colony interaction model was employed to assess the compatibility of these strains to coexist in mixed biofilms. We identified highly competitive B. velezensis strains, which cannot coexist with other Bacillus spp. Using confocal laser scanning microscopy along with a specific dye for extracellular DNA, we uncovered the importance of extracellular DNA for the formation of B. licheniformis biofilms. Altogether, the results highlight the heterogeneity in both genome and biofilm structure among Bacillus spp. isolated from biofilms present within livestock buildings.IMPORTANCELittle is known about the microbial communities that develop on farms in direct contact with animals. Nonpathogenic strains of Bacillus velezensis, Bacillus subtilis, and Bacillus licheniformis were found in biofilm samples collected from surfaces in contact with animals. Significant genetic and phenotypic diversity was described among these Bacillus strains. The strains do not possess mobile antibiotic resistance genes in their genomes and have a strong capacity to form structured biofilms. Among these species, B. velezensis was noted for its high competitiveness compared with the other Bacillus spp. Additionally, the importance of extracellular DNA in the formation of B. licheniformis biofilms was observed. These findings provide insights for the management of these surface microbiota that can influence animal health, such as the use of competitive strains to minimize the establishment of undesirable bacteria or enzymes capable of specifically deconstructing biofilms.}, }
@article {pmid39157765, year = {2024}, author = {de Santana, CO and Spealman, P and Oliveira, E and Gresham, D and de Jesus, T and Chinalia, F}, title = {Prokaryote communities along a source-to-estuary river continuum in the Brazilian Atlantic Forest.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17900}, pmid = {39157765}, issn = {2167-8359}, mesh = {Brazil ; *Rivers/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Geologic Sediments/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; Forests ; Estuaries ; Biodiversity ; Archaea/genetics/classification/isolation &amp; purification ; Microbiota ; }, abstract = {The activities of microbiomes in river sediments play an important role in sustaining ecosystem functions by driving many biogeochemical cycles. However, river ecosystems are frequently affected by anthropogenic activities, which may lead to microbial biodiversity loss and/or changes in ecosystem functions and related services. While parts of the Atlantic Forest biome stretching along much of the eastern coast of South America are protected by governmental conservation efforts, an estimated 89% of these areas in Brazil are under threat. This adds urgency to the characterization of prokaryotic communities in this vast and highly diverse biome. Here, we present prokaryotic sediment communities in the tropical Juliana River system at three sites, an upstream site near the river source in the mountains (Source) to a site in the middle reaches (Valley) and an estuarine site near the urban center of Ituberá (Mangrove). The diversity and composition of the communities were compared at these sites, along with environmental conditions, the former by using qualitative and quantitative analyses of 16S rRNA gene amplicons. While the communities included distinct populations at each site, a suite of core taxa accounted for the majority of the populations at all sites. Prokaryote diversity was highest in the sediments of the Mangrove site and lowest at the Valley site. The highest number of genera exclusive to a given site was found at the Source site, followed by the Mangrove site, which contained some archaeal genera not present at the freshwater sites. Copper (Cu) concentrations were related to differences in communities among sites, but none of the other environmental factors we determined was found to have a significant influence. This may be partly due to an urban imprint on the Mangrove site by providing organic carbon and nutrients via domestic effluents.}, }
@article {pmid39155010, year = {2024}, author = {Wong, LC and Rodenburg, U and Leite, RR and Korthals, GW and Pover, J and Koerten, H and Kuramae, EE and Bodelier, PLE}, title = {Exploring microbial diversity and interactions for asbestos modifying properties.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175577}, doi = {10.1016/j.scitotenv.2024.175577}, pmid = {39155010}, issn = {1879-1026}, mesh = {*Biodegradation, Environmental ; *Bacteria/metabolism/classification ; Fungi/metabolism ; Asbestos ; Soil Microbiology ; Iron/metabolism ; Asbestos, Serpentine ; }, abstract = {Asbestos poses a substantial environmental health risk, and biological treatment offers a promising approach to mitigate its impact by altering its chemical composition. However, the dynamics of microbial co-inoculation in asbestos bioremediation remain poorly understood. This study investigates the effect of microbial single cultures and co-cultures on modifying crocidolite and chrysotile fibers, focusing on the extraction of iron and magnesium. Seventy bacterial and eighty-three fungal strains were isolated from five diverse sites, characterized phylogenetically using the 16S rRNA gene and ITS region, respectively, and assessed for siderophore and organic acid production. Most bacterial strains were identified as Pseudomonas, while Penicillium predominated among fungal strains. Ten bacterial and 25 fungal strains were found to produce both organic compounds. Four microbial co-cultures (one bacterium-bacterium, two fungus-bacterium, and one fungus-fungus) exhibiting synergistic effects in plate assays, alongside their respective single cultures, were incubated with crocidolite and chrysotile. ICP-OES analysis revealed that in crocidolite, the co-culture HRF19-HRB12 removed more iron than their single cultures, while Penicillium TPF36 showed the highest iron removal. The co-culture of two Pseudomonas strains (HRB12-RB5) exhibited the highest magnesium concentration in the supernatant. In chrysotile, the co-culture HRB12-RB5 removed more iron than their individual cultures, with Penicillium TFSF27 exhibiting the highest iron concentration in the solution. Penicillium TFSF27 and the co-culture TFSF27-TPF36 demonstrated the highest magnesium removal. SEM-XRMA analysis showed a significant reduction in iron and magnesium content, confirming elemental extraction from the fibers' structure. This study significantly broadens the range of microbial strains capable of modifying asbestos fibers and underscores the potential of microbial co-cultures in asbestos remediation.}, }
@article {pmid39150265, year = {2024}, author = {Longhi, G and Lugli, GA and Tarracchini, C and Fontana, F and Bianchi, MG and Carli, E and Bussolati, O and van Sinderen, D and Turroni, F and Ventura, M}, title = {From raw milk cheese to the gut: investigating the colonization strategies of Bifidobacterium mongoliense.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {9}, pages = {e0124424}, pmid = {39150265}, issn = {1098-5336}, support = {PE00000003//National Recovery and Resilience Plan (NRRP)/ ; SFI/12/RC/2273a//Irish Government's National Development Plan/ ; SFI/12/RC/2273b//Irish Government's National Development Plan/ ; }, mesh = {*Cheese/microbiology ; *Bifidobacterium/genetics/metabolism/growth &amp; development ; Humans ; *Milk/microbiology ; *Gastrointestinal Microbiome ; Animals ; Italy ; }, abstract = {The microbial ecology of raw milk cheeses is determined by bacteria originating from milk and milk-producing animals. Recently, it has been shown that members of the Bifidobacterium mongoliense species may become transmitted along the Parmigiano Reggiano cheese production chain and ultimately may colonize the consumer intestine. However, there is a lack of knowledge regarding the molecular mechanisms that mediate the interaction between B. mongoliense and the human gut. Based on 128 raw milk cheeses collected from different Italian regions, we isolated and characterized 10 B. mongoliense strains. Comparative genomics allowed us to unveil the presence of enzymes required for the degradation of sialylated host-glycans in B. mongoliense, corroborating the appreciable growth on de Man-Rogosa-Sharpe (MRS) medium supplemented with 3'-sialyllactose (3'-SL) or 6'-sialyllactose (6'-SL). The B. mongoliense BMONG18 was chosen, due to its superior ability to utilize 3'-SL and mucin as representative strain, to investigate its behavior when co-inoculated with other bifidobacterial species. Conversely, members of other bifidobacterial species did not appear to benefit from the presence of BMONG18, highlighting a competitive scenario for nutrient acquisition. Transcriptomic data of BMONG18 reveal no significant differences in gene expression when cultivated in a gut simulating medium (GSM), regardless of whether cheese was included or not. Furthermore, BMONG18 was shown to exhibit high adhesion capabilities to HT29-MTX human cells, in line with its colonization ability of a human host.IMPORTANCEFermented foods are nourishments produced through controlled microbial growth that play an essential role in worldwide human nutrition. Research interest in fermented foods has increased since the 80s, driven by growing awareness of their potential health benefits beyond mere nutritional content. Bifidobacterium mongoliense, previously identified throughout the production process of Parmigiano Reggiano cheese, was found to be capable of establishing itself in the intestines of its consumers. Our study underscores molecular mechanisms through which this bifidobacterial species, derived from food, interacts with the host and other gut microbiota members.}, }
@article {pmid39150230, year = {2024}, author = {Li, J and Yang, X and Zhang, X and Zhang, L}, title = {Effects and mechanisms of microbial ecology and diversity on phytoremediation of cadmium-contaminated soil under the influence of biodegradable organic acids.}, journal = {International journal of phytoremediation}, volume = {26}, number = {14}, pages = {2392-2403}, doi = {10.1080/15226514.2024.2391025}, pmid = {39150230}, issn = {1549-7879}, mesh = {*Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Cadmium/metabolism ; *Bacillus megaterium/metabolism ; *Soil Microbiology ; *Lolium/metabolism ; Rhizosphere ; Citric Acid/metabolism ; Bacteria/metabolism ; }, abstract = {In recent years, heavy metal pollution has become a global environmental problem and poses a great threat to the health of people and ecosystems. Therefore, strategies for the effective remediation of Cd from contaminated soil are urgently needed. In this study, ryegrass was utilized as a remediation plant, and its remediation potential was enhanced through the application of Citric Acid (CA) in conjunction with Bacillus megaterium (B. megaterium). The P3 treatment (CA + Bacillus megaterium) exhibited a significantly higher efficiency in promoting cadmium extraction by ryegrass, resulting in a 1.79-fold increase in shoot cadmium accumulation compared to the control group (CK) with no Bacillus megaterium or CA. Moreover, the P3 treatment led to an increased abundance of Actinobacteriota, Acidobacteriota, and Patescibacteria in the rhizosphere. The concentration of amino derivatives (such as betaine, sulfolithocholylglycine, N-alpha-acetyl-lysine, glycocholic acid, arginyl-threonine) showed significant upregulation following the P3 treatment. In summary, this study proposes a viable approach for phytoremediation of soil contaminated with cadmium by harnessing the mobilizing abilities of soil bacteria.}, }
@article {pmid39148674, year = {2024}, author = {Dyczko, D and Błażej, P and Kiewra, D}, title = {The influence of forest habitat type on Ixodes ricinus infections with Rickettsia spp. in south-western Poland.}, journal = {Current research in parasitology &amp; vector-borne diseases}, volume = {6}, number = {}, pages = {100200}, pmid = {39148674}, issn = {2667-114X}, abstract = {This study investigates the prevalence of Rickettsia spp. in Ixodes ricinus tick populations in different forest habitat types (broadleaf forest, mixed broadleaf and coniferous forest, and coniferous forest) in south-western Poland. During the survey periods from April to June 2018 and 2019 a total of 494 I. ricinus ticks, including 374 nymphs, 60 females and 60 males, were tested for Rickettsia infections by nested PCR targeting the gltA gene. The overall infection rate was 42.3%; however, we observed statistically significant year-to-year variation. Infection rates varied between tick developmental stages and were significantly influenced by forest habitat type. As assessed by a generalized linear mixed model (GLMM), the highest infection rates were observed in mixed broadleaf and coniferous forests, while coniferous forests had a significant negative effect on infection prevalence. DNA sequencing of selected samples confirmed the predominance of Rickettsia helvetica (91.2%) and less frequent Rickettsia monacensis (8.8%). This study suggests that the forest habitat types can influence Rickettsia spp. infection in tick populations; however, a comprehensive understanding of all factors influencing the level of infection requires future study.}, }
@article {pmid39143010, year = {2024}, author = {Ozbayram, EG and Kleinsteuber, S and Sträuber, H and Schroeder, BG and da Rocha, UN and Corrêa, FB and Harms, H and Nikolausz, M}, title = {Three-domain microbial communities in the gut of Pachnoda marginata larvae: A comparative study revealing opposing trends in gut compartments.}, journal = {Environmental microbiology reports}, volume = {16}, number = {4}, pages = {e13324}, pmid = {39143010}, issn = {1758-2229}, mesh = {Animals ; *Larva/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Eukaryota/classification/genetics/isolation &amp; purification ; Phylogeny ; Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {This study aimed to examine the bacterial, methanogenic archaeal, and eukaryotic community structure in both the midgut and hindgut of Pachnoda marginata larvae using an amplicon sequencing approach. The goal was to investigate how various diets and the soil affect the composition of these three-domain microbial communities within the gut of insect larvae. The results indicated a notable variation in the microbial community composition among the gut compartments. The majority of the bacterial community in the hindgut was composed of Ruminococcaceae and Christensenellaceae. Nocardiaceae, Microbacteriaceae, and Lachnospiraceae were detected in midgut samples from larvae feeding on the leaf diet, whereas Sphingomonadaceae, Rhodobacteraceae, and Promicromonasporaceae dominated the bacterial community of midgut of larvae feeding on the straw diet. The diet was a significant factor that influenced the methanogenic archaeal and eukaryotic community patterns. The methanogenic communities in the two gut compartments significantly differed from each other, with the midgut communities being more similar to those in the soil. A higher diversity of methanogens was observed in the midgut samples of both diets compared to the hindgut. Overall, the microbiota of the hindgut was more host-specific, while the assembly of the midgut was more influenced by the environmental microorganisms.}, }
@article {pmid39142044, year = {2024}, author = {Battulga, B and Nakayama, M and Matsuoka, S and Kondo, T and Atarashi-Andoh, M and Koarashi, J}, title = {Dynamics and functions of microbial communities in the plastisphere in temperate coastal environments.}, journal = {Water research}, volume = {264}, number = {}, pages = {122207}, doi = {10.1016/j.watres.2024.122207}, pmid = {39142044}, issn = {1879-2448}, mesh = {*Biofilms ; *Bacteria/genetics/classification ; Fungi/genetics ; Microbiota ; Microplastics ; Japan ; Geologic Sediments/microbiology ; Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbial attachment and biofilm formation on microplastics (MPs <5 mm in size) in the environment have received growing attention. However, there is limited knowledge of microbial function and their effect on the properties and behavior of MPs in the environment. In this study, microbial communities in the plastisphere were explored to understand microbial ecology as well as their impact on aquatic ecosystems. Using the amplicon sequencing of 16S and internal transcribed spacer (ITS) genes, we uncovered the composition and diversity of bacterial and fungal communities in samples of MPs (fiber, film, foam, and fragment), surface water, bottom sediment, and coastal sand in two contrasting coastal areas of Japan. Differences in microbial diversity and taxonomic composition were detected depending on sample type (MPs, water, sediment, and sand) and the research site. Although relatively higher bacterial and fungal gene counts were determined in MP fragments and foams from the research sites, there were no significant differences in microbial community composition depending on the morphotypes of MPs. Given the colonization by hydrocarbon-degrading communities and the presence of pathogens on MPs, the complex processes of microbial taxa influence the characteristics of MP-associated biofilms, and thus, the properties of MPs. This study highlights the metabolic functions of microbes in MP-associated biofilms, which could be key to uncovering the true impact of plastic debris on the global ecosystem.}, }
@article {pmid39141295, year = {2024}, author = {Turbant, F and Blache, A and Węgrzyn, G and Achouak, W and Wien, F and Arluison, V}, title = {Use of Synchrotron Radiation Circular Dichroism to Analyze the Interaction and Insertion of Proteins into Bacterial Outer Membrane Vesicles.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2843}, number = {}, pages = {73-94}, pmid = {39141295}, issn = {1940-6029}, mesh = {*Circular Dichroism/methods ; *Synchrotrons ; *Bacterial Outer Membrane Proteins/chemistry/metabolism ; Bacterial Outer Membrane/metabolism/chemistry ; Protein Structure, Secondary ; Lipid Bilayers/metabolism/chemistry ; }, abstract = {Circular dichroism (CD) is a spectroscopic technique commonly used for the analysis of proteins. Particularly, it allows the determination of protein secondary structure content in various media, including the membrane environment. In this chapter, we present how CD applications can be used to analyze the interaction of proteins with bacterial outer membrane vesicles (OMVs). Most CD studies characterizing the structure of proteins inserted into membranes rely on artificial lipid bilayers, mimicking natural membranes. Nevertheless, these artificial models lack the important features of the true membrane, especially for the outer membrane of Gram-negative bacteria. These features include lipid diversity, glycosylation, and asymmetry. Here, we show how to analyze the interactions of proteins, either integral or peripheral, with OMVs in solution and with supported membranes of OMVs, using conventional CD and orientated circular dichroism (OCD). We explain how to decipher the spectroscopic signals to obtain information on the molecular structure of the protein upon its interaction with an OMV and through its potential insertion into an OMV membrane.}, }
@article {pmid39141097, year = {2024}, author = {Papazachariou, V and Fernández-Juárez, V and Parfrey, LW and Riemann, L}, title = {Nitrogen Fixation and Microbial Communities Associated with Decomposing Seagrass Leaves in Temperate Coastal Waters.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {106}, pmid = {39141097}, issn = {1432-184X}, mesh = {*Nitrogen Fixation ; *Plant Leaves/microbiology ; *Seawater/microbiology/chemistry ; *Microbiota ; *Zosteraceae/microbiology/metabolism ; Nitrogen/metabolism/analysis ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Denmark ; Cyanobacteria/metabolism/genetics/classification/isolation &amp; purification ; }, abstract = {Seagrass meadows play pivotal roles in coastal biochemical cycles, with nitrogen fixation being a well-established process associated with living seagrass. Here, we tested the hypothesis that nitrogen fixation is also associated with seagrass debris in Danish coastal waters. We conducted a 52-day in situ experiment to investigate nitrogen fixation (proxied by acetylene reduction) and dynamics of the microbial community (16S rRNA gene amplicon sequencing) and the nitrogen fixing community (nifH DNA/RNA amplicon sequencing) associated with decomposing Zostera marina leaves. The leaves harboured distinct microbial communities, including distinct nitrogen fixers, relative to the surrounding seawater and sediment throughout the experiment. Nitrogen fixation rates were measurable on most days, but highest on days 3 (dark, 334.8 nmol N g[-1] dw h[-1]) and 15 (light, 194.6 nmol N g[-1] dw h[-1]). Nitrogen fixation rates were not correlated with the concentration of inorganic nutrients in the surrounding seawater or with carbon:nitrogen ratios in the leaves. The composition of nitrogen fixers shifted from cyanobacterial Sphaerospermopsis to heterotrophic genera like Desulfopila over the decomposition period. On the days with highest fixation, nifH RNA gene transcripts were mainly accounted for by cyanobacteria, in particular by Sphaerospermopsis and an unknown taxon (order Nostocales), alongside Proteobacteria. Our study shows that seagrass debris in temperate coastal waters harbours substantial nitrogen fixation carried out by cyanobacteria and heterotrophic bacteria that are distinct relative to the surrounding seawater and sediments. This suggests that seagrass debris constitutes a selective environment where degradation is affected by the import of nitrogen via nitrogen fixation.}, }
@article {pmid39140100, year = {2024}, author = {Crous, PW and Jurjević, &#x17d; and Balashov, S and De la Peña-Lastra, S and Mateos, A and Pinruan, U and Rigueiro-Rodríguez, A and Osieck, ER and Altés, A and Czachura, P and Esteve-Raventós, F and Gunaseelan, S and Kaliyaperumal, M and Larsson, E and Luangsa-Ard, JJ and Moreno, G and Pancorbo, F and Piątek, M and Sommai, S and Somrithipol, S and Asif, M and Delgado, G and Flakus, A and Illescas, T and Kezo, K and Khamsuntorn, P and Kubátová, A and Labuda, R and Lavoise, C and Lebel, T and Lueangjaroenkit, P and Maciá-Vicente, JG and Paz, A and Saba, M and Shivas, RG and Tan, YP and Wingfield, MJ and Aas, T and Abramczyk, B and Ainsworth, AM and Akulov, A and Alvarado, P and Armada, F and Assyov, B and Avchar, R and Avesani, M and Bezerra, JL and Bhat, JD and Bilański, P and Bily, DS and Boccardo, F and Bozok, F and Campos, JC and Chaimongkol, S and Chellappan, N and Costa, MM and Dalecká, M and Darmostuk, V and Daskalopoulos, V and Dearnaley, J and Dentinger, BTM and De Silva, NI and Dhotre, D and Carlavilla, JR and Doungsa-Ard, C and Dovana, F and Erhard, A and Ferro, LO and Gallegos, SC and Giles, CE and Gore, G and Gorfer, M and Guard, FE and Hanson, S&#xc5; and Haridev, P and Jankowiak, R and Jeffers, SN and Kandemir, H and Karich, A and Kisło, K and Kiss, L and Krisai-Greilhuber, I and Latha, KPD and Lorenzini, M and Lumyong, S and Manimohan, P and Manjón, JL and Maula, F and Mazur, E and Mesquita, NLS and Młynek, K and Mongkolsamrit, S and Morán, P and Murugadoss, R and Nagarajan, M and Nalumpang, S and Noisripoom, W and Nosalj, S and Novaes, QS and Nowak, M and Pawłowska, J and Peiger, M and Pereira, OL and Pinto, A and Plaza, M and Polemis, E and Polhorský, A and Ramos, DO and Raza, M and Rivas-Ferreiro, M and Rodriguez-Flakus, P and Ruszkiewicz-Michalska, M and Sánchez, A and Santos, A and Schüller, A and Scott, PA and Şen, I and Shelke, D and Śliwa, L and Solheim, H and Sonawane, H and Strašiftáková, D and Stryjak-Bogacka, M and Sudsanguan, M and Suwannarach, N and Suz, LM and Syme, K and Taşkın, H and Tennakoon, DS and Tomka, P and Vaghefi, N and Vasan, V and Vauras, J and Wiktorowicz, D and Villarreal, M and Vizzini, A and Wrzosek, M and Yang, X and Yingkunchao, W and Zapparoli, G and Zervakis, GI and Groenewald, JZ}, title = {Fungal Planet description sheets: 1614-1696.}, journal = {Fungal systematics and evolution}, volume = {13}, number = {}, pages = {183-440}, pmid = {39140100}, issn = {2589-3831}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Baobabopsis sabindy in leaves of Eragrostis spartinoides, Cortinarius magentiguttatus among deep leaf litter, Laurobasidium azarandamiae from uredinium of Puccinia alyxiae on Alyxia buxifolia, Marasmius pseudoelegans on well-rotted twigs and litter in mixed wet sclerophyll and subtropical rainforest. Bolivia, Favolaschia luminosa on twigs of Byttneria hirsuta, Lecanora thorstenii on bark, in savannas with shrubs and trees. Brazil, Asterina costamaiae on leaves of Rourea bahiensis, Purimyces orchidacearum (incl. Purimyces gen. nov.) as root endophyte on Cattleya locatellii. Bulgaria, Monosporascus bulgaricus and Monosporascus europaeus isolated from surface-sterilised, asymptomatic roots of Microthlaspi perfoliatum. Finland, Inocybe undatolacera on a lawn, near Betula pendula. France, Inocybe querciphila in humus of mixed forest. Germany, Arrhenia oblongispora on bare soil attached to debris of herbaceous plants and grasses. Greece, Tuber aereum under Quercus coccifera and Acer sempervirens. India, Alfoldia lenyadriensis from the gut of a Platynotus sp. beetle, Fulvifomes subramanianii on living Albizzia amara, Inosperma pavithrum on soil, Phylloporia parvateya on living Lonicera sp., Tropicoporus maritimus on living Peltophorum pterocarpum. Indonesia, Elsinoe atypica on leaf of Eucalyptus pellita. Italy, Apiotrichum vineum from grape wine, Cuphopyllus praecox among grass. Madagascar, Pisolithus madagascariensis on soil under Intsia bijuga. Netherlands, Cytosporella calamagrostidis and Periconia calamagrostidicola on old leaves of Calamagrostis arenaria, Hyaloscypha caricicola on leaves of Carex sp., Neoniesslia phragmiticola (incl. Neoniesslia gen. nov.) on leaf sheaths of standing dead culms of Phragmites australis, Neptunomyces juncicola on culms of Juncus maritimus, Zenophaeosphaeria calamagrostidis (incl. Zenophaeosphaeria gen. nov.) on culms of Calamagrostis arenaria. Norway, Hausneria geniculata (incl. Hausneria gen. nov.) from a gallery of Dryocoetes alni on Alnus incana. Pakistan, Agrocybe auriolus on leaf litter of Eucalyptus camaldulensis, Rhodophana rubrodisca in nutrient-rich loamy soil with Morus alba. Poland, Cladosporium nubilum from hypersaline brine, Entomortierella ferrotolerans from soil at mines and postmining sites, Pseudopezicula epiphylla from sooty mould community on Quercus robur, Quixadomyces sanctacrucensis from resin of Pinus sylvestris, Szafranskia beskidensis (incl. Szafranskia gen. nov.) from resin of Abies alba. Portugal, Ascocoryne laurisilvae on degraded wood of Laurus nobilis, Hygrocybe madeirensis in laurel forests, Hygrocybula terracocta (incl. Hygrocybula gen. nov.) on mossy areas of laurel forests planted with Cryptomeria japonica. Republic of Kenya, Penicillium gorferi from a sterile chicken feather embedded in a soil sample. Slovakia, Cerinomyces tatrensis on bark of Pinus mugo, Metapochonia simonovicovae from soil. South Africa, Acremonium agapanthi on culms of Agapanthus praecox, Alfaria elegiae on culms of Elegia ebracteata, Beaucarneamyces stellenboschensis (incl. Beaucarneamyces gen. nov.) on dead leaves of Beaucarnea stricta, Gardeniomyces kirstenboschensis (incl. Gardeniomyces gen. nov.) rotting fruit of Gardenia thunbergia, Knufia dianellae on dead leaves of Dianella caerulea, Lomaantha quercina on twigs of Quercus suber. Melanina restionis on dead leaves of Restio duthieae, Microdochium buffelskloofinum on seeds of Eragrostis cf. racemosa, Thamnochortomyces kirstenboschensis (incl. Thamnochortomyces gen. nov.) on culms of Thamnochortus fraternus, Tubeufia hagahagana on leaves of Hypoxis angustifolia, Wingfieldomyces cypericola on dead leaves of Cyperus papyrus. Spain, Geastrum federeri in soil under Quercus suber and Q. canariensis, Geastrum nadalii in calcareous soil under Juniperus, Quercus, Cupressus, Pinus and Robinia, Hygrocybe garajonayensis in laurel forests, Inocybe cistophila on acidic soil under Cistus ladanifer, Inocybe sabuligena in a mixed Quercus ilex subsp. ballota/Juniperus thurifera open forest, Mycena calongei on mossy bark base of Juniperus oxycedrus, Rhodophana ulmaria on soil in Ulmus minor forest, Tuber arriacaense in soil under Populus pyramidalis, Volvariella latispora on grassy soils in a Quercus ilex ssp. rotundifolia stand. Sweden, Inocybe iota in alpine heath on calcareous soil. Thailand, Craterellus maerimensis and Craterellus sanbuakwaiensis on laterite and sandy soil, Helicocollum samlanense on scale insects, Leptosporella cassiae on dead twigs of Cassia fistula, Oxydothis coperniciae on dead leaf of Copernicia alba, Russula mukdahanensis on soil, Trechispora sangria on soil, Trechispora sanpatongensis on soil. Türkiye, Amanita corylophila in a plantation of Corylus avellana. Ukraine, Pararthrophiala adonis (incl. Pararthrophiala gen. nov.) on dead stems of Adonis vernalis. USA, Cladorrhinum carnegieae from Carnegiea gigantea, Dematipyriformia americana on swab from basement wall, Dothiora americana from outside air, Dwiroopa aeria from bedroom air, Lithohypha cladosporioides from hospital swab, Macroconia verruculosa on twig of Ilex montana, associated with black destroyed ascomycetous fungus and Biatora sp., Periconia floridana from outside air, Phytophthora fagacearum from necrotic leaves and shoots of Fagus grandifolia, Queenslandipenidiella californica on wood in crawlspace. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Jurjević Z, Balashov S, De la Peña-Lastra S, Mateos A, Pinruan U, Rigueiro-Rodríguez A, Osieck ER, Altés A, Czachura P, Esteve-Raventós F, Gunaseelan S, Kaliyaperumal M, Larsson E, Luangsa-ard JJ, Moreno G, Pancorbo F, Piątek M, Sommai S, Somrithipol S, Asif M, Delgado G, Flakus A, Illescas T, Kezo K, Khamsuntorn P, Kubátová A, Labuda R, Lavoise C, Lebel T, Lueangjaroenkit P, Maciá-Vicente JG, Paz A, Saba M, Shivas RG, Tan YP, Wingfield MJ, Aas T, Abramczyk B, Ainsworth AM, Akulov A, Alvarado P, Armada F, Assyov B, Avchar R, Avesani M, Bezerra JL, Bhat JD, Bilański P, Bily DS, Boccardo F, Bozok F, Campos JC, Chaimongkol S, Chellappan N, Costa MM, Dalecká M, Darmostuk V, Daskalopoulos V, Dearnaley J, Dentinger BTM, De Silva NI, Dhotre D, Carlavilla JR, Doungsa-ard C, Dovana F, Erhard A, Ferro LO, Gallegos SC, Giles CE, Gore G, Gorfer M, Guard FE, Hanson S-A, Haridev P, Jankowiak R, Jeffers SN, Kandemir H, Karich A, Kisło K, Kiss L, Krisai-Greilhuber I, Latha KPD, Lorenzini M, Lumyong S, Manimohan P, Manjón JL, Maula F, Mazur E, Mesquita NLS, Młynek K, Mongkolsamrit S, Morán P, Murugadoss R, Nagarajan M, Nalumpang S, Noisripoom W, Nosalj S, Novaes QS, Nowak M, Pawłowska J, Peiger M, Pereira OL, Pinto A, Plaza M, Polemis E, Polhorský A, Ramos DO, Raza M, Rivas-Ferreiro M, Rodriguez-Flakus P, Ruszkiewicz-Michalska M, Sánchez A, Santos A, Schüller A, Scott PA, Şen İ, Shelke D, Śliwa L, Solheim H, Sonawane H, Strašiftáková D, Stryjak-Bogacka M, Sudsanguan M, Suwannarach N, Suz LM, Syme K, Taşkın H, Tennakoon DS, Tomka P, Vaghefi N, Vasan V, Vauras J, Wiktorowicz D, Villarreal M, Vizzini A, Wrzosek M, Yang X, Yingkunchao W, Zapparoli G, Zervakis GI, Groenewald JZ (2024). Fungal Planet description sheets: 1614-1696. Fungal Systematics and Evolution 13: 183-440. doi: 10.3114/fuse.2024.13.11.}, }
@article {pmid39136489, year = {2024}, author = {Brar, G and Floden, M and McFrederick, Q and Rajamohan, A and Yocum, G and Bowsher, J}, title = {Environmentally acquired gut-associated bacteria are not critical for growth and survival in a solitary bee, Megachile rotundata.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {9}, pages = {e0207623}, pmid = {39136489}, issn = {1098-5336}, support = {RII Track-2 FEC18268341826834//National Science Foundation (NSF)/ ; IOS-1557940//National Science Foundation (NSF)/ ; ARS 3060-21220-032-00D//U.S. Department of Agriculture (USDA)/ ; ARS 3060-21220-032-00D//U.S. Department of Agriculture (USDA)/ ; }, mesh = {Animals ; Bees/microbiology/growth &amp; development ; *Gastrointestinal Microbiome ; *Larva/microbiology/growth &amp; development ; *Pollen/microbiology ; Female ; Bacteria/classification/genetics/isolation &amp; purification/growth &amp; development ; Lactobacillaceae/genetics/growth &amp; development/physiology/isolation &amp; purification ; }, abstract = {Social bees have been extensively studied for their gut microbial functions, but the significance of the gut microbiota in solitary bees remains less explored. Solitary bee, Megachile rotundata females provision their offspring with pollen from various plant species, harboring a diverse microbial community that colonizes larvae guts. The Apilactobacillus is the most abundant microbe, but evidence concerning the effects of Apilactobacillus and other provision microbes on growth and survival are lacking. We hypothesized that the presence of Apilactobacillus in abundance would enhance larval and prepupal development, weight, and survival, while the absence of intact microbial communities was expected to have a negative impact on bee fitness. We reared larvae on pollen provisions with naturally collected microbial communities (Natural pollen) or devoid of microbial communities (Sterile pollen). We also assessed the impact of introducing Apilactobacillus micheneri by adding it to both types of pollen provisions. Feeding larvae with sterile pollen + A. micheneri led to the highest mortality rate, followed by natural pollen + A. micheneri, and sterile pollen. Larval development was significantly delayed in groups fed with sterile pollen. Interestingly, larval and prepupal weights did not significantly differ across treatments compared to natural pollen-fed larvae. 16S rRNA gene sequencing found a dominance of Sodalis, when A. micheneri was introduced to natural pollen. The presence of Sodalis with abundant A. micheneri suggests potential crosstalk between both, shaping bee nutrition and health. Hence, this study highlights that the reliance on nonhost-specific environmental bacteria may not impact fitness of M. rotundata.IMPORTANCEThis study investigates the impact of environmentally acquired gut microbes of solitary bee fitness with insights into the microbial ecology of bee and their health. While the symbiotic microbiome is well-studied in social bees, the role of environmental acquired microbiota in solitary bees remains unclear. Assessing this relationship in a solitary pollinator, the leaf-cutting bee, Megachile rotundata, we discovered that this bee species does not depend on the diverse environmental bacteria found in pollen for either its larval growth or survival. Surprisingly, high concentrations of the most abundant pollen bacteria, Apilactobacillus micheneri did not consistently benefit bee fitness, but caused larval mortality. Our findings also suggest an interaction between Apilactobacillus and the Sodalis and perhaps their role in bee nutrition. Hence, this study provides significant insights that contribute to understanding the fitness, conservation, and pollination ecology of other solitary bee species in the future.}, }
@article {pmid39133233, year = {2024}, author = {Kwiatkowska, K and Ormaniec, P}, title = {Microbial Succession on Microplastics in Wastewater Treatment Plants: Exploring the Complexities of Microplastic-Microbiome Interactions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {105}, pmid = {39133233}, issn = {1432-184X}, mesh = {*Microplastics/analysis ; *Wastewater/microbiology/chemistry ; *Biofilms ; *Microbiota ; *Sewage/microbiology/chemistry ; Waste Disposal, Fluid ; Water Pollutants, Chemical/analysis ; Bacteria/classification/metabolism ; Plastics/chemistry ; }, abstract = {Despite some effectiveness of wastewater treatment processes, microplastics accumulate in sewage sludge and their further use may contribute to the release of plastic microplastics into the environment. There is an urgent need to reduce the amount of microplastics in sewage sludge. Plastic particles serve as solid substrates for various microorganisms, promoting the formation of microbial biofilms with different metabolic activities. The biofilm environment associated with microplastics will determine the efficiency of treatment processes, especially biological methods, and the mechanisms of organic compound conversion. A significant source of microplastics is the land application of sewage sludge from wastewater treatment plants. The detrimental impact of microplastics affects soil enzymatic activity, soil microorganisms, flora, fauna, and plant production. This review article summarizes the development of research related to microplastics and discusses the issue of microplastic introduction from sewage sludge. Given that microplastics can contain complex composite polymers and form a plastisphere, further research is needed to understand their potential environmental impact, pathogenicity, and the characteristics of biofilms in wastewater treatment systems. The article also discusses the physicochemical properties of microplastics in wastewater treatment plants and their role in biofilm formation. Then, the article explained the impact of these properties on the possibility of the formation of biofilms on their surface due to the peculiar structure of microorganisms and also characterized what factors enable the formation of specific plastisphere in wastewater treatment plants. It highlights the urgent need to understand the basic information about microplastics to assess environmental toxicity more rationally, enabling better pollution control and the development of regulatory standards to manage microplastics entering the environment.}, }
@article {pmid39132685, year = {2025}, author = {Ye, D and Liu, Y and Li, J and Zhou, J and Cao, J and Wu, Y and Wang, X and Fang, Y and Ye, X and Zou, J and Ma, Q}, title = {Competitive dynamics and balance between Streptococcus mutans and commensal streptococci in oral microecology.}, journal = {Critical reviews in microbiology}, volume = {51}, number = {3}, pages = {532-543}, doi = {10.1080/1040841X.2024.2389386}, pmid = {39132685}, issn = {1549-7828}, mesh = {*Mouth/microbiology ; Humans ; Biofilms/growth &amp; development ; *Dental Caries/microbiology ; *Streptococcus mutans/physiology/growth &amp; development ; *Streptococcus/physiology/growth &amp; development ; Microbiota ; }, abstract = {Dental caries, as a biofilm-related disease, is closely linked to dysbiosis in microbial ecology within dental biofilms. Beyond its impact on oral health, bacteria within the oral cavity pose systemic health risks by potentially entering the bloodstream, thereby increasing susceptibility to bacterial endocarditis, among other related diseases. Streptococcus mutans, a principal cariogenic bacterium, possesses virulence factors crucial to the pathogenesis of dental caries. Its ability to adhere to tooth surfaces, produce glucans for biofilm formation, and metabolize sugars into lactic acid contributes to enamel demineralization and the initiation of carious lesions. Its aciduricity and ability to produce bacteriocins enable a competitive advantage, allowing it to thrive in acidic environments and dominate in changing oral microenvironments. In contrast, commensal streptococci, such as Streptococcus sanguinis, Streptococcus gordonii, and Streptococcus salivarius, act as primary colonizers and compete with S. mutans for adherence sites and nutrients during biofilm formation. This competition involves the production of alkali, peroxides, and antibacterial substances, thereby inhibiting S. mutans growth and maintaining microbial balance. This dynamic interaction influences the balance of oral microbiota, with disruptions leading to shifts in microbial composition that are marked by rapid increases in S. mutans abundance, contributing to the onset of dental caries. Thus, understanding the dynamic interactions between commensal and pathogenic bacteria in oral microecology is important for developing effective strategies to promote oral health and prevent dental caries. This review highlights the roles and competitive interactions of commensal bacteria and S. mutans in oral microecology, emphasizing the importance of maintaining oral microbial balance for health, and discusses the pathological implications of perturbations in this balance.}, }
@article {pmid39128495, year = {2025}, author = {De Pessemier, B and López, CD and Taelman, S and Verdonck, M and Chen, Y and Stockman, A and Lambert, J and Van de Wiele, T and Callewaert, C}, title = {Comparative Whole Metagenome Analysis in Lesional and Nonlesional Scalp Areas of Patients with Psoriasis Capitis and Healthy Individuals.}, journal = {The Journal of investigative dermatology}, volume = {145}, number = {3}, pages = {605-617.e14}, doi = {10.1016/j.jid.2024.07.020}, pmid = {39128495}, issn = {1523-1747}, mesh = {Humans ; *Psoriasis/microbiology/pathology ; *Metagenome ; Male ; Female ; *Scalp/microbiology/pathology ; Adult ; Middle Aged ; *Microbiota/genetics ; Metagenomics ; Staphylococcus aureus/isolation &amp; purification/genetics ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Psoriasis is an immune-mediated inflammatory disorder, where the majority of the patients suffer from psoriasis capitis or scalp psoriasis. Current therapeutics remain ineffective to treat scalp lesions. In this study, we present a whole-metagenome characterization of the scalp microbiome in psoriasis capitis. We investigated how changes in the homeostatic cutaneous microbiome correlate with the condition and identified metagenomic biomarkers (taxonomic, functional, virulence factors, antimicrobial resistance genes) that could partly explain its emergence. Within this study, 83 top and back scalp samples from healthy individuals and 64 lesional and nonlesional scalp samples from subjects with untreated psoriasis capitis were analyzed. Using qPCR targeting the 16S and 18S ribosomal RNA genes, we found a significant decrease in microbial load within scalp regions affected by psoriasis compared with that in their nonlesional counterparts. Metagenomic analysis revealed that psoriatic lesions displayed significant lower Cutibacterium species (including C. modestum, C. namnetense, C. granulosum, C. porci), along with an elevation in Staphylococcus aureus. A heightened relative presence of efflux pump protein-encoding genes was detected, suggesting potential antimicrobial resistance mechanisms. These mechanisms are known to specifically target human antimicrobial peptides (including cathelicidin LL-37), which are frequently encountered within psoriasis lesions. These shifts in microbial community dynamics may contribute to psoriasis disease pathogenesis.}, }
@article {pmid39126446, year = {2025}, author = {Izumi, H}, title = {Abundances of ectomycorrhizal exploration types show the type-dependent temporal dynamics over the seasons-a controlled growth container experiment.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {28}, number = {4}, pages = {633-641}, pmid = {39126446}, issn = {1618-1905}, mesh = {*Mycorrhizae/classification/growth &amp; development/physiology/isolation &amp; purification ; Seasons ; *Quercus/microbiology/growth &amp; development ; Soil Microbiology ; Symbiosis ; Forests ; Trees/microbiology ; }, abstract = {Ectomycorrhizas are ubiquitous symbiotic associations between host trees and soil fungi. While the seasonal changes of the taxonomic community structure of ectomycorrhizal fungi have been studied extensively, the temporal dynamics of ectomycorrhizal exploration types which have been proposed for elucidating the functional roles of ectomycorrhizas have not been fully examined. The purpose of the study is to test the hypothesis of whether the abundance of the exploration types in the hosts with different phenology shows different temporal patterns over the seasons. Two host species, deciduous Quercus acutissima and evergreen Q. glauca, were planted in growth containers with natural forest soils and were grown in single or combined species treatment, under similar environmental conditions and in shared soil spore banks of the ectomycorrhizal fungi. The ectomycorrhizal exploration types that occurred on these two host species in two different treatments were observed for two growing seasons. The observed exploration types, namely contact, short-distance, and long-distance type as well as the overall abundance of the ectomycorrhizas showed distinct temporal patterns although no specific response to the host seasonal phenology was found. The abundances of the contact type showed no relation to the seasons whereas those of the short- and the long-distance type increased with time. The formation of the long-distance type was strongly influenced by the host species treatments while that of the other two types was not so. Therefore, the different exploration types demonstrate distinct temporal patterns depending on the types but no specific seasonal responses.}, }
@article {pmid39123264, year = {2024}, author = {Rothrock, MJ and Zwirzitz, B and Al Hakeem, WG and Oladeinde, A and Guard, JY and Li, X}, title = {16S amplicon-based microbiome biomapping of a commercial broiler hatchery.}, journal = {Animal microbiome}, volume = {6}, number = {1}, pages = {46}, pmid = {39123264}, issn = {2524-4671}, abstract = {Hatcheries, where eggs from multiple breeder farms are incubated and hatched before being sent to different broiler farms, represent a nexus point in the commercial production of broilers in the United States. Considering all downstream microbial quality and safety aspects of broiler production (live production, processing, consumer use) can be potentially affected by the hatchery, a better understanding of microbial ecology within commercial hatcheries is essential. Therefore, a commercial broiler hatchery was biomapped using 16S rRNA amplicon-based microbiome analyses of four sample type categories (Air, Egg, Water, Facility) across five different places in the pre-hatch, hatch, and post-hatch areas. While distinct microbiota were found for each sample type category and hatchery area, microbial community analyses revealed that Egg microbiota trended towards clustering with the facility-related samples when moving from the prehatch to post-hatch areas, highlighting the potential effect of the hatchery environment in shaping the pre-harvest broiler-related microbiota. Prevalence analyses revealed 20 ASVs (Core20) present in the core microbiota of all sample types and areas, with each ASV possessing a unique distribution throughout the hatchery. Interestingly, three Enterobacteriaceae ASVs were in the Core20, including Salmonella. Subsequent analyses showed that Salmonella, while a minor prehatch and hatch Core20ASV, dominated the Enterobacteriaceae niche and total microbiota in the chick pad feces in the post-hatch area of the hatchery, and the presence of this Salmonella ASV in the post-hatch feces was associated with swabs of breakroom tables. These findings highlight the complexity of commercial hatchery microbiota, including identifying chick pad feces and breakroom tables as potentially important sampling or disinfection targets for hatchery managers to focus their Salmonella mitigation efforts to reduce loads entering live production farms.}, }
@article {pmid39122657, year = {2024}, author = {Brenzinger, K and Glatter, T and Hakobyan, A and Meima-Franke, M and Zweers, H and Liesack, W and Bodelier, PLE}, title = {Exploring modes of microbial interactions with implications for methane cycling.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {9}, pages = {}, pmid = {39122657}, issn = {1574-6941}, support = {5535/1-1//DFG/ ; 870.15.073/NWO_/Dutch Research Council/Netherlands ; }, mesh = {*Methane/metabolism ; *Microbial Interactions ; *Volatile Organic Compounds/metabolism ; *Carbon Dioxide/metabolism ; Methylomonas/metabolism/genetics ; Proteomics ; Proteome ; Heterotrophic Processes ; Oxygenases/metabolism/genetics ; }, abstract = {Methanotrophs are the sole biological sink of methane. Volatile organic compounds (VOCs) produced by heterotrophic bacteria have been demonstrated to be a potential modulating factor of methane consumption. Here, we identify and disentangle the impact of the volatolome of heterotrophic bacteria on the methanotroph activity and proteome, using Methylomonas as model organism. Our study unambiguously shows how methanotrophy can be influenced by other organisms without direct physical contact. This influence is mediated by VOCs (e.g. dimethyl-polysulphides) or/and CO2 emitted during respiration, which can inhibit growth and methane uptake of the methanotroph, while other VOCs had a stimulating effect on methanotroph activity. Depending on whether the methanotroph was exposed to the volatolome of the heterotroph or to CO2, proteomics revealed differential protein expression patterns with the soluble methane monooxygenase being the most affected enzyme. The interaction between methanotrophs and heterotrophs can have strong positive or negative effects on methane consumption, depending on the species interacting with the methanotroph. We identified potential VOCs involved in the inhibition while positive effects may be triggered by CO2 released by heterotrophic respiration. Our experimental proof of methanotroph-heterotroph interactions clearly calls for detailed research into strategies on how to mitigate methane emissions.}, }
@article {pmid39122033, year = {2024}, author = {de Menezes, AB and Gashchak, S and Wood, MD and Beresford, NA}, title = {Relationships between radiation, wildfire and the soil microbial communities in the Chornobyl Exclusion Zone.}, journal = {The Science of the total environment}, volume = {950}, number = {}, pages = {175381}, doi = {10.1016/j.scitotenv.2024.175381}, pmid = {39122033}, issn = {1879-1026}, mesh = {*Wildfires ; *Chernobyl Nuclear Accident ; *Soil Microbiology ; *Microbiota ; *Soil Pollutants, Radioactive/analysis ; Radiation Monitoring ; Soil/chemistry ; Bacteria/classification ; Ukraine ; Forests ; }, abstract = {There is considerable uncertainty regarding radiation's effects on biodiversity in natural complex ecosystems typically subjected to multiple environmental disturbances and stresses. In this study we characterised the relationships between soil microbial communities and estimated total absorbed dose rates to bacteria, grassy vegetation and trees in the Red Forest region of the Chornobyl Exclusion Zone. Samples were taken from sites of contrasting ecological histories and along burn and no burn areas following a wildfire. Estimated total absorbed dose rates to bacteria reached levels one order of magnitude higher than those known to affect bacteria in laboratory studies. Sites with harsher ecological conditions, notably acidic pH and low soil moisture, tended to have higher radiation contamination levels. No relationship between the effects of fire and radiation were observed. Microbial groups that correlated with high radiation sites were mostly classified to taxa associated with high environmental stress habitats or stress resistance traits. Distance-based linear models and co-occurrence analysis revealed that the effects of radiation on the soil microbiome were minimal. Hence, the association between high radiation sites and specific microbial groups is more likely a result of the harsher ecological conditions in these sites, rather than due to radiation itself. In this study, we provide a starting point for understanding the relationship between soil microbial communities and estimated total absorbed radiation dose rates to different components of an ecosystem highly contaminated with radiation. Our results suggest that soil microbiomes adapted to natural soil conditions are more likely to be resistant to ionising radiation than expected from laboratory studies, which demonstrates the importance of assessing the impact of ionising radiation on soil microbial communities under field conditions.}, }
@article {pmid39119822, year = {2024}, author = {West, NJ and Landa, M and Obernosterer, I}, title = {Differential association of key bacterial groups with diatoms and Phaeocystis spp. during spring blooms in the Southern Ocean.}, journal = {MicrobiologyOpen}, volume = {13}, number = {4}, pages = {e1428}, pmid = {39119822}, issn = {2045-8827}, support = {LEFE-CYBER//Centre National de la Recherche Scientifique/ ; //Institut Polaire Fran&#xe7;ais Paul Emile Victor/ ; 10-BLAN-0614//Agence Nationale de la Recherche/ ; }, mesh = {*Diatoms/classification ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; *Oceans and Seas ; Haptophyta/classification/growth &amp; development ; Phytoplankton/classification/growth &amp; development ; Phylogeny ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Seasons ; }, abstract = {Interactions between phytoplankton and heterotrophic bacteria significantly influence the cycling of organic carbon in the ocean, with many of these interactions occurring at the micrometer scale. We explored potential associations between specific phytoplankton and bacteria in two size fractions, 0.8-3 µm and larger than 3 µm, at three naturally iron-fertilized stations and one high nutrient low chlorophyll station in the Southern Ocean. The composition of phytoplankton and bacterial communities was determined by sequencing the rbcL gene and 16S rRNA gene from DNA and RNA extracts, which represent presence and potential activity, respectively. Diatoms, particularly Thalassiosira, contributed significantly to the DNA sequences in the larger size fractions, while haptophytes were dominant in the smaller size fraction. Correlation analysis between the most abundant phytoplankton and bacterial operational taxonomic units revealed strong correlations between Phaeocystis and picoeukaryotes with SAR11, SAR116, Magnetospira, and Planktomarina. In contrast, most Thalassiosira operational taxonomic units showed the highest correlations with Polaribacter, Sulfitobacteria, Erythrobacter, and Sphingobium, while Fragilariopsis, Haslea, and Thalassionema were correlated with OM60, Fluviicola, and Ulvibacter. Our in-situ observations suggest distinct associations between phytoplankton and bacterial taxa, which could play crucial roles in nutrient cycling in the Southern Ocean.}, }
@article {pmid39118147, year = {2024}, author = {Xiong, Y and Mueller, RS and Feng, S and Guo, X and Pan, C}, title = {Proteomic stable isotope probing with an upgraded Sipros algorithm for improved identification and quantification of isotopically labeled proteins.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {148}, pmid = {39118147}, issn = {2049-2618}, support = {R01 AT011618/AT/NCCIH NIH HHS/United States ; R01AT011618/NH/NIH HHS/United States ; }, mesh = {*Proteomics/methods ; *Isotope Labeling ; *Algorithms ; Escherichia coli/metabolism ; Carbon Isotopes/metabolism ; Tandem Mass Spectrometry/methods ; Proteome ; }, abstract = {BACKGROUND: Proteomic stable isotope probing (SIP) is used in microbial ecology to trace a non-radioactive isotope from a labeled substrate into de novo synthesized proteins in specific populations that are actively assimilating and metabolizing the substrate in a complex microbial community. The Sipros algorithm is used in proteomic SIP to identify variably labeled proteins and quantify their isotopic enrichment levels (atom%) by performing enrichment-resolved database searching.<br><br>RESULTS: In this study, Sipros was upgraded to improve the labeled protein identification, isotopic enrichment quantification, and database searching speed. The new Sipros 4 was compared with the existing Sipros 3, Calisp, and MetaProSIP in terms of the number of identifications and the accuracy and precision of atom% quantification on both the peptide and protein levels using standard E. coli cultures with 1.07 atom%, 2 atom%, 5 atom%, 25 atom%, 50 atom%, and 99 atom% [13]C enrichment. Sipros 4 outperformed Calisp and MetaProSIP across all samples, especially in samples with&#x2009;&#x2265;&#x2009;5 atom% [13]C labeling. The computational speed on Sipros 4 was&#x2009;>&#x2009;20 times higher than Sipros 3 and was on par with the overall speed of Calisp- and MetaProSIP-based pipelines. Sipros 4 also demonstrated higher sensitivity for the detection of labeled proteins in two [13]C-SIP experiments on a real-world soil community. The labeled proteins were used to trace [13]C from [13]C-methanol and [13]C-labeled plant exudates to the consuming soil microorganisms and their newly synthesized proteins.<br><br>CONCLUSION: Overall, Sipros 4 improved the quality of the proteomic SIP results and reduced the computational cost of SIP database searching, which will make proteomic SIP more useful and accessible to the border community. Video Abstract.}, }
@article {pmid39113789, year = {2024}, author = {Strik, DPBTB and Ganigue, R}, title = {Editorial: Microbial chain elongation-carbon recovering biorefineries for the circular economy.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {12}, number = {}, pages = {1448975}, pmid = {39113789}, issn = {2296-4185}, }
@article {pmid39113100, year = {2024}, author = {Nieto, EE and Jurburg, SD and Steinbach, N and Festa, S and Morelli, IS and Coppotelli, BM and Chatzinotas, A}, title = {DNA stable isotope probing reveals the impact of trophic interactions on bioaugmentation of soils with different pollution histories.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {146}, pmid = {39113100}, issn = {2049-2618}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Soil Pollutants/metabolism ; *Biodegradation, Environmental ; *RNA, Ribosomal, 16S/genetics ; *RNA, Ribosomal, 18S/genetics ; *Bacteria/metabolism/classification/genetics ; Biomass ; Carbon Isotopes/metabolism ; Food Chain ; Polycyclic Aromatic Hydrocarbons/metabolism ; Isotope Labeling ; }, abstract = {BACKGROUND: Bioaugmentation is considered a sustainable and cost-effective methodology to recover contaminated environments, but its outcome is highly variable. Predation is a key top-down control mechanism affecting inoculum establishment, however, its effects on this process have received little attention. This study focused on the impact of trophic interactions on bioaugmentation success in two soils with different pollution exposure histories. We inoculated a [13]C-labelled pollutant-degrading consortium in these soils and tracked the fate of the labelled biomass through stable isotope probing (SIP) of DNA. We identified active bacterial and eukaryotic inoculum-biomass consumers through amplicon sequencing of 16S rRNA and 18S rRNA genes coupled to a novel enrichment factor calculation.<br><br>RESULTS: Inoculation effectively increased PAH removal in the&#xa0;short-term, but not in&#xa0;the long-term polluted soil. A decrease in the relative abundance of the inoculated genera was observed already on day 15 in the long-term polluted soil, while growth of these genera was observed in the short-term polluted soil, indicating establishment of the inoculum. In both soils, eukaryotic genera dominated as early incorporators of [13]C-labelled biomass, while bacteria incorporated the labelled biomass at the end of the incubation period, probably through cross-feeding. We also found different successional patterns between the two soils. In the short-term polluted soil, Cercozoa and Fungi genera predominated as early incorporators, whereas Ciliophora, Ochrophyta and Amoebozoa were the predominant genera in the long-term polluted soil.<br><br>CONCLUSION: Our results showed differences in the inoculum establishment and predator community responses, affecting bioaugmentation efficiency. This highlights the need to further study predation effects on inoculum survival to increase the applicability of inoculation-based technologies. Video Abstract.}, }
@article {pmid39110233, year = {2024}, author = {Wei, L and Wang, Y and Li, N and Zhao, N and Xu, S}, title = {Bacteria-Like Gaiella Accelerate Soil Carbon Loss by Decomposing Organic Matter of Grazing Soils in Alpine Meadows on the Qinghai-Tibet Plateau.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {104}, pmid = {39110233}, issn = {1432-184X}, support = {2023-ZJ-767//Qinghai Province Applied Basic Research Program/ ; 2023-ZJ-767//Qinghai Province Applied Basic Research Program/ ; LHZX-2020-02//Joint Special Project of Sanjiangyuan National Park/ ; LHZX-2020-02//Joint Special Project of Sanjiangyuan National Park/ ; }, mesh = {*Soil Microbiology ; Tibet ; *Carbon/metabolism/analysis ; *Soil/chemistry ; *Grassland ; Animals ; Carbon Sequestration ; Herbivory ; Bacteria/metabolism/classification ; }, abstract = {The alpine meadows of the Qinghai-Tibet Plateau have significant potential for storing soil carbon, which is important to global carbon sequestration. Grazing is a major threat to its potential for carbon sequestration. However, grazing poses a major threat to this potential by speeding up the breakdown of organic matter in the soil and releasing carbon, which may further lead to positive carbon-climate change feedback and threaten ecological security. Therefore, in order to accurately explore the driving mechanism and regulatory factors of soil organic matter decomposition in grazing alpine meadows on the Qinghai-Tibet Plateau, we took the grazing sample plots of typical alpine meadows as the research object and set up grazing intensities of different life cycles, aiming to explore the relationship and main regulatory factors of grazing on soil organic matter decomposition and soil microorganisms. The results show the following: (1) soil microorganisms, especially Acidobacteria and Acidobacteria, drove the decomposition of organic matter in the soil, thereby accelerating the release of soil carbon, which was not conducive to soil carbon sequestration in grassland; (2) the grazing triggering effect formed a positive feedback with soil microbial carbon release, accelerating the decomposition of organic matter and soil carbon loss; and (3) the grazing ban and light grazing were more conducive to slowing down soil organic matter decomposition and increasing soil carbon sequestration.}, }
@article {pmid39109653, year = {2024}, author = {Corich, L and Losasso, C and Meneghel, A and Blarasin, FI and Basaglia, G and Corich, MA}, title = {The first case of urosepsis caused by Corynebacterium aurimucosum in an immunocompetent patient.}, journal = {Future microbiology}, volume = {19}, number = {11}, pages = {963-970}, pmid = {39109653}, issn = {1746-0921}, mesh = {Humans ; *Corynebacterium/isolation &amp; purification/genetics/pathogenicity/classification ; Aged ; Female ; *Corynebacterium Infections/microbiology/diagnosis/drug therapy ; *Sepsis/microbiology/drug therapy ; *Urinary Tract Infections/microbiology/drug therapy/diagnosis ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {Non-diphtheroid Corynebacterium sepsis is rare and has affected only immunocompromised or particularly predisposed patients so far. We present the first case of urosepsis caused by Corynebacterium aurimucosum in a 67-year-old woman, without any known immunodeficiencies and in absence of any immunosuppressive therapy, admitted to the hospital for fever and acute dyspnea. This work suggests a new approach in evaluating the isolation of Corynebacteria, especially if isolated from blood. In particular, it highlights the potential infectious role of C. aurimucosum (often considered a contaminant and only rarely identified as an etiological agent of infections) and its clinical consequences, detailing also interesting aspects about its microbiological diagnosis and relative therapy and clarifying contrasting data of literature.}, }
@article {pmid39109421, year = {2024}, author = {Alfahl, Z and Biggins, S and Higgins, O and Chueiri, A and Smith, TJ and Morris, D and O'Dwyer, J and Hynds, PD and Burke, LP and O'Connor, L}, title = {A rapid on-site loop-mediated isothermal amplification technology as an early warning system for the detection of Shiga toxin-producing Escherichia coli in water.}, journal = {Microbiology (Reading, England)}, volume = {170}, number = {8}, pages = {}, pmid = {39109421}, issn = {1465-2080}, mesh = {*Nucleic Acid Amplification Techniques/methods ; *Shiga-Toxigenic Escherichia coli/genetics/isolation &amp; purification ; *Water Microbiology ; Molecular Diagnostic Techniques/methods/instrumentation ; Sensitivity and Specificity ; Rivers/microbiology ; Shiga Toxin 1/genetics ; Groundwater/microbiology ; }, abstract = {Shiga toxin-producing Escherichia coli (STEC) is an important waterborne pathogen capable of causing serious gastrointestinal infections with potentially fatal complications, including haemolytic-uremic syndrome. All STEC serogroups harbour genes that encode at least one Shiga toxin (stx1 and/or stx2), which constitute the primary virulence factors of STEC. Loop-mediated isothermal amplification (LAMP) enables rapid real-time pathogen detection with a high degree of specificity and sensitivity. The aim of this study was to develop and validate an on-site portable diagnostics workstation employing LAMP technology to permit rapid real-time STEC detection in environmental water samples. Water samples (n=28) were collected from groundwater wells (n=13), rivers (n=12), a turlough (n=2) and an agricultural drain (n=1) from the Corrib catchment in Galway. Water samples (100 ml) were passed through a 0.22 µm filter, and buffer was added to elute captured cells. Following filtration, eluates were tested directly using LAMP assays targeting stx1, stx2 and E. coli phoA genes. The portable diagnostics workstation was used in field studies to demonstrate the on-site testing capabilities of the instrument. Real-time PCR assays targeting stx1 and stx2 genes were used to confirm the results. The limit of detection for stx1, stx2 and phoA LAMP assays were 2, 2 and 6 copies, respectively. Overall, stx1, stx2 and phoA genes were detected by LAMP in 15/28 (53.6 %), 9/28 (32.2 %) and 24/28 (85.7 %) samples, respectively. For confirmation, the LAMP results for stx1 and stx2 correlated perfectly (100 %) with those obtained using PCR. The portable diagnostics workstation exhibited high sensitivity throughout the on-site operation, and the average time from sample collection to final result was 40 min. We describe a simple, transferable and efficient diagnostic technology for on-site molecular analysis of various water sources. This method allows on-site testing of drinking water, enabling evidence-based decision-making by public health and water management authorities.}, }
@article {pmid39109205, year = {2024}, author = {Zhu, L and Chen, L and Lin, B and Xu, Y and Dong, W and Lv, Y and Tang, J and Zhang, G and Zhang, L and Yang, S and Yang, Q and Chen, S}, title = {Deciphering the microbial succession and color formation mechanism of "green-covering and red-heart" Guanyin Tuqu.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1412503}, pmid = {39109205}, issn = {1664-302X}, abstract = {"Green-covering and red-heart" Guanyin Tuqu (GRTQ), as a type of special fermentation starter, is characterized by the "green-covering" formed on the surface of Guanyin Tuqu (SQ) and the "red-heart" in the center of Guanyin Tuqu (CQ). However, the mechanisms that promote temporal succession in the GRTQ microbial ecology and the formation of "green-covering and red-heart" characteristics remain unclear. Herein, we correlated the temporal profiles of microbial community succession with the main environmental variables (temperature, moisture, and acidity) and spatial position (center and surface) in GRTQ throughout fermentation. According to the results of high-throughput sequencing and culture-dependent methods, the microbial communities in the CQ and SQ demonstrated functional complementarity. For instance, the bacterial richness index of the CQ was greater than that of SQ, and the fungal richness index of the SQ was greater than that of CQ at the later stage of fermentation. Furthermore, Saccharomycopsis, Saccharomyces, Aspergillus, Monascus, Lactobacillus, Bacillus, Rhodanobacter, and Chitinophaga were identified as the dominant microorganisms in the center, while the surface was represented by Saccharomycopsis, Aspergillus, Monascus, Lactobacillus, Acetobacter, and Weissella. By revealing the physiological characteristics of core microorganisms at different spatial positions of GRTQ, such as Aspergillus clavatus and Monascus purpureus, as well as their interactions with environmental factors, we elucidated the color formation mechanism behind the phenomenon of "green" outside and "red" inside. This study provides fundamental information support for optimizing the production process of GRTQ.}, }
@article {pmid39107417, year = {2024}, author = {Cordovez, V and Carrión, VJ and Rivas Torres, G and Ortiz, DA and Cabrera, W and Balian, H and Vivanco, AK and Pérez-Jaramillo, JE and Chaves, J and Pazmiño, DA and van 't Hof, P and Raaijmakers, JM}, title = {Darwin's expedition revisited to reveal the evolution of plant-microbe interactions on Galápagos.}, journal = {Nature microbiology}, volume = {9}, number = {8}, pages = {1903-1905}, pmid = {39107417}, issn = {2058-5276}, support = {GSC fund 17150//Universidad San Francisco de Quito (USFQ)/ ; }, mesh = {*Plants/microbiology ; Ecuador ; *Biological Evolution ; Host-Pathogen Interactions ; Plant Diseases/microbiology ; }, }
@article {pmid39106714, year = {2024}, author = {Qing, J and Li, C and Zhi, H and Zhang, L and Wu, J and Li, Y}, title = {Exploring macrophage heterogeneity in IgA nephropathy: Mechanisms of renal impairment and current therapeutic targets.}, journal = {International immunopharmacology}, volume = {140}, number = {}, pages = {112748}, doi = {10.1016/j.intimp.2024.112748}, pmid = {39106714}, issn = {1878-1705}, mesh = {*Glomerulonephritis, IGA/metabolism/immunology ; Humans ; *Macrophages/immunology/metabolism ; Kidney/pathology/metabolism/immunology ; Male ; Female ; Glomerular Filtration Rate ; Adult ; Single-Cell Analysis ; }, abstract = {The lack of understanding of the mechanism of renal injury in IgA nephropathy (IgAN) hinders the development of personalized treatment plans and targeted therapies. Improved insight into the cause of renal dysfunction in IgAN is necessary to enhance the effectiveness of strategies for slowing the progression of the disease. This study examined single cell RNA sequencing (scRNA seq) and bulk-RNA seq data and found that the gene expression of renal intrinsic cells (RIC) was significantly changed in patients with renal impairment, with a primary focus on energy metabolism. We discovered a clear metabolic reprogramming of RIC during renal function impairment (RF) using the 'scMetabolism' package, which manifested as a weakening of oxidative phosphorylation, alterations in fatty acid metabolism, and changes in glycolysis. Cellular communication analysis revealed that communication between macrophages (Ma) and RIC became more active and impacted cell function through the ligand-receptor-transcription factor (L-R-TF) axis in patients with RF. Our studies showed a notable upsurge in the expression of gene CLU and the infiltration of CLU[+] Ma in patients with RF. CLU is a multifunctional protein, extensively involved in processes such as cell apoptosis and immune responses. Data obtained from the Nephroseq V5 database and multiplex immunohistochemistry (mIHC) were used to validate the findings, which were found to be robustly correlated with estimated glomerular filtration rate (eGFR) of the IgAN patients, as demonstrated by linear regression (LR). This study provides new insights into the cellular and molecular changes that occur in IgAN during renal impairment, revealing that elevated expression of CLU and CLU[+] Ma percolation are common features in patients with RF. These findings offer potential targets and strategies for personalized management and targeted therapy of IgAN.}, }
@article {pmid39106212, year = {2024}, author = {Pottie, I and Vázquez Fernández, R and Van de Wiele, T and Briers, Y}, title = {Phage lysins for intestinal microbiome modulation: current challenges and enabling techniques.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2387144}, pmid = {39106212}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Bacteriophages/physiology ; Animals ; *Endopeptidases/metabolism ; Bacteria/genetics/metabolism/virology/classification ; Probiotics ; Anti-Bacterial Agents/pharmacology ; Bacterial Infections/microbiology/drug therapy/therapy ; Viral Proteins/metabolism/genetics ; Peptidoglycan/metabolism ; }, abstract = {The importance of the microbiota in the intestinal tract for human health has been increasingly recognized. In this perspective, microbiome modulation, a targeted alteration of the microbial composition, has gained interest. Phage lysins, peptidoglycan-degrading enzymes encoded by bacteriophages, are a promising new class of antibiotics currently under clinical development for treating bacterial infections. Due to their high specificity, lysins are considered microbiome-friendly. This review explores the opportunities and challenges of using lysins as microbiome modulators. First, the high specificity of endolysins, which can be further modulated using protein engineering or targeted delivery methods, is discussed. Next, obstacles and possible solutions to assess the microbiome-friendliness of lysins are considered. Finally, lysin delivery to the intestinal tract is discussed, including possible delivery methods such as particle-based and probiotic vehicles. Mapping the hurdles to developing lysins as microbiome modulators and identifying possible ways to overcome these hurdles can help in their development. In this way, the application of these innovative antimicrobial agents can be expanded, thereby taking full advantage of their characteristics.}, }
@article {pmid39105581, year = {2024}, author = {Zhu, Y-X and Yang, T-Y and Deng, J-H and Yin, Y and Song, Z-R and Du, Y-Z}, title = {Stochastic processes drive divergence of bacterial and fungal communities in sympatric wild insect species despite sharing a common diet.}, journal = {mSphere}, volume = {9}, number = {8}, pages = {e0038624}, pmid = {39105581}, issn = {2379-5042}, support = {BK20231330//JST | Natural Science Foundation of Jiangsu Province (Jiangsu Natural Science Foundation)/ ; }, mesh = {Animals ; *Insecta/microbiology ; *Fungi/classification/genetics ; *Microbiota ; *Sympatry ; *Bacteria/classification/genetics/isolation &amp; purification ; *Stochastic Processes ; *Diet ; Mycobiome ; Citrus/microbiology ; }, abstract = {UNLABELLED: Arthropods harbor complex microbiota that play a pivotal role in host fitness. While multiple factors, like host species and diet, shape microbiota in arthropods, their impact on community assembly in wild insects remains largely unknown. In this study, we surveyed bacterial and fungal community assembly in nine sympatric wild insect species that share a common citrus fruit diet. Source tracking analysis suggested that these insects acquire some bacteria and fungi from the citrus fruit with varying degrees. Although sharing a common diet led to microbiota convergence, the diversity, composition, and network of both bacterial and fungal communities varied significantly among surveyed insect groups. Null model analysis indicated that stochastic processes, particularly dispersal limitation and drift, are primary drivers of structuring insect bacterial and fungal communities. Importantly, the influence of each community assembly process varied strongly depending on the host species. Thus, we proposed a speculative view that the host specificity of the microbiome and mycobiome assembly is widespread in wild insects despite sharing the same regional species pool. Overall, this research solidifies the importance of host species in shaping microbiomes and mycobiomes, providing novel insights into their assembly mechanisms in wild insects.<br><br>IMPORTANCE: Since the microbiome has been shown to impact insect fitness, a mechanistic understanding of community assembly has potentially significant applications but remains largely unexplored. In this paper, we investigate bacterial and fungal community assembly in nine sympatric wild insect species that share a common diet. The main findings indicate that stochastic processes drive the divergence of microbiomes and mycobiomes in nine sympatric wild insect species. These findings offer novel insights into the assembly mechanisms of microbiomes and mycobiomes in wild insects.}, }
@article {pmid39103310, year = {2024}, author = {Liu, J and Xu, G and Zhao, S and He, J}, title = {Plastisphere Microbiomes Respiring Persistent Organohalide Pollutants.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {33}, pages = {14740-14752}, doi = {10.1021/acs.est.4c02251}, pmid = {39103310}, issn = {1520-5851}, mesh = {*Microbiota ; Plastics ; Persistent Organic Pollutants/metabolism ; Bacteria/metabolism ; Halogenated Diphenyl Ethers/metabolism ; Biodegradation, Environmental ; }, abstract = {Plastics are invading nearly all ecosystems on earth, acting as emerging repositories for toxic organic pollutants and thereby imposing substantial threats to ecological integrity. The colonization of plastics by microorganisms, forming the plastisphere, has garnered attention due to its potential influence on biogeochemical cycles. However, the capability of plastisphere microorganisms to attenuate organohalide pollutants remains to be evaluated. This study revealed that the plastisphere, collected from coastal ecosystems, harbors unique microbiomes, while the natural accumulation of organohalide pollutants on plastics may favor the proliferation of organohalide-respiring bacteria (OHRB). Laboratory tests further elucidated the high potential of plastisphere microbiota to reductively dehalogenate a variety of organohalide pollutants. Notably, over 70% tested plastisphere completely debrominated tetrabromobisphenol A (TBBPA) and polybrominated diphenyl ethers (PBDEs) to nonhalogenated products, whereas polychlorinated biphenyls (PCBs) were converted to lower congeners under anaerobic conditions. Dehalococcoides, Dehalogenimonas, and novel Dehalococcoidia populations might contribute to the observed dehalogenation based on their growth during incubation and positive correlations with the quantity of halogens removed. Intriguingly, large fractions of these OHRB populations were identified in a lack of the currently known TBBPA/PBDEs/PCBs reductive dehalogenase (RDase) genes, suggesting the presence of novel RDase genes. Microbial community analyses identified organohalides as a crucial factor in determining the composition, diversity, interaction, and assembly of microbes derived from the plastisphere. Collectively, this study underscores the overlooked roles of the plastisphere in the natural attenuation of persistent organohalide pollutants and sheds light on the unignorable impacts of organohalide compounds on the microbial ecology of the plastisphere.}, }
@article {pmid39101559, year = {2024}, author = {Brar, NK and Dhariwal, A and Shekhar, S and Junges, R and Hakansson, AP and Petersen, FC}, title = {HAMLET, a human milk protein-lipid complex, modulates amoxicillin induced changes in an ex vivo biofilm model of the oral microbiome.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1406190}, pmid = {39101559}, issn = {1664-302X}, abstract = {Challenges from infections caused by biofilms and antimicrobial resistance highlight the need for novel antimicrobials that work in conjunction with antibiotics and minimize resistance risk. In this study we investigated the composite effect of HAMLET (human alpha-lactalbumin made lethal to tumor cells), a human milk protein-lipid complex and amoxicillin on microbial ecology using an ex vivo oral biofilm model with pooled saliva samples. HAMLET was chosen due to its multi-targeted antimicrobial mechanism, together with its synergistic effect with antibiotics on single species pathogens, and low risk of resistance development. The combination of HAMLET and low concentrations of amoxicillin significantly reduced biofilm viability, while each of them alone had little or no impact. Using a whole metagenomics approach, we found that the combination promoted a remarkable shift in overall microbial composition compared to the untreated samples. A large proportion of the bacterial species in the combined treatment were Lactobacillus crispatus, a species with probiotic effects, whereas it was only detected in a minor fraction in untreated samples. Although resistome analysis indicated no major shifts in alpha-diversity, the results showed the presence of TEM beta-lactamase genes in low proportions in all treated samples but absence in untreated samples. Our study illustrates HAMLET's capability to alter the effects of amoxicillin on the oral microbiome and potentially favor the growth of selected probiotic bacteria when in combination. The findings extend previous knowledge on the combined effects of HAMLET and antibiotics against target pathogens to include potential modulatory effects on polymicrobial biofilms of human origin.}, }
@article {pmid39101364, year = {2024}, author = {Elias Masiques, N and Vossen, E and De Vrieze, J and De Smet, S and Van Hecke, T}, title = {The formation of sulfur metabolites during in vitro gastrointestinal digestion of fish, white meat and red meat is affected by the addition of fructo-oligosaccharides.}, journal = {Food &amp; function}, volume = {15}, number = {17}, pages = {8729-8739}, doi = {10.1039/d4fo00928b}, pmid = {39101364}, issn = {2042-650X}, mesh = {Animals ; *Fermentation ; *Oligosaccharides/metabolism ; *Red Meat/analysis ; Cattle ; *Digestion ; Swine ; *Chickens ; Fishes/metabolism ; Gastrointestinal Tract/metabolism ; Sulfur/metabolism ; Meat/analysis ; Humans ; Fatty Acids, Volatile/metabolism ; Ammonia/metabolism ; }, abstract = {The formation of sulfur metabolites during large intestinal fermentation of red meat may affect intestinal health. In this study, four muscle sources with varying heme-Fe content (beef, pork, chicken and salmon), with or without fructo-oligosaccharides (FOS), were exposed to an in vitro gastrointestinal digestion and fermentation model, after which the formation of sulfur metabolites, protein fermentation metabolites, and short (SCFA) and branched (BCFA) chain fatty acids was assessed. When FOS were present during muscle fermentation, levels of SCFA (+54%) and H2S (+36%) increased, whereas levels of CS2 (-37%), ammonia (-60%) and indole (-30%) decreased, and the formation of dimethyl sulfides and phenol was suppressed. Red meat fermentation was not accompanied by higher H2S formation, but beef ferments tended to contain 33 to 49% higher CS2 levels compared to the ferments of other muscle sources. In conclusion, there is a greater effect on sulfur fermentation by the addition of FOS to the meats, than the intrinsic heme-Fe content of meat.}, }
@article {pmid39098418, year = {2024}, author = {Zhang, M and Duan, T and Luo, Y and Zhang, H and Li, W and Wang, X and Han, J}, title = {Impact mechanisms of various surfactants on the biodegradation of phenanthrene in soil: Bioavailability and microbial community responses.}, journal = {The Science of the total environment}, volume = {950}, number = {}, pages = {175225}, doi = {10.1016/j.scitotenv.2024.175225}, pmid = {39098418}, issn = {1879-1026}, mesh = {*Phenanthrenes/metabolism ; *Surface-Active Agents/metabolism ; *Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Soil Microbiology ; Soil/chemistry ; Biological Availability ; Microbiota/drug effects ; Polysorbates ; Glycolipids ; }, abstract = {The present study was conducted to systematically explore the mechanisms underlying the impact of various surfactants (CTAB, SDBS, Tween 80 and rhamnolipid) at different doses (10, 100 and 1000 mg/kg) on the biodegradation of a model polycyclic aromatic hydrocarbon (PAH) by indigenous soil microorganisms, focusing on bioavailability and community responses. The cationic surfactant CTAB inhibited the biodegradation of phenanthrene within the whole tested dosage range by decreasing its bioavailability and adversely affecting soil microbial communities. Appropriate doses of SDBS (1000 mg/kg), Tween 80 (100, 1000 mg/kg) and rhamnolipid at all amendment levels promoted the transformation of phenanthrene from the very slow desorption fraction (Fvslow) to bioavailable fractions (rapid and slow desorption fractions, Frapid and Fslow), assessed via Tenax extraction. However, only Tween 80 and rhamnolipid at these doses significantly improved both the rates and extents of phenanthrene biodegradation by 22.1-204.3 and 38.4-76.7 %, respectively, while 1000 mg/kg SDBS had little effect on phenanthrene removal. This was because the inhibitory effects of anionic surfactant SDBS, especially at high doses, on the abundance, diversity and activity of soil microbial communities surpassed the bioavailability enhancement in dominating biodegradation. In contrast, the nonionic surfactant Tween 80 and biosurfactant rhamnolipid enhanced the bioavailability of phenanthrene for degradation and also that to specific degrading bacterial genera, which stimulated their growth and increased the abundance of the related nidA degradation gene. Moreover, they promoted the total microbial/bacterial biomass, community diversity and polyphenol oxidase activity by providing available substrates and nutrients. These findings contribute to the design of suitable surfactant types and dosages for mitigating the environmental risk of PAHs and simultaneously benefiting microbial ecology in soil through bioremediation.}, }
@article {pmid39095861, year = {2024}, author = {Anthony, WE and Allison, SD and Broderick, CM and Chavez Rodriguez, L and Clum, A and Cross, H and Eloe-Fadrosh, E and Evans, S and Fairbanks, D and Gallery, R and Gontijo, JB and Jones, J and McDermott, J and Pett-Ridge, J and Record, S and Rodrigues, JLM and Rodriguez-Reillo, W and Shek, KL and Takacs-Vesbach, T and Blanchard, JL}, title = {From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {56}, pmid = {39095861}, issn = {2524-6372}, support = {DE-AC05-76RL01830//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; 89233218CNA000001//U.S. Department of Energy/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; }, abstract = {Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.}, }
@article {pmid39095500, year = {2024}, author = {}, title = {Bringing microbial ecology into focus.}, journal = {Nature microbiology}, volume = {9}, number = {8}, pages = {1901-1902}, pmid = {39095500}, issn = {2058-5276}, mesh = {*Ecology ; Microbiota ; Humans ; Bacteria/genetics/classification/metabolism ; }, }
@article {pmid39095499, year = {2024}, author = {Carreira, C and Lønborg, C and Acharya, B and Aryal, L and Buivydaite, Z and Borim Corrêa, F and Chen, T and Lorenzen Elberg, C and Emerson, JB and Hillary, L and Khadka, RB and Langlois, V and Mason-Jones, K and Netherway, T and Sutela, S and Trubl, G and Wa Kang'eri, A and Wang, R and White, RA and Winding, A and Zhao, T and Sapkota, R}, title = {Integrating viruses into soil food web biogeochemistry.}, journal = {Nature microbiology}, volume = {9}, number = {8}, pages = {1918-1928}, pmid = {39095499}, issn = {2058-5276}, support = {NNF21OC0072586//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 36223//Villum Fonden (Villum Foundation)/ ; 1127-00033B//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; }, mesh = {*Soil Microbiology ; *Food Chain ; *Viruses/genetics/classification/isolation &amp; purification ; *Soil/chemistry ; *Microbiota ; Animals ; Plants/virology/microbiology ; Ecosystem ; Bacteria/virology/metabolism/genetics ; }, abstract = {The soil microbiome is recognized as an essential component of healthy soils. Viruses are also diverse and abundant in soils, but their roles in soil systems remain unclear. Here we argue for the consideration of viruses in soil microbial food webs and describe the impact of viruses on soil biogeochemistry. The soil food web is an intricate series of trophic levels that span from autotrophic microorganisms to plants and animals. Each soil system encompasses contrasting and dynamic physicochemical conditions, with labyrinthine habitats composed of particles. Conditions are prone to shifts in space and time, and this variability can obstruct or facilitate interactions of microorganisms and viruses. Because viruses can infect all domains of life, they must be considered as key regulators of soil food web dynamics and biogeochemical cycling. We highlight future research avenues that will enable a more robust understanding of the roles of viruses in soil function and health.}, }
@article {pmid39094415, year = {2024}, author = {Song, Y and Cao, X and Li, SA and Li, Z and Grossart, HP and Ma, H}, title = {Human activities-impacted lake dissolved organic matter (DOM) affects phycosphere microbial diversity and DOM diversification via carbon metabolism.}, journal = {Journal of environmental management}, volume = {367}, number = {}, pages = {122011}, doi = {10.1016/j.jenvman.2024.122011}, pmid = {39094415}, issn = {1095-8630}, mesh = {*Lakes/microbiology ; *Carbon/metabolism ; Humans ; Benzopyrans ; Bacteria/metabolism ; }, abstract = {Photosynthetic carbon sequestration and microbial carbon metabolism are major processes of algae-bacteria interactions, affecting pollutant degradation as well as fundamental biogeochemical cycles in aquatic systems. Human-induced land-use changes greatly alter the molecular composition and input of terrestrial dissolved organic matter (DOM) in inland lakes. However, how the origin of DOM leads to varying effects on phycosphere microbial communities or molecular composition of DOM, e.g., via carbon metabolism, has been little studied in freshwater. Here, we incubated the cyanobacterium Microcystis aeruginosa and a bacterial community from natural lakes to establish an alga-bacteria model system. This allowed us to investigate how DOM from different sources affects phycosphere microbial diversity and DOM diversification. We showed that Suwannee River fulvic acid (SRFA), Suwannee River natural organic matter (SRNOM) and cropland lake DOM promote algal growth, whereas DOM from an urban lake inhibits algal growth. Algal metabolites and DOM together shaped the chemotaxis response of phycosphere communities. High-resolution mass spectrometry analysis demonstrated that DOM chemo-diversity tended to become uniform after interactions of diverse DOM sources with the algae-bacteria symbiosis system. Molecular thermodynamic analysis of DOM based on a substrate-explicit model further verified that microbial interactions render DOM less bioavailable and thus increase recalcitrant DOM formation. Metabolome analysis uncovered that DOM addition intensifies metabolic pathways related to labile and recalcitrant DOM utilization (mainly lignin/carboxyl-rich alicyclic molecule (CRAM)-like DOM, unsaturated hydrocarbon), whereby cofactor and vitamin metabolism represented an extremely strong activity in all metabolic pathways. Our results highlight covariation and interactions of DOM with microbial metabolism at the molecular level and expands our understanding of microbially mediated DOM shaping aquatic carbon cycling.}, }
@article {pmid39088119, year = {2024}, author = {Ferreira, P and Benabderrahim, MA and Hamza, H and Marchesini, A and Rejili, M and Castro, J and Tavares, RM and Costa, D and Sebastiani, F and Lino-Neto, T}, title = {Exploring the Influence of Date Palm Cultivars on Soil Microbiota.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {103}, pmid = {39088119}, issn = {1432-184X}, support = {2019-SECTION2-15; PRIMA/0001/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2019-SECTION2-15; PRIMA/0001/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2019-SECTION2-15; PRIMA/0001/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2019-SECTION2-15; PRIMA/0001/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {*Soil Microbiology ; *Phoeniceae/microbiology/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Fungi/genetics/classification/isolation &amp; purification/physiology ; Genotype ; Plant Roots/microbiology ; Soil/chemistry ; }, abstract = {Plants thrive in diverse environments, where root-microbe interactions play a pivotal role. Date palm (Phoenix dactylifera L.), with its genetic diversity and resilience, is an ideal model for studying microbial adaptation to different genotypes and stresses. This study aimed to analyze the bacterial and fungal communities associated with traditional date palm cultivars and the widely cultivated "Deglet Nour" were explored using metabarcoding approaches. The microbial diversity analysis identified a rich community with 13,189 bacterial and 6442 fungal Amplicon Sequence Variants (ASVs). Actinobacteriota, Proteobacteria, and Bacteroidota dominated bacterial communities, while Ascomycota dominated fungal communities. Analysis of the microbial community revealed the emergence of two distinct clusters correlating with specific date palm cultivars, but fungal communities showed higher sensitivity to date palm genotype variations compared to bacterial communities. The commercial cultivar "Deglet Nour" exhibited a unique microbial composition enriched in pathogenic fungal taxa, which was correlated with its genetic distance. Overall, our study contributes to understanding the complex interactions between date palm genotypes and soil microbiota, highlighting the genotype role in microbial community structure, particularly among fungi. These findings suggest correlations between date palm genotype, stress tolerance, and microbial assembly, with implications for plant health and resilience. Further research is needed to elucidate genotype-specific microbial interactions and their role in enhancing plant resilience to environmental stresses.}, }
@article {pmid39087852, year = {2024}, author = {Wu, T and Bafort, Q and Mortier, F and Almeida-Silva, F and Natran, A and Van de Peer, Y}, title = {The immediate metabolomic effects of whole-genome duplication in the greater duckweed, Spirodela polyrhiza.}, journal = {American journal of botany}, volume = {111}, number = {8}, pages = {e16383}, pmid = {39087852}, issn = {1537-2197}, support = {833522/ERC_/European Research Council/International ; }, mesh = {*Araceae/genetics/metabolism ; *Genome, Plant ; *Metabolomics ; *Gene Duplication ; Metabolome ; Polyploidy ; Biomass ; }, abstract = {PREMISE: In plants, whole-genome duplication (WGD) is a common mutation with profound evolutionary potential. Given the costs associated with a superfluous genome copy, polyploid establishment is enigmatic. However, in the right environment, immediate phenotypic changes following WGD can facilitate establishment. Metabolite abundances are the direct output of the cell's regulatory network and determine much of the impact of environmental and genetic change on the phenotype. While it is well known that an increase in the bulk amount of genetic material can increase cell size, the impact of gene dosage multiplication on the metabolome remains largely unknown.<br><br>METHODS: We used untargeted metabolomics on four genetically distinct diploid-neoautotetraploid pairs of the greater duckweed, Spirodela polyrhiza, to investigate how WGD affects metabolite abundances per cell and per biomass.<br><br>RESULTS: Autopolyploidy increased metabolite levels per cell, but the response of individual metabolites varied considerably. However, the impact on metabolite level per biomass was restricted because the increased cell size reduced the metabolite concentration per cell. Nevertheless, we detected both quantitative and qualitative effects of WGD on the metabolome. Many effects were strain-specific, but some were shared by all four strains.<br><br>CONCLUSIONS: The nature and impact of metabolic changes after WGD depended strongly on the genotype. Dosage effects have the potential to alter the plant metabolome qualitatively and quantitatively, but were largely balanced out by the reduction in metabolite concentration due to an increase in cell size in this species.}, }
@article {pmid39085652, year = {2024}, author = {Brinch, C and Otani, S and Munk, P and van den Beld, M and Franz, E and Aarestrup, FM}, title = {Discovery of Vibrio cholerae in Urban Sewage in Copenhagen, Denmark.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {102}, pmid = {39085652}, issn = {1432-184X}, support = {NNF16OC0021856//Novo Nordisk Fonden/ ; NNF16OC0021856//Novo Nordisk Fonden/ ; NNF16OC0021856//Novo Nordisk Fonden/ ; NNF16OC0021856//Novo Nordisk Fonden/ ; VEO 874735//Horizon 2020 Framework Programme/ ; VEO 874735//Horizon 2020 Framework Programme/ ; VEO 874735//Horizon 2020 Framework Programme/ ; VEO 874735//Horizon 2020 Framework Programme/ ; VEO 874735//Horizon 2020 Framework Programme/ ; VEO 874735//Horizon 2020 Framework Programme/ ; }, mesh = {Denmark ; *Sewage/microbiology ; *Vibrio cholerae/genetics/isolation &amp; purification/classification ; Genome, Bacterial ; Wastewater/microbiology ; Cholera/microbiology/epidemiology ; }, abstract = {We report the discovery of a persistent presence of Vibrio cholerae at very low abundance in the inlet of a single wastewater treatment plant in Copenhagen, Denmark at least since 2015. Remarkably, no environmental or locally transmitted clinical case of V. cholerae has been reported in Denmark for more than 100 years. We, however, have recovered a near-complete genome out of 115 metagenomic sewage samples taken over the past 8 years, despite the extremely low relative abundance of one V. cholerae read out of 500,000 sequenced reads. Due to the very low relative abundance, routine screening of the individual samples did not reveal V. cholerae. The recovered genome lacks the gene responsible for cholerae toxin production, but although this strain may not pose an immediate public health risk, our finding illustrates the importance, challenges, and effectiveness of wastewater-based pathogen surveillance.}, }
@article {pmid39085298, year = {2024}, author = {Vidal-Verdú, &#xc0; and Torrent, D and Iglesias, A and Latorre-Pérez, A and Abendroth, C and Corbín-Agustí, P and Peretó, J and Porcar, M}, title = {The highly differentiated gut of Pachnoda marginata hosts sequential microbiomes: microbial ecology and potential applications.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {65}, pmid = {39085298}, issn = {2055-5008}, support = {ACIF/2021/110//Generalitat Valenciana (Regional Government of Valencia)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; *Coleoptera/microbiology ; Metagenomics/methods ; Phylogeny ; Gastrointestinal Tract/microbiology ; Sequence Analysis, DNA/methods ; }, abstract = {Insect gut microbiomes play a crucial role in the insect development and are shaped, among other factors, by the specialized insect diet habits as well as the morphological structure of the gut. Rose chafers (Pachnoda spp.; Coleoptera: Scarabaeidae) have a highly differentiated gut characterized by a pronounced hindgut dilation which resembles a miniaturized rumen. Specifically, the species Pachnoda marginata has not been previously studied in detail in terms of microbial ecology. Here, we show a fine scale study of the highly compartmentalized gut of P. marginata by using amplicon and metagenomic sequencing to shed light on the bacterial, archaeal and fungal communities thriving in each section of the gut. We found a microbial gradient along the gut from aerobic (foregut) to strictly anaerobic communities (hindgut). In addition, we have characterized interesting biological activities and metabolic pathways of gut microbial communities related to cellulose degradation, methane production and sulfate reduction. Taken together, our results reveal the highly diverse microbial community and the potential of P. marginata gut as a source of industrially relevant microbial diversity.}, }
@article {pmid39083238, year = {2024}, author = {Romano, I and Ventorino, V and Schettino, M and Magaraci, G and Pepe, O}, title = {Changes in Soil Microbial Communities Induced by Biodegradable and Polyethylene Mulch Residues Under Three Different Temperatures.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {101}, pmid = {39083238}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Biodegradation, Environmental ; *Temperature ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Fungi/genetics/metabolism/classification ; *Polyethylene ; *Microbiota ; *Soil/chemistry ; Biodegradable Plastics/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Mulching is a common method increasing crop yield and achieving out-of-season production; nevertheless, their removal poses a significant environmental danger. In this scenario, the use of biodegradable plastic mulches comes up as a solution to increase the sustainability of this practice, as they can be tilled in soil without risk for the environment. In this context, it is important to study the microbial response to this practice, considering their direct involvement in plastic biodegradation. This study evaluated the biodegradation of three commercial mulch residues: one conventional non-biodegradable mulch versus two biodegradable ones (white and black compostable Mater-Bi mulches). The experiment was conducted under three incubation temperatures (room temperature 20-25 °C, 30 °C, and 45 °C) for a 6-month trial using fallow agricultural soil. Soil without plastic mulch residues was used as a control. White mater-bi biodegradable mulch residues showed higher degradation rates up to 88.90% at 30 °C, and up to 69.15% at room temperature. Furthermore, incubation at 45 °C determines the absence of degradation for all types of mulch considered. Moreover, bacterial alpha diversity was primarily influenced by plastic type and temperature, while fungal populations were mainly affected by temperature. Beta diversity was impacted by all experimental variables. Predicted functional genes crucial for degrading complex substrates, including those encoding hydrolases, cutinases, cellobiosidases, and lipases, were derived from 16S rRNA gene sequencing data. Cluster analysis based on predicted enzyme-encoding gene abundance revealed two clusters, mainly linked to sampling time. Finally, core microbiome analysis identified dominant bacterial and fungal taxa in various soil-plastic ecosystems during degradation, pinpointing species potentially involved in plastic breakdown. The present study allows an assessment of how different temperatures affect the degradation of mulch residues in soil, providing important insights for different climatic growing zones. It also fills a gap in the literature by directly comparing the effects of biodegradable and polyethylene mulches on soil microbial communities.}, }
@article {pmid39081364, year = {2024}, author = {Schmitz, DA and Wechsler, T and Mignot, I and Kümmerli, R}, title = {Predicting bacterial interaction outcomes from monoculture growth and supernatant assays.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae045}, pmid = {39081364}, issn = {2730-6151}, abstract = {How to derive principles of community dynamics and stability is a central question in microbial ecology. Bottom-up experiments, in which a small number of bacterial species are mixed, have become popular to address it. However, experimental setups are typically limited because co-culture experiments are labor-intensive and species are difficult to distinguish. Here, we use a four-species bacterial community to show that information from monoculture growth and inhibitory effects induced by secreted compounds can be combined to predict the competitive rank order in the community. Specifically, integrative monoculture growth parameters allow building a preliminary competitive rank order, which is then adjusted using inhibitory effects from supernatant assays. While our procedure worked for two different media, we observed differences in species rank orders between media. We then parameterized computer simulations with our empirical data to show that higher order species interactions largely follow the dynamics predicted from pairwise interactions with one important exception. The impact of inhibitory compounds was reduced in higher order communities because their negative effects were spread across multiple target species. Altogether, we formulated three simple rules of how monoculture growth and supernatant assay data can be combined to establish a competitive species rank order in an experimental four-species community.}, }
@article {pmid39081075, year = {2024}, author = {Bontemps, Z and Paranjape, K and Guy, L}, title = {Host-bacteria interactions: ecological and evolutionary insights from ancient, professional endosymbionts.}, journal = {FEMS microbiology reviews}, volume = {48}, number = {4}, pages = {}, pmid = {39081075}, issn = {1574-6976}, support = {F23-0260//Helge Ax:son Johnsons Foundation/ ; //NSERC/ ; }, mesh = {*Symbiosis ; *Host Microbial Interactions/physiology ; *Biological Evolution ; Gammaproteobacteria/genetics/physiology/classification ; Animals ; Bacteria/genetics/classification ; Ecosystem ; }, abstract = {Interactions between eukaryotic hosts and their bacterial symbionts drive key ecological and evolutionary processes, from regulating ecosystems to the evolution of complex molecular machines and processes. Over time, endosymbionts generally evolve reduced genomes, and their relationship with their host tends to stabilize. However, host-bacteria relationships may be heavily influenced by environmental changes. Here, we review these effects on one of the most ancient and diverse endosymbiotic groups, formed by-among others-Legionellales, Francisellaceae, and Piscirickettsiaceae. This group is referred to as Deep-branching Intracellular Gammaproteobacteria (DIG), whose last common ancestor presumably emerged about 2 Ga ago. We show that DIGs are globally distributed, but generally at very low abundance, and are mainly identified in aquatic biomes. Most DIGs harbour a type IVB secretion system, critical for host-adaptation, but its structure and composition vary. Finally, we review the different types of microbial interactions that can occur in diverse environments, with direct or indirect effects on DIG populations. The increased use of omics technologies on environmental samples will allow a better understanding of host-bacterial interactions and help unravel the definition of DIGs as a group from an ecological, molecular, and evolutionary perspective.}, }
@article {pmid39080099, year = {2024}, author = {Tiusanen, M and Becker-Scarpitta, A and Wirta, H}, title = {Distinct Communities and Differing Dispersal Routes in Bacteria and Fungi of Honey Bees, Honey, and Flowers.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {100}, pmid = {39080099}, issn = {1432-184X}, support = {201801360//Koneen S&#xe4;&#xe4;ti&#xf6;/ ; }, mesh = {Bees/microbiology ; Animals ; *Flowers/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/isolation &amp; purification/genetics ; *Honey/microbiology/analysis ; *Microbiota ; Finland ; Pollination ; DNA Barcoding, Taxonomic ; Seasons ; }, abstract = {Microbiota, the communities of microbes on and in organisms or organic matter, are essential for the functioning of ecosystems. How microbes are shared and transmitted delineates the formation of a microbiota. As pollinators forage, they offer a route to transfer microbes among the flowering plants, themselves, and their nests. To assess how the two components of the microbiota, bacteria and fungi, in pollination communities are shared and transferred, we focused on the honey bee Apis mellifera and collected honey bee, honey (representing the hive microbiota), and flower samples three times during the summer in Finland. We identified the bacteria and fungi by DNA metabarcoding. To determine the impact of honey bees' flower choices on the honey bee and hive microbiota, we identified also plant DNA in honey. The bacterial communities of honey bees, honey, and flowers all differ greatly from each other, while the fungal communities of honey bees and honey are very similar, yet different from flowers. The time of the summer and the sampling area influence all these microbiota. For flowers, the plant identity impacts both bacterial and fungal communities' composition the most. For the dispersal pathways of bacteria to honey bees, they are acquired directly from the honey and indirectly from flowers through the honey, while fungi are directly transmitted to honey bees from flowers. Overall, the distinctiveness of the microbiota of honey bees, honey, and the surrounding flowers suggests the sharing of microbes among them occurs but plays a minor role for the established microbiota.}, }
@article {pmid39079336, year = {2024}, author = {Zhang, Y and Li, X and Ren, A and Yao, M and Chen, C and Zhang, H and van der Meer, W and Liu, G}, title = {Impacts of water treatments on bacterial communities of biofilm and loose deposits in drinking water distribution systems.}, journal = {Environment international}, volume = {190}, number = {}, pages = {108893}, doi = {10.1016/j.envint.2024.108893}, pmid = {39079336}, issn = {1873-6750}, mesh = {*Biofilms/growth &amp; development/drug effects ; *Drinking Water/microbiology ; *Water Purification/methods ; *Water Supply ; *Bacteria ; Water Microbiology ; }, abstract = {Treated drinking water is delivered to customers through drinking water distribution systems (DWDSs). Although studies have focused on exploring the microbial ecology of DWDSs, knowledge about the effects of different water treatments on the bacterial community of biofilm and loose deposits in DWDS is limited. This study assessed the effects of additional treatments on the bacterial communities developed in 10 months' old pilot DWDSs. The results showed a similar bacterial community in the pipe-wall biofilm, which was dominated by Novosphingobium spp. (20-82 %) and Sphingomonas spp. (11-53 %), regardless of the treatment applied. The bacterial communities that were retained in the distribution systems (including pipe-wall biofilm and loose deposits) were similar to the particle-associated bacteria (PAB) in the corresponding supply water. The additional treatments showed clear effects of the removal and/or introduction of particles. The genera Aeromonas spp., Clostridium spp., Legionella spp., and Pseudomonas spp., which contain opportunistic pathogenic species, were only detected among the PAB in ion exchange system. Our study demonstrated that the biofilm community is consistent across treatments, and the contribution from bacteria in loose deposits is important but can be controlled by removing particles. These findings offer more insight into the origin and development of microbial ecology in DWDSs and suggest paths for further research on the possibility of managing the microbial ecology in distribution systems.}, }
@article {pmid39079302, year = {2024}, author = {Zhou, W and Huang, D and Chen, S and Wang, G and Li, R and Xu, W and Lei, Y and Xiao, R and Yin, L and Chen, H and Li, F}, title = {Microplastic dilemma: Assessing the unexpected trade-offs between biodegradable and non-biodegradable forms on plant health, cadmium uptake, and sediment microbial ecology.}, journal = {Journal of hazardous materials}, volume = {477}, number = {}, pages = {135240}, doi = {10.1016/j.jhazmat.2024.135240}, pmid = {39079302}, issn = {1873-3336}, mesh = {*Cadmium/metabolism/toxicity ; *Microplastics/toxicity/metabolism ; *Soil Microbiology ; *Geologic Sediments/microbiology/chemistry ; *Soil Pollutants/metabolism ; Biodegradation, Environmental ; Plant Roots/metabolism/microbiology ; Biodegradable Plastics/metabolism ; Plants/metabolism ; Plant Development/drug effects ; }, abstract = {Despite extensive substitution of biodegradable plastics (BPs) for conventional plastics (CPs), research on their environmental ecological consequences as microplastics (MPs) is scarce. This study aimed to fill this gap by investigating the impacts of six prototypical MPs (categorized into BMPs and CMPs) on plant growth, cadmium (Cd) translocation, and bacterial communities in contaminated sediments. Results showed both BMPs and CMPs hindered plant development; yet interestingly, BMPs provoked more pronounced physiological and biochemical changes alongside increased oxidative stress due to reactive oxygen species accumulation. Notably, most MP types promoted the absorption of Cd by plant roots potentially via a "dilution effect". BMPs also induced larger shifts in soil microbial metabolic functions compared to CMPs. Ramlibacter was identified as a key biomarker distinguishing BMPs from CMPs, with link to multiple N metabolic pathways and N assimilation. This study offers novel insights into intricate biochemical mechanisms and environmental chemistry behaviors underpinning MP-Cd interactions within the plant-microbe-sediment system, emphasizing BMPs' higher potential ecological risks based on their significant effects on plant health and microbial ecology. This work contributes to enhancing the comprehensive understanding of their ecological implications and potential threats to environmental security.}, }
@article {pmid39077993, year = {2024}, author = {Jirsová, D and Wideman, JG}, title = {Integrated overview of stramenopile ecology, taxonomy, and heterotrophic origin.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39077993}, issn = {1751-7370}, support = {2119963//National Science Foundation/ ; GBMF9201//Gordon and Betty Moore Foundation/ ; CZ.02.01.01/00/22_010/0008117//VEDA FELLOWSHIPS within the Operational program Jan Amos Komensky/ ; }, mesh = {Biological Evolution ; *Heterotrophic Processes ; Phylogeny ; Plastids/genetics ; *Stramenopiles/classification/genetics ; }, abstract = {Stramenopiles represent a significant proportion of aquatic and terrestrial biota. Most biologists can name a few, but these are limited to the phototrophic (e.g. diatoms and kelp) or parasitic species (e.g. oomycetes, Blastocystis), with free-living heterotrophs largely overlooked. Though our attention is slowly turning towards heterotrophs, we have only a limited understanding of their biology due to a lack of cultured models. Recent metagenomic and single-cell investigations have revealed the species richness and ecological importance of stramenopiles-especially heterotrophs. However, our lack of knowledge of the cell biology and behaviour of these organisms leads to our inability to match species to their particular ecological functions. Because photosynthetic stramenopiles are studied independently of their heterotrophic relatives, they are often treated separately in the literature. Here, we present stramenopiles as a unified group with shared synapomorphies and evolutionary history. We introduce the main lineages, describe their important biological and ecological traits, and provide a concise update on the origin of the ochrophyte plastid. We highlight the crucial role of heterotrophs and mixotrophs in our understanding of stramenopiles with the goal of inspiring future investigations in taxonomy and life history. To understand each of the many diversifications within stramenopiles-towards autotrophy, osmotrophy, or parasitism-we must understand the ancestral heterotrophic flagellate from which they each evolved. We hope the following will serve as a primer for new stramenopile researchers or as an integrative refresher to those already in the field.}, }
@article {pmid39074063, year = {2024}, author = {Nyathi, M and Dhlamini, Z and Ncube, T}, title = {Cloning Cellulase Genes from Victoria Falls Rainforest Decaying Logs Metagenome.}, journal = {Polish journal of microbiology}, volume = {73}, number = {3}, pages = {343-348}, pmid = {39074063}, issn = {2544-4646}, mesh = {*Cellulase/genetics/metabolism ; *Metagenome ; *Rainforest ; Soil Microbiology ; Cloning, Molecular ; Hydrogen-Ion Concentration ; Escherichia coli/genetics ; Temperature ; Metagenomics ; Bacteria/genetics/classification/enzymology/isolation &amp; purification ; }, abstract = {The Victoria Falls rainforest is a protected site whose forest floors harbor a host of cellulolytic microorganisms involved in biomass degradation. This study collected decaying logs and soil from the rainforest for bioprospecting cellulases from their metagenomes. Metagenomic DNA was isolated from the compound sample. Degenerate cellulase primers were used to amplify cellulase genes in the metagenome. The resulting amplicons cloned into Z-competent Escherichia coli DH5α were analyzed by functional screening for the production of cellulase extracellularly. Functional screening of the clones resulted in one clone (Clone-i) testing positive for extracellular cellulase production. Submerged fermentation of Clone-i was carried out for cellulase production. The cellulases were characterized to determine their activity's optimum pH and temperature. The diversity of the cellulases produced by Clone-i was determined. Clone-i's optimum enzyme activity was observed after 72 hours of incubation at 50°C and pH 5. Clone-i produced 80% more exoglucanases as compared to endoglucanases. The cellulolytic Clone-i' isolate shows Victoria Falls rainforest's potential as an enzyme bioprospecting site, reflecting that metagenomics is a valuable tool in microbial ecology.}, }
@article {pmid39073401, year = {2024}, author = {Williams, SE and Varliero, G and Lurgi, M and Stach, JEM and Race, PR and Curnow, P}, title = {Diversity and structure of the deep-sea sponge microbiome in the equatorial Atlantic Ocean.}, journal = {Microbiology (Reading, England)}, volume = {170}, number = {7}, pages = {}, pmid = {39073401}, issn = {1465-2080}, mesh = {*Porifera/microbiology ; *Microbiota ; *Archaea/classification/genetics/isolation &amp; purification ; Animals ; Atlantic Ocean ; *Bacteria/classification/genetics/isolation &amp; purification ; *Phylogeny ; Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; }, abstract = {Sponges (phylum Porifera) harbour specific microbial communities that drive the ecology and evolution of the host. Understanding the structure and dynamics of these communities is emerging as a primary focus in marine microbial ecology research. Much of the work to date has focused on sponges from warm and shallow coastal waters, while sponges from the deep ocean remain less well studied. Here, we present a metataxonomic analysis of the microbial consortia associated with 23 individual deep-sea sponges. We identify a high abundance of archaea relative to bacteria across these communities, with certain sponge microbiomes comprising more than 90 % archaea. Specifically, the archaeal family Nitrosopumilaceae is prolific, comprising over 99 % of all archaeal reads. Our analysis revealed that sponge microbial communities reflect the host sponge phylogeny, indicating a key role for host taxonomy in defining microbiome composition. Our work confirms the contribution of both evolutionary and environmental processes to the composition of microbial communities in deep-sea sponges.}, }
@article {pmid39073317, year = {2024}, author = {Bahri, S and Bouazizi, S and Nahdi, A and Mlika, M and Hamdi, M and Jameleddine, S}, title = {Insights on the Tunisian Prickly Pear Molasses as a Potential Antifibrotic and Antioxidant Candidate against Lung Fibrosis.}, journal = {Chemistry &amp; biodiversity}, volume = {21}, number = {11}, pages = {e202401030}, doi = {10.1002/cbdv.202401030}, pmid = {39073317}, issn = {1612-1880}, support = {//Tunisian Ministry of Higher Education/ ; //Scientific Research/ ; }, mesh = {Animals ; *Antioxidants/pharmacology/chemistry ; *Rats, Wistar ; Rats ; *Pulmonary Fibrosis/drug therapy/chemically induced/metabolism/pathology ; *Molasses ; Male ; Bleomycin ; Oxidative Stress/drug effects ; Pyrus/chemistry ; Tunisia ; Antifibrotic Agents/pharmacology/chemistry ; Disease Models, Animal ; Lung/drug effects/pathology/metabolism ; }, abstract = {Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive interstitial disease leading to pulmonary damage and respiratory failure. We aimed to investigate the effect of prickly pear molasses (PPM) on an experimental model of pulmonary fibrosis induced by bleomycin (BLM) in Wistar rat. Animals were divided into 5 groups: the control group (G1), the BLM group (G2) and three groups (G3, G4, G5) receiving a single intra-tracheal injection of BLM (4 mg/kg) and PPM (at 2, 4.5 and10 %) that was introduced into the diet one week before BLM injection and continued for 3 weeks. Our phytochemical results revealed significant polyphenol and flavonoid content. LCMS analysis revealed the presence of Sinapinic acid, t-ferulic acid, t-cinnamic acid, Caffeic acid, gallic acid and vallinic acid among others. Our histological study revealed significant decrease in collagen deposition in the groups of rats treated with 4.5 % and 10 % molasses compared to BLM group. Oxidative stress in pulmonary tissues was investigated using catalase (CAT), superoxide dismutase (SOD), and malondialdehyde (MDA) assays. Treatment with PPM normalized the disturbance in the level of these oxidative markers in G3,G4, G5 compared to G2. In conclusion, PPM exhibit antifibrotic and antioxidant activities in BLM model of lung fibrosis.}, }
@article {pmid39073180, year = {2024}, author = {Bielčik, M and Schlägel, UE and Schäfer, M and Aguilar-Trigueros, CA and Lakovic, M and Sosa-Hernández, MA and Hammer, EC and Jeltsch, F and Rillig, MC}, title = {Aligning spatial ecological theory with the study of clonal organisms: the case of fungal coexistence.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {99}, number = {6}, pages = {2211-2233}, doi = {10.1111/brv.13119}, pmid = {39073180}, issn = {1469-185X}, support = {GRK 2118//Deutsche Forschungsgemeinschaft/ ; SCHL 2259/1-1.//Deutsche Forschungsgemeinschaft/ ; 100619639//Fachagentur Nachwachsende Rohstoffe/ ; }, mesh = {*Fungi/physiology ; *Ecosystem ; Models, Biological ; }, abstract = {Established ecological theory has focused on unitary organisms, and thus its concepts have matured into a form that often hinders rather than facilitates the ecological study of modular organisms. Here, we use the example of filamentous fungi to develop concepts that enable integration of non-unitary (modular) organisms into the established community ecology theory, with particular focus on its spatial aspects. In doing so, we provide a link between fungal community ecology and modern coexistence theory (MCT). We first show how community processes and predictions made by MCT can be used to define meaningful scales in fungal ecology. This leads to the novel concept of the unit of community interactions (UCI), a promising conceptual tool for applying MCT to communities of modular organisms with indeterminate clonal growth and hierarchical individuality. We outline plausible coexistence mechanisms structuring fungal communities, and show at what spatial scales and in what habitats they are most likely to act. We end by describing challenges and opportunities for empirical and theoretical research in fungal competitive coexistence.}, }
@article {pmid39071402, year = {2024}, author = {Dieppa-Colón, E and Martin, C and Anantharaman, K}, title = {Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39071402}, issn = {2692-8205}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; T32 GM135066/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are extremely underexplored. Phages are classified as virulent or temperate based on their life cycles. Temperate phages adopt the lysogenic mode of infection, where the genome integrates into the host cell genome forming a prophage. Prophages enable viral genome replication without host cell lysis, and often contribute novel and beneficial traits to the host genome. Current phage research predominantly focuses on lytic phages, leaving a significant gap in knowledge regarding prophages, including their biology, diversity, and ecological roles.<br><br>RESULTS: Here we develop and describe Prophage-DB, a database of prophages, their proteins, and associated metadata that will serve as a resource for viral genomics and microbial ecology. To create the database, we identified and characterized prophages from genomes in three of the largest publicly available databases. We applied several state-of-the-art tools in our pipeline to annotate these viruses, cluster and taxonomically classify them, and detect their respective auxiliary metabolic genes. In total, we identify and characterize over 350,000 prophages and 35,000 auxiliary metabolic genes. Our prophage database is highly representative based on statistical results and contains prophages from a diverse set of archaeal and bacterial hosts which show a wide environmental distribution.<br><br>CONCLUSION: Prophages are particularly overlooked in viral ecology and merit increased attention due to their vital implications for microbiomes and their hosts. Here, we created Prophage-DB to advance our comprehension of prophages in microbiomes through a comprehensive characterization of prophages in publicly available genomes. We propose that Prophage-DB will serve as a valuable resource for advancing phage research, offering insights into viral taxonomy, host relationships, auxiliary metabolic genes, and environmental distribution.}, }
@article {pmid39066818, year = {2024}, author = {Castellano-Hinojosa, A and Tortosa, G and Fernández-Zambrano, A and Correa-Galeote, D and Bedmar, EJ and Medina-Sánchez, JM}, title = {Strong Saharan Dust Deposition Events Alter Microbial Diversity and Composition in Sediments of High-Mountain Lakes of Sierra Nevada (Spain).}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {99}, pmid = {39066818}, issn = {1432-184X}, support = {A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; A-RNM-237-UGR18//FEDER/Junta de Andaluc&#xed;a-Consejer&#xed;a de Econom&#xed;a y Conocimiento/Proyecto/ ; PID2020-118872RB-I00//MICIN/AEI/10.13039/501100011033/ ; LifeWatch-2019-10-UGR-01//Ministry of Science and Innovation through the FEDER funds from the Spanish Pluriregional Operational Program 2014-2020 (POPE), LifeWatch-ERIC action line/ ; }, mesh = {*Geologic Sediments/microbiology/chemistry ; *Lakes/microbiology/chemistry ; *Dust/analysis ; Spain ; *Biodiversity ; *Bacteria/classification/genetics/isolation &amp; purification ; Microbiota ; Africa, Northern ; }, abstract = {Mediterranean high-mountain lakes are being increasingly affected by strong Saharan dust deposition events. However, the ecological impacts of these severe atmospheric episodes remain largely unknown. We examined the effects of a strong Saharan dust intrusion to the Iberian Peninsula in 2022 on the physicochemical parameters and prokaryotic communities in sediments of nine high-mountain lakes of Sierra Nevada (Spain) located above 2800 m.a.s.l and in different orientations (north vs. south). A previous year (2021), with lower Saharan dust deposition with respect to 2022, was used for interannual comparisons. The strong dust deposition to the high-mountain lakes resulted in a significant increase in sediment nutrient availability which was linked to changes in the composition of prokaryotic communities. Decreases in alpha diversity and changes in beta diversity of prokaryotic communities were mainly observed in lakes located in the south compared to the north orientation likely because the former was more affected by the atmospheric dust deposition episode. Dust intrusion to the high-mountain lakes resulted in significant changes in the relative abundance of specific genera involved in important nutrient cycling processes such as phosphate solubilization, nitrogen fixation, nitrification, and denitrification. Saharan dust deposition also increased predicted microbial functionality in all lakes. Our findings show that severe atmospheric dust inputs to remote high-mountain lakes of Sierra Nevada can have significant biogeochemical and biodiversity consequences through changes in nutrient availability and prokaryotic communities in sediments of these freshwater ecosystems. This information contributes to understanding how Mediterranean high-mountain lakes of Sierra Nevada face strong intrusions of Saharan dust and their ecological consequences.}, }
@article {pmid39065051, year = {2024}, author = {Du, W and Li, J and Zhang, G and Yu, K and Liu, S}, title = {Spatiotemporal Variations in Co-Occurrence Patterns of Planktonic Prokaryotic Microorganisms along the Yangtze River.}, journal = {Microorganisms}, volume = {12}, number = {7}, pages = {}, pmid = {39065051}, issn = {2076-2607}, support = {52100171//National Natural Science Foundation of China/ ; BYESS2023103//Young Elite Scientist Sponsorship Program by Beijing Association for Science and Technology/ ; }, abstract = {Bacteria and archaea are foundational life forms on Earth and play crucial roles in the development of our planet's biological hierarchy. Their interactions influence various aspects of life, including eukaryotic cell biology, molecular biology, and ecological dynamics. However, the coexistence network patterns of these microorganisms within natural river ecosystems, vital for nutrient cycling and environmental health, are not well understood. To address this knowledge gap, we systematically explored the non-random coexistence patterns of planktonic bacteria and archaea in the 6000-km stretch of the Yangtze River by using high-throughput sequencing technology. By analyzing the O/R ratio, representing the divergence between observed (O%) and random (R%) co-existence incidences, and the module composition, we found a preference of both bacteria and archaea for intradomain associations over interdomain associations. Seasons notably influenced the co-existence of bacteria and archaea, and archaea played a more crucial role in spring as evidenced by their predominant presence of interphyla co-existence and more species as keystone ones. The autumn network was characterized by a higher node or edge number, greater graph density, node degree, degree centralization, and nearest neighbor degree, indicating a more complex and interconnected structure. Landforms markedly affected microbial associations, with more complex networks and more core species found in plain and non-source areas. Distance-decay analysis suggested the importance of geographical distance in shaping bacteria and archaea co-existence patterns (more pronounced in spring). Natural, nutrient, and metal factors, including water temperature, NH4[+]-N, Fe, Al, and Ni were identified as crucial determinants shaping the co-occurrence patterns. Overall, these findings revealed the dynamics of prokaryotic taxa coexistence patterns in response to varying environmental conditions and further contributed to a broader understanding of microbial ecology in freshwater biogeochemical cycling.}, }
@article {pmid39065031, year = {2024}, author = {Sapp, PA and Townsend, JR and Kirby, TO and Govaert, M and Duysburgh, C and Verstrepen, L and Marzorati, M and Marshall, TM and Esposito, R}, title = {AG1[®], a Novel Synbiotic, Maintains Gut Barrier Function following Inflammatory Challenge in a Caco-2/THP1-Blue™ Co-Culture Model.}, journal = {Microorganisms}, volume = {12}, number = {7}, pages = {}, pmid = {39065031}, issn = {2076-2607}, support = {n/a//Athletic Greens International (Carson City, NV 89701)/ ; }, abstract = {Nutritional interventions to reduce gastrointestinal (GI) permeability are of significant interest to physically active adults and those experiencing chronic health conditions. This in vitro study was designed to assess the impact of AG1, a novel synbiotic, on GI permeability following an inflammatory challenge. Interventions [AG1 (vitamins/minerals, pre-/probiotics, and phytonutrients) and control (control medium)] were fed separately into a human GI tract model (stomach, small intestine, and colon). In the colonic phase, the GI contents were combined with fecal inocula from three healthy human donors. GI permeability was evaluated with transepithelial electrical resistance (TEER) in a Caco-2 (apical)/THP1-Blue™ (basolateral) co-culture model. The apical side received sodium butyrate (positive control) or Caco-2 complete medium (negative control) during baseline testing. In the 24 h experiment, the apical side received colonic simulation isolates from the GI model, and the basolateral side was treated with Caco-2 complete medium, then 6 h treatment with lipopolysaccharide. TEER was assessed at 0 h and 24 h, and inflammatory markers were measured at 30 h in triplicate. Paired samples t-tests were used to evaluate endpoint mean difference (MD) for AG1 vs. control. TEER was higher for AG1 (mean ± SD: 99.89 ± 1.32%) vs. control (mean ± SD: 92.87 ± 1.22%) following activated THP1-induced damage [MD: 7.0% (p < 0.05)]. AG1 maintained TEER similar to the level of the negative control [-0.1% (p = 0.02)]. No differences in inflammatory markers were observed. These in vitro data suggest that acute supplementation with AG1 might stimulate protective effects on GI permeability. These changes may be driven by SCFA production due to the pre-/probiotic properties of AG1, but more research is needed.}, }
@article {pmid39062734, year = {2024}, author = {Zhang, H and Li, S and Zhou, S and Guo, W and Chen, P and Li, Y and Wu, W}, title = {Divergence of Phyllosphere Microbial Community Assemblies and Components of Volatile Organic Compounds between the Invasive Sphagneticola trilobata, the Native Sphagneticola calendulacea and Their Hybrids, and Its Implications for Invasiveness.}, journal = {Genes}, volume = {15}, number = {7}, pages = {}, pmid = {39062734}, issn = {2073-4425}, support = {2023KCXTD017//Guangdong Province University Innovative Team Project: Innovation and Development Application of Ornamental Plant Germplasm with Lingnan Characteristics/ ; }, mesh = {*Volatile Organic Compounds/metabolism ; *Microbiota ; *Introduced Species ; Brassicaceae/microbiology/genetics ; China ; }, abstract = {Closely-related plant groups with distinct microbiomes, chemistries and ecological characteristics represent tractable models to explore mechanisms shaping species spread, competitive dynamics and community assembly at the interface of native and introduced ranges. We investigated phyllosphere microbial communities, volatile organic compound (VOC) compositions, and potential interactions among introduced S. trilobata, native S. calendulacea and their hybrid in South China. S. trilobata exhibited higher α diversity but significantly different community composition compared to the native and hybrid groups. However, S. calendulacea and the hybrid shared certain microbial taxa, suggesting potential gene flow or co-existence. The potent antimicrobial VOC profile of S. trilobata, including unique compounds like p-cymene (13.33%), likely contributes to its invasion success. The hybrid's intermediate microbial and VOC profiles suggest possible consequences for species distribution, genetic exchange, and community assembly in heterogeneous environments. This hybrid deserves further study as both an opportunity for and threat to diversity maintenance. These differentiating yet connected plant groups provide insight into ecological and evolutionary dynamics shaping microbiome structure, species co-occurrence and competitive outcomes during biological exchange and habitat transformation. An interdisciplinary approach combining chemical and microbial ecology may reveal mechanisms underlying community stability and change, informing management of species spread in a globalized world.}, }
@article {pmid39061809, year = {2024}, author = {Hriňová, K and Dlapová, J and Kubala, B and Kormanová, &#x13d; and Levarski, Z and Struhárňanská, E and Turňa, J and Stuchlík, S}, title = {Production of Reverse Transcriptase and DNA Polymerase in Bacterial Expression Systems.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {11}, number = {7}, pages = {}, pmid = {39061809}, issn = {2306-5354}, support = {APVV-17-0333//Slovak Research and Development Agency/ ; APVV-21-0215//Slovak Research and Development Agency/ ; APVV-21-0227//Slovak Research and Development Agency/ ; APVV-22-0161//Slovak Research and Development Agency/ ; }, abstract = {DNA amplification and reverse transcription enzymes have proven to be invaluable in fast and reliable diagnostics and research applications because of their processivity, specificity, and robustness. Our study focused on the production of mutant Taq DNA polymerase and mutant M-MLV reverse transcriptase in the expression hosts Vibrio natriegens and Escherichia coli under various expression conditions. We also examined nonspecific extracellular production in V. natriegens. Intracellularly, M-MLV was produced in V. natriegens at the level of 11% of the total cell proteins (TCPs) compared with 16% of TCPs in E. coli. We obtained a soluble protein that accounted for 11% of the enzyme produced in V. natriegens and 22% of the enzyme produced in E. coli. Taq pol was produced intracellularly in V. natriegens at the level of 30% of TCPs compared with 26% of TCPs in E. coli. However, Taq pol was almost non-soluble in E. coli, whereas in V. natriegens, we obtained a soluble protein that accounted for 23% of the produced enzyme. We detected substantial extracellular production of Taq pol. Thus, V. natriegens is a suitable alternative host with the potential for production of recombinant proteins.}, }
@article {pmid39060935, year = {2024}, author = {Baptista, MS and Lee, CK and Monteiro, MR and Torgo, L and Cary, SC and Magalhães, C}, title = {Soils of two Antarctic Dry Valleys exhibit unique microbial community structures in response to similar environmental disturbances.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {52}, pmid = {39060935}, issn = {2524-6372}, abstract = {BACKGROUND: Isolating the effects of deterministic variables (e.g., physicochemical conditions) on soil microbial communities from those of neutral processes (e.g., dispersal) remains a major challenge in microbial ecology. In this study, we disturbed soil microbial communities of two McMurdo Dry Valleys of Antarctica exhibiting distinct microbial biogeographic patterns, both devoid of aboveground biota and different in macro- and micro-physicochemical conditions. We modified the availability of water, nitrogen, carbon, copper ions, and sodium chloride salts in a laboratory-based experiment and monitored the microbial communities for up to two months. Our aim was to mimic a likely scenario in the near future, in which similar selective pressures will be applied to both valleys. We hypothesized that, given their unique microbial communities, the two valleys would select for different microbial populations when subjected to the same disturbances.<br><br>RESULTS: The two soil microbial communities, subjected to the same disturbances, did not respond similarly as reflected in both 16S rRNA genes and transcripts. Turnover of the two microbial communities showed a contrasting response to the same environmental disturbances and revealed different potentials for adaptation to change. These results suggest that the heterogeneity between these microbial communities, reflected in their strong biogeographic patterns, was maintained even when subjected to the same selective pressure and that the 'rare biosphere', at least in these samples, were deeply divergent and did not act as a reservoir for microbiota that enabled convergent responses to change in environmental conditions.<br><br>CONCLUSIONS: Our findings strongly support the occurrence of endemic microbial communities that show a structural resilience to environmental disturbances, spanning a wide range of physicochemical conditions. In the highly arid and nutrient-limited environment of the Dry Valleys, these results provide direct evidence of microbial biogeographic patterns that can shape the communities' response in the face of future environmental changes.}, }
@article {pmid39059201, year = {2024}, author = {Bai, X and Samari-Kermani, M and Schijven, J and Raoof, A and Dinkla, IJT and Muyzer, G}, title = {Enhancing slow sand filtration for safe drinking water production: interdisciplinary insights into Schmutzdecke characteristics and filtration performance in mini-scale filters.}, journal = {Water research}, volume = {262}, number = {}, pages = {122059}, doi = {10.1016/j.watres.2024.122059}, pmid = {39059201}, issn = {1879-2448}, mesh = {*Filtration ; *Drinking Water/microbiology ; *Water Purification/methods ; *Sand ; *Escherichia coli ; Silicon Dioxide/chemistry ; Biofilms ; }, abstract = {The demand for safe drinking water is constantly challenged by increasing biohazards. One widely used solution is implementing indoor-operated slow sand filtration (SSF) as one of the final barriers in water production. SSF has gained popularity due to its low energy consumption and efficient removal of biohazards, especially microorganisms, without using chemicals. SSF involves both physical-chemical and biological removal, particularly in the "Schmutzdecke", which is a biofilm-like layer on the sand bed surface. To achieve the optimal performance of SSF, a systematic understanding of the influence of SSF operating parameters on the Schmutzdecke development and filter filtration performance is required. Our study focused on three operational parameters, i.e., sand material, sand size, and the addition of an inoculum (suspension of matured Schmutzdecke), on the mini-scale filters. The effects of these parameters on the Schmutzdecke development and SSF removal performance were studied by biochemical analyses and 16S amplicon sequencing, together with spiking experiments with Escherichia coli (E. coli) in the mini-scale filters. Our results indicate that the mini-scale filters successfully developed Schmutzdeckes and generated bacterial breakthrough curves efficiently. The sand size and material were found to have an impact on Schmutzdecke's development. The addition of inoculum to new filters did not induce significant changes in the microbial community composition of the Schmutzdecke, but we observed positive effects of faster Schmutzdecke development and better removal performance in some inoculated filters. Our study highlights the value of mini-scale filters for SSF studies, which provide insights into Schmutzdecke microbial ecology and bacterial removal with significantly reduced requirements of materials and effort as compared to larger-scale filters. We found that operational parameters have a greater impact on the Schmutzdecke biochemical characteristics and removal performances than on the microbial community composition. This suggests that Schmutzdecke characteristics may provide more reliable predictors of SSF removal performance, which could help to improve safe drinking water production.}, }
@article {pmid39055957, year = {2024}, author = {Zhang, Y and Gan, G and Li, Y and Li, W and Jiang, Y and Wang, P and Hu, J and Wang, N and Quan, X and Liu, J and Raza, W and Xu, Y and Hohmann, P and Jousset, A and Wang, Y and Shen, Q and Jiang, G and Wei, Z}, title = {Exploring the temporal dynamics of a disease suppressive rhizo-microbiome in eggplants.}, journal = {iScience}, volume = {27}, number = {7}, pages = {110319}, pmid = {39055957}, issn = {2589-0042}, abstract = {The rhizosphere microbiome is important for plant health, yet their contributions to disease resistance and assembly dynamics remain unclear. This study employed rhizosphere microbiome transplantation (RMT) to delineate the impact of the rhizosphere microbiome and the immune response of eggplant (Solanum melongena) on resistance to bacterial wilt caused by Ralstonia solanacearum. We first identified disease-suppressive and disease-conducive rhizosphere microbiome in a susceptible tomato recipient. Using a non-destructive rhizobox and 16S rRNA amplicon sequencing, we monitored the dynamics of both microbiome types during the eggplant development. Most differences were observed at the early stage and then diminished over time. The suppressive microbiome maintained a higher proportion of initial community members throughout eggplant development and exhibited stronger deterministic processes in the early stage, underscoring the importance of plant selection in recruiting protective microbes for rhizosphere immunity. Our study sheds light on the development of microbiome-based strategies for plant disease management and resistance breeding.}, }
@article {pmid39052866, year = {2024}, author = {}, title = {Correction to: Alpine soil microbial ecology in a changing world.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {8}, pages = {}, doi = {10.1093/femsec/fiae085}, pmid = {39052866}, issn = {1574-6941}, }
@article {pmid39052865, year = {2024}, author = {Vuilleumier, S and Barthelmebs, L and Corcoll, N and Hery, M and G Karpouzas, D and Wick, LY}, title = {Editorial: thematic issue on microbial ecotoxicology.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {8}, pages = {}, pmid = {39052865}, issn = {1574-6941}, mesh = {*Ecotoxicology ; }, }
@article {pmid39051617, year = {2024}, author = {Pluym, T and Waegenaar, F and De Gusseme, B and Boon, N}, title = {Microbial drinking water monitoring now and in the future.}, journal = {Microbial biotechnology}, volume = {17}, number = {7}, pages = {e14532}, pmid = {39051617}, issn = {1751-7915}, support = {1S02022N//Fonds Wetenschappelijk Onderzoek/ ; 1S26823N//Fonds Wetenschappelijk Onderzoek/ ; S006221N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {*Drinking Water/microbiology ; *Bacteria/genetics/isolation &amp; purification/classification ; Humans ; Water Microbiology ; Environmental Monitoring/methods ; }, abstract = {Over time, humanity has addressed microbial water contamination in various ways. Historically, individuals resorted to producing beer to combat the issue. Fast forward to the 19th century, and we witnessed a scientific approach by Robert Koch. His groundbreaking gelatine plating method aimed to identify and quantify bacteria, with a proposed limit of 100 colony-forming units per millilitre (CFU/mL) to avoid Cholera outbreaks. Despite considerable advancements in plating techniques through experimentation with media compositions and growth temperatures, the reliance on a century-old method for water safety remains the state-of-the-art. Even though most countries succeed in producing qualitative water at the end of the production centres, it is difficult to control, and guarantee, the same quality during distribution. Rather than focusing solely on specific sampling points, we propose a holistic examination of the entire water network to ensure comprehensive safety. Current practices leave room for uncertainties, especially given the low concentrations of pathogens. Innovative methods like flow cytometry and flow cytometric fingerprinting offer the ability to detect changes in the microbiome of drinking water. Additionally, molecular techniques and emerging sequencing technologies, such as third-generation sequencing (MinION), mark a significant leap forward, enhancing detection limits and emphasizing the identification of unwanted genes rather than the unwanted bacteria/microorganisms itself. Over the last decades, there has been the realization that the drinking water distribution networks are complex ecosystems that, beside bacteria, comprise of viruses, protozoans and even isopods. Sequencing techniques to find eukaryotic DNA are necessary to monitor the entire microbiome of the drinking water distribution network. Or will artificial intelligence, big data and machine learning prove to be the way to go for (microbial) drinking water monitoring? In essence, it is time to transcend century-old practices and embrace modern technologies to ensure the safety of our drinking water from production to consumption.}, }
@article {pmid39047455, year = {2024}, author = {Blair, MF and Vaidya, R and Salazar-Benites, G and Bott, CB and Pruden, A}, title = {Relating microbial community composition to treatment performance in an ozone-biologically active carbon filtration potable reuse treatment train.}, journal = {Water research}, volume = {262}, number = {}, pages = {122091}, doi = {10.1016/j.watres.2024.122091}, pmid = {39047455}, issn = {1879-2448}, mesh = {*Ozone ; *Water Purification/methods ; *Filtration ; Microbiota ; Charcoal/chemistry ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Treatment trains that couple ozone (O3) with biologically active carbon (BAC) filtration are of interest as a lower cost, more sustainable, membrane-free approach to water reuse. However, little is known about the microbial communities that are the fundamental drivers of O3-BAC treatment. The objective of this study was to demonstrate microbial community profiling as a diagnostic tool for assessing the functionality, biological stability, and resilience of coupled physical, chemical, advanced oxidative and biological processes employed in water reuse treatment. We utilized 16S rRNA gene amplicon sequencing to profile the bacterial microbiota over time throughout a potable reuse train employing coagulation, flocculation, sedimentation, ozonation, BAC filtration, granular activated carbon (GAC) adsorption, and UV disinfection. A distinct baseline microbiota was associated with each stage of treatment (ANOSIM, p < 0.05, r-stat = 0.52), each undergoing succession with time and operational shifts. Ozonation resulted in the sharpest shifts (i.e., 83.3 % average change in Genus level relative abundances, when adjusted O3:TOC ratio > 1), and also variance, in microbial community composition. Adjustment in O3:TOC ratios, temperature, filter-aid polymer, monochloramine quenching agent, and empty-bed contact time also resulted in measurable changes in the baseline microbial community composition of individual processes, but to a lesser degree. Of these, supplementation of nitrogen and phosphorus resulted in the strongest bifurcation, especially in the microbial communities inhabiting the BAC (ANOSIM: p < 0.05, BAC5 r-stat = 0.32; BAC10 r-stat = 0.54) and GAC (ANOSIM: p < 0.05, GAC10 r-stat = 0.54; GAC20 r-stat = 0.63) units. Additionally, we found that the BAC microbial community was responsive to an inoculation of microbially active media, which resulted in improved TOC removal. The findings of this study improve understanding of bacterial dynamics occurring in advanced water treatment trains and can inform improved system design and operation.}, }
@article {pmid39046569, year = {2024}, author = {Chen, X and Zhang, W and Geng, M and Shen, J and Wang, J}, title = {Carbon and Nutrient Limitations of Microbial Metabolism in Xingkai Lake, China: Abiotic and Biotic Drivers.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {97}, pmid = {39046569}, issn = {1432-184X}, support = {42230507//National Natural Science Foundation of China/ ; 42225708//National Natural Science Foundation of China/ ; }, mesh = {*Lakes/microbiology/chemistry ; China ; *Carbon/metabolism ; *Phosphorus/metabolism/analysis ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; *Fungi/metabolism/classification ; *Nitrogen/metabolism ; *Geologic Sediments/microbiology ; *Microbiota ; Nutrients/metabolism/analysis ; }, abstract = {Microbial communities are crucial for water quality and biogeochemical cycling in freshwaters. Microbes secrete extracellular enzymes to decompose organic matter for their needs of nutrients and scarce elements. Yet, there is a lack of knowledge on microbial metabolic limitations in freshwaters, especially in lake sediments. Here, we examined the carbon, nitrogen, and phosphorus-acquiring extracellular enzyme activities and the bacterial and fungal communities of 30 sediments across Xingkai Lake, the largest freshwater lake in Northeast Asia. We further analyzed the microbial metabolic limitations via extracellular enzyme stoichiometry and explored the direct and indirect effects of abiotic and biotic factors on the limitations. We found that microbial metabolisms were primarily limited by phosphorus in Xingkai Lake. For instance, microbial carbon and phosphorus limitations were closely correlated to abiotic factors like water depth, total dissolved solids, sediment total carbon, and conductivity. The metabolic limitations were also affected by biotic factors, such as showing positive relationships with the alpha and beta diversity of bacteria, and with the beta diversity of fungi. In addition, community compositions of bacteria and fungi were mainly correlated to abiotic factors such as total carbon and dissolved organic carbon, respectively. Collectively, microbial metabolic limitations were affected directly or indirectly by abiotic factors and microbial communities. Our findings indicate that microbial metabolic limitations are not only driven by bacteria and fungi but also by abiotic factors such as water depth and total nitrogen, and thus provide empirical evidence for effective management of freshwater lakes under climate warming and intensified human activities.}, }
@article {pmid39046558, year = {2024}, author = {Xie, G and Sun, C and Gong, Y and Luo, W and Tang, X}, title = {Beyond the Bloom: Unraveling the Diversity, Overlap, and Stability of Free-Living and Particle-Attached Bacterial Communities in a Cyanobacteria-Dominated Hypereutrophic Lake.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {96}, pmid = {39046558}, issn = {1432-184X}, support = {WGKQ2022032//West Anhui University/ ; 41971062//National Natural Science Foundation of China/ ; }, mesh = {*Lakes/microbiology ; *Cyanobacteria/genetics/classification ; *Eutrophication ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; Seasons ; Ecosystem ; China ; }, abstract = {In aquatic ecosystems with low nutrient levels, organic aggregates (OAs) act as nutrient hotspots, hosting a diverse range of microbial species compared to those in the water column. Lake eutrophication, marked by intensified and prolonged cyanobacterial blooms, significantly impacts material and energy cycling processes, potentially altering the ecological traits of both free-living (FL) and particle-attached (PA) bacteria. However, the extent to which observed patterns of FL and PA bacterial diversity, community assembly, and stability extend to hypereutrophic lakes remains understudied. To address this gap, we investigated bacterial diversity, composition, assembly processes, and stability within hypereutrophic Lake Xingyun. Our results revealed that FL bacterial communities exhibited higher α-diversity than PA counterparts, coupled with discernible taxonomic compositions. Both bacterial communities showed distinct seasonality, influenced by cyanobacterial bloom intensity. Environmental factors accounted for 71.1% and 54.2% of the variation among FL and PA bacteria, respectively. The assembly of the PA bacterial community was predominantly stochastic, while FL assembly was more deterministic. The FL network demonstrated greater stability, complexity, and negative interactions, indicative of competitive relationships, while the PA network showed a prevalence of positive correlations, suggesting mutualistic interactions. Importantly, these findings differ from observations in oligotrophic, mesotrophic, and eutrophic lakes. Overall, this research provides valuable insights into the interplay among bacterial fractions, enhancing our understanding of nutrient status and cyanobacterial blooms in shaping bacterial communities.}, }
@article {pmid39046491, year = {2024}, author = {Soto-Cortés, E and Marroquín-Rodríguez, M and Basanta, MD and Maldonado-López, Y and Parra-Olea, G and Rebollar, EA}, title = {Host Species and Environment Shape the Skin Microbiota of Mexican Axolotls.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {98}, pmid = {39046491}, issn = {1432-184X}, support = {CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; IN205521//PAPIIT/UNAM/ ; }, mesh = {Animals ; *Skin/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Mexico ; *Fungi/classification/isolation &amp; purification/genetics ; Ambystoma mexicanum/microbiology ; Host Specificity ; Environment ; Biodiversity ; }, abstract = {Skin microbiomes in amphibians are complex systems that can be influenced by biotic and abiotic factors. In this study, we examined the effect of host species and environmental conditions on the skin bacterial and fungal microbiota of four obligate paedomorphic salamander species, commonly known as axolotls (Ambystoma andersoni, A. dumerilii, A. mexicanum, and A. taylori), all of them endemic to the Trans-Mexican Volcanic Belt. We found that despite their permanent aquatic lifestyle, these species present a host-specific skin microbiota that is distinct from aquatic communities. We identified skin-associated taxa that were unique to each host species and that differentiated axolotl species based on alpha and beta diversity metrics. Moreover, we identified a set of microbial taxa that were shared across hosts with high relative abundances across skin samples. Specifically, bacterial communities were dominated by Burkholderiales and Pseudomonadales bacterial orders and Capnodiales and Pleosporales fungal orders. Host species and environmental variables collectively explained more microbial composition variation in bacteria (R2 = 0.46) in comparison to fungi (R2 = 0.2). Our results contribute to a better understanding of the factors shaping the diversity and composition of skin microbial communities in Ambystoma. Additional studies are needed to disentangle the effects of specific host associated and environmental factors that could influence the skin microbiome of these endangered species.}, }
@article {pmid39043275, year = {2024}, author = {Fernández-Blanco, C and Pereira, A and Veiga, MC and Kennes, C and Ganigué, R}, title = {Comprehensive comparative study on n-caproate production by Clostridium kluyveri: batch vs. continuous operation modes.}, journal = {Bioresource technology}, volume = {408}, number = {}, pages = {131138}, doi = {10.1016/j.biortech.2024.131138}, pmid = {39043275}, issn = {1873-2976}, mesh = {*Ethanol/metabolism ; *Clostridium kluyveri/metabolism ; *Caproates/metabolism ; Batch Cell Culture Techniques ; Bioreactors ; Fermentation ; Acetates/metabolism ; Oxidation-Reduction ; }, abstract = {Recently, there has been notable interest in researching and industrially producing medium-chain carboxylic acids (MCCAs) like n-caproate and n-caprylate via chain elongation process. This study presents a comprehensive assessment of the behavior and MCCA production profiles of Clostridium kluyveri in batch and continuous modes, at different ethanol:acetate molar ratios (1.5:1, 3.5:1 and 5.5:1). The highest n-caproate concentration, 12.9 ± 0.67 g/L (92.9 ± 1.39 % MCCA selectivity), was achieved in batch mode at a 3.5:1 ratio. Interestingly, higher ratios favored batch mode selectivity over continuous mode when this was equal or higher to 3.5:1. Steady state operation yielded the highest n-caproate (9.5 ± 0.13 g/L) and n-caprylate (0.35 ± 0.020 g/L) concentrations at the 3.5:1 ratio. Increased ethanol:acetate ratios led to a higher excessive ethanol oxidation (EEO) in both operational modes, potentially limiting n-caproate production and selectivity, especially at the 5.5:1 ratio. Overall, this study reports the efficient MCCA production of both batch and continuous modes by C. kluyveri.}, }
@article {pmid39043163, year = {2024}, author = {DeWitt, ME and Sanders, JW}, title = {Tropical Diseases in the United States: Beyond Poverty - Advancing an Ecological Framework in Tropical Medicine.}, journal = {The American journal of tropical medicine and hygiene}, volume = {111}, number = {3}, pages = {449-451}, pmid = {39043163}, issn = {1476-1645}, mesh = {*Tropical Medicine ; Humans ; *Poverty ; United States/epidemiology ; }, }
@article {pmid39039555, year = {2024}, author = {Wang, D and Liu, L and Xu, X and Wang, C and Wang, Y and Deng, Y and Zhang, T}, title = {Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {134}, pmid = {39039555}, issn = {2049-2618}, mesh = {*Bacteriophages/genetics/classification/physiology/isolation &amp; purification ; *Sewage/virology/microbiology ; *Wastewater/virology/microbiology ; *Bacteria/virology/genetics/classification ; Biofilms ; Metagenomics ; Water Purification/methods ; Microbiota ; }, abstract = {BACKGROUND: Understanding the interactions and dynamics of microbiotas within biological wastewater treatment systems is essential for ensuring their stability and long-term sustainability. In this study, we developed a systematic framework employing multi-omics and Hi-C sequencing to extensively investigate prokaryotic and phage communities within a hybrid biofilm and activated sludge system.<br><br>RESULTS: We uncovered distinct distribution&#xa0;patterns, metabolic capabilities, and activities of functional prokaryotes through the analysis of 454 reconstructed prokaryotic genomes. Additionally, we reconstructed a phage catalog comprising 18,645 viral operational taxonomic units (vOTUs) with high length and contiguity using hybrid assembly, and a distinct distribution of phages was depicted between activated sludge (AS) and biofilm. Importantly, 1340 host-phage pairs were established using Hi-C and conventional in silico methods, unveiling the host-determined phage prevalence. The majority of predicted hosts were found to be involved in various crucial metabolic processes, highlighting the potential vital roles of phages in influencing substance metabolism within this system. Moreover, auxiliary metabolic genes (AMGs) related to various categories (e.g., carbohydrate degradation, sulfur metabolism, transporter) were predicted. Subsequent activity analysis emphasized their potential ability to mediate host metabolism during infection. We also profiled the temporal dynamics of phages and their associated hosts using 13-month time-series metagenomic data, further demonstrating their tight interactions. Notably, we observed lineage-specific infection patterns, such as&#xa0;potentially host abundance- or phage/host ratio-driven phage population changes.<br><br>CONCLUSIONS: The insights gained from this research contribute to the growing body of knowledge surrounding interactions and dynamics of host-phage and pave the way for further exploration and potential applications in the field of microbial ecology. Video Abstract.}, }
@article {pmid39039015, year = {2024}, author = {Vanharanta, M and Santoro, M and Villena-Alemany, C and Piiparinen, J and Piwosz, K and Grossart, HP and Labrenz, M and Spilling, K}, title = {Microbial remineralization processes during postspring-bloom with excess phosphate available in the northern Baltic Sea.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {8}, pages = {}, pmid = {39039015}, issn = {1574-6941}, support = {731065//European Commission/ ; 2021/03/Y/NZ8/00076//National Science Centre, Poland/ ; GR1540/37-1//DFG/ ; }, mesh = {*Seawater/microbiology/chemistry ; *Phosphates/metabolism ; *Bacteria/metabolism/genetics/growth &amp; development ; *Phosphorus/metabolism ; *Carbon/metabolism ; *Nitrogen/metabolism ; Finland ; Oceans and Seas ; Eutrophication ; Heterotrophic Processes ; }, abstract = {The phosphorus (P) concentration is increasing in parts of the Baltic Sea following the spring bloom. The fate of this excess P-pool is an open question, and here we investigate the role of microbial degradation processes in the excess P assimilation phase. During a 17-day-long mesocosm experiment in the southwest Finnish archipelago, we examined nitrogen, phosphorus, and carbon acquiring extracellular enzyme activities in three size fractions (<0.2, 0.2-3, and >3 µm), bacterial abundance, production, community composition, and its predicted metabolic functions. The mesocosms received carbon (C) and nitrogen (N) amendments individually and in combination (NC) to distinguish between heterotrophic and autotrophic processes. Alkaline phosphatase activity occurred mainly in the dissolved form and likely contributed to the excess phosphate conditions together with grazing. At the beginning of the experiment, peptidolytic and glycolytic enzymes were mostly produced by free-living bacteria. However, by the end of the experiment, the NC-treatment induced a shift in peptidolytic and glycolytic activities and degradation of phosphomonoesters toward the particle-associated fraction, likely as a consequence of higher substrate availability. This would potentially promote retention of nutrients in the surface as opposed to sedimentation, but direct sedimentation measurements are needed to verify this hypothesis.}, }
@article {pmid39030648, year = {2024}, author = {Moretti, LG and Crusciol, CAC and Leite, MFA and Momesso, L and Bossolani, JW and Costa, OYA and Hungria, M and Kuramae, EE}, title = {Diverse bacterial consortia: key drivers of rhizosoil fertility modulating microbiome functions, plant physiology, nutrition, and soybean grain yield.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {50}, pmid = {39030648}, issn = {2524-6372}, support = {2016/23699-8; 2018/14892-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 151120/2020-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, abstract = {Soybean cultivation in tropical regions relies on symbioses with nitrogen-fixing Bradyrhizobium and plant growth-promoting bacteria (PGPBs), reducing environmental impacts of N fertilizers and pesticides. We evaluate the effects of soybean inoculation with different bacterial consortia combined with PGPBs or microbial secondary metabolites (MSMs) on rhizosoil chemistry, plant physiology, plant nutrition, grain yield, and rhizosphere microbial functions under field conditions over three growing seasons with four treatments: standard inoculation of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens consortium (SI); SI plus foliar spraying with Bacillus subtilis (SI + Bs); SI plus foliar spraying with Azospirillum brasilense (SI + Az); and SI plus seed application of MSMs enriched in lipo-chitooligosaccharides extracted from B. diazoefficiens and Rhizobium tropici (SI + MSM). Rhizosphere microbial composition, diversity, and function was assessed by metagenomics. The relationships between rhizosoil chemistry, plant nutrition, grain yield, and the abundance of microbial taxa and functions were determined by generalized joint attribute modeling. The bacterial consortia had the most significant impact on rhizosphere soil fertility, which in turn affected the bacterial community, plant physiology, nutrient availability, and production. Cluster analysis identified microbial groups and functions correlated with shifts in rhizosoil chemistry and plant nutrition. Bacterial consortia positively modulated specific genera and functional pathways involved in biosynthesis of plant secondary metabolites, amino acids, lipopolysaccharides, photosynthesis, bacterial secretion systems, and sulfur metabolism. The effects of the bacterial consortia on the soybean holobiont, particularly the rhizomicrobiome and rhizosoil fertility, highlight the importance of selecting appropriate consortia for desired outcomes. These findings have implications for microbial-based agricultural practices that enhance crop productivity, quality, and sustainability.}, }
@article {pmid39030520, year = {2024}, author = {Joo, M and Nam, S}, title = {Adolescent gut microbiome imbalance and its association with immune response in inflammatory bowel diseases and obesity.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {268}, pmid = {39030520}, issn = {1471-2180}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Adolescent ; *RNA, Ribosomal, 16S/genetics ; *Obesity/microbiology/immunology ; Female ; Male ; *Bacteria/classification/genetics/isolation &amp; purification ; *Phylogeny ; Inflammatory Bowel Diseases/microbiology/immunology ; Crohn Disease/microbiology/immunology ; Colitis, Ulcerative/microbiology/immunology ; Dysbiosis/microbiology ; Prevotella/genetics/classification/isolation &amp; purification ; Faecalibacterium prausnitzii/genetics ; Feces/microbiology ; }, abstract = {BACKGROUND: Recently, there has been an increase in the number of studies focusing on the association between the gut microbiome and obesity or inflammatory diseases, especially in adults. However, there is a lack of studies investigating the association between gut microbiome and gastrointestinal (GI) diseases in adolescents.<br><br>METHOD: We obtained 16S rRNA-seq datasets for gut microbiome analysis from 202 adolescents, comprising ulcerative colitis (UC), Crohn's disease (CD), obesity (Ob), and healthy controls (HC). We utilized Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to acquire Operational Taxonomic Units (OTUs). Subsequently, we analyzed Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO) terms and pathway enrichment for the identified OTUs.<br><br>RESULTS: In this study, we investigated the difference between the gut microbiomes in adolescents with GI diseases and those in healthy adolescents using 202 samples of 16S rRNA sequencing data. The distribution of the six main gut microbiota (i.e., unclassified Dorea, unclassified Lachnospiraceae, unclassified Ruminococcus, Faecalibacterium prausnitzii, Prevotella copri, unclassified Sutterella) was different based on the status of obesity and inflammatory diseases. Dysbiosis was observed within Lachnospiraceae in adolescents with inflammatory diseases (i.e., UC and CD), and in adolescents with obesity within Prevotella and Sutterella. More specifically, our results showed that the relative abundance of Faecalibacterium prausnitzii and unclassified Lachnospiraceae was more than 10% and 8% higher, respectively, in the UC group compared to the CD, Ob, and HC groups. Additionally, the Ob group had over 20% and over 3% higher levels of Prevotella copri and unclassified Sutterella, respectively, compared to the UC, CD, and HC groups. Also, inspecting associations between the six specific microbiota and KO terms, we found that the six microbiota -relating KO terms were associated with NOD-like receptor signaling. These six taxa differences may affect the immune system and inflammatory response by affecting NOD-like receptor signaling in the host during critical adolescence.<br><br>CONCLUSION: In this study, we discovered that dysbiosis of the microbial community had varying degrees of influence on the inflammatory and immune response pathways in adolescents with inflammatory diseases and obesity.}, }
@article {pmid39030408, year = {2024}, author = {Gilbert, JA and Hartmann, EM}, title = {The indoors microbiome and human health.}, journal = {Nature reviews. Microbiology}, volume = {22}, number = {12}, pages = {742-755}, pmid = {39030408}, issn = {1740-1534}, mesh = {Humans ; *Microbiota ; Air Microbiology ; Air Pollution, Indoor ; Built Environment ; }, abstract = {Indoor environments serve as habitat for humans and are replete with various reservoirs and niches for microorganisms. Microorganisms enter indoor spaces with their human and non-human hosts, as well as via exchange with outdoor sources, such as ventilation and plumbing. Once inside, many microorganisms do not survive, especially on dry, barren surfaces. Even reduced, this microbial biomass has critical implications for the health of human occupants. As urbanization escalates, exploring the intersection of the indoor environment with the human microbiome and health is increasingly vital. The indoor microbiome, a complex ecosystem of microorganisms influenced by human activities and environmental factors, plays a pivotal role in modulating infectious diseases and fostering healthy immune development. Recent advancements in microbiome research shed light on this unique ecological system, highlighting the need for innovative approaches in creating health-promoting living spaces. In this Review, we explore the microbial ecology of built environments - places where humans spend most of their lives - and its implications for immune, endocrine and neurological health. We further propose strategies to harness the indoor microbiome for better health outcomes.}, }
@article {pmid39029405, year = {2024}, author = {Kozaeva, E and Eida, AA and Gunady, EF and Dangl, JL and Conway, JM and Brophy, JA}, title = {Roots of synthetic ecology: microbes that foster plant resilience in the changing climate.}, journal = {Current opinion in biotechnology}, volume = {88}, number = {}, pages = {103172}, doi = {10.1016/j.copbio.2024.103172}, pmid = {39029405}, issn = {1879-0429}, mesh = {*Microbiota/physiology ; *Climate Change ; *Plants/microbiology ; Plant Development ; Ecosystem ; Synthetic Biology ; Ecology ; Plant Roots/microbiology ; }, abstract = {Microbes orchestrate nearly all major biogeochemical processes. The ability to program their influence on plant growth and development is attractive for sustainable agriculture. However, the complexity of microbial ecosystems and our limited understanding of the mechanisms by which plants and microbes interact with each other and the environment make it challenging to use microbiomes to influence plant growth. Novel technologies at the intersection of microbial ecology, systems biology, and bioengineering provide new tools to probe the role of plant microbiomes across environments. Here, we summarize recent studies on plant and microbe responses to abiotic stresses, showcasing key molecules and micro-organisms that are important for plant health. We highlight opportunities to use synthetic microbial communities to understand the complexity of plant-microbial interactions and discuss future avenues of programming ecology to improve plant and ecosystem health.}, }
@article {pmid39025292, year = {2024}, author = {Guo, X and Zhao, W and Yin, D and Mei, Z and Wang, F and Tiedje, J and Ling, S and Hu, S and Xu, T}, title = {Aspirin altered antibiotic resistance genes response to sulfonamide in the gut microbiome of zebrafish.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {359}, number = {}, pages = {124566}, doi = {10.1016/j.envpol.2024.124566}, pmid = {39025292}, issn = {1873-6424}, mesh = {*Zebrafish/genetics ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Sulfonamides/pharmacology ; *Aspirin/pharmacology ; *Drug Resistance, Microbial/genetics ; *Anti-Bacterial Agents/pharmacology ; Sulfamethoxazole/pharmacology ; Water Pollutants, Chemical ; Bacteria/genetics/drug effects ; }, abstract = {Pharmaceuticals are widespread in aquatic environments and might contribute to the prevalence of antibiotic resistance. However, the co-effect of antibiotics and non-antibiotic pharmaceuticals on the gut microbiome of fish is poorly understood. In this study, we characterized the variation of the zebrafish gut microbiome and resistome after exposure to sulfamethoxazole (SMX) and aspirin under different treatments. SMX contributed to the significant increase in the antibiotic resistance genes (ARGs) richness and abundance with 46 unique ARGs and five mobile genetic elements (MGEs) detected. Combined exposure to SMX and aspirin enriched total ARGs abundance and rearranged microbiota under short-term exposure. Exposure time was more responsible for resistome and the gut microbiome than exposure concentrations. Perturbation of the gut microbiome contributed to the functional variation related to RNA processing and modification, cell motility, signal transduction mechanisms, and defense mechanisms. A strong significant positive correlation (R = 0.8955, p < 0.001) was observed between total ARGs and MGEs regardless of different treatments revealing the key role of MGEs in ARGs transmission. Network analysis indicated most of the potential ARGs host bacteria belonged to Proteobacteria. Our study suggested that co-occurrence of non-antibiotics and antibiotics could accelerate the spread of ARGs in gut microbial communities and MGEs played a key role.}, }
@article {pmid39021442, year = {2024}, author = {Bowers, RM and Gonzalez-Pena, V and Wardhani, K and Goudeau, D and Blow, MJ and Udwary, D and Klein, D and Vill, AC and Brito, IL and Woyke, T and Malmstrom, RR and Gawad, C}, title = {scMicrobe PTA: near complete genomes from single bacterial cells.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae085}, pmid = {39021442}, issn = {2730-6151}, support = {DP2 CA239145/CA/NCI NIH HHS/United States ; }, abstract = {Microbial genomes produced by standard single-cell amplification methods are largely incomplete. Here, we show that primary template-directed amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard multiple displacement amplification-based approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.}, }
@article {pmid39021414, year = {2024}, author = {Marin, C and Migura-García, L and Rodríguez, JC and Ventero, MP and Pérez-Gracia, MT and Vega, S and Tort-Miró, C and Marco-Fuertes, A and Lorenzo-Rebenaque, L and Montoro-Dasi, L}, title = {Swine farm environmental microbiome: exploring microbial ecology and functionality across farms with high and low sanitary status.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1401561}, pmid = {39021414}, issn = {2297-1769}, abstract = {INTRODUCTION: Stringent regulations in pig farming, such as antibiotic control and the ban on certain additives and disinfectants, complicate disease control efforts. Despite the evolution of microbial communities inside the house environment, they maintain stability over the years, exhibiting characteristics specific to each type of production and, in some cases, unique to a particular company or farm production type. In addition, some infectious diseases are recurrent in specific farms, while other farms never present these diseases, suggesting a connection between the presence of these microorganisms in animals or their environment. Therefore, the aim of this study was to characterise environmental microbiomes of farms with high and low sanitary status, establishing the relationships between both, health status, environmental microbial ecology and its functionality.<br><br>METHODS: For this purpose, 6 pig farms were environmentally sampled. Farms were affiliated with a production company that handle the majority of the pigs slaughtered in Spain. This study investigated the relationship among high health and low health status farms using high throughput 16S rRNA gene sequencing. In addition, to identify ecologically relevant functions and potential pathogens based on the 16S rRNA gene sequences obtained, functional Annotation with PROkaryotic TAXa (FAPROTAX) was performed.<br><br>RESULTS AND DISCUSSION: This study reveals notable differences in microbial communities between farms with persistent health issues and those with good health outcomes, suggesting a need for protocols tailored to address specific challenges. The variation in microbial populations among farms underscores the need for specific and eco-friendly cleaning and disinfection protocols. These measures are key to enhancing the sustainability of livestock farming, ensuring safer products and boosting competitive edge in the market.}, }
@article {pmid39019971, year = {2024}, author = {Grafmüller, J and Möllmer, J and Muehe, EM and Kammann, CI and Kray, D and Schmidt, HP and Hagemann, N}, title = {Granulation compared to co-application of biochar plus mineral fertilizer and its impacts on crop growth and nutrient leaching.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {16555}, pmid = {39019971}, issn = {2045-2322}, mesh = {*Charcoal/chemistry ; *Fertilizers ; *Crops, Agricultural/growth &amp; development ; *Minerals/chemistry ; Nitrogen/chemistry ; Brassica/growth &amp; development ; Soil/chemistry ; Nutrients ; Agriculture/methods ; Magnesium/chemistry ; }, abstract = {Mechanized biochar field application remains challenging due to biochar's poor flowability and bulk density. Granulation of biochar with fertilizer provides a product ready for application with well-established machinery. However, it's unknown whether granulated biochar-based fertilizers (gBBF) are as effective as co-application of non-granulated biochar with fertilizer. Here, we compared a gBBF with a mineral compound fertilizer (control), and with a non-granulated biochar that was co-applied at a rate of 1.1 t ha[-1] with the fertilizer in a white cabbage greenhouse pot trial. Half the pots received heavy rain simulation treatments to investigate nutrient leaching. Crop yields were not significantly increased by biochar without leaching compared to the control. With leaching, cabbage yield increased with gBBF and biochar-co-application by 14% (p > 0.05) and 34% (p < 0.05), respectively. Nitrogen leaching was reduced by 26-35% with both biochar amendments. Biochar significantly reduced potassium, magnesium, and sulfur leaching. Most nitrogen associated with gBBF was released during the trial and the granulated biochar regained its microporosity. Enriching fertilizers with biochar by granulation or co-application can improve crop yields and decrease nutrient leaching. While the gBBF yielded less biomass compared to biochar co-application, improved mechanized field application after granulation could facilitate the implementation of biochar application in agriculture.}, }
@article {pmid39018765, year = {2024}, author = {Bittleston, LS}, title = {Connecting microbial community assembly and function.}, journal = {Current opinion in microbiology}, volume = {80}, number = {}, pages = {102512}, doi = {10.1016/j.mib.2024.102512}, pmid = {39018765}, issn = {1879-0364}, mesh = {*Microbiota ; *Bacteria/genetics/classification/metabolism ; Biodiversity ; Humans ; }, abstract = {Microbial ecology is moving away from purely descriptive analyses to experiments that can determine the underlying mechanisms driving changes in community assembly and function. More species-rich microbial communities generally have higher functional capabilities depending on if there is positive selection of certain species or complementarity among different species. When building synthetic communities or laboratory enrichment cultures, there are specific choices that can increase the number of species able to coexist. Higher resource complexity or the addition of physical niches are two of the many factors leading to greater biodiversity and associated increases in functional capabilities. We can use principles from community ecology and knowledge of microbial physiology to generate improved microbiomes for use in medicine, agriculture, or environmental management.}, }
@article {pmid39017940, year = {2024}, author = {Kim, YS and Yun, HS and Lee, JH and Lee, KL and Choi, JS and Won, DH and Kim, YJ and Kim, HS and Yoon, HS}, title = {Comparison of Metabarcoding and Microscopy Methodologies to Analyze Diatom Communities in Five Estuaries Along the Southern Coast of the Korean Peninsula.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {95}, pmid = {39017940}, issn = {1432-184X}, support = {2016R1A6A1A05011910//National Research Foundation of Korea/ ; 2016R1A6A1A05011910//National Research Foundation of Korea/ ; 2021R1I1A205551711//National Research Foundation of Korea/ ; }, mesh = {*Diatoms/classification/growth &amp; development ; *DNA Barcoding, Taxonomic ; *Microscopy/methods ; *Estuaries ; Republic of Korea ; Biodiversity ; Phylogeny ; Ecosystem ; }, abstract = {The study of microalgal communities is critical for understanding aquatic ecosystems. These communities primarily comprise diatoms (Heterokontophyta), with two methods commonly used to study them: Microscopy and metabarcoding. However, these two methods often deliver different results; thus, their suitability for analyzing diatom communities is frequently debated and evaluated. This study used these two methods to analyze the diatom communities in identical water samples and compare the results. The taxonomy of the species constituting the diatom communities was confirmed, and both methods showed that species belonging to the orders Bacillariales and Naviculales (class Bacillariophyceae) are the most diverse. In the lower taxonomic levels (family, genus, and species), microscopy tended to show a bias toward detecting diatom species (Nitzschia frustulum, Nitzschia inconspicua, Nitzschia intermedia, Navicula gregaria, Navicula perminuta, Navicula recens, Navicula sp.) belonging to the Bacillariaceae and Naviculaceae families. The results of the two methods differed in identifying diatom species in the communities and analyzing their structural characteristics. These results are consistent with the fact that diatoms belonging to the genera Nitzschia and Navicula are abundant in the communities; furthermore, only the Illumina MiSeq data showed the abundance of the Melosira and Entomoneis genera. The results obtained from microscopy were superior to those of Illumina MiSeq regarding species-level identification. Based on the results obtained via microscopy and Illumina MiSeq, it was revealed that neither method is perfect and that each has clear strengths and weaknesses. Therefore, to analyze diatom communities effectively and accurately, these two methods should be combined.}, }
@article {pmid39012154, year = {2024}, author = {Salazar-Jaramillo, L and de la Cuesta-Zuluaga, J and Chica, LA and Cadavid, M and Ley, RE and Reyes, A and Escobar, JS}, title = {Gut microbiome diversity within Clostridia is negatively associated with human obesity.}, journal = {mSystems}, volume = {9}, number = {8}, pages = {e0062724}, pmid = {39012154}, issn = {2379-5077}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology ; Male ; Adult ; Female ; Cross-Sectional Studies ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Body Mass Index ; }, abstract = {UNLABELLED: Clostridia are abundant in the human gut and comprise families associated with host health such as Oscillospiraceae, which has been correlated with leanness. However, culturing bacteria within this family is challenging, leading to their detection primarily through 16S rRNA amplicon sequencing, which has a limited ability to unravel diversity at low taxonomic levels, or by shotgun metagenomics, which is hindered by its high costs and complexity. In this cross-sectional study involving 114 Colombian adults, we used an amplicon-based sequencing strategy with alternative markers-gyrase subunit B (gyrB) and DNA K chaperone heat protein 70 (dnaK)-that evolve faster than the 16S rRNA gene. Comparing the diversity and abundance observed with the three markers in our cohort, we found a reduction in the diversity of Clostridia, particularly within Lachnospiraceae and Oscillospiraceae among obese individuals [as measured by the body mass index (BMI)]. Within Lachnospiraceae, the diversity of Ruminococcus_A negatively correlated with BMI. Within Oscillospiraceae, the genera CAG-170 and Vescimonas also exhibited this negative correlation. In addition, the abundance of Vescimonas was negatively correlated with BMI. Leveraging shotgun metagenomic data, we conducted a phylogenetic and genomic characterization of 120 metagenome-assembled genomes from Vescimonas obtained from a larger sample of the same cohort. We identified 17 of the 72 reported species. The functional annotation of these genomes showed the presence of multiple carbohydrate-active enzymes, particularly glycosyl transferases and glycoside hydrolases, suggesting potential beneficial roles in fiber degradation, carbohydrate metabolism, and butyrate production.<br><br>IMPORTANCE: The gut microbiota is diverse across various taxonomic levels. At the intra-species level, it comprises multiple strains, some of which may be host-specific. However, our understanding of fine-grained diversity has been hindered by the use of the conserved 16S rRNA gene. While shotgun metagenomics offers higher resolution, it remains costly, may fail to identify specific microbes in complex samples, and requires extensive computational resources and expertise. To address this, we employed a simple and cost-effective analysis of alternative genetic markers to explore diversity within Clostridia, a crucial group within the human gut microbiota whose diversity may be underestimated. We found high intra-species diversity for certain groups and associations with obesity. Notably, we identified Vescimonas, an understudied group. Making use of metagenomic data, we inferred functionality, uncovering potential beneficial roles in dietary fiber and carbohydrate degradation, as well as in short-chain fatty acid production.}, }
@article {pmid39012115, year = {2024}, author = {Luyt, NA and de Witt, RN and Divol, B and Patterton, HG and Setati, ME and Taillandier, P and Bauer, FF}, title = {Physical cell-cell contact elicits specific transcriptomic responses in wine yeast species.}, journal = {Microbiology spectrum}, volume = {12}, number = {8}, pages = {e0057223}, pmid = {39012115}, issn = {2165-0497}, support = {UID85055//National Research Foundation (NRF)/ ; UID83471//National Research Foundation (NRF)/ ; }, mesh = {*Wine/microbiology ; *Saccharomyces cerevisiae/genetics/metabolism ; *Transcriptome ; *Fermentation ; *Gene Expression Regulation, Fungal ; Saccharomycetales/genetics/metabolism ; Gene Expression Profiling ; Vitis/microbiology/genetics ; Cell Wall/metabolism/genetics ; Fungal Proteins/genetics/metabolism ; Microbial Interactions ; }, abstract = {Fermenting grape juice provides a habitat for a well-mapped and evolutionarily relevant microbial ecosystem consisting of many natural or inoculated strains of yeasts and bacteria. The molecular nature of many of the ecological interactions within this ecosystem remains poorly understood, with the partial exception of interactions of a metabolic nature such as competition for nutrients and production of toxic metabolites/peptides. Data suggest that physical contact between species plays a significant role in the phenotypic outcome of interspecies interactions. However, the molecular nature of the mechanisms regulating these phenotypes remains unknown. Here, we present a transcriptomic analysis of physical versus metabolic contact between two wine relevant yeast species, Saccharomyces cerevisiae and Lachancea thermotolerans. The data show that these species respond to the physical presence of the other species. In S. cerevisiae, physical contact results in the upregulation of genes involved in maintaining cell wall integrity, cell wall structural components, and genes involved in the production of H2S. In L. thermotolerans, HSP stress response genes were the most significantly upregulated gene family. Both yeasts downregulated genes belonging to the FLO family, some of which play prominent roles in cellular adhesion. qPCR analysis indicates that the expression of some of these genes is regulated in a species-specific manner, suggesting that yeasts adjust gene expression to specific biotic challenges or interspecies interactions. These findings provide fundamental insights into yeast interactions and evolutionary adaptations of these species to the wine ecosystem.IMPORTANCEWithin the wine ecosystem, yeasts are the most relevant contributors to alcoholic fermentation and wine organoleptic characteristics. While some studies have described yeast-yeast interactions during alcoholic fermentation, such interactions remain ill-defined, and little is understood regarding the molecular mechanisms behind many of the phenotypes observed when two or more species are co-cultured. In particular, no study has investigated transcriptional regulation in response to physical interspecies cell-cell contact, as opposed to the generally better understood/characterized metabolic interactions. These data are of direct relevance to our understanding of microbial ecological interactions in general while also creating opportunities to improve ecosystem-based biotechnological applications such as wine fermentation. Furthermore, the presence of competitor species has rarely been considered an evolutionary biotic selection pressure. In this context, the data reveal novel gene functions. This, and further such analysis, is likely to significantly enlarge the genome annotation space.}, }
@article {pmid39011025, year = {2024}, author = {Alam, M and Pandit, B and Moin, A and Iqbal, UN}, title = {Invisible Inhabitants of Plants and a Sustainable Planet: Diversity of Bacterial Endophytes and their Potential in Sustainable Agriculture.}, journal = {Indian journal of microbiology}, volume = {64}, number = {2}, pages = {343-366}, pmid = {39011025}, issn = {0046-8991}, abstract = {Uncontrolled usage of chemical fertilizers, climate change due to global warming, and the ever-increasing demand for food have necessitated sustainable agricultural practices. Removal of ever-increasing environmental pollutants, treatment of life-threatening diseases, and control of drug-resistant pathogens are also the need of the present time to maintain the health and hygiene of nature, as well as human beings. Research on plant-microbe interactions is paving the way to ameliorate all these sustainably. Diverse bacterial endophytes inhabiting the internal tissues of different parts of the plants promote the growth and development of their hosts by different mechanisms, such as through nutrient acquisition, phytohormone production and modulation, protection from biotic or abiotic challenges, assisting in flowering and root development, etc. Notwithstanding, efficient exploitation of endophytes in human welfare is hindered due to scarce knowledge of the molecular aspects of their interactions, community dynamics, in-planta activities, and their actual functional potential. Modern "-omics-based" technologies and genetic manipulation tools have empowered scientists to explore the diversity, dynamics, roles, and functional potential of endophytes, ultimately empowering humans to better use them in sustainable agricultural practices, especially in future harsh environmental conditions. In this review, we have discussed the diversity of bacterial endophytes, factors (biotic as well as abiotic) affecting their diversity, and their various plant growth-promoting activities. Recent developments and technological advancements for future research, such as "-omics-based" technologies, genetic engineering, genome editing, and genome engineering tools, targeting optimal utilization of the endophytes in sustainable agricultural practices, or other purposes, have also been discussed.}, }
@article {pmid39010847, year = {2024}, author = {Qing, J and Zhang, L and Li, C and Li, Y}, title = {Mendelian randomization analysis revealed that albuminuria is the key factor affecting socioeconomic status in CKD patients.}, journal = {Renal failure}, volume = {46}, number = {2}, pages = {2367705}, pmid = {39010847}, issn = {1525-6049}, mesh = {Humans ; *Mendelian Randomization Analysis ; *Albuminuria ; *Renal Insufficiency, Chronic/complications ; *Social Class ; *Glomerular Filtration Rate ; }, abstract = {Previous studies indicate a strong correlation between the incidence of chronic kidney disease (CKD) and lower economic status. However, these studies often struggle to delineate a clear cause-effect relationship, leaving healthcare providers uncertain about how to manage kidney disease in a way that improves patients' financial outcomes. Our study aimed to explore and establish a causal relationship between CKD and socioeconomic status, identifying critical influencing factors. We utilized summary meta-analysis data from the CKDGen Consortium and UK Biobank. Genetic variants identified from these sources served as instrumental variables (IVs) to estimate the association between CKD and socioeconomic status. The presence or absence of CKD, estimated glomerular filtration rate (eGFR), and albuminuria were used as exposures, while income and regional deprivation were analyzed as outcomes. We employed the R packages 'TwoSampleMR' and 'Mendelianrandomization' to conduct both univariable and multivariable Mendelian randomization (MR) analyses, assessing for potential pleiotropy and heterogeneity. Our univariable MR analysis revealed a significant causal relationship between high levels of albuminuria and lower income (OR = 0.84, 95% CI: 0.73-0.96, p = 0.013), with no significant pleiotropy detected. In the multivariable MR analysis, both CKD (OR = 0.867, 95% CI: 0.786-0.957, p = 0.0045) and eGFR (OR = 0.065, 95% CI: 0.010-0.437, p = 0.0049) exhibited significant effects on income. This study underscores that higher albuminuria levels in CKD patients are associated with decreased income and emphasizes the importance of effective management and treatment of albuminuria in CKD patients to mitigate both social and personal economic burdens.}, }
@article {pmid39008123, year = {2024}, author = {Núñez-Muñoz, LA and Sánchez-García, ME and Calderón-Pérez, B and De la Torre-Almaraz, R and Ruiz-Medrano, R and Xoconostle-Cázares, B}, title = {Metagenomic Analysis of Rhizospheric Bacterial Community of Citrus Trees Expressing Phloem-Directed Antimicrobials.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {93}, pmid = {39008123}, issn = {1432-184X}, support = {SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; SENASICA-CINVESTAV 2017//Servicio Nacional de Sanidad e Inocuidad Agroalimentaria (SENASICA)/ ; CF-2023-G-231//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; }, mesh = {*Rhizosphere ; *Phloem/microbiology/metabolism ; *Soil Microbiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota ; *Plant Diseases/microbiology ; *Citrus/microbiology ; Plants, Genetically Modified/microbiology/genetics ; Phylogeny ; Metagenomics ; Muramidase/metabolism/genetics ; Plant Proteins/genetics/metabolism ; beta-Defensins/genetics ; RNA, Ribosomal, 16S/genetics ; Anti-Infective Agents/pharmacology/metabolism ; Citrus sinensis/microbiology ; Plant Roots/microbiology ; }, abstract = {Huanglongbing, also known as citrus greening, is currently the most devastating citrus disease with limited success in prevention and mitigation. A promising strategy for Huanglongbing control is the use of antimicrobials fused to a carrier protein (phloem protein of 16 kDa or PP16) that targets vascular tissues. This study investigated the effects of genetically modified citrus trees expressing Citrus sinensis PP16 (CsPP16) fused to human lysozyme and β-defensin-2 on the soil microbiome diversity using 16S amplicon analysis. The results indicated that there were no significant alterations in alpha diversity, beta diversity, phylogenetic diversity, differential abundance, or functional prediction between the antimicrobial phloem-overexpressing plants and the control group, suggesting minimal impact on microbial community structure. However, microbiota diversity analysis revealed distinct bacterial assemblages between the rhizosphere soil and root environments. This study helps to understand the ecological implications of crops expressing phloem-targeted antimicrobials for vascular disease management, with minimal impact on soil microbiota.}, }
@article {pmid39008061, year = {2024}, author = {Helmy, KG and Abu-Hussien, SH}, title = {Root Rot Management in Common Bean (Phaseolus vulgaris L.) Through Integrated Biocontrol Strategies using Metabolites from Trichoderma harzianum, Serratia marcescens, and Vermicompost Tea.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {94}, pmid = {39008061}, issn = {1432-184X}, mesh = {*Phaseolus/microbiology ; *Plant Diseases/microbiology/prevention &amp; control ; *Serratia marcescens/physiology/metabolism ; *Rhizoctonia/physiology ; *Plant Roots/microbiology ; Biological Control Agents/pharmacology ; Pest Control, Biological ; Antibiosis ; Hypocreales/physiology/metabolism ; Egypt ; Composting ; Soil Microbiology ; }, abstract = {Common bean (Phaseolus vulgaris L.) is an essential food staple and source of income for small-holder farmers across Africa. However, yields are greatly threatened by fungal diseases like root rot induced by Rhizoctonia solani. This study aimed to evaluate an integrated approach utilizing vermicompost tea (VCT) and antagonistic microbes for effective and sustainable management of R. solani root rot in common beans. Fourteen fungal strains were first isolated from infected common bean plants collected across three Egyptian governorates, with R. solani being the most virulent isolate with 50% dominance. Subsequently, the antagonistic potential of vermicompost tea (VCT), Serratia sp., and Trichoderma sp. was assessed against this destructive pathogen. Combinations of 10% VCT and the biocontrol agent isolates displayed potent inhibition of R. solani growth in vitro, prompting in planta testing. Under greenhouse conditions, integrated applications of 5 or 10% VCT with Serratia marcescens, Trichoderma harzianum, or effective microorganisms (EM1) afforded up to 95% protection against pre- and post-emergence damping-off induced by R. solani in common bean cv. Giza 6. Similarly, under field conditions, combining VCT with EM1 (VCT + EM1) or Trichoderma harzianum (VCT + Trichoderma harzianum) substantially suppressed disease severity by 65.6% and 64.34%, respectively, relative to untreated plants. These treatments also elicited defense enzyme activity and distinctly improved growth parameters including 136.68% and 132.49% increases in pod weight per plant over control plants. GC-MS profiling of Trichoderma harzianum, Serratia marcescens, and vermicompost tea (VCT) extracts revealed unique compounds dominated by cyclic pregnane, fatty acid methyl esters, linoleic acid derivatives, and free fatty acids like oleic, palmitic, and stearic acids with confirmed biocontrol and plant growth-promoting activities. The results verify VCT-mediated delivery of synergistic microbial consortia as a sustainable platform for integrated management of debilitating soil-borne diseases, enhancing productivity and incomes for smallholder bean farmers through regeneration of soil health. Further large-scale validation can pave the adoption of this climate-resilient approach for securing food and nutrition security.}, }
@article {pmid39007602, year = {2024}, author = {Jensen, N and Maldonado-Gomez, M and Krishnakumar, N and Weng, C-Y and Castillo, J and Razi, D and Kalanetra, K and German, JB and Lebrilla, CB and Mills, DA and Taft, DH}, title = {Dietary fiber monosaccharide content alters gut microbiome composition and fermentation.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {8}, pages = {e0096424}, pmid = {39007602}, issn = {1098-5336}, support = {R01DK124193//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; F32HD093185//HHS | National Institutes of Health (NIH)/ ; //Mars (Mars Incorporated)/ ; F32 HD093185/HD/NICHD NIH HHS/United States ; R01 DK124193/DK/NIDDK NIH HHS/United States ; //Gut Microbiome Yogurt and Probiotics Fellowship/ ; //Bill and Melinda Gates Foundation (GF)/ ; }, mesh = {*Fermentation ; *Gastrointestinal Microbiome ; *Dietary Fiber/metabolism ; *Monosaccharides/metabolism/analysis ; Animals ; *Bacteria/classification/metabolism/genetics ; Feces/microbiology/chemistry ; Fatty Acids, Volatile/metabolism ; }, abstract = {UNLABELLED: Members of the mammalian gut microbiota metabolize diverse complex carbohydrates that are not digested by the host, which are collectively labeled "dietary fiber." While the enzymes and transporters that each strain uses to establish a nutrient niche in the gut are often exquisitely specific, the relationship between carbohydrate structure and microbial ecology is imperfectly understood. The present study takes advantage of recent advances in complex carbohydrate structure determination to test the effects of fiber monosaccharide composition on microbial fermentation. Fifty-five fibers with varied monosaccharide composition were fermented by a pooled feline fecal inoculum in a modified MiniBioReactor array system over a period of 72 hours. The content of the monosaccharides glucose and xylose was significantly associated with the reduction of pH during fermentation, which was also predictable from the concentrations of the short-chain fatty acids lactic acid, propionic acid, and the signaling molecule indole-3-acetic acid. Microbiome diversity and composition were also predictable from monosaccharide content and SCFA concentration. In particular, the concentrations of lactic acid and propionic acid correlated with final alpha diversity and were significantly associated with the relative abundance of several of the genera, including Lactobacillus and Dubosiella. Our results suggest that monosaccharide composition offers a generalizable method to compare any dietary fiber of interest and uncover links between diet, gut microbiota, and metabolite production.<br><br>IMPORTANCE: The survival of a microbial species in the gut depends on the availability of the nutrients necessary for that species to survive. Carbohydrates in the form of non-host digestible fiber are of particular importance, and the set of genes possessed by each species for carbohydrate consumption can vary considerably. Here, differences in the monosaccharides that are the building blocks of fiber are considered for their impact on both the survival of different species of microbes and on the levels of microbial fermentation products produced. This work demonstrates that foods with similar monosaccharide content will have consistent effects on the survival of microbial species and on the production of microbial fermentation products.}, }
@article {pmid39003240, year = {2024}, author = {Vass, M and Székely, AJ and Carlsson-Graner, U and Wikner, J and Andersson, A}, title = {Microeukaryote community coalescence strengthens community stability and elevates diversity.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {8}, pages = {}, pmid = {39003240}, issn = {1574-6941}, support = {2018-05973//Swedish Research Council/ ; }, mesh = {*Biodiversity ; *Diatoms/growth &amp; development ; *Fungi/genetics/classification/growth &amp; development ; Rivers/microbiology ; Seawater/microbiology ; Ciliophora/growth &amp; development/genetics ; Cercozoa/genetics/growth &amp; development ; Microbiota ; Eukaryota/growth &amp; development ; }, abstract = {Mixing of entire microbial communities represents a frequent, yet understudied phenomenon. Here, we mimicked estuarine condition in a microcosm experiment by mixing a freshwater river community with a brackish sea community and assessed the effects of both environmental and community coalescences induced by varying mixing processes on microeukaryotic communities. Signs of shifted community composition of coalesced communities towards the sea parent community suggest asymmetrical community coalescence outcome, which, in addition, was generally less impacted by environmental coalescence. Community stability, inferred from community cohesion, differed among river and sea parent communities, and increased following coalescence treatments. Generally, community coalescence increased alpha diversity and promoted competition from the introduction (or emergence) of additional (or rare) species. These competitive interactions in turn had community stabilizing effect as evidenced by the increased proportion of negative cohesion. The fate of microeukaryotes was influenced by mixing ratios and frequencies (i.e. one-time versus repeated coalescence). Namely, diatoms were negatively impacted by coalescence, while fungi, ciliates, and cercozoans were promoted to varying extents, depending on the mixing ratios of the parent communities. Our study suggests that the predictability of coalescence outcomes was greater when the sea parent community dominated the final community, and this predictability was further enhanced when communities collided repeatedly.}, }
@article {pmid39003046, year = {2025}, author = {Lamprea Pineda, PA and Demeestere, K and Alvarado-Alvarado, AA and Devlieghere, F and Boon, N and Van Langenhove, H and Walgraeve, C}, title = {Degradation of gaseous hydrocarbons in aerated stirred bioreactors inoculated with Rhodococcus erythropolis: Effect of the carbon source and SIFT-MS method development.}, journal = {Journal of environmental sciences (China)}, volume = {147}, number = {}, pages = {268-281}, doi = {10.1016/j.jes.2023.10.020}, pmid = {39003046}, issn = {1001-0742}, mesh = {*Rhodococcus/metabolism ; *Bioreactors/microbiology ; *Biodegradation, Environmental ; *Hydrocarbons/metabolism ; Carbon/metabolism ; Air Pollutants/metabolism/analysis ; Mass Spectrometry ; Toluene/metabolism ; Xylenes/metabolism ; Butanes/metabolism ; Benzene Derivatives ; Pentanes ; }, abstract = {The study of microbial hydrocarbons removal is of great importance for the development of future bioremediation strategies. In this study, we evaluated the removal of a gaseous mixture containing toluene, m-xylene, ethylbenzene, cyclohexane, butane, pentane, hexane and heptane in aerated stirred bioreactors inoculated with Rhodococcus erythropolis and operated under non-sterile conditions. For the real-time measurement of hydrocarbons, a novel systematic approach was implemented using Selected-Ion Flow Tube Mass Spectrometry (SIFT-MS). The effect of the carbon source (∼9.5 ppmv) on (i) the bioreactors' performance (BR1: dosed with only cyclohexane as a single hydrocarbon versus BR2: dosed with a mixture of the 8 hydrocarbons) and (ii) the evolution of microbial communities over time were investigated. The results showed that cyclohexane reached a maximum removal efficiency (RE) of 53% ± 4% in BR1. In BR2, almost complete removal of toluene, m-xylene and ethylbenzene, being the most water-soluble and easy-to-degrade carbon sources, was observed. REs below 32% were obtained for the remaining compounds. By exposing the microbial consortium to only the five most recalcitrant hydrocarbons, REs between 45% ± 5% and 98% ± 1% were reached. In addition, we observed that airborne microorganisms populated the bioreactors and that the type of carbon source influenced the microbial communities developed. The abundance of species belonging to the genus Rhodococcus was below 10% in all bioreactors at the end of the experiments. This work provides fundamental insights to understand the complex behavior of gaseous hydrocarbon mixtures in bioreactors, along with a systematic approach for the development of SIFT-MS methods.}, }
@article {pmid39002491, year = {2024}, author = {Meroz, N and Livny, T and Friedman, J}, title = {Quantifying microbial interactions: concepts, caveats, and applications.}, journal = {Current opinion in microbiology}, volume = {80}, number = {}, pages = {102511}, doi = {10.1016/j.mib.2024.102511}, pmid = {39002491}, issn = {1879-0364}, mesh = {*Microbial Interactions ; Ecosystem ; Microbiota ; Bacteria/metabolism/genetics ; }, abstract = {Microbial communities are fundamental to every ecosystem on Earth and hold great potential for biotechnological applications. However, their complex nature hampers our ability to study and understand them. A common strategy to tackle this complexity is to abstract the community into a network of interactions between its members - a phenomenological description that captures the overall effects of various chemical and physical mechanisms that underpin these relationships. This approach has proven useful for numerous applications in microbial ecology, including predicting community dynamics and stability and understanding community assembly and evolution. However, care is required in quantifying and interpreting interactions. Here, we clarify the concept of an interaction and discuss when interaction measurements are useful despite their context-dependent nature. Furthermore, we categorize different approaches for quantifying interactions, highlighting the research objectives each approach is best suited for.}, }
@article {pmid39001714, year = {2024}, author = {Williams, TA and Davin, AA and Szánthó, LL and Stamatakis, A and Wahl, NA and Woodcroft, BJ and Soo, RM and Eme, L and Sheridan, PO and Gubry-Rangin, C and Spang, A and Hugenholtz, P and Szöllősi, GJ}, title = {Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39001714}, issn = {1751-7370}, support = {GBMF9741//Gordon and Betty Moore Foundation/ ; 714774//European Union's Horizon 2020 Research and Innovation Programme/ ; /ERC_/European Research Council/International ; 947317//European Union's Horizon 2020 Research and Innovation Programme/ ; 735929LPI//Simons Foundation/ ; FL150100038//Australian Research Council Laureate Fellowship/ ; 812811//Simons Foundation/ ; 101087081//European Union's Horizon Europe ERA Chair Program/ ; URF150571//Royal Society University Research Fellowship/ ; }, mesh = {*Phylogeny ; *Archaea/genetics/classification ; Bacteria/genetics/classification ; Evolution, Molecular ; Genome, Bacterial ; Symbiosis ; Ecology ; }, abstract = {In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host-microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature, and oxygen use offer enormous potential for understanding the rich tapestry of microbial life.}, }
@article {pmid38995161, year = {2024}, author = {Seixas, MH and Munroe, JS and Eggleston, EM}, title = {Bacterial diversity and geomicrobiology of Winter Wonderland ice cave, Utah, USA.}, journal = {MicrobiologyOpen}, volume = {13}, number = {4}, pages = {e1426}, pmid = {38995161}, issn = {2045-8827}, support = {//Middlebury College/ ; }, mesh = {Utah ; *Bacteria/classification/genetics/isolation &amp; purification ; *Caves/microbiology ; *Ice ; Soil Microbiology ; Biodiversity ; Microscopy, Electron, Scanning ; Seasons ; Water Microbiology ; }, abstract = {The Winter Wonderland ice cave, located at an elevation of 3140 m above sea level in the Uinta Mountains of northern Utah, USA, maintains a constant sub-zero temperature. Seasonal snowmelt and rain enter the cave, freeze on the surface of the existing ice, and contribute to a 3-m-thick layered ice mass. This ice mass contains organic matter and cryogenic cave carbonates (CCCs) that date back centuries. In this study, samples of ice, liquid water, and exposed CCCs were collected to examine the bacterial communities within the cave and to determine if these communities vary spatially and between sample types. Flow cytometry showed that cell counts are an order of magnitude higher in liquid water samples than in ice. Epifluorescence microscopy and scanning electron microscopy imaging revealed potential coccoid and bacillus microbial morphologies in water samples and putative cells or calcite spherules in the CCCs. The diversity of bacteria associated with soil, identified through sequence-based analysis, supports the hypothesis that water enters the cave by filtering through soil and bedrock. A differential abundance of bacterial taxa was observed between sample types, with the greatest diversity found in CCCs. This supports a geomicrobiological framework where microbes aggregate in the water, sink into a concentrated layer, and precipitate out of the ice with the CCCs, thereby reducing the cell counts in the ice. These CCCs may provide essential nutrients for the bacteria or could themselves be products of biomineralization.}, }
@article {pmid38995046, year = {2024}, author = {Gibson, C and Jauffur, S and Guo, B and Frigon, D}, title = {Activated sludge microbial community assembly: the role of influent microbial community immigration.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {8}, pages = {e0059824}, pmid = {38995046}, issn = {1098-5336}, support = {RGPIN-2016-06498, STPGP-521349-18//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; McGill Engineering Doctoral Award//Faculty of Engineering, McGill University (Faculty of Engineering, McGill)/ ; }, mesh = {*Sewage/microbiology ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; Wastewater/microbiology ; Waste Disposal, Fluid/methods ; }, abstract = {Wastewater treatment plants (WWTPs) are host to diverse microbial communities and receive a constant influx of microbes from influent wastewater. However, the impact of immigrants on the structure and activities of the activated sludge (AS) microbial community remains unclear. To gain insight on this phenomenon known as perpetual community coalescence, the current study utilized controlled manipulative experiments that decoupled the influent wastewater composition from the microbial populations to reveal the fundamental mechanisms involved in immigration between sewers and AS-WWTP. The immigration dynamics of heterotrophs were analyzed by harvesting wastewater biomass solids from three different sewer systems and adding to synthetic wastewater. Immigrating influent populations were observed to contribute up to 14% of the sequencing reads in the AS. By modeling the net growth rate of taxa, it was revealed that immigrants primarily exhibited low or negative net growth rates. By developing a protocol to reproducibly grow AS-WWTP communities in the lab, we have laid down the foundational principles for the testing of operational factors creating community variations with low noise and appropriate replication. Understanding the processes that drive microbial community diversity and assembly is a key question in microbial ecology. In the future, this knowledge can be used to manipulate the structure of microbial communities and improve system performance in WWTPs.IMPORTANCEIn biological wastewater treatment processes, the microbial community composition is essential in the performance and stability of the system. This study developed a reproducible protocol to investigate the impact of influent immigration (or perpetual coalescence of the sewer and activated sludge communities) with appropriate reproducibility and controls, allowing intrinsic definitions of core and immigrant populations to be established. The method developed herein will allow sequential manipulative experiments to be performed to test specific hypothesis and optimize wastewater treatment processes to meet new treatment goals.}, }
@article {pmid38993674, year = {2024}, author = {Huang, C and Liu, D and Yang, S and Huang, Y and Wei, X and Zhang, P and Lin, J and Xu, B and Liu, Y and Guo, D and Li, Y and Li, J and Zhang, H}, title = {Effect of time-restricted eating regimen on weight loss is mediated by gut microbiome.}, journal = {iScience}, volume = {27}, number = {7}, pages = {110202}, pmid = {38993674}, issn = {2589-0042}, abstract = {Time-restricted eating (TRE) is a promising obesity management strategy, but weight-loss efficacy varies among participants, and the underlying mechanism is unclear. The study aimed to investigate the role of gut microbiota in weight-loss response during long-term TRE intervention. We analyzed data from 51 obese adults in a 12-month TRE program, categorizing them into distinct weight loss groups (DG) and moderate weight loss groups (MG) based on their TRE responses. Shotgun metagenomic sequencing analysis revealed a significant increase in species closely associated with weight loss effectiveness and metabolic parameter changes in the DG group. Pathways related to fatty acid biosynthesis, glycogen biosynthesis, and nucleotide metabolism were reduced in the DG group and enhanced in the MG group. Next, we identified nine specific species at baseline that contributed better responses to TRE intervention and significant weight loss. Collectively, gut microbiota contributes to responsiveness heterogeneity in TRE and can predict weight-loss effectiveness.}, }
@article {pmid38992757, year = {2024}, author = {Zeng, X and Liu, Y and Wang, Q and Ma, H and Li, X and Wang, Q and Yang, Q}, title = {Tanning wastewater restructured nitrogen-transforming bacteria communities and promoted N2O emissions in receiving river riparian sediments.}, journal = {Environmental research}, volume = {260}, number = {}, pages = {119580}, doi = {10.1016/j.envres.2024.119580}, pmid = {38992757}, issn = {1096-0953}, mesh = {*Rivers/microbiology/chemistry ; *Wastewater/microbiology/chemistry/analysis ; *Geologic Sediments/microbiology/chemistry ; *Nitrogen/analysis ; *Tanning ; Water Pollutants, Chemical/analysis ; Bacteria ; Denitrification ; Nitrous Oxide/analysis ; }, abstract = {Physicochemical and toxicological characterization of leather tanning wastewater has been widely documented. However, few reports have examined the response of denitrification N2 and N2O emissions in riparian sediments of tannery wastewater-receiving rivers. In this study, [15]N-nitrate labeling was used to reveal the effects of tanning wastewater on denitrification N2 and N2O emission in a wastewater-receiving river (the old Mang River, OMR). OMR riparian sediments were highly polluted with total organic carbon (93.39 mg/kg), total nitrogen (5.00 g/kg) and heavy metals; specifically, Cr, Zn, Cd, and Pb were found at concentrations 47.3, 5.8, 1.6, 4.3, and 2.8 times that in a nearby parallel river without tanning wastewater input (the new Mang River, NMR), respectively. The denitrification N2 emission rates (0.0015 nmol N · g[-1] h[-1]) of OMR riparian sediments were significantly reduced by 2.5 times compared with those from the NMR (p < 0.05), but the N2O emission rates (0.31 nmol N · g[-1] h[-1]) were significantly increased (4.1 times, p < 0.05). Although the dominant nitrogen-transforming bacteria phylum was Proteobacteria in the riparian sediments of both rivers, 11 nitrogen-transforming bacteria genera in the OMR were found to be significantly enriched; five of these were related to pollutant degradation based on linear discriminant analysis (LDA >3). The average activity of the electron transport system in the OMR was 6.3 times lower than that of the NMR (p < 0.05). Among pollution factors, heavy metal complex pollution was the dominant factor driving variations in N2O emissions, microbial community structure, and electron transport system activity. These results provide a new understanding and reference for the treatment of tanning wastewater-receiving rivers.}, }
@article {pmid38987492, year = {2024}, author = {Ng, MS and Soon, N and Afiq-Rosli, L and Kunning, I and Mana, RR and Chang, Y and Wainwright, BJ}, title = {Highly Diverse Symbiodiniaceae Types Hosted by Corals in a Global Hotspot of Marine Biodiversity.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {92}, pmid = {38987492}, issn = {1432-184X}, mesh = {*Anthozoa/microbiology ; Animals ; *Biodiversity ; *Dinoflagellida/genetics/classification/physiology ; *Symbiosis ; *Coral Reefs ; Papua New Guinea ; Phylogeny ; High-Throughput Nucleotide Sequencing ; }, abstract = {Symbiotic dinoflagellates in the genus Symbiodiniaceae play vital roles in promoting resilience and increasing stress tolerance in their coral hosts. While much of the world's coral succumb to the stresses associated with increasingly severe and frequent thermal bleaching events, live coral cover in Papua New Guinea (PNG) remains some of the highest reported globally despite the historically warm waters surrounding the country. Yet, in spite of the high coral cover in PNG and the acknowledged roles Symbiodiniaceae play within their hosts, these communities have not been characterized in this global biodiversity hotspot. Using high-throughput sequencing of the ITS2 rDNA gene, we profiled the endosymbionts of four coral species, Diploastrea heliopora, Pachyseris speciosa, Pocillopora acuta, and Porites lutea, across six sites in PNG. Our findings reveal patterns of Cladocopium and Durusdinium dominance similar to other reefs in the Coral Triangle, albeit with much greater intra- and intergenomic variation. Host- and site-specific variations in Symbiodiniaceae type profiles were observed across collection sites, appearing to be driven by environmental conditions. Notably, the extensive intra- and intergenomic variation, coupled with many previously unreported sequences, highlight PNG as a potential hotspot of symbiont diversity. This work represents the first characterization of the coral-symbiont community structure in the PNG marine biodiversity hotspot, serving as a baseline for future studies.}, }
@article {pmid38987022, year = {2024}, author = {Litchman, E and Villéger, S and Zinger, L and Auguet, JC and Thuiller, W and Munoz, F and Kraft, NJB and Philippot, L and Violle, C}, title = {Refocusing the microbial rare biosphere concept through a functional lens.}, journal = {Trends in ecology &amp; evolution}, volume = {39}, number = {10}, pages = {923-936}, doi = {10.1016/j.tree.2024.06.005}, pmid = {38987022}, issn = {1872-8383}, mesh = {*Microbiota ; Ecosystem ; Biodiversity ; }, abstract = {The influential concept of the rare biosphere in microbial ecology has underscored the importance of taxa occurring at low abundances yet potentially playing key roles in communities and ecosystems. Here, we refocus the concept of rare biosphere through a functional trait-based lens and provide a framework to characterize microbial functional rarity, a combination of numerical scarcity across space or time and trait distinctiveness. We demonstrate how this novel interpretation of the rare biosphere, rooted in microbial functions, can enhance our mechanistic understanding of microbial community structure. It also sheds light on functionally distinct microbes, directing conservation efforts towards taxa harboring rare yet ecologically crucial functions.}, }
@article {pmid38985714, year = {2024}, author = {Ugwuanyi, IR and Steele, A and Glamoclija, M}, title = {Microbial Ecology of an Arctic Travertine Geothermal Spring: Implications for Biosignature Preservation and Astrobiology.}, journal = {Astrobiology}, volume = {24}, number = {7}, pages = {734-753}, doi = {10.1089/ast.2023.0130}, pmid = {38985714}, issn = {1557-8070}, mesh = {Arctic Regions ; *Exobiology ; *Hot Springs/microbiology/chemistry ; Mars ; Silicon Dioxide/chemistry ; Svalbard ; Carbonates/chemistry/analysis ; Microbiota ; Temperature ; Biofilms ; }, abstract = {Jotun springs in Svalbard, Norway, is a rare warm environment in the Arctic that actively forms travertine. In this study, we assessed the microbial ecology of Jotun's active (aquatic) spring and dry spring transects. We evaluated the microbial preservation potential and mode, as well as the astrobiological relevance of the travertines to marginal carbonates mapped at Jezero Crater on Mars (the Mars 2020 landing site). Our results revealed that microbial communities exhibited spatial dynamics controlled by temperature, fluid availability, and geochemistry. Amorphous carbonates and silica precipitated within biofilm and on the surface of filamentous microorganisms. The water discharged at the source is warm, with near neutral pH, and undersaturated in silica. Hence, silicification possibly occurred through cooling, dehydration, and partially by a microbial presence or activities that promote silica precipitation. CO2 degassing and possible microbial contributions induced calcite precipitation and travertine formation. Jotun revealed that warm systems that are not very productive in carbonate formation may still produce significant carbonate buildups and provide settings favorable for fossilization through silicification and calcification. Our findings suggest that the potential for amorphous silica precipitation may be essential for Jezero Crater's marginal carbonates because it significantly increases the preservation potential of putative martian organisms.}, }
@article {pmid38983631, year = {2024}, author = {Hawes, I and García-Maldonado, JQ and Falcón, LI}, title = {Editorial: Exploring microbial mat communities in extreme environments.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1440619}, doi = {10.3389/fmicb.2024.1440619}, pmid = {38983631}, issn = {1664-302X}, }
@article {pmid38982970, year = {2024}, author = {Jiang, J and Xiang, X and Zhou, Q and Zhou, L and Bi, X and Khanal, SK and Wang, Z and Chen, G and Guo, G}, title = {Optimization of a Novel Engineered Ecosystem Integrating Carbon, Nitrogen, Phosphorus, and Sulfur Biotransformation for Saline Wastewater Treatment Using an Interpretable Machine Learning Approach.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {29}, pages = {12989-12999}, doi = {10.1021/acs.est.4c03160}, pmid = {38982970}, issn = {1520-5851}, mesh = {*Phosphorus/metabolism ; *Nitrogen/metabolism ; *Sulfur/metabolism ; *Machine Learning ; *Wastewater/chemistry ; *Carbon/metabolism ; Biotransformation ; Ecosystem ; Waste Disposal, Fluid/methods ; Denitrification ; }, abstract = {The denitrifying sulfur (S) conversion-associated enhanced biological phosphorus removal (DS-EBPR) process for treating saline wastewater is characterized by its unique microbial ecology that integrates carbon (C), nitrogen (N), phosphorus (P), and S biotransformation. However, operational instability arises due to the numerous parameters and intricates bacterial interactions. This study introduces a two-stage interpretable machine learning approach to predict S conversion-driven P removal efficiency and optimize DS-EBPR process. Stage one utilized the XGBoost regression model, achieving an R[2] value of 0.948 for predicting sulfate reduction (SR) intensity from anaerobic parameters with feature engineering. Stage two involved the CatBoost classification and regression model integrating anoxic parameters with the predicted SR values for predicting P removal, reaching an accuracy of 94% and an R[2] value of 0.93, respectively. This study identified key environmental factors, including SR intensity (20-45 mg S/L), influent P concentration (<9.0 mg P/L), mixed liquor volatile suspended solids (MLVSS)/mixed liquor suspended solids (MLSS) ratio (0.55-0.72), influent C/S ratio (0.5-1.0), anoxic reaction time (5-6 h), and MLSS concentration (>6.50 g/L). A user-friendly graphic interface was developed to facilitate easier optimization and control. This approach streamlines the determination of optimal conditions for enhancing P removal in the DS-EBPR process.}, }
@article {pmid38982962, year = {2024}, author = {Sbibih, Y and Saddari, A and Alla, I and Abdesselami, O and Ben Moussa, C and Ezrari, S and Benaissa, E and Ben Lahlou, Y and Elouennass, M and Maleb, A}, title = {Microbial ecology of protective isolation room: Air and Surfaces.}, journal = {La Tunisie medicale}, volume = {102}, number = {7}, pages = {394-398}, pmid = {38982962}, issn = {2724-7031}, mesh = {Humans ; *Air Microbiology ; *Cross Infection/prevention &amp; control/epidemiology/microbiology ; Prospective Studies ; Patients' Rooms/organization &amp; administration/statistics &amp; numerical data ; Patient Isolation/methods ; Hospitals, University ; Immunocompromised Host ; Tunisia/epidemiology ; }, abstract = {INTRODUCTION: Healthcare-associated infections pose a significant public health burden, leading to morbidity, mortality, prolonged hospital stays, and substantial social and economic costs. Immunocompromised patients are at a heightened risk of nosocomial infections.<br><br>AIM: This prospective study conducted at Mohammed VI University Hospital of Oujda aimed to assess the microbial ecology of surfaces and air in an immunosuppressed patient room compared to a double hospitalization room.<br><br>METHODS: Microbiological air purity tests were conducted employing both the sedimentation method and the collision method with the assistance of Microflow Alpha. The sedimentation method used Mueller Hinton with 5% human blood, facilitating the free fall of contaminated dust particles. The collection program employed was set for 10 minutes per 1 m3. For surface sampling, swabs were taken from a 25 cm2 surface. The swabs were immediately forwarded to the Microbiology Laboratory. We carried out both macroscopic and microscopic identification of colonies, followed by definitive biochemical identification using the BD phoenixTM system. Antibiotic susceptibility was assessed through agar diffusion on Muller Hinton medium coupled with the determination of the minimum inhibitory concentration.<br><br>RESULTS: The results revealed a decreased bacterial count within the protective isolation room, in contrast to the standard hospital room. We noted the predominance of coagulase-negative Staphylococcus spp and Bacillus spp. Staphylococcus aureus and Aspergillus spp, common pathogens in healthcare-associated infections, were notably absent in the protective isolation room. The findings underline the pivotal role of hospital environments in the transmission of healthcare-associated infections.<br><br>CONCLUSION: The protective isolation room demonstrated effective control of microbial contamination, with fewer and less resistant germs. The study highlighted the significance of air treatment systems in preventing the spread of opportunistic infections. Our study underscored the critical role of microbiological cleanliness in preventing nosocomial infections.}, }
@article {pmid38982749, year = {2024}, author = {Schrecengost, A and Rotterová, J and Poláková, K and Čepička, I and Beinart, RA}, title = {Divergent marine anaerobic ciliates harbor closely related Methanocorpusculum endosymbionts.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38982749}, issn = {1751-7370}, support = {//Simons Foundation Early Career Investigator in Marine Microbial Ecology and Evolution Award/ ; 1330406//United States National Science Foundation EPSCoR Track II Cooperative Agreement Award/ ; 23-06004S//Czech Science Foundation/ ; OIA-1655221//National Science Foundation EPSCoR/ ; //Vini&#x10d;n&#xe1; Microscopy Core Facility/ ; LM2023050//MEYS CR/ ; 1919588//National Science Foundation Major Research Instrumentation/ ; }, mesh = {*Symbiosis ; *Ciliophora/classification/genetics/physiology ; *Phylogeny ; Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; *Geologic Sediments/microbiology ; RNA, Ribosomal, 18S/genetics ; DNA, Archaeal/genetics/chemistry ; Sequence Analysis, DNA ; Seawater/microbiology/parasitology ; }, abstract = {Ciliates are a diverse group of protists known for their ability to establish various partnerships and thrive in a wide variety of oxygen-depleted environments. Most anaerobic ciliates harbor methanogens, one of the few known archaea living intracellularly. These methanogens increase the metabolic efficiency of host fermentation via syntrophic use of host end-product in methanogenesis. Despite the ubiquity of these symbioses in anoxic habitats, patterns of symbiont specificity and fidelity are not well known. We surveyed two unrelated, commonly found groups of anaerobic ciliates, the Plagiopylea and Metopida, isolated from anoxic marine sediments. We sequenced host 18S rRNA and symbiont 16S rRNA marker genes as well as the symbiont internal transcribed spacer region from our cultured ciliates to identify hosts and their associated methanogenic symbionts. We found that marine ciliates from both of these co-occurring, divergent groups harbor closely related yet distinct intracellular archaea within the Methanocorpusculum genus. The symbionts appear to be stable at the host species level, but at higher taxonomic levels, there is evidence that symbiont replacements have occurred. Gaining insight into this unique association will deepen our understanding of the complex transmission modes of marine microbial symbionts, and the mutualistic microbial interactions occurring across domains of life.}, }
@article {pmid38980056, year = {2024}, author = {Henson, MW and Thrash, JC}, title = {Microbial ecology of northern Gulf of Mexico estuarine waters.}, journal = {mSystems}, volume = {9}, number = {8}, pages = {e0131823}, pmid = {38980056}, issn = {2379-5077}, support = {Simons Investigator in Aquatic Microbial Ecology Award//Simons Foundation (SF)/ ; Marine Microbiology Postdoctoral Fellowship//Simons Foundation (SF)/ ; LEQSF[2014-2017]-RDA-06//Louisiana Board of Regents (LBR)/ ; Lerner Gray grant//American Museum of Natural History (AMNH)/ ; Gulf Research Program Early Career Research Fellowship//National Academies of Sciences, Engineering, and Medicine (NASEM)/ ; LEEC Grant//Louisiana Department of Fish and Wildlife/ ; }, mesh = {Gulf of Mexico ; *Estuaries ; Bacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology/chemistry ; Louisiana ; Microbiota ; Water Microbiology ; Ecosystem ; Salinity ; }, abstract = {Estuarine and coastal ecosystems are of high economic and ecological importance, owing to their diverse communities and the disproportionate role they play in carbon cycling, particularly in carbon sequestration. Organisms inhabiting these environments must overcome strong natural fluctuations in salinity, nutrients, and turbidity, as well as numerous climate change-induced disturbances such as land loss, sea level rise, and, in some locations, increasingly severe tropical cyclones that threaten to disrupt future ecosystem health. The northern Gulf of Mexico (nGoM) along the Louisiana coast contains dozens of estuaries, including the Mississippi-Atchafalaya River outflow, which dramatically influence the region due to their vast upstream watershed. Nevertheless, the microbiology of these estuaries and surrounding coastal environments has received little attention. To improve our understanding of microbial ecology in the understudied coastal nGoM, we conducted a 16S rRNA gene amplicon survey at eight sites and multiple time points along the Louisiana coast and one inland swamp spanning freshwater to high brackish salinities, totaling 47 duplicated Sterivex (0.2-2.7 µm) and prefilter (>2.7 µm) samples. We cataloged over 13,000 Amplicon Sequence ariants (ASVs) from common freshwater and marine clades such as SAR11 (Alphaproteobacteria), Synechococcus (Cyanobacteria), and acI and Candidatus Actinomarina (Actinobacteria). We observed correlations with freshwater or marine habitats in many organisms and characterized a group of taxa with specialized distributions across brackish water sites, supporting the hypothesis of an endogenous brackish-water community. Additionally, we observed brackish-water associations for several aquatic clades typically considered marine or freshwater taxa, such as SAR11 subclade II, SAR324, and the acI Actinobacteria. The data presented here expand the geographic coverage of microbial ecology in estuarine communities, help delineate the native and transitory members of these environments, and provide critical aquatic microbiological baseline data for coastal and estuarine sites in the nGoM.IMPORTANCEEstuarine and coastal waters are diverse ecosystems influenced by tidal fluxes, interconnected wetlands, and river outflows, which are of high economic and ecological importance. Microorganisms play a pivotal role in estuaries as "first responders" and ecosystem architects, yet despite their ecological importance, they remain underrepresented in microbial studies compared to open ocean environments. This leads to substantial knowledge gaps that are important for understanding global biogeochemical cycling and making decisions about conservation and management strategies in these environments. Our study makes key contributions to the microbial ecology of estuarine and coastal habitats in the northern Gulf of Mexico. Our microbial community data support the concept of a globally distributed, core brackish microbiome and emphasize previously underrecognized brackish-water taxa. Given the projected worsening of land loss, oil spills, and natural disasters in this region, our results will serve as important baseline data for researchers investigating the microbial communities found across estuaries.}, }
@article {pmid38980052, year = {2024}, author = {Flinkstrom, Z and Bryson, S and Candry, P and Winkler, M-KH}, title = {Metagenomic clustering links specific metabolic functions to globally relevant ecosystems.}, journal = {mSystems}, volume = {9}, number = {8}, pages = {e0057324}, pmid = {38980052}, issn = {2379-5077}, support = {DE-SC0020356//U.S. Department of Energy (DOE)/ ; }, mesh = {*Metagenomics/methods ; *Metagenome/genetics ; Ecosystem ; Cluster Analysis ; Microbiota/genetics ; }, abstract = {UNLABELLED: Metagenomic sequencing has advanced our understanding of biogeochemical processes by providing an unprecedented view into the microbial composition of different ecosystems. While the amount of metagenomic data has grown rapidly, simple-to-use methods to analyze and compare across studies have lagged behind. Thus, tools expressing the metabolic traits of a community are needed to broaden the utility of existing data. Gene abundance profiles are a relatively low-dimensional embedding of a metagenome's functional potential and are, thus, tractable for comparison across many samples. Here, we compare the abundance of KEGG Ortholog Groups (KOs) from 6,539 metagenomes from the Joint Genome Institute's Integrated Microbial Genomes and Metagenomes (JGI IMG/M) database. We find that samples cluster into terrestrial, aquatic, and anaerobic ecosystems with marker KOs reflecting adaptations to these environments. For instance, functional clusters were differentiated by the metabolism of antibiotics, photosynthesis, methanogenesis, and surprisingly GC content. Using this functional gene approach, we reveal the broad-scale patterns shaping microbial communities and demonstrate the utility of ortholog abundance profiles for representing a rapidly expanding body of metagenomic data.<br><br>IMPORTANCE: Metagenomics, or the sequencing of DNA from complex microbiomes, provides a view into the microbial composition of different environments. Metagenome databases were created to compile sequencing data across studies, but it remains challenging to compare and gain insight from these large data sets. Consequently, there is a need to develop accessible approaches to extract knowledge across metagenomes. The abundance of different orthologs (i.e., genes that perform a similar function across species) provides a simplified representation of a metagenome's metabolic potential that can easily be compared with others. In this study, we cluster the ortholog abundance profiles of thousands of metagenomes from diverse environments and uncover the traits that distinguish them. This work provides a simple to use framework for functional comparison and advances our understanding of how the environment shapes microbial communities.}, }
@article {pmid38979877, year = {2024}, author = {Overgaard, CK and Jamy, M and Radutoiu, S and Burki, F and Dueholm, MKD}, title = {Benchmarking long-read sequencing strategies for obtaining ASV-resolved rRNA operons from environmental microeukaryotes.}, journal = {Molecular ecology resources}, volume = {24}, number = {7}, pages = {e13991}, doi = {10.1111/1755-0998.13991}, pmid = {38979877}, issn = {1755-0998}, support = {9041-00236B//Danmarks Frie Forskningsfond/ ; 2021-04055//Vetenskapsr&#xe5;det/ ; 101044505/ERC_/European Research Council/International ; }, mesh = {*Eukaryota/genetics/classification ; *Computational Biology/methods ; *High-Throughput Nucleotide Sequencing/methods ; *rRNA Operon/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA/methods ; Phylogeny ; }, abstract = {The use of short-read metabarcoding for classifying microeukaryotes is challenged by the lack of comprehensive 18S rRNA reference databases. While recent advances in high-throughput long-read sequencing provide the potential to greatly increase the phylogenetic coverage of these databases, the performance of different sequencing technologies and subsequent bioinformatics processing remain to be evaluated, primarily because of the absence of well-defined eukaryotic mock communities. To address this challenge, we created a eukaryotic rRNA operon clone-library and turned it into a precisely defined synthetic eukaryotic mock community. This mock community was then used to evaluate the performance of three long-read sequencing strategies (PacBio circular consensus sequencing and two Nanopore approaches using unique molecular identifiers) and three tools for resolving amplicons sequence variants (ASVs) (USEARCH, VSEARCH, and DADA2). We investigated the sensitivity of the sequencing techniques based on the number of detected mock taxa, and the accuracy of the different ASV-calling tools with a specific focus on the presence of chimera among the final rRNA operon ASVs. Based on our findings, we provide recommendations and best practice protocols for how to cost-effectively obtain essentially error-free rRNA operons in high-throughput. An agricultural soil sample was used to demonstrate that the sequencing and bioinformatic results from the mock community also translates to highly diverse natural samples, which enables us to identify previously undescribed microeukaryotic lineages.}, }
@article {pmid38974332, year = {2024}, author = {Johnston, JT and Quoc, BN and Abrahamson, B and Candry, P and Ramon, C and Cash, KJ and Saccomano, SC and Samo, TJ and Ye, C and Weber, PK and Winkler, MH and Mayali, X}, title = {Increasing aggregate size reduces single-cell organic carbon incorporation by hydrogel-embedded wetland microbes.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae086}, pmid = {38974332}, issn = {2730-6151}, abstract = {Microbial degradation of organic carbon in sediments is impacted by the availability of oxygen and substrates for growth. To better understand how particle size and redox zonation impact microbial organic carbon incorporation, techniques that maintain spatial information are necessary to quantify elemental cycling at the microscale. In this study, we produced hydrogel microspheres of various diameters (100, 250, and 500 μm) and inoculated them with an aerobic heterotrophic bacterium isolated from a freshwater wetland (Flavobacterium sp.), and in a second experiment with a microbial community from an urban lacustrine wetland. The hydrogel-embedded microbial populations were incubated with [13]C-labeled substrates to quantify organic carbon incorporation into biomass via nanoSIMS. Additionally, luminescent nanosensors enabled spatially explicit measurements of oxygen concentrations inside the microspheres. The experimental data were then incorporated into a reactive-transport model to project long-term steady-state conditions. Smaller (100 μm) particles exhibited the highest microbial cell-specific growth per volume, but also showed higher absolute activity near the surface compared to the larger particles (250 and 500 μm). The experimental results and computational models demonstrate that organic carbon availability was not high enough to allow steep oxygen gradients and as a result, all particle sizes remained well-oxygenated. Our study provides a foundational framework for future studies investigating spatially dependent microbial activity in aggregates using isotopically labeled substrates to quantify growth.}, }
@article {pmid38973247, year = {2024}, author = {Akay, C and Ulrich, N and Rocha, U and Ding, C and Adrian, L}, title = {Sequential Anaerobic-Aerobic Treatment Enhances Sulfamethoxazole Removal: From Batch Cultures to Observations in a Large-Scale Wastewater Treatment Plant.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {28}, pages = {12609-12620}, pmid = {38973247}, issn = {1520-5851}, mesh = {*Sulfamethoxazole/metabolism ; *Wastewater/chemistry ; Anaerobiosis ; Waste Disposal, Fluid ; Water Pollutants, Chemical/metabolism ; Aerobiosis ; }, abstract = {Sulfamethoxazole (SMX) passes through conventional wastewater treatment plants (WWTPs) mainly unaltered. Under anoxic conditions sulfate-reducing bacteria can transform SMX but the fate of the transformation products (TPs) and their prevalence in WWTPs remain unknown. Here, we report the anaerobic formation and aerobic degradation of SMX TPs. SMX biotransformation was observed in nitrate- and sulfate-reducing enrichment cultures. We identified 10 SMX TPs predominantly showing alterations in the heterocyclic and N[4]-arylamine moieties. Abiotic oxic incubation of sulfate-reducing culture filtrates led to further degradation of the major anaerobic SMX TPs. Upon reinoculation under oxic conditions, all anaerobically formed TPs, including the secondary TPs, were degraded. In samples collected at different stages of a full-scale municipal WWTP, anaerobically formed SMX TPs were detected at high concentrations in the primary clarifier and digested sludge units, where anoxic conditions were prevalent. Contrarily, their concentrations were lower in oxic zones like the biological treatment and final effluent. Our results suggest that anaerobically formed TPs were eliminated in the aerobic treatment stages, consistent with our observations in batch biotransformation experiments. More generally, our findings highlight the significance of varying redox states determining the fate of SMX and its TPs in engineered environments.}, }
@article {pmid38971962, year = {2024}, author = {Zhang, W and Zhang, F and Wu, Y and Liu, J and Fahad, S and Li, Z and Zhao, S and Qiu, Z and Zhu 朱, M&#x58a8;}, title = {Powdery Mildew of Xanthium strumarium Caused by Podosphaera xanthii in central China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-05-24-1062-PDN}, pmid = {38971962}, issn = {0191-2917}, abstract = {Xanthium strumarium, known as cocklebur, is an annual herb and has been used in traditional Chinese medicine. In October 2020, powdery mildew-like disease signs and symptoms were observed on X. strumarium grown in a crop field, Xinxiang city, Henan Province, China (35.36076° N, 113.93467° E). The specimen (PX-XS2023) was stored in Xinxiang Key Laboratory of Plant Stress Biology. White colonies in irregular or coalesced circular shaped-lesions were abundant on both ad- and abaxial surfaces of leaves and covered up to 99 % of the leaf area. Some of the infected leaves were senesced. More than 70 % of plants (n = 130) exhibited these signs and symptoms. Conidiophores were straight or slightly curved, 55 to 160 × 11 to 13 μm composed of foot-cells, shorter cells and conidia. Conidia were ellipsoid to oval, 29 to 40 × 14 to 20 μm (n = 50), with a length/width ration of 2.0 to 2.5, containing fibrosin bodies. Dark brown to black chasmothecia were found on infected leaves. The appendages were mycelium-shaped and at the base of scattered or gregarious chasmothecia (n = 50, 70 to 120 μm in diameter). Asci were 55 to 80 × 50 to 65 μm (n=30). These morphological characteristics were consistent with those of Podosphaera xanthii (Braun and Cook 2012). The internal transcribed spacer (ITS) region and Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) region of the fungus (PX-XS2023) were amplified and sequenced with primers ITS1/ITS4 (White et al. 1990) and GAPDH1/GAPDH3R (Bradshaw et al. 2022) according to a previously reported method (Zhu et al. 2022). The resulting sequences were respectively deposited into GenBank (Accession No. MW300956 and PP236083). BLASTn analysis indicated that the sequences were respectively 99.82 % (564/565) and 100% (272/272) identical to P. xanthii (MT260063 and ON075658). The phylogenetic analysis indicated that the strain PX-XS2023 and P. xanthii were clustered into a same branch. Therefore, the causal agent of powdery mildew on X. strumarium was P. xanthii. To conduct pathogenicity assays, mature leaves of five healthy X. strumarium (height in 50 centimeters) were inoculated with fungal conidia by gently pressing surfaces of infested leaves onto leaves of healthy plants (Zhu et al. 2020). Five untreated plants served as controls. The controls and inoculated plants were separately maintained in greenhouses (humidity, 60%; light/dark, 16 h/8 h; temperature, 18°C). Eight days post-inoculation, signs of powdery mildew were detectable on inoculated plants, however, the controls were asymptomatic. Thus, the fungal pathogen was morphologically and molecularly identified and confirmed as P. xanthii. This powdery mildew caused by P. xanthii was previously reported on X. strumarium in Korea, Russia and India (Farr and Rossman, 2021). In addition, P. xanthii was recorded on X. strumarium in Xinjiang Province, China (Tai 1979). However, this is the first report of P. xanthii on X. strumarium in central China, where is around 3000 km away from Xinjiang Province with geographically differences. The sudden presence of powdery mildew caused by P. xanthii may adversely affect plant health and thus reduce medical value of X. strumarium. Therefore, the identification and confirmation of P. xanthii infecting X. strumarium enhance the knowledge on the hosts of this pathogen in China and will provide fundamental information for disease control in the future.}, }
@article {pmid38969462, year = {2024}, author = {Chen, Y and Zhou, H and Gao, H and Su, Z and Li, X and Qi, P and Li, T and Hu, C and Li, Z and Bi, Z and Xing, X and Yang, J and Chen, C and Ma, K and Chen, J}, title = {Comprehensive comparison of water quality risk and microbial ecology between new and old cast iron pipe distribution systems.}, journal = {Journal of environmental sciences (China)}, volume = {146}, number = {}, pages = {55-66}, doi = {10.1016/j.jes.2023.05.020}, pmid = {38969462}, issn = {1001-0742}, mesh = {*Iron ; *Water Quality ; *Biofilms ; Corrosion ; *Water Supply ; Water Microbiology ; Drinking Water/microbiology/chemistry ; Drug Resistance, Microbial/genetics ; Environmental Monitoring ; Water Pollutants, Chemical/analysis ; Trihalomethanes/analysis ; }, abstract = {The effects of cast iron pipe corrosion on water quality risk and microbial ecology in drinking water distribution systems (DWDSs) were investigated. It was found that trihalomethane (THMs) concentration and antibiotic resistance genes (ARGs) increased sharply in the old DWDSs. Under the same residual chlorine concentration conditions, the adenosine triphosphate concentration in the effluent of old DWDSs (Eff-old) was significantly higher than that in the effluent of new DWDSs. Moreover, stronger bioflocculation ability and weaker hydrophobicity coexisted in the extracellular polymeric substances of Eff-old, meanwhile, iron particles could be well inserted into the structure of the biofilms to enhance the mechanical strength and stability of the biofilms, hence enhancing the formation of THMs. Old DWDSs significantly influenced the microbial community of bulk water and triggered stronger microbial antioxidant systems response, resulting in higher ARGs abundance. Corroded cast iron pipes induced a unique interaction system of biofilms, chlorine, and corrosion products. Therefore, as the age of cast iron pipes increases, the fluctuation of water quality and microbial ecology should be paid more attention to maintain the safety of tap water.}, }
@article {pmid38969457, year = {2024}, author = {Chen, SC and Musat, F and Richnow, HH and Krüger, M}, title = {Microbial diversity and oil biodegradation potential of northern Barents Sea sediments.}, journal = {Journal of environmental sciences (China)}, volume = {146}, number = {}, pages = {283-297}, doi = {10.1016/j.jes.2023.12.010}, pmid = {38969457}, issn = {1001-0742}, mesh = {*Geologic Sediments/microbiology/chemistry ; *Biodegradation, Environmental ; Arctic Regions ; *Microbiota ; Petroleum/metabolism ; Bacteria/classification/metabolism/genetics ; Archaea/metabolism/classification/genetics ; Water Pollutants, Chemical/analysis/metabolism ; Biodiversity ; }, abstract = {The Arctic, an essential ecosystem on Earth, is subject to pronounced anthropogenic pressures, most notable being the climate change and risks of crude oil pollution. As crucial elements of Arctic environments, benthic microbiomes are involved in climate-relevant biogeochemical cycles and hold the potential to remediate upcoming contamination. Yet, the Arctic benthic microbiomes are among the least explored biomes on the planet. Here we combined geochemical analyses, incubation experiments, and microbial community profiling to detail the biogeography and biodegradation potential of Arctic sedimentary microbiomes in the northern Barents Sea. The results revealed a predominance of bacterial and archaea phyla typically found in the deep marine biosphere, such as Chloroflexi, Atribacteria, and Bathyarcheaota. The topmost benthic communities were spatially structured by sedimentary organic carbon, lacking a clear distinction among geographic regions. With increasing sediment depth, the community structure exhibited stratigraphic variability that could be correlated to redox geochemistry of sediments. The benthic microbiomes harbored multiple taxa capable of oxidizing hydrocarbons using aerobic and anaerobic pathways. Incubation of surface sediments with crude oil led to proliferation of several genera from the so-called rare biosphere. These include Alkalimarinus and Halioglobus, previously unrecognized as hydrocarbon-degrading genera, both harboring the full genetic potential for aerobic alkane oxidation. These findings increase our understanding of the taxonomic inventory and functional potential of unstudied benthic microbiomes in the Arctic.}, }
@article {pmid38969451, year = {2024}, author = {Ma, B and Zheng, L and Xie, B and Ma, L and Jia, M and Xie, C and Hu, C and Ulbricht, M and Wei, Y}, title = {Sustainable wastewater treatment and reuse in space.}, journal = {Journal of environmental sciences (China)}, volume = {146}, number = {}, pages = {237-240}, doi = {10.1016/j.jes.2023.08.023}, pmid = {38969451}, issn = {1001-0742}, mesh = {*Wastewater ; *Waste Disposal, Fluid/methods ; *Water Purification/methods ; Space Flight ; }, abstract = {Exploring the vast extraterrestrial space is an inevitable trend with continuous human development. Water treatment and reuse are crucial in the limited and closed space that is available in spaceships or long-term use space bases that will be established in the foreseeable future. Dedicated water treatment technologies have experienced iterative development for more than 60 years since the first manned spaceflight was successfully launched. Herein, we briefly review the related wastewater characteristics and the history of water treatment in space stations, and we focus on future challenges and perspectives, aiming at providing insights for optimizing wastewater treatment technologies and closing the water cycle in future.}, }
@article {pmid38968348, year = {2024}, author = {Miettinen, TP and Gomez, AL and Wu, Y and Wu, W and Usherwood, TR and Hwang, Y and Roller, BRK and Polz, MF and Manalis, SR}, title = {Cell size, density, and nutrient dependency of unicellular algal gravitational sinking velocities.}, journal = {Science advances}, volume = {10}, number = {27}, pages = {eadn8356}, pmid = {38968348}, issn = {2375-2548}, mesh = {*Cell Size ; *Nutrients/metabolism ; Gravitation ; Phytoplankton/physiology/metabolism ; Photosynthesis ; Microalgae/metabolism ; }, abstract = {Eukaryotic phytoplankton, also known as algae, form the basis of marine food webs and drive marine carbon sequestration. Algae must regulate their motility and gravitational sinking to balance access to light at the surface and nutrients in deeper layers. However, the regulation of gravitational sinking remains largely unknown, especially in motile species. Here, we quantify gravitational sinking velocities according to Stokes' law in diverse clades of unicellular marine microalgae to reveal the cell size, density, and nutrient dependency of sinking velocities. We identify a motile algal species, Tetraselmis sp., that sinks faster when starved due to a photosynthesis-driven accumulation of carbohydrates and a loss of intracellular water, both of which increase cell density. Moreover, the regulation of cell sinking velocities is connected to proliferation and can respond to multiple nutrients. Overall, our work elucidates how cell size and density respond to environmental conditions to drive the vertical migration of motile algae.}, }
@article {pmid38965531, year = {2024}, author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV}, title = {Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {148}, pmid = {38965531}, issn = {1741-7007}, support = {Intramural Research Program//U.S. National Library of Medicine/ ; }, mesh = {*Gene Transfer, Horizontal ; *Microbiota/genetics ; Biodiversity ; Symbiosis/genetics ; Models, Theoretical ; Models, Biological ; }, abstract = {BACKGROUND: Microbiomes are generally characterized by high diversity of coexisting microbial species and strains, and microbiome composition typically remains stable across a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. Therefore, the long-term persistence of microbiome diversity calls for an explanation.<br><br>RESULTS: To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis were obtained, namely, pure competition, host-parasite relationship, and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environment.<br><br>CONCLUSIONS: The results of this modeling study show that basic phenomena that are universal in microbial communities, namely, environmental variation and HGT, provide for stabilization and persistence of microbial diversity, and emergence of ecological complexity.}, }
@article {pmid38964855, year = {2024}, author = {Zhao, F and Wang, B and Cui, Q and Wu, Y}, title = {Genetically modified indigenous Pseudomonas aeruginosa drove bacterial community to change positively toward microbial enhanced oil recovery applications.}, journal = {Journal of applied microbiology}, volume = {135}, number = {7}, pages = {}, doi = {10.1093/jambio/lxae168}, pmid = {38964855}, issn = {1365-2672}, support = {31700117//National Natural Science Foundation of China/ ; 6096//Qufu Normal University/ ; }, mesh = {*Pseudomonas aeruginosa/genetics/metabolism ; *Petroleum/metabolism ; *Surface-Active Agents/metabolism ; Biodegradation, Environmental ; Bacteria/genetics/metabolism/classification ; Hydrocarbons/metabolism ; Microbiota ; }, abstract = {AIMS: Microbial enhanced oil recovery (MEOR) is cost-effective and eco-friendly for oil exploitation. Genetically modified biosurfactants-producing high-yield strains are promising for ex-situ MEOR. However, can they survive and produce biosurfactants in petroleum reservoirs for in-situ MEOR? What is their effect on the native bacterial community?<br><br>METHODS AND RESULTS: A genetically modified indigenous biosurfactants-producing strain Pseudomonas aeruginosa PrhlAB was bioaugmented in simulated reservoir environments. Pseudomonas aeruginosa PrhlAB could stably colonize in simulated reservoirs. Biosurfactants (200&#xa0;mg l-1) were produced in simulated reservoirs after bio-augmenting strain PrhlAB. The surface tension of fluid was reduced to 32.1 mN m-1. Crude oil was emulsified with an emulsification index of 60.1%. Bio-augmenting strain PrhlAB stimulated the MEOR-related microbial activities. Hydrocarbon-degrading bacteria and biosurfactants-producing bacteria were activated, while the hydrogen sulfide-producing bacteria were inhibited. Bio-augmenting P. aeruginosa PrhlAB reduced the diversity of bacterial community, and gradually simplified the species composition. Bacteria with oil displacement potential became dominant genera, such as Shewanella, Pseudomonas, and Arcobacter.<br><br>CONCLUSIONS: Culture-based and sequence-based analyses reveal that genetically modified biosurfactants-producing strain P. aeruginosa PrhlAB are promising for in-situ MEOR as well.}, }
@article {pmid38962127, year = {2024}, author = {Lange, E and Kranert, L and Krüger, J and Benndorf, D and Heyer, R}, title = {Microbiome modeling: a beginner's guide.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1368377}, pmid = {38962127}, issn = {1664-302X}, abstract = {Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in human health, environmental processes, and biotechnological applications and interact with each other, their environment, and hosts via ecological interactions. Our understanding of microbiomes is still limited and hampered by their complexity. A concept improving this understanding is systems biology, which focuses on the holistic description of biological systems utilizing experimental and computational methods. An important set of such experimental methods are metaomics methods which analyze microbiomes and output lists of molecular features. These lists of data are integrated, interpreted, and compiled into computational microbiome models, to predict, optimize, and control microbiome behavior. There exists a gap in understanding between microbiologists and modelers/bioinformaticians, stemming from a lack of interdisciplinary knowledge. This knowledge gap hinders the establishment of computational models in microbiome analysis. This review aims to bridge this gap and is tailored for microbiologists, researchers new to microbiome modeling, and bioinformaticians. To achieve this goal, it provides an interdisciplinary overview of microbiome modeling, starting with fundamental knowledge of microbiomes, metaomics methods, common modeling formalisms, and how models facilitate microbiome control. It concludes with guidelines and repositories for modeling. Each section provides entry-level information, example applications, and important references, serving as a valuable resource for comprehending and navigating the complex landscape of microbiome research and modeling.}, }
@article {pmid38960913, year = {2024}, author = {Bischof, PSP and Bartolomaeus, TUP and Löber, U and Bleidorn, C}, title = {Microbiome Dynamics and Functional Composition in Coelopa frigida (Diptera, Coelopidae): Insights into Trophic Specialization of Kelp Flies.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {91}, pmid = {38960913}, issn = {1432-184X}, support = {F01KI1909A//Bundesministerium f&#xfc;r Bildung und Forschung/ ; }, mesh = {Animals ; *Diptera/microbiology ; *Larva/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Phylogeny ; *Bacteria/classification/genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic ; Kelp/microbiology ; }, abstract = {Coelopidae (Diptera), known as kelp flies, exhibit an ecological association with beached kelp and other rotting seaweeds. This unique trophic specialization necessitates significant adaptations to overcome the limitations of an algal diet. We aimed to investigate whether the flies' microbiome could be one of these adaptive mechanisms. Our analysis focused on assessing composition and diversity of adult and larval microbiota of the kelp fly Coelopa frigida. Feeding habits of the larvae of this species have been subject of numerous studies, with debates whether they directly consume kelp or primarily feed on associated bacteria. By using a 16S rRNA metabarcoding approach, we found that the larval microbiota displayed considerably less diversity than adults, heavily dominated by only four operational taxonomic units (OTUs). Phylogenetic placement recovered the most dominant OTU of the larval microbiome, which is the source of more than half of all metabarcoding sequence reads, as an undescribed genus of Orbaceae (Gammaproteobacteria). Interestingly, this OTU is barely found among the 15 most abundant taxa of the adult microbiome, where it is responsible for less than 2% of the metabarcoding sequence reads. The other three OTUs dominating the larval microbiome have been assigned as Psychrobacter (Gammaproteobacteria), Wohlfahrtiimonas (Gammaproteobacteria), and Cetobacterium (Fusobacteriota). Moreover, we also uncovered a distinct shift in the functional composition between the larval and adult stages, where our taxonomic profiling suggests a significant decrease in functional diversity in larval samples. Our study offers insights into the microbiome dynamics and functional composition of Coelopa frigida.}, }
@article {pmid38960411, year = {2024}, author = {Mafune, KK and Kasson, MT and Winkler, MH}, title = {Building blocks toward sustainable biofertilizers: variation in arbuscular mycorrhizal spore germination when immobilized with diazotrophic bacteria in biodegradable hydrogel beads.}, journal = {Journal of applied microbiology}, volume = {135}, number = {7}, pages = {}, doi = {10.1093/jambio/lxae167}, pmid = {38960411}, issn = {1365-2672}, support = {2021 postdoctoral//Washington Research Foundation/ ; //Mycological Society of America/ ; 2023-67013-4017//National Institute of Food and Agriculture/ ; }, mesh = {*Mycorrhizae/physiology ; *Spores, Fungal/growth &amp; development ; *Hydrogels ; *Azospirillum brasilense/metabolism ; *Fertilizers/analysis ; Alginates ; }, abstract = {AIM: We investigated whether there was interspecies and intraspecies variation in spore germination of 12 strains of arbuscular mycorrhizal fungi when co-entrapped with the diazotrophic plant growth-promoting bacteria, Azospirillum brasilense Sp7 in alginate hydrogel beads.<br><br>METHODS AND RESULTS: Twelve Rhizophagus irregularis, Rhizophagus intraradices, and Funneliformis mosseae strains were separately combined with a live culture of Azospirillum brasilense Sp7. Each fungal-bacterial consortia was supplemented with sodium alginate to a 2% concentration (v/v) and cross-linked in calcium chloride (2%&#xa0;w/v) to form biodegradable hydrogel beads. One hundred beads from each combination (total of 1200) were fixed in solidified modified Strullu and Romand media. Beads were observed for successful spore germination and bacterial growth over 14 days. In all cases, successful growth of A. brasilense was observed. For arbuscular mycorrhizal fungi, interspecies variation in spore germination was observed, with R. intraradices having the highest germination rate (64.3%), followed by R. irregularis (45.5%) and F. mosseae (40.3%). However, a difference in intraspecies germination was only observed among strains of R. irregularis and F. mosseae. Despite having varying levels of germination, even the strains with the lowest potential were still able to establish with the plant host Brachypodium distachyon in a model system.<br><br>CONCLUSIONS: Arbuscular mycorrhizal spore germination varied across strains when co-entrapped with a diazotrophic plant growth-promoting bacteria. This demonstrates that hydrogel beads containing a mixed consortium hold potential as a sustainable biofertilizer and that compatibility tests remain an important building block when aiming to create a hydrogel biofertilizer that encases a diversity of bacteria and fungi. Moving forward, further studies should be conducted to test the efficacy of these hydrogel biofertilizers on different crops across varying climatic conditions in order to optimize their potential.}, }
@article {pmid38959887, year = {2024}, author = {Perruzza, L and Rezzonico Jost, T and Raneri, M and Gargari, G and Palatella, M and De Ponte Conti, B and Seehusen, F and Heckmann, J and Viemann, D and Guglielmetti, S and Grassi, F}, title = {Protection from environmental enteric dysfunction and growth improvement in malnourished newborns by amplification of secretory IgA.}, journal = {Cell reports. Medicine}, volume = {5}, number = {7}, pages = {101639}, pmid = {38959887}, issn = {2666-3791}, mesh = {Animals ; *Immunoglobulin A, Secretory/metabolism ; *Malnutrition/immunology ; Mice ; Female ; *Gastrointestinal Microbiome ; Animals, Newborn ; Humans ; Apyrase/metabolism ; Infant, Newborn ; }, abstract = {Environmental enteric dysfunction (EED) is a condition associated with malnutrition that can progress to malabsorption and villous atrophy. Severe EED results in linear growth stunting, slowed neurocognitive development, and unresponsiveness to oral vaccines. Prenatal exposure to malnutrition and breast feeding by malnourished mothers replicates EED. Pups are characterized by deprivation of secretory IgA (SIgA) and altered development of the gut immune system and microbiota. Extracellular ATP (eATP) released by microbiota limits T follicular helper (Tfh) cell activity and SIgA generation in Peyer's patches (PPs). Administration of a live biotherapeutic releasing the ATP-degrading enzyme apyrase to malnourished pups restores SIgA levels and ameliorates stunted growth. SIgA is instrumental in improving the growth and intestinal immune competence of mice while they are continuously fed a malnourished diet. The analysis of microbiota composition suggests that amplification of endogenous SIgA may exert a dominant function in correcting malnourishment dysbiosis and its consequences on host organisms, irrespective of the actual microbial ecology.}, }
@article {pmid38958675, year = {2024}, author = {Dendooven, L and Pérez-Hernández, V and Navarro-Pérez, G and Tlalmis-Corona, J and Navarro-Noya, YE}, title = {Spatial and Temporal Shifts of Endophytic Bacteria in Conifer Seedlings of Abies religiosa (Kunth) Schltdl. &amp; Cham.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {90}, pmid = {38958675}, issn = {1432-184X}, support = {591213//Consejo Nacional de Humanidades Ciencia y Tecnolog&#xed;a (CONAHCyT)/ ; INFR-2015-01-253217//Consejo Nacional de Humanidades Ciencia y Tecnolog&#xed;a (CONAHCyT)/ ; }, mesh = {*Seedlings/microbiology/growth &amp; development ; *Bacteria/classification/genetics/isolation &amp; purification ; *Endophytes/classification/isolation &amp; purification/physiology/genetics ; *RNA, Ribosomal, 16S/genetics ; *Abies/microbiology ; *Plant Roots/microbiology ; Soil Microbiology ; Biodiversity ; Microbiota ; DNA, Bacterial/genetics ; }, abstract = {Endophytes play an important role in plant development, survival, and establishment, but their temporal dynamics in young conifer plants are still largely unknown. In this study, the bacterial community was determined by metabarcoding of the 16S rRNA gene in the rhizoplane, roots, and aerial parts of 1- and 5-month-old seedlings of natural populations of Abies religiosa (Kunth) Schltdl. &amp; Cham. In 1-month-old seedlings, Pseudomonas dominated aerial parts (relative abundance 71.6%) and roots (37.9%). However, the roots exhibited significantly higher bacterial species richness than the aerial parts, with the dissimilarity between these plant sections mostly explained by the loss of bacterial amplification sequence variants. After 5 months, Mucilaginibacter dominated in the rhizoplane (9.0%), Streptomyces in the roots (12.2%), and Pseudomonas in the aerial parts (18.1%). The bacterial richness and community structure differed significantly between the plant sections, and these variations were explained mostly by 1-for-1 substitution. The relative abundance of putative metabolic pathways significantly differed between the plant sections at both 1 and 5 months. All the dominant bacterial genera (e.g., Pseudomonas and Burkholderia-Caballeronia-Paraburkholderia) have been reported to have plant growth-promoting capacities and/or antagonism against pathogens, but what defines their role for plant development has still to be determined. This investigation improves our understanding of the early plant-bacteria interactions essential for natural regeneration of A. religiosa forest.}, }
@article {pmid38955825, year = {2024}, author = {Pan, H and Wattiez, R and Gillan, D}, title = {Soil Metaproteomics for Microbial Community Profiling: Methodologies and Challenges.}, journal = {Current microbiology}, volume = {81}, number = {8}, pages = {257}, pmid = {38955825}, issn = {1432-0991}, support = {No.2023-BSBA-024//Joint Funds of the Natural Science Foundation of Liaoning Province of China/ ; }, mesh = {*Soil Microbiology ; *Proteomics/methods ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota ; Fungi/classification/genetics/metabolism/isolation &amp; purification ; Soil/chemistry ; Computational Biology/methods ; }, abstract = {Soil represents a complex and dynamic ecosystem, hosting a myriad of microorganisms that coexist and play vital roles in nutrient cycling and organic matter transformation. Among these microorganisms, bacteria and fungi are key members of the microbial community, profoundly influencing the fate of nitrogen, sulfur, and carbon in terrestrial environments. Understanding the intricacies of soil ecosystems and the biological processes orchestrated by microbial communities necessitates a deep dive into their composition and metabolic activities. The advent of next-generation sequencing and 'omics' techniques, such as metagenomics and metaproteomics, has revolutionized our understanding of microbial ecology and the functional dynamics of soil microbial communities. Metagenomics enables the identification of microbial community composition in soil, while metaproteomics sheds light on the current biological functions performed by these communities. However, metaproteomics presents several challenges, both technical and computational. Factors such as the presence of humic acids and variations in extraction methods can influence protein yield, while the absence of high-resolution mass spectrometry and comprehensive protein databases limits the depth of protein identification. Notwithstanding these limitations, metaproteomics remains a potent tool for unraveling the intricate biological processes and functions of soil microbial communities. In this review, we delve into the methodologies and challenges of metaproteomics in soil research, covering aspects such as protein extraction, identification, and bioinformatics analysis. Furthermore, we explore the applications of metaproteomics in soil bioremediation, highlighting its potential in addressing environmental challenges.}, }
@article {pmid38955821, year = {2024}, author = {Weisse, T and Pröschold, T and Kammerlander, B and Sonntag, B and Schicker, L}, title = {Numerical and Thermal Response of the Bacterivorous Ciliate Colpidium kleini, a Species Potentially at Risk of Extinction by Rising Water Temperatures.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {89}, pmid = {38955821}, issn = {1432-184X}, support = {P 32714/FWF_/Austrian Science Fund FWF/Austria ; DOC fForte 22883//&#xd6;sterreichischen Akademie der Wissenschaften/ ; 10.55776/P32714//Austrian Science Fund/ ; }, mesh = {*Ciliophora/physiology/growth &amp; development/classification/isolation &amp; purification ; Lakes/microbiology/parasitology ; Temperature ; Phylogeny ; Extinction, Biological ; Bacteria/classification/isolation &amp; purification/genetics ; }, abstract = {We investigated the food-dependent growth and thermal response of the freshwater ciliate Colpidium kleini using numerical response (NR) experiments. This bacterivorous ciliate occurs in lotic water and the pelagial of lakes and ponds. The C. kleini strain used in this work was isolated from a small alpine lake and identified by combining detailed morphological inspections with molecular phylogeny. Specific growth rates (rmax) were measured from 5 to 21 °C. The ciliate did not survive at 22 °C. The threshold bacterial food levels (0.3 - 2.2 × 10[6] bacterial cells mL[-1]) matched the bacterial abundance in the alpine lake from which C. kleini was isolated. The food threshold was notably lower than previously reported for C. kleini and two other Colpidium species. The threshold was similar to levels reported for oligotrich and choreotrich ciliates if expressed in terms of bacterial biomass (0.05 - 0.43 mg C L[-1]). From the NR results, we calculated physiological mortality rates at zero food concentration. The mean mortality (0.55 ± 0.17 d[-1]) of C. kleini was close to the mean estimate obtained for other planktonic ciliates that do not encyst. We used the data obtained by the NR experiments to fit a thermal performance curve (TPC). The TPC yielded a temperature optimum at 17.3 °C for C. kleini, a maximum upper thermal tolerance limit of 21.9 °C, and a thermal safety margin of 4.6 °C. We demonstrated that combining NR with TPC analysis is a powerful tool to predict better a species' fitness in response to temperature and food.}, }
@article {pmid38954336, year = {2024}, author = {Benammar, L and Menasria, T and Dibi, AR}, title = {Deciphering the geochemical influences on bacterial diversity and communities among two Algerian hot springs.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {32}, pages = {44848-44862}, pmid = {38954336}, issn = {1614-7499}, mesh = {*Hot Springs/microbiology ; Algeria ; *Bacteria ; *RNA, Ribosomal, 16S ; Biodiversity ; Archaea ; }, abstract = {Northeastern Algeria boasts numerous hot springs, yet these hydrothermal sites remain largely unexplored for their microbial ecology. The present study explores the bacterial abundance and diversity within two distinct Algerian hot springs (Hammam Saïda and Hammam Debagh) and investigates the link between the prevailing bacteria with geochemical parameters. High-throughput 16S rRNA gene sequencing of water and sediment samples revealed a bacterial dominance of 99.85-91.16% compared to Archaea (0.14-0.66%) in both springs. Interestingly, Saïda hot spring, characterized by higher temperatures and sodium content, harbored a community dominated by Pseudomonadota (51.13%), whereas Debagh, a Ca-Cl-SO4 type spring, was primarily populated by Bacillota with 55.33%. Bacteroidota displayed even distribution across both sites. Additional phyla, including Chloroflexota, Deinococcota, Cyanobacteriota, and Chlorobiota, were also present. Environmental factors, particularly temperature, sodium, potassium, and alkalinity, significantly influenced bacterial diversity and composition. These findings shed light on the interplay between distinct microbial communities and their associated geochemical properties, providing valuable insights for future research on biogeochemical processes in these unique ecosystems driven by distinct environmental conditions, including potential applications in bioremediation and enzyme discovery.}, }
@article {pmid38952448, year = {2024}, author = {Aqueel, R and Badar, A and Ijaz, UZ and Malik, KA}, title = {Microbial influencers and cotton leaf curl disease (CLCuD) susceptibility: a network perspective.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1381883}, pmid = {38952448}, issn = {1664-302X}, abstract = {Biotic stresses, such as plant viruses, e.g., cotton leaf curl virus (CLCuV), can alter root-associated and leaf-associated microbial diversities in plants. There are complex ecological dynamics at play, with each microbe contributing to a multitude of biotic and abiotic interactions, thus deciding the stability of the plant's ecosystem in response to the disease. Deciphering these networks of interactions is a challenging task. The inferential research in microbiome is also at a nascent stage, often constrained by the underlying analytical assumptions and the limitations with respect to the depth of sequencing. There is also no real consensus on network-wide statistics to identify the influential microbial players in a network. Guided by the latest developments in network science, including recently published metrics such as Integrated View of Influence (IVI) and some other centrality measures, this study provides an exposé of the most influential nodes in the rhizospheric and phyllospheric microbial networks of the cotton leaf curl disease (CLCuD) susceptible, partially tolerant, and resistant cotton varieties. It is evident from our results that the CLCuD-resistant Gossypium arboreum possesses an equal share of keystone species, which helps it to withstand ecological pressures. In the resistant variety, the phyllosphere harbors the most influential nodes, whereas in the susceptible variety, they are present in the rhizosphere. Based on hubness score, spreading score, and IVI, the top 10 occurring keystone species in the FDH-228 (resistant) variety include Actinokineospora, Cohnella, Thermobacillus, Clostridium, Desulfofarcimen, and MDD-D21. Elusimicrobia, Clostridium-sensu-stricto_12, Candidatus woesebacteria, and Dyella were identified as the most influential nodes in the PFV-1 (partially tolerant) variety. In the PFV-2 (susceptible) variety, the keystone species were identified as Georginia, Nesterenkonia, Elusimicrobia MVP-88, Acetivibrio, Tepedisphaerales, Chelatococcus, Nitrosospira, and RCP2-54. This concept deciphers the diseased and healthy plant's response to viral disease, which may be microbially mediated.}, }
@article {pmid38949619, year = {2024}, author = {Jibrin, MO and Sharma, A and Mavian, CN and Timilsina, S and Kaur, A and Iruegas-Bocardo, F and Potnis, N and Minsavage, GV and Coutinho, TA and Creswell, TC and Egel, DS and Francis, DM and Kebede, M and Miller, SA and Montelongo, MJ and Nikolaeva, E and Pianzzola, MJ and Pruvost, O and Quezado-Duval, AM and Ruhl, GE and Shutt, VM and Maynard, E and Maeso, DC and Siri, MI and Trueman, CL and Salemi, M and Vallad, GE and Roberts, PD and Jones, JB and Goss, EM}, title = {Phylodynamic Insights into Global Emergence and Diversification of the Tomato Pathogen Xanthomonas hortorum pv. gardneri.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {37}, number = {10}, pages = {712-720}, doi = {10.1094/MPMI-04-24-0035-R}, pmid = {38949619}, issn = {0894-0282}, mesh = {*Solanum lycopersicum/microbiology ; *Plant Diseases/microbiology ; *Xanthomonas/genetics/pathogenicity ; *Phylogeny ; *Genetic Variation ; Genome, Bacterial ; }, abstract = {The emergence of plant pathogens is often associated with waves of unique evolutionary and epidemiological events. Xanthomonas hortorum pv. gardneri is one of the major pathogens causing bacterial spot disease of tomatoes. After its first report in the 1950s, there were no formal reports on this pathogen until the 1990s, despite active global research on the pathogens that cause tomato and pepper bacterial spot disease. Given the recently documented global distribution of X. hortorum pv. gardneri, our objective was to examine genomic diversification associated with its emergence. We sequenced the genomes of X. hortorum pv. gardneri strains collected in eight countries to examine global population structure and pathways of emergence using phylodynamic analysis. We found that strains isolated post-1990 group by region of collection and show minimal impact of recombination on genetic variation. A period of rapid geographic expansion in X. hortorum pv. gardneri is associated with acquisition of a large plasmid conferring copper tolerance by horizontal transfer and coincides with the burgeoning hybrid tomato seed industry through the 1980s. The ancestry of X. hortorum pv. gardneri is consistent with introduction to hybrid tomato seed production and dissemination during the rapid increase in trade of hybrid seeds. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.}, }
@article {pmid38946903, year = {2024}, author = {Malfent, F and Zehl, M and Kirkegaard, RH and Oberhofer, M and Zotchev, SB}, title = {Genomes and secondary metabolomes of Streptomyces spp. isolated from Leontopodium nivale ssp. alpinum.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1408479}, pmid = {38946903}, issn = {1664-302X}, abstract = {Bacterial endophytes dwelling in medicinal plants represent an as yet underexplored source of bioactive natural products with the potential to be developed into drugs against various human diseases. For the first time, several Streptomyces spp. were isolated from the rare and endangered traditional medicinal plant Leontopodium nivale ssp. alpinum, also known as Edelweiss. In the search for novel natural products, nine endophytic Streptomyces spp. from Edelweiss were investigated via genome sequencing and analysis, followed by fermentation in different media and investigation of secondary metabolomes. A total of 214 secondary metabolite biosynthetic gene clusters (BGCs), of which 35 are presumably unique, were identified by the bioinformatics tool antiSMASH in the genomes of these isolates. LC-MS analyses of the secondary metabolomes of these isolates revealed their potential to produce both known and presumably novel secondary metabolites, whereby most of the identified molecules could be linked to their cognate BGCs. This work sets the stage for further investigation of endophytic streptomycetes from Edelweiss aimed at the discovery and characterization of novel bioactive natural products.}, }
@article {pmid38946328, year = {2024}, author = {Langlois, GA}, title = {Past-President address: My journey in microbial ecology-footprints in the sand, island hopping, supply chains, and technology bridges.}, journal = {The Journal of eukaryotic microbiology}, volume = {71}, number = {4}, pages = {e13037}, doi = {10.1111/jeu.13037}, pmid = {38946328}, issn = {1550-7408}, mesh = {*Ecology ; Eukaryota/physiology ; History, 20th Century ; History, 21st Century ; }, abstract = {This paper highlights and honors the connectivity among protistan researchers, using my own research journey as a backdrop, with attention to the supply chain of ideas, supporters, and other influencers who helped to shape and guide my career by sharing their ideas, protocols, skills, and enthusiasm. In looking back at the journey, the supply chain in my career has also included changes in the conceptual framework for my research studies, converging with a continuous flow of ideas and support from colleagues and mentors. To illustrate the complex map of ideas and supporters, this paper will examine technological advances, paradigm shifts in ecological constructs, geographical considerations, breakthroughs in peritrich biology, and the importance of an integrated perspective as we navigate the changing realities of today's scientific challenges.}, }
@article {pmid38946115, year = {2024}, author = {Zayed, N and Vertommen, R and Simoens, K and Bernaerts, K and Boon, N and Srivastava, MG and Braem, A and Van Holm, W and Castro, AB and Teughels, W}, title = {How well do antimicrobial mouth rinses prevent dysbiosis in an in vitro periodontitis biofilm model?.}, journal = {Journal of periodontology}, volume = {95}, number = {9}, pages = {880-891}, doi = {10.1002/JPER.23-0674}, pmid = {38946115}, issn = {1943-3670}, mesh = {*Biofilms/drug effects ; Humans ; *Dysbiosis/prevention &amp; control ; *Mouthwashes/pharmacology/therapeutic use ; *Periodontitis/prevention &amp; control/microbiology ; Microscopy, Electron, Scanning ; Chlorhexidine/pharmacology/analogs &amp; derivatives/therapeutic use ; Interleukin-8 ; In Vitro Techniques ; Anti-Infective Agents/pharmacology/therapeutic use ; Durapatite ; Anti-Infective Agents, Local/pharmacology/therapeutic use ; Microbiota/drug effects ; }, abstract = {BACKGROUND: Periodontal diseases are associated with dysbiosis in the oral microbial communities. Managing oral biofilms is therefore key for preventing these diseases. Management protocols often include over-the-counter antimicrobial mouth rinses, which lack data on their effects on the oral microbiome's ecology, bacterial composition, metabolic activity, and dysbiosis resilience. This study examined the efficacy of antimicrobial mouth rinses to halt dysbiosis in in vitro oral biofilms under periodontitis-simulating conditions.<br><br>METHODS: Multispecies oral biofilms were grown on hydroxyapatite discs (HADs) and rinsed daily with one of six mouth rinses. Positive and negative controls were included. After three rinses, biofilms were analyzed with viability quantitative polymerase chain reaction and visualized using scanning electron microscopy. Supernatants of rinsed biofilms were used for metabolic activity analysis. In addition, human oral keratinocytes were exposed to rinsed biofilms to assess their inflammatory response. All outputs were analyzed for correlation using Spearman coefficient.<br><br>RESULTS: Product-related changes were observed in the rinsed biofilms. Three of the six tested mouth rinses could significantly prevent dysbiosis with &#x2265;30% reduction in pathobiont abundance relative to the control. These biofilms had lower metabolic activity, and the exposed human oral keratinocyte produced less interleukin-8. Interleukin-8 production correlated to both pathobiont quantity and the metabolic activity of the biofilms.<br><br>CONCLUSION: Some mouth rinses could support biofilm resilience and stop dysbiosis evolution in the biofilm model, with a clear product-related effect. Such mouth rinses can be considered for patients under maintenance/supportive periodontal therapy to prevent/delay disease recurrence. Others are more useful for different periodontal therapy stages.}, }
@article {pmid38945268, year = {2024}, author = {Tom, WA and Judy, JV and Kononoff, PJ and Fernando, SC}, title = {Influence of empirically derived filtering parameters, amplicon sequence variant, and operational taxonomic unit pipelines on assessing rumen microbial diversity.}, journal = {Journal of dairy science}, volume = {107}, number = {11}, pages = {9209-9234}, doi = {10.3168/jds.2023-24479}, pmid = {38945268}, issn = {1525-3198}, mesh = {Animals ; *Rumen/microbiology ; Cattle ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; }, abstract = {Microbes play an important role in human and animal health, as well as animal productivity. The host microbial interactions within ruminants play a critical role in animal health and productivity and provide up to 70% of the animal's energy needs in the form of fermentation products. As such, many studies have investigated microbial community composition to understand the microbial community changes and factors that affect microbial colonization and persistence. Advances in next-generation sequencing technologies and the low cost of sequencing have led many studies to use 16S rDNA-based analysis tools for interrogation of microbiomes at a much finer scale than traditional culturing. However, methods that rely on single base pair differences for bacterial taxa clustering may inflate or underestimate diversity, leading to inaccurate identification of bacterial diversity. Therefore, in this study, we sequenced mock communities of known membership and abundance to establish filtration parameters to reduce the inflation of microbial diversity due to PCR and sequencing errors. Additionally, we evaluated the effect of the resulting filtering parameters proposed using established bioinformatic pipelines on a study consisting of Holstein and Jersey cattle to identify breed and treatment effects on the bacterial community composition and the impact of filtering on global microbial community structure analysis and results. Filtration resulted in a sharp reduction in bacterial taxa identified, yet retain most sequencing data (retaining >79% of sequencing reads) when analyzed using 3 different microbial analysis pipelines (DADA2, Mothur, USEARCH). After filtration, conclusions from α-diversity and β-diversity tests showed very similar results across all analysis methods. The mock community-based filtering parameters proposed in this study help provide a more realistic estimation of bacterial diversity. Additionally, filtration reduced the variation between microbiome analysis methods and helped to identify microbial community differences that could have been missed due to the large animal-to-animal variation observed in the unfiltered data. As such, we believe the new filtering parameters described in this study will help to obtain diversity estimates that are closer to realistic values, improve the ability to detecting microbial community differences, and help to better understand microbial community changes in 16S rDNA-based studies.}, }
@article {pmid38943017, year = {2024}, author = {Pires, CS and Costa, L and Barbosa, SG and Sequeira, JC and Cachetas, D and Freitas, JP and Martins, G and Machado, AV and Cavaleiro, AJ and Salvador, AF}, title = {Microplastics Biodegradation by Estuarine and Landfill Microbiomes.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {88}, pmid = {38943017}, issn = {1432-184X}, support = {UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2023.01617.BD//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04469/2020 unit, with DOI 10.54499/UIDB/04469/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; NORTE-01-0145-FEDER-000080//European Regional Development Fund/ ; }, mesh = {*Biodegradation, Environmental ; *Microbiota ; *Microplastics/metabolism ; *Waste Disposal Facilities ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Water Pollutants, Chemical/metabolism ; Polyesters/metabolism ; Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Estuaries ; Polyethylene/metabolism ; Polyethylene Terephthalates/metabolism ; }, abstract = {Plastic pollution poses a worldwide environmental challenge, affecting wildlife and human health. Assessing the biodegradation capabilities of natural microbiomes in environments contaminated with microplastics is crucial for mitigating the effects of plastic pollution. In this work, we evaluated the potential of landfill leachate (LL) and estuarine sediments (ES) to biodegrade polyethylene (PE), polyethylene terephthalate (PET), and polycaprolactone (PCL), under aerobic, anaerobic, thermophilic, and mesophilic conditions. PCL underwent extensive aerobic biodegradation with LL (99 ± 7%) and ES (78 ± 3%) within 50-60 days. Under anaerobic conditions, LL degraded 87 ± 19% of PCL in 60 days, whereas ES showed minimal biodegradation (3 ± 0.3%). PE and PET showed no notable degradation. Metataxonomics results (16S rRNA sequencing) revealed the presence of highly abundant thermophilic microorganisms assigned to Coprothermobacter sp. (6.8% and 28% relative abundance in anaerobic and aerobic incubations, respectively). Coprothermobacter spp. contain genes encoding two enzymes, an esterase and a thermostable monoacylglycerol lipase, that can potentially catalyze PCL hydrolysis. These results suggest that Coprothermobacter sp. may be pivotal in landfill leachate microbiomes for thermophilic PCL biodegradation across varying conditions. The anaerobic microbial community was dominated by hydrogenotrophic methanogens assigned to Methanothermobacter sp. (21%), pointing at possible syntrophic interactions with Coprothermobacter sp. (a H2-producer) during PCL biodegradation. In the aerobic experiments, fungi dominated the eukaryotic microbial community (e.g., Exophiala (41%), Penicillium (17%), and Mucor (18%)), suggesting that aerobic PCL biodegradation by LL involves collaboration between fungi and bacteria. Our findings bring insights on the microbial communities and microbial interactions mediating plastic biodegradation, offering valuable perspectives for plastic pollution mitigation.}, }
@article {pmid38942024, year = {2024}, author = {Harder, CB and Miyauchi, S and Virágh, M and Kuo, A and Thoen, E and Andreopoulos, B and Lu, D and Skrede, I and Drula, E and Henrissat, B and Morin, E and Kohler, A and Barry, K and LaButti, K and Salamov, A and Lipzen, A and Merényi, Z and Hegedüs, B and Baldrian, P and Stursova, M and Weitz, H and Taylor, A and Koriabine, M and Savage, E and Grigoriev, IV and Nagy, LG and Martin, F and Kauserud, H}, title = {Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations.}, journal = {Cell genomics}, volume = {4}, number = {7}, pages = {100586}, pmid = {38942024}, issn = {2666-979X}, mesh = {*Genome, Fungal/genetics ; *Agaricales/genetics ; Phylogeny ; DNA Transposable Elements/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Plants/microbiology/genetics ; }, abstract = {Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.}, }
@article {pmid38940921, year = {2024}, author = {Picariello, E and De Nicola, F}, title = {Recover of Soil Microbial Community Functions in Beech and Turkey Oak Forests After Coppicing Interventions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {86}, pmid = {38940921}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Fagus/microbiology ; *Quercus/microbiology ; *Forests ; *Microbiota ; *Soil/chemistry ; *Seasons ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Biodiversity ; Forestry ; Trees/microbiology ; Ecosystem ; }, abstract = {Forest management influences the occurrence of tree species, the organic matter input to the soil decomposer system, and hence, it can alter soil microbial community and key ecosystem functions it performs. In this study, we compared the potential effect of different forest management, coppice and high forest, on soil microbial functional diversity, enzyme activities and chemical-physical soil properties in two forests, turkey oak and beech, during summer and autumn. We hypothesized that coppicing influences soil microbial functional diversity with an overall decrease. Contrary to our hypothesis, in summer, the functional diversity of soil microbial community was higher in both coppice forests, suggesting a resilience response of the microbial communities in the soil after tree cutting, which occurred 15-20 years ago. In beech forest under coppice management, a higher content of soil organic matter (but also of soil recalcitrant and stable organic carbon) compared to high forest can explain the higher soil microbial functional diversity and metabolic activity. In turkey oak forest, although differences in functional diversity of soil microbial community between management were observed, for the other investigated parameters, the differences were mainly linked to seasonality. The findings highlight that the soil organic matter preservation depends on the type of forest, but the soil microbial community was able to recover after about 15 years from coppice intervention in both forest ecosystems. Thus, the type of management implemented in these forest ecosystems, not negatively affecting soil organic matter pool, preserving microbial community and potentially soil ecological functions, is sustainable in a scenario of climate change.}, }
@article {pmid38940862, year = {2024}, author = {Ljaljević Grbić, M and Dimkić, I and Janakiev, T and Kosel, J and Tavzes, &#x10c; and Popović, S and Knežević, A and Legan, L and Retko, K and Ropret, P and Unković, N}, title = {Uncovering the Role of Autochthonous Deteriogenic Biofilm Community: Rožanec Mithraeum Monument (Slovenia).}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {87}, pmid = {38940862}, issn = {1432-184X}, support = {451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; 451-03-47/2023-01/200178//Ministry of Education, Science, and Technological Development of the Republic of Serbia/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; BI-RS/20-21-013 and J7-3147//Slovenian Research Agency (ARRS)/ ; }, mesh = {*Biofilms ; *Lichens/microbiology/physiology ; *Calcium Carbonate ; Slovenia ; Ascomycota/physiology ; Mycobiome ; }, abstract = {The primary purpose of the study, as part of the planned conservation work, was to uncover all aspects of autochthonous biofilm pertaining to the formation of numerous deterioration symptoms occurring on the limestone Rožanec Mithraeum monument in Slovenia. Using state-of-the-art sequencing technologies combining mycobiome data with observations made via numerous light and spectroscopic (FTIR and Raman) microscopy analyses pointed out to epilithic lichen Gyalecta jenensis and its photobiont, carotenoid-rich Trentepohlia aurea, as the origin of salmon-hued pigmented alterations of limestone surface. Furthermore, the development of the main deterioration symptom on the monument, i.e., biopitting, was instigated by the formation of typical endolithic thalli and ascomata of representative Verrucariaceae family (Verrucaria sp.) in conjunction with the oxalic acid-mediated dissolution of limestone. The domination of lichenized fungi, as the main deterioration agents, both on the relief and surrounding limestone, was additionally supported by the high relative abundance of lichenized and symbiotroph groups in FUNGuild analysis. Obtained results not only upgraded knowledge of this frequently occurring but often overlooked group of extremophilic stone heritage deteriogens but also provided a necessary groundwork for the development of efficient biocontrol formulation applicable in situ for the preservation of similarly affected limestone monuments.}, }
@article {pmid38940768, year = {2024}, author = {Baroncelli, R and Cobo-Díaz, JF and Benocci, T and Peng, M and Battaglia, E and Haridas, S and Andreopoulos, W and LaButti, K and Pangilinan, J and Lipzen, A and Koriabine, M and Bauer, D and Le Floch, G and Mäkelä, MR and Drula, E and Henrissat, B and Grigoriev, IV and Crouch, JA and de Vries, RP and Sukno, SA and Thon, MR}, title = {Genome evolution and transcriptome plasticity is associated with adaptation to monocot and dicot plants in Colletotrichum fungi.}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {38940768}, issn = {2047-217X}, mesh = {*Colletotrichum/genetics/pathogenicity ; *Transcriptome ; *Genome, Fungal ; *Evolution, Molecular ; Phylogeny ; Adaptation, Physiological/genetics ; Gene Expression Profiling/methods ; Plant Diseases/microbiology/genetics ; }, abstract = {BACKGROUND: Colletotrichum fungi infect a wide diversity of monocot and dicot hosts, causing diseases on almost all economically important plants worldwide. Colletotrichum is also a suitable model for studying gene family evolution on a fine scale to uncover events in the genome associated with biological changes.<br><br>RESULTS: Here we present the genome sequences of 30 Colletotrichum species covering the diversity within the genus. Evolutionary analyses revealed that the Colletotrichum ancestor diverged in the late Cretaceous in parallel with the diversification of flowering plants. We provide evidence of independent host jumps from dicots to monocots during the evolution of Colletotrichum, coinciding with a progressive shrinking of the plant cell wall degradative arsenal and expansions in lineage-specific gene families. Comparative transcriptomics of 4 species adapted to different hosts revealed similarity in gene content but high diversity in the modulation of their transcription profiles on different plant substrates. Combining genomics and transcriptomics, we identified a set of core genes such as specific transcription factors, putatively involved in plant cell wall degradation.<br><br>CONCLUSIONS: These results indicate that the ancestral Colletotrichum were associated with dicot plants and certain branches progressively adapted to different monocot hosts, reshaping the gene content and its regulation.}, }
@article {pmid38940583, year = {2024}, author = {Xie, G and Sun, C and Luo, W and Gong, Y and Tang, X}, title = {Distinct ecological niches and community dynamics: understanding free-living and particle-attached bacterial communities in an oligotrophic deep lake.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {7}, pages = {e0071424}, pmid = {38940583}, issn = {1098-5336}, support = {41971062, 42371065//MOST | National Natural Science Foundation of China (NSFC)/ ; WGKQ2022032//West Anhui University ()/ ; }, mesh = {*Lakes/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; China ; *Microbiota ; Ecosystem ; Seasons ; }, abstract = {Oligotrophic deep-water lakes are unique and sensitive ecosystems with limited nutrient availability. Understanding bacterial communities within these lakes is crucial for assessing ecosystem health, biogeochemical cycling, and responses to environmental changes. In this study, we investigated the seasonal and vertical dynamics of both free-living (FL) and particle-attached (PA) bacteria in Lake Fuxian, a typical oligotrophic deep freshwater lake in southeast China. Our findings revealed distinct seasonal and vertical dynamics of FL and PA bacterial communities, driven by similar physiochemical environmental factors. PA bacteria exhibited higher α- and β-diversity and were enriched with Proteobacteria, Cyanobacteria, Firmicutes, Patescibacteria, Planctomycetota, and Verrucomicrobiota, while FL bacteria were enriched with Actinobacteria and Bacteroidota. FL bacteria showed enrichment in putative functions related to chemoheterotrophy and aerobic anoxygenic photosynthesis, whereas the PA fraction was enriched with intracellular parasites (mainly contributed by Rickettsiales, Chlamydiales, and Legionellales) and nitrogen metabolism functions. Deterministic processes predominantly shaped the assembly of both FL and PA bacterial communities, with stochastic processes playing a greater role in the FL fraction. Network analysis revealed extensive species interactions, with a higher proportion of positively correlated edges in the PA network, indicating mutualistic or cooperative interactions. Cyanobium, Comamonadaceae, and Roseomonas were identified as keystone taxa in the PA network, underscoring potential cooperation between autotrophic and heterotrophic bacteria in organic particle microhabitats. Overall, the disparities in bacterial diversity, community composition, putative function, and network characteristics between FL and PA fractions highlight their adaptation to distinct ecological niches within these unique lake ecosystems.IMPORTANCEUnderstanding the diversity of microbial communities, their assembly mechanisms, and their responses to environmental changes is fundamental to the study of aquatic microbial ecology. Oligotrophic deep-water lakes are fragile ecosystems with limited nutrient resources, rendering them highly susceptible to environmental fluctuations. Examining different bacterial types within these lakes offers valuable insights into the intricate mechanisms governing community dynamics and adaptation strategies across various scales. In our investigation of oligotrophic deep freshwater Lake Fuxian in China, we explored the seasonal and vertical dynamics of two bacterial types: free-living (FL) and particle-attached (PA). Our findings unveiled distinct patterns in the diversity, composition, and putative functions of these bacteria, all shaped by environmental factors. Understanding these subtleties provides insight into bacterial interactions, thereby influencing the overall ecosystem functioning. Ultimately, our research illuminates the adaptation and roles of FL and PA bacteria within these unique lake environments, contributing significantly to our broader comprehension of ecosystem stability and health.}, }
@article {pmid38939048, year = {2024}, author = {Shi, Q and Sun, L and Gao, J and Li, F and Chen, D and Shi, T and Tan, Y and Chang, H and Liu, X and Kang, J and Lu, F and Huang, Z and Zhao, H}, title = {Effects of sodium lauryl sulfate and postbiotic toothpaste on oral microecology.}, journal = {Journal of oral microbiology}, volume = {16}, number = {1}, pages = {2372224}, pmid = {38939048}, issn = {2000-2297}, abstract = {The diversity and delicate balance of the oral microbiome contribute to oral health, with its disruption leading to oral and systemic diseases. Toothpaste includes elements like traditional additives such as sodium lauryl sulfate (SLS) as well as novel postbiotics derived from probiotics, which are commonly employed for maintaining oral hygiene and a healthy oral cavity. However, the response of the oral microbiota to these treatments remains poorly understood. In this study, we systematically investigated the impact of SLS, and toothpaste containing postbiotics (hereafter, postbiotic toothpaste) across three systems: biofilms, animal models, and clinical populations. SLS was found to kill bacteria in both preformed biofilms (mature biofilms) and developing biofilms (immature biofilms), and disturbed the microbial community structure by increasing the number of pathogenic bacteria. SLS also destroyed periodontal tissue, promoted alveolar bone resorption, and enhanced the extent of inflammatory response level. The postbiotic toothpaste favored bacterial homeostasis and the normal development of the two types of biofilms in vitro, and attenuated periodontitis and gingivitis in vivo via modulation of oral microecology. Importantly, the postbiotic toothpaste mitigated the adverse effects of SLS when used in combination, both in vitro and in vivo. Overall, the findings of this study describe the impact of toothpaste components on oral microflora and stress the necessity for obtaining a comprehensive understanding of oral microbial ecology by considering multiple aspects.}, }
@article {pmid38938005, year = {2024}, author = {Chaudhary, DK and Kim, SE and Park, HJ and Kim, KH}, title = {Unveiling the Bacterial Community across the Stomach, Hepatopancreas, Anterior Intestine, and Posterior Intestine of Pacific Whiteleg Shrimp.}, journal = {Journal of microbiology and biotechnology}, volume = {34}, number = {6}, pages = {1260-1269}, pmid = {38938005}, issn = {1738-8872}, mesh = {Animals ; *Penaeidae/microbiology ; *Hepatopancreas/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; Republic of Korea ; *Intestines/microbiology ; Phylogeny ; Stomach/microbiology ; Biodiversity ; Aquaculture ; DNA, Bacterial/genetics ; }, abstract = {The gastrointestinal (GI) tract of shrimp, which is comprised of the stomach, hepatopancreas, and intestine, houses microbial communities that play crucial roles in immune defense, nutrient absorption, and overall health. While the intestine's microbiome has been well-studied, there has been limited research investigating the stomach and hepatopancreas. The present study addresses this gap by profiling the bacterial community in these interconnected GI segments of Pacific whiteleg shrimp. To this end, shrimp samples were collected from a local aquaculture farm in South Korea, and 16S rRNA gene amplicon sequencing was performed. The results revealed significant variations in bacterial diversity and composition among GI segments. The stomach and hepatopancreas exhibited higher Proteobacteria abundance, while the intestine showed a more diverse microbiome, including Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Chloroflexi, and Verrucomicrobia. Genera such as Oceaniovalibus, Streptococcus, Actibacter, Ilumatobacter, and Litorilinea dominated the intestine, while Salinarimonas, Sphingomonas, and Oceaniovalibus prevailed in the stomach and hepatopancreas. It is particularly notable that Salinarimonas, which is associated with nitrate reduction and pollutant degradation, was prominent in the hepatopancreas. Overall, this study provides insights into the microbial ecology of the Pacific whiteleg shrimp's GI tract, thus enhancing our understanding of shrimp health with the aim of supporting sustainable aquaculture practices.}, }
@article {pmid38937989, year = {2024}, author = {Wu, H and Mu, C and Li, X and Fan, W and Shen, L and Zhu, W}, title = {Breed-Driven Microbiome Heterogeneity Regulates Intestinal Stem Cell Proliferation via Lactobacillus-Lactate-GPR81 Signaling.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {11}, number = {33}, pages = {e2400058}, pmid = {38937989}, issn = {2198-3844}, support = {32030104//National Natural Science Foundation of China/ ; 2022YFD1300402//National Key Research and Development Program of China/ ; }, mesh = {Animals ; *Cell Proliferation/physiology ; *Stem Cells/metabolism/cytology ; *Lactobacillus/metabolism/genetics ; *Receptors, G-Protein-Coupled/metabolism/genetics ; *Gastrointestinal Microbiome/physiology/genetics ; Swine ; *Lactic Acid/metabolism ; Signal Transduction/physiology ; Wnt Signaling Pathway/physiology/genetics ; Jejunum/microbiology/metabolism/cytology ; Obesity/metabolism/microbiology ; Intestinal Mucosa/metabolism/microbiology/cytology ; }, abstract = {Genetically lean and obese individuals have distinct intestinal microbiota and function. However, the underlying mechanisms of the microbiome heterogeneity and its regulation on epithelial function such as intestinal stem cell (ISC) fate remain unclear. Employing pigs of genetically distinct breeds (obese Meishan and lean Yorkshire), this study reveals transcriptome-wide variations in microbial ecology of the jejunum, characterized by enrichment of active Lactobacillus species, notably the predominant Lactobacillus amylovorus (L. amylovorus), and lactate metabolism network in obese breeds. The L. amylovorus-dominant heterogeneity is paralleled with epithelial functionality difference as reflected by highly expressed GPR81, more proliferative ISCs and activated Wnt/β-catenin signaling. Experiments using in-house developed porcine jejunal organoids prove that live L. amylovorus and its metabolite lactate promote intestinal organoid growth. Mechanistically, L. amylovorus and lactate activate Wnt/β-catenin signaling in a GPR81-dependent manner to promote ISC-mediated epithelial proliferation. However, heat-killed L. amylovorus fail to cause these changes. These findings uncover a previously underrepresented role of L. amylovorus in regulating jejunal stem cells via Lactobacillus-lactate-GPR81 axis, a key mechanism bridging breed-driven intestinal microbiome heterogeneity with ISC fate. Thus, results from this study provide new insights into the role of gut microbiome and stem cell interactions in maintaining intestinal homeostasis.}, }
@article {pmid38936927, year = {2024}, author = {Shen, CL and Wankhade, UD and Shankar, K and Najjar, RS and Feresin, RG and Elmassry, MM and Dufour, JM and Kaur, G and Chintapalli, SV and Piccolo, BD and Dunn, DM and Cao, JJ}, title = {Effects of Statin and Annatto-extracted Tocotrienol Supplementation on Glucose Homeostasis, Bone Microstructure, and Gut Microbiota Composition in Obese Mice.}, journal = {In vivo (Athens, Greece)}, volume = {38}, number = {4}, pages = {1557-1570}, pmid = {38936927}, issn = {1791-7549}, support = {P30 DK048520/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Tocotrienols/pharmacology/administration &amp; dosage ; Mice ; *Homeostasis/drug effects ; *Obesity/drug therapy/metabolism ; Male ; *Dietary Supplements ; *Bone and Bones/drug effects/metabolism/pathology ; *Hydroxymethylglutaryl-CoA Reductase Inhibitors/pharmacology ; *Diet, High-Fat/adverse effects ; Bixaceae/chemistry ; Mice, Obese ; Plant Extracts/pharmacology/administration &amp; dosage ; Glucose/metabolism ; Mice, Inbred C57BL ; Insulin Resistance ; Blood Glucose ; Disease Models, Animal ; Liver/drug effects/metabolism/pathology ; Biomarkers ; Carotenoids ; }, abstract = {BACKGROUND/AIM: This study examined the effects of tocotrienols (TT) in conjunction with statin on glucose homeostasis, bone microstructure, gut microbiome, and systemic and liver inflammatory markers in obese C57BL/6J mice.<br><br>MATERIALS AND METHODS: Forty male C57BL/6J mice were fed a high-fat diet (HFD) and assigned into four groups in a 2 (no statin vs. 120 mg statin/kg diet)&#xd7;2 (no TT vs. 400 mg TT/kg diet) factorial design for 14 weeks.<br><br>RESULTS: Statin and TT improved glucose tolerance only when each was given alone, and only statin supplementation decreased insulin resistance. Consistently, only statin supplementation decreased serum insulin levels and HOMA-IR. Pancreatic insulin was also increased with statin treatment. Statin and TT, alone or in combination, reduced the levels of serum IL-6, but only TT attenuated the increased serum leptin levels induced by a HFD. Statin supplementation increased bone area/total area and connectivity density at LV-4, while TT supplementation increased bone area/total area and trabecular number, but decreased trabecular separation at the distal femur. Statin supplementation, but not TT, reduced hepatic inflammatory cytokine gene expression. Neither TT supplementation nor statin supplementation statistically altered microbiome species evenness or richness. However, they altered the relative abundance of certain microbiome species. Most notably, both TT and statin supplementation increased the relative abundance of Lachnospiraceae UCG-006.<br><br>CONCLUSION: TT and statin collectively benefit bone microstructure, glucose homeostasis, and microbial ecology in obese mice. Such changes may be, in part, associated with suppression of inflammation in the host.}, }
@article {pmid38936916, year = {2024}, author = {Morikawa, T and Paudel, D and Uehara, O and Ariwansa, D and Kobayashi, Y and Yang, J and Yoshida, K and Abiko, Y}, title = {Effects of Laurus nobilis Leaf Extract (LAURESH[®]) on Oral and Gut Microbiota Diversity in Mice.}, journal = {In vivo (Athens, Greece)}, volume = {38}, number = {4}, pages = {1758-1766}, pmid = {38936916}, issn = {1791-7549}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Plant Leaves/chemistry ; Mice ; *Plant Extracts/pharmacology ; *Laurus/chemistry ; *RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Biodiversity ; Feces/microbiology ; Bacteria/classification/drug effects/genetics/isolation &amp; purification ; Male ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND/AIM: The leaves of Laurus nobilis have been used for culinary purposes for many years and have recently been shown to have beneficial effects on human health by altering microbiota composition. However, the effects of L. nobilis on the diversity of microbiomes in the oral cavity and gut remain unknown. Therefore, in this study, we examined the effects of an extract of L. nobilis on the diversity of microbiomes in the oral cavity and gut in mice.<br><br>MATERIALS AND METHODS: C57BL/6J mice were randomly divided into two groups and fed a standard diet (SD) and a standard diet containing 5% LAURESH[&#xae;], a laurel extract (SDL). After 10 weeks, oral swabs and fecal samples were collected. The bacterial DNA extracted from the oral swabs and feces was used for microbiota analysis using 16S rRNA sequencing. The sequencing data were analyzed using the Quantitative Insights into Microbial Ecology 2 in the DADA2 pipeline and 16S rRNA database.<br><br>RESULTS: The &#x3b1;-diversity of the oral microbiome was significantly greater in the SDL group than in the SD group. The &#x3b2;-diversity of the oral microbiome was also significantly different between the groups. Moreover, the taxonomic abundance analysis showed that five bacteria in the gut were significantly different among the groups. Furthermore, the SDL diet increased the abundance of beneficial gut bacteria, such as Akkermansia sp.<br><br>CONCLUSION: Increased diversity of the oral microbiome and proportion of Akkermansia sp. in the gut microbiome induced by L. nobilis consumption may benefit oral and gut health.}, }
@article {pmid38936824, year = {2024}, author = {Chen, YC and Destouches, L and Cook, A and Fedorec, AJH}, title = {Synthetic microbial ecology: engineering habitats for modular consortia.}, journal = {Journal of applied microbiology}, volume = {135}, number = {7}, pages = {}, doi = {10.1093/jambio/lxae158}, pmid = {38936824}, issn = {1365-2672}, support = {EP/W524335/1//Engineering and Physical Sciences Research Council/ ; BB/T008709/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Microbial Consortia ; *Synthetic Biology/methods ; *Microbiota ; *Ecosystem ; Ecology ; }, abstract = {Microbiomes, the complex networks of micro-organisms and the molecules through which they interact, play a crucial role in health and ecology. Over at least the past two decades, engineering biology has made significant progress, impacting the bio-based industry, health, and environmental sectors; but has only recently begun to explore the engineering of microbial ecosystems. The creation of synthetic microbial communities presents opportunities to help us understand the dynamics of wild ecosystems, learn how to manipulate and interact with existing microbiomes for therapeutic and other purposes, and to create entirely new microbial communities capable of undertaking tasks for industrial biology. Here, we describe how synthetic ecosystems can be constructed and controlled, focusing on how the available methods and interaction mechanisms facilitate the regulation of community composition and output. While experimental decisions are dictated by intended applications, the vast number of tools available suggests great opportunity for researchers to develop a diverse array of novel microbial ecosystems.}, }
@article {pmid38935596, year = {2024}, author = {O'Brien, JM and Blais, N and Butler, C and White, N and Bustead, A and Figler, C and Wells, M and Anderson, G and Yuhas, A and Ernakovich, JG}, title = {Ten "simple" rules for non-Indigenous researchers engaging Indigenous communities in Arctic research.}, journal = {PLoS computational biology}, volume = {20}, number = {6}, pages = {e1012093}, pmid = {38935596}, issn = {1553-7358}, mesh = {Arctic Regions ; Humans ; *Indigenous Peoples ; Research Personnel ; }, }
@article {pmid38935504, year = {2024}, author = {Luo, S and Zhang, X and Zhou, X}, title = {Temporospatial dynamics and host specificity of honeybee gut bacteria.}, journal = {Cell reports}, volume = {43}, number = {7}, pages = {114408}, doi = {10.1016/j.celrep.2024.114408}, pmid = {38935504}, issn = {2211-1247}, mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome ; *Host Specificity ; *Bacteria/genetics ; Host Microbial Interactions/physiology ; }, abstract = {Honeybees are important pollinators worldwide, with their gut microbiota playing a crucial role in maintaining their health. The gut bacteria of honeybees consist of primarily five core lineages that are spread through social interactions. Previous studies have provided a basic understanding of the composition and function of the honeybee gut microbiota, with recent advancements focusing on analyzing diversity at the strain level and changes in bacterial functional genes. Research on honeybee gut microbiota across different regions globally has provided insights into microbial ecology. Additionally, recent findings have shed light on the mechanisms of host specificity of honeybee gut bacteria. This review explores the temporospatial dynamics in honeybee gut microbiota, discussing the reasons and mechanisms behind these fluctuations. This synopsis provides insights into host-microbe interactions and is invaluable for honeybee health.}, }
@article {pmid38935220, year = {2024}, author = {Parra, B and Lutz, VT and Brøndsted, L and Carmona, JL and Palomo, A and Nesme, J and Van Hung Le, V and Smets, BF and Dechesne, A}, title = {Characterization and Abundance of Plasmid-Dependent Alphatectivirus Bacteriophages.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {85}, pmid = {38935220}, issn = {1432-184X}, support = {101026675//European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant/ ; 002200000279//VRID Postdoctorado from Vicerrector&#xed;a de Investigaci&#xf3;n y Desarrollo, Universidad de Concepci&#xf3;n/ ; P-PhanFARE (23046)//Villum Fonden/ ; }, mesh = {*Plasmids/genetics ; *Wastewater/virology/microbiology ; *Bacteriophages/genetics/isolation &amp; purification/physiology/classification ; Genome, Viral ; Escherichia coli/virology/genetics ; Host Specificity ; Pseudomonas putida/virology/genetics ; Salmonella enterica/virology/genetics ; Phylogeny ; }, abstract = {Antimicrobial resistance (AMR) is a major public health threat, exacerbated by the ability of bacteria to rapidly disseminate antimicrobial resistance genes (ARG). Since conjugative plasmids of the incompatibility group P (IncP) are ubiquitous mobile genetic elements that often carry ARG and are broad-host-range, they are important targets to prevent the dissemination of AMR. Plasmid-dependent phages infect plasmid-carrying bacteria by recognizing components of the conjugative secretion system as receptors. We sought to isolate plasmid-dependent phages from wastewater using an avirulent strain of Salmonella enterica carrying the conjugative IncP plasmid pKJK5. Irrespective of the site, we only obtained bacteriophages belonging to the genus Alphatectivirus. Eleven isolates were sequenced, their genomes analyzed, and their host range established using S. enterica, Escherichia coli, and Pseudomonas putida carrying diverse conjugative plasmids. We confirmed that Alphatectivirus are abundant in domestic and hospital wastewater using culture-dependent and culture-independent approaches. However, these results are not consistent with their low or undetectable occurrence in metagenomes. Therefore, overall, our results emphasize the importance of performing phage isolation to uncover diversity, especially considering the potential of plasmid-dependent phages to reduce the spread of ARG carried by conjugative plasmids, and to help combat the AMR crisis.}, }
@article {pmid38933974, year = {2024}, author = {Rezende, GS and Rocha, FI and Funnicelli, MIG and Malavazi, I and Crauwels, S and Brandao, MM and Cunha, AF}, title = {Metabarcoding analysis reveals an interaction among distinct groups of bacteria associated with three different varietals of grapes used for wine production in Brazil.}, journal = {Heliyon}, volume = {10}, number = {11}, pages = {e32283}, pmid = {38933974}, issn = {2405-8440}, abstract = {Grapes are globally popular with wine production being one of the most well-known uses of grapes worldwide. Brazil has a growing wine industry, and the Serra Gaúcha region is a significant contributor to the country's wine production. Nonetheless, other states are increasing their relevance in this segment. Environmental factors and the soil microbiome (bacteria and fungi) heavily influence grape quality, shaping the crucial "terroir" for wines. Here, soil quality was assessed through nutrient analysis and bacteria microbial diversity, which could significantly impact grape health and final wine attributes. Soil samples from São Paulo's vineyards, focusing on Syrah, Malbec, and Cabernet Sauvignon, underwent chemical and microbial analysis via 16S rRNA metabarcoding and highlighted significant differences in soil composition between vineyards. Statistical analyses including PCA and CAP showcased region-based separation and intricate associations between microbiota, region, and grape variety. Correlation analysis pinpointed microbial genera linked to specific soil nutrients. Random Forest analysis identified abundant bacterial genera per grape variety and the Network analysis revealed varied co-occurrence patterns, with Cabernet Sauvignon exhibiting complex microbial interactions. This study unveils complex relationships between soil microbiota, nutrients, and diverse grape varieties in distinct vineyard regions. Understanding how these specific microorganisms are associated with grapes can improve vineyard management, grape quality, and wine production. It can also potentially optimize soil health, bolster grapevine resilience against pests and diseases, and contribute to the unique character of wines known as terroir.}, }
@article {pmid38933028, year = {2024}, author = {Stemple, B and Gulliver, D and Sarkar, P and Tinker, K and Bibby, K}, title = {Metagenome-assembled genomes provide insight into the metabolic potential during early production of Hydraulic Fracturing Test Site 2 in the Delaware Basin.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1376536}, pmid = {38933028}, issn = {1664-302X}, abstract = {Demand for natural gas continues to climb in the United States, having reached a record monthly high of 104.9 billion cubic feet per day (Bcf/d) in November 2023. Hydraulic fracturing, a technique used to extract natural gas and oil from deep underground reservoirs, involves injecting large volumes of fluid, proppant, and chemical additives into shale units. This is followed by a "shut-in" period, during which the fracture fluid remains pressurized in the well for several weeks. The microbial processes that occur within the reservoir during this shut-in period are not well understood; yet, these reactions may significantly impact the structural integrity and overall recovery of oil and gas from the well. To shed light on this critical phase, we conducted an analysis of both pre-shut-in material alongside production fluid collected throughout the initial production phase at the Hydraulic Fracturing Test Site 2 (HFTS 2) located in the prolific Wolfcamp formation within the Permian Delaware Basin of west Texas, USA. Specifically, we aimed to assess the microbial ecology and functional potential of the microbial community during this crucial time frame. Prior analysis of 16S rRNA sequencing data through the first 35 days of production revealed a strong selection for a Clostridia species corresponding to a significant decrease in microbial diversity. Here, we performed a metagenomic analysis of produced water sampled on Day 33 of production. This analysis yielded three high-quality metagenome-assembled genomes (MAGs), one of which was a Clostridia draft genome closely related to the recently classified Petromonas tenebris. This draft genome likely represents the dominant Clostridia species observed in our 16S rRNA profile. Annotation of the MAGs revealed the presence of genes involved in critical metabolic processes, including thiosulfate reduction, mixed acid fermentation, and biofilm formation. These findings suggest that this microbial community has the potential to contribute to well souring, biocorrosion, and biofouling within the reservoir. Our research provides unique insights into the early stages of production in one of the most prolific unconventional plays in the United States, with important implications for well management and energy recovery.}, }
@article {pmid38932970, year = {2024}, author = {Ponce, MA and Maille, JM and Stoll, I and James, A and Bruce, A and Kim, TN and Scully, ED and Morrison, WR}, title = {Microbial vectoring capacity by internal- and external-infesting stored product insects after varying dispersal periods between novel food patches: An underestimated risk.}, journal = {Ecology and evolution}, volume = {14}, number = {6}, pages = {e11368}, pmid = {38932970}, issn = {2045-7758}, abstract = {Understanding the ability of internal- and external-infesting stored product insects to vector microbes is important for estimating the relative risk that insects pose to postharvest commodities as they move between habitat patches and in the landscape. Thus, the aim of the current study was to evaluate and compare the microbial growth in novel food patches at different dispersal periods by different populations of Sitophilus oryzae (e.g., internal-infesting) and Lasioderma serricorne (e.g., external-infesting). Adults of both species collected from laboratory colonies or field-captured populations were either placed immediately in a novel food patch, or given a dispersal period of 24 or 72 h in a sterilized environment before entering a surrogate food patch. Vectored microbes in new food patches were imaged after 3 or 5 days of foraging, and microbial growth was processed using ImageJ while fungal species were identified through sequencing the ITS4/5 ribosomal subunit. We found that increasing dispersal time resulted in multiple-fold reductions in microbial growth surrogate food patches by L. serricorne but not S. oryzae. This was likely attributable to higher mobility by S. oryzae than L. serricorne. A total of 20 morphospecies were identified from 13 genera among the 59 sequences, with a total of 23% and 16% classified as Aspergillus and Penicillium spp. Our data suggest that there is a persistent risk of microbial contamination by both species, which has important food safety implications at food facilities.}, }
@article {pmid38930577, year = {2024}, author = {Hernández-Zulueta, J and Rubio-Bueno, S and Zamora-Tavares, MDP and Vargas-Ponce, O and Rodríguez-Troncoso, AP and Rodríguez-Zaragoza, FA}, title = {Metabarcoding the Bacterial Assemblages Associated with Toxopneustes roseus in the Mexican Central Pacific.}, journal = {Microorganisms}, volume = {12}, number = {6}, pages = {}, pmid = {38930577}, issn = {2076-2607}, abstract = {The Mexican Central Pacific (MCP) region has discontinuous coral ecosystems with different protection and anthropogenic disturbance. Characterizing the bacterial assemblage associated with the sea urchin Toxopneustes roseus and its relationship with environmental variables will contribute to understanding the species' physiology and ecology. We collected sea urchins from coral ecosystems at six sites in the MCP during the summer and winter for two consecutive years. The spatial scale represented the most important variation in the T. roseus bacteriome, particularly because of Isla Isabel National Park (PNII). Likewise, spatial differences correlated with habitat structure variables, mainly the sponge and live coral cover. The PNII exhibited highly diverse bacterial assemblages compared to other sites, characterized by families associated with diseases and environmental stress (Saprospiraceae, Flammeovirgaceae, and Xanthobacteraceae). The remaining five sites presented a constant spatiotemporal pattern, where the predominance of the Campylobacteraceae and Helicobacteraceae families was key to T. roseus' holobiont. However, the dominance of certain bacterial families, such as Enterobacteriaceae, in the second analyzed year suggests that Punto B and Islas e islotes de Bahía Chamela Sanctuary were exposed to sewage contamination. Overall, our results improve the understanding of host-associated bacterial assemblages in specific time and space and their relationship with the environmental condition.}, }
@article {pmid38928853, year = {2024}, author = {Tata, A and Massaro, A and Miano, B and Petrin, S and Antonelli, P and Peruzzo, A and Pezzuto, A and Favretti, M and Bragolusi, M and Zacometti, C and Losasso, C and Piro, R}, title = {A Snapshot, Using a Multi-Omic Approach, of the Metabolic Cross-Talk and the Dynamics of the Resident Microbiota in Ripening Cheese Inoculated with Listeria innocua.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {12}, pages = {}, pmid = {38928853}, issn = {2304-8158}, support = {RC IZSVe 11/2018//Ministero della Salute/ ; }, abstract = {Raw milk cheeses harbor complex microbial communities. Some of these microorganisms are technologically essential, but undesirable microorganisms can also be present. While most of the microbial dynamics and cross-talking studies involving interaction between food-derived bacteria have been carried out on agar plates in laboratory-controlled conditions, the present study evaluated the modulation of the resident microbiota and the changes of metabolite production directly in ripening raw milk cheese inoculated with Listeria innocua strains. Using a proxy of the pathogenic Listeria monocytogenes, we aimed to establish the key microbiota players and chemical signals that characterize Latteria raw milk cheese over 60 days of ripening time. The microbiota of both the control and Listeria-inoculated cheeses was analyzed using 16S rRNA targeted amplicon sequencing, while direct analysis in real time mass spectrometry (DART-HRMS) was applied to investigate the differences in the metabolic profiles of the cheeses. The diversity analysis showed the same microbial diversity trend in both the control cheese and the inoculated cheese, while the taxonomic analysis highlighted the most representative genera of bacteria in both the control and inoculated cheese: Lactobacillus and Streptococcus. On the other hand, the metabolic fingerprints revealed that the complex interactions between resident microbiota and L. innocua were governed by continuously changing chemical signals. Changes in the amounts of small organic acids, hydroxyl fatty acids, and antimicrobial compounds, including pyroglutamic acid, hydroxy-isocaproic acid, malic acid, phenyllactic acid, and lactic acid, were observed over time in the L. innocua-inoculated cheese. In cheese that was inoculated with L. innocua, Streptococcus was significantly correlated with the volatile compounds carboxylbenzaldheyde and cyclohexanecarboxylic acid, while Lactobacillus was positively correlated with some volatile and flavor compounds (cyclohexanecarboxylic acid, pyroxidal acid, aminobenzoic acid, and vanillic acid). Therefore, we determined the metabolic markers that characterize a raw milk cheese inoculated with L. innocua, the changes in these markers with the ripening time, and the positive correlation of flavor and volatile compounds with the resident microbiota. This multi-omics approach could suggest innovative food safety strategies based on the enhanced management of undesirable microorganisms by means of strain selection in raw matrices and the addition of specific antimicrobial metabolites to prevent the growth of undesirable microorganisms.}, }
@article {pmid38928813, year = {2024}, author = {Vale, ADS and Pereira, CMT and De Dea Lindner, J and Rodrigues, LRS and Kadri, NKE and Pagnoncelli, MGB and Kaur Brar, S and Soccol, CR and Pereira, GVM}, title = {Exploring Microbial Influence on Flavor Development during Coffee Processing in Humid Subtropical Climate through Metagenetic-Metabolomics Analysis.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {12}, pages = {}, pmid = {38928813}, issn = {2304-8158}, support = {440343/2022-4//National Council for Scientific and Technological Development/ ; }, abstract = {Research into microbial interactions during coffee processing is essential for developing new methods that adapt to climate change and improve flavor, thus enhancing the resilience and quality of global coffee production. This study aimed to investigate how microbial communities interact and contribute to flavor development in coffee processing within humid subtropical climates. Employing Illumina sequencing for microbial dynamics analysis, and high-performance liquid chromatography (HPLC) integrated with gas chromatography-mass spectrometry (GC-MS) for metabolite assessment, the study revealed intricate microbial diversity and associated metabolic activities. Throughout the fermentation process, dominant microbial species included Enterobacter, Erwinia, Kluyvera, and Pantoea from the prokaryotic group, and Fusarium, Cladosporium, Kurtzmaniella, Leptosphaerulina, Neonectria, and Penicillium from the eukaryotic group. The key metabolites identified were ethanol, and lactic, acetic, and citric acids. Notably, the bacterial community plays a crucial role in flavor development by utilizing metabolic versatility to produce esters and alcohols, while plant-derived metabolites such as caffeine and linalool remain stable throughout the fermentation process. The undirected network analysis revealed 321 interactions among microbial species and key substances during the fermentation process, with Enterobacter, Kluyvera, and Serratia showing strong connections with sugar and various volatile compounds, such as hexanal, benzaldehyde, 3-methylbenzaldehyde, 2-butenal, and 4-heptenal. These interactions, including inhibitory effects by Fusarium and Cladosporium, suggest microbial adaptability to subtropical conditions, potentially influencing fermentation and coffee quality. The sensory analysis showed that the final beverage obtained a score of 80.83 ± 0.39, being classified as a specialty coffee by the Specialty Coffee Association (SCA) metrics. Nonetheless, further enhancements in acidity, body, and aftertaste could lead to a more balanced flavor profile. The findings of this research hold substantial implications for the coffee industry in humid subtropical regions, offering potential strategies to enhance flavor quality and consistency through controlled fermentation practices. Furthermore, this study contributes to the broader understanding of how microbial ecology interplays with environmental factors to influence food and beverage fermentation, a topic of growing interest in the context of climate change and sustainable agriculture.}, }
@article {pmid38927252, year = {2024}, author = {Huang, Y and Chen, Y and Xie, H and Feng, Y and Chen, S and Bao, B}, title = {Effects of Inducible Nitric Oxide Synthase (iNOS) Gene Knockout on the Diversity, Composition, and Function of Gut Microbiota in Adult Zebrafish.}, journal = {Biology}, volume = {13}, number = {6}, pages = {}, pmid = {38927252}, issn = {2079-7737}, support = {2022YFD2400103//the National Key R&amp;D Program of China/ ; 2021N3016//the Regional Development Project of Fujian/ ; }, abstract = {The gut microbiota constitutes a complex ecosystem that has an important impact on host health. In this study, genetically engineered zebrafish with inducible nitric oxide synthase (iNOS or NOS2) knockout were used as a model to investigate the effects of nos2a/nos2b gene single knockout and nos2 gene double knockout on intestinal microbiome composition and function. Extensive 16S rRNA sequencing revealed substantial changes in microbial diversity and specific taxonomic abundances, yet it did not affect the functional structure of the intestinal tissues. Notably, iNOS-deficient zebrafish demonstrated a decrease in Vibrio species and an increase in Aeromonas species, with more pronounced effects observed in double knockouts. Further transcriptomic analysis of the gut in double iNOS knockout zebrafish indicated significant alterations in immune-related and metabolic pathways, including the complement and PPAR signaling pathways. These findings underscore the crucial interplay between host genetics and gut microbiota, indicating that iNOS plays a key role in modulating the gut microbial ecology, host immune system, and metabolic responses.}, }
@article {pmid38926469, year = {2024}, author = {Martin, LC and O'Hare, MA and Ghielmetti, G and Twesigomwe, D and Kerr, TJ and Gumbo, R and Buss, PE and Kitchin, N and Hemmings, SMJ and Miller, MA and Goosen, WJ}, title = {Short-read full-length 16S rRNA amplicon sequencing for characterisation of the respiratory bacteriome of captive and free-ranging African elephants (Loxodonta africana).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {14768}, pmid = {38926469}, issn = {2045-2322}, support = {S007355//American Association of Zoo Veterinarians/ ; 86949//National Research Foundation, South Africa/ ; MND200409511840//National Research Foundation/ ; /WT_/Wellcome Trust/United Kingdom ; 222941/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; S005651//American Association of Zoo Veterinarians/ ; PMDS22052113333//National Research Foundation/ ; }, mesh = {Animals ; *Elephants/microbiology/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Respiratory System/microbiology ; Animals, Zoo/microbiology ; Sequence Analysis, DNA/methods ; Animals, Wild/microbiology ; Phylogeny ; }, abstract = {Hypervariable region sequencing of the 16S ribosomal RNA (rRNA) gene plays a critical role in microbial ecology by offering insights into bacterial communities within specific niches. While providing valuable genus-level information, its reliance on data from targeted genetic regions limits its overall utility. Recent advances in sequencing technologies have enabled characterisation of the full-length 16S rRNA gene, enhancing species-level classification. Although current short-read platforms are cost-effective and precise, they lack full-length 16S rRNA amplicon sequencing capability. This study aimed to evaluate the feasibility of a modified 150 bp paired-end full-length 16S rRNA amplicon short-read sequencing technique on the Illumina iSeq 100 and 16S rRNA amplicon assembly workflow by utilising a standard mock microbial community and subsequently performing exploratory characterisation of captive (zoo) and free-ranging African elephant (Loxodonta africana) respiratory microbiota. Our findings demonstrate that, despite generating assembled amplicons averaging 869 bp in length, this sequencing technique provides taxonomic assignments consistent with the theoretical composition of the mock community and respiratory microbiota of other mammals. Tentative bacterial signatures, potentially representing distinct respiratory tract compartments (trunk and lower respiratory tract) were visually identified, necessitating further investigation to gain deeper insights into their implication for elephant physiology and health.}, }
@article {pmid38926391, year = {2024}, author = {Brown, CL and Maile-Moskowitz, A and Lopatkin, AJ and Xia, K and Logan, LK and Davis, BC and Zhang, L and Vikesland, PJ and Pruden, A}, title = {Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5412}, pmid = {38926391}, issn = {2041-1723}, support = {1545756//National Science Foundation (NSF)/ ; 2004751//National Science Foundation (NSF)/ ; 2125798//National Science Foundation (NSF)/ ; 4813//Water Research Foundation (WRF)/ ; }, mesh = {*Gene Transfer, Horizontal ; *Sewage/microbiology ; *Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/classification/metabolism ; Water Purification/methods ; Metagenomics/methods ; Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid/methods ; Drug Resistance, Bacterial/genetics ; Selection, Genetic ; }, abstract = {Activated sludge is the centerpiece of biological wastewater treatment, as it facilitates removal of sewage-associated pollutants, fecal bacteria, and pathogens from wastewater through semi-controlled microbial ecology. It has been hypothesized that horizontal gene transfer facilitates the spread of antibiotic resistance genes within the wastewater treatment plant, in part because of the presence of residual antibiotics in sewage. However, there has been surprisingly little evidence to suggest that sewage-associated antibiotics select for resistance at wastewater treatment plants via horizontal gene transfer or otherwise. We addressed the role of sewage-associated antibiotics in promoting antibiotic resistance using lab-scale sequencing batch reactors fed field-collected wastewater, metagenomic sequencing, and our recently developed bioinformatic tool Kairos. Here, we found confirmatory evidence that fluctuating levels of antibiotics in sewage are associated with horizontal gene transfer of antibiotic resistance genes, microbial ecology, and microdiversity-level differences in resistance gene fate in activated sludge.}, }
@article {pmid38923208, year = {2024}, author = {Bosch, J and Lebre, PH and Marais, E and Maggs-Kölling, G and Cowan, DA}, title = {Kinetics and pathways of sub-lithic microbial community (hypolithon) development.}, journal = {Environmental microbiology reports}, volume = {16}, number = {3}, pages = {e13290}, pmid = {38923208}, issn = {1758-2229}, support = {//University of Pretoria/ ; 113308//National Research Foundation/ ; 137954//National Research Foundation/ ; 95565//National Research Foundation/ ; }, mesh = {*Soil Microbiology ; *Cyanobacteria/genetics/isolation &amp; purification/growth &amp; development/classification/metabolism ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Desert Climate ; Namibia ; Kinetics ; Phylogeny ; DNA, Bacterial/genetics ; Soil/chemistry ; }, abstract = {Type I hypolithons are microbial communities dominated by Cyanobacteria. They adhere to the underside of semi-translucent rocks in desert pavements, providing them with a refuge from the harsh abiotic stresses found on the desert soil surface. Despite their crucial role in soil nutrient cycling, our understanding of their growth rates and community development pathways remains limited. This study aimed to quantify the dynamics of hypolithon formation in the pavements of the Namib Desert. We established replicate arrays of sterile rock tiles with varying light transmission in two areas of the Namib Desert, each with different annual precipitation regimes. These were sampled annually over 7 years, and the samples were analysed using eDNA extraction and 16S rRNA gene amplicon sequencing. Our findings revealed that in the zone with higher precipitation, hypolithon formation became evident in semi-translucent rocks 3 years after the arrays were set up. This coincided with a Cyanobacterial 'bloom' in the adherent microbial community in the third year. In contrast, no visible hypolithon formation was observed at the array set up in the hyper-arid zone. This study provides the first quantitative evidence of the kinetics of hypolithon development in hot desert environments, suggesting that development rates are strongly influenced by precipitation regimes.}, }
@article {pmid38922748, year = {2024}, author = {Pérez-Pazos, E and Beidler, KV and Narayanan, A and Beatty, BH and Maillard, F and Bancos, A and Heckman, KA and Kennedy, PG}, title = {Fungi rather than bacteria drive early mass loss from fungal necromass regardless of particle size.}, journal = {Environmental microbiology reports}, volume = {16}, number = {3}, pages = {e13280}, pmid = {38922748}, issn = {1758-2229}, support = {SCW1632//Department of Energy Office of Biological and Environmental Research Genomic Science Program/ ; 2038293//National Science Foundation/ ; }, mesh = {*Bacteria/classification/genetics/isolation &amp; purification/growth &amp; development/metabolism ; *Particle Size ; Fungi/growth &amp; development/classification/genetics/physiology ; Soil Microbiology ; Hydrogen-Ion Concentration ; Ascomycota/growth &amp; development/physiology ; }, abstract = {Microbial necromass is increasingly recognized as an important fast-cycling component of the long-term carbon present in soils. To better understand how fungi and bacteria individually contribute to the decomposition of fungal necromass, three particle sizes (>500, 250-500, and <250 μm) of Hyaloscypha bicolor necromass were incubated in laboratory microcosms inoculated with individual strains of two fungi and two bacteria. Decomposition was assessed after 15 and 28 days via necromass loss, microbial respiration, and changes in necromass pH, water content, and chemistry. To examine how fungal-bacterial interactions impact microbial growth on necromass, single and paired cultures of bacteria and fungi were grown in microplates containing necromass-infused media. Microbial growth was measured after 5 days through quantitative PCR. Regardless of particle size, necromass colonized by fungi had higher mass loss and respiration than both bacteria and uninoculated controls. Fungal colonization increased necromass pH, water content, and altered chemistry, while necromass colonized by bacteria remained mostly unaltered. Bacteria grew significantly more when co-cultured with a fungus, while fungal growth was not significantly affected by bacteria. Collectively, our results suggest that fungi act as key early decomposers of fungal necromass and that bacteria may require the presence of fungi to actively participate in necromass decomposition.}, }
@article {pmid38922446, year = {2024}, author = {Filek, K and Vuković, BB and Žižek, M and DiBello, A and Kanjer, L and Trotta, A and Corrente, M and Bosak, S}, title = {Correction to: Loggerhead Sea Turtles as Hosts of Diverse Bacterial and Fungal Communities.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {84}, doi = {10.1007/s00248-024-02405-z}, pmid = {38922446}, issn = {1432-184X}, }
@article {pmid38921731, year = {2024}, author = {Wang, C and Defoirdt, T and Rajkovic, A}, title = {The Effect of Caco-2 Cells on Sporulation and Enterotoxin Expression by Foodborne Clostridium perfringens.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {6}, pages = {}, pmid = {38921731}, issn = {2076-0817}, support = {201808630020//China Scholarship Council/ ; BOF20/BAS/120//Special Research Fund of Ghent University/ ; 1506419N//Research Foundation - Flanders/ ; }, mesh = {Humans ; Caco-2 Cells ; *Clostridium perfringens/genetics ; *Enterotoxins/metabolism/genetics ; *Spores, Bacterial/genetics ; *Coculture Techniques ; Clostridium Infections/microbiology/metabolism ; Epithelial Cells/metabolism/microbiology ; Foodborne Diseases/microbiology ; }, abstract = {Clostridium perfringens enterotoxin (Cpe)-producing strains cause gastrointestinal infections in humans and account for the second-largest number of all foodborne outbreaks caused by bacterial toxins. The Cpe toxin is only produced during sporulation; this process might be affected when C. perfringens comes into contact with host cells. The current study determined how the cpe expression levels and spore formation changed over time during co-culture with Caco-2 cells (as a model of intestinal epithelial cells). In co-culture with Caco-2 cells, total C. perfringens cell counts first decreased and then remained more or less stable, whereas spore counts were stable over the whole incubation period. The cpe mRNA level in the co-culture with Caco-2 cells increased more rapidly than in the absence of Caco-2 cells (3.9-fold higher levels in coculture than in the absence of Caco-2 cells after 8 h of incubation). Finally, we found that cpe expression is inhibited by a cue released by Caco-2 cells (8.3-fold lower levels in the presence of supernatants of Caco-2 cells than in the absence of the supernatants after 10 h of incubation); as a consequence, the increased expression in co-culture with Caco-2 cells must be caused by a factor associated with the Caco-2 cells.}, }
@article {pmid38920365, year = {2024}, author = {Givati, S and Forchielli, E and Aharonovich, D and Barak, N and Weissberg, O and Belkin, N and Rahav, E and Segrè, D and Sher, D}, title = {Diversity in the utilization of different molecular classes of dissolved organic matter by heterotrophic marine bacteria.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {7}, pages = {e0025624}, pmid = {38920365}, issn = {1098-5336}, support = {RGP0020/2016//Human Frontier Science Program (HFSP)/ ; NSFOCE-BSF 1635070//United States-Israel Binational Science Foundation (BSF)/ ; 1786/20//Israel Science Foundation (ISF)/ ; }, mesh = {*Seawater/microbiology ; *Heterotrophic Processes ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Mediterranean Sea ; Microbiota ; Amino Acids/metabolism ; Organic Chemicals/metabolism ; }, abstract = {UNLABELLED: Heterotrophic marine bacteria utilize and recycle dissolved organic matter (DOM), impacting biogeochemical cycles. It is currently unclear to what extent distinct DOM components can be used by different heterotrophic clades. Here, we ask how a natural microbial community from the Eastern Mediterranean Sea (EMS) responds to different molecular classes of DOM (peptides, amino acids, amino sugars, disaccharides, monosaccharides, and organic acids) comprising much of the biomass of living organisms. Bulk bacterial activity increased after 24 h for all treatments relative to the control, while glucose and ATP uptake decreased or remained unchanged. Moreover, while the per-cell uptake rate of glucose and ATP decreased, that of Leucin significantly increased for amino acids, reflecting their importance as common metabolic currencies in the marine environment. Pseudoalteromonadaceae dominated the peptides treatment, while different Vibrionaceae strains became dominant in response to amino acids and amino sugars. Marinomonadaceae grew well on organic acids, and Alteromonadaseae on disaccharides. A comparison with a recent laboratory-based study reveals similar peptide preferences for Pseudoalteromonadaceae, while Alteromonadaceae, for example, grew well in the lab on many substrates but dominated in seawater samples only when disaccharides were added. We further demonstrate a potential correlation between the genetic capacity for degrading amino sugars and the dominance of specific clades in these treatments. These results highlight the diversity in DOM utilization among heterotrophic bacteria and complexities in the response of natural communities.<br><br>IMPORTANCE: A major goal of microbial ecology is to predict the dynamics of natural communities based on the identity of the organisms, their physiological traits, and their genomes. Our results show that several clades of heterotrophic bacteria each grow in response to one or more specific classes of organic matter. For some clades, but not others, growth in a complex community is similar to that of isolated strains in laboratory monoculture. Additionally, by measuring how the entire community responds to various classes of organic matter, we show that these results are ecologically relevant, and propose that some of these resources are utilized through common uptake pathways. Tracing the path between different resources to the specific microbes that utilize them, and identifying commonalities and differences between different natural communities and between them and lab cultures, is an important step toward understanding microbial community dynamics and predicting how communities will respond to perturbations.}, }
@article {pmid38918384, year = {2024}, author = {Dueholm, MKD and Andersen, KS and Korntved, AC and Rudkjøbing, V and Alves, M and Bajón-Fernández, Y and Batstone, D and Butler, C and Cruz, MC and Davidsson, &#xc5; and Erijman, L and Holliger, C and Koch, K and Kreuzinger, N and Lee, C and Lyberatos, G and Mutnuri, S and O'Flaherty, V and Oleskowicz-Popiel, P and Pokorna, D and Rajal, V and Recktenwald, M and Rodríguez, J and Saikaly, PE and Tooker, N and Vierheilig, J and De Vrieze, J and Wurzbacher, C and Nielsen, PH}, title = {MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5361}, pmid = {38918384}, issn = {2041-1723}, support = {Dark Matter and grant 13351//Villum Fonden (Villum Foundation)/ ; 6111-00617 A//Det Frie Forskningsr&#xe5;d (Danish Council for Independent Research)/ ; }, mesh = {*Archaea/genetics/classification/metabolism ; *RNA, Ribosomal, 16S/genetics ; Anaerobiosis ; *Bacteria/genetics/classification/metabolism ; *Microbiota/genetics ; *Biodiversity ; *Phylogeny ; Wastewater/microbiology ; Bioreactors/microbiology ; Methane/metabolism ; Sequence Analysis, DNA ; }, abstract = {Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84-99% and 18-61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.}, }
@article {pmid38918217, year = {2024}, author = {Duong, HL and Paufler, S and Harms, H and Maskow, T and Schlosser, D}, title = {Biocalorimetry-aided monitoring of fungal pretreatment of lignocellulosic agricultural residues.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {394}, pmid = {38918217}, issn = {1432-0614}, support = {911 Program//B&#x1ed9; Gi&#xe1;o d&#x1ee5;c v&#xe0; &#xd0;&#xe0;o t&#x1ea1;o/ ; }, mesh = {*Lignin/metabolism ; *Triticum/microbiology/chemistry ; *Fungi/metabolism ; Fermentation ; Hydrolysis ; Agriculture/methods ; }, abstract = {The present study aimed to investigate whether and how non-invasive biocalorimetric measurements could serve for process monitoring of fungal pretreatment during solid-state fermentation (SSF) of lignocellulosic agricultural residues such as wheat straw. Seven filamentous fungi representing different lignocellulose decay types were employed. Water-soluble sugars being immediately available after fungal pretreatment and those becoming water-extractable after enzymatic digestion of pretreated wheat straw with hydrolysing (hemi)cellulases were considered to constitute the total bioaccessible sugar fraction. The latter was used to indicate the success of pretreatments and linked to corresponding species-specific metabolic heat yield coefficients (YQ/X) derived from metabolic heat flux measurements during fungal wheat straw colonisation. An YQ/X range of about 120 to 140 kJ/g was seemingly optimal for pretreatment upon consideration of all investigated fungi and application of a non-linear Gaussian fitting model. Upon exclusion from analysis of the brown-rot basidiomycete Gloeophyllum trabeum, which differs from all other here investigated fungi in employing extracellular Fenton chemistry for lignocellulose decomposition, a linear relationship where amounts of total bioaccessible sugars were suggested to increase with increasing YQ/X values was obtained. It remains to be elucidated whether an YQ/X range being optimal for fungal pretreatment could firmly be established, or if the sugar accessibility for post-treatment generally increases with increasing YQ/X values as long as "conventional" enzymatic, i.e. (hemi)cellulase-based, lignocellulose decomposition mechanisms are operative. In any case, metabolic heat measurement-derived parameters such as YQ/X values may become very valuable tools supporting the assessment of the suitability of different fungal species for pretreatment of lignocellulosic substrates. KEY POINTS: • Biocalorimetry was used to monitor wheat straw pretreatment with seven filamentous fungi. • Metabolic heat yield coefficients (YQ/X) seem to indicate pretreatment success. • YQ/X values may support the selection of suitable fungal strains for pretreatment.}, }
@article {pmid38917910, year = {2024}, author = {Gao, Y and Heng, S and Wang, J and Liu, Z and Liu, Y and Chen, B and Han, Y and Li, W and Lu, X and Zhen, G}, title = {Bioelectrochemically altering microbial ecology in upflow anaerobic sludge blanket to enhance methanogenesis fed with high-sulfate methanolic wastewater.}, journal = {Bioresource technology}, volume = {406}, number = {}, pages = {131026}, doi = {10.1016/j.biortech.2024.131026}, pmid = {38917910}, issn = {1873-2976}, mesh = {*Wastewater/microbiology ; *Methanol/metabolism ; *Methane/metabolism ; *Sulfates/metabolism ; *Sewage/microbiology ; Anaerobiosis ; Bioreactors/microbiology ; Electrodes ; }, abstract = {A bioelectrochemical upflow anaerobic sludge blanket (BE-UASB) was constructed and compared with the traditional UASB to investigate the role of bioelectrocatalysis in modulating methanogenesis and sulfidogensis involved within anaerobic treatment of high-sulfate methanolic wastewater (COD/SO4[2-] ratio ≤ 2). Methane production rate for BE-UASB was 1.4 times higher than that of the single UASB, while SO4[2-] removal stabilized at 16.7%. Bioelectrocatalysis selectively enriched key functional anaerobes and stimulated the secretion of extracellular polymeric substances, especially humic acids favoring electron transfer, thereby accelerating the electroactive biofilms development of electrodes. Methanomethylovorans was the dominant genus (35%) to directly convert methanol to CH4. Methanobacterium as CO2 electroreduction methane-producing archaea appeared only on electrodes. Acetobacterium exhibited anode-dependence, which provided acetate for sulfate-reducing bacteria (norank Syntrophobacteraceae and Desulfomicrobium) through synergistic coexistence. This study confirmed that BE-UASB regulated the microbial ecology to achieve efficient removal and energy recovery of high-sulfate methanolic wastewater.}, }
@article {pmid38917500, year = {2024}, author = {Zhang, D and Calmanovici, B and Marican, H and Reisser, J and Summers, S}, title = {The assembly and ecological roles of biofilms attached to plastic debris of Ashmore reef.}, journal = {Marine pollution bulletin}, volume = {205}, number = {}, pages = {116651}, doi = {10.1016/j.marpolbul.2024.116651}, pmid = {38917500}, issn = {1879-3363}, mesh = {*Biofilms ; *Plastics ; Australia ; Microbiota ; Seawater/microbiology ; Coral Reefs ; Bacteria ; Waste Products ; }, abstract = {Plastic pollution in the ocean is a global environmental hazard aggravated by poor management of plastic waste and growth of annual plastic consumption. Microbial communities colonizing the plastic's surface, the plastisphere, has gained global interest resulting in numerous efforts to characterize the plastisphere. However, there are insufficient studies deciphering the underlying metabolic processes governing the function of the plastisphere and the plastic they reside upon. Here, we collected plastic and seawater samples from Ashmore Reef in Australia to examine the planktonic microbes and plastic associated biofilm (PAB) to investigate the ecological impact, pathogenic potential, and plastic degradation capabilities of PAB in Ashmore Reef, as well as the role and impact of bacteriophages on PAB. Using high-throughput metagenomic sequencing, we demonstrated distinct microbial communities between seawater and PAB. Similar numbers of pathogenic bacteria were found in both sample types, yet plastic and seawater select for different pathogen populations. Virulence Factor analysis further illustrated stronger pathogenic potential in PAB, highlighting the pathogenicity of environmental PAB. Furthermore, functional analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed xenobiotic degradation and fatty acid degradation to be enriched in PABs. In addition, construction of metagenome-assembled genomes (MAG) and functional analysis further demonstrated the presence of a complete Polyethylene (PE) degradation pathway in multiple Proteobacteria MAGs, especially in Rhodobacteriaceae sp. Additionally, we identified viral population presence in PAB, revealing the key role of bacteriophages in shaping these communities within the PAB. Our result provides a comprehensive overview of the various ecological processes shaping microbial community on marine plastic debris.}, }
@article {pmid38916294, year = {2024}, author = {Chadwick, GL and Dury, GA and Nayak, DD}, title = {Physiological and transcriptomic response to methyl-coenzyme M reductase limitation in Methanosarcina acetivorans.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {7}, pages = {e0222023}, pmid = {38916294}, issn = {1098-5336}, support = {//Searle Scholars Program (SSP)/ ; Beckman Young Investigator Award//Arnold and Mabel Beckman Foundation (AMBF)/ ; Simons Early Career Investigator in Marine Microbial Ecology and Evolution//Simons Foundation (SF)/ ; Packard Fellowship in Science and Engineering//David and Lucile Packard Foundation (PF)/ ; Chan-Zuckerberg Biohub - San Francisco Investigator//Chan Zuckerberg Initiative (CZI)/ ; 5T32GM06698-14//HHS | National Institutes of Health (NIH)/ ; //Adolph C. and Mary Sprague Miller Institute for Basic Research in Science, University of California Berkeley (MIBRS)/ ; }, mesh = {*Methanosarcina/genetics/enzymology/metabolism ; *Oxidoreductases/metabolism/genetics ; *Transcriptome ; Methane/metabolism ; Archaeal Proteins/genetics/metabolism ; Gene Expression Regulation, Archaeal ; Operon ; }, abstract = {UNLABELLED: Methyl-coenzyme M reductase (MCR) catalyzes the final step of methanogenesis, the microbial metabolism responsible for nearly all biological methane emissions to the atmosphere. Decades of biochemical and structural research studies have generated detailed insights into MCR function in vitro, yet very little is known about the interplay between MCR and methanogen physiology. For instance, while it is routinely stated that MCR catalyzes the rate-limiting step of methanogenesis, this has not been categorically tested. In this study, to gain a more direct understanding of MCR's control on the growth of Methanosarcina acetivorans, we generate a strain with an inducible mcr operon on the chromosome, allowing for careful control of MCR expression. We show that MCR is not growth rate-limiting in substrate-replete batch cultures. However, through careful titration of MCR expression, growth-limiting state(s) can be obtained. Transcriptomic analysis of M. acetivorans experiencing MCR limitation reveals a global response with hundreds of differentially expressed genes across diverse functional categories. Notably, MCR limitation leads to strong induction of methylsulfide methyltransferases, likely due to insufficient recycling of metabolic intermediates. In addition, the mcr operon is not transcriptionally regulated, i.e., it is constitutively expressed, suggesting that the overabundance of MCR might be beneficial when cells experience nutrient limitation or stressful conditions. Altogether, we show that there is a wide range of cellular MCR concentrations that can sustain optimal growth, suggesting that other factors such as anabolic reactions might be rate-limiting for methanogenic growth.<br><br>IMPORTANCE: Methane is a potent greenhouse gas that has contributed to ca. 25% of global warming in the post-industrial era. Atmospheric methane is primarily of biogenic origin, mostly produced by microorganisms called methanogens. Methyl-coenzyme M reductase (MCR) catalyzes methane formatio in methanogens. Even though MCR comprises ca. 10% of the cellular proteome, it is hypothesized to be growth-limiting during methanogenesis. In this study, we show that Methanosarcina acetivorans cells grown in substrate-replicate batch cultures produce more MCR than its cellular demand for optimal growth. The tools outlined in this study can be used to refine metabolic models of methanogenesis and assay lesions in MCR in a higher-throughput manner than isolation and biochemical characterization of pure protein.}, }
@article {pmid38915372, year = {2024}, author = {Levi, EE and Jeppesen, E and Nejstgaard, JC and Davidson, TA}, title = {Chlorophyll-a determinations in mesocosms under varying nutrient and temperature treatments: in-situ fluorescence sensors versus in-vitro measurements.}, journal = {Open research Europe}, volume = {4}, number = {}, pages = {69}, pmid = {38915372}, issn = {2732-5121}, abstract = {Harmful algal blooms (HABs) are a significant threat to freshwater ecosystems, and monitoring for changes in biomass is therefore important. Fluorescence in-situ sensors enable rapid and high frequency real-time data collection and have been widely used to determine chlorophyll- a (Chla) concentrations that are used as an indicator of the total algal biomass. However, conversion of fluorescence to equivalent-Chla concentrations is often complicated due to biofouling, phytoplankton composition and the type of equipment used. Here, we validated measurements from 24 Chla and 12 phycocyanin (cyanobacteria indicator) fluorescence in-situ sensors (Cyclops-7F, Turner Designs) against spectrophotometrically (in-vitro) determined Chla and tested a data-cleaning procedure for eliminating data errors and impacts of non-photochemical quenching (i.e. light-induced decrease in fluorescence intensity). The test was done across a range of freshwater plankton communities in 24 mesocosms (i.e. experimental tanks) with a 2x3 (high and low nutrient x ambient, IPCC-A2 and IPCC-A2+50% temperature scenarios) factorial design. For most mesocosms (tanks), we found accurate (r [2] ≥ 0.7) calibration of in-situ Chla fluorescence data using simple linear regression. An exception was tanks with high in-situ phycocyanin fluorescence, for which multiple regressions were employed, which increased the explained variance by >10%. Another exception was the low Chla concentration tanks (r [2] < 0.5). Our results also show that the high frequency in-situ fluorescence data recorded the timing of sudden Chla variations, while less frequent in-vitro sampling sometimes missed these or, when recorded, the duration of changes was inaccurately determined. Fluorescence in-situ sensors are particularly useful to detect and quantify sudden phytoplankton biomass variations through high frequency measurements, especially when using appropriate data-cleaning methods and accounting for factors that can impact the fluorescence readings. Nevertheless, corroborating these data with in-vitro Chla assessments would provide additional validation for the early warnings provided by sensor data.}, }
@article {pmid38912052, year = {2024}, author = {Goldman, SL and Sanders, JG and Sprockett, DD and Landers, A and Yan, W and Moeller, AH}, title = {Hackflex library preparation enables low-cost metagenomic profiling.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae075}, pmid = {38912052}, issn = {2730-6151}, support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; T32 AI145821/AI/NIAID NIH HHS/United States ; }, abstract = {Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations <1 ng/μL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.}, }
@article {pmid38910491, year = {2024}, author = {Kommana, G and Hupfer, M and Woodhouse, JN and Grossart, HP and Goldhammer, T}, title = {Reduced greenhouse gas emissions from particulate organic matter degradation in iron-enriched sediments.}, journal = {Environmental science. Processes &amp; impacts}, volume = {26}, number = {7}, pages = {1227-1244}, doi = {10.1039/d4em00185k}, pmid = {38910491}, issn = {2050-7895}, mesh = {*Geologic Sediments/chemistry ; *Greenhouse Gases/analysis ; *Iron ; Particulate Matter/analysis ; Germany ; Air Pollutants/analysis ; Environmental Monitoring ; Biodegradation, Environmental ; Water Pollutants, Chemical/analysis ; }, abstract = {Iron (Fe) plays an important role in the biogeochemical cycling of carbon and nutrients in aquatic systems. Reactive Fe phases can interact with organic carbon and facilitate the removal of carbon from the biogeochemical cycle; however, this important ecosystem function is often strongly controlled by Fe availability. Due to pollution from lignite mining in the Lusatian province in Northeast Germany, large amounts of iron and sulfate are released into the fluvial-lacustrine system of the Spree River. It was hypothesized that the input of freshly precipitated iron oxyhydroxides from mining areas (e.g., ferrihydrite) alter the biodegradation of particulate organic matter (POM) in downstream lacustrine sediments. To investigate the Fe-dependent degradation of POM, slurries mimicking iron-polluted sediments (85 mg Fe per g, 116 mg Fe per g, and 149 mg Fe per g dry weight) were incubated with plankton or leaf POM under anoxic and oxic headspace conditions, and CO2 and CH4 emissions, water chemistry, and stable isotopes of dissolved inorganic carbon were measured. The experiments revealed that (i) with an increasing Fe content, the CO2 and CH4 emissions were gradually reduced, (ii) CO2 and CH4 production was higher during plankton degradation than during leaf decomposition, and (iii) under oxic conditions, CO2 production was higher and CH4 production was lower when compared to the treatments under anoxic conditions. These findings demonstrate that while benthic mineralization of fresh POM typically releases greenhouse gases into the water column, the availability of iron oxyhydroxides can contribute to reduced greenhouse gas emissions from sediments. This is of considerable relevance for future carbon budgets of similar mining-affected, iron-polluted fluvial-lacustrine river systems.}, }
@article {pmid38909617, year = {2024}, author = {Kullberg, RFJ and Wikki, I and Haak, BW and Kauko, A and Galenkamp, H and Peters-Sengers, H and Butler, JM and Havulinna, AS and Palmu, J and McDonald, D and Benchraka, C and Abdel-Aziz, MI and Prins, M and Maitland van der Zee, AH and van den Born, BJ and Jousilahti, P and de Vos, WM and Salomaa, V and Knight, R and Lahti, L and Nieuwdorp, M and Niiranen, T and Wiersinga, WJ}, title = {Association between butyrate-producing gut bacteria and the risk of infectious disease hospitalisation: results from two observational, population-based microbiome studies.}, journal = {The Lancet. Microbe}, volume = {5}, number = {9}, pages = {100864}, doi = {10.1016/S2666-5247(24)00079-X}, pmid = {38909617}, issn = {2666-5247}, mesh = {Humans ; Middle Aged ; Adult ; *Hospitalization/statistics &amp; numerical data ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Aged ; Finland/epidemiology ; *Butyrates/metabolism ; *RNA, Ribosomal, 16S/genetics/analysis ; Netherlands/epidemiology ; Young Adult ; *Bacteria/genetics/classification/isolation &amp; purification ; Feces/microbiology ; Adolescent ; Communicable Diseases/microbiology/epidemiology ; Cohort Studies ; Risk Factors ; }, abstract = {BACKGROUND: Microbiota alterations are common in patients hospitalised for severe infections, and preclinical models have shown that anaerobic butyrate-producing gut bacteria protect against systemic infections. However, the relationship between microbiota disruptions and increased susceptibility to severe infections in humans remains unclear. We investigated the relationship between gut microbiota and the risk of future infection-related hospitalisation in two large population-based cohorts.<br><br>METHODS: In this observational microbiome study, gut microbiota were characterised using 16S rRNA gene sequencing in independent population-based cohorts from the Netherlands (HELIUS study; derivation cohort) and Finland (FINRISK 2002 study; validation cohort). HELIUS was conducted in Amsterdam, Netherlands, and included adults (aged 18-70 years at inclusion) who were randomly sampled from the municipality register of Amsterdam. FINRISK 2002 was conducted in six regions in Finland and is a population survey that included a random sample of adults (aged 25-74 years). In both cohorts, participants completed questionnaires, underwent a physical examination, and provided a faecal sample at inclusion (Jan 3, 2013, to Nov 27, 2015, for HELIUS participants and Jan 21 to April 19, 2002, for FINRISK participants. For inclusion in our study, a faecal sample needed to be provided and successfully sequenced, and national registry data needed to be available. Primary predictor variables were microbiota composition, diversity, and relative abundance of butyrate-producing bacteria. Our primary outcome was hospitalisation or mortality due to any infectious disease during 5-7-year follow-up after faecal sample collection, based on national registry data. We examined associations between microbiota and infection risk using microbial ecology and Cox proportional hazards.<br><br>FINDINGS: We profiled gut microbiota from 10&#x2009;699 participants (4248 [39&#xb7;7%] from the derivation cohort and 6451&#xa0;[60&#xb7;3%] from the validation cohort). 602 (5&#xb7;6%) participants (152 [3&#xb7;6%] from the derivation cohort; 450 [7&#xb7;0%] from the validation cohort) were hospitalised or died due to infections during follow-up. Gut microbiota composition of these participants differed from those without hospitalisation for infections (derivation p=0&#xb7;041; validation p=0&#xb7;0002). Specifically, higher relative abundance of butyrate-producing bacteria was associated with a reduced risk of hospitalisation for infections (derivation cohort cause-specific hazard ratio 0&#xb7;75 [95% CI 0&#xb7;60-0&#xb7;94] per 10% increase in butyrate producers, p=0&#xb7;013; validation cohort 0&#xb7;86 [0&#xb7;77-0&#xb7;96] per 10% increase, p=0&#xb7;0077). These associations remained unchanged following adjustment for demographics, lifestyle, antibiotic exposure, and comorbidities.<br><br>INTERPRETATION: Gut microbiota composition, specifically colonisation with butyrate-producing bacteria, was associated with protection against hospitalisation for infectious diseases in the general population across two independent European cohorts. Further studies should investigate whether modulation of the microbiome can reduce the risk of severe infections.<br><br>FUNDING: Amsterdam UMC, Porticus, National Institutes of Health, Netherlands Organisation for Health Research and Development (ZonMw), and Leducq Foundation.}, }
@article {pmid38906896, year = {2024}, author = {Schorn, S and Graf, JS and Littmann, S and Hach, PF and Lavik, G and Speth, DR and Schubert, CJ and Kuypers, MMM and Milucka, J}, title = {Persistent activity of aerobic methane-oxidizing bacteria in anoxic lake waters due to metabolic versatility.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {5293}, pmid = {38906896}, issn = {2041-1723}, mesh = {*Methane/metabolism ; *Lakes/microbiology ; *Oxidation-Reduction ; Anaerobiosis ; Methylococcaceae/metabolism/genetics ; Metagenomics ; Oxygen/metabolism ; }, abstract = {Lacustrine methane emissions are strongly mitigated by aerobic methane-oxidizing bacteria (MOB) that are typically most active at the oxic-anoxic interface. Although oxygen is required by the MOB for the first step of methane oxidation, their occurrence in anoxic lake waters has raised the possibility that they are capable of oxidizing methane further anaerobically. Here, we investigate the activity and growth of MOB in Lake Zug, a permanently stratified freshwater lake. The rates of anaerobic methane oxidation in the anoxic hypolimnion reached up to 0.2 µM d[-1]. Single-cell nanoSIMS measurements, together with metagenomic and metatranscriptomic analyses, linked the measured rates to MOB of the order Methylococcales. Interestingly, their methane assimilation activity was similar under hypoxic and anoxic conditions. Our data suggest that these MOB use fermentation-based methanotrophy as well as denitrification under anoxic conditions, thus offering an explanation for their widespread presence in anoxic habitats such as stratified water columns. Thus, the methane sink capacity of anoxic basins may have been underestimated by not accounting for the anaerobic MOB activity.}, }
@article {pmid38904568, year = {2024}, author = {Ganier, C and Callewaert, C and Matos, TR and Sonkoly, E and Dyring-Andersen, B and Rajan, N}, title = {Young ESDR: Engaging and Nurturing the Next-Generation Skin Research Community.}, journal = {The Journal of investigative dermatology}, volume = {144}, number = {11}, pages = {2349-2350}, doi = {10.1016/j.jid.2024.05.004}, pmid = {38904568}, issn = {1523-1747}, }
@article {pmid38902915, year = {2024}, author = {Kerr, BJ and Anderson, CL and Pearce, SC and Schweer, WP}, title = {Dietary isoacids effects on growth, nitrogen, and energy digestibility, and fecal volatile fatty acids and microbial ecology in finishing pigs.}, journal = {Journal of animal science}, volume = {102}, number = {}, pages = {}, pmid = {38902915}, issn = {1525-3163}, mesh = {Animals ; *Feces/chemistry/microbiology ; *Animal Feed/analysis ; *Digestion/drug effects ; *Diet/veterinary ; *Fatty Acids, Volatile/metabolism ; Female ; *Nitrogen/metabolism ; *Animal Nutritional Physiological Phenomena ; Swine/growth &amp; development ; Energy Metabolism/drug effects ; }, abstract = {Isoacids are branched ketoacids which when fed to ruminants have been shown to enhance the growth of fiber-digesting organisms. Ninety finishing gilts were individually fed dietary treatments consisting of diet type: corn-soybean meal (CSBM), a diet containing 40% distillers dried grains with solubles (DDGS), or a diet containing 40% sugar beet pulp (SBP); in combination with either no feed additive (CNT), the addition of 0.50% isobutyrate (IB), or the addition of a 0.88% mix of isobutyrate, isovalerate, and 2-methylbutyrate (MX). Gilts consumed an average of 2.171 kg/d over the 28-d trial. On d 26, fresh fecal samples were collected for determination of apparent total tract digestibility (ATTD) of gross energy (GE) and nitrogen (N), determination of fecal volatile fatty acids (VFA), and evaluation of microbial ecology. There was no interaction between diet type and isoacid addition, and no main effect of isoacid or diet type on alpha or Shannon microbial diversity measures (P > 0.05). There was no interaction between isoacid addition and diet type, and no main effect of isoacid addition on microbial beta diversity (P > 0.05), but differences were observed in microbial beta diversity due to diet type (P ≤ 0.05). There was no interaction between diet type and isoacid addition observed in fecal VFA concentrations (P > 0.05), with only minor differences in fecal VFA concentrations noted due to isoacid addition (P ≤ 0.05). The interaction between diet type and isoacid addition on ATTD of dietary GE and N (P ≤ 0.01) was large because the addition of IB did not affect the ATTD of GE or N in pigs fed the CSBM diet, but increased ATTD of GE and N in pigs fed diets containing DDGS and decreased the ATTD of GE and N in pigs fed diets containing SBP. In contrast, adding a blend of isoacids (i.e., MX) reduced the ATTD of GE and N, regardless of diet type. There was no interaction between diet type and isoacid addition, and no effect of isoacid addition was observed on pig performance (P > 0.05). Diet type did not affect average daily gain (P > 0.05), but pigs fed diets containing DDGS or SBP consumed less feed (P = 0.01) and exhibited greater GF ratios compared to pigs fed the low-fiber CSBM diet (P ≤ 0.05). In conclusion, there was little to no effect of isoacid addition on microbial ecology, fecal VFA concentrations, ATTD of GE or N, or pig performance, but the improvement in ATTD of GE and N in pigs fed diets containing DDGS when IB was added warrants further investigation.}, }
@article {pmid38896653, year = {2024}, author = {Elliott, JFK and McLeod, DV and Taylor, TB and Westra, ER and Gandon, S and Watson, BNJ}, title = {Conditions for the spread of CRISPR-Cas immune systems into bacterial populations.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38896653}, issn = {1751-7370}, support = {BB/T008741/1//Biotechnology and Biological Sciences Research Council SWBio DTP/ ; DH150169//Royal Society Dorothy Hodgkin Fellowship/ ; NE/S001921/1//Natural Environment Research Council/ ; BB/X010600/1//Biotechnology and Biological Sciences Research Council Discovery Fellowship/ ; }, mesh = {*CRISPR-Cas Systems ; *Bacteriophages/genetics ; *Bacteria/genetics/virology/classification ; Pseudomonas aeruginosa/virology/genetics/immunology ; Gene Transfer, Horizontal ; Clustered Regularly Interspaced Short Palindromic Repeats ; }, abstract = {Bacteria contain a wide variety of innate and adaptive immune systems which provide protection to the host against invading genetic material, including bacteriophages (phages). It is becoming increasingly clear that bacterial immune systems are frequently lost and gained through horizontal gene transfer. However, how and when new immune systems can become established in a bacterial population have remained largely unstudied. We developed a joint epidemiological and evolutionary model that predicts the conditions necessary for the spread of a CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) immune system into a bacterial population lacking this system. We found that whether bacteria carrying CRISPR-Cas will spread (increase in frequency) into a bacterial population depends on the abundance of phages and the difference in the frequency of phage resistance mechanisms between bacteria carrying a CRISPR-Cas immune system and those not (denoted as ${f}_{\Delta }$). Specifically, the abundance of cells carrying CRISPR-Cas will increase if there is a higher proportion of phage resistance (either via CRISPR-Cas immunity or surface modification) in the CRISPR-Cas-possessing population than in the cells lacking CRISPR-Cas. We experimentally validated these predictions in a model using Pseudomonas aeruginosa PA14 and phage DMS3vir. Specifically, by varying the initial ratios of different strains of bacteria that carry alternative forms of phage resistance, we confirmed that the spread of cells carrying CRISPR-Cas through a population can be predicted based on phage density and the relative frequency of resistance phenotypes. Understanding which conditions promote the spread of CRISPR-Cas systems helps to predict when and where these defences can become established in bacterial populations after a horizontal gene transfer event, both in ecological and clinical contexts.}, }
@article {pmid38896454, year = {2024}, author = {Zhang, Y and Quensen, J and Chen, B and Li, H and Tiedje, J and Sun, W and Qian, X}, title = {Paenalcaligenes faecalis sp. nov., a novel species of the family Alcaligenaceae isolated from chicken faeces.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {6}, pages = {}, doi = {10.1099/ijsem.0.006429}, pmid = {38896454}, issn = {1466-5034}, mesh = {Animals ; *Base Composition ; *Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Chickens/microbiology ; *Feces/microbiology ; *DNA, Bacterial/genetics ; *Nucleic Acid Hybridization ; *Bacterial Typing Techniques ; *Sequence Analysis, DNA ; *Alcaligenaceae/genetics/classification/isolation &amp; purification ; Fatty Acids ; Genome, Bacterial ; }, abstract = {A Gram-negative, motile, rod-shaped aerobic and alkalogenic bacterium, designated as strain YLCF04[T], was isolated from chicken faeces. Its growth was optimal at 28 °C (range, 10-40 °C), pH 8 (range, pH 6-9) and in 1 % (w/v) NaCl (range, 0-10 %). It was classified to the genus Paenalcaligenes and was most closely related to Paenalcaligenes hominis CCUG 53761A[T] (97.5 % similarity) based on 16S rRNA gene sequence analysis. Average nucleotide identity and digital DNA-DNA hybridization values between YLCF04[T] and P. hominis CCUG 53761A[T] were 76.3 and 18.2 %, respectively. Strain YLCF04[T] has a genome size of 2.7 Mb with DNA G+C content of 46.3 mol%. Based on its phylogenetic, genomic, phenotypic and biochemical characteristics, strain YLCF04[T] represents a novel species of the genus Paenalcaligenes, for which the name Paenalcaligenes faecalis sp. nov. is proposed. The type strain is YLCF04[T] (=CCTCC AB 2022359[T]= KCTC 92789[T]).}, }
@article {pmid38895568, year = {2024}, author = {Puente-Sánchez, F and Macías-Pérez, LA and Campbell, KL and Royo-Llonch, M and Balagué, V and Sánchez, P and Tamames, J and Mundy, CJ and Pedrós-Alió, C}, title = {Bacterioplankton taxa compete for iron along the early spring-summer transition in the Arctic Ocean.}, journal = {Ecology and evolution}, volume = {14}, number = {6}, pages = {e11546}, pmid = {38895568}, issn = {2045-7758}, abstract = {Microbial assemblages under the sea ice of the Dease Strait, Canadian Arctic, were sequenced for metagenomes of a small size fraction (0.2-3 μm). The community from early March was typical for this season, with Alpha- and Gammaproteobacteria as the dominant taxa, followed by Thaumarchaeota and Bacteroidetes. Toward summer, Bacteroidetes, and particularly the genus Polaribacter, became increasingly dominant, followed by the Gammaproteobacteria. Analysis of genes responsible for microbial acquisition of iron showed an abundance of ABC transporters for divalent cations and ferrous iron. The most abundant transporters, however, were the outer membrane TonB-dependent transporters of iron-siderophore complexes. The abundance of iron acquisition genes suggested this element was essential for the microbial assemblage. Interestingly, Gammaproteobacteria were responsible for most of the siderophore synthesis genes. On the contrary, Bacteroidetes did not synthesize siderophores but accounted for most of the transporters, suggesting a role as cheaters in the competition for siderophores as public goods. This cheating ability of the Bacteroidetes may have contributed to their dominance in the summer.}, }
@article {pmid38894967, year = {2024}, author = {Zou, C and Yi, X and Li, H and Bizic, M and Berman-Frank, I and Gao, K}, title = {Correlation of methane production with physiological traits in Trichodesmium IMS 101 grown with methylphosphonate at different temperatures.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1396369}, pmid = {38894967}, issn = {1664-302X}, abstract = {The diazotrophic cyanobacterium Trichodesmium has been recognized as a potentially significant contributor to aerobic methane generation via several mechanisms including the utilization of methylphophonate (MPn) as a source of phosphorus. Currently, there is no information about how environmental factors regulate methane production by Trichodesmium. Here, we grew Trichodesmium IMS101 at five temperatures ranging from 16 to 31°C, and found that its methane production rates increased with rising temperatures to peak (1.028 ± 0.040 nmol CH4 μmol POC[-1] day[-1]) at 27°C, and then declined. Its specific growth rate changed from 0.03 ± 0.01 d[-1] to 0.34 ± 0.02 d[-1], with the optimal growth temperature identified between 27 and 31°C. Within the tested temperature range the Q10 for the methane production rate was 4.6 ± 0.7, indicating a high sensitivity to thermal changes. In parallel, the methane production rates showed robust positive correlations with the assimilation rates of carbon, nitrogen, and phosphorus, resulting in the methane production quotients (molar ratio of carbon, nitrogen, or phosphorus assimilated to methane produced) of 227-494 for carbon, 40-128 for nitrogen, and 1.8-3.4 for phosphorus within the tested temperature range. Based on the experimental data, we estimated that the methane released from Trichodesmium can offset about 1% of its CO2 mitigation effects.}, }
@article {pmid38892722, year = {2024}, author = {Thompson, RS and Bowers, SJ and Vargas, F and Hopkins, S and Kelley, T and Gonzalez, A and Lowry, CA and Dorrestein, PC and Vitaterna, MH and Turek, FW and Knight, R and Wright, KP and Fleshner, M}, title = {A Prebiotic Diet Containing Galactooligosaccharides and Polydextrose Produces Dynamic and Reproducible Changes in the Gut Microbial Ecosystem in Male Rats.}, journal = {Nutrients}, volume = {16}, number = {11}, pages = {}, pmid = {38892722}, issn = {2072-6643}, support = {N00014-15-1-2809//Office of Naval Research/ ; }, mesh = {Animals ; *Prebiotics ; Male ; *Gastrointestinal Microbiome/drug effects ; *Rats, Sprague-Dawley ; *Oligosaccharides/pharmacology/administration &amp; dosage ; *Glucans ; Rats ; Bile Acids and Salts/metabolism ; Feces/microbiology ; Bacteria/classification/metabolism ; RNA, Ribosomal, 16S ; Diet/methods ; }, abstract = {Despite substantial evidence supporting the efficacy of prebiotics for promoting host health and stress resilience, few experiments present evidence documenting the dynamic changes in microbial ecology and fecal microbially modified metabolites over time. Furthermore, the literature reports a lack of reproducible effects of prebiotics on specific bacteria and bacterial-modified metabolites. The current experiments examined whether consumption of diets enriched in prebiotics (galactooligosaccharides (GOS) and polydextrose (PDX)), compared to a control diet, would consistently impact the gut microbiome and microbially modified bile acids over time and between two research sites. Male Sprague Dawley rats were fed control or prebiotic diets for several weeks, and their gut microbiomes and metabolomes were examined using 16S rRNA gene sequencing and untargeted LC-MS/MS analysis. Dietary prebiotics altered the beta diversity, relative abundance of bacterial genera, and microbially modified bile acids over time. PICRUSt2 analyses identified four inferred functional metabolic pathways modified by the prebiotic diet. Correlational network analyses between inferred metabolic pathways and microbially modified bile acids revealed deoxycholic acid as a potential network hub. All these reported effects were consistent between the two research sites, supporting the conclusion that dietary prebiotics robustly changed the gut microbial ecosystem. Consistent with our previous work demonstrating that GOS/PDX reduces the negative impacts of stressor exposure, we propose that ingesting a diet enriched in prebiotics facilitates the development of a health-promoting gut microbial ecosystem.}, }
@article {pmid38892504, year = {2024}, author = {Duysburgh, C and Govaert, M and Guillemet, D and Marzorati, M}, title = {Co-Supplementation of Baobab Fiber and Arabic Gum Synergistically Modulates the In Vitro Human Gut Microbiome Revealing Complementary and Promising Prebiotic Properties.}, journal = {Nutrients}, volume = {16}, number = {11}, pages = {}, pmid = {38892504}, issn = {2072-6643}, mesh = {*Gastrointestinal Microbiome ; *Prebiotics ; *Gum Arabic/therapeutic use ; *Adansonia ; *Plant Preparations/therapeutic use ; Metabolome ; Metagenome ; Colon/microbiology ; }, abstract = {Arabic gum, a high molecular weight heteropolysaccharide, is a promising prebiotic candidate as its fermentation occurs more distally in the colon, which is the region where most chronic colonic diseases originate. Baobab fiber could be complementary due to its relatively simple structure, facilitating breakdown in the proximal colon. Therefore, the current study aimed to gain insight into how the human gut microbiota was affected in response to long-term baobab fiber and Arabic gum supplementation when tested individually or as a combination of both, allowing the identification of potential complementary and/or synergetic effects. The validated Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]), an in vitro gut model simulating the entire human gastrointestinal tract, was used. The microbial metabolic activity was examined, and quantitative 16S-targeted Illumina sequencing was used to monitor the gut microbial composition. Moreover, the effect on the gut microbial metabolome was quantitatively analyzed. Repeated administration of baobab fiber, Arabic gum, and their combination had a significant effect on the metabolic activity, diversity index, and community composition of the microbiome present in the simulated proximal and distal colon with specific impacts on Bifidobacteriaceae and Faecalibacterium prausnitzii. Despite the lower dosage strategy (2.5 g/day), co-supplementation of both compounds resulted in some specific synergistic prebiotic effects, including a biological activity throughout the entire colon, SCFA synthesis including a synergy on propionate, specifically increasing abundance of Akkermansiaceae and Christensenellaceae in the distal colon region, and enhancing levels of spermidine and other metabolites of interest (such as serotonin and ProBetaine).}, }
@article {pmid38891933, year = {2024}, author = {Carpio, LE and Olivares, M and Benítez-Paez, A and Serrano-Candelas, E and Barigye, SJ and Sanz, Y and Gozalbes, R}, title = {Comparative Binding Study of Gliptins to Bacterial DPP4-like Enzymes for the Treatment of Type 2 Diabetes Mellitus (T2DM).}, journal = {International journal of molecular sciences}, volume = {25}, number = {11}, pages = {}, pmid = {38891933}, issn = {1422-0067}, support = {reference INNTAL32/19/002, INNTA3/2021/16 and INNTA3/2022/20//Agencia Valenciana de la innovaci&#xf3;/ ; grant PID2020-119536RB-I00//Spanish Ministry of Science, Innovation and Universities (MCIU)/ ; APOTIP/2021/035//Generalitat Valenciana/ ; CEX2021-001189-S/MCIU/AEI/10.13039/501100011033//Spanish Government MCIU/AEI/ ; }, mesh = {Humans ; Bacteria/metabolism ; Bacterial Proteins/metabolism/chemistry ; Binding Sites ; *Diabetes Mellitus, Type 2/metabolism/drug therapy ; *Dipeptidyl Peptidase 4/metabolism/chemistry ; *Dipeptidyl-Peptidase IV Inhibitors/pharmacology ; *Gastrointestinal Microbiome ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Binding ; }, abstract = {The role of the gut microbiota and its interplay with host metabolic health, particularly in the context of type 2 diabetes mellitus (T2DM) management, is garnering increasing attention. Dipeptidyl peptidase 4 (DPP4) inhibitors, commonly known as gliptins, constitute a class of drugs extensively used in T2DM treatment. However, their potential interactions with gut microbiota remain poorly understood. In this study, we employed computational methodologies to investigate the binding affinities of various gliptins to DPP4-like homologs produced by intestinal bacteria. The 3D structures of DPP4 homologs from gut microbiota species, including Segatella copri, Phocaeicola vulgatus, Bacteroides uniformis, Parabacteroides merdae, and Alistipes sp., were predicted using computational modeling techniques. Subsequently, molecular dynamics simulations were conducted for 200 ns to ensure the stability of the predicted structures. Stable structures were then utilized to predict the binding interactions with known gliptins through molecular docking algorithms. Our results revealed binding similarities of gliptins toward bacterial DPP4 homologs compared to human DPP4. Specifically, certain gliptins exhibited similar binding scores to bacterial DPP4 homologs as they did with human DPP4, suggesting a potential interaction of these drugs with gut microbiota. These findings could help in understanding the interplay between gliptins and gut microbiota DPP4 homologs, considering the intricate relationship between the host metabolism and microbial communities in the gut.}, }
@article {pmid38890249, year = {2024}, author = {Plewa-Tutaj, K and Krzyściak, P and Dobrzycka, A}, title = {Mycological air contamination level and biodiversity of airborne fungi isolated from the zoological garden air - preliminary research.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {30}, pages = {43066-43079}, pmid = {38890249}, issn = {1614-7499}, support = {2022/06/X/NZ8/00430//National Science Center, Poland/ ; }, mesh = {*Air Microbiology ; *Fungi/isolation &amp; purification/classification ; *Biodiversity ; Animals ; *Environmental Monitoring ; Gardens ; Animals, Zoo/microbiology ; }, abstract = {The aim of this paper was to evaluate the degree of mycological air contamination and determine the taxonomic diversity of airborne fungi residing in the air of 20 different animal facilities in a zoological garden. The concentrations of fungi in the zoological garden were measured using a MAS-100 air sampler. The collected microorganisms were identified using the combination of molecular and morphological methods. The fungal concentration ranged from 50 to 3.65 × 10[4] CFU/m[3] during the whole study. The quantitative analysis of the fungal aerosol showed that the obtained concentration values were lower than the recommended permissible limits (5 × 10[4] CFU/m[3] for fungi). Environmental factors, including temperature and relative humidity, exerted a varying effect on the presence and concentration of isolated fungi. Relative humidity was shown to correlate positively with the concentration of fungal spores in the air of the facilities studied (rho = 0.57, p < 0.0021). In parallel, no significant correlation was established between temperature and total fungal concentration (rho = - 0.1, p < 0.2263). A total of 112 fungal strains belonging to 50 species and 10 genera were isolated. Penicillium was the dominant genera, including 58.9% of total fungal strains, followed by Aspergillus 25.89%, Cladosporium 3.57%, Talaromyces 3.57%, Mucor 1.78%, Schizophyllum 1.78%, Syncephalastrum 0.89%, Alternaria 0.89%, Absidia 0.89%, and Cunninghamella 0.89%. Our preliminary studies provide basic information about the fungal concentrations, as well as their biodiversity in zoological garden. Further studies are needed to generate additional data from long-term sampling in order to increase our understanding of airborne fungal composition in the zoological garden.}, }
@article {pmid38888768, year = {2024}, author = {Sanderson, H and White, AP}, title = {Methods for Genomic Epidemiology of Bacterial Pathogens: Example Salmonella.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2813}, number = {}, pages = {19-37}, pmid = {38888768}, issn = {1940-6029}, mesh = {*Salmonella/genetics ; Humans ; *Genomics/methods ; *Salmonella Infections/microbiology/epidemiology ; *Phylogeny ; *Genome, Bacterial ; *Molecular Epidemiology/methods ; Virulence Factors/genetics ; Disease Outbreaks ; Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences/genetics ; }, abstract = {Genomics has revolutionized how we characterize and monitor infectious diseases for public health. The surveillance and characterization of Salmonella has improved drastically within the past decade. In this chapter, we discuss the prerequisites for good bacterial genomics studies and make note of advantages and disadvantages of this research approach. We discuss methods for outbreak detection and the evolutionary and epidemiological characterization of Salmonella spp. We provide an outline for determining the sequence type and serotype of isolates, building a core genome phylogenetic tree, and detecting antimicrobial resistance genes, virulence factors, and mobile genetic elements. These methods can be used to study other pathogenic bacterial species.}, }
@article {pmid38888737, year = {2024}, author = {Sagar, A and Rai, S and Sharma, S and Perveen, K and Bukhari, NA and Sayyed, RZ and Mastinu, A}, title = {Molecular Characterization Reveals Biodiversity and Biopotential of Rhizobacterial Isolates of Bacillus Spp.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {83}, pmid = {38888737}, issn = {1432-184X}, mesh = {*Bacillus/isolation &amp; purification/genetics/metabolism ; *Soil Microbiology ; *Biodiversity ; India ; Plant Roots/microbiology ; Cicer/microbiology/growth &amp; development ; Solanum lycopersicum/microbiology/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Phylogeny ; Antibiosis ; Siderophores/metabolism ; Indoleacetic Acids/metabolism ; }, abstract = {Bacillus species appearas the most attractive plant growth-promoting rhizobacteria (PGPR) and alternative to synthetic chemical pesticides. The present study examined the antagonistic potential of spore forming-Bacilli isolated from organic farm soil samples of Allahabad, India. Eighty-seven Bacillus strains were isolated and characterized based on their morphological, plant growth promoting traits and molecular characteristics. The diversity analysis used 16S-rDNA, BOX-element, and enterobacterial repetitive intergenic consensus. Two strains, PR30 and PR32, later identified as Bacillus sp., exhibited potent in vitro antagonistic activity against Ralstonia solanaceorum. These isolates produced copious amounts of multiple PGP traits, such as indole-3-acetic acid (40.0 and 54.5 μg/mL), phosphate solubilization index (PSI) (4.4 and 5.3), ammonia, siderophore (3 and 4 cm), and 1-aminocyclopropane-1-carboxylate deaminase (8.1and 9.2 μM/mg//h) and hydrogen cyanide. These isolates were subjected to the antibiotic sensitivity test. The two potent isolates based on the higher antagonistic and the best plant growth-promoting ability were selected for plant growth-promoting response studies in tomatoe, broccoli, and chickpea. In the pot study, Bacillus subtilis (PR30 and PR31) showed significant improvement in seed germination (27-34%), root length (20-50%), shoot length (20-40%), vigor index (50-75%), carotenoid content (0.543-1.733), and lycopene content (2.333-2.646 mg/100 g) in tomato, broccoli, and chickpea. The present study demonstrated the production of multiple plant growth-promoting traits by the isolates and their potential as effective bioinoculants for plant growth promotion and biocontrol of phytopathogens.}, }
@article {pmid38886127, year = {2024}, author = {Piwosz, K and Villena-Alemany, C and Całkiewicz, J and Mujakić, I and Náhlík, V and Dean, J and Koblížek, M}, title = {Response of aerobic anoxygenic phototrophic bacteria to limitation and availability of organic carbon.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {7}, pages = {}, pmid = {38886127}, issn = {1574-6941}, support = {2021/03/Y/NZ8/00076//National Science Centre, Poland/ ; }, mesh = {*Carbon/metabolism ; *Phototrophic Processes ; Heterotrophic Processes ; Lakes/microbiology ; Bacteria, Aerobic/metabolism/growth &amp; development ; Light ; Ecosystem ; Bacteria/metabolism/growth &amp; development/genetics ; }, abstract = {Aerobic anoxygenic phototrophic (AAP) bacteria are an important component of freshwater bacterioplankton. They can support their heterotrophic metabolism with energy from light, enhancing their growth efficiency. Based on results from cultures, it was hypothesized that photoheterotrophy provides an advantage under carbon limitation and facilitates access to recalcitrant or low-energy carbon sources. However, verification of these hypotheses for natural AAP communities has been lacking. Here, we conducted whole community manipulation experiments and compared the growth of AAP bacteria under carbon limited and with recalcitrant or low-energy carbon sources under dark and light (near-infrared light, λ > 800 nm) conditions to elucidate how they profit from photoheterotrophy. We found that AAP bacteria induce photoheterotrophic metabolism under carbon limitation, but they overcompete heterotrophic bacteria when carbon is available. This effect seems to be driven by physiological responses rather than changes at the community level. Interestingly, recalcitrant (lignin) or low-energy (acetate) carbon sources inhibited the growth of AAP bacteria, especially in light. This unexpected observation may have ecosystem-level consequences as lake browning continues. In general, our findings contribute to the understanding of the dynamics of AAP bacteria in pelagic environments.}, }
@article {pmid38884913, year = {2024}, author = {Obregón-Gutierrez, P and Aragón, V and Correa-Fiz, F}, title = {Analysis of the Nasal Microbiota in Healthy and Diseased Pigs.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2815}, number = {}, pages = {93-113}, pmid = {38884913}, issn = {1940-6029}, mesh = {Animals ; *Microbiota/genetics ; Swine/microbiology ; *RNA, Ribosomal, 16S/genetics ; Nose/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Swine Diseases/microbiology ; Sequence Analysis, DNA/methods ; }, abstract = {Massive sequencing of a fragment of 16S rRNA gene allows the characterization of bacterial communities in different body sites: the microbiota. Nasal microbiota can be analyzed by DNA extraction from nasal swabs, amplification of the specific fragment of interest, and posterior sequencing. The raw sequences obtained need to go through a computational process to check their quality and then assign the taxonomy. Here, we will describe the complete process from sampling to get the microbial diversity of nasal microbiota in health and disease.}, }
@article {pmid38878412, year = {2024}, author = {Zheng, P and Mao, A and Meng, S and Yu, F and Zhang, S and Lun, J and Li, J and Hu, Z}, title = {Assembly mechanism of microbial community under different seasons in Shantou sea area.}, journal = {Marine pollution bulletin}, volume = {205}, number = {}, pages = {116550}, doi = {10.1016/j.marpolbul.2024.116550}, pmid = {38878412}, issn = {1879-3363}, mesh = {*Seasons ; *Microbiota ; *Seawater/microbiology ; Bacteria/classification ; Phylogeny ; Biodiversity ; China ; Oceans and Seas ; }, abstract = {Coastal areas are often affected by a variety of climates, and microbial composition patterns are conducive to adaptation to these environments. In this study, the composition and pattern of microbial communities in the Shantou sea from four seasons were analyzed. The diversity of microbial community was significant differences under different seasons (p < 0.01). Meanwhile, dissolved oxygen levels, temperature were key factors to shift microbial communities. The assembly mechanism of microbial communities was constructed by the iCAMP (Infer community assembly mechanism by the phylogenetic bin-based null). Interestingly, the analyses revealed that drift was the predominant driver of this process (44.5 %), suggesting that microbial community assembly in this setting was dominated by stochastic processes. For example, Vibrio was found to be particularly susceptible to stochastic processes, indicating that the pattern of bacterial community was governed by stochastic processes. Thus, these results offering novel insight into the regulation of microbial ecology in marine environments.}, }
@article {pmid38876584, year = {2024}, author = {Kothe, CI and Carøe, C and Mazel, F and Zilber, D and Cruz-Morales, P and Mohellibi, N and Evans, JD}, title = {Novel misos shape distinct microbial ecologies: opportunities for flavourful sustainable food innovation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {189}, number = {}, pages = {114490}, doi = {10.1016/j.foodres.2024.114490}, pmid = {38876584}, issn = {1873-7145}, mesh = {*Fermentation ; *Bacteria/classification/genetics/metabolism ; *Food Microbiology ; Taste ; Fermented Foods/microbiology ; Microbiota ; Japan ; Metagenomics ; }, abstract = {Fermentation is resurgent around the world as people seek healthier, more sustainable, and tasty food options. This study explores the microbial ecology of miso, a traditional Japanese fermented paste, made with novel regional substrates to develop new plant-based foods. Eight novel miso varieties were developed using different protein-rich substrates: yellow peas, Gotland lentils, and fava beans (each with two treatments: standard and nixtamalisation), as well as rye bread and soybeans. The misos were produced at Noma, a restaurant in Copenhagen, Denmark. Samples were analysed with biological and technical triplicates at the beginning and end of fermentation. We also incorporated in this study six samples of novel misos produced following the same recipe at Inua, a former affiliate restaurant of Noma in Tokyo, Japan. To analyse microbial community structure and diversity, metabarcoding (16S and ITS) and shotgun metagenomic analyses were performed. The misos contain a greater range of microbes than is currently described for miso in the literature. The composition of the novel yellow pea misos was notably similar to the traditional soybean ones, suggesting they are a good alternative, which supports our culinary collaborators' sensory conclusions. For bacteria, we found that overall substrate had the strongest effect, followed by time, treatment (nixtamalisation), and geography. For fungi, there was a slightly stronger effect of geography and a mild effect of substrate, and no significant effects for treatment or time. Based on an analysis of metagenome-assembled genomes (MAGs), strains of Staphylococccus epidermidis differentiated according to substrate. Carotenoid biosynthesis genes in these MAGs appeared in strains from Japan but not from Denmark, suggesting a possible gene-level geographical effect. The benign and possibly functional presence of S. epidermidis in these misos, a species typically associated with the human skin microbiome, suggests possible adaptation to the miso niche, and the flow of microbes between bodies and foods in certain fermentation as more common than is currently recognised. This study improves our understanding of miso ecology, highlights the potential for developing novel misos using diverse local ingredients, and suggests how fermentation innovation can contribute to studies of microbial ecology and evolution.}, }
@article {pmid38876281, year = {2024}, author = {Ponce-Jahen, SJ and Valenzuela, EI and Rangel-Mendez, JR and Sánchez-Carrillo, S and Cervantes, FJ}, title = {Anoxic nitrification with carbon-based materials as terminal electron acceptors.}, journal = {Bioresource technology}, volume = {406}, number = {}, pages = {130961}, doi = {10.1016/j.biortech.2024.130961}, pmid = {38876281}, issn = {1873-2976}, mesh = {*Nitrification ; *Carbon/chemistry ; Electrons ; Graphite/chemistry ; Phylogeny ; Oxidation-Reduction ; Ammonium Compounds/metabolism ; Anaerobiosis ; Nitrates/metabolism ; Bacteria/metabolism ; }, abstract = {This study investigates the potential of humic substances (HS) and graphene oxide (GO), as extracellular electron acceptors (EEA) for nitrification, aiming to explore alternatives to sustain this process in wastewater treatment systems. Experimental results demonstrate the conversion of ammonium to nitrate (up to 87 % of conversion) coupled to the reduction of either HS or GO by anaerobic consortia. Electron balance confirmed the contribution of HS and GO to ammonium oxidation. Tracer analysis in incubations performed with [15]NH4[+] demonstrated [15]NO3[-] as the main product with a minor fraction ending as [29]N2. Phylogenetic analysis identified Firmicutes, Euryarchaeota, and Chloroflexi as the microbial lineages potentially involved in anoxic nitrification linked to HS reduction. This study introduces a new avenue for research in which carbon-based materials with electron-accepting capacity may support the anoxic oxidation of ammonium, for instance in bioelectrochemical systems in which carbon-based anodes could support this novel process.}, }
@article {pmid38874336, year = {2024}, author = {Tomazelli, D and Klauberg-Filho, O and Mendes, LW and Goss-Souza, D}, title = {The impact of land-use changes and management intensification on bacterial communities in the last decade: a review.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {7}, pages = {e0030924}, pmid = {38874336}, issn = {1098-5336}, support = {1/CX/CSRD VA/United States ; }, mesh = {*Soil Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; Brazil ; *Agriculture/methods ; *Microbiota ; Biodiversity ; Soil/chemistry ; }, abstract = {In the last decade, advances in soil bacterial ecology have contributed to increasing agricultural production. Brazil is the world leading agriculture producer and leading soil biodiversity reservoir. Meanwhile, there is still a significant gap in the knowledge regarding the soil microscopic life and its interactions with agricultural practices, and the replacement of natural vegetation by agroecosystems is yet to be unfolded. Through high throughput DNA sequencing, scientists are now exploring the complexity of soil bacterial communities and their relationship with soil and environmental characteristics. This study aimed to investigate the progress of bacterial ecology studies in Brazil over the last 10 years, seeking to understand the effect of the conversion of natural vegetation in agricultural systems on the diversity and structure of the soil microbial communities. We conducted a systematic search for scientific publication databases. Our systematic search has matched 62 scientific articles from three different databases. Most of the studies were placed in southeastern and northern Brazil, with no records of studies about microbial ecology in 17 out of 27 Brazilian states. Out of the 26 studies that examined the effects of replacing natural vegetation with agroecosystems, most authors concluded that changes in soil pH and vegetation cover replacement were the primary drivers of shifts in microbial communities. Understanding the ecology of the bacteria inhabiting Brazilian soils in agroecosystems is paramount for developing more efficient soil management strategies and cleaner agricultural technologies.}, }
@article {pmid38873612, year = {2024}, author = {Pulvirenti, F and Giufrè, M and Pentimalli, TM and Camilli, R and Milito, C and Villa, A and Sculco, E and Cerquetti, M and Pantosti, A and Quinti, I}, title = {Oropharyngeal microbial ecosystem perturbations influence the risk for acute respiratory infections in common variable immunodeficiency.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1371118}, pmid = {38873612}, issn = {1664-3224}, mesh = {Humans ; *Common Variable Immunodeficiency/microbiology/immunology/complications ; *Oropharynx/microbiology ; Male ; Female ; Middle Aged ; Adult ; *Respiratory Tract Infections/microbiology/immunology ; *Dysbiosis ; Microbiota ; Prospective Studies ; Aged ; RNA, Ribosomal, 16S/genetics ; Acute Disease ; Bacteria/classification/genetics ; Case-Control Studies ; }, abstract = {BACKGROUND: The respiratory tract microbiome is essential for human health and well-being and is determined by genetic, lifestyle, and environmental factors. Patients with Common Variable Immunodeficiency (CVID) suffer from respiratory and intestinal tract infections, leading to chronic diseases and increased mortality rates. While CVID patients' gut microbiota have been analyzed, data on the respiratory microbiome ecosystem are limited.<br><br>OBJECTIVE: This study aims to analyze the bacterial composition of the oropharynx of adults with CVID and its link with clinical and immunological features and risk for respiratory acute infections.<br><br>METHODS: Oropharyngeal samples from 72 CVID adults and 26 controls were collected in a 12-month prospective study. The samples were analyzed by metagenomic bacterial 16S ribosomal RNA sequencing and processed using the Quantitative Insights Into Microbial Ecology (QIME) pipeline. Differentially abundant species were identified and used to build a dysbiosis index. A machine learning model trained on microbial abundance data was used to test the power of microbiome alterations to distinguish between healthy individuals and CVID patients.<br><br>RESULTS: Compared to controls, the oropharyngeal microbiome of CVID patients showed lower alpha- and beta-diversity, with a relatively increased abundance of the order Lactobacillales, including the family Streptococcaceae. Intra-CVID analysis identified age >45 years, COPD, lack of IgA, and low residual IgM as associated with a reduced alpha diversity. Expansion of Haemophilus and Streptococcus genera was observed in patients with undetectable IgA and COPD, independent from recent antibiotic use. Patients receiving azithromycin as antibiotic prophylaxis had a higher dysbiosis score. Expansion of Haemophilus and Anoxybacillus was associated with acute respiratory infections within six months.<br><br>CONCLUSIONS: CVID patients showed a perturbed oropharynx microbiota enriched with potentially pathogenic bacteria and decreased protective species. Low residual levels of IgA/IgM, chronic lung damage, anti antibiotic prophylaxis contributed to respiratory dysbiosis.}, }
@article {pmid38873164, year = {2024}, author = {Rodríguez-Cruz, UE and Castelán-Sánchez, HG and Madrigal-Trejo, D and Eguiarte, LE and Souza, V}, title = {Uncovering novel bacterial and archaeal diversity: genomic insights from metagenome-assembled genomes in Cuatro Cienegas, Coahuila.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1369263}, pmid = {38873164}, issn = {1664-302X}, abstract = {A comprehensive study was conducted in the Cuatro Ciénegas Basin (CCB) in Coahuila, Mexico, which is known for its diversity of microorganisms and unique physicochemical properties. The study focused on the "Archaean Domes" (AD) site in the CCB, which is characterized by an abundance of hypersaline, non-lithifying microbial mats. In AD, we analyzed the small domes and circular structures using metagenome assembly genomes (MAGs) with the aim of expanding our understanding of the prokaryotic tree of life by uncovering previously unreported lineages, as well as analyzing the diversity of bacteria and archaea in the CCB. A total of 325 MAGs were identified, including 48 Archaea and 277 Bacteria. Remarkably, 22 archaea and 104 bacteria could not be classified even at the genus level, highlighting the remarkable novel diversity of the CCB. Besides, AD site exhibited significant diversity at the phylum level, with Proteobacteria being the most abundant, followed by Desulfobacteria, Spirochaetes, Bacteroidetes, Nanoarchaeota, Halobacteriota, Cyanobacteria, Planctomycetota, Verrucomicrobiota, Actinomycetes and Chloroflexi. In Archaea, the monophyletic groups of MAGs belonged to the Archaeoglobi, Aenigmarchaeota, Candidate Nanoarchaeota, and Halobacteriota. Among Bacteria, monophyletic groups were also identified, including Spirochaetes, Proteobacteria, Planctomycetes, Actinobacteria, Verrucomicrobia, Bacteroidetes, Candidate Bipolaricaulota, Desulfobacteria, and Cyanobacteria. These monophyletic groups were possibly influenced by geographic isolation, as well as the extreme and fluctuating environmental conditions in the pond AD, such as stoichiometric imbalance of C:N:P of 122:42:1, fluctuating pH (5-9.8) and high salinity (5.28% to saturation).}, }
@article {pmid38870896, year = {2024}, author = {de la Cuesta-Zuluaga, J and Boldt, L and Maier, L}, title = {Response, resistance, and recovery of gut bacteria to human-targeted drug exposure.}, journal = {Cell host &amp; microbe}, volume = {32}, number = {6}, pages = {786-793}, doi = {10.1016/j.chom.2024.05.009}, pmid = {38870896}, issn = {1934-6069}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects ; Xenobiotics/pharmacology ; Symbiosis ; Gastrointestinal Tract/microbiology/drug effects ; Drug Resistance, Bacterial ; Host Microbial Interactions/drug effects ; }, abstract = {Survival strategies of human-associated microbes to drug exposure have been mainly studied in the context of bona fide pathogens exposed to antibiotics. Less well understood are the survival strategies of non-pathogenic microbes and host-associated commensal communities to the variety of drugs and xenobiotics to which humans are exposed. The lifestyle of microbial commensals within complex communities offers a variety of ways to adapt to different drug-induced stresses. Here, we review the responses and survival strategies employed by gut commensals when exposed to drugs-antibiotics and non-antibiotics-at the individual and community level. We also discuss the factors influencing the recovery and establishment of a new community structure following drug exposure. These survival strategies are key to the stability and resilience of the gut microbiome, ultimately influencing the overall health and well-being of the host.}, }
@article {pmid38869727, year = {2024}, author = {Dyczko, D and Krysmann, A and Kolanek, A and Borczyk, B and Kiewra, D}, title = {Bacterial pathogens in Ixodes ricinus collected from lizards Lacerta agilis and Zootoca vivipara in urban areas of Wrocław, SW Poland- preliminary study.}, journal = {Experimental &amp; applied acarology}, volume = {93}, number = {2}, pages = {409-420}, pmid = {38869727}, issn = {1572-9702}, mesh = {Animals ; Female ; Male ; *Anaplasma/isolation &amp; purification/genetics ; *Borrelia/isolation &amp; purification/genetics ; Cities ; *Ixodes/microbiology/physiology ; Larva/microbiology/physiology ; *Lizards/parasitology/microbiology ; Nymph/microbiology/physiology ; Poland ; *Rickettsia/genetics/isolation &amp; purification ; }, abstract = {The aim of this study was to determine the level of infection of Ixodes ricinus ticks with pathogens (Borrelia spp., Rickettsia spp., and Anaplasma spp.) collected from Lacerta agilis and Zootoca vivipara lizards in the urban areas of Wrocław (SW Poland). The study was carried out in July-August 2020. Lizards were caught by a noose attached to a pole or by bare hands, identified by species, and examined for the presence of ticks. Each lizard was then released at the site of capture. Ticks were removed with tweezers, identified by species using keys, and molecular tests were performed for the presence of pathogens. From 28 lizards (17 specimens of Z. vivipara and 11 specimens of L. agilis) a total of 445 ticks, including 321 larvae and 124 nymphs, identified as I. ricinus were collected. A larger number of ticks were obtained from L. agilis compared to Z. vivipara. Molecular tests for the presence of pathogens were performed on 445 specimens of I. ricinus. The nested PCR method for the fla gene allowed the detection of Borrelia spp. in 9.4% of ticks, and it was higher in ticks from L. agilis (12.0%) than from Z. vivipara (1.0%). The RFLP method showed the presence of three species, including two belonging to the B. burgdorferi s.l. complex (B. lusitaniae and B. afzelii), and B. miyamotoi. The overall level of infection of Rickettsia spp. was 19.3%, including 27.2% in ticks collected from Z. vivipara and 17.0% from L. agilis. Sequencing of randomly selected samples confirmed the presence of R. helvetica. DNA of Anaplasma spp. was detected only in one pool of larvae collected from L. agilis, and sample sequencing confirmed the presence of (A) phagocytophilum. The research results indicate the important role of lizards as hosts of ticks and their role in maintaining pathogens in the environment including urban agglomeration as evidenced by the first recorded presence of (B) miyamotoi and (A) phagocytophilum in I. ricinus ticks collected from L. agilis. However, confirmation of the role of sand lizards in maintaining (B) miyamotoi and A. phagocytophilum requires more studies and sampling of lizard tissue.}, }
@article {pmid38868805, year = {2024}, author = {Riello, GBC and da Silva, PM and da Silva Oliveira, FA and de Oliveira, RTG and da Silva, FER and da Frota França, IG and Melo, VMM and Miyajima, F and Pinheiro, RF and Danielle S, M}, title = {Gut Microbiota Composition Correlates with Disease Severity in Myelodysplastic Syndrome.}, journal = {International journal of hematology-oncology and stem cell research}, volume = {18}, number = {2}, pages = {192-201}, pmid = {38868805}, issn = {2008-3009}, abstract = {The myelodysplastic syndrome (MDS) is a heterogeneous group of clonal disorders of hematopoietic progenitor cells related to ineffective hematopoiesis and an increased risk of transformation to acute myelogenous leukemia. MDS is divided into categories, namely lineage dysplasia (MDS-SLD), MDS with ring sideroblasts (MDS-RS), MDS with multilineage dysplasia (MDS-MLD), MDS with excess blasts (MDS-EB). The International Prognostic Classification System (IPSS) ranks the patients as very low, low, intermediate, high, and very high based on disease evolution and survival rates. Evidence points to toll-like receptor (TLR) abnormal signaling as an underlying mechanism of this disease, providing a link between MDS and immune dysfunction. Microbial signals, such as lipopolysaccharides from gram-negative bacteria, can activate or suppress TLRs. Therefore, we hypothesized that MDS patients present gut microbiota alterations associated with disease subtypes and prognosis. To test this hypothesis, we sequenced the 16S rRNA gene from fecal samples of 30 MDS patients and 16 healthy elderly controls. We observed a negative correlation between Prevotella spp. and Akkermansia spp. in MDS patients compared with the control group. High-risk patients presented a significant increase in the genus Prevotella spp. compared to the other risk categories. There was a significant reduction in the abundance of the genus Akkermansia spp. in high-risk patients compared with low- and intermediate-risk. There was a significant decrease in the genus Ruminococcus spp. in MDS-EB patients compared with controls. Our findings show a new association between gut dysbiosis and higher-risk MDS, with a predominance of gram-negative bacteria.}, }
@article {pmid38868511, year = {2024}, author = {Li, M and Hu, J and Wei, Z and Jousset, A and Pommier, T and Yu, X and Xu, Y and Shen, Q}, title = {Synthetic microbial communities: Sandbox and blueprint for soil health enhancement.}, journal = {iMeta}, volume = {3}, number = {1}, pages = {e172}, pmid = {38868511}, issn = {2770-596X}, abstract = {We summarize here the use of SynComs in improving various dimensions of soil health, including fertility, pollutant removal, soil-borne disease suppression, and soil resilience; as well as a set of useful guidelines to assess and understand the principles for designing SynComs to enhance soil health. Finally, we discuss the next stages of SynComs applications, including highly diverse and multikingdom SynComs targeting several functions simultaneously.}, }
@article {pmid38867105, year = {2025}, author = {Mahjoubi, M and Cherif, H and Aliyu, H and Chouchane, H and Cappello, S and Neifar, M and Mapelli, F and Souissi, Y and Borin, S and Cowan, DA and Cherif, A}, title = {Brucella pituitosa strain BU72, a new hydrocarbonoclastic bacterium through exopolysaccharide-based surfactant production.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {28}, number = {2}, pages = {299-313}, pmid = {38867105}, issn = {1618-1905}, mesh = {*Brucella/metabolism/genetics/classification/growth &amp; development ; *Surface-Active Agents/metabolism/chemistry ; *Hydrocarbons/metabolism ; Biodegradation, Environmental ; *Polysaccharides, Bacterial/metabolism/chemistry ; Metals, Heavy/metabolism/toxicity ; Genome, Bacterial ; Petroleum/metabolism ; Spectroscopy, Fourier Transform Infrared ; }, abstract = {Hydrocarbon and heavy metal pollution are amongst the most severe and prevalent environmental problems due to their toxicity and persistence. Bioremediation using microorganisms is considered one of the most effective ways to treat polluted sites. In the present study, we unveil the bioremediation potential of Brucella pituitosa strain BU72. Besides its ability to grow on multiple hydrocarbons as the sole carbon source and highly tolerant to several heavy metals, BU72 produces different exopolysaccharide-based surfactants (EBS) when grown with glucose or with crude oil as sole carbon source. These EBS demonstrated particular and specific functional groups as determined by Fourier transform infrared (FTIR) spectral analysis that showed a strong absorption peak at 3250 cm[-1] generated by the -OH group for both EBS. The FTIR spectra of the produced EBS revealed major differences in functional groups and protein content. To better understand the EBS production coupled with the degradation of hydrocarbons and heavy metal resistance, the genome of strain BU72 was sequenced. Annotation of the genome revealed multiple genes putatively involved in EBS production pathways coupled with resistance to heavy metals genes such as arsenic tolerance and cobalt-zinc-cadmium resistance. The genome sequence analysis showed the potential of BU72 to synthesise secondary metabolites and the presence of genes involved in plant growth promotion. Here, we describe the physiological, metabolic, and genomic characteristics of Brucella pituitosa strain BU72, indicating its potential as a bioremediation agent.}, }
@article {pmid38865907, year = {2024}, author = {Wang, L and Lee, E and Barlaz, MA and de Los Reyes, FL}, title = {Linking microbial population dynamics in anaerobic bioreactors to food waste type and decomposition stage.}, journal = {Waste management (New York, N.Y.)}, volume = {186}, number = {}, pages = {77-85}, doi = {10.1016/j.wasman.2024.06.004}, pmid = {38865907}, issn = {1879-2456}, mesh = {*Bioreactors/microbiology ; Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; Refuse Disposal/methods ; Solid Waste/analysis ; Bacteria/metabolism/genetics/classification ; Vegetables/microbiology ; Methane/metabolism ; Fruit/microbiology ; Garbage ; Food Loss and Waste ; }, abstract = {A key question in anaerobic microbial ecology is how microbial communities develop over different stages of waste decomposition and whether these changes are specific to waste types. We destructively sampled over time 26 replicate bioreactors cultivated on fruit/vegetable waste (FVW) and meat waste (MW) based on pre-defined waste components and composition. To characterize community shifts, we examined 16S rRNA genes from both the leachate and solid fractions of the waste. Waste decomposition occurred faster in FVW than MW, as accumulation of ammonia in MW reactors led to inhibition of methanogenesis. We identified population succession during different stages of waste decomposition and linked specific populations to different waste types. Community analyses revealed underrepresentation of methanogens in the leachate fractions, emphasizing the importance of consistent and representative sampling when characterizing microbial communities in solid waste.}, }
@article {pmid38861460, year = {2024}, author = {Wutkowska, M and Tláskal, V and Bordel, S and Stein, LY and Nweze, JA and Daebeler, A}, title = {Leveraging genome-scale metabolic models to understand aerobic methanotrophs.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38861460}, issn = {1751-7370}, support = {21-17322M//Czech Science Foundation/ ; }, mesh = {*Methane/metabolism ; Oxidation-Reduction ; Aerobiosis ; Metabolic Networks and Pathways/genetics ; Models, Biological ; }, abstract = {Genome-scale metabolic models (GEMs) are valuable tools serving systems biology and metabolic engineering. However, GEMs are still an underestimated tool in informing microbial ecology. Since their first application for aerobic gammaproteobacterial methane oxidizers less than a decade ago, GEMs have substantially increased our understanding of the metabolism of methanotrophs, a microbial guild of high relevance for the natural and biotechnological mitigation of methane efflux to the atmosphere. Particularly, GEMs helped to elucidate critical metabolic and regulatory pathways of several methanotrophic strains, predicted microbial responses to environmental perturbations, and were used to model metabolic interactions in cocultures. Here, we conducted a systematic review of GEMs exploring aerobic methanotrophy, summarizing recent advances, pointing out weaknesses, and drawing out probable future uses of GEMs to improve our understanding of the ecology of methane oxidizers. We also focus on their potential to unravel causes and consequences when studying interactions of methane-oxidizing bacteria with other methanotrophs or members of microbial communities in general. This review aims to bridge the gap between applied sciences and microbial ecology research on methane oxidizers as model organisms and to provide an outlook for future studies.}, }
@article {pmid38860973, year = {2024}, author = {Deehan, EC and Zhang, Z and Nguyen, NK and Perez-Muñoz, ME and Cole, J and Riva, A and Berry, D and Prado, CM and Walter, J}, title = {Adaptation to tolerate high doses of arabinoxylan is associated with fecal levels of Bifidobacterium longum.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2363021}, pmid = {38860973}, issn = {1949-0984}, support = {741623/ERC_/European Research Council/International ; }, mesh = {*Xylans/metabolism ; Humans ; *Feces/microbiology/chemistry ; Male ; Female ; *Dietary Fiber/metabolism ; Middle Aged ; *Gastrointestinal Microbiome/drug effects ; *Bifidobacterium longum/metabolism ; Adult ; Dietary Supplements/analysis ; Fermentation ; Aged ; Adaptation, Physiological ; }, abstract = {Dietary fiber supplements are a strategy to close the 'fiber gap' and induce targeted modulations of the gut microbiota. However, higher doses of fiber supplements cause gastrointestinal (GI) symptoms that differ among individuals. What determines these inter-individual differences is insufficiently understood. Here we analyzed findings from a six-week randomized controlled trial that evaluated GI symptoms to corn bran arabinoxylan (AX; n = 15) relative to non-fermentable microcrystalline cellulose (MCC; n = 16) at efficacious supplement doses of 25 g/day (females) or 35 g/day (males) in adults with excess weight. Self-reported flatulence, bloating, and stomach aches were evaluated weekly. Bacterial taxa involved in AX fermentation were identified by bioorthogonal non-canonical amino acid tagging. Associations between GI symptoms, fecal microbiota features, and diet history were systematically investigated. AX supplementation increased symptoms during the first three weeks relative to MCC (p < 0.05, Mann-Whitney tests), but subjects 'adapted' with symptoms reverting to baseline levels toward the end of treatment. Symptom adaptations were individualized and correlated with the relative abundance of Bifidobacterium longum at baseline (rs = 0.74, p = 0.002), within the bacterial community that utilized AX (rs = 0.69, p = 0.006), and AX-induced shifts in acetate (rs = 0.54, p = 0.039). Lower baseline consumption of animal-based foods and higher whole grains associated with less severity and better adaptation. These findings suggest that humans do 'adapt' to tolerate efficacious fiber doses, and this process is linked to their microbiome and dietary factors known to interact with gut microbes, providing a basis for the development of strategies for improved tolerance of dietary fibers.}, }
@article {pmid38860825, year = {2024}, author = {Paillet, T and Lamy-Besnier, Q and Figueroa, C and Petit, M-A and Dugat-Bony, E}, title = {Dynamics of the viral community on the surface of a French smear-ripened cheese during maturation and persistence across production years.}, journal = {mSystems}, volume = {9}, number = {7}, pages = {e0020124}, pmid = {38860825}, issn = {2379-5077}, mesh = {*Cheese/microbiology/virology ; *Bacteriophages/genetics/isolation &amp; purification ; Bacteria/virology/genetics/isolation &amp; purification ; Microbiota ; Food Microbiology ; France ; Metagenomics ; Virome ; }, abstract = {The surface of smear-ripened cheeses constitutes a dynamic microbial ecosystem resulting from the successive development of different microbial groups such as lactic acid bacteria, fungi, and ripening bacteria. Recent studies indicate that a viral community, mainly composed of bacteriophages, also represents a common and substantial part of the cheese microbiome. However, the composition of this community, its temporal variations, and associations between bacteriophages and their hosts remain poorly characterized. Here, we studied a French smear-ripened cheese by both viral metagenomics and 16S metabarcoding approaches to assess both the succession of phages and bacterial communities on the cheese surface during cheese ripening and their temporal variations in ready-to-eat cheeses over the years of production. We observed a clear transition of the phage community structure during ripening with a decreased relative abundance of viral species (vOTUs) associated with Lactococcus phages, which were replaced by vOTUs associated with phages infecting ripening bacteria such as Brevibacterium, Glutamicibacter, Pseudoalteromonas, and Vibrio. The dynamics of the phage community was strongly associated with bacterial successions observed on the cheese surface. Finally, while some variations in the distribution of phages were observed in ready-to-eat cheeses produced at different dates spanning more than 4 years of production, the most abundant phages were detected throughout. This result revealed the long-term persistence of the dominant phages in the cheese production environment. Together, these findings offer novel perspectives on the ecology of bacteriophages in smear-ripened cheese and emphasize the significance of incorporating bacteriophages in the microbial ecology studies of fermented foods.IMPORTANCEThe succession of diverse microbial populations is critical for ensuring the production of high-quality cheese. We observed a temporal succession of phages on the surface of a smear-ripened cheese, with new phage communities showing up when ripening bacteria start covering this surface. Interestingly, the final phage community of this cheese is also consistent over large periods of time, as the same bacteriophages were found in cheese products from the same manufacturer made over 4 years. This research highlights the importance of considering these bacteriophages when studying the microbial life of fermented foods like cheese.}, }
@article {pmid38858788, year = {2024}, author = {Silva, DP and Villela, HDM and Santos, HF and Duarte, GAS and Ribeiro, JR and Ghizelini, AM and Vilela, CLS and Rosado, PM and Fazolato, CS and Santoro, EP and Carmo, FL and Ximenes, DS and Soriano, AU and Rachid, CTCC and Thurber, RLV and Peixoto, RS}, title = {Correction: Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {105}, pmid = {38858788}, issn = {2049-2618}, }
@article {pmid38857239, year = {2024}, author = {Martinez-Villegas, L and Lado, P and Klompen, H and Wang, S and Cummings, C and Pesapane, R and Short, SM}, title = {The microbiota of Amblyomma americanum reflects known westward expansion.}, journal = {PloS one}, volume = {19}, number = {6}, pages = {e0304959}, pmid = {38857239}, issn = {1932-6203}, mesh = {Animals ; *Microbiota ; Female ; Male ; *Amblyomma/microbiology ; United States ; Ixodidae/microbiology ; }, abstract = {Amblyomma americanum, a known vector of multiple tick-borne pathogens, has expanded its geographic distribution across the United States in the past decades. Tick microbiomes may play a role shaping their host's life history and vectorial capacity. Bacterial communities associated with A. americanum may reflect, or enable, geographic expansion and studying the microbiota will improve understanding of tick-borne disease ecology. We examined the microbiota structure of 189 adult ticks collected in four regions encompassing their historical and current geographic distribution. Both geographic region of origin and sex were significant predictors of alpha diversity. As in other tick models, within-sample diversity was low and uneven given the presence of dominant endosymbionts. Beta diversity analyses revealed that bacterial profiles of ticks of both sexes collected in the West were significantly different from those of the Historic range. Biomarkers were identified for all regions except the historical range. In addition, Bray-Curtis dissimilarities overall increased with distance between sites. Relative quantification of ecological processes showed that, for females and males, respectively, drift and dispersal limitation were the primary drivers of community assembly. Collectively, our findings highlight how microbiota structural variance discriminates the western-expanded populations of A. americanum ticks from the Historical range. Spatial autocorrelation, and particularly the detection of non-selective ecological processes, are indicative of geographic isolation. We also found that prevalence of Ehrlichia chaffeensis, E. ewingii, and Anaplasma phagocytophilum ranged from 3.40-5.11% and did not significantly differ by region. Rickettsia rickettsii was absent from our samples. Our conclusions demonstrate the value of synergistic analysis of biogeographic and microbial ecology data in investigating range expansion in A. americanum and potentially other tick vectors as well.}, }
@article {pmid38855766, year = {2024}, author = {Tong, L and Jun, L and He, J and Min, Y and Guoqing, D and Yuting, H and Huaxing, Z and Huan, W and Tingshuang, P}, title = {Differences in environmental microbial community responses under rice-crab co-culture and crab monoculture models under cyanobacterial bloom.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1327520}, pmid = {38855766}, issn = {1664-302X}, abstract = {Cyanobacterial blooms (CBs) present significant challenges to Chinese mitten crab (CMC) culture, posing hazards to the aquatic microbial ecology. However, the current focus on the microbial ecological changes within the CMC culture system under the influence of CBs is somewhat insufficient. There's an urgent need to analyze the microbial ecosystem of the CMC culture system under CBs. This study employed 16S rRNA gene amplicon sequencing to investigate the dynamics of the environmental microbial community in both the rice-crab co-culture (RC) and crab monoculture (CM) models. The results revealed that cyanobacteria reached high levels in the CM water in July, while they began to increase in the RC water in August. Notably, OTU147 (uncultured bacterium g_Planktothrix NIVA-CYA 15), identified as the dominant taxon associated with CBs, showed a significant linear relationship with TP, NO2 [-]-N, and the N:P ratio. TP, TN, NO2 [-]-N, and CODMn had a more pronounced impact on the structure of bacterial communities and cyanobacterial taxa in the water. The bacterial community structure involved in carbon metabolism displayed temporal succession in the water. The co-occurrence network of the bacterial community primarily consisted of Chloroflexi, Proteobacteria, and Firnicutes in the sediment, and Actinobacteria, Proteobacteria, Chloroflexi, and Bacteroidota in the water. In contrast, the co-occurrence network included different peripheral species in the sediment and water. Keystone species were predominantly represented by OTU22 (uncultured actinobacterium g_ hgcI clade) and OTU12 (uncultured Opitutae bacterium g_ norank) in the RC water, and by OTU25 (uncultured bacterium g_ Limnohabitans) in the CM water. TP, TN, NO2 [-]-N, and CODMn were identified as the primary environmental factors influencing these keystone taxa within the culture water. In conclusion, this study on the microbial ecology of the CMC culture system under the influence of CBs provides valuable insights that can be instrumental in subsequent management efforts.}, }
@article {pmid38852236, year = {2024}, author = {Xu, Y and Yu, Z and Liu, C and Hu, Y and Zhang, J and Liu, J and Chen, X and Liu, J and Wang, G and Liu, X and Jin, J and Li, Y}, title = {Variability in soybean yield responses to elevated atmospheric CO2: Insights from non-structural carbohydrate remobilisation during seed filling.}, journal = {Plant physiology and biochemistry : PPB}, volume = {213}, number = {}, pages = {108802}, doi = {10.1016/j.plaphy.2024.108802}, pmid = {38852236}, issn = {1873-2690}, mesh = {*Glycine max/metabolism/growth &amp; development/drug effects/physiology ; *Carbon Dioxide/metabolism/pharmacology ; *Photosynthesis/drug effects ; *Carbohydrate Metabolism ; *Seeds/metabolism/growth &amp; development/drug effects ; }, abstract = {The increasing atmospheric CO2 concentration (e[CO2]) has mixed effects on soybean most varieties' yield. This study elucidated the effect of e[CO2] on soybean yield and the underlying mechanisms related to photosynthetic capacity, non-structural carbohydrate (NSC) accumulation, and remobilisation. Four soybean cultivars were cultivated in open-top chambers at two CO2 levels. Photosynthesis rates were determined from R2 to R6. Plants were sampled at R5 and R8 to determine carbohydrate concentrations. There were significant variations in yield responses among the soybean cultivars under e[CO2], from no change in DS1 to a 22% increase in SN14. DS1 and SN14 had the smallest and largest increase, respectively, in daily carbon assimilation capacity. Under e[CO2], DS1, MF5, and XHJ had an increase in Ci, at which point the transition from Rubisco-limited to ribulose-1,5-bisphosphate regeneration-limited photosynthesis occurred, in contrast with SN14. Thus, the cultivars might have distinct mechanisms that enhance photosynthesis under e[CO2] conditions. A positive correlation was between daily carbon assimilation response to e[CO2] and soybean yield, emphasising the importance of enhanced photosynthate accumulation before the R5 stage in determining yield response to e[CO2]. E[CO2] significantly influenced NSC accumulation in vegetative organs at R5, with variation among cultivars. There was enhanced NSC remobilisation during seed filling, indicating cultivar-specific responses to the remobilisation of sucrose and soluble sugars, excluding sucrose and starch. A positive correlation was between leaf and stem NSC remobilisation and yield response to e[CO2], emphasising the role of genetic differences in carbohydrate remobilisation mechanisms in determining soybean yield variation under elevated CO2 levels.}, }
@article {pmid38849711, year = {2024}, author = {Doménech-Pascual, A and Carrasco-Barea, L and Gich, F and Boadella, J and Freixinos Campillo, Z and Gómez Cerezo, R and Butturini, A and Romaní, AM}, title = {Differential response of bacteria and fungi to drought on the decomposition of Sarcocornia fruticosa woody stems in a saline stream.}, journal = {Environmental microbiology}, volume = {26}, number = {6}, pages = {e16661}, doi = {10.1111/1462-2920.16661}, pmid = {38849711}, issn = {1462-2920}, support = {PID2021-123735OB-C2/MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovaci&#xf3;n/ ; RTI2018-097950-B-C2//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PCI2020-120702-2/AEI/10.13039/501.100.011.033//Agencia Estatal de Investigaci&#xf3;n/ ; 2021 FISDU 00297//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; }, mesh = {*Droughts ; *Bacteria/metabolism/classification ; *Fungi/metabolism ; *Rivers/microbiology ; *Salinity ; *Plant Stems/microbiology/metabolism ; Ecosystem ; }, abstract = {Inland saline ecosystems suffer multiple stresses (e.g., high radiation, salinity, water scarcity) that may compromise essential ecosystem functions such as organic matter decomposition. Here, we investigated the effects of drought on microbial colonization and decomposition of Sarcocornia fruticosa woody stems across different habitats in a saline watershed: on the dry floodplain, submerged in the stream channel and at the shoreline (first submerged, then emerged). Unexpectedly, weight loss was not enhanced in the submerged stems, while decomposition process differed between habitats. On the floodplain, it was dominated by fungi and high cellulolytic activity; in submerged conditions, a diverse community of bacteria and high ligninolytic activity dominated; and, on the shoreline, enzyme activities were like submerged conditions, but with a fungal community similar to the dry conditions. Results indicate distinct degradation paths being driven by different stress factors: strong water scarcity and photodegradation in dry conditions, and high salinity and reduced oxygen in wet conditions. This suggests that fungi are more resistant to drought, and bacteria to salinity. Overall, in saline watersheds, variations in multiple stress factors exert distinct environmental filters on bacteria and fungi and their role in the decomposition of plant material, affecting carbon cycling and microbial interactions.}, }
@article {pmid38849299, year = {2024}, author = {Papazlatani, C and Garbeva, P and Huerta Lwanga, E}, title = {Effect of microplastic pollution on the gut microbiome of anecic and endogeic earthworms.}, journal = {FEMS microbiology letters}, volume = {371}, number = {}, pages = {}, pmid = {38849299}, issn = {1574-6968}, mesh = {*Oligochaeta/microbiology/drug effects ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Microplastics/toxicity ; Bacteria/classification/drug effects/isolation &amp; purification/genetics ; Soil Pollutants/toxicity ; Soil Microbiology ; }, abstract = {Microplastic (MP) pollution constitutes an emerging type of pollution threatening both aquatic and terrestrial ecosystems. The impact on aquatic ecosystems has been extensively studied, but the effect on terrestrial ecosystems and their inhabitants is mostly underexplored. In this study, we explored the effect of MP pollution on gut bacterial microbiome of endogeic (Aporrectodea caliginosa) and anecic (Lumbricus terrestris) earthworms. The experiments were performed in sandy soil with 0.2% of low-density polyethylene MPs (LDPE MPs). We observed that the endogeic earthworms had 100% survival, while anecic earthworms survived 25 days in the control (i.e. in absence of MPs) and 21 days in the treatment with LDPE MPs. The main driver of shifts in the diversity and composition of the bacterial communities in the gut of tested earthworms was the lifestyle of the worms, followed by the presence of MPs. The bacterial microbiome diversity was significantly different among the two types of earthworms, and the highest bacterial diversity was found in the gut of the endogeic earthworms. The effect of MPs on gut bacterial microbiome was clearly observed in the changes in the relative abundance of several phyla and families of the bacterial communities in both types of earthworms, although it was most evident in the anecic earthworms. The Actinobacteriota, Proteobacteria, and Firmicutes were the main groups enhanced in the MP treatments, suggesting enrichment of the bacterial communities with potential plastic degraders.}, }
@article {pmid38844497, year = {2024}, author = {Serra Moncadas, L and Hofer, C and Bulzu, PA and Pernthaler, J and Andrei, AS}, title = {Author Correction: Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4830}, doi = {10.1038/s41467-024-49328-4}, pmid = {38844497}, issn = {2041-1723}, }
@article {pmid38842339, year = {2024}, author = {Kortenbosch, HH and van Leuven, F and van den Heuvel, C and Schoustra, SE and Zwaan, BJ and Snelders, E}, title = {Catching some air: a method to spatially quantify aerial triazole resistance in Aspergillus fumigatus.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {7}, pages = {e0027124}, pmid = {38842339}, issn = {1098-5336}, support = {GROEN.2019.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; }, mesh = {*Aspergillus fumigatus/drug effects/genetics ; *Drug Resistance, Fungal ; *Air Microbiology ; *Triazoles/pharmacology ; *Antifungal Agents/pharmacology ; Spores, Fungal/drug effects/genetics ; Environmental Monitoring/methods ; }, abstract = {Airborne triazole-resistant spores of the human fungal pathogen Aspergillus fumigatus are a significant human health problem as the agricultural use of triazoles has been selecting for cross-resistance to life-saving clinical triazoles. However, how to quantify exposure to airborne triazole-resistant spores remains unclear. Here, we describe a method for cost-effective wide-scale outdoor air sampling to measure both spore abundance as well as antifungal resistance fractions. We show that prolonged outdoor exposure of sticky seals placed in delta traps, when combined with a two-layered cultivation approach, can regionally yield sufficient colony-forming units (CFUs) for the quantitative assessment of aerial resistance levels at a spatial scale that was up to now unfeasible. When testing our method in a European pilot sampling 12 regions, we demonstrate that there are significant regional differences in airborne CFU numbers, and the triazole-resistant fraction of airborne spores is widespread and varies between 0 and 0.1 for itraconazole (∼4 mg/L) and voriconazole (∼2 mg/L). Our efficient and accessible air sampling protocol opens up extensive options for fine-scale spatial sampling and surveillance studies of airborne A. fumigatus.IMPORTANCEAspergillus fumigatus is an opportunistic fungal pathogen that humans and other animals are primarily exposed to through inhalation. Due to the limited availability of antifungals, resistance to the first choice class of antifungals, the triazoles, in A. fumigatus can make infections by this fungus untreatable and uncurable. Here, we describe and validate a method that allows for the quantification of airborne resistance fractions and quick genotyping of A. fumigatus TR-types. Our pilot study provides proof of concept of the suitability of the method for use by citizen-scientists for large-scale spatial air sampling. Spatial air sampling can open up extensive options for surveillance, health-risk assessment, and the study of landscape-level ecology of A. fumigatus, as well as investigating the environmental drivers of triazole resistance.}, }
@article {pmid38840338, year = {2024}, author = {Olson, EG and Dittoe, DK and Micciche, AC and Stock, DA and Rubinelli, PM and Rothrock, MJ and Ricke, SC}, title = {Microbiome analyses of poultry feeds: Part II. Comparison of different poultry feeds.}, journal = {Journal of environmental science and health. Part. B, Pesticides, food contaminants, and agricultural wastes}, volume = {59}, number = {8}, pages = {448-482}, doi = {10.1080/03601234.2024.2361596}, pmid = {38840338}, issn = {1532-4109}, mesh = {Animals ; *Animal Feed/analysis ; *Poultry/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/isolation &amp; purification ; Chickens/microbiology ; Microbiota ; }, abstract = {Within the realm of poultry feed mill operations, the persistent concern over microbial feed quality necessitates the establishment of a robust baseline for enhancing and sustaining the standards of commercial feeds. This dual-phase investigation, comprising Parts I, was previously published, and the current study presented here as Part II aimed to illuminate this baseline using 16S rRNA gene sequencing. In Part II, nine distinct commercial poultry feeds formulated as starters, growers, starter/growers, or supplements, the selected feeds underwent genomic DNA extraction, amplification with custom dual-indexed primers, and subsequent Illumina MiSeq sequencing. Through data analysis in QIIME2-2021.4 and R Studio, the study unveils alpha (Kruskal-Wallis) and beta (ANOSIM) diversity, taxonomic differences (ANCOM), and core microbiomes (core_members), deeming main and pairwise effects statistically significant at p < 0.05 and Q < 0.05. Notably, the investigation identified 30% common core microbial members across the nine feed types, shedding light on potential foodborne poultry pathogens such as Helicobacter and Campylobacter. Probiotic-associated feeds exhibited distinct microbial communities, emphasizing the need to explore their impact on the early poultry gastrointestinal tract (GIT) further.}, }
@article {pmid38840053, year = {2024}, author = {Ullah, I and Ullah, S and Amin, F and Al-Hawadi, JS and Okla, MK and Alaraidh, IA and AbdElgawad, H and Liu, K and Harrison, MT and Saud, S and Hassan, S and Nawaz, T and Zhu, M and Liu, H and Fahad, S}, title = {Germination responses of Lens Culiunaris L. seeds to osmotic potentials at cardinal temperatures using hydrothermal time model.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {502}, pmid = {38840053}, issn = {1471-2229}, mesh = {*Germination/physiology ; *Seeds/physiology/growth &amp; development ; *Lens Plant/physiology/growth &amp; development ; *Temperature ; Water/metabolism ; Models, Biological ; Osmotic Pressure ; }, abstract = {BACKGROUND: Lentil is a significant legume that are consumed as a staple food and have a significant economic impact around the world. The purpose of the present research on lentil was to assess the hydrothermal time model's capacity to explain the dynamics of Lens culinaris L. var. Markaz-09 seed germination, as well as to ascertain the germination responses at various sub-optimal temperatures (T) and water potentials (Ψ). In order to study lentil seed germination (SG) behavior at variable water potentials (Ψs) and temperatures (Ts). A lab experiment employing the hydrothermal time model was created. Seeds were germinated at six distinct temperatures: 15 [0]С, 20 [0]С, 25 [0]С, 30 [0]С, 35 [0]С, and 40 [0]С, with five Ψs of 0, -0.3, -0.6, -0.9, and - 1.2 MPa in a PEG-6000 (Polyethylene glycol 6000) solution.<br><br>RESULTS: The results indicated that the agronomic parameters like Germination index (GI), Germination energy (GE), Timson germination index (TGI), were maximum in 25 [0]C at (-0.9&#xa0;MPa) and lowest at 40 [0]C in 0&#xa0;MPa. On other hand, mean germination time (MGT) value was highest at 15 [0]C in -1.2&#xa0;MPa and minimum at 40 [0]C in (-0.6&#xa0;MPa) while Mean germination rate (MGR) was maximum at 40 [0]C in (0&#xa0;MPa) and minimum at 15 [0]C in (-0.6&#xa0;MPa).<br><br>CONCLUSIONS: The HTT model eventually defined the germination response of Lens culinaris L. var. Markaz-09 (Lentil) for all Ts and &#x3a8;s, allowing it to be employed as a predictive tool in Lens culinaris L. var. Markaz-09 (Lentil) seed germination simulation models.}, }
@article {pmid38839775, year = {2024}, author = {Ray, K and Basak, SK and Giri, CK and Kotal, HN and Mandal, A and Chatterjee, K and Saha, S and Biswas, B and Mondal, S and Das, I and Ghosh, A and Bhadury, P and Joshi, R}, title = {Ecological restoration at pilot-scale employing site-specific rationales for small-patch degraded mangroves in Indian Sundarbans.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {12952}, pmid = {38839775}, issn = {2045-2322}, support = {BT/PR7501/BCE/8/982/2013//Department of Biotechnology, Government of India; Science and Engineering Research Board, Department of Science and Technology, Government of India/ ; File No. BT/PR30531/BCE/8/1496/2018//Department of Biotechnology, Government of India; Science and Engineering Research Board, Department of Science and Technology, Government of India/ ; EMR/2016/005262//Department of Biotechnology, Government of India; Science and Engineering Research Board, Department of Science and Technology, Government of India/ ; }, mesh = {*Wetlands ; India ; *Conservation of Natural Resources/methods ; Ecosystem ; Environmental Restoration and Remediation/methods ; Pilot Projects ; Bayes Theorem ; }, abstract = {To date, degraded mangrove ecosystem restoration accomplished worldwide primarily aligns towards rehabilitation with monotypic plantations, while ecological restoration principles are rarely followed in these interventions. However, researchers admit that most of these initiatives' success rate is not appreciable often. An integrative framework of ecological restoration for degraded mangroves where site-specific observations could be scientifically rationalized, with co-located reference pristine mangroves as the target ecosystem to achieve is currently distinctively lacking. Through this experimental scale study, we studied the suitability of site-specific strategies to ecologically restore degraded mangrove patches vis-à-vis the conventional mono-species plantations in a highly vulnerable mangrove ecosystem in Indian Sundarbans. This comprehensive restoration framework was trialed in small discrete degraded mangrove patches spanning ~ 65 ha. Site-specific key restoration components applied are statistically validated through RDA analyses and Bayesian t-tests. 25 quantifiable metrics evaluate the restoration success of a ~ 3 ha degraded mangrove patch with Ridgeline distribution, Kolmogorov-Smirnov (K-S) tests, and Mahalanobis Distance (D[2]) measure to prove the site's near-equivalence to pristine reference in multiple ecosystem attributes. This restoration intervention irrevocably establishes the greater potential of this framework in the recovery of ecosystem functions and self-sustenance compared to that of predominant monoculture practices for vulnerable mangroves.}, }
@article {pmid38839017, year = {2024}, author = {Ruan, SY and Luo, HW and Tang, XR and Qi, JY}, title = {Effects of 3-year organic farming management on soil antibiotic resistant genes and virulence factors in a double rice cropping system.}, journal = {The Science of the total environment}, volume = {944}, number = {}, pages = {173722}, doi = {10.1016/j.scitotenv.2024.173722}, pmid = {38839017}, issn = {1879-1026}, mesh = {*Oryza/microbiology ; *Soil Microbiology ; *Organic Agriculture/methods ; *Virulence Factors/genetics ; China ; *Soil/chemistry ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; }, abstract = {Investigating the antibiotic resistance genes (ARGs) and virulence factors (VFs) within soil microbial communities is crucial for understanding microbial ecology and the evolution of antibiotic resistance. However, the study of ARGs, VFs, and their predominant microbial hosts in soils under varying rice production management practices remains largely underexplored. To this end, a three-year field experiment was conducted under organic management within a double rice cropping system in South China. The study revealed that, in contrast to conventional management (CK), organic farming practices did not significantly alter the total reads of ARGs and VFs. However, there was a notable alteration in the ARGs abundance at the antibiotic class level, such as an increase (P < 0.05) in the abundance of Multidrug ARGs (by 1.7 %) and a decrease (P < 0.05) in Rifamycin (by 17.5 %) and Fosfomycin ARGs (by 15.3 %). Furthermore, a significant shift in VFs was observed under organic farming compared to CK, characterized by an increase (P < 0.05) in offensive VFs and a decrease (P < 0.05) in nonspecific VFs and the regulation of virulence-associated genes. Key microbial taxa identified as influencing ARGs and VFs in the tested soil samples, e.g., Proteobacteria. The findings highlight the need for more detailed attention to soil ecology within organic rice production systems in South China, particularly concerning the significant alterations observed in ARGs and VFs.}, }
@article {pmid38839005, year = {2024}, author = {David, GM and Pimentel, IM and Rehsen, PM and Vermiert, AM and Leese, F and Gessner, MO}, title = {Multiple stressors affecting microbial decomposer and litter decomposition in restored urban streams: Assessing effects of salinization, increased temperature, and reduced flow velocity in a field mesocosm experiment.}, journal = {The Science of the total environment}, volume = {943}, number = {}, pages = {173669}, doi = {10.1016/j.scitotenv.2024.173669}, pmid = {38839005}, issn = {1879-1026}, mesh = {*Rivers/chemistry/microbiology ; *Salinity ; Biodegradation, Environmental ; Ecosystem ; Plant Leaves ; Alnus ; Temperature ; Environmental Monitoring ; }, abstract = {A multitude of anthropogenic stressors impact biological communities and ecosystem processes in urban streams. Prominent among them are salinization, increased temperature, and altered flow regimes, all of which can affect microbial decomposer communities and litter decomposition, a fundamental ecosystem process in streams. Impairments caused by these stressors individually or in combination and recovery of communities and ecosystem processes after release from these stressors are not well understood. To improve our understanding of multiple stressors impacts we performed an outdoor stream mesocosm experiment with 64 experimental units to assess the response of microbial litter decomposers and decomposition. The three stressors we applied in a full-factorial design were increased salinity (NaCl addition, 0.53 mS cm[-1] above ambient), elevated temperature (3.5 °C above ambient), and reduced flow velocity (3.5 vs 14.2 cm s[-1]). After two weeks of stressor exposure (first sampling) and two subsequent weeks of recovery (second sampling), we determined leaf-associated microbial respiration, fungal biomass, and the sporulation activity and community composition of aquatic hyphomycetes in addition to decomposition rates of black alder (Alnus glutinosa) leaves confined in fine-mesh litter bags. Microbial colonization of the litter was accompanied by significant mass loss in all mesocosms. However, there was little indication that mass loss, microbial respiration, fungal biomass, sporulation rate or community composition of aquatic hyphomycetes was strongly affected by either single stressors or their interactions. Two exceptions were temperature effects on sporulation and decomposition rate. Similarly, no notable differences among mesocosms were observed after the recovery phase. These results suggest that microbial decomposers and leaf litter decomposition are either barely impaired by exposure to the tested stressors at the levels applied in our experiment, or that communities in restored urban streams are well adapted to cope with these stressor levels.}, }
@article {pmid38832805, year = {2024}, author = {Freitas, ASd and Zagatto, LFG and Rocha, GS and Pellegrinetti, TA and Alves, LdCM and Lara, VMd and Mandro, JA and Martins, GL and Muniz, AW and Hanada, RE and Würdig Roesch, LF and Tsai, SM}, title = {Bacterial genomes recovered from litter's metagenomes in Amazonian Dark Earths.}, journal = {Microbiology resource announcements}, volume = {13}, number = {7}, pages = {e0042224}, pmid = {38832805}, issn = {2576-098X}, support = {2021/10.626-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; 314806/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 01.02.016301.00293/2021//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Amazonas (FAPEAM)/ ; 2020/08927-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; }, abstract = {Here, we report 27 metagenome-assembled bacterial genomes (MAGs) from litter samples of a secondary forest located in Brazil over an Amazonian Dark Earth pool. The data set includes members from the phyla Pseudomonadata (14 MAGs), Actinomycetota (7 MAGs), Bacteroidota (4 MAGs), Bacillota (1 MAG), and Bdellovibrionota (1 MAG).}, }
@article {pmid38831142, year = {2024}, author = {Chen, D and Tian, C and Yuan, H and Zhai, W and Chang, Z}, title = {Nitrogen Removal Performance and Microbial Community Structure of IMTA Ponds (Apostistius japonicus-Penaeus japonicus-Ulva).}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {82}, pmid = {38831142}, issn = {1432-184X}, support = {2023YFD2401704//National Key Research and Development Program of China/ ; CARS-48//Agriculture Research System of China/ ; No.2023TD50//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; }, mesh = {*Nitrogen/metabolism ; *Aquaculture ; *Denitrification ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Ponds/microbiology ; *Microbiota ; Animals ; *Penaeidae/microbiology ; *Nitrous Oxide/metabolism/analysis ; Geologic Sediments/microbiology ; Oxidation-Reduction ; Ammonium Compounds/metabolism ; }, abstract = {Denitrification and anaerobic ammonium oxidation (anammox) are key processes for nitrogen removal in aquaculture, reducing the accumulated nitrogen nutrients to nitrogen gas or nitrous oxide gas. Complete removal of nitrogen from aquaculture systems is an important measure to solve environmental pollution. In order to evaluate the nitrogen removal potential of marine aquaculture ponds, this study investigated the denitrification and anammox rates, the flux of nitrous oxide (N2O) at the water-air interface, the sediment microbial community structure, and the gene expression associated with the nitrogen removal process in integrated multi-trophic aquaculture (IMTA) ponds (Apostistius japonicus-Penaeus japonicus-Ulva) with different culture periods. The results showed that the denitrification and anammox rates in sediments increased with the increase of cultivation periods and depth, and there was no significant difference in nitrous oxide gas flux at the water-air interface between different cultivation periods (p > 0.05). At the genus and phylum levels, the abundance of microorganisms related to nitrogen removal reactions in sediments changed significantly with the increase of cultivation period and depth, and was most significantly affected by the concentration of particulate organic nitrogen (PON) in sediments. The expression of denitrification gene (narG, nirS, nosZ) in surface sediments was significantly higher than that in deep sediments (p < 0.05), and was negatively correlated with denitrification rate. All samples had a certain anammox capacity, but no known anammox bacteria were found in the microbial diversity detection, and the expression of gene (hzsB) related to the anammox process was extremely low, which may indicate the existence of an unknown anammox bacterium. The data of this study showed that the IMTA culture pond had a certain potential for nitrogen removal, and whether it could make a contribution to reducing the pollution of culture wastewater still needed additional practice and evaluation, and also provided a theoretical basis for the nitrogen removal research of coastal mariculture ponds.}, }
@article {pmid38830709, year = {2024}, author = {Mugani, R and El Khalloufi, F and Kasada, M and Redouane, EM and Haida, M and Aba, RP and Essadki, Y and Zerrifi, SEA and Herter, SO and Hejjaj, A and Aziz, F and Ouazzani, N and Azevedo, J and Campos, A and Putschew, A and Grossart, HP and Mandi, L and Vasconcelos, V and Oudra, B}, title = {Monitoring of toxic cyanobacterial blooms in Lalla Takerkoust reservoir by satellite imagery and microcystin transfer to surrounding farms.}, journal = {Harmful algae}, volume = {135}, number = {}, pages = {102631}, doi = {10.1016/j.hal.2024.102631}, pmid = {38830709}, issn = {1878-1470}, mesh = {*Microcystins/metabolism/analysis ; *Harmful Algal Bloom ; *Microcystis/physiology/growth &amp; development ; *Satellite Imagery ; *Environmental Monitoring/methods ; Cyanobacteria/physiology/growth &amp; development ; Indonesia ; Synechococcus/physiology ; Lakes/microbiology ; }, abstract = {Cyanobacterial harmful algal blooms (CyanoHABs) threaten public health and freshwater ecosystems worldwide. In this study, our main goal was to explore the dynamics of cyanobacterial blooms and how microcystins (MCs) move from the Lalla Takerkoust reservoir to the nearby farms. We used Landsat imagery, molecular analysis, collecting and analyzing physicochemical data, and assessing toxins using HPLC. Our investigation identified two cyanobacterial species responsible for the blooms: Microcystis sp. and Synechococcus sp. Our Microcystis strain produced three MC variants (MC-RR, MC-YR, and MC-LR), with MC-RR exhibiting the highest concentrations in dissolved and intracellular toxins. In contrast, our Synechococcus strain did not produce any detectable toxins. To validate our Normalized Difference Vegetation Index (NDVI) results, we utilized limnological data, including algal cell counts, and quantified MCs in freeze-dried Microcystis bloom samples collected from the reservoir. Our study revealed patterns and trends in cyanobacterial proliferation in the reservoir over 30 years and presented a historical map of the area of cyanobacterial infestation using the NDVI method. The study found that MC-LR accumulates near the water surface due to the buoyancy of Microcystis. The maximum concentration of MC-LR in the reservoir water was 160 µg L[-1]. In contrast, 4 km downstream of the reservoir, the concentration decreased by a factor of 5.39 to 29.63 µgL[-1], indicating a decrease in MC-LR concentration with increasing distance from the bloom source. Similarly, the MC-YR concentration decreased by a factor of 2.98 for the same distance. Interestingly, the MC distribution varied with depth, with MC-LR dominating at the water surface and MC-YR at the reservoir outlet at a water depth of 10 m. Our findings highlight the impact of nutrient concentrations, environmental factors, and transfer processes on bloom dynamics and MC distribution. We emphasize the need for effective management strategies to minimize toxin transfer and ensure public health and safety.}, }
@article {pmid38830413, year = {2024}, author = {Kerfahi, D and Dong, K and Tripathi, B and Adams, JM}, title = {Global comparison shows that soil bacterial communities in extreme pH soils are more structured by deterministic processes.}, journal = {The Science of the total environment}, volume = {942}, number = {}, pages = {173662}, doi = {10.1016/j.scitotenv.2024.173662}, pmid = {38830413}, issn = {1879-1026}, mesh = {*Soil Microbiology ; Hydrogen-Ion Concentration ; *Soil/chemistry ; *Bacteria ; Microbiota ; }, abstract = {A major aim of microbial ecology is the search for basic 'rules' that dominate variation in microbial communities. An earlier comparison of several soil successional series showed that pH explained variation in the relative importance of stochastic versus deterministic processes in bacterial communities. In neutral pH soils, bacterial communities were more strongly influenced by stochastic processes than in low or high pH soils. Here, we took a broad level approach to attempt a more definitive answer of whether soil pH dominates bacterial community structuring using the global database of 237 samples. The beta-NTI showed that at both a global and continental scale, samples with low pH were dominated by deterministic processes, while in samples at around neutral pH, stochastic processes dominated. At high pH, stochasticity dominated on the global scale, but on several continents, the beta-NTI showed determinism predominating. Overall, it appears that bacterial community structuring is strongly and predictably affected by pH, with the most consistent difference observed between determinism at low pH and stochasticity at neutral pH. There is a need for hypothesis testing to explain why this trend exists. It is possible that at low pH, there is a greater selection for consortia to exploit resources, which leads to more predictable, deterministic combinations of species co-occurring. Additionally, the high energy demands for homeostasis and the constraints from the lack of available nutrient resources may impose greater niche-based competition, resulting in more deterministic community structuring at low pH.}, }
@article {pmid38829422, year = {2024}, author = {Jurado, V and Martin-Pozas, T and Fernandez-Cortes, A and Calaforra, JM and Sanchez-Moral, S and Saiz-Jimenez, C}, title = {Gypsum Cave Biofilm Communities are Strongly Influenced by Bat- And Arthropod-Related Fungi.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {80}, pmid = {38829422}, issn = {1432-184X}, mesh = {*Caves/microbiology ; *Chiroptera/microbiology/physiology ; Animals ; *Biofilms ; *Fungi/classification/physiology/genetics/isolation &amp; purification ; *Arthropods/microbiology ; *Calcium Sulfate ; Spain ; Biodiversity ; Mycobiome ; Soil Microbiology ; }, abstract = {The Gypsum Karst of Sorbas, Almeria, southeast Spain, includes a few caves whose entrances are open and allow the entry and roosting of numerous bats. Caves are characterized by their diversity of gypsum speleothems, such as stalactites, coralloids, gypsum crusts, etc. Colored biofilms can be observed on the walls of most caves, among which the Covadura and C3 caves were studied. The objective was to determine the influence that bat mycobiomes may have on the fungal communities of biofilms. The results indicate that the fungi retrieved from white and yellow biofilms in Covadura Cave (Ascomycota, Mortierellomycota, Basidiomycota) showed a wide diversity, depending on their location, and were highly influenced by the bat population, the guano and the arthropods that thrive in the guano, while C3 Cave was more strongly influenced by soil- and arthropod-related fungi (Ascomycota, Mortierellomycota), due to the absence of roosting bats.}, }
@article {pmid38829379, year = {2024}, author = {Gwokyalya, R and Herren, JK and Weldon, CW and Ndlela, S and Gichuhi, J and Ongeso, N and Wairimu, AW and Ekesi, S and Mohamed, SA}, title = {Shaping the Microbial Landscape: Parasitoid-Driven Modifications of Bactrocera dorsalis Microbiota.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {81}, pmid = {38829379}, issn = {1432-184X}, mesh = {Animals ; *Tephritidae/microbiology/parasitology ; *Wasps/microbiology/physiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *Gastrointestinal Microbiome ; *Larva/microbiology/parasitology/growth &amp; development ; *RNA, Ribosomal, 16S/genetics ; Fungi/genetics/physiology ; Host-Parasite Interactions ; Microbiota ; Dysbiosis/microbiology/parasitology ; }, abstract = {Koinobiont endoparasitoids regulate the physiology of their hosts through altering host immuno-metabolic responses, processes which function in tandem to shape the composition of the microbiota of these hosts. Here, we employed 16S rRNA and ITS amplicon sequencing to investigate whether parasitization by the parasitoid wasps, Diachasmimorpha longicaudata (Ashmaed) (Hymenoptera: Braconidae) and Psyttalia cosyrae (Wilkinson) (Hymenoptera: Braconidae), induces gut dysbiosis and differentially alter the gut microbial (bacteria and fungi) communities of an important horticultural pest, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae). We further investigated the composition of bacterial communities of adult D. longicaudata and P. cosyrae to ascertain whether the adult parasitoids and parasitized host larvae share microbial taxa through transmission. We demonstrated that parasitism by D. longicaudata induced significant gut perturbations, resulting in the colonization and increased relative abundance of pathogenic gut bacteria. Some pathogenic bacteria like Stenotrophomonas and Morganella were detected in both the guts of D. longicaudata-parasitized B. dorsalis larvae and adult D. longicaudata wasps, suggesting a horizontal transfer of microbes from the parasitoid to the host. The bacterial community of P. cosyrae adult wasps was dominated by Arsenophonus nasoniae, whereas that of D. longicaudata adults was dominated by Paucibater spp. and Pseudomonas spp. Parasitization by either parasitoid wasp was associated with an overall reduction in fungal diversity and evenness. These findings indicate that unlike P. cosyrae which is avirulent to B. dorsalis, parasitization by D. longicaudata induces shifts in the gut bacteriome of B. dorsalis larvae to a pathobiont-dominated community. This mechanism possibly enhances its virulence against the pest, further supporting its candidacy as an effective biocontrol agent of this frugivorous tephritid fruit fly pest.}, }
@article {pmid38828615, year = {2024}, author = {Ramirez-Puebla, ST and Mark Welch, JL and Borisy, GG}, title = {Improved Visualization of Oral Microbial Consortia.}, journal = {Journal of dental research}, volume = {103}, number = {13}, pages = {1421-1427}, pmid = {38828615}, issn = {1544-0591}, support = {R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 GM126257/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biofilms ; Humans ; *Microbial Consortia ; *Tongue/microbiology ; In Situ Hybridization, Fluorescence/methods ; Actinomyces ; Streptococcus salivarius ; }, abstract = {Bacteria on the tongue dorsum (TD) form consortia tens to hundreds of microns in diameter organized around a core of epithelial cells. Whole-mount preparations have been instrumental in revealing their organization and specific microbial associations. However, their thickness and intricate 3-dimensional complexity present challenges for a comprehensive spatial analysis. To overcome these challenges, we employed a complementary approach: embedding in hydrophilic plastic followed by sectioning and postsectioning labeling. Samples were labeled by hybridization with multiplexed fluorescent oligonucleotide probes and visualized by spectral imaging and linear unmixing. Application of this strategy to TD biofilms improved the visualization of bacteria that were difficult to resolve in whole-mount imaging. Actinomyces, previously detected as patches, became resolved at the single-cell level. The filamentous taxa Leptotrichia and Lachnospiraceae, located at the core of the consortium, were regularly visualized whereas previously they were rarely detected when using whole mounts. Streptococcus salivarius, heterogeneously detected in whole mounts, were regularly and homogenously observed. Two-dimensional images provide valuable information about the organization of bacterial biofilms. However, they offer only a single plane of view for objects that can extend to hundreds of microns in thickness, and information obtained from such images may not always reflect the complexity of a 3-dimensional object. We combined serial physical sectioning with optical sectioning to facilitate the 3-dimensional reconstruction of consortia, spanning over 100 µm in thickness. Our work showcases the use of hydrophilic plastic embedding and sectioning for examining the structure of TD biofilms through spectral imaging fluorescence in situ hybridization. The result was improved visualization of important members of the human oral microbiome. This technique serves as a complementary method to the previously employed whole-mount analysis, offering its own set of advantages and limitations. Addressing the spatial complexity of bacterial consortia demands a multifaceted approach for a comprehensive and effective analysis.}, }
@article {pmid38827504, year = {2024}, author = {Gupta, VVSR and Tiedje, JM}, title = {Ranking environmental and edaphic attributes driving soil microbial community structure and activity with special attention to spatial and temporal scales.}, journal = {mLife}, volume = {3}, number = {1}, pages = {21-41}, pmid = {38827504}, issn = {2770-100X}, abstract = {The incredibly complex soil microbial communities at small scales make their analysis and identification of reasons for the observed structures challenging. Microbial community structure is mainly a result of the inoculum (dispersal), the selective advantages of those organisms under the habitat-based environmental attributes, and the ability of those colonizers to sustain themselves over time. Since soil is protective, and its microbial inhabitants have long adapted to varied soil conditions, significant portions of the soil microbial community structure are likely stable. Hence, a substantial portion of the community will not correlate to often measured soil attributes. We suggest that the drivers be ranked on the basis of their importance to the fundamental needs of the microbes: (i) those that supply energy, i.e., organic carbon and electron acceptors; (ii) environmental effectors or stressors, i.e., pH, salt, drought, and toxic chemicals; (iii) macro-organism associations, i.e., plants and their seasonality, animals and their fecal matter, and soil fauna; and (iv) nutrients, in order, N, P, and probably of lesser importance, other micronutrients, and metals. The relevance of drivers also varies with spatial and time scales, for example, aggregate to field to regional, and persistent to dynamic populations to transcripts, and with the extent of phylogenetic difference, hence phenotypic differences in organismal groups. We present a summary matrix to provide guidance on which drivers are important for particular studies, with special emphasis on a wide range of spatial and temporal scales, and illustrate this with genomic and population (rRNA gene) data from selected studies.}, }
@article {pmid38827283, year = {2024}, author = {Viladomat Jasso, M and García-Ulloa, M and Zapata-Peñasco, I and Eguiarte, LE and Souza, V}, title = {Metagenomic insight into taxonomic composition, environmental filtering and functional redundancy for shaping worldwide modern non-lithifying microbial mats.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17412}, pmid = {38827283}, issn = {2167-8359}, mesh = {*Metagenomics ; Archaea/genetics/classification ; Mexico ; Bacteria/genetics/classification ; Ecosystem ; Microbiota/genetics ; Metagenome ; Geologic Sediments/microbiology ; }, abstract = {Modern microbial mats are relictual communities mostly found in extreme environments worldwide. Despite their significance as representatives of the ancestral Earth and their important roles in biogeochemical cycling, research on microbial mats has largely been localized, focusing on site-specific descriptions and environmental change experiments. Here, we present a global comparative analysis of non-lithifying microbial mats, integrating environmental measurements with metagenomic data from 62 samples across eight sites, including two new samples from the recently discovered Archaean Domes from Cuatro Ciénegas, Mexico. Our results revealed a notable influence of environmental filtering on both taxonomic and functional compositions of microbial mats. Functional redundancy appears to confer resilience to mats, with essential metabolic pathways conserved across diverse and highly contrasting habitats. We identified six highly correlated clusters of taxa performing similar ecological functions, suggesting niche partitioning and functional specialization as key mechanisms shaping community structure. Our findings provide insights into the ecological principles governing microbial mats, and lay the foundation for future research elucidating the intricate interplay between environmental factors and microbial community dynamics.}, }
@article {pmid38825932, year = {2024}, author = {Li, SQ and Song, Y and Zhou, F and Chen, MY and Chen, LG and Zhou, JP}, title = {[Primary biliary cholangitis and autoimmune hepatitis overlap syndrome complicated with skin and soft tissue infection of lower limb during corticosteroids treatment: a case report].}, journal = {Zhonghua nei ke za zhi}, volume = {63}, number = {6}, pages = {618-620}, doi = {10.3760/cma.j.cn112138-20231030-00263}, pmid = {38825932}, issn = {0578-1426}, mesh = {Humans ; Adrenal Cortex Hormones/adverse effects ; Cholangitis/chemically induced ; *Hepatitis, Autoimmune/etiology/drug therapy ; Liver Cirrhosis, Biliary/drug therapy/complications ; Lower Extremity ; }, }
@article {pmid38820701, year = {2024}, author = {Wang, Z and Fu, X and Kuramae, EE}, title = {Insight into farming native microbiome by bioinoculant in soil-plant system.}, journal = {Microbiological research}, volume = {285}, number = {}, pages = {127776}, doi = {10.1016/j.micres.2024.127776}, pmid = {38820701}, issn = {1618-0623}, mesh = {*Soil Microbiology ; *Microbiota/physiology ; *Soil/chemistry ; *Agriculture/methods ; Bacteria/classification/metabolism/isolation &amp; purification/genetics ; Crops, Agricultural/microbiology ; Plants/microbiology ; Microbial Interactions ; }, abstract = {Applying beneficial microorganisms (BM) as bioinoculants presents a promising soil-amendment strategy while impacting the native microbiome, which jointly alters soil-plant performance. Leveraging the untapped potential of native microbiomes alongside bioinoculants may enable farmers to sustainably regulate soil-plant systems via natural bioresources. This review synthesizes literature on native microbiome responses to BMs and their interactive effects on soil and plant performance. We highlight that native microbiomes harbor both microbial "helpers" that can improve soil fertility and plant productivity, as well as "inhibitors" that hinder these benefits. To harness the full potential of resident microbiome, it is crucial to elucidate their intricate synergistic and antagonistic interplays with introduced BMs and clarify the conditions that facilitate durable BM-microbiome synergies. Hence, we indicate current challenges in predicting these complex microbial interactions and propose corresponding strategies for microbiome breeding via BM bioinoculant. Overall, fully realizing the potential of BMs requires clarifying their interactions with native soil microbiomes and judiciously engineering microbiome to harness helpful microbes already present within agroecosystems.}, }
@article {pmid38819559, year = {2024}, author = {Sanchez, FB and Sato Guima, SE and Setubal, JC}, title = {How to Obtain and Compare Metagenome-Assembled Genomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2802}, number = {}, pages = {135-163}, pmid = {38819559}, issn = {1940-6029}, mesh = {*Metagenome/genetics ; *Metagenomics/methods ; Software ; Computational Biology/methods ; Databases, Genetic ; Sequence Analysis, DNA/methods ; Genome, Bacterial ; }, abstract = {Metagenome-assembled genomes, or MAGs, are genomes retrieved from metagenome datasets. In the vast majority of cases, MAGs are genomes from prokaryotic species that have not been isolated or cultivated in the lab. They, therefore, provide us with information on these species that are impossible to obtain otherwise, at least until new cultivation methods are devised. Thanks to improvements and cost reductions of DNA sequencing technologies and growing interest in microbial ecology, the rise in number of MAGs in genome repositories has been exponential. This chapter covers the basics of MAG retrieval and processing and provides a practical step-by-step guide using a real dataset and state-of-the-art tools for MAG analysis and comparison.}, }
@article {pmid38819147, year = {2024}, author = {Sumner, DY}, title = {Oxygenation of Earth's atmosphere induced metabolic and ecologic transformations recorded in the Lomagundi-Jatuli carbon isotopic excursion.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {6}, pages = {e0009324}, pmid = {38819147}, issn = {1098-5336}, mesh = {*Earth, Planet ; *Atmosphere/chemistry ; *Carbon Isotopes/analysis/metabolism ; Oxygen/metabolism ; Methane/metabolism ; Bacteria/metabolism/genetics/classification ; Cyanobacteria/metabolism/genetics ; }, abstract = {The oxygenation of Earth's atmosphere represents the quintessential transformation of a planetary surface by microbial processes. In turn, atmospheric oxygenation transformed metabolic evolution; molecular clock models indicate the diversification and ecological expansion of respiratory metabolisms in the several hundred million years following atmospheric oxygenation. Across this same interval, the geological record preserves [13]C enrichment in some carbonate rocks, called the Lomagundi-Jatuli excursion (LJE). By combining data from geologic and genomic records, a self-consistent metabolic evolution model emerges for the LJE. First, fermentation and methanogenesis were major processes remineralizing organic carbon before atmospheric oxygenation. Once an ozone layer formed, shallow water and exposed environments were shielded from UVB/C radiation, allowing the expansion of cyanobacterial primary productivity. High primary productivity and methanogenesis led to preferential removal of [12]C into organic carbon and CH4. Extreme and variable [13]C enrichments in carbonates were caused by [13]C-depleted CH4 loss to the atmosphere. Through time, aerobic respiration diversified and became ecologically widespread, as did other new metabolisms. Respiration displaced fermentation and methanogenesis as the dominant organic matter remineralization processes. As CH4 loss slowed, dissolved inorganic carbon in shallow environments was no longer highly [13]C enriched. Thus, the loss of extreme [13]C enrichments in carbonates marks the establishment of a new microbial mat ecosystem structure, one dominated by respiratory processes distributed along steep redox gradients. These gradients allowed the exchange of metabolic by-products among metabolically diverse organisms, providing novel metabolic opportunities. Thus, the microbially induced oxygenation of Earth's atmosphere led to the transformation of microbial ecosystems, an archetypal example of planetary microbiology.IMPORTANCEThe oxygenation of Earth's atmosphere represents the most extensive known chemical transformation of a planetary surface by microbial processes. In turn, atmospheric oxygenation transformed metabolic evolution by providing oxidants independent of the sites of photosynthesis. Thus, the evolutionary changes during this interval and their effects on planetary-scale biogeochemical cycles are fundamental to our understanding of the interdependencies among genomes, organisms, ecosystems, elemental cycles, and Earth's surface chemistry through time.}, }
@article {pmid38819146, year = {2024}, author = {Tang, S and Wu, G and Liu, Y and Xue, B and Zhang, S and Zhang, W and Jia, Y and Xie, Q and Liang, C and Wang, L and Heng, H and Wei, W and Shi, X and Hu, Y and Yang, J and Zhao, L and Wang, X and Zhao, L and Yuan, H}, title = {Guild-level signature of gut microbiome for diabetic kidney disease.}, journal = {mBio}, volume = {15}, number = {7}, pages = {e0073524}, pmid = {38819146}, issn = {2150-7511}, support = {P30 ES005022/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetic Nephropathies/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Female ; *Feces/microbiology ; Middle Aged ; *Metagenomics ; Adult ; Aged ; *Metagenome ; }, abstract = {UNLABELLED: Current microbiome signatures for chronic diseases such as diabetic kidney disease (DKD) are mainly based on low-resolution taxa such as genus or phyla and are often inconsistent among studies. In microbial ecosystems, bacterial functions are strain specific, and taxonomically different bacteria tend to form co-abundance functional groups called guilds. Here, we identified guild-level signatures for DKD by performing in-depth metagenomic sequencing and conducting genome-centric and guild-based analysis on fecal samples from 116 DKD patients and 91 healthy subjects. Redundancy analysis on 1,543 high-quality metagenome-assembled genomes (HQMAGs) identified 54 HQMAGs that were differentially distributed among the young healthy control group, elderly healthy control group, early-stage DKD patients (EDG), and late-stage DKD patients (LDG). Co-abundance network analysis classified the 54 HQMAGs into two guilds. Compared to guild 2, guild 1 contained more short-chain fatty acid biosynthesis genes and fewer genes encoding uremic toxin indole biosynthesis, antibiotic resistance, and virulence factors. Guild indices, derived from the total abundance of guild members and their diversity, delineated DKD patients from healthy subjects and between different severities of DKD. Age-adjusted partial Spearman correlation analysis showed that the guild indices were correlated with DKD disease progression and with risk indicators of poor prognosis. We further validated that the random forest classification model established with the 54 HQMAGs was also applicable for classifying patients with end-stage renal disease and healthy subjects in an independent data set. Therefore, this genome-level, guild-based microbial analysis strategy may identify DKD patients with different severity at an earlier stage to guide clinical interventions.<br><br>IMPORTANCE: Traditionally, microbiome research has been constrained by the reliance on taxonomic classifications that may not reflect the functional dynamics or the ecological interactions within microbial communities. By transcending these limitations with a genome-centric and guild-based analysis, our study sheds light on the intricate and specific interactions between microbial strains and diabetic kidney disease (DKD). We have unveiled two distinct microbial guilds with opposite influences on host health, which may redefine our understanding of microbial contributions to disease progression. The implications of our findings extend beyond mere association, providing potential pathways for intervention and opening new avenues for patient stratification in clinical settings. This work paves the way for a paradigm shift in microbiome research in DKD and potentially other chronic kidney diseases, from a focus on taxonomy to a more nuanced view of microbial ecology and function that is more closely aligned with clinical outcomes.}, }
@article {pmid38818274, year = {2023}, author = {Fu, Y and Dou, Q and Smalla, K and Wang, Y and Johnson, TA and Brandt, KK and Mei, Z and Liao, M and Hashsham, SA and Schäffer, A and Smidt, H and Zhang, T and Li, H and Stedtfeld, R and Sheng, H and Chai, B and Virta, M and Jiang, X and Wang, F and Zhu, YG and Tiedje, JM}, title = {Gut microbiota research nexus: One Health relationship between human, animal, and environmental resistomes.}, journal = {mLife}, volume = {2}, number = {4}, pages = {350-364}, pmid = {38818274}, issn = {2770-100X}, abstract = {The emergence and rapid spread of antimicrobial resistance is of global public health concern. The gut microbiota harboring diverse commensal and opportunistic bacteria that can acquire resistance via horizontal and vertical gene transfers is considered an important reservoir and sink of antibiotic resistance genes (ARGs). In this review, we describe the reservoirs of gut ARGs and their dynamics in both animals and humans, use the One Health perspective to track the transmission of ARG-containing bacteria between humans, animals, and the environment, and assess the impact of antimicrobial resistance on human health and socioeconomic development. The gut resistome can evolve in an environment subject to various selective pressures, including antibiotic administration and environmental and lifestyle factors (e.g., diet, age, gender, and living conditions), and interventions through probiotics. Strategies to reduce the abundance of clinically relevant antibiotic-resistant bacteria and their resistance determinants in various environmental niches are needed to ensure the mitigation of acquired antibiotic resistance. With the help of effective measures taken at the national, local, personal, and intestinal management, it will also result in preventing or minimizing the spread of infectious diseases. This review aims to improve our understanding of the correlations between intestinal microbiota and antimicrobial resistance and provide a basis for the development of management strategies to mitigate the antimicrobial resistance crisis.}, }
@article {pmid38818270, year = {2023}, author = {Liu, J and Xu, G and Zhao, S and He, J}, title = {Resilience and functional redundancy of methanogenic digestion microbiome safeguard recovery of methanogenesis activity under the stress induced by microplastics.}, journal = {mLife}, volume = {2}, number = {4}, pages = {378-388}, pmid = {38818270}, issn = {2770-100X}, abstract = {Microplastics and nanoplastics are emerging pollutants that substantially influence biological element cycling in natural ecosystems. Plastics are also prevalent in sewage, and they accumulate in waste-activated sludge (WAS). However, the impacts of plastics on the methanogenic digestion of WAS and the underpinning microbiome remain underexplored, particularly during long-term operation. In this study, we found that short-term exposure to individual microplastics and nanoplastics (polyethylene, polyvinyl chloride, polystyrene, and polylactic acid) at a low concentration (10 particles/g sludge) slightly enhanced methanogenesis by 2.1%-9.0%, whereas higher levels (30-200 particles/g sludge) suppressed methanogenesis by 15.2%-30.1%. Notably, the coexistence of multiple plastics, particularly at low concentrations, showed synergistic suppression of methanogenesis. Unexpectedly, methanogenesis activity completely recovered after long-term exposure to plastics, despite obvious suppression of methanogenesis by initial plastic exposure. The inhibition of methanogenesis by plastics could be attributed to the stimulated generation of reactive oxygen species. The stress induced by plastics dramatically decreased the relative abundance of methanogens but showed marginal influence on putative hydrolytic and fermentation populations. Nonetheless, the digestion sludge microbiome exhibited resilience and functional redundancy, contributing to the recovery of methanogenesis during the long-term operation of digesters. Plastics also increased the complexity, modularity, and negative interaction ratios of digestion sludge microbiome networks, but their influence on community assembly varied. Interestingly, a unique plastisphere was observed, the networks and assembly of which were distinct from the sludge microbiome. Collectively, the comprehensive evaluation of the influence of microplastics and nanoplastics on methanogenic digestion, together with the novel ecological insights, contribute to better understanding and manipulating this engineered ecosystem in the face of increasing plastic pollution.}, }
@article {pmid38817815, year = {2023}, author = {Wu, L and Yang, Y and Ning, D and Gao, Q and Yin, H and Xiao, N and Zhou, BY and Chen, S and He, Q and Zhou, J}, title = {Assessing mechanisms for microbial taxa and community dynamics using process models.}, journal = {mLife}, volume = {2}, number = {3}, pages = {239-252}, pmid = {38817815}, issn = {2770-100X}, abstract = {Disentangling the assembly mechanisms controlling community composition, structure, distribution, functions, and dynamics is a central issue in ecology. Although various approaches have been proposed to examine community assembly mechanisms, quantitative characterization is challenging, particularly in microbial ecology. Here, we present a novel approach for quantitatively delineating community assembly mechanisms by combining the consumer-resource model with a neutral model in stochastic differential equations. Using time-series data from anaerobic bioreactors that target microbial 16S rRNA genes, we tested the applicability of three ecological models: the consumer-resource model, the neutral model, and the combined model. Our results revealed that model performances varied substantially as a function of population abundance and/or process conditions. The combined model performed best for abundant taxa in the treatment bioreactors where process conditions were manipulated. In contrast, the neutral model showed the best performance for rare taxa. Our analysis further indicated that immigration rates decreased with taxa abundance and competitions between taxa were strongly correlated with phylogeny, but within a certain phylogenetic distance only. The determinism underlying taxa and community dynamics were quantitatively assessed, showing greater determinism in the treatment bioreactors that aligned with the subsequent abnormal system functioning. Given its mechanistic basis, the framework developed here is expected to be potentially applicable beyond microbial ecology.}, }
@article {pmid38816803, year = {2024}, author = {Saeed, S and Ullah, S and Amin, F and Al-Hawadi, JS and Okla, MK and Alaraidh, IA and AbdElgawad, H and Liu, K and Harrison, MT and Saud, S and Hassan, S and Nawaz, T and Zhu, M and Liu, H and Khan, MA and Fahad, S}, title = {Salicylic acid and Tocopherol improve wheat (Triticum aestivum L.) Physio-biochemical and agronomic features grown in deep sowing stress: a way forward towards sustainable production.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {477}, pmid = {38816803}, issn = {1471-2229}, mesh = {*Triticum/growth &amp; development/metabolism/drug effects ; *Salicylic Acid/pharmacology/metabolism ; *Tocopherols/metabolism ; *Germination/drug effects ; Seeds/drug effects/growth &amp; development ; Antioxidants/metabolism ; Stress, Physiological ; Sustainable Development ; Chlorophyll/metabolism ; }, abstract = {BACKGROUND: The rate of germination and other physiological characteristics of seeds that are germinating are impacted by deep sowing. Based on the results of earlier studies, conclusions were drawn that deep sowing altered the physio-biochemical and agronomic characteristics of wheat (Triticum aestivum L.).<br><br>RESULTS: In this study, seeds of wheat were sown at 2 (control) and 6&#xa0;cm depth and the impact of exogenously applied salicylic acid and tocopherol (Vitamin-E) on its physio-biochemical and agronomic features was assessed. As a result, seeds grown at 2&#xa0;cm depth witnessed an increase in mean germination time, germination percentage, germination rate index, germination energy, and seed vigor index. In contrast, 6&#xa0;cm deep sowing resulted in negatively affecting all the aforementioned agronomic characteristics. In addition, deep planting led to a rise in MDA, glutathione reductase, and antioxidants enzymes including APX, POD, and SOD concentration. Moreover, the concentration of chlorophyll a, b, carotenoids, proline, protein, sugar, hydrogen peroxide, and agronomic attributes was boosted significantly with exogenously applied salicylic acid and tocopherol under deep sowing stress.<br><br>CONCLUSIONS: The results of the study showed that the depth of seed sowing has an impact on agronomic and physio-biochemical characteristics and that the negative effects of deep sowing stress can be reduced by applying salicylic acid and tocopherol to the leaves.}, }
@article {pmid38816227, year = {2024}, author = {Carrillo-Barragan, P}, title = {Clean your own house first: integrating sustainability into microbiology labs.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {7}, pages = {}, pmid = {38816227}, issn = {1574-6941}, support = {//University of Basel/ ; }, mesh = {*Laboratories ; Environmental Microbiology ; Sustainable Development ; Microbiology ; Conservation of Natural Resources ; }, abstract = {Microbiology laboratories are pivotal hubs for exploring the potential of microorganisms and addressing global challenges. Particularly, Environmental Microbiology facilities hold substantial influence in advancing knowledge and capabilities crucial for achieving the United Nations Sustainable Development Goals. This raises the imperative of integrating sustainable practices to mitigate the environmental impact of research activities and foster a culture of responsibility. Such an approach not only aligns with global sustainability objectives but also catalyses innovative, eco-conscious methodologies in scientific research aimed at tackling pressing environmental issues. Concerns regarding the environmental footprint of laboratory practices have stimulated innovative improvements within the scientific community, ranging from resource-efficient initiatives to the management of essential commodities like water and energy. This perspective discusses specific areas where microbiology laboratories can enhance their sustainability efforts, drawing on reports and case studies of pioneering groups. Additionally, it explores potential collaborators to support these endeavours and emphasises the pivotal role of early career researchers in driving this transition. By initiating discussions and sparking curiosity within the environmental microbial community, this commentary seeks to propel the microbial ecology field toward a greener future, starting from within the laboratory environment.}, }
@article {pmid38814337, year = {2024}, author = {Filek, K and Vuković, BB and Žižek, M and Kanjer, L and Trotta, A and Di Bello, A and Corrente, M and Bosak, S}, title = {Loggerhead Sea Turtles as Hosts of Diverse Bacterial and Fungal Communities.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {79}, pmid = {38814337}, issn = {1432-184X}, support = {UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; }, mesh = {Animals ; *Turtles/microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; Microbiota ; Cloaca/microbiology ; Mycobiome ; Biodiversity ; Gastrointestinal Microbiome ; Biofilms ; }, abstract = {Research on microbial communities associated with wild animals provides a valuable reservoir of knowledge that could be used for enhancing their rehabilitation and conservation. The loggerhead sea turtle (Caretta caretta) is a globally distributed species with its Mediterranean population categorized as least concern according to the IUCN Red List of Threatened Species as a result of robust conservation efforts. In our study, we aimed to further understand their biology in relation to their associated microorganisms. We investigated epi- and endozoic bacterial and endozoic fungal communities of cloaca, oral mucosa, carapace biofilm. Samples obtained from 18 juvenile, subadult, and adult turtles as well as 8 respective enclosures, over a 3-year period, were analysed by amplicon sequencing of 16S rRNA gene and ITS2 region of nuclear ribosomal gene. Our results reveal a trend of decreasing diversity of distal gut bacterial communities with the age of turtles. Notably, Tenacibaculum species show higher relative abundance in juveniles than in adults. Differential abundances of taxa identified as Tenacibaculum, Moraxellaceae, Cardiobacteriaceae, and Campylobacter were observed in both cloacal and oral samples in addition to having distinct microbial compositions with Halioglobus taxa present only in oral samples. Fungal communities in loggerheads' cloaca were diverse and varied significantly among individuals, differing from those of tank water. Our findings expand the known microbial diversity repertoire of loggerhead turtles, highlighting interesting taxa specific to individual body sites. This study provides a comprehensive view of the loggerhead sea turtle bacterial microbiota and marks the first report of distal gut fungal communities that contributes to establishing a baseline understanding of loggerhead sea turtle holobiont.}, }
@article {pmid38814057, year = {2024}, author = {Chen, M and Grégoire, DS and Bain, JG and Blowes, DW and Hug, LA}, title = {Legacy copper/nickel mine tailings potentially harbor novel iron/sulfur cycling microorganisms within highly variable communities.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {6}, pages = {e0014324}, pmid = {38814057}, issn = {1098-5336}, support = {ORF-RE09-061//Ontario Research Fund - Research Excellence/ ; //Canada Research Chairs (Chaires de recherche du Canada)/ ; //Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; }, mesh = {*Mining ; *Sulfur/metabolism ; *Iron/metabolism ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; *Copper/metabolism/analysis ; *Nickel/metabolism ; Ontario ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Biodegradation, Environmental ; }, abstract = {The oxidation of sulfide-bearing mine tailings catalyzed by acidophilic iron and sulfur-oxidizing bacteria releases toxic metals and other contaminants into soil and groundwater as acid mine drainage. Understanding the environmental variables that control the community structure and metabolic activity of microbes indigenous to tailings (especially the abiotic stressors of low pH and high dissolved metal content) is crucial to developing sustainable bioremediation strategies. We determined the microbial community composition along two continuous vertical gradients of Cu/Ni mine tailings at each of two tailings impoundments near Sudbury, Ontario. 16S rRNA amplicon data showed high variability in community diversity and composition between locations, as well as at different depths within each location. A temporal comparison for one tailings location showed low fluctuation in microbial communities across 2 years. Differences in community composition correlated most strongly with pore-water pH, Eh, alkalinity, salinity, and the concentration of several dissolved metals (including iron, but not copper or nickel). The relative abundances of individual genera differed in their degrees of correlation with geochemical factors. Several abundant lineages present at these locations have not previously been associated with mine tailings environments, including novel species predicted to be involved in iron and sulfur cycling.IMPORTANCEMine tailings represent a significant threat to North American freshwater, with legacy tailings areas generating acid mine drainage (AMD) that contaminates rivers, lakes, and aquifers. Microbial activity accelerates AMD formation through oxidative metabolic processes but may also ameliorate acidic tailings by promoting secondary mineral precipitation and immobilizing dissolved metals. Tailings exhibit high geochemical variation within and between mine sites and may harbor many novel extremophiles adapted to high concentrations of toxic metals. Characterizing the unique microbiomes associated with tailing environments is key to identifying consortia that may be used as the foundation for innovative mine-waste bioremediation strategies. We provide an in-depth analysis of microbial diversity at four copper/nickel mine tailings impoundments, describe how communities (and individual lineages) differ based on geochemical gradients, predict organisms involved in AMD transformations, and identify taxonomically novel groups present that have not previously been observed in mine tailings.}, }
@article {pmid38812552, year = {2024}, author = {Zhu, W and Chang, L and Zhang, M and Chen, Q and Sui, L and Shen, C and Jiang, J}, title = {Microbial diversity in mountain-dwelling amphibians: The combined effects of host and climatic factors.}, journal = {iScience}, volume = {27}, number = {6}, pages = {109907}, pmid = {38812552}, issn = {2589-0042}, abstract = {Comprehending the determinants of host-associated microbiota is pivotal in microbial ecology. Yet, the links between climatic factors and variations in host-associated microbiota necessitate further clarification. Mountain-dwelling amphibians, with limited dispersal abilities, serve as valuable models for addressing these questions. Our study, using 126 amphibian-associated microbial samples (64 gut and 62 skin) and 101 environmental microbial samples (51 soil and 50 water) from the eastern Tibetan Plateau, revealed host factors as primary drivers of the variations in host-associated microbiota. However, climatic factors contributed to additional variations in gut microbial beta-diversity and skin microbial function. Water microbiota were identified as a significant contributor to the amphibian-associated microbiomes, with their climate-driven variations mediating an indirect association between the variations in climatic factors and host-associated microbiota. These findings extend our understanding of the assembly of host-associated microbiota in amphibians, emphasizing the significance of microbiota in evaluating the impact of climate change on animals.}, }
@article {pmid38812371, year = {2024}, author = {Liu, J and Wu, Y and Zhang, W and Fahad, S and Qiu, Z and Zhu 朱, M&#x58a8;}, title = {Podosphaera xanthii Causing Powdery Mildew on Salvia farinacea in Central China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-03-24-0591-PDN}, pmid = {38812371}, issn = {0191-2917}, abstract = {Salvia farinacea, commonly referred as mealycup sage, is a perennial herbaceous plant belonging to the Salvia genus of the Lamiaceae family. It originates from the Mediterranean region, North America, and Europe and is globally cultivated due to its appealing and captivating flowers. Moreover, mealycup sage is utilized as traditional Chinese medicinal plant for treatment of cardiovascular diseases (Li et al. 2018). In October 2023, powdery mildew-like symptoms were observed on Salvia farinacea plants cultivated in a garden located in Xinxiang City, Henan Province, China (113.93, 35.29). The leaves were covered with white and thin masses of mycelia, conidiophores and conidia of the fungus. About 100 plants were checked and 90 % were infected. There were a large number of white colonies with irregular or continuous round lesions on the adaxial and abaxial surfaces of the leaves, covering approximately 80% of the leaf area. The slightly or straight curved conidiophores (n = 30) were 46 to 145× 8 to 11 μm in size and consisted of foot cells, shorter cells and conidia. The ellipsoidal to oval conidia (n = 30), containing fibrosin bodies, were 24 to 35 × 12 to 19 μm in size and had a length/width ratio of 1.8 to 2.1. No chasmothecia were observed on leaves. These morphological features were consistent with those of Podosphaera xanthii (Braun and Cook 2012). Following the previously described method (White et al. 1990; Bradshaw et al. 2022; Zhu et al. 2022a), the sequences of ITS and Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) regions were amplified with specific primers ITS1/ITS4 (ITS1 5'-TCCGTAGGTGAACCTGCGG-3' ; ITS4 5'-TCCTCCGCTTATTGATATGC-3') and PMGAPDH1/PMGAPDH3R (PMGAPDH1 5'-GGAATGGCTATGCGTGTACC-3'; PMGAPDH3R 5'-CCCCATTCGTTGTCGTACCATG-3'), and the resulting sequences were uploaded in GenBank (Accession No. OR761885 and PP236082, respectively). BLASTn analysis showed that the sequence shared 560/565 (99%) and 272/272 (100%) homology with P. xanthii (MW301281) on Impatiens balsamina (Zhu et al. 2022b) and with P. xanthii (ON075658) on Cucumis melo (Bradshaw et al. 2022), respectively. The phylogenetic analysis clearly illustrated that the collected isolate of P. xanthii clustered in the same clade. The pathogenicity was tested according to the method previously described (Zhu et al. 2021). The fungus was inoculated onto the leaf surfaces of three healthy plants by blowing conidia from infected leaves with pressurized air. Non-inoculated plants were treated as control. Both the control and inoculated plants were separately placed in growth chambers under 60% humidity; light/dark, 16 h/8 h; and a temperature of 18°C. After a period of 12-15 days, the leaves of the inoculated plants exhibited signs of powdery mildew, whereas the control group remained unaffected. Therefore, the fungal pathogen was identified and confirmed as P. xanthii (isolate PXSF202310). Previously, P. xanthii was reported on Impatiens balsamina and S. farinacea from China and Korea (Zhu et al. 2021; Choi et al. 2022). As far as we know, this is the first documentation of P. xanthii on S. farinacea in central China. The presence of P. xanthii can lead to a deterioration in plant health and stunted growth, thereby negatively impacting both the decorative and medicinal value of S. farinacea. The recognition of P. xanthii on S. farinacea enhances our comprehension of this pathogen hosts and provides fundamental information for forthcoming disease control studies.}, }
@article {pmid38812269, year = {2024}, author = {Przybylska, MS and Violle, C and Vile, D and Scheepens, JF and Munoz, F and Tenllado, &#xc1; and Vinyeta, M and Le Roux, X and Vasseur, F}, title = {Can plants build their niche through modulation of soil microbial activities linked with nitrogen cycling? A test with Arabidopsis thaliana.}, journal = {The New phytologist}, volume = {243}, number = {2}, pages = {620-635}, doi = {10.1111/nph.19870}, pmid = {38812269}, issn = {1469-8137}, support = {ANR-17-CE02-0018-01//Agence Nationale de la Recherche/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft/ ; ERC-StG-2014-639706-CONSTRAINTS/ERC_/European Research Council/International ; ERC-StG-2020-949843/ERC_/European Research Council/International ; }, mesh = {*Arabidopsis/genetics/metabolism/microbiology ; *Nitrogen Cycle ; *Soil Microbiology ; *Biomass ; Nitrogen/metabolism ; Soil/chemistry ; Genotype ; Nitrification ; Denitrification ; Ecosystem ; }, abstract = {In natural systems, different plant species have been shown to modulate specific nitrogen (N) cycling processes so as to meet their N demand, thereby potentially influencing their own niche. This phenomenon might go beyond plant interactions with symbiotic microorganisms and affect the much less explored plant interactions with free-living microorganisms involved in soil N cycling, such as nitrifiers and denitrifiers. Here, we investigated variability in the modulation of soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively), and their ratio (NEA : DEA), across 193 Arabidopsis thaliana accessions. We studied the genetic and environmental determinants of such plant-soil interactions, and effects on plant biomass production in the next generation. We found that NEA, DEA, and NEA : DEA varied c. 30-, 15- and 60-fold, respectively, among A. thaliana genotypes and were related to genes linked with stress response, flowering, and nitrate nutrition, as well as to soil parameters at the geographic origin of the analysed genotypes. Moreover, plant-mediated N cycling activities correlated with the aboveground biomass of next-generation plants in home vs away nonautoclaved soil, suggesting a transgenerational impact of soil biotic conditioning on plant performance. Altogether, these findings suggest that nutrient-based plant niche construction may be much more widespread than previously thought.}, }
@article {pmid38811807, year = {2024}, author = {Eliette, AS and Elodie, B and Arnaud, M and Tiffany, R and Aymé, S and Pascal, P}, title = {Idiosyncratic invasion trajectories of human bacterial pathogens facing temperature disturbances in soil microbial communities.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {12375}, pmid = {38811807}, issn = {2045-2322}, support = {773830//European Commission One Health EJP/ ; 773830//European Commission One Health EJP/ ; 773830//European Commission One Health EJP/ ; }, mesh = {*Soil Microbiology ; *Listeria monocytogenes/physiology ; Humans ; *Microbiota ; Klebsiella pneumoniae/physiology ; Temperature ; Biodiversity ; }, abstract = {Current knowledge about effects of disturbance on the fate of invaders in complex microbial ecosystems is still in its infancy. In order to investigate this issue, we compared the fate of Klebsiella pneumoniae (Kp) and Listeria monocytogenes (Lm) in soil microcosms. We then used environmental disturbances (freeze-thaw or heat cycles) to compare the fate of both invaders and manipulate soil microbial diversity. Population dynamics of the two pathogens was assessed over 50 days of invasion while microbial diversity was measured at times 0, 20 and 40 days. The outcome of invasion was strain-dependent and the response of the two invaders to disturbance differed. Resistance to Kp invasion was higher under the conditions where resident microbial diversity was the highest while a significant drop of diversity was linked to a higher persistence. In contrast, Lm faced stronger resistance to invasion in heat-treated microcosms where diversity was the lowest. Our results show that diversity is not a universal proxy of resistance to microbial invasion, indicating the need to properly assess other intrinsic properties of the invader, such as its metabolic repertoire, or the array of interactions between the invader and resident communities.}, }
@article {pmid38810265, year = {2024}, author = {Li, C and Wang, L and Tong, C and Li, H and Qin, Z and Zeng, X and Chang, Y and Li, M and Yang, Q}, title = {Molecular Insights into the Defense of Dioscorea opposita Cultivar Tiegun Callus Against Pathogenic and Endophytic Fungal Infection Through Transcriptome Analysis.}, journal = {Phytopathology}, volume = {114}, number = {8}, pages = {1893-1903}, doi = {10.1094/PHYTO-04-24-0125-R}, pmid = {38810265}, issn = {0031-949X}, mesh = {*Dioscorea/microbiology/genetics ; *Alternaria/physiology/pathogenicity ; *Plant Diseases/microbiology/immunology ; *Endophytes/physiology/genetics ; Penicillium/genetics/physiology/pathogenicity ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Transcriptome ; }, abstract = {Dioscorea opposita cultivar Tiegun is an economically important crop with high nutritional and medicinal value. Plants can activate complex and diverse defense mechanisms after infection by pathogenic fungi. Moreover, endophytic fungi can also trigger the plant immune system to resist pathogen invasion. However, the study of the effects of endophytic fungi on plant infection lags far behind that of pathogenic fungi, and the underlying mechanism is not fully understood. Here, the black spot pathogen Alternaria alternata and the endophytic fungus Penicillium halotolerans of Tiegun were identified and used to infect calli. The results showed that A. alternata could cause more severe membrane lipid peroxidation, whereas P. halotolerans could rapidly increase the activity of the plant antioxidant enzymes superoxide dismutase, peroxidase, and catalase; thus, the degree of damage to the callus caused by P. halotolerans was weaker than that caused by A. alternata. RNA sequencing analysis revealed that various plant defense pathways, such as phenylpropanoid biosynthesis, flavonoid biosynthesis, plant hormone signal transduction, and the mitogen-activated protein kinase signaling pathway, play important roles in triggering the plant immune response during fungal infection. Furthermore, the tryptophan metabolism, betalain biosynthesis, fatty acid degradation, flavonoid biosynthesis, tyrosine metabolism, and isoquinoline alkaloid biosynthesis pathways may accelerate the infection of pathogenic fungi, and the ribosome biogenesis pathway in eukaryotes may retard the damage caused by endophytic fungi. This study lays a foundation for exploring the infection mechanism of yam pathogens and endophytic fungi and provides insight for effective fungal disease control in agriculture.}, }
@article {pmid38808529, year = {2024}, author = {Demircan, T and Gül, S and Taşçı, EA}, title = {Can Microbiome Modulate Regenerative Capacity? A Comparative Microbiome Study Reveals a Dominant Presence of Flavobacteriaceae in Blastema Tissue During Axolotl Limb Regeneration.}, journal = {Omics : a journal of integrative biology}, volume = {28}, number = {6}, pages = {291-302}, doi = {10.1089/omi.2024.0075}, pmid = {38808529}, issn = {1557-8100}, mesh = {Animals ; *Regeneration ; *Microbiota/genetics ; *Ambystoma mexicanum/microbiology/physiology ; *RNA, Ribosomal, 16S/genetics ; *Extremities/microbiology ; Phylogeny ; }, abstract = {The axolotl (Ambystoma mexicanum) is renowned for its remarkable regenerative capabilities, which are not diminished by the transition from a neotenic to a metamorphic state. This study explored the microbiome dynamics in axolotl limb regeneration by examining the microbial communities present in neotenic and metamorphic axolotls at two critical stages of limb regeneration: pre-amputation and during blastema formation. Utilizing 16S rRNA amplicon sequencing, we investigated the variations in microbiome profiles associated with different developmental and regenerative states. Our findings reveal a distinct separation in the microbiome profiles of neotenic and metamorphic samples, with a clear demarcation in microbial composition at both the phylum and genus levels. In neotenic 0DPA samples, Proteobacteria and Firmicutes were the most abundant, whereas in neotenic 7DPA samples, Proteobacteria and Bacteroidetes dominated. Conversely, metamorphic samples displayed a higher abundance of Firmicutes and Bacteroidetes at 0DPA and Proteobacteria and Firmicutes at 7DPA. Alpha and beta diversity analyses, along with dendrogram construction, demonstrated significant variations within and between the sample groups, suggesting a strong influence of both developmental stage and regenerative state on the microbiome. Notably, Flavobacterium and Undibacterium emerged as distinctive microbial entities in neotenic 7DPA samples, highlighting potential key players in the microbial ecology of regeneration. These findings suggest that the axolotl's microbiome is dynamically responsive to blastema formation, and they underscore the potential influence of microbial communities on the regeneration process. This study lays the groundwork for future research into the mechanisms by which the microbiome may modulate regenerative capacity.}, }
@article {pmid38806848, year = {2024}, author = {Banchi, E and Manna, V and Muggia, L and Celussi, M}, title = {Marine Fungal Diversity and Dynamics in the Gulf of Trieste (Northern Adriatic Sea).}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {78}, pmid = {38806848}, issn = {1432-184X}, mesh = {*Seawater/microbiology ; *Fungi/genetics/classification/isolation &amp; purification ; *Biodiversity ; *RNA, Ribosomal, 18S/genetics/analysis ; Mycobiome ; DNA, Fungal/genetics ; DNA Barcoding, Taxonomic ; Phylogeny ; DNA, Ribosomal Spacer/genetics/analysis ; Ascomycota/genetics/classification/isolation &amp; purification ; }, abstract = {Fungi contribute to different important ecological processes, including decomposition of organic matter and nutrient cycling, but in the marine environment the main factors influencing their diversity and dynamics at the spatial and temporal levels are still largely unclear. In this study, we performed DNA metabarcoding on seawater sampled monthly over a year and a half in the Gulf of Trieste (northern Adriatic Sea), targeting the internal transcribed spacer (ITS) and the 18S rRNA gene regions. The fungal communities were diverse, very dynamic, and belonged predominantly to marine taxa. Samples could be clustered in two groups, mainly based on the high (> 30%) or low relative proportion of the ascomycetes Parengyodontium album, which emerged as a key taxon in this area. Dissolved and particulate organic C:N ratio played important roles in shaping the mycoplankton assemblages, suggesting that differently bioavailable organic matter pools may be utilized by different consortia. The proportion of fungal over total reads was 31% for ITS and 0.7% for 18S. ITS had the highest taxonomic resolution but low power to detect early divergent fungal lineages. Our results on composition, distribution, and environmental drivers extended our knowledge of the structure and function of the mycobiome of coastal waters.}, }
@article {pmid38806738, year = {2024}, author = {Wissner, JL and Parada-Fabián, JC and Márquez-Velázquez, NA and Escobedo-Hinojosa, W and Gaudêncio, SP and Prieto-Davó, A}, title = {Diversity and Bioprospection of Gram-positive Bacteria Derived from a Mayan Sinkhole.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {77}, pmid = {38806738}, issn = {1432-184X}, support = {POSTDOC//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; POSTDOC//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; LA/P/0140/2020//FCT-Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia, IP/ ; PAIP 5000-9149//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico, Facultad de Qu&#xed;mica/ ; A1-S-10785//Consejo Nacional de Ciencia Humanidades y Tecnolog&#xed;a (CONAHCyT) Ciencia B&#xe1;sica/ ; }, mesh = {*Geologic Sediments/microbiology ; Mexico ; *Biodiversity ; *Gram-Positive Bacteria/isolation &amp; purification/genetics/classification ; *RNA, Ribosomal, 16S/genetics ; Bioprospecting ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Seawater/microbiology ; }, abstract = {Water-filled sinkholes known locally as cenotes, found on the Yucatán Peninsula, have remarkable biodiversity. The primary objective of this study was to explore the biotechnological potential of Gram-positive cultivable bacteria obtained from sediment samples collected at the coastal cenote Pol-Ac in Yucatán, Mexico. Specifically, the investigation aimed to assess production of hydrolytic enzymes and antimicrobial compounds. 16 S rRNA gene sequencing led to the identification of 49 Gram-positive bacterial isolates belonging to the phyla Bacillota (n = 29) and Actinomycetota (n = 20) divided into the common genera Bacillus and Streptomyces, as well as the genera Virgibacillus, Halobacillus, Metabacillus, Solibacillus, Neobacillus, Rossellomorea, Nocardiopsis and Corynebacterium. With growth at 55ºC, 21 of the 49 strains were classified as moderately thermotolerant. All strains were classified as halotolerant and 24 were dependent on marine water for growth. Screening for six extracellular hydrolytic enzymes revealed gelatinase, amylase, lipase, cellulase, protease and chitinase activities in 93.9%, 67.3%, 63.3%, 59.2%, 59.2% and 38.8%, of isolated strains, respectively. The genes for polyketide synthases type I, were detected in 24 of the strains. Of 18 strains that achieved > 25% inhibition of growth in the bacterial pathogen Staphylococcus aureus ATCC 6538, 4 also inhibited growth in Escherichia coli ATCC 35,218. Isolates Streptomyces sp. NCA_378 and Bacillus sp. NCA_374 demonstrated 50-75% growth inhibition against at least one of the two pathogens tested, along with significant enzymatic activity across all six extracellular enzymes. This is the first comprehensive report on the biotechnological potential of Gram-positive bacteria isolated from sediments in the cenotes of the Yucatán Peninsula.}, }
@article {pmid38805423, year = {2024}, author = {Fournier, C and Fiedler, A and Weidele, M and Kautz, H and Schleheck, D}, title = {Description of a 'plankton filtration bias' in sequencing-based bacterial community analysis and of an Arduino microcontroller-based flowmeter device that can help to resolve it.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0303937}, pmid = {38805423}, issn = {1932-6203}, mesh = {*Filtration/instrumentation/methods ; *Plankton/genetics ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/isolation &amp; purification ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Lakes/microbiology ; Phylogeny ; Biomass ; }, abstract = {Diversity studies of aquatic picoplankton (bacterioplankton) communities using size-class filtration, DNA extraction, PCR and sequencing of phylogenetic markers, require a robust methodological pipeline, since biases have been demonstrated essentially at all levels, including DNA extraction, primer choice and PCR. Even different filtration volumes of the same plankton sample and, thus, different biomass loading of the filters, can distort the sequencing results. In this study, we designed an Arduino microcontroller-based flowmeter that records the decrease of initial (maximal) flowrate as proxy for increasing biomass loading and clogging of filters during plankton filtration. The device was tested using freshwater plankton of Lake Constance, and total DNA was extracted and an 16S rDNA amplicon was sequenced. We confirmed that different filtration volumes used for the same water sample affect the sequencing results. Differences were visible in alpha and beta diversities and across all taxonomic ranks. Taxa most affected were typical freshwater Actinobacteria and Bacteroidetes, increasing up to 38% and decreasing up to 29% in relative abundance, respectively. In another experiment, a lake water sample was filtered undiluted and three-fold diluted, and each filtration was stopped once the flowrate had reduced to 50% of initial flowrate, hence, at the same degree of filter clogging. The three-fold diluted sample required three-fold filtration volumes, while equivalent amounts of total DNA were extracted and differences across all taxonomic ranks were not statistically significant compared to the undiluted controls. In conclusion, this work confirms a volume/biomass-dependent bacterioplankton filtration bias for sequencing-based community analyses and provides an improved procedure for controlling biomass loading during filtrations and recovery of equivalent amounts of DNA from samples independent of the plankton density. The application of the device can also avoid the distorting of sequencing results as caused by the plankton filtration bias.}, }
@article {pmid38804464, year = {2024}, author = {Lappan, R and Thakar, J and Molares Moncayo, L and Besser, A and Bradley, JA and Goordial, J and Trembath-Reichert, E and Greening, C}, title = {The atmosphere: a transport medium or an active microbial ecosystem?.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38804464}, issn = {1751-7370}, support = {RGY0058/2022//Human Frontier Science Program/ ; }, mesh = {*Atmosphere ; *Ecosystem ; Microbiota ; Air Microbiology ; Biodiversity ; Bacteria/metabolism/classification/growth &amp; development ; }, abstract = {The atmosphere may be Earth's largest microbial ecosystem. It is connected to all of Earth's surface ecosystems and plays an important role in microbial dispersal on local to global scales. Despite this grand scale, surprisingly little is understood about the atmosphere itself as a habitat. A key question remains unresolved: does the atmosphere simply transport microorganisms from one location to another, or does it harbour adapted, resident, and active microbial communities that overcome the physiological stressors and selection pressures the atmosphere poses to life? Advances in extreme microbiology and astrobiology continue to push our understanding of the limits of life towards ever greater extremes of temperature, pressure, salinity, irradiance, pH, and water availability. Earth's atmosphere stands as a challenging, but potentially surmountable, extreme environment to harbour living, active, resident microorganisms. Here, we confront the current understanding of the atmosphere as a microbial habitat, highlighting key advances and limitations. We pose major ecological and mechanistic questions about microbial life in the atmosphere that remain unresolved and frame the problems and technical pitfalls that have largely hindered recent developments in this space, providing evidence-based insights to drive future research in this field. New innovations supported by rigorous technical standards are needed to enable progress in understanding atmospheric microorganisms and their influence on global processes of weather, climate, nutrient cycling, biodiversity, and microbial connectivity, especially in the context of rapid global change.}, }
@article {pmid38804108, year = {2024}, author = {Ochoa-Hueso, R and Eldridge, DJ and Berdugo, M and Trivedi, P and Sokoya, B and Cano-Díaz, C and Abades, S and Alfaro, F and Bamigboye, AR and Bastida, F and Blanco-Pastor, JL and de Los Rios, A and Durán, J and Geisen, S and Grebenc, T and Illán, JG and Liu, YR and Makhalanyane, TP and Mamet, S and Molina-Montenegro, MA and Moreno, JL and Nahberger, TU and Peñaloza-Bojacá, GF and Plaza, C and Rey, A and Rodríguez, A and Siebe, C and Singh, BK and Teixido, AL and Torres-Díaz, C and Wang, L and Wang, J and Wang, J and Zaady, E and Zhou, X and Zhou, XQ and Tedersoo, L and Delgado-Baquerizo, M}, title = {Unearthing the soil-borne microbiome of land plants.}, journal = {Global change biology}, volume = {30}, number = {5}, pages = {e17295}, doi = {10.1111/gcb.17295}, pmid = {38804108}, issn = {1365-2486}, support = {LRB17\1019//British Ecological Society/ ; J4-1766//Slovenian Research Agency/ ; GOPC-CA-20-0001//Junta de Andaluc&#xed;a/ ; P20_00323//Junta de Andaluc&#xed;a/ ; EMC21_00207//Junta de Andaluc&#xed;a/ ; GO2022-01//Junta de Andaluc&#xed;a/ ; PID2019-106004RA-I00//Spanish Ministry of Science and Innovation/ ; PID2020-115813RA-I00//Spanish Ministry of Science and Innovation/ ; TED2021-130908B-C41//Spanish Ministry of Science and Innovation/ ; }, mesh = {*Soil Microbiology ; *Microbiota ; *Embryophyta ; Biodiversity ; Soil/chemistry ; }, abstract = {Plant-soil biodiversity interactions are fundamental for the functioning of terrestrial ecosystems. Yet, the existence of a set of globally distributed topsoil microbial and small invertebrate organisms consistently associated with land plants (i.e., their consistent soil-borne microbiome), together with the environmental preferences and functional capabilities of these organisms, remains unknown. We conducted a standardized field survey under 150 species of land plants, including 58 species of bryophytes and 92 of vascular plants, across 124 locations from all continents. We found that, despite the immense biodiversity of soil organisms, the land plants evaluated only shared a small fraction (less than 1%) of all microbial and invertebrate taxa that were present across contrasting climatic and soil conditions and vegetation types. These consistent taxa were dominated by generalist decomposers and phagotrophs and their presence was positively correlated with the abundance of functional genes linked to mineralization. Finally, we showed that crossing environmental thresholds in aridity (aridity index of 0.65, i.e., the transition from mesic to dry ecosystems), soil pH (5.5; i.e., the transition from acidic to strongly acidic soils), and carbon (less than 2%, the lower limit of fertile soils) can result in drastic disruptions in the associations between land plants and soil organisms, with potential implications for the delivery of soil ecosystem processes under ongoing global environmental change.}, }
@article {pmid38804043, year = {2024}, author = {Owens, LA and Thurber, MI and Goldberg, TL}, title = {CRISPR-Cas9-mediated host signal reduction for 18S metabarcoding of host-associated eukaryotes.}, journal = {Molecular ecology resources}, volume = {24}, number = {6}, pages = {e13980}, pmid = {38804043}, issn = {1755-0998}, support = {R01 AG049395/AG/NIA NIH HHS/United States ; R37 AG049395/AG/NIA NIH HHS/United States ; T32 AI007414/AI/NIAID NIH HHS/United States ; 1R21AI163592-01/HI/NHLBI NIH HHS/United States ; T32AI007414/HI/NHLBI NIH HHS/United States ; 1R01AG049395-01/HI/NHLBI NIH HHS/United States ; R21 AI163592/AI/NIAID NIH HHS/United States ; }, mesh = {*CRISPR-Cas Systems ; *Eukaryota/genetics ; *DNA Barcoding, Taxonomic/methods ; *RNA, Ribosomal, 18S/genetics ; Metagenomics/methods ; Humans ; Animals ; }, abstract = {Metabarcoding-based methods for identification of host-associated eukaryotes have the potential to revolutionize parasitology and microbial ecology, yet significant technical challenges remain. In particular, highly abundant host reads can mask the presence of less-abundant target organisms, especially for sample types rich in host DNA (e.g., blood and tissues). Here, we present a new CRISPR-Cas9-mediated approach designed to reduce host signal by selective amplicon digestion, thus enriching clinical samples for eukaryotic endosymbiont sequences during metabarcoding. Our method achieves a nearly 76% increased efficiency in host signal reduction compared with no treatment and a nearly 60% increased efficiency in host signal reduction compared with the most commonly used published method. Furthermore, the application of our method to clinical samples allows for the detection of parasite infections that would otherwise have been missed.}, }
@article {pmid38802328, year = {2024}, author = {Fu, Y and Hu, F and Wang, F and Xu, M and Jia, Z and Amelung, W and Mei, Z and Han, X and Virta, M and Jiang, X and Tiedje, JM}, title = {Distinct Assembly Patterns of Soil Antibiotic Resistome Revealed by Land-Use Changes over 30 Years.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {23}, pages = {10216-10226}, doi = {10.1021/acs.est.3c10423}, pmid = {38802328}, issn = {1520-5851}, mesh = {*Soil/chemistry ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Anti-Bacterial Agents/pharmacology ; }, abstract = {Compared with the ever-growing information about the anthropogenic discharge of nutrients, metals, and antibiotics on the disturbance of antibiotic resistance genes (ARGs), less is known about how the potential natural stressors drive the evolutionary processes of antibiotic resistance. This study examined how soil resistomes evolved and differentiated over 30 years in various land use settings with spatiotemporal homogeneity and minimal human impact. We found that the contents of soil organic carbon, nitrogen, soil microbial biomass, and bioavailable heavy metals, as well as related changes in the antibiotic resistome prevalence including diversity and abundance, declined in the order of grassland > cropland > bareland. Sixty-nine remaining ARGs and 14 mobile genetic elements (MGEs) were shared among three land uses. Multiple factors (i.e., soil properties, heavy metals, bacterial community, and MGEs) contributed to the evolutionary changes of the antibiotic resistome, wherein the resistome profile was dominantly driven by MGEs from both direct and indirect pathways, supported by a partial least-squares path model analysis. Our results suggest that pathways to mitigate ARGs in soils can coincide with land degradation processes, posing a challenge to the common goal of managing our environment sustainably.}, }
@article {pmid38801800, year = {2024}, author = {Oesterle, I and Ayeni, KI and Ezekiel, CN and Berry, D and Rompel, A and Warth, B}, title = {Insights into the early-life chemical exposome of Nigerian infants and potential correlations with the developing gut microbiome.}, journal = {Environment international}, volume = {188}, number = {}, pages = {108766}, doi = {10.1016/j.envint.2024.108766}, pmid = {38801800}, issn = {1873-6750}, support = {P 32326/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Nigeria ; *Milk, Human/chemistry/microbiology ; Infant ; Female ; *Feces/microbiology/chemistry ; Exposome ; Xenobiotics/analysis ; Infant, Newborn ; RNA, Ribosomal, 16S ; Environmental Pollutants/analysis ; Adult ; Male ; }, abstract = {Early-life exposure to natural and synthetic chemicals can impact acute and chronic health conditions. Here, a suspect screening workflow anchored on high-resolution mass spectrometry was applied to elucidate xenobiotics in breast milk and matching stool samples collected from Nigerian mother-infant pairs (n = 11) at three time points. Potential correlations between xenobiotic exposure and the developing gut microbiome, as determined by 16S rRNA gene amplicon sequencing, were subsequently explored. Overall, 12,192 and 16,461 features were acquired in the breast milk and stool samples, respectively. Following quality control and suspect screening, 562 and 864 features remained, respectively, with 149 of these features present in both matrices. Taking advantage of 242 authentic reference standards measured for confirmatory purposes of food bio-actives and toxicants, 34 features in breast milk and 68 features in stool were identified and semi-quantified. Moreover, 51 and 78 features were annotated with spectral library matching, as well as 416 and 652 by in silico fragmentation tools in breast milk and stool, respectively. The analytical workflow proved its versatility to simultaneously determine a diverse panel of chemical classes including mycotoxins, endocrine-disrupting chemicals (EDCs), antibiotics, plasticizers, perfluorinated alkylated substances (PFAS), and pesticides, although it was originally optimized for polyphenols. Spearman rank correlation of the identified features revealed significant correlations between chemicals of the same classification such as polyphenols. One-way ANOVA and differential abundance analysis of the data obtained from stool samples revealed that molecules of plant-based origin elevated as complementary foods were introduced to the infants' diets. Annotated compounds in the stool, such as tricetin, positively correlated with the genus Blautia. Moreover, vulgaxanthin negatively correlated with Escherichia-Shigella. Despite the limited sample size, this exploratory study provides high-quality exposure data of matched biospecimens obtained from mother-infant pairs in sub-Saharan Africa and shows potential correlations between the chemical exposome and the gut microbiome.}, }
@article {pmid38801423, year = {2024}, author = {Ramírez-Pool, JA and Calderón-Pérez, B and Ruiz-Medrano, R and Ortiz-Castro, R and Xoconostle-Cazares, B}, title = {Bacillus Strains as Effective Biocontrol Agents Against Phytopathogenic Bacteria and Promoters of Plant Growth.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {76}, pmid = {38801423}, issn = {1432-184X}, mesh = {*Bacillus/physiology ; *Arabidopsis/microbiology/growth &amp; development ; *Plant Diseases/prevention &amp; control/microbiology ; Quorum Sensing ; Chromobacterium/physiology/growth &amp; development ; Biological Control Agents/pharmacology ; Plant Development ; Seedlings/microbiology/growth &amp; development ; Soil Microbiology ; }, abstract = {Modern crop production relies on the application of chemical pesticides and fertilizers causing environmental and economic challenges. In response, less environmentally impactful alternatives have emerged such as the use of beneficial microorganisms. These microorganisms, particularly plant growth-promoting bacteria (PGPB), have demonstrated their ability to enhance plant growth, protect against various stresses, and reduce the need for chemical inputs. Among the PGPB, Bacillus species have garnered attention due to their adaptability and commercial potential. Recent reports have highlighted Bacillus strains as biocontrol agents against phytopathogenic bacteria while concurrently promoting plant growth. We also examined Bacillus plant growth-promoting abilities in Arabidopsis thaliana seedlings. In this study, we assessed the potential of various Bacillus strains to control diverse phytopathogenic bacteria and inhibit quorum sensing using Chromobacterium violaceum as a model system. In conclusion, our results suggest that bacteria of the genus Bacillus hold significant potential for biotechnological applications. This includes developments aimed at reducing agrochemical use, promoting sustainable agriculture, and enhancing crop yield and protection.}, }
@article {pmid38801001, year = {2024}, author = {Timmis, K and Hallsworth, JE and McGenity, TJ and Armstrong, R and Colom, MF and Karahan, ZC and Chavarría, M and Bernal, P and Boyd, ES and Ramos, JL and Kaltenpoth, M and Pruzzo, C and Clarke, G and López-Garcia, P and Yakimov, MM and Perlmutter, J and Greening, C and Eloe-Fadrosh, E and Verstraete, W and Nunes, OC and Kotsyurbenko, O and Nikel, PI and Scavone, P and Häggblom, MM and Lavigne, R and Le Roux, F and Timmis, JK and Parro, V and Michán, C and García, JL and Casadevall, A and Payne, SM and Frey, J and Koren, O and Prosser, JI and Lahti, L and Lal, R and Anand, S and Sood, U and Offre, P and Bryce, CC and Mswaka, AY and Jores, J and Kaçar, B and Blank, LM and Maaßen, N and Pope, PB and Banciu, HL and Armitage, J and Lee, SY and Wang, F and Makhalanyane, TP and Gilbert, JA and Wood, TK and Vasiljevic, B and Soberón, M and Udaondo, Z and Rojo, F and Tamang, JP and Giraud, T and Ropars, J and Ezeji, T and Müller, V and Danbara, H and Averhoff, B and Sessitsch, A and Partida-Martínez, LP and Huang, W and Molin, S and Junier, P and Amils, R and Wu, XL and Ron, E and Erten, H and de Martinis, ECP and Rapoport, A and Öpik, M and Pokatong, WDR and Stairs, C and Amoozegar, MA and Serna, JG}, title = {A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society.}, journal = {Microbial biotechnology}, volume = {17}, number = {5}, pages = {e14456}, pmid = {38801001}, issn = {1751-7915}, mesh = {*Microbiology/education ; Humans ; Biotechnology ; }, abstract = {EXECUTIVE SUMMARY: Microbes are all pervasive in their distribution and influence on the functioning and well-being of humans, life in general and the planet. Microbially-based technologies contribute hugely to the supply of important goods and services we depend upon, such as the provision of food, medicines and clean water. They also offer mechanisms and strategies to mitigate and solve a wide range of problems and crises facing humanity at all levels, including those encapsulated in the sustainable development goals (SDGs) formulated by the United Nations. For example, microbial technologies can contribute in multiple ways to decarbonisation and hence confronting global warming, provide sanitation and clean water to the billions of people lacking them, improve soil fertility and hence food production and develop vaccines and other medicines to reduce and in some cases eliminate deadly infections. They are the foundation of biotechnology, an increasingly important and growing business sector and source of employment, and the centre of the bioeconomy, Green Deal, etc. But, because microbes are largely invisible, they are not familiar to most people, so opportunities they offer to effectively prevent and solve problems are often missed by decision-makers, with the negative consequences this entrains. To correct this lack of vital knowledge, the International Microbiology Literacy Initiative-the IMiLI-is recruiting from the global microbiology community and making freely available, teaching resources for a curriculum in societally relevant microbiology that can be used at all levels of learning. Its goal is the development of a society that is literate in relevant microbiology and, as a consequence, able to take full advantage of the potential of microbes and minimise the consequences of their negative activities. In addition to teaching about microbes, almost every lesson discusses the influence they have on sustainability and the SDGs and their ability to solve pressing problems of societal inequalities. The curriculum thus teaches about sustainability, societal needs and global citizenship. The lessons also reveal the impacts microbes and their activities have on our daily lives at the personal, family, community, national and global levels and their relevance for decisions at all levels. And, because effective, evidence-based decisions require not only relevant information but also critical and systems thinking, the resources also teach about these key generic aspects of deliberation. The IMiLI teaching resources are learner-centric, not academic microbiology-centric and deal with the microbiology of everyday issues. These span topics as diverse as owning and caring for a companion animal, the vast range of everyday foods that are produced via microbial processes, impressive geological formations created by microbes, childhood illnesses and how they are managed and how to reduce waste and pollution. They also leverage the exceptional excitement of exploration and discovery that typifies much progress in microbiology to capture the interest, inspire and motivate educators and learners alike. The IMiLI is establishing Regional Centres to translate the teaching resources into regional languages and adapt them to regional cultures, and to promote their use and assist educators employing them. Two of these are now operational. The Regional Centres constitute the interface between resource creators and educators-learners. As such, they will collect and analyse feedback from the end-users and transmit this to the resource creators so that teaching materials can be improved and refined, and new resources added in response to demand: educators and learners will thereby be directly involved in evolution of the teaching resources. The interactions between educators-learners and resource creators mediated by the Regional Centres will establish dynamic and synergistic relationships-a global societally relevant microbiology education ecosystem-in which creators also become learners, teaching resources are optimised and all players/stakeholders are empowered and their motivation increased. The IMiLI concept thus embraces the principle of teaching societally relevant microbiology embedded in the wider context of societal, biosphere and planetary needs, inequalities, the range of crises that confront us and the need for improved decisioning, which should ultimately lead to better citizenship and a humanity that is more sustainable and resilient.<br><br>ABSTRACT: The biosphere of planet Earth is a microbial world: a vast reactor of countless microbially driven chemical transformations and energy transfers that push and pull many planetary geochemical processes, including the cycling of the elements of life, mitigate or amplify climate change (e.g., Nature Reviews Microbiology, 2019, 17, 569) and impact the well-being and activities of all organisms, including humans. Microbes are both our ancestors and creators of the planetary chemistry that allowed us to evolve (e.g., Life's engines: How microbes made earth habitable, 2023). To understand how the biosphere functions, how humans can influence its development and live more sustainably with the other organisms sharing it, we need to understand the microbes. In a recent editorial (Environmental Microbiology, 2019, 21, 1513), we advocated for improved microbiology literacy in society. Our concept of microbiology literacy is not based on knowledge of the academic subject of microbiology, with its multitude of component topics, plus the growing number of additional topics from other disciplines that become vitally important elements of current microbiology. Rather it is focused on microbial activities that impact us-individuals/communities/nations/the human world-and the biosphere and that are key to reaching informed decisions on a multitude of issues that regularly confront us, ranging from personal issues to crises of global importance. In other words, it is knowledge and understanding essential for adulthood and the transition to it, knowledge and understanding that must be acquired early in life in school. The 2019 Editorial marked the launch of the International Microbiology Literacy Initiative, the IMiLI. HERE, WE PRESENT: our concept of how microbiology literacy may be achieved and the rationale underpinning it; the type of teaching resources being created to realise the concept and the framing of microbial activities treated in these resources in the context of sustainability, societal needs and responsibilities and decision-making; and the key role of Regional Centres that will translate the teaching resources into local languages, adapt them according to local cultural needs, interface with regional educators and develop and serve as hubs of microbiology literacy education networks. The topics featuring in teaching resources are learner-centric and have been selected for their inherent relevance, interest and ability to excite and engage. Importantly, the resources coherently integrate and emphasise the overarching issues of sustainability, stewardship and critical thinking and the pervasive interdependencies of processes. More broadly, the concept emphasises how the multifarious applications of microbial activities can be leveraged to promote human/animal, plant, environmental and planetary health, improve social equity, alleviate humanitarian deficits and causes of conflicts among peoples and increase understanding between peoples (Microbial Biotechnology, 2023, 16(6), 1091-1111). Importantly, although the primary target of the freely available (CC BY-NC 4.0) IMiLI teaching resources is schoolchildren and their educators, they and the teaching philosophy are intended for all ages, abilities and cultural spectra of learners worldwide: in university education, lifelong learning, curiosity-driven, web-based knowledge acquisition and public outreach. The IMiLI teaching resources aim to promote development of a global microbiology education ecosystem that democratises microbiology knowledge.}, }
@article {pmid38799067, year = {2024}, author = {Vargas-Sánchez, M and Alcocer, J and Puche, E and Sánchez-Carrillo, S}, title = {Abiotic processes control carbon dioxide dynamics in temperate karst lakes.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17393}, pmid = {38799067}, issn = {2167-8359}, mesh = {*Lakes/chemistry ; *Carbon Dioxide/analysis/metabolism ; Spain ; *Seasons ; Environmental Monitoring/methods ; Carbon Cycle ; Phytoplankton/metabolism ; }, abstract = {Inland waters are crucial in the carbon cycle, contributing significantly to the global CO2 fluxes. Carbonate lakes may act as both sources and sinks of CO2 depending on the interactions between the amount of dissolved inorganic carbon (DIC) inputs, lake metabolisms, and geochemical processes. It is often difficult to distinguish the dominant mechanisms driving CO2 dynamics and their effects on CO2 emissions. This study was undertaken in three groundwater-fed carbonate-rich lakes in central Spain (Ruidera Lakes), severely polluted with nitrates from agricultural overfertilization. Diel and seasonal (summer and winter) changes in CO2 concentration (CCO2) DIC, and CO2 emissions-(FCO2)-, as well as physical and chemical variables, including primary production and phytoplanktonic chlorophyll-a were measured. In addition, δ[13]C-DIC, δ[13]C-CO2 in lake waters, and δ[13]C of the sedimentary organic matter were measured seasonally to identify the primary CO2 sources and processes. While the lakes were consistently CCO2 supersaturated and FCO2 was released to the atmosphere during both seasons, the highest CCO2 and DIC were in summer (0.36-2.26 µmol L[-1]). Our results support a strong phosphorus limitation for primary production in these lakes, which impinges on CO2 dynamics. External DIC inputs to the lake waters primarily drive the CCO2 and, therefore, the FCO2. The δ[13]C-DIC signatures below -12‰ confirmed the primary geogenic influence on DIC. As also suggested by the high values on the calcite saturation index, the Miller-Tans plot revealed that the CO2 source in the lakes was close to the signature provided by the fractionation of δ[13]C-CO2 from calcite precipitation. Therefore, the main contribution behind the CCO2 values found in these karst lakes should be attributed to the calcite precipitation process, which is temperature-dependent according to the seasonal change observed in δ[13]C-DIC values. Finally, co-precipitation of phosphate with calcite could partly explain the observed low phytoplankton production in these lakes and the impact on the contribution to increasing greenhouse gas emissions. However, as eutrophication increases and the soluble reactive phosphorus (SRP) content increases, the co-precipitation of phosphate is expected to be progressively inhibited. These thresholds must be assessed to understand how the CO3[2-] ions drive lake co-precipitation dynamics. Carbonate regions extend over 15% of the Earth's surface but seem essential in the CO2 dynamics at a global scale.}, }
@article {pmid38798771, year = {2024}, author = {Mahalak, KK and Liu, L and Bobokalonov, J and Narrowe, AB and Firrman, J and Bittinger, K and Hu, W and Jones, SM and Moustafa, AM}, title = {Supplementation with soluble or insoluble rice-bran fibers increases short-chain fatty acid producing bacteria in the gut microbiota in vitro.}, journal = {Frontiers in nutrition}, volume = {11}, number = {}, pages = {1304045}, pmid = {38798771}, issn = {2296-861X}, abstract = {INTRODUCTION: Studies have shown that a diet high in fiber and prebiotics has a positive impact on human health due largely to the fermentation of these compounds by the gut microbiota. One underutilized source of fiber may be rice bran, a waste product of rice processing that is used most frequently as an additive to livestock feed but may be a good source of fibers and other phenolic compounds as a human diet supplement. Previous studies focused on specific compounds extracted from rice bran showed that soluble fibers extracted from rice bran can improve glucose response and reduce weight gain in mouse models. However, less is known about changes in the human gut microbiota in response to regular rice bran consumption.<br><br>METHODS: In this study, we used a Simulator of the Human Intestinal Microbial Ecology (SHIME&#xae;) to cultivate the human gut microbiota of 3 different donors in conditions containing either soluble or insoluble fiber fractions from rice bran. Using 16S rRNA amplicon sequencing and targeted metabolomics via Gas Chromatography-Mass Spectrometry, we explored how gut microbial communities developed provided different supplemental fiber sources.<br><br>RESULTS: We found that insoluble and soluble fiber fractions increased short-chain fatty acid production, indicating that both fractions were fermented. However, there were differences in response between donors, for example the gut microbiota from donor 1 increased acetic acid production with both fiber types compared with control; whereas for donors 2 and 3, butanoic acid production increased with ISF and SF supplementation. Both soluble and insoluble rice bran fractions increased the abundance of Bifidobacterium and Lachnospiraceae taxa.<br><br>DISCUSSION: Overall, analysis of the effect of soluble and insoluble rice bran fractions on the human in vitro gut microbiota and the metabolites produced revealed individually variant responses to these prebiotics.}, }
@article {pmid38798271, year = {2024}, author = {Almeida-Silva, F and Prost-Boxoen, L and Van de Peer, Y}, title = {hybridexpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors.}, journal = {The New phytologist}, volume = {243}, number = {2}, pages = {811-819}, pmid = {38798271}, issn = {1469-8137}, support = {833522/ERC_/European Research Council/International ; 833522//H2020 European Research Council/ ; 11H0426N//Fonds Wetenschappelijk Onderzoek/ ; BOF.MET.2021.0005.01//Bijzonder Onderzoeksfonds UGent/ ; }, mesh = {*Software ; *Hybridization, Genetic ; *Gene Expression Profiling ; *Oryza/genetics ; *Transcriptome/genetics ; Gossypium/genetics ; Hybrid Vigor/genetics ; Gene Expression Regulation, Plant ; Plant Roots/genetics ; Polyploidy ; }, abstract = {Hybridization, the process of crossing individuals from diverse genetic backgrounds, plays a pivotal role in evolution, biological invasiveness, and crop breeding. At the transcriptional level, hybridization often leads to complex nonadditive effects, presenting challenges for understanding its consequences. Although standard transcriptomic analyses exist to compare hybrids to their progenitors, such analyses have not been implemented in a software package, hindering reproducibility. We introduce hybridexpress, an R/Bioconductor package designed to facilitate the analysis, visualization, and comparison of gene expression patterns in hybrid triplets (hybrids and their progenitors). hybridexpress provides users with a user-friendly and comprehensive workflow that includes all standard comparative analyses steps, including data normalization, calculation of midparent expression values, sample clustering, expression-based gene classification into categories and classes, and overrepresentation analysis for functional terms. We illustrate the utility of hybridexpress through comparative transcriptomic analyses of cotton allopolyploidization and rice root trait heterosis. hybridexpress is designed to streamline comparative transcriptomic studies of hybrid triplets, advancing our understanding of evolutionary dynamics in allopolyploids, and enhancing plant breeding strategies. hybridexpress is freely accessible from Bioconductor (https://bioconductor.org/packages/HybridExpress) and its source code is available on GitHub (https://github.com/almeidasilvaf/HybridExpress).}, }
@article {pmid38794902, year = {2024}, author = {Fricker, AD and Yao, T and Lindemann, SR and Flores, GE}, title = {Enrichment and characterization of human-associated mucin-degrading microbial consortia by sequential passage.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {7}, pages = {}, pmid = {38794902}, issn = {1574-6941}, support = {SC1 GM136546/GM/NIGMS NIH HHS/United States ; SC1GM136546/NH/NIH HHS/United States ; }, mesh = {Humans ; *Mucins/metabolism ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Microbial Consortia ; *Fermentation ; Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome ; Akkermansia/metabolism ; Desulfovibrio/metabolism/genetics/classification ; Bacteroides/metabolism/genetics/classification/growth &amp; development ; }, abstract = {Mucin is a glycoprotein secreted throughout the mammalian gastrointestinal tract that can support endogenous microorganisms in the absence of complex polysaccharides. While several mucin-degrading bacteria have been identified, the interindividual differences in microbial communities capable of metabolizing this complex polymer are not well described. To determine whether community assembly on mucin is deterministic across individuals or whether taxonomically distinct but functionally similar mucin-degrading communities are selected across fecal inocula, we used a 10-day in vitro sequential batch culture fermentation from three human donors with mucin as the sole carbon source. For each donor, 16S rRNA gene amplicon sequencing was used to characterize microbial community succession, and the short-chain fatty acid profile was determined from the final community. All three communities reached a steady-state by day 7 in which the community composition stabilized. Taxonomic comparisons amongst communities revealed that one of the final communities had Desulfovibrio, another had Akkermansia, and all three shared other members, such as Bacteroides. Metabolic output differences were most notable for one of the donor's communities, with significantly less production of acetate and propionate than the other two communities. These findings demonstrate the feasibility of developing stable mucin-degrading communities with shared and unique taxa. Furthermore, the mechanisms and efficiencies of mucin degradation across individuals are important for understanding how this community-level process impacts human health.}, }
@article {pmid38792792, year = {2024}, author = {Jiao, F and Qian, L and Wu, J and Zhang, D and Zhang, J and Wang, M and Sui, X and Zhang, X}, title = {Diversity and Composition of Soil Acidobacterial Communities in Different Temperate Forest Types of Northeast China.}, journal = {Microorganisms}, volume = {12}, number = {5}, pages = {}, pmid = {38792792}, issn = {2076-2607}, support = {LBH-Q21167//Heilongjiang Province Postdoctoral Research Start-up Fund Project/ ; }, abstract = {To gain an in-depth understanding of the diversity and composition of soil Acidobacteria in five different forest types in typical temperate forest ecosystems and to explore their relationship with soil nutrients. The diversity of soil Acidobacteria was determined by high-throughput sequencing technology. Soil Acidobacteria's alpha-diversity index and soil nutrient content differed significantly among different forest types. β-diversity and the composition of soil Acidobacteria also varied across forest types. Acidobacterial genera, such as Acidobacteria_Gp1, Acidobacteria_Gp4, and Acidobacteria_Gp17, play key roles in different forests. The RDA analyses pointed out that the soil pH, available nitrogen (AN), carbon to nitrogen (C/N) ratio, available phosphorus (AP), total carbon (TC), and total phosphorus (TP) were significant factors affecting soil Acidobacteria in different forest types. In this study, the diversity and composition of soil Acidobacteria under different forest types in a temperate forest ecosystem were analyzed, revealing the complex relationship between them and soil physicochemical properties. These findings not only enhance our understanding of soil microbial ecology but also provide important guidance for ecological conservation and restoration strategies for temperate forest ecosystems.}, }
@article {pmid38790992, year = {2024}, author = {Roszkowska, P and Klimczak, E and Ostrycharz, E and Rączka, A and Wojciechowska-Koszko, I and Dybus, A and Cheng, YH and Yu, YH and Mazgaj, S and Hukowska-Szematowicz, B}, title = {Small Intestinal Bacterial Overgrowth (SIBO) and Twelve Groups of Related Diseases-Current State of Knowledge.}, journal = {Biomedicines}, volume = {12}, number = {5}, pages = {}, pmid = {38790992}, issn = {2227-9059}, abstract = {The human gut microbiota creates a complex microbial ecosystem, characterized by its high population density, wide diversity, and complex interactions. Any imbalance of the intestinal microbiome, whether qualitative or quantitative, may have serious consequences for human health, including small intestinal bacterial overgrowth (SIBO). SIBO is defined as an increase in the number of bacteria (10[3]-10[5] CFU/mL), an alteration in the bacterial composition, or both in the small intestine. The PubMed, Science Direct, Web of Science, EMBASE, and Medline databases were searched for studies on SIBO and related diseases. These diseases were divided into 12 groups: (1) gastrointestinal disorders; (2) autoimmune disease; (3) cardiovascular system disease; (4) metabolic disease; (5) endocrine disorders; (6) nephrological disorders; (7) dermatological diseases; (8) neurological diseases (9); developmental disorders; (10) mental disorders; (11) genetic diseases; and (12) gastrointestinal cancer. The purpose of this comprehensive review is to present the current state of knowledge on the relationships between SIBO and these 12 disease groups, taking into account risk factors and the causal context. This review fills the evidence gap on SIBO and presents a biological-medical approach to the problem, clearly showing the groups and diseases having a proven relationship with SIBO, as well as indicating groups within which research should continue to be expanded.}, }
@article {pmid38790880, year = {2024}, author = {Ding, Y and Wang, L and Wang, H and Li, H}, title = {Dynamic Succession of Natural Microbes during the Ecolly Grape Growth under Extremely Simplified Eco-Cultivation.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {10}, pages = {}, pmid = {38790880}, issn = {2304-8158}, support = {LYNJ202110//research and application of key technologies for sustainable development of wine industry/ ; }, abstract = {The composition and continuous succession of natural microbial communities during grape growth play important roles in grape health and flavor quality as well as in characterizing the regional wine terroir. This study explored the diversity and dynamics of fruit epidermal microbes at each growth and developmental stage of Ecolly grapes under an extremely simplified eco-cultivation model, analyzed microbial interactions and associations of weather parameters to specific communities, and emphasized metabolic functional characteristics of microecology. The results indicated that the natural microbial community changed significantly during the grape growth phase. The dominant fungal genera mainly included Gibberella, Alternaria, Filobasidium, Naganishia, Ascochyta, Apiotrichum, Comoclathris, and Aureobasidium, and the dominant bacterial genera mainly contained Sediminibacterium, Ralstonia, Pantoea, Bradyrhizobium, Brevundimonas, Mesorhizobium, Planococcus, and Planomicrobium. In summary, filamentous fungi gradually shifted to basidiomycetous yeasts along with fruit ripening, with a decline in the number of Gram-negative bacteria and a relative increase in Gram-positive bacteria. The community assembly process reflects the fact that microbial ecology may be influenced by a variety of factors, but the fungal community was more stable, and the bacterial community fluctuated more from year to year, which may reflect their response to weather conditions over the years. Overall, our study helps to comprehensively profile the ecological characteristics of the grape microbial system, highlights the natural ecological viticulture concept, and promotes the sustainable development of the grape and wine industry.}, }
@article {pmid38790838, year = {2024}, author = {Ayed, L and M'hir, S and Nuzzolese, D and Di Cagno, R and Filannino, P}, title = {Harnessing the Health and Techno-Functional Potential of Lactic Acid Bacteria: A Comprehensive Review.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {10}, pages = {}, pmid = {38790838}, issn = {2304-8158}, abstract = {This review examines the techno-functional properties of lactic acid bacteria (LABs) in the food industry, focusing on their potential health benefits. We discuss current findings related to the techno-functionality of LAB, which includes acidification, proteolytic and lipolytic features, and a variety of other biochemical activities. These activities include the production of antimicrobial compounds and the synthesis of exopolysaccharides that improve food safety and consumer sensory experience. LABs are also known for their antioxidant abilities, which help reduce oxidative reactions in foods and improve their functional properties. In addition, LABs' role as probiotics is known for their promising effects on gut health, immune system modulation, cholesterol control, and general wellbeing. Despite these advantages, several challenges hinder the effective production and use of probiotic LABs, such as maintaining strain viability during storage and transport as well as ensuring their efficacy in the gastrointestinal tract. Our review identifies these critical barriers and suggests avenues for future research.}, }
@article {pmid38788571, year = {2024}, author = {Liu, J and Zhao, R and Feng, J and Fu, W and Cao, L and Zhang, J and Lei, Y and Liang, J and Lin, L and Li, X and Li, B}, title = {Bacterial assembly and succession patterns in conventional and advanced drinking water systems: From source to tap.}, journal = {Journal of hazardous materials}, volume = {473}, number = {}, pages = {134613}, doi = {10.1016/j.jhazmat.2024.134613}, pmid = {38788571}, issn = {1873-3336}, mesh = {*Drinking Water/microbiology ; *Bacteria/classification/genetics/metabolism ; *Water Purification/methods ; *Water Microbiology ; Halogenation ; Filtration ; Biodiversity ; Water Supply ; }, abstract = {Bacteria are pivotal to drinking water treatment and public health. However, the mechanisms of bacterial assembly and their impact on species coexistence remain largely unexplored. This study explored the assembly and succession of bacterial communities in two full-scale drinking water systems over one year. We observed a decline in bacterial biomass, diversity, and co-occurrence network complexity along the treatment processes, except for the biological activated carbon filtration stage. The conventional plant showed higher bacterial diversity than the advanced plant, despite similar bacterial concentrations and better removal efficiency. The biological activated carbon filter exhibited high phylogenetic diversity, indicating enhanced bacterial metabolic functionality for organic matter removal. Chlorination inactivated most bacteria but favored some chlorination-resistant and potentially pathogenic species, such as Burkholderia, Bosea, Brevundimonas, and Acinetobacter. Moreover, the spatiotemporal dynamics of the bacterial continuum were primarily driven by stochastic processes, explaining more than 78% of the relative importance. The advanced plant's bacterial community was less influenced by dispersal limitation and more by homogeneous selection. The stochastic process regulated bacterial diversity and influenced the complexity of the species co-occurrence network. These findings deepen our understanding of microbial ecological mechanisms and species interactions, offering insights for enhancing hygienic safety in drinking water systems.}, }
@article {pmid38786909, year = {2024}, author = {Jawień, P and Pfitzner, WP and Schaffner, F and Kiewra, D}, title = {Mosquitoes (Diptera: Culicidae) of Poland: An Update of Species Diversity and Current Challenges.}, journal = {Insects}, volume = {15}, number = {5}, pages = {}, pmid = {38786909}, issn = {2075-4450}, abstract = {This article presents the current state of knowledge of mosquito species (Diptera: Culicidae) occurring in Poland. In comparison to the most recently published checklists (1999 and 2007), which listed 47 mosquito species, four species (Aedes japonicus, Anopheles daciae, Anopheles hyrcanus, and Anopheles petragnani) are added to the Polish fauna. Our new checklist of Polish mosquito fauna includes 51 species of mosquitoes from five genera: Aedes (30), Anopheles (8), Coquillettidia (1), Culiseta (7), and Culex (5). Aspects of the ecology and biology of the Polish mosquito fauna, with particular emphasis on newly recorded species, are discussed.}, }
@article {pmid38786897, year = {2024}, author = {Dyczko, D and Plewa-Tutaj, K and Kiewra, D}, title = {Entomopathogenic Fungi in Forest Habitats of Ixodes ricinus.}, journal = {Insects}, volume = {15}, number = {5}, pages = {}, pmid = {38786897}, issn = {2075-4450}, abstract = {(1) Background: In addition to the microclimate, host availability, and tick microbiota, soil environmental microorganisms can affect tick populations. This study aimed to (1) determine the presence and diversity of entomopathogenic fungi (EF) in forests, where ticks are abundant, and (2) estimate the effectiveness of the isolated EF strains against Ixodes ricinus. (2) Methods: EF were isolated using the trap insect method from soil collected from tick sites. A bioassay was used to estimate the effectiveness of EF against ticks. (3) Results: The presence of EF was found in all tested forest habitat types. A total of 53 strains belonging to the genera Metarhizium, Beauveria, and Isaria were isolated. All the six strains subjected to the bioassay showed potential efficacy against both adult and nymphal stages of I. ricinus; however, the strains differed in their effectiveness. The most effective isolate against I. ricinus was the soil environmental strain of Metarhizium anisopliae. (4) Conclusion: The study indicates that tick habitats can be the source of entomopathogenic fungi, which have a lethal effect on ticks, as demonstrated in preliminary laboratory tests with I. ricinus. However, for practical use, extensive field tests and further research on application methods and long-term effects are necessary to develop effective and sustainable tick management strategies.}, }
@article {pmid38782346, year = {2024}, author = {Liu, Y and Delgado-Baquerizo, M and Bing, H and Wang, Y and Wang, J and Chen, J and Qiu, S and Zhu, H and Wu, Y and Fang, L and Chang, R}, title = {Warming-induced shifts in alpine soil microbiome: An ecosystem-scale study with environmental context-dependent insights.}, journal = {Environmental research}, volume = {255}, number = {}, pages = {119206}, doi = {10.1016/j.envres.2024.119206}, pmid = {38782346}, issn = {1096-0953}, mesh = {*Soil Microbiology ; *Microbiota ; Tibet ; Soil/chemistry ; Global Warming ; Ecosystem ; Altitude ; Climate Change ; }, abstract = {Climate warming is a pressing global issue with substantial impacts on soil health and function. However, the influence of environmental context on the responses of soil microorganisms to warming remains largely elusive, particularly in alpine ecosystems. This study examined the responses of the soil microbiome to in situ experimental warming across three elevations (3850 m, 4100 m, and 4250 m) in the meadow of Gongga Mountain, eastern Tibetan Plateau. Our findings demonstrate that soil microbial diversity is highly resilient to warming, with significant impacts observed only at specific elevations. Furthermore, the influence of warming on the composition of the soil microbial community is also elevation-dependent, underscoring the importance of local environmental context in shaping microbial evolution in alpine soils under climate warming. Notably, we identified soil moisture at 3850 m and carbon-to-nitrogen ratio at 4250 m as indirect predictors regulating the responses of microbial diversity to warming at specific elevations. These findings underscore the paramount importance of considering pre-existing environmental conditions in predicting the response of alpine soil microbiomes to climate warming. Our study provides novel insights into the intricate interactions between climate warming, soil microbiome, and environmental context in alpine ecosystems, illuminating the complex mechanisms governing soil microbial ecology in these fragile and sensitive environments.}, }
@article {pmid38781750, year = {2024}, author = {Bouchali, R and Mandon, C and Danty-Berger, E and Géloën, A and Marjolet, L and Youenou, B and Pozzi, ACM and Vareilles, S and Galia, W and Kouyi, GL and Toussaint, JY and Cournoyer, B}, title = {Runoff microbiome quality assessment of a city center rainwater harvesting zone shows a differentiation of pathogen loads according to human mobility patterns.}, journal = {International journal of hygiene and environmental health}, volume = {260}, number = {}, pages = {114391}, doi = {10.1016/j.ijheh.2024.114391}, pmid = {38781750}, issn = {1618-131X}, mesh = {*Rain ; Humans ; *Microbiota ; *Water Microbiology ; *Cities ; *Bacteria/isolation &amp; purification/classification/genetics ; *Environmental Monitoring/methods ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; }, abstract = {The hygienic quality of urban surfaces can be impaired by multiple sources of microbiological contaminants. These surfaces can trigger the development of multiple bacterial taxa and favor their spread during rain events through the circulation of runoff waters. These runoff waters are commonly directed toward sewer networks, stormwater infiltration systems or detention tanks prior a release into natural water ways. With water scarcity becoming a major worldwide issue, these runoffs are representing an alternative supply for some usage like street cleaning and plant watering. Microbiological hazards associated with these urban runoffs, and surveillance guidelines must be defined to favor these uses. Runoff microbiological quality from a recently implemented city center rainwater harvesting zone was evaluated through classical fecal indicator bacteria (FIB) assays, quantitative PCR and DNA meta-barcoding analyses. The incidence of socio-urbanistic patterns on the organization of these urban microbiomes were investigated. FIB and DNA from Human-specific Bacteroidales and pathogens such as Staphylococcus aureus were detected from most runoffs and showed broad distribution patterns. 16S rRNA DNA meta-barcoding profilings further identified core recurrent taxa of health concerns like Acinetobacter, Mycobacterium, Aeromonas and Pseudomonas, and divided these communities according to two main groups of socio-urbanistic patterns. One of these was highly impacted by heavy traffic, and showed recurrent correlation networks involving bacterial hydrocarbon degraders harboring significant virulence properties. The tpm-based meta-barcoding approach identified some of these taxa at the species level for more than 30 genera. Among these, recurrent pathogens were recorded such as P. aeruginosa, P. paraeruginosa, and Aeromonas caviae. P. aeruginosa and A. caviae tpm reads were found evenly distributed over the study site but those of P. paraeruginosa were higher among sub-catchments impacted by heavy traffic. Health risks associated with these runoff P. paraeruginosa emerging pathogens were high and associated with strong cytotoxicity on A549 lung cells. Recurrent detections of pathogens in runoff waters highlight the need of a microbiological surveillance prior allowing their use. Good microbiological quality can be obtained for certain typologies of sub-catchments with good hygienic practices but not all. A reorganization of Human mobility and behaviors would likely trigger changes in these bacterial diversity patterns and reduce the occurrences of the most hazardous groups.}, }
@article {pmid38780093, year = {2024}, author = {Beaver, RC and Neufeld, JD}, title = {Microbial ecology of the deep terrestrial subsurface.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38780093}, issn = {1751-7370}, support = {//Nuclear Waste Management Organization/ ; //Ontario Research Fund: Research Excellence/ ; //Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Archaea/classification/isolation &amp; purification/metabolism ; *Bacteria/classification/isolation &amp; purification/metabolism/genetics ; *Soil Microbiology ; Microbiota ; Ecosystem ; }, abstract = {The terrestrial subsurface hosts microbial communities that, collectively, are predicted to comprise as many microbial cells as global surface soils. Although initially thought to be associated with deposited organic matter, deep subsurface microbial communities are supported by chemolithoautotrophic primary production, with hydrogen serving as an important source of electrons. Despite recent progress, relatively little is known about the deep terrestrial subsurface compared to more commonly studied environments. Understanding the composition of deep terrestrial subsurface microbial communities and the factors that influence them is of importance because of human-associated activities including long-term storage of used nuclear fuel, carbon capture, and storage of hydrogen for use as an energy vector. In addition to identifying deep subsurface microorganisms, recent research focuses on identifying the roles of microorganisms in subsurface communities, as well as elucidating myriad interactions-syntrophic, episymbiotic, and viral-that occur among community members. In recent years, entirely new groups of microorganisms (i.e. candidate phyla radiation bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoloarchaeota, Nanoarchaeota archaea) have been discovered in deep terrestrial subsurface environments, suggesting that much remains unknown about this biosphere. This review explores the historical context for deep terrestrial subsurface microbial ecology and highlights recent discoveries that shape current ecological understanding of this poorly explored microbial habitat. Additionally, we highlight the need for multifaceted experimental approaches to observe phenomena such as cryptic cycles, complex interactions, and episymbiosis, which may not be apparent when using single approaches in isolation, but are nonetheless critical to advancing our understanding of this deep biosphere.}, }
@article {pmid38779669, year = {2024}, author = {Kou, Z and Liu, K and Qiao, Z and Wang, Y and Li, Y and Li, Y and Yu, X and Han, W}, title = {The alterations of oral, airway and intestine microbiota in chronic obstructive pulmonary disease: a systematic review and meta-analysis.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1407439}, pmid = {38779669}, issn = {1664-3224}, mesh = {*Pulmonary Disease, Chronic Obstructive/microbiology ; Humans ; *Gastrointestinal Microbiome ; Mouth/microbiology ; Microbiota ; Bacteria/classification/genetics ; }, abstract = {BACKGROUND: Increasing evidence indicates the microbial ecology of chronic obstructive pulmonary disease (COPD) is intricately associated with the disease's status and severity, and distinct microbial ecological variations exist between COPD and healthy control (HC). This systematic review and meta-analysis aimed to summarize microbial diversity indices and taxa relative abundance of oral, airway, and intestine microbiota of different stages of COPD and HC to make comparisons.<br><br>METHODS: A comprehensive systematic literature search was conducted in PubMed, Embase, the Web of Science, and the Cochrane Library databases to identify relevant English articles on the oral, airway, and intestine microbiota in COPD published between 2003 and 8 May 2023. Information on microbial diversity indices and taxa relative abundance of oral, airway, and intestine microbiota was collected for comparison between different stages of COPD and HC.<br><br>RESULTS: A total of 20 studies were included in this review, involving a total of 337 HC participants, 511 COPD patients, and 154 AECOPD patients. We observed that no significant differences in alpha diversity between the participant groups, but beta diversity was significantly different in half of the included studies. Compared to HC, Prevotella, Streptococcus, Actinomyces, and Veillonella of oral microbiota in SCOPD were reduced at the genus level. Most studies supported that Haemophilus, Lactobacillus, and Pseudomonas were increased, but Veillonella, Prevotella, Actinomyces, Porphyromonas, and Atopobium were decreased at the genus level in the airway microbiota of SCOPD. However, the abundance of Haemophilus, Lactobacillus and Pseudomonas genera exhibited an increase, whereas Actinomyces and Porphyromonas showed a decrease in the airway microbiota of AECOPD compared to HC. And Lachnospira of intestine microbiota in SCOPD was reduced at the genus level.<br><br>CONCLUSION: The majority of published research findings supported that COPD exhibited decreased alpha diversity compared to HC. However, our meta-analysis does not confirm it. In order to further investigate the characteristics and mechanisms of microbiome in the oral-airway- intestine axis of COPD patients, larger-scale and more rigorous studies are needed.<br><br>PROSPERO (https://www.crd.york.ac.uk/prospero/), identifier CRD42023418726.}, }
@article {pmid38779326, year = {2024}, author = {Mellouk, A and Mahmood, T and Jlali, M and Vieco-Saiz, N and Michel, V and Cozannet, P and Ozbek, S and Mercier, Y and Devillard, E and Consuegra, J}, title = {Potential of guar gum as a leaky gut model in broilers: Digestibility, performance, and microbiota responses.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {17}, number = {}, pages = {177-187}, pmid = {38779326}, issn = {2405-6383}, abstract = {Diet is a major modulator of animal resilience and its three pillars: host's immune response, gut microbiota, and intestinal barrier. In the present study, we endeavour to delineate a challenging condition aimed to degrade these pillars and elucidate its impact on broiler performance and nutrient digestibility. To attain this objective, we opted to use guar gum (GG) as a source of galactomannan. A series of three in vivo experiments were conducted employing conventional or semi-purified diets, supplemented with or without GG during the grower phase (14-28 d). Our findings demonstrate a substantial decline in animal performance metrics such as body weight (reduced by 29%, P < 0.001), feed intake (decreased by 12%, P < 0.001), and feed conversion ratio (up to 58% increase, P < 0.001) in the presence of GG at 2%. The supplementation of a semi-purified diet with incremental doses of GG resulted in a linear reduction (P < 0.001) in the apparent total tract digestibility of dry matter and apparent metabolisable energy. Additionally, a marked reduction in ileal endogenous losses, as well as apparent and standardised digestibility of all amino acids with varying proportions (P < 0.05), was observed. These alterations were accompanied by disrupted gut integrity assessed by fluorescein isothiocyanate-dextran (FITC-d) (P < 0.001) as well as an inflammatory status characterised by elevated levels of acute-phase proteins, namely orosomucoid and serum amyloid A in the sera (P = 0.03), and increased mRNA expression levels of IL-1, IL-6, IL-8, Inos, and K203 genes in the ileum, along with a decrease in IgA levels in the gut lumen (P < 0.05). Microbial ecology and activity were characterised by reduced diversity and richness (Shannon index, P = 0.005) in the presence of GG. Consequently, our results revealed diminished levels of short-chain fatty acids (P = 0.01) and their producer genera, such as Clostridium_XIVa and Blautia, in the gut caeca, coupled with excessive accumulation of lactate (17-fold increase, P < 0.01) in the presence of GG at 2%. In addition to providing a more comprehensive characterisation of the GG supplementation as a leaky gut model, our results substantiate a thorough understanding of the intricate adjustments and interplay between the intestinal barrier, immune response, and microbiota. Furthermore, they underscore the significance of feed components in modulating these dynamics.}, }
@article {pmid38779128, year = {2024}, author = {Eckmann, CA and Bachy, C and Wittmers, F and Strauss, J and Blanco-Bercial, L and Vergin, KL and Parsons, RJ and Kudela, RM and Johnson, R and Bolaños, LM and Giovannoni, SJ and Carlson, CA and Worden, AZ}, title = {Recurring seasonality exposes dominant species and niche partitioning strategies of open ocean picoeukaryotic algae.}, journal = {Communications earth &amp; environment}, volume = {5}, number = {1}, pages = {266}, pmid = {38779128}, issn = {2662-4435}, abstract = {Ocean spring phytoplankton blooms are dynamic periods important to global primary production. We document vertical patterns of a diverse suite of eukaryotic algae, the prasinophytes, in the North Atlantic Subtropical Gyre with monthly sampling over four years at the Bermuda Atlantic Time-series Study site. Water column structure was used to delineate seasonal stability periods more ecologically relevant than seasons defined by calendar dates. During winter mixing, tiny prasinophytes dominated by Class II comprise 46 ± 24% of eukaryotic algal (plastid-derived) 16S rRNA V1-V2 amplicons, specifically Ostreococcus Clade OII, Micromonas commoda, and Bathycoccus calidus. In contrast, Class VII are rare and Classes I and VI peak during warm stratified periods when surface eukaryotic phytoplankton abundances are low. Seasonality underpins a reservoir of genetic diversity from multiple prasinophyte classes during warm periods that harbor ephemeral taxa. Persistent Class II sub-species dominating the winter/spring bloom period retreat to the deep chlorophyll maximum in summer, poised to seed the mixed layer upon winter convection, exposing a mechanism for initiating high abundances at bloom onset. Comparisons to tropical oceans reveal broad distributions of the dominant sub-species herein. This unparalleled window into temporal and spatial niche partitioning of picoeukaryotic primary producers demonstrates how key prasinophytes prevail in warm oceans.}, }
@article {pmid38775958, year = {2024}, author = {Starr, K and Montesanto, F and Perisho, E and Aluthge, N and Pegg, M and Fernando, SC}, title = {Gut Microbial Composition of Cyprinella lutrensis (Red Shiner) and Notropis stramineus (Sand Shiner): Insights from Wild Fish Populations.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {75}, pmid = {38775958}, issn = {1432-184X}, support = {20-121 &amp; 18-176//Nebraska Environmental Trust/ ; 20-121 &amp; 18-176//Nebraska Environmental Trust/ ; NC 1189//National Institute of Food and Agriculture/ ; 2022-33522-38219//National Institute of Food and Agriculture/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteria/classification/isolation &amp; purification/genetics ; *Cyprinidae/microbiology ; *Rivers/microbiology ; RNA, Ribosomal, 16S/genetics ; Nebraska ; }, abstract = {The gut microbiome is a highly intricate ecosystem that exerts a pivotal influence on the host's physiology. Characterizing fish microbiomes is critical to understanding fish physiology and health, but little is known about the ecology and colonization dynamics of microorganisms inhabiting fish species. In this study, we investigated the bacterial communities of two small-bodied fish species, Cyprinella lutrensis (red shiner) and Notropis stramineus (sand shiner), two fish species where gut microbiomes have not been investigated previously and surrounding waters, collected from rivers in Nebraska, USA. Our study focused on evaluating microbial diversity in small-bodied fish and identifying autochthonous microbes present within these species irrespective of location to better understand bacterial community composition and possible roles of such bacterial species. Our results revealed that both red shiner and sand shiner exhibited gut bacterial communities dominated by typical bacterial phyla found in freshwater fish. The phylum Bacteroidota was minimally abundant in both species and significantly lower in relative abundance compared to the surrounding water microbial community. Furthermore, we found that the gut microbiomes of red shiner and sand shiner differed from the microbial community in the surrounding water, suggesting that these fish species contain host-associated bacterial species that may provide benefits to the host such as nutrient digestion and colonization resistance of environmental pathogens. The fish gut bacterial communities were sensitive to environmental conditions such as turbidity, dissolved oxygen, temperature, and total nitrogen. Our findings also show bacterial community differences between fish species; although they shared notable similarities in bacterial taxa at phyla level composition, ASV level analysis of bacterial taxa displayed compositional differences. These findings contribute to a better understanding of the gut bacterial composition of wild, freshwater, small-bodied fish and highlight the influence of intrinsic (host) and environmental factors on shaping the bacterial composition.}, }
@article {pmid38773211, year = {2024}, author = {Fischer, FC and Schulze-Makuch, D and Heinz, J}, title = {Microbial preference for chlorate over perchlorate under simulated shallow subsurface Mars-like conditions.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {11537}, pmid = {38773211}, issn = {2045-2322}, support = {455070607//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Perchlorates/metabolism ; *Mars ; *Chlorates/metabolism ; *Extraterrestrial Environment ; Aspergillus niger/metabolism ; Saccharomycetales/metabolism ; Water/chemistry ; Microbial Viability ; }, abstract = {The Martian surface and shallow subsurface lacks stable liquid water, yet hygroscopic salts in the regolith may enable the transient formation of liquid brines. This study investigated the combined impact of water scarcity, UV exposure, and regolith depth on microbial survival under Mars-like environmental conditions. Both vegetative cells of Debaryomyces hansenii and Planococcus halocryophilus, alongside with spores of Aspergillus niger, were exposed to an experimental chamber simulating Martian environmental conditions (constant temperatures of about - 11 °C, low pressure of approximately 6 mbar, a CO2 atmosphere, and 2 h of daily UV irradiation). We evaluated colony-forming units (CFU) and water content at three different regolith depths before and after exposure periods of 3 and 7 days, respectively. Each organism was tested under three conditions: one without the addition of salts to the regolith, one containing sodium chlorate, and one with sodium perchlorate. Our results reveal that the residual water content after the exposure experiments increased with regolith depth, along with the organism survival rates in chlorate-containing and salt-free samples. The survival rates of the three organisms in perchlorate-containing regolith were consistently lower for all organisms and depths compared to chlorate, with the most significant difference being observed at a depth of 10-12 cm, which corresponds to the depth with the highest residual water content. The postulated reason for this is an increase in the salt concentration at this depth due to the freezing of water, showing that for these organisms, perchlorate brines are more toxic than chlorate brines under the experimental conditions. This underscores the significance of chlorate salts when considering the habitability of Martian environments.}, }
@article {pmid38773116, year = {2024}, author = {Huang, WRH and Braam, C and Kretschmer, C and Villanueva, SL and Liu, H and Ferik, F and van der Burgh, AM and Boeren, S and Wu, J and Zhang, L and Nürnberger, T and Wang, Y and Seidl, MF and Evangelisti, E and Stuttmann, J and Joosten, MHAJ}, title = {Receptor-like cytoplasmic kinases of different subfamilies differentially regulate SOBIR1/BAK1-mediated immune responses in Nicotiana benthamiana.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4339}, pmid = {38773116}, issn = {2041-1723}, support = {201706990001//China Scholarship Council (CSC)/ ; E032-2017-01 55851//CONCYTEC | Fondo Nacional de Desarrollo Cient&#xed;fico, Tecnol&#xf3;gico y de Innovaci&#xf3;n Tecnol&#xf3;gica (Cienciactiva)/ ; }, mesh = {*Nicotiana/immunology/microbiology/genetics/metabolism ; *Plant Proteins/metabolism/genetics ; *Plant Immunity/genetics ; *Protein Serine-Threonine Kinases/metabolism/genetics ; *Plant Diseases/microbiology/immunology ; Phytophthora/pathogenicity ; Protein Kinases/metabolism/genetics ; Phosphorylation ; Gene Expression Regulation, Plant ; Reactive Oxygen Species/metabolism ; Signal Transduction ; }, abstract = {Cell-surface receptors form the front line of plant immunity. The leucine-rich repeat (LRR)-receptor-like kinases SOBIR1 and BAK1 are required for the functionality of the tomato LRR-receptor-like protein Cf-4, which detects the secreted effector Avr4 of the pathogenic fungus Fulvia fulva. Here, we show that the kinase domains of SOBIR1 and BAK1 directly phosphorylate each other and that residues Thr522 and Tyr469 of the kinase domain of Nicotiana benthamiana SOBIR1 are required for its kinase activity and for interacting with signalling partners, respectively. By knocking out multiple genes belonging to different receptor-like cytoplasmic kinase (RLCK)-VII subfamilies in N. benthamiana:Cf-4, we show that members of RLCK-VII-6, -7, and -8 differentially regulate the Avr4/Cf-4-triggered biphasic burst of reactive oxygen species. In addition, members of RLCK-VII-7 play an essential role in resistance against the oomycete pathogen Phytophthora palmivora. Our study provides molecular evidence for the specific roles of RLCKs downstream of SOBIR1/BAK1-containing immune complexes.}, }
@article {pmid38772810, year = {2024}, author = {Zai, X and Cordovez, V and Zhu, F and Zhao, M and Diao, X and Zhang, F and Raaijmakers, JM and Song, C}, title = {C4 cereal and biofuel crop microbiomes.}, journal = {Trends in microbiology}, volume = {32}, number = {11}, pages = {1119-1131}, doi = {10.1016/j.tim.2024.04.008}, pmid = {38772810}, issn = {1878-4380}, mesh = {*Biofuels/microbiology ; *Microbiota/physiology ; *Edible Grain/microbiology ; *Crops, Agricultural/microbiology ; Setaria Plant/genetics/microbiology ; Climate Change ; }, abstract = {Microbiomes provide multiple life-support functions for plants, including nutrient acquisition and tolerance to abiotic and biotic stresses. Considering the importance of C4 cereal and biofuel crops for food security under climate change conditions, more attention has been given recently to C4 plant microbiome assembly and functions. Here, we review the current status of C4 cereal and biofuel crop microbiome research with a focus on beneficial microbial traits for crop growth and health. We highlight the importance of environmental factors and plant genetics in C4 crop microbiome assembly and pinpoint current knowledge gaps. Finally, we discuss the potential of foxtail millet as a C4 model species and outline future perspectives of C4 plant microbiome research.}, }
@article {pmid38771894, year = {2024}, author = {Van Hee, S and Alınç, T and Weldegergis, BT and Dicke, M and Colazza, S and Peri, E and Jacquemyn, H and Cusumano, A and Lievens, B}, title = {Differential effects of plant-beneficial fungi on the attraction of the egg parasitoid Trissolcus basalis in response to Nezara viridula egg deposition.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0304220}, pmid = {38771894}, issn = {1932-6203}, mesh = {Animals ; *Beauveria/physiology ; *Capsicum/parasitology/microbiology ; *Wasps/physiology ; *Oviposition ; Volatile Organic Compounds/metabolism ; Female ; Trichoderma/physiology ; Host-Parasite Interactions ; Ovum ; Herbivory ; }, abstract = {There is increasing evidence that plant-associated microorganisms play important roles in defending plants against insect herbivores through both direct and indirect mechanisms. While previous research has shown that these microbes can modify the behaviour and performance of insect herbivores and their natural enemies, little is known about their effect on egg parasitoids which utilize oviposition-induced plant volatiles to locate their hosts. In this study, we investigated how root inoculation of sweet pepper (Capsicum annuum) with the plant-beneficial fungi Beauveria bassiana ARSEF 3097 or Trichoderma harzianum T22 influences the olfactory behaviour of the egg parasitoid Trissolcus basalis following egg deposition by its host Nezara viridula. Olfactometer assays showed that inoculation by T. harzianum significantly enhanced the attraction of the egg parasitoid, while B. bassiana had the opposite effect. However, no variation was observed in the chemical composition of plant volatiles. Additionally, fitness-related traits of the parasitoids (wasp body size) were not altered by any of the two fungi, suggesting that fungal inoculation did not indirectly affect host quality. Altogether, our results indicate that plant inoculation with T. harzianum T22 can be used to enhance attraction of egg parasitoids, which could be a promising strategy in manipulating early plant responses against pest species and improving sustainable crop protection. From a more fundamental point of view, our findings highlight the importance of taking into account the role of microorganisms when studying the intricate interactions between plants, herbivores and their associated egg parasitoids.}, }
@article {pmid38771538, year = {2024}, author = {Song, S and Sun, Z and Xu, G and Xu, H}, title = {Continuous warming drives the colonization dynamics of periphytic ciliate fauna in marine environments.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {25}, pages = {37326-37336}, pmid = {38771538}, issn = {1614-7499}, support = {31672308//The Natural Science Foundation of China/ ; 41076089//The Natural Science Foundation of China/ ; }, mesh = {*Ciliophora/physiology ; *Global Warming ; *Ecosystem ; Temperature ; }, abstract = {In order to evaluate the influence of global warming on the ecosystem processes in marine environments, the changes in colonization dynamics of periphytic microbiota were studied using the periphytic ciliate communities as the test organism fauna under a continuous warming gradient of 22℃ (control), 25℃, 28℃, 31℃, and 34 ℃. The results demonstrated that (1) the test ciliate communities generally showed a similar temporal pattern in within the colonization process under the water temperatures from 22 up to 28℃; however, (2) the colonization dynamics were significantly changed, and the fitness of colonization curves to the MacArthur-Wilson model equation was failed under the temperature increased by 6 ℃, and (3) the loading or assimilative capacity of the test aquatic ecosystem was decreased with the increase of water temperature. Therefore, this study suggests that continuous warming may significantly drive the colonization dynamics of periphytic ciliates in marine ecosystems.}, }
@article {pmid38771339, year = {2024}, author = {Jiao, Y and Zhang, G and Ai, X and Wang, X}, title = {Comparison of the Effects of LDPE and PBAT Film Residues on Soil Microbial Ecology.}, journal = {Current microbiology}, volume = {81}, number = {7}, pages = {185}, pmid = {38771339}, issn = {1432-0991}, support = {52200109//National Natural Science Foundation of China/ ; 202102310278//State Scholarship Fund and the Key R&amp;D and Promotion Project of Henan Province/ ; }, mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Polyethylene/chemistry ; Polyesters/metabolism ; Soil/chemistry ; Soil Pollutants/analysis ; Microbiota ; }, abstract = {The plastic film is extensively applied with limited recycling, leading to the long-run residue accumulation in soil, which offers a distinctive habitat for microorganisms, and creates a plastisphere. In this study, traditional low-density polyethylene (LDPE) plastic film and biodegradable polybutylene adipate terephthalate (PBAT) plastic film materials were selected to test their effects on soil microbial ecology. Based on high-throughput sequencing, compared to the soil environment, the alpha-diversity of bacterial communities in plastisphere was lower, and the abundance of Actinobacteria increased. Plastic film residues, as bacterial habitats, exhibited greater heterogeneity and harbor unique bacterial communities. The communities were distinguished between plastisphere and soil environment by means of a random-forest (RF) machine-learning model. Prominent distinctions emerged among bacterial functions between soil environment and plastisphere, especially regarding organics degradation. The neutral model and null model indicated that the constitution of bacterial communities was dominated by random processes except in LDPE plastisphere. The bacterial co-occurrence network of the plastisphere exhibited higher complexity and modularity. This study contributes to our comprehending of characteristics of plastisphere bacterial communities in soil environment and the associated ecological risks of plastic film residues accumulation.}, }
@article {pmid38771320, year = {2024}, author = {Wang, Y and Zou, Q}, title = {Deciphering Microbial Adaptation in the Rhizosphere: Insights into Niche Preference, Functional Profiles, and Cross-Kingdom Co-occurrences.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {74}, pmid = {38771320}, issn = {1432-184X}, support = {62102269, 62373080//National Natural Science Foundation of China/ ; }, mesh = {*Rhizosphere ; *Soil Microbiology ; *Fungi/genetics/classification/physiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota ; *Adaptation, Physiological ; Ecosystem ; Bacterial Physiological Phenomena ; }, abstract = {Rhizosphere microbial communities are to be as critical factors for plant growth and vitality, and their adaptive differentiation strategies have received increasing amounts of attention but are poorly understood. In this study, we obtained bacterial and fungal amplicon sequences from the rhizosphere and bulk soils of various ecosystems to investigate the potential mechanisms of microbial adaptation to the rhizosphere environment. Our focus encompasses three aspects: niche preference, functional profiles, and cross-kingdom co-occurrence patterns. Our findings revealed a correlation between niche similarity and nucleotide distance, suggesting that niche adaptation explains nucleotide variation among some closely related amplicon sequence variants (ASVs). Furthermore, biological macromolecule metabolism and communication among abundant bacteria increase in the rhizosphere conditions, suggesting that bacterial function is trait-mediated in terms of fitness in new habitats. Additionally, our analysis of cross-kingdom networks revealed that fungi act as intermediaries that facilitate connections between bacteria, indicating that microbes can modify their cooperative relationships to adapt. Overall, the evidence for rhizosphere microbial community adaptation, via differences in gene and functional and co-occurrence patterns, elucidates the adaptive benefits of genetic and functional flexibility of the rhizosphere microbiota through niche shifts.}, }
@article {pmid38765607, year = {2024}, author = {Wu, S and Qu, Z and Chen, D and Wu, H and Caiyin, Q and Qiao, J}, title = {Deciphering and designing microbial communities by genome-scale metabolic modelling.}, journal = {Computational and structural biotechnology journal}, volume = {23}, number = {}, pages = {1990-2000}, pmid = {38765607}, issn = {2001-0370}, abstract = {Microbial communities are shaped by the complex interactions among organisms and the environment. Genome-scale metabolic models (GEMs) can provide deeper insights into the complexity and ecological properties of various microbial communities, revealing their intricate interactions. Many researchers have modified GEMs for the microbial communities based on specific needs. Thus, GEMs need to be comprehensively summarized to better understand the trends in their development. In this review, we summarized the key developments in deciphering and designing microbial communities using different GEMs. A timeline of selected highlights in GEMs indicated that this area is evolving from the single-strain level to the microbial community level. Then, we outlined a framework for constructing GEMs of microbial communities. We also summarized the models and resources of static and dynamic community-level GEMs. We focused on the role of external environmental and intracellular resources in shaping the assembly of microbial communities. Finally, we discussed the key challenges and future directions of GEMs, focusing on the integration of GEMs with quorum sensing mechanisms, microbial ecology interactions, machine learning algorithms, and automatic modeling, all of which contribute to consortia-based applications in different fields.}, }
@article {pmid38763283, year = {2024}, author = {Liu, S and Shi, Y and Chen, J and Zhang, Z and Cao, H and Li, W and Ye, M}, title = {Interspecific barrier effect driven by heavy metals makes soil bacterial functional assembly more stochastic.}, journal = {Environmental research}, volume = {253}, number = {}, pages = {119153}, doi = {10.1016/j.envres.2024.119153}, pmid = {38763283}, issn = {1096-0953}, mesh = {*Soil Microbiology ; *Metals, Heavy/toxicity/analysis ; *Soil Pollutants/toxicity/analysis ; *Bacteria/genetics/classification/drug effects ; China ; Stochastic Processes ; Microbiota/drug effects ; }, abstract = {Residual heavy metals in soils will destroy microbial community stability and influence its aggregation. However, exploring microbial ecology under heavy-metal stress still requires a conjoint analysis of bacterial interspecies communication and the community diversity maintenance mechanism. In this study, soil samples were collected from a heavy-metal-contaminated site in China to investigate the ecological response of indigenous microbial communities through high-throughput sequencing. Results showed that bacterial taxa and functions generated unusual decoupling phenomena. There were no significant differences in the diversity of species with the increase in concentration of heavy metals (Hg, Se, and Cr), but the functional diversity was lost. Also, the average niche breadth of bacterial species increased from 1.70 to 2.28, but community stability declined and the species assembly was always a deterministic process (NST <0.5). After the bacterial functional assembly changed from a stochastic process to a deterministic process (NST <0.5), it was transformed into a stochastic process (NST >0.5) again under the stress of high-concentration heavy metals, indicating that the collective stress resistance of bacterial communities changed from positive mutation into passive functional propagation. The research results can provide new insight into understanding the adaptive evolution of communities and ecosystem restoration under the stress of soil heavy metals.}, }
@article {pmid38762502, year = {2024}, author = {Awala, SI and Gwak, JH and Kim, Y and Jung, MY and Dunfield, PF and Wagner, M and Rhee, SK}, title = {Nitrous oxide respiration in acidophilic methanotrophs.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4226}, pmid = {38762502}, issn = {2041-1723}, mesh = {*Nitrous Oxide/metabolism ; *Methane/metabolism ; Hydrogen-Ion Concentration ; Oxidoreductases/metabolism/genetics ; Oxygen/metabolism ; Oxidation-Reduction ; Anaerobiosis ; Methanol/metabolism ; Hydrogen/metabolism ; Oxygenases/metabolism/genetics ; }, abstract = {Aerobic methanotrophic bacteria are considered strict aerobes but are often highly abundant in hypoxic and even anoxic environments. Despite possessing denitrification genes, it remains to be verified whether denitrification contributes to their growth. Here, we show that acidophilic methanotrophs can respire nitrous oxide (N2O) and grow anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen. We study two strains that possess N2O reductase genes: Methylocella tundrae T4 and Methylacidiphilum caldifontis IT6. We show that N2O respiration supports growth of Methylacidiphilum caldifontis at an extremely acidic pH of 2.0, exceeding the known physiological pH limits for microbial N2O consumption. Methylocella tundrae simultaneously consumes N2O and CH4 in suboxic conditions, indicating robustness of its N2O reductase activity in the presence of O2. Furthermore, in O2-limiting conditions, the amount of CH4 oxidized per O2 reduced increases when N2O is added, indicating that Methylocella tundrae can direct more O2 towards methane monooxygenase. Thus, our results demonstrate that some methanotrophs can respire N2O independently or simultaneously with O2, which may facilitate their growth and survival in dynamic environments. Such metabolic capability enables these bacteria to simultaneously reduce the release of the key greenhouse gases CO2, CH4, and N2O.}, }
@article {pmid38762482, year = {2024}, author = {Min, K and Glowacki, AJ and Bosma, ML and McGuire, JA and Tian, S and McAdoo, K and DelSasso, A and Fourre, T and Gambogi, RJ and Milleman, J and Milleman, KR}, title = {Quantitative analysis of the effects of essential oil mouthrinses on clinical plaque microbiome: a parallel-group, randomized trial.}, journal = {BMC oral health}, volume = {24}, number = {1}, pages = {578}, pmid = {38762482}, issn = {1472-6831}, mesh = {Humans ; *Mouthwashes/therapeutic use ; *Oils, Volatile/therapeutic use/pharmacology ; *Dental Plaque/microbiology ; *Microbiota/drug effects ; Adult ; *Gingivitis/microbiology/prevention &amp; control ; Male ; Female ; Anti-Infective Agents, Local/therapeutic use ; Salicylates/therapeutic use ; Young Adult ; Middle Aged ; Drug Combinations ; Terpenes ; }, abstract = {BACKGROUND: The rich diversity of microorganisms in the oral cavity plays an important role in the maintenance of oral health and development of detrimental oral health conditions. Beyond commonly used qualitative microbiome metrics, such as relative proportions or diversity, both the species-level identification and quantification of bacteria are key to understanding clinical disease associations. This study reports the first-time application of an absolute quantitative microbiome analysis using spiked DNA standards and shotgun metagenome sequencing to assess the efficacy and safety of product intervention on dental plaque microbiome.<br><br>METHODS: In this parallel-group, randomized clinical trial, essential oil mouthrinses, including LISTERINE&#xae; Cool Mint Antiseptic (LCM), an alcohol-containing prototype mouthrinse (ACPM), and an alcohol-free prototype mouthrinse (AFPM), were compared against a hydroalcohol control rinse on clinical parameters and the oral microbiome of subjects with moderate gingivitis. To enable a sensitive and clinically meaningful measure of bacterial abundances, species were categorized according to their associations with oral conditions based on published literature and quantified using known amounts of spiked DNA standards.<br><br>RESULTS: Multivariate analysis showed that both LCM and ACPM shifted the dysbiotic microbiome composition of subjects with gingivitis to a healthier state after 4 weeks of twice-daily use, resembling the composition of subjects with clinically healthy oral conditions recruited for observational reference comparison at baseline. The essential oil-containing mouthrinses evaluated in this study showed statistically significant reductions in clinical gingivitis and plaque measurements when compared to the hydroalcohol control rinse after 6 weeks of use.<br><br>CONCLUSIONS: By establishing a novel quantitative method for microbiome analysis, this study sheds light on the mechanisms of LCM mouthrinse efficacy on oral microbial ecology, demonstrating that repeated usage non-selectively resets a gingivitis-like oral microbiome toward that of a healthy oral cavity.<br><br>TRIAL REGISTRATION: The trial was registered on ClinicalTrials.gov on 10/06/2021. The registration number is NCT04921371.}, }
@article {pmid38761763, year = {2024}, author = {Wang, Z and Lü, C and Wang, Y and Gomes, RL and Clarke, CJ and Gomes, HI}, title = {Zero-valent iron (ZVI) facilitated in-situ selenium (Se) immobilization and its recovery by magnetic separation: Mechanisms and implications for microbial ecology.}, journal = {Journal of hazardous materials}, volume = {473}, number = {}, pages = {134591}, doi = {10.1016/j.jhazmat.2024.134591}, pmid = {38761763}, issn = {1873-3336}, mesh = {*Selenium/chemistry ; *Iron/chemistry ; *Water Pollutants, Chemical/chemistry ; *Geologic Sediments/microbiology/chemistry ; Bacteria/metabolism/genetics ; Biodegradation, Environmental ; RNA, Ribosomal, 16S/genetics ; Magnetic Phenomena ; }, abstract = {Selenium (Se(VI)) is environmentally toxic. One of the most popular reducing agents for Se(VI) remediation is zero-valent iron (ZVI). However, most ZVI studies were carried out in water matrices, and the recovery of reduced Se has not been investigated. A water-sediment system constructed using natural sediment was employed here to study in-situ Se remediation and recovery. A combined effect of ZVI and unacclimated microorganisms from natural sediment was found in Se(VI) removal in the water phase with a removal efficiency of 92.7 ± 1.1% within 7 d when 10 mg L[-1] Se(VI) was present. Soluble Se(VI) was removed from the water and precipitated to the sediment phase (74.8 ± 0.1%), which was enhanced by the addition of ZVI (83.3 ± 0.3%). The recovery proportion of the immobilized Se was 34.2 ± 0.1% and 92.5 ± 0.2% through wet and dry magnetic separation with 1 g L[-1] ZVI added, respectively. The 16 s rRNA sequencing revealed the variations in the microbial communities in response to ZVI and Se, which the magnetic separation could potentially mitigate in the long term. This study provides a novel technique to achieve in-situ Se remediation and recovery by combining ZVI reduction and magnetic separation.}, }
@article {pmid38760758, year = {2024}, author = {Min, K and Bosma, ML and John, G and McGuire, JA and DelSasso, A and Milleman, J and Milleman, KR}, title = {Quantitative analysis of the effects of brushing, flossing, and mouthrinsing on supragingival and subgingival plaque microbiota: 12-week clinical trial.}, journal = {BMC oral health}, volume = {24}, number = {1}, pages = {575}, pmid = {38760758}, issn = {1472-6831}, mesh = {Humans ; *Dental Plaque/microbiology ; *Gingivitis/microbiology ; *Mouthwashes/therapeutic use ; Female ; *Microbiota/drug effects ; Adult ; *Toothbrushing/methods ; Male ; *Dental Devices, Home Care ; Single-Blind Method ; Middle Aged ; Salicylates/therapeutic use ; Drug Combinations ; Terpenes/therapeutic use/pharmacology ; Bacterial Load/drug effects ; Anti-Infective Agents, Local/therapeutic use ; Young Adult ; }, abstract = {BACKGROUND: Translational microbiome research using next-generation DNA sequencing is challenging due to the semi-qualitative nature of relative abundance data. A novel method for quantitative analysis was applied in this 12-week clinical trial to understand the mechanical vs. chemotherapeutic actions of brushing, flossing, and mouthrinsing against the supragingival dental plaque microbiome. Enumeration of viable bacteria using vPCR was also applied on supragingival plaque for validation and on subgingival plaque to evaluate interventional effects below the gingival margin.<br><br>METHODS: Subjects with gingivitis were enrolled in a single center, examiner-blind, virtually supervised, parallel group controlled clinical trial. Subjects with gingivitis were randomized into brushing only (B); brushing and flossing (BF); brushing and rinsing with Listerine&#xae; Cool Mint&#xae; Antiseptic (BA); brushing and rinsing with Listerine&#xae; Cool Mint&#xae; Zero (BZ); or brushing, flossing, and rinsing with Listerine&#xae; Cool Mint&#xae; Zero (BFZ). All subjects brushed twice daily for 1&#xa0;min with a sodium monofluorophosphate toothpaste and a soft-bristled toothbrush. Subjects who flossed used unflavored waxed dental floss once daily. Subjects assigned to mouthrinses rinsed twice daily. Plaque specimens were collected at the baseline visit and after 4 and 12 weeks of intervention. Bacterial cell number quantification was achieved by adding reference amounts of DNA controls to plaque samples prior to DNA extraction, followed by shallow shotgun metagenome sequencing.<br><br>RESULTS: 286 subjects completed the trial. The metagenomic data for supragingival plaque showed significant reductions in Shannon-Weaver diversity, species richness, and total and categorical bacterial abundances (commensal, gingivitis, and malodor) after 4 and 12 weeks for the BA, BZ, and BFZ groups compared to the B group, while no significant differences were observed between the B and BF groups. Supragingival plaque vPCR further validated these results, and subgingival plaque vPCR demonstrated significant efficacy for the BFZ intervention only.<br><br>CONCLUSIONS: This publication reports on a successful application of a quantitative method of microbiome analysis in a clinical trial demonstrating the sustained and superior efficacy of essential oil mouthrinses at controlling dental plaque compared to mechanical methods. The quantitative microbiological data in this trial also reinforce the safety and mechanism of action of EO mouthrinses against plaque microbial ecology and highlights the importance of elevating EO mouthrinsing as an integral part of an oral hygiene regimen.<br><br>TRIAL REGISTRATION: The trial was registered on ClinicalTrials.gov on 31/10/2022. The registration number is NCT05600231.}, }
@article {pmid38758374, year = {2024}, author = {Nie, X and Zhao, Z and Zhang, X and Bastías, DA and Nan, Z and Li, C}, title = {Endophytes Alleviate Drought-Derived Oxidative Damage in Achnatherum inebrians Plants Through Increasing Antioxidants and Regulating Host Stress Responses.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {73}, pmid = {38758374}, issn = {1432-184X}, support = {31772665//The National Nature Science Foundation of China/ ; jbky-2022-ey21//The Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Endophytes/metabolism/physiology ; *Antioxidants/metabolism ; *Oxidative Stress ; *Droughts ; *Epichloe/physiology/genetics/metabolism ; Gene Expression Regulation, Plant ; Stress, Physiological ; }, abstract = {Endophytes generally increase antioxidant contents of plants subjected to environmental stresses. However, the mechanisms by which endophytes alter the accumulation of antioxidants in plant tissues are not entirely clear. We hypothesized that, in stress situations, endophytes would simultaneously reduce oxidative damage and increase antioxidant contents of plants and that the accumulation of antioxidants would be a consequence of the endophyte ability to regulate the expression of plant antioxidant genes. We investigated the effects of the fungal endophyte Epichloë gansuensis (C.J. Li &amp; Nan) on oxidative damage, antioxidant contents, and expression of representative genes associated with antioxidant pathways in Achnatherum inebrians (Hance) Keng plants subjected to low (15%) and high (60%) soil moisture conditions. Gene expression levels were measured using RNA-seq. As expected, the endophyte reduced the oxidative damage by 17.55% and increased the antioxidant contents by 53.14% (on average) in plants subjected to low soil moisture. In line with the accumulation of antioxidants in plant tissues, the endophyte increased the expression of most plant genes associated with the biosynthesis of antioxidants (e.g., MIOX, crtB, gpx) while it reduced the expression of plant genes related to the metabolization of antioxidants (e.g., GST, PRODH, ALDH). Our findings suggest that endophyte ability of increasing antioxidant contents in plants may reduce the oxidative damage caused by stresses and that the fungal regulation of plant antioxidants would partly explain the accumulation of these compounds in plant tissues.}, }
@article {pmid38756954, year = {2024}, author = {Wang, F and Xiang, L and Sze-Yin Leung, K and Elsner, M and Zhang, Y and Guo, Y and Pan, B and Sun, H and An, T and Ying, G and Brooks, BW and Hou, D and Helbling, DE and Sun, J and Qiu, H and Vogel, TM and Zhang, W and Gao, Y and Simpson, MJ and Luo, Y and Chang, SX and Su, G and Wong, BM and Fu, TM and Zhu, D and Jobst, KJ and Ge, C and Coulon, F and Harindintwali, JD and Zeng, X and Wang, H and Fu, Y and Wei, Z and Lohmann, R and Chen, C and Song, Y and Sanchez-Cid, C and Wang, Y and El-Naggar, A and Yao, Y and Huang, Y and Cheuk-Fung Law, J and Gu, C and Shen, H and Gao, Y and Qin, C and Li, H and Zhang, T and Corcoll, N and Liu, M and Alessi, DS and Li, H and Brandt, KK and Pico, Y and Gu, C and Guo, J and Su, J and Corvini, P and Ye, M and Rocha-Santos, T and He, H and Yang, Y and Tong, M and Zhang, W and Suanon, F and Brahushi, F and Wang, Z and Hashsham, SA and Virta, M and Yuan, Q and Jiang, G and Tremblay, LA and Bu, Q and Wu, J and Peijnenburg, W and Topp, E and Cao, X and Jiang, X and Zheng, M and Zhang, T and Luo, Y and Zhu, L and Li, X and Barceló, D and Chen, J and Xing, B and Amelung, W and Cai, Z and Naidu, R and Shen, Q and Pawliszyn, J and Zhu, YG and Schaeffer, A and Rillig, MC and Wu, F and Yu, G and Tiedje, JM}, title = {Emerging contaminants: A One Health perspective.}, journal = {Innovation (Cambridge (Mass.))}, volume = {5}, number = {4}, pages = {100612}, pmid = {38756954}, issn = {2666-6758}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; P42 ES027706/ES/NIEHS NIH HHS/United States ; }, abstract = {Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health. Despite global efforts to mitigate legacy pollutants, the continuous introduction of new substances remains a major threat to both people and the planet. In response, global initiatives are focusing on risk assessment and regulation of emerging contaminants, as demonstrated by the ongoing efforts to establish the UN's Intergovernmental Science-Policy Panel on Chemicals, Waste, and Pollution Prevention. This review identifies the sources and impacts of emerging contaminants on planetary health, emphasizing the importance of adopting a One Health approach. Strategies for monitoring and addressing these pollutants are discussed, underscoring the need for robust and socially equitable environmental policies at both regional and international levels. Urgent actions are needed to transition toward sustainable pollution management practices to safeguard our planet for future generations.}, }
@article {pmid38756730, year = {2024}, author = {Akashi, M and Takemura, M and Suzuki, S}, title = {Continuous year-round isolation of giant viruses from brackish shoreline soils.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1402690}, pmid = {38756730}, issn = {1664-302X}, abstract = {Giant viruses, categorized under Nucleocytoviricota, are believed to exist ubiquitously in natural environments. However, comprehensive reports on isolated giant viruses remain scarce, with limited information available on unrecoverable strains, viral proliferation sites, and natural hosts. Previously, the author highlighted Pandoravirus hades, Pandoravirus persephone, and Mimivirus sp. styx, isolated from brackish water soil, as potential hotspots for giant virus multiplication. This study presents findings from nearly a year of monthly sampling within the same brackish water region after isolating the three aforementioned strains. This report details the recurrent isolation of a wide range of giant viruses. Each month, four soil samples were randomly collected from an approximately 5 × 10 m plot, comprising three soil samples and one water sample containing sediment from the riverbed. Acanthamoeba castellanii was used as a host for virus isolation. These efforts consistently yielded at least one viral species per month, culminating in a total of 55 giant virus isolates. The most frequently isolated species was Mimiviridae (24 isolates), followed by Marseilleviridae (23 isolates), Pandoravirus (6 isolates), and singular isolates of Pithovirus and Cedratvirus. Notably, viruses were not consistently isolated from any of the four samples every month, with certain sites yielding no viruses. Cluster analysis based on isolate numbers revealed that soil samples from May and water and sediment samples from January produced the highest number of viral strains. These findings underscore brackish coastal soil as a significant site for isolating numerous giant viruses, highlighting the non-uniform distribution along coastlines.}, }
@article {pmid38755460, year = {2024}, author = {Flores-Almaraz, VS and Truong, C and Hernández-Oaxaca, D and Reyes-Galindo, V and Mastretta-Yanes, A and Jaramillo-Correa, JP and Salas-Lizana, R}, title = {Foliar mycobiome remains unaltered under urban air-pollution but differentially express stress-related genes.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {72}, pmid = {38755460}, issn = {1432-184X}, support = {grant 778409//CONAHCyT Becas Nacionales/ ; grant 308488//CONAHCYT FORDECYT-PRONACES/ ; grant 308488//CONAHCYT FORDECYT-PRONACES/ ; grant 308488//CONAHCYT FORDECYT-PRONACES/ ; Project 319083//CONAHCyT PRONACES Sistemas Socioecol&#xf3;gicos 2021/ ; Project 319083//CONAHCyT PRONACES Sistemas Socioecol&#xf3;gicos 2021/ ; Project 319083//CONAHCyT PRONACES Sistemas Socioecol&#xf3;gicos 2021/ ; }, mesh = {*Mycobiome ; *Fungi/genetics/classification/isolation &amp; purification ; *Plant Leaves/microbiology ; Mexico ; *Air Pollution/adverse effects ; Ozone ; Stress, Physiological ; Cities ; }, abstract = {Air pollution caused by tropospheric ozone contributes to the decline of forest ecosystems; for instance, sacred fir, Abies religiosa (Kunth) Schltdl. &amp; Cham. forests in the peri-urban region of Mexico City. Individual trees within these forests exhibit variation in their response to ozone exposure, including the severity of visible symptoms in needles. Using RNA-Seq metatranscriptomic data and ITS2 metabarcoding, we investigated whether symptom variation correlates with the taxonomic and functional composition of fungal mycobiomes from needles collected in this highly polluted area in the surroundings of Mexico City. Our findings indicate that ozone-related symptoms do not significantly correlate with changes in the taxonomic composition of fungal mycobiomes. However, genes coding for 30 putative proteins were differentially expressed in the mycobiome of asymptomatic needles, including eight genes previously associated with resistance to oxidative stress. These results suggest that fungal communities likely play a role in mitigating the oxidative burst caused by tropospheric ozone in sacred fir. Our study illustrates the feasibility of using RNA-Seq data, accessible from global sequence repositories, for the characterization of fungal communities associated with plant tissues, including their gene expression.}, }
@article {pmid38755154, year = {2024}, author = {Schmider, T and Hestnes, AG and Brzykcy, J and Schmidt, H and Schintlmeister, A and Roller, BRK and Teran, EJ and Söllinger, A and Schmidt, O and Polz, MF and Richter, A and Svenning, MM and Tveit, AT}, title = {Physiological basis for atmospheric methane oxidation and methanotrophic growth on air.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4151}, pmid = {38755154}, issn = {2041-1723}, support = {295910//Norges Forskningsr&#xe5;d (Research Council of Norway)/ ; 315129//Norges Forskningsr&#xe5;d (Research Council of Norway)/ ; }, mesh = {*Methane/metabolism ; *Oxidation-Reduction ; *Carbon Monoxide/metabolism ; *Hydrogen/metabolism ; Atmosphere/chemistry ; Air ; Nitrogen/metabolism ; Greenhouse Gases/metabolism ; }, abstract = {Atmospheric methane oxidizing bacteria (atmMOB) constitute the sole biological sink for atmospheric methane. Still, the physiological basis allowing atmMOB to grow on air is not well understood. Here we assess the ability and strategies of seven methanotrophic species to grow with air as sole energy, carbon, and nitrogen source. Four species, including three outside the canonical atmMOB group USCα, enduringly oxidized atmospheric methane, carbon monoxide, and hydrogen during 12 months of growth on air. These four species exhibited distinct substrate preferences implying the existence of multiple metabolic strategies to grow on air. The estimated energy yields of the atmMOB were substantially lower than previously assumed necessary for cellular maintenance in atmMOB and other aerobic microorganisms. Moreover, the atmMOB also covered their nitrogen requirements from air. During growth on air, the atmMOB decreased investments in biosynthesis while increasing investments in trace gas oxidation. Furthermore, we confirm that a high apparent specific affinity for methane is a key characteristic of atmMOB. Our work shows that atmMOB grow on the trace concentrations of methane, carbon monoxide, and hydrogen present in air and outlines the metabolic strategies that enable atmMOB to mitigate greenhouse gases.}, }
@article {pmid38755019, year = {2024}, author = {Vaccalluzzo, A and Pino, A and Grimaldi, RL and Caggia, C and Cianci, S and Randazzo, CL}, title = {Lacticaseibacillus rhamnosus TOM 22.8 (DSM 33500) is an effective strategy for managing vaginal dysbiosis, rising the lactobacilli population.}, journal = {Journal of applied microbiology}, volume = {135}, number = {5}, pages = {}, doi = {10.1093/jambio/lxae110}, pmid = {38755019}, issn = {1365-2672}, support = {//Uriach/ ; }, mesh = {Female ; Humans ; *Probiotics/administration &amp; dosage/therapeutic use ; *Lacticaseibacillus rhamnosus ; *Dysbiosis/microbiology ; *Vagina/microbiology ; Adult ; Middle Aged ; Young Adult ; Quality of Life ; Lactobacillus ; Vaginosis, Bacterial/microbiology/drug therapy ; }, abstract = {AIM: The present study is a single-centre, randomized, controlled clinical trial aimed to evaluate the effectiveness of the probiotic Lacticaseibacillus rhamnosus TOM 22.8 (DSM 33500) strain, orally administrated, to treat vaginal dysbiosis.<br><br>METHODS AND RESULTS: Overall, 80 women, with signs and symptoms of vaginal dysbiosis, were enrolled and allocated to the treatment group (A, n=60), who took 1 capsule of the probiotic strain for 10 consecutive days, or the non-treatment group (B, n=20), who did not receive any treatment. Clinical (vaginal signs and symptoms; pH of the vaginal fluid; Amsel criteria; Nugent score; Lactobacillary grade) and microbiological examinations were performed at baseline (T0), 10 days (T1), and 30 (T2) days after the oral administration of the probiotic TOM 22.8 strain. The latter resulted in a restoration of the physiological pH, accompanied by remission or attenuation of clinical signs and symptoms as well as the improvement of the quality of life (QoL). Microbiological data revealed a significant reduction of potentially pathogenic bacteria.<br><br>CONCLUSION: The administration of the L. rhamnosus TOM 22.8 probiotic strain could be proposed as an effective strategy for the treatment of vaginal dysbiosis.}, }
@article {pmid38754710, year = {2024}, author = {Thomé, PC and Wolinska, J and Van Den Wyngaert, S and Reñé, A and Ilicic, D and Agha, R and Grossart, HP and Garcés, E and Monaghan, MT and Strassert, JFH}, title = {Phylogenomics including new sequence data of phytoplankton-infecting chytrids reveals multiple independent lifestyle transitions across the phylum.}, journal = {Molecular phylogenetics and evolution}, volume = {197}, number = {}, pages = {108103}, doi = {10.1016/j.ympev.2024.108103}, pmid = {38754710}, issn = {1095-9513}, mesh = {*Phylogeny ; *Chytridiomycota/genetics/classification ; *Phytoplankton/genetics/classification ; Genomics ; }, abstract = {Parasitism is the most common lifestyle on Earth and has emerged many times independently across the eukaryotic tree of life. It is frequently found among chytrids (Chytridiomycota), which are early-branching unicellular fungi that feed osmotrophically via rhizoids as saprotrophs or parasites. Chytrids are abundant in most aquatic and terrestrial environments and fulfil important ecosystem functions. As parasites, they can have significant impacts on host populations. They cause global amphibian declines and influence the Earth's carbon cycle by terminating algal blooms. To date, the evolution of parasitism within the chytrid phylum remains unclear due to the low phylogenetic resolution of rRNA genes for the early diversification of fungi, and because few parasitic lineages have been cultured and genomic data for parasites is scarce. Here, we combine transcriptomics, culture-independent single-cell genomics and a phylogenomic approach to overcome these limitations. We newly sequenced 29 parasitic taxa and combined these with existing data to provide a robust backbone topology for the diversification of Chytridiomycota. Our analyses reveal multiple independent lifestyle transitions between parasitism and saprotrophy among chytrids and multiple host shifts by parasites. Based on these results and the parasitic lifestyle of other early-branching holomycotan lineages, we hypothesise that the chytrid last common ancestor was a parasite of phytoplankton.}, }
@article {pmid38754295, year = {2024}, author = {Verstraete, W}, title = {Nitrogen and me - How little did we, and do we know about "stikstof - azote - nitrogen"?.}, journal = {Water research}, volume = {258}, number = {}, pages = {121687}, doi = {10.1016/j.watres.2024.121687}, pmid = {38754295}, issn = {1879-2448}, mesh = {Humans ; *Agriculture ; Fertilizers ; History, 20th Century ; *Nitrogen ; }, abstract = {This retrospective article reflects on the complex and evolving relationship between humans and nitrogen over several decades. Raised on a Flemish farm, the author's early experiences with nitrogen in agriculture - both its benefits and dangers - laid the foundation for a lifelong interest in this element. The article traverses a broad range of topics related to nitrogen, highlighting its critical role in various historical, agricultural, environmental, and industrial contexts. The narrative begins with a historical overview of nitrogen's role in agriculture and warfare. The development of industrial processes like the Haber and Ostwald methods transformed nitrogen into a key ingredient for both fertilizers and explosives. The dual nature of nitrogen - as a life-giver in agriculture and a destructive component in warfare and also in biodiversity - is an important theme. The article delves into the environmental impacts of nitrogen, particularly in the context of modern agriculture and industrialization. Issues like fertilization, water contamination, and the challenges of managing nitrogenous waste highlight the complex interplay between human activities and environmental health. Technological advancements are explored, including the development of bioaugmentation methods and the potential of genetic engineering in optimizing nitrogen fixation. Throughout the narrative, personal anecdotes are weaved with scientific information, offering a unique perspective on the historical and contemporary challenges of managing nitrogen. The discussion extends to the broader implications of nitrogen management in the context of sustainability, climate change, and global food security and its overall regulatory space. All these considerations call for a re-evaluation of our relationship with nitrogen, advocating for innovative solutions and systemic thinking to address the multifaceted challenges posed by this essential, yet often problematic element.}, }
@article {pmid38752760, year = {2024}, author = {Barnett, SE and Shade, A}, title = {Seven years of microbial community metagenomes from temperate soils affected by an ongoing coal seam fire.}, journal = {Microbiology resource announcements}, volume = {13}, number = {6}, pages = {e0019824}, pmid = {38752760}, issn = {2576-098X}, support = {1749544//National Science Foundation (NSF)/ ; }, abstract = {We examined the dynamics of soil microbiomes under heat press disturbance from an underground coal mine fire in Centralia, PA. Here, we present metagenomic sequencing and assembly data from soil microbiomes across seven consecutive years at repeatedly sampled fire-affected sites along with unaffected reference sites.}, }
@article {pmid38750737, year = {2024}, author = {Kaijser, W and Lorenz, AW and Brauer, VS and Burfeid-Castellanos, A and David, GM and Nuy, JK and Baikova, D and Beszteri, B and Gillmann, SM and Kiesel, J and Mayombo, NAS and Peters, K and Rettig, K and Rolauffs, P and Haase, P and Hering, D}, title = {Differential associations of five riverine organism groups with multiple stressors.}, journal = {The Science of the total environment}, volume = {934}, number = {}, pages = {173105}, doi = {10.1016/j.scitotenv.2024.173105}, pmid = {38750737}, issn = {1879-1026}, mesh = {*Rivers/microbiology ; *Environmental Monitoring ; Animals ; *Biodiversity ; Fungi ; Diatoms/physiology ; Invertebrates/physiology ; Fishes ; Bacteria/classification ; Water Pollutants, Chemical/analysis ; }, abstract = {The decline of river and stream biodiversity results from multiple simultaneous occuring stressors, yet few studies explore responses explore responses across various taxonomic groups at the same locations. In this study, we address this shortcoming by using a coherent data set to study the association of nine commonly occurring stressors (five chemical, one morphological and three hydraulic) with five taxonomic groups (bacteria, fungi, diatoms, macro-invertebrates and fish). According to studies on single taxonomic groups, we hypothesise that gradients of chemical stressors structure community composition of all taxonomic groups, while gradients of hydraulic and morphological stressors are mainly related to larger organisms such as benthic macro-invertebrates and fish. Organisms were sampled over two years at 20 sites in two catchments: a recently restored urban lowland catchment (Boye) and a moderately disturbed rural mountainous catchment (Kinzig). Dissimilarity matrices were computed for each taxonomic group within a catchment. Taxonomic dissimilarities between sites were linked to stressor dissimilarities using multivariable Generalized Linear Mixed Models. Stressor gradients were longer in the Boye, but did in contrast to the Kinzig not cover low stress intensities. Accordingly, responses of the taxonomic groups were stronger in the Kinzig catchment than in the recently restored Boye catchment. The discrepancy between catchments underlines that associations to stressors strongly depend on which part of the stressor gradient is covered in a catchment. All taxonomic groups were related to conductivity. Bacteria, fungi and macro-invertebrates change with dissolved oxygen, and bacteria and fungi with total nitrogen. Morphological and hydraulic stressors had minor correlations with bacteria, fungi and diatoms, while macro-invertebrates were strongly related to fine sediment and discharge, and fish to high flow peaks. The results partly support our hypotheses about the differential associations of the different taxonomic groups with the stressors.}, }
@article {pmid38750646, year = {2024}, author = {Huusko, K and Manninen, OH and Myrsky, E and Stark, S}, title = {Soil fungal and bacterial communities reflect differently tundra vegetation state transitions and soil physico-chemical properties.}, journal = {The New phytologist}, volume = {243}, number = {1}, pages = {407-422}, doi = {10.1111/nph.19808}, pmid = {38750646}, issn = {1469-8137}, support = {323504//Biotieteiden ja Ymp&#xe4;rist&#xf6;n Tutkimuksen Toimikunta/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Fungi/physiology ; *Bacteria/classification ; *Tundra ; Finland ; Chemical Phenomena ; Plants/microbiology ; }, abstract = {Strong disturbances may induce ecosystem transitions into new alternative states that sustain through plant-soil interactions, such as the transition of dwarf shrub-dominated into graminoid-dominated vegetation by herbivory in tundra. Little evidence exists on soil microbial communities in alternative states, and along the slow process of ecosystem return into the predisturbance state. We analysed vegetation, soil microbial communities and activities as well as soil physico-chemical properties in historical reindeer enclosures in northernmost Finland in the following plot types: control heaths in the surrounding tundra; graminoid-dominated; 'shifting'; and recovered dwarf shrub-dominated vegetation inside enclosures. Soil fungal communities followed changes in vegetation, whereas bacterial communities were more affected by soil physico-chemical properties. Graminoid plots were characterized by moulds, pathotrophs and dark septate endophytes. Ericoid mycorrhizal and saprotrophic fungi were typical for control and recovered plots. Soil microbial communities inside the enclosures showed historical contingency, as their spatial variation was high in recovered plots despite the vegetation being more homogeneous. Self-maintaining feedback loops between plant functional types, soil microbial communities, and carbon and nutrient mineralization act effectively to stabilize alternative vegetation states, but once predisturbance vegetation reestablishes itself, soil microbial communities and physico-chemical properties return back towards their predisturbance state.}, }
@article {pmid38749545, year = {2024}, author = {Sato, Y}, title = {Transcriptome analysis: a powerful tool to understand individual microbial behaviors and interactions in ecosystems.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {88}, number = {8}, pages = {850-856}, doi = {10.1093/bbb/zbae064}, pmid = {38749545}, issn = {1347-6947}, support = {17H04716//Japan Society for the Promotion of Science/ ; JPMJFR2174//Japan Science and Technology Agency/ ; }, mesh = {*Ecosystem ; *Gene Expression Profiling/methods ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; Transcriptome ; Microbiota/genetics ; Bacteria/genetics/metabolism/classification ; Microbial Interactions/genetics ; Metagenome ; }, abstract = {Transcriptome analysis is a powerful tool for studying microbial ecology, especially individual microbial functions in an ecosystem and their interactions. With the development of high-throughput sequencing technology, great progress has been made in analytical methods for microbial communities in natural environments. 16S rRNA gene amplicon sequencing (ie microbial community structure analysis) and shotgun metagenome analysis have been widely used to determine the composition and potential metabolic capability of microorganisms in target environments without requiring culture. However, even if the types of microorganisms present and their genes are known, it is difficult to determine what they are doing in an ecosystem. Gene expression analysis (transcriptome analysis; RNA-seq) is a powerful tool to address these issues. The history and basic information of gene expression analysis, as well as examples of studies using this method to analyze microbial ecosystems, are presented.}, }
@article {pmid38749241, year = {2024}, author = {Kutralam-Muniasamy, G and Shruti, VC and Pérez-Guevara, F}, title = {Plastisphere-hosted viruses: A review of interactions, behavior, and effects.}, journal = {Journal of hazardous materials}, volume = {472}, number = {}, pages = {134533}, doi = {10.1016/j.jhazmat.2024.134533}, pmid = {38749241}, issn = {1873-3336}, mesh = {*Viruses ; Plastics ; Virus Physiological Phenomena ; Biofilms ; Ecosystem ; Microplastics ; }, abstract = {Microbial communities, including bacteria, diatoms, and fungi, colonize plastic surfaces, forming biofilms known as the "plastisphere." Recent research has revealed that plastispheres also host a wide range of viruses, sparking interest in microbial ecology and virology. This shared habitat allows viruses to replicate, interact, infect, and spread, potentially impacting the environment and human health. Consequently, viruses attached to microplastics are now recognized to have broad effects on cellular and immune responses. However, the ecology and implications of viruses hosted in plastisphere habitats remain poorly understood, highlighting their fundamental importance as a subject of study. This review explores various pathways for virus attachment to plastispheres, factors influencing these interactions, their impacts within plastisphere and host-associated environments, and associated issues. It also summarizes current research and identifies knowledge gaps. We anticipate that this paper will help improve our predictive understanding of plastisphere viruses in natural settings and emphasizes the need for more research in real-world environments to advance the field.}, }
@article {pmid38748252, year = {2024}, author = {Perez-Bou, L and Gonzalez-Martinez, A and Cabrera, JJ and Juarez-Jimenez, B and Rodelas, B and Gonzalez-Lopez, J and Correa-Galeote, D}, title = {Design and Validation of Primer Sets for the Detection and Quantification of Antibiotic Resistance Genes in Environmental Samples by Quantitative PCR.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {71}, pmid = {38748252}, issn = {1432-184X}, mesh = {*DNA Primers/genetics ; *Real-Time Polymerase Chain Reaction/methods ; *Wastewater/microbiology ; *Genes, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects/isolation &amp; purification/classification ; }, abstract = {The high prevalence of antibiotic resistant bacteria (ARB) in several environments is a great concern threatening human health. Particularly, wastewater treatment plants (WWTP) become important contributors to the dissemination of ARB to receiving water bodies, due to the inefficient management or treatment of highly antibiotic-concentrated wastewaters. Hence, it is vital to develop molecular tools that allow proper monitoring of the genes encoding resistances to these important therapeutic compounds (antibiotic resistant genes, ARGs). For an accurate quantification of ARGs, there is a need for sensitive and robust qPCR assays supported by a good design of primers and validated protocols. In this study, eleven relevant ARGs were selected as targets, including aadA and aadB (conferring resistance to aminoglycosides); ampC, blaTEM, blaSHV, and mecA (resistance to beta-lactams); dfrA1 (resistance to trimethoprim); ermB (resistance to macrolides); fosA (resistance to fosfomycin); qnrS (resistance to quinolones); and tetA(A) (resistance to tetracyclines). The in silico design of the new primer sets was performed based on the alignment of all the sequences of the target ARGs (orthology grade > 70%) deposited in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, allowing higher coverages of the ARGs' biodiversity than those of several primers described to date. The adequate design and performance of the new molecular tools were validated in six samples, retrieved from both natural and engineered environments related to wastewater treatment. The hallmarks of the optimized qPCR assays were high amplification efficiency (> 90%), good linearity of the standard curve (R[2] > 0.980), repeatability and reproducibility across experiments, and a wide linear dynamic range. The new primer sets and methodology described here are valuable tools to upgrade the monitorization of the abundance and emergence of the targeted ARGs by qPCR in WWTPs and related environments.}, }
@article {pmid38747602, year = {2024}, author = {Sudo, M and Osvatic, J and Taylor, JD and Dufour, SC and Prathep, A and Wilkins, LGE and Rattei, T and Yuen, B and Petersen, JM}, title = {SoxY gene family expansion underpins adaptation to diverse hosts and environments in symbiotic sulfide oxidizers.}, journal = {mSystems}, volume = {9}, number = {6}, pages = {e0113523}, pmid = {38747602}, issn = {2379-5077}, support = {VRG14-021//Vienna Science and Technology Fund (WWTF)/ ; DOC 69/FWF_/Austrian Science Fund FWF/Austria ; 802494//EC | European Research Council (ERC)/ ; Grant-DOI 10.55776/DOC69//Austrian Science Fund (FWF) DocFunds/ ; 10.55776/COE7//University of Vienna/ ; SEP-210693430//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, mesh = {Animals ; Adaptation, Physiological/genetics ; Bacteria/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Genome, Bacterial ; Hydrothermal Vents/microbiology ; Multigene Family ; *Oxidation-Reduction ; Phylogeny ; *Sulfides/metabolism ; Sulfur/metabolism ; *Symbiosis/genetics ; Bivalvia ; }, abstract = {Sulfur-oxidizing bacteria (SOB) have developed distinct ecological strategies to obtain reduced sulfur compounds for growth. These range from specialists that can only use a limited range of reduced sulfur compounds to generalists that can use many different forms as electron donors. Forming intimate symbioses with animal hosts is another highly successful ecological strategy for SOB, as animals, through their behavior and physiology, can enable access to sulfur compounds. Symbioses have evolved multiple times in a range of animal hosts and from several lineages of SOB. They have successfully colonized a wide range of habitats, from seagrass beds to hydrothermal vents, with varying availability of symbiont energy sources. Our extensive analyses of sulfur transformation pathways in 234 genomes of symbiotic and free-living SOB revealed widespread conservation in metabolic pathways for sulfur oxidation in symbionts from different host species and environments, raising the question of how they have adapted to such a wide range of distinct habitats. We discovered a gene family expansion of soxY in these genomes, with up to five distinct copies per genome. Symbionts harboring only the "canonical" soxY were typically ecological "specialists" that are associated with specific host subfamilies or environments (e.g., hydrothermal vents, mangroves). Conversely, symbionts with multiple divergent soxY genes formed versatile associations across diverse hosts in various marine environments. We hypothesize that expansion and diversification of the soxY gene family could be one genomic mechanism supporting the metabolic flexibility of symbiotic SOB enabling them and their hosts to thrive in a range of different and dynamic environments.IMPORTANCESulfur metabolism is thought to be one of the most ancient mechanisms for energy generation in microorganisms. A diverse range of microorganisms today rely on sulfur oxidation for their metabolism. They can be free-living, or they can live in symbiosis with animal hosts, where they power entire ecosystems in the absence of light, such as in the deep sea. In the millions of years since they evolved, sulfur-oxidizing bacteria have adopted several highly successful strategies; some are ecological "specialists," and some are "generalists," but which genetic features underpin these ecological strategies are not well understood. We discovered a gene family that has become expanded in those species that also seem to be "generalists," revealing that duplication, repurposing, and reshuffling existing genes can be a powerful mechanism driving ecological lifestyle shifts.}, }
@article {pmid38747384, year = {2024}, author = {Tanabe, TS and Bach, E and D'Ermo, G and Mohr, MG and Hager, N and Pfeiffer, N and Guiral, M and Dahl, C}, title = {A cascade of sulfur transferases delivers sulfur to the sulfur-oxidizing heterodisulfide reductase-like complex.}, journal = {Protein science : a publication of the Protein Society}, volume = {33}, number = {6}, pages = {e5014}, pmid = {38747384}, issn = {1469-896X}, support = {57388731//Deutscher Akademischer Austauschdienst/Hubert Curien Procope program/ ; 40444VM//Deutscher Akademischer Austauschdienst/Hubert Curien Procope program/ ; //Studienstiftung des Deutschen Volkes/ ; 351/13-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Sulfur/metabolism ; *Oxidation-Reduction ; *Sulfurtransferases/metabolism/chemistry/genetics ; *Oxidoreductases/metabolism/chemistry ; *Bacterial Proteins/metabolism/chemistry/genetics ; }, abstract = {A heterodisulfide reductase-like complex (sHdr) and novel lipoate-binding proteins (LbpAs) are central players of a wide-spread pathway of dissimilatory sulfur oxidation. Bioinformatic analysis demonstrate that the cytoplasmic sHdr-LbpA systems are always accompanied by sets of sulfur transferases (DsrE proteins, TusA, and rhodaneses). The exact composition of these sets may vary depending on the organism and sHdr system type. To enable generalizations, we studied model sulfur oxidizers from distant bacterial phyla, that is, Aquificota and Pseudomonadota. DsrE3C of the chemoorganotrophic Alphaproteobacterium Hyphomicrobium denitrificans and DsrE3B from the Gammaproteobacteria Thioalkalivibrio sp. K90mix, an obligate chemolithotroph, and Thiorhodospira sibirica, an obligate photolithotroph, are homotrimers that donate sulfur to TusA. Additionally, the hyphomicrobial rhodanese-like protein Rhd442 exchanges sulfur with both TusA and DsrE3C. The latter is essential for sulfur oxidation in Hm. denitrificans. TusA from Aquifex aeolicus (AqTusA) interacts physiologically with AqDsrE, AqLbpA, and AqsHdr proteins. This is particularly significant as it establishes a direct link between sulfur transferases and the sHdr-LbpA complex that oxidizes sulfane sulfur to sulfite. In vivo, it is unlikely that there is a strict unidirectional transfer between the sulfur-binding enzymes studied. Rather, the sulfur transferases form a network, each with a pool of bound sulfur. Sulfur flux can then be shifted in one direction or the other depending on metabolic requirements. A single pair of sulfur-binding proteins with a preferred transfer direction, such as a DsrE3-type protein towards TusA, may be sufficient to push sulfur into the sink where it is further metabolized or needed.}, }
@article {pmid38746754, year = {2024}, author = {Shan, Z and Chen, H and Deng, Y and He, D and Ren, L}, title = {An abrupt regime shift of bacterioplankton community from weak to strong thermal pollution in a subtropical bay.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1395583}, pmid = {38746754}, issn = {1664-302X}, abstract = {Thermal pollution from the cooling system of the nuclear power plants greatly changes the environmental and the ecological conditions of the receiving marine water body, but we know little about their impact on the steady-state transition of marine bacterioplankton communities. In this study, we used high-throughput sequencing based on the 16S rRNA gene to investigate the impact of the thermal pollution on the bacterioplankton communities in a subtropical bay (the Daya Bay). We observed that thermal pollution from the cooling system of the nuclear power plant caused a pronounced thermal gradient ranging from 19.6°C to 24.12°C over the whole Daya Bay. A temperature difference of 4.5°C between the northern and southern parts of the bay led to a regime shift in the bacterioplankton community structure. In the three typical scenarios of regime shifts, the steady-state transition of bacterioplankton community structure in response to temperature increasing was more likely consistent with an abrupt regime shift rather than a smooth regime or a discontinuous regime model. Water temperature was a decisive factor on the regime shift of bacterioplankton community structure. High temperature significantly decreased bacterioplankton diversity and shifted its community compositions. Cyanobium and Synechococcus of Cyanobacteria, NS5 marine group of Bacteroidota, and Vibrio of Gammaproteobacteria were found that favored high temperature environments. Furthermore, the increased water temperature significantly altered the community assembly of bacterioplankton in Daya Bay, with a substantial decrease in the proportion of drift and others, and a marked increase in the proportion of homogeneous selection. In summary, we proposed that seawater temperature increasing induced by the thermal pollution resulted in an abrupt regime shift of bacterioplankton community in winter subtropical bay. Our research might broad our understanding of marine microbial ecology under future conditions of global warming.}, }
@article {pmid38746391, year = {2024}, author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Krulilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I}, title = {CAIM: Coverage-based Analysis for Identification of Microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38746391}, issn = {2692-8205}, support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 CA143130/CA/NCI NIH HHS/United States ; }, abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic (WMS) approach. In this study, we developed a new bioinformatics tool, CAIM, for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consitently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similality of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and primary 44 liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.}, }
@article {pmid38740585, year = {2024}, author = {Bin, X and Wang, P and Shen, Y and Xiang, X and Jafir, M and Wan, X}, title = {Investigation of Fungal Community Structure in the Gut of the Stag Beetle Dorcus hopei (Coleoptera; Lucanidae): Comparisons Among Developmental Stages.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {70}, pmid = {38740585}, issn = {1432-184X}, support = {31872276//National Natural Science Foundation of China/ ; 31872276//National Natural Science Foundation of China/ ; 31872276//National Natural Science Foundation of China/ ; 31872276//National Natural Science Foundation of China/ ; 31872276//National Natural Science Foundation of China/ ; 31872276//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Coleoptera/microbiology/growth &amp; development ; *Larva/growth &amp; development/microbiology ; *Fungi/genetics/classification/physiology ; *Gastrointestinal Microbiome ; Pupa/growth &amp; development/microbiology ; Mycobiome ; Biodiversity ; Symbiosis ; High-Throughput Nucleotide Sequencing ; }, abstract = {Stag beetles, recognized as common saproxylic insects, are valued for their vibrant coloration and distinctive morphology. These beetles play a crucial ecological role in decomposition and nutrient cycling, serving as a vital functional component in ecosystem functioning. Although previous studies have confirmed that stag beetles are predominantly fungivores, the fluctuations in their intestinal fungal communities at different developmental stages remain poorly understood. In the current study, high-throughput sequencing was employed to investigate the dynamic changes within intestinal fungal communities at various developmental stages in the stag beetle Dorcus hopei. Results showed that microbial diversity was higher during the larval stage than during the pupal and adult stages. Furthermore, significant differences were identified in the composition of the intestinal fungal communities across the larval, pupal, and adult stages, suggesting that developmental transitions may be crucial factors contributing to variations in fungal community composition and diversity. Dominant genera included Candida, Scheffersomyces, Phaeoacremonium, and Trichosporon. Functional predictions indicated a greater diversity and relative abundance of endosymbiotic fungi in the larval gut, suggesting a potential dependency of larvae on beneficial gut fungi for nutrient acquisition. Additionally, the application of abundance-based β-null deviation and niche width analyses revealed that the adult gut exerted a stronger selection pressure on its fungal community, favoring certain taxa. This selection process culminates in a more robust co-occurrence network of fungal communities within the adult gut, thereby enhancing their adaptability to environmental fluctuations. This study advances our understanding of the intestinal fungal community structure in stag beetles, providing a crucial theoretical foundation for the development of saproxylic beetle resources, biomass energy utilization, plastic degradation strategies, and beetle conservation efforts.}, }
@article {pmid38740197, year = {2024}, author = {Ibrahim, SS and Ionescu, D and Grossart, HP}, title = {Tapping into fungal potential: Biodegradation of plastic and rubber by potent Fungi.}, journal = {The Science of the total environment}, volume = {934}, number = {}, pages = {173188}, doi = {10.1016/j.scitotenv.2024.173188}, pmid = {38740197}, issn = {1879-1026}, mesh = {*Biodegradation, Environmental ; *Plastics/metabolism ; *Fungi/metabolism ; *Rubber/metabolism ; Polyurethanes ; }, abstract = {Plastic polymers are present in most aspects of routine daily life. Their increasing leakage into the environment poses a threat to environmental, animal, and human health. These polymers are often resistant to microbial degradation and are predicted to remain in the environment for tens to hundreds of years. Fungi have been shown to degrade complex polymers and are considered good candidates for bioremediation (biological pollutant reduction) of plastics. Therefore, we screened 18 selected fungal strains for their ability to degrade polyurethane (PU), polyethylene (PE), and tire rubber. As a proxy for plastic polymer mineralization, we quantified O2 consumption and CO2 production in an enclosed biodegradation system providing plastic as the sole carbon source. In contrast to most studies we demonstrated that the tested fungi attach to, and colonize the different plastic polymers without any pretreatment of the plastics and in the absence of sugars, which were suggested essential for priming the degradation process. Functional polymer groups identified by Fourier-transform infrared spectroscopy (FTIR), and changes in fungal morphology as seen in light and scanning electron microscopy (SEM) were used as indicators of fungal adaptation to growth on PU as a substrate. Thereby, SEM analysis revealed new morphological structures and deformation of the cell wall of several fungal strains when colonizing PU and utilizing this plastic polymer for cell growth. Strains of Fusarium, Penicillium, Botryotinia cinerea EN41, and Trichoderma demonstrated a high potential to degrade PU, rubber, and PE. Growing on PU, over 90 % of the O2 was consumed in <14 days with 300-500 ppm of CO2 generated in parallel. Our study highlights a high bioremediation potential of some fungal strains to efficiently degrade plastic polymers, largely dependent on plastic type.}, }
@article {pmid38739959, year = {2024}, author = {Kazmi, SSUH and Tayyab, M and Pastorino, P and Barcelò, D and Yaseen, ZM and Grossart, HP and Khan, ZH and Li, G}, title = {Decoding the molecular concerto: Toxicotranscriptomic evaluation of microplastic and nanoplastic impacts on aquatic organisms.}, journal = {Journal of hazardous materials}, volume = {472}, number = {}, pages = {134574}, doi = {10.1016/j.jhazmat.2024.134574}, pmid = {38739959}, issn = {1873-3336}, mesh = {*Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; *Aquatic Organisms/drug effects/genetics ; Animals ; *Transcriptome/drug effects ; Nanoparticles/toxicity/chemistry ; }, abstract = {The pervasive and steadily increasing presence of microplastics/nanoplastics (MPs/NPs) in aquatic environments has raised significant concerns regarding their potential adverse effects on aquatic organisms and their integration into trophic dynamics. This emerging issue has garnered the attention of (eco)toxicologists, promoting the utilization of toxicotranscriptomics to unravel the responses of aquatic organisms not only to MPs/NPs but also to a wide spectrum of environmental pollutants. This review aims to systematically explore the broad repertoire of predicted molecular responses by aquatic organisms, providing valuable intuitions into complex interactions between plastic pollutants and aquatic biota. By synthesizing the latest literature, present analysis sheds light on transcriptomic signatures like gene expression, interconnected pathways and overall molecular mechanisms influenced by various plasticizers. Harmful effects of these contaminants on key genes/protein transcripts associated with crucial pathways lead to abnormal immune response, metabolic response, neural response, apoptosis and DNA damage, growth, development, reproductive abnormalities, detoxification, and oxidative stress in aquatic organisms. However, unique challenge lies in enhancing the fingerprint of MPs/NPs, presenting complicated enigma that requires decoding their specific impact at molecular levels. The exploration endeavors, not only to consolidate existing knowledge, but also to identify critical gaps in understanding, push forward the frontiers of knowledge about transcriptomic signatures of plastic contaminants. Moreover, this appraisal emphasizes the imperative to monitor and mitigate the contamination of commercially important aquatic species by MPs/NPs, highlighting the pivotal role that regulatory frameworks must play in protecting all aquatic ecosystems. This commitment aligns with the broader goal of ensuring the sustainability of aquatic resources and the resilience of ecosystems facing the growing threat of plastic pollutants.}, }
@article {pmid38736980, year = {2024}, author = {Ahmad, R and Liaquat, M and Sammi, S and Al-Hawadi, JS and Jahangir, M and Mumtaz, A and Khan, I and Okla, MK and Alaraidh, IA and AbdElgawad, H and Liu, K and Harrison, MT and Saud, S and Hassan, S and Nawaz, T and Zhu, M and Liu, H and Adnan, M and Sadiq, A and Rahman, TU and Asghari, BH and Fahad, S}, title = {Physicochemical and nutritional profiles of wild adlay (Coix lacryma-jobi Linn) accessions by GC, FTIR, and spectrophotometer.}, journal = {Food chemistry: X}, volume = {22}, number = {}, pages = {101418}, pmid = {38736980}, issn = {2590-1575}, abstract = {Purpose of current study was to determine physicochemical, triglyceride composition, and functional groups of wild adlay accessions (brown, black, yellow, grey, green, off white, and purple) to find out its scope as cereal crop. Triglycerides, minerals and functional groups were determined through Gas chromatography, spectrophotometer and Fourier Transform Infrared (FTIR) spectrophotometer respectively. Results revealed variation among bulk densities, specific densities, percent empty spaces, and corresponding grain counts per 10 g of sample are useful in distinguishing brown, black, yellow, grey, green, off white, and purple wild adlay accessions. Specific density and grain count per 10 g sample was significantly related. No statistical relationship exists among the pronounced physical characteristics. Brown adlay expressed the highest protein, fat, and fiber contents 15.82%, 4.76% and 2.37% respectively. Protein, fat, ash, and fiber percent contents were found comparable to cultivated adlay. Spectrophotometric analysis revealed macro elements including phosphorus, potassium, calcium, and sodium in the range 0.3% - 2.2% and micro elements boron, iron, copper, zinc, and manganese in the range 1.6 mg/kg - 20.8 mg/kg. Gas chromatography showed polyunsaturated fatty acids (PUFA) constitute the primary fraction (39% ± 7.2) of wild adlay triglycerides. Linoleic and palmitic acids were present as prominent fatty acids, 43.5% ±1.4 and 26.3% ±1.4 respectively. Infra-red frequencies distinguished functional groups in narrow band and fingerprint region of protein in association with out of plane region leading to structural differences among adlay accessions. Comparison of major distinguishing vibrational frequencies among different flours indicated black adlay containing highest functional groups appeared promising for varietal development.}, }
@article {pmid38734822, year = {2024}, author = {Breedt, G and Korsten, L and Gokul, JK}, title = {Influence of Soil Phosphate on Rhizobacterial Performance in Affecting Wheat Yield.}, journal = {Current microbiology}, volume = {81}, number = {7}, pages = {170}, pmid = {38734822}, issn = {1432-0991}, mesh = {*Triticum/microbiology/growth &amp; development ; *Phosphates/metabolism ; *Soil Microbiology ; *Soil/chemistry ; *Rhizosphere ; Fertilizers/analysis ; Paenibacillus/metabolism/genetics/growth &amp; development ; Phosphorus/metabolism ; }, abstract = {As a primary nutrient in agricultural soils, phosphorus plays a crucial but growth-limiting role for plants due to its complex interactions with various soil elements. This often results in excessive phosphorus fertilizer application, posing concerns for the environment. Agri-research has therefore shifted focus to increase fertilizer-use efficiency and minimize environmental impact by leveraging plant growth-promoting rhizobacteria. This study aimed to evaluate the in-field incremental effect of inorganic phosphate concentration (up to 50 kg/ha/P) on the ability of two rhizobacterial isolates, Lysinibacillus sphaericus (T19), Paenibacillus alvei (T29), from the previous Breedt et al. (Ann Appl Biol 171:229-236, 2017) study on maize in enhancing the yield of commercially grown Duzi® cultivar wheat. Results obtained from three seasons of field trials revealed a significant relationship between soil phosphate concentration and the isolates' effectiveness in improving wheat yield. Rhizospheric samples collected at flowering during the third season, specifically to assess phosphatase enzyme activity at the different soil phosphate levels, demonstrated a significant decrease in soil phosphatase activity when the phosphorus rate reached 75% for both isolates. Furthermore, in vitro assessments of inorganic phosphate solubilization by both isolates at five increments of tricalcium phosphate-amended Pikovskaya media found that only isolate T19 was capable of solubilizing tricalcium at concentrations exceeding 3 mg/ml. The current study demonstrates the substantial influence of inorganic phosphate on the performance of individual rhizobacterial isolates, highlighting that this is an essential consideration when optimizing these isolates to increase wheat yield in commercial cultivation.}, }
@article {pmid38733792, year = {2024}, author = {Musat, F and Kjeldsen, KU and Rotaru, AE and Chen, SC and Musat, N}, title = {Archaea oxidizing alkanes through alkyl-coenzyme M reductases.}, journal = {Current opinion in microbiology}, volume = {79}, number = {}, pages = {102486}, doi = {10.1016/j.mib.2024.102486}, pmid = {38733792}, issn = {1879-0364}, mesh = {*Alkanes/metabolism ; *Archaea/enzymology/genetics/metabolism ; *Oxidation-Reduction ; *Oxidoreductases/metabolism/genetics ; *Phylogeny ; Electron Transport ; Archaeal Proteins/metabolism/genetics/chemistry ; Gene Transfer, Horizontal ; Bacteria/enzymology/genetics/metabolism/classification ; }, abstract = {This review synthesizes recent discoveries of novel archaea clades capable of oxidizing higher alkanes, from volatile ones like ethane to longer-chain alkanes like hexadecane. These archaea, termed anaerobic multicarbon alkane-oxidizing archaea (ANKA), initiate alkane oxidation using alkyl-coenzyme M reductases, enzymes similar to the methyl-coenzyme M reductases of methanogenic and anaerobic methanotrophic archaea (ANME). The polyphyletic alkane-oxidizing archaea group (ALOX), encompassing ANME and ANKA, harbors increasingly complex alkane degradation pathways, correlated with the alkane chain length. We discuss the evolutionary trajectory of these pathways emphasizing metabolic innovations and the acquisition of metabolic modules via lateral gene transfer. Additionally, we explore the mechanisms by which archaea couple alkane oxidation with the reduction of electron acceptors, including electron transfer to partner sulfate-reducing bacteria (SRB). The phylogenetic and functional constraints that shape ALOX-SRB associations are also discussed. We conclude by highlighting the research needs in this emerging research field and its potential applications in biotechnology.}, }
@article {pmid38730059, year = {2024}, author = {Kimura, K and Okuro, T}, title = {Cyanobacterial Biocrust on Biomineralized Soil Mitigates Freeze-Thaw Effects and Preserves Structure and Ecological Functions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {69}, pmid = {38730059}, issn = {1432-184X}, support = {JPMJSA1906//Science and Technology Research Partnership for Sustainable Development/ ; JP22H01310//Japan Society for the Promotion of Science/ ; JPMEERF20205001//Environment Research and Technology Development Fund/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Freezing ; *Cyanobacteria/metabolism/chemistry ; Carbonates/chemistry/metabolism ; Ecosystem ; Sporosarcina/metabolism/growth &amp; development ; }, abstract = {Biocrust inoculation and microbially induced carbonate precipitation (MICP) are tools used in restoring degraded arid lands. It remains unclear whether the ecological functions of the two tools persist when these methods are combined and subjected to freeze-thaw (FT) cycles. We hypothesized a synergetic interaction between MICP treatment and biocrust under FT cycles, which would allow both components to retain their ecological functions. We grew cyanobacterial (Nostoc commune) biocrusts on bare soil and on MICP (Sporosarcina pasteurii)-treated soil, subjecting them to repeated FT cycles simulating the Mongolian climate. Generalized linear modeling revealed that FT cycling did not affect physical structure or related functions but could increase the productivity and reduce the nutrient condition of the crust. The results confirm the high tolerance of MICP-treated soil and biocrust to FT cycling. MICP treatment + biocrust maintained higher total carbohydrate content under FT stress. Our study indicates that biocrust on biomineralized soil has a robust enough structure to endure FT cycling during spring and autumn and to promote restoration of degraded lands.}, }
@article {pmid38729708, year = {2024}, author = {Garcia-Gutierrez, E and Monteoliva García, G and Bodea, I and Cotter, PD and Iguaz, A and Garre, A}, title = {A secondary model for the effect of pH on the variability in growth fitness of Listeria innocua strains.}, journal = {Food research international (Ottawa, Ont.)}, volume = {186}, number = {}, pages = {114314}, doi = {10.1016/j.foodres.2024.114314}, pmid = {38729708}, issn = {1873-7145}, mesh = {*Listeria/growth &amp; development/classification ; Hydrogen-Ion Concentration ; *Food Microbiology ; Models, Biological ; Colony Count, Microbial ; Risk Assessment ; }, abstract = {Variability in microbial growth is a keystone of modern Quantitative Microbiological Risk Assessment (QMRA). However, there are still significant knowledge gaps on how to model variability, with the most common assumption being that variability is constant. This is implemented by an error term (with constant variance) added on top of the secondary growth model (for the square root of the growth rate). However, this may go against microbial ecology principles, where differences in growth fitness among bacterial strains would be more prominent in the vicinity of the growth limits than at optimal growth conditions. This study coins the term "secondary models for variability", evaluating whether they should be considered in QMRA instead of the constant strain variability hypothesis. For this, 21 strains of Listeria innocua were used as case study, estimating their growth rate by the two-fold dilution method at pH between 5 and 10. Estimates of between-strain variability and experimental uncertainty were obtained for each pH using mixed-effects models, showing the lowest variability at optimal growth conditions, increasing towards the growth limits. Nonetheless, the experimental uncertainty also increased towards the extremes, evidencing the need to analyze both sources of variance independently. A secondary model was thus proposed, relating strain variability and pH conditions. Although the modelling approach certainly has some limitations that would need further experimental validation, it is an important step towards improving the description of variability in QMRA, being the first model of this type in the field.}, }
@article {pmid38728984, year = {2024}, author = {Yuan, Y and Zhang, G and Fang, H and Peng, S and Xia, Y and Wang, F}, title = {The ecology of the sewer systems: Microbial composition, function, assembly, and network in different spatial locations.}, journal = {Journal of environmental management}, volume = {359}, number = {}, pages = {121107}, doi = {10.1016/j.jenvman.2024.121107}, pmid = {38728984}, issn = {1095-8630}, mesh = {*Sewage/microbiology ; RNA, Ribosomal, 16S/genetics ; Wastewater/microbiology ; Ecology ; Corrosion ; Microbiota ; }, abstract = {Microbial induced concrete corrosion (MICC) is the primary deterioration affecting global sewers. Disentangling ecological mechanisms in the sewer system is meaningful for implementing policies to protect sewer pipes using trenchless technology. It is necessary to understand microbial compositions, interaction networks, functions, alongside assembly processes in sewer microbial communities. In this study, sewer wastewater samples and microbial samples from the upper part (UP), middle part (MP) and bottom part (BP) of different pipes were collected for 16S rRNA gene amplicon analysis. It was found that BP harbored distinct microbial communities and the largest proportion of unique species (1141) compared to UP and MP. The community in BP tended to be more clustered. Furthermore, significant differences in microbial functions existed in different spatial locations, including the carbon cycle, nitrogen cycle and sulfur cycle. Active microbial sulfur cycling indicated the corrosion risk of MICC. Among the environmental factors, the oxidation‒reduction potential drove changes in BP, while sulfate managed changes in UP and BP. Stochasticity dominated community assembly in the sewer system. Additionally, the sewer microbial community exhibited numerous positive links. BP possessed a more complex, modular network with higher modularity. These deep insights into microbial ecology in the sewer system may guide engineering safety and disaster prevention in sewer infrastructure.}, }
@article {pmid38728226, year = {2024}, author = {Ma, T and Rothschild, J and Halabeya, F and Zilman, A and Milstein, JN}, title = {Mechanics limits ecological diversity and promotes heterogeneity in confined bacterial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {20}, pages = {e2322321121}, pmid = {38728226}, issn = {1091-6490}, support = {RGPIN-2019-06520//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; RGPIN-2022-04909//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; 207-2019-2020-Q4-00576//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; }, mesh = {*Escherichia coli/physiology ; Models, Biological ; Biodiversity ; Ecosystem ; }, abstract = {Multispecies bacterial populations often inhabit confined and densely packed environments where spatial competition determines the ecological diversity of the community. However, the role of mechanical interactions in shaping the ecology is still poorly understood. Here, we study a model system consisting of two populations of nonmotile Escherichia coli bacteria competing within open, monolayer microchannels. The competitive dynamics is observed to be biphasic: After seeding, either one strain rapidly fixates or both strains orient into spatially stratified, stable communities. We find that mechanical interactions with other cells and local spatial constraints influence the resulting community ecology in unexpected ways, severely limiting the overall diversity of the communities while simultaneously allowing for the establishment of stable, heterogeneous populations of bacteria displaying disparate growth rates. Surprisingly, the populations have a high probability of coexisting even when one strain has a significant growth advantage. A more coccus morphology is shown to provide a selective advantage, but agent-based simulations indicate this is due to hydrodynamic and adhesion effects within the microchannel and not from breaking of the nematic ordering. Our observations are qualitatively reproduced by a simple Pólya urn model, which suggests the generality of our findings for confined population dynamics and highlights the importance of early colonization conditions on the resulting diversity and ecology of bacterial communities. These results provide fundamental insights into the determinants of community diversity in dense confined ecosystems where spatial exclusion is central to competition as in organized biofilms or intestinal crypts.}, }
@article {pmid38727217, year = {2024}, author = {Thomas, MJN and Brockhurst, MA and Coyte, KZ}, title = {What makes a temperate phage an effective bacterial weapon?.}, journal = {mSystems}, volume = {9}, number = {6}, pages = {e0103623}, pmid = {38727217}, issn = {2379-5077}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/T014342/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 220243/Z/20/Z//Wellcome Trust (WT)/ ; 226047/Z/22/Z//Wellcome Trust (WT)/ ; }, mesh = {*Lysogeny ; *Pseudomonas aeruginosa/virology ; Bacteriophages/genetics/physiology ; }, abstract = {UNLABELLED: Temperate bacteriophages (phages) are common features of bacterial genomes and can act as self-amplifying biological weapons, killing susceptible competitors and thus increasing the fitness of their bacterial hosts (lysogens). Despite their prevalence, however, the key characteristics of an effective temperate phage weapon remain unclear. Here, we use systematic mathematical analyses coupled with experimental tests to understand what makes an effective temperate phage weapon. We find that effectiveness is controlled by phage life history traits-in particular, the probability of lysis and induction rate-but that the optimal combination of traits varies with the initial frequency of a lysogen within a population. As a consequence, certain phage weapons can be detrimental when their hosts are rare yet beneficial when their hosts are common, while subtle changes in individual life history traits can completely reverse the impact of an individual phage weapon on lysogen fitness. We confirm key predictions of our model experimentally, using temperate phages isolated from the clinically relevant Liverpool epidemic strain of Pseudomonas aeruginosa. Through these experiments, we further demonstrate that nutrient availability can also play a critical role in driving frequency-dependent patterns in phage-mediated competition. Together, these findings highlight the complex and context-dependent nature of temperate phage weapons and the importance of both ecological and evolutionary processes in shaping microbial community dynamics more broadly.<br><br>IMPORTANCE: Temperate bacteriophages-viruses that integrate within bacterial DNA-are incredibly common within bacterial genomes and can act as powerful self-amplifying weapons. Bacterial hosts that carry temperate bacteriophages can thus gain a fitness advantage within a given niche by killing competitors. But what makes an effective phage weapon? Here, we first use a simple mathematical model to explore the factors determining bacteriophage weapon utility. Our models suggest that bacteriophage weapons are nuanced and context-dependent; an individual bacteriophage may be beneficial or costly depending upon tiny changes to how it behaves or the bacterial community it inhabits. We then confirm these mathematical predictions experimentally, using phages isolated from cystic fibrosis patients. But, in doing so, we also find that another factor-nutrient availability-plays a key role in shaping bacteriophage-mediated competition. Together, our results provide new insights into how temperate bacteriophages modulate bacterial communities.}, }
@article {pmid38726295, year = {2024}, author = {Casero, JJD and Rovedder, APM and Vargas, LK}, title = {Editorial: Plant-microbe interactions in forest ecosystems, volume II.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1414383}, pmid = {38726295}, issn = {1664-462X}, }
@article {pmid38724726, year = {2024}, author = {Bobonis, J and Yang, ALJ and Voogdt, CGP and Typas, A}, title = {TAC-TIC, a high-throughput genetics method to identify triggers or blockers of bacterial toxin-antitoxin systems.}, journal = {Nature protocols}, volume = {19}, number = {8}, pages = {2231-2249}, pmid = {38724726}, issn = {1750-2799}, mesh = {*Toxin-Antitoxin Systems/genetics ; *Escherichia coli/genetics ; Bacterial Toxins/genetics/metabolism ; Bacteriophages/genetics ; High-Throughput Screening Assays/methods ; Conjugation, Genetic ; }, abstract = {Toxin-antitoxin systems (TAs) are abundant in bacterial chromosomes and can arrest growth under stress, but usually remain inactive. TAs have been increasingly implicated in halting the growth of infected bacteria from bacteriophages or foreign genetic elements[1,2] to protect the population (abortive infection, Abi). The vast diversity and abundance of TAs and other Abi systems[3] suggest they play an important immunity role, yet what allows them to sense attack remains largely enigmatic. Here, we describe a method called toxin activation-inhibition conjugation (TAC-TIC), which we used to identify gene products that trigger or block the toxicity of phage-defending tripartite retron-TAs[4]. TAC-TIC employs high-density arrayed mobilizable gene-overexpression libraries, which are transferred into cells carrying the full TA system or only its toxic component, on inducible vectors. The double-plasmid transconjugants are then pinned on inducer-containing agar plates and their colony fitness is quantified to identify gene products that trigger a TA to inhibit growth (TAC), or that block it from acting (TIC). TAC-TIC is optimized for the Singer ROTOR pinning robot, but can also be used with other robots or manual pinners, and allows screening tens of thousands of genes against any TA or Abi (with toxicity) within a week. Finally, we present a dual conjugation donor/cloning strain (Escherichia coli DATC), which accelerates the construction of TAC-TIC gene-donor libraries from phages, enabling the use of TAC-TIC for identifying TA triggers and antidefense mechanisms in phage genomes.}, }
@article {pmid38723661, year = {2024}, author = {Tschitschko, B and Esti, M and Philippi, M and Kidane, AT and Littmann, S and Kitzinger, K and Speth, DR and Li, S and Kraberg, A and Tienken, D and Marchant, HK and Kartal, B and Milucka, J and Mohr, W and Kuypers, MMM}, title = {Rhizobia-diatom symbiosis fixes missing nitrogen in the ocean.}, journal = {Nature}, volume = {630}, number = {8018}, pages = {899-904}, pmid = {38723661}, issn = {1476-4687}, mesh = {Carbon/metabolism ; *Diatoms/metabolism/physiology ; *Nitrogen/metabolism ; *Nitrogen Fixation ; *Oceans and Seas ; Photosynthesis ; Phylogeny ; *Rhizobium/classification/metabolism/physiology ; *Seawater/microbiology/chemistry ; *Symbiosis ; Cyanobacteria/isolation &amp; purification/metabolism ; Atlantic Ocean ; }, abstract = {Nitrogen (N2) fixation in oligotrophic surface waters is the main source of new nitrogen to the ocean[1] and has a key role in fuelling the biological carbon pump[2]. Oceanic N2 fixation has been attributed almost exclusively to cyanobacteria, even though genes encoding nitrogenase, the enzyme that fixes N2 into ammonia, are widespread among marine bacteria and archaea[3-5]. Little is known about these non-cyanobacterial N2 fixers, and direct proof that they can fix nitrogen in the ocean has so far been lacking. Here we report the discovery of a non-cyanobacterial N2-fixing symbiont, 'Candidatus Tectiglobus diatomicola', which provides its diatom host with fixed nitrogen in return for photosynthetic carbon. The N2-fixing symbiont belongs to the order Rhizobiales and its association with a unicellular diatom expands the known hosts for this order beyond the well-known N2-fixing rhizobia-legume symbioses on land[6]. Our results show that the rhizobia-diatom symbioses can contribute as much fixed nitrogen as can cyanobacterial N2 fixers in the tropical North Atlantic, and that they might be responsible for N2 fixation in the vast regions of the ocean in which cyanobacteria are too rare to account for the measured rates.}, }
@article {pmid38722447, year = {2024}, author = {Hu, Y and Cai, J and Song, Y and Li, G and Gong, Y and Jiang, X and Tang, X and Shao, K and Gao, G}, title = {Sediment DNA Records the Critical Transition of Bacterial Communities in the Arid Lake.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {68}, pmid = {38722447}, issn = {1432-184X}, support = {2019YFA0607100//Key Technologies Research and Development Program/ ; U2003205//National Natural Science Foundation of China/ ; 2022xjkk1504//The third Xinjiang Scientific Expedition/ ; }, mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; China ; *DNA, Bacterial/genetics ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Microbiota ; }, abstract = {It is necessary to predict the critical transition of lake ecosystems due to their abrupt, non-linear effects on social-economic systems. Given the promising application of paleolimnological archives to tracking the historical changes of lake ecosystems, it is speculated that they can also record the lake's critical transition. We studied Lake Dali-Nor in the arid region of Inner Mongolia because of the profound shrinking the lake experienced between the 1300 s and the 1600 s. We reconstructed the succession of bacterial communities from a 140-cm-long sediment core at 4-cm intervals and detected the critical transition. Our results showed that the historical trajectory of bacterial communities from the 1200 s to the 2010s was divided into two alternative states: state1 from 1200 to 1300 s and state2 from 1400 to 2010s. Furthermore, in the late 1300 s, the appearance of a tipping point and critical slowing down implied the existence of a critical transition. By using a multi-decadal time series from the sedimentary core, with general Lotka-Volterra model simulations, local stability analysis found that bacterial communities were the most unstable as they approached the critical transition, suggesting that the collapse of stability triggers the community shift from an equilibrium state to another state. Furthermore, the most unstable community harbored the strongest antagonistic and mutualistic interactions, which may imply the detrimental role of interaction strength on community stability. Collectively, our study showed that sediment DNA can be used to detect the critical transition of lake ecosystems.}, }
@article {pmid38722171, year = {2024}, author = {Stice, SP and Jan, H-H and Chen, H-C and Nwosu, L and Shin, GY and Weaver, S and Coutinho, T and Kvitko, BH and Baltrus, DA}, title = {Erratum for Stice et al., "Pantailocins: phage-derived bacteriocins from Pantoea ananatis and Pantoea stewartii subsp. indologenes".}, journal = {Applied and environmental microbiology}, volume = {90}, number = {6}, pages = {e0062924}, doi = {10.1128/aem.00629-24}, pmid = {38722171}, issn = {1098-5336}, }
@article {pmid38718505, year = {2024}, author = {Liu, S and Zhang, Z and Zhao, C and Zhang, M and Han, F and Hao, J and Wang, X and Shan, X and Zhou, W}, title = {Nonlinear responses of biofilm bacteria to alkyl-chain length of parabens by DFT calculation.}, journal = {Journal of hazardous materials}, volume = {472}, number = {}, pages = {134460}, doi = {10.1016/j.jhazmat.2024.134460}, pmid = {38718505}, issn = {1873-3336}, mesh = {*Parabens/chemistry/toxicity ; *Biofilms/drug effects ; Bacteria/drug effects ; Density Functional Theory ; Quorum Sensing/drug effects ; }, abstract = {Parabens can particularly raise significant concerns regarding the disruption of microbial ecology due to their antimicrobial properties. However, the responses of biofilm bacteria to diverse parabens with different alkyl-chain length remains unclear. Here, theoretical calculations and bioinformatic analysis were performed to decipher the influence of parabens varying alkyl-chain lengths on the biofilm bacteria. Our results showed that the disturbances in bacterial community did not linearly response to the alkyl-chain length of parabens, and propylparaben (PrP), with median chain length, had more severe impact on bacterial community. Despite the fact that paraben lethality linearly increased with chain length, the PrP had a higher chemical reactions potential than parabens with shorter or longer alkyl-chain. The chemical reactions potential was critical in the nonlinear responses of bacterial community to alkyl-chain length of parabens. PrP could impose selective pressure to disturb the bacterial community, because it had a more profound contribution to deterministic assembly process. Furthermore, N-acyl-homoserine lactones was also significantly promoted under PrP exposure, confirming that PrP could affect the bacterial community by influencing the quorum-sensing system. Overall, our study reveals the nonlinear responses of bacterial communities to the alkyl-chain lengths of parabens and provides insightful perspectives for the better regulation of parabens. ENVIRONMENTAL IMPLICATION: Parabens are recognized as emerging organic pollutants, which specially raise great concerns due to their antimicrobial properties disturbing microbial ecology. However, few study have addressed the relationship between bacterial community responses and the molecular structural features of parabens with different alkyl-chain length. This investigation revealed nonlinear responses of the bacterial community to the alkyl-chain length of parabens through DFT calculation and bioinformatic analysis and identified the critical roles of chemical reactions potential in nonlinear responses of bacterial community. Our results benefit the precise evaluation of ecological hazards posed by parabens and provide useful insights for better regulation of parabens.}, }
@article {pmid38714759, year = {2024}, author = {Lee, KS and Landry, Z and Athar, A and Alcolombri, U and Pramoj Na Ayutthaya, P and Berry, D and de Bettignies, P and Cheng, JX and Csucs, G and Cui, L and Deckert, V and Dieing, T and Dionne, J and Doskocil, O and D'Souza, G and García-Timermans, C and Gierlinger, N and Goda, K and Hatzenpichler, R and Henshaw, RJ and Huang, WE and Iermak, I and Ivleva, NP and Kneipp, J and Kubryk, P and Küsel, K and Lee, TK and Lee, SS and Ma, B and Martínez-Pérez, C and Matousek, P and Meckenstock, RU and Min, W and Mojzeš, P and Müller, O and Kumar, N and Nielsen, PH and Notingher, I and Palatinszky, M and Pereira, FC and Pezzotti, G and Pilat, Z and Plesinger, F and Popp, J and Probst, AJ and Riva, A and Saleh, AAE and Samek, O and Sapers, HM and Schubert, OT and Stubbusch, AKM and Tadesse, LF and Taylor, GT and Wagner, M and Wang, J and Yin, H and Yue, Y and Zenobi, R and Zini, J and Sarkans, U and Stocker, R}, title = {MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data.}, journal = {Nature microbiology}, volume = {9}, number = {5}, pages = {1152-1156}, pmid = {38714759}, issn = {2058-5276}, support = {GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 542395//Simons Foundation/ ; }, mesh = {*Spectrum Analysis, Raman/methods ; *Internet ; Humans ; Databases, Factual ; }, }
@article {pmid38712704, year = {2024}, author = {Vandermaesen, J and Daly, AJ and Mawarda, PC and Baetens, JM and De Baets, B and Boon, N and Springael, D}, title = {Cooperative interactions between invader and resident microbial community members weaken the negative diversity-invasion relationship.}, journal = {Ecology letters}, volume = {27}, number = {5}, pages = {e14433}, doi = {10.1111/ele.14433}, pmid = {38712704}, issn = {1461-0248}, support = {266039//EU FP7/ ; G0D0322N//Fonds Wetenschappelijk Onderzoek/ ; BELSPO P7/25//Belgian Science Policy (BELSPO)/ ; }, mesh = {*Microbiota ; Benzamides ; Microbial Interactions ; Phyllobacteriaceae/physiology ; Groundwater/microbiology ; Biodiversity ; }, abstract = {The negative diversity-invasion relationship observed in microbial invasion studies is commonly explained by competition between the invader and resident populations. However, whether this relationship is affected by invader-resident cooperative interactions is unknown. Using ecological and mathematical approaches, we examined the survival and functionality of Aminobacter niigataensis MSH1 to mineralize 2,6-dichlorobenzamide (BAM), a groundwater micropollutant affecting drinking water production, in sand microcosms when inoculated together with synthetic assemblies of resident bacteria. The assemblies varied in richness and in strains that interacted pairwise with MSH1, including cooperative and competitive interactions. While overall, the negative diversity-invasion relationship was retained, residents engaging in cooperative interactions with the invader had a positive impact on MSH1 survival and functionality, highlighting the dependency of invasion success on community composition. No correlation existed between community richness and the delay in BAM mineralization by MSH1. The findings suggest that the presence of cooperative residents can alleviate the negative diversity-invasion relationship.}, }
@article {pmid38712077, year = {2024}, author = {Letourneau, J and Carrion, VM and Jiang, S and Osborne, OW and Holmes, ZC and Fox, A and Epstein, P and Tan, CY and Kirtley, M and Surana, NK and David, LA}, title = {Interplay between particle size and microbial ecology in the gut microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38712077}, issn = {2692-8205}, support = {R01 DK116187/DK/NIDDK NIH HHS/United States ; R01 DK128611/DK/NIDDK NIH HHS/United States ; }, abstract = {Physical particles can serve as critical abiotic factors that structure the ecology of microbial communities. For non-human vertebrate gut microbiomes, fecal particle size (FPS) has been known to be shaped by chewing efficiency and diet. However, little is known about what drives FPS in the human gut. Here, we analyzed FPS by laser diffraction across a total of 76 individuals and found FPS to be strongly individualized. Surprisingly, a behavioral intervention with 41 volunteers designed to increase chewing efficiency did not impact FPS. Dietary patterns could also not be associated with FPS. Instead, we found evidence that mammalian and human gut microbiomes shaped FPS. Fecal samples from germ-free and antibiotic-treated mice exhibited increased FPS relative to colonized mice. In humans, markers of longer transit time were correlated with smaller FPS. Gut microbiota diversity and composition were also associated with FPS. Finally, ex vivo culture experiments using human fecal microbiota from distinct donors showed that differences in microbiota community composition can drive variation in particle size. Together, our results support an ecological model in which the human gut microbiome plays a key role in reducing the size of food particles during digestion, and that the microbiomes of individuals vary in this capacity. These new insights also suggest FPS in humans to be governed by processes beyond those found in other mammals and emphasize the importance of gut microbiota in shaping their own abiotic environment.}, }
@article {pmid38711157, year = {2024}, author = {Jurburg, SD and Blowes, SA and Shade, A and Eisenhauer, N and Chase, JM}, title = {Synthesis of recovery patterns in microbial communities across environments.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {79}, pmid = {38711157}, issn = {2049-2618}, support = {FZT 118, 202548816//Deutsche Forschungsgemeinschaft/ ; FZT 118, 202548816//Deutsche Forschungsgemeinschaft/ ; FZT 118, 202548816//Deutsche Forschungsgemeinschaft/ ; FZT 118, 202548816//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Microbiota ; *Soil Microbiology ; *Bayes Theorem ; Animals ; *Bacteria/classification/genetics/isolation &amp; purification ; Mammals/microbiology ; Biodiversity ; Water Microbiology ; }, abstract = {BACKGROUND: Disturbances alter the diversity and composition of microbial communities. Yet a generalized empirical assessment of microbiome responses to disturbance across different environments is needed to understand the factors driving microbiome recovery, and the role of the environment in driving these patterns.<br><br>RESULTS: To this end, we combined null models with Bayesian generalized linear models to examine 86 time series of disturbed mammalian, aquatic, and soil microbiomes up to 50&#xa0;days following disturbance. Overall, disturbances had the strongest effect on mammalian microbiomes, which lost taxa and later recovered their richness, but not their composition. In contrast, following disturbance, aquatic microbiomes tended away from their pre-disturbance composition over time. Surprisingly, across all environments, we found no evidence of increased compositional dispersion (i.e., variance) following disturbance, in contrast to the expectations of the Anna Karenina Principle.<br><br>CONCLUSIONS: This is the first study to systematically compare secondary successional dynamics across disturbed microbiomes, using a consistent temporal scale and modeling approach. Our findings show that the recovery of microbiomes is environment-specific, and helps to reconcile existing, environment-specific research into a unified perspective. Video Abstract.}, }
@article {pmid38710359, year = {2024}, author = {Lambert, S and Vercauteren, M and Catarino, AI and Li, Y and Van Landuyt, J and Boon, N and Everaert, G and De Rijcke, M and Janssen, CR and Asselman, J}, title = {Aerosolization of micro- and nanoplastics via sea spray: Investigating the role of polymer type, size, and concentration, and potential implications for human exposure.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {351}, number = {}, pages = {124105}, doi = {10.1016/j.envpol.2024.124105}, pmid = {38710359}, issn = {1873-6424}, mesh = {*Aerosols ; Humans ; *Microplastics/analysis ; *Seawater/chemistry ; *Plastics ; *Particle Size ; Polymers/chemistry ; Air Pollutants/analysis ; Inhalation Exposure/statistics &amp; numerical data ; Environmental Monitoring/methods ; Environmental Exposure ; Nanoparticles ; }, abstract = {Micro- and nanoplastics (MNPs) can enter the atmosphere via sea spray aerosols (SSAs), but the effects of plastic characteristics on the aerosolization process are unclear. Furthermore, the importance of the transport of MNPs via these SSAs as a possible new exposure route for human health remains unknown. The aim of this study was two-fold: (1) to examine if a selection of factors affects aerosolization processes of MNPs, and (2) to estimate human exposure to MNPs via aerosols inhalation. A laboratory-based bubble bursting mechanism, simulating the aerosolization process at sea, was used to investigate the influence of MNP as well as seawater characteristics. To determine the potential human exposure to microplastics via inhalation of SSAs, the results of the laboratory experiments were extrapolated to the field based on sea surface microplastic concentrations and the volume of inhaled aerosols. Enrichment seemed to be influenced by MNP size, concentration and polymer type. With higher enrichment for smaller particles and denser polymers. Experiments with different concentrations showed a larger range of variability but nonetheless lower concentrations seemed to result in higher enrichment, presumably due to lower aggregation. In addition to the MNP characteristics, the type of seawater used seemed to influence the aerosolization process. Our human exposure estimate to microplastic via inhalation of sea spray aerosols shows that in comparison with reported inhaled concentrations in urban and indoor environments, this exposure route seems negligible for microplastics. Following the business-as-usual scenario on plastic production, the daily plastic inhalation in coastal areas in 2100 is estimated to increase but remain far below 1 particle per day. This study shows that aerosolization of MNPs is a new plastic transport pathway to be considered, but in terms of human exposure it seems negligible compared to other more important sources of MNPs, based on current reported environmental concentrations.}, }
@article {pmid38708804, year = {2024}, author = {Burr, DJ and Drauschke, J and Kanevche, K and Kümmel, S and Stryhanyuk, H and Heberle, J and Perfumo, A and Elsaesser, A}, title = {Stable Isotope Probing-nanoFTIR for Quantitation of Cellular Metabolism and Observation of Growth-Dependent Spectral Features.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {20}, number = {36}, pages = {e2400289}, doi = {10.1002/smll.202400289}, pmid = {38708804}, issn = {1613-6829}, support = {462858357//Deutsche Forschungsgemeinschaft/ ; Freigeist//Volkswagen Foundation/ ; 50WB1623//Bundesministerium f&#xfc;r Wirtschaft und Energie/ ; 50WB2023//Bundesministerium f&#xfc;r Wirtschaft und Energie/ ; }, mesh = {Spectroscopy, Fourier Transform Infrared/methods ; *Carbon Isotopes/chemistry ; Microscopy, Atomic Force ; Isotope Labeling/methods ; Nanotechnology/methods ; Escherichia coli/metabolism/growth &amp; development ; Glucose/metabolism ; }, abstract = {This study utilizes nanoscale Fourier transform infrared spectroscopy (nanoFTIR) to perform stable isotope probing (SIP) on individual bacteria cells cultured in the presence of [13]C-labelled glucose. SIP-nanoFTIR simultaneously quantifies single-cell metabolism through infrared spectroscopy and acquires cellular morphological information via atomic force microscopy. The redshift of the amide I peak corresponds to the isotopic enrichment of newly synthesized proteins. These observations of single-cell translational activity are comparable to those of conventional methods, examining bulk cell numbers. Observing cells cultured under conditions of limited carbon, SIP- nanoFTIR is used to identify environmentally-induced changes in metabolic heterogeneity and cellular morphology. Individuals outcompeting their neighboring cells will likely play a disproportionately large role in shaping population dynamics during adverse conditions or environmental fluctuations. Additionally, SIP-nanoFTIR enables the spectroscopic differentiation of specific cellular growth phases. During cellular replication, subcellular isotope distribution becomes more homogenous, which is reflected in the spectroscopic features dependent on the extent of [13]C-[13]C mode coupling or to specific isotopic symmetries within protein secondary structures. As SIP-nanoFTIR captures single-cell metabolism, environmentally-induced cellular processes, and subcellular isotope localization, this technique offers widespread applications across a variety of disciplines including microbial ecology, biophysics, biopharmaceuticals, medicinal science, and cancer research.}, }
@article {pmid38707845, year = {2024}, author = {Rivas-Santisteban, J and Yubero, P and Robaina-Estévez, S and González, JM and Tamames, J and Pedrós-Alió, C}, title = {Quantifying microbial guilds.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae042}, pmid = {38707845}, issn = {2730-6151}, abstract = {The ecological role of microorganisms is of utmost importance due to their multiple interactions with the environment. However, assessing the contribution of individual taxonomic groups has proven difficult despite the availability of high throughput data, hindering our understanding of such complex systems. Here, we propose a quantitative definition of guild that is readily applicable to metagenomic data. Our framework focuses on the functional character of protein sequences, as well as their diversifying nature. First, we discriminate functional sequences from the whole sequence space corresponding to a gene annotation to then quantify their contribution to the guild composition across environments. In addition, we identify and distinguish functional implementations, which are sequence spaces that have different ways of carrying out the function. In contrast, we found that orthology delineation did not consistently align with ecologically (or functionally) distinct implementations of the function. We demonstrate the value of our approach with two case studies: the ammonia oxidation and polyamine uptake guilds from the Malaspina circumnavigation cruise, revealing novel ecological dynamics of the latter in marine ecosystems. Thus, the quantification of guilds helps us to assess the functional role of different taxonomic groups with profound implications on the study of microbial communities.}, }
@article {pmid38706006, year = {2024}, author = {Liew, KJ and Shahar, S and Shamsir, MS and Shaharuddin, NB and Liang, CH and Chan, KG and Pointing, SB and Sani, RK and Goh, KM}, title = {Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {29}, pmid = {38706006}, issn = {2524-6372}, support = {FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4//Malaysia Fundamental Research Grant Scheme (FRGS)/ ; FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4//Malaysia Fundamental Research Grant Scheme (FRGS)/ ; FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4//Malaysia Fundamental Research Grant Scheme (FRGS)/ ; FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4//Malaysia Fundamental Research Grant Scheme (FRGS)/ ; FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4//Malaysia Fundamental Research Grant Scheme (FRGS)/ ; 4J549//UTM QuickWin grant/ ; 4J549//UTM QuickWin grant/ ; T2EP30123-0028//Singapore Ministry of Education ARC Tier 2 fund/ ; 1736255, 1849206, and 1920954//National Science Foundation/ ; }, abstract = {BACKGROUND: Hot spring biofilms provide a window into the survival strategies of microbial communities in extreme environments and offer potential for biotechnological applications. This study focused on green and brown biofilms thriving on submerged plant litter within the Sungai Klah hot spring in Malaysia, characterised by temperatures of 58-74 °C. Using Illumina shotgun metagenomics and Nanopore ligation sequencing, we investigated the microbial diversity and functional potential of metagenome-assembled genomes (MAGs) with specific focus on biofilm formation, heat stress response, and carbohydrate catabolism.<br><br>RESULTS: Leveraging the power of both Illumina short-reads and Nanopore long-reads, we employed an Illumina-Nanopore hybrid assembly approach to construct MAGs with enhanced quality. The dereplication process, facilitated by the dRep tool, validated the efficiency of the hybrid assembly, yielding MAGs that reflected the intricate microbial diversity of these extreme ecosystems. The comprehensive analysis of these MAGs uncovered intriguing insights into the survival strategies of thermophilic taxa in the hot spring biofilms. Moreover, we examined the plant litter degradation potential within the biofilms, shedding light on the participation of diverse microbial taxa in the breakdown of starch, cellulose, and hemicellulose. We highlight that Chloroflexota and Armatimonadota MAGs exhibited a wide array of glycosyl hydrolases targeting various carbohydrate substrates, underscoring their metabolic versatility in utilisation of carbohydrates at elevated temperatures.<br><br>CONCLUSIONS: This study advances understanding of microbial ecology on plant litter under elevated temperature by revealing the functional adaptation of MAGs from hot spring biofilms. In addition, our findings highlight potential for biotechnology application through identification of thermophilic lignocellulose-degrading enzymes. By demonstrating the efficiency of hybrid assembly utilising Illumina-Nanopore reads, we highlight the value of combining multiple sequencing methods for a more thorough exploration of complex microbial communities.}, }
@article {pmid38705066, year = {2024}, author = {Shao, YH and Wu, JH and Chen, HW}, title = {Comammox Nitrospira cooperate with anammox bacteria in a partial nitritation-anammox membrane bioreactor treating low-strength ammonium wastewater at high loadings.}, journal = {Water research}, volume = {257}, number = {}, pages = {121698}, doi = {10.1016/j.watres.2024.121698}, pmid = {38705066}, issn = {1879-2448}, mesh = {*Bioreactors/microbiology ; *Wastewater/microbiology ; *Ammonium Compounds/metabolism ; Bacteria/metabolism ; Waste Disposal, Fluid/methods ; Nitrogen/metabolism ; Nitrification ; Nitrites/metabolism ; Oxidation-Reduction ; }, abstract = {Research has revealed that comammox Nitrospira and anammox bacteria engage in dynamic interactions in partial nitritation-anammox reactors, where they compete for ammonium and nitrite or comammox Nitrospria supply nitrite to anammox bacteria. However, two gaps in the literature are present: the know-how to manipulate the interactions to foster a stable and symbiotic relationship and the assessment of how effective this partnership is for treating low-strength ammonium wastewater at high hydraulic loads. In this study, we employed a membrane bioreactor designed to treat synthetic ammonium wastewater at a concentration of 60 mg N/L, reaching a peak loading of 0.36 g N/L/day by gradually reducing the hydraulic retention time to 4 hr. Throughout the experiment, the reactor achieved an approximately 80 % nitrogen removal rate through strategically adjusting intermittent aeration at every stage. Notably, the genera Ca. Kuenena, Nitrosomonas, and Nitrospira collectively constituted approximately 40 % of the microbial community. Under superior intermittent aeration conditions, the expression of comammox amoA was consistently higher than that of Nitrospira nxrB and AOB amoA in the biofilm, despite the higher abundance of Nitrosomonas than comammox Nitrospira, implying that the biofilm environment is favorable for fostering cooperation between comammox and anammox bacteria. We then assessed the in situ activity of comammox Nitrospira in the reactor by selectively suppressing Nitrosomonas using 1-octyne, thereby confirming that comammox Nitrospira played the primary role in facilitating the nitritation (33.1 % of input ammonium) rather than complete nitrification (7.3 % of input ammonium). Kinetic analysis revealed a specific ammonia-oxidizing rate 5.3 times higher than the nitrite-oxidizing rate in the genus Nitrospira, underscoring their critical role in supplying nitrite. These findings provide novel insights into the cooperative interplay between comammox Nitrospira and anammox bacteria, potentially reshaping the management of nitrogen cycling in engineered environments, and aiding the development of microbial ecology-driven wastewater treatment technologies.}, }
@article {pmid38703220, year = {2024}, author = {Zhao, L and Zhang, S and Xiao, R and Zhang, C and Lyu, Z and Zhang, F}, title = {Diversity and Functionality of Bacteria Associated with Different Tissues of Spider Heteropoda venatoria Revealed through Integration of High-Throughput Sequencing and Culturomics Approaches.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {67}, pmid = {38703220}, issn = {1432-184X}, mesh = {Animals ; *Spiders/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *High-Throughput Nucleotide Sequencing ; *RNA, Ribosomal, 16S/genetics ; Female ; Gastrointestinal Microbiome ; Humans ; Phylogeny ; Biodiversity ; Anti-Bacterial Agents/pharmacology ; Pesticides ; }, abstract = {Spiders host a diverse range of bacteria in their guts and other tissues, which have been found to play a significant role in their fitness. This study aimed to investigate the community diversity and functional characteristics of spider-associated bacteria in four tissues of Heteropoda venatoria using HTS of the 16S rRNA gene and culturomics technologies, as well as the functional verification of the isolated strains. The results of HTS showed that the spider-associated bacteria in different tissues belonged to 34 phyla, 72 classes, 170 orders, 277 families, and 458 genera. Bacillus was found to be the most abundant bacteria in the venom gland, silk gland, and ovary, while Stenotrophomonas, Acinetobacter, and Sphingomonas were dominant in the gut microbiota. Based on the amplicon sequencing results, 21 distinct cultivation conditions were developed using culturomics to isolate bacteria from the ovary, gut, venom gland, and silk gland. A total of 119 bacterial strains, representing 4 phyla and 25 genera, with Bacillus and Serratia as the dominant genera, were isolated. Five strains exhibited high efficiency in degrading pesticides in the in vitro experiments. Out of the 119 isolates, 28 exhibited antibacterial activity against at least one of the tested bacterial strains, including the pathogenic bacteria Staphylococcus aureus, Acinetobacter baumanii, and Enterococcus faecalis. The study also identified three strains, GL312, PL211, and PL316, which exhibited significant cytotoxicity against MGC-803. The crude extract from the fermentation broth of strain PL316 was found to effectively induce apoptosis in MGC-803 cells. Overall, this study offers a comprehensive understanding of the bacterial community structure associated with H. venatoria. It also provides valuable insights into discovering novel antitumor natural products for gastric cancer and xenobiotic-degrading bacteria of spiders.}, }
@article {pmid38702804, year = {2024}, author = {Das, R and Mishra, P and Mishra, B and Jha, R}, title = {Effect of in ovo feeding of xylobiose and xylotriose on plasma immunoglobulin, cecal metabolites production, microbial ecology, and metabolic pathways in broiler chickens.}, journal = {Journal of animal science and biotechnology}, volume = {15}, number = {1}, pages = {62}, pmid = {38702804}, issn = {1674-9782}, abstract = {BACKGROUND: Dietary supplementation of xylooligosaccharides (XOS) has been found to influence gut health by manipulating cecal microbiota and producing microbe-origin metabolites. But no study investigated and compared the effect of in ovo feeding of xylobiose (XOS2) and xylotriose (XOS3) in chickens. This study investigated the effect of in ovo feeding of these XOS compounds on post-hatch gut health parameters in chickens. A total of 144 fertilized chicken eggs were divided into three groups: a) non-injected control (CON), b) XOS2, and c) XOS3. On the 17[th] embryonic day, the eggs of the XOS2 and XOS3 groups were injected with 3 mg of XOS2 and XOS3 diluted in 0.5 mL of 0.85% normal saline through the amniotic sac. After hatching, the chicks were raised for 21 d. Blood was collected on d 14 to measure plasma immunoglobulin. Cecal digesta were collected for measuring short-chain fatty acids (SCFA) on d 14 and 21, and for microbial ecology and microbial metabolic pathway analyses on d 7 and 21.<br><br>RESULTS: The results were considered significantly different at P&#x2009;<&#x2009;0.05. ELISA quantified plasma IgA and IgG on d 14 chickens, revealing no differences among the treatments. Gas chromatography results showed no significant differences in the concentrations of cecal SCFAs on d 14 but significant differences on d&#xa0;21. However, the SCFA concentrations were lower in the XOS3 than in the CON group on d 21. The cecal metagenomics data showed that the abundance of the family Clostridiaceae significantly decreased on d 7, and the abundance of the family Oscillospiraceae increased on d 21 in the XOS2 compared to the CON. There was a reduction in the relative abundance of genus Clostridium sensu stricto&#xa0;1&#xa0;in the XOS2 compared to the CON on d 7 and the genus Ruminococcus torques in both XOS2 and XOS3 groups compared to the CON on d 21. The XOS2 and XOS3 groups reduced the genes for chondroitin sulfate degradation I and L-histidine degradation I pathways, which contribute to improved gut health, respectively, in the microbiome on d 7. In contrast, on d 21, the XOS2 and XOS3 groups enriched the thiamin salvage II, L-isoleucine biosynthesis IV, and O-antigen building blocks biosynthesis (E. coli) pathways, which are indicative of improved gut health. Unlike the XOS3 and CON, the microbiome enriched the pathways associated with energy enhancement, including flavin biosynthesis I, sucrose degradation III, and Calvin-Benson-Bassham cycle pathways, in the XOS2 group on d 21.<br><br>CONCLUSION: In ovo XOS2 and XOS3 feeding promoted beneficial bacterial growth and reduced harmful bacteria at the family and genus levels. The metagenomic-based microbial metabolic pathway profiling predicted a favorable change in the availability of cecal metabolites in the XOS2 and XOS3 groups. The modulation of microbiota and metabolic pathways suggests that in ovo XOS2 and XOS3 feeding improved gut health during the post-hatch period of broilers.}, }
@article {pmid38700528, year = {2024}, author = {Purahong, W and Ji, L and Wu, YT}, title = {Community Assembly Processes of Deadwood Mycobiome in a Tropical Forest Revealed by Long-Read Third-Generation Sequencing.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {66}, pmid = {38700528}, issn = {1432-184X}, support = {MOST 107-2311-B-020-002//Ministry of Science and Technology, Taiwan/ ; }, mesh = {*Mycobiome ; *Wood/microbiology ; *Fungi/genetics/classification/isolation &amp; purification ; *Forests ; Tropical Climate ; Phylogeny ; High-Throughput Nucleotide Sequencing ; Biodiversity ; }, abstract = {Despite the importance of wood-inhabiting fungi on nutrient cycling and ecosystem functions, their ecology, especially related to their community assembly, is still highly unexplored. In this study, we analyzed the wood-inhabiting fungal richness, community composition, and phylogenetics using PacBio sequencing. Opposite to what has been expected that deterministic processes especially environmental filtering through wood-physicochemical properties controls the community assembly of wood-inhabiting fungal communities, here we showed that both deterministic and stochastic processes can highly contribute to the community assembly processes of wood-inhabiting fungi in this tropical forest. We demonstrated that the dynamics of stochastic and deterministic processes varied with wood decomposition stages. The initial stage was mainly governed by a deterministic process (homogenous selection), whereas the early and later decomposition stages were governed by the stochastic processes (ecological drift). Deterministic processes were highly contributed by wood physicochemical properties (especially macronutrients and hemicellulose) rather than soil physicochemical factors. We elucidated that fine-scale fungal-fungal interactions, especially the network topology, modularity, and keystone taxa of wood-inhabiting fungal communities, strongly differed in an initial and decomposing deadwood. This current study contributes to a better understanding of the ecological processes of wood-inhabiting fungi in tropical regions where the knowledge of wood-inhabiting fungi is highly limited.}, }
@article {pmid38700397, year = {2024}, author = {Havlena, ZE and Hose, LD and DuChene, HR and Baker, GM and Powell, JD and Labrado, AL and Brunner, B and Jones, DS}, title = {Origin and modern microbial ecology of secondary mineral deposits in Lehman Caves, Great Basin National Park, NV, USA.}, journal = {Geobiology}, volume = {22}, number = {3}, pages = {e12594}, doi = {10.1111/gbi.12594}, pmid = {38700397}, issn = {1472-4669}, support = {80NSSC20K0619//NASA Exobiology/ ; //Rocky Mountain Association of Geologists/ ; }, mesh = {*Caves/microbiology ; *Minerals/analysis ; *Bacteria/classification/metabolism ; Nevada ; Archaea/metabolism ; Geologic Sediments/microbiology/chemistry ; Parks, Recreational ; RNA, Ribosomal, 16S/genetics ; Sulfuric Acids ; Phylogeny ; Microbiota ; Calcium Sulfate/chemistry ; Microscopy, Electron, Scanning ; }, abstract = {Lehman Caves is an extensively decorated high desert cave that represents one of the main tourist attractions in Great Basin National Park, Nevada. Although traditionally considered a water table cave, recent studies identified abundant speleogenetic features consistent with a hypogenic and, potentially, sulfuric acid origin. Here, we characterized white mineral deposits in the Gypsum Annex (GA) passage to determine whether these secondary deposits represent biogenic minerals formed during sulfuric acid corrosion and explored microbial communities associated with these and other mineral deposits throughout the cave. Powder X-ray diffraction (pXRD), scanning electron microscopy with electron dispersive spectroscopy (SEM-EDS), and electron microprobe analyses (EPMA) showed that, while most white mineral deposits from the GA contain gypsum, they also contain abundant calcite, silica, and other phases. Gypsum and carbonate-associated sulfate isotopic values of these deposits are variable, with δ[34]SV-CDT between +9.7‰ and +26.1‰, and do not reflect depleted values typically associated with replacement gypsum formed during sulfuric acid speleogenesis. Petrographic observations show that the sulfates likely co-precipitated with carbonate and SiO2 phases. Taken together, these data suggest that the deposits resulted from later-stage meteoric events and not during an initial episode of sulfuric acid speleogenesis. Most sedimentary and mineral deposits in Lehman Caves have very low microbial biomass, with the exception of select areas along the main tour route that have been impacted by tourist traffic. High-throughput 16S rRNA gene amplicon sequencing showed that microbial communities in GA sediments are distinct from those in other parts of the cave. The microbial communities that inhabit these oligotrophic secondary mineral deposits include OTUs related to known ammonia-oxidizing Nitrosococcales and Thaumarchaeota, as well as common soil taxa such as Acidobacteriota and Proteobacteria. This study reveals microbial and mineralogical diversity in a previously understudied cave and expands our understanding of the geomicrobiology of desert hypogene cave systems.}, }
@article {pmid38697936, year = {2024}, author = {Nair, GR and Kooverjee, BB and de Scally, S and Cowan, DA and Makhalanyane, TP}, title = {Changes in nutrient availability substantially alter bacteria and extracellular enzymatic activities in Antarctic soils.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {6}, pages = {}, pmid = {38697936}, issn = {1574-6941}, support = {UID 110717//National Research Foundation of South Africa/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Nitrogen/metabolism ; *Bacteria/genetics/enzymology/metabolism ; *Nutrients/metabolism ; *Soil/chemistry ; *Microbiota ; *Carbon/metabolism ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In polar regions, global warming has accelerated the melting of glacial and buried ice, resulting in meltwater run-off and the mobilization of surface nutrients. Yet, the short-term effects of altered nutrient regimes on the diversity and function of soil microbiota in polyextreme environments such as Antarctica, remains poorly understood. We studied these effects by constructing soil microcosms simulating augmented carbon, nitrogen, and moisture. Addition of nitrogen significantly decreased the diversity of Antarctic soil microbial assemblages, compared with other treatments. Other treatments led to a shift in the relative abundances of these microbial assemblages although the distributional patterns were random. Only nitrogen treatment appeared to lead to distinct community structural patterns, with increases in abundance of Proteobacteria (Gammaproteobateria) and a decrease in Verrucomicrobiota (Chlamydiae and Verrucomicrobiae).The effects of extracellular enzyme activities and soil parameters on changes in microbial taxa were also significant following nitrogen addition. Structural equation modeling revealed that nutrient source and extracellular enzyme activities were positive predictors of microbial diversity. Our study highlights the effect of nitrogen addition on Antarctic soil microorganisms, supporting evidence of microbial resilience to nutrient increases. In contrast with studies suggesting that these communities may be resistant to change, Antarctic soil microbiota responded rapidly to augmented nutrient regimes.}, }
@article {pmid38697548, year = {2024}, author = {Hendry, MJ and Kirk, L and Warner, J and Shaw, S and Peyton, BM and Schmeling, E and Barbour, SL}, title = {Selenate bioreduction in a large in situ field trial.}, journal = {The Science of the total environment}, volume = {933}, number = {}, pages = {172869}, doi = {10.1016/j.scitotenv.2024.172869}, pmid = {38697548}, issn = {1879-1026}, mesh = {*Water Pollutants, Chemical/metabolism/analysis ; *Selenic Acid/metabolism ; *Biodegradation, Environmental ; British Columbia ; Coal Mining ; Selenium/metabolism/analysis ; Mining ; }, abstract = {Removing selenium (Se) from mine effluent is a common challenge. A long-term, in situ experiment was conducted to bioremediate large volumes (up to 7500 m[c] d[-1]) of Se(VI)-contaminated water (mean 87 μg L[-1]) by injecting the water into a saturated waste rock fill (SRF) at a coal mining operation in Elk Valley, British Columbia, Canada. To stimulate/maintain biofilm growth in the SRF, labile organic carbon (methanol) and nutrients were added to the water prior to its injection. A conservative tracer (Br[-]) was also added to track the migration of injected water across the SRF, identify wells with minimal dilution and used to quantify the extent of bioreduction. The evolution of the Se species through the SRF was monitored in time and space for 201 d. Selenium concentrations of <3.8 μg L[-1] were attained in monitoring wells located 38 m from the injection wells after 114 to 141 d of operation. Concentrations of Se species in water samples from complementary long-term (351-498 d) column experiments using influent Se(VI) concentrations of 1.0 mg L[-1] were consistent with the results of the in situ experiment. Solid samples collected at the completion of the column experiments confirmed the presence of indigenous Se-reducing bacteria and that the sequestered Se was present as insoluble Se(0), likely in Se-S ring compounds. Based on the success of this ongoing bioremediation experiment, this technology is being applied at other mine sites.}, }
@article {pmid38696469, year = {2024}, author = {Freilich, MA and Poirier, C and Dever, M and Alou-Font, E and Allen, J and Cabornero, A and Sudek, L and Choi, CJ and Ruiz, S and Pascual, A and Farrar, JT and Johnston, TMS and D'Asaro, EA and Worden, AZ and Mahadevan, A}, title = {3D intrusions transport active surface microbial assemblages to the dark ocean.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {19}, pages = {e2319937121}, pmid = {38696469}, issn = {1091-6490}, support = {N00014-16-1-3130//DOD | USN | Office of Naval Research (ONR)/ ; GBMF 3788//Gordon and Betty Moore Foundation (GBMF)/ ; Dimensions 2230811//National Science Foundation (NSF)/ ; N/A//DOD | National Defense Science and Engineering Graduate (NDSEG)/ ; Martin Fellowship//MIT | Environmental Solutions Initiative, Massachusetts Institute of Technology (ESI)/ ; Montrym Fund//MIT | Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology (EAPS, MIT)/ ; N00014-18-1-2416//DOD | USN | Office of Naval Research (ONR)/ ; N00014-18-1-2139//DOD | USN | Office of Naval Research (ONR)/ ; N00014-18-1-2431//DOD | USN | Office of Naval Research (ONR)/ ; }, mesh = {*Seawater/microbiology/chemistry ; *Bacteria/metabolism ; *Oceans and Seas ; Carbon/metabolism ; Carbon Cycle ; Chlorophyll/metabolism ; Ecosystem ; Phytoplankton/metabolism ; Seasons ; Biomass ; Microbiota/physiology ; Oxygen/metabolism ; }, abstract = {Subtropical oceans contribute significantly to global primary production, but the fate of the picophytoplankton that dominate in these low-nutrient regions is poorly understood. Working in the subtropical Mediterranean, we demonstrate that subduction of water at ocean fronts generates 3D intrusions with uncharacteristically high carbon, chlorophyll, and oxygen that extend below the sunlit photic zone into the dark ocean. These contain fresh picophytoplankton assemblages that resemble the photic-zone regions where the water originated. Intrusions propagate depth-dependent seasonal variations in microbial assemblages into the ocean interior. Strikingly, the intrusions included dominant biomass contributions from nonphotosynthetic bacteria and enrichment of enigmatic heterotrophic bacterial lineages. Thus, the intrusions not only deliver material that differs in composition and nutritional character from sinking detrital particles, but also drive shifts in bacterial community composition, organic matter processing, and interactions between surface and deep communities. Modeling efforts paired with global observations demonstrate that subduction can flux similar magnitudes of particulate organic carbon as sinking export, but is not accounted for in current export estimates and carbon cycle models. Intrusions formed by subduction are a particularly important mechanism for enhancing connectivity between surface and upper mesopelagic ecosystems in stratified subtropical ocean environments that are expanding due to the warming climate.}, }
@article {pmid38695873, year = {2024}, author = {Roh, H and Kannimuthu, D}, title = {Genomic and Transcriptomic Diversification of Flagellin Genes Provides Insight into Environmental Adaptation and Phylogeographic Characteristics in Aeromonas hydrophila.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {65}, pmid = {38695873}, issn = {1432-184X}, mesh = {*Flagellin/genetics ; *Aeromonas hydrophila/genetics/physiology ; *Transcriptome ; Phylogeography ; Adaptation, Physiological/genetics ; Phylogeny ; Biofilms/growth &amp; development ; }, abstract = {Aeromonas hydrophila is an opportunistic motile pathogen with a broad host range, infecting both terrestrial and aquatic animals. Environmental and geographical conditions exert selective pressure on both geno- and phenotypes of pathogens. Flagellin, directly exposed to external environments and containing important immunogenic epitopes, may display significant variability in response to external conditions. In this study, we conducted a comparative analysis of ~ 150 A. hydrophila genomes, leading to the identification of six subunits of the flagellin gene (fla-1 to fla-4, flaA, and flaB). Individual strains harbored different composition of flagellin subunits and copies. The composition of subunits showed distinct patterns depending on environmental sources. Strains from aquatic environments were mainly comprised of fla-1 to fla-4 subunits, while terrestrial strains predominated in groups harboring flaA and flaB subunits. Each flagellin showed varying levels of expression, with flaA and flaB demonstrating significantly higher expression compared to others. One of the chemotaxis pathways that control flagellin movement through a two-component system was significantly upregulated in flaA(+ 1)/flaB(+ 1) group, whereas flaA and flaB showed different transcriptomic expressions. The genes positively correlated with flaA expression were relevant to biofilm formation and bacterial chemotaxis, but flaB showed a negative correlation with the genes in ABC transporters and quorum sensing pathway. However, the expression patterns of fla-2 to fla-4 were identical. This suggests various types of flagellin subunits may have different biological functions. The composition and expression levels of flagellin subunits could provide valuable insights into the adaptation of A. hydrophila and the differences among strains in response to various external environments.}, }
@article {pmid38694807, year = {2024}, author = {Sumithra, TG and Sharma, SRK and Suresh, G and Gop, AP and Surya, S and Gomathi, P and Anil, MK and Sajina, KA and Reshma, KJ and Ebeneezar, S and Narasimapallavan, I and Gopalakrishnan, A}, title = {Mechanistic insights into the early life stage microbiota of silver pompano (Trachinotus blochii).}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1356828}, pmid = {38694807}, issn = {1664-302X}, abstract = {INTRODUCTION: Deep investigations of host-associated microbiota can illuminate microbe-based solutions to improve production in an unprecedented manner. The poor larval survival represents the critical bottleneck in sustainable marine aquaculture practices. However, little is known about the microbiota profiles and their governing eco-evolutionary processes of the early life stages of marine teleost, impeding the development of suitable beneficial microbial management strategies. The study provides first-hand mechanistic insights into microbiota and its governing eco-evolutionary processes in early life stages of a tropical marine teleost model, Trachinotus blochii.<br><br>METHODS: The microbiota profiles and their dynamics from the first day of hatching till the end of metamorphosis and that of fingerling's gut during the routine hatchery production were studied using 16S rRNA amplicon-based high-throughput sequencing. Further, the relative contributions of various external factors (rearing water, live feed, microalgae, and formulated feed) to the microbiota profiles at different ontogenies was also analyzed.<br><br>RESULTS: A less diverse but abundant core microbial community (~58% and 54% in the whole microbiota and gut microbiota, respectively) was observed throughout the early life stages, supporting 'core microbiota' hypothesis. Surprisingly, there were two well-differentiated clusters in the whole microbiota profiles, &#x2264;10 DPH (days post-hatching) and&#x2009;>&#x2009;10 DPH samples. The levels of microbial taxonomic signatures of stress indicated increased stress in the early stages, a possible explanation for increased mortality during early life stages. Further, the results suggested an adaptive mechanism for establishing beneficial strains along the ontogenetic progression. Moreover, the highly transient microbiota in the early life stages became stable along the ontogenetic progression, hypothesizing that the earlier life stages will be the best window to influence the microbiota. The egg microbiota also crucially affected the microbial community. Noteworthily, both water and the feed microbiota significantly contributed to the early microbiota, with the feed microbiota having a more significant contribution to fish microbiota. The results illustrated that rotifer enrichment would be the optimal medium for the early larval microbiota manipulations.<br><br>CONCLUSION: The present study highlighted the crucial foundations for the microbial ecology of T. blochii during early life stages with implications to develop suitable beneficial microbial management strategies for sustainable mariculture production.}, }
@article {pmid38694752, year = {2024}, author = {Brame, JE and Liddicoat, C and Abbott, CA and Edwards, RA and Robinson, JM and Gauthier, NE and Breed, MF}, title = {The macroecology of butyrate-producing bacteria via metagenomic assessment of butyrate production capacity.}, journal = {Ecology and evolution}, volume = {14}, number = {5}, pages = {e11239}, pmid = {38694752}, issn = {2045-7758}, abstract = {Butyrate-producing bacteria are found in many outdoor ecosystems and host organisms, including humans, and are vital to ecosystem functionality and human health. These bacteria ferment organic matter, producing the short-chain fatty acid butyrate. However, the macroecological influences on their biogeographical distribution remain poorly resolved. Here we aimed to characterise their global distribution together with key explanatory climatic, geographical and physicochemical variables. We developed new normalised butyrate production capacity (BPC) indices derived from global metagenomic (n = 13,078) and Australia-wide soil 16S rRNA (n = 1331) data, using Geographic Information System (GIS) and modelling techniques to detail their ecological and biogeographical associations. The highest median BPC scores were found in anoxic and fermentative environments, including the human (BPC = 2.99) and non-human animal gut (BPC = 2.91), and in some plant-soil systems (BPC = 2.33). Within plant-soil systems, roots (BPC = 2.50) and rhizospheres (BPC = 2.34) had the highest median BPC scores. Among soil samples, geographical and climatic variables had the strongest overall effects on BPC scores (variable importance score range = 0.30-0.03), with human population density also making a notable contribution (variable importance score = 0.20). Higher BPC scores were in soils from seasonally productive sandy rangelands, temperate rural residential areas and sites with moderate-to-high soil iron concentrations. Abundances of butyrate-producing bacteria in outdoor soils followed complex ecological patterns influenced by geography, climate, soil chemistry and hydrological fluctuations. These new macroecological insights further our understanding of the ecological patterns of outdoor butyrate-producing bacteria, with implications for emerging microbially focused ecological and human health policies.}, }
@article {pmid38691424, year = {2024}, author = {Xiong, X and Othmer, HG and Harcombe, WR}, title = {Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38691424}, issn = {1751-7370}, support = {R01 GM121498/GM/NIGMS NIH HHS/United States ; R01-GM121498/NH/NIH HHS/United States ; }, mesh = {*Escherichia coli/drug effects/genetics/growth &amp; development ; *Anti-Bacterial Agents/pharmacology ; *Symbiosis ; *Salmonella enterica/drug effects/genetics ; Coculture Techniques ; Microbial Interactions ; Ampicillin/pharmacology ; Drug Resistance, Bacterial ; }, abstract = {Antibiotic persistence (heterotolerance) allows a subpopulation of bacteria to survive antibiotic-induced killing and contributes to the evolution of antibiotic resistance. Although bacteria typically live in microbial communities with complex ecological interactions, little is known about how microbial ecology affects antibiotic persistence. Here, we demonstrated within a synthetic two-species microbial mutualism of Escherichia coli and Salmonella enterica that the combination of cross-feeding and community spatial structure can emergently cause high antibiotic persistence in bacteria by increasing the cell-to-cell heterogeneity. Tracking ampicillin-induced death for bacteria on agar surfaces, we found that E. coli forms up to 55 times more antibiotic persisters in the cross-feeding coculture than in monoculture. This high persistence could not be explained solely by the presence of S. enterica, the presence of cross-feeding, average nutrient starvation, or spontaneous resistant mutations. Time-series fluorescent microscopy revealed increased cell-to-cell variation in E. coli lag time in the mutualistic co-culture. Furthermore, we discovered that an E. coli cell can survive antibiotic killing if the nearby S. enterica cells on which it relies die first. In conclusion, we showed that the high antibiotic persistence phenotype can be an emergent phenomenon caused by a combination of cross-feeding and spatial structure. Our work highlights the importance of considering spatially structured interactions during antibiotic treatment and understanding microbial community resilience more broadly.}, }
@article {pmid38691215, year = {2024}, author = {Tokash-Peters, AG and Niyonzima, JD and Kayirangwa, M and Muhayimana, S and Tokash, IW and Jabon, JD and Lopez, SG and Kearns, PJ and Woodhams, DC}, title = {Mosquito Microbiomes of Rwanda: Characterizing Mosquito Host and Microbial Communities in the Land of a Thousand Hills.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {64}, pmid = {38691215}, issn = {1432-184X}, support = {DGE 1249946//Directorate for Biological Sciences/ ; 1950051//Directorate for Biological Sciences/ ; 1947684//National Science Foundation/ ; 1947684//National Science Foundation/ ; }, mesh = {Rwanda ; Animals ; *Microbiota ; *Culicidae/microbiology ; *Wolbachia/genetics/isolation &amp; purification/classification ; *Bacteria/classification/genetics/isolation &amp; purification ; Mosquito Vectors/microbiology ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Serratia/genetics/isolation &amp; purification/classification ; Electron Transport Complex IV/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {Mosquitoes are a complex nuisance around the world and tropical countries bear the brunt of the burden of mosquito-borne diseases. Rwanda has had success in reducing malaria and some arboviral diseases over the last few years, but still faces challenges to elimination. By building our understanding of in situ mosquito communities in Rwanda at a disturbed, human-occupied site and at a natural, preserved site, we can build our understanding of natural mosquito microbiomes toward the goal of implementing novel microbial control methods. Here, we examined the composition of collected mosquitoes and their microbiomes at two diverse sites using Cytochrome c Oxidase I sequencing and 16S V4 high-throughput sequencing. The majority (36 of 40 species) of mosquitoes captured and characterized in this study are the first-known record of their species for Rwanda but have been characterized in other nations in East Africa. We found significant differences among mosquito genera and among species, but not between mosquito sexes or catch method. Bacteria of interest for arbovirus control, Asaia, Serratia, and Wolbachia, were found in abundance at both sites and varied greatly by species.}, }
@article {pmid38691135, year = {2024}, author = {Salem, MA and Nour El-Din, HT and Hashem, AM and Aziz, RK}, title = {Genome-Scale Investigation of the Regulation of azoR Expression in Escherichia coli Using Computational Analysis and Transposon Mutagenesis.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {63}, pmid = {38691135}, issn = {1432-184X}, mesh = {*DNA Transposable Elements/genetics ; *Gene Expression Regulation, Bacterial ; *Escherichia coli Proteins/genetics/metabolism ; *Escherichia coli/genetics/metabolism ; *Nitroreductases/genetics/metabolism ; NADH, NADPH Oxidoreductases/genetics/metabolism ; Mutagenesis ; Genome, Bacterial ; Computational Biology ; Mutagenesis, Insertional ; }, abstract = {Bacterial azoreductases are enzymes that catalyze the reduction of ingested or industrial azo dyes. Although azoreductase genes have been well identified and characterized, the regulation of their expression has not been systematically investigated. To determine how different factors affect the expression of azoR, we extracted and analyzed transcriptional data from the Gene Expression Omnibus (GEO) resource, then confirmed computational predictions by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Results showed that azoR expression was lower with higher glucose concentration, agitation speed, and incubation temperature, but higher at higher culture densities. Co-expression and clustering analysis indicated ten genes with similar expression patterns to azoR: melA, tpx, yhbW, yciK, fdnG, fpr, nfsA, nfsB, rutF, and chrR (yieF). In parallel, constructing a random transposon library in E. coli K-12 and screening 4320 of its colonies for altered methyl red (MR)-decolorizing activity identified another set of seven genes potentially involved in azoR regulation. Among these genes, arsC, relA, plsY, and trmM were confirmed as potential azoR regulators based on the phenotypic decolorization activity of their transposon mutants, and the expression of arsC and relA was confirmed, by qRT-PCR, to significantly increase in E. coli K-12 in response to different MR concentrations. Finally, the significant decrease in azoR transcription upon transposon insertion in arsC and relA (as compared to its expression in wild-type E. coli) suggests their probable involvement in azoR regulation. In conclusion, combining in silico analysis and random transposon mutagenesis suggested a set of potential regulators of azoR in E. coli.}, }
@article {pmid38690316, year = {2024}, author = {Rivera-Lopez, EO and Nieves-Morales, R and Melendez-Martinez, G and Paez-Diaz, JA and Rodriguez-Carrio, SM and Rodriguez-Ramos, J and Morales-Valle, L and Rios-Velazquez, C}, title = {Sea cucumber (Holothuria glaberrima) intestinal microbiome dataset from Puerto Rico, generated by shotgun sequencing.}, journal = {Data in brief}, volume = {54}, number = {}, pages = {110421}, pmid = {38690316}, issn = {2352-3409}, abstract = {The sea cucumber (H. glaberrima) is a species found in the shallow waters near coral reefs and seagrass beds in Puerto Rico. To characterize the microbial taxonomic composition and functional profiles present in the sea cucumber, total DNA was obtained from their intestinal system, fosmid libraries constructed, and subsequent sequencing was performed. The diversity profile displayed that the most predominant domain was Bacteria (76.56 %), followed by Viruses (23.24 %) and Archaea (0.04 %). Within the 11 phyla identified, the most abundant was Proteobacteria (73.16 %), followed by Terrabacteria group (3.20 %) and Fibrobacterota, Chlorobiota, Bacteroidota (FCB) superphylum (1.02 %). The most abundant species were Porvidencia rettgeri (21.77 %), Pseudomonas stutzeri (14.78 %), and Alcaligenes faecalis (5.00 %). The functional profile revealed that the most abundant functions are related to transporters, MISC (miscellaneous information systems), organic nitrogen, energy, and carbon utilization. The data collected in this project on the diversity and functional profiles of the intestinal system of the H. glaberrima provided a detailed view of its microbial ecology. These findings may motivate comparative studies aimed at understanding the role of the microbiome in intestinal regeneration.}, }
@article {pmid38688974, year = {2024}, author = {Morigasaki, S and Matsui, M and Ohtsu, I and Doi, Y and Kawano, Y and Nakai, R and Iwasaki, W and Hayashi, H and Takaya, N}, title = {Temporal and fertilizer-dependent dynamics of soil bacterial communities in buckwheat fields under long-term management.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {9896}, pmid = {38688974}, issn = {2045-2322}, support = {JP19H05688//Japan Society for the Promotion of Science/ ; JP19H05683//Japan Society for the Promotion of Science/ ; JP19H05679//Japan Society for the Promotion of Science/ ; }, mesh = {*Fagopyrum ; *Soil Microbiology ; *Fertilizers ; *Bacteria/genetics/classification ; *RNA, Ribosomal, 16S/genetics ; *Soil/chemistry ; Microbiota ; Nitrogen/metabolism/analysis ; Agriculture/methods ; }, abstract = {This study integrated bacterial community and soil chemicals to characterize the soil ecosystem in an open upland field managed by six controlled fertilizer programs using the minimum amount of pesticides. Amplicon sequencing the 16S rRNA gene revealed that inorganic nitrogen fertilizer and compost altered the diversity and structure of the soil bacterial community throughout buckwheat (Fagopyrum esculentum Moench 'Hitachiakisoba') cultivation. The bacterial community comprised three clusters that contained bacteria that are prevalent in soils fertilized with nitrogen (cluster 1, 340 taxa), without nitrogen and compost (cluster 2, 234 taxa), and with compost-fertilized (cluster 3, 296 taxa). Cluster 2 contained more taxa in Actinobacteriota and less in Acidobacteriota, and cluster 3 contained more taxa in Gemmatimonadota compared with the other clusters. The most frequent taxa in cluster 1 were within the Chloroflexi phylum. The bacterial community structure correlated with soil chemical properties including pH, total organic carbon, SO4[2-], soluble Ca[2+]. A co-occurrence network of bacterial taxa and chemicals identified key bacterial groups comprising the center of a community network that determined topology and dynamics of the network. Temporal dynamics of the bacterial community structure indicated that Burkholderiales were associated with buckwheat ripening, indicating plant-bacteria interaction in the ecosystem.}, }
@article {pmid38688113, year = {2024}, author = {Ghani, MI and Yi, B and Rehmani, MS and Wei, X and Siddiqui, JA and Fan, R and Liu, Y and El-Sheikh, MA and Chen, X and Ahmad, P}, title = {Potential of melatonin and Trichoderma harzianum inoculation in ameliorating salt toxicity in watermelon: Insights into antioxidant system, leaf ultrastructure, and gene regulation.}, journal = {Plant physiology and biochemistry : PPB}, volume = {211}, number = {}, pages = {108639}, doi = {10.1016/j.plaphy.2024.108639}, pmid = {38688113}, issn = {1873-2690}, mesh = {*Citrullus/microbiology/drug effects/metabolism ; *Melatonin/pharmacology ; *Antioxidants/metabolism ; *Plant Leaves/drug effects/metabolism ; *Gene Expression Regulation, Plant/drug effects ; Salt Stress ; Hypocreales ; Photosynthesis/drug effects ; Oxidative Stress/drug effects ; }, abstract = {Melatonin (MT) is an extensively studied biomolecule with dual functions, serving as an antioxidant and a signaling molecule. Trichoderma Harzianum (TH) is widely recognized for its effectiveness as a biocontrol agent against many plant pathogens. However, the interplay between seed priming and MT (150 μm) in response to NaCl (100 mM) and its interaction with TH have rarely been investigated. This study aimed to evaluate the potential of MT and TH, alone and in combination, to mitigate salt stress (SS) in watermelon plants. The findings of this study revealed a significant decline in the morphological, physiological, and biochemical indices of watermelon seedlings exposed to SS. However, MT and TH treatments reduced the negative impact of salt stress. The combined application of MT and TH exerted a remarkable positive effect by increasing the growth, photosynthetic and gas exchange parameters, chlorophyll fluorescence indices, and ion balance (decreasing Na[+] and enhancing K[+]). MT and TH effectively alleviated oxidative injury by inhibiting hydrogen peroxide formation in saline and non-saline environments, as established by reduced lipid peroxidation and electrolyte leakage. Moreover, oxidative injury induced by SS on the cells was significantly mitigated by regulation of the antioxidant system, AsA-GSH-related enzymes, the glyoxalase system, augmentation of osmolytes, and activation of several genes involved in the defense system. Additionally, the reduction in oxidative damage was examined by chloroplast integrity via transmission electron microscopy (TEM). Overall, the results of this study provide a promising contribution of MT and TH in safeguarding the watermelon crop from oxidative damage induced by salt stress.}, }
@article {pmid38685217, year = {2024}, author = {Liu, Z and Zhang, J and Fan, C and Sun, S and An, X and Sun, Y and Gao, T and Zhang, D}, title = {Influence of Bacillus subtilis strain Z-14 on microbial ecology of cucumber rhizospheric vermiculite infested with fusarium oxysporum f. sp. cucumerinum.}, journal = {Pesticide biochemistry and physiology}, volume = {201}, number = {}, pages = {105875}, doi = {10.1016/j.pestbp.2024.105875}, pmid = {38685217}, issn = {1095-9939}, mesh = {*Fusarium/genetics/physiology ; *Cucumis sativus/microbiology ; *Rhizosphere ; *Bacillus subtilis/genetics/physiology/metabolism ; *Soil Microbiology ; *Plant Diseases/microbiology/prevention &amp; control ; Aluminum Silicates ; Plant Roots/microbiology ; }, abstract = {Fusarium oxysporum (FO) is a typical soil-borne pathogenic fungus, and the cucumber wilt disease caused by F. oxysporum f. sp. cucumerinum (FOC) seriously affects crop yield and quality. Vermiculite is increasingly being used as a culture substrate; nevertheless, studies exploring the effectiveness and mechanisms of biocontrol bacteria in this substrate are limited. In this study, vermiculite was used as a culture substrate to investigate the control effect of Bacillus subtilis strain Z-14 on cucumber wilt and the rhizospheric microecology, focusing on colonization ability, soil microbial diversity, and rhizosphere metabolome. Pot experiments showed that Z-14 effectively colonized the cucumber roots, achieving a controlled efficacy of 61.32% for wilt disease. It significantly increased the abundance of Bacillus and the expression of NRPS and PKS genes, while reducing the abundance of FO in the rhizosphere. Microbial diversity sequencing showed that Z-14 reduced the richness and diversity of the rhizosphere bacterial community, increased the richness and diversity of the fungal community, and alleviated the effect of FO on the community structure of the cucumber rhizosphere. The metabolomics analysis revealed that Z-14 affected ABC transporters, amino acid synthesis, and the biosynthesis of plant secondary metabolites. Additionally, Z-14 increased the contents of phenylacetic acid, capsidol, and quinolinic acid, all of which were related to the antagonistic activity in the rhizosphere. Z-14 exhibited a significant control effect on cucumber wilt and influenced the microflora and metabolites in rhizospheric vermiculite, providing a theoretical basis for further understanding the control effect and mechanism of cucumber wilt in different culture substrates.}, }
@article {pmid38684474, year = {2024}, author = {Cohen, Y and Johnke, J and Abed-Rabbo, A and Pasternak, Z and Chatzinotas, A and Jurkevitch, E}, title = {Unbalanced predatory communities and a lack of microbial degraders characterize the microbiota of a highly sewage-polluted Eastern-Mediterranean stream.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {6}, pages = {}, pmid = {38684474}, issn = {1574-6941}, support = {CH 731/2-1//Deutsche Forschungsgemeinschaft/ ; 1583/12//Israel Science Foundation/ ; }, mesh = {*Sewage/microbiology ; *Microbiota ; *Rivers/microbiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Water Microbiology ; Bdellovibrio/genetics/metabolism ; }, abstract = {Wastewater pollution of water resources takes a heavy toll on humans and on the environment. In highly polluted water bodies, self-purification is impaired, as the capacity of the riverine microbes to regenerate the ecosystem is overwhelmed. To date, information on the composition, dynamics and functions of the microbial communities in highly sewage-impacted rivers is limited, in particular in arid and semi-arid environments. In this year-long study of the highly sewage-impacted Al-Nar/Kidron stream in the Barr al-Khalil/Judean Desert east of Jerusalem, we show, using 16S and 18S rRNA gene-based community analysis and targeted qPCR, that both the bacterial and micro-eukaryotic communities, while abundant, exhibited low stability and diversity. Hydrolyzers of organics compounds, as well as nitrogen and phosphorus recyclers were lacking, pointing at reduced potential for regeneration. Furthermore, facultative bacterial predators were almost absent, and the obligate predators Bdellovibrio and like organisms were found at very low abundance. Finally, the micro-eukaryotic predatory community differed from those of other freshwater environments. The lack of essential biochemical functions may explain the stream's inability to self-purify, while the very low levels of bacterial predators and the disturbed assemblages of micro-eukaryote predators present in Al-Nar/Kidron may contribute to community instability and disfunction.}, }
@article {pmid38683238, year = {2024}, author = {Cowan, DA and Albers, SV and Antranikian, G and Atomi, H and Averhoff, B and Basen, M and Driessen, AJM and Jebbar, M and Kelman, Z and Kerou, M and Littlechild, J and Müller, V and Schönheit, P and Siebers, B and Vorgias, K}, title = {Extremophiles in a changing world.}, journal = {Extremophiles : life under extreme conditions}, volume = {28}, number = {2}, pages = {26}, pmid = {38683238}, issn = {1433-4909}, mesh = {*Extremophiles/metabolism/physiology ; Sustainable Development ; Adaptation, Physiological ; Extreme Environments ; Biotechnology ; }, abstract = {Extremophiles and their products have been a major focus of research interest for over 40 years. Through this period, studies of these organisms have contributed hugely to many aspects of the fundamental and applied sciences, and to wider and more philosophical issues such as the origins of life and astrobiology. Our understanding of the cellular adaptations to extreme conditions (such as acid, temperature, pressure and more), of the mechanisms underpinning the stability of macromolecules, and of the subtleties, complexities and limits of fundamental biochemical processes has been informed by research on extremophiles. Extremophiles have also contributed numerous products and processes to the many fields of biotechnology, from diagnostics to bioremediation. Yet, after 40 years of dedicated research, there remains much to be discovered in this field. Fortunately, extremophiles remain an active and vibrant area of research. In the third decade of the twenty-first century, with decreasing global resources and a steadily increasing human population, the world's attention has turned with increasing urgency to issues of sustainability. These global concerns were encapsulated and formalized by the United Nations with the adoption of the 2030 Agenda for Sustainable Development and the presentation of the seventeen Sustainable Development Goals (SDGs) in 2015. In the run-up to 2030, we consider the contributions that extremophiles have made, and will in the future make, to the SDGs.}, }
@article {pmid38683223, year = {2024}, author = {Kunzler, M and Schlechter, RO and Schreiber, L and Remus-Emsermann, MNP}, title = {Hitching a Ride in the Phyllosphere: Surfactant Production of Pseudomonas spp. Causes Co-swarming of Pantoea eucalypti 299R.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {62}, pmid = {38683223}, issn = {1432-184X}, mesh = {*Pantoea/genetics/metabolism/physiology/growth &amp; development ; *Pseudomonas/metabolism/genetics/growth &amp; development/physiology ; *Surface-Active Agents/metabolism ; }, abstract = {Here, we demonstrate the beneficial effect of surfactant-producing pseudomonads on Pantoea eucalypti 299R. We conducted a series of experiments in environments of increasing complexity. P. eucalypti 299R (Pe299R), and Pseudomonas sp. FF1 (Pff1) or Pe299R and surfactant-production deficient Pseudomonas sp. FF1::ΔviscB (Pff1ΔviscB) were co-inoculated in broth, on swarming agar plates, and on plants. In broth, there were no differences in the growth dynamics of Pe299R when growing in the presence of Pff1 or Pff1ΔviscB. By contrast, on swarming agar plates, Pe299R was able to co-swarm with Pff1 which led to a significant increase in Pe299R biomass compared to Pe299R growing with Pff1ΔviscB or in monoculture. Finally in planta, and using the single-cell bioreporter for reproductive success (CUSPER), we found a temporally distinct beneficial effect of Pff1 on co-inoculated Pe299R subpopulations that did not occur in the presence of Pff1ΔviscB. We tested three additional surfactant-producing pseudomonads and their respective surfactant knockout mutants on PE299R on swarming agar showing similar results. This led us to propose a model for the positive effect of surfactant production during leaf colonization. Our results indicate that co-motility might be common during leaf colonization and adds yet another facet to the already manyfold roles of surfactants.}, }
@article {pmid38682902, year = {2024}, author = {Song, H-S and Lee, N-R and Kessell, AK and McCullough, HC and Park, S-Y and Zhou, K and Lee, D-Y}, title = {Kinetics-based inference of environment-dependent microbial interactions and their dynamic variation.}, journal = {mSystems}, volume = {9}, number = {5}, pages = {e0130523}, pmid = {38682902}, issn = {2379-5077}, support = {2020R1A2C2007192//National Research Foundation of Korea (NRF)/ ; 32136-05-1- HD050//MAFRA | Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET)/ ; //Nebraska Tobacco Settlement Biomedical Research Development Fund (NTSBRDF)/ ; 2125155//National Science Foundation (NSF)/ ; 2021R1F1A1064592//National Research Foundation of Korea (NRF)/ ; }, mesh = {*Microbial Interactions/physiology ; Kinetics ; *Escherichia coli/metabolism ; Models, Biological ; Environment ; }, abstract = {Microbial communities in nature are dynamically evolving as member species change their interactions subject to environmental variations. Accounting for such context-dependent dynamic variations in interspecies interactions is critical for predictive ecological modeling. In the absence of generalizable theoretical foundations, we lack a fundamental understanding of how microbial interactions are driven by environmental factors, significantly limiting our capability to predict and engineer community dynamics and function. To address this issue, we propose a novel theoretical framework that allows us to represent interspecies interactions as an explicit function of environmental variables (such as substrate concentrations) by combining growth kinetics and a generalized Lotka-Volterra model. A synergistic integration of these two complementary models leads to the prediction of alterations in interspecies interactions as the outcome of dynamic balances between positive and negative influences of microbial species in mixed relationships. The effectiveness of our method was experimentally demonstrated using a synthetic consortium of two Escherichia coli mutants that are metabolically dependent (due to an inability to synthesize essential amino acids) but competitively grow on a shared substrate. The analysis of the E. coli binary consortium using our model not only showed how interactions between the two amino acid auxotrophic mutants are controlled by the dynamic shifts in limiting substrates but also enabled quantifying previously uncharacterizable complex aspects of microbial interactions, such as asymmetry in interactions. Our approach can be extended to other ecological systems to model their environment-dependent interspecies interactions from growth kinetics.IMPORTANCEModeling environment-controlled interspecies interactions through separate identification of positive and negative influences of microbes in mixed relationships is a new capability that can significantly improve our ability to understand, predict, and engineer the complex dynamics of microbial communities. Moreover, the prediction of microbial interactions as a function of environmental variables can serve as valuable benchmark data to validate modeling and network inference tools in microbial ecology, the development of which has often been impeded due to the lack of ground truth information on interactions. While demonstrated against microbial data, the theory developed in this work is readily applicable to general community ecology to predict interactions among macroorganisms, such as plants and animals, as well as microorganisms.}, }
@article {pmid38680790, year = {2024}, author = {García, FM and Guerrero, SIB and la Peña, CG and Gutiérrez, DRA and Rodríguez, QKS and Herrera, CAM and Paniagua, FV and Velásquez, CD and Montoya, AC and Núñez, LMV}, title = {Bacteria in the blood of healthy stray dogs infested by ticks in northern Mexico.}, journal = {Journal of advanced veterinary and animal research}, volume = {11}, number = {1}, pages = {132-138}, pmid = {38680790}, issn = {2311-7710}, abstract = {OBJECTIVE: The objectives of this study were to determine the richness, abundance, and diversity of bacteria in stray dogs (Canis lupus familiaris) infested by ticks in Comarca Lagunera, northern Mexico, and to establish their pathogenic and or/zoonotic potential.<br><br>MATERIALS AND METHODS: Blood samples from 12 dogs were collected, and their deoxyribonucleic acid was extracted. The V3-V4 region of the 16S ribosomal ribunocleic acid gene was amplified by polymerase chain reaction. Next-generation sequencing (NGS) was performed on a MiSeq Illumina platform, and the data were analyzed using quantitative insights into microbial ecology.<br><br>RESULTS: The operational taxonomic units resulted in 23 phyla, 54 classes, 89 orders, 189 families, 586 genera, and 620 bacterial species; among them, 64 species and/or bacterial genera with pathogenic or zoonotic potential were identified, some of which have been reported in the literature as relevant to public health (Anaplasma phagocytophilum, Brucella spp., Clostridium spp., Corynebacterium affermentants, Cutibacterium spp., Dietzia spp., Ehrlichia canis, Fusobacterium necrophorum, Leptotrichia spp., Mycobacterium spp., Paracoccus spp., and Roseomonas gilardii).<br><br>CONCLUSION: This research offers relevant information on the prevalence of tick-borne diseases as well as other potential zoonotic diseases in the blood of stray dogs parasitized by ticks in northern Mexico. New molecular biology and massive NGS techniques may play an important role in the study and documentation of bacterial profiles from animals in close proximity to humans.}, }
@article {pmid38679176, year = {2024}, author = {Guo, Z and Ma, XS and Ni, SQ}, title = {Journey of the swift nitrogen transformation: Unveiling comammox from discovery to deep understanding.}, journal = {Chemosphere}, volume = {358}, number = {}, pages = {142093}, doi = {10.1016/j.chemosphere.2024.142093}, pmid = {38679176}, issn = {1879-1298}, mesh = {*Nitrogen/metabolism ; *Ammonia/metabolism ; *Bacteria/metabolism/genetics ; *Oxidation-Reduction ; *Nitrogen Cycle ; Nitrification ; Ecosystem ; }, abstract = {COMplete AMMonia OXidizer (comammox) refers to microorganisms that have the function of oxidizing NH4[+] to NO3[-] alone. The discovery of comammox overturned the two-step theory of nitrification in the past century and triggered many important scientific questions about the nitrogen cycle in nature. This comprehensive review delves into the origin and discovery of comammox, providing a detailed account of its detection primers, clades metabolic variations, and environmental factors. An in-depth analysis of the ecological niche differentiation among ammonia oxidizers was also discussed. The intricate role of comammox in anammox systems and the relationship between comammox and nitrogen compound emissions are also discussed. Finally, the relationship between comammox and anammox is displayed, and the future research direction of comammox is prospected. This review reveals the metabolic characteristics and distribution patterns of comammox in ecosystems, providing new perspectives for understanding nitrogen cycling and microbial ecology. Additionally, it offers insights into the potential application value and prospects of comammox.}, }
@article {pmid38678007, year = {2024}, author = {Wang, X and Tang, Y and Yue, X and Wang, S and Yang, K and Xu, Y and Shen, Q and Friman, VP and Wei, Z}, title = {The role of rhizosphere phages in soil health.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {5}, pages = {}, pmid = {38678007}, issn = {1574-6941}, support = {2022YFC3501501//National Key Research and Development Program of China/ ; 42325704//National Natural Science Foundation of China/ ; //Nanjing Agricultural University/ ; }, mesh = {*Soil Microbiology ; *Rhizosphere ; *Bacteriophages/genetics ; *Microbiota ; *Bacteria/virology/genetics ; Gene Transfer, Horizontal ; Plants/microbiology/virology ; Ecosystem ; }, abstract = {While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation, and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness, and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.}, }
@article {pmid38676557, year = {2024}, author = {Glasl, B and Luter, HM and Damjanovic, K and Kitzinger, K and Mueller, AJ and Mahler, L and Engelberts, JP and Rix, L and Osvatic, JT and Hausmann, B and Séneca, J and Daims, H and Pjevac, P and Wagner, M}, title = {Co-occurring nitrifying symbiont lineages are vertically inherited and widespread in marine sponges.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38676557}, issn = {1751-7370}, support = {T 1218//Austrian Science Fund/ ; }, mesh = {Animals ; *Porifera/microbiology ; *Symbiosis ; *Nitrification ; *Archaea/genetics/classification/metabolism/isolation &amp; purification ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Phylogeny ; *Ammonia/metabolism ; Nitrites/metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Metagenome ; }, abstract = {Ammonia-oxidizing archaea and nitrite-oxidizing bacteria are common members of marine sponge microbiomes. They derive energy for carbon fixation and growth from nitrification-the aerobic oxidation of ammonia to nitrite and further to nitrate-and are proposed to play essential roles in the carbon and nitrogen cycling of sponge holobionts. In this study, we characterize two novel nitrifying symbiont lineages, Candidatus Nitrosokoinonia and Candidatus Nitrosymbion in the marine sponge Coscinoderma matthewsi using a combination of molecular tools, in situ visualization, and physiological rate measurements. Both represent a new genus in the ammonia-oxidizing archaeal class Nitrososphaeria and the nitrite-oxidizing bacterial order Nitrospirales, respectively. Furthermore, we show that larvae of this viviparous sponge are densely colonized by representatives of Ca. Nitrosokoinonia and Ca. Nitrosymbion indicating vertical transmission. In adults, the representatives of both symbiont genera are located extracellularly in the mesohyl. Comparative metagenome analyses and physiological data suggest that ammonia-oxidizing archaeal symbionts of the genus Ca. Nitrosokoinonia strongly rely on endogenously produced nitrogenous compounds (i.e. ammonium, urea, nitriles/cyanides, and creatinine) rather than on exogenous ammonium sources taken up by the sponge. Additionally, the nitrite-oxidizing bacterial symbionts of the genus Ca. Nitrosymbion may reciprocally support the ammonia-oxidizers with ammonia via the utilization of sponge-derived urea and cyanate. Comparative analyses of published environmental 16S rRNA gene amplicon data revealed that Ca. Nitrosokoinonia and Ca. Nitrosymbion are widely distributed and predominantly associated with marine sponges and corals, suggesting a broad relevance of our findings.}, }
@article {pmid38675977, year = {2024}, author = {Król, N and Chitimia-Dobler, L and Dobler, G and Kiewra, D and Czułowska, A and Obiegala, A and Zajkowska, J and Juretzek, T and Pfeffer, M}, title = {Identification of New Microfoci and Genetic Characterization of Tick-Borne Encephalitis Virus Isolates from Eastern Germany and Western Poland.}, journal = {Viruses}, volume = {16}, number = {4}, pages = {}, pmid = {38675977}, issn = {1999-4915}, support = {61508669//Pfizer (Germany)/ ; }, mesh = {*Encephalitis Viruses, Tick-Borne/genetics/classification/isolation &amp; purification ; Animals ; Poland ; Germany/epidemiology ; *Phylogeny ; *Encephalitis, Tick-Borne/virology/epidemiology ; Humans ; Ixodes/virology ; }, abstract = {(1) Background: Tick-borne encephalitis (TBE) is the most important tick-borne viral disease in Eurasia, although effective vaccines are available. Caused by the tick-borne encephalitis virus (TBEV, syn. Orthoflavivirus encephalitidis), in Europe, it is transmitted by ticks like Ixodes ricinus and Dermacentor reticulatus. TBEV circulates in natural foci, making it endemic to specific regions, such as southern Germany and northeastern Poland. Our study aimed to identify new TBEV natural foci and genetically characterize strains in ticks in previously nonendemic areas in Eastern Germany and Western Poland. (2) Methods: Ticks were collected from vegetation in areas reported by TBE patients. After identification, ticks were tested for TBEV in pools of a maximum of 10 specimens using real-time RT-PCR. From the positive TBEV samples, E genes were sequenced. (3) Results: Among 8400 ticks from 19 sites, I. ricinus (n = 4784; 56.9%) was predominant, followed by D. reticulatus (n = 3506; 41.7%), Haemaphysalis concinna (n = 108; 1.3%), and I. frontalis (n = 2; <0.1%). TBEV was detected in 19 pools originating in six sites. The phylogenetic analyses revealed that TBEV strains from Germany and Poland clustered with other German strains, as well as those from Finland and Estonia. (4) Conclusions: Although there are still only a few cases are reported from these areas, people spending much time outdoors should consider TBE vaccination.}, }
@article {pmid38674735, year = {2024}, author = {Isokpehi, RD and Kim, Y and Krejci, SE and Trivedi, VD}, title = {Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential.}, journal = {Microorganisms}, volume = {12}, number = {4}, pages = {}, pmid = {38674735}, issn = {2076-2607}, support = {U41 HG006941/HG/NHGRI NIH HHS/United States ; U41HG006941/NH/NIH HHS/United States ; }, abstract = {Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.}, }
@article {pmid38674704, year = {2024}, author = {Wang, H and Pijl, A and Liu, B and Wamelink, W and Korthals, GW and Costa, OYA and Kuramae, EE}, title = {A Comparison of Different Protocols for the Extraction of Microbial DNA Inhabiting Synthetic Mars Simulant Soil.}, journal = {Microorganisms}, volume = {12}, number = {4}, pages = {}, pmid = {38674704}, issn = {2076-2607}, abstract = {Compared with typical Earth soil, Martian soil and Mars simulant soils have distinct properties, including pH > 8.0 and high contents of silicates, iron-rich minerals, sulfates, and metal oxides. This unique soil matrix poses a major challenge for extracting microbial DNA. In particular, mineral adsorption and the generation of destructive hydroxyl radicals through cationic redox cycling may interfere with DNA extraction. This study evaluated different protocols for extracting microbial DNA from Mars Global Simulant (MGS-1), a Mars simulant soil. Two commercial kits were tested: the FastDNA SPIN Kit for soil ("MP kit") and the DNeasy PowerSoil Pro Kit ("PowerSoil kit"). MGS-1 was incubated with living soil for five weeks, and DNA was extracted from aliquots using the kits. After extraction, the DNA was quantified with a NanoDrop spectrophotometer and used as the template for 16S rRNA gene amplicon sequencing and qPCR. The MP kit was the most efficient, yielding approximately four times more DNA than the PowerSoil kit. DNA extracted using the MP kit with 0.5 g soil resulted in 28,642-37,805 16S rRNA gene sequence reads and 30,380-42,070 16S rRNA gene copies, whereas the 16S rRNA gene could not be amplified from DNA extracted using the PowerSoil kit. We suggest that the FastDNA SPIN Kit is the best option for studying microbial communities in Mars simulant soils.}, }
@article {pmid38672854, year = {2024}, author = {Daval, C and Tran, T and Verdier, F and Martin, A and Alexandre, H and Grandvalet, C and Tourdot-Maréchal, R}, title = {Identification of Key Parameters Inducing Microbial Modulation during Backslopped Kombucha Fermentation.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {8}, pages = {}, pmid = {38672854}, issn = {2304-8158}, support = {PO FEDER-FSE Bourgogne 2014/2020//European Regional Development Fund/ ; }, abstract = {The aim of this study was to assess the impact of production parameters on the reproducibility of kombucha fermentation over several production cycles based on backslopping. Six conditions with varying oxygen accessibility (specific interface surface) and initial acidity (through the inoculation rate) of the cultures were carried out and compared to an original kombucha consortium and a synthetic consortium assembled from yeasts and bacteria isolated from the original culture. Output parameters monitored were microbial populations, biofilm weight, key physico-chemical parameters and metabolites. Results highlighted the existence of phases in microbial dynamics as backslopping cycles progressed. The transitions between phases occurred faster for the synthetic consortium compared to the original kombucha. This led to microbial dynamics and fermentative kinetics that were reproducible over several cycles but that could also deviate and shift abruptly to different behaviors. These changes were mainly induced by an increase in the Saccharomyces cerevisiae population, associated with an intensification of sucrose hydrolysis, sugar consumption and an increase in ethanol content, without any significant acceleration in the rate of acidification. The study suggests that the reproducibility of kombucha fermentations relies on high biodiversity to slow down the modulations of microbial dynamics induced by the sustained rhythm of backslopping cycles.}, }
@article {pmid38670213, year = {2024}, author = {Sun, Y and Du, P and Li, H and Zhou, K and Shou, L and Chen, J and Meng Li, }, title = {Prokaryotic community assembly patterns and nitrogen metabolic potential in oxygen minimum zone of Yangtze Estuary water column.}, journal = {Environmental research}, volume = {252}, number = {Pt 3}, pages = {119011}, doi = {10.1016/j.envres.2024.119011}, pmid = {38670213}, issn = {1096-0953}, mesh = {*Estuaries ; China ; *Nitrogen/metabolism/analysis ; *Oxygen/metabolism/analysis ; Bacteria/metabolism/genetics/classification ; RNA, Ribosomal, 16S ; Nitrogen Cycle ; }, abstract = {It is predicted that oxygen minimum zones (OMZs) in the ocean will expand as a consequence of global warming and environmental pollution. This will affect the overall microbial ecology and microbial nitrogen cycle. As one of the world's largest alluvial estuaries, the Yangtze Estuary has exhibited a seasonal OMZ since the 1980s. In this study, we have uncovered the microbial composition, the patterns of community assembly and the potential for microbial nitrogen cycling within the water column of the Yangtze Estuary, with a particular focus on OMZ. Based on the 16 S rRNA gene sequencing, a specific spatial variation in the composition of prokaryotic communities was observed for each water layer, with the Proteobacteria (46.1%), Bacteroidetes (20.3%), and Cyanobacteria (10.3%) dominant. Stochastic and deterministic processes together shaped the community assembly in the water column. Further, pH was the most important environmental factor influencing prokaryotic composition in the surface water, followed by silicate, PO4[3-], and distance offshore (p < 0.05). Water depth, NH4[+], and PO4[3-] were the main factors in the bottom water (p < 0.05). At last, species analysis and marker gene annotation revealed candidate nitrogen cycling performers, and a rich array of nitrogen cycling potential in the bottom water of the Yangtze Estuary. The determined physiochemical parameters and potential for nitrogen respiration suggested that organic nitrogen and NO3[-] (or NO2[-]) are the preferred nitrogen sources for microorganisms in the Yangtze Estuary OMZ. These findings are expected to advance research on the ecological responses of estuarine oxygen minimum zones (OMZs) to future global climate perturbations.}, }
@article {pmid38668461, year = {2024}, author = {Takács, E and Lázár, D and Siakwa, A and Klátyik, S and Mörtl, M and Kocsányi, L and Barócsi, A and Lenk, S and Lengyel, E and Székács, A}, title = {Ecotoxicological Evaluation of Safener and Antimicrobial Additives in Isoxaflutole-Based Herbicide Formulations.}, journal = {Toxics}, volume = {12}, number = {4}, pages = {}, pmid = {38668461}, issn = {2305-6304}, support = {NVKP_16-1-2016-0049//Hungarian National Research, Development and Innovation Office within the National Com-petitiveness and Excellence Program/ ; NKFIH-3524-1/2022//National Research, Development and Innovation Fund by the Hungarian Ministry of Culture and Innovation/ ; TKP2021-NVA-22//Thematic Excellence Program 2021, National Defense, National Security Sub-Program/ ; }, abstract = {The environmental load by isoxaflutole and its formulated herbicide products has increasingly become apparent because, after the ban of atrazine, isoxaflutole has become its replacement active ingredient (a.i.). Obtaining information regarding the fate of this a.i. in environmental matrices and its ecotoxicological effects on aquatic organisms is essential for the risk assessment of the herbicide. In this study, the effects of Merlin Flexx- and Merlin WG75 formulated isoxaflutole-based herbicide products and two selected additives (cyprosulfamide safener and 1,2-benzisothiazol-3(2H)-one antimicrobial agent) were investigated on Raphidocelis subcapitata in growth inhibition assays. In ecotoxicological tests, two conventional (optical density and chlorophyll-a content) and two induced fluorescence-based (Fv*/Fp: efficiency of the photosystem PSII and Rfd* changes in the observed ratio of fluorescence decrease) endpoints were determined by UV-spectrophotometer and by our FluoroMeter Module, respectively. Furthermore, dissipation of isoxaflutole alone and in its formulated products was examined by an HPLC-UV method. In ecotoxicological assays, the fluorescence-based Rfd* was observed as the most sensitive endpoint. In this study, the effects of the safener cyprosulfamide and the antimicrobial agent 1,2-benzisothiazol-3(2H)-one on R. subcapitata is firstly reported. The results indicated that the isoxaflutole-equivalent toxicity of the mixture of the isoxaflutole-safener-antimicrobial agent triggered lower toxicity (EC50 = 2.81 ± 0.22 mg/L) compared to the individual effect of the a.i. (EC50 = 0.02 ± 0.00 mg/L). The Merlin Flexx formulation (EC50 = 27.04 ± 1.41 mg/L) was found to be approximately 50-fold less toxic than Merlin WG75, which can be explained by the different chemical characteristics and quantity of additives in them. The additives influenced the dissipation of the a.i. in Z8 medium, as the DT50 value decreased by approximately 1.2- and 3.5-fold under light and dark conditions, respectively.}, }
@article {pmid38668249, year = {2024}, author = {Plewa-Tutaj, K and Twarużek, M and Kosicki, R and Soszczyńska, E}, title = {Analysis of Mycotoxins and Cytotoxicity of Airborne Molds Isolated from the Zoological Garden-Screening Research.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {4}, pages = {}, pmid = {38668249}, issn = {2076-0817}, support = {DEC390 2022/06/X/NZ8/00430//National Science Centre, Poland/ ; }, mesh = {*Mycotoxins/toxicity/analysis ; *Air Microbiology ; *Penicillium/isolation &amp; purification/metabolism ; *Aspergillus/isolation &amp; purification/metabolism ; Animals ; Fungi/isolation &amp; purification/drug effects/genetics ; Chromatography, High Pressure Liquid ; Animals, Zoo/microbiology ; Gardens ; Tandem Mass Spectrometry ; }, abstract = {OBJECTIVE: The objective of this paper was to assess the airborne mold contamination, secondary metabolite profiles, and cytotoxicity of the dominant fungal species isolated from the air in selected rooms at a Zoological Garden.<br><br>MATERIALS AND METHODS: Fungal concentrations were measured with MAS-100 air samplers. The collected airborne fungi were identified using a combination of morphological and molecular methods. The cytotoxicity of 84 strains belonging to two Penicillium and Aspergillus genera was determined using the quantitative colorimetric MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium salt) assay. The mycotoxins were detected using high-performance liquid chromatography (HPLC) with a mass spectrometry detector.<br><br>RESULTS: The ITS gene was amplified and sequenced to identify the 132 species. For mycotoxicological and cytotoxicity analyses, 52 Penicillium isolates and 32 Aspergillus representatives were selected. Cytotoxicity was confirmed in 97.6% of cases analyzed. Using the LC-MS/MS method, 42 out of 84 strains produced at least one of the following toxins: ochratoxin A, ochratoxin B, patulin, gliotoxin, roquefortine C, griseofulvin, sterigmatocystin, fumonisin B2, moniliformin, and mycophenolic acid.<br><br>CONCLUSIONS: Analytical methods for assessing the presence of mycotoxins in fungal isolates collected directly from the air have proven to be an effective tool. Our research provides new information on the occurrence of potentially toxin-producing molds within a zoo.}, }
@article {pmid38665977, year = {2023}, author = {Crous, PW and Costa, MM and Kandemir, H and Vermaas, M and Vu, D and Zhao, L and Arumugam, E and Flakus, A and Jurjević, &#x17d; and Kaliyaperumal, M and Mahadevakumar, S and Murugadoss, R and Shivas, RG and Tan, YP and Wingfield, MJ and Abell, SE and Marney, TS and Danteswari, C and Darmostuk, V and Denchev, CM and Denchev, TT and Etayo, J and Gené, J and Gunaseelan, S and Hubka, V and Illescas, T and Jansen, GM and Kezo, K and Kumar, S and Larsson, E and Mufeeda, KT and Piątek, M and Rodriguez-Flakus, P and Sarma, PVSRN and Stryjak-Bogacka, M and Torres-Garcia, D and Vauras, J and Acal, DA and Akulov, A and Alhudaib, K and Asif, M and Balashov, S and Baral, HO and Baturo-Cieśniewska, A and Begerow, D and Beja-Pereira, A and Bianchinotti, MV and Bilański, P and Chandranayaka, S and Chellappan, N and Cowan, DA and Custódio, FA and Czachura, P and Delgado, G and De Silva, NI and Dijksterhuis, J and Dueñas, M and Eisvand, P and Fachada, V and Fournier, J and Fritsche, Y and Fuljer, F and Ganga, KGG and Guerra, MP and Hansen, K and Hywel-Jones, N and Ismail, AM and Jacobs, CR and Jankowiak, R and Karich, A and Kemler, M and Kisło, K and Klofac, W and Krisai-Greilhuber, I and Latha, KPD and Lebeuf, R and Lopes, ME and Lumyong, S and Maciá-Vicente, JG and Maggs-Kölling, G and Magistà, D and Manimohan, P and Martín, MP and Mazur, E and Mehrabi-Koushki, M and Miller, AN and Mombert, A and Ossowska, EA and Patejuk, K and Pereira, OL and Piskorski, S and Plaza, M and Podile, AR and Polhorský, A and Pusz, W and Raza, M and Ruszkiewicz-Michalska, M and Saba, M and Sánchez, RM and Singh, R and Śliwa, L and Smith, ME and Stefenon, VM and Strasiftáková, D and Suwannarach, N and Szczepańska, K and Telleria, MT and Tennakoon, DS and Thines, M and Thorn, RG and Urbaniak, J and van der Vegte, M and Vasan, V and Vila-Viçosa, C and Voglmayr, H and Wrzosek, M and Zappelini, J and Groenewald, JZ}, title = {Fungal Planet description sheets: 1550-1613.}, journal = {Persoonia}, volume = {51}, number = {}, pages = {280-417}, pmid = {38665977}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Argentina, Neocamarosporium halophilum in leaf spots of Atriplex undulata. Australia, Aschersonia merianiae on scale insect (Coccoidea), Curvularia huamulaniae isolated from air, Hevansia mainiae on dead spider, Ophiocordyceps poecilometigena on Poecilometis sp. Bolivia, Lecanora menthoides on sandstone, in open semi-desert montane areas, Sticta monlueckiorum corticolous in a forest, Trichonectria epimegalosporae on apothecia of corticolous Megalospora sulphurata var. sulphurata, Trichonectria puncteliae on the thallus of Punctelia borreri. Brazil, Catenomargarita pseudocercosporicola (incl. Catenomargarita gen. nov.) hyperparasitic on Pseudocercospora fijiensis on leaves of Musa acuminata, Tulasnella restingae on protocorms and roots of Epidendrum fulgens. Bulgaria, Anthracoidea umbrosae on Carex spp. Croatia, Hymenoscyphus radicis from surface-sterilised, asymptomatic roots of Microthlaspi erraticum, Orbilia multiserpentina on wood of decorticated branches of Quercus pubescens. France, Calosporella punctatispora on dead corticated twigs of Aceropalus. French West Indies (Martinique), Eutypella lechatii on dead corticated palm stem. Germany, Arrhenia alcalinophila on loamy soil. Iceland, Cistella blauvikensis on dead grass (Poaceae). India, Fulvifomes maritimus on living Peltophorum pterocarpum, Fulvifomes natarajanii on dead wood of Prosopis juliflora, Fulvifomes subazonatus on trunk of Azadirachta indica, Macrolepiota bharadwajii on moist soil near the forest, Narcissea delicata on decaying elephant dung, Paramyrothecium indicum on living leaves of Hibiscus hispidissimus, Trichoglossum syamviswanathii on moist soil near the base of a bamboo plantation. Iran, Vacuiphoma astragalicola from stem canker of Astragalus sarcocolla. Malaysia, Neoeriomycopsis fissistigmae (incl. Neoeriomycopsidaceae fam. nov.) on leaf spots on flower Fissistigma sp. Namibia, Exophiala lichenicola lichenicolous on Acarospora cf. luederitzensis. Netherlands, Entoloma occultatum on soil, Extremus caricis on dead leaves of Carex sp., Inocybe pseudomytiliodora on loamy soil. Norway, Inocybe guldeniae on calcareous soil, Inocybe rupestroides on gravelly soil. Pakistan, Hymenagaricus brunneodiscus on soil. Philippines, Ophiocordyceps philippinensis parasitic on Asilus sp. Poland, Hawksworthiomyces ciconiae isolated from Ciconia ciconia nest, Plectosphaerella vigrensis from leaf spots on Impatiens noli-tangere, Xenoramularia epitaxicola from sooty mould community on Taxus baccata. Portugal, Inocybe dagamae on clay soil. Saudi Arabia, Diaporthe jazanensis on branches of Coffea arabica. South Africa, Alternaria moraeae on dead leaves of Moraea sp., Bonitomyces buffels-kloofinus (incl. Bonitomyces gen. nov.) on dead twigs of unknown tree, Constrictochalara koukolii on living leaves of Itea rhamnoides colonised by a Meliola sp., Cylindromonium lichenophilum on Parmelina tiliacea, Gamszarella buffelskloofina (incl. Gamszarella gen. nov.) on dead insect, Isthmosporiella africana (incl. Isthmosporiella gen. nov.) on dead twigs of unknown tree, Nothoeucasphaeria buffelskloofina (incl. Nothoeucasphaeria gen. nov.), on dead twigs of unknown tree, Nothomicrothyrium beaucarneae (incl. Nothomicrothyrium gen. nov.) on dead leaves of Beaucarnea stricta, Paramycosphaerella proteae on living leaves of Protea caffra, Querciphoma foliicola on leaf litter, Rachicladosporium conostomii on dead twigs of Conostomium natalense var. glabrum, Rhamphoriopsis synnematosa on dead twig of unknown tree, Waltergamsia mpumalanga on dead leaves of unknown tree. Spain, Amanita fulvogrisea on limestone soil, in mixed forest, Amanita herculis in open Quercus forest, Vuilleminia beltraniae on Cistus symphytifolius. Sweden, Pachyella pulchella on decaying wood on sand-silt riverbank. Thailand, Deniquelata cassiae on dead stem of Cassia fistula, Stomiopeltis thailandica on dead twigs of Magnolia champaca. Ukraine, Circinaria podoliana on natural limestone outcrops, Neonematogonum carpinicola (incl. Neonematogonum gen. nov.) on dead branches of Carpinus betulus. USA, Exophiala wilsonii water from cooling tower, Hygrophorus aesculeticola on soil in mixed forest, and Neocelosporium aereum from air in a house attic. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Costa MM, Kandemir H, et al. 2023. Fungal Planet description sheets: 1550-1613. Persoonia 51: 280-417. doi: 10.3767/persoonia.2023.51.08.}, }
@article {pmid38664322, year = {2024}, author = {Vincent, J and Tenore, A and Mattei, MR and Frunzo, L}, title = {Modelling Plasmid-Mediated Horizontal Gene Transfer in Biofilms.}, journal = {Bulletin of mathematical biology}, volume = {86}, number = {6}, pages = {63}, pmid = {38664322}, issn = {1522-9602}, support = {861088//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; }, mesh = {*Biofilms/growth &amp; development ; *Gene Transfer, Horizontal ; *Plasmids/genetics ; *Mathematical Concepts ; *Models, Biological ; *Models, Genetic ; Conjugation, Genetic ; Anti-Bacterial Agents/pharmacology ; }, abstract = {In this study, we present a mathematical model for plasmid spread in a growing biofilm, formulated as a nonlocal system of partial differential equations in a 1-D free boundary domain. Plasmids are mobile genetic elements able to transfer to different phylotypes, posing a global health problem when they carry antibiotic resistance factors. We model gene transfer regulation influenced by nearby potential receptors to account for recipient-sensing. We also introduce a promotion function to account for trace metal effects on conjugation, based on literature data. The model qualitatively matches experimental results, showing that contaminants like toxic metals and antibiotics promote plasmid persistence by favoring plasmid carriers and stimulating conjugation. Even at higher contaminant concentrations inhibiting conjugation, plasmid spread persists by strongly inhibiting plasmid-free cells. The model also replicates higher plasmid density in biofilm's most active regions.}, }
@article {pmid38663208, year = {2024}, author = {Ceballos-Escalera, A and Pous, N and Bañeras, L and Balaguer, MD and Puig, S}, title = {Advancing towards electro-bioremediation scaling-up: On-site pilot plant for successful nitrate-contaminated groundwater treatment.}, journal = {Water research}, volume = {256}, number = {}, pages = {121618}, doi = {10.1016/j.watres.2024.121618}, pmid = {38663208}, issn = {1879-2448}, mesh = {*Groundwater/chemistry ; *Nitrates/metabolism ; *Biodegradation, Environmental ; *Water Pollutants, Chemical ; Pilot Projects ; *Water Purification/methods ; Denitrification ; Spain ; Bioreactors ; }, abstract = {The potential of nitrate electro-bioremediation has been fully demonstrated at the laboratory scale, although it has not yet been fully implemented due to the challenges associated with scaling-up bioelectrochemical reactors and their on-site operation. This study describes the initial start-up and subsequent stable operation of an electro-bioremediation pilot plant for the treatment of nitrate-contaminated groundwater on-site (Navata site, Spain). The pilot plant was operated under continuous flow mode for 3 months, producing an effluent suitable for drinking water in terms of nitrates and nitrites (<50 mg NO3[-] L[-1]; 0 mg NO2[-] L[-1]). A maximum nitrate removal rate of 0.9 ± 0.1 kg NO3[-] m[-3] d[-1] (efficiency 82 ± 18 %) was achieved at a cathodic hydraulic retention time (HRTcat) of 2.0 h with a competitive energy consumption of 4.3 ± 0.4 kWh kg[-1] NO3[-]. Under these conditions, the techno-economic analysis estimated an operational cost of 0.40 € m[-3]. Simultaneously, microbiological analyses revealed structural heterogeneity in the reactor, with denitrification functionality concentrated predominantly from the centre to the upper section of the reactor. The most abundant groups were Pseudomonadaceae, Rhizobiaceae, Gallionellaceae, and Xanthomonadaceae. In conclusion, this pilot plant represents a significant advancement in implementing this technology on a larger scale, validating its effectiveness in terms of nitrate removal and cost-effectiveness. Moreover, the results validate the electro-bioremediation in a real environment and encourage further investigation of its potential as a water treatment.}, }
@article {pmid38662665, year = {2024}, author = {Hulatt, CJ and Suzuki, H and Détain, A and Wijffels, RH and Leya, T and Posewitz, MC}, title = {The genome of the Arctic snow alga Limnomonas spitsbergensis (Chlamydomonadales).}, journal = {G3 (Bethesda, Md.)}, volume = {14}, number = {7}, pages = {}, pmid = {38662665}, issn = {2160-1836}, support = {749910//Marie Sk&#x142;odowska-Curie Individual Fellowship/ ; //European Union's Horizon 2020/ ; //Posewitz lab/ ; //Colorado School of Mines/ ; //National Center for Genome Resources/ ; NN9634K//UNINETT Sigma-2 Compute Infrastructure/ ; }, mesh = {Arctic Regions ; *Snow/microbiology ; *Molecular Sequence Annotation ; Phylogeny ; Chlorophyta/genetics ; Genomics/methods ; }, abstract = {Snow algae are a diverse group of extremophilic microeukaryotes found on melting polar and alpine snowfields. They play an important role in the microbial ecology of the cryosphere, and their propagation on snow and ice surfaces may in part accelerate climate-induced melting of these systems. High-quality snow algae genomes are needed for studies on their unique physiology, adaptive mechanisms, and genome evolution under multiple forms of stress, including cold temperatures and intense sunlight. Here, we assembled and annotated the genome of Limnomonas spitsbergensis, a cryophilic biciliate green alga originally isolated from melting snow on Svalbard, in the Arctic. The L. spitsbergensis genome assembly is based primarily on the use of PacBio long reads and secondly Illumina short reads, with an assembly size of 260.248 Mb in 124 contigs. A combination of 3 alternative annotation strategies was used including protein homology, RNA-seq evidence, and PacBio full-length transcript isoforms. The best merged set of annotations identified 18,277 protein-coding genes, which were 95.2% complete based on Benchmarking Universal Single-Copy Orthologs analysis. We also provide the annotated mitogenome, which is a relatively large 77.942 kb circular mapping sequence containing extensive repeats. The L. spitsbergensis genome will provide a new resource for research on snow algae adaptation, behavior, and natural selection in unique, low-temperature terrestrial environments that are under threat from climate change.}, }
@article {pmid38662575, year = {2024}, author = {Liu, X and Salles, JF}, title = {Bridging ecological assembly process and community stability upon bacterial invasions.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38662575}, issn = {1751-7370}, mesh = {*Soil Microbiology ; *Escherichia coli/genetics ; *Microbiota ; Ecosystem ; Microbial Interactions ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Understanding the link between microbial community stability and assembly processes is crucial in microbial ecology. Here, we investigated whether the impact of biotic disturbances would depend on the processes controlling community assembly. For that, we performed an experiment using soil microcosms in which microbial communities assembled through different processes were invaded by Escherichia coli. We show that the ecological assembly process of the resident community plays a significant role in invader-resident competition, invader survival, and compositional stability of the resident community. Specifically, the resident communities primarily assembled through stochastic processes were more susceptible to invader survival. Besides, E. coli invasion acts as a biotic selection pressure, leading to competition between the invader and resident taxa, suppressing the stochasticity in the resident community. Taken together, this study provides empirical evidence for the interpretation of microbial community assemblage on their (potential) ecosystem functions and services, such as the prevention of pathogen establishment and the pathogenic states of soil microbiomes.}, }
@article {pmid38662080, year = {2024}, author = {Ezhumalai, G and Arun, M and Manavalan, A and Rajkumar, R and Heese, K}, title = {A Holistic Approach to Circular Bioeconomy Through the Sustainable Utilization of Microalgal Biomass for Biofuel and Other Value-Added Products.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {61}, pmid = {38662080}, issn = {1432-184X}, mesh = {*Microalgae/metabolism/growth &amp; development ; *Biofuels ; *Biomass ; Cyanobacteria/metabolism ; Seaweed/metabolism ; Carbon Dioxide/metabolism ; }, abstract = {Emissions from transportation and industry primarily cause global warming, leading to floods, glacier melt, and rising seas. Widespread greenhouse gas emissions and resulting global warming pose significant risks to the environment, economy, and society. The need for alternative fuels drives the development of third-generation feedstocks: microalgae, seaweed, and cyanobacteria. These microalgae offer traits like rapid growth, high lipid content, non-competition with human food, and growth on non-arable land using brackish or waste water, making them promising for biofuel. These unique phototrophic organisms use sunlight, water, and carbon dioxide (CO2) to produce biofuels, biochemicals, and more. This review delves into the realm of microalgal biofuels, exploring contemporary methodologies employed for lipid extraction, significant value-added products, and the challenges inherent in their commercial-scale production. While the cost of microalgae bioproducts remains high, utilizing wastewater nutrients for cultivation could substantially cut production costs. Furthermore, this review summarizes the significance of biocircular economy approaches, which encompass the utilization of microalgal biomass as a feed supplement and biofertilizer, and biosorption of heavy metals and dyes. Besides, the discussion extends to the in-depth analysis and future prospects on the commercial potential of biofuel within the context of sustainable development. An economically efficient microalgae biorefinery should prioritize affordable nutrient inputs, efficient harvesting techniques, and the generation of valuable by-products.}, }
@article {pmid38661241, year = {2024}, author = {Xiong, H and Zhang, X and Zeng, H and Xie, S and Yi, S}, title = {Experience of diet in patients with inflammatory bowel disease: A thematic synthesis of qualitative studies.}, journal = {Journal of clinical nursing}, volume = {33}, number = {8}, pages = {3283-3293}, doi = {10.1111/jocn.17186}, pmid = {38661241}, issn = {1365-2702}, mesh = {Humans ; *Inflammatory Bowel Diseases/diet therapy/psychology ; *Qualitative Research ; *Diet/psychology/methods ; Adult ; Male ; Female ; Middle Aged ; }, abstract = {AIM: To synthesise the dietary expesriences of patients with inflammatory bowel disease by reviewing relevant qualitative studies.<br><br>BACKGROUND: Diet plays a crucial role in the development and progression of inflammatory bowel disease (IBD). There is no specific diet that can be recommended for all patients. We conducted a synthesis of qualitative studies to gain a comprehensive understanding of the dietary management experience of patients with IBD, aiming to provide better dietary guidance in the future.<br><br>DESIGN: A qualitative synthesis was conducted following the Thomas and Harden method and reported following the ENTREQ statement.<br><br>METHODS: Qualitative studies were systematically searched in five electronic databases: PubMed, PsycINFO, Embase, CINAHL, and Web of Science. There was no time limit for publication, and all database searches were up to 10 May, 2023. The Joanna Briggs Institute Qualitative Assessment and Review Instrument was utilised to appraise the quality of the included studies. Data for inclusion in articles were extracted and analysed using a thematic synthesis method.<br><br>RESULTS: Six studies involving 119 patients were eventually included. The studies were conducted in six different countries. Four major themes were identified: the diet of patients with IBD is completely different from the normal one; manage symptoms and live with the disease by modifying diet; psychological adjustment to eating (be frustrated; worried and afraid; feel ashamed; growth and resilience); barriers and challenges (barriers from perceived social support; conflicts between diet and nutrition; challenges from food hedonism and cravings).<br><br>CONCLUSIONS: Patients with IBD highlighted the distinction between their diet and the normal diet. Dietary modifications were used as a way to manage symptoms and live with the disease. In addition to physical symptoms, patients experienced diet-related psychological changes. Dietary modifications in patients with IBD encounters difficulties and challenges, necessitating prompt guidance and intervention. (1) The implementation of dietary modifications in patients with IBD encounters numerous obstacles and complexities, necessitating prompt guidance and intervention.<br><br>No patient or public contribution.<br><br>REGISTRATION: The protocol was registered with PROSPERO (CRD42023391545).}, }
@article {pmid38660030, year = {2024}, author = {Lourenço, KS and Suleiman, AKA and Pijl, A and Dimitrov, MR and Cantarella, H and Kuramae, EE}, title = {Mix-method toolbox for monitoring greenhouse gas production and microbiome responses to soil amendments.}, journal = {MethodsX}, volume = {12}, number = {}, pages = {102699}, pmid = {38660030}, issn = {2215-0161}, abstract = {In this study, we adopt an interdisciplinary approach, integrating agronomic field experiments with soil chemistry, molecular biology techniques, and statistics to investigate the impact of organic residue amendments, such as vinasse (a by-product of sugarcane ethanol production), on soil microbiome and greenhouse gas (GHG) production. The research investigates the effects of distinct disturbances, including organic residue application alone or combined with inorganic N fertilizer on the environment. The methods assess soil microbiome dynamics (composition and function), GHG emissions, and plant productivity. Detailed steps for field experimental setup, soil sampling, soil chemical analyses, determination of bacterial and fungal community diversity, quantification of genes related to nitrification and denitrification pathways, measurement and analysis of gas fluxes (N2O, CH4, and CO2), and determination of plant productivity are provided. The outcomes of the methods are detailed in our publications (Lourenço et al., 2018a; Lourenço et al., 2018b; Lourenço et al., 2019; Lourenço et al., 2020). Additionally, the statistical methods and scripts used for analyzing large datasets are outlined. The aim is to assist researchers by addressing common challenges in large-scale field experiments, offering practical recommendations to avoid common pitfalls, and proposing potential analyses, thereby encouraging collaboration among diverse research groups.•Interdisciplinary methods and scientific questions allow for exploring broader interconnected environmental problems.•The proposed method can serve as a model and protocol for evaluating the impact of soil amendments on soil microbiome, GHG emissions, and plant productivity, promoting more sustainable management practices.•Time-series data can offer detailed insights into specific ecosystems, particularly concerning soil microbiota (taxonomy and functions).}, }
@article {pmid38659931, year = {2024}, author = {Prochera, A and Muppirala, AN and Kuziel, GA and Soualhi, S and Shepherd, A and Sun, L and Issac, B and Rosenberg, HJ and Karim, F and Perez, K and Smith, KH and Archibald, TH and Rakoff-Nahoum, S and Hagen, SJ and Rao, M}, title = {Enteric glia regulate Paneth cell secretion and intestinal microbial ecology.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38659931}, issn = {2692-8205}, support = {K08 DK110532/DK/NIDDK NIH HHS/United States ; P50 HD105351/HD/NICHD NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 DK135707/DK/NIDDK NIH HHS/United States ; R01 DK130836/DK/NIDDK NIH HHS/United States ; R01 AI171100/AI/NIAID NIH HHS/United States ; }, abstract = {Glial cells of the enteric nervous system (ENS) interact closely with the intestinal epithelium and secrete signals that influence epithelial cell proliferation and barrier formation in vitro. Whether these interactions are important in vivo, however, is unclear because previous studies reached conflicting conclusions [1]. To better define the roles of enteric glia in steady state regulation of the intestinal epithelium, we characterized the glia in closest proximity to epithelial cells and found that the majority express PLP1 in both mice and humans. To test their functions using an unbiased approach, we genetically depleted PLP1[+] cells in mice and transcriptionally profiled the small and large intestines. Surprisingly, glial loss had minimal effects on transcriptional programs and the few identified changes varied along the gastrointestinal tract. In the ileum, where enteric glia had been considered most essential for epithelial integrity, glial depletion did not drastically alter epithelial gene expression but caused a modest enrichment in signatures of Paneth cells, a secretory cell type important for innate immunity. In the absence of PLP1[+] glia, Paneth cell number was intact, but a subset appeared abnormal with irregular and heterogenous cytoplasmic granules, suggesting a secretory deficit. Consistent with this possibility, ileal explants from glial-depleted mice secreted less functional lysozyme than controls with corresponding effects on fecal microbial composition. Collectively, these data suggest that enteric glia do not exert broad effects on the intestinal epithelium but have an essential role in regulating Paneth cell function and gut microbial ecology.}, }
@article {pmid38658559, year = {2024}, author = {Chen, KH and Feng, J and Bodelier, PLE and Yang, Z and Huang, Q and Delgado-Baquerizo, M and Cai, P and Tan, W and Liu, YR}, title = {Metabolic coupling between soil aerobic methanotrophs and denitrifiers in rice paddy fields.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3471}, pmid = {38658559}, issn = {2041-1723}, support = {32071595//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32371731//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42177022//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Methane/metabolism ; *Oryza/metabolism/microbiology ; *Denitrification ; *Soil Microbiology ; *Oxidation-Reduction ; China ; *Soil/chemistry ; Aerobiosis ; Bacteria/metabolism/genetics/classification ; Nitrous Oxide/metabolism ; Phylogeny ; Carbon Isotopes/metabolism ; Metagenome ; }, abstract = {Paddy fields are hotspots of microbial denitrification, which is typically linked to the oxidation of electron donors such as methane (CH4) under anoxic and hypoxic conditions. While several anaerobic methanotrophs can facilitate denitrification intracellularly, whether and how aerobic CH4 oxidation couples with denitrification in hypoxic paddy fields remains virtually unknown. Here we combine a ~3300 km field study across main rice-producing areas of China and [13]CH4-DNA-stable isotope probing (SIP) experiments to investigate the role of soil aerobic CH4 oxidation in supporting denitrification. Our results reveal positive relationships between CH4 oxidation and denitrification activities and genes across various climatic regions. Microcosm experiments confirm that CH4 and methanotroph addition promote gene expression involved in denitrification and increase nitrous oxide emissions. Moreover, [13]CH4-DNA-SIP analyses identify over 70 phylotypes harboring genes associated with denitrification and assimilating [13]C, which are mostly belonged to Rubrivivax, Magnetospirillum, and Bradyrhizobium. Combined analyses of [13]C-metagenome-assembled genomes and [13]C-metabolomics highlight the importance of intermediates such as acetate, propionate and lactate, released during aerobic CH4 oxidation, for the coupling of CH4 oxidation with denitrification. Our work identifies key microbial taxa and pathways driving coupled aerobic CH4 oxidation and denitrification, with important implications for nitrogen management and greenhouse gas regulation in agroecosystems.}, }
@article {pmid38658525, year = {2024}, author = {Arthofer, P and Panhölzl, F and Delafont, V and Hay, A and Reipert, S and Cyran, N and Wienkoop, S and Willemsen, A and Sifaoui, I and Arberas-Jiménez, I and Schulz, F and Lorenzo-Morales, J and Horn, M}, title = {A giant virus infecting the amoeboflagellate Naegleria.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3307}, pmid = {38658525}, issn = {2041-1723}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; 101039843//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 891572//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; P37198-B//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; }, mesh = {*Genome, Viral/genetics ; *Giant Viruses/genetics/classification/ultrastructure/isolation &amp; purification/physiology ; *Naegleria/genetics/virology ; Naegleria fowleri/genetics/isolation &amp; purification ; Phylogeny ; Humans ; }, abstract = {Giant viruses (Nucleocytoviricota) are significant lethality agents of various eukaryotic hosts. Although metagenomics indicates their ubiquitous distribution, available giant virus isolates are restricted to a very small number of protist and algal hosts. Here we report on the first viral isolate that replicates in the amoeboflagellate Naegleria. This genus comprises the notorious human pathogen Naegleria fowleri, the causative agent of the rare but fatal primary amoebic meningoencephalitis. We have elucidated the structure and infection cycle of this giant virus, Catovirus naegleriensis (a.k.a. Naegleriavirus, NiV), and show its unique adaptations to its Naegleria host using fluorescence in situ hybridization, electron microscopy, genomics, and proteomics. Naegleriavirus is only the fourth isolate of the highly diverse subfamily Klosneuvirinae, and like its relatives the NiV genome contains a large number of translation genes, but lacks transfer RNAs (tRNAs). NiV has acquired genes from its Naegleria host, which code for heat shock proteins and apoptosis inhibiting factors, presumably for host interactions. Notably, NiV infection was lethal to all Naegleria species tested, including the human pathogen N. fowleri. This study expands our experimental framework for investigating giant viruses and may help to better understand the basic biology of the human pathogen N. fowleri.}, }
@article {pmid38657743, year = {2024}, author = {Atasoy, M and Scott, WT and Regueira, A and Mauricio-Iglesias, M and Schaap, PJ and Smidt, H}, title = {Biobased short chain fatty acid production - Exploring microbial community dynamics and metabolic networks through kinetic and microbial modeling approaches.}, journal = {Biotechnology advances}, volume = {73}, number = {}, pages = {108363}, doi = {10.1016/j.biotechadv.2024.108363}, pmid = {38657743}, issn = {1873-1899}, mesh = {Bioreactors/microbiology ; *Fatty Acids, Volatile/metabolism ; Kinetics ; *Metabolic Networks and Pathways ; Models, Biological ; *Microbiota ; }, abstract = {In recent years, there has been growing interest in harnessing anaerobic digestion technology for resource recovery from waste streams. This approach has evolved beyond its traditional role in energy generation to encompass the production of valuable carboxylic acids, especially volatile fatty acids (VFAs) like acetic acid, propionic acid, and butyric acid. VFAs hold great potential for various industries and biobased applications due to their versatile properties. Despite increasing global demand, over 90% of VFAs are currently produced synthetically from petrochemicals. Realizing the potential of large-scale biobased VFA production from waste streams offers significant eco-friendly opportunities but comes with several key challenges. These include low VFA production yields, unstable acid compositions, complex and expensive purification methods, and post-processing needs. Among these, production yield and acid composition stand out as the most critical obstacles impacting economic viability and competitiveness. This paper seeks to offer a comprehensive view of combining complementary modeling approaches, including kinetic and microbial modeling, to understand the workings of microbial communities and metabolic pathways in VFA production, enhance production efficiency, and regulate acid profiles through the integration of omics and bioreactor data.}, }
@article {pmid38657507, year = {2024}, author = {Fu, Y and Jia, F and Su, J and Xu, X and Zhang, Y and Li, X and Jiang, X and Schäffer, A and Virta, M and Tiedje, JM and Wang, F}, title = {Co-occurrence patterns of gut microbiome, antibiotic resistome and the perturbation of dietary uptake in captive giant pandas.}, journal = {Journal of hazardous materials}, volume = {471}, number = {}, pages = {134252}, doi = {10.1016/j.jhazmat.2024.134252}, pmid = {38657507}, issn = {1873-3336}, mesh = {Animals ; *Ursidae/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Feces/microbiology ; *Diet ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects/classification ; RNA, Ribosomal, 16S/genetics ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; Drug Resistance, Bacterial/genetics ; }, abstract = {The microbiome is a key source of antibiotic resistance genes (ARGs), significantly influenced by diet, which highlights the interconnectedness between diet, gut microbiome, and ARGs. Currently, our understanding is limited on the co-occurrence among gut microbiome, antibiotic resistome in the captive giant panda and the perturbation of dietary uptake, especially for the composition and forms in dietary nutrition. Here, a qPCR array with 384 primer sets and 16 S rRNA gene amplicon sequencing were used to characterize the antibiotic resistome and microbiomes in panda feces, dietary bamboo, and soil around the habitat. Diet nutrients containing organic and mineral substances in soluble and insoluble forms were also quantified. Organic and mineral components in water-unextractable fractions were 7.5 to 139 and 637 to 8695 times higher than those in water-extractable portions in bamboo and feces, respectively, while the latter contributed more to the variation (67.5 %) of gut microbiota. Streptococcus, Prevotellaceae, and Bacteroides were the dominant genera in giant pandas. The ARG patterns in panda guts showed higher diversity in old individuals but higher abundance in young ones, driven directly by the bacterial community change and mobile genetic element mediation and indirectly by dietary intervention. Our results suggest that dietary nutrition mainly accounts for the shift of gut microbiota, while bacterial community and mobile genetic elements influenced the variation of gut antibiotic resistome.}, }
@article {pmid38657451, year = {2024}, author = {Guo, D and Tian, K and Peng, X and Liu, S and Xu, X and Tian, W}, title = {Cadmium/zinc stresses and plant cultivation influenced soil microflora: a pot experiment conducted in field.}, journal = {Ecotoxicology and environmental safety}, volume = {277}, number = {}, pages = {116384}, doi = {10.1016/j.ecoenv.2024.116384}, pmid = {38657451}, issn = {1090-2414}, mesh = {*Soil Microbiology ; *Cadmium/toxicity ; *Zinc/toxicity ; *Soil Pollutants/toxicity ; *Rhizosphere ; *Biodegradation, Environmental ; *Fungi/drug effects ; *Bacteria/drug effects/genetics ; Soil/chemistry ; Microbiota/drug effects ; Metals, Heavy/toxicity ; Stress, Physiological ; }, abstract = {It's of great challenge to address for heavy metal-contaminated soil. Once the farmland is contaminated with heavy metals, the microbial ecology of the plant rhizosphere will change, which in turn impacts crop productivity and quality. However, few studies have explored the effects of heavy metals on plant rhizosphere microbes in farmland and the role that plant cultivation plays in such a phytoremediation practice. In this study, the impacts of comfrey (Symphytum officinale L.) cultivation and the stresses of cadmium/zinc (Cd/Zn) on rhizosphere soil microflora were examined. Microbial DNA was collected from soils to evaluate the prevalence of bacteria and fungi communities in rhizosphere soils. High-throughput 16 S rRNA sequencing was used to determine the diversity of the bacterial and fungal communities. The results showed that growing comfrey on polluted soils reduced the levels of Cd and Zn from the vertical profile. Both the comfrey growth and Cd/Zn stresses affected the community of rhizosphere microorganisms (bacteria or fungi). Additionally, the analysis of PCoA and NMDS indicated that the cultivation of comfrey significantly changed the bacterial composition and structure of unpolluted soil. Comfrey cultivation in polluted and unpolluted soils did not result in much variance in the fungi's species composition, but the fungal compositions of the two-type soils were noticeably different. This work provided a better understanding of the impacts of Cd/Zn stresses and comfrey cultivation on rhizosphere microbial community, as well as new insight into phytoremediation of heavy metal-contaminated soils.}, }
@article {pmid38655503, year = {2024}, author = {Horstmann, L and Lipus, D and Bartholomäus, A and Arens, F and Airo, A and Ganzert, L and Zamorano, P and Schulze-Makuch, D and Wagner, D}, title = {Persistent microbial communities in hyperarid subsurface habitats of the Atacama Desert: Insights from intracellular DNA analysis.}, journal = {PNAS nexus}, volume = {3}, number = {4}, pages = {pgae123}, pmid = {38655503}, issn = {2752-6542}, abstract = {Desert environments constitute one of the largest and yet most fragile ecosystems on Earth. Under the absence of regular precipitation, microorganisms are the main ecological component mediating nutrient fluxes by using soil components, like minerals and salts, and atmospheric gases as a source for energy and water. While most of the previous studies on microbial ecology of desert environments have focused on surface environments, little is known about microbial life in deeper sediment layers. Our study is extending the limited knowledge about microbial communities within the deeper subsurface of the hyperarid core of the Atacama Desert. By employing intracellular DNA extraction and subsequent 16S rRNA sequencing of samples collected from a soil pit in the Yungay region of the Atacama Desert, we unveiled a potentially viable microbial subsurface community residing at depths down to 4.20 m. In the upper 80 cm of the playa sediments, microbial communities were dominated by Firmicutes taxa showing a depth-related decrease in biomass correlating with increasing amounts of soluble salts. High salt concentrations are possibly causing microbial colonization to cease in the lower part of the playa sediments between 80 and 200 cm depth. In the underlying alluvial fan deposits, microbial communities reemerge, possibly due to gypsum providing an alternative water source. The discovery of this deeper subsurface community is reshaping our understanding of desert soils, emphasizing the need to consider subsurface environments in future explorations of arid ecosystems.}, }
@article {pmid38654537, year = {2024}, author = {Zhu 朱墨, M and Zhang, W and Duan, X and Yan, S and Cai, Y and Gong, S and Fahad, S and Qiu, Z}, title = {Biocontrol Potential of Cladosporium sphaerospermum Against the Wheat Powdery Mildew Fungus Blumeria graminis f. sp. tritici.}, journal = {Plant disease}, volume = {108}, number = {10}, pages = {2983-2988}, doi = {10.1094/PDIS-02-24-0433-SC}, pmid = {38654537}, issn = {0191-2917}, mesh = {*Ascomycota/physiology ; *Cladosporium/physiology ; *Triticum/microbiology ; *Plant Diseases/microbiology/prevention &amp; control ; Spores, Fungal/physiology ; Pest Control, Biological ; Biomass ; }, abstract = {Cladosporium spp. are known to be mycoparasites and inhibit phytopathogenic fungi. However, so far, little information is available on the impact of Cladosporium spp. on powdery mildews. Based on the morphological characteristics and molecular analysis, C. sphaerospermum was identified as a mycoparasite on the wheat powdery mildew fungus Blumeria graminis f. sp. tritici (Bgt), recently named B. graminis s. str. C. sphaerospermum was capable of preventing colony formation and conidial distribution of Bgt. The biomasses of Bgt notably decreased by 1.3, 2.2, 3.6, and 3.8 times at 2, 4, 6, and 8 days postinoculation (dpi), respectively. In addition, biomasses of C. sphaerospermum at 2, 4, 6, and 8 dpi significantly increased to 5.6, 13.9, 18.2, and 67.3 times, respectively. In vitro, C. sphaerospermum exudates significantly impaired appressorial formation of Bgt. Thus, C. sphaerospermum acts as a potential biological control agent by suppressing the formation, distribution, and development of Bgt conidia and is a viable alternative for managing the wheat powdery mildew. These results suggest that C. sphaerospermum is an antagonistic parasite of the wheat powdery mildew fungus and, hence, provide new knowledge about the biological control of phytopathogenic fungi.}, }
@article {pmid38653968, year = {2024}, author = {Serra Moncadas, L and Hofer, C and Bulzu, PA and Pernthaler, J and Andrei, AS}, title = {Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3421}, pmid = {38653968}, issn = {2041-1723}, support = {PZ00P3_193240//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {*Genome, Bacterial ; *Bacteria/genetics/classification ; *Fresh Water/microbiology ; *Phylogeny ; *Adaptation, Physiological/genetics ; Metagenomics/methods ; Evolution, Molecular ; Genome Size ; Proteome/genetics/metabolism ; }, abstract = {The emergence of bacterial species is rooted in their inherent potential for continuous evolution and adaptation to an ever-changing ecological landscape. The adaptive capacity of most species frequently resides within the repertoire of genes encoding the secreted proteome (SP), as it serves as a primary interface used to regulate survival/reproduction strategies. Here, by applying evolutionary genomics approaches to metagenomics data, we show that abundant freshwater bacteria exhibit biphasic adaptation states linked to the eco-evolutionary processes governing their genome sizes. While species with average to large genomes adhere to the dominant paradigm of evolution through niche adaptation by reducing the evolutionary pressure on their SPs (via the augmentation of functionally redundant genes that buffer mutational fitness loss) and increasing the phylogenetic distance of recombination events, most of the genome-reduced species exhibit a nonconforming state. In contrast, their SPs reflect a combination of low functional redundancy and high selection pressure, resulting in significantly higher levels of conservation and invariance. Our findings indicate that although niche adaptation is the principal mechanism driving speciation, freshwater genome-reduced bacteria often experience extended periods of adaptive stasis. Understanding the adaptive state of microbial species will lead to a better comprehension of their spatiotemporal dynamics, biogeography, and resilience to global change.}, }
@article {pmid38653406, year = {2024}, author = {Wu, T and Ding, J and Zhao, YJ and Ding, L and Zang, Y and Sun, HJ and Zhong, L and Pang, JW and Li, Y and Ren, NQ and Yang, SS}, title = {Microplastics shaped performance, microbial ecology and community assembly in simultaneous nitrification, denitrification and phosphorus removal process.}, journal = {The Science of the total environment}, volume = {929}, number = {}, pages = {172651}, doi = {10.1016/j.scitotenv.2024.172651}, pmid = {38653406}, issn = {1879-1026}, mesh = {*Nitrification ; *Denitrification ; *Phosphorus/metabolism ; *Water Pollutants, Chemical/metabolism/analysis ; *Waste Disposal, Fluid/methods ; *Microplastics ; Wastewater ; Microbiota ; }, abstract = {The widespread use of microplastics (MPs) has led to an increase in their discharge to wastewater treatment plants. However, the knowledge of impact of MPs on macro-performance and micro-ecology in simultaneous nitrification, denitrification, and phosphorus removal (SNDPR) systems is limited, hampering the understanding of potential risks posed by MPs. This study firstly comprehensively investigated the performance, species interactions, and community assembly under polystyrene (PS) and polyvinyl chloride (PVC) exposure in SNDPR systems. The results showed under PS (1, 10 mg/L) and PVC (1, 10 mg/L) exposure, total nitrogen removal was reduced by 3.38-10.15 %. PS and PVC restrained the specific rates of nitrite and nitrate reduction (SNIRR, SNRR), as well as the activities of nitrite and nitrate reductase enzymes (NIR, NR). The specific ammonia oxidation rate (SAOR) and activity of ammonia oxidase enzyme (AMO) were reduced only at 10 mg/L PVC. PS and PVC enhanced the size of co-occurrence networks, niche breadth, and number of key species while decreasing microbial cooperation by 5.85-13.48 %. Heterogeneous selection dominated microbial community assembly, and PS and PVC strengthened the contribution of stochastic processes. PICRUSt prediction further revealed some important pathways were blocked by PS and PVC. Together, the reduced TN removal under PS and PVC exposure can be attributed to the inhibition of SAOR, SNRR, and SNIRR, the restrained activities of NIR, NR, and AMO, the changes in species interactions and community assembly mechanisms, and the suppression of some essential metabolic pathways. This paper offers a new perspective on comprehending the effects of MPs on SNDPR systems.}, }
@article {pmid38651910, year = {2024}, author = {Rodríguez-Ramos, J and Nicora, CD and Purvine, SO and Borton, MA and McGivern, BB and Hoyt, DW and Lipton, MS and Wrighton, KC}, title = {Untargeted, tandem mass spectrometry metaproteome of Columbia River sediments.}, journal = {Microbiology resource announcements}, volume = {13}, number = {6}, pages = {e0003324}, pmid = {38651910}, issn = {2576-098X}, support = {P30 CA016058/CA/NCI NIH HHS/United States ; Award 1781//Joint Genome Institute Large-scale sequencing award/ ; DE-AC05-76RL01830//Office of Biological and Environmental Research/ ; DE-SC0018170//Subsurface Biogeochemical Research program/ ; }, abstract = {Rivers are critical ecosystems that impact global biogeochemical cycles. Nonetheless, a mechanistic understanding of river microbial metabolisms and their influences on geochemistry is lacking. Here, we announce metaproteomes of river sediments that are paired with metagenomes and metabolites, enabling an understanding of the microbial underpinnings of river respiration.}, }
@article {pmid38648266, year = {2024}, author = {Ramoneda, J and Fan, K and Lucas, JM and Chu, H and Bissett, A and Strickland, MS and Fierer, N}, title = {Ecological relevance of flagellar motility in soil bacterial communities.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38648266}, issn = {1751-7370}, support = {P2EZP3_199849/SNSF_/Swiss National Science Foundation/Switzerland ; 2131837//US National Science Foundation/ ; }, mesh = {*Flagella/genetics/physiology ; *Soil Microbiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Metagenomics ; Bacterial Physiological Phenomena ; Carbon/metabolism ; Soil/chemistry ; Metagenome ; Genome, Bacterial ; }, abstract = {Flagellar motility is a key bacterial trait as it allows bacteria to navigate their immediate surroundings. Not all bacteria are capable of flagellar motility, and the distribution of this trait, its ecological associations, and the life history strategies of flagellated taxa remain poorly characterized. We developed and validated a genome-based approach to infer the potential for flagellar motility across 12 bacterial phyla (26 192 unique genomes). The capacity for flagellar motility was associated with a higher prevalence of genes for carbohydrate metabolism and higher maximum potential growth rates, suggesting that flagellar motility is more prevalent in environments with higher carbon availability. To test this hypothesis, we applied a method to infer the prevalence of flagellar motility in whole bacterial communities from metagenomic data and quantified the prevalence of flagellar motility across four independent field studies that each captured putative gradients in soil carbon availability (148 metagenomes). We observed a positive relationship between the prevalence of bacterial flagellar motility and soil carbon availability in all datasets. Since soil carbon availability is often correlated with other factors that could influence the prevalence of flagellar motility, we validated these observations using metagenomic data from a soil incubation experiment where carbon availability was directly manipulated with glucose amendments. This confirmed that the prevalence of bacterial flagellar motility is consistently associated with soil carbon availability over other potential confounding factors. This work highlights the value of combining predictive genomic and metagenomic approaches to expand our understanding of microbial phenotypic traits and reveal their general environmental associations.}, }
@article {pmid38648112, year = {2024}, author = {Temple, C and Blouin, AG and Boezen, D and Botermans, M and Durant, L and De Jonghe, K and de Koning, P and Goedefroit, T and Minet, L and Steyer, S and Verdin, E and Zwart, M and Massart, S}, title = {Biological Characterization of Physostegia Chlorotic Mottle Virus, an Emergent Virus Infecting Vegetables in Diversified Production Systems.}, journal = {Phytopathology}, volume = {114}, number = {7}, pages = {1680-1688}, doi = {10.1094/PHYTO-06-23-0194-R}, pmid = {38648112}, issn = {0031-949X}, mesh = {*Plant Diseases/virology ; *Hemiptera/virology ; *Vegetables/virology ; Solanum lycopersicum/virology ; Animals ; Switzerland ; Insect Vectors/virology ; Crops, Agricultural/virology ; Host Specificity ; }, abstract = {In 2014, Physostegia chlorotic mottle virus (PhCMoV) was discovered in Austria in Physostegia virginiana. Subsequent collaborative efforts established a link between the virus and severe fruit symptoms on important crops such as tomato, eggplant, and cucumber across nine European countries. Thereafter, specific knowledge gaps, which are crucial to assess the risks PhCMoV can pose for production and how to manage it, needed to be addressed. In this study, the transmission, prevalence, and disease severity of PhCMoV were examined. This investigation led to the identification of PhCMoV presence in a new country, Switzerland. Furthermore, our research indicates that the virus was already present in Europe 30 years ago. Bioassays demonstrated PhCMoV can result in up to 100% tomato yield losses depending on the phenological stage of the plant at the time of infection. PhCMoV was found to naturally infect 12 new host plant species across eight families, extending its host range to 21 plant species across 15 plant families. The study also identified a polyphagous leafhopper (genus Anaceratagallia) as a natural vector of PhCMoV. Overall, PhCMoV was widespread in small-scale diversified vegetable farms in Belgium where tomato is grown in soil under tunnels, occurring in approximately one-third of such farms. However, outbreaks were sporadic and were associated at least once with the cultivation in tomato tunnels of perennial plants that can serve as a reservoir host for the virus and its vector. To further explore this phenomenon and manage the virus, studying the ecology of the vector would be beneficial.}, }
@article {pmid38647288, year = {2024}, author = {Waegenaar, F and García-Timermans, C and Van Landuyt, J and De Gusseme, B and Boon, N}, title = {Impact of operational conditions on drinking water biofilm dynamics and coliform invasion potential.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {5}, pages = {e0004224}, pmid = {38647288}, issn = {1098-5336}, support = {1S02022N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; S006221N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; }, mesh = {*Biofilms/growth &amp; development ; *Drinking Water/microbiology ; *Enterobacteriaceae/physiology/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Water Quality ; Water Purification ; Water Microbiology ; Water Supply ; }, abstract = {UNLABELLED: Biofilms within drinking water distribution systems serve as a habitat for drinking water microorganisms. However, biofilms can negatively impact drinking water quality by causing water discoloration and deterioration and can be a reservoir for unwanted microorganisms. In this study, we investigated whether indicator organisms for drinking water quality, such as coliforms, can settle in mature drinking water biofilms. Therefore, a biofilm monitor consisting of glass rings was used to grow and sample drinking water biofilms. Two mature drinking water biofilms were characterized by flow cytometry, ATP measurements, confocal laser scanning microscopy, and 16S rRNA sequencing. Biofilms developed under treated chlorinated surface water supply exhibited lower cell densities in comparison with biofilms resulting from treated groundwater. Overall, the phenotypic as well as the genotypic characteristics were significantly different between both biofilms. In addition, the response of the biofilm microbiome and possible biofilm detachment after minor water quality changes were investigated. Limited changes in pH and free chlorine addition, to simulate operational changes that are relevant for practice, were evaluated. It was shown that both biofilms remained resilient. Finally, mature biofilms were prone to invasion of the coliform, Serratia fonticola. After spiking low concentrations (i.e., ±100 cells/100 mL) of the coliform to the corresponding bulk water samples, the coliforms were able to attach and get established within the mature biofilms. These outcomes emphasize the need for continued research on biofilm detachment and its implications for water contamination in distribution networks.<br><br>IMPORTANCE: The revelation that even low concentrations of coliforms can infiltrate into mature drinking water biofilms highlights a potential public health concern. Nowadays, the measurement of coliform bacteria is used as an indicator for fecal contamination and to control the effectiveness of disinfection processes and the cleanliness and integrity of distribution systems. In Flanders (Belgium), 533 out of 18,840 measurements exceeded the established norm for the coliform indicator parameter in 2021; however, the source of microbial contamination is mostly unknown. Here, we showed that mature biofilms, are susceptible to invasion of Serratia fonticola. These findings emphasize the importance of understanding and managing biofilms in drinking water distribution systems, not only for their potential to influence water quality, but also for their role in harboring and potentially disseminating pathogens. Further research into biofilm detachment, long-term responses to operational changes, and pathogen persistence within biofilms is crucial to inform strategies for safeguarding drinking water quality.}, }
@article {pmid38646773, year = {2024}, author = {Weng, LY and Luan, DD and Zhou, DP and Guo, QG and Wang, GZ and Zhang, JL}, title = {Improving crop health by synthetic microbial communities: Progress and prospects.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {35}, number = {3}, pages = {847-857}, doi = {10.13287/j.1001-9332.202403.028}, pmid = {38646773}, issn = {1001-9332}, mesh = {*Crops, Agricultural/growth &amp; development/microbiology ; *Microbiota ; *Rhizosphere ; Soil Microbiology ; Synthetic Biology/methods ; Agriculture/methods ; }, abstract = {Crop health directly affects yields and food security. At present, agrochemicals such as fertilizers and pesticides are mainly used in agricultural production to promote crop health. However, long-term excessive utilization of agrochemicals will damage the ecological environment of farmlands and increase the safety risk of agricultural products. It is urgent to explore efficient and environment-friendly agricultural products. Rhizosphere microbiome are considered as the second genome of plants, which are closely related to crop health. Understanding the key functional microbes, microbe-microbe interactions, and plant-microbe interactions are fundamental for exploring the potential of beneficial microbes in promoting crop health. However, due to the heterogeneity and complexity of the natural environment, stimulating the function of indigenous microorganisms remains uncertain. Synthetic microbial community (SynCom) is an artificial combination of two or more different strain isolates of microorganisms, with different taxonomic, genetic, or functional characteristic. Because of the advantages of maintaining species diversity and community stability, SynCom has been widely applied in the fields of human health, environmental governance and industrial production, and may also have great potential in promoting crop health. We summarized the concept and research status of SynCom, expounded the principles and methods of constructing SynCom, and analyzed the research on the promotion of crop health by exploring the mechanism of plant-microbe interactions, promoting plant growth and development, and improving stress resistance. Finally, we envisaged the future prospects to guide the using SynCom to improve crop health.}, }
@article {pmid38643981, year = {2024}, author = {Haller, F and Jimenez, K and Baumgartner, M and Lang, M and Klotz, A and Jambrich, M and Busslinger, G and Müllauer, L and Khare, V and Gasche, C}, title = {Nfe2l2/NRF2 Deletion Attenuates Tumorigenesis and Increases Bacterial Diversity in a Mouse Model of Lynch Syndrome.}, journal = {Cancer prevention research (Philadelphia, Pa.)}, volume = {17}, number = {7}, pages = {311-324}, doi = {10.1158/1940-6207.CAPR-23-0478}, pmid = {38643981}, issn = {1940-6215}, support = {P32302FW//Austrian Science Fund (FWF)/ ; }, mesh = {Animals ; *NF-E2-Related Factor 2/metabolism/genetics ; Mice ; *Colorectal Neoplasms, Hereditary Nonpolyposis/genetics/pathology/metabolism ; *MutS Homolog 2 Protein/genetics/metabolism ; Humans ; *Mice, Inbred C57BL ; *Disease Models, Animal ; Carcinogenesis/genetics/pathology ; Mice, Knockout ; Female ; Intestinal Mucosa/pathology/metabolism/microbiology ; Male ; }, abstract = {Lynch syndrome (LS) is the most prevalent heritable form of colorectal cancer. Its early onset and high lifetime risk for colorectal cancer emphasize the necessity for effective chemoprevention. NFE2L2 (NRF2) is often considered a potential druggable target, and many chemopreventive compounds induce NRF2. However, although NRF2 counteracts oxidative stress, it is also overexpressed in colorectal cancer and may promote tumorigenesis. In this study, we evaluated the role of NRF2 in the prevention of LS-associated neoplasia. We found increased levels of NRF2 in intestinal epithelia of mice with intestinal epithelium-specific Msh2 deletion (MSH2ΔIEC) compared with C57BL/6 (wild-type) mice, as well as an increase in downstream NRF2 targets NAD(P)H dehydrogenase (quinone 1) and glutamate-cysteine ligase catalytic subunit. Likewise, NRF2 levels were increased in human MSH2-deficient LS tumors compared with healthy human controls. In silico analysis of a publicly accessible RNA sequencing LS dataset also found an increase in downstream NRF2 targets. Upon crossing MSH2ΔIEC with Nrf2null (MSH2ΔIECNrf2null) mice, we unexpectedly found reduced tumorigenesis in MSH2ΔIECNrf2null mice compared with MSH2ΔIEC mice after 40 weeks, which occurred despite an increase in oxidative damage in MSH2ΔIECNrf2null mice. The loss of NRF2 impaired proliferation as seen by Ki67 intestinal staining and in organoid cultures. This was accompanied by diminished WNT/β-catenin signaling, but apoptosis was unaffected. Microbial α-diversity increased over time with the loss of NRF2 based upon 16S rRNA gene amplicon sequencing of murine fecal samples. Altogether, we show that NRF2 protein levels are increased in MSH2 deficiency and associated neoplasia, but the loss of NRF2 attenuates tumorigenesis. Activation of NRF2 may not be a feasible strategy for chemoprevention in LS. Prevention Relevance: Patients with LS have an early onset and high lifetime risk for colorectal cancer. In this study, we show that NRF2 protein levels are increased in MSH2 deficiency and associated neoplasia, but the loss of NRF2 attenuates tumorigenesis. This suggests that NRF2 may not be a tumor suppressor in this specific context.}, }
@article {pmid38643524, year = {2024}, author = {Mishra, S and Zhang, X and Yang, X}, title = {Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition.}, journal = {Microbiological research}, volume = {284}, number = {}, pages = {127726}, doi = {10.1016/j.micres.2024.127726}, pmid = {38643524}, issn = {1618-0623}, mesh = {Bacteria/genetics/classification/metabolism ; Metagenomics ; Microbiota/physiology ; *Plant Development ; *Plant Roots/microbiology ; *Plants/microbiology ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.}, }
@article {pmid38642761, year = {2024}, author = {Wu, WF and Li, XY and Chen, SC and Jin, BJ and Wu, CY and Li, G and Sun, CL and Zhu, YG and Lin, XY}, title = {Nitrogen fertilization modulates rice phyllosphere functional genes and pathogens through fungal communities.}, journal = {The Science of the total environment}, volume = {929}, number = {}, pages = {172622}, doi = {10.1016/j.scitotenv.2024.172622}, pmid = {38642761}, issn = {1879-1026}, mesh = {*Oryza/microbiology ; *Fertilizers ; *Nitrogen ; *Fungi/physiology ; Mycobiome ; Agriculture ; Microbiota ; Plant Leaves/microbiology ; }, abstract = {The phyllosphere is a vital yet often neglected habitat hosting diverse microorganisms with various functions. However, studies regarding how the composition and functions of the phyllosphere microbiome respond to agricultural practices, like nitrogen fertilization, are limited. This study investigated the effects of long-term nitrogen fertilization with different levels (CK, N90, N210, N330) on the functional genes and pathogens of the rice phyllosphere microbiome. Results showed that the relative abundance of many microbial functional genes in the rice phyllosphere was significantly affected by nitrogen fertilization, especially those involved in C fixation and denitrification genes. Different nitrogen fertilization levels have greater effects on fungal communities than bacteria communities in the rice phyllosphere, and network analysis and structural equation models further elucidate that fungal communities not only changed bacterial-fungal inter-kingdom interactions in the phyllosphere but also contributed to the variation of biogeochemical cycle potential. Besides, the moderate nitrogen fertilization level (N210) was associated with an enrichment of beneficial microbes in the phyllosphere, while also resulting in the lowest abundance of pathogenic fungi (1.14 %). In contrast, the highest abundance of pathogenic fungi (1.64 %) was observed in the highest nitrogen fertilization level (N330). This enrichment of pathogen due to high nitrogen level was also regulated by the fungal communities, as revealed through SEM analysis. Together, we demonstrated that the phyllosphere fungal communities were more sensitive to the nitrogen fertilization levels and played a crucial role in influencing phyllosphere functional profiles including element cycling potential and pathogen abundance. This study expands our knowledge regarding the role of phyllosphere fungal communities in modulating the element cycling and plant health in sustainable agriculture.}, }
@article {pmid38638900, year = {2024}, author = {Yang, W and Li, X and Yan, H and Sun, Y and Wu, D and Du, Y and Luo, Y}, title = {Recruitment of beneficial cucumber rhizosphere microbes mediated by amino acid secretion induced by biocontrol Bacillus subtilis isolate 1JN2.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1379566}, pmid = {38638900}, issn = {1664-302X}, abstract = {INTRODUCTION: At present, the use of beneficial microorganisms to control cucumber Fusarium wilt is a widely used method, and the rhizosphere microecological reset is one of the mechanisms involved. However, how biocontrol strains reshape cucumber rhizosphere microecology remains to be further studied.<br><br>METHODS: The composition changes of cucumber root exudates induced by biocontrol strain 1JN2, the microbial ecology of cucumber rhizosphere and the colonization ability of biocontrol strain 1JN2 in cucumber rhizosphere were analyzed through UHPLC-MS/MS analysis, Illumina high-throughput sequencing and SEM, respectively.<br><br>RESULTS: First, cucumber plants treated with biocontrol Bacillus 1JN2 reduced the disease severity of Fusarium wilt by 60%. Significant changes in cucumber root exudates were found after 1JN2 inoculation and the contents of four amino acids including glutamine, tryptophan, glycine and glutamic acid were significantly increased. Second, It was found that the bacterial diversity in the rhizosphere of cucumber was significantly increased in both the strain treatment group and the amino acid mixture treatment group, The number of Bacillus was the largest in all dominant populations, exceeded 20% in all treatment groups. The bacteria of Hydrogenispora and Vicinamibacteria were significantly increased after treatment.<br><br>DISCUSSION: Overall, the results demonstrated that amino acid substances in cucumber root exudates induced by biocontrol strain 1JN2 can shift the cucumber root microenvironment and prevent the occurrence of Fusarium wilt disease.}, }
@article {pmid38638570, year = {2024}, author = {Verbeelen, T and Fernandez, CA and Nguyen, TH and Gupta, S and Leroy, B and Wattiez, R and Vlaeminck, SE and Leys, N and Ganigué, R and Mastroleo, F}, title = {Radiotolerance of N-cycle bacteria and their transcriptomic response to low-dose space-analogue ionizing irradiation.}, journal = {iScience}, volume = {27}, number = {5}, pages = {109596}, pmid = {38638570}, issn = {2589-0042}, abstract = {The advancement of regenerative life support systems (RLSS) is crucial to allow long-distance space travel. Within the Micro-Ecological Life Support System Alternative (MELiSSA), efficient nitrogen recovery from urine and other waste streams is vital to produce liquid fertilizer to feed food and oxygen production in subsequent photoautotrophic processes. This study explores the effects of ionizing radiation on nitrogen cycle bacteria that transform urea to nitrate. In particular, we assess the radiotolerance of Comamonas testosteroni, Nitrosomonas europaea, and Nitrobacter winogradskyi after exposure to acute γ-irradiation. Moreover, a comprehensive whole transcriptome analysis elucidates the effects of spaceflight-analogue low-dose ionizing radiation on the individual axenic strains and on their synthetic community o. This research sheds light on how the spaceflight environment could affect ureolysis and nitrification processes from a transcriptomic perspective.}, }
@article {pmid38636749, year = {2024}, author = {Xu, Y and Niu, C and Liang, S and Guo, J and Li, K and Zhang, J and Li, J and Jin, Y and Bai, J and Dai, J and Lu, C}, title = {An inulin-based glycovesicle for pathogen-targeted drug delivery to ameliorate salmonellosis.}, journal = {International journal of biological macromolecules}, volume = {267}, number = {Pt 2}, pages = {131656}, doi = {10.1016/j.ijbiomac.2024.131656}, pmid = {38636749}, issn = {1879-0003}, mesh = {Animals ; *Inulin/pharmacology/chemistry ; Mice ; *Anti-Bacterial Agents/pharmacology/chemistry ; *Salmonella Infections/drug therapy/microbiology ; *Gastrointestinal Microbiome/drug effects ; Drug Delivery Systems ; Levofloxacin/pharmacology ; Micelles ; Drug Carriers/chemistry ; Nanoparticles/chemistry ; }, abstract = {The gut microbiota plays a significant role in the pathogenesis and remission of inflammatory bowel disease. However, conventional antibiotic therapies may alter microbial ecology and lead to dysbiosis of the gut microbiome, which greatly limits therapeutic efficacy. To address this challenge, novel nanomicelles that couple inulin with levofloxacin via disulfide bonds for the treatment of salmonellosis were developed in this study. Owing to their H2S-responsiveness, the nanomicelles can target the inflamed colon and rapidly release levofloxacin to selectively fight against enteric pathogens. Moreover, the embedded inulin can serve as prebiotic fiber to increase the amount of Bifidobacteria and Lactobacilli in mice with salmonellosis, thus maintaining the intestinal mechanical barrier and regulating the balance of the intestinal flora. Therefore, multifunctional nanomicelles had a better curative effect than pure levofloxacin on ameliorating inflammation in vivo. The pathogen-targeted glycovesicle represents a promising drug delivery platform to maximize the efficacy of antibacterial drugs for the treatment of inflammatory bowel disease.}, }
@article {pmid38636461, year = {2024}, author = {Zafar, H and Saier, MH}, title = {An Insider's Perspective about the Pathogenic Relevance of Gut Bacterial Transportomes.}, journal = {Microbial physiology}, volume = {34}, number = {1}, pages = {133-141}, pmid = {38636461}, issn = {2673-1673}, support = {R01 GM077402/GM/NIGMS NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Bacteria/metabolism/pathogenicity ; Animals ; Biological Transport ; Bacterial Proteins/metabolism ; Host Microbial Interactions/physiology ; Carrier Proteins/metabolism ; Gastrointestinal Tract/microbiology ; }, abstract = {BACKGROUND: The gut microbiome is integral to host health, hosting complex interactions between the host and numerous microbial species in the gastrointestinal tract. Key among the molecular mechanisms employed by gut bacteria are transportomes, consisting of diverse transport proteins crucial for bacterial adaptation to the dynamic, nutrient-rich environment of the mammalian gut. These transportomes facilitate the movement of a wide array of molecules, impacting both the host and the microbial community.<br><br>SUMMARY: This communication explores the significance of transportomes in gut bacteria, focusing on their role in nutrient acquisition, competitive interactions among microbes, and potential pathogenicity. It delves into the transportomes of key gut bacterial species like E. coli, Salmonella, Bacteroides, Lactobacillus, Clostridia, and Bifidobacterium, examining the functions of predicted transport proteins. The overview synthesizes recent research efforts, highlighting how these transportomes influence host-microbe interactions and contribute to the microbial ecology of the gut.<br><br>KEY MESSAGES: Transportomes are vital for the survival and adaptation of bacteria in the gut, enabling the import and export of various nutrients and molecules. The complex interplay of transport proteins not only supports bacterial growth and competition but also has implications for host health, potentially contributing to pathogenic processes. Understanding the pathogenic potential of transportomes in major gut bacterial species provides insights into gut health and disease, offering avenues for future research and therapeutic strategies.}, }
@article {pmid38634861, year = {2024}, author = {Lee, HJ and Whang, KS}, title = {Falsiroseomonas oryziterrae sp. nov., and Falsiroseomonas oryzae sp. nov., isolated from rice paddy soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {4}, pages = {}, doi = {10.1099/ijsem.0.006349}, pmid = {38634861}, issn = {1466-5034}, mesh = {*Oryza ; Base Composition ; Cardiolipins ; Fatty Acids/chemistry ; Phosphatidylethanolamines ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Amino Acids ; Nucleotides ; Phosphatidylcholines ; Phosphatidylglycerols ; Soil ; }, abstract = {Three Gram-stain-negative, aerobic, non-motile and coccobacilli-shaped bacterial strains, designated as NPKOSM-4[T], NPKOSM-8 and MO-31[T], were isolated from rice paddy soil. They had 96.5-100 % 16S rRNA gene sequence similarity to each other, and strains NPKOSM-4[T] and NPKOSM-8 showed 100 % 16S rRNA gene sequence similarity, confirming that they were the same species. Comparative analysis of 16S rRNA genes with closely related type strains showed that three isolates were most closely related to Falsiroseomonas terricola EM0302[T] (96.1-97.8 %), Falsiroseomonas wooponensis WW53[T] (95.51-96.3 %) and Falsiroseomonas bella CQN31[T] (96.0-96.5 %), respectively. The genomes of strains NPKOSM-4[T] and MO-31[T] consisted of 4 632 875 and 6 455 771 bps, respectively, with 72.0 and 72.1 mol% G+C content. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values between strains NPKOSM-4[T] and MO-31[T] and type strains of Falsiroseomonas species were lower than the cut-offs (≥95 % for ANI, ≥95-96 % for AAI and ≥ 70 % for dDDH) required to define a bacterial species. The major fatty acids of strains NPKOSM-4[T], NPKOSM-8 and MO-31[T] were C18 : 1 ω7c and C18 : 1 2-OH (<10 %) and the predominant quinone was Q-10. The polar lipids of strain NPKOSM-4[T] were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified aminophospholipid and three unidentified aminolipids. The polar lipid profiles of strain MO-31[T] contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified aminolipid and three unidentified lipids. Based on their distinctive phenotypic, phylogenetic, and chemotaxonomic characteristics, strains NPKOSM-4[T], NPKOSM-8 and MO-31[T] are considered to represent two novel species of the genus Falsiroseomonas, for which the names Falsiroseomonas oryziterrae sp. nov. [to accommodate strains NPKOSM-4[T] (= KACC 22135[T]=JCM 34745[T]), NPKOSM-8 (=KACC 22134=JCM 34746)] and Falsiroseomonas oryzae sp. nov. [to accommodate strain MO-31[T] (= KACC 22465[T]=JCM 35532[T])] are proposed.}, }
@article {pmid38634692, year = {2024}, author = {Zimmermann, J and Piecyk, A and Sieber, M and Petersen, C and Johnke, J and Moitinho-Silva, L and Künzel, S and Bluhm, L and Traulsen, A and Kaleta, C and Schulenburg, H}, title = {Gut-associated functions are favored during microbiome assembly across a major part of C. elegans life.}, journal = {mBio}, volume = {15}, number = {5}, pages = {e0001224}, pmid = {38634692}, issn = {2150-7511}, support = {261376515//Deutsche Forschungsgemeinschaft (DFG)/ ; 261376515//Deutsche Forschungsgemeinschaft (DFG)/ ; 261376515//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {Animals ; *Caenorhabditis elegans/microbiology/physiology ; *Gastrointestinal Microbiome/physiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Host Microbial Interactions ; Gastrointestinal Tract/microbiology ; Microbiota ; }, abstract = {UNLABELLED: The microbiome expresses a variety of functions that influence host biology. The range of functions depends on the microbiome's composition, which can change during the host's lifetime due to neutral assembly processes, host-mediated selection, and environmental conditions. To date, the exact dynamics of microbiome assembly, the underlying determinants, and the effects on host-associated functions remain poorly understood. Here, we used the nematode Caenorhabditis elegans and a defined community of fully sequenced, naturally associated bacteria to study microbiome dynamics and functions across a major part of the worm's lifetime of hosts under controlled experimental conditions. Bacterial community composition initially shows strongly declining levels of stochasticity, which increases during later time points, suggesting selective effects in younger animals as opposed to more random processes in older animals. The adult microbiome is enriched in genera Ochrobactrum and Enterobacter compared to the direct substrate and a host-free control environment. Using pathway analysis, metabolic, and ecological modeling, we further find that the lifetime assembly dynamics increase competitive strategies and gut-associated functions in the host-associated microbiome, indicating that the colonizing bacteria benefit the worm. Overall, our study introduces a framework for studying microbiome assembly dynamics based on stochastic, ecological, and metabolic models, yielding new insights into the processes that determine host-associated microbiome composition and function.<br><br>IMPORTANCE: The microbiome plays a crucial role in host biology. Its functions depend on the microbiome composition that can change during a host's lifetime. To date, the dynamics of microbiome assembly and the resulting functions still need to be better understood. This study introduces a new approach to characterize the functional consequences of microbiome assembly by modeling both the relevance of stochastic processes and metabolic characteristics of microbial community changes. The approach was applied to experimental time-series data obtained for the microbiome of the nematode Caenorhabditis elegans across the major part of its lifetime. Stochastic processes played a minor role, whereas beneficial bacteria as well as gut-associated functions enriched in hosts. This indicates that the host might actively shape the composition of its microbiome. Overall, this study provides a framework for studying microbiome assembly dynamics and yields new insights into C. elegans microbiome functions.}, }
@article {pmid38634606, year = {2024}, author = {Vandepol, NS and Shade, A}, title = {Is everything everywhere? A hands-on activity to engage undergraduates with key concepts in quantitative microbial biogeography.}, journal = {Journal of microbiology &amp; biology education}, volume = {25}, number = {2}, pages = {e0017023}, pmid = {38634606}, issn = {1935-7877}, support = {1749544//National Science Foundation/ ; //The Michigan State University Certification in College Teaching within the Graduate School in partnership with the College of Natural Sciences/ ; //The French Centre National de la Recherche Scientifique (CNRS)/ ; }, abstract = {The ubiquity and ease with which microbial cells disperse over space is a key concept in microbiology, especially in microbial ecology. The phenomenon prompted Baas Becking's famous "everything is everywhere" statement that now acts as the null hypothesis in studies that test the dispersal limitation of microbial taxa. Despite covering the content in lectures, exam performance indicated that the concepts of dispersal and biogeography challenged undergraduate students in an upper-level Microbial Ecology course. Therefore, we iteratively designed a hands-on classroom activity to supplement the lecture content and reinforce fundamental microbial dispersal and biogeography concepts while also building quantitative reasoning and teamwork skills. In a class period soon after the lecture, the students formed three-to-five-person teams to engage in the activity, which included a hands-on dispersal simulation and worksheet to guide discussion. The simulation involved stepwise neutral immigration or emigration and then environmental selection on a random community of microbial taxa represented by craft poms. The students recorded the results at each step as microbial community data. A field guide was provided to identify the taxonomy based on the pom phenotype and a reference to each taxon's preferred environmental niches. The worksheet guided a reflection of student observations during the simulation. It also sharpened quantitative thinking by prompting the students to summarize and visualize their and other teams' microbial community data and then to compare the observed community distributions to the idealized expectation given only selection without dispersal. We found that the activity improved student performance on exam questions and general student satisfaction and comfort with the biogeography concepts. Activity instructions and a list of needed materials are included for instructors to reproduce for their classrooms.}, }
@article {pmid38632086, year = {2024}, author = {Chen, H and Zwaenepoel, A and Van de Peer, Y}, title = {wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {5}, pages = {}, pmid = {38632086}, issn = {1367-4811}, support = {3G032219//Research Foundation-Flanders/ ; //Ghent University/ ; }, mesh = {*Polyploidy ; *Genome, Plant ; *Gene Duplication ; *Phylogeny ; Evolution, Molecular ; Software ; Genomics/methods ; }, abstract = {MOTIVATION: Major improvements in sequencing technologies and genome sequence assembly have led to a huge increase in the number of available genome sequences. In turn, these genome sequences form an invaluable source for evolutionary, ecological, and comparative studies. One kind of analysis that has become routine is the search for traces of ancient polyploidy, particularly for plant genomes, where whole-genome duplication (WGD) is rampant.<br><br>RESULTS: Here, we present a major update of a previously developed tool wgd, namely wgd v2, to look for remnants of ancient polyploidy, or WGD. We implemented novel and improved previously developed tools to (a) construct KS age distributions for the whole-paranome (collection of all duplicated genes in a genome), (b) unravel intragenomic and intergenomic collinearity resulting from WGDs, (c) fit mixture models to age distributions of gene duplicates, (d) correct substitution rate variation for phylogenetic placement of WGDs, and (e) date ancient WGDs via phylogenetic dating of WGD-retained gene duplicates. The applicability and feasibility of wgd v2 for the identification and the relative and absolute dating of ancient WGDs is demonstrated using different plant genomes.<br><br>wgd v2 is open source and available at https://github.com/heche-psb/wgd.}, }
@article {pmid38631226, year = {2024}, author = {Rubin-Blum, M and Makovsky, Y and Rahav, E and Belkin, N and Antler, G and Sisma-Ventura, G and Herut, B}, title = {Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea.}, journal = {Marine environmental research}, volume = {198}, number = {}, pages = {106497}, doi = {10.1016/j.marenvres.2024.106497}, pmid = {38631226}, issn = {1879-0291}, mesh = {Mediterranean Sea ; *Archaea/genetics/metabolism ; *Seawater/microbiology ; *Bacteria/metabolism/genetics/classification ; *Microbiota ; Carbon/metabolism ; Salts ; Methane/metabolism ; }, abstract = {Discharge of gas-rich brines fuels productive chemosynthetic ecosystems in the deep sea. In these salty, methanic and sulfidic brines, microbial communities adapt to specific niches along the physicochemical gradients. However, the molecular mechanisms that underpin these adaptations are not fully known. Using metagenomics, we investigated the dense (∼10[6] cell ml[-1]) microbial communities that occupy small deep-sea brine pools found in the Southeastern Mediterranean Sea (1150 m water depth, ∼22 °C, ∼60 PSU salinity, sulfide, methane, ammonia reaching millimolar levels, and oxygen usually depleted), reaching high productivity rates of 685 μg C L[-1] d[-1] ex-situ. We curated 266 metagenome-assembled genomes of bacteria and archaea from the several pools and adjacent sediment-water interface, highlighting the dominance of a single Sulfurimonas, which likely fuels its autotrophy using sulfide oxidation or inorganic sulfur disproportionation. This lineage may be dominant in its niche due to genome streamlining, limiting its metabolic repertoire, particularly by using a single variant of sulfide: quinone oxidoreductase. These primary producers co-exist with ANME-2c archaea that catalyze the anaerobic oxidation of methane. Other lineages can degrade the necromass aerobically (Halomonas and Alcanivorax), or anaerobically through fermentation of macromolecules (e.g., Caldatribacteriota, Bipolaricaulia, Chloroflexota, etc). These low-abundance organisms likely support the autotrophs, providing energy-rich H2, and vital organics such as vitamin B12.}, }
@article {pmid38630182, year = {2024}, author = {Nithyapriya, S and Sundaram, L and Eswaran, SUD and Perveen, K and Alshaikh, NA and Sayyed, RZ and Mastinu, A}, title = {Purification and Characterization of Desferrioxamine B of Pseudomonas fluorescens and Its Application to Improve Oil Content, Nutrient Uptake, and Plant Growth in Peanuts.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {60}, pmid = {38630182}, issn = {1432-184X}, support = {RSP2024R358//King Saud University/ ; }, mesh = {*Arachis ; Deferoxamine ; *Pseudomonas fluorescens ; India ; RNA, Ribosomal, 16S/genetics ; Nutrients ; Siderophores ; Iron ; Soil ; }, abstract = {Microorganisms produce siderophores, which are low-molecular-weight iron chelators when iron availability is limited. The present analyzed the role of LNPF1 as multifarious PGPR for improving growth parameters and nutrient content in peanut and soil nutrients. Such multifarious PGPR strains can be used as effective bioinoculants for peanut farming. In this work, rhizosphere bacteria from Zea mays and Arachis hypogaea plants in the Salem area of Tamil Nadu, India, were isolated and tested for biochemical attributes and characteristics that stimulate plant growth, such as the production of hydrogen cyanide, ammonia (6 µg/mL), indole acetic acid (76.35 µg/mL), and solubilizing phosphate (520 µg/mL). The 16S rRNA gene sequences identified the isolate LNPF1 as Pseudomonas fluorescens with a similarity percentage of 99% with Pseudomonas sp. Isolate LNPF1 was evaluated for the production of siderophore. Siderophore-rich supernatant using a Sep Pack C18 column and Amberlite-400 Resin Column (λmax 264) produced 298 mg/L and 50 mg/L of siderophore, respectively. The characterization of purified siderophore by TLC, HPLC, FTIR, and 2D-NMR analysis identified the compound as desferrioxamine, a hydroxamate siderophore. A pot culture experiment determined the potential of LNPF1 to improve iron and oil content and photosynthetic pigments in Arachis hypogaea L. and improve soil nutrient content. Inoculation of A. hypogea seeds with LNPF1 improved plant growth parameters such as leaf length (60%), shoot length (22%), root length (54.68%), fresh weight (47.28%), dry weight (37%), and number of nuts (66.66) compared to the control (untreated seeds). This inoculation also improved leaf iron content (43.42), short iron content (38.38%), seed iron (46.72%), seed oil (31.68%), carotenoid (64.40%), and total chlorophyll content (98.%) compared to control (untreated seeds). Bacterized seeds showed a substantial increase in nodulation (61.65%) and weight of individual nodules (95.97) vis-à-vis control. The results of the present study indicated that P. fluorescens might be utilized as a potential bioinoculant to improve growth, iron content, oil content, number of nuts and nodules of Arachishypogaea L., and enrich soil nutrients.}, }
@article {pmid38629830, year = {2024}, author = {Castro, AE and Montecillo, AD and Villanueva, RMD and Obusan, MCM}, title = {Bacterial community profiles of select tributaries of Laguna Lake in the Philippines.}, journal = {Microbiology resource announcements}, volume = {13}, number = {5}, pages = {e0116123}, pmid = {38629830}, issn = {2576-098X}, abstract = {Laguna Lake is known for its ecological, economic, and cultural importance. Effects of urbanization and accumulation of emerging pollutants have been associated with its water quality; however, the microbial ecology of its tributaries remains to be explored. We report bacterial community profiles from shotgun metagenomes of its select tributary waters.}, }
@article {pmid38628677, year = {2024}, author = {Kim, M and Park, T and Park, C and Baek, YC and Cho, A and Lee, HG and Kim, E and Bok, EY and Jung, YH and Hur, TY and Do, YJ}, title = {Impact of rumen cannulation surgery on rumen microbiota composition in Hanwoo steers.}, journal = {Journal of animal science and technology}, volume = {66}, number = {2}, pages = {353-365}, pmid = {38628677}, issn = {2055-0391}, abstract = {Rumen cannulation is a surgical technique used to collect rumen contents from ruminants. However, rumen cannulation surgery may potentially impact the composition of the rumen microbiota. This study aimed to examine the longitudinal alterations in the rumen microbiota composition of Hanwoo steers after cannulation surgery. In this study, eight Hanwoo steers were used; four steers underwent rumen cannulation surgery (cannulation group), while the remaining four were left intact (control group). Rumen samples were collected from all eight steers using the stomach tubing method on the day before surgery (day 0) and on postoperative days 1, 4, 7, 10, 14, 17, 21, 24, and 28, resulting in 80 samples (10 timepoints × 8 animals). The microbiota of all 80 samples were analyzed using 16S rRNA gene amplicon sequencing with Quantitative Insights into Microbial Ecology version 2 (QIIME2). There were no significant differences (p > 0.05) in all major phyla and most major genera representing at least 0.5% of total sequences across all 80 samples between the control and cannulation groups on the preoperative and postoperative days. However, while the alpha diversity indices did not differ (p > 0.05) between the two groups on the preoperative day, they significantly differed (p < 0.05) between the two groups on the postoperative days. Further, the overall microbial distribution based on both unweighted and weighted principal coordinate analysis plots significantly differed (p < 0.05) between the two groups on both the preoperative and postoperative days. Orthogonal polynomial contrasts indicated that major genera and microbial diversity in the cannulation group decreased following surgery but returned to their initial states by postoperative day 28. In conclusion, this study demonstrates that rumen cannulation surgery affects some major taxa and microbial diversity, suggesting that the rumen cannulation method can alter the composition of rumen microbiota in Hanwoo steers.}, }
@article {pmid38627476, year = {2024}, author = {Ridley, RS and Conrad, RE and Lindner, BG and Woo, S and Konstantinidis, KT}, title = {Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {8798}, pmid = {38627476}, issn = {2045-2322}, support = {2136146//National Science Foundation/ ; }, mesh = {Humans ; *Multiomics ; *Plastics ; Polymers ; Biotransformation ; Biodegradation, Environmental ; }, abstract = {Despite increasing efforts across various disciplines, the fate, transport, and impact of synthetic plastics on the environment and public health remain poorly understood. To better elucidate the microbial ecology of plastic waste and its potential for biotransformation, we conducted a large-scale analysis of all publicly available meta-omic studies investigating plastics (n = 27) in the environment. Notably, we observed low prevalence of known plastic degraders throughout most environments, except for substantial enrichment in riverine systems. This indicates rivers may be a highly promising environment for discovery of novel plastic bioremediation products. Ocean samples associated with degrading plastics showed clear differentiation from non-degrading polymers, showing enrichment of novel putative biodegrading taxa in the degraded samples. Regarding plastisphere pathogenicity, we observed significant enrichment of antimicrobial resistance genes on plastics but not of virulence factors. Additionally, we report a co-occurrence network analysis of 10 + million proteins associated with the plastisphere. This analysis revealed a localized sub-region enriched with known and putative plastizymes-these may be useful for deeper investigation of nature's ability to biodegrade man-made plastics. Finally, the combined data from our meta-analysis was used to construct a publicly available database, the Plastics Meta-omic Database (PMDB)-accessible at plasticmdb.org. These data should aid in the integrated exploration of the microbial plastisphere and facilitate research efforts investigating the fate and bioremediation potential of environmental plastic waste.}, }
@article {pmid38626537, year = {2024}, author = {Ali, A and Wang, N and Wang, Q and Xu, G and Xu, H}, title = {An approach to evaluating seasonal responses to acute toxicity of antibiotic nitrofurazone on periphytic ciliated protist communities in marine environments.}, journal = {European journal of protistology}, volume = {94}, number = {}, pages = {126081}, doi = {10.1016/j.ejop.2024.126081}, pmid = {38626537}, issn = {1618-0429}, mesh = {*Seasons ; *Nitrofurazone/pharmacology ; *Ciliophora/drug effects ; China ; Water Pollutants, Chemical/toxicity ; Anti-Bacterial Agents/pharmacology ; Seawater ; }, abstract = {Periphytic protists including ciliates are the primary components of microbial communities in which they play a vital role in the progression of food webs by moving resources from lower to higher trophic levels. However, the toxic effects of veterinary antibiotics on periphytic protists across four seasons are minimally understood. Therefore, in this study, a 1-year survey was conducted with the antibiotic nitrofurazone (NFZ) applied at concentrations of 0.0, 1.5, 3.0, 6.0, and 12.0 mg/L. Samples of protist communities were collected using microscope glass slides during four seasons in the coastal waters of the Yellow Sea, Qingdao, northern China. The abundance of protists dropped with an increase in NFZ concentrations, and almost all species were dead at a concentration of 12.0 mg/L. The 12 h-LC50 values of NFZ for the protist biota were similar among the four seasons, despite significant seasonal variability in the community structure. The present results suggest that the periphytic protist biota may be used as a biomarker for assessing the ecotoxicity of NFZ in marine environments regardless of the year season.}, }
@article {pmid38625060, year = {2024}, author = {Garvin, ZK and Abades, SR and Trefault, N and Alfaro, FD and Sipes, K and Lloyd, KG and Onstott, TC}, title = {Prevalence of trace gas-oxidizing soil bacteria increases with radial distance from Polloquere hot spring within a high-elevation Andean cold desert.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38625060}, issn = {1751-7370}, support = {/NASA/NASA/United States ; //Astrobiology Early Career Collaboration Award/ ; //High Meadows Environmental Institute at Princeton University/ ; //Walbridge Fund Graduate Award/ ; G110-21-W8189//W.M. Keck Foundation/ ; 1170995//National Fund for Scientific and Technological Development/ ; //National Science Foundation/ ; 2121637//Frontier Research in Earth Sciences/ ; 2151015//Division of Ocean Sciences/ ; }, mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Desert Climate ; *Hot Springs/microbiology ; *Oxidation-Reduction ; Carbon Monoxide/metabolism ; Hydrogen/metabolism ; Microbiota ; Altitude ; Soil/chemistry ; }, abstract = {High-elevation arid regions harbor microbial communities reliant on metabolic niches and flexibility to survive under biologically stressful conditions, including nutrient limitation that necessitates the utilization of atmospheric trace gases as electron donors. Geothermal springs present "oases" of microbial activity, diversity, and abundance by delivering water and substrates, including reduced gases. However, it is unknown whether these springs exhibit a gradient of effects, increasing their impact on trace gas-oxidizers in the surrounding soils. We assessed whether proximity to Polloquere, a high-altitude geothermal spring in an Andean salt flat, alters the diversity and metabolic structure of nearby soil bacterial populations compared to the surrounding cold desert. Recovered DNA and metagenomic analyses indicate that the spring represents an oasis for microbes in this challenging environment, supporting greater biomass with more diverse metabolic functions in proximal soils that declines sharply with radial distance from the spring. Despite the sharp decrease in biomass, potential rates of atmospheric hydrogen (H2) and carbon monoxide (CO) uptake increase away from the spring. Kinetic estimates suggest this activity is due to high-affinity trace gas consumption, likely as a survival strategy for energy/carbon acquisition. These results demonstrate that Polloquere regulates a gradient of diverse microbial communities and metabolisms, culminating in increased activity of trace gas-oxidizers as the influence of the spring yields to that of the regional salt flat environment. This suggests the spring holds local importance within the context of the broader salt flat and potentially represents a model ecosystem for other geothermal systems in high-altitude desert environments.}, }
@article {pmid38624181, year = {2024}, author = {Manck, LE and Coale, TH and Stephens, BM and Forsch, KO and Aluwihare, LI and Dupont, CL and Allen, AE and Barbeau, KA}, title = {Iron limitation of heterotrophic bacteria in the California Current System tracks relative availability of organic carbon and iron.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38624181}, issn = {1751-7370}, support = {OCE-1026607//NSF/ ; DGE-1144086//NSF/ ; 729162//Simons Postdoctoral Fellowship in Marine Microbial Ecology/ ; OCE-1558453//NSF/ ; OCE-1756884//NSF/ ; 970820//Simons Collaboration on Principles of Microbial Ecosystems/ ; OCE-1558841//NSF/ ; }, mesh = {*Iron/metabolism ; *Carbon/metabolism ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Seawater/microbiology ; California ; *Heterotrophic Processes ; Microbiota ; }, abstract = {Iron is an essential nutrient for all microorganisms of the marine environment. Iron limitation of primary production has been well documented across a significant portion of the global surface ocean, but much less is known regarding the potential for iron limitation of the marine heterotrophic microbial community. In this work, we characterize the transcriptomic response of the heterotrophic bacterial community to iron additions in the California Current System, an eastern boundary upwelling system, to detect in situ iron stress of heterotrophic bacteria. Changes in gene expression in response to iron availability by heterotrophic bacteria were detected under conditions of high productivity when carbon limitation was relieved but when iron availability remained low. The ratio of particulate organic carbon to dissolved iron emerged as a biogeochemical proxy for iron limitation of heterotrophic bacteria in this system. Iron stress was characterized by high expression levels of iron transport pathways and decreased expression of iron-containing enzymes involved in carbon metabolism, where a majority of the heterotrophic bacterial iron requirement resides. Expression of iron stress biomarkers, as identified in the iron-addition experiments, was also detected insitu. These results suggest iron availability will impact the processing of organic matter by heterotrophic bacteria with potential consequences for the marine biological carbon pump.}, }
@article {pmid38622815, year = {2024}, author = {Riquelme Del Río, B and Sepulveda-Jauregui, A and Salas-Rabaza, JA and Mackenzie, R and Thalasso, F}, title = {Fine-Scale Spatial Variability of Greenhouse Gas Emissions From a Subantarctic Peatland Bog.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {17}, pages = {7393-7402}, pmid = {38622815}, issn = {1520-5851}, mesh = {*Greenhouse Gases/analysis ; *Wetlands ; *Methane/analysis ; Carbon Dioxide/analysis ; Soil/chemistry ; Ecosystem ; Sphagnopsida ; Environmental Monitoring ; }, abstract = {Peatlands are recognized as crucial greenhouse gas sources and sinks and have been extensively studied. Their emissions exhibit high spatial heterogeneity when measured on site using flux chambers. However, the mechanism by which this spatial variability behaves on a very fine scale remains unclear. This study investigates the fine-scale spatial variability of greenhouse gas emissions from a subantarctic Sphagnum peatland bog. Using a recently developed skirt chamber, methane emissions and ecosystem respiration (as carbon dioxide) were measured at a submeter scale resolution, at five specific 3 × 3 m plots, which were examined across the site throughout a single campaign during the Austral summer season. The results indicated that methane fluxes were significantly less homogeneously distributed compared with ecosystem respiration. Furthermore, we established that the spatial variation scale, i.e., the minimum spatial domain over which notable changes in methane emissions and ecosystem respiration occur, was <0.56 m[2]. Factors such as ground height relative to the water table and vegetation coverage were analyzed. It was observed that Tetroncium magellanicum exhibited a notable correlation with higher methane fluxes, likely because of the aerenchymatous nature of this species, facilitating gas transport. This study advances understanding of gas exchange patterns in peatlands but also emphasizes the need for further efforts for characterizing spatial dynamics at a very fine scale for precise greenhouse gas budget assessment.}, }
@article {pmid38621490, year = {2024}, author = {Cheng, J and Robles-Lecompte, A and McKenna, AM and Chang, NB}, title = {Deciphering linkages between DON and the microbial community for nitrogen removal using two green sorption media in a surface water filtration system.}, journal = {Chemosphere}, volume = {357}, number = {}, pages = {142042}, doi = {10.1016/j.chemosphere.2024.142042}, pmid = {38621490}, issn = {1879-1298}, mesh = {*Nitrogen/metabolism ; *Filtration/methods ; Water Pollutants, Chemical/metabolism/analysis ; Water Purification/methods ; Biodegradation, Environmental ; Denitrification ; Adsorption ; Microbiota ; Florida ; Aluminum Oxide/chemistry ; Waste Disposal, Fluid/methods ; }, abstract = {The presence of dissolved organic nitrogen (DON) in stormwater treatment processes is a continuous challenge because of the intertwined nature of its decomposition, bioavailability, and biodegradability and its unclear molecular characteristics. In this paper, 21 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in combination with quantitative polymerase chain reaction was applied to elucidate the molecular change of DON and microbial population dynamics in a field-scale water filtration system filled with two specialty adsorbents for comparison in South Florida where the dry and wet seasons are distinctive annually. The adsorbents included CPS (clay-perlite and sand sorption media) and ZIPGEM (zero-valent iron and perlite-based green environmental media). Our study revealed that seasonal effects can significantly influence the dynamic characteristics and biodegradability of DON. The microbial population density in the filter beds indicated that three microbial species in the nitrogen cycle were particularly thrived for denitrification, dissimilatory nitrate reduction to ammonium, and anaerobic ammonium oxidation via competition and commensalism relationships during the wet season. Also, there was a decrease in the compositional complexity and molecular weight of the DON groups (CnHmOpN1, CnHmOpN2, CnHmOpN3, and CnHmOpN4), revealed by the 21 T FT-ICR MS bioassay, driven by a microbial population quantified by polymerase chain reaction from the dry to the wet season. These findings indirectly corroborate the assumption that the metabolism of microorganisms is much more vigorous in the wet season. The results affirm that the sustainable materials (CPS and ZIPGEM) can sustain nitrogen removal intermittently by providing a suitable living environment in which the metabolism of microbial species can be cultivated and enhanced to facilitate physico-chemical nitrogen removal across the two types of green sorption media.}, }
@article {pmid38619794, year = {2024}, author = {Van Holm, W and Zayed, N and Lauwens, K and Saghi, M and Axelsson, J and Aktan, MK and Braem, A and Simoens, K and Vanbrabant, L and Proost, P and Van Holm, B and Maes, P and Boon, N and Bernaerts, K and Teughels, W}, title = {Oral Biofilm Composition, Dissemination to Keratinocytes, and Inflammatory Attenuation Depend on Probiotic and Synbiotic Strain Specificity.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {38619794}, issn = {1867-1314}, support = {C24/17/086//KU Leuven/ ; C16/17/010//KU Leuven/ ; C16/17/010//KU Leuven/ ; C24/17/086//KU Leuven/ ; G091218N//Fonds Wetenschappelijk Onderzoek/ ; G091218N//Fonds Wetenschappelijk Onderzoek/ ; }, abstract = {Several inflammatory diseases are characterized by a disruption in the equilibrium between the host and its microbiome. Due to the increase in resistance, the use of antibiotics for the widespread, nonspecific killing of microorganisms is at risk. Pro-microbial approaches focused on stimulating or introducing beneficial species antagonistic toward pathobionts may be a viable alternative for restoring the host-microbiome equilibrium. Unfortunately, not all potential probiotic or synbiotic species and even subspecies (to strain level) are equally effective for the designated pathology, leading to conflicting accounts of their efficacy. To assess the extent of these species- and strain-specific effects, 13 probiotic candidates were evaluated for their probiotic and synbiotic potential with glycerol on in vitro oral biofilms, dissemination from biofilms to keratinocytes, and anti-inflammatory activity. Species- and strain-specific effects and efficacies were observed in how they functioned as probiotics or synbiotics by influencing oral pathobionts and commensals within biofilms and affected the dissemination of pathobionts to keratinocytes, ranging from ineffective strains to strains that reduced pathobionts by 3 + log. In addition, a minority of the candidates exhibited the ability to mitigate the inflammatory response of LPS-stimulated monocytes. For a comprehensive assessment of probiotic therapy for oral health, a judicious selection of fully characterized probiotic strains that are specifically tailored to the designated pathology is required. This approach aims to challenge the prevailing perception of probiotics, shifting the focus away from "form over function." Rather than using unproven, hypothetical probiotic strains from known genera or species, one should choose strains that are actually functional in resolving the desired pathology before labelling them probiotics.}, }
@article {pmid38619730, year = {2024}, author = {Zhu, H and Li, S and Wu, Z and Xiong, X and Lin, P and Liu, B and He, D and Liu, G}, title = {Diversity Patterns of Eukaryotic Phytoplankton in the Medog Section of the Yarlung Zangbo River.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {59}, pmid = {38619730}, issn = {1432-184X}, mesh = {*Ecosystem ; *Rivers ; Biodiversity ; Biomass ; Phytoplankton ; }, abstract = {As one of the important biodiversity conservation areas in China, the ecosystem in the lower reaches of the Yarlung Zangbo River is fragile, and is particularly sensitive to global changes. To reveal the diversity pattern of phytoplankton, the metabarcode sequencing was employed in the Medog section of the lower reaches of the Yarlung Zangbo River during autumn 2019 in present study. The phytoplankton assemblies can be significantly divided into the main stem and the tributaries; there are significant differences in the phytoplankton biomass, alpha and beta diversity between the main stem and the tributaries. While both the main stem and the tributaries are affected by dispersal limitation, the phytoplankton assemblages in the entire lower reaches are primarily influenced by heterogeneous selection. Community dissimilarity and assembly process were significantly correlated with turbidity, electrical conductivity, and nitrogen nutrition. The tributaries were the main source of the increase in phytoplankton diversity in the lower reaches of the Yarlung Zangbo River. Such diversity pattern of phytoplankton in the lower reach may be caused by the special habitat in Medog, that is, the excessive flow velocity, and the significant spatial heterogeneity in physical and chemical factors between stem and tributaries. Based on the results and conclusions obtained in present study, continuous long-term monitoring is essential to assess and quantify the impact of global changes on phytoplankton.}, }
@article {pmid38618866, year = {2024}, author = {Zha, Z and Wang, R and Wang, Q and Chen, F and Ye, Z and Li, Y}, title = {A fast and efficient liquid chromatography-tandem mass spectrometry method for measuring l- and d-amino acids in the urine of patients with immunoglobulin A nephropathy.}, journal = {Biomedical chromatography : BMC}, volume = {38}, number = {6}, pages = {e5866}, doi = {10.1002/bmc.5866}, pmid = {38618866}, issn = {1099-0801}, support = {82170716//National Science Foundation of China/ ; 81870333//National Science Foundation of China/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; //College Science and Technology Innovation Project of Shanxi Education Department/ ; }, mesh = {Humans ; *Tandem Mass Spectrometry/methods ; *Amino Acids/urine ; *Glomerulonephritis, IGA/urine ; Chromatography, Liquid/methods ; Male ; Adult ; Female ; Middle Aged ; Reproducibility of Results ; Biomarkers/urine ; Stereoisomerism ; Linear Models ; Case-Control Studies ; Young Adult ; }, abstract = {Immunoglobulin nephropathy (IgAN) stands as the most prevalent primary glomerular nephropathy globally, typically diagnosed through an invasive renal biopsy. Emerging research suggests the significant involvement of chiral amino acids in kidney disease progression. This study introduces a nonderivative LC-tandem mass spectrometry approach, offering efficient separation outcomes within 15 min for identifying chiral amino acids in human urine samples. Subsequently, using this method, the analysis of l- and d-amino acids in the urine of both patients with IgAN and healthy individuals was conducted. Fourteen d-amino acids and 20 l-amino acids were identified in the urine samples obtained from 17 patients with IgAN and 21 healthy individuals. The results indicated notable variances in the concentrations of both l- and d-amino acids between the IgAN and healthy control groups. In contrast to the healthy group, the IgAN group exhibited higher mean urine concentrations of most l-amino acids and lower concentrations of d-amino acids. Furthermore, correlations between amino acids and clinical markers were investigated. These results propose a novel method for monitoring trace amino acids in urine samples and introduce a new concept for potential markers of IgAN.}, }
@article {pmid38617439, year = {2024}, author = {Ogaya, Y and Kadota, T and Hamada, M and Nomura, R and Nakano, K}, title = {Characterization of the unique oral microbiome of children harboring Helicobacter pylori in the oral cavity.}, journal = {Journal of oral microbiology}, volume = {16}, number = {1}, pages = {2339158}, pmid = {38617439}, issn = {2000-2297}, abstract = {OBJECTIVE: Helicobacter pylori infection is acquired in childhood via the oral cavity, although its relationship with the characteristics of the oral microbiome has not been elucidated. In this study, we performed comprehensive analysis of the oral microbiome in children and adults with or without H. pylori in the oral cavity.<br><br>METHODS: Bacterial DNA was extracted from 41 adult and 21 child saliva specimens, and H. pylori was detected using PCR. 16S rRNA gene amplification was performed for next-generation sequencing. Bioinformatic analyses were conducted using Quantitative Insights into Microbial Ecology 2 (QIIME 2).<br><br>RESULTS: Faith's phylogenetic diversity analysis showed a significant difference between H. pylori-negative adult and child specimens in terms of &#x3b1;-diversity (p&#x2009;<&#x2009;0.05), while no significant difference was observed between H. pylori-positive adult and child specimens. There was also a significant difference in &#x3b2;-diversity between H. pylori-positive and negative child specimens (p&#x2009;<&#x2009;0.05). Taxonomic analysis at the genus level revealed that Porphyromonas was the only bacterium that was significantly more abundant in both H. pylori-positive adults and children than in corresponding negative specimens (p&#x2009;<&#x2009;0.01 and p&#x2009;<&#x2009;0.05, respectively).<br><br>CONCLUSION: These results suggest unique oral microbiome characteristics in children with H. pylori infection in the oral cavity.}, }
@article {pmid38613756, year = {2024}, author = {Costa, JL and Silva, LG and Veras, STS and Gavazza, S and Florencio, L and Motteran, F and Kato, MT}, title = {Use of nitrate, sulphate, and iron (III) as electron acceptors to improve the anaerobic degradation of linear alkylbenzene sulfonate: effects on removal potential and microbiota diversification.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {38613756}, issn = {1614-7499}, support = {APQ-0603-3.07/14//Funda&#xe7;&#xe3;o de Amparo &#xe0; Ci&#xea;ncia e Tecnologia do Estado de Pernambuco/ ; CAPES-PrInt//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; finance code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; process number 88887.467533/2019-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, abstract = {Linear alkylbenzene sulfonate (LAS) is a synthetic anionic surfactant that is found in certain amounts in wastewaters and even in water bodies, despite its known biodegradability. This study aimed to assess the influence of nitrate, sulphate, and iron (III) on LAS anaerobic degradation and biomass microbial diversity. Batch reactors were inoculated with anaerobic biomass, nutrients, LAS (20 mg L[-1]), one of the three electron acceptors, and ethanol (40 mg L[-1]) as a co-substrate. The control treatments, with and without co-substrate, showed limited LAS biodegradation efficiencies of 10 ± 2% and 0%, respectively. However, when nitrate and iron (III) were present without co-substrate, biodegradation efficiencies of 53 ± 4% and 75 ± 3% were achieved, respectively, which were the highest levels observed. Clostridium spp. was prominent in all treatments, while Alkaliphilus spp. and Bacillus spp. thrived in the presence of iron, which had the most significant effect on LAS biodegradation. Those microorganisms were identified as crucial in affecting the LAS anaerobic degradation. The experiments revealed that the presence of electron acceptors fostered the development of a more specialised microbiota, especially those involved in the LAS biodegradation. A mutual interaction between the processes of degradation and adsorption was also shown.}, }
@article {pmid38613638, year = {2024}, author = {Cai, Y and Chen, Z and Chen, E and Zhang, D and Wei, T and Sun, M and Lian, Y}, title = {Succinic Acid Ameliorates Concanavalin A-Induced Hepatitis by Altering the Inflammatory Microenvironment and Expression of BCL-2 Family Proteins.}, journal = {Inflammation}, volume = {47}, number = {6}, pages = {2000-2012}, pmid = {38613638}, issn = {1573-2576}, support = {2021J05278//Fujian Provincial Natural Science Foundation/ ; 2021QNB017//The Health Science Foundation of Fujian Youth Program/ ; 82303109//National Natural Science Foundation of China/ ; 2022J05299//Natural Science Foundation of Fujian Province, China/ ; 2021B002//Cross-Strait Postdoctoral Exchange Funding Program of Fujian Province, China/ ; }, mesh = {Animals ; *Concanavalin A/toxicity ; *Succinic Acid/pharmacology ; Mice ; *Hepatitis, Autoimmune/drug therapy/metabolism/pathology ; *Proto-Oncogene Proteins c-bcl-2/metabolism ; *Apoptosis/drug effects ; Liver/drug effects/pathology/metabolism ; Male ; Cellular Microenvironment/drug effects ; Kupffer Cells/drug effects/metabolism ; Chemical and Drug Induced Liver Injury/drug therapy/metabolism/pathology ; Inflammation/drug therapy/metabolism ; }, abstract = {Autoimmune hepatitis (AIH) is a severe immune-mediated inflammatory liver disease that currently lacks feasible drug treatment methods. Our study aimed to evaluate the protective effect of succinic acid against AIH and provide a reliable method for the clinical treatment of AIH. We performed an in vivo study of the effects of succinic acid on concanavalin A (ConA)-induced liver injury in mice. We examined liver transaminase levels, performed hematoxylin and eosin (HE) staining, and observed apoptotic phenotypes in mice. We performed flow cytometry to detect changes in the number of neutrophils and monocytes, and used liposomes to eliminate the liver Kupffer cells and evaluate their role. We performed bioinformatics analysis, reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and western blotting to detect mitochondrial apoptosis-induced changes in proteins from the B-cell lymphoma 2(Bcl-2) family. Succinic acid ameliorated ConA-induced AIH in a concentration-dependent manner, as reflected in the survival curve. HE and TUNEL staining and terminal deoxynucleotidyl transferase dUTP nick end labeling revealed decreased alanine transaminase and aspartate aminotransferase levels, and reduced liver inflammation and apoptosis. RT-qPCR and enzyme-linked immunosorbent assay revealed that succinic acid significantly reduced liver pro-inflammatory cytokine levels. Flow cytometry revealed significantly decreased levels of liver neutrophils. Moreover, the protective effect of succinic acid disappeared after the Kupffer cells were eliminated, confirming their important role in the effect. Bioinformatics analysis, RT-qPCR, and western blotting showed that succinic acid-induced changes in proteins from the Bcl-2 family involved mitochondrial apoptosis, indicating the molecular mechanism underlying the protective effect of succinic acid. Succinic acid ameliorated ConA-induced liver injury by regulating immune balance, inhibiting pro-inflammatory factors, and promoting anti-apoptotic proteins in the liver. This study provides novel insights into the biological functions and therapeutic potential of succinic acid in the treatment of autoimmune liver injury.}, }
@article {pmid38606974, year = {2024}, author = {Cardoso, PM and Hill, LJ and Villela, HDM and Vilela, CLS and Assis, JM and Rosado, PM and Rosado, JG and Chacon, MA and Majzoub, ME and Duarte, GAS and Thomas, T and Peixoto, RS}, title = {Localization and symbiotic status of probiotics in the coral holobiont.}, journal = {mSystems}, volume = {9}, number = {5}, pages = {e0026124}, pmid = {38606974}, issn = {2379-5077}, support = {FCC/1/1976-40-01,BAS/1/1095-01-0//King Abdullah University of Science and Technology (KAUST)/ ; }, mesh = {*Anthozoa/microbiology/physiology ; *Symbiosis/physiology ; Animals ; *Probiotics/pharmacology ; In Situ Hybridization, Fluorescence ; Halomonas/physiology ; Microbiota/physiology ; }, abstract = {UNLABELLED: Corals establish symbiotic relationships with microorganisms, especially endosymbiotic photosynthetic algae. Although other microbes have been commonly detected in coral tissues, their identity and beneficial functions for their host are unclear. Here, we confirm the beneficial outcomes of the inoculation of bacteria selected as probiotics and use fluorescence in situ hybridization (FISH) to define their localization in the coral Pocillopora damicornis. Our results show the first evidence of the inherent presence of Halomonas sp. and Cobetia sp. in native coral tissues, even before their inoculation. Furthermore, the relative enrichment of these coral tissue-associated bacteria through their inoculation in corals correlates with health improvements, such as increases in photosynthetic potential, and productivity. Our study suggests the symbiotic status of Halomonas sp. and Cobetia sp. in corals by indicating their localization within coral gastrodermis and epidermis and correlating their increased relative abundance through active inoculation with beneficial outcomes for the holobiont. This knowledge is crucial to facilitate the screening and application of probiotics that may not be transient members of the coral microbiome.<br><br>IMPORTANCE: Despite the promising results indicating the beneficial outcomes associated with the application of probiotics in corals and some scarce knowledge regarding the identity of bacterial cells found within the coral tissue, the correlation between these two aspects is still missing. This gap limits our understanding of the actual diversity of coral-associated bacteria and whether these symbionts are beneficial. Some researchers, for example, have been suggesting that probiotic screening should only focus on the very few known tissue-associated bacteria, such as Endozoicomonas sp., assuming that the currently tested probiotics are not tissue-associated. Here, we provide specific FISH probes for Halomonas sp. and Cobetia sp., expand our knowledge of the identity of coral-associated bacteria and confirm the probiotic status of the tested probiotics. The presence of these beneficial microorganisms for corals (BMCs) inside host tissues and gastric cavities also supports the notion that direct interactions with the host may underpin their probiotic role. This is a new breakthrough; these results argue against the possibility that the positive effects of BMCs are due to factors that are not related to a direct symbiotic interaction, for example, that the host simply feeds on inoculated bacteria or that the bacteria change the water quality.}, }
@article {pmid38602612, year = {2024}, author = {Xie, Y and Fan, Y and Su, M and Wang, Y and Zhang, G}, title = {Characteristics of the oral microbiota in patients with primary Sjögren's syndrome.}, journal = {Clinical rheumatology}, volume = {43}, number = {6}, pages = {1939-1947}, pmid = {38602612}, issn = {1434-9949}, support = {2019-106-21//Shantou Medical Health Science and Technology Plan/ ; A2019244//Medical Science Research Foundation of Guangdong Province/ ; }, mesh = {Humans ; *Sjogren's Syndrome/microbiology ; Female ; Middle Aged ; *Saliva/microbiology ; *Microbiota ; Male ; Adult ; *Mouth/microbiology ; *RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Aged ; High-Throughput Nucleotide Sequencing ; Dental Plaque/microbiology ; Dental Caries/microbiology ; }, abstract = {OBJECTIVE: Primary Sjögren's syndrome (pSS) is an autoimmune disease with unknown etiology that is considered to be related to environmental and genetic factors. The aim of this study was to clarify the oral microflora characteristics of pSS patients and to reveal the connection between oral bacterial composition and dental caries using a high-throughput sequencing technique.<br><br>METHODS: Thirty-five pSS patients and 20 healthy controls were enrolled in this study. We collected saliva and plaque samples from pSS patients and saliva samples from healthy controls. We used 16S ribosomal DNA (16S rDNA) high-throughput sequencing targeting the V3-V4 hypervariable region to determine the composition and structure of the microbiota in the three sample sets. Finally, bioinformatics analyses, including the diversity of the microbiota, species differences, and functional prediction were performed.<br><br>RESULTS: In the alpha diversity and beta diversity analysis, the Chao1 (P&#x2009;<&#x2009;0.01), observed species (P&#x2009;<&#x2009;0.01), and PD whole tree indices (P&#x2009;<&#x2009;0.01) were significantly lower in the saliva and plaque samples of pSS patients than in the saliva samples of healthy controls, but the Shannon (P&#x2009;<&#x2009;0.01) and Simpson indices (P&#x2009;<&#x2009;0.01) were significantly higher in the healthy controls, and their total diversity significantly differed. In the main flora composition at the genus level (top 10), we identified Prevotella and Veillonella as more enriched in the saliva of pSS patients and Fusobacterium, Actinomyces, and Leptotrichia as more enriched in the plaque of pSS patients. Predictive functional analysis showed that the oral microbiota of pSS patients was related to translation, metabolism of cofactors and vitamins, and nucleotide metabolism.<br><br>CONCLUSIONS: The oral microbial ecology of patients with pSS is dysregulated, resulting in a decrease in overall diversity. Prevotella and Veillonella may be related to pSS, while Fusobacterium, Actinomyces, and Leptotrichia may be related to dental caries in pSS patients. Key Points &#x2022; This study revealed differences in the oral microbial composition of patients with pSS compared to healthy controls. &#x2022; We included a plaque group of pSS patients to identify the microbiota related to pSS and dental caries. &#x2022; Prevotella and Veillonella may contribute to pSS, and Fusobacterium, Actinomyces, and Leptotrichia are associated with dental caries in pSS patients.}, }
@article {pmid38602532, year = {2024}, author = {Xing, H and Chen, W and Liu, Y and Cahill, JF}, title = {Local Community Assembly Mechanisms and the Size of Species Pool Jointly Explain the Beta Diversity of Soil Fungi.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {58}, pmid = {38602532}, issn = {1432-184X}, support = {31670531 and 32071645//National Natural Science Foundation of China/ ; 2022JBGS04 and 2023JBGS06//Research Project of Baishanzu National Park/ ; }, mesh = {China ; Forests ; Gamma Rays ; *Microbiota ; *Mycorrhizae ; Soil ; }, abstract = {Fungi play vital regulatory roles in terrestrial ecosystems. Local community assembly mechanisms, including deterministic and stochastic processes, as well as the size of regional species pools (gamma diversity), typically influence overall soil microbial community beta diversity patterns. However, there is limited evidence supporting their direct and indirect effects on beta diversity of different soil fungal functional groups in forest ecosystems. To address this gap, we collected 1606 soil samples from a 25-ha subtropical forest plot in southern China. Our goal was to determine the direct effects and indirect effects of regional species pools on the beta diversity of soil fungi, specifically arbuscular mycorrhizal (AM), ectomycorrhizal (EcM), plant-pathogenic, and saprotrophic fungi. We quantified the effects of soil properties, mycorrhizal tree abundances, and topographical factors on soil fungal diversity. The beta diversity of plant-pathogenic fungi was predominantly influenced by the size of the species pool. In contrast, the beta diversity of EcM fungi was primarily driven indirectly through community assembly processes. Neither of them had significant effects on the beta diversity of AM and saprotrophic fungi. Our results highlight that the direct and indirect effects of species pools on the beta diversity of soil functional groups of fungi can significantly differ even within a relatively small area. They also demonstrate the independent and combined effects of various factors in regulating the diversities of soil functional groups of fungi. Consequently, it is crucial to study the fungal community not only as a whole but also by considering different functional groups within the community.}, }
@article {pmid38602492, year = {2024}, author = {Machushynets, NV and Al Ayed, K and Terlouw, BR and Du, C and Buijs, NP and Willemse, J and Elsayed, SS and Schill, J and Trebosc, V and Pieren, M and Alexander, FM and Cochrane, SA and Liles, MR and Medema, MH and Martin, NI and van Wezel, GP}, title = {Discovery and Derivatization of Tridecaptin Antibiotics with Altered Host Specificity and Enhanced Bioactivity.}, journal = {ACS chemical biology}, volume = {19}, number = {5}, pages = {1106-1115}, pmid = {38602492}, issn = {1554-8937}, mesh = {*Anti-Bacterial Agents/pharmacology/chemistry ; *Pseudomonas aeruginosa/drug effects ; Humans ; *Microbial Sensitivity Tests ; Host Specificity ; Drug Discovery ; Lipopeptides/pharmacology/chemistry ; Peptides ; }, abstract = {The prevalence of multidrug-resistant (MDR) pathogens combined with a decline in antibiotic discovery presents a major challenge for health care. To refill the discovery pipeline, we need to find new ways to uncover new chemical entities. Here, we report the global genome mining-guided discovery of new lipopeptide antibiotics tridecaptin A5 and tridecaptin D, which exhibit unusual bioactivities within their class. The change in the antibacterial spectrum of Oct-TriA5 was explained solely by a Phe to Trp substitution as compared to Oct-TriA1, while Oct-TriD contained 6 substitutions. Metabolomic analysis of producer Paenibacillus sp. JJ-21 validated the predicted amino acid sequence of tridecaptin A5. Screening of tridecaptin analogues substituted at position 9 identified Oct-His9 as a potent congener with exceptional efficacy against Pseudomonas aeruginosa and reduced hemolytic and cytotoxic properties. Our work highlights the promise of tridecaptin analogues to combat MDR pathogens.}, }
@article {pmid38598334, year = {2024}, author = {Wei, X and Tsai, MS and Liang, L and Jiang, L and Hung, CJ and Jelliffe-Pawlowski, L and Rand, L and Snyder, M and Jiang, C}, title = {Vaginal microbiomes show ethnic evolutionary dynamics and positive selection of Lactobacillus adhesins driven by a long-term niche-specific process.}, journal = {Cell reports}, volume = {43}, number = {4}, pages = {114078}, doi = {10.1016/j.celrep.2024.114078}, pmid = {38598334}, issn = {2211-1247}, mesh = {Humans ; *Vagina/microbiology ; Female ; *Microbiota/genetics ; *Lactobacillus/genetics ; Adhesins, Bacterial/genetics ; Ethnicity/genetics ; Adult ; Evolution, Molecular ; Pregnancy ; Selection, Genetic ; Biological Evolution ; }, abstract = {The vaginal microbiome's composition varies among ethnicities. However, the evolutionary landscape of the vaginal microbiome in the multi-ethnic context remains understudied. We perform a systematic evolutionary analysis of 351 vaginal microbiome samples from 35 multi-ethnic pregnant women, in addition to two validation cohorts, totaling 462 samples from 90 women. Microbiome alpha diversity and community state dynamics show strong ethnic signatures. Lactobacillaceae have a higher ratio of non-synonymous to synonymous polymorphism and lower nucleotide diversity than non-Lactobacillaceae in all ethnicities, with a large repertoire of positively selected genes, including the mucin-binding and cell wall anchor genes. These evolutionary dynamics are driven by the long-term evolutionary process unique to the human vaginal niche. Finally, we propose an evolutionary model reflecting the environmental niches of microbes. Our study reveals the extensive ethnic signatures in vaginal microbial ecology and evolution, highlighting the importance of studying the host-microbiome ecosystem from an evolutionary perspective.}, }
@article {pmid38593340, year = {2024}, author = {Suárez-Moo, P and Prieto-Davó, A}, title = {Biosynthetic potential of the sediment microbial subcommunities of an unexplored karst ecosystem and its ecological implications.}, journal = {MicrobiologyOpen}, volume = {13}, number = {2}, pages = {e1407}, pmid = {38593340}, issn = {2045-8827}, support = {//Consejo Nacional de Humanidades Ciencias y Tecnolog&#xed;as (CONAHCYT), M&#xe9;xico project A1-S-10785 (APD) and postdoctoral fellowship (362331) (PSM)/ ; }, mesh = {Bacteria/genetics ; Metagenome ; *Microbiota ; Multigene Family ; *Bacillaceae/genetics ; *Biological Products ; Biosynthetic Pathways/genetics ; }, abstract = {Microbial communities from various environments have been studied in the quest for new natural products with a broad range of applications in medicine and biotechnology. We employed an enrichment method and genome mining tools to examine the biosynthetic potential of microbial communities in the sediments of a coastal sinkhole within the karst ecosystem of the Yucatán Peninsula, Mexico. Our investigation led to the detection of 203 biosynthetic gene clusters (BGCs) and 55 secondary metabolites (SMs) within 35 high-quality metagenome-assembled genomes (MAGs) derived from these subcommunities. The most abundant types of BGCs were Terpene, Nonribosomal peptide-synthetase, and Type III polyketide synthase. Some of the in silico identified BGCs and SMs have been previously reported to exhibit biological activities against pathogenic bacteria and fungi. Others could play significant roles in the sinkhole ecosystem, such as iron solubilization and osmotic stress protection. Interestingly, 75% of the BGCs showed no sequence homology with bacterial BGCs previously reported in the MiBIG database. This suggests that the microbial communities in this environment could be an untapped source of genes encoding novel specialized compounds. The majority of the BGCs were identified in pathways found in the genus Virgibacillus, followed by Sporosarcina, Siminovitchia, Rhodococcus, and Halomonas. The latter, along with Paraclostridium and Lysinibacillus, had the highest number of identified BGC types. This study offers fresh insights into the potential ecological role of SMs from sediment microbial communities in an unexplored environment, underscoring their value as a source of novel natural products.}, }
@article {pmid38593079, year = {2024}, author = {Zhong, Q and Liao, B and Liu, J and Shen, W and Wang, J and Wei, L and Ma, Y and Dong, PT and Bor, B and McLean, JS and Chang, Y and Shi, W and Cen, L and Wu, M and Liu, J and Li, Y and He, X and Le, S}, title = {Episymbiotic Saccharibacteria TM7x modulates the susceptibility of its host bacteria to phage infection and promotes their coexistence.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {16}, pages = {e2319790121}, pmid = {38593079}, issn = {1091-6490}, support = {R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 GM110243/GM/NIGMS NIH HHS/United States ; R01 AI087946/AI/NIAID NIH HHS/United States ; R01 GM124378/GM/NIGMS NIH HHS/United States ; R01 AI152421/AI/NIAID NIH HHS/United States ; R01 DE030943/DE/NIDCR NIH HHS/United States ; R01 AI132818/AI/NIAID NIH HHS/United States ; R01 DE031274/DE/NIDCR NIH HHS/United States ; S10 OD023603/OD/NIH HHS/United States ; }, mesh = {Humans ; *Bacteriophages/physiology ; Symbiosis ; Bacteria/genetics ; }, abstract = {Bacteriophages (phages) play critical roles in modulating microbial ecology. Within the human microbiome, the factors influencing the long-term coexistence of phages and bacteria remain poorly investigated. Saccharibacteria (formerly TM7) are ubiquitous members of the human oral microbiome. These ultrasmall bacteria form episymbiotic relationships with their host bacteria and impact their physiology. Here, we showed that during surface-associated growth, a human oral Saccharibacteria isolate (named TM7x) protects its host bacterium, a Schaalia odontolytica strain (named XH001) against lytic phage LC001 predation. RNA-Sequencing analysis identified in XH001 a gene cluster with predicted functions involved in the biogenesis of cell wall polysaccharides (CWP), whose expression is significantly down-regulated when forming a symbiosis with TM7x. Through genetic work, we experimentally demonstrated the impact of the expression of this CWP gene cluster on bacterial-phage interaction by affecting phage binding. In vitro coevolution experiments further showed that the heterogeneous populations of TM7x-associated and TM7x-free XH001, which display differential susceptibility to LC001 predation, promote bacteria and phage coexistence. Our study highlights the tripartite interaction between the bacterium, episymbiont, and phage. More importantly, we present a mechanism, i.e., episymbiont-mediated modulation of gene expression in host bacteria, which impacts their susceptibility to phage predation and contributes to the formation of "source-sink" dynamics between phage and bacteria in biofilm, promoting their long-term coexistence within the human microbiome.}, }
@article {pmid38591008, year = {2024}, author = {Kang, M and Liu, L and Grossart, HP}, title = {Spatio-temporal variations of methane fluxes in sediments of a deep stratified temperate lake.}, journal = {iScience}, volume = {27}, number = {4}, pages = {109520}, pmid = {38591008}, issn = {2589-0042}, abstract = {Spatio-temporal variability of sediment-mediated methane (CH4) production in freshwater lakes causes large uncertainties in predicting global lake CH4 emissions under different climate change and eutrophication scenarios. We conducted extensive sediment incubation experiments to investigate CH4 fluxes in Lake Stechlin, a deep, stratified temperate lake. Our results show contrasting spatial patterns in CH4 fluxes between littoral and profundal sites. The littoral sediments, ∼33% of the total sediment surface area, contributed ∼86.9% of the annual CH4 flux at the sediment-water interface. Together with sediment organic carbon quality, seasonal stratification is responsible for the striking spatial difference in sediment CH4 production between littoral and profundal zones owing to more sensitive CH4 production than oxidation to warming. While profundal sediments produce a relatively small amount of CH4, its production increases markedly as anoxia spreads in late summer. Our measurements indicate that future lake CH4 emissions will increase due to climate warming and concomitant hypoxia/anoxia.}, }
@article {pmid38589480, year = {2024}, author = {Sanchis Pla, L and van Gestel, J}, title = {Exploring the microbial savanna: predator-prey interactions in the soil.}, journal = {Molecular systems biology}, volume = {20}, number = {5}, pages = {477-480}, pmid = {38589480}, issn = {1744-4292}, support = {101116560//ERC Starting Grant/ ; }, mesh = {*Soil Microbiology ; Grassland ; Animals ; Food Chain ; Predatory Behavior ; Soil/chemistry ; }, abstract = {Soils host complex multi-trophic communities with diverse, mostly microbial, predator and prey species, including numerous bacterivorous protists and bacterial prey. The molecular mechanisms underlying microbial predator-prey interactions have thus far mainly been explored using reductionist methods, outside the soil environment and independent from the broader life history strategies that microbes display in soils. In this Comment, we advocate for an integrative research approach, combining molecular systems biology and microbial ecology, to investigate how predator-prey interactions shape microbial life history strategies and thereby population dynamics in natural soil communities.}, }
@article {pmid38587642, year = {2024}, author = {Srinivasan, S and Jnana, A and Murali, TS}, title = {Modeling Microbial Community Networks: Methods and Tools for Studying Microbial Interactions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {56}, pmid = {38587642}, issn = {1432-184X}, support = {CRG/2022/003227//Science and Engineering Research Board/ ; }, mesh = {Humans ; *Microbial Interactions ; *Microbiota ; Microbial Consortia ; Coculture Techniques ; Community Networks ; }, abstract = {Microbial interactions function as a fundamental unit in complex ecosystems. By characterizing the type of interaction (positive, negative, neutral) occurring in these dynamic systems, one can begin to unravel the role played by the microbial species. Towards this, various methods have been developed to decipher the function of the microbial communities. The current review focuses on the various qualitative and quantitative methods that currently exist to study microbial interactions. Qualitative methods such as co-culturing experiments are visualized using microscopy-based techniques and are combined with data obtained from multi-omics technologies (metagenomics, metabolomics, metatranscriptomics). Quantitative methods include the construction of networks and network inference, computational models, and development of synthetic microbial consortia. These methods provide a valuable clue on various roles played by interacting partners, as well as possible solutions to overcome pathogenic microbes that can cause life-threatening infections in susceptible hosts. Studying the microbial interactions will further our understanding of complex less-studied ecosystems and enable design of effective frameworks for treatment of infectious diseases.}, }
@article {pmid38587527, year = {2024}, author = {Garcia Mendez, DF and Egan, S and Wist, J and Holmes, E and Sanabria, J}, title = {Meta-analysis of the Microbial Diversity Cultured in Bioreactors Simulating the Gut Microbiome.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {57}, pmid = {38587527}, issn = {1432-184X}, support = {FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Bioreactors ; Feces ; }, abstract = {Understanding the intricate ecological interactions within the gut microbiome and unravelling its impact on human health is a challenging task. Bioreactors are valuable tools that have contributed to our understanding of gut microbial ecology. However, there is a lack of studies describing and comparing the microbial diversity cultivated in these models. This knowledge is crucial for refining current models to reflect the gastrointestinal microbiome accurately. In this study, we analysed the microbial diversity of 1512 samples from 18 studies available in public repositories that employed cultures performed in batches and various bioreactor models to cultivate faecal microbiota. Community structure comparison between samples using t-distributed stochastic neighbour embedding and the Hellinger distance revealed a high variation between projects. The main driver of these differences was the inter-individual variation between the donor faecal inocula. Moreover, there was no overlap in the structure of the microbial communities between studies using the same bioreactor platform. In addition, α-diversity analysis using Hill numbers showed that highly complex bioreactors did not exhibit higher diversities than simpler designs. However, analyses of five projects in which the samples from the faecal inoculum were also provided revealed an amplicon sequence variants enrichment in bioreactors compared to the inoculum. Finally, a comparative analysis of the taxonomy of the families detected in the projects and the GMRepo database revealed bacterial families exclusively found in the bioreactor models. These findings highlight the potential of bioreactors to enrich low-abundance microorganisms from faecal samples, contributing to uncovering the gut microbial "dark matter".}, }
@article {pmid38585661, year = {2024}, author = {Hill, LJ and Messias, CSMA and Vilela, CLS and Garritano, AN and Villela, HDM and do Carmo, FL and Thomas, T and Peixoto, RS}, title = {Bacteria associated with the in hospite Symbiodiniaceae's phycosphere.}, journal = {iScience}, volume = {27}, number = {4}, pages = {109531}, pmid = {38585661}, issn = {2589-0042}, abstract = {Symbiotic interactions between Symbiodiniaceae and bacteria are still poorly explored, especially those in hospite. Here, we adapted a technique that allows for the enrichment of intact and metabolically active in hospite Symbiodiniaceae cells (ihSC) and their associated bacteria from the tissue of the model coral Pocillopora damicornis, using a discontinuous gradient of solution of isotonic Percoll (SIP). The ihSC were concentrated in the 50% SIP fraction, as determined by microscopy. The presence of bacteria associated with ihSC was confirmed by fluorescence in situ hybridization, while microbiome analysis indicated that bacteria of the families Halieaceae, Flavobacteriaceae, and Alcanivoraceae are significantly associated with ihSC. Extracellular vesicles that could be exuding molecules were detected on the symbiosome membranes. Our technique and data contribute to elucidate ihSC-bacteria interactions.}, }
@article {pmid38585291, year = {2023}, author = {Hobusch, U and Scheuch, M and Heuckmann, B and Hodžić, A and Hobusch, GM and Rammel, C and Pfeffer, A and Lengauer, V and Froehlich, DE}, title = {One Health Education Nexus: enhancing synergy among science-, school-, and teacher education beyond academic silos.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1337748}, pmid = {38585291}, issn = {2296-2565}, mesh = {Humans ; Ecosystem ; *One Health ; *Teacher Training ; Students ; Schools ; Health Education ; Educational Status ; }, abstract = {INTRODUCTION: The fact that the daily lives of billions of people were affected by the medical, social, and political aspects of the SARS-CoV-2 pandemic shows the need to anchor the understanding of One Health in society. Hence, promoting awareness and deepening the understanding of the interrelation between human health, animal health, and ecosystems must be accomplished through quality education, as advocated by UN Sustainable Development Goal 4. The often-questioned and discussed measures taken by governments to control the global pandemic between 2020 and 2023 can be seen as an opportunity to meet the educational needs of civil society solutions in multi-stakeholder settings between public, universities, and schools.<br><br>METHODS: This paper focuses on the integration of One Health principles in educational frameworks, particularly within the context of the higher education teaching framework "Teaching Clinic." This master-level course in the domain of pre-service teacher education serves as a potent vehicle for facilitating One Health Education, bridging the gap between research, higher education, and schools. Through the presentation of two case studies, this article demonstrates how the Teaching Clinic approach fosters interdisciplinary perspectives and provides a dynamic learning environment for pre-service teachers, as well as for pupils involved in the educational process.<br><br>RESULTS: In both cases, the integration of educational One Health school teaching-learning settings effectively enhanced pupils' understanding of complex topics and engaged them in active learning experiences. Pre-service teachers played a crucial role in developing, implementing, and evaluating these interventions. In Case I, pupils demonstrated proficiency in analyzing data and evaluating mathematical models, while in Case II, the chosen instructional approach facilitated One Health knowledge acquisition and enjoyment among pupils. These results underscore the potential of the One Health Teaching Clinic as a valuable educational framework for enhancing teaching and learning outcomes for pre-service teachers and fostering pupil engagement in socio-scientific One Health-related topics.<br><br>DISCUSSION: The discussion delves into the significance of breaking down disciplinary silos and the crucial role of teacher education in promoting a holistic approach to education, emphasizing the intersectionality of One Health Education and Education for Sustainable Development. This article underpins the significance of collaborative efforts across multiple (scientific) disciplines and across secondary and tertiary education levels to reach a nexus. Moreover, it emphasizes the alignment of this approach with the 2030 Agenda, Education for Sustainable Development, and Sustainable Development Goals, highlighting the potential for collective action toward a more sustainable future.}, }
@article {pmid38581683, year = {2024}, author = {Loos, D and Filho, APDC and Dutilh, BE and Barber, AE and Panagiotou, G}, title = {A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists.}, journal = {Cell reports}, volume = {43}, number = {4}, pages = {114046}, doi = {10.1016/j.celrep.2024.114046}, pmid = {38581683}, issn = {2211-1247}, support = {/ERC_/European Research Council/International ; }, mesh = {*Soil Microbiology ; *Fungi/genetics/classification ; *Microbiota/genetics ; *Bacteria/genetics/classification ; Humans ; Biodiversity ; Genomics/methods ; Phylogeny ; }, abstract = {Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat change, we analyze thousands of genera detected in 1,580 host, soil, and aquatic samples. This large-scale analysis identifies 48 bacterial and 4 fungal genera that are abundant across the three biomes, demonstrating fitness in diverse environmental conditions. Samples containing these generalists have significantly higher alpha diversity. These generalists play a significant role in shaping cross-kingdom community structure, boasting larger genomes with more secondary metabolism and antimicrobial resistance genes. Conversely, 30 bacterial and 19 fungal genera are only found in a single habitat, suggesting a limited ability to adapt to different and changing environments. These findings contribute to our understanding of microbial niche breadth and its consequences for global biodiversity loss.}, }
@article {pmid38581020, year = {2024}, author = {Douillard, FP and Derman, Y and Jian, C and Korpela, K and Saxén, H and Salonen, A and de Vos, WM and Korkeala, H and Lindström, M}, title = {Case report: Aberrant fecal microbiota composition of an infant diagnosed with prolonged intestinal botulism.}, journal = {Gut pathogens}, volume = {16}, number = {1}, pages = {20}, pmid = {38581020}, issn = {1757-4749}, abstract = {BACKGROUND: Intestinal botulism is primarily reported in small babies as a condition known as infant botulism. The condition results from the ingestion of environmental or foodborne spores of botulinum neurotoxin (BoNT) producing Clostridia, usually Clostridium botulinum, and subsequent spore germination into active botulinum neurotoxinogenic cultures in the gut. It is generally considered that small babies are susceptible to C. botulinum colonization because of their immature gut microbiota. Yet, it is poorly understood which host factors contribute to the clinical outcome of intestinal botulism. We previously reported a case of infant botulism where the infant recovered clinically in six weeks but continued to secrete C. botulinum cells and/or BoNT in the feces for seven months.<br><br>CASE PRESENTATION: To further understand the microbial ecology behind this exceptionally long-lasting botulinum neurotoxinogenic colonization, we characterized the infant fecal microbiota using 16S rRNA gene amplicon sequencing over the course of disease and recovery. C. botulinum could be detected in the infant fecal samples at low levels through the acute phase of the disease and three months after recovery. Overall, we observed a temporal delay in the maturation of the infant fecal microbiota associated with a persistently high-level bifidobacterial population and a low level of Lachnospiraceae, Bacteroidaceae and Ruminococcaceae compared to healthy infants over time.<br><br>CONCLUSION: This study brings novel insights into the infant fecal composition associated with intestinal botulism and provides a basis for a more systematic analysis of the gut microbiota of infants diagnosed with botulism. A better understanding of the gut microbial ecology associated with infant botulism may support the development of prophylactic strategies against this life-threatening disease in small babies.}, }
@article {pmid38579997, year = {2024}, author = {Cao, Y and Li, Y and Jia, L and Wang, Q and Niu, T and Yang, Q and Wang, Q and Zeng, X and Wang, R and Yue, L}, title = {Long-term and combined heavy-metal contamination forms a unique microbiome and resistome: A case study in a Yellow River tributary sediments.}, journal = {Environmental research}, volume = {252}, number = {Pt 1}, pages = {118861}, doi = {10.1016/j.envres.2024.118861}, pmid = {38579997}, issn = {1096-0953}, mesh = {*Metals, Heavy/toxicity/analysis ; *Geologic Sediments/microbiology/chemistry ; *Rivers/microbiology/chemistry ; *Microbiota/drug effects ; *Water Pollutants, Chemical/analysis/toxicity ; China ; Environmental Monitoring ; Bacteria/genetics/drug effects ; }, abstract = {Microorganisms have developed mechanisms to adapt to environmental stress, but how microbial communities adapt to long-term and combined heavy-metal contamination under natural environmental conditions remains unclear. Specifically, this study analyzed the characteristics of heavy metal composition, microbial community, and heavy metal resistance genes (MRGs) in sediments along Mang River, a tributary of the Yellow River, which has been heavily polluted by industrial production for more than 40 years. The results showed that the concentrations of Cr, Zn, Pb, Cu and As in most sediments were higher than the ambient background values. Bringing the heavy metals speciation and concentration into the risk evaluation method, two-thirds of the sediment samples were at or above the moderate risk level, and the ecological risk of combined heavy metals in the sediments decreased along the river stream. The high ecological risk of heavy metals affected the microbial community structure, metabolic pathways and MRG distribution. The formation of a HM-resistant microbiome possibly occurred through the spread of insertion sequences (ISs) carrying multiple MRGs, the types of ISs carrying MRGs outnumber those of plasmids, and the quantity of MRGs on ISs is also higher than that on plasmids. These findings could improve our understanding of the adaptation mechanism of microbial communities to long-term combined heavy metal contamination.}, }
@article {pmid38578091, year = {2024}, author = {Morrison, BH and Jones, JL and Dzwonkowski, B and Krause, JW}, title = {Tracking Vibrio: population dynamics and ecology of Vibrio parahaemolyticus and V. vulnificus in an Alabama estuary.}, journal = {Microbiology spectrum}, volume = {12}, number = {5}, pages = {e0367423}, pmid = {38578091}, issn = {2165-0497}, support = {U19 FD005923/FD/FDA HHS/United States ; #5U19FD005923-04//HHS | U.S. Food and Drug Administration (FDA)/ ; }, mesh = {*Vibrio parahaemolyticus/isolation &amp; purification/growth &amp; development ; *Vibrio vulnificus/isolation &amp; purification/growth &amp; development ; *Estuaries ; Alabama ; Population Dynamics ; Salinity ; Vibrio Infections/microbiology/epidemiology ; Seawater/microbiology ; Water Microbiology ; }, abstract = {UNLABELLED: Vibrio is a genus of halophilic, gram-negative bacteria found in estuaries around the globe. Integral parts of coastal cultures often involve contact with vectors of pathogenic Vibrio spp. (e.g., consuming raw shellfish). High rates of mortality from certain Vibrio spp. infections demonstrate the need for an improved understanding of Vibrio spp. dynamics in estuarine regions. Our study assessed meteorological, hydrographic, and biological correlates of Vibrio parahaemolyticus and V. vulnificus at 10 sites in the Eastern Mississippi Sound System (EMSS) from April to October 2019. During the sampling period, median abundances of V. parahaemolyticus and V. vulnificus were 2.31 log MPN/L and 2.90 log MPN/L, respectively. Vibrio spp. dynamics were largely driven by site-based variation, with sites closest to freshwater inputs having the highest abundances. The E-W wind scalar, which affects Ekman transport, was a novel Vibrio spp. correlate observed. A potential salinity effect on bacterial-particle associations was identified, where V. vulnificus was associated with larger particles in conditions outside of their optimal salinity. Additionally, V. vulnificus abundances were correlated to those of harmful algal species that did not dominate community chlorophyll. Correlates from this study may be used to inform the next iteration of regionally predictive Vibrio models and may lend additional insight to Vibrio spp. ecology in similar systems.<br><br>IMPORTANCE: Vibrio spp. are bacteria found in estuaries worldwide; some species can cause illness and infections in humans. Relationships between Vibrio spp. abundance, salinity, and temperature are well documented, but correlations to other environmental parameters are less understood. This study identifies unique correlates (e.g., E-W wind scalar and harmful algal species) that could potentially inform the next iteration of predictive Vibrio models for the EMSS region. Additionally, these correlates may allow existing environmental monitoring efforts to be leveraged in providing data inputs for future Vibrio risk models. An observed correlation between salinity and V. vulnificus/particle-size associations suggests that predicted environmental changes may affect the abundance of Vibrio spp. in certain reservoirs, which may alter which vectors present the greatest vibrio risk.}, }
@article {pmid38575035, year = {2024}, author = {Zheng, W and Wu, Q and Guo, X and Zhou, P and Wu, J and Yan, W}, title = {Rocky desertification succession alters soil microbial communities and survival strategies in the karst context.}, journal = {The Science of the total environment}, volume = {927}, number = {}, pages = {172171}, doi = {10.1016/j.scitotenv.2024.172171}, pmid = {38575035}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Microbiota ; *Fungi ; *Soil/chemistry ; Archaea/genetics/physiology ; Ecosystem ; Conservation of Natural Resources ; }, abstract = {Rocky desertification is one of the most ecological problems in the karst context. Although extensive research has been conducted to explore how to restore and protect, the responses of soil fungi and archaea to rocky desertification succession remain limited. Here, four grades of rocky desertification in a karst ecosystem were selected, amplicon sequencing analysis was conducted to investigate fungal and archaeal community adaptation in response to rocky desertification succession. Our findings revealed that the diversity and community structure of fungi and archaea in soils declined with the aggravation of rocky desertification. As the rocky desertification succession intensified, microbial interactions shifted from cooperation to competition. Microbial survival strategies were K-strategist and r-strategist dominated in the early and late stages of succession, respectively. Additionally, the driving factors affecting microorganisms have shifted from vegetation diversity to soil properties as the intensification of rocky desertification. Collectively, our study highlighted that plant diversity and soil properties play important roles on soil microbiomes in fragile karst ecosystems and that environmental factors induced by human activities might still be the dominant factor exacerbating rocky desertification, which could significantly enrich our understanding of microbial ecology within karst ecosystems.}, }
@article {pmid38574431, year = {2024}, author = {Cunha, ICMD and Silva, AVRD and Boleta, EHM and Pellegrinetti, TA and Zagatto, LFG and Zagatto, SDSS and Chaves, MG and Mendes, R and Patreze, CM and Tsai, SM and Mendes, LW}, title = {The interplay between the inoculation of plant growth-promoting rhizobacteria and the rhizosphere microbiome and their impact on plant phenotype.}, journal = {Microbiological research}, volume = {283}, number = {}, pages = {127706}, doi = {10.1016/j.micres.2024.127706}, pmid = {38574431}, issn = {1618-0623}, mesh = {*Rhizosphere ; Plants/microbiology ; Bacteria/genetics ; *Microbiota ; Soil/chemistry ; Phenotype ; Soil Microbiology ; Plant Roots/microbiology ; }, abstract = {Microbial inoculation stands as a pivotal strategy, fostering symbiotic relationships between beneficial microorganisms and plants, thereby enhancing nutrient uptake, bolstering resilience against environmental stressors, and ultimately promoting healthier and more productive plant growth. However, while the advantageous roles of inoculants are widely acknowledged, the precise and nuanced impacts of inoculation on the intricate interactions of the rhizosphere microbiome remain significantly underexplored. This study explores the impact of bacterial inoculation on soil properties, plant growth, and the rhizosphere microbiome. By employing various bacterial strains and a synthetic community (SynCom) as inoculants in common bean plants, the bacterial and fungal communities in the rhizosphere were assessed through 16 S rRNA and ITS gene sequencing. Concurrently, soil chemical parameters, plant traits, and gene expression were evaluated. The findings revealed that bacterial inoculation generally decreased pH and V%, while increasing H+Al and m% in the rhizosphere. It also decreased gene expression in plants related to detoxification, photosynthesis, and defense mechanisms, while enhancing bacterial diversity in the rhizosphere, potentially benefiting plant health. Specific bacterial strains showed varied impacts on rhizosphere microbiome assembly, predominantly affecting rhizospheric bacteria more than fungi, indirectly influencing soil conditions and plants. Notably, Paenibacillus polymyxa inoculation improved plant nitrogen (by 5.2%) and iron levels (by 28.1%), whereas Bacillus cereus boosted mycorrhization rates (by 70%). Additionally, inoculation led to increased complexity in network interactions within the rhizosphere (∼15%), potentially impacting plant health. Overall, the findings highlight the significant impact of introducing bacteria to the rhizosphere, enhancing nutrient availability, microbial diversity, and fostering beneficial plant-microbe interactions.}, }
@article {pmid38571798, year = {2024}, author = {Rani, V and Horváth, Z and Nejstgaard, JC and Fierpasz, &#xc1; and Pálffy, K and Vad, CF}, title = {Food density drives diet shift of the invasive mysid shrimp, Limnomysis benedeni.}, journal = {Ecology and evolution}, volume = {14}, number = {4}, pages = {e11202}, pmid = {38571798}, issn = {2045-7758}, abstract = {Understanding the diet preferences and food selection of invasive species is crucial to better predict their impact on community structure and ecosystem functioning. Limnomysis benedeni, a Ponto-Caspian invasive mysid shrimp, is one of the most successful invaders in numerous European river and lake ecosystems. While existing studies suggest potentially strong trophic impact due to high predation pressure on native plankton communities, little is known of its food selectivity between phyto- and zooplankton, under different food concentrations. Here, we therefore investigated the feeding selectivity of L. benedeni on two commonly occurring prey organisms in freshwaters, the small rotifer zooplankton Brachionus calyciflorus together with the microphytoplankton Cryptomonas sp. present in increasing densities. Our results demonstrated a clear shift in food selection, with L. benedeni switching from B. calyciflorus to Cryptomonas sp. already when the two prey species were provided in equal biomasses. Different functional responses were observed for the two food types, indicating somewhat different foraging mechanisms for each food type. These findings provide experimental evidence on the feeding flexibility of invasive mysid shrimps and potential implications for trophic interactions in invaded ecosystems.}, }
@article {pmid38567263, year = {2023}, author = {Crous, PW and Osieck, ER and Shivas, RG and Tan, YP and Bishop-Hurley, SL and Esteve-Raventós, F and Larsson, E and Luangsa-Ard, JJ and Pancorbo, F and Balashov, S and Baseia, IG and Boekhout, T and Chandranayaka, S and Cowan, DA and Cruz, RHSF and Czachura, P and De la Peña-Lastra, S and Dovana, F and Drury, B and Fell, J and Flakus, A and Fotedar, R and Jurjević, &#x17d; and Kolecka, A and Mack, J and Maggs-Kölling, G and Mahadevakumar, S and Mateos, A and Mongkolsamrit, S and Noisripoom, W and Plaza, M and Overy, DP and Piątek, M and Sandoval-Denis, M and Vauras, J and Wingfield, MJ and Abell, SE and Ahmadpour, A and Akulov, A and Alavi, F and Alavi, Z and Altés, A and Alvarado, P and Anand, G and Ashtekar, N and Assyov, B and Banc-Prandi, G and Barbosa, KD and Barreto, GG and Bellanger, JM and Bezerra, JL and Bhat, DJ and Bilański, P and Bose, T and Bozok, F and Chaves, J and Costa-Rezende, DH and Danteswari, C and Darmostuk, V and Delgado, G and Denman, S and Eichmeier, A and Etayo, J and Eyssartier, G and Faulwetter, S and Ganga, KGG and Ghosta, Y and Goh, J and Góis, JS and Gramaje, D and Granit, L and Groenewald, M and Gulden, G and Gusmão, LFP and Hammerbacher, A and Heidarian, Z and Hywel-Jones, N and Jankowiak, R and Kaliyaperumal, M and Kaygusuz, O and Kezo, K and Khonsanit, A and Kumar, S and Kuo, CH and Læssøe, T and Latha, KPD and Loizides, M and Luo, SM and Maciá-Vicente, JG and Manimohan, P and Marbach, PAS and Marinho, P and Marney, TS and Marques, G and Martín, MP and Miller, AN and Mondello, F and Moreno, G and Mufeeda, KT and Mun, HY and Nau, T and Nkomo, T and Okrasińska, A and Oliveira, JPAF and Oliveira, RL and Ortiz, DA and Pawłowska, J and Pérez-De-Gregorio, M&#xc0; and Podile, AR and Portugal, A and Privitera, N and Rajeshkumar, KC and Rauf, I and Rian, B and Rigueiro-Rodríguez, A and Rivas-Torres, GF and Rodriguez-Flakus, P and Romero-Gordillo, M and Saar, I and Saba, M and Santos, CD and Sarma, PVSRN and Siquier, JL and Sleiman, S and Spetik, M and Sridhar, KR and Stryjak-Bogacka, M and Szczepańska, K and Taşkın, H and Tennakoon, DS and Thanakitpipattana, D and Trovão, J and Türkekul, I and van Iperen, AL and van 't Hof, P and Vasquez, G and Visagie, CM and Wingfield, BD and Wong, PTW and Yang, WX and Yarar, M and Yarden, O and Yilmaz, N and Zhang, N and Zhu, YN and Groenewald, JZ}, title = {Fungal Planet description sheets: 1478-1549.}, journal = {Persoonia}, volume = {50}, number = {}, pages = {158-310}, pmid = {38567263}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Aschersonia mackerrasiae on whitefly, Cladosporium corticola on bark of Melaleuca quinquenervia, Penicillium nudgee from soil under Melaleuca quinquenervia, Pseudocercospora blackwoodiae on leaf spot of Persoonia falcata, and Pseudocercospora dalyelliae on leaf spot of Senna alata. Bolivia, Aspicilia lutzoniana on fully submersed siliceous schist in high-mountain streams, and Niesslia parviseta on the lower part and apothecial discs of Erioderma barbellatum on a twig. Brazil, Cyathus bonsai on decaying wood, Geastrum albofibrosum from moist soil with leaf litter, Laetiporus pratigiensis on a trunk of a living unknown hardwood tree species, and Scytalidium synnematicum on dead twigs of unidentified plant. Bulgaria, Amanita abscondita on sandy soil in a plantation of Quercus suber. Canada, Penicillium acericola on dead bark of Acer saccharum, and Penicillium corticola on dead bark of Acer saccharum. China, Colletotrichum qingyuanense on fruit lesion of Capsicum annuum. Denmark, Helminthosphaeria leptospora on corticioid Neohypochnicium cremicolor. Ecuador (Galapagos), Phaeosphaeria scalesiae on Scalesia sp. Finland, Inocybe jacobssonii on calcareous soils in dry forests and park habitats. France, Cortinarius rufomyrrheus on sandy soil under Pinus pinaster, and Periconia neominutissima on leaves of Poaceae. India, Coprinopsis fragilis on decaying bark of logs, Filoboletus keralensis on unidentified woody substrate, Penicillium sankaranii from soil, Physisporinus tamilnaduensis on the trunk of Azadirachta indica, and Poronia nagaraholensis on elephant dung. Iran, Neosetophoma fici on infected leaves of Ficus elastica. Israel, Cnidariophoma eilatica (incl. Cnidariophoma gen. nov.) from Stylophora pistillata. Italy, Lyophyllum obscurum on acidic soil. Namibia, Aureobasidium faidherbiae on dead leaf of Faidherbia albida, and Aureobasidium welwitschiae on dead leaves of Welwitschia mirabilis. Netherlands, Gaeumannomycella caricigena on dead culms of Carex elongata, Houtenomyces caricicola (incl. Houtenomyces gen. nov.) on culms of Carex disticha, Neodacampia ulmea (incl. Neodacampia gen. nov.) on branch of Ulmus laevis, Niesslia phragmiticola on dead standing culms of Phragmites australis, Pseudopyricularia caricicola on culms of Carex disticha, and Rhodoveronaea nieuwwulvenica on dead bamboo sticks. Norway, Arrhenia similis half-buried and moss-covered pieces of rotting wood in grass-grown path. Pakistan, Mallocybe ahmadii on soil. Poland, Beskidomyces laricis (incl. Beskidomyces gen. nov.) from resin of Larix decidua ssp. polonica, Lapidomyces epipinicola from sooty mould community on Pinus nigra, and Leptographium granulatum from a gallery of Dendroctonus micans on Picea abies. Portugal, Geoglossum azoricum on mossy areas of laurel forest areas planted with Cryptomeria japonica, and Lunasporangiospora lusitanica from a biofilm covering a biodeteriorated limestone wall. Qatar, Alternaria halotolerans from hypersaline sea water, and Alternaria qatarensis from water sample collected from hypersaline lagoon. South Africa, Alfaria thamnochorti on culm of Thamnochortus fraternus, Knufia aloeicola on Aloe gariepensis, Muriseptatomyces restionacearum (incl. Muriseptatomyces gen. nov.) on culms of Restionaceae, Neocladosporium arctotis on nest of cases of bag worm moths (Lepidoptera, Psychidae) on Arctotis auriculata, Neodevriesia scadoxi on leaves of Scadoxus puniceus, Paraloratospora schoenoplecti on stems of Schoenoplectus lacustris, Tulasnella epidendrea from the roots of Epidendrum × obrienianum, and Xenoidriella cinnamomi (incl. Xenoidriella gen. nov.) on leaf of Cinnamomum camphora. South Korea, Lemonniera fraxinea on decaying leaves of Fraxinus sp. from pond. Spain, Atheniella lauri on the bark of fallen trees of Laurus nobilis, Halocryptovalsa endophytica from surface-sterilised, asymptomatic roots of Salicornia patula, Inocybe amygdaliolens on soil in mixed forest, Inocybe pityusarum on calcareous soil in mixed forest, Inocybe roseobulbipes on acidic soils, Neonectria borealis from roots of Vitis berlandieri × Vitis rupestris, Sympoventuria eucalyptorum on leaves of Eucalyptus sp., and Tuber conchae from soil. Sweden, Inocybe bidumensis on calcareous soil. Thailand, Cordyceps sandindaengensis on Lepidoptera pupa, buried in soil, Ophiocordyceps kuchinaraiensis on Coleoptera larva, buried in soil, and Samsoniella winandae on Lepidoptera pupa, buried in soil. Taiwan region (China), Neophaeosphaeria livistonae on dead leaf of Livistona rotundifolia. Türkiye, Melanogaster anatolicus on clay loamy soils. UK, Basingstokeomyces allii (incl. Basingstokeomyces gen. nov.) on leaves of Allium schoenoprasum. Ukraine, Xenosphaeropsis corni on recently dead stem of Cornus alba. USA, Nothotrichosporon aquaticum (incl. Nothotrichosporon gen. nov.) from water, and Periconia philadelphiana from swab of coil surface. Morphological and culture characteristics for these new taxa are supported by DNA barcodes. Citation: Crous PW, Osieck ER, Shivas RG, et al. 2023. Fungal Planet description sheets: 1478-1549. Persoonia 50: 158- 310. https://doi.org/10.3767/persoonia.2023.50.05.}, }
@article {pmid38562743, year = {2024}, author = {Matz, LM and Shah, NS and Porterfield, L and Stuyck, OM and Jochum, MD and Kayed, R and Taglialatela, G and Urban, RJ and Buffington, SA}, title = {Microbial determinants of dementia risk in subjects of Mexican descent with type 2 diabetes living in South Texas.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {38562743}, support = {P30 ES030285/ES/NIEHS NIH HHS/United States ; T32 AG067952/AG/NIA NIH HHS/United States ; UL1 TR001439/TR/NCATS NIH HHS/United States ; }, abstract = {Type 2 diabetes (T2D) is a common forerunner of neurodegeneration and dementia, including Alzheimer's Disease (AD), yet the underlying mechanisms remain unresolved. Individuals of Mexican descent living in South Texas have increased prevalence of comorbid T2D and early onset AD, despite low incidence of the predisposing APOE-e4 variant and an absence of the phenotype among relatives residing in Mexico - suggesting a role for environmental factors in coincident T2D and AD susceptibility. Here, in a small clinical trial, we show dysbiosis of the human gut microbiome could contribute to neuroinflammation and risk for AD in this population. Divergent Gastrointestinal Symptom Rating Scale (GSRS) responses, despite no differences in expressed dietary preferences, provided the first evidence for altered gut microbial ecology among T2D subjects (sT2D) versus population-matched healthy controls (HC). Metataxonomic 16S rRNA sequencing of participant stool revealed a decrease in alpha diversity of sT2D versus HC gut communities and identified BMI as a driver of gut community structure. Linear discriminant analysis effect size (LEfSe) identified a significant decrease in the relative abundance of the short-chain fatty acid-producing taxa Lachnospiraceae, Faecalibacterium, and Alistipes and an increase in pathobionts Escherichia-Shigella, Enterobacter, and Clostridia innocuum among sT2D gut microbiota, as well as differentially abundant gene and metabolic pathways. These results suggest characterization of the gut microbiome of individuals with T2D could identify key actors among "disease state" microbiota which may increase risk for or accelerate the onset of neurodegeneration. Furthermore, they identify candidate microbiome-targeted approaches for prevention and treatment of neuroinflammation in AD.}, }
@article {pmid38562476, year = {2024}, author = {Zhang, R and Zhang, H and Yang, C and Li, H and Wu, J}, title = {Effects of water stress on nutrients and enzyme activity in rhizosphere soils of greenhouse grape.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1376849}, pmid = {38562476}, issn = {1664-302X}, abstract = {In grape cultivation, incorrect water regulation will lead to significant water wastage, which in turn will change soil structure and disrupt soil nutrient cycling processes. This study aimed to investigate the effects of different water regulation treatments [by setting moderate water stress (W1), mild water stress (W2), and adequate water availability (CK)] on soil physical-chemical properties and enzyme activity in greenhouse grape during the growing season. The result showed that the W2 treatment had a negative impact on the build-up of dissolved organic carbon (DOC), nitrate nitrogen (NO3-N), and available phosphorus (AP). Throughout the reproductive period, the W1 and W2 treatments decreased the soil's microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) contents, and MBC was more vulnerable to water stress. During the growth period, the trends of urease, catalase, and sucrase activities in different soil depth were ranked as 10-20 cm > 0-10 cm > 20-40 cm. The urease activity in 0-10 cm soil was suppressed by both W1 and W2 treatments, while the invertase activity in various soil layers under W1 treatment differed substantially. The W1 treatment also reduced the catalase activity in the 20-40 cm soil layer in the grape growth season. These findings suggested that W2 treatment can conserve water and enhance microbial ecology of greenhouse grape soils. Therefore, W2 treatment was the most effective water regulation measure for local greenhouse grape cultivation.}, }
@article {pmid38562261, year = {2024}, author = {Zünd, JN and Plüss, S and Mujezinovic, D and Menzi, C and von Bieberstein, PR and de Wouters, T and Lacroix, C and Leventhal, GE and Pugin, B}, title = {A flexible high-throughput cultivation protocol to assess the response of individuals' gut microbiota to diet-, drug-, and host-related factors.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae035}, pmid = {38562261}, issn = {2730-6151}, abstract = {The anaerobic cultivation of fecal microbiota is a promising approach to investigating how gut microbial communities respond to specific intestinal conditions and perturbations. Here, we describe a flexible protocol using 96-deepwell plates to cultivate stool-derived gut microbiota. Our protocol aims to address gaps in high-throughput culturing in an anaerobic chamber. We characterized the influence of the gas phase on the medium chemistry and microbial physiology and introduced a modular medium preparation process to enable the testing of several conditions simultaneously. Furthermore, we identified a medium formulation that maximized the compositional similarity of ex vivo cultures and donor microbiota while limiting the bloom of Enterobacteriaceae. Lastly, we validated the protocol by demonstrating that cultivated fecal microbiota responded similarly to dietary fibers (resistant dextrin, soluble starch) and drugs (ciprofloxacin, 5-fluorouracil) as reported in vivo. This high-throughput cultivation protocol has the potential to facilitate culture-dependent studies, accelerate the discovery of gut microbiota-diet-drug-host interactions, and pave the way to personalized microbiota-centered interventions.}, }
@article {pmid38555787, year = {2024}, author = {Mugani, R and El Khalloufi, F and Redouane, EM and Haida, M and Aba, RP and Essadki, Y and El Amrani Zerrifi, S and Hejjaj, A and Ouazzani, N and Campos, A and Grossart, HP and Mandi, L and Vasconcelos, V and Oudra, B}, title = {Unlocking the potential of bacterioplankton-mediated microcystin degradation and removal: A bibliometric analysis of sustainable water treatment strategies.}, journal = {Water research}, volume = {255}, number = {}, pages = {121497}, doi = {10.1016/j.watres.2024.121497}, pmid = {38555787}, issn = {1879-2448}, mesh = {*Microcystins/metabolism ; *Water Purification/methods ; Biodegradation, Environmental ; *Plankton/metabolism ; Bibliometrics ; Bacteria/metabolism ; }, abstract = {Microcystins (MCs) constitute a significant threat to human and environmental health, urging the development of effective removal methods for these toxins. In this review, we explore the potential of MC-degrading bacteria as a solution for the removal of MCs from water. The review insights into the mechanisms of action employed by these bacteria, elucidating their ability to degrade and thus remove MCs. After, the review points out the influence of the structural conformation of MCs on their removal, particularly their stability at different water depths within different water bodies. Then, we review the crucial role played by the production of MCs in ensuring the survival and safeguarding of the enzymatic activities of Microcystis cells. This justifies the need for developing effective and sustainable methods for removing MCs from aquatic ecosystems, given their critical ecological function and potential toxicity to humans and animals. Thereafter, challenges and limitations associated with using MC-degrading bacteria in water treatment are discussed, emphasizing the need for further research to optimize the selection of bacterial strains used for MCs biodegradation. The interaction of MCs-degrading bacteria with sediment particles is also crucial for their toxin removal potential and its efficiency. By presenting critical information, this review is a valuable resource for researchers, policymakers, and stakeholders involved in developing sustainable and practical approaches to remove MCs. Our review highlights the potential of various applications of MC-degrading bacteria, including multi-soil-layering (MSL) technologies. It emphasizes the need for ongoing research to optimize the utilization of MC-degrading bacteria in water treatment, ultimately ensuring the safety and quality of water sources. Moreover, this review highlights the value of bibliometric analyses in revealing research gaps and trends, providing detailed insights for further investigations. Specifically, we discuss the importance of employing advanced genomics, especially combining various OMICS approaches to identify and optimize the potential of MCs-degrading bacteria.}, }
@article {pmid38555472, year = {2024}, author = {Pan, J and Zhang, Z and Li, Y and Yu, J and You, Z and Li, C and Wang, S and Zhu, M and Ren, F and Zhang, X and Sun, Y and Wang, S}, title = {A microbial knowledge graph-based deep learning model for predicting candidate microbes for target hosts.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {3}, pages = {}, pmid = {38555472}, issn = {1477-4054}, support = {2022FY101100//Science &amp; Technology Fundamental Resources Investigation Program/ ; 62325308//National Science Fund for Distinguished Young Scholars of China/ ; 32170114//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Deep Learning ; Pattern Recognition, Automated ; Neural Networks, Computer ; Algorithms ; Bacteria ; }, abstract = {Predicting interactions between microbes and hosts plays critical roles in microbiome population genetics and microbial ecology and evolution. How to systematically characterize the sophisticated mechanisms and signal interplay between microbes and hosts is a significant challenge for global health risks. Identifying microbe-host interactions (MHIs) can not only provide helpful insights into their fundamental regulatory mechanisms, but also facilitate the development of targeted therapies for microbial infections. In recent years, computational methods have become an appealing alternative due to the high risk and cost of wet-lab experiments. Therefore, in this study, we utilized rich microbial metagenomic information to construct a novel heterogeneous microbial network (HMN)-based model named KGVHI to predict candidate microbes for target hosts. Specifically, KGVHI first built a HMN by integrating human proteins, viruses and pathogenic bacteria with their biological attributes. Then KGVHI adopted a knowledge graph embedding strategy to capture the global topological structure information of the whole network. A natural language processing algorithm is used to extract the local biological attribute information from the nodes in HMN. Finally, we combined the local and global information and fed it into a blended deep neural network (DNN) for training and prediction. Compared to state-of-the-art methods, the comprehensive experimental results show that our model can obtain excellent results on the corresponding three MHI datasets. Furthermore, we also conducted two pathogenic bacteria case studies to further indicate that KGVHI has excellent predictive capabilities for potential MHI pairs.}, }
@article {pmid38555095, year = {2024}, author = {Brame, JE and Warbrick, I and Heke, D and Liddicoat, C and Breed, MF}, title = {Short-term passive greenspace exposures have little effect on nasal microbiomes: A cross-over exposure study of a Māori cohort.}, journal = {Environmental research}, volume = {252}, number = {Pt 1}, pages = {118814}, doi = {10.1016/j.envres.2024.118814}, pmid = {38555095}, issn = {1096-0953}, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; Air Microbiology ; Air Pollutants/analysis ; Bacteria/genetics/classification/isolation &amp; purification ; Cohort Studies ; Cross-Over Studies ; Environmental Exposure ; Maori People ; *Microbiota ; New Zealand ; *Nose/microbiology ; Parks, Recreational ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Indigenous health interventions have emerged in New Zealand aimed at increasing people's interactions with and exposure to macro and microbial diversity. Urban greenspaces provide opportunities for people to gain such exposures. However, the dynamics and pathways of microbial transfer from natural environments onto a person remain poorly understood. Here, we analysed bacterial 16S rRNA amplicons in air samples (n = 7) and pre- and post-exposure nasal samples (n = 238) from 35 participants who had 30-min exposures in an outdoor park. The participants were organised into two groups: over eight days each group had two outdoor park exposures and two indoor office exposures, with a cross-over study design and washout days between exposure days. We investigated the effects of participant group, location (outdoor park vs. indoor office), and exposures (pre vs. post) on the nasal bacterial community composition and three key suspected health-associated bacterial indicators (alpha diversity, generic diversity of Gammaproteobacteria, and read abundances of butyrate-producing bacteria). The participants had distinct nasal bacterial communities, but these communities did not display notable shifts in composition following exposures. The community composition and key health bacterial indicators were stable throughout the trial period, with no clear or consistent effects of group, location, or exposure. We conclude that 30-min exposure periods to urban greenspaces are unlikely to create notable changes in the nasal microbiome of visitors, which contrasts with previous research. Our results suggest that longer exposures or activities that involves closer interaction with microbial rich ecological components (e.g., soil) are required for greenspace exposures to result in noteworthy changes in the nasal microbiome.}, }
@article {pmid38554019, year = {2024}, author = {Hohagen, M and Sánchez, L and Herbst, AJ and Kählig, H and Shin, JW and Berry, D and Del Favero, G and Kleitz, F}, title = {MANNosylation of Mesoporous Silica Nanoparticles Modifies TLR4 Localization and NF-κB Translocation in T24 Bladder Cancer Cells.}, journal = {Advanced healthcare materials}, volume = {13}, number = {17}, pages = {e2304150}, pmid = {38554019}, issn = {2192-2659}, support = {//University of Vienna/ ; IBS-R004//Institute for Basic Science/ ; }, mesh = {Humans ; *Toll-Like Receptor 4/metabolism ; *Silicon Dioxide/chemistry ; *Nanoparticles/chemistry ; *NF-kappa B/metabolism ; *Urinary Bladder Neoplasms/metabolism/pathology ; *Mannose/chemistry ; Cell Line, Tumor ; Bacterial Adhesion/drug effects ; Caveolin 1/metabolism ; Porosity ; Lipopolysaccharides ; }, abstract = {D-mannose is widely used as non-antibiotic treatment for bacterial urinary tract infections. This application is based on a well-studied mechanism of binding to the type 1 bacterial pili and, therefore, blocking bacteria adhesion to the uroepithelial cells. To implement D-mannose into carrier systems, the mechanism of action of the sugar in the bladder environment is also relevant and requires investigation. Herein, two different MANNosylation strategies using mesoporous silica nanoparticles (MSNs) are described. The impact of different chemical linkers on bacterial adhesion and bladder cell response is studied via confocal microscopy imaging of the MSN interactions with the respective organisms. Cytotoxicity is assessed and the expression of Toll-like receptor 4 (TLR4) and caveolin-1 (CAV-1), in the presence or absence of simulated infection with bacterial lipopolysaccharide (LPS), is evaluated using the human urinary bladder cancer cell line T24. Further, localisation of the transcription factor NF-κB due to the MANNosylated materials is examined over time. The results show that MANNosylation modifies bacterial adhesion to the nanomaterials and significantly affects TLR4, caveolin-1, and NF-κB in bladder cells. These elements are essential components of the inflammatory cascade/pathogens response during urinary tract infections. These findings demonstrate that MANNosylation is a versatile tool to design hybrid nanocarriers for targeted biomedical applications.}, }
@article {pmid38553666, year = {2024}, author = {Ma, ZS}, title = {Towards a unified medical microbiome ecology of the OMU for metagenomes and the OTU for microbes.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {137}, pmid = {38553666}, issn = {1471-2105}, mesh = {Animals ; Humans ; Metagenome ; *Microbiota/genetics ; *Gastrointestinal Microbiome ; Biodiversity ; Sequence Analysis, DNA ; Metagenomics/methods ; }, abstract = {BACKGROUND: Metagenomic sequencing technologies offered unprecedented opportunities and also challenges to microbiology and microbial ecology particularly. The technology has revolutionized the studies of microbes and enabled the high-profile human microbiome and earth microbiome projects. The terminology-change from microbes to microbiomes signals that our capability to count and classify microbes (microbiomes) has achieved the same or similar level as we can for the biomes (macrobiomes) of plants and animals (macrobes). While the traditional investigations of macrobiomes have usually been conducted through naturalists' (Linnaeus &amp; Darwin) naked eyes, and aerial and satellite images (remote-sensing), the large-scale investigations of microbiomes have been made possible by DNA-sequencing-based metagenomic technologies. Two major types of metagenomic sequencing technologies-amplicon sequencing and whole-genome (shotgun sequencing)-respectively generate two contrastingly different categories of metagenomic reads (data)-OTU (operational taxonomic unit) tables representing microorganisms and OMU (operational metagenomic unit), a new term coined in this article to represent various cluster units of metagenomic genes.<br><br>RESULTS: The ecological science of microbiomes based on the OTU representing microbes has been unified with the classic ecology of macrobes (macrobiomes), but the unification based on OMU representing metagenomes has been rather limited. In a previous series of studies, we have demonstrated the applications of several classic ecological theories (diversity, composition, heterogeneity, and biogeography) to the studies of metagenomes. Here I push the envelope for the unification of OTU and OMU again by demonstrating the applications of metacommunity assembly and ecological networks to the metagenomes of human gut microbiomes. Specifically, the neutral theory of biodiversity (Sloan's near neutral model), Ning et al.stochasticity framework, core-periphery network, high-salience skeleton network, special trio-motif, and positive-to-negative ratio are applied to analyze the OMU tables from whole-genome sequencing technologies, and demonstrated with seven human gut metagenome datasets from the human microbiome project.<br><br>CONCLUSIONS: All of the ecological theories demonstrated previously and in this article, including diversity, composition, heterogeneity, stochasticity, and complex network analyses, are equally applicable to OMU metagenomic analyses, just as to OTU analyses. Consequently, I strongly advocate the unification of OTU/OMU (microbiomes) with classic ecology of plants and animals (macrobiomes) in the context of medical ecology.}, }
@article {pmid38552803, year = {2024}, author = {Petra de Oliveira Barros, V and Macedo Silva, JR and Maciel Melo, VM and Terceiro, PS and Nunes de Oliveira, I and Duarte de Freitas, J and Francisco da Silva Moura, O and Xavier de Araújo-Júnior, J and Erlanny da Silva Rodrigues, E and Maraschin, M and Thompson, FL and Landell, MF}, title = {Biosurfactants production by marine yeasts isolated from zoanthids and characterization of an emulsifier produced by Yarrowia lipolytica LMS 24B.}, journal = {Chemosphere}, volume = {355}, number = {}, pages = {141807}, doi = {10.1016/j.chemosphere.2024.141807}, pmid = {38552803}, issn = {1879-1298}, mesh = {*Yarrowia/metabolism ; Surface-Active Agents/chemistry ; Kerosene ; *Petroleum/analysis ; Hydrocarbons/metabolism ; Carbon/metabolism ; Biodegradation, Environmental ; }, abstract = {The present study investigates the potential for biosurfactant production of 19 marine yeast species obtained from zoanthids. Using the emulsification index test to screen the samples produced by the marine yeasts, we verified that five isolates exhibited an emulsification index ≥50%. Additional tests were performed on such isolates, including oil displacement, drop collapse, Parafilm M assay, and surface tension measurement. The tolerance of produced biosurfactants for environmental conditions was also analyzed, especially considering the media's temperature, pH, and salinity. Moreover, the surfactant's ability to emulsify different hydrocarbon sources and to metabolize kerosene as the sole carbon source was evaluated in vitro. Our results demonstrate that yeast biosurfactants can emulsify hydrocarbon sources under different physicochemical conditions and metabolize kerosene as a carbon source. Considering the Yarrowia lipolytica LMS 24B as the yeast model for biosurfactant production from the cell's wall biomass, emulsification indexes of 61.2% were obtained, even at a high temperature of 120 °C. Furthermore, the Fourier-transform middle infrared spectroscopy (FTIR) analysis of the biosurfactant's chemical composition revealed the presence of distinct functional groups assigned to a glycoprotein complex. Considering the status of developing new bioproducts and bioprocesses nowadays, our findings bring a new perspective to biosurfactant production by marine yeasts, especially Y. lipolytica LMS 24B. In particular, the presented results validate the relevance of marine environments as valuable sources of genetic resources, i.e., yeast strains capable of metabolizing and emulsifying petroleum derivatives.}, }
@article {pmid38549428, year = {2024}, author = {Männistö, MK and Ahonen, SHK and Ganzert, L and Tiirola, M and Stark, S and Häggblom, MM}, title = {Bacterial and fungal communities in sub-Arctic tundra heaths are shaped by contrasting snow accumulation and nutrient availability.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {4}, pages = {}, pmid = {38549428}, issn = {1574-6941}, support = {252323//Academy of Finland/ ; OCE 2129351//National Science Foundation/ ; }, mesh = {*Ecosystem ; *Mycobiome ; Snow ; Tundra ; Bacteria/genetics ; Soil/chemistry ; Seasons ; Climate Change ; Nutrients ; Arctic Regions ; }, abstract = {Climate change is affecting winter snow conditions significantly in northern ecosystems but the effects of the changing conditions for soil microbial communities are not well-understood. We utilized naturally occurring differences in snow accumulation to understand how the wintertime subnivean conditions shape bacterial and fungal communities in dwarf shrub-dominated sub-Arctic Fennoscandian tundra sampled in mid-winter, early, and late growing season. Phospholipid fatty acid (PLFA) and quantitative PCR analyses indicated that fungal abundance was higher in windswept tundra heaths with low snow accumulation and lower nutrient availability. This was associated with clear differences in the microbial community structure throughout the season. Members of Clavaria spp. and Sebacinales were especially dominant in the windswept heaths. Bacterial biomass proxies were higher in the snow-accumulating tundra heaths in the late growing season but there were only minor differences in the biomass or community structure in winter. Bacterial communities were dominated by members of Alphaproteobacteria, Actinomycetota, and Acidobacteriota and were less affected by the snow conditions than the fungal communities. The results suggest that small-scale spatial patterns in snow accumulation leading to a mosaic of differing tundra heath vegetation shapes bacterial and fungal communities as well as soil carbon and nutrient availability.}, }
@article {pmid38549276, year = {2024}, author = {Gao, J and Chen, L and Wang, J and Zhao, W and Zhang, J and Qin, Z and Wang, M and Chen, X and Li, M and Yang, Q}, title = {Response of the Symbiotic Microbial Community of Dioscorea opposita Cultivar Tiegun to Root-Knot Nematode Infection.}, journal = {Plant disease}, volume = {108}, number = {8}, pages = {2472-2483}, doi = {10.1094/PDIS-01-24-0169-RE}, pmid = {38549276}, issn = {0191-2917}, mesh = {Animals ; *Dioscorea/microbiology/parasitology ; *Plant Roots/microbiology/parasitology ; *Plant Diseases/parasitology/microbiology ; *Soil Microbiology ; *Symbiosis ; *Tylenchoidea/physiology ; *Rhizosphere ; *Microbiota ; Bacteria/classification/genetics/isolation &amp; purification ; Nematoda/physiology/microbiology ; }, abstract = {Yam is an important medicinal and edible dual-purpose plant with high economic value. However, nematode damage severely affects its yield and quality. One of the major effects of nematode infestations is the secondary infection of pathogenic bacteria or fungi through entry wounds made by the nematodes. Understanding the response of the symbiotic microbial community of yam plants to nematodes is crucial for controlling such a disease. In this study, we investigated the rhizosphere and how endophytic microbiomes shift after nematode infection during the tuber expansion stage in the Dioscorea opposita Thunb. cultivar Tiegun. Our results revealed that soil depth affected the abundance of nematodes, and the relative number of Meloidogyne incognita was higher in the diseased soil at a depth of 16 to 40 cm than those at a depth of 0 to 15 and 41 to 70 cm. The abundance of and interactions among soil microbiota members were significantly correlated with root-knot nematode (RKN) parasitism at various soil depths. However, the comparison of the microbial α-diversity and composition between healthy and diseased rhizosphere soil showed no difference. Compared with healthy soils, the co-occurrence networks of M. incognita-infested soils included a higher ratio of positive correlations linked to plant health. In addition, we detected a higher abundance of certain taxonomic groups belonging to Chitinophagaceae and Xanthobacteraceae in the rhizosphere of RKN-infested plants. The nematodes, besides causing direct damage to plants, also possess the ability to act synergistically with other pathogens, especially Ramicandelaber and Fusarium, leading to the development of disease complexes. In contrast to soil samples, RKN parasitism specifically had a significant effect on the composition and assembly of the root endophytic microbiota. The RKN colonization impacted a wide variety of endophytic microbiomes, including Pseudomonas, Sphingomonas, Rhizobium, Neocosmospora, and Fusarium. This study revealed the relationship between RKN disease and changes in the rhizosphere and endophytic microbial community, which may provide novel insights that help improve biological management of yam RKNs.}, }
@article {pmid38548725, year = {2024}, author = {Giordano, N and Gaudin, M and Trottier, C and Delage, E and Nef, C and Bowler, C and Chaffron, S}, title = {Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {2721}, pmid = {38548725}, issn = {2041-1723}, support = {862923//European Commission (EC)/ ; }, mesh = {*Ecosystem ; Phylogeny ; *Bacteria/genetics ; Aquatic Organisms/genetics ; Oceans and Seas ; }, abstract = {Marine microorganisms form complex communities of interacting organisms that influence central ecosystem functions in the ocean such as primary production and nutrient cycling. Identifying the mechanisms controlling their assembly and activities is a major challenge in microbial ecology. Here, we integrated Tara Oceans meta-omics data to predict genome-scale community interactions within prokaryotic assemblages in the euphotic ocean. A global genome-resolved co-activity network revealed a significant number of inter-lineage associations across diverse phylogenetic distances. Identified co-active communities include species displaying smaller genomes but encoding a higher potential for quorum sensing, biofilm formation, and secondary metabolism. Community metabolic modelling reveals a higher potential for interaction within co-active communities and points towards conserved metabolic cross-feedings, in particular of specific amino acids and group B vitamins. Our integrated ecological and metabolic modelling approach suggests that genome streamlining and metabolic auxotrophies may act as joint mechanisms shaping bacterioplankton community assembly in the global ocean surface.}, }
@article {pmid38548158, year = {2024}, author = {Yang, S and Zuo, J and Grossart, HP and Dai, G and Liu, J and Song, L and Gan, N}, title = {Evaluating microcystinase A-based approach on microcystins degradation during harvested cyanobacterial blooms.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {348}, number = {}, pages = {123878}, doi = {10.1016/j.envpol.2024.123878}, pmid = {38548158}, issn = {1873-6424}, mesh = {Microcystins/metabolism ; Reproducibility of Results ; *Cyanobacteria/metabolism ; *Microcystis/metabolism ; Biomass ; }, abstract = {Addressing notorious and worldwide Microcystis blooms, mechanical algae harvesting is an effective emergency technology for bloom mitigation and removal of nutrient loads in waterbodies. However, the absence of effective methods for removal of cyanobacterial toxins, e.g., microcystins (MCs), poses a challenge to recycle the harvested Microcystis biomass. In this study, we therefore introduced a novel approach, the "captured biomass-MlrA enzymatic MC degradation", by enriching microcystinase A (MlrA) via fermentation and spraying it onto salvaged Microcystis slurry to degrade all MCs. After storing the harvested Microcystis slurry, a rapid release of extracellular MCs occurred within the initial 8 h, reaching a peak concentration of 5.33 μg/mL at 48 h during the composting process. Upon spraying the recombinant MlrA crude extract (about 3.36 U) onto the Microcystis slurry in a ratio of 0.1% (v/v), over 95% of total MCs were degraded within a 24-h period. Importantly, we evaluated the reliability and safety of using MlrA extracts to degrade MCs. Results showed that organic matter/nutrient contents, e.g. soluble proteins, polysaccharides, phycocyanin and carotenoids, were not significantly altered. Furthermore, the addition of MlrA extracts did not significantly change the bacterial community composition and diversity in the Microcystis slurry, indicating that the MlrA extracts did not increase the risk of pathogenic bacteria. Our study provides an effective and promising method for the pre-treatment of harvested Microcystis biomass, highlighting an ecologically sustainable framework for addressing Microcystis blooms.}, }
@article {pmid38547998, year = {2024}, author = {Li, Y and Schütte, W and Dekeukeleire, M and Janssen, C and Boon, N and Asselman, J and Lebeer, S and Spacova, I and De Rijcke, M}, title = {The immunostimulatory activity of sea spray aerosols: bacteria and endotoxins activate TLR4, TLR2/6, NF-κB and IRF in human cells.}, journal = {The Science of the total environment}, volume = {927}, number = {}, pages = {171969}, doi = {10.1016/j.scitotenv.2024.171969}, pmid = {38547998}, issn = {1879-1026}, mesh = {Humans ; *NF-kappa B/metabolism ; *Aerosols ; *Endotoxins ; Toll-Like Receptor 4/metabolism ; Interferon Regulatory Factors/metabolism ; Toll-Like Receptor 2/metabolism ; Bacteria ; Air Pollutants ; Belgium ; Immunity, Innate ; }, abstract = {Frequent exposure to sea spray aerosols (SSA) containing marine microorganisms and bioactive compounds may influence human health. However, little is known about potential immunostimulation by SSA exposure. This study focuses on the effects of marine bacteria and endotoxins in SSA on several receptors and transcription factors known to play a key role in the human innate immune system. SSA samples were collected in the field (Ostend, Belgium) or generated in the lab using a marine aerosol reference tank (MART). Samples were characterized by their sodium contents, total bacterial counts, and endotoxin concentrations. Human reporter cells were exposed to SSA to investigate the activation of toll-like receptor 4 (TLR4) in HEK-Blue hTLR4 cells and TLR2/6 in HEK-Blue hTLR2/6 cells, as well as the activation of nuclear factor kappa B (NF-κB) and interferon regulatory factors (IRF) in THP1-Dual monocytes. These responses were then correlated to the total bacterial counts and endotoxin concentrations to explore dose-effect relationships. Field SSA contained from 3.0 × 10[3] to 6.0 × 10[5] bacteria/m[3] air (averaging 2.0 ± 1.9 × 10[5] bacteria/m[3] air) and an endotoxin concentration ranging from 7 to 1217 EU/m[3] air (averaging 389 ± 434 EU/m[3] air). In contrast, MART SSA exhibited elevated levels of total bacterial count (from 2.0 × 10[5] to 2.4 × 10[6], averaging 7.3 ± 5.5 × 10[5] cells/m[3] air) and endotoxin concentration from 536 to 2191 (averaging 1310 ± 513 EU/m[3] air). SSA samples differentially activated TLR4, TLR2/6, NF-κB and IRF. These immune responses correlated dose-dependently with the total bacterial counts, endotoxin levels, or both. This study sheds light on the immunostimulatory potential of SSA and its underlying mechanisms, highlighting the need for further research to deepen our understanding of the health implications of SSA exposure.}, }
@article {pmid38546802, year = {2024}, author = {Stephenson, MM and Coleman, ME and Azzolina, NA}, title = {Trends in Burdens of Disease by Transmission Source (USA, 2005-2020) and Hazard Identification for Foods: Focus on Milkborne Disease.}, journal = {Journal of epidemiology and global health}, volume = {14}, number = {3}, pages = {787-816}, pmid = {38546802}, issn = {2210-6014}, mesh = {Humans ; *Foodborne Diseases/epidemiology ; United States/epidemiology ; *Disease Outbreaks/statistics &amp; numerical data ; Animals ; *Milk/microbiology ; Cost of Illness ; Hazard Analysis and Critical Control Points/methods ; Food Microbiology ; }, abstract = {BACKGROUND: Robust solutions to global, national, and regional burdens of communicable and non-communicable diseases, particularly related to diet, demand interdisciplinary or transdisciplinary collaborations to effectively inform risk analysis and policy decisions.<br><br>OBJECTIVE: U.S. outbreak data for 2005-2020 from all transmission sources were analyzed for trends in the burden of infectious disease and foodborne outbreaks.<br><br>METHODS: Outbreak data from 58 Microsoft Access[&#xae;] data tables were structured using systematic queries and pivot tables for analysis by transmission source, pathogen, and date. Trends were examined using graphical representations, smoothing splines, Spearman's rho rank correlations, and non-parametric testing for trend. Hazard Identification was conducted based on the number and severity of illnesses.<br><br>RESULTS: The evidence does not support increasing trends in the burden of infectious foodborne disease, though strongly increasing trends were observed for other transmission sources. Morbidity and mortality were dominated by person-to-person transmission; foodborne and other transmission sources accounted for small portions of the disease burden. Foods representing the greatest hazards associated with the four major foodborne bacterial diseases were identified. Fatal foodborne disease was dominated by fruits, vegetables, peanut butter, and pasteurized dairy.<br><br>CONCLUSION: The available evidence conflicts with assumptions of zero risk for pasteurized milk and increasing trends in the burden of illness for raw milk. For future evidence-based risk management, transdisciplinary risk analysis methodologies are essential to balance both communicable and non-communicable diseases and both food safety and food security, considering scientific, sustainable, economic, cultural, social, and political factors to support health and wellness for humans and ecosystems.}, }
@article {pmid38544331, year = {2024}, author = {Wang, C and Defoirdt, T and Rajkovic, A}, title = {The impact of indole and mucin on sporulation, biofilm formation, and enterotoxin production in foodborne Clostridium perfringens.}, journal = {Journal of applied microbiology}, volume = {135}, number = {4}, pages = {}, doi = {10.1093/jambio/lxae083}, pmid = {38544331}, issn = {1365-2672}, support = {201808630020//China Scholarship Council/ ; BOF20/BAS/120//Ghent University/ ; 1506419N//Research Foundation Flanders/ ; }, mesh = {*Clostridium perfringens/genetics ; *Enterotoxins/genetics ; Mucins/metabolism ; Spores, Bacterial ; Biofilms ; }, abstract = {AIMS: Indole and mucin are compounds found in the host environment as they are produced by the host or by the host-associated microbiota. This study investigated whether indole and mucin impact Clostridium perfringens growth and sporulation, as well as enterotoxin production and biofilm formation.<br><br>METHODS AND RESULTS: There was no impact on growth of Cl. perfringens for up to 400&#xa0;&#xb5;M indole and 240&#xa0;mg/l mucin, and neither indole nor mucin affected sporulation. Reverse-transcriptase qPCR showed that mucin strongly upregulated the expression of Cl. perfringens enterotoxin (up to 121-fold increase), whereas indole had a much more modest effect (2-fold). This was also reflected in increased Cl. perfringens enterotoxin levels in mucin-treated Cl. perfringens (as assessed by a reversed passive latex agglutination assay). Finally, mucin and indole significantly increased biofilm formation of Cl. perfringens, although the effect size was relatively small (less than 1.5 fold).<br><br>CONCLUSION: These results indicate that Cl. perfringens can sense its presence in a host environment by responding to mucin, and thereby markedly increased enterotoxin production.}, }
@article {pmid38543583, year = {2024}, author = {Pandey, S and Blache, A and Achouak, W}, title = {Insights into Bacterial Extracellular Vesicle Biogenesis, Functions, and Implications in Plant-Microbe Interactions.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, pmid = {38543583}, issn = {2076-2607}, abstract = {Plant-microbe interactions play a crucial role in shaping plant health and survival. In recent years, the role of extracellular vesicles (EVs) in mediating intercellular communication between plants and microbes has emerged as an intriguing area of research. EVs serve as important carriers of bioactive molecules and genetic information, facilitating communication between cells and even between different organisms. Pathogenic bacteria leverage extracellular vesicles (EVs) to amplify their virulence, exploiting their cargo rich in toxins and virulence factors. Conversely, beneficial microbes initiate EV secretion to stimulate plant immune responses and nurture symbiotic relationships. The transfer of EV-packed small RNAs (sRNAs) has been demonstrated to facilitate the modulation of immune responses. Furthermore, harnessing the potential of EVs holds promise for the development of innovative diagnostic tools and sustainable crop protection strategies. This review highlights the biogenesis and functions of EVs in bacteria and their importance in plant defense, and paves the way for future research in this exciting field.}, }
@article {pmid38543493, year = {2024}, author = {Heczko, P}, title = {Editorial for Special Issue "Effects of Probiotics on Health".}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, pmid = {38543493}, issn = {2076-2607}, abstract = {Since 1987, when Professor Sherwood Gorbach discovered, characterized, and commercialized the first probiotic Lactobacillus rhamnosus GG, a total of over 17,000 publications have been indexed in PubMed under "probiotic" and "health", which is an extensive amount of research on the specific bacteria and yeasts defined as "live microorganisms that, when administered in adequate amounts, exert a health benefit on the host" [...].}, }
@article {pmid38543484, year = {2024}, author = {Rosa-Masegosa, A and Rodriguez-Sanchez, A and Gorrasi, S and Fenice, M and Gonzalez-Martinez, A and Gonzalez-Lopez, J and Muñoz-Palazon, B}, title = {Microbial Ecology of Granular Biofilm Technologies for Wastewater Treatment: A Review.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, pmid = {38543484}, issn = {2076-2607}, abstract = {Nowadays, the discharge of wastewater is a global concern due to the damage caused to human and environmental health. Wastewater treatment has progressed to provide environmentally and economically sustainable technologies. The biological treatment of wastewater is one of the fundamental bases of this field, and the employment of new technologies based on granular biofilm systems is demonstrating success in tackling the environmental issues derived from the discharge of wastewater. The granular-conforming microorganisms must be evaluated as functional entities because their activities and functions for removing pollutants are interconnected with the surrounding microbiota. The deep knowledge of microbial communities allows for the improvement in system operation, as the proliferation of microorganisms in charge of metabolic roles could be modified by adjustments to operational conditions. This is why engineering must consider the intrinsic microbiological aspects of biological wastewater treatment systems to obtain the most effective performance. This review provides an extensive view of the microbial ecology of biological wastewater treatment technologies based on granular biofilms for mitigating water pollution.}, }
@article {pmid38543271, year = {2024}, author = {Srivastava, MG and Kamarudin, NHN and Aktan, MK and Zheng, K and Zayed, N and Yongabi, D and Wagner, P and Teughels, W and Boccaccini, AR and Braem, A}, title = {pH-Triggered Controlled Release of Chlorhexidine Using Chitosan-Coated Titanium Silica Composite for Dental Infection Prevention.}, journal = {Pharmaceutics}, volume = {16}, number = {3}, pages = {}, pmid = {38543271}, issn = {1999-4923}, support = {STG/17/024, C32/18/059//KU Leuven/ ; }, abstract = {Peri-implantitis is a growing pathological concern for dental implants which aggravates the occurrence of revision surgeries. This increases the burden on both hospitals and the patients themselves. Research is now focused on the development of materials and accompanying implants designed to resist biofilm formation. To enhance this endeavor, a smart method of biofilm inhibition coupled with limiting toxicity to the host cells is crucial. Therefore, this research aims to establish a proof-of-concept for the pH-triggered release of chlorhexidine (CHX), an antiseptic commonly used in mouth rinses, from a titanium (Ti) substrate to inhibit biofilm formation on its surface. To this end, a macroporous Ti matrix is filled with mesoporous silica (together referred to as Ti/SiO2), which acts as a diffusion barrier for CHX from the CHX feed side to the release side. To limit release to acidic conditions, the release side of Ti/SiO2 is coated with crosslinked chitosan (CS), a pH-responsive and antimicrobial natural polymer. Scanning electron microscopy coupled with energy dispersive X-ray spectroscopy (SEM/EDX) and Fourier transform infrared (FTIR) spectroscopy confirmed successful CS film formation and crosslinking on the Ti/SiO2 disks. The presence of the CS coating reduced CHX release by 33% as compared to non-coated Ti/SiO2 disks, thus reducing the antiseptic exposure to the environment in normal conditions. Simultaneous differential scanning calorimetry and thermogravimetric analyzer (SDT) results highlighted the thermal stability of the crosslinked CS films. Quartz crystal microbalance with dissipation monitoring (QCM-D) indicated a clear pH response for crosslinked CS coatings in an acidic medium. This pH response also influenced CHX release through a Ti/SiO2/CS disk where the CHX release was higher than the average trend in the neutral medium. Finally, the antimicrobial study revealed a significant reduction in biofilm formation for the CS-coated samples compared to the control sample using viability quantitative polymerase chain reaction (v-qPCR) measurements, which were also corroborated using SEM imaging. Overall, this study investigates the smart triggered release of pharmaceutical agents aimed at inhibiting biofilm formation, with potential applicability to implant-like structures.}, }
@article {pmid38542054, year = {2024}, author = {Barathan, M and Ng, SL and Lokanathan, Y and Ng, MH and Law, JX}, title = {Unseen Weapons: Bacterial Extracellular Vesicles and the Spread of Antibiotic Resistance in Aquatic Environments.}, journal = {International journal of molecular sciences}, volume = {25}, number = {6}, pages = {}, pmid = {38542054}, issn = {1422-0067}, support = {DIP-2023-011//National University of Malaysia/ ; FF-2021-518//Faculty of Medicine, Universiti Kebangsaan Malaysia/ ; }, mesh = {*Ecosystem ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Multiple, Bacterial ; *Extracellular Vesicles ; Genes, Bacterial ; }, abstract = {This paper sheds light on the alarming issue of antibiotic resistance (ABR) in aquatic environments, exploring its detrimental effects on ecosystems and public health. It examines the multifaceted role of antibiotic use in aquaculture, agricultural runoff, and industrial waste in fostering the development and dissemination of resistant bacteria. The intricate interplay between various environmental factors, horizontal gene transfer, and bacterial extracellular vesicles (BEVs) in accelerating the spread of ABR is comprehensively discussed. Various BEVs carrying resistance genes like blaCTX-M, tetA, floR, and sul/I, as well as their contribution to the dominance of multidrug-resistant bacteria, are highlighted. The potential of BEVs as both a threat and a tool in combating ABR is explored, with promising strategies like targeted antimicrobial delivery systems and probiotic-derived EVs holding significant promise. This paper underscores the urgency of understanding the intricate interplay between BEVs and ABR in aquatic environments. By unraveling these unseen weapons, we pave the way for developing effective strategies to mitigate the spread of ABR, advocating for a multidisciplinary approach that includes stringent regulations, enhanced wastewater treatment, and the adoption of sustainable practices in aquaculture.}, }
@article {pmid38539868, year = {2024}, author = {M'hir, S and Ayed, L and De Pasquale, I and Fanizza, E and Tlais, AZA and Comparelli, R and Verni, M and Latronico, R and Gobbetti, M and Di Cagno, R and Filannino, P}, title = {Comparison of Milk Kefirs Obtained from Cow's, Ewe's and Goat's Milk: Antioxidant Role of Microbial-Derived Exopolysaccharides.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, pmid = {38539868}, issn = {2076-3921}, abstract = {Different types of milk are used in the production of milk kefir, but little information is available on the release of potentially antioxidant exopolysaccharides (EPS). The aim of this study was to investigate whether the microbial dynamics and EPS release are dependent on the milk substrate. In our study, the inoculated microbial consortium was driven differently by each type of milk (cow, ewe, and goat). This was evident in the sugar consumption, organic acid production, free amino release, and EPS production. The amount and the composition of the secreted EPS varied depending on the milk type, with implications for the structure and functional properties of the EPS. The low EPS yield in ewe's milk was associated with a higher lactic acid production and thus with the use of carbon sources oriented towards energy production. Depending on the milk used as substrate, the EPS showed different monosaccharide and FT-IR profiles, microstructures, and surface morphologies. These differences affected the antiradical properties and reducing power of the EPS. In particular, EPS extracted from cow's milk had a higher antioxidant activity than other milk types, and the antioxidant activity was concentration dependent.}, }
@article {pmid38539229, year = {2024}, author = {Villena-Alemany, C and Mujakić, I and Fecskeová, LK and Woodhouse, J and Auladell, A and Dean, J and Hanusová, M and Socha, M and Gazulla, CR and Ruscheweyh, HJ and Sunagawa, S and Silva Kavagutti, V and Andrei, A&#x15e; and Grossart, HP and Ghai, R and Koblížek, M and Piwosz, K}, title = {Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {65}, pmid = {38539229}, issn = {2049-2618}, support = {19-28778X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 19-28778X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 19-28778X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 19-28778X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 19-28778X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 2021/03/Y/NZ8/00076//Polska Akademia Nauk/ ; }, mesh = {*Phototrophic Processes ; *Lakes/microbiology ; Bacteria/genetics ; Biomass ; Bacteria, Aerobic/genetics/metabolism ; Phytoplankton/genetics ; }, abstract = {BACKGROUND: Aerobic anoxygenic phototrophic (AAP) bacteria are heterotrophic bacteria that supply their metabolism with light energy harvested by bacteriochlorophyll-a-containing reaction centers. Despite their substantial contribution to bacterial biomass, microbial food webs, and carbon cycle, their phenology in freshwater lakes remains unknown. Hence, we investigated seasonal variations of AAP abundance and community composition biweekly across 3 years in a temperate, meso-oligotrophic freshwater lake.<br><br>RESULTS: AAP bacteria displayed a clear seasonal trend with a spring maximum following the bloom of phytoplankton and a secondary maximum in autumn. As the AAP bacteria represent a highly diverse assemblage of species, we followed their seasonal succession using the amplicon sequencing of the pufM marker gene. To enhance the accuracy of the taxonomic assignment, we developed new pufM primers that generate longer amplicons and compiled the currently largest database of pufM genes, comprising 3633 reference sequences spanning all phyla known to contain AAP species. With this novel resource, we demonstrated that the majority of the species appeared during specific phases of the seasonal cycle, with less than 2% of AAP species detected during the whole year. AAP community presented an indigenous freshwater nature characterized by high resilience and heterogenic adaptations to varying conditions of the freshwater environment.<br><br>CONCLUSIONS: Our findings highlight the substantial contribution of AAP bacteria to the carbon flow and ecological dynamics of lakes and unveil a recurrent and dynamic seasonal succession of the AAP community. By integrating this information with the indicator of primary production (Chlorophyll-a) and existing ecological models, we show that AAP bacteria play a pivotal role in the recycling of dissolved organic matter released during spring phytoplankton bloom. We suggest a potential role of AAP bacteria within the context of the PEG model and their consideration in further ecological models.}, }
@article {pmid38537828, year = {2024}, author = {Madge Pimentel, I and Baikova, D and Buchner, D and Burfeid Castellanos, A and David, GM and Deep, A and Doliwa, A and Hadžiomerović, U and Mayombo, NAS and Prati, S and Spyra, MA and Vermiert, AM and Beisser, D and Dunthorn, M and Piggott, JJ and Sures, B and Tiegs, SD and Leese, F and Beermann, AJ}, title = {Assessing the response of an urban stream ecosystem to salinization under different flow regimes.}, journal = {The Science of the total environment}, volume = {926}, number = {}, pages = {171849}, doi = {10.1016/j.scitotenv.2024.171849}, pmid = {38537828}, issn = {1879-1026}, mesh = {Animals ; *Ecosystem ; *Rivers ; Invertebrates/physiology ; Fresh Water ; Sodium Chloride ; }, abstract = {Urban streams are exposed to a variety of anthropogenic stressors. Freshwater salinization is a key stressor in these ecosystems that is predicted to be further exacerbated by climate change, which causes simultaneous changes in flow parameters, potentially resulting in non-additive effects on aquatic ecosystems. However, the effects of salinization and flow velocity on urban streams are still poorly understood as multiple-stressor experiments are often conducted at pristine rather than urban sites. Therefore, we conducted a mesocosm experiment at the Boye River, a recently restored stream located in a highly urbanized area in Western Germany, and applied recurrent pulses of salinity along a gradient (NaCl, 9 h daily of +0 to +2.5 mS/cm) in combination with normal and reduced current velocities (20 cm/s vs. 10 cm/s). Using a comprehensive assessment across multiple organism groups (macroinvertebrates, eukaryotic algae, fungi, parasites) and ecosystem functions (primary production, organic-matter decomposition), we show that flow velocity reduction has a pervasive impact, causing community shifts for almost all assessed organism groups (except fungi) and inhibiting organic-matter decomposition. Salinization affected only dynamic components of community assembly by enhancing invertebrate emigration via drift and reducing fungal reproduction. We caution that the comparatively small impact of salt in our study can be due to legacy effects from past salt pollution by coal mining activities >30 years ago. Nevertheless, our results suggest that urban stream management should prioritize the continuity of a minimum discharge to maintain ecosystem integrity. Our study exemplifies a holistic approach for the assessment of multiple-stressor impacts on streams, which is needed to inform the establishment of a salinity threshold above which mitigation actions must be taken.}, }
@article {pmid38537819, year = {2024}, author = {Tobias-Hünefeldt, SP and van Beusekom, JEE and Russnak, V and Dähnke, K and Streit, WR and Grossart, HP}, title = {Seasonality, rather than estuarine gradient or particle suspension/sinking dynamics, determines estuarine carbon distributions.}, journal = {The Science of the total environment}, volume = {926}, number = {}, pages = {171962}, doi = {10.1016/j.scitotenv.2024.171962}, pmid = {38537819}, issn = {1879-1026}, mesh = {*Carbon/analysis ; Dissolved Organic Matter ; *Greenhouse Gases/analysis ; Estuaries ; Particulate Matter/analysis ; Rivers ; }, abstract = {Estuaries are important components of the global carbon cycle; exchanging carbon between aquatic, atmospheric, and terrestrial environments, representing important loci for blue carbon storage and greenhouse gas emissions. However, how estuarine gradients affect sinking/suspended particles, and dissolved organic matter dynamic interactions remains unexplored. We fractionated suspended/sinking particles to assess and characterise carbon fate differences. We investigated bacterial colonisation (SYBR Green I) and exopolymer concentrations (TEP/CSP) with microscopy staining techniques. C/H/N and dry weight analysis identified particle composition differences. Meanwhile, nutrient and carbon analysis, and excitation and emission matrix evaluations with a subsequent parallel factor (PARAFAC) analysis characterised dissolved organic matter. The lack of clear salinity driven patterns in our study are presumably due to strong mixing forces and high particle heterogeneity along the estuary, with only density differences between suspended and sinking particles. Elbe estuary particles' organic portion is made up of marine-like (sinking) and terrestrial-like (suspended) signatures. Salinity did not have a significant role in microbial degradation and carbon composition, although brackish estuary portions were more biologically active. Indicative of increased degradation rates, leading to decreased greenhouse gas emissions, which are especially relevant for estuaries, with their disproportionate greenhouse gas emissions. Bacterial colonisation decreased seawards, indicative of decreased degradation, and shifts in microbial community composition and functions. Our findings span diverse strands of research, concerning steady carbon contributions from both marine and terrestrial sources, carbon aromaticity, humification index, and bioavailability. Their integration highlights the importance of the Elbe estuary as a model system, providing robust information for future policy decisions affecting dissolved and particulate matter dynamics within the Elbe Estuary.}, }
@article {pmid38537644, year = {2024}, author = {Kawa, D and Thiombiano, B and Shimels, MZ and Taylor, T and Walmsley, A and Vahldick, HE and Rybka, D and Leite, MFA and Musa, Z and Bucksch, A and Dini-Andreote, F and Schilder, M and Chen, AJ and Daksa, J and Etalo, DW and Tessema, T and Kuramae, EE and Raaijmakers, JM and Bouwmeester, H and Brady, SM}, title = {The soil microbiome modulates the sorghum root metabolome and cellular traits with a concomitant reduction of Striga infection.}, journal = {Cell reports}, volume = {43}, number = {4}, pages = {113971}, pmid = {38537644}, issn = {2211-1247}, mesh = {*Sorghum/microbiology/metabolism ; *Striga/physiology ; *Plant Roots/microbiology/metabolism/parasitology ; *Microbiota ; *Soil Microbiology ; Metabolome ; Plant Diseases/microbiology/parasitology ; }, abstract = {Sorghum bicolor is among the most important cereals globally and a staple crop for smallholder farmers in sub-Saharan Africa. Approximately 20% of sorghum yield is lost annually in Africa due to infestation with the root parasitic weed Striga hermonthica. Existing Striga management strategies are not singularly effective and integrated approaches are needed. Here, we demonstrate the functional potential of the soil microbiome to suppress Striga infection in sorghum. We associate this suppression with microbiome-mediated induction of root endodermal suberization and aerenchyma formation and with depletion of haustorium-inducing factors, compounds required for the initial stages of Striga infection. We further identify specific bacterial taxa that trigger the observed Striga-suppressive traits. Collectively, our study describes the importance of the soil microbiome in the early stages of root infection by Striga and pinpoints mechanisms of Striga suppression. These findings open avenues to broaden the effectiveness of integrated Striga management practices.}, }
@article {pmid38537571, year = {2024}, author = {Jing, J and Garbeva, P and Raaijmakers, JM and Medema, MH}, title = {Strategies for tailoring functional microbial synthetic communities.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38537571}, issn = {1751-7370}, mesh = {*Microbiota ; Soil/chemistry ; Soil Microbiology ; Microbial Interactions ; }, abstract = {Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity of soil microorganisms and their complex interactions make it challenging to pinpoint the main players important for the life support functions microbes can provide to plants, including enhanced tolerance to (a)biotic stress factors. Designing simplified microbial synthetic communities (SynComs) helps reduce this complexity to unravel the molecular and chemical basis and interplay of specific microbiome functions. While SynComs have been successfully employed to dissect microbial interactions or reproduce microbiome-associated phenotypes, the assembly and reconstitution of these communities have often been based on generic abundance patterns or taxonomic identities and co-occurrences but have only rarely been informed by functional traits. Here, we review recent studies on designing functional SynComs to reveal common principles and discuss multidimensional approaches for community design. We propose a strategy for tailoring the design of functional SynComs based on integration of high-throughput experimental assays with microbial strains and computational genomic analyses of their functional capabilities.}, }
@article {pmid38535593, year = {2024}, author = {Cristino, S and Pascale, MR and Marino, F and Derelitto, C and Salaris, S and Orsini, M and Squarzoni, S and Grottola, A and Girolamini, L}, title = {Characterization of a Novel Species of Legionella Isolated from a Healthcare Facility: Legionella resiliens sp. nov.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, pmid = {38535593}, issn = {2076-0817}, mesh = {*Legionella/genetics/isolation &amp; purification ; *Phylogeny ; Fatty Acids/analysis ; Water Microbiology ; Health Facilities ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Base Composition/genetics ; Bacterial Typing Techniques ; Humans ; Whole Genome Sequencing ; }, abstract = {Two Legionella-like isolates, 8cVS16[T] and 9fVS26, were isolated from a water distribution system (WDS) in a healthcare facility. Cells were Gram- and Ziehl Neelsen-stain-negative, rod-shaped, motile, and exhibited a blue-white fluorescence under Wood's lamp at 365 nm. The strains grew in a range of 32-37 °C on BCYE with L-cysteine (Cys+), GVPC, and MWY agar medium, with a positive reaction for oxidase, catalase, and gelatinase. The dominant fatty acids were summed features 3 (C16:1ω7c/C16:1ω6c) (27.7%), C16:0 iso (17.5%), and C16:0 (16.3%), and Q13 as the major ubiquinone. The mip and rpoB gene sequences showed a similarity of 96.7% and 92.4%, with L. anisa (ATCC 35292[T]). The whole genomes sequencing (WGS) performed displayed a GC content of 38.21 mol% for both. The digital DNA-DNA hybridization (dDDH) analysis demonstrated the separation of the two strains from the phylogenetically most related L. anisa (ATCC 35292[T]), with ≤43% DNA-DNA relatedness. The Average Nucleotide Identity (ANI) between the two strains and L. anisa (ATCC 35292[T]) was 90.74%, confirming that the two isolates represent a novel species of the genus Legionella. The name proposed for this species is Legionella resiliens sp. nov., with 8cVS16[T] (=DSM 114356[T] = CCUG 76627[T]) as the type strain.}, }
@article {pmid38531380, year = {2024}, author = {Skinner, JP and Palar, S and Allen, C and Raderstorf, A and Blake, P and Morán Reyes, A and Berg, RN and Muse, C and Robles, A and Hamdan, N and Chu, MY and Delgado, AG}, title = {Acetylene Tunes Microbial Growth During Aerobic Cometabolism of Trichloroethene.}, journal = {Environmental science &amp; technology}, volume = {58}, number = {14}, pages = {6274-6283}, pmid = {38531380}, issn = {1520-5851}, mesh = {*Trichloroethylene/metabolism ; Acetylene/metabolism ; Biodegradation, Environmental ; Bacteria/metabolism ; Biomass ; *Groundwater ; }, abstract = {Microbial aerobic cometabolism is a possible treatment approach for large, dilute trichloroethene (TCE) plumes at groundwater contaminated sites. Rapid microbial growth and bioclogging pose a persistent problem in bioremediation schemes. Bioclogging reduces soil porosity and permeability, which negatively affects substrate distribution and contaminant treatment efficacy while also increasing the operation and maintenance costs of bioremediation. In this study, we evaluated the ability of acetylene, an oxygenase enzyme-specific inhibitor, to decrease biomass production while maintaining aerobic TCE cometabolism capacity upon removal of acetylene. We first exposed propane-metabolizing cultures (pure and mixed) to 5% acetylene (v v[-1]) for 1, 2, 4, and 8 d and we then verified TCE aerobic cometabolic activity. Exposure to acetylene overall decreased biomass production and TCE degradation rates while retaining the TCE degradation capacity. In the mixed culture, exposure to acetylene for 1-8 d showed minimal effects on the composition and relative abundance of TCE cometabolizing bacterial taxa. TCE aerobic cometabolism and incubation conditions exerted more notable effects on microbial ecology than did acetylene. Acetylene appears to be a viable approach to control biomass production that may lessen the likelihood of bioclogging during TCE cometabolism. The findings from this study may lead to advancements in aerobic cometabolism remediation technologies for dilute plumes.}, }
@article {pmid38530469, year = {2024}, author = {Maraci, &#xd6; and Antonatou-Papaioannou, A and Jünemann, S and Schneeberger, K and Schulze, M and Scheffler, I and Caspers, BA}, title = {Bats, Bacteria, and Bat Smell V.2.0: Repeatable Sex-Specific Differences in Scent Organ Microbiota.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {55}, pmid = {38530469}, issn = {1432-184X}, support = {SCHN 1584/2-1//Deutsche Forschungsgemeinschaft/ ; SCHN 1584/2-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; Male ; Female ; Odorants ; Smell ; *Chiroptera ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Bacteria ; Pheromones/metabolism ; *Microbiota/genetics ; }, abstract = {Reproducibility is a fundamental principle in science, ensuring reliable and valid findings. However, replication studies are scarce, particularly in ecology, due to the emphasis on novelty for publication. We explored the possibility of replicating original findings in the field of microbial and chemical ecology by conducting a conceptual replication of a previous study analysing the sex-specific differences in the microbial communities inhabiting the wing sacs, a scent organ with crucial functions in olfactory communication, of greater sac-winged bat (Saccopteryx bilineata). In the original study, the skin swabs from the antebrachial wing sacs of the males and wing sac rudiments of the females were analysed using culture-dependent methods to test sex-specific differences. The authors demonstrated that males have lower microbial richness and different microbial composition than females. We attempted to reproduce these findings using 16S rRNA sequencing, which offers improved accuracy in pinpointing microbial members than culture-dependent methods because of advanced statistical methods. Our study validated the original study's findings: Males had a lower microbial richness, and the community composition differed between the sexes. Furthermore, in the current study, males had an increased abundance of bacteria that might potentially be involved in odour production and degradation of malodorous substances and antimicrobial production. Our conceptual replication study corroborated that microbes can play a role in shaping their host's olfactory phenotype and consequently influence sexual selection. Furthermore, the current study emphasises the importance of replication efforts and hopefully encourages a culture that values replication studies in scientific practice.}, }
@article {pmid38528797, year = {2024}, author = {Avila Santos, AP and de Almeida, BLS and Bonidia, RP and Stadler, PF and Stefanic, P and Mandic-Mulec, I and Rocha, U and Sanches, DS and de Carvalho, ACPLF}, title = {BioDeepfuse: a hybrid deep learning approach with integrated feature extraction techniques for enhanced non-coding RNA classification.}, journal = {RNA biology}, volume = {21}, number = {1}, pages = {1-12}, pmid = {38528797}, issn = {1555-8584}, support = {2023/00264-0//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior [CAPES] - Universidade de S&#xe3;o Paulo [USP]/ ; 109981//Canada&#x2019;s International Development Research Centre [IDRC]/ ; J1-4411//ARIS project/ ; }, mesh = {*Deep Learning ; RNA, Untranslated/genetics ; Algorithms ; RNA ; Neural Networks, Computer ; }, abstract = {The accurate classification of non-coding RNA (ncRNA) sequences is pivotal for advanced non-coding genome annotation and analysis, a fundamental aspect of genomics that facilitates understanding of ncRNA functions and regulatory mechanisms in various biological processes. While traditional machine learning approaches have been employed for distinguishing ncRNA, these often necessitate extensive feature engineering. Recently, deep learning algorithms have provided advancements in ncRNA classification. This study presents BioDeepFuse, a hybrid deep learning framework integrating convolutional neural networks (CNN) or bidirectional long short-term memory (BiLSTM) networks with handcrafted features for enhanced accuracy. This framework employs a combination of k-mer one-hot, k-mer dictionary, and feature extraction techniques for input representation. Extracted features, when embedded into the deep network, enable optimal utilization of spatial and sequential nuances of ncRNA sequences. Using benchmark datasets and real-world RNA samples from bacterial organisms, we evaluated the performance of BioDeepFuse. Results exhibited high accuracy in ncRNA classification, underscoring the robustness of our tool in addressing complex ncRNA sequence data challenges. The effective melding of CNN or BiLSTM with external features heralds promising directions for future research, particularly in refining ncRNA classifiers and deepening insights into ncRNAs in cellular processes and disease manifestations. In addition to its original application in the context of bacterial organisms, the methodologies and techniques integrated into our framework can potentially render BioDeepFuse effective in various and broader domains.}, }
@article {pmid38526664, year = {2024}, author = {Roy, R and Paul, P and Chakraborty, P and Malik, M and Das, S and Chatterjee, S and Maity, A and Dasgupta, M and Sarker, RK and Sarkar, S and Das Gupta, A and Tribedi, P}, title = {Cuminaldehyde and Tobramycin Forestall the Biofilm Threats of Staphylococcus aureus: A Combinatorial Strategy to Evade the Biofilm Challenges.}, journal = {Applied biochemistry and biotechnology}, volume = {196}, number = {11}, pages = {7588-7613}, pmid = {38526664}, issn = {1559-0291}, support = {R&amp;D/2020/F2//The Neotia University/ ; }, mesh = {*Biofilms/drug effects/growth &amp; development ; *Tobramycin/pharmacology ; *Staphylococcus aureus/drug effects/physiology ; *Benzaldehydes/pharmacology ; *Cymenes/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Reactive Oxygen Species/metabolism ; Microbial Sensitivity Tests ; Xanthophylls/pharmacology ; Humans ; }, abstract = {Staphylococcus aureus, an opportunistic Gram-positive pathogen, is known for causing various infections in humans, primarily by forming biofilms. The biofilm-induced antibiotic resistance has been considered a significant medical threat. Combinatorial therapy has been considered a reliable approach to combat antibiotic resistance by using multiple antimicrobial agents simultaneously, targeting bacteria through different mechanisms of action. To this end, we examined the effects of two molecules, cuminaldehyde (a natural compound) and tobramycin (an antibiotic), individually and in combination, against staphylococcal biofilm. Our experimental observations demonstrated that cuminaldehyde (20 μg/mL) in combination with tobramycin (0.05 μg/mL) exhibited efficient reduction in biofilm formation compared to their individual treatments (p < 0.01). Additionally, the combination showed an additive interaction (fractional inhibitory concentration value 0.66) against S. aureus. Further analysis revealed that the effective combination accelerated the buildup of reactive oxygen species (ROS) and increased the membrane permeability of the bacteria. Our findings also specified that the cuminaldehyde in combination with tobramycin efficiently reduced biofilm-associated pathogenicity factors of S. aureus, including fibrinogen clumping ability, hemolysis property, and staphyloxanthin production. The selected concentrations of tobramycin and cuminaldehyde demonstrated promising activity against the biofilm development of S. aureus on catheter models without exerting antimicrobial effects. In conclusion, the combination of tobramycin and cuminaldehyde presented a successful strategy for combating staphylococcal biofilm-related healthcare threats. This combinatorial approach holds the potential for controlling biofilm-associated infections caused by S. aureus.}, }
@article {pmid38524670, year = {2023}, author = {Yount, TA and Murtha, AN and Cecere, AG and Miyashiro, TI}, title = {Quorum sensing facilitates interpopulation signaling by Vibrio fischeri within the light organ of Euprymna scolopes.}, journal = {Israel journal of chemistry}, volume = {63}, number = {5-6}, pages = {}, pmid = {38524670}, issn = {0021-2148}, support = {R01 GM129133/GM/NIGMS NIH HHS/United States ; }, abstract = {Quorum sensing is an intercellular signaling mechanism that enables bacterial cells to coordinate population-level behaviors. How quorum sensing functions in natural habitats remains poorly understood. Vibrio fischeri is a bacterial symbiont of the Hawaiian bobtail squid Euprymna scolopes and depends on LuxI/LuxR quorum sensing to produce the symbiotic trait of bioluminescence. A previous study demonstrated that animals emit light when co-colonized by a Δlux mutant, which lacks several genes within the lux operon that are necessary for bioluminescence production, and a LuxI[-] mutant, which cannot synthesize the quorum signaling molecule N-3-oxohexanoyl-homoserine lactone. Here, we build upon that observation and show that populations of LuxI[-] feature elevated promoter activity for the lux operon. We find that population structures comprising of Δlux and LuxI[-] are attenuated within the squid, but a wild-type strain enables the LuxI[-] strain type to be maintained in vivo. These experimental results support a model of interpopulation signaling, which provides basic insight into how quorum sensing functions within the natural habitats found within a host.}, }
@article {pmid38521905, year = {2024}, author = {Wu, J and Lv, Y and Hao, P and Zhang, Z and Zheng, Y and Chen, E and Fan, Y}, title = {Immunological profile of lactylation-related genes in Crohn's disease: a comprehensive analysis based on bulk and single-cell RNA sequencing data.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {300}, pmid = {38521905}, issn = {1479-5876}, support = {82300630//National Natural Science Foundation of China/ ; 2022GGB011//Project of Young and Middle-aged Backbone Talents Cultivation/ ; 2021J011329//Fujian Provincial Natural Science Foundation/ ; 2021QNB017//Health Science Foundation of Fujian Youth Program/ ; }, mesh = {Humans ; *Crohn Disease/genetics ; Databases, Factual ; Lactic Acid ; Sequence Analysis, RNA ; }, abstract = {BACKGROUND: Crohn's disease (CD) is a disease characterized by intestinal immune dysfunction, often accompanied by metabolic abnormalities. Disturbances in lactate metabolism have been found in the intestine of patients with CD, but studies on the role of lactate and related Lactylation in the pathogenesis of CD are still unknown.<br><br>METHODS: We identified the core genes associated with Lactylation by downloading and merging three CD-related datasets (GSE16879, GSE75214, and GSE112366) from the GEO database, and analyzed the functions associated with the hub genes and the correlation between their expression levels and immune infiltration through comprehensive analysis. We explored the Lactylation levels of different immune cells using single-cell data and further analyzed the differences in Lactylation levels between inflammatory and non-inflammatory sites.<br><br>RESULTS: We identified six Lactylation-related hub genes that are highly associated with CD. Further analysis revealed that these six hub genes were highly correlated with the level of immune cell infiltration. To further clarify the effect of Lactylation on immune cells, we analyzed single-cell sequencing data of immune cells from inflammatory and non-inflammatory sites in CD patients and found that there were significant differences in the levels of Lactylation between different types of immune cells, and that the levels of Lactylation were significantly higher in immune cells from inflammatory sites.<br><br>CONCLUSIONS: These results suggest that Lactylation-related genes and their functions are closely associated with changes in inflammatory cells in CD patients.}, }
@article {pmid38519354, year = {2024}, author = {,  and Jurburg, SD and Álvarez Blanco, MJ and Chatzinotas, A and Kazem, A and König-Ries, B and Babin, D and Smalla, K and Cerecetto, V and Fernandez-Gnecco, G and Covacevich, F and Viruel, E and Bernaschina, Y and Leoni, C and Garaycochea, S and Terra, JA and Fresia, P and Figuerola, ELM and Wall, LG and Covelli, JM and Agnello, AC and Nieto, EE and Festa, S and Dominici, LE and Allegrini, M and Zabaloy, MC and Morales, ME and Erijman, L and Coniglio, A and Cassán, FD and Nievas, S and Roldán, DM and Menes, R and Jauri, PV and Marrero, CS and Massa, AM and Revetria, MAM and Fernández-Scavino, A and Pereira-Mora, L and Martínez, S and Frene, JP}, title = {Datathons: fostering equitability in data reuse in ecology.}, journal = {Trends in microbiology}, volume = {32}, number = {5}, pages = {415-418}, doi = {10.1016/j.tim.2024.02.010}, pmid = {38519354}, issn = {1878-4380}, mesh = {Argentina ; *Biodiversity ; *Ecology ; *Microbiota ; Uruguay ; }, abstract = {Approaches to rapidly collecting global biodiversity data are increasingly important, but biodiversity blind spots persist. We organized a three-day Datathon event to improve the openness of local biodiversity data and facilitate data reuse by local researchers. The first Datathon, organized among microbial ecologists in Uruguay and Argentina assembled the largest microbiome dataset in the region to date and formed collaborative consortia for microbiome data synthesis.}, }
@article {pmid38518769, year = {2024}, author = {Pristner, M and Wasinger, D and Seki, D and Klebermaß-Schrehof, K and Berger, A and Berry, D and Wisgrill, L and Warth, B}, title = {Neuroactive metabolites and bile acids are altered in extremely premature infants with brain injury.}, journal = {Cell reports. Medicine}, volume = {5}, number = {4}, pages = {101480}, pmid = {38518769}, issn = {2666-3791}, mesh = {Infant, Newborn ; Infant ; Humans ; *Infant, Extremely Premature ; Chromatography, Liquid/methods ; *Bile Acids and Salts ; RNA, Ribosomal, 16S/genetics ; Tandem Mass Spectrometry ; }, abstract = {The gut microbiome is associated with pathological neurophysiological evolvement in extremely premature infants suffering from brain injury. The exact underlying mechanism and its associated metabolic signatures in infants are not fully understood. To decipher metabolite profiles linked to neonatal brain injury, we investigate the fecal and plasma metabolome of samples obtained from a cohort of 51 extremely premature infants at several time points, using liquid chromatography (LC)-high-resolution mass spectrometry (MS)-based untargeted metabolomics and LC-MS/MS-based targeted analysis for investigating bile acids and amidated bile acid conjugates. The data are integrated with 16S rRNA gene amplicon gut microbiome profiles as well as patient cytokine, growth factor, and T cell profiles. We find an early onset of differentiation in neuroactive metabolites between infants with and without brain injury. We detect several bacterially derived bile acid amino acid conjugates in plasma and feces. These results provide insights into the early-life metabolome of extremely premature infants.}, }
@article {pmid38516656, year = {2024}, author = {Brait, N and Hackl, T and Morel, C and Exbrayat, A and Gutierrez, S and Lequime, S}, title = {A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {vead088}, pmid = {38516656}, issn = {2057-1577}, abstract = {Large-scale metagenomic and -transcriptomic studies have revolutionized our understanding of viral diversity and abundance. In contrast, endogenous viral elements (EVEs), remnants of viral sequences integrated into host genomes, have received limited attention in the context of virus discovery, especially in RNA-Seq data. EVEs resemble their original viruses, a challenge that makes distinguishing between active infections and integrated remnants difficult, affecting virus classification and biases downstream analyses. Here, we systematically assess the effects of EVEs on a prototypical virus discovery pipeline, evaluate their impact on data integrity and classification accuracy, and provide some recommendations for better practices. We examined EVEs and exogenous viral sequences linked to Orthomyxoviridae, a diverse family of negative-sense segmented RNA viruses, in 13 genomic and 538 transcriptomic datasets of Culicinae mosquitoes. Our analysis revealed a substantial number of viral sequences in transcriptomic datasets. However, a significant portion appeared not to be exogenous viruses but transcripts derived from EVEs. Distinguishing between transcribed EVEs and exogenous virus sequences was especially difficult in samples with low viral abundance. For example, three transcribed EVEs showed full-length segments, devoid of frameshift and nonsense mutations, exhibiting sufficient mean read depths that qualify them as exogenous virus hits. Mapping reads on a host genome containing EVEs before assembly somewhat alleviated the EVE burden, but it led to a drastic reduction of viral hits and reduced quality of assemblies, especially in regions of the viral genome relatively similar to EVEs. Our study highlights that our knowledge of the genetic diversity of viruses can be altered by the underestimated presence of EVEs in transcriptomic datasets, leading to false positives and altered or missing sequence information. Thus, recognizing and addressing the influence of EVEs in virus discovery pipelines will be key in enhancing our ability to capture the full spectrum of viral diversity.}, }
@article {pmid38514851, year = {2024}, author = {Silva, DEO and Costa, RM and Campos, JR and Rocha, SMB and de Araujo Pereira, AP and Melo, VMM and Oliveira, FAS and de Alcantara Neto, F and Mendes, LW and Araujo, ASF}, title = {Short-term restoration practices change the bacterial community in degraded soil from the Brazilian semiarid.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {6845}, pmid = {38514851}, issn = {2045-2322}, mesh = {*Soil ; RNA, Ribosomal, 16S/genetics ; Brazil ; *Bacteria/genetics ; Acidobacteria/genetics ; Soil Microbiology ; }, abstract = {Land degradation by deforestation adversely impacts soil properties, and long-term restoration practices have been reported to potentially reverse these effects, particularly on soil microorganisms. However, there is limited knowledge regarding the short-term effects of restoration on the soil bacterial community in semiarid areas. This study evaluates the bacterial community in soils experiencing degradation (due to slash-and-burn deforestation) and restoration (utilizing stone cordons and revegetation), in comparison to a native soil in the Brazilian semiarid region. Three areas were selected: (a) under degradation; (b) undergoing short-term restoration; and (c) a native area, and the bacterial community was assessed using 16S rRNA sequencing on soil samples collected during both dry and rainy seasons. The dry and rainy seasons exhibited distinct bacterial patterns, and native sites differed from degraded and restoration sites. Chloroflexi and Proteobacteria phyla exhibited higher prevalence in degraded and restoration sites, respectively, while Acidobacteria and Actinobacteria were more abundant in sites undergoing restoration compared to degraded sites. Microbial connections varied across sites and seasons, with an increase in nodes observed in the native site during the dry season, more edges and positive connections in the restoration site, and a higher occurrence of negative connections in the degradation site during the rainy season. Niche occupancy analysis revealed that degradation favored specialists over generalists, whereas restoration exhibited a higher prevalence of generalists compared to native sites. Specifically, degraded sites showed a higher abundance of specialists in contrast to restoration sites. This study reveals that land degradation impacts the soil bacterial community, leading to differences between native and degraded sites. Restoring the soil over a short period alters the status of the bacterial community in degraded soil, fostering an increase in generalist microbes that contribute to enhanced soil stability.}, }
@article {pmid38512483, year = {2024}, author = {Zhan, Y and Wang, E and Zhou, Y and He, G and Lv, P and Wang, L and Zhou, T and Miao, X and Chen, C and Li, Q}, title = {Facilitating Effects of Reductive Soil Disinfestation on Soil Health and Physiological Properties of Panax ginseng.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {54}, pmid = {38512483}, issn = {1432-184X}, mesh = {Soil/chemistry ; *Panax ; Agriculture/methods ; *Microbiota ; *Mycobiome ; Soil Microbiology ; }, abstract = {Chemical soil fumigation (CSF) and reductive soil disinfestation (RSD) have been proven to be effective agricultural strategies to improve soil quality, restructure microbial communities, and promote plant growth in soil degradation remediation. However, it is still unclear how RSD and CSF ensure soil and plant health by altering fungal communities. Field experiments were conducted to investigate the effects of CSF with chloropicrin, and RSD with animal feces on soil properties, fungal communities and functional composition, and plant physiological characteristics were evaluated. Results showed that RSD and CSF treatment improved soil properties, restructured fungal community composition and structure, enhanced fungal interactions and functions, and facilitated plant growth. There was a significant increase in OM, AN, and AP contents in the soil with both CSF and RSD treatments compared to CK. Meanwhile, compared with CK and CSF, RSD treatment significantly increased biocontrol Chaetomium relative abundance while reducing pathogenic Neonectria relative abundance, indicating that RSD has strong inhibition potential. Furthermore, the microbial network of RSD treatment was more complex and interconnected, and the functions of plant pathogens, and animal pathogen were decreased. Importantly, RSD treatment significantly increased plant SOD, CAT, POD activity, SP, Ca, Zn content, and decreased MDA, ABA, Mg, K, and Fe content. In summary, RSD treatment is more effective than CSF treatment, by stimulating the proliferation of probiotic communities to further enhance soil health and plant disease resistance.}, }
@article {pmid38509266, year = {2024}, author = {Djotan, AKG and Matsushita, N and Fukuda, K}, title = {Year-round dynamics of arbuscular mycorrhizal fungi communities in the roots and surrounding soils of Cryptomeria japonica.}, journal = {Mycorrhiza}, volume = {34}, number = {1-2}, pages = {119-130}, pmid = {38509266}, issn = {1432-1890}, support = {JP22H02382//Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {*Mycorrhizae/genetics ; Soil/chemistry ; Ecosystem ; *Cryptomeria/genetics ; Plant Roots/microbiology ; Soil Microbiology ; Trees ; DNA, Fungal/genetics ; Fungi/genetics ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) live simultaneously inside and outside of host plant roots for a functional mycorrhizal symbiosis. Still, the year-round dynamics and relationships between soil properties and AMF communities of trees in forest ecosystems remain unclear. We collected paired root and soil samples of the same Cryptomeria japonica trees at two forest sites (five trees at each site) every 2 months over a year. Total DNA was extracted from roots and soil separately and soil physicochemical properties were measured. With Illumina's next-generation amplicon sequencing targeting the small subunit of fungal ribosomal DNA, we clarified seasonal dynamics of soil properties and AMF communities. Soil pH and total phosphorus showed significant seasonality while total carbon, nitrogen, and C/N did not. Only pH was a good predictor of the composition and dynamics of the AMF community. The total AMF community (roots + soil) showed significant seasonality because of variation from May to September. Root and soil AMF communities were steady year-round, however, with similar species richness but contained significantly different AMF assemblages in any sampling month. Despite the weak seasonality in the communities, the top two dominant OTUs showed significant but different shifts between roots and soils across seasons with strong antagonistic relationships. In conclusion, few dominant AMF taxa are dynamically shifting between the roots and soils of C. japonica to respond to seasonal and phenological variations in their microhabitats. AMF inhabiting forest ecosystems may have high environmental plasticity to sustain a functional symbiosis regardless of seasonal variations that occur in the soil.}, }
@article {pmid38508742, year = {2024}, author = {Nishimura, Y and Yamada, K and Okazaki, Y and Ogata, H}, title = {DiGAlign: Versatile and Interactive Visualization of Sequence Alignment for Comparative Genomics.}, journal = {Microbes and environments}, volume = {39}, number = {1}, pages = {}, pmid = {38508742}, issn = {1347-4405}, mesh = {*Software ; *User-Computer Interface ; Sequence Alignment ; Genomics ; Genome ; }, abstract = {With the explosion of available genomic information, comparative genomics has become a central approach to understanding microbial ecology and evolution. We developed DiGAlign (https://www.genome.jp/digalign/), a web server that provides versatile functionality for comparative genomics with an intuitive interface. It allows the user to perform the highly customizable visualization of a synteny map by simply uploading nucleotide sequences of interest, ranging from a specific region to the whole genome landscape of microorganisms and viruses. DiGAlign will serve a wide range of biological researchers, particularly experimental biologists, with multifaceted features that allow the rapid characterization of genomic sequences of interest and the generation of a publication-ready figure.}, }
@article {pmid38508273, year = {2024}, author = {O'Donnell, C and Thorn, C and Roskam, E and Friel, R and Kirwan, SF and Waters, SM and O'Flaherty, V}, title = {Novel oxidising feed additives reduce in vitro methane emissions using the rumen simulation technique.}, journal = {The Science of the total environment}, volume = {926}, number = {}, pages = {171808}, doi = {10.1016/j.scitotenv.2024.171808}, pmid = {38508273}, issn = {1879-1026}, mesh = {Animals ; Female ; *Rumen ; *Propionates/metabolism ; Methane/metabolism ; Magnesium Oxide/metabolism ; Diet ; Silage/analysis ; Ruminants ; Acetates/metabolism ; Oxygen/metabolism ; Animal Feed/analysis ; Fermentation ; Digestion ; Lactation ; }, abstract = {Enteric methane (CH4) produced by ruminant livestock is a potent greenhouse gas and represents significant energy loss for the animal. The novel application of oxidising compounds as antimethanogenic agents with future potential to be included in ruminant feeds, was assessed across two separate experiments in this study. Low concentrations of oxidising agents, namely urea hydrogen peroxide (UHP) with and without potassium iodide (KI), and magnesium peroxide (MgO2), were investigated for their effects on CH4 production, total gas production (TGP), volatile fatty acid (VFA) profiles, and nutrient disappearance in vitro using the rumen simulation technique. In both experiments, the in vitro diet consisted of 50:50 grass silage:concentrate on a dry matter basis. Treatment concentrations were based on the amount of oxygen delivered and expressed in terms of fold concentration. In Experiment 1, four treatments were tested (Control, 1× UHP + KI, 1× UHP, and 0.5× UHP + KI), and six treatments were assessed in Experiment 2 (Control, 0.5× UHP + KI, 0.5× UHP, 0.25× UHP + KI, 0.25× UHP, and 0.12× MgO2). All treatments in this study had a reducing effect on CH4 parameters. A dose-dependent reduction of TGP and CH4 parameters was observed, where treatments delivering higher levels of oxygen resulted in greater CH4 suppression. 1× UHP + KI reduced TGP by 28 % (p = 0.611), CH4% by 64 % (p = 0.075) and CH4 mmol/g digestible organic matter by 71 % (p = 0.037). 0.12× MgO2 reduced CH4 volume by 25 % (p > 0.05) without affecting any other parameters. Acetate-to-propionate ratios were reduced by treatments in both experiments (p < 0.01). Molar proportions of acetate and butyrate were reduced, while propionate and valerate were increased in UHP treatments. High concentrations of UHP affected the degradation of neutral detergent fibre in the forage substrate. Future in vitro work should investigate alternative slow-release oxygen sources aimed at prolonging CH4 suppression.}, }
@article {pmid38508106, year = {2024}, author = {Luo, Y and Pang, J and Pan, S and Wang, J and Jiang, X and Xu, Q and Zhang, H and Ruan, C and Ren, J and Zhang, C and Shi, J}, title = {Penicillium oxalicum SL2-enhanced nanoscale zero-valent iron effectively reduces Cr(VI) and shifts soil microbiota.}, journal = {Journal of hazardous materials}, volume = {469}, number = {}, pages = {134058}, doi = {10.1016/j.jhazmat.2024.134058}, pmid = {38508106}, issn = {1873-3336}, mesh = {*Chromium/analysis/metabolism ; *Environmental Restoration and Remediation ; Iron ; *Penicillium ; Soil ; Urease ; *Water Pollutants, Chemical/analysis ; }, abstract = {Most current researches focus solely on reducing soil chromium availability. It is difficult to reduce soil Cr(VI) concentration below 5.0 mg kg[-1] using single remediation technology. This study introduced a sustainable soil Cr(VI) reduction and stabilization system, Penicillium oxalicum SL2-nanoscale zero-valent iron (nZVI), and investigated its effect on Cr(VI) reduction efficiency and microbial ecology. Results showed that P. oxalicum SL2-nZVI effectively reduced soil total Cr(VI) concentration from 187.1 to 3.4 mg kg[-1] within 180 d, and remained relatively stable at 360 d. The growth curve of P. oxalicum SL2 and microbial community results indicated that γ-ray irradiation shortened the adaptation time of P. oxalicum SL2 and facilitated its colonization in soil. P. oxalicum SL2 colonization activated nZVI and its derivatives, and increased soil iron bioavailability. After restoration, the negative effect of Cr(VI) on soil microorganisms was markedly alleviated. Cr(VI), Fe(II), bioavailable Cr/Fe, Eh, EC and urease (SUE) were the key environmental factors of soil microbiota. Notably, Penicillium significantly stimulated the growth of urease-positive bacteria, Arthrobacter, Pseudarthrobacter, and Microvirga, synergistically reducing soil chromium availability. The combination of P. oxalicum SL2 and nZVI is expected to form a green, economical and long-lasting Cr(VI) reduction stabilization strategy.}, }
@article {pmid38507071, year = {2024}, author = {Martin-Pozas, T and Nováková, A and Jurado, V and Cuezva, S and Fernandez-Cortes, A and Saiz-Jimenez, C and Sanchez-Moral, S}, title = {A Second Fungal Outbreak in Castañar Cave, Spain, Discloses the Fragility of Subsurface Ecosystems.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {53}, pmid = {38507071}, issn = {1432-184X}, support = {PID2019-110603RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-114978GB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2019-110603RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2019-110603RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-114978GB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2019-110603RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {*Fungi/genetics ; Spain/epidemiology ; *Ecosystem ; Caves/microbiology ; Disease Outbreaks ; }, abstract = {Castañar is a cave with strict visitor control measures since it was open to public visits in 2003. However, in recent years, the cave suffered two fungal outbreaks, the first in 2008 and controlled by cleaning the contaminated sediments and subsequent closure of the cave until 2014. The cave was reopened but limited to a maximum of 450 visitors/year. Despite these restrictions on visit, the cave experienced a second outbreak in 2021, originating from the installation of a steel grating walkway, aiming at protecting the ground sediments from the visitors' footsteps. Here, we conducted an analysis using Next-Generation Sequencing and culture-dependent techniques to investigate the fungal communities related to the second outbreak and compare with those present before the cave suffered the outbreak. The results show that the most abundant fungi involved in the 2021 outbreak were already detected in 2020, and even in 2008 and 2009, although the main species that originating both outbreaks were different, likely due to the different carbon sources introduced into the cave.}, }
@article {pmid38502221, year = {2024}, author = {Saati-Santamaría, Z and Flores-Félix, JD and Igual, JM and Velázquez, E and García-Fraile, P and Martínez-Molina, E}, title = {Speciation Features of Ferdinandcohnia quinoae sp. nov to Adapt to the Plant Host.}, journal = {Journal of molecular evolution}, volume = {92}, number = {2}, pages = {169-180}, pmid = {38502221}, issn = {1432-1432}, support = {SA293P18//Junta de Castilla y Le&#xf3;n/ ; }, mesh = {*Fatty Acids ; Phylogeny ; *Plants/genetics ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; }, abstract = {The bacterial strain SECRCQ15[T] was isolated from seeds of Chenopodium quinoa in Spain. Phylogenetic, chemotaxonomic, and phenotypic analyses, as well as genome similarity indices, support the classification of the strain into a novel species of the genus Ferdinandcohnia, for which we propose the name Ferdinandcohnia quinoae sp. nov. To dig deep into the speciation features of the strain SECRCQ15[T], we performed a comparative genomic analysis of the genome of this strain and those of the type strains of species from the genus Ferdinandcohnia. We found several genes related with plant growth-promoting mechanisms within the SECRCQ15[T] genome. We also found that singletons of F. quinoae SECRCQ15[T] are mainly related to the use of carbohydrates, which is a common trait of plant-associated bacteria. To further reveal speciation events in this strain, we revealed genes undergoing diversifying selection (e.g., genes encoding ribosomal proteins) and functions likely lost due to pseudogenization. Also, we found that this novel species contains 138 plant-associated gene-cluster functions that are unique within the genus Ferdinandcohnia. These features may explain both the ecological and taxonomical differentiation of this new taxon.}, }
@article {pmid38500703, year = {2024}, author = {Dreyling, L and Penone, C and Schenk, NV and Schmitt, I and Dal Grande, F}, title = {Biotic interactions outweigh abiotic factors as drivers of bark microbial communities in Central European forests.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae012}, pmid = {38500703}, issn = {2730-6151}, abstract = {Bark surfaces are extensive areas within forest ecosystems, which provide an ideal habitat for microbial communities, through their longevity and seasonal stability. Here we provide a comprehensive account of the bark surface microbiome of living trees in Central European forests, and identify drivers of diversity and community composition. We examine algal, fungal, and bacterial communities and their interactions using metabarcoding on samples from over 750 trees collected in the Biodiversity Exploratories in northern, central, and southern Germany. We show that mutual biotic influence is more important than the abiotic environment with regard to community composition, whereas abiotic conditions and geography are more important for alpha diversity. Important abiotic factors are the relative humidity and light availability, which decrease the algal and bacterial alpha diversity but strongly increase fungal alpha diversity. In addition, temperature is important in shaping the microbial community, with higher temperature leading to homogeneous communities of dominant fungi, but high turnover in bacterial communities. Changes in the community dissimilarity of one organismal group occur in close relation to changes in the other two, suggesting that there are close interactions between the three major groups of the bark surface microbial communities, which may be linked to beneficial exchange. To understand the functioning of the forest microbiome as a whole, we need to further investigate the functionality of interactions within the bark surface microbiome and combine these results with findings from other forest habitats such as soil or canopy.}, }
@article {pmid38499207, year = {2024}, author = {Kodama, T and Takehara, T}, title = {Molecular Genealogy of Metabolic-associated Hepatocellular Carcinoma.}, journal = {Seminars in liver disease}, volume = {44}, number = {2}, pages = {147-158}, pmid = {38499207}, issn = {1098-8971}, support = {JP23ama221410,JP23ck0106793,JP23fk0210131//Japan Agency for Medical Research and Development/ ; JP23ama221410//Japan Agency for Medical Research and Development/ ; JP23ck0106793//Japan Agency for Medical Research and Development/ ; JP23fk0210131//Japan Agency for Medical Research and Development/ ; }, mesh = {Humans ; *Carcinoma, Hepatocellular/genetics ; *Liver Neoplasms/genetics ; *Tumor Microenvironment ; *Genetic Predisposition to Disease ; Animals ; Non-alcoholic Fatty Liver Disease/genetics ; Lipid Metabolism/genetics ; Insulin Resistance ; Membrane Proteins/genetics ; Diabetes Mellitus, Type 2/genetics ; Oxidative Stress ; Obesity/genetics/complications ; Risk Factors ; Polymorphism, Single Nucleotide ; Acyltransferases/genetics ; Adaptor Proteins, Signal Transducing ; Phospholipases A2, Calcium-Independent ; }, abstract = {This review examines the latest epidemiological and molecular pathogenic findings of metabolic-associated hepatocellular carcinoma (HCC). Its increasing prevalence is a significant concern and reflects the growing burden of obesity and metabolic diseases, including metabolic dysfunction-associated steatotic liver disease, formerly known as nonalcoholic fatty liver disease, and type 2 diabetes. Metabolic-associated HCC has unique molecular abnormality and distinctive gene expression patterns implicating aberrations in bile acid, fatty acid metabolism, oxidative stress, and proinflammatory pathways. Furthermore, a notable frequency of single nucleotide polymorphisms in genes such as patatin-like phospholipase domain-containing 3, transmembrane 6 superfamily member 2, glucokinase regulator, and membrane-bound O-acyltransferase domain-containing 7 has been observed. The tumor immune microenvironment of metabolic-associated HCC is characterized by unique phenotypes of macrophages, neutrophils, and T lymphocytes. Additionally, the pathogenesis of metabolic-associated HCC is influenced by abnormal lipid metabolism, insulin resistance, and dysbiosis. In conclusion, deciphering the intricate interactions among metabolic processes, genetic predispositions, inflammatory responses, immune regulation, and microbial ecology is imperative for the development of novel therapeutic and preventative measures against metabolic-associated HCC.}, }
@article {pmid38498218, year = {2024}, author = {Greipel, E and Nagy, K and Csákvári, E and Dér, L and Galajda, P and Kutasi, J}, title = {Chemotactic Interactions of Scenedesmus sp. and Azospirillum brasilense Investigated by Microfluidic Methods.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {52}, pmid = {38498218}, issn = {1432-184X}, mesh = {*Azospirillum brasilense ; *Scenedesmus/metabolism ; Microfluidics ; Oxaloacetic Acid/metabolism ; Plant Growth Regulators/metabolism ; Plants/metabolism ; }, abstract = {The use of algae for industrial, biotechnological, and agricultural purposes is spreading globally. Scenedesmus species can play an essential role in the food industry and agriculture due to their favorable nutrient content and plant-stimulating properties. Previous research and the development of Scenedesmus-based foliar fertilizers raised several questions about the effectiveness of large-scale algal cultivation and the potential effects of algae on associative rhizobacteria. In the microbiological practice applied in agriculture, bacteria from the genus Azospirillum are one of the most studied plant growth-promoting, associative, nitrogen-fixing bacteria. Co-cultivation with Azospirillum species may be a new way of optimizing Scenedesmus culturing, but the functioning of the co-culture system still needs to be fully understood. It is known that Azospirillum brasilense can produce indole-3-acetic acid, which could stimulate algae growth as a plant hormone. However, the effect of microalgae on Azospirillum bacteria is unclear. In this study, we investigated the behavior of Azospirillum brasilense bacteria in the vicinity of Scenedesmus sp. or its supernatant using a microfluidic device consisting of physically separated but chemically coupled microchambers. Following the spatial distribution of bacteria within the device, we detected a positive chemotactic response toward the microalgae culture. To identify the metabolites responsible for this behavior, we tested the chemoeffector potential of citric acid and oxaloacetic acid, which, according to our HPLC analysis, were present in the algae supernatant in 0.074 mg/ml and 0.116 mg/ml concentrations, respectively. We found that oxaloacetic acid acts as a chemoattractant for Azospirillum brasilense.}, }
@article {pmid38497641, year = {2024}, author = {Dean, CJ and Peña-Mosca, F and Ray, T and Wehri, TJ and Sharpe, K and Antunes, AM and Doster, E and Fernandes, L and Calles, VF and Bauman, C and Godden, S and Heins, B and Pinedo, P and Machado, VS and Caixeta, LS and Noyes, NR}, title = {Exploring associations between the teat apex metagenome and Staphylococcus aureus intramammary infections in primiparous cows under organic directives.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {4}, pages = {e0223423}, pmid = {38497641}, issn = {1098-5336}, mesh = {Female ; Cattle ; Animals ; Staphylococcus aureus/genetics ; Metagenome ; Case-Control Studies ; *Mastitis, Bovine/epidemiology/microbiology ; *Staphylococcal Infections/epidemiology/veterinary/microbiology ; Milk/microbiology ; Mammary Glands, Animal/microbiology ; }, abstract = {UNLABELLED: The primary objective of this study was to identify associations between the prepartum teat apex microbiome and the presence of Staphylococcus aureus intramammary infections (IMI) in primiparous cows during the first 5 weeks after calving. We performed a case-control study using shotgun metagenomics of the teat apex and culture-based milk data collected longitudinally from 710 primiparous cows on five organic dairy farms. Cases had higher odds of having S. aureus metagenomic DNA on the teat apex prior to parturition compared to controls (OR = 38.9, 95% CI: 14.84-102.21). Differential abundance analysis confirmed this association, with cases having a 23.8 higher log fold change (LFC) in the abundance of S. aureus in their samples compared to controls. Of the most prevalent microorganisms in controls, those associated with a lower risk of post-calving S. aureus IMI included Microbacterium phage Min 1 (OR = 0.37, 95% CI: 0.25-0.53), Corynebacterium efficiens (OR = 0.53, 95% CI: 0.30-0.94), Kocuria polaris (OR = 0.54, 95% CI: 0.35-0.82), Micrococcus terreus (OR = 0.64, 95% CI: 0.44-0.93), and Dietzia alimentaria (OR = 0.45, 95% CI: 0.26-0.75). Genes encoding for Microcin B17 AMPs were the most prevalent on the teat apex of cases and controls (99.7% in both groups). The predicted abundance of genes encoding for Microcin B17 was also higher in cases compared to controls (LFC 0.26).<br><br>IMPORTANCE: Intramammary infections (IMI) caused by Staphylococcus aureus remain an important problem for the dairy industry. The microbiome on the external skin of the teat apex may play a role in mitigating S. aureus IMI risk, in particular the production of antimicrobial peptides (AMPs) by commensal microbes. However, current studies of the teat apex microbiome utilize a 16S approach, which precludes the detection of genomic features such as genes that encode for AMPs. Therefore, further research using a shotgun metagenomic approach is needed to understand what role prepartum teat apex microbiome dynamics play in IMI risk.}, }
@article {pmid38494494, year = {2024}, author = {Liu, X and Salles, JF}, title = {Lose-lose consequences of bacterial community-driven invasions in soil.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {57}, pmid = {38494494}, issn = {2049-2618}, mesh = {*Soil ; Soil Microbiology ; Bacteria/genetics/metabolism ; *Microbiota ; }, abstract = {BACKGROUND: Community-driven invasion, also known as community coalescence, occurs widely in natural ecosystems. Despite that, our knowledge about the process and mechanisms controlling community-driven invasion in soil ecosystems is lacking. Here, we performed a set of coalescence experiments in soil microcosms and assessed impacts up to 60 days after coalescence by quantifying multiple traits (compositional, functional, and metabolic) of the invasive and coalescent communities.<br><br>RESULTS: Our results showed that coalescences significantly triggered changes in the resident community's succession trajectory and functionality (carbohydrate metabolism), even when the size of the invasive community is small (~&#x2009;5% of the resident density) and 99% of the invaders failed to survive. The invasion impact was mainly due to the high suppression of constant residents (65% on average), leading to a lose-lose situation where both invaders and residents suffered with coalescence. Our results showed that surviving residents could benefit from the coalescence, which supports the theory of "competition-driven niche segregation" at the microbial community level. Furthermore, the result showed that both short- and long-term coalescence effects were predicted by similarity and unevenness indexes of compositional, functional, and metabolic traits of invasive communities. This indicates the power of multi-level traits in monitoring microbial community succession. In contrast, the varied importance of different levels of traits suggests that competitive processes depend on the composition of the invasive community.<br><br>CONCLUSIONS: Our results shed light on the process and consequence of community coalescences and highlight that resource competition between invaders and residents plays a critical role in soil microbial community coalescences. These findings provide valuable insights for understanding and predicting soil microbial community succession in frequently disturbed natural and agroecosystems. Video Abstract.}, }
@article {pmid38493536, year = {2024}, author = {Mekonnen, YT and Savini, F and Indio, V and Seguino, A and Giacometti, F and Serraino, A and Candela, M and De Cesare, A}, title = {Systematic review on microbiome-related nutritional interventions interfering with the colonization of foodborne pathogens in broiler gut to prevent contamination of poultry meat.}, journal = {Poultry science}, volume = {103}, number = {5}, pages = {103607}, pmid = {38493536}, issn = {1525-3171}, mesh = {Animals ; *Chickens ; *Gastrointestinal Microbiome ; *Poultry Diseases/prevention &amp; control/microbiology ; Meat/analysis ; Probiotics/administration &amp; dosage/pharmacology ; Animal Feed/analysis ; Food Microbiology ; Foodborne Diseases/veterinary/prevention &amp; control/microbiology ; Diet/veterinary ; }, abstract = {This systematic review aimed to compile the available body of knowledge about microbiome-related nutritional interventions contributing to improve the chicken health and having an impact on the reduction of colonization by foodborne pathogens in the gut. Original research articles published between 2012 and 2022 were systematically searched in Scopus and PubMed. A total of 1,948 articles were retrieved and 140 fulfilled the inclusion criteria. Overall, 73 papers described 99 interventions against colonization by Escherichia coli and related organisms; 10 papers described 15 interventions against Campylobacter spp.; 36 papers described 54 interventions against Salmonella; 40 papers described 54 interventions against Clostridium perfringens. A total of 197 microbiome-related interventions were identified as effective against one or more of the listed pathogens and included probiotics (n = 80), prebiotics (n = 23), phytobiotics (n = 25), synbiotics (n = 12), organic acids (n = 12), enzymes (n = 4), essential oils (n = 14) and combination of these (n = 27). The identified interventions were mostly administered in the feed (173/197) or through oral gavage (11/197), in the drinking water (7/197), in ovo (2/197), intra amniotic (2/197), in fresh or reused litter (1/197) or both in the feed and water (1/197). The interventions enhanced the beneficial microbial communities in the broiler gut as Lactic acid bacteria, mostly Lactobacillus spp., or modulated multiple microbial populations. The mechanisms promoting the fighting against colonization by foodborne pathogens included competitive exclusion, production of short chain fatty acids, decrease of gut pH, restoration of the microbiome after dysbiosis events, promotion of a more stable microbial ecology, expression of genes improving the integrity of intestinal mucosa, enhancing of mucin production and improvement of host immune response. All the studies extracted from the literature described in vivo trials but performed on a limited number of animals under experimental settings. Moreover, they detailed the effect of the intervention on the chicken gut without details on further impact on poultry meat safety.}, }
@article {pmid38493186, year = {2024}, author = {Wu, L and Wang, XW and Tao, Z and Wang, T and Zuo, W and Zeng, Y and Liu, YY and Dai, L}, title = {Data-driven prediction of colonization outcomes for complex microbial communities.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {2406}, pmid = {38493186}, issn = {2041-1723}, support = {U19 AI095219/AI/NIAID NIH HHS/United States ; U01 HL089856/HL/NHLBI NIH HHS/United States ; R01 AI141529/AI/NIAID NIH HHS/United States ; R01 HD093761/HD/NICHD NIH HHS/United States ; UH3 OD023268/OD/NIH HHS/United States ; RF1 AG067744/AG/NIA NIH HHS/United States ; K25 HL166208/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; Feces/microbiology ; *Enterococcus faecium ; Microbial Interactions ; Enterococcus faecalis ; }, abstract = {Microbial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the colonization of exogenous species in complex communities remains a fundamental challenge in microbial ecology, mainly due to our limited knowledge of the diverse mechanisms governing microbial dynamics. Here, we propose a data-driven approach independent of any dynamics model to predict colonization outcomes of exogenous species from the baseline compositions of microbial communities. We systematically validate this approach using synthetic data, finding that machine learning models can predict not only the binary colonization outcome but also the post-invasion steady-state abundance of the invading species. Then we conduct colonization experiments for commensal gut bacteria species Enterococcus faecium and Akkermansia muciniphila in hundreds of human stool-derived in vitro microbial communities, confirming that the data-driven approaches can predict the colonization outcomes in experiments. Furthermore, we find that while most resident species are predicted to have a weak negative impact on the colonization of exogenous species, strongly interacting species could significantly alter the colonization outcomes, e.g., Enterococcus faecalis inhibits the invasion of E. faecium invasion. The presented results suggest that the data-driven approaches are powerful tools to inform the ecology and management of microbial communities.}, }
@article {pmid38492828, year = {2024}, author = {Malik, M and Das, S and Chakraborty, P and Paul, P and Roy, R and Das Gupta, A and Sarkar, S and Chatterjee, S and Maity, A and Dasgupta, M and Sarker, RK and Tribedi, P}, title = {Application of cuminaldehyde and ciprofloxacin for the effective control of biofilm assembly of Pseudomonas aeruginosa: A combinatorial study.}, journal = {Microbial pathogenesis}, volume = {190}, number = {}, pages = {106624}, doi = {10.1016/j.micpath.2024.106624}, pmid = {38492828}, issn = {1096-1208}, mesh = {*Biofilms/drug effects ; *Ciprofloxacin/pharmacology ; *Pseudomonas aeruginosa/drug effects/physiology ; *Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; *Benzaldehydes/pharmacology ; *Reactive Oxygen Species/metabolism ; Virulence Factors ; Cymenes/pharmacology ; Drug Synergism ; Cell Membrane Permeability/drug effects ; Humans ; }, abstract = {Pseudomonas aeruginosa is widely associated with biofilm-mediated antibiotic resistant chronic and acute infections which constitute a persistent healthcare challenges. Addressing this threat requires exploration of novel therapeutic strategies involving the combination of natural compounds and conventional antibiotics. Hence, our study has focused on two compounds; cuminaldehyde and ciprofloxacin, which were strategically combined to target the biofilm challenge of P. aeruginosa. The minimum inhibitory concentration (MIC) of cuminaldehyde and ciprofloxacin was found to be 400 μg/mL and 0.4 μg/mL, respectively. Moreover, the fractional inhibitory concentration index (FICI = 0.62) indicated an additive interaction prevailed between cuminaldehyde and ciprofloxacin. Subsequently, sub-MIC doses of cuminaldehyde (25 μg/mL) and ciprofloxacin (0.05 μg/mL) were selected for an array of antibiofilm assays which confirmed their biofilm inhibitory potential without exhibiting any antimicrobial activity. Furthermore, selected doses of the mentioned compounds could manage biofilm on catheter surface by inhibiting and disintegrating existing biofilm. Additionally, the test combination of the mentioned compounds reduced virulence factors secretion, accumulated reactive oxygen species and increased cell-membrane permeability. Thus, the combination of cuminaldehyde and ciprofloxacin demonstrates potential in combating biofilm-associated Pseudomonal threats.}, }
@article {pmid38492604, year = {2024}, author = {Zhao, S and Zheng, Q and Wang, H and Fan, X}, title = {Nitrogen in landfills: Sources, environmental impacts and novel treatment approaches.}, journal = {The Science of the total environment}, volume = {924}, number = {}, pages = {171725}, doi = {10.1016/j.scitotenv.2024.171725}, pmid = {38492604}, issn = {1879-1026}, abstract = {Nitrogen (N) accumulation in landfills is a pressing environmental concern due to its diverse sources and significant environmental impacts. However, there is relatively limited attention and research focus on N in landfills as it is overshadowed by other more prominent pollutants. This study comprehensively examines the sources of N in landfills, including food waste contributing to 390 million tons of N annually, industrial discharges, and sewage treatment plant effluents. The environmental impacts of N in landfills are primarily manifested in N2O emissions and leachate with high N concentrations. To address these challenges, this study presents various mitigation and management strategies, including N2O reduction measures and novel NH4[+] removal techniques, such as electrochemical technologies, membrane separation processes, algae-based process, and other advanced oxidation processes. However, a more in-depth understanding of the complexities of N cycling in landfills is required, due to the lack of long-term monitoring data and the presence of intricate interactions and feedback mechanisms. To ultimately achieve optimized N management and minimized adverse environmental impacts in landfill settings, future prospects should emphasize advancements in monitoring and modeling technologies, enhanced understanding of microbial ecology, implementation of circular economy principles, application of innovative treatment technologies, and comprehensive landfill design and planning.}, }
@article {pmid38491554, year = {2024}, author = {Xu, G and Zhao, S and Rogers, MJ and Chen, C and He, J}, title = {Global prevalence of organohalide-respiring bacteria dechlorinating polychlorinated biphenyls in sewage sludge.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {54}, pmid = {38491554}, issn = {2049-2618}, support = {R-302-000-198720//Ng Teng Fong Charitable Foundation (NTFCF)/ ; MOE-00003301//The Ministry of Education, Singapore/ ; }, mesh = {Humans ; *Polychlorinated Biphenyls/analysis ; Sewage ; *Chloroflexi/genetics ; Prevalence ; Biodegradation, Environmental ; Bacteria/genetics/metabolism ; *Environmental Pollutants/analysis ; Geologic Sediments/microbiology ; }, abstract = {BACKGROUND: Massive amounts of sewage sludge are generated during biological sewage treatment and are commonly subjected to anaerobic digestion, land application, and landfill disposal. Concurrently, persistent organic pollutants (POPs) are frequently found in sludge treatment and disposal systems, posing significant risks to both human health and wildlife. Metabolically versatile microorganisms originating from sewage sludge are inevitably introduced to sludge treatment and disposal systems, potentially affecting the fate of POPs. However, there is currently a dearth of comprehensive assessments regarding the capability of sewage sludge microbiota from geographically disparate regions to attenuate POPs and the underpinning microbiomes.<br><br>RESULTS: Here we report the global prevalence of organohalide-respiring bacteria (OHRB) known for their capacity to attenuate POPs in sewage sludge, with an occurrence frequency of ~50% in the investigated samples (605 of 1186). Subsequent laboratory tests revealed microbial reductive dechlorination of polychlorinated biphenyls (PCBs), one of the most notorious categories of POPs, in 80 out of 84 sludge microcosms via various pathways. Most chlorines were removed from the para- and meta-positions of PCBs; nevertheless, ortho-dechlorination of PCBs also occurred widely, although to lower extents. Abundances of several well-characterized OHRB genera (Dehalococcoides, Dehalogenimonas, and Dehalobacter) and uncultivated Dehalococcoidia lineages increased during incubation and were positively correlated with PCB dechlorination, suggesting their involvement in dechlorinating PCBs. The previously identified PCB reductive dehalogenase (RDase) genes pcbA4 and pcbA5 tended to coexist in most sludge microcosms, but the low ratios of these RDase genes to OHRB abundance also indicated the existence of currently undescribed RDases in sewage sludge. Microbial community analyses revealed a positive correlation between biodiversity and PCB dechlorination activity although there was an apparent threshold of community co-occurrence network complexity beyond which dechlorination activity decreased.<br><br>CONCLUSIONS: Our findings that sludge microbiota exhibited nearly ubiquitous dechlorination of PCBs indicate widespread and nonnegligible impacts of sludge microbiota on the fate of POPs in sludge treatment and disposal systems. The existence of diverse OHRB also suggests sewage sludge as an alternative source to obtain POP-attenuating consortia and calls for further exploration of OHRB populations in sewage sludge. Video Abstract.}, }
@article {pmid38488929, year = {2024}, author = {Dayang Najwa, AB and Elexson, N and Dalene, L and Teng, ST}, title = {Vibrio Species and Cyanobacteria: Understanding Their Association in Local Shrimp Farm Using Canonical Correspondence Analysis (CCA).}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {51}, pmid = {38488929}, issn = {1432-184X}, mesh = {Animals ; *Vibrio ; *Cyanobacteria ; Ponds ; Water ; Aquaculture ; *Vibrio parahaemolyticus ; *Penaeidae/microbiology ; }, abstract = {In aquatic environments, Vibrio and cyanobacteria establish varying relationships influenced by environmental factors. To investigate their association, this study spanned 5 months at a local shrimp farm, covering the shrimp larvae stocking cycle until harvesting. A total of 32 samples were collected from pond A (n = 6), pond B (n = 6), effluent (n = 10), and influent (n = 10). Vibrio species and cyanobacteria density were observed, and canonical correspondence analysis (CCA) assessed their correlation. CCA revealed a minor correlation (p = 0.847, 0.255, 0.288, and 0.304) between Vibrio and cyanobacteria in pond A, pond B, effluent, and influent water, respectively. Notably, Vibrio showed a stronger correlation with pH (6.14-7.64), while cyanobacteria correlated with pH, salinity (17.4-24 ppt), and temperature (30.8-31.5 °C), with salinity as the most influential factor. This suggests that factors beyond cyanobacteria influence Vibrio survival. Future research could explore species-specific relationships, regional dynamics, and multidimensional landscapes to better understand Vibrio-cyanobacteria connections. Managing water parameters may prove more efficient in controlling vibriosis in shrimp farms than targeting cyanobacterial populations.}, }
@article {pmid38488280, year = {2024}, author = {Giacomini, JJ and Torres-Morales, J and Tang, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Spatial ecology of Haemophilus and Aggregatibacter in the human oral cavity.}, journal = {Microbiology spectrum}, volume = {12}, number = {4}, pages = {e0401723}, pmid = {38488280}, issn = {2165-0497}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; Aggregatibacter/physiology ; Phylogeny ; *Ecosystem ; *Haemophilus/genetics ; Mouth ; }, abstract = {UNLABELLED: Haemophilus and Aggregatibacter are two of the most common bacterial genera in the human oral cavity, encompassing both commensals and pathogens of substantial ecological and medical significance. In this study, we conducted a metapangenomic analysis of oral Haemophilus and Aggregatibacter species to uncover genomic diversity, phylogenetic relationships, and habitat specialization within the human oral cavity. Using three metrics-pangenomic gene content, phylogenomics, and average nucleotide identity (ANI)-we first identified distinct species and sub-species groups among these genera. Mapping of metagenomic reads then revealed clear patterns of habitat specialization, such as Aggregatibacter species predominantly in dental plaque, a distinctive Haemophilus parainfluenzae sub-species group on the tongue dorsum, and H. sp. HMT-036 predominantly in keratinized gingiva and buccal mucosa. In addition, we found that supragingival plaque samples contained predominantly only one out of the three taxa, H. parainfluenzae, Aggregatibacter aphrophilus, and A. sp. HMT-458, suggesting independent niches or a competitive relationship. Functional analyses revealed the presence of key metabolic genes, such as oxaloacetate decarboxylase, correlated with habitat specialization, suggesting metabolic versatility as a driving force. Additionally, heme synthesis distinguishes H. sp. HMT-036 from closely related Haemophilus haemolyticus, suggesting that the availability of micronutrients, particularly iron, was important in the evolutionary ecology of these species. Overall, our study exemplifies the power of metapangenomics to identify factors that may affect ecological interactions within microbial communities, including genomic diversity, habitat specialization, and metabolic versatility.<br><br>IMPORTANCE: Understanding the microbial ecology of the mouth is essential for comprehending human physiology. This study employs metapangenomics to reveal that various Haemophilus and Aggregatibacter species exhibit distinct ecological preferences within the oral cavity of healthy individuals, thereby supporting the site-specialist hypothesis. Additionally, it was observed that the gene pool of different Haemophilus species correlates with their ecological niches. These findings shed light on the significance of key metabolic functions in shaping microbial distribution patterns and interspecies interactions in the oral ecosystem.}, }
@article {pmid38485445, year = {2024}, author = {Harris, TD and Reinl, KL and Azarderakhsh, M and Berger, SA and Berman, MC and Bizic, M and Bhattacharya, R and Burnet, SH and Cianci-Gaskill, JA and Domis, LNS and Elfferich, I and Ger, KA and Grossart, HF and Ibelings, BW and Ionescu, D and Kouhanestani, ZM and Mauch, J and McElarney, YR and Nava, V and North, RL and Ogashawara, I and Paule-Mercado, MCA and Soria-Píriz, S and Sun, X and Trout-Haney, JV and Weyhenmeyer, GA and Yokota, K and Zhan, Q}, title = {What makes a cyanobacterial bloom disappear? A review of the abiotic and biotic cyanobacterial bloom loss factors.}, journal = {Harmful algae}, volume = {133}, number = {}, pages = {102599}, doi = {10.1016/j.hal.2024.102599}, pmid = {38485445}, issn = {1878-1470}, mesh = {*Cyanobacteria/physiology ; *Harmful Algal Bloom ; }, abstract = {Cyanobacterial blooms present substantial challenges to managers and threaten ecological and public health. Although the majority of cyanobacterial bloom research and management focuses on factors that control bloom initiation, duration, toxicity, and geographical extent, relatively little research focuses on the role of loss processes in blooms and how these processes are regulated. Here, we define a loss process in terms of population dynamics as any process that removes cells from a population, thereby decelerating or reducing the development and extent of blooms. We review abiotic (e.g., hydraulic flushing and oxidative stress/UV light) and biotic factors (e.g., allelopathic compounds, infections, grazing, and resting cells/programmed cell death) known to govern bloom loss. We found that the dominant loss processes depend on several system specific factors including cyanobacterial genera-specific traits, in situ physicochemical conditions, and the microbial, phytoplankton, and consumer community composition. We also address loss processes in the context of bloom management and discuss perspectives and challenges in predicting how a changing climate may directly and indirectly affect loss processes on blooms. A deeper understanding of bloom loss processes and their underlying mechanisms may help to mitigate the negative consequences of cyanobacterial blooms and improve current management strategies.}, }
@article {pmid38485438, year = {2024}, author = {Woodhouse, JN and Burford, MA and Neilan, BA and Jex, A and Tichkule, S and Sivonen, K and Fewer, DP and Grossart, HP and Willis, A}, title = {Long-term stability of the genome structure of the cyanobacterium, Dolichospermum in a deep German lake.}, journal = {Harmful algae}, volume = {133}, number = {}, pages = {102600}, doi = {10.1016/j.hal.2024.102600}, pmid = {38485438}, issn = {1878-1470}, support = {/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Lakes/microbiology ; *Cyanobacteria/genetics ; Phytoplankton ; Biomass ; Phosphorus ; }, abstract = {Dolichospermum is a cyanobacterial genus commonly associated with toxic blooms in lakes and brackish water bodies worldwide, and is a long-term resident of Lake Stechlin, northeastern Germany. In recent decades, shifts in the phosphorus loading and phytoplankton species composition have seen increased biomass of Dolichospermum during summer blooms from 1998, peaking around 2005, and declining after 2020. Cyanobacteria are known to rapidly adapt to new environments, facilitated by genome adaptation. To investigate the changes in genomic features that may have occurred in Lake Stechlin Dolichospermum during this time of increased phosphorus loading and higher biomass, whole genome sequence analysis was performed on samples of ten akinetes isolated from ten, 1 cm segments of a sediment core, representing a ∼45-year period from 1970 to 2017. Comparison of these genomes with genomes of extant isolates revealed a clade of Dolichospermum that clustered with the ADA-6 genus complex, with remarkable genome stability, without gene gain or loss events in response to recent environmental changes. The genome characteristics indicate that this species is suited to a deep-chlorophyll maximum, including additional light-harvesting and phosphorus scavenging genes. Population SNP analysis revealed two sub-populations that shifted in dominance as the lake transitioned between oligotrophic and eutrophic conditions. Overall, the results show little change within the population, despite diversity between extant populations from different geographic locations and the in-lake changes in phosphorus concentrations.}, }
@article {pmid38484962, year = {2024}, author = {Fang, X and Colina Blanco, AE and Christl, I and Le Bars, M and Straub, D and Kleindienst, S and Planer-Friedrich, B and Zhao, FJ and Kappler, A and Kretzschmar, R}, title = {Simultaneously decreasing arsenic and cadmium in rice by soil sulfate and limestone amendment under intermittent flooding.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {347}, number = {}, pages = {123786}, doi = {10.1016/j.envpol.2024.123786}, pmid = {38484962}, issn = {1873-6424}, mesh = {Cadmium/analysis ; *Arsenic/analysis ; Calcium Carbonate ; Soil ; *Oryza ; Sulfates ; Clay ; Sulfur Oxides ; Sand ; *Soil Pollutants/analysis ; *Oxides ; *Calcium Compounds ; }, abstract = {Water management in paddy soils can effectively reduce the soil-to-rice grain transfer of either As or Cd, but not of both elements simultaneously due to the higher mobility of As under reducing and Cd under oxidizing soil conditions. Limestone amendment, the common form of liming, is well known for decreasing Cd accumulation in rice grown on acidic soils. Sulfate amendment was suggested to effectively decrease As accumulation in rice, especially under intermittent soil flooding. To study the unknown effects of combined sulfate and limestone amendment under intermittent flooding for simultaneously decreasing As and Cd in rice, we performed a pot experiment using an acidic sandy loam paddy soil. We also included a clay loam paddy soil to study the role of soil texture in low-As rice production under intermittent flooding. We found that liming not only decreased rice Cd concentrations but also greatly decreased dimethylarsenate (DMA) accumulation in rice. We hypothesize that this is due to suppressed sulfate reduction, As methylation, and As thiolation by liming in the sulfate-amended soil and a higher share of deprotonated DMA at higher pH which is taken up less readily than protonated DMA. Decreased gene abundance of potential soil sulfate-reducers by liming further supported our hypothesis. Combined sulfate and limestone amendment to the acidic sandy loam soil produced rice with 43% lower inorganic As, 72% lower DMA, and 68% lower Cd compared to the control soil without amendment. A tradeoff between soil aeration and water availability was observed for the clay loam soil, suggesting difficulties to decrease As in rice while avoiding plant water stress under intermittent flooding in fine-textured soils. Our results suggest that combining sulfate amendment, liming, and intermittent flooding can help to secure rice safety when the presence of both As and Cd in coarse-textured soils is of concern.}, }
@article {pmid38483479, year = {2024}, author = {Mermans, F and De Baets, H and García-Timermans, C and Teughels, W and Boon, N}, title = {Unlocking the mechanism of action: a cost-effective flow cytometry approach for accelerating antimicrobial drug development.}, journal = {Microbiology spectrum}, volume = {12}, number = {4}, pages = {e0393123}, pmid = {38483479}, issn = {2165-0497}, support = {G0B2719N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; }, mesh = {Humans ; *Cephalothin ; Flow Cytometry ; Cost-Benefit Analysis ; *Anti-Infective Agents/pharmacology ; Drug Development ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antimicrobial resistance is one of the greatest challenges to global health. While the development of new antimicrobials can combat resistance, low profitability reduces the number of new compounds brought to market. Elucidating the mechanism of action is crucial for developing new antimicrobials. This can become expensive as there are no universally applicable pipelines. Phenotypic heterogeneity of microbial populations resulting from antimicrobial treatment can be captured through flow cytometric fingerprinting. Since antimicrobials are classified into limited groups, the mechanism of action of known compounds can be used for predictive modeling. We demonstrate a cost-effective flow cytometry approach for determining the mechanism of action of new compounds. Cultures of Actinomyces viscosus and Fusobacterium nucleatum were treated with different antimicrobials and measured by flow cytometry. A Gaussian mixture mask was applied over the data to construct phenotypic fingerprints. Fingerprints were used to assess statistical differences between mechanism of action groups and to train random forest classifiers. Classifiers were then used to predict the mechanism of action of cephalothin. Statistical differences were found among the different mechanisms of action groups. Pairwise comparison showed statistical differences for 35 out of 45 pairs for A. viscosus and for 32 out of 45 pairs for F. nucleatum after 3.5 h of treatment. The best-performing random forest classifier yielded a Matthews correlation coefficient of 0.92 and the mechanism of action of cephalothin could be successfully predicted. These findings suggest that flow cytometry can be a cheap and fast alternative for determining the mechanism of action of new antimicrobials.IMPORTANCEIn the context of the emerging threat of antimicrobial resistance, the development of novel antimicrobials is a commonly employed strategy to combat resistance. Elucidating the mechanism of action of novel compounds is crucial in this development but can become expensive, as no universally applicable pipelines currently exist. We present a novel flow cytometry-based approach capable of determining the mechanism of action swiftly and cost-effectively. The workflow aims to accelerate drug discovery and could help facilitate a more targeted approach for antimicrobial treatment of patients.}, }
@article {pmid38481338, year = {2024}, author = {Sun, J and Zhao, J and Liu, M and Li, J and Cheng, J and Li, W and Yuan, M and Xiao, S and Xue, C}, title = {SreC-dependent adaption to host iron environments regulates the transition of trophic stages and developmental processes of Curvularia lunata.}, journal = {Molecular plant pathology}, volume = {25}, number = {3}, pages = {e13444}, pmid = {38481338}, issn = {1364-3703}, support = {31271992//National Natural Science Foundation of China/ ; 2022JH2/101300168//Liaoning Provincial Applied Basic Program/ ; }, mesh = {*Iron/metabolism ; *Fungal Proteins/genetics/metabolism ; Virulence ; *Curvularia ; }, abstract = {Plant pathogens are challenged by host-derived iron starvation or excess during infection, but the mechanism of plant pathogens rapidly adapting to the dynamic host iron environments to assimilate iron for invasion and colonization remains largely unexplored. Here, we found that the GATA transcription factor SreC in Curvularia lunata is required for virulence and adaption to the host iron excess environment. SreC directly binds to the ATGWGATAW element in an iron-dependent manner to regulate the switch between different iron assimilation pathways, conferring adaption to host iron environments in different trophic stages of C. lunata. SreC also regulates the transition of trophic stages and developmental processes in C. lunata. SreC-dependent adaption to host iron environments is essential to the infectious growth and survival of C. lunata. We also demonstrate that CgSreA (a SreC orthologue) plays a similar role in Colletotrichum graminicola. We conclude that Sre mediates adaption to the host iron environment during infection, and the function is conserved in hemibiotrophic fungi.}, }
@article {pmid38480488, year = {2024}, author = {Munley, JA and Kelly, LS and Park, G and Drury, SK and Gillies, GS and Coldwell, PS and Kannan, KB and Bible, LE and Efron, PA and Nagpal, R and Mohr, AM}, title = {Acute emergence of the intestinal pathobiome after postinjury pneumonia.}, journal = {The journal of trauma and acute care surgery}, volume = {97}, number = {1}, pages = {65-72}, pmid = {38480488}, issn = {2163-0763}, support = {R01 GM105893/GM/NIGMS NIH HHS/United States ; T32 GM008721/GM/NIGMS NIH HHS/United States ; T32 HL160491/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; *Rats, Sprague-Dawley ; Female ; Male ; Rats ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Sex Factors ; Disease Models, Animal ; Sepsis/microbiology ; Pneumonia/microbiology/etiology ; }, abstract = {BACKGROUND: Previous preclinical studies have demonstrated sex-specific alterations in the gut microbiome following traumatic injury or sepsis alone; however, the impact of host sex on dysbiosis in the setting of postinjury sepsis acutely is unknown. We hypothesized that multicompartmental injury with subsequent pneumonia would result in host sex-specific dysbiosis.<br><br>METHODS: Male and proestrus female Sprague-Dawley rats (n = 8/group) were subjected to either multicompartmental trauma (PT) (lung contusion, hemorrhagic shock, cecectomy, bifemoral pseudofracture), PT plus 2-hour daily restraint stress (PT/RS), PT with postinjury day 1 Pseudomonas aeruginosa pneumonia (PT-PNA), PT/RS with pneumonia (PT/RS-PNA), or naive controls. Fecal microbiome was measured on days 0 and 2 using high-throughput 16S rRNA sequencing and Quantitative Insights Into Microbial Ecology 2 bioinformatics analyses. Microbial &#x3b1;-diversity was assessed using Chao1 (number of different unique species) and Shannon (species richness and evenness) indices. &#x3b2;-diversity was assessed using principal coordinate analysis. Significance was defined as p < 0.05.<br><br>RESULTS: All groups had drastic declines in the Chao1 (&#x3b1;-diversity) index compared with naive controls (p < 0.05). Groups PT-PNA and PT/RS-PNA resulted in different &#x3b2;-diversity arrays compared with uninfected counterparts (PT, PT/RS) (p = 0.001). Postinjury sepsis cohorts showed a loss of commensal bacteria along with emergence of pathogenic bacteria, with blooms of Proteus in PT-PNA and Escherichia-Shigella group in PT/RS-PNA compared with other cohorts. At day 2, PT-PNA resulted in &#x3b2;-diversity, which was unique between males and females (p = 0.004). Microbiome composition in PT-PNA males was dominated by Anaerostipes and Parasuterella , whereas females had increased Barnesiella and Oscillibacter . The PT/RS males had an abundance of Gastranaerophilales and Muribaculaceae .<br><br>CONCLUSION: Multicompartmental trauma complicated by sepsis significantly diminishes diversity and alters microbial composition toward a severely dysbiotic state early after injury, which varies between males and females. These findings highlight the role of sex in postinjury sepsis and the pathobiome, which may influence outcomes after severe trauma and sepsis.}, }
@article {pmid38477597, year = {2024}, author = {Miliotis, G and Sengupta, P and Hameed, A and Chuvochina, M and McDonagh, F and Simpson, AC and Parker, CW and Singh, NK and Rekha, PD and Morris, D and Raman, K and Kyrpides, NC and Hugenholtz, P and Venkateswaran, K}, title = {Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov.}, journal = {mBio}, volume = {15}, number = {4}, pages = {e0018124}, pmid = {38477597}, issn = {2150-7511}, support = {FutureCare Seed Fund//University of Galway (NUI Galway)/ ; 2012 Space Biology NNH12ZTT001N grant no. 19-12829-26//National Aeronautics and Space Administration (NASA)/ ; DP220100900//Australian Research Council Discovery Project/ ; //U.S. Department of Energy Joint Genome Institute, DOE Office of Science User Facility, U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231/ ; }, mesh = {Humans ; *Fatty Acids/analysis ; *Ceftazidime ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Base Composition ; Nucleic Acid Hybridization ; Spores/chemistry ; Nucleotides ; DNA ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; Bacterial Typing Techniques ; }, abstract = {UNLABELLED: A comprehensive microbial surveillance was conducted at NASA's Mars 2020 spacecraft assembly facility (SAF), where whole-genome sequencing (WGS) of 110 bacterial strains was performed. One isolate, designated 179-BFC-A-HS[T], exhibited less than 80% average nucleotide identity (ANI) to known species, suggesting a novel organism. This strain demonstrated high-level resistance [minimum inhibitory concentration (MIC) >256 mg/L] to third-generation cephalosporins, including ceftazidime, cefpodoxime, combination ceftazidime/avibactam, and the fourth-generation cephalosporin cefepime. The results of a comparative genomic analysis revealed that 179-BFC-A-HS[T] is most closely related to Virgibacillus halophilus 5B73C[T], sharing an ANI of 78.7% and a digital DNA-DNA hybridization (dDDH) value of 23.5%, while their 16S rRNA gene sequences shared 97.7% nucleotide identity. Based on these results and the recent recognition that the genus Virgibacillus is polyphyletic, strain 179-BFC-A-HS[T] is proposed as a novel species of a novel genus, Tigheibacillus jepli gen. nov., sp. nov (type strain 179-BFC-A-HS[T] = DSM 115946[T] = NRRL B-65666[T]), and its closest neighbor, V. halophilus, is proposed to be reassigned to this genus as Tigheibacillus halophilus comb. nov. (type strain 5B73C[T] = DSM 21623[T] = JCM 21758[T] = KCTC 13935[T]). It was also necessary to reclassify its second closest neighbor Virgibacillus soli, as a member of a novel genus Paracerasibacillus, reflecting its phylogenetic position relative to the genus Cerasibacillus, for which we propose Paracerasibacillus soli comb. nov. (type strain CC-YMP-6[T] = DSM 22952[T] = CCM 7714[T]). Within Amphibacillaceae (n = 64), P. soli exhibited 11 antibiotic resistance genes (ARG), while T. jepli encoded for 3, lacking any known β-lactamases, suggesting resistance from variant penicillin-binding proteins, disrupting cephalosporin efficacy. P. soli was highly resistant to azithromycin (MIC >64 mg/L) yet susceptible to cephalosporins and penicillins.<br><br>IMPORTANCE: The significance of this research extends to understanding microbial survival and adaptation in oligotrophic environments, such as those found in SAF. Whole-genome sequencing of several strains isolated from Mars 2020 mission assembly cleanroom facilities, including the discovery of the novel species Tigheibacillus jepli, highlights the resilience and antimicrobial resistance (AMR) in clinically relevant antibiotic classes of microbes in nutrient-scarce settings. The study also redefines the taxonomic classifications within the Amphibacillaceae family, aligning genetic identities with phylogenetic data. Investigating ARG and virulence factors (VF) across these strains illuminates the microbial capability for resistance under resource-limited conditions while emphasizing the role of human-associated VF in microbial survival, informing sterilization practices and microbial management in similar oligotrophic settings beyond spacecraft assembly cleanrooms such as pharmaceutical and medical industry cleanrooms.}, }
@article {pmid38476936, year = {2024}, author = {Dittoe, DK and Feye, KM and Ovall, C and Thompson, HA and Ricke, SC}, title = {Exploiting the microbiota of organic and inorganic acid-treated raw poultry products to improve shelf-life.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1348159}, pmid = {38476936}, issn = {1664-302X}, abstract = {INTRODUCTION: Targeted amplicon sequencing of the 16S rRNA delineates the complex microbial interactions that occur during food spoilage, providing a tool to intensively screen microbiota response to antimicrobial processing aids and interventions. The current research determines the microbiota and spoilage indicator (total aerobes and lactic acid bacteria; LAB) response to inorganic and organic antimicrobial intervention use on the shelf-life of fresh, never-frozen, skin-on, bone-in chicken wings.<br><br>METHODS: Wings (n=200) were sourced from local processor and either not treated (NT) or treated with 15-s dips of tap water (TW), organic (peracetic acid; PAA), inorganic acids (sodium bisulfate; SBS), and their combination (SBS + PAA). Wings were stored (4&#xb0;C) and rinsed in neutralizing Buffered Peptone Water (BPW) for 1 min on d 0, 7, 14, and 21 post-treatment. Spoilage indicators, aerobic mesophiles and LAB, were quantified from rinsates. Genomic DNA of d 14 and 21 rinsates were extracted, and V4 of 16S rRNA gene was sequenced. Sequences were analyzed using QIIME2.2019.7. APC and LAB counts were reported as Log10 CFU/g of chicken and analyzed in R Studio as a General Linear Model using ANOVA. Pairwise differences were determined using Tukey's HSD (P&#xa3;0.05).<br><br>RESULTS: Spoilage was indicated for all products by day 21 according to APC counts (>7 Log10 CFU/g); however, wings treated with SBS and SBS + PAA demonstrated a 7-day extended shelf-life compared to those treated with NT, TW, or PAA. The interaction of treatment and time impacted the microbial diversity and composition (p < 0.05), with those treated with SBS having a lower richness and evenness compared to those treated with the controls (NT and TW; p < 0.05, Q < 0.05). On d 14, those treated with SBS and SBS + PAA had lower relative abundance of typical spoilage population while having a greater relative abundance of Bacillus spp. (~70 and 50% of population; ANCOM p < 0.05). By d 21, the Bacillus spp. populations decreased below 10% of the population among those treated with SBS and SBS + PAA.<br><br>DISCUSSION: Therefore, there are differential effects on the microbial community depending on the chemical intervention used with organic and inorganic acids, impacting the microbial ecology differently.}, }
@article {pmid38476935, year = {2024}, author = {Indong, RA and Park, JM and Hong, JK and Lyou, ES and Han, T and Hong, JK and Lee, TK and Lee, JI}, title = {A simple protocol for cultivating the bacterivorous soil nematode Caenorhabditis elegans in its natural ecology in the laboratory.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1347797}, pmid = {38476935}, issn = {1664-302X}, abstract = {The complex interplay between an animal and its surrounding environment requires constant attentive observation in natural settings. Moreover, how ecological interactions are affected by an animal's genes is difficult to ascertain outside the laboratory. Genetic studies with the bacterivorous nematode Caenorhabditis elegans have elucidated numerous relationships between genes and functions, such as physiology, behaviors, and lifespan. However, these studies use standard laboratory culture that does not reflect C. elegans true ecology. C. elegans is found growing in nature and reproduced in large numbers in soils enriched with rotting fruit or vegetation, a source of abundant and diverse microbes that nourish the thriving populations of nematodes. We developed a simple mesocosm we call soil-fruit-natural-habitat that simulates the natural ecology of C. elegans in the laboratory. Apples were placed on autoclaved potted soils, and after a soil microbial solution was added, the mesocosm was subjected to day-night, temperature, and humidity cycling inside a growth chamber. After a period of apple-rotting, C elegans were added, and the growing worm population was observed. We determined optimal conditions for the growth of C. elegans and then performed an ecological succession experiment observing worm populations every few days. Our data showed that the mesocosm allows abundant growth and reproduction of C. elegans that resembles populations of the nematode found in rotting fruit in nature. Overall, our study presents a simple protocol that allows the cultivation of C. elegans in a natural habitat in the laboratory for a broad group of scientists to study various aspects of animal and microbial ecology.}, }
@article {pmid38475926, year = {2024}, author = {Suarez, C and Rosenqvist, T and Dimitrova, I and Sedlacek, CJ and Modin, O and Paul, CJ and Hermansson, M and Persson, F}, title = {Biofilm colonization and succession in a full-scale partial nitritation-anammox moving bed biofilm reactor.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {51}, pmid = {38475926}, issn = {2049-2618}, support = {2018-01423//Svenska Forskningsr&#xe5;det Formas/ ; 2019-00432//Svenska Forskningsr&#xe5;det Formas/ ; 2019-00432//Svenska Forskningsr&#xe5;det Formas/ ; 2018-01423//Svenska Forskningsr&#xe5;det Formas/ ; 2020-01905//Svenska Forskningsr&#xe5;det Formas/ ; ZK74//Austrian Science Fund/ ; }, mesh = {*Ammonia ; *Anaerobic Ammonia Oxidation ; Phylogeny ; Sewage/microbiology ; Bacteria ; Bioreactors/microbiology ; Nitrogen ; Biofilms ; Oxidation-Reduction ; }, abstract = {BACKGROUND: Partial nitritation-anammox (PNA) is a biological nitrogen removal process commonly used in wastewater treatment plants for the treatment of warm and nitrogen-rich sludge liquor from anaerobic digestion, often referred to as sidestream wastewater. In these systems, biofilms are frequently used to retain biomass with aerobic ammonia-oxidizing bacteria (AOB) and anammox bacteria, which together convert ammonium to nitrogen gas. Little is known about how these biofilm communities develop, and whether knowledge about the assembly of biofilms in natural communities can be applied to PNA biofilms.<br><br>RESULTS: We followed the start-up of a full-scale PNA moving bed biofilm reactor for 175 days using shotgun metagenomics. Environmental filtering likely restricted initial biofilm colonization, resulting in low phylogenetic diversity, with the initial microbial community comprised mainly of Proteobacteria. Facilitative priority effects allowed further biofilm colonization, with the growth of initial aerobic colonizers promoting the arrival and growth of anaerobic taxa like methanogens and anammox bacteria. Among the early colonizers were known 'oligotrophic' ammonia oxidizers including comammox Nitrospira and Nitrosomonas cluster 6a AOB. Increasing the nitrogen load in the bioreactor allowed colonization by 'copiotrophic' Nitrosomonas cluster 7 AOB and resulted in the exclusion of the initial ammonia- and nitrite oxidizers.<br><br>CONCLUSIONS: We show that complex dynamic processes occur in PNA microbial communities before a stable bioreactor process is achieved. The results of this study not only contribute to our knowledge about biofilm assembly and PNA bioreactor start-up but could also help guide strategies for the successful implementation of PNA bioreactors. Video Abstract.}, }
@article {pmid38471203, year = {2024}, author = {Malinowski, N and Morgan, MJ and Wylie, J and Walsh, T and Domingos, S and Metcalfe, S and Kaksonen, AH and Barnhart, EP and Mueller, R and Peyton, BM and Puzon, GJ}, title = {Prokaryotic microbial ecology as an ecosurveillance tool for eukaryotic pathogen colonisation: Meiothermus and Naegleria fowleri.}, journal = {Water research}, volume = {254}, number = {}, pages = {121426}, doi = {10.1016/j.watres.2024.121426}, pmid = {38471203}, issn = {1879-2448}, mesh = {*Naegleria fowleri ; Prospective Studies ; *Drinking Water ; Bacteria ; Biofilms ; }, abstract = {Naegleria fowleri has been detected in drinking water distribution systems (DWDS) in Australia, Pakistan and the United States and is the causative agent of the highly fatal disease primary amoebic meningoencephalitis. Previous small scale field studies have shown that Meiothermus may be a potential biomarker for N. fowleri. However, correlations between predictive biomarkers in small sample sizes often breakdown when applied to larger more representative datasets. This study represents one of the largest and most rigorous temporal investigations of Naegleria fowleri colonisation in an operational DWDS in the world and measured the association of Meiothermus and N. fowleri over a significantly larger space and time in the DWDS. A total of 232 samples were collected from five sites over three-years (2016-2018), which contained 29 positive N. fowleri samples. Two specific operational taxonomic units assigned to M. chliarophilus and M. hypogaeus, were significantly associated with N. fowleri presence. Furthermore, inoculation experiments demonstrated that Meiothermus was required to support N. fowleri growth in field-collected biofilms. This validates Meiothermus as prospective biological tool to aid in the identification and surveillance of N. fowleri colonisable sites.}, }
@article {pmid38470030, year = {2024}, author = {Tittes, C and Nijland, J and Schoentag, AMC and Hackl, T and Di Cianni, N and Marchfelder, A and Quax, TEF}, title = {Development of a genetic system for Haloferax gibbonsii LR2-5, model host for haloarchaeal viruses.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {4}, pages = {e0012924}, pmid = {38470030}, issn = {1098-5336}, support = {//Deutsche Forschungsgemeinschaft (DFG)/ ; //EC | European Research Council (ERC)/ ; }, mesh = {*Haloferax/genetics ; Gene Deletion ; *Haloferax volcanii/genetics/metabolism ; Promoter Regions, Genetic ; *Viruses/genetics ; *Archaeal Proteins/genetics ; }, abstract = {UNLABELLED: Archaeal viruses are among the most enigmatic members of the virosphere, and their diverse morphologies raise many questions about their infection mechanisms. The study of molecular mechanisms underlying virus-host interactions hinges upon robust model organisms with a system for gene expression and deletion. Currently, there are only a limited number of archaea that have associated viruses and have a well-developed genetic system. Here, we report the development of a genetic system for the euryarchaeon Haloferax gibbonsii LR2-5. This strain can be infected by multiple viruses and is a model for the study of virus-host interactions. We created a Hfx. gibbonsii LR2-5 ∆pyrE strain, resulting in uracil auxotrophy, which could be used as a selection marker. An expression plasmid carrying a pyrE gene from the well-established Haloferax volcanii system was tested for functionality. Expression of a GFP-MinD fusion under a tryptophan inducible promoter was fully functional and showed similar cellular localization as in Hfx. volcanii. Thus, the plasmids of the Hfx. volcanii system can be used directly for the Hfx. gibbonsii LR2-5 genetic system, facilitating the transfer of tools between the two. Finally, we tested for the functionality of gene deletions by knocking out two genes of the archaeal motility structure, the archaellum. These deletion mutants were as expected non-motile and the phenotype of one deletion could be rescued by the expression of the deleted archaellum gene from a plasmid. Thus, we developed a functional genetic toolbox for the euryarchaeal virus host Hfx. gibbonsii LR2-5, which will propel future studies on archaeal viruses.<br><br>IMPORTANCE: Species from all domains of life are infected by viruses. In some environments, viruses outnumber their microbial hosts by a factor of 10, and viruses are the most important predators of microorganisms. While much has been discovered about the infection mechanisms of bacterial and eukaryotic viruses, archaeal viruses remain understudied. Good model systems are needed to study their virus-host interactions in detail. The salt-loving archaeon Haloferax gibbonsii LR2-5 has been shown to be infected by a variety of different viruses and, thus, is an excellent model to study archaeal viruses. By establishing a genetic system, we have significantly expanded the toolbox for this model organism, which will fuel our understanding of infection strategies of the underexplored archaeal viruses.}, }
@article {pmid38467467, year = {2024}, author = {Powell, ME and McCoy, SJ}, title = {Divide and conquer: Spatial and temporal resource partitioning structures benthic cyanobacterial mats.}, journal = {Journal of phycology}, volume = {60}, number = {2}, pages = {254-272}, doi = {10.1111/jpy.13443}, pmid = {38467467}, issn = {1529-8817}, support = {DGE-2040435//National Science Foundation/ ; OCE-2239425//National Science Foundation/ ; }, mesh = {*Ecosystem ; *Cyanobacteria/metabolism ; Sulfur/metabolism ; Carbon/metabolism ; }, abstract = {Benthic cyanobacterial mats are increasing in abundance worldwide with the potential to degrade ecosystem structure and function. Understanding mat community dynamics is thus critical for predicting mat growth and proliferation and for mitigating any associated negative effects. Carbon, nitrogen, and sulfur cycling are the predominant forms of nutrient cycling discussed within the literature, while metabolic cooperation and viral interactions are understudied. Although many forms of nutrient cycling in mats have been assessed, the links between niche dynamics, microbial interactions, and nutrient cycling are not well described. Here, we present an updated review on how nutrient cycling and microbial community interactions in mats are structured by resource partitioning via spatial and temporal heterogeneity and succession. We assess community interactions and nutrient cycling at both intramat and metacommunity scales. Additionally, we present ideas and recommendations for research in this area, highlighting top-down control, boundary layers, and metabolic cooperation as important future directions.}, }
@article {pmid38466433, year = {2024}, author = {Ważny, R and Jędrzejczyk, RJ and Rozpądek, P and Domka, A and Tokarz, KM and Janicka, M and Turnau, K}, title = {Bacteria Associated with Spores of Arbuscular Mycorrhizal Fungi Improve the Effectiveness of Fungal Inocula for Red Raspberry Biotization.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {50}, pmid = {38466433}, issn = {1432-184X}, mesh = {*Mycorrhizae/physiology ; *Rubus ; Spores, Fungal ; Plants/microbiology ; Bacteria ; Chlorophyll ; Water ; }, abstract = {Intensive crop production leads to the disruption of the symbiosis between plants and their associated microorganisms, resulting in suboptimal plant productivity and lower yield quality. Therefore, it is necessary to improve existing methods and explore modern, environmentally friendly approaches to crop production. One of these methods is biotization, which involves the inoculation of plants with appropriately selected symbiotic microorganisms which play a beneficial role in plant adaptation to the environment. In this study, we tested the possibility of using a multi-microorganismal inoculum composed of arbuscular mycorrhizal fungi (AMF) and AMF spore-associated bacteria for biotization of the red raspberry. Bacteria were isolated from the spores of AMF, and their plant growth-promoting properties were tested. AMF inocula were supplemented with selected bacterial strains to investigate their effect on the growth and vitality of the raspberry. The investigations were carried out in the laboratory and on a semi-industrial scale in a polytunnel where commercial production of seedlings is carried out. In the semi-industrial experiment, we tested the growth parameters of plants and physiological response of the plant to temporary water shortage. We isolated over fifty strains of bacteria associated with spores of AMF. Only part of them showed plant growth-promoting properties, and six of these (belonging to the Paenibacillus genus) were used for the inoculum. AMF inoculation and co-inoculation of AMF and bacteria isolated from AMF spores improved plant growth and vitality in both experimental setups. Plant dry weight was improved by 70%, and selected chlorophyll fluorescence parameters (the contribution of light to primary photochemistry and fraction of reaction centre chlorophyll per chlorophyll of the antennae) were increased. The inoculum improved carbon assimilation, photosynthetic rate, stomatal conductance and transpiration after temporary water shortage. Raspberry biotization with AMF and bacteria associated with spores has potential applications in horticulture where ecological methods based on plant microorganism interaction are in demand.}, }
@article {pmid38465733, year = {2024}, author = {Javourez, U and Matassa, S and Vlaeminck, SE and Verstraete, W}, title = {Ruminations on sustainable and safe food: Championing for open symbiotic cultures ensuring resource efficiency, eco-sustainability and affordability.}, journal = {Microbial biotechnology}, volume = {17}, number = {3}, pages = {e14436}, pmid = {38465733}, issn = {1751-7915}, mesh = {Animals ; *Ruminants ; *Biotechnology ; Fermentation ; Animal Feed ; Costs and Cost Analysis ; }, abstract = {Microbes are powerful upgraders, able to convert simple substrates to nutritional metabolites at rates and yields surpassing those of higher organisms by a factor of 2 to 10. A summary table highlights the superior efficiencies of a whole array of microbes compared to conventionally farmed animals and insects, converting nitrogen and organics to food and feed. Aiming at the most resource-efficient class of microbial proteins, deploying the power of open microbial communities, coined here as 'symbiotic microbiomes' is promising. For instance, a production train of interest is to develop rumen-inspired technologies to upgrade fibre-rich substrates, increasingly available as residues from emerging bioeconomy initiatives. Such advancements offer promising perspectives, as currently only 5%-25% of the available cellulose is recovered by ruminant livestock systems. While safely producing food and feed with open cultures has a long-standing tradition, novel symbiotic fermentation routes are currently facing much higher market entrance barriers compared to axenic fermentation. Our global society is at a pivotal juncture, requiring a shift towards food production systems that not only embrace the environmental and economic sustainability but also uphold ethical standards. In this context, we propose to re-examine the place of spontaneous or natural microbial consortia for safe future food and feed biotech developments, and advocate for intelligent regulatory practices. We stress that reconsidering symbiotic microbiomes is key to achieve sustainable development goals and defend the need for microbial biotechnology literacy education.}, }
@article {pmid38465465, year = {2024}, author = {Van Goethem, MW and Marasco, R and Hong, PY and Daffonchio, D}, title = {The antibiotic crisis: On the search for novel antibiotics and resistance mechanisms.}, journal = {Microbial biotechnology}, volume = {17}, number = {3}, pages = {e14430}, pmid = {38465465}, issn = {1751-7915}, support = {//King Abdullah University of Science and Technology (KAUST)/ ; }, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Ecosystem ; Bacteria/genetics ; Drug Resistance, Microbial ; Agriculture ; }, abstract = {In the relentless battle for human health, the proliferation of antibiotic-resistant bacteria has emerged as an impending catastrophe of unprecedented magnitude, potentially driving humanity towards the brink of an unparalleled healthcare crisis. The unyielding advance of antibiotic resistance looms as the foremost threat of the 21st century in clinical, agricultural and environmental arenas. Antibiotic resistance is projected to be the genesis of the next global pandemic, with grim estimations of tens of millions of lives lost annually by 2050. Amidst this impending calamity, our capacity to unearth novel antibiotics has languished, with the past four decades marred by a disheartening 'antibiotic discovery void'. With nearly 80% of our current antibiotics originating from natural or semi-synthetic sources, our responsibility is to cast our investigative nets into uncharted ecological niches teeming with microbial strife, the so-called 'microbial oases of interactions'. Within these oases of interactions, where microorganisms intensively compete for space and nutrients, a dynamic and ever-evolving microbial 'arms race' is constantly in place. Such a continuous cycle of adaptation and counter-adaptation is a fundamental aspect of microbial ecology and evolution, as well as the secrets to unique, undiscovered antibiotics, our last bastion against the relentless tide of resistance. In this context, it is imperative to invest in research to explore the competitive realms, like the plant rhizosphere, biological soil crusts, deep sea hydrothermal vents, marine snow and the most modern plastisphere, in which competitive interactions are at the base of the microorganisms' struggle for survival and dominance in their ecosystems: identify novel antibiotic by targeting microbial oases of interactions could represent a 'missing piece of the puzzle' in our fight against antibiotic resistance.}, }
@article {pmid38461750, year = {2024}, author = {Michielsen, S and Vercelli, GT and Cordero, OX and Bachmann, H}, title = {Spatially structured microbial consortia and their role in food fermentations.}, journal = {Current opinion in biotechnology}, volume = {87}, number = {}, pages = {103102}, doi = {10.1016/j.copbio.2024.103102}, pmid = {38461750}, issn = {1879-0429}, mesh = {*Fermentation ; *Microbial Consortia/physiology ; *Food Microbiology ; }, abstract = {Microbial consortia are important for the fermentation of foods. They bring combined functionalities to the fermented product, but stability and product consistency of fermentations with complex consortia can be hard to control. Some of these consortia, such as water- and milk-kefir and kombucha, grow as multispecies aggregates or biofilms, in which micro-organisms taking part in a fermentation cascade are spatially organized. The spatial organization of micro-organisms in these aggregates can impact what metabolic interactions are realized in the consortia, ultimately affecting the growth dynamics and evolution of microbes. A better understanding of such spatially structured communities is of interest from the perspective of microbial ecology and biotechnology, as multispecies aggregates can be used to valorize energy-rich substrates, such as plant-based substrates or side streams from the food industry.}, }
@article {pmid38458948, year = {2024}, author = {Fu, S and Wang, Q and Wang, R and Zhang, Y and Lan, R and He, F and Yang, Q}, title = {Corrigendum to "Horizontal transfer of antibiotic resistance genes within the bacterial communities in aquacultural environment" [Sci. Total Environ. 820 (2022) 153286].}, journal = {The Science of the total environment}, volume = {922}, number = {}, pages = {171434}, doi = {10.1016/j.scitotenv.2024.171434}, pmid = {38458948}, issn = {1879-1026}, }
@article {pmid38457521, year = {2024}, author = {Colombi, E and Bertels, F and Doulcier, G and McConnell, E and Pichugina, T and Sohn, KH and Straub, C and McCann, HC and Rainey, PB}, title = {Rapid dissemination of host metabolism-manipulating genes via integrative and conjugative elements.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {11}, pages = {e2309263121}, pmid = {38457521}, issn = {1091-6490}, support = {MAU1709//Royal Society of New Zealand | Marsden Fund (Royal Society of New Zealand Marsden Fund)/ ; SFB1182 Project C4//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {Phylogeny ; *Conjugation, Genetic ; *Gene Transfer, Horizontal/genetics ; Biological Evolution ; DNA Transposable Elements/genetics ; }, abstract = {Integrative and conjugative elements (ICEs) are self-transmissible mobile elements that transfer functional genetic units across broad phylogenetic distances. Accessory genes shuttled by ICEs can make significant contributions to bacterial fitness. Most ICEs characterized to date encode readily observable phenotypes contributing to symbiosis, pathogenicity, and antimicrobial resistance, yet the majority of ICEs carry genes of unknown function. Recent observations of rapid acquisition of ICEs in a pandemic lineage of Pseudomonas syringae pv. actinidae led to investigation of the structural and functional diversity of these elements. Fifty-three unique ICE types were identified across the P. syringae species complex. Together they form a distinct family of ICEs (PsICEs) that share a distant relationship to ICEs found in Pseudomonas aeruginosa. PsICEs are defined by conserved backbone genes punctuated by an array of accessory cargo genes, are highly recombinogenic, and display distinct evolutionary histories compared to their bacterial hosts. The most common cargo is a recently disseminated 16-kb mobile genetic element designated Tn6212. Deletion of Tn6212 did not alter pathogen growth in planta, but mutants displayed fitness defects when grown on tricarboxylic acid (TCA) cycle intermediates. RNA-seq analysis of a set of nested deletion mutants showed that a Tn6212-encoded LysR regulator has global effects on chromosomal gene expression. We show that Tn6212 responds to preferred carbon sources and manipulates bacterial metabolism to maximize growth.}, }
@article {pmid38453959, year = {2024}, author = {Guerrero-Egido, G and Pintado, A and Bretscher, KM and Arias-Giraldo, LM and Paulson, JN and Spaink, HP and Claessen, D and Ramos, C and Cazorla, FM and Medema, MH and Raaijmakers, JM and Carrión, VJ}, title = {bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {2072}, pmid = {38453959}, issn = {2041-1723}, mesh = {*Genome, Bacterial/genetics ; *Pseudomonas syringae/genetics ; Workflow ; Genomics/methods ; }, abstract = {Bacteria have an extensive adaptive ability to live in close association with eukaryotic hosts, exhibiting detrimental, neutral or beneficial effects on host growth and health. However, the genes involved in niche adaptation are mostly unknown and their functions poorly characterized. Here, we present bacLIFE (https://github.com/Carrion-lab/bacLIFE) a streamlined computational workflow for genome annotation, large-scale comparative genomics, and prediction of lifestyle-associated genes (LAGs). As a proof of concept, we analyzed 16,846 genomes from the Burkholderia/Paraburkholderia and Pseudomonas genera, which led to the identification of hundreds of genes potentially associated with a plant pathogenic lifestyle. Site-directed mutagenesis of 14 of these predicted LAGs of unknown function, followed by plant bioassays, showed that 6 predicted LAGs are indeed involved in the phytopathogenic lifestyle of Burkholderia plantarii and Pseudomonas syringae pv. phaseolicola. These 6 LAGs encompassed a glycosyltransferase, extracellular binding proteins, homoserine dehydrogenases and hypothetical proteins. Collectively, our results highlight bacLIFE as an effective computational tool for prediction of LAGs and the generation of hypotheses for a better understanding of bacteria-host interactions.}, }
@article {pmid38452350, year = {2024}, author = {Boutin, S and Lussier, E and Laforest-Lapointe, I}, title = {Investigating the spatiotemporal dynamics of apple tree phyllosphere bacterial and fungal communities across cultivars in orchards.}, journal = {Canadian journal of microbiology}, volume = {70}, number = {6}, pages = {238-251}, doi = {10.1139/cjm-2023-0215}, pmid = {38452350}, issn = {1480-3275}, mesh = {*Malus/microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Plant Leaves/microbiology ; Spatio-Temporal Analysis ; Biodiversity ; Mycobiome ; Flowers/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The phyllosphere, a reservoir of diverse microbial life associated with plant health, harbors microbial communities that are subject to various complex ecological processes acting at multiple scales. In this study, we investigated the determinants of the spatiotemporal variation in bacterial and fungal communities within the apple tree phyllosphere, employing 16S and ITS amplicon sequencing. Our research assessed the impact of key factors-plant compartment, site, time, and cultivar-on the composition and diversity of leaf and flower microbial communities. Our analyses, based on samples collected from three cultivars in three orchards in 2022, revealed that site and time are the strongest drivers of apple tree phyllosphere microbial communities. Conversely, plant compartment and cultivar exhibited minor roles in explaining community composition and diversity. Predominantly, bacterial communities comprised Hymenobacter (25%) and Sphingomonas (10%), while the most relatively abundant fungal genera included Aureobasidium (27%) and Sporobolomyces (10%). Additionally, our results show a gradual decrease in alpha-diversity throughout the growth season. These findings emphasize the necessity to consider local microbial ecology dynamics in orchards, especially as many groups worldwide aim for the development of biocontrol strategies (e.g., by manipulating plant-microbe interactions). More research is needed to improve our understanding of the determinants of time and site-specific disparities within apple tree phyllosphere microbial communities across multiple years, locations, and cultivars.}, }
@article {pmid38452018, year = {2024}, author = {Du, Z and Behrens, SF}, title = {Effect of target gene sequence evenness and dominance on real-time PCR quantification of artificial sulfate-reducing microbial communities.}, journal = {PloS one}, volume = {19}, number = {3}, pages = {e0299930}, pmid = {38452018}, issn = {1932-6203}, mesh = {Real-Time Polymerase Chain Reaction/methods ; Phylogeny ; Reproducibility of Results ; *Sulfates ; *Microbiota/genetics ; }, abstract = {Quantitative real-time PCR of phylogenetic and functional marker genes is among the most commonly used techniques to quantify the abundance of microbial taxa in environmental samples. However, in most environmental applications, the approach is a rough assessment of population abundance rather than an exact absolute quantification method because of PCR-based estimation biases caused by multiple factors. Previous studies on these technical issues have focused on primer or template sequence features or PCR reaction conditions. However, how target gene sequence characteristics (e.g., evenness and dominance) in environmental samples affect qPCR quantifications has not been well studied. Here, we compared three primer sets targeting the beta subunit of the dissimilatory sulfite reductase (dsrB) to investigate qPCR quantification performance under different target gene sequence evenness and dominance conditions using artificial gBlock template mixtures designed accordingly. Our results suggested that the qPCR quantification performance of all tested primer sets was determined by the comprehensive effect of the target gene sequence evenness and dominance in environmental samples. Generally, highly degenerate primer sets have equivalent or better qPCR quantification results than a more target-specific primer set. Low template concentration in this study (~105 copies/L) will exaggerate the qPCR quantification results difference among tested primer sets. Improvements to the accuracy and reproducibility of qPCR assays for gene copy number quantification in environmental microbiology and microbial ecology studies should be based on prior knowledge of target gene sequence information acquired by metagenomic analysis or other approaches, careful selection of primer sets, and proper reaction conditions optimization.}, }
@article {pmid38450400, year = {2024}, author = {Duarte, RDC and Iannetta, PPM and Gomes, AM and Vasconcelos, MW}, title = {More than a meat- or synthetic nitrogen fertiliser-substitute: a review of legume phytochemicals as drivers of 'One Health' via their influence on the functional diversity of soil- and gut-microbes.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1337653}, pmid = {38450400}, issn = {1664-462X}, abstract = {Legumes are essential to healthy agroecosystems, with a rich phytochemical content that impacts overall human and animal well-being and environmental sustainability. While these phytochemicals can have both positive and negative effects, legumes have traditionally been bred to produce genotypes with lower levels of certain plant phytochemicals, specifically those commonly termed as 'antifeedants' including phenolic compounds, saponins, alkaloids, tannins, and raffinose family oligosaccharides (RFOs). However, when incorporated into a balanced diet, such legume phytochemicals can offer health benefits for both humans and animals. They can positively influence the human gut microbiome by promoting the growth of beneficial bacteria, contributing to gut health, and demonstrating anti-inflammatory and antioxidant properties. Beyond their nutritional value, legume phytochemicals also play a vital role in soil health. The phytochemical containing residues from their shoots and roots usually remain in-field to positively affect soil nutrient status and microbiome diversity, so enhancing soil functions and benefiting performance and yield of following crops. This review explores the role of legume phytochemicals from a 'one health' perspective, examining their on soil- and gut-microbial ecology, bridging the gap between human nutrition and agroecological science.}, }
@article {pmid38448699, year = {2024}, author = {Tao, F and Houlton, BZ and Frey, SD and Lehmann, J and Manzoni, S and Huang, Y and Jiang, L and Mishra, U and Hungate, BA and Schmidt, MWI and Reichstein, M and Carvalhais, N and Ciais, P and Wang, YP and Ahrens, B and Hugelius, G and Hocking, TD and Lu, X and Shi, Z and Viatkin, K and Vargas, R and Yigini, Y and Omuto, C and Malik, AA and Peralta, G and Cuevas-Corona, R and Di Paolo, LE and Luotto, I and Liao, C and Liang, YS and Saynes, VS and Huang, X and Luo, Y}, title = {Reply to: Model uncertainty obscures major driver of soil carbon.}, journal = {Nature}, volume = {627}, number = {8002}, pages = {E4-E6}, pmid = {38448699}, issn = {1476-4687}, mesh = {*Uncertainty ; }, }
@article {pmid38446847, year = {2024}, author = {Koslová, A and Hackl, T and Bade, F and Sanchez Kasikovic, A and Barenhoff, K and Schimm, F and Mersdorf, U and Fischer, MG}, title = {Endogenous virophages are active and mitigate giant virus infection in the marine protist Cafeteria burkhardae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {11}, pages = {e2314606121}, pmid = {38446847}, issn = {1091-6490}, support = {5734//Gordon and Betty Moore Foundation (GBMF)/ ; ALTF 1150-2018//European Molecular Biology Organization (EMBO)/ ; }, mesh = {Humans ; Virophages ; *Giant Viruses/genetics ; *Stramenopiles/genetics ; *Virus Diseases ; Antiviral Agents ; }, abstract = {Endogenous viral elements (EVEs) are common genetic passengers in various protists. Some EVEs represent viral fossils, whereas others are still active. The marine heterotrophic flagellate Cafeteria burkhardae contains several EVE types related to the virophage mavirus, a small DNA virus that parasitizes the lytic giant virus CroV. We hypothesized that endogenous virophages may act as an antiviral defense system in protists, but no protective effect of virophages in wild host populations has been shown so far. Here, we tested the activity of virophage EVEs and studied their impact on giant virus replication. We found that endogenous mavirus-like elements (EMALEs) from globally distributed Cafeteria populations produced infectious virus particles specifically in response to CroV infection. However, reactivation was stochastic, often inefficient, and poorly reproducible. Interestingly, only one of eight EMALE types responded to CroV infection, implying that other EMALEs may be linked to different giant viruses. We isolated and cloned several reactivated virophages and characterized their particles, genomes, and infection dynamics. All tested virophages inhibited the production of CroV during coinfection, thereby preventing lysis of the host cultures in a dose-dependent manner. Comparative genomics of different C. burkhardae strains revealed that inducible EMALEs are common and are not linked to specific geographic locations. We demonstrate that naturally occurring virophage EVEs reactivate upon giant virus infection, thus providing a striking example that eukaryotic EVEs can become active under specific conditions. Moreover, our results support the hypothesis that virophages can act as an adaptive antiviral defense system in protists.}, }
@article {pmid38441415, year = {2024}, author = {Lee, HJ and Hwang, JS and Lee, EK and Whang, KS}, title = {Erythrobacter oryzae sp. nov., isolated from rice paddy soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {3}, pages = {}, doi = {10.1099/ijsem.0.006287}, pmid = {38441415}, issn = {1466-5034}, mesh = {*Sphingomonadaceae ; *Oryza ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Base Composition ; Fatty Acids/chemistry ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; }, abstract = {Two novel bacterial strains, designated as COR-2[T] and CR-8, were isolated from paddy soil. These isolates were aerobic, Gram-stain-negative, non-spore-forming, non-motile, rod-shaped, and formed orange-coloured colonies. Phylogenetic analysis based on 16S rRNA gene sequences showed that two strains formed a clear phylogenetic lineage with the genus Erythrobacter. Strains COR-2[T] and CR-8 showed 99.9 % 16S rRNA gene sequence similarity. Both strains had the highest 16S rRNA gene similarity of 99.1-99.7 % to Erythrobacter colymbi TPW-24[T], Erythrobacter donghaensis SW-132[T] and Erythrobacter tepidarius DSM 10594[T], respectively. The genome of strain COR-2[T] comprised 3 559 918 bp and the genomic DNA G + C content was 67.7 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain COR-2[T] and its closely related species of the genus Erythrobacter were 79.3-85.5% and 24.1-29.1 %, respectively. The major respiratory quinone was Q-10, while the major fatty acids were C18 : 1 ω7c and C17 : 1 ω6c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, two unidentified phospholipids and eight unidentified lipids. Based on phylogenetic and phenotypic considerations, the two strains [COR-2[T] (type strain; = KACC 22941[T]=JCM 35529[T]) and CR-8 (= KACC 22945=JCM 35530)] are considered to represent novel species of the genus Erythrobacter, for which the name Erythrobacter oryzae sp. nov. is proposed.}, }
@article {pmid38440286, year = {2024}, author = {Zeng, L and Noeparvar, P and Burne, RA and Glezer, BS}, title = {Genetic characterization of glyoxalase pathway in oral streptococci and its contribution to interbacterial competition.}, journal = {Journal of oral microbiology}, volume = {16}, number = {1}, pages = {2322241}, pmid = {38440286}, issn = {2000-2297}, support = {R01 DE012236/DE/NIDCR NIH HHS/United States ; }, abstract = {OBJECTIVES: To analyze contributions to microbial ecology of Reactive Electrophile Species (RES), including methylglyoxal, generated during glycolysis.<br><br>METHODS: Genetic analyses were performed on the glyoxalase pathway in Streptococcus mutans (SM) and Streptococcus sanguinis (SS), followed by phenotypic assays and transcription analysis.<br><br>RESULTS: Deleting glyoxalase I (lguL) reduced RES tolerance to a far greater extent in SM than in SS, decreasing the competitiveness of SM against SS. Although SM displays a greater RES tolerance than SS, lguL-null mutants of either species showed similar tolerance; a finding consistent with the ability of methylglyoxal to induce the expression of lguL in SM, but not in SS. A novel paralogue of lguL (named gloA2) was identified in most streptococci. SM mutant &#x2206;gloA2SM showed little change in methylglyoxal tolerance yet a significant growth defect and increased autolysis on fructose, a phenotype reversed by the addition of glutathione, or by the deletion of a fructose: phosphotransferase system (PTS) that generates fructose-1-phosphate (F-1-P).<br><br>CONCLUSIONS: Fructose contributes to RES generation in a PTS-specific manner, and GloA2 may be required to degrade certain RES derived from F-1-P. This study reveals the critical roles of RES in fitness and interbacterial competition and the effects of PTS in modulating RES metabolism.}, }
@article {pmid38439944, year = {2024}, author = {Ma, H and Liu, J and Mo, L and Arias-Giraldo, LM and Xiang, M and Liu, X}, title = {Wild plant species with broader precipitation niches exhibit stronger host selection in rhizosphere microbiome assembly.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycad015}, pmid = {38439944}, issn = {2730-6151}, abstract = {Plants actively recruit microbes from the soil, forming species-specific root microbiomes. However, their relationship with plant adaptations to temperature and precipitation remains unclear. Here we examined the host-selected and conserved microbiomes of 13 native plant species in the Xilingol steppe, Inner Mongolia, a semi-arid region in China. By calculating the global precipitation and temperature niches of these plants, considering plant phylogenetic distances, and analyzing functional traits, we found that these factors significantly influenced the rhizosphere microbiome assembly. We further quantified the strength of host selection and observed that plants with wider precipitation niches exhibited greater host selection strength in their rhizosphere microbiome assembly and higher rhizosphere bacterial diversity. In general, the rhizosphere microbiome showed a stronger link to plant precipitation niches than temperature niches. Haliangium exhibited consistent responsiveness to host characteristics. Our findings offer novel insights into host selection effects and the ecological determinants of wild plant rhizosphere microbiome assembly, with implications for steering root microbiomes of wild plants and understanding plant-microbiome evolution.}, }
@article {pmid38436268, year = {2024}, author = {Wang, Q and Cole, JR}, title = {Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification.}, journal = {Microbiology resource announcements}, volume = {13}, number = {4}, pages = {e0106323}, pmid = {38436268}, issn = {2576-098X}, abstract = {The RDP Classifier is one of the most popular machine learning approaches for taxonomic classification due to its robustness and relatively high accuracy. Both the RDP taxonomy and RDP Classifier have been updated to incorporate newly described taxa and recent changes to prokaryotic nomenclature.}, }
@article {pmid38436256, year = {2024}, author = {Ling, J and Hryckowian, AJ}, title = {Re-framing the importance of Group B Streptococcus as a gut-resident pathobiont.}, journal = {Infection and immunity}, volume = {92}, number = {9}, pages = {e0047823}, pmid = {38436256}, issn = {1098-5522}, support = {R35 GM150996/GM/NIGMS NIH HHS/United States ; R35GM150996//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; DGE-2137424//NSF | National Science Foundation Graduate Research Fellowship Program (GRFP)/ ; 1U48DP006383//UW-Madison Prevention Research Center/ ; Gift//Judy L. and Sal A. Troia/ ; }, mesh = {*Streptococcus agalactiae ; Humans ; *Streptococcal Infections/microbiology ; *Gastrointestinal Microbiome/physiology ; Gastrointestinal Tract/microbiology ; Animals ; }, abstract = {Streptococcus agalactiae (Group B Streptococcus, GBS) is a Gram-positive bacterial species that causes disease in humans across the lifespan. While antibiotics are used to mitigate GBS infections, it is evident that antibiotics disrupt human microbiomes (which can predispose people to other diseases later in life), and antibiotic resistance in GBS is on the rise. Taken together, these unintended negative impacts of antibiotics highlight the need for precision approaches for minimizing GBS disease. One possible approach involves selectively depleting GBS in its commensal niches before it can cause disease at other body sites or be transmitted to at-risk individuals. One understudied commensal niche of GBS is the adult gastrointestinal (GI) tract, which may predispose colonization at other body sites in individuals at risk for GBS disease. However, a better understanding of the host-, microbiome-, and GBS-determined variables that dictate GBS GI carriage is needed before precise GI decolonization approaches can be developed. In this review, we synthesize current knowledge of the diverse body sites occupied by GBS as a pathogen and as a commensal. We summarize key molecular factors GBS utilizes to colonize different host-associated niches to inform future efforts to study GBS in the GI tract. We also discuss other GI commensals that are pathogenic in other body sites to emphasize the broader utility of precise de-colonization approaches for mitigating infections by GBS and other bacterial pathogens. Finally, we highlight how GBS treatments could be improved with a more holistic understanding of GBS enabled by continued GI-focused study.}, }
@article {pmid38430754, year = {2024}, author = {Yan, X and Li, S and Abdullah Al, M and Mo, Y and Zuo, J and Grossart, HP and Zhang, H and Yang, Y and Jeppesen, E and Yang, J}, title = {Community stability of free-living and particle-attached bacteria in a subtropical reservoir with salinity fluctuations over 3 years.}, journal = {Water research}, volume = {254}, number = {}, pages = {121344}, doi = {10.1016/j.watres.2024.121344}, pmid = {38430754}, issn = {1879-2448}, mesh = {*Ecosystem ; Salinity ; Lakes/microbiology ; Bacteria/genetics ; *Microbiota/physiology ; Aquatic Organisms ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Changes in salinity have a profound influence on ecological services and functions of inland freshwater ecosystems, as well as on the shaping of microbial communities. Bacterioplankton, generally classified into free-living (FL) and particle-attached (PA) forms, are main components of freshwater ecosystems and play key functional roles for biogeochemical cycling and ecological stability. However, there is limited knowledge about the responses of community stability of both FL and PA bacteria to salinity fluctuations. Here, we systematically explored changes in community stability of both forms of bacteria based on high-frequency sampling in a shallow urban reservoir (Xinglinwan Reservoir) in subtropical China for 3 years. Our results indicated that (1) salinity was the strongest environmental factor determining FL and PA bacterial community compositions - rising salinity increased the compositional stability of both bacterial communities but decreased their α-diversity. (2) The community stability of PA bacteria was significantly higher than that of FL at high salinity level with low salinity variance scenarios, while the opposite was found for FL bacteria, i.e., their stability was higher than PA bacteria at low salinity level with high variance scenarios. (3) Both bacterial traits (e.g., bacterial genome size and interaction strength of rare taxa) and precipitation-induced factors (e.g., changes in salinity and particle) likely contributed collectively to differences in community stability of FL and PA bacteria under different salinity scenarios. Our study provides additional scientific basis for ecological management, protection and restoration of urban reservoirs under changing climatic and environmental conditions.}, }
@article {pmid38430049, year = {2024}, author = {Barnett, SE and Shade, A}, title = {Arrive and wait: Inactive bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance.}, journal = {Ecology letters}, volume = {27}, number = {3}, pages = {e14393}, doi = {10.1111/ele.14393}, pmid = {38430049}, issn = {1461-0248}, support = {1749544//National Science Foundation/ ; }, mesh = {Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; *Resilience, Psychological ; Soil Microbiology ; Bacteria/genetics ; *Microbiota/physiology ; }, abstract = {Long-term (press) disturbances like the climate crisis and other anthropogenic pressures are fundamentally altering ecosystems and their functions. Many critical ecosystem functions, such as biogeochemical cycling, are facilitated by microbial communities. Understanding the functional consequences of microbiome responses to press disturbances requires ongoing observations of the active populations that contribute to functions. This study leverages a 7-year time series of a 60-year-old coal seam fire (Centralia, Pennsylvania, USA) to examine the resilience of soil bacterial microbiomes to a press disturbance. Using 16S rRNA and 16S rRNA gene amplicon sequencing, we assessed the interannual dynamics of the active subset and the 'whole' bacterial community. Contrary to our hypothesis, the whole communities demonstrated greater resilience than active subsets, suggesting that inactive members contributed to overall structural resilience. Thus, in addition to selection mechanisms of active populations, perceived microbiome resilience is also supported by mechanisms of dispersal, persistence, and revival from the local dormant pool.}, }
@article {pmid38427046, year = {2024}, author = {Alvarenga, DO and Priemé, A and Rousk, K}, title = {The Feather Moss Hylocomium splendens Affects the Transcriptional Profile of a Symbiotic Cyanobacterium in Relation to Acquisition and Turnover of Key Nutrients.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {49}, pmid = {38427046}, issn = {1432-184X}, support = {947719/ERC_/European Research Council/International ; }, mesh = {Symbiosis ; Nitrogen Fixation ; *Bryopsida/genetics/metabolism/microbiology ; *Bryophyta ; *Cyanobacteria/metabolism ; Amino Acids/metabolism ; }, abstract = {Moss-cyanobacteria symbioses were proposed to be based on nutrient exchange, with hosts providing C and S while bacteria provide N, but we still lack understanding of the underlying molecular mechanisms of their interactions. We investigated how contact between the ubiquitous moss Hylocomium splendens and its cyanobiont affects nutrient-related gene expression of both partners. We isolated a cyanobacterium from H. splendens and co-incubated it with washed H. splendens shoots. Cyanobacterium and moss were also incubated separately. After 1 week, we performed acetylene reduction assays to estimate N2 fixation and RNAseq to evaluate metatranscriptomes. Genes related to N2 fixation and the biosynthesis of several amino acids were up-regulated in the cyanobiont when hosted by the moss. However, S-uptake and the biosynthesis of the S-containing amino acids methionine and cysteine were down-regulated in the cyanobiont while the degradation of selenocysteine was up-regulated. In contrast, the number of differentially expressed genes in the moss was much lower, and almost no transcripts related to nutrient metabolism were affected. It is possible that, at least during the early stage of this symbiosis, the cyanobiont receives few if any nutrients from the host in return for N, suggesting that moss-cyanobacteria symbioses encompass relationships that are more plastic than a constant mutualist flow of nutrients.}, }
@article {pmid38426066, year = {2024}, author = {Yue, Y and Hao, H and Wang, Q and Xiao, T and Zhang, Y and Chen, Q and Chen, H and Zhang, J}, title = {Dynamics of the soil microbial community associated with Morchella cultivation: diversity, assembly mechanism and yield prediction.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1345231}, pmid = {38426066}, issn = {1664-302X}, abstract = {INTRODUCTION: The artificial cultivation of morels has been a global research focus owing to production variability. Understanding the microbial ecology in cultivated soil is essential to increase morel yield and alleviate pathogen harm.<br><br>METHODS: A total of nine Morchella cultivation experiments in four soil field types, forest, paddy, greenhouse, and orchard in Shanghai city were performed to determine the potential ecological relationship between Morchella growth and soil microbial ecology.<br><br>RESULTS: Generally, significant variation was observed in the soil microbial diversity and composition between the different experimental field types. The niche width analysis indicated that the bacterial habitat niche breadth was significantly greater than the fungal community width, which was further confirmed by a null model that revealed that homogeneous selection could explain 46.26 and 53.64% of the variance in the bacterial and fungal assemblies, respectively. Moreover, the neutral community model revealed that stochastic processes dominate the bacterial community in forests and paddies and both the bacterial and fungal communities in orchard crops, whereas deterministic processes mostly govern the fungal community in forests and paddies and both the bacterial and the fungal communities in greenhouses. Furthermore, co-occurrence patterns were constructed, and the results demonstrated that the dynamics of the soil microbial community are related to fluctuations in soil physicochemical characteristics, especially soil potassium. Importantly, structural equation modeling further demonstrated that the experimental soil type significantly affects the potassium content of the soil, which can directly or indirectly promote Morchella yield by inhibiting soil fungal richness.<br><br>DISCUSSION: This was the first study to predict morel yield through soil potassium fertilizer and soil fungal community richness, which provides new insights into deciphering the importance of microbial ecology in morel agroecosystems.}, }
@article {pmid38425054, year = {2024}, author = {Law, SR and Mathes, F and Paten, AM and Alexandre, PA and Regmi, R and Reid, C and Safarchi, A and Shaktivesh, S and Wang, Y and Wilson, A and Rice, SA and Gupta, VVSR}, title = {Life at the borderlands: microbiomes of interfaces critical to One Health.}, journal = {FEMS microbiology reviews}, volume = {48}, number = {2}, pages = {}, pmid = {38425054}, issn = {1574-6976}, support = {//CSIRO/ ; }, mesh = {Animals ; Humans ; *One Health ; *Microbiota ; Biological Evolution ; Soil Microbiology ; Plants/microbiology ; }, abstract = {Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome-host relationships, specifically at interfaces critical to One Health-a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.}, }
@article {pmid38424049, year = {2024}, author = {Zhong, ZP and Du, J and Köstlbacher, S and Pjevac, P and Orlić, S and Sullivan, MB}, title = {Viral potential to modulate microbial methane metabolism varies by habitat.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1857}, pmid = {38424049}, issn = {2041-1723}, support = {3790//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 1759874//National Science Foundation (NSF)/ ; 1829831//National Science Foundation (NSF)/ ; NA//OSU | Byrd Polar and Climate Research Center, Ohio State University (Byrd Polar and Climate Research Center of The Ohio State University)/ ; }, mesh = {Animals ; Methane/metabolism ; Ecosystem ; *Viruses/genetics ; Metagenome ; *Euryarchaeota/genetics ; }, abstract = {Methane is a potent greenhouse gas contributing to global warming. Microorganisms largely drive the biogeochemical cycling of methane, yet little is known about viral contributions to methane metabolism (MM). We analyzed 982 publicly available metagenomes from host-associated and environmental habitats containing microbial MM genes, expanding the known MM auxiliary metabolic genes (AMGs) from three to 24, including seven genes exclusive to MM pathways. These AMGs are recovered on 911 viral contigs predicted to infect 14 prokaryotic phyla including Halobacteriota, Methanobacteriota, and Thermoproteota. Of those 24, most were encoded by viruses from rumen (16/24), with substantially fewer by viruses from environmental habitats (0-7/24). To search for additional MM AMGs from an environmental habitat, we generate metagenomes from methane-rich sediments in Vrana Lake, Croatia. Therein, we find diverse viral communities, with most viruses predicted to infect methanogens and methanotrophs and some encoding 13 AMGs that can modulate host metabolisms. However, none of these AMGs directly participate in MM pathways. Together these findings suggest that the extent to which viruses use AMGs to modulate host metabolic processes (e.g., MM) varies depending on the ecological properties of the habitat in which they dwell and is not always predictable by habitat biogeochemical properties.}, }
@article {pmid38423404, year = {2024}, author = {Das, S and Malik, M and Dastidar, DG and Roy, R and Paul, P and Sarkar, S and Chakraborty, P and Maity, A and Dasgupta, M and Gupta, AD and Chatterjee, S and Sarker, RK and Maiti, D and Tribedi, P}, title = {Piperine, a phytochemical prevents the biofilm city of methicillin-resistant Staphylococcus aureus: A biochemical approach to understand the underlying mechanism.}, journal = {Microbial pathogenesis}, volume = {189}, number = {}, pages = {106601}, doi = {10.1016/j.micpath.2024.106601}, pmid = {38423404}, issn = {1096-1208}, mesh = {Humans ; *Methicillin-Resistant Staphylococcus aureus ; Anti-Bacterial Agents/pharmacology/metabolism ; *Staphylococcal Infections ; Biofilms ; Phytochemicals/pharmacology ; DNA/metabolism ; Microbial Sensitivity Tests ; *Alkaloids ; *Piperidines ; *Benzodioxoles ; *Polyunsaturated Alkamides ; }, abstract = {Methicillin-resistant Staphylococcus aureus (MRSA), a drug-resistant human pathogen causes several nosocomial as well as community-acquired infections involving biofilm machinery. Hence, it has gained a wide interest within the scientific community to impede biofilm-induced MRSA-associated health complications. The current study focuses on the utilization of a natural bioactive compound called piperine to control the biofilm development of MRSA. Quantitative assessments like crystal violet, total protein recovery, and fluorescein-di-acetate (FDA) hydrolysis assays, demonstrated that piperine (8 and 16 μg/mL) could effectively compromise the biofilm formation of MRSA. Light and scanning electron microscopic image analysis confirmed the same. Further investigation revealed that piperine could reduce extracellular polysaccharide production by down-regulating the expression of icaA gene. Besides, piperine could reduce the cell-surface hydrophobicity of MRSA, a crucial factor of biofilm formation. Moreover, the introduction of piperine could interfere with microbial motility indicating the interaction of piperine with the quorum-sensing components. A molecular dynamics study showed a stable binding between piperine and AgrA protein (regulator of quorum sensing) suggesting the possible meddling of piperine in quorum-sensing of MRSA. Additionally, the exposure to piperine led to the accumulation of intracellular reactive oxygen species (ROS) and potentially heightened cell membrane permeability in inhibiting microbial biofilm formation. Besides, piperine could reduce the secretion of diverse virulence factors from MRSA. Further exploration revealed that piperine interacted with extracellular DNA (e-DNA), causing disintegration by weakening the biofilm architecture. Conclusively, this study suggests that piperine could be a potential antibiofilm molecule against MRSA-associated biofilm infections.}, }
@article {pmid38419638, year = {2024}, author = {Boase, K and Santini, T and Watkin, E}, title = {Microbes of biotechnological importance in acidic saline lakes in the Yilgarn Craton, Western Australia.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1308797}, pmid = {38419638}, issn = {1664-302X}, abstract = {Acidic salt lakes are environments that harbor an array of biologically challenging conditions. Through 16S rRNA, 18S rRNA, and ITS amplicon sequencing of eight such lakes across the Yilgarn Craton of Western Australia, we aim to understand the microbial ecology of these lakes with a focus on iron- and sulfur-oxidizing and reducing microorganisms that have theoretical application in biomining industries. In spite of the biological challenges to life in these lakes, the microbial communities were highly diverse. Redundancy analysis of soil samples revealed sulfur, ammonium, organic carbon, and potassium were significant diversities of the microbial community composition. The most abundant microbes with a hypothetical application in biomining include the genus 9 M32 of the Acidithiobacillus family, Alicyclobacillus and Acidiphilium, all of which are possible iron- and/or sulfur-oxidizing bacteria. It is evident through this study that these lakes harbor multiple organisms with potential in biomining industries that should be exploited and studied further.}, }
@article {pmid38412470, year = {2024}, author = {Shi, TL and Jia, KH and Bao, YT and Nie, S and Tian, XC and Yan, XM and Chen, ZY and Li, ZC and Zhao, SW and Ma, HY and Zhao, Y and Li, X and Zhang, RG and Guo, J and Zhao, W and El-Kassaby, YA and Müller, N and Van de Peer, Y and Wang, XR and Street, NR and Porth, I and An, X and Mao, JF}, title = {High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar.}, journal = {Plant physiology}, volume = {195}, number = {1}, pages = {652-670}, pmid = {38412470}, issn = {1532-2548}, support = {2022YFD2200103//National Key R&amp;D Program of China/ ; 32171816//National Natural Science Foundation of China/ ; }, mesh = {*Populus/genetics ; *Alleles ; *Genome, Plant/genetics ; Gene Expression Regulation, Plant ; Haplotypes/genetics ; Hybridization, Genetic ; Machine Learning ; }, abstract = {Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid "84K" (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.}, }
@article {pmid38411098, year = {2024}, author = {Moreno, CM and Bernish, M and Meyer, MG and Li, Z and Waite, N and Cohen, NR and Schofield, O and Marchetti, A}, title = {Molecular physiology of Antarctic diatom natural assemblages and bloom event reveal insights into strategies contributing to their ecological success.}, journal = {mSystems}, volume = {9}, number = {3}, pages = {e0130623}, pmid = {38411098}, issn = {2379-5077}, support = {PLR1440435//National Science Foundation (NSF)/ ; OPP1745036//National Science Foundation (NSF)/ ; }, mesh = {*Diatoms/genetics ; Antarctic Regions ; Phytoplankton/genetics ; Oceans and Seas ; Plankton/metabolism ; Iron/metabolism ; }, abstract = {UNLABELLED: The continental shelf of the Western Antarctic Peninsula (WAP) is a highly variable system characterized by strong cross-shelf gradients, rapid regional change, and large blooms of phytoplankton, notably diatoms. Rapid environmental changes coincide with shifts in plankton community composition and productivity, food web dynamics, and biogeochemistry. Despite the progress in identifying important environmental factors influencing plankton community composition in the WAP, the molecular basis for their survival in this oceanic region, as well as variations in species abundance, metabolism, and distribution, remains largely unresolved. Across a gradient of physicochemical parameters, we analyzed the metabolic profiles of phytoplankton as assessed through metatranscriptomic sequencing. Distinct phytoplankton communities and metabolisms closely mirrored the strong gradients in oceanographic parameters that existed from coastal to offshore regions. Diatoms were abundant in coastal, southern regions, where colder and fresher waters were conducive to a bloom of the centric diatom, Actinocyclus. Members of this genus invested heavily in growth and energy production; carbohydrate, amino acid, and nucleotide biosynthesis pathways; and coping with oxidative stress, resulting in uniquely expressed metabolic profiles compared to other diatoms. We observed strong molecular evidence for iron limitation in shelf and slope regions of the WAP, where diatoms in these regions employed iron-starvation induced proteins, a geranylgeranyl reductase, aquaporins, and urease, among other strategies, while limiting the use of iron-containing proteins. The metatranscriptomic survey performed here reveals functional differences in diatom communities and provides further insight into the environmental factors influencing the growth of diatoms and their predicted response to changes in ocean conditions.<br><br>IMPORTANCE: In the Southern Ocean, phytoplankton must cope with harsh environmental conditions such as low light and growth-limiting concentrations of the micronutrient iron. Using metratranscriptomics, we assessed the influence of oceanographic variables on the diversity of the phytoplankton community composition and on the metabolic strategies of diatoms along the Western Antarctic Peninsula, a region undergoing rapid climate change. We found that cross-shelf differences in oceanographic parameters such as temperature and variable nutrient concentrations account for most of the differences in phytoplankton community composition and metabolism. We opportunistically characterized the metabolic underpinnings of a large bloom of the centric diatom Actinocyclus in coastal waters of the WAP. Our results indicate that physicochemical differences from onshore to offshore are stronger than between southern and northern regions of the WAP; however, these trends could change in the future, resulting in poleward shifts in functional differences in diatom communities and phytoplankton blooms.}, }
@article {pmid38411061, year = {2024}, author = {Zhang, Y and Deng, Y and Wang, C and Li, S and Lau, FTK and Zhou, J and Zhang, T}, title = {Effects of operational parameters on bacterial communities in Hong Kong and global wastewater treatment plants.}, journal = {mSystems}, volume = {9}, number = {3}, pages = {e0133323}, pmid = {38411061}, issn = {2379-5077}, support = {T21-604/19-R//Hong Kong Theme Based Research Scheme/ ; GRF17206120//Hong Kong General Research Fund/ ; DEMP-2017-03//Hong Kong DSD/ ; }, mesh = {Wastewater ; Sewage/microbiology ; Hong Kong/epidemiology ; Bacteria/genetics ; *Water Purification ; *Environmental Pollutants ; }, abstract = {UNLABELLED: Wastewater treatment plants (WWTPs) are indispensable biotechnology facilities for modern cities and play an essential role in modern urban infrastructure by employing microorganisms to remove pollutants in wastewater, thus protecting public health and the environment. This study conducted a 13-month bacterial community survey of six full-scale WWTPs in Hong Kong with samples of influent, activated sludge (AS), and effluent to explore their synchronism and asynchronism of bacterial community. Besides, we compared AS results of six Hong Kong WWTPs with data from 1,186 AS amplicon data in 269 global WWTPs and a 9-year metagenomic sequencing survey of a Hong Kong WWTP. Our results showed the compositions of bacterial communities varied and the bacterial community structure of AS had obvious differences across Hong Kong WWTPs. The co-occurrence analysis identified 40 pairs of relationships that existed among Hong Kong WWTPs to show solid associations between two species and stochastic processes took large proportions for the bacterial community assembly of six WWTPs. The abundance and distribution of the functional bacteria in worldwide and Hong Kong WWTPs were examined and compared, and we found that ammonia-oxidizing bacteria had more diversity than nitrite-oxidizing bacteria. Besides, Hong Kong WWTPs could make great contributions to the genome mining of microbial dark matter in the global "wanted list." Operational parameters had important effects on OTUs' abundance, such as the temperature to the genera of Tetrasphaera, Gordonia and Nitrospira. All these results obtained from this study can deepen our understanding of the microbial ecology in WWTPs and provide foundations for further studies.<br><br>IMPORTANCE: Wastewater treatment plants (WWTPs) are an indispensable component of modern cities, as they can remove pollutants in wastewater to prevent anthropogenic activities. Activated sludge (AS) is a fundamental wastewater treatment process and it harbors a highly complex microbial community that forms the main components and contains functional groups. Unveiling "who is there" is a long-term goal of the research on AS microbiology. High-throughput sequencing provides insights into the inventory diversity of microbial communities to an unprecedented level of detail. At present, the analysis of communities in WWTPs usually comes from a specific WWTP and lacks comparisons and verification among different WWTPs. The wide-scale and long-term sampling project and research in this study could help us evaluate the AS community more accurately to find the similarities and different results for different WWTPs in Hong Kong and other regions of the world.}, }
@article {pmid38410391, year = {2024}, author = {Duysburgh, C and Miclotte, L and Green, JB and Watts, KT and Sardi, MI and Chakrabarti, A and Khafipour, E and Marzorati, M}, title = {Saccharomyces cerevisiae derived postbiotic alters gut microbiome metabolism in the human distal colon resulting in immunomodulatory potential in vitro.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1358456}, pmid = {38410391}, issn = {1664-302X}, abstract = {The yeast-based postbiotic EpiCor is a well-studied formulation, consisting of a complex mixture of bioactive molecules. In clinical studies, EpiCor postbiotic has been shown to reduce intestinal symptoms in a constipated population and support mucosal defense in healthy subjects. Anti-inflammatory potential and butyrogenic properties have been reported in vitro, suggesting a possible link between EpiCor's gut modulatory activity and immunomodulation. The current study used a standardized in vitro gut model, the Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]), to obtain a deeper understanding on host-microbiome interactions and potential microbiome modulation following repeated EpiCor administration. It was observed that EpiCor induced a functional shift in carbohydrate fermentation patterns in the proximal colon environment. Epicor promoted an increased abundance of Bifidobacterium in both the proximal and distal colon, affecting overall microbial community structure. Co-occurrence network analysis at the phylum level provided additional evidence of changes in the functional properties of microbial community promoted by EpiCor, increasing positive associations between Actinobacteria with microbes belonging to the Firmicutes phylum. These results, together with a significant increase in butyrate production provide additional support of EpiCor benefits to gut health. Investigation of host-microbiome interactions confirmed the immunomodulatory potential of the applied test product. Specific microbial alterations were observed in the distal colon, with metabotyping indicating that specific metabolic pathways, such as bile acid and tryptophan metabolism, were affected following EpiCor supplementation. These results, especially considering many effects were seen distally, further strengthen the position of EpiCor as a postbiotic with health promoting functionality in the gut, which could be further assessed in vivo.}, }
@article {pmid38409540, year = {2024}, author = {Xu, T and Novotny, A and Zamora-Terol, S and Hambäck, PA and Winder, M}, title = {Dynamics of Gut Bacteria Across Different Zooplankton Genera in the Baltic Sea.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {48}, pmid = {38409540}, issn = {1432-184X}, support = {2016-04685//Swedish Research Council/ ; 2016-04685//Swedish Research Council/ ; }, mesh = {Animals ; Zooplankton/genetics ; RNA, Ribosomal, 16S/genetics/metabolism ; Bacteria ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; *Rotifera ; }, abstract = {In aquatic ecosystems, zooplankton-associated bacteria potentially have a great impact on the structure of ecosystems and trophic networks by providing various metabolic pathways and altering the ecological niche of host species. To understand the composition and drivers of zooplankton gut microbiota, we investigated the associated microbial communities of four zooplankton genera from different seasons in the Baltic Sea using the 16S rRNA gene. Among the 143 ASVs (amplified sequence variants) observed belonging to heterotrophic bacteria, 28 ASVs were shared across all zooplankton hosts over the season, and these shared core ASVs represented more than 25% and up to 60% of relative abundance in zooplankton hosts but were present at low relative abundance in the filtered water. Zooplankton host identity had stronger effects on bacterial composition than seasonal variation, with the composition of gut bacterial communities showing host-specific clustering patterns. Although bacterial compositions and dominating core bacteria were different between zooplankton hosts, higher gut bacteria diversity and more bacteria contributing to the temporal variation were found in Temora and Pseudocalanus, compared to Acartia and Synchaeta. Diet diatom and filamentous cyanobacteria negatively correlated with gut bacteria diversity, but the difference in diet composition did not explain the dissimilarity of gut bacteria composition, suggesting a general effect of diet on the inner conditions in the zooplankton gut. Synchaeta maintained high stability of gut bacterial communities with unexpectedly low bacteria-bacteria interactions as compared to the copepods, indicating host-specific regulation traits. Our results suggest that the patterns of gut bacteria dynamics are host-specific and the variability of gut bacteria is not only related to host taxonomy but also related to host behavior and life history traits.}, }
@article {pmid38408899, year = {2024}, author = {Banerjee, A and Ghosh, A and Saha, B and Bhadury, P and De, P}, title = {Surface Charge-Switchable Antifouling Block Copolymer with Bacteriostatic Properties.}, journal = {Langmuir : the ACS journal of surfaces and colloids}, volume = {40}, number = {10}, pages = {5314-5325}, doi = {10.1021/acs.langmuir.3c03771}, pmid = {38408899}, issn = {1520-5827}, mesh = {*Biofouling/prevention &amp; control ; Proteins/metabolism ; Cations/chemistry ; Cell Membrane/metabolism ; Polymers/chemistry ; Surface Properties ; }, abstract = {Zwitterionic polymers are an emerging family of effective, low-fouling materials that can withstand unintended interactions with biological systems while exhibiting enhanced activity in bacterial matrix deterioration and biofilm eradication. Herein, we modularly synthesized an amphiphilic block copolymer, ZABCP, featuring potential bacteriostatic properties composed of a charge-switchable polyzwitterionic segment and a redox-sensitive pendant disulfide-labeled polymethacrylate block. The leucine-appended polyzwitterionic segment with alternatively positioned cationic amine and anionic carboxylate functionalities undergoes charge alterations (+ve → 0 → -ve) on pH variation. By introducing appropriate amphiphilicity, ZABCP forms distinct vesicles with redox-sensitive bilayer membranes and zwitterionic shielding coronas, enabling switching of surface charge. ZABCP vesicles exhibit 180 ± 20 nm hydrodynamic diameter, and its charge switching behavior in response to pH was confirmed by the change of zeta potential value from -23 to +36 mV. The binding interaction between ZABCP vesicles with lysozyme and pepsin proteins strengthens when the surface charge shifts from neutral (pH 7.4) to either anionic or cationic. This surface-charge-switchable phenomenon paves the way for implementing cationic ZABCP vesicles for bacterial cell growth inhibition, which is shown by the pronounced transition of cellular morphology, including clustering, aggregation, or elongation as well as membrane disruption for both Bacillus subtilis (Gram-positive) and Escherichia coli (Gram-negative). Such enhanced bacteriostatic activity could be ascribed to a strong electrostatic interaction between cationic vesicles and negatively charged bacterial membranes, leading to cell membrane disruption. Overall, this study provides a tailor-made approach to adopt low-fouling properties and potential bacteriostatic activity using zwitterionic polymers through precise control of pH.}, }
@article {pmid38407642, year = {2024}, author = {Wang, Y and Xue, D and Chen, X and Qiu, Q and Chen, H}, title = {Structure and Functions of Endophytic Bacterial Communities Associated with Sphagnum Mosses and Their Drivers in Two Different Nutrient Types of Peatlands.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {47}, pmid = {38407642}, issn = {1432-184X}, support = {2022376//the Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 2021JDTD011//the Youth Science and Technology Innovation Team Program of Sichuan Province of China/ ; QNTS202201//the Youth Innovation Program of CIB/ ; 42001093//the National Natural Science Foundation of China/ ; 2019QZKK0304//the Second Tibetan Plateau Scientific Expedition/ ; }, mesh = {*Ecosystem ; RNA, Ribosomal, 16S/genetics ; *Sphagnopsida ; Bacteria/genetics ; Carbon ; Nitrogen ; Nutrients ; }, abstract = {Sphagnum mosses are keystone plant species in the peatland ecosystems that play a crucial role in the formation of peat, which shelters a broad diversity of endophytic bacteria with important ecological functions. In particular, methanotrophic and nitrogen-fixing endophytic bacteria benefit Sphagnum moss hosts by providing both carbon and nitrogen. However, the composition and abundance of endophytic bacteria from different species of Sphagnum moss in peatlands of different nutrient statuses and their drivers remain unclear. This study used 16S rRNA gene amplicon sequencing to examine endophytic bacterial communities in Sphagnum mosses and measured the activity of methanotrophic microbial by the [13]C-CH4 oxidation rate. According to the results, the endophytic bacterial community structure varied among Sphagnum moss species and Sphagnum capillifolium had the highest endophytic bacterial alpha diversity. Moreover, chlorophyll, phenol oxidase, carbon contents, and water retention capacity strongly shaped the communities of endophytic bacteria. Finally, Sphagnum palustre in Hani (SP) had a higher methane oxidation rate than S. palustre in Taishanmiao. This result is associated with the higher average relative abundance of Methyloferula an obligate methanotroph in SP. In summary, this work highlights the effects of Sphagnum moss characteristics on the endophytic bacteriome. The endophytic bacteriome is important for Sphagnum moss productivity, as well as for carbon and nitrogen cycles in Sphagnum moss peatlands.}, }
@article {pmid38407587, year = {2024}, author = {Kempraj, V and Auth, J and Cha, DH and Mason, CJ}, title = {Impact of Larval Food Source on the Stability of the Bactrocera dorsalis Microbiome.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {46}, pmid = {38407587}, issn = {1432-184X}, support = {2040-22430-028-000-D//USDA ARS/ ; 2040-43000-018-000-D//USDA ARS/ ; 2040-22430-028-000-D//USDA ARS/ ; 60-2040-3-003//Animal and Plant Health Inspection Service/ ; }, mesh = {Humans ; Female ; Animals ; Larva ; RNA, Ribosomal, 16S/genetics ; *Fruit ; *Tephritidae ; }, abstract = {Bacterial symbionts are crucial to the biology of Bactrocera dorsalis. With larval diet (fruit host) being a key factor that determines microbiome composition and with B. dorsalis using more than 400 fruits as hosts, it is unclear if certain bacterial symbionts are preserved and are passed on to B. dorsalis progenies despite changes in larval diet. Here, we conducted a fly rearing experiment to characterize diet-induced changes in the microbiome of female B. dorsalis. In order to explicitly investigate the impacts of larval diet on the microbiome, including potential stable bacterial constituents of B. dorsalis, we performed 16S rRNA sequencing on the gut tissues of teneral female flies reared from four different host fruits (guava, mango, papaya, and rose apple) infested using a single cohort of wild B. dorsalis that emerged from tropical almond (mother flies). Although B. dorsalis-associated microbiota were predominantly shaped by the larval diet, some major bacterial species from the mother flies were retained in progenies raised on different larval diets. With some variation, Klebsiella (ASV 1 and 2), Morganella (ASV 3), and Providencia (ASV 6) were the major bacterial symbionts that were stable and made up 0.1-80% of the gut and ovipositor microbiome of female teneral flies reared on different host fruits. Our results suggest that certain groups of bacteria are stably associated with female B. dorsalis across larval diets. These findings provide a basis for unexplored research on symbiotic bacterial function in B. dorsalis and may aid in the development of novel management techniques against this devastating pest of horticultural importance.}, }
@article {pmid38405409, year = {2024}, author = {Hoffbeck, C and Middleton, DMRL and Lamar, SK and Keall, SN and Nelson, NJ and Taylor, MW}, title = {Gut microbiome of the sole surviving member of reptile order Rhynchocephalia reveals biogeographic variation, influence of host body condition and a substantial core microbiota in tuatara across New Zealand.}, journal = {Ecology and evolution}, volume = {14}, number = {2}, pages = {e11073}, pmid = {38405409}, issn = {2045-7758}, abstract = {Tuatara are the sole extant species in the reptile order Rhynchocephalia. They are ecologically and evolutionarily unique, having been isolated geographically for ~84 million years and evolutionarily from their closest living relatives for ~250 million years. Here we report the tuatara gut bacterial community for the first time. We sampled the gut microbiota of translocated tuatara at five sanctuaries spanning a latitudinal range of ~1000 km within Aotearoa New Zealand, as well as individuals from the source population on Takapourewa (Stephens Island). This represents a first look at the bacterial community of the order Rhynchocephalia and provides the opportunity to address several key hypotheses, namely that the tuatara gut microbiota: (1) differs from those of other reptile orders; (2) varies among geographic locations but is more similar at sites with more similar temperatures and (3) is shaped by tuatara body condition, parasitism and ambient temperature. We found significant drivers of the microbiota in sampling site, tuatara body condition, parasitism and ambient temperature, suggesting the importance of these factors when considering tuatara conservation. We also derived a 'core' community of shared bacteria across tuatara at many sites, despite their geographic range and isolation. Remarkably, >70% of amplicon sequence variants could not be assigned to known genera, suggesting a largely undescribed gut bacterial community for this ancient host species.}, }
@article {pmid38403716, year = {2024}, author = {Nayman, EI and Schwartz, BA and Polmann, M and Gumabong, AC and Nieuwdorp, M and Cickovski, T and Mathee, K}, title = {Differences in gut microbiota between Dutch and South-Asian Surinamese: potential implications for type 2 diabetes mellitus.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {4585}, pmid = {38403716}, issn = {2045-2322}, support = {09150182010020//ZONMW-VICI/ ; }, mesh = {Humans ; Female ; Ethnicity ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2/epidemiology ; Adenosine Deaminase ; Minority Groups ; Intercellular Signaling Peptides and Proteins ; Fatty Acids, Volatile ; }, abstract = {Gut microbiota, or the collection of diverse microorganisms in a specific ecological niche, are known to significantly impact human health. Decreased gut microbiota production of short-chain fatty acids (SCFAs) has been implicated in type 2 diabetes mellitus (T2DM) disease progression. Most microbiome studies focus on ethnic majorities. This study aims to understand how the microbiome differs between an ethnic majority (the Dutch) and minority (the South-Asian Surinamese (SAS)) group with a lower and higher prevalence of T2DM, respectively. Microbiome data from the Healthy Life in an Urban Setting (HELIUS) cohort were used. Two age- and gender-matched groups were compared: the Dutch (n = 41) and SAS (n = 43). Microbial community compositions were generated via DADA2. Metrics of microbial diversity and similarity between groups were computed. Biomarker analyses were performed to determine discriminating taxa. Bacterial co-occurrence networks were constructed to examine ecological patterns. A tight microbiota cluster was observed in the Dutch women, which overlapped with some of the SAS microbiota. The Dutch gut contained a more interconnected microbial ecology, whereas the SAS network was dispersed, i.e., contained fewer inter-taxonomic correlational relationships. Bacteroides caccae, Butyricicoccus, Alistipes putredinis, Coprococcus comes, Odoribacter splanchnicus, and Lachnospira were enriched in the Dutch gut. Haemophilus, Bifidobacterium, and Anaerostipes hadrus discriminated the SAS gut. All but Lachnospira and certain strains of Haemophilus are known to produce SCFAs. The Dutch gut microbiome was distinguished from the SAS by diverse, differentially abundant SCFA-producing taxa with significant cooperation. The dynamic ecology observed in the Dutch was not detected in the SAS. Among several potential gut microbial biomarkers, Haemophilus parainfluenzae likely best characterizes the ethnic minority group, which is more predisposed to T2DM. The higher prevalence of T2DM in the SAS may be associated with the gut dysbiosis observed.}, }
@article {pmid38402967, year = {2024}, author = {Zhou, P and Li, D and Zhang, C and Ping, Q and Wang, L and Li, Y}, title = {Comparison of different sewage sludge pretreatment technologies for improving sludge solubilization and anaerobic digestion efficiency: A comprehensive review.}, journal = {The Science of the total environment}, volume = {921}, number = {}, pages = {171175}, doi = {10.1016/j.scitotenv.2024.171175}, pmid = {38402967}, issn = {1879-1026}, mesh = {Anaerobiosis ; *Sewage/microbiology ; *Ultrasonics ; Methane/chemistry ; Hydrolysis ; Waste Disposal, Fluid ; Bioreactors ; }, abstract = {Anaerobic digestion (AD) of sewage sludge reduces organic solids and produces methane, but the complex nature of sludge, especially the difficulty in solubilization, limits AD efficiency. Pretreatments, by destroying sludge structure and promoting disintegration and hydrolysis, are valuable strategies to enhance AD performance. There is a plethora of reviews on sludge pretreatments, however, quantitative comparisons from multiple perspectives across different pretreatments remain scarce. This review categorized various pretreatments into three groups: Physical (ultrasonic, microwave, thermal hydrolysis, electric decomposition, and high pressure homogenization), chemical (acid, alkali, Fenton, calcium peroxide, and ozone), and biological (microaeration, exogenous bacteria, and exogenous hydrolase) pretreatments. The optimal conditions of various pretreatments and their impacts on enhancing AD efficiency were summarized; the effects of different pretreatments on microbial community in the AD system were comprehensively compared. The quantitative comparison based on dissolution degree of COD (DDCOD) indicted that the sludge solubilization performance is in the order of physical, chemical, and biological pretreatments, although with each below 40 % DDCOD. Biological pretreatment, particularly microaeration and exogenous bacteria, excel in AD enhancement. Pretreatments alter microbial ecology, favoring Firmicutes and Methanosaeta (acetotrophic methanogens) over Proteobacteria and Methanobacterium (hydrogenotrophic methanogens). Most pretreatments have unfavorable energy and economic outcomes, with electric decomposition and microaeration being exceptions. On the basis of the overview of the above pretreatments, a full energy and economy assessment for sewage sludge treatment was suggested. Finally, challenges associated with sludge pretreatments and AD were analyzed, and future research directions were proposed. This review may broaden comprehension of sludge pretreatments and AD, and provide an objective basis for the selection of sludge pretreatment technologies.}, }
@article {pmid38402751, year = {2024}, author = {Rosenqvist, T and Chan, S and Ahlinder, J and Salomonsson, EN and Suarez, C and Persson, KM and Rådström, P and Paul, CJ}, title = {Inoculation with adapted bacterial communities promotes development of full scale slow sand filters for drinking water production.}, journal = {Water research}, volume = {253}, number = {}, pages = {121203}, doi = {10.1016/j.watres.2024.121203}, pmid = {38402751}, issn = {1879-2448}, mesh = {*Drinking Water ; *Water Purification/methods ; Bacteria/genetics ; *Microbiota ; Firmicutes ; Filtration/methods ; Silicon Dioxide/chemistry ; }, abstract = {Gravity-driven filtration through slow sand filters (SSFs) is one of the oldest methods for producing drinking water. As water passes through a sand bed, undesired microorganisms and chemicals are removed by interactions with SSF biofilm and its resident microbes. Despite their importance, the processes through which these microbial communities form are largely unknown, as are the factors affecting these processes. In this study, two SSFs constructed using different sand sources were compared to an established filter and observed throughout their maturation process. One SSF was inoculated through addition of sand scraped from established filters, while the other was not inoculated. The operational and developing microbial communities of SSFs, as well as their influents and effluents, were studied by sequencing of 16S ribosomal rRNA genes. A functional microbial community resembling that of the established SSF was achieved in the inoculated SSF, but not in the non-inoculated SSF. Notably, the non-inoculated SSF had significantly (p < 0.01) higher abundances of classes Armatimonadia, Elusimicrobia, Fimbriimonadia, OM190 (phylum Planctomycetota), Parcubacteria, Vampirivibrionia and Verrucomicrobiae. Conversely, it had lower abundances of classes Anaerolineae, Bacilli, bacteriap25 (phylum Myxococcota), Blastocatellia, Entotheonellia, Gemmatimonadetes, lineage 11b (phylum Elusimicrobiota), Nitrospiria, Phycisphaerae, subgroup 22 (phylum Acidobacteriota) and subgroup 11 (phylum Acidobacteriota). Poor performance of neutral models showed that the assembly and dispersal of SSF microbial communities was mainly driven by selection. The temporal turnover of microbial species, as estimated through the scaling exponent of the species-time relationship, was twice as high in the non-inoculated filter (0.946 ± 0.164) compared to the inoculated filter (0.422 ± 0.0431). This study shows that the addition of an inoculum changed the assembly processes within SSFs. Specifically, the rate at which new microorganisms were observed in the biofilm was reduced. The reduced temporal turnover may be driven by inoculating taxa inhibiting growth, potentially via secondary metabolite production. This in turn would allow the inoculation community to persist and contribute to SSF function.}, }
@article {pmid38402201, year = {2024}, author = {Zhu, H and Li, M and Bi, D and Yang, H and Gao, Y and Song, F and Zheng, J and Xie, R and Zhang, Y and Liu, H and Yan, X and Kong, C and Zhu, Y and Xu, Q and Wei, Q and Qin, H}, title = {Fusobacterium nucleatum promotes tumor progression in KRAS p.G12D-mutant colorectal cancer by binding to DHX15.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1688}, pmid = {38402201}, issn = {2041-1723}, support = {81972221//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; 81801564//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; 81902422//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; 82072634//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; }, mesh = {Animals ; Humans ; Mice ; Carcinogenesis/genetics ; *Colorectal Neoplasms/pathology ; *Fusobacterium nucleatum/genetics ; Proto-Oncogene Proteins p21(ras)/genetics ; RNA Helicases ; }, abstract = {Fusobacterium nucleatum (F. nucleatum) promotes intestinal tumor growth and its relative abundance varies greatly among patients with CRC, suggesting the presence of unknown, individual-specific effectors in F. nucleatum-dependent carcinogenesis. Here, we identify that F. nucleatum is enriched preferentially in KRAS p.G12D mutant CRC tumor tissues and contributes to colorectal tumorigenesis in Villin-Cre/Kras[G12D+/-] mice. Additionally, Parabacteroides distasonis (P. distasonis) competes with F. nucleatum in the G12D mouse model and human CRC tissues with the KRAS mutation. Orally gavaged P. distasonis in mice alleviates the F. nucleatum-dependent CRC progression. F. nucleatum invades intestinal epithelial cells and binds to DHX15, a protein of RNA helicase family expressed on CRC tumor cells, mechanistically involving ERK/STAT3 signaling. Knock out of Dhx15 in Villin-Cre/Kras[G12D+/-] mice attenuates the CRC phenotype. These findings reveal that the oncogenic effect of F. nucleatum depends on somatic genetics and gut microbial ecology and indicate that personalized modulation of the gut microbiota may provide a more targeted strategy for CRC treatment.}, }
@article {pmid38401719, year = {2024}, author = {Martin-Pozas, T and Cuezva, S and Fernandez-Cortes, A and Gonzalez-Pumariega, M and Elez, J and Duarte, E and de la Rasilla, M and Canaveras, JC and Saiz-Jimenez, C and Sanchez-Moral, S}, title = {Adaptive response of prokaryotic communities to extreme pollution flooding in a Paleolithic rock art cave (Pindal Cave, northern Spain).}, journal = {The Science of the total environment}, volume = {921}, number = {}, pages = {171137}, doi = {10.1016/j.scitotenv.2024.171137}, pmid = {38401719}, issn = {1879-1026}, mesh = {Animals ; Cattle ; *Ecosystem ; Spain ; Floods ; Prokaryotic Cells ; *Microbiota ; Nitrogen ; Mammals ; }, abstract = {A flood event affecting Pindal Cave, a UNESCO World Heritage site, introduced a substantial amount of external sediments and waste into the cave. This event led to the burial of preexisting sediments, altering the biogeochemical characteristics of the cave ecosystem by introducing heightened levels of organic matter, nitrogen compounds, phosphorus, and heavy metals. The sediments included particulate matter and waste from a cattle farm located within the water catchment area of the cavity, along with diverse microorganisms, reshaping the cave microbial community. This study addresses the ongoing influence of a cattle farm on the cave ecosystem and aims to understand the adaptive responses of the underground microbial community to the sudden influx of waste allochthonous material. Here, we show that the flood event had an immediate and profound effect on the cave microbial community, marked by a significant increase in methanogenic archaea, denitrifying bacteria, and other microorganisms commonly associated with mammalian intestinal tracts. Furthermore, our findings reveal that one year after the flood, microorganisms related to the flood decreased, while the increase in inorganic forms of ammonium and nitrate suggests potential nitrification, aligning with increased abundances of corresponding functional genes involved in nitrogen cycling. The results reveal that the impact of pollution was neither recent nor isolated, and it was decisive in stopping livestock activity near the cave. The influence of the cattle farm has persisted since its establishment over the impluvium area, and this influence endures even a year after the flood. Our study emphasizes the dynamic interplay between natural events, anthropogenic activities, and microbial communities, offering insights into the resilience of cave ecosystems. Understanding microbial adaptation in response to environmental disturbances, as demonstrated in this cave ecosystem, has implications for broader ecological studies and underscores the importance of considering temporal dynamics in conservation efforts.}, }
@article {pmid38401169, year = {2024}, author = {Vieira, HH and Bulzu, PA and Kasalický, V and Haber, M and Znachor, P and Piwosz, K and Ghai, R}, title = {Isolation of a widespread giant virus implicated in cryptophyte bloom collapse.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38401169}, issn = {1751-7370}, support = {20-12496X//Grant Agency of the Czech Republic/ ; GACR 23-06806S//Grant Agency of the Czech Republic/ ; 22-33245S//Czech Science Foundation/ ; 2021/03/Y/NZ8/00076//National Science Centre/ ; }, mesh = {Humans ; *Giant Viruses ; Phytoplankton ; Cryptophyta/genetics ; Eukaryota ; *Viruses ; }, abstract = {Photosynthetic cryptophytes are ubiquitous protists that are major participants in the freshwater phytoplankton bloom at the onset of spring. Mortality due to change in environmental conditions and grazing have been recognized as key factors contributing to bloom collapse. In contrast, the role of viral outbreaks as factors terminating phytoplankton blooms remains unknown from freshwaters. Here, we isolated and characterized a cryptophyte virus contributing to the annual collapse of a natural cryptophyte spring bloom population. This viral isolate is also representative for a clade of abundant giant viruses (phylum Nucleocytoviricota) found in freshwaters all over the world.}, }
@article {pmid38400045, year = {2024}, author = {Johnson, ML and Zwart, MP}, title = {Robust Approaches to the Quantitative Analysis of Genome Formula Variation in Multipartite and Segmented Viruses.}, journal = {Viruses}, volume = {16}, number = {2}, pages = {}, pmid = {38400045}, issn = {1999-4915}, support = {016.Vidi.171.061/NWO_/Dutch Research Council/Netherlands ; }, mesh = {*Viruses/genetics ; Genome, Viral ; Biological Evolution ; }, abstract = {When viruses have segmented genomes, the set of frequencies describing the abundance of segments is called the genome formula. The genome formula is often unbalanced and highly variable for both segmented and multipartite viruses. A growing number of studies are quantifying the genome formula to measure its effects on infection and to consider its ecological and evolutionary implications. Different approaches have been reported for analyzing genome formula data, including qualitative description, applying standard statistical tests such as ANOVA, and customized analyses. However, these approaches have different shortcomings, and test assumptions are often unmet, potentially leading to erroneous conclusions. Here, we address these challenges, leading to a threefold contribution. First, we propose a simple metric for analyzing genome formula variation: the genome formula distance. We describe the properties of this metric and provide a framework for understanding metric values. Second, we explain how this metric can be applied for different purposes, including testing for genome-formula differences and comparing observations to a reference genome formula value. Third, we re-analyze published data to illustrate the applications and weigh the evidence for previous conclusions. Our re-analysis of published datasets confirms many previous results but also provides evidence that the genome formula can be carried over from the inoculum to the virus population in a host. The simple procedures we propose contribute to the robust and accessible analysis of genome-formula data.}, }
@article {pmid38399791, year = {2024}, author = {Stroeva, AR and Klyukina, AA and Vidishcheva, ON and Poludetkina, EN and Solovyeva, MA and Pyrkin, VO and Gavirova, LA and Birkeland, NK and Akhmanov, GG and Bonch-Osmolovskaya, EA and Merkel, AY}, title = {Structure of Benthic Microbial Communities in the Northeastern Part of the Barents Sea.}, journal = {Microorganisms}, volume = {12}, number = {2}, pages = {}, pmid = {38399791}, issn = {2076-2607}, support = {20-54-20001//Russian Foundation for Basic Research/ ; }, abstract = {The Barents Sea shelf is one of the most economically promising regions in the Arctic in terms of its resources and geographic location. However, benthic microbial communities of the northeastern Barents Sea are still barely studied. Here, we present a detailed systematic description of the structures of microbial communities located in the sediments and bottom water of the northeastern Barents Sea based on 16S rRNA profiling and a qPCR assessment of the total prokaryotic abundance in 177 samples. Beta- and alpha-diversity analyses revealed a clear difference between the microbial communities of diverse sediment layers and bottom-water fractions. We identified 101 microbial taxa whose representatives had statistically reliable distribution patterns between these ecotopes. Analysis of the correlation between microbial community structure and geological data yielded a number of important results-correlations were found between the abundance of individual microbial taxa and bottom relief, thickness of marine sediments, presence of hydrotrolite interlayers, and the values of pH and Eh. We also demonstrated that a relatively high abundance of prokaryotes in sediments can be caused by the proliferation of Deltaproteobacteria representatives, in particular, sulfate and iron reducers.}, }
@article {pmid38395561, year = {2024}, author = {Aswathi, KN and Shirke, A and Praveen, A and Murthy, PS}, title = {Functioning of Saccharomyces cerevisiae in honey coffee (Coffea canephora) and their effect on metabolites, volatiles and flavor profiles.}, journal = {Food research international (Ottawa, Ont.)}, volume = {180}, number = {}, pages = {114092}, doi = {10.1016/j.foodres.2024.114092}, pmid = {38395561}, issn = {1873-7145}, mesh = {Saccharomyces cerevisiae/metabolism ; *Coffea/chemistry ; *Honey ; *Yeast, Dried ; Sugars/metabolism ; }, abstract = {Post-harvesting and microbial activity of coffee play a critical role in the metabolites and the sensory quality of the brew. The pulped natural/honey coffee process is an improvised semi-dry technique consisting of prolonged fermentation of depulped coffee beans excluding washing steps. The starter culture application in coffee industry plays an important role to enhance the cup quality. This work focuses on the fermentation of pulped natural/honey Robusta coffee with a starter culture (Saccharomyces cerevisiae MTCC 173) and the identification of fermentation patterns through [1]H NMR, microbial ecology, volatomics and organoleptics of brew. Fermentation was accelerated by yeast populace (10 cfu log/mL) for 192 h. Principal compound analysis performed on [1]H NMR led to the investigation of metabolites such as sugars, alkaloids, alcohols, organic acids and amino acids. Detection of some sugars and organic acids represented that the starter cultures imparted few metabolic changes during the process. A major activity of sugars in fermentation with 83.3 % variance in PC 1 and 16.7 % in PC 2 was observed. The chemical characteristics such as carbohydrates (41.88 ± 0.77 mg/g), polyphenols (34.16 ± 0.79 mg/g), proteins (58.54 ± 0.66 mg/g), caffeine (26.54 ± 0.06 mg/g), and CGA (21.83 ± 0.04 mg/g) were also evaluated. The heatmap-based visualization of GC-MS accorded characterization of additional 5 compounds in treated (T) coffee contributing to sweet, fruity and caramelly odor notes compared to untreated (UT). The sensory outlines 72.5 in T and 70.5 in UT scores. Preparation of honey coffee with Saccharomyces cerevisiae is the first report, which modulated the flavor and quality of coffee.}, }
@article {pmid38395158, year = {2024}, author = {Li, XM and Hu, HF and Chen, SC}, title = {Artificial light at night causes community instability of bacterial community in urban soils.}, journal = {The Science of the total environment}, volume = {921}, number = {}, pages = {171129}, doi = {10.1016/j.scitotenv.2024.171129}, pmid = {38395158}, issn = {1879-1026}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Ecosystem ; *Soil ; Light Pollution ; Environment ; Bacteria ; Light ; }, abstract = {Urban soils host diverse bacteria crucial for ecosystem functions and urban health. As urbanization rises, artificial light at night (ALAN) imposes disturbances on soil ecosystems, yet how ALAN affects the structure and stability of soil bacterial community remains unclear. Here we coupled a short-term incubation experiment, community profiling, network analysis, and in situ field survey to assess the ecological impacts of ALAN. We showed that ALAN influenced bacterial compositions and shifted the bacterial network to a less stable phase, altering denitrification potential. Such transition in community stability probably resulted from an ALAN-induced decrease in competition and/or an increase in facilitation, in line with the Stress Gradient Hypothesis. Similar destabilizing effects were also detected in bacterial networks in multiple urban soils subjected to different levels of ALAN stress, supporting the action of ALAN on naturally-occurring soil bacterial communities. Overall, our findings highlight ALAN as a new form of anthropogenic stress that jeopardizes the stability of soil bacterial community, which would facilitate ecological projection of expanding ALAN exposure.}, }
@article {pmid38393401, year = {2024}, author = {Minahan, NT and Chen, CH and Chuang, YC and Tsai, KH and Shen, WC and Guo, YL}, title = {Fungal Spore Richness and Abundance of Allergenic Taxa: Comparing a Portable Impactor and Passive Trap Indoors and Outdoors in an Urban Setting.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {45}, pmid = {38393401}, issn = {1432-184X}, mesh = {*Allergens ; Spores, Fungal/genetics ; *Fungi/genetics ; Air Microbiology ; Environmental Monitoring ; }, abstract = {Fungal spores are common airborne allergens, and fungal richness has been implicated in allergic disease. Amplicon sequencing of environmental DNA from air samples is a promising method to estimate fungal spore richness with semi-quantification of hundreds of taxa and can be combined with quantitative PCR to derive abundance estimates. However, it remains unclear how the choice of air sampling method influences these estimates. This study compared active sampling with a portable impactor and passive sampling with a passive trap over different durations to estimate fungal spore richness and the abundance of allergenic taxa. Air sampling was conducted indoors and outdoors at 12 residences, including repeated measurements with a portable impactor and passive traps with 1-day and 7-day durations. ITS2 amplicon sequence data were transformed to spore equivalents estimated by quantitative PCR, repeated active samples were combined, and abundance-based rarefaction was performed to standardize sample coverage for estimation of genus-level richness and spore abundance. Rarefied fungal richness was similar between methods indoors but higher for passive traps with a 7-day duration outdoors. Rarefied abundance of allergenic genera was similar between methods but some genera had lower abundance for passive traps with a 1-day duration, which differed indoors and outdoors indicating stochasticity in the collection of spores on collocated samplers. This study found that similar estimates of fungal spore richness and abundance of allergenic taxa can be obtained using a portable impactor or a passive trap within one day and that increased passive sample duration provides limited additional information.}, }
@article {pmid38391651, year = {2024}, author = {Hoffstadt, K and Nikolausz, M and Krafft, S and Bonatelli, ML and Kumar, V and Harms, H and Kuperjans, I}, title = {Optimization of the Ex Situ Biomethanation of Hydrogen and Carbon Dioxide in a Novel Meandering Plug Flow Reactor: Start-Up Phase and Flexible Operation.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {11}, number = {2}, pages = {}, pmid = {38391651}, issn = {2306-5354}, support = {KESW-1-2-032A-B//European Regional Development Fund (ERDF)/ ; }, abstract = {With the increasing use of renewable energy resources for the power grid, the need for long-term storage technologies, such as power-to-gas systems, is growing. Biomethanation provides the opportunity to store energy in the form of the natural gas-equivalent biomethane. This study investigates a novel plug flow reactor that employs a helical static mixer for the biological methanation of hydrogen and carbon dioxide. In tests, the reactor achieved an average methane production rate of 2.5 LCH4LR∗d (methane production [LCH4] per liter of reactor volume [LR] per day [d]) with a maximum methane content of 94%. It demonstrated good flexibilization properties, as repeated 12 h downtimes did not negatively impact the process. The genera Methanothermobacter and Methanobacterium were predominant during the initial phase, along with volatile organic acid-producing, hydrogenotrophic, and proteolytic bacteria. The average ratio of volatile organic acid to total inorganic carbon increased to 0.52 ± 0.04, while the pH remained stable at an average of pH 8.1 ± 0.25 from day 32 to 98, spanning stable and flexible operation modes. This study contributes to the development of efficient flexible biological methanation systems for sustainable energy storage and management.}, }
@article {pmid38388537, year = {2024}, author = {Faller, L and Leite, MFA and Kuramae, EE}, title = {Enhancing phosphate-solubilising microbial communities through artificial selection.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1649}, pmid = {38388537}, issn = {2041-1723}, mesh = {*Phosphates ; Ecosystem ; Soil Microbiology ; Agriculture ; Soil ; *Microbiota/genetics ; }, abstract = {Microbial communities, acting as key drivers of ecosystem processes, harbour immense potential for sustainable agriculture practices. Phosphate-solubilising microorganisms, for example, can partially replace conventional phosphate fertilisers, which rely on finite resources. However, understanding the mechanisms and engineering efficient communities poses a significant challenge. In this study, we employ two artificial selection methods, environmental perturbation, and propagation, to construct phosphate-solubilising microbial communities. To assess trait transferability, we investigate the community performance in different media and a hydroponic system with Chrysanthemum indicum. Our findings reveal a distinct subset of phosphate-solubilising bacteria primarily dominated by Klebsiella and Enterobacterales. The propagated communities consistently demonstrate elevated levels of phosphate solubilisation, surpassing the starting soil community by 24.2% in activity. The increased activity of propagated communities remains consistent upon introduction into the hydroponic system. This study shows the efficacy of community-level artificial selection, particularly through propagation, as a tool for successfully modifying microbial communities to enhance phosphate solubilisation.}, }
@article {pmid38385702, year = {2024}, author = {Zhao, Y and Ling, N and Liu, X and Li, C and Jing, X and Hu, J and Rui, J}, title = {Altitudinal patterns of alpine soil ammonia-oxidizing community structure and potential nitrification rate.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {3}, pages = {e0007024}, pmid = {38385702}, issn = {1098-5336}, support = {41771293//MOST | National Natural Science Foundation of China (NSFC)/ ; 42277100//MOST | National Natural Science Foundation of China (NSFC)/ ; 20JR5RA308//Outstanding Youth Foundation of Gansu Province/ ; lzujbky-2019-ct01//Fundamental Research Funds for Central Universities of China/ ; lzujbky-2022-ct04//Fundamental Research Funds for Central Universities of China/ ; }, mesh = {*Bacteria/genetics ; *Soil/chemistry ; Ammonia ; Nitrification ; Oxidation-Reduction ; Soil Microbiology ; Archaea/genetics ; Phylogeny ; }, abstract = {Nitrogen availability limits the net primary productivity in alpine meadows on the Qinghai-Tibetan Plateau, which is regulated by ammonia-oxidizing microorganisms. However, little is known about the elevational patterns of soil ammonia oxidizers in alpine meadows. Here, we investigated the potential nitrification rate (PNR), abundance, and community diversity of soil ammonia-oxidizing microorganisms along the altitudinal gradient between 3,200 and 4,200 m in Qinghai-Tibetan alpine meadows. We found that both PNR and amoA gene abundance declined from 3,400 to 4,200 m but lowered at 3,200 m, possibly due to intense substrate competition and biological nitrification inhibition from grasses. The primary contributors to soil nitrification were ammonia-oxidizing archaea (AOA), and their proportionate share of soil nitrification increased with altitude in comparison to ammonia-oxidizing bacteria (AOB). The alpha diversity of AOA increased by higher temperature and plant richness at low elevations, while decreased by higher moisture and low legume biomass at middle elevations. In contrast, the alpha diversity of AOB increased along elevation. The elevational patterns of AOA and AOB communities were primarily driven by temperature, soil moisture, and vegetation. These findings suggest that elevation-induced climate changes, such as shifts in temperature and water conditions, could potentially alter the soil nitrification process in alpine meadows through changes in vegetation and soil properties, which provide new insights into how soil ammonia oxidizers respond to climate change in alpine meadows.IMPORTANCEThe importance of this study is revealing that elevational patterns and nitrification contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities were primarily driven by temperature, soil moisture, and vegetation. Compared to AOB, the relative contribution of AOA to soil nitrification increased at higher elevations. The research highlights the potential impact of elevation-induced climate change on nitrification processes in alpine meadows, mediated by alterations in vegetation and soil properties. By providing new insights into how ammonia oxidizers respond to climate change, this study contributes valuable knowledge to the field of microbial ecology and helps predict ecological responses to environmental changes in alpine meadows.}, }
@article {pmid38380980, year = {2024}, author = {Van Gerrewey, T and Navarrete, O and Vandecruys, M and Perneel, M and Boon, N and Geelen, D}, title = {Bacterially enhanced plant-growing media for controlled environment agriculture.}, journal = {Microbial biotechnology}, volume = {17}, number = {2}, pages = {e14422}, pmid = {38380980}, issn = {1751-7915}, support = {HBC.2017.0209//Agentschap Innoveren en Ondernemen/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Agriculture ; *Bacteria/genetics ; Plants/genetics ; Soil/chemistry ; Plant Roots/microbiology ; Soil Microbiology ; }, abstract = {Microbe-plant interactions in the root zone not only shape crop performance in soil but also in hydroponic cultivation systems. The biological and physicochemical properties of the plant-growing medium determine the root-associated microbial community and influence bacterial inoculation effectiveness, which affects plant growth. This study investigated the combined impact of plant-growing media composition and bacterial community inoculation on the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Ten plant-growing media were composed of varying raw materials, including black peat, white peat, coir pith, wood fibre, composted bark, green waste compost, perlite and sand. In addition, five different bacterial community inocula (BCI S1-5) were collected from the roots of lettuce obtained at different farms. After inoculation and cultivation inside a vertical farm, lettuce root-associated bacterial community structures, diversity and compositions were determined by evaluating 16S rRNA gene sequences. The study revealed distinct bacterial community structures among experimental replicates, highlighting the influence of raw material variations on root-associated bacterial communities, even at the batch level. However, bacterial community inoculation allowed modulation of the root-associated bacterial communities independently from the plant-growing medium composition. Bacterial diversity was identified as a key determinant of plant growth performance with green waste compost introducing Bacilli and Actinobacteria, and bacterial community inoculum S3 introducing Pseudomonas, which positively correlated with plant growth. These findings challenge the prevailing notion of hydroponic cultivation systems as sterile environments and highlight the significance of proper plant-growing media raw material selection and bacterial community inoculation in shaping root-associated microbiomes that provide stability through microbial diversity. This study supports the concept of creating bacterially enhanced plant-growing media to promote plant growth in controlled environment agriculture.}, }
@article {pmid38380088, year = {2024}, author = {Savaglia, V and Lambrechts, S and Tytgat, B and Vanhellemont, Q and Elster, J and Willems, A and Wilmotte, A and Verleyen, E and Vyverman, W}, title = {Geology defines microbiome structure and composition in nunataks and valleys of the Sør Rondane Mountains, East Antarctica.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1316633}, pmid = {38380088}, issn = {1664-302X}, abstract = {Understanding the relation between terrestrial microorganisms and edaphic factors in the Antarctic can provide insights into their potential response to environmental changes. Here we examined the composition of bacterial and micro-eukaryotic communities using amplicon sequencing of rRNA genes in 105 soil samples from the Sør Rondane Mountains (East Antarctica), differing in bedrock or substrate type and associated physicochemical conditions. Although the two most widespread taxa (Acidobacteriota and Chlorophyta) were relatively abundant in each sample, multivariate analysis and co-occurrence networks revealed pronounced differences in community structure depending on substrate type. In moraine substrates, Actinomycetota and Cercozoa were the most abundant bacterial and eukaryotic phyla, whereas on gneiss, granite and marble substrates, Cyanobacteriota and Metazoa were the dominant bacterial and eukaryotic taxa. However, at lower taxonomic level, a distinct differentiation was observed within the Cyanobacteriota phylum depending on substrate type, with granite being dominated by the Nostocaceae family and marble by the Chroococcidiopsaceae family. Surprisingly, metazoans were relatively abundant according to the 18S rRNA dataset, even in samples from the most arid sites, such as moraines in Austkampane and Widerøefjellet ("Dry Valley"). Overall, our study shows that different substrate types support distinct microbial communities, and that mineral soil diversity is a major determinant of terrestrial microbial diversity in inland Antarctic nunataks and valleys.}, }
@article {pmid38378706, year = {2024}, author = {Papin, M and Philippot, L and Breuil, MC and Bru, D and Dreux-Zigha, A and Mounier, A and Le Roux, X and Rouard, N and Spor, A}, title = {Survival of a microbial inoculant in soil after recurrent inoculations.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {4177}, pmid = {38378706}, issn = {2045-2322}, support = {ANR-20-CE02-0014//Agence Nationale de la Recherche/ ; }, mesh = {*Agricultural Inoculants ; Soil ; Nitrates ; Agriculture ; *Pseudomonas fluorescens ; Soil Microbiology ; }, abstract = {Microbial inoculants are attracting growing interest in agriculture, but their efficacy remains unreliable in relation to their poor survival, partly due to the competition with the soil resident community. We hypothesised that recurrent inoculation could gradually alleviate this competition and improve the survival of the inoculant while increasing its impact on the resident bacterial community. We tested the effectiveness of such strategy with four inoculation sequences of Pseudomonas fluorescens strain B177 in soil microcosms with increasing number and frequency of inoculation, compared to a non-inoculated control. Each sequence was carried out at two inoculation densities (10[6] and 10[8] cfu.g soil[-1]). The four-inoculation sequence induced a higher abundance of P. fluorescens, 2 weeks after the last inoculation. No impact of inoculation sequences was observed on the resident community diversity and composition. Differential abundance analysis identified only 28 out of 576 dominants OTUs affected by the high-density inoculum, whatever the inoculation sequence. Recurrent inoculations induced a strong accumulation of nitrate, not explained by the abundance of nitrifying or nitrate-reducing microorganisms. In summary, inoculant density rather than inoculation pattern matters for inoculation effect on the resident bacterial communities, while recurrent inoculation allowed to slightly enhance the survival of the inoculant and strongly increased soil nitrate content.}, }
@article {pmid38376218, year = {2024}, author = {Kridler, MR and Viney, IA and Custer, JM and Schlottman, B and Bartelme, R and Carini, P}, title = {Draft genome sequences of Arthrobacter sp. AZCC_0090 and Mycobacterium sp. AZCC_0083 isolated from oligotrophic subsurface forest soil in the Santa Catalina mountains of Southern Arizona.}, journal = {Microbiology resource announcements}, volume = {13}, number = {3}, pages = {e0108923}, pmid = {38376218}, issn = {2576-098X}, support = {IOS-2141605//National Science Foundation (NSF)/ ; DGE-2137419//National Science Foundation (NSF)/ ; //Technology and Research Initiative Fund-WEES/ ; }, abstract = {Here, we present the genomes of two soil actinobacteria: Arthrobacter sp. strain AZCC_0090 and Mycobacterium sp. strain AZCC_0083, isolated from oligotrophic subsurface soils in Southern Arizona, USA.}, }
@article {pmid38376179, year = {2024}, author = {Bisesi, AT and Möbius, W and Nadell, CD and Hansen, EG and Bowden, SD and Harcombe, WR}, title = {Bacteriophage specificity is impacted by interactions between bacteria.}, journal = {mSystems}, volume = {9}, number = {3}, pages = {e0117723}, pmid = {38376179}, issn = {2379-5077}, support = {IOS-2019304//National Science Foundation (NSF)/ ; IOS-2017879//National Science Foundation (NSF)/ ; BB/V011464/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {*Bacteriophages/physiology ; Bacteria ; Escherichia coli/physiology ; Bacterial Physiological Phenomena ; Symbiosis ; }, abstract = {UNLABELLED: Predators play a central role in shaping community structure, function, and stability. The degree to which bacteriophage predators (viruses that infect bacteria) evolve to be specialists with a single bacterial prey species versus generalists able to consume multiple types of prey has implications for their effect on microbial communities. The presence and abundance of multiple bacterial prey types can alter selection for phage generalists, but less is known about how interactions between prey shape predator specificity in microbial systems. Using a phenomenological mathematical model of phage and bacterial populations, we find that the dominant phage strategy depends on prey ecology. Given a fitness cost for generalism, generalist predators maintain an advantage when prey species compete, while specialists dominate when prey are obligately engaged in cross-feeding interactions. We test these predictions in a synthetic microbial community with interacting strains of Escherichia coli and Salmonella enterica by competing a generalist T5-like phage able to infect both prey against P22vir, an S. enterica-specific phage. Our experimental data conform to our modeling expectations when prey species are competing or obligately mutualistic, although our results suggest that the in vitro cost of generalism is caused by a combination of biological mechanisms not anticipated in our model. Our work demonstrates that interactions between bacteria play a role in shaping ecological selection on predator specificity in obligately lytic bacteriophages and emphasizes the diversity of ways in which fitness trade-offs can manifest.<br><br>IMPORTANCE: There is significant natural diversity in how many different types of bacteria a bacteriophage can infect, but the mechanisms driving this diversity are unclear. This study uses a combination of mathematical modeling and an in vitro system consisting of Escherichia coli, Salmonella enterica, a T5-like generalist phage, and the specialist phage P22vir to highlight the connection between bacteriophage specificity and interactions between their potential microbial prey. Mathematical modeling suggests that competing bacteria tend to favor generalist bacteriophage, while bacteria that benefit each other tend to favor specialist bacteriophage. Experimental results support this general finding. The experiments also show that the optimal phage strategy is impacted by phage degradation and bacterial physiology. These findings enhance our understanding of how complex microbial communities shape selection on bacteriophage specificity, which may improve our ability to use phage to manage antibiotic-resistant microbial infections.}, }
@article {pmid38376167, year = {2024}, author = {Hegarty, B and Riddell V, J and Bastien, E and Langenfeld, K and Lindback, M and Saini, JS and Wing, A and Zhang, J and Duhaime, M}, title = {Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods.}, journal = {mSystems}, volume = {9}, number = {3}, pages = {e0110523}, pmid = {38376167}, issn = {2379-5077}, support = {DGE1256260, 2055455, DGE134012//National Science Foundation (NSF)/ ; NA17OAR4320152//DOC | National Oceanic and Atmospheric Administration (NOAA)/ ; Blue Sky Initiative//College of Engineering, University of Michigan/ ; }, mesh = {Ecosystem ; *Viruses ; Metagenomics/methods ; Databases, Nucleic Acid ; }, abstract = {UNLABELLED: Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral identification tools. However, the effectiveness of this strategy is unknown. Here, we benchmarked combinations of six widely used informatics tools for viral identification and analysis (VirSorter, VirSorter2, VIBRANT, DeepVirFinder, CheckV, and Kaiju), called "rulesets." Rulesets were tested against mock metagenomes composed of taxonomically diverse sequence types and diverse aquatic metagenomes to assess the effects of the degree of viral enrichment and habitat on tool performance. We found that six rulesets achieved equivalent accuracy [Matthews Correlation Coefficient (MCC) = 0.77, Padj ≥ 0.05]. Each contained VirSorter2, and five used our "tuning removal" rule designed to remove non-viral contamination. While DeepVirFinder, VIBRANT, and VirSorter were each found once in these high-accuracy rulesets, they were not found in combination with each other: combining tools does not lead to optimal performance. Our validation suggests that the MCC plateau at 0.77 is partly caused by inaccurate labeling within reference sequence databases. In aquatic metagenomes, our highest MCC ruleset identified more viral sequences in virus-enriched (44%-46%) than in cellular metagenomes (7%-19%). While improved algorithms may lead to more accurate viral identification tools, this should be done in tandem with careful curation of sequence databases. We recommend using the VirSorter2 ruleset and our empirically derived tuning removal rule. Our analysis provides insight into methods for in silico viral identification and will enable more robust viral identification from metagenomic data sets.<br><br>IMPORTANCE: The identification of viruses from environmental metagenomes using informatics tools has offered critical insights in microbial ecology. However, it remains difficult for researchers to know which tools optimize viral recovery for their specific study. In an attempt to recover more viruses, studies are increasingly combining the outputs from multiple tools without validating this approach. After benchmarking combinations of six viral identification tools against mock metagenomes and environmental samples, we found that these tools should only be combined cautiously. Two to four tool combinations maximized viral recovery and minimized non-viral contamination compared with either the single-tool or the five- to six-tool ones. By providing a rigorous overview of the behavior of in silico viral identification strategies and a pipeline to replicate our process, our findings guide the use of existing viral identification tools and offer a blueprint for feature engineering of new tools that will lead to higher-confidence viral discovery in microbiome studies.}, }
@article {pmid38373802, year = {2024}, author = {O'Hara, E and Zaheer, R and Andrés-Lasheras, S and McAllister, TA and Gruninger, RJ}, title = {Evaluating the liver abscess microbiota of beef cattle during a reduction in tylosin supplementation shows differences according to abscess size and fraction.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {4}, pages = {}, pmid = {38373802}, issn = {1574-6941}, support = {//Agriculture and Agri-Food Canada/ ; //Genome Alberta/ ; ANH.02.19//Beef Cattle Research Council/ ; }, mesh = {Cattle ; Animals ; Tylosin/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Liver Abscess/veterinary/epidemiology/microbiology ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Dietary Supplements/analysis ; *Microbiota ; Animal Feed/analysis ; }, abstract = {Liver abscesses (LA) resulting from bacterial infection in cattle pose a significant global challenge to the beef and dairy industries. Economic losses from liver discounts at slaughter and reduced animal performance drive the need for effective mitigation strategies. Tylosin phosphate supplementation is widely used to reduce LA occurrence, but concerns over antimicrobial overuse emphasize the urgency to explore alternative approaches. Understanding the microbial ecology of LA is crucial to this, and we hypothesized that a reduced timeframe of tylosin delivery would alter LA microbiomes. We conducted 16S rRNA sequencing to assess severe liver abscess bacteriomes in beef cattle supplemented with in-feed tylosin. Our findings revealed that shortening tylosin supplementation did not notably alter microbial communities. Additionally, our findings highlighted the significance of sample processing methods, showing differing communities in bulk purulent material and the capsule-adhered material. Fusobacterium or Bacteroides ASVs dominated LA, alongside probable opportunistic gut pathogens and other microbes. Moreover, we suggest that liver abscess size correlates with microbial community composition. These insights contribute to our understanding of factors impacting liver abscess microbial ecology and will be valuable in identifying antibiotic alternatives. They underscore the importance of exploring varied approaches to address LA while reducing reliance on in-feed antibiotics.}, }
@article {pmid38373396, year = {2025}, author = {Jaber, D and Younes, N and Khalil, E and Albsoul-Younes, A and Zawiah, M and Al-Bakri, AG}, title = {Studying Microbial Ecology of Diabetic Foot Infections: Significance of PCR Analysis for Prudent Antimicrobial Stewardship.}, journal = {The international journal of lower extremity wounds}, volume = {24}, number = {2}, pages = {497-505}, doi = {10.1177/15347346241230288}, pmid = {38373396}, issn = {1552-6941}, mesh = {*Diabetic Foot/microbiology/drug therapy/diagnosis ; Humans ; *Antimicrobial Stewardship/methods ; *Polymerase Chain Reaction/methods ; Male ; Female ; Middle Aged ; Aged ; *Anti-Bacterial Agents/therapeutic use ; Methicillin-Resistant Staphylococcus aureus/isolation &amp; purification ; }, abstract = {This study presents a comprehensive investigation into the microbial ecology of diabetic foot infections (DFIs), using molecular-polymerase chain reaction (PCR) analysis to accurately identify the causative agents. One hundred DFI patients were recruited and classified using the Depth Extent Phase and Associated Etiology (DEPA) score according to their severity. Results revealed polymicrobial infections in 75% of cases, predominantly featuring Staphylococcus epidermidis (83%) and Staphylococcus aureus (63%). Importantly, 20% of samples exhibited facultative anaerobes Bacteroides fragilis or Clostridium perfringens, exclusively in high DEPA score ulcers. Candida albicans coinfection was identified in 19.2% of cases, underscoring the need for mycological evaluation. Empirical antimicrobial therapy regimens were tailored to DEPA severity, yet our findings highlighted a potential gap in methicillin-resistant Staphylococcus aureus (MRSA) coverage. Despite an 88% prevalence of methicillin-resistant Staphylococci, vancomycin usage was suboptimal. This raises concerns about the underestimation of MRSA risk and the need for tailored antibiotic guidelines. Our study demonstrates the efficacy of molecular-PCR analysis in identifying diverse microbial communities in DFIs, influencing targeted antibiotic choices. The results advocate for refined antimicrobial guidelines, considering regional variations in microbial patterns and judiciously addressing multidrug-resistant strains. This research contributes crucial insights for optimizing DFIs management and helps the physicians to have a fast decision in selection the suitable antibiotic for each patient and to decrease the risk of bacterial resistance from the improper use of broad-spectrum empirical therapies.}, }
@article {pmid38370212, year = {2024}, author = {Taherkhani, H and KavianFar, A and Aminnezhad, S and Lanjanian, H and Ahmadi, A and Azimzadeh, S and Masoudi-Nejad, A}, title = {Deciphering the impact of microbial interactions on COPD exacerbation: An in-depth analysis of the lung microbiome.}, journal = {Heliyon}, volume = {10}, number = {4}, pages = {e24775}, pmid = {38370212}, issn = {2405-8440}, abstract = {In microbiome studies, the diversity and types of microbes have been extensively explored; however, the significance of microbial ecology is equally paramount. The comprehension of metabolic interactions among the wide array of microorganisms in the lung microbiota is indispensable for understanding chronic pulmonary disease and for the development of potent treatments. In this investigation, metabolic networks were simulated, and ecological theory was employed to assess the diagnosis of COPD, subsequently suggesting innovative treatment strategies for COPD exacerbation. Lung sputum 16S rRNA paired-end data from 112 COPD patients were utilized, and a supervised machine-learning algorithm was applied to identify taxa associated with sex and mortality. Subsequently, an OTU table with Greengenes 99 % dataset was generated. Finally, the interactions between bacterial species were analyzed using a simulated metabolic network. A total of 1781 OTUs and 1740 bacteria at the genus level were identified. We employed an additional dataset to validate our analyses. Notably, among the more abundant genera, Pseudomonas was detected in females, while Lactobacillus was detected in males. Additionally, a decrease in bacterial diversity was observed during COPD exacerbation, and mortality was associated with the high abundance of the Staphylococcus and Pseudomonas genera. Moreover, an increase in Proteobacteria abundance was observed during COPD exacerbations. In contrast, COPD patients exhibited decreased levels of Firmicutes and Bacteroidetes. Significant connections between microbial ecology and bacterial diversity in COPD patients were discovered, highlighting the critical role of microbial ecology in the understanding of COPD. Through the simulation of metabolic interactions among bacteria, the observed dysbiosis in COPD was elucidated. Furthermore, the prominence of anaerobic bacteria in COPD patients was revealed to be influenced by parasitic relationships. These findings have the potential to contribute to improved clinical management strategies for COPD patients.}, }
@article {pmid38367872, year = {2024}, author = {Tuts, L and Rasschaert, G and Heyndrickx, M and Boon, N and Eppinger, R and Becue, I}, title = {Detection of antibiotic residues in groundwater with a validated multiresidue UHPLC-MS/MS quantification method.}, journal = {Chemosphere}, volume = {352}, number = {}, pages = {141455}, doi = {10.1016/j.chemosphere.2024.141455}, pmid = {38367872}, issn = {1879-1298}, mesh = {Animals ; Humans ; Anti-Bacterial Agents/analysis ; Chromatography, High Pressure Liquid/methods ; Tandem Mass Spectrometry/methods ; Lactams, Macrocyclic/analysis ; Sulfanilamide/analysis ; Chloramphenicol/analysis ; Sulfonamides/analysis ; Lincosamides ; Pleuromutilins ; *Groundwater ; Macrolides/analysis ; *Drug Residues/analysis ; }, abstract = {The occurrence of antibiotic residues in the environment has received considerable attention because of their potential to select for bacterial resistance. The overuse of antibiotics in human medicine and animal production results in antibiotic residues entering the aquatic environment, but concentrations are currently not well determined. This study investigates the occurrence of antibiotics in groundwater in areas strongly related to agriculture and the antibiotic treatment of animals. A multiresidue method was validated according to EU Regulation 2021/808, to allow (semi-)quantitative analysis of 78 antibiotics from 10 different classes: β-lactams, sulfonamides, tetracyclines, lincosamides, amphenicols, (fluoro)quinolones, macrolides, pleuromutilins, ansamycins and diaminopyrimidines using ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). This method was used to test different storage conditions of these water samples during a stability study over a period of 2 weeks. Sulfonamides, lincosamides and pleuromutilins were the most stable. Degradation was most pronounced for β-lactam antibiotics, macrolides and ansamycins. To maintain stability, storage of samples at -18 °C is preferred. With the validated method, antibiotic residues were detected in groundwater, sampled from regions associated with intensive livestock farming in Flanders (Belgium). Out of 50 samples, 14% contained at least one residue. Concentrations were low, ranging from < LOD to 0.03 μg/L. Chloramphenicol, oxolinic acid, tetracycline and sulfonamides (sulfadiazine, sulfadoxine, sulfamethazine and sulfisoxazole) were detected. This study presents a new method for the quantification of antibiotic residues, which was applied to investigate the presence of antibiotic residues in groundwater in Flanders.}, }
@article {pmid38367838, year = {2024}, author = {González-Feijoo, R and Santás-Miguel, V and Arenas-Lago, D and Álvarez-Rodríguez, E and Núñez-Delgado, A and Arias-Estévez, M and Pérez-Rodríguez, P}, title = {Effectiveness of cork and pine bark powders as biosorbents for potentially toxic elements present in aqueous solution.}, journal = {Environmental research}, volume = {250}, number = {}, pages = {118455}, doi = {10.1016/j.envres.2024.118455}, pmid = {38367838}, issn = {1096-0953}, mesh = {*Pinus/chemistry ; *Quercus/chemistry ; *Plant Bark/chemistry ; Adsorption ; *Water Pollutants, Chemical/analysis/chemistry ; Powders/chemistry ; Hydrogen-Ion Concentration ; Metals, Heavy/analysis/chemistry ; }, abstract = {Cork oak and pine bark, two of the most prolific byproducts of the European forestry sector, were assessed as biosorbents for eliminating potentially toxic elements (PTEs) from water-based solutions. Our research suggests that bioadsorption stands out as a viable and environmental eco-friendly technology, presenting a sustainable method for the extraction of PTEs from polluted water sources. This study aimed to evaluate and compare the efficiency of cork powder and pine bark powder as biosorbents. Specifically, the adsorption of Fe, Cu, Zn, Cd, Ni, Pb and Sn at equilibrium were studied through batch experiments by varying PTEs concentrations, pH, and ionic strength. Results from adsorption-desorption experiments demonstrate the remarkable capacity of both materials to retain the studied PTE. Cork powder and pine bark powder exhibited the maximum retention capacity for Fe and Cd, while they performed poorly for Pb and Sn, respectively. Nevertheless, pine bark showed a slightly lower retention capacity than cork. Increasing the pH resulted in cork showing the highest adsorption for Zn and the lowest for Sn, while for pine bark, Cd was the most adsorbed, and Sn was the least adsorbed, respectively. The highest adsorption of both materials occurred at pH 3.5-5, depending on the PTE tested. The ionic strength also influenced the adsorption of the various PTEs for both materials, with decreased adsorption as ionic strength increased. The findings suggest that both materials could be effective for capturing and eliminating the examined PTEs, albeit with different efficiencies. Remarkably, pine bark demonstrated superior adsorption capabilities, which were observed to vary based on the specific element and the experimental conditions. These findings contribute to elucidating the bio-adsorption potential of these natural materials, specifically their suitability in mitigating PTEs pollution, and favoring the recycling and revalorization of byproducts that might otherwise be considered residue.}, }
@article {pmid38367043, year = {2024}, author = {LeBlanc, NR and Harrigian, FC}, title = {Green Waste Compost Impacts Microbial Functions Related to Carbohydrate Use and Active Dispersal in Plant Pathogen-Infested Soil.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {44}, pmid = {38367043}, issn = {1432-184X}, support = {2038-22430-003-000-D//Agricultural Research Service/ ; }, mesh = {Soil/chemistry ; Soil Microbiology ; *Composting ; *Fusarium ; Bacteria/genetics ; Sequence Analysis ; }, abstract = {The effects of compost on physical and chemical characteristics of soil are well-studied but impacts on soil microbiomes are poorly understood. This research tested effects of green waste compost on bacterial communities in soil infested with the plant pathogen Fusarium oxysporum. Compost was added to pathogen-infested soil and maintained in mesocosms in a greenhouse experiment and replicated growth chamber experiments. Bacteria and F. oxysporum abundance were quantified using quantitative PCR. Taxonomic and functional characteristics of bacterial communities were measured using shotgun metagenome sequencing. Compost significantly increased bacterial abundance 8 weeks after amendment in one experiment. Compost increased concentrations of chemical characteristics of soil, including phosphorus, potassium, organic matter, and pH. In all experiments, compost significantly reduced abundance of F. oxysporum and altered the taxonomic composition of soil bacterial communities. Sixteen bacterial genera were significantly increased from compost in every experiment, potentially playing a role in pathogen suppression. In all experiments, there was a consistent negative effect of compost on functions related to carbohydrate use and a positive effect on bacteria with flagella. Results from this work demonstrate that compost can reduce the abundance of soilborne plant pathogens and raise questions about the role of microbes in plant pathogen suppression.}, }
@article {pmid38366262, year = {2024}, author = {Wang, J and Zhu, YG and Tiedje, JM and Ge, Y}, title = {Global biogeography and ecological implications of cobamide-producing prokaryotes.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38366262}, issn = {1751-7370}, support = {42307162//National Natural Science Foundation of China/ ; 2019QZKK0308//Second Tibetan Plateau Scientific Expedition and Research Program/ ; DBI-1759892//US National Science Foundation/ ; //Institute for Cyber-Enabled Research at Michigan State University/ ; }, mesh = {*Cobamides ; Metagenome ; *Microbiota ; Soil ; }, abstract = {Cobamides, a class of essential coenzymes synthesized only by a subset of prokaryotes, are model nutrients in microbial interaction studies and play significant roles in global ecosystems. Yet, their spatial patterns and functional roles remain poorly understood. Herein, we present an in-depth examination of cobamide-producing microorganisms, drawn from a comprehensive analysis of 2862 marine and 2979 soil metagenomic samples. A total of 1934 nonredundant metagenome-assembled genomes (MAGs) potentially capable of producing cobamides de novo were identified. The cobamide-producing MAGs are taxonomically diverse but habitat specific. They constituted only a fraction of all the recovered MAGs, with the majority of MAGs being potential cobamide users. By mapping the distribution of cobamide producers in marine and soil environments, distinct latitudinal gradients were observed: the marine environment showed peak abundance at the equator, whereas soil environments peaked at mid-latitudes. Importantly, significant and positive links between the abundance of cobamide producers and the diversity and functions of microbial communities were observed, as well as their promotional roles in essential biogeochemical cycles. These associations were more pronounced in marine samples than in soil samples, which suggests a heightened propensity for microorganisms to engage in cobamide sharing in fluid environments relative to the more spatially restricted soil environment. These findings shed light on the global patterns and potential ecological roles of cobamide-producing microorganisms in marine and soil ecosystems, enhancing our understanding of large-scale microbial interactions.}, }
@article {pmid38365962, year = {2024}, author = {Paes da Costa, D and das Graças Espíndola da Silva, T and Sérgio Ferreira Araujo, A and Prudêncio de Araujo Pereira, A and William Mendes, L and Dos Santos Borges, W and Felix da França, R and Alberto Fragoso de Souza, C and Alves da Silva, B and Oliveira Silva, R and Valente de Medeiros, E}, title = {Soil fertility impact on recruitment and diversity of the soil microbiome in sub-humid tropical pastures in Northeastern Brazil.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {3919}, pmid = {38365962}, issn = {2045-2322}, mesh = {*Soil ; RNA, Ribosomal, 16S/genetics/metabolism ; Brazil ; Bacteria ; *Microbiota/genetics ; Soil Microbiology ; }, abstract = {Soil fertility is key point to pastures systems and drives the microbial communities and their functionality. Therefore, an understanding of the interaction between soil fertility and microbial communities can increase our ability to manage pasturelands and maintain their soil functioning and productivity. This study probed the influence of soil fertility on microbial communities in tropical pastures in Brazil. Soil samples, gathered from the top 20 cm of twelve distinct areas with diverse fertility levels, were analyzed via 16S rRNA sequencing. The soils were subsequently classified into two categories, namely high fertility (HF) and low fertility (LF), using the K-Means clustering. The random forest analysis revealed that high fertility (HF) soils had more bacterial diversity, predominantly Proteobacteria, Nitrospira, Chloroflexi, and Bacteroidetes, while Acidobacteria increased in low fertility (LF) soils. High fertility (HF) soils exhibited more complex network interactions and an enrichment of nitrogen-cycling bacterial groups. Additionally, functional annotation based on 16S rRNA varied between clusters. Microbial groups in HF soil demonstrated enhanced functions such as nitrate reduction, aerobic ammonia oxidation, and aromatic compound degradation. In contrast, in the LF soil, the predominant processes were ureolysis, cellulolysis, methanol oxidation, and methanotrophy. Our findings expand our knowledge about how soil fertility drives bacterial communities in pastures.}, }
@article {pmid38365802, year = {2024}, author = {Fenibo, EO and Nkuna, R and Matambo, T}, title = {Impact of artisanal refining activities on bacterial diversity in a Niger Delta fallow land.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {3866}, pmid = {38365802}, issn = {2045-2322}, mesh = {RNA, Ribosomal, 16S/genetics/metabolism ; Niger ; *Soil Pollutants/metabolism ; Soil Microbiology ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; *Microbiota/genetics ; *Petroleum/metabolism ; Hydrocarbons/metabolism ; Soil/chemistry ; DNA/metabolism ; }, abstract = {Hydrocarbon pollution is a major ecological problem facing oil-producing countries, especially in the Niger Delta region of Nigeria. In this study, a site that had been previously polluted by artisanal refining activity was investigated using 16S rRNA Illumina high-throughput sequencing technology and bioinformatics tools. These were used to investigate the bacterial diversity in soil with varying degrees of contamination, determined with a gas chromatography-flame ionization detector (GC-FID). Soil samples were collected from a heavily polluted (HP), mildly polluted (MP), and unpolluted (control sample, CS) portion of the study site. DNA was extracted using the Zymo Research (ZR) Fungi/Bacteria DNA MiniPrep kit, followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized based on the V3 and V4 hypervariable regions of the 16S rRNA gene. QIIME (Quantitative Insights Into Microbial Ecology) 2 software was used to analyse the sequence data. The final data set covered 20,640 demultiplexed high-quality reads and a total of 160 filtered bacterial OTUs. Proteobacteria dominated samples HP and CS, while Actinobacteria dominated sample MP. Denitratisoma, Pseudorhodoplanes, and Spirilospora were the leading genera in samples HP, CS, and MP respectively. Diversity analysis indicated that CS [with 25.98 ppm of total petroleum hydrocarbon (TPH)] is more diverse than HP (with 490,630 ppm of TPH) and MP (with 5398 ppm of TPH). A functional prediction study revealed that six functional modules dominated the dataset, with metabolism covering up to 70%, and 11 metabolic pathways. This study demonstrates that a higher hydrocarbon concentration in soil adversely impacts microbial diversity, creating a narrow bacterial diversity dominated by hydrocarbon-degrading species, in addition to the obvious land and ecosystem degradation caused by artisanal refining activities. Overall, the artisanal refining business is significantly driving ecosystem services losses in the Niger Delta, which calls for urgent intervention, with focus on bioremediation.}, }
@article {pmid38365260, year = {2024}, author = {Díez-Vives, C and Riesgo, A}, title = {High compositional and functional similarity in the microbiome of deep-sea sponges.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365260}, issn = {1751-7370}, support = {100010434//'la Caixa' Foundation/ ; PID2019-105769GB-I00//Spanish Ministry of Science and Innovation/ ; 796011//Marie Sk&#x142;odowska-Curie Individual Fellowships Grant Agreement/ ; }, mesh = {Animals ; Bacteria/genetics/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; *Microbiota ; Water/metabolism ; *Porifera ; }, abstract = {Sponges largely depend on their symbiotic microbes for their nutrition, health, and survival. This is especially true in high microbial abundance (HMA) sponges, where filtration is usually deprecated in favor of a larger association with prokaryotic symbionts. Sponge-microbiome association is substantially less understood for deep-sea sponges than for shallow water species. This is most unfortunate, since HMA sponges can form massive sponge grounds in the deep sea, where they dominate the ecosystems, driving their biogeochemical cycles. Here, we assess the microbial transcriptional profile of three different deep-sea HMA sponges in four locations of the Cantabrian Sea and compared them to shallow water HMA and LMA (low microbial abundance) sponge species. Our results reveal that the sponge microbiome has converged in a fundamental metabolic role for deep-sea sponges, independent of taxonomic relationships or geographic location, which is shared in broad terms with shallow HMA species. We also observed a large number of redundant microbial members performing the same functions, likely providing stability to the sponge inner ecosystem. A comparison between the community composition of our deep-sea sponges and another 39 species of HMA sponges from deep-sea and shallow habitats, belonging to the same taxonomic orders, suggested strong homogeneity in microbial composition (i.e. weak species-specificity) in deep sea species, which contrasts with that observed in shallow water counterparts. This convergence in microbiome composition and functionality underscores the adaptation to an extremely restrictive environment with the aim of exploiting the available resources.}, }
@article {pmid38365254, year = {2024}, author = {Layoun, P and López-Pérez, M and Haro-Moreno, JM and Haber, M and Thrash, JC and Henson, MW and Kavagutti, VS and Ghai, R and Salcher, MM}, title = {Flexible genomic island conservation across freshwater and marine Methylophilaceae.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365254}, issn = {1751-7370}, support = {19-23469S//Czech Science Foundation/ ; KA131//University of South Bohemia, Faculty of Science, Department of Ecosystem Biology/ ; 116/2019/P//Grant Agency of the University of South Bohemia in &#x10c;esk&#xe9; Bud&#x11b;jovice/ ; }, mesh = {*Methylophilaceae ; Genome, Bacterial ; Genomic Islands ; Phylogeny ; Lakes ; }, abstract = {The evolutionary trajectory of Methylophilaceae includes habitat transitions from freshwater sediments to freshwater and marine pelagial that resulted in genome reduction (genome-streamlining) of the pelagic taxa. However, the extent of genetic similarities in the genomic structure and microdiversity of the two genome-streamlined pelagic lineages (freshwater "Ca. Methylopumilus" and the marine OM43 lineage) has so far never been compared. Here, we analyzed complete genomes of 91 "Ca. Methylopumilus" strains isolated from 14 lakes in Central Europe and 12 coastal marine OM43 strains. The two lineages showed a remarkable niche differentiation with clear species-specific differences in habitat preference and seasonal distribution. On the other hand, we observed a synteny preservation in their genomes by having similar locations and types of flexible genomic islands (fGIs). Three main fGIs were identified: a replacement fGI acting as phage defense, an additive fGI harboring metabolic and resistance-related functions, and a tycheposon containing nitrogen-, thiamine-, and heme-related functions. The fGIs differed in relative abundances in metagenomic datasets suggesting different levels of variability ranging from strain-specific to population-level adaptations. Moreover, variations in one gene seemed to be responsible for different growth at low substrate concentrations and a potential biogeographic separation within one species. Our study provides a first insight into genomic microdiversity of closely related taxa within the family Methylophilaceae and revealed remarkably similar dynamics involving mobile genetic elements and recombination between freshwater and marine family members.}, }
@article {pmid38365250, year = {2024}, author = {Sher, AW and Aufrecht, JA and Herrera, D and Zimmerman, AE and Kim, YM and Munoz, N and Trejo, JB and Paurus, VL and Cliff, JB and Hu, D and Chrisler, WB and Tournay, RJ and Gomez-Rivas, E and Orr, G and Ahkami, AH and Doty, SL}, title = {Dynamic nitrogen fixation in an aerobic endophyte of Populus.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365250}, issn = {1751-7370}, support = {#50774//Environmental Molecular Sciences Laboratory/ ; //United States Department of Energy Office of Science/ ; DE-SC0021137//Office of Biological and Environmental Research/ ; }, mesh = {*Nitrogen Fixation/physiology ; *Populus/genetics/metabolism ; Endophytes/genetics ; Oxidoreductases/genetics ; In Situ Hybridization, Fluorescence ; Nitrogenase/genetics/metabolism ; Nitrogen ; }, abstract = {Biological nitrogen fixation by microbial diazotrophs can contribute significantly to nitrogen availability in non-nodulating plant species. In this study of molecular mechanisms and gene expression relating to biological nitrogen fixation, the aerobic nitrogen-fixing endophyte Burkholderia vietnamiensis, strain WPB, isolated from Populus trichocarpa served as a model for endophyte-poplar interactions. Nitrogen-fixing activity was observed to be dynamic on nitrogen-free medium with a subset of colonies growing to form robust, raised globular like structures. Secondary ion mass spectrometry (NanoSIMS) confirmed that N-fixation was uneven within the population. A fluorescent transcriptional reporter (GFP) revealed that the nitrogenase subunit nifH is not uniformly expressed across genetically identical colonies of WPB and that only ~11% of the population was actively expressing the nifH gene. Higher nifH gene expression was observed in clustered cells through monitoring individual bacterial cells using single-molecule fluorescence in situ hybridization. Through 15N2 enrichment, we identified key nitrogenous metabolites and proteins synthesized by WPB and employed targeted metabolomics in active and inactive populations. We cocultivated WPB Pnif-GFP with poplar within a RhizoChip, a synthetic soil habitat, which enabled direct imaging of microbial nifH expression within root epidermal cells. We observed that nifH expression is localized to the root elongation zone where the strain forms a unique physical interaction with the root cells. This work employed comprehensive experimentation to identify novel mechanisms regulating both biological nitrogen fixation and beneficial plant-endophyte interactions.}, }
@article {pmid38365248, year = {2024}, author = {Gottel, NR and Hill, MS and Neal, MJ and Allard, SM and Zengler, K and Gilbert, JA}, title = {Biocontrol in built environments to reduce pathogen exposure and infection risk.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365248}, issn = {1751-7370}, support = {UCSD 2223669//NSF ENG-EPSRC EFRI ELiS/ ; 80NSSC19K1604//NASA ROSBIO/ ; }, mesh = {Humans ; *Microbiota ; Bacteria/genetics ; *Bacillus ; Anti-Bacterial Agents ; Built Environment ; }, abstract = {The microbiome of the built environment comprises bacterial, archaeal, fungal, and viral communities associated with human-made structures. Even though most of these microbes are benign, antibiotic-resistant pathogens can colonize and emerge indoors, creating infection risk through surface transmission or inhalation. Several studies have catalogued the microbial composition and ecology in different built environment types. These have informed in vitro studies that seek to replicate the physicochemical features that promote pathogenic survival and transmission, ultimately facilitating the development and validation of intervention techniques used to reduce pathogen accumulation. Such interventions include using Bacillus-based cleaning products on surfaces or integrating bacilli into printable materials. Though this work is in its infancy, early research suggests the potential to use microbial biocontrol to reduce hospital- and home-acquired multidrug-resistant infections. Although these techniques hold promise, there is an urgent need to better understand the microbial ecology of built environments and to determine how these biocontrol solutions alter species interactions. This review covers our current understanding of microbial ecology of the built environment and proposes strategies to translate that knowledge into effective biocontrol of antibiotic-resistant pathogens.}, }
@article {pmid38365244, year = {2024}, author = {Yu, XA and McLean, C and Hehemann, JH and Angeles-Albores, D and Wu, F and Muszyński, A and Corzett, CH and Azadi, P and Kujawinski, EB and Alm, EJ and Polz, MF}, title = {Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365244}, issn = {1751-7370}, support = {DE-SC0008743//United States Department of Energy/ ; DE-SC0015662//United States Department of Energy/ ; }, mesh = {Bacteria/genetics ; *Seaweed ; *Microbiota ; }, abstract = {Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes.}, }
@article {pmid38365240, year = {2024}, author = {Shen, L and Liu, Y and Chen, L and Lei, T and Ren, P and Ji, M and Song, W and Lin, H and Su, W and Wang, S and Rooman, M and Pucci, F}, title = {Genomic basis of environmental adaptation in the widespread poly-extremophilic Exiguobacterium group.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365240}, issn = {1751-7370}, support = {U21A20176//National Natural Science Foundation of China/ ; 2019QZKK0503//Second Tibetan Plateau Scientific Expedition and Research/ ; 92251304//National Natural Science Foundation of China/ ; swzy202008//Open Project Fund of Anhui Provincial Key Laboratory of Protection and Utilization of Important Biological Resources/ ; 2022AH010012//Anhui Provincial Engineering Research Centre for Molecular Detection and Diagnostics/ ; }, mesh = {*Exiguobacterium ; *Extremophiles ; Genomics ; Phylogeny ; Proteins ; }, abstract = {Delineating cohesive ecological units and determining the genetic basis for their environmental adaptation are among the most important objectives in microbiology. In the last decade, many studies have been devoted to characterizing the genetic diversity in microbial populations to address these issues. However, the impact of extreme environmental conditions, such as temperature and salinity, on microbial ecology and evolution remains unclear so far. In order to better understand the mechanisms of adaptation, we studied the (pan)genome of Exiguobacterium, a poly-extremophile bacterium able to grow in a wide range of environments, from permafrost to hot springs. To have the genome for all known Exiguobacterium type strains, we first sequenced those that were not yet available. Using a reverse-ecology approach, we showed how the integration of phylogenomic information, genomic features, gene and pathway enrichment data, regulatory element analyses, protein amino acid composition, and protein structure analyses of the entire Exiguobacterium pangenome allows to sharply delineate ecological units consisting of mesophilic, psychrophilic, halophilic-mesophilic, and halophilic-thermophilic ecotypes. This in-depth study clarified the genetic basis of the defined ecotypes and identified some key mechanisms driving the environmental adaptation to extreme environments. Our study points the way to organizing the vast microbial diversity into meaningful ecologically units, which, in turn, provides insight into how microbial communities adapt and respond to different environmental conditions in a changing world.}, }
@article {pmid38365232, year = {2024}, author = {Zheng, Y and Wang, B and Gao, P and Yang, Y and Xu, B and Su, X and Ning, D and Tao, Q and Li, Q and Zhao, F and Wang, D and Zhang, Y and Li, M and Winkler, MH and Ingalls, AE and Zhou, J and Zhang, C and Stahl, DA and Jiang, J and Martens-Habbena, W and Qin, W}, title = {Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365232}, issn = {1751-7370}, support = {548565//Simons Postdoctoral Fellowship in Marine Microbial Ecology/ ; //Florida Agricultural Experiment Station Hatch project/ ; //National Natural Science Foundation of China/ ; 2020Z01//Shanghai Sheshan National Geophysical Observatory/ ; 20200925173954005//Stable Support Plan Program of Shenzhen Natural Science Fund/ ; ZDSYS201802081843490//Southern University of Science and Technology/ ; //Shenzhen Key Laboratory of Marine Archaea Geo-Omics/ ; 2020KCXTD023//the Innovation Team Project of Universities/ ; //National Natural Science Foundation of China/ ; //Fundamental Research Funds for the Central Universities of China/ ; 92051114//National Natural Science Foundation of China/ ; }, mesh = {*Archaea ; *Ammonia/metabolism ; Ecosystem ; RNA, Ribosomal, 16S/genetics/metabolism ; Oxidation-Reduction ; Phylogeny ; Soil ; Soil Microbiology ; }, abstract = {Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.}, }
@article {pmid38363394, year = {2024}, author = {Duan, Y and Li, Y and Zhao, J and Zhang, J and Luo, C and Jia, R and Liu, X}, title = {Changes in Microbial Composition During the Succession of Biological Soil Crusts in Alpine Hulun Buir Sandy Land, China.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {43}, pmid = {38363394}, issn = {1432-184X}, mesh = {Ecosystem ; Soil ; Sand ; Soil Microbiology ; *Lichens ; *Cyanobacteria ; *Microbiota ; Nitrogen ; Phosphorus ; China ; }, abstract = {Biological soil crusts (biocrusts) are considered "desert ecosystem engineers" because they play a vital role in the restoration and stability maintenance of deserts, including those cold sandy land ecosystems at high latitudes, which are especially understudied. Microorganisms participate in the formation and succession of biocrusts, contributing to soil properties' improvement and the stability of soil aggregates, and thus vegetation development. Accordingly, understanding the composition and successional characteristics of microorganisms is a prerequisite for analyzing the ecological functions of biocrusts and related applications. Here, the Hulun Buir Sandy Land region in northeastern China-lying at the highest latitude of any sandy land in the country-was selected for study. Through a field investigation and next-generation sequencing (Illumina MiSeq PE300 Platform), our goal was to assess the shifts in diversity and community composition of soil bacteria and fungi across different stages during the succession of biocrusts in this region, and to uncover the main factors involved in shaping their soil microbial community. The results revealed that the nutrient enrichment capacity of biocrusts for available nitrogen, total nitrogen, total phosphorus, total content of water-soluble salt, available potassium, soil organic matter, and available phosphorus was progressively enhanced by the succession of cyanobacterial crusts to lichen crusts and then to moss crusts. In tandem, soil bacterial diversity increased as biocrust succession proceeded but fungal diversity decreased. A total of 32 bacterial phyla and 11 fungal phyla were identified, these also known to occur in other desert ecosystems. Among those taxa, the relative abundance of Proteobacteria and Cyanobacteria significantly increased and decreased, respectively, along the cyanobacterial crust-lichen-moss crust successional gradient. However, for Actinobacteria, Chloroflexi, and Acidobacteria their changed relative abundance was significantly hump-shaped, increasing in the shift from cyanobacterial crust to lichen crust, and then decreasing as lichen crust shifted to moss crust. In this process, the improved soil properties effectively enhanced soil bacterial and fungal community composition. Altogether, these findings broaden our understanding about how soil microbial properties can change during the succession of biocrusts in high-latitude, cold sandy land ecosystems.}, }
@article {pmid38362164, year = {2024}, author = {Pasciullo Boychuck, S and Brenner, LJ and Gagorik, CN and Schamel, JT and Baker, S and Tran, E and vonHoldt, BM and Koepfli, KP and Maldonado, JE and DeCandia, AL}, title = {The gut microbiomes of Channel Island foxes and island spotted skunks exhibit fine-scale differentiation across host species and island populations.}, journal = {Ecology and evolution}, volume = {14}, number = {2}, pages = {e11017}, pmid = {38362164}, issn = {2045-7758}, abstract = {California's Channel Islands are home to two endemic mammalian carnivores: island foxes (Urocyon littoralis) and island spotted skunks (Spilogale gracilis amphiala). Although it is rare for two insular terrestrial carnivores to coexist, these known competitors persist on both Santa Cruz Island and Santa Rosa Island. We hypothesized that examination of their gut microbial communities would provide insight into the factors that enable this coexistence, as microbial symbionts often reflect host evolutionary history and contemporary ecology. Using rectal swabs collected from island foxes and island spotted skunks sampled across both islands, we generated 16S rRNA amplicon sequencing data to characterize their gut microbiomes. While island foxes and island spotted skunks both harbored the core mammalian microbiome, host species explained the largest proportion of variation in the dataset. We further identified intraspecific variation between island populations, with greater differentiation observed between more specialist island spotted skunk populations compared to more generalist island fox populations. This pattern may reflect differences in resource utilization following fine-scale niche differentiation. It may further reflect evolutionary differences regarding the timing of intraspecific separation. Considered together, this study contributes to the growing catalog of wildlife microbiome studies, with important implications for understanding how eco-evolutionary processes enable the coexistence of terrestrial carnivores-and their microbiomes-in island environments.}, }
@article {pmid38361649, year = {2024}, author = {Parks, M and Lee, JS and Camua, K and Hollender, E}, title = {Turtle species and ecology drive carapace microbiome diversity in three seasonally interconnected wetland habitats.}, journal = {Access microbiology}, volume = {6}, number = {1}, pages = {}, pmid = {38361649}, issn = {2516-8290}, abstract = {Different species of freshwater turtles exhibit primary behaviours ranging from aerial basking to benthic bottom-walking, cycle between wet and dry conditions at different time intervals, and undertake short-distance overland movements between aquatic habitats. These behaviours in turn may impact the accumulation of microbes on external shell surfaces of turtles and provide novel niches for differentiation of microbial communities. We assessed microbial diversity using 16S and 18S rRNA metabarcoding on carapace surfaces of six species of freshwater turtles residing in three adjacent and seasonally interconnected wetland habitats in southeast Oklahoma (United States). Communities were highly diverse, with nearly 4200 prokaryotic and 500 micro-eukaryotic amplicon sequence variants recovered, and included taxa previously reported as common or differentially abundant on turtle shells. The 16S rRNA alpha diversity tended to be highest for two species of benthic turtles, while 18S rRNA alpha diversity was highest for two basking and one shallow-water benthic species. Beta diversity of communities was more strongly differentiated by turtle species than by collection site, and ordination patterns were largely reflective of turtle species' primary habits (i.e. benthic, basking, or benthic-basking). Our data support that freshwater turtles could play a role in microbial ecology and evolution in freshwater habitats and warrant additional exploration including in areas with high native turtle diversity and inter-habitat turtle movements.}, }
@article {pmid38357595, year = {2024}, author = {Fickling, NW and Abbott, CA and Brame, JE and Cando-Dumancela, C and Liddicoat, C and Robinson, JM and Breed, MF}, title = {Light-dark cycles may influence in situ soil bacterial networks and diurnally-sensitive taxa.}, journal = {Ecology and evolution}, volume = {14}, number = {2}, pages = {e11018}, pmid = {38357595}, issn = {2045-7758}, abstract = {Soil bacterial taxa have important functional roles in ecosystems (e.g. nutrient cycling, soil formation, plant health). Many factors influence their assembly and regulation, with land cover types (e.g. open woodlands, grasslands), land use types (e.g. nature reserves, urban green space) and plant-soil feedbacks being well-studied factors. However, changes in soil bacterial communities in situ over light-dark cycles have received little attention, despite many plants and some bacteria having endogenous circadian rhythms that could influence soil bacterial communities. We sampled surface soils in situ across 24-h light-dark cycles (at 00:00, 06:00, 12:00, 18:00) at two land cover types (remnant vegetation vs. cleared, grassy areas) and applied 16S rRNA amplicon sequencing to investigate changes in bacterial communities. We show that land cover type strongly affected soil bacterial diversity, with soils under native vegetation expressing 15.4%-16.4% lower alpha diversity but 4.9%-10.6% greater heterogeneity than soils under cleared vegetation. In addition, we report time-dependent and site-specific changes in bacterial network complexity and between 598-922 ASVs showing significant changes in relative abundance across times. Native site node degree (bacterial interactions) at the phylum level was 16.0% higher in the early morning than in the afternoon/evening. Our results demonstrate for the first time that light-dark cycles have subtle yet important effects on soil bacterial communities in situ and that land cover influences these dynamics. We provide a new view of soil microbial ecology and suggest that future studies should consider the time of day when sampling soil bacteria.}, }
@article {pmid38356049, year = {2024}, author = {van Bergeijk, DA and Augustijn, HE and Elsayed, SS and Willemse, J and Carrión, VJ and Du, C and Urem, M and Grigoreva, LV and Cheprasov, MY and Grigoriev, S and Jansen, H and Wintermans, B and Budding, AE and Spaink, HP and Medema, MH and van Wezel, GP}, title = {Taxonomic and metabolic diversity of Actinomycetota isolated from faeces of a 28,000-year-old mammoth.}, journal = {Environmental microbiology}, volume = {26}, number = {2}, pages = {e16589}, doi = {10.1111/1462-2920.16589}, pmid = {38356049}, issn = {1462-2920}, support = {//Universiteit Leiden/ ; 101055020-COMMUNITY//European Research Council/International ; 948770-DECIPHER//European Research Council/International ; }, mesh = {Animals ; Phylogeny ; *Mammoths ; Genomics ; *Streptomyces/genetics ; *Actinomycetales ; Feces ; }, abstract = {Ancient environmental samples, including permafrost soils and frozen animal remains, represent an archive with microbial communities that have barely been explored. This yet unexplored microbial world is a genetic resource that may provide us with new evolutionary insights into recent genomic changes, as well as novel metabolic pathways and chemistry. Here, we describe Actinomycetota Micromonospora, Oerskovia, Saccharopolyspora, Sanguibacter and Streptomyces species were successfully revived and their genome sequences resolved. Surprisingly, the genomes of these bacteria from an ancient source show a large phylogenetic distance to known strains and harbour many novel biosynthetic gene clusters that may well represent uncharacterised biosynthetic potential. Metabolic profiles of the strains display the production of known molecules like antimycin, conglobatin and macrotetrolides, but the majority of the mass features could not be dereplicated. Our work provides insights into Actinomycetota isolated from an ancient source, yielding unexplored genomic information that is not yet present in current databases.}, }
@article {pmid38356037, year = {2024}, author = {Xian, WD and Ding, J and Chen, J and Qu, W and Cao, P and Tang, C and Liu, X and Zhang, Y and Li, JL and Wang, P and Li, WJ and Wang, J}, title = {Distinct Assembly Processes Structure Planktonic Bacterial Communities Among Near- and Offshore Ecosystems in the Yangtze River Estuary.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {42}, pmid = {38356037}, issn = {1432-184X}, mesh = {*Ecosystem ; *Rivers/microbiology ; Plankton/genetics ; Estuaries ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Water ; }, abstract = {The estuarine system functions as natural filters due to its ability to facilitate material transformation, planktonic bacteria play a crucial role in the cycling of complex nutrients and pollutants within estuaries, and understanding the community composition and assembly therein is crucial for comprehending bacterial ecology within estuaries. Despite extensive investigations into the composition and community assembly of two bacterial fractions (free-living, FLB; particle-attached, PAB), the process by which bacterioplankton communities in these two habitats assemble in the nearshore and offshore zones of estuarine ecosystems remains poorly understood. In this study, we conducted sampling in the Yangtze River Estuary (YRE) to investigate potential variations in the composition and community assembly of FLB and PAB in nearshore and offshore regions. We collected 90 samples of surface, middle, and bottom water from 16 sampling stations and performed 16S rRNA gene amplicon analysis along with environmental factor measurements. The results unveiled that the nearshore communities demonstrated significantly greater species richness and Chao1 indices compared to the offshore communities. In contrast, the nearshore communities had lower values of Shannon and Simpson indices. When compared to the FLB, the PAB exhibit a higher level of biodiversity and abundance. However, no distinct alpha and beta diversity differences were observed between the bottom, middle, and surface water layers. The community assembly analysis indicated that nearshore communities are predominantly shaped by deterministic processes, particularly due to heterogeneous selection of PAB; In contrast, offshore communities are governed more by stochastic processes, largely due to homogenizing dispersal of FLB. Consequently, the findings of this study demonstrate that nearshore and PAB communities exhibit higher levels of species diversity, while stochastic and deterministic processes exert distinct influences on communities among near- and offshore regions. This study further sheds new light on our understanding of the mechanisms governing bacterial communities in estuarine ecosystems.}, }
@article {pmid38354254, year = {2024}, author = {Doré, H and Eisenberg, AR and Junkins, EN and Leventhal, GE and Ganesh, A and Cordero, OX and Paul, BG and Valentine, DL and O'Malley, MA and Wilbanks, EG}, title = {Targeted hypermutation of putative antigen sensors in multicellular bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {9}, pages = {e2316469121}, pmid = {38354254}, issn = {1091-6490}, support = {W911NF-19-2-0026//DOD | USA | AFC | CCDC | Army Research Office (ARO)/ ; W911NF-19-D-0001//DOD | USA | AFC | CCDC | Army Research Office (ARO)/ ; 508543//Joint Genome Institute (JGI)/ ; }, mesh = {*Bacteria/genetics ; Archaea/genetics ; Metagenome ; Retroelements ; *Bacteriophages/genetics ; }, abstract = {Diversity-generating retroelements (DGRs) are used by bacteria, archaea, and viruses as a targeted mutagenesis tool. Through error-prone reverse transcription, DGRs introduce random mutations at specific genomic loci, enabling rapid evolution of these targeted genes. However, the function and benefits of DGR-diversified proteins in cellular hosts remain elusive. We find that 82% of DGRs from one of the major monophyletic lineages of DGR reverse transcriptases are encoded by multicellular bacteria, which often have two or more DGR loci in their genomes. Using the multicellular purple sulfur bacterium Thiohalocapsa sp. PB-PSB1 as an example, we characterized nine distinct DGR loci capable of generating 10[282] different combinations of target proteins. With environmental metagenomes from individual Thiohalocapsa aggregates, we show that most of PB-PSB1's DGR target genes are diversified across its biogeographic range, with spatial heterogeneity in the diversity of each locus. In Thiohalocapsa PB-PSB1 and other bacteria hosting this lineage of cellular DGRs, the diversified target genes are associated with NACHT-domain anti-phage defenses and putative ternary conflict systems previously shown to be enriched in multicellular bacteria. We propose that these DGR-diversified targets act as antigen sensors that confer a form of adaptive immunity to their multicellular consortia, though this remains to be experimentally tested. These findings could have implications for understanding the evolution of multicellularity, as the NACHT-domain anti-phage systems and ternary systems share both domain homology and conceptual similarities with the innate immune and programmed cell death pathways of plants and metazoans.}, }
@article {pmid38351424, year = {2024}, author = {Morelle, J and Bastos, A and Frankenbach, S and Frommlet, JC and Campbell, DA and Lavaud, J and Serôdio, J}, title = {The Photoprotective Behavior of a Motile Benthic Diatom as Elucidated from the Interplay Between Cell Motility and Physiological Responses to a Light Microgradient Using a Novel Experimental Setup.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {40}, pmid = {38351424}, issn = {1432-184X}, mesh = {*Diatoms/physiology ; Photosynthesis ; Chlorophyll ; Light ; Cell Movement ; }, abstract = {It has long been hypothesized that benthic motile pennate diatoms use phototaxis to optimize photosynthesis and minimize photoinhibitory damage by adjusting their position within vertical light gradients in coastal benthic sediments. However, experimental evidence to test this hypothesis remains inconclusive, mainly due to methodological difficulties in studying cell behavior and photosynthesis over realistic spatial microscale gradients of irradiance and cell position. In this study, a novel experimental approach was developed and used to test the hypothesis of photosynthesis optimization through motility, based on the combination of single-cell in vivo chlorophyll fluorometry and microfluidic chips. The approach allows the concurrent study of behavior and photosynthetic activity of individual cells of the epipelic diatom species Craspedostauros britannicus exposed to a light microgradient of realistic dimensions, simulating the irradiance and distance scales of light microgradients in benthic sediments. Following exposure to light, (i) cells explored their light environment before initiating light-directed motility; (ii) cells used motility to lower their light dose, when exposed to the highest light intensities; and (iii) motility was combined with reversible non-photochemical quenching, to allow cells to avoid photoinhibition. The results of this proof-of-concept study not only strongly support the photoprotective nature of photobehavior in the studied species but also revealed considerable variability in how individual cells reacted to a light microgradient. The experimental setup can be readily applied to study motility and photosynthetic light responses of other diatom species or natural assemblages, as well as other photoautotrophic motile microorganisms, broadening the toolset for experimental microbial ecology research.}, }
@article {pmid38351266, year = {2024}, author = {Arbulu, S and Kjos, M}, title = {Revisiting the Multifaceted Roles of Bacteriocins : The Multifaceted Roles of Bacteriocins.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {41}, pmid = {38351266}, issn = {1432-184X}, support = {101029099//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 296906//Norges Forskningsr&#xe5;d/ ; }, mesh = {*Bacteriocins/pharmacology ; Biofilms ; Bacteria ; Peptides ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Bacteriocins are gene-encoded antimicrobial peptides produced by bacteria. These peptides are heterogeneous in terms of structure, antimicrobial activities, biosynthetic clusters, and regulatory mechanisms. Bacteriocins are widespread in nature and may contribute to microbial diversity due to their capacity to target specific bacteria. Primarily studied as food preservatives and therapeutic agents, their function in natural settings is however less known. This review emphasizes the ecological significance of bacteriocins as multifunctional peptides by exploring bacteriocin distribution, mobility, and their impact on bacterial population dynamics and biofilms.}, }
@article {pmid38348184, year = {2024}, author = {Wang, W and Dong, Y and Guo, W and Zhang, X and Degen, AA and Bi, S and Ding, L and Chen, X and Long, R}, title = {Linkages between rumen microbiome, host, and environment in yaks, and their implications for understanding animal production and management.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1301258}, pmid = {38348184}, issn = {1664-302X}, abstract = {Livestock on the Qinghai-Tibetan Plateau is of great importance for the livelihood of the local inhabitants and the ecosystem of the plateau. The natural, harsh environment has shaped the adaptations of local livestock while providing them with requisite eco-services. Over time, unique genes and metabolic mechanisms (nitrogen and energy) have evolved which enabled the yaks to adapt morphologically and physiologically to the Qinghai-Tibetan Plateau. The rumen microbiota has also co-evolved with the host and contributed to the host's adaptation to the environment. Understanding the complex linkages between the rumen microbiota, the host, and the environment is essential to optimizing the rumen function to meet the growing demands for animal products while minimizing the environmental impact of ruminant production. However, little is known about the mechanisms of host-rumen microbiome-environment linkages and how they ultimately benefit the animal in adapting to the environment. In this review, we pieced together the yak's adaptation to the Qinghai-Tibetan Plateau ecosystem by summarizing the natural selection and nutritional features of yaks and integrating the key aspects of its rumen microbiome with the host metabolic efficiency and homeostasis. We found that this homeostasis results in higher feed digestibility, higher rumen microbial protein production, higher short-chain fatty acid (SCFA) concentrations, and lower methane emissions in yaks when compared with other low-altitude ruminants. The rumen microbiome forms a multi-synergistic relationship among the rumen microbiota services, their communities, genes, and enzymes. The rumen microbial proteins and SCFAs act as precursors that directly impact the milk composition or adipose accumulation, improving the milk or meat quality, resulting in a higher protein and fat content in yak milk and a higher percentage of protein and abundant fatty acids in yak meat when compared to dairy cow or cattle. The hierarchical interactions between the climate, forage, rumen microorganisms, and host genes have reshaped the animal's survival and performance. In this review, an integrating and interactive understanding of the host-rumen microbiome environment was established. The understanding of these concepts is valuable for agriculture and our environment. It also contributes to a better understanding of microbial ecology and evolution in anaerobic ecosystems and the host-environment linkages to improve animal production.}, }
@article {pmid38346660, year = {2024}, author = {Durán-Viseras, A and Lindner, BG and Hatt, JK and Lai, A and Wallace, R and Ginn, O and Brown, J and Konstantinidis, KT}, title = {Metagenomic insights into the impact of litter from poultry Concentrated Animal Feeding Operations (CAFOs) to adjacent soil and water microbial communities.}, journal = {The Science of the total environment}, volume = {920}, number = {}, pages = {170772}, doi = {10.1016/j.scitotenv.2024.170772}, pmid = {38346660}, issn = {1879-1026}, mesh = {Humans ; Animals ; Poultry ; Soil ; Metagenome ; Chickens ; Water ; *Microbiota ; *Anti-Infective Agents ; Anti-Bacterial Agents ; Metagenomics ; }, abstract = {In recent decades, human food consumption has led to an increased demand for animal-based foods, particularly chicken meat production. The state of Georgia, USA is one of the top broiler chicken producers in the United States, where animals are raised in Concentrated Animal Feeding Operations (CAFOs). Without proper management, CAFOs could negatively impact the environment and become a public health risk as a source of water and air pollution and/or by spreading antimicrobial resistance genes. In this study, we used metagenome sequencing to investigate the impact of the application of the CAFO's litter on adjacent soils and downstream creek waters in terms of microbial diversity and antimicrobial resistance profile changes. Our data indicate that while a few microbial groups increased in abundance within a short period of time after litter application, these populations subsequently decreased to levels similar to those found prior to the litter application or to below the detection limit of our metagenome sequencing effort. Microbial taxonomic composition analyses, relative abundance of Metagenome-Assembled Genomes (MAGs) and detection of Antimicrobial Resistance Genes (ARGs) allow us to conclude that this practice of litter application had a negligible effect on the microbiome or resistome profile of these soils and nearby waterways, likely due to its dilution in the field and/or outcompetition by indigenous microbes, revealing a minimal impact of these poultry facilities on the natural microbial communities.}, }
@article {pmid38345372, year = {2024}, author = {Campbell, BC and Greenfield, P and Barnhart, EP and Gong, S and Midgley, DJ and Paulsen, IT and George, SC}, title = {Krumholzibacteriota and Deltaproteobacteria contain rare genetic potential to liberate carbon from monoaromatic compounds in subsurface coal seams.}, journal = {mBio}, volume = {15}, number = {3}, pages = {e0173523}, pmid = {38345372}, issn = {2150-7511}, mesh = {*Coal/microbiology ; Carbon/metabolism ; Methane/metabolism ; *Deltaproteobacteria/metabolism ; }, abstract = {Biogenic methane in subsurface coal seam environments is produced by diverse consortia of microbes. Although this methane is useful for global energy security, it remains unclear which microbes can liberate carbon from the coal. Most of this carbon is relatively resistant to biodegradation, as it is contained within aromatic rings. Thus, to explore for coal-degrading taxa in the subsurface, this study reconstructed relevant metagenome-assembled genomes (MAGs) from coal seams by using a key genomic marker for the anaerobic degradation of monoaromatic compounds as a guide: the benzoyl-CoA reductase gene (bcrABCD). Three MAGs were identified with this genetic potential. The first represented a novel taxon from the Krumholzibacteriota phylum, which this study is the first to describe. This Krumholzibacteriota MAG contained a full set of genes for benzoyl-CoA dearomatization, in addition to other genes for anaerobic catabolism of monoaromatics. Analysis of Krumholzibacteriota MAGs from other environments revealed that this genetic potential may be common, and thus, Krumholzibacteriota may be important organisms for the liberation of recalcitrant carbon in a broad range of environments. Moreover, the assembly and characterization of two Syntrophorhabdus aromaticivorans MAGs from different continents and a Syntrophaceae sp. MAG implicate the Deltaproteobacteria class in coal seam monoaromatic degradation. Each of these taxa are potential rate-limiting organisms for subsurface coal-to-methane biodegradation. Their description here provides some understanding of their function within the coal seam microbiome and will help inform future efforts in coal bed methane stimulation, anoxic bioremediation of organic pollutants, and assessments of anoxic, subsurface carbon cycling and emissions.IMPORTANCESubsurface coal seams are highly anoxic, oligotrophic environments, where the main source of carbon is "locked away" within aromatic rings. Despite these challenges, many coal seams accumulate biogenic methane, implying that the coal seam microbiome is "unlocking" this carbon source in situ. For over two decades, researchers have endeavored to understand which organisms perform these processes. This study provides the first descriptions of organisms with this genetic potential from the coal seam environment. Here, we report metagenomic insights into carbon liberation from aromatic molecules and the degradation pathways involved and describe a Krumholzibacteriota, two Syntrophorhabdus aromaticivorans, and a Syntrophaceae MAG that contain this genetic potential. This is also the first time that the Krumholzibacteriota phylum has been implicated in anaerobic dearomatization of aromatic hydrocarbons. This potential is identified here in numerous MAGs from other terrestrial and marine subsurface habitats, implicating the Krumholzibacteriota in carbon-cycling processes across a broad range of environments.}, }
@article {pmid38344937, year = {2024}, author = {Ugolini, GS and Wang, M and Secchi, E and Pioli, R and Ackermann, M and Stocker, R}, title = {Microfluidic approaches in microbial ecology.}, journal = {Lab on a chip}, volume = {24}, number = {5}, pages = {1394-1418}, pmid = {38344937}, issn = {1473-0189}, mesh = {Animals ; *Microfluidics/methods ; *Ecology ; }, abstract = {Microbial life is at the heart of many diverse environments and regulates most natural processes, from the functioning of animal organs to the cycling of global carbon. Yet, the study of microbial ecology is often limited by challenges in visualizing microbial processes and replicating the environmental conditions under which they unfold. Microfluidics operates at the characteristic scale at which microorganisms live and perform their functions, thus allowing for the observation and quantification of behaviors such as growth, motility, and responses to external cues, often with greater detail than classical techniques. By enabling a high degree of control in space and time of environmental conditions such as nutrient gradients, pH levels, and fluid flow patterns, microfluidics further provides the opportunity to study microbial processes in conditions that mimic the natural settings harboring microbial life. In this review, we describe how recent applications of microfluidic systems to microbial ecology have enriched our understanding of microbial life and microbial communities. We highlight discoveries enabled by microfluidic approaches ranging from single-cell behaviors to the functioning of multi-cellular communities, and we indicate potential future opportunities to use microfluidics to further advance our understanding of microbial processes and their implications.}, }
@article {pmid38344169, year = {2024}, author = {Pertierra, LR and Varliero, G and Barbosa, A and Biersma, EM and Convey, P and Chown, SL and Cowan, D and De Los Rios, A and Escribano-Alvarez, P and Fontaneto, D and Fraser, C and Harris, M and Hughes, K and Griffiths, H and le Roux, P and Liu, XP and Lynch, H and Majewska, R and Martinez, PA and Molina-Montenegro, M and Olalla-Tarraga, MA and Peck, L and Quesada, A and Ronquillo, C and Ropert-Coudert, Y and Sancho, L and Terauds, A and Vianna, J and Wilmotte, A and Hortal, J and Greve, M}, title = {TerrANTALife 1.0 Biodiversity data checklist of known Antarctic terrestrial and freshwater life forms.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e106199}, pmid = {38344169}, issn = {1314-2828}, abstract = {BACKGROUND: Incomplete species inventories for Antarctica represent a key challenge for comprehensive ecological research and conservation in the region. Additionally, data required to understand population dynamics, rates of evolution, spatial ranges, functional traits, physiological tolerances and species interactions, all of which are fundamental to disentangle the different functional elements of Antarctic biodiversity, are mostly missing. However, much of the fauna, flora and microbiota in the emerged ice-free land of the continent have an uncertain presence and/or unresolved status, with entire biodiversity compendia of prokaryotic groups (e.g. bacteria) being missing. All the available biodiversity information requires consolidation, cross-validation, re-assessment and steady systematic inclusion in order to create a robust catalogue of biodiversity for the continent.<br><br>NEW INFORMATION: We compiled, completed and revised eukaryotic species inventories present in terrestrial and freshwater ecosystems in Antarctica in a new living database: terrANTALife (version 1.0). The database includes the first integration in a compendium for many groups of eukaryotic microorganisms. We also introduce a first catalogue of amplicon sequence variants (ASVs) of prokaryotic biodiversity. Available compendia and literature to date were searched for Antarctic terrestrial and freshwater species, integrated, taxonomically harmonised and curated by experts to create comprehensive checklists of Antarctic organisms. The final inventories comprises 470 animal species (including vertebrates, free-living invertebrates and parasites), 306 plants (including all Viridiplantae: embryophytes and green algae), 997 fungal species and 434 protists (sensu lato). We also provide a first account for many groups of microorganisms, including non-lichenised fungi and multiple groups of eukaryotic unicellular species (Stramenophila, Alveolata and Rhizaria (SAR), Chromists and Amoeba), jointly referred to as "protists". In addition, we identify 1753 bacterial (obtained from 348117 ASVs) and 34 archaeal genera (from 1848 ASVs), as well as, at least, 14 virus families. We formulate a basic tree of life in Antarctica with the main lineages listed in the region and their "known-accepted-species" numbers.}, }
@article {pmid38343862, year = {2024}, author = {Lin, H and Chen, Y and Abror, G and Price, M and Morris, A and Sun, J and Palella, F and Chew, KW and Brown, TT and Rinaldo, CR and Peddada, SD}, title = {The effect of sexual behavior on HIV-1 seroconversion is mediated by the gut microbiome and proinflammatory cytokines.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {38343862}, issn = {2693-5015}, support = {U01 HL146208/HL/NHLBI NIH HHS/United States ; S10 OD023402/OD/NIH HHS/United States ; ZIA ES103390/ImNIH/Intramural NIH HHS/United States ; U01 HL146201/HL/NHLBI NIH HHS/United States ; U01 HL146204/HL/NHLBI NIH HHS/United States ; U01 HL146240/HL/NHLBI NIH HHS/United States ; }, abstract = {The association between HIV-1 seroconversion and gut dysbiosis is well documented, and its association with sexual activity is also widely recognized. However, it is not known whether the gut dysbiosis mediates the effects of high-risk sexual behavior on HIV-1 seroconversion. In this report we focused on men who engaged in high-risk sexual behavior where they had receptive anal intercourse with multiple men. We demonstrate that proinflammatory cytokines, sCD14 and sCD163, and gut microbiota mediate the effects of this high-risk sexual behavior on subsequent HIV seroconversion. We discovered changes in the gut microbial ecology, prior to seroconversion, both in terms of the composition as well as inter-relationships among the commensal species. Furthermore, these changes correlate with future HIV seroconversion. Specifically, as the number of sexual partners increased, we discovered in a "dose-response" manner, a decrease in the abundance of commensal and short-chain fatty acid-producing species, A. muciniphila, B. caccae, B. fragilis, B. uniformis, Bacteroides spp., Butyricimonas spp., and Odoribacter spp, and an increase in proinflammatory species Dehalobacterium spp. and Methanobrevibacter spp. These changes were also observed among subsequent HIV seroconverters. Interestingly, we also discovered a reduction in correlations among these commensal and short-chain fatty acid producing bacteria in a "dose-response" manner with the number of sexual partners. Our mediation analysis not only provides a conceptual model for the disease process but also provides clues for future clinical interventions that will manipulate the gut microbiota to treat high-risk subjects to prevent HIV seroconversion.}, }
@article {pmid38338599, year = {2024}, author = {Bodie, AR and Wythe, LA and Dittoe, DK and Rothrock, MJ and O'Bryan, CA and Ricke, SC}, title = {Alternative Additives for Organic and Natural Ready-to-Eat Meats to Control Spoilage and Maintain Shelf Life: Current Perspectives in the United States.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, pmid = {38338599}, issn = {2304-8158}, abstract = {Food additives are employed in the food industry to enhance the color, smell, and taste of foods, increase nutritional value, boost processing efficiency, and extend shelf life. Consumers are beginning to prioritize food ingredients that they perceive as supporting a healthy lifestyle, emphasizing ingredients they deem acceptable as alternative or "clean-label" ingredients. Ready-to-eat (RTE) meat products can be contaminated with pathogens and spoilage microorganisms after the cooking step, contributing to food spoilage losses and increasing the risk to consumers for foodborne illnesses. More recently, consumers have advocated for no artificial additives or preservatives, which has led to a search for antimicrobials that meet these demands but do not lessen the safety or quality of RTE meats. Lactates and diacetates are used almost universally to extend the shelf life of RTE meats by reducing spoilage organisms and preventing the outgrowth of the foodborne pathogen Listeria monocytogenes. These antimicrobials applied to RTE meats tend to be broad-spectrum in their activities, thus affecting overall microbial ecology. It is to the food processing industry's advantage to target spoilage organisms and pathogens specifically.}, }
@article {pmid38337180, year = {2024}, author = {Finn, DR}, title = {A metagenomic alpha-diversity index for microbial functional biodiversity.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {3}, pages = {}, pmid = {38337180}, issn = {1574-6941}, support = {522758166//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Metagenome ; *Biodiversity ; RNA, Ribosomal ; Ecosystem ; }, abstract = {Alpha-diversity indices are an essential tool for describing and comparing biodiversity. Microbial ecologists apply indices originally intended for, or adopted by, macroecology to address questions relating to taxonomy (conserved marker) and function (metagenome-based data). In this Perspective piece, I begin by discussing the nature and mathematical quirks important for interpreting routinely employed alpha-diversity indices. Secondly, I propose a metagenomic alpha-diversity index (MD) that measures the (dis)similarity of protein-encoding genes within a community. MD has defined limits, whereby a community comprised mostly of similar, poorly diverse protein-encoding genes pulls the index to the lower limit, while a community rich in divergent homologs and unique genes drives it toward the upper limit. With data acquired from an in silico and three in situ metagenome studies, I derive MD and typical alpha-diversity indices applied to taxonomic (ribosomal rRNA) and functional (all protein-encoding) genes, and discuss their relationships with each other. Not all alpha-diversity indices detect biological trends, and taxonomic does not necessarily follow functional biodiversity. Throughout, I explain that protein Richness and MD provide complementary and easily interpreted information, while probability-based indices do not. Finally, considerations regarding the unique nature of microbial metagenomic data and its relevance for describing functional biodiversity are discussed.}, }
@article {pmid38332550, year = {2024}, author = {Louw, NL and Wolfe, BE and Uricchio, LH}, title = {A phylogenomic perspective on interspecific competition.}, journal = {Ecology letters}, volume = {27}, number = {2}, pages = {e14359}, doi = {10.1111/ele.14359}, pmid = {38332550}, issn = {1461-0248}, support = {1942063//National Science Foundation/ ; 2021362//National Science Foundation/ ; }, mesh = {Phylogeny ; *Genome ; *Genomics ; Biological Evolution ; Phenotype ; }, abstract = {Evolutionary processes may have substantial impacts on community assembly, but evidence for phylogenetic relatedness as a determinant of interspecific interaction strength remains mixed. In this perspective, we consider a possible role for discordance between gene trees and species trees in the interpretation of phylogenetic signal in studies of community ecology. Modern genomic data show that the evolutionary histories of many taxa are better described by a patchwork of histories that vary along the genome rather than a single species tree. If a subset of genomic loci harbour trait-related genetic variation, then the phylogeny at these loci may be more informative of interspecific trait differences than the genome background. We develop a simple method to detect loci harbouring phylogenetic signal and demonstrate its application through a proof-of-principle analysis of Penicillium genomes and pairwise interaction strength. Our results show that phylogenetic signal that may be masked genome-wide could be detectable using phylogenomic techniques and may provide a window into the genetic basis for interspecific interactions.}, }
@article {pmid38332365, year = {2024}, author = {Amaral, RR and Love, RM and Braga, T and Souza Côrtes, MI and Rachid, CTCC and Rôças, IN and Siqueira, JF}, title = {Impact of root canal preparation using two single-file systems on the intra-radicular microbiome of teeth with primary apical periodontitis.}, journal = {Clinical oral investigations}, volume = {28}, number = {2}, pages = {139}, pmid = {38332365}, issn = {1436-3771}, mesh = {Humans ; *Root Canal Preparation ; Dental Pulp Cavity/microbiology ; Root Canal Therapy ; *Periapical Periodontitis/microbiology ; Bacteria ; }, abstract = {OBJECTIVES: This study aimed to describe the effects of two single-file systems on the diversity of the endodontic microbiome of teeth with primary asymptomatic apical periodontitis.<br><br>MATERIALS AND METHODS: The root canals from single-rooted teeth with apical periodontitis were prepared using either the Reciproc Blue (RB) or the XP-endo Shaper (XPS) instrument system. The latter was followed by a supplementary step with the XP-endo Finisher (XPF) instrument. For irrigation, 5.25% sodium hypochlorite was used. Root canal samples were taken at the baseline (S1), after preparation (S2), and after the supplementary step (S3). DNA was extracted and subjected to high-throughput sequencing using the MiSeq Illumina platform.<br><br>RESULTS: Samples from 10 teeth from the RB and 7 from the XPS group were subjected to DNA sequencing. Initial samples differed significantly from post-preparation samples in bacterial diversity, with no significant difference when comparing the two instrument systems. The most dominant phyla in S2 were Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, and Actinobacteria. The same phyla were found to dominate baseline samples and samples taken after using XPF, but with differences in the ranking of the most dominant ones. At the genus level, the most dominant genera identified after RB instrumentation were Bacteroidaceae [G-1], Fusobacterium, and Staphylococcus, while the most dominant genera after XPS instrumentation were Fusobacterium and Porphyromonas. These genera were also dominant in the initial samples.<br><br>CONCLUSIONS: Both treatment protocols had measurable effects on the root canal microbial diversity, with no significant differences between them. Most of the dominant taxa involved in the primary infection and probably in the aetiology of apical periodontitis were eliminated or substantially reduced.<br><br>CLINICAL RELEVANCE: The most dominant taxa that persisted after instrumentation were Fusobacterium, Porphyromonas, Staphylococcus, and Bacteroidaceae [G-1].}, }
@article {pmid38332161, year = {2024}, author = {McDougall, FK and Speight, N and Funnell, O and Boardman, WSJ and Power, ML}, title = {Dynamics of Antimicrobial Resistance Carriage in Koalas (Phascolarctos Cinereus) and Pteropid Bats (Pteropus Poliocephalus) Before, During and After Wildfires.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {39}, pmid = {38332161}, issn = {1432-184X}, mesh = {Humans ; Animals ; *Chiroptera ; *Wildfires ; *Phascolarctidae ; Anti-Bacterial Agents/pharmacology ; Australia ; Drug Resistance, Bacterial/genetics ; Animals, Wild ; }, abstract = {In the 2019-2020 summer, wildfires decimated the Australian bush environment and impacted wildlife species, including koalas (Phascolarctos cinereus) and grey headed flying fox pups (Pteropid bats, Pteropus poliocephalus). Consequently, hundreds of koalas and thousands of bat pups entered wildlife hospitals with fire-related injuries/illness, where some individuals received antimicrobial therapy. This study investigated the dynamics of antimicrobial resistance (AMR) in pre-fire, fire-affected and post-fire koalas and Pteropid bat pups. PCR and DNA sequencing were used to screen DNA samples extracted from faeces (koalas and bats) and cloacal swabs (koalas) for class 1 integrons, a genetic determinant of AMR, and to identify integron-associated antibiotic resistance genes. Class 1 integrons were detected in 25.5% of koalas (68 of 267) and 59.4% of bats (92 of 155). Integrons contained genes conferring resistance to aminoglycosides, trimethoprim and beta-lactams. Samples were also screened for blaTEM (beta-lactam) resistance genes, which were detected in 2.6% of koalas (7 of 267) and 25.2% of bats (39 of 155). Integron occurrence was significantly higher in fire-affected koalas in-care compared to wild pre-fire koalas (P < 0.0001). Integron and blaTEM occurrence were not significantly different in fire-affected bats compared to pre-fire bats (P > 0.05), however, their occurrence was significantly higher in fire-affected bats in-care compared to wild fire-affected bats (P < 0.0001 and P = 0.0488 respectively). The observed shifts of AMR dynamics in wildfire-impacted species flags the need for judicious antibiotic use when treating fire-affected wildlife to minimise unwanted selective pressure and negative treatment outcomes associated with carriage of resistance genes and antibiotic resistant bacteria.}, }
@article {pmid38331994, year = {2024}, author = {Tao, X and Yang, Z and Feng, J and Jian, S and Yang, Y and Bates, CT and Wang, G and Guo, X and Ning, D and Kempher, ML and Liu, XJA and Ouyang, Y and Han, S and Wu, L and Zeng, Y and Kuang, J and Zhang, Y and Zhou, X and Shi, Z and Qin, W and Wang, J and Firestone, MK and Tiedje, JM and Zhou, J}, title = {Experimental warming accelerates positive soil priming in a temperate grassland ecosystem.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1178}, pmid = {38331994}, issn = {2041-1723}, support = {DE-SC0004601//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; DE-SC0020163//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; DE-SC0010570//DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)/ ; 41825016//National Natural Science Foundation of China (National Science Foundation of China)/ ; EF-2025558//NSF | BIO | Division of Environmental Biology (DEB)/ ; DEB-2129235//NSF | BIO | Division of Environmental Biology (DEB)/ ; }, mesh = {*Ecosystem ; *Grassland ; Soil ; Carbon ; Climate Change ; }, abstract = {Unravelling biosphere feedback mechanisms is crucial for predicting the impacts of global warming. Soil priming, an effect of fresh plant-derived carbon (C) on native soil organic carbon (SOC) decomposition, is a key feedback mechanism that could release large amounts of soil C into the atmosphere. However, the impacts of climate warming on soil priming remain elusive. Here, we show that experimental warming accelerates soil priming by 12.7% in a temperate grassland. Warming alters bacterial communities, with 38% of unique active phylotypes detected under warming. The functional genes essential for soil C decomposition are also stimulated, which could be linked to priming effects. We incorporate lab-derived information into an ecosystem model showing that model parameter uncertainty can be reduced by 32-37%. Model simulations from 2010 to 2016 indicate an increase in soil C decomposition under warming, with a 9.1% rise in priming-induced CO2 emissions. If our findings can be generalized to other ecosystems over an extended period of time, soil priming could play an important role in terrestrial C cycle feedbacks and climate change.}, }
@article {pmid38331428, year = {2024}, author = {Lee Díaz, AS and Minchev, Z and Raaijmakers, JM and Pozo, MJ and Garbeva, P}, title = {Impact of bacterial and fungal inoculants on the resident rhizosphere microbiome and the volatilome of tomato plants under leaf herbivory stress.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {2}, pages = {}, pmid = {38331428}, issn = {1574-6941}, support = {765290//European Union/ ; }, mesh = {*Agricultural Inoculants ; *Solanum lycopersicum ; Rhizosphere ; Herbivory ; Soil Microbiology ; Bacteria/genetics ; *Microbiota ; }, abstract = {Various studies have addressed the impact of microbial inoculants on the composition of the resident microbiome. How microbial inoculants impact plant metabolism and interact with the resident rhizobiota under herbivory stress remains elusive. Here, we investigated the impact of two bacterial and two fungal inoculants, inoculated as single species and as a synthetic community, on the rhizosphere microbiome and volatilome of tomato plants (Solanum lycopersicum) comparing nonstress conditions to exposed to leaf herbivory by Spodoptera exigua. Based on amplicon sequencing analysis, rhizobacterial community composition was significantly affected by all four inoculants and the magnitude of this effect was dependent on herbivory stress. Fungal community composition was altered by the microbial inoculants but independent of herbivory stress. The rhizosphere volatilome was impacted by the microbial inoculation and differences between treatments were evened under herbivory stress. Each microbial inoculant caused unique changes in the volatilome of stressed plants but also shared similar responses, in particular the enhanced production of dimethyl disulfide and benzothiazole. In conclusion, the introduction of microbial inoculants in the tomato rhizosphere caused unique as well as common changes in the rhizosphere microbiome and volatilome, but these changes were minor compared to the microbiome changes induced by herbivory stress.}, }
@article {pmid38329329, year = {2024}, author = {Amill, F and Gauthier, J and Rautio, M and Derome, N}, title = {Characterization of gill bacterial microbiota in wild Arctic char (Salvelinus alpinus) across lakes, rivers, and bays in the Canadian Arctic ecosystems.}, journal = {Microbiology spectrum}, volume = {12}, number = {3}, pages = {e0294323}, pmid = {38329329}, issn = {2165-0497}, support = {//UL | Sentinelle Nord, Universit&#xe9; Laval (Sentinel North)/ ; //Canada First Research Excellence Fund (CFREF)/ ; //Polar Knowledge Canada (PKC)/ ; }, mesh = {Animals ; Bays ; Canada ; Dysbiosis ; Gills ; *Lakes ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Trout/genetics/metabolism ; Water/metabolism ; }, abstract = {Teleost gill mucus has a highly diverse microbiota, which plays an essential role in the host's fitness and is greatly influenced by the environment. Arctic char (Salvelinus alpinus), a salmonid well adapted to northern conditions, faces multiple stressors in the Arctic, including water chemistry modifications, that could negatively impact the gill microbiota dynamics related to the host's health. In the context of increasing environmental disturbances, we aimed to characterize the taxonomic distribution of transcriptionally active taxa within the bacterial gill microbiota of Arctic char in the Canadian Arctic in order to identify active bacterial composition that correlates with environmental factors. For this purpose, a total of 140 adult anadromous individuals were collected from rivers, lakes, and bays belonging to five Inuit communities located in four distinct hydrologic basins in the Canadian Arctic (Nunavut and Nunavik) during spring (May) and autumn (August). Various environmental factors were collected, including latitudes, water and air temperatures, oxygen concentration, pH, dissolved organic carbon (DOC), salinity, and chlorophyll-a concentration. The taxonomic distribution of transcriptionally active taxa within the gill microbiota was quantified by 16S rRNA gene transcripts sequencing. The results showed differential bacterial activity between the different geographical locations, explained by latitude, salinity, and, to a lesser extent, air temperature. Network analysis allowed the detection of a potential dysbiosis signature (i.e., bacterial imbalance) in fish gill microbiota from Duquet Lake in the Hudson Strait and the system Five Mile Inlet connected to the Hudson Bay, both showing the lowest alpha diversity and connectivity between taxa.IMPORTANCEThis paper aims to decipher the complex relationship between Arctic char (Salvelinus alpinus) and its symbiotic microbial consortium in gills. This salmonid is widespread in the Canadian Arctic and is the main protein and polyunsaturated fatty acids source for Inuit people. The influence of environmental parameters on gill microbiota in wild populations remains poorly understood. However, assessing the Arctic char's active gill bacterial community is essential to look for potential pathogens or dysbiosis that could threaten wild populations. Here, we concluded that Arctic char gill microbiota was mainly influenced by latitude and air temperature, the latter being correlated with water temperature. In addition, a dysbiosis signature detected in gill microbiota was potentially associated with poor fish health status recorded in these disturbed environments. With those results, we hypothesized that rapid climate change and increasing anthropic activities in the Arctic might profoundly disturb Arctic char gill microbiota, affecting their survival.}, }
@article {pmid38328439, year = {2024}, author = {Jaeger, JW and Brandt, A and Gui, W and Yergaliyev, T and Hernández-Arriaga, A and Muthu, MM and Edlund, K and Elashy, A and Molinaro, A and Möckel, D and Sarges, J and Halibasic, E and Trauner, M and Kahles, F and Rolle-Kampczyk, U and Hengstler, J and Schneider, CV and Lammers, T and Marschall, HU and von Bergen, M and Camarinha-Silva, A and Bergheim, I and Trautwein, C and Schneider, KM}, title = {Microbiota modulation by dietary oat beta-glucan prevents steatotic liver disease progression.}, journal = {JHEP reports : innovation in hepatology}, volume = {6}, number = {3}, pages = {100987}, pmid = {38328439}, issn = {2589-5559}, abstract = {BACKGROUND &amp; AIMS: Changes in gut microbiota in metabolic dysfunction-associated steatotic liver disease (MASLD) are important drivers of disease progression towards fibrosis. Therefore, reversing microbial alterations could ameliorate MASLD progression. Oat beta-glucan, a non-digestible polysaccharide, has shown promising therapeutic effects on hyperlipidemia associated with MASLD, but its impact on gut microbiota and most importantly MASLD-related fibrosis remains unknown.<br><br>METHODS: We performed detailed metabolic phenotyping, including assessments of body composition, glucose tolerance, and lipid metabolism, as well as comprehensive characterization of the gut-liver axis in a western-style diet (WSD)-induced model of MASLD and assessed the effect of a beta-glucan intervention on early and advanced liver disease. Gut microbiota were modulated using broad-spectrum antibiotic treatment.<br><br>RESULTS: Oat beta-glucan supplementation did not affect WSD-induced body weight gain or glucose intolerance and the metabolic phenotype remained largely unaffected. Interestingly, oat beta-glucan dampened MASLD-related inflammation, which was associated with significantly reduced monocyte-derived macrophage infiltration and fibroinflammatory gene expression, as well as strongly reduced fibrosis development. Mechanistically, this protective effect was not mediated by changes in bile acid composition or signaling, but was dependent on gut microbiota and was lost upon broad-spectrum antibiotic treatment. Specifically, oat beta-glucan partially reversed unfavorable changes in gut microbiota, resulting in an expansion of protective taxa, including Ruminococcus, and Lactobacillus followed by reduced translocation of Toll-like receptor ligands.<br><br>CONCLUSIONS: Our findings identify oat beta-glucan as a highly efficacious food supplement that dampens inflammation and fibrosis development in diet-induced MASLD. These results, along with its favorable dietary profile, suggest that it may be a cost-effective and well-tolerated approach to preventing MASLD progression and should be assessed in clinical studies.<br><br>IMPACT AND IMPLICATIONS: Herein, we investigated the effect of oat beta-glucan on the gut-liver axis and fibrosis development in a mouse model of metabolic dysfunction-associated steatotic liver disease (MASLD). Beta-glucan significantly reduced inflammation and fibrosis in the liver, which was associated with favorable shifts in gut microbiota that protected against bacterial translocation and activation of fibroinflammatory pathways. Together, oat beta-glucan may be a cost-effective and well-tolerated approach to prevent MASLD progression and should be assessed in clinical studies.}, }
@article {pmid38327124, year = {2024}, author = {Rudzki, EN and Antonson, ND and Jones, TM and Schelsky, WM and Trevelline, BK and Hauber, ME and Kohl, KD}, title = {Host avian species and environmental conditions influence the microbial ecology of brood parasitic brown-headed cowbird nestlings: What rules the roost?.}, journal = {Molecular ecology}, volume = {33}, number = {6}, pages = {e17289}, doi = {10.1111/mec.17289}, pmid = {38327124}, issn = {1365-294X}, support = {1953226//US National Science Foundation/ ; 2026836//US National Science Foundation/ ; 2139321//US National Science Foundation/ ; 2305848//US National Science Foundation/ ; }, mesh = {Animals ; *Parasites ; RNA, Ribosomal, 16S/genetics ; Nesting Behavior ; *Passeriformes ; }, abstract = {The role of species interactions, as well as genetic and environmental factors, all likely contribute to the composition and structure of the gut microbiome; however, disentangling these independent factors under field conditions represents a challenge for a functional understanding of gut microbial ecology. Avian brood parasites provide unique opportunities to investigate these questions, as brood parasitism results in parasite and host nestlings being raised in the same nest, by the same parents. Here we utilized obligate brood parasite brown-headed cowbird nestlings (BHCO; Molothrus ater) raised by several different host passerine species to better understand, via 16S rRNA sequencing, the microbial ecology of brood parasitism. First, we compared faecal microbial communities of prothonotary warbler nestlings (PROW; Protonotaria citrea) that were either parasitized or non-parasitized by BHCO and communities among BHCO nestlings from PROW nests. We found that parasitism by BHCO significantly altered both the community membership and community structure of the PROW nestling microbiota, perhaps due to the stressful nest environment generated by brood parasitism. In a second dataset, we compared faecal microbiotas from BHCO nestlings raised by six different host passerine species. Here, we found that the microbiota of BHCO nestlings was significantly influenced by the parental host species and the presence of an inter-specific nestmate. Thus, early rearing environment is important in determining the microbiota of brood parasite nestlings and their companion nestlings. Future work may aim to understand the functional effects of this microbiota variability on nestling performance and fitness.}, }
@article {pmid38325783, year = {2024}, author = {Wang, B and Hu, K and Li, C and Zhang, Y and Hu, C and Liu, Z and Ding, J and Chen, L and Zhang, W and Fang, J and Zhang, H}, title = {Geographic distribution of bacterial communities of inland waters in China.}, journal = {Environmental research}, volume = {249}, number = {}, pages = {118337}, doi = {10.1016/j.envres.2024.118337}, pmid = {38325783}, issn = {1096-0953}, mesh = {China ; *Bacteria/genetics/classification/isolation &amp; purification ; *RNA, Ribosomal, 16S/analysis/genetics ; Biodiversity ; Water Microbiology ; Fresh Water/microbiology ; }, abstract = {Microorganisms are integral to freshwater ecological functions and, reciprocally, their activity and diversity are shaped by the ecosystem state. Yet, the diversity of bacterial community and its driving factors at a large scale remain elusive. To bridge this knowledge gap, we delved into an analysis of 16S RNA gene sequences extracted from 929 water samples across China. Our analyses revealed that inland water bacterial communities showed a weak latitudinal diversity gradient. We found 530 bacterial genera with high relative abundance of hgcI clade. Among them, 29 core bacterial genera were identified, that is strongly linked to mean annual temperature and nutrient loadings. We also detected a non-linear response of bacterial network complexity to the increasing of human pressure. Mantel analysis suggested that MAT, HPI and P loading were the major factors driving bacterial communities in inland waters. The map of taxa abundance showed that the abundant CL500-29 marine group in eastern and southern China indicated high eutrophication risk. Our findings enhance our understanding of the diversity and large-scale biogeographic pattern of bacterial communities of inland waters and have important implications for microbial ecology.}, }
@article {pmid38325494, year = {2024}, author = {Forsmark, B and Bizjak, T and Nordin, A and Rosenstock, NP and Wallander, H and Gundale, MJ}, title = {Shifts in microbial community composition and metabolism correspond with rapid soil carbon accumulation in response to 20 years of simulated nitrogen deposition.}, journal = {The Science of the total environment}, volume = {918}, number = {}, pages = {170741}, doi = {10.1016/j.scitotenv.2024.170741}, pmid = {38325494}, issn = {1879-1026}, mesh = {*Nitrogen/analysis ; Soil ; Carbon ; Forests ; *Microbiota ; Soil Microbiology ; }, abstract = {Anthropogenic nitrogen (N) deposition and fertilization in boreal forests frequently reduces decomposition and soil respiration and enhances C storage in the topsoil. This enhancement of the C sink can be as strong as the aboveground biomass response to N additions and has implications for the global C cycle, but the mechanisms remain elusive. We hypothesized that this effect would be associated with a shift in the microbial community and its activity, and particularly by fungal taxa reported to be capable of lignin degradation and organic N acquisition. We sampled the organic layer below the intact litter of a Norway spruce (Picea abies (L.) Karst) forest in northern Sweden after 20 years of annual N additions at low (12.5 kg N ha[-1] yr[-1]) and high (50 kg N ha[-1] yr[-1]) rates. We measured microbial biomass using phospholipid fatty-acid analysis (PLFA) and ergosterol measurements and used ITS metagenomics to profile the fungal community of soil and fine-roots. We probed the metabolic activity of the soil community by measuring the activity of extracellular enzymes and evaluated its relationships with the most N responsive soil fungal species. Nitrogen addition decreased the abundance of fungal PLFA markers and changed the fungal community in humus and fine-roots. Specifically, the humus community changed in part due to a shift from Oidiodendron pilicola, Cenococcum geophilum, and Cortinarius caperatus to Tylospora fibrillosa and Russula griseascens. These microbial community changes were associated with decreased activity of Mn-peroxidase and peptidase, and an increase in the activity of C acquiring enzymes. Our results show that the rapid accumulation of C in the humus layer frequently observed in areas with high N deposition is consistent with a shift in microbial metabolism, where decomposition associated with organic N acquisition is downregulated when inorganic N forms are readily available.}, }
@article {pmid38325456, year = {2024}, author = {Redouane, EM and Núñez, A and Achouak, W and Barakat, M and Alex, A and Martins, JC and Tazart, Z and Mugani, R and Zerrifi, SEA and Haida, M and García, AM and Campos, A and Lahrouni, M and Oufdou, K and Vasconcelos, V and Oudra, B}, title = {Microcystin influence on soil-plant microbiota: Unraveling microbiota modulations and assembly processes in the rhizosphere of Vicia faba.}, journal = {The Science of the total environment}, volume = {918}, number = {}, pages = {170634}, doi = {10.1016/j.scitotenv.2024.170634}, pmid = {38325456}, issn = {1879-1026}, mesh = {*Vicia faba ; Soil ; Microcystins/toxicity ; Rhizosphere ; *Cyanobacteria ; *Microbiota ; Soil Microbiology ; Plant Roots/metabolism ; }, abstract = {Microcystins (MCs) are frequently detected in cyanobacterial bloom-impacted waterbodies and introduced into agroecosystems via irrigation water. They are widely known as phytotoxic cyanotoxins, which impair the growth and physiological functions of crop plants. However, their impact on the plant-associated microbiota is scarcely tackled and poorly understood. Therefore, we aimed to investigate the effect of MCs on microbiota-inhabiting bulk soil (BS), root adhering soil (RAS), and root tissue (RT) of Vicia faba when exposed to 100 μg L[-1] MCs in a greenhouse pot experiment. Under MC exposure, the structure, co-occurrence network, and assembly processes of the bacterial microbiota were modulated with the greatest impact on RT-inhabiting bacteria, followed by BS and, to a lesser extent, RAS. The analyses revealed a significant decrease in the abundances of several Actinobacteriota-related taxa within the RT microbiota, including the most abundant and known genus of Streptomyces. Furthermore, MCs significantly increased the abundance of methylotrophic bacteria (Methylobacillus, Methylotenera) and other Proteobacteria-affiliated genera (e.g., Paucibacter), which are supposed to degrade MCs. The co-occurrence network of the bacterial community in the presence of MCs was less complex than the control network. In MC-exposed RT, the turnover in community composition was more strongly driven by deterministic processes, as proven by the beta-nearest taxon index. Whereas in MC-treated BS and RAS, both deterministic and stochastic processes can influence community assembly to some extent, with a relative dominance of deterministic processes. Altogether, these results suggest that MCs may reshape the structure of the microbiota in the soil-plant system by reducing bacterial taxa with potential phytobeneficial traits and increasing other taxa with the potential capacity to degrade MCs.}, }
@article {pmid38324120, year = {2024}, author = {Scaini, A and Mulligan, J and Berg, H and Brangarí, A and Bukachi, V and Carenzo, S and Chau Thi, D and Courtney-Mustaphi, C and Ekblom, A and Fjelde, H and Fridahl, M and Hansson, A and Hicks, L and Höjer, M and Juma, B and Kain, JH and Kariuki, RW and Kim, S and Lane, P and Leizeaga, A and Lindborg, R and Livsey, J and Lyon, SW and Marchant, R and McConville, JR and Munishi, L and Nilsson, D and Olang, L and Olin, S and Olsson, L and Rogers, PM and Rousk, J and Sandén, H and Sasaki, N and Shoemaker, A and Smith, B and Thai Huynh Phuong, L and Varela Varela, A and Venkatappa, M and Vico, G and Von Uexkull, N and Wamsler, C and Wondie, M and Zapata, P and Zapata Campos, MJ and Manzoni, S and Tompsett, A}, title = {Pathways from research to sustainable development: Insights from ten research projects in sustainability and resilience.}, journal = {Ambio}, volume = {53}, number = {4}, pages = {517-533}, pmid = {38324120}, issn = {1654-7209}, support = {2016-06359//Vetenskapsr&#xe5;det/ ; 2016-06355//Vetenskapsr&#xe5;det/ ; 2016-06297//Vetenskapsr&#xe5;det/ ; 2016-06300//Vetenskapsr&#xe5;det/ ; 2016-06327//Vetenskapsr&#xe5;det/ ; 2016-06329//Vetenskapsr&#xe5;det/ ; 2016-06334//Vetenskapsr&#xe5;det/ ; 2016-06289//Vetenskapsr&#xe5;det/ ; 2016-06313//Vetenskapsr&#xe5;det/ ; 2016-06389//Vetenskapsr&#xe5;det/ ; }, mesh = {Humans ; *Resilience, Psychological ; }, abstract = {Drawing on collective experience from ten collaborative research projects focused on the Global South, we identify three major challenges that impede the translation of research on sustainability and resilience into better-informed choices by individuals and policy-makers that in turn can support transformation to a sustainable future. The three challenges comprise: (i) converting knowledge produced during research projects into successful knowledge application; (ii) scaling up knowledge in time when research projects are short-term and potential impacts are long-term; and (iii) scaling up knowledge across space, from local research sites to larger-scale or even global impact. Some potential pathways for funding agencies to overcome these challenges include providing targeted prolonged funding for dissemination and outreach, and facilitating collaboration and coordination across different sites, research teams, and partner organizations. By systematically documenting these challenges, we hope to pave the way for further innovations in the research cycle.}, }
@article {pmid38322759, year = {2023}, author = {Yang, X and Narvaez-Bravo, C and Zhang, P}, title = {Driving forces shaping the microbial ecology in meat packing plants.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1333696}, pmid = {38322759}, issn = {1664-302X}, abstract = {Meat production is a complex system, continually receiving animals, water, air, and workers, all of which serve as carriers of bacteria. Selective pressures involved in different meat processing stages such as antimicrobial interventions and low temperatures, may promote the accumulation of certain residential microbiota in meat cutting facilities. Bacteria including human pathogens from all these sources can contaminate meat surfaces. While significant advancements have been made in enhancing hygienic standards and pathogen control measures in meat plants, resulting in a notable reduction in STEC recalls and clinical cases, STEC still stands as a predominant contributor to foodborne illnesses associated with beef and occasionally with pork. The second-and third-generation sequencing technology has become popular in microbiota related studies and provided a better image of the microbial community in the meat processing environments. In this article, we reviewed the potential factors influencing the microbial ecology in commercial meat processing facilities and conducted a meta-analysis on the microbiota data published in the last 10 years. In addition, the mechanisms by which bacteria persist in meat production environments have been discussed with a focus on the significant human pathogen E. coli O157:H7 and generic E. coli, an indicator often used for the hygienic condition in food production.}, }
@article {pmid38319112, year = {2024}, author = {Guo, J and Ning, H and Li, Y and Xu, Q and Shen, Q and Ling, N and Guo, S}, title = {Assemblages of rhizospheric and root endospheric mycobiota and their ecological associations with functional traits of rice.}, journal = {mBio}, volume = {15}, number = {3}, pages = {e0273323}, pmid = {38319112}, issn = {2150-7511}, support = {32372808//National Natural Science Foundation of China (NSFC)/ ; 41977080//National Natural Science Foundation of China (NSFC)/ ; U2003210//National Natural Science Foundation of China (NSFC)/ ; 202206193000001, 20220816113416001//Shenzhen Science and Technology Program/ ; JCYJ20230807111217035//Shenzhen Science and Technology Program/ ; 2019QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; }, mesh = {*Oryza ; *Microbiota ; Bacteria ; Fungi ; Plant Roots/microbiology ; Soil Microbiology ; Rhizosphere ; Soil/chemistry ; }, abstract = {UNLABELLED: The soil-root interface harbors complex fungal communities that play vital roles in the fitness of host plants. However, little is known about the assembly rules and potential functions of rhizospheric and endospheric mycobiota. A greenhouse experiment was conducted to explore the fungal communities inhabiting the rhizosphere and roots of 87 rice cultivars at the tillering stage via amplicon sequencing of the fungal internal transcribed spacer 1 region. The potential relationships between these communities and host plant functional traits were also investigated using Procrustes analysis, generalized additive model fitting, and correlation analysis. The fungal microbiota exhibited greater richness, higher diversity, and lower structural variability in the rhizosphere than in the root endosphere. Compared with the root endosphere, the rhizosphere supported a larger coabundance network, with greater connectivity and stronger cohesion. Null model-based analyses revealed that dispersal limitation was primarily responsible for rhizosphere fungal community assembly, while ecological drift was the dominant process in the root endosphere. The community composition of fungi in the rhizosphere was shown to be more related to plant functional traits, such as the root/whole plant biomass, root:shoot biomass ratio, root/shoot nitrogen (N) content, and root/shoot/whole plant N accumulation, than to that in the root endosphere. Overall, at the early stage of rice growth, diverse and complex rhizospheric fungal communities are shaped by stochastic-based processes and exhibit stronger associations with plant functional traits.<br><br>IMPORTANCE: The assembly processes and functions of root-associated mycobiota are among the most fascinating yet elusive topics in microbial ecology. Our results revealed that stochastic forces (dispersal limitation or ecological drift) act on fungal community assembly in both the rice rhizosphere and root endosphere at the early stage of plant growth. In addition, high covariations between the rhizosphere fungal community compositions and plant functional trait profiles were clearly demonstrated in the present study. This work provides empirical evidence of the root-associated fungal assembly principles and ecological relationships of plant functional traits with rhizospheric and root endospheric mycobiota, thereby potentially providing novel perspectives for enhancing plant performance.}, }
@article {pmid38317822, year = {2024}, author = {Kop, LFM and Koch, H and Jetten, MSM and Daims, H and Lücker, S}, title = {Metabolic and phylogenetic diversity in the phylum Nitrospinota revealed by comparative genome analyses.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycad017}, pmid = {38317822}, issn = {2730-6151}, abstract = {The most abundant known nitrite-oxidizing bacteria in the marine water column belong to the phylum Nitrospinota. Despite their importance in marine nitrogen cycling and primary production, there are only few cultured representatives that all belong to the class Nitrospinia. Moreover, although Nitrospinota were traditionally thought to be restricted to marine environments, metagenome-assembled genomes have also been recovered from groundwater. Over the recent years, metagenomic sequencing has led to the discovery of several novel classes of Nitrospinota (UBA9942, UBA7883, 2-12-FULL-45-22, JACRGO01, JADGAW01), which remain uncultivated and have not been analyzed in detail. Here, we analyzed a nonredundant set of 98 Nitrospinota genomes with focus on these understudied Nitrospinota classes and compared their metabolic profiles to get insights into their potential role in biogeochemical element cycling. Based on phylogenomic analysis and average amino acid identities, the highly diverse phylum Nitrospinota could be divided into at least 33 different genera, partly with quite distinct metabolic capacities. Our analysis shows that not all Nitrospinota are nitrite oxidizers and that members of this phylum have the genomic potential to use sulfide and hydrogen for energy conservation. This study expands our knowledge of the phylogeny and potential ecophysiology of the phylum Nitrospinota and offers new avenues for the isolation and cultivation of these elusive bacteria.}, }
@article {pmid38317643, year = {2024}, author = {Vlasselaer, L and Crauwels, S and Lievens, B and De Coninck, B}, title = {Unveiling the microbiome of hydroponically cultivated lettuce: impact of Phytophthora cryptogea infection on plant-associated microorganisms.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {3}, pages = {}, pmid = {38317643}, issn = {1574-6941}, support = {HBC.2020.3181//VLAIO/ ; }, mesh = {Lactuca ; *Phytophthora/genetics ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology ; *Microbiota/genetics ; Rhizosphere ; Flavobacterium/genetics ; Soil Microbiology ; }, abstract = {Understanding the complex interactions between plants and their associated microorganisms is crucial for optimizing plant health and productivity. While microbiomes of soil-bound cultivated crops are extensively studied, microbiomes of hydroponically cultivated crops have received limited attention. To address this knowledge gap, we investigated the rhizosphere and root endosphere of hydroponically cultivated lettuce. Additionally, we sought to explore the potential impact of the oomycete pathogen Phytophthora cryptogea on these microbiomes. Root samples were collected from symptomatic and nonsymptomatic plants in three different greenhouses. Amplicon sequencing of the bacterial 16S rRNA gene revealed significant alterations in the bacterial community upon P. cryptogea infection, particularly in the rhizosphere. Permutational multivariate analysis of variance (perMANOVA) revealed significant differences in microbial communities between plants from the three greenhouses, and between symptomatic and nonsymptomatic plants. Further analysis uncovered differentially abundant zero-radius operational taxonomic units (zOTUs) between symptomatic and nonsymptomatic plants. Interestingly, members of Pseudomonas and Flavobacterium were positively associated with symptomatic plants. Overall, this study provides valuable insights into the microbiome of hydroponically cultivated plants and highlights the influence of pathogen invasion on plant-associated microbial communities. Further research is required to elucidate the potential role of Pseudomonas and Flavobacterium spp. in controlling P. cryptogea infections within hydroponically cultivated lettuce greenhouses.}, }
@article {pmid38315121, year = {2024}, author = {Han, K and Li, J and Yang, D and Zhuang, Q and Zeng, H and Rong, C and Yue, J and Li, N and Gu, C and Chen, L and Chen, C}, title = {Detecting horizontal gene transfer with metagenomics co-barcoding sequencing.}, journal = {Microbiology spectrum}, volume = {12}, number = {3}, pages = {e0360223}, pmid = {38315121}, issn = {2165-0497}, support = {2021YFF0703805//MOST | National Key Research and Development Program of China (NKPs)/ ; 82102447//MOST | National Natural Science Foundation of China (NSFC)/ ; DFL20191801//Beijing Hospital Authority/ ; Z201100005520040//Beijing Municipal Science and Technology Commission, Adminitrative Commission of Zhongguancun Science Park/ ; QML20230701//Beijing Hospitals Authority Youth Programme/ ; }, mesh = {Animals ; Humans ; Mice ; *Gene Transfer, Horizontal ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; Bacteria/genetics ; DNA ; }, abstract = {Horizontal gene transfer (HGT) is the process through which genetic information is transferred between different genomes and that played a crucial role in bacterial evolution. HGT can enable bacteria to rapidly acquire antibiotic resistance and bacteria that have acquired resistance is spreading within the microbiome. Conventional methods of characterizing HGT patterns include short-read metagenomic sequencing (short-reads mNGS), long-read sequencing, and single-cell sequencing. These approaches present several limitations, such as short-read fragments, high amounts of input DNA, and sequencing costs, respectively. Here, we attempt to circumvent present limitations to detect HGT by developing a metagenomics co-barcode sequencing workflow (MECOS) and applying it to the human and mouse gut microbiomes. In addition to that, we have over 10-fold increased contig length compared to short-reads mNGS; we also obtained exceeding 30 million paired reads with co-barcode information. Applying the novel bioinformatic pipeline, we integrated this co-barcoding information and the context information from long reads, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Specifically, we detected approximately 3,000 HGT blocks in individual samples, encompassing ~6,000 genes and ~100 taxonomic groups, including loci conferring tetracycline resistance through ribosomal protection. MECOS provides a valuable tool for investigating HGT and advance our understanding on the evolution of natural microbial communities within hosts.IMPORTANCEIn this study, to better identify horizontal gene transfer (HGT) in individual samples, we introduce a new co-barcoding sequencing system called metagenomics co-barcoding sequencing (MECOS), which has three significant improvements: (i) long DNA fragment extraction, (ii) a special transposome insertion, (iii) hybridization of DNA to barcode beads, and (4) an integrated bioinformatic pipeline. Using our approach, we have over 10-fold increased contig length compared to short-reads mNGS, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Our results indicate the presence of approximately 3,000 HGT blocks, involving roughly 6,000 genes and 100 taxonomic groups in individual samples. Notably, these HGT events are predominantly enriched in genes that confer tetracycline resistance via ribosomal protection. MECOS is a useful tool for investigating HGT and the evolution of natural microbial communities within hosts, thereby advancing our understanding of microbial ecology and evolution.}, }
@article {pmid38313259, year = {2024}, author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV}, title = {Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38313259}, issn = {2692-8205}, abstract = {Microbiomes are generally characterized by high diversity of coexisting microbial species and strains that remains stable within a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis obtained, namely, pure competition, host-parasite relationship and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environments. These findings show that basic phenomena that are universal in microbial communities, environmental variation and HGT, provide for stabilization of microbial diversity and ecological complexity.}, }
@article {pmid38312729, year = {2024}, author = {Wang, Y and Long, C and Yin, L and Liu, R and Liao, Y and He, G and Liu, Z}, title = {Effects of simulated acid rain on hydrochemical factors and microbial community structure in red soil aquifers.}, journal = {RSC advances}, volume = {14}, number = {7}, pages = {4482-4491}, pmid = {38312729}, issn = {2046-2069}, abstract = {Acid rain can lower the pH of groundwater and affect its hydrogeochemistry and microbial ecology. However, the effects of acid rain on the hydrogeochemistry and microbial ecology of red soil groundwater systems in southern China are poorly understood. Previous research had mainly investigated the sources and patterns of groundwater acidification, but not the microbial mechanisms that contribute to this process and their associations with hydrochemical factors. To address this knowledge gap, we conducted a soil column experiment to simulate the infiltration of acid rain through various filter materials (coarse, medium, and fine sand) and to examine the hydrochemical and microbial features of the infiltrate, which can reveal how simulated acid rain (pH 3.5-7.0) alters the hydrochemistry and microbial community composition in red soil aquifers. The results showed that the pH of the leachate decreased due to simulated acid rain, and that the leaching efficiency of nitrogen and metal ions was influenced by the particle size of the filter media. Illumina 16S rRNA gene sequencing revealed that the leachate was dominated by Proteobacteria, Patescibacteria, Actinobacteria, and Acidobacteria, with Proteobacteria accounting for 67.04-74.69% of the bacterial community and containing a high proportion of nitrifying and denitrifying bacteria. Additionally, several genera with heavy metal tolerance, such as Burkholderia-Caballeronia-Paraburkholderia, Delftia, Methylversatilis, Aquicella, and Ralstonia, were widely distributed in the leachate, indicating the strong adaptive capacity of the microbial population. A correlation analysis between the hydrochemical factors and the microbial community structure revealed that pH was the most influential factor, followed by NO2[-]-N, Fe, Al, Cu, Mn, and others. These results indicate that acidification modifies the hydrochemical conditions of the aquifer, creating an environment that is unfavorable for microbial growth and survival. However, some microorganisms may acquire resistance genes to cope with environmental changes.}, }
@article {pmid38311160, year = {2024}, author = {Guo, M and Shang, X and Ma, Y and Zhang, K and Zhang, L and Zhou, Y and Gong, Z and Miao, R}, title = {Biochars assisted phytoremediation of polycyclic aromatic hydrocarbons contaminated agricultural soil: Dynamic responses of functional genes and microbial community.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {345}, number = {}, pages = {123476}, doi = {10.1016/j.envpol.2024.123476}, pmid = {38311160}, issn = {1873-6424}, mesh = {*Polycyclic Aromatic Hydrocarbons/analysis ; Soil/chemistry ; Biodegradation, Environmental ; *Soil Pollutants/analysis ; Soil Microbiology ; Bacteria/genetics/metabolism ; *Microbiota ; *Charcoal ; }, abstract = {A biochar-intensified phytoremediation experiment was designed to investigate the dynamic effects of different biochars on polycyclic aromatic hydrocarbon (PAH) removal in ryegrass rhizosphere contaminated soil. Maize and wheat straw biochar pyrolyzed at 300 °C and 500 °C were amended into PAH-contaminated soil, and then ryegrass (Lolium multiflorum L.) was planted for 90 days. Spearman's correlations among PAH removal, enzyme activity, abundance of PAH-ring hydroxylating dioxygenase (PAH-RHDα), and fungal and bacterial community structure were analyzed to elucidate the microbial degradation mechanisms during the combined remediation process. The results showed that 500 °C wheat straw biochar had higher surface area and more nutrients, and significantly accelerated the phytoremediation of PAHs (62.5 %), especially for high molecular weight PAH in contaminated soil. The activities of urease and dehydrogenase and the abundance of total and PAH-degrading bacteria, which improved with time by biochar and ryegrass, had a positive correlation with the removal rate of PAHs. Biochar enhanced the abundance of gram-negative (GN) PAH-RHDα genes. The GN PAH-degraders, Sphingomonas, bacteriap25, Haliangium, and Dongia may play vital roles in PAH degradation in biochar-amended rhizosphere soils. Principal coordinate analysis indicated that biochar led to significant differences in fungal community structures before 30 days, while the diversity of the bacterial community composition depended on planting ryegrass after 60 days. These findings imply that the structural reshaping of microbial communities results from incubation time and the selection of biochar and ryegrass in PAH-contaminated soils. Applying 500 °C wheat straw biochar could enhance the rhizoremediation of PAH-contaminated soil and benefit the soil microbial ecology.}, }
@article {pmid38307852, year = {2024}, author = {Jimonet, P and Druart, C and Blanquet-Diot, S and Boucinha, L and Kourula, S and Le Vacon, F and Maubant, S and Rabot, S and Van de Wiele, T and Schuren, F and Thomas, V and Walther, B and Zimmermann, M and , }, title = {Gut Microbiome Integration in Drug Discovery and Development of Small Molecules.}, journal = {Drug metabolism and disposition: the biological fate of chemicals}, volume = {52}, number = {4}, pages = {274-287}, doi = {10.1124/dmd.123.001605}, pmid = {38307852}, issn = {1521-009X}, mesh = {Animals ; Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Drug Discovery ; Drug Interactions ; }, abstract = {Human microbiomes, particularly in the gut, could have a major impact on the efficacy and toxicity of drugs. However, gut microbial metabolism is often neglected in the drug discovery and development process. Medicen, a Paris-based human health innovation cluster, has gathered more than 30 international leading experts from pharma, academia, biotech, clinical research organizations, and regulatory science to develop proposals to facilitate the integration of microbiome science into drug discovery and development. Seven subteams were formed to cover the complementary expertise areas of 1) pharma experience and case studies, 2) in silico microbiome-drug interaction, 3) in vitro microbial stability screening, 4) gut fermentation models, 5) animal models, 6) microbiome integration in clinical and regulatory aspects, and 7) microbiome ecosystems and models. Each expert team produced a state-of-the-art report of their respective field highlighting existing microbiome-related tools at every stage of drug discovery and development. The most critical limitations are the growing, but still limited, drug-microbiome interaction data to produce predictive models and the lack of agreed-upon standards despite recent progress. In this paper we will report on and share proposals covering 1) how microbiome tools can support moving a compound from drug discovery to clinical proof-of-concept studies and alert early on potential undesired properties stemming from microbiome-induced drug metabolism and 2) how microbiome data can be generated and integrated in pharmacokinetic models that are predictive of the human situation. Examples of drugs metabolized by the microbiome will be discussed in detail to support recommendations from the working group. SIGNIFICANCE STATEMENT: Gut microbial metabolism is often neglected in the drug discovery and development process despite growing evidence of drugs' efficacy and safety impacted by their interaction with the microbiome. This paper will detail existing microbiome-related tools covering every stage of drug discovery and development, current progress, and limitations, as well as recommendations to integrate them into the drug discovery and development process.}, }
@article {pmid38305149, year = {2024}, author = {Mukhia, S and Kumar, A and Kumar, R}, title = {Bacterial community distribution and functional potentials provide key insights into their role in the ecosystem functioning of a retreating Eastern Himalayan glacier.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {3}, pages = {}, pmid = {38305149}, issn = {1574-6941}, support = {45/17/2020-/BIO/BMS//Indian Council of Medical Research/ ; DBT/JRF/BET-17/I/2017/AL/367//Department of Biotechnology/ ; DST/INSPIRE/04/2014/001280//Department of Science and Technology/ ; SRG/2019/001071//Science and Engineering Research Board/ ; }, mesh = {*Ecosystem ; Ice Cover ; Metagenomics ; Bacteria ; Metagenome ; *Microbiota ; Proteobacteria/genetics ; Sulfur/metabolism ; }, abstract = {Himalayan glaciers are receding at an exceptional rate, perturbing the local biome and ecosystem processes. Understanding the microbial ecology of an exclusively microbe-driven biome provides insights into their contributions to the ecosystem functioning through biogeochemical fluxes. Here, we investigated the bacterial communities and their functional potential in the retreating East Rathong Glacier (ERG) of Sikkim Himalaya. Amplicon-based taxonomic classification revealed the dominance of the phyla Proteobacteria, Bacteroidota, and candidate Patescibacteria in the glacial sites. Further, eight good-quality metagenome-assembled genomes (MAGs) of Proteobacteria, Patescibacteria, Acidobacteriota, and Choloflexota retrieved from the metagenomes elucidated the microbial contributions to nutrient cycling. The ERG MAGs showed aerobic respiration as a primary metabolic feature, accompanied by carbon fixation and complex carbon degradation potentials. Pathways for nitrogen metabolism, chiefly dissimilatory nitrate reduction and denitrification, and a complete sulphur oxidation enzyme complex for sulphur metabolism were identified in the MAGs. We observed that DNA repair and oxidative stress response genes complemented with osmotic and periplasmic stress and protein chaperones were vital for adaptation against the intense radiation and stress conditions of the extreme Himalayan niche. Current findings elucidate the microbiome and associated functional potentials of a vulnerable glacier, emphasizing their significant ecological roles in a changing glacial ecosystem.}, }
@article {pmid38305133, year = {2024}, author = {Ramakodi, MP}, title = {Merging and concatenation of sequencing reads: a bioinformatics workflow for the comprehensive profiling of microbiome from amplicon data.}, journal = {FEMS microbiology letters}, volume = {371}, number = {}, pages = {}, doi = {10.1093/femsle/fnae009}, pmid = {38305133}, issn = {1574-6968}, mesh = {RNA, Ribosomal, 18S/genetics ; Workflow ; *Microbiota/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A comprehensive profiling of microbial diversity is essential to understand the ecosystem functions. Universal primer sets such as the 515Y/926R could amplify a part of 16S and 18S rRNA and infer the diversity of prokaryotes and eukaryotes. However, the analyses of mixed sequencing data pose a bioinformatics challenge; the 16S and 18S rRNA sequences need to be separated first and analysed individually/independently due to variations in the amplicon length. This study describes an alternative strategy, a merging and concatenation workflow, to analyse the mixed amplicon data without separating the 16S and 18S rRNA sequences. The workflow was tested with 24 mock community (MC) samples, and the analyses resolved the composition of prokaryotes and eukaryotes adequately. In addition, there was a strong correlation (cor = 0.950; P-value = 4.754e-10) between the observed and expected abundances in the MC samples, which suggests that the computational approach could infer the microbial proportions accurately. Further, 18 samples collected from the Sundarbans mangrove region were analysed as a case study. The analyses identified Proteobacteria, Bacteroidota, Actinobacteriota, Cyanobacteria, and Crenarchaeota as dominant bacterial phyla and eukaryotic divisions such as Metazoa, Gyrista, Cryptophyta, Chlorophyta, and Dinoflagellata were found to be dominant in the samples. Thus, the results support the applicability of the method in environmental microbiome research. The merging and concatenation workflow presented here requires considerably less computational resources and uses widely/commonly used bioinformatics packages, saving researchers analyses time (for equivalent sample numbers, compared to the conventional approach) required to infer the diversity of major microbial domains from mixed amplicon data at comparable accuracy.}, }
@article {pmid38303015, year = {2024}, author = {Mejías-Molina, C and Pico-Tomàs, A and Martínez-Puchol, S and Itarte, M and Torrell, H and Canela, N and Borrego, CM and Corominas, L and Rusiñol, M and Bofill-Mas, S}, title = {Wastewater-based epidemiology applied at the building-level reveals distinct virome profiles based on the age of the contributing individuals.}, journal = {Human genomics}, volume = {18}, number = {1}, pages = {10}, pmid = {38303015}, issn = {1479-7364}, support = {202103-30//Fundaci&#xf3; la Marat&#xf3; de TV3/ ; 202103-30//Fundaci&#xf3; la Marat&#xf3; de TV3/ ; 202103-30//Fundaci&#xf3; la Marat&#xf3; de TV3/ ; 202103-30//Fundaci&#xf3; la Marat&#xf3; de TV3/ ; ICRA-ENV 2017 SGR 1124//Consolidated Research Group grants/ ; ICRA-ENV 2017 SGR 1124//Consolidated Research Group grants/ ; }, mesh = {Humans ; Wastewater ; Wastewater-Based Epidemiological Monitoring ; Virome/genetics ; *Viruses/genetics ; *Virus Diseases ; }, abstract = {BACKGROUND: Human viruses released into the environment can be detected and characterized in wastewater. The study of wastewater virome offers a consolidated perspective on the circulation of viruses within a population. Because the occurrence and severity of viral infections can vary across a person's lifetime, studying the virome in wastewater samples contributed by various demographic segments can provide valuable insights into the prevalence of viral infections within these segments. In our study, targeted enrichment sequencing was employed to characterize the human virome in wastewater at a building-level scale. This was accomplished through passive sampling of wastewater in schools, university settings, and nursing homes in two cities in Catalonia. Additionally, sewage from a large urban wastewater treatment plant was analysed to serve as a reference for examining the collective excreted human virome.<br><br>RESULTS: The virome obtained from influent wastewater treatment plant samples showcased the combined viral presence from individuals of varying ages, with astroviruses and human bocaviruses being the most prevalent, followed by human adenoviruses, polyomaviruses, and papillomaviruses. Significant variations in the viral profiles were observed among the different types of buildings studied. Mamastrovirus 1 was predominant in school samples, salivirus and human polyomaviruses JC and BK in the university settings while nursing homes showed a more balanced distribution of viral families presenting papillomavirus and picornaviruses and, interestingly, some viruses linked to immunosuppression.<br><br>CONCLUSIONS: This study shows the utility of building-level wastewater-based epidemiology as an effective tool for monitoring the presence of viruses circulating within specific age groups. It provides valuable insights for public health monitoring and epidemiological studies.}, }
@article {pmid38302681, year = {2024}, author = {Wdowiak-Wróbel, S and Kalita, M and Palusińska-Szysz, M and Marek-Kozaczuk, M and Sokołowski, W and Coutinho, TA}, title = {Pantoea trifolii sp. nov., a novel bacterium isolated from Trifolium rubens root nodules.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {2698}, pmid = {38302681}, issn = {2045-2322}, support = {PL-RPA2/07/TRIFOMIKRO/2019//Narodowe Centrum Bada&#x144; i Rozwoju/ ; POL180702349288//National Research Foundation/ ; }, mesh = {Sequence Analysis, DNA ; *Pantoea/genetics ; *Trifolium/genetics ; RNA, Ribosomal, 16S/genetics ; DNA ; Phylogeny ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Bacterial Typing Techniques ; Nucleic Acid Hybridization ; }, abstract = {A novel bacterium, designated strain MMK2[T], was isolated from a surface-sterilised root nodule of a Trifolium rubens plant growing in south-eastern Poland. Cells were Gram negative, non-spore forming and rod shaped. The strain had the highest 16S rRNA gene sequence similarity with P. endophytica (99.4%), P. leporis (99.4%) P. rwandensis (98.8%) and P. rodasii (98.45%). Phylogenomic analysis clearly showed that strain MMK2[T] and an additional strain, MMK3, should reside in the genus Pantoea and that they were most closely related to P. endophytica and P. leporis. Genome comparisons showed that the novel strain shared 82.96-93.50% average nucleotide identity and 26.2-53. 2% digital DNA:DNA hybridization with closely related species. Both strains produced siderophores and were able to solubilise phosphates. The MMK2[T] strain was also able to produce indole-3-acetic acid. The tested strains differed in their antimicrobial activity, but both were able to inhibit the growth of Sclerotinia sclerotiorum 10Ss01. Based on the results of the phenotypic, phylogenomic, genomic and chemotaxonomic analyses, strains MMK2[T] and MMK3 belong to a novel species in the genus Pantoea for which the name Pantoea trifolii sp. nov. is proposed with the type strain MMK2[T] (= DSM 115063[T] = LMG 33049[T]).}, }
@article {pmid38302544, year = {2024}, author = {Prasoodanan P K, V and Kumar, S and Dhakan, DB and Waiker, P and Saxena, R and Sharma, VK}, title = {Metagenomic exploration of Andaman region of the Indian Ocean.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {2717}, pmid = {38302544}, issn = {2045-2322}, mesh = {Indian Ocean ; *Ecosystem ; RNA, Ribosomal, 16S/genetics ; Metagenome ; *Microbiota/genetics ; Water ; Seawater ; }, abstract = {Ocean microbiome is crucial for global biogeochemical cycles and primary productivity. Despite numerous studies investigating the global ocean microbiomes, the microbiome composition of the Andaman region of the Indian Ocean remains largely unexplored. While this region harbors pristine biological diversity, the escalating anthropogenic activities along coastal habitats exert an influence on the microbial ecology and impact the aquatic ecosystems. We investigated the microbiome composition in the coastal waters of the Andaman Islands by 16S rRNA gene amplicon and metagenomic shotgun sequencing approaches and compared it with the Tara Oceans Consortium. In the coastal waters of the Andaman Islands, a significantly higher abundance and diversity of Synechococcus species was observed with a higher abundance of photosynthesis pigment-related genes to adapt to variable light conditions and nutrition. In contrast, Prochlorococcus species showed higher abundance in open ocean water samples of the Indian Ocean region, with a relatively limited functional diversity. A higher abundance of antibiotic-resistance genes was also noted in the coastal waters region. We also updated the ocean microbiome gene catalog with 93,172 unique genes from the Andaman coastal water microbiome. This study provides valuable insights into the Indian Ocean microbiome and supplements the global marine microbial ecosystem studies.}, }
@article {pmid38299778, year = {2024}, author = {León-Sobrino, C and Ramond, JB and Coclet, C and Kapitango, RM and Maggs-Kölling, G and Cowan, DA}, title = {Temporal dynamics of microbial transcription in wetted hyperarid desert soils.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {3}, pages = {}, pmid = {38299778}, issn = {1574-6941}, support = {113308//University of Pretoria/ ; }, mesh = {*Ecosystem ; Soil ; Desert Climate ; Soil Microbiology ; *Microbiota/genetics ; Water ; RNA, Messenger ; }, abstract = {Rainfall is rare in hyperarid deserts but, when it occurs, it triggers large biological responses essential for the long-term maintenance of the ecosystem. In drylands, microbes play major roles in nutrient cycling, but their responses to short-lived opportunity windows are poorly understood. Due to its ephemeral nature, mRNA is ideally suited to study microbiome dynamics upon abrupt changes in the environment. We analyzed microbial community transcriptomes after simulated rainfall in a Namib Desert soil over 7 days. Using total mRNA from dry and watered plots we infer short-term functional responses in the microbiome. A rapid two-phase cycle of activation and return to basal state was completed in a short period. Motility systems activated immediately, whereas competition-toxicity increased in parallel to predator taxa and the drying of soils. Carbon fixation systems were downregulated, and reactivated upon return to a near-dry state. The chaperone HSP20 was markedly regulated by watering across all major bacteria, suggesting a particularly important role in adaptation to desiccated ecosystems. We show that transcriptomes provide consistent and high resolution information on microbiome processes in a low-biomass environment, revealing shared patterns across taxa. We propose a structured dispersal-predation dynamic as a central driver of desert microbial responses to rainfall.}, }
@article {pmid38297006, year = {2024}, author = {Maza-Márquez, P and Lee, MD and Bebout, BM}, title = {Community ecology and functional potential of bacteria, archaea, eukarya and viruses in Guerrero Negro microbial mat.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {2561}, pmid = {38297006}, issn = {2045-2322}, mesh = {Archaea/genetics ; Bacteria/genetics ; Eukaryota/genetics ; Phylogeny ; Viruses/genetics ; *Microbiota ; }, abstract = {In this study, the microbial ecology, potential environmental adaptive mechanisms, and the potential evolutionary interlinking of genes between bacterial, archaeal and viral lineages in Guerrero Negro (GN) microbial mat were investigated using metagenomic sequencing across a vertical transect at millimeter scale. The community composition based on unique genes comprised bacteria (98.01%), archaea (1.81%), eukarya (0.07%) and viruses (0.11%). A gene-focused analysis of bacteria archaea, eukarya and viruses showed a vertical partition of the community. The greatest coverages of genes of bacteria and eukarya were detected in first layers, while the highest coverages of genes of archaea and viruses were found in deeper layers. Many genes potentially related to adaptation to the local environment were detected, such as UV radiation, multidrug resistance, oxidative stress, heavy metals, salinity and desiccation. Those genes were found in bacterial, archaeal and viral lineages with 6477, 44, and 1 genes, respectively. The evolutionary histories of those genes were studied using phylogenetic analysis, showing an interlinking between domains in GN mat.}, }
@article {pmid38296863, year = {2024}, author = {Bååth, E and Kritzberg, ES}, title = {Temperature Adaptation of Aquatic Bacterial Community Growth Is Faster in Response to Rising than to Falling Temperature.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {38}, pmid = {38296863}, issn = {1432-184X}, mesh = {Temperature ; *Cold Temperature ; *Lakes ; Bacteria/metabolism ; Seasons ; }, abstract = {Bacteria are key organisms in energy and nutrient cycles, and predicting the effects of temperature change on bacterial activity is important in assessing global change effects. A changing in situ temperature will affect the temperature adaptation of bacterial growth in lake water, both long term in response to global change, and short term in response to seasonal variations. The rate of adaptation may, however, depend on whether temperature is increasing or decreasing, since bacterial growth and turnover scale with temperature. Temperature adaptation was studied for winter (in situ temperature 2.5 °C) and summer communities (16.5 °C) from a temperate lake in Southern Sweden by exposing them to a temperature treatment gradient between 0 and 30 °C in ~ 5 °C increments. This resulted mainly in a temperature increase for the winter and a decrease for the summer community. Temperature adaptation of bacterial community growth was estimated as leucine incorporation using a temperature Sensitivity Index (SI, log growth at 35 °C/4 °C), where higher values indicate adaptation to higher temperatures. High treatment temperatures resulted in higher SI within days for the winter community, resulting in an expected level of community adaptation within 2 weeks. Adaptation for the summer community was also correlated to treatment temperature, but the rate of adaption was slower. Even after 5 weeks, the bacterial community had not fully adapted to the lowest temperature conditions. Thus, during periods of increasing temperature, the bacterial community will rapidly adapt to function optimally, while decreasing temperature may result in long periods of non-optimal functioning.}, }
@article {pmid38294246, year = {2024}, author = {Kashani, M and Engle, MA and Kent, DB and Gregston, T and Cozzarelli, IM and Mumford, AC and Varonka, MS and Harris, CR and Akob, DM}, title = {Illegal dumping of oil and gas wastewater alters arid soil microbial communities.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {2}, pages = {e0149023}, pmid = {38294246}, issn = {1098-5336}, support = {//DOI | U.S. Geological Survey (USGS)/ ; }, mesh = {*Wastewater ; Soil Microbiology ; Soil/chemistry ; Phylogeny ; Desert Climate ; *Microbiota ; Hydrocarbons ; }, abstract = {The Permian Basin, underlying southeast New Mexico and west Texas, is one of the most productive oil and gas (OG) provinces in the United States. Oil and gas production yields large volumes of wastewater with complex chemistries, and the environmental health risks posed by these OG wastewaters on sensitive desert ecosystems are poorly understood. Starting in November 2017, 39 illegal dumps, as defined by federal and state regulations, of OG wastewater were identified in southeastern New Mexico, releasing ~600,000 L of fluid onto dryland soils. To evaluate the impacts of these releases, we analyzed changes in soil geochemistry and microbial community composition by comparing soils from within OG wastewater dump-affected samples to unaffected zones. We observed significant changes in soil geochemistry for all dump-affected compared with control samples, reflecting the residual salts and hydrocarbons from the OG-wastewater release (e.g., enriched in sodium, chloride, and bromide). Microbial community structure significantly (P < 0.01) differed between dump and control zones, with soils from dump areas having significantly (P < 0.01) lower alpha diversity and differences in phylogenetic composition. Dump-affected soil samples showed an increase in halophilic and halotolerant taxa, including members of the Marinobacteraceae, Halomonadaceae, and Halobacteroidaceae, suggesting that the high salinity of the dumped OG wastewater was exerting a strong selective pressure on microbial community structure. Taxa with high similarity to known hydrocarbon-degrading organisms were also detected in the dump-affected soil samples. Overall, this study demonstrates the potential for OG wastewater exposure to change the geochemistry and microbial community dynamics of arid soils.IMPORTANCEThe long-term environmental health impacts resulting from releases of oil and gas (OG) wastewater, typically brines with varying compositions of ions, hydrocarbons, and other constituents, are understudied. This is especially true for sensitive desert ecosystems, where soil microbes are key primary producers and drivers of nutrient cycling. We found that releases of OG wastewater can lead to shifts in microbial community composition and function toward salt- and hydrocarbon-tolerant taxa that are not typically found in desert soils, thus altering the impacted dryland soil ecosystem. Loss of key microbial taxa, such as those that catalyze organic carbon cycling, increase arid soil fertility, promote plant health, and affect soil moisture retention, could result in cascading effects across the sensitive desert ecosystem. By characterizing environmental changes due to releases of OG wastewater to soils overlying the Permian Basin, we gain further insights into how OG wastewater may alter dryland soil microbial functions and ecosystems.}, }
@article {pmid38293374, year = {2024}, author = {Choi, YJ and Lim, JY and Kang, MJ and Choi, JY and Yang, JH and Chung, YB and Park, SH and Min, SG and Lee, MA}, title = {Changes in bacterial composition and metabolite profiles during kimchi fermentation with different garlic varieties.}, journal = {Heliyon}, volume = {10}, number = {2}, pages = {e24283}, pmid = {38293374}, issn = {2405-8440}, abstract = {Garlic, a key ingredient in kimchi, is an indispensable source of lactic acid bacteria, which are essential for fermentation. This study explored the effects of various garlic varieties on kimchi fermentation, focusing on changes in microbial communities and metabolite profiles. We observed that the type of garlic used did not significantly alter the microbial community. However, the presence of garlic itself made a significant difference. Specifically, kimchi with garlic showed higher abundance of Leuconostoc and Weissella, which are bacteria primarily responsible for kimchi fermentation. Additionally, kimchi containing garlic had increased levels of mannitol and fructose, which significantly influence taste; however, lactic acid and putrescine levels were decreased. Therefore, the addition of garlic directly contributes to the flavor profile of kimchi. Sixty-two metabolites were identified using gas chromatography and mass spectrometry. The variety of garlic added influenced the metabolite profiles of kimchi, particularly in the later stages of fermentation. These profiles were categorized based on the garlic's origin, whether from southern or northern ecotypes (R[2]X = 0.933, R[2]Y = 0.986, Q[2] = 0.878). These findings confirm that both the presence and the variety of garlic significantly impact the microbial ecology and metabolites during kimchi fermentation, underscoring its essential role in the process.}, }
@article {pmid38293109, year = {2024}, author = {Leleiwi, I and Kokkinias, K and Kim, Y and Baniasad, M and Shaffer, M and Sabag-Daigle, A and Daly, RA and Flynn, RM and Wysocki, VH and Ahmer, BMM and Borton, MA and Wrighton, KC}, title = {Gut microbiome carbon and sulfur metabolisms support Salmonella during pathogen infection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.01.16.575907}, pmid = {38293109}, issn = {2692-8205}, abstract = {Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and an ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting the microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome, here we performed multi-omics approaches on fecal microbial communities from untreated and Salmonella -infected mice. Reconstructed genomes recruited metatranscriptomic and metabolomic data providing a strain-resolved view of the expressed metabolisms of the microbiome during Salmonella infection. This data informed possible Salmonella interactions with members of the gut microbiome that were previously uncharacterized. Salmonella- induced inflammation significantly reduced the diversity of transcriptionally active members in the gut microbiome, yet increased gene expression was detected for 7 members, with Luxibacter and Ligilactobacillus being the most active. Metatranscriptomic insights from Salmonella and other persistent taxa in the inflamed microbiome further expounded the necessity for oxidative tolerance mechanisms to endure the host inflammatory responses to infection. In the inflamed gut lactate was a key metabolite, with microbiota production and consumption reported amongst transcriptionally active members. We also showed that organic sulfur sources could be converted by gut microbiota to yield inorganic sulfur pools that become oxidized in the inflamed gut, resulting in thiosulfate and tetrathionate that supports Salmonella respiration. Advancement of pathobiome understanding beyond inferences from prior amplicon-based approaches can hold promise for infection mitigation, with the active community outlined here offering intriguing organismal and metabolic therapeutic targets.}, }
@article {pmid38289133, year = {2024}, author = {Op De Beeck, M and Troein, C and Peterson, C and Tunlid, A and Persson, P}, title = {Elucidating fungal decomposition of organic matter at sub-micrometer spatial scales using optical photothermal infrared (O-PTIR) microspectroscopy.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {2}, pages = {e0148923}, pmid = {38289133}, issn = {1098-5336}, support = {2020-04293//Vetenskapsr&#xe5;det (VR)/ ; 2021-05188//Vetenskapsr&#xe5;det (VR)/ ; }, mesh = {*Basidiomycota ; *Mycorrhizae ; Hyphae ; Cellulose ; Spectrophotometry, Infrared/methods ; }, abstract = {In microbiological studies, a common goal is to link environmental factors to microbial activities. Both environmental factors and microbial activities are typically derived from bulk samples. It is becoming increasingly clear that such bulk environmental parameters poorly represent the microscale environments microorganisms experience. Using infrared (IR) microspectroscopy, the spatial distribution of chemical compound classes can be visualized, making it a useful tool for studying the interactions between microbial cells and their microenvironments. The spatial resolution of conventional IR microspectroscopy has been limited by the diffraction limit of IR light. The recent development of optical photothermal infrared (O-PTIR) microspectroscopy has pushed the spatial resolution of IR microspectroscopy beyond this diffraction limit, allowing the distribution of chemical compound classes to be visualized at sub-micrometer spatial scales. To examine the potential and limitations of O-PTIR microspectroscopy to probe the interactions between fungal cells and their immediate environments, we imaged the decomposition of cellulose films by cells of the ectomycorrhizal fungus Paxillus involutus and compared O-PTIR results using conventional IR microspectroscopy. Whereas the data collected with conventional IR microspectroscopy indicated that P. involutus has only a very limited ability to decompose cellulose films, O-PTIR data suggested that the ability of P. involutus to decompose cellulose was substantial. Moreover, the O-PTIR method enabled the identification of a zone located outside the fungal hyphae where the cellulose was decomposed by oxidation. We conclude that O-PTIR can provide valuable new insights into the abilities and mechanisms by which microorganisms interact with their surrounding environments.IMPORTANCEInfrared (IR) microspectroscopy allows the spatial distribution of chemical compound classes to be visualized. The use of conventional IR microspectroscopy in microbiological studies has been restricted by limited spatial resolution. Recent developments in laser technology have enabled a new class of IR microspectroscopy instruments to be developed, pushing the spatial resolution beyond the diffraction limit of IR light to approximately 500 nm. This improved spatial resolution now allows microscopic observations of changes in chemical compounds to be made, making IR microspectroscopy a useful tool to investigate microscale changes in chemistry that are caused by microbial activity. We show these new possibilities using optical photothermal infrared microspectroscopy to visualize the changes in cellulose substrates caused by oxidation by the ectomycorrhizal fungus Paxillus involutus at the interface between individual fungal hyphae and cellulose substrates.}, }
@article {pmid38289092, year = {2024}, author = {Bontemps, Z and Moënne-Loccoz, Y and Hugoni, M}, title = {Stochastic and deterministic assembly processes of microbial communities in relation to natural attenuation of black stains in Lascaux Cave.}, journal = {mSystems}, volume = {9}, number = {2}, pages = {e0123323}, pmid = {38289092}, issn = {2379-5077}, support = {//DRAC Nouvelle Aquitaine/ ; }, mesh = {*Coloring Agents ; *Microbiota ; Caves ; }, abstract = {Community assembly processes are complex and understanding them represents a challenge in microbial ecology. Here, we used Lascaux Cave as a stable, confined environment to quantify the importance of stochastic vs deterministic processes during microbial community dynamics across the three domains of life in relation to an anthropogenic disturbance that had resulted in the side-by-side occurrence of a resistant community (unstained limestone), an impacted community (present in black stains), and a resilient community (attenuated stains). Metabarcoding data showed that the microbial communities of attenuated stains, black stains, and unstained surfaces differed, with attenuated stains being in an intermediate position. We found four scenarios to explain community response to disturbance in stable conditions for the three domains of life. Specifically, we proposed the existence of a fourth, not-documented yet scenario that concerns the always-rare microbial taxa, where stochastic processes predominate even after disturbance but are replaced by deterministic processes during post-disturbance recovery. This suggests a major role of always-rare taxa in resilience, perhaps because they might provide key functions required for ecosystem recovery.IMPORTANCEThe importance of stochastic vs deterministic processes in cave microbial ecology has been a neglected topic so far, and this work provided an opportunity to do so in a context related to the dynamics of black-stain alterations in Lascaux, a UNESCO Paleolithic cave. Of particular significance was the discovery of a novel scenario for always-rare microbial taxa in relation to disturbance, in which stochastic processes are replaced later by deterministic processes during post-disturbance recovery, i.e., during attenuation of black stains.}, }
@article {pmid38286834, year = {2024}, author = {Wang, X and Liu, Y and Qing, C and Zeng, J and Dong, J and Xia, P}, title = {Analysis of diversity and function of epiphytic bacterial communities associated with macrophytes using a metagenomic approach.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {37}, pmid = {38286834}, issn = {1432-184X}, mesh = {*Ecosystem ; Lakes ; Metagenome ; Bacteria/genetics/metabolism ; *Potamogetonaceae/genetics/microbiology ; Nitrogen/metabolism ; }, abstract = {Epiphytic bacteria constitute a vital component of aquatic ecosystems, pivotal in regulating elemental cycling. Despite their significance, the diversity and functions of epiphytic bacterial communities adhering to various submerged macrophytes remain largely unexplored. In this study, we employed a metagenomic approach to investigate the diversity and function of epiphytic bacterial communities associated with six submerged macrophytes: Ceratophyllum demersum, Hydrilla verticillata, Myriophyllum verticillatum, Potamogeton lucens, Stuckenia pectinata, and Najas marina. The results revealed that the predominant epiphytic bacterial species for each plant type included Pseudomonas spp., Microbacterium spp., and Stenotrophomonas rhizophila. Multiple comparisons and linear discriminant analysis effect size indicated a significant divergence in the community composition of epiphytic bacteria among the six submerged macrophytes, with 0.3-1% of species uniquely identified. Epiphytic bacterial richness associated with S. pectinata significantly differed from that of both C. demersum and H. verticillata, although no significant differences were observed in diversity and evenness. Functionally, notable variations were observed in the relative abundances of genes associated with carbon, nitrogen, and phosphorus cycling within epiphytic bacterial communities on the submerged macrophyte hosts. Among these communities, H. verticillata exhibited enrichment in genes related to the 3-hydroxypropionate bicycle and nitrogen assimilation, translocation, and denitrification. Conversely, M. verticillatum showcased enrichment in genes linked to the reductive citric acid cycle (Arnon-Buchanan cycle), reductive pentose phosphate cycle (Calvin cycle), polyphosphate degradation, and organic nitrogen metabolism. In summary, our findings offer valuable insights into the diversity and function of epiphytic bacteria on submerged macrophyte leaves, shedding light on their roles in lake ecosystems.}, }
@article {pmid38286067, year = {2024}, author = {Lamprea-Pineda, PA and Demeestere, K and González-Cortés, JJ and Boon, N and Devlieghere, F and Van Langenhove, H and Walgraeve, C}, title = {Addition of (bio)surfactants in the biofiltration of hydrophobic volatile organic compounds in air.}, journal = {Journal of environmental management}, volume = {353}, number = {}, pages = {120132}, doi = {10.1016/j.jenvman.2024.120132}, pmid = {38286067}, issn = {1095-8630}, mesh = {Humans ; Surface-Active Agents/chemistry ; *Volatile Organic Compounds ; Hexanes ; Polysorbates ; Cyclohexanes ; *Saponins ; Filtration/methods ; }, abstract = {The removal of volatile organic compounds (VOCs) in air is of utmost importance to safeguard both environmental quality and human well-being. However, the low aqueous solubility of hydrophobic VOCs results in poor removal in waste gas biofilters (BFs). In this study, we evaluated the addition of (bio)surfactants in three BFs (BF1 and BF2 mixture of compost and wood chips (C + WC), and BF3 filled with expanded perlite) to enhance the removal of cyclohexane and hexane from a polluted gas stream. Experiments were carried out to select two (bio)surfactants (i.e., Tween 80 and saponin) out of five (sodium dodecyl sulfate (SDS), Tween 80, surfactin, rhamnolipid and saponin) from a physical-chemical (i.e., decreasing VOC gas-liquid partitioning) and biological (i.e., the ability of the microbial consortium to grow on the (bio)surfactants) point of view. The results show that adding Tween 80 at 1 critical micelle concentration (CMC) had a slight positive effect on the removal of both VOCs, in BF1 (e.g., 7.0 ± 0.6 g cyclohexane m[-3] h[-1], 85 ± 2% at 163 s; compared to 6.7 ± 0.4 g cyclohexane m[-3] h[-1], 76 ± 2% at 163 s and 0 CMC) and BF2 (e.g., 4.3 ± 0.4 g hexane m[-3] h[-1], 27 ± 2% at 82 s; compared to 3.1 ± 0.7 g hexane m[-3] h[-1], 16 ± 4% at 82 s and 0 CMC), but a negative effect in BF3 at either 1, 3 and 9 CMC (e.g., 2.4 ± 0.4 g hexane m[-3] h[-1], 30 ± 4% at 163 s and 1 CMC; compared to 4.6 ± 1.0 g hexane m[-3] h[-1], 43 ± 8% at 163 s and 0 CMC). In contrast, the performance of all BFs improved with the addition of saponin, particularly at 3 CMC. Notably, in BF3, the elimination capacity (EC) and removal efficiency (RE) doubled for both VOCs (i.e., 9.1 ± 0.6 g cyclohexane m[-3] h[-1], 49 ± 3%; 4.3 ± 0.3 g hexane m[-3] h[-1], 25 ± 3%) compared to no biosurfactant addition (i.e., 4.5 ± 0.4 g cyclohexane m[-3] h[-1], 23 ± 3%; hexane 2.2 ± 0.5 g m[-3] h[-1], 10 ± 2%) at 82 s. Moreover, the addition of the (bio)surfactants led to a shift in the microbial consortia, with a different response in BF1-BF2 compared to BF3. This study evaluates for the first time the use of saponin in BFs, it demonstrates that cyclohexane and hexane RE can be improved by (bio)surfactant addition, and it provides recommendations for future studies in this field.}, }
@article {pmid38282644, year = {2024}, author = {Schauberger, C and Thamdrup, B and Lemonnier, C and Trouche, B and Poulain, J and Wincker, P and Arnaud-Haond, S and Glud, RN and Maignien, L}, title = {Metagenome-assembled genomes of deep-sea sediments: changes in microbial functional potential lag behind redox transitions.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycad005}, pmid = {38282644}, issn = {2730-6151}, abstract = {Hadal sediments are hotspots of microbial activity in the deep sea and exhibit strong biogeochemical gradients. But although these gradients are widely assumed to exert selective forces on hadal microbial communities, the actual relationship between biogeochemistry, functional traits, and microbial community structure remains poorly understood. We tested whether the biogeochemical conditions in hadal sediments select for microbes based on their genomic capacity for respiration and carbohydrate utilization via a metagenomic analysis of over 153 samples from the Atacama Trench region (max. depth = 8085 m). The obtained 1357 non-redundant microbial genomes were affiliated with about one-third of all known microbial phyla, with more than half belonging to unknown genera. This indicated that the capability to withstand extreme hydrostatic pressure is a phylogenetically widespread trait and that hadal sediments are inhabited by diverse microbial lineages. Although community composition changed gradually over sediment depth, these changes were not driven by selection for respiratory or carbohydrate degradation capability in the oxic and nitrogenous zones, except in the case of anammox bacteria and nitrifying archaea. However, selection based on respiration and carbohydrate degradation capacity did structure the communities of the ferruginous zone, where aerobic and nitrogen respiring microbes declined exponentially (half-life = 125-419 years) and were replaced by subsurface communities. These results highlight a delayed response of microbial community composition to selective pressure imposed by redox zonation and indicated that gradual changes in microbial composition are shaped by the high-resilience and slow growth of microbes in the seafloor.}, }
@article {pmid38281398, year = {2024}, author = {Van Peteghem, L and Sakarika, M and Matassa, S and Pikaar, I and Ganigué, R and Rabaey, K}, title = {Corrigendum to "Towards new carbon-neutral food systems: Combining carbon capture and utilization with microbial protein production" [Bioresour. Technol. 349 (2022) 126853].}, journal = {Bioresource technology}, volume = {395}, number = {}, pages = {130362}, doi = {10.1016/j.biortech.2024.130362}, pmid = {38281398}, issn = {1873-2976}, }
@article {pmid38280409, year = {2024}, author = {Yao, S and Swanson, CS and Cheng, Z and He, Q and Yuan, H}, title = {Alternating polarity as a novel strategy for building synthetic microbial communities capable of robust Electro-Methanogenesis.}, journal = {Bioresource technology}, volume = {395}, number = {}, pages = {130374}, doi = {10.1016/j.biortech.2024.130374}, pmid = {38280409}, issn = {1873-2976}, mesh = {RNA, Ribosomal, 16S/genetics ; Biofuels ; Charcoal ; Bayes Theorem ; *Microbiota ; *Euryarchaeota/genetics ; Methane ; }, abstract = {Electro-methanogenic microbial communities can produce biogas with high efficiency and have attracted extensive research interest. In this study an alternating polarity strategy was developed to build electro-methanogenic communities. In two-chamber bioelectrochemical systems amended with activated carbon, the electrode potential was alternated between +0.8 V and -0.4 V vs. standard hydrogen electrode every three days. Cumulative biogas production under alternating polarity increased from 45 L/L/kg-activated carbon after start-up to 125 L/L/kg after the 4th enrichment, significantly higher than that under intermittent cathode (-0.4 V/open circuit), continuous cathode (-0.4 V), and open circuit. The communities assembled under alternating polarity were electroactive and structurally different from those assembled under other conditions. One Methanobacterium population and two Geobacter populations were consistently abundant and active in the communities. Their 16S rRNA was up-regulated by electrode potentials. Bayesian networks inferred close associations between these populations. Overall, electro-methanogenic communities have been successfully assembled with alternating polarity.}, }
@article {pmid38279257, year = {2024}, author = {Córdova-Espinoza, MG and González-Vázquez, R and Barron-Fattel, RR and Gónzalez-Vázquez, R and Vargas-Hernández, MA and Albores-Méndez, EM and Esquivel-Campos, AL and Mendoza-Pérez, F and Mayorga-Reyes, L and Gutiérrez-Nava, MA and Medina-Quero, K and Escamilla-Gutiérrez, A}, title = {Aptamers: A Cutting-Edge Approach for Gram-Negative Bacterial Pathogen Identification.}, journal = {International journal of molecular sciences}, volume = {25}, number = {2}, pages = {}, pmid = {38279257}, issn = {1422-0067}, mesh = {Humans ; *Aptamers, Nucleotide ; SELEX Aptamer Technique ; Gram-Negative Bacteria/genetics ; Bacteria ; *Communicable Diseases ; }, abstract = {Early and accurate diagnoses of pathogenic microorganisms is essential to correctly identify diseases, treating infections, and tracking disease outbreaks associated with microbial infections, to develop precautionary measures that allow a fast and effective response in epidemics and pandemics, thus improving public health. Aptamers are a class of synthetic nucleic acid molecules with the potential to be used for medical purposes, since they can be directed towards any target molecule. Currently, the use of aptamers has increased because they are a useful tool in the detection of specific targets. We present a brief review of the use of aptamers to detect and identify bacteria or even some toxins with clinical importance. This work describes the advances in the technology of aptamers, with the purpose of providing knowledge to develop new aptamers for diagnoses and treatment of different diseases caused by infectious microorganisms.}, }
@article {pmid38278954, year = {2024}, author = {Ma, X and Vanneste, S and Chang, J and Ambrosino, L and Barry, K and Bayer, T and Bobrov, AA and Boston, L and Campbell, JE and Chen, H and Chiusano, ML and Dattolo, E and Grimwood, J and He, G and Jenkins, J and Khachaturyan, M and Marín-Guirao, L and Mesterházy, A and Muhd, DD and Pazzaglia, J and Plott, C and Rajasekar, S and Rombauts, S and Ruocco, M and Scott, A and Tan, MP and Van de Velde, J and Vanholme, B and Webber, J and Wong, LL and Yan, M and Sung, YY and Novikova, P and Schmutz, J and Reusch, TBH and Procaccini, G and Olsen, JL and Van de Peer, Y}, title = {Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment.}, journal = {Nature plants}, volume = {10}, number = {2}, pages = {240-255}, pmid = {38278954}, issn = {2055-0278}, support = {833522/ERC_/European Research Council/International ; }, mesh = {*Alismatales/genetics ; *Zosteraceae/genetics ; Ecosystem ; }, abstract = {We present chromosome-level genome assemblies from representative species of three independently evolved seagrass lineages: Posidonia oceanica, Cymodocea nodosa, Thalassia testudinum and Zostera marina. We also include a draft genome of Potamogeton acutifolius, belonging to a freshwater sister lineage to Zosteraceae. All seagrass species share an ancient whole-genome triplication, while additional whole-genome duplications were uncovered for C. nodosa, Z. marina and P. acutifolius. Comparative analysis of selected gene families suggests that the transition from submerged-freshwater to submerged-marine environments mainly involved fine-tuning of multiple processes (such as osmoregulation, salinity, light capture, carbon acquisition and temperature) that all had to happen in parallel, probably explaining why adaptation to a marine lifestyle has been exceedingly rare. Major gene losses related to stomata, volatiles, defence and lignification are probably a consequence of the return to the sea rather than the cause of it. These new genomes will accelerate functional studies and solutions, as continuing losses of the 'savannahs of the sea' are of major concern in times of climate change and loss of biodiversity.}, }
@article {pmid38278226, year = {2024}, author = {Sabrekov, AF and Semenov, MV and Terentieva, IE and Krasnov, GS and Kharitonov, SL and Glagolev, MV and Litti, YV}, title = {Anaerobic methane oxidation is quantitatively important in deeper peat layers of boreal peatlands: Evidence from anaerobic incubations, in situ stable isotopes depth profiles, and microbial communities.}, journal = {The Science of the total environment}, volume = {916}, number = {}, pages = {170213}, doi = {10.1016/j.scitotenv.2024.170213}, pmid = {38278226}, issn = {1879-1026}, mesh = {*Carbon Dioxide/analysis ; Anaerobiosis ; Methane/metabolism ; Soil ; RNA, Ribosomal, 16S ; Acetates ; *Microbiota ; Isotopes ; }, abstract = {Boreal peatlands store most of their carbon in layers deeper than 0.5 m under anaerobic conditions, where carbon dioxide and methane are produced as terminal products of organic matter degradation. Since the global warming potential of methane is much greater than that of carbon dioxide, the balance between the production rates of these gases is important for future climate predictions. Herein, we aimed to understand whether anaerobic methane oxidation (AMO) could explain the high CO2/CH4 anaerobic production ratios that are widely observed for the deeper peat layers of boreal peatlands. Furthermore, we quantified the metabolic pathways of methanogenesis to examine whether hydrogenotrophic methanogenesis is a dominant methane production pathway for the presumably recalcitrant deeper peat. To assess the CH4 cycling in deeper peat, we combined laboratory anaerobic incubations with a pathway-specific inhibitor, in situ depth patterns of stable isotopes in CH4, and 16S rRNA gene amplicon sequencing for three representative boreal peatlands in Western Siberia. We found up to a 69 % reduction in CH4 production due to AMO, which largely explained the high CO2/CH4 anaerobic production ratios and the in situ depth-related patterns of δ[13]C and δD in methane. The absence of acetate accumulation after inhibiting acetotrophic methanogenesis and the presence of sulfate- and nitrate-reducing anaerobic acetate oxidizers in the deeper peat indicated that these microorganisms use SO4[2-] and NO3[-] as electron acceptors. Acetotrophic methanogenesis dominated net CH4 production in the deeper peat, accounting for 81 ± 13 %. Overall, anaerobic oxidation is quantitatively important for the methane cycle in the deeper layers of boreal peatlands, affecting both methane and its main precursor concentrations.}, }
@article {pmid38276724, year = {2024}, author = {Hassan, Z and Westerhoff, HV}, title = {Arsenic Contamination of Groundwater Is Determined by Complex Interactions between Various Chemical and Biological Processes.}, journal = {Toxics}, volume = {12}, number = {1}, pages = {}, pmid = {38276724}, issn = {2305-6304}, abstract = {At a great many locations worldwide, the safety of drinking water is not assured due to pollution with arsenic. Arsenic toxicity is a matter of both systems chemistry and systems biology: it is determined by complex and intertwined networks of chemical reactions in the inanimate environment, in microbes in that environment, and in the human body. We here review what is known about these networks and their interconnections. We then discuss how consideration of the systems aspects of arsenic levels in groundwater may open up new avenues towards the realization of safer drinking water. Along such avenues, both geochemical and microbiological conditions can optimize groundwater microbial ecology vis-à-vis reduced arsenic toxicity.}, }
@article {pmid38275746, year = {2023}, author = {Seppi, M and Pasqualini, J and Facchin, S and Savarino, EV and Suweis, S}, title = {Emergent Functional Organization of Gut Microbiomes in Health and Diseases.}, journal = {Biomolecules}, volume = {14}, number = {1}, pages = {}, pmid = {38275746}, issn = {2218-273X}, mesh = {Humans ; *Gastrointestinal Microbiome ; Dysbiosis ; *Microbiota ; Metagenome ; Metagenomics ; }, abstract = {Continuous and significant progress in sequencing technologies and bioinformatics pipelines has revolutionized our comprehension of microbial communities, especially for human microbiomes. However, most studies have focused on studying the taxonomic composition of the microbiomes and we are still not able to characterize dysbiosis and unveil the underlying ecological consequences. This study explores the emergent organization of functional abundances and correlations of gut microbiomes in health and disease. Leveraging metagenomic sequences, taxonomic and functional tables are constructed, enabling comparative analysis. First, we show that emergent taxonomic and functional patterns are not useful to characterize dysbiosis. Then, through differential abundance analyses applied to functions, we reveal distinct functional compositions in healthy versus unhealthy microbiomes. In addition, we inquire into the functional correlation structure, revealing significant differences between the healthy and unhealthy groups, which may significantly contribute to understanding dysbiosis. Our study demonstrates that scrutinizing the functional organization in the microbiome provides novel insights into the underlying state of the microbiome. The shared data structure underlying the functional and taxonomic compositions allows for a comprehensive macroecological examination. Our findings not only shed light on dysbiosis, but also underscore the importance of studying functional interrelationships for a nuanced understanding of the dynamics of the microbial community. This research proposes a novel approach, bridging the gap between microbial ecology and functional analyses, promising a deeper understanding of the intricate world of the gut microbiota and its implications for human health.}, }
@article {pmid38274012, year = {2023}, author = {Ulčar, B and Regueira, A and Podojsteršek, M and Boon, N and Ganigué, R}, title = {Why do lactic acid bacteria thrive in chain elongation microbiomes?.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {11}, number = {}, pages = {1291007}, pmid = {38274012}, issn = {2296-4185}, abstract = {Efficient waste management is necessary to transition towards a more sustainable society. An emerging trend is to use mixed culture biotechnology to produce chemicals from organic waste. Insights into the metabolic interactions between community members and their growth characterization are needed to mediate knowledge-driven bioprocess development and optimization. Here, a granular sludge bioprocess for the production of caproic acid through sugar-based chain elongation metabolism was established. Lactic acid and chain-elongating bacteria were identified as the two main functional guilds in the granular community. The growth features of the main community representatives (isolate Limosilactobacillus musocae G03 for lactic acid bacteria and type strain Caproiciproducens lactatifermentans for chain-elongating bacteria) were characterized. The measured growth rates of lactic acid bacteria (0.051 ± 0.005 h[-1]) were two times higher than those of chain-elongating bacteria (0.026 ± 0.004 h[-1]), while the biomass yields of lactic acid bacteria (0.120 ± 0.005 g biomass/g glucose) were two times lower than that of chain-elongating bacteria (0.239 ± 0.007 g biomass/g glucose). This points towards differential growth strategies, with lactic acid bacteria resembling that of a r-strategist and chain-elongating bacteria resembling that of a K-strategist. Furthermore, the half-saturation constant of glucose for L. mucosae was determined to be 0.35 ± 0.05 g/L of glucose. A linear trend of caproic acid inhibition on the growth of L. mucosae was observed, and the growth inhibitory caproic acid concentration was predicted to be 13.6 ± 0.5 g/L, which is the highest reported so far. The pre-adjustment of L. mucosae to 4 g/L of caproic acid did not improve the overall resistance to it, but did restore the growth rates at low caproic acid concentrations (1-4 g/L) to the baseline values (i.e., growth rate at 0 g/L of caproic acid). High resistance to caproic acid enables lactic acid bacteria to persist and thrive in the systems intended for caproic acid production. Here, insights into the growth of two main functional guilds of sugar-based chain elongation systems are provided which allows for a better understanding of their interactions and promotes future bioprocess design and optimization.}, }
@article {pmid38273535, year = {2024}, author = {Lewis, ASL and Lau, MP and Jane, SF and Rose, KC and Be'eri-Shlevin, Y and Burnet, SH and Clayer, F and Feuchtmayr, H and Grossart, HP and Howard, DW and Mariash, H and Delgado Martin, J and North, RL and Oleksy, I and Pilla, RM and Smagula, AP and Sommaruga, R and Steiner, SE and Verburg, P and Wain, D and Weyhenmeyer, GA and Carey, CC}, title = {Anoxia begets anoxia: A positive feedback to the deoxygenation of temperate lakes.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17046}, doi = {10.1111/gcb.17046}, pmid = {38273535}, issn = {1365-2486}, support = {//College of Science Roundtable at Virginia Tech/ ; //Cornell Atkinson Center for Sustainability, Cornell University/ ; GR1540/37-1//Deutsche Forschungsgemeinschaft/ ; //EMALCSA Chair/ ; //Institute for Critical Technology and Applied Science/ ; //Leibniz-Institut f&#xfc;r Gew&#xe4;sser&#xf6;kologie und Binnenfischerei/ ; //LTSER Platform Tyrolean Alps (LTER-Austria)/ ; C01X2205//Ministry of Business, Innovation and Employment/ ; //Missouri Department of Natural Resources/ ; 1737424//National Science Foundation/ ; 1753639//National Science Foundation/ ; 1754265//National Science Foundation/ ; 1840995//National Science Foundation/ ; 1933016//National Science Foundation/ ; 2019528//National Science Foundation/ ; 2048031//National Science Foundation/ ; NE/R016429/1//Natural Environment Research Council/ ; //Oak Ridge National Laboratory/ ; 2020-01091//Svenska Forskningsr&#xe5;det Formas/ ; 2020-03222//Vetenskapsr&#xe5;det/ ; //Water Power Technologies Office/ ; }, mesh = {Humans ; *Lakes ; Chlorophyll A/analysis ; *Environmental Monitoring/methods ; Feedback ; Hypoxia ; Phosphorus/analysis ; Oxygen ; Eutrophication ; }, abstract = {Declining oxygen concentrations in the deep waters of lakes worldwide pose a pressing environmental and societal challenge. Existing theory suggests that low deep-water dissolved oxygen (DO) concentrations could trigger a positive feedback through which anoxia (i.e., very low DO) during a given summer begets increasingly severe occurrences of anoxia in following summers. Specifically, anoxic conditions can promote nutrient release from sediments, thereby stimulating phytoplankton growth, and subsequent phytoplankton decomposition can fuel heterotrophic respiration, resulting in increased spatial extent and duration of anoxia. However, while the individual relationships in this feedback are well established, to our knowledge, there has not been a systematic analysis within or across lakes that simultaneously demonstrates all of the mechanisms necessary to produce a positive feedback that reinforces anoxia. Here, we compiled data from 656 widespread temperate lakes and reservoirs to analyze the proposed anoxia begets anoxia feedback. Lakes in the dataset span a broad range of surface area (1-126,909 ha), maximum depth (6-370 m), and morphometry, with a median time-series duration of 30 years at each lake. Using linear mixed models, we found support for each of the positive feedback relationships between anoxia, phosphorus concentrations, chlorophyll a concentrations, and oxygen demand across the 656-lake dataset. Likewise, we found further support for these relationships by analyzing time-series data from individual lakes. Our results indicate that the strength of these feedback relationships may vary with lake-specific characteristics: For example, we found that surface phosphorus concentrations were more positively associated with chlorophyll a in high-phosphorus lakes, and oxygen demand had a stronger influence on the extent of anoxia in deep lakes. Taken together, these results support the existence of a positive feedback that could magnify the effects of climate change and other anthropogenic pressures driving the development of anoxia in lakes around the world.}, }
@article {pmid38273527, year = {2024}, author = {Fontaine, S and Abbadie, L and Aubert, M and Barot, S and Bloor, JMG and Derrien, D and Duchene, O and Gross, N and Henneron, L and Le Roux, X and Loeuille, N and Michel, J and Recous, S and Wipf, D and Alvarez, G}, title = {Plant-soil synchrony in nutrient cycles: Learning from ecosystems to design sustainable agrosystems.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17034}, doi = {10.1111/gcb.17034}, pmid = {38273527}, issn = {1365-2486}, support = {ANR-20-PCA-0006//ANR/ ; //European Union/ ; //INRAE-CNRS/ ; //ISITE Clermont-Ferrand/ ; }, mesh = {Humans ; *Soil ; *Ecosystem ; Agriculture ; Plants ; Carbon ; }, abstract = {Redesigning agrosystems to include more ecological regulations can help feed a growing human population, preserve soils for future productivity, limit dependency on synthetic fertilizers, and reduce agriculture contribution to global changes such as eutrophication and warming. However, guidelines for redesigning cropping systems from natural systems to make them more sustainable remain limited. Synthetizing the knowledge on biogeochemical cycles in natural ecosystems, we outline four ecological systems that synchronize the supply of soluble nutrients by soil biota with the fluctuating nutrient demand of plants. This synchrony limits deficiencies and excesses of soluble nutrients, which usually penalize both production and regulating services of agrosystems such as nutrient retention and soil carbon storage. In the ecological systems outlined, synchrony emerges from plant-soil and plant-plant interactions, eco-physiological processes, soil physicochemical processes, and the dynamics of various nutrient reservoirs, including soil organic matter, soil minerals, atmosphere, and a common market. We discuss the relative importance of these ecological systems in regulating nutrient cycles depending on the pedoclimatic context and on the functional diversity of plants and microbes. We offer ideas about how these systems could be stimulated within agrosystems to improve their sustainability. A review of the latest advances in agronomy shows that some of the practices suggested to promote synchrony (e.g., reduced tillage, rotation with perennial plant cover, crop diversification) have already been tested and shown to be effective in reducing nutrient losses, fertilizer use, and N2 O emissions and/or improving biomass production and soil carbon storage. Our framework also highlights new management strategies and defines the conditions for the success of these nature-based practices allowing for site-specific modifications. This new synthetized knowledge should help practitioners to improve the long-term productivity of agrosystems while reducing the negative impact of agriculture on the environment and the climate.}, }
@article {pmid38273522, year = {2024}, author = {Lí, JT and Hicks, LC and Brangarí, AC and Tájmel, D and Cruz-Paredes, C and Rousk, J}, title = {Subarctic winter warming promotes soil microbial resilience to freeze-thaw cycles and enhances the microbial carbon use efficiency.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17040}, doi = {10.1111/gcb.17040}, pmid = {38273522}, issn = {1365-2486}, support = {202006100130//Distinguished International Students Scholarship/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; 2022-01478//Svenska Forskningsr&#xe5;det Formas/ ; 2020-03858//Vetenskapsr&#xe5;det/ ; 2020-04083//Vetenskapsr&#xe5;det/ ; 4.3-2021-00164//Vetenskapsr&#xe5;det/ ; }, mesh = {*Soil Microbiology ; Seasons ; Soil/chemistry ; Carbon ; *Resilience, Psychological ; Climate Change ; }, abstract = {Climate change is predicted to cause milder winters and thus exacerbate soil freeze-thaw perturbations in the subarctic, recasting the environmental challenges that soil microorganisms need to endure. Historical exposure to environmental stressors can facilitate the microbial resilience to new cycles of that same stress. However, whether and how such microbial memory or stress legacy can modulate microbial responses to cycles of frost remains untested. Here, we conducted an in situ field experiment in a subarctic birch forest, where winter warming resulted in a substantial increase in the number and intensity of freeze-thaw events. After one season of winter warming, which raised mean surface and soil (-8 cm) temperatures by 2.9 and 1.4°C, respectively, we investigated whether the in situ warming-induced increase in frost cycles improved soil microbial resilience to an experimental freeze-thaw perturbation. We found that the resilience of microbial growth was enhanced in the winter warmed soil, which was associated with community differences across treatments. We also found that winter warming enhanced the resilience of bacteria more than fungi. In contrast, the respiration response to freeze-thaw was not affected by a legacy of winter warming. This translated into an enhanced microbial carbon-use efficiency in the winter warming treatments, which could promote the stabilization of soil carbon during such perturbations. Together, these findings highlight the importance of climate history in shaping current and future dynamics of soil microbial functioning to perturbations associated with climate change, with important implications for understanding the potential consequences on microbial-mediated biogeochemical cycles.}, }
@article {pmid38272989, year = {2024}, author = {Laanbroek, HJ and Rains, MC and Verhoeven, JTA and Whigham, DF}, title = {The effect of intentional summer flooding for mosquito control on the nitrogen dynamics of impounded Avicennia germinans mangrove forests.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {2165}, pmid = {38272989}, issn = {2045-2322}, mesh = {*Wetlands ; *Avicennia ; Ecosystem ; Mosquito Control ; Nitrogen/analysis ; Plant Breeding ; Forests ; Soil/chemistry ; }, abstract = {Coastal wetlands such as mangrove forests are breeding grounds for nuisance-causing insects. Rotational Impoundment Management (RIM) for mosquito control involves annual summer inundation of impounded mangrove forests with estuarine water during the summer half year. However, in addition to controlling mosquitos, RIM may change biogeochemical pathways. This study set out to investigate how RIM quantitatively affects physicochemical soil characteristics and potential nitrifying and denitrifying activities (PNA and PDA), which are key in the global nitrogen cycle. Before and after the implementation of RIM, soil samples were collected annually in habitats differing in size and abundance of black mangroves (Avicennia germinans) in an impoundment with RIM and in an adjacent impoundment with a more open connection to the lagoon. Compared to the non-managed impoundment, soil moisture content, total nitrogen and PDA increased, while salinity decreased after the start of annual summer flooding, but only in the dwarf habitat. In the sparse and dense habitats, total nitrogen and PDA increased independently of summer flooding, whereas soil moisture content and salinity were not affected by RIM. Labile organic nitrogen increased only in the RIM impoundment, irrespective of the habitat type. PNA was generally not affected with time, except in the dwarf habitat in the absence of intentional summer flooding where it increased. Changes in the non-managed impoundment adjacent to the RIM impoundment demonstrate the importance of groundwater exchange in linked ecosystems. The consequences of interventions in the management of mangrove impoundments and adjacent forests for the nitrogen budget are discussed.}, }
@article {pmid38271645, year = {2024}, author = {De Bondt, Y and Verdonck, C and Brandt, MJ and De Vuyst, L and Gänzle, MG and Gobbetti, M and Zannini, E and Courtin, CM}, title = {Wheat Sourdough Breadmaking: A Scoping Review.}, journal = {Annual review of food science and technology}, volume = {15}, number = {1}, pages = {265-282}, doi = {10.1146/annurev-food-110923-034834}, pmid = {38271645}, issn = {1941-1421}, mesh = {*Bread/microbiology ; *Fermentation ; *Triticum ; Food Handling ; Humans ; Food Microbiology ; Taste ; Nutritive Value ; }, abstract = {Using sourdough in breadmaking can enhance bread's shelf-life and flavor compared to exclusive baker's yeast use and is believed to increase its nutritional quality and healthiness. Previous research established insight into the microbial ecology of sourdough, but the link between leavening agent use, processing, and bread quality remains elusive. However, such knowledge is key for standardization, research on the health benefits, and the definition of sourdough bread. In this systematic scoping review, we analyzed 253 studies and identified large variations in the type and amount of leavening agent, fermentation conditions, and bread quality (specific loaf volume and acidification). The interrelation between these elements and their effect on the extent of fermentation is discussed, together with issues preventing proper comparison of breadmaking procedures. With this review, we want to contribute to the dialogue concerning the definition of sourdough-type bread products and the research into the health benefits attributed to them.}, }
@article {pmid38267517, year = {2024}, author = {Acuña, JJ and Rilling, JI and Inostroza, NG and Zhang, Q and Wick, LY and Sessitsch, A and Jorquera, MA}, title = {Variovorax sp. strain P1R9 applied individually or as part of bacterial consortia enhances wheat germination under salt stress conditions.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {2070}, pmid = {38267517}, issn = {2045-2322}, support = {1221228//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; 1201386//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; }, mesh = {*Triticum ; Salt Stress ; Plant Development ; Salt Tolerance ; *Comamonadaceae ; *Magnesium ; *Radioisotopes ; }, abstract = {Endophytes isolated from extremophile plants are interesting microbes for improving the stress tolerance of agricultural plants. Here, we isolated and characterized endophytic bacteria showing plant growth-promoting (PGP) traits from plants in two extreme Chilean biomes (Atacama Desert and Chilean Patagonia). Forty-two isolates were characterized as both halotolerant auxin producers (2-51 mg L[-1]) and 1-aminocyclopropane-1-carboxylate (ACC)-degrading bacteria (15-28 µmol αKB mg protein[-1] h[-1]). The most efficient isolates were tested as single strains, in dual and triple consortia, or in combination with previously reported PGP rhizobacteria (Klebsiella sp. 27IJA and 8LJA) for their impact on the germination of salt-exposed (0.15 M and 0.25 M NaCl) wheat seeds. Interestingly, strain P1R9, identified as Variovorax sp., enhanced wheat germination under salt stress conditions when applied individually or as part of bacterial consortia. Under salt stress, plants inoculated with dual consortia containing the strain Variovorax sp. P1R9 showed higher biomass (41%) and reduced lipid peroxidation (33-56%) than uninoculated plants. Although the underlying mechanisms remain elusive, our data suggest that the application of Variovorax sp. P1R9, alone or as a member of PGP consortia, may improve the salt stress tolerance of wheat plants.}, }
@article {pmid38265481, year = {2024}, author = {He, B and Li, Q and Zou, S and Bai, X and Li, W and Chen, Y}, title = {Dynamic Changes of Soil Microbial Communities During the Afforestation of Pinus Armandii in a Karst Region of Southwest China.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {36}, pmid = {38265481}, issn = {1432-184X}, support = {Qiankehe Jichu-ZK [2021] 231//the Project of Guizhou Science and Technology Fund/ ; Bikelianhe [2023] 10 and 24//the Project of Bijie Science and Technology Fund/ ; Bikelianhe [2023] 10 and 24//the Project of Bijie Science and Technology Fund/ ; Bkhzdzx [2021]1//Bijie Science and Technology Major Project/ ; Bikelianhezi Guigongcheng [2021] 8//the Opening Fund for Guizhou Province Key Laboratory of Ecological Protection and Restoration of Typical Plateau Wetlands/ ; [2022]096//the Technology Top Talent Project in Department of Education of Guizhou Province/ ; Qianjiaohe KY [2022]120 and 123//the Support Plan for Young Science and Technology talents of Guizhou Province Education Department/ ; }, mesh = {*Microbiota ; *Mycobiome ; China ; *Pinus ; Soil ; }, abstract = {Clarifying the response of soil microbial communities to vegetation restoration is essential to comprehend biogeochemical processes and ensure the long-term viability of forest development. To assess the variations in soil microbial communities throughout the growth of Pinus armandii plantations in the karst region, we utilized the "space instead of time" approach and selected four P. armandii stands with ages ranging from 10 to 47 years, along with a grassland control. The microbial community structure was determined by conducting Illumina sequencing of the 16 S rRNA gene and the ITS gene, respectively. The results demonstrated that afforestation with P. armandii significantly influenced soil microbial communities, as indicated by notable differences in bacterial and fungal composition and diversity between the plantations and the control. However, soil microbe diversity did not display significant variation across stand ages. Moreover, the bacterial community exhibited higher responsiveness to age gradients compared to the fungal community. Soil physicochemical factors play a critical role in elucidating microbial diversity and community composition variations during restoration processes. TN, AN, TP, AP, SOC, AK, and pH were the most significant influencing factors for the composition of bacterial community, while TC, SOC, pH, and TCa were the most significant influencing factors for the composition of fungal community. Our findings indicate substantial changes in soil bacterial and fungal communities across successive stages of development. Additionally, the changes in dominant bacteria and fungi characteristics across the age gradient were primarily attributed to variations in the prevailing soil conditions and chemical factors.}, }
@article {pmid38261090, year = {2024}, author = {Deschamps, C and Denis, S and Humbert, D and Priymenko, N and Chalancon, S and De Bodt, J and Van de Wiele, T and Ipharraguerre, I and Alvarez-Acero, I and Achard, C and Apper, E and Blanquet-Diot, S}, title = {Canine Mucosal Artificial Colon: development of a new colonic in vitro model adapted to dog sizes.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {166}, pmid = {38261090}, issn = {1432-0614}, mesh = {Dogs ; Animals ; *Ecosystem ; Colon ; *Actinobacteria ; Ammonia ; Anaerobiosis ; }, abstract = {Differences in dog breed sizes are an important determinant of variations in digestive physiology, mainly related to the large intestine. In vitro gut models are increasingly used as alternatives to animal experiments for technical, cost, societal, and regulatory reasons. Up to now, only one in vitro model of the canine colon incorporates the dynamics of different canine gut regions, yet no adaptations exist to reproduce size-related digestive parameters. To address this limitation, we developed a new model of the canine colon, the CANIne Mucosal ARtificial COLon (CANIM-ARCOL), simulating main physiochemical (pH, transit time, anaerobiosis), nutritional (ileal effluent composition), and microbial (lumen and mucus-associated microbiota) parameters of this ecosystem and adapted to three dog sizes (i.e., small under 10 kg, medium 10-30 kg, and large over 30 kg). To validate the new model regarding microbiota composition and activities, in vitro fermentations were performed in bioreactors inoculated with stools from 13 dogs (4 small, 5 medium, and 4 large). After a stabilization period, microbiota profiles clearly clustered depending on dog size. Bacteroidota and Firmicutes abundances were positively correlated with dog size both in vitro and in vivo, while opposite trends were observed for Actinobacteria and Proteobacteria. As observed in vivo, microbial activity also increased with dog size in vitro, as evidenced from gas production, short-chain fatty acids, ammonia, and bile acid dehydroxylation. In line with the 3R regulation, CANIM-ARCOL could be a relevant platform to assess bilateral interactions between food and pharma compounds and gut microbiota, capturing inter-individual or breed variabilities. KEY POINTS: • CANIM-ARCOL integrates main canine physicochemical and microbial colonic parameters • Gut microbiota associated to different dog sizes is accurately maintained in vitro • The model can help to move toward personalized approach considering dog body weight.}, }
@article {pmid38261068, year = {2024}, author = {Pei, P and Aslam, M and Wang, H and Ye, P and Li, T and Liang, H and Lin, Q and Chen, W and Du, H}, title = {Diversity and ecological function of urease-producing bacteria in the cultivation environment of Gracilariopsis lemaneiformis.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {35}, pmid = {38261068}, issn = {1432-184X}, support = {2022fjscq02//the Open Program of Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province/ ; 2022fjscq02//the Open Program of Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province/ ; 41976125//the National Natural Science Foundation of China/ ; 42206116//the Natural Science Foundation of China grants/ ; 2022KCXTD008//the Program for University Innovation Team of Guangdong Province/ ; 2018KCXTD012//the Team Project of Department of Education of Guangdong Province/ ; }, mesh = {*Urease ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Seaweed ; Nitrogen ; Urea ; }, abstract = {Urease-producing bacteria (UPB) provide inorganic nitrogen for primary producers by hydrolyzing urea, and play an important role in marine nitrogen cycle. However, there is still an incomplete understanding of UPB and their ecological functions in the cultivation environment of the red macroalgae Gracilariopsis lemaneiformis. This study comprehensively analyzed the diversity of culturable UPB and explored their effects on urea uptake by G. lemaneiformis. A total of 34 isolates belonging to four main bacterial phyla i.e. (Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria) were identified through 16S rRNA sequencing and were screened for UPB by urea agar chromogenic medium assay and ureC gene cloning. Our data revealed that only 8 strains contained urease. All of these UPB exhibited different urease activities, which were determined by the Berthelot reaction colorimetry assay. Additionally, the UPB strain (G13) isolated from G. lemaneiformis with higher urease activity was selected for co-culture with G. lemaneiformis to explore its role in promoting or inhibiting nitrogen uptake by macroalgae. The results showed a significant increase in urea consumption in the culture medium and the total cellular nitrogen in G. lemaneiformis in the UPB-co culture group compared to the sterile group. This suggests that the selected UPB strain positively influences nitrogen uptake by G. lemaneiformis. Similarly, isotopic assays revealed that the δ[15]N content of G. lemaneiformis was significantly higher in the UPB-co culture than in the control group, where δ[15]N-urea was the only nitrogen source in the culture medium. This indicates that the UPB helped G. lemaneiformis to absorb more nitrogen from urea. Moreover, the highest content of δ[15]N was found in G. lemaneiformis with epiphytic bacteria compared to sterilized (i.e. control), showing that epiphytic bacteria, along with UPB, have a compound effect in helping G. lemaneiformis absorb more nitrogen from urea. Taken together, these results provide unique insight into the ecological role of UPB and suggest that urease from macroalgae environment-associated bacteria might be an important player in marine nitrogen cycling.}, }
@article {pmid38261023, year = {2024}, author = {Herren, P and Dunn, AM and Meyling, NV and Savio, C and Hesketh, H}, title = {Effect of CO2 Concentrations on Entomopathogen Fitness and Insect-Pathogen Interactions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {34}, pmid = {38261023}, issn = {1432-184X}, support = {859850//Horizon 2020 Framework Programme/ ; }, mesh = {Animals ; *Carbon Dioxide ; Insecta ; Larva ; *Bacillus thuringiensis ; Biological Control Agents ; }, abstract = {Numerous insect species and their associated microbial pathogens are exposed to elevated CO2 concentrations in both artificial and natural environments. However, the impacts of elevated CO2 on the fitness of these pathogens and the susceptibility of insects to pathogen infections are not well understood. The yellow mealworm, Tenebrio molitor, is commonly produced for food and feed purposes in mass-rearing systems, which increases risk of pathogen infections. Additionally, entomopathogens are used to control T. molitor, which is also a pest of stored grains. It is therefore important to understand how elevated CO2 may affect both the pathogen directly and impact on host-pathogen interactions. We demonstrate that elevated CO2 concentrations reduced the viability and persistence of the spores of the bacterial pathogen Bacillus thuringiensis. In contrast, conidia of the fungal pathogen Metarhizium brunneum germinated faster under elevated CO2. Pre-exposure of the two pathogens to elevated CO2 prior to host infection did not affect the survival probability of T. molitor larvae. However, larvae reared at elevated CO2 concentrations were less susceptible to both pathogens compared to larvae reared at ambient CO2 concentrations. Our findings indicate that whilst elevated CO2 concentrations may be beneficial in reducing host susceptibility in mass-rearing systems, they may potentially reduce the efficacy of the tested entomopathogens when used as biological control agents of T. molitor larvae. We conclude that CO2 concentrations should be carefully selected and monitored as an additional environmental factor in laboratory experiments investigating insect-pathogen interactions.}, }
@article {pmid38260895, year = {2023}, author = {Tan, H and Du, XH and Bonito, G and Masaphy, S}, title = {Editorial: Morels: physiology, genetics, and interactions with the environment.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1352719}, pmid = {38260895}, issn = {1664-302X}, }
@article {pmid38260330, year = {2024}, author = {Caty, SN and Alvarez-Buylla, A and Vasek, C and Tapia, EE and Martin, NA and McLaughlin, T and Weber, PK and Mayali, X and Coloma, LA and Morris, MM and O'Connell, LA}, title = {A toxic environment selects for specialist microbiome in poison frogs.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38260330}, issn = {2692-8205}, support = {DP2 HD102042/HD/NICHD NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; }, abstract = {Shifts in microbiome community composition can have large effects on host health. It is therefore important to understand how perturbations, like those caused by the introduction of exogenous chemicals, modulate microbiome community composition. In poison frogs within the family Dendrobatidae, the skin microbiome is exposed to the alkaloids that the frogs sequester from their diet and use for defense. Given the demonstrated antimicrobial effects of these poison frog alkaloids, these compounds may be structuring the skin microbial community. To test this, we first characterized microbial communities from chemically defended and closely related non-defended frogs from Ecuador. Then we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of a single frog species. In both the field and lab experiments, we found that alkaloid-exposed microbiomes are more species rich and phylogenetically diverse, with an increase in rare taxa. To better understand the strain-specific behavior in response to alkaloids, we cultured microbial strains from poison frog skin and found the majority of strains exhibited either enhanced growth or were not impacted by the addition of DHQ. Additionally, stable isotope tracing coupled to nanoSIMS suggests that some of these strains are able to metabolize DHQ. Taken together, these data suggest that poison frog chemical defenses open new niches for skin-associated microbes with specific adaptations, including the likely metabolism of alkaloids, that enable their survival in this toxic environment. This work helps expand our understanding of how exposure to exogenous compounds like alkaloids can impact host microbiomes.}, }
@article {pmid38259105, year = {2024}, author = {Hoang, DQ and Wilson, LR and Scheftgen, AJ and Suen, G and Currie, CR}, title = {Disturbance-diversity relationships of microbial communities change based on growth substrate.}, journal = {mSystems}, volume = {9}, number = {2}, pages = {e0088723}, pmid = {38259105}, issn = {2379-5077}, support = {T32 GM007215/GM/NIGMS NIH HHS/United States ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria ; Cellulose ; Glucose ; }, abstract = {Disturbance events can impact ecological community dynamics. Understanding how communities respond to disturbances and how those responses can vary is a challenge in microbial ecology. In this study, we grew a previously enriched specialized microbial community on either cellulose or glucose as a sole carbon source and subjected them to one of five different disturbance regimes of varying frequencies ranging from low to high. Using 16S rRNA gene amplicon sequencing, we show that the community structure is largely driven by substrate, but disturbance frequency affects community composition and successional dynamics. When grown on cellulose, bacteria in the genera Cellvibrio, Lacunisphaera, and Asticcacaulis are the most abundant microbes. However, Lacunisphaera is only abundant in the lower disturbance frequency treatments, while Asticcacaulis is more abundant in the highest disturbance frequency treatment. When grown on glucose, the most abundant microbes are two Pseudomonas sequence variants and a Cohnella sequence variant that is only abundant in the highest disturbance frequency treatment. Communities grown on cellulose exhibited a greater range of diversity (1.95-7.33 Hill 1 diversity) that peaks at the intermediate disturbance frequency treatment or one disturbance every 3 days. Communities grown on glucose, however, ranged from 1.63 to 5.19 Hill 1 diversity with peak diversity at the greatest disturbance frequency treatment. These results demonstrate that the dynamics of a microbial community can vary depending on substrate and the disturbance frequency and may potentially explain the variety of diversity-disturbance relationships observed in microbial systems.IMPORTANCEA generalizable diversity-disturbance relationship (DDR) of microbial communities remains a contentious topic. Various microbial systems have different DDRs. Rather than finding support or refuting specific DDRs, we investigated the underlying factors that lead to different DDRs. In this study, we measured a cellulose-enriched microbial community's response to a range of disturbance frequencies from high to low, across two different substrates: cellulose and glucose. We demonstrate that the community displays a unimodal DDR when grown on cellulose and a monotonically increasing DDR when grown on glucose. Our findings suggest that the same community can display different DDRs. These results suggest that the range of DDRs we observe across different microbial systems may be due to the nutritional resources microbial communities can access and the interactions between bacteria and their environment.}, }
@article {pmid38259093, year = {2024}, author = {Fadum, JM and Borton, MA and Daly, RA and Wrighton, KC and Hall, EK}, title = {Dominant nitrogen metabolisms of a warm, seasonally anoxic freshwater ecosystem revealed using genome resolved metatranscriptomics.}, journal = {mSystems}, volume = {9}, number = {2}, pages = {e0105923}, pmid = {38259093}, issn = {2379-5077}, support = {P30 CA046934/CA/NCI NIH HHS/United States ; }, mesh = {*Ecosystem ; Nitrates/analysis ; Lakes/chemistry ; Organic Chemicals ; *Ammonium Compounds ; Water ; Nitrogen ; }, abstract = {Nitrogen (N) availability is one of the principal drivers of primary productivity across aquatic ecosystems. However, the microbial communities and emergent metabolisms that govern N cycling in tropical lakes are both distinct from and poorly understood relative to those found in temperate lakes. This latitudinal difference is largely due to the warm (>20°C) temperatures of tropical lake anoxic hypolimnions (deepest portion of a stratified water column), which result in unique anaerobic metabolisms operating without the temperature constraints found in lakes at temperate latitudes. As such, tropical hypolimnions provide a platform for exploring microbial membership and functional diversity. To better understand N metabolism in warm anoxic waters, we combined measurements of geochemistry and water column thermophysical structure with genome-resolved metatranscriptomic analyses of the water column microbiome in Lake Yojoa, Honduras. We sampled above and below the oxycline in June 2021, when the water column was stratified, and again at the same depths and locations in January 2022, when the water column was mixed. We identified 335 different lineages and significantly different microbiome membership between seasons and, when stratified, between depths. Notably, nrfA (indicative of dissimilatory nitrate reduction to ammonium) was upregulated relative to other N metabolism genes in the June hypolimnion. This work highlights the taxonomic and functional diversity of microbial communities in warm and anoxic inland waters, providing insight into the contemporary microbial ecology of tropical ecosystems as well as inland waters at higher latitudes as water columns continue to warm in the face of global change.IMPORTANCEIn aquatic ecosystems where primary productivity is limited by nitrogen (N), whether continuously, seasonally, or in concert with additional nutrient limitations, increased inorganic N availability can reshape ecosystem structure and function, potentially resulting in eutrophication and even harmful algal blooms. Whereas microbial metabolic processes such as mineralization and dissimilatory nitrate reduction to ammonium increase inorganic N availability, denitrification removes bioavailable N from the ecosystem. Therefore, understanding these key microbial mechanisms is critical to the sustainable management and environmental stewardship of inland freshwater resources. This study identifies and characterizes these crucial metabolisms in a warm, seasonally anoxic ecosystem. Results are contextualized by an ecological understanding of the study system derived from a multi-year continuous monitoring effort. This unique data set is the first of its kind in this largely understudied ecosystem (tropical lakes) and also provides insight into microbiome function and associated taxa in warm, anoxic freshwaters.}, }
@article {pmid38256774, year = {2024}, author = {Reyes-Ardila, WL and Rugeles-Silva, PA and Duque-Zapata, JD and Vélez-Martínez, GA and Tarazona Pulido, L and Cardona Tobar, KM and Díaz Gallo, SA and Muñoz Flórez, JE and Díaz-Ariza, LA and López-Alvarez, D}, title = {Exploring Genomics and Microbial Ecology: Analysis of Bidens pilosa L. Genetic Structure and Soil Microbiome Diversity by RAD-Seq and Metabarcoding.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, pmid = {38256774}, issn = {2223-7747}, support = {FP44842-221-2018//Pontificia Universidad Javeriana/ ; FP44842-221-2018//Ministry of Science, Technology, and Innovation, the Ministry of National Education/ ; FP44842-221-2018//Ministry of Industry, Commerce and Tourism/ ; FP44842-221-2018//ICETEX/ ; FP44842-221-2018//Ministry of National Education/ ; }, abstract = {Bidens pilosa L., native to South America and commonly used for medicinal purposes, has been understudied at molecular and genomic levels and in its relationship with soil microorganisms. In this study, restriction site-associated DNA markers (RADseq) techniques were implemented to analyze genetic diversity and population structure, and metabarcoding to examine microbial composition in soils from Palmira, Sibundoy, and Bogotá, Colombia. A total of 2,984,123 loci and 3485 single nucleotide polymorphisms (SNPs) were identified, revealing a genetic variation of 12% between populations and 88% within individuals, and distributing the population into three main genetic groups, FST = 0.115 (p < 0.001) and FIT = 0.013 (p > 0.05). In the soil analysis, significant correlations were found between effective cation exchange capacity (ECEC) and apparent density, soil texture, and levels of Mg and Fe, as well as negative correlations between ECEC and Mg, and Mg, Fe, and Ca. Proteobacteria and Ascomycota emerged as the predominant bacterial and fungal phyla, respectively. Analyses of alpha, beta, and multifactorial diversity highlight the influence of ecological and environmental factors on these microbial communities, revealing specific patterns of clustering and association between bacteria and fungi in the studied locations.}, }
@article {pmid38254227, year = {2024}, author = {Gul, F and Herrema, H and Davids, M and Keating, C and Nasir, A and Ijaz, UZ and Javed, S}, title = {Gut microbial ecology and exposome of a healthy Pakistani cohort.}, journal = {Gut pathogens}, volume = {16}, number = {1}, pages = {5}, pmid = {38254227}, issn = {1757-4749}, support = {NE/L011956/1//Natural Environment Research Council/ ; EP/P029329/1//Engineering and Physical Sciences Research Council/ ; }, abstract = {BACKGROUND: Pakistan is a multi-ethnic society where there is a disparity between dietary habits, genetic composition, and environmental exposures. The microbial ecology of healthy Pakistani gut in the context of anthropometric, sociodemographic, and dietary patterns holds interest by virtue of it being one of the most populous countries, and also being a Lower Middle Income Country (LMIC).<br><br>METHODS: 16S rRNA profiling of healthy gut microbiome of normo-weight healthy Pakistani individuals from different regions of residence is performed with additional meta-data collected through filled questionnaires. The current health status is then linked to dietary patterns through [Formula: see text] test of independence and Generalized Linear Latent Variable Model (GLLVM) where distribution of individual microbes is regressed against all recorded sources of variability. To identify the core microbiome signature, a dynamic approach is used that considers into account species occupancy as well as consistency across assumed grouping of samples including organization by gender and province of residence. Fitting neutral modeling then revealed core microbiome that is selected by the environment.<br><br>RESULTS: A strong determinant of disparity is by province of residence. It is also established that the male microbiome is better adapted to the local niche than the female microbiome, and that there is microbial taxonomic and functional diversity in different ethnicities, dietary patterns and lifestyle habits. Some microbial genera, such as, Megamonas, Porphyromonas, Haemophilus, Klebsiella and Finegoldia showed significant associations with consumption of pickle, fresh fruits, rice, and cheese. Our analyses suggest current health status being associated with the diet, sleeping patterns, employment status, and the medical history.<br><br>CONCLUSIONS: This study provides a snapshot of the healthy core Pakistani gut microbiome by focusing on the most populous provinces and ethnic groups residing in predominantly urban areas. The study serves a reference dataset for exploring variations in disease status and designing personalized dietary and lifestyle interventions to promote gut health, particularly in LMICs settings.}, }
@article {pmid38253620, year = {2024}, author = {Zeng, J and Xie, C and Huang, Z and Cho, CH and Chan, H and Li, Q and Ashktorab, H and Smoot, DT and Wong, SH and Yu, J and Gong, W and Liang, C and Xu, H and Chen, H and Liu, X and Wu, JCY and Ip, M and Gin, T and Zhang, L and Chan, MTV and Hu, W and Wu, WKK}, title = {LOX-1 acts as an N[6]-methyladenosine-regulated receptor for Helicobacter pylori by binding to the bacterial catalase.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {669}, pmid = {38253620}, issn = {2041-1723}, mesh = {Animals ; Humans ; Mice ; *Adenosine/analogs &amp; derivatives ; Catalase/metabolism ; *Helicobacter Infections/metabolism ; *Helicobacter pylori/metabolism ; RNA, Messenger/genetics ; *Scavenger Receptors, Class E/genetics ; }, abstract = {The role of N[6]-methyladenosine (m[6]A) modification of host mRNA during bacterial infection is unclear. Here, we show that Helicobacter pylori infection upregulates host m[6]A methylases and increases m[6]A levels in gastric epithelial cells. Reducing m[6]A methylase activity via hemizygotic deletion of methylase-encoding gene Mettl3 in mice, or via small interfering RNAs targeting m[6]A methylases, enhances H. pylori colonization. We identify LOX-1 mRNA as a key m[6]A-regulated target during H. pylori infection. m[6]A modification destabilizes LOX-1 mRNA and reduces LOX-1 protein levels. LOX-1 acts as a membrane receptor for H. pylori catalase and contributes to bacterial adhesion. Pharmacological inhibition of LOX-1, or genetic ablation of Lox-1, reduces H. pylori colonization. Moreover, deletion of the bacterial catalase gene decreases adhesion of H. pylori to human gastric sections. Our results indicate that m[6]A modification of host LOX-1 mRNA contributes to protection against H. pylori infection by downregulating LOX-1 and thus reducing H. pylori adhesion.}, }
@article {pmid38251984, year = {2024}, author = {Shoemaker, WR and Grilli, J}, title = {Investigating macroecological patterns in coarse-grained microbial communities using the stochastic logistic model of growth.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {38251984}, issn = {2050-084X}, support = {2010885//National Science Foundation/ ; }, mesh = {Logistic Models ; Phylogeny ; *Biological Evolution ; Biodiversity ; *Microbiota ; }, abstract = {The structure and diversity of microbial communities are intrinsically hierarchical due to the shared evolutionary history of their constituents. This history is typically captured through taxonomic assignment and phylogenetic reconstruction, sources of information that are frequently used to group microbes into higher levels of organization in experimental and natural communities. Connecting community diversity to the joint ecological dynamics of the abundances of these groups is a central problem of community ecology. However, how microbial diversity depends on the scale of observation at which groups are defined has never been systematically examined. Here, we used a macroecological approach to quantitatively characterize the structure and diversity of microbial communities among disparate environments across taxonomic and phylogenetic scales. We found that measures of biodiversity at a given scale can be consistently predicted using a minimal model of ecology, the Stochastic Logistic Model of growth (SLM). This result suggests that the SLM is a more appropriate null-model for microbial biodiversity than alternatives such as the Unified Neutral Theory of Biodiversity. Extending these within-scale results, we examined the relationship between measures of biodiversity calculated at different scales (e.g. genus vs. family), an empirical pattern previously evaluated in the context of the Diversity Begets Diversity (DBD) hypothesis (Madi et al., 2020). We found that the relationship between richness estimates at different scales can be quantitatively predicted assuming independence among community members, demonstrating that the DBD can be sufficiently explained using the SLM as a null model of ecology. Contrastingly, only by including correlations between the abundances of community members (e.g. as the consequence of interactions) can we predict the relationship between estimates of diversity at different scales. The results of this study characterize novel microbial patterns across scales of organization and establish a sharp demarcation between recently proposed macroecological patterns that are not and are affected by ecological interactions.}, }
@article {pmid38251877, year = {2024}, author = {Schloss, PD}, title = {Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses.}, journal = {mSphere}, volume = {9}, number = {2}, pages = {e0035423}, pmid = {38251877}, issn = {2379-5042}, support = {R01 CA215574/CA/NCI NIH HHS/United States ; U01 CA264071/CA/NCI NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; }, abstract = {UNLABELLED: Considering it is common to find as much as 100-fold variation in the number of 16S rRNA gene sequences across samples in a study, researchers need to control for the effect of uneven sequencing effort. How to do this has become a contentious question. Some have argued that rarefying or rarefaction is "inadmissible" because it omits valid data. A number of alternative approaches have been developed to normalize and rescale the data that purport to be invariant to the number of observations. I generated community distributions based on 12 published data sets where I was able to assess the ability of multiple methods to control for uneven sequencing effort. Rarefaction was the only method that could control for variation in uneven sequencing effort when measuring commonly used alpha and beta diversity metrics. Next, I compared the false detection rate and power to detect true differences between simulated communities with a known effect size using various alpha and beta diversity metrics. Although all methods of controlling for uneven sequencing effort had an acceptable false detection rate when samples were randomly assigned to two treatment groups, rarefaction was consistently able to control for differences in sequencing effort when sequencing depth was confounded with treatment group. Finally, the statistical power to detect differences in alpha and beta diversity metrics was consistently the highest when using rarefaction. These simulations underscore the importance of using rarefaction to normalize the number of sequences across samples in amplicon sequencing analyses.<br><br>IMPORTANCE: Sequencing 16S rRNA gene fragments has become a fundamental tool for understanding the diversity of microbial communities and the factors that affect their diversity. Due to technical challenges, it is common to observe wide variation in the number of sequences that are collected from different samples within the same study. However, the diversity metrics used by microbial ecologists are sensitive to differences in sequencing effort. Therefore, tools are needed to control for the uneven levels of sequencing. This simulation-based analysis shows that despite a longstanding controversy, rarefaction is the most robust approach to control for uneven sequencing effort. The controversy started because of confusion over the definition of rarefaction and violation of assumptions that are made by methods that have been borrowed from other fields. Microbial ecologists should use rarefaction.}, }
@article {pmid38248928, year = {2023}, author = {Masigol, H and Retter, A and Pourmoghaddam, MJ and Amini, H and Taheri, SR and Mostowfizadeh-Ghalamfarsa, R and Kimiaei, M and Grossart, HP}, title = {Opening Pandora's Box: Neglected Biochemical Potential of Permafrost-Associated Fungal Communities in a Warming Climate.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {10}, number = {1}, pages = {}, pmid = {38248928}, issn = {2309-608X}, support = {DFG GR1540/37-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Permafrost, a vast storage reservoir of frozen organic matter, is rapidly thawing due to climate change, releasing previously preserved carbon into the environment. This phenomenon has significant consequences for microbial communities, including fungi, inhabiting permafrost-associated regions. In this review, we delve into the intricate interplay between permafrost thawing and fungal diversity and functionality with an emphasis on thermokarst lakes. We explore how the release of organic carbon from thawing permafrost alters the composition and activities of fungal communities, emphasizing the potential for shifts in taxonomic diversity and functional gene expression. We discuss the formation of thermokarst lakes, as an example of permafrost thaw-induced ecological disruptions and their impact on fungal communities. Furthermore, we analyze the repercussions of these changes, including effects on nutrient cycling, plant productivity, and greenhouse gas (GHG) emissions. By elucidating the multifaceted relationship between permafrost thaw and aquatic fungi, this review provides valuable insights into the ecological consequences of ongoing climate change in permafrost-affected regions.}, }
@article {pmid38248338, year = {2024}, author = {Kirby, TO and Sapp, PA and Townsend, JR and Govaert, M and Duysburgh, C and Marzorati, M and Marshall, TM and Esposito, R}, title = {AG1[®] Induces a Favorable Impact on Gut Microbial Structure and Functionality in the Simulator of Human Intestinal Microbial Ecosystem[®] Model.}, journal = {Current issues in molecular biology}, volume = {46}, number = {1}, pages = {557-569}, pmid = {38248338}, issn = {1467-3045}, support = {N/A//Athletic Greens International/ ; }, abstract = {Modulation of the human gut microbiome has become an area of interest in the nutraceutical space. We explored the effect of the novel foundational nutrition supplement AG1[®] on the composition of human microbiota in an in vitro experimental design. Employing the Simulator of Human Intestinal Microbial Ecosystem (SHIME[®]) model, AG1[®] underwent digestion, absorption, and subsequent colonic microenvironment simulation under physiologically relevant conditions in healthy human fecal inocula. Following 48 h of colonic simulation, the gut microbiota were described using shallow shotgun, whole genome sequencing. Metagenomic data were used to describe changes in community structure (alpha diversity, beta diversity, and changes in specific taxa) and community function (functional heterogeneity and changes in specific bacterial metabolic pathways). Results showed no significant change in alpha diversity, but a significant effect of treatment and donor and an interaction between the treatment and donor effect on structural heterogeneity likely stemming from the differential enrichment of eight bacterial taxa. Similar findings were observed for community functional heterogeneity likely stemming from the enrichment of 20 metabolic pathways characterized in the gene ontology term database. It is logical to conclude that an acute dose of AG1 has significant effects on gut microbial composition that may translate into favorable effects in humans.}, }
@article {pmid38246125, year = {2024}, author = {Mahony, J}, title = {Biological and bioinformatic tools for the discovery of unknown phage-host combinations.}, journal = {Current opinion in microbiology}, volume = {77}, number = {}, pages = {102426}, doi = {10.1016/j.mib.2024.102426}, pmid = {38246125}, issn = {1879-0364}, mesh = {*Bacteriophages/genetics ; Artificial Intelligence ; Computational Biology ; *Microbiota ; Metagenomics ; }, abstract = {The field of microbial ecology has been transformed by metagenomics in recent decades and has culminated in vast datasets that facilitate the bioinformatic dissection of complex microbial communities. Recently, attention has turned from defining the microbiota composition to the interactions and relationships that occur between members of the microbiota. Within complex microbiota, the identification of bacteriophage-host combinations has been a major challenge. Recent developments in artificial intelligence tools to predict protein structure and function as well as the relationships between bacteria and their infecting bacteriophages allow a strategic approach to identifying and validating phage-host relationships. However, biological validation of these predictions remains essential and will serve to improve the existing predictive tools. In this review, I provide an overview of the most recent developments in both bioinformatic and experimental approaches to predicting and experimentally validating unknown phage-host combinations.}, }
@article {pmid38244618, year = {2024}, author = {Yalçın, G and Yıldız, D and Calderó-Pascual, M and Yetim, S and Şahin, Y and Parakatselaki, ME and Avcı, F and Karakaya, N and Ladoukakis, ED and Berger, SA and Ger, KA and Jeppesen, E and Beklioğlu, M}, title = {Quality matters: Response of bacteria and ciliates to different allochthonous dissolved organic matter sources as a pulsed disturbance in shallow lakes.}, journal = {The Science of the total environment}, volume = {916}, number = {}, pages = {170140}, doi = {10.1016/j.scitotenv.2024.170140}, pmid = {38244618}, issn = {1879-1026}, mesh = {Animals ; *Ecosystem ; *Lakes/microbiology ; Dissolved Organic Matter ; Bacteria ; Biomass ; Plankton ; }, abstract = {Shallow lake ecosystems are particularly prone to disturbances such as pulsed dissolved organic matter (allochthonous-DOM; hereafter allo-DOM) loadings from catchments. However, the effects of allo-DOM with contrasting quality (in addition to quantity) on the planktonic communities of microbial loop are poorly understood. To determine the impact of different qualities of pulsed allo-DOM disturbance on the coupling between bacteria and ciliates, we conducted a mesocosm experiment with two different allo-DOM sources added to mesocosms in a single-pulse disturbance event: Alder tree leaf extract, a more labile (L) source and HuminFeed® (HF), a more recalcitrant source. Allo-DOM sources were used as separate treatments and in combination (HFL) relative to the control without allo-DOM additions (C). Our results indicate that the quality of allo-DOM was a major regulator of planktonic microbial community biomass and/or composition through which both bottom-up and top-down forces were involved. Bacteria biomass showed significant nonlinear responses in L and HFL with initial increases followed by decreases to pre-pulse conditions. Ciliate biomass was significantly higher in L compared to all other treatments. In terms of composition, bacterivore ciliate abundance was significantly higher in both L and HFL treatments, mainly driven by the bacterial biomass increase in the same treatments. GAMM models showed negative interaction between metazoan zooplankton biomass and ciliates, but only in the L treatment, indicating top-down control on ciliates. Ecosystem stability analyses revealed overperformance, high resilience and full recovery of bacteria in the HFL and L treatments, while ciliates showed significant shift in compositional stability in HFL and L with incomplete taxonomic recovery. Our study highlights the importance of allo-DOM quality shaping the response within the microbial loop not only through triggering different scenarios in biomass, but also the community composition, stability, and species interactions (top-down and bottom-up) in bacteria and plankton.}, }
@article {pmid38244196, year = {2024}, author = {Truter, M and Koopman, JE and Jordaan, K and Tsamkxao, LO and Cowan, DA and Underdown, SJ and Ramond, JB and Rifkin, RF}, title = {Documenting the diversity of the Namibian Ju|'hoansi intestinal microbiome.}, journal = {Cell reports}, volume = {43}, number = {2}, pages = {113690}, doi = {10.1016/j.celrep.2024.113690}, pmid = {38244196}, issn = {2211-1247}, mesh = {Animals ; Humans ; *Gastrointestinal Microbiome ; Prevotella ; *Saccharomycetales ; }, abstract = {We investigate the bacterial and fungal composition and functionality of the Ju|'hoansi intestinal microbiome (IM). The Juǀ'hoansi are a hunter-gatherer community residing in northeastern Namibia. They formerly subsisted by hunting and gathering but have been increasingly exposed to industrial dietary sources, medicines, and lifestyle features. They present an opportunity to study the evolution of the human IM in situ, from a predominantly hunter-gatherer to an increasingly Western urban-forager-farmer lifestyle. Their bacterial IM resembles that of typical hunter-gatherers, being enriched for genera such as Prevotella, Blautia, Faecalibacterium, Succinivibrio, and Treponema. Fungal IM inhabitants include animal pathogens and plant saprotrophs such as Fusarium, Issatchenkia, and Panellus. Our results suggest that diet and culture exert a greater influence on Ju|'hoansi IM composition than age, self-identified biological sex, and medical history. The Ju|'hoansi exhibit a unique core IM composition that diverges from the core IMs of other populations.}, }
@article {pmid38244160, year = {2024}, author = {Wang, N and Wang, Q and Song, S and Sun, Z and Zhao, A and Ali, A and Xu, G and Zhong, X and Wang, F and Xu, H}, title = {Microplastics drive community dynamics of periphytic protozoan fauna in marine environments.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {9}, pages = {13327-13334}, pmid = {38244160}, issn = {1614-7499}, support = {31672308//The Natural Science Foundation of China/ ; 41076089//The Natural Science Foundation of China/ ; ZR2022QD065//the Youth Project of the Natural Science Foundation of Shandong Province, China/ ; }, mesh = {Ecosystem ; Biodiversity ; Environmental Monitoring ; Microplastics ; Plastics ; *Ciliophora/physiology ; *Water Pollutants, Chemical/toxicity ; }, abstract = {The pollution of microplastics (MPs) to the marine environment has become a widespread focus of attention. To assess MP-induced ecotoxicity on marine ecosystems, periphytic protozoan communities were used as test organisms and exposed to five concentrations of MPs: 0, 1, 5, 25, and 125 mg l[-1]. Protozoan samples were collected using microscope slides from coastal waters of the Yellow Sea, northern China. A total of 13 protozoan species were identified and represented different tolerance to MP-induced ecotoxicity. Inhibition effects of MPs on the test protozoan communities were clearly shown in terms of both the species richness and individual abundance and followed linear relationships to MP concentrations. The community patterns were driven by MPs and significantly shifted at concentrations over 5 mg l[-1]. Our findings demonstrated that MPs may induce the community-level ecotoxic response of periphytic protozoan fauna and followed significant community dynamics. Thus, it is suggested that periphytic protozoan fauna may be used as useful community-based test model organisms for evaluating MP-induced ecotoxicity in marine environments.}, }
@article {pmid38243487, year = {2023}, author = {Saintillan, D}, title = {Dispersion of run-and-tumble microswimmers through disordered media.}, journal = {Physical review. E}, volume = {108}, number = {6-1}, pages = {064608}, doi = {10.1103/PhysRevE.108.064608}, pmid = {38243487}, issn = {2470-0053}, abstract = {Understanding the transport properties of microorganisms and self-propelled particles in porous media has important implications for human health as well as microbial ecology. In free space, most microswimmers perform diffusive random walks as a result of the interplay of self-propulsion and orientation decorrelation mechanisms such as run-and-tumble dynamics or rotational diffusion. In an unstructured porous medium, collisions with the microstructure result in a decrease in the effective spatial diffusivity of the particles from its free-space value. Here, we analyze this problem for a simple model system consisting of noninteracting point particles performing run-and-tumble dynamics through a two-dimensional disordered medium composed of a random distribution of circular obstacles, in the absence of Brownian diffusion or hydrodynamic interactions. The particles are assumed to collide with the obstacles as hard spheres and subsequently slide on the obstacle surface with no frictional resistance while maintaining their orientation, until they either escape or tumble. We show that the variations in the long-time diffusivity can be described by a universal dimensionless hindrance function f(ϕ,Pe) of the obstacle area fraction ϕ and Péclet number Pe, or ratio of the swimmer run length to the obstacle size. We analytically derive an asymptotic expression for the hindrance function valid for dilute media (Peϕ≪1), and its extension to denser media is obtained using stochastic simulations. As we explain, the model is also easily generalized to describe dispersion in three dimensions.}, }
@article {pmid38241807, year = {2024}, author = {Wang, D and Han, I and McCullough, K and Klaus, S and Lee, J and Srinivasan, V and Li, G and Wang, ZL and Bott, CB and McQuarrie, J and Stinson, BM and deBarbadillo, C and Dombrowski, P and Barnard, J and Gu, AZ}, title = {Side-Stream Enhanced Biological Phosphorus Removal (S2EBPR) enables effective phosphorus removal in a pilot-scale A-B stage shortcut nitrogen removal system for mainstream municipal wastewater treatment.}, journal = {Water research}, volume = {251}, number = {}, pages = {121050}, doi = {10.1016/j.watres.2023.121050}, pmid = {38241807}, issn = {1879-2448}, mesh = {*Sewage ; Denitrification ; Phosphorus/metabolism ; Rivers ; Nitrogen ; RNA, Ribosomal, 16S ; Phylogeny ; Nitrites ; Pilot Projects ; Bioreactors ; *Water Purification/methods ; Polyphosphates/metabolism ; Carbon ; }, abstract = {While the adsorption/bio-oxidation (A/B) process has been widely studied for carbon capture and shortcut nitrogen (N) removal, its integration with enhanced biological phosphorus (P) removal (EBPR) has been considered challenging and thus unexplored. Here, full-scale pilot testing with an integrated system combining A-stage high-rate activated sludge with B-stage partial (de)nitrification/anammox and side-stream EBPR (HRAS-P(D)N/A-S2EBPR) was conducted treating real municipal wastewater. The results demonstrated that, despite the relatively low influent carbon load, the B-stage P(D)N-S2EBPR system could achieve effective P removal performance, with the carbon supplement and redirection of the A-stage sludge fermentate to the S2EBPR. The novel process configuration design enabled a system shift in carbon flux and distribution for efficient EBPR, and provided unique selective factors for ecological niche partitioning among different key functionally relevant microorganisms including polyphosphate accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs). The combined nitrite from B-stage to S2EBPR and aerobic-anoxic conditions in our HRAS-P(D)N/A-S2EBPR system promoted DPAOs for simultaneous internal carbon-driven denitrification via nitrite and P removal. 16S rRNA gene-based oligotyping analysis revealed high phylogenetic microdiversity within the Accumulibacter population and discovered coexistence of certain oligotypes of Accumulibacter and Competibacter correlated with efficient P removal. Single-cell Raman micro-spectroscopy-based phenotypic profiling showed high phenotypic microdiversity in the active PAO community and the involvement of unidentified PAOs and internal carbon-accumulating organisms that potentially played an important role in system performance. This is the first pilot study to demonstrate that the P(D)N-S2EBPR system could achieve shortcut N removal and influent carbon-independent EBPR simultaneously, and the results provided insights into the effects of incorporating S2EBPR into A/B process on metabolic activities, microbial ecology, and resulted system performance.}, }
@article {pmid38236289, year = {2024}, author = {Bergman, I and Lindström, ES and Sassenhagen, I}, title = {Ciliate Grazing on the Bloom-Forming Microalga Gonyostomum semen.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {33}, pmid = {38236289}, issn = {1432-184X}, support = {146-300-188//Olle Engkvists Stiftelse/ ; 146-300-188//Olle Engkvists Stiftelse/ ; }, mesh = {Ecosystem ; *Microalgae ; Semen ; Carbon ; *Ciliophora ; Lakes ; }, abstract = {The freshwater raphidophyte Gonyostomum semen forms extensive summer blooms in northern European humic lakes. The development of these blooms might be facilitated by a lack of natural top-down control, as few zooplankton species are able to prey on these large algal cells (up to 100 μm) that expel trichocysts upon physical stress. In this study, we describe a small ciliate species (< 17 μm) that preys on G. semen by damaging the cell membrane until cytoplasm and organelles spill out. Sequencing of clonal cultures of the ciliate tentatively identified it as the prostomatid species Urotricha pseudofurcata. Grazing experiments illustrated that feeding by U. cf. pseudofurcata can significantly reduce cell concentrations of the microalga. However, differences in cell size and growth rate between two investigated ciliate strains resulted in noticeably different grazing pressure. Environmental sequencing data from five different lakes supported potential interactions between the two species. Urotricha cf. pseudofurcata might, thus, play an important role in aquatic ecosystems that are regularly dominated by G. semen, reducing the abundance of this bloom-forming microalga and enabling transfer of organic carbon to higher trophic levels.}, }
@article {pmid38236100, year = {2023}, author = {Singh, A and Sharma, P and Singh, A and Agarwal, C and Patel M, G and Ganapathy, K}, title = {RELEVANCE FOR DIAGNOSIS, THERAPY, AND STRATEGIES OF GUT MICROBES DYSBIOSIS IN CHRONIC KIDNEY DISEASE: A SYSTEMATIC REVIEW.}, journal = {Georgian medical news}, volume = {}, number = {344}, pages = {57-63}, pmid = {38236100}, issn = {1512-0112}, mesh = {Humans ; Animals ; Rats ; Dysbiosis/diagnosis ; *Gastrointestinal Microbiome ; Quality of Life ; Inflammation ; *Renal Insufficiency, Chronic/complications/diagnosis/therapy ; }, abstract = {Dysbiosis and weakened gastrointestinal barrier function have been identified as potential regulators of Chronic Kidney Disease (CKD). The complex connection among gut micro biota and CKD is provided in this study, with particular attention to how inflammation contributes to the CKD path physiology. It establishes the inverse association between CKD and gut microbial dysbiosis by exploring the collision of CKD about the organization and capabilities of the gut micro biota. The possibility of new diagnostic tools in measuring the dynamic changes within the gut microbial ecology illustrates the importance of accurately diagnosing gut micro biota abnormalities in CKD. Additionally, the study explores the targeted medicines that focus on gut micro biota in CKD. Using data from both human clinical trials and rat models, the study demonstrates the variety of therapeutic approaches and their ability to limit the rate of development of CKD and its accompanying problems. The study we performed was based on the Preferred Reporting Items for Systematic reviews and Meta Analyses (PRISMA) approach. The findings show the significance of investigating the relationship between gut micro biota and CKD, paving up the possibility for new therapeutic strategies to improve the patient outcomes and quality of life. The present understanding of CKD-induced modifications to the gut micro biota and the ensuing effects on gastrointestinal health, emphasizing studies, will be highlighted in this review.}, }
@article {pmid38236032, year = {2024}, author = {Hozalski, RM and Zhao, X and Kim, T and LaPara, TM}, title = {On-site filtration of large sample volumes improves the detection of opportunistic pathogens in drinking water distribution systems.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {2}, pages = {e0165823}, pmid = {38236032}, issn = {1098-5336}, support = {M.L. 2018 Chp. 214 Art. 4 Sec. 02 Subd. 04f//Minnesota Environment and Natural Resources Trust Fund (ENRTF)/ ; }, mesh = {*Drinking Water/microbiology ; *Legionella pneumophila ; Propidium/*analogs &amp; derivatives ; *Mycobacterium/genetics ; Water Microbiology ; Water Supply ; *Legionella/genetics ; *Azides ; }, abstract = {In this study, we compared conventional vacuum filtration of small volumes through disc membranes (effective sample volumes for potable water: 0.3-1.0 L) with filtration of high volumes using ultrafiltration (UF) modules (effective sample volumes for potable water: 10.6-84.5 L) for collecting bacterial biomass from raw, finished, and tap water at seven drinking water systems. Total bacteria, Legionella spp., Legionella pneumophila, Mycobacterium spp., and Mycobacterium avium complex in these samples were enumerated using both conventional quantitative PCR (qPCR) and viability qPCR (using propidium monoazide). In addition, PCR-amplified gene fragments were sequenced for microbial community analysis. The frequency of detection (FOD) of Legionella spp. in finished and tap water samples was much greater using UF modules (83% and 77%, respectively) than disc filters (24% and 33%, respectively). The FODs for Mycobacterium spp. in raw, finished, and tap water samples were also consistently greater using UF modules than disc filters. Furthermore, the number of observed operational taxonomic units and diversity index values for finished and tap water samples were often substantially greater when using UF modules as compared to disc filters. Conventional and viability qPCR yielded similar results, suggesting that membrane-compromised cells represented a minor fraction of total bacterial biomass. In conclusion, our research demonstrates that large-volume filtration using UF modules improved the detection of opportunistic pathogens at the low concentrations typically found in public drinking water systems and that the majority of bacteria in these systems appear to be viable in spite of disinfection with free chlorine and/or chloramine.IMPORTANCEOpportunistic pathogens, such as Legionella pneumophila, are a growing public health concern. In this study, we compared sample collection and enumeration methods on raw, finished, and tap water at seven water systems throughout the State of Minnesota, USA. The results showed that on-site filtration of large water volumes (i.e., 500-1,000 L) using ultrafiltration membrane modules improved the frequency of detection of relatively rare organisms, including opportunistic pathogens, compared to the common approach of filtering about 1 L using disc membranes. Furthermore, results from viability quantitative PCR (qPCR) with propidium monoazide were similar to conventional qPCR, suggesting that membrane-compromised cells represent an insignificant fraction of microorganisms. Results from these ultrafiltration membrane modules should lead to a better understanding of the microbial ecology of drinking water distribution systems and their potential to inoculate premise plumbing systems with opportunistic pathogens where conditions are more favorable for their growth.}, }
@article {pmid38235197, year = {2023}, author = {Meesters, C and Weldegergis, BT and Dicke, M and Jacquemyn, H and Lievens, B}, title = {Limited effects of plant-beneficial fungi on plant volatile composition and host-choice behavior of Nesidiocoris tenuis.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1322719}, pmid = {38235197}, issn = {1664-462X}, abstract = {Biological control using plant-beneficial fungi has gained considerable interest as a sustainable method for pest management, by priming the plant for enhanced defense against pathogens and insect herbivores. However, despite promising outcomes, little is known about how different fungal strains mediate these beneficial effects. In this study, we evaluated whether inoculation of tomato seeds with the plant-beneficial fungi Beauveria bassiana ARSEF 3097, Metarhizium brunneum ARSEF 1095 and Trichoderma harzianum T22 affected the plant's volatile organic compound (VOC) profile and the host-choice behavior of Nesidiocoris tenuis, an emerging pest species in NW-European tomato cultivation, and the related zoophytophagous biocontrol agent Macrolophus pygmaeus. Results indicated that fungal inoculation did not significantly alter the VOC composition of tomato plants. However, in a two-choice cage assay where female insects were given the option to select between control plants and fungus-inoculated plants, N. tenuis preferred control plants over M. brunneum-inoculated plants. Nearly 72% of all N. tenuis individuals tested chose the control treatment. In all other combinations tested, no significant differences were found for none of the insects. We conclude that inoculation of tomato with plant-beneficial fungi had limited effects on plant volatile composition and host-choice behavior of insects. However, the observation that N. tenuis was deterred from the crop when inoculated with M. brunneum and attracted to non-inoculated plants may provide new opportunities for future biocontrol based on a push-pull strategy.}, }
@article {pmid38234383, year = {2022}, author = {Tan, YP and Bishop-Hurley, SL and Shivas, RG and Cowan, DA and Maggs-Kölling, G and Maharachchikumbura, SSN and Pinruan, U and Bransgrove, KL and De la Peña-Lastra, S and Larsson, E and Lebel, T and Mahadevakumar, S and Mateos, A and Osieck, ER and Rigueiro-Rodríguez, A and Sommai, S and Ajithkumar, K and Akulov, A and Anderson, FE and Arenas, F and Balashov, S and Bañares, &#xc1; and Berger, DK and Bianchinotti, MV and Bien, S and Bilański, P and Boxshall, AG and Bradshaw, M and Broadbridge, J and Calaça, FJS and Campos-Quiroz, C and Carrasco-Fernández, J and Castro, JF and Chaimongkol, S and Chandranayaka, S and Chen, Y and Comben, D and Dearnaley, JDW and Ferreira-Sá, AS and Dhileepan, K and Díaz, ML and Divakar, PK and Xavier-Santos, S and Fernández-Bravo, A and Gené, J and Guard, FE and Guerra, M and Gunaseelan, S and Houbraken, J and Janik-Superson, K and Jankowiak, R and Jeppson, M and Jurjević, &#x17d; and Kaliyaperumal, M and Kelly, LA and Kezo, K and Khalid, AN and Khamsuntorn, P and Kidanemariam, D and Kiran, M and Lacey, E and Langer, GJ and López-Llorca, LV and Luangsa-Ard, JJ and Lueangjaroenkit, P and Lumbsch, HT and Maciá-Vicente, JG and Mamatha Bhanu, LS and Marney, TS and Marqués-Gálvez, JE and Morte, A and Naseer, A and Navarro-Ródenas, A and Oyedele, O and Peters, S and Piskorski, S and Quijada, L and Ramírez, GH and Raja, K and Razzaq, A and Rico, VJ and Rodríguez, A and Ruszkiewicz-Michalska, M and Sánchez, RM and Santelices, C and Savitha, AS and Serrano, M and Leonardo-Silva, L and Solheim, H and Somrithipol, S and Sreenivasa, MY and Stępniewska, H and Strapagiel, D and Taylor, T and Torres-Garcia, D and Vauras, J and Villarreal, M and Visagie, CM and Wołkowycki, M and Yingkunchao, W and Zapora, E and Groenewald, JZ and Crous, PW}, title = {Fungal Planet description sheets: 1436-1477.}, journal = {Persoonia}, volume = {49}, number = {}, pages = {261-350}, pmid = {38234383}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Argentina, Colletotrichum araujiae on leaves, stems and fruits of Araujia hortorum. Australia, Agaricus pateritonsus on soil, Curvularia fraserae on dying leaf of Bothriochloa insculpta, Curvularia millisiae from yellowing leaf tips of Cyperus aromaticus, Marasmius brunneolorobustus on well-rotted wood, Nigrospora cooperae from necrotic leaf of Heteropogon contortus, Penicillium tealii from the body of a dead spider, Pseudocercospora robertsiorum from leaf spots of Senna tora, Talaromyces atkinsoniae from gills of Marasmius crinis-equi and Zasmidium pearceae from leaf spots of Smilaxglyciphylla. Brazil, Preussia bezerrensis from air. Chile, Paraconiothyrium kelleni from the rhizosphere of Fragaria chiloensis subsp. chiloensis f. chiloensis. Finland, Inocybe udicola on soil in mixed forest with Betula pendula, Populus tremula, Picea abies and Alnus incana. France, Myrmecridium normannianum on dead culm of unidentified Poaceae. Germany, Vexillomyces fraxinicola from symptomless stem wood of Fraxinus excelsior. India, Diaporthe limoniae on infected fruit of Limonia acidissima, Didymella naikii on leaves of Cajanus cajan, and Fulvifomes mangroviensis on basal trunk of Aegiceras corniculatum. Indonesia, Penicillium ezekielii from Zea mays kernels. Namibia, Neocamarosporium calicoremae and Neocladosporium calicoremae on stems of Calicorema capitata, and Pleiochaeta adenolobi on symptomatic leaves of Adenolobus pechuelii. Netherlands, Chalara pteridii on stems of Pteridium aquilinum, Neomackenziella juncicola (incl. Neomackenziella gen. nov.) and Sporidesmiella junci from dead culms of Juncus effusus. Pakistan, Inocybe longistipitata on soil in a Quercus forest. Poland, Phytophthora viadrina from rhizosphere soil of Quercus robur, and Septoria krystynae on leaf spots of Viscum album. Portugal (Azores), Acrogenospora stellata on dead wood or bark. South Africa, Phyllactinia greyiae on leaves of Greyia sutherlandii and Punctelia anae on bark of Vachellia karroo. Spain, Anteaglonium lusitanicum on decaying wood of Prunus lusitanica subsp. lusitanica, Hawksworthiomyces riparius from fluvial sediments, Lophiostoma carabassense endophytic in roots of Limbarda crithmoides, and Tuber mohedanoi from calcareus soils. Spain (Canary Islands), Mycena laurisilvae on stumps and woody debris. Sweden, Elaphomyces geminus from soil under Quercus robur. Thailand, Lactifluus chiangraiensis on soil under Pinus merkusii, Lactifluus nakhonphanomensis and Xerocomus sisongkhramensis on soil under Dipterocarpus trees. Ukraine, Valsonectria robiniae on dead twigs of Robinia hispida. USA, Spiralomyces americanus (incl. Spiralomyces gen. nov.) from office air. Morphological and culture characteristics are supported by DNA barcodes. Citation: Tan YP, Bishop-Hurley SL, Shivas RG, et al. 2022. Fungal Planet description sheets: 1436-1477. Persoonia 49: 261-350. https://doi.org/10.3767/persoonia.2022.49.08.}, }
@article {pmid38232435, year = {2024}, author = {Cagri Ozturk, R and Feyzioglu, AM and Capkin, E and Yildiz, I and Altinok, I}, title = {Effects of environmental parameters on spatial and temporal distribution of marine microbial communities in the southern Black Sea.}, journal = {Marine environmental research}, volume = {195}, number = {}, pages = {106344}, doi = {10.1016/j.marenvres.2024.106344}, pmid = {38232435}, issn = {1879-0291}, mesh = {*Seawater/chemistry ; RNA, Ribosomal, 16S/genetics ; Black Sea ; Bacteria/genetics ; *Microbiota ; Water ; }, abstract = {The Black Sea is a unique environment with strong and permanent vertical stratification, with a thin layer of oxic zone above and a permanent anoxic zone below. Few high-throughput genomic surveys have been conducted to examine microbiota in the Black Sea. Yet, there is no study on the seasonal and vertical variation in microbial community compositions, driving forces and mechanisms of community assembly. In this study, seasonal, vertical, and spatial microbial assemblages were studied in terms of diversity, abundance, and community structure using 16S rRNA metabarcoding. 16S rRNA metabarcoding confirmed seasonal changes in microbial communities and the presence of distinct microbial groups among different water layers. Taxa belonging to Cyanobiaceae contributed a large fraction of the total biomass and were the most abundant autotrophic bacteria found across the whole water column, including hydrogen sulfide-containing anoxic zone. Temperature, salinity, water density, conductivity, light, chlorophyll-a, O2, NO3, NH3, PO4, Si, and H2S had a significant influence on the vertical bacterial community assemblages. The copper mine discharge system at 180 m did not affect microbial community structure and composition. Temperature seemed to be a primary factor in the variance between shallow depths. In conclusion, the lack of light, low dissolved oxygen levels, and low temperature do not restrict microbial diversity, as proven by the higher diversity observed in deeper zones. Wastewater in Black Sea region may be discharged into the Black Sea to depth of 180 m or deeper without impacting microbial ecology.}, }
@article {pmid38229613, year = {2023}, author = {Pavan, S and Gorthi, SP and Prabhu, AN and Das, B and Mutreja, A and Vasudevan, K and Shetty, V and Ramamurthy, T and Ballal, M}, title = {Dysbiosis of the Beneficial Gut Bacteria in Patients with Parkinson's Disease from India.}, journal = {Annals of Indian Academy of Neurology}, volume = {26}, number = {6}, pages = {908-916}, pmid = {38229613}, issn = {0972-2327}, abstract = {OBJECTIVES: Recent advancement in understanding neurological disorders has revealed the involvement of dysbiosis of the gut microbiota in the pathophysiology of Parkinson's disease (PD). We sequenced microbial DNA using fecal samples collected from PD cases and healthy controls (HCs) to evaluate the role of gut microbiota.<br><br>METHODS: Full-length bacterial 16S rRNA gene sequencing of fecal samples was performed using amplified polymerase chain reaction (PCR) products on the GridION Nanopore sequencer. Sequenced data were analyzed using web-based tools BugSeq and MicrobiomeAnalyst.<br><br>RESULTS: We found that certain bacterial families like Clostridia UCG 014, Cristensenellaceae, and Oscillospiraceae are higher in abundance, and Lachinospiracea, Coriobacteriaceae and genera associated with short-chain fatty acid production, Faecalibacterium, Fusicatenibacter, Roseburia and Blautia, are lower in abundance among PD cases when compared with the HC. Genus Akkermansia, Dialister, Bacteroides, and Lachnospiraceae NK4A136 group positively correlated with constipation in PD.<br><br>CONCLUSION: Observations from this study support the other global research on the PD gut microbiome background and provide fresh insight into the gut microbial composition of PD patients from a south Indian population. We report a higher abundance of Clostridia UCG 014 group, previously not linked to PD.}, }
@article {pmid38228918, year = {2024}, author = {Alonso, A and Boyero, L and Solla, A and Ferreira, V}, title = {Dieback and Replacement of Riparian Trees May Impact Stream Ecosystem Functioning.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {32}, pmid = {38228918}, issn = {1432-184X}, mesh = {*Ecosystem ; Trees ; Rivers/microbiology ; Biomass ; Nitrogen ; Plant Leaves/microbiology ; *Alnus/microbiology ; }, abstract = {Alders are nitrogen (N)-fixing riparian trees that promote leaf litter decomposition in streams through their high-nutrient leaf litter inputs. While alders are widespread across Europe, their populations are at risk due to infection by the oomycete Phytophthora ×alni, which causes alder dieback. Moreover, alder death opens a space for the establishment of an aggressive N-fixing invasive species, the black locust (Robinia pseudoacacia). Shifts from riparian vegetation containing healthy to infected alder and, eventually, alder loss and replacement with black locust may alter the key process of leaf litter decomposition and associated microbial decomposer assemblages. We examined this question in a microcosm experiment comparing three types of leaf litter mixtures: one representing an original riparian forest composed of healthy alder (Alnus lusitanica), ash (Fraxinus angustifolia), and poplar (Populus nigra); one with the same species composition where alder had been infected by P. ×alni; and one where alder had been replaced with black locust. The experiment lasted six weeks, and every two weeks, microbially driven decomposition, fungal biomass, reproduction, and assemblage structure were measured. Decomposition was highest in mixtures with infected alder and lowest in mixtures with black locust, reflecting differences in leaf nutrient concentrations. Mixtures with alder showed distinct fungal assemblages and higher sporulation rates than mixtures with black locust. Our results indicate that alder loss and its replacement with black locust may alter key stream ecosystem processes and assemblages, with important changes already occurring during alder infection. This highlights the importance of maintaining heathy riparian forests to preserve proper stream ecosystem functioning.}, }
@article {pmid38228915, year = {2024}, author = {Iqbal, Z and Ahmad, M and Raza, MA and Hilger, T and Rasche, F}, title = {Phosphate-Solubilizing Bacillus sp. Modulate Soil Exoenzyme Activities and Improve Wheat Growth.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {31}, pmid = {38228915}, issn = {1432-184X}, mesh = {*Phosphates ; Triticum/microbiology ; *Bacillus ; Soil ; Phosphorus ; Bacillus subtilis ; Soil Microbiology ; }, abstract = {Phosphorus (P) is a vital mineral nutrient in agriculture and its deficiency results in reduced growth, yield, and grain quality in cereals. Much of the applied P in agriculture becomes fixed in soils, limiting its accessibility to plants. Thus, investigating sustainable strategies to release fixed P resources and enhance plant uptake is crucial. This study explored how plant-associated bacteria employ phosphate solubilizing mechanisms to improve P availability. The growth patterns of four bacterial strains, namely Bacillus subtilis ZE15 and ZR3, along with Bacillus megaterium ZE32 and ZR19, were examined in Pikovskaya's broth culture with and without the addition of insoluble phosphorus (P). In the absence of P amendment, most strains reached a stationary growth phase by the fourth day. However, their responses diverged when exposed to P-amended media. Particularly, ZE15 demonstrated the highest P solubilization capability, achieving up to 130 µg mL[-1] solubilization in vitro. All strains produced organic acids in Pikovskaya's broth culture. A comparison of the influence of Ca3(PO4)2 revealed significantly greater organic acid quantities in the presence of insoluble P. Notably, strain ZE15 exhibited the highest phosphate esterase activity (3.65 nmol g[-1] dry matter), while strain ZE32 showed the highest ß-D glucosidase activity (2.81 nmol g[-1] dry matter) in the presence of insoluble P. The ability of Bacillus species to solubilize P in combination with increased exoenzyme activity in the rhizosphere could be used in future studies to support P uptake through enhanced solubilization and mineralization.}, }
@article {pmid38225668, year = {2024}, author = {Terzin, M and Laffy, PW and Robbins, S and Yeoh, YK and Frade, PR and Glasl, B and Webster, NS and Bourne, DG}, title = {The road forward to incorporate seawater microbes in predictive reef monitoring.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {5}, pmid = {38225668}, issn = {2524-6372}, abstract = {Marine bacterioplankton underpin the health and function of coral reefs and respond in a rapid and sensitive manner to environmental changes that affect reef ecosystem stability. Numerous meta-omics surveys over recent years have documented persistent associations of opportunistic seawater microbial taxa, and their associated functions, with metrics of environmental stress and poor reef health (e.g. elevated temperature, nutrient loads and macroalgae cover). Through positive feedback mechanisms, disturbance-triggered heterotrophic activity of seawater microbes is hypothesised to drive keystone benthic organisms towards the limit of their resilience and translate into shifts in biogeochemical cycles which influence marine food webs, ultimately affecting entire reef ecosystems. However, despite nearly two decades of work in this space, a major limitation to using seawater microbes in reef monitoring is a lack of a unified and focused approach that would move beyond the indicator discovery phase and towards the development of rapid microbial indicator assays for (near) real-time reef management and decision-making. By reviewing the current state of knowledge, we provide a comprehensive framework (defined as five phases of research and innovation) to catalyse a shift from fundamental to applied research, allowing us to move from descriptive to predictive reef monitoring, and from reactive to proactive reef management.}, }
@article {pmid38224372, year = {2024}, author = {Syiemiong, D and Rabha, J}, title = {Unveiling nature's treasures: actinobacteria from Meghalaya's mining sites as sources of bioactive compounds.}, journal = {Archives of microbiology}, volume = {206}, number = {2}, pages = {64}, pmid = {38224372}, issn = {1432-072X}, mesh = {*Actinobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria ; *Actinomycetales ; *Nocardia ; }, abstract = {Coal and sillimanite mining sites present unique ecological niches favoring the growth of actinobacteria, a group of Gram-positive bacteria known for producing a wide array of bioactive compounds. Isolating these bacteria from such environments could unveil novel compounds with potential biotechnological applications. This study involved the isolation of actinobacteria from two mining sites in Meghalaya, India. The dominant genera from both sites were Streptomyces, Amycolatopsis, Nocardia, and Streptosporangium. Metabolic pathway prediction from 16S rRNA gene revealed several pathways beneficial for plant growth. Exploration of biosynthetic genes indicated a prevalence of the type-II polyketide synthase gene. Sequencing the ketosynthase-alpha domain of the gene led to predictions of various bioactive secondary metabolites. Around 44% of the isolates demonstrated antimicrobial properties, with some also displaying plant growth-promoting traits. Amycolatopsis SD-15 exhibited promising results in planta when tested on tomato plants. These findings highlight the potential of actinobacteria from Meghalaya's mining sites across medical, agricultural, and industrial domains.}, }
@article {pmid38223759, year = {2024}, author = {Liu, B and Lee, CW and Bong, CW and Wang, AJ}, title = {Investigating Escherichia coli habitat transition from sediments to water in tropical urban lakes.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e16556}, pmid = {38223759}, issn = {2167-8359}, mesh = {*Escherichia coli ; *Lakes/microbiology ; Water Microbiology ; Water Quality ; Ecosystem ; }, abstract = {BACKGROUND: Escherichia coli is a commonly used faecal indicator bacterium to assess the level of faecal contamination in aquatic habitats. However, extensive studies have reported that sediment acts as a natural reservoir of E. coli in the extraintestinal environment. E. coli can be released from the sediment, and this may lead to overestimating the level of faecal contamination during water quality surveillance. Thus, we aimed to investigate the effects of E. coli habitat transition from sediment to water on its abundance in the water column.<br><br>METHODS: This study enumerated the abundance of E. coli in the water and sediment at five urban lakes in the Kuala Lumpur-Petaling Jaya area, state of Selangor, Malaysia. We developed a novel method for measuring habitat transition rate of sediment E. coli to the water column, and evaluated the effects of habitat transition on E. coli abundance in the water column after accounting for its decay in the water column.<br><br>RESULTS: The abundance of E. coli in the sediment ranged from below detection to 12,000 cfu g[-1], and was about one order higher than in the water column (1 to 2,300 cfu mL[-1]). The habitat transition rates ranged from 0.03 to 0.41 h[-1]. In contrast, the E. coli decay rates ranged from 0.02 to 0.16 h[-1]. In most cases (>80%), the habitat transition rates were higher than the decay rates in our study.<br><br>DISCUSSION: Our study provided a possible explanation for the persistence of E. coli in tropical lakes. To the best of our knowledge, this is the first quantitative study on habitat transition of E. coli from sediments to water column.}, }
@article {pmid38218325, year = {2024}, author = {Eberhardt, N and Santamarina, BG and Enghardt, ML and Rohland, O and Hussain, I and Tannert, A and Thieme, L and Rubio, I and Jürgen Rödel,  and Bettina Löffler,  and Arndt, HD and Bauer, M and Busch, A}, title = {The effects of photoactivated ciprofloxacin and bile acids on biofilms on bile duct catheters.}, journal = {International journal of antimicrobial agents}, volume = {63}, number = {4}, pages = {107086}, doi = {10.1016/j.ijantimicag.2024.107086}, pmid = {38218325}, issn = {1872-7913}, mesh = {Humans ; *Ciprofloxacin/pharmacology ; *Bile Acids and Salts/pharmacology ; Pilot Projects ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Biofilms ; Bile Ducts ; Catheters ; Escherichia coli ; }, abstract = {OBJECTIVES: This study examined the potential of a novel photoactivatable ciprofloxacin to act against bacterial infections and microbiomes related to biliary diseases. It also evaluated treatment by combining the impact of bile acids and antibiotics on biofilms. Innovative strategies were evaluated to address the elusive bile duct microbiome resulting in biofilm-related infections linked to biliary catheters. The healthy biliary system is considered sterile, but bile microbiomes can occur in disease, and these correlate with hepatobiliary diseases. Causes include biofilms that form on internal-external biliary drainage catheters. These biliary catheters were used to noninvasively study the otherwise elusive bile microbiome for a pilot study.<br><br>METHODS: A new photoactivatable antibiotic was tested for efficacy against human-derived pathogenic bacterial isolates - Salmonella enterica and Escherichia coli - and catheter-derived bile duct microbiomes. In addition, the effect of bile acids on the antibiotic treatment of biofilms was quantified using crystal violet staining, confocal laser scanning microscopy, and biofilm image analysis. Two novel approaches for targeting biliary biofilms were tested.<br><br>RESULTS: A photoactivated antibiotic based on ciprofloxacin showed efficacy in preventing biofilm formation and reducing bacterial viability without harming eukaryotic cells. Furthermore, combination treatment of antibiotics with bile acids, such as ursodesoxycholic acid, mildly influenced biofilm biomass but reduced bacterial survival within biofilms.<br><br>CONCLUSION: Bile acids, in addition to their endocrine and paracrine functions, may enhance antibiotic killing of bacterial biofilms compared with antibiotics alone. These approaches hold promise for treating biliary infections such as cholangitis.}, }
@article {pmid38217646, year = {2024}, author = {Blache, A and Achouak, W}, title = {Extraction and Purification of Outer Membrane Vesicles and Their Associated RNAs.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2741}, number = {}, pages = {11-24}, pmid = {38217646}, issn = {1940-6029}, mesh = {*Gram-Negative Bacteria/genetics ; Escherichia coli/genetics ; RNA, Bacterial/genetics/metabolism ; Bacterial Outer Membrane Proteins/genetics/metabolism ; *Extracellular Vesicles/metabolism ; }, abstract = {Outer membrane vesicles (OMVs), produced by Gram negative-bacteria and sRNAs, are key players in cell-to-cell communication and interactions of bacteria with the environment. OMVs act as information carriers and encapsulate various molecules such as proteins, lipids, metabolites, and RNAs. OMVs and sRNAs play a broad range of functions from pathogenesis to stress resistance, to biofilm formation and both mediate interkingdom signaling. Various studies indicate that there is a mechanism of intercellular communication mediated by OMV-derived bacterial RNAs that is conserved among certain bacterial species. Here we describe methods for the extraction and purification of vesicles produced by Gram-negative bacteria, such as Pseudomonas brassicacearum and Escherichia coli, and address methods for the extraction of OMVs-derived sRNA and techniques for the analysis of sRNAs.}, }
@article {pmid38217094, year = {2024}, author = {Garuglieri, E and Marasco, R and Odobel, C and Chandra, V and Teillet, T and Areias, C and Sánchez-Román, M and Vahrenkamp, V and Daffonchio, D}, title = {Searching for microbial contribution to micritization of shallow marine sediments.}, journal = {Environmental microbiology}, volume = {26}, number = {2}, pages = {e16573}, doi = {10.1111/1462-2920.16573}, pmid = {38217094}, issn = {1462-2920}, support = {OSR#4097//King Abdullah University of Science and Technology/ ; }, mesh = {*Geologic Sediments/chemistry ; Carbonates ; Calcium Carbonate ; *Microbiota ; }, abstract = {Micritization is an early diagenetic process that gradually alters primary carbonate sediment grains through cycles of dissolution and reprecipitation of microcrystalline calcite (micrite). Typically observed in modern shallow marine environments, micritic textures have been recognized as a vital component of storage and flow in hydrocarbon reservoirs, attracting scientific and economic interests. Due to their endolithic activity and the ability to promote nucleation and reprecipitation of carbonate crystals, microorganisms have progressively been shown to be key players in micritization, placing this process at the boundary between the geological and biological realms. However, published research is mainly based on geological and geochemical perspectives, overlooking the biological and ecological complexity of microbial communities of micritized sediments. In this paper, we summarize the state-of-the-art and research gaps in micritization from a microbial ecology perspective. Since a growing body of literature successfully applies in vitro and in situ 'fishing' strategies to unveil elusive microorganisms and expand our knowledge of microbial diversity, we encourage their application to the study of micritization. By employing these strategies in micritization research, we advocate promoting an interdisciplinary approach/perspective to identify and understand the overlooked/neglected microbial players and key pathways governing this phenomenon and their ecology/dynamics, reshaping our comprehension of this process.}, }
@article {pmid38216372, year = {2024}, author = {Pogoreutz, C and Ziegler, M}, title = {Frenemies on the reef? Resolving the coral-Endozoicomonas association.}, journal = {Trends in microbiology}, volume = {32}, number = {5}, pages = {422-434}, doi = {10.1016/j.tim.2023.11.006}, pmid = {38216372}, issn = {1878-4380}, mesh = {Animals ; *Anthozoa/microbiology/physiology ; *Coral Reefs ; Microbiota ; Phylogeny ; *Symbiosis ; }, abstract = {Stony corals are poster child holobionts due to their intimate association with diverse microorganisms from all domains of life. We are only beginning to understand the diverse functions of most of these microbial associates, including potential main contributors to holobiont health and resilience. Among these, bacteria of the elusive genus Endozoicomonas are widely perceived as beneficial symbionts based on their genomic potential and their high prevalence and ubiquitous presence in coral tissues. Simultaneously, evidence of pathogenic and parasitic Endozoicomonas lineages in other marine animals is emerging. Synthesizing the current knowledge on the association of Endozoicomonas with marine holobionts, we challenge the perception of a purely mutualistic coral-Endozoicomonas relationship and propose directions to elucidate its role along the symbiotic spectrum.}, }
@article {pmid38214516, year = {2024}, author = {Weller, DL and Murphy, CM and Love, TMT and Danyluk, MD and Strawn, LK}, title = {Methodological differences between studies confound one-size-fits-all approaches to managing surface waterways for food and water safety.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {2}, pages = {e0183523}, pmid = {38214516}, issn = {1098-5336}, support = {P30 ES001247/ES/NIEHS NIH HHS/United States ; 2019-51181-30016//U.S. Department of Agriculture (USDA)/ ; //VT | Virginia Agricultural Experiment Station, Virginia Polytechnic Institute and State University (VAES)/ ; }, mesh = {*Escherichia coli ; Environmental Microbiology ; Salmonella ; *Listeria ; Food ; Food Microbiology ; Food Safety ; }, abstract = {Even though differences in methodology (e.g., sample volume and detection method) have been shown to affect observed microbial water quality, multiple sampling and laboratory protocols continue to be used for water quality monitoring. Research is needed to determine how these differences impact the comparability of findings to generate best management practices and the ability to perform meta-analyses. This study addresses this knowledge gap by compiling and analyzing a data set representing 2,429,990 unique data points on at least one microbial water quality target (e.g., Salmonella presence and Escherichia coli concentration). Variance partitioning analysis was used to quantify the variance in likelihood of detecting each pathogenic target that was uniquely and jointly attributable to non-methodological versus methodological factors. The strength of the association between microbial water quality and select methodological and non-methodological factors was quantified using conditional forest and regression analysis. Fecal indicator bacteria concentrations were more strongly associated with non-methodological factors than methodological factors based on conditional forest analysis. Variance partitioning analysis could not disentangle non-methodological and methodological signals for pathogenic Escherichia coli, Salmonella, and Listeria. This suggests our current perceptions of foodborne pathogen ecology in water systems are confounded by methodological differences between studies. For example, 31% of total variance in likelihood of Salmonella detection was explained by methodological and/or non-methodological factors, 18% was jointly attributable to both methodological and non-methodological factors. Only 13% of total variance was uniquely attributable to non-methodological factors for Salmonella, highlighting the need for standardization of methods for microbiological water quality testing for comparison across studies.IMPORTANCEThe microbial ecology of water is already complex, without the added complications of methodological differences between studies. This study highlights the difficulty in comparing water quality data from projects that used different sampling or laboratory methods. These findings have direct implications for end users as there is no clear way to generalize findings in order to characterize broad-scale ecological phenomenon and develop science-based guidance. To best support development of risk assessments and guidance for monitoring and managing waters, data collection and methods need to be standardized across studies. A minimum set of data attributes that all studies should collect and report in a standardized way is needed. Given the diversity of methods used within applied and environmental microbiology, similar studies are needed for other microbiology subfields to ensure that guidance and policy are based on a robust interpretation of the literature.}, }
@article {pmid38212738, year = {2024}, author = {Varliero, G and Lebre, PH and Adams, B and Chown, SL and Convey, P and Dennis, PG and Fan, D and Ferrari, B and Frey, B and Hogg, ID and Hopkins, DW and Kong, W and Makhalanyane, T and Matcher, G and Newsham, KK and Stevens, MI and Weigh, KV and Cowan, DA}, title = {Biogeographic survey of soil bacterial communities across Antarctica.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {9}, pmid = {38212738}, issn = {2049-2618}, support = {310030_215119/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Humans ; Antarctic Regions ; Phylogeny ; *Soil ; *Cyanobacteria ; Biodiversity ; Soil Microbiology ; }, abstract = {BACKGROUND: Antarctica and its unique biodiversity are increasingly at risk from the effects of global climate change and other human influences. A significant recent element underpinning strategies for Antarctic conservation has been the development of a system of Antarctic Conservation Biogeographic Regions (ACBRs). The datasets supporting this classification are, however, dominated by eukaryotic taxa, with contributions from the bacterial domain restricted to Actinomycetota and Cyanobacteriota. Nevertheless, the ice-free areas of the Antarctic continent and the sub-Antarctic islands are dominated in terms of diversity by bacteria. Our study aims to generate a comprehensive phylogenetic dataset of Antarctic bacteria with wide geographical coverage on the continent and sub-Antarctic islands, to investigate whether bacterial diversity and distribution is reflected in the current ACBRs.<br><br>RESULTS: Soil bacterial diversity and community composition did not fully conform with the ACBR classification. Although 19% of the variability was explained by this classification, the largest differences in bacterial community composition were between the broader continental and maritime Antarctic regions, where a degree of structural overlapping within continental and maritime bacterial communities was apparent, not fully reflecting the division into separate ACBRs. Strong divergence in soil bacterial community composition was also apparent between the Antarctic/sub-Antarctic islands and the Antarctic mainland. Bacterial communities were partially shaped by bioclimatic conditions, with 28% of dominant genera showing habitat preferences connected to at least one of the bioclimatic variables included in our analyses. These genera were also reported as indicator taxa for the ACBRs.<br><br>CONCLUSIONS: Overall, our data indicate that the current ACBR subdivision of the Antarctic continent does not fully reflect bacterial distribution and diversity in Antarctica. We observed considerable overlap in the structure of soil bacterial communities within the maritime Antarctic region and within the continental Antarctic region. Our results also suggest that bacterial communities might be impacted by regional climatic and other environmental changes. The dataset developed in this study provides a comprehensive baseline that will provide a valuable tool for biodiversity conservation efforts on the continent. Further studies are clearly required, and we emphasize the need for more extensive campaigns to systematically sample and characterize Antarctic and sub-Antarctic soil microbial communities. Video Abstract.}, }
@article {pmid38212192, year = {2024}, author = {Ayeni, KI and Berry, D and Ezekiel, CN and Warth, B}, title = {Enhancing microbiome research in sub-Saharan Africa.}, journal = {Trends in microbiology}, volume = {32}, number = {2}, pages = {111-115}, doi = {10.1016/j.tim.2023.11.003}, pmid = {38212192}, issn = {1878-4380}, mesh = {Humans ; Africa South of the Sahara ; *Microbiota ; }, abstract = {While there are lighthouse examples of microbiome research in sub-Saharan Africa (SSA), a significant proportion of local researchers face several challenges. Here, we highlight prevailing issues limiting microbiome research in SSA and suggest potential technological, societal, and research-based solutions. We emphasize the need for considerable investment in infrastructures, training, and appropriate funding to democratize modern technologies with a view to providing useful data to improve human health.}, }
@article {pmid38211751, year = {2024}, author = {Busch, A and Roy, S and Helbing, DL and Colic, L and Opel, N and Besteher, B and Walter, M and Bauer, M and Refisch, A}, title = {Gut microbiome in atypical depression.}, journal = {Journal of affective disorders}, volume = {349}, number = {}, pages = {277-285}, doi = {10.1016/j.jad.2024.01.060}, pmid = {38211751}, issn = {1573-2517}, mesh = {Humans ; Depression ; *Depressive Disorder, Major/diagnosis ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Recent studies showed that immunometabolic dysregulation is related to unipolar major depressive disorder (MDD) and that it more consistently maps to MDD patients endorsing an atypical symptom profile, characterized by energy-related symptoms including increased appetite, weight gain, and hypersomnia. Despite the documented influence of the microbiome on immune regulation and energy homeostasis, studies have not yet investigated microbiome differences among clinical groups in individuals with MDD.<br><br>METHODS: Fifteen MDD patients with atypical features according to the Diagnostic and Statistical Manual of Mental Disorders (DSM-5)-5, forty-four MDD patients not fulfilling the DSM-5 criteria for the atypical subtype, and nineteen healthy controls were included in the study. Participants completed detailed clinical assessment and stool samples were collected. Samples were sequenced for the prokaryotic 16S rRNA gene, in the V3-V4 variable regions. Only samples with no antibiotic exposure in the previous 12&#xa0;months and a minimum of >2000 quality-filtered reads were included in the analyses.<br><br>RESULTS: There were no statistically significant differences in alpha- and beta-diversity between the MDD groups and healthy controls. However, within the atypical MDD group, there was an increase in the Verrucomicrobiota phylum, with Akkermansia as the predominant bacterial genus.<br><br>LIMITATIONS: Cross-sectional data, modest sample size, and significantly increased body mass index in the atypical MDD group.<br><br>CONCLUSIONS: There were no overall differences among the investigated groups. However, differences were found at several taxonomic levels. Studies in larger longitudinal samples with relevant confounders are needed to advance the understanding of the microbial influences on the clinical heterogeneity of depression.}, }
@article {pmid38206365, year = {2024}, author = {Reyes-Reyes, EM and Brown, J and Trial, MD and Chinnasamy, D and Wiegand, JP and Bradford, D and Brinton, RD and Rodgers, KE}, title = {Vivaria housing conditions expose sex differences in brain oxidation, microglial activation, and immune system states in aged hAPOE4 mice.}, journal = {Experimental brain research}, volume = {242}, number = {3}, pages = {543-557}, pmid = {38206365}, issn = {1432-1106}, support = {P01 AG026572/AG/NIA NIH HHS/United States ; P30 AG072980/AG/NIA NIH HHS/United States ; R01 AG057931/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Mice ; Animals ; Female ; Male ; Aged ; Infant ; *Apolipoprotein E4/genetics/metabolism ; Microglia/pathology ; *Alzheimer Disease/genetics ; Housing Quality ; Sex Characteristics ; CD8-Positive T-Lymphocytes/metabolism/pathology ; Brain/metabolism ; Immune System/metabolism/pathology ; Mice, Transgenic ; }, abstract = {Apolipoprotein E ε4 allele (APOE4) is the predominant genetic risk factor for late-onset Alzheimer's disease (AD). APOE4 mouse models have provided advances in the understanding of disease pathogenesis, but unaccounted variables like rodent housing status may hinder translational outcomes. Non-sterile aspects like food and bedding can be major sources of changes in rodent microflora. Alterations in intestinal microbial ecology can cause mucosal barrier impairment and increase pro-inflammatory signals. The present study examined the role of sterile and non-sterile food and housing on redox indicators and the immune status of humanized-APOE4 knock-in mice (hAPOe4). hAPOE4 mice were housed under sterile conditions until 22 months of age, followed by the transfer of a cohort of mice to non-sterile housing for 2 months. At 24 months of age, the redox/immunologic status was evaluated by flow cytometry/ELISA. hAPOE4 females housed under non-sterile conditions exhibited: (1) higher neuronal and microglial oxygen radical production and (2) lower CD68[+] microglia (brain) and CD8[+] T cells (periphery) compared to sterile-housed mice. In contrast, hAPOE4 males in non-sterile housing exhibited: (1) higher MHCII[+] microglia and CD11b[+]CD4[+] T cells (brain) and (2) higher CD11b[+]CD4[+] T cells and levels of lipopolysaccharide-binding protein and inflammatory cytokines in the periphery relative to sterile-housed mice. This study demonstrated that sterile vs. non-sterile housing conditions are associated with the activation of redox and immune responses in the brain and periphery in a sex-dependent manner. Therefore, housing status may contribute to variable outcomes in both the brain and periphery.}, }
@article {pmid38202384, year = {2023}, author = {Wang, B and Sun, M and Wang, Y and Yan, T and Li, Y and Wu, X and Wang, Y and Zhuang, W}, title = {Cadmium-Tolerant Bacterium Strain Cdb8-1 Contributed to the Remediation of Cadmium Pollution through Increasing the Growth and Cadmium Uptake of Chinese Milk Vetch (Astragalus sinicus L.) in Cadmium-Polluted Soils.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {1}, pages = {}, pmid = {38202384}, issn = {2223-7747}, support = {32271916//National Natural Science Foundation of China/ ; JSPKLB202211//Independent Scientific Research Project of Institute of Botany, Jiangsu Province, and Chinese Academy of Sciences/ ; }, abstract = {Cadmium (Cd) pollution has attracted global attention because it not only jeopardizes soil microbial ecology and crop production, but also threatens human health. As of now, microbe-assisted phytoremediation has proven to be a promising approach for the revegetation of Cd-contaminated soil. Therefore, it is important to find such tolerant microorganisms. In the present study, we inoculated a bacteria strain tolerant to Cd, Cdb8-1, to Cd-contaminated soils and then explored the effects of Cdb8-1 inoculation on the performance of the Chinese milk vetch. The results showed plant height, root length, and fresh and dry weight of Chinese milk vetch grown in Cdb8-1-inoculated soils increased compared to the non-inoculated control group. The inoculation of Cd-contaminated soils with Cdb8-1 also enhanced their antioxidant defense system and decreased the H2O2 and malondialdehyde (MDA) contents, which alleviated the phytotoxicity of Cd. The inoculation of Cdb8-1 in Cd-contaminated soils attenuated the contents of total and available Cd in the soil and augmented the BCF and TF of Chinese milk vetch, indicating that the combined application of Cd-tolerant bacteria Cdb8-1 and Chinese milk vetch is a potential solution to Cd-contaminated soils.}, }
@article {pmid38200027, year = {2024}, author = {Verbeelen, T and Fernandez, CA and Nguyen, TH and Gupta, S and Aarts, R and Tabury, K and Leroy, B and Wattiez, R and Vlaeminck, SE and Leys, N and Ganigué, R and Mastroleo, F}, title = {Whole transcriptome analysis highlights nutrient limitation of nitrogen cycle bacteria in simulated microgravity.}, journal = {NPJ microgravity}, volume = {10}, number = {1}, pages = {3}, pmid = {38200027}, issn = {2373-8065}, support = {4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; 4000129030//Federaal Wetenschapsbeleid (Belgian Federal Science Policy Office)/ ; }, abstract = {Regenerative life support systems (RLSS) will play a vital role in achieving self-sufficiency during long-distance space travel. Urine conversion into a liquid nitrate-based fertilizer is a key process in most RLSS. This study describes the effects of simulated microgravity (SMG) on Comamonas testosteroni, Nitrosomonas europaea, Nitrobacter winogradskyi and a tripartite culture of the three, in the context of nitrogen recovery for the Micro-Ecological Life Support System Alternative (MELiSSA). Rotary cell culture systems (RCCS) and random positioning machines (RPM) were used as SMG analogues. The transcriptional responses of the cultures were elucidated. For CO2-producing C. testosteroni and the tripartite culture, a PermaLife[TM] PL-70 cell culture bag mounted on an in-house 3D-printed holder was applied to eliminate air bubble formation during SMG cultivation. Gene expression changes indicated that the fluid dynamics in SMG caused nutrient and O2 limitation. Genes involved in urea hydrolysis and nitrification were minimally affected, while denitrification-related gene expression was increased. The findings highlight potential challenges for nitrogen recovery in space.}, }
@article {pmid38199186, year = {2024}, author = {Truong, D and Changey, F and Rondags, E and Framboisier, X and Etienne, M and Guedon, E}, title = {Evaluation of short-circuited electrodes in combination with dark fermentation for promoting biohydrogen production process.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {157}, number = {}, pages = {108631}, doi = {10.1016/j.bioelechem.2023.108631}, pmid = {38199186}, issn = {1878-562X}, mesh = {Fermentation ; *Manure ; *Bioreactors ; Hydrogen ; Electrodes ; }, abstract = {Short-circuited electrodes, in combination with dark fermentation, were evaluated in a biohydrogen production process. The system is based on an innovative design of a non-compartmented electromicrobial bioreactor with a conductive tubular membrane as cathode and a graphite felt as anode. In particular, the electrode specialization occurred when the bioreactor was inoculated with manure as the whole medium and when a vacuum was applied in the tubular membrane, for allowing continuous extraction of gaseous species (H2, CH4, CO2) from the bioreactor. This specialization of the electrodes as anode and cathode was further confirmed by microbial ecology analysis of biofilms and by cyclic voltammetry measurements. In these experimental conditions, the potential of the electrochemical system (short-circuited electrodes) reached values as low as -320 mV vs. SHE, associated with a significant bioH2 production. Moreover, a higher bioH2 production occurred and a potential of the electrochemical system as low as -429 mV vs SHE was temporarily observed, when additional heat treatments of the whole manure were applied in order to remove methanogen microorganisms (i.e., hydrogen consumers). In the bioreactor, the higher production of bioH2 would be promoted by electrofermentation from the current flow observed between short-circuited anode and cathode.}, }
@article {pmid38193259, year = {2024}, author = {De Paepe, E and Plekhova, V and Vangeenderhuysen, P and Baeck, N and Bullens, D and Claeys, T and De Graeve, M and Kamoen, K and Notebaert, A and Van de Wiele, T and Van Den Broeck, W and Vanlede, K and Van Winckel, M and Vereecke, L and Elliott, C and Cox, E and Vanhaecke, L}, title = {Integrated gut metabolome and microbiome fingerprinting reveals that dysbiosis precedes allergic inflammation in IgE-mediated pediatric cow's milk allergy.}, journal = {Allergy}, volume = {79}, number = {4}, pages = {949-963}, doi = {10.1111/all.16005}, pmid = {38193259}, issn = {1398-9995}, support = {//Fonds Wetenschappelijk Onderzoek/ ; //Bijzonder Onderzoeksfonds UGent/ ; }, mesh = {Humans ; Child ; Child, Preschool ; Cattle ; Female ; Mice ; Animals ; *Milk Hypersensitivity ; Dysbiosis ; RNA, Ribosomal, 16S ; *Microbiota ; Inflammation ; Allergens ; Lactoglobulins ; Immunoglobulin E ; Metabolome ; }, abstract = {BACKGROUND: IgE-mediated cow's milk allergy (IgE-CMA) is one of the first allergies to arise in early childhood and may result from exposure to various milk allergens, of which β-lactoglobulin (BLG) and casein are the most important. Understanding the underlying mechanisms behind IgE-CMA is imperative for the discovery of novel biomarkers and the design of innovative treatment and prevention strategies.<br><br>METHODS: We report a longitudinal in&#xa0;vivo murine model, in which two mice strains (BALB/c and C57Bl/6) were sensitized to BLG using either cholera toxin or an oil emulsion (n&#x2009;=&#x2009;6 per group). After sensitization, mice were challenged orally, their clinical signs monitored, antibody (IgE and IgG1) and cytokine levels (IL-4 and IFN-&#x3b3;) measured, and fecal samples subjected to metabolomics. The results of the murine models were further extrapolated to fecal microbiome-metabolome data from our population of IgE-CMA (n&#x2009;=&#x2009;22) and healthy (n&#x2009;=&#x2009;23) children (Trial: NCT04249973), on which polar metabolomics, lipidomics and 16S rRNA metasequencing were performed. In&#xa0;vitro gastrointestinal digestions and multi-omics corroborated the microbial origin of proposed metabolic changes.<br><br>RESULTS: During mice sensitization, we observed multiple microbially derived metabolic alterations, most importantly bile acid, energy and tryptophan metabolites, that preceded allergic inflammation. We confirmed microbial dysbiosis, and its associated effect on metabolic alterations in our patient cohort, through in&#xa0;vitro digestions and multi-omics, which was accompanied by metabolic signatures of low-grade inflammation.<br><br>CONCLUSION: Our results indicate that gut dysbiosis precedes allergic inflammation and nurtures a chronic low-grade inflammation in children on elimination diets, opening important new opportunities for future prevention and treatment strategies.}, }
@article {pmid38191744, year = {2024}, author = {Nawata, K and Kadoya, A and Suzuki, S}, title = {Persistence of Marine Bacterial Plasmid in the House Fly (Musca domestica): Marine-Derived Antimicrobial Resistance Genes Have a Chance of Invading the Human Environment.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {30}, pmid = {38191744}, issn = {1432-184X}, support = {KAKENHI 20H00633//Japanese Society of Promotion of Science/ ; Endowed Chair Program//The Sumitomo Electric Industries Group Corporate Social Responsibility Foundation/ ; }, mesh = {Animals ; Humans ; Anti-Bacterial Agents/pharmacology ; *Houseflies ; Angiotensin Receptor Antagonists ; Escherichia coli/genetics ; Angiotensin-Converting Enzyme Inhibitors ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; Enterobacteriaceae/genetics ; *Anti-Infective Agents ; }, abstract = {The house fly is known to be a vector of antibiotic-resistant bacteria (ARB) in animal farms. It is also possible that the house fly contributes to the spread of ARB and antibiotic resistance genes (ARGs) among various environments. We hypothesized that ARB and ARGs present in marine fish and fishery food may gain access to humans via the house fly. We show herein that pAQU1, a marine bacterial ARG-bearing plasmid, persists in the house fly intestine for 5 days after fly ingestion of marine bacteria. In the case of Escherichia coli bearing the same plasmid, the persistence period exceeded 7 days. This interval is sufficient for transmission to human environments, meaning that the house fly is capable of serving as a vector of marine-derived ARGs. Time course monitoring of the house fly intestinal microflora showed that the initial microflora was occupied abundantly with Enterobacteriaceae. Experimentally ingested bacteria dominated the intestinal environment immediately following ingestion; however, after 72 h, the intestinal microflora recovered to resemble that observed at baseline, when diverse genera of Enterobacteriaceae were seen. Given that pAQU1 in marine bacteria and E. coli were detected in fly excrement (defined here as any combination of feces and regurgitated material) at 7 days post-bacterial ingestion, we hypothesize that the house fly may serve as a vector for transmission of ARGs from marine items and fish to humans via contamination with fly excrement.}, }
@article {pmid38191681, year = {2024}, author = {de Pontes, JS and Oehl, F and Pereira, CD and de Toledo Machado, CT and Coyne, D and da Silva, DKA and Maia, LC}, title = {Heterogeneity in Arbuscular Mycorrhizal Fungi and Plant Communities of the Brazilian Cerrado, Transitional Areas toward the Caatinga, and the Atlantic Forest.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {29}, pmid = {38191681}, issn = {1432-184X}, mesh = {*Mycorrhizae/genetics ; Brazil ; Forests ; Rainforest ; *Microbiota ; Soil ; }, abstract = {The Cerrado is the most diverse tropical savanna worldwide and the second-largest biome in South America. The objective of this study was to understand the heterogeneity and dynamics of arbuscular mycorrhizal fungi (AMF) in different types of natural Cerrado vegetation and areas that are transitioning to dryer savannas or tropical rainforests and to elucidate the driving factors responsible for the differences between these ecosystems. Twenty-one natural sites were investigated, including typical Cerrado forest, typical Caatinga, Atlantic Rainforest, transitions between Cerrado and Caatinga, Cerrado areas near Caatinga or rainforest, and Carrasco sites. Spores were extracted from the soils, counted, and morphologically analyzed. In total, 82 AMF species were detected. AMF species richness varied between 36 and 51, with the highest richness found in the area transitioning between Cerrado and Caatinga, followed by areas of Cerrado close to Caatinga and typical Cerrado forest. The types of Cerrado vegetation and the areas transitioning to the Caatinga shared the highest numbers of AMF species (32-38). Vegetation, along with chemical and physical soil parameters, affected the AMF communities, which may also result from seasonal rainfall patterns. The Cerrado has a great AMF diversity and is, consequently, a natural refuge for AMF. The plant and microbial communities as well as the diversity of habitats require urgent protection within the Cerrado, as it represents a key AMF hotspot.}, }
@article {pmid38190944, year = {2024}, author = {Kim, G and Yang, H and Lee, J and Cho, KS}, title = {Comparative analysis of hydrogen production and bacterial communities in mesophilic and thermophilic consortia using multiple inoculum sources.}, journal = {Chemosphere}, volume = {350}, number = {}, pages = {141144}, doi = {10.1016/j.chemosphere.2024.141144}, pmid = {38190944}, issn = {1879-1298}, mesh = {Fermentation ; *Food ; *Refuse Disposal ; Bacteria ; Hydrogen ; Bioreactors ; }, abstract = {This study investigates the hydrogen (H2) production performance and bacterial communities in mesophilic (37 °C) and thermophilic (50 °C) H2-producing consortia derived from different inoculum sources and utilizing food waste as a substrate. This study found notable variations in H2 production characteristics among these consortia. Among the mesophilic consortia (MC), the W-MC obtained with wetland (W) as the inoculum source exhibited the highest hydrogen production (3900 mL·L[-1] and 117 mL·L[-1]·h[-1]), while among the thermophilic consortia (TC), the FP-TC obtained with forest puddle sediment (FP) as the inoculum source showed the highest performance (2112 mL·L[-1] and 127 mL·L[-1]·h[-1]). This study reveals that the choice of inoculum source plays a crucial role in determining hydrogen production efficiency. Furthermore, the bacterial community analysis demonstrated varying microbial diversity and richness in different inoculum sources. Clostridium, a well-known H2-producing bacterium, was found in both mesophilic and thermophilic consortia and showed a positive correlation with H2 production. Other bacteria, such as Sporanaerobacter, Caproiciproducens, and Caldibacillus, also exhibited significant correlations with H2 production, suggesting their potential roles in the process. The study highlights the complex interactions between bacterial communities and hydrogen production performance, shedding light on the critical factors influencing this renewable energy source. Overall, this study contributes to our understanding of the microbial ecology and the factors affecting hydrogen production in different temperature conditions, which can have practical implications for optimizing biohydrogen production processes using organic waste substrates.}, }
@article {pmid38190786, year = {2024}, author = {Zhao, A and Wang, Q and Xu, H and Xu, G}, title = {Effects of continuous warming on homogeneity of periphytic protozoan fauna in marine ecosystems.}, journal = {Marine pollution bulletin}, volume = {199}, number = {}, pages = {116017}, doi = {10.1016/j.marpolbul.2023.116017}, pmid = {38190786}, issn = {1879-3363}, mesh = {*Ecosystem ; *Environmental Biomarkers ; Temperature ; }, abstract = {As a powerful biological indicator, multivariate dispersion in a community is widely used to evaluate the biological evaluation of environmental heterogeneity. To investigate the effects of persistent warming on microbial fauna in marine environments, the periphytic protozoan communities were used as test organisms and incubated in five temperature-controlled circulation system at 22 (control), 25, 28, 31 and 34 °C, respectively. The results showed that (1) there was a clear variation in species occurrence, and the α-/γ-diversity measures decreased with the increase of temperatures; (2) the compositional pattern was significantly driven by the persistent warming compared to community pattern from species-abundance data; and (3) both traditional β-diversity and multivariate dispersion measures on species compositional matrix were significantly correlative with changes in the temperature. Therefore, it is suggested that continuous temperature fluctuations have a greater impact on homogeneity of species composition of protozoan communities than that of their community structure.}, }
@article {pmid38187389, year = {2023}, author = {Roland, MM and Peacock, TE and Hall, N and Mohammed, AD and Ball, R and Jolly, A and Alexeev, S and Dopkins, N and Nagarkatti, M and Nagarkatti, P and Kubinak, JL}, title = {B-cell-specific MhcII regulates microbiota composition in a primarily IgA-independent manner.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1253674}, pmid = {38187389}, issn = {1664-3224}, support = {P20 GM103641/GM/NIGMS NIH HHS/United States ; R01 AI155887/AI/NIAID NIH HHS/United States ; R56 AI162986/AI/NIAID NIH HHS/United States ; S10 OD032271/OD/NIH HHS/United States ; }, mesh = {Animals ; Mice ; Antilymphocyte Serum ; B-Lymphocytes ; Homeodomain Proteins/genetics ; *Immunoglobulin A ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Genes, MHC Class II ; }, abstract = {BACKGROUND: The expression of major histocompatibility complex class II (MhcII) molecules on B cells is required for the development of germinal centers (GCs) in lymphoid follicles; the primary sites for the generation of T-cell-dependent (TD) antibody responses. Peyer's patches (PPs) are secondary lymphoid tissues (SLOs) in the small intestine (SI) that give rise to high-affinity, TD antibodies (mainly immunoglobulin A (IgA)) generated against the microbiota. While several studies have demonstrated that MhcII antigen presentation by other immune cells coordinate TD IgA responses and regulate microbiota composition, whether or not B-cell-specific MhcII influences gut microbial ecology is unknown.<br><br>METHODS: Here, we developed a novel Rag1 [-/-] adoptive co-transfer model to answer this question. In this model, Rag1 [-/-] mice were reconstituted with na&#xef;ve CD4[+] T cells and either MhcII-sufficient or MhcII-deficient na&#xef;ve B cells. Subsequent to this, resulting shifts in microbiota composition was characterized via 16S rRNA gene sequencing of SI-resident and fecal bacterial communities.<br><br>RESULTS: Results from our experiments indicate that SLO development and reconstitution of an anti-commensal TD IgA response can be induced in Rag1 [-/-] mice receiving T cells and MhcII-sufficient B cells, but not in mice receiving T cells and MhcII-deficient B cells. Results from our 16S experiments confirmed that adaptive immunity is a relevant host factor shaping microbial ecology in the gut, and that its impact was most pronounced on SI-resident bacterial communities.<br><br>CONCLUSION: Our data also clearly establishes that MhcII-mediated cognate interactions between B cells and T cells regulates this effect by maintaining species richness in the gut, which is a phenotype commonly associated with good health. Finally, contrary to expectations, our experimental results indicate that IgA was not responsible for driving any of the effects on the microbiota ascribed to the loss of B cell-specific MhcII. Collectively, results from our experiments support that MhcII-mediated antigen presentation by B cells regulates microbiota composition and promotes species richness through an IgA-independent mechanism.}, }
@article {pmid38185942, year = {2024}, author = {Zayed, N and Munjaković, H and Aktan, MK and Simoens, K and Bernaerts, K and Boon, N and Braem, A and Pamuk, F and Saghi, M and Van Holm, W and Fidler, A and Gašperšič, R and Teughels, W}, title = {Electrolyzed Saline Targets Biofilm Periodontal Pathogens In Vitro.}, journal = {Journal of dental research}, volume = {103}, number = {3}, pages = {243-252}, doi = {10.1177/00220345231216660}, pmid = {38185942}, issn = {1544-0591}, mesh = {Humans ; *Interleukin-8 ; Dysbiosis ; Biofilms ; *Anti-Infective Agents ; Inflammation ; }, abstract = {Preventing the development and recurrence of periodontal diseases often includes antimicrobial mouthrinses to control the growth of the periodontal pathogens. Most antimicrobials are nonselective, targeting the symbiotic oral species as well as the dysbiosis-inducing ones. This affects the overall microbial composition and metabolic activity and consequently the host-microbe interactions, which can be detrimental (associated with inflammation) or beneficial (health-associated). Consequently, guiding the antimicrobial effect for modulating the microbial composition to a health-associated one should be considered. For such an approach, this study investigated electrolyzed saline as a novel rinse. Electrolyzed saline was prepared from sterile saline using a portable electrolysis device. Multispecies oral homeostatic and dysbiotic biofilms were grown on hydroxyapatite discs and rinsed daily with electrolyzed saline (EOS). Corresponding positive (NaOCl) and negative (phosphate-buffered saline) controls were included. After 3 rinses, biofilms were analyzed with viability quantitative polymerase chain reaction and scanning electron microscopy. Supernatants of rinsed biofilms were used for metabolic activity analysis (high-performance liquid chromatography) through measuring organic acid content. In addition, human oral keratinocytes (HOKs) were exposed to EOS to test biocompatibility (cytotoxicity and inflammation induction) and also to rinsed biofilms to assess their immunogenicity after rinsing. Rinsing the dysbiotic biofilms with EOS could reduce the counts of the pathobionts (>3 log10 Geq/mm[2] reduction) and avert biofilm dysbiosis (≤1% pathobiont abundance), leading to the dominance of commensal species (≥99%), which altered both biofilm metabolism and interleukin 8 (IL-8) induction in HOKs. EOS had no harmful effects on homeostatic biofilms. The scanning electron micrographs confirmed the same. In addition, tested concentrations of EOS did not have any cytotoxic effects and did not induce IL-8 production in HOKs. EOS showed promising results for diverting dysbiosis in in vitro rinsed biofilms and controlling key periopathogens, with no toxic effects on commensal species or human cells. This novel rinsing should be considered for clinical applications.}, }
@article {pmid38185393, year = {2024}, author = {Wang, L and Zheng, M and Liu, J and Jin, Z and Wang, C and Gao, M and Zhang, H and Zhang, X and Xia, X}, title = {LDLa containing C-type lectin mediates phagocytosis of V.anguillarum and regulates immune effector genes in shrimp.}, journal = {Fish &amp; shellfish immunology}, volume = {145}, number = {}, pages = {109361}, doi = {10.1016/j.fsi.2024.109361}, pmid = {38185393}, issn = {1095-9947}, mesh = {Animals ; Lectins, C-Type/genetics ; Phagocytosis ; *Bacterial Infections ; Receptors, Pattern Recognition/genetics ; Bacteria/metabolism ; Crustacea/metabolism ; *Penaeidae ; Immunity, Innate/genetics ; Hemocytes ; Arthropod Proteins/genetics ; }, abstract = {C-type lectins (CTLs) function as pattern recognition receptors (PRRs) by recognizing invading microorganisms, thereby triggering downstream immune events against infected pathogens. In this study, a novel CTL containing a low-density lipoprotein receptor class A (LDLa) domain was obtained from Litopenaeus vannamei, designed as LvLDLalec. Stimulation by the bacterial pathogen Vibrio anguillarum (V. anguillarum) resulted in remarkable up-regulation of LvLDLalec, as well as release of LvLDLalec into hemolymph. The rLvLDLalec protein possessed broad-spectrum bacterial binding and agglutinating activities, as well as hemocyte attachment ability. Importantly, LvLDLalec facilitated the bacterial clearance in shrimp hemolymph and protected shrimp from bacterial infection. Further studies revealed that LvLDLalec promoted hemocytes phagocytosis against V. anguillarum and lysosomes were involved in the process. Meanwhile, LvLDLalec participated in humoral immunity through activating and inducing nuclear translocation of Dorsal to regulate phagocytosis-related genes and antimicrobial peptides (AMPs) genes, thereby accelerated the removal of invading pathogens in vivo and improved the survival rate of L. vannamei. These results unveil that LvLDLalec serves as a PRR participate in cellular and humoral immunity exerting opsonin activity to play vital roles in the immune regulatory system of L. vannamei.}, }
@article {pmid38182675, year = {2024}, author = {Zhou, Y and Meng, F and Ochieng, B and Xu, J and Zhang, L and Kimirei, IA and Feng, M and Zhu, L and Wang, J}, title = {Climate and Environmental Variables Drive Stream Biofilm Bacterial and Fungal Diversity on Tropical Mountainsides.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {28}, pmid = {38182675}, issn = {1432-184X}, mesh = {*Rivers ; Tanzania ; Bacteria/genetics ; Biofilms ; *Microbiota ; }, abstract = {High mountain freshwater systems are particularly sensitive to the impacts of global warming and relevant environmental changes. Microorganisms contribute substantially to biogeochemical processes, yet their distribution patterns and driving mechanism in alpine streams remain understudied. Here, we examined the bacterial and fungal community compositions in stream biofilm along the elevational gradient of 745-1874 m on Mt. Kilimanjaro and explored their alpha and beta diversity patterns and the underlying environmental drivers. We found that the species richness and evenness monotonically increased towards higher elevations for bacteria, while were non-significant for fungi. However, both bacterial and fungal communities showed consistent elevational distance-decay relationships, i.e., the dissimilarity of assemblage composition increased with greater elevational differences. Bacterial alpha diversity patterns were mainly affected by chemical variables such as total nitrogen and phosphorus, while fungi were affected by physical variables such as riparian shading and stream width. Notably, climatic variables such as mean annual temperature strongly affected the elevational succession of bacterial and fungal community compositions. Our study is the first exploration of microbial biodiversity and their underlying driving mechanisms for stream ecosystems in tropical alpine regions. Our findings provide insights on the response patterns of tropical aquatic microbial community composition and diversity under climate change.}, }
@article {pmid38181473, year = {2024}, author = {Zhao, A and Zhong, X and Xu, H and Xu, G}, title = {Continuous warming shifts the community pattern of periphytic protozoan fauna in marine environments.}, journal = {Marine pollution bulletin}, volume = {199}, number = {}, pages = {116016}, doi = {10.1016/j.marpolbul.2023.116016}, pmid = {38181473}, issn = {1879-3363}, mesh = {*Ecosystem ; Environmental Monitoring/methods ; *Ciliophora ; Food Chain ; Environmental Biomarkers ; Biodiversity ; }, abstract = {Protozoan fauna is playing an important role in the functioning of microbial food webs by transferring the flux of material and energy from low to high tropic levels in marine ecosystems. To assess effects of elevated temperature on the marine ecosystem, periphytic protozoan communities were used as the test microbial fauna, and were incubated in a temperature-controlled circulation system in a successive temperature gradient of 22 (control), 25, 28, 31 and 34 °C. The results showed that: (1) the test microbial fauna was shifted in both species composition and community structure; (2) the average taxonomic distinctness represented a clear decreasing trend, (3) while the variation in taxonomic distinctness significantly increased with increase of water temperature; and (4) the community pattern was significantly departed from an expectation when temperature increased by 12 °C. These results suggested that Protozoa may be used as a useful bioindicator of global warming in marine ecosystems.}, }
@article {pmid38179971, year = {2024}, author = {Price, CE and Valls, RA and Ramsey, AR and Loeven, NA and Jones, JT and Barrack, KE and Schwartzman, JD and Royce, DB and Cramer, RA and Madan, JC and Ross, BD and Bliska, J and O'Toole, GA}, title = {Intestinal Bacteroides modulates inflammation, systemic cytokines, and microbial ecology via propionate in a mouse model of cystic fibrosis.}, journal = {mBio}, volume = {15}, number = {2}, pages = {e0314423}, pmid = {38179971}, issn = {2150-7511}, support = {R01 ES033988/ES/NIEHS NIH HHS/United States ; P30 DK117469/DK/NIDDK NIH HHS/United States ; R35 GM142685/GM/NIGMS NIH HHS/United States ; T32 HL134598/HL/NHLBI NIH HHS/United States ; T32 AI007363/AI/NIAID NIH HHS/United States ; }, mesh = {Child ; Infant ; Humans ; Mice ; Animals ; *Cystic Fibrosis/complications ; Cystic Fibrosis Transmembrane Conductance Regulator ; Propionates ; Bacteroides/genetics ; Caco-2 Cells ; Inflammation/complications ; Disease Models, Animal ; Dysbiosis/complications ; Escherichia coli ; }, abstract = {Persons with cystic fibrosis (CF), starting in early life, show intestinal microbiome dysbiosis characterized in part by a decreased relative abundance of the genus Bacteroides. Bacteroides is a major producer of the intestinal short chain fatty acid propionate. We demonstrate here that cystic fibrosis transmembrane conductance regulator-defective (CFTR-/-) Caco-2 intestinal epithelial cells are responsive to the anti-inflammatory effects of propionate. Furthermore, Bacteroides isolates inhibit the IL-1β-induced inflammatory response of CFTR-/- Caco-2 intestinal epithelial cells and do so in a propionate-dependent manner. The introduction of Bacteroides-supplemented stool from infants with cystic fibrosis into the gut of Cftr[F508del] mice results in higher propionate in the stool as well as the reduction in several systemic pro-inflammatory cytokines. Bacteroides supplementation also reduced the fecal relative abundance of Escherichia coli, indicating a potential interaction between these two microbes, consistent with previous clinical studies. For a Bacteroides propionate mutant in the mouse model, pro-inflammatory cytokine KC is higher in the airway and serum compared with the wild-type (WT) strain, with no significant difference in the absolute abundance of these two strains. Taken together, our data indicate the potential multiple roles of Bacteroides-derived propionate in the modulation of systemic and airway inflammation and mediating the intestinal ecology of infants and children with CF. The roles of Bacteroides and the propionate it produces may help explain the observed gut-lung axis in CF and could guide the development of probiotics to mitigate systemic and airway inflammation for persons with CF.IMPORTANCEThe composition of the gut microbiome in persons with CF is correlated with lung health outcomes, a phenomenon referred to as the gut-lung axis. Here, we demonstrate that the intestinal microbe Bacteroides decreases inflammation through the production of the short-chain fatty acid propionate. Supplementing the levels of Bacteroides in an animal model of CF is associated with reduced systemic inflammation and reduction in the relative abundance of the opportunistically pathogenic group Escherichia/Shigella in the gut. Taken together, these data demonstrate a key role for Bacteroides and microbially produced propionate in modulating inflammation, gut microbial ecology, and the gut-lung axis in cystic fibrosis. These data support the role of Bacteroides as a potential probiotic in CF.}, }
@article {pmid38179905, year = {2024}, author = {Huffines, JT and Boone, RL and Kiedrowski, MR}, title = {Temperature influences commensal-pathogen dynamics in a nasal epithelial cell co-culture model.}, journal = {mSphere}, volume = {9}, number = {1}, pages = {e0058923}, pmid = {38179905}, issn = {2379-5042}, support = {P30 DK072482/DK/NIDDK NIH HHS/United States ; T32 GM008111/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Temperature ; Coculture Techniques ; *Staphylococcus aureus ; Dysbiosis ; *Sinusitis/microbiology ; Epithelial Cells/microbiology ; Inflammation ; Chronic Disease ; }, abstract = {Chronic rhinosinusitis (CRS) is an inflammatory disease of the paranasal sinuses, and microbial dysbiosis associated with CRS is thought to be a key driver of host inflammation that contributes to disease progression. Staphylococcus aureus is a common upper respiratory tract (URT) pathobiont associated with higher carriage rates in CRS populations, where S. aureus-secreted toxins can be identified in CRS tissues. Although many genera of bacteria colonize the URT, few account for the majority of sequencing reads. These include S. aureus and several species belonging to the genus Corynebacterium, including Corynebacterium propinquum and Corynebacterium pseudodiphtheriticum, which are observed at high relative abundance in the healthy URT. Studies have examined bacterial interactions between major microbionts of the URT and S. aureus, but few have done so in the context of a healthy versus diseased URT environment. Here, we examine the role of temperature in commensal, pathogen, and epithelial dynamics using an air-liquid interface cell culture model mimicking the nasal epithelial environment. Healthy URT temperatures change from the nares to the nasopharynx and are increased during disease. Temperatures representative of the healthy URT increase persistence and aggregate formation of commensal C. propinquum and C. pseudodiphtheriticum, reduce S. aureus growth, and lower epithelial cytotoxicity compared to higher temperatures correlating with the diseased CRS sinus. Dual-species colonization revealed species-specific interactions between Corynebacterium species and S. aureus dependent on temperature. Our findings suggest URT mucosal temperature plays a significant role in mediating polymicrobial and host-bacterial interactions that may exacerbate microbial dysbiosis in chronic URT diseases.IMPORTANCEChronic rhinosinusitis is a complex inflammatory disease with a significant healthcare burden. Although presence of S. aureus and microbial dysbiosis are considered mediators of inflammation in CRS, no studies have examined the influence of temperature on S. aureus interactions with the nasal epithelium and the dominant genus of the healthy URT, Corynebacterium. Interactions between Corynebacterium species and S. aureus have been documented in several studies, but none to date have examined how environmental changes in the URT may alter their interactions with the epithelium or each other. This study utilizes a polarized epithelial cell culture model at air-liquid interface to study the colonization and spatial dynamics of S. aureus and clinical isolates of Corynebacterium from people with CRS to characterize the role temperature has in single- and dual-species dynamics on the nasal epithelium.}, }
@article {pmid38179459, year = {2023}, author = {Parsons, RJ and Liu, S and Longnecker, K and Yongblah, K and Johnson, C and Bolaños, LM and Comstock, J and Opalk, K and Kido Soule, MC and Garley, R and Carlson, CA and Temperton, B and Bates, NR}, title = {Suboxic DOM is bioavailable to surface prokaryotes in a simulated overturn of an oxygen minimum zone, Devil's Hole, Bermuda.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1287477}, pmid = {38179459}, issn = {1664-302X}, abstract = {Oxygen minimum zones (OMZs) are expanding due to increased sea surface temperatures, subsequent increased oxygen demand through respiration, reduced oxygen solubility, and thermal stratification driven in part by anthropogenic climate change. Devil's Hole, Bermuda is a model ecosystem to study OMZ microbial biogeochemistry because the formation and subsequent overturn of the suboxic zone occur annually. During thermally driven stratification, suboxic conditions develop, with organic matter and nutrients accumulating at depth. In this study, the bioavailability of the accumulated dissolved organic carbon (DOC) and the microbial community response to reoxygenation of suboxic waters was assessed using a simulated overturn experiment. The surface inoculated prokaryotic community responded to the deep (formerly suboxic) 0.2 μm filtrate with cell densities increasing 2.5-fold over 6 days while removing 5 μmol L[-1] of DOC. After 12 days, the surface community began to shift, and DOC quality became less diagenetically altered along with an increase in SAR202, a Chloroflexi that can degrade recalcitrant dissolved organic matter (DOM). Labile DOC production after 12 days coincided with an increase of Nitrosopumilales, a chemoautotrophic ammonia oxidizing archaea (AOA) that converts ammonia to nitrite based on the ammonia monooxygenase (amoA) gene copy number and nutrient data. In comparison, the inoculation of the deep anaerobic prokaryotic community into surface 0.2 μm filtrate demonstrated a die-off of 25.5% of the initial inoculum community followed by a 1.5-fold increase in cell densities over 6 days. Within 2 days, the prokaryotic community shifted from a Chlorobiales dominated assemblage to a surface-like heterotrophic community devoid of Chlorobiales. The DOM quality changed to less diagenetically altered material and coincided with an increase in the ribulose-1,5-bisphosphate carboxylase/oxygenase form I (cbbL) gene number followed by an influx of labile DOM. Upon reoxygenation, the deep DOM that accumulated under suboxic conditions is bioavailable to surface prokaryotes that utilize the accumulated DOC initially before switching to a community that can both produce labile DOM via chemoautotrophy and degrade the more recalcitrant DOM.}, }
@article {pmid38175304, year = {2024}, author = {Marčiulynas, A and Menkis, A}, title = {Long-term Dynamics of Fungal Communities Inhabiting Decaying Stumps of Quercus robur.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {27}, pmid = {38175304}, issn = {1432-184X}, mesh = {*Mycobiome ; *Quercus ; High-Throughput Nucleotide Sequencing ; Trees ; Wood ; }, abstract = {We studied the diversity, composition, and long-term dynamics of wood-inhabiting fungi in Quercus robur stumps left after commercial tree harvesting in Lithuania. Sampling of wood was carried out at three sites and from stumps, which were 10-, 20-, 30-, 40-, and 50-year-old. DNA was isolated from wood samples and fungal communities analyzed using high-throughput sequencing. Results showed that stump age had a limited effect on fungal diversity. The development of fungal communities in oak stums was found to be a slow process as fungal communities remained similar for decades, while larger changes were only detected in older stumps. The most common fungi were Eupezizella sp. (18.4%), Hyphodontia pallidula (12.9%), Mycena galericulata (8.3%), and Lenzites betulinus (7.1%). Fistulina hepatica, which is a red-listed wood-decay oak fungus, was also detected at a low relative abundance in stump wood. In the shortage of suitable substrate, oak stumps may provide habitats for long-term survival of different fungal species, including red-listed and oak-related fungi.}, }
@article {pmid38175217, year = {2024}, author = {Grandhay, C and Prétot, E and Klaba, V and Celle, H and Normand, AC and Bertrand, X and Grenouillet, F}, title = {Yeast Biodiversity of Karst Waters: Interest of Four Culture Media and an Improved MALDI-TOF MS Database.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {26}, pmid = {38175217}, issn = {1432-184X}, mesh = {Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Culture Media ; *Drinking Water ; Biodiversity ; }, abstract = {Karst aquifers are a significant source of drinking water and highly vulnerable to pollution and microbial contamination. Microbiological regulations for the quality of drinking water mostly focus on bacterial levels and lack guidance concerning fungal contamination. Moreover, there is no standardised microbial analysis methodology for identifying fungi in water. Our main objective was to establish the most effective culture and identification methodology to examine yeast diversity in karst waters. We assessed the comparative efficacy of four culture media (CHROMagar Candida, dichloran glycerol 18% [DG18], dichloran rose Bengal chloramphenicol [DRBC], and SYMPHONY agar) for yeast isolation from karst water samples. Furthermore, we investigated the comprehensiveness of databases used in MALDI-TOF mass spectrometry (MALDI-TOF MS) for identifying environmental yeast species. In total, we analysed 162 water samples, allowing the identification of 2479 yeast isolates. We demonstrate that a combination of four culture media, each with distinct specifications, more efficiently covers a wide range of yeast species in karst water than a combination of only two or three. Supplementation of a MALDI-TOF MS database is also critical for analysing environmental microbial samples and improved the identification of yeast biodiversity. This study is an initial step towards standardising the analysis of fungal biodiversity in karst waters, enabling a better understanding of the significance of this environmental reservoir in relation to public health.}, }
@article {pmid38172411, year = {2024}, author = {Kankonkar, HT and Khandeparker, RS}, title = {Halotolerant Bacteria from Genus Nesterenkonia sandarakina VSA9 as a Potential Polyhydroxyalkanoate Producer.}, journal = {Current microbiology}, volume = {81}, number = {1}, pages = {53}, pmid = {38172411}, issn = {1432-0991}, mesh = {*Polyhydroxyalkanoates ; Phylogeny ; *Micrococcaceae/metabolism ; Bacteria/genetics/metabolism ; Acyltransferases/metabolism ; }, abstract = {Nesterenkonia sandarakina VSA9 pigmented bacteria isolated from Sargassum is being reported to produce polyhydroxyalkanoates (PHA) deduced through detecting the presence of pha C gene using the molecular method. The PHA synthase gene was of type I which has been concluded from the phylogenetic tree and multiple sequence analysis. The amino acid analysis of pha C gene confirms the involvement of the lipase box having a sequence of G-Y-C-I-G-G with cysteine as the active center of the PHA synthase. Homology modeling predicted the 3D protein structure which is similar to the PHA synthase of Chromobacterium sp. USM2. The solvent extract of N. sandarakina VSA9 showed the presence of Carotenoid compound with maximum wavelength at 475 nm. The study's findings could have far-reaching implications, contributing to advancements in the biotechnology, industrial processes, and sustainable practices. The simultaneous production of carotenoids and PHAs by N. sandarakina VSA9 presents exciting opportunities for the development of innovative and environmentally friendly applications.}, }
@article {pmid38171425, year = {2024}, author = {Gao, T and Tian, H and Xiang, L and Wang, Z and Fu, Y and Shi, J and Wen, X and Jiang, X and He, W and Hashsham, SA and Wang, F}, title = {Characteristics of bacterial community and extracellular enzymes in response to atrazine application in black soil.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {343}, number = {}, pages = {123286}, doi = {10.1016/j.envpol.2023.123286}, pmid = {38171425}, issn = {1873-6424}, mesh = {*Atrazine/analysis ; Soil ; Soil Microbiology ; *Herbicides/analysis ; Bacteria/metabolism ; *Soil Pollutants/analysis ; Biomarkers/metabolism ; Biodegradation, Environmental ; }, abstract = {The ecological functioning of black soil largely depends on the activities of various groups of microorganisms. However, little is known about how atrazine, a widely used herbicide with known harmful effects on the environment, influences the microbial ecology of black soil, and the extracellular enzymes related to the carbon, nitrogen and phosphorus cycles. Here, we evaluated the change in extracellular enzymes and bacterial community characteristics in black soil after exposure to various concentrations of atrazine. Low concentrations of applied atrazine (10 - 20 mg kg[-1]) were almost completely degraded after 120 days. At high concentrations (80 - 100 mg kg[-1]), about 95% of the applied atrazine was degraded over the same period. Additionally, linear fitting of data indicated that the total enzymatic activity index (TEI) and bacterial α-diversity index were negatively correlated with atrazine applied concentration. The atrazine had a greater effect on bacterial beta diversity after 120 days, which differentiated species clusters treated with low and high atrazine concentrations. Soil bacterial community structure and function were affected by atrazine, especially at high atrazine concentrations (80 - 100 mg kg[-1]). Key microorganisms such as Sphingomonas and Nocardioides were identified as biomarkers for atrazine dissipation. Functional prediction indicated that most metabolic pathways might be involved in atrazine dissipation. Overall, the findings enhance our understanding of the factors driving atrazine degradation in black soil and supports the use of biomarkers as indicators of atrazine dissipation.}, }
@article {pmid38171124, year = {2024}, author = {Soni, K and Kothamasi, D and Chandra, R}, title = {Municipal wastewater treatment plant showing a potential reservoir for clinically relevant MDR bacterial strains co-occurrence of ESBL genes and integron-integrase genes.}, journal = {Journal of environmental management}, volume = {351}, number = {}, pages = {119938}, doi = {10.1016/j.jenvman.2023.119938}, pmid = {38171124}, issn = {1095-8630}, mesh = {Humans ; beta-Lactamases/genetics ; Integrons/genetics ; Integrases ; Bacteria ; Anti-Bacterial Agents/pharmacology ; Escherichia coli ; Wastewater ; *Bacillus ; *Water Purification ; Drug Resistance, Multiple ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {Municipal wastewater treatment plants (MWWTPs) are a milieu for co-occurrence of multiple antibiotic resistance genes (ARGs). This facilitates mixing and genetic exchange; and promotes dissemination of multidrug resistance (MDR) to wastewater bacterial communities which is hazardous for the effluent receiving environment. This study investigated the co-occurrence of extended-spectrum beta-lactamase (ESBL) genes (blaTEM, blaCTX-M, blaSHV, blaOXA), and integron-integrase genes (intI1, intI2, intI3) in MDR bacteria isolated from the Bharwara MWWTP in Lucknow, India. Thirty-one MDR bacterial colonies resistant to three or more antibiotics were isolated from three treatment stages of this MWWTP. Six of these: Staphylococcus aureus, Serratia marcescens, Salmonella enterica, Shigella sonnei, Escherichia coli, and Bacillus sp. Had co-occurrence of ESBL and integron-integrase genes. These six isolates were examined for the occurrence of MDR efflux genes (qacA, acrB) and ARGs (aac(3)-1, qnrA1, tetA, vanA) and tested for resistance against 12 different antibiotics. The highest resistance was against penicillin-G (100%) and lowest for chloramphenicol (16.66%). Bacillus sp. Isolate BWKRC6 had the highest co-occurrence of antibiotic resistance-determining genes and was resistant to all the 12 antibiotics tested. The co-occurrence of ESBL, integron-integrase, antibiotic resistance-determining and MDR efflux genes in bacteria isolated from the Bharwara MWWTP indicates that the wastewaters of this treatment plant may have become a hotspot for MDR bacteria and may present human and environmental health hazards. Therefore, there is need for a rapid action to limit the spread of this threat. Public regulatory authorities must urgently implement measures to prevent MWWTPs becoming reservoirs for evolution of antibiotic resistance genes and development of antibiotic resistance.}, }
@article {pmid38169617, year = {2023}, author = {Song, W and Wu, F and Yan, Y and Li, Y and Wang, Q and Hu, X and Li, Y}, title = {Gut microbiota landscape and potential biomarker identification in female patients with systemic lupus erythematosus using machine learning.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1289124}, pmid = {38169617}, issn = {2235-2988}, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Lupus Erythematosus, Systemic/diagnosis ; Biomarkers ; Machine Learning ; }, abstract = {OBJECTIVES: Systemic Lupus Erythematosus (SLE) is a complex autoimmune disease that disproportionately affects women. Early diagnosis and prevention are crucial for women's health, and the gut microbiota has been found to be strongly associated with SLE. This study aimed to identify potential biomarkers for SLE by characterizing the gut microbiota landscape using feature selection and exploring the use of machine learning (ML) algorithms with significantly dysregulated microbiotas (SDMs) for early identification of SLE patients. Additionally, we used the SHapley Additive exPlanations (SHAP) interpretability framework to visualize the impact of SDMs on the risk of developing SLE in females.<br><br>METHODS: Stool samples were collected from 54 SLE patients and 55 Negative Controls (NC) for microbiota analysis using 16S rRNA sequencing. Feature selection was performed using Elastic Net and Boruta on species-level taxonomy. Subsequently, four ML algorithms, namely logistic regression (LR), Adaptive Boosting (AdaBoost), Random Forest (RF), and eXtreme gradient boosting (XGBoost), were used to achieve early identification of SLE with SDMs. Finally, the best-performing algorithm was combined with SHAP to explore how SDMs affect the risk of developing SLE in females.<br><br>RESULTS: Both alpha and beta diversity were found to be different in SLE group. Following feature selection, 68 and 21 microbiota were retained in Elastic Net and Boruta, respectively, with 16 microbiota overlapping between the two, i.e., SDMs for SLE. The four ML algorithms with SDMs could effectively identify SLE patients, with XGBoost performing the best, achieving Accuracy, Sensitivity, Specificity, Positive Predictive Value, Negative Predictive Value, and AUC values of 0.844, 0.750, 0.938, 0.923, 0.790, and 0.930, respectively. The SHAP interpretability framework showed a complex non-linear relationship between the relative abundance of SDMs and the risk of SLE, with Escherichia_fergusonii having the largest SHAP value.<br><br>CONCLUSIONS: This study revealed dysbiosis in the gut microbiota of female SLE patients. ML classifiers combined with SDMs can facilitate early identification of female patients with SLE, particularly XGBoost. The SHAP interpretability framework provides insight into the impact of SDMs on the risk of SLE and may inform future scientific treatment for SLE.}, }
@article {pmid38169416, year = {2024}, author = {Kim, K and Jinno, C and Li, X and Bravo, D and Cox, E and Ji, P and Liu, Y}, title = {Impact of an oligosaccharide-based polymer on the metabolic profiles and microbial ecology of weanling pigs experimentally infected with a pathogenic E. coli.}, journal = {Journal of animal science and biotechnology}, volume = {15}, number = {1}, pages = {1}, pmid = {38169416}, issn = {1674-9782}, support = {W4002 and NC1202//National Institute of Food and Agriculture/ ; }, abstract = {BACKGROUND: Our previous study has reported that supplementation of oligosaccharide-based polymer enhances gut health and disease resistance of pigs infected with enterotoxigenic E. coli (ETEC) F18 in a manner similar to carbadox. The objective of this study was to investigate the impacts of oligosaccharide-based polymer or antibiotic on the host metabolic profiles and colon microbiota of weaned pigs experimentally infected with ETEC F18.<br><br>RESULTS: Multivariate analysis highlighted the differences in the metabolic profiles of serum and colon digesta which were predominantly found between pigs supplemented with oligosaccharide-based polymer and antibiotic. The relative abundance of metabolic markers of immune responses and nutrient metabolisms, such as amino acids and carbohydrates, were significantly differentiated between the oligosaccharide-based polymer and antibiotic groups (q&#x2009;<&#x2009;0.2 and fold change&#x2009;>&#x2009;2.0). In addition, pigs in antibiotic had a reduced (P&#x2009;<&#x2009;0.05) relative abundance of Lachnospiraceae and Lactobacillaceae, whereas had greater (P&#x2009;<&#x2009;0.05) Clostridiaceae and Streptococcaceae in the colon digesta on d 11 post-inoculation (PI) compared with d 5 PI.<br><br>CONCLUSIONS: The impact of oligosaccharide-based polymer on the metabolic and microbial profiles of pigs is not fully understood, and further exploration is needed. However, current research suggest that various mechanisms are involved in the enhanced disease resistance and performance in ETEC-challenged pigs by supplementing this polymer.}, }
@article {pmid38167150, year = {2024}, author = {Alahmad, A and Harir, M and Fochesato, S and Tulumello, J and Walker, A and Barakat, M and Ndour, PMS and Schmitt-Kopplin, P and Cournac, L and Laplaze, L and Heulin, T and Achouak, W}, title = {Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {1}, pmid = {38167150}, issn = {2049-2618}, support = {ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; ANR grant RootAdapt ANR17-CE20-0022-01//French Agence Nationale de la Recherche/ ; }, mesh = {*Pennisetum/genetics ; RNA, Ribosomal, 16S/genetics/metabolism ; Plant Roots/microbiology ; *Microbiota ; Soil/chemistry ; Plants/microbiology ; Exudates and Transudates ; Soil Microbiology ; Rhizosphere ; }, abstract = {BACKGROUND: The rhizosheath, a cohesive soil layer firmly adhering to plant roots, plays a vital role in facilitating water and mineral uptake. In pearl millet, rhizosheath formation is genetically controlled and influenced by root exudates. Here, we investigated the impact of root exudates on the microbiota composition, interactions, and assembly processes, and rhizosheath structure in pearl millet using four distinct lines with contrasting soil aggregation abilities.<br><br>RESULTS: Utilizing 16S rRNA gene and ITS metabarcoding for microbiota profiling, coupled with FTICR-MS metabonomic analysis of metabolite composition in distinct plant compartments and root exudates, we revealed substantial disparities in microbial diversity and interaction networks. The &#xdf;-NTI analysis highlighted bacterial rhizosphere turnover driven primarily by deterministic processes, showcasing prevalent homogeneous selection in root tissue (RT) and root-adhering soil (RAS). Conversely, fungal communities were more influenced by stochastic processes. In bulk soil assembly, a combination of deterministic and stochastic mechanisms shapes composition, with deterministic factors exerting a more pronounced role. Metabolic profiles across shoots, RT, and RAS in different pearl millet lines mirrored their soil aggregation levels, emphasizing the impact of inherent plant traits on microbiota composition and unique metabolic profiles in RT and exudates. Notably, exclusive presence of antimicrobial compounds, including DIMBOA and H-DIMBOA, emerged in root exudates and RT of low aggregation lines.<br><br>CONCLUSIONS: This research underscores the pivotal influence of root exudates in shaping the root-associated microbiota composition across pearl millet lines, entwined with their soil aggregation capacities. These findings underscore the interconnectedness of root exudates and microbiota, which jointly shape rhizosheath structure, deepening insights into soil-plant-microbe interactions and ecological processes shaping rhizosphere microbial communities. Deciphering plant-microbe interactions and their contribution to soil aggregation and microbiota dynamics holds promise for the advancement of sustainable agricultural strategies. Video Abstract.}, }
@article {pmid38166159, year = {2024}, author = {Chen, X and He, C and Zhang, Q and Bayakmetov, S and Wang, X}, title = {Modularized Design and Construction of Tunable Microbial Consortia with Flexible Topologies.}, journal = {ACS synthetic biology}, volume = {13}, number = {1}, pages = {183-194}, pmid = {38166159}, issn = {2161-5063}, support = {R01 EB031893/EB/NIBIB NIH HHS/United States ; R01 GM131405/GM/NIGMS NIH HHS/United States ; }, mesh = {*Microbial Consortia/genetics ; *Bacteria/genetics ; }, abstract = {Complex and fluid bacterial community compositions are critical to diversity, stability, and function. However, quantitative and mechanistic descriptions of the dynamics of such compositions are still lacking. Here, we develop a modularized design framework that allows for bottom-up construction and the study of synthetic bacterial consortia with different topologies. We showcase the microbial consortia design and building process by constructing amensalism and competition consortia using only genetic circuit modules to engineer different strains to form the community. Functions of modules and hosting strains are validated and quantified to calibrate dynamic parameters, which are then directly fed into a full mechanistic model to accurately predict consortia composition dynamics for both amensalism and competition without further fitting. More importantly, such quantitative understanding successfully identifies the experimental conditions to achieve coexistence composition dynamics. These results illustrate the process of both computationally and experimentally building up bacteria consortia complexity and hence achieve robust control of such fluid systems.}, }
@article {pmid38165515, year = {2024}, author = {Fowler, AE and McFrederick, QS and Adler, LS}, title = {Pollen Diet Diversity does not Affect Gut Bacterial Communities or Melanization in a Social and Solitary Bee Species.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {25}, doi = {10.1007/s00248-023-02323-6}, pmid = {38165515}, issn = {1432-184X}, support = {GNE19-200-33243//Northeast SARE/ ; AFRI-2018-08591//U.S. Department of Agriculture/ ; }, mesh = {Bees ; Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Diet/veterinary ; Medicago sativa ; Pollen ; }, abstract = {Pollinators face many stressors, including reduced floral diversity. A low-diversity diet can impair organisms' ability to cope with additional stressors, such as pathogens, by altering the gut microbiome and/or immune function, but these effects are understudied for most pollinators. We investigated the impact of pollen diet diversity on two ecologically and economically important generalist pollinators, the social bumble bee (Bombus impatiens) and the solitary alfalfa leafcutter bee (Megachile rotundata). We experimentally tested the effect of one-, two-, or three-species pollen diets on gut bacterial communities in both species, and the melanization immune response in B. impatiens. Pollen diets included dandelion (Taraxacum officinale), staghorn sumac (Rhus typhina), and hawthorn (Crataegus sp.) alone, each pair-wise combination, or a mix of all three species. We fed bees their diet for 7 days and then dissected out guts and sequenced 16S rRNA gene amplicons to characterize gut bacterial communities. To assess melanization in B. impatiens, we inserted microfilament implants into the bee abdomen and measured melanin deposition on the implant. We found that pollen diet did not influence gut bacterial communities in M. rotundata. In B. impatiens, pollen diet composition, but not diversity, affected gut bacterial richness in older, but not newly-emerged bees. Pollen diet did not affect the melanization response in B. impatiens. Our results suggest that even a monofloral, low-quality pollen diet such as dandelion can support diverse gut bacterial communities in captive-reared adults of these bee species. These findings shed light on the effects of reduced diet diversity on bee health.}, }
@article {pmid38165150, year = {2024}, author = {Kanchongkittiphon, W and Nopnipa, S and Mathuranyanon, R and Nonthabenjawan, N and Sritournok, S and Manuyakorn, W and Wanapaisan, P}, title = {Characterization of gut microbiome profile in children with confirmed wheat allergy.}, journal = {Asian Pacific journal of allergy and immunology}, volume = {}, number = {}, pages = {}, doi = {10.12932/AP-080623-1626}, pmid = {38165150}, issn = {0125-877X}, abstract = {BACKGROUND: Food allergies pose serious health risks, including life-threatening anaphylactic reactions, increased morbidity, and reduced quality of life. Wheat allergy is a common concern in Asia. There is growing interest in understanding the potential association between dysregulation of the gut microbiome and the development of food allergies.<br><br>OBJECTIVE: This study aimed to explore the gut microbiome of Thai children with wheat allergy and its potential association with allergic responses.<br><br>METHODS: Microbial abundance was assessed using Quantitative Insights into Microbial Ecology 2 (QIIME2) microbiome analysis based on 16S rDNA data. The correlation between microbial richness and relevant parameters was evaluated using the Spearman correlation analysis. Additionally, the microbial community functions were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2).<br><br>RESULTS: The gut microbiome analysis revealed significant differences between the two groups at the phylum and genus levels. Firmicutes (p = 0.012) and Verrucomicrobia (p < 0.001) were enriched in wheat-allergic children, whereas specific gut microbes such as Megamonas (p = 0.04), Romboutsia (p < 0.001), Fusobacterium (p < 0.001), Clostridium senso stricto1 (p < 0.001), and Turicibacter (p < 0.001) were more abundant in healthy children. Anaerostripes (p = 0.011), Erysipelatoclostridium (p < 0.001), Prevotella 2 (p < 0.001), Ruminiclostridium 5 (p < 0.001), and Clostridium innnocuum (p < 0.001) were enriched in children with a confirmed wheat allergy. Functional analysis indicated disparities in the pathways related to arginine and polyamine biosynthesis.<br><br>CONCLUSION: These findings offer valuable insights into the gut microbiome of children with wheat allergy and its potential impact on symptom severity, laying the groundwork for further research and interventions aimed at addressing this health concern.}, }
@article {pmid38163403, year = {2024}, author = {Dufour, OK and Hoffman, E and Sleith, RS and Katz, LA and Weiner, AKM and Sehein, TR}, title = {Testate amoebae (Arcellinida, Amoebozoa) community diversity in New England bogs and fens assessed through lineage-specific amplicon sequencing.}, journal = {European journal of protistology}, volume = {92}, number = {}, pages = {126049}, pmid = {38163403}, issn = {1618-0429}, support = {R15 HG010409/HG/NHGRI NIH HHS/United States ; }, mesh = {*Amoeba/genetics ; Ecosystem ; Wetlands ; Phylogeny ; *Amoebozoa ; *Lobosea ; New England ; }, abstract = {Testate amoebae (order Arcellinida) are abundant in freshwater ecosystems, including low pH bogs and fens. Within these environments, Arcellinida are considered top predators in microbial food webs and their tests are useful bioindicators of paleoclimatic changes and anthropogenic pollutants. Accurate species identifications and characterizations of diversity are important for studies of paleoclimate, microbial ecology, and environmental change; however, morphological species definitions mask cryptic diversity, which is a common phenomenon among microbial eukaryotes. Lineage-specific primers recently designed to target Arcellinida for amplicon sequencing successfully captured a poorly-described yet diverse fraction of the microbial eukaryotic community. Here, we leveraged the application of these newly-designed primers to survey the diversity of Arcellinida in four low-pH New England bogs and fens, investigating variation among bogs (2018) and then across seasons and habitats within two bogs (2019). Three OTUs represented 66% of Arcellinida reads obtained across all habitats surveyed. 103 additional OTUs were present in lower abundance with some OTUs detected in only one sampling location, suggesting habitat specificity. By establishing a baseline for Arcellinida diversity, we provide a foundation to monitor key taxa in habitats that are predicted to change with increasing anthropogenic pressure and rapid climate change.}, }
@article {pmid38162520, year = {2023}, author = {Capeding, MRZ and Phee, LCM and Ming, C and Noti, M and Vidal, K and Le Carrou, G and Frézal, A and Moll, JM and Vogt, JK and Myers, PN and Nielsen, BH and Boulangé, CL and Samuel, TM and Berger, B and Cercamondi, CI}, title = {Safety, efficacy, and impact on gut microbial ecology of a Bifidobacterium longum subspecies infantis LMG11588 supplementation in healthy term infants: a randomized, double-blind, controlled trial in the Philippines.}, journal = {Frontiers in nutrition}, volume = {10}, number = {}, pages = {1319873}, pmid = {38162520}, issn = {2296-861X}, abstract = {INTRODUCTION: Bifidobacterium longum subspecies infantis (B. infantis) may play a key role in infant gut development. This trial evaluated safety, tolerability, and efficacy of B. infantis LMG11588 supplementation.<br><br>METHODS: This randomized, placebo-controlled, double-blind study conducted in the Philippines included healthy breastfed and/or formula-fed infants (14-21&#x2009;days old) randomized for 8&#x2009;weeks to a control group (CG; n&#x2009;=&#x2009;77), or any of two B. infantis experimental groups (EGs): low (Lo-EG; 1*10[8] CFU/day; n&#x2009;=&#x2009;75) or high dose (Hi-EG; 1.8*10[10] CFU/day; n&#x2009;=&#x2009;76). Primary endpoint was weight gain; secondary endpoints included stooling patterns, gastrointestinal symptoms, adverse events, fecal microbiome, biomarkers, pH, and organic acids.<br><br>RESULTS: Non-inferiority in weight gain was demonstrated for Hi-EG and Lo-EG vs. CG. Overall, probiotic supplementation promoted mushy-soft stools, fewer regurgitation episodes, and increased fecal acetate production, which was more pronounced in the exclusively breastfed infants (EBF) and positively correlated with B. infantis abundance. In EBF, fecal pro-inflammatory cytokines (IL-1 beta, IL-8) were reduced. Strain-level metagenomic analysis allowed attributing the increased abundance of B. infantis in EGs versus CG, to LMG11588 probiotic colonization. Colonization by autochthonous B. infantis strains was similar between groups.<br><br>DISCUSSION: B. infantis LMG11588 supplementation was associated with normal infant growth, was safe and well-tolerated and promoted a Bifidobacterium-rich microbiota driven by B. infantis LMG11588 colonization without disturbing the natural dispersal of autochthonous B. infantis strains. In EBF, supplementation stimulated microbial metabolic activity and beneficially modulated enteric inflammation.}, }
@article {pmid38162026, year = {2023}, author = {Modolon, F and Schultz, J and Duarte, G and Vilela, CLS and Thomas, T and Peixoto, RS}, title = {In situ devices can culture the microbial dark matter of corals.}, journal = {iScience}, volume = {26}, number = {12}, pages = {108374}, pmid = {38162026}, issn = {2589-0042}, abstract = {Most microorganisms found in environmental samples have never been cultured and can often only be explored through molecular or microscopic approaches. Here, we adapt the use of in situ diffusion-based devices to culture "yet-to-be-cultured" microorganisms associated with coral mucus and compare this with a traditional culturing method. The culturability of microorganisms associated with mucus of the coral Pocillopora damicornis increased by 420% and 570% with diffusion growth chambers and microwell chip devices, respectively, compared with the traditional method tested. The obtained cultures represent up to 64.4% of the total diversity of amplicon sequence variants (ASVs) found in the mucus of the coral P. damicornis. In addition, some previously uncultured microorganisms, such as members of the family Nitrosopumilaceae and halophilic/halotolerant bacteria were cultured. Our results validate alternative microbial culturing strategies to culture coral-associated microorganisms, while significantly increasing the culturability of previous microbial dark matter.}, }
@article {pmid38159169, year = {2023}, author = {Wang, G and Wang, X and Yang, Z and Wang, S and Li, W and Shang, S and Luo, Y and Wang, L}, title = {Effects of Fusarium solani on the Growth and Development of Anoplophora glabripennis Larvae.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {23}, pmid = {38159169}, issn = {1432-184X}, mesh = {Animals ; Larva/microbiology ; *Coleoptera/microbiology ; *Fusarium ; }, abstract = {Anoplophora glabripennis (Asian longhorned beetle) is a wood-boring pest that can inhabit a wide range of healthy deciduous host trees in native and non-native habitats. Lignocellulose degradation plays a major role in the acquisition of nutrients during the growth and development of A. glabripennis larvae. In this study, the lignocellulose degradation capacity of Fusarium solani, a fungal symbiont of A. glabripennis, was investigated in fermentation culture and in four host tree species. The impact of F. solani on larval growth and survival parameters was assessed. Fermentation culture demonstrated continuous and stable production of lignocellulolytic enzymes over the cultivation period. Furthermore, F. solani was able to degrade host tree lignocellulose, as shown by decreased soluble sugar and cellulose contents and an increase in protein content. No significant differences in larval survival were observed in larvae fed with or without F. solani. However, weight and head capsule width were higher in larvae fed on F. solani, and gut lignocellulose activities were elevated in fed larvae. Our results indicate a role for F. solani in the predigestion of lignocellulose during the colonization and parasitic stages of A. glabripennis larval development, and also the F. solani an important symbiotic partner to A. glabripennis, lowering barriers to colonization and development in a range of habitats.}, }
@article {pmid38159125, year = {2023}, author = {Hao, Z and Wang, Q and Wang, J and Deng, Y and Yan, Z and Tian, L and Jiang, H}, title = {Water Level Fluctuations Modulate the Microbiomes Involved in Biogeochemical Cycling in Floodplains.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {24}, pmid = {38159125}, issn = {1432-184X}, support = {51839011//National Natural Science Foundation of China/ ; }, mesh = {*Water ; Nitrates ; *Microbiota/genetics ; Metagenome ; Nitrogen/metabolism ; }, abstract = {Drastic changes in hydrological conditions within floodplain ecosystems create distinct microbial habitats. However, there remains a lack of exploration regarding the variations in microbial function potentials across the flooding and drought seasons. In this study, metagenomics and environmental analyses were employed in floodplains that experience hydrological variations across four seasons. Analysis of functional gene composition, encompassing nitrogen, carbon, and sulfur metabolisms, revealed apparent differences between the flooding and drought seasons. The primary environmental drivers identified were water level, overlying water depth, submergence time, and temperature. Specific modules, e.g., the hydrolysis of β-1,4-glucosidic bond, denitrification, and dissimilatory/assimilatory nitrate reduction to ammonium, exhibited higher relative abundance in summer compared to winter. It is suggested that cellulose degradation was potentially coupled with nitrate reduction during the flooding season. Phylogenomic analysis of metagenome-assembled genomes (MAGs) unveiled that the Desulfobacterota lineage possessed abundant nitrogen metabolism genes supported by pathway reconstruction. Variation of relative abundance implied its environmental adaptability to both the wet and dry seasons. Furthermore, a novel order was found within Methylomirabilota, containing nitrogen reduction genes in the MAG. Overall, this study highlights the crucial role of hydrological factors in modulating microbial functional diversity and generating genomes with abundant nitrogen metabolism potentials.}, }
@article {pmid38157893, year = {2024}, author = {Guarin, TC and Li, L and Haak, L and Teel, L and Pagilla, KR}, title = {Contaminants of emerging concern reduction and microbial community characterization across a three-barrier advanced water treatment system.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169637}, doi = {10.1016/j.scitotenv.2023.169637}, pmid = {38157893}, issn = {1879-1026}, mesh = {Charcoal/chemistry ; RNA, Ribosomal, 16S ; *Water Pollutants, Chemical/chemistry ; *Water Purification/methods ; Filtration/methods ; *Ozone/chemistry ; *Drinking Water ; }, abstract = {This research investigated the removal of contaminants of emerging concern (CECs) and characterized the microbial community across an advanced water treatment (AWT) train consisting of Coagulation/Flocculation/Clarification/Granular Media Filtration (CFCGMF), Ozone-Biological Activated Carbon Filtration (O3/BAC), Granular Activated Carbon filtration, Ultraviolet Disinfection, and Cartridge Filtration (GAC/UV/CF). The AWT train successfully met the goals of CECs and bulk organics removal. The microbial community at each treatment step of the AWT train was characterized using 16S rRNA sequencing on the Illumina MiSeq platform generated from DNA extracted from liquid and solid (treatment media) samples taken along the treatment train. Differences in the microbial community structure were observed. The dominant operational taxonomic units (OTU) decreased along the treatment train, but the treatment steps did impact the microbial community composition downstream of each unit process. These results provide insights into microbial ecology in advanced water treatment systems, which are influenced and shaped by each treatment step, the microbial community interactions, and their potential metabolic contribution to CECs degradation.}, }
@article {pmid38157796, year = {2024}, author = {Wang, L and Nabi, F and Yi, W and Wang, D and Zhu, Y and Jiang, X}, title = {Low-dose thiram exposure elicits dysregulation of the gut microbial ecology in broiler chickens.}, journal = {Ecotoxicology and environmental safety}, volume = {270}, number = {}, pages = {115879}, doi = {10.1016/j.ecoenv.2023.115879}, pmid = {38157796}, issn = {1090-2414}, mesh = {Animals ; Thiram/toxicity ; Chickens/genetics ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Fungicides, Industrial/toxicity ; Bacteria/genetics ; }, abstract = {Thiram, a typical fungicide pesticide, is widely used in agricultural production. The presence of thiram residues is not only due to over-utilization, but is also primarily attributed to long-term accumulation. However, there is a paucity of information regarding the impact of prolonged utilization of thiram at low doses on the gut microbiota, particularly with respect to gut fungi. Our objective is to explore the effect of thiram on broilers from the perspective of gut microbiota, which includes both bacteria and fungi. We developed a long-term low-dose thiram model to simulate thiram residue and employed 16 S rRNA and ITS gene sequencing to investigate the diversity and profile of gut microbiota between group CC (normal diet) and TC (normal diet supplemented with 5 mg/kg thiram). The results revealed that low doses of thiram had a detrimental effect on broiler's growth performance, resulting in an approximate reduction of 669.33 g in their final body weight at day 45. Our findings indicated that low-dose thiram had a negative impact on the gut bacterial composition, leading to a notable reduction in the abundance of Merdibacter, Paenibacillus, Macrococcus, Fournierella, and Anaeroplasma (p < 0.05) compared to the CC group. Conversely, the relative level of Myroides was significantly increased (p < 0.05) in response to thiram exposure. In gut fungi, thiram significantly enhanced the diversity and richness of gut fungal populations (p < 0.05), as evidenced by the notable increase in alpha indices, i.e. ACE (CC: 346.49 ± 117.27 vs TC: 787.27 ± 379.14, p < 0.05), Chao 1 (CC: 317.63 ± 69.13 vs TC: 504.85 ± 104.50, p < 0.05), Shannon (CC: 1.28 ± 1.19 vs TC: 5.39 ± 2.66, p < 0.05), Simpson (CC: 0.21 ± 0.21 vs TC: 0.78 ± 0.34, p < 0.05). Furthermore, the abundance of Ascomycota, Kickxellomycota, and Glomeromycota were significantly increased (p < 0.05) by exposure to thiram, conversely, the level of Basidiomycota was decreased (p < 0.05) in the TC group compared to the CC group. Overall, this study demonstrated that low doses of thiram induced significant changes in the composition and abundance of gut microbiota in broilers, with more pronounced changes observed in the gut fungal community as compared to the gut bacterial community. Importantly, our findings further emphasize the potential risks associated with low dose thiram exposure and have revealed a novel discovery indicating that significant alterations in gut fungi may serve as the crucial factor contributing to the detrimental effects exerted by thiram residues.}, }
@article {pmid38157058, year = {2023}, author = {Chowaniec, K and Styburski, J and Kozioł, S and Pisańska, Z and Skubała, K}, title = {Dune Blowouts as Microbial Hotspots and the Changes of Overall Microbial Activity and Photosynthetic Biomass Along with Succession of Biological Soil Crusts.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {22}, pmid = {38157058}, issn = {1432-184X}, support = {U1U/W18/NO/28.34//Faculty of Biology, Jagiellonian University/ ; }, mesh = {Biomass ; *Ecosystem ; *Soil ; Soil Microbiology ; Desert Climate ; }, abstract = {Biological soil crust (BSC) constitutes a consortium of cyanobacteria, algae, lichen, mosses, and heterotrophic microorganisms, forming a miniature ecosystem within the uppermost soil layer. The biomass of different organisms forming BSC and their activity changes along with succession. Previous studies focused primarily on BSC in hyper-arid/arid regions, whereas the ecophysiology of BSC in temperate climates is still not well recognized. In order to determine changes in overall microbial activity and photosynthetic biomass in BSC at different stages of the succession of inland sandy grasslands, we analyzed dehydrogenase activity and determined the content of photosynthetic pigments. We also compared these parameters between BSC developed on the dune ridges and aeolian blowouts in the initial stage of succession. Our study revealed a significant increase in both photosynthetic biomass and overall microbial activity in BSC as the succession of inland shifting sands progresses. We found that chl a concentration in BSC could be considered a useful quantitative indicator of both the presence of photoautotrophs and the degree of soil crust development in warm-summer humid continental climates. The photosynthetic biomass was closely related to increased microbial activity in BSC, which suggests that photoautotrophs constitute a major BSC component. Dune blowouts constitute environmental niches facilitating the development of BSC, compared to dune ridges. High biomass of microorganisms in the dune blowouts may be associated with a high amount of organic material and more favorable moisture conditions. We conclude that deflation fields are key places for keeping a mosaic of habitats in the area of shifting sands and can be a reservoir of microorganisms supporting further settlement of dune slopes by BSC.}, }
@article {pmid38156301, year = {2023}, author = {Wani, AK and Ahmad, S and Américo-Pinheiro, JHP and Tizro, N and Singh, R}, title = {Building the taxonomic profile of the Riniaie Marwah hot spring of Kishtwar in Jammu and Kashmir: the first high-throughput sequencing-based metagenome study.}, journal = {Iranian journal of microbiology}, volume = {15}, number = {6}, pages = {723-733}, pmid = {38156301}, issn = {2008-3289}, abstract = {BACKGROUND AND OBJECTIVES: Rinaie Marwah hot spring Kishtwar (RMHSK) is one of the geothermal springs located at 33°51'51″N 75°32'07″E with an elevation of 2134 meters above sea level in Jammu and Kashmir, India. We aimed to study the microbial diversity of this geothermal spring using metagenomics.<br><br>MATERIALS AND METHODS: In the present study, physiochemical parameters including temperature (65-75&#xb0;C), pH (6. 9-8. 8), hardness (250 ppm), and mineral content was measured along with the microbial diversity using Illumina MiSeq metagenome-based 16s amplicon sequencing (V3-V4). The sequence reads were classified taxonomically into 31 phyla, 71 classes, 152 orders, 256 families, 410 genus, and 665 species. QIIME 2 (Quantitative Insights into Microbial Ecology), an extensible, powerful, and decentralized analytical tool, was used for taxonomic analysis.<br><br>RESULTS: Bacteroidota (32. 57%) was the dominant phylum, Bacteroidia (32. 51%) the dominant class, Bacteroidales (16. 6%) the dominant order, and Lentimicrobiaceae (14. 23%) was the dominant family per the abundance analysis. Shannon (2. 28) and Chao 1 (87. 0) diversity indices support the existence of higher microbial diversity in RMHSK (50717 OTUs).<br><br>CONCLUSION: The microbial diversity of RMHSK is reported for the first time through a metagenomic study. Identification of microorganisms with characteristics that are relevant to industries.}, }
@article {pmid38153618, year = {2023}, author = {Xiong, L and Li, Y and Zeng, K and Wei, Y and Li, H and Ji, X}, title = {Revealing viral diversity in the Napahai plateau wetland based on metagenomics.}, journal = {Antonie van Leeuwenhoek}, volume = {117}, number = {1}, pages = {3}, pmid = {38153618}, issn = {1572-9699}, support = {32160294, 42267059//National Natural Science Foundation of China/ ; }, mesh = {*Wetlands ; Ecosystem ; Phylogeny ; China ; *Bacteriophages ; }, abstract = {We focused on exploring the diversity of viruses in the Napahai plateau wetland, a unique ecosystem located in Yunnan, China. While viruses in marine environments have been extensively studied for their influence on microbial metabolism and biogeochemical cycles, little is known about their composition and function in plateau wetlands. Metagenomic analysis was employed to investigate the viral diversity and biogeochemical impacts in the Napahai wetland. It revealed that the Caudoviricetes and Malgrandaviricetes class level was the most abundant viral category based on phylogenetic analysis. Additionally, a gene-sharing network highlighted the presence of numerous unexplored viruses and demonstrated their unique characteristics and significant variation within the viral community of the Napahai wetland. Furthermore, the study identified the auxiliary metabolic genes (AMGs). AMGs provide phages with additional functions, such as protection against host degradation and involvement in metabolic pathways, such as the pentose phosphate pathway and DNA biosynthesis. The viruses in the Napahai wetland were found to influence carbon, nitrogen, sulfur, and amino acid metabolism, indirectly contributing to biogeochemical cycling through these AMGs. Overall, the research sheds light on the diverse and unique viral communities in the Napahai plateau wetland and emphasizes the significant roles of viruses in microbial ecology. The findings contribute to a deeper understanding of the characteristics and ecological functions of viral communities in plateau wetland ecosystems.}, }
@article {pmid38153543, year = {2023}, author = {Ciric, M and Šaraba, V and Budin, C and de Boer, T and Nikodinovic-Runic, J}, title = {Polyurethane-Degrading Potential of Alkaline Groundwater Bacteria.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {21}, pmid = {38153543}, issn = {1432-184X}, support = {870292//EU Horizon 2020 Research and Innovation Programme - BioICEP/ ; 451-03-47/2023-01/200042//Ministry of Science, Innovation and Technological Development of the Republic of Serbia/ ; }, mesh = {Humans ; Polyurethanes ; *Comamonadaceae ; DNA, Ribosomal ; *Groundwater ; Pseudomonas ; Suppuration ; }, abstract = {Plastic waste is a global environmental burden and long-lasting plastic polymers, including ubiquitous and toxic polyurethanes (PUs), rapidly accumulate in the water environments. In this study, samples were collected from the three alkaline groundwater occurrences in the geotectonic regions of the Pannonian basin of northern Serbia (Torda and Slankamen Banja) and Inner Dinarides of western Serbia (Mokra Gora) with aim to isolate and identify bacteria with plastic- and lignocellulose-degrading potential, that could be applied to reduce the burden of environmental plastic pollution. The investigated occurrences belong to cold, mildly alkaline (pH: 7.6-7.9) brackish and hyperalkaline (pH: 11.5) fresh groundwaters of the SO4 - Na + K, Cl - Na + K and OH, Cl - Ca, Na + K genetic type. Full-length 16S rDNA sequencing, using Oxford Nanopore sequencing device, was performed with DNA extracted from colonies obtained by cultivation of all groundwater samples, as well as with DNA extracted directly from one groundwater sample. The most abundant genera belong to Pseudomonas, Acidovorax, Kocuria and Methylotenera. All screened isolates (100%) had the ability to grow on at least 3 of the tested plastic and lignocellulosic substrates, with 53.9% isolates degrading plastic substrate Impranil® DLN-SD (SD), a model compound for PUs degradation. Isolates degrading SD that were identified by partial 16S rDNA sequencing belong to the Stenotrophomonas, Pseudomonas, Paraburkholderia, Aeromonas, Vibrio and Acidovorax genera. Taking into account that plastics, including commonly produced PUs, are widespread in groundwater, identification of PUs-degrading bacteria may have potential applications in bioremediation of groundwater polluted with this polymer.}, }
@article {pmid38151633, year = {2024}, author = {Paulino, PG and Abuin-Denis, L and Maitre, A and Piloto-Sardiñas, E and Obregon, D and Santos, HA and Cabezas-Cruz, A}, title = {Dissecting the impact of Anaplasma phagocytophilum infection on functional networks and community stability of the tick microbiome.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {27}, number = {4}, pages = {1205-1218}, pmid = {38151633}, issn = {1618-1905}, support = {E-26/211.312/2021//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 313753/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; SGCE - RAPPORT No 0300//Collectivit&#xe9; de Corse/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche/ ; }, mesh = {*Anaplasma phagocytophilum/physiology/genetics ; Animals ; *Ixodes/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; Ehrlichiosis/microbiology ; Nymph/microbiology ; Gastrointestinal Microbiome/physiology ; }, abstract = {CONTEXT: Pathogens can manipulate microbial interactions to ensure survival, potentially altering the functional patterns and microbiome assembly. The present study investigates how Anaplasma phagocytophilum infection affects the functional diversity, composition, and assembly of the Ixodes scapularis microbiome, with a focus on high central pathways-those characterized by elevated values in centrality metrics such as eigenvector, betweenness, and degree measures, in the microbial community.<br><br>METHODS: Using previously published data from nymphs' gut V4 region's amplicons of bacterial 16S rRNA, we predicted the functional diversity and composition in control and A. phagocytophilum-infected ticks and inferred co-occurrence networks of taxa and ubiquitous pathways in each condition to associate the high central pathways to the microbial community assembly.<br><br>RESULTS: Although no differences were observed concerning pathways richness and diversity, there was a significant impact on taxa and functional assembly when ubiquitous pathways in each condition were filtered. Moreover, a notable shift was observed in the microbiome's high central functions. Specifically, pathways related to the degradation of nucleosides and nucleotides emerged as the most central functions in response to A. phagocytophilum infection. This finding suggests a reconfiguration of functional relationships within the microbial community, potentially influenced by the pathogen's limited metabolic capacity. This limitation implies that the tick microbiome may provide additional metabolic resources to support the pathogen's functional needs.<br><br>CONCLUSIONS: Understanding the metabolic interactions within the tick microbiome can enhance our knowledge of pathogen colonization mechanisms and uncover new disease control and prevention strategies. For example, certain pathways that were more abundant or highly central during infection may represent potential targets for microbiota-based vaccines.}, }
@article {pmid38148858, year = {2023}, author = {Khan, A and Singh, AV and Gautam, SS and Agarwal, A and Punetha, A and Upadhayay, VK and Kukreti, B and Bundela, V and Jugran, AK and Goel, R}, title = {Microbial bioformulation: a microbial assisted biostimulating fertilization technique for sustainable agriculture.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1270039}, pmid = {38148858}, issn = {1664-462X}, abstract = {Addressing the pressing issues of increased food demand, declining crop productivity under varying agroclimatic conditions, and the deteriorating soil health resulting from the overuse of agricultural chemicals, requires innovative and effective strategies for the present era. Microbial bioformulation technology is a revolutionary, and eco-friendly alternative to agrochemicals that paves the way for sustainable agriculture. This technology harnesses the power of potential microbial strains and their cell-free filtrate possessing specific properties, such as phosphorus, potassium, and zinc solubilization, nitrogen fixation, siderophore production, and pathogen protection. The application of microbial bioformulations offers several remarkable advantages, including its sustainable nature, plant probiotic properties, and long-term viability, positioning it as a promising technology for the future of agriculture. To maintain the survival and viability of microbial strains, diverse carrier materials are employed to provide essential nourishment and support. Various carrier materials with their unique pros and cons are available, and choosing the most appropriate one is a key consideration, as it substantially extends the shelf life of microbial cells and maintains the overall quality of the bioinoculants. An exemplary modern bioformulation technology involves immobilizing microbial cells and utilizing cell-free filters to preserve the efficacy of bioinoculants, showcasing cutting-edge progress in this field. Moreover, the effective delivery of bioformulations in agricultural fields is another critical aspect to improve their overall efficiency. Proper and suitable application of microbial formulations is essential to boost soil fertility, preserve the soil's microbial ecology, enhance soil nutrition, and support crop physiological and biochemical processes, leading to increased yields in a sustainable manner while reducing reliance on expensive and toxic agrochemicals. This manuscript centers on exploring microbial bioformulations and their carrier materials, providing insights into the selection criteria, the development process of bioformulations, precautions, and best practices for various agricultural lands. The potential of bioformulations in promoting plant growth and defense against pathogens and diseases, while addressing biosafety concerns, is also a focal point of this study.}, }
@article {pmid38148389, year = {2023}, author = {Petrović, M and Janakiev, T and Grbić, ML and Unković, N and Stević, T and Vukićević, S and Dimkić, I}, title = {Insights into Endophytic and Rhizospheric Bacteria of Five Sugar Beet Hybrids in Terms of Their Diversity, Plant-Growth Promoting, and Biocontrol Properties.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {19}, pmid = {38148389}, issn = {1432-184X}, mesh = {Bacillus subtilis ; Bacillus ; Plant Development ; Endophytes ; Plant Roots/microbiology ; Phosphates ; *Beta vulgaris ; }, abstract = {Sugar beet is the most important crop for sugar production in temperate zones. The plant microbiome is considered an important factor in crop productivity and health. Here, we investigated the bacterial diversity of seeds, roots, and rhizosphere of five sugar beet hybrids named Eduarda (ED), Koala (KO), Tibor (T), Tajfun (TF), and Cercospora-resistant (C). A culture-independent next-generation sequencing approach was used for the further investigation of seed-borne endophytes. Hybrid-associated bacteria were evaluated for their plant growth-promoting (PGP) characteristics, antagonistic activity towards Cercospora beticola and several Fusarium strains in dual culture assays, and drought and salinity tolerance. High-throughput sequencing revealed that the Proteobacteria phylum was most dominant in the seeds of all hybrids, followed by Cyanobacteria and Actinobacteriota. The predominant genus in all hybrids was Pantoea, followed by Pseudomonas, Acinetobacter, Chalicogloea, Corynebacterium, Enterobacter, Enterococcus, Glutamicibacter, Kosakonia, and Marinilactibacillus. Unique genera in the hybrids were Pleurocapsa and Arthrobacter (T), Klebsiella (TF), Apibacter (ED), and Alloscardovia (KO). The genera that were most represented in one hybrid were Weissella and Staphylococcus (TF); Streptococcus (T); Gardnerella, Prevotella, and Rothia (KO); and Gilliamella, Lactobacillus, and Snodgrassella (ED). Thirty-two bacteria out of 156 isolates from the rhizosphere, roots, and seeds were selected with respect to various plant growth-promoting activities in vitro, i.e., nitrogen fixation, phosphate solubilization, siderophore production, indole-3-acetic acid production, 1-aminocyclopropane-1-carboxylic acid deaminase activity, hydrogen cyanide production, exoenzymatic activity (amylase, protease, lipase, cellulase, xylanase, mannanases, gelatinase, and pectinase), mitigation of environmental stresses, and antifungal activity. Mixta theicola KO3-44, Providencia vermicola ED3-10, Curtobacterium pusillum ED2-6, and Bacillus subtilis KO3-18 had the highest potential to promote plant growth due to their multiple abilities (nitrogen fixation, phosphate solubilization, production of siderophores, and IAA). The best antagonistic activity towards phytopathogenic fungi was found for Bacillus velezensis C3-19, Paenibacillus polymyxa C3-36 and Bacillus halotolerans C3-16/2.1. Only four isolates B. velezensis T2-23, B. subtilis T3-4, B. velezensis ED2-2, and Bacillus halotolerans C3-16/2.1 all showed enzymatic activity, with the exception of xylanase production. B. halotolerans C3-16/2.1 exhibited the greatest tolerance to salinity, while two B. subtilis strains (C3-62 and TF2-1) grew successfully at the maximum concentration of PEG. The current study demonstrates that sugar beet-associated bacteria have a wide range of beneficial traits and are therefore highly promising for the formulation of biological control and PGP agents.}, }
@article {pmid38148362, year = {2023}, author = {Ofek, T and Trabelcy, B and Izhaki, I and Halpern, M}, title = {Vibrio cholerae O1 Inhabit Intestines and Spleens of Fish in Aquaculture Ponds.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {20}, pmid = {38148362}, issn = {1432-184X}, support = {2728/17//the India-Israel Joint UGC-ISF/ ; 2015103//the United States-Israel Binational Science Foundation, BSF/ ; }, mesh = {Animals ; *Vibrio cholerae O1 ; Cholera Toxin ; Ponds ; Spleen ; *Cholera/epidemiology ; Intestines ; Fishes ; }, abstract = {Vibrio cholerae is the causative agent of cholera, an acute diarrheal disease that spreads locally and globally in epidemics and pandemics. Although it was discovered that fish harbor V. cholerae strains in their intestines, most investigations revealed non-toxic V. cholerae serogroups in fish. Due to the rarity of toxigenic V. cholerae serogroups, it is difficult to cultivate these strains from environmental samples. Hence, here we aimed to uncover evidence of the occurrence of toxigenic V. cholerae in the intestines and spleens of various fish species. By using molecular detection tools, we show that V. cholerae O1 and strains positive for the cholera toxin inhabit both healthy and diseased fish intestines and spleens, suggesting that fish may serve as intermediate vectors of toxigenic V. cholerae. No significant differences were found between the abundance of toxigenic V. cholerae (either O1 or cholera toxin positive strains) in the healthy and the diseased fish intestines or spleens. In conclusion, a variety of fish species may serve as potential vectors and reservoirs of toxigenic V. cholerae as they form a link between the other reservoirs of V. cholerae (chironomids, copepods, and waterbirds). Similarly, they may aid in the spread of this bacterium between water bodies.}, }
@article {pmid38147140, year = {2023}, author = {Lee, H and Chaudhary, DK and Lim, OB and Kim, DU}, title = {Paenibacillus silvisoli sp. nov. and Paenibacillus humicola sp. nov., isolated from forest soil.}, journal = {Archives of microbiology}, volume = {206}, number = {1}, pages = {42}, pmid = {38147140}, issn = {1432-072X}, support = {NIBR202203112//National Institute of Biological Resources/ ; }, mesh = {Phylogeny ; *Cardiolipins ; Forests ; *Paenibacillus/genetics ; DNA ; }, abstract = {During the study of microbial ecology of forest soil, two circular, white-colored bacterial colonies were isolated and labeled as strains TW38[T] and TW40[T]. Both strains were catalase positive and oxidase negative. Strains TW38[T] and TW40[T] demonstrated growth within a temperature range of 10-37 °C and 18-37 °C, respectively, and thrived within a pH range of 5.5-9.0 and 6.0-8.0, respectively. Both strains grew at 0-2.0% (w/v) NaCl concentrations. The phylogenetic analysis indicated that strains TW38[T] and TW40[T] affiliated to the genus Paenibacillus, with the closest neighbors being Paenibacillus montanisoli RA17[T] (98.6%) and Paenibacillus arachidis E3[T] (95.4%), respectively. In both strains, the sole respiratory quinone was MK-7, the signature fatty acid was antiso-C15:0, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. The digital DNA-DNA hybridization and the average nucleotide identity values between TW38[T], TW40[T], and closest reference strains were < 29.0% and < 85.0%, respectively. The DNA G+C content of TW38[T] and TW40[T] was 54.5% and 57.1%, respectively. In general, the phylogenetic, genomics, chemotaxonomic, and phenotypic data support the differentiation of TW38[T] and TW40[T] from other closest members of the genus Paenibacillus. Thus, we conclude both strains TW38[T] and TW40[T] represent novel species of the genus Paenibacillus, for which the name Paenibacillus silvisoli sp. nov. and Paenibacillus humicola sp. nov. are proposed, respectively. The type strain of Paenibacillus silvisoli is TW38[T] (= KCTC 43468[T] = NBRC 116015[T]) and type strain of Paenibacillus humicola is TW40[T] (= KCTC 43469[T] = NBRC 116016[T]).}, }
@article {pmid38146666, year = {2024}, author = {Sveen, TR and Viketoft, M and Bengtsson, J and Bahram, M}, title = {Core taxa underpin soil microbial community turnover during secondary succession.}, journal = {Environmental microbiology}, volume = {26}, number = {1}, pages = {e16561}, doi = {10.1111/1462-2920.16561}, pmid = {38146666}, issn = {1462-2920}, support = {2021-03724//The Swedish Research Council/ ; //The Swedish University of Agricultural Sciences (early career grant)/ ; 2020-00807//The Swedish Research Council Formas/ ; }, mesh = {*Soil ; Phylogeny ; Soil Microbiology ; Forests ; *Microbiota/genetics ; Bacteria/genetics ; Grassland ; }, abstract = {Understanding the processes that underpin the community assembly of bacteria is a key challenge in microbial ecology. We studied soil bacterial communities across a large-scale successional gradient of managed and abandoned grasslands paired with mature forest sites to disentangle drivers of community turnover and assembly. Diversity partitioning and phylogenetic null-modelling showed that bacterial communities in grasslands remain compositionally stable following abandonment and secondary succession but they differ markedly from fully afforested sites. Zeta diversity analyses revealed the persistence of core microbial taxa that both reflected and differed from whole-scale community turnover patterns. Differences in soil pH and C:N were the main drivers of community turnover between paired grassland and forest sites and the variability of pH within successional stages was a key factor related to the relative dominance of deterministic assembly processes. Our results indicate that grassland microbiomes could be compositionally resilient to abandonment and secondary succession and that the major changes in microbial communities between grasslands and forests occur fairly late in the succession when trees have established as the dominant vegetation. We also show that core taxa may show contrasting responses to management and abandonment in grasslands.}, }
@article {pmid38146049, year = {2024}, author = {Santos, LRC and Barros, PSDR and Monteiro, DA and Tabosa, JN and de Melo, AF and de Lyra, MDCCP and Oliveira, JRS and Fernandes Júnior, PI and de Freitas, ADS and Rachid, CTCDC}, title = {Influences of plant organ, genotype, and cultivation site on the endophytic bacteriome of maize (Zea mays L.) in the semi-arid region of Pernambuco, Brazil.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {55}, number = {1}, pages = {789-797}, pmid = {38146049}, issn = {1678-4405}, mesh = {*Zea mays/microbiology ; Brazil ; Endophytes/genetics ; Bacteria/genetics ; *Actinomycetales ; Genotype ; Plant Roots/microbiology ; }, abstract = {Endophytic bacteria play a crucial role in plant development and adaptation, and the knowledge of how endophytic bacteria assemblage is influenced by cultivation site and plant genotype is an important step to achieve microbiome manipulation. This work aimed to study the roots and stems of endophytic bacteriome of four maize genotypes cultivated in two regions of the semi-arid region of Pernambuco - Brazil. Our hypothesis is that the endophytic community assemblage will be influenced by plant genotypes and cultivation region. Metabarcoding sequencing data revealed significant differences in alfa diversity in function of both factors, genotypes, and maize organs. Beta diversity analysis showed that the bacterial communities differ mainly in function of the plant organ. The most abundant genera found in the samples were Leifsonia, Bacillus, Klebsiella, Streptomyces, and Bradyrhizobium. To understand ecological interactions within each compartment, we constructed co-occurrence network for each organ. This analysis revealed important differences in network structure and complexity and suggested that Leifsonia (the main genera found) had distinct ecological roles depending on the plant organ. Our data showed that root endophytic maize bacteria would be influenced by cultivation site, but not by genotype. We believe that, collectively, our data not only characterize the bacteriome associated with this plant and how different factors shape it, but also increase the knowledge to select potential bacteria for bioinoculant production.}, }
@article {pmid38143001, year = {2024}, author = {Shi, B and Cheng, X and Jiang, S and Pan, J and Zhu, D and Lu, Z and Jiang, Y and Liu, C and Guo, H and Xie, J}, title = {Unveiling the power of COD/N on constructed wetlands in a short-term experiment: Exploring microbiota co-occurrence patterns and assembly dynamics.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169568}, doi = {10.1016/j.scitotenv.2023.169568}, pmid = {38143001}, issn = {1879-1026}, mesh = {*Denitrification ; Wetlands ; Biological Oxygen Demand Analysis ; Nitrification ; *Microbiota ; Nitrogen/chemistry ; Water ; Waste Disposal, Fluid/methods ; }, abstract = {Constructed wetlands (CWs) are a cost-effective and environmentally friendly wastewater treatment technology. The influent chemical oxygen demand (COD)/nitrogen (N) ratio (CNR) plays a crucial role in microbial activity and purification performance. However, the effects of CNR changes on microbial diversity, interactions, and assembly processes in CWs are not well understood. In this study, we conducted comprehensive mechanistic experiments to investigate the response of CWs to changes in influent CNR, focusing on the effluent, rhizosphere, and substrate microbiota. Our goal is to provide new insights into CW management by integrating microbial ecology and environmental engineering perspectives. We constructed two groups of horizontal subsurface flow constructed wetlands (HFCWs) and set up three influent CNRs to analyse the microbial responses and nutrient removal. The results indicated that increasing influent CNR led to a decrease in microbial α-diversity and niche width. Genera involved in nitrogen removal and denitrification, such as Rhodobacter, Desulfovibrio, and Zoogloea, were enriched under medium/high CNR conditions, resulting in higher nitrate (NO3[-]-N) removal (up to 99 %) than that under lower CNR conditions (<60 %). Environmental factors, including water temperature (WT), pH, and phosphorus (P), along with CNR-induced COD and NO3[-]-N play important roles in microbial succession in HFCWs. The genus Nitrospira, which is involved in nitrification, exhibited a significant negative correlation (p < 0.05) with WT, COD, and P. Co-occurrence network analysis revealed that increasing influent CNR reduced the complexity of the network structure and increased microbial competition. Analysis using null models demonstrated that the microbial community assembly in HFCWs was primarily driven by stochastic processes under increasing influent CNR conditions. Furthermore, HFCWs with more stochastic microbial communities exhibited better denitrification performance (NO3[-]-N removal). Overall, this study enhances our understanding of nutrient removal, microbial co-occurrence, and assembly mechanisms in CWs under varying influent CNRs.}, }
@article {pmid38140550, year = {2023}, author = {Vickos, U and Camasta, M and Grandi, N and Scognamiglio, S and Schindler, T and Belizaire, MRD and Lango-Yaya, E and Koyaweda, GW and Senzongo, O and Pounguinza, S and Estimé, KKJF and N'yetobouko, S and Gadia, CLB and Feiganazoui, DA and Le Faou, A and Orsini, M and Perno, CF and Zinzula, L and Rafaï, CD}, title = {COVID-19 Genomic Surveillance in Bangui (Central African Republic) Reveals a Landscape of Circulating Variants Linked to Validated Antiviral Targets of SARS-CoV-2 Proteome.}, journal = {Viruses}, volume = {15}, number = {12}, pages = {}, pmid = {38140550}, issn = {1999-4915}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Humans ; *SARS-CoV-2/genetics ; Proteome ; *COVID-19/epidemiology ; Central African Republic/epidemiology ; Phylogeny ; Genomics ; Antiviral Agents ; }, abstract = {Since its outbreak, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spread rapidly, causing the Coronavirus Disease 19 (COVID-19) pandemic. Even with the vaccines' administration, the virus continued to circulate due to inequal access to prevention and therapeutic measures in African countries. Information about COVID-19 in Africa has been limited and contradictory, and thus regional studies are important. On this premise, we conducted a genomic surveillance study about COVID-19 lineages circulating in Bangui, Central African Republic (CAR). We collected 2687 nasopharyngeal samples at four checkpoints in Bangui from 2 to 22 July 2021. Fifty-three samples tested positive for SARS-CoV-2, and viral genomes were sequenced to look for the presence of different viral strains. We performed phylogenetic analysis and described the lineage landscape of SARS-CoV-2 circulating in the CAR along 15 months of pandemics and in Africa during the study period, finding the Delta variant as the predominant Variant of Concern (VoC). The deduced aminoacidic sequences of structural and non-structural genes were determined and compared to reference and reported isolates from Africa. Despite the limited number of positive samples obtained, this study provides valuable information about COVID-19 evolution at the regional level and allows for a better understanding of SARS-CoV-2 circulation in the CAR.}, }
@article {pmid38139130, year = {2023}, author = {Popov, IV and Popov, IV and Krikunova, AA and Lipilkina, TA and Derezina, TN and Chikindas, ML and Venema, K and Ermakov, AM}, title = {Gut Microbiota Composition of Insectivorous Synanthropic and Fructivorous Zoo Bats: A Direct Metagenomic Comparison.}, journal = {International journal of molecular sciences}, volume = {24}, number = {24}, pages = {}, pmid = {38139130}, issn = {1422-0067}, support = {23-14-00316//Russian Science Foundation/ ; Agreement 075-10-2021-093, Project [IMB-2102]//Ministry of Science and Higher Education of the Russian Federation/ ; //K.V. was supported by the Dutch Province of Limburg with a grant to the Centre for Healthy Eating &amp; Food Innovation (HEFI) of Maastricht University-campus Venlo/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Chiroptera ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Bacteria/genetics ; }, abstract = {Bats are natural reservoirs for many emerging viral diseases. That is why their virome is widely studied. But at the same time, studies of their bacterial gut microbiota are limited, creating a degree of uncertainty about the role of bats in global microbial ecology. In this study, we analyzed gut microbiota of insectivorous Nyctalus noctula and Vespertilio murinus from rehabilitation centers from Rostov-on-Don and Moscow, respectively, and fructivorous Carollia perspicillata from the Moscow Zoo based on V3-V4 16S rRNA metagenomic sequencing. We revealed that microbial diversity significantly differs between the insectivorous and fructivorous species studied, while the differences between N. noctula and V. murinus are less pronounced, which shows that bats' gut microbiota is not strictly species-specific and depends more on diet type. In the gut microbiota of synanthropic bats, we observed bacteria that are important for public health and animal welfare such as Bacteroides, Enterobacter, Clostridiaceae, Enterococcus, Ureaplasma, Faecalibacterium, and Helicobacter, as well as some lactic acid bacteria such as Pediococcus, Lactobacillus, Lactococcus, and Weisella. All these bacteria, except for Bacteroides and Weisella, were significantly less abundant in C. perspicillata. This study provides a direct metagenomic comparison of synanthropic insectivorous and zoo fructivorous bats, suggesting future directions for studying these animals' role in microbial ecology.}, }
@article {pmid38138049, year = {2023}, author = {Lourenço, KS and Cantarella, H and Kuramae, EE}, title = {Carbon and Nutrients from Organic Residues Modulate the Dynamics of Prokaryotic and Fungal Communities.}, journal = {Microorganisms}, volume = {11}, number = {12}, pages = {}, pmid = {38138049}, issn = {2076-2607}, abstract = {Inputs of carbon (C) and nutrients from organic residues may select specific microbes and shape the soil microbial community. However, little is known about the abiotic filtering of the same residues with different nutrient concentrations applied to the soil. In our study, we explored how applying organic residue, vinasse, as fertilizer in its natural state (V) versus its concentrated form (CV) impacts soil microbiota. We conducted two field experiments, evaluating soil prokaryotic and fungal communities over 24 and 45 days with vinasse (V or CV) plus N fertilizer. We used 16S rRNA gene and ITS amplicon sequencing. Inorganic N had no significant impact on bacterial and fungal diversity compared to the control. However, the varying concentrations of organic C and nutrients in vinasse significantly influenced the soil microbiome structure, with smaller effects observed for V compared to CV. Prokaryotic and fungal communities were not correlated (co-inertia: RV coefficient = 0.1517, p = 0.9708). Vinasse did not change the total bacterial but increased the total fungal abundance. A higher C input enhanced the prokaryotic but reduced the fungal diversity. Our findings highlight vinasse's role as an abiotic filter shaping soil microbial communities, with distinct effects on prokaryotic and fungal communities. Vinasse primarily selects fast-growing microorganisms, shedding light on the intricate dynamics between organic residues, nutrient concentrations, and soil microbes.}, }
@article {pmid38137974, year = {2023}, author = {Pérez, G and Krause, SMB and Bodelier, PLE and Meima-Franke, M and Pitombo, L and Irisarri, P}, title = {Interactions between Cyanobacteria and Methane Processing Microbes Mitigate Methane Emissions from Rice Soils.}, journal = {Microorganisms}, volume = {11}, number = {12}, pages = {}, pmid = {38137974}, issn = {2076-2607}, support = {CSIC-4562//Comisi&#xf3;n Sectorial de Investigaci&#xf3;n Cient&#xed;fica/ ; POS_EXT_2016_1_133774//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n/ ; 32050410288//National Science Foundation of China 568 (NSFC), International (Regional) Cooperation and Exchange Program/ ; }, abstract = {Cyanobacteria play a relevant role in rice soils due to their contribution to soil fertility through nitrogen (N2) fixation and as a promising strategy to mitigate methane (CH4) emissions from these systems. However, information is still limited regarding the mechanisms of cyanobacterial modulation of CH4 cycling in rice soils. Here, we focused on the response of methane cycling microbial communities to inoculation with cyanobacteria in rice soils. We performed a microcosm study comprising rice soil inoculated with either of two cyanobacterial isolates (Calothrix sp. and Nostoc sp.) obtained from a rice paddy. Our results demonstrate that cyanobacterial inoculation reduced CH4 emissions by 20 times. Yet, the effect on CH4 cycling microbes differed for the cyanobacterial strains. Type Ia methanotrophs were stimulated by Calothrix sp. in the surface layer, while Nostoc sp. had the opposite effect. The overall pmoA transcripts of Type Ib methanotrophs were stimulated by Nostoc. Methanogens were not affected in the surface layer, while their abundance was reduced in the sub surface layer by the presence of Nostoc sp. Our results indicate that mitigation of methane emission from rice soils based on cyanobacterial inoculants depends on the proper pairing of cyanobacteria-methanotrophs and their respective traits.}, }
@article {pmid38136731, year = {2023}, author = {Balcha, ES and Gómez, F and Gemeda, MT and Bekele, FB and Abera, S and Cavalazzi, B and Woldesemayat, AA}, title = {Shotgun Metagenomics-Guided Prediction Reveals the Metal Tolerance and Antibiotic Resistance of Microbes in Poly-Extreme Environments in the Danakil Depression, Afar Region.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {38136731}, issn = {2079-6382}, abstract = {The occurrence and spread of antibiotic resistance genes (ARGs) in environmental microorganisms, particularly in poly-extremophilic bacteria, remain underexplored and have received limited attention. This study aims to investigate the prevalence of ARGs and metal resistance genes (MRGs) in shotgun metagenome sequences obtained from water and salt crust samples collected from Lake Afdera and the Assale salt plain in the Danakil Depression, northern Ethiopia. Potential ARGs were characterized by the comprehensive antibiotic research database (CARD), while MRGs were identified by using BacMetScan V.1.0. A total of 81 ARGs and 39 MRGs were identified at the sampling sites. We found a copA resistance gene for copper and the β-lactam encoding resistance genes were the most abundant the MRG and ARG in the study area. The abundance of MRGs is positively correlated with mercury (Hg) concentration, highlighting the importance of Hg in the selection of MRGs. Significant correlations also exist between heavy metals, Zn and Cd, and ARGs, which suggests that MRGs and ARGs can be co-selected in the environment contaminated by heavy metals. A network analysis revealed that MRGs formed a complex network with ARGs, primarily associated with β-lactams, aminoglycosides, and tetracyclines. This suggests potential co-selection mechanisms, posing concerns for both public health and ecological balance.}, }
@article {pmid38133854, year = {2024}, author = {Chatterjee, S and Paul, P and Chakraborty, P and Das, S and Das Gupta, A and Roy, R and Malik, M and Sarkar, S and Sarker, RK and Tribedi, P}, title = {Combinatorial application of cuminaldehyde and gentamicin shows enhanced antimicrobial and antibiofilm action on Pseudomonas aeruginosa.}, journal = {Folia microbiologica}, volume = {69}, number = {4}, pages = {823-834}, pmid = {38133854}, issn = {1874-9356}, mesh = {*Biofilms/drug effects ; *Pseudomonas aeruginosa/drug effects/physiology ; *Gentamicins/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; *Benzaldehydes/pharmacology ; Cymenes/pharmacology ; Virulence Factors ; Drug Synergism ; Humans ; }, abstract = {The emergence of biofilm-induced drug tolerance poses a critical challenge to public healthcare management. Pseudomonas aeruginosa, a gram-negative opportunistic bacterium, is involved in various biofilm-associated infections in human hosts. Towards this direction, in the present study, a combinatorial approach has been explored as it is a demonstrably effective strategy for managing microbial infections. Thus, P. aeruginosa has been treated with cuminaldehyde (a naturally occurring phytochemical) and gentamicin (an aminoglycoside antibiotic) in connection to the effective management of the biofilm challenges. It was also observed that the test molecules could show increased antimicrobial activity against P. aeruginosa. A fractional inhibitory concentration index (FICI) of 0.65 suggested an additive interaction between cuminaldehyde and gentamicin. Besides, a series of experiments such as crystal violet assay, estimation of extracellular polymeric substance (EPS), and microscopic images indicated that an enhanced antibiofilm activity was obtained when the selected compounds were applied together on P. aeruginosa. Furthermore, the combination of the selected compounds was found to reduce the secretion of virulence factors from P. aeruginosa. Taken together, this study suggested that the combinatorial application of cuminaldehyde and gentamicin could be considered an effective approach towards the control of biofilm-linked infections caused by P. aeruginosa.}, }
@article {pmid38133759, year = {2024}, author = {Hidalgo, J and Artetxe, U and Becerril, JM and Gómez-Sagasti, MT and Epelde, L and Vilela, J and Garbisu, C}, title = {Biological remediation treatments improve the health of a mixed contaminated soil before significantly reducing contaminant levels.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {4}, pages = {6010-6024}, pmid = {38133759}, issn = {1614-7499}, support = {Project Phy2SUDOE - SOE4/P5/E1021//Interreg/ ; AGL 2015-64481-C2-1-R//Ministerio de Econom&#xed;a y Competitividad/ ; AGL2016-76592-R//Ministerio de Econom&#xed;a y Competitividad/ ; UPV/EHU-GV IT-1648-22//Eusko Jaurlaritza/ ; }, mesh = {Sewage ; *Soil Pollutants/analysis ; Biodegradation, Environmental ; Soil ; *Polychlorinated Biphenyls ; Soil Microbiology ; }, abstract = {The remediation of mixed contaminated soil is challenging as it often requires actions to minimize metal-induced risks while degrading organic contaminants. Here, the effectiveness of different bioremediation strategies, namely, rhizoremediation with native plant species, mycoremediation with Pleurotus ostreatus spent mushroom substrate, and biostimulation with organic by-products (i.e., composted sewage sludge and spent mushroom substrate), for the recovery of a mixed contaminated soil from an abandoned gravel pit was studied. The combination of biostimulation and rhizoremediation led to the most significant increase in soil health, according to microbial indicator values. The application of composted sewage sludge led to the highest reduction in anthracene and polychlorinated biphenyls concentrations. None of the strategies managed to decrease contamination levels below regulatory limits, but they did enhance soil health. It was concluded that the biological remediation treatments improved soil functioning in a short time, before the concentration of soil contaminants was significantly reduced.}, }
@article {pmid38127978, year = {2023}, author = {Liuu, S and Nepelska, M and Pfister, H and Gamelas Magalhaes, J and Chevalier, G and Strozzi, F and Billerey, C and Maresca, M and Nicoletti, C and Di Pasquale, E and Pechard, C and Bardouillet, L and Girardin, SE and Boneca, IG and Doré, J and Blottière, HM and Bonny, C and Chene, L and Cultrone, A}, title = {Identification of a muropeptide precursor transporter from gut microbiota and its role in preventing intestinal inflammation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {52}, pages = {e2306863120}, pmid = {38127978}, issn = {1091-6490}, support = {FP7/2007-2013//European community's Seventh Framework Programme/ ; FP7/2007-2013//European community's Seventh framework Programme/ ; }, mesh = {Humans ; Mice ; Animals ; *Gastrointestinal Microbiome ; Peptidoglycan/metabolism ; Intestines/pathology ; Inflammation/metabolism ; Membrane Transport Proteins/metabolism ; Anti-Inflammatory Agents/metabolism ; Dextran Sulfate ; *Colitis/metabolism ; Disease Models, Animal ; Colon/metabolism ; Mice, Inbred C57BL ; }, abstract = {The gut microbiota is a considerable source of biologically active compounds that can promote intestinal homeostasis and improve immune responses. Here, we used large expression libraries of cloned metagenomic DNA to identify compounds able to sustain an anti-inflammatory reaction on host cells. Starting with a screen for NF-κB activation, we have identified overlapping clones harbouring a heterodimeric ATP-binding cassette (ABC)-transporter from a Firmicutes. Extensive purification of the clone's supernatant demonstrates that the ABC-transporter allows for the efficient extracellular accumulation of three muropeptide precursor, with anti-inflammatory properties. They induce IL-10 secretion from human monocyte-derived dendritic cells and proved effective in reducing AIEC LF82 epithelial damage and IL-8 secretion in human intestinal resections. In addition, treatment with supernatants containing the muropeptide precursor reduces body weight loss and improves histological parameters in Dextran Sulfate Sodium (DSS)-treated mice. Until now, the source of peptidoglycan fragments was shown to come from the natural turnover of the peptidoglycan layer by endogenous peptidoglycan hydrolases. This is a report showing an ABC-transporter as a natural source of secreted muropeptide precursor and as an indirect player in epithelial barrier strengthening. The mechanism described here might represent an important component of the host immune homeostasis.}, }
@article {pmid38126787, year = {2024}, author = {Walsh, C and Stallard-Olivera, E and Fierer, N}, title = {Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology.}, journal = {mBio}, volume = {15}, number = {2}, pages = {e0205023}, pmid = {38126787}, issn = {2150-7511}, support = {Graduate Research Assistantship//Cooperative Institute for Research in Environmental Sciences (CIRES)/ ; }, mesh = {*Machine Learning ; Algorithms ; *Microbiota ; }, abstract = {Due to the complex nature of microbiome data, the field of microbial ecology has many current and potential uses for machine learning (ML) modeling. With the increased use of predictive ML models across many disciplines, including microbial ecology, there is extensive published information on the specific ML algorithms available and how those algorithms have been applied. Thus, our goal is not to summarize the breadth of ML models available or compare their performances. Rather, our goal is to provide more concrete and actionable information to guide microbial ecologists in how to select, run, and interpret ML algorithms to predict the taxa or genes associated with particular sample categories or environmental gradients of interest. Such microbial data often have unique characteristics that require careful consideration of how to apply ML models and how to interpret the associated results. This review is intended for practicing microbial ecologists who may be unfamiliar with some of the intricacies of ML models. We provide examples and discuss common opportunities and pitfalls specific to applying ML models to the types of data sets most frequently collected by microbial ecologists.}, }
@article {pmid38125540, year = {2023}, author = {Dhivahar, J and Parthasarathy, A and Krishnan, K and Kovi, BS and Pandian, GN}, title = {Bat-associated microbes: Opportunities and perils, an overview.}, journal = {Heliyon}, volume = {9}, number = {12}, pages = {e22351}, pmid = {38125540}, issn = {2405-8440}, abstract = {The potential biotechnological uses of bat-associated bacteria are discussed briefly, indicating avenues for biotechnological applications of bat-associated microbes. The uniqueness of bats in terms of their lifestyle, genomes and molecular immunology may predispose bats to act as disease reservoirs. Molecular phylogenetic analysis has shown several instances of bats harbouring the ancestral lineages of bacterial (Bartonella), protozoal (Plasmodium, Trypanosoma cruzi) and viral (SARS-CoV2) pathogens infecting humans. Along with the transmission of viruses from bats, we also discuss the potential roles of bat-associated bacteria, fungi, and protozoan parasites in emerging diseases. Current evidence suggests that environmental changes and interactions between wildlife, livestock, and humans contribute to the spill-over of infectious agents from bats to other hosts. Domestic animals including livestock may act as intermediate amplifying hosts for bat-origin pathogens to transmit to humans. An increasing number of studies investigating bat pathogen diversity and infection dynamics have been published. However, whether or how these infectious agents are transmitted both within bat populations and to other hosts, including humans, often remains unknown. Metagenomic approaches are uncovering the dynamics and distribution of potential pathogens in bat microbiomes, which might improve the understanding of disease emergence and transmission. Here, we summarize the current knowledge on bat zoonoses of public health concern and flag the gaps in the knowledge to enable further research and allocation of resources for tackling future outbreaks.}, }
@article {pmid38115223, year = {2024}, author = {Euler, S and Jeffrey, LC and Maher, DT and Johnston, SG and Sugimoto, R and Tait, DR}, title = {Microbiome mediating methane and nitrogen transformations in a subterranean estuary.}, journal = {Environmental microbiology}, volume = {26}, number = {1}, pages = {e16558}, doi = {10.1111/1462-2920.16558}, pmid = {38115223}, issn = {1462-2920}, support = {DE180100535//Australian Research Council/ ; }, mesh = {*Greenhouse Gases ; Estuaries ; Methane ; Dissolved Organic Matter ; Nitrogen ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Ammonium Compounds ; }, abstract = {Subterranean estuaries (STEs) are important coastal biogeochemical reactors facilitating unique niches for microbial communities. A common approach in determining STE greenhouse gas and nutrient fluxes is to use terrestrial endmembers, not accounting for microbially mediated transformations throughout the STE. As such, the microbial ecology and spatial distribution of specialists that cycle compounds in STEs remain largely underexplored. In this study, we applied 16S rRNA amplicon sequencing with paired biogeochemical characterisations to spatially evaluate microbial communities transforming greenhouse gases and nutrients in an STE. We show that methanogens are most prevalent at the terrestrial end (up to 2.81% relative abundance) concomitant to the highest porewater methane, carbon dioxide and dissolved organic carbon concentrations (0.41 ± 0.02 μM, 273.31 ± 6.05 μM and 0.51 ± 0.02 mM, respectively). Lower ammonium concentrations corresponded with abundant nitrifying and ammonia-oxidising prokaryotes in the mixing zone (up to 11.65% relative abundance). Methane, ammonium and dissolved organic carbon concentrations all decreased by >50% from the terrestrial to the oceanic end of the 15 m transect. This study highlights the STE's hidden microbiome zonation, as well as the importance of accounting for microbial transformations mitigating nutrient and greenhouse gas fluxes to the coastal ecosystems.}, }
@article {pmid38114339, year = {2024}, author = {Sutherland, WJ and Bennett, C and Brotherton, PNM and Butchart, SHM and Butterworth, HM and Clarke, SJ and Esmail, N and Fleishman, E and Gaston, KJ and Herbert-Read, JE and Hughes, AC and James, J and Kaartokallio, H and Le Roux, X and Lickorish, FA and Newport, S and Palardy, JE and Pearce-Higgins, JW and Peck, LS and Pettorelli, N and Primack, RB and Primack, WE and Schloss, IR and Spalding, MD and Ten Brink, D and Tew, E and Timoshyna, A and Tubbs, N and Watson, JEM and Wentworth, J and Wilson, JD and Thornton, A}, title = {A horizon scan of global biological conservation issues for 2024.}, journal = {Trends in ecology &amp; evolution}, volume = {39}, number = {1}, pages = {89-100}, doi = {10.1016/j.tree.2023.11.001}, pmid = {38114339}, issn = {1872-8383}, mesh = {*Ecosystem ; *Biodiversity ; Conservation of Natural Resources ; Forecasting ; Food ; }, abstract = {We present the results of our 15th horizon scan of novel issues that could influence biological conservation in the future. From an initial list of 96 issues, our international panel of scientists and practitioners identified 15 that we consider important for societies worldwide to track and potentially respond to. Issues are novel within conservation or represent a substantial positive or negative step-change with global or regional extents. For example, new sources of hydrogen fuel and changes in deep-sea currents may have profound impacts on marine and terrestrial ecosystems. Technological advances that may be positive include benchtop DNA printers and the industrialisation of approaches that can create high-protein food from air, potentially reducing the pressure on land for food production.}, }
@article {pmid38112791, year = {2023}, author = {Yue, Y and Yang, Z and Wang, F and Chen, X and Huang, Y and Ma, J and Cai, L and Yang, M}, title = {Effects of Cascade Reservoirs on Spatiotemporal Dynamics of the Sedimentary Bacterial Community: Co-occurrence Patterns, Assembly Mechanisms, and Potential Functions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {18}, pmid = {38112791}, issn = {1432-184X}, mesh = {*Ecosystem ; Biodiversity ; Fresh Water ; Rivers/microbiology ; *Microbiota ; Bacteria/genetics ; China ; Nitrogen ; }, abstract = {Dam construction as an important anthropogenic activity significantly influences ecological processes in altered freshwater bodies. However, the effects of multiple cascade dams on microbial communities have been largely overlooked. In this study, the spatiotemporal distribution, co-occurrence relationships, assembly mechanisms, and functional profiles of sedimentary bacterial communities were systematically investigated in 12 cascade reservoirs across two typical karst basins in southwest China over four seasons. A significant spatiotemporal heterogeneity was observed in bacterial abundance and diversity. Co-occurrence patterns in the Wujiang Basin exhibited greater edge counts, graph density, average degree, robustness, and reduced modularity, suggesting more intimate and stronger ecological interactions among species than in the Pearl River Basin. Furthermore, Armatimonadota and Desulfobacterota, identified as keystone species, occupied a more prominent niche than the dominant species. A notable distance-decay relationship between geographical distance and community dissimilarities was identified in the Pearl River Basin. Importantly, in the Wujiang Basin, water temperature emerged as the primary seasonal variable steering the deterministic process of bacterial communities, whereas 58.5% of the explained community variance in the neutral community model (NCM) indicated that stochastic processes governed community assembly in the Pearl River Basin. Additionally, principal component analysis (PCA) revealed more pronounced seasonal dynamics in nitrogen functional compositions than spatial variation in the Wujiang Basin. Redundancy analysis (RDA) results indicated that in the Wujiang Basin, environmental factors and in Pearl River Basin, geographical distance, reservoir age, and hydraulic retention time (HRT), respectively, influenced the abundance of nitrogen-related genes. Notably, these findings offer novel insights: building multiple cascade reservoirs could lead to a cascading decrease in biodiversity and resilience in the river-reservoir ecosystem.}, }
@article {pmid38112441, year = {2024}, author = {Foxall, RL and Means, J and Marcinkiewicz, AL and Schillaci, C and DeRosia-Banick, K and Xu, F and Hall, JA and Jones, SH and Cooper, VS and Whistler, CA}, title = {Inoviridae prophage and bacterial host dynamics during diversification, succession, and Atlantic invasion of Pacific-native Vibrio parahaemolyticus.}, journal = {mBio}, volume = {15}, number = {1}, pages = {e0285123}, pmid = {38112441}, issn = {2150-7511}, support = {R/SFA-4//UNH | New Hampshire Sea Grant, University of New Hampshire (NHSG)/ ; R-HCE-3//UNH | New Hampshire Sea Grant, University of New Hampshire (NHSG)/ ; R/SFA-13//UNH | New Hampshire Sea Grant, University of New Hampshire (NHSG)/ ; NH00698//UNH | COLSA | New Hampshire Agricultural Experiment Station (NHAES)/ ; NH00625//UNH | COLSA | New Hampshire Agricultural Experiment Station (NHAES)/ ; NH00658//UNH | COLSA | New Hampshire Agricultural Experiment Station (NHAES)/ ; }, mesh = {Prophages ; *Vibrio parahaemolyticus/genetics ; Inoviridae ; Ecosystem ; Bacteria ; *Bacteriophages/genetics ; }, abstract = {An understanding of the processes that contribute to the emergence of pathogens from environmental reservoirs is critical as changing climate precipitates pathogen evolution and population expansion. Phylogeographic analysis of Vibrio parahaemolyticus hosts combined with the analysis of their Inoviridae phage resolved ambiguities of diversification dynamics which preceded successful Atlantic invasion by the epidemiologically predominant ST36 lineage. It has been established experimentally that filamentous phage can limit host recombination, but here, we show that phage loss is linked to rapid bacterial host diversification during epidemic spread in natural ecosystems alluding to a potential role for ubiquitous inoviruses in the adaptability of pathogens. This work paves the way for functional analyses to define the contribution of inoviruses in the evolutionary dynamics of environmentally transmitted pathogens.}, }
@article {pmid38111463, year = {2024}, author = {Li, C and Gillings, MR and Zhang, C and Chen, Q and Zhu, D and Wang, J and Zhao, K and Xu, Q and Leung, PH and Li, X and Liu, J and Jin, L}, title = {Ecology and risks of the global plastisphere as a newly expanding microbial habitat.}, journal = {Innovation (Cambridge (Mass.))}, volume = {5}, number = {1}, pages = {100543}, pmid = {38111463}, issn = {2666-6758}, abstract = {Plastic offers a new niche for microorganisms, the plastisphere. The ever-increasing emission of plastic waste makes it critical to understand the microbial ecology of the plastisphere and associated effects. Here, we present a global fingerprint of the plastisphere, analyzing samples collected from freshwater, seawater, and terrestrial ecosystems. The plastisphere assembles a distinct microbial community that has a clearly higher heterogeneity and a more deterministically dominated assembly compared to natural habitats. New coexistence patterns-loose and fragile networks with mostly specialist linkages among microorganisms that are rarely found in natural habitats-are seen in the plastisphere. Plastisphere microbiomes generally have a great potential to metabolize organic compounds, which could accelerate carbon turnover. Microorganisms involved in the nitrogen cycle are also altered in the plastisphere, especially in freshwater plastispheres, where a high abundance of denitrifiers may increase the release of nitrite (aquatic toxicant) and nitrous oxide (greenhouse gas). Enrichment of animal, plant, and human pathogens means that the plastisphere could become an increasingly mobile reservoir of harmful microorganisms. Our findings highlight that if the trajectory of plastic emissions is not reversed, the expanding plastisphere could pose critical planetary health challenges.}, }
@article {pmid38110747, year = {2023}, author = {Steinberger, Y and Doniger, T and Applebaum, I and Sherman, C and Rotbart, N}, title = {Effects of Vineyard Agro-management Practices on Soil Bacterial Community Composition, and Diversity.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {17}, pmid = {38110747}, issn = {1432-184X}, mesh = {Humans ; *Soil/chemistry ; Farms ; Soil Microbiology ; Agriculture ; Bacteria/genetics ; *Microbiota ; }, abstract = {Changes in land use strongly affect soil biological and physico-chemical structure and characteristics, which are strongly related to agricultural conversion of natural habitats to man-made usage. These are among the most important and not always beneficial changes, affecting loss of habitats. In Golan Heights basaltic soils, vineyards are currently a driving force in land-use change. Such changes could have an important effect on soil microbial community that play an important role in maintaining stable functioning of soil ecosystems. This study investigated the microbial communities in five different agro-managements using molecular tools that can clarify the differences in microbial community structure and function. Significant differences in soil microbial community composition were found. However, no differences in alpha diversity or functionality were found between the treatments. To the best of our knowledge, this is the first report indicating that the bacterial community in different agro-managements provide an insight into the potential function of a vineyard system.}, }
@article {pmid38110491, year = {2023}, author = {Elsayed, SS and van der Heul, HU and Xiao, X and Nuutila, A and Baars, LR and Wu, C and Metsä-Ketelä, M and van Wezel, GP}, title = {Unravelling key enzymatic steps in C-ring cleavage during angucycline biosynthesis.}, journal = {Communications chemistry}, volume = {6}, number = {1}, pages = {281}, pmid = {38110491}, issn = {2399-3669}, support = {16439//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; }, abstract = {Angucyclines are type II polyketide natural products, often characterized by unusual structural rearrangements through B- or C-ring cleavage of their tetracyclic backbone. While the enzymes involved in B-ring cleavage have been extensively studied, little is known of the enzymes leading to C-ring cleavage. Here, we unravel the function of the oxygenases involved in the biosynthesis of lugdunomycin, a highly rearranged C-ring cleaved angucycline derivative. Targeted deletion of the oxygenase genes, in combination with molecular networking and structural elucidation, showed that LugOI is essential for C12 oxidation and maintaining a keto group at C6 that is reduced by LugOII, resulting in a key intermediate towards C-ring cleavage. An epoxide group is then inserted by LugOIII, and stabilized by the novel enzyme LugOV for the subsequent cleavage. Thus, for the first time we describe the oxidative enzymatic steps that form the basis for a wide range of rearranged angucycline natural products.}, }
@article {pmid38108886, year = {2023}, author = {Morrill, A and Forbes, MR and Vesterinen, EJ and Tamminen, M and Sääksjärvi, IE and Kaunisto, KM}, title = {Molecular Characterisation of Faecal Bacterial Assemblages Among Four Species of Syntopic Odonates.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {16}, pmid = {38108886}, issn = {1432-184X}, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics ; Ecology ; Feces ; Host Specificity ; *Odonata ; }, abstract = {Factors such as host species, phylogeny, diet, and both timing and location of sampling are thought to influence the composition of gut-associated bacteria in insects. In this study, we compared the faecal-associated bacterial taxa for three Coenagrion and one Enallagma damselfly species. We expected high overlap in representation of bacterial taxa due to the shared ecology and diet of these species. Using metabarcoding based on the 16S rRNA gene, we identified 1513 sequence variants, representing distinct bacterial 'taxa'. Intriguingly, the damselfly species showed somewhat different magnitudes of richness of ZOTUs, ranging from 480 to 914 ZOTUs. In total, 921 (or 60.8% of the 1513) distinct ZOTUs were non-shared, each found only in one species, and then most often in only a single individual. There was a surfeit of these non-shared incidental ZOTUs in the Enallagma species accounting for it showing the highest bacterial richness and accounting for a sample-wide pattern of more single-species ZOTUs than expected, based on comparisons to the null model. Future studies should address the extent to which faecal bacteria represent non-incidental gut bacteria and whether abundant and shared taxa are true gut symbionts. Pictures of odonates adopted from Norske Art databank under Creative Commons License (CC BY 4.0).}, }
@article {pmid38107863, year = {2023}, author = {Vandeweyer, D and Bruno, D and Bonelli, M and IJdema, F and Lievens, B and Crauwels, S and Casartelli, M and Tettamanti, G and De Smet, J}, title = {Bacterial biota composition in gut regions of black soldier fly larvae reared on industrial residual streams: revealing community dynamics along its intestinal tract.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1276187}, pmid = {38107863}, issn = {1664-302X}, abstract = {Some insect species have gained attention as efficient bioconverters of low-value organic substrates (i.e., residual streams) into high-value biomass. Black soldier fly (BSF) (Hermetia illucens) larvae are particularly interesting for bioconversion due to their ability to grow on a wide range of substrates, including low-value industrial residual streams. This is in part due to the plasticity of the gut microbiota of polyphagous insects, like BSF. Gut microbiota composition varies depending on rearing substrates, via a mechanism that might support the recruitment of microorganisms that facilitate digestion of a specific substrate. At the same time, specific microbial genera do persist on different substrates via unknown mechanisms. This study aimed to offer insights on this microbial plasticity by investigating how the composition of the bacterial community present in the gut of BSF larvae responds to two industrial residual streams: swill (a mixture of catering and supermarket leftovers) and distiller's dried grains with solubles. The bacterial biota composition of substrates, whole larvae at the beginning of the rearing period and at harvest, rearing residues, and larval gut regions were investigated through 16S rRNA gene sequencing. It was observed that both substrate and insect development influenced the bacterial composition of the whole larvae. Zooming in on the gut regions, there was a clear shift in community composition from a higher to a lower diversity between the anterior/middle midgut and the posterior midgut/hindgut, indicating a selective pressure occurring in the middle midgut region. Additionally, the abundance of the bacterial biota was always high in the hindgut, while its diversity was relatively low. Even more, the bacterial community in the hindgut was found to be relatively more conserved over the different substrates, harboring members of the BSF core microbiota. We postulate a potential role of the hindgut as a reservoir for insect-associated microbes. This warrants further research on that underexplored region of the intestinal tract. Overall, these findings contribute to our understanding of the bacterial biota structure and dynamics along the intestinal tract, which can aid microbiome engineering efforts to enhance larval performance on (industrial) residual streams.}, }
@article {pmid38105519, year = {2024}, author = {Pinto, S and Benincà, E and Galazzo, G and Jonkers, D and Penders, J and Bogaards, JA}, title = {Heterogeneous associations of gut microbiota with Crohn's disease activity.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2292239}, pmid = {38105519}, issn = {1949-0984}, mesh = {Humans ; *Crohn Disease/microbiology ; *Gastrointestinal Microbiome ; Inflammation ; Bacteria/genetics ; Bacteroidetes ; }, abstract = {The multi-factorial involvement of gut microbiota with Crohn's disease (CD) necessitates robust analysis to uncover possible associations with particular microbes. CD has been linked to specific bacteria, but reported associations vary widely across studies. This inconsistency may result from heterogeneous associations across individual patients, resulting in no apparent or only weak relationships with the means of bacterial abundances. We investigated the relationship between bacterial relative abundances and disease activity in a longitudinal cohort of CD patients (n = 57) and healthy controls (n = 15). We applied quantile regression, a statistical technique that allows investigation of possible relationships outside the mean response. We found several significant and mostly negative associations with CD, especially in lower quantiles of relative abundance on family or genus level. Associations found by quantile regression deviated from the mean response in relative abundances of Coriobacteriaceae, Pasteurellaceae, Peptostreptococcaceae, Prevotellaceae, and Ruminococcaceae. For the family Streptococcaceae we found a significant elevation in relative abundance for patients experiencing an exacerbation relative to those who remained without self-reported symptoms or measurable inflammation. Our analysis suggests that specific bacterial families are related to CD and exacerbation, but associations vary between patients due to heterogeneity in disease course, medication history, therapy response, gut microbiota composition and historical contingency. Our study underscores that microbial diversity is reduced in the gut of CD patients, but suggests that the process of diversity loss is rather irregular with respect to specific taxonomic groups. This novel insight may advance our ecological understanding of this complex disease.}, }
@article {pmid38103698, year = {2024}, author = {Yuan, J and Yang, L and Yu, P and Tang, N and Liu, L and Wang, W and Wang, P and Yang, Q and Guo, S and Li, J}, title = {Comparison and development of scanning electron microscope techniques for delicate plant tissues.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {340}, number = {}, pages = {111963}, doi = {10.1016/j.plantsci.2023.111963}, pmid = {38103698}, issn = {1873-2259}, mesh = {Microscopy, Electron, Scanning ; *Plants ; Temperature ; *Water ; }, abstract = {Cell deformation often occurs during sample preparation and imaging with scanning electron microscope (SEM), especially with delicate samples, which influences the accuracy of the results. Here we investigate the influence of several preparation methods on cell deformation, using water content and tissue hardness as indicators to classify "delicate" samples of plant species. The degree of deformation in samples resulting from five preparation methods was measured at the tissue and single-cell levels, revealing that a cryo- and methanol-fixation produced lower degrees of tissue dimension deformation and better preservation of cell shape for delicate samples, while for harder tissues, other preparation methods for a dehydrated specimen are also suitable. Stability and image quality of delicate samples could be improved with the application of a cryo-protectant combined with a lower cryo-stage temperature, e.g. - 30 °C. We show that the sample stability under the beam was improved by combining larger sample size and cryo-stage application. Furthermore, the influence of adaxial and abaxial tissue surfaces, the accelerating voltage, and sputter coating time on sample stability and image quality was evaluated. Our study is valuable for artifact reduction and easy application of SEM.}, }
@article {pmid38102317, year = {2023}, author = {Modra, H and Ulmann, V and Gersl, M and Babak, V and Konecny, O and Hubelova, D and Caha, J and Kudelka, J and Falkinham, JO and Pavlik, I}, title = {River Sediments Downstream of Villages in a Karstic Watershed Exhibited Increased Numbers and Higher Diversity of Nontuberculous Mycobacteria.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {15}, pmid = {38102317}, issn = {1432-184X}, mesh = {*Nontuberculous Mycobacteria ; *Rivers ; Prevalence ; Water Quality ; Phosphorus ; }, abstract = {The impact of residential villages on the nontuberculous mycobacteria (NTM) in streams flowing through them has not been studied in detail. Water and sediments of streams are highly susceptible to anthropogenic inputs such as surface water flows. This study investigated the impact of seven residential villages in a karst watershed on the prevalence and species spectrum of NTM in water and sediments. Higher NTM species diversity (i.e., 19 out of 28 detected) was recorded downstream of the villages and wastewater treatment plants (WWTPs) compared to sampling sites upstream (i.e., 5). Significantly, higher Zn and lower silicon concentrations were detected in sediments inside the village and downstream of the WWTP's effluents. Higher phosphorus concentration in sediment was downstream of WWTPs compared to other sampling sites. The effluent from the WWTPs had a substantial impact on water quality parameters with significant increases in total phosphorus, anions (Cl[-]and N-NH3[-]), and cations (Na[+] and K[+]). The results provide insights into NTM numbers and species diversity distribution in a karst watershed and the impact of urban areas. Although in this report the focus is on the NTM, it is likely that other water and sediment microbes will be influenced as well.}, }
@article {pmid38098978, year = {2023}, author = {Gonzalez, OA and Kirakodu, SS and Ebersole, JL}, title = {DAMPs and alarmin gene expression patterns in aging healthy and diseased mucosal tissues.}, journal = {Frontiers in oral health}, volume = {4}, number = {}, pages = {1320083}, pmid = {38098978}, issn = {2673-4842}, support = {P20 GM103538/GM/NIGMS NIH HHS/United States ; P40 RR003640/RR/NCRR NIH HHS/United States ; }, abstract = {INTRODUCTION: Periodontitis is delineated by a dysbiotic microbiome at sites of lesions accompanied by a dysregulated persistent inflammatory response that undermines the integrity of the periodontium. The interplay of the altered microbial ecology and warning signals from host cells would be a critical feature for maintaining or re-establishing homeostasis in these tissues.<br><br>METHODS: This study used a nonhuman primate model (Macaca mulatta) with naturally-occurring periodontitis (n&#x2009;=&#x2009;34) and experimental ligature-induced periodontitis (n&#x2009;=&#x2009;36) to describe the features of gene expression for an array of damage-associate molecular patterns (DAMPs) or alarmins within the gingival tissues. The animals were age stratified into: &#x2264;3 years (Young), 7-12 years (Adolescent), 12-15 years (Adult) and 17-23 years (Aged). Gingival tissue biopsies were examined via microarray. The analysis focused on 51 genes representative of the DAMPs/alarmins family of host cell warning factors and 18 genes associated with tissue destructive processed in the gingival tissues. Bacterial plaque samples were collected by curette sampling and 16S rRNA gene sequences used to describe the oral microbiome.<br><br>RESULTS: A subset of DAMPs/alarmins were expressed in healthy and naturally-occurring periodontitis tissues in the animals and suggested local effects on gingival tissues leading to altered levels of DAMPs/alarmins related to age and disease. Significant differences from adult healthy levels were most frequently observed in the young and adolescent animals with few representatives in this gene array altered in the healthy aged gingival tissues. Of the 51 target genes, only approximately &#x2153; were altered by &#x2265;1.5-fold in any of the age groups of animals during disease, with those increases observed during disease initiation. Distinctive positive and negative correlations were noted with the DAMP/alarmin gene levels and comparative expression changes of tissue destructive molecules during disease across the age groups. Finally, specific correlations of DAMP/alarmin genes and relative abundance of particular microbes were observed in health and resolution samples in younger animals, while increased correlations during disease in the older groups were noted.<br><br>CONCLUSIONS: Thus, using this human-like preclinical model of induced periodontitis, we demonstrated the dynamics of the activation of the DAMP/alarmin warning system in the gingival tissues that showed some specific differences based on age.}, }
@article {pmid38098078, year = {2023}, author = {Huete-Stauffer, TM and Logares, R and Ansari, MI and Røstad, A and Calleja, ML and Morán, XAG}, title = {Increased prokaryotic diversity in the Red Sea deep scattering layer.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {87}, pmid = {38098078}, issn = {2524-6372}, support = {CCF-2017/2018//King Abdullah University of Science and Technology/ ; RYC-2013-12554//Ministerio de Econom&#xed;a y Competitividad/ ; }, abstract = {BACKGROUND: The diel vertical migration (DVM) of fish provides an active transport of labile dissolved organic matter (DOM) to the deep ocean, fueling the metabolism of heterotrophic bacteria and archaea. We studied the impact of DVM on the mesopelagic prokaryotic diversity of the Red Sea focusing on the mesopelagic deep scattering layer (DSL) between 450-600 m.<br><br>RESULTS: Despite the general consensus of homogeneous conditions in the mesopelagic layer, we observed variability in physico-chemical variables (oxygen, inorganic nutrients, DOC) in the depth profiles. We also identified distinct seasonal indicator prokaryotes inhabiting the DSL, representing between 2% (in spring) to over 10% (in winter) of total 16S rRNA gene sequences. The dominant indicator groups were Alteromonadales in winter, Vibrionales in spring and Microtrichales in summer. Using multidimensional scaling analysis, the DSL samples showed divergence from the surrounding mesopelagic layers and were distributed according to depth (47% of variance explained). We identified the sources of diversity that contribute to the DSL by analyzing the detailed profiles of spring, where 3 depths were sampled in the mesopelagic. On average, 7% was related to the epipelagic, 34% was common among the other mesopelagic waters and 38% was attributable to the DSL, with 21% of species being unique to this layer.<br><br>CONCLUSIONS: We conclude that the mesopelagic physico-chemical properties shape a rather uniform prokaryotic community, but that the 200&#xa0;m deep DSL contributes uniquely and in a high proportion to the diversity of the Red Sea mesopelagic.}, }
@article {pmid38097563, year = {2023}, author = {Riva, A and Rasoulimehrabani, H and Cruz-Rubio, JM and Schnorr, SL and von Baeckmann, C and Inan, D and Nikolov, G and Herbold, CW and Hausmann, B and Pjevac, P and Schintlmeister, A and Spittler, A and Palatinszky, M and Kadunic, A and Hieger, N and Del Favero, G and von Bergen, M and Jehmlich, N and Watzka, M and Lee, KS and Wiesenbauer, J and Khadem, S and Viernstein, H and Stocker, R and Wagner, M and Kaiser, C and Richter, A and Kleitz, F and Berry, D}, title = {Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {8210}, pmid = {38097563}, issn = {2041-1723}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; P 27831/FWF_/Austrian Science Fund FWF/Austria ; P27831-B28//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; 741623//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {*Inulin/metabolism ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria ; Prebiotics ; }, abstract = {Prebiotics are defined as non-digestible dietary components that promote the growth of beneficial gut microorganisms. In many cases, however, this capability is not systematically evaluated. Here, we develop a methodology for determining prebiotic-responsive bacteria using the popular dietary supplement inulin. We first identify microbes with a capacity to bind inulin using mesoporous silica nanoparticles functionalized with inulin. 16S rRNA gene amplicon sequencing of sorted cells revealed that the ability to bind inulin was widespread in the microbiota. We further evaluate which taxa are metabolically stimulated by inulin and find that diverse taxa from the phyla Firmicutes and Actinobacteria respond to inulin, and several isolates of these taxa can degrade inulin. Incubation with another prebiotic, xylooligosaccharides (XOS), in contrast, shows a more robust bifidogenic effect. Interestingly, the Coriobacteriia Eggerthella lenta and Gordonibacter urolithinfaciens are indirectly stimulated by the inulin degradation process, expanding our knowledge of inulin-responsive bacteria.}, }
@article {pmid38096695, year = {2024}, author = {Wang, Q and Sun, Z and Song, S and Ali, A and Xu, H}, title = {Can salinity variability drive the colonization dynamics of periphytic protozoan fauna in marine environments?.}, journal = {Marine pollution bulletin}, volume = {198}, number = {}, pages = {115882}, doi = {10.1016/j.marpolbul.2023.115882}, pmid = {38096695}, issn = {1879-3363}, mesh = {*Biodiversity ; Environmental Monitoring ; Salinity ; *Ciliophora ; Logistic Models ; Ecosystem ; }, abstract = {To investigate effects of salinity variability on colonization dynamics of periphytic protozoan fauna, a 21-day study was conducted in temperature-controlled circulation systems (TCCSs). Periphytic protozoan communities were incubated using glass slides as artificial substrata in five TCCS aquaria with a large-scale salinity gradient of 9, 19, 29 (control), 39, and 49 PSU, respectively. The colonization dynamics were observed on days 3, 5, 7, 10, 14, and 21. The colonization dynamics were well fitted to the MacArthur-Wilson and logistic model equations in colonization and growth curves in all five treatments, respectively. However, the maximum species richness and abundance were reduced, and the colonization patterns were significantly shifted in four treatments with salinity changed by 20 PSU compared to the control (29 PSU). Thus, it is suggested that the large-scale salinity variability may reduce the species richness significantly and affect colonization dynamics of periphytic protozoan fauna in marine environments.}, }
@article {pmid38095470, year = {2024}, author = {Guo, Q and Gong, L}, title = {Compared with pure forest, mixed forest alters microbial diversity and increases the complexity of interdomain networks in arid areas.}, journal = {Microbiology spectrum}, volume = {12}, number = {1}, pages = {e0264223}, pmid = {38095470}, issn = {2165-0497}, support = {2021XJKK0900//the third comprehensive scientific investigtion project in xinjiang/ ; }, mesh = {*Soil Microbiology ; Forests ; Trees ; *Microbiota ; Soil/chemistry ; }, abstract = {The results provide a comparative study of the response of soil microbial ecology to the afforestation of different tree species and deepen the understanding of the factors controlling soil microbial community structure.}, }
@article {pmid38095319, year = {2024}, author = {Forman-Ankjaer, B and Hvid-Jensen, F and Kobel, CM and Greve, T}, title = {Short communication: first case of bacteraemia caused by Dielma fastidiosa in a patient hospitalized with diverticulitis.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {132}, number = {2}, pages = {130-133}, doi = {10.1111/apm.13367}, pmid = {38095319}, issn = {1600-0463}, mesh = {Phylogeny ; Firmicutes ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Humans ; *Bacteremia/diagnosis ; Likelihood Functions ; *Diverticulitis ; }, abstract = {Dielma fastidiosa is a gram-negative, anaerobic rod belonging to the family Erysipelotrichaceae. D. fastidiosa has previously been isolated in human stool samples as part of the commensal flora; however, prior to this case, it has never been identified as a human pathogen. We present the first case of bacteraemia with D. fastidiosa. Bacterial growth in the blood culture bottle was detected by the automated blood culture system BacT/ALERT 3D. Culturing was performed, and bacterial colonies were identified as D. fastidiosa using MALDI-TOF MS. A subsequent whole-genome sequencing using Illumina NovaSeq was performed, and a phylogenetic tree depicting all available sequences of D. fastidiosa was generated. The reference MALDI-TOF spectrum and species identification was compared with the previously published spectrum. Whole-genome sequencing confirmed the tentative MALDI-TOF species identification. Notably, the maximum-likelihood-based phylogenetic analysis placed the D. fastidiosa isolate from this clinical case within the known variation of the eight publicly available sequences of this species. We identified D. fastidiosa by whole-genome sequencing followed by maximum-likelihood analysis as a possible pathogen in this case of bacteraemia in a patient hospitalized with diverticulitis.}, }
@article {pmid38094622, year = {2023}, author = {Ollison, GA and Hu, SK and Hopper, JV and Stewart, BP and Beatty, JL and Caron, DA}, title = {Physiology governing diatom vs. dinoflagellate bloom and decline in coastal Santa Monica Bay.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1287326}, pmid = {38094622}, issn = {1664-302X}, abstract = {Algal blooms on the Southern California coast are typically dominated by diatom and dinoflagellate taxa, and are governed by their physiological responses to environmental cues; however, we lack a predictive understanding of the environmental controls underlying the establishment and persistence of these distinct bloom events. In this study, we examined gene expression among the numerically dominant diatom and dinoflagellate taxa during spring upwelling bloom events to compare the physiological underpinnings of diatom vs. dinoflagellate bloom dynamics. Diatoms, which bloomed following upwelling events, expressed genes related to dissolved inorganic nitrogen utilization, and genes related to the catabolism of chitin that may have prolonged their bloom duration following nitrogen depletion. Conversely, dinoflagellates bloomed under depleted inorganic nitrogen conditions, exhibited less variation in transcriptional activity, and expressed few genes associated with dissolved inorganic nutrients during their bloom. Dinoflagellate profiles exhibited evidence of proteolysis and heterotrophy that may have enabled them to bloom to high abundances under depleted inorganic nutrients. Taken together, diatom and dinoflagellate transcriptional profiles illustrated guild-specific physiologies that are tuned to respond to and thrive under distinct environmental "windows of opportunity."}, }
@article {pmid38091083, year = {2023}, author = {Perez-Bou, L and Muñoz-Palazon, B and Gonzalez-Lopez, J and Gonzalez-Martinez, A and Correa-Galeote, D}, title = {Deciphering the Role of WWTPs in Cold Environments as Hotspots for the Dissemination of Antibiotic Resistance Genes.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {14}, pmid = {38091083}, issn = {1432-184X}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Wastewater ; Waste Disposal, Fluid ; Genes, Bacterial/genetics ; Ecosystem ; Drug Resistance, Microbial/genetics ; Sewage/microbiology ; }, abstract = {Cold environments are the most widespread extreme habitats in the world. However, the role of wastewater treatment plants (WWTPs) in the cryosphere as hotspots in antibiotic resistance dissemination has not been well established. Hence, a snapshot of the resistomes of WWTPs in cold environments, below 5 °C, was provided to elucidate their role in disseminating antibiotic resistance genes (ARGs) to the receiving waterbodies. The resistomes of two natural environments from the cold biosphere were also determined. Quantitative PCR analysis of the aadA, aadB, ampC, blaSHV, blaTEM, dfrA1, ermB, fosA, mecA, qnrS, and tetA(A) genes indicated strong prevalences of these genetic determinants in the selected environments, except for the mecA gene, which was not found in any of the samples. Notably, high abundances of the aadA, ermB, and tetA(A) genes were found in the influents and activated sludge, highlighting that WWTPs of the cryosphere are critical hotspots for disseminating ARGs, potentially worsening the resistance of bacteria to some of the most commonly prescribed antibiotics. Besides, the samples from non-disturbed cold environments had large quantities of ARGs, although their ARG profiles were highly dissimilar. Hence, the high prevalences of ARGs lend support to the fact that antibiotic resistance is a common issue worldwide, including environmentally fragile cold ecosystems.}, }
@article {pmid38088973, year = {2023}, author = {Liu, ZS and Wang, KH and Cai, M and Yang, ML and Wang, XK and Ma, HL and Yuan, YH and Wu, LH and Li, DF and Liu, SJ}, title = {Agromyces chromiiresistens sp. nov., Novosphingobium album sp. nov., Sphingobium arseniciresistens sp. nov., Sphingomonas pollutisoli sp. nov., and Salinibacterium metalliresistens sp. nov.: five new members of Microbacteriaceae and Sphingomonadaceae from polluted soil.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1289110}, pmid = {38088973}, issn = {1664-302X}, abstract = {There are many unidentified microbes in polluted soil needing to be explored and nominated to benefit the study of microbial ecology. In this study, a taxonomic research was carried out on five bacterial strains which were isolated and cultivated from polycyclic aromatic hydrocarbons, and heavy metals polluted soil of an abandoned coking plant. Phylogenetical analysis showed that they belonged to the phyla Proteobacteria and Actinobacteria, and their 16S rRNA gene sequence identities were lower than 98.5% to any known and validly nominated bacterial species, suggesting that they were potentially representing new species. Using polyphasic taxonomic approaches, the five strains were classified as new species of the families Microbacteriaceae and Sphingomonadaceae. Genome sizes of the five strains ranged from 3.07 to 6.60 Mb, with overall DNA G+C contents of 63.57-71.22 mol%. The five strains had average nucleotide identity of 72.38-87.38% and digital DNA-DNA hybridization of 14.0-34.2% comparing with their closely related type strains, which were all below the thresholds for species delineation, supporting these five strains as novel species. Based on the phylogenetic, phylogenomic, and phenotypic characterizations, the five novel species are proposed as Agromyces chromiiresistens (type strain H3Y2-19a[T] = CGMCC 1.61332[T]), Salinibacterium metalliresistens (type strain H3M29-4[T] = CGMCC 1.61335T), Novosphingobium album (type strain H3SJ31-1[T] = CGMCC 1.61329[T]), Sphingomonas pollutisoli (type strain H39-1-10[T] = CGMCC 1.61325[T]), and Sphingobium arseniciresistens (type strain H39-3-25[T] = CGMCC 1.61326[T]). Comparative genome analysis revealed that the species of the family Sphingomonadaceae represented by H39-1-10[T], H39-3-25[T], and H3SJ31-1[T] possessed more functional protein-coding genes for the degradation of aromatic pollutants than the species of the family Microbacteriaceae represented by H3Y2-19a[T] and H3M29-4[T]. Furthermore, their capacities of resisting heavy metals and metabolizing aromatic compounds were investigated. The results indicated that strains H3Y2-19a[T] and H39-3-25[T] were robustly resistant to chromate (VI) and/or arsenite (III). Strains H39-1-10[T] and H39-3-25[T] grew on aromatic compounds, including naphthalene, as carbon sources even in the presence of chromate (VI) and arsenite (III). These features reflected their adaptation to the polluted soil environment.}, }
@article {pmid38088573, year = {2024}, author = {Lücking, G and Albrecht, K and Märtlbauer, E and Schauer, K}, title = {Draft genome sequences of two thermophilic, spore-forming Aeribacillus pallidus strains isolated from dairy products.}, journal = {Microbiology resource announcements}, volume = {13}, number = {1}, pages = {e0089623}, pmid = {38088573}, issn = {2576-098X}, abstract = {The presence of thermophilic spore-forming bacteria is challenging in industrial food processing. The presented genome sequences of Aeribacillus pallidus, isolated from raw milk and cocoa powder, provide insights into how to prevent damage to minimally processed foods and products with extended shelf life, such as milk products.}, }
@article {pmid38087672, year = {2024}, author = {Effenberger, M and Grander, C and Hausmann, B and Enrich, B and Pjevac, P and Zoller, H and Tilg, H}, title = {Apelin and the gut microbiome: Potential interaction in human MASLD.}, journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver}, volume = {56}, number = {6}, pages = {932-940}, doi = {10.1016/j.dld.2023.11.023}, pmid = {38087672}, issn = {1878-3562}, mesh = {Humans ; *Apelin/blood ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Case-Control Studies ; Aged ; *Carcinoma, Hepatocellular/microbiology/blood ; *Liver Cirrhosis/microbiology/blood ; Liver Neoplasms/microbiology ; Apelin Receptors/metabolism ; Cytokines/blood ; Feces/microbiology/chemistry ; Adult ; }, abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a leading cause of chronic liver disease with increasing numbers worldwide. Adipokines like apelin (APLN) can act as key players in the complex pathophysiology of MASLD.<br><br>AIMS: Investigating the role of APLN in MASLD.<br><br>METHODS: Fecal and blood samples were collected in a MASLD cohort and healthy controls (HC). MASLD patients with liver fibrosis and MASLD-associated hepatocellular carcinoma (HCC) were included into the study. Systemic concentration of Apelin, Apelin receptor (APLNR) and circulating cytokines were measured in serum samples.<br><br>RESULTS: Apelin concentration correlated with the Fib-4 score and was elevated in MASLD patients (mild fibrosis, mF (Fib-4 <3.25) and severe fibrosis, sF (Fib-4 >3.25)) as well as in MASLD-associated HCC patients compared to HC. In accordance APLNR and circulating cytokines were also elevated in mF and sF. In contrast apelin levels were negatively associated with liver survival at three and five years. Changes in taxa composition at phylum level showed an increase of Enterobactericae, Prevotellaceae and Lactobacillaceae in patients with sF compared to mF. We could also observe an association between apelin concentrations and bacterial lineages (phyla).<br><br>CONCLUSIONS: Circulating apelin is associated with liver fibrosis and HCC. In addition, there might exist an interaction between systemic apelin and the gut microbiome.}, }
@article {pmid38087002, year = {2023}, author = {Montaño-Salazar, S and Quintanilla, E and Sánchez, JA}, title = {Microbial shifts associated to ENSO-derived thermal anomalies reveal coral acclimation at holobiont level.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {22049}, pmid = {38087002}, issn = {2045-2322}, mesh = {Animals ; *Anthozoa/microbiology ; El Nino-Southern Oscillation ; Biodiversity ; Acclimatization ; Cold Temperature ; Bacteria ; Coral Reefs ; }, abstract = {The coral microbiome conforms a proxy to study effects of changing environmental conditions. However, scarce information exists regarding microbiome dynamics and host acclimation in response to environmental changes associated to global-scale disturbances. We assessed El Niño Southern Oscillation (ENSO)-derived thermal anomalies shifts in the bacterial microbiome of Pacifigorgia cairnsi (Gorgoniidae: Octocorallia) from the remote island of Malpelo in the Tropical Eastern Pacific. Malpelo is a hot spot of biodiversity and lacks direct coastal anthropogenic impacts. We evaluated the community composition and predicted functional profiles of the microbiome during 2015, 2017 and 2018, including different phases of ENSO cycle. The bacterial community diversity and composition between the warming and cooling phase were similar, but differed from the neutral phase. Relative abundances of different microbiome core members such as Endozoicomonas and Mycoplasma mainly drove these differences. An acclimated coral holobiont is suggested not just to warm but also to cold stress by embracing similar microbiome shifts and functional redundancy that allow maintaining coral's viability under thermal stress. Responses of the microbiome of unperturbed sea fans such as P. cairnsi in Malpelo could be acting as an extended phenotype facilitating the acclimation at the holobiont level.}, }
@article {pmid38086476, year = {2024}, author = {Zhang, M and Zhao, B and Yan, Y and Cheng, Z and Li, Z and Han, L and Sun, Y and Zheng, Y and Xia, Y}, title = {Comamonas-dominant microbial community in carbon poor aquitard sediments revealed by metagenomic-based growth rate investigation.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169203}, doi = {10.1016/j.scitotenv.2023.169203}, pmid = {38086476}, issn = {1879-1026}, mesh = {Metagenome ; *Arsenic/analysis ; Carbon/metabolism ; *Microbiota ; Bacteria/metabolism ; Geologic Sediments/chemistry ; }, abstract = {The microbiological ecology of a low-nutrient shallow aquifer with high arsenic content in the Yinchuan Plain was investigated in this study. Amplicon sequencing data from five samples (depths: 1.5 m, 3.5 m, 11.2 m, 19.3 m, and 25.5 m) revealed diverse and adaptable microbial community. Among the microbial community, Comamonas was the most prominent, accounting for 10.52 % of the total. This genus displayed high growth rates, with a maximum growth rate of 12.06 d[-1] and a corresponding doubling time of 1.38 days, as determined through an analysis of codon usage bias. Functional annotation of Metagenome-Assembled Genomes (MAGs) for samples at 1.5 m and 11.2 m depths revealed Comamonas' metabolic versatility, including various carbon pathways, assimilative sulfate reduction (ASR), and dissimilatory reduction to ammonium (DNRA). The TPM (Transcripts Per Kilobase of exon model per Million mapped reads) of MAGs at 11.2 m sample was 15.7 and 12.3. The presence of arsenic resistance genes in Comamonas aligns with sediment arsenic levels (65.8 mg/kg for 1.5 m depth, 32.8 mg/kg for 11.2 m depth). This study highlights the role of Comamonas as a 'generalist' bacteria in challenging oligotrophic sediments, emphasizing the significance of such organisms in community stability and ecological functions. ENVIRONMENTAL IMPLICATION: Low-biomass limits the microbial activity and biogeochemical study in oligotrophic environments, which is the typical condition for underground aquatic ecosystems. Facilitated by growth rate estimation, our research focuses on active functional microorganisms and their biogeochemical metabolic in oligotrophic aquifer sediments, revealing their impact on the environment and response to arsenic threats. Findings illuminate the metabolic advantage of a 'generalist life-style' in carbon-scarce environments and contribute to a broader understanding of bacterial ecosystems and environmental impacts in oligotrophic aquifer sediments worldwide.}, }
@article {pmid38085721, year = {2023}, author = {Coleman, ME and Oscar, TP and Negley, TL and Stephenson, MM}, title = {Suppression of pathogens in properly refrigerated raw milk.}, journal = {PloS one}, volume = {18}, number = {12}, pages = {e0289249}, pmid = {38085721}, issn = {1932-6203}, mesh = {Humans ; Animals ; Milk ; Food Microbiology ; Pilot Projects ; Colony Count, Microbial ; Salmonella ; *Escherichia coli O157 ; *Listeria monocytogenes ; }, abstract = {Conflicting claims exist regarding pathogen growth in raw milk. A small pilot study was designed to provide definitive data on trends for pathogen growth and decline in raw bovine milk hygienically produced for direct human consumption. An independent laboratory conducted the study, monitoring growth and decline of pathogens inoculated into raw milk. Raw milk samples were inoculated with foodborne pathogens (Campylobacter, E. coli O157:H7, Listeria monocytogenes, or Salmonella) at lower (<162 colony forming units (CFU) per mL) and higher levels (<8,300 CFU/mL). Samples were stored at 4.4°C and quantified over time after inoculation (days 0, 3, 6, 9, 12, and 14) by standard culture-based methods. Statistical analysis of trends using the Mann-Kendall Trend Test and Analysis of Variance were conducted for 48 time series observations. Evidence of pathogen growth was documented for L. monocytogenes in 8 of 12 replicates (P = 0.001 to P = 0.028). Analysis of variance confirmed significant increases for L. monocytogenes at both initial levels in week 2. No evidence of growth was documented over 14 days for the three pathogens predominantly associated with raw milk outbreaks in the US (Campylobacter, E. coli O157:H7, and Salmonella). Further research is needed to characterize parameters for pathogen growth and decline to support re-assessment of risks that were based on incorrect assumptions about interactions of pathogens with the raw milk microbiota.}, }
@article {pmid38082204, year = {2024}, author = {Li, X and Yu, S and Cheng, Z and Chang, X and Yun, Y and Jiang, M and Chen, X and Wen, X and Li, H and Zhu, W and Xu, S and Xu, Y and Wang, X and Zhang, C and Wu, Q and Hu, J and Lin, Z and Aury, JM and Van de Peer, Y and Wang, Z and Zhou, X and Wang, J and Lü, P and Zhang, L}, title = {Origin and evolution of the triploid cultivated banana genome.}, journal = {Nature genetics}, volume = {56}, number = {1}, pages = {136-142}, pmid = {38082204}, issn = {1546-1718}, support = {833522//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {*Musa/genetics ; *Fusarium/genetics ; Triploidy ; Plant Breeding ; Transcription Factors/genetics ; Plant Diseases/genetics ; }, abstract = {Most fresh bananas belong to the Cavendish and Gros Michel subgroups. Here, we report chromosome-scale genome assemblies of Cavendish (1.48 Gb) and Gros Michel (1.33 Gb), defining three subgenomes, Ban, Dh and Ze, with Musa acuminata ssp. banksii, malaccensis and zebrina as their major ancestral contributors, respectively. The insertion of repeat sequences in the Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 RGA2 (resistance gene analog 2) promoter was identified in most diploid and triploid bananas. We found that the receptor-like protein (RLP) locus, including Foc race 1-resistant genes, is absent in the Gros Michel Ze subgenome. We identified two NAP (NAC-like, activated by apetala3/pistillata) transcription factor homologs specifically and highly expressed in fruit that directly bind to the promoters of many fruit ripening genes and may be key regulators of fruit ripening. Our genome data should facilitate the breeding and super-domestication of bananas.}, }
@article {pmid38082143, year = {2023}, author = {Botero Rute, LM and Caro-Quintero, A and Acosta-González, A}, title = {Enhancing the Conventional Culture: the Evaluation of Several Culture Media and Growth Conditions Improves the Isolation of Ruminal Bacteria.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {13}, pmid = {38082143}, issn = {1432-184X}, mesh = {Cattle ; Animals ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; *Rumen/microbiology ; Bacteria ; *Microbiota ; }, abstract = {The rumen microbiota is critical in cattle digestion. Still, its low cultivability makes it difficult to study its ecological function and biotechnological potential. To improve the recovery of ruminal microorganisms, this study combined the evaluation of several cultivation parameters with metabarcoding analysis. The parameters tested comprised eight media cultures, three sample dilutions (10[-2], 10[-6], 10[-12]), and two incubation times (3 and 7 days). Bacterial populations were determined through Illumina sequencing of 16S rRNA from three biological replicates. The results indicate that none of the culture media recovered all rumen populations and that there was an altered relative abundance of the dominant phyla. In the rumen, Bacteroidetes and Firmicutes comprised 75% and 15% of the relative abundance, respectively, while in the culture media, these were 15% and 60%, respectively. Principal coordinate analysis (PCoA) of the bacterial community revealed significant shifts in population composition due to dilution, with 10[-2] and 10[-6] dilutions clustered closely while the 10[-12] dilution differed markedly. In contrast, incubation duration did not influence population diversity. According to the results, two media, CAN and KNT, were selected based on their ability to recover more similar populations compared to the rumen sample. The metataxonomic study showed that CAN media had consistent reproducibility over time, while KNT showed enrichment of different taxa due to the use of rumen fluid as a substrate. From these, 64 pure cultures were obtained and 54 were identified through 16S rRNA gene sequencing. Being Streptococcus the most frequently isolated genus, this prevalence contrasts with the liquid media composition, underscoring the importance of refining single colony isolation strategies. Although no culture medium could replicate the native rumen bacterial population perfectly, our findings highlight the potential of CAN and KNT media in recovering populations that are more closely aligned to natural rumen conditions. In conclusion, our study emphasizes the importance of integrating molecular approaches in selecting suitable cultivation media and parameters to depict rumen bacteria accurately.}, }
@article {pmid38078767, year = {2024}, author = {Smith, AB and Specker, JT and Hewlett, KK and Scoggins, TR and Knight, M and Lustig, AM and Li, Y and Evans, KM and Guo, Y and She, Q and Christopher, MW and Garrett, TJ and Moustafa, AM and Van Tyne, D and Prentice, BM and Zackular, JP}, title = {Liberation of host heme by Clostridioides difficile-mediated damage enhances Enterococcus faecalis fitness during infection.}, journal = {mBio}, volume = {15}, number = {1}, pages = {e0165623}, pmid = {38078767}, issn = {2150-7511}, support = {K22 AI137220/AI/NIAID NIH HHS/United States ; R21 AI164018/AI/NIAID NIH HHS/United States ; U19 AI174998/AI/NIAID NIH HHS/United States ; R03 AI168491/AI/NIAID NIH HHS/United States ; L40 AI147162/AI/NIAID NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Clostridioides difficile ; Enterococcus faecalis ; *Clostridium Infections/microbiology ; Bacteria ; *Gastrointestinal Microbiome ; }, abstract = {Clostridioides difficile and Enterococcus faecalis are two pathogens of great public health importance. Both bacteria colonize the human gastrointestinal tract where they are known to interact in ways that worsen disease outcomes. We show that the damage associated with C. difficile infection (CDI) releases nutrients that benefit E. faecalis. One particular nutrient, heme, allows E. faecalis to use oxygen to generate energy and grow better in the gut. Understanding the mechanisms of these interspecies interactions could inform therapeutic strategies for CDI.}, }
@article {pmid38078555, year = {2024}, author = {Zhang, X and Dai, H and Huang, Y and Liu, K and Li, X and Zhang, S and Fu, S and Jiao, S and Chen, C and Dong, B and Yang, Z and Cui, Y and Li, H and Liu, S}, title = {Species pool, local assembly processes: Disentangling the mechanisms determining bacterial α- and β-diversity during forest secondary succession.}, journal = {Molecular ecology}, volume = {33}, number = {4}, pages = {e17241}, doi = {10.1111/mec.17241}, pmid = {38078555}, issn = {1365-294X}, support = {31700383//Natural Science Foundation of China/ ; 31800375//Natural Science Foundation of China/ ; 31930078//Natural Science Foundation of China/ ; 32071556//Natural Science Foundation of China/ ; U1904204//Natural Science Foundation of China/ ; 222300420036//Natural Science Foundation of Henan Province/ ; //the Fundamental Research Funds of Northwest A&amp;F University/ ; QCYRCXM-2022-347//the high-level innovation and entrepreneurship talent project of Qinchuangyuan/ ; }, mesh = {*Biodiversity ; Forests ; Ecology ; *Microbiota ; Bacteria/genetics ; Soil ; Ecosystem ; }, abstract = {Across ecology, and particularly within microbial ecology, there is limited understanding how the generation and maintenance of diversity. Although recent work has shown that both local assembly processes and species pools are important in structuring microbial communities, the relative contributions of these mechanisms remain an important question. Moreover, the roles of local assembly processes and species pools are drastically different when explicitly considering the potential for saturation or unsaturation, yet this issue is rarely addressed. Thus, we established a conceptual model that incorporated saturation theory into the microbiological domain to advance the understanding of mechanisms controlling soil bacterial diversity during forest secondary succession. Conceptual model hypotheses were tested by coupling soil bacterial diversity, local assembly processes and species pools using six different forest successional chronosequences distributed across multiple climate zones. Consistent with the unsaturated case proposed in our conceptual framework, we found that species pool consistently affected α-diversity, even while local assembly processes on local richness operate. In contrast, the effects of species pool on β-diversity disappeared once local assembly processes were taken into account, and changes in environmental conditions during secondary succession led to shifts in β-diversity through mediation of the strength of heterogeneous selection. Overall, this study represents one of the first to demonstrate that most local bacterial communities might be unsaturated, where the effect of species pool on α-diversity is robust to the consideration of multiple environmental influences, but β-diversity is constrained by environmental selection.}, }
@article {pmid38076468, year = {2024}, author = {Nikita, R and Ghosh, A and Yash,  and Kumar, C and Mandal, A and Saini, N and Dubey, SK and Gogoi, K and Rajts, F and Belton, B and Bhadury, P}, title = {Dataset of biological community structure in Deepor Beel using eDNA approach-A RAMSAR wetland of Assam, India.}, journal = {Data in brief}, volume = {52}, number = {}, pages = {109786}, pmid = {38076468}, issn = {2352-3409}, abstract = {Deepor Beel, located in the state of Assam in India, is a Wetland of International Importance with a Wildlife Sanctuary and is the only RAMSAR site in the state. Though of invaluable ecological significance, the wetland is facing anthropogenic stressors, leading to rapid degradation of ecological health. In December 2022, surface water was collected from six stations of Deepor Beel to elucidate biological communities using the eDNA approach. At the time of sampling, in-situ environmental parameters were measured in triplicates. The dissolved nutrients and concentrations of metals and metalloids were estimated using UV-Vis Spectrophotometry and ICP-MS approaches respectively. The study revealed a high concentration of dissolved nitrate in the surface water. High-throughput sequencing using Nanopore sequencing chemistry in a MinION platform indicated the overwhelming abundance of Moraxellaceae (Prokaryotes) and Eumetazoa (Eukaryotes). The abundance of Cyprinidae were also encountered in the studied wetland reflecting the biodiversity of fish populations. High nitrate along with elucidated microbial signals are crucial to designate ecological health status of Deeper Beel. This study is aimed at generating baseline information to aid long-term monitoring and restoration of the Deepor Beel as well as the first comprehensive assessment of a RAMSAR Site located in northeast of India.}, }
@article {pmid38075488, year = {2024}, author = {Wang, X and Guo, K and Rabaey, K and Prévoteau, A}, title = {(Bio)electrochemistry for the environment, ready for ignition?.}, journal = {Environmental science and ecotechnology}, volume = {17}, number = {}, pages = {100336}, pmid = {38075488}, issn = {2666-4984}, }
@article {pmid38073168, year = {2023}, author = {Kumar, G and Bhadury, P}, title = {Exploring the influences of geographical variation on sequence signatures in the human gut microbiome.}, journal = {Journal of genetics}, volume = {102}, number = {}, pages = {}, pmid = {38073168}, issn = {0973-7731}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Firmicutes/genetics ; Bacteroidetes/genetics ; Geography ; }, abstract = {Geography shapes the structure and function of human gut microbiomes. In this study, we have explored the available human gut microbiome 16S rRNA sequence datasets of cohorts representing large geographical gradients. The 16S rRNA sequences representing V3-V4 as well as V4 regions generated using Illumina sequencing chemistry in the MiSeq platform encompassing the United States of America, Chile, South Africa, Kuwait, and Malaysia were subjected to in-depth computational biology analyses. Firmicutes and Bacteroidetes were the most dominant phyla present in all studied cohorts but Actinobacteria was exclusively present in high abundance in cohorts from Malaysia (15.99%). The relative abundance of five families, namely Bacteroidaceae, Ruminococcaceae, Prevotellaceae, Clostridiaceae, and Eubacteriaceae were highest representing the studied cohorts. The permutational multivariate analysis of variance (PERMANOVA) showed that the dissimilarity in the gut microbiome structure of cohorts representing studied countries was significant (R[2] = 0.28, P<0.001). The calculated Firmicutes to Bacteroidetes (F : B) ratio was found to be lowest in cohorts from South Africa (1.11) and Chile (0.95). The cohorts from South Africa exhibited the highest alpha diversity based on Hill numbers at q=0, whereas at q=1 and 2, cohorts from Malaysia had the highest alpha diversity. The beta diversity analysis revealed that cohorts from Chile formed a distinct cluster among all the studied geographical locations. For the first time, the study also showed that cohorts from Malaysia representing short geographical distances exhibited distinct intrapopulation differences in the gut microbiome and may not be influenced by cultural and genetic factors.}, }
@article {pmid38072930, year = {2023}, author = {Sakarika, M and Kerckhof, FM and Van Peteghem, L and Pereira, A and Van Den Bossche, T and Bouwmeester, R and Gabriels, R and Van Haver, D and Ulčar, B and Martens, L and Impens, F and Boon, N and Ganigué, R and Rabaey, K}, title = {The nutritional composition and cell size of microbial biomass for food applications are defined by the growth conditions.}, journal = {Microbial cell factories}, volume = {22}, number = {1}, pages = {254}, pmid = {38072930}, issn = {1475-2859}, support = {CO2PERATE//Agentschap Innoveren en Ondernemen/ ; HBC.2019.2601//Agentschap Innoveren en Ondernemen/ ; HBC.2018.0188//Agentschap Innoveren en Ondernemen/ ; HBC.2020.2205//Agentschap Innoveren en Ondernemen/ ; 1286824N//Fonds Wetenschappelijk Onderzoek/ ; 1S27821N//Fonds Wetenschappelijk Onderzoek/ ; BOF19/STA/044//Universiteit Gent/ ; }, mesh = {Biomass ; *Amino Acids ; *Proteome ; Cysteine ; Cell Size ; }, abstract = {BACKGROUND: It is increasingly recognized that conventional food production systems are not able to meet the globally increasing protein needs, resulting in overexploitation and depletion of resources, and environmental degradation. In this context, microbial biomass has emerged as a promising sustainable protein alternative. Nevertheless, often no consideration is given on the fact that the cultivation conditions affect the composition of microbial cells, and hence their quality and nutritional value. Apart from the properties and nutritional quality of the produced microbial food (ingredient), this can also impact its sustainability. To qualitatively assess these aspects, here, we investigated the link between substrate availability, growth rate, cell composition and size of Cupriavidus necator and Komagataella phaffii.<br><br>RESULTS: Biomass with decreased nucleic acid and increased protein content was produced at low growth rates. Conversely, high rates resulted in larger cells, which could enable more efficient biomass harvesting. The proteome allocation varied across the different growth rates, with more ribosomal proteins at higher rates, which could potentially affect the techno-functional properties of the biomass. Considering the distinct amino acid profiles established for the different cellular components, variations in their abundance impacts the product quality leading to higher cysteine and phenylalanine content at low growth rates. Therefore, we hint that costly external amino acid supplementations that are often required to meet the nutritional needs could be avoided by carefully applying conditions that enable targeted growth rates.<br><br>CONCLUSION: In summary, we demonstrate tradeoffs between nutritional quality and production rate, and we discuss the microbial biomass properties that vary according to the growth conditions.}, }
@article {pmid38072911, year = {2023}, author = {Arnolds, KL and Higgins, RC and Crandall, J and Li, G and Linger, JG and Guarnieri, MT}, title = {Risk Assessment of Industrial Microbes Using a Terrestrial Mesocosm Platform.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {12}, pmid = {38072911}, issn = {1432-184X}, support = {DE-AC36-08GO28308//U.S. Department of Energy/ ; DE-AC36-08GO28308//U.S. Department of Energy/ ; DE-AC36-08GO28308//U.S. Department of Energy/ ; DE-AC36-08GO28308//U.S. Department of Energy/ ; DE-AC36-08GO28308//U.S. Department of Energy/ ; DE-AC36-08GO28308//U.S. Department of Energy/ ; }, mesh = {*Ecosystem ; Saccharomyces cerevisiae/genetics ; Soil Microbiology ; *Microbiota ; Soil ; Risk Assessment ; }, abstract = {Industrial microbes and bio-derived products have emerged as an integral component of the bioeconomy, with an array of agricultural, bioenergy, and biomedical applications. However, the rapid development of microbial biotechnology raises concerns related to environmental escape of laboratory microbes, detection and tracking thereof, and resultant impact upon native ecosystems. Indeed, though wild-type and genetically modified microbes are actively deployed in industrial bioprocesses, an understanding of microbial interactivity and impact upon the environment is severely lacking. In particular, the persistence and sustained ecosystem impact of industrial microbes following laboratory release or unintentional laboratory escape remains largely unexplored. Herein, we investigate the applicability of soil-sorghum mesocosms for the ecological risk assessment of the industrial microbe, Saccharomyces cerevisiae. We developed and applied a suite of diagnostic and bioinformatic analyses, including digital droplet PCR, microscopy, and phylogenomic analyses to assess the impacts of a terrestrial ecosystem perturbation event over a 30-day time course. The platform enables reproducible, high-sensitivity tracking of S. cerevisiae in a complex soil microbiome and analysis of the impact upon abiotic soil characteristics and soil microbiome population dynamics and diversity. The resultant data indicate that even though S. cerevisiae is relatively short-lived in the soil, a single perturbation event can have sustained impact upon mesocosm soil composition and underlying microbial populations in our system, underscoring the necessity for more comprehensive risk assessment and development of mitigation and biocontainment strategies in industrial bioprocesses.}, }
@article {pmid38072409, year = {2023}, author = {Ide, H and Ishii, K and Takahashi, Y and Fujitani, H and Tsuneda, S}, title = {Effects of Co-existing Heterotrophs on Physiology of and Nitrogen Metabolism in Autotrophic Nitrite-oxidizing Candidatus Nitrotoga.}, journal = {Microbes and environments}, volume = {38}, number = {4}, pages = {}, pmid = {38072409}, issn = {1347-4405}, mesh = {*Nitrites/metabolism ; Oxidation-Reduction ; *Gallionellaceae/metabolism ; Nitrogen/metabolism ; }, abstract = {Interactions between autotrophic nitrifiers and heterotrophs have attracted considerable attention in microbial ecology. However, the mechanisms by which heterotrophs affect the physiological activity of and nitrogen metabolism in autotrophic nitrite oxidizers remain unclear. We herein focused on nitrite-oxidizing Candidatus Nitrotoga and compared an axenic culture including only Ca. Nitrotoga with a co-culture of both Ca. Nitrotoga and Acidovorax in physiological experiments and transcriptomics. In the co-culture with Acidovorax, nitrite consumption by Ca. Nitrotoga was promoted, and some genes relevant to nitrogen metabolism in Ca. Nitrotoga were highly expressed. These results provide insights into the mechanisms by which co-existing heterotrophs affect autotrophic nitrifiers.}, }
@article {pmid38070605, year = {2024}, author = {Suman, J and Sredlova, K and Fraraccio, S and Jerabkova, M and Strejcek, M and Kabickova, H and Cajthaml, T and Uhlik, O}, title = {Transformation of hydroxylated polychlorinated biphenyls by bacterial 2-hydroxybiphenyl 3-monooxygenase.}, journal = {Chemosphere}, volume = {349}, number = {}, pages = {140909}, doi = {10.1016/j.chemosphere.2023.140909}, pmid = {38070605}, issn = {1879-1298}, mesh = {Animals ; *Polychlorinated Biphenyls/metabolism ; Hydroxylation ; Mixed Function Oxygenases/metabolism ; Bacteria/metabolism ; }, abstract = {Monohydroxylated PCBs (OH-PCBs) are an (eco)toxicologically significant group of compounds, as they arise from the oxidation of polychlorinated biphenyls (PCBs) and, at the same time, may exert even more severe toxic effects than their parent PCB molecules. Despite having been widely detected in environmental samples, plants, and animals, information on the fate of OH-PCBs in the environment is scarce, including on the enzymatic machinery behind their degradation. To date, only a few bacterial taxa capable of OH-PCB transformation have been reported. In this study, we aimed to obtain a deeper insight into the transformation of OH-PCBs in soil bacteria and isolated a Pseudomonas sp. strain P1B16 based on its ability to use o-phenylphenol (2-PP) which, when exposed to the Delor 103-derived OH-PCB mixture, depleted a wide spectrum of mono-, di, and trichlorinated OH-PCBs. In the P1B16 genome, a region designated as hbp was identified, which bears a set of putative genes involved in the transformation of OH-PCBs, namely hbpA encoding for a putative flavin-dependent 2-hydroxybiphenyl monooxygenase, hbpC (2,3-dihydroxybiphenyl-1,2-dioxygenase), hbpD (2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase), and the transcriptional activator-encoding gene hbpR. The hbpA coding sequence was heterologously expressed, purified, and its substrate specificity was investigated towards the Delor 103-derived OH-PCB mixture, individual OH-PCBs, and multiple (chlorinated) phenolics. Apart from 2-PP and 2-chlorophenol, HbpA was also demonstrated to transform a range of OH-PCBs, including a 3-hydroxy-2,2',4',5,5'-pentachlorobiphenyl. Importantly, this is the first direct evidence of HbpA homologs being involved in the degradation of OH-PCBs. Moreover, using a P1B16-based biosensor strain, the specific induction of hbp genes by 2-PP, 3-phenylphenol, 4-phenylphenol, and the OH-PCB mixture was demonstrated. This study provides direct evidence on the specific enzymatic machinery responsible for the transformation of OH-PCBs in bacteria, with many implications in ecotoxicology, environmental restoration, and microbial ecology in habitats burdened with PCB contamination.}, }
@article {pmid38070053, year = {2024}, author = {Deng, W and Bai, NE and Qi, FL and Yang, XY and She, R and Xiao, W}, title = {Temporal dynamics of the microbial heterogeneity-diversity relationship in microcosmic systems.}, journal = {Oecologia}, volume = {204}, number = {1}, pages = {35-46}, pmid = {38070053}, issn = {1432-1939}, support = {32371557//National Natural Science Foundation of China/ ; 2019QZKK2002//Second Tibetan Plateau Scientifc Expedition and Research Program/ ; }, mesh = {Animals ; *Biodiversity ; *Plants ; Ecosystem ; }, abstract = {Spatial heterogeneity significantly enhances biodiversity, representing one of the ecology's most enduring paradigms. However, many studies have found decreasing, humped, and neutral correlations between spatial heterogeneity and biodiversity (heterogeneity-diversity relationships, HDR). These findings have pushed this widely accepted theory back into controversy. Microbial HDR research has lagged compared to that of plants and animals. Nevertheless, microbes have features that add a temporal-scale perspective to HDR research that is critical to understanding patterns of HDR. In this study, 157 microcosms with different types spatial heterogeneity were set up to map the HDR of microorganisms and their temporal dynamics using high-throughput sequencing techniques. The results show that the following: 1. Spatial heterogeneity can significantly alter microbial diversity in microcosmic systems. Changes in microbial diversity, in turn, lead to changes in environmental conditions. These changes caused microorganisms to exhibit increasing, decreasing, humped, U-shaped, and neutral HDR patterns. 2. The emergence of HDR patterns is characterized by temporal dynamics. Additionally, the HDR patterns generated by spatial structural and compositional heterogeneity exhibit inconsistent emergence times. These results suggest that the temporal dynamics of HDR may be one of the reasons for the coexistence of multiple patterns in previous studies. The feedback regulation between spatial heterogeneity-biodiversity-environmental conditions is an essential reason for the temporally dynamics of HDR patterns. All future ecological studies should pay attention to the temporal dynamic patterns of ecological factors.}, }
@article {pmid38067489, year = {2023}, author = {Singh, SK and Shrivastava, S and Mishra, AK and Kumar, D and Pandey, VK and Srivastava, P and Pradhan, B and Behera, BC and Bahuguna, A and Baek, KH}, title = {Friedelin: Structure, Biosynthesis, Extraction, and Its Potential Health Impact.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {23}, pages = {}, pmid = {38067489}, issn = {1420-3049}, mesh = {Humans ; *Triterpenes/chemistry ; Anti-Inflammatory Agents ; Antioxidants/pharmacology ; Phytochemicals ; }, abstract = {Pharmaceutical companies are investigating more source matrices for natural bioactive chemicals. Friedelin (friedelan-3-one) is a pentacyclic triterpene isolated from various plant species from different families as well as mosses and lichen. The fundamental compounds of these friedelane triterpenoids are abundantly found in cork tissues and leaf materials of diverse plant genera such as Celastraceae, Asteraceae, Fabaceae, and Myrtaceae. They possess many pharmacological effects, including anti-inflammatory, antioxidant, anticancer, and antimicrobial activities. Friedelin also has an anti-insect effect and the ability to alter the soil microbial ecology, making it vital to agriculture. Ultrasound, microwave, supercritical fluid, ionic liquid, and acid hydrolysis extract friedelin with reduced environmental impact. Recently, the high demand for friedelin has led to the development of CRISPR/Cas9 technology and gene overexpression plasmids to produce friedelin using genetically engineered yeast. Friedelin with low cytotoxicity to normal cells can be the best phytochemical for the drug of choice. The review summarizes the structural interpretation, biosynthesis, physicochemical properties, quantification, and various forms of pharmacological significance.}, }
@article {pmid38067008, year = {2023}, author = {Popov, IV and Berezinskaia, IS and Popov, IV and Martiusheva, IB and Tkacheva, EV and Gorobets, VE and Tikhmeneva, IA and Aleshukina, AV and Tverdokhlebova, TI and Chikindas, ML and Venema, K and Ermakov, AM}, title = {Cultivable Gut Microbiota in Synanthropic Bats: Shifts of Its Composition and Diversity Associated with Hibernation.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {23}, pages = {}, pmid = {38067008}, issn = {2076-2615}, support = {23-14-00316//Russian Science Foundation/ ; agreement 075-10-2021-093, Project [IMB-2102]//Ministry of Science and Higher Education of the Russian Federation/ ; K.V. was supported by the Dutch Province of Limburg with a grant to the Centre for Healthy Eating &amp; Food Innovation (HEFI) of Maastricht University-campus Venlo.//Centre for Healthy Eating &amp; Food Innovation (HEFI)/ ; }, abstract = {The role of bats in the global microbial ecology no doubt is significant due to their unique immune responses, ability to fly, and long lifespan, all contributing to pathogen spread. Some of these animals hibernate during winter, which results in the altering of their physiology. However, gut microbiota shifts during hibernation is little studied. In this research, we studied cultivable gut microbiota composition and diversity of Nyctalus noctula before, during, and after hibernation in a bat rehabilitation center. Gut microorganisms were isolated on a broad spectrum of culture media, counted, and identified with mass spectrometry. Linear modeling was used to investigate associations between microorganism abundance and N. noctula physiological status, and alpha- and beta-diversity indexes were used to explore diversity changes. As a result, most notable changes were observed in Serratia liquefaciens, Hafnia alvei, Staphylococcus sciuri, and Staphylococcus xylosus, which were significantly more highly abundant in hibernating bats, while Citrobacter freundii, Klebsiella oxytoca, Providencia rettgeri, Citrobacter braakii, and Pedicoccus pentosaceus were more abundant in active bats before hibernation. The alpha-diversity was the lowest in hibernating bats, while the beta-diversity differed significantly among all studied periods. Overall, this study shows that hibernation contributes to changes in bat cultivable gut microbiota composition and diversity.}, }
@article {pmid38066493, year = {2023}, author = {Shuanglian, Y and Huiling, Z and Xunting, L and Yifang, D and Yufen, L and Shanshan, X and Lijuan, S and Yunpeng, L}, title = {Establishment and validation of early prediction model for hypertriglyceridemic severe acute pancreatitis.}, journal = {Lipids in health and disease}, volume = {22}, number = {1}, pages = {218}, pmid = {38066493}, issn = {1476-511X}, support = {3502Z20204007//Xiamen Key Programs of Medicine and Health/ ; 3502Z20199172//Xiamen Priority Programs of Medicine and Health/ ; 2023zsyyhlky-010//Nursing research Programs of Zhongshan Hospital Xiamen University/ ; }, mesh = {Humans ; *Pancreatitis/diagnosis ; Severity of Illness Index ; Acute Disease ; Ascites ; Retrospective Studies ; Prognosis ; Biomarkers ; C-Reactive Protein ; *Hypertriglyceridemia ; }, abstract = {BACKGROUND: The prevalence of hypertriglyceridaemia-induced acute pancreatitis (HTG-AP) is increasing due to improvements in living standards and dietary changes. However, currently, there is no clinical multifactor scoring system specific to HTG-AP. This study aimed to screen the predictors of HTG-SAP and combine several indicators to establish and validate a visual model for the early prediction of HTG-SAP.<br><br>METHODS: The clinical data of 266 patients with HTG-SAP were analysed. Patients were classified into severe (N&#x2009;=&#x2009;42) and non-severe (N&#x2009;=&#x2009;224) groups according to the Atlanta classification criteria. Several statistical analyses, including one-way analysis, least absolute shrinkage with selection operator (LASSO) regression model, and binary logistic regression analysis, were used to evaluate the data.<br><br>RESULTS: The univariate analysis showed that several factors showed no statistically significant differences, including the number of episodes of pancreatitis, abdominal pain score, and several blood diagnostic markers, such as lactate dehydrogenase (LDH), serum calcium (Ca[2+]), C-reactive protein (CRP), and the incidence of pleural effusion, between the two groups (P&#x2009;<&#x2009;0.000). LASSO regression analysis identified six candidate predictors: CRP, LDH, Ca[2+], procalcitonin (PCT), ascites, and Balthazar computed tomography grade. Binary logistic regression multivariate analysis showed that CRP, LDH, Ca[2+], and ascites were independent predictors of HTG-SAP, and the area under the curve (AUC) values were 0.886, 0.893, 0.872, and 0.850, respectively. The AUC of the newly established HTG-SAP model was 0.960 (95% confidence interval: 0.936-0.983), which was higher than that of the bedside index for severity in acute pancreatitis (BISAP) score, modified CT severity index, Ranson score, and Japanese severity score (JSS) CT grade (AUC: 0.794, 0.796, 0.894 and 0.764, respectively). The differences were significant (P&#x2009;<&#x2009;0.01), except for the JSS prognostic indicators (P&#x2009;=&#x2009;0.130). The Hosmer-Lemeshow test showed that the predictive results of the model were highly consistent with the actual situation (P&#x2009;>&#x2009;0.05). The decision curve analysis plot suggested that clinical intervention can benefit patients when the model predicts that they are at risk for developing HTG-SAP.<br><br>CONCLUSIONS: CRP, LDH, Ca[2+], and ascites are independent predictors of HTG-SAP. The prediction model constructed based on these indicators has a high accuracy, sensitivity, consistency, and practicability in predicting HTG-SAP.}, }
@article {pmid38065941, year = {2023}, author = {Zhou, Y and Yang, Z and Liu, J and Li, X and Wang, X and Dai, C and Zhang, T and Carrión, VJ and Wei, Z and Cao, F and Delgado-Baquerizo, M and Li, X}, title = {Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {8126}, pmid = {38065941}, issn = {2041-1723}, mesh = {Soil ; *Microbiota ; *Fabaceae ; Arachis ; Rhizosphere ; Crop Production ; Soil Microbiology ; Plant Roots ; }, abstract = {It is widely known that some soils have strong levels of disease suppression and prevent the establishment of pathogens in the rhizosphere of plants. However, what soils are better suppressing disease, and how management can help us to boost disease suppression remain unclear. Here, we used field, greenhouse and laboratory experiments to investigate the effect of management (monocropping and rotation) on the capacity of rhizosphere microbiomes in suppressing peanut root rot disease. Compared with crop rotations, monocropping resulted in microbial assemblies that were less effective in suppressing root rot diseases. Further, the depletion of key rhizosphere taxa in monocropping, which were at a disadvantage in the competition for limited exudates resources, reduced capacity to protect plants against pathogen invasion. However, the supplementation of depleted strains restored rhizosphere resistance to pathogen. Taken together, our findings highlight the role of native soil microbes in fighting disease and supporting plant health, and indicate the potential of using microbial inocula to regenerate the natural capacity of soil to fight disease.}, }
@article {pmid38063370, year = {2024}, author = {Tamames, J and Jiménez-Lalana, D and Redondo, &#xc1; and Martínez-García, S and de Los Rios, A}, title = {In situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day.}, journal = {Molecular ecology resources}, volume = {24}, number = {2}, pages = {e13909}, doi = {10.1111/1755-0998.13909}, pmid = {38063370}, issn = {1755-0998}, mesh = {*Metagenome ; *Microbiota/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Spain ; }, abstract = {We present here a complete system for metagenomic analysis that allows performing the sequencing and analysis of a medium-size metagenome in less than one day. This unprecedented development was possible due to the conjunction of state-of-the-art experimental and computational advances: a portable laboratory suitable for DNA extraction and sequencing with nanopore technology; the powerful metagenomic analysis pipeline SqueezeMeta, capable to provide a complete analysis in a few hours and using scarce computational resources; and tools for the automatic inspection of the results via a graphical user interface, that can be coupled to a web server to allow remote visualization of data (SQMtools and SQMxplore). We have tested the feasibility of our approach in the sequencing of the microbiota associated to volcanic rocks in La Palma, Canary Islands. Also, we did a two-day sampling campaign of marine waters in which the results obtained on the first day guided the experimental design of the second day. We demonstrate that it is possible to generate metagenomic information in less than one day, making it feasible to obtain taxonomic and functional profiles fast and efficiently, even in field conditions. This capacity can be used in the further to perform real-time functional and taxonomic monitoring of microbial communities in remote areas.}, }
@article {pmid38060022, year = {2023}, author = {Abu Bakar, N and Lau, BYC and González-Aravena, M and Smykla, J and Krzewicka, B and Karsani, SA and Alias, SA}, title = {Geographical Diversity of Proteomic Responses to Cold Stress in the Fungal Genus Pseudogymnoascus.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {11}, pmid = {38060022}, issn = {1432-184X}, support = {Postgraduate sponsorship//Majlis Amanah Rakyat/ ; HICoE grant (IOES-2014G)//Ministry of Higher Education, Malaysia/ ; UMRP (RP026A-18SUS)//Universiti Malaya/ ; }, mesh = {*Cold-Shock Response ; Proteomics ; *Ascomycota ; Soil Microbiology ; Soil ; Antarctic Regions ; Cold Temperature ; }, abstract = {In understanding stress response mechanisms in fungi, cold stress has received less attention than heat stress. However, cold stress has shown its importance in various research fields. The following study examined the cold stress response of six Pseudogymnoascus spp. isolated from various biogeographical regions through a proteomic approach. In total, 2541 proteins were identified with high confidence. Gene Ontology enrichment analysis showed diversity in the cold stress response pathways for all six Pseudogymnoascus spp. isolates, with metabolic and translation-related processes being prominent in most isolates. 25.6% of the proteins with an increase in relative abundance were increased by more than 3.0-fold. There was no link between the geographical origin of the isolates and the cold stress response of Pseudogymnoascus spp. However, one Antarctic isolate, sp3, showed a distinctive cold stress response profile involving increased flavin/riboflavin biosynthesis and methane metabolism. This Antarctic isolate (sp3) was also the only one that showed decreased phospholipid metabolism in cold stress conditions. This work will improve our understanding of the mechanisms of cold stress response and adaptation in psychrotolerant soil microfungi, with specific attention to the fungal genus Pseudogymnoascus.}, }
@article {pmid38059790, year = {2023}, author = {Martinez-Gutierrez, CA and Uyeda, JC and Aylward, FO}, title = {A timeline of bacterial and archaeal diversification in the ocean.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {38059790}, issn = {2050-084X}, support = {IIBR-2141862//National Science Foundation/ ; Early Career Award in Marine Microbial Ecology and Evolution//Simons Foundation/ ; }, mesh = {*Archaea/genetics ; Phylogeny ; *Cyanobacteria ; Oxygen ; Oceans and Seas ; Seawater/microbiology ; }, abstract = {Microbial plankton play a central role in marine biogeochemical cycles, but the timing in which abundant lineages diversified into ocean environments remains unclear. Here, we reconstructed the timeline in which major clades of bacteria and archaea colonized the ocean using a high-resolution benchmarked phylogenetic tree that allows for simultaneous and direct comparison of the ages of multiple divergent lineages. Our findings show that the diversification of the most prevalent marine clades spans throughout a period of 2.2 Ga, with most clades colonizing the ocean during the last 800 million years. The oldest clades - SAR202, SAR324, Ca. Marinimicrobia, and Marine Group II - diversified around the time of the Great Oxidation Event, during which oxygen concentration increased but remained at microaerophilic levels throughout the Mid-Proterozoic, consistent with the prevalence of some clades within these groups in oxygen minimum zones today. We found the diversification of the prevalent heterotrophic marine clades SAR11, SAR116, SAR92, SAR86, and Roseobacter as well as the Marine Group I to occur near to the Neoproterozoic Oxygenation Event (0.8-0.4 Ga). The diversification of these clades is concomitant with an overall increase of oxygen and nutrients in the ocean at this time, as well as the diversification of eukaryotic algae, consistent with the previous hypothesis that the diversification of heterotrophic bacteria is linked to the emergence of large eukaryotic phytoplankton. The youngest clades correspond to the widespread phototrophic clades Prochlorococcus, Synechococcus, and Crocosphaera, whose diversification happened after the Phanerozoic Oxidation Event (0.45-0.4 Ga), in which oxygen concentrations had already reached their modern levels in the atmosphere and the ocean. Our work clarifies the timing at which abundant lineages of bacteria and archaea colonized the ocean, thereby providing key insights into the evolutionary history of lineages that comprise the majority of prokaryotic biomass in the modern ocean.}, }
@article {pmid38057381, year = {2023}, author = {Oliveira, FR and Lansac-Tôha, FM and Meira, BR and Progênio, M and Velho, LFM}, title = {Influence of Ecological Multiparameters on Facets of β-Diversity of Freshwater Plankton Ciliates.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {10}, pmid = {38057381}, issn = {1432-184X}, mesh = {*Ecosystem ; Plankton ; Phylogeny ; Fresh Water ; Biodiversity ; *Ciliophora ; Water ; }, abstract = {Understanding the relative importance of the factors that drive global patterns of biodiversity is among the major topics of ecological and biogeographic research. In freshwater bodies, spatial, temporal, abiotic, and biotic factors are important structurers of these ecosystems and can trigger distinct responses according to the facet of biodiversity considered. The objective was to evaluate how different facets of β-diversity (taxonomic, functional, and phylogenetic) based on data from the planktonic ciliate community of a Neotropical floodplain, are influenced by temporal, spatial, abiotic, and biotic factors. The research was conducted in the upper Paraná River floodplain between the years 2010 and 2020 in different water bodies. All predictors showed significant importance on the facets of β-diversity, except the abiotic predictors on species composition data, for the taxonomic facet. The functional and phylogenetic facets were mostly influenced by abiotic, biotic, and spatial factors. For temporal predictors, results showed influence on taxonomic (structure and composition data) and functional (structure data) facets. Also, a fraction of shared explanation between the temporal and abiotic components was observed for the distinct facets. Significant declines in β-diversity in continental ecosystems have been evidenced, especially those with drastic implications for ecosystemic services. Therefore, the preservation of a high level of diversity in water bodies, also involving phylogenetic and functional facets, should be a priority in conservation plans and goals, to ensure the maintenance of important ecological processes involving ciliates.}, }
@article {pmid38055943, year = {2023}, author = {Rodríguez, MA and Fernández, LA and Daisley, BA and Reynaldi, FJ and Allen-Vercoe, E and Thompson, GJ}, title = {Probiotics and in-hive fermentation as a source of beneficial microbes to support the gut microbial health of honey bees.}, journal = {Journal of insect science (Online)}, volume = {23}, number = {6}, pages = {}, pmid = {38055943}, issn = {1536-2442}, support = {//Comisi&#xf3;n de Investigaciones Cient&#xed;ficas Buenos Aires/ ; //Global Affairs Canada Emerging Leaders/ ; //Americas Scholarship Program/ ; //Mar&#xed;a Agustina Rodr&#xed;guez/ ; //Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; Anti-Bacterial Agents/immunology/pharmacology/therapeutic use ; *Beekeeping/methods ; *Bees/drug effects/immunology/microbiology ; *Fermentation/immunology ; *Gastrointestinal Microbiome/immunology ; *Probiotics/pharmacology/therapeutic use ; }, abstract = {Managed populations of honey bees (Apis mellifera Linnaeus; Hymenoptera: Apidae) are regularly exposed to infectious diseases. Good hive management including the occasional application of antibiotics can help mitigate infectious outbreaks, but new beekeeping tools and techniques that bolster immunity and help control disease transmission are welcome. In this review, we focus on the applications of beneficial microbes for disease management as well as to support hive health and sustainability within the apicultural industry. We draw attention to the latest advances in probiotic approaches as well as the integration of fermented foods (such as water kefir) with disease-fighting properties that might ultimately be delivered to hives as an alternative or partial antidote to antibiotics. There is substantial evidence from in vitro laboratory studies that suggest beneficial microbes could be an effective method for improving disease resistance in honey bees. However, colony level evidence is lacking and there is urgent need for further validation via controlled field trials experimentally designed to test defined microbial compositions against specific diseases of interest.}, }
@article {pmid38054947, year = {2024}, author = {Knight, T and Sureka, S}, title = {A New Paradigm for Threat Agnostic Biodetection: Biological Intelligence (BIOINT).}, journal = {Health security}, volume = {22}, number = {1}, pages = {31-38}, pmid = {38054947}, issn = {2326-5108}, mesh = {Humans ; *Intelligence ; }, }
@article {pmid38054712, year = {2024}, author = {Schloss, PD}, title = {Waste not, want not: revisiting the analysis that called into question the practice of rarefaction.}, journal = {mSphere}, volume = {9}, number = {1}, pages = {e0035523}, pmid = {38054712}, issn = {2379-5042}, support = {R01 CA215574/CA/NCI NIH HHS/United States ; U01 CA264071/CA/NCI NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Computer Simulation ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; }, abstract = {In 2014, McMurdie and Holmes published the provocatively titled "Waste not, want not: why rarefying microbiome data is inadmissible." The claims of their study have significantly altered how microbiome researchers control for the unavoidable uneven sequencing depths that are inherent in modern 16S rRNA gene sequencing. Confusion over the distinction between the definitions of rarefying and rarefaction continues to cloud the interpretation of their results. More importantly, the authors made a variety of problematic choices when designing and analyzing their simulations. I identified 11 factors that could have compromised the results of the original study. I reproduced the original simulation results and assessed the impact of those factors on the underlying conclusion that rarefying data is inadmissible. Throughout, the design of the original study made choices that caused rarefying and rarefaction to appear to perform worse than they truly did. Most important were the approaches used to assess ecological distances, the removal of samples with low sequencing depth, and not accounting for conditions where sequencing effort is confounded with treatment group. Although the original study criticized rarefying for the arbitrary removal of valid data, repeatedly rarefying data many times (i.e., rarefaction) incorporates all the data. In contrast, it is the removal of rare taxa that would appear to remove valid data. Overall, I show that rarefaction is the most robust approach to control for uneven sequencing effort when considered across a variety of alpha and beta diversity metrics.IMPORTANCEOver the past 10 years, the best method for normalizing the sequencing depth of samples characterized by 16S rRNA gene sequencing has been contentious. An often cited article by McMurdie and Holmes forcefully argued that rarefying the number of sequence counts was "inadmissible" and should not be employed. However, I identified a number of problems with the design of their simulations and analysis that compromised their results. In fact, when I reproduced and expanded upon their analysis, it was clear that rarefaction was actually the most robust approach for controlling for uneven sequencing effort across samples. Rarefaction limits the rate of falsely detecting and rejecting differences between treatment groups. Far from being "inadmissible", rarefaction is a valuable tool for analyzing microbiome sequence data.}, }
@article {pmid38054526, year = {2023}, author = {Altaisaikhan, A and Yoshihara, K and Hata, T and Miyata, N and Asano, Y and Suematsu, T and Kadota, Y and Sudo, N}, title = {Dietary supplementation with 1-kestose induces altered locomotor activity and increased striatal dopamine levels with a change in gut microbiota in male mice.}, journal = {Physiological reports}, volume = {11}, number = {23}, pages = {e15882}, pmid = {38054526}, issn = {2051-817X}, support = {JP20H04106//KAKENHI/ ; JP23K18276//KAKENHI/ ; 2020-192//Smoking Research Foundation (SRF)/ ; }, mesh = {Mice ; Animals ; Male ; *Dopamine ; *Gastrointestinal Microbiome ; Trisaccharides ; Prebiotics ; }, abstract = {1-Kestose (KES), a dietary fiber and prebiotic carbohydrate, benefits various physiological functions. This study aimed to examine whether diets supplemented with KES over three consecutive generations could significantly affect some host physiological aspects, including behavioral phenotypes and gut microbial ecology. Mice that received KES-supplemented diets for three generations demonstrated increased activity compared with those fed diets lacking KES. Furthermore, the KES group showed increased striatal dopamine (DA) and serotonin (5-HT) levels. The observed increase in DA levels within the striatum was positively correlated with locomotor activity in the KES group but not in the control (CON) group. The α-diversities were significantly lower in the KES group compared to the CON group. The three-dimensional principal coordinate analysis revealed a substantial distinction between the KES and CON groups across each generation. At the genus level, most gut microbiota genera exhibited lower abundances in the KES group than in the CON group, except for Bifidobacteria and Akkermansia. Spearman's rank-order analysis indicated significant negative correlations between the striatal DA levels and α-diversity values. These findings suggest that prolonged supplementation with KES may stimulate increased locomotor activity along with elevated striatal DA levels, which are potentially associated with KES-induced alterations in the gut microbiota.}, }
@article {pmid38053549, year = {2023}, author = {Song, W and Li, H and Zhou, Y and Liu, X and Li, Y and Wang, M and Li, DD and Tu, Q}, title = {Discordant patterns between nitrogen-cycling functional traits and taxa in distant coastal sediments reveal important community assembly mechanisms.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1291242}, pmid = {38053549}, issn = {1664-302X}, abstract = {A central question in microbial ecology is how immense microbes are assembled in changing natural environments while executing critical ecosystem functions. Over the past decade, effort has been made to unravel the contribution of stochasticity and determinism to the compositional of microbial communities. However, most studies focus on microbial taxa, ignoring the importance of functional traits. By employing shotgun metagenomic sequencing and state-of-the-art bioinformatics approaches, this study comprehensively investigated the microbially mediated nitrogen (N) cycling processes in two geographically distant coastal locations. Both shotgun and 16S rRNA gene amplicon sequencing demonstrated significantly differed taxonomic compositions between the two sites. The relative abundance of major microbial phyla, such as Pseudomonadota, Thaumarchaeota, and Bacteroidota, significantly differed. In contrast, high homogeneity was observed for N-cycling functional traits. Statistical analyses suggested that N-cycling taxonomic groups were more related to geographic distance, whereas microbial functional traits were more influenced by environmental factors. Multiple community assembly models demonstrated that determinism strongly governed the microbial N-cycling functional traits, whereas their carrying taxonomic groups were highly stochastic. Such discordant patterns between N-cycling functional traits and taxa demonstrated an important mechanism in microbial ecology in which essential ecosystem functions are stably maintained despite geographic distance and stochastic community assembly.}, }
@article {pmid38053159, year = {2023}, author = {Costa, LSAS and de Faria, MR and Chiaramonte, JB and Mendes, LW and Sepo, E and de Hollander, M and Fernandes, JMC and Carrión, VJ and Bettiol, W and Mauchline, TH and Raaijmakers, JM and Mendes, R}, title = {Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {85}, pmid = {38053159}, issn = {2524-6372}, support = {BB/N016246/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X010953/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {BACKGROUND: Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere microbiome. Here, we studied this remarkable phenomenon for Bipolaris sorokiniana in two wheat cultivars differing in resistance to this fungal root pathogen.<br><br>RESULTS: The results showed that repeated exposure of the susceptible wheat cultivar to the pathogen led to a significant reduction in disease severity after five successive growth cycles. Surprisingly, the resistant wheat cultivar, initially included as a control, showed the opposite pattern with an increase in disease severity after repeated pathogen exposure. Amplicon analyses revealed that the bacterial families Chitinophagaceae, Anaerolineaceae and Nitrosomonadaceae were associated with disease suppressiveness in the susceptible wheat cultivar; disease suppressiveness in the resistant wheat cultivar was also associated with Chitinophagaceae and a higher abundance of Comamonadaceae. Metagenome analysis led to the selection of 604 Biosynthetic Gene Clusters (BGCs), out of a total of 2,571 identified by AntiSMASH analysis, that were overrepresented when the soil entered the disease suppressive state. These BGCs are involved in the biosynthesis of terpenes, non-ribosomal peptides, polyketides, aryl polyenes and post-translationally modified peptides.<br><br>CONCLUSION: Combining taxonomic and functional profiling we identified key changes in the rhizosphere microbiome during disease suppression. This illustrates how the host plant relies on the rhizosphere microbiome as the first line of defense to fight soil-borne pathogens. Microbial taxa and functions identified here can be used in novel strategies to control soil-borne fungal pathogens.}, }
@article {pmid38049781, year = {2023}, author = {Thapa, S and Zhou, S and O'Hair, J and Al Nasr, K and Ropelewski, A and Li, H}, title = {Exploring the microbial diversity and characterization of cellulase and hemicellulase genes in goat rumen: a metagenomic approach.}, journal = {BMC biotechnology}, volume = {23}, number = {1}, pages = {51}, pmid = {38049781}, issn = {1472-6750}, support = {2018-38821-27737//USDA-NIFA/ ; 2018-38821-27737//USDA-NIFA/ ; 2018-38821-27737//USDA-NIFA/ ; OCI 1053575//NSF/ ; }, mesh = {Animals ; *Cellulase/metabolism ; Metagenome ; Goats/genetics/metabolism/microbiology ; Rumen/metabolism/microbiology ; Escherichia coli/genetics ; Bacteria ; *Cellulases/genetics ; Cellulose ; }, abstract = {BACKGROUND: Goat rumen microbial communities are perceived as one of the most potential biochemical reservoirs of multi-functional enzymes, which are applicable to enhance wide array of bioprocesses such as the hydrolysis of cellulose and hemi-cellulose into fermentable sugar for biofuel and other value-added biochemical production. Even though, the limited understanding of rumen microbial genetic diversity and the absence of effective screening culture methods have impeded the full utilization of these potential enzymes. In this study, we applied culture independent metagenomics sequencing approach to isolate, and identify microbial communities in goat rumen, meanwhile, clone and functionally characterize novel cellulase and xylanase genes in goat rumen bacterial communities.<br><br>RESULTS: Bacterial DNA samples were extracted from goat rumen fluid. Three genomic libraries were sequenced using Illumina HiSeq 2000 for paired-end 100-bp (PE100) and Illumina HiSeq 2500 for paired-end 125-bp (PE125). A total of 435gb raw reads were generated. Taxonomic analysis using Graphlan revealed that Fibrobacter, Prevotella, and Ruminococcus are the most abundant genera of bacteria in goat rumen. SPAdes assembly and prodigal annotation were performed. The contigs were also annotated using the DOE-JGI pipeline. In total, 117,502 CAZymes, comprising endoglucanases, exoglucanases, beta-glucosidases, xylosidases, and xylanases, were detected in all three samples. Two genes with predicted cellulolytic/xylanolytic activities were cloned and expressed in E. coli BL21(DE3). The endoglucanases and xylanase enzymatic activities of the recombinant proteins were confirmed using substrate plate assay and dinitrosalicylic acid (DNS) analysis. The 3D structures of endoglucanase A and endo-1,4-beta xylanase was predicted using the Swiss Model. Based on the 3D structure analysis, the two enzymes isolated from goat's rumen metagenome are unique with only 56-59% similarities to those homologous proteins in protein data bank (PDB) meanwhile, the structures of the enzymes also displayed greater stability, and higher catalytic activity.<br><br>CONCLUSIONS: In summary, this study provided the database resources of bacterial metagenomes from goat's rumen fluid, including gene sequences with annotated functions and methods for gene isolation and over-expression of cellulolytic enzymes; and a wealth of genes in the metabolic pathways affecting food and nutrition of ruminant animals.}, }
@article {pmid38047964, year = {2023}, author = {Guo, D and Ge, J and Tang, Z and Tian, B and Li, W and Li, C and Xu, L and Luo, J}, title = {Dynamic Gut Microbiota of Apolygus lucorum Across Different Life Stages Reveals Potential Pathogenic Bacteria for Facilitating the Pest Management.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {9}, pmid = {38047964}, issn = {1432-184X}, mesh = {Adult ; Animals ; Humans ; *Gastrointestinal Microbiome ; Firmicutes ; Proteobacteria ; China ; Nymph ; Serratia/genetics ; }, abstract = {Insect's gut microbiota has diverse effects on their fitness, and a comprehensive understanding of gut microbiota functions requires analyzing its diversity. Apolygus lucorum is a highly destructive pest that threatens many economically important crops in China. This study investigated the gut microbiota of A. lucorum across its life cycle using both culture-dependent and culture-independent methods. A total of 87 gut bacterial isolates were identified, belonging to 4 phyla, 27 families, and 45 genera, while Miseq sequencing detected 91 amplicon sequence variants (ASVs) assigned to 5 phyla, 28 families, and 39 genera. Proteobacteria and Firmicutes were the predominant phyla, with Staphylococcus and Serratia as the major genera. There were significant differences in the relative abundance of these genera between the nymph and adult stages. Staphylococcus was significantly more abundant in nymphs than it in adults, while Serratia was significantly more abundant in sexually mature adults than in other developmental stages. Notably, Serratia is a common opportunistic pathogen in many insects. Injecting the gut-dominant isolate Serratia marcescens verified its high pathogenicity. Additionally, immune indicators of the bug at different developmental stages supported the hypothesis that Serratia is a pathogen of A. lucorum. This study provides a foundation for understanding the role of gut bacteria in the life history of A. lucorum and developing new pest control strategies based on microbes.}, }
@article {pmid38047636, year = {2023}, author = {Hill, MS and Gilbert, JA}, title = {Microbiology of the built environment: harnessing human-associated built environment research to inform the study and design of animal nests and enclosures.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {87}, number = {4}, pages = {e0012121}, pmid = {38047636}, issn = {1098-5557}, mesh = {Animals ; Humans ; *Built Environment ; *Environmental Microbiology ; }, abstract = {SUMMARYOver the past decade, hundreds of studies have characterized the microbial communities found in human-associated built environments (BEs). These have focused primarily on how the design and use of our built spaces have shaped human-microbe interactions and how the differential selection of certain taxa or genetic traits has influenced health outcomes. It is now known that the more removed humans are from the natural environment, the greater the risk for the development of autoimmune and allergic diseases, and that indoor spaces can be harsh, selective environments that can increase the emergence of antimicrobial-resistant and virulent phenotypes in surface-bound communities. However, despite the abundance of research that now points to the importance of BEs in determining human-microbe interactions, only a fraction of non-human animal structures have been comparatively explored. It is here, in the context of human-associated BE research, that we consider the microbial ecology of animal-built natural nests and burrows, as well as artificial enclosures, and point to areas of primary interest for future research.}, }
@article {pmid38047236, year = {2023}, author = {Lupatelli, CA and Attard, A and Kuhn, ML and Cohen, C and Thomen, P and Noblin, X and Galiana, E}, title = {Automated high-content image-based characterization of microorganism behavioral diversity and distribution.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {5640-5649}, pmid = {38047236}, issn = {2001-0370}, abstract = {Microorganisms have evolved complex systems to respond to environmental signals. Gradients of particular molecules and elemental ions alter the behavior of microbes and their distribution within their environment. Microdevices coupled with automated image-based methods are now employed to analyze the instantaneous distribution and motion behaviors of microbial species in controlled environments at small temporal scales, mimicking, to some extent, macro conditions. Such technologies have so far been adopted for investigations mainly on individual species. Similar versatile approaches must now be developed for the characterization of multiple and complex interactions between a microbial community and its environment. Here, we provide a comprehensive step-by-step method for the characterization of species-specific behavior in a synthetic mixed microbial suspension in response to an environmental driver. By coupling accessible microfluidic devices with automated image analysis approaches, we evaluated the behavioral response of three morphologically different telluric species (Phytophthora parasitica, Vorticella microstoma, Enterobacter aerogenes) to a potassium gradient driver. Using the TrackMate plug-in algorithm, we performed morphometric and then motion analyses to characterize the response of each microbial species to the driver. Such an approach enabled to confirm the different morphological features of the three species and simultaneously characterize their specific motion in reaction to the driver and their co-interaction dynamics. By increasing the complexity of suspensions, this approach could be integrated in a framework for phenotypic analysis in microbial ecology research, helping to characterize how key drivers influence microbiota assembly at microbiota host-environment interfaces.}, }
@article {pmid38042956, year = {2023}, author = {Alfonso, S and Mente, E and Fiocchi, E and Manfrin, A and Dimitroglou, A and Papaharisis, L and Barkas, D and Toomey, L and Boscarato, M and Losasso, C and Peruzzo, A and Stefani, A and Zupa, W and Spedicato, MT and Nengas, I and Lembo, G and Carbonara, P}, title = {Growth performance, gut microbiota composition, health and welfare of European sea bass (Dicentrarchus labrax) fed an environmentally and economically sustainable low marine protein diet in sea cages.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {21269}, pmid = {38042956}, issn = {2045-2322}, support = {Grant no. 817737//European Union's Horizon 2020 research and innovation programme/ ; }, mesh = {Animals ; *Bass/metabolism ; *Gastrointestinal Microbiome ; Diet ; Fish Oils/metabolism ; Fatty Acids/metabolism ; Diet, Protein-Restricted ; Animal Feed/analysis ; }, abstract = {The large use of fish meal/fish oil in carnivorous fish feeds is the main concern regarding environmental sustainability of aquaculture. Here, we evaluated the effects of an innovative diet, designed to be (1) environmentally sustainable by lowering the marine protein content while being (2) cost effective by using sustainable alternative raw materials with acceptable cost and produced on an industrial scale, on growth performance, gut microbiota composition, health and welfare of European sea bass (Dicentrarchus labrax), a key species of the Mediterranean marine aquaculture, reared in sea cages. Results show that the specific growth rate of fish fed the low marine protein diet was significantly lower than those fed conventional diet (0.67% vs 0.69%). Fatty acid profile of fillets from fish fed a low marine protein diet presented significant lower n-6 and higher n-3 content when compared to conventional ones. Then, a significant increase in the abundance of Vibrio and reduction of Photobacterium were found in the gut of fish fed with the low marine protein diet but effects on sea bass health needs further investigation. Finally, no major health and welfare alterations for fish fed the low marine protein diet were observed, combined with a potential slight benefit related to humoral immunity. Overall, these results suggest that despite the low marine protein diet moderately affects growth performance, it nevertheless may enhance environmental and economic sustainability of the sea bass aquaculture.}, }
@article {pmid38040657, year = {2023}, author = {Baril, X and Constant, P}, title = {Carbon amendments in soil microcosms induce uneven response on H2 oxidation activity and microbial community composition.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {12}, pages = {}, pmid = {38040657}, issn = {1574-6941}, support = {RGPIN-2018-05262//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Carbon/metabolism ; *Hydrogenase/genetics/metabolism ; Oxidation-Reduction ; Soil ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Hydrogen/metabolism ; Bacteria ; *Microbiota ; Cellulose/metabolism ; Sucrose/metabolism ; }, abstract = {High-affinity H2-oxidizing bacteria (HA-HOB) thriving in soil are responsible for the most important sink of atmospheric H2. Their activity increases with soil organic carbon content, but the incidence of different carbohydrate fractions on the process has received little attention. Here we tested the hypothesis that carbon amendments impact HA-HOB activity and diversity differentially depending on their recalcitrance and their concentration. Carbon sources (sucrose, starch, cellulose) and application doses (0, 0.1, 1, 3, 5% Ceq soildw-1) were manipulated in soil microcosms. Only 0.1% Ceq soildw-1 cellulose treatment stimulated the HA-HOB activity. Sucrose amendments induced the most significant changes, with an abatement of 50% activity at 1% Ceq soildw-1. This was accompanied with a loss of bacterial and fungal alpha diversity and a reduction of high-affinity group 1 h/5 [NiFe]-hydrogenase gene (hhyL) abundance. A quantitative classification framework was elaborated to assign carbon preference traits to 16S rRNA gene, ITS and hhyL genotypes. The response was uneven at the taxonomic level, making carbon preference a difficult trait to predict. Overall, the results suggest that HA-HOB activity is more susceptible to be stimulated by low doses of recalcitrant carbon, while labile carbon-rich environment is an unfavorable niche for HA-HOB, inducing catabolic repression of hydrogenase.}, }
@article {pmid38038797, year = {2024}, author = {Mustaq, S and Moin, A and Pandit, B and Tiwary, BK and Alam, M}, title = {Phyllobacteriaceae: a family of ecologically and metabolically diverse bacteria with the potential for different applications.}, journal = {Folia microbiologica}, volume = {69}, number = {1}, pages = {17-32}, pmid = {38038797}, issn = {1874-9356}, mesh = {Humans ; *Phyllobacteriaceae/genetics ; Phylogeny ; Bacteria/genetics ; *Fabaceae/microbiology ; Nitrogen/metabolism ; DNA, Bacterial/metabolism ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {The family Phyllobacteriaceae is a heterogeneous assemblage of more than 146 species of bacteria assigned to its existing 18 genera. Phylogenetic analyses have shown great phylogenetic diversity and also suggested about incorrect classification of several species that need to be reassessed for their proper phylogenetic classification. However, almost 50% of the family members belong to the genus Mesorhizobium only, of which the majority are symbiotic nitrogen fixers associated with different legumes. Other major genera are Phyllobacterium, Nitratireductor, Aquamicrobium, and Aminobacter. Nitrogen-fixing, legume nodulating members are present in Aminobacter and Phyllobacterium as well. Aquamicrobium spp. can degrade environmental pollutants, like 2,4-dichlorophenol, 4-chloro-2-methylphenol, and 4-chlorophenol. Chelativorans, Pseudaminobacter, Aquibium, and Oricola are the other genera that contain multiple species having diverse metabolic capacities, the rest being single-membered genera isolated from varied environments. In addition, heavy metal and antibiotic resistance, chemolithoautotrophy, poly-β-hydroxybutyrate storage, cellulase production, etc., are the other notable characteristics of some of the family members. In this report, we have comprehensively reviewed each of the species of the family Phyllobacteriaceae in their eco-physiological aspects and found that the family is rich with ecologically and metabolically highly diverse bacteria having great potential for human welfare and environmental clean-up.}, }
@article {pmid38036921, year = {2023}, author = {Gallardo-Becerra, L and Cervantes-Echeverría, M and Cornejo-Granados, F and Vazquez-Morado, LE and Ochoa-Leyva, A}, title = {Perspectives in Searching Antimicrobial Peptides (AMPs) Produced by the Microbiota.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {8}, pmid = {38036921}, issn = {1432-184X}, support = {Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; PAPIIT UNAM (IN219723)//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; PAPIIT UNAM (IN219723)//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; PAPIIT UNAM (IN219723)//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; PAPIIT UNAM (IN219723)//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; PAPIIT UNAM (IN219723)//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, mesh = {Humans ; *Antimicrobial Cationic Peptides/genetics/pharmacology ; Antimicrobial Peptides ; Bacteria/genetics ; *Microbiota/genetics ; Anti-Bacterial Agents ; }, abstract = {Changes in the structure and function of the microbiota are associated with various human diseases. These microbial changes can be mediated by antimicrobial peptides (AMPs), small peptides produced by the host and their microbiota, which play a crucial role in host-bacteria co-evolution. Thus, by studying AMPs produced by the microbiota (microbial AMPs), we can better understand the interactions between host and bacteria in microbiome homeostasis. Additionally, microbial AMPs are a new source of compounds against pathogenic and multi-resistant bacteria. Further, the growing accessibility to metagenomic and metatranscriptomic datasets presents an opportunity to discover new microbial AMPs. This review examines the structural properties of microbiota-derived AMPs, their molecular action mechanisms, genomic organization, and strategies for their identification in any microbiome data as well as experimental testing. Overall, we provided a comprehensive overview of this important topic from the microbial perspective.}, }
@article {pmid38036897, year = {2023}, author = {Hernández-Pelegrín, L and Ros, VID and Herrero, S and Crava, CM}, title = {Non-retroviral Endogenous Viral Elements in Tephritid Fruit Flies Reveal Former Viral Infections Not Related to Known Circulating Viruses.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {7}, pmid = {38036897}, issn = {1432-184X}, mesh = {Animals ; RNA, Small Interfering/genetics/metabolism ; *Viruses/genetics ; *RNA Viruses/genetics ; *Virus Diseases ; *Diptera ; }, abstract = {A wide variety of insect-specific non-retroviral RNA viruses specifically infect insects. During viral infection, fragments of viral sequences can integrate into the host genomes creating non-retroviral endogenous viral elements (nrEVEs). Although the exact function of nrEVEs is so far unknown, some studies suggest that nrEVEs may interfere with virus replication by producing PIWI-interacting RNAs (piRNAs) that recognize and degrade viral RNAs through sequence complementarity. In this article, we identified the nrEVEs repertoire of ten species within the dipteran family Tephritidae (true fruit flies), which are considered a major threat to agriculture worldwide. Our results suggest that each of these species contains nrEVEs, although in limited numbers, and that nrEVE integration may have occurred both before and after speciation. Furthermore, the majority of nrEVEs originated from viruses with negative single-stranded RNA genomes and represent structural viral functions. Notably, these nrEVEs exhibit low similarity to currently known circulating viruses. To explore the potential role of nrEVEs, we investigated their transcription pattern and the production of piRNAs in different tissues of Ceratitis capitata. We successfully identified piRNAs that are complementary to the sequence of one nrEVE in C. capitata, thereby highlighting a potential link between nrEVEs and the piRNA pathway. Overall, our results provide valuable insights into the comparative landscape of nrEVEs in true fruit flies, contributing to the understanding of the intimate relation between fruit flies and their past and present viral pathogens.}, }
@article {pmid38033596, year = {2023}, author = {Zhang, M and Kong, Z and Fu, H and Shu, X and Xue, Q and Lai, H and Guo, Q}, title = {Rhizosphere microbial ecological characteristics of strawberry root rot.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1286740}, pmid = {38033596}, issn = {1664-302X}, abstract = {INTRODUCTION: Strawberry (Fragaria × ananassa Duch.) holds a preeminent position among small fruits globally due to its delectable fruits and significant economic value. However, strawberry cultivation is hampered by various plant diseases, hindering the sustainable development of the strawberry industry. The occurrence of plant diseases is closely linked to imbalance in rhizosphere microbial community structure.<br><br>METHODS: In the present study, a systematic analysis of the differences and correlations among non-culturable microorganisms, cultivable microbial communities, and soil nutrients in rhizosphere soil, root surface soil, and non-rhizosphere soil of healthy and diseased strawberry plants affected by root rot was conducted. The goal was to explore the relationship between strawberry root rot occurrence and rhizosphere microbial community structure.<br><br>RESULTS: According to the results, strawberry root rot altered microbial community diversity, influenced fungal community composition in strawberry roots, reduced microbial interaction network stability, and enriched more endophytic-phytopathogenic bacteria and saprophytic bacteria. In addition, the number of bacteria isolated from the root surface soil of diseased plants was significantly higher than that of healthy plants.<br><br>DISCUSSION: In summary, the diseased strawberry plants changed microbial community diversity, fungal species composition, and enriched functional microorganisms significantly, in addition to reshaping the microbial co-occurrence network. The results provide a theoretical basis for revealing the microecological mechanism of strawberry root rot and the ecological prevention and control of strawberry root rot from a microbial ecology perspective.}, }
@article {pmid38033562, year = {2023}, author = {Farmer, M and Rajasabhai, R and Tarpeh, W and Tyo, K and Wells, G}, title = {Meta-omic profiling reveals ubiquity of genes encoding for the nitrogen-rich biopolymer cyanophycin in activated sludge microbiomes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1287491}, pmid = {38033562}, issn = {1664-302X}, abstract = {Recovering nitrogen (N) from municipal wastewater is a promising approach to prevent nutrient pollution, reduce energy use, and transition toward a circular N bioeconomy, but remains a technologically challenging endeavor. Existing N recovery techniques are optimized for high-strength, low-volume wastewater. Therefore, developing methods to concentrate dilute N from mainstream wastewater will bridge the gap between existing technologies and practical implementation. The N-rich biopolymer cyanophycin is a promising candidate for N bioconcentration due to its pH-tunable solubility characteristics and potential for high levels of accumulation. However, the cyanophycin synthesis pathway is poorly explored in engineered microbiomes. In this study, we analyzed over 3,700 publicly available metagenome assembled genomes (MAGs) and found that the cyanophycin synthesis gene cphA was ubiquitous across common activated sludge bacteria. We found that cphA was present in common phosphorus accumulating organisms (PAO) Ca. 'Accumulibacter' and Tetrasphaera, suggesting potential for simultaneous N and P bioconcentration in the same organisms. Using metatranscriptomic data, we confirmed the expression of cphA in lab-scale bioreactors enriched with PAO. Our findings suggest that cyanophycin synthesis is a ubiquitous metabolic activity in activated sludge microbiomes. The possibility of combined N and P bioconcentration could lower barriers to entry for N recovery, since P concentration by PAO is already a widespread biotechnology in municipal wastewater treatment. We anticipate this work to be a starting point for future evaluations of combined N and P bioaccumulation, with the ultimate goal of advancing widespread adoption of N recovery from municipal wastewater.}, }
@article {pmid38030916, year = {2023}, author = {Mlewski, EC and Saona, LA and Boidi, FJ and Chiappero, MF and Vaieretti, MV and Soria, M and Farías, ME and Izquierdo, AE}, title = {Exploring Soil Bacterial Diversity in Relation to Edaphic Physicochemical Properties of High-altitude Wetlands from Argentine Puna.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {6}, pmid = {38030916}, issn = {1432-184X}, support = {PICT 2018-4129//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica FONCYT/ ; PICT2018-04228//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica FONCYT/ ; PICT2018-04228//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica FONCYT/ ; PICT2018-04228//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica FONCYT/ ; }, mesh = {Humans ; *Ecosystem ; Wetlands ; Soil/chemistry ; Altitude ; Bacteria/genetics ; *Microbiota ; Soil Microbiology ; }, abstract = {High Andean wetlands, particularly those known as vegas or bofedales, are essential conservation ecosystems due to their significant contribution to ecosystem services. The soil microbial communities in these ecosystems play a crucial role in fundamental processes such as decomposition and nutrient cycling, sustaining life in the region. However, at present, these microbial communities are poorly understood. In order to contribute to this knowledge, we aimed to characterize and compare the microbial communities from soils of seven Argentine Puna vegas and to analyze their association with soil physicochemical characteristics. Proteobacteria (Gamma and Alphaproteobacteria) was the dominant phylum across all vegas, followed in abundance by Actinobacteriota, Desulfobacterota, and Chloroflexi. Furthermore, the abundance of specific bacterial families and genera varied significantly between the vegas; some of them can be associated with plant growth-promoting bacteria such as Rhodomicrobium in La Quebradita and Quebrada del Diablo, Bacillus in Antofalla and Las Quinuas. Laguna Negra showed no shared ASVs with abundance in genera such as Sphingomonas and Pseudonocardia. The studied vegas also differed in their soil physicochemical properties; however, associations between the composition of microbial communities with the edaphic parameters measured were not found. These results suggest that other environmental factors (e.g., geographic, climatic, and plant communities' characteristics) could determine soil microbial diversity patterns. Further investigations are needed to be focused on understanding the composition and function of microorganisms in the soil associated with specific vegetation types in these high-altitude wetlands, which will provide valuable insights into the ecological dynamics of these ecosystems for conservation strategies.}, }
@article {pmid38030815, year = {2023}, author = {Zhang, N and Zhu, W and Zhang, S and Liu, T and Gong, L and Wang, Z and Zhang, W and Cui, Y and Wu, Q and Li, J and Yu, H and El-Omar, EM and Hao, J and Lu, W}, title = {A Novel Bifidobacterium/Klebsiella Ratio in Characterization Analysis of the Gut and Bile Microbiota of CCA Patients.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {5}, pmid = {38030815}, issn = {1432-184X}, mesh = {Humans ; Bifidobacterium/genetics ; Klebsiella/genetics ; RNA, Ribosomal, 16S/genetics ; Bile ; *Gastrointestinal Microbiome ; *Microbiota ; Firmicutes/genetics ; Bacteroidetes/genetics ; Feces/microbiology ; }, abstract = {Cholangiocarcinoma (CCA) is a serious health problem worldwide. The gut and bile microbiota have not been clearly characterized in patients with CCA, and better noninvasive diagnostic approaches for CCA need to be established. The aim of this study was to investigate the characteristics of the gut and bile microbiota in CCA patients. Forty-two CCA patients and 16 healthy normal controls (HNCs) were enrolled. DNA was extracted from fecal and bile samples and subjected to 16S rRNA gene analysis. We found that there were significant differences in the species diversity, structure, and composition of the microbial communities between the CCA group and the HNC grouAt the phylum level, compared with that in the HNC group, the relative abundance of Firmicutes and Actinobacteriota was significantly decreased in the CCA group, whereas Proteobacteria and Bacteroidota were significantly enriched. The Firmicutes/Bacteroidota (F/B) ratio significantly decreased in the CCA group compared to the HNC grouThe relative abundance of Klebsiella in the CCA group was significantly higher than that in the HNC group, while the relative abundance of Bifidobacterium was significantly decreased. The Bifidobacterium/Klebsiella (B/K) ratio was established as a novel biomarker and was found to be significantly decreased in the CCA group compared with the HNC grouOur findings provide evidence supporting the use of Klebsiella and Bifidobacterium as noninvasive intestinal microbiomarkers for improving the diagnosis of CCA.}, }
@article {pmid38029116, year = {2023}, author = {Ouamba, AJK and Gagnon, M and Varin, T and Chouinard, PY and LaPointe, G and Roy, D}, title = {Phylogenetic variation in raw cow milk microbiota and the impact of forage combinations and use of silage inoculants.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1175663}, pmid = {38029116}, issn = {1664-302X}, abstract = {INTRODUCTION: The microbiota of bulk tank raw milk is known to be closely related to that of microbial niches of the on-farm environment. Preserved forage types are partof this ecosystem and previous studies have shown variations in their microbial ecology. However, little is known of the microbiota of forage ration combinations and the transfer rates of associated species to milk.<br><br>METHODS: We identified raw milk bacteria that may originate from forage rations encompassing either hay (H) or grass/legume silage uninoculated (GL) as the only forage type, or a combination of GL and corn silage uninoculated (GLC), or grass/legume and corn silage both inoculated (GLICI). Forage and milk samples collected in the fall and spring from 24 dairy farms were analyzed using 16S rRNA gene high-throughput sequencing following a treatment with propidium monoazide to account for viable cells.<br><br>RESULTS AND DISCUSSION: Three community types separating H, GL, and GLICI forage were identified. While the H community was co-dominated by Enterobacteriaceae, Microbacteriaceae, Beijerinckiaceae, and Sphingomonadaceae, the GL and GLICI communities showed high proportions of Leuconostocaceae and Acetobacteraceae, respectively. Most of the GLC and GLICI rations were similar, suggesting that in the mixed forage rations involving grass/legume and corn silage, the addition of inoculant in one or both types of feed does not considerably change the microbiota. Raw milk samples were not grouped in the same way, as the GLC milk was phylogenetically different from that of GLICI across sampling periods. Raw milk communities, including the GLICI group for which cows were fed inoculated forage, were differentiated by Enterobacteriaceae and other Proteobacteria, instead of by lactic acid bacteria. Of the 113 amplicon sequence variants (ASVs) shared between forage rations and corresponding raw milk, bacterial transfer rates were estimated at 18 to 31%. Silage-based forage rations, particularly those including corn, share more ASVs with raw milk produced on corresponding farms compared to that observed in the milk from cows fed hay. These results show the relevance of cow forage rations as sources of bacteria that contaminate milk and serve to advance our knowledge of on-farm raw milk contamination.}, }
@article {pmid38029109, year = {2023}, author = {Crosby, KC and Rojas, M and Sharma, P and Johnson, MA and Mazloom, R and Kvitko, BH and Smits, THM and Venter, SN and Coutinho, TA and Heath, LS and Palmer, M and Vinatzer, BA}, title = {Genomic delineation and description of species and within-species lineages in the genus Pantoea.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1254999}, pmid = {38029109}, issn = {1664-302X}, support = {R25 GM072767/GM/NIGMS NIH HHS/United States ; }, abstract = {As the name of the genus Pantoea ("of all sorts and sources") suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus Pantoea. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.}, }
@article {pmid38029094, year = {2023}, author = {Semenov, M and Li, H and Luo, Y and Deng, Y and Kuzyakov, Y}, title = {Editorial: Microbial regulation of soil carbon cycling in terrestrial ecosystems.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1295624}, pmid = {38029094}, issn = {1664-302X}, }
@article {pmid38029079, year = {2023}, author = {Koepper, S and Clark, KF and McClure, JT and Revie, CW and Stryhn, H and Thakur, KK}, title = {Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1245818}, pmid = {38029079}, issn = {1664-302X}, abstract = {The shell microbial community of lobsters-a key factor in the development of epizootic shell disease (ESD)-is still insufficiently researched in Atlantic Canada and many knowledge gaps remain. This study aimed to establish a baseline description and analysis of the shell microbiome of apparently healthy lobsters from four locations in the region. More than 180 lobster shell swab samples were collected from New Brunswick, Nova Scotia and Prince Edward Island (PEI). PacBio long-read 16S rDNA sequencing and bioinformatic analyses in QIIME2 identified the shell-associated bacteria. The shell microbiome of healthy lobsters consisted mainly of the bacterial classes Gammaproteobacteria, Saprospiria, Verrucomicrobiae, Alphaproteobacteria, Flavobacteriia, Acidimicrobiia and Planctomycetia. The microbial composition differed regionally and seasonally, with some classes showing decreased or increased relative abundances in the PEI samples as well as in the winter and spring samples in Nova Scotia. The core shell microbiome included potentially pathogenic as well as beneficial bacterial taxa, of which some were present only in certain regions. Bacterial taxa that have previously been associated with ESD were present on healthy lobsters in Atlantic Canada, but their frequency differed by location, sampling time, and moult stage. This study indicated that geographical and seasonal factors influenced the shell microbiome of apparently healthy lobsters more than host factors such as sex, size, and moult stage. Our results provide valuable reference microbial data from lobsters in a disease-free state.}, }
@article {pmid38026034, year = {2023}, author = {Gjini, E and Madec, S}, title = {Towards a mathematical understanding of invasion resistance in multispecies communities.}, journal = {Royal Society open science}, volume = {10}, number = {11}, pages = {231034}, pmid = {38026034}, issn = {2054-5703}, abstract = {Multispecies community composition and dynamics are key to health and disease across biological systems, a prominent example being microbial ecosystems. Explaining the forces that govern diversity and resilience in the microbial consortia making up our body's defences remains a challenge. In this, theoretical models are crucial, to bridge the gap between species dynamics and underlying mechanisms and to develop analytic insight. Here we propose a replicator equation framework to model multispecies dynamics where an explicit notion of invasion resistance of a system emerges and can be studied explicitly. For illustration, we derive the conceptual link between such replicator equation and N microbial species' growth and interaction traits, stemming from micro-scale environmental modification. Within this replicator framework, mean invasion fitness arises, evolves dynamically, and may undergo critical predictable shifts with global environmental changes. This mathematical approach clarifies the key role of this resident system trait for invader success, and highlights interaction principles among N species that optimize their collective resistance to invasion. We propose this model based on the replicator equation as a powerful new avenue to study, test and validate mechanisms of invasion resistance and colonization in multispecies microbial ecosystems and beyond.}, }
@article {pmid38026022, year = {2023}, author = {Tarnowski, MJ and Varliero, G and Scown, J and Phelps, E and Gorochowski, TE}, title = {Soil as a transdisciplinary research catalyst: from bioprospecting to biorespecting.}, journal = {Royal Society open science}, volume = {10}, number = {11}, pages = {230963}, pmid = {38026022}, issn = {2054-5703}, abstract = {The vast microbial biodiversity of soils is beginning to be observed and understood by applying modern DNA sequencing techniques. However, ensuring this potentially valuable information is used in a fair and equitable way remains a challenge. Here, we present a public engagement project that explores this topic through collaborative research of soil microbiomes at six urban locations using nanopore-based DNA sequencing. The project brought together researchers from the disciplines of synthetic biology, environmental humanities and microbial ecology, as well as school students aged 14-16 years old, to gain a broader understanding of views on the use of data from the environment. Discussions led to the transformation of 'bioprospecting', a metaphor with extractive connotations which is often used to frame environmental DNA sequencing studies, towards a more collaborative approach-'biorespecting'. This shift in terminology acknowledges that genetic information contained in soil arises as a result of entire ecosystems, including the people involved in its creation. Therefore, any use of sequence information should be accountable to the ecosystems from which it arose. As knowledge can arise from ecosystems and communities, science and technology should acknowledge this link and reciprocate with care and benefit-sharing to help improve the wellbeing of future generations.}, }
@article {pmid38023904, year = {2023}, author = {Fu, X and Huang, Y and Fu, Q and Qiu, Y and Zhao, J and Li, J and Wu, X and Yang, Y and Liu, H and Yang, X and Chen, H}, title = {Critical transition of soil microbial diversity and composition triggered by plant rhizosphere effects.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1252821}, pmid = {38023904}, issn = {1664-462X}, abstract = {Over the years, microbial community composition in the rhizosphere has been extensively studied as the most fascinating topic in microbial ecology. In general, plants affect soil microbiota through rhizodeposits and changes in abiotic conditions. However, a consensus on the response of microbiota traits to the rhizosphere and bulk soils in various ecosystems worldwide regarding community diversity and structure has not been reached yet. Here, we conducted a meta-analysis of 101 studies to investigate the microbial community changes between the rhizosphere and bulk soils across various plant species (maize, rice, vegetables, other crops, herbaceous, and woody plants). Our results showed that across all plant species, plant rhizosphere effects tended to reduce the rhizosphere soil pH, especially in neutral or slightly alkaline soils. Beta-diversity of bacterial community was significantly separated between into rhizosphere and bulk soils. Moreover, r-strategists and copiotrophs (e.g. Proteobacteria and Bacteroidetes) enriched by 24-27% in the rhizosphere across all plant species, while K-strategists and oligotrophic (e.g. Acidobacteria, Gemmatimonadete, Nitrospirae, and Planctomycetes) decreased by 15-42% in the rhizosphere. Actinobacteria, Firmicutes, and Chloroflexi are also depleted by in the plant rhizosphere compared with the bulk soil by 7-14%. The Actinobacteria exhibited consistently negative effect sizes across all plant species, except for maize and vegetables. In Firmicutes, both herbaceous and woody plants showed negative responses to rhizosphere effects, but those in maize and rice were contrarily enriched in the rhizosphere. With regards to Chloroflexi, apart from herbaceous plants showing a positive effect size, the plant rhizosphere effects were consistently negative across all other plant types. Verrucomicrobia exhibited a significantly positive effect size in maize, whereas herbaceous plants displayed a negative effect size in the rhizosphere. Overall, our meta-analysis exhibited significant changes in microbial community structure and diversity responding to the plant rhizosphere effects depending on plant species, further suggesting the importance of plant rhizosphere to environmental changes influencing plants and subsequently their controls over the rhizosphere microbiota related to nutrient cycling and soil health.}, }
@article {pmid38016221, year = {2024}, author = {Zhang, X and Wang, Y and Jiao, P and Zhang, M and Deng, Y and Jiang, C and Liu, XW and Lou, L and Li, Y and Zhang, XX and Ma, L}, title = {Microbiome-functionality in anaerobic digesters: A critical review.}, journal = {Water research}, volume = {249}, number = {}, pages = {120891}, doi = {10.1016/j.watres.2023.120891}, pmid = {38016221}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Bioreactors/microbiology ; *Microbiota ; Methane/metabolism ; Metabolic Networks and Pathways ; }, abstract = {Microbially driven anaerobic digestion (AD) processes are of immense interest due to their role in the biovalorization of biowastes into renewable energy resources. The function-versatile microbiome, interspecies syntrophic interactions, and trophic-level metabolic pathways are important microbial components of AD. However, the lack of a comprehensive understanding of the process hampers efforts to improve AD efficiency. This study presents a holistic review of research on the microbial and metabolic "black box" of AD processes. Recent research on microbiology, functional traits, and metabolic pathways in AD, as well as the responses of functional microbiota and metabolic capabilities to optimization strategies are reviewed. The diverse ecophysiological traits and cooperation/competition interactions of the functional guilds and the biomanipulation of microbial ecology to generate valuable products other than methane during AD are outlined. The results show that AD communities prioritize cooperation to improve functional redundancy, and the dominance of specific microbes can be explained by thermodynamics, resource allocation models, and metabolic division of labor during cross-feeding. In addition, the multi-omics approaches used to decipher the ecological principles of AD consortia are summarized in detail. Lastly, future microbial research and engineering applications of AD are proposed. This review presents an in-depth understanding of microbiome-functionality mechanisms of AD and provides critical guidance for the directional and efficient bioconversion of biowastes into methane and other valuable products.}, }
@article {pmid38015286, year = {2023}, author = {Liu, D and Wei, L}, title = {Epigenetic Regulation in Response to CO2 Fluctuation in Marine Microalga Nannochloropsis oceanica.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {4}, pmid = {38015286}, issn = {1432-184X}, mesh = {*Carbon Dioxide ; Epigenesis, Genetic ; Histones/genetics ; *Microalgae/genetics ; Adaptation, Physiological ; Carbon ; }, abstract = {Microalgae often undergo different CO2 experiment in their habitat. To adapt to low CO2, carbon concentrating mechanism (CCM) could be launched in majority of microalgae and CCM are regulated at RNA level are well known. However, epigenetic modifications and their potential regulation of the transcription of masked genes at the genome level in response to CO2 fluctuation remain unclear. Here epigenetic regulation in response to CO2 fluctuation and epigenome-association with phenotypic plasticity of CCM are firstly uncovered in marine microalga Nannochloropsis oceanica IMET1. The result showed that lysine butyrylation (Kbu) and histone H3K9m2 modifications were present in N. oceanica IMET1. Moreover, Kbu modification positively regulated gene expression. In response to CO2 fluctuation, there were 5,438 and 1,106 genes regulated by Kbu and H3K9m2 in Nannochloropsis, respectively. Gained or lost histone methylations were closely associated with activating or repressing gene expressions. Differential modifications were mainly enriched in carbon fixation, photorespiration, photosynthesis, and lipid metabolism etc. Massive genome-wide epigenetic reprogramming was observed after N. oceanica cells shifted from high CO2 to low CO2. Particularly, we firstly noted that the transcription of the key low CO2 responsive carbonic anhydrase (CA5), a key component involved in CCM stress signaling, was potentially regulated by bivalent Kbu-H3K9m2 modifications in microalgae. This study provides novel insights into the relationship between gene transcription and epigenetic modification in Nannochloropsis, which will lay foundation on genetic improvement of CCM at epigenetic level.}, }
@article {pmid38008827, year = {2023}, author = {Zhu, YL and Huang, YJ and Nuerhamanti, N and Bai, XY and Wang, HN and Zhu, XY and Zhang, W}, title = {The Composition and Diversity of the Rhizosphere Bacterial Community of Ammodendron bifolium Growing in the Takeermohuer Desert Are Different from Those in the Nonrhizosphere.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {2}, pmid = {38008827}, issn = {1432-184X}, support = {32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; }, mesh = {*Ecosystem ; Rhizosphere ; Bacteria/genetics ; Proteobacteria ; Acidobacteria ; *Fabaceae ; Soil/chemistry ; Plants ; Nitrogen ; Soil Microbiology ; }, abstract = {Soil microorganisms play important roles in vegetation establishment and soil biogeochemical cycling. Ammodendron bifolium is a dominant sand-fixing (i.e., stabilizing sand dunes) and endangered plant in the Takeermohuer Desert, and the bacterial community associated with this plant rhizosphere is still unclear. In this study, we investigated the composition and diversity of the bacterial community from the A. bifolium rhizosphere and bulk soil at different soil depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) using culture and high-throughput sequencing methods. We preliminarily analyzed the edaphic factors influencing the structure of bacterial communities. The results showed that the high-salinity Takeermohuer Desert has an oligotrophic environment, while the A. bifolium rhizosphere exhibited a relatively nutrient-rich environment due to higher contents of soil organic matter (SOM) and soil alkaline nitrogen (SAN) than bulk soil. The dominant bacterial groups in the desert were Actinobacteria (39.8%), Proteobacteria (17.4%), Acidobacteria (10.2%), Bacteroidetes (6.3%), Firmicutes (6.3%), Chloroflexi (5.6%), and Planctomycetes (5.0%) at the phylum level. However, the relative abundances of Proteobacteria (20.2%) and Planctomycetes (6.1%) were higher in the rhizosphere, and those of Firmicutes (9.8%) and Chloroflexi (6.9%) were relatively higher in barren bulk soil. A large number of Actinobacteria were detected in all soil samples, of which the most abundant genera were Streptomyces (5.4%) and Actinomadura (8.2%) in the bulk soil and rhizosphere, respectively. The Chao1 and PD_whole_tree indices in the rhizosphere soil were significantly higher than those in the bulk soil at the same soil depth and tended to decrease with increasing soil depth. Co-occurrence network analyses showed that the keystone species in the Takeermohuer Desert were the phyla Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi. Furthermore, the major edaphic factors affecting the rhizosphere bacterial community were electrical conductivity (EC), SOM, soil total nitrogen (STN), SAN, and soil available potassium (SAK), while the major edaphic factors affecting the bacterial community in bulk soil were distance and ratio of carbon to nitrogen (C/N). We concluded that the A. bifolium rhizosphere bacterial community is different from that of the nonrhizosphere in composition, structure, diversity, and driving factors, which may improve our understanding of the relationship between plant and bacterial communities and lay a theoretical foundation for A. bifolium species conservation in desert ecosystems.}, }
@article {pmid38008821, year = {2023}, author = {Fuster, M and Ruiz, T and Lamarque, A and Coulon, M and Legrand, B and Sabart, M and Latour, D and Mallet, C}, title = {Cyanosphere Dynamic During Dolichospermum Bloom: Potential Roles in Cyanobacterial Proliferation.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {3}, pmid = {38008821}, issn = {1432-184X}, mesh = {*Cyanobacteria/genetics ; *Microcystis ; *Microbiota ; Cell Proliferation ; Lakes ; Eutrophication ; }, abstract = {Under the effect of global change, management of cyanobacterial proliferation becomes increasingly pressing. Given the importance of interactions within microbial communities in aquatic ecosystems, a handful of studies explored the potential relations between cyanobacteria and their associated bacterial community (i.e., cyanosphere). Yet, most of them specifically focused on the ubiquitous cyanobacteria Microcystis, overlooking other genera. Here, based on 16s rDNA metabarcoding analysis, we confirmed the presence of cyanosphere representing up to 30% of the total bacterial community diversity, during bloom episode of another preponderant cyanobacterial genus, Dolichospermum. Moreover, we highlighted a temporal dynamic of this cyanosphere. A sPLS-DA model permits to discriminate three important dates and 220 OTUs. With their affiliations, we were able to show how these variations potentially imply a turnover in ecological functions depending on bloom phases. Although more studies are necessary to quantify the impacts of these variations, we argue that cyanosphere can have an important, yet underestimated, role in the modulation of cyanobacterial blooms.}, }
@article {pmid38006200, year = {2023}, author = {Houldcroft, CJ and Underdown, S}, title = {Infectious disease in the Pleistocene: Old friends or old foes?.}, journal = {American journal of biological anthropology}, volume = {182}, number = {4}, pages = {513-531}, doi = {10.1002/ajpa.24737}, pmid = {38006200}, issn = {2692-7691}, support = {//Oxford Brookes University/ ; }, mesh = {Animals ; Humans ; Friends ; *Hominidae ; *Communicable Diseases/epidemiology ; Genome ; DNA ; }, abstract = {The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.}, }
@article {pmid38004650, year = {2023}, author = {Aponte, H and Sulbaran-Bracho, Y and Mondaca, P and Vidal, C and Pérez, R and Meier, S and Cornejo, P and Rojas, C}, title = {Biochemical, Catabolic, and PGP Activity of Microbial Communities and Bacterial Strains from the Root Zone of Baccharis linearis in a Mediterranean Mine Tailing.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004650}, issn = {2076-2607}, support = {3210752//FONDECYT/ ; InES19-FRO19101//MINEDUC/ ; }, abstract = {The management of mine tailings (MT) is commonly workload heavy, intrusive, and expensive. Phytostabilization offers a promising approach for MT management; however, it poses challenges due to the unfavorable physicochemical properties of these wastes. Nevertheless, native microorganisms capable of supporting plant growth and development could enhance the efficacy of phytostabilization. This study assesses the biological activity of microbial communities from the root zone of Baccharis linearis, which is naturally present in MT, in order to evaluate their biotechnological potential for phytostabilization. The root zone and bulk samples were collected from B. linearis plants located within a MT in the Mediterranean zone of Chile. Enzyme activities related to the cycling of C, N, and P were assessed. The community-level physiological profile was evaluated using the MicroResp[TM] system. Bacterial plant growth-promoting (PGP) traits and colony forming units (CFU) were evaluated through qualitative and microbiological methods, respectively. CFU, enzyme activities, and CLPP were higher in the root zone compared with the bulk samples. Five bacterial strains from the root zone exhibited PGP traits such as P solubilization and N acquisition, among others. The presence of microbial communities in the root zone of B. linearis with PGP traits suggests their potential to enhance the ecological management of MT through phytostabilization programs.}, }
@article {pmid38001901, year = {2023}, author = {Macedo-Viñas, M and Lucas, A}, title = {Evolution of Microbial Flora Colonizing Burn Wounds during Hospitalization in Uruguay.}, journal = {Biomedicines}, volume = {11}, number = {11}, pages = {}, pmid = {38001901}, issn = {2227-9059}, abstract = {(1) Background: Infections are a main cause of morbidity and mortality among burn patients. The spectrum of microorganisms depends on the epidemiological context and treatment practices. We aimed to describe the evolution of microbial flora colonizing burn wounds among patients hospitalized during 15 or more days at the National Burn Center in 2015. (2) Methods: Demographic data, length of stay, total body surface area burn, and status at discharge were collected from electronic records and culture results from the laboratory database. (3) Results: Among 98 included patients, 87 were colonized. The mean length of stay was 39 days overall and 16 days in the ICU. Acinetobacter spp., Enterococcus spp., and Staphylococcus aureus predominated. Fifty-six patients harbored multidrug-resistant bacteria and had a significantly greater TBSA. The mean time to colonization was 6 days overall and 14 days for multidrug-resistant bacteria; it was significantly longer for methicillin-resistant S. aureus than for methicillin-susceptible S. aureus. (4) Conclusions: This is the first report describing the dynamics of microbial colonization of burn wounds in Uruguay. Similarities were found with reports elsewhere, but early colonization with yeasts and the absence of Streptococcus pyogenes were unique. Each burn center needs to monitor its microbial ecology to tailor their antimicrobial strategies effectively.}, }
@article {pmid38000643, year = {2024}, author = {Jiang, M and Khunjar, W and Li, A and Chandran, K}, title = {Divergent microbial structure still results in convergent microbial function during arrested anaerobic digestion of food waste at different hydraulic retention times.}, journal = {Bioresource technology}, volume = {393}, number = {}, pages = {130069}, doi = {10.1016/j.biortech.2023.130069}, pmid = {38000643}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Food Loss and Waste ; Food ; RNA, Ribosomal, 16S/genetics ; *Refuse Disposal ; Bioreactors ; Fatty Acids, Volatile/metabolism ; Methane ; }, abstract = {In this study, two arrested anaerobic digestion bioreactors, fed with food waste, operated under different hydraulic retention times (HRTs) exhibited similar total volatile fatty acid (VFA) yields (p = 0.09). 16S rRNA gene sequencing revealed distinct microbial structure (p = 0.02) at the two HRTs. However, between the two HRTs, there were no differences in potential (DNA) and extant (mRNA) functionality for the production of acetic (AA)-, propionic (PA)-, butyric (BA)- and valeric-acid (VA), as indicated by the metagenome and metatranscriptome data, respectively. The highest potential and extant functionality for PA production in the reactor microbiomes mirrored the highest abundance of PA in the reactor effluents. Meta-omics analysis of BA production indicated possible metabolite exchange across different community members. Notably, the basis for similar VFA production performance observed under the HRTs tested lies in the community-level redundancy in convergent acidification functions and pathways, rather than trends in community-level structure alone.}, }
@article {pmid38000642, year = {2024}, author = {Wu, K and Leliveld, T and Zweers, H and Rijnaarts, H and Langenhoff, A and Fernandes, TV}, title = {Impact of mixed microalgal and bacterial species on organic micropollutants removal in photobioreactors under natural light.}, journal = {Bioresource technology}, volume = {393}, number = {}, pages = {130083}, doi = {10.1016/j.biortech.2023.130083}, pmid = {38000642}, issn = {1873-2976}, mesh = {Photobioreactors/microbiology ; *Microalgae ; *Chlorella ; Sewage ; Bacteria ; Biomass ; }, abstract = {Single microalgae species are effective at the removal of various organic micropollutants (OMPs), however increased species diversity might enhance this removal. Sixteen OMPs were added to 2 continuous photobioreactors, one inoculated with Chlorella sorokiniana and the other with a microalgal-bacterial community, for 112 d under natural light. Three media were sequentially used in 3 Periods: I) synthetic sewage (d 0-28), II) 10x diluted anaerobically digested black water (AnBW) (d 28-94) and III) 5x diluted AnBW (d 94-112). Twelve OMPs were removed > 30 %, while 4 were < 10 % removed. Removal efficiencies were similar for 9 OMPs, yet the mixed community showed a 2-3 times higher removal capacity (µg OMP/g dry weight) than C. sorokiniana during Period II pseudo steady state. The removal decreased drastically in Period III due to overgrowth of filamentous green algae. This study shows for the first time how microbial community composition and abundance are key for OMPs removal.}, }
@article {pmid37999395, year = {2023}, author = {Hernanz-Torrijos, M and Ortega, MJ and Úbeda, B and Bartual, A}, title = {Polyunsaturated Aldehydes Profile in the Diatom Cyclotella cryptica Is Sensitive to Changes in Its Phycosphere Bacterial Assemblages.}, journal = {Marine drugs}, volume = {21}, number = {11}, pages = {}, pmid = {37999395}, issn = {1660-3397}, support = {RTI2018-101272-B-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; Plan Propio UCA 2022-2023//University of C&#xe1;diz/ ; }, mesh = {*Diatoms/chemistry ; Aldehydes/pharmacology/chemistry ; Oceans and Seas ; Bacteria ; Marine Biology ; }, abstract = {Diatoms are responsible for the fixation of ca. 20% of the global CO2 and live associated with bacteria that utilize the organic substances produced by them. Current research trends in marine microbial ecology show which diatom and bacteria interact mediated through the production and exchange of infochemicals. Polyunsaturated aldehydes (PUA) are organic molecules released by diatoms that are considered to have infochemical properties. In this work, we investigated the possible role of PUA as a mediator in diatom-bacteria interactions. To this end, we compare the PUA profile of a newly isolated oceanic PUA producer diatom, Cyclotella cryptica, co-cultured with and without associated bacteria at two phosphate availability conditions. We found that the PUA profile of C. cryptica cultured axenically was different than its profile when it was co-cultured with autochthonous (naturally associated) and non-autochthonous bacteria (unnaturally inoculated). We also observed that bacterial presence significantly enhanced diatom growth and that C. cryptica modulated the percentage of released PUA in response to the presence of bacteria, also depending on the consortium type. Based on our results, we propose that this diatom could use released PUA as a specific organic matter sign to attract beneficial bacteria for constructing its own phycosphere, for more beneficial growth.}, }
@article {pmid37997641, year = {2024}, author = {Tájmel, D and Cruz-Paredes, C and Rousk, J}, title = {Heat wave-induced microbial thermal trait adaptation and its reversal in the Subarctic.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17032}, doi = {10.1111/gcb.17032}, pmid = {37997641}, issn = {1365-2486}, support = {9036-00004B//Danmarks Frie Forskningsfond/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; 2020-04083//Vetenskapsr&#xe5;det/ ; 4.3-2021-00164//Vetenskapsr&#xe5;det/ ; }, mesh = {*Ecosystem ; *Hot Temperature ; Soil Microbiology ; Climate Change ; Temperature ; Soil/chemistry ; Carbon ; }, abstract = {Climate change predictions suggest that arctic and subarctic ecosystems will be particularly affected by rising temperatures and extreme weather events, including severe heat waves. Temperature is one of the most important environmental factors controlling and regulating microbial decomposition in soils; therefore, it is critical to understand its impact on soil microorganisms and their feedback to climate warming. We conducted a warming experiment in a subarctic birch forest in North Sweden to test the effects of summer heat waves on the thermal trait distributions that define the temperature dependences for microbial growth and respiration. We also determined the microbial temperature dependences 10 and 12 months after the heat wave simulation had ended to investigate the persistence of the thermal trait shifts. As a result of warming, the bacterial growth temperature dependence shifted to become warm-adapted, with a similar trend for fungal growth. For respiration, there was no shift in the temperature dependence. The shifts in thermal traits were not accompanied by changes in α- or β-diversity of the microbial community. Warming increased the fungal-to-bacterial growth ratio by 33% and decreased the microbial carbon use efficiency by 35%, and both these effects were caused by the reduction in moisture the warming treatments caused, while there was no evidence that substrate depletion had altered microbial processes. The warm-shifted bacterial thermal traits were partially restored within one winter but only fully recovered to match ambient conditions after 1 year. To conclude, a summer heat wave in the Subarctic resulted in (i) shifts in microbial thermal trait distributions; (ii) lower microbial process rates caused by decreased moisture, not substrate depletion; and (iii) no detectable link between the microbial thermal trait shifts and community composition changes.}, }
@article {pmid37994377, year = {2024}, author = {Lyche Solheim, A and Gundersen, H and Mischke, U and Skjelbred, B and Nejstgaard, JC and Guislain, ALN and Sperfeld, E and Giling, DP and Haande, S and Ballot, A and Moe, SJ and Stephan, S and Walles, TJW and Jechow, A and Minguez, L and Ganzert, L and Hornick, T and Hansson, TH and Stratmann, CN and Järvinen, M and Drakare, S and Carvalho, L and Grossart, HP and Gessner, MO and Berger, SA}, title = {Lake browning counteracts cyanobacteria responses to nutrients: Evidence from phytoplankton dynamics in large enclosure experiments and comprehensive observational data.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17013}, doi = {10.1111/gcb.17013}, pmid = {37994377}, issn = {1365-2486}, support = {603378, 226273//European Union FP7/ ; 731065//European Union H2020/ ; 01LC1501, 033L041B//German Federal Ministry of Education and Research/ ; GE 1775/2-1//German Research Foundation/ ; K45/2017, SAW-2015-IGB-1//Leibniz Association/ ; //Morsa River Basin authority, Norway/ ; }, mesh = {*Phytoplankton ; Lakes/microbiology ; Humic Substances ; Eutrophication ; *Cyanobacteria ; Nutrients ; Phosphorus/analysis ; China ; }, abstract = {Lakes worldwide are affected by multiple stressors, including climate change. This includes massive loading of both nutrients and humic substances to lakes during extreme weather events, which also may disrupt thermal stratification. Since multi-stressor effects vary widely in space and time, their combined ecological impacts remain difficult to predict. Therefore, we combined two consecutive large enclosure experiments with a comprehensive time-series and a broad-scale field survey to unravel the combined effects of storm-induced lake browning, nutrient enrichment and deep mixing on phytoplankton communities, focusing particularly on potentially toxic cyanobacterial blooms. The experimental results revealed that browning counteracted the stimulating effect of nutrients on phytoplankton and caused a shift from phototrophic cyanobacteria and chlorophytes to mixotrophic cryptophytes. Light limitation by browning was identified as the likely mechanism underlying this response. Deep-mixing increased microcystin concentrations in clear nutrient-enriched enclosures, caused by upwelling of a metalimnetic Planktothrix rubescens population. Monitoring data from a 25-year time-series of a eutrophic lake and from 588 northern European lakes corroborate the experimental results: Browning suppresses cyanobacteria in terms of both biovolume and proportion of the total phytoplankton biovolume. Both the experimental and observational results indicated a lower total phosphorus threshold for cyanobacterial bloom development in clearwater lakes (10-20 μg P L[-1]) than in humic lakes (20-30 μg P L[-1]). This finding provides management guidance for lakes receiving more nutrients and humic substances due to more frequent extreme weather events.}, }
@article {pmid37991947, year = {2023}, author = {Arya, S and George, AB and O'Dwyer, JP}, title = {Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {48}, pages = {e2307313120}, pmid = {37991947}, issn = {1091-6490}, support = {376199//Simons Foundation (SF)/ ; }, mesh = {*Microbiota ; *Machine Learning ; }, abstract = {Microbiome engineering offers the potential to leverage microbial communities to improve outcomes in human health, agriculture, and climate. To translate this potential into reality, it is crucial to reliably predict community composition and function. But a brute force approach to cataloging community function is hindered by the combinatorial explosion in the number of ways we can combine microbial species. An alternative is to parameterize microbial community outcomes using simplified, mechanistic models, and then extrapolate these models beyond where we have sampled. But these approaches remain data-hungry, as well as requiring an a priori specification of what kinds of mechanisms are included and which are omitted. Here, we resolve both issues by introducing a mechanism-agnostic approach to predicting microbial community compositions and functions using limited data. The critical step is the identification of a sparse representation of the community landscape. We then leverage this sparsity to predict community compositions and functions, drawing from techniques in compressive sensing. We validate this approach on in silico community data, generated from a theoretical model. By sampling just [Formula: see text]1% of all possible communities, we accurately predict community compositions out of sample. We then demonstrate the real-world application of our approach by applying it to four experimental datasets and showing that we can recover interpretable, accurate predictions on composition and community function from highly limited data.}, }
@article {pmid37991578, year = {2023}, author = {Liu, HH and Chen, L and Shao, HB and Gao, S and Hong, XY and Bing, XL}, title = {Environmental Factors and the Symbiont Cardinium Influence the Bacterial Microbiome of Spider Mites Across the Landscape.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {1}, pmid = {37991578}, issn = {1432-184X}, support = {32001905 and 32020103011//National Natural Science Foundation of China/ ; 32001905 and 32020103011//National Natural Science Foundation of China/ ; 2022YFC2601000//National Key Research and Development Program of China/ ; BK20211213//Natural Science Foundation of Jiangsu Province/ ; KJQN202110//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Humans ; Animals ; *Tetranychidae ; RNA, Ribosomal, 16S/genetics ; Bacteroidetes/genetics ; *Arthropods ; *Microbiota ; }, abstract = {Microbes play a key role in the biology, ecology, and evolution of arthropods. Despite accumulating data on microbial communities in arthropods that feed on plants using piercing-sucking mouthparts, we still lack a comprehensive understanding of the composition and assembly factors of the microbiota, particularly in field-collected spider mites. Here, we applied 16S rRNA amplicon sequencing to investigate the characters of the bacterial community in 140 samples representing 420 mite individuals, belonging to eight Tetranychus species (Acari: Tetranychidae) collected from 26 sites in China. The results showed that the bacterial composition of spider mites varied significantly among different species, locations, and plants. The environment showed a significant influence on the bacterial community of spider mites, with different relative contributions. Latitude and precipitation were found to be the main factors influencing the bacterial community composition. The dissimilarity of bacterial community and geographical distance between mite locations were significantly correlated. The assembly of spider mite bacterial communities seemed to be mainly influenced by stochastic processes. Furthermore, the symbiont Cardinium was found to be important in shaping the microbiota of many Tetranychus species. The relative abundance of Cardinium was > 50% in T. viennensis, T. urticae G, T. urticae R, and T. turkestani. Removing Cardinium reads from our analysis significantly changed Shannon diversity index and weighted beta diversity in these species. Altogether, this study provides novel insights into bacterial diversity patterns that contribute to our knowledge of the symbiotic relationships between arthropods and their bacterial communities.}, }
@article {pmid37989722, year = {2024}, author = {Yuan, M and Na, M and Hicks, LC and Rousk, J}, title = {Limiting resources for soil microbial growth in climate change simulation treatments in the subarctic.}, journal = {Ecology}, volume = {105}, number = {1}, pages = {e4210}, doi = {10.1002/ecy.4210}, pmid = {37989722}, issn = {1939-9170}, support = {KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; 2020-03858//The Swedish Research Council Vetenskapsr&#xe5;det/ ; 2020-04083//The Swedish Research Council Vetenskapsr&#xe5;det/ ; 4.3-2021-00164//Swedish Research Council's/ ; }, mesh = {*Ecosystem ; *Climate Change ; Soil ; Soil Microbiology ; Tundra ; Arctic Regions ; Plants ; Carbon ; Nitrogen ; Bacteria ; }, abstract = {The microbial use of resources to sustain life and reproduce influences for example, decomposition and plant nutrient provisioning. The study of "limiting factors" has shed light on the interaction between plants and their environment. Here, we investigated whether carbon (C), nitrogen (N), or phosphorus (P) was limiting for soil microorganisms in a subarctic tundra heath, and how changes in resource availability associated with climate change affected this. We studied samples in which changes in resource availability due to climate warming were simulated by the addition of birch litter and/or inorganic N. To these soils, we supplied factorial C (as glucose), N (as NH4 NO3), and P (as KH2 PO4 /K2 HPO4) additions ("limiting factor assays," LFA), to determine the limiting factors. The combination of C and P induced large growth responses in all soils and, combined with a systematic tendency for growth increases by C, this suggested that total microbial growth was primarily limited by C and secondarily by P. The C limitation was alleviated by the field litter treatment and strengthened by N fertilization. The microbial growth response to the LFA-C and LFA-P addition was strongest in the field-treatment that combined litter and N addition. We also found that bacteria were closer to P limitation than fungi. Our results suggest that, under a climate change scenario, increased C availability resulting from Arctic greening, treeline advance, and shrubification will reduce the microbial C limitation, while increased N availability resulting from warming will intensify the microbial C limitation. Our results also suggest that the synchronous increase of both C and N availability might lead to a progressive P limitation of microbial growth, primarily driven by bacteria being closer to P limitation. These shifts in microbial resource limitation might lead to a microbial targeting of the limiting element from organic matter, and also trigger competition for nutrients between plants and microorganisms, thus modulating the productivity of the ecosystem.}, }
@article {pmid37987191, year = {2023}, author = {Garbisu, C and Alkorta, I}, title = {A case for the importance of following antibiotic resistant bacteria throughout the soil food web.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {45}, number = {12}, pages = {e2300153}, doi = {10.1002/bies.202300153}, pmid = {37987191}, issn = {1521-1878}, support = {PID2020-116495RB-I00//MCIN/AEI/10.13039/501100011033/ ; IT1578-22//Basque Government/ ; //JRL Environmental Antibiotic Resistance/ ; }, mesh = {Animals ; *Soil ; *Bacteria/genetics ; Manure/microbiology ; Food Chain ; Ecosystem ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Genes, Bacterial ; }, abstract = {It is necessary to complement next-generation sequencing data on the soil resistome with theoretical knowledge provided by ecological studies regarding the spread of antibiotic resistant bacteria (ARB) in the abiotic and, especially, biotic fraction of the soil ecosystem. Particularly, when ARB enter agricultural soils as a consequence of the application of animal manure as fertilizer, from a microbial ecology perspective, it is important to know their fate along the soil food web, that is, throughout that complex network of feeding interactions among members of the soil biota that has crucial effects on species richness and ecosystem productivity and stability. It is critical to study how the ARB that enter the soil through the application of manure can reach other taxonomical groups (e.g., fungi, protists, nematodes, arthropods, earthworms), paying special attention to their presence in the gut microbiomes of mesofauna-macrofauna and to the possibilities for horizontal gene transfer of antibiotic resistant genes.}, }
@article {pmid37986012, year = {2023}, author = {Basbas, C and Garzon, A and Schlesener, C and van Heule, M and Profeta, R and Weimer, BC and Silva-Del-Rio, N and Byrne, BA and Karle, B and Aly, SS and Lima, FS and Pereira, RV}, title = {Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {59}, pmid = {37986012}, issn = {2524-4671}, abstract = {BACKGROUND: The goal of this study was to assess the microbial ecology and diversity present in the uterus of post-partum dairy cows with and without metritis from 24 commercial California dairy farms using shotgun metagenomics. A set subset of 95 intrauterine swab samples, taken from a larger selection of 307 individual cow samples previously collected, were examined for α and β diversity and differential abundance associated with metritis. Cows within 21 days post-partum were categorized into one of three clinical groups during sample collection: control (CT, n = 32), defined as cows with either no vaginal discharge or a clear, non-purulent mucus vaginal discharge; metritis (MET, n = 33), defined as a cow with watery, red or brown colored, and fetid vaginal discharge; and purulent discharge cows (PUS, n = 31), defined as a non-fetid purulent or mucopurulent vaginal discharge.<br><br>RESULTS: All three clinical groups (CT, MET, and PUS) were highly diverse, with the top 12 most abundant genera accounting for 10.3%, 8.8%, and 10.1% of mean relative abundance, respectively. The &#x3b1; diversity indices revealed a lower diversity from samples collected from MET and PUS when compared to CT cows. PERMANOVA statistical testing revealed a significant difference (P adjusted&#x2009;<&#x2009;0.01) in the diversity of genera between CT and MET samples (R2&#x2009;=&#x2009;0.112, P&#x2009;=&#x2009;0.003) and a non-significant difference between MET and PUS samples (R2&#x2009;=&#x2009;0.036, P&#x2009;=&#x2009;0.046). ANCOM-BC analysis revealed that from the top 12 most abundant genera, seven genera were increased in the natural log fold change (LFC) of abundance in MET when compared to CT samples: Bacteroides, Clostridium, Fusobacterium, Phocaeicola, Porphyromonas, Prevotella, and Streptococcus. Two genera, Dietzia and Microbacterium, were decreased in natural LFC of abundance when comparing MET (regardless of treatment) and CT, while no changes in natural LFC of abundance were observed for Escherichia, Histophilus, and Trueperella.<br><br>CONCLUSIONS: The results presented here, are the current deepest shotgun metagenomic analyses conducted on the bovine uterine microbiome to date (mean of 256,425 genus-level reads per sample). Our findings support that uterine samples from cows without metritis (CT) had increased &#x3b1;-diversity but decreased &#x3b2;-diversity when compared to metritis or PUS cows, characteristic of dysbiosis. In summary, our findings highlight that MET cows have an increased abundance of Bacteroides, Porphyromonas, and Fusobacterium when compared to CT and PUS, and support the need for further studies to better understand their potential causal role in metritis pathogenesis.}, }
@article {pmid37984648, year = {2024}, author = {Bhattarai, B and Bhattacharjee, AS and Coutinho, FH and Goel, R}, title = {Investigating the viral ecology and contribution to the microbial ecology in full-scale mesophilic anaerobic digesters.}, journal = {Chemosphere}, volume = {349}, number = {}, pages = {140743}, doi = {10.1016/j.chemosphere.2023.140743}, pmid = {37984648}, issn = {1879-1298}, mesh = {Anaerobiosis ; *Bioreactors/microbiology ; *Methane/metabolism ; Bacteria/metabolism ; Sewage ; }, abstract = {In an attempt to assess the diversity of viruses and their potential to modulate the metabolism of functional microorganisms in anaerobic digesters, we collected digestate from three mesophilic anaerobic digesters in full-scale wastewater treatment plants treating real municipal wastewater. The reads were analyzed using bioinformatics algorithms to elucidate viral diversity, identify their potential role in modulating the metabolism of functional microorganisms, and provide essential genomic information for the potential use of virus-mediated treatment in controlling the anaerobic digester microbiome. We found that Siphoviridae was the dominant family in mesophilic anaerobic digesters, followed by Myoviridae and Podoviridae. Lysogeny was prevalent in mesophilic anaerobic digesters as the majority of metagenome-assembled genomes contained at least one viral genome within them. One virus within the genome of an acetoclastic methanogen (Methanothrix soehngenii) was observed with a gene (fwdE) acquired via lateral transfer from hydrogenotrophic methanogens. The virus-mediated acquisition of fwdE gene enables possibility of mixotrophic methanogenesis in Methanothrix soehngenii. This evidence highlighted that lysogeny provides fitness advantage to methanogens in anaerobic digesters by adding flexibility to changing substrates. Similarly, we found auxiliary metabolic genes, such as cellulase and alpha glucosidase, of bacterial origin responsible for sludge hydrolysis in viruses. Additionally, we discovered novel viral genomes and provided genomic information on viruses infecting acidogenic, acetogenic, and pathogenic bacteria that can potentially be used for virus-mediated treatment to deal with the souring problem in anaerobic digesters and remove pathogens from biosolids before land application. Collectively, our study provides a genome-level understanding of virome in conjunction with the microbiome in anaerobic digesters that can be used to optimize the anaerobic digestion process for efficient biogas generation.}, }
@article {pmid37982643, year = {2023}, author = {Lo, H-Y and Wink, K and Nitz, H and Kästner, M and Belder, D and Müller, JA and Kaster, A-K}, title = {scMAR-Seq: a novel workflow for targeted single-cell genomics of microorganisms using radioactive labeling.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0099823}, pmid = {37982643}, issn = {2379-5077}, mesh = {Workflow ; *Genomics/methods ; *Microfluidics/methods ; }, abstract = {A central question in microbial ecology is which member of a community performs a particular metabolism. Several sophisticated isotope labeling techniques are available for analyzing the metabolic function of populations and individual cells in a community. However, these methods are generally either insufficiently sensitive or throughput-limited and thus have limited applicability for the study of complex environmental samples. Here, we present a novel approach that combines highly sensitive radioisotope tracking, microfluidics, high-throughput sorting, and single-cell genomics to simultaneously detect and identify individual microbial cells based solely on their in situ metabolic activity, without prior information on community structure.}, }
@article {pmid37981701, year = {2023}, author = {Sadeghi, J and Chaganti, SR and Johnson, TB and Heath, DD}, title = {Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {258}, pmid = {37981701}, issn = {2049-2618}, mesh = {Animals ; Phylogeny ; *Microbiota/genetics ; Fishes ; *Gastrointestinal Microbiome/genetics ; Water ; }, abstract = {BACKGROUND: While many studies have reported that the structure of the gut and skin microbiota is driven by both species-specific and habitat-specific factors, the relative importance of host-specific versus environmental factors in wild vertebrates remains poorly understood. The aim of this study was to determine the diversity and composition of fish skin, gut, and surrounding water bacterial communities (hereafter referred to as microbiota) and assess the extent to which host habitat and phylogeny predict microbiota similarity. Skin swabs and gut samples from 334 fish belonging to 17 species were sampled in three Laurentian Great Lakes (LGLs) habitats (Detroit River, Lake Erie, Lake Ontario). We also collected and filtered water samples at the time of fish collection. We analyzed bacterial community composition using 16S metabarcoding and tested for community variation.<br><br>RESULTS: We found that the water microbiota was distinct from the fish microbiota, although the skin microbiota more closely resembled the water microbiota. We also found that environmental (sample location), habitat, fish diet, and host species factors shape and promote divergence or convergence of the fish microbiota. Since host species significantly affected both gut and skin microbiota (separately from host species effects), we tested for phylosymbiosis using pairwise host species phylogenetic distance versus bacterial community dissimilarity. We found significant phylogenetic effects on bacterial community dissimilarity, consistent with phylosymbiosis for both the fish skin and gut microbiota, perhaps reflecting the longstanding co-evolutionary relationship between the host species and their microbiomes.<br><br>CONCLUSIONS: Analyzing the gut and skin mucus microbiota across diverse fish species in complex natural ecosystems such as the LGLs provides insights into the potential for habitat and species-specific effects on the microbiome, and ultimately the health, of the host. Video Abstract.}, }
@article {pmid37980777, year = {2023}, author = {Acosta, DJ and Alper, HS}, title = {Advances in enzymatic and organismal technologies for the recycling and upcycling of petroleum-derived plastic waste.}, journal = {Current opinion in biotechnology}, volume = {84}, number = {}, pages = {103021}, doi = {10.1016/j.copbio.2023.103021}, pmid = {37980777}, issn = {1879-0429}, mesh = {Mutation ; *Petroleum ; Polymers ; Recycling ; Plastics ; }, abstract = {Biological catalysts are emerging with the capability to depolymerize a wide variety of plastics. Improving and discovering these catalysts has leveraged a range of tools, including microbial ecology studies, high-throughput selections, and computationally guided mutational studies. In this review, we discuss the prospects for biological solutions to plastic recycling and upcycling with a focus on major advances in polyethylene terephthalate depolymerization, expanding the range of polymers with known biological catalysts, and the utilization of derived products. We highlight several recent improvements in enzymes and reaction properties, the discovery of a wide variety of novel plastic-depolymerizing biocatalysts, and how depolymerization products can be utilized in recycling and upcycling.}, }
@article {pmid37979870, year = {2024}, author = {Xiao, Z and Lu, C and Wu, Z and Li, X and Ding, K and Zhu, Z and Han, R and Zhao, J and Ge, T and Li, G and Zhu, YG}, title = {Continuous cropping disorders of eggplants (Solanum melongena L.) and tomatoes (Solanum lycopersicum L.) in suburban agriculture: Microbial structure and assembly processes.}, journal = {The Science of the total environment}, volume = {909}, number = {}, pages = {168558}, doi = {10.1016/j.scitotenv.2023.168558}, pmid = {37979870}, issn = {1879-1026}, mesh = {*Solanum lycopersicum ; *Solanum melongena ; Soil Microbiology ; Agriculture ; Bacteria/genetics ; Soil/chemistry ; Rhizosphere ; }, abstract = {Deciphering the intricate relationships between microorganisms and plants remains a formidable challenge in plant microbial ecology, an area that holds promise for optimizing microbial interventions to enhance stress resilience and agricultural yields. In our investigation, we procured samples during 2019 and 2022 from a suburban agricultural greenhouse. Our study delineated the composition of bacterial and fungal communities across various ecological niches-namely, the rhizosphere soil, bulk soil, and phyllosphere of healthy, Ralstonia solanacearum-infected, and dead eggplants and tomatoes. The structure and composition of both fungal and bacterial communities change significantly under the influence of the host genotype across all samples. In the tomato or eggplant groups, bacterial wilt exerts a more pronounced impact on the bacterial community than on the fungal community. We speculate that the rhizosphere of healthy eggplants and tomatoes harbored more antibiotic-producing (e.g., Amycolatopsis and Penicillium) and biocontrol (e.g., Bacillus) strains, which can lead to have lower absolute abundance of R. solanacearum. In the context of R. solanacearum invasion, deterministic processes were responsible for shaping 70.67 % and 80.63 % of the bacterial community assembly in the rhizosphere of eggplants and tomatoes, respectively. Deterministic processes dominated the assembly of fungal communities in the rhizosphere of R. solanacearum-infected eggplants, whereas the opposite was true in the tomatoes. Homogeneous selection emerged as the predominant force governing the bacterial community assembly in the rhizospheres of R. solanacearum-infected eggplants and tomatoes. The bacterial co-occurrence networks in healthy rhizosphere soil were characterized by reduced vulnerability and enhanced stability (i.e., robustness index) and complexity (i.e., cohesion index), compared to their infected counterparts. In summary, complex microbial networks in rhizosphere soils are more resistant to invasion by soil-borne pathogens. The dynamics of bacterial interactions and community assembly processes are pivotal for effective microbiome management and offer predictive insights into the ecological ramifications of R. solanacearum invasions.}, }
@article {pmid37977011, year = {2023}, author = {Scaria, SS and Balasubramanian, B and Dandin, VS and Meyyazhagan, A and Pappuswamy, M and Sattanathan, G and Liu, WC and Kadanthottu Sebastian, J and Park, S}, title = {Review on impacts of micro- and nano-plastic on aquatic ecosystems and mitigation strategies.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {265}, number = {}, pages = {106759}, doi = {10.1016/j.aquatox.2023.106759}, pmid = {37977011}, issn = {1879-1514}, mesh = {Animals ; Humans ; *Ecosystem ; Microplastics/toxicity ; Plastics/toxicity ; *Water Pollutants, Chemical/toxicity ; Food Chain ; }, abstract = {The rapid proliferation of microplastics (MPs) and nanoplastics (NPs) in our environment presents a formidable hazard to both biotic and abiotic components. These pollutants originate from various sources, including commercial production and the breakdown of larger plastic particles. Widespread contamination of the human body, agroecosystems, and animals occurs through ingestion, entry into the food chain, and inhalation. Consequently, the imperative to devise innovative methods for MPs and NPs remediation has become increasingly apparent. This review explores the current landscape of strategies proposed to mitigate the escalating threats associated with plastic waste. Among the array of methods in use, microbial remediation emerges as a promising avenue for the decomposition and reclamation of MPs and NPs. In response to the growing concern, numerous nations have already implemented or are in the process of adopting regulations to curtail MPs and NPs in aquatic habitats. This paper aims to address this gap by delving into the environmental fate, behaviour, transport, ecotoxicity, and management of MPs and NPs particles within the context of nanoscience, microbial ecology, and remediation technologies. Key findings of this review encompass the intricate interdependencies between MPs and NPs and their ecosystems. The ecological impact, from fate to ecotoxicity, is scrutinized in light of the burgeoning environmental imperative. As a result, this review not only provides an encompassing understanding of the ecological ramifications of MPs and NPs but also highlights the pressing need for further research, innovation, and informed interventions.}, }
@article {pmid37976624, year = {2023}, author = {Liu, S and Lin, Y and Liu, T and Xu, X and Wang, J and Chen, Q and Sun, W and Dang, C and Ni, J}, title = {Planktonic/benthic Bathyarchaeota as a "gatekeeper" enhance archaeal nonrandom co-existence and deterministic assembling in the Yangtze River.}, journal = {Water research}, volume = {247}, number = {}, pages = {120829}, doi = {10.1016/j.watres.2023.120829}, pmid = {37976624}, issn = {1879-2448}, mesh = {Humans ; *Archaea/genetics ; *Plankton ; Geologic Sediments/microbiology ; Rivers/microbiology ; Water ; Carbon ; RNA, Ribosomal, 16S ; Phylogeny ; DNA, Archaeal ; }, abstract = {Archaea, the third proposed domain of life, mediate carbon and nutrient cycling in global natural habitats. Compared with bacteria, our knowledge about archaeal ecological modes in large freshwater environments subject to varying natural and human factors is limited. By metabarcoding analysis of 303 samples, we provided the first integrate biogeography about archaeal compositions, co-existence networks, and assembling processes within a 6000 km continuum of the Yangtze River. Our study revealed that, among the major phyla, water samples owned a higher proportion of Thaumarchaeota (62.8%), while sediments had higher proportions of Euryarchaeota (33.4%) and Bathyarchaeota (18.8%). A decline of polarization in phylum abundance profile was observed from plateau/mountain/hill to basin/plain areas, which was attributed to the increase of nutrients and metals. Planktonic and benthic Bathyarchaeota tended to co-occur with both major (e.g., methanogens or Thermoplasmata) and minor (e.g., Asgard or DPANN) taxa in the non-random networks, harboring the highest richness and abundances of keystone species and contributing the most positively to edge number, node degree, and nearest neighbor degree. Furthermore, we noted significantly positive contributions of Bathyarchaeota abundance and network complexity to the dominance of deterministic process in archaeal assembly (water: 65.3%; sediments: 92.6%), since higher carbon metabolic versatility of Bathyarchaeota would benefit archaeal symbiotic relations. Stronger deterministic assembling was identified at the lower-reach plain, and higher concentrations of ammonium and aluminum separately functioning as nutrition and agglomerator were the main environmental drivers. We lastly found that the Three Gorges Dam caused a simultaneous drop of benthic Bathyarchaeota abundance, network co-existence, and deterministic effects immediately downstream due to riverbed erosion as a local interference. These findings highlight that Bathyarchaeota are a "gatekeeper" to promote fluvial archaeal diversity, stability, and predictability under varying macroscopic and microscopic factors, expanding our knowledge about microbial ecology in freshwater biogeochemical cycling globally.}, }
@article {pmid37975506, year = {2023}, author = {Lequime, S}, title = {The sociality continuum of viruses: a commentary on Leeks et al. 2023.}, journal = {Journal of evolutionary biology}, volume = {36}, number = {11}, pages = {1568-1570}, doi = {10.1111/jeb.14247}, pmid = {37975506}, issn = {1420-9101}, mesh = {*Onions ; *Viruses/genetics ; Evolution, Molecular ; }, }
@article {pmid37974054, year = {2023}, author = {Minnebo, Y and De Paepe, K and Raes, J and Van de Wiele, T}, title = {Eating patterns contribute to shaping the gut microbiota in the mucosal simulator of the human intestinal microbial ecosystem.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {12}, pages = {}, doi = {10.1093/femsec/fiad149}, pmid = {37974054}, issn = {1574-6941}, support = {30770923//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Feeding Behavior ; Colon/microbiology ; Feces/microbiology ; }, abstract = {Eating patterns, i.e. meal frequency and circadian timing of meals, are often modified in weight loss and metabolic healing strategies. However, in-depth research into the effects on the gut microbiome remains scarce, particularly across various colon regions and niches. We identified eating patterns to contribute in shaping the in vitro gut biomass production, metabolism, and microbial community compositions by subjecting four faecal microbiomes to a pattern that is standardized for a dynamic gut model (feeding at 09, 17, and 01 h), a typical Western (breakfast, lunch, and dinner at 09, 13, and 19 h, respectively), and a time-restricted pattern (single meal at 09 h). While eating patterns moderately affected the microbiome (2.4% and 1.8% significant variation in proportional and quantitative microbial compositions, respectively), significant changes were noted in the time-restricted pattern, including increased Bacteroides, Butyricicoccus, Dialister, and Faecalibacterium abundances. Sampling every 4 h revealed no significant circadian fluctuations in biomass production, microbial community compositions, or functionality. Longer fasting times favoured the growth of slower-growing species, such as Akkermansia, Dialister, and Parasutterella over faster-growers, such as Pseudomonas and Stenotrophomonas. Our findings illustrate the importance of recording and considering eating patterns as a gut microbiome determinant in in vivo and in vitro dietary intervention studies.}, }
@article {pmid37973932, year = {2023}, author = {Feliu-Paradeda, L and Puig, S and Bañeras, L}, title = {Design and validation of a multiplex PCR method for the simultaneous quantification of Clostridium acetobutylicum, Clostridium carboxidivorans and Clostridium cellulovorans.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {20073}, pmid = {37973932}, issn = {2045-2322}, support = {PCI2019-111932-2//Ministerio de Ciencia e Innovaci&#xf3;n/ ; 2021 FISDU00132//Generalitat de Catalunya/ ; UdG-AG-575//Universitat de Girona/ ; }, mesh = {*Clostridium acetobutylicum/genetics ; *Clostridium cellulovorans/genetics ; Multiplex Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Clostridium/genetics ; Butanols ; 1-Butanol ; Fermentation ; }, abstract = {Co-cultures of clostridia with distinct physiological properties have emerged as an alternative to increase the production of butanol and other added-value compounds from biomass. The optimal performance of mixed tandem cultures may depend on the stability and fitness of each species in the consortium, making the development of specific quantification methods to separate their members crucial. In this study, we developed and tested a multiplex qPCR method targeting the 16S rRNA gene for the simultaneous quantification of Clostridium acetobutylicum, Clostridium carboxidivorans and Clostridium cellulovorans in co-cultures. Designed primer pairs and probes could specifically quantify the three Clostridium species with no cross-reactions thus allowing significant changes in their growth kinetics in the consortia to be detected and correlated with productivity. The method was used to test a suitable medium composition for simultaneous growth of the three species. We show that higher alcohol productions were obtained when combining C. carboxidivorans and C. acetobutylicum compared to individual cultures, and further improved (> 90%) in the triplet consortium. Altogether, the methodology could be applied to fermentation processes targeting butanol productions from lignocellulosic feedstocks with a higher substrate conversion efficiency.}, }
@article {pmid37971428, year = {2023}, author = {Silcocks, M and Chang, X and Thuong Thuong, NT and Qin, Y and Minh Ha, DT and Khac Thai, PV and Vijay, S and Anh Thu, DD and Ngoc Ha, VT and Ngoc Nhung, H and Huu Lan, N and Quynh Nhu, NT and Edwards, D and Nath, A and Pham, K and Duc Bang, N and Hong Chau, TT and Thwaites, G and Heemskerk, AD and Chuen Khor, C and Teo, YY and Inouye, M and Ong, RT-H and Caws, M and Holt, KE and Dunstan, SJ}, title = {Evolution and transmission of antibiotic resistance is driven by Beijing lineage Mycobacterium tuberculosis in Vietnam.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0256223}, pmid = {37971428}, issn = {2165-0497}, support = {/WT_/Wellcome Trust/United Kingdom ; U19 AI162583/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Mycobacterium tuberculosis/genetics ; Antitubercular Agents/pharmacology/therapeutic use ; Beijing ; Vietnam/epidemiology ; Genotype ; *Tuberculosis, Multidrug-Resistant/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Mutation ; }, abstract = {Drug-resistant tuberculosis (TB) infection is a growing and potent concern, and combating it will be necessary to achieve the WHO's goal of a 95% reduction in TB deaths by 2035. While prior studies have explored the evolution and spread of drug resistance, we still lack a clear understanding of the fitness costs (if any) imposed by resistance-conferring mutations and the role that Mtb genetic lineage plays in determining the likelihood of resistance evolution. This study offers insight into these questions by assessing the dynamics of resistance evolution in a high-burden Southeast Asian setting with a diverse lineage composition. It demonstrates that there are clear lineage-specific differences in the dynamics of resistance acquisition and transmission and shows that different lineages evolve resistance via characteristic mutational pathways.}, }
@article {pmid37971255, year = {2023}, author = {Martínez-Alvarez, L and Ramond, J-B and Vikram, S and León-Sobrino, C and Maggs-Kölling, G and Cowan, DA}, title = {With a pinch of salt: metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {12}, pages = {e0062923}, pmid = {37971255}, issn = {1098-5336}, support = {113308//National Research Foundation (NRF)/ ; }, mesh = {*Bacteria/genetics ; Desert Climate ; Soil Microbiology ; Sodium Chloride ; *Microbiota ; }, abstract = {The hyperarid Namib Desert is one of the oldest deserts on Earth. It contains multiple clusters of playas which are saline-rich springs surrounded by halite evaporites. Playas are of great ecological importance, and their indigenous (poly)extremophilic microorganisms are potentially involved in the precipitation of minerals such as carbonates and sulfates and have been of great biotechnological importance. While there has been a considerable amount of microbial ecology research performed on various Namib Desert edaphic microbiomes, little is known about the microbial communities inhabiting its multiple playas. In this work, we provide a comprehensive taxonomic and functional potential characterization of the microbial, including viral, communities of sediment mats and halites from two distant salt pans of the Namib Desert, contributing toward a better understanding of the ecology of this biome.}, }
@article {pmid37970641, year = {2023}, author = {Spencer-Williams, I and Meyer, M and DePas, W and Elliott, E and Haig, SJ}, title = {Assessing the Impacts of Lead Corrosion Control on the Microbial Ecology and Abundance of Drinking-Water-Associated Pathogens in a Full-Scale Drinking Water Distribution System.}, journal = {Environmental science &amp; technology}, volume = {57}, number = {48}, pages = {20360-20369}, pmid = {37970641}, issn = {1520-5851}, mesh = {*Drinking Water/microbiology ; RNA, Ribosomal, 16S/genetics ; Corrosion ; Nontuberculous Mycobacteria/genetics ; Phosphates ; Water Microbiology ; }, abstract = {Increases in phosphate availability in drinking water distribution systems (DWDSs) from the use of phosphate-based corrosion control strategies may result in nutrient and microbial community composition shifts in the DWDS. This study assessed the year-long impacts of full-scale DWDS orthophosphate addition on both the microbial ecology and density of drinking-water-associated pathogens that infect the immunocompromised (DWPIs). Using 16S rRNA gene amplicon sequencing and droplet digital PCR, drinking water microbial community composition and DWPI density were examined. Microbial community composition analysis suggested significant compositional changes after the orthophosphate addition. Significant increases in total bacterial density were observed after orthophosphate addition, likely driven by a 2 log 10 increase in nontuberculous mycobacteria (NTM). Linear effect models confirmed the importance of phosphate addition with phosphorus concentration explaining 17% and 12% of the variance in NTM and L. pneumophila density, respectively. To elucidate the impact of phosphate on NTM aggregation, a comparison of planktonic and aggregate fractions of NTM cultures grown at varying phosphate concentrations was conducted. Aggregation assay results suggested that higher phosphate concentrations cause more disaggregation, and the interaction between phosphate and NTM is species specific. This work reveals new insight into the consequences of orthophosphate application on the DWDS microbiome and highlights the importance of proactively monitoring the DWDS for DWPIs.}, }
@article {pmid37970497, year = {2023}, author = {Lee, JH and Kim, S and Kim, ES and Keum, GB and Doo, H and Kwak, J and Pandey, S and Cho, JH and Ryu, S and Song, M and Cho, JH and Kim, S and Kim, HB}, title = {Comparative analysis of the pig gut microbiome associated with the pig growth performance.}, journal = {Journal of animal science and technology}, volume = {65}, number = {4}, pages = {856-864}, pmid = {37970497}, issn = {2055-0391}, abstract = {There are a variety of microorganisms in the animal intestine, and it has been known that they play important roles in the host such as suppression of potentially pathogenic microorganisms, modulation of the gut immunity. In addition, the gut microbiota and the livestock growth performance have long been known to be related. Therefore, we evaluated the interrelation between the growth performance and the gut microbiome of the pigs from 3 different farms, with pigs of varied ages ready to be supplied to the market. When pigs reached average market weight of 118 kg, the average age of pigs in three different farms were < 180 days, about 190 days, and > 200 days, respectively. Fecal samples were collected from pigs of age of 70 days, 100 days, 130 days, and 160 days. The output data of the 16S rRNA gene sequencing by the Illumina Miseq platform was filtered and analyzed using Quantitative Insights into Microbial Ecology (QIIME)2, and the statistical analysis was performed using Statistical Analysis of Metagenomic Profiles (STAMP). The results of this study showed that the gut microbial communities shifted as pigs aged along with significant difference in the relative abundance of different phyla and genera in different age groups of pigs from each farm. Even though, there was no statistical differences among groups in terms of Chao1, the number of observed operational taxonomic units (OTUs), and the Shannon index, our results showed higher abundances of Bifidobacterium, Clostridium and Lactobacillus in the feces of pigs with rapid growth rate. These results will help us to elucidate important gut microbiota that can affect the growth performance of pigs.}, }
@article {pmid37968548, year = {2024}, author = {Naidoo, Y and Pierneef, RE and Cowan, DA and Valverde, A}, title = {Characterization of the soil resistome and mobilome in Namib Desert soils.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {27}, number = {4}, pages = {967-975}, pmid = {37968548}, issn = {1618-1905}, mesh = {*Soil Microbiology ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Desert Climate ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; Gene Transfer, Horizontal ; Soil/chemistry ; Genes, Bacterial ; Interspersed Repetitive Sequences ; }, abstract = {The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics.}, }
@article {pmid37968339, year = {2023}, author = {Sadiq, FA and De Reu, K and Steenackers, H and Van de Walle, A and Burmølle, M and Heyndrickx, M}, title = {Dynamic social interactions and keystone species shape the diversity and stability of mixed-species biofilms - an example from dairy isolates.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {118}, pmid = {37968339}, issn = {2730-6151}, support = {101025683//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; 35906//Villum Fonden (Villum Foundation)/ ; }, abstract = {Identifying interspecies interactions in mixed-species biofilms is a key challenge in microbial ecology and is of paramount importance given that interactions govern community functionality and stability. We previously reported a bacterial four-species biofilm model comprising Stenotrophomonas rhizophila, Bacillus licheniformis, Microbacterium lacticum, and Calidifontibacter indicus that were isolated from the surface of a dairy pasteuriser after cleaning and disinfection. These bacteria produced 3.13-fold more biofilm mass compared to the sum of biofilm masses in monoculture. The present study confirms that the observed community synergy results from dynamic social interactions, encompassing commensalism, exploitation, and amensalism. M. lacticum appears to be the keystone species as it increased the growth of all other species that led to the synergy in biofilm mass. Interactions among the other three species (in the absence of M. lacticum) also contributed towards the synergy in biofilm mass. Biofilm inducing effects of bacterial cell-free-supernatants were observed for some combinations, revealing the nature of the observed synergy, and addition of additional species to dual-species combinations confirmed the presence of higher-order interactions within the biofilm community. Our findings provide understanding of bacterial interactions in biofilms which can be used as an interaction-mediated approach for cultivating, engineering, and designing synthetic bacterial communities.}, }
@article {pmid37966591, year = {2024}, author = {Heinrichs, ME and Piedade, GJ and Popa, O and Sommers, P and Trubl, G and Weissenbach, J and Rahlff, J}, title = {Breaking the Ice: A Review of Phages in Polar Ecosystems.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2738}, number = {}, pages = {31-71}, pmid = {37966591}, issn = {1940-6029}, mesh = {*Bacteriophages ; Ecosystem ; Biomass ; Biological Evolution ; Cell Death ; *Viroids ; }, abstract = {Bacteriophages, or phages, are viruses that infect and replicate within bacterial hosts, playing a significant role in regulating microbial populations and ecosystem dynamics. However, phages from extreme environments such as polar regions remain relatively understudied due to challenges such as restricted ecosystem access and low biomass. Understanding the diversity, structure, and functions of polar phages is crucial for advancing our knowledge of the microbial ecology and biogeochemistry of these environments. In this review, we will explore the current state of knowledge on phages from the Arctic and Antarctic, focusing on insights gained from -omic studies, phage isolation, and virus-like particle abundance data. Metagenomic studies of polar environments have revealed a high diversity of phages with unique genetic characteristics, providing insights into their evolutionary and ecological roles. Phage isolation studies have identified novel phage-host interactions and contributed to the discovery of new phage species. Virus-like particle abundance and lysis rate data, on the other hand, have highlighted the importance of phages in regulating bacterial populations and nutrient cycling in polar environments. Overall, this review aims to provide a comprehensive overview of the current state of knowledge about polar phages, and by synthesizing these different sources of information, we can better understand the diversity, dynamics, and functions of polar phages in the context of ongoing climate change, which will help to predict how polar ecosystems and residing phages may respond to future environmental perturbations.}, }
@article {pmid37966223, year = {2023}, author = {Liu, S and Greenhut, IV and Heist, EP and Heist, MR and Moe, LA}, title = {Bacterial community dynamics during distilled spirit fermentation: influence of mash recipes and fermentation processes.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0162423}, pmid = {37966223}, issn = {2165-0497}, mesh = {*Saccharomyces cerevisiae ; Fermentation ; *Ethanol ; Bacteria/genetics ; Sugars ; }, abstract = {Production of ethanol from sugars and yeast is an ancient, ostensibly simple process. The source of sugars varies depending on the desired product and can include fruits, vegetables, molasses, honey, or grains, among other things. The source of yeast can be natural in the case of spontaneous ferments, but dry yeast addition is typical for large-scale fermentations. While the polymicrobial nature of some alcoholic fermentations is appreciated (e.g., for wine), most grain-based ethanol producers view microbes, apart from the added yeast, as "contaminants" meant to be controlled in order to maximize efficiency of ethanol production per unit of sugar. Nonetheless, despite rigorous cleaning-in-place measures and cooking the mash, bacteria are routinely cultured from these fermentations. We now know that bacteria can contribute to fermentation efficiency on an industrial scale, yet nothing is known about the makeup and stability of microbial communities in distilled spirit fermentations. The work here establishes the roles of mash recipes and distillery practices in microbial community assembly and dynamics over the course of fermentation. This represents an important first step in appreciating the myriad roles of bacteria in the production of distilled spirits.}, }
@article {pmid37966203, year = {2023}, author = {Miliotis, G and McDonagh, F and Singh, NK and O'Connor, L and Tuohy, A and Morris, D and Venkateswaran, K}, title = {Genomic analysis reveals the presence of emerging pathogenic Klebsiella lineages aboard the International Space Station.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0189723}, pmid = {37966203}, issn = {2165-0497}, support = {2021_ECRAward//University of Galway (NUI Galway)/ ; Space Biology NNH12ZTT001N grant no. 19-12829-26//National Aeronautics and Space Administration (NASA)/ ; }, mesh = {Humans ; *Space Flight ; Bacteria/genetics ; Klebsiella/genetics ; Plasmids ; Genomics ; Klebsiella pneumoniae/genetics ; }, abstract = {The International Space Station (ISS) is a unique, hermetically sealed environment, subject to environmental pressures not encountered on Earth, including microgravity and radiation (cosmic ionising/UV). While bacteria's adaptability during spaceflight remains elusive, recent research suggests that it may be species and even clone-specific. Considering the documented spaceflight-induced suppression of the human immune system, a deper understanding of the genomics of potential human pathogens in space could shed light on species and lineages of medical astromicrobiological significance. In this study, we used hybrid assembly methods and comparative genomics to deliver a comprehensive genomic characterization of 10 Klebsiella isolates retrieved from the ISS. Our analysis unveiled that Klebsiella quasipneumoniae ST138 demonstrates both spatial and temporal persistence aboard the ISS, showing evidence of genomic divergence from its Earth-based ST138 lineage. Moreover, we characterized plasmids from Klebsiella species of ISS origin, which harbored genes for disinfectant resistance and enhanced thermotolerance, suggestin possible adaptive advantages. Furthermore, we identified a mobile genetic element containing a hypervirulence-associated locus belonging to a Klebsiella pneumoniae isolate of the "high-risk" ST101 clone. Our work provides insights into the adaptability and persistence of Klebsiella species during spaceflight, highlighting the importance of understanding the dynamics of potential pathogenic bacteria in such environments.}, }
@article {pmid37965618, year = {2023}, author = {Ogola, HJO and Ijoma, GN and Edokpayi, JN}, title = {Sediment microbiome diversity and functional profiles of unprotected arid-tropical natural wetlands in South Africa revealed by shotgun metagenomics data.}, journal = {Data in brief}, volume = {51}, number = {}, pages = {109726}, pmid = {37965618}, issn = {2352-3409}, abstract = {The Limpopo province, located in the arid-tropical region in northeastern South Africa, is renowned for its diverse natural wetlands, some of which are currently unprotected. These wetlands play a crucial role in preserving biodiversity, purifying water, controlling floods, and supporting agricultural production for rural communities. Unfortunately, human activities such as agricultural effluents, run-offs, domestic wastewater, and plastics pollution, along with the impacts of climate change, are mounting pressures on these ecosystems. However, there is limited information on the microbial ecology of natural wetlands in this region, considering the changing anthropogenic activities. The data presented represents the first report on the microbial and functional diversity of sediment microbiomes associated with unprotected arid-tropical natural wetlands in South Africa. Metagenomic shotgun sequencing was performed on sediment samples from ten different wetlands using the Illumina NextSeq 2000 platform. Taxonomic profiling of 328,625,930 high-quality sequencing reads using the MetaPhlAn v3.0 pipeline revealed that Bacteria were the most abundant kingdom (54.5 %), followed by Viruses (0.40 %), Archaea (0.01 %), and Eukaryota (0.36 %). Among bacteria, the most prevalent taxa belonged to the phylum Proteobacteria, particularly the classes Gammaproteobacteria and Betaproteobacteria, which accounted for 83 % of bacterial sequences. The Terrabacteria group, consisting of the phyla Firmicutes and Actinobacteria, made up 3 % of the bacterial population. The abundance of these top bacterial taxa varied across different wetland samples, both at the genus and species levels. In addition, hierarchical clustering based on Bray-Curtis dissimilarity distances of fungal, protist, archaea, and virus species showed distinct clustering of sediment samples from different wetlands. Functional annotation of the metagenomes identified 1224-1702 enzyme classes, 84,833-198,397 gene families, and 280-400 pathways across the various wetland sediments. The data provide crucial baseline information on the microbial and functional diversity of sediment communities in arid tropical wetlands. This knowledge will contribute to a better understanding of these unique environments and can aid in their management and conservation efforts in rural South Africa.}, }
@article {pmid37964521, year = {2023}, author = {Brunetti, AE and Lyra, ML and Monteiro, JPC and Zurano, JP and Baldo, D and Haddad, CFB and Moeller, AH}, title = {Convergence of gut microbiota in myrmecophagous amphibians.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {2011}, pages = {20232223}, pmid = {37964521}, issn = {1471-2954}, support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome ; Biological Evolution ; *Microbiota ; Mammals/microbiology ; Anura ; RNA, Ribosomal, 16S ; }, abstract = {The gut microbiome composition of terrestrial vertebrates is known to converge in response to common specialized dietary strategies, like leaf-eating (folivory) or ant- and termite-eating (myrmecophagy). To date, such convergence has been studied in mammals and birds, but has been neglected in amphibians. Here, we analysed 15 anuran species (frogs and toads) representing five Neotropical families and demonstrated the compositional convergence of the gut microbiomes of distantly related myrmecophagous species. Specifically, we found that the gut microbial communities of bufonids and microhylids, which have independently evolved myrmecophagy, were significantly more similar than expected based on their hosts' evolutionary divergence. Conversely, we found that gut microbiome composition was significantly associated with host evolutionary history in some cases. For instance, the microbiome composition of Xenohyla truncata, one of the few known amphibians that eat fruits, was not different from those of closely related tree frogs with an arthropod generalist diet. Bacterial taxa overrepresented in myrmecophagous species relative to other host families include Paludibacter, Treponema, and Rikenellaceae, suggesting diet-mediated selection and prey-to-predator transmission likely driving the observed compositional convergence. This study provides a basis for examining the roles of the gut microbiome in host tolerance and sequestration of toxic alkaloids from ants and termites.}, }
@article {pmid37961388, year = {2023}, author = {Karim, S and Zenzal, TJ and Beati, L and Sen, R and Adegoke, A and Kumar, D and Downs, LP and Keko, M and Nussbaum, A and Becker, DJ and Moore, FR}, title = {Ticks without borders: Microbial communities of immature Neotropical tick species parasitizing migratory landbirds along northern Gulf of Mexico.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37961388}, issn = {2692-8205}, support = {P20 GM103476/GM/NIGMS NIH HHS/United States ; }, abstract = {The long-distance, seasonal migrations of birds make them an effective ecological bridge for the movement of ticks. The introduction of exotic tick species to new geographical regions can lead to the emergence of novel tick-borne pathogens or the re-emergence of previously eradicated ones. This study assessed the prevalence of exotic tick species parasitizing resident, short-distance, and long-distance songbirds during spring and autumn at stopover sites in the northern Gulf of Mexico using the mitochondrial 12S rDNA gene. Birds were captured for tick collection from six different sites from late August to early November in both 2018 and 2019. The highest number of ticks were collected in the 2019 season. Most ticks were collected off the Yellow-breasted Chat (Icteria virens) and Common Yellowthroat (Geothlypis trichas), and 54% of the total ticks collected were from Grand Chenier, LA. A high throughput 16S ribosomal RNA sequencing approach was followed to characterize the microbial communities and identify pathogenic microbes in all tick samples. Tick microbial communities, diversity, and community structure were determined using quantitative insight into microbial ecology (QIIME). The sparse correlations for compositional data (SparCC) approach was then used to construct microbial network maps and infer microbial correlations. A total of 421 individual ticks in the genera Amblyomma, Haemaphysalis, and Ixodes were recorded from 28 songbird species, of which Amblyomma and Amblyomma longirostre was the most abundant tick genus and species, respectively. Microbial profiles showed that Proteobacteria was the most abundant phylum. The most abundant bacteria include the pathogenic Rickettsia and endosymbiont Francisella, Candidatus Midichloria, and Spiroplasma. BLAST analysis and phylogenetic reconstruction of the Rickettsia sequences revealed the highest similarities to pathogenic spotted and non-spotted fever groups, including R. buchneri, R. conorii, R. prowazekii, R. bellii, R. australis, R. parkeri, R. monacensis, and R. monteiroi. Permutation multivariate analysis of variance revealed that the relative abundance of Francisella and Rickettsia drives microbial patterns across the tick genera. We also observed a higher percentage of positive correlations in microbe-microbe interactions among members of the microbial communities. Network analysis suggested a negative correlation between a) Francisella and Rickettsia and, b) Francisella and Cutibacterium. Lastly, mapping the distributions of bird species parasitized during spring migrations highlighted geographic hotspots where migratory songbirds could disperse ticks and their pathogens at stopover sites or upon arrival to their breeding grounds, the latter showing means dispersal distances from 421-5003 kilometers. These findings strongly highlight the potential role of migratory birds in the epidemiology of tick-borne pathogens.}, }
@article {pmid37959068, year = {2023}, author = {Bettera, L and Levante, A and Bancalari, E and Bottari, B and Cirlini, M and Neviani, E and Gatti, M}, title = {Lacticaseibacillus Strains Isolated from Raw Milk: Screening Strategy for Their Qualification as Adjunct Culture in Cheesemaking.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {21}, pages = {}, pmid = {37959068}, issn = {2304-8158}, support = {FIL-Quota Incentivante//University of Parma/ ; }, abstract = {The microbial ecology fundamentals of raw milk and long-ripened cheeses consist of a complex interaction between starter lactic acid bacteria (SLAB) and non-starter LAB (NSLAB). Although NSLAB aromatic properties are paramount, other phenotypic traits need to be considered for their use as adjunct cultures, such as the capability to endure technological parameters encountered during cheesemaking. The present study focused on the isolation and characterization of NSLAB from spontaneously fermented raw cow's milk coming from 20 dairies that produce Grana Padano PDO cheese. From 122 isolates, the screening process selected the 10 most diverse strains belonging to Lacticaseibacillus spp. to be phenotypically characterized. The strains were tested for their growth performance in milk in combination with the application of technological stresses, for their ability to produce volatile compounds after their growth in milk, and for their ability to use different nutrient sources and resist chemicals. The complex characterization qualified the strains 5959_Lbparacasei and 5296_Lbparacasei as the best candidates to be used as adjunct strains in the production of raw milk and long-ripened cheeses, provided that antibiotic resistance is measured before their employment. Other strains with interesting aromatic capabilities but lower heat resistance were 5293_Lbparacasei, 5649_Lbparacasei and 5780_Lbparacasei, which could be candidates as adjunct strains for uncooked cheese production.}, }
@article {pmid37957741, year = {2023}, author = {Moldovan, OT and Carrell, AA and Bulzu, PA and Levei, E and Bucur, R and Sitar, C and Faur, L and Mirea, IC and Șenilă, M and Cadar, O and Podar, M}, title = {The gut microbiome mediates adaptation to scarce food in Coleoptera.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {80}, pmid = {37957741}, issn = {2524-6372}, support = {R01 DE024463/DE/NIDCR NIH HHS/United States ; R01DE024463/NH/NIH HHS/United States ; }, abstract = {Beetles are ubiquitous cave invertebrates worldwide that adapted to scarce subterranean resources when they colonized caves. Here, we investigated the potential role of gut microbiota in the adaptation of beetles to caves from different climatic regions of the Carpathians. The beetles' microbiota was host-specific, reflecting phylogenetic and nutritional adaptation. The microbial community structure further resolved conspecific beetles by caves suggesting microbiota-host coevolution and influences by local environmental factors. The detritivore species hosted a variety of bacteria known to decompose and ferment organic matter, suggesting turnover and host cooperative digestion of the sedimentary microbiota and allochthonous-derived nutrients. The cave Carabidae, with strong mandibula, adapted to predation and scavenging of animal and plant remains, had distinct microbiota dominated by symbiotic lineages Spiroplasma or Wolbachia. All beetles had relatively high levels of fermentative Carnobacterium and Vagococcus involved in lipid accumulation and a reduction of metabolic activity, and both features characterize adaptation to caves.}, }
@article {pmid37956766, year = {2024}, author = {Dong, CD and Huang, CP and Chen, CW and Hung, CM}, title = {The remediation of marine sediments containing polycyclic aromatic hydrocarbons by peroxymonosulfate activated with Sphagnum moss-derived biochar and its benthic microbial ecology.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {341}, number = {}, pages = {122912}, doi = {10.1016/j.envpol.2023.122912}, pmid = {37956766}, issn = {1873-6424}, mesh = {*Sphagnopsida ; *Polycyclic Aromatic Hydrocarbons ; Peroxides ; Carbon ; Geologic Sediments/chemistry ; }, abstract = {This research was to study the efficiency of Sphagnum moss-derived biochar (SMBC) in removing polycyclic aromatic hydrocarbons (PAHs) from marine sediment using a peroxymonosulfate (PMS)-based carbon-advanced oxidation process (PMS-CAOPs). Sphagnum moss-derived biochar (SMBC) was generated via a simple thermochemical process for PMS activation toward enhancing decontamination of sediments. At pH 6, the SMBC/PMS system achieved a PAH removal efficiency exceeding 78% in 12 h reaction time. Moreover, PAHs of 6-, 5-, 4-, 3-, and 2-ring structures exhibited 98%, 74%, 68%, 85%, and 91%, of removal, respectively. The SMBC activation of PMS generated both radicals (SO4[•-] and HO•) and nonradical ([1]O2), species responsible for PAHs degradation, attributed primarily to inherent iron and carbon moieties. The significant PAHs degradation efficiency showcased by the SMBC/PMS process holds promise for augmenting the performance of indigenous benthic microbial activity in sediment treatment contexts. The response of sediment microbial communities to PAH-induced stress was particularly associated with the Proteobacteria phylum, specifically the Sulfurovum genus. The findings of the present study highlight the efficacy of environmentally benign reactive radical/nonradical-based PMS-CAOP using pristine carbon materials, offering a sustainable strategy for sediment treatment.}, }
@article {pmid37956735, year = {2024}, author = {Cohen, E and Azriel, S and Auster, O and Gal, A and Mikhlin, S and Crauwels, S and Rahav, G and Gal-Mor, O}, title = {A new Salmonella enterica serovar that was isolated from a wild sparrow presents a distinct genetic, metabolic and virulence profile.}, journal = {Microbes and infection}, volume = {26}, number = {3}, pages = {105249}, doi = {10.1016/j.micinf.2023.105249}, pmid = {37956735}, issn = {1769-714X}, mesh = {Animals ; Mice ; *Salmonella enterica/genetics ; Salmonella typhimurium/genetics ; Serogroup ; *Salmonella Infections, Animal/microbiology ; *Sparrows ; Virulence/genetics ; *Arsenic ; }, abstract = {Salmonella enterica is a ubiquitous and clinically-important bacterial pathogen, able to infect and cause different diseases in a wide range of hosts. Here, we report the isolation and characterization of a new S. enterica serovar (13,23:i:-; S. Tirat-Zvi), belonging to the Havana supper-lineage that was isolated from a wild house sparrow (Passer domesticus) in Israel. Whole genome sequencing and complete assembly of its genome indicated a plasmid-free, 4.7 Mb genome that carries the Salmonella pathogenicity islands 1-6, 9, 19 and an integrative and conjugative element (ICE), encoding arsenic resistance genes. Phenotypically, S. Tirat-Zvi isolate TZ282 was motile, readily formed biofilm, more versatile in carbon source utilization than S. Typhimurium and highly tolerant to arsenic, but impaired in host cell invasion. In-vivo infection studies indicated that while S. Tirat-Zvi was able to infect and cause an acute inflammatory enterocolitis in young chicks, it was compromised in mice colonization and did not cause an inflammatory colitis in mice compared to S. Typhimurium. We suggest that these phenotypes reflect the distinctive ecological niche of this new serovar and its evolutionary adaptation to passerine birds, as a permissive host. Moreover, these results further illuminate the genetic, phenotypic and ecological diversity of S. enterica pathovars.}, }
@article {pmid37956179, year = {2023}, author = {Sauters, TJC and Roth, C and Murray, D and Sun, S and Floyd Averette, A and Onyishi, CU and May, RC and Heitman, J and Magwene, PM}, title = {Amoeba predation of Cryptococcus: A quantitative and population genomic evaluation of the accidental pathogen hypothesis.}, journal = {PLoS pathogens}, volume = {19}, number = {11}, pages = {e1011763}, pmid = {37956179}, issn = {1553-7374}, support = {R01 AI039115/AI/NIAID NIH HHS/United States ; R01 AI050113/AI/NIAID NIH HHS/United States ; R01 AI133654/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Humans ; Mice ; *Amoeba/microbiology ; Metagenomics ; Predatory Behavior ; *Cryptococcus neoformans/genetics ; *Cryptococcosis/genetics/microbiology ; }, abstract = {The "Amoeboid Predator-Fungal Animal Virulence Hypothesis" posits that interactions with environmental phagocytes shape the evolution of virulence traits in fungal pathogens. In this hypothesis, selection to avoid predation by amoeba inadvertently selects for traits that contribute to fungal escape from phagocytic immune cells. Here, we investigate this hypothesis in the human fungal pathogens Cryptococcus neoformans and Cryptococcus deneoformans. Applying quantitative trait locus (QTL) mapping and comparative genomics, we discovered a cross-species QTL region that is responsible for variation in resistance to amoeba predation. In C. neoformans, this same QTL was found to have pleiotropic effects on melanization, an established virulence factor. Through fine mapping and population genomic comparisons, we identified the gene encoding the transcription factor Bzp4 that underlies this pleiotropic QTL and we show that decreased expression of this gene reduces melanization and increases susceptibility to amoeba predation. Despite the joint effects of BZP4 on amoeba resistance and melanin production, we find no relationship between BZP4 genotype and escape from macrophages or virulence in murine models of disease. Our findings provide new perspectives on how microbial ecology shapes the genetic architecture of fungal virulence, and suggests the need for more nuanced models for the evolution of pathogenesis that account for the complexities of both microbe-microbe and microbe-host interactions.}, }
@article {pmid37954239, year = {2023}, author = {Al-Khlifeh, E and Khadem, S and Hausmann, B and Berry, D}, title = {Microclimate shapes the phylosymbiosis of rodent gut microbiota in Jordan's Great Rift Valley.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1258775}, pmid = {37954239}, issn = {1664-302X}, abstract = {Host phylogeny and the environment play vital roles in shaping animal microbiomes. However, the effects of these variables on the diversity and richness of the gut microbiome in different bioclimatic zones remain underexplored. In this study, we investigated the effects of host phylogeny and bioclimatic zone on the diversity and composition of the gut microbiota of two heterospecific rodent species, the spiny mouse Acomys cahirinus and the house mouse Mus musculus, in three bioclimatic zones of the African Great Rift Valley (GRV). We confirmed host phylogeny using the D-loop sequencing method and analyzed the influence of host phylogeny and bioclimatic zone parameters on the rodent gut microbiome using high-throughput amplicon sequencing of 16S rRNA gene fragments. Phylogenetic analysis supported the morphological identification of the rodents and revealed a marked genetic difference between the two heterospecific species. We found that bioclimatic zone had a significant effect on the gut microbiota composition while host phylogeny did not. Microbial alpha diversity of heterospecific hosts was highest in the Mediterranean forest bioclimatic zone, followed by the Irano-Turanian shrubland, and was lowest in the Sudanian savanna tropical zone. The beta diversity of the two rodent species showed significant differences across the Mediterranean, Irano-Turanian, and Sudanian regions. The phyla Firmicutes and Bacteroidetes were highly abundant, and Deferribacterota, Cyanobacteria and Proteobacteria were also prominent. Amplicon sequence variants (ASVs) were identified that were unique to the Sudanian bioclimatic zone. The core microbiota families recovered in this study were consistent among heterospecific hosts. However, diversity decreased in conspecific host populations found at lower altitudes in Sudanian bioclimatic zone. The composition of the gut microbiota is linked to the adaptation of the host to its environment, and this study underscores the importance of incorporating climatic factors such as elevation and ambient temperature, in empirical microbiome research and is the first to describe the rodent gut microbiome from the GRV.}, }
@article {pmid37951257, year = {2024}, author = {Ye, J and Li, J and Li, L and Zhang, S and Chen, J and Zhu, D and Zhang, C and Xie, B and Zhang, B and Hou, K}, title = {Trends in global ambient fine particulate matter pollution and diabetes mortality rates attributable to it in the 1990-2019: 30 years systematic analysis of global burden of disease.}, journal = {The Science of the total environment}, volume = {908}, number = {}, pages = {168358}, doi = {10.1016/j.scitotenv.2023.168358}, pmid = {37951257}, issn = {1879-1026}, mesh = {Humans ; Particulate Matter ; Global Burden of Disease ; *Diabetes Mellitus/epidemiology ; Environmental Pollution ; Environmental Exposure ; *Air Pollution ; Quality-Adjusted Life Years ; }, abstract = {AIM: To analyze the trends in ambient fine particulate matter pollution (PM2.5) and the age-standardized mortality rate (ASMR) of diabetes attributable to it from 1990 to 2019 by region, country, and socio-economic development status.<br><br>METHODS: The main data, including the summary exposure value (SEV) of ambient PM2.5 and the ASMR of diabetes due to ambient PM2.5, was collected from the Global Burden of Disease 2019 database. The socio-demographic index (SDI) was employed for assessing a particular region or country's degree of socio-economic development. Joinpoint regression analysis was used to assess the changes of ambient PM2.5 and ASMR of diabetes attributable to it.<br><br>RESULTS: Globally, the SEV of ambient PM2.5 increased from 15.65&#xa0;&#x3bc;g/m[3] in 1990 to 26.22&#xa0;&#x3bc;g/m[3] in 2019, with an annual average percent change (AAPC) of 1.788 (95&#xa0;% CI 1.687-1.889) &#x3bc;g/m[3]. The ASMR of diabetes attributable to ambient PM2.5 increased from 1.57 per 100,000 population in 1990 to 2.47 per 100.000 population in 2019 (AAPC&#xa0;=&#xa0;1.569 [95&#xa0;% CI 1.42-1.718]). Most regions and countries had an increase of SEV of ambient PM2.5 and ASMR of diabetes attributable to ambient PM2.5. The largest increase of SEV of ambient PM2.5 was observed in South Asia (AAPC&#xa0;=&#xa0;3.556 [95&#xa0;% CI 3.329-3.875]), while the largest increase of ASMR of diabetes was in Central Asia (AAPC&#xa0;=&#xa0;5.170 [95%CI 4.696-5.647]). Moreover, the increase of SEV of ambient PM2.5 and ASMR of diabetes attributable to it were positively associated with SDI in low SDI countries (SDI&#xa0;<&#xa0;0.46), whereas the opposite result was observed when SDI&#xa0;&#x2265;&#xa0;0.46.<br><br>CONCLUSION: From 1990 to 2019, the population's exposure to ambient PM2.5 and ASMR of diabetes attributable to it increased generally, especially in low-middle SDI regions. Ambient PM2.5 remains a threat to global health. Greater investment in ambient PM2.5 and the mortality attributable to it are needed.}, }
@article {pmid37950563, year = {2023}, author = {White, A and Giannetto, M and Mulla, L and Del Rosario, A and Lim, T and Culver, E and Timmer, M and Bushell, J and Lambert, MR and Hernández-Gómez, O}, title = {Bacterial communities of the threatened Western Pond Turtle may be impacted by land use.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {12}, pages = {}, doi = {10.1093/femsec/fiad143}, pmid = {37950563}, issn = {1574-6941}, support = {//David H. Smith Postdoctoral Fellowship/ ; //Association of Zoos and Aquariums Saving Animals From Extinction Western Pond Turtle Range-wide Conservation Coalition Grant/ ; //Northern California Herpetological Society/ ; }, mesh = {Animals ; *Turtles/microbiology ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Fresh Water ; }, abstract = {As semi-aquatic species that use both terrestrial and aquatic habitats, freshwater turtles and their microbial communities are especially sensitive to the impacts of habitat disturbance. In this study, we use 16S rRNA amplicon sequencing to characterize the shell and cloacal bacterial communities of turtles in the San Francisco Bay Area. We captured western pond turtles (Actinemys/Emys marmorata) across eight sites located in urban and rural environments, along with invasive red-eared sliders (Trachemys scripta elegans). We assessed differences in western pond turtle bacterial communities diversity/composition between shell and cloacal samples and evaluated how alpha/beta diversity metrics were influenced by habitat quality. We found phylum-level bacterial taxonomic turnover in the bacterial communities of western pond turtles relative to the host tissue substrate samples. Our findings indicate that location identity elicits a high degree of lower-level (i.e. species/genus) bacterial taxonomic turnover. Further, we found that samples originating from good quality habitat had poorer shell bacterial communities but more diverse cloacal ones. The shell bacterial communities of red-eared sliders overlapped with those western pond turtles suggesting the existence of microbial dispersal between these two species. Our results add to our current understanding of turtle symbiont microbial ecology by establishing patterns of bacterial symbiont variation in an urban to rural gradient.}, }
@article {pmid37942081, year = {2023}, author = {Han, X and Beck, K and Bürgmann, H and Frey, B and Stierli, B and Frossard, A}, title = {Synthetic oligonucleotides as quantitative PCR standards for quantifying microbial genes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1279041}, pmid = {37942081}, issn = {1664-302X}, abstract = {Real-time quantitative PCR (qPCR) has been widely used to quantify gene copy numbers in microbial ecology. Despite its simplicity and straightforwardness, establishing qPCR assays is often impeded by the tedious process of producing qPCR standards by cloning the target DNA into plasmids. Here, we designed double-stranded synthetic DNA fragments from consensus sequences as qPCR standards by aligning microbial gene sequences (10-20 sequences per gene). Efficiency of standards from synthetic DNA was compared with plasmid standards by qPCR assays for different phylogenetic marker and functional genes involved in carbon (C) and nitrogen (N) cycling, tested with DNA extracted from a broad range of soils. Results showed that qPCR standard curves using synthetic DNA performed equally well to those from plasmids for all the genes tested. Furthermore, gene copy numbers from DNA extracted from soils obtained by using synthetic standards or plasmid standards were comparable. Our approach therefore demonstrates that a synthetic DNA fragment as qPCR standard provides comparable sensitivity and reliability to a traditional plasmid standard, while being more time- and cost-efficient.}, }
@article {pmid37941937, year = {2023}, author = {Zhang, H and Wei, T and Li, Q and Fu, L and He, L and Wang, Y}, title = {Metagenomic 16S rDNA reads of in situ preserved samples revealed microbial communities in the Yongle blue hole.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16257}, pmid = {37941937}, issn = {2167-8359}, mesh = {DNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Water ; *Microbiota/genetics ; Sulfates ; }, abstract = {Our knowledge on biogeochemistry and microbial ecology of marine blue holes is limited due to challenges in collecting multilayered water column and oxycline zones. In this study, we collected samples from 16 water layers in Yongle blue hole (YBH) located in the South China Sea using the in situ microbial filtration and fixation (ISMIFF) apparatus. The microbial communities based on 16S rRNA metagenomic reads for the ISMIFF samples showed high microbial diversity and consistency among samples with similar dissolved oxygen levels. At the same depth of the anoxic layer, the ISMIFF samples were dominated by sulfate-reducing bacteria from Desulfatiglandales (17.96%). The sulfide concentration is the most significant factor that drives the division of microbial communities in YBH, which might support the prevalence of sulfate-reducing microorganisms in the anoxic layers. Our results are different from the microbial community structures of a Niskin sample of this study and the reported samples collected in 2017, in which a high relative abundance of Alteromonadales (26.59%) and Thiomicrospirales (38.13%), and Arcobacteraceae (11.74%) was identified. We therefore demonstrate a new profile of microbial communities in YBH probably due to the effect of sampling and molecular biological methods, which provides new possibilities for further understanding of the material circulation mechanism of blue holes and expanding anoxic marine water zones under global warming.}, }
@article {pmid37941395, year = {2022}, author = {Blumberg, K and Miller, M and Ponsero, A and Hurwitz, B}, title = {Ontology-driven analysis of marine metagenomics: what more can we learn from our data?.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {37941395}, issn = {2047-217X}, mesh = {*Ecology ; *Microbiota/genetics ; Metagenome ; Metagenomics ; }, abstract = {BACKGROUND: The proliferation of metagenomic sequencing technologies has enabled novel insights into the functional genomic potentials and taxonomic structure of microbial communities. However, cyberinfrastructure efforts to manage and enable the reproducible analysis of sequence data have not kept pace. Thus, there is increasing recognition of the need to make metagenomic data discoverable within machine-searchable frameworks compliant with the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles for data stewardship. Although a variety of metagenomic web services exist, none currently leverage the hierarchically structured terminology encoded within common life science ontologies to programmatically discover data.<br><br>RESULTS: Here, we integrate large-scale marine metagenomic datasets with community-driven life science ontologies into a novel FAIR web service. This approach enables the retrieval of data discovered by intersecting the knowledge represented within ontologies against the functional genomic potential and taxonomic structure computed from marine sequencing data. Our findings highlight various microbial functional and taxonomic patterns relevant to the ecology of prokaryotes in various aquatic environments.<br><br>CONCLUSIONS: In this work, we present and evaluate a novel Semantic Web architecture that can be used to ask novel biological questions of existing marine metagenomic datasets. Finally, the FAIR ontology searchable data products provided by our API can be leveraged by future research efforts.}, }
@article {pmid37938301, year = {2022}, author = {McDaniel, EA and van Steenbrugge, JJM and Noguera, DR and McMahon, KD and Raaijmakers, JM and Medema, MH and Oyserman, BO}, title = {TbasCO: trait-based comparative 'omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {111}, pmid = {37938301}, issn = {2730-6151}, support = {MCB-1518130//National Science Foundation (NSF)/ ; MCB-1518130//National Science Foundation (NSF)/ ; }, abstract = {A grand challenge in microbial ecology is disentangling the traits of individual populations within complex communities. Various cultivation-independent approaches have been used to infer traits based on the presence of marker genes. However, marker genes are not linked to traits with complete fidelity, nor do they capture important attributes, such as the timing of gene expression or coordination among traits. To address this, we present an approach for assessing the trait landscape of microbial communities by statistically defining a trait attribute as a shared transcriptional pattern across multiple organisms. Leveraging the KEGG pathway database as a trait library and the Enhanced Biological Phosphorus Removal (EBPR) model microbial ecosystem, we demonstrate that a majority (65%) of traits present in 10 or more genomes have niche-differentiating expression attributes. For example, while many genomes containing high-affinity phosphorus transporter pstABCS display a canonical attribute (e.g. up-regulation under phosphorus starvation), we identified another attribute shared by many genomes where transcription was highest under high phosphorus conditions. Taken together, we provide a novel framework for unravelling the functional dynamics of uncultivated microorganisms by assigning trait-attributes through genome-resolved time-series metatranscriptomics.}, }
@article {pmid37934729, year = {2023}, author = {Vasileiou, D and Karapiperis, C and Baltsavia, I and Chasapi, A and Ahrén, D and Janssen, PJ and Iliopoulos, I and Promponas, VJ and Enright, AJ and Ouzounis, CA}, title = {CGG toolkit: Software components for computational genomics.}, journal = {PLoS computational biology}, volume = {19}, number = {11}, pages = {e1011498}, pmid = {37934729}, issn = {1553-7358}, mesh = {Reproducibility of Results ; *Genomics/methods ; *Software ; Computational Biology/methods ; Genome ; }, abstract = {Public-domain availability for bioinformatics software resources is a key requirement that ensures long-term permanence and methodological reproducibility for research and development across the life sciences. These issues are particularly critical for widely used, efficient, and well-proven methods, especially those developed in research settings that often face funding discontinuities. We re-launch a range of established software components for computational genomics, as legacy version 1.0.1, suitable for sequence matching, masking, searching, clustering and visualization for protein family discovery, annotation and functional characterization on a genome scale. These applications are made available online as open source and include MagicMatch, GeneCAST, support scripts for CoGenT-like sequence collections, GeneRAGE and DifFuse, supported by centrally administered bioinformatics infrastructure funding. The toolkit may also be conceived as a flexible genome comparison software pipeline that supports research in this domain. We illustrate basic use by examples and pictorial representations of the registered tools, which are further described with appropriate documentation files in the corresponding GitHub release.}, }
@article {pmid37934609, year = {2023}, author = {Qiao, N and Gaur, G and Modesto, M and Chinnici, F and Scarafile, D and Borruso, L and Marin, AC and Spiezio, C and Valente, D and Sandri, C and Gänzle, MG and Mattarelli, P}, title = {Physiological and genomic characterization of Lactiplantibacillus plantarum isolated from Indri indri in Madagascar.}, journal = {Journal of applied microbiology}, volume = {134}, number = {11}, pages = {}, doi = {10.1093/jambio/lxad255}, pmid = {37934609}, issn = {1365-2672}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; //Canada Research Chairs/ ; //China Scholarship Council/ ; }, mesh = {Animals ; *Indriidae/metabolism ; Madagascar ; Coumaric Acids/metabolism ; *Lactobacillus plantarum/genetics/metabolism ; Genomics ; *Anti-Infective Agents/metabolism ; }, abstract = {AIMS: Indri indri is a lemur of Madagascar which is critically endangered. The analysis of the microbial ecology of the intestine offers tools to improve conservation efforts. This study aimed to achieve a functional genomic analysis of three Lactiplantibacillus plantarum isolates from indris.<br><br>METHODS AND RESULTS: Samples were obtained from 18 indri; 3 isolates of Lp. plantarum were obtained from two individuals. The three isolates were closely related to each other, with <10 single nucleotide polymorphisms, suggesting that the two individuals shared diet-associated microbes. The genomes of the three isolates were compared to 96 reference strains of Lp. plantarum. The three isolates of Lp. plantarum were not phenotypically resistant to antibiotics but shared all 17 genes related to antimicrobial resistance that are part of the core genome of Lp. plantarum. The genomes of the three indri isolates of Lp. plantarum also encoded for the 6 core genome genes coding for enzymes related to metabolism of hydroxybenzoic and hydroxycinnamic acids. The phenotype for metabolism of hydroxycinnamic acids by indri isolates of Lp. plantarum matched the genotype.<br><br>CONCLUSIONS: Multiple antimicrobial resistance genes and gene coding for metabolism of phenolic compounds were identified in the genomes of the indri isolates, suggesting that Lp. plantarum maintains antimicrobial resistance in defense of antimicrobial plant secondary pathogens and that their metabolism by intestinal bacteria aids digestion of plant material by primate hosts.}, }
@article {pmid37933257, year = {2023}, author = {Ochoa-Sánchez, M and Acuña Gomez, EP and Moreno, L and Moraga, CA and Gaete, K and Eguiarte, LE and Souza, V}, title = {Body site microbiota of Magellanic and king penguins inhabiting the Strait of Magellan follow species-specific patterns.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16290}, pmid = {37933257}, issn = {2167-8359}, mesh = {Animals ; *Spheniscidae ; RNA, Ribosomal, 16S ; *Microbiota ; Soil ; }, abstract = {Animal hosts live in continuous interaction with bacterial partners, yet we still lack a clear understanding of the ecological drivers of animal-associated bacteria, particularly in seabirds. Here, we investigated the effect of body site in the structure and diversity of bacterial communities of two seabirds in the Strait of Magellan: the Magellanic penguin (Spheniscus magellanicus) and the king penguin (Aptenodytes patagonicus). We used 16S rRNA gene sequencing to profile bacterial communities associated with body sites (chest, back, foot) of both penguins and the nest soil of Magellanic penguin. Taxonomic composition showed that Moraxellaceae family (specifically Psychrobacter) had the highest relative abundance across body sites in both penguin species, whereas Micrococacceae had the highest relative abundance in nest soil. We were able to detect a bacterial core among 90% of all samples, which consisted of Clostridium sensu stricto and Micrococcacea taxa. Further, the king penguin had its own bacterial core across its body sites, where Psychrobacter and Corynebacterium were the most prevalent taxa. Microbial alpha diversity across penguin body sites was similar in most comparisons, yet we found subtle differences between foot and chest body sites of king penguins. Body site microbiota composition differed across king penguin body sites, whereas it remained similar across Magellanic penguin body sites. Interestingly, all Magellanic penguin body site microbiota composition differed from nest soil microbiota. Finally, bacterial abundance in penguin body sites fit well under a neutral community model, particularly in the king penguin, highlighting the role of stochastic process and ecological drift in microbiota assembly of penguin body sites. Our results represent the first report of body site bacterial communities in seabirds specialized in subaquatic foraging. Thus, we believe it represents useful baseline information that could serve for long-term comparisons that use marine host microbiota to survey ocean health.}, }
@article {pmid37932283, year = {2023}, author = {Simpson, AC and Sengupta, P and Zhang, F and Hameed, A and Parker, CW and Singh, NK and Miliotis, G and Rekha, PD and Raman, K and Mason, CE and Venkateswaran, K}, title = {Phylogenomics, phenotypic, and functional traits of five novel (Earth-derived) bacterial species isolated from the International Space Station and their prevalence in metagenomes.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {19207}, pmid = {37932283}, issn = {2045-2322}, support = {R01 MH117406/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Prevalence ; Phenotype ; *Paenibacillus/genetics ; Fatty Acids/analysis ; DNA ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Bacterial Typing Techniques ; }, abstract = {With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habitats, and how microbes survive, proliferate and spread in space conditions, is becoming more important. The microbial tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-stain-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the ISS. The analysis of their 16S rRNA gene sequences revealed > 99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing was undertaken. For all strains, the gyrB gene exhibited < 93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average nucleotide identity and digital DNA-DNA hybridization values, when compared to any known bacterial species, were < 94% and <50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including β-lactone and type III polyketide synthase (T3PKS) clusters. Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10[T] (= NRRL B-65660[T] = DSM 115933[T]), Leifsonia virtsii F6_8S_P_1A[T] (= NRRL B-65661[T] = DSM 115931[T]), Leifsonia williamsii F6_8S_P_1B[T] (= NRRL B-65662[T] = DSM 115932[T]), Paenibacillus vandeheii F6_3S_P_1C[T] (= NRRL B-65663[T] = DSM 115940[T]), and Sporosarcina highlanderae F6_3S_P_2[T] (= NRRL B-65664[T] = DSM 115943[T]). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.}, }
@article {pmid37931689, year = {2024}, author = {Álvarez-Pérez, S and Lievens, B and de Vega, C}, title = {Floral nectar and honeydew microbial diversity and their role in biocontrol of insect pests and pollination.}, journal = {Current opinion in insect science}, volume = {61}, number = {}, pages = {101138}, doi = {10.1016/j.cois.2023.101138}, pmid = {37931689}, issn = {2214-5753}, mesh = {Animals ; *Plant Nectar ; *Pollination ; Insecta ; Carbohydrates ; Ecosystem ; }, abstract = {Sugar-rich plant-related secretions, such as floral nectar and honeydew, that are commonly used as nutrient sources by insects and other animals, are also the ecological niche for diverse microbial communities. Recent research has highlighted the great potential of nectar and honeydew microbiomes in biological pest control and improved pollination, but the exploitation of these microbiomes requires a deep understanding of their community dynamics and plant-microbe-insect interactions. Additionally, the successful application of microbes in crop fields is conditioned by diverse ecological, legal, and ethical challenges that should be taken into account. In this article, we provide an overview of the nectar and honeydew microbiomes and discuss their potential applications in sustainable agricultural practices.}, }
@article {pmid37931135, year = {2023}, author = {Naik, AT and Kamensky, KM and Hellum, AM and Moisander, PH}, title = {Disturbance frequency directs microbial community succession in marine biofilms exposed to shear.}, journal = {mSphere}, volume = {8}, number = {6}, pages = {e0024823}, pmid = {37931135}, issn = {2379-5042}, support = {N00014220-1-2170//DOD | USN | Office of Naval Research (ONR)/ ; Multi-Institutional Collaborative Seed Funding//University of Massachusetts Dartmouth (UMD)/ ; N00014-16-1-3051//Michigan State University (MSU)/ ; }, mesh = {*Biofilms ; *Microbiota ; Prokaryotic Cells ; }, abstract = {Disturbances are major drivers of community succession in many microbial systems; however, relatively little is known about marine biofilm community succession, especially under antifouling disturbance. Antifouling technologies exert strong local disturbances on marine biofilms, and resulting biomass losses can be accompanied by shifts in biofilm community composition and succession. We address this gap in knowledge by bridging microbial ecology with antifouling technology development. We show that disturbance by shear can strongly alter marine biofilm community succession, acting as a selective filter influenced by frequency of exposure. Examining marine biofilm succession patterns with and without shear revealed stable associations between key prokaryotic and eukaryotic taxa, highlighting the importance of cross-domain assessment in future marine biofilm research. Describing how compounded top-down and bottom-up disturbances shape the succession of marine biofilms is valuable for understanding the assembly and stability of these complex microbial communities and predicting species invasiveness.}, }
@article {pmid37926855, year = {2023}, author = {Minnebo, Y and Delbaere, K and Goethals, V and Raes, J and Van de Wiele, T and De Paepe, K}, title = {Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {240}, pmid = {37926855}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Butyrates/metabolism ; Nutrients ; Fermentation ; Carbohydrates ; Feces/microbiology ; }, abstract = {BACKGROUND: Transit time is an important modulator of the human gut microbiome. The inability to modify transit time as the sole variable hampers mechanistic in vivo microbiome research. We singled out gut transit time in an unprecedented in vitro approach by subjecting faecal microbial communities from six individuals with either short, medium or long in vivo transit times, to three different colonic transit times of 21, 32 and 63 h in the validated human gut in vitro model, SHIME.<br><br>RESULTS: Transit time was identified as the single most important driver of microbial cell concentrations (52%), metabolic activity (45%) and quantitative (24%) and proportional (22%) community composition. Deceleration of transit was characterised by a significant decrease of specific Bifidobacterium and Veillonella spp. and increase of specific fibre degrading bacteria and nutrient specialists, such as Bacteroides, Prevotella, Ruminococcus, Bilophila and Akkermansia spp. These microbial communities reached a higher population density and net carbohydrate fermentation, leading to an increased SCFA production at longer transit times. In contrast, the carbohydrate-to-biomass production efficiency was increased at shorter transits, particularly in well-adapted faecal microbiomes from donors with short in vivo transit. Said adaptation was also reflected in the carbohydrate-to-SCFA conversion efficiency which varied with donor, but also colon region and SCFA chain length. A long transit time promoted propionate production, whereas butyrate production and butyrate producers were selectively enriched in the proximal colon at medium transit time.<br><br>CONCLUSION: Microbial growth rates and nutrient utilisation efficiency mediate the species-specific gut microbiota response to in vitro transit time variation, which is the main driver of in vitro microbial load, metabolism and community composition. Given the in vivo transit time variation within and between individuals, the personalisation of in vitro transit time based on in vivo data is required to accurately study intra- and inter-individual differences in gut microbiome structure, functionality and interactions with host and environmental modulators. Video Abstract.}, }
@article {pmid37925991, year = {2023}, author = {Chen, C and Li, P and Yin, M and Wang, J and Sun, Y and Ju, W and Liu, L and Li, ZH}, title = {Deciphering characterization of seasonal variations in microbial communities of marine ranching: Diversity, co-occurrence network patterns, and assembly processes.}, journal = {Marine pollution bulletin}, volume = {197}, number = {}, pages = {115739}, doi = {10.1016/j.marpolbul.2023.115739}, pmid = {37925991}, issn = {1879-3363}, mesh = {Seasons ; *Microbiota ; Temperature ; Microbial Consortia ; Bacteria ; }, abstract = {Offshore coastal marine ranching ecosystems are one of the most productive ecosystems. The results showed that the composition and structure of the microbial communities varied considerably with the season. Co-occurrence network analysis demonstrated that the microbial network was more complex in summer and positively correlated links (cooperative or symbiotic) were dominated in autumn and winter. Null model indicated that the ecological processes of the bacterial communities were mainly governed by deterministic processes (mainly homogeneous selection) in summer. For microeukaryotic communities, assembly processes were more regulated by stochastic processes in all seasons. For rare taxa, assembly processes were regulated by stochastic processes and were not affected by seasonality. Changes in water temperature due to seasonal variations were the main, but not the only, environmental factor driving changes in microbial communities. This study will improve the understanding of offshore coastal ecosystems through the perspective of microbial ecology.}, }
@article {pmid37925029, year = {2024}, author = {Ghosh, A and Yash,  and Kumar, C and Bhadury, P}, title = {Cascading effects of trace metals enrichment on phytoplankton communities of the River Ganga in South Asia.}, journal = {Chemosphere}, volume = {347}, number = {}, pages = {140607}, doi = {10.1016/j.chemosphere.2023.140607}, pmid = {37925029}, issn = {1879-1298}, mesh = {Phytoplankton ; Rivers ; Ecosystem ; Asia, Southern ; *Arsenic/toxicity ; *Diatoms ; *Trace Elements/pharmacology ; Iron/pharmacology ; }, abstract = {Globally freshwater ecosystems and associated biota including phytoplankton communities are at extreme risk from trace metal pollution originating from geogenic as well as from anthropogenic sources such as release of untreated industrial effluents. In the present study influence of iron- and arsenic-enrichments on structure and metabolism of phytoplankton communities of River Ganga, one of the largest rivers of South Asia, was assessed under laboratory-based microcosm experiments. Surface water samples were collected and subsequently enriched with higher than recommended concentrations of iron (10 mg/L) and arsenic (10 μg/L). The set-up comprised of nine containers of 25 L volume with three containers each for iron- and arsenic-enrichment and was maintained for 30 days. Trace metal enrichment rapidly changed the phytoplankton community structure and chemistry of nutrients uptake. Iron-enrichment prompted diatom blooms comprising of Thalassiosira, succeeded by green algae Coelastrum. Arsenic-enrichment maintained cyanobacteria for longer time-spans compared to the control and iron-enriched containers but significantly lesser abundance of diatoms. Variations in community composition was also reflected in nutrient uptake rates with silicate release in the arsenic-enriched containers at the end of the experiment. Changes in macronutrient dynamics also altered genus growth rates wherein both iron- and arsenic appeared to lower the death rate of Thalassosira but stimulated growth of other genera including Skeletonema and Pandorina. Iron appeared to influence lesser number of genera compared to arsenic which altered growth rates of both diatoms and green algae. This consequently influenced the gross primary productivity values which lowered both in the iron- and arsenic-enriched containers compared to the control owing to decrease in phytoplankton diversity. Iron appeared to drive phytoplankton communities toward a less general and more specialized composition with high abundance of selective species comprising of small diatoms such as Thalassiosira, whereas arsenic appears to select for green algal enrichment in freshwater ecosystems.}, }
@article {pmid37920817, year = {2023}, author = {Talavera-Marcos, S and Parras-Moltó, M and Aguirre de Cárcer, D}, title = {Leveraging phylogenetic signal to unravel microbiome function and assembly rules.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {5165-5173}, pmid = {37920817}, issn = {2001-0370}, abstract = {Clarifying the general rules behind microbial community assembly will foster the development of microbiome-based technological solutions. Here, we study microbial community assembly through a computational analysis of phylogenetic core groups (PCGs): discrete portions of the bacterial phylogeny with high prevalence in the ecosystem under study. We first show that the existence of PCGs was a predominant feature of the varied set of microbial ecosystems studied. Then, we re-analyzed an in vitro experimental dataset using a PCG-based approach, drawing only from its community composition data and from publicly available genomic databases. Using mainly genome scale metabolic models and population dynamics modeling, we obtained ecological insights on metabolic niche structure and population dynamics comparable to those gained after canonical experimentation. Thus, leveraging phylogenetic signal to help unravel microbiome function and assembly rules offers a potential avenue to gain further insight on Earth's microbial ecosystems.}, }
@article {pmid37920261, year = {2023}, author = {Poirier, S and Coeuret, G and Champomier-Vergès, MC and Desmonts, MH and Werner, D and Feurer, C and Frémaux, B and Guillou, S and Luong, NM and Rué, O and Loux, V and Zagorec, M and Chaillou, S and , }, title = {Holistic integration of omics data reveals the drivers that shape the ecology of microbial meat spoilage scenarios.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1286661}, pmid = {37920261}, issn = {1664-302X}, abstract = {BACKGROUND: The use of omics data for monitoring the microbial flow of fresh meat products along a production line and the development of spoilage prediction tools from these data is a promising but challenging task. In this context, we produced a large multivariate dataset (over 600 samples) obtained on the production lines of two similar types of fresh meat products (poultry and raw pork sausages). We describe a full analysis of this dataset in order to decipher how the spoilage microbial ecology of these two similar products may be shaped differently depending on production parameter characteristics.<br><br>METHODS: Our strategy involved a holistic approach to integrate unsupervised and supervised statistical methods on multivariate data (OTU-based microbial diversity; metabolomic data of volatile organic compounds; sensory measurements; growth parameters), and a specific selection of potential uncontrolled (initial microbiota composition) or controlled (packaging type; lactate concentration) drivers.<br><br>RESULTS: Our results demonstrate that the initial microbiota, which is shown to be very different between poultry and pork sausages, has a major impact on the spoilage scenarios and on the effect that a downstream parameter such as packaging type has on the overall evolution of the microbial community. Depending on the process, we also show that specific actions on the pork meat (such as deboning and defatting) elicit specific food spoilers such as Dellaglioa algida, which becomes dominant during storage. Finally, ecological network reconstruction allowed us to map six different metabolic pathways involved in the production of volatile organic compounds involved in spoilage. We were able connect them to the different bacterial actors and to the influence of packaging type in an overall view. For instance, our results demonstrate a new role of Vibrionaceae in isopropanol production, and of Latilactobacillus fuchuensis and Lactococcus piscium in methanethiol/disylphide production. We also highlight a possible commensal behavior between Leuconostoc carnosum and Latilactobacillus curvatus around 2,3-butanediol metabolism.<br><br>CONCLUSION: We conclude that our holistic approach combined with large-scale multi-omic data was a powerful strategy to prioritize the role of production parameters, already known in the literature, that shape the evolution and/or the implementation of different meat spoilage scenarios.}, }
@article {pmid37920009, year = {2023}, author = {Yuan, X and Song, W and Li, Y and Wang, Q and Qing, J and Zhi, W and Han, H and Qin, Z and Gong, H and Hou, G and Li, Y}, title = {Using Bayesian networks with tabu algorithm to explore factors related to chronic kidney disease with mental illness: A cross-sectional study.}, journal = {Mathematical biosciences and engineering : MBE}, volume = {20}, number = {9}, pages = {16194-16211}, doi = {10.3934/mbe.2023723}, pmid = {37920009}, issn = {1551-0018}, mesh = {Humans ; Cross-Sectional Studies ; Bayes Theorem ; Algorithms ; *Renal Insufficiency, Chronic/epidemiology ; *Mental Disorders/epidemiology ; }, abstract = {While Bayesian networks (BNs) offer a promising approach to discussing factors related to many diseases, little attention has been poured into chronic kidney disease with mental illness (KDMI) using BNs. This study aimed to explore the complex network relationships between KDMI and its related factors and to apply Bayesian reasoning for KDMI, providing a scientific reference for its prevention and treatment. Data was downloaded from the online open database of CHARLS 2018, a population-based longitudinal survey. Missing values were first imputed using Random Forest, followed by propensity score matching (PSM) for class balancing regarding KDMI. Elastic Net was then employed for variable selection from 18 variables. Afterwards, the remaining variables were included in BNs model construction. Structural learning of BNs was achieved using tabu algorithm and the parameter learning was conducted using maximum likelihood estimation. After PSM, 427 non-KDMI cases and 427 KDMI cases were included in this study. Elastic Net identified 11 variables significantly associated with KDMI. The BNs model comprised 12 nodes and 24 directed edges. The results suggested that diabetes, physical activity, education levels, sleep duration, social activity, self-report on health and asset were directly related factors for KDMI, whereas sex, age, residence and Internet access represented indirect factors for KDMI. BN model not only allows for the exploration of complex network relationships between related factors and KDMI, but also could enable KDMI risk prediction through Bayesian reasoning. This study suggests that BNs model holds great prospects in risk factor detection for KDMI.}, }
@article {pmid37919394, year = {2023}, author = {Dougherty, PE and Nielsen, TK and Riber, L and Lading, HH and Forero-Junco, LM and Kot, W and Raaijmakers, JM and Hansen, LH}, title = {Widespread and largely unknown prophage activity, diversity, and function in two genera of wheat phyllosphere bacteria.}, journal = {The ISME journal}, volume = {17}, number = {12}, pages = {2415-2425}, pmid = {37919394}, issn = {1751-7370}, support = {NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 801199//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; }, mesh = {*Prophages/genetics ; *Triticum ; Bacteria/genetics ; }, abstract = {Environmental bacteria host an enormous number of prophages, but their diversity and natural functions remain largely elusive. Here, we investigate prophage activity and diversity in 63 Erwinia and Pseudomonas strains isolated from flag leaves of wheat grown in a single field. Introducing and validating Virion Induction Profiling Sequencing (VIP-Seq), we identify and quantify the activity of 120 spontaneously induced prophages, discovering that some phyllosphere bacteria produce more than 10[8] virions/mL in overnight cultures, with significant induction also observed in planta. Sequence analyses and plaque assays reveal E. aphidicola prophages contribute a majority of intraspecies genetic diversity and divide their bacterial hosts into antagonistic factions engaged in widespread microbial warfare, revealing the importance of prophage-mediated microdiversity. When comparing spontaneously active prophages with predicted prophages we also find insertion sequences are strongly correlated with non-active prophages. In conclusion, we discover widespread and largely unknown prophage diversity and function in phyllosphere bacteria.}, }
@article {pmid37914532, year = {2023}, author = {Ray, AE and Tribbia, DZ and Cowan, DA and Ferrari, BC}, title = {Clearing the air: unraveling past and guiding future research in atmospheric chemosynthesis.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {87}, number = {4}, pages = {e0004823}, pmid = {37914532}, issn = {1098-5557}, support = {FT170100341, DP220103430//Department of Education and Training | Australian Research Council (ARC)/ ; 4406//Department of the Environment and Energy | Australian Antarctic Division (AAD)/ ; }, mesh = {*Carbon Monoxide/metabolism ; *Gases ; Hydrogen/metabolism ; Soil ; Methane/metabolism ; Water ; }, abstract = {Atmospheric chemosynthesis is a recently proposed form of chemoautotrophic microbial primary production. The proposed process relies on the oxidation of trace concentrations of hydrogen (≤530 ppbv), carbon monoxide (≤90 ppbv), and methane (≤1,870 ppbv) gases using high-affinity enzymes. Atmospheric hydrogen and carbon monoxide oxidation have been primarily linked to microbial growth in desert surface soils scarce in liquid water and organic nutrients, and low in photosynthetic communities. It is well established that the oxidation of trace hydrogen and carbon monoxide gases widely supports the persistence of microbial communities in a diminished metabolic state, with the former potentially providing a reliable source of metabolic water. Microbial atmospheric methane oxidation also occurs in oligotrophic desert soils and is widespread throughout copiotrophic environments, with established links to microbial growth. Despite these findings, the direct link between trace gas oxidation and carbon fixation remains disputable. Here, we review the supporting evidence, outlining major gaps in our understanding of this phenomenon, and propose approaches to validate atmospheric chemosynthesis as a primary production process. We also explore the implications of this minimalistic survival strategy in terms of nutrient cycling, climate change, aerobiology, and astrobiology.}, }
@article {pmid37914126, year = {2024}, author = {Abkar, L and Moghaddam, HS and Fowler, SJ}, title = {Microbial ecology of drinking water from source to tap.}, journal = {The Science of the total environment}, volume = {908}, number = {}, pages = {168077}, doi = {10.1016/j.scitotenv.2023.168077}, pmid = {37914126}, issn = {1879-1026}, mesh = {*Drinking Water/analysis ; Water Supply ; *Water Purification/methods ; Sanitary Engineering ; Public Health ; Water Microbiology ; }, abstract = {As drinking water travels from its source, through various treatment processes, hundreds to thousands of kilometres of distribution network pipes, to the taps in private homes and public buildings, it is exposed to numerous environmental changes, as well as other microbes living in both water and on surfaces. This review aims to identify the key locations and factors that are associated with changes in the drinking water microbiome throughout conventional urban drinking water systems from the source to the tap water. Over the past 15 years, improvements in cultivation-independent methods have enabled studies that allow us to answer such questions. As a result, we are beginning to move towards predicting the impacts of disturbances and interventions resulting ultimately in management of drinking water systems and microbial communities rather than mere observation. Many challenges still exist to achieve effective management, particularly within the premise plumbing environment, which exhibits diverse and inconsistent conditions that may lead to alterations in the microbiota, potentially presenting public health risks. Finally, we recommend the establishment of global collaborative projects on the drinking water microbiome that will enhance our current knowledge and lead to tools for operators and researchers alike to improve global access to high-quality drinking water.}, }
@article {pmid37909775, year = {2023}, author = {Mason, G and Footer, MJ and Rojas, ER}, title = {Mechanosensation induces persistent bacterial growth during bacteriophage predation.}, journal = {mBio}, volume = {14}, number = {6}, pages = {e0276622}, pmid = {37909775}, issn = {2150-7511}, support = {R35 GM143057/GM/NIGMS NIH HHS/United States ; 5R35GM143057-02//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {*Escherichia coli/virology/growth &amp; development ; *Bacteriophages/physiology/growth &amp; development ; }, abstract = {Bacteria and bacteriophage form one of the most important predator-prey relationships on earth, yet how the long-term stability of this ecological interaction is achieved is unclear. Here, we demonstrate that Escherichia coli can rapidly grow during bacteriophage predation if they are doing so in spatially confined environments. This discovery revises our understanding of bacteria-bacteriophage population dynamics in many real-world environments where bacteria grow in confinement, such as the gut and the soil. Additionally, this result has clear implications for the potential of bacteriophage therapy and the role of mechanosensation during bacterial pathogenesis.}, }
@article {pmid37909659, year = {2024}, author = {Quiroga, MV and Stegen, JC and Mataloni, G and Cowan, D and Lebre, PH and Valverde, A}, title = {Microdiverse bacterial clades prevail across Antarctic wetlands.}, journal = {Molecular ecology}, volume = {33}, number = {1}, pages = {e17189}, doi = {10.1111/mec.17189}, pmid = {37909659}, issn = {1365-294X}, support = {PICT 2016-2517//ANPCyT - Argentina/ ; PICT 2020-3113//ANPCyT - Argentina/ ; //European Union/ ; //Instituto Ant&#xe1;rtico Argentino - Direcci&#xf3;n Nacional del Ant&#xe1;rtico/ ; CLU-2019-05 IRNASA/CSIC//Junta de Castilla y Le&#xf3;n/ ; //NRF - South Africa/ ; Contract DE-AC05-76RL01830 -JCS//U.S. Department of Energy-BER program/ ; }, mesh = {Phylogeny ; Antarctic Regions ; *Wetlands ; Bacteria/genetics ; *Microbiota ; }, abstract = {Antarctica's extreme environmental conditions impose selection pressures on microbial communities. Indeed, a previous study revealed that bacterial assemblages at the Cierva Point Wetland Complex (CPWC) are shaped by strong homogeneous selection. Yet which bacterial phylogenetic clades are shaped by selection processes and their ecological strategies to thrive in such extreme conditions remain unknown. Here, we applied the phyloscore and feature-level βNTI indexes coupled with phylofactorization to successfully detect bacterial monophyletic clades subjected to homogeneous (HoS) and heterogenous (HeS) selection. Remarkably, only the HoS clades showed high relative abundance across all samples and signs of putative microdiversity. The majority of the amplicon sequence variants (ASVs) within each HoS clade clustered into a unique 97% sequence similarity operational taxonomic unit (OTU) and inhabited a specific environment (lotic, lentic or terrestrial). Our findings suggest the existence of microdiversification leading to sub-taxa niche differentiation, with putative distinct ecotypes (consisting of groups of ASVs) adapted to a specific environment. We hypothesize that HoS clades thriving in the CPWC have phylogenetically conserved traits that accelerate their rate of evolution, enabling them to adapt to strong spatio-temporally variable selection pressures. Variable selection appears to operate within clades to cause very rapid microdiversification without losing key traits that lead to high abundance. Variable and homogeneous selection, therefore, operate simultaneously but on different aspects of organismal ecology. The result is an overall signal of homogeneous selection due to rapid within-clade microdiversification caused by variable selection. It is unknown whether other systems experience this dynamic, and we encourage future work evaluating the transferability of our results.}, }
@article {pmid37903921, year = {2023}, author = {Jansson, JK and McClure, R and Egbert, RG}, title = {Soil microbiome engineering for sustainability in a changing environment.}, journal = {Nature biotechnology}, volume = {41}, number = {12}, pages = {1716-1728}, pmid = {37903921}, issn = {1546-1696}, mesh = {*Soil ; *Microbiota/genetics ; Soil Microbiology ; Synthetic Biology ; Biotechnology ; }, abstract = {Recent advances in microbial ecology and synthetic biology have the potential to mitigate damage caused by anthropogenic activities that are deleteriously impacting Earth's soil ecosystems. Here, we discuss challenges and opportunities for harnessing natural and synthetic soil microbial communities, focusing on plant growth promotion under different scenarios. We explore current needs for microbial solutions in soil ecosystems, how these solutions are being developed and applied, and the potential for new biotechnology breakthroughs to tailor and target microbial products for specific applications. We highlight several scientific and technological advances in soil microbiome engineering, including characterization of microbes that impact soil ecosystems, directing how microbes assemble to interact in soil environments, and the developing suite of gene-engineering approaches. This Review underscores the need for an interdisciplinary approach to understand the composition, dynamics and deployment of beneficial soil microbiomes to drive efforts to mitigate or reverse environmental damage by restoring and protecting healthy soil ecosystems.}, }
@article {pmid37902333, year = {2023}, author = {van der Meij, A and Elsayed, SS and Du, C and Willemse, J and Wood, TM and Martin, NI and Raaijmakers, JM and van Wezel, GP}, title = {The plant stress hormone jasmonic acid evokes defensive responses in streptomycetes.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {11}, pages = {e0123923}, pmid = {37902333}, issn = {1098-5336}, support = {14221//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; }, mesh = {*Plant Growth Regulators ; *Amino Acids ; Anti-Bacterial Agents ; Hormones ; }, abstract = {Microorganisms that live on or inside plants can influence plant growth and health. Among the plant-associated bacteria, streptomycetes play an important role in defense against plant diseases, but the underlying mechanisms are not well understood. Here, we demonstrate that the plant hormones jasmonic acid (JA) and methyl jasmonate directly affect the life cycle of streptomycetes by modulating antibiotic synthesis and promoting faster development. Moreover, the plant hormones specifically stimulate the synthesis of the polyketide antibiotic actinorhodin in Streptomyces coelicolor. JA is then modified in the cell by amino acid conjugation, thereby quenching toxicity. Collectively, these results provide new insight into the impact of a key plant hormone on diverse phenotypic responses of streptomycetes.}, }
@article {pmid37901816, year = {2023}, author = {Li, Y and Hou, Y and Hou, Q and Long, M and Wang, Z and Rillig, MC and Liao, Y and Yong, T}, title = {Soil microbial community parameters affected by microplastics and other plastic residues.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1258606}, pmid = {37901816}, issn = {1664-302X}, abstract = {INTRODUCTION: The impact of plastics on terrestrial ecosystems is receiving increasing attention. Although of great importance to soil biogeochemical processes, how plastics influence soil microbes have yet to be systematically studied. The primary objectives of this study are to evaluate whether plastics lead to divergent responses of soil microbial community parameters, and explore the potential driving factors.<br><br>METHODS: We performed a meta-analysis of 710 paired observations from 48 published articles to quantify the impact of plastic on the diversity, biomass, and functionality of soil microbial communities.<br><br>RESULTS AND DISCUSSION: This study indicated that plastics accelerated soil organic carbon loss (effect size&#x2009;=&#x2009;-0.05, p&#x2009;=&#x2009;0.004) and increased microbial functionality (effect size&#x2009;=&#x2009;0.04, p&#x2009;=&#x2009;0.003), but also reduced microbial biomass (effect size&#x2009;=&#x2009;-0.07, p&#x2009;<&#x2009;0.001) and the stability of co-occurrence networks. Polyethylene significantly reduced microbial richness (effect size&#x2009;=&#x2009;-0.07, p&#x2009;<&#x2009;0.001) while polypropylene significantly increased it (effect size&#x2009;=&#x2009;0.17, p&#x2009;<&#x2009;0.001). Degradable plastics always had an insignificant effect on the microbial community. The effect of the plastic amount on microbial functionality followed the "hormetic dose-response" model, the infection point was about 40&#x2009;g/kg. Approximately 3564.78&#x2009;&#x3bc;m was the size of the plastic at which the response of microbial functionality changed from positive to negative. Changes in soil pH, soil organic carbon, and total nitrogen were significantly positively correlated with soil microbial functionality, biomass, and richness (R[2]&#x2009;=&#x2009;0.04-0.73, p&#x2009;<&#x2009;0.05). The changes in microbial diversity were decoupled from microbial community structure and functionality. We emphasize the negative impacts of plastics on soil microbial communities such as microbial abundance, essential to reducing the risk of ecological surprise in terrestrial ecosystems. Our comprehensive assessment of plastics on soil microbial community parameters deepens the understanding of environmental impacts and ecological risks from this emerging pollution.}, }
@article {pmid37897125, year = {2023}, author = {Seppey, CVW and Cabrol, L and Thalasso, F and Gandois, L and Lavergne, C and Martinez-Cruz, K and Sepulveda-Jauregui, A and Aguilar-Muñoz, P and Astorga-España, MS and Chamy, R and Dellagnezze, BM and Etchebehere, C and Fochesatto, GJ and Gerardo-Nieto, O and Mansilla, A and Murray, A and Sweetlove, M and Tananaev, N and Teisserenc, R and Tveit, AT and Van de Putte, A and Svenning, MM and Barret, M}, title = {Biogeography of microbial communities in high-latitude ecosystems: Contrasting drivers for methanogens, methanotrophs and global prokaryotes.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {3364-3386}, doi = {10.1111/1462-2920.16526}, pmid = {37897125}, issn = {1462-2920}, support = {Project MATCH C16B03//ECOS sud CONICYT/ ; grant no. 256132/H30//ECOS sud CONICYT/ ; project METHANOBASE (ELAC2014_DCC-0092)//ERANet-LAC program/ ; //French Ministries of Foreign Affairs and International Development (MAEDI)/ ; //German Federal Ministry of Education and Research, WISNA program/ ; grant no. 277238//Mexican National Council for Science and Technology (CONACYT)/ ; //National Education, Superior Education and Research (MENESR)/ ; MillenniumScienceInitiativeProgram-ICN2021_002//Chilean National Agency of Research and Development (ANID)/ ; }, mesh = {*Microbiota/genetics ; *Euryarchaeota/genetics ; Wetlands ; Soil/chemistry ; Methane ; }, abstract = {Methane-cycling is becoming more important in high-latitude ecosystems as global warming makes permafrost organic carbon increasingly available. We explored 387 samples from three high-latitudes regions (Siberia, Alaska and Patagonia) focusing on mineral/organic soils (wetlands, peatlands, forest), lake/pond sediment and water. Physicochemical, climatic and geographic variables were integrated with 16S rDNA amplicon sequences to determine the structure of the overall microbial communities and of specific methanogenic and methanotrophic guilds. Physicochemistry (especially pH) explained the largest proportion of variation in guild composition, confirming species sorting (i.e., environmental filtering) as a key mechanism in microbial assembly. Geographic distance impacted more strongly beta diversity for (i) methanogens and methanotrophs than the overall prokaryotes and, (ii) the sediment habitat, suggesting that dispersal limitation contributed to shape the communities of methane-cycling microorganisms. Bioindicator taxa characterising different ecological niches (i.e., specific combinations of geographic, climatic and physicochemical variables) were identified, highlighting the importance of Methanoregula as generalist methanogens. Methylocystis and Methylocapsa were key methanotrophs in low pH niches while Methylobacter and Methylomonadaceae in neutral environments. This work gives insight into the present and projected distribution of methane-cycling microbes at high latitudes under climate change predictions, which is crucial for constraining their impact on greenhouse gas budgets.}, }
@article {pmid37895286, year = {2023}, author = {Aboushaala, K and Wong, AYL and Barajas, JN and Lim, P and Al-Harthi, L and Chee, A and Forsyth, CB and Oh, CD and Toro, SJ and Williams, FMK and An, HS and Samartzis, D}, title = {The Human Microbiome and Its Role in Musculoskeletal Disorders.}, journal = {Genes}, volume = {14}, number = {10}, pages = {}, pmid = {37895286}, issn = {2073-4425}, support = {R21 AR079679/AR/NIAMS NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Bacteria ; *Musculoskeletal Diseases ; Oxygen ; }, abstract = {Musculoskeletal diseases (MSDs) are characterized as injuries and illnesses that affect the musculoskeletal system. MSDs affect every population worldwide and are associated with substantial global burden. Variations in the makeup of the gut microbiota may be related to chronic MSDs. There is growing interest in exploring potential connections between chronic MSDs and variations in the composition of gut microbiota. The human microbiota is a complex community consisting of viruses, archaea, bacteria, and eukaryotes, both inside and outside of the human body. These microorganisms play crucial roles in influencing human physiology, impacting metabolic and immunological systems in health and disease. Different body areas host specific types of microorganisms, with facultative anaerobes dominating the gastrointestinal tract (able to thrive with or without oxygen), while strict aerobes prevail in the nasal cavity, respiratory tract, and skin surfaces (requiring oxygen for development). Together with the immune system, these bacteria have coevolved throughout time, forming complex biological relationships. Changes in the microbial ecology of the gut may have a big impact on health and can help illnesses develop. These changes are frequently impacted by lifestyle choices and underlying medical disorders. The potential for safety, expenses, and efficacy of microbiota-based medicines, even with occasional delivery, has attracted interest. They are, therefore, a desirable candidate for treating MSDs that are chronic and that may have variable progression patterns. As such, the following is a narrative review to address the role of the human microbiome as it relates to MSDs.}, }
@article {pmid37894228, year = {2023}, author = {Jech, SD and Day, N and Barger, NN and Antoninka, A and Bowker, MA and Reed, S and Tucker, C}, title = {Cultivating Resilience in Dryland Soils: An Assisted Migration Approach to Biological Soil Crust Restoration.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, pmid = {37894228}, issn = {2076-2607}, support = {RC18-1322//Department of Defense Strategic Environmental Research and Development Program/ ; NA//Canyonlands Research Center/ ; NA//Wildlife Conservation Society Climate Adaptation Fund/ ; }, abstract = {Land use practices and climate change have driven substantial soil degradation across global drylands, impacting ecosystem functions and human livelihoods. Biological soil crusts, a common feature of dryland ecosystems, are under extensive exploration for their potential to restore the stability and fertility of degraded soils through the development of inoculants. However, stressful abiotic conditions often result in the failure of inoculation-based restoration in the field and may hinder the long-term success of biocrust restoration efforts. Taking an assisted migration approach, we cultivated biocrust inocula sourced from multiple hot-adapted sites (Mojave and Sonoran Deserts) in an outdoor facility at a cool desert site (Colorado Plateau). In addition to cultivating inoculum from each site, we created an inoculum mixture of biocrust from the Mojave Desert, Sonoran Desert, and Colorado Plateau. We then applied two habitat amelioration treatments to the cultivation site (growth substrate and shading) to enhance soil stability and water availability and reduce UV stress. Using marker gene sequencing, we found that the cultivated mixed inoculum comprised both local- and hot-adapted cyanobacteria at the end of cultivation but had similar cyanobacterial richness as each unmixed inoculum. All cultivated inocula had more cyanobacterial 16S rRNA gene copies and higher cyanobacterial richness when cultivated with a growth substrate and shade. Our work shows that it is possible to field cultivate biocrust inocula sourced from different deserts, but that community composition shifts toward that of the cultivation site unless habitat amelioration is employed. Future assessments of the function of a mixed inoculum in restoration and its resilience in the face of abiotic stressors are needed to determine the relative benefit of assisted migration compared to the challenges and risks of this approach.}, }
@article {pmid37883861, year = {2024}, author = {Zhang, X and Luther, AK and Rabaey, K and Prévoteau, A}, title = {Periodic polarization duty cycle tunes performance and adhesion of anodic electroactive biofilms.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {155}, number = {}, pages = {108581}, doi = {10.1016/j.bioelechem.2023.108581}, pmid = {37883861}, issn = {1878-562X}, mesh = {*Geobacter ; Biofilms ; Electrodes ; Carbon ; *Bioelectric Energy Sources ; }, abstract = {Periodic polarization can improve the performance of anodic electroactive biofilms (EABs). The impact of the half-period duration was previously investigated at constant duty cycle (50%), i.e., the proportion of a period during which the electrode is polarized. Here, we cultured eight EABs on glassy carbon electrodes at four different duty cycles (50%, 67%, 80% and 91%) by varying the time interval under open circuit conditions, while keeping the polarization duration at 10 s. The shorter duty cycles slightly slowed initial growth but produced EABs generating higher faradaic currents. The total charge recovery over 38 days increased with decreasing duty cycles from 0.53 kC.cm[-2] (duty cycle of 91%) to 1.65 kC.cm[-2] (50%). EABs with the shortest duty cycle fully detached twice from the electrode surface, but detachments were quickly followed by the formation of more efficient EABs. We then carried out controlled removal of some aged and low current-producing EABs by applying a 30 s cathodic current (H2 evolution at -15 mA.cm[-2]) and observed the subsequent rapid development of fresh EABs displaying better electrochemical performance. Our results illustrate that well-chosen dynamic controls of electrode potentials can substantially improve the average current production of EABs, or allow a simple replacement of underperforming EABs.}, }
@article {pmid37878053, year = {2023}, author = {Maisnam, P and Jeffries, TC and Szejgis, J and Bristol, D and Singh, BK and Eldridge, DJ and Horn, S and Chieppa, J and Nielsen, UN}, title = {Severe Prolonged Drought Favours Stress-Tolerant Microbes in Australian Drylands.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3097-3110}, pmid = {37878053}, issn = {1432-184X}, support = {DP150104199; DP190101968//Australian Research Council/ ; }, mesh = {Humans ; Ecosystem ; Droughts ; Soil Microbiology ; Australia ; Soil/chemistry ; Bacteria/genetics ; *Chytridiomycota ; *Microbiota ; }, abstract = {Drylands comprise one-third of Earth's terrestrial surface area and support over two billion people. Most drylands are projected to experience altered rainfall regimes, including changes in total amounts and fewer but larger rainfall events interspersed by longer periods without rain. This transition will have ecosystem-wide impacts but the long-term effects on microbial communities remain poorly quantified. We assessed belowground effects of altered rainfall regimes (+ 65% and -65% relative to ambient) at six sites in arid and semi-arid Australia over a period of three years (2016-2019) coinciding with a significant natural drought event (2017-2019). Microbial communities differed significantly among semi-arid and arid sites and across years associated with variation in abiotic factors, such as pH and carbon content, along with rainfall. Rainfall treatments induced shifts in microbial community composition only at a subset of the sites (Milparinka and Quilpie). However, differential abundance analyses revealed that several taxa, including Acidobacteria, TM7, Gemmatimonadates and Chytridiomycota, were more abundant in the wettest year (2016) and that their relative abundance decreased in drier years. By contrast, the relative abundance of oligotrophic taxa such as Actinobacteria, Alpha-proteobacteria, Planctomycetes, and Ascomycota and Basidiomycota, increased during the prolonged drought. Interestingly, fungi were shown to be more sensitive to the prolonged drought and to rainfall treatment than bacteria with Basidiomycota mostly dominant in the reduced rainfall treatment. Moreover, correlation network analyses showed more positive associations among stress-tolerant dominant taxa following the drought (i.e., 2019 compared with 2016). Our result indicates that such stress-tolerant taxa play an important role in how whole communities respond to changes in aridity. Such knowledge provides a better understanding of microbial responses to predicted increases in rainfall variability and the impact on the functioning of semi-arid and arid ecosystems.}, }
@article {pmid37878052, year = {2023}, author = {Chen, M and Su, S and Zhang, C and Zhu, J and Feng, W and Chen, H and Jiang, J and Lu, Z and Liu, W and Gan, J}, title = {The Role of Biogeography in Shaping Intestinal Flora and Influence on Fatty Acid Composition in Red Swamp Crayfish (Procambarus clarkii).}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3111-3127}, pmid = {37878052}, issn = {1432-184X}, mesh = {Animals ; *Gastrointestinal Microbiome ; Astacoidea/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Fatty Acids ; }, abstract = {Intestinal microbiota plays an important role in promoting digestion, metabolism, and immunity. Intestinal microbiota and fatty acids are important indicators to evaluate the health and nutritional composition of Procambarus clarkii. They have been shown to be strongly influence by environmental and genetic factors. However, it is not clear whether environmental factors have a greater impact on the intestinal microbiota and fatty acid composition of crayfish. The link between the intestinal microbial communities and fatty acid (FA) compositions of red swamp crayfish from different geographical has not yet been studied. Thus, the current paper focuses on the influence of different environments on the fatty acids in muscles of crayfish and the possible existence between gut microbiota and fatty acids. Therefore, in this study, we compared the fatty acid compositions and intestinal microbiota of five crayfish populations from different geographical locations. The results were further analyzed to determine whether there is a relationship between geographical location, fatty acid compositions and intestinal microbiota. The gut microbial communities of the crayfish populations were characterized using 16S rRNA high-throughput gene sequencing. The results showed that there were significant differences in FA compositions of crayfish populations from different geographical locations. A similar trend was observed in the gut microbiome, which also varied significantly according to geographic location. Interestingly, the analysis revealed that there was a relationship between fatty acid compositions and intestinal microbes, revealed by alpha diversity analysis and cluster analysis. However, further studies of the interactions between the P. clarkii gut microbiota and biochemical composition are needed, which will ultimately reveal the complexity of microbial ecosystems with potential applications in aquaculture and species conservation.}, }
@article {pmid37877729, year = {2023}, author = {Eng, AY and Narayanan, A and Alster, CJ and DeAngelis, KM}, title = {Thermal adaptation of soil microbial growth traits in response to chronic warming.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {11}, pages = {e0082523}, pmid = {37877729}, issn = {1098-5336}, support = {DEB-1749206, DEB-1832110//National Science Foundation (NSF)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; }, mesh = {*Soil ; *Global Warming ; Soil Microbiology ; Climate Change ; Biomass ; }, abstract = {Soils are the largest terrestrial carbon sink and the foundation of our food, fiber, and fuel systems. Healthy soils are carbon sinks, storing more carbon than they release. This reduces the amount of carbon dioxide released into the atmosphere and buffers against climate change. Soil microbes drive biogeochemical cycling and contribute to soil health through organic matter breakdown, plant growth promotion, and nutrient distribution. In this study, we determined how soil microbial growth traits respond to long-term soil warming. We found that bacterial isolates from warmed plots showed evidence of adaptation of optimum growth temperature. This suggests that increased microbial biomass and growth in a warming world could result in greater carbon storage. As temperatures increase, greater microbial activity may help reduce the soil carbon feedback loop. Our results provide insight on how atmospheric carbon cycling and soil health may respond in a warming world.}, }
@article {pmid37877306, year = {2023}, author = {Zhu, B and Gu, H and He, J and Li, F and Yu, J and Liu, W and Chen, Q and Lai, Y and Yu, S}, title = {The impact of smash-ridge tillage on agronomic traits of tobacco plants, soil enzymatic activity, microbial community structure, and functional diversity.}, journal = {Plant signaling &amp; behavior}, volume = {18}, number = {1}, pages = {2260640}, pmid = {37877306}, issn = {1559-2324}, mesh = {*Soil/chemistry ; Nicotiana/genetics ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Agriculture/methods ; *Microbiota ; }, abstract = {Smash-ridge tillage is a novel cultivation technique that significantly influences the quality of arable land and crop yield. In this study, we employed high-throughput 16S rRNA sequencing and Biolog-ECO methods to systematically investigate the impact of smash-ridge tillage on soil microbial community structure and functional diversity. The results demonstrate that both ST30 and ST50 treatments significantly enhance the average plant height, average plant diameter, average fresh root weight, stem fresh weight, and leaf area of tobacco plants, with the ST50 treatment exhibiting superior performance. Furthermore, both ST30 and ST50 treatments exhibit significantly higher soil enzyme activity and microbial community diversity compared to the CK treatment. They also improve the soil microbial utilization of carbon sources. Additionally, the ST50-treated soil samples demonstrate 15 microbial functional pathways that exceed those of the CK and ST30 treatments. In conclusion, the Smash-ridge tillage treatment at a depth of 50 cm yields more favorable results. This study provides a theoretical foundation for enhancing soil quality in Smash-ridge tillage by elucidating the mechanisms through which it impacts soil microbial ecology.}, }
@article {pmid37875737, year = {2023}, author = {Dahl, SA and Seifert, J and Camarinha-Silva, A and Cheng, YC and Hernández-Arriaga, A and Hudler, M and Windisch, W and König, A}, title = {Microbiota and Nutrient Portraits of European Roe Deer (Capreolus capreolus) Rumen Contents in Characteristic Southern German Habitats.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3082-3096}, pmid = {37875737}, issn = {1432-184X}, mesh = {Animals ; Rumen/microbiology ; *Deer ; Forests ; Bacteria ; Nutrients ; *Microbiota ; }, abstract = {Roe deer (Capreolus capreolus) are found in various habitats, from pure forest cultures to agricultural areas and mountains. In adapting to the geographically and seasonally differentiating food supply, they depend, above all, on an adapted microbiome. However, knowledge about the microbiome of wild ruminants still needs to be improved. There are only a few publications for individual species with a low number of samples. This study aims to identify a core microbiota for Bavarian roe deer and present nutrient and microbiota portraits of the individual habitat types. This study investigated the roe deer's rumen (reticulorumen) content from seven different characteristic Bavarian habitat types. The focus was on the composition of nutrients, fermentation products, and the rumen bacterial community. A total of 311 roe deer samples were analysed, with the most even possible distribution per habitat, season, age class, and gender. Significant differences in nutrient concentrations and microbial composition were identified for the factors habitat, season, and age class. The highest crude protein content (plant protein and microbial) in the rumen was determined in the purely agricultural habitat (AG), the highest value of non-fibre carbohydrates in the alpine mountain forest, and the highest fibre content (neutral detergent fibre, NDF) in the pine forest habitat. Maximum values for fibre content go up to 70% NDF. The proportion of metabolites (ammonia, lactate, total volatile fatty acids) was highest in the Agriculture-Beech-Forest habitat (ABF). Correlations can be identified between adaptations in the microbiota and specific nutrient concentrations, as well as in strong fluctuations in ingested forage. In addition, a core bacterial community comprising five genera could be identified across all habitats, up to 44% of total relative abundance. As with all wild ruminants, many microbial genera remain largely unclassified at various taxonomic levels. This study provides a more in-depth insight into the diversity and complexity of the roe deer rumen microbiota. It highlights the key microorganisms responsible for converting naturally available nutrients of different botanical origins.}, }
@article {pmid37875201, year = {2024}, author = {Chen, S and Kuramae, EE and Jia, Z and Liu, B}, title = {Stable isotope probing reveals compositional and functional shifts in active denitrifying communities along the soil profile in an intensive agricultural area.}, journal = {The Science of the total environment}, volume = {907}, number = {}, pages = {167968}, doi = {10.1016/j.scitotenv.2023.167968}, pmid = {37875201}, issn = {1879-1026}, mesh = {*Soil ; *Nitrates/analysis ; Agriculture ; DNA ; Isotopes ; Denitrification ; Soil Microbiology ; }, abstract = {Denitrifying microbial communities in the vadose zone play an essential role in eliminating the nitrate leached from agricultural practices. This nitrate could otherwise contaminate groundwater and threaten public health. Here, we utilized stable isotope probing combined with amplicon sequencing and functional gene quantification to inspect the composition and function of heterotrophic denitrifying microorganisms along a 9-m soil profile in an intensive agricultural area. Dramatic differences in the composition of the active denitrifiers were uncovered between the surface soil and deep layers of the vadose zone. The main denitrifying bacterial taxa identified from [13]C-DNA fractions were Pseudomonadaceae (Pseudomonas), Rhodocyclaceae (Azoarcus), and Burkholderiaceae in the surface soil (0-0.2 m), and were Pseudomonadaceae (Pseudomonas), Burkholderiaceae, Bacillaceae (Bacillus), and Paenibacillaceae (Ammoniphilus) in the deep layers (0.5-9.0 m). Analysis of the functional genes (nirS, nirK, and nosZ) in isotope-labeled DNA revealed an upward nos/nir ratio with increasing soil depth, which may account for the higher nitrous oxide emission potential in the surface soil, as compared to the deeper sand-rich, low organic carbon layers. This study improves our understanding of active denitrifying microbes in the vadose zone and helps in developing techniques to reduce nitrate pollution in groundwater.}, }
@article {pmid37874854, year = {2023}, author = {George, AB and O'Dwyer, J}, title = {Universal abundance fluctuations across microbial communities, tropical forests, and urban populations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {44}, pages = {e2215832120}, pmid = {37874854}, issn = {1091-6490}, support = {376199//Simons Foundation (SF)/ ; 220020439//James S. McDonnell Foundation (JSMF)/ ; }, mesh = {Humans ; Urban Population ; *Forests ; Population Dynamics ; *Microbiota ; Cities ; }, abstract = {The growth of complex populations, such as microbial communities, forests, and cities, occurs over vastly different spatial and temporal scales. Although research in different fields has developed detailed, system-specific models to understand each individual system, a unified analysis of different complex populations is lacking; such an analysis could deepen our understanding of each system and facilitate cross-pollination of tools and insights across fields. Here, we use a shared framework to analyze time-series data of the human gut microbiome, tropical forest, and urban employment. We demonstrate that a single, three-parameter model of stochastic population dynamics can reproduce the empirical distributions of population abundances and fluctuations in all three datasets. The three parameters characterizing a species measure its mean abundance, deterministic stability, and stochasticity. Our analysis reveals that, despite the vast differences in scale, all three systems occupy a similar region of parameter space when time is measured in generations. In other words, although the fluctuations observed in these systems may appear different, this difference is primarily due to the different physical timescales associated with each system. Further, we show that the distribution of temporal abundance fluctuations is described by just two parameters and derive a two-parameter functional form for abundance fluctuations to improve risk estimation and forecasting.}, }
@article {pmid37871765, year = {2024}, author = {Brandt, A and Csarmann, K and Hernández-Arriaga, A and Baumann, A and Staltner, R and Halilbasic, E and Trauner, M and Camarinha-Silva, A and Bergheim, I}, title = {Antibiotics attenuate diet-induced nonalcoholic fatty liver disease without altering intestinal barrier dysfunction.}, journal = {The Journal of nutritional biochemistry}, volume = {123}, number = {}, pages = {109495}, doi = {10.1016/j.jnutbio.2023.109495}, pmid = {37871765}, issn = {1873-4847}, mesh = {Male ; Mice ; Animals ; *Non-alcoholic Fatty Liver Disease/etiology/metabolism ; Liver/metabolism ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Mice, Inbred C57BL ; Diet/adverse effects ; Inflammation/metabolism ; *Gastrointestinal Diseases ; Fructose/metabolism ; Diet, High-Fat ; }, abstract = {To date the role of the alterations of intestinal microbiota in the development of intestinal barrier dysfunction in settings of nonalcoholic fatty liver disease (NAFLD) has not been fully understood. Here, we assessed the effect of antibiotics on development of NAFLD and their impact on intestinal barrier dysfunction. Male C57BL/6J mice were either pair-fed a liquid control diet (C) or fat- and fructose-rich diet (FFr) +/- antibiotics (AB, ampicillin/vancomycin/metronidazole/gentamycin) for 7 weeks. Fasting blood glucose was determined and markers of liver damage, inflammation, intestinal barrier function, and microbiota composition were assessed. The development of hepatic steatosis with early signs of inflammation found in FFr-fed mice was significantly abolished in FFr+AB-fed mice. Also, while prevalence of bacteria in feces was not detectable and TLR4 ligand levels in portal plasma were at the level of controls in FFr+AB-fed mice, impairments of intestinal barrier function like an increased permeation of xylose and iNOS protein levels persisted to a similar extent in both FFr-fed groups irrespective of AB use. Exposure of everted small intestinal tissue sacs of naïve mice to fructose resulted in a significant increase in tissue permeability and loss of tight junction proteins, being not affected by the presence of AB, whereas the concomitant treatment of tissue sacs with the NOS inhibitor aminoguanidine attenuated these alterations. Taken together, our data suggest that intestinal barrier dysfunction in diet-induced NAFLD in mice may not be predominantly dependent on changes in intestinal microbiota but rather that fructose-induced alterations of intestinal NO-homeostasis might be critically involved.}, }
@article {pmid37866247, year = {2023}, author = {Kleikamp, HBC and Grouzdev, D and Schaasberg, P and van Valderen, R and van der Zwaan, R and Wijgaart, RV and Lin, Y and Abbas, B and Pronk, M and van Loosdrecht, MCM and Pabst, M}, title = {Metaproteomics, metagenomics and 16S rRNA sequencing provide different perspectives on the aerobic granular sludge microbiome.}, journal = {Water research}, volume = {246}, number = {}, pages = {120700}, doi = {10.1016/j.watres.2023.120700}, pmid = {37866247}, issn = {1879-2448}, mesh = {*Sewage/chemistry ; RNA, Ribosomal, 16S/genetics ; Bioreactors ; *Microbiota ; Metagenome ; Metagenomics/methods ; }, abstract = {The tremendous progress in sequencing technologies has made DNA sequencing routine for microbiome studies. Additionally, advances in mass spectrometric techniques have extended conventional proteomics into the field of microbial ecology. However, systematic studies that provide a better understanding of the complementary nature of these 'omics' approaches, particularly for complex environments such as wastewater treatment sludge, are urgently needed. Here, we describe a comparative metaomics study on aerobic granular sludge from three different wastewater treatment plants. For this, we employed metaproteomics, whole metagenome, and 16S rRNA amplicon sequencing to study the same granule material with uniform size. We furthermore compare the taxonomic profiles using the Genome Taxonomy Database (GTDB) to enhance the comparability between the different approaches. Though the major taxonomies were consistently identified in the different aerobic granular sludge samples, the taxonomic composition obtained by the different omics techniques varied significantly at the lower taxonomic levels, which impacts the interpretation of the nutrient removal processes. Nevertheless, as demonstrated by metaproteomics, the genera that were consistently identified in all techniques cover the majority of the protein biomass. The established metaomics data and the contig classification pipeline are publicly available, which provides a valuable resource for further studies on metabolic processes in aerobic granular sludge.}, }
@article {pmid37860776, year = {2023}, author = {Yitbarek, S and Guittar, J and Knutie, SA and Ogbunugafor, CB}, title = {Deconstructing taxa x taxa xenvironment interactions in the microbiota: A theoretical examination.}, journal = {iScience}, volume = {26}, number = {10}, pages = {107875}, pmid = {37860776}, issn = {2589-0042}, abstract = {A major objective of microbial ecology is to identify how the composition of microbial taxa shapes host phenotypes. However, most studies focus on pairwise interactions and ignore the potentially significant effects of higher-order microbial interactions.Here, we quantify the effects of higher-order interactions among taxa on host infection risk. We apply our approach to an in silico dataset that is built to resemble a population of insect hosts with gut-associated microbial communities at risk of infection from an intestinal parasite across a breadth of nutrient environmental contexts.We find that the effect of higher-order interactions is considerable and can change appreciably across environmental contexts. Furthermore, we show that higher-order interactions can stabilize community structure thereby reducing host susceptibility to parasite invasion.Our approach illustrates how incorporating the effects of higher-order interactions among gut microbiota across environments can be essential for understanding their effects on host phenotypes.}, }
@article {pmid37858824, year = {2024}, author = {Niu, S and Xie, J and Wang, G and Li, Z and Zhang, K and Li, H and Xia, Y and Tian, J and Yu, E and Xie, W and Gong, W}, title = {Community assembly patterns and processes of bacteria in a field-scale aquaculture wastewater treatment system.}, journal = {The Science of the total environment}, volume = {907}, number = {}, pages = {167913}, doi = {10.1016/j.scitotenv.2023.167913}, pmid = {37858824}, issn = {1879-1026}, mesh = {Wastewater ; Bacteria ; *Microbiota ; Aquaculture ; *Water Purification ; }, abstract = {Microbial communities are responsible for the biological treatment of wastewater, however, our comprehension of their diversity, assembly patterns, and functions remains limited. In this study, we analyzed bacterial communities in both water and sediment samples. These samples were gathered from a novel field-scale aquaculture wastewater treatment system (FAWTS), which employs a multi-stage purification process to eliminate nutrients from pond culture wastewater. Significant variations were observed in bacterial diversity and composition across various ponds within the system and at different stages of the culture. Notably, the bacterial community in the FAWTS displayed a distinct species abundance distribution. The influence of dispersal-driven processes on shaping FAWTS communities was found to be relatively weak. The utilization of neutral and null models unveiled that the assembly of microbial communities was primarily governed by stochastic processes. Moreover, environmental factors variables such as total nitrogen (TN), dissolved oxygen (DO), and temperature were found to be associated with both the composition and assembly of bacterial communities, influencing the relative significance of stochastic processes. Furthermore, we discovered a close relationship between that bacterial community composition and system functionality. These findings hold significant implications for microbial ecologists and environmental engineers, as they can collaboratively refine operational strategies while preserving biodiversity. This, in turn, promotes the stability and efficiency of the FAWTS. In summary, our study contributes to an enhanced mechanistic understanding of microbial community diversity, assembly patterns, and functionality within the FAWTS, offering valuable insights into both microbial ecology and wastewater treatment processes.}, }
@article {pmid37855643, year = {2023}, author = {Villabona, N and Moran, N and Hammer, T and Reyes, A}, title = {Conserved, yet disruption-prone, gut microbiomes in neotropical bumblebees.}, journal = {mSphere}, volume = {8}, number = {6}, pages = {e0013923}, pmid = {37855643}, issn = {2379-5042}, support = {R35 GM131738/GM/NIGMS NIH HHS/United States ; }, mesh = {Bees ; Animals ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota ; Ecology ; }, abstract = {Social bees are an important model for the ecology and evolution of gut microbiomes. These bees harbor ancient, specific, and beneficial gut microbiomes and are crucial pollinators. However, most of the research has concentrated on managed honeybees and bumblebees in the temperate zone. Here we used 16S rRNA gene sequencing to characterize gut microbiomes in wild neotropical bumblebee communities from Colombia. We also analyzed drivers of microbiome structure across our data and previously published data from temperate bumblebees. Our results show that lineages of neotropical bumblebees not only retained their ancient gut bacterial symbionts during dispersal from North America but also are prone to major disruption, a shift that is strongly associated with parasite infection. Finally, we also found that microbiomes are much more strongly structured by host phylogeny than by geography, despite the very different environmental conditions and plant communities in the two regions.}, }
@article {pmid37852481, year = {2024}, author = {Zammit, I and Badia, S and Mejías-Molina, C and Rusiñol, M and Bofill-Mas, S and Borrego, CM and Corominas, L}, title = {Zooming in to the neighborhood level: A year-long wastewater-based epidemiology monitoring campaign for COVID-19 in small intraurban catchments.}, journal = {The Science of the total environment}, volume = {907}, number = {}, pages = {167811}, doi = {10.1016/j.scitotenv.2023.167811}, pmid = {37852481}, issn = {1879-1026}, mesh = {Humans ; *COVID-19/epidemiology ; SARS-CoV-2 ; Wastewater ; Wastewater-Based Epidemiological Monitoring ; }, abstract = {In recent years, wastewater-based epidemiology (WBE) has emerged as a valuable and cost-effective tool for monitoring the prevalence of COVID-19. Large-scale monitoring efforts have been implemented in numerous countries, primarily focusing on sampling at the entrance of wastewater treatment plants (WWTPs) to cover a large population. However, sampling at a finer spatial scale, such as at the neighborhood level (NGBs), pose new challenges, including the absence of composite sampling infrastructure and increased uncertainty due to the dynamics of small catchments. This study aims to investigate the feasibility and accuracy of WBE when deployed at the neighborhood level (sampling in sewers) compared to the city level (sampling at the entrance of a WWTP). To achieve this, we deployed specific WBE sampling stations at the intraurban scale within three NGBs in Barcelona, Spain. The study period covers the 5th and the 6th waves of COVID-19 in Spain, spanning from March 2021 to March 2022, along with the WWTP downstream from the NGBs. The results showed a strong correlation between the dynamics of COVID-19 clinical cases and wastewater SARS-CoV-2 loads at both the NGB and city levels. Notably, during the 5th wave, which was dominated by the Delta SARS-CoV-2 variant, wastewater loads were higher than during the 6th wave (Omicron variant), despite a lower number of clinical cases recorded during the 5th wave. The correlations between wastewater loads and clinical cases at the NGB level were stronger than at the WWTP level. However, the early warning potential varied across neighborhoods and waves, with some cases showing a one-week early warning and others lacking any significant early warning signal. Interestingly, the prevalence of COVID-19 did not exhibit major differences among NGBs with different socioeconomic statuses.}, }
@article {pmid37848722, year = {2023}, author = {Rizaludin, MS and Garbeva, P and Zwart, M and Hu, J}, title = {Microbial volatiles mediate bacterial evolutionary dynamics.}, journal = {The ISME journal}, volume = {17}, number = {12}, pages = {2144-2146}, pmid = {37848722}, issn = {1751-7370}, }
@article {pmid37844340, year = {2023}, author = {Li, Z and Ma, H and Hong, Z and Zhang, T and Cao, M and Cui, F and Grossart, HP}, title = {Phytoplankton interspecific interactions modified by symbiotic fungi and bacterial metabolites under environmentally relevant hydrogen peroxide concentrations stress.}, journal = {Water research}, volume = {246}, number = {}, pages = {120739}, doi = {10.1016/j.watres.2023.120739}, pmid = {37844340}, issn = {1879-2448}, mesh = {Phytoplankton ; Hydrogen Peroxide/pharmacology ; Symbiosis ; *Chlorella vulgaris ; *Cyanobacteria ; *Microcystis/metabolism ; Water ; Fungi ; Microcystins/metabolism ; }, abstract = {Hydrogen peroxide (H2O2), which accumulates in water and triggers oxidative stress for aquatic microbes, has been shown to have profound impacts on planktonic microbial community dynamics including cyanobacterial bloom formation. Yet, potential effects of H2O2 on interspecific relationships of phytoplankton-microbe symbiotic interactions remain unclear. Here, we investigated effects of environmentally relevant H2O2 concentrations on interspecific microbial relationships in algae-microbe symbiosis. Microbes play a crucial role in the competition between M. aeruginosa and Chlorella vulgaris at low H2O2 concentrations (∼400 nM), in which fungi and bacteria protect Microcystis aeruginosa from oxidative stress. Moreover, H2O2 stimulated the synthesis and release of extracellular microcystin-LR from Microcystis aeruginosa, while intracellular microcystin-LR concentrations remained at a relatively constant level. In the presence of H2O2, loss of organoheterocyclic compounds, organic acids and ketones contributed to the growth of M. aeruginosa, but the reduction of vitamins inhibited it. Regulation of interspecific relationships by H2O2 is achieved by its action on fungal species and bacterial secretory metabolites. This study explored the response of phytoplankton interspecific relationships in symbiotic phytoplankton-microbe interactions to environmentally relevant H2O2 concentrations stress, providing a theoretical basis for understanding the formation of harmful-algae blooming and impact of photochemical properties of water on aquatic ecological safety and stability.}, }
@article {pmid37843656, year = {2023}, author = {Znamínko, M and Falteisek, L and Vrbická, K and Klímová, P and Christiansen, JR and Jørgensen, CJ and Stibal, M}, title = {Methylotrophic Communities Associated with a Greenland Ice Sheet Methane Release Hotspot.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3057-3067}, pmid = {37843656}, issn = {1432-184X}, support = {A32524//Hartmann Fonden/ ; 0135-00229B//Danish Independent Research Fund/ ; LL2004 'MARCH4G'//Czech Ministry of Education, Youth and Sports/ ; }, mesh = {Greenland ; *Ice Cover/microbiology ; *Methane/analysis ; Climate ; Seasons ; }, abstract = {Subglacial environments provide conditions suitable for the microbial production of methane, an important greenhouse gas, which can be released from beneath the ice as a result of glacial melting. High gaseous methane emissions have recently been discovered at Russell Glacier, an outlet of the southwestern margin of the Greenland Ice Sheet, acting not only as a potential climate amplifier but also as a substrate for methane consuming microorganisms. Here, we describe the composition of the microbial assemblage exported in meltwater from the methane release hotspot at Russell Glacier and its changes over the melt season and as it travels downstream. We found that a substantial part (relative abundance 27.2% across the whole dataset) of the exported assemblage was made up of methylotrophs and that the relative abundance of methylotrophs increased as the melt season progressed, likely due to the seasonal development of the glacial drainage system. The methylotrophs were dominated by representatives of type I methanotrophs from the Gammaproteobacteria; however, their relative abundance decreased with increasing distance from the ice margin at the expense of type II methanotrophs and/or methylotrophs from the Alphaproteobacteria and Betaproteobacteria. Our results show that subglacial methane release hotspot sites can be colonized by microorganisms that can potentially reduce methane emissions.}, }
@article {pmid37843655, year = {2023}, author = {Sudhakari, PA and Ramisetty, BCM}, title = {An Eco-evolutionary Model on Surviving Lysogeny Through Grounding and Accumulation of Prophages.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3068-3081}, pmid = {37843655}, issn = {1432-184X}, mesh = {Humans ; Lysogeny ; Prophages/genetics ; Escherichia coli/genetics ; *Superinfection/genetics ; Wastewater ; *Bacteriophages/genetics ; Genome, Bacterial ; }, abstract = {Temperate phages integrate into the bacterial genomes propagating along with the bacterial genomes. Multiple phage elements, representing diverse prophages, are present in most bacterial genomes. The evolutionary events and the ecological dynamics underlying the accumulation of prophage elements in bacterial genomes have yet to be understood. Here, we show that the local wastewater had 7% of lysogens (hosting mitomycin C-inducible prophages), and they showed resistance to superinfection by their corresponding lysates. Genomic analysis of four lysogens and four non-lysogens revealed the presence of multiple prophages (belonging to Myoviridae and Siphoviridae) in both lysogens and non-lysogens. For large-scale comparison, 2180 Escherichia coli genomes isolated from various sources across the globe and 523 genomes specifically isolated from diverse wastewaters were analyzed. A total of 15,279 prophages were predicted among 2180 E. coli genomes and 2802 prophages among 523 global wastewater isolates, with a mean of ~ 5 prophages per genome. These observations indicate that most putative prophages are relics of past bacteria-phage conflicts; they are "grounded" prophages that cannot excise from the bacterial genome. Prophage distribution analysis based on the sequence homology suggested the random distribution of E. coli prophages within and between E. coli clades. The independent occurrence pattern of these prophages indicates extensive horizontal transfers across the genomes. We modeled the eco-evolutionary dynamics to reconstruct the events that could have resulted in the prophage accumulation accounting for infection, superinfection immunity, and grounding. In bacteria-phage conflicts, the bacteria win by grounding the prophage, which could confer superinfection immunity.}, }
@article {pmid37836513, year = {2023}, author = {Perreau, C and Thabuis, C and Verstrepen, L and Ghyselinck, J and Marzorati, M}, title = {Ex Vivo Colonic Fermentation of NUTRIOSE[®] Exerts Immuno-Modulatory Properties and Strong Anti-Inflammatory Effects.}, journal = {Nutrients}, volume = {15}, number = {19}, pages = {}, pmid = {37836513}, issn = {2072-6643}, support = {//Roquette/ ; }, mesh = {Humans ; *Dextrins ; Fermentation ; *Lipopolysaccharides/metabolism ; Caco-2 Cells ; Colon/metabolism ; Fatty Acids, Volatile/metabolism ; Immunity ; Anti-Inflammatory Agents/pharmacology/metabolism ; }, abstract = {NUTRIOSE[®] (Roquette, Lestrem, France) is a resistant dextrin with well-established prebiotic effects. This study evaluated the indirect effects of pre-digested NUTRIOSE[®] on host immune response and gut barrier integrity. Fecal samples from eight healthy donors were inoculated in a Colon-on-a-plate[®] system (ProDigest, Ghent, Belgium) with or without NUTRIOSE[®] supplementation. Following 48 h fermentation, colonic suspensions were tested in a Caco-2/THP1-Blue™ co-culture system to determine their effects on gut barrier activity (transepithelial electrical resistance) and immune response following lipopolysaccharide stimulation. Additionally, changes in short-chain fatty acid levels (SCFA) and microbial community composition following a 48 h fermentation in the Colon-on-a-plate[®] system were measured. Across all donors, immune-mediated intestinal barrier damage was significantly reduced with NUTRIOSE[®]-supplemented colonic suspensions versus blank. Additionally, IL-6 and IL-10 levels were significantly increased, and the level of the neutrophil chemoattractant IL-8 was significantly decreased with NUTRIOSE[®]-supplemented colonic suspensions versus blank in the co-culture models following lipopolysaccharide stimulation. These beneficial effects of NUTRIOSE[®] supplementation were likely due to increased acetate and propionate levels and the enrichment of SCFA-producing bacteria. NUTRIOSE[®] was well fermented by the colonic bacteria of all eight donors and had protective effects on inflammation-induced disruption of the intestinal epithelial barrier and strong anti-inflammatory effects.}, }
@article {pmid37833155, year = {2023}, author = {Munley, JA and Kelly, LS and Park, G and Gillies, GS and Pons, EE and Kannan, KB and Bible, LE and Efron, PA and Nagpal, R and Mohr, AM}, title = {Sex-specific intestinal dysbiosis persists after multicompartmental injury.}, journal = {Surgery}, volume = {174}, number = {6}, pages = {1453-1462}, doi = {10.1016/j.surg.2023.08.023}, pmid = {37833155}, issn = {1532-7361}, support = {R01 GM105893/GM/NIGMS NIH HHS/United States ; }, mesh = {Female ; Male ; Rats ; Animals ; Rats, Sprague-Dawley ; *Dysbiosis/etiology ; RNA, Ribosomal, 16S ; *Multiple Trauma ; Computational Biology ; }, abstract = {BACKGROUND: Preclinical studies of the gut microbiome after severe traumatic injury have demonstrated severe dysbiosis in males, with sex-specific microbial differences up to 2 days after injury. However, the impact of host sex on injury-driven dysbiosis over time remains unknown. We hypothesized that sex-specific differences in intestinal microbiome diversity and composition after traumatic injury with and without stress would persist after 7 days.<br><br>METHODS: Male and proestrus female Sprague-Dawley rats (n&#xa0;= 8/group) were subjected to either polytrauma (lung contusion, hemorrhagic shock, cecectomy, bifemoral pseudofractures), polytrauma plus chronic restraint stress, or na&#xef;ve controls. The fecal microbiome was measured on days 0, 3, and 7 using 16S rRNA sequencing and Quantitative Insights into Microbial Ecology bioinformatics analyses. Microbial alpha-diversity (Chao1 and Shannon indices) and beta-diversity were assessed. Analyses were performed in GraphPad and "R," with significance defined as P < .05.<br><br>RESULTS: Polytrauma and polytrauma plus chronic restraint stress reduced alpha-diversity (Chao1, Shannon) within 3 days postinjury, which persisted up to day 7 in both sexes; polytrauma and polytrauma plus chronic restraint stress females had significantly decreased Chao1 compared to male counterparts at day 7 (P&#xa0;= .02). At day 7, the microbiome composition in polytrauma females had higher proportion of Mucispirillum, whereas polytrauma plus chronic restraint stress males demonstrated elevated abundance of Ruminococcus and Akkermansia.<br><br>CONCLUSION: Multicompartmental trauma induces intestinal dysbiosis that is sex-specific with persistence of decreased diversity and unique "pathobiome" signatures in females after 1 week. These findings underline sex as an important biological variable that may influence variable host-specific responses and outcomes after severe trauma and critical illness. This underscores the need to consider precision medicine strategies to ameliorate these outcomes.}, }
@article {pmid37831075, year = {2023}, author = {Xu, H and Xiao, Q and Dai, Y and Chen, D and Zhang, C and Jiang, Y and Xie, J}, title = {Selected Bacteria Are Critical for Karst River Carbon Sequestration via Integrating Multi-omics and Hydrochemistry Data.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3043-3056}, pmid = {37831075}, issn = {1432-184X}, mesh = {*Rivers/chemistry ; *Carbon Sequestration ; Dissolved Organic Matter ; Leucine/metabolism ; Multiomics ; Carbon/metabolism ; Bacteria/genetics/metabolism ; Water/metabolism ; }, abstract = {Recalcitrant dissolved organic carbon (RDOC) produced by microbial carbon pumps (MCPs) in the ocean is crucial for carbon sequestration and regulating climate change in the history of Earth. However, the importance of microbes on RDOC formation in terrestrial aquatic systems, such as rivers and lakes, remains to be determined. By integrating metagenomic (MG) and metatranscriptomic (MT) sequencing, we defined the microbial communities and their transcriptional activities in both water and silt of a typical karst river, the Lijiang River, in Southwest China. Betaproteobacteria predominated in water, serving as the most prevalent population remodeling components of dissolved organic carbon (DOC). Binning method recovered 45 metagenome-assembled genomes (MAGs) from water and silt. Functional annotation of MAGs showed Proteobacteria was less versatile in degrading complex carbon, though cellulose and chitin utilization genes were widespread in this phylum, whereas Bacteroidetes had high potential for the utilization of macro-molecular organic carbon. Metabolic remodeling revealed that increased shared metabolites within the bacterial community are associated with increased concentration of DOC, highlighting the significance of microbial cooperation during producing and remodeling of carbon components. Beta-oxidation, leucine degradation, and mevalonate (MVA) modules were significantly positively correlated with the concentration of RDOC. Blockage of the leucine degradation pathway in Limnohabitans and UBA4660-related MAGs were associated with decreased RDOC in the karst river, while the Fluviicola-related MAG containing a complete leucine degradation pathway was positively correlated with RDOC concentration. Collectively, our study revealed the linkage between bacteria metabolic processes and carbon sequestration. This provided novel insights into the microbial roles in karst-rivers carbon sink.}, }
@article {pmid37830797, year = {2023}, author = {Stapelfeldt, HRD and Lanclos, VC and Henson, MW and Thrash, JC}, title = {Draft genome sequence of the BAL58 Betaproteobacteria representative strain LSUCC0117.}, journal = {Microbiology resource announcements}, volume = {12}, number = {11}, pages = {e0062023}, pmid = {37830797}, issn = {2576-098X}, support = {Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation (SF)/ ; OCE-1945279//National Science Foundation (NSF)/ ; }, abstract = {Here, we present the draft genome sequence of strain LSUCC0117, a representative of the abundant aquatic BAL58 Betaproteobacteria group which we isolated from a coastal site in the northern Gulf of Mexico. The genome is estimated at over 99% complete, with a genome size of 2,687,225 bp.}, }
@article {pmid37828283, year = {2023}, author = {Kothamasi, D and Vermeylen, S and Deepika, S}, title = {Are ecological processes that select beneficial traits in agricultural microbes nature's intellectual property rights?.}, journal = {Nature biotechnology}, volume = {41}, number = {10}, pages = {1381-1384}, pmid = {37828283}, issn = {1546-1696}, support = {894188//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; }, mesh = {*Intellectual Property ; *Agriculture ; Bacteria ; }, }
@article {pmid37823651, year = {2023}, author = {Tran, WC and Sullivan, B and Kitzmiller, CE and Choudoir, M and Simoes, R and Dayarathne, N and DeAngelis, KM}, title = {Draft genome sequence of Paenibacillus sp. strain RC67, an isolate from a long-term forest soil warming experiment in Petersham, Massachusetts.}, journal = {Microbiology resource announcements}, volume = {12}, number = {11}, pages = {e0037323}, pmid = {37823651}, issn = {2576-098X}, support = {DEB-1749206, DEB-1456610, DEB-1832210//National Science Foundation (NSF)/ ; }, abstract = {Paenibacillus sp. strain RC67 was isolated from the Harvard Forest long-term soil warming experiment. The assembled genome is a single contig with 7,963,753 bp and 99.4% completion. Genome annotation suggests that the isolate is of a novel bacterial species.}, }
@article {pmid37822474, year = {2023}, author = {Callewaert, C and Pezavant, M and Vandaele, R and Meeus, B and Vankrunkelsven, E and Van Goethem, P and Plumacker, A and Misset, B and Darcis, G and Piret, S and De Vleeschouwer, L and Staelens, F and Van Varenbergh, K and Tombeur, S and Ottevaere, A and Montag, I and Vandecandelaere, P and Jonckheere, S and Vandekerckhove, L and Tobback, E and Wieers, G and Marot, JC and Anseeuw, K and D'Hoore, L and Tuyls, S and De Tavernier, B and Catteeuw, J and Lotfi, A and Melnik, A and Aksenov, A and Grandjean, D and Stevens, M and Gasthuys, F and Guyot, H}, title = {Sniffing out safety: canine detection and identification of SARS-CoV-2 infection from armpit sweat.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {1185779}, pmid = {37822474}, issn = {2296-858X}, abstract = {Detection dogs were trained to detect SARS-CoV-2 infection based on armpit sweat odor. Sweat samples were collected using cotton pads under the armpits of negative and positive human patients, confirmed by qPCR, for periods of 15-30 min. Multiple hospitals and organizations throughout Belgium participated in this study. The sweat samples were stored at -20°C prior to being used for training purposes. Six dogs were trained under controlled atmosphere conditions for 2-3 months. After training, a 7-day validation period was conducted to assess the dogs' performances. The detection dogs exhibited an overall sensitivity of 81%, specificity of 98%, and an accuracy of 95%. After validation, training continued for 3 months, during which the dogs' performances remained the same. Gas chromatography/mass spectrometry (GC/MS) analysis revealed a unique sweat scent associated with SARS-CoV-2 positive sweat samples. This scent consisted of a wide variety of volatiles, including breakdown compounds of antiviral fatty acids, skin proteins and neurotransmitters/hormones. An acceptability survey conducted in Belgium demonstrated an overall high acceptability and enthusiasm toward the use of detection dogs for SARS-CoV-2 detection. Compared to qPCR and previous canine studies, the detection dogs have good performances in detecting SARS-CoV-2 infection in humans, using frozen sweat samples from the armpits. As a result, they can be used as an accurate pre-screening tool in various field settings alongside the PCR test.}, }
@article {pmid37821698, year = {2023}, author = {Pavlopoulos, GA and Baltoumas, FA and Liu, S and Selvitopi, O and Camargo, AP and Nayfach, S and Azad, A and Roux, S and Call, L and Ivanova, NN and Chen, IM and Paez-Espino, D and Karatzas, E and ,  and Iliopoulos, I and Konstantinidis, K and Tiedje, JM and Pett-Ridge, J and Baker, D and Visel, A and Ouzounis, CA and Ovchinnikov, S and Buluç, A and Kyrpides, NC}, title = {Unraveling the functional dark matter through global metagenomics.}, journal = {Nature}, volume = {622}, number = {7983}, pages = {594-602}, pmid = {37821698}, issn = {1476-4687}, support = {DP5 OD026389/OD/NIH HHS/United States ; P20 GM103475/GM/NIGMS NIH HHS/United States ; }, mesh = {Cluster Analysis ; *Metagenome/genetics ; *Metagenomics/methods ; *Proteins/chemistry/classification/genetics ; Databases, Protein ; Protein Conformation ; *Microbiology ; }, abstract = {Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities[1,2]. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database[3]. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.}, }
@article {pmid37821652, year = {2023}, author = {Yost, RT and Fowler, AE and Adler, LS}, title = {Gut Transplants from Bees Fed an Antipathogenic Pollen Diet Do Not Confer Pathogen Resistance to Recipients.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3133-3137}, pmid = {37821652}, issn = {1432-184X}, support = {2128221//National Science Foundation/ ; NE2001//U.S. Department of Agriculture/ ; }, mesh = {Bees ; Animals ; Pollen ; Diet/veterinary ; *Microbiota ; *Gastrointestinal Microbiome ; Crithidia ; *Biological Products ; }, abstract = {Pollinators are threatened by diverse stressors, including microbial pathogens such as Crithidia bombi. Consuming sunflower pollen dramatically reduces C. bombi infection in the bumble bee Bombus impatiens, but the mechanism behind this medicinal effect is unclear. We asked whether diet mediates resistance to C. bombi through changes in the gut microbiome. We hypothesized that sunflower pollen changes the gut microbiome, which in turn reduces Crithidia infection. To test this, we performed a gut transplant experiment. We fed donor bees either a sunflower pollen treatment or buckwheat pollen as a control treatment and then inoculated recipient bees with homogenized guts from either sunflower-fed or buckwheat-fed donor bees. All recipient bees were then fed a wildflower pollen diet. Two days after the transplant, we infected recipients with C. bombi, and 2 days later, we provided another donor gut transplant. To quantify infection, we performed both fecal screens and dissections of the recipient bees. We found no significant differences in C. bombi infection intensity or presence between bees that received sunflower-fed microbiomes versus buckwheat-fed microbiomes. This suggests that sunflower pollen's effects on pathogen resistance are not mediated by gut microbiota.}, }
@article {pmid37820474, year = {2023}, author = {Ma, L and Roman, M and Alhadidi, A and Jia, M and Martini, F and Xue, Y and Verliefde, A and Gutierrez, L and Cornelissen, E}, title = {Fate of organic micropollutants during brackish water desalination for drinking water production in decentralized capacitive electrodialysis.}, journal = {Water research}, volume = {245}, number = {}, pages = {120625}, doi = {10.1016/j.watres.2023.120625}, pmid = {37820474}, issn = {1879-2448}, mesh = {*Drinking Water ; *Water Purification ; Sodium Chloride ; Ions ; Adsorption ; Saline Waters ; }, abstract = {Capacitive electrodialysis (CED) is an emerging and promising desalination technology for decentralized drinking water production. Brackish water, often used as a drinking water source, may contain organic micropollutants (OMPs), thus raising environmental and health concerns. This study investigated the transport of OMPs in a fully-functional decentralized CED system for drinking water production under realistic operational conditions. Eighteen environmentally-relevant OMPs (20 µg L[-1]) with different physicochemical properties (charge, size, hydrophobicity) were selected and added to the feed water. The removal of OMPs was significantly lower than that of salts (∼94%), mainly due to their lower electrical mobility and higher steric hindrance. The removal of negatively-charged OMPs reached 50% and was generally higher than that of positively-charged OMPs (31%), whereas non-charged OMPs were barely transported. Marginal adsorption of OMPs was found under moderate water recovery (50%), in contrast to significant adsorption of charged OMPs under high water recovery (80%). The five-month operation demonstrated that the CED system could reliably produce water with low salt ions and TOC concentrations, meeting the respective WHO requirements. The specific energy consumption of the CED stack under 80% water recovery was 0.54 kWh m[-3], which is competitive to state-of-the-art RO, ED, and emerging MCDI in brackish water desalination. Under this condition, the total OPEX was 2.43 € m[-3], of which the cost of membrane replacement contributed significantly. Although the CED system proved to be a robust, highly adaptive, and fully automated technology for decentralized drinking water production, it was not highly efficient in removing OMPs, especially non-charged OMPs.}, }
@article {pmid37819096, year = {2023}, author = {Khot, V and Strous, M and Dong, X and Kiesser, AK}, title = {Viral diversity and dynamics and CRISPR-Cas-mediated immunity in a robust alkaliphilic cyanobacterial consortium.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0221723}, pmid = {37819096}, issn = {2165-0497}, support = {//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; //Canada First Research Excellence Fund (CFREF)/ ; //Alberta Innovates (AI)/ ; Alberta Graduate Excellence//Government of Alberta (Alberta Government)/ ; Faculty of Graduate Studies Doctoral Scholarship//University of Calgary (U of C)/ ; }, mesh = {CRISPR-Cas Systems ; *Cyanobacteria/genetics ; *Viruses ; }, abstract = {Biotechnology applications utilizing the function of microbial communities have become increasingly important solutions as we strive for sustainable applications. Although viral infections are known to have a significant impact on microbial turnover and nutrient cycling, viral dynamics have remained largely overlooked in these engineered communities. Predatory perturbations to the functional stability of these microbial biotechnology applications must be investigated in order to design more robust applications. In this study, we closely examine virus-microbe dynamics in a model microbial community used in a biotechnology application. Our findings suggest that viral dynamics change significantly with environmental conditions and that microbial immunity may play an important role in maintaining functional stability. We present this study as a comprehensive template for other researchers interested in exploring predatory dynamics in engineered microbial communities.}, }
@article {pmid37819078, year = {2023}, author = {Svet, L and Parijs, I and Isphording, S and Lories, B and Marchal, K and Steenackers, HP}, title = {Competitive interactions facilitate resistance development against antimicrobials.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {10}, pages = {e0115523}, pmid = {37819078}, issn = {1098-5336}, mesh = {*Anti-Infective Agents/pharmacology ; Biofilms ; Bacteria/genetics ; Phenotype ; Sulfathiazoles/pharmacology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {While the evolution of antimicrobial resistance is well studied in free-living bacteria, information on resistance development in dense and diverse biofilm communities is largely lacking. Therefore, we explored how the social interactions in a duo-species biofilm composed of the brewery isolates Pseudomonas rhodesiae and Raoultella terrigena influence the adaptation to the broad-spectrum antimicrobial sulfathiazole. Previously, we showed that the competition between these brewery isolates enhances the antimicrobial tolerance of P. rhodesiae. Here, we found that this enhanced tolerance in duo-species biofilms is associated with a strongly increased antimicrobial resistance development in P. rhodesiae. Whereas P. rhodesiae was not able to evolve resistance against sulfathiazole in monospecies conditions, it rapidly evolved resistance in the majority of the duo-species communities. Although the initial presence of R. terrigena was thus required for P. rhodesiae to acquire resistance, the resistance mechanisms did not depend on the presence of R. terrigena. Whole genome sequencing of resistant P. rhodesiae clones showed no clear mutational hot spots. This indicates that the acquired resistance phenotype depends on complex interactions between low-frequency mutations in the genetic background of the strains. We hypothesize that the increased tolerance in duo-species conditions promotes resistance by enhancing the selection of partially resistant mutants and opening up novel evolutionary trajectories that enable such genetic interactions. This hypothesis is reinforced by experimentally excluding potential effects of increased initial population size, enhanced mutation rate, and horizontal gene transfer. Altogether, our observations suggest that the community mode of life and the social interactions therein strongly affect the accessible evolutionary pathways toward antimicrobial resistance.IMPORTANCEAntimicrobial resistance is one of the most studied bacterial properties due to its enormous clinical and industrial relevance; however, most research focuses on resistance development of a single species in isolation. In the present study, we showed that resistance evolution of brewery isolates can differ greatly between single- and mixed-species conditions. Specifically, we observed that the development of antimicrobial resistance in certain species can be significantly enhanced in co-culture as compared to the single-species conditions. Overall, the current study emphasizes the need of considering the within bacterial interactions in microbial communities when evaluating antimicrobial treatments and resistance evolution.}, }
@article {pmid37818230, year = {2023}, author = {Grander, C and Meyer, M and Steinacher, D and Claudel, T and Hausmann, B and Pjevac, P and Grabherr, F and Oberhuber, G and Grander, M and Brigo, N and Jukic, A and Schwärzler, J and Weiss, G and Adolph, TE and Trauner, M and Tilg, H}, title = {24-Norursodeoxycholic acid ameliorates experimental alcohol-related liver disease and activates hepatic PPARγ.}, journal = {JHEP reports : innovation in hepatology}, volume = {5}, number = {11}, pages = {100872}, pmid = {37818230}, issn = {2589-5559}, support = {P 29379/FWF_/Austrian Science Fund FWF/Austria ; P 33070/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {BACKGROUND &amp; AIMS: Alcohol-related liver disease (ALD) is a global healthcare challenge with limited treatment options. 24-Norursodeoxycholic acid (NorUDCA) is a synthetic bile acid with anti-inflammatory properties in experimental and human cholestatic liver diseases. In the present study, we explored the efficacy of norUDCA in experimental ALD.<br><br>METHODS: NorUDCA was tested in a preventive and therapeutic setting in an experimental ALD model (Lieber-DeCarli diet enriched with ethanol). Liver disease was phenotypically evaluated using histology and biochemical methods, and anti-inflammatory properties and peroxisome proliferator-activated receptor gamma activation by norUDCA were evaluated in cellular model systems.<br><br>RESULTS: NorUDCA administration ameliorated ethanol-induced liver injury, reduced hepatocyte death, and reduced the expression of hepatic pro-inflammatory cytokines including tumour necrosis factor (Tnf), Il-1&#x3b2;, Il-6, and Il-10. NorUDCA shifted hepatic macrophages towards an anti-inflammatory M2 phenotype. Further, norUDCA administration altered the composition of the intestinal microbiota, specifically increasing the abundance of Roseburia, Enterobacteriaceae, and Clostridum spp. In a&#xa0;therapeutic model, norUDCA also ameliorated ethanol-induced liver injury. Moreover, norUDCA suppressed lipopolysaccharide-induced IL-6 expression in human peripheral blood mononuclear cells and evoked peroxisome proliferator-activated receptor gamma activation.<br><br>CONCLUSIONS: NorUDCA ameliorated experimental ALD, protected against hepatic inflammation, and affected gut microbial commensalism. NorUDCA could serve as a novel therapeutic agent in the future management of patients with ALD.<br><br>IMPACT AND IMPLICATIONS: Alcohol-related liver disease is a global healthcare concern with limited treatment options. 24-Norursodeoxycholic acid (NorUDCA) is a modified bile acid, which was proven to be effective in human cholestatic liver diseases. In the present study, we found a protective effect of norUDCA in experimental alcoholic liver disease. For patients with ALD, norUDCA could be a potential new treatment option.}, }
@article {pmid37816903, year = {2023}, author = {Abdolahpur Monikh, F and Baun, A and Hartmann, NB and Kortet, R and Akkanen, J and Lee, JS and Shi, H and Lahive, E and Uurasjärvi, E and Tufenkji, N and Altmann, K and Wiesner, Y and Grossart, HP and Peijnenburg, W and Kukkonen, JVK}, title = {Exposure protocol for ecotoxicity testing of microplastics and nanoplastics.}, journal = {Nature protocols}, volume = {18}, number = {11}, pages = {3534-3564}, pmid = {37816903}, issn = {1750-2799}, support = {965367//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 964766//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {Humans ; *Microplastics/analysis/toxicity ; Plastics/toxicity ; *Water Pollutants, Chemical/analysis/chemistry/toxicity ; }, abstract = {Despite the increasing concern about the harmful effects of micro- and nanoplastics (MNPs), there are no harmonized guidelines or protocols yet available for MNP ecotoxicity testing. Current ecotoxicity studies often use commercial spherical particles as models for MNPs, but in nature, MNPs occur in variable shapes, sizes and chemical compositions. Moreover, protocols developed for chemicals that dissolve or form stable dispersions are currently used for assessing the ecotoxicity of MNPs. Plastic particles, however, do not dissolve and also show dynamic behavior in the exposure medium, depending on, for example, MNP physicochemical properties and the medium's conditions such as pH and ionic strength. Here we describe an exposure protocol that considers the particle-specific properties of MNPs and their dynamic behavior in exposure systems. Procedure 1 describes the top-down production of more realistic MNPs as representative of MNPs in nature and particle characterization (e.g., using thermal extraction desorption-gas chromatography/mass spectrometry). Then, we describe exposure system development for short- and long-term toxicity tests for soil (Procedure 2) and aquatic (Procedure 3) organisms. Procedures 2 and 3 explain how to modify existing ecotoxicity guidelines for chemicals to target testing MNPs in selected exposure systems. We show some examples that were used to develop the protocol to test, for example, MNP toxicity in marine rotifers, freshwater mussels, daphnids and earthworms. The present protocol takes between 24 h and 2 months, depending on the test of interest and can be applied by students, academics, environmental risk assessors and industries.}, }
@article {pmid37816747, year = {2023}, author = {Rahlff, J and Esser, SP and Plewka, J and Heinrichs, ME and Soares, A and Scarchilli, C and Grigioni, P and Wex, H and Giebel, HA and Probst, AJ}, title = {Marine viruses disperse bidirectionally along the natural water cycle.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {6354}, pmid = {37816747}, issn = {2041-1723}, mesh = {*Ecosystem ; Water Cycle ; Seawater/analysis ; *Viruses/genetics ; Aerosols/analysis ; }, abstract = {Marine viruses in seawater have frequently been studied, yet their dispersal from neuston ecosystems at the air-sea interface towards the atmosphere remains a knowledge gap. Here, we show that 6.2% of the studied virus population were shared between air-sea interface ecosystems and rainwater. Virus enrichment in the 1-mm thin surface microlayer and sea foams happened selectively, and variant analysis proved virus transfer to aerosols collected at ~2 m height above sea level and rain. Viruses detected in rain and these aerosols showed a significantly higher percent G/C base content compared to marine viruses. CRISPR spacer matches of marine prokaryotes to foreign viruses from rainwater prove regular virus-host encounters at the air-sea interface. Our findings on aerosolization, adaptations, and dispersal support transmission of viruses along the natural water cycle.}, }
@article {pmid37816673, year = {2023}, author = {Byers, AK and Condron, LM and O'Callaghan, M and Waller, L and Dickie, IA and Wakelin, SA}, title = {Plant species identity and plant-induced changes in soil physicochemistry-but not plant phylogeny or functional traits - shape the assembly of the root-associated soil microbiome.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {11}, pages = {}, pmid = {37816673}, issn = {1574-6941}, mesh = {*Soil Microbiology ; Phylogeny ; Soil ; *Microbiota ; Bacteria/genetics ; Plants/microbiology ; Plant Roots/microbiology ; Rhizosphere ; }, abstract = {The root-associated soil microbiome contributes immensely to support plant health and performance against abiotic and biotic stressors. Understanding the processes that shape microbial assembly in root-associated soils is of interest in microbial ecology and plant health research. In this study, 37 plant species were grown in the same soil mixture for 10 months, whereupon the root-associated soil microbiome was assessed using amplicon sequencing. From this, the contribution of direct and indirect plant effects on microbial assembly was assessed. Plant species and plant-induced changes in soil physicochemistry were the most significant factors that accounted for bacterial and fungal community variation. Considering that all plants were grown in the same starting soil mixture, our results suggest that plants, in part, shape the assembly of their root-associated soil microbiome via their effects on soil physicochemistry. With the increase in phylogenetic ranking from plant species to class, we observed declines in the degree of community variation attributed to phylogenetic origin. That is, plant-microbe associations were unique to each plant species, but the phylogenetic associations between plant species were not important. We observed a large degree of residual variation (> 65%) not accounted for by any plant-related factors, which may be attributed to random community assembly.}, }
@article {pmid37814279, year = {2023}, author = {Liu, W and Liu, H and Wang, Y and Zhao, Z and Balasubramanian, B and Jha, R}, title = {Effects of Enteromorpha prolifera polysaccharides on growth performance, intestinal barrier function and cecal microbiota in yellow-feathered broilers under heat stress.}, journal = {Journal of animal science and biotechnology}, volume = {14}, number = {1}, pages = {132}, pmid = {37814279}, issn = {1674-9782}, support = {32002196//National Nature Science Foundation of China/ ; }, abstract = {BACKGROUND: Global warming leading to heat stress (HS) is becoming a major challenge for broiler production. This study aimed to explore the protective effects of seaweed (Enteromorpha prolifera) polysaccharides (EPS) on the intestinal barrier function, microbial ecology, and performance of broilers under HS. A total of 144 yellow-feathered broilers (male, 56 days old) with 682.59 ± 7.38 g were randomly assigned to 3 groups: 1) TN (thermal neutral zone, 23.6 ± 1.8 °C), 2) HS (heat stress, 33.2 ± 1.5 °C for 10 h/d), and 3) HSE (HS + 0.1% EPS). Each group contained 6 replicates with 8 broilers per replicate. The study was conducted for 4 weeks; feed intake and body weights were measured at the end of weeks 2 and 4. At the end of the feeding trial, small intestine samples were collected for histomorphology, antioxidant, secretory immunoglobulin A (sIgA) content, apoptosis, gene and protein expression analysis; cecal contents were also collected for microbiota analysis based on 16S rDNA sequencing.<br><br>RESULTS: Dietary EPS promoted the average daily gain (ADG) of broilers during 3-4 weeks of HS (P&#x2009;<&#x2009;0.05). At the end of HS on broilers, the activity of total superoxide dismutase (T-SOD), glutathione S-transferase (GST), and the content of sIgA in jejunum were improved by EPS supplementation (P&#x2009;<&#x2009;0.05). Besides, dietary EPS reduced the epithelial cell apoptosis of jejunum and ileum in heat-stressed broilers (P&#x2009;<&#x2009;0.05). Addition of EPS in HS group broilers' diet upregulated the relative mRNA expression of Occludin, ZO-1, &#x3b3;-GCLc and IL-10 of the jejunum (P&#x2009;<&#x2009;0.05), whereas downregulated the relative mRNA expression of NF-&#x3ba;B p65, TNF-&#x3b1; and IL-1&#x3b2; of the jejunum (P&#x2009;<&#x2009;0.05). Dietary EPS increased the protein expression of Occludin and ZO-1, whereas it reduced the protein expression of NF-&#x3ba;B p65 and MLCK (P&#x2009;<&#x2009;0.01) and tended to decrease the protein expression of TNF-&#x3b1; (P&#x2009;=&#x2009;0.094) in heat-stressed broilers. Furthermore, the proportions of Bacteroides and Oscillospira among the three groups were positively associated with jejunal apoptosis and pro-inflammatory cytokine expression (P&#x2009;<&#x2009;0.05) and negatively correlated with jejunal Occludin level (P&#x2009;<&#x2009;0.05). However, the proportions of Lactobacillus, Barnesiella, Subdoligranulum, Megasphaera, Collinsella, and Blautia among the three groups were positively related to ADG (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: EPS can be used as a feed additive in yellow-feathered broilers. It effectively improves growth performance and alleviates HS-induced intestinal injury by relieving inflammatory damage and improving the tight junction proteins expression. These beneficial effects may be related to inhibiting NF-&#x3ba;B/MLCK signaling pathway activation and regulation of cecal microbiota.}, }
@article {pmid37813267, year = {2024}, author = {Biagioli, F and Coleine, C and Delgado-Baquerizo, M and Feng, Y and Saiz-Jimenez, C and Selbmann, L}, title = {Outdoor climate drives diversity patterns of dominant microbial taxa in caves worldwide.}, journal = {The Science of the total environment}, volume = {906}, number = {}, pages = {167674}, doi = {10.1016/j.scitotenv.2023.167674}, pmid = {37813267}, issn = {1879-1026}, mesh = {Caves/microbiology ; Bacteria/metabolism ; *Microbiota ; Geography ; *Mycobiome ; }, abstract = {The cave microbiota is assumed to be shaped by indoor microclimate, biotic and abiotic factors, which are largely dependent from outside environmental conditions; however, this knowledge is available at local or regional scales only. To address this knowledge gap, we reanalyzed over 1050 bacterial and fungal communities of caves worldwide, and found that outdoor temperature and rainfall play a critical role in explaining differences in microbial diversity patterns of global caves, selecting specific dominant taxa across gradients of growing aridity conditions with arid climate leading to a reduction in total cave microbial diversity. Moreover, we found that fungal (from 186 to 1908 taxa) and bacterial (from 467 to 1619 taxa) diversity increased under temperate-tropical and temperate-continental climatic regions, respectively, highlighting an opposite preference for the two microbial compartments. We hypothesized that outdoor geographical, climatic variables and lithology are critical epistatic drivers in assembling microbial communities and their dominant taxa, whose ecological responses could be useful to predict the fate of these subterranean environments in the context of climate change. Our work elucidates the intimate connection between caves microbiota and surface ecosystems highlighting the sensitivity of cave microbial communities to climatic changes and environmental degradation. This work also provides a natural benchmark for the biogeographic information for caves globally and for protection strategies aiming at conservation of underground environments.}, }
@article {pmid37812012, year = {2023}, author = {Kocurek, B and Ramachandran, P and Grim, CJ and Morin, P and Howard, L and Ottesen, A and Timme, R and Leonard, SR and Rand, H and Strain, E and Tadesse, D and Pettengill, JB and Lacher, DW and Mammel, M and Jarvis, KG}, title = {Application of quasimetagenomics methods to define microbial diversity and subtype Listeria monocytogenes in dairy and seafood production facilities.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0148223}, pmid = {37812012}, issn = {2165-0497}, mesh = {Humans ; *Listeria monocytogenes/genetics ; Food Microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Seafood ; }, abstract = {In developed countries, the human diet is predominated by food commodities, which have been manufactured, processed, and stored in a food production facility. Little is known about the application of metagenomic sequencing approaches for detecting foodborne pathogens, such as L. monocytogenes, and characterizing microbial diversity in food production ecosystems. In this work, we investigated the utility of 16S rRNA amplicon and quasimetagenomic sequencing for the taxonomic and phylogenetic classification of Listeria culture enrichments of environmental swabs collected from dairy and seafood production facilities. We demonstrated that single-nucleotide polymorphism (SNP) analyses of L. monocytogenes metagenome-assembled genomes (MAGs) from quasimetagenomic data sets can achieve similar resolution as culture isolate whole-genome sequencing. To further understand the impact of genome coverage on MAG SNP cluster resolution, an in silico downsampling approach was employed to reduce the percentage of target pathogen sequence reads, providing an initial estimate of required MAG coverage for subtyping resolution of L. monocytogenes.}, }
@article {pmid37812006, year = {2023}, author = {Phillips, EK and Shaffer, JMC and Henson, MW and Coelho, JT and Martin, MO and Thrash, JC}, title = {Genome sequences of four agarolytic bacteria from the Bacteroidia and Gammaproteobacteria.}, journal = {Microbiology resource announcements}, volume = {12}, number = {11}, pages = {e0066723}, pmid = {37812006}, issn = {2576-098X}, support = {Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation (SF)/ ; OCE-1945279, EF-2125191//National Science Foundation (NSF)/ ; }, abstract = {Here we present the genomes of four marine agarolytic bacteria belonging to the Bacteroidota and Proteobacteria. Two genomes are closed and two are in draft form, but all are at least 99% complete and offer new opportunities to study agar-degradation in marine bacteria.}, }
@article {pmid37811990, year = {2023}, author = {He, D and Yao, X and Zhang, P and Liu, W and Huang, J and Sun, H and Wang, N and Zhang, X and Wang, H and Zhang, H and Ao, X and Xie, F}, title = {Effects of continuous cropping on fungal community diversity and soil metabolites in soybean roots.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0178623}, pmid = {37811990}, issn = {2165-0497}, support = {LJKZ0678//Project of Scientific Research in Education Department of Liaoning Province, China/ ; 22-318-2-05//Project of Science and technology of Shenyang, China/ ; LJKZ0630//Project of Scientific Research in Education Department of Liaoning province, China/ ; }, mesh = {*Soil ; *Mycobiome ; Glycine max ; Rhizosphere ; Soil Microbiology ; Crops, Agricultural/microbiology ; }, abstract = {Soybean yield can be affected by soybean soil fungal communities in different tillage patterns. Soybean is an important food crop with great significance worldwide. Continuous cultivation resulted in soil nutrient deficiencies, disordered metabolism of root exudates, fungal pathogen accumulation, and an altered microbial community, which brought a drop in soybean output. In this study, taking the soybean agroecosystem in northeast China, we revealed the microbial ecology and soil metabolites spectrum, especially the diversity and composition of soil fungi and the correlation of pathogenic fungi, and discussed the mechanisms and the measures of alleviating the obstacles.}, }
@article {pmid37810791, year = {2023}, author = {McKenney, EA and Nichols, LM and Alvarado, S and Hardy, S and Kemp, K and Polmanteer, R and Shoemaker, A and Dunn, RR}, title = {Sourdough starters exhibit similar succession patterns but develop flour-specific climax communities.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16163}, pmid = {37810791}, issn = {2167-8359}, mesh = {*Flour/microbiology ; RNA, Ribosomal, 16S/genetics ; Fermentation ; *Bacteria/genetics ; Lactobacillus/genetics ; }, abstract = {The microbial fermentation behind sourdough bread is among our oldest technologies, yet there are many opportunities for sourdough science to learn from traditional bakers. We analyzed 16S rRNA sequences in R to assess the bacterial community structure and performance of 40 starters grown from 10 types of flour over 14 days, and identified six distinct stages of succession. At each stage, bacterial taxa correlate with determinants of bread quality including pH, rise, and aromatic profile. Day 1 starter cultures were dominated by microorganisms commonly associated with plants and flour, and by aromas similar to toasted grain/cereal. Bacterial diversity peaked from days 2-6 as taxa shifted from opportunistic/generalist bacteria associated with flour inputs, toward specialized climax bacterial communities (days 10-14) characterized by acid-tolerant taxa and fruity (p < 3.03e-03), sour (p < 1.60e-01), and fermented (p < 1.47e-05) aromas. This collection of traits changes predictably through time, regardless of flour type, highlighting patterns of bacterial constraints and dynamics that are conserved across systems and scales. Yet, while sourdough climax communities exhibit similar markers of maturity (i.e., pH ≤ 4 and enriched in Lactobacillus (mean abundance 48.1%), Pediococcus (mean abundance 22.7%), and/or Gluconobacter (mean abundance 19.1%)), we also detected specific taxa and aromas associated with each type of flour. Our results address important ecological questions about the relationship between community structure and starter performance, and may enable bakers to deliberately select for specific sourdough starter and bread characteristics.}, }
@article {pmid37807043, year = {2023}, author = {Hayes, MG and Langille, MGI and Gu, H}, title = {Cross-study analyses of microbial abundance using generalized common factor methods.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {380}, pmid = {37807043}, issn = {1471-2105}, support = {CGS-M Alexander Graham Bell Scholarship//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN/05108-2017//Natural Sciences and Engineering Research Council of Canada/ ; Scotia Scholars Award//Nova Scotia Health Research Foundation/ ; }, mesh = {*Metagenome ; *Microbiota/genetics ; Metagenomics/methods ; Genomics ; Computational Biology/methods ; }, abstract = {BACKGROUND: By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to a new frontier in microbial ecology, promising the ability to leverage the microbiome to make crucial advancements in the environmental and biomedical sciences. However, this is challenging, as genomic data are high-dimensional, sparse, and noisy. Much of this noise reflects the exact conditions under which sequencing took place, and is so significant that it limits consensus-based validation of study results.<br><br>RESULTS: We propose an ensemble approach for cross-study exploratory analyses of microbial abundance data in which we first estimate the variance-covariance matrix of the underlying abundances from each dataset on the log scale assuming Poisson sampling, and subsequently model these covariances jointly so as to find a shared low-dimensional subspace of the feature space.<br><br>CONCLUSIONS: By viewing the projection of the latent true abundances onto this common structure, the variation is pared down to that which is shared among all datasets, and is likely to reflect more generalizable biological signal than can be inferred from individual datasets. We investigate several ways of achieving this, demonstrate that they work well on simulated and real metagenomic data in terms of signal retention and interpretability, and recommend a particular implementation.}, }
@article {pmid37805972, year = {2023}, author = {Pandit, B and Moin, A and Mondal, A and Banik, A and Alam, M}, title = {Characterization of a biofilm-forming, amylase-producing, and heavy-metal-bioremediating strain Micrococcus sp. BirBP01 isolated from oligotrophic subsurface lateritic soil.}, journal = {Archives of microbiology}, volume = {205}, number = {11}, pages = {351}, pmid = {37805972}, issn = {1432-072X}, mesh = {Micrococcus/genetics/metabolism ; Soil ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Metals, Heavy/metabolism ; Bacteria/genetics ; Biofilms ; *Soil Pollutants/metabolism ; Biodegradation, Environmental ; }, abstract = {Lateritic soil is the reddish to brown-colored soil composed mainly of iron or aluminium oxides, hydroxides, or oxyhydroxides. Information on bacteria that inhabit this soil type, their ecological role, and metabolic potential are scarce. We have isolated and partially characterized a bacterial strain BirBP01 from a lead, calcium, and magnesium-rich, oligotrophic subsurface lateritic soil-sample collected from 12-feet deep horizon of a laterite mining pit in Birbhum district, India. The isolate is a biofilm-forming, Gram-positive bacterium having a sarcinae arrangement, mesophilic, slightly alkaliphilic, able to produce amylase, and resistant against multiple heavy-metals. BirBP01 has the ability to bioremediate 51% of Pb, 30% of Zn, and 22% of Cu through biosorption, possibly into the biofilm matrix. The bioremediating ability of the bacterium alleviated the inhibitory effect of heavy-metals on the germination of chickpea (Cicer arietinum L.) seeds. 16S rRNA gene-based phylogenetic analysis revealed that BirBP01 is a member of the genus Micrococcus. It showed more than 99% identity of the 16S rRNA gene sequence, and clustered within the same branch of the phylogenetic tree, with strains of M. yunnanensis, M. endophyticus, and M. luteus. The ability to produce amylase, and bioremediate heavy-metals signify that Micrococcus sp. BirBP01 could be potentially a good candidate for industrial applications, and to clean up heavy-metal contaminated sites.}, }
@article {pmid37804686, year = {2024}, author = {Çömlekcioğlu, U and Jezierska, S and Opsomer, G and Pascottini, OB}, title = {Uterine microbial ecology and disease in cattle: A review.}, journal = {Theriogenology}, volume = {213}, number = {}, pages = {66-78}, doi = {10.1016/j.theriogenology.2023.09.016}, pmid = {37804686}, issn = {1879-3231}, mesh = {Female ; Cattle ; Animals ; Dysbiosis/veterinary ; *Cattle Diseases/prevention &amp; control/microbiology ; Uterus/microbiology ; *Endometritis/veterinary ; Bacteria ; *Uterine Diseases/veterinary/microbiology ; }, abstract = {Due to the critical contribution of the uterine-associated microbiota in reproductive health, physiology, and performance, culture-independent methods have been increasingly employed to unravel key aspects of microbial ecology in the uterus of cattle. Nowadays, we know that bacterial diversity is crucial to maintain uterine health, however, there is still no consensus on the exact composition of a healthy uterine microbiota (or eubiosis). Generally, loss of bacterial diversity (or dysbiosis) contributes to the development of uterine infections, associated with increased relative abundances of Bacteroides, Fusobacterium, Trueperella, and Porphyromonas. Uterine infections are highly prevalent and gravely influence the profitability of cattle operations, animal welfare, and public health. Thus, understanding the dynamics of uterine microbial ecology is essential to develop effective strategies focused on preventing and mitigating the adverse effects of uterine dysbiosis as well as assisting in the process of restoring the core, healthy uterine microbiota. The aim of this review is to summarize research conducted in the microbial ecology of bovine uteri. We discuss the origin of the uterine microflora of healthy cows and the factors influencing its composition. In addition, we review the biology of specific pathogens that are known to increase in abundance during the occurrence of uterine disease. Lastly, we provide an overview of the bacterial biofilm in the bovine endometrium, and we briefly summarize the rationale for the use of probiotics to prevent uterine disease in cattle.}, }
@article {pmid37803760, year = {2023}, author = {Tadielo, LE and Dos Santos, EAR and Possebon, FS and Schmiedt, JA and Juliano, LCB and Cerqueira-Cézar, CK and de Oliveira, JP and Sampaio, ANDCE and Melo, PRL and Caron, EFF and Pinto, JPAN and Bersot, LDS and Pereira, JG}, title = {Characterization of microbial ecology, Listeria monocytogenes, and Salmonella sp. on equipment and utensil surfaces in Brazilian poultry, pork, and dairy industries.}, journal = {Food research international (Ottawa, Ont.)}, volume = {173}, number = {Pt 2}, pages = {113422}, doi = {10.1016/j.foodres.2023.113422}, pmid = {37803760}, issn = {1873-7145}, mesh = {Animals ; Swine ; *Listeria monocytogenes ; Poultry ; Food Microbiology ; Dairying ; *Pork Meat ; Brazil ; RNA, Ribosomal, 16S ; *Red Meat ; Escherichia coli ; Salmonella/genetics ; }, abstract = {This study aimed to evaluate the level of counting by indicator microorganisms, identify the microbial ecology, detect Listeria monocytogenes and Salmonella sp., and determine the presence of virulence genes and biofilm formation. A total of 480 samples were collected from the surfaces of the equipment and utensils using sterile swabs for the detection of L. monocytogenes and Salmonella sp. and counting mesophilic aerobes, Enterobacteriaceae, Escherichia coli, and Pseudomonas sp. The microbial ecology was evaluated by sequencing the 16S rRNA gene. Genes for virulence and biofilm formation were analyzed and adhesion capacity was evaluated for L. monocytogenes and Salmonella sp. The mesophilic aerobe count was the highest in the dairy processing facility, followed by the pork and poultry slaughterhouses. L. monocytogenes was detected in all facilities, with the highest detection in the pork slaughterhouse, followed by the poultry and dairy facilities. Salmonella sp. was only detected in the dairy. Isolates of L. monocytogenes and Salmonella sp. showed poor adhesion to polystyrene surfaces, virulence genes, and biofilm formation. The frequent contaminants in the slaughterhouses were Pseudomonas, Acinetobacter, and Aeromonas in poultry, Acinetobacter, Pseudomonas, and Brevundimonas in pork, and Pseudomonas, Kocuria, and Staphylococcus in dairy. Our results provide useful information to understand the microbiological risks associated with contamination.}, }
@article {pmid37803713, year = {2023}, author = {Podduturi, R and da Silva David, G and da Silva, RJ and Hyldig, G and Jørgensen, NOG and Agerlin Petersen, M}, title = {Characterization and finding the origin of off-flavor compounds in Nile tilapia cultured in net cages in hydroelectric reservoirs, São Paulo State, Brazil.}, journal = {Food research international (Ottawa, Ont.)}, volume = {173}, number = {Pt 2}, pages = {113375}, doi = {10.1016/j.foodres.2023.113375}, pmid = {37803713}, issn = {1873-7145}, mesh = {Animals ; *Cichlids ; Brazil ; *Volatile Organic Compounds ; Naphthols/analysis/chemistry ; }, abstract = {An increasing demand for fish products has led to an intensive aquaculture production in Brazil, and cultivation of fish constituted 860 × 10[3] tons in 2022, contributing to the 87% of total fish consumption. Nile tilapia constitutes almost half of the aquaculture production, and most tilapia farms use floating net cages. One of the major constraints of intensive fish production is production of off-flavors. Release of nutrients by the fish leads to deterioration of the water quality and stimulates growth of microorganisms, also including off-flavor producing species. The objective of this study was to determine levels of taste and odor compounds (geosmin, 2-MIB and a selection of volatile compounds) and their impact on the flavor quality of Nile tilapia produced in net cages in reservoirs in São Paulo State, Brazil. GC-MS analysis of fish and water from six different farms showed concentrations of geosmin in the water from 1 to 8 ng/L, while geosmin in fish flesh ranged from 40 to 750 ng/kg. The level of 2-MIB in water was 2 to 25 ng/L, and 0 to 800 ng/kg fish. The GC-MS analysis also revealed presence of more than 100 volatile organic compounds in the fish flesh, consisting of aldehydes, alcohols, benzene derivatives, hydrocarbons, ketones and few other compounds. Geosmin and 2-MIB related flavor notes were detected in all fish by a sensory panel, and a high correlation between the chemical and sensory analyses was found. The potential impact of the volatile organic compounds on the fish flavor is discussed. Analysis of the water quality in the reservoirs indicated that levels of geosmin and 2-MIB levels were highly influenced by the nutrient levels in the water.}, }
@article {pmid37802356, year = {2024}, author = {Sarkodie, EK and Jiang, L and Li, K and Guo, Z and Yang, J and Shi, J and Peng, Y and Wu, X and Huang, S and Deng, Y and Jiang, H and Liu, H and Liu, X}, title = {The influence of cysteine in transformation of Cd fractionation and microbial community structure and functional profile in contaminated paddy soil.}, journal = {The Science of the total environment}, volume = {906}, number = {}, pages = {167535}, doi = {10.1016/j.scitotenv.2023.167535}, pmid = {37802356}, issn = {1879-1026}, mesh = {Humans ; Cadmium/analysis ; Cysteine ; Soil/chemistry ; *Microbiota ; Sulfur ; Nitrogen ; *Soil Pollutants/analysis ; *Oryza ; }, abstract = {Remediating cadmium (Cd) contaminated paddy soil is vital for agroecology, food safety, and human health. Soil washing is more feasible to reduce remediation method due to its high efficiency. However, green, low-cost and more efficient washing agents are still required. In this study, we investigated the ability of cysteine as a washing agent for soil washing to remove Cd from contaminated paddy soil. Through a batch experiment, we evaluated the removal efficiency of cysteine as a washing agent by comparing their removal rate with that of a microbial inoculant and sulphuric acid as other washing agents. The transformation of Cd fractionation and microbial community structure and functional profile in paddy soils after cysteine leaching was studied by using sequential extraction and high-throughput sequencing. Results showed that cysteine had better efficiency in the removal of Cd from paddy soil in comparison to sulphuric acid and the microbial inoculant, and could achieve a maximum removal rate of 97 % Cd in paddy soil. Cysteine decreased the proportion of Cd in the exchangeable fraction, carbonate bound fraction, iron and manganese bound fraction, and organic matter bound fraction and was best for the removal of the residual fraction, which contributed to its higher Cd removal ability. Considering the economic benefits of the reagents used, cysteine was shown to be economically feasible for use as a leaching agent. In addition, cysteine could significantly increase the relative abundance of Thermochromatium, Sideroxydans, Streptacidiphilus, and Frankia which promoted the nitrogen and sulfur metabolism in the paddy soil. In summary, this study revealed that cysteine was readily available, cheap, non-toxic, highly efficient, and even has fertilizing properties, making it eco-friendly and ideal for remediation of Cd-contaminated paddy soils. Besides, the health of paddy soils would also benefit from cysteine's promotion of microbial nitrogen and sulfur metabolism.}, }
@article {pmid37800904, year = {2023}, author = {Ettinger, CL and Wu-Woods, J and Kurbessoian, T and Brown, DJ and Souza Pacheco, Id and Vindiola, BG and Walling, LL and Atkinson, PW and Byrne, FJ and Redak, R and Stajich, JE}, title = {Geographical survey of the mycobiome and microbiome of Southern California glassy-winged sharpshooters.}, journal = {mSphere}, volume = {8}, number = {5}, pages = {e0026723}, pmid = {37800904}, issn = {2379-5042}, mesh = {Xylella ; RNA, Ribosomal, 16S/genetics ; *Mycobiome ; *Microbiota ; Animals ; *Hemiptera/microbiology ; Geography ; }, abstract = {The glassy-winged sharpshooter, Homalodisca vitripennis Germar, is an invasive xylem-feeding leafhopper with a devastating economic impact on California agriculture through transmission of the plant pathogen, Xylella fastidiosa. While studies have focused on X. fastidiosa or known symbionts of H. vitripennis, little work has been done at the scale of the microbiome (the bacterial community) or mycobiome (the fungal community). Here, we characterize the mycobiome and the microbiome of H. vitripennis across Southern California and explore correlations with captivity and host insecticide resistance status. Using high-throughput sequencing of the ribosomal internal transcribed spacer 1 region and the 16S rRNA gene to profile the mycobiome and microbiome, respectively, we found that while the H. vitripennis mycobiome significantly varied across Southern California, the microbiome did not. We also observed a significant difference in both the mycobiome and microbiome between captive and wild H. vitripennis. Finally, we found that the mycobiome, but not the microbiome, was correlated with insecticide resistance status in wild H. vitripennis. This study serves as a foundational look at the H. vitripennis mycobiome and microbiome across Southern California. Future work should explore the putative link between microbes and insecticide resistance status and investigate whether microbial communities should be considered in H. vitripennis management practices. IMPORTANCE The glassy-winged sharpshooter is an invasive leafhopper that feeds on the xylem of plants and transmits the devastating pathogen, Xylella fastidiosa, resulting in significant economic damage to California's agricultural system. While studies have focused on this pathogen or obligate symbionts of the glassy-winged sharpshooter, there is limited knowledge of the bacterial and fungal communities that make up its microbiome and mycobiome. To address this knowledge gap, we explored the composition of the mycobiome and the microbiome of the glassy-winged sharpshooter across Southern California and identified differences associated with geography, captivity, and host insecticide resistance status. Understanding sources of variation in the microbial communities associated with the glassy-winged sharpshooter is an important consideration for developing management strategies to control this invasive insect. This study is a first step toward understanding the role microbes may play in the glassy-winged sharpshooter's resistance to insecticides.}, }
@article {pmid37799598, year = {2023}, author = {Wang, H and Yan, B and Wu, Y and Yin, M and Wang, M and Fu, C}, title = {Microbial community diversity and potential functionality in response to dam construction along the Three Gorge Reservoir, China.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1218806}, pmid = {37799598}, issn = {1664-302X}, abstract = {River and reservoir bacterial communities are the most basic part of river biomes and ecosystem structure, and play an important role in river biological processes. Yet, it remains unclear how highly regulated dam reservoirs affect both soil and sediment bacterial communities. A temporal distribution pattern of bacterial communities was investigated using Illumina MiSeq sequencing in a transition section of the Three Gorges Reservoir (TGR). In total, 106,682 features belong to the bacteria kingdom, encompassing 95 phyla, 228 classes, 514 orders, 871 families, 1959 genera, and 3,053 species. With water level regulation, Shannon diversity index, and observed species differed significantly, with no significant difference in Simpson evenness. Both in the high water level period (October) and the low water level period (June), Proteobacteria, Acidobacteri, and Chloroflexi were the most abundant phyla. Whereas, based on PCA plots and Circos plot, the microbial community structure has changed significantly. LEfSe method was used to identify the classified bacterial taxa with significant abundance differences between the low water level and high water level periods. KOs (KEGG Orthology) pathway enrichment analysis were conducted to investigate functional and related metabolic pathways in groups. To some extent, it can be inferred that water level regulation affects community growth by affecting the metabolism of the microbial community.}, }
@article {pmid37798675, year = {2023}, author = {Avila Santos, AP and Kabiru Nata'ala, M and Kasmanas, JC and Bartholomäus, A and Keller-Costa, T and Jurburg, SD and Tal, T and Camarinha-Silva, A and Saraiva, JP and Ponce de Leon Ferreira de Carvalho, AC and Stadler, PF and Sipoli Sanches, D and Rocha, U}, title = {The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {48}, pmid = {37798675}, issn = {2524-4671}, abstract = {BACKGROUND: Metagenomic data can shed light on animal-microbiome relationships and the functional potential of these communities. Over the past years, the generation of metagenomics data has increased exponentially, and so has the availability and reusability of data present in public repositories. However, identifying which datasets and associated metadata are available is not straightforward. We created the Animal-Associated Metagenome Metadata Database (AnimalAssociatedMetagenomeDB - AAMDB) to facilitate the identification and reuse of publicly available non-human, animal-associated metagenomic data, and metadata. Further, we used the AAMDB to (i) annotate common and scientific names of the species; (ii) determine the fraction of vertebrates and invertebrates; (iii) study their biogeography; and (iv) specify whether the animals were wild, pets, livestock or used for medical research.<br><br>RESULTS: We manually selected metagenomes associated with non-human animals from SRA and MG-RAST. &#xa0;Next, we standardized and curated 51 metadata attributes (e.g., host, compartment, geographic coordinates, and country). The AAMDB version 1.0 contains 10,885 metagenomes associated with 165 different species from 65 different countries.&#xa0;From the collected metagenomes, 51.1% were recovered from animals associated with medical research or grown for human consumption (i.e., mice, rats, cattle, pigs, and poultry). Further, we observed an over-representation of animals collected in temperate regions (89.2%) and a lower representation of samples from the polar zones, with only 11 samples in total. The most common genus among invertebrate animals was Trichocerca (rotifers).<br><br>CONCLUSION: Our work may guide host species selection in novel animal-associated metagenome research, especially in biodiversity and conservation studies. The data available in our database will allow scientists to perform meta-analyses and test new hypotheses (e.g., host-specificity, strain heterogeneity, and biogeography of animal-associated metagenomes), leveraging existing data. The AAMDB WebApp is a user-friendly interface that is publicly available at https://webapp.ufz.de/aamdb/ .}, }
@article {pmid37796897, year = {2023}, author = {Diao, M and Dyksma, S and Koeksoy, E and Ngugi, DK and Anantharaman, K and Loy, A and Pester, M}, title = {Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction.}, journal = {FEMS microbiology reviews}, volume = {47}, number = {5}, pages = {}, pmid = {37796897}, issn = {1574-6976}, support = {P 31996-B/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Oxidation-Reduction ; *Bacteria/metabolism ; *Archaea/metabolism ; Sulfates/metabolism ; Sulfites/metabolism ; Sulfur/metabolism ; Phylogeny ; }, abstract = {Sulfate/sulfite-reducing microorganisms (SRM) are ubiquitous in nature, driving the global sulfur cycle. A hallmark of SRM is the dissimilatory sulfite reductase encoded by the genes dsrAB. Based on analysis of 950 mainly metagenome-derived dsrAB-carrying genomes, we redefine the global diversity of microorganisms with the potential for dissimilatory sulfate/sulfite reduction and uncover genetic repertoires that challenge earlier generalizations regarding their mode of energy metabolism. We show: (i) 19 out of 23 bacterial and 2 out of 4 archaeal phyla harbor uncharacterized SRM, (ii) four phyla including the Desulfobacterota harbor microorganisms with the genetic potential to switch between sulfate/sulfite reduction and sulfur oxidation, and (iii) the combination as well as presence/absence of different dsrAB-types, dsrL-types and dsrD provides guidance on the inferred direction of dissimilatory sulfur metabolism. We further provide an updated dsrAB database including > 60% taxonomically resolved, uncultured family-level lineages and recommendations on existing dsrAB-targeted primers for environmental surveys. Our work summarizes insights into the inferred ecophysiology of newly discovered SRM, puts SRM diversity into context of the major recent changes in bacterial and archaeal taxonomy, and provides an up-to-date framework to study SRM in a global context.}, }
@article {pmid37794496, year = {2023}, author = {Lühken, R and Becker, N and Dyczko, D and Sauer, FG and Kliemke, K and Schmidt-Chanasit, J and Rydzanicz, K}, title = {First record of Anopheles (Anopheles) hyrcanus (Pallas 1771) (Diptera: Culicidae) in Poland.}, journal = {Parasites &amp; vectors}, volume = {16}, number = {1}, pages = {345}, pmid = {37794496}, issn = {1756-3305}, support = {BMBF//Bundesministerium f&#xfc;r Bildung und Forschung/ ; BMBF//Bundesministerium f&#xfc;r Bildung und Forschung/ ; BMBF//Bundesministerium f&#xfc;r Bildung und Forschung/ ; }, mesh = {Animals ; *Culicidae ; *Anopheles/parasitology ; Poland ; Mosquito Vectors ; Climate ; Europe ; }, abstract = {The spatial distribution of mosquito species in the course of globalization and climate warming is highly dynamic. Different studies have demonstrated the spread and establishment of thermophilic mosquito species, potentially increasing the prevalence of 'nuisance' mosquitoes and the local transmission of pathogens. Here we report the first recorded sampling of Anopheles hyrcanus in Wrocław, southwest Poland. This is the most northern detection of this species to date in Europe. Future spread and population development of this potential vector of malaria parasites, viruses or zoonotic helminths, such as Dirofilaria spp., must be monitored carefully. Potential factors underlying the spread of this species are discussed.}, }
@article {pmid37794421, year = {2023}, author = {Xiang, S and Chen, Z and Dai, Z and Wang, F}, title = {Global burden of lower respiratory infections attributable to secondhand smoke among children under 5 years of age, 2010-2019: a systematic analysis of the global burden of disease study 2019.}, journal = {BMC public health}, volume = {23}, number = {1}, pages = {1920}, pmid = {37794421}, issn = {1471-2458}, mesh = {Humans ; Child ; Child, Preschool ; Global Burden of Disease ; *Tobacco Smoke Pollution/adverse effects ; Quality-Adjusted Life Years ; *Respiratory Tract Infections/epidemiology ; Risk Factors ; Global Health ; }, abstract = {BACKGROUND: Epidemiological trends of lower respiratory infections (LRIs) attributable to secondhand smoke (SHS) among children under 5 years since smoking bans have been increasingly applied globally remain unclear. Here, we aimed to estimate the spatiotemporal trends of the global, regional, and national burden of LRIs attributable to SHS among children under 5 years old between 2010 and 2019.<br><br>METHODS: Data on the deaths, and disability adjusted life years (DALYs) of the disease burden was retrieved from the Global Burden of Disease (GBD) 2019 for 204 countries and territories between 2010 and 2019. The rates per 100,000 population, along with 95% uncertainty intervals, as well as population-attributable fraction (PAF) was presented for each estimate.<br><br>RESULTS: In 2019, an estimated 6.94% (3.80-10.12%) of under-5 LRIs deaths were attributable to SHS globally, with an under-5 mortality rate of 7.02 per 100,000, a decrease of 5.77% since 2010. Similarly, 6.95% (3.81-10.13%) of LRIs DALYs were due to SHS among children under 5 years, with a rate in under-5s of 619.36 DALYs per 100,000, and also a 5.77% decrease since 2010. Azerbaijan, Turkmenistan, and Papua New Guinea showed the highest under-5 mortality and DALYs burden rates of LRIs attributable to SHS in 2019. In contrast, the PAF was stagnant over the past ten years and there is even a year-on-year upward trend in South Asia. Nationally, in 2019, Bosnia and Herzegovina, Armenia, and Montenegro showed the highest PAFSHS of LRIs burden among children under 5 years of age. In addition, the burden was heavier in children under 1 year of age and was significantly negatively associated with sociodemographic index.<br><br>CONCLUSIONS: SHS remains a risk factor that cannot be ignored for LRIs burden worldwide. Hence, governments and health systems should continue to take steps to reduce SHS pollution among young children to mitigate this burden.}, }
@article {pmid37794084, year = {2023}, author = {Hettiarachchi, A and Cnockaert, M and Joossens, M and Gekière, A and Meeus, I and Vereecken, NJ and Michez, D and Smagghe, G and Vandamme, P}, title = {The wild solitary bees Andrena vaga, Anthophora plumipes, Colletes cunicularius, and Osmia cornuta microbiota are host specific and dominated by endosymbionts and environmental microorganisms.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3013-3026}, pmid = {37794084}, issn = {1432-184X}, mesh = {Bees ; Animals ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Mycobiome ; Bacteria ; *Spiroplasma ; }, abstract = {We characterized the microbial communities of the crop, midgut, hindgut, and ovaries of the wild solitary bees Andrena vaga, Anthophora plumipes, Colletes cunicularius, and Osmia cornuta through 16S rRNA gene and ITS2 amplicon sequencing and a large-scale isolation campaign. The bacterial communities of these bees were dominated by endosymbionts of the genera Wolbachia and Spiroplasma. Bacterial and yeast genera representing the remaining predominant taxa were linked to an environmental origin. While only a single sampling site was examined for Andrena vaga, Anthophora plumipes, and Colletes cunicularius, and two sampling sites for Osmia cornuta, the microbiota appeared to be host specific: bacterial, but not fungal, communities generally differed between the analyzed bee species, gut compartments and ovaries. This may suggest a selective process determined by floral and host traits. Many of the gut symbionts identified in the present study are characterized by metabolic versatility. Whether they exert similar functionalities within the bee gut and thus functional redundancy remains to be elucidated.}, }
@article {pmid37794025, year = {2023}, author = {Li, X and Chen, D and Carrión, VJ and Revillini, D and Yin, S and Dong, Y and Zhang, T and Wang, X and Delgado-Baquerizo, M}, title = {Author Correction: Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {6188}, doi = {10.1038/s41467-023-41564-4}, pmid = {37794025}, issn = {2041-1723}, }
@article {pmid37792090, year = {2023}, author = {Rippel, TM and Wimp, GM}, title = {Succession of Fungal Communities and Their Functional Profiles in a Decaying Foundation Species.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3003-3012}, pmid = {37792090}, issn = {1432-184X}, mesh = {*Mycobiome ; Ecosystem ; Fungi/physiology ; Soil Microbiology ; Plant Leaves/microbiology ; Biomass ; Plants ; Soil ; }, abstract = {Dead plant biomass from foundation plant species is fundamental for the survival of coastal salt marshes because dead biomass aids in the vertical accretion of the ecosystem. Fungi regulate the decomposition of dead biomass, and thus play an essential role for marsh survival. Despite their importance, little is known about the compositional and functional changes of fungal communities in plant matter throughout senescence and litter decomposition. Here, we analyzed how fungal communities and their functionality change in the foundation plant species Spartina patens, which builds vast amounts of dead plant biomass (thatch) on the soil surface. We analyzed the chemical and fungal properties of live biomass, standing dead biomass (dead biomass shortly after senescence), upper thatch (top layer of litter on the soil surface), and lower thatch (bottom layer of litter on the soil surface) during September and November of 2021. We found that the chemical and fungal properties of different S. patens biomass types followed a predictable litter decomposition pattern. Notably, live biomass, standing dead biomass, upper thatch, and lower thatch all hosted unique fungal communities and litter chemistry. Functional groups present in live biomass (pathogens, epiphytes, and mycoparasites) were lost during senescence and later replaced by diverse saprotrophs. The abundance of lignocellulose saprotrophs increased throughout decomposition, with the highest abundance occurring in lower thatch. These results suggest a predictable succession of fungal communities through the senescence and decomposition of the foundation species S. patens. Our study highlights the diversity of fungal communities in a disappearing foundation species.}, }
@article {pmid37792089, year = {2023}, author = {Sun, J and Zhou, H and Cheng, H and Chen, Z and Yang, J and Wang, Y and Jing, C}, title = {Depth-Dependent Distribution of Prokaryotes in Sediments of the Manganese Crust on Nazimov Guyots of the Magellan Seamounts.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3027-3042}, pmid = {37792089}, issn = {1432-184X}, mesh = {*Bacteria/genetics ; *Manganese ; Geologic Sediments/microbiology ; Nickel ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Cobalt ; }, abstract = {Deep ocean polymetallic nodules, rich in cobalt, nickel, and titanium which are commonly used in high-technology and biotechnology applications, are being eyed for green energy transition through deep-sea mining operations. Prokaryotic communities underneath polymetallic nodules could participate in deep-sea biogeochemical cycling, however, are not fully described. To address this gap, we collected sediment cores from Nazimov guyots, where polymetallic nodules exist, to explore the diversity and vertical distribution of prokaryotic communities. Our 16S rRNA amplicon sequencing data, quantitative PCR results, and phylogenetic beta diversity indices showed that prokaryotic diversity in the surficial layers (0-8 cm) was > 4-fold higher compared to deeper horizons (8-26 cm), while heterotrophs dominated in all sediment horizons. Proteobacteria was the most abundant taxon (32-82%) across all sediment depths, followed by Thaumarchaeota (4-37%), Firmicutes (2-18%), and Planctomycetes (1-6%). Depth was the key factor controlling prokaryotic distribution, while heavy metals (e.g., iron, copper, nickel, cobalt, zinc) can also influence significantly the downcore distribution of prokaryotic communities. Analyses of phylogenetic diversity showed that deterministic processes governing prokaryotic assembly in surficial layers, contrasting with stochastic influences in deep layers. This was further supported from the detection of a more complex prokaryotic co-occurrence network in the surficial layer which suggested more diverse prokaryotic communities existed in the surface vs. deeper sediments. This study expands current knowledge on the vertical distribution of benthic prokaryotic diversity in deep sea settings underneath polymetallic nodules, and the results reported might set a baseline for future mining decisions.}, }
@article {pmid37791342, year = {2023}, author = {Kamiya, S}, title = {Microbial ecology between Clostridioides difficile and gut microbiota.}, journal = {Bioscience of microbiota, food and health}, volume = {42}, number = {4}, pages = {229-235}, pmid = {37791342}, issn = {2186-6953}, abstract = {Clostridioides difficile colonizes a polymicrobial environment in the intestine and is a causative agent for antibiotic-associated diarrhea (AAD) and pseudomembranous colitis (PMC). The most important virulence factors of C. difficile are bacterial toxins, and three toxins (toxin A, toxin B, and binary toxin) are produced by toxigenic strains. Other virulence factors include spores, flagella, capsules, biofilms, hydrolytic enzymes and adhesins. C. difficile infection (CDI) is specifically diagnosed by anaerobic culture and toxin detection by either nucleic acid amplification test (NAAT) or enzyme-linked immunosorbent assay (ELISA). For treatment of CDI, metronidazole, vancomycin and fidaxomicin are used based on the severity of CDI. Mutual interaction between C. difficile and gut microbiota is associated with pathogenesis of CDI, and decreased microbial diversity with altered gut microbiome was detected in CDI patients. Restoration of certain gut microbiota is considered to be potentially effective for the prevention and treatment of CDI, and an ideal goal for CDI patients is restoration of the gut microbiota to a healthy state. Fecal microbiota transplantation (FMT) is a highly successful method of microbiome restoration and has been reported to be effective for the prevention of recurrent CDI. In addition, approaches to restoring the gut microbiota by using probioitcs and live biotherapeutic products (LBPs) are currently being studied to examine the effect on CDI. Further microbial ecological research on C. difficile and gut microbiota could lead to a better understanding of the pathogenesis and treatment of CDI.}, }
@article {pmid37783827, year = {2023}, author = {Skwara, A and Gowda, K and Yousef, M and Diaz-Colunga, J and Raman, AS and Sanchez, A and Tikhonov, M and Kuehn, S}, title = {Statistically learning the functional landscape of microbial communities.}, journal = {Nature ecology &amp; evolution}, volume = {7}, number = {11}, pages = {1823-1833}, pmid = {37783827}, issn = {2397-334X}, support = {R01 GM151538/GM/NIGMS NIH HHS/United States ; T32 GM150375/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; Biomass ; Soil ; Models, Theoretical ; }, abstract = {Microbial consortia exhibit complex functional properties in contexts ranging from soils to bioreactors to human hosts. Understanding how community composition determines function is a major goal of microbial ecology. Here we address this challenge using the concept of community-function landscapes-analogues to fitness landscapes-that capture how changes in community composition alter collective function. Using datasets that represent a broad set of community functions, from production/degradation of specific compounds to biomass generation, we show that statistically inferred landscapes quantitatively predict community functions from knowledge of species presence or absence. Crucially, community-function landscapes allow prediction without explicit knowledge of abundance dynamics or interactions between species and can be accurately trained using measurements from a small subset of all possible community compositions. The success of our approach arises from the fact that empirical community-function landscapes appear to be not rugged, meaning that they largely lack high-order epistatic contributions that would be difficult to fit with limited data. Finally, we show that this observation holds across a wide class of ecological models, suggesting community-function landscapes can be efficiently inferred across a broad range of ecological regimes. Our results open the door to the rational design of consortia without detailed knowledge of abundance dynamics or interactions.}, }
@article {pmid37782571, year = {2023}, author = {Schnyder, E and Bodelier, PLE and Hartmann, M and Henneberger, R and Niklaus, PA}, title = {Experimental erosion of microbial diversity decreases soil CH4 consumption rates.}, journal = {Ecology}, volume = {104}, number = {12}, pages = {e4178}, doi = {10.1002/ecy.4178}, pmid = {37782571}, issn = {1939-9170}, support = {144065 to Pascal A. Niklaus.//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Ecosystem ; *Soil ; Bacteria/genetics ; Biodiversity ; Wetlands ; Methane ; Soil Microbiology ; }, abstract = {Biodiversity-ecosystem functioning (BEF) experiments have predominantly focused on communities of higher organisms, in particular plants, with comparably little known to date about the relevance of biodiversity for microbially driven biogeochemical processes. Methanotrophic bacteria play a key role in Earth's methane (CH4) cycle by removing atmospheric CH4 and reducing emissions from methanogenesis in wetlands and landfills. Here, we used a dilution-to-extinction approach to simulate diversity loss in a methanotrophic landfill cover soil community. Replicate samples were diluted 10[1] -10[7] -fold, preincubated under a high CH4 atmosphere for microbial communities to recover to comparable size, and then incubated for 86 days at constant or diurnally cycling temperature. We hypothesize that (1) CH4 consumption decreases as methanotrophic diversity is lost, and (2) this effect is more pronounced under variable temperatures. Net CH4 consumption was determined by gas chromatography. Microbial community composition was determined by DNA extraction and sequencing of amplicons specific to methanotrophs and bacteria (pmoA and 16S gene fragments). The richness of operational taxonomic units (OTU) of methanotrophic and nonmethanotrophic bacteria decreased approximately linearly with log-dilution. CH4 consumption decreased with the number of OTUs lost, independent of community size. These effects were independent of temperature cycling. The diversity effects we found occured in relatively diverse communities, challenging the notion of high functional redundancy mediating high resistance to diversity erosion in natural microbial systems. The effects also resemble the ones for higher organisms, suggesting that BEF relationships are universal across taxa and spatial scales.}, }
@article {pmid37779539, year = {2022}, author = {Caparrós, E and Cenit, MC and Muriel, J and Benítez-Páez, A and Moreno, MV and González-Delgado, P and Rubio, G and Sanz, Y and Fernández, J}, title = {Intestinal microbiota is modified in pediatric food protein-induced enterocolitis syndrome.}, journal = {The journal of allergy and clinical immunology. Global}, volume = {1}, number = {4}, pages = {217-224}, pmid = {37779539}, issn = {2772-8293}, abstract = {BACKGROUND: Food protein-induced enterocolitis syndrome (FPIES) is a non-IgE-mediated food hypersensitivity that affects the gastrointestinal system, especially in children, who often present with more severe clinical manifestations than adults do. Although its pathogenesis is poorly understood and biomarkers are still lacking, scientific evidence suggests that gut microbiota may play an important role in the development of FPIES.<br><br>OBJECTIVE: We aimed to compare the composition of gut microbiota in children with FPIES with that in age- and sex-matched healthy controls.<br><br>METHODS: We analyzed the gut microbiota profiles in fecal samples of 17 patients with FPIES (case patients) and 12 age-matched healthy children (controls) by tag sequencing of the 16S ribosomal RNA gene hypervariable V4-V5 regions. Subjects' sociodemographic, clinical, and food diary variables were described and compared between groups by using inferential statistical tests. Nonparametric linear discriminant analysis was performed for intestinal microbiota data.<br><br>RESULTS: Patients with confirmed cases FPIES (n&#xa0;= 17; average patient age, 7.5&#xa0;&#xb1; 3.2 years) and controls without FPIES or any atopy (n&#xa0;= 12, average patient age, 6.9&#xa0;&#xb1; 2.7 years) were included. Fish was the main FPIES-inducing allergen in 65% of the cases. The patients with FPIES showed higher proportions of Lachnospiraceae spp (P&#xa0;< .0286) and a lower proportion of Ruminococcaceae spp (P&#xa0;< .0066), Lactobacillaceae spp (P&#xa0;< .0075), and Leuconostocaceae spp (P&#xa0;< .0173) than the controls.<br><br>CONCLUSIONS: Our data clearly show a different gut microbial signature in patients with FPIES, suggesting a new potential avenue for aiding the diagnosis and clinical management of FPIES. Larger studies are needed to confirm these results.}, }
@article {pmid37778560, year = {2024}, author = {Buenaño-Vargas, C and Gagliano, MC and Paulo, LM and Bartle, A and Graham, A and van Veelen, HPJ and O'Flaherty, V}, title = {Acclimation of microbial communities to low and moderate salinities in anaerobic digestion.}, journal = {The Science of the total environment}, volume = {906}, number = {}, pages = {167470}, doi = {10.1016/j.scitotenv.2023.167470}, pmid = {37778560}, issn = {1879-1026}, mesh = {*Wastewater ; Anaerobiosis ; Sewage/microbiology ; Waste Disposal, Fluid ; Salinity ; Bioreactors/microbiology ; Bacteria ; *Microbiota ; }, abstract = {In recent years anaerobic digestion (AD) has been investigated as suitable biotechnology to treat wastewater at elevated salinities. However, when starting up AD reactors with inocula that are not adapted to salinity, low concentrations of sodium (Na[+]) in the influent can already cause disintegration of microbial aggregates and wash-out. This study investigated biomass acclimation to 5 g Na[+/]L of two different non-adapted inocula in two lab-scale hybrid expanded granular sludge bed (EGSB)-anaerobic filter (AF) reactors fed with synthetic wastewater. After an initial biomass disintegration, new aggregates were formed relatively fast (i.e., after 95 days of operation), indicating microbial community adaptation. The newly formed microbial aggregates accumulated Na[+] at the expense of calcium (Ca[2+]), but this did not hamper biomass retention or process performance. The hybrid reactor configuration, including a pumice stone filter in the upper section, and the low up-flow velocities applied, were key features for retaining the biomass within the system. This reactor configuration can be easily applied and represents a low-cost alternative for acclimating biomass to saline effluents, even in existing digesters. When the acclimated biomass was transferred from EGSB to an up-flow anaerobic sludge blanket (UASB) reactor configuration also fed with saline synthetic wastewater, more dense aggregates in the form of granules were obtained. The performances of the UASB inoculated with the acclimated biomass were comparable to another reactor seeded with saline-adapted granular sludge from a full-scale plant. Regardless of the inoculum origin, a defined core microbiome of Bacteria (Thermovirga, Bacteroidetes vadinHA17, Blvii28 wastewater-sludge group, Mesotoga, and Synergistaceae) and Archaea (Methanosaeta and Methanobacterium) was detected, highlighting the importance of these microbial groups in developing halotolerance and maintaining AD process stability.}, }
@article {pmid37778079, year = {2023}, author = {Sabach, O and Buhnik-Rosenblau, K and Kesten, I and Freilich, S and Freilich, S and Kashi, Y}, title = {The rise of the sourdough: Genome-scale metabolic modeling-based approach to design sourdough starter communities with tailored-made properties.}, journal = {International journal of food microbiology}, volume = {407}, number = {}, pages = {110402}, doi = {10.1016/j.ijfoodmicro.2023.110402}, pmid = {37778079}, issn = {1879-3460}, mesh = {Saccharomyces cerevisiae/genetics/metabolism ; Fermentation ; *Lactobacillales/metabolism ; *Yeast, Dried ; Bacteria ; Pediococcus ; Bread/microbiology ; Flour/microbiology ; Food Microbiology ; }, abstract = {Sourdough starters harbor microbial consortia that benefit the final product's aroma and volume. The complex nature of these spontaneously developed communities raises challenges in predicting the fermentation phenotypes. Herein, we demonstrated for the first time in this field the potential of genome-scale metabolic modeling (GEMs) in the study of sourdough microbial communities. Broad in-silico modeling of microbial growth was applied on communities composed of yeast (Saccharomyces cerevisiae) and different Lactic Acid Bacteria (LAB) species, which mainly predominate in sourdough starters. Simulations of model-represented communities associated specific bacterial compositions with sourdough phenotypes. Based on ranking the phenotypic performances of different combinations, Pediococcus spp. - Lb. sakei group members were predicted to have an optimal effect considering the increase in S. cerevisiae growth abilities and overall CO2 secretion rates. Flux Balance Analysis (FBA) revealed mutual relationships between the Pediococcus spp. - Lb. sakei group members and S. cerevisiae through bidirectional nutrient dependencies, and further underlined that these bacteria compete with the yeast over nutrients to a lesser extent than the rest LAB species. Volatile compounds (VOCs) production was further modeled, identifying species-specific and community-related VOCs production profiles. The in-silico models' predictions were validated by experimentally building synthetic sourdough communities and assessing the fermentation phenotypes. The Pediococcus spp. - Lb. sakei group was indeed associated with increased yeast cell counts and fermentation rates, demonstrating a 25 % increase in the average leavening rates during the first 10 fermentation hours compared to communities with a lower representation of these group members. Overall, these results provide a possible novel strategy towards the de-novo design of sourdough starter communities with tailored-made characterizations, including a shortened leavening period.}, }
@article {pmid37778064, year = {2023}, author = {Niu, G and Wang, R and Zhou, H and Yang, J and Lu, X and Han, X and Huang, J}, title = {Nitrogen addition and mowing had only weak interactive effects on macronutrients in plant-soil systems of a typical steppe in Inner Mongolia.}, journal = {Journal of environmental management}, volume = {347}, number = {}, pages = {119121}, doi = {10.1016/j.jenvman.2023.119121}, pmid = {37778064}, issn = {1095-8630}, mesh = {*Ecosystem ; *Soil ; Nitrogen ; Plants ; China ; Nutrients ; Grassland ; }, abstract = {Effective management of macronutrients is pivotal in the optimization and provisioning of ecosystem services in grassland areas, particularly in degraded grasslands. In such instances where mowing and nitrogen (N) fertilization have emerged as predominant management strategies, nutrient management is especially important. However, the precise effects of these concurrent practices on the distribution of macronutrients in plant-soil systems remain unclear. Here we evaluated the effects of 12 years of N addition (2, 10, and 50 g N m[-2] year[-1]) and mowing on the concentrations and pools of six macronutrients (i.e., N; phosphorus P; sulfur S, calcium Ca, magnesium Mg, and potassium K) in three plant components (aboveground plants, litter, and belowground roots) at the community level and in the soil in a typical steppe in Inner Mongolia. Our results revealed that N addition generally raised the N concentration in the entire plant-soil system, regardless of whether plots were mowed. Higher N addition (10 and 50 g N m[-2] year[-1]) also led to higher concentrations of P (+22%, averaging two N addition rates), S (+16%), K (+22%), Ca (+22%), and Mg (+24%) in plants but lower concentrations of these nutrients in the litter. Similar decreases in K (-9%), Ca (-46%), and Mg (-8%) were observed in the roots. In light of the observed increases in vegetation biomass and the lack of pronounced changes in soil bulk density, we found that the ecosystem N enrichment resulted in increased pools of all measured macronutrients in plants, litter, and roots (with the exception of Ca in the roots) while concurrently decreased the pools of P (-20%, averaging two higher N addition rates), S (-12%), K (-10%), Ca (-37%), and Mg (-19%) in the soil, with no obvious effect of the mowing practice. Overall, mowing exhibited a very limited capacity to alleviate the effects of long-term N addition on macronutrients in the plant-soil system. These findings highlight the importance of considering the distribution of macronutrients across distinct plant organs and the dynamic nutrient interplay between plants and soil, particularly in the context of long-term fertilization and mowing practices, when formulating effective grassland management strategies.}, }
@article {pmid37777451, year = {2023}, author = {Tsirigotaki, M and Galanakis, E}, title = {Impact of vaccines on Staphylococcus aureus colonization: A systematic review and meta-analysis.}, journal = {Vaccine}, volume = {41}, number = {44}, pages = {6478-6487}, doi = {10.1016/j.vaccine.2023.09.034}, pmid = {37777451}, issn = {1873-2518}, abstract = {BACKGROUND: Concerns regarding vaccine effects on microbial ecology have led to interest in the non-targeted effects of vaccinations.<br><br>OBJECTIVES: To systematically review the literature related to the impact of vaccines on S. aureus carriage.<br><br>METHODS: We conducted a systematic search of MEDLINE, Scopus and clinical trials.gov for studies that assessed vaccine effects on S. aureus carriage in children and adults using predefined inclusion and exclusion criteria. Generic inverse variance meta-analysis was done using random-effects models.<br><br>RESULTS: Of 1,686 studies screened, 34 were eligible for inclusion, of which 22 were observational and 12 randomized controlled studies (RCTs). 88.2% (30/34) provided data on pneumococcal conjugate vaccines (PCV), 23.5% on influenza vaccines (8/34), 6% on other vaccines (2/34) and 20.6% on more than one vaccine (7/34). Most studies tested nasopharyngeal specimens (82.3%, 28/34). Among children aged more than 18-24&#xa0;months, evidence suggested no effect of PCV on S. aureus colonization [2 RCTs, pooled OR 1.09 (95% CI 0.94-1.25), p 0.25; 7 observational studies, pooled OR: 1.02 (95% CI 0.83-1.25), p 0.86]. A transient increase in S. aureus carriage in PCV-vaccinated infants 9-15&#xa0;months was shown [2 RCTs, pooled OR 1.11 (95% CI 1.00-1.23), p 0.06; 4 observational studies, pooled OR 1.64 (95% CI 1.00-2.68), p 0.05]. A reduction in S. aureus carriage was observed after influenza vaccination [4 observational studies; OR 0.85 (95% CI 0.78-0.94), p 0.0001]. Based on the Grading of Recommendations Assessment, Development and Evaluation, the quality of evidence was considered low for randomized and very low for non-randomized trials.<br><br>CONCLUSION: Evidence did not suggest long-term effects of pneumococcal vaccinations on S. aureus nasopharyngeal carriage in children, however transient niche changes may occur in infants. Influenza vaccination was related to decreased rates of S. aureus carriage. Data regarding other vaccines is scarce. Further research and ongoing surveillance are needed to monitor colonization changes.}, }
@article {pmid37775010, year = {2023}, author = {Shen, Z and Yu, B and Shao, K and Gao, G and Tang, X}, title = {Warming reduces microeukaryotic diversity, network complexity and stability.}, journal = {Environmental research}, volume = {238}, number = {Pt 2}, pages = {117235}, doi = {10.1016/j.envres.2023.117235}, pmid = {37775010}, issn = {1096-0953}, mesh = {*Ecosystem ; *Climate Change ; Analysis of Variance ; Temperature ; }, abstract = {Unraveling how climate warming affects microorganisms and the underlying mechanisms has been a hot topic in climate change and microbial ecology. To date, many studies have reported microbial responses to climate warming, especially in soil ecosystems, however, knowledge of how warming influences microeukaryotic diversity, network complexity and stability in lake ecosystems, in particular the possible underlying mechanisms, is largely unknown. To address this gap, we conducted 20 mesocosms spanning five temperature scenarios (26 °C, 27.5 °C, 29 °C, 30.5 °C, and 32 °C) in Lake Bosten, a hotspot for studying climate change, and investigated microeukaryotic communities using 18S rRNA gene sequencing. Our results demonstrated that warming, time, and their interactions significantly reduced microeukaryotic α-diversity (two-way ANOVA: P＜0.01). Although warming did not significantly affect microeukaryotic community structure (ANOSIM: P＞0.05), it enhanced species turnover. Microeukaryotic networks exhibited distinct co-occurrence patterns and topological properties across temperature scenarios. Warming reduced network complexity and stability, as well as altered species interactions. Collectively, these findings are likely to have implications for ecological management of lake ecosystems, in particular semi-arid and arid regions, and for predicting ecological consequences of climate change.}, }
@article {pmid37774017, year = {2023}, author = {Wielscher, M and Pfisterer, K and Samardzic, D and Balsini, P and Bangert, C and Jäger, K and Buchberger, M and Selitsch, B and Pjevac, P and Willinger, B and Weninger, W}, title = {The phageome in normal and inflamed human skin.}, journal = {Science advances}, volume = {9}, number = {39}, pages = {eadg4015}, pmid = {37774017}, issn = {2375-2548}, mesh = {Humans ; *Virome ; Skin/microbiology ; *Microbiota ; Metagenome ; Bacteria/genetics ; DNA, Viral/genetics ; }, abstract = {Dysbiosis of skin microbiota drives the progression of atopic dermatitis (AD). The contribution of bacteriophages to bacterial community compositions in normal and inflamed skin is unknown. Using shotgun metagenomics from skin swabs of healthy individuals and patients with AD, we found 13,586 potential viral contiguous DNA sequences, which could be combined into 164 putative viral genomes including 133 putative phages. The Shannon diversity index for the viral metagenome-assembled genomes (vMAGs) did not correlate with AD. In total, we identified 28 vMAGs that differed significantly between normal and AD skin. Quantitative polymerase chain reaction validation of three complete vMAGs revealed their independence from host bacterium abundance. Our data indicate that normal and inflamed skin harbor distinct phageomes and suggest a causative relationship between changing viral and bacterial communities as a driver of skin pathology.}, }
@article {pmid37771751, year = {2023}, author = {Arikawa, K and Hosokawa, M}, title = {Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {4508-4518}, pmid = {37771751}, issn = {2001-0370}, abstract = {Owing to the ineffectiveness of traditional culture techniques for the vast majority of microbial species, culture-independent analyses utilizing next-generation sequencing and bioinformatics have become essential for gaining insight into microbial ecology and function. This mini-review focuses on two essential methods for obtaining genetic information from uncultured prokaryotes, metagenomics and single-cell genomics. We analyzed the registration status of uncultured prokaryotic genome data from major public databases and assessed the advantages and limitations of both the methods. Metagenomics generates a significant quantity of sequence data and multiple prokaryotic genomes using straightforward experimental procedures. However, in ecosystems with high microbial diversity, such as soil, most genes are presented as brief, disconnected contigs, and lack association of highly conserved genes and mobile genetic elements with individual species genomes. Although technically more challenging, single-cell genomics offers valuable insights into complex ecosystems by providing strain-resolved genomes, addressing issues in metagenomics. Recent technological advancements, such as long-read sequencing, machine learning algorithms, and in silico protein structure prediction, in combination with vast genomic data, have the potential to overcome the current technical challenges and facilitate a deeper understanding of uncultured microbial ecosystems and microbial dark matter genes and proteins. In light of this, it is imperative that continued innovation in both methods and technologies take place to create high-quality reference genome databases that will support future microbial research and industrial applications.}, }
@article {pmid37771273, year = {2023}, author = {Staller, K and Olén, O and Söderling, J and Roelstraete, B and Törnblom, H and Kuo, B and Nguyen, LH and Ludvigsson, JF}, title = {Antibiotic use as a risk factor for irritable bowel syndrome: Results from a nationwide, case-control study.}, journal = {Alimentary pharmacology &amp; therapeutics}, volume = {58}, number = {11-12}, pages = {1175-1184}, doi = {10.1111/apt.17736}, pmid = {37771273}, issn = {1365-2036}, support = {K23DK120945/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Humans ; *Irritable Bowel Syndrome/drug therapy/epidemiology/diagnosis ; Case-Control Studies ; Anti-Bacterial Agents/adverse effects ; Risk Factors ; Sweden/epidemiology ; }, abstract = {BACKGROUND: The microbiome plays an important role in the pathophysiology of irritable bowel syndrome (IBS). Antibiotic use can fundamentally alter gut microbial ecology. We examined the association of antibiotic use with IBS in a large population-based investigation.<br><br>METHODS: A case-control study with prospectively collected data on 29,111 adult patients diagnosed with IBS in Sweden between 2007 and 2016 matched with 135,172 controls. Using a comprehensive histopathology cohort, the Swedish Patient Register, and the Prescribed Drug Register, we identified all consecutive cases of IBS in addition to cumulative antibiotic dispensations accrued until 1&#x2009;year prior to IBS (exclusionary period) for cases and time of matching for up to five general population controls matched on the basis of age, sex, country and calendar year. Conditional logistic regression estimated multivariable-adjusted odds ratios (ORs) and 95% confidence intervals (CIs) for the risk of IBS.<br><br>RESULTS: Patients with IBS (n&#x2009;=&#x2009;29,111) were more likely than controls (n&#x2009;=&#x2009;135,172) to have used antibiotics up to 1&#x2009;year prior to diagnosis (74.9% vs. 57.8%). After multivariable adjustment, this translated to a more than twofold increased odds of IBS (OR 2.21, 95% CI 2.14-2.28) that did not differ according to age, sex, year of IBS diagnosis or IBS subtype. Compared to none, 1-2 (OR 1.67, 95% CI 1.61-1.73) and &#x2265;3 antibiotics dispensations (OR 3.36, 95% CI 3.24-3.49) were associated with increased odds of IBS (p for trend <0.001) regardless of the antibiotic class.<br><br>CONCLUSIONS: Prior antibiotics use was associated with an increased odds of IBS with the highest risk among people with multiple antibiotics dispensations.}, }
@article {pmid38868338, year = {2023}, author = {Wan, W and Grossart, HP and He, D and Liu, W and Wang, S and Yang, Y}, title = {Differentiation strategies for planktonic bacteria and eukaryotes in response to aggravated algal blooms in urban lakes.}, journal = {iMeta}, volume = {2}, number = {1}, pages = {e84}, pmid = {38868338}, issn = {2770-596X}, abstract = {Aggravated algal blooms potentially decreased environmental heterogeneity. Different strategies of planktonic bacteria and eukaryotes in response to aggravated algal blooms. Environmental constraints of plankton showed different patterns over time.}, }
@article {pmid38818334, year = {2023}, author = {Zhu, YG and Zhu, D and Rillig, MC and Yang, Y and Chu, H and Chen, QL and Penuelas, J and Cui, HL and Gillings, M}, title = {Ecosystem Microbiome Science.}, journal = {mLife}, volume = {2}, number = {1}, pages = {2-10}, pmid = {38818334}, issn = {2770-100X}, abstract = {The microbiome contributes to multiple ecosystem functions and services through its interactions with a complex environment and other organisms. To date, however, most microbiome studies have been carried out on individual hosts or particular environmental compartments. This greatly limits a comprehensive understanding of the processes and functions performed by the microbiome and its dynamics at an ecosystem level. We propose that the theory and tools of ecosystem ecology be used to investigate the connectivity of microorganisms and their interactions with the biotic and abiotic environment within entire ecosystems and to examine their contributions to ecosystem services. Impacts of natural and anthropogenic stressors on ecosystems will likely cause cascading effects on the microbiome and lead to unpredictable outcomes, such as outbreaks of emerging infectious diseases or changes in mutualistic interactions. Despite enormous advances in microbial ecology, we are yet to study microbiomes of ecosystems as a whole. Doing so would establish a new framework for microbiome study: Ecosystem Microbiome Science. The advent and application of molecular and genomic technologies, together with data science and modeling, will accelerate progress in this field.}, }
@article {pmid38868331, year = {2023}, author = {Li, C and Jin, L and Zhang, C and Li, S and Zhou, T and Hua, Z and Wang, L and Ji, S and Wang, Y and Gan, Y and Liu, J}, title = {Destabilized microbial networks with distinct performances of abundant and rare biospheres in maintaining networks under increasing salinity stress.}, journal = {iMeta}, volume = {2}, number = {1}, pages = {e79}, pmid = {38868331}, issn = {2770-596X}, abstract = {Global changes such as seawater intrusion and freshwater resource salinization increase environmental stress imposed on the aquatic microbiome. A strong predictive understanding of the responses of the aquatic microbiome to environmental stress will help in coping with the "gray rhino" events in the environment, thereby contributing to an ecologically sustainable future. Considering that microbial ecological networks are tied to the stability of ecosystem functioning and that abundant and rare biospheres with different biogeographic patterns are important drivers of ecosystem functioning, the roles of abundant and rare biospheres in maintaining ecological networks need to be clarified. Here we showed that, with the increasing salinity stress induced by the freshwater-to-seawater transition, the microbial diversity reduced significantly and the taxonomic structure experienced a strong succession. The complexity and stability of microbial ecological networks were diminished by the increasing stress. The composition of the microorganisms supporting the networks underwent sharp turnovers during the freshwater-to-seawater transition, with the abundant biosphere behaving more robustly than the rare biosphere. Notably, the abundant biosphere played a much more important role than the rare biosphere in stabilizing ecological networks under low-stress environments, but the difference between their relative importance narrowed significantly with the increasing stress, suggesting that the environmental stress weakened the "Matthew effect" in the microbial world. With in-depth insights into the aquatic microbial ecology under stress, our findings highlight the importance of adjusting conservation strategies for the abundant and rare biospheres to maintain ecosystem functions and services in response to rising environmental stress.}, }
@article {pmid38868349, year = {2023}, author = {Fu, S and Wang, R and Xu, Z and Zhou, H and Qiu, Z and Shen, L and Yang, Q}, title = {Metagenomic sequencing combined with flow cytometry facilitated a novel microbial risk assessment framework for bacterial pathogens in municipal wastewater without cultivation.}, journal = {iMeta}, volume = {2}, number = {1}, pages = {e77}, pmid = {38868349}, issn = {2770-596X}, abstract = {A workflow that combined metagenomic sequencing with flow cytometry was developed. The absolute abundance of pathogens was accurately estimated in mock communities and real samples. Metagenome-assembled genomes binned from metagenomic data set is robust in phylogenetic analysis and virulence profiling.}, }
@article {pmid38665803, year = {2023}, author = {Schilling, OS and Nagaosa, K and Schilling, TU and Brennwald, MS and Sohrin, R and Tomonaga, Y and Brunner, P and Kipfer, R and Kato, K}, title = {Revisiting Mt Fuji's groundwater origins with helium, vanadium and environmental DNA tracers.}, journal = {Nature water}, volume = {1}, number = {1}, pages = {60-73}, pmid = {38665803}, issn = {2731-6084}, abstract = {Known locally as the water mountain, for millennia Japan's iconic Mt Fuji has provided safe drinking water to millions of people via a vast network of groundwater and freshwater springs. Groundwater, which is recharged at high elevations, flows down Fuji's flanks within three basaltic aquifers, ultimately forming countless pristine freshwater springs among Fuji's foothills. Here we challenge the current conceptual model of Fuji being a simple system of laminar groundwater flow with little to no vertical exchange between its three aquifers. This model contrasts strongly with Fuji's extreme tectonic instability due to its unique location on top of the only known continental trench-trench-trench triple junction, its complex geology and its unusual microbial spring water communities. On the basis of a unique combination of microbial environmental DNA, vanadium and helium tracers, we provide evidence for prevailing deep circulation and a previously unknown deep groundwater contribution to Fuji's freshwater springs. The most substantial deep groundwater upwelling has been found along Japan's most tectonically active region, the Fujikawa-kako Fault Zone. Our findings broaden the hydrogeological understanding of Fuji and demonstrate the vast potential of combining environmental DNA, on-site noble gas and trace element analyses for groundwater science.}, }
@article {pmid38665197, year = {2023}, author = {Simister, RL and Iulianella Phillips, BP and Wickham, AP and Cayer, EM and Hart, CJR and Winterburn, PA and Crowe, SA}, title = {DNA sequencing, microbial indicators, and the discovery of buried kimberlites.}, journal = {Communications earth &amp; environment}, volume = {4}, number = {1}, pages = {387}, pmid = {38665197}, issn = {2662-4435}, abstract = {Population growth and technological advancements are placing growing demand on mineral resources. New and innovative exploration technologies that improve detection of deeply buried mineralization and host rocks are required to meet these demands. Here we used diamondiferous kimberlite ore bodies as a test case and show that DNA amplicon sequencing of soil microbial communities resolves anomalies in microbial community composition and structure that reflect the surface expression of kimberlites buried under 10 s of meters of overburden. Indicator species derived from laboratory amendment experiments were employed in an exploration survey in which the species distributions effectively delineated the surface expression of buried kimberlites. Additional indicator species derived directly from field observations improved the blind discovery of kimberlites buried beneath similar overburden types. Application of DNA sequence-based analyses of soil microbial communities to mineral deposit exploration provides a powerful illustration of how genomics technologies can be leveraged in the discovery of critical new resources.}, }
@article {pmid38665180, year = {2023}, author = {Naz, N and Harandi, BF and Newmark, J and Kounaves, SP}, title = {Microbial growth in actual martian regolith in the form of Mars meteorite EETA79001.}, journal = {Communications earth &amp; environment}, volume = {4}, number = {1}, pages = {381}, pmid = {38665180}, issn = {2662-4435}, abstract = {Studies to understand the growth of organisms on Mars are hampered by the use of simulants to duplicate martian mineralogy and chemistry. Even though such materials are improving, no terrestrial simulant can replace a real martian sample. Here we report the use of actual martian regolith, in the form of Mars meteorite EETA79001 sawdust, to demonstrate its ability to support the growth of four microorganisms, E. coli. Eucapsis sp., Chr20-20201027-1, and P. halocryophilus, for up to 23 days under terrestrial conditions using regolith:water ratios from 4:1 to 1:10. If the EETA79001 sawdust is widely representative of regolith on the martian surface, our results imply that microbial life under appropriate conditions could have been present on Mars in the past and/or today in the subsurface, and that the regolith does not contain any bactericidal agents. The results of our study have implications not only for putative martian microbial life but also for building bio-sustainable human habitats on Mars.}, }
@article {pmid38867909, year = {2022}, author = {Zhu, YX and Yang, R and Wang, XY and Wen, T and Gong, MH and Shen, Y and Xu, JY and Zhao, DS and Du, YZ}, title = {Gut microbiota composition in the sympatric and diet-sharing Drosophila simulans and Dicranocephalus wallichii bowringi shaped largely by community assembly processes rather than regional species pool.}, journal = {iMeta}, volume = {1}, number = {4}, pages = {e57}, pmid = {38867909}, issn = {2770-596X}, abstract = {Clarifying the mechanisms underlying microbial community assembly from regional microbial pools is a central issue of microbial ecology, but remains largely unexplored. Here, we investigated the gut bacterial and fungal microbiome assembly processes and potential sources in Drosophila simulans and Dicranocephalus wallichii bowringi, two wild, sympatric insect species that share a common diet of waxberry. While some convergence was observed, the diversity, composition, and network structure of the gut microbiota significantly differed between these two host species. Null model analyses revealed that stochastic processes (e.g., drift, dispersal limitation) play a principal role in determining gut microbiota from both hosts. However, the strength of each ecological process varied with the host species. Furthermore, the source-tracking analysis showed that only a minority of gut microbiota within D. simulans and D. wallichii bowringi are drawn from a regional microbial pool from waxberries, leaves, or soil. Results from function prediction implied that host species-specific gut microbiota might arise partly through host functional requirement and specific selection across host-microbiota coevolution. In conclusion, our findings uncover the importance of community assembly processes over regional microbial pools in shaping sympatric insect gut microbiome structure and function.}, }
@article {pmid37938751, year = {2022}, author = {Jia, X and Dini-Andreote, F and Salles, JF}, title = {Unravelling the interplay of ecological processes structuring the bacterial rare biosphere.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {96}, pmid = {37938751}, issn = {2730-6151}, abstract = {Most ecological communities harbor many rare species (i.e., the rare biosphere), however, relatively little is known about how distinct ecological processes structure their existence. Here, we used spatiotemporal data on soil bacterial communities along a natural ecosystem gradient to model the relative influences of assembly processes structuring the rare and common biospheres. We found a greater influence of homogeneous selection (i.e., imposed by spatiotemporally constant variables) mediating the assembly of the rare biosphere, whereas the common biosphere was mostly governed by variable selection (i.e., imposed by spatial and/or temporal fluctuating variables). By partitioning the different types of rarity, we found homogeneous selection to explain the prevalence of permanently rare taxa, thus suggesting their persistence at low abundances to be restrained by physiological traits. Conversely, the dynamics of conditionally rare taxa were mostly structured by variable selection, which aligns with the ability of these taxa to switch between rarity and commonness as responses to environmental spatiotemporal variations. Taken together, our study contributes to the establishment of a link between conceptual and empirical developments in the ecology of the soil microbial rare biosphere. Besides, this study provides a framework to better understand, model, and predict the existence and dynamics of microbial rare biospheres across divergent systems and scales.}, }
@article {pmid37938754, year = {2022}, author = {Díaz Rodríguez, CA and Díaz-García, L and Bunk, B and Spröer, C and Herrera, K and Tarazona, NA and Rodriguez-R, LM and Overmann, J and Jiménez, DJ}, title = {Novel bacterial taxa in a minimal lignocellulolytic consortium and their potential for lignin and plastics transformation.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {89}, pmid = {37938754}, issn = {2730-6151}, abstract = {The understanding and manipulation of microbial communities toward the conversion of lignocellulose and plastics are topics of interest in microbial ecology and biotechnology. In this study, the polymer-degrading capability of a minimal lignocellulolytic microbial consortium (MELMC) was explored by genome-resolved metagenomics. The MELMC was mostly composed (>90%) of three bacterial members (Pseudomonas protegens; Pristimantibacillus lignocellulolyticus gen. nov., sp. nov; and Ochrobactrum gambitense sp. nov) recognized by their high-quality metagenome-assembled genomes (MAGs). Functional annotation of these MAGs revealed that Pr. lignocellulolyticus could be involved in cellulose and xylan deconstruction, whereas Ps. protegens could catabolize lignin-derived chemical compounds. The capacity of the MELMC to transform synthetic plastics was assessed by two strategies: (i) annotation of MAGs against databases containing plastic-transforming enzymes; and (ii) predicting enzymatic activity based on chemical structural similarities between lignin- and plastics-derived chemical compounds, using Simplified Molecular-Input Line-Entry System and Tanimoto coefficients. Enzymes involved in the depolymerization of polyurethane and polybutylene adipate terephthalate were found to be encoded by Ps. protegens, which could catabolize phthalates and terephthalic acid. The axenic culture of Ps. protegens grew on polyhydroxyalkanoate (PHA) nanoparticles and might be a suitable species for the industrial production of PHAs in the context of lignin and plastic upcycling.}, }
@article {pmid38818216, year = {2022}, author = {Guo, X and Yuan, M and Lei, J and Shi, Z and Zhou, X and Li, J and Deng, Y and Yang, Y and Wu, L and Luo, Y and Tiedje, JM and Zhou, J}, title = {Climate warming restructures seasonal dynamics of grassland soil microbial communities.}, journal = {mLife}, volume = {1}, number = {3}, pages = {245-256}, pmid = {38818216}, issn = {2770-100X}, abstract = {Soil microbial community's responses to climate warming alter the global carbon cycle. In temperate ecosystems, soil microbial communities function along seasonal cycles. However, little is known about how the responses of soil microbial communities to warming vary when the season changes. In this study, we investigated the seasonal dynamics of soil bacterial community under experimental warming in a temperate tall-grass prairie ecosystem. Our results showed that warming significantly (p = 0.001) shifted community structure, such that the differences of microbial communities between warming and control plots increased nonlinearly (R [2] = 0.578, p = 0.021) from spring to winter. Also, warming significantly (p < 0.050) increased microbial network complexity and robustness, especially during the colder seasons, despite large variations in network size and complexity in different seasons. In addition, the relative importance of stochastic processes in shaping the microbial community decreased by warming in fall and winter but not in spring and summer. Our study indicates that climate warming restructures the seasonal dynamics of soil microbial community in a temperate ecosystem. Such seasonality of microbial responses to warming may enlarge over time and could have significant impacts on the terrestrial carbon cycle.}, }
@article {pmid38234686, year = {2022}, author = {Crous, PW and Boers, J and Holdom, D and Osieck, ER and Steinrucken, TV and Tan, YP and Vitelli, JS and Shivas, RG and Barrett, M and Boxshall, AG and Broadbridge, J and Larsson, E and Lebel, T and Pinruan, U and Sommai, S and Alvarado, P and Bonito, G and Decock, CA and De la Peña-Lastra, S and Delgado, G and Houbraken, J and Maciá-Vicente, JG and Raja, HA and Rigueiro-Rodríguez, A and Rodríguez, A and Wingfield, MJ and Adams, SJ and Akulov, A and Al-Hidmi, T and Antonín, V and Arauzo, S and Arenas, F and Armada, F and Aylward, J and Bellanger, JM and Berraf-Tebbal, A and Bidaud, A and Boccardo, F and Cabero, J and Calledda, F and Corriol, G and Crane, JL and Dearnaley, JDW and Dima, B and Dovana, F and Eichmeier, A and Esteve-Raventós, F and Fine, M and Ganzert, L and García, D and Torres-Garcia, D and Gené, J and Gutiérrez, A and Iglesias, P and Istel, &#x141; and Jangsantear, P and Jansen, GM and Jeppson, M and Karun, NC and Karich, A and Khamsuntorn, P and Kokkonen, K and Kolařík, M and Kubátová, A and Labuda, R and Lagashetti, AC and Lifshitz, N and Linde, C and Loizides, M and Luangsa-Ard, JJ and Lueangjaroenkit, P and Mahadevakumar, S and Mahamedi, AE and Malloch, DW and Marincowitz, S and Mateos, A and Moreau, PA and Miller, AN and Molia, A and Morte, A and Navarro-Ródenas, A and Nebesářová, J and Nigrone, E and Nuthan, BR and Oberlies, NH and Pepori, AL and Rämä, T and Rapley, D and Reschke, K and Robicheau, BM and Roets, F and Roux, J and Saavedra, M and Sakolrak, B and Santini, A and Ševčíková, H and Singh, PN and Singh, SK and Somrithipol, S and Spetik, M and Sridhar, KR and Starink-Willemse, M and Taylor, VA and van Iperen, AL and Vauras, J and Walker, AK and Wingfield, BD and Yarden, O and Cooke, AW and Manners, AG and Pegg, KG and Groenewald, JZ}, title = {Fungal Planet description sheets: 1383-1435.}, journal = {Persoonia}, volume = {48}, number = {}, pages = {261-371}, pmid = {38234686}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Agaricus albofoetidus, Agaricus aureoelephanti and Agaricus parviumbrus on soil, Fusarium ramsdenii from stem cankers of Araucaria cunninghamii, Keissleriella sporoboli from stem of Sporobolus natalensis, Leptosphaerulina queenslandica and Pestalotiopsis chiaroscuro from leaves of Sporobolus natalensis, Serendipita petricolae as endophyte from roots of Eriochilus petricola, Stagonospora tauntonensis from stem of Sporobolus natalensis, Teratosphaeria carnegiei from leaves of Eucalyptus grandis × E. camaldulensis and Wongia ficherai from roots of Eragrostis curvula. Canada, Lulworthia fundyensis from intertidal wood and Newbrunswickomyces abietophilus (incl. Newbrunswickomyces gen. nov.) on buds of Abies balsamea. Czech Republic, Geosmithia funiculosa from a bark beetle gallery on Ulmus minor and Neoherpotrichiella juglandicola (incl. Neoherpotrichiella gen. nov.) from wood of Juglans regia. France, Aspergillus rouenensis and Neoacrodontium gallica (incl. Neoacrodontium gen. nov.) from bore dust of Xestobium rufovillosum feeding on Quercus wood, Endoradiciella communis (incl. Endoradiciella gen. nov.) endophytic in roots of Microthlaspi perfoliatum and Entoloma simulans on soil. India, Amanita konajensis on soil and Keithomyces indicus from soil. Israel, Microascus rothbergiorum from Stylophora pistillata. Italy, Calonarius ligusticus on soil. Netherlands, Appendopyricularia juncicola (incl. Appendopyricularia gen. nov.), Eriospora juncicola and Tetraploa juncicola on dead culms of Juncus effusus, Gonatophragmium physciae on Physcia caesia and Paracosmospora physciae (incl. Paracosmospora gen. nov.) on Physcia tenella, Myrmecridium phragmitigenum on dead culm of Phragmites australis, Neochalara lolae on stems of Pteridium aquilinum, Niesslia nieuwwulvenica on dead culm of undetermined Poaceae, Nothodevriesia narthecii (incl. Nothodevriesia gen. nov.) on dead leaves of Narthecium ossifragum and Parastenospora pini (incl. Parastenospora gen. nov.) on dead twigs of Pinus sylvestris. Norway, Verticillium bjoernoeyanum from sand grains attached to a piece of driftwood on a sandy beach. Portugal, Collybiopsis cimrmanii on the base of living Quercus ilex and amongst dead leaves of Laurus and herbs. South Africa, Paraproliferophorum hyphaenes (incl. Paraproliferophorum gen. nov.) on living leaves of Hyphaene sp. and Saccothecium widdringtoniae on twigs of Widdringtonia wallichii. Spain, Cortinarius dryosalor on soil, Cyphellophora endoradicis endophytic in roots of Microthlaspi perfoliatum, Geoglossum lauri-silvae on soil, Leptographium gemmatum from fluvial sediments, Physalacria auricularioides from a dead twig of Castanea sativa, Terfezia bertae and Tuber davidlopezii in soil. Sweden, Alpova larskersii, Inocybe alpestris and Inocybe boreogodeyi on soil. Thailand, Russula banwatchanensis, Russula purpureoviridis and Russula lilacina on soil. Ukraine, Nectriella adonidis on overwintered stems of Adonis vernalis. USA, Microcyclus jacquiniae from living leaves of Jacquinia keyensis and Penicillium neoherquei from a minute mushroom sporocarp. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Boers J, Holdom D, et al. 2022. Fungal Planet description sheets: 1383-1435. Persoonia 48: 261-371. https://doi.org/10.3767/persoonia.2022.48.08.}, }
@article {pmid37938693, year = {2022}, author = {Zauner, S and Vogel, M and Polzin, J and Yuen, B and Mußmann, M and El-Hacen, EM and Petersen, JM}, title = {Microbial communities in developmental stages of lucinid bivalves.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {56}, pmid = {37938693}, issn = {2730-6151}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; P 31010/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Bivalves from the family Lucinidae host sulfur-oxidizing bacterial symbionts, which are housed inside specialized gill epithelial cells and are assumed to be acquired from the environment. However, little is known about the Lucinidae life cycle and symbiont acquisition in the wild. Some lucinid species broadcast their gametes into the surrounding water column, however, a few have been found to externally brood their offspring by the forming gelatinous egg masses. So far, symbiont transmission has only been investigated in one species that reproduces via broadcast spawning. Here, we show that the lucinid Loripes orbiculatus from the West African coast forms egg masses and these are dominated by diverse members of the Alphaproteobacteria, Clostridia, and Gammaproteobacteria. The microbial communities of the egg masses were distinct from those in the environments surrounding lucinids, indicating that larvae may shape their associated microbiomes. The gill symbiont of the adults was undetectable in the developmental stages, supporting horizontal transmission of the symbiont with environmental symbiont acquisition after hatching from the egg masses. These results demonstrate that L. orbiculatus acquires symbionts from the environment independent of the host's reproductive strategy (brooding or broadcast spawning) and reveal previously unknown associations with microbes during lucinid early development.}, }
@article {pmid37938753, year = {2022}, author = {Alcolombri, U and Pioli, R and Stocker, R and Berry, D}, title = {Single-cell stable isotope probing in microbial ecology.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {55}, pmid = {37938753}, issn = {2730-6151}, support = {P 27831/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Environmental and host-associated microbiomes are typically diverse assemblages of organisms performing myriad activities and engaging in a network of interactions that play out in spatially structured contexts. As the sum of these activities and interactions give rise to overall microbiome function, with important consequences for environmental processes and human health, elucidating specific microbial activities within complex communities is a pressing challenge. Single-cell stable isotope probing (SC-SIP) encompasses multiple techniques that typically utilize Raman microspectroscopy or nanoscale secondary ion mass spectrometry (NanoSIMS) to enable spatially resolved tracking of isotope tracers in cells, cellular components, and metabolites. SC-SIP techniques are uniquely suited for illuminating single-cell activities in microbial communities and for testing hypotheses about cellular functions generated for example from meta-omics datasets. Here, we illustrate the insights enabled by SC-SIP techniques by reviewing selected applications in microbiology and offer a perspective on their potential for future research.}, }
@article {pmid38868712, year = {2022}, author = {Xi, J and Lei, B and Liu, YX and Ding, Z and Liu, J and Xu, T and Hou, L and Han, S and Qian, X and Ma, Y and Xue, Q and Gao, J and Gu, J and Tiedje, JM and Lin, Y}, title = {Microbial community roles and chemical mechanisms in the parasitic development of Orobanche cumana.}, journal = {iMeta}, volume = {1}, number = {3}, pages = {e31}, pmid = {38868712}, issn = {2770-596X}, abstract = {Orobanche cumana Wallr. is a holoparasite weed that extracts water and nutrients from its host the sunflower, thereby causing yield reductions and quality losses. However, the number of O. cumana parasites in the same farmland is distinctly different. The roots of some hosts have been heavily parasitized, while others have not been parasitized. What are the factors contributing to this phenomenon? Is it possible that sunflower interroot microorganisms are playing a regulatory role in this phenomenon? The role of the microbial community in this remains unclear. In this study, we investigated the rhizosphere soil microbiome for sunflowers with different degrees of O. cumana parasitism, that is, healthy, light infection, moderate infection, and severe infection on the sunflower roots. The microbial structures differed significantly according to the degree of parasitism, where Xanthomonadaceae was enriched in severe infections. Metagenomic analyses revealed that amino acid, carbohydrate, energy, and lipid metabolism were increased in the rhizosphere soils of severely infected sunflowers, which were attributed to the proliferation of Lysobacter. Lysobacter antibioticus (HX79) was isolated and its capacity to promote O. cumana seed germination and increase the germ tube length was confirmed by germination and pot experiments. Cyclo(Pro-Val), an active metabolite of strain HX79, was identified and metabolomic and molecular docking approaches confirmed it was responsible for promoting O. cumana seed germination and growth. And we found that Pseudomonas mandelii HX1 inhibited the growth of O. cumana in the host rhizosphere soil. Our findings clarify the role of rhizosphere microbiota in regulating the parasite O. cumana to possibly facilitate the development of a new weed suppression strategy.}, }
@article {pmid37938683, year = {2022}, author = {Marasco, R and Fusi, M and Ramond, JB and Van Goethem, MW and Seferji, K and Maggs-Kölling, G and Cowan, DA and Daffonchio, D}, title = {The plant rhizosheath-root niche is an edaphic "mini-oasis" in hyperarid deserts with enhanced microbial competition.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {47}, pmid = {37938683}, issn = {2730-6151}, abstract = {Plants have evolved unique morphological and developmental adaptations to cope with the abiotic stresses imposed by (hyper)arid environments. Such adaptations include the formation of rhizosheath-root system in which mutualistic plant-soil microbiome associations are established: the plant provides a nutrient-rich and shielded environment to microorganisms, which in return improve plant-fitness through plant growth promoting services. We hypothesized that the rhizosheath-root systems represent refuge niches and resource islands for the desert edaphic microbial communities. As a corollary, we posited that microorganisms compete intensively to colonize such "oasis" and only those beneficial microorganisms improving host fitness are preferentially selected by plant. Our results show that the belowground rhizosheath-root micro-environment is largely more hospitable than the surrounding gravel plain soil with higher nutrient and humidity contents, and cooler temperatures. By combining metabarcoding and shotgun metagenomics, we demonstrated that edaphic microbial biomass and community stability increased from the non-vegetated soils to the rhizosheath-root system. Concomitantly, non-vegetated soil communities favored autotrophy lifestyle while those associated with the plant niches were mainly heterotrophs and enriched in microbial plant growth promoting capacities. An intense inter-taxon microbial competition is involved in the colonization and homeostasis of the rhizosheath zone, as documented by significant enrichment of antibiotic resistance genes and CRISPR-Cas motifs. Altogether, our results demonstrate that rhizosheath-root systems are "edaphic mini-oases" and microbial diversity hotspots in hyperarid deserts. However, to colonize such refuge niches, the desert soil microorganisms compete intensively and are therefore prepared to outcompete potential rivals.}, }
@article {pmid37938286, year = {2022}, author = {Yeh, YC and Fuhrman, JA}, title = {Contrasting diversity patterns of prokaryotes and protists over time and depth at the San-Pedro Ocean Time series.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {36}, pmid = {37938286}, issn = {2730-6151}, support = {1737409//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 3779//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 549943//Simons Foundation/ ; }, abstract = {Community dynamics are central in microbial ecology, yet we lack studies comparing diversity patterns among marine protists and prokaryotes over depth and multiple years. Here, we characterized microbes at the San-Pedro Ocean Time series (2005-2018), using SSU rRNA gene sequencing from two size fractions (0.2-1 and 1-80 μm), with a universal primer set that amplifies from both prokaryotes and eukaryotes, allowing direct comparisons of diversity patterns in a single set of analyses. The 16S + 18S rRNA gene composition in the small size fraction was mostly prokaryotic (>92%) as expected, but the large size fraction unexpectedly contained 46-93% prokaryotic 16S rRNA genes. Prokaryotes and protists showed opposite vertical diversity patterns; prokaryotic diversity peaked at mid-depth, protistan diversity at the surface. Temporal beta-diversity patterns indicated prokaryote communities were much more stable than protists. Although the prokaryotic communities changed monthly, the average community stayed remarkably steady over 14 years, showing high resilience. Additionally, particle-associated prokaryotes were more diverse than smaller free-living ones, especially at deeper depths, contributed unexpectedly by abundant and diverse SAR11 clade II. Eukaryotic diversity was strongly correlated with the diversity of particle-associated prokaryotes but not free-living ones, reflecting that physical associations result in the strongest interactions, including symbioses, parasitism, and decomposer relationships.}, }
@article {pmid37938248, year = {2022}, author = {Song, J and Beule, L and Jongmans-Hochschulz, E and Wichels, A and Gerdts, G}, title = {The travelling particles: community dynamics of biofilms on microplastics transferred along a salinity gradient.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {35}, pmid = {37938248}, issn = {2730-6151}, support = {03F0789B//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 03F0789B//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 03F0789B//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 03F0789B//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 03F0789B//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; }, abstract = {Microplastics (MP), as novel substrata for microbial colonization within aquatic ecosystems, are a matter of growing concern due to their potential to propagate foreign or invasive species across different environments. MP are known to harbour a diversity of microorganisms, yet little is understood of the dynamics of their biofilms and their capacity to successfully displace these microorganisms across different aquatic ecosystems typically marked by steep salinity gradients. To address this, we performed an in situ sequential incubation experiment to simulate MP transport from riverine to coastal seawaters using synthetic (high-density polyethylene, HDPE and tyre wear, TW) and natural (Wood) substrata. Bacterial communities on incubated particles were compared to each other as well as to those in surrounding waters, and their dynamics along the gradient investigated. All communities differed significantly from each other in their overall structure along the salinity gradient and were shaped by different ecological processes. While HDPE communities were governed by environmental selection, those on TW and Wood were dominated by stochastic events of dispersal and drift. Upon transfer into coastal seawaters, an almost complete turnover was observed among HDPE and TW communities. While synthetic particles displaced a minor proportion of communities across the salinity gradient, some of these comprised putatively pathogenic and resistant taxa. Our findings present an extensive assessment of MP biofilms and their dynamics upon displacement across different aquatic systems, presenting new insights into the role of MP as transport vectors.}, }
@article {pmid39131681, year = {2022}, author = {Movva, R and Murtaza, N and Giri, R and Png, CW and Davies, J and Alabbas, S and Oancea, I and O'Cuiv, P and Morrison, M and Begun, J and Florin, TH}, title = {Successful Manipulation of the Gut Microbiome to Treat Spontaneous and Induced Murine Models of Colitis.}, journal = {Gastro hep advances}, volume = {1}, number = {3}, pages = {359-374}, pmid = {39131681}, issn = {2772-5723}, abstract = {BACKGROUND AND AIMS: There is clinical interest in the sustainability or otherwise of prebiotic, microbial, and antibiotic treatments to both prevent and treat inflammatory bowel diseases. This study examined the role of antibiotic manipulation of the gut microbiome to treat spontaneous and induced murine models of colitis.<br><br>METHODS: Symptomatic, histological, molecular, and microbial ecology and bioinformatic readouts were used to study the effect of a 10-day antibiotic cocktail and then follow-up over 2 months in the spontaneous Winnie colitis mouse preclinical model of ulcerative colitis and also the indirect antibiotic and Winnie microbiotic gavage effects in an acute dextran sodium sulfate-induced colitis model in wild-type mice.<br><br>RESULTS: The antibiotics elicited a striking reduction in both colitis symptoms and blinded histological colitis scores, together with a convergence of the microbial taxonomy of the spontaneous colitis and wild-type control mice, toward a taxonomic phenotype usually considered to be dysbiotic. The improvement in colitis was sustained over the following 8 weeks although the microbial taxonomy changed. In&#xa0;vitro, fecal waters from the antibiotic-treated colitis and wild-type mice suppressed the inflammatory tenor of colonic epithelial cells, and gavaged cecal slurries from these mice moderated the acute induced colitis.<br><br>CONCLUSION: The results clearly show the possibility of a sustained remission of colitis by microbial manipulation, which is relevant to clinical management of inflammatory bowel diseases. The beneficial effects appeared to depend on the microbial metabolome rather than its taxonomy.}, }
@article {pmid38647867, year = {2022}, author = {Dzulkarnain, ELN and Audu, JO and Wan Dagang, WRZ and Abdul-Wahab, MF}, title = {Microbiomes of biohydrogen production from dark fermentation of industrial wastes: current trends, advanced tools and future outlook.}, journal = {Bioresources and bioprocessing}, volume = {9}, number = {1}, pages = {16}, pmid = {38647867}, issn = {2197-4365}, support = {MyBrainSC scholarship//Ministry of Higher Education, Malaysia/ ; 05G24//Universiti Teknologi Malaysia/ ; 09G86//Universiti Teknologi Malaysia/ ; }, abstract = {Biohydrogen production through dark fermentation is very attractive as a solution to help mitigate the effects of climate change, via cleaner bioenergy production. Dark fermentation is a process where organic substrates are converted into bioenergy, driven by a complex community of microorganisms of different functional guilds. Understanding of the microbiomes underpinning the fermentation of organic matter and conversion to hydrogen, and the interactions among various distinct trophic groups during the process, is critical in order to assist in the process optimisations. Research in biohydrogen production via dark fermentation is currently advancing rapidly, and various microbiology and molecular biology tools have been used to investigate the microbiomes. We reviewed here the different systems used and the production capacity, together with the diversity of the microbiomes used in the dark fermentation of industrial wastes, with a special emphasis on palm oil mill effluent (POME). The current challenges associated with biohydrogen production were also included. Then, we summarised and discussed the different molecular biology tools employed to investigate the intricacy of the microbial ecology associated with biohydrogen production. Finally, we included a section on the future outlook of how microbiome-based technologies and knowledge can be used effectively in biohydrogen production systems, in order to maximise the production output.}, }
@article {pmid38867731, year = {2022}, author = {Jiao, S and Chu, H and Zhang, B and Wei, X and Chen, W and Wei, G}, title = {Linking soil fungi to bacterial community assembly in arid ecosystems.}, journal = {iMeta}, volume = {1}, number = {1}, pages = {e2}, pmid = {38867731}, issn = {2770-596X}, abstract = {Revealing the roles of biotic factors in driving community assembly, which is crucial for the understanding of biodiversity and ecosystem functions, is a fundamental but infrequently investigated subject in microbial ecology. Here, combining a cross-biome observational study with an experimental microcosm study, we provided evidence to reveal the major roles of biotic factors (i.e., soil fungi and cross-kingdom species associations) in determining soil bacterial biogeography and community assembly in complex terrestrial ecosystems of the arid regions of northwest China. The results showed that the soil fungal richness mediates the balance of assembly processes of bacterial communities, and stochastic assembly processes decreased with increasing fungal richness. Our results further suggest that the predicted increase in aridity conditions due to climate change will reduce bacterial α-diversity, particularly in desert soils and subsurface layer, and induce more negative species associations. Together, our study represents a significant advance in linking soil fungi to the mechanisms underlying bacterial biogeographic patterns and community assembly in arid ecosystems under climate aridity and land-use change scenarios.}, }
@article {pmid37938679, year = {2022}, author = {Junkins, EN and McWhirter, JB and McCall, LI and Stevenson, BS}, title = {Environmental structure impacts microbial composition and secondary metabolism.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {15}, pmid = {37938679}, issn = {2730-6151}, support = {80NSSC19K0479//National Aeronautics and Space Administration (NASA)/ ; 80NSSC19K0479//National Aeronautics and Space Administration (NASA)/ ; }, abstract = {Determining the drivers of microbial community assembly is a central theme of microbial ecology, and chemical ecologists seek to characterize how secondary metabolites mediate these assembly patterns. Environmental structure affects how communities assemble and what metabolic pathways aid in that assembly. Here, we bridged these two perspectives by addressing the chemical drivers of community assembly within a spatially structured landscape with varying oxygen availability. We hypothesized that structured environments would favor higher microbial diversity and metabolite diversity. We anticipated that the production of a compound would be more advantageous in a structured environment (less mixing) compared to an unstructured environment (more mixing), where the molecule would have a diminished local effect. We observed this to be partially true in our experiments: structured environments had similar microbial diversity compared to unstructured environments but differed significantly in the metabolites produced. We also found that structured environments selected for communities with higher evenness, rather than communities with higher richness. This supports the idea that when characterizing the drivers of community assembly, it matters less about who is there and more about what they are doing. Overall, these data contribute to a growing effort to approach microbial community assembly with interdisciplinary tools and perspectives.}, }
@article {pmid37938685, year = {2022}, author = {Jiang, G and Zhang, Y and Gan, G and Li, W and Wan, W and Jiang, Y and Yang, T and Zhang, Y and Xu, Y and Wang, Y and Shen, Q and Wei, Z and Dini-Andreote, F}, title = {Exploring rhizo-microbiome transplants as a tool for protective plant-microbiome manipulation.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {10}, pmid = {37938685}, issn = {2730-6151}, abstract = {The development of strategies for effectively manipulating and engineering beneficial plant-associated microbiomes is a major challenge in microbial ecology. In this sense, the efficacy and potential implications of rhizosphere microbiome transplant (RMT) in plant disease management have only scarcely been explored in the literature. Here, we initially investigated potential differences in rhizosphere microbiomes of 12 Solanaceae eggplant varieties and accessed their level of resistance promoted against bacterial wilt disease caused by the pathogen Ralstonia solanacearum, in a 3-year field trial. We elected 6 resistant microbiomes and further tested the broad feasibility of using RMT from these donor varieties to a susceptible model Solanaceae tomato variety MicroTom. Overall, we found the rhizosphere microbiome of resistant varieties to enrich for distinct and specific bacterial taxa, of which some displayed significant associations with the disease suppression. Quantification of the RMT efficacy using source tracking analysis revealed more than 60% of the donor microbial communities to successfully colonize and establish in the rhizosphere of recipient plants. RTM from distinct resistant donors resulted in different levels of wilt disease suppression, reaching up to 47% of reduction in disease incidence. Last, we provide a culture-dependent validation of potential bacterial taxa associated with antagonistic interactions with the pathogen, thus contributing to a better understanding of the potential mechanism associated with the disease suppression. Our study shows RMT from appropriate resistant donors to be a promising tool to effectively modulate protective microbiomes and promote plant health. Together we advocate for future studies aiming at understanding the ecological processes and mechanisms mediating rates of coalescence between donor and recipient microbiomes in the plant rhizosphere.}, }
@article {pmid38089065, year = {2022}, author = {Berkhout, M and Zoetendal, E and Plugge, C and Belzer, C}, title = {Use of synthetic communities to study microbial ecology of the gut.}, journal = {Microbiome research reports}, volume = {1}, number = {1}, pages = {4}, pmid = {38089065}, issn = {2771-5965}, abstract = {The application of in vitro synthetic microbial communities is an excellent approach to model the ecological interactions between microbes in the human gastrointestinal tract. Although DNA-based studies have provided a wealth of information, they do not consider the ecological properties of the human gut microbiota. Ecological interactions between gut microbes of interest can be studied by applying synthetic communities. This review describes the considerations that should be taken into account when constructing a synthetic community by discussing example research questions that can be answered by using a synthetic microbial community, the choice of microbial species, the growth conditions, possible reactor setups, and the parameters to analyze.}, }
@article {pmid37938641, year = {2021}, author = {Röttjers, L and Vandeputte, D and Raes, J and Faust, K}, title = {Null-model-based network comparison reveals core associations.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {36}, pmid = {37938641}, issn = {2730-6151}, support = {STG/16/006//KU Leuven (Katholieke Universiteit Leuven)/ ; STG/16/006//KU Leuven (Katholieke Universiteit Leuven)/ ; 801747//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 801747//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 30770923//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; 30770923//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; }, abstract = {Microbial network construction and analysis is an important tool in microbial ecology. Such networks are often constructed from statistically inferred associations and may not represent ecological interactions. Hence, microbial association networks are error prone and do not necessarily reflect true community structure. We have developed anuran, a toolbox for investigation of noisy networks with null models. Such models allow researchers to generate data under the null hypothesis that all associations are random, supporting identification of nonrandom patterns in groups of association networks. This toolbox compares multiple networks to identify conserved subsets (core association networks, CANs) and other network properties that are shared across all networks. We apply anuran to a time series of fecal samples from 20 women to demonstrate the existence of CANs in a subset of the sampled individuals. Moreover, we use data from the Global Sponge Project to demonstrate that orders of sponges have a larger CAN than expected at random. In conclusion, this toolbox is a resource for investigators wanting to compare microbial networks across conditions, time series, gradients, or hosts.}, }
@article {pmid37938227, year = {2021}, author = {Reitmeier, S and Hitch, TCA and Treichel, N and Fikas, N and Hausmann, B and Ramer-Tait, AE and Neuhaus, K and Berry, D and Haller, D and Lagkouvardos, I and Clavel, T}, title = {Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {31}, pmid = {37938227}, issn = {2730-6151}, abstract = {16S rRNA gene amplicon sequencing is a popular approach for studying microbiomes. However, some basic concepts have still not been investigated comprehensively. We studied the occurrence of spurious sequences using defined microbial communities based on data either from the literature or generated in three sequencing facilities and analyzed via both operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) approaches. OTU clustering and singleton removal, a commonly used approach, delivered approximately 50% (mock communities) to 80% (gnotobiotic mice) spurious taxa. The fraction of spurious taxa was generally lower based on ASV analysis, but varied depending on the gene region targeted and the barcoding system used. A relative abundance of 0.25% was found as an effective threshold below which the analysis of spurious taxa can be prevented to a large extent in both OTU- and ASV-based analysis approaches. Using this cutoff improved the reproducibility of analysis, i.e., variation in richness estimates was reduced by 38% compared with singleton filtering using six human fecal samples across seven sequencing runs. Beta-diversity analysis of human fecal communities was markedly affected by both the filtering strategy and the type of phylogenetic distances used for comparison, highlighting the importance of carefully analyzing data before drawing conclusions on microbiome changes. In summary, handling of artifact sequences during bioinformatic processing of 16S rRNA gene amplicon data requires careful attention to avoid the generation of misleading findings. We propose the concept of effective richness to facilitate the comparison of alpha-diversity across studies.}, }
@article {pmid37938246, year = {2021}, author = {Hill, JE and Raaijmakers, JM and Smidt, H}, title = {Editorial.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {10}, doi = {10.1038/s43705-021-00013-3}, pmid = {37938246}, issn = {2730-6151}, }
@article {pmid37769814, year = {2023}, author = {Zinzula, L and Scholz, J and Nagy, I and Di Guardo, G and Orsini, M}, title = {Biophysical characterization of the cetacean morbillivirus haemagglutinin glycoprotein.}, journal = {Virus research}, volume = {336}, number = {}, pages = {199231}, pmid = {37769814}, issn = {1872-7492}, abstract = {Cetacean morbillivirus (CeMV) is an enveloped, non-segmented, negative-stranded RNA virus that infects marine mammals, spreading across species and causing lethal disease outbreaks worldwide. Among the eight proteins encoded by the CeMV genome, the haemagglutinin (H) glycoprotein is responsible for the virus attachment to host cell receptors. CeMV H represents an attractive target for antiviral and diagnostic research, yet the elucidation of the molecular mechanisms underlying its role in infection and inter-species transmission was hampered thus far due to the unavailability of recombinant versions of the protein. Here we present the cloning, expression and purification of a recombinant CeMV H ectodomain (rH-ecto), providing an initial characterization of its biophysical and structural properties. Sodium dodecyl sulphate - polyacrylamide gel electrophoresis (PAGE) combined to Western blot analysis and periodic acid Schiff assay showed that CeMV rH-ecto is purifiable at homogeneity from insect cells as a secreted, soluble and glycosylated protein. Miniaturized differential scanning fluorimetry, Blue Native PAGE and size exclusion chromatography coupled to multiangle light scattering revealed that CeMV rH-ecto is globularly folded, thermally stable and exists in solution in the oligomeric states of dimer and multiple of dimers. Furthermore, negative stain electron microscopy single particle analysis allowed us to delineate a low-resolution molecular architecture of the CeMV rH-ecto dimer, which recapitulates native assemblies from other morbilliviral H proteins, such as those from measles virus and canine distemper virus. This set of experiments by orthogonal techniques validates the CeMV rH-ecto as an experimental model for future biochemical studies on its structure and functions.}, }
@article {pmid37768303, year = {2023}, author = {Kiewra, D and Krysmann, A}, title = {Interactions between hard ticks (Ixodidae) and bacterial tick-borne pathogens.}, journal = {Annals of parasitology}, volume = {69}, number = {1}, pages = {7-16}, doi = {10.17420/ap6901.502}, pmid = {37768303}, issn = {2299-0631}, mesh = {Animals ; Humans ; *Ixodidae ; *Tick-Borne Diseases ; *Rickettsia/genetics ; *Ticks ; Europe ; *Ixodes ; }, abstract = {In Europe, ticks are particularly important vectors of pathogens known as tick-borne pathogens (TBP). TBP can influence hosts, including domestic animals and humans as well as ticks. This review focuses on interactions between hard ticks and medically and veterinary significant bacterial pathogens i.e. Borrelia burgdorferi s.l., Anaplasma spp, and Rickettsia spp. The interactions between ticks and bacteria include among others the impact on gene expression and tick behaviour. Infection with TBP may influence tick salivary proteins and midgut receptors. Infection with B. burgdorferi s.l. changes the bahaviour of the tick allowing them for longer questing and increased mobility, while A. phagocytophilum increases survive in low temperatures by upregulating the expression of antifreeze glycoprotein (IAFGP). Whereas Rickettsia spp. increases ticks attraction towards the 900 MHz electromagnetic field.}, }
@article {pmid37768099, year = {2023}, author = {Ghesquière, J and Simoens, K and Koos, E and Boon, N and Teughels, W and Bernaerts, K}, title = {Spatiotemporal monitoring of a periodontal multispecies biofilm model: demonstration of prebiotic treatment responses.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {10}, pages = {e0108123}, pmid = {37768099}, issn = {1098-5336}, mesh = {Humans ; *Bacteria ; Streptococcus gordonii/physiology ; Fusobacterium nucleatum ; Streptococcus sanguis ; Streptococcus oralis ; Biofilms ; *Periodontitis ; Arginine/metabolism ; Porphyromonas gingivalis/physiology ; }, abstract = {Biofilms are complex polymicrobial communities which are often associated with human infections such as the oral disease periodontitis. Studying these complex communities under controlled conditions requires in vitro biofilm model systems that mimic the natural environment as close as possible. This study established a multispecies periodontal model in the drip flow biofilm reactor in order to mimic the continuous flow of nutrients at the air-liquid interface in the oral cavity. The design is engineered to enable real-time characterization. A community of five bacteria, Streptococcus gordonii-GFPmut3*, Streptococcus oralis-GFPmut3*, Streptococcus sanguinis-pVMCherry, Fusobacterium nucleatum, and Porphyromonas gingivalis-SNAP26 is visualized using two distinct fluorescent proteins and the SNAP-tag. The biofilm in the reactor develops into a heterogeneous, spatially uniform, dense, and metabolically active biofilm with relative cell abundances similar to those in a healthy individual. Metabolic activity, structural features, and bacterial composition of the biofilm remain stable from 3 to 6 days. As a proof of concept for our periodontal model, the 3 days developed biofilm is exposed to a prebiotic treatment with L-arginine. Multifaceted effects of L-arginine on the oral biofilm were validated by this model setup. L-arginine showed to inhibit growth and incorporation of the pathogenic species and to reduce biofilm thickness and volume. Additionally, L-arginine is metabolized by Streptococcus gordonii-GFPmut3* and Streptococcus sanguinis-pVMCherry, producing high levels of ornithine and ammonium in the biofilm. In conclusion, our drip flow reactor setup is promising in studying spatiotemporal behavior of a multispecies periodontal community.ImportancePeriodontitis is a multifactorial chronic inflammatory disease in the oral cavity associated with the accumulation of microorganisms in a biofilm. Not the presence of the biofilm as such, but changes in the microbiota (i.e., dysbiosis) drive the development of periodontitis, resulting in the destruction of tooth-supporting tissues. In this respect, novel treatment approaches focus on maintaining the health-associated homeostasis of the resident oral microbiota. To get insight in dynamic biofilm responses, our research presents the establishment of a periodontal biofilm model including Streptococcus gordonii, Streptococcus oralis, Streptococcus sanguinis, Fusobacterium nucleatum, and Porphyromonas gingivalis. The added value of the model setup is the combination of simulating continuously changing natural mouth conditions with spatiotemporal biofilm profiling using non-destructive characterization tools. These applications are limited for periodontal biofilm research and would contribute in understanding treatment mechanisms, short- or long-term exposure effects, the adaptation potential of the biofilm and thus treatment strategies.}, }
@article {pmid37767604, year = {2023}, author = {Bustos-Lobato, L and Rus, MJ and Saúco, C and Simon-Soro, A}, title = {Oral microbial biomap in the drought environment: Sjogren's syndrome.}, journal = {Molecular oral microbiology}, volume = {38}, number = {5}, pages = {400-407}, doi = {10.1111/omi.12435}, pmid = {37767604}, issn = {2041-1014}, mesh = {Humans ; *Sjogren's Syndrome/microbiology ; Droughts ; Ecosystem ; Saliva/microbiology ; }, abstract = {Sjogren's syndrome (SS) is an autoimmune disease that affects primarily the salivary glands, making perturbations in the oral ecosystem and potential factors of salivary flow that influence the onset and development of the disease. The oral cavity contains diverse microorganisms that inhabit various niches such as the oral microbial "biomap." It does not seem specific enough to establish a characteristic microbiome, given the diversity of clinical manifestations, variable rates of salivary secretion, and influential risk factors in patients with SS. This review discusses the biogeography of the oral microbiome in patients with SS such as saliva, tongue, tooth, mucosa, and gum. The microorganisms that were more abundant in the different oral niches were Gram-positive species, suggesting a higher survival of cell wall bacteria in this arid oral environment. Reduced salivary flow appears not to be linked to the cause of dysbiosis alone but influences host-associated risk factors. However, much work remains to be done to establish the role of the microbiome in the etiopathogenesis of autoimmune diseases such as SS. Future studies of the microbiome in autoimmunity will shed light on the role of specific microorganisms that have never been linked before with SS.}, }
@article {pmid37767299, year = {2023}, author = {Cai, J and Pan, R and Lin, J and Liu, J and Zhang, L and Wen, X and Chen, X and Zhang, X}, title = {Improved EfficientNet for corn disease identification.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1224385}, pmid = {37767299}, issn = {1664-462X}, abstract = {INTRODUCTION: Corn is one of the world's essential crops, and the presence of corn diseases significantly affects both the yield and quality of corn. Accurate identification of corn diseases in real time is crucial to increasing crop yield and improving farmers' income. However, in real-world environments, the complexity of the background, irregularity of the disease region, large intraclass variation, and small interclass variation make it difficult for most convolutional neural network models to achieve disease recognition under such conditions. Additionally, the low accuracy of existing lightweight models forces farmers to compromise between accuracy and real-time.<br><br>METHODS: To address these challenges, we propose FCA-EfficientNet. Building upon EfficientNet, the fully-convolution-based coordinate attention module allows the network to acquire spatial information through convolutional structures. This enhances the network's ability to focus on disease regions while mitigating interference from complex backgrounds. Furthermore, the adaptive fusion module is employed to fuse image information from different scales, reducing interference from the background in disease recognition. Finally, through multiple experiments, we have determined the network structure that achieves optimal performance.<br><br>RESULTS: Compared to other widely used deep learning models, this proposed model exhibits outstanding performance in terms of accuracy, precision, recall, and F1 score. Furthermore, the model has a parameter count of 3.44M and Flops of 339.74M, which is lower than most lightweight network models. We designed and implemented a corn disease recognition application and deployed the model on an Android device with an average recognition speed of 92.88ms, which meets the user's needs.<br><br>DISCUSSION: Overall, our model can accurately identify corn diseases in realistic environments, contributing to timely and effective disease prevention and control.}, }
@article {pmid37766415, year = {2023}, author = {Bohórquez-Herrera, J and Abad Matías, ID and Gutiérrez Castañeda, CG}, title = {Impact of different environmental pollution processes on bacterial key-indicators in tropical rivers: scoping review.}, journal = {FEMS microbiology letters}, volume = {370}, number = {}, pages = {}, doi = {10.1093/femsle/fnad098}, pmid = {37766415}, issn = {1574-6968}, support = {//Universidad de Cartagena/ ; }, abstract = {Freshwater ecosystems are an essential resource for human use and natural populations, but they are exposed to different sources of man-made pollution. This study analyses how different environmental pollution processes influence the structure of bacterial communities in tropical rivers. A scoping review was performed to characterize the bacterial communities in freshwater ecosystems in tropical regions that have been reported to be associated with pollution of different kinds. The statistical analyses allowed us to categorize the genera found into three large groups (pollution generalists, middle types, and pollution specialists) according to the types of pollutants with which they were associated. The results show that Escherichia has a greater association with fecal contamination, while Enterococcus is more associated with domestic wastewater and organic and synthetic chemicals. The present study proposes Streptomyces as a potential indicator of waters with microbial contamination, as well as some other genera as possible indicators of waters with heavy metal contamination.}, }
@article {pmid37760211, year = {2023}, author = {Verstrepen, L and Calatayud-Arroyo, M and Duysburgh, C and De Medts, J and Ekmay, RD and Marzorati, M}, title = {Amino Acid Digestibility of Different Formulations of Torula Yeast in an In Vitro Porcine Gastrointestinal Digestion Model and Their Protective Effects on Barrier Function and Inflammation in a Caco-2/THP1Co-Culture Model.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {18}, pages = {}, pmid = {37760211}, issn = {2076-2615}, support = {//Arbiom Inc./ ; }, abstract = {Single-cell protein from torula yeast (Cyberlindnera jadinii) grown on lignocellulosic biomass has been proven to be an excellent alternative protein source for animal feed. This study aimed to evaluate the amino acid (AA) digestibility by estimating intestinal absorption from three yeast-based ingredients, produced by cultivating C. jadinii on hydrolysate, using either mixed woody species (drum- (WDI) or spray-dried (WSI)) or corn dextrose (drum-dried (DDI)) as the carbon source. Further, the protective effect of intestinal digests on activated THP1-Blue™-induced epithelial damage and cytokine profile was evaluated. Total protein content from these three ingredients ranged from 34 to 45%, while the AA dialysis showed an estimated bioaccessibility between 41 and 58%, indicating good digestibility of all test products. A protective effect against epithelial-induced damage was observed for two of the three tested products. Torula yeast cultivated on wood and drum-dried (WDI) and torula yeast cultivated on wood and spray-dried (WSI) significantly increased transepithelial electrical resistance (TEER) values (111-147%, p < 0.05), recovering the epithelial barrier from the inflammation-induced damage in a dose-dependent manner. Further, WSI digests significantly reduced IL8 (250.8 ± 28.1 ng/mL), IL6 (237.9 ± 1.8 pg/mL) and TNF (2797.9 ± 216.3 pg/mL) compared to the blank control (IL8 = 485.7 ± 74.4 ng/mL, IL6 = 478.7 ± 58.9 pg/mL; TNF = 4273.5 ± 20.9 pg/mL) (p < 0.05). These results align with previous in vivo studies, supporting torula yeast-based ingredients as a high-quality protein source for pigs, protecting the intestinal barrier from inflammatory damage, and reducing the pro-inflammatory response. We provided novel insights into the mechanisms behind the health improvement of pigs fed on torula yeast-based ingredients, with potential applications for designing nutritional interventions to recover intestinal homeostasis during critical production periods, such as weaning.}, }
@article {pmid37756318, year = {2023}, author = {Zhang, X and Yao, C and Zhang, B and Tan, W and Gong, J and Wang, GY and Zhao, J and Lin, X}, title = {Dynamics of Benthic Nitrate Reduction Pathways and Associated Microbial Communities Responding to the Development of Seasonal Deoxygenation in a Coastal Mariculture Zone.}, journal = {Environmental science &amp; technology}, volume = {57}, number = {40}, pages = {15014-15025}, doi = {10.1021/acs.est.3c03994}, pmid = {37756318}, issn = {1520-5851}, mesh = {Nitrates/analysis ; Chlorophyll A ; Seasons ; Organic Chemicals ; *Ammonium Compounds ; Nitrogen/analysis ; *Microbiota ; Oxygen ; Denitrification ; }, abstract = {Intensive mariculture activities result in eutrophication and enhance coastal deoxygenation. Deoxygenation profoundly influences nitrate reduction processes and further the fate of nitrogen (N) in coastal systems. Herein, [15]N isotope labeling, real-time PCR, and high-throughput sequencing techniques were jointly used to investigate the participation and seasonal dynamics of sediment nitrate reduction pathways and the succession of functional microbial communities during the development of seasonal deoxygenation in a coastal aquaculture zone. Denitrification dominated benthic nitrate reduction (46.26-80.91%). Both denitrification and dissimilatory nitrate reduction to ammonium were significantly enhanced by summer deoxygenation (dissolved oxygen levels fell to 2.94 ± 0.28 mg L[-1]), while anammox remained unchanged. The abundance of the nitrous oxide reductase gene nosZ increased during deoxygenation. The community of the nosZ gene was sensitive to deoxygenation, with Azospirillum and Ruegeria accounting for the majority. Pelobacter was overwhelming in the nrfA gene (encoding dissimilatory nitrite reductase) community, which was less affected by deoxygenation. The variations of benthic nitrate reduction processes were driven by bottom water oxygen combined with temperature, chlorophyll a, and microbial gene abundances and community compositions. Our results implicated that seasonal oxygen-deficient zones could be substantial N sinks of coastal ecosystems and important for N balance. Effective management measures need to be developed to avoid further exacerbation of coastal deoxygenation and maintain the sustainable development of mariculture.}, }
@article {pmid37755230, year = {2023}, author = {Bareia, T and Pollak, S and Guler, P and Puyesky, S and Eldar, A}, title = {Major distinctions between the two oligopeptide permease systems of Bacillus subtilis with respect to signaling, development and evolutionary divergence.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {9}, pages = {}, pmid = {37755230}, issn = {1465-2080}, mesh = {*Bacillus subtilis/genetics ; Biological Evolution ; *Biological Phenomena ; Signal Transduction ; Oligopeptides ; }, abstract = {Oligopeptide-permeases (Opps) are used by bacteria to import short peptides. In addition to their metabolic benefit, imported short peptides are used in many Gram-positive bacteria as signalling molecules of the RRNPP super-family of quorum-sensing systems, making Opps an integral part of cell–cell communication. In some Gram-positive bacteria there exist multiple Opps and the relative importance of those to RRNPP quorum sensing are not fully clear. Specifically, in Bacillus subtilis , the Gram-positive model species, there exist two homologous oligopeptide permeases named Opp and App. Previous work showed that the App system is mutated in lab strain 168 and its recovery partially complements an Opp mutation for several developmental processes. Yet, the nature of the impact of App on signalling and development in wild-type strains, where both permeases are active was not studied. Here we re-examine the impact of the two permease systems. We find that App has a minor contribution to biofilm formation, surfactin production and phage infection compared to the effect of Opp. This reduced effect is also reflected in its lower ability to import the signals of four different Rap-Phr RRNPP systems. Further analysis of the App system revealed that, unlike Opp, some App genes have undergone horizontal transfer, resulting in two distinct divergent alleles of this system in B. subtilis strains. We found that both alleles were substantially better adapted than the Opp system to import an exogenous RRNPP signal of the Bacillus cereus group PlcR-PapR system. In summary, we find that the App system has only a minor role in signalling but may still be crucial for the import of other peptides.}, }
@article {pmid37754985, year = {2023}, author = {Marsaux, B and Moens, F and Marzorati, M and Van de Wiele, T}, title = {The Intricate Connection between Bacterial α-Diversity and Fungal Engraftment in the Human Gut of Healthy and Impaired Individuals as Studied Using the In Vitro SHIME[®] Model.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {9}, pages = {}, pmid = {37754985}, issn = {2309-608X}, support = {812969//Marie Sklodowska-Curie/ ; BOF22/GOA/031//UGent special research fund/ ; }, abstract = {From the estimated 2.2 to 3.8 million fungal species existing on Earth, only a minor fraction actively colonizes the human gastrointestinal tract. In fact, these fungi only represent 0.1% of the gastrointestinal biosphere. Despite their low abundance, fungi play dual roles in human health-both beneficial and detrimental. Fungal infections are often associated with bacterial dysbiosis following antibiotic use, yet our understanding of gut fungi-bacteria interactions remains limited. Here, we used the SHIME[®] gut model to explore the colonization of human fecal-derived fungi across gastrointestinal compartments. We accounted for the high inter-individual microbial diversity by using fecal samples from healthy adults, healthy babies, and Crohn's disease patients. Using quantitative Polymerase Chain Reaction and targeted next-generation sequencing, we demonstrated that SHIME[®]-colonized mycobiomes change upon loss of transient colonizers. In addition, SHIME[®] reactors from Crohn's disease patients contained comparable bacterial levels as healthy adults but higher fungal concentrations, indicating unpredictable correlations between fungal levels and total bacterial counts. Our findings rather link higher bacterial α-diversity to limited fungal growth, tied to colonization resistance. Hence, while healthy individuals had fewer fungi engrafting the colonic reactors, low α-diversity in impaired (Crohn's disease patients) or immature (babies) microbiota was associated with greater fungal abundance. To validate, antibiotic-treated healthy colonic microbiomes demonstrated increased fungal colonization susceptibility, and bacterial taxa that were negatively correlated with fungal expansion were identified. In summary, fungal colonization varied individually and transiently, and bacterial resistance to fungal overgrowth was more related with specific bacterial genera than total bacterial load. This study sheds light on fungal-bacterial dynamics in the human gut.}, }
@article {pmid37754764, year = {2023}, author = {Barbosa, C and Tamayo-Leiva, J and Alcorta, J and Salgado, O and Daniele, L and Morata, D and Díez, B}, title = {Effects of hydrogeochemistry on the microbial ecology of terrestrial hot springs.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0024923}, pmid = {37754764}, issn = {2165-0497}, abstract = {Temperature, pH, and hydrochemistry of terrestrial hot springs play a critical role in shaping thermal microbial communities. However, the interactions of biotic and abiotic factors at this terrestrial-aquatic interface are still not well understood on a global scale, and the question of how underground events influence microbial communities remains open. To answer this, 11 new samples obtained from the El Tatio geothermal field were analyzed by 16S rRNA amplicon sequencing (V4 region), along with 191 samples from previous publications obtained from the Taupo Volcanic Zone, the Yellowstone Plateau Volcanic Field, and the Eastern Tibetan Plateau, with their temperature, pH, and major ion concentration. Microbial alpha diversity was lower in acid-sulfate waters, and no significant correlations were found with temperature. However, moderate correlations were observed between chemical parameters such as pH (mostly constrained to temperatures below 70°C), SO4 [2-] and abundances of members of the phyla Armatimonadota, Deinococcota, Chloroflexota, Campilobacterota, and Thermoplasmatota. pH and SO4 [2-] gradients were explained by phase separation of sulfur-rich hydrothermal fluids and oxidation of reduced sulfur in the steam phase, which were identified as key processes shaping these communities. Ordination and permutational analysis of variance showed that temperature, pH, and major element hydrochemistry explain only 24% of the microbial community structure. Therefore, most of the variance remained unexplained, suggesting that other environmental or biotic factors are also involved and highlighting the environmental complexity of the ecosystem and its great potential to test niche theory ecological associated questions. IMPORTANCE This is the first approach to investigate whether geothermal processes could have an influence on the ecology of thermal microbial communities on a global scale. In addition to temperature and pH, microbial communities are structured by sulfate concentrations, which depends on the tectono-magmatic settings (such as the depth of magmatic chambers) and the local settings (such as the availability of a confining layer separating NaCl waters from steam after phase separation) and the possibility of mixing with more diluted fluids. Comparison of microbial communities from different geothermal areas by homogeneous sequence processing showed that no significant geographic distance decay was detected on the microbial communities according to Bray-Curtis, Jaccard, unweighted, and weighted Unifrac similarity/dissimilarity indices. Instead, an ancient potential divergence in the same taxonomic groups is suggested between globally distant thermal zones.}, }
@article {pmid37754664, year = {2023}, author = {Djemiel, C and Dequiedt, S and Bailly, A and Tripied, J and Lelièvre, M and Horrigue, W and Jolivet, C and Bispo, A and Saby, N and Valé, M and Maron, P-A and Ranjard, L and Terrat, S}, title = {Biogeographical patterns of the soil fungal:bacterial ratio across France.}, journal = {mSphere}, volume = {8}, number = {5}, pages = {e0036523}, pmid = {37754664}, issn = {2379-5042}, mesh = {Humans ; *Soil/chemistry ; *Environmental Biomarkers ; Soil Microbiology ; Bacteria/genetics ; France ; Carbon ; }, abstract = {Soils are one of the major reservoirs of biological diversity on our planet because they host a huge richness of microorganisms. The fungal:bacterial (F:B) ratio targets two major functional groups of organisms in soils and can improve our understanding of their importance and efficiency for soil functioning. To better decipher the variability of this ratio and rank the environmental parameters involved, we used the French Soil Quality Monitoring Network (RMQS)-one of the most extensive and a priori-free soil sampling surveys, based on a systematic 16 km × 16 km grid and including more than 2,100 samples. F:B ratios, measured by quantitative PCR targeting the 18S and 16S rDNA genes, turned out to be heterogenously distributed and spatially structured in geographical patterns across France. These distribution patterns differed from bacterial or fungal densities taken separately, supporting the hypothesis that the F:B ratio is not the mere addition of each density but rather results from the complex interactions of the two functional groups. The F:B ratios were mainly influenced by soil characteristics and land management. Among soil characteristics, the pH and, to a lesser extent, the organic carbon content and the carbon:nitrogen (C:N) ratio were the main drivers. These results improved our understanding of soil microbial communities, and from an operational point of view, they suggested that the F:B ratio should be a useful new bioindicator of soil status. The resulting dataset can be considered as a first step toward building up a robust repository essential to any bioindicator and aimed at guiding and helping decision making. IMPORTANCE In the face of human disturbances, microbial activity can be impacted and, e.g., can result in the release of large amounts of soil carbon into the atmosphere, with global impacts on temperature. Therefore, the development and the regular use of soil bioindicators are essential to (i) improve our knowledge of soil microbial communities and (ii) guide and help decision makers define suitable soil management strategies. Bacterial and fungal communities are key players in soil organic matter turnover, but with distinct physiological and ecological characteristics. The fungal:bacterial ratio targets these two major functional groups by investigating their presence and their equilibrium. The aim of our study is to characterize this ratio at a territorial scale and rank the environmental parameters involved so as to further develop a robust repository essential to the interpretation of any bioindicator of soil quality.}, }
@article {pmid37752280, year = {2023}, author = {Dong, M and Kuramae, EE and Zhao, M and Li, R and Shen, Q and Kowalchuk, GA}, title = {Tomato growth stage modulates bacterial communities across different soil aggregate sizes and disease levels.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {104}, pmid = {37752280}, issn = {2730-6151}, support = {41977044//National Natural Science Foundation of China (National Science Foundation of China)/ ; 202006850020//China Scholarship Council (CSC)/ ; }, abstract = {Soil aggregates contain distinct physio-chemical properties across different size classes. These differences in micro-habitats support varied microbial communities and modulate the effect of plant on microbiome, which affect soil functions such as disease suppression. However, little is known about how the residents of different soil aggregate size classes are impacted by plants throughout their growth stages. Here, we examined how tomato plants impact soil aggregation and bacterial communities within different soil aggregate size classes. Moreover, we investigated whether aggregate size impacts the distribution of soil pathogen and their potential inhibitors. We collected samples from different tomato growth stages: before-planting, seedling, flowering, and fruiting stage. We measured bacterial density, community composition, and pathogen abundance using qPCR and 16 S rRNA gene sequencing. We found the development of tomato growth stages negatively impacted root-adhering soil aggregation, with a gradual decrease of large macro-aggregates (1-2 mm) and an increase of micro-aggregates (<0.25 mm). Additionally, changes in bacterial density and community composition varied across soil aggregate size classes. Furthermore, the pathogen exhibited a preference to micro-aggregates, while macro-aggregates hold a higher abundance of potential pathogen-inhibiting taxa and predicted antibiotic-associated genes. Our results indicate that the impacts of tomatoes on soil differ for different soil aggregate size classes throughout different plant growth stages, and plant pathogens and their potential inhibitors have different habitats within soil aggregate size classes. These findings highlight the importance of fine-scale heterogeneity of soil aggregate size classes in research on microbial ecology and agricultural sustainability, further research focuses on soil aggregates level could help identify candidate tax involved in suppressing pathogens in the virtual micro-habitats.}, }
@article {pmid37750468, year = {2023}, author = {Wang, Z and Ishii, S and Novak, PJ}, title = {Quantification of depth-dependent microbial growth in encapsulated systems.}, journal = {Microbial biotechnology}, volume = {16}, number = {11}, pages = {2094-2104}, pmid = {37750468}, issn = {1751-7915}, mesh = {In Situ Hybridization, Fluorescence ; *Biofilms ; *Alginates ; }, abstract = {Encapsulated systems have been widely used in environmental applications to selectively retain and protect microorganisms. The permeable matrix used for encapsulation, however, limits the accessibility of existing analytical methods to study the behaviour of the encapsulated microorganisms. Here, we present a novel method that overcomes these limitations and enables direct observation and enumeration of encapsulated microbial colonies over a range of spatial and temporal scales. The method involves embedding, cross-sectioning, and analysing the system via fluorescence in situ hybridization and retains the structure of encapsulants and the morphology of encapsulated colonies. The major novelty of this method lies in its ability to distinguish between, and subsequently analyse, multiple microorganisms within a single encapsulation matrix across depth. Our results demonstrated the applicability and repeatability of this method with alginate-encapsulated pure (Nitrosomonas europaea) and enrichment cultures (anammox enrichment). The use of this method can potentially reveal interactions between encapsulated microorganisms and their surrounding matrix, as well as quantitatively validate predictions from mathematical models, thereby advancing our understanding of microbial ecology in encapsulated or even biofilm systems and facilitating the optimization of these systems.}, }
@article {pmid37749300, year = {2023}, author = {Mueller, AJ and Daebeler, A and Herbold, CW and Kirkegaard, RH and Daims, H}, title = {Cultivation and genomic characterization of novel and ubiquitous marine nitrite-oxidizing bacteria from the Nitrospirales.}, journal = {The ISME journal}, volume = {17}, number = {11}, pages = {2123-2133}, pmid = {37749300}, issn = {1751-7370}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; P 30570/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Nitrites/metabolism ; Oxidation-Reduction ; *Bacteria ; Ammonia/metabolism ; Nitrification ; Genomics ; Phylogeny ; }, abstract = {Nitrospirales, including the genus Nitrospira, are environmentally widespread chemolithoautotrophic nitrite-oxidizing bacteria. These mostly uncultured microorganisms gain energy through nitrite oxidation, fix CO2, and thus play vital roles in nitrogen and carbon cycling. Over the last decade, our understanding of their physiology has advanced through several new discoveries, such as alternative energy metabolisms and complete ammonia oxidizers (comammox Nitrospira). These findings mainly resulted from studies of terrestrial species, whereas less attention has been given to marine Nitrospirales. In this study, we cultured three new marine Nitrospirales enrichments and one isolate. Three of these four NOB represent new Nitrospira species while the fourth represents a novel genus. This fourth organism, tentatively named "Ca. Nitronereus thalassa", represents the first cultured member of a Nitrospirales lineage that encompasses both free-living and sponge-associated nitrite oxidizers, is highly abundant in the environment, and shows distinct habitat distribution patterns compared to the marine Nitrospira species. Partially explaining this, "Ca. Nitronereus thalassa" harbors a unique combination of genes involved in carbon fixation and respiration, suggesting differential adaptations to fluctuating oxygen concentrations. Furthermore, "Ca. Nitronereus thalassa" appears to have a more narrow substrate range compared to many other marine nitrite oxidizers, as it lacks the genomic potential to utilize formate, cyanate, and urea. Lastly, we show that the presumed marine Nitrospirales lineages are not restricted to oceanic and saline environments, as previously assumed.}, }
@article {pmid37748600, year = {2023}, author = {Lamprea Pineda, PA and Demeestere, K and González-Cortés, JJ and Alvarado-Alvarado, AA and Boon, N and Devlieghere, F and Van Langenhove, H and Walgraeve, C}, title = {Effect of inoculum type, packing material and operational conditions on the biofiltration of a mixture of hydrophobic volatile organic compounds in air.}, journal = {The Science of the total environment}, volume = {904}, number = {}, pages = {167326}, doi = {10.1016/j.scitotenv.2023.167326}, pmid = {37748600}, issn = {1879-1026}, mesh = {*Volatile Organic Compounds/analysis ; Filtration/methods ; Hexanes ; Biodegradation, Environmental ; Cyclohexanes ; Toluene ; *Air Pollutants/analysis ; Bioreactors/microbiology ; }, abstract = {The emission of volatile organic compounds (VOCs) into the atmosphere causes negative environmental and health effects. Biofiltration is known to be an efficient and cost-effective treatment technology for the removal of VOCs in waste gas streams. However, little is known on the removal of VOC mixtures and the effect of operational conditions, particularly for hydrophobic VOCs, and on the microbial populations governing the biofiltration process. In this study, we evaluated the effect of inoculum type (acclimated activated sludge (A-AS) versus Rhodococcus erythropolis) and packing material (mixture of compost and wood chips (C + WC) versus expanded perlite) on the removal of a mixture of hydrophobic VOCs (toluene, cyclohexane and hexane) in three biofilters (BFs), i.e., BF1: C + WC and R. erythropolis; BF2: C + WC and A-AS; and BF3: expanded perlite and R. erythropolis. The BFs were operated for 374 days at varying inlet loads (ILs) and empty bed residence times (EBRTs). The results showed that the VOCs were removed in the following order: toluene > cyclohexane > hexane, which corresponds to their air-water partitioning coefficient and thus bioavailability of each VOC. Toluene is the most hydrophilic VOC, while hexane is the most hydrophobic. BF2 outperformed BF1 and BF3 in each operational phase, with average maximum elimination capacities (ECmax) of 21 ± 3 g toluene m[-3] h[-1] (removal efficiency (RE): 100 %; EBRT: 82 s), 11 ± 2 g cyclohexane m[-3] h[-1] (RE: 86 ± 6 %; EBRT: 163 s) and 6.2 ± 0.9 g hexane m[-3] h[-1] (RE: 96 ± 4 %; EBRT: 245 s). Microbial analysis showed that despite having different inocula, the genera Rhodococcus, Mycobacterium and/or Pseudonocardia dominated in all BFs but at different relative abundances. This study provides new insights into the removal of difficult-to-degrade VOC mixtures with limited research to date on biofiltration.}, }
@article {pmid37748072, year = {2023}, author = {Maegele, I and Rupp, S and Özbek, S and Guse, A and Hambleton, EA and Holstein, TW}, title = {A predatory gastrula leads to symbiosis-independent settlement in Aiptasia.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {40}, pages = {e2311872120}, pmid = {37748072}, issn = {1091-6490}, mesh = {Animals ; *Sea Anemones ; Symbiosis ; Gastrula ; *Anthozoa ; *Asteraceae ; *Dinoflagellida ; Larva ; }, abstract = {The planula larvae of the sea anemone Aiptasia have so far not been reported to complete their life cycle by undergoing metamorphosis into adult forms. This has been a major obstacle in their use as a model for coral-dinoflagellate endosymbiosis. Here, we show that Aiptasia larvae actively feed on crustacean nauplii, displaying a preference for live prey. This feeding behavior relies on functional stinging cells, indicative of complex neuronal control. Regular feeding leads to significant size increase, morphological changes, and efficient settlement around 14 d postfertilization. Surprisingly, the presence of dinoflagellate endosymbionts does not affect larval growth or settlement dynamics but is crucial for sexual reproduction. Our findings finally close Aiptasia's life cycle and highlight the functional nature of its larvae, as in Haeckel's Gastrea postulate, yet reveal its active carnivory, thus contributing to our understanding of early metazoan evolution.}, }
@article {pmid37747940, year = {2023}, author = {Murali, R and Yu, H and Speth, DR and Wu, F and Metcalfe, KS and Crémière, A and Laso-Pèrez, R and Malmstrom, RR and Goudeau, D and Woyke, T and Hatzenpichler, R and Chadwick, GL and Connon, SA and Orphan, VJ}, title = {Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea.}, journal = {PLoS biology}, volume = {21}, number = {9}, pages = {e3002292}, pmid = {37747940}, issn = {1545-7885}, mesh = {*Archaea ; Anaerobiosis ; *Sulfates/metabolism ; Geologic Sediments/microbiology ; Bacteria/genetics ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we used comparative metagenomics and phylogenetics to investigate the metabolic adaptation among the 4 main syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a, and Seep-SRB1g) and identified features associated with their syntrophic lifestyle that distinguish them from their non-syntrophic evolutionary neighbors in the phylum Desulfobacterota. We show that the protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved between the syntrophic lineages. In contrast, the proteins involved in electron transfer within the SRB inner membrane differ between clades, indicative of convergent evolution in the adaptation to a syntrophic lifestyle. Our analysis suggests that in most cases, this adaptation likely occurred after the acquisition of the DIET complexes in an ancestral clade and involve horizontal gene transfers within pathways for electron transfer (CbcBA) and biofilm formation (Pel). We also provide evidence for unique adaptations within syntrophic SRB clades, which vary depending on the archaeal partner. Among the most widespread syntrophic SRB, Seep-SRB1a, subclades that specifically partner ANME-2a are missing the cobalamin synthesis pathway, suggestive of nutritional dependency on its partner, while closely related Seep-SRB1a partners of ANME-2c lack nutritional auxotrophies. Our work provides insight into the features associated with DIET-based syntrophy and the adaptation of SRB towards it.}, }
@article {pmid37746209, year = {2022}, author = {Yamaguchi, S and Fujioka, T and Yoshimi, A and Kumagai, T and Umemura, M and Abe, K and Machida, M and Kawai, K}, title = {Discovery of a gene cluster for the biosynthesis of novel cyclic peptide compound, KK-1, in Curvularia clavata.}, journal = {Frontiers in fungal biology}, volume = {3}, number = {}, pages = {1081179}, pmid = {37746209}, issn = {2673-6128}, abstract = {KK-1, a cyclic depsipeptide with 10 residues produced by a filamentous fungus Curvularia clavata BAUA-2787, is a promising pesticide active compound with high activity against many plant pathogens, especially Botrytis cinerea. As a first step toward the future mass production of KK-1 through synthetic biological approaches, we aimed to identify the genes responsible for the KK-1 biosynthesis. To achieve this, we conducted whole genome sequencing and transcriptome analysis of C. clavata BAUA-2787 to predict the KK-1 biosynthetic gene cluster. We then generated the overexpression and deletion mutants for each cluster gene using our originally developed transformation system for this fungus, and analyzed the KK-1 production and the cluster gene expression levels to confirm their involvement in KK-1 biosynthesis. As a result of these, a region of approximately 71 kb was found, containing 10 open reading frames, which were co-induced during KK-1 production, as a biosynthetic gene cluster. These include kk1B, which encodes nonribosomal peptide synthetase with a domain structure that is consistent with the structural features of KK-1, and kk1F, which encodes a transcription factor. The overexpression of kk1F increased the expression of the entire cluster genes and, consequently, improved KK-1 production, whereas its deletion decreased the expression of the entire cluster genes and almost eliminated KK-1 production, demonstrating that the protein encoded by kk1F regulates the expressions of the other nine cluster genes cooperatively as the pathway-specific transcription factor. Furthermore, the deletion of each cluster gene caused a reduction in KK-1 productivity, indicating that each gene is involved in KK-1 production. The genes kk1A, kk1D, kk1H, and kk1I, which showed a significant decrease in KK-1 productivity due to deletion, were presumed to be directly involved in KK-1 structure formation, including the biosynthesis of the constituent residues. kk1C, kk1E, kk1G, and kk1J, which maintained a certain level of KK-1 productivity despite deletion, were possibly involved in promoting or assisting KK-1 production, such as extracellular transportation and the removal of aberrant units incorporated into the peptide chain.}, }
@article {pmid37746167, year = {2022}, author = {Koizumi, A and Miyazawa, K and Ogata, M and Takahashi, Y and Yano, S and Yoshimi, A and Sano, M and Hidaka, M and Nihira, T and Nakai, H and Kimura, S and Iwata, T and Abe, K}, title = {Cleavage of α-1,4-glycosidic linkages by the glycosylphosphatidylinositol-anchored α-amylase AgtA decreases the molecular weight of cell wall α-1,3-glucan in Aspergillus oryzae.}, journal = {Frontiers in fungal biology}, volume = {3}, number = {}, pages = {1061841}, pmid = {37746167}, issn = {2673-6128}, abstract = {Aspergillus fungi contain α-1,3-glucan with a low proportion of α-1,4-glucan as a major cell wall polysaccharide. Glycosylphosphatidylinositol (GPI)-anchored α-amylases are conserved in Aspergillus fungi. The GPI-anchored α-amylase AmyD in Aspergillus nidulans has been reported to directly suppress the biosynthesis of cell wall α-1,3-glucan but not to degrade it in vivo. However, the detailed mechanism of cell wall α-1,3-glucan biosynthesis regulation by AmyD remains unclear. Here we focused on AoAgtA, which is encoded by the Aspergillus oryzae agtA gene, an ortholog of the A. nidulans amyD gene. Similar to findings in A. nidulans, agtA overexpression in A. oryzae grown in submerged culture decreased the amount of cell wall α-1,3-glucan and led to the formation of smaller hyphal pellets in comparison with the wild-type strain. We analyzed the enzymatic properties of recombinant (r)AoAgtA produced in Pichia pastoris and found that it degraded soluble starch, but not linear bacterial α-1,3-glucan. Furthermore, rAoAgtA cleaved 3-α-maltotetraosylglucose with a structure similar to the predicted boundary structure between the α-1,3-glucan main chain and a short spacer composed of α-1,4-linked glucose residues in cell wall α-1,3-glucan. Interestingly, rAoAgtA randomly cleaved only the α-1,4-glycosidic bonds of 3-α-maltotetraosylglucose, indicating that AoAgtA may cleave the spacer in cell wall α-1,3-glucan. Consistent with this hypothesis, heterologous overexpression of agtA in A. nidulans decreased the molecular weight of cell wall α-1,3-glucan. These in vitro and in vivo properties of AoAgtA suggest that GPI-anchored α-amylases can degrade the spacer α-1,4-glycosidic linkages in cell wall α-1,3-glucan before its insolubilization, and this spacer cleavage decreases the molecular weight of cell wall α-1,3-glucan in vivo.}, }
@article {pmid37746119, year = {2023}, author = {Tamano, K and Brown, DW and Yoshimi, A}, title = {Editorial: The use of metabolic engineering techniques to increase the productivity of primary and secondary metabolites within filamentous fungi.}, journal = {Frontiers in fungal biology}, volume = {4}, number = {}, pages = {1178290}, pmid = {37746119}, issn = {2673-6128}, }
@article {pmid37744927, year = {2023}, author = {Frates, ES and Spietz, RL and Silverstein, MR and Girguis, P and Hatzenpichler, R and Marlow, JJ}, title = {Natural and anthropogenic carbon input affect microbial activity in salt marsh sediment.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1235906}, pmid = {37744927}, issn = {1664-302X}, abstract = {Salt marshes are dynamic, highly productive ecosystems positioned at the interface between terrestrial and marine systems. They are exposed to large quantities of both natural and anthropogenic carbon input, and their diverse sediment-hosted microbial communities play key roles in carbon cycling and remineralization. To better understand the effects of natural and anthropogenic carbon on sediment microbial ecology, several sediment cores were collected from Little Sippewissett Salt Marsh (LSSM) on Cape Cod, MA, USA and incubated with either Spartina alterniflora cordgrass or diesel fuel. Resulting shifts in microbial diversity and activity were assessed via bioorthogonal non-canonical amino acid tagging (BONCAT) combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Both Spartina and diesel amendments resulted in initial decreases of microbial diversity as well as clear, community-wide shifts in metabolic activity. Multi-stage degradative frameworks shaped by fermentation were inferred based on anabolically active lineages. In particular, the metabolically versatile Marinifilaceae were prominent under both treatments, as were the sulfate-reducing Desulfovibrionaceae, which may be attributable to their ability to utilize diverse forms of carbon under nutrient limited conditions. By identifying lineages most directly involved in the early stages of carbon processing, we offer potential targets for indicator species to assess ecosystem health and highlight key players for selective promotion of bioremediation or carbon sequestration pathways.}, }
@article {pmid37744490, year = {2023}, author = {Petrin, S and Orsini, M and Massaro, A and Olsen, JE and Barco, L and Losasso, C}, title = {Phenotypic and genotypic antimicrobial resistance correlation and plasmid characterization in Salmonella spp. isolates from Italy reveal high heterogeneity among serovars.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1221351}, pmid = {37744490}, issn = {2296-2565}, mesh = {Animals ; Humans ; Serogroup ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Phenotype ; Salmonella/genetics ; Italy ; Aminoglycosides ; }, abstract = {INTRODUCTION: The spread of antimicrobial resistance among zoonotic pathogens such as Salmonella is a serious health threat, and mobile genetic elements (MGEs) carrying antimicrobial resistance genes favor this phenomenon. In this work, phenotypic antimicrobial resistance to commonly used antimicrobials was studied, and the antimicrobial resistance genes (ARGs) and plasmid replicons associated with the resistances were determined.<br><br>METHODS: Eighty-eight Italian Salmonella enterica strains (n&#x2009;=&#x2009;88), from human, animal and food sources, isolated between 2009 and 2019, were selected to represent serovars with different frequency of isolation in human cases of salmonellosis. The presence of plasmid replicons was also investigated.<br><br>RESULTS AND DISCUSSION: Resistances to sulphonamides (23.9%), ciprofloxacin (27.3%), ampicillin (29.5%), and tetracycline (32.9%) were the most found phenotypes. ARGs identified in the genomes correlated with the phenotypical results, with blaTEM-1B, sul1, sul2, tetA and tetB genes being frequently identified. Point mutations in gyrA and parC genes were also detected, in addition to many different aminoglycoside-modifying genes, which, however, did not cause phenotypic resistance to aminoglycosides. Many genomes presented plasmid replicons, however, only a limited number of ARGs were predicted to be located on the contigs carrying these replicons. As an expectation of this, multiple ARGs were identified on contigs with IncQ1 plasmid replicon in strains belonging to the monophasic variant of Salmonella Typhimurium. In general, high variability in ARGs and plasmid replicons content was observed among isolates, highlighting a high level of heterogeneity in Salmonella enterica. Irrespective of the serovar., many of the ARGs, especially those associated with critically and highly important antimicrobials for human medicine were located together with plasmid replicons, thus favoring their successful dissemination.}, }
@article {pmid37737949, year = {2023}, author = {Li, X and Chen, S and Zhao, L and Zeng, X and Liu, Y and Li, C and Yang, Q}, title = {Effect of lactic acid bacteria by different concentrations of copper based on non-target metabolomic analysis.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {49}, pages = {107568-107579}, pmid = {37737949}, issn = {1614-7499}, mesh = {Animals ; Humans ; *Copper/chemistry ; *Lactobacillales ; Bacteria ; Intestines ; Mammals ; }, abstract = {Copper (Cu) is an essential element for mammals, but excess intake can have detrimental health consequences. However, Cu is no longer present in the "Limit of Contaminants in Foods" promulgated in 2022. The potential impact of different Cu (II) concentrations on human health remains unclear. In this study, a strain of lactic acid bacteria (LAB), namely, Lactiplantibacillus plantarum CICC 23121 (L23121), was selected as a prebiotic indicator strain to indirectly assess the effects of food-limited Cu (II) concentrations (issued by Tolerance limit of copper in foods in 1994) on the functions of intestinal microbes. We used non-target metabolomics, automatic growth curve detector, scanning electron microscopy (SEM), and Fourier transform infrared spectroscopy (FTIR) to investigate the effects of Cu (II) on L23121. The study revealed shows that the 50% minimum inhibitory concentration (MIC50) of Cu (II) for most lactic acid bacteria was 4 mg/L. At low Cu (II) concentrations (≤ 4 mg/L), the pentose phosphate pathway and pyrimidine metabolism of the lactic acid bacteria were affected, resulting in a decrease in the content of beneficial secondary metabolites and a significant decrease in the cell activity. As Cu (II) concentrations increase (≥ 6 mg/L), the key amino acid and lipid metabolisms were affected, leading to the inhibition of growth and primary metabolite production of the bacteria. Under high concentration of Cu (II) (6 mg/L), the surface adhesion of the bacteria was distorted and covered with significantly large particles, and the functional groups of the cells were significantly shifted. As a probiotic, the abundance of lactic acid bacteria in the intestine is significantly reduced, which will inevitably seriously damage intestinal homeostasis. Thus, to protect human intestinal microbes' health, it is recommended to limit the concentration of Cu in food to less than 4 mg/L.}, }
@article {pmid37737839, year = {2023}, author = {Lee, HJ and Whang, KS}, title = {Oryzibacter oryziterrae gen. nov., sp. nov., isolated from rice paddy soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {9}, pages = {}, doi = {10.1099/ijsem.0.006033}, pmid = {37737839}, issn = {1466-5034}, mesh = {*Oryza ; Base Composition ; Fatty Acids/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Soil ; }, abstract = {A novel Gram-stain-negative, aerobic, motile and pleomorphic rod-shaped bacterial strain, designated COJ-58[T], was isolated from rice paddy soil. Strain COJ-58[T] grew optimally at 20-30 °C, at pH 5.0-8.0 and with 0-1.0 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain COJ-58[T] forms a distinct lineage within the family Pleomorphomonadaceae, with highest similarity to Pleomorphomonas carboxyditropha SVCO-16[T] (95.9 %), Pleomorphomonas koreensis Y9[T] (95.8 %), Pleomorphomonas oryzae F-7[T] (95.7 %) and Pleomorphomonas diazotrophica R5-392[T] (95.6 %), respectively. The average nucleotide identity, digital DNA-DNA hybridization, average amino acid identity and percentage of conserved proteins values between the genomes of strain COJ-58[T] and its closely related taxa are ≤77.2 %, ≤21.6 %, ≤68.3 % and ≤61.3 %, respectively. The genome size of strain COJ-58[T] is 4.9 Mb and the genomic DNA G + C content is 63.7 mol%. The major fatty acids are C18 : 1 ω7c, C16 : 0 and summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I). The differential phenotypic and genotypic characteristics of strain COJ-58[T] indicate that it represents a novel genus and species, for which the name Oryzibacter oryziterrae gen. nov., sp. nov. is proposed, with strain COJ-58[T] (=KACC 22108[T]=JCM 34744[T]) as the type strain.}, }
@article {pmid37737625, year = {2023}, author = {Turner, TL and Mitra, SD and Kochan, TJ and Pincus, NB and Lebrun-Corbin, M and Cheung, BH and Gatesy, SW and Afzal, T and Nozick, SH and Ozer, EA and Hauser, AR}, title = {Taxonomic characterization of Pseudomonas hygromyciniae sp. nov., a novel species discovered from a commercially purchased antibiotic.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0183821}, pmid = {37737625}, issn = {2165-0497}, support = {K24 AI104831/AI/NIAID NIH HHS/United States ; R01 AI118257/AI/NIAID NIH HHS/United States ; R21 AI153953/AI/NIAID NIH HHS/United States ; R21 AI164254/AI/NIAID NIH HHS/United States ; }, abstract = {In an attempt to identify novel bacterial species, microbiologists have examined a wide range of environmental niches. We describe the serendipitous discovery of a novel gram-negative bacterial species from a different type of extreme niche: a purchased vial of antibiotic. The vial of antibiotic hygromycin B was found to be factory contaminated with a bacterial species, which we designate Pseudomonas hygromyciniae sp. nov. The proposed novel species belongs to the P. fluorescens complex and is most closely related to P. brenneri, P. proteolytica, and P. fluorescens. The type strain Pseudomonas hygromyciniae sp. nov. strain SDM007[T] (SDM007[T]) harbors a novel 250 kb megaplasmid which confers resistance to hygromycin B and contains numerous other genes predicted to encode replication and conjugation machinery. SDM007[T] grows in hygromycin concentrations of up to 5 mg/mL but does not use the antibiotic as a carbon or nitrogen source. While unable to grow at 37°C ruling out its ability to infect humans, it grows and survives at temperatures between 4 and 30°C. SDM007[T] can infect plants, as demonstrated by the lettuce leaf model, and is highly virulent in the Galleria mellonella infection model but is unable to infect mammalian A549 cells. These findings indicate that commercially manufactured antibiotics represent another extreme environment that may support the growth of novel bacterial species. IMPORTANCE Physical and biological stresses in extreme environments may select for bacteria not found in conventional environments providing researchers with the opportunity to not only discover novel species but to uncover new enzymes, biomolecules, and biochemical pathways. This strategy has been successful in harsh niches such as hot springs, deep ocean trenches, and hypersaline brine pools. Bacteria belonging to the Pseudomonas species are often found to survive in these unusual environments, making them relevant to healthcare, food, and manufacturing industries. Their ability to survive in a variety of environments is mainly due to the high genotypic and phenotypic diversity displayed by this genus. In this study, we discovered a novel Pseudomonas sp. from a desiccated environment of a sealed antibiotic bottle that was considered sterile. A close genetic relationship with its phylogenetic neighbors reiterated the need to use not just DNA-based tools but also biochemical characteristics to accurately classify this organism.}, }
@article {pmid37737001, year = {2023}, author = {Bernadus, JBB and Pelealu, J and Kandou, GD and Pinaria, AG and Mamahit, JME and Tallei, TE}, title = {Metagenomic Insight into the Microbiome and Virome Associated with Aedes aegypti Mosquitoes in Manado (North Sulawesi, Indonesia).}, journal = {Infectious disease reports}, volume = {15}, number = {5}, pages = {549-563}, pmid = {37737001}, issn = {2036-7430}, abstract = {The aim of this study was to investigate the microbial diversity encompassing bacteria, fungi, and viruses within the composite microbial community associated with Aedes aegypti mosquitoes in Manado, Indonesia, using a whole-genome shotgun metagenomics approach. Female mosquitoes were collected and grouped into pools of 50 individuals, from which genomic DNA (gDNA) and RNA were extracted separately. Whole-genome shotgun metagenomics were performed on gDNA samples. The bioinformatics analysis encompassed quality assessment, taxonomic classification, and visualization. The evaluation of the microbial community entailed an assessment of taxa abundance and diversity using Kraken version 2.1.2. The study delineated the prevalence of dominant bacterial phyla, including Proteobacteria, with varying abundance of Firmicutes, Bacteroidota, and Actinobacteria, and notable occurrence of Tenericutes. Furthermore, the presence of the fungal phylum Ascomycota was also detected. Among the identified barcodes, Barcode04 emerged as the most abundant and diverse, while Barcode06 exhibited greater evenness. Barcode03, 05, and 07 displayed moderate richness and diversity. Through an analysis of the relative abundance, a spectrum of viruses within Ae. aegypti populations was unveiled, with Negarnaviricota constituting the most prevalent phylum, followed by Nucleocytoviricota, Uroviricota, Artverviricota, Kitrinoviricota, Peploviricota, Phixviricota, and Cossaviricota. The presence of Negarnaviricota viruses raises pertinent public health concerns. The presence of other viral phyla underscores the intricate nature of virus-mosquito interactions. The analysis of viral diversity provides valuable insights into the range of viruses carried by Ae. aegypti. The community exhibits low biodiversity, with a few dominant species significantly influencing its composition. This has implications for healthcare and ecological management, potentially simplifying control measures but also posing risks if the dominant species are harmful. This study enriches our comprehension of the microbiome and virome associated with Ae. aegypti mosquitoes, emphasizing the importance of further research to fully comprehend their ecological significance and impact on public health. The findings shed light on the microbial ecology of Ae. aegypti, offering potential insights into mosquito biology, disease transmission, and strategies for vector control. Future studies should endeavor to establish specific associations with Ae. aegypti, elucidate the functional roles of the identified microbial and viral species, and investigate their ecological implications.}, }
@article {pmid37725513, year = {2023}, author = {Yang, J and Bowring, JZ and Krusche, J and Lehmann, E and Bejder, BS and Silva, SF and Bojer, MS and Grunert, T and Peschel, A and Ingmer, H}, title = {Cross-species communication via agr controls phage susceptibility in Staphylococcus aureus.}, journal = {Cell reports}, volume = {42}, number = {9}, pages = {113154}, doi = {10.1016/j.celrep.2023.113154}, pmid = {37725513}, issn = {2211-1247}, mesh = {Humans ; Staphylococcus aureus/metabolism ; *Bacteriophages/metabolism ; Staphylococcus/metabolism ; Glycosyltransferases/metabolism ; *Staphylococcal Infections ; Bacterial Proteins/metabolism ; Quorum Sensing ; }, abstract = {Bacteria use quorum sensing (QS) to coordinate group behavior in response to cell density, and some bacterial viruses (phages) also respond to QS. In Staphylococcus aureus, the agr-encoded QS system relies on accumulation of auto-inducing cyclic peptides (AIPs). Other staphylococci also produce AIPs of which many inhibit S. aureus agr. We show that agr induction reduces expression of tarM, encoding a glycosyltransferase responsible for α-N-acetylglucosamine modification of the major S. aureus phage receptor, the wall teichoic acids. This allows lytic phage Stab20 and related phages to infect and kill S. aureus. However, in mixed communities, producers of inhibitory AIPs like S. haemolyticus, S. caprae, and S. pseudintermedius inhibit S. aureus agr, thereby impeding phage infection. Our results demonstrate that cross-species interactions dramatically impact phage susceptibility. These interactions likely influence microbial ecology and impact the efficacy of phages in medical and biotechnological applications such as phage therapy.}, }
@article {pmid37725094, year = {2023}, author = {Rossetto Marcelino, V}, title = {The value of connections.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {37725094}, issn = {2050-084X}, mesh = {*Gastrointestinal Microbiome ; }, abstract = {High proportions of gut bacteria that produce their own food can be an indicator for poor gut health.}, }
@article {pmid37724869, year = {2023}, author = {Leroux, N and Sylvain, FE and Holland, A and Luis Val, A and Derome, N}, title = {Gut microbiota of an Amazonian fish in a heterogeneous riverscape: integrating genotype, environment, and parasitic infections.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0275522}, pmid = {37724869}, issn = {2165-0497}, abstract = {A number of key factors can structure the gut microbiota of fish such as environment, diet, health state, and genotype. Mesonauta festivus, an Amazonian cichlid, is a relevant model organism to study the relative contribution of these factors on the community structure of fish gut microbiota. M. festivus has well-studied genetic populations and thrives in rivers with drastically divergent physicochemical characteristics. Here, we collected 167 fish from 12 study sites and used 16S and 18S rRNA metabarcoding approaches to characterize the gut microbiome structure of M. festivus. These data sets were analyzed in light of the host fish genotypes (genotyping-by-sequencing) and an extensive characterization of environmental physico-chemical parameters. We explored the relative contribution of environmental dissimilarity, the presence of parasitic taxa, and phylogenetic relatedness on structuring the gut microbiota. We documented occurrences of Nyctotherus sp. infecting a fish and linked its presence to a dysbiosis of the host gut microbiota. Moreover, we detected the presence of helminths which had a minor impact on the gut microbiota of their host. In addition, our results support a higher impact of the phylogenetic relatedness between fish rather than environmental similarity between sites of study on structuring the gut microbiota for this Amazonian cichlid. Our study in a heterogeneous riverscape integrates a wide range of factors known to structure fish gut microbiomes. It significantly improves understanding of the complex relationship between fish, their parasites, their microbiota, and the environment. IMPORTANCE The gut microbiota is known to play important roles in its host immunity, metabolism, and comportment. Its taxonomic composition is modulated by a complex interplay of factors that are hard to study simultaneously in natural systems. Mesonauta festivus, an Amazonian cichlid, is an interesting model to simultaneously study the influence of multiple variables on the gut microbiota. In this study, we explored the relative contribution of the environmental conditions, the presence of parasitic infections, and the genotype of the host on structuring the gut microbiota of M. festivus in Amazonia. Our results highlighted infections by a parasitic ciliate that caused a disruption of the gut microbiota and by parasitic worms that had a low impact on the microbiota. Finally, our results support a higher impact of the genotype than the environment on structuring the microbiota for this fish. These findings significantly improve understanding of the complex relationship among fish, their parasites, their microbiota, and the environment.}, }
@article {pmid37724866, year = {2023}, author = {van der Loos, LM and De Coninck, L and Zell, R and Lequime, S and Willems, A and De Clerck, O and Matthijnssens, J}, title = {Highly divergent CRESS DNA and picorna-like viruses associated with bleached thalli of the green seaweed Ulva.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0025523}, pmid = {37724866}, issn = {2165-0497}, abstract = {Marine macroalgae (seaweeds) are important primary producers and foundation species in coastal ecosystems around the world. Seaweeds currently contribute to an estimated 51% of the global mariculture production, with a long-term growth rate of 6% per year, and an estimated market value of more than US$11.3 billion. Viral infections could have a substantial impact on the ecology and aquaculture of seaweeds, but surprisingly little is known about virus diversity in macroalgal hosts. Using metagenomic sequencing, we characterized viral communities associated with healthy and bleached specimens of the commercially important green seaweed Ulva. We identified 20 putative new and divergent viruses, of which the majority belonged to the Circular Rep-Encoding Single-Stranded (CRESS) DNA viruses [single-stranded (ss)DNA genomes], Durnavirales [double-stranded (ds)RNA], and Picornavirales (ssRNA). Other newly identified RNA viruses were related to the Ghabrivirales, the Mitoviridae, and the Tombusviridae. Bleached Ulva samples contained particularly high viral read numbers. While reads matching assembled CRESS DNA viruses and picorna-like viruses were nearly absent from the healthy Ulva samples (confirmed by qPCR), they were very abundant in the bleached specimens. Therefore, bleaching in Ulva could be caused by one or a combination of the identified viruses but may also be the result of another causative agent or abiotic stress, with the viruses simply proliferating in already unhealthy seaweed tissue. This study highlights how little we know about the diversity and ecology of seaweed viruses, especially in relation to the health and diseases of the algal host, and emphasizes the need to better characterize the algal virosphere. IMPORTANCE Green seaweeds of the genus Ulva are considered a model system to study microbial interactions with the algal host. Remarkably little is known, however, about viral communities associated with green seaweeds, especially in relation to the health of the host. In this study, we characterized the viral communities associated with healthy and bleached Ulva. Our findings revealed the presence of 20 putative novel viruses associated with Ulva, encompassing both DNA and RNA viruses. The majority of these viruses were found to be especially abundant in bleached Ulva specimens. This is the first step toward understanding the role of viruses in the ecology and aquaculture of this green seaweed.}, }
@article {pmid37723328, year = {2023}, author = {Sasi, R and Suchithra, TV}, title = {Wastewater microbial diversity versus molecular analysis at a glance: a mini-review.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {54}, number = {4}, pages = {3033-3039}, pmid = {37723328}, issn = {1678-4405}, mesh = {*Wastewater ; Phylogeny ; *Microbiota ; Genomics ; Nitrogen/metabolism ; Phosphorus/metabolism ; Bioreactors/microbiology ; Sewage/microbiology ; }, abstract = {Microorganisms play a vital role in biological wastewater treatment by converting organic and toxic materials into harmless substances. Understanding microbial communities' structure, taxonomy, phylogeny, and metabolic activities is essential to improve these processes. Molecular microbial ecology employs molecular techniques to study community profiles and phylogenetic information since culture-dependent approaches have limitations in providing a comprehensive understanding of microbial diversity in a system. Genomic advancements such as DNA hybridization, microarray analysis, sequencing, and reverse sample genome probing have enabled the detailed characterization of microbial communities in wastewater treatment facilities. This mini-review summarizes the current state of knowledge on the diversity of microorganisms in wastewater treatment plants, emphasizing critical microbial processes such as nitrogen and phosphorus removal.}, }
@article {pmid37723166, year = {2023}, author = {Ye, H and Borusak, S and Eberl, C and Krasenbrink, J and Weiss, AS and Chen, SC and Hanson, BT and Hausmann, B and Herbold, CW and Pristner, M and Zwirzitz, B and Warth, B and Pjevac, P and Schleheck, D and Stecher, B and Loy, A}, title = {Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5533}, pmid = {37723166}, issn = {2041-1723}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; I 2320/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Humans ; Animals ; Mice ; *Affect ; Bile Acids and Salts ; *Salmonella enterica ; Taurine ; Sulfur ; }, abstract = {Taurine-respiring gut bacteria produce H2S with ambivalent impact on host health. We report the isolation and ecophysiological characterization of a taurine-respiring mouse gut bacterium. Taurinivorans muris strain LT0009 represents a new widespread species that differs from the human gut sulfidogen Bilophila wadsworthia in its sulfur metabolism pathways and host distribution. T. muris specializes in taurine respiration in vivo, seemingly unaffected by mouse diet and genotype, but is dependent on other bacteria for release of taurine from bile acids. Colonization of T. muris in gnotobiotic mice increased deconjugation of taurine-conjugated bile acids and transcriptional activity of a sulfur metabolism gene-encoding prophage in other commensals, and slightly decreased the abundance of Salmonella enterica, which showed reduced expression of galactonate catabolism genes. Re-analysis of metagenome data from a previous study further suggested that T. muris can contribute to protection against pathogens by the commensal mouse gut microbiota. Together, we show the realized physiological niche of a key murine gut sulfidogen and its interactions with selected gut microbiota members.}, }
@article {pmid37722685, year = {2023}, author = {Jacobovitz, MR and Hambleton, EA and Guse, A}, title = {Unlocking the Complex Cell Biology of Coral-Dinoflagellate Symbiosis: A Model Systems Approach.}, journal = {Annual review of genetics}, volume = {57}, number = {}, pages = {411-434}, doi = {10.1146/annurev-genet-072320-125436}, pmid = {37722685}, issn = {1545-2948}, support = {/ERC_/European Research Council/International ; }, mesh = {Animals ; *Anthozoa/genetics ; Symbiosis/genetics ; Ecosystem ; *Dinoflagellida/genetics ; Systems Analysis ; }, abstract = {Symbiotic interactions occur in all domains of life, providing organisms with resources to adapt to new habitats. A prime example is the endosymbiosis between corals and photosynthetic dinoflagellates. Eukaryotic dinoflagellate symbionts reside inside coral cells and transfer essential nutrients to their hosts, driving the productivity of the most biodiverse marine ecosystem. Recent advances in molecular and genomic characterization have revealed symbiosis-specific genes and mechanisms shared among symbiotic cnidarians. In this review, we focus on the cellular and molecular processes that underpin the interaction between symbiont and host. We discuss symbiont acquisition via phagocytosis, modulation of host innate immunity, symbiont integration into host cell metabolism, and nutrient exchange as a fundamental aspect of stable symbiotic associations. We emphasize the importance of using model systems to dissect the cellular complexity of endosymbiosis, which ultimately serves as the basis for understanding its ecology and capacity to adapt in the face of climate change.}, }
@article {pmid37719127, year = {2023}, author = {Castañeda-Molina, Y and Marulanda-Moreno, SM and Saldamando-Benjumea, C and Junca, H and Moreno-Herrera, CX and Cadavid-Restrepo, G}, title = {Microbiome analysis of Spodoptera frugiperda (Lepidoptera, Noctuidae) larvae exposed to Bacillus thuringiensis (Bt) endotoxins.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15916}, pmid = {37719127}, issn = {2167-8359}, mesh = {Animals ; Spodoptera ; Larva ; *Bacillus thuringiensis/genetics ; Endotoxins ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Anti-Bacterial Agents ; }, abstract = {BACKGROUND: Spodoptera frugiperda (or fall armyworm, FAW) is a polyphagous pest native to Western Hemisphere and recently discovered in the Eastern Hemisphere. In Colombia, S. frugiperda is recognized as a pest of economic importance in corn. The species has genetically differentiated into two host populations named "corn" and "rice" strains. In 2012, a study made in central Colombia demonstrated that the corn strain is less susceptible to Bacillus thuringiensis (Bt) endotoxins (Cry1Ac and Cry 1Ab) than the rice strain. In this country, Bt transgenic corn has been extensively produced over the last 15 years. Since gut microbiota plays a role in the physiology and immunity of insects, and has been implicated in promoting the insecticidal activity of Bt, in this study an analysis of the interaction between Bt endotoxins and FAW gut microbiota was made. Also, the detection of endosymbionts was performed here, as they might have important implications in the biological control of a pest.<br><br>METHODS: The composition and diversity of microbiomes associated with larval specimens of S. frugiperda(corn strain) was investigated in a bioassay based on six treatments in the presence/absence of Bt toxins and antibiotics (Ab) through bacterial isolate analyses and by high throughput sequencing of the bacterial 16S rRNA gene. Additionally, species specific primers were used, to detect endosymbionts from gonads in S. frugiperda corn strain.<br><br>RESULTS: Firmicutes, Proteobacteria and Bacteroidota were the most dominant bacterial phyla found in S. frugiperda corn strain. No significant differences in bacteria species diversity and richness among the six treatments were found. Two species of Enterococcus spp., E. mundtii and E. casseliflavus were detected in treatments with Bt and antibiotics, suggesting that they are less susceptible to both of them. Additionally, the endosymbiont Arsenophonus was also identified on treatments in presence of Bt and antibiotics. The results obtained here are important since little knowledge exists about the gut microbiota on this pest and its interaction with Bt endotoxins. Previous studies made in Lepidoptera suggest that alteration of gut microbiota can be used to improve the management of pest populations, demonstrating the relevance of the results obtained in this work.}, }
@article {pmid37717747, year = {2023}, author = {Farrell, ML and Chueiri, A and Maguire, M and Kovářová, A and Miliotis, G and O'Connor, L and McDonagh, F and Duane, S and Cormican, M and Devane, G and Tuohy, A and DeLappe, N and De Bock, F and Burke, LP and Morris, D}, title = {Longitudinal carriage of antimicrobial resistant Enterobacterales in healthy individuals in Ireland - Assessing the impact of recreational water use on duration of carriage.}, journal = {The Science of the total environment}, volume = {905}, number = {}, pages = {167100}, doi = {10.1016/j.scitotenv.2023.167100}, pmid = {37717747}, issn = {1879-1026}, mesh = {Humans ; *Escherichia coli/genetics ; Enterobacteriaceae/genetics ; Ireland/epidemiology ; beta-Lactamases/genetics ; Feces ; *Anti-Infective Agents ; Anti-Bacterial Agents ; }, abstract = {The increasing prevalence of extended-spectrum beta-lactamase (ESBL) producing Enterobacterales (ESBL-PE) and carbapenemase-producing Enterobacterales (CPE) is a major public health concern worldwide. Despite the associated risk of infection from gut colonisation with a resistant Enterobacterales, the incidence and duration of carriage in healthy individuals is poorly studied. This "persistence study" is the first in Ireland to assess the longitudinal carriage of ESBL-PE and CPE in healthy individuals. A cohort of 45 participants, 22 of whom were colonised with ESBL-PE, was recruited from a recently completed point prevalence study that investigated colonisation in recreational water users (WU) versus controls. Six bi-monthly faecal samples per participant were analysed for CPE and ESBL-PE over one year and the relationship between persistent colonisation and exposure to natural waters was investigated. For 11 of 45 participants (24.4 %) ESBL-E. coli (ESBL-EC) was detected in at least one sample. Genomic analysis revealed that six participants harboured the same ESBL-EC strains as identified in the preceding study. ESBL-EC persisted in the gut for a median duration of 10.3 months (range 4-23 months), consistent with previous research. Five participants (11.1 %) carried ESBL-EC for the entire study year. The carbapenemase gene blaIMI-2 was detected once. Colonisation was higher in water users during the non-bathing season (n = 10, November 2021-April 2022), than during the bathing season (n = 5, May 2022-September 2022) [relative risk 1.99 (95 % CI 0.34-11.71)]. However, overall WU were less likely to be colonised with ESBL-EC than controls (19 % vs 25 % respectively, RR 0.76, CI 0.24-2.34). Further research is warranted to better understand the factors influencing the persistence of gut colonisation with ESBL-EC and CPE and to what extent bathing water quality impacts colonisation for those regularly exposed.}, }
@article {pmid37717325, year = {2023}, author = {Sandeep, R and Muscolino, JF and Macêdo, WV and Piculell, M and Christensson, M and Poulsen, JS and Nielsen, JL and Vergeynst, L}, title = {Effect of biofilm thickness on the activity and community composition of phosphorus accumulating bacteria in a moving bed biofilm reactor.}, journal = {Water research}, volume = {245}, number = {}, pages = {120599}, doi = {10.1016/j.watres.2023.120599}, pmid = {37717325}, issn = {1879-2448}, abstract = {Can biofilms enhance the rates of phosphorus removal in wastewater treatment? In order to narrow the scientific gap on the effect of biofilm thickness on the activity and microbial community of phosphorus-accumulating bacteria, this study investigated biofilms of 30 to 1000 µm thickness in a moving bed biofilm reactor. Measurements on 5 different biofilm carriers showed that biomass-specific phosphorus release and uptake rates increased as a function of biofilm thickness for biofilms thinner than about 110 µm but were lower for thicker biofilms of about 550-1000 µm. The reduced phosphorus uptake and release rates in the thickest biofilms can result from substrate mass transfer limitations whereas the low activity in the thinnest biofilms can be related to a too high turnover rate in the biofilm due to heterotrophic growth. Additionally, the microbial ecology of the different biofilms confirms the observed phosphorus uptake and release rates. The results from the full-length 16S rRNA gene sequencing of the bacterial community showed that the thicker biofilms were characterized by higher relative abundance (40-58%) of potential phosphorus accumulating genera Zoogloea, Acinetobacter, Dechloromonas and Ca. Accumulibacter. In contrast, the thinner biofilms were dominated by the genus Ferribacterium (34-60%), which might be competing with phosphorus-accumulating bacteria as indicated by the relatively high acetate uptake rates in the thinner biofilms. It is concluded that there is an optimal biofilm thickness of 100-500 µm, at which the phosphorus accumulating bacteria have the highest activity.}, }
@article {pmid37715042, year = {2023}, author = {Candry, P and Chadwick, GL and Caravajal-Arroyo, JM and Lacoere, T and Winkler, MH and Ganigué, R and Orphan, VJ and Rabaey, K}, title = {Trophic interactions shape the spatial organization of medium-chain carboxylic acid producing granular biofilm communities.}, journal = {The ISME journal}, volume = {17}, number = {11}, pages = {2014-2022}, pmid = {37715042}, issn = {1751-7370}, mesh = {*Carboxylic Acids ; *Biofilms ; Bacteria ; Lactic Acid ; Sugars ; }, abstract = {Granular biofilms producing medium-chain carboxylic acids (MCCA) from carbohydrate-rich industrial feedstocks harbor highly streamlined communities converting sugars to MCCA either directly or via lactic acid as intermediate. We investigated the spatial organization and growth activity patterns of MCCA producing granular biofilms grown on an industrial side stream to test (i) whether key functional guilds (lactic acid producing Olsenella and MCCA producing Oscillospiraceae) stratified in the biofilm based on substrate usage, and (ii) whether spatial patterns of growth activity shaped the unique, lenticular morphology of these biofilms. First, three novel isolates (one Olsenella and two Oscillospiraceae species) representing over half of the granular biofilm community were obtained and used to develop FISH probes, revealing that key functional guilds were not stratified. Instead, the outer 150-500 µm of the granular biofilm consisted of a well-mixed community of Olsenella and Oscillospiraceae, while deeper layers were made up of other bacteria with lower activities. Second, nanoSIMS analysis of [15]N incorporation in biofilms grown in normal and lactic acid amended conditions suggested Oscillospiraceae switched from sugars to lactic acid as substrate. This suggests competitive-cooperative interactions may govern the spatial organization of these biofilms, and suggests that optimizing biofilm size may be a suitable process engineering strategy. Third, growth activities were similar in the polar and equatorial biofilm peripheries, leaving the mechanism behind the lenticular biofilm morphology unexplained. Physical processes (e.g., shear hydrodynamics, biofilm life cycles) may have contributed to lenticular biofilm development. Together, this study develops an ecological framework of MCCA-producing granular biofilms that informs bioprocess development.}, }
@article {pmid37713796, year = {2023}, author = {Cai, X and Hu, Y and Zhou, S and Meng, D and Xia, S and Wang, H}, title = {Unraveling bacterial and eukaryotic communities in secondary water supply systems: Dynamics, assembly, and health implications.}, journal = {Water research}, volume = {245}, number = {}, pages = {120597}, doi = {10.1016/j.watres.2023.120597}, pmid = {37713796}, issn = {1879-2448}, mesh = {Water ; Eukaryota ; Bacteria ; Water Supply ; *Amoeba ; *Microbiota ; }, abstract = {Secondary water supply systems (SWSSs) are crucial water supply infrastructures for high-rise buildings in metropolitan cities. In recent years, they have garnered public attention due to increased microbial risks. However, our understanding of SWSS microbial ecology, particularly concerning the composition of eukaryotes and the underlying mechanisms driving microbial dynamics and assembly in SWSSs, remains elusive. Herein, we conducted a comprehensive investigation on both eukaryotes and bacteria along the water transportation pathway and across various microbial habitats (water, biofilm, and sediment) in SWSSs. Sequencing results revealed that eukaryotes within SWSSs predominantly consist of protists (average abundance: 31.23%) and metazoans (20.91%), while amoebae accounted for 4.71% of the total. During water transportation from the distribution mains to taps, both bacterial and eukaryotic communities exhibited significant community shifts, and higher degrees of variation were observed for eukaryotic community among different locations within SWSSs. The normalized stochasticity ratio (NST) analysis demonstrated that bacterial community assembly was governed by stochastic processes, while eukaryotic community assembly was primarily shaped by deterministic processes. Within SWSS tanks, bacterial communities significantly varied across water, biofilm, and sediment, whereas eukaryotic communities showed minor differences among these habitats. The co-occurrence networks analysis revealed that tank biofilm and sediment harbored more eukaryote-bacterium linkages than water, suggesting biofilm and sediment might be hotspots for inter-kingdom interactions. We also applied FEAST analysis to track the source of tap water microbiota, results of which showed that household-tap bacteria mainly originated from tank water. In contrast, tank biofilm was identified as the primary microbial source to eukaryotes in household tap water. Additionally, engineering factors such as tank materials significantly affected amoeba community, and the SWSS configuration was found to influence Legionella and Mycobacterium abundances in SWSSs. Overall, results of our study shed light on the microbial ecology in SWSS and provide insights into SWSS management and health risk control.}, }
@article {pmid37712979, year = {2023}, author = {Li, Y and Yang, H and Su, Y and Gong, X and Yao, B and Cheng, L}, title = {Phosphorus Coupled with High Nitrogen Addition Exerts a Great Influence on Soil Bacterial Community in a Semiarid Grassland.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2993-3002}, pmid = {37712979}, issn = {1432-184X}, mesh = {*Ecosystem ; *Soil/chemistry ; Grassland ; Nitrogen/chemistry ; Phosphorus ; Bacteria/genetics ; Soil Microbiology ; China ; }, abstract = {Nitrogen (N) and phosphorus (P) addition, either individually or in combination, has been demonstrated to enhance plant productivity in grassland ecosystems. Soil bacterial community, which is the driver of litter decomposition and nutrient cycling, is assumed to control responses of terrestrial ecosystem structure and function to N and P addition. Using a high-throughput Illumina MiSeq sequencing platform, we conducted a 9-year field experiment of N (0, 5, 10, and 20 g N m[-2] yr[-1]) and P (0 and 10 g P m[-2] yr[-1]) additions in the Inner Mongolian steppes to elucidate long-term effects of N and P addition on soil bacterial richness, diversity and composition. We found that N addition reduced the relative abundance of Acidobacteria, Chloroflexi, and Nitrospirae, while increased that of Bacteroides. The results showed that the bacterial biomarker was enriched in P addition treatments, either individually or combined with N addition. Both N and P addition altered the bacterial community structure, while only N addition greatly decreased bacterial richness and diversity. More importantly, we showed that all of these effects were most significant in N3P treatment (20 g N m[-2] yr[-1] and 10 g P m[-2] yr[-1]), implying that P coupled with a high-level N addition exerted a great influence on soil bacterial community. Structural equation models revealed that N and P addition had a great direct effect on soil bacterial community and an indirect effect on it mainly by changing the litter biomass. Our findings highlighted that severe niche differentiation was induced by P along with a high-level N, further emphasizing the importance of simultaneously evaluating response of soil bacterial community to N and P addition, especially in the context of increasing anthropogenic nutrient additions.}, }
@article {pmid37711620, year = {2023}, author = {Rosel-Pech, C and Pinto-Cardoso, S and Chávez-Torres, M and Montufar, N and Osuna-Padilla, I and Ávila-Ríos, S and Reyes-Terán, G and Aguirre-Alvarado, C and Matías Juan, NA and Pérez-Lorenzana, H and Vázquez-Rosales, JG and Bekker-Méndez, VC}, title = {Distinct fecal microbial signatures are linked to sex and chronic immune activation in pediatric HIV infection.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1244473}, pmid = {37711620}, issn = {1664-3224}, mesh = {Adult ; Child ; Humans ; Female ; Male ; *HIV Infections ; RNA, Ribosomal, 16S/genetics ; *Aging, Premature ; Anti-Bacterial Agents ; Disease Progression ; }, abstract = {INTRODUCTION: Our understanding of HIV-associated gut microbial dysbiosis in children perinatally-infected with HIV (CLWH) lags behind that of adults living with HIV. Childhood represents a critical window for the gut microbiota. Any disturbances, including prolonged exposure to HIV, antiretroviral drugs, and antibiotics are likely to have a significant impact on long-term health, resulting in a less resilient gut microbiome. The objective of our study was to characterize the gut microbiota in CLWH, and compare it with HIV-unexposed and -uninfected children.<br><br>METHODS: We enrolled 31 children aged 3 to 15 years; 15 were CLWH and 16 were HUU. We assessed dietary patterns and quality; quantified soluble and cellular markers of HIV disease progression by flow cytometry, enzyme-linked immunosorbent and multiplex-bead assays, and profiled the gut microbiota by 16S rRNA sequencing. We explored relationships between the gut microbiota, antibiotic exposure, dietary habits, soluble and cellular markers and host metadata.<br><br>RESULTS: Children had a Western-type diet, their median health eating index score was 67.06 (interquartile range 58.76-74.66). We found no discernable impact of HIV on the gut microbiota. Alpha diversity metrics did not differ between CLWH and HUU. Sex impacted the gut microbiota (R-squared= 0.052, PERMANOVA p=0.024). Male children had higher microbial richness compared with female children. Two taxa were found to discriminate female from male children independently from HIV status: Firmicutes for males, and Bacteroides for females. Markers of HIV disease progression were comparable between CLWH and HUU, except for the frequency of exhausted CD4+ T cells (PD-1+) which was increased in CLWH (p=0.0024 after adjusting for confounders). Both the frequency of exhausted CD4+ and activated CD4+ T cells (CD38+ HLADR+) correlated positively with the relative abundance of Proteobacteria (rho=0.568. false discovery rate (FDR)-adjusted p= 0.029, and rho=0.62, FDR-adjusted p=0.0126, respectively).<br><br>CONCLUSION: The gut microbiota of CLWH appears similar to that of HUU, and most markers of HIV disease progression are normalized with long-term ART, suggesting a beneficial effect of the latter on the gut microbial ecology. The relationship between exhausted and activated CD4+ T cells and Proteobacteria suggests a connection between the gut microbiome, and premature aging in CLWH.}, }
@article {pmid37711139, year = {2023}, author = {Vijay, S and Nair, RR and Sharan, D and Jakkala, K and Ajitkumar, P}, title = {Percoll discontinuous density gradient centrifugation method for the fractionation of the subpopulations of Mycobacterium smegmatis and Mycobacterium tuberculosis from in vitro cultures.}, journal = {MethodsX}, volume = {11}, number = {}, pages = {102344}, pmid = {37711139}, issn = {2215-0161}, abstract = {Bacterial populations in the in vitro laboratory cultures, environment, and patients contain metabolically different subpopulations that respond differently to stress agents, including antibiotics, and emerge as stress tolerant or resistant strains. To contain the emergence of such strains, it is important to study the features of the metabolic status and response of the subpopulations to stress agents. For this purpose, an efficient method is required for the fractionation and isolation of the subpopulations from the cultures. Here we describe in detail the manual setting up of a simple, easy-to-do, reproducibly robust Percoll discontinuous density gradient centrifugation for the fractionation of subpopulations of short-sized cells (SCs) and normal/long-sized cells (NCs) from Mycobacterium smegmatis and Mycobacterium tuberculosis cultures, which we had reported earlier. About 90-98% enrichment was obtained respectively for SCs and NCs for M. smegmatis and 69-67% enrichment was obtained respectively for the SCs and NCs for M. tuberculosis.•The Percoll discontinuous density gradient centrifugation helps the fractionation and isolation of mycobacterial subpopulations that differ in density.•The method offers a consistently reproducible high enrichment of the subpopulations of SCs and NCs from the in vitro cultures of M. smegmatis and M. tuberculosis.•Our earlier reports on the consistency in the differential response of the subpopulations, enriched using the method, to oxidative, nitrite, and antibiotic stress proves its validity.}, }
@article {pmid37708771, year = {2023}, author = {Sentenac, H and Loyau, A and Zoccarato, L and Jassey, VEJ and Grossart, HP and Schmeller, DS}, title = {Biofilm community composition is changing in remote mountain lakes with a relative increase in potentially toxigenic algae.}, journal = {Water research}, volume = {245}, number = {}, pages = {120547}, doi = {10.1016/j.watres.2023.120547}, pmid = {37708771}, issn = {1879-2448}, abstract = {Mountain lakes provide clear drinking water to humankind but are strongly impacted by global change. Benthic biofilms are crucial for maintaining water quality in these oligotrophic lakes, yet little is known about the effects of global change on mountain biofilm communities. By combining analyses of metabarcoding data on 16S and 18S rRNA genes with climatic and environmental data, we investigated global change effects on the composition of biofilm prokaryotic and micro-eukaryotic assemblages in a five-year monitoring program of 26 Pyrenean lakes (2016-2020). Using time-decay relationships and within-lake dissimilarity modelling, we show that the composition of both prokaryotic and micro-eukaryotic biofilm communities significantly shifted and their biodiversity declined from 2016 to 2020. In particular, analyses of temporal trends with linear mixed models indicated an increase in the richness and relative abundance of cyanobacteria, including potentially toxigenic cyanobacteria, and a concomitant decrease in diatom richness and relative abundance. While these compositional shifts may be due to several drivers of global change acting simultaneously on mountain lake biota, water pH and hardness were, from our data, the main environmental variables associated with changes for both prokaryotic and micro-eukaryotic assemblages. Water pH and hardness increased in our lakes over the study period, and are known to increase in Pyrenean lakes due to the intensification of rock weathering as a result of climate change. Given predicted climate trends and if water pH and hardness do cause some changes in benthic biofilms, those changes might be further exacerbated in the future. Such biofilm compositional shifts may induce cascading effects in mountain food webs, threatening the resilience of the entire lake ecosystem. The rise in potentially toxigenic cyanobacteria also increases intoxication risks for humans, pets, wild animals, and livestock that use mountain lakes. Therefore, our study has implications for water quality, ecosystem health, public health, as well as local economies (pastoralism, tourism), and highlights the possible impacts of global change on mountain lakes.}, }
@article {pmid37708391, year = {2023}, author = {Ionescu, D and Volland, JM and Contarini, PE and Gros, O}, title = {Genomic Mysteries of Giant Bacteria: Insights and Implications.}, journal = {Genome biology and evolution}, volume = {15}, number = {9}, pages = {}, pmid = {37708391}, issn = {1759-6653}, mesh = {*Genomics ; Bacteria/genetics ; Archaea/genetics ; Biological Evolution ; }, abstract = {Bacteria and Archaea are traditionally regarded as organisms with a simple morphology constrained to a size of 2-3 µm. Nevertheless, the history of microbial research is rich in the description of giant bacteria exceeding tens and even hundreds of micrometers in length or diameter already from its early days, for example, Beggiatoa spp., to the present, for example, Candidatus Thiomargarita magnifica. While some of these giants are still being studied, some were lost to science, with merely drawings and photomicrographs as evidence for their existence. The physiology and biogeochemical role of giant bacteria have been studied, with a large focus on those involved in the sulfur cycle. With the onset of the genomic era, no special emphasis has been given to this group, in an attempt to gain a novel, evolutionary, and molecular understanding of the phenomenon of bacterial gigantism. The few existing genomic studies reveal a mysterious world of hyperpolyploid bacteria with hundreds to hundreds of thousands of chromosomes that are, in some cases, identical and in others, extremely different. These studies on giant bacteria reveal novel organelles, cellular compartmentalization, and novel mechanisms to combat the accumulation of deleterious mutations in polyploid bacteria. In this perspective paper, we provide a brief overview of what is known about the genomics of giant bacteria and build on that to highlight a few burning questions that await to be addressed.}, }
@article {pmid37705860, year = {2024}, author = {Mills, S and Trego, AC and Prevedello, M and De Vrieze, J and O'Flaherty, V and Lens, PNL and Collins, G}, title = {Unifying concepts in methanogenic, aerobic, and anammox sludge granulation.}, journal = {Environmental science and ecotechnology}, volume = {17}, number = {}, pages = {100310}, pmid = {37705860}, issn = {2666-4984}, abstract = {The retention of dense and well-functioning microbial biomass is crucial for effective pollutant removal in several biological wastewater treatment technologies. High solids retention is often achieved through aggregation of microbial communities into dense, spherical aggregates known as granules, which were initially discovered in the 1980s. These granules have since been widely applied in upflow anaerobic digesters for waste-to-energy conversions. Furthermore, granular biomass has been applied in aerobic wastewater treatment and anaerobic ammonium oxidation (anammox) technologies. The mechanisms underpinning the formation of methanogenic, aerobic, and anammox granules are the subject of ongoing research. Although each granule type has been extensively studied in isolation, there has been a lack of comparative studies among these granulation processes. It is likely that there are some unifying concepts that are shared by all three sludge types. Identifying these unifying concepts could allow a unified theory of granulation to be formed. Here, we review the granulation mechanisms of methanogenic, aerobic, and anammox granular sludge, highlighting several common concepts, such as the role of extracellular polymeric substances, cations, and operational parameters like upflow velocity and shear force. We have then identified some unique features of each granule type, such as different internal structures, microbial compositions, and quorum sensing systems. Finally, we propose that future research should prioritize aspects of microbial ecology, such as community assembly or interspecies interactions in individual granules during their formation and growth.}, }
@article {pmid37702500, year = {2023}, author = {Deng, T and He, Z and Xu, M and Dong, M and Guo, J and Sun, G and Huang, H}, title = {Species' functional traits and interactions drive nitrate-mediated sulfur-oxidizing community structure and functioning.}, journal = {mBio}, volume = {14}, number = {5}, pages = {e0156723}, pmid = {37702500}, issn = {2150-7511}, mesh = {*Ecosystem ; Nitrates ; *Microbiota ; Sulfur ; Phenotype ; Oxidation-Reduction ; }, abstract = {Understanding the processes and mechanisms governing microbial community assembly and their linkages to ecosystem functioning has long been a core issue in microbial ecology. An in-depth insight still requires combining with analyses of species' functional traits and microbial interactions. Our study showed how species' functional traits and interactions determined microbial community structure and functions by a well-controlled laboratory experiment with nitrate-mediated sulfur oxidation systems using high-throughput sequencing and culture-dependent technologies. The results provided solid evidences that species' functional traits and interactions were the intrinsic factors determining community structure and function. More importantly, our study established quantitative links between community structure and function based on species' functional traits and interactions, which would have important implications for the design and synthesis of microbiomes with expected functions.}, }
@article {pmid37695394, year = {2023}, author = {Wei, N and Tan, J}, title = {Correction to: Environment and Host Genetics Influence the Biogeography of Plant Microbiome Structure.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2869}, doi = {10.1007/s00248-023-02300-z}, pmid = {37695394}, issn = {1432-184X}, }
@article {pmid37692385, year = {2023}, author = {Fan, R and Liu, Y and Bin, Y and Huang, J and Yi, B and Tang, X and Li, Y and Cai, Y and Yang, Z and Yang, M and Song, J and Pan, Q and Liu, Z and Ghani, MI and Hu, X and Chen, X}, title = {Identification of Colletotrichum aenigma as the new causal agent of leaf blight disease on Aucuba japonica Thunb., and screenings of effective fungicides for its sustainable management.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1222844}, pmid = {37692385}, issn = {1664-302X}, abstract = {Aucuba japonica Thunb is an evergreen woody ornamental plant with significant economic and ecological values. It also produces aucubin, showing a variety of biological activities. It is widely planted in the southwest region of China, including karst landscape areas in Guizhou Province. In January 2022, a serious leaf blight disease was observed on the leaves of A. japonica in the outdoor gardens of Guizhou University, Guiyang, Guizhou, China. The causal agent was identified as Colletotrichum aenigma through amplification and sequencing of the internal transcribed spacer (ITS) region, translation of the chitin synthase (CHS) and actin (ACT) genes, and morphological characterizations. Koch's postulates were confirmed by its pathogenicity on healthy leaves, including re-isolation and identification. To our knowledge, this is the first report of C. aenigma causing leaf blight on A. japonica worldwide. To identify pathogen characteristics that could be utilized for future disease management, the effects of temperature and light on mycelial growth, conidia production, and conidial germination, and the effects of humidity on conidial germination were studied. Optimal temperatures for mycelial growth of C. aenigma BY827 were 25-30°C, while 15°C and 35°C were favorable for conidia production. Concurrently, alternating 10-h light and 14-h dark, proved to be beneficial for mycelial growth and conidial germination. Additionally, conidial germination was enhanced at 90% humidity. In vitro screenings of ten chemical pesticides to assess their efficacy in suppressing C. aenigma representative strain BY827. Among them, difenoconazole showed the best inhibition rate, with an EC50 (concentration for 50% of maximal effect) value of 0.0148 μg/ml. Subsequently, field experiment results showed that difenoconazole had the highest control efficiency on A. japonica leaf blight (the decreasing rate of disease incidence and decreasing rate of disease index were 44.60 and 47.75%, respectively). Interestingly, we discovered that C. aenigma BY827 may develop resistance to mancozeb, which is not reported yet among Colletotrichum spp. strains. In conclusion, our study provided new insights into the causal agent of A. japonica leaf blight, and the effective fungicides evaluated provided an important basis and potential resource for the sustainable control of A. japonica leaf blight caused by C. aenigma in the field.}, }
@article {pmid37692384, year = {2023}, author = {Mermans, F and Mattelin, V and Van den Eeckhoudt, R and García-Timermans, C and Van Landuyt, J and Guo, Y and Taurino, I and Tavernier, F and Kraft, M and Khan, H and Boon, N}, title = {Opportunities in optical and electrical single-cell technologies to study microbial ecosystems.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1233705}, pmid = {37692384}, issn = {1664-302X}, abstract = {New techniques are revolutionizing single-cell research, allowing us to study microbes at unprecedented scales and in unparalleled depth. This review highlights the state-of-the-art technologies in single-cell analysis in microbial ecology applications, with particular attention to both optical tools, i.e., specialized use of flow cytometry and Raman spectroscopy and emerging electrical techniques. The objectives of this review include showcasing the diversity of single-cell optical approaches for studying microbiological phenomena, highlighting successful applications in understanding microbial systems, discussing emerging techniques, and encouraging the combination of established and novel approaches to address research questions. The review aims to answer key questions such as how single-cell approaches have advanced our understanding of individual and interacting cells, how they have been used to study uncultured microbes, which new analysis tools will become widespread, and how they contribute to our knowledge of ecological interactions.}, }
@article {pmid37692382, year = {2023}, author = {Amon, CER and Fossou, RK and Ebou, AET and Koua, DK and Kouadjo, CG and Brou, YC and Voko Bi, DRR and Cowan, DA and Zézé, A}, title = {The core bacteriobiome of Côte d'Ivoire soils across three vegetation zones.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1220655}, pmid = {37692382}, issn = {1664-302X}, abstract = {The growing understanding that soil bacteria play a critical role in ecosystem servicing has led to a number of large-scale biogeographical surveys of soil microbial diversity. However, most of such studies have focused on northern hemisphere regions and little is known of either the detailed structure or function of soil microbiomes of sub-Saharan African countries. In this paper, we report the use of high-throughput amplicon sequencing analyses to investigate the biogeography of soil bacteria in soils of Côte d'Ivoire. 45 surface soil samples were collected from Côte d'Ivoire, representing all major biomes, and bacterial community composition was assessed by targeting the V4-V5 hypervariable region of the 16S ribosomal RNA gene. Causative relationships of both soil physicochemical properties and climatic data on bacterial community structure were infered. 48 phyla, 92 classes, 152 orders, 356 families, and 1,234 genera of bacteria were identified. The core bacteriobiome consisted of 10 genera ranked in the following order of total abundance: Gp6, Gaiella, Spartobacteria_genera_incertae_sedis, WPS-1_genera_incertae_sedis, Gp4, Rhodoplanes, Pseudorhodoplanes, Bradyrhizobium, Subdivision3_genera_incertae_sedis, and Gp3. Some of these genera, including Gp4 and WPS-1_genera_incertae_sedis, were unequally distributed between forest and savannah areas while other taxa (Bradyrhizobium and Rhodoplanes) were consistently found in all biomes. The distribution of the core genera, together with the 10 major phyla, was influenced by several environmental factors, including latitude, pH, Al and K. The main pattern of distribution that was observed for the core bacteriobiome was the vegetation-independent distribution scheme. In terms of predicted functions, all core bacterial taxa were involved in assimilatory sulfate reduction, while atmospheric dinitrogen (N2) reduction was only associated with the genus Bradyrhizobium. This work, which is one of the first such study to be undertaken at this scale in Côte d'Ivoire, provides insights into the distribution of bacterial taxa in Côte d'Ivoire soils, and the findings may serve as biological indicator for land management in Côte d'Ivoire.}, }
@article {pmid37691494, year = {2023}, author = {Mödl, B and Awad, M and Zwolanek, D and Scharf, I and Schwertner, K and Milovanovic, D and Moser, D and Schmidt, K and Pjevac, P and Hausmann, B and Krauß, D and Mohr, T and Svinka, J and Kenner, L and Casanova, E and Timelthaler, G and Sibilia, M and Krieger, S and Eferl, R}, title = {Defects in microvillus crosslinking sensitize to colitis and inflammatory bowel disease.}, journal = {EMBO reports}, volume = {24}, number = {10}, pages = {e57084}, pmid = {37691494}, issn = {1469-3178}, support = {ERC-2015-AdG TNT-Tumors 694883//EC | European Research Council (ERC)/ ; P35069-B//Austrian Science Fund (FWF)/ ; P33430//Austrian Science Fund (FWF)/ ; P 32900/FWF_/Austrian Science Fund FWF/Austria ; P32900-B//Austrian Science Fund (FWF)/ ; DOC 59-833//Austrian Science Fund (FWF)/ ; 766214//EC | Horizon 2020 Framework Programme (H2020)/ ; }, mesh = {Animals ; Mice ; *Microvilli/metabolism/pathology ; Humans ; *Inflammatory Bowel Diseases/metabolism/pathology/genetics ; *Intestinal Mucosa/metabolism/pathology ; Colitis/chemically induced/metabolism/pathology/genetics ; Cadherins/metabolism/genetics ; Mice, Knockout ; Enterocytes/metabolism/pathology ; Disease Models, Animal ; Dextran Sulfate ; Epithelial Cells/metabolism/pathology ; Permeability ; Mice, Inbred C57BL ; }, abstract = {Intestinal epithelial cells are covered by the brush border, which consists of densely packed microvilli. The Intermicrovillar Adhesion Complex (IMAC) links the microvilli and is required for proper brush border organization. Whether microvillus crosslinking is involved in the intestinal barrier function or colitis is currently unknown. We investigate the role of microvillus crosslinking in colitis in mice with deletion of the IMAC component CDHR5. Electron microscopy shows pronounced brush border defects in CDHR5-deficient mice. The defects result in severe mucosal damage after exposure to the colitis-inducing agent DSS. DSS increases the permeability of the mucus layer and brings bacteria in direct contact with the disorganized brush border of CDHR5-deficient mice. This correlates with bacterial invasion into the epithelial cell layer which precedes epithelial apoptosis and inflammation. Single-cell RNA sequencing data of patients with ulcerative colitis reveals downregulation of CDHR5 in enterocytes of diseased areas. Our results provide experimental evidence that a combination of microvillus crosslinking defects with increased permeability of the mucus layer sensitizes to inflammatory bowel disease.}, }
@article {pmid37690780, year = {2023}, author = {Cantu-Jungles, TM and Hamaker, BR}, title = {Tuning Expectations to Reality: Don't Expect Increased Gut Microbiota Diversity with Dietary Fiber.}, journal = {The Journal of nutrition}, volume = {153}, number = {11}, pages = {3156-3163}, doi = {10.1016/j.tjnut.2023.09.001}, pmid = {37690780}, issn = {1541-6100}, mesh = {*Gastrointestinal Microbiome ; Health Promotion ; Motivation ; Dietary Fiber/pharmacology ; *Microbiota ; }, abstract = {Dietary approaches, particularly those including fiber supplementation, can be used to promote health benefits by shaping gut microbial communities. Whereas community diversity measures, such as richness and evenness, are often used in microbial ecology to make sense of these complex and vast microbial ecosystems, it is less clear how these concepts apply when dietary fiber supplementation is given. In this perspective, we summarize and demonstrate how factors including experimental approach, number of bacteria sharing a dietary fiber, and initial relative abundances of bacteria that use a fiber can significantly affect diversity outcomes in fiber fermentation studies. We also show that a reduction in alpha diversity is possible, and perhaps expected, for most approaches that use fermentable fibers to beneficially shape the gut microbial community while still achieving health-related improvements.}, }
@article {pmid37689957, year = {2023}, author = {Wang, S and De Paepe, K and Van de Wiele, T and Fu, X and Wang, S and Zhang, B and Huang, Q}, title = {Starch-entrapped microspheres enhance gut microbiome-mediated anti-obesity effects of resistant starch in high-fat diet induced obese C57BL/6J mice.}, journal = {Food research international (Ottawa, Ont.)}, volume = {172}, number = {}, pages = {113215}, doi = {10.1016/j.foodres.2023.113215}, pmid = {37689957}, issn = {1873-7145}, mesh = {Animals ; Mice ; Mice, Inbred C57BL ; *Resistant Starch ; Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Dysbiosis ; Microspheres ; Obesity ; Starch/pharmacology ; Amylose ; }, abstract = {The prevalence of obesity is growing worldwide and has been extensively linked to gut microbiota dysbiosis. In addition to exercise and physical activity, fiber-rich foods may be a first-line prophylactic to manage obesity. This study investigated in vivo dietary intervention with high-amylose maize starch (HAMS) and starch-entrapped microspheres (MS) to treat high-fat diet induced metabolic disorder and gut microbiome dysbiosis in mice. MS more efficiently controlled body weight as well as adipose tissue mass compared to HAMS. Furthermore, MS significantly reduced blood glucose, insulin, lipid and pro-inflammatory cytokine levels compared to the high-fat diet, while the effects of HAMS were less pronounced. The MS-altered gut microbiota composition favoring Streptococcaceae, Bacilli, Firmicutes and unclassified Clostridiales was predicted to promote fatty acid, pantothenate and Coenzyme A biosynthesis. In line with this, elevated fecal short chain fatty acid (SCFA), in particular, propionate concentration was observed in MS-fed mice. Our study provides novel insights into the mechanistic action of MS on intestinal homeostasis, providing a basis for future dietary therapeutic applications.}, }
@article {pmid37688636, year = {2023}, author = {Garrido, AG and Machado, LF and Pereira, CM and Abrantes, DP and Calderon, EN and Zilberberg, C}, title = {Marine Heatwave Caused Differentiated Dysbiosis in Photosymbiont Assemblages of Corals and Hydrocorals During El Niño 2015/2016.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2959-2969}, pmid = {37688636}, issn = {1432-184X}, mesh = {Animals ; *Anthozoa ; El Nino-Southern Oscillation ; Dysbiosis ; Coral Reefs ; Climate Change ; }, abstract = {Reef corals have been threatened by climate change, with more frequent and intense bleaching events leading to extensive coral mortality and loss of coral cover worldwide. In the face of this, the corals' photosymbiont assemblages have received special attention as a key to better understand the bleaching process and its recovery. To assess the effects of thermal anomalies, the coral Mussismilia harttii and the hydrocoral Millepora alcicornis were monitored through the El Niño 2015/2016 at a Southwestern Atlantic (SWA) coral reef. A severe bleaching event (57% of colonies bleached) was documented, triggered by a < 3 °C-week heatwave, but no mortality was detected. The hydrocoral was more susceptible than the scleractinian, displaying bleaching symptoms earlier and experiencing a longer and more intense bleaching event. The composition of photosymbionts in the M. alcicornis population was affected only at the rare biosphere level (< 5% relative abundance), with the emergence of new symbionts after bleaching. Conversely, a temporary dysbiosis was observed in the M. harttii population, with one of the dominant symbiodiniaceans decreasing in relative abundance at the peak of the bleaching, which negatively affected the total β-diversity. After colonies' complete recovery, symbiodiniaceans' dominances returned to normal levels in both hosts. These results highlight critical differences in how the two coral species cope with bleaching and contribute to the understanding of the role of photosymbionts throughout the bleaching-recovery process.}, }
@article {pmid37687396, year = {2023}, author = {Galinytė, D and Balčiūnaitė-Murzienė, G and Karosienė, J and Morudov, D and Naginienė, R and Baranauskienė, D and Šulinskienė, J and Kudlinskienė, I and Savickas, A and Savickienė, N}, title = {Determination of Heavy Metal Content: Arsenic, Cadmium, Mercury, and Lead in Cyano-Phycocyanin Isolated from the Cyanobacterial Biomass.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {17}, pages = {}, pmid = {37687396}, issn = {2223-7747}, abstract = {Cyano-phycocyanin (C-PC) is a light-absorbing biliprotein found in cyanobacteria, commonly known as blue-green algae. Due to its antioxidative, anti-inflammatory, and anticancer properties, this protein is a promising substance in medicine and pharmaceuticals. However, cyanobacteria tend to bind heavy metals from the environment, making it necessary to ensure the safety of C-PC for the development of pharmaceutical products, with C-PC isolated from naturally collected cyanobacterial biomass. This study aimed to determine the content of the most toxic heavy metals, arsenic (As), cadmium (Cd), mercury (Hg), and lead (Pb) in C-PC isolated from different cyanobacterial biomasses collected in the Kaunas Lagoon during 2019-2022, and compare them with the content of heavy metals in C-PC isolated from cultivated Spirulina platensis (S. platensis). Cyanobacteria of Aphanizomenon flos-aquae (A. flos-aquae) dominated the biomass collected in 2019, while the genus Microcystis dominated the biomasses collected in the years 2020 and 2022. Heavy metals were determined using inductively coupled plasma mass spectrometry (ICP-MS). ICP-MS analysis revealed higher levels of the most investigated heavy metals (Pb, Cd, and As) in C-PC isolated from the biomass with the dominant Microcystis spp. compared to C-PC isolated from the biomass with the predominant A. flos-aquae. Meanwhile, C-PC isolated from cultivated S. platensis exhibited lower concentrations of As and Pb than C-PC isolated from naturally collected cyanobacterial biomass.}, }
@article {pmid37687181, year = {2023}, author = {Tom, A and Jacob, J and Mathews, M and Rajagopal, R and Alfarhan, A and Barcelo, D and Narayanankutty, A}, title = {Synthesis of Bis-Chalcones and Evaluation of Its Effect on Peroxide-Induced Cell Death and Lipopolysaccharide-Induced Cytokine Production.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {17}, pages = {}, pmid = {37687181}, issn = {1420-3049}, mesh = {*Antioxidants/pharmacology ; *Chalcones/pharmacology ; Lipopolysaccharides/pharmacology ; Cell Death ; Peroxides ; Cytokines ; }, abstract = {Plant secondary metabolites are important sources of biologically active compounds with wide pharmacological potentials. Among the different classes, the chalcones form integral pharmacologically active agents. Natural chalcones and bis-chalcones exhibit high antioxidant and anti-inflammatory properties in various experiments. Studies are also underway to explore more biologically active bis-chalcones by chemical synthesis of these compounds. In this study, the effects of six synthetic bis-chalcones were evaluated in intestinal epithelial cells (IEC-6); further, the anti-inflammatory potentials were studied in lipopolysaccharide-induced cytokine production in macrophages. The synthesized bis-chalcones differ from each other first of all by the nature of the aromatic cores (functional group substitution, and their position) and by the size of a central alicycle. The exposure of IEC-6 cells to peroxide radicals reduced the cell viability; however, pre-treatment with the bis-chalcones improved the cell viability in these cells. The mechanism of action was observed to be the increased levels of glutathione and antioxidant enzyme activities. Further, these bis-chalcones also inhibited the LPS-stimulation-induced inflammatory cytokine production in RAW 264.7 macrophages. Overall, the present study indicated the cytoprotective and anti-inflammatory abilities of synthetic bis-chalcones.}, }
@article {pmid37684546, year = {2023}, author = {Liu, N and Huang, Z and Fang, Y and Dong, Z}, title = {Impacts of Thermal Drainage on Bacterial Diversity and Community Construction in Tianwan Nuclear Power Plant.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2981-2992}, pmid = {37684546}, issn = {1432-184X}, mesh = {*Ecosystem ; *Nuclear Power Plants ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Drainage ; Carbon ; }, abstract = {As one of the low-carbon and high-efficient energy sources, nuclear power is developing vigorously to alleviate the crisis of global climate warming and realize carbon neutrality goals. Meanwhile, the ecological effect of thermal drainage in the nuclear power plant is significantly remarkable, which environmental assessment system has not yet referred to microorganisms. The rapid response of microbial diversity and community structure to environmental changes is crucial for ecosystem stability. This study investigated the bacterial diversity, community construction, and the co-occurrence patterns by 16S rRNA gene amplicon sequencing among gradient warming regions in Tianwan Nuclear Power Plant. The alpha diversity of the high warming region was the lowest in summer, which was dominated by Proteobacteria, whereas the highest bacterial diversity presented in high warming regions in winter, which harbored higher proportions of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. The spatial distribution of bacterial communities showed clear separation especially in summer. Strong correlations were between community compositions and environmental factors, such as salinity, DO, TN, and temperature in summer. Furthermore, remarkable seasonality in bacterial co-occurrence patterns was discovered: the robustness of the bacterial co-occurrence network was promoted in winter, while the complexity and robustness were decreased in summer due to the warming of thermal drainage. These findings reveal the potential factors underpinning the influence of thermal drainage on bacterial community structure, which make it possible to predict the ecological effect of the nuclear power plants by exploring how the microbial assembly is likely to respond to the temperature and other environmental changes.}, }
@article {pmid37684545, year = {2023}, author = {Huang, R and Tang, C and Zhao, Y and Liu, L and Chen, J and Shi, Z and Yan, Z}, title = {Unveiling the Biochar-Respiratory Growth of Methanosarcina acetivorans Involving Extracellular Polymeric Substances.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2970-2980}, pmid = {37684545}, issn = {1432-184X}, support = {22008142//National Natural Science Foundation of China/ ; ZR2022YQ31//Natural Science Foundation of Shandong Province/ ; BK20200232//Natural Science Foundation of Jiangsu Province/ ; Qilu Youth Talent Program//Shandong University/ ; }, mesh = {*Methanosarcina/genetics ; *Extracellular Polymeric Substance Matrix ; Electron Transport ; Methane ; }, abstract = {Biochar can be applied to diverse natural and engineered anaerobic systems. Biochar plays biogeochemical roles during its production, storage, and environmental dynamics, one of which is related to the global methane flux governed by methanotrophs and methanogens. Our understanding of relevant mechanisms is currently limited to the roles of biochar in methanotrophic growth, but less is known about the roles of biochar in methanogenic growth. Here, we demonstrated that biochar enhanced the methanogenic growth of a model methanogen, Methanosarcina acetivorans, and the role of biochar as an electron acceptor during methanogenic growth was confirmed, which is referred to as biochar-respiratory growth. The biochar-respiratory growth of M. acetivorans promoted the secretion of extracellular polymeric substances (EPS) with augmented electron transfer capabilities, and the removal of EPS significantly attenuated extracellular electron transfer. Identification and quantification of prosthetic cofactors for EPS suggest an important role of flavin and F420 in extracellular electron transfer. Transcriptomic analysis provided additional insights into the biochar-respiratory growth of M. acetivorans, showing that there was a positive response in transcriptional regulation to the favorable growth environment provided by biochar, which stimulated global methanogenesis. Our results shed more light on the in situ roles of biochar in the ecophysiology of methanogens in diverse anaerobic environments.}, }
@article {pmid37682693, year = {2024}, author = {Wilberts, L and Vuts, J and Caulfield, JC and Thomas, G and Withall, DM and Wäckers, F and Birkett, MA and Jacquemyn, H and Lievens, B}, title = {Effects of root inoculation of entomopathogenic fungi on olfactory-mediated behavior and life-history traits of the parasitoid Aphidius ervi (Haliday) (Hymenoptera: Braconidae).}, journal = {Pest management science}, volume = {80}, number = {2}, pages = {307-316}, doi = {10.1002/ps.7762}, pmid = {37682693}, issn = {1526-4998}, support = {1S79919N//Fonds Wetenschappelijk Onderzoek/ ; C24E/19/052//KU Leuven/ ; BB/X010953/1//Growing Health Institute Strategic Programme funded by the Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BBS/OS/CP/000001//Industrial Strategy Challenge Fund funded by the Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {Animals ; *Parasites ; Pest Control, Biological ; *Wasps/physiology ; Plants ; Nicotiana ; *Aphids/physiology ; *Capsicum ; }, abstract = {BACKGROUND: Although most biological control programs use multiple biological agents to manage pest species, to date only a few programs have combined the use of agents from different guilds. Using sweet pepper (Capsicum annuum L.), the entomopathogenic fungus Akanthomyces muscarius ARSEF 5128, the tobacco peach aphid Myzus persicae var. nicotianae and the aphid parasitoid Aphidius ervi as the experimental model, we explored whether root inoculation with an entomopathogenic fungus is compatible with parasitoid wasps for enhanced biocontrol of aphids.<br><br>RESULTS: In dual-choice behavior experiments, A. ervi was significantly attracted to the odor of M. persicae-infested C. annuum plants that had been inoculated with A. muscarius, compared to noninoculated infested plants. There was no significant difference in attraction to the odor of uninfested plants. Myzus persicae-infested plants inoculated with A. muscarius emitted significantly higher amounts of indole, (E)-nerolidol, (3E,7E)-4,8,12-trimethyltrideca-1,3,7,11-tetraene and one unidentified terpene compared to noninoculated infested plants. Coupled gas chromatography-electroantennography, using the antennae of A. ervi, confirmed the physiological activity of these elevated compounds. Inoculation of plants with A. muscarius did not affect parasitism rate nor parasitoid longevity, but significantly increased the speed of mummy formation in parasitized aphids on fungus-inoculated plants.<br><br>CONCLUSION: Our data suggest that root inoculation of C. annuum with A. muscarius ARSEF 5128 alters the olfactory-mediated behavior of parasitoids, but has little effect on parasitism efficiency or life-history parameters. However, increased attraction of parasitoids towards M. persicae-infested plants when inoculated by entomopathogenic fungi can accelerate host localization and hence improve biocontrol efficacy. &#xa9; 2023 Society of Chemical Industry.}, }
@article {pmid37680522, year = {2023}, author = {You, Y and Zhang, W and Cai, M and Guo, Q and Wang, J and Cai, Y and Lin, J}, title = {Discovery of fecal microbial signatures in patients with ankylosing spondylitis.}, journal = {Archives of rheumatology}, volume = {38}, number = {2}, pages = {217-229}, pmid = {37680522}, issn = {2618-6500}, abstract = {OBJECTIVES: This study aimed to investigate the characteristics of the gut microbiota in Chinese patients with ankylosing spondylitis (AS) and healthy controls in Quanzhou aiming to explore the correlation between microbiome changes and AS activities.<br><br>PATIENTS AND METHODS: In this study, high-throughput sequencing of the gene of 16S ribosomal RNA (16S rRNA) in fecal samples from 40 AS patients and 40 healthy controls, for a total of 80 participants (70 males, 10 females; mean age 33.7&#xb1;10.7 years; range, 15 to 58 years), was conducted between January 2018 and January 2019. Alpha and beta diversity were analyzed using the QIIME (Quantitative Insights Into Microbial Ecology) software, and differences were analyzed using Student's t-test, linear discriminant analysis coupled with effect size and Metastats. Finally, a correlation network was constructed using Pearson's analysis.<br><br>RESULTS: The alpha index values of the AS group were not significantly different from those of the control group. At the genus level, eight genera, Ruminiclostridium_9, Fusicatenibacter, Adlercreutzia, CAG-56, Intestinimonas, Lachnospira, Bacteroides, and Pseudoflavonifractor, were significantly enriched in patients with AS, whereas the abundance of uncultured_bacterium_f_Saccharimonadaceae, Prevotella_7, uncultured_bacterium_f_ Enterobacteriaceae, Cronobacter, Prevotellaceae_NK3B31_group, and Weissella were significantly decreased in patients with AS. In addition, diseaserelated gut microbial communities were detected in patients with AS.<br><br>CONCLUSION: We found differences in the gut microbiome between the patients with AS and controls and identified potential disease activity-related bacterial communities.}, }
@article {pmid37676325, year = {2023}, author = {Sun, P and Wang, M and Zheng, W and Li, S and Zhu, X and Chai, X and Zhao, S}, title = {Unbalanced diets enhance the complexity of gut microbial network but destabilize its stability and resistance.}, journal = {Stress biology}, volume = {3}, number = {1}, pages = {20}, pmid = {37676325}, issn = {2731-0450}, abstract = {Stability is a fundamental ecological property of the gut microbiota and is associated with host health. Numerous studies have shown that unbalanced dietary components disturb the gut microbial composition and thereby contribute to the onset and progression of disease. However, the impact of unbalanced diets on the stability of the gut microbiota is poorly understood. In the present study, four-week-old mice were fed a plant-based diet high in refined carbohydrates or a high-fat diet for four weeks to simulate a persistent unbalanced diet. We found that persistent unbalanced diets significantly reduced the gut bacterial richness and increased the complexity of bacterial co-occurrence networks. Furthermore, the gut bacterial response to unbalanced diets was phylogenetically conserved, which reduced network modularity and enhanced the proportion of positive associations between community taxon, thereby amplifying the co-oscillation of perturbations among community species to destabilize gut microbial communities. The disturbance test revealed that the gut microbiota of mice fed with unbalanced diets was less resistant to antibiotic perturbation and pathogenic bacteria invasion. This study may fill a gap in the mechanistic understanding of the gut microbiota stability in response to diet and provide new insights into the gut microbial ecology.}, }
@article {pmid37676037, year = {2023}, author = {Danevčič, T and Spacapan, M and Dragoš, A and Kovács, &#xc1;T and Mandic-Mulec, I}, title = {DegQ is an important policing link between quorum sensing and regulated adaptative traits in Bacillus subtilis.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0090823}, pmid = {37676037}, issn = {2165-0497}, abstract = {Quorum sensing (QS) is a widespread bacterial communication system that controls important adaptive traits in a cell density-dependent manner. However, mechanisms by which QS-regulated traits are linked within the cell and mechanisms by which these links affect adaptation are not well understood. In this study, Bacillus subtilis was used as a model bacterium to investigate the link between the ComQXPA QS system, DegQ, surfactin and protease production in planktonic and biofilm cultures. The work tests two alternative hypotheses predicting that hypersensitivity of the QS signal-deficient mutant (comQ::kan) to exogenously added ComX, resulting in increased surfactin production, is linked to an additional genetic locus, or alternatively, to overexpression of the ComX receptor ComP. Results are in agreement with the first hypothesis and show that the P srfAA hypersensitivity of the comQ::kan mutant is linked to a 168 strain-specific mutation in the P degQ region. Hence, the markerless ΔcomQ mutant lacking this mutation is not overresponsive to ComX. Such hyper-responsiveness is specific for the P srfAA and not detected in another ComX-regulated promoter, the P aprE , which is under the positive control by DegQ. Our results suggest that DegQ by exerting differential effect on P srfAA and P aprE acts as a policing mechanism and the intracellular link, which guards the cell from an overinvestment into surfactin production. IMPORTANCE DegQ levels are known to regulate surfactin synthesis and extracellular protease production, and DegQ is under the control of the ComX-dependent QS. DegQ also serves as an important policing link between these QS-regulated processes, preventing overinvestment in these costly processes. This work highlights the importance of DegQ, which acts as the intracellular link between ComX production and the response by regulating extracellular degradative enzyme synthesis and surfactin production.}, }
@article {pmid37675430, year = {2023}, author = {Edwards, J and Hoffbeck, C and West, AG and Pas, A and Taylor, MW}, title = {16S rRNA gene-based microbiota profiles from diverse avian faeces are largely independent of DNA preservation and extraction method.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1239167}, pmid = {37675430}, issn = {1664-302X}, abstract = {The avian gut microbiota has been the subject of considerable recent attention, with potential implications for diverse fields such as the poultry industry, microbial ecology, and conservation. Faecal microbiotas are frequently used as a non-invasive proxy for the gut microbiota, however the extraction of high-quality microbial DNA from avian faeces has often proven challenging. Here we aimed to evaluate the performance of two DNA preservation methods (95% ethanol and RNAlater) and five extraction approaches (IndiSpin Pathogen Kit, QIAamp PowerFecal Pro DNA Kit, MicroGEM PrepGEM Bacteria Kit, ZymoBIOMICS DNA Miniprep Kit, and an in-house phase separation-based method) for studying the avian gut microbiota. Systematic testing of the efficacy of these approaches on faecal samples from an initial three avian species (chicken, ostrich, and the flightless parrot kākāpō) revealed substantial differences in the quality, quantity and integrity of extracted DNA, but negligible influence of applied method on 16S rRNA gene-based microbiota profiles. Subsequent testing with a selected combination of preservation and extraction method on 10 further phylogenetically and ecologically diverse avian species reiterated the efficacy of the chosen approach, with bacterial community structure clustering strongly by technical replicates for a given avian species. Our finding that marked differences in extraction efficacy do not appear to influence 16S rRNA gene-based bacterial community profiles provides an important foundation for ongoing research on the avian gut microbiota.}, }
@article {pmid37674014, year = {2023}, author = {Cornish, CM and Bergholz, P and Schmidt, K and Sweetman, J}, title = {How Benthic Sediment Microbial Communities Respond to Glyphosate and Its Metabolite: a Microcosm Experiment.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2949-2958}, pmid = {37674014}, issn = {1432-184X}, mesh = {RNA, Ribosomal, 16S/genetics ; *Water Pollutants, Chemical/analysis ; *Herbicides/pharmacology ; *Microbiota ; Glyphosate ; }, abstract = {Glyphosate is the most commonly used agricultural herbicide in the world. In aquatic ecosystems, glyphosate often adsorbs to benthic substrates or is metabolized and degraded by microorganisms. The effects of glyphosate on microbial communities vary widely as microorganisms respond differently to exposure. To help understand the impacts of glyphosate on the sediment microbiome, we conducted a microcosm experiment examining the responses of benthic sediment microbial communities to herbicide treatments. Sediments from a prairie pothole wetland were collected, and 16S rRNA gene sequencing was used to analyze community composition 2-h and 14-days after a single treatment of low (0.07 ppm), medium (0.7 ppm), or high (7 ppm) glyphosate, aminomethylphosphonic acid (glyphosate metabolite), or a glyphosate-based commercial formula. We found no significant differences in microbial community composition across treatments, concentration levels, or day of sampling. These findings suggest that microbial species in the Prairie Pothole Region of North America may be tolerant to glyphosate exposure.}, }
@article {pmid37671861, year = {2023}, author = {Roller, BRK and Hellerschmied, C and Wu, Y and Miettinen, TP and Gomez, AL and Manalis, SR and Polz, MF}, title = {Single-cell mass distributions reveal simple rules for achieving steady-state growth.}, journal = {mBio}, volume = {14}, number = {5}, pages = {e0158523}, pmid = {37671861}, issn = {2150-7511}, support = {Life Sciences Project Award-572792//Simons Foundation (SF)/ ; }, mesh = {Reproducibility of Results ; Cell Division ; *Bacteria ; Culture Media ; Biomass ; }, abstract = {Microbiologists have watched clear liquid turn cloudy for over 100 years. While the cloudiness of a culture is proportional to its total biomass, growth rates from optical density measurements are challenging to interpret when cells change size. Many bacteria adjust their size at different steady-state growth rates, but also when shifting between starvation and growth. Optical density cannot disentangle how mass is distributed among cells. Here, we use single-cell mass measurements to demonstrate that a population of cells in batch culture achieves a stable mass distribution for only a short period of time. Achieving steady-state growth in rich medium requires low initial biomass concentrations and enough time for individual cell mass accumulation and cell number increase via cell division to balance out. Steady-state growth is important for reliable cell mass distributions and experimental reproducibility. We discuss how mass variation outside of steady-state can impact physiology, ecology, and evolution experiments.}, }
@article {pmid37669892, year = {2023}, author = {Hellal, J and Lise, B and Annette, B and Aurélie, C and Giulia, C and Simon, C and Cristiana, CL and Caroline, C and Nicolas, G and Marina, H and Fabrice, ML and Jean, M and Soizic, M and Carmen, P and Stéphane, P and Agnès, R and Stéphane, V}, title = {Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {10}, pages = {}, pmid = {37669892}, issn = {1574-6941}, mesh = {Ecotoxicology ; *Environmental Pollutants/toxicity ; Environmental Pollution ; *Environmental Restoration and Remediation ; Risk Assessment ; }, abstract = {Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment. They also play key roles in the fate of pollutants through the degradation, transformation, and transfer of organic or inorganic compounds. Thus, they are crucial for the development of nature-based solutions to reduce pollution and of bio-based solutions for environmental risk assessment of chemicals. At the intersection between microbial ecology, toxicology, and biogeochemistry, microbial ecotoxicology is a fast-expanding research area aiming to decipher the interactions between pollutants and microorganisms. This perspective paper gives an overview of the main research challenges identified by the Ecotoxicomic network within the emerging One Health framework and in the light of ongoing interest in biological approaches to environmental remediation and of the current state of the art in microbial ecology. We highlight prevailing knowledge gaps and pitfalls in exploring complex interactions among microorganisms and their environment in the context of chemical pollution and pinpoint areas of research where future efforts are needed.}, }
@article {pmid37668400, year = {2023}, author = {Du, H and Pan, J and Zhang, C and Yang, X and Wang, C and Lin, X and Li, J and Liu, W and Zhou, H and Yu, X and Mo, S and Zhang, G and Zhao, G and Qu, W and Jiang, C and Tian, Y and He, Z and Liu, Y and Li, M}, title = {Analogous assembly mechanisms and functional guilds govern prokaryotic communities in mangrove ecosystems of China and South America.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0157723}, pmid = {37668400}, issn = {2165-0497}, abstract = {As an important coastal "blue carbon sink," mangrove ecosystems contain microbial communities with an as-yet-unknown high species diversity. Exploring the assemblage and structure of sediment microbial communities therein can aid in a better understanding of their ecosystem functioning, such as carbon sequestration and other biogeochemical cycles in mangrove wetlands. However, compared to other biomes, the study of mangrove sediment microbiomes is limited, especially in diverse mangrove ecosystems at a large spatial scale, which may harbor microbial communities with distinct compositions and functioning. Here, we analyzed 380 sediment samples from 13 and 8 representative mangrove ecosystems, respectively, in China and South America and compared their microbial features. Although the microbial community compositions exhibited strong distinctions, the community assemblage in the two locations followed analogous patterns: the assemblages of the entire community, abundant taxa, rare taxa, and generalists were predominantly driven by stochastic processes with significant distance-decay patterns, while the assembly of specialists was more likely related to the behaviors of other organisms in or surrounding the mangrove ecosystems. In addition, co-occurrence and topological network analysis of mangrove sediment microbiomes underlined the dominance of sulfate-reducing prokaryotes in both the regions. Moreover, we found that more than 70% of the keystone and hub taxa were sulfate-reducing prokaryotes, implying their important roles in maintaining the linkage and stability of the mangrove sediment microbial communities. This study fills a gap in the large-scale analysis of microbiome features covering distantly located and diverse mangrove ecosystems. Here, we propose a suggestion to the Mangrove Microbiome Initiative that 16S rRNA sequencing protocols should be standardized with a unified primer to facilitate the global-scale analysis of mangrove microbiomes and further comparisons with the reference data sets from other biomes.IMPORTANCEMangrove wetlands are important ecosystems possessing valuable ecological functions for carbon storage, species diversity maintenance, and coastline stabilization. These functions are greatly driven or supported by microorganisms that make essential contributions to biogeochemical cycles in mangrove ecosystems. The mechanisms governing the microbial community assembly, structure, and functions are vital to microbial ecology but remain unclear. Moreover, studying these mechanisms of mangrove microbiomes at a large spatial scale can provide a more comprehensive insight into their universal features and can help untangle microbial interaction patterns and microbiome functions. In this study, we compared the mangrove microbiomes in a large spatial range and found that the assembly patterns and key functional guilds of the Chinese and South American mangrove microbiomes were analogous. The entire communities exhibited significant distance-decay patterns and were strongly governed by stochastic processes, while the assemblage of specialists may be merely associated with the behaviors of the organisms in mangrove ecosystems. Furthermore, our results highlight the dominance of sulfate-reducing prokaryotes in mangrove microbiomes and their key roles in maintaining the stability of community structure and functions.}, }
@article {pmid37668159, year = {2023}, author = {Van den Eeckhoudt, R and Christiaens, AS and Ceyssens, F and Vangalis, V and Verstrepen, KJ and Boon, N and Tavernier, F and Kraft, M and Taurino, I}, title = {Full-electric microfluidic platform to capture, analyze and selectively release single cells.}, journal = {Lab on a chip}, volume = {23}, number = {19}, pages = {4276-4286}, doi = {10.1039/d3lc00645j}, pmid = {37668159}, issn = {1473-0189}, mesh = {*Microfluidics ; Automation ; Cell Movement ; Cell Size ; *Dielectric Spectroscopy ; Saccharomyces cerevisiae ; }, abstract = {Current single-cell technologies require large and expensive equipment, limiting their use to specialized labs. In this paper, we present for the first time a microfluidic device which demonstrates a combined method for full-electric cell capturing, analyzing, and selectively releasing with single-cell resolution. All functionalities are experimentally demonstrated on Saccharomyces cerevisiae. Our microfluidic platform consists of traps centered around a pair of individually accessible coplanar electrodes, positioned under a microfluidic channel. Using this device, we validate our novel Two-Voltage method for trapping single cells by positive dielectrophoresis (pDEP). Cells are attracted to the trap when a high voltage (VH) is applied. A low voltage (VL) holds the already trapped cell in place without attracting additional cells, allowing full control over the number of trapped cells. After trapping, the cells are analyzed by broadband electrochemical impedance spectroscopy. These measurements allow the detection of single cells and the extraction of cell parameters. Additionally, these measurements show a strong correlation between average phase change and cell size, enabling the use of our system for size measurements in biological applications. Finally, our device allows selectively releasing trapped cells by turning off the pDEP signal in their trap. The experimental results show the techniques potential as a full-electric single-cell analysis tool with potential for miniaturization and automation which opens new avenues towards small-scale, high throughput single-cell analysis and sorting lab-on-CMOS devices.}, }
@article {pmid37667323, year = {2023}, author = {Rodríguez-Pastor, R and Hasik, AZ and Knossow, N and Bar-Shira, E and Shahar, N and Gutiérrez, R and Zaman, L and Harrus, S and Lenski, RE and Barrick, JE and Hawlena, H}, title = {Bartonella infections are prevalent in rodents despite efficient immune responses.}, journal = {Parasites &amp; vectors}, volume = {16}, number = {1}, pages = {315}, pmid = {37667323}, issn = {1756-3305}, support = {DEB-1813069//National Science Foundation/ ; 1391/15//Israel Science Foundation/ ; }, mesh = {Animals ; *Bartonella Infections/epidemiology/veterinary ; *Bartonella ; Immunoglobulin G ; Kinetics ; Immunity ; }, abstract = {BACKGROUND: Pathogens face strong selection from host immune responses, yet many host populations support pervasive pathogen populations. We investigated this puzzle in a model system of Bartonella and rodents from Israel's northwestern Negev Desert. We chose to study this system because, in this region, 75-100% of rodents are infected with Bartonella at any given time, despite an efficient immunological response. In this region, Bartonella species circulate in three rodent species, and we tested the hypothesis that at least one of these hosts exhibits a waning immune response to Bartonella, which allows reinfections.<br><br>METHODS: We inoculated captive animals of all three rodent species with the same Bartonella strain, and we quantified the bacterial dynamics and Bartonella-specific immunoglobulin G antibody kinetics over a period of 139&#xa0;days after the primary inoculation, and then for 60&#xa0;days following reinoculation with the same strain.<br><br>RESULTS: Contrary to our hypothesis, we found a strong, long-lasting immunoglobulin G antibody response, with protective immunological memory in all three rodent species. That response prevented reinfection upon exposure of the rodents to the same Bartonella strain.<br><br>CONCLUSIONS: This study constitutes an initial step toward understanding how the interplay between traits of Bartonella and their hosts influences the epidemiological dynamics of these pathogens in nature.}, }
@article {pmid37667132, year = {2023}, author = {Lv, H and Li, X and He, D and Chen, X and Liu, M and Lan, Y and Zhao, J and Wang, H and Yan, Z}, title = {Genotype-Controlled Vertical Transmission Exerts Selective Pressure on Community Assembly of Salvia miltiorrhiza.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2934-2948}, pmid = {37667132}, issn = {1432-184X}, mesh = {*Salvia miltiorrhiza/genetics/metabolism ; Fungi/genetics ; Endophytes/genetics ; *Microbiota/genetics ; Soil ; Seedlings ; Plant Roots/microbiology ; }, abstract = {The plant's endophytic fungi play an important role in promoting host development and metabolism. Studies have shown that the factors affecting the assembly of the endophyte community mainly include host genotype, vertical transmission, and soil origin. However, we do not know the role of vertically transmitted endohytic fungi influences on the host-plant's endophytic community assembly. Salvia miltiorrhiza from three production areas were used as research objects; we constructed three production area genotypes of S. miltiorrhiza regenerated seedlings simultaneously. Based on high-throughput sequencing, we analyzed the effects of genotype, soil origin, and vertical transmission on endophytic fungal communities. The results show that the community of soil origins significantly affected the endophytic fungal community in the regenerated seedlings of S. miltiorrhiza. The influence of genotype on community composition occurs through a specific mechanism. Genotype may selectively screen certain communities into the seed, thereby exerting selection pressure on the community composition process of offspring. As the number of offspring increases gradually, the microbiota, controlled by genotype and transmitted vertically, stabilizes, ultimately resulting in a significant effect of genotype on community composition.Furthermore, we observed that the taxa influencing the active ingredients are also selected as the vertically transmitted community. Moreover, the absence of an initial vertically transmitted community in S. miltiorrhiza makes it more vulnerable to infection by pathogenic fungi. Therefore, it is crucial to investigate and comprehend the selection model of the vertically transmitted community under varying genotypes and soil conditions. This research holds significant implications for enhancing the quality and yield of medicinal plants and economic crops.}, }
@article {pmid37666974, year = {2023}, author = {Lin, Q and Li, L and De Vrieze, J and Li, C and Fang, X and Li, X}, title = {Functional conservation of microbial communities determines composition predictability in anaerobic digestion.}, journal = {The ISME journal}, volume = {17}, number = {11}, pages = {1920-1930}, pmid = {37666974}, issn = {1751-7370}, mesh = {Anaerobiosis ; *Microbiota ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal ; Bioreactors ; Microbial Consortia/genetics ; }, abstract = {A major challenge in managing and engineering microbial communities is determining whether and how microbial community responses to environmental alterations can be predicted and explained, especially in microorganism-driven systems. We addressed this challenge by monitoring microbial community responses to the periodic addition of the same feedstock throughout anaerobic digestion, a typical microorganism-driven system where microorganisms degrade and transform the feedstock. The immediate and delayed response consortia were assemblages of microorganisms whose abundances significantly increased on the first or third day after feedstock addition. The immediate response consortia were more predictable than the delayed response consortia and showed a reproducible and predictable order-level composition across multiple feedstock additions. These results stood in both present (16 S rRNA gene) and potentially active (16 S rRNA) microbial communities and in different feedstocks with different biodegradability and were validated by simulation modeling. Despite substantial species variability, the immediate response consortia aligned well with the reproducible CH4 production, which was attributed to the conservation of expressed functions by the response consortia throughout anaerobic digestion, based on metatranscriptomic data analyses. The high species variability might be attributed to intraspecific competition and contribute to biodiversity maintenance and functional redundancy. Our results demonstrate reproducible and predictable microbial community responses and their importance in stabilizing system functions.}, }
@article {pmid37664629, year = {2023}, author = {Simon, LM and Flocco, C and Burkart, F and Methner, A and Henke, D and Rauer, L and Müller, CL and Vogel, J and Quaisser, C and Overmann, J and Simon, S}, title = {Microbial fingerprints reveal interaction between museum objects, curators, and visitors.}, journal = {iScience}, volume = {26}, number = {9}, pages = {107578}, pmid = {37664629}, issn = {2589-0042}, abstract = {Microbial communities reside at the interface between humans and their environment. Whether the microbiome can be leveraged to gain information on human interaction with museum objects is unclear. To investigate this, we selected objects from the Museum für Naturkunde and the Pergamonmuseum in Berlin, Germany, varying in material and size. Using swabs, we collected 126 samples from natural and cultural heritage objects, which were analyzed through 16S rRNA sequencing. By comparing the microbial composition of touched and untouched objects, we identified a microbial signature associated with human skin microbes. Applying this signature to cultural heritage objects, we identified areas with varying degrees of exposure to human contact on the Ishtar gate and Sam'al gate lions. Furthermore, we differentiated objects touched by two different individuals. Our findings demonstrate that the microbiome of museum objects provides insights into the level of human contact, crucial for conservation, heritage science, and potentially provenance research.}, }
@article {pmid37662195, year = {2023}, author = {Hoang, DQ and Wilson, LR and Scheftgen, AJ and Suen, G and Currie, CR}, title = {Disturbance-Diversity Relationships of Microbial Communities Change Based on Growth Substrate.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37662195}, issn = {2692-8205}, support = {T32 GM007215/GM/NIGMS NIH HHS/United States ; }, abstract = {Disturbance events can impact ecological community dynamics. Understanding how communities respond to disturbances, and how those responses can vary, is a challenge in microbial ecology. In this study, we grew a previously enriched specialized microbial community on either cellulose or glucose as a sole carbon source, and subjected them to one of five different disturbance regimes of varying frequencies ranging from low to high. Using 16S rRNA gene amplicon sequencing, we show that community structure is largely driven by substrate, but disturbance frequency affects community composition and successional dynamics. When grown on cellulose, bacteria in the genera Cellvibrio, Lacunisphaera, and Asticaccacaulis are the most abundant microbes. However, Lacunisphaera is only abundant in the lower disturbance frequency treatments, while Asticaccaulis is more abundant in the highest disturbance frequency treatment. When grown on glucose, the most abundant microbes are two Pseudomonas sequence variants, and a Cohnella sequence variant that is only abundant in the highest disturbance frequency treatment. Communities grown on cellulose exhibited a greater range of diversity (0.67-1.99 Shannon diversity and 1.38-5.25 Inverse Simpson diversity) that peak at the intermediate disturbance frequency treatment, or 1 disturbance every 3 days. Communities grown on glucose, however, ranged from 0.49-1.43 Shannon diversity and 1.37- 3.52 Inverse Simpson with peak diversity at the greatest disturbance frequency treatment. These results demonstrate that the dynamics of a microbial community can vary depending on substrate and the disturbance frequency, and may potentially explain the variety of diversity-disturbance relationships observed in microbial ecosystems.}, }
@article {pmid37658881, year = {2023}, author = {Owashi, Y and Minami, T and Kikuchi, T and Yoshida, A and Nakano, R and Kageyama, D and Adachi-Hagimori, T}, title = {Microbiome of Zoophytophagous Biological Control Agent Nesidiocoris tenuis.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2923-2933}, pmid = {37658881}, issn = {1432-184X}, mesh = {Humans ; Animals ; Biological Control Agents ; *Hemiptera/genetics ; RNA, Ribosomal, 16S/genetics ; *Rickettsia/genetics ; *Spiroplasma ; *Wolbachia/genetics ; *Microbiota ; Symbiosis ; }, abstract = {Many insects are associated with endosymbionts that influence the feeding, reproduction, and distribution of their hosts. Although the small green mirid, Nesidiocoris tenuis (Reuter) (Hemiptera: Miridae), a zoophytophagous predator that feeds on plants as well as arthropods, is a globally important biological control agent, its microbiome has not been sufficiently studied. In the present study, we assessed the microbiome variation in 96 N. tenuis individuals from 14 locations throughout Japan, based on amplicon sequencing of the 16S ribosomal RNA gene. Nine major bacteria associated with N. tenuis were identified: Rickettsia, two strains of Wolbachia, Spiroplasma, Providencia, Serratia, Pseudochrobactrum, Lactococcus, and Stenotrophomonas. Additionally, a diagnostic PCR analysis for three typical insect reproductive manipulators, Rickettsia, Wolbachia, and Spiroplasma, was performed on a larger sample size (n = 360) of N. tenuis individuals; the most prevalent symbiont was Rickettsia (69.7%), followed by Wolbachia (39.2%) and Spiroplasma (6.1%). Although some symbionts were co-infected, their prevalence did not exhibit any specific tendency, such as a high frequency in specific infection combinations. The infection frequency of Rickettsia was significantly correlated with latitude and temperature, while that of Wolbachia and Spiroplasma was significantly correlated with host plants. The predominance of these bacteria and the absence of obligate symbionts suggested that the N. tenuis microbiome is typical for predatory arthropods rather than sap-feeding insects. Rickettsia and Wolbachia were vertically transmitted rather than horizontally transmitted from the prey. The functional validation of each symbiont would be warranted to develop N. tenuis as a biological control agent.}, }
@article {pmid37659544, year = {2023}, author = {Kazmi, SSUH and Saqib, HSA and Pastorino, P and Grossart, HP and Yaseen, ZM and Abualreesh, MH and Liu, W and Wang, Z}, title = {Influence of the antibiotic nitrofurazone on community dynamics of marine periphytic ciliates: Evidence from community-based bioassays.}, journal = {The Science of the total environment}, volume = {904}, number = {}, pages = {166687}, doi = {10.1016/j.scitotenv.2023.166687}, pmid = {37659544}, issn = {1879-1026}, mesh = {*Ecosystem ; Nitrofurazone/toxicity ; Anti-Bacterial Agents/toxicity ; Environmental Monitoring ; Biodiversity ; *Ciliophora ; }, abstract = {Marine periphytic ciliates play a pivotal role in shaping coastal ecosystems dynamics, thereby acting as robust biological indicators of aquatic ecosystem health and functionality. However, the understanding of the effects of veterinary antibiotics on composition and structure of periphytic ciliate communities remains limited. Therefore, this research investigates the influence of the veterinary antibiotic nitrofurazone on the community dynamics of marine periphytic ciliates through bioassay experiments conducted over a one-year cycle. Various concentrations of nitrofurazone were administered to the tested ciliate assemblages, and subsequent changes in community composition, abundance, and diversity were quantitatively analyzed. The research revealed significant alterations in periphytic ciliate communities following exposure to nitrofurazone. Concentration-dependent (0-8 mg L[-1]) decrease in ciliates abundance, accompanied by shifts in species composition, community structure, and community patterns were observed. Comprehensive assessment of diversity metrics indicated significant changes in species richness and evenness in the presence of nitrofurazone, potentially disrupting the stability of ciliate communities. Furthermore, nitrofurazone significantly influenced the community structure of ciliates in all seasons (winter: R[2] = 0.489; spring: R[2] = 0.666; summer: R[2] = 0.700, autumn: R[2] = 0.450), with high toxic potential in treatments 4 and 8 mg L[-1]. Differential abundances of ciliates varied across seasons and nitrofurazone treatments, some orders like Pleurostomatida were consistently affected, while others (i.e., Strombidida and Philasterida) showed irregular distributions or were evenly affected (e.g., Urostylida and Synhymeniida). Retrieved contrasting patterns between nitrofurazone and community responses underscore the broad response repertoire exhibited by ciliates to antibiotic exposure, suggesting potential cascading effects on associated ecological processes in the periphyton community. These findings significantly enhance the understanding of the ecological impacts of nitrofurazone on marine periphytic ciliate communities, emphasizing the imperative for vigilant monitoring and regulation of veterinary antibiotics to protect marine ecosystem health and biodiversity. Further research is required to explore the long-term effects of nitrofurazone exposure and evaluate potential strategies to reduce the ecological repercussions of antibiotics in aquatic environments, with a particular focus on nitrofurazone.}, }
@article {pmid37659520, year = {2023}, author = {Schulz, G and van Beusekom, JEE and Jacob, J and Bold, S and Schöl, A and Ankele, M and Sanders, T and Dähnke, K}, title = {Low discharge intensifies nitrogen retention in rivers - A case study in the Elbe River.}, journal = {The Science of the total environment}, volume = {904}, number = {}, pages = {166740}, doi = {10.1016/j.scitotenv.2023.166740}, pmid = {37659520}, issn = {1879-1026}, mesh = {*Rivers ; *Nitrates/analysis ; Ecosystem ; Environmental Monitoring/methods ; Nitrogen/analysis ; Eutrophication ; Harmful Algal Bloom ; Water ; }, abstract = {Eutrophication due to excessive nutrient inputs is a major threat to coastal ecosystems worldwide, causing harmful algae blooms, seagrass loss and hypoxia. Decisions to combat eutrophication in the North Sea were made in the 1980s. Despite significant improvements during recent decades, high nitrogen loads and resulting eutrophication problems remain. In this study, long-term changes in nitrogen inputs to the Elbe Estuary (Germany) were characterized based on nitrogen data provided by the Elbe River Basin Community from 1985 to 2019. Additionally, surface water samples were taken at the weir separating the river from the estuary from 2011 to 2021 to characterize dissolved inorganic nitrogen concentrations and nitrate stable isotope composition. The findings suggest a close coupling of river discharge with the riverine nitrogen cycle. Nitrogen loads decreased disproportionately with decreasing discharge. This decrease is due to intensified nitrogen retention in the Elbe catchment, which can double nitrogen retention compared to average discharge conditions. Phytoplankton growth was enhanced by long residence times and high light availability at low water levels. This suggests that the recent decreases in nitrogen loads in the Elbe River were not only a result of management measures in the catchment but were also amplified by a recent long-lasting drought in the catchment. Based on projections from the Intergovernmental Panel on Climate Change, more frequent and extensive droughts are anticipated, which may lead to future seasonal shifts to nitrate limitation in the lower Elbe River.}, }
@article {pmid37658593, year = {2023}, author = {Ahmmed, MK and Bhowmik, S and Ahmmed, F and Giteru, SG and Islam, SS and Hachem, M and Hussain, MA and Kanwugu, ON and Agyei, D and Defoirdt, T}, title = {Utilisation of probiotics for disease management in giant freshwater prawn (Macrobrachium rosenbergii): Administration methods, antagonistic effects and immune response.}, journal = {Journal of fish diseases}, volume = {46}, number = {12}, pages = {1321-1336}, doi = {10.1111/jfd.13850}, pmid = {37658593}, issn = {1365-2761}, support = {//Bijzonder Onderzoeksfonds UGent/ ; //University of Otago/ ; //Ural Federal University/ ; }, mesh = {Animals ; *Palaemonidae ; *Fish Diseases ; *Probiotics/therapeutic use ; Fresh Water ; Immunity ; Disease Management ; }, abstract = {The giant freshwater prawn (Macrobrachium rosenbergii) is a high-yielding prawn variety well-received worldwide due to its ability to adapt to freshwater culture systems. Macrobrachium rosenbergii is an alternative to shrimp typically obtained from marine and brackish aquaculture systems. However, the use of intensive culture systems can lead to disease outbreaks, particularly in larval and post-larval stages, caused by pathogenic agents such as viruses, bacteria, fungi, yeasts and protozoans. White tail disease (viral), white spot syndrome (viral) and bacterial necrosis are examples of economically significant diseases. Given the increasing antibiotic resistance of disease-causing microorganisms, probiotics have emerged as promising alternatives for disease control. Probiotics are live active microbes that are introduced into a target host in an adequate number or dose to promote its health. In the present paper, we first discuss the diseases that occur in M. rosenbergii production, followed by an in-depth discussion on probiotics. We elaborate on the common methods of probiotics administration and explain the beneficial health effects of probiotics as immunity enhancers. Moreover, we discuss the antagonistic effects of probiotics on pathogenic microorganisms. Altogether, this paper provides a comprehensive overview of disease control in M. rosenbergii aquaculture through the use of probiotics, which could enhance the sustainability of prawn culture.}, }
@article {pmid37657296, year = {2023}, author = {Fu, S and Zhang, Y and Wang, R and Qiu, Z and Song, W and Yang, Q and Shen, L}, title = {A novel culture-enriched metagenomic sequencing strategy effectively guarantee the microbial safety of drinking water by uncovering the low abundance pathogens.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118737}, doi = {10.1016/j.jenvman.2023.118737}, pmid = {37657296}, issn = {1095-8630}, mesh = {*Metagenome ; *Drinking Water ; Phylogeny ; Anti-Bacterial Agents ; Risk Management ; }, abstract = {Assessing the presence of waterborne pathogens and antibiotic resistance genes (ARGs) is crucial for managing the environmental quality of drinking water sources. However, detecting low abundance pathogens in such settings is challenging. In this study, a workflow was developed to enrich for broad spectrum pathogens from drinking water samples. A mock community was used to evaluate the effectiveness of various enrichment broths in detecting low-abundance pathogens. Monthly metagenomic surveillance was conducted in a drinking water source from May to September 2021, and water samples were subjected to five enrichment procedures for 6 h to recover the majority of waterborne bacterial pathogens. Oxford Nanopore Technology (ONT) was used for metagenomic sequencing of enriched samples to obtain high-quality pathogen genomes. The results showed that selective enrichment significantly increased the proportions of targeted bacterial pathogens. Compared to direct metagenomic sequencing of untreated water samples, targeted enrichment followed by ONT sequencing significantly improved the detection of waterborne pathogens and the quality of metagenome-assembled genomes (MAGs). Eighty-six high-quality MAGs, including 70 pathogen MAGs, were obtained from ONT sequencing, while only 12 MAGs representing 10 species were obtained from direct metagenomic sequencing of untreated water samples. In addition, ONT sequencing improved the recovery of mobile genetic elements and the accuracy of phylogenetic analysis. This study highlights the urgent need for efficient methodologies to detect and manage microbial risks in drinking water sources. The developed workflow provides a cost-effective approach for environmental management of drinking water sources with microbial risks. The study also uncovered pathogens that were not detected by traditional methods, thereby advancing microbial risk management of drinking water sources.}, }
@article {pmid37656873, year = {2023}, author = {Cantoran, A and Maillard, F and Baldrian, P and Kennedy, PG}, title = {Defining a core microbial necrobiome associated with decomposing fungal necromass.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {9}, pages = {}, doi = {10.1093/femsec/fiad098}, pmid = {37656873}, issn = {1574-6941}, mesh = {Animals ; Carbon ; Ecosystem ; Forests ; *Mycobiome ; *Mycorrhizae ; }, abstract = {Despite growing interest in fungal necromass decomposition due to its importance in soil carbon retention, whether a consistent group of microorganisms is associated with decomposing necromass remains unresolved. Here, we synthesize knowledge on the composition of the bacterial and fungal communities present on decomposing fungal necromass from a variety of fungal species, geographic locations, habitats, and incubation times. We found that there is a core group of both bacterial and fungal genera (i.e. a core fungal necrobiome), although the specific size of the core depended on definition. Based on a metric that included both microbial frequency and abundance, we demonstrate that the core is taxonomically and functionally diverse, including bacterial copiotrophs and oligotrophs as well as fungal saprotrophs, ectomycorrhizal fungi, and both fungal and animal parasites. We also show that the composition of the core necrobiome is notably dynamic over time, with many core bacterial and fungal genera having specific associations with the early, middle, or late stages of necromass decomposition. While this study establishes the existence of a core fungal necrobiome, we advocate that profiling the composition of fungal necromass decomposer communities in tropical environments and other terrestrial biomes beyond forests is needed to fill key knowledge gaps regarding the global nature of the fungal necrobiome.}, }
@article {pmid37656196, year = {2023}, author = {Fagre, AC and Islam, A and Reeves, WK and Kading, RC and Plowright, RK and Gurley, ES and McKee, CD}, title = {Bartonella Infection in Fruit Bats and Bat Flies, Bangladesh.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2910-2922}, pmid = {37656196}, issn = {1432-184X}, mesh = {Animals ; Phylogeny ; Bangladesh/epidemiology ; *Chiroptera ; Genetic Variation ; *Bartonella Infections/epidemiology/veterinary/microbiology ; *Bartonella/genetics ; DNA ; }, abstract = {Bats harbor diverse intracellular Bartonella bacteria, but there is limited understanding of the factors that influence transmission over time. Investigation of Bartonella dynamics in bats could reveal general factors that control transmission of multiple bat-borne pathogens, including viruses. We used molecular methods to detect Bartonella DNA in paired bat (Pteropus medius) blood and bat flies in the family Nycteribiidae collected from a roost in Faridpur, Bangladesh between September 2020 and January 2021. We detected high prevalence of Bartonella DNA in bat blood (35/55, 64%) and bat flies (59/60, 98%), with sequences grouping into three phylogenetic clades. Prevalence in bat blood increased over the study period (33% to 90%), reflecting an influx of juvenile bats in the population and an increase in the prevalence of bat flies. Discordance between infection status and the clade/genotype of detected Bartonella was also observed in pairs of bats and their flies, providing evidence that bat flies take blood meals from multiple bat hosts. This evidence of bat fly transfer between hosts and the changes in Bartonella prevalence during a period of increasing nycteribiid density support the role of bat flies as vectors of bartonellae. The study provides novel information on comparative prevalence and genetic diversity of Bartonella in pteropodid bats and their ectoparasites, as well as demographic factors that affect Bartonella transmission and potentially other bat-borne pathogens.}, }
@article {pmid37655448, year = {2023}, author = {Wang, Y and Li, Q and Zhang, J and Liu, P and Zheng, H and Chen, L and Wang, Z and Tan, C and Zhang, M and Zhang, H and Miao, W and Wang, Y and Xuan, X and Yi, G and Wang, P}, title = {Ring1a protects against colitis through regulating mucosal immune system and colonic microbial ecology.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2251646}, pmid = {37655448}, issn = {1949-0984}, mesh = {Animals ; Mice ; *Colitis/genetics/microbiology ; *Gastrointestinal Microbiome ; Immune System ; Metronidazole/pharmacology ; Prevotella/genetics ; }, abstract = {Inflammatory bowel disease (IBD) represents a prominent chronic immune-mediated inflammatory disorder, yet its etiology remains poorly comprehended, encompassing intricate interactions between genetics, immunity, and the gut microbiome. This study uncovers a novel colitis-associated risk gene, namely Ring1a, which regulates the mucosal immune response and intestinal microbiota. Ring1a deficiency exacerbates colitis by impairing the immune system. Concomitantly, Ring1a deficiency led to a Prevotella genus-dominated pathogenic microenvironment, which can be horizontally transmitted to co-housed wild type (WT) mice, consequently intensifying dextran sodium sulfate (DSS)-induced colitis. Furthermore, we identified a potential mechanism linking the altered microbiota in Ring1aKO mice to decreased levels of IgA, and we demonstrated that metronidazole administration could ameliorate colitis progression in Ring1aKO mice, likely by reducing the abundance of the Prevotella genus. We also elucidated the immune landscape of DSS colitis and revealed the disruption of intestinal immune homeostasis associated with Ring1a deficiency. Collectively, these findings highlight Ring1a as a prospective candidate risk gene for colitis and suggest metronidazole as a potential therapeutic option for clinically managing Prevotella genus-dominated colitis.}, }
@article {pmid37655346, year = {2023}, author = {Gutierrez, T and Liu, H}, title = {Editorial: Rising stars in aquatic microbiology: 2022.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1265720}, doi = {10.3389/fmicb.2023.1265720}, pmid = {37655346}, issn = {1664-302X}, }
@article {pmid37653502, year = {2023}, author = {Zehentner, B and Scherer, S and Neuhaus, K}, title = {Non-canonical transcriptional start sites in E. coli O157:H7 EDL933 are regulated and appear in surprisingly high numbers.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {243}, pmid = {37653502}, issn = {1471-2180}, mesh = {*Escherichia coli O157/genetics ; Transcription Initiation Site ; *Enterohemorrhagic Escherichia coli ; Cell Cycle ; Culture Media ; }, abstract = {Analysis of genome wide transcription start sites (TSSs) revealed an unexpected complexity since not only canonical TSS of annotated genes are recognized by RNA polymerase. Non-canonical TSS were detected antisense to, or within, annotated genes as well new intergenic (orphan) TSS, not associated with known genes. Previously, it was hypothesized that many such signals represent noise or pervasive transcription, not associated with a biological function. Here, a modified Cappable-seq protocol allows determining the primary transcriptome of the enterohemorrhagic E. coli O157:H7 EDL933 (EHEC). We used four different growth media, both in exponential and stationary growth phase, replicated each thrice. This yielded 19,975 EHEC canonical and non-canonical TSS, which reproducibly occurring in three biological replicates. This questions the hypothesis of experimental noise or pervasive transcription. Accordingly, conserved promoter motifs were found upstream indicating proper TSSs. More than 50% of 5,567 canonical and between 32% and 47% of 10,355 non-canonical TSS were differentially expressed in different media and growth phases, providing evidence for a potential biological function also of non-canonical TSS. Thus, reproducible and environmentally regulated expression suggests that a substantial number of the non-canonical TSSs may be of unknown function rather than being the result of noise or pervasive transcription.}, }
@article {pmid37653010, year = {2023}, author = {Gralka, M and Pollak, S and Cordero, OX}, title = {Genome content predicts the carbon catabolic preferences of heterotrophic bacteria.}, journal = {Nature microbiology}, volume = {8}, number = {10}, pages = {1799-1808}, pmid = {37653010}, issn = {2058-5276}, mesh = {*Carbon/metabolism ; Bacteria ; Heterotrophic Processes ; *Microbiota/genetics ; Genomics ; }, abstract = {Heterotrophic bacteria-bacteria that utilize organic carbon sources-are taxonomically and functionally diverse across environments. It is challenging to map metabolic interactions and niches within microbial communities due to the large number of metabolites that could serve as potential carbon and energy sources for heterotrophs. Whether their metabolic niches can be understood using general principles, such as a small number of simplified metabolic categories, is unclear. Here we perform high-throughput metabolic profiling of 186 marine heterotrophic bacterial strains cultured in media containing one of 135 carbon substrates to determine growth rates, lag times and yields. We show that, despite high variability at all levels of taxonomy, the catabolic niches of heterotrophic bacteria can be understood in terms of their preference for either glycolytic (sugars) or gluconeogenic (amino and organic acids) carbon sources. This preference is encoded by the total number of genes found in pathways that feed into the two modes of carbon utilization and can be predicted using a simple linear model based on gene counts. This allows for coarse-grained descriptions of microbial communities in terms of prevalent modes of carbon catabolism. The sugar-acid preference is also associated with genomic GC content and thus with the carbon-nitrogen requirements of their encoded proteome. Our work reveals how the evolution of bacterial genomes is structured by fundamental constraints rooted in metabolism.}, }
@article {pmid37652144, year = {2023}, author = {Low, KE and Tingley, JP and Klassen, L and King, ML and Xing, X and Watt, C and Hoover, SER and Gorzelak, M and Abbott, DW}, title = {Carbohydrate flow through agricultural ecosystems: Implications for synthesis and microbial conversion of carbohydrates.}, journal = {Biotechnology advances}, volume = {69}, number = {}, pages = {108245}, doi = {10.1016/j.biotechadv.2023.108245}, pmid = {37652144}, issn = {1873-1899}, mesh = {Animals ; *Carbohydrates/chemistry ; Carbohydrate Metabolism ; Agriculture ; Soil/chemistry ; *Microbiota ; }, abstract = {Carbohydrates are chemically and structurally diverse biomolecules, serving numerous and varied roles in agricultural ecosystems. Crops and horticulture products are inherent sources of carbohydrates that are consumed by humans and non-human animals alike; however carbohydrates are also present in other agricultural materials, such as soil and compost, human and animal tissues, milk and dairy products, and honey. The biosynthesis, modification, and flow of carbohydrates within and between agricultural ecosystems is intimately related with microbial communities that colonize and thrive within these environments. Recent advances in -omics techniques have ushered in a new era for microbial ecology by illuminating the functional potential for carbohydrate metabolism encoded within microbial genomes, while agricultural glycomics is providing fresh perspective on carbohydrate-microbe interactions and how they influence the flow of functionalized carbon. Indeed, carbohydrates and carbohydrate-active enzymes are interventions with unrealized potential for improving carbon sequestration, soil fertility and stability, developing alternatives to antimicrobials, and circular production systems. In this manner, glycomics represents a new frontier for carbohydrate-based biotechnological solutions for agricultural systems facing escalating challenges, such as the changing climate.}, }
@article {pmid37650927, year = {2023}, author = {Ho, HVN and Dunigan, DD and Salsbery, ME and Agarkova, IV and Al Ameeli, Z and Van Etten, JL and DeLong, JP}, title = {Viral Chemotaxis of Paramecium Bursaria Altered by Algal Endosymbionts.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2904-2909}, pmid = {37650927}, issn = {1432-184X}, support = {1736030//Directorate for Biological Sciences/ ; }, mesh = {*Paramecium ; Chemotaxis ; *Phycodnaviridae ; Symbiosis ; }, abstract = {Chemotaxis is widespread across many taxa and often aids resource acquisition or predator avoidance. Species interactions can modify the degree of movement facilitated by chemotaxis. In this study, we investigated the influence of symbionts on Paramecium bursaria's chemotactic behavior toward chloroviruses. To achieve this, we performed choice experiments using chlorovirus and control candidate attractors (virus stabilization buffer and pond water). We quantified the movement of Paramecia grown with or without algal and viral symbionts toward each attractor. All Paramecia showed some chemotaxis toward viruses, but cells without algae and viruses showed the most movement toward viruses. Thus, the endosymbiotic algae (zoochlorellae) appeared to alter the movement of Paramecia toward chloroviruses, but it was not clear that ectosymbiotic viruses (chlorovirus) also had this effect. The change in behavior was consistent with a change in swimming speed, but a change in attraction remains possible. The potential costs and benefits of chemotactic movement toward chloroviruses for either the Paramecia hosts or its symbionts remain unclear.}, }
@article {pmid37649628, year = {2023}, author = {Levante, A and Bertani, G and Marrella, M and Mucchetti, G and Bernini, V and Lazzi, C and Neviani, E}, title = {The microbiota of Mozzarella di Bufala Campana PDO cheese: a study across the manufacturing process.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1196879}, pmid = {37649628}, issn = {1664-302X}, abstract = {INTRODUCTION: Mozzarella di Bufala Campana PDO cheese (MBC) is a globally esteemed Italian cheese. The traditional cheesemaking process of MBC relies on natural whey starter culture, water buffalo's milk, and the local agroecosystem.<br><br>METHODS: In this study, the microbial ecology of intermediate samples of MBC production, coming from two dairies with slightly different cheesemaking technology (dairy M large producer, and dairy C medium-small), was investigated using 16S rRNA amplicon sequencing. This research aimed to provide insights into the dynamics of microbial consortia involved in various cheesemaking steps.<br><br>RESULTS AND DISCUSSION: All samples, except for raw buffalo milk, exhibited a core microbiome predominantly composed of Streptococcus spp. and Lactobacillus spp., albeit with different ratios between the two genera across the two MBC producers. Notably, the microbiota of the brine from both dairies, analyzed using 16S amplicon sequencing for the first time, was dominated by the Lactobacillus and Streptococcus genera, while only dairy C showed the presence of minor genera such as Pediococcus and Lentilactobacillus. Intriguingly, the final mozzarella samples from both producers displayed an inversion in the dominance of Lactobacillus spp. over Streptococcus spp. in the microbiota compared to curd samples, possibly attributable to the alleviation of thermal stress following the curd stretching step. In conclusion, the different samples from the two production facilities did not exhibit significant differences in terms of the species involved in MBC cheesemaking. This finding confirms that the key role in the MBC cheesemaking process lies with a small-sized microbiome primarily composed of Streptococcus and Lactobacillus spp.}, }
@article {pmid37649327, year = {2024}, author = {Mariën, Q and Regueira, A and Ganigué, R}, title = {Steerable isobutyric and butyric acid production from CO2 and H2 by Clostridium luticellarii.}, journal = {Microbial biotechnology}, volume = {17}, number = {1}, pages = {e14321}, pmid = {37649327}, issn = {1751-7915}, support = {ERDF (UE)//Galician Competitive Research Group/ ; GRC ED431C 2021/37//Galician Competitive Research Group/ ; BOF19/STA/044//Bijzonder Onderzoeksfonds UGent/ ; 1SC5722N//Fonds Wetenschappelijk Onderzoek/ ; ED481B-2021-012//Xunta de Galicia/ ; }, mesh = {Butyric Acid/metabolism ; *Isobutyrates ; *Carbon Dioxide ; Acetic Acid ; Fermentation ; *Clostridium ; }, abstract = {Clostridium luticellarii is a recently discovered acetogen that is uniquely capable of producing butyric and isobutyric acid from various substrates (e.g. methanol), but it is unclear which factors influence its (iso)butyric acid production from H2 and CO2 . We aimed to investigate the autotrophic metabolism of C. luticellarii by identifying the necessary growth conditions and examining the effects of pH and metabolite levels on product titers and selectivity. Results show that autotrophic growth of C. luticellarii requires the addition of complex nutrient sources and the absence of shaking conditions. Further experiments combined with thermodynamic calculations identified pH as a key parameter governing the direction of metabolic fluxes. At circumneutral pH (~6.5), acetic acid is the sole metabolic end product but C. luticellarii possesses the unique ability to co-oxidize organic acids such as valeric acid under high H2 partial pressures (>1 bar). Conversely, mildly acidic pH (≤5.5) stimulates the production of butyric and isobutyric acid while partly halting the oxidation of organic acids. Additionally, elevated acetic acid concentrations stimulated butyric and isobutyric acid production up to a combined selectivity of 53 ± 3%. Finally, our results suggest that isobutyric acid is produced by a reversible isomerization of butyric acid, but valeric and caproic acid are not isomerized. These combined insights can inform future efforts to optimize and scale-up the production of valuable chemicals from CO2 using C. luticellarii.}, }
@article {pmid37643688, year = {2023}, author = {McEvoy, N and O'Connor, A and McDonagh, F and Lonappan, AM and Farrell, ML and Kovarova, A and Burke, L and Ryan, K and Hallahan, B and Miliotis, G}, title = {Complete genome of an inhibitor-resistant blaTEM-30 encoding Escherichia coli sequence type 127 isolate identified in human saliva with a high genotypic virulence load.}, journal = {Journal of global antimicrobial resistance}, volume = {35}, number = {}, pages = {44-47}, doi = {10.1016/j.jgar.2023.08.014}, pmid = {37643688}, issn = {2213-7173}, mesh = {Humans ; *Escherichia coli ; Virulence/genetics ; *Escherichia coli Infections ; Phylogeny ; Saliva ; Virulence Factors/genetics ; Genotype ; Anti-Bacterial Agents/pharmacology ; }, abstract = {OBJECTIVES: Escherichia coli sequence type (ST) 127 is a pandemic lineage that belongs to the extraintestial pathogenic (ExPEC) family, mainly associated with urinary tract infections and bloodstream infections. Here, we report the complete genome of an E. coli ST 127 isolate which was identified in the saliva of a patient with treatment-resistant schizophrenia (TRS) exhibiting no signs of infection. The objective of this work is to determine the mobile genetic elements (MGEs), antibiotic resistance genes (ARGs), and virulence factors (VFs) that contribute to the pathogenicity of such ST127 isolates.<br><br>METHODS: Whole-genome sequencing (WGS) of isolate GABEEC10 was performed using DNABseq and Nanopore MinION platforms. Hybrid assembly of GABEEC10 was conducted with Unicycler v. 0.5.0. and annotated using PROKKA v1.14.5. Comparative genomics and phylogenomics were conducted using average nucleotide identity (ANI) and approximately-maximum-likelihood phylogenetic inference. ARGs, VFs, and serotyping were identified with Abricate v1.0.0 using CARD, vfdb, and EcOH databases, respectively.<br><br>RESULTS: Escherichia coli salivary isolate GABEEC10 was identified to belong to phylogroup B2 and have a serotype of O6 H31 with a total genome length of 4,940,530 bp and a mean guanine-cytosine (GC) content of 50.40 %. GABEEC10 was identified to have a highly virulent genotype with the presence of 84 VFs in addition to 44 ARGs, including an acquired blaTEM-30. The strain was identified to additionally carry four mobilisable plasmids.<br><br>CONCLUSION: We report the complete genome of E. coli GABAEEC10 that can be used for gaining insights into the pathogenicity, drug resistance mechanisms, and dissemination patterns of the emerging pandemic lineage ST 127.}, }
@article {pmid37640259, year = {2023}, author = {Ikeda, T and Ogawa, T and Aono, T}, title = {Dethiobiotin uptake and utilization by bacteria possessing bioYB operon.}, journal = {Research in microbiology}, volume = {174}, number = {8}, pages = {104131}, doi = {10.1016/j.resmic.2023.104131}, pmid = {37640259}, issn = {1769-7123}, mesh = {*Biotin/metabolism ; Biological Transport ; *Operon ; Bacteria/genetics/metabolism ; }, abstract = {Biotin is an essential vitamin for all organisms. Some bacteria cannot synthesize biotin and live by acquiring biotin from the environment. Bacterial biotin transporters (BioY) are classified into three mechanistic types. The first forms the BioMNY complex with ATPase (BioM) and transmembrane protein (BioN). The second relies on a promiscuous energy coupling module. The third functions independently. One-third of bioY genes spread in bacteria cluster with bioM and bioN on the genomes, and the rest does not. Interestingly, some bacteria have the bioY gene clustering with bioB gene, which encodes biotin synthase, an enzyme that converts dethiobiotin to biotin, on their genome. This bioY-bioB cluster is observed even though these bacteria cannot synthesize biotin. Azorhizobium caulinodans ORS571, a rhizobium of tropical legume Sesbania rostrata, is one of such bacteria. In this study using this bacterium, we demonstrated that the BioY linked to BioB could transport not only biotin but also dethiobiotin, and the combination of BioY and BioB contributed to the growth of A. caulinodans ORS571 in a biotin-deficient but dethiobiotin-sufficient environment. We propose that such environment universally exists in the natural world, and the identification of such environment will be a new subject in the field of microbial ecology.}, }
@article {pmid37639796, year = {2023}, author = {Mei, Z and Fu, Y and Wang, F and Xiang, L and Hu, F and Harindintwali, JD and Wang, M and Virta, M and Hashsham, SA and Jiang, X and Tiedje, JM}, title = {Magnetic biochar/quaternary phosphonium salt reduced antibiotic resistome and pathobiome on pakchoi leaves.}, journal = {Journal of hazardous materials}, volume = {460}, number = {}, pages = {132388}, doi = {10.1016/j.jhazmat.2023.132388}, pmid = {37639796}, issn = {1873-3336}, mesh = {Humans ; *Sodium Chloride ; *Anti-Bacterial Agents/pharmacology ; Plant Leaves ; Soil ; Vegetables ; Magnetic Phenomena ; }, abstract = {Antibiotic resistance genes (ARGs) and human pathogenic bacteria (HPB) in leafy vegetable is a matter of concern as they can be transferred from soil, atmosphere, and foliar sprays, and poses a potential risk to public health. While traditional disinfection technologies are effective in reducing the presence of ARGs and HPB in soil. A new technology, foliar spraying with magnetic biochar/quaternary ammonium salt (MBQ), was demonstrated and applied to the leaf surface. High-throughput quantitative PCR targeting 96 valid ARGs and 16 S rRNA sequencing were used to assess its efficacy in reducing ARGs and HPB. The results showed that spraying MBQ reduced 97.0 ± 0.81% of "high-risk ARGs", associated with seven classes of antibiotic resistance in pakchoi leaves within two weeks. Water washing could further reduce "high-risk ARGs" from pakchoi leaves by 19.8%- 24.6%. The relative abundance of HPB closely related to numerous ARGs was reduced by 15.2 ± 0.23% with MBQ application. Overall, this study identified the potential risk of ARGs from leafy vegetables and clarified the significant implications of MBQ application for human health as it offers a promising strategy for reducing ARGs and HPB in leafy vegetables.}, }
@article {pmid37637623, year = {2023}, author = {Ratna, HVK and Jeyaraman, M and Yadav, S and Jeyaraman, N and Nallakumarasamy, A}, title = {Is Dysbiotic Gut the Cause of Low Back Pain?.}, journal = {Cureus}, volume = {15}, number = {7}, pages = {e42496}, pmid = {37637623}, issn = {2168-8184}, abstract = {Low back pain (LBP) is the foremost cause of disability that affects the day-to-day activities of millions of people worldwide. The putative trigger of LBP is linked to the gut microbiome (GM) and its dysbiotic environment. With the concept of GM, various disease pathogenesis has been revisited with plausible crosstalks and micromolecular mimicry. In the normal intervertebral disc (IVD), Firmicutes and Actinobacteria were found in abundance. The blood-disc barrier protects IVD from systemic infection, resists inflammation, and halts the immune surveillance of the inner aspects of IVD. The insights into microbial ecology will broaden our horizons in GM and IVD degeneration in LBP cases. However, an improved understanding of GM and back pain has to be explored in large-scale individuals with varied timescales to validate the above findings. The role of GM (diet, prebiotics, probiotics, and fecal microbiota transplantation) in pain modulation can form novel therapies in cases of LBP.}, }
@article {pmid37637134, year = {2023}, author = {White, C and Antell, E and Schwartz, SL and Lawrence, JE and Keren, R and Zhou, L and Yu, K and Zhuang, W and Alvarez-Cohen, L}, title = {Synergistic interactions between anammox and dissimilatory nitrate reducing bacteria sustains reactor performance across variable nitrogen loading ratios.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1243410}, pmid = {37637134}, issn = {1664-302X}, abstract = {Anaerobic ammonium oxidizing (anammox) bacteria are utilized for high efficiency nitrogen removal from nitrogen-laden sidestreams in wastewater treatment plants. The anammox bacteria form a variety of competitive and mutualistic interactions with heterotrophic bacteria that often employ denitrification or dissimilatory nitrate reduction to ammonium (DNRA) for energy generation. These interactions can be heavily influenced by the influent ratio of ammonium to nitrite, NH4[+]:NO2[-], where deviations from the widely acknowledged stoichiometric ratio (1:1.32) have been demonstrated to have deleterious effects on anammox efficiency. Thus, it is important to understand how variable NH4[+]:NO2[-] ratios impact the microbial ecology of anammox reactors. We observed the response of the microbial community in a lab scale anammox membrane bioreactor (MBR) to changes in the influent NH4[+]:NO2[-] ratio using both 16S rRNA gene and shotgun metagenomic sequencing. Ammonium removal efficiency decreased from 99.77 ± 0.04% when the ratio was 1:1.32 (prior to day 89) to 90.85 ± 0.29% when the ratio was decreased to 1:1.1 (day 89-202) and 90.14 ± 0.09% when the ratio was changed to 1:1.13 (day 169-200). Over this same timespan, the overall nitrogen removal efficiency (NRE) remained relatively unchanged (85.26 ± 0.01% from day 0-89, compared to 85.49 ± 0.01% from day 89-169, and 83.04 ± 0.01% from day 169-200). When the ratio was slightly increased to 1:1.17-1:1.2 (day 202-253), the ammonium removal efficiency increased to 97.28 ± 0.45% and the NRE increased to 88.21 ± 0.01%. Analysis of 16 S rRNA gene sequences demonstrated increased relative abundance of taxa belonging to Bacteroidetes, Chloroflexi, and Ignavibacteriae over the course of the experiment. The relative abundance of Planctomycetes, the phylum to which anammox bacteria belong, decreased from 77.19% at the beginning of the experiment to 12.24% by the end of the experiment. Analysis of metagenome assembled genomes (MAGs) indicated increased abundance of bacteria with nrfAH genes used for DNRA after the introduction of lower influent NH4[+]:NO2[-] ratios. The high relative abundance of DNRA bacteria coinciding with sustained bioreactor performance indicates a mutualistic relationship between the anammox and DNRA bacteria. Understanding these interactions could support more robust bioreactor operation at variable nitrogen loading ratios.}, }
@article {pmid37637113, year = {2023}, author = {Huang, J and Li, J and Zhou, W and Cheng, Y and Li, J}, title = {Effect of different rice transplanting patterns on microbial community in water, sediment, and Procambarus clarkii intestine in rice-crayfish system.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1233815}, pmid = {37637113}, issn = {1664-302X}, abstract = {Although the microbial ecology of integrated rice-crayfish farming systems is receiving increasing attention with the expanding application area in China, the effects of rice transplanting patterns on the microbial community of water, sediment and Procambarus clarkii intestine in rice-crayfish system has yet to be determined. This study explored the microbial community present in water, sediment and intestine samples from three transplant patterns (rice crayfish with wide-narrow row transplanting, rice-crayfish with normal transplanting and pond-crayfish, abbreviated as RC-W, RC, and PC, respectively) using high-throughput sequencing. The results showed that the dominant microbial taxa from sediment, surrounding water, and intestine at phylum level were Proteobacteria, Chloroflexi, Cyanobacteria, Actinobacteria, Bacteroidetes. The patterns of rice transplanting had significant effects on microbial biodiversity and species composition in surrounding water. The OTUs community richness of water under RC group was significantly higher than that of PC group and RC-W group. The OTU relative abundance of top 10 operational taxonomic units had significantly different (p < 0.05) in the water samples from the three groups. The intestinal OTU community richness of Procambarus clarkii in the three groups was positively correlated with the community richness of water. The proximity between intestinal and water samples in PCA diagram indicated that their species composition was more similar. The results also showed that rice transplanting patterns can affect intestinal microbial biodiversity of Procambarus clarkii and the intestinal microbial biodiversity correlated with water bodies. Although the intestinal microbial diversity of crayfish in RC-W group was lower than that in RC group, the relative abundance of potential pathogenic bacteria, such as Vibrio, Aeromonas, in intestine of the crayfish in the RC-W group was significantly decreased under rice wide-narrow row transplanting model. Redundancy analysis revealed that environmental parameters, such as pH, DO, nitrate, which regulate the composition of microbial community structures. This study provides an understanding for microbial response to different rice transplanting pattern in rice-crayfish farming system.}, }
@article {pmid37635954, year = {2024}, author = {Romans-Casas, M and Feliu-Paradeda, L and Tedesco, M and Hamelers, HVM and Bañeras, L and Balaguer, MD and Puig, S and Dessì, P}, title = {Selective butyric acid production from CO2 and its upgrade to butanol in microbial electrosynthesis cells.}, journal = {Environmental science and ecotechnology}, volume = {17}, number = {}, pages = {100303}, pmid = {37635954}, issn = {2666-4984}, abstract = {Microbial electrosynthesis (MES) is a promising carbon utilization technology, but the low-value products (i.e., acetate or methane) and the high electric power demand hinder its industrial adoption. In this study, electrically efficient MES cells with a low ohmic resistance of 15.7 mΩ m[2] were operated galvanostatically in fed-batch mode, alternating periods of high CO2 and H2 availability. This promoted acetic acid and ethanol production, ultimately triggering selective (78% on a carbon basis) butyric acid production via chain elongation. An average production rate of 14.5 g m[-2] d[-1] was obtained at an applied current of 1.0 or 1.5 mA cm[-2], being Megasphaera sp. the key chain elongating player. Inoculating a second cell with the catholyte containing the enriched community resulted in butyric acid production at the same rate as the previous cell, but the lag phase was reduced by 82%. Furthermore, interrupting the CO2 feeding and setting a constant pH2 of 1.7-1.8 atm in the cathode compartment triggered solventogenic butanol production at a pH below 4.8. The efficient cell design resulted in average cell voltages of 2.6-2.8 V and a remarkably low electric energy requirement of 34.6 kWhel kg[-1] of butyric acid produced, despite coulombic efficiencies being restricted to 45% due to the cross-over of O2 and H2 through the membrane. In conclusion, this study revealed the optimal operating conditions to achieve energy-efficient butyric acid production from CO2 and suggested a strategy to further upgrade it to valuable butanol.}, }
@article {pmid37635262, year = {2023}, author = {Zhai, X and Castro-Mejía, JL and Gobbi, A and Aslampaloglou, A and Kot, W and Nielsen, DS and Deng, L}, title = {The impact of storage buffer and storage conditions on fecal samples for bacteriophage infectivity and metavirome analyses.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {193}, pmid = {37635262}, issn = {2049-2618}, mesh = {Humans ; *Bacteriophages/genetics ; DNA, Bacterial ; Feces ; Metagenome ; RNA ; }, abstract = {BACKGROUND: There is an increasing interest in investigating the human gut virome for its influence on the gut bacterial community and its putative influence on the trajectory towards health or disease. Most gut virome studies are based on sequencing of stored fecal samples. However, relatively little is known about how conventional storage buffers and storage conditions affect the infectivity of bacteriophages and influence the downstream metavirome sequencing.<br><br>RESULTS: We demonstrate that the infectivity and genome recovery rate of different spiked bacteriophages (T4, c2 and Phi X174) are variable and highly dependent on storage buffers. Regardless of the storage temperature and timespan, all tested phages immediately lost 100% (DNA/RNA Shield) or more than 90% (StayRNA and RNAlater) of their infectivity. Generally, in SM buffer at 4&#xa0;&#xb0;C phage infectivity was preserved for up to 30 days and phage DNA integrity was maintained for up to 100&#xa0;days. While in CANVAX, the most effective buffer, all spiked phage genomes were preserved for at least 100&#xa0;days. Prolonged storage time (500&#xa0;days) at -&#xa0;80&#xa0;&#xb0;C impacted viral diversity differently in the different buffers. Samples stored in CANVAX or DNA/RNA Shield buffer had the least shifts in metavirome composition, after prolonged storage, but they yielded more contigs classified as "uncharacterised". Moreover, in contrast to the SM buffer, these storage buffers yielded a higher fraction of bacterial DNA in metavirome-sequencing libraries. We demonstrated that the latter was due to inactivation of the DNases employed to remove extra-cellular DNA during virome extraction. The latter could be partly avoided by employing additional washing steps prior to virome extraction.<br><br>CONCLUSION: Fecal sample storage buffers and storage conditions (time and temperature) strongly influence bacteriophage infectivity and viral composition as determined by plaque assay and metavirome sequencing. The choice of buffer had a larger effect than storage temperature and storage time on the quality of the viral sequences and analyses. Based on these results, we recommend storage of fecal virome samples at in SM buffer at 4&#xa0;&#xb0;C for the isolation of viruses and at -&#xa0;80&#xa0;&#xb0;C for metagenomic applications if practically feasible (i.e., access to cold storage). For fecal samples stored in other buffers, samples should be cleared of these buffers before viral extraction and sequencing. Video Abstract.}, }
@article {pmid37635076, year = {2024}, author = {Barman, D and Dkhar, MS}, title = {Purification and characterization of moderately thermostable raw-starch digesting α-amylase from endophytic Streptomyces mobaraensis DB13 associated with Costus speciosus.}, journal = {The Journal of general and applied microbiology}, volume = {69}, number = {6}, pages = {293-300}, doi = {10.2323/jgam.2023.08.001}, pmid = {37635076}, issn = {1349-8037}, mesh = {*alpha-Amylases/metabolism/chemistry/isolation &amp; purification ; *Streptomyces/enzymology ; *Enzyme Stability ; *Starch/metabolism ; Hydrogen-Ion Concentration ; *Molecular Weight ; Kinetics ; *Temperature ; Endophytes/enzymology/metabolism/genetics ; Substrate Specificity ; Bacterial Proteins/metabolism/chemistry/isolation &amp; purification/genetics ; Electrophoresis, Polyacrylamide Gel ; }, abstract = {Endophytic actinobacteria are known to produce various enzymes with potential industrial applications. Alpha-amylase is an important class of industrial enzyme with a multi-dimensional utility. The present experiment was designed to characterize a moderately thermostable α-amylase producing endophytic Streptomyces mobaraensis DB13 isolated from Costus speciosus (J. Koenig) Sm. The enzyme was purified using 60% ammonium sulphate precipitation, dialysis, and Sephadex G-100 column chromatography. Based on 12% SDS-PAGE, the molecular weight of the purified α-amylase was estimated to be 55 kDa. The maximum α-amylase activity was achieved at pH 7.0, 50°C and it retained 80% of its activity at both pH 7.0 and 8.0 after incubation for 2 h. The α-mylase activity is strongly enhanced by Ca[2+], Mg[2+], and inhibited by Ba[2+]. The activity remains stable in the presence of Tween-80, SDS, PMSF, and Triton X-100; however, β-mercaptoethanol, EDTA, and H2O2 reduced the activity. The kinetic parameters Km and Vmax values for this α-amylase were calculated as 2.53 mM and 29.42 U/mL respectively. The α-amylase had the ability to digest various raw starches at a concentration of 10 mg/mL at pH 7.0, 50°C, where maize and rice are the preferred substrates. The digestion starts after 4 h of incubation, which reaches maximum after 48 h of incubation. These results suggest that S. mobaraensis DB13 is a potential source of moderately thermostable α-amylase enzyme, that effciently hydrolyzes raw starch. It suggesting that this α-amylase is a promising candidate to be use for industrial purposes.}, }
@article {pmid37633274, year = {2023}, author = {Pérez-Cobas, AE and Ginevra, C and Rusniok, C and Jarraud, S and Buchrieser, C}, title = {The respiratory tract microbiome, the pathogen load, and clinical interventions define severity of bacterial pneumonia.}, journal = {Cell reports. Medicine}, volume = {4}, number = {9}, pages = {101167}, pmid = {37633274}, issn = {2666-3791}, mesh = {Humans ; *Pneumonia, Bacterial/diagnosis ; Respiratory System ; *Coinfection ; Dysbiosis ; *Microbiota ; }, abstract = {Bacterial pneumonia is a considerable problem worldwide. Here, we follow the inter-kingdom respiratory tract microbiome (RTM) of a unique cohort of 38 hospitalized patients (n = 97 samples) with pneumonia caused by Legionella pneumophila. The RTM composition is characterized by diversity drops early in hospitalization and ecological species replacement. RTMs with the highest bacterial and fungal loads show low diversity and pathogen enrichment, suggesting high biomass as a biomarker for secondary and/or co-infections. The RTM structure is defined by a "commensal" cluster associated with a healthy RTM and a "pathogen" enriched one, suggesting that the cluster equilibrium drives the microbiome to recovery or dysbiosis. Legionella biomass correlates with disease severity and co-morbidities, while clinical interventions influence the RTM dynamics. Fungi, archaea, and protozoa seem to contribute to progress of pneumonia. Thus, the interplay of the RTM equilibrium, the pathogen load dynamics, and clinical interventions play a critical role in patient recovery.}, }
@article {pmid37633148, year = {2024}, author = {Guo, T and Wang, T and Chen, L and Zheng, B}, title = {Whole-grain highland barley premade biscuit prepared by hot-extrusion 3D printing: Printability and nutritional assessment.}, journal = {Food chemistry}, volume = {432}, number = {}, pages = {137226}, doi = {10.1016/j.foodchem.2023.137226}, pmid = {37633148}, issn = {1873-7072}, mesh = {*Nutrition Assessment ; *Hordeum ; Functional Food ; Corn Oil ; Printing, Three-Dimensional ; }, abstract = {In this study, to explore the possibility of applying whole-grain highland barley (HB) in functional food, HB premade biscuit was created by hot-extrusion 3D printing (HEP) for the first time, and its printability and nutritional functions were evaluated. The rheology results showed 20% (w/w) HB suspension with 9% corn oil addition had better printability due to the formation of a structure with higher elasticity and stronger resistance to deformation. Moreover, the obtained premade biscuit had lower predicted glycemic index (pGI) and starch digestibility. Meanwhile, in vivo experiment results showed it could affect the glycolipid metabolism, ameliorate the high fat diet (HFD)-induced metabolic disorders and maintain the balance of the gut microbial ecology. This could be attributed to the decrease in Firmicutes/Bacteroidetes ratio and the proliferation of propionate-producing probiotics, especially Veilonella, Weissella and Desulfovibrio. Overall, this study could provide basic data and innovative approaches to prepare nutritional whole-grain foods.}, }
@article {pmid37632540, year = {2023}, author = {Seward, J and Bräuer, S and Beckett, P and Roy-Léveillée, P and Emilson, E and Watmough, S and Basiliko, N}, title = {Recovery of Smelter-Impacted Peat and Sphagnum Moss: a Microbial Perspective.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2894-2903}, pmid = {37632540}, issn = {1432-184X}, mesh = {Ecosystem ; *Sphagnopsida ; Soil/chemistry ; *Metals, Heavy ; Ontario ; }, abstract = {Peatlands store approximately one-half of terrestrial soil carbon and one-tenth of non-glacial freshwater. Some of these important ecosystems are located near heavy metal emitting smelters. To improve the understanding of smelter impacts and potential recovery after initial pollution controls in the 1970s (roughly 50 years of potential recovery), we sampled peatlands along a distance gradient of 134 km from a smelter in Sudbury, Ontario, Canada, an area with over a century of nickel (Ni) and copper (Cu) mining activity. This work is aimed at evaluating potential shifts in bacterial and archaeal community structures in Sphagnum moss and its underlying peat within smelter-impacted poor fens. In peat, total Ni and Cu concentrations were higher (0.062-0.067 and 0.110-0.208 mg/g, respectively) at sites close to the smelter and exponentially dropped with distance from the smelter. This exponential decrease in Ni concentrations was also observed in Sphagnum. 16S rDNA amplicon sequencing showed that peat and Sphagnum moss host distinct microbiomes with peat accommodating a more diverse community structure. The microbiomes of Sphagnum were dominated by Proteobacteria (62.5%), followed by Acidobacteria (11.9%), with no observable trends with distance from the smelter. Dominance of Acidobacteria (32.4%) and Proteobacteria (29.6%) in peat was reported across all sites. No drift in taxonomy was seen across the distance gradient or from the reference sites, suggesting a potential microbiome recovery toward that of the reference peatlands microbiomes after decades of pollution controls. These results advance the understanding of peat and Sphagnum moss microbiomes, as well as depict the sensitivities and the resilience of peatland ecosystems.}, }
@article {pmid37630470, year = {2023}, author = {Won, S and Shin, C and Kang, HY}, title = {Potential Self-Attenuation of Arsenic by Indigenous Microorganisms in the Nakdong River.}, journal = {Microorganisms}, volume = {11}, number = {8}, pages = {}, pmid = {37630470}, issn = {2076-2607}, support = {NRF- 2020R1I1A3068585//National Research Foundation of Korea/ ; }, abstract = {The toxic element arsenic (As) has become the major focus of global research owing to its harmful effects on human health, resulting in the establishment of several guidelines to prevent As contamination. The widespread industrial use of As has led to its accumulation in the environment, increasing the necessity to develop effective remediation technologies. Among various treatments, such as chemical, physical, and biological treatments, used to remediate As-contaminated environments, biological methods are the most economical and eco-friendly. Microbial oxidation of arsenite (As(III)) to arsenate (As(V)) is a primary detoxification strategy for As remediation as it reduces As toxicity and alters its mobility in the environment. Here, we evaluated the self-detoxification potential of microcosms isolated from Nakdong River water by investigating the autotrophic and heterotrophic oxidation of As(III) to As(V). Experimental data revealed that As(III) was oxidized to As(V) during the autotrophic and heterotrophic growth of river water microcosms. However, the rate of oxidation was significantly higher under heterotrophic conditions because of the higher cell growth and density in an organic-matter-rich environment compared to that under autotrophic conditions without the addition of external organic matter. At an As(III) concentration > 5 mM, autotrophic As(III) oxidation remained incomplete, even after an extended incubation time. This inhibition can be attributed to the toxic effect of the high contaminant concentration on bacterial growth and the acidification of the growth medium with the oxidation of As(III) to As(V). Furthermore, we isolated representative pure cultures from both heterotrophic- and autotrophic-enriched cultures. The new isolates revealed new members of As(III)-oxidizing bacteria in the diversified bacterial community. This study highlights the natural process of As attenuation within river systems, showing that microcosms in river water can detoxify As under both organic-matter-rich and -deficient conditions. Additionally, we isolated the bacterial strains HTAs10 and ATAs5 from the microcosm which can be further investigated for potential use in As remediation systems. Our findings provide insights into the microbial ecology of As(III) oxidation in river ecosystems and provide a foundation for further investigations into the application of these bacteria for bioremediation.}, }
@article {pmid37624441, year = {2023}, author = {Pinheiro Alves de Souza, Y and Schloter, M and Weisser, W and Schulz, S}, title = {Deterministic Development of Soil Microbial Communities in Disturbed Soils Depends on Microbial Biomass of the Bioinoculum.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2882-2893}, pmid = {37624441}, issn = {1432-184X}, mesh = {Biomass ; *Soil ; Soil Microbiology ; Bacteria/genetics ; Archaea/genetics ; *Microbiota ; }, abstract = {Despite its enormous importance for ecosystem services, factors driving microbial recolonization of soils after disturbance are still poorly understood. Here, we compared the microbial recolonization patterns of a disturbed, autoclaved soil using different amounts of the original non-disturbed soil as inoculum. By using this approach, we manipulated microbial biomass, but did not change microbial diversity of the inoculum. We followed the development of a new soil microbiome after reinoculation over a period of 4 weeks using a molecular barcoding approach as well as qPCR. Focus was given on the assessment of bacteria and archaea. We could show that 1 week after inoculation in all inoculated treatments bacterial biomass exceeded the values from the original soil as a consequence of high dissolved organic carbon (DOC) concentrations in the disturbed soil resulting from the disturbance. This high biomass was persistent over the complete experimental period. In line with the high DOC concentrations, in the first 2 weeks of incubation, copiotrophic bacteria dominated the community, which derived from the inoculum used. Only in the disturbed control soils which did not receive a microbial inoculum, recolonization pattern differed. In contrast, archaeal biomass did not recover over the experimental period and recolonization was strongly triggered by amount of inoculated original soil added. Interestingly, the variability between replicates of the same inoculation density decreased with increasing biomass in the inoculum, indicating a deterministic development of soil microbiomes if higher numbers of cells are used for reinoculation.}, }
@article {pmid37624156, year = {2023}, author = {Cao, Y and Wang, R and Liu, Y and Li, Y and Jia, L and Yang, Q and Zeng, X and Li, X and Wang, Q and Wang, R and Riaz, L}, title = {Improved Calculations of Heavy Metal Toxicity Coefficients for Evaluating Potential Ecological Risk in Sediments Based on Seven Major Chinese Water Systems.}, journal = {Toxics}, volume = {11}, number = {8}, pages = {}, pmid = {37624156}, issn = {2305-6304}, support = {U1904205//Key Project of the National Natural Science Foundation of China-Henan Joint Fund/ ; NSFC 42277409//National Natural Science Foundation of China/ ; 22B180006//Educational Commission of the Henan Province of China/ ; 21A180014//Key Project of Natural Science of the Education Department of Henan Province of China/ ; 212102110322//Science and Technology Project of Henan Province/ ; }, abstract = {Several methods have been used to assess heavy metal contamination in sediments. However, an assessment that considers both composite heavy metal speciation and concentration is necessary to accurately study ecological risks. This study improved the potential ecological risk index method and calculated the toxicity coefficients of seven heavy metals: Arsenic (As), Cadmium (Cd), Chromium (Cr), Copper (Cu), Nickel (Ni), Lead (Pb), and Zinc (Zn). The newly calculated toxicity coefficients were validated by using previously published heavy metal distribution data of the Henan section of the Yellow River. The calculation procedure is based on the principle that the abundance of heavy metals in the environment and their bioavailable forms affect the toxicity of heavy metals. The toxicity coefficients for the seven heavy metals were calculated as follows: As = 10, Cd = 20, Cr = 5, Cu = 2, Ni = 5, Pb = 5, Zn = 1. Ecological risk assessment of the Henan section of the Yellow River using the improved toxicity coefficients revealed that the ecological risk of Cd and total heavy metals is higher than previous calculations, reaching the strength and moderate risk levels, respectively. The improved potential ecological risk index method is more sensitive to heavy metal pollution and thus provides a better indication of ecological risk. This is a necessary improvement to provide more accurate pollution assessments.}, }
@article {pmid37620628, year = {2023}, author = {Chen, X and Li, Q and Chen, D and Zhao, L and Xiao, C}, title = {Restoration Measures of Fencing after Tilling Guided Succession of Grassland Soil Microbial Community Structure to Natural Grassland in the Sanjiangyuan Agro-pasture Ecotone of the Qinghai-Tibetan Plateau.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2870-2881}, pmid = {37620628}, issn = {1432-184X}, support = {2019QZKK040104//the Second Tibetan Plateau Scientific Expedition and Research (STEP) Program/ ; 2021FY100705//the Special Project on National Science and Technology Basic Resources Investigation of China/ ; 31770501//the National Natural Science Foundation of China/ ; }, mesh = {*Soil/chemistry ; Grassland ; Tibet ; Soil Microbiology ; Plants ; *Microbiota ; }, abstract = {In the fragile Sanjiangyuan (SJY) agro-pasture ecotone of the Qinghai-Tibetan Plateau (QTP), planting and fencing have been used to alleviate grassland degradation and to provide high-quality grass seeds for the implementation of the project of "grain for green". The soil microbe is the major driving factor in maintaining plant productivity and soil nutrient cycling. However, few studies have explored the effects of planting and fencing on soil microorganisms in the SJY agro-pasture ecotone. We explored the effects of tilling (TG) and fencing after tilling (FTG) on soil microbial communities to reveal the effects of restoration measures on soil microbes and to provide a reference in assessing and improving ecosystem structure. The results showed that restoration measures increased soil microbial species diversity and significantly changed their community structure. We found, the microbial composition was more complex under FTG, and its fungal variability was higher and more similar to that of natural grassland. Additionally, restoration measures resulted in fungal co-occurrence network was more edges, higher density, larger diameter and more positive interactions. This was due to the management of the vegetation-soil microenvironment by FTG inducing a differentiation of microbial community structure. In summary, the implementation of FTG could change the microenvironment in the SJY agro-pasture ecotone, so that variation in the structure of microbial community tended toward that of natural grassland, and increased the stability of microbial co-occurrence network, which was more obvious in the fungal community. HIGHLIGHTS: • Restoration measures have changed the vegetation characteristics and soil microenvironment. • Fencing after tilling (FTG) has brought the microenvironment closer to natural grassland. • FTG significantly increased microbial unique ASVs. The number of fungal unique ASVs was similar to that of natural grassland. • FTG resulted in changes in microbial community structure towards natural grasslands and increased the stability of the microbial co-occurrence network, which was more apparent in the fungal community.}, }
@article {pmid37620398, year = {2023}, author = {De Micco, V and Amitrano, C and Mastroleo, F and Aronne, G and Battistelli, A and Carnero-Diaz, E and De Pascale, S and Detrell, G and Dussap, CG and Ganigué, R and Jakobsen, &#xd8;M and Poulet, L and Van Houdt, R and Verseux, C and Vlaeminck, SE and Willaert, R and Leys, N}, title = {Plant and microbial science and technology as cornerstones to Bioregenerative Life Support Systems in space.}, journal = {NPJ microgravity}, volume = {9}, number = {1}, pages = {69}, pmid = {37620398}, issn = {2373-8065}, abstract = {Long-term human space exploration missions require environmental control and closed Life Support Systems (LSS) capable of producing and recycling resources, thus fulfilling all the essential metabolic needs for human survival in harsh space environments, both during travel and on orbital/planetary stations. This will become increasingly necessary as missions reach farther away from Earth, thereby limiting the technical and economic feasibility of resupplying resources from Earth. Further incorporation of biological elements into state-of-the-art (mostly abiotic) LSS, leading to bioregenerative LSS (BLSS), is needed for additional resource recovery, food production, and waste treatment solutions, and to enable more self-sustainable missions to the Moon and Mars. There is a whole suite of functions crucial to sustain human presence in Low Earth Orbit (LEO) and successful settlement on Moon or Mars such as environmental control, air regeneration, waste management, water supply, food production, cabin/habitat pressurization, radiation protection, energy supply, and means for transportation, communication, and recreation. In this paper, we focus on air, water and food production, and waste management, and address some aspects of radiation protection and recreation. We briefly discuss existing knowledge, highlight open gaps, and propose possible future experiments in the short-, medium-, and long-term to achieve the targets of crewed space exploration also leading to possible benefits on Earth.}, }
@article {pmid37619629, year = {2023}, author = {Wang, SH and Yuan, SW and Che, FF and Wan, X and Wang, YF and Yang, DH and Yang, HJ and Zhu, D and Chen, P}, title = {Strong bacterial stochasticity and fast fungal turnover in Taihu Lake sediments, China.}, journal = {Environmental research}, volume = {237}, number = {Pt 2}, pages = {116954}, doi = {10.1016/j.envres.2023.116954}, pmid = {37619629}, issn = {1096-0953}, abstract = {Understanding the assembly and turnover of microbial communities is crucial for gaining insights into the diversity and functioning of lake ecosystems, a fundamental and central issue in microbial ecology. The ecosystem of Taihu Lake has been significantly jeopardized due to urbanization and industrialization. In this study, we examined the diversity, assembly, and turnover of bacterial and fungal communities in Taihu Lake sediment. The results revealed strong bacterial stochasticity and fast fungal turnover in the sediment. Significant heterogeneity was observed among all sediment samples in terms of environmental factors, especially ORP, TOC, and TN, as well as microbial community composition and alpha diversity. For instance, the fungal richness index exhibited an approximate 3-fold variation. Among the environmental factors, TOC, TN, and pH had a more pronounced influence on the bacterial community composition compared to the fungal community composition. Interestingly, species replacement played a dominant role in microbial beta diversity, with fungi exhibiting a stronger pattern. In contrast, stochastic processes governed the community assembly of both bacteria and fungi, but were more pronounced for bacteria (R[2] = 0.7 vs. 0.5). These findings deepen the understanding of microbial assembly and turnover in sediments under environmental stress and provide essential insights for maintaining the multifunctionality of lake ecosystems.}, }
@article {pmid37615431, year = {2023}, author = {Armour, CR and Sovacool, KL and Close, WL and Topçuoğlu, BD and Wiens, J and Schloss, PD}, title = {Machine learning classification by fitting amplicon sequences to existing OTUs.}, journal = {mSphere}, volume = {8}, number = {5}, pages = {e0033623}, pmid = {37615431}, issn = {2379-5042}, support = {R01 CA215574/CA/NCI NIH HHS/United States ; R01CA215574/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Algorithms ; *Microbiota/genetics ; }, abstract = {The ability to use 16S rRNA gene sequence data to train machine learning classification models offers the opportunity to diagnose patients based on the composition of their microbiome. In some applications, the taxonomic resolution that provides the best models may require the use of de novo operational taxonomic units (OTUs) whose composition changes when new data are added. We previously developed a new reference-based approach, OptiFit, that fits new sequence data to existing de novo OTUs without changing the composition of the original OTUs. While OptiFit produces OTUs that are as high quality as de novo OTUs, it is unclear whether this method for fitting new sequence data into existing OTUs will impact the performance of classification models relative to models trained and tested only using de novo OTUs. We used OptiFit to cluster sequences into existing OTUs and evaluated model performance in classifying a dataset containing samples from patients with and without colonic screen relevant neoplasia (SRN). We compared the performance of this model to standard methods including de novo and database-reference-based clustering. We found that using OptiFit performed as well or better in classifying SRNs. OptiFit can streamline the process of classifying new samples by avoiding the need to retrain models using reclustered sequences. IMPORTANCE There is great potential for using microbiome data to aid in diagnosis. A challenge with de novo operational taxonomic unit (OTU)-based classification models is that 16S rRNA gene sequences are often assigned to OTUs based on similarity to other sequences in the dataset. If data are generated from new patients, the old and new sequences must be reclustered to OTUs and the classification model retrained. Yet there is a desire to have a single, validated model that can be widely deployed. To overcome this obstacle, we applied the OptiFit clustering algorithm to fit new sequence data to existing OTUs allowing for reuse of the model. A random forest model implemented using OptiFit performed as well as the traditional reassign and retrain approach. This result shows that it is possible to train and apply machine learning models based on OTU relative abundance data that do not require retraining or the use of a reference database.}, }
@article {pmid37614461, year = {2023}, author = {Kandeel, SA and Megahed, AA}, title = {Editorial: Infectious diseases, microbial ecology, and antimicrobial resistance dynamics in food animals.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1266980}, pmid = {37614461}, issn = {2297-1769}, }
@article {pmid37610498, year = {2023}, author = {Wei, N and Tan, J}, title = {Environment and Host Genetics Influence the Biogeography of Plant Microbiome Structure.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2858-2868}, pmid = {37610498}, issn = {1432-184X}, support = {030869//Holden Arboretum/ ; LEQSF(2023-26)-RD-A-14//Louisiana Board of Regents/ ; 10635//Gordon and Betty Moore Foundation/ ; }, mesh = {*Microbiota/genetics ; Bacteria/genetics ; *Araceae/microbiology ; }, abstract = {To understand how microbiota influence plant populations in nature, it is important to examine the biogeographic distribution of plant-associated microbiomes and the underlying mechanisms. However, we currently lack a fundamental understanding of the biogeography of plant microbiomes across populations and the environmental and host genetic factors that shape their distribution. Leveraging the broad distribution and extensive genetic variation in duckweeds (the Lemna species complex), we identified key factors that governed plant microbiome diversity and compositional variation geographically. In line with the microbial biogeography of free-living microbiomes, we observed higher bacterial richness in temperate regions relative to lower latitudes in duckweed microbiomes (with 10% higher in temperate populations). Our analyses revealed that higher temperature and sodium concentration in aquatic environments showed a negative impact on duckweed bacterial richness, whereas temperature, precipitation, pH, and concentrations of phosphorus and calcium, along with duckweed genetic variation, influenced the biogeographic variation of duckweed bacterial community composition. Analyses of plant microbiome assembly processes further revealed that niche-based selection played an important role (26%) in driving the biogeographic variation of duckweed bacterial communities, alongside the contributions of dispersal limitation (33%) and drift (39%). These findings add significantly to our understanding of host-associated microbial biogeography and provide important insights for predicting plant microbiome vulnerability and resilience under changing climates and intensifying anthropogenic activities.}, }
@article {pmid37608162, year = {2023}, author = {Fecchio, A and Bell, JA and Williams, EJ and Dispoto, JH and Weckstein, JD and de Angeli Dutra, D}, title = {Co-infection with Leucocytozoon and Other Haemosporidian Parasites Increases with Latitude and Altitude in New World Bird Communities.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2838-2846}, pmid = {37608162}, issn = {1432-184X}, support = {DEB-1503804//National Science Foundation/ ; }, mesh = {Animals ; *Parasites ; *Coinfection/veterinary ; Bayes Theorem ; Altitude ; *Bird Diseases/epidemiology/parasitology ; Birds ; *Haemosporida ; Prevalence ; }, abstract = {Establishing how environmental gradients and host ecology drive spatial variation in infection rates and diversity of pathogenic organisms is one of the central goals in disease ecology. Here, we identified the predictors of concomitant infection and lineage richness of blood parasites in New Word bird communities. Our multi-level Bayesian models revealed that higher latitudes and elevations played a determinant role in increasing the probability of a bird being co-infected with Leucocytozoon and other haemosporidian parasites. The heterogeneity in both single and co-infection rates was similarly driven by host attributes and temperature, with higher probabilities of infection in heavier migratory host species and at cooler localities. Latitude, elevation, host body mass, migratory behavior, and climate were also predictors of Leucocytozoon lineage richness across the New World avian communities, with decreasing parasite richness at higher elevations, rainy and warmer localities, and in heavier and resident host species. Increased parasite richness was found farther from the equator, confirming a reverse Latitudinal Diversity Gradient pattern for this parasite group. The increased rates of Leucocytozoon co-infection and lineage richness with increased latitude are in opposition with the pervasive assumption that pathogen infection rates and diversity are higher in tropical host communities.}, }
@article {pmid37607924, year = {2023}, author = {Li, X and Chen, D and Carrión, VJ and Revillini, D and Yin, S and Dong, Y and Zhang, T and Wang, X and Delgado-Baquerizo, M}, title = {Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5090}, pmid = {37607924}, issn = {2041-1723}, mesh = {*Fusariosis ; *Microbiota ; *Fusarium ; Metagenome ; Hydrogen-Ion Concentration ; }, abstract = {Soil-borne pathogens pose a major threat to food production worldwide, particularly under global change and with growing populations. Yet, we still know very little about how the soil microbiome regulates the abundance of soil pathogens and their impact on plant health. Here we combined field surveys with experiments to investigate the relationships of soil properties and the structure and function of the soil microbiome with contrasting plant health outcomes. We find that soil acidification largely impacts bacterial communities and reduces the capacity of soils to combat fungal pathogens. In vitro assays with microbiomes from acidified soils further highlight a declined ability to suppress Fusarium, a globally important plant pathogen. Similarly, when we inoculate healthy plants with an acidified soil microbiome, we show a greatly reduced capacity to prevent pathogen invasion. Finally, metagenome sequencing of the soil microbiome and untargeted metabolomics reveals a down regulation of genes associated with the synthesis of sulfur compounds and reduction of key traits related to sulfur metabolism in acidic soils. Our findings suggest that changes in the soil microbiome and disruption of specific microbial processes induced by soil acidification can play a critical role for plant health.}, }
@article {pmid37607131, year = {2023}, author = {Klapper, FA and Kiel, C and Bellstedt, P and Vyverman, W and Pohnert, G}, title = {Structure Elucidation of the First Sex-Inducing Pheromone of a Diatom.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {62}, number = {43}, pages = {e202307165}, doi = {10.1002/anie.202307165}, pmid = {37607131}, issn = {1521-3773}, support = {FWO G001521N, BOF/GOA No. 01G01715//European Marine Biological Resource Centre Belgium/ ; Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Diatoms are abundant unicellular microalgae, responsible for ≈20 % of global photosynthetic CO2 fixation. Nevertheless, we know little about fundamental aspects of their biology, such as their sexual reproduction. Pheromone-mediated chemical communication is crucial for successful mating. An attraction pheromone was identified in the diatom Seminavis robusta, but metabolites priming cells for sex and synchronizing search and mating behavior remained elusive. These sex-inducing pheromones (SIP) induce cell cycle arrest and trigger the production of the attraction pheromone. Here we describe the challenging structure elucidation of an S. robusta SIP. Guided by metabolomics, a candidate metabolite was identified and elucidated by labeling experiments, NMR, ESI MS[n] analyses, and chemical transformations. The use of negative ion mode MS was essential to decipher the unprecedented hydroxyproline and β-sulfated aspartate-containing cyclic heptapeptide that acts in femtomolar concentrations.}, }
@article {pmid37606945, year = {2023}, author = {Ricks, KD and Ricks, NJ and Yannarell, AC}, title = {Patterns of Plant Salinity Adaptation Depend on Interactions with Soil Microbes.}, journal = {The American naturalist}, volume = {202}, number = {3}, pages = {276-287}, doi = {10.1086/725393}, pmid = {37606945}, issn = {1537-5323}, mesh = {Humans ; *Salinity ; Acclimatization ; *Infertility ; Phenotype ; Soil ; }, abstract = {AbstractAs plant-microbe interactions are both ubiquitous and critical in shaping plant fitness, patterns of plant adaptation to their local environment may be influenced by these interactions. Identifying the contribution of soil microbes to plant adaptation may provide insight into the evolution of plant traits and their microbial symbioses. To this end, we assessed the contribution of soil microbes to plant salinity adaptation by growing 10 populations of Bromus tectorum, collected from habitats differing in their salinity, in the greenhouse under either high-salinity or nonsaline conditions and with or without soil microbial partners. Across two live soil inoculum treatments, we found evidence for adaptation of these populations to their home salinity environment. However, when grown in sterile soils, plants were slightly maladapted to their home salinity environment. As plants were on average more fit in sterile soils, pathogenic microbes may have been significant drivers of plant fitness herein. Consequently, we hypothesized that the plant fitness advantage in their home salinity may have been due to increased plant resistance to pathogenic attack in those salinity environments. Our results highlight that plant-microbe interactions may partially mediate patterns of plant adaptation as well as be important selective agents in plant evolution.}, }
@article {pmid37606696, year = {2023}, author = {Theodorescu, M and Bucur, R and Bulzu, PA and Faur, L and Levei, EA and Mirea, IC and Cadar, O and Ferreira, RL and Souza-Silva, M and Moldovan, OT}, title = {Environmental Drivers of the Moonmilk Microbiome Diversity in Some Temperate and Tropical Caves.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2847-2857}, pmid = {37606696}, issn = {1432-184X}, mesh = {*Caves/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota ; Proteobacteria/genetics ; }, abstract = {Moonmilk is a cave deposit that was used for medical and cosmetic purposes and has lately raised interest for its antimicrobial potential. We studied five moonmilk samples from four caves with different microclimatic conditions, two temperate in north-western and northern Romania (Ferice, Fața Apei, and Izvorul Tăușoarelor caves) and one tropical in Minas Gerais, Brazil (Nestor Cave). The physicochemical and mineralogical analyses confirmed the presence of calcite and dolomite as the main phase in the moonmilk. A 16S rRNA gene-based metabarcoding approach showed the most abundant bacteria phyla Proteobacteria, GAL15, Actinobacteriota, and Acidobacteriota. The investigated caves differed in the dominant orders of bacteria, with the highest distance between the Romanian and Nestor Cave samples. Climate and, implicitly, the soil microbiome can be responsible for some differences we found between all the samples. However, other factors can be involved in shaping the moonmilk microbiome, as differences were found between samples in the same cave (Ferice). In our five moonmilk samples, 1 phylum, 70 orders (~ 36%), and 252 genera (~ 47%) were unclassified, which hints at the great potential of cave microorganisms for future uses.}, }
@article {pmid37604894, year = {2023}, author = {Utzeri, VJ and Cilli, E and Fontani, F and Zoboli, D and Orsini, M and Ribani, A and Latorre, A and Lissovsky, AA and Pillola, GL and Bovo, S and Gruppioni, G and Luiselli, D and Fontanesi, L}, title = {Ancient DNA re-opens the question of the phylogenetic position of the Sardinian pika Prolagus sardus (Wagner, 1829), an extinct lagomorph.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13635}, pmid = {37604894}, issn = {2045-2322}, mesh = {Animals ; *DNA, Ancient ; Phylogeny ; *Lagomorpha ; Biological Evolution ; Archaeology ; }, abstract = {Palaeogenomics is contributing to refine our understanding of many major evolutionary events at an unprecedented resolution, with relevant impacts in several fields, including phylogenetics of extinct species. Few extant and extinct animal species from Mediterranean regions have been characterised at the DNA level thus far. The Sardinian pika, Prolagus sardus (Wagner, 1829), was an iconic lagomorph species that populated Sardinia and Corsica and became extinct during the Holocene. There is a certain scientific debate on the phylogenetic assignment of the extinct genus Prolagus to the family Ochotonidae (one of the only two extant families of the order Lagomorpha) or to a separated family Prolagidae, or to the subfamily Prolaginae within the family Ochotonidae. In this study, we successfully reconstructed a portion of the mitogenome of a Sardinian pika dated to the Neolithic period and recovered from the Cabaddaris cave, an archaeological site in Sardinia. Our calibrated phylogeny may support the hypothesis that the genus Prolagus is an independent sister group to the family Ochotonidae that diverged from the Ochotona genus lineage about 30 million years ago. These results may contribute to refine the phylogenetic interpretation of the morphological peculiarities of the Prolagus genus already described by palaeontological studies.}, }
@article {pmid37604501, year = {2023}, author = {Kuzyk, SB and Messner, K and Plouffe, J and Ma, X and Wiens, K and Yurkov, V}, title = {Diverse aerobic anoxygenic phototrophs synthesize bacteriochlorophyll in oligotrophic rather than copiotrophic conditions, suggesting ecological niche.}, journal = {Environmental microbiology}, volume = {25}, number = {11}, pages = {2653-2665}, doi = {10.1111/1462-2920.16482}, pmid = {37604501}, issn = {1462-2920}, mesh = {Humans ; *Bacteriochlorophylls ; Phylogeny ; Bacteria, Aerobic/genetics ; Ecosystem ; Photosynthesis ; *Alphaproteobacteria ; }, abstract = {While investigating aerobic anoxygenic phototrophs (AAP) from Lake Winnipeg's bacterial community, over 500 isolates were obtained. Relatives of 20 different species were examined simultaneously, identifying conditions for optimal growth or pigment production to determine features that may unify this group of phototrophs. All were distributed among assorted α-Proteobacterial families including Erythrobacteraceae, Sphingomonadaceae, Sphingosinicellaceae, Acetobacteraceae, Methylobacteriaceae, and Rhodobacteraceae. Major phenotypic characteristics matched phylogenetic association, including pigmentation, morphology, metal transformations, tolerances, lipid configurations, and enzyme activities, which distinctly separated each taxonomic family. While varying pH and temperature had a limited independent impact on pigment production, bacteriochlorophyll synthesis was distinctly promoted under low nutrient conditions, whereas copiotrophy repressed its production but enhanced carotenoid yield. New AAP diversity was also reported by revealing strains related to non-phototrophic Rubellimicrobium and Sphingorhabdus, as well as spread throughout Roseomonas, Sphingomonas, and Methylobacterium/Methylorubrum, which previously only had a few known photosynthetic members. This study exemplified the overwhelming diversity of AAP in a single aquatic environment, confirming cultivation continues to be of importance in microbial ecology to discover functionality in both new and previously reported cohorts of bacteria as specific laboratory conditions were required to promote aerobic bacteriochlorophyll production.}, }
@article {pmid37603734, year = {2023}, author = {Lee, H and Bloxham, B and Gore, J}, title = {Resource competition can explain simplicity in microbial community assembly.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {35}, pages = {e2212113120}, pmid = {37603734}, issn = {1091-6490}, mesh = {*Ecology ; Laboratories ; *Microbiota ; }, abstract = {Predicting the composition and diversity of communities is a central goal in ecology. While community assembly is considered hard to predict, laboratory microcosms often follow a simple assembly rule based on the outcome of pairwise competitions. This assembly rule predicts that a species that is excluded by another species in pairwise competition cannot survive in a multispecies community with that species. Despite the empirical success of this bottom-up prediction, its mechanistic origin has remained elusive. In this study, we elucidate how this simple pattern in community assembly can emerge from resource competition. Our geometric analysis of a consumer-resource model shows that trio community assembly is always predictable from pairwise outcomes when one species grows faster than another species on every resource. We also identify all possible trio assembly outcomes under three resources and find that only two outcomes violate the assembly rule. Simulations demonstrate that pairwise competitions accurately predict trio assembly with up to 100 resources and the assembly of larger communities containing up to twelve species. We then further demonstrate accurate quantitative prediction of community composition using the harmonic mean of pairwise fractions. Finally, we show that cross-feeding between species does not decrease assembly rule prediction accuracy. Our findings highlight that simple community assembly can emerge even in ecosystems with complex underlying dynamics.}, }
@article {pmid37601377, year = {2023}, author = {Flocco, CG and Methner, A and Burkart, F and Geppert, A and Overmann, J}, title = {Touching the (almost) untouchable: a minimally invasive workflow for microbiological and biomolecular analyses of cultural heritage objects.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1197837}, pmid = {37601377}, issn = {1664-302X}, abstract = {Microbiological and biomolecular approaches to cultural heritage research have expanded the established research horizon from the prevalent focus on the cultural objects' conservation and human health protection to the relatively recent applications to provenance inquiry and assessment of environmental impacts in a global context of a changing climate. Standard microbiology and molecular biology methods developed for other materials, specimens, and contexts could, in principle, be applied to cultural heritage research. However, given certain characteristics common to several heritage objects-such as uniqueness, fragility, high value, and restricted access, tailored approaches are required. In addition, samples of heritage objects may yield low microbial biomass, rendering them highly susceptible to cross-contamination. Therefore, dedicated methodology addressing these limitations and operational hurdles is needed. Here, we review the main experimental challenges and propose a standardized workflow to study the microbiome of cultural heritage objects, illustrated by the exploration of bacterial taxa. The methodology was developed targeting the challenging side of the spectrum of cultural heritage objects, such as the delicate written record, while retaining flexibility to adapt and/or upscale it to heritage artifacts of a more robust constitution or larger dimensions. We hope this tailored review and workflow will facilitate the interdisciplinary inquiry and interactions among the cultural heritage research community.}, }
@article {pmid37597041, year = {2023}, author = {Cleary, DFR and de Voogd, NJ and Stuij, TM and Swierts, T and Oliveira, V and Polónia, ARM and Louvado, A and Gomes, NCM and Coelho, FJRC}, title = {A Study of Sponge Symbionts from Different Light Habitats.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2819-2837}, pmid = {37597041}, issn = {1432-184X}, mesh = {Animals ; Biodiversity ; Phylogeny ; Bacteria/genetics ; Seawater/microbiology ; *Microbiota ; Water ; *Porifera ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The amount of available light plays a key role in the growth and development of microbial communities. In the present study, we tested to what extent sponge-associated prokaryotic communities differed between specimens of the sponge species Cinachyrella kuekenthali and Xestospongia muta collected in dimly lit (caves and at greater depths) versus illuminated (shallow water) habitats. In addition to this, we also collected samples of water, sediment, and another species of Cinachyrella, C. alloclada. Overall, the biotope (sponge host species, sediment, and seawater) proved the major driver of variation in prokaryotic community composition. The light habitat, however, also proved a predictor of compositional variation in prokaryotic communities of both C. kuekenthali and X. muta. We used an exploratory technique based on machine learning to identify features (classes, orders, and OTUs), which distinguished X. muta specimens sampled in dimly lit versus illuminated habitat. We found that the classes Alphaproteobacteria and Rhodothermia and orders Puniceispirillales, Rhodospirillales, Rhodobacterales, and Thalassobaculales were associated with specimens from illuminated, i.e., shallow water habitat, while the classes Dehalococcoidia, Spirochaetia, Entotheonellia, Nitrospiria, Schekmanbacteria, and Poribacteria, and orders Sneathiellales and Actinomarinales were associated with specimens sampled from dimly lit habitat. There was, however, considerable variation within the different light habitats highlighting the importance of other factors in structuring sponge-associated bacterial communities.}, }
@article {pmid37594520, year = {2023}, author = {Martínez, LT and Marchant, M and Díaz, RTA and Arrojo, M&#xc1; and Muñoz, P}, title = {Benthic Foraminifera as Pollution Biomarkers: a Morphological Approach.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2802-2818}, pmid = {37594520}, issn = {1432-184X}, support = {1130511//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; 170124//Fondo de Equipamiento Cient&#xed;fico y Tecnol&#xf3;gico/ ; }, mesh = {*Water Pollutants, Chemical/analysis ; Geologic Sediments/chemistry ; *Foraminifera/chemistry ; Environmental Monitoring/methods ; *Metals, Heavy/toxicity/analysis ; Biomarkers ; }, abstract = {Coastal areas are often intervened by anthropic activities, which increase the contamination of toxic agents such as heavy metals. This causes adverse morphological effects on benthic microorganisms, such as foraminifera. This group is one of the most susceptible to environmental deterioration, so they can be used as pollution biomarkers by identifying shell abnormalities. Therefore, 28 sediment samples from northern Chile were analyzed, calculating the Abnormality Index-FAI and its spatio-temporal distributions in benthic foraminifera, as well as the minimum and maximum abnormality percentages and their relationship with heavy metal concentrations, using a generalized non-linear model and a principal component analysis. The results indicated a proportion of abnormal shells within the ranges described for polluted areas conditions, revealing environmental stress conditions. This reflected a change in the environmental conditions in the most recent sediments of the bay. The highest FAI values were observed to the southwest of the bay, caused by the local current system. The species Bolivina seminuda, Buliminella elegantissima, and Epistominella exigua presented a greater number of deformities, allowing them to be used as contamination biomarkers. A significant correlation was found between Ti, Mn, Ni, Va, and Ba with decreased chamber sizes, wrong coiling, scars, and number of abnormality types. This suggests the effect of the particular geochemical conditions of the area on the heavy metals that cause toxic effects on foraminifera. These analyses are an efficient tool for identifying the effects of environmental stress before they occur in higher organisms, mitigating the environmental impact on marine biodiversity.}, }
@article {pmid37594170, year = {2023}, author = {Hambleton, EA}, title = {How corals get their nutrients.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {37594170}, issn = {2050-084X}, mesh = {Animals ; *Nutrients ; *Anthozoa ; Cell Wall ; }, abstract = {Algae living inside corals provide sugars for their host by digesting their own cell walls.}, }
@article {pmid37590550, year = {2022}, author = {de Almeida, OGG and De Martinis, ECP}, title = {Multitargeted Analyses are Instrumental for Microbial Ecology Studies.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {187}, pages = {}, doi = {10.3791/64789}, pmid = {37590550}, issn = {1940-087X}, }
@article {pmid37586176, year = {2023}, author = {Bai, X and Dinkla, IJT and Muyzer, G}, title = {Shedding light on the total and active core microbiomes in slow sand filters for drinking water production.}, journal = {Water research}, volume = {243}, number = {}, pages = {120404}, doi = {10.1016/j.watres.2023.120404}, pmid = {37586176}, issn = {1879-2448}, mesh = {Humans ; *Drinking Water ; Filtration/methods ; *Water Purification/methods ; *Microbiota ; Bacteria/genetics ; Silicon Dioxide/chemistry ; }, abstract = {Slow sand filters (SSF) are widely used in the production of drinking water as a last barrier in the removal of pathogens. This removal mainly depends on the 'Schmutzdecke', a biofilm-like layer on the surface of the sand bed. Most previous studies focused on the total community as revealed by DNA analysis rather than on the active community, which may lead to an incorrect understanding of the SSF ecology. In the current study, we determined and compared the DNA- (total) and RNA-displayed (active) communities in the Schmutzdecke layer from 10 full-scale slow sand filters and further explored the SSF core microbiome in terms of both presence (DNA) and activity (RNA). Discrepancies were observed between the total and the active community, although there was a consistent grouping in the PCoA analysis. The DNA-displayed community may be somewhat inflated, while the RNA-displayed community could reveal low abundance (or rare) but active community members. The overall results imply that both DNA (presence) and RNA (activity) data should be considered to prevent the underestimation of organisms of functional importance but lower abundance. Microbial communities of studied mature Schmutzdecke were shaped by the influent water. Nevertheless, a core microbiome was shared by the mature Schmutzdeckes from independent filters, representing the dominant and consistent microbial community composition in slow sand filters. In the DNA samples, a total of 33 VSC families ('very strict core', with a relative abundance >0.1% and 100% prevalence) were observed across all filters. Among the RNA samples, there were 18 VSC families, including 16 families that overlapped with the DNA VSC families and 2 unique RNA VSC families. The core microbial community structure was influenced by the operational parameters, including the Schmutzdecke age and the sand size, and was less influenced by water flow. In addition, indicator organisms ('biomarkers') for the Schmutzdecke age, which show the longest duration that SSF can maintain a good operation, were observed in our study. The abundant presence of bacteria belonging to bacteriap25 and Caldilineaceae was associated with older Schmutzdeckes, revealing longer periods of stable operation performance of the filter, while the high abundance of bacteria belonging to Bdellovibrionaceae and Bryobacteraceae related to short periods of stable operation performance.}, }
@article {pmid37579703, year = {2023}, author = {Li, Z and Wang, J and Fan, J and Yue, H and Zhang, X}, title = {Marine toxin domoic acid alters protistan community structure and assembly process in sediments.}, journal = {Marine environmental research}, volume = {191}, number = {}, pages = {106131}, doi = {10.1016/j.marenvres.2023.106131}, pmid = {37579703}, issn = {1879-0291}, mesh = {*Marine Toxins ; Kainic Acid/toxicity ; Eukaryota ; *Microbiota ; }, abstract = {Domoic acid (DA)-producing algal blooms have been the issue of worldwide concerns in recent decades, but there has never been any attempt to investigate the effects of DA on microbial ecology in marine environments. Protists are considered to be key regulators of microbial activity, community structure and evolution, we therefore explore the effect of DA on the ecology of protists via metagenome in this work. The results indicate that trace amounts of DA can act as a stressor to alter alpha and beta diversity of protistan community. Among trophic functional groups, consumers and phototrophs are negative responders of DA, implying DA is potentially capable of functional-level effects in the ocean. Moreover, microecological theory reveals that induction of DA increases the role of deterministic processes in microbial community assembly, thus altering the biotic relationships and successional processes in symbiotic patterns. Finally, we demonstrate that the mechanism by which DA shapes protistan ecological network is by acting on phototrophs, which triggers cascading effects in networks and eventually leading to shifts in ecological succession of protists. Overall, our results present the first perspective regarding the effects of DA on marine microbial ecology, which will supplement timely information on the ecological impacts of DA in the ocean.}, }
@article {pmid37573698, year = {2023}, author = {Song, Y and Zhang, S and Lu, J and Duan, R and Chen, H and Ma, Y and Si, T and Luo, M}, title = {Reed restoration decreased nutrients in wetlands with dredged sediments: Microbial community assembly and function in rhizosphere.}, journal = {Journal of environmental management}, volume = {344}, number = {}, pages = {118700}, doi = {10.1016/j.jenvman.2023.118700}, pmid = {37573698}, issn = {1095-8630}, mesh = {*Rhizosphere ; Wetlands ; Bacteria ; Archaea ; *Microbiota ; Plants ; Nutrients ; Geologic Sediments/chemistry ; }, abstract = {Using dredged sediments as substrate for aquatic plants is a low-cost and ecological friendly way for in situ aquatic ecological restoration. However, the limited information available about how aquatic plant restoration affects the microbial ecology and nutrients in dredged sediments. In this study, nutrient contents, enzyme activities, and bacterial and archaeal communities in vertical sediment layers were determined in bulk and reed zones of wetlands constructed with dredged sediments in west Lake Taihu for three years. Reed restoration significantly decreased total nitrogen, total phosphorus, and organic carbon contents and increased alkaline phosphatase, urease, and sucrase activities compared to bulk area. Bacterial communities in vertical sediment layers had higher similarity in reed zone in comparison to bulk zone, and many bacterial and archaeal genera were only detected in reed rhizosphere zones. Compared with the bulk zone, the reed restoration area has a higher abundance of phylum Actinobacteriota, Hydrothermarchaeota, and class α-proteobacteria. The assembly process of the bacterial and archaeal communities was primarily shaped by dispersal limitation (67.03% and 32.97%, respectively), and stochastic processes were enhanced in the reed recovery area. Network analysis show that there were more complicated interactions among bacteria and archaea and low-abundance taxa were crucial in maintaining the microbial community stability in rhizosphere of reed zone. PICRUST2 analysis demonstrate that reed restoration promotes metabolic pathways related to C and N cycle in dredged sediments. These data highlight that using dredged sediments as substrates for aquatic plants can transform waste material into a valuable resource, enhancing the benefits to the environment.}, }
@article {pmid37567875, year = {2023}, author = {Molbert, N and Ghanavi, HR and Johansson, T and Mostadius, M and Hansson, MC}, title = {An evaluation of DNA extraction methods on historical and roadkill mammalian specimen.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13080}, pmid = {37567875}, issn = {2045-2322}, mesh = {Animals ; *Chloroform ; *DNA/genetics ; Phenol ; Phenols ; Mammals/genetics ; Silicon Dioxide ; }, abstract = {Guidelines identifying appropriate DNA extraction methods for both museum and modern biological samples are scarce or non-existent for mammalian species. Yet, obtaining large-scale genetic material collections are vital for conservation and management purposes. In this study, we evaluated five protocols making use of either spin-column, organic solvents, or magnetic bead-based methods for DNA extraction on skin samples from both modern, traffic-killed (n = 10) and museum (n = 10) samples of European hedgehogs, Ericaneus europaeus. We showed that phenol-chloroform or silica column (NucleoSpin Tissue) protocols yielded the highest amount of DNA with satisfactory purity compared with magnetic bead-based protocols, especially for museum samples. Furthermore, extractions using the silica column protocol appeared to produce longer DNA fragments on average than the other methods tested. Our investigation demonstrates that both commercial extraction kits and phenol-chloroform protocol retrieve acceptable DNA concentrations for downstream processes, from degraded remnants of traffic-killed and museum samples of mammalian specimens. Although all the tested methods could be applied depending on the research questions and laboratory conditions, commercial extraction kits may be preferred due to their effectiveness, safety and the higher quality of the DNA extractions.}, }
@article {pmid37567306, year = {2023}, author = {Schroll, M and Liu, L and Einzmann, T and Keppler, F and Grossart, HP}, title = {Methane accumulation and its potential precursor compounds in the oxic surface water layer of two contrasting stratified lakes.}, journal = {The Science of the total environment}, volume = {903}, number = {}, pages = {166205}, doi = {10.1016/j.scitotenv.2023.166205}, pmid = {37567306}, issn = {1879-1026}, abstract = {Methane (CH4) supersaturation in oxygenated waters is a widespread phenomenon despite the traditional perception of strict anoxic methanogenesis. This notion has recently been challenged by successive findings of processes and mechanisms that produce CH4 in oxic environments. While some of the processes contributing to the vertical accumulation of CH4 in the oxygenated upper water layers of freshwater lakes have been identified, temporal variations as well as drivers are still poorly understood. In this study, we investigated the accumulation of CH4 in oxic water layers of two contrasting lakes in Germany: Lake Willersinnweiher (shallow, monomictic, eutrophic) and Lake Stechlin (deep, dimictic, eutrophic) from 2019 to 2020. The dynamics of isotopic values of CH4 and the role of potential precursor compounds of oxic CH4 production were explored. During the study period, persistent strong CH4 supersaturation (relative to air) was observed in the surface waters, mostly concentrated around the thermocline. The magnitude of vertical CH4 accumulation strongly varied over season and was generally more pronounced in shallow Lake Willersinnweiher. In both lakes, increases in CH4 concentrations from the surface to the thermocline mostly coincided with an enrichment in [13]C-CH4 and [2]H-CH4, indicating a complex interaction of multiple processes such as CH4 oxidation, CH4 transport from littoral sediments and oxic CH4 production, sustaining and controlling this CH4 supersaturation. Furthermore, incubation experiments with [13]C- and [2]H-labelled methylated P-, N- and C- compounds clearly showed that methylphosphonate, methylamine and methionine acted as potent precursors of accumulating CH4 and at least partly sustained CH4 supersaturation. This highlights the need to better understand the mechanisms underlying CH4 accumulation by focusing on production and transport pathways of CH4 and its precursor compounds, e.g., produced via phytoplankton. Such knowledge forms the foundation to better predict aquatic CH4 dynamics and its subsequent rates of emission to the atmosphere.}, }
@article {pmid37564072, year = {2023}, author = {Michoud, G and Kohler, TJ and Ezzat, L and Peter, H and Nattabi, JK and Nalwanga, R and Pramateftaki, P and Styllas, M and Tolosano, M and De Staercke, V and Schön, M and Marasco, R and Daffonchio, D and Bourquin, M and Busi, SB and Battin, TJ}, title = {The dark side of the moon: first insights into the microbiome structure and function of one of the last glacier-fed streams in Africa.}, journal = {Royal Society open science}, volume = {10}, number = {8}, pages = {230329}, pmid = {37564072}, issn = {2054-5703}, abstract = {The glaciers on Africa's 'Mountains of the Moon' (Rwenzori National Park, Uganda) are predicted to disappear within the next decades owing to climate change. Consequently, the glacier-fed streams (GFSs) that drain them will vanish, along with their resident microbial communities. Despite the relevance of microbial communities for performing ecosystem processes in equatorial GFSs, their ecology remains understudied. Here, we show that the benthic microbiome from the Mt. Stanley GFS is distinct at several levels from other GFSs. Specifically, several novel taxa were present, and usually common groups such as Chrysophytes and Polaromonas exhibited lower relative abundances compared to higher-latitude GFSs, while cyanobacteria and diatoms were more abundant. The rich primary producer community in this GFS likely results from the greater environmental stability of the Afrotropics, and accordingly, heterotrophic processes dominated in the bacterial community. Metagenomics revealed that almost all prokaryotes in the Mt. Stanley GFS are capable of organic carbon oxidation, while greater than 80% have the potential for fermentation and acetate oxidation. Our findings suggest a close coupling between photoautotrophs and other microbes in this GFS, and provide a glimpse into the future for high-latitude GFSs globally where primary production is projected to increase with ongoing glacier shrinkage.}, }
@article {pmid37563275, year = {2023}, author = {Epp Schmidt, D and Maul, JE and Yarwood, SA}, title = {Quantitative Amplicon Sequencing Is Necessary to Identify Differential Taxa and Correlated Taxa Where Population Sizes Differ.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2790-2801}, pmid = {37563275}, issn = {1432-184X}, support = {1828910//NSF/ ; }, mesh = {*Bacteria/genetics ; Population Density ; *Microbiota/genetics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {High-throughput, multiplexed-amplicon sequencing has become a core tool for understanding environmental microbiomes. As researchers have widely adopted sequencing, many open-source analysis pipelines have been developed to compare microbiomes using compositional analysis frameworks. However, there is increasing evidence that compositional analyses do not provide the information necessary to accurately interpret many community assembly processes. This is especially true when there are large gradients that drive distinct community assembly processes. Recently, sequencing has been combined with Q-PCR (among other sources of total quantitation) to generate "Quantitative Sequencing" (QSeq) data. QSeq more accurately estimates the true abundance of taxa, is a more reliable basis for inferring correlation, and, ultimately, can be more reliably related to environmental data to infer community assembly processes. In this paper, we use a combination of published data sets, synthesis, and empirical modeling to offer guidance for which contexts QSeq is advantageous. As little as 5% variation in total abundance among experimental groups resulted in more accurate inference by QSeq than compositional methods. Compositional methods for differential abundance and correlation unreliably detected patterns in abundance and covariance when there was greater than 20% variation in total abundance among experimental groups. Whether QSeq performs better for beta diversity analysis depends on the question being asked, and the analytic strategy (e.g., what distance metric is being used); for many questions and methods, QSeq and compositional analysis are equivalent for beta diversity analysis. QSeq is especially useful for taxon-specific analysis; QSeq transformation and analysis should be the default for answering taxon-specific questions of amplicon sequence data. Publicly available bioinformatics pipelines should incorporate support for QSeq transformation and analysis.}, }
@article {pmid37555066, year = {2023}, author = {Mashamaite, L and Lebre, PH and Varliero, G and Maphosa, S and Ortiz, M and Hogg, ID and Cowan, DA}, title = {Microbial diversity in Antarctic Dry Valley soils across an altitudinal gradient.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1203216}, pmid = {37555066}, issn = {1664-302X}, abstract = {INTRODUCTION: The Antarctic McMurdo Dry Valleys are geologically diverse, encompassing a wide variety of soil habitats. These environments are largely dominated by microorganisms, which drive the ecosystem services of the region. While altitude is a well-established driver of eukaryotic biodiversity in these Antarctic ice-free areas (and many non-Antarctic environments), little is known of the relationship between altitude and microbial community structure and functionality in continental Antarctica.<br><br>METHODS: We analysed prokaryotic and lower eukaryotic diversity from soil samples across a 684 m altitudinal transect in the lower Taylor Valley, Antarctica and performed a phylogenic characterization of soil microbial communities using short-read sequencing of the 16S rRNA and ITS marker gene amplicons.<br><br>RESULTS AND DISCUSSION: Phylogenetic analysis showed clear altitudinal trends in soil microbial composition and structure. Cyanobacteria were more prevalent in higher altitude samples, while the highly stress resistant Chloroflexota and Deinococcota were more prevalent in lower altitude samples. We also detected a shift from Basidiomycota to Chytridiomycota with increasing altitude. Several genera associated with trace gas chemotrophy, including Rubrobacter and Ornithinicoccus, were widely distributed across the entire transect, suggesting that trace-gas chemotrophy may be an important trophic strategy for microbial survival in oligotrophic environments. The ratio of trace-gas chemotrophs to photoautotrophs was significantly higher in lower altitude samples. Co-occurrence network analysis of prokaryotic communities showed some significant differences in connectivity within the communities from different altitudinal zones, with cyanobacterial and trace-gas chemotrophy-associated taxa being identified as potential keystone taxa for soil communities at higher altitudes. By contrast, the prokaryotic network at low altitudes was dominated by heterotrophic keystone taxa, thus suggesting a clear trophic distinction between soil prokaryotic communities at different altitudes. Based on these results, we conclude that altitude is an important driver of microbial ecology in Antarctic ice-free soil habitats.}, }
@article {pmid37552473, year = {2023}, author = {Jiang, Z and Liu, S and Zhang, D and Sha, Z}, title = {The Diversity and Metabolism of Culturable Nitrate-Reducing Bacteria from the Photic Zone of the Western North Pacific Ocean.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2781-2789}, pmid = {37552473}, issn = {1432-184X}, mesh = {*Nitrates ; Pacific Ocean ; Chlorophyll A ; *Thiosulfates ; Seawater/microbiology ; Sulfur/metabolism ; Nitrogen/metabolism ; Carbon ; Chitin ; Phylogeny ; }, abstract = {To better understand bacterial communities and metabolism under nitrogen deficiency, 154 seawater samples were obtained from 5 to 200 m at 22 stations in the photic zone of the Western North Pacific Ocean. Total 634 nitrate-utilizing bacteria were isolated using selective media and culture-dependent methods, and 295 of them were positive for nitrate reduction. These nitrate-reducing bacteria belonged to 19 genera and 29 species and among them, Qipengyuania flava, Roseibium aggregatum, Erythrobacter aureus, Vibrio campbellii, and Stappia indica were identified from all tested seawater layers of the photic zone and at almost all stations. Twenty-nine nitrate-reducing strains representing different species were selected for further the study of nitrogen, sulfur, and carbon metabolism. All 29 nitrate-reducing isolates contained genes encoding dissimilatory nitrate reduction or assimilatory nitrate reduction. Six nitrate-reducing isolates can oxidize thiosulfate based on genomic analysis and activity testing, indicating that nitrate-reducing thiosulfate-oxidizing bacteria exist in the photic zone. Five nitrate-reducing isolates obtained near the chlorophyll a-maximum layer contained a dimethylsulfoniopropionate synthesis gene and three of them contained both dimethylsulfoniopropionate synthesis and cleavage genes. This suggests that nitrate-reducing isolates may participate in dimethylsulfoniopropionate synthesis and catabolism in photic seawater. The presence of multiple genes for chitin degradation and extracellular peptidases may indicate that almost all nitrate-reducing isolates (28/29) can use chitin and proteinaceous compounds as important sources of carbon and nitrogen. Collectively, these results reveal culturable nitrate-reducing bacterial diversity and have implications for understanding the role of such strains in the ecology and biogeochemical cycles of nitrogen, sulfur, and carbon in the oligotrophic marine photic zone.}, }
@article {pmid37550791, year = {2023}, author = {Pitiriga, V and Bakalis, J and Theodoridou, K and Dimitroulia, E and Saroglou, G and Tsakris, A}, title = {Comparison of microbial colonization rates between central venous catheters and peripherally inserted central catheters.}, journal = {Antimicrobial resistance and infection control}, volume = {12}, number = {1}, pages = {74}, pmid = {37550791}, issn = {2047-2994}, mesh = {Humans ; *Central Venous Catheters/adverse effects ; *Catheterization, Central Venous/adverse effects/methods ; Retrospective Studies ; Critical Illness ; *Catheter-Related Infections/prevention &amp; control ; Risk Factors ; *Sepsis ; *Anti-Infective Agents ; }, abstract = {BACKGROUND: Central venous catheters (CVCs) and peripherally inserted central catheters (PICCs), have been widely used as intravascular devices in critically ill patients. However, they might evoke complications, such as catheter colonization that has been considered as predisposing factor for central line-associated bloodstream infections (CLABSIs). Although numerous studies have compared the risk of bloodstream infections between PICCs and CVCs, comparative studies on their colonization rates are limited.<br><br>OBJECTIVES: The episodes of catheter colonization in critically ill patients with CVCs or PICCs were retrospectively analysed during a two-year period in a Greek tertiary care hospital and colonization rates, microbial profiles and antimicrobial susceptibility&#xa0;patterns were compared.<br><br>METHODS: Clinical and laboratory data of consecutive hospitalized critically-ill patients who underwent PICC and CVC placement between May 2017-May 2019 were analysed. All catheters were examined by the semiquantitative culture technique for bacterial pathogens, either as a routine process after catheter removal or after suspicion of infection. Species identification and antimicrobial resistance patterns were determined by the Vitek2 automated system.<br><br>RESULTS: During the survey period a total of 122/1187 (10.28%) catheter colonization cases were identified among CVCs and 19/639 (2.97%) cases among PICCs (p&#x2009;=&#x2009;0.001). The colonization rate was 12.48/1000 catheter-days for the&#xa0;CVC group and 1.71/1000 catheter-days for the&#xa0;PICC group (p&#x2009;<&#x2009;0.001). The colonization rate per 1000 catheter-days due to multidrug-resistant organisms (MDROs) was 3.85 in all study cases, 7.26 (71/122) in the&#xa0;CVC group and 0.63 (7/19) in the&#xa0;PICC group (p&#x2009;<&#x2009;0.001). Within the&#xa0;CVC group, the most common microorganism isolated was MDR Acinetobacter baumannii (n&#x2009;=&#x2009;38, 31.1%) followed by MDR Klebsiella pneumoniae (n&#x2009;=&#x2009;20, 16.4%). In the&#xa0;PICC group, the predominant microorganism isolated was Candida spp. (n&#x2009;=&#x2009;5, 23.8%) followed by MDR K. pneumoniae and MDR A. baumannii in equal numbers (n&#x2009;=&#x2009;3, 14.2%).<br><br>CONCLUSION: PICC lines were associated with significantly lower colonization rates comparing to the&#xa0;CVC&#xa0;ones. In addition, patterns of microbial colonization revealed a trend over the predominance of MDR gram-negatives in CVCs suggesting that PICCs might be a&#xa0;safer alternative for prolonged inpatient intravascular access. Prevention programs directed by local microbial ecology may diminish catheter colonization rates and CLABSIs.}, }
@article {pmid37550373, year = {2023}, author = {Yu, L and Khachaturyan, M and Matschiner, M and Healey, A and Bauer, D and Cameron, B and Cusson, M and Emmett Duffy, J and Joel Fodrie, F and Gill, D and Grimwood, J and Hori, M and Hovel, K and Hughes, AR and Jahnke, M and Jenkins, J and Keymanesh, K and Kruschel, C and Mamidi, S and Menning, DM and Moksnes, PO and Nakaoka, M and Pennacchio, C and Reiss, K and Rossi, F and Ruesink, JL and Schultz, ST and Talbot, S and Unsworth, R and Ward, DH and Dagan, T and Schmutz, J and Eisen, JA and Stachowicz, JJ and Van de Peer, Y and Olsen, JL and Reusch, TBH}, title = {Author Correction: Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina).}, journal = {Nature plants}, volume = {9}, number = {8}, pages = {1370}, doi = {10.1038/s41477-023-01504-y}, pmid = {37550373}, issn = {2055-0278}, }
@article {pmid37548146, year = {2023}, author = {Ruiz, J and de Celis, M and Diaz-Colunga, J and Vila, JC and Benitez-Dominguez, B and Vicente, J and Santos, A and Sanchez, A and Belda, I}, title = {Predictability of the community-function landscape in wine yeast ecosystems.}, journal = {Molecular systems biology}, volume = {19}, number = {9}, pages = {e11613}, pmid = {37548146}, issn = {1744-4292}, mesh = {*Saccharomyces cerevisiae/genetics ; *Wine ; Ecosystem ; Phylogeny ; Fermentation ; Yeasts ; }, abstract = {Predictively linking taxonomic composition and quantitative ecosystem functions is a major aspiration in microbial ecology, which must be resolved if we wish to engineer microbial consortia. Here, we have addressed this open question for an ecological function of major biotechnological relevance: alcoholic fermentation in wine yeast communities. By exhaustively phenotyping an extensive collection of naturally occurring wine yeast strains, we find that most ecologically and industrially relevant traits exhibit phylogenetic signal, allowing functional traits in wine yeast communities to be predicted from taxonomy. Furthermore, we demonstrate that the quantitative contributions of individual wine yeast strains to the function of complex communities followed simple quantitative rules. These regularities can be integrated to quantitatively predict the function of newly assembled consortia. Besides addressing theoretical questions in functional ecology, our results and methodologies can provide a blueprint for rationally managing microbial processes of biotechnological relevance.}, }
@article {pmid37547726, year = {2023}, author = {Gibson, E and Zimmerman, NB}, title = {Urban biogeography of fungal endophytes across San Francisco.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15454}, pmid = {37547726}, issn = {2167-8359}, mesh = {Humans ; Endophytes/genetics ; Cities ; San Francisco ; Hot Temperature ; *Fungi, Unclassified ; Plants/microbiology ; Trees/microbiology ; *Microbiota ; }, abstract = {In natural and agricultural systems, the plant microbiome-the microbial organisms associated with plant tissues and rhizosphere soils-has been shown to have important effects on host physiology and ecology, yet we know little about how these plant-microbe relationships play out in urban environments. Here we characterize the composition of fungal communities associated with living leaves of one of the most common sidewalk trees in the city of San Francisco, California. We focus our efforts on endophytic fungi (asymptomatic microfungi that live inside healthy leaves), which have been shown in other systems to have large ecological effects on the health of their plant hosts. Specifically, we characterized the foliar fungal microbiome of Metrosideros excelsa (Myrtaceae) trees growing in a variety of urban environmental conditions. We used high-throughput culturing, PCR, and Sanger sequencing of the internal transcribed spacer nuclear ribosomal DNA (ITS nrDNA) region to quantify the composition and structure of fungal communities growing within healthy leaves of 30 M. excelsa trees from six distinct sites, which were selected to capture the range of environmental conditions found within city limits. Sequencing resulted in 854 high-quality ITS sequences. These sequences clustered into 85 Operational Taxonomic Units (97% OTUs). We found that these communities encompass relatively high alpha (within) and beta (between-site) diversity. Because the communities are all from the same host tree species, and located in relatively close geographical proximity to one another, these analyses suggest that urban environmental factors such as heat islands or differences in vegetation or traffic density (and associated air quality) may potentially be influencing the composition of these fungal communities. These biogeographic patterns provide evidence that plant microbiomes in urban environments can be as dynamic and complex as their natural counterparts. As human populations continue to transition out of rural areas and into cities, understanding the factors that shape environmental microbial communities in urban ecosystems stands to become increasingly important.}, }
@article {pmid37544074, year = {2023}, author = {Fu, S and Wang, R and Zhang, J and Xu, Z and Yang, X and Yang, Q}, title = {Temporal variability of microbiome in the different plankton hosts revealed distinct environmental persistence of Vibrio parahaemolyticus in shrimp farms.}, journal = {Microbiological research}, volume = {275}, number = {}, pages = {127464}, doi = {10.1016/j.micres.2023.127464}, pmid = {37544074}, issn = {1618-0623}, mesh = {Plankton/genetics ; *Vibrio parahaemolyticus/genetics ; *Chlorella ; Hemolysin Proteins/genetics ; *Microbiota/genetics ; Aquaculture ; }, abstract = {Plankton-bacteria interactions may play essential roles in maintaining the persistence of pathogenic Vibrio spp. However, the actual plankton host of the toxigenic Vibrio parahaemolyticus that harbors thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH) remains unclear. To answer this question, we measured the abundance of toxigenic and nontoxigenic Vibrio parahaemolyticus in different types of plankton by most probable number (MPN)-PCR. We next investigated the dynamics of the microbiomes of rearing water, copepods, Chlorella, four predominant diatom genera (Nitzschia, Melosira, Skeletonema and Chaetoceros) and the gut of the shrimp in two recirculated shrimp farming systems from April to September using high-throughput 16 S rRNA amplicon sequencing. The survival of trh-positive and trh-negative V. parahaemolyticus in seawater and different plankton hosts was examined under low temperature and starvation conditions. The results showed that copepods harbored the highest proportion of trh-positive V. parahaemolyticus, followed by diatoms. Chitinous diatoms (CD) harbored a high proportion of Vibrionaceae, of which a high abundance of V. parahaemolyticus was found in summer. In contrast, Vibrio spp. is rarely found in Chlorella and nonchitinous diatoms. Taxon-specific associations were also observed, including a relatively high abundance of Vibrio and Halodesulfovibrio on copepods and covariation of Aeromonas and Bacillus inside the Chlorella. The survival assays showed that, in comparison to trh-negative V. parahaemolyticus, trh-positive V. parahaemolyticus showed better survival in copepods and CD under starvation conditions and maintained high persistence in the above hosts at low temperature. In conclusion, the results herein suggested that chitinous plankton might provide protection for V. parahaemolyticus, especially trh-positive V. parahaemolyticus, and improve their persistence under harsh conditions. Our study provided in-depth insights into the persistence of V. parahaemolyticus in the environment, which would promote targeted disease prevention measures.}, }
@article {pmid37543702, year = {2023}, author = {Tang, L and O'Dwyer, J and Kimyon, &#xd6; and Manefield, MJ}, title = {Microbial community composition of food waste before anaerobic digestion.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12703}, pmid = {37543702}, issn = {2045-2322}, mesh = {Anaerobiosis ; Food ; RNA, Ribosomal, 16S/genetics ; *Refuse Disposal ; *Microbiota/genetics ; Bacteria/genetics ; Bioreactors/microbiology ; Methane ; Sewage/microbiology ; }, abstract = {Anaerobic digestion is widely used to process and recover value from food waste. Commercial food waste anaerobic digestion facilities seek improvements in process efficiency to enable higher throughput. There is limited information on the composition of microbial communities in food waste prior to digestion, limiting rational exploitation of the catalytic potential of microorganisms in pretreatment processes. To address this knowledge gap, bacterial and fungal communities in food waste samples from a commercial anaerobic digestion facility were characterised over 3 months. The abundance of 16S rRNA bacterial genes was approximately five orders of magnitude higher than the abundance of the fungal intergenic spacer (ITS) sequence, suggesting the numerical dominance of bacteria over fungi in food waste before anaerobic digestion. Evidence for the mass proliferation of bacteria in food waste during storage prior to anaerobic digestion is presented. The composition of the bacterial community shows variation over time, but lineages within the Lactobacillaceae family are consistently dominant. Nitrogen content and pH are correlated to community variation. These findings form a foundation for understanding the microbial ecology of food waste and provide opportunities to further improve the throughput of anaerobic digestion.}, }
@article {pmid37542810, year = {2023}, author = {De Paepe, J and Garcia Gragera, D and Arnau Jimenez, C and Rabaey, K and Vlaeminck, SE and Gòdia, F}, title = {Continuous cultivation of microalgae yields high nutrient recovery from nitrified urine with limited supplementation.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118500}, doi = {10.1016/j.jenvman.2023.118500}, pmid = {37542810}, issn = {1095-8630}, mesh = {Humans ; *Microalgae/metabolism ; Calcium/metabolism ; Edetic Acid/metabolism ; Magnesium ; Nutrients ; Photobioreactors ; Phosphorus/metabolism ; Dietary Supplements ; Biomass ; Nitrogen/metabolism ; }, abstract = {Microalgae can play a key role in the bioeconomy, particularly in combination with the valorisation of waste streams as cultivation media. Urine is an example of a widely available nutrient-rich waste stream, and alkaline stabilization and subsequent full nitrification in a bioreactor yields a stable nitrate-rich solution. In this study, such nitrified urine served as a culture medium for the edible microalga Limnospira indica. In batch cultivation, nitrified urine without additional supplements yielded a lower biomass concentration, nutrient uptake and protein content compared to modified Zarrouk medium, as standard medium. To enhance the nitrogen uptake efficiency and biomass production, nitrified urine was supplemented with potentially limiting elements. Limited amounts of phosphorus (36 mg L[-1]), magnesium (7.9 mg L[-1]), calcium (12.2 mg L[-1]), iron (2.0 mg L[-1]) and EDTA (88.5 mg Na2-EDTA.2H2O L[-1]) rendered the nitrified urine matrix as effective as modified Zarrouk medium in terms of biomass production (OD750 of 1.2), nutrient uptake (130 mg N L[-1]) and protein yield (47%) in batch culture. Urine precipitates formed by alkalinisation could in principle supply enough phosphorus, calcium and magnesium, requiring only external addition of iron, EDTA and inorganic carbon. Subsequently, the suitability of supplemented nitrified urine as a culture medium was confirmed in continuous Limnospira cultivation in a CSTR photobioreactor. This qualifies nitrified urine as a valuable and sustainable microalgae growth medium, thereby creating novel nutrient loops on Earth and in Space, i.e., in regenerative life support systems for human deep-space missions.}, }
@article {pmid37542791, year = {2023}, author = {van den Bergh, SG and Chardon, I and Meima-Franke, M and Costa, OYA and Korthals, GW and de Boer, W and Bodelier, PLE}, title = {The intrinsic methane mitigation potential and associated microbes add product value to compost.}, journal = {Waste management (New York, N.Y.)}, volume = {170}, number = {}, pages = {17-32}, doi = {10.1016/j.wasman.2023.07.027}, pmid = {37542791}, issn = {1879-2456}, abstract = {Conventional agricultural activity reduces the uptake of the potent greenhouse gas methane by agricultural soils. However, the recently observed improved methane uptake capacity of agricultural soils after compost application is promising but needs mechanistic understanding. In this study, the methane uptake potential and microbiomes involved in methane cycling were assessed in green compost and household-compost with and without pre-digestion. In bottle incubations of different composts with both high and near-atmospheric methane concentrations (∼10.000 &amp; ∼10 ppmv, respectively), green compost showed the highest potential methane uptake rates (up to 305.19 ± 94.43 nmol h[-1] g dw compost[-1] and 25.19 ± 6.75 pmol h[-1] g dw compost[-1], respectively). 16S, pmoA and mcrA amplicon sequencing revealed that its methanotrophic and methanogenic communities were dominated by type Ib methanotrophs, and more specifically by Methylocaldum szegediense and other Methylocaldum species, and Methanosarcina species, respectively. Ordination analyses showed that the abundance of type Ib methanotrophic bacteria was the main steering factor of the intrinsic methane uptake rates of composts, whilst the ammonium content was the main limiting factor, being most apparent in household composts. These results emphasize the potential of compost to contribute to methane mitigation, providing added value to compost as a product for industrial, commercial, governmental and public interests relevant to waste management. Compost could serve as a vector for the introduction of active methanotrophic bacteria in agricultural soils, potentially improving the methane uptake potential of agricultural soils and contributing to global methane mitigation, which should be the focus of future research.}, }
@article {pmid37542538, year = {2023}, author = {Niu, J and Chen, D and Shang, C and Xiao, L and Wang, Y and Zeng, W and Zheng, X and Chen, Z and Du, X and Chen, X}, title = {Niche Differentiation of Biofilm Microorganisms in a Full-scale Municipal Drinking Water Distribution System in China and Their Implication for Biofilm Control.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2770-2780}, pmid = {37542538}, issn = {1432-184X}, mesh = {*Drinking Water ; Water Quality ; Bacteria/genetics ; Proteobacteria ; Biofilms ; Archaea/genetics ; *Bacillus ; Water Supply ; Water Microbiology ; }, abstract = {Biofilms on the inner surface of a drinking water distribution system (DWDS) affect water quality and stability. Understanding the niche differentiation of biofilm microbial communities is necessary for the efficient control of DWDS biofilms. However, biofilm studies are difficult to conduct in the actual DWDS because of inaccessibility to the pipes buried underground. Taking the opportunity of infrastructure construction and relevant pipeline replacement in China, biofilms in a DWDS (a water main and its branch pipes) were collected in situ, followed by analysis on the abundances and community structures of bacterial and archaeal using quantitative PCR and high-throughput sequencing, respectively. Results showed that archaea were detected only in the biofilms of the water main, with a range of 9.4×10[3]~1.1×10[5] copies/cm[2]. By contrast, bacteria were detected in the biofilms of branch pipes and the distal part of the water main, with a range of 8.8×10[3]~9.6×10[6] copies/cm[2]. Among the biofilm samples, the archaeal community in the central part of the water main showed the highest richness and diversity. Nitrosopumilus was found to be predominant (86.22%) in the biofilms of the proximal part of the water main. However, Methanobrevibacter (87.15%) predominated in the distal part of the water main. The bacterial community of the water main and branch pipes was primarily composed of Firmicutes and Proteobacteria at the phylum level, respectively. Regardless of archaea or bacteria, only few operational taxonomic units (OTUs) (<0.5% of total OTUs) were shared by all the biofilms, indicating the niche differentiation of biofilm microorganisms. Moreover, the high Mn content in the biofilms of the distal sampling location (D3) in the water main was linked to the predominance of Bacillus. Functional gene prediction revealed that the proportion of infectious disease-related genes was 0.44-0.67% in the tested biofilms. Furthermore, functional genes related to the resistance of the bacterial community to disinfections and antibiotics were detected in all the samples, that is, glutathione metabolism-relating genes (0.14-0.65%) and beta-lactam resistance gene (0.01-0.05%). The results of this study indicate the ubiquity of archaea and bacteria in the biofilms of water main and branch pipes, respectively, and pipe diameters could be a major influencing factor on bacterial community structure. In the water main, the key finding was the predominant existence of archaea, particularly Nitrosopumilus and methanogen. Hence, their routine monitoring and probable influences on water quality in pipelines with large diameter should be given more attention. Besides, since Mn-related Bacillus and suspected pathogenic Enterococcus were detected in the biofilm, supplementation of disinfectant may be a feasible strategy for inhibiting their growth and ensuring water quality. In addition, the monitoring on their abundance variation could help to determine the frequency and methods of pipeline maintenance.}, }
@article {pmid37542537, year = {2023}, author = {Ren, Z and Ye, S and Li, H and Huang, X and Chen, L and Cao, S and Chen, T}, title = {Biological Interactions and Environmental Influences Shift Microeukaryotes in Permafrost Active Layer Soil Across the Qinghai-Tibet Plateau.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2756-2769}, pmid = {37542537}, issn = {1432-184X}, mesh = {Animals ; *Permafrost ; Tibet ; Soil/chemistry ; *Microbiota ; *Arthropods ; Soil Microbiology ; *Ciliophora/genetics ; }, abstract = {Permafrost active layer soils are harsh environments with thaw/freeze cycles and sub-zero temperatures, harboring diverse microorganisms. However, the distribution patterns, assembly mechanism, and driving forces of soil microeukaryotes in permafrost remain largely unknown. In this study, we investigated microeukaryotes in permafrost active layer across the Qinghai-Tibet Plateau (QTP) using 18S rRNA gene sequencing. The results showed that the microbial eukaryotic communities were dominated by Nematozoa, Ciliophora, Ascomycota, Cercozoa, Arthropoda, and Basidiomycota in terms of relative abundance and operational taxonomic unit (OTU) richness. Nematozoa had the highest relative abundance, while Ciliophora had the highest OTU richness. These phyla had strong interactions between each other. Their alpha diversity and community structure were differently influenced by the factors associated to location, climate, and soil properties, particularly the soil properties. Significant but weak distance-decay relationships with different slopes were established for the communities of these dominant phyla, except for Basidiomycota. According to the null model, community assemblies of Nematozoa and Cercozoa were dominated by heterogeneous selection, Ciliophora and Ascomycota were dominated by dispersal limitation, while Arthropoda and Basidiomycota were highly dominated by non-dominant processes. The assembly mechanisms can be jointly explained by biotic interactions, organism treats, and environmental influences. Modules in the co-occurrence network of the microeukaryotes were composed by members from different taxonomic groups. These modules also had interactions and responded to different environmental factors, within which, soil properties had strong influences on these modules. The results suggested the importance of biological interactions and soil properties in structuring microbial eukaryotic communities in permafrost active layer soil across the QTP.}, }
@article {pmid37541415, year = {2023}, author = {He, Q and Yan, X and Wang, H and Ji, Y and Li, J and Liu, L and Bi, P and Xu, P and Xu, B and Ma, J}, title = {Towards a better understanding of the anaerobic/oxic/anoxic-aerobic granular sludge process (AOA-AGS) for simultaneous low-strength wastewater treatment and in situ sludge reduction from ambient to winter temperatures.}, journal = {Environmental research}, volume = {236}, number = {Pt 2}, pages = {116822}, doi = {10.1016/j.envres.2023.116822}, pmid = {37541415}, issn = {1096-0953}, abstract = {The new anaerobic/oxic/anoxic-aerobic granular sludge (AOA-AGS) merits the advantages of effective carbon utilization and low-carbon treatment. However, low temperature poses stressing concerns and the resisting mechanism remains much unknown. Herein, an AOA-AGS process was configured for simultaneous nitrification, denitrification and phosphorus removal (SNDPR) with low-strength wastewater from ambient (>15 °C) to winter temperatures (<15 °C). Results showed that simultaneously advanced nutrients removal, and dramatic in situ sludge reduction (Yobs of 0.093 g MLSS/g COD) were gained regardless of seasonally decreasing temperatures. Winter temperatures even amplified Candidatus Competibacter predominating from 20.11% to 34.74%, which laid the core basis for endogenous denitrification, sludge minimization and temperature resistance. A removal model was thus proposed given the observed functional groups, and doubts were also raised for future investigations. This study would aid a better understanding on the microbial ecology and engineering aspects of the new AOA-AGS process treating low-strength wastewater at low temperatures.}, }
@article {pmid37537784, year = {2023}, author = {Guan, X and Zhao, Z and Jiang, J and Fu, L and Liu, J and Pan, Y and Gao, S and Wang, B and Chen, Z and Wang, X and Sun, H and Jiang, B and Dong, Y and Zhou, Z}, title = {Succession and assembly mechanisms of seawater prokaryotic communities along an extremely wide salinity gradient.}, journal = {Environmental microbiology reports}, volume = {15}, number = {6}, pages = {545-556}, pmid = {37537784}, issn = {1758-2229}, support = {2022JH2/101300155//Applied Basic Research Project of Liaoning Province/ ; 2022XTCX0504//Fundamental Research Funds of Liaoning Academy of Agricultural Sciences/ ; 2021RT08//Innovation and Entrepreneurship Program for High-level Talent of Dalian/ ; 2021921071//Liaoning BaiQianWan Talents Program/ ; }, mesh = {*Archaea/genetics ; Salinity ; Prokaryotic Cells ; Seawater ; *Microbiota ; Sodium Chloride ; }, abstract = {Salinity is an important environmental factor in microbial ecology for affecting the microbial communities in diverse environments. Understanding the salinity adaptation mechanisms of a microbial community is a significant issue, while most previous studies only covered a narrow salinity range. Here, variations in seawater prokaryotic communities during the whole salt drying progression (salinity from 3% to 25%) were investigated. According to high-throughput sequencing results, the diversity, composition, and function of seawater prokaryotic communities varied significantly along the salinity gradient, expressing as decreased diversity, enrichment of some halophilic archaea, and powerful nitrate reduction in samples with high salt concentrations. More importantly, a sudden and dramatic alteration of prokaryotic communities was observed when salinity reached 16%, which was recognized as the change point. Combined with the results of network analysis, we found the increasing of complexity but decreasing of stability in prokaryotic communities when salinity exceeded the change point. Moreover, prokaryotic communities became more deterministic when salinity exceeded the change point due to the niche adaptation of halophilic species. Our study showed that substantial variations in seawater prokaryotic communities along an extremely wide salinity gradient, and also explored the underlying mechanisms regulating these changes.}, }
@article {pmid37537681, year = {2023}, author = {Mendes, LW and Raaijmakers, JM and de Hollander, M and Sepo, E and Gómez Expósito, R and Chiorato, AF and Mendes, R and Tsai, SM and Carrión, VJ}, title = {Impact of the fungal pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root microbiome.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {68}, pmid = {37537681}, issn = {2524-6372}, support = {2014/03217-3, 2015/00251-9, 2020/00469-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 408191/2018-0, 307670/2021-0, 302591/2019-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 88887.185941/2018-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, abstract = {BACKGROUND: Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective success. If and how invading fungal root pathogens can disrupt microbiome assembly and gene expression is still largely unknown. Here, we investigated the impact of the fungal pathogen Fusarium oxysporum (fox) on the assembly of rhizosphere and endosphere microbiomes of a fox-susceptible and fox-resistant common bean cultivar.<br><br>RESULTS: Integration of 16S-amplicon, shotgun metagenome as well as metatranscriptome sequencing with community ecology analysis showed that fox infections significantly changed the composition and gene expression of the root microbiome in a cultivar-dependent manner. More specifically, fox infection led to increased microbial diversity, network complexity, and a higher proportion of the genera Flavobacterium, Bacillus, and Dyadobacter in the rhizosphere of the fox-resistant cultivar compared to the fox-susceptible cultivar. In the endosphere, root infection also led to changes in community assembly, with a higher abundance of the genera Sinorhizobium and Ensifer in the fox-resistant cultivar. Metagenome and metatranscriptome analyses further revealed the enrichment of terpene biosynthesis genes with a potential role in pathogen suppression in the fox-resistant cultivar upon fungal pathogen invasion.<br><br>CONCLUSION: Collectively, these results revealed a cultivar-dependent enrichment of specific bacterial genera and the activation of putative disease-suppressive functions in the rhizosphere and endosphere microbiome of common bean under siege.}, }
@article {pmid37535084, year = {2023}, author = {Pan, Q and Shikano, I and Liu, TX and Felton, GW}, title = {Correction to: Helicoverpa zea-Associated Gut Bacteria as Drivers in Shaping Plant Anti-herbivore Defense in Tomato.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2183}, doi = {10.1007/s00248-023-02281-z}, pmid = {37535084}, issn = {1432-184X}, }
@article {pmid37535083, year = {2023}, author = {Šaraba, V and Milovanovic, J and Nikodinovic-Runic, J and Budin, C and de Boer, T and Ciric, M}, title = {Brackish Groundwaters Contain Plastic- and Cellulose-Degrading Bacteria.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2747-2755}, pmid = {37535083}, issn = {1432-184X}, mesh = {*Cellulose/metabolism ; Ecosystem ; Plastics ; Bacteria ; *Groundwater ; }, abstract = {The selected brackish groundwater occurrences in the geotectonic regions of Inner Dinarides of western Serbia (Obrenovačka Banja) and Serbian crystalline core (Lomnički Kiseljak and Velika Vrbnica) were sampled for isolation and identification of plastic- and lignocellulose-degrading bacteria, as well as for the assessment of their enzymatic potential. The examined occurrences belong to the cold and warm (subthermal), weakly alkaline, neutral, and weakly acidic groundwater, and their genetic types are HCO3-Na + K and HCO3-Ca, Mg. The most abundant genera identified by next-generation 16S sequencing of cultivated groundwater samples belong to Aeromonas and Exiguobacterium. Of isolates screened on plastic and lignocellulosic substrates, 85.3% demonstrated growth and/or degrading activity on at least one tested substrate, with 27.8% isolates degrading plastic substrate Impranil® DLN-SD (SD), 1.9% plastic substrate bis(2-hydroxyethyl)terephthalate, and 5.6% carboxymethyl cellulose (CMC). Isolates degrading SD that were identified by 16S rDNA sequencing belonged to genera Stenotrophomonas, Flavobacterium, Pantoea, Enterobacter, Pseudomonas, Serratia, Acinetobacter, and Proteus, while isolates degrading CMC belonged to genera Rhizobium and Shewanella. All investigated brackish groundwaters harbor bacteria with potential in degradation of plastics or cellulose. Taking into account that microplastics contamination of groundwater resources is becoming a significant problem, the finding of plastic-degrading bacteria may have potential in bioremediation treatments of polluted groundwater. Subterranean ecosystems, which are largely untapped resources of biotechnologically relevant enzymes, are not traditionally considered the environment of choice for screening for plastic- and cellulose-degrading bacteria and therefore deserve a special attention from this aspect.}, }
@article {pmid37533451, year = {2023}, author = {Pandey, S and Kim, ES and Cho, JH and Song, M and Doo, H and Kim, S and Keum, GB and Kwak, J and Ryu, S and Choi, Y and Kang, J and Lee, JJ and Kim, HB}, title = {Swine gut microbiome associated with non-digestible carbohydrate utilization.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1231072}, pmid = {37533451}, issn = {2297-1769}, abstract = {Non-digestible carbohydrates are an unavoidable component in a pig's diet, as all plant-based feeds contain different kinds of non-digestible carbohydrates. The major types of non-digestible carbohydrates include non-starch polysaccharides (such as cellulose, pectin, and hemicellulose), resistant starch, and non-digestible oligosaccharides (such as fructo-oligosaccharide and xylo-oligosaccharide). Non-digestible carbohydrates play a significant role in balancing the gut microbial ecology and overall health of the swine by promoting the production of short chain fatty acids. Although non-digestible carbohydrates are rich in energy, swine cannot extract this energy on their own due to the absence of enzymes required for their degradation. Instead, they rely on gut microbes to utilize these carbohydrates for energy production. Despite the importance of non-digestible carbohydrate degradation, limited studies have been conducted on the swine gut microbes involved in this process. While next-generation high-throughput sequencing has aided in understanding the microbial compositions of the swine gut, specific information regarding the bacteria involved in non-digestible carbohydrate degradation remains limited. Therefore, it is crucial to investigate and comprehend the bacteria responsible for the breakdown of non-digestible carbohydrates in the gut. In this mini review, we have discussed the major bacteria involved in the fermentation of different types of non-digestible carbohydrates in the large intestine of swine, shedding light on their potential roles and contributions to swine nutrition and health.}, }
@article {pmid37532947, year = {2023}, author = {Jabir, T and Jain, A and Vipindas, PV and Krishnan, KP}, title = {Stochastic Processes Dominate in the Water Mass-Based Segregation of Diazotrophs in a High Arctic Fjord (Svalbard).}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2733-2746}, pmid = {37532947}, issn = {1432-184X}, mesh = {*Estuaries ; *Water ; Svalbard ; Nitrogen Fixation/genetics ; Nitrogen ; Stochastic Processes ; }, abstract = {Nitrogen-fixing or diazotrophic microbes fix atmospheric nitrogen (N2) to ammonia (NH3[+]) using nitrogenase enzyme and play a crucial role in regulating marine primary productivity and carbon dioxide sequestration. However, there is a lack of information about the diversity, structure, and environmental regulations of the diazotrophic communities in the high Arctic fjords, such as Kongsfjorden. Here, we employed nifH gene sequencing to clarify variations in composition, community structure, and assembly mechanism among the diazotrophs of the salinity-driven stratified waters of Kongsfjorden. The principal environmental and ecological drivers of the observed variations were identified. The majority of the nifH gene sequences obtained in the present study belonged to cluster I and cluster III nifH phylotypes, accounting for 65% and 25% of the total nifH gene sequences. The nifH gene diversity and composition, irrespective of the size fractions (free-living and particle attached), showed a clear separation among water mass types, i.e., Atlantic-influenced versus glacier-influenced water mass. Higher nifH gene diversity and relative abundances of non-cyanobacterial nifH OTUs, affiliated with uncultured Rhizobiales, Burkholderiales, Alteromonadaceae, Gallionellaceae (cluster I) and uncultured Deltaproteobacteria including Desulfuromonadaceae (cluster III), were prevalent in GIW while uncultured Gammaproteobacteria and Desulfobulbaceae were abundant in AIW. The diazotrophic community assembly was dominated by stochastic processes, principally ecological drift, and to lesser degrees dispersal limitation and homogeneous dispersal. Differences in the salinity and dissolved oxygen content lead to the vertical segregation of diazotrophs among water mass types. These findings suggest that water column stratification affects the composition and assembly mechanism of diazotrophic communities and thus could affect nitrogen fixation in the Arctic fjord.}, }
@article {pmid37531050, year = {2023}, author = {Zhang, D and Sun, J and Wang, D and Peng, S and Wang, Y and Lin, X and Yang, X and Hua, Q and Wu, P}, title = {Comparison of bacterial and fungal communities structure and dynamics during chicken manure and pig manure composting.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {41}, pages = {94347-94360}, pmid = {37531050}, issn = {1614-7499}, support = {BK20201110//Natural Science Foundation of Jiangsu Province/ ; 2021BEE02025//Key Research and Development Program of Ningxia/ ; NMKJXM202009//Science and Technology Major Project of Inner Mongolia/ ; }, mesh = {Animals ; Swine ; *Mycobiome ; Manure/microbiology ; Chickens/genetics ; *Composting ; RNA, Ribosomal, 16S ; Soil ; Bacteria/genetics ; *Actinomycetales/genetics ; }, abstract = {Composting is a sustainable and eco-friendly technology that turns animal waste into organic fertilizers. It remains unclear whether differences exist in the structure of microbial communities during different livestock manure composting. This study analyzed the dynamic change of bacterial and fungal communities, metabolic function, and trophic mode during chicken manure (CM) and pig manure (PM) composting based on 16S rRNA and ITS sequencing. Environmental factors were investigated for their impact on microbial communities. During composting, bacterial diversity decreased and then increased, while fungal diversity slightly increased and then decreased. Saccharomonospora and Aspergillus were the dominant genera and key microorganisms in CM and PM, respectively, which played crucial roles in sustaining the stability of the ecological network structure in the microbial ecology and participating in metabolism. Saccharomonospora gradually increased, while Aspergillus increased at first and then decreased. PM had better microbial community stability and more keystone taxa than CM. In CM and PM, the primary function of bacterial communities was metabolism, while saprotroph was the primary trophic mode of fungal communities. Dissolved organic carbon (DOC) was the primary factor influencing the structure and function of microbial communities in CM and PM. In addition to DOC, pH and moisture were important factors affecting the fungal communities in CM and PM, respectively. These results show that the succession of bacteria and fungi in CM and PM proceeded in a similar pattern, but there are still some differences in the dominant genus and their responses to environmental factors.}, }
@article {pmid37528183, year = {2023}, author = {Wang, L and Wang, J and Yuan, J and Tang, Z and Wang, J and Zhang, Y}, title = {Long-Term Organic Fertilization Strengthens the Soil Phosphorus Cycle and Phosphorus Availability by Regulating the pqqC- and phoD-Harboring Bacterial Communities.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2716-2732}, pmid = {37528183}, issn = {1432-184X}, mesh = {*Soil/chemistry ; *Phosphorus/metabolism ; Fertilizers/analysis ; Carbon ; Bacteria/genetics/metabolism ; Soil Microbiology ; Minerals ; Fertilization ; }, abstract = {The pqqC and phoD genes encode pyrroloquinoline quinone synthase and alkaline phosphomonoesterase (ALP), respectively. These genes play a crucial role in regulating the solubilization of inorganic phosphorus (Pi) and the mineralization of organic phosphorus (Po), making them valuable markers for P-mobilizing bacterial. However, there is limited understanding of how the interplay between soil P-mobilizing bacterial communities and abiotic factors influences P transformation and availability in the context of long-term fertilization scenarios. We used real-time polymerase chain reaction and high-throughput sequencing to explore the characteristics of soil P-mobilizing bacterial communities and their relationships with key physicochemical properties and P fractions under long-term fertilization scenarios. In a 38-year fertilization experiment, six fertilization treatments were selected. These treatments were sorted into three groups: the non-P-amended group, including no fertilization and mineral NK fertilizer; the sole mineral-P-amended group, including mineral NP and NPK fertilizer; and the organically amended group, including sole organic fertilizer and organic fertilizer plus mineral NPK fertilizer. The organically amended group significantly increased soil labile P (Ca2-P and enzyme-P) and Olsen-P content and proportion but decreased non-labile P (Ca10-P) proportion compared with the sole mineral-P-amended group, indicating enhanced P availability in the soil. Meanwhile, the organically amended group significantly increased soil ALP activity and pqqC and phoD gene abundances, indicating that organic fertilization promotes the activity and abundance of microorganisms involved in P mobilization processes. Interestingly, the organically amended group dramatically reshaped the community structure of P-mobilizing bacteria and increased the relative abundance of Acidiphilium, Panacagrimonas, Hansschlegelia, and Beijerinckia. These changes had a greater positive impact on ALP activity, labile P, and Olsen-P content compared to the abundance of P-mobilizing genes alone, indicating their importance in driving P mobilization processes. Structural equation modeling indicated that soil organic carbon and Po modulated the relationship between P-mobilizing bacterial communities and labile P and Olsen-P, highlighting the influence of SOC and Po on the functioning of P-mobilizing bacteria and their impact on P availability. Overall, our study demonstrates that organic fertilization has the potential to reshape the structure of P-mobilizing bacterial communities, leading to increased P mobilization and availability in the soil. These findings contribute to our understanding of the mechanisms underlying P cycling in agricultural systems and provide valuable insights for enhancing microbial P mobilization through organic fertilization.}, }
@article {pmid37527741, year = {2023}, author = {Antonelli, P and Peruzzo, A and Mancin, M and Boscolo Anzoletti, A and Dall'Ara, S and Orsini, M and Bordin, P and Arcangeli, G and Zanolin, B and Barco, L and Losasso, C}, title = {Tetrodotoxin in bivalve mollusks: An integrated study towards the comprehension of the influencing factors of a newly native phenomenon.}, journal = {Chemosphere}, volume = {339}, number = {}, pages = {139682}, doi = {10.1016/j.chemosphere.2023.139682}, pmid = {37527741}, issn = {1879-1298}, mesh = {Animals ; Tetrodotoxin/toxicity ; *Tandem Mass Spectrometry ; Comprehension ; *Bivalvia ; Neurotoxins ; Phytoplankton ; }, abstract = {Tetrodotoxins (TTXs) are potent neurotoxins named after the Tetraodontidae fish family. The ingestion of TTX-contaminated flesh can cause neurotoxic symptoms and can lead to death. In 2017 symptoms the European Food Safety Authority (EFSA) recognized the threat to food safety resulting from TTX exposure via food consumption and, thus, proposed a safety limit of 44 μg/kg of TTX in marine gastropods and bivalves. To date, however, TTXs have not yet been included in the list of biotoxins to be monitored within the European Union, even though, in a few cases, levels of TTX found were higher than the EFSA limit. The origin of TTX production is debated and the roles of both biotic and abiotic factors on TTX-mediated toxic events remain unclear. In order to meet these knowledge requests the present study was aimed to investigate the role of seawater temperature, pH, water conductivity, and oxygen saturation, along with the marine phytoplankton community and the bacterial community of mussels and oysters on the accumulation of TTX and analogues in the bivalves. Abiotic parameters were measured by means of a multi-parametric probe, phytoplankton community was analyzed by optic microscopy while microbial community was described by amplicon metataxonomic sequencing, TTXs concentration in the collected matrices were measured by HILIC-MS/MS. A possible role of seawater pH and temperature, among the investigated abiotic factors, in regulating the occurrence of TTXs was found. Regarding biotic variables, a possible influence of Vibrio, Shewanella and Flavobacteriaceae in the occurrence of TTXs was found. Concurrently, Prorocentrum cordatum cell numbers were correlated to the incidence of TTX in mussels. The results herein collected suggest that environmental variables play a consistent part in the occurrence of TTX in the edible bivalve habitats, and there are also indications of a potential role played by specific bacteria taxa in association with phytoplankton.}, }
@article {pmid37527740, year = {2023}, author = {Wang, Y and Gao, Y and Lu, X and Gadow, SI and Zhuo, G and Hu, W and Song, Y and Zhen, G}, title = {Bioelectrochemical anaerobic membrane bioreactor enables high methane production from methanolic wastewater: Roles of microbial ecology and microstructural integrity of anaerobic biomass.}, journal = {Chemosphere}, volume = {339}, number = {}, pages = {139676}, doi = {10.1016/j.chemosphere.2023.139676}, pmid = {37527740}, issn = {1879-1298}, mesh = {*Wastewater ; *Methanol ; Sewage/chemistry ; Anaerobiosis ; Biomass ; Methane/metabolism ; Bioreactors ; Waste Disposal, Fluid ; Membranes, Artificial ; }, abstract = {The disintegration of anaerobic sludge and blockage of membrane pores has impeded the practical application of anaerobic membrane bioreactor (AnMBR) in treating methanolic wastewater. In this study, bioelectrochemical system (BES) was integrated into AnMBR to alleviate sludge dispersion and membrane fouling as well as enhance bioconversion of methanol. Bioelectrochemical regulation effect induced by BES enhanced methane production rate from 4.94 ± 0.52 to 5.39 ± 0.37 L/Lreactor/d by accelerating the enrichment of electroactive microorganisms and the agglomeration of anaerobic sludge via the adhesive and chemical bonding force. 16 S rRNA gene high-throughput sequencing demonstrated that bioelectrochemical stimulation had modified the metabolic pathways by regulating the key functional microbial communities. Methanogenesis via the common methylotrophic Methanomethylovorans was partially substituted by the hydrogenotrophic Candidatus_Methanofastidiosum, etc. The metabolic behaviors of methanol are bioelectrochemistry-dependent, and controlling external voltage is thus an effective strategy for ensuring robust electron transfer, low membrane fouling, and long-term process stability.}, }
@article {pmid37525505, year = {2024}, author = {Effelsberg, N and Kobusch, I and Schollenbruch, H and Linnemann, S and Bang, C and Franke, A and Köck, R and Boelhauve, M and Mellmann, A}, title = {Pilot study on nasal microbiota dynamics and MRSA carriage of a pig cohort housed on straw bedding.}, journal = {Molecular microbiology}, volume = {122}, number = {3}, pages = {403-412}, doi = {10.1111/mmi.15136}, pmid = {37525505}, issn = {1365-2958}, support = {01KI2009A//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 01KI2009B//Bundesministerium f&#xfc;r Bildung und Forschung/ ; }, mesh = {Animals ; *Methicillin-Resistant Staphylococcus aureus/genetics/isolation &amp; purification ; Swine ; *Staphylococcal Infections/microbiology ; *Microbiota ; *Housing, Animal ; *RNA, Ribosomal, 16S/genetics ; *Carrier State/microbiology ; *Nose/microbiology ; Pilot Projects ; Bedding and Linens/microbiology ; Swine Diseases/microbiology ; }, abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) can be transmitted between pigs and humans on farms. Hence, the reduction of MRSA carriage in pigs could decrease the risk of zoonotic transmission. Recently, straw bedding has been found to significantly reduce MRSA carriage in pigs. The mechanisms behind this effect remain unclear but changes in the nasal microbiome may play a role. In this exploratory study, the nasal microbiota of pigs kept on straw was examined using V1/V2 16S rRNA gene sequencing. Nasal swabs were collected from 13 pigs at six different time points during the course of a full fattening cycle resulting in 74 porcine samples. In addition, straw samples were collected at each time point. Eleven out of 13 pigs were MRSA positive at housing-in. We found a strong temporal pattern in the microbial communities. Both microbial diversity and abundance of Staphylococcus species peaked in week 5 after introduction to the straw stable decreased in week 10, when all pigs turned MRSA-negative, and increased again toward the end of the fattening period. These findings show that the introduction of pigs into a new environment has a huge impact on their nasal microbiota, which might lead to unfavorable conditions for MRSA. Moreover, other Staphylococcus species may play a role in eliminating MRSA carriage. We designed a follow-up study including two different husbandry systems to further assess these effects.}, }
@article {pmid37523041, year = {2024}, author = {Li, S and Young, T and Archer, S and Lee, K and Alfaro, AC}, title = {Gut microbiome resilience of green-lipped mussels, Perna canaliculus, to starvation.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {27}, number = {2}, pages = {571-580}, pmid = {37523041}, issn = {1618-1905}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Perna ; RNA, Ribosomal, 16S/genetics ; *Resilience, Psychological ; Bacteria/genetics ; }, abstract = {Host gut microbiomes play an important role in animal health and resilience to conditions, such as malnutrition and starvation. These host-microbiome relationships are poorly understood in the marine mussel Perna canaliculus, which experiences significant variations in food quantity and quality in coastal areas. Prolonged starvation may be a contributory factor towards incidences of mass mortalities in farmed mussel populations, resulting in highly variable production costs and unreliable market supplies. Here, we examine the gut microbiota of P. canaliculus in response to starvation and subsequent re-feeding using high-throughput amplicon sequencing of the 16S rRNA gene. Mussels showed no change in bacterial species richness when subjected to a 14-day starvation, followed by re-feeding/recovery. However, beta bacteria diversity revealed significant shifts (PERMANOVA p-value < 0.001) in community structure in the starvation group and no differences in the subsequent recovery group (compared to the control group) once they were re-fed, highlighting their recovery capability and resilience. Phylum-level community profiles revealed an elevation in dominance of Proteobacteria (ANCOM-BC p-value <0.001) and Bacteroidota (ANCOM-BC p-value = 0.04) and lower relative abundance of Cyanobacteria (ANCOM-BC p-value = 0.01) in the starvation group compared to control and recovery groups. The most abundant genus-level shifts revealed relative increases of the heterotroph Halioglobus (p-value < 0.05) and lowered abundances of the autotroph Synechococcus CC9902 in the starvation group. Furthermore, a SparCC correlation network identified co-occurrence of a cluster of genera with elevated relative abundance in the starved mussels that were positively correlated with Synechococcus CC9902. The findings from this work provide the first insights into the effect of starvation on the resilience capacity of Perna canaliculus gut microbiota, which is of central importance to understanding the effect of food variation and limitation in farmed mussels.}, }
@article {pmid37520283, year = {2023}, author = {Wentzien, NM and Fernández-González, AJ and Villadas, PJ and Valverde-Corredor, A and Mercado-Blanco, J and Fernández-López, M}, title = {Thriving beneath olive trees: The influence of organic farming on microbial communities.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {3575-3589}, pmid = {37520283}, issn = {2001-0370}, abstract = {Soil health and root-associated microbiome are interconnected factors involved in plant health. The use of manure amendment on agricultural fields exerts a direct benefit on soil nutrient content and water retention, among others. However, little is known about the impact of manure amendment on the root-associated microbiome, particularly in woody species. In this study, we aimed to evaluate the effects of ovine manure on the microbial communities of the olive rhizosphere and root endosphere. Two adjacent orchards subjected to conventional (CM) and organic (OM) management were selected. We used metabarcoding sequencing to assess the bacterial and fungal communities. Our results point out a clear effect of manure amendment on the microbial community. Fungal richness and diversity were increased in the rhizosphere. The fungal biomass in the rhizosphere was more than doubled, ranging from 1.72 × 10[6] ± 1.62 × 10[5] (CM) to 4.54 × 10[6] ± 8.07 × 10[5] (OM) copies of the 18 S rRNA gene g[-1] soil. Soil nutrient content was also enhanced in the OM orchard. Specifically, oxidable organic matter, total nitrogen, nitrate, phosphorous, potassium and sulfate concentrations were significantly increased in the OM orchard. Moreover, we predicted a higher abundance of bacteria in OM with metabolic functions involved in pollutant degradation and defence against pathogens. Lastly, microbial co-occurrence network showed more positive interactions, complexity and shorter geodesic distance in the OM orchard. According to our results, manure amendment on olive orchards represents a promising tool for positively modulating the microbial community in direct contact with the plant.}, }
@article {pmid37516570, year = {2023}, author = {Parizadeh, M and Arrieta, MC}, title = {The global human gut microbiome: genes, lifestyles, and diet.}, journal = {Trends in molecular medicine}, volume = {29}, number = {10}, pages = {789-801}, doi = {10.1016/j.molmed.2023.07.002}, pmid = {37516570}, issn = {1471-499X}, mesh = {Humans ; *Gastrointestinal Microbiome ; Bacteria ; *Microbiota ; Diet ; Life Style ; }, abstract = {A growing number of human gut microbiome studies consistently describe differences between human populations. Here, we review how factors related to host genetics, ethnicity, lifestyle, and geographic location help explain this variation. Studies from contrasting environmental scenarios point to diet and lifestyle as the most influential. The effect of human migration and displacement demonstrates how the microbiome adapts to newly adopted lifestyles and contributes to the profound biological and health consequences attributed to migration. This information strongly suggests against a universal scale for healthy or dysbiotic gut microbiomes, and prompts for additional microbiome population surveys, particularly from less industrialized nations. Considering these important differences will be critical for designing strategies to diagnose and restore dysbiosis in various human populations.}, }
@article {pmid37515622, year = {2023}, author = {Mi, JX and Liu, KL and Ding, WL and Zhang, MH and Wang, XF and Shaukat, A and Rehman, MU and Jiao, XL and Huang, SC}, title = {Comparative analysis of the gut microbiota of wild wintering whooper swans (Cygnus Cygnus), captive black swans (Cygnus Atratus), and mute swans (Cygnus Olor) in Sanmenxia Swan National Wetland Park of China.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {41}, pages = {93731-93743}, pmid = {37515622}, issn = {1614-7499}, support = {No. 32202876//National Natural Science Foundation of China/ ; No. 30501374//Special Support Fund for High-level Talents of Henan Agricultural University/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Wetlands ; Ecosystem ; RNA, Ribosomal, 16S ; *Anseriformes ; Birds ; Ducks ; China ; }, abstract = {The gastrointestinal microbiota, a complex ecosystem, is involved in the physiological activities of hosts and the development of diseases. Birds occupy a critical ecological niche in the ecosystem, performing a variety of ecological functions and possessing a complex gut microbiota composition. However, the gut microbiota of wild and captive birds has received less attention in the same region. We profiled the fecal gut microbiome of wild wintering whooper swans (Cygnus Cygnus; Cyg group, n = 25), captive black swans (Cygnus Atratus; Atr group, n = 20), and mute swans (Cygnus Olor; Olor group, n = 30) using 16S rRNA gene sequencing to reveal differences in the gut microbial ecology. The results revealed that the three species of swans differed significantly in terms of the alpha and beta diversity of their gut microbiota, as measured by ACE, Chao1, Simpson and Shannon indices, principal coordinates analysis (PCoA) and non-metricmulti-dimensional scaling (NMDS) respectively. Based on the results of the linear discriminant analysis effect size (LEfSe) and random forest analysis, we found that there were substantial differences in the relative abundance of Gottschalkia, Trichococcus, Enterococcus, and Kurthia among the three groups. Furthermore, an advantageous pattern of interactions between microorganisms was shown by the association network analysis. Among these, Gottschalkia had the higher area under curve (AUC), which was 0.939 (CI = 0.879-0.999), indicating that it might be used as a biomarker to distinguish between wild and captive black swans. Additionally, PICRUSt2 predictions indicated significant differences in gut microbiota functions between wild and captive trumpeter swans, with the gut microbiota functions of Cyg group focusing on carbohydrate metabolism, membrane transport, cofactor, and vitamin metabolism pathways, the Atr group on lipid metabolism, and the Olor group on cell motility, amino acid metabolism, and replication and repair pathways. These findings showed that the gut microbiota of wild and captive swans differed, which is beneficial to understand the gut microecology of swans and to improve regional wildlife conservation strategies.}, }
@article {pmid37512939, year = {2023}, author = {Mourgela, RN and Kioukis, A and Pourjam, M and Lagkouvardos, I}, title = {Large-Scale Integration of Amplicon Data Reveals Massive Diversity within Saprospirales, Mostly Originating from Saline Environments.}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, pmid = {37512939}, issn = {2076-2607}, abstract = {The order Saprospirales, a group of bacteria involved in complex degradation pathways, comprises three officially described families: Saprospiraceae, Lewinellaceae, and Haliscomenobacteraceae. These collectively contain 17 genera and 31 species. The current knowledge on Saprospirales diversity is the product of traditional isolation methods, with the inherited limitations of culture-based approaches. This study utilized the extensive information available in public sequence repositories combined with recent analytical tools to evaluate the global evidence-based diversity of the Saprospirales order. Our analysis resulted in 1183 novel molecular families, 15,033 novel molecular genera, and 188 K novel molecular species. Of those, 7 novel families, 464 novel genera, and 1565 species appeared in abundances at ≥0.1%. Saprospirales were detected in various environments, such as saline water, freshwater, soil, various hosts, wastewater treatment plants, and other bioreactors. Overall, saline water was the environment showing the highest prevalence of Saprospirales, with bioreactors and wastewater treatment plants being the environments where they occurred with the highest abundance. Lewinellaceae was the family containing the majority of the most prevalent species detected, while Saprospiraceae was the family with the majority of the most abundant species found. This analysis should prime researchers to further explore, in a more targeted way, the Saprospirales proportion of microbial dark matter.}, }
@article {pmid37512925, year = {2023}, author = {St-Pierre, B and Perez Palencia, JY and Samuel, RS}, title = {Impact of Early Weaning on Development of the Swine Gut Microbiome.}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, pmid = {37512925}, issn = {2076-2607}, support = {Hatch projects SD00H719-20 and SD00H682-19//South Dakota State University Agricultural Experiment Station / USDA National Institute of Food and Agriculture/ ; }, abstract = {Considering that pigs are naturally weaned between 12 and 18 weeks of age, the common practice in the modern swine industry of weaning as early as between two and four weeks of age increases challenges during this transition period. Indeed, young pigs with an immature gut are suddenly separated from the sow, switched from milk to a diet consisting of only solid ingredients, and subjected to a new social hierarchy from mixing multiple litters. From the perspective of host gut development, weaning under these conditions causes a regression in histological structure as well as in digestive and barrier functions. While the gut is the main center of immunity in mature animals, the underdeveloped gut of early weaned pigs has yet to contribute to this function until seven weeks of age. The gut microbiota or microbiome, an essential contributor to the health and nutrition of their animal host, undergoes dramatic alterations during this transition, and this descriptive review aims to present a microbial ecology-based perspective on these events. Indeed, as gut microbial communities are dependent on cross-feeding relationships, the change in substrate availability triggers a cascade of succession events until a stable composition is reached. During this process, the gut microbiota is unstable and prone to dysbiosis, which can devolve into a diseased state. One potential strategy to accelerate maturation of the gut microbiome would be to identify microbial species that are critical to mature swine gut microbiomes, and develop strategies to facilitate their establishment in early post-weaning microbial communities.}, }
@article {pmid37512843, year = {2023}, author = {Cowan, DA and Cary, SC and DiRuggiero, J and Eckardt, F and Ferrari, B and Hopkins, DW and Lebre, PH and Maggs-Kölling, G and Pointing, SB and Ramond, JB and Tribbia, D and Warren-Rhodes, K}, title = {'Follow the Water': Microbial Water Acquisition in Desert Soils.}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, pmid = {37512843}, issn = {2076-2607}, support = {80256//National Research Foundation/ ; }, abstract = {Water availability is the dominant driver of microbial community structure and function in desert soils. However, these habitats typically only receive very infrequent large-scale water inputs (e.g., from precipitation and/or run-off). In light of recent studies, the paradigm that desert soil microorganisms are largely dormant under xeric conditions is questionable. Gene expression profiling of microbial communities in desert soils suggests that many microbial taxa retain some metabolic functionality, even under severely xeric conditions. It, therefore, follows that other, less obvious sources of water may sustain the microbial cellular and community functionality in desert soil niches. Such sources include a range of precipitation and condensation processes, including rainfall, snow, dew, fog, and nocturnal distillation, all of which may vary quantitatively depending on the location and geomorphological characteristics of the desert ecosystem. Other more obscure sources of bioavailable water may include groundwater-derived water vapour, hydrated minerals, and metabolic hydro-genesis. Here, we explore the possible sources of bioavailable water in the context of microbial survival and function in xeric desert soils. With global climate change projected to have profound effects on both hot and cold deserts, we also explore the potential impacts of climate-induced changes in water availability on soil microbiomes in these extreme environments.}, }
@article {pmid37511881, year = {2023}, author = {Walther-Antonio, M and Schulze-Makuch, D}, title = {The Hypothesis of a "Living Pulse" in Cells.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, pmid = {37511881}, issn = {2075-1729}, abstract = {Motility is a great biosignature and its pattern is characteristic for specific microbes. However, motion does also occur within the cell by the myriads of ongoing processes within the cell and the exchange of gases and nutrients with the outside environment. Here, we propose that the sum of these processes in a microbial cell is equivalent to a pulse in complex organisms and suggest a first approach to measure the "living pulse" in microorganisms. We emphasize that if a "living pulse" can be shown to exist, it would have far-reaching applications, such as for finding life in extreme environments on Earth and in extraterrestrial locations, as well as making sure that life is not present where it should not be, such as during medical procedures and in the food processing industry.}, }
@article {pmid37511821, year = {2023}, author = {Schulze-Makuch, D and Irwin, LN}, title = {Life Unknown: Preliminary Scheme for a Magnetotrophic Organism.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, pmid = {37511821}, issn = {2075-1729}, abstract = {No magnetotrophic organism on Earth is known to use magnetic fields as an energy source or the storage of information. However, a broad diversity of life forms is sensitive to magnetic fields and employs them for orientation and navigation, among other purposes. If the magnetic field strength were much larger, such as that on planets around neutron stars or magnetars, metabolic energy could be obtained from these magnetic fields in principle. Here, we introduce three hypothetical models of magnetotrophic organisms that obtain energy via the Lorentz force. Even if an organism uses magnetic fields only as an energy source, but otherwise is relying on biochemistry, this organism would be by definition a magnetotrophic form of life as we do not know it.}, }
@article {pmid37511182, year = {2023}, author = {Turbant, F and Waeytens, J and Blache, A and Esnouf, E and Raussens, V and Węgrzyn, G and Achouak, W and Wien, F and Arluison, V}, title = {Interactions and Insertion of Escherichia coli Hfq into Outer Membrane Vesicles as Revealed by Infrared and Orientated Circular Dichroism Spectroscopies.}, journal = {International journal of molecular sciences}, volume = {24}, number = {14}, pages = {}, pmid = {37511182}, issn = {1422-0067}, support = {101004806//Trans-National Access (TNA) of Molecular-Scale Biophysics Research Infrastructure (MOSBRI)/ ; 08254//IEA/PICS CNRS/ ; ANR-11-IDEX-0003-02//Investissements d'Avenir &#xbb; program, through the "ADI 2021 Paris Saclay/ ; 2016/21/N/NZ1/02850//National Science Center Poland/ ; 531-D020-D242-23//University of Gdansk/ ; }, mesh = {Escherichia coli/genetics/metabolism ; Circular Dichroism ; *Escherichia coli Proteins/genetics/metabolism ; *RNA, Small Untranslated/genetics ; Host Factor 1 Protein/genetics/metabolism ; RNA, Bacterial/genetics ; Gene Expression Regulation, Bacterial ; }, abstract = {The possible carrier role of Outer Membrane Vesicles (OMVs) for small regulatory noncoding RNAs (sRNAs) has recently been demonstrated. Nevertheless, to perform their function, these sRNAs usually need a protein cofactor called Hfq. In this work we show, by using a combination of infrared and circular dichroism spectroscopies, that Hfq, after interacting with the inner membrane, can be translocated into the periplasm, and then be exported in OMVs, with the possibility to be bound to sRNAs. Moreover, we provide evidence that Hfq interacts with and is inserted into OMV membranes, suggesting a role for this protein in the release of sRNA outside the vesicle. These findings provide clues to the mechanism of host-bacteria interactions which may not be defined solely by protein-protein and protein-outer membrane contacts, but also by the exchange of RNAs, and in particular sRNAs.}, }
@article {pmid37509218, year = {2023}, author = {Li, G and Jin, Y and Chen, B and Lin, A and Wang, E and Xu, F and Hu, G and Xiao, C and Liu, H and Hou, X and Zhang, B and Song, J}, title = {Exploring the Relationship between the Gut Mucosal Virome and Colorectal Cancer: Characteristics and Correlations.}, journal = {Cancers}, volume = {15}, number = {14}, pages = {}, pmid = {37509218}, issn = {2072-6694}, support = {Nos. 81873553//National Natural Science Foundation of China/ ; Nos. 81800465//National Natural Science Foundation of China/ ; }, abstract = {The fecal virome has been reported to be associated with CRC. However, little is known about the mucosal virome signature in CRC. This study aimed to determine the viral community within CRC tissues and their contributions to colorectal carcinogenesis. Colonic mucosal biopsies were harvested from patients with CRC (biopsies of both neoplasia and adjacent normal tissue (CRC-A)) and healthy controls (HC). The shot-gun metagenomic sequencing of virus-like particles (VLPs) was performed on the biopsies. Viral community, functional pathways, and their correlations to clinical data were analyzed. Fluorescence in situ hybridizations (FISH) for the localization of viruses in the intestine was performed, as well as quantitative PCR for the detection of Torque teno virus load in human mucosal VLP DNA. A greater number and proportion of core species were found in CRC tissues than in CRC-A and HC tissues. The diversity of the mucosal virome in CRC tissues was significantly increased compared to that in HC and CRC-A tissues. The mucosal virome signature of CRC tissues were significantly different from those of HC and CRC-A tissues at the species level. The abundances of eukaryotic viruses from the Anelloviridae family and its sub-species Torque teno virus (TTV) were significantly higher in CRC patients than in HC. Furthermore, increased levels of TTV in the intestinal lamina propria were found in the CRC group. Multiple viral functions of TTV associated with carcinogenesis were enriched in CRC tissues. We revealed for the first time that the mucosal virobiota signature of CRC is characterized by a higher diversity and more eukaryotic viruses. The enrichment of TTV species in CRC tissues suggests that they may play an oncogenic role in CRC. Targeting eukaryotic viruses in the gut may provide novel strategies for the prevention and treatment of CRC.}, }
@article {pmid37507629, year = {2024}, author = {Daba, G and Daelemans, R and Berecha, G and Geerinck, MWJ and Verreth, C and Crauwels, S and Lievens, B and Honnay, O}, title = {Genetic diversity and structure of the coffee leaf rust fungus Hemileia vastatrix across different coffee management systems in Ethiopia.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {27}, number = {2}, pages = {525-534}, pmid = {37507629}, issn = {1618-1905}, mesh = {*Coffea/genetics/microbiology ; Ethiopia ; *Basidiomycota/genetics ; Polymorphism, Genetic ; Plant Diseases/microbiology ; }, abstract = {Although coffee leaf rust (CLR), caused by Hemileia vastatrix, poses an increasing threat to coffee production in Ethiopia, little is known regarding its genetic diversity and structure and how these are affected by coffee management. Here, we used genetic fingerprinting based on sequence-related amplified polymorphism (SRAP) markers to genotype H. vastatrix samples from different coffee shrubs, across 40 sites, covering four coffee production systems (forest coffee, semi plantation coffee, home garden coffee, and plantation coffee) and different altitudes in Ethiopia. In total, 96 H. vastatrix samples were successfully genotyped with three primer combinations, producing a total of 79 scorable bands. We found 35.44% of amplified bands to be polymorphic, and the polymorphic information content (PIC) was 0.45, suggesting high genetic diversity among our CLR isolates. We also found significant isolation-by-distance across the samples investigated and detected significant differences in fungal genetic composition among plantation coffee and home garden coffee and a marginally significant difference among plantation coffee and forest coffee. Furthermore, we found a significant effect of altitude on CLR genetic composition in the forest coffee and plantation systems. Our results suggest that both spore dispersal and different selection pressures in the different coffee management systems are likely responsible for the observed high genetic diversity and genetic structure of CLR isolates in Ethiopia. When selecting Ethiopian coffee genotypes for crop improvement, it is important that these genotypes carry some resistance against CLR. Because our study shows large variation in genetic composition across relatively short geographical distances, a broad selection of rust isolates must be used for coffee resistance screening.}, }
@article {pmid37507489, year = {2023}, author = {Daraz, U and Erhunmwunse, AS and Dubeux, JCB and Mackowiak, C and Guerra, VA and Hsu, CM and Ma, J and Li, Y and Yang, X and Liao, HL and Wang, XB}, title = {Soil Bacterial Communities Across Seven Rhizoma Peanut Cultivars (Arachis glabrata Benth.) Respond to Seasonal Variation.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2703-2715}, pmid = {37507489}, issn = {1432-184X}, mesh = {*Soil ; Seasons ; *Arachis/microbiology ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Soil Microbiology ; }, abstract = {Soil microorganisms play key roles in soil nutrient transformations and have a notable effect on plant growth and health. Different plant genotypes can shape soil microbial patterns via the secretion of root exudates and volatiles, but it is uncertain how a difference in soil microorganisms induced by crop cultivars will respond to short-term seasonal variations. A field experiment was conducted to assess the changes in soil bacterial communities of seven rhizoma peanut (Arachis glabrata Benth, RP) cultivars across two growing seasons, April (Spring season) and October (Fall season). Soils' bacterial communities were targeted using 16S rRNA gene amplicon sequencing. Bacterial community diversity and taxonomic composition among rhizoma peanut cultivars were significantly affected by seasons, cultivars, and their interactions (p < 0.05). Alpha diversity, as estimated by the OTU richness and Simpson index, was around onefold decrease in October than in April across most of the RP cultivars, while the soils from Arblick and Latitude had around one time higher alpha diversity in both seasons compared with other cultivars. Beta diversity differed significantly in April (R = 0.073, p < 0.01) and October (R = 0.084, p < 0.01) across seven cultivars. Bacterial dominant taxa (at phylum and genus level) were strongly affected by seasons and varied towards more dominant groups that have functional potentials involved in nutrient cycling from April to October. A large shift in water availability induced by season variations in addition to host cultivar's effects can explain the observed patterns in diversity, composition, and co-occurrence of bacterial taxa. Overall, our results demonstrate an overriding effect of short-term seasonal variations on soil bacterial communities associated with different crop cultivars. The findings suggest that season-induced shifts in environmental conditions could exert stronger impacts on soil microorganisms than the finer-scale rhizosphere effect from crop cultivars, and consequently influence largely microbe-mediated soil processes and crop health in agricultural ecosystems.}, }
@article {pmid37507488, year = {2023}, author = {Gonçalves, OS and Santana, MF}, title = {Uncovering the Secrets of Slow-Growing Bacteria in Tropical Savanna Soil Through Isolation and Genomic Analysis.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2687-2702}, pmid = {37507488}, issn = {1432-184X}, mesh = {*Soil ; RNA, Ribosomal, 16S/genetics/metabolism ; *Grassland ; Bacteria ; Genomics ; Soil Microbiology ; Phylogeny ; }, abstract = {One gram of soil holds ten billion bacteria of thousands of different species, but most remain unknown, and one of the serious issues is intrinsic to slow-growing bacteria. In this study, we aimed to isolate and characterize slow-growing bacteria from Brazilian Cerrado soil. Over a period of 4 weeks, we conducted an incubation process and selected a total of 92 isolates. These isolates, consisting mostly of slow-growing bacteria, have the ability to thrive in low-water conditions and possess features that promote plant growth. To identify the isolated bacteria, we performed 16S rRNA sequencing analysis and found that the slow-growing strains were genetically similar to known bacterial species but also belonged to a novel group of species. The new strains identified were Caballeronia sp., Neobacillus sp., Bradyrhizobium sp., and high GC Gram-positive species. Furthermore, we conducted growth experiments using various culture media and temperature conditions. These experiments revealed an extended lag phase for five strains, indicating their slow growth characteristics. Genomic analysis of these five slow-growing bacteria showed their potential to participate in biogeochemical cycles, metabolize various carbohydrates, encode proteins with a role in promoting plant growth and have biosynthetic potential for secondary metabolites. Taken together, our findings reveal the untapped potential of slow-growing bacteria in tropical savanna soils.}, }
@article {pmid37507453, year = {2023}, author = {Villela, H and Modolon, F and Schultz, J and Delgadillo-Ordoñez, N and Carvalho, S and Soriano, AU and Peixoto, RS}, title = {Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12273}, pmid = {37507453}, issn = {2045-2322}, mesh = {*Hydrocarbons/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; *Petroleum/metabolism ; Bacteria/genetics ; Alkanes/metabolism ; Biodegradation, Environmental ; }, abstract = {Here we report the oil degradation genetic potential of six oil-degrading bacteria (ODB), previously used as a bioremediation consortium, isolated from the hydrocoral Millepora alcicornis and seawater. The strains were identified as Halomonas sp. (LC_1), Cobetia sp. (LC_6), Pseudoalteromonas shioyasakiensis (LC_2), Halopseudomonas aestusnigri (LC_3), Shewanella algae (LC_4), and Brucella intermedia (LC_5). The taxonomic identification differed from that of the original paper when we used whole genome gene markers instead of just 16S rRNA gene. Genes responsible for the degradation of aromatic hydrocarbons and n-alkanes were found in all genomes, although different (and complementary) steps of the metabolic pathways were unique to each strain. Genes for naphthalene and toluene degradation were found in various strains. We annotated quinate degradation genes in LC_6, while LC_3 and LC_5 presented genes for biosurfactant and rhamnolipid biosynthesis. We also annotated genes related to beneficial mechanisms for corals, such as genes involved in nitrogen and DMSP metabolism, cobalamin biosynthesis and antimicrobial compounds production. Our findings reinforce the importance of using bacterial consortia for bioremediation approaches instead of single strains, due to their complementary genomic arsenals. We also propose a genome-based framework to select complementary ODB that can provide additional benefits to coral health.}, }
@article {pmid37507436, year = {2023}, author = {Melaugh, G and Martinez, VA and Baker, P and Hill, PJ and Howell, PL and Wozniak, DJ and Allen, RJ}, title = {Distinct types of multicellular aggregates in Pseudomonas aeruginosa liquid cultures.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {52}, pmid = {37507436}, issn = {2055-5008}, support = {BB/R012415/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 AI077628/AI/NIAID NIH HHS/United States ; R01 AI134895/AI/NIAID NIH HHS/United States ; R01 AI143916/AI/NIAID NIH HHS/United States ; }, mesh = {*Biofilms ; *Pseudomonas aeruginosa ; Polysaccharides, Bacterial/metabolism ; DNA ; }, abstract = {Pseudomonas aeruginosa forms suspended multicellular aggregates when cultured in liquid media. These aggregates may be important in disease, and/or as a pathway to biofilm formation. The polysaccharide Psl and extracellular DNA (eDNA) have both been implicated in aggregation, but previous results depend strongly on the experimental conditions. Here we develop a quantitative microscopy-based method for assessing changes in the size distribution of suspended aggregates over time in growing cultures. For exponentially growing cultures of P. aeruginosa PAO1, we find that aggregation is mediated by cell-associated Psl, rather than by either eDNA or secreted Psl. These aggregates arise de novo within the culture via a growth process that involves both collisions and clonal growth, and Psl non-producing cells do not aggregate with producers. In contrast, we find that stationary phase (overnight) cultures contain a different type of multicellular aggregate, in which both eDNA and Psl mediate cohesion. Our findings suggest that the physical and biological properties of multicellular aggregates may be very different in early-stage vs late-stage bacterial cultures.}, }
@article {pmid37505287, year = {2023}, author = {Feckler, A and Baudy-Groh, P and Friedrichs, L and Gonçalves, S and Lüderwald, S and Risse-Buhl, U and Bundschuh, M}, title = {Diatoms Reduce Decomposition of and Fungal Abundance on Less Recalcitrant Leaf Litter via Negative Priming.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2674-2686}, pmid = {37505287}, issn = {1432-184X}, support = {2017-0507//Vetenskapsr&#xe5;det/ ; }, mesh = {*Diatoms/metabolism ; Fungi/metabolism ; Rivers ; Plant Leaves/microbiology ; Carbon/metabolism ; Ecosystem ; }, abstract = {Heterotrophic microbial decomposers colonize submerged leaf litter in close spatial proximity to periphytic algae that exude labile organic carbon during photosynthesis. These exudates are conjectured to affect microbial decomposers' abundance, resulting in a stimulated (positive priming) or reduced (negative priming) leaf litter decomposition. Yet, the occurrence, direction, and intensity of priming associated with leaf material of differing recalcitrance remains poorly tested. To assess priming, we submerged leaf litter of differing recalcitrance (Alnus glutinosa [alder; less recalcitrant] and Fagus sylvatica [beech; more recalcitrant]) in microcosms and quantified bacterial, fungal, and diatom abundance as well as leaf litter decomposition over 30 days in absence and presence of light. Diatoms did not affect beech decomposition but reduced alder decomposition by 20% and alder-associated fungal abundance by 40% in the treatments including all microbial groups and light, thus showing negative priming. These results suggest that alder-associated heterotrophs acquired energy from diatom exudates rather than from leaf litter. Moreover, it is suggested that these heterotrophs have channeled energy to alternative (reproductive) pathways that may modify energy and nutrient availability for the remaining food web and result in carbon pools protected from decomposition in light-exposed stream sections.}, }
@article {pmid37505057, year = {2024}, author = {Choudhary, M and Minsavage, GV and Goss, EM and Timilsina, S and Coutinho, TA and Vallad, GE and Paret, ML and Jones, JB}, title = {Whole-Genome-Sequence-Based Classification of Xanthomonas euvesicatoria pv. eucalypti and Computational Analysis of the Type III Secretion System.}, journal = {Phytopathology}, volume = {114}, number = {1}, pages = {47-60}, doi = {10.1094/PHYTO-05-23-0150-R}, pmid = {37505057}, issn = {0031-949X}, mesh = {Type III Secretion Systems ; Phylogeny ; *Eucalyptus ; Plant Diseases/microbiology ; *Xanthomonas ; }, abstract = {Xanthomonas spp. infect a wide range of annual and perennial plants. Bacterial blight in young seedlings of Eucalyptus spp. in Indonesia was originally identified as X. perforans. However, these strains failed to elicit a hypersensitive response (HR) on either tomatoes or peppers. Two of the strains, EPK43 and BCC 972, when infiltrated into tomato and pepper leaves, failed to grow to significant levels in comparison with well-characterized X. euvesicatoria pv. perforans (Xp) strains. Furthermore, spray inoculation of 'Bonny Best' tomato plants with a bacterial suspension of the Eucalyptus strains resulted in no obvious symptoms. We sequenced the whole genomes of eight strains isolated from two Eucalyptus species between 2007 and 2015. The strains had average nucleotide identities (ANIs) of at least 97.8 with Xp and X. euvesicatoria pv. euvesicatoria (Xeu) strains, both of which are causal agents of bacterial spot of tomatoes and peppers. A comparison of the Eucalyptus strains revealed that the ANI values were >99.99% with each other. Core genome phylogeny clustered all Eucalyptus strains with X. euvesicatoria pv. rosa. They formed separate clades, which included X. euvesicatoria pv. alangii, X. euvesicatoria pv. citrumelonis, and X. euvesicatoria pv. alfalfae. Based on ANI, phylogenetic relationships, and pathogenicity, we designated these Eucalyptus strains as X. euvesicatoria pv. eucalypti (Xee). Comparative analysis of sequenced strains provided unique profiles of type III secretion effectors. Core effector XopD, present in all pathogenic Xp and Xeu strains, was absent in the Xee strains. Comparison of the hrp clusters of Xee, Xp, and Xeu genomes revealed that HrpE in Xee strains was very different from that in Xp and Xeu. To determine if it was functional, we deleted the gene and complemented with the Xee hrpE, confirming it was essential for secretion of type III effectors. HrpE has a hypervariable N-terminus in Xanthomonas spp., in which the N-terminus of Xee strains differs significantly from those of Xeu and Xp strains.}, }
@article {pmid37500801, year = {2023}, author = {Esser, SP and Rahlff, J and Zhao, W and Predl, M and Plewka, J and Sures, K and Wimmer, F and Lee, J and Adam, PS and McGonigle, J and Turzynski, V and Banas, I and Schwank, K and Krupovic, M and Bornemann, TLV and Figueroa-Gonzalez, PA and Jarett, J and Rattei, T and Amano, Y and Blaby, IK and Cheng, JF and Brazelton, WJ and Beisel, CL and Woyke, T and Zhang, Y and Probst, AJ}, title = {A predicted CRISPR-mediated symbiosis between uncultivated archaea.}, journal = {Nature microbiology}, volume = {8}, number = {9}, pages = {1619-1633}, pmid = {37500801}, issn = {2058-5276}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Archaea/genetics/metabolism ; *Symbiosis/genetics ; Genomics ; Plasmids ; DNA/metabolism ; }, abstract = {CRISPR-Cas systems defend prokaryotic cells from invasive DNA of viruses, plasmids and other mobile genetic elements. Here, we show using metagenomics, metatranscriptomics and single-cell genomics that CRISPR systems of widespread, uncultivated archaea can also target chromosomal DNA of archaeal episymbionts of the DPANN superphylum. Using meta-omics datasets from Crystal Geyser and Horonobe Underground Research Laboratory, we find that CRISPR spacers of the hosts Candidatus Altiarchaeum crystalense and Ca. A. horonobense, respectively, match putative essential genes in their episymbionts' genomes of the genus Ca. Huberiarchaeum and that some of these spacers are expressed in situ. Metabolic interaction modelling also reveals complementation between host-episymbiont systems, on the basis of which we propose that episymbionts are either parasitic or mutualistic depending on the genotype of the host. By expanding our analysis to 7,012 archaeal genomes, we suggest that CRISPR-Cas targeting of genomes associated with symbiotic archaea evolved independently in various archaeal lineages.}, }
@article {pmid37496156, year = {2022}, author = {Wolfsberger, W and Chhugani, K and Shchubelka, K and Frolova, A and Salyha, Y and Zlenko, O and Arych, M and Dziuba, D and Parkhomenko, A and Smolanka, V and Gümüş, ZH and Sezgin, E and Diaz-Lameiro, A and Toth, VR and Maci, M and Bortz, E and Kondrashov, F and Morton, PM and Łabaj, PP and Romero, V and Hlávka, J and Mangul, S and Oleksyk, TK}, title = {Scientists without borders: lessons from Ukraine.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {37496156}, issn = {2047-217X}, support = {R33 CA263705/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Ukraine ; *Armed Conflicts ; *Science ; }, abstract = {Conflicts and natural disasters affect entire populations of the countries involved and, in addition to the thousands of lives destroyed, have a substantial negative impact on the scientific advances these countries provide. The unprovoked invasion of Ukraine by Russia, the devastating earthquake in Turkey and Syria, and the ongoing conflicts in the Middle East are just a few examples. Millions of people have been killed or displaced, their futures uncertain. These events have resulted in extensive infrastructure collapse, with loss of electricity, transportation, and access to services. Schools, universities, and research centers have been destroyed along with decades' worth of data, samples, and findings. Scholars in disaster areas face short- and long-term problems in terms of what they can accomplish now for obtaining grants and for employment in the long run. In our interconnected world, conflicts and disasters are no longer a local problem but have wide-ranging impacts on the entire world, both now and in the future. Here, we focus on the current and ongoing impact of war on the scientific community within Ukraine and from this draw lessons that can be applied to all affected countries where scientists at risk are facing hardship. We present and classify examples of effective and feasible mechanisms used to support researchers in countries facing hardship and discuss how these can be implemented with help from the international scientific community and what more is desperately needed. Reaching out, providing accessible training opportunities, and developing collaborations should increase inclusion and connectivity, support scientific advancements within affected communities, and expedite postwar and disaster recovery.}, }
@article {pmid37491575, year = {2023}, author = {Kim, JM and Yoo, SY and An, JS and Woo, JJ and Cho, YD and Park, HE and Karm, MH}, title = {Effect of a multichannel oral irrigator on periodontal health and the oral microbiome.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12043}, pmid = {37491575}, issn = {2045-2322}, mesh = {Humans ; Administration, Oral ; Dental Plaque Index ; *Microbiota ; *Periodontal Diseases ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Oral biofilms or dental plaques are one of the major etiological factors for diverse oral diseases. We aimed to evaluate the effect of a multichannel oral irrigator (MCOI) on periodontal health in 29 participants randomly divided into two groups: the MCOI group and the control group. To evaluate the effect of the MCOI on periodontal health, the modified Quigley Hein Plaque Index (PI), Mühlemann-Son Sulcus Bleeding Index (SBI), bleeding on probing (BOP), and swelling were evaluated and compared before and after MCOI use for 3 days. Although PI and SBI showed statistically significant increases in the control group, the MCOI group showed no significant changes in either parameter. Moreover, the percentage of BOP was significantly lower in the MCOI group. Saliva samples were analyzed by 16s rRNA amplicon sequencing to investigate changes in the oral microbiome. Sequencing results showed that Porphyromonas spp. were significantly increased in the control group, whereas no significant change was detected in the MCOI group. Using the MCOI, enriched populations and functional pathways were detected in pioneer species comprising non-mutans streptococci. These findings provide evidence of the effectiveness of the MCOI in maintaining periodontal health and a healthy microbial ecology in the oral cavity.}, }
@article {pmid37486583, year = {2023}, author = {Zaman, R and Antonioli, F and Shah, A and Ullah, A and May, C and Klutsch, JG and Erbilgin, N}, title = {A Pine in Distress: How Infection by Different Pathogenic Fungi Affect Lodgepole Pine Chemical Defenses.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2666-2673}, pmid = {37486583}, issn = {1432-184X}, mesh = {Animals ; *Pinus/microbiology ; *Coleoptera/microbiology ; *Weevils ; Canada ; Terpenes ; }, abstract = {In North America, lodgepole pine is frequently subjected to attacks by various biotic agents that compromise its ability to defend against subsequent attacks by insect herbivores. We investigated whether infections of lodgepole pine by different pathogenic fungal species have varying effects on its defense chemistry. We selected two common pathogens, Atropellis canker, Atropellis piniphila, and western gall rust, Endocronartium harknessii, affecting mature lodgepole pine trees in western Canada. We also included three ophiostomatoid fungi Grosmannia clavigera, Ophiostoma montium, and Leptographium longiclavatum associated with the mountain pine beetle (Dendroctonus ponderosae), because they are commonly used to investigate induced defenses of host trees of bark beetles. We collected phloem samples from lodgepole pines infected with the rust or the canker and healthy lodgepole pines in the same stand. We also inoculated mature lodgepole pines with the three fungal symbionts and collected phloem samples 2 weeks later when the defense chemistry was at its highest level. Different fungal species differentially altered the terpene chemistry of lodgepole pine trees. E. harknessii and the fungal symbionts altered the terpene chemistry in a similar pattern while trees responded to the infection by the A. piniphila differently. Our study highlights the importance of considering specific biotic stress agents in tree susceptibility or resistance to the subsequent attacks by insect herbivores, such as mountain pine beetle.}, }
@article {pmid37485515, year = {2023}, author = {Němečková, K and Mareš, J and Procházková, L and Culka, A and Košek, F and Wierzchos, J and Nedbalová, L and Dudák, J and Tymlová, V and Žemlička, J and Kust, A and Zima, J and Nováková, E and Jehlička, J}, title = {Gypsum endolithic phototrophs under moderate climate (Southern Sicily): their diversity and pigment composition.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1175066}, pmid = {37485515}, issn = {1664-302X}, abstract = {In this study, we used microscopic, spectroscopic, and molecular analysis to characterize endolithic colonization in gypsum (selenites and white crystalline gypsum) from several sites in Sicily. Our results showed that the dominant microorganisms in these environments are cyanobacteria, including: Chroococcidiopsis sp., Gloeocapsopsis pleurocapsoides, Gloeocapsa compacta, and Nostoc sp., as well as orange pigmented green microalgae from the Stephanospherinia clade. Single cell and filament sequencing coupled with 16S rRNA amplicon metagenomic profiling provided new insights into the phylogenetic and taxonomic diversity of the endolithic cyanobacteria. These organisms form differently pigmented zones within the gypsum. Our metagenomic profiling also showed differences in the taxonomic composition of endoliths in different gypsum varieties. Raman spectroscopy revealed that carotenoids were the most common pigments present in the samples. Other pigments such as gloeocapsin and scytonemin were also detected in the near-surface areas, suggesting that they play a significant role in the biology of endoliths in this environment. These pigments can be used as biomarkers for basic taxonomic identification, especially in case of cyanobacteria. The findings of this study provide new insights into the diversity and distribution of phototrophic microorganisms and their pigments in gypsum in Southern Sicily. Furthemore, this study highlights the complex nature of endolithic ecosystems and the effects of gypsum varieties on these communities, providing additional information on the general bioreceptivity of these environments.}, }
@article {pmid37485507, year = {2023}, author = {Thiele, S and Vader, A and Thomson, S and Saubrekka, K and Petelenz, E and Müller, O and Bratbak, G and Øvreås, L}, title = {Seasonality of the bacterial and archaeal community composition of the Northern Barents Sea.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1213718}, pmid = {37485507}, issn = {1664-302X}, abstract = {The Barents Sea is a transition zone between the Atlantic and the Arctic Ocean. The ecosystem in this region is highly variable, and a seasonal baseline of biological factors is needed to monitor the effects of global warming. In this study, we report the results from the investigations of the bacterial and archaeal community in late winter, spring, summer, and early winter along a transect through the northern Barents Sea into the Arctic Ocean east of Svalbard using 16S rRNA metabarcoding. Winter samples were dominated by members of the SAR11 clade and a community of nitrifiers, namely Cand. Nitrosopumilus and LS-NOB (Nitrospinia), suggest a prevalence of chemoautotrophic metabolisms. During spring and summer, members of the Gammaproteobacteria (mainly members of the SAR92 and OM60(NOR5) clades, Nitrincolaceae) and Bacteroidia (mainly Polaribacter, Formosa, and members of the NS9 marine group), which followed a succession based on their utilization of different phytoplankton-derived carbon sources, prevailed. Our results indicate that Arctic marine bacterial and archaeal communities switch from carbon cycling in spring and summer to nitrogen cycling in winter and provide a seasonal baseline to study the changes in these processes in response to the effects of climate change.}, }
@article {pmid37485503, year = {2023}, author = {Van Holm, W and Lauwens, K and De Wever, P and Schuermans, A and Zayed, N and Pamuk, F and Saghi, M and Fardim, P and Bernaerts, K and Boon, N and Teughels, W}, title = {Probiotics for oral health: do they deliver what they promise?.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1219692}, pmid = {37485503}, issn = {1664-302X}, abstract = {Probiotics have demonstrated oral health benefits by influencing the microbiome and the host. Although promising, their current use is potentially constrained by several restrictions. One such limiting factor lies in the prevailing preparation of a probiotic product. To commercialize the probiotic, a shelf stable product is achieved by temporarily inactivating the live probiotic through drying or freeze drying. Even though a lyophilized probiotic can be kept dormant for an extended period of time, their viability can be severely compromised, making their designation as probiotics questionable. Additionally, does the application of an inactive probiotic directly into the oral cavity make sense? While the dormancy may allow for survival on its way towards the gut, does it affect their capacity for oral colonisation? To evaluate this, 21 probiotic product for oral health were analysed for the number of viable (probiotic), culturable (CFU) and dead (postbiotic) cells, to verify whether the commercial products indeed contain what they proclaim. After isolating and uniformly lyophilizing three common probiotic species in a simple yet effective lyoprotective medium, the adhesion to saliva covered hydroxyapatite discs of lyophilized probiotics was compared to fresh or reactivated lyophilized probiotics. Unfortunately, many of the examined products failed to contain the claimed amounts of viable cells, but also the strains used were inadequately characterized and lacked clinical evidence for that unknown strain, questioning their label of a 'probiotic'. Additionally, lyophilized probiotics demonstrated low adhesive capacity compared to their counterparts, prompting the question of why fresh or reactivated probiotics are not currently used.}, }
@article {pmid37482337, year = {2023}, author = {Santás-Miguel, V and Arias-Estévez, M and Rodríguez-Seijo, A and Arenas-Lago, D}, title = {Use of metal nanoparticles in agriculture. A review on the effects on plant germination.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {334}, number = {}, pages = {122222}, doi = {10.1016/j.envpol.2023.122222}, pmid = {37482337}, issn = {1873-6424}, mesh = {*Metal Nanoparticles/toxicity ; Silver/toxicity ; Agriculture/methods ; Soil ; *Nanoparticles ; Nanotechnology ; Germination ; }, abstract = {Agricultural nanotechnology has become a powerful tool to help crops and improve agricultural production in the context of a growing world population. However, its application can have some problems with the development of harvests, especially during germination. This review evaluates nanoparticles with essential (Cu, Fe, Ni and Zn) and non-essential (Ag and Ti) elements on plant germination. In general, the effect of nanoparticles depends on several factors (dose, treatment time, application method, type of nanoparticle and plant). In addition, pH and ionic strength are relevant when applying nanoparticles to the soil. In the case of essential element nanoparticles, Fe nanoparticles show better results in improving nutrient uptake, improving germination, and the possibility of magnetic properties could favor their use in the removal of pollutants. In the case of Cu and Zn nanoparticles, they can be beneficial at low concentrations, while their excess presents toxicity and negatively affects germination. About nanoparticles of non-essential elements, both Ti and Ag nanoparticles can be helpful for nutrient uptake. However, their potential effects depend highly on the crop type, particle size and concentration. Overall, nanotechnology in agriculture is still in its early stages of development, and more research is needed to understand potential environmental and public health impacts.}, }
@article {pmid37482010, year = {2023}, author = {Pan, Y and Sun, RZ and Wang, Y and Chen, GL and Fu, YY and Yu, HQ}, title = {Carbon source shaped microbial ecology, metabolism and performance in denitrification systems.}, journal = {Water research}, volume = {243}, number = {}, pages = {120330}, doi = {10.1016/j.watres.2023.120330}, pmid = {37482010}, issn = {1879-2448}, mesh = {*Carbon/chemistry ; *Denitrification ; Methanol ; Glycerol ; Bioreactors/microbiology ; Acetates ; Glucose ; Nitrogen/metabolism ; Nitrates/metabolism ; }, abstract = {The limited information on microbial interactions and metabolic patterns in denitrification systems, especially those fed with different carbon sources, has hindered the establishment of ecological linkages between microscale connections and macroscopic reactor performance. In this work, denitrification performance, metabolic patterns, and ecological structure were investigated in parallel well-controlled bioreactors with four representative carbon sources, i.e., methanol, glycerol, acetate, and glucose. After long-term acclimation, significant differences were observed among the four bioreactors in terms of denitrification rates, organic utilization, and heterotrophic bacterial yields. Different carbon sources induced the succession of denitrifying microbiota toward different ecological structures and exhibited distinct metabolic patterns. Methanol-fed reactors showed distinctive microbial carbon utilization pathways and a more intricate microbial interaction network, leading to significant variations in organic utilization and metabolite production compared to other carbon sources. Three keystone taxa belonging to the Verrucomicrobiota phylum, SJA-15 order and the Kineosphaera genus appeared as network hubs in the methanol, glycerol, and acetate-fed systems, playing essential roles in their ecological functions. Several highly connected species were also identified within the glucose-fed system. The close relationship between microbial metabolites, ecological structures, and system performances suggests that this complex network relationship may greatly contribute to the efficient operation of bioreactors.}, }
@article {pmid37482007, year = {2023}, author = {Wang, M and Wang, X and Zhou, S and Chen, Z and Chen, M and Feng, S and Li, J and Shu, W and Cao, B}, title = {Strong succession in prokaryotic association networks and community assembly mechanisms in an acid mine drainage-impacted riverine ecosystem.}, journal = {Water research}, volume = {243}, number = {}, pages = {120343}, doi = {10.1016/j.watres.2023.120343}, pmid = {37482007}, issn = {1879-2448}, mesh = {*Ecosystem ; Mining ; *Microbiota ; Microbial Consortia ; Fresh Water ; Iron ; }, abstract = {Acid mine drainage (AMD) serves as an ideal model system for investigating microbial ecology, interaction, and assembly mechanism in natural environments. While previous studies have explored the structure and function of microbial communities in AMD, the succession patterns of microbial association networks and underlying assembly mechanisms during natural attenuation processes remain elusive. Here, we investigated prokaryotic microbial diversity and community assembly along an AMD-impacted river, from the extremely acidic, heavily polluted headwaters to the nearly neutral downstream sites. Microbial diversity was increased along the river, and microbial community composition shifted from acidophile-dominated to freshwater taxa-dominated communities. The complexity and relative modularity of the microbial networks were also increased, indicating greater network stability during succession. Deterministic processes, including abiotic selection of pH and high contents of sulfur and iron, governed community assembly in the headwaters. Although the stochasticity ratio was increased downstream, manganese content, microbial negative cohesion, and relative modularity played important roles in shaping microbial community structure. Overall, this study provides valuable insights into the ecological processes that govern microbial community succession in AMD-impacted riverine ecosystems. These findings have important implications for in-situ remediation of AMD contamination.}, }
@article {pmid37480518, year = {2023}, author = {O'Brien, L and Siboni, N and Seymour, JR and Balzer, M and Mitrovic, S}, title = {Tributary Inflows to a Regulated River Influence Bacterial Communities and Increase Bacterial Carbon Assimilation.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2642-2654}, pmid = {37480518}, issn = {1432-184X}, mesh = {*Rivers/chemistry ; *Carbon ; Ecosystem ; Water ; Bacteria/genetics ; }, abstract = {Inflows from unregulated tributaries change the physical, chemical, and biotic conditions in receiving regulated rivers, impacting microbial community structure and metabolic function. Understanding how tributary inflows affect bacterial carbon production (BCP) is integral to understanding energy transfer in riverine ecosystems. To investigate the role of tributary inflows on bacterial community composition and BCP, a ~90th percentile natural flow event was sampled over 5 days along the Lachlan River and its tributaries within the Murray-Darling Basin of eastern Australia. Increased tributary inflows after rainfall corresponded with a significantly different and more diverse bacterial community in the regulated mainstem. The major contributor to this difference was an increase in relative abundance of bacterial groups with a potential metabolic preference for humic substances (Burkholderiaceae Polynucleobacter, Alcaligenaceae GKS98 freshwater group, Saccharimonadia) and a significant decrease in Spirosomaceae Pseudarcicella, known to metabolise algal exudates. Increases in orthophosphate and river discharge explained 31% of community change, suggesting a combination of resource delivery and microbial community coalescence as major drivers. BCP initially decreased significantly with tributary inflows, but the total load of carbon assimilated by bacteria increased by up to 20 times with flow due to increased water volume. The significant drivers of BCP were dissolved organic carbon, water temperature, and conductivity. Notably, BCP was not correlated with bacterial diversity or community composition. Tributary inflows were shown to alter mainstem bacterial community structure and metabolic function to take advantage of fresh terrestrial dissolved organic material, resulting in substantial changes to riverine carbon assimilation over small times scales.}, }
@article {pmid37480517, year = {2023}, author = {Aguado-López, D and Bartolomé, C and Lopes, AR and Henriques, D and Segura, SK and Maside, X and Pinto, MA and Higes, M and Martín-Hernández, R}, title = {Frequent Parasitism of Apis mellifera by Trypanosomatids in Geographically Isolated Areas with Restricted Beekeeping Movements.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2655-2665}, pmid = {37480517}, issn = {1432-184X}, support = {project No. SBPLY/19/180501/000334//Consejer&#xed;a de Educaci&#xf3;n, Cultura y Deportes, of the Junta de Castilla - La Mancha (European Regional development Fund)/ ; Grant no. PRE2018-084878, RTA2017-00004-C02-01//Ministerio de Asuntos Econ&#xf3;micos y Transformaci&#xf3;n Digital/ ; program COMPETE 2020-POCI//Programa Operacional para a Competividade e Internacionaliza&#xe7;&#xe3;o/ ; project BeeHappy (POCI-01-0145-FEDER-029871)//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/143627/2019//Funda&#xe7;ao para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0007/2021//SusTEC/ ; INCRECYT program//European Social Funds/ ; }, mesh = {Animals ; Bees ; *Beekeeping ; *Trypanosomatina/genetics/parasitology ; Crithidia/genetics/parasitology ; Symbiosis ; Azores ; }, abstract = {Trypanosomatids form a group of high prevalence protozoa that parasitise honey bees, with Lotmaria passim as the predominant species worldwide. However, the knowledge about the ecology of trypanosomatids in isolated areas is limited. The Portuguese archipelagos of Madeira and Azores provide an interesting setting to investigate these parasites because of their geographic isolation, and because they harbour honey bee populations devoid of two major enemies: Varroa destructor and Nosema ceranae. Hence, a total of 661 honey bee colonies from Madeira and the Azores were analysed using different molecular techniques, through which we found a high prevalence of trypanosomatids despite the isolation of these islands. L. passim was the predominant species and, in most colonies, was the only one found, even on islands free of V. destructor and/or N. ceranae with severe restrictions on colony movements to prevent the spread of them. However, islands with V. destructor had a significantly higher prevalence of L. passim and, conversely, islands with N. ceranae did not shown any significant correlation with the trypanosomatid. Crithidia bombi was detected in Madeira and on three islands of the Azores, almost always coincident with L. passim. By contrast, Crithidia mellificae was not detected in any sample. A high-throughput sequencing analysis distinguished two main haplotypes of L. passim, which accounted for 98% of the total sequence reads. This work suggests that L. passim and C. bombi are parasites that have been associated with honey bees predating the spread of V. destructor and N. ceranae.}, }
@article {pmid37479828, year = {2023}, author = {Ravindhiran, R and Sivarajan, K and Sekar, JN and Murugesan, R and Dhandapani, K}, title = {Listeria monocytogenes an Emerging Pathogen: a Comprehensive Overview on Listeriosis, Virulence Determinants, Detection, and Anti-Listerial Interventions.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2231-2251}, pmid = {37479828}, issn = {1432-184X}, mesh = {Animals ; Humans ; *Listeria monocytogenes/genetics ; *Listeria ; Virulence ; Food Microbiology ; *Listeriosis/diagnosis/epidemiology/microbiology ; Virulence Factors/genetics ; }, abstract = {Listeria monocytogenes, the third most deleterious zoonotic pathogen, is a major causative agent of animal and human listeriosis, an infection related to the consumption of contaminated food products. Even though, this pathogen has been responsible for the outbreaks of foodborne infections in the early 1980s, the major outbreaks have been reported during the past two decades. Listeriosis infection in the host is a rare but life-threatening disease with major public health and economic implications. Extensive reports on listeriosis outbreaks are associated with milk and milk products, meat and meat products, and fresh produce. This bacterium can adapt to any environmental and stress conditions, making it a prime causative agent for major foodborne diseases. The pathogen could survive an antibiotic treatment and persist in the host cell, thereby escaping the standard diagnostic practices. The current review strives to provide concise information on the epidemiology, serotypes, and pathogenesis of the L. monocytogenes to decipher the knowledge on the endurance of the pathogen inside the host and food products as a vehicle for Listeria contaminations. In addition, various detection methods for Listeria species from food samples and frontline regimens of L. monocytogenes treatment have also been discussed.}, }
@article {pmid37479827, year = {2023}, author = {Hirata, K and Asahi, T and Kataoka, K}, title = {Spatial and Sexual Divergence of Gut Bacterial Communities in Field Cricket Teleogryllus occipitalis (Orthoptera: Gryllidae).}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2627-2641}, pmid = {37479827}, issn = {1432-184X}, mesh = {Animals ; Female ; Male ; *Gastrointestinal Microbiome ; *Gryllidae ; RNA, Ribosomal, 16S/genetics ; *Cricket Sport ; Bacteria/genetics ; }, abstract = {The insect gut is colonized by microbes that confer a myriad of beneficial services to the host, including nutritional support, immune enhancement, and even influence behavior. Insect gut microbes show dynamic changes due to the gut compartments, sex, and seasonal and geographic influences. Crickets are omnivorous hemimetabolous insects that have sex-specific roles, such as males producing chirping sounds for communication and exhibiting fighting behavior. However, limited information is available on their gut bacterial communities, hampering studies on functional compartmentalization of the gut and sex-specific roles of the gut microbiota in omnivorous insects. Here, we report a metagenomic analysis of the gut bacteriome of the field cricket Teleogryllus occipitalis using 16S rRNA V3-V4 amplicon sequencing to identify sex- and compartment-dependent influences on its diversity and function. The structure of the gut microbiota is strongly influenced by their gut compartments rather than sex. The species richness and diversity analyses revealed large difference in the bacterial communities between the gut compartments while minor differences were observed between the sexes. Analysis of relative abundance and predicted functions revealed that nitrogen- and oxygen-dependent metabolism and amino acid turnover were subjected to functional compartmentalization in the gut. Comparisons between the sexes revealed differences in the gut microbiota, reflecting efficiency in energy use, including glycolytic and carbohydrate metabolism, suggesting a possible involvement in egg production in females. This study provides insights into the gut compartment dependent and sex-specific roles of host-gut symbiont interactions in crickets and the industrial production of crickets.}, }
@article {pmid37478594, year = {2023}, author = {Tang, Y and Wang, C and Holm, PE and Hansen, HCB and Brandt, KK}, title = {Impacts of biochar materials on copper speciation, bioavailability, and toxicity in chromated copper arsenate polluted soil.}, journal = {Journal of hazardous materials}, volume = {459}, number = {}, pages = {132067}, doi = {10.1016/j.jhazmat.2023.132067}, pmid = {37478594}, issn = {1873-3336}, mesh = {Humans ; Copper/toxicity ; *Trace Elements ; Biological Availability ; *Soil Pollutants/metabolism ; Charcoal ; Soil ; Triticum/metabolism ; }, abstract = {Trace element polluted soils pose risks to human and environmental health. Biochar can decrease trace element bioavailability in soils, but their resulting ability to reduce soil toxicity may vary significantly depending on feedstocks used, pyrolysis conditions, and the target pollutants. Chromated copper arsenate (CCA) polluted sites are common, but only very few types of biochar have been tested for these sites. Hence, we tested fourteen well-characterized biochar materials for their ability to bind Cu and reduce toxicity in a CCA polluted soil in a 56-day experiment. Biochar (1%, wt/wt) increased plant (wheat, Triticum aestivum L.) shoot and root growth by 6-58% and 0-73%, reduced soil toxicity to Arthrobacter globiformis by 7-55%, decreased bioavailable Cu (Pseudomonas fluorescens bioreporter) by 5-65%, and decreased free Cu[2+] ion activities by 27-89%. The A. globiformis solid-contact test constituted a sensitive ecotoxicological endpoint and deserves further attention for assessment of soil quality. Oil seed rape straw biochar generally performed better than other tested biochar materials. Biochar performance was positively correlated with its high cation exchange capacity, multiple surface functional groups, and high nitrogen and phosphorus content. Our results pave the way for future selection of feedstocks for creation of modified biochar materials with optimal performance in CCA polluted soil.}, }
@article {pmid37476672, year = {2023}, author = {Zhang, Y and Wang, R}, title = {The human gut phageome: composition, development, and alterations in disease.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1213625}, pmid = {37476672}, issn = {1664-302X}, abstract = {The human gastrointestinal tract is colonized by a large number of microorganisms, including bacteria, archaea, viruses, and eukaryotes. The bacterial community has been widely confirmed to have a significant impact on human health, while viruses, particularly phages, have received less attention. Phages are viruses that specifically infect bacteria. They are abundant in the biosphere and exist in a symbiotic relationship with their host bacteria. Although the application of high-throughput sequencing and bioinformatics technology has greatly improved our understanding of the genomic diversity, taxonomic composition, and spatio-temporal dynamics of the human gut phageome, there is still a large portion of sequencing data that is uncharacterized. Preliminary studies have predicted that the phages play a crucial role in driving microbial ecology and evolution. Prior to exploring the function of phages, it is necessary to address the obstacles that hinder establishing a comprehensive sequencing database with sufficient biological properties and understanding the impact of phage-bacteria interactions on human health. In this study, we provide an overview of the human gut phageome, including its composition, structure, and development. We also explore the various factors that may influence the phageome based on current research, including age, diet, ethnicity, and geographical location. Additionally, we summarize the relationship between the phageome and human diseases, such as IBD, IBS, obesity, diabetes, and metabolic syndrome.}, }
@article {pmid37474781, year = {2023}, author = {Yu, L and Khachaturyan, M and Matschiner, M and Healey, A and Bauer, D and Cameron, B and Cusson, M and Emmett Duffy, J and Joel Fodrie, F and Gill, D and Grimwood, J and Hori, M and Hovel, K and Hughes, AR and Jahnke, M and Jenkins, J and Keymanesh, K and Kruschel, C and Mamidi, S and Menning, DM and Moksnes, PO and Nakaoka, M and Pennacchio, C and Reiss, K and Rossi, F and Ruesink, JL and Schultz, ST and Talbot, S and Unsworth, R and Ward, DH and Dagan, T and Schmutz, J and Eisen, JA and Stachowicz, JJ and Van de Peer, Y and Olsen, JL and Reusch, TBH}, title = {Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina).}, journal = {Nature plants}, volume = {9}, number = {8}, pages = {1207-1220}, pmid = {37474781}, issn = {2055-0278}, mesh = {*Ecosystem ; *Zosteraceae/genetics ; Canada ; Phylogeography ; Oceans and Seas ; }, abstract = {Currents are unique drivers of oceanic phylogeography and thus determine the distribution of marine coastal species, along with past glaciations and sea-level changes. Here we reconstruct the worldwide colonization history of eelgrass (Zostera marina L.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Two west-to-east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival of Z. marina in the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present there for ~243 ky (thousand years). Mediterranean populations were founded ~44 kya, while extant distributions along western and eastern Atlantic shores were founded at the end of the Last Glacial Maximum (~19 kya), with at least one major refuge being the North Carolina region. The recent colonization and five- to sevenfold lower genomic diversity of the Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans.}, }
@article {pmid37470815, year = {2023}, author = {Lee, K and Bogdanova, A and Missaoui, A}, title = {Host Genetic Background Effect on Vertical Seed Transmission of Epichloë Endophyte Strains in Tall Fescue.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2618-2626}, pmid = {37470815}, issn = {1432-184X}, mesh = {Endophytes/genetics ; *Lolium/genetics/microbiology ; *Epichloe/genetics ; Poaceae ; Seeds/microbiology ; *Festuca/microbiology ; }, abstract = {Tall fescue (Lolium arundinaceum (Schreb.) Darbysh.) is a cool-season perennial grass widely grown for forage and turf. Tall fescue lives in association with a fungal endophyte that helps the grass overcome abiotic and biotic stressors. The endophyte is asexual and transmits vertically from the tall fescue plant to the next generation through the seed. Producers of endophyte-infected tall fescue must have endophyte infection in at least 70% of their seed. Therefore, endophyte seed transmission is vital in breeding and seed production. Transfer of endophytes from their native host to different backgrounds of elite tall fescue cultivars can lead to a low seed transmission of the endophyte to the seed. This study screened 23 previously uncharacterized endophyte strains for transmissibility when artificially inoculated into continental and Mediterranean-type host tall fescue. We found no correlation between the rate of successful inoculation and the seed transmission rate of the endophyte in the new host. Nor did the seed transmission rate of the endophyte strains in their native host correlate with the seed transmission rate of the endophyte in the new host. Five strains exhibited seed transmission above 70% in both Mediterranean and Continental host backgrounds and will be characterized further for potential use in cultivar development.}, }
@article {pmid37469593, year = {2023}, author = {Riedel, T and Bunk, B and Schröttner, P}, title = {Editorial: Characterization of rare and recently first described human pathogenic bacteria.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1212627}, pmid = {37469593}, issn = {2235-2988}, mesh = {Humans ; *Bacteria/genetics ; *Genome, Bacterial ; }, }
@article {pmid37468677, year = {2023}, author = {Banas, I and Esser, SP and Turzynski, V and Soares, A and Novikova, P and May, P and Moraru, C and Hasenberg, M and Rahlff, J and Wilmes, P and Klingl, A and Probst, AJ}, title = {Spatio-functional organization in virocells of small uncultivated archaea from the deep biosphere.}, journal = {The ISME journal}, volume = {17}, number = {10}, pages = {1789-1792}, pmid = {37468677}, issn = {1751-7370}, support = {863664/ERC_/European Research Council/International ; }, mesh = {*Archaea/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Viruses/genetics ; DNA, Viral/genetics ; }, abstract = {Despite important ecological roles posited for virocells (i.e., cells infected with viruses), studying individual cells in situ is technically challenging. We introduce here a novel correlative microscopic approach to study the ecophysiology of virocells. By conducting concerted virusFISH, 16S rRNA FISH, and scanning electron microscopy interrogations of uncultivated archaea, we linked morphologies of various altiarchaeal cells to corresponding phylogenetic signals and indigenous virus infections. While uninfected cells exhibited moderate separation between fluorescence signals of ribosomes and DNA, virocells displayed complete cellular segregation of chromosomal DNA from viral DNA, the latter co-localizing with host ribosome signals. A similar spatial separation was observed in dividing cells, with viral signals congregating near ribosomes at the septum. These observations suggest that replication of these uncultivated viruses occurs alongside host ribosomes, which are used to generate the required proteins for virion assembly. Heavily infected cells sometimes displayed virus-like particles attached to their surface, which agree with virus structures in cells observed via transmission electron microscopy. Consequently, this approach is the first to link genomes of uncultivated viruses to their respective structures and host cells. Our findings shed new light on the complex ecophysiology of archaeal virocells in deep subsurface biofilms and provide a solid framework for future in situ studies of virocells.}, }
@article {pmid37466247, year = {2024}, author = {Avasthi, I and Lerner, H and Grings, J and Gräber, C and Schleheck, D and Cölfen, H}, title = {Biodegradable Mineral Plastics.}, journal = {Small methods}, volume = {8}, number = {4}, pages = {e2300575}, doi = {10.1002/smtd.202300575}, pmid = {37466247}, issn = {2366-9608}, support = {//Carl-Zeiss Foundation/ ; }, abstract = {Mineral plastics are a promising class of bio-inspired materials that offer exceptional properties, like self-heal ability, stretchability in the hydrogel state, and high hardness, toughness, transparency, and non-flammability in the dry state along with reversible transformation into the hydrogel by addition of water. This enables easy reshape-ability and recycling like the solubility in mild acids to subsequently form mineral plastics again by base addition. However, current mineral plastics rely on petrochemistry, are hardly biodegradable, and thus persistent in nature. This work presents the next generation of mineral plastics, which are bio-based and biodegradable, making them a promising, new class of polymers for the development of environmentally friendly materials. Physically cross-linked (poly)glutamic-acid (PGlu)-based mineral plastics are synthesized using various alcohol-water mixtures, metal ion ratios and molecular weights. The rheological properties are easily adjusted using these parameters. The general procedure involves addition of equimolar solution of CaCl2 to PGlu in equal volumes followed by addition of iPrOH (iPrOH:H2O = 1:1) under vigorous stirring conditions. The ready biodegradability of PGlu/CaFe mineral plastic is confirmed in this study where the elements N, Ca, and Fe present in it tend to act as additional nutrients, supporting the growth of microorganisms and consequently, promoting the biodegradation process.}, }
@article {pmid37461605, year = {2023}, author = {Simpson, AC and Sengupta, P and Zhang, F and Hameed, A and Parker, CW and Singh, NK and Miliotis, G and Rekha, PD and Raman, K and Mason, CE and Venkateswaran, K}, title = {Phylogenetic affiliations and genomic characterization of novel bacterial species and their abundance in the International Space Station.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {37461605}, issn = {2693-5015}, support = {R01 MH117406/MH/NIMH NIH HHS/United States ; }, abstract = {BACKGROUND: With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habits, and how microbes survive, proliferate and spread in space conditions, is coming more and more important. The Microbial Tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the International Space Station (ISS).<br><br>RESULTS: The analysis of their 16S rRNA gene sequences revealed <99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing (WGS) was undertaken. For all strains, the gyrB gene exhibited <93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average ucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values, when compared to any known bacterial species, were less than <94% and 50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including &#x3b2;-lactone and type III polyketide synthase (T3PKS) clusters.<br><br>CONCLUSIONS: Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10[T] (=NRRL B-65660[T]), Leifsonia virtsii, F6_8S_P_1A[T] (=NRRL B-65661[T]), Leifsonia williamsii, F6_8S_P_1B[T] (=NRRL B- 65662[T] and DSMZ 115932[T]), Paenibacillus vandeheii, F6_3S_P_1C[T](=NRRL B-65663[T] and DSMZ 115940[T]), and Sporosarcina highlanderae F6_3S_P_2 T(=NRRL B-65664[T] and DSMZ 115943[T]). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.}, }
@article {pmid37459919, year = {2023}, author = {Wang, L and Zhu, L and Liang, C and Huang, X and Liu, Z and Huo, J and Zhang, Y and Zhang, Y and Chen, L and Xu, H and Li, X and Xu, L and Kuang, M and Wong, CC and Yu, J}, title = {Targeting N6-methyladenosine reader YTHDF1 with siRNA boosts antitumor immunity in NASH-HCC by inhibiting EZH2-IL-6 axis.}, journal = {Journal of hepatology}, volume = {79}, number = {5}, pages = {1185-1200}, doi = {10.1016/j.jhep.2023.06.021}, pmid = {37459919}, issn = {1600-0641}, abstract = {BACKGROUND &amp; AIMS: RNA N[6]-methyladenosine (m[6]A) reader protein YTHDF1 has been implicated in cancer; however, its role in hepatocellular carcinoma (HCC), especially in non-alcoholic steatohepatitis-associated HCC (NASH-HCC), remains unknown. Here, we investigated the functional role of YTHDF1 in NASH-HCC and its interplay with the tumor immune microenvironment.<br><br>METHODS: Hepatocyte-specific Ythdf1-overexpressing mice were subjected to a NASH-HCC-inducing diet. Tumor-infiltrating immune cells were profiled with single-cell RNA-sequencing, flow cytometry, and immunostaining. The molecular target of YTHDF1 was elucidated with RNA-sequencing, m[6]A-sequencing, YTHDF1 RNA immunoprecipitation-sequencing, proteomics, and ribosome-profiling. Ythdf1 in NASH-HCC models was targeted by lipid nanoparticle (LNP)-encapsulated small-interfering Ythdf1.<br><br>RESULTS: YTHDF1 is overexpressed in tumor tissues compared to adjacent peri-tumor tissues from patients with NASH-HCC. Liver-specific Ythdf1 overexpression drives tumorigenesis in dietary models of spontaneous NASH-HCC. Single-cell RNA-sequencing and flow cytometry revealed that Ythdf1 induced accumulation of myeloid-derived suppressor cells (MDSCs) and suppressed cytotoxic CD8[+] T-cell function. Mechanistically, Ythdf1 expression in NASH-HCC cells induced the secretion of IL-6, which mediated MDSC recruitment and activation, leading to CD8[+] T-cell dysfunction. EZH2 mRNA was identified as a key YTHDF1 target. YTHDF1 binds to m[6]A-modified EZH2 mRNA and promotes EZH2 translation. EZH2 in turn increased expression and secretion of IL-6. Ythdf1 knockout synergized with anti-PD-1 treatment to suppress tumor growth in NASH-HCC allografts. Furthermore, therapeutic targeting of Ythdf1 using LNP-encapsulated small-interfering RNA significantly increased the efficacy of anti-PD-1 blockade in NASH-HCC allografts.<br><br>CONCLUSIONS: We identified that YTHDF1 promotes NASH-HCC tumorigenesis via EZH2-IL-6 signaling, which recruits and activates MDSCs to cause cytotoxic CD8[+] T-cell dysfunction. YTHDF1 may be a novel therapeutic target to improve responses to anti-PD-1 immunotherapy in NASH-HCC.<br><br>IMPACT AND IMPLICATIONS: YTHDF1, a N[6]-methyladenosine reader, is upregulated in patients with non-alcoholic steatohepatitis (NASH)-associated hepatocellular carcinoma (HCC); however, its role in modulating the tumor immune microenvironment in NASH-HCC remains unclear. Here, we show that Ythdf1 mediates immunosuppression in NASH-HCC and that targeting YTHDF1 in combination with immune checkpoint blockade elicits robust antitumor immune responses. Our findings suggest novel therapeutic targets for potentiating the efficacy of immune checkpoint blockade in NASH-HCC and provide the rationale for developing YTHDF1 inhibitors for the treatment of NASH-HCC.}, }
@article {pmid37459796, year = {2023}, author = {Sabbe, K and D'Haen, L and Boon, N and Ganigué, R}, title = {Predicting the performance of chain elongating microbiomes through flow cytometric fingerprinting.}, journal = {Water research}, volume = {243}, number = {}, pages = {120323}, doi = {10.1016/j.watres.2023.120323}, pmid = {37459796}, issn = {1879-2448}, mesh = {Fermentation ; *Caproates ; Flow Cytometry ; Bioreactors/microbiology ; *Microbiota ; }, abstract = {As part of the circular bio-economy paradigm shift, waste management and valorisation practices have moved away from sanitation and towards the production of added-value compounds. Recently, the development of mixed culture bioprocess for the conversion of waste(water) to platform chemicals, such as medium chain carboxylic acids, has attracted significant interest. Often, the microbiology of these novel bioprocesses is less diverse and more prone to disturbances, which can lead to process failure. This issue can be tackled by implementing an advanced monitoring strategy based on the microbiology of the process. In this study, flow cytometry was used to monitor the microbiology of lactic acid chain elongation for the production of caproic acid, and assess its performance both qualitatively and quantitatively. Two continuous stirred tank reactors for chain elongation were monitored flow cytometrically for over 336 days. Through community typing, four specific community types could be identified and correlated to both a specific functionality and genotypic diversity. Additionally, the machine-learning algorithms trained in this study demonstrated the ability to predict production rates of, amongst others, caproic acid with high accuracy in the present (R[2] > 0.87) and intermediate accuracy in the near future (R[2] > 0.63). The identification of specific community types and the development of predictive algorithms form the basis of advanced bioprocess monitoring based on flow cytometry, and have the potential to improve bioprocess control and optimization, leading to better product quality and yields.}, }
@article {pmid37458953, year = {2024}, author = {Vélez-Martínez, GA and Reyes-Ardila, WL and Duque-Zapata, JD and Rugeles-Silva, PA and Muñoz Flórez, JE and López-Álvarez, D}, title = {Soil bacteria and fungi communities are shaped by elevation influences in Colombian forest and páramo natural ecosystems.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {27}, number = {2}, pages = {377-391}, pmid = {37458953}, issn = {1618-1905}, mesh = {*Ecosystem ; *Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; Colombia ; Bacteria/genetics ; Forests ; Fungi/genetics ; Soil Microbiology ; }, abstract = {The influence of elevation on natural terrestrial ecosystems determines the arrangements of microbial communities in soils to be associated with biotic and abiotic factors. To evaluate changes of fungi and bacteria at the community level along an elevational gradient (between 1000 and 3800 m.a.s.l.), physicochemical measurements of soils, taxonomic identifications of plants, and metabarcoding sequences of the 16S rRNA gene for bacteria and the ITS1 region for fungi were obtained. The bacterial taxonomic composition showed that Acidobacteriota increased in abundance with elevation, while Actinobacteriota and Verrucomicrobiota decreased. Furthermore, Firmicutes and Proteobacteria maintained maximum levels of abundance at intermediate elevations (1200 and 2400 m.a.s.l.). In fungi, Ascomycota was more abundant at higher elevations, Basidiomycota tended to dominate at lower elevations, and Mortierellomycota had a greater presence at intermediate sites. These results correlated with the edaphic parameters of decreasing pH and increasing organic carbon and available nitrogen with elevation. In addition, the Shannon index found a greater diversity in bacteria than fungi, but both showed a unimodal pattern with maximum values in the Andean Forest at 2400 m.a.s.l. Through the microbial characterization of the ecosystems, the elevational gradient, soil properties, and vegetation were found to exert significant effects on microbial communities and alpha diversity indices. We conclude that the most abundant soil microorganisms at the sampling points differed in abundance and diversity according to the variations in factors influencing ecological communities.}, }
@article {pmid37458790, year = {2023}, author = {Huang, S and Lentendu, G and Fujinuma, J and Shiono, T and Kubota, Y and Mitchell, EAD}, title = {Soil Micro-eukaryotic Diversity Patterns Along Elevation Gradient Are Best Estimated by Increasing the Number of Elevation Steps Rather than Within Elevation Band Replication.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2606-2617}, pmid = {37458790}, issn = {1432-184X}, support = {182531/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Soil ; *Biodiversity ; Soil Microbiology ; Japan ; Nitrogen ; }, abstract = {The development of high-throughput sequencing (HTS) of environmental DNA (eDNA) has stimulated the study of soil microbial diversity patterns and drivers at all scales. However, given the heterogeneity of soils, a challenge is to define effective and efficient sampling protocols that allow sound comparison with other records, especially vegetation. In studies of elevational diversity pattern, a trade-off is choosing between replication within elevation bands vs. sampling more elevation bands. We addressed this question for soil protists along an elevation gradient on Mt. Asahi, Hokkaido, Japan. We compared two sampling approaches: (1) the replicate strategy (five replicates at six elevational bands, total = 30) and (2) the transect strategy (one sample in each of 16 different elevational bands). Despite a nearly twofold lower sampling effort, the transect strategy yielded congruent results compared to the replicate strategy for the estimation of elevational alpha diversity pattern: the regression coefficients between diversity indices and elevation did not differ between the two options. Furthermore, for a given total number of samples, gamma diversity estimated across the entire transect was higher when sampling more elevational bands as compared to replication from fewer elevational bands. Beta diversity (community composition turnover) was lower within a given elevational band than between adjacent bands and increased with elevation distance. In redundancy analyses, soil organic matter-related variable (the first principal component of soil organic matter, water content, total organic carbon, and nitrogen by whom were highly correlated) and elevation best explained elevational beta diversity pattern for both sampling approaches. Taken together, our results suggest that sampling a single plot per elevation band will be sufficient to obtain a good estimate of soil micro-eukaryotic diversity patterns along elevation gradients. This study demonstrated the effectiveness of the transect strategy in estimating diversity patterns along elevation gradients which is instructive for future environmental or even experimental studies. While not advocating for completely replacing replication-based sampling practices, it is important to note that both replicate and transect strategies have their merits and can be employed based on specific research goals and resource limitations.}, }
@article {pmid37458590, year = {2023}, author = {Masuda, T and Inomura, K and Mareš, J and Kodama, T and Shiozaki, T and Matsui, T and Suzuki, K and Takeda, S and Deutsch, C and Prášil, O and Furuya, K}, title = {Coexistence of Dominant Marine Phytoplankton Sustained by Nutrient Specialization.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0400022}, pmid = {37458590}, issn = {2165-0497}, mesh = {Phytoplankton ; Ecosystem ; Seawater/microbiology ; Nitrates ; *Synechococcus ; Nitrogen ; *Ammonium Compounds ; }, abstract = {Prochlorococcus and Synechococcus are the two dominant picocyanobacteria in the low-nutrient surface waters of the subtropical ocean, but the basis for their coexistence has not been quantitatively demonstrated. Here, we combine in situ microcosm experiments and an ecological model to show that this coexistence can be sustained by specialization in the uptake of distinct nitrogen (N) substrates at low-level concentrations that prevail in subtropical environments. In field incubations, the response of both Prochlorococcus and Synechococcus to nanomolar N amendments demonstrates N limitation of growth in both populations. However, Prochlorococcus showed a higher affinity to ammonium, whereas Synechococcus was more adapted to nitrate uptake. A simple ecological model demonstrates that the differential nutrient preference inferred from field experiments with these genera may sustain their coexistence. It also predicts that as the supply of NO3[-] decreases, as expected under climate warming, the dominant genera should undergo a nonlinear shift from Synechococcus to Prochlorococcus, a pattern that is supported by subtropical field observations. Our study suggests that the evolution of differential nutrient affinities is an important mechanism for sustaining the coexistence of genera and that climate change is likely to shift the relative abundance of the dominant plankton genera in the largest biomes in the ocean. IMPORTANCE Our manuscript addresses the following fundamental question in microbial ecology: how do different plankton using the same essential nutrients coexist? Prochlorococcus and Synechococcus are the two dominant picocyanobacteria in the low-nutrient surface waters of the subtropical ocean, which support a significant amount of marine primary production. The geographical distributions of these two organisms are largely overlapping, but the basis for their coexistence in these biomes remains unclear. In this study, we combined in situ microcosm experiments and an ecosystem model to show that the coexistence of these two organisms can arise from specialization in the uptake of distinct nitrogen substrates; Prochlorococcus prefers ammonium, whereas Synechococcus prefers nitrate when these nutrients exist at low concentrations. Our framework can be used for simulating and predicting the coexistence in the future ocean and may provide hints toward understanding other similar types of coexistence.}, }
@article {pmid37458207, year = {2023}, author = {Seto, M and Kondoh, M}, title = {Microbial redox cycling enhances ecosystem thermodynamic efficiency and productivity.}, journal = {Ecology letters}, volume = {26}, number = {10}, pages = {1714-1725}, doi = {10.1111/ele.14287}, pmid = {37458207}, issn = {1461-0248}, support = {JPMEERF20214103//Environmental Restoration and Conservation Agency/ ; JP19H05641//Japan Society for the Promotion of Science/ ; JP19K06853//Japan Society for the Promotion of Science/ ; JP21H05315//Japan Society for the Promotion of Science/ ; JP22K06390//Japan Society for the Promotion of Science/ ; JP23H04652//Japan Society for the Promotion of Science/ ; }, mesh = {*Ecosystem ; *Symbiosis/physiology ; Thermodynamics ; }, abstract = {Microbial life in low-energy ecosystems relies on individual energy conservation, optimizing energy use in response to interspecific competition and mutualistic interspecific syntrophy. Our study proposes a novel community-level strategy for increasing energy use efficiency. By utilizing an oxidation-reduction (redox) reaction network model that represents microbial redox metabolic interactions, we investigated multiple species-level competition and cooperation within the network. Our results suggest that microbial functional diversity allows for metabolic handoffs, which in turn leads to increased energy use efficiency. Furthermore, the mutualistic division of labour and the resulting complexity of redox pathways actively drive material cycling, further promoting energy exploitation. Our findings reveal the potential of self-organized ecological interactions to develop efficient energy utilization strategies, with important implications for microbial ecosystem functioning and the co-evolution of life and Earth.}, }
@article {pmid37454793, year = {2023}, author = {Qi, L and Li, R and Wu, Y and Ibeanusi, V and Chen, G}, title = {Spatial distribution and assembly processes of bacterial communities in northern Florida freshwater springs.}, journal = {Environmental research}, volume = {235}, number = {}, pages = {116584}, doi = {10.1016/j.envres.2023.116584}, pmid = {37454793}, issn = {1096-0953}, mesh = {*Ecosystem ; Phylogeny ; Florida ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Fresh Water ; *Microbiota ; }, abstract = {Freshwater microorganisms are an essential component of the global biogeochemical cycle and a significant contributory factor in water quality. Unraveling the mechanisms controlling microbial community spatial distribution is crucial for the assessment of water quality and health of aquatic ecosystems. This research provided a comprehensive analysis of microbial communities in Florida freshwater springs. The 16S rRNA gene sequencing and bioinformatics analyses revealed the bacterial compositional heterogeneity as well as numerous unique ASVs and biomarkers in different springs. Statistical analysis showed both geographic distance and environmental variables contributed to regional bacterial community variation, while nitrate was the dominant environmental stressor that shaped the bacterial communities. The phylogenetic bin-based null model characterized both deterministic and stochastic factors contributing to community assembly in Florida springs, with the majority of bins dominated by ecological drift. Mapping of predicted pathways to the MetaCyc database revealed the inconsistency between microbial taxonomic and functional profiles, implying the functional redundancy pattern. Collectively, our work sheds insights into the microbial spatial distribution, community assembly, and function traits in one of the world's most productive aquifers. Therefore, this work provides a unique view of the health of Florida's artesian springs and offers new perspectives for freshwater quality assessment and sustainable management.}, }
@article {pmid37453005, year = {2023}, author = {Nagpal, S and Mande, SS}, title = {Environmental insults and compensative responses: when microbiome meets cancer.}, journal = {Discover oncology}, volume = {14}, number = {1}, pages = {130}, pmid = {37453005}, issn = {2730-6011}, support = {PhD Sponsorship//Tata Consultancy Services/ ; }, abstract = {Tumor microenvironment has recently been ascribed a new hallmark-the polymorphic microbiome. Accumulating evidence regarding the tissue specific territories of tumor-microbiome have opened new and interesting avenues. A pertinent question is regarding the functional consequence of the interface between host-microbiome and cancer. Given microbial communities have predominantly been explored through an ecological perspective, it is important that the foundational aspects of ecological stress and the fight to 'survive and thrive' are accounted for tumor-micro(b)environment as well. Building on existing evidence and classical microbial ecology, here we attempt to characterize the ecological stresses and the compensative responses of the microorganisms inside the tumor microenvironment. What insults would microbes experience inside the cancer jungle? How would they respond to these insults? How the interplay of stress and microbial quest for survival would influence the fate of tumor? This work asks these questions and tries to describe this underdiscussed ecological interface of the tumor and its microbiota. It is hoped that a larger scientific thought on the importance of microbial competition sensing vis-à-vis tumor-microenvironment would be stimulated.}, }
@article {pmid37452612, year = {2024}, author = {Hoque, E and Fritscher, J}, title = {Are anaerobic fungi crucial hidden players of microbiomes in anoxic environment?.}, journal = {Critical reviews in microbiology}, volume = {50}, number = {5}, pages = {540-563}, doi = {10.1080/1040841X.2023.2224425}, pmid = {37452612}, issn = {1549-7828}, mesh = {*Anaerobiosis ; *Microbiota ; Biofilms ; *Environment ; Fossils/microbiology ; *Mucor/classification/genetics/isolation &amp; purification ; *Aquatic Organisms/isolation &amp; purification ; DNA, Fungal/genetics ; Geologic Sediments/microbiology ; Adaptation, Physiological ; Groundwater/microbiology ; }, abstract = {Anaerobic fungi are known to migrate and establish a 3D network of biofilms (microbiomes) and live invisible in the rumen and terrestrial subsurface, deep-sea - marine, and anoxic environment. They deserve our attention to understand anoxic fungal ecology and functions and develop new products and solutions. Such fungi activate unique genes to produce various polysaccharidases deemed essential for degrading plants' lignocellulosic materials. Nutrient release, recycling, and physical support by anaerobic fungi are crucial for microbiome formation. Multiple reports point to the ability of strictly anaerobic and facultative fungi to adapt and live in anoxic subsurface. Deep-sea sediments and natural anoxic methane-emitting salty waters of sulfidic springs offer suitable habitats for developing prokaryotic-fungal microbiomes. Researchers found a billion-year-old fossil of the fungus-prokaryotic sulfate-reducing consortium buried in deep-sea biospheres. Fungal spores' ability to migrate, even after germination, through sandy layers demonstrates their potential to move up and down porous geological layers or rock fissures. Selective fungal affinity to specific wood in wood chip arrays might help differentiate viable anaerobic fungi from an anoxic environment for their rapid collection and investigation. New collection methods, cultivation, gene expression, and drug and enzyme activity analyses can boost anaerobic fungal research.}, }
@article {pmid37452527, year = {2023}, author = {Soder-Walz, JM and Wasmund, K and Deobald, D and Vicent, T and Adrian, L and Marco-Urrea, E}, title = {Respiratory protein interactions in Dehalobacter sp. strain 8M revealed through genomic and native proteomic analyses.}, journal = {Environmental microbiology}, volume = {25}, number = {11}, pages = {2604-2620}, doi = {10.1111/1462-2920.16464}, pmid = {37452527}, issn = {1462-2920}, mesh = {*Proteomics ; *Bacteria/genetics ; Genomics ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Dehalobacter (Firmicutes) encompass obligate organohalide-respiring bacteria used for bioremediation of groundwater contaminated with halogenated organics. Various aspects of their biochemistry remain unknown, including the identities and interactions of respiratory proteins. Here, we sequenced the genome of Dehalobacter sp. strain 8M and analysed its protein expression. Strain 8M encodes 22 reductive dehalogenase homologous (RdhA) proteins. RdhA D8M_v2_40029 (TmrA) was among the two most abundant proteins during growth with trichloromethane and 1,1,2-trichloroethane. To examine interactions of respiratory proteins, we used blue native gel electrophoresis together with dehalogenation activity tests and mass spectrometry. The highest activities were found in gel slices with the highest abundance of TmrA. Protein distributions across gel lanes provided biochemical evidence that the large and small subunits of the membrane-bound [NiFe] uptake hydrogenase (HupL and HupS) interacted strongly and that HupL/S interacted weakly with RdhA. Moreover, the interaction of RdhB and membrane-bound b-type cytochrome HupC was detected. RdhC proteins, often encoded in rdh operons but without described function, migrated in a protein complex not associated with HupL/S or RdhA. This study provides the first biochemical evidence of respiratory protein interactions in Dehalobacter, discusses implications for the respiratory architecture and advances the molecular comprehension of this unique respiratory chain.}, }
@article {pmid37449414, year = {2023}, author = {Ni, G and Leung, PM and Daebeler, A and Guo, J and Hu, S and Cook, P and Nicol, GW and Daims, H and Greening, C}, title = {Nitrification in acidic and alkaline environments.}, journal = {Essays in biochemistry}, volume = {67}, number = {4}, pages = {753-768}, pmid = {37449414}, issn = {1744-1358}, mesh = {*Nitrification ; *Ammonia/metabolism ; Ecosystem ; Oxidation-Reduction ; Bacteria/metabolism ; }, abstract = {Aerobic nitrification is a key process in the global nitrogen cycle mediated by microorganisms. While nitrification has primarily been studied in near-neutral environments, this process occurs at a wide range of pH values, spanning ecosystems from acidic soils to soda lakes. Aerobic nitrification primarily occurs through the activities of ammonia-oxidising bacteria and archaea, nitrite-oxidising bacteria, and complete ammonia-oxidising (comammox) bacteria adapted to these environments. Here, we review the literature and identify knowledge gaps on the metabolic diversity, ecological distribution, and physiological adaptations of nitrifying microorganisms in acidic and alkaline environments. We emphasise that nitrifying microorganisms depend on a suite of physiological adaptations to maintain pH homeostasis, acquire energy and carbon sources, detoxify reactive nitrogen species, and generate a membrane potential at pH extremes. We also recognize the broader implications of their activities primarily in acidic environments, with a focus on agricultural productivity and nitrous oxide emissions, as well as promising applications in treating municipal wastewater.}, }
@article {pmid37446198, year = {2023}, author = {Gu, X and Cao, Z and Zhao, L and Seswita-Zilda, D and Zhang, Q and Fu, L and Li, J}, title = {Metagenomic Insights Reveal the Microbial Diversity and Associated Algal-Polysaccharide-Degrading Enzymes on the Surface of Red Algae among Remote Regions.}, journal = {International journal of molecular sciences}, volume = {24}, number = {13}, pages = {}, pmid = {37446198}, issn = {1422-0067}, support = {RFSOCC2023-2025//Impact and Response of Antarctic Seas to Climate Change/ ; RFSOCC2023-2025//Jiang Li/ ; }, mesh = {Metagenomics ; Bacteria/genetics/metabolism ; *Rhodophyta/genetics ; Metagenome ; *Seaweed ; Polysaccharides/metabolism ; }, abstract = {Macroalgae and macroalgae-associated bacteria together constitute the most efficient metabolic cycling system in the ocean. Their interactions, especially the responses of macroalgae-associated bacteria communities to algae in different geographical locations, are mostly unknown. In this study, metagenomics was used to analyze the microbial diversity and associated algal-polysaccharide-degrading enzymes on the surface of red algae among three remote regions. There were significant differences in the macroalgae-associated bacteria community composition and diversity among the different regions. At the phylum level, Proteobacteria, Bacteroidetes, and Actinobacteria had a significantly high relative abundance among the regions. From the perspective of species diversity, samples from China had the highest macroalgae-associated bacteria diversity, followed by those from Antarctica and Indonesia. In addition, in the functional prediction of the bacterial community, genes associated with amino acid metabolism, carbohydrate metabolism, energy metabolism, metabolism of cofactors and vitamins, and membrane transport had a high relative abundance. Canonical correspondence analysis and redundancy analysis of environmental factors showed that, without considering algae species and composition, pH and temperature were the main environmental factors affecting bacterial community structure. Furthermore, there were significant differences in algal-polysaccharide-degrading enzymes among the regions. Samples from China and Antarctica had high abundances of algal-polysaccharide-degrading enzymes, while those from Indonesia had extremely low abundances. The environmental differences between these three regions may impose a strong geographic differentiation regarding the biodiversity of algal microbiomes and their expressed enzyme genes. This work expands our knowledge of algal microbial ecology, and contributes to an in-depth study of their metabolic characteristics, ecological functions, and applications.}, }
@article {pmid37442613, year = {2023}, author = {Demarquest, G and Lajoie, G}, title = {Bacterial endophytes of sugar maple leaves vary more idiosyncratically than epiphytes across a large geographic area.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {9}, pages = {}, doi = {10.1093/femsec/fiad079}, pmid = {37442613}, issn = {1574-6941}, mesh = {Humans ; *Ecosystem ; Endophytes ; *Acer ; Bacteria/genetics ; Plants ; Plant Leaves/microbiology ; }, abstract = {Bacteria from the leaf surface and the leaf tissue have been attributed with several beneficial properties for their plant host. Though physically connected, the microbial ecology of these compartments has mostly been studied separately such that we lack an integrated understanding of the processes shaping their assembly. We sampled leaf epiphytes and endophytes from the same individuals of sugar maple across the northern portion of its range to evaluate if their community composition was driven by similar processes within and across populations differing in plant traits and overall abiotic environment. Leaf compartment explained most of the variation in community diversity and composition across samples. Leaf epiphytic communities were driven more by host and site characteristics than endophytic communities, whose community composition was more idiosyncratic across samples. Our results suggest a greater importance of priority effects and opportunistic colonization in driving community assembly of leaf endophytes. Understanding the comparative assembly of bacterial communities at the surface and inside plant leaves may be particularly useful for leveraging their respective potential for improving the health of plants in natural and anthropized ecosystems.}, }
@article {pmid37440561, year = {2023}, author = {Fiedler, S and Schrader, H and Theobalt, N and Hofmann, I and Geiger, T and Arndt, D and Wanke, R and Schwaiger, J and Blutke, A}, title = {Standardized tissue sampling guidelines for histopathological and molecular analyses of rainbow trout (Oncorhynchus mykiss) in ecotoxicological studies.}, journal = {PloS one}, volume = {18}, number = {7}, pages = {e0288542}, pmid = {37440561}, issn = {1932-6203}, mesh = {Animals ; *Oncorhynchus mykiss ; Ecotoxicology ; Reproducibility of Results ; *Water Pollutants, Chemical/toxicity ; }, abstract = {In ecotoxicology, evaluation of toxicities and no observed effect concentrations (NOEC) of test compounds in experimental fish is commonly based on molecular-, biochemical- and analytical chemistry analyses of organ/tissue samples and the assessment of (histo-) pathological lesions. Standardization of organ/tissue sampling locations, sample numbers, and sample processing contributes to warrant the reproducibility and inter- and intra-study comparability of analysis results. The present article provides the first comprehensive tissue sampling guidelines specifically adapted to rainbow trout (Oncorhynchus mykiss) as a frequently used fish species in ecotoxicological studies. A broad spectrum of ~40 different organs and tissues is covered. Appropriate sampling locations, sample sizes and sample numbers for subsequent routine histopathological evaluation (all organs/tissue) and for molecular analyses (~30 organs/tissues) are described in detail and illustrated with schematic drawings and representative macroscopic and histological images. These field-proven sampling guidelines were developed based on the pertinent literature and practical experience in ecotoxicological fish studies. They are intended to serve as a standard reference for any routine ecotoxicological study using rainbow trout as a test system. A broad application of the featured tissue sampling procedures will help to improve the reproducibility of analyses and to reduce inter- and intra-study variability induced by sampling bias and (normal) inter-sample morphological variation, and will therefore provide a robust basis for reliable characterization of toxicity and NOEC identification of diverse test substances and aquatic pollutants.}, }
@article {pmid37438876, year = {2023}, author = {Basile, A and Heinken, A and Hertel, J and Smarr, L and Li, W and Treu, L and Valle, G and Campanaro, S and Thiele, I}, title = {Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2226921}, pmid = {37438876}, issn = {1949-0984}, support = {757922/ERC_/European Research Council/International ; RF1 AG058942/AG/NIA NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *Microbiota ; Inflammation ; Liver ; Anti-Bacterial Agents ; Escherichia coli ; }, abstract = {We report the first use of constraint-based microbial community modeling on a single individual with episodic inflammation of the gastrointestinal tract, who has a well documented set of colonic inflammatory biomarkers, as well as metagenomically-sequenced fecal time series covering seven dates over 16 months. Between the first two time steps the individual was treated with both steroids and antibiotics. Our methodology enabled us to identify numerous time-correlated microbial species and metabolites. We found that the individual's dynamical microbial ecology in the disease state led to time-varying in silico overproduction, compared to healthy controls, of more than 24 biologically important metabolites, including methane, thiamine, formaldehyde, trimethylamine N-oxide, folic acid, serotonin, histamine, and tryptamine. The microbe-metabolite contribution analysis revealed that some Dialister species changed metabolic pathways according to the inflammation phases. At the first time point, characterized by the highest levels of serum (complex reactive protein) and fecal (calprotectin) inflammation biomarkers, they produced L-serine or formate. The production of the compounds, through a cascade effect, was mediated by the interaction with pathogenic Escherichia coli strains and Desulfovibrio piger. We integrated the microbial community metabolic models of each time point with a male whole-body, organ-resolved model of human metabolism to track the metabolic consequences of dysbiosis at different body sites. The presence of D. piger in the gut microbiome influenced the sulfur metabolism with a domino effect affecting the liver. These results revealed large longitudinal variations in an individual's gut microbiome ecology and metabolite production, potentially impacting other organs in the body. Future simulations with more time points from an individual could permit us to assess how external drivers, such as diet change or medical interventions, drive microbial community dynamics.}, }
@article {pmid37438797, year = {2023}, author = {Nguyen, LH and Okin, D and Drew, DA and Battista, VM and Jesudasen, SJ and Kuntz, TM and Bhosle, A and Thompson, KN and Reinicke, T and Lo, CH and Woo, JE and Caraballo, A and Berra, L and Vieira, J and Huang, CY and Das Adhikari, U and Kim, M and Sui, HY and Magicheva-Gupta, M and McIver, L and Goldberg, MB and Kwon, DS and Huttenhower, C and Chan, AT and Lai, PS}, title = {Metagenomic assessment of gut microbial communities and risk of severe COVID-19.}, journal = {Genome medicine}, volume = {15}, number = {1}, pages = {49}, pmid = {37438797}, issn = {1756-994X}, support = {K01 DK120742/DK/NIDDK NIH HHS/United States ; K23 DK125838/DK/NIDDK NIH HHS/United States ; UL1 TR002541/TR/NCATS NIH HHS/United States ; T32 HL116275/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; Post-Acute COVID-19 Syndrome ; *COVID-19 ; *Microbiota ; Metagenome ; *Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure.<br><br>METHODS: We profiled 127 hospitalized patients with COVID-19 (n&#x2009;=&#x2009;79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites.<br><br>RESULTS: Forty-eight species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or "long COVID," suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with classifying whether stool was obtained from patients with severe vs. moderate COVID-19, a finding that was externally validated in an independent cohort. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease.<br><br>CONCLUSIONS: Here, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to expand upon these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention.}, }
@article {pmid37438590, year = {2023}, author = {Nava, V and Chandra, S and Aherne, J and Alfonso, MB and Antão-Geraldes, AM and Attermeyer, K and Bao, R and Bartrons, M and Berger, SA and Biernaczyk, M and Bissen, R and Brookes, JD and Brown, D and Cañedo-Argüelles, M and Canle, M and Capelli, C and Carballeira, R and Cereijo, JL and Chawchai, S and Christensen, ST and Christoffersen, KS and de Eyto, E and Delgado, J and Dornan, TN and Doubek, JP and Dusaucy, J and Erina, O and Ersoy, Z and Feuchtmayr, H and Frezzotti, ML and Galafassi, S and Gateuille, D and Gonçalves, V and Grossart, HP and Hamilton, DP and Harris, TD and Kangur, K and Kankılıç, GB and Kessler, R and Kiel, C and Krynak, EM and Leiva-Presa, &#xc0; and Lepori, F and Matias, MG and Matsuzaki, SS and McElarney, Y and Messyasz, B and Mitchell, M and Mlambo, MC and Motitsoe, SN and Nandini, S and Orlandi, V and Owens, C and Özkundakci, D and Pinnow, S and Pociecha, A and Raposeiro, PM and Rõõm, EI and Rotta, F and Salmaso, N and Sarma, SSS and Sartirana, D and Scordo, F and Sibomana, C and Siewert, D and Stepanowska, K and Tavşanoğlu, &#xdc;N and Tereshina, M and Thompson, J and Tolotti, M and Valois, A and Verburg, P and Welsh, B and Wesolek, B and Weyhenmeyer, GA and Wu, N and Zawisza, E and Zink, L and Leoni, B}, title = {Plastic debris in lakes and reservoirs.}, journal = {Nature}, volume = {619}, number = {7969}, pages = {317-322}, pmid = {37438590}, issn = {1476-4687}, mesh = {Ecosystem ; *Lakes/chemistry ; *Plastics/analysis/classification ; *Water Pollution/analysis/statistics &amp; numerical data ; Surveys and Questionnaires ; Urbanization ; *Water Supply ; Human Activities ; }, abstract = {Plastic debris is thought to be widespread in freshwater ecosystems globally[1]. However, a lack of comprehensive and comparable data makes rigorous assessment of its distribution challenging[2,3]. Here we present a standardized cross-national survey that assesses the abundance and type of plastic debris (>250 μm) in freshwater ecosystems. We sample surface waters of 38 lakes and reservoirs, distributed across gradients of geographical position and limnological attributes, with the aim to identify factors associated with an increased observation of plastics. We find plastic debris in all studied lakes and reservoirs, suggesting that these ecosystems play a key role in the plastic-pollution cycle. Our results indicate that two types of lakes are particularly vulnerable to plastic contamination: lakes and reservoirs in densely populated and urbanized areas and large lakes and reservoirs with elevated deposition areas, long water-retention times and high levels of anthropogenic influence. Plastic concentrations vary widely among lakes; in the most polluted, concentrations reach or even exceed those reported in the subtropical oceanic gyres, marine areas collecting large amounts of debris[4]. Our findings highlight the importance of including lakes and reservoirs when addressing plastic pollution, in the context of pollution management and for the continued provision of lake ecosystem services.}, }
@article {pmid37436063, year = {2023}, author = {Smets, W and Chock, MK and Walsh, CM and Vanderburgh, CQ and Kau, E and Lindow, SE and Fierer, N and Koskella, B}, title = {Leaf side determines the relative importance of dispersal versus host filtering in the phyllosphere microbiome.}, journal = {mBio}, volume = {14}, number = {4}, pages = {e0111123}, pmid = {37436063}, issn = {2150-7511}, mesh = {*Bacteria/genetics ; *Microbiota ; Plants/microbiology ; Plant Leaves/microbiology ; }, abstract = {Leaves harbor distinct microbial communities that can have an important impact on plant health and microbial ecosystems worldwide. Nevertheless, the ecological processes that shape the composition of leaf microbial communities remain unclear, with previous studies reporting contradictory results regarding the importance of bacterial dispersal versus host selection. This discrepancy could be driven in part because leaf microbiome studies typically consider the upper and lower leaf surfaces as a single entity despite these habitats possessing considerable anatomical differences. We characterized the composition of bacterial phyllosphere communities from the upper and lower leaf surfaces across 24 plant species. Leaf surface pH and stomatal density were found to shape phyllosphere community composition, and the underside of leaves had lower richness and higher abundances of core community members than upper leaf surfaces. We found fewer endemic bacteria on the upper leaf surfaces, suggesting that dispersal is more important in shaping these communities, with host selection being a more important force in microbiome assembly on lower leaf surfaces. Our study illustrates how changing the scale in which we observe microbial communities can impact our ability to resolve and predict microbial community assembly patterns on leaf surfaces. IMPORTANCE Leaves can harbor hundreds of different bacterial species that form unique communities for every plant species. Bacterial communities on leaves are really important because they can, for example, protect their host against plant diseases. Usually, bacteria from the whole leaf are considered when trying to understand these communities; however, this study shows that the upper and lower sides of a leaf have a very different impact on how these communities are shaped. It seems that the bacteria on the lower leaf side are more closely associated with the plant host, and communities on the upper leaf side are more impacted by immigrating bacteria. This can be really important when we want to treat, for example, crops in the field with beneficial bacteria or when trying to understand host-microbe interactions on the leaves.}, }
@article {pmid37434715, year = {2023}, author = {Trexler, RV and Van Goethem, MW and Goudeau, D and Nath, N and Malmstrom, RR and Northen, TR and Couradeau, E}, title = {BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1176751}, pmid = {37434715}, issn = {1664-302X}, abstract = {Determining which microorganisms are active within soil communities remains a major technical endeavor in microbial ecology research. One promising method to accomplish this is coupling bioorthogonal non-canonical amino acid tagging (BONCAT) with fluorescence activated cell sorting (FACS) which sorts cells based on whether or not they are producing new proteins. Combined with shotgun metagenomic sequencing (Seq), we apply this method to profile the diversity and potential functional capabilities of both active and inactive microorganisms in a biocrust community after being resuscitated by a simulated rain event. We find that BONCAT-FACS-Seq is capable of discerning the pools of active and inactive microorganisms, especially within hours of applying the BONCAT probe. The active and inactive components of the biocrust community differed in species richness and composition at both 4 and 21 h after the wetting event. The active fraction of the biocrust community is marked by taxa commonly observed in other biocrust communities, many of which play important roles in species interactions and nutrient transformations. Among these, 11 families within the Firmicutes are enriched in the active fraction, supporting previous reports indicating that the Firmicutes are key early responders to biocrust wetting. We highlight the apparent inactivity of many Actinobacteria and Proteobacteria through 21 h after wetting, and note that members of the Chitinophagaceae, enriched in the active fraction, may play important ecological roles following wetting. Based on the enrichment of COGs in the active fraction, predation by phage and other bacterial members, as well as scavenging and recycling of labile nutrients, appear to be important ecological processes soon after wetting. To our knowledge, this is the first time BONCAT-FACS-Seq has been applied to biocrust samples, and therefore we discuss the potential advantages and shortcomings of coupling metagenomics to BONCAT to intact soil communities such as biocrust. In all, by pairing BONCAT-FACS and metagenomics, we are capable of highlighting the taxa and potential functions that typifies the microbes actively responding to a rain event.}, }
@article {pmid37433981, year = {2023}, author = {Gomes, AFF and de Almeida, LG and Cônsoli, FL}, title = {Comparative Genomics of Pesticide-Degrading Enterococcus Symbionts of Spodoptera frugiperda (Lepidoptera: Noctuidae) Leads to the Identification of Two New Species and the Reappraisal of Insect-Associated Enterococcus Species.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2583-2605}, pmid = {37433981}, issn = {1432-184X}, support = {140835/2019-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2010/13714-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2011/50877-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {Animals ; Spodoptera/genetics ; *Insecticides ; *Pesticides ; Larva ; Enterococcus/genetics ; Genomics ; DNA ; Zea mays ; }, abstract = {Enterococcus species have been described as core members of the microbial community of Spodoptera frugiperda (Lepidoptera: Noctuidae) and have been previously reported as insecticide degrading agents. This study aimed to investigate the molecular composition of these microbial symbionts of S. frugiperda to better understand their association with the host and their potential for insecticide metabolization. Through phenotypic assays and comparative genomic analyses of several pesticide-degrading Enterococcus isolated from the gut of S. frugiperda larvae, we identified two new species: Enterococcus entomosocium n. sp. and Enterococcus spodopteracolus n. sp. Their identities as new species were confirmed by whole genome alignment, utilizing cut-offs of 95-96% for the average nucleotide identity (ANI) and 70% for the digital DNA: DNA hybridization (dDDH) values. The systematic positioning of these new species within the genus Enterococcus was resolved using genome-based analysis, revealing Enterococcus casseliflavus as a sister group of E. entomosocium n. sp., and Enterococcus mundtii as a sister group of E. spodopteracolus n. sp. Comparative genomic analyses of several isolates of E. entomosocium n. sp. and E. spodopteracolus n. sp. provided a better assessment of the interactions established in the symbiotic association with S. frugiperda and led to the discovery of misidentified new species of Enterococcus associated with insects. Our analyses indicated that the potential of E. entomosocium n. sp. and E. spodopteracolus n. sp. to metabolize different pesticides arises from molecular mechanisms that result in rapid evolution of new phenotypes in response to environmental stressors, in this case, the pesticides their host insect is exposed to.}, }
@article {pmid37433980, year = {2023}, author = {Candelori, A and Di Giuseppe, G and Villalobo, E and Sjödin, A and Vallesi, A}, title = {Bipolar Biogeographical Distribution of Parafrancisella Bacteria Carried by the Ciliate Euplotes.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3128-3132}, pmid = {37433980}, issn = {1432-184X}, support = {PNRA18_00152//PNRA (Programma Nazionale di Ricerca in Antartide)/ ; }, mesh = {Phylogeny ; *Euplotes/genetics/microbiology ; *Francisella ; Cytoplasm ; Antarctic Regions ; }, abstract = {Parafrancisella adeliensis, a Francisella-like endosymbiont, was found to reside in the cytoplasm of an Antarctic strain of the bipolar ciliate species, Euplotes petzi. To inquire whether Euplotes cells collected from distant Arctic and peri-Antarctic sites host Parafrancisella bacteria, wild-type strains of the congeneric bipolar species, E. nobilii, were screened for Parafrancisella by in situ hybridization and 16S gene amplification and sequencing. Results indicate that all Euplotes strains analyzed contained endosymbiotic bacteria with 16S nucleotide sequences closely similar to the P. adeliensis 16S gene sequence. This finding suggests that Parafrancisella/Euplotes associations are not endemic to Antarctica, but are common in both the Antarctic and Arctic regions.}, }
@article {pmid37432727, year = {2023}, author = {Wang, J and Shi, K and Jing, Z and Ge, Y}, title = {Metagenomic Evidence for Cobamide Producers Driving Prokaryotic Co-occurrence Associations and Potential Function in Wastewater Treatment Plants.}, journal = {Environmental science &amp; technology}, volume = {57}, number = {29}, pages = {10640-10651}, doi = {10.1021/acs.est.3c02181}, pmid = {37432727}, issn = {1520-5851}, mesh = {*Cobamides ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Cobamides are required by most organisms but are only produced by specific prokaryotic taxa. These commonly shared cofactors play significant roles in shaping the microbial community and ecosystem function. Wastewater treatment plants (WWTPs) are the world's most common biotechnological systems; knowledge about sharing of cobamides among microorganisms is predicted to be important to decipher the complex microbial relationships in these systems. Herein, we explored prokaryotic potential cobamide producers in global WWTP systems based on metagenomic analyses. A set of 8253 metagenome-assembled genomes (MAGs) were recovered and 1276 (15.5%) of them were identified as cobamide producers, which could potentially be used for the practical biological manipulation of WWTP systems. Moreover, 8090 of the total recovered MAGs (98.0%) contained at least one enzyme family dependent on cobamides, indicating the sharing of cobamides among microbial members in WWTP systems. Importantly, our results showed that the relative abundance and number of cobamide producers improved the complexity of microbial co-occurrence networks and most nitrogen, sulfur, and phosphorus cycling gene abundances, indicating the significance of cobamides in microbial ecology and their potential function in WWTP systems. These findings enhance the knowledge of cobamide producers and their functions in WWTP systems, which has important implications for improving the efficiency of microbial wastewater treatment processes.}, }
@article {pmid37432469, year = {2023}, author = {DiPietro, AG and Bryant, SA and Zanger, MM and Williamson, KE}, title = {Understanding Viral Impacts in Soil Microbial Ecology Through the Persistence and Decay of Infectious Bacteriophages.}, journal = {Current microbiology}, volume = {80}, number = {9}, pages = {276}, pmid = {37432469}, issn = {1432-0991}, mesh = {*Bacteriophages ; Soil Microbiology ; Ecology ; Fresh Water ; Soil ; }, abstract = {Marine bacteriophages have been well characterized in terms of decay rates, population dynamics in relation to their hosts, and their impacts on biogeochemical cycles in the global ocean. Knowledge in soil bacteriophage ecology lags considerably behind, with few studies documenting population dynamics with hosts and even fewer reporting phage decay rates. By using sterile soil or aquatic microcosms inoculated with single bacteriophage isolates, phage decay rates (loss of infectivity over time) were determined, independent of host interactions, for 5 model phage isolates. Decay rates varied by phage from 0.11-2.07% h[-1] in soils to 0.07-0.28% h[-1] in aquatic microcosms. For phages incubated in both soil and aquatic microcosms, the observed decay rate was consistently higher in soil microcosms than in aquatic microcosms by at least a factor of two. However, when decay rates for soil phage isolates in the present study were compared to those reported for marine and freshwater phage isolates from previous studies, the decay constants for soil phages were, on average, 4 times lower than those for aquatic phages. Slower rates of phage decay in soils indicate a lower turnover rate, which may have subsequent and potentially far-reaching impacts on virus-mediated mortality and bacterial activity. The wide range of decay rates observed in the present study and the lack of information on this critical aspect of virus-host dynamics in soil emphasizes the need for continued research in this field.}, }
@article {pmid37431054, year = {2022}, author = {Seo, H and Lee, S and Park, H and Jo, S and Kim, S and Rahim, MA and Ul-Haq, A and Barman, I and Lee, Y and Seo, A and Kim, M and Jung, IY and Song, HY}, title = {Characteristics and Microbiome Profiling of Korean Gochang Bokbunja Vinegar by the Fermentation Process.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {20}, pages = {}, pmid = {37431054}, issn = {2304-8158}, support = {2021040D288//Gochang Bokbunja vinegar Research Project/ ; Soonchunhyang University Research Fund//Soonchunhyang University/ ; }, abstract = {As NGS (next-generation sequencing) technology develops, metagenomics-based microbial ecology, that is, microbiome research, has recently led to the science of fermented food. Based on the above technology, a study was conducted to understand the characteristics of vinegar made from bokbunja, a local crop in Gochang-gun, Korea. Physicochemical characteristics of vinegar, organic acid analysis, microbial community analysis, and electronic tongue analysis were explored while fermenting the vinegar for 70 days under eight fermentation conditions according to the concentration of bokbunja liquid (100% or 50%), type of fermenter (porcelain jar or stainless container), and fermentation environment (natural outdoor conditions or temperature/oxygen controlled). As a result, distinct microbial community patterns were found in the stage of acetic acid fermentation and, accordingly, this fermentation of Gochang vinegar is classified into three categories. Vinegar prepared by the traditional method of outdoor fermentation using jars showed characteristics of "Acetobacter (42.1%)/Lactobacillus (56.9%) fusion fermentation". Under conditions where oxygen and temperature were controlled indoors using jars, characteristics of "Komagataeibacter (90.2%) fermentation" were found. "Lactobacillus (92.2%) fermentation" characteristics were discovered under natural outdoor conditions using stainless steel containers. These fermentation pattern differences were related to taxonomic phylogenetic diversity, which was also considered involved in determining organic acid production and taste. These results will be helpful as a scientific basis for understanding the fermentation characteristics of Gochang vinegar and developing high-value-added traditional vinegar products.}, }
@article {pmid37428189, year = {2023}, author = {Rellegadla, S and Prajapat, G and Jain, S and Agrawal, A}, title = {Microbial communities succession post to polymer flood demonstrate a role in enhanced oil recovery.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {17}, pages = {5531-5544}, pmid = {37428189}, issn = {1432-0614}, support = {IMP/2018/000589//SERB Department of Science and Technology/ ; BT/PR25132/NER/95/1034/2017//Department of Biotechnology, Ministry of Science and Technology, India/ ; 09/1131(0028)/2019-EMR-I//CSIR India/ ; }, abstract = {The role of indigenous microbial communities in residual oil extraction following a recovery process is not well understood. This study investigated the dynamics of resident microbial communities in oil-field simulating sand pack bioreactors after the polymer flooding stage resumed with waterflooding and explored their contribution to the oil extraction process. The microbial community succession was studied through high-throughput sequencing of 16S rRNA genes. The results revealed alternating dominance of minority populations, including Dietzia sps., Acinetobacter sps., Soehngenia sps., and Paracoccus sps., in each bioreactor following the flooding process. Additionally, the post-polymer waterflooding stage led to higher oil recovery, with hydroxyethylcellulose, tragacanth gum, and partially hydrolyzed polyacrylamide polymer-treated bioreactors yielding additional recovery of 4.36%, 5.39%, and 3.90% residual oil in place, respectively. The dominant microbial communities were previously reported to synthesize biosurfactants and emulsifiers, as well as degrade and utilize hydrocarbons, indicating their role in aiding the recovery process. However, the correlation analysis of the most abundant taxa showed that some species were more positively correlated with the oil recovery process, while others acted as competitors for the carbon source. The study also found that higher biomass favored the plugging of high permeability zones in the reservoir, facilitating the dislodging of crude oil in new channels. In conclusion, this study suggests that microbial populations significantly shift upon polymer treatment and contribute synergistically to the oil recovery process depending on the characteristics of the polymers injected. KEY POINTS: • Post-polymer flooded microbial ecology shows unique indigenous microbial consortia. • Injected polymers are observed to act as enrichment substrates by resident communities. • The first study to show successive oil recovery stage post-polymer flood without external influence.}, }
@article {pmid37426976, year = {2023}, author = {Wang, M and Cernava, T}, title = {Editorial: The phyllosphere microbiome.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1234843}, pmid = {37426976}, issn = {1664-462X}, }
@article {pmid37423403, year = {2023}, author = {Melo-Bolívar, JF and Ruiz Pardo, RY and Quintanilla-Carvajal, MX and Díaz, LE and Alzate, JF and Junca, H and Rodríguez Orjuela, JA and Villamil Diaz, LM}, title = {Evaluation of dietary single probiotic isolates and probiotic multistrain consortia in growth performance, gut histology, gut microbiota, immune regulation, and infection resistance of Nile tilapia, Oreochromis niloticus, shows superior monostrain performance.}, journal = {Fish &amp; shellfish immunology}, volume = {140}, number = {}, pages = {108928}, doi = {10.1016/j.fsi.2023.108928}, pmid = {37423403}, issn = {1095-9947}, mesh = {Animals ; *Cichlids ; *Gastrointestinal Microbiome ; *Probiotics/pharmacology ; Diet/veterinary ; *Tilapia ; Animal Feed/analysis ; *Fish Diseases ; Dietary Supplements ; }, abstract = {The probiotic potential of a designed bacterial consortia isolated from a competitive exclusion culture originally obtained from the intestinal contents of tilapia juveniles were evaluated on Nile tilapia alevins. The growth performance, intestinal histology, microbiota effects, resistance to Streptococcus agalactiae challenge, and immune response were assessed. In addition, the following treatments were included in a commercial feed: A12+M4+M10 (Lactococcus lactis A12, Priestia megaterium M4, and Priestia sp. M10), M4+M10 (P. megaterium M4, and Priestia sp. M10) and the single bacteria as controls; A12 (L. lactis A12), M4 (P. megaterium M4), M10 (Priestia sp. M10), also a commercial feed without any probiotic addition was included as a control. The results showed that all probiotic treatments improved the growth performance, intestinal histology, and resistance during experimental infection with S. agalactiae in comparison to the control fish. Also, the administration of probiotics resulted in the modulation of genes associated with the innate and adaptive immune systems that were non-dependent on microbial colonization. Surprisingly, L. lactis A12 alone induced benefits in fish compared to the microbial consortia, showing the highest increase in growth rate, survival during experimental infection with S. agalactiae, increased intestinal fold length, and the number of differentially expressed genes. Lastly, we conclude that a competitive exclusion culture is a reliable source of probiotics, and monostrain L. lactis A12 has comparable or even greater probiotic potential than the bacterial consortia.}, }
@article {pmid37422225, year = {2023}, author = {Villar-dePablo, M and Ascaso, C and Rodríguez-Pérez, E and Urizal, M and Wierzchos, J and Pérez-Ortega, S and de Los Ríos, A}, title = {Innovative approaches to accurately assess the effectiveness of biocide-based treatments to fight biodeterioration of Cultural Heritage monuments.}, journal = {The Science of the total environment}, volume = {897}, number = {}, pages = {165318}, doi = {10.1016/j.scitotenv.2023.165318}, pmid = {37422225}, issn = {1879-1026}, mesh = {*Disinfectants/pharmacology ; *Cyanobacteria ; *Ascomycota ; Microscopy ; }, abstract = {The development of diagnostic methods to accurately assess the effects of treatments on lithobiont colonization remains a challenge for the conservation of Cultural Heritage monuments. In this study, we tested the efficacy of biocide-based treatments on microbial colonization of a dolostone quarry, in the short and long-term, using a dual analytical strategy. We applied a metabarcoding approach to characterize fungal and bacterial communities over time, integrated with microscopy techniques to analyze the interactions of microorganisms with the substrate and evaluate the effectiveness. These communities were dominated by the bacterial phyla Actinobacteriota, Proteobacteria and Cyanobacteria, and the fungal order Verrucariales, which include taxa previously reported as biodeteriogenic agents and observed here associated with biodeterioration processes. Following the treatments, changes over time in the abundance profiles depend on taxa. While Cyanobacteriales, Cytophagales and Verrucariales decreased in abundance, other groups, such as Solirubrobacteriales, Thermomicrobiales and Pleosporales increased. These patterns could be related not only to the specific effects of the biocide on the different taxa, but also to different recolonization abilities of those organisms. The different susceptibility to treatments could be associated with the inherent cellular properties of different taxa, but differences in biocide penetration to endolithic microhabitats could be involved. Our results demonstrate the importance of both removing epilithic colonization and applying biocides to act against endolithic forms. Recolonization processes could also explain some of the taxon-dependent responses, especially in the long-term. Taxa showing resistance, and those benefiting from nutrient accumulation in the form of cellular debris following treatments, may have an advantage in colonizing treated areas, pointing to the need for long-term monitoring of a wide range of taxa. This study highlights the potential utility of combining metabarcoding and microscopy to analyze the effects of treatments and design appropriate strategies to combat biodeterioration and establish preventive conservation protocols.}, }
@article {pmid37419360, year = {2023}, author = {Martin-Pozas, T and Fernandez-Cortes, A and Cuezva, S and Cañaveras, JC and Benavente, D and Duarte, E and Saiz-Jimenez, C and Sanchez-Moral, S}, title = {New insights into the structure, microbial diversity and ecology of yellow biofilms in a Paleolithic rock art cave (Pindal Cave, Asturias, Spain).}, journal = {The Science of the total environment}, volume = {897}, number = {}, pages = {165218}, doi = {10.1016/j.scitotenv.2023.165218}, pmid = {37419360}, issn = {1879-1026}, mesh = {*Caves/microbiology ; Spain ; *Bacteria ; Ecology ; Biofilms ; }, abstract = {In the absence of sunlight, caves harbor a great diversity of microbial colonies to extensive biofilms with different sizes and colors visible to the naked eye. One of the most widespread and visible types of biofilm are those with yellow hues that can constitute a serious problem for the conservation of cultural heritage in many caves, such as Pindal Cave (Asturias, Spain). This cave, declared a World Heritage Site by UNESCO for its Paleolithic parietal art, shows a high degree of development of yellow biofilms that represents a real threat to the conservation of painted and engraved figures. This study aims to: 1) identify the microbial structures and the most characteristic taxa composing the yellow biofilms, 2) seek the linked microbiome reservoir primarily contributing to their growth; 3) seed light on the driving vectors that contribute to their formation and determine the subsequent proliferation and spatial distribution. To achieve this goal, we used amplicon-based massive sequencing, in combination with other techniques such as microscopy, in situ hybridization and environmental monitoring, to compare the microbial communities of yellow biofilms with those of drip waters, cave sediments and exterior soil. The results revealed microbial structures related to the phylum Actinomycetota and the most characteristic bacteria in yellow biofilms, represented by the genera wb1-P19, Crossiella, Nitrospira, and Arenimonas. Our findings suggest that sediments serve as potential reservoirs and colonization sites for these bacteria that can develop into biofilms under favorable environmental and substrate conditions, with a particular affinity for speleothems and rugged-surfaced rocks found in condensation-prone areas. This study presents an exhaustive study of microbial communities of yellow biofilms in a cave, which could be used as a procedure for the identification of similar biofilms in other caves and to design effective conservation strategies in caves with valuable cultural heritage.}, }
@article {pmid37419243, year = {2023}, author = {Loyola-Fonseca, SC and Campello, AF and Rodrigues, RCV and Alves, FRF and Brasil, SC and Vilela, CLS and Gonçalves, LS and Provenzano, JC and Siqueira, JF and Rôças, IN}, title = {Disinfection and Shaping of Vertucci Class II Root Canals after Preparation with Two Instrument Systems and Supplementary Ultrasonic Activation of Sodium Hypochlorite.}, journal = {Journal of endodontics}, volume = {49}, number = {9}, pages = {1183-1190}, doi = {10.1016/j.joen.2023.06.017}, pmid = {37419243}, issn = {1878-3554}, mesh = {*Dental Pulp Cavity/diagnostic imaging/microbiology ; *Sodium Hypochlorite/therapeutic use ; X-Ray Microtomography ; Disinfection ; Ultrasonics ; Root Canal Preparation ; }, abstract = {INTRODUCTION: This study compared disinfection and shaping after root canal preparation with either XP-endo Shaper or TruNatomy instrument systems, supplemented by ultrasonic activation of sodium hypochlorite (NaOCl) with either stainless-steel (SS) or nickel-titanium (NiTi) inserts.<br><br>METHODS: Mesial roots from mandibular molars with Vertucci class II configuration were divided into 2 groups (n&#xa0;=&#xa0;24) based on anatomically paired micro-computed tomography (micro-CT) analyses. Pre and postpreparation micro-CT scans were obtained to evaluate the shaping performance. The canals were contaminated with a mixed bacterial culture for 30&#xa0;days and then subjected to preparation with either XP-endo Shaper or TruNatomy instruments using NaOCl irrigation. Supplementary ultrasonic activation of NaOCl was conducted using either an SS (TruNatomy group) or NiTi (XP-endo Shaper group) insert. Bacteriological samples were taken from the canals before preparation (S1), after preparation (S2), and after the supplementary approach (S3). Bacterial reduction was evaluated using a quantitative real-time polymerase chain reaction.<br><br>RESULTS: Preparation with both instrument systems significantly reduced bacterial counts (P&#xa0;<&#xa0;.01). After preparation, 36% (TruNatomy) and 35% (XP-endo Shaper) were negative for bacteria. These values increased to 59% and 65% after ultrasonic activation with the SS and NiTi inserts, respectively. The quantitative data in S2 showed that XP-endo Shaper promoted a significantly higher bacterial reduction than TruNatomy (P&#xa0;<&#xa0;.05). No significant intragroup differences were observed after ultrasonic activation (P&#xa0;>&#xa0;.05), probably because the SS insert promoted a significantly higher S2-to-S3 reduction than the NiTi insert (P&#xa0;<&#xa0;.01). Micro-CT analysis revealed no significant differences in the unprepared areas between the groups (P&#xa0;>&#xa0;.05).<br><br>CONCLUSIONS: The XP-endo Shaper caused a significantly higher bacterial reduction than TruNatomy in Vertucci class II canals. Better antibacterial results after ultrasonic activation were observed for the SS ultrasonic inserts than for the NiTi inserts.}, }
@article {pmid37418833, year = {2024}, author = {Crump, BC and Bowen, JL}, title = {The Microbial Ecology of Estuarine Ecosystems.}, journal = {Annual review of marine science}, volume = {16}, number = {}, pages = {335-360}, doi = {10.1146/annurev-marine-022123-101845}, pmid = {37418833}, issn = {1941-0611}, mesh = {Animals ; Humans ; *Wetlands ; Estuaries ; Food Chain ; Carbon ; *Microbiota ; }, abstract = {Human civilization relies on estuaries, and many estuarine ecosystem services are provided by microbial communities. These services include high rates of primary production that nourish harvests of commercially valuable species through fisheries and aquaculture, the transformation of terrestrial and anthropogenic materials to help ensure the water quality necessary to support recreation and tourism, and mutualisms that maintain blue carbon accumulation and storage. Research on the ecology that underlies microbial ecosystem services in estuaries has expanded greatly across a range of estuarine environments, including water, sediment, biofilms, biological reefs, and stands of seagrasses, marshes, and mangroves. Moreover, the application of new molecular tools has improved our understanding of the diversity and genomic functions of estuarine microbes. This review synthesizes recent research on microbial habitats in estuaries and the contributions of microbes to estuarine food webs, elemental cycling, and interactions with plants and animals, and highlights novel insights provided by recent advances in genomics.}, }
@article {pmid37417553, year = {2023}, author = {Jansma, J and Thome, NU and Schwalbe, M and Chatziioannou, AC and Elsayed, SS and van Wezel, GP and van den Abbeele, P and van Hemert, S and El Aidy, S}, title = {Dynamic effects of probiotic formula ecologic®825 on human small intestinal ileostoma microbiota: a network theory approach.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2232506}, pmid = {37417553}, issn = {1949-0984}, mesh = {Adult ; Humans ; *Gastrointestinal Microbiome ; *Microbiota ; *Probiotics/pharmacology ; Propionates/pharmacology ; Enterobacteriaceae ; }, abstract = {The gut microbiota plays a pivotal role in health and disease. The use of probiotics as microbiota-targeted therapies is a promising strategy to improve host health. However, the molecular mechanisms involved in such therapies are often not well understood, particularly when targeting the small intestinal microbiota. In this study, we investigated the effects of a probiotic formula (Ecologic®825) on the adult human small intestinal ileostoma microbiota. The results showed that supplementation with the probiotic formula led to a reduction in the growth of pathobionts, such as Enterococcaceae and Enterobacteriaceae, and a decrease in ethanol production. These changes were associated with significant alterations in nutrient utilization and resistance to perturbations. These probiotic mediated alterations which coincided with an initial increase in lactate production and decrease in pH were followed by a sharp increase in the levels of butyrate and propionate. Moreover, the probiotic formula increased the production of multiple N-acyl amino acids in the stoma samples. The study demonstrates the utility of network theory in identifying novel microbiota-targeted therapies and improving existing ones. Overall, the findings provide insights into the dynamic molecular mechanisms underlying probiotic therapies, which can aid in the development of more effective treatments for a range of conditions.}, }
@article {pmid37415044, year = {2023}, author = {King, NG and Uribe, R and Moore, PJ and Earp, HS and Gouraguine, A and Hinostroza, D and Perez-Matus, A and Smith, K and Smale, DA}, title = {Multiscale Spatial Variability and Stability in the Structure and Diversity of Bacterial Communities Associated with the Kelp Eisenia cokeri in Peru.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2574-2582}, pmid = {37415044}, issn = {1432-184X}, support = {MR/S032827/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Kelp/microbiology ; Ecosystem ; Peru ; Bacteria/genetics ; Biodiversity ; *Microbiota ; }, abstract = {Ecological communities are structured by a range of processes that operate over a range of spatial scales. While our understanding of such biodiversity patterns in macro-communities is well studied, our understanding at the microbial level is still lacking. Bacteria can be free living or associated with host eukaryotes, forming part of a wider "microbiome," which is fundamental for host performance and health. For habitat forming foundation-species, host-bacteria relationships likely play disproportionate roles in mediating processes for the wider ecosystem. Here, we describe host-bacteria communities across multiple spatial scales (i.e., from 10s of m to 100s of km) in the understudied kelp, Eisenia cokeri, in Peru. We found that E. cokeri supports a distinct bacterial community compared to the surrounding seawater, but the structure of these communities varied markedly at the regional (~480 km), site (1-10 km), and individual (10s of m) scale. The marked regional-scale differences we observed may be driven by a range of processes, including temperature, upwelling intensity, or regional connectivity patterns. However, despite this variability, we observed consistency in the form of a persistent core community at the genus level. Here, the genera Arenicella, Blastopirellula, Granulosicoccus, and Litorimonas were found in >80% of samples and comprised ~53% of total sample abundance. These genera have been documented within bacterial communities associated with kelps and other seaweed species from around the world and may be important for host function and wider ecosystem health in general.}, }
@article {pmid37415043, year = {2023}, author = {Shao, Q and Lin, Z and Xu, Z and Zhu, Z and Zhou, C and Yan, X}, title = {Integrated Biogeography and Assembly Mechanisms of Microeukaryotic Communities in Coastal Waters Near Shellfish Cultivation.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2560-2573}, pmid = {37415043}, issn = {1432-184X}, support = {2022J195//Natural Science Foundation of Ningbo/ ; 2022S116//Public Welfare Science and Technology Project of Ningbo/ ; 2018YFD0900702//National Key Research and Development Program of China/ ; }, mesh = {Animals ; Ecosystem ; Plankton/genetics ; *Diatoms ; China ; *Dinoflagellida/genetics ; *Arthropods ; Shellfish ; }, abstract = {The Lianjiang coast in the East China Sea is a typical subtropical marine ecosystem, and shellfish cultivation occupies almost all of the available tidal flats. Many studies have investigated the effects of shellfish cultivation on benthic organisms and sediments, while the impact of shellfish cultivation on plankton ecosystems is still poorly understood. This study investigated the biogeographical patterns of microeukaryotic communities from Lianjiang coastal waters in four seasons using 18S ribosomal RNA gene amplicon sequencing. Microeukaryotes were mainly comprised of Dinoflagellata, Diatomea, Arthropoda, Ciliophora, Chlorophyta, Protalveolata, Cryptophyceae, and Ochrophyta, and presented significant differences in three habitats (the aquaculture area, confluent area, and offshore area) and four seasons. Similarity percentage analysis revealed that Paracalanus parvus, Heterocapsa rotundata, Bestiolina similis, and five additional key taxa contributed to spatio-temporal differences. Seasonal environmental and spatial factors explained 27.47% of microeukaryotic community variation on average, with 11.11% of the variation shared. Environmental variables, particularly depth, pH, and nitrite concentration, were strongly associated with the microeukaryotic community compositions. The neutral community model further demonstrated that stochastic processes were sufficient in shaping substantial variation in microeukaryotic communities across four seasons, which may reveal the remaining unexplained microeukaryotic community variation. We further divided four seasons into the aquaculture stages and non-aquaculture stages, and speculated that aquaculture activities may increase the dispersal limitation of microeukaryotes in coastal waters, especially for the big bodied-microbes like Arthropoda. The results provide a better understanding of the biogeographical patterns, processes, and mechanisms of microeukaryotic communities near shellfish cultivation.}, }
@article {pmid37408642, year = {2023}, author = {Kasahara, K and Leygeber, M and Seiffarth, J and Ruzaeva, K and Drepper, T and Nöh, K and Kohlheyer, D}, title = {Enabling oxygen-controlled microfluidic cultures for spatiotemporal microbial single-cell analysis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1198170}, pmid = {37408642}, issn = {1664-302X}, abstract = {Microfluidic cultivation devices that facilitate O2 control enable unique studies of the complex interplay between environmental O2 availability and microbial physiology at the single-cell level. Therefore, microbial single-cell analysis based on time-lapse microscopy is typically used to resolve microbial behavior at the single-cell level with spatiotemporal resolution. Time-lapse imaging then provides large image-data stacks that can be efficiently analyzed by deep learning analysis techniques, providing new insights into microbiology. This knowledge gain justifies the additional and often laborious microfluidic experiments. Obviously, the integration of on-chip O2 measurement and control during the already complex microfluidic cultivation, and the development of image analysis tools, can be a challenging endeavor. A comprehensive experimental approach to allow spatiotemporal single-cell analysis of living microorganisms under controlled O2 availability is presented here. To this end, a gas-permeable polydimethylsiloxane microfluidic cultivation chip and a low-cost 3D-printed mini-incubator were successfully used to control O2 availability inside microfluidic growth chambers during time-lapse microscopy. Dissolved O2 was monitored by imaging the fluorescence lifetime of the O2-sensitive dye RTDP using FLIM microscopy. The acquired image-data stacks from biological experiments containing phase contrast and fluorescence intensity data were analyzed using in-house developed and open-source image-analysis tools. The resulting oxygen concentration could be dynamically controlled between 0% and 100%. The system was experimentally tested by culturing and analyzing an E. coli strain expressing green fluorescent protein as an indirect intracellular oxygen indicator. The presented system allows for innovative microbiological research on microorganisms and microbial ecology with single-cell resolution.}, }
@article {pmid37406718, year = {2023}, author = {Lv, T and Wang, D and Hui, J and Cheng, W and Ai, H and Qin, L and Huang, M and Feng, M and Wu, Y}, title = {Effect of return activated sludge diversion ratio on phosphorus removal performance in side-stream enhanced biological phosphorus removal (S2EBPR) process.}, journal = {Environmental research}, volume = {235}, number = {}, pages = {116546}, doi = {10.1016/j.envres.2023.116546}, pmid = {37406718}, issn = {1096-0953}, mesh = {*Sewage ; *Phosphorus ; Bioreactors ; Wastewater ; Carbon ; }, abstract = {In this study, a lab-scale continuous flow side-stream enhanced biological phosphorus (P) removal (S2EBPR) reactor was operated for 247 days treating synthetic wastewater with influent carbon to phosphorus (C/P) ratio of 25.0 g COD/g P and influent PO4[3-]-P of 7.4 ± 0.3 mg P/L. The effect of the return activated sludge (RAS) diversion ratio on S2EBPR reactor was investigated by comparing P removal performance, microbial activity, and community structure. The results showed that the RAS diversion ratio of 8.0%, by yielding a side-stream sludge retention time (SRTSS) of ∼60 h, resulted in the lowest effluent PO4[3-]-P concentration of 0.5 ± 0.3 mg P/L. The results of in situ process profiles and ex situ P release and uptake batch tests under different RAS diversion conditions showed that the more anaerobic P release was obtained in the side-stream reactor, the higher the P removal efficiency and EBPR activity were achieved. The stoichiometric ratios observed in EBPR activity tests indicated a polyphosphate accumulating organisms (PAOs) metabolism mainly dependent on the glycolysis pathway. The results of microbial ecology analysis revealed that the optimized SRTSS would give a competitive advantage to PAOs in the S2EBPR process. By obtaining statistically reliable results, this study would provide guidance for wastewater treatment plants to achieve optimal P removal performance in S2EBPR configuration.}, }
@article {pmid37406090, year = {2023}, author = {Pollak, S}, title = {Plant DNA in feces as a nutritional crystal ball.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {29}, pages = {e2309172120}, pmid = {37406090}, issn = {1091-6490}, mesh = {*DNA, Plant/analysis ; Feces/chemistry ; }, }
@article {pmid37405949, year = {2023}, author = {Almeida-Silva, F and Van de Peer, Y}, title = {Whole-genome Duplications and the Long-term Evolution of Gene Regulatory Networks in Angiosperms.}, journal = {Molecular biology and evolution}, volume = {40}, number = {7}, pages = {}, pmid = {37405949}, issn = {1537-1719}, mesh = {Phylogeny ; *Gene Regulatory Networks ; *Magnoliopsida/genetics ; Gene Duplication ; Evolution, Molecular ; Genome, Plant ; Polyploidy ; }, abstract = {Angiosperms have a complex history of whole-genome duplications (WGDs), with varying numbers and ages of WGD events across clades. These WGDs have greatly affected the composition of plant genomes due to the biased retention of genes belonging to certain functional categories following their duplication. In particular, regulatory genes and genes encoding proteins that act in multiprotein complexes have been retained in excess following WGD. Here, we inferred protein-protein interaction (PPI) networks and gene regulatory networks (GRNs) for seven well-characterized angiosperm species and explored the impact of both WGD and small-scale duplications (SSDs) in network topology by analyzing changes in frequency of network motifs. We found that PPI networks are enriched in WGD-derived genes associated with dosage-sensitive intricate systems, and strong selection pressures constrain the divergence of WGD-derived genes at the sequence and PPI levels. WGD-derived genes in network motifs are mostly associated with dosage-sensitive processes, such as regulation of transcription and cell cycle, translation, photosynthesis, and carbon metabolism, whereas SSD-derived genes in motifs are associated with response to biotic and abiotic stress. Recent polyploids have higher motif frequencies than ancient polyploids, whereas WGD-derived network motifs tend to be disrupted on the longer term. Our findings demonstrate that both WGD and SSD have contributed to the evolution of angiosperm GRNs, but in different ways, with WGD events likely having a more significant impact on the short-term evolution of polyploids.}, }
@article {pmid37405460, year = {2023}, author = {Suzuki, K and Katashima, K and Miki, T and Igarashi, H and Xu, Q and Ohkubo, S and Iwaishi, S and Harada, N}, title = {Bacterial Community Composition Under Paddy Conditions Is More Strongly Affected by the Difference in Soil Type than by Field Management.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2552-2559}, pmid = {37405460}, issn = {1432-184X}, mesh = {*Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Bacteria/genetics ; Agriculture/methods ; }, abstract = {In this study, we aimed to investigate the effects of soil type and field management on bacterial communities in paddy soils, taking into account the differences in soil physicochemical properties. We collected soil samples from 51 paddy fields in six prefectures in Japan. The paddy fields were managed under organic regimes (26 fields), natural-farming regimes (12 fields), or conventional regimes (13 fields). The paddy fields were classified into four soil types: andosol, gray lowland soil, gley soil, and gray upland soil. Soil DNA was extracted from the soil samples collected 2 to 10 weeks after the flooding, and the 16S rRNA gene amplicon sequencing analysis was performed. The bacterial community compositions were dominated by the phylum Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, and Firmicutes in all fields. The difference in soil type had significant effects on α-diversities of the bacterial communities, although the field management had no effect. The soil bacterial communities in the gley soils and gray upland soils individually formed different groups from those in the other soils, while the andosol and gray lowland soils tended to form relatively similar bacterial communities. On the other hand, the effects of the field management were estimated to be smaller than those of soil type. The β-diversity of the bacterial community compositions were significantly correlated with soil pH, total nitrogen content, total carbon content, and divalent iron content. Our results suggest that the soil microbial community in paddy fields may be strongly influenced by soil physiochemical properties derived from differences in soil type.}, }
@article {pmid37404190, year = {2023}, author = {Kosmopoulos, JC and Campbell, DE and Whitaker, RJ and Wilbanks, EG}, title = {Horizontal Gene Transfer and CRISPR Targeting Drive Phage-Bacterial Host Interactions and Coevolution in "Pink Berry" Marine Microbial Aggregates.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {7}, pages = {e0017723}, pmid = {37404190}, issn = {1098-5336}, support = {T32 DK077653/DK/NIDDK NIH HHS/United States ; T32 DK077653-29//HHS | National Institutes of Health (NIH)/ ; }, mesh = {Humans ; *Bacteriophages/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Transfer, Horizontal ; Fruit ; Host Microbial Interactions ; }, abstract = {Bacteriophages (phages), which are viruses that infect bacteria, are the most abundant components of microbial communities and play roles in community dynamics and host evolution. However, the study of phage-host interactions is hindered by a paucity of model systems from natural environments. Here, we investigate phage-host interactions in the "pink berry" consortia, which are naturally occurring, low-diversity, macroscopic bacterial aggregates that are found in the Sippewissett Salt Marsh (Falmouth, MA, USA). We leverage metagenomic sequence data and a comparative genomics approach to identify eight compete phage genomes, infer their bacterial hosts from host-encoded clustered regularly interspaced short palindromic repeats (CRISPRs), and observe the potential evolutionary consequences of these interactions. Seven of the eight phages identified infect known pink berry symbionts, namely, Desulfofustis sp. PB-SRB1, Thiohalocapsa sp. PB-PSB1, and Rhodobacteraceae sp. A2, and they are largely divergent from known viruses. In contrast to the conserved bacterial community structure of pink berries, the distribution of these phages across aggregates is highly variable. Two phages persisted over a period of seven years with high sequence conservation, allowing us to identify gene gain and loss. Increased nucleotide variation in a conserved phage capsid gene that is commonly targeted by host CRISPR systems suggests that CRISPRs may drive phage evolution in pink berries. Finally, we identified a predicted phage lysin gene that was horizontally transferred to its bacterial host, potentially via a transposon intermediary. Taken together, our results demonstrate that pink berry consortia contain diverse and variable phages as well as provide evidence for phage-host coevolution via multiple mechanisms in a natural microbial system. IMPORTANCE Phages, which are viruses that infect bacteria, are important components of all microbial systems, in which they drive the turnover of organic matter by lysing host cells, facilitate horizontal gene transfer (HGT), and coevolve with their bacterial hosts. Bacteria resist phage infection, which is often costly or lethal, through a diversity of mechanisms. One of these mechanisms is CRISPR systems, which encode arrays of phage-derived sequences from past infections to block subsequent infection with related phages. Here, we investigate the bacteria and phage populations from a simple marine microbial community, known as "pink berries", found in salt marshes of Falmouth, Massachusetts, as a model of phage-host coevolution. We identify eight novel phages and characterize a case of putative CRISPR-driven phage evolution as well as an instance of HGT between a phage and its host, together suggesting that phages have large evolutionary impacts in a naturally occurring microbial community.}, }
@article {pmid37404136, year = {2023}, author = {Li, H and Zhou, H and Yang, S and Dai, X}, title = {Stochastic and Deterministic Assembly Processes in Seamount Microbial Communities.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {7}, pages = {e0070123}, pmid = {37404136}, issn = {1098-5336}, mesh = {*Ecosystem ; China ; }, abstract = {Seamounts are ubiquitous in the ocean. However, little is known about how seamount habitat features influence the local microbial community. In this study, the microbial populations of sediment cores from sampling depths of 0.1 to 35 cm from 10 seamount summit sites with a water depth of 1,850 to 3,827 m across the South China Sea (SCS) Basin were analyzed. Compared with nonseamount ecosystems, isolated seamounts function as oases for microbiomes, with average moderate to high levels of microbial abundance, richness, and diversity, and they harbor distinct microbial communities. The distinct characteristics of different seamounts provide a high level of habitat heterogeneity, resulting in the wide range of microbial community diversity observed across all seamounts. Using dormant thermospores as tracers to study the effect of dispersal by ocean currents, the observed distance-decay biogeography across different seamounts shaped simultaneously by the seamounts' naturally occurring heterogeneous habitat and the limitation of ocean current dispersal was found. We also established a framework that links initial community assembly with successional dynamics in seamounts. Seamounts provide resource-rich and dynamic environments, which leads to a dominance of stochasticity during initial community establishment in surface sediments. However, a progressive increase in deterministic environmental selection, correlated with resource depletion in subsurface sediments, leads to the selective growth of rare species of surface sediment communities in shaping the subsurface community. Overall, the study indicates that seamounts are a previously ignored oasis in the deep sea. This study also provides a case study for understanding the microbial ecology in globally widespread seamounts. IMPORTANCE Although there are approximately 25 million seamounts in the ocean, surprisingly little is known about seamount microbial ecology. We provide evidence that seamounts are island-like habitats harboring microbial communities distinct from those of nonseamount habitats, and they exhibit a distance-decay pattern. Environmental selection and dispersal limitation simultaneously shape the observed biogeography. Coupling empirical data with a null mode revealed a shift in the type and strength, which controls microbial community assembly and succession from the seamount surface to the subsurface sediments as follows: (i) community assembly is initially primarily driven by stochastic processes such as dispersal limitation, and (ii) changes in the subsurface environment progressively increase the importance of environmental selection. This case study contributes to the mechanistic understanding essential for a predictive microbial ecology of seamounts.}, }
@article {pmid37402057, year = {2023}, author = {Hkiri, N and Aounallah, F and Fouzai, K and Chouchani, C and Asses, N}, title = {Ability of marine-derived fungi isolated from polluted saline environment for enzymatic hydrocarbon remediation.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {54}, number = {3}, pages = {1983-2000}, pmid = {37402057}, issn = {1678-4405}, mesh = {*Lignin/metabolism ; Laccase/genetics/metabolism ; Peroxidases/metabolism ; Fungi/metabolism ; *Petroleum/metabolism ; Biodegradation, Environmental ; }, abstract = {Marine-derived fungi have attracted much attention due to their ability to present a new biosynthetic diversity. About 50 fungal isolates were obtained from Tunisian Mediterranean seawater and then screened for the presence of lignin-peroxidase (LiP), manganese-dependent peroxidase (MnP), and laccase (Lac) activities. The results obtained from both qualitative and quantitative assays showed that four of marine fungi isolates had a high potential to produce lignin-degrading enzymes. They were characterized taxonomically by a molecular method, based on international spacer (ITS) rDNA sequence analysis, as Chaetomium jodhpurense (MH667651.1), Chaetomium maderasense (MH665977.1), Paraconiothyrium variabile (MH667653.1), and Phoma betae (MH667655.1) which have been reported as producers of ligninolytic enzyme in the literature. The enzymatic activities and culture conditions were optimized using a Fractional Factorial design (2 [7- 4]). Then, fungal strains were incubated with the addition of 1% of crude oil in 50% of seawater for 25 days to evaluate their abilities to simultaneously degrade hydrocarbon compounds and to produce ligninolytic enzymes. The strain P. variabile exhibited the highest crude oil degradation rate (48.3%). Significant production of ligninolytic enzymes was recorded during the degradation process, which reached 2730 U/L for the MnP, 410 U/L for LiP, and 168.5 U/L for Lac. The FTIR and GC-MS analysis confirmed that the isolates rapidly biodegrade crude oil under ecological and economic conditions.}, }
@article {pmid37401933, year = {2023}, author = {Chen, L and Xin, X and Li, J and Han, C and Xiong, W and Luo, Y and Sun, R and Zhang, J}, title = {Phosphorus Fertilization Boosts Mineral-Associated Soil Organic Carbon Formation Associated with Phagotrophic Protists.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2541-2551}, pmid = {37401933}, issn = {1432-184X}, support = {42177332//National Natural Science Foundation of China/ ; XDA24020104 and XDA28020203//Strategic Priority Research Program of Chinese Academy of Sciences/ ; 2022YFD1500203 and 2022YFD1500401//National Key Research and Development Program of China/ ; 2023325//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; CARS-03-15 and CARS-52//China Agriculture Research System/ ; }, mesh = {*Soil ; *Phosphorus/metabolism ; Carbon/metabolism ; Soil Microbiology ; Minerals/metabolism ; Bacteria/genetics/metabolism ; Fertilizers/analysis ; Fertilization ; }, abstract = {Long-term fertilization affects soil organic C accumulation. A growing body of research has revealed critical roles of bacteria in soil organic C accumulation, particularly through mineral-associated organic C (MAOC) formation. Protists are essential components of soil microbiome, but the relationships between MAOC formation and protists under long-term fertilization remain unclear. Here, we used cropland soil from a long-term fertilization field trial and conducted two microcosm experiments with [13]C-glucose addition to investigate the effects of N and P fertilizations on MAOC formation and the relationships with protists. The results showed that long-term fertilization (especially P fertilization) significantly (P < 0.05) increased [13]C-MAOC content. Compared with P-deficient treatment, P replenishment enriched the number of protists (mainly Amoebozoa and Cercozoa) and bacteria (mainly Acidobacteriota, Bacteroidota, and Gammaproteobacteria), and significantly (P < 0.001) promoted the abundances of bacterial functional genes controlling C, N, P, and S metabolisms. The community composition of phagotrophic protists prominently (P < 0.001) correlated with the bacterial community composition, bacterial functional gene abundance, and [13]C-MAOC content. Co-occurrence networks of phagotrophic protists and bacteria were more connected in soil with the N inoculum added than in soil with the NP inoculum added. P replenishment strengthened bacterial [13]C assimilation (i.e., [13]C-phospholipid fatty acid content), which negatively (P < 0.05) correlated with the number and relative abundance of phagotrophic Cercozoa. Together, these results suggested that P fertilization boosts MAOC formation associated with phagotrophic protists. Our study paves the way for future research to harness the potential of protists to promote belowground C accrual in agroecosystems.}, }
@article {pmid37396621, year = {2023}, author = {Moens, F and Vandevijver, G and De Blaiser, A and Larsson, A and Spreafico, F and Augustijns, P and Marzorati, M}, title = {The Dynamic Intestinal Absorption Model (Diamod®), an in vitro tool to study the interconnected kinetics of gastrointestinal solubility, supersaturation, precipitation, and intestinal permeation processes of oral drugs.}, journal = {International journal of pharmaceutics: X}, volume = {5}, number = {}, pages = {100177}, pmid = {37396621}, issn = {2590-1567}, abstract = {This study aimed at developing the Diamod® as a dynamic gastrointestinal transfer model with physically interconnected permeation. The Diamod® was validated by studying the impact of the intraluminal dilution of a cyclodextrin-based itraconazole solution and the negative food effect for indinavir sulfate for which clinical data are available demonstrating that the systemic exposure was strongly mediated by interconnected solubility, precipitation, and permeation processes. The Diamod® accurately simulated the impact of water intake on the gastrointestinal behavior of a Sporanox® solution. Water intake significantly decreased the duodenal solute concentrations of itraconazole as compared to no intake of water. Despite this duodenal behavior the amount of permeated itraconazole was not affected by water intake as observed in vivo. Next to this, the Diamod® accurately simulated the negative food effect for indinavir sulfate. Different fasted and fed state experiments demonstrated that this negative food effect was mediated by an increased stomach pH, entrapment of indinavir in colloidal structures and the slower gastric emptying of indinavir under fed state conditions. Therefore, it can be concluded that the Diamod® is a useful in vitro model to mechanistically study the gastrointestinal performance of drugs.}, }
@article {pmid37395875, year = {2023}, author = {Simon, MP and Schatz, M and Böhm, L and Papp, I and Grossart, HP and Andersen, TJ and Bálint, M and Düring, RA}, title = {Dissent in the sediment? Lake sediments as archives of short- and long-range impact of anthropogenic activities in northeastern Germany.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {36}, pages = {85867-85888}, pmid = {37395875}, issn = {1614-7499}, support = {DFG BA 4843/2-1//Deutsche Forschungsgemeinschaft/ ; K314/2020//Deutsche Forschungsgemeinschaft/ ; K314/2020//Leibniz-Gemeinschaft/ ; }, mesh = {DDT/analysis ; Lakes/analysis ; Anthropogenic Effects ; Dissent and Disputes ; *Water Pollutants, Chemical/analysis ; *Pesticides/analysis ; *Hydrocarbons, Chlorinated/analysis ; Geologic Sediments/chemistry ; Environmental Monitoring/methods ; China ; }, abstract = {The suitability of lake sediment cores to reconstruct past inputs, regional pollution, and usage patterns of pesticides has been shown previously. Until now, no such data exist for lakes in eastern Germany. Therefore, 10 sediment cores (length 1 m) of 10 lakes in eastern Germany, the territory of the former German Democratic Republic (GDR), were collected and cut into 5-10-mm layers. In each layer, concentrations of trace elements (TEs) As, Cd, Cr, Cu, Ni, Pb, S, and Zn, as well as of organochlorine pesticides (OCPs), i.e., dichlorodiphenyltrichloroethane (DDT) and hexachlorocyclohexane (HCH), were analyzed. A miniaturized solid-liquid extraction technique in conjunction with headspace solid-phase microextraction (HS-SPME) and gas chromatography-mass spectrometry (GC-MS) was used for the latter. The progression of TE concentrations over time is uniform. It follows a trans-regional pattern and is indicative of activity and policy making in West Germany before 1990 instead of those in the GDR. Of OCPs, only transformation products of DDT were found. Congener ratios indicate a mainly aerial input. In the lakes' profiles, several regional features and responses to national policies and measures are visible. Dichlorodiphenyldichloroethane (DDD) concentrations reflect the history of DDT use in the GDR. Lake sediments proved to be suitable to archive short- and long-range impacts of anthropogenic activity. Our data can be used to complement and validate other forms of environmental pollution long-term monitoring and to check for the efficiency of pollution countermeasures in the past.}, }
@article {pmid37393557, year = {2023}, author = {Madrigal-Trejo, D and Sánchez-Pérez, J and Espinosa-Asuar, L and Valdivia-Anistro, JA and Eguiarte, LE and Souza, V}, title = {A Metagenomic Time-Series Approach to Assess the Ecological Stability of Microbial Mats in a Seasonally Fluctuating Environment.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2252-2270}, pmid = {37393557}, issn = {1432-184X}, support = {IG200319//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; 970341//Consejo Nacional de Ciencia y Tecnolog&#xed;a (CONACYT)/ ; R20F009//http://dx.doi.org/10.13039/501100020884/ ; }, mesh = {Metagenome ; *Cyanobacteria/genetics ; Archaea/genetics ; *Microbiota ; Bacteroidetes/genetics ; }, abstract = {Microbial mats are complex ecological assemblages that have been present in the rock record since the Precambrian and can still be found in extant marginalized environments. These structures are considered highly stable ecosystems. In this study, we evaluate the ecological stability of dome-forming microbial mats in a modern, water-level fluctuating, hypersaline pond located in the Cuatro Ciénegas Basin, Mexico. We conducted metagenomic sampling of the site from 2016 to 2019 and detected 2250 genera of Bacteria and Archaea, with only <20 belonging to the abundant taxa (>1%). The microbial community was dominated by Proteobacteria, Euryarchaeota, Bacteroidetes, Firmicutes, and Cyanobacteria, and was compositionally sensitive to disturbances, leading to high taxonomic replacement even at the phylum level, with a significant increase in Archaea from [Formula: see text]1-4% to [Formula: see text]33% throughout the 2016-2019 study period. Although a core community represented most of the microbial community (>75%), relative abundances shifted significantly between samples, as demonstrated by changes in the abundance of Coleofasciculus from 10.2% in 2017 to 0.05% in 2019. Although functional differences between seasons were subtle, co-occurrence networks suggest differential ecological interactions between the seasons, with the addition of a new module during the rainy season and the potential shift in hub taxa. Functional composition was slightly more similar between samples, but basic processes such as carbohydrate, amino acid, and nucleic acid metabolisms were widely distributed among samples. Major carbon fixation processes included sulfur oxidation, nitrogen fixation, and photosynthesis (both oxygenic and anoxygenic), as well as the Wood-Ljundgahl and Calvin cycles.}, }
@article {pmid37392205, year = {2023}, author = {Woźniak, M and Tyśkiewicz, R and Siebielec, S and Gałązka, A and Jaroszuk-Ściseł, J}, title = {Metabolic Profiling of Endophytic Bacteria in Relation to Their Potential Application as Components of Multi-Task Biopreparations.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2527-2540}, pmid = {37392205}, issn = {1432-184X}, mesh = {Humans ; *Ecosystem ; *Bacteria ; Endophytes ; Crops, Agricultural ; Stress, Physiological ; }, abstract = {Agricultural crops are exposed to various abiotic and biotic stresses that can constrain crop productivity. Focusing on a limited subset of key groups of organisms has the potential to facilitate the monitoring of the functions of human-managed ecosystems. Endophytic bacteria can enhance plant stress resistance and can help plants to cope with the negative impacts of stress factors through the induction of different mechanisms, influencing plant biochemistry and physiology. In this study, we characterise endophytic bacteria isolated from different plants based on their metabolic activity and ability to synthesise 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD), the activity of hydrolytic exoenzymes, the total phenolic compounds (TPC) and iron-complexing compounds (ICC). Test GEN III MicroPlate indicated that the evaluated endophytes are highly metabolically active, and the best used substrates were amino acids, which may be important in selecting potential carrier components for bacteria in biopreparations. The ACCD activity of strain ES2 (Stenotrophomonas maltophilia) was the highest, whereas that of strain ZR5 (Delftia acidovorans) was the lowest. Overall, the obtained results indicated that ∼91.3% of the isolates were capable of producing at least one of the four hydrolytic enzymes. In addition, most of the tested strains produced ICC and TPC, which play a significant role in reducing stress in plants. The results of this study suggest that the tested endophytic bacterial strains can potentially be used to mitigate climate change-associated stresses in plants and to inhibit plant pathogens.}, }
@article {pmid37392204, year = {2023}, author = {Berçot, MR and Queiroz, PRM and Grynberg, P and Togawa, R and Martins, &#xc9;S and Rocha, GT and Monnerat, RG}, title = {Distribution and Genetic Diversity of Genes from Brazilian Bacillus thuringiensis Strains Toxic to Agricultural Insect Pests Revealed by Real-Time PCR.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2515-2526}, pmid = {37392204}, issn = {1432-184X}, mesh = {Animals ; *Bacillus thuringiensis/genetics ; Endotoxins/genetics/chemistry ; Real-Time Polymerase Chain Reaction ; Bacillus thuringiensis Toxins ; Brazil ; Bacterial Proteins/genetics/chemistry ; Insecta ; Genetic Variation ; Hemolysin Proteins/genetics/chemistry ; }, abstract = {Bacillus thuringiensis is a Gram-positive aerobic bacterium and the most used biopesticide worldwide. Given the importance of B. thuringiensis strain characterization for the development of new bioinsecticides or transgenic events and the identification and classification of new B. thuringiensis genes and strains to understand its distribution and diversity, this work is aimed at creating a gene identification system based on qPCR reactions utilizing core B. thuringiensis genes cry1, cry2, cry3, cry4, cry5, app6, cry7, cry8, cry9, cry10, cry11, vpb1, vpa2, vip3, cyt1, and cyt2 for the characterization of 257 strains of B. thuringiensis. This system was based on the Invertebrate Bacteria Collection from Embrapa Genetic Resources and Biotechnology and analyzed (a) the degree of correlation between the distribution of these strains and the origin of the substrate from which the strain was isolated and (b) between its distribution and geoclimatic conditions. This study made it possible to observe that the cry1, cry2, and vip3A/B genes occur homogeneously in the Brazilian territory, and some genes are found in specific regions. The biggest reservoir of variability is within B. thuringiensis strains in each region, and it is suggested that both geoclimatic conditions and regional crops interfere with the genetic diversity of the B. thuringiensis strains present in the region, and B. thuringiensis strains can constantly exchange genetic information.}, }
@article {pmid37391884, year = {2023}, author = {Grosicki, GJ and Pugh, J and Wosinska, L and Quilter, K and Mattimoe, D and Allen, J and Joyce, SA and O'Sullivan, O and Close, GL}, title = {Ultra-Endurance triathlon competition shifts fecal metabolome independent of changes to microbiome composition.}, journal = {Journal of applied physiology (Bethesda, Md. : 1985)}, volume = {135}, number = {3}, pages = {549-558}, doi = {10.1152/japplphysiol.00024.2023}, pmid = {37391884}, issn = {1522-1601}, mesh = {Humans ; Male ; Female ; Physical Endurance/physiology ; *Athletic Performance/physiology ; Swimming/physiology ; *Microbiota ; Metabolome ; }, abstract = {Understanding changes to gut microbiota composition and metabolic output in response to acute exercise may be necessary for understanding the mechanisms mediating the long-term health and performance benefits of exercise. Our primary objective was to characterize acute changes in the fecal microbiome and metabolome following participation in an ultra-endurance (3.9 km swim, 180.2 km bike, 42.2 km run) triathlon. An exploratory aim was to determine associations between athlete-specific factors [race performance (i.e., completion time) and lifetime years of endurance training] with pre-race gut microbiota and metabolite profiles. Stool samples from 12 triathletes (9 males/3 females; 43 ± 14 yr, 23 ± 2 kg/m[2]) were collected ≤48 h before and the first bowel movement following race completion. Intra- and inter-individual diversity of bacterial species and individual bacterial taxa were unaltered following race completion (P > 0.05). However, significant reductions (P < 0.05) in free and secondary bile acids [deoxycholic acid (DCA), 12-keto-lithocholic acid (12-ketoLCA)] and short-chain fatty acids (butyric and pivalic acids), and significant increases (P < 0.05) in long-chain fatty acids (oleic and palmitoleic acids) were observed. Exploratory analyses revealed several associations between pre-race bacterial taxa and fecal metabolites with race performance and lifetime history of endurance training (P < 0.05). These findings suggest that 1) acute ultra-endurance exercise shifts microbial metabolism independent of changes to community composition and 2) athlete performance level and training history relate to resting-state gut microbial ecology.NEW &amp; NOTEWORTHY This is the first study to characterize acute changes in gut microbial ecology and metabolism following an ultra-endurance triathlon. We demonstrate changes in gut microbial community function, but not structure, as well as several associations between gut microbiome and fecal metabolome characteristics with race completion time and lifetime history of endurance training. These data add to a small but growing body of literature seeking to characterize the acute and chronic effects of exercise on the gut microbial ecosystem.}, }
@article {pmid37391045, year = {2023}, author = {Abele, M and Doll, E and Bayer, FP and Meng, C and Lomp, N and Neuhaus, K and Scherer, S and Kuster, B and Ludwig, C}, title = {Unified Workflow for the Rapid and In-Depth Characterization of Bacterial Proteomes.}, journal = {Molecular &amp; cellular proteomics : MCP}, volume = {22}, number = {8}, pages = {100612}, pmid = {37391045}, issn = {1535-9484}, mesh = {*Proteome/analysis ; *Proteomics/methods ; Workflow ; Peptides/chemistry ; Escherichia coli ; }, abstract = {Bacteria are the most abundant and diverse organisms among the kingdoms of life. Due to this excessive variance, finding a unified, comprehensive, and safe workflow for quantitative bacterial proteomics is challenging. In this study, we have systematically evaluated and optimized sample preparation, mass spectrometric data acquisition, and data analysis strategies in bacterial proteomics. We investigated workflow performances on six representative species with highly different physiologic properties to mimic bacterial diversity. The best sample preparation strategy was a cell lysis protocol in 100% trifluoroacetic acid followed by an in-solution digest. Peptides were separated on a 30-min linear microflow liquid chromatography gradient and analyzed in data-independent acquisition mode. Data analysis was performed with DIA-NN using a predicted spectral library. Performance was evaluated according to the number of identified proteins, quantitative precision, throughput, costs, and biological safety. With this rapid workflow, over 40% of all encoded genes were detected per bacterial species. We demonstrated the general applicability of our workflow on a set of 23 taxonomically and physiologically diverse bacterial species. We could confidently identify over 45,000 proteins in the combined dataset, of which 30,000 have not been experimentally validated before. Our work thereby provides a valuable resource for the microbial scientific community. Finally, we grew Escherichia coli and Bacillus cereus in replicates under 12 different cultivation conditions to demonstrate the high-throughput suitability of the workflow. The proteomic workflow we present in this manuscript does not require any specialized equipment or commercial software and can be easily applied by other laboratories to support and accelerate the proteomic exploration of the bacterial kingdom.}, }
@article {pmid37389724, year = {2024}, author = {Das, S and Roy, R and Paul, P and Chakraborty, P and Chatterjee, S and Malik, M and Sarkar, S and Das Gupta, A and Maiti, D and Tribedi, P}, title = {Piperine, a Plant Alkaloid, Exhibits Efficient Disintegration of the Pre-existing Biofilm of Staphylococcus aureus: a Step Towards Effective Management of Biofilm Threats.}, journal = {Applied biochemistry and biotechnology}, volume = {196}, number = {3}, pages = {1272-1291}, pmid = {37389724}, issn = {1559-0291}, support = {R&amp;D/2020/F2//The Neotia University/ ; }, mesh = {Humans ; Staphylococcus aureus ; Biofilms ; *Alkaloids/pharmacology ; Benzodioxoles/pharmacology ; *Staphylococcal Infections ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Piperidines ; *Polyunsaturated Alkamides ; }, abstract = {Staphylococcus aureus causes a range of chronic infections in humans by exploiting its biofilm machinery and drug-tolerance property. Although several strategies have been proposed to eradicate biofilm-linked issues, here, we have explored whether piperine, a bioactive plant alkaloid, can disintegrate an already existing Staphylococcal biofilm. Towards this direction, the cells of S. aureus were allowed to develop biofilm first followed by treatment with the test concentrations (8 and 16 µg/mL) of piperine. In this connection, several assays such as total protein recovery assay, crystal violet assay, extracellular polymeric substances (EPS) measurement assay, fluorescein diacetate hydrolysis assay, and fluorescence microscopic image analysis confirmed the biofilm-disintegrating property of piperine against S. aureus. Piperine reduced the cellular auto-aggregation by decreasing the cell surface hydrophobicity. On further investigation, we observed that piperine could down regulate the dltA gene expression that might reduce the cell surface hydrophobicity of S. aureus. It was also observed that the piperine-induced accumulation of reactive oxygen species (ROS) could enhance biofilm disintegration by decreasing the cell surface hydrophobicity of the test organism. Together, all the observations suggested that piperine could be used as a potential molecule for the effective management of the pre-existing biofilm of S. aureus.}, }
@article {pmid37387230, year = {2024}, author = {Falkenberg, R and Sigl, L and Fochler, M}, title = {From 'making lists' to conducting 'well-rounded' studies: Epistemic re-orientations in soil microbial ecology.}, journal = {Social studies of science}, volume = {54}, number = {1}, pages = {78-104}, pmid = {37387230}, issn = {1460-3659}, mesh = {*Soil ; *Soil Microbiology ; }, abstract = {Soil microbial ecology is a relatively young research field that became established around the middle of the 20th century and has grown considerably since then. We analyze two epistemic re-orientations in the field, asking how possibilities for creating do-able problems within current conditions of research governance and researchers' collective sense-making about new, more desirable modes of research were intertwined in these developments. We show that a first re-orientation towards molecular omics studies was comparably straightforward to bring about, because it allowed researchers to gain resources for their work and to build careers-in other words, to create do-able problems. Yet, over time this mode of research developed into a scientific bandwagon from which researchers found it difficult to depart, even as they considered this kind of work as producing mostly descriptive studies rather than exploring interesting and important ecological questions. Researchers currently wish to re-orient their field again, towards a new mode of conducting 'well-rounded' interdisciplinary and ecologically-relevant studies. This re-orientation is, however, not easy to put into practice. In contrast to omics studies, this new mode of research does not easily enable the creation of do-able problems for two reasons. First, it is not as readily 'packaged' and hence more difficult to align with institutional and funding frameworks as well as with demands for productivity and career building. Second, while the first re-orientation was part of a broader exciting bandwagon across the life sciences and promised apparent discoveries, the current re-orientation goes along with a different sense of novelty, exploring complex environmental relations and building an understanding at the intersection of disciplines, instead of pushing a clearly circumscribed frontier. Ultimately, our analysis raises questions about whether current conditions of research governance structurally privilege particular kinds of scientific re-orientation over others.}, }
@article {pmid37387175, year = {2023}, author = {Grover, S and Markin, A and Anderson, TK and Eulenstein, O}, title = {Phylogenetic diversity statistics for all clades in a phylogeny.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {39 Suppl 1}, pages = {i177-i184}, pmid = {37387175}, issn = {1367-4811}, support = {75N93021C00015/AI/NIAID NIH HHS/United States ; }, mesh = {Phylogeny ; *Biological Evolution ; *Algorithms ; Computer Simulation ; Software ; }, abstract = {The classic quantitative measure of phylogenetic diversity (PD) has been used to address problems in conservation biology, microbial ecology, and evolutionary biology. PD is the minimum total length of the branches in a phylogeny required to cover a specified set of taxa on the phylogeny. A general goal in the application of PD has been identifying a set of taxa of size k that maximize PD on a given phylogeny; this has been mirrored in active research to develop efficient algorithms for the problem. Other descriptive statistics, such as the minimum PD, average PD, and standard deviation of PD, can provide invaluable insight into the distribution of PD across a phylogeny (relative to a fixed value of k). However, there has been limited or no research on computing these statistics, especially when required for each clade in a phylogeny, enabling direct comparisons of PD between clades. We introduce efficient algorithms for computing PD and the associated descriptive statistics for a given phylogeny and each of its clades. In simulation studies, we demonstrate the ability of our algorithms to analyze large-scale phylogenies with applications in ecology and evolutionary biology. The software is available at https://github.com/flu-crew/PD_stats.}, }
@article {pmid37383638, year = {2023}, author = {McAtee, TB and Pinnell, LJ and Powledge, SA and Wolfe, CA and Morley, PS and Richeson, JT}, title = {Effects of respiratory virus vaccination and bovine respiratory disease on the respiratory microbiome of feedlot cattle.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1203498}, pmid = {37383638}, issn = {1664-302X}, abstract = {INTRODUCTION: The objectives of this study were to evaluate the impacts of two modified-live virus (MLV) vaccination protocols and respiratory disease (BRD) occurrence on the microbial community composition of the nasopharynx in feedlot cattle.<br><br>METHODS: The treatment groups included in this randomized controlled trial included: 1) no viral respiratory vaccination (CON), 2) intranasal, trivalent, MLV respiratory vaccine in addition to a parenteral BVDV type I and II vaccine (INT), and 3) parenteral, pentavalent, MLV respiratory vaccination against the same agents (INJ). Calves (n = 525) arrived in 5 truckload blocks and were stratified by body weight, sex, and presence of a pre-existing identification ear-tag. A total of 600 nasal swab samples were selected for DNA extraction and subsequent 16S rRNA gene sequencing to characterize the microbiome of the upper respiratory tract. Nasal swabs collected on d 28 from healthy cattle were used to evaluate the impact of vaccination on upper respiratory tract (URT) microbial communities.<br><br>RESULTS: Firmicutes were less abundant in INT calves (n = 114; P < 0.05) and this difference was attributed to decreased relative abundance (RA) of Mycoplasma spp. (P = 0.04). Mannheimia and Pasteurella had lower RA in INT (P < 0.05). The microbiome in healthy animals on d 28 had increased Proteobacteria (largely Moraxella spp.) and decreased Firmicutes (comprised almost exclusively of Mycoplasma spp.) compared to animals that were treated for or died from BRD (P < 0.05). Cattle that died had a greater RA of Mycoplasma spp. in their respiratory microbiome on d 0 (P < 0.02). Richness was similar on d 0 and 28, but diversity increased for all animals on d 28 (P>0.05).}, }
@article {pmid37383354, year = {2023}, author = {Kim, S and Kwak, J and Song, M and Cho, J and Kim, ES and Keum, GB and Doo, H and Pandey, S and Cho, JH and Ryu, S and Kim, S and Im, YM and Kim, HB}, title = {Effects of Lacticaseibacillus casei (Lactobacillus casei) and Saccharomyces cerevisiae mixture on growth performance, hematological parameters, immunological responses, and intestinal microbiome in weaned pigs.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1140718}, pmid = {37383354}, issn = {2297-1769}, abstract = {INTRODUCTION: This study was conducted to evaluate the effects of Lacticaseibacillus casei (Lactobacillus casei) and Saccharomyces cerevisiae mixture on growth performance, hematological parameters, immunological responses, and gut microbiome in weaned pigs.<br><br>METHODS: A total of 300 crossbred pigs [(Landrace &#xd7; Yorkshire]&#x2009;&#xd7;&#x2009;Duroc; 8.87&#x2009;&#xb1;&#x2009;0.34&#x2009; kg of average initial body weight [BW]; 4&#x2009; weeks of age) were divided into two dietary treatments (15 pigs/pen, 10 replicates/treatment) using a randomized complete block design (block&#x2009;=&#x2009;BW): control (CON) and the effective microorganism (MEM). The CON was not treated, while the MEM was treated with the mixture of L. casei (1 &#xd7; 10[7]&#x2009;CFU/mL) and S. cerevisiae (1 &#xd7; 10[7]&#x2009;CFU/mL) at 3&#x2009;mL/pig/day for 4&#x2009; weeks via the drinking water supply. Two feces and one blood sample from the randomly selected pigs in each pen were collected on D1 and D28 after weaning. Pigs were individually weighed, and pen feed intakes were recorded to evaluate pig growth performance. For the gut microbiome analysis, 16S rRNA gene hypervariable regions (V5 to V6) were sequenced using the Illumina MiSeq platform, and Quantitative Insight into Microbial Ecology (QIIME) and Microbiome Helper pipeline were used for 16S rRNA gene sequence analysis.<br><br>RESULTS AND DISCUSSION: The daily weight gain and feed efficiency of MEM were significantly higher than those of CON (p&#x2009;<&#x2009;0.001). There were no significant differences in hematological parameters and immune responses between CON and MEM. However, MEM had significantly lower Treponema genus, whereas significantly higher Lactobacillus and Roseburia genera compared to CON. Overall, our data showed that L. casei and S. cerevisiae mixture could promote growth performance through the modulation of gut microbiota in pigs. This study will help to understand the correlation between the growth performance and the gut microbiome.}, }
@article {pmid37382454, year = {2023}, author = {Liu, W and Cui, X and Wang, X and Shen, C and Ji, L and Zhang, M and Wong, MH and Zhang, J and Shan, S}, title = {Sugarcane mosaic virus reduced bacterial diversity and network complexity in the maize root endosphere.}, journal = {mSystems}, volume = {8}, number = {4}, pages = {e0019823}, pmid = {37382454}, issn = {2379-5077}, mesh = {*Microbiota/genetics ; RNA, Ribosomal, 16S ; Potyvirus ; Soil Microbiology ; *Zea mays/genetics ; Plant Roots/microbiology ; Endophytes/genetics ; Bacteria/genetics ; }, abstract = {Sugarcane mosaic virus (SCMV) causes mosaic disease in crops such as maize and sugarcane by its vector-an aphid-and is transmitted top-down into the root system. However, understanding of the effects of the aphid-borne virus on root-associated microbes after plant invasion remains limited. The current project investigated maize root-associated (rhizosphere and endosphere) bacterial communities, potential interspecies interaction, and assembly processes in response to SCMV invasion based on 16S rRNA gene amplicon sequencing. SCMV was detected in the roots 9 days after inoculation, and leaf mosaic and chlorosis appeared. The SCMV invasion markedly reduced the α-diversity of endosphere bacteria compared with uninoculated controls (Mock). The connectivity and complexity of the bacterial co-occurrence network in the root endosphere decreased after SCMV invasion, implying that the plant virus may alter root endophyte-microbial interactions. Moreover, a signature that deviates more from stochastic processes was observed in virus-infected plants. Unexpectedly, the rhizosphere bacterial communities were rarely affected by the viral invasion. This study lays the foundation for elucidating the fate of the microbial component of the plant holobiont following aphid-borne virus exposure. IMPORTANCE Biotic (e.g., soil-borne viruses) stress can alter root-associated bacterial communities, essential in maintaining host plant growth and health. However, the regulation of root-associated microorganisms by plant viruses from shoots is still largely unknown. Our results show that plant virus invasion leads to reduced and simpler inter-microbial communication in the maize endosphere. In addition, stochastic processes act on bacterial community assembly in both rhizosphere and endosphere, and bacterial communities in virus-invaded plant endosphere tend to shift toward deterministic processes. Our study highlights the negative effects of plant viruses on root endophytes from the microbial ecology perspective, which may be microbially mediated mechanisms of plant diseases.}, }
@article {pmid37382302, year = {2023}, author = {Puente-Sánchez, F and Hoetzinger, M and Buck, M and Bertilsson, S}, title = {Exploring environmental intra-species diversity through non-redundant pangenome assemblies.}, journal = {Molecular ecology resources}, volume = {23}, number = {7}, pages = {1724-1736}, doi = {10.1111/1755-0998.13826}, pmid = {37382302}, issn = {1755-0998}, support = {892961//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 2019-02336//Svenska Forskningsr&#xe5;det Formas/ ; 2017-04422//Vetenskapsr&#xe5;det/ ; 2018-05973//Vetenskapsr&#xe5;det/ ; }, mesh = {Phylogeny ; *Bacteria/genetics ; Metagenome ; Algorithms ; *Microbiota ; Metagenomics/methods ; }, abstract = {At the genome level, microorganisms are highly adaptable both in terms of allele and gene composition. Such heritable traits emerge in response to different environmental niches and can have a profound influence on microbial community dynamics. As a consequence, any individual genome or population will contain merely a fraction of the total genetic diversity of any operationally defined "species", whose ecological potential can thus be only fully understood by studying all of their genomes and the genes therein. This concept, known as the pangenome, is valuable for studying microbial ecology and evolution, as it partitions genomes into core (present in all the genomes from a species, and responsible for housekeeping and species-level niche adaptation among others) and accessory regions (present only in some, and responsible for intra-species differentiation). Here we present SuperPang, an algorithm producing pangenome assemblies from a set of input genomes of varying quality, including metagenome-assembled genomes (MAGs). SuperPang runs in linear time and its results are complete, non-redundant, preserve gene ordering and contain both coding and non-coding regions. Our approach provides a modular view of the pangenome, identifying operons and genomic islands, and allowing to track their prevalence in different populations. We illustrate this by analysing intra-species diversity in Polynucleobacter, a bacterial genus ubiquitous in freshwater ecosystems, characterized by their streamlined genomes and their ecological versatility. We show how SuperPang facilitates the simultaneous analysis of allelic and gene content variation under different environmental pressures, allowing us to study the drivers of microbial diversification at unprecedented resolution.}, }
@article {pmid37379878, year = {2023}, author = {Abel, SM and Wu, F and Primpke, S and Gerdts, G and Brandt, A}, title = {Journey to the deep: plastic pollution in the hadal of deep-sea trenches.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {333}, number = {}, pages = {122078}, doi = {10.1016/j.envpol.2023.122078}, pmid = {37379878}, issn = {1873-6424}, mesh = {*Plastics/analysis ; *Water Pollutants, Chemical/analysis ; Environmental Pollution/analysis ; Microplastics ; Oceans and Seas ; }, abstract = {The global increase of plastic production, linked with an overall plastic misuse and waste mismanagement, leads to an inevitable increase of plastic debris that ends up in our oceans. One of the major sinks of this pollution is the deep-sea floor, which is hypothesized to accumulate in its deepest points, the hadal trenches. Little is known about the magnitude of pollution in these trenches, given the remoteness of these environments, numerous factors influencing the input and sinking behavior of plastic debris from shallower environments. This study represents to the best of our knowledge the largest survey of (macro)plastic debris sampled at hadal depths, down to 9600 m. Industrial packaging and material assignable to fishing activities were the most common debris items in the Kuril Kamchatka trench, most likely deriving from long-distance transport by the Kuroshio extension current (KE) or from regional marine traffic and fishing activities. The chemical analysis by (Attenuated Total Reflection Fourier transform infrared (ATR-FTIR) spectroscopy revealed that the main polymers detected were polyethylene (PE), polypropylene (PP) and nylon. Plastic waste is reaching the depths of the trench, although some of the items were only partially broken down. This finding suggests that complete breakdown into secondary microplastics (MP) may not always occur at the sea surface or though the water column. Due to increased brittleness, plastic debris may break apart upon reaching the hadal trench floor where plastic degrading factors were thought to be, coming off. The KKT's remote location and high sedimentation rates make it a potential site for high levels of plastic pollution, potentially making it one of the world's most heavily contaminated marine areas and an oceanic plastic deposition zone.}, }
@article {pmid37378294, year = {2023}, author = {Xie, P and Huang, K and Deng, A and Mo, P and Xiao, F and Wu, F and Xiao, D and Wang, Y}, title = {The diversity and abundance of bacterial and fungal communities in the rhizosphere of Cathaya argyrophylla are affected by soil physicochemical properties.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1111087}, pmid = {37378294}, issn = {1664-302X}, abstract = {Cathaya argyrophylla is an ancient Pinaceae species endemic to China that is listed on the IUCN Red List. Although C. argyrophylla is an ectomycorrhizal plant, the relationship between its rhizospheric soil microbial community and soil properties related to the natural habitat remains unknown. High-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences was used to survey the C. argyrophylla soil community at four natural spatially distributed points in Hunan Province, China, and functional profiles were predicted using PICRUSt2 and FUNGuild. The dominant bacterial phyla included Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi, and the dominant genus was Acidothermus. The dominant fungal phyla were Basidiomycota and Ascomycota, while Russula was the dominant genus. Soil properties were the main factors leading to changes in rhizosphere soil bacterial and fungal communities, with nitrogen being the main driver of changes in soil microbial communities. The metabolic capacities of the microbial communities were predicted to identify differences in their functional profiles, including amino acid transport and metabolism, energy production and conversion, and the presence of fungi, including saprotrophs and symbiotrophs. These findings illuminate the soil microbial ecology of C. argyrophylla, and provide a scientific basis for screening rhizosphere microorganisms that are suitable for vegetation restoration and reconstruction for this important threatened species.}, }
@article {pmid37375921, year = {2023}, author = {Qi, Y and Ma, L and Ghani, MI and Peng, Q and Fan, R and Hu, X and Chen, X}, title = {Effects of Drought Stress Induced by Hypertonic Polyethylene Glycol (PEG-6000) on Passiflora edulis Sims Physiological Properties.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {37375921}, issn = {2223-7747}, support = {2021-229, HZJD [2022]001//Guizhou Provincial Science and Technology Program/ ; Guike AA21196003//Science and Technology Base &amp; Talent Project of Guangxi Province/ ; 2021YFD1100303-3//National Key Research and Development Program of China/ ; 2019-04//Guizhou University Cultivation Project/ ; }, abstract = {Passion fruit is known to be sensitive to drought, and in order to study the physiological and biochemical changes that occur in passion fruit seedlings under drought stress, a hypertonic polyethylene glycol (PEG) solution (5%, 10%, 15%, and 20%) was used to simulate drought stress in passion fruit seedlings. We explored the physiological changes in passion fruit seedlings under drought stress induced by PEG to elucidate their response to drought stress and provide a theoretical basis for drought-resistant cultivation of passion fruit seedlings. The results show that drought stress induced by PEG had a significant effect on the growth and physiological indices of passion fruit. Drought stress significantly decreased fresh weight, chlorophyll content, and root vitality. Conversely, the contents of soluble protein (SP), proline (Pro), and malondialdehyde (MDA) increased gradually with the increasing PEG concentration and prolonged stress duration. After nine days, the SP, Pro and MDA contents were higher in passion fruit leaves and roots under 20% PEG treatments compared with the control. Additionally, with the increase in drought time, the activities of antioxidant enzymes such as peroxidase (POD), superoxide dismutase (SOD) and catalase (CAT) showed an increasing trend and then a decreasing trend, and they reached the highest value at the sixth day of drought stress. After rehydration, SP, Pro and MDA contents in the leaves and roots of passion fruit seedlings was reduced. Among all the stress treatments, 20% PEG had the most significant effect on passion fruit seedlings. Therefore, our study demonstrated sensitive concentrations of PEG to simulate drought stress on passion fruit and revealed the physiological adaptability of passion fruit to drought stress.}, }
@article {pmid37375077, year = {2023}, author = {Xu, ZS and Ju, T and Yang, X and Gänzle, M}, title = {A Meta-Analysis of Bacterial Communities in Food Processing Facilities: Driving Forces for Assembly of Core and Accessory Microbiomes across Different Food Commodities.}, journal = {Microorganisms}, volume = {11}, number = {6}, pages = {}, pmid = {37375077}, issn = {2076-2607}, support = {Food Microbiology and Probiotics//Canada Research Chairs/ ; Accelerate Fellowship//Mitacs/ ; }, abstract = {Microbial spoilage is a major cause of food waste. Microbial spoilage is dependent on the contamination of food from the raw materials or from microbial communities residing in food processing facilities, often as bacterial biofilms. However, limited research has been conducted on the persistence of non-pathogenic spoilage communities in food processing facilities, or whether the bacterial communities differ among food commodities and vary with nutrient availability. To address these gaps, this review re-analyzed data from 39 studies from various food facilities processing cheese (n = 8), fresh meat (n = 16), seafood (n = 7), fresh produce (n = 5) and ready-to-eat products (RTE; n = 3). A core surface-associated microbiome was identified across all food commodities, including Pseudomonas, Acinetobacter, Staphylococcus, Psychrobacter, Stenotrophomonas, Serratia and Microbacterium. Commodity-specific communities were additionally present in all food commodities except RTE foods. The nutrient level on food environment surfaces overall tended to impact the composition of the bacterial community, especially when comparing high-nutrient food contact surfaces to floors with an unknown nutrient level. In addition, the compositions of bacterial communities in biofilms residing in high-nutrient surfaces were significantly different from those of low-nutrient surfaces. Collectively, these findings contribute to a better understanding of the microbial ecology of food processing environments, the development of targeted antimicrobial interventions and ultimately the reduction of food waste and food insecurity and the promotion of food sustainability.}, }
@article {pmid37375028, year = {2023}, author = {Villeneuve, K and Turcotte-Blais, V and Lazar, CS}, title = {Effect of Snowmelt on Groundwater Bacterial Community Composition and Potential Role of Surface Environments as Microbial Seed Bank in Two Distinct Aquifers from the Region of Quebec, Canada.}, journal = {Microorganisms}, volume = {11}, number = {6}, pages = {}, pmid = {37375028}, issn = {2076-2607}, support = {RGPIN-2019-06670//Natural Sciences and Engineering Research Council/ ; Aquatic Environmental Genomics//Canada Research Chairs/ ; }, abstract = {Events of groundwater recharge are associated with changes in the composition of aquifer microbial communities but also abiotic conditions. Modification in the structure of the community can be the result of different environmental condition favoring or hindering certain taxa, or due to the introduction of surface-derived taxa. Yet, in both cases, the local hydrogeochemical settings of the aquifer is likely to affect the amount of variation observed. Therefore, in our study, we used 16S rRNA gene sequencing to assess how microbial communities change in response to snowmelt and the potential connectivity between subsurface and surface microbiomes in two distinct aquifers located in the region of Vaudreuil-Soulanges (Québec, Canada). At both sites, we observed an increase in groundwater level and decrease in temperature following the onset of snow melt in March 2019. Bacterial community composition of each aquifer was significantly different (p < 0.05) between samples collected prior and after groundwater recharge. Furthermore, microbial source tracking results suggested a low contribution of surface environments to the groundwater microbiome except for in the months associated with recharge (March 2019 and April 2019). Overall, despite differences in soil permeability between both sites, the period of snow melt was followed by important changes in the composition of microbial communities from aquifers.}, }
@article {pmid37375009, year = {2023}, author = {Satari, L and Iglesias, A and Porcar, M}, title = {The Microbiome of Things: Appliances, Machines, and Devices Hosting Artificial Niche-Adapted Microbial Communities.}, journal = {Microorganisms}, volume = {11}, number = {6}, pages = {}, pmid = {37375009}, issn = {2076-2607}, support = {ID101000470//European Union (MICRO4BIOGAS project)/ ; }, abstract = {As it is the case with natural substrates, artificial surfaces of man-made devices are home to a myriad of microbial species. Artificial products are not necessarily characterized by human-associated microbiomes; instead, they can present original microbial populations shaped by specific environmental-often extreme-selection pressures. This review provides a detailed insight into the microbial ecology of a range of artificial devices, machines, and appliances, which we argue are specific microbial niches that do not necessarily fit in the "build environment" microbiome definition. Instead, we propose here the Microbiome of Things (MoT) concept analogous to the Internet of Things (IoT) because we believe it may be useful to shed light on human-made, but not necessarily human-related, unexplored microbial niches.}, }
@article {pmid37374902, year = {2023}, author = {Heczko, P and Kozień, &#x141; and Strus, M}, title = {Special Issue "An Update on Lactobacillus": Editorial.}, journal = {Microorganisms}, volume = {11}, number = {6}, pages = {}, pmid = {37374902}, issn = {2076-2607}, abstract = {As indicated in the introduction to this Special Issue, as of 2020, the original genus Lactobacillus comprised over 260 recognized species, a figure which is probably much higher now [...].}, }
@article {pmid37369788, year = {2023}, author = {Fukui, Y and Abe, M and Kobayashi, M}, title = {Effects of Hyphomonas Strains on the Growth of Red Algae Pyropia Species by Attaching Specifically to Their Rhizoids.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2502-2514}, pmid = {37369788}, issn = {1432-184X}, mesh = {*Rhodophyta ; *Seaweed ; Seawater ; Bacteria ; Vitamins ; }, abstract = {Bacteria and marine macroalgae form close associations, while various bacteria affect the morphogenesis and growth of macroalgae. Hyphomonas strains exhibit normal morphogenetic activity in protoplasts of the red alga Pyropia yezoensis (nori). However, the effects of the bacteria on the growth of Pyropia from protoplast cells to regenerated thalli remain unknown. Here, we assessed the growth of P. yezoensis and Pyropia tenera using combined cultures of three Hyphomonas strains (LNM10-16, SCM-2, and LNM-9) and three algal media (artificial seawater with vitamins, artificial seawater, and natural seawater) over 7 weeks. Third week after culture, the three Hyphomonas strains showed almost similar levels of normal growth activity for both Pyropia species. However, at 7 weeks, significant differences were observed among the three Hyphomonas strains in terms of length, length-to-width ratio, and normal morphology of Pyropia thalli. LNM10-16 significantly promoted the thalli length and length-to-width ratios of both Pyropia species in artificial seawater without vitamins and natural seawater, compared with the other two Hyphomonas strains. P. yezoensis cultured in artificial seawater with vitamins showed a much higher demand for LNM10-16 in development of the thalli length than P. tenera. These results may be explained by differences in the growth activities of Hyphomonas strains and the nutrient requirements of Pyropia species. Furthermore, the bacteria were more specifically attached to the rhizoid surfaces of both species. This study is the first to reveal that Hyphomonas strains affect the growth of Pyropia species by attaching to their rhizoids.}, }
@article {pmid37365511, year = {2023}, author = {Chang, Y and Sun, H and Liu, S and He, Y and Zhao, S and Wang, J and Wang, T and Zhang, J and Gao, J and Yang, Q and Li, M and Zhao, X}, title = {Identification of BBX gene family and its function in the regulation of microtuber formation in yam.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {354}, pmid = {37365511}, issn = {1471-2164}, support = {5101049470215//Postdoctor Initiative Foundation of Henan Normal University/ ; 21A180013//Colleges and Universities in Henan Province Key Scientific Research Project Funding Scheme/ ; CARS-21//Agriculture Research System of China/ ; 224200510011//The Zhongyuan high level talents special support plan-Science and Technology Innovation Leading Talents/ ; 2021YFD1600100//Special National Key Research and Development Plan/ ; 81274019//National Natural Science Foundation of China/ ; 5201049160163//Henan Normal University and Wen County People's Government Jointly Build National Yam Germplasm Resource Garden Project/ ; }, mesh = {*Dioscorea/genetics/metabolism ; Gene Expression Profiling ; Multigene Family ; Photoperiod ; Circadian Rhythm ; Gene Expression Regulation, Plant ; Plant Proteins/metabolism ; }, abstract = {BBX proteins play important roles in all of the major light-regulated developmental processes. However, no systematic analysis of BBX gene family regarding the regulation of photoperiodic microtuber formation has been previously performed in yam. In this study, a systematic analysis on the BBX gene family was conducted in three yam species, with the results, indicating that this gene plays a role in regulating photoperiodic microtuber formation. These analyses included identification the BBX gene family in three yam species, their evolutionary relationships, conserved domains, motifs, gene structure, cis-acting elements, and expressional patterns. Based on these analyses, DoBBX2/DoCOL5 and DoBBX8/DoCOL8 showing the most opposite pattern of expression during microtuber formation were selected as candidate genes for further investigation. Gene expression analysis showed DoBBX2/DoCOL5 and DoBBX8/DoCOL8 were highest expressed in leaves and exhibited photoperiod responsive expression patterns. Besides, the overexpression of DoBBX2/DoCOL5 and DoBBX8/DoCOL8 in potato accelerated tuber formation under short-day (SD) conditions, whereas only the overexpression of DoBBX8/DoCOL8 enhanced the accelerating effect of dark conditions on tuber induction. Tuber number was increased in DoBBX8/DoCOL8 overexpressing plants under dark, as well as in DoBBX2/DoCOL5 overexpressing plants under SD. Overall, the data generated in this study may form the basis of future functional characterizations of BBX genes in yam, especially regarding their regulation of microtuber formation via the photoperiodic response pathway.}, }
@article {pmid37364132, year = {2023}, author = {Schleyer, G and Kuhlisch, C and Ziv, C and Ben-Dor, S and Malitsky, S and Schatz, D and Vardi, A}, title = {Lipid biomarkers for algal resistance to viral infection in the ocean.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {27}, pages = {e2217121120}, pmid = {37364132}, issn = {1091-6490}, support = {101053543/ERC_/European Research Council/International ; }, mesh = {Humans ; *Viruses ; Phytoplankton/metabolism ; *Haptophyta/metabolism ; *Virus Diseases ; Biomarkers/metabolism ; Oceans and Seas ; Lipids ; }, abstract = {Marine viruses play a key role in regulating phytoplankton populations, greatly affecting the biogeochemical cycling of major nutrients in the ocean. Resistance to viral infection has been reported for various phytoplankton species under laboratory conditions. Nevertheless, the occurrence of resistant cells in natural populations is underexplored due to the lack of sensitive tools to detect these rare phenotypes. Consequently, our current understanding of the ecological importance of resistance and its underlying mechanisms is limited. Here, we sought to identify lipid biomarkers for the resistance of the bloom-forming alga Emiliania huxleyi to its specific virus, E. huxleyi virus (EhV). By applying an untargeted lipidomics approach, we identified a group of glycosphingolipid (GSL) biomarkers that characterize resistant E. huxleyi strains and were thus termed resistance-specific GSLs (resGSLs). Further, we detected these lipid biomarkers in E. huxleyi isolates collected from induced E. huxleyi blooms and in samples collected during an open-ocean E. huxleyi bloom, indicating that resistant cells predominantly occur during the demise phase of the bloom. Last, we show that the GSL composition of E. huxleyi cultures that recover following infection and gain resistance to the virus resembles that of resistant strains. These findings highlight the metabolic plasticity and coevolution of the GSL biosynthetic pathway and underscore its central part in this host-virus arms race.}, }
@article {pmid37362850, year = {2023}, author = {McDonagh, F and Cormican, M and Morris, D and Burke, L and Singh, NK and Venkateswaran, K and Miliotis, G}, title = {Medical Astro-Microbiology: Current Role and Future Challenges.}, journal = {Journal of the Indian Institute of Science}, volume = {}, number = {}, pages = {1-26}, pmid = {37362850}, issn = {0970-4140}, abstract = {The second and third decades of the twenty-first century are marked by a flourishing of space technology which may soon realise human aspirations of a permanent multiplanetary presence. The prevention, control and management of infection with microbial pathogens is likely to play a key role in how successful human space aspirations will become. This review considers the emerging field of medical astro-microbiology. It examines the current evidence regarding the risk of infection during spaceflight via host susceptibility, alterations to the host's microbiome as well as exposure to other crew members and spacecraft's microbiomes. It also considers the relevance of the hygiene hypothesis in this regard. It then reviews the current evidence related to infection risk associated with microbial adaptability in spaceflight conditions. There is a particular focus on the International Space Station (ISS), as one of the only two crewed objects in low Earth orbit. It discusses the effects of spaceflight related stressors on viruses and the infection risks associated with latent viral reactivation and increased viral shedding during spaceflight. It then examines the effects of the same stressors on bacteria, particularly in relation to changes in virulence and drug resistance. It also considers our current understanding of fungal adaptability in spaceflight. The global public health and environmental risks associated with a possible re-introduction to Earth of invasive species are also briefly discussed. Finally, this review examines the largely unknown microbiology and infection implications of celestial body habitation with an emphasis placed on Mars. Overall, this review summarises much of our current understanding of medical astro-microbiology and identifies significant knowledge gaps.}, }
@article {pmid37356531, year = {2023}, author = {Wang, H and Lin, L and Zhang, L and Han, P and Ju, F}, title = {Microbiome assembly mechanism and functional potential in enhanced biological phosphorus removal system enriched with Tetrasphaera-related polyphosphate accumulating organisms.}, journal = {Environmental research}, volume = {233}, number = {}, pages = {116494}, doi = {10.1016/j.envres.2023.116494}, pmid = {37356531}, issn = {1096-0953}, mesh = {*Phosphorus ; Polyphosphates/metabolism ; Phylogeny ; RNA, Ribosomal, 16S ; *Actinomycetales/genetics/metabolism ; Bacteria/genetics/metabolism ; Bioreactors ; Sewage/microbiology ; }, abstract = {Tetrasphaera-related polyphosphate accumulating organisms (PAOs) are the key functional guilds for enhanced biological phosphorus removal (EBPR) systems. Their biomass enrichment can be enhanced by the nitrification inhibitor allylthiourea (ATU). However, the underlying assembly mechanism and the functional potential of the EBPR microbiome regulated by ATU are unclear. This study investigates the effect of ATU on microbiome assembly and functional potential by closely following the microbiota dynamics in an EBPR system enriched with Tetrasphaera-related PAOs for 288-days before, during and after ATU addition. The results showed that ATU addition increased microbiota structural similarity and compositional convergence, and enhanced determinism in the assembly of EBPR microbiome. During exposure to ATU, Tetrasphaera-related PAOs were governed by homogeneous selection and the dominant species revealed by 16S rRNA gene-based phylogenetic analysis shifted from clade III to clade I. Meanwhile, ATU supply promoted significant enrichment of functional genes involved in phosphate transport (pit) and polyphosphate synthesis and degradation (ppk1 and ppk2), whereas both Nitrosomonas and ammonia monooxygenase-encoding genes (amoA/B/C) assignable to this group of nitrifying bacteria decreased. Moreover, ATU addition relieved the significant abundance correlation between filamentous bacteria Ca. Promineofilum and denitrifying Brevundimonas (FDR-adjusted P < 0.01), damaging their potential synergic or cooperative interactions, thus weakening their competitiveness against Tetrasphaera-related PAOs. Notably, ATU withdrawn created opportunistic conditions for the unexpected explosive growth and predominance of Thiothrix filaments, leading to a serious bulking event. Our study provides new insights into the microbial ecology of Tetrasphaera-related PAOs in EBPR system, which could guide the establishment of an efficient microbiota for EBPR.}, }
@article {pmid37356163, year = {2023}, author = {Yuan, W and Xu, EG and Li, L and Zhou, A and Peijnenburg, WJGM and Grossart, HP and Liu, W and Yang, Y}, title = {Tracing and trapping micro- and nanoplastics: Untapped mitigation potential of aquatic plants?.}, journal = {Water research}, volume = {242}, number = {}, pages = {120249}, doi = {10.1016/j.watres.2023.120249}, pmid = {37356163}, issn = {1879-2448}, abstract = {Micro- and nanoplastics are emerging concerns due to their environmental ubiquity and currently largely unknown ecological impacts. Leveraging on a recently developed method using europium-doped polystyrene particles (PS-Eu), our present work aimed to accurately trace the uptake and transport of micro- and nanoplastics in aquatic plants and shed insights into the potential of different aquatic plants for trapping and removal of plastics from water environment. Seedlings of Vallisneria denseserrulata Makino (submerged plant), Iris tectorum Maxim (emergent plant), and Eichhornia crassipes Solms (floating plant) were exposed to 100 nm and 2 μm PS-Eu in freshwater (5 μg/mL) or sediments (5 μg/g) for 8 weeks. Fluorescence imaging clearly evidenced that PS-Eu mainly accumulated in the intercellular space and were transported from roots to leaves via the apoplastic path and vascular bundle. Mass spectrum analysis demonstrated that up to 6250 μg/g nanoplastics were trapped in aquatic plants (mainly in roots) with a bioconcentration factor of 306.5, depending on exposure routes and plant species. Owing to their excellent capture capability and high tolerance to plastic exposures, floating plants like E. crassipes are promising for immobilizing and removing fine plastics from the water environment.}, }
@article {pmid37354976, year = {2023}, author = {Kable, ME and Chin, EL and Huang, L and Stephensen, CB and Lemay, DG}, title = {Association of Estimated Daily Lactose Consumption, Lactase Persistence Genotype (rs4988235), and Gut Microbiota in Healthy Adults in the United States.}, journal = {The Journal of nutrition}, volume = {153}, number = {8}, pages = {2163-2173}, doi = {10.1016/j.tjnut.2023.06.025}, pmid = {37354976}, issn = {1541-6100}, mesh = {Male ; Female ; Humans ; Adult ; United States ; Lactose ; *Lactose Intolerance/genetics ; *Gastrointestinal Microbiome/genetics ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; Dairy Products ; Lactase/genetics ; Genotype ; }, abstract = {BACKGROUND: Lactase persistence (LP) is a heritable trait in which lactose can be digested throughout adulthood. Lactase nonpersistent (LNP) individuals who consume lactose may experience microbial adaptations in response to undigested lactose.<br><br>OBJECTIVES: The objective of the study was to estimate lactose from foods reported in the Automated Self-Administered 24-Hour Dietary Assessment Tool (ASA24) and determine the interaction between lactose consumption, LP genotype, and gut microbiome in an observational cross-sectional study of healthy adults in the United States (US).<br><br>METHODS: Average daily lactose consumption was estimated for 279 healthy US adults, genotyped for the lactase gene -13910G>A polymorphism (rs4988235) by matching ASA24-reported foods to foods in the Nutrition Coordinating Center Food and Nutrient Database. Analysis of covariance was used to identify whether the A genotype (LP) influenced lactose and total dairy consumption, with total energy intake and weight as covariates. The 16S rRNA V4/V5 region, amplified from bacterial DNA extracted from each frozen stool sample, was sequenced using Illumina MiSeq (300 bp paired-end) and analyzed using Quantitative Insights Into Microbial Ecology (QIIME)2 (version 2019.10). Differential abundances of bacterial taxa were analyzed using DESeq2 likelihood ratio tests.<br><br>RESULTS: Across a diverse set of ethnicities, LP subjects consumed more lactose than LNP subjects. Lactobacillaceae abundance was highest in LNP subjects who consumed more than 12.46 g/d (upper tercile). Within Caucasians and Hispanics, family Lachnospiraceae was significantly enriched in the gut microbiota of LNP individuals consuming the upper tercile of lactose across both sexes.<br><br>CONCLUSIONS: Elevated lactose consumption in individuals with the LNP genotype is associated with increased abundance of family Lactobacillaceae and Lachnospriaceae, taxa that contain multiple genera capable of utilizing lactose. This trial was registered on clinicaltrials.gov as NCT02367287.}, }
@article {pmid37350274, year = {2023}, author = {Rupp, ME and Van Schooneveld, TC and Starlin, R and Quick, J and Snyder, GM and Passaretti, CL and Stevens, MP and Cawcutt, K}, title = {Hospital return-to-work practices for healthcare providers infected with severe acute respiratory coronavirus virus 2 (SARS-CoV-2).}, journal = {Infection control and hospital epidemiology}, volume = {44}, number = {12}, pages = {2081-2084}, doi = {10.1017/ice.2023.133}, pmid = {37350274}, issn = {1559-6834}, mesh = {Humans ; *COVID-19 ; SARS-CoV-2 ; Return to Work ; Hospitals ; Health Personnel ; }, abstract = {A survey of academic medical-center hospital epidemiologists indicated substantial deviation from Centers for Disease Control and Prevention guidance regarding healthcare providers (HCPs) recovering from coronavirus disease 2019 (COVID-19) returning to work. Many hospitals continue to operate under contingency status and have HCPs return to work earlier than recommended.}, }
@article {pmid37348760, year = {2023}, author = {Eudy, BJ and Odle, J and Lin, X and Maltecca, C and Walter, KR and McNulty, NP and Fellner, V and Jacobi, SK}, title = {Dietary Prebiotic Oligosaccharides and Arachidonate Alter the Fecal Microbiota and Mucosal Lipid Composition of Suckling Pigs.}, journal = {The Journal of nutrition}, volume = {153}, number = {8}, pages = {2249-2262}, doi = {10.1016/j.tjnut.2023.06.019}, pmid = {37348760}, issn = {1541-6100}, mesh = {Animals ; Swine ; *Prebiotics ; *Microbiota ; Oligosaccharides/pharmacology/analysis ; Feces/microbiology ; Intestinal Mucosa ; Lipids ; }, abstract = {BACKGROUND: Early intestinal development is important to infant vitality, and optimal formula composition can promote gut health.<br><br>OBJECTIVES: The objectives were to evaluate the effects of arachidonate (ARA) and/or prebiotic oligosaccharide (PRE) supplementation in formula on the development of the microbial ecosystem and colonic health parameters.<br><br>METHODS: Newborn piglets were fed 4 formulas containing ARA [0.5 compared with 2.5% of dietary fatty acids (FAs)] and PRE (0 compared with 8 g/L, containing a 1:1 mixture of galactooligosaccharides and polydextrose) in a 2 x 2 factorial design for 22 d. Fecal samples were collected weekly and analyzed for relative microbial abundance. Intestinal samples were collected on day 22 and analyzed for mucosal FAs, pH, and short-chain FAs (SCFAs).<br><br>RESULTS: PRE supplementation significantly increased genera within Bacteroidetes and Firmicutes, including Anaerostipes, Mitsuokella, Prevotella, Clostridium IV, and Bulleidia, and resulted in progressive separation from controls as determined by Principal Coordinates Analysis. Concentrations of SCFA increased from 70.98 to 87.37 mM, with an accompanying reduction in colonic pH. ARA supplementation increased the ARA content of the colonic mucosa from 2.35-5.34% of total FAs. PRE supplementation also altered mucosal FA composition, resulting in increased linoleic acid (11.52-16.33% of total FAs) and ARA (2.35-5.16% of total FAs).<br><br>CONCLUSIONS: Prebiotic supplementation during the first 22 d of life altered the gut microbiota of piglets and increased the abundance of specific bacterial genera. These changes correlated with increased SCFA, which may benefit intestinal development. Although dietary ARA did not alter the microbiota, it increased the ARA content of the colonic mucosa, which may support intestinal development and epithelial repair. Prebiotic supplementation also increased unsaturation of FAs in the colonic mucosa. Although the mechanism requires further investigation, it may be related to altered microbial ecology or biohydrogenation of FA.}, }
@article {pmid37347668, year = {2023}, author = {Verbeelen, T and Van Houdt, R and Leys, N and Ganigué, R and Mastroleo, F}, title = {RNA extraction protocol from low-biomass bacterial Nitrosomonas europaea and Nitrobacter winogradskyi cultures for whole transcriptome studies.}, journal = {STAR protocols}, volume = {4}, number = {3}, pages = {102358}, pmid = {37347668}, issn = {2666-1667}, mesh = {*Nitrosomonas europaea/genetics ; Nitrosomonas/genetics ; Transcriptome/genetics ; Biomass ; Bacteria/genetics ; RNA ; *Nitrobacter ; }, abstract = {RNA-sequencing for whole transcriptome analysis requires high-quality RNA in adequate amounts, which can be difficult to generate with low-biomass-producing bacteria where sample volume is limited. We present an RNA extraction protocol for low-biomass-producing autotrophic bacteria Nitrosomonas europaea and Nitrobacter winogradskyi cultures. We describe steps for sample collection, lysozyme-based enzymatic lysis, and a commercial silica-column-based RNA extraction. We then detail evaluation of RNA yield and quality for downstream applications such as RNA-Seq. For complete details on the use and execution of this protocol, please refer to Verbeelen et al.[1].}, }
@article {pmid37346753, year = {2023}, author = {Petrin, S and Wijnands, L and Benincà, E and Mughini-Gras, L and Delfgou-van Asch, EHM and Villa, L and Orsini, M and Losasso, C and Olsen, JE and Barco, L}, title = {Assessing phenotypic virulence of Salmonella enterica across serovars and sources.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1184387}, pmid = {37346753}, issn = {1664-302X}, abstract = {INTRODUCTION: Whole genome sequencing (WGS) is increasingly used for characterizing foodborne pathogens and it has become a standard typing technique for surveillance and research purposes. WGS data can help assessing microbial risks and defining risk mitigating strategies for foodborne pathogens, including Salmonella enterica.<br><br>METHODS: To test the hypothesis that (combinations of) different genes can predict the probability of infection [P(inf)] given exposure to a certain pathogen strain, we determined P(inf) based on invasion potential of 87 S. enterica strains belonging to 15 serovars isolated from animals, foodstuffs and human patients, in an in vitro gastrointestinal tract (GIT) model system. These genomes were sequenced with WGS and screened for genes potentially involved in virulence. A random forest (RF) model was applied to assess whether P(inf) of a strain could be predicted based on the presence/absence of those genes. Moreover, the association between P(inf) and biofilm formation in different experimental conditions was assessed.<br><br>RESULTS AND DISCUSSION: P(inf) values ranged from 6.7E-05 to 5.2E-01, showing variability both among and within serovars. P(inf) values also varied between isolation sources, but no unambiguous pattern was observed in the tested serovars. Interestingly, serovars causing the highest number of human infections did not show better ability to invade cells in the GIT model system, with strains belonging to other serovars displaying even higher infectivity. The RF model did not identify any virulence factor as significant P(inf) predictors. Significant associations of P(inf) with biofilm formation were found in all the different conditions for a limited number of serovars, indicating that the two phenotypes are governed by different mechanisms and that the ability to form biofilm does not correlate with the ability to invade epithelial cells. Other omics techniques therefore seem more promising as alternatives to identify genes associated with P(inf), and different hypotheses, such as gene expression rather than presence/absence, could be tested to explain phenotypic virulence [P(inf)].}, }
@article {pmid37345931, year = {2023}, author = {Aldeguer-Riquelme, B and Antón, J and Santos, F}, title = {Distribution, abundance, and ecogenomics of the Palauibacterales, a new cosmopolitan thiamine-producing order within the Gemmatimonadota phylum.}, journal = {mSystems}, volume = {8}, number = {4}, pages = {e0021523}, pmid = {37345931}, issn = {2379-5077}, mesh = {*Ecosystem ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics ; Metagenome/genetics ; Lakes ; }, abstract = {The phylum Gemmatimonadota comprises mainly uncultured microorganisms that inhabit different environments such as soils, freshwater lakes, marine sediments, sponges, or corals. Based on 16S rRNA gene studies, the group PAUC43f is one of the most frequently retrieved Gemmatimonadota in marine samples. However, its physiology and ecological roles are completely unknown since, to date, not a single PAUC43f isolate or metagenome-assembled genome (MAG) has been characterized. Here, we carried out a broad study of the distribution, abundance, ecotaxonomy, and metabolism of PAUC43f, for which we propose the name of Palauibacterales. This group was detected in 4,965 16S rRNA gene amplicon datasets, mainly from marine sediments, sponges, corals, soils, and lakes, reaching up to 34.3% relative abundance, which highlights its cosmopolitan character, mainly salt-related. The potential metabolic capabilities inferred from 52 Palauibacterales MAGs recovered from marine sediments, sponges, and saline soils suggested a facultative aerobic and chemoorganotrophic metabolism, although some members may also oxidize hydrogen. Some Palauibacterales species might also play an environmental role as N2O consumers as well as suppliers of serine and thiamine. When compared to the rest of the Gemmatimonadota phylum, the biosynthesis of thiamine was one of the key features of the Palauibacterales. Finally, we show that polysaccharide utilization loci (PUL) are widely distributed within the Gemmatimonadota so that they are not restricted to Bacteroidetes, as previously thought. Our results expand the knowledge about this cryptic phylum and provide new insights into the ecological roles of the Gemmatimonadota in the environment. IMPORTANCE Despite advances in molecular and sequencing techniques, there is still a plethora of unknown microorganisms with a relevant ecological role. In the last years, the mostly uncultured Gemmatimonadota phylum is attracting scientific interest because of its widespread distribution and abundance, but very little is known about its ecological role in the marine ecosystem. Here we analyze the global distribution and potential metabolism of the marine Gemmatimonadota group PAUC43f, for which we propose the name of Palauibacterales order. This group presents a saline-related character and a chemoorganoheterotrophic and facultatively aerobic metabolism, although some species might oxidize H2. Given that Palauibacterales is potentially able to synthesize thiamine, whose auxotrophy is the second most common in the marine environment, we propose Palauibacterales as a key thiamine supplier to the marine communities. This finding suggests that Gemmatimonadota could have a more relevant role in the marine environment than previously thought.}, }
@article {pmid37343911, year = {2023}, author = {Andrade, L and P Ryan, M and P Burke, L and Hynds, P and Weatherill, J and O'Dwyer, J}, title = {Assessing antimicrobial and metal resistance genes in Escherichia coli from domestic groundwater supplies in rural Ireland.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {333}, number = {}, pages = {121970}, doi = {10.1016/j.envpol.2023.121970}, pmid = {37343911}, issn = {1873-6424}, mesh = {Animals ; Cattle ; Humans ; Swine ; *Escherichia coli/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Ecosystem ; Ireland ; *Anti-Infective Agents/pharmacology ; Microbial Sensitivity Tests ; }, abstract = {Natural ecosystems can become significant reservoirs and/or pathways for antimicrobial resistance (AMR) dissemination, with the potential to affect nearby microbiological, animal, and ultimately human communities. This is further accentuated in environments that provide direct human exposure, such as drinking water. To date, however, few studies have investigated AMR dissemination potential and the presence of co-selective stressors (e.g., metals/metalloids) in groundwater environments of human health significance. Accordingly, the present study analysed samples from rural (drinking) groundwater supplies (i.e., private wells) in the Republic of Ireland, where land use is dominated by livestock grazing activities. In total, 48 Escherichia coli isolates tested phenotypically for antimicrobial susceptibility in an earlier study were further subject to whole genome sequencing (WGS) and corresponding water samples were further analysed for trace metal/metalloid concentrations. Eight isolates (i.e., 16.7%) were genotypically resistant to antimicrobials, confirming prior phenotypic results through the identification of ten antimicrobial resistance genes (ARGs); namely: aph(3″)-lb (strA; n=7), aph(6)-Id (strA; n = 6), blaTEM (n = 6), sul2 (n = 6), tetA (n = 4), floR (n = 2), dfrA5 (n = 1), tetB (n = 1), and tetY (n = 1). Additional bioinformatic analysis revealed that all ARGs were plasmid-borne, except for two of the six sul2 genes, and that 31.2% of all tested isolates (n = 15) and 37.5% of resistant ones (n = 3) carried virulence genes. Study results also found no significant relationships between metal concentrations and ARG abundance. Additionally, just one genetic linkage was identified between ARGs and a metal resistance gene (MRG), namely merA, a mercury-resistant gene found on the same plasmid as blaTEM, dfrA5, strA, strB, and sul2 in the only isolate of inferred porcine (as opposed to bovine) origin. Overall, findings suggest that ARG (and MRG) acquisition may be occurring prior to groundwater ingress, and are likely a legacy issue arising from agricultural practices.}, }
@article {pmid37342144, year = {2023}, author = {Wilberts, L and Rojas-Preciado, N and Jacquemyn, H and Lievens, B}, title = {Fungal strain and crop cultivar affect growth of sweet pepper plants after root inoculation with entomopathogenic fungi.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1196765}, pmid = {37342144}, issn = {1664-462X}, abstract = {As endophytes, entomopathogenic fungi can protect plants against biotic and abiotic stresses and at the same time promote plant growth and plant health. To date, most studies have investigated whether Beauveria bassiana can enhance plant growth and plant health, while only little is known about other entomopathogenic fungi. In this study, we evaluated whether root inoculation of the entomopathogenic fungi Akanthomyces muscarius ARSEF 5128, B. bassiana ARSEF 3097 and Cordyceps fumosorosea ARSEF 3682 can promote plant growth of sweet pepper (Capsicum annuum L.), and whether effects are cultivar-dependent. Plant height, stem diameter, number of leaves, canopy area, and plant weight were assessed four weeks following inoculation in two independent experiments using two cultivars of sweet pepper (cv. 'IDS RZ F1' and cv. 'Maduro'). Results showed that the three entomopathogenic fungi were able to enhance plant growth, particularly canopy area and plant weight. Further, results showed that effects significantly depended on cultivar and fungal strain, with the strongest fungal effects obtained for cv. 'IDS RZ F1', especially when inoculated with C. fumosorosea. We conclude that inoculation of sweet pepper roots with entomopathogenic fungi can stimulate plant growth, but effects depend on fungal strain and crop cultivar.}, }
@article {pmid37339946, year = {2023}, author = {Ma, L and Liu, KW and Li, Z and Hsiao, YY and Qi, Y and Fu, T and Tang, GD and Zhang, D and Sun, WH and Liu, DK and Li, Y and Chen, GZ and Liu, XD and Liao, XY and Jiang, YT and Yu, X and Hao, Y and Huang, J and Zhao, XW and Ke, S and Chen, YY and Wu, WL and Hsu, JL and Lin, YF and Huang, MD and Li, CY and Huang, L and Wang, ZW and Zhao, X and Zhong, WY and Peng, DH and Ahmad, S and Lan, S and Zhang, JS and Tsai, WC and Van de Peer, Y and Liu, ZJ}, title = {Diploid and tetraploid genomes of Acorus and the evolution of monocots.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3661}, pmid = {37339946}, issn = {2041-1723}, mesh = {*Tetraploidy ; *Acorus ; Phylogeny ; Diploidy ; Genome ; }, abstract = {Monocots are a major taxon within flowering plants, have unique morphological traits, and show an extraordinary diversity in lifestyle. To improve our understanding of monocot origin and evolution, we generate chromosome-level reference genomes of the diploid Acorus gramineus and the tetraploid Ac. calamus, the only two accepted species from the family Acoraceae, which form a sister lineage to all other monocots. Comparing the genomes of Ac. gramineus and Ac. calamus, we suggest that Ac. gramineus is not a potential diploid progenitor of Ac. calamus, and Ac. calamus is an allotetraploid with two subgenomes A, and B, presenting asymmetric evolution and B subgenome dominance. Both the diploid genome of Ac. gramineus and the subgenomes A and B of Ac. calamus show clear evidence of whole-genome duplication (WGD), but Acoraceae does not seem to share an older WGD that is shared by most other monocots. We reconstruct an ancestral monocot karyotype and gene toolkit, and discuss scenarios that explain the complex history of the Acorus genome. Our analyses show that the ancestors of monocots exhibit mosaic genomic features, likely important for that appeared in early monocot evolution, providing fundamental insights into the origin, evolution, and diversification of monocots.}, }
@article {pmid37338413, year = {2023}, author = {Bittleston, LS and Wolock, CJ and Maeda, J and Infante, V and Ané, JM and Pierce, NE and Pringle, A}, title = {Carnivorous Nepenthes Pitchers with Less Acidic Fluid House Nitrogen-Fixing Bacteria.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {7}, pages = {e0081223}, pmid = {37338413}, issn = {1098-5336}, mesh = {Animals ; *Nitrogen-Fixing Bacteria ; RNA, Ribosomal, 16S/genetics ; Insecta ; Bacteria/genetics ; Nitrogen/analysis ; Alkynes ; }, abstract = {Carnivorous pitcher plants are uniquely adapted to nitrogen limitation, using pitfall traps to acquire nutrients from insect prey. Pitcher plants in the genus Sarracenia may also use nitrogen fixed by bacteria inhabiting the aquatic microcosms of their pitchers. Here, we investigated whether species of a convergently evolved pitcher plant genus, Nepenthes, might also use bacterial nitrogen fixation as an alternative strategy for nitrogen capture. First, we constructed predicted metagenomes of pitcher organisms from three species of Singaporean Nepenthes using 16S rRNA sequence data and correlated predicted nifH abundances with metadata. Second, we used gene-specific primers to amplify and quantify the presence or absence of nifH directly from 102 environmental samples and identified potential diazotrophs with significant differential abundance in samples that also had positive nifH PCR tests. Third, we analyzed nifH in eight shotgun metagenomes from four additional Bornean Nepenthes species. Finally, we conducted an acetylene reduction assay using greenhouse-grown Nepenthes pitcher fluids to confirm nitrogen fixation is indeed possible within the pitcher habitat. Results show active acetylene reduction can occur in Nepenthes pitcher fluid. Variation in nifH from wild samples correlates with Nepenthes host species identity and pitcher fluid acidity. Nitrogen-fixing bacteria are associated with more neutral fluid pH, while endogenous Nepenthes digestive enzymes are most active at low fluid pH. We hypothesize Nepenthes species experience a trade-off in nitrogen acquisition; when fluids are acidic, nitrogen is primarily acquired via plant enzymatic degradation of insects, but when fluids are neutral, Nepenthes plants take up more nitrogen via bacterial nitrogen fixation. IMPORTANCE Plants use different strategies to obtain the nutrients that they need to grow. Some plants access their nitrogen directly from the soil, while others rely on microbes to access the nitrogen for them. Carnivorous pitcher plants generally trap and digest insect prey, using plant-derived enzymes to break down insect proteins and generate a large portion of the nitrogen that they subsequently absorb. In this study, we present results suggesting that bacteria living in the fluids formed by Nepenthes pitcher plants can fix nitrogen directly from the atmosphere, providing an alternative pathway for plants to access nitrogen. These nitrogen-fixing bacteria are only likely to be present when pitcher plant fluids are not strongly acidic. Interestingly, the plant's enzymes are known to be more active under strongly acidic conditions. We propose a potential trade-off where pitcher plants sometimes access nitrogen using their own enzymes to digest prey and at other times take advantage of bacterial nitrogen fixation.}, }
@article {pmid37338363, year = {2023}, author = {Ye, L and Yang, X and Zhang, B and Zhou, J and Tian, H and Zhang, X and Li, X}, title = {Seasonal Succession of Fungal Communities in Native Truffle (Tuber indicum) Ecosystems.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {7}, pages = {e0019523}, pmid = {37338363}, issn = {1098-5336}, mesh = {Ecosystem ; Seasons ; *Mycobiome ; *Ascomycota ; *Mycorrhizae ; Soil ; Soil Microbiology ; }, abstract = {Truffles are a rare underground fungus and one of the most expensive, and sought-after kitchen ingredients in the world. Microbial ecology plays an important role in the annual growth cycle of truffles, but fungal communities in native truffle ecosystems are still largely unknown, especially for Tuber indicum from China. In this study, the spatial and temporal dynamics of soil physicochemical properties and fungal communities were described associated with four T. indicum-producing plots (TPPs) and one non-truffle-producing plot in four successive growing seasons. A total of 160 biological samples were collected, 80 of which were used for the determination of 10 soil physicochemical indices and 80 for Illumina-based analysis of the fungal microbiome. Soil physicochemical properties and fungal communities exhibited considerable seasonal variation. Ascomycetes, Basidiomycetes, and Mucormycoides dominated. The core microbiome work on the microecological changes in TPPs, and the identified core members contribute to the seasonal succession of communities. The genus Tuber occupies a central position in healthy TPPs. There was a strong correlation between soil physicochemical properties and fungal communities. The genus Tuber showed a positive correlation with Ca, Mg, and total nitrogen, but a negative correlation with total phosphorus and available potassium. This study describes the complex ecological dynamics of soil physicochemical indices and fungal communities occurring during the annual cycle of Tuber indicum, and highlights the succession of core communities in truffle plots, which contribute to better protection of native truffle ecosystems and control of mycorrhizal fungal contamination in artificial truffle plantations in China. IMPORTANCE The spatial and temporal dynamics of soil physicochemical properties and fungal communities associated with four Tuber indicum-producing plots and one non truffle producing plot in four different growing seasons are described. Soil physicochemical properties and fungal communities exhibited considerable seasonal variation. This study examines the complex ecological dynamics of soil physicochemical indices and fungal communities occurring during the annual cycle of Tuber indicum and highlights the succession of core communities in truffle plots, which contributes to better protection of native truffle ecosystems and control of mycorrhizal fungal contamination in artificial truffle plantations in China.}, }
@article {pmid37338299, year = {2023}, author = {Hurst, JH and Kelly, MS}, title = {Leveraging the human microbiota to target bacterial respiratory pathogens: new paths toward an expanded antimicrobial armamentarium.}, journal = {mBio}, volume = {14}, number = {4}, pages = {e0085423}, pmid = {37338299}, issn = {2150-7511}, support = {K01 AI173398/AI/NIAID NIH HHS/United States ; }, mesh = {Child ; Humans ; Moraxella catarrhalis/drug effects ; *Anti-Infective Agents ; *Respiratory Tract Infections/drug therapy/microbiology ; Anti-Bacterial Agents/pharmacology/therapeutic use ; }, abstract = {Acute respiratory infections are the most frequent infections across the lifespan and are the leading infectious cause of death among children globally. Bacterial respiratory infections are routinely treated with antibiotics, nearly all of which are derived from microbial natural products. Unfortunately, antibiotic-resistant bacteria are an increasingly frequent cause of respiratory infections, and there are few new antibiotics in development that target these pathogens. In the article by Stubbendieck et al., the authors identified Rothia species that demonstrate in vitro and ex vivo growth inhibition of the respiratory pathobiont Moraxella catarrhalis. The authors present experiments suggesting that this activity is mediated at least in part through the secretion of a novel peptidoglycan endopeptidase that targets the M. catarrhalis cell wall. In this commentary, we discuss these findings in the context of the urgent threat of antimicrobial resistance and highlight the promise of the human respiratory microbiota as a source of novel biotherapeutics.}, }
@article {pmid37336018, year = {2023}, author = {Liu, H and Wang, Y and Shi, X}, title = {Co-existing antibiotics alter the enantioselective dissipation characteristics of zoxamide and drive combined impact on soil microenvironment.}, journal = {Journal of environmental management}, volume = {344}, number = {}, pages = {118340}, doi = {10.1016/j.jenvman.2023.118340}, pmid = {37336018}, issn = {1095-8630}, mesh = {Anti-Bacterial Agents/pharmacology ; Soil ; Stereoisomerism ; *Oxytetracycline/analysis ; Tetracycline ; Sulfamethoxazole ; Bacteria ; *Soil Pollutants/analysis ; }, abstract = {Co-existence of antibiotics (ABX) in soil may expand the environmental harm of pesticide pollution. Our study investigated the combined effects of five antibiotics chlortetracycline (CTC), oxytetracycline (OTC), tetracycline (TC), sulfamethoxazole (SMX), enrofloxacin (ENR) on enantioselective fate of zoxamide (ZXM) and soil health. The results showed that S-(+)-ZXM preferentially dissipated in soil. ABX prolonged dissipation half-life and reduced enantioselectivity of ZXM. Soil was detected to be more acidic after long-term treatment of ZXM and ABX. Lowest soil available N, P, K were found in ZXM + SMX, ZXM + OTC and ZXM + SMX groups at 80 days, respectively. ABX had demonstrated effective promotion of catalase (S-CAT), urease (S-UE) and negative impact on dehydrogenase (S-DHA), sucrase (S-SC) activities. Bacteria Lysobacter, Sphingomonas and fungus Mortierella were identified as the most dominant genera, which possessed as potential microbial resources for removal of composite pollution from ZXM and ABX. SMX and TC, SMX, ENR, respectively, contributed to the alteration of bacteria and fungi community abundance. Soil acidity, available N and enzyme activity showed stronger correlations with bacteria and fungi compared to other environmental factors. Our findings highlighted the interactions between ZXM and ABX from the perspective of soil microenvironment changes. Moreover, a theoretical basis for the mechanism was actively provided.}, }
@article {pmid37333658, year = {2023}, author = {Schultz, J and Modolon, F and Peixoto, RS and Rosado, AS}, title = {Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1167718}, pmid = {37333658}, issn = {1664-302X}, abstract = {More than 20,000 species of prokaryotes (less than 1% of the estimated number of Earth's microbial species) have been described thus far. However, the vast majority of microbes that inhabit extreme environments remain uncultured and this group is termed "microbial dark matter." Little is known regarding the ecological functions and biotechnological potential of these underexplored extremophiles, thus representing a vast untapped and uncharacterized biological resource. Advances in microbial cultivation approaches are key for a detailed and comprehensive characterization of the roles of these microbes in shaping the environment and, ultimately, for their biotechnological exploitation, such as for extremophile-derived bioproducts (extremozymes, secondary metabolites, CRISPR Cas systems, and pigments, among others), astrobiology, and space exploration. Additional efforts to enhance culturable diversity are required due to the challenges imposed by extreme culturing and plating conditions. In this review, we summarize methods and technologies used to recover the microbial diversity of extreme environments, while discussing the advantages and disadvantages associated with each of these approaches. Additionally, this review describes alternative culturing strategies to retrieve novel taxa with their unknown genes, metabolisms, and ecological roles, with the ultimate goal of increasing the yields of more efficient bio-based products. This review thus summarizes the strategies used to unveil the hidden diversity of the microbiome of extreme environments and discusses the directions for future studies of microbial dark matter and its potential applications in biotechnology and astrobiology.}, }
@article {pmid37333098, year = {2023}, author = {Grodner, B and Shi, H and Farchione, O and Vill, AC and Ntekas, I and Diebold, PJ and Zipfel, WR and Brito, IL and Vlaminck, I}, title = {Spatial Mapping of Mobile Genetic Elements and their Cognate Hosts in Complex Microbiomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37333098}, issn = {2692-8205}, support = {DP2 AI138242/AI/NIAID NIH HHS/United States ; R33 CA235302/CA/NCI NIH HHS/United States ; S10 OD018516/OD/NIH HHS/United States ; }, abstract = {The frequent exchange of mobile genetic elements (MGEs) between bacteria accelerates the spread of functional traits, including antimicrobial resistance, within the human microbiome. Yet, progress in understanding these intricate processes has been hindered by the lack of tools to map the spatial spread of MGEs in complex microbial communities, and to associate MGEs to their bacterial hosts. To overcome this challenge, we present an imaging approach that pairs single molecule DNA Fluorescence In Situ Hybridization (FISH) with multiplexed ribosomal RNA FISH, thereby enabling the simultaneous visualization of both MGEs and host bacterial taxa. We used this methodology to spatially map bacteriophage and antimicrobial resistance (AMR) plasmids in human oral biofilms, and we studied the heterogeneity in their spatial distributions and demonstrated the ability to identify their host taxa. Our data revealed distinct clusters of both AMR plasmids and prophage, coinciding with densely packed regions of host bacteria in the biofilm. These results suggest the existence of specialized niches that maintain MGEs within the community, possibly acting as local hotspots for horizontal gene transfer. The methods introduced here can help advance the study of MGE ecology and address pressing questions regarding antimicrobial resistance and phage therapy.}, }
@article {pmid37331053, year = {2023}, author = {Araujo, FF and Salvador, GLO and Lupatini, GC and Pereira, APA and Costa, RM and de Aviz, RO and de Alcantara Neto, F and Mendes, LW and Araujo, ASF}, title = {Exploring the diversity and composition of soil microbial communities in different soybean-maize management systems.}, journal = {Microbiological research}, volume = {274}, number = {}, pages = {127435}, doi = {10.1016/j.micres.2023.127435}, pmid = {37331053}, issn = {1618-0623}, mesh = {*Soil/chemistry ; Zea mays/microbiology ; Glycine max ; Soil Microbiology ; *Microbiota ; }, abstract = {Soybean-maize are cultivated in different management systems, such as no-tillage and pastures, which presents potential to add organic residues, and it can potentially impacts the soil microbial community present in these systems. Thus, this study aimed to examine the effects of different soybean-maize management practices on the diversity and composition of soil microbial communities. Specifically, 16 S rRNA amplicon sequencing was used to investigate whether the use of pasture species in a fallowing system influences microbial communities in a soybean-maize rotation system, as compared to conventional tillage and no-tillage systems. The results indicate that the inclusion of the pasture species Urochloa brizantha in soybean-maize management systems leads to distinct responses within the soil microbial community. It was found that different soybean-maize management systems, particularly those with U. brizantha, affected the microbial community, likely due to the management applied to this pasture species. The system with 3 years of fallowing before soybean-maize showed the lowest microbial richness (∼2000 operational taxonomic units) and diversity index (∼6.0). Proteobacteria (∼30%), Acidobacteria (∼15%), and Verrucomicrobia (∼10%) were found to be the most abundant phyla in the soil under tropical native vegetation, while soils under cropland had an increased abundance of Firmicutes (∼30% to ∼50%) and Actinobacteria (∼30% to ∼35%). To summarize, this study identified the impacts of various soybean-maize management practices on the soil microbial community and emphasized the advantages of adding U. brizantha as a fallow species.}, }
@article {pmid37327546, year = {2023}, author = {Ostermeyer, P and Folens, K and Verbruggen, F and Bonin, L and Hennebel, T and Korneel, R}, title = {A sulfate reducing bioreactor controlled by an electrochemical system enables near-zero chemical treatment of metallurgical wastewater.}, journal = {Water research}, volume = {242}, number = {}, pages = {120215}, doi = {10.1016/j.watres.2023.120215}, pmid = {37327546}, issn = {1879-2448}, mesh = {*Wastewater ; *Sulfates/chemistry ; Sewage/chemistry ; Metals ; Bioreactors ; Waste Disposal, Fluid/methods ; }, abstract = {Metallurgical wastewaters are characterized by a low pH (<4), high concentrations of sulfate (15 gSO4[2-] L[-1]), and metal(loid)s. Current treatment requires the consumption of chemicals such as alkali and high levels of waste sludge generation. In this study, we have shown that combining water electrolysis and sulfate reducing bioreactors enables the in-situ generation of base and H2, eliminating the need for base and electron donor addition, resulting in the near-zero treatment of metallurgical wastewater. By extracting cations from the effluent of the system to the bioreactor, the bioreactor pH could be maintained by the in-situ production of alkali. The current for pH control varied between 112-753 mol electrons per m[3] wastewater or 5-48 A m[-2] electrode area. High concentrations of sulfate in the influent and addition of CO2 increased the current required to maintain a steady bioreactor pH. On the other hand, a high sulfate reduction rate and increased influent pH lowered the current required for pH control. Moreover, the current efficiency varied from 14% to 91% and increased with higher pH and cation (Na[+], NH4[+], K[+], Mg[2+], Ca[2+]) concentrations in the middle compartment of the electrochemical cell. The salinity was lowered from 70-120 mS cm[-1] in the influent to 5-20 mS cm[-1] in the system effluent. The energy consumption of the electrochemical pH control varied between 10 and 100 kWh m[-3] and was affected by the conductivity of the wastewater. Industrial wastewater was treated successfully with an average energy consumption of 39 ± 7 kWh m[-3], removing sulfate from 15 g SO4[2-] L[-1] to 0.5 ± 0.5 g SO4[2-] L[-1] at a reduction rate of 20 ± 1 gSO4[2-] L[-1] d[-1]..Metal(loid)s such as As, Cd, Cu, Pb, Te, Tl, Ni and Zn were removed to levels of 1-50 µg L[-1].}, }
@article {pmid37326636, year = {2023}, author = {Dos Santos Ribeiro, P and Carvalho, NB and Aburjaile, F and Sousa, T and Veríssimo, G and Gomes, T and Neves, F and Blanco, L and Lima, JA and de Oliveira, D and Jaiswal, AK and Brenig, B and Soares, S and Ramos, R and Matiuzzi, M and Góes-Neto, A and Figueira, CP and Costa, F and Ristow, P and Azevedo, V}, title = {Environmental Biofilms from an Urban Community in Salvador, Brazil, Shelter Previously Uncharacterized Saprophytic Leptospira.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2488-2501}, pmid = {37326636}, issn = {1432-184X}, support = {001//Coordination for the Improvement of Higher Education Personnel (Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior - CAPES)/ ; 423415/2021-2//National Council for Scientific and Technological Development (CNPq) Universal project/ ; 23038.000776/2017-54//INCT IN-TREE/ ; }, mesh = {Animals ; Rats ; *Leptospira/genetics ; *Leptospirosis/microbiology ; Brazil ; Biofilms ; DNA ; }, abstract = {Biofilms are complex microecosystems with valuable ecological roles that can shelter a variety of microorganisms. Spirochetes from the genus Leptospira have been observed to form biofilms in vitro, in rural environments, and in the kidneys of reservoir rats. The genus Leptospira is composed of pathogenic and non-pathogenic species, and the description of new species is ongoing due to the advent of whole genome sequencing. Leptospires have increasingly been isolated from water and soil samples. To investigate the presence of Leptospira in environmental biofilms, we collected three distinct samples of biofilms formed in an urban setting with poor sanitation: Pau da Lima, in Salvador, Bahia, Brazil. All biofilm samples were negative for the presence of pathogenic leptospires via conventional PCR, but cultures containing saprophytic Leptospira were identified. Whole genomes were generated and analyzed for twenty isolates obtained from these biofilms. For species identification, we used digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analysis. The obtained isolates were classified into seven presumptive species from the saprophytic S1 clade. ANI and dDDH analysis suggest that three of those seven species were new. Classical phenotypic tests confirmed the novel isolated bacteria as saprophytic Leptospira. The isolates presented typical morphology and ultrastructure according to scanning electron microscopy and formed biofilms under in vitro conditions. Our data indicate that a diversity of saprophytic Leptospira species survive in the Brazilian poorly sanitized urban environment, in a biofilm lifestyle. We believe our results contribute to a better understanding of Leptospira biology and ecology, considering biofilms as natural environmental reservoirs for leptospires.}, }
@article {pmid37323900, year = {2023}, author = {Ho, PM and Nazeer, RR and Welch, M}, title = {Therapeutic interventions alter ecological interactions among cystic fibrosis airway microbiota.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1178131}, pmid = {37323900}, issn = {1664-302X}, support = {NC/P001564/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; }, abstract = {The airways of people with cystic fibrosis (CF) often harbor a diverse microbiota and in recent years, much effort has been invested in cataloguing these. In spite of providing a wealth of insight, this cataloguing tells us little about how the organisms interact with one another in the CF airways. However, such relationships can be inferred using the theoretical framework of the Lotka-Volterra (LV) model. In the current work, we use a generalized Lotka-Volterra model to interrogate the nationwide data collected and curated by the UK CF Registry. This longitudinal dataset (covering the period 2008-2020) contains annual depositions that record the presence/absence of microbial taxa in each patient, their medication, and their CF genotype. Specifically, we wanted to identify trends in ecological relationships between the CF microbiota at a nationwide level, and whether these are potentially affected by medication. Our results show that some medications have a distinct influence on the microbial interactome, especially those that potentially influence the "gut-lung axis" or mucus viscosity. In particular, we found that patients treated with a combination of antimicrobial agents (targeting the airway microbiota), digestive enzymes (assisting in the assimilation of dietary fats and carbohydrates), and DNase (to reduce mucus viscosity) displayed a distinctly different airway interactome compared with patients treated separately with these medications.}, }
@article {pmid37323646, year = {2023}, author = {Rodrigues-Filho, JL and Macêdo, RL and Sarmento, H and Pimenta, VRA and Alonso, C and Teixeira, CR and Pagliosa, PR and Netto, SA and Santos, NCL and Daura-Jorge, FG and Rocha, O and Horta, P and Branco, JO and Sartor, R and Muller, J and Cionek, VM}, title = {From ecological functions to ecosystem services: linking coastal lagoons biodiversity with human well-being.}, journal = {Hydrobiologia}, volume = {850}, number = {12-13}, pages = {2611-2653}, pmid = {37323646}, issn = {0018-8158}, abstract = {In this review we highlight the relevance of biodiversity that inhabit coastal lagoons, emphasizing how species functions foster processes and services associated with this ecosystem. We identified 26 ecosystem services underpinned by ecological functions performed by bacteria and other microbial organisms, zooplankton, polychaetae worms, mollusks, macro-crustaceans, fishes, birds, and aquatic mammals. These groups present high functional redundancy but perform complementary functions that result in distinct ecosystem processes. Because coastal lagoons are located in the interface between freshwater, marine and terrestrial ecosystems, the ecosystem services provided by the biodiversity surpass the lagoon itself and benefit society in a wider spatial and historical context. The species loss in coastal lagoons due to multiple human-driven impacts affects the ecosystem functioning, influencing negatively the provision of all categories of services (i.e., supporting, regulating, provisioning and cultural). Because animals' assemblages have unequal spatial and temporal distribution in coastal lagoons, it is necessary to adopt ecosystem-level management plans to protect habitat heterogeneity and its biodiversity, ensuring the provision of services for human well-being to multi-actors in the coastal zone.}, }
@article {pmid37318372, year = {2023}, author = {Rani, S and Sørensen, MT and Estellé, J and Noel, SJ and Nørskov, N and Krogh, U and Foldager, L and Højberg, O}, title = {Gastrointestinal Microbial Ecology of Weaned Piglets Fed Diets with Different Levels of Glyphosate.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0061523}, pmid = {37318372}, issn = {2165-0497}, mesh = {Animals ; Swine ; *Dysbiosis ; *Gastrointestinal Tract ; Diet/veterinary ; Stomach ; Cecum ; Acids ; }, abstract = {Glyphosate possesses antimicrobial properties, and the present study investigated potential effects of feed glyphosate on piglet gastrointestinal microbial ecology. Weaned piglets were allocated to four diets (glyphosate contents [mg/kg feed]: 0 mg/kg control [CON; i.e., basal diet with no glyphosate added], 20 mg/kg as Glyphomax commercial herbicide [GM20], and 20 mg/kg [IPA20] and 200 mg/kg [IPA200] as glyphosate isopropylamine [IPA] salt). Piglets were sacrificed after 9 and 35 days of treatment, and stomach, small intestine, cecum, and colon digesta were analyzed for glyphosate, aminomethylphosphonic acid (AMPA), organic acids, pH, dry matter content, and microbiota composition. Digesta glyphosate contents reflected dietary levels (on day 35, 0.17, 16.2, 20.5, and 207.5 mg/kg colon digesta, respectively). Overall, we observed no significant glyphosate-associated effects on digesta pH, dry matter content, and-with few exceptions-organic acid levels. On day 9, only minor gut microbiota changes were observed. On day 35, we observed a significant glyphosate-associated decrease in species richness (CON, 462; IPA200, 417) and in the relative abundance of certain Bacteroidetes genera: CF231 (CON, 3.71%; IPA20, 2.33%; IPA200, 2.07%) and g_0.24 (CON, 3.69%; IPA20, 2.07%; IPA200, 1.75%) in cecum. No significant changes were observed at the phylum level. In the colon, we observed a significant glyphosate-associated increase in the relative abundance of Firmicutes (CON, 57.7%; IPA20, 69.4%; IPA200, 66.1%) and a decrease in Bacteroidetes (CON, 32.6%; IPA20, 23.5%). Significant changes were only observed for few genera, e.g., g_0.24 (CON, 7.12%; IPA20, 4.59%; IPA200, 4.00%). In conclusion, exposing weaned piglets to glyphosate-amended feed did not affect gastrointestinal microbial ecology to a degree that was considered actual dysbiosis, e.g., no potential pathogen bloom was observed. IMPORTANCE Glyphosate residues can be found in feed made from genetically modified glyphosate-resistant crops treated with glyphosate or from conventional crops, desiccated with glyphosate before harvest. If these residues affect the gut microbiota to an extent that is unfavorable to livestock health and productivity, the widespread use of glyphosate on feed crops may need to be reconsidered. Few in vivo studies have been conducted to investigate potential impact of glyphosate on the gut microbial ecology and derived health issues of animals, in particular livestock, when exposed to dietary glyphosate residues. The aim of the present study was therefore to investigate potential effects on the gastrointestinal microbial ecology of newly weaned piglets fed glyphosate-amended diets. Piglets did not develop actual gut dysbiosis when fed diets, containing a commercial herbicide formulation or a glyphosate salt at the maximum residue level, defined by the European Union for common feed crops, or at a 10-fold-higher level.}, }
@article {pmid37318344, year = {2023}, author = {Diner, RE and Zimmer-Faust, A and Cooksey, E and Allard, S and Kodera, SM and Kunselman, E and Garodia, Y and Verhougstraete, MP and Allen, AE and Griffith, J and Gilbert, JA}, title = {Host and Water Microbiota Are Differentially Linked to Potential Human Pathogen Accumulation in Oysters.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {7}, pages = {e0031823}, pmid = {37318344}, issn = {1098-5336}, support = {K12 GM068524/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Humans ; Water ; *Ostreidae/microbiology ; *Vibrio parahaemolyticus ; *Vibrio vulnificus ; *Bivalvia ; Bacteria/genetics ; }, abstract = {Oysters play an important role in coastal ecology and are a globally popular seafood source. However, their filter-feeding lifestyle enables coastal pathogens, toxins, and pollutants to accumulate in their tissues, potentially endangering human health. While pathogen concentrations in coastal waters are often linked to environmental conditions and runoff events, these do not always correlate with pathogen concentrations in oysters. Additional factors related to the microbial ecology of pathogenic bacteria and their relationship with oyster hosts likely play a role in accumulation but are poorly understood. In this study, we investigated whether microbial communities in water and oysters were linked to accumulation of Vibrio parahaemolyticus, Vibrio vulnificus, or fecal indicator bacteria. Site-specific environmental conditions significantly influenced microbial communities and potential pathogen concentrations in water. Oyster microbial communities, however, exhibited less variability in microbial community diversity and accumulation of target bacteria overall and were less impacted by environmental differences between sites. Instead, changes in specific microbial taxa in oyster and water samples, particularly in oyster digestive glands, were linked to elevated levels of potential pathogens. For example, increased levels of V. parahaemolyticus were associated with higher relative abundances of cyanobacteria, which could represent an environmental vector for Vibrio spp. transport, and with decreased relative abundance of Mycoplasma and other key members of the oyster digestive gland microbiota. These findings suggest that host and microbial factors, in addition to environmental variables, may influence pathogen accumulation in oysters. IMPORTANCE Bacteria in the marine environment cause thousands of human illnesses annually. Bivalves are a popular seafood source and are important in coastal ecology, but their ability to concentrate pathogens from the water can cause human illness, threatening seafood safety and security. To predict and prevent disease, it is critical to understand what causes pathogenic bacteria to accumulate in bivalves. In this study, we examined how environmental factors and host and water microbial communities were linked to potential human pathogen accumulation in oysters. Oyster microbial communities were more stable than water communities, and both contained the highest concentrations of Vibrio parahaemolyticus at sites with warmer temperatures and lower salinities. High oyster V. parahaemolyticus concentrations corresponded with abundant cyanobacteria, a potential vector for transmission, and a decrease in potentially beneficial oyster microbes. Our study suggests that poorly understood factors, including host and water microbiota, likely play a role in pathogen distribution and pathogen transmission.}, }
@article {pmid37317205, year = {2023}, author = {Maatouk, M and Rolain, JM and Bittar, F}, title = {Using Genomics to Decipher the Enigmatic Properties and Survival Adaptation of Candidate Phyla Radiation.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317205}, issn = {2076-2607}, support = {M&#xe9;diterran&#xe9;e Infection 10-IAHU-03//Agence Nationale de la Recherche/ ; }, abstract = {Microbial ecology is a critical field for understanding the composition, diversity, and functions of microorganisms in various environmental and health-related processes. The discovery of Candidate Phyla Radiation (CPR) through culture-independent methods has introduced a new division of microbes characterized by a symbiotic/parasitic lifestyle, small cell size, and small genome. Despite being poorly understood, CPRs have garnered significant attention in recent years due to their widespread detection in a variety of environmental and clinical samples. These microorganisms have been found to exhibit a high degree of genetic diversity compared to other microbes. Several studies have shed light on their potential importance in global biogeochemical cycles and their impact on various human activities. In this review, we provide a systematic overview of the discovery of CPRs. We then focus on describing how the genomic characteristics of CPRs have helped them interact with and adapt to other microbes in different ecological niches. Future works should focus on discovering the metabolic capacities of CPRs and, if possible, isolating them to obtain a better understanding of these microorganisms.}, }
@article {pmid37317127, year = {2023}, author = {Varliero, G and Lebre, PH and Frey, B and Fountain, AG and Anesio, AM and Cowan, DA}, title = {Glacial Water: A Dynamic Microbial Medium.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317127}, issn = {2076-2607}, support = {129227//National Research Foundation/ ; }, abstract = {Microbial communities and nutrient dynamics in glaciers and ice sheets continuously change as the hydrological conditions within and on the ice change. Glaciers and ice sheets can be considered bioreactors as microbiomes transform nutrients that enter these icy systems and alter the meltwater chemistry. Global warming is increasing meltwater discharge, affecting nutrient and cell export, and altering proglacial systems. In this review, we integrate the current understanding of glacial hydrology, microbial activity, and nutrient and carbon dynamics to highlight their interdependence and variability on daily and seasonal time scales, as well as their impact on proglacial environments.}, }
@article {pmid37317116, year = {2023}, author = {Malajacan, GT and Nacario, MAG and Obusan, MCM and Rivera, WL}, title = {Host-Associated Bacteroides 16S rDNA-Based Markers for Source Tracking of Fecal Pollution in Laguna Lake, Philippines.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317116}, issn = {2076-2607}, support = {N/A//Department of Science and Technology/ ; }, abstract = {Sources of fecal contamination in Laguna Lake, Philippines, were identified using a library-independent microbial source tracking method targeting host-associated Bacteroides 16S rDNA-based markers. Water samples from nine lake stations were assessed for the presence of the fecal markers HF183 (human), BoBac (cattle), Pig-2-Bac (swine), and DuckBac (duck) from August 2019 to January 2020. HF183 (average concentration = 1.91 log10 copies/mL) was the most frequently detected, while Pig-2-Bac (average concentration = 2.47 log10 copies/mL) was the most abundant. The detected marker concentrations in different stations corresponded to the land use patterns around the lake. Generally, all marker concentrations were higher during the wet season (August-October), suggesting the effect of rainfall-associated factors on the movement and retention of markers from sources. There was a significant association (ρ = 0.45; p < 0.001) between phosphate and the concentration of HF183, suggesting domestic sewage-derived pollution. The markers had acceptable sensitivity and specificity, i.e., HF183 (S = 0.88; R = 0.99), Pig-2-Bac (S = 1.00; R = 1.00), and DuckBac (S = 0.94; R = 1.00), and therefore may be used for the continuous monitoring of fecal pollution in the lake and in designing interventions to improve the quality of the lake water.}, }
@article {pmid37317051, year = {2023}, author = {Wang, M and Sun, X and Cao, B and Chiariello, NR and Docherty, KM and Field, CB and Gao, Q and Gutknecht, JLM and Guo, X and He, G and Hungate, BA and Lei, J and Niboyet, A and Le Roux, X and Shi, Z and Shu, W and Yuan, M and Zhou, J and Yang, Y}, title = {Long-term elevated precipitation induces grassland soil carbon loss via microbe-plant-soil interplay.}, journal = {Global change biology}, volume = {29}, number = {18}, pages = {5429-5444}, doi = {10.1111/gcb.16811}, pmid = {37317051}, issn = {1365-2486}, support = {//G. Evelyn Hutchinson postdoctoral fellowship from Yale Institute for Biospheric Studies at Yale University/ ; //The Simons Foundation postdoctoral fellowship in Marine Microbial Ecology/ ; 2019A1515110345//Guangdong Basis and Applied Basic Research Foundation grant/ ; 2021A1515011497//Guangdong Basis and Applied Basic Research Foundation grant/ ; 20223BBG74S02//Key Technology R&amp;D Program of Jiangxi Province/ ; 41825016//National Natural Science Foundation of China/ ; 41877048//National Natural Science Foundation of China/ ; 42007297//National Natural Science Foundation of China/ ; DE-SC0004601//Office of Science and Office of Biological and Environmental Research (DOE-BER) of the U.S. Department of Energy Genomic Science Program/ ; DE-SC0010715//Office of Science and Office of Biological and Environmental Research (DOE-BER) of the U.S. Department of Energy Genomic Science Program/ ; //Office of the Vice President for Research at the University of Oklahoma/ ; 2019FY100700//Science &amp; Technology Fundamental Resources Investigation Program/ ; //The French CNRS/INSU-EC2CO Program (project INTERACT)/ ; //The French Institute of Agriculture, Food and Environment Research (INRAE, ECODIV Department)/ ; //The Morgan Family Foundation/ ; //The Packard Foundation/ ; 2019QZKK0503//The Second Tibetan Plateau Scientific Expedition and Research (STEP) Program/ ; DEB-0092642//US National Science Foundation/ ; DEB-0445324//US National Science Foundation/ ; }, mesh = {*Grassland ; Carbon ; Climate Change ; *Microbiota ; Nitrogen ; }, abstract = {Global climate models predict that the frequency and intensity of precipitation events will increase in many regions across the world. However, the biosphere-climate feedback to elevated precipitation (eP) remains elusive. Here, we report a study on one of the longest field experiments assessing the effects of eP, alone or in combination with other climate change drivers such as elevated CO2 (eCO2), warming and nitrogen deposition. Soil total carbon (C) decreased after a decade of eP treatment, while plant root production decreased after 2 years. To explain this asynchrony, we found that the relative abundances of fungal genes associated with chitin and protein degradation increased and were positively correlated with bacteriophage genes, suggesting a potential viral shunt in C degradation. In addition, eP increased the relative abundances of microbial stress tolerance genes, which are essential for coping with environmental stressors. Microbial responses to eP were phylogenetically conserved. The effects of eP on soil total C, root production, and microbes were interactively affected by eCO2 . Collectively, we demonstrate that long-term eP induces soil C loss, owing to changes in microbial community composition, functional traits, root production, and soil moisture. Our study unveils an important, previously unknown biosphere-climate feedback in Mediterranean-type water-limited ecosystems, namely how eP induces soil C loss via microbe-plant-soil interplay.}, }
@article {pmid37316492, year = {2023}, author = {Cuypers, WL and Meysman, P and Weill, FX and Hendriksen, RS and Beyene, G and Wain, J and Nair, S and Chattaway, MA and Perez-Sepulveda, BM and Ceyssens, PJ and de Block, T and Lee, WWY and Pardos de la Gandara, M and Kornschober, C and Moran-Gilad, J and Veldman, KT and Cormican, M and Torpdahl, M and Fields, PI and Černý, T and Hardy, L and Tack, B and Mellor, KC and Thomson, N and Dougan, G and Deborggraeve, S and Jacobs, J and Laukens, K and Van Puyvelde, S}, title = {A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3517}, pmid = {37316492}, issn = {2041-1723}, support = {BBS/E/F/000PR10349/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MC_PC_16093/MRC_/Medical Research Council/United Kingdom ; BB/CCG1720/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Ethiopia/epidemiology ; Genomics ; Salmonella/genetics ; }, abstract = {Antimicrobial resistant Salmonella enterica serovar Concord (S. Concord) is known to cause severe gastrointestinal and bloodstream infections in patients from Ethiopia and Ethiopian adoptees, and occasional records exist of S. Concord linked to other countries. The evolution and geographical distribution of S. Concord remained unclear. Here, we provide a genomic overview of the population structure and antimicrobial resistance (AMR) of S. Concord by analysing genomes from 284 historical and contemporary isolates obtained between 1944 and 2022 across the globe. We demonstrate that S. Concord is a polyphyletic serovar distributed among three Salmonella super-lineages. Super-lineage A is composed of eight S. Concord lineages, of which four are associated with multiple countries and low levels of AMR. Other lineages are restricted to Ethiopia and horizontally acquired resistance to most antimicrobials used for treating invasive Salmonella infections in low- and middle-income countries. By reconstructing complete genomes for 10 representative strains, we demonstrate the presence of AMR markers integrated in structurally diverse IncHI2 and IncA/C2 plasmids, and/or the chromosome. Molecular surveillance of pathogens such as S. Concord supports the understanding of AMR and the multi-sector response to the global AMR threat. This study provides a comprehensive baseline data set essential for future molecular surveillance.}, }
@article {pmid37314477, year = {2023}, author = {An, Y and Braga, MP and Garcia, SL and Grudzinska-Sterno, M and Hambäck, PA}, title = {Host Phylogeny Structures the Gut Bacterial Community Within Galerucella Leaf Beetles.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2477-2487}, pmid = {37314477}, issn = {1432-184X}, support = {#2019-4980//The Swedish Research Council Vetenskapsr&#xe5;det to PAH/ ; }, mesh = {Animals ; *Coleoptera/microbiology ; Phylogeny ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Insecta ; Bacteria/genetics ; }, abstract = {Gut microbes play important roles for their hosts. Previous studies suggest that host-microbial systems can form long-term associations over evolutionary time and the dynamic changes of the intestinal system may represent major driving forces and contribute to insect dietary diversification and speciation. Our study system includes a set of six closely related leaf beetle species (Galerucella spp.) and our study aims to separate the roles of host phylogeny and ecology in determining the gut microbial community and to identify eventual relationship between host insects and gut bacteria. We collected adult beetles from their respective host plants and quantified their microbial community using 16S rRNA sequencing. The results showed that the gut bacteria community composition was structured by host beetle phylogeny, where more or less host-specific gut bacteria interact with the different Galerucella species. For example, the endosymbiotic bacteria Wolbachia was found almost exclusively in G. nymphaea and G. sagittariae. Diversity indicators also suggested that α- and β-diversities of gut bacteria communities varied among host beetle species. Overall, our results suggest a phylogenetically controlled co-occurrence pattern between the six closely related Galerucella beetles and their gut bacteria, indicating the potential of co-evolutionary processes occurring between hosts and their gut bacterial communities.}, }
@article {pmid37310275, year = {2023}, author = {Saati-Santamaría, Z}, title = {Global Map of Specialized Metabolites Encoded in Prokaryotic Plasmids.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0152323}, pmid = {37310275}, issn = {2165-0497}, mesh = {Humans ; *Bacteria/genetics ; Secondary Metabolism/genetics ; Plasmids/genetics ; *Multigene Family ; }, abstract = {Plasmids are the main mobile elements responsible for horizontal gene transfer (HGT) in microorganisms. These replicons extend the metabolic spectrum of their host cells by carrying functional genes. However, it is still unknown to what extent plasmids carry biosynthetic gene clusters (BGCs) related to the production of secondary or specialized metabolites (SMs). Here, we analyzed 9,183 microbial plasmids to unveil their potential to produce SMs, finding a large diversity of cryptic BGCs in a few varieties of prokaryotic host taxa. Some of these plasmids harbored 15 or more BGCs, and many others were exclusively dedicated to mobilizing BGCs. We found an occurrence pattern of BGCs within groups of homologous plasmids shared by a common taxon, mainly in host-associated microbes (e.g., Rhizobiales, Enterobacteriaceae members). Our results add to the knowledge of the ecological functions and potential industrial uses of plasmids and shed light on the dynamics and evolution of SMs in prokaryotes. IMPORTANCE Plasmids are mobile DNA elements that can be shared among microbial cells, and they are useful for bringing to fruition some microbial ecological traits. However, it is not known to what extent plasmids harbor genes related to the production of specialized/secondary metabolites (SMs). In microbes, these metabolites are frequently useful for defense purposes, signaling, etc. In addition, these molecules usually have biotechnological and clinical applications. Here, we analyzed the content, dynamics, and evolution of genes related to the production of SMs in >9,000 microbial plasmids. Our results confirm that some plasmids act as a reservoir of SMs. We also found that some families of biosynthetic gene clusters are exclusively present in some groups of plasmids shared among closely related microbes. Host-associated bacteria (e.g., plant and human microbes) harbor the majority of specialized metabolites encoded in plasmids. These results provide new knowledge about microbial ecological traits and might enable the discovery of novel metabolites.}, }
@article {pmid37308155, year = {2023}, author = {Timmis, K and Verstraete, W and Regina, VR and Hallsworth, JE}, title = {The Pareto principle: To what extent does it apply to resource acquisition in stable microbial communities and thereby steer their geno-/ecotype compositions and interactions between their members?.}, journal = {Environmental microbiology}, volume = {25}, number = {7}, pages = {1221-1231}, doi = {10.1111/1462-2920.16438}, pmid = {37308155}, issn = {1462-2920}, mesh = {*Ecotype ; Genotype ; *Microbiota/genetics ; }, abstract = {The Pareto principle, or 20:80 rule, describes resource distribution in stable communities whereby 20% of community members acquire 80% of a key resource. In this Burning Question, we ask to what extent the Pareto principle applies to the acquisition of limiting resources in stable microbial communities; how it may contribute to our understanding of microbial interactions, microbial community exploration of evolutionary space, and microbial community dysbiosis; and whether it can serve as a benchmark of microbial community stability and functional optimality?}, }
@article {pmid37303746, year = {2023}, author = {Martinez-Rabert, E and Sloan, WT and Gonzalez-Cabaleiro, R}, title = {Multiscale models driving hypothesis and theory-based research in microbial ecology.}, journal = {Interface focus}, volume = {13}, number = {4}, pages = {20230008}, pmid = {37303746}, issn = {2042-8898}, abstract = {Hypothesis and theory-based studies in microbial ecology have been neglected in favour of those that are descriptive and aim for data-gathering of uncultured microbial species. This tendency limits our capacity to create new mechanistic explanations of microbial community dynamics, hampering the improvement of current environmental biotechnologies. We propose that a multiscale modelling bottom-up approach (piecing together sub-systems to give rise to more complex systems) can be used as a framework to generate mechanistic hypotheses and theories (in-silico bottom-up methodology). To accomplish this, formal comprehension of the mathematical model design is required together with a systematic procedure for the application of the in-silico bottom-up methodology. Ruling out the belief that experimentation before modelling is indispensable, we propose that mathematical modelling can be used as a tool to direct experimentation by validating theoretical principles of microbial ecology. Our goal is to develop methodologies that effectively integrate experimentation and modelling efforts to achieve superior levels of predictive capacity.}, }
@article {pmid37303745, year = {2023}, author = {Sloan, WT and Gómez-Borraz, TL}, title = {Engineering biology in the face of uncertainty.}, journal = {Interface focus}, volume = {13}, number = {4}, pages = {20230001}, pmid = {37303745}, issn = {2042-8898}, abstract = {Combining engineering and biology surely must be a route to delivering solutions to the world's most pressing problems in depleting resources, energy and the environment. Engineers and biologists have long recognized the power in coupling their disciplines and have evolved a healthy variety of approaches to realizing technologies. Yet recently, there has been a movement to narrow the remit of engineering biology. Its definition as 'the application of engineering principles to the design of biological systems' ought to encompass a broad church. However, the emphasis is firmly on construction '…of novel biological devices and systems from standardized artificial parts' within cells. Thus, engineering biology has become synonymous with synthetic biology, despite the many longstanding technologies that use natural microbial communities. The focus on the nuts and bolts of synthetic organisms may be deflecting attention from the significant challenge of delivering solutions at scale, which cuts across all engineering biology, synthetic and natural. Understanding, let alone controlling, every component of an engineered system is an unrealistic goal. To realize workable solutions in a timely manner we must develop systematic ways of engineering biology in the face of the uncertainties that are inherent in biological systems and that arise through lack of knowledge.}, }
@article {pmid37303743, year = {2023}, author = {Sierocinski, P and Stilwell, P and Padfield, D and Bayer, F and Buckling, A}, title = {The ecology of scale: impact of volume on coalescence and function in methanogenic communities.}, journal = {Interface focus}, volume = {13}, number = {4}, pages = {20220089}, pmid = {37303743}, issn = {2042-8898}, abstract = {Engineered ecosystems span multiple volume scales, from a nano-scale to thousands of cubic metres. Even the largest industrial systems are tested in pilot scale facilities. But does scale affect outcomes? Here we look at comparing different size laboratory anaerobic fermentors to see if and how the volume of the community affects the outcome of community coalescence (combining multiple communities) on community composition and function. Our results show that there is an effect of scale on biogas production. Furthermore, we see a link between community evenness and volume, with smaller scale communities having higher evenness. Despite those differences, the overall patterns of community coalescence are very similar at all scales, with coalescence leading to levels of biogas production comparable with that of the best-performing component community. The increase in biogas with increasing volume plateaus, suggesting there is a volume where productivity stays stable over large volumes. Our findings are reassuring for ecologists studying large ecosystems and industries operating pilot scale facilities, as they support the validity of pilot scale studies in this field.}, }
@article {pmid37302588, year = {2023}, author = {Rosinger, C and Rousk, J and Bonkowski, M and Rethemeyer, J and Jaeschke, A}, title = {Rewetting the hyper-arid Atacama Desert soil reactivates a carbon-starved microbial decomposer community and also triggers archaeal metabolism.}, journal = {The Science of the total environment}, volume = {892}, number = {}, pages = {164785}, doi = {10.1016/j.scitotenv.2023.164785}, pmid = {37302588}, issn = {1879-1026}, mesh = {*Archaea ; Soil ; Carbon ; Glycerol ; Soil Microbiology ; Bacteria ; *Microbiota ; Fatty Acids ; Phospholipids ; }, abstract = {Extreme environmental conditions make soils of the hyper-arid Atacama Desert one of the most hostile habitats for life on the planet. During the short intervals of moisture availability that occur, it remains unresolved how soil microorganisms physiologically respond to such dramatic environmental changes. Therefore, we simulated a precipitation event - without (H2O) and with (H2O + C) labile carbon (C) supplementation - and investigated the responses in microbial communities (using phospholipid fatty acids (PLFAs) and archaeal glycerol dialkyl glycerol tetraether (GDGTs)) and physiology (by means of respiration, bacterial and fungal growth and C-use efficiency (CUE)) during a five-day incubation. We demonstrated that bacterial and fungal growth does occur in these extreme soils following rewetting, albeit at 100-10,000-fold lower rates compared to previously studied soil systems. C supplementation increased levels of bacterial growth and respiration responses by 5- and 50-fold, respectively, demonstrating a C-limited microbial decomposer community. While the microbial CUE following rewetting was c. 14 %, the addition of labile C during rewetting resulted in a substantial reduction (c. 1.6 %). Consistent with these interpretations, the PLFA composition clearly shifted from saturated towards more unsaturated and branched PLFAs, which could arise from (i) a physiological adaptation of the cell membrane to changing osmotic conditions or (ii) a community composition shift. Significant increases in total PLFA concentrations were solely found with H2O + C addition. Contrary to other recent studies, we found evidence for a metabolically active archaeal community in these hyper-arid soils upon rewetting. We conclude that (i) microorganisms in this extreme soil habitat can be activated and grow within days following rewetting, (ii) available C is the limiting factor for microbial growth and biomass gains, and (iii) that an optimization of tolerating the extreme conditions while maintaining a high CUE comes at the expense of very poor resource-use efficiency during high resource availability.}, }
@article {pmid37302271, year = {2023}, author = {Sakarika, M and Ganigué, R and Rabaey, K}, title = {Corrigendum to "Methylotrophs: from C1 compounds to food" [Curr Opin Biotechnol 75 (2022) 102685].}, journal = {Current opinion in biotechnology}, volume = {82}, number = {}, pages = {102964}, doi = {10.1016/j.copbio.2023.102964}, pmid = {37302271}, issn = {1879-0429}, }
@article {pmid37301781, year = {2023}, author = {Zhu, YL and Huang, YJ and Nuerhamanti, N and Bai, XY and Wang, HN and Zhu, XY and Zhang, W}, title = {Composition and Distribution Characteristics of Rhizosphere Bacterial Community of Ammodendron bifolium Growing in Takeermohuer Desert Are Different from Those in Non-rhizosphere.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2461-2476}, pmid = {37301781}, issn = {1432-184X}, support = {32160309//National Science Foundation of China/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; }, mesh = {*Rhizosphere ; Bacteria ; Proteobacteria ; Acidobacteria ; *Fabaceae ; Soil/chemistry ; Nitrogen ; Soil Microbiology ; }, abstract = {Soil microorganisms play important roles in vegetation establishment and soil biogeochemical cycling. Ammodendron bifolium is a dominant sand-fixing and endangered plant in Takeermohuer Desert, and bacterial community associated with this plant rhizosphere is still unclear. In this study, we studied the composition and diversity of bacterial community from A. bifolium rhizosphere and bulk soil at different soil depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) using traditional bacterial isolation and high-throughput sequencing approaches, and preliminarily analyzed the edaphic factors influencing the structure of bacterial communities. Results showed that Takeermohuer Desert with high salinity has been an oligotrophic environment, while the rhizosphere exhibited eutrophication resulting from high content SOM (soil organic matter) and SAN (soil alkaline nitrogen) compared with bulk soil. The dominant bacterial groups in the desert were Actinobacteria (39.8%), Proteobacteria (17.4%), Acidobacteria (10.2%), Bacteroidetes (6.3%), Firmicutes (6.3%), Chloroflexi (5.6%), and Planctomycetes (5.0%) at the phyla level. However, the relative abundances of Proteobacteria (20.2%) and Planctomycetes (6.1%) were higher in eutrophic rhizosphere, and Firmicutes (9.8%) and Chloroflexi (6.9%) relatively higher in barren bulk soil. A large number of Actinobacteria were detected in all soil samples, of which the most abundant genus was Streptomyces (5.4%) and Actinomadura (8.2%) in the bulk soil and rhizosphere, respectively. The Chao1 and PD indexes in rhizosphere were significantly higher than those in bulk soil at the same soil depth, and tended to decrease with increasing soil depth. Co-occurrence network analyses showed that the keystone species in Takeermohuer Desert were Actinobacteria, Acidobacteria, Proteobacteria, and Chlorofexi. Furthermore, the major environmental factors affecting rhizosphere bacterial community were EC (electrical conductivity), SOM, STN (soil total nitrogen), SAN, and SAK (soil available potassium), while bulk soil were distance and C/N (STC/STN). We concluded that A. bifolium rhizosphere bacterial community is different from non-rhizosphere in composition, distribution, and environmental influencing factors, which will have important significances for understanding their ecological functions and maintaining biodiversity.}, }
@article {pmid37300728, year = {2023}, author = {Wasmund, K and Trueba-Santiso, A and Vicent, T and Adrian, L and Vuilleumier, S and Marco-Urrea, E}, title = {Proteogenomics of the novel Dehalobacterium formicoaceticum strain EZ94 highlights a key role of methyltransferases during anaerobic dichloromethane degradation.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {33}, pages = {80602-80612}, pmid = {37300728}, issn = {1614-7499}, support = {CTM2016-75587-C2-1-R//Agencia Estatal de Investigaci&#xf3;n/ ; PID2019-103989RB-100//Agencia Estatal de Investigaci&#xf3;n/ ; BES-2014-070817//Ministerio de Econom&#xed;a y Competitividad/ ; ANR-17-CE07-0009//Agence Nationale de la Recherche/ ; }, mesh = {Proteome/metabolism ; Anaerobiosis ; *Proteogenomics ; Peptococcaceae ; Methylene Chloride ; Biodegradation, Environmental ; Methyltransferases/metabolism ; }, abstract = {Dichloromethane (DCM, methylene chloride) is a toxic, high-volume industrial pollutant of long-standing. Anaerobic biodegradation is crucial for its removal from contaminated environments, yet prevailing mechanisms remain unresolved, especially concerning dehalogenation. In this study, we obtained an assembled genome of a novel DCM-degrading strain, Dehalobacterium formicoaceticum strain EZ94, from a stable DCM-degrading consortium, and we analyzed its proteome during degradation of DCM. A gene cluster recently predicted to play a major role in anaerobic DCM catabolism (the mec cassette) was found. Methyltransferases and other proteins encoded by the mec cassette were among the most abundant proteins produced, suggesting their involvement in DCM catabolism. Reductive dehalogenases were not detected. Genes and corresponding proteins for a complete Wood-Ljungdahl pathway, which could enable further metabolism of DCM carbon, were also found. Unlike for the anaerobic DCM degrader "Ca. F. warabiya," no genes for metabolism of the quaternary amines choline and glycine betaine were identified. This work provides independent and supporting evidence that mec-associated methyltransferases are key to anaerobic DCM metabolism.}, }
@article {pmid37296446, year = {2023}, author = {Peral-Aranega, E and Saati-Santamaría, Z and Ayuso-Calles, M and Kostovčík, M and Veselská, T and Švec, K and Rivas, R and Kolařik, M and García-Fraile, P}, title = {New insight into the bark beetle ips typographus bacteriome reveals unexplored diversity potentially beneficial to the host.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {53}, pmid = {37296446}, issn = {2524-6372}, support = {19-09072S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; }, abstract = {BACKGROUND: Ips typographus (European spruce bark beetle) is the most destructive pest of spruce forests in Europe. As for other animals, it has been proposed that the microbiome plays important roles in the biology of bark beetles. About the bacteriome, there still are many uncertainties regarding the taxonomical composition, insect-bacteriome interactions, and their potential roles in the beetle ecology. Here, we aim to deep into the ecological functions and taxonomical composition of I. typographus associated bacteria.<br><br>RESULTS: We assessed the metabolic potential of a collection of isolates obtained from different life stages of I. typographus beetles. All strains showed the capacity to hydrolyse one or more complex polysaccharides into simpler molecules, which may provide an additional carbon source to its host. Also, 83.9% of the strains isolated showed antagonistic effect against one or more entomopathogenic fungi, which could assist the beetle in its fight against this pathogenic threat. Using culture-dependent and -independent techniques, we present a taxonomical analysis of the bacteriome associated with the I. typographus beetle during its different life stages. We have observed an evolution of its bacteriome, which is diverse at the larval phase, substantially diminished in pupae, greater in the teneral adult phase, and similar to that of the larval stage in mature adults. Our results suggest that taxa belonging to the Erwiniaceae family, and the Pseudoxanthomonas and Pseudomonas genera, as well as an undescribed genus within the Enterobactereaceae family, are part of the core microbiome and may perform vital roles in maintaining beetle fitness.<br><br>CONCLUSION: Our results indicate that isolates within the bacteriome of I. typographus beetle have the metabolic potential to increase beetle fitness by proving additional and assimilable carbon sources for the beetle, and by antagonizing fungi entomopathogens. Furthermore, we observed that isolates from adult beetles are more likely to have these capacities but those obtained from larvae showed strongest antifungal activity. Our taxonomical analysis showed that Erwinia typographi, Pseudomonas bohemica, and Pseudomonas typographi species along with Pseudoxanthomonas genus, and putative new taxa belonging to the Erwiniaceae and Enterobacterales group are repeatedly present within the bacteriome of I. typographus beetles, indicating that these species might be part of the core microbiome. In addition to Pseudomonas and Erwinia group, Staphylococcus, Acinetobacter, Curtobacterium, Streptomyces, and Bacillus genera seem to also have interesting metabolic capacities but are present in a lower frequency. Future studies involving bacterial-insect interactions or analysing other potential roles would provide more insights into the bacteriome capacity to be beneficial to the beetle.}, }
@article {pmid37296336, year = {2023}, author = {Yu, T and Nie, J and Zang, H and Zeng, Z and Yang, Y}, title = {Peanut-based Rotation Stabilized Diazotrophic Communities and Increased Subsequent Wheat Yield.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2447-2460}, pmid = {37296336}, issn = {1432-184X}, support = {2016YFD0300205-01//National Key Research and Development Program of China/ ; 31901470//National Natural Science Foundation of China/ ; }, mesh = {*Agriculture/methods ; Arachis ; Triticum ; Soil/chemistry ; *Fabaceae ; Nitrogen/analysis ; }, abstract = {The introduction of legumes into rotations can improve nitrogen use efficiency and crop yield; however, its microbial mechanism involved remains unclear. This study aimed to explore the temporal impact of peanut introduction on microorganisms related to nitrogen metabolism in rotation systems. In this study, the dynamics of diazotrophic communities in two crop seasons and wheat yields of two rotation systems: winter wheat - summer maize (WM) and spring peanut → winter wheat - summer maize (PWM) in the North China Plain were investigated. Our results showed that peanut introduction increased wheat yield and biomass by 11.6% (p < 0.05) and 8.9%, respectively. Lower Chao1 and Shannon indexes of the diazotrophic communities were detected in soils that sampling in June compared with those sampling in September, although no difference was found between WM and PWM. Principal co-ordinates analysis (PCoA) showed that rotation system significantly changed the diazotrophic community structures (PERMANOVA; p < 0.05). Compared with WM, the genera of Azotobacter, Skermanella, Azohydromonas, Rhodomicrobium, Azospirillum, Unclassified_f_Opitutaceae, and Unclassified_f_Rhodospirillaceae were significantly enriched (p < 0.05) in PWM. Furthermore, rotation system and sampling time significantly influenced soil properties, which significantly correlated with the top 15 genera in relative abundance. Partial least squares path modeling (PLS-PM) analysis further showed that the diazotrophic community diversity (alpha- and beta-diversity) and soil properties (pH, SOC and TN) significantly affected wheat yield. In conclusion, legume inclusion has the potential to stabilize diazotrophic community structure at the temporal scales and increase subsequent crop yield.}, }
@article {pmid37294090, year = {2023}, author = {Upadhyay, V and Suryawanshi, RK and Tasoff, P and McCavitt-Malvido, M and Kumar, RG and Murray, VW and Noecker, C and Bisanz, JE and Hswen, Y and Ha, CWY and Sreekumar, B and Chen, IP and Lynch, SV and Ott, M and Lee, S and Turnbaugh, PJ}, title = {Mild SARS-CoV-2 infection results in long-lasting microbiota instability.}, journal = {mBio}, volume = {14}, number = {4}, pages = {e0088923}, pmid = {37294090}, issn = {2150-7511}, support = {K08 HL165106/HL/NHLBI NIH HHS/United States ; R01 DK114034/DK/NIDDK NIH HHS/United States ; R01 AT011117/AT/NCCIH NIH HHS/United States ; F31 AI164671/AI/NIAID NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; R01 AR074500/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; Mice ; Mice, Inbred C57BL ; SARS-CoV-2 ; *COVID-19 ; *Microbiota ; Mammals ; }, abstract = {Viruses targeting mammalian cells can indirectly alter the gut microbiota, potentially compounding their phenotypic effects. Multiple studies have observed a disrupted gut microbiota in severe cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection that require hospitalization. Yet, despite demographic shifts in disease severity resulting in a large and continuing burden of non-hospitalized infections, we still know very little about the impact of mild SARS-CoV-2 infection on the gut microbiota in the outpatient setting. To address this knowledge gap, we longitudinally sampled 14 SARS-CoV-2-positive subjects who remained outpatient and 4 household controls. SARS-CoV-2 cases exhibited a significantly less stable gut microbiota relative to controls. These results were confirmed and extended in the K18-humanized angiotensin-converting enzyme 2 mouse model, which is susceptible to SARS-CoV-2 infection. All of the tested SARS-CoV-2 variants significantly disrupted the mouse gut microbiota, including USA-WA1/2020 (the original variant detected in the USA), Delta, and Omicron. Surprisingly, despite the fact that the Omicron variant caused the least severe symptoms in mice, it destabilized the gut microbiota and led to a significant depletion in Akkermansia muciniphila. Furthermore, exposure of wild-type C57BL/6J mice to SARS-CoV-2 disrupted the gut microbiota in the absence of severe lung pathology. IMPORTANCE Taken together, our results demonstrate that even mild cases of SARS-CoV-2 can disrupt gut microbial ecology. Our findings in non-hospitalized individuals are consistent with studies of hospitalized patients, in that reproducible shifts in gut microbial taxonomic abundance in response to SARS-CoV-2 have been difficult to identify. Instead, we report a long-lasting instability in the gut microbiota. Surprisingly, our mouse experiments revealed an impact of the Omicron variant, despite producing the least severe symptoms in genetically susceptible mice, suggesting that despite the continued evolution of SARS-CoV-2, it has retained its ability to perturb the intestinal mucosa. These results will hopefully renew efforts to study the mechanisms through which Omicron and future SARS-CoV-2 variants alter gastrointestinal physiology, while also considering the potentially broad consequences of SARS-CoV-2-induced microbiota instability for host health and disease.}, }
@article {pmid37293832, year = {2023}, author = {Mortier, C and Quintelier, K and De Craemer, AS and Renson, T and Deroo, L and Dumas, E and Verheugen, E and Coudenys, J and Decruy, T and Lukasik, Z and Van Gassen, S and Saeys, Y and Hoorens, A and Lobatón, T and Van den Bosch, F and Van de Wiele, T and Venken, K and Elewaut, D}, title = {Gut Inflammation in Axial Spondyloarthritis Patients is Characterized by a Marked Type 17 Skewed Mucosal Innate-like T Cell Signature.}, journal = {Arthritis &amp; rheumatology (Hoboken, N.J.)}, volume = {75}, number = {11}, pages = {1969-1982}, doi = {10.1002/art.42627}, pmid = {37293832}, issn = {2326-5205}, mesh = {Humans ; Interleukin-17/metabolism ; Nuclear Receptor Subfamily 1, Group F, Member 3 ; Leukocytes, Mononuclear/metabolism ; Inflammation/metabolism ; *Spondylarthritis/metabolism ; *Spondylitis, Ankylosing ; Mucous Membrane/metabolism ; }, abstract = {OBJECTIVE: Patients with spondyloarthritis (SpA) often present with microscopic signs of gut inflammation, a risk factor for progressive disease. We investigated whether mucosal innate-like T cells are involved in dysregulated interleukin-23 (IL-23)/IL-17 responses in the gut-joint axis in SpA.<br><br>METHODS: Ileal and colonic intraepithelial lymphocytes (IELs), lamina propria lymphocytes (LPLs), and paired peripheral blood mononuclear cells (PBMCs) were isolated from treatment-naive patients with nonradiographic axial SpA with (n&#xa0;=&#xa0;11) and without (n&#xa0;=&#xa0;14) microscopic gut inflammation and healthy controls (n&#xa0;=&#xa0;15) undergoing ileocolonoscopy. The presence of gut inflammation was assessed histopathologically. Immunophenotyping of innate-like T cells and conventional T cells was performed using intracellular flow cytometry. Unsupervised clustering analysis was done by FlowSOM technology. Serum IL-17A levels were measured via Luminex.<br><br>RESULTS: Microscopic gut inflammation in nonradiographic axial SpA was characterized by increased ileal intraepithelial &#x3b3;&#x3b4;-hi T cells, a &#x3b3;&#x3b4;-T cell subset with elevated &#x3b3;&#x3b4;-T cell receptor expression. &#x3b3;&#x3b4;-hi T cells&#xa0;were also increased in PBMCs of patients with nonradiographic axial SpA versus healthy controls and were strongly associated with Ankylosing Spondylitis Disease Activity Score. The abundance of mucosal-associated invariant T cells and invariant natural killer T cells was unaltered. Innate-like T cells in the inflamed gut showed increased ROR&#x3b3;t, IL-17A, and IL-22 levels with loss of T-bet, a signature that was less pronounced in conventional T cells. Presence of gut inflammation was associated with higher serum IL-17A levels. In patients treated with tumor necrosis factor blockade, the proportion of &#x3b3;&#x3b4;-hi cells and ROR&#x3b3;t expression in blood was completely restored.<br><br>CONCLUSION: Intestinal innate-like T cells display marked type 17 skewing in the inflamed gut mucosa of patients with nonradiographic axial SpA. &#x3b3;&#x3b4;-hi T cells are linked to intestinal inflammation and disease activity in SpA.}, }
@article {pmid37291701, year = {2023}, author = {Suarez, C and Hackl, T and Wilen, BM and Persson, F and Hagelia, P and Jetten, MSM and Dalcin Martins, P}, title = {Novel and unusual genes for nitrogen and metal cycling in Planctomycetota- and KSB1-affiliated metagenome-assembled genomes reconstructed from a marine subsea tunnel.}, journal = {FEMS microbiology letters}, volume = {370}, number = {}, pages = {}, pmid = {37291701}, issn = {1574-6968}, mesh = {*Metagenome ; *Planctomycetes ; Nitrogen ; RNA, Ribosomal, 16S/genetics ; Manganese ; Iron ; Oxidation-Reduction ; }, abstract = {The Oslofjord subsea road tunnel is a unique environment in which the typically anoxic marine deep subsurface is exposed to oxygen. Concrete biodeterioration and steel corrosion in the tunnel have been linked to the growth of iron- and manganese-oxidizing biofilms in areas of saline water seepage. Surprisingly, previous 16S rRNA gene surveys of biofilm samples revealed microbial communities dominated by sequences affiliated with nitrogen-cycling microorganisms. This study aimed to identify microbial genomes with metabolic potential for novel nitrogen- and metal-cycling reactions, representing biofilm microorganisms that could link these cycles and play a role in concrete biodeterioration. We reconstructed 33 abundant, novel metagenome-assembled genomes (MAGs) affiliated with the phylum Planctomycetota and the candidate phylum KSB1. We identified novel and unusual genes and gene clusters in these MAGs related to anaerobic ammonium oxidation, nitrite oxidation, and other nitrogen-cycling reactions. Additionally, 26 of 33 MAGs also had the potential for iron, manganese, and arsenite cycling, suggesting that bacteria represented by these genomes might couple these reactions. Our results expand the diversity of microorganisms putatively involved in nitrogen and metal cycling, and contribute to our understanding of potential biofilm impacts on built infrastructure.}, }
@article {pmid37287124, year = {2023}, author = {Klein-Gordon, JM and Johnson, KB and Loper, JE and Stockwell, VO}, title = {Contribution of Native Plasmids of Pantoea vagans C9-1 to Epiphytic Fitness and Fire Blight Management on Apple and Pear Flowers and Fruits.}, journal = {Phytopathology}, volume = {113}, number = {12}, pages = {2187-2196}, doi = {10.1094/PHYTO-04-23-0144-SA}, pmid = {37287124}, issn = {0031-949X}, mesh = {*Malus/microbiology ; Fruit ; *Pantoea/genetics ; *Pyrus/microbiology ; Plant Diseases/prevention &amp; control/microbiology ; Plasmids ; *Erwinia amylovora/genetics ; Flowers/microbiology ; }, abstract = {Pantoea vagans C9-1 (C9-1) is a biological control bacterium that is applied to apple and pear trees during bloom for suppression of fire blight, caused by Erwinia amylovora. Strain C9-1 has three megaplasmids: pPag1, pPag2, and pPag3. Prior bioinformatic studies predicted these megaplasmids have a role in environmental fitness and/or biocontrol efficacy. Plasmid pPag3 is part of the large Pantoea plasmid (LPP-1) group that is present in all Pantoea spp. and has been hypothesized to contribute to environmental colonization and persistence, while pPag2 is less common. We assessed fitness of C9-1 derivatives cured of pPag2 and/or pPag3 on pear and apple flowers and fruit in experimental orchards. We also assessed the ability of a C9-1 derivative lacking pPag3 to reduce populations of E. amylovora on flowers and disease incidence. Previously, we determined that tolerance to stresses imposed in vitro was compromised in derivatives of C9-1 lacking pPag2 and/or pPag3; however, in this study, the loss of pPag2 and/or pPag3 did not consistently reduce the fitness of C9-1 on flowers in orchards. Over the summer, pPag3 contributed to survival of C9-1 on developing apple and pear fruit in two of five trials, whereas loss of pPag2 did not significantly affect survival of C9-1. We also found that loss of pPag3 did not affect C9-1's ability to reduce E. amylovora populations or fire blight incidence on apple flowers. Our findings partially support prior hypotheses that LPP-1 in Pantoea species contributes to persistence on plant surfaces but questions whether LPP-1 facilitates host colonization.}, }
@article {pmid37286586, year = {2023}, author = {Leung, H and Xiong, L and Ni, Y and Busch, A and Bauer, M and Press, AT and Panagiotou, G}, title = {Impaired flux of bile acids from the liver to the gut reveals microbiome-immune interactions associated with liver damage.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {35}, pmid = {37286586}, issn = {2055-5008}, mesh = {Mice ; Animals ; Bile Acids and Salts ; Ecosystem ; *Cholestasis/complications/pathology ; *Liver Diseases/complications ; Cytokines ; *Gastrointestinal Microbiome ; }, abstract = {Currently, there is evidence that alteration in the gut ecosystem contributes to the development of liver diseases, however, the complex mechanisms involved are still unclear. We induced cholestasis in mice by bile duct ligation (BDL), mirroring the phenotype of a bile duct obstruction, to understand how gut microbiota alterations caused by an impaired flow of bile acid to the gut contribute to the pathogenesis and progression of liver disease. We performed longitudinal stool, heart, and liver sampling using mice receiving BDL and controls receiving sham operation (ShamOP). Shotgun metagenomics profiling using fecal samples taken before and on day 1, day 3, and day 7 after surgery was performed, and the cytokines and clinical chemistry profiles from heart blood, as well as the liver bile acids profile, were measured. The BDL surgery reshaped the microbiome of mice, resulting in highly distinct characteristics compared to the ShamOP. Our analysis of the microbiome pathways and ECs revealed that BDL reduces the production of hepatoprotective compounds in the gut, such as biotin, spermidine, arginine, and ornithine, which were negatively associated with inflammatory cytokines (IL-6, IL-23, MCP-1). The reduction of the functional potential of the gut microbiota in producing those hepatoprotective compounds is associated with the decrease of beneficial bacteria species from Anaerotruncus, Blautia, Eubacterium, and Lachnoclostridium genera, as well as the increase of disease-associated bacteria e.g., Escherichia coli and Entercoccus faecalis. Our findings advances our knowledge of the gut microbiome-bile acids-liver triangle, which may serve as a potential therapeutic strategy for liver diseases.}, }
@article {pmid37285553, year = {2023}, author = {McKinlay, JB}, title = {Are Bacteria Leaky? Mechanisms of Metabolite Externalization in Bacterial Cross-Feeding.}, journal = {Annual review of microbiology}, volume = {77}, number = {}, pages = {277-297}, doi = {10.1146/annurev-micro-032521-023815}, pmid = {37285553}, issn = {1545-3251}, mesh = {*Bacteria ; Homeostasis ; }, abstract = {The metabolism of a bacterial cell stretches beyond its boundaries, often connecting with the metabolism of other cells to form extended metabolic networks that stretch across communities, and even the globe. Among the least intuitive metabolic connections are those involving cross-feeding of canonically intracellular metabolites. How and why are these intracellular metabolites externalized? Are bacteria simply leaky? Here I consider what it means for a bacterium to be leaky, and I review mechanisms of metabolite externalization from the context of cross-feeding. Despite common claims, diffusion of most intracellular metabolites across a membrane is unlikely. Instead, passive and active transporters are likely involved, possibly purging excess metabolites as part of homeostasis. Re-acquisition of metabolites by a producer limits the opportunities for cross-feeding. However, a competitive recipient can stimulate metabolite externalization and initiate a positive-feedback loop of reciprocal cross-feeding.}, }
@article {pmid37285121, year = {2023}, author = {Tran, PQ and Bachand, SC and Hotvedt, JC and Kieft, K and McDaniel, EA and McMahon, KD and Anantharaman, K}, title = {Physiological and genomic evidence of cysteine degradation and aerobic hydrogen sulfide production in freshwater bacteria.}, journal = {mSystems}, volume = {8}, number = {3}, pages = {e0020123}, pmid = {37285121}, issn = {2379-5077}, support = {Hatch project 1025641//U.S. Department of Agriculture (USDA)/ ; CSP 394//Joint Genome Institute (JGI)/ ; //Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; }, mesh = {*Hydrogen Sulfide/metabolism ; Cysteine/metabolism ; Ecosystem ; Sulfides/metabolism ; Bacteria/genetics ; Sulfur/metabolism ; Lakes/microbiology ; Oxygen/metabolism ; Genomics ; }, abstract = {The sulfur-containing amino acid cysteine is abundant in the environment, including in freshwater lakes. Biological cysteine degradation can result in hydrogen sulfide (H2S), a toxic and ecologically relevant compound that is a central player in biogeochemical cycling in aquatic environments. Here, we investigated the ecological significance of cysteine in oxic freshwater, using isolated cultures, controlled experiments, and multiomics. We screened bacterial isolates enriched from natural lake water for their ability to produce H2S when provided cysteine. We identified 29 isolates (Bacteroidota, Proteobacteria, and Actinobacteria) that produced H2S. To understand the genomic and genetic basis for cysteine degradation and H2S production, we further characterized three isolates using whole-genome sequencing (using a combination of short-read and long-read sequencing) and tracked cysteine and H2S levels over their growth ranges: Stenotrophomonas maltophilia (Gammaproteobacteria), S. bentonitica (Gammaproteobacteria), and Chryseobacterium piscium (Bacteroidota). Cysteine decreased and H2S increased, and all three genomes had genes involved in cysteine degradation. Finally, to assess the presence of these organisms and genes in the environment, we surveyed a 5-year time series of metagenomic data from the same isolation source (Lake Mendota, Madison, WI, USA) and identified their presence throughout the time series. Overall, our study shows that diverse isolated bacterial strains can use cysteine and produce H2S under oxic conditions, and we show evidence using metagenomic data that this process may occur more broadly in natural freshwater lakes. Future considerations of sulfur cycling and biogeochemistry in oxic environments should account for H2S production from the degradation of organosulfur compounds. IMPORTANCE Hydrogen sulfide (H2S), a naturally occurring gas with both biological and abiotic origins, can be toxic to living organisms. In aquatic environments, H2S production typically originates from anoxic (lacking oxygen) environments, such as sediments, or the bottom layers of thermally stratified lakes. However, the degradation of sulfur-containing amino acids such as cysteine, which all cells and life forms rely on, can be a source of ammonia and H2S in the environment. Unlike other approaches for biological H2S production such as dissimilatory sulfate reduction, cysteine degradation can occur in the presence of oxygen. Yet, little is known about how cysteine degradation influences sulfur availability and cycling in freshwater lakes. In our study, we identified diverse bacteria from a freshwater lake that can produce H2S in the presence of O2. Our study highlights the ecological importance of oxic H2S production in natural ecosystems and necessitates a change in our outlook on sulfur biogeochemistry.}, }
@article {pmid37283549, year = {2023}, author = {Oba, PM and Carroll, MQ and Sieja, KM and Yang, X and Epp, TY and Warzecha, CM and Varney, JL and Fowler, JW and Coon, CN and Swanson, KS}, title = {Effects of a Saccharomyces cerevisiae fermentation product on fecal characteristics, metabolite concentrations, and microbiota populations of dogs undergoing transport stress.}, journal = {Journal of animal science}, volume = {101}, number = {}, pages = {}, pmid = {37283549}, issn = {1525-3163}, mesh = {Dogs ; Female ; Male ; Animals ; *Saccharomyces cerevisiae/metabolism ; Fermentation ; Diet/veterinary ; Dietary Supplements/analysis ; Feces/microbiology ; *Microbiota ; Bacteria ; Animal Feed/analysis ; }, abstract = {Previously, a Saccharomyces cerevisiae fermentation product (SCFP) positively altered fecal microbiota, fecal metabolites, and immune cell function of adult dogs. Our objective was to determine the fecal characteristics, microbiota, and metabolites of SCFP-supplemented dogs subjected to transport stress. All procedures were approved by the Four Rivers Kennel IACUC prior to experimentation. Thirty-six adult dogs (18 male, 18 female; age: 7.1 ± 0.77 yr; body weight: 28.97 ± 3.67 kg) were randomly assigned to be controls or receive SCFP supplementation (250 mg/dog/d) (N = 18/group) for 11 wk. At that time, fresh fecal samples were collected before and after transport in a hunting dog trailer with individual kennels. The trailer was driven 40 miles round trip for about 45 min. Fecal microbiota data were evaluated using Quantitative Insights Into Microbial Ecology 2, while all other data were analyzed using the Mixed Models procedure of Statistical Analysis System. Effects of treatment, transport, and treatment × transport were tested, with P < 0.05 being considered significant. Transport stress increased fecal indole concentrations and relative abundances of fecal Actinobacteria, Collinsella, Slackia, Ruminococcus, and Eubacterium. In contrast, relative abundances of fecal Fusobacteria, Streptococcus, and Fusobacterium were reduced by transport. Fecal characteristics, metabolites, and bacterial alpha and beta diversity measures were not affected by diet alone. Several diet × transport interactions were significant, however. Following transport, relative abundance of fecal Turicibacter increased in SCFP-supplemented dogs, but decreased in controls. Following transport, relative abundances of fecal Proteobacteria, Bacteroidetes, Prevotella, and Sutterella increased in controls, but not in SCFP-supplemented dogs. In contrast, relative abundances of fecal Firmicutes, Clostridium, Faecalibacterium, and Allobaculum increased and fecal Parabacteroides and Phascolarctobacterium decreased after transport stress in SCFP-supplemented dogs, but not in controls. Our data demonstrate that both transport stress and SCFP alter fecal microbiota in dogs, with transport being the primary cause for shifts. SCFP supplementation may provide benefits to dogs undergoing transport stress, but more research is necessary to determine proper dosages. More research is also necessary to determine if and how transport stress impacts gastrointestinal microbiota and other indicators of health.}, }
@article {pmid37280438, year = {2023}, author = {Ndour, PMS and Bargaz, A and Rchiad, Z and Pawlett, M and Clark, IM and Mauchline, TH and Harris, J and Lyamlouli, K}, title = {Microbial Catabolic Activity: Methods, Pertinence, and Potential Interest for Improving Microbial Inoculant Efficiency.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2211-2230}, pmid = {37280438}, issn = {1432-184X}, mesh = {*Soil/chemistry ; *Agricultural Inoculants ; Carbon ; Agriculture/methods ; Soil Microbiology ; }, abstract = {Microbial catabolic activity (MCA) defined as the degrading activity of microorganisms toward various organic compounds for their growth and energy is commonly used to assess soil microbial function potential. For its measure, several methods are available including multi-substrate-induced respiration (MSIR) measurement which allow to estimate functional diversity using selected carbon substrates targeting specific biochemical pathways. In this review, the techniques used to measure soil MCA are described and compared with respect to their accuracy and practical use. Particularly the efficiency of MSIR-based approaches as soil microbial function indicators was discussed by (i) showing their sensitivity to different agricultural practices including tillage, amendments, and cropping systems and (ii) by investigating their relationship with soil enzyme activities and some soil chemical properties (pH, soil organic carbon, cation exchange capacity). We highlighted the potential of these MSIR-based MCA measurements to improve microbial inoculant composition and to determine their potential effects on soil microbial functions. Finally, we have proposed ideas for improving MCA measurement notably through the use of molecular tools and stable isotope probing which can be combined with classic MSIR methods. Graphical abstract describing the interrelation between the different parts and the concepts developed in the review.}, }
@article {pmid37280212, year = {2023}, author = {Weyhenmeyer, GA and Obertegger, U and Rudebeck, H and Jakobsson, E and Jansen, J and Zdorovennova, G and Bansal, S and Block, BD and Carey, CC and Doubek, JP and Dugan, H and Erina, O and Fedorova, I and Fischer, JM and Grinberga, L and Grossart, HP and Kangur, K and Knoll, LB and Laas, A and Lepori, F and Meier, J and Palshin, N and Peternell, M and Pulkkanen, M and Rusak, JA and Sharma, S and Wain, D and Zdorovennov, R}, title = {Author Correction: Towards critical white ice conditions in lakes under global warming.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3283}, doi = {10.1038/s41467-023-39005-3}, pmid = {37280212}, issn = {2041-1723}, }
@article {pmid37280177, year = {2023}, author = {Gralka, M}, title = {Searching for Principles of Microbial Ecology Across Levels of Biological Organization.}, journal = {Integrative and comparative biology}, volume = {63}, number = {6}, pages = {1520-1531}, pmid = {37280177}, issn = {1557-7023}, mesh = {Animals ; *Ecosystem ; *Microbiota ; Ecology ; }, abstract = {Microbial communities play pivotal roles in ecosystems across different scales, from global elemental cycles to household food fermentations. These complex assemblies comprise hundreds or thousands of microbial species whose abundances vary over time and space. Unraveling the principles that guide their dynamics at different levels of biological organization, from individual species, their interactions, to complex microbial communities, is a major challenge. To what extent are these different levels of organization governed by separate principles, and how can we connect these levels to develop predictive models for the dynamics and function of microbial communities? Here, we will discuss recent advances that point towards principles of microbial communities, rooted in various disciplines from physics, biochemistry, and dynamical systems. By considering the marine carbon cycle as a concrete example, we demonstrate how the integration of levels of biological organization can offer deeper insights into the impact of increasing temperatures, such as those associated with climate change, on ecosystem-scale processes. We argue that by focusing on principles that transcend specific microbiomes, we can pave the way for a comprehensive understanding of microbial community dynamics and the development of predictive models for diverse ecosystems.}, }
@article {pmid37279442, year = {2023}, author = {Suzzi, AL and Stat, M and Gaston, TF and Huggett, MJ}, title = {Spatial patterns in host-associated and free-living bacterial communities across six temperate estuaries.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {7}, pages = {}, pmid = {37279442}, issn = {1574-6941}, mesh = {Animals ; *Estuaries ; Australia ; Bacteria/genetics ; Seawater/microbiology ; *Microbiota ; }, abstract = {A major goal of microbial ecology is to establish the importance of spatial and environmental factors in driving community variation. Their relative importance likely varies across spatial scales, but focus has primarily been on free-living communities within well-connected aquatic environments rather than less connected island-like habitats such as estuaries, and key host-associated communities within these systems. Here we sampled both free-living (seawater and sediment) and host-associated (estuarine fish hindgut microbiome, Pelates sexlineatus) communities across six temperate Australian estuaries spanning ∼500 km. We find that spatial and environmental factors have different influences on these communities, with seawater demonstrating strong distance-decay relationships (R = -0.69) and significant associations with a range of environmental variables. Distance-decay relationships were weak for sediment communities but became stronger over smaller spatial scales (within estuaries, R = -0.5), potentially reflecting environmental filtering across biogeochemical gradients or stochastic processes within estuary sediments. Finally, P. sexlineatus hindgut microbiome communities displayed weak distance-decay relationships (R = -0.36), and limited variation explained by environmental variables, indicating the significance of host-related factors in driving community variation. Our findings provide important ecological insights into the spatial distributions and driving forces of both free-living and host-associated bacterial patterns across temperate estuarine systems.}, }
@article {pmid37278908, year = {2023}, author = {Gao, H and Wu, M and Liu, H and Ou, Y and Zhang, T and Duan, X}, title = {Unraveling the Positive Effect of Soil Moisture on the Bioaugmentation of Petroleum-Contaminated Soil Using Bioinformatics.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2436-2446}, pmid = {37278908}, issn = {1432-184X}, mesh = {*Petroleum ; Soil/chemistry ; *Soil Pollutants/analysis ; Soil Microbiology ; Biodegradation, Environmental ; Hydrocarbons/metabolism ; Bacteria/genetics/metabolism ; Computational Biology ; }, abstract = {Petroleum contamination is a severe threat to the soil environment. Previous studies have demonstrated that petroleum degradation efficiency is promoted by enhancing soil moisture content (MC). However, the effects of MC on soil microbial ecological functions during bioremediation remain unclear. Here, we investigated the impacts of 5% and 15% of moisture contents on petroleum degradation, soil microbial structures and functions, and the related genes using high-throughput sequencing and gene function prediction. Results indicated that petroleum biodegradation efficiency was increased by 8.06% in the soils with 15% MC when compared to that with 5% of MC. The complexity and stability of soil microbial community structures with 15% MC were higher than those in the soils with 5% MC when hydrocarbon-degrading bacterial flora (HDBF) were inoculated into the soils. Fifteen percent of moisture content strengthened the interaction of the bacterial community network and reduced the loss of some key bacteria species including Mycobacterium, Sphingomonas, and Gemmatimonas. Some downregulated gene pathways relating to bioaugmentation were enhanced in the soils with 15% MC. The results suggested that the dynamic balances of microbial communities and the metabolic interactions by 15% MC treatment are the driving forces for the enhancement of bioremediation in petroleum-contaminated soil.}, }
@article {pmid37278524, year = {2023}, author = {Dedrick, S and Warrier, V and Lemon, KP and Momeni, B}, title = {When does a Lotka-Volterra model represent microbial interactions? Insights from in vitro nasal bacterial communities.}, journal = {mSystems}, volume = {8}, number = {3}, pages = {e0075722}, pmid = {37278524}, issn = {2379-5077}, support = {R35 GM141806/GM/NIGMS NIH HHS/United States ; R01 GM117174/GM/NIGMS NIH HHS/United States ; T32 HL007427/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; Microbial Interactions ; Models, Theoretical ; Models, Biological ; Bacteria ; }, abstract = {To alter microbial community composition for therapeutic purposes, an accurate and reliable modeling framework capable of predicting microbial community outcomes is required. Lotka-Volterra (LV) equations have been utilized to describe a breadth of microbial communities, yet, the conditions in which this modeling framework is successful remain unclear. Here, we propose that a set of simple in vitro experiments-growing each member in cell-free spent medium obtained from other members-can be used as a test to decide whether an LV model is appropriate for describing microbial interactions of interest. We show that for LV to be a good candidate, the ratio of growth rate to carrying capacity of each isolate when grown in the cell-free spent media of other isolates should remain constant. Using an in vitro community of human nasal bacteria as a tractable system, we find that LV can be a good approximation when the environment is low-nutrient (i.e., when growth is limited by the availability of nutrients) and complex (i.e., when multiple resources, rather than a few, determine growth). These findings can help clarify the range of applicability of LV models and reveal when a more complex model may be necessary for predictive modeling of microbial communities. IMPORTANCE Although mathematical modeling can be a powerful tool to draw useful insights in microbial ecology, it is crucial to know when a simplified model adequately represents the interactions of interest. Here, we take advantage of bacterial isolates from the human nasal passages as a tractable model system and conclude that the commonly used Lotka-Volterra model can represent interactions among microbes well when the environment is complex (with many interaction mediators) and low-nutrient. Our work highlights the importance of considering both realism and simplicity when choosing a model to represent microbial interactions.}, }
@article {pmid37278360, year = {2023}, author = {Zayed, N and Ghesquière, J and Kamarudin, NHN and Bernaerts, K and Boon, N and Braem, A and Van Holm, W and Teughels, W}, title = {Oral Biofilm Cryotherapy as a Novel Ecological Modulation Approach.}, journal = {Journal of dental research}, volume = {102}, number = {9}, pages = {1038-1046}, doi = {10.1177/00220345231172688}, pmid = {37278360}, issn = {1544-0591}, mesh = {*Anti-Infective Agents ; Bacterial Load ; Biofilms ; Cryotherapy ; }, abstract = {Oral cryotherapy is used in dentistry as a safe, simple, and low-cost treatment for a variety of oral lesions. It is well known for its ability to aid in the healing process. However, its effect on oral biofilms is unknown. As a result, the purpose of this study was to assess the effects of cryotherapy on in vitro oral biofilms. In vitro multispecies oral biofilms were grown on the surface of hydroxyapatite discs in symbiotic or dysbiotic states. CryoPen X+ was used to treat the biofilms, whereas untreated biofilms served as control. One set of biofilms was collected for study immediately after cryotherapy, whereas another group was reincubated for 24 h to permit biofilm recovery. Changes in biofilm structure were analyzed with a confocal laser scanning microscope (CLSM) and a scanning electron microscope (SEM), while biofilm ecology and community compositional changes were analyzed with viability DNA extraction and quantitative polymerase chain reaction (v-qPCR) analysis. One cryo-cycle immediately reduced biofilm load by 0.2 to 0.4 log10 Geq/mL, which increased with additional treatment cycles. Although the bacterial load of the treated biofilms recovered to the same level as the control biofilms within 24 h, the CLSM detected structural alterations. Compositional alterations were also detected by SEM, corroborating the v-qPCR findings that showed ≈≤10% incidence of pathogenic species compared to nontreated biofilms that encompassed ≈45% and 13% pathogenic species in dysbiotic and symbiotic biofilms, respectively. Spray cryotherapy showed promising results in a novel conceptual approach to the control of oral biofilms. Acting selectively by targeting oral pathobionts and retaining commensals, spray cryotherapy could modify the ecology of in vitro oral biofilms to become more symbiotic and prevent the evolution of dysbiosis without the use of antiseptics/antimicrobials.}, }
@article {pmid37275175, year = {2023}, author = {Timmusk, S and Pall, T and Raz, S and Fetsiukh, A and Nevo, E}, title = {The potential for plant growth-promoting bacteria to impact crop productivity in future agricultural systems is linked to understanding the principles of microbial ecology.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1141862}, pmid = {37275175}, issn = {1664-302X}, abstract = {Global climate change poses challenges to land use worldwide, and we need to reconsider agricultural practices. While it is generally accepted that biodiversity can be used as a biomarker for healthy agroecosystems, we must specify what specifically composes a healthy microbiome. Therefore, understanding how holobionts function in native, harsh, and wild habitats and how rhizobacteria mediate plant and ecosystem biodiversity in the systems enables us to identify key factors for plant fitness. A systems approach to engineering microbial communities by connecting host phenotype adaptive traits would help us understand the increased fitness of holobionts supported by genetic diversity. Identification of genetic loci controlling the interaction of beneficial microbiomes will allow the integration of genomic design into crop breeding programs. Bacteria beneficial to plants have traditionally been conceived as "promoting and regulating plant growth". The future perspective for agroecosystems should be that microbiomes, via multiple cascades, define plant phenotypes and provide genetic variability for agroecosystems.}, }
@article {pmid37272971, year = {2023}, author = {Zhang, Y and Wang, M and Cheng, W and Huang, C and Ren, J and Zhai, H and Niu, L}, title = {Temporal and Spatial Variation Characteristics and Influencing Factors of Bacterial Community in Urban Landscape Lakes.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2424-2435}, pmid = {37272971}, issn = {1432-184X}, support = {51809211//National Natural Science Foundation of China/ ; 20JY045//Shaanxi Provincial Education Department/ ; 2018M633548//China Postdoctoral Science Foundation/ ; }, mesh = {Humans ; *Lakes/microbiology ; Bacteria/genetics ; Proteobacteria ; *Actinobacteria ; Seasons ; China ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Urban landscape lakes are closely related to human activity, but there are limited studies on their bacterial community characteristics and risks to human health. In this study, four different types of urban landscape lakes in Xi'an were selected, and the bacterial community structures in different seasons were analyzed by Illumina Nova high-throughput sequencing technology. Seasonal variations in bacterial communities were analyzed by linear discriminant analysis, STAMP difference analysis, and nonmetric multidimensional scaling. Redundancy analysis was used to investigate the influencing factors. Furthermore, the metabolic functions of bacterial communities were predicted by Tax4Fun. There were clear seasonal differences in the α-diversity of bacteria, with bacterial diversity being higher in winter than in summer in the four urban landscape lakes, and the diversity of different water sources was different; the distributions of Proteobacteria, Actinobacteria, Chloroflexi, and Verrucomicrobia had significant seasonal differences; and the dominant bacteria at the genus level had obvious temporal and spatial differences. Furthermore, a variety of environmental factors had an impact on bacterial communities, and temperature, DO, and nitrogen were the primary factors affecting the seasonal variation in bacteria. There are also significant seasonal differences in the metabolic functions of bacterial communities. These results are helpful for understanding the current status of bacteria in the aquatic environments of such urban landscape lakes.}, }
@article {pmid37272815, year = {2023}, author = {Tang, K and Tao, L and Wang, Y and Wang, Q and Fu, C and Chen, B and Zhang, Z and Fu, Y}, title = {Temporal Variations in the Gut Microbiota of the Globally Endangered Sichuan Partridge (Arborophila rufipectus): Implications for Adaptation to Seasonal Dietary Change and Conservation.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {6}, pages = {e0074723}, pmid = {37272815}, issn = {1098-5336}, mesh = {Animals ; *Gastrointestinal Microbiome ; Seasons ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria/genetics ; Endangered Species ; Animals, Wild ; *Galliformes/genetics ; }, abstract = {Host-associated microbiotas are known to influence host health by aiding digestion, metabolism, nutrition, physiology, immune function, and pathogen resistance. Although an increasing number of studies have investigated the avian microbiome, there is a lack of research on the gut microbiotas of wild birds, especially endangered pheasants. Owing to the difficulty of characterizing the dynamics of dietary composition, especially in omnivores, how the gut microbiotas of birds respond to seasonal dietary changes remains poorly understood. The Sichuan partridge (Arborophila rufipectus) is an endangered pheasant species with a small population endemic to the mountains of southwest China. Here, 16S rRNA sequencing and Tax4Fun were used to characterize and compare community structure and functions of the gut microbiota in the Sichuan partridges across three critical periods of their annual life cycle (breeding, postbreeding wandering, and overwintering). We found that the microbial communities were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Cyanobacteria throughout the year. Diversity of the gut microbiotas was highest during postbreeding wandering and lowest during the overwintering periods. Seasonal dietary changes and reassembly of the gut microbial community occurred consistently. Composition, diversity, and functions of the gut microbiota exhibited diet-associated variations, which might facilitate host adaptation to diverse diets in response to environmental shifts. Moreover, 28 potential pathogenic genera were detected, and their composition differed significantly between the three periods. Investigation of the wild bird gut microbiota dynamics has enhanced our understanding of diet-microbiota associations over the annual life cycle of birds, aiding in the integrative conservation of this endangered bird. IMPORTANCE Characterizing the gut microbiotas of wild birds across seasons will shed light on their annual life cycle. Due to sampling difficulties and the lack of detailed dietary information, studies on how the gut microbiota adapts to seasonal dietary changes of wild birds are scarce. Based on more detailed dietary composition, we found a seasonal reshaping pattern of the gut microbiota of Sichuan partridges corresponding to their seasonal dietary changes. The variation in diet and gut microbiota potentially facilitated the diversity of dietary niches of this endangered pheasant, revealing a seasonal diet-microbiota association across the three periods of the annual cycle. In addition, identifying a variety of potentially pathogenic bacterial genera aids in managing the health and improving survival of Sichuan partridges. Incorporation of microbiome research in the conservation of endangered species contributes to our comprehensive understanding the diet-host-microbiota relationship in wild birds and refinement of conservation practices.}, }
@article {pmid37272792, year = {2023}, author = {Wu, X and Gushgari-Doyle, S and Lui, LM and Hendrickson, AJ and Liu, Y and Jagadamma, S and Nielsen, TN and Justice, NB and Simmons, T and Hess, NJ and Joyner, DC and Hazen, TC and Arkin, AP and Chakraborty, R}, title = {Distinct Depth-Discrete Profiles of Microbial Communities and Geochemical Insights in the Subsurface Critical Zone.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {6}, pages = {e0050023}, pmid = {37272792}, issn = {1098-5336}, mesh = {*Bacteria/metabolism ; *Microbiota ; Carbon/metabolism ; Tennessee ; }, abstract = {Microbial assembly and metabolic potential in the subsurface critical zone (SCZ) are substantially impacted by subsurface geochemistry and hydrogeology, selecting for microbes distinct from those in surficial soils. In this study, we integrated metagenomics and geochemistry to elucidate how microbial composition and metabolic potential are shaped and impacted by vertical variations in geochemistry and hydrogeology in terrestrial subsurface sediment. A sediment core from an uncontaminated, pristine well at Oak Ridge Field Research Center in Oak Ridge, Tennessee, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone, was used in this study. Our results showed that subsurface microbes were highly localized and that communities were rarely interconnected. Microbial community composition as well as metabolic potential in carbon and nitrogen cycling varied even over short vertical distances. Further analyses indicated a strong depth-related covariation of community composition with a subset of 12 environmental variables. An analysis of dissolved organic carbon (DOC) quality via ultrahigh resolution mass spectrometry suggested that the SCZ was generally a low-carbon environment, with the relative portion of labile DOC decreasing and that of recalcitrant DOC increasing along the depth, selecting microbes from copiotrophs to oligotrophs and also impacting the microbial metabolic potential in the carbon cycle. Our study demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolism in the SCZ. IMPORTANCE In this study, we explored the links between geochemical parameters, microbial community structure and metabolic potential across the depth of sediment, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone. Our results revealed that microbes in the terrestrial subsurface can be highly localized, with communities rarely being interconnected along the depth. Overall, our research demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolic potential in different depths of subsurface terrestrial sediment. Such studies correlating microbial community analyses and geochemistry analyses, including high resolution mass spectrometry analyses of natural organic carbon, will further the fundamental understanding of microbial ecology and biogeochemistry in subsurface terrestrial ecosystems and will benefit the future development of predictive models on nutrient turnover in these environments.}, }
@article {pmid37272710, year = {2023}, author = {Miller, SE and Colman, AS and Waldbauer, JR}, title = {Metaproteomics reveals functional partitioning and vegetational variation among permafrost-affected Arctic soil bacterial communities.}, journal = {mSystems}, volume = {8}, number = {3}, pages = {e0123822}, pmid = {37272710}, issn = {2379-5077}, mesh = {*Permafrost/microbiology ; Bacteria/genetics ; Tundra ; Soil/chemistry ; Plants ; Acidobacteria ; *Alphaproteobacteria ; *Betaproteobacteria ; Carbon/metabolism ; }, abstract = {Microbial activity in Arctic soils controls the cycling of significant stores of organic carbon and nutrients. We studied in situ processes in Alaskan soils using original metaproteomic methods in order to relate important heterotrophic functions to microbial taxa and to understand the microbial response to Arctic greening. Major bacterial groups show strong metabolic specialization in organic topsoils. α-/β-/γ-Proteobacteria specialized in the acquisition of small, soluble compounds, whereas Acidobacteria, Actinobacteria, and other detritosphere groups specialized in the degradation of plant-derived polymers. α-/β-/γ-Proteobacteria dominated the expression of transporters for common root exudates and limiting nitrogenous compounds, supporting an ecological model of dependence upon plants for carbon and competition with plants for nitrogen. Detritosphere groups specialized in distinct substrates, with Acidobacteria producing the most enzymes for hemicellulose depolymerization. Acidobacteria was the most active group across the three plant ecotypes sampled-the largely nonvascular, lower biomass intertussock and the largely vascular, higher biomass tussock and shrub. Functional partitioning among bacterial groups was stable between plant ecotypes, but certain functions associated with α-/β-/γ-Proteobacteria were more strongly expressed in higher biomass ecotypes. We show that refined metaproteomic approaches can elucidate soil microbial ecology as well as biogeochemical trajectories of major carbon stocks. IMPORTANCE The Arctic is warming twice as fast as the rest of the planet, and Arctic soils currently store twice as much carbon as the entire atmosphere-two facts that make understanding how Arctic soil microbial communities are responding to climate change particularly urgent. Greening of vegetation cover across the Arctic landscape is one of the most prominent climate-driven shifts in Arctic terrestrial ecology, with potentially profound effects on biogeochemical cycling by the soil microbiome. Here we use metaproteomics to document microbial metabolic functions that drive soil carbon and nutrient cycling processes in an Arctic tundra landscape. We identify functional roles among bacterial taxonomic groups that are largely stable across vegetation types, with certain functions strongly expressed by rhizosphere groups reflecting a community metabolic response to greening.}, }
@article {pmid37270320, year = {2023}, author = {M Venturini, A and B Gontijo, J and A Mandro, J and Berenguer, E and Peay, KG and M Tsai, S and Bohannan, BJM}, title = {Soil microbes under threat in the Amazon Rainforest.}, journal = {Trends in ecology &amp; evolution}, volume = {38}, number = {8}, pages = {693-696}, doi = {10.1016/j.tree.2023.04.014}, pmid = {37270320}, issn = {1872-8383}, mesh = {*Soil ; *Ecosystem ; Rainforest ; Biodiversity ; Climate Change ; }, abstract = {Soil microorganisms are sensitive indicators of land-use and climate change in the Amazon, revealing shifts in important processes such as greenhouse gas (GHG) production, but they have been overlooked in conservation and management initiatives. Integrating soil biodiversity with other disciplines while expanding sampling efforts and targeted microbial groups is crucially needed.}, }
@article {pmid37268771, year = {2023}, author = {Listmann, L and Peters, C and Rahlff, J and Esser, SP and Schaum, CE}, title = {Seasonality and Strain Specificity Drive Rapid Co-evolution in an Ostreococcus-Virus System from the Western Baltic Sea.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2414-2423}, pmid = {37268771}, issn = {1432-184X}, support = {CLICCS//Exzellenzcluster Ozean der Zukunft/ ; Start up Prof. Dr. Elisa Schaum//University of Hamburg, Germany/ ; RA3432/1-1//DFG/ ; 730984//Assemble Plus/ ; }, mesh = {*Ecosystem ; Phytoplankton/genetics ; *Chlorophyta ; }, abstract = {Marine viruses are a major driver of phytoplankton mortality and thereby influence biogeochemical cycling of carbon and other nutrients. Phytoplankton-targeting viruses are important components of ecosystem dynamics, but broad-scale experimental investigations of host-virus interactions remain scarce. Here, we investigated in detail a picophytoplankton (size 1 µm) host's responses to infections by species-specific viruses from distinct geographical regions and different sampling seasons. Specifically, we used Ostreococcus tauri and O. mediterraneus and their viruses (size ca. 100 nm). Ostreococcus sp. is globally distributed and, like other picoplankton species, play an important role in coastal ecosystems at certain times of the year. Further, Ostreococcus sp. is a model organism, and the Ostreococcus-virus system is well-known in marine biology. However, only few studies have researched its evolutionary biology and the implications thereof for ecosystem dynamics. The Ostreococcus strains used here stem from different regions of the Southwestern Baltic Sea that vary in salinity and temperature and were obtained during several cruises spanning different sampling seasons. Using an experimental cross-infection set-up, we explicitly confirm species and strain specificity in Ostreococcus sp. from the Baltic Sea. Moreover, we found that the timing of virus-host co-existence was a driver of infection patterns as well. In combination, these findings prove that host-virus co-evolution can be rapid in natural systems.}, }
@article {pmid37268258, year = {2023}, author = {Yu, Y and Fu, D and Zhou, H and Su, J and Chen, S and Lv, G}, title = {Potential application of Atractylodes macrocephala Koidz. as a natural drug for bone mass regulation: A review.}, journal = {Journal of ethnopharmacology}, volume = {315}, number = {}, pages = {116718}, doi = {10.1016/j.jep.2023.116718}, pmid = {37268258}, issn = {1872-7573}, mesh = {*Atractylodes ; *Oils, Volatile ; China ; Plant Extracts/pharmacology ; Anti-Inflammatory Agents/pharmacology ; }, abstract = {The root of Atractylodes macrocephala Koidz. (AM) has been used for thousands of years in China, and it's extracts contain various constituents, such as volatile oils, polysaccharides, and lactones, with a myriad of pharmacological effects, including improves the healthy state of the gastrointestinal system and regulating immunity, hormone secretion, anti-inflammatory, antibacterial, antioxidation, anti-aging, and antitumor properties. Recently, researchers have focused on the effect of AM in regulating bone mass; therefore, its potential mechanism of action in regulating bone mass needs to be elucidated.<br><br>AIM OF REVIEW: This study reviewed the known and possible mechanisms of bone mass regulation by AM.<br><br>MATERIALS AND METHODS: Cochrane, Medline via PubMed, Embase, CENTRAL, CINAHL, Web of Science, Chinese biomedical literature database, Chinese Science and Technology Periodical Database, and Wanfang Database were used to search AM root extracts-related studies. The retrieval date was from the establishment of the database to January 1, 2023.<br><br>RESULTS: By summarizing 119 natural active substances that have been isolated from AM root to date, we explored its possible targets and pathways (such as Hedgehog, Wnt/&#x3b2;-catenin, and BMP/Smads pathways etc.) for bone growth and presented our position on possible future research/perspectives in the regulation of bone mass using this plant.<br><br>CONCLUSIONS: AM root extracts (incuding aqueous, ethanol etc.) promotes osteogenesis and inhibits osteoclastogenesis. These functions promote the absorption of nutrients, regulate gastrointestinal motility and intestinal microbial ecology, regulate endocrine function, strengthen bone immunity, and exert anti-inflammatory and antioxidant effects.}, }
@article {pmid37266990, year = {2023}, author = {Nikolaidis, M and Hesketh, A and Frangou, N and Mossialos, D and Van de Peer, Y and Oliver, SG and Amoutzias, GD}, title = {A panoramic view of the genomic landscape of the genus Streptomyces.}, journal = {Microbial genomics}, volume = {9}, number = {6}, pages = {}, pmid = {37266990}, issn = {2057-5858}, mesh = {*Genomics ; *Streptomyces/genetics/metabolism ; Codon ; Multigene Family ; }, abstract = {We delineate the evolutionary plasticity of the ecologically and biotechnologically important genus Streptomyces, by analysing the genomes of 213 species. Streptomycetes genomes demonstrate high levels of internal homology, whereas the genome of their last common ancestor was already complex. Importantly, we identify the species-specific fingerprint proteins that characterize each species. Even among closely related species, we observed high interspecies variability of chromosomal protein-coding genes, species-level core genes, accessory genes and fingerprints. Notably, secondary metabolite biosynthetic gene clusters (smBGCs), carbohydrate-active enzymes (CAZymes) and protein-coding genes bearing the rare TTA codon demonstrate high intraspecies and interspecies variability, which emphasizes the need for strain-specific genomic mining. Highly conserved genes, such as those specifying genus-level core proteins, tend to occur in the central region of the chromosome, whereas those encoding proteins with evolutionarily volatile species-level fingerprints, smBGCs, CAZymes and TTA-codon-bearing genes are often found towards the ends of the linear chromosome. Thus, the chromosomal arms emerge as the part of the genome that is mainly responsible for rapid adaptation at the species and strain level. Finally, we observed a moderate, but statistically significant, correlation between the total number of CAZymes and three categories of smBGCs (siderophores, e-Polylysin and type III lanthipeptides) that are related to competition among bacteria.}, }
@article {pmid37264467, year = {2023}, author = {Wainwright, BJ and Millar, T and Bowen, L and Semon, L and Hickman, KJE and Lee, JN and Yeo, ZY and Zahn, G}, title = {The core mangrove microbiome reveals shared taxa potentially involved in nutrient cycling and promoting host survival.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {47}, pmid = {37264467}, issn = {2524-6372}, support = {IG20-SI003 &amp; A-0007210-00-00//Yale-NUS College/ ; IG20-SI003 &amp; A-0007210-00-00//Yale-NUS College/ ; IG20-SI003 &amp; A-0007210-00-00//Yale-NUS College/ ; IG20-SI003 &amp; A-0007210-00-00//Yale-NUS College/ ; IG20-SI003 &amp; A-0007210-00-00//Yale-NUS College/ ; IG20-SI003 &amp; A-0007210-00-00//Yale-NUS College/ ; IG20-SI003 &amp; A-0007210-00-00//Yale-NUS College/ ; IG20-SI003 &amp; A-0007210-00-00//Yale-NUS College/ ; }, abstract = {BACKGROUND: Microbes have fundamental roles underpinning the functioning of our planet, they are involved in global carbon and nutrient cycling, and support the existence of multicellular life. The mangrove ecosystem is nutrient limited and if not for microbial cycling of nutrients, life in this harsh environment would likely not exist. The mangroves of Southeast Asia are the oldest and most biodiverse on the planet, and serve vital roles helping to prevent shoreline erosion, act as nursery grounds for many marine species and sequester carbon. Despite these recognised benefits and the importance of microbes in these ecosystems, studies examining the mangrove microbiome in Southeast Asia are scarce.cxs RESULTS: Here we examine the microbiome of Avicenia alba and Sonneratia alba and identify a core microbiome of 81 taxa. A further eight taxa (Pleurocapsa, Tunicatimonas, Halomonas, Marinomonas, Rubrivirga, Altererythrobacte, Lewinella, and Erythrobacter) were found to be significantly enriched in mangrove tree compartments suggesting key roles in this microbiome. The majority of those identified are involved in nutrient cycling or have roles in the production of compounds that promote host survival.<br><br>CONCLUSION: The identification of a core microbiome furthers our understanding of mangrove microbial biodiversity, particularly in Southeast Asia where studies such as this are rare. The identification of significantly different microbial communities between sampling sites suggests environmental filtering is occurring, with hosts selecting for a microbial consortia most suitable for survival in their immediate environment. As climate change advances, many of these microbial communities are predicted to change, however, without knowing what is currently there, it is impossible to determine the magnitude of any deviations. This work provides an important baseline against which change in microbial community can be measured.}, }
@article {pmid37264141, year = {2023}, author = {Zehnle, H and Laso-Pérez, R and Lipp, J and Riedel, D and Benito Merino, D and Teske, A and Wegener, G}, title = {Candidatus Alkanophaga archaea from Guaymas Basin hydrothermal vent sediment oxidize petroleum alkanes.}, journal = {Nature microbiology}, volume = {8}, number = {7}, pages = {1199-1212}, pmid = {37264141}, issn = {2058-5276}, mesh = {Archaea ; *Petroleum/metabolism ; *Hydrothermal Vents ; Anaerobiosis ; Alkanes/metabolism ; Sulfates/metabolism ; }, abstract = {Methanogenic and methanotrophic archaea produce and consume the greenhouse gas methane, respectively, using the reversible enzyme methyl-coenzyme M reductase (Mcr). Recently, Mcr variants that can activate multicarbon alkanes have been recovered from archaeal enrichment cultures. These enzymes, called alkyl-coenzyme M reductase (Acrs), are widespread in the environment but remain poorly understood. Here we produced anoxic cultures degrading mid-chain petroleum n-alkanes between pentane (C5) and tetradecane (C14) at 70 °C using oil-rich Guaymas Basin sediments. In these cultures, archaea of the genus Candidatus Alkanophaga activate the alkanes with Acrs and completely oxidize the alkyl groups to CO2. Ca. Alkanophaga form a deep-branching sister clade to the methanotrophs ANME-1 and are closely related to the short-chain alkane oxidizers Ca. Syntrophoarchaeum. Incapable of sulfate reduction, Ca. Alkanophaga shuttle electrons released from alkane oxidation to the sulfate-reducing Ca. Thermodesulfobacterium syntrophicum. These syntrophic consortia are potential key players in petroleum degradation in heated oil reservoirs.}, }
@article {pmid37263428, year = {2023}, author = {Van Peteghem, L and Matassa, S and Rabaey, K and Sakarika, M}, title = {Microbial protein from recovered nitrogen: Nutritional quality, safety, and feasibility assessment.}, journal = {The Science of the total environment}, volume = {892}, number = {}, pages = {164525}, doi = {10.1016/j.scitotenv.2023.164525}, pmid = {37263428}, issn = {1879-1026}, mesh = {Adult ; Humans ; Nitrogen/metabolism ; Feasibility Studies ; Nutritive Value ; Biomass ; *Metals, Heavy ; Amino Acids ; Lipids ; *Pesticides ; }, abstract = {In contrast to traditional agriculture, microbial protein (MP) production is highly efficient in nitrogen (N) usage and can be employed to valorize a variety of recovered resources, thereby increasing the overall sustainability of food production. The present study aimed to establish the potential of seven recovered N sources originating from different waste streams for MP production using ethanol and acetate as growth substrates. The evaluation was based on specific growth rate, biomass yield, nutritional quality (i.e. macromolecular composition, amino acid (AA) and lipid profile) and food safety (i.e. concentration of heavy metals, polyaromatic hydrocarbons (PAH), pesticides and antibiotics) of the MP. The majority of the recovered N sources did not affect the kinetics and had a minor impact on the biomass yield, compared to their commercial equivalents. The nutritional content of the biomass was similar to soy flour and did not show major variations in AA and lipid profile for the different recovered N sources. Considering the heavy metal content, an average-weighing adult should not consume >53-213 g of the microbial biomass produced on recovered N per day due to its high copper content. A substantial amount of PAH were also found in the biomass. A daily consumption of 20 g/person/day would impose 2.0-2.8 times higher dietary exposure than the mean PAH exposure through nutrition in the EU, indicating a potential concern for human health. On the other hand, the biomass was free of antibiotics, and the traces of pesticides found did not raise any major concern for food applications. Based on the results of this work, no evidence was found to restrict the application of microbial biomass produced on recovered nitrogen as food.}, }
@article {pmid37260833, year = {2023}, author = {Myers, KS and Ingle, AT and Walters, KA and Fortney, NW and Scarborough, MJ and Donohue, TJ and Noguera, DR}, title = {Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {11}, number = {}, pages = {1197175}, pmid = {37260833}, issn = {2296-4185}, abstract = {The liquid residue resulting from various agroindustrial processes is both rich in organic material and an attractive source to produce a variety of chemicals. Using microbial communities to produce chemicals from these liquid residues is an active area of research, but it is unclear how to deploy microbial communities to produce specific products from the different agroindustrial residues. To address this, we fed anaerobic bioreactors one of several agroindustrial residues (carbohydrate-rich lignocellulosic fermentation conversion residue, xylose, dairy manure hydrolysate, ultra-filtered milk permeate, and thin stillage from a starch bioethanol plant) and inoculated them with a microbial community from an acid-phase digester operated at the wastewater treatment plant in Madison, WI, United States. The bioreactors were monitored over a period of months and sampled to assess microbial community composition and extracellular fermentation products. We obtained metagenome assembled genomes (MAGs) from the microbial communities in each bioreactor and performed comparative genomic analyses to identify common microorganisms, as well as any community members that were unique to each reactor. Collectively, we obtained a dataset of 217 non-redundant MAGs from these bioreactors. This metagenome assembled genome dataset was used to evaluate whether a specific microbial ecology model in which medium chain fatty acids (MCFAs) are simultaneously produced from intermediate products (e.g., lactic acid) and carbohydrates could be applicable to all fermentation systems, regardless of the feedstock. MAGs were classified using a multiclass classification machine learning algorithm into three groups, organisms fermenting the carbohydrates to intermediate products, organisms utilizing the intermediate products to produce MCFAs, and organisms producing MCFAs directly from carbohydrates. This analysis revealed common biological functions among the microbial communities in different bioreactors, and although different microorganisms were enriched depending on the agroindustrial residue tested, the results supported the conclusion that the microbial ecology model tested was appropriate to explain the MCFA production potential from all agricultural residues.}, }
@article {pmid37260392, year = {2023}, author = {Putman, LI and Schaerer, LG and Wu, R and Kulas, DG and Zolghadr, A and Ong, RG and Shonnard, DR and Techtmann, SM}, title = {Deconstructed Plastic Substrate Preferences of Microbial Populations from the Natural Environment.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0036223}, pmid = {37260392}, issn = {2165-0497}, mesh = {*Plastics/metabolism ; *Polyethylene/metabolism ; RNA, Ribosomal, 16S/genetics ; Polyethylene Terephthalates/metabolism ; Bacteria ; }, abstract = {Over half of the world's plastic waste is landfilled, where it is estimated to take hundreds of years to degrade. Given the continued use and disposal of plastic products, it is vital that we develop fast and effective ways to utilize plastic waste. Here, we explore the potential of tandem chemical and biological processing to process various plastics quickly and effectively. Four samples of compost or sediment were used to set up enrichment cultures grown on mixtures of compounds, including disodium terephthalate and terephthalic acid (monomers of polyethylene terephthalate), compounds derived from the chemical deconstruction of polycarbonate, and pyrolysis oil derived from high-density polyethylene plastics. Established enrichment communities were also grown on individual substrates to investigate the substrate preferences of different taxa. Biomass harvested from the cultures was characterized using 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing. These data reveal low-diversity microbial communities structured by differences in culture inoculum, culture substrate source plastic type, and time. Microbial populations from the classes Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Acidobacteriae were significantly enriched when grown on substrates derived from high-density polyethylene and polycarbonate. The metagenomic data contain abundant aromatic and aliphatic hydrocarbon degradation genes relevant to the biodegradation of deconstructed plastic substrates used here. We show that microbial populations from diverse environments are capable of growth on substrates derived from the chemical deconstruction or pyrolysis of multiple plastic types and that paired chemical and biological processing of plastics should be further developed for industrial applications to manage plastic waste. IMPORTANCE The durability and impermeable nature of plastics have made them a popular material for numerous applications, but these same qualities make plastics difficult to dispose of, resulting in massive amounts of accumulated plastic waste in landfills and the natural environment. Since plastic use and disposal are projected to increase in the future, novel methods to effectively break down and dispose of current and future plastic waste are desperately needed. We show that the products of chemical deconstruction or pyrolysis of plastic can successfully sustain the growth of low-diversity microbial communities. These communities were enriched from multiple environmental sources and are capable of degrading complex xenobiotic carbon compounds. This study demonstrates that tandem chemical and biological processing can be used to degrade multiple types of plastics over a relatively short period of time and may be a future avenue for the mitigation of rapidly accumulating plastic waste.}, }
@article {pmid37259890, year = {2023}, author = {Geisen, S and Lara, E and Mitchell, E}, title = {Contemporary issues, current best practice and ways forward in soil protist ecology.}, journal = {Molecular ecology resources}, volume = {23}, number = {7}, pages = {1477-1487}, doi = {10.1111/1755-0998.13819}, pmid = {37259890}, issn = {1755-0998}, mesh = {*Ecosystem ; *Soil ; Eukaryota/genetics ; Ecology ; Biodiversity ; Bacteria ; }, abstract = {Soil protists are increasingly studied due to a release from previous methodological constraints and the acknowledgement of their immense diversity and functional importance in ecosystems. However, these studies often lack sufficient depth in knowledge, which is visible in the form of falsely used terms and false- or over-interpreted data with conclusions that cannot be drawn from the data obtained. As we welcome that also non-experts include protists in their still mostly bacterial and/or fungal-focused studies, our aim here is to help avoid some common errors. We provide suggestions for current terms to use when working on soil protists, like protist instead of protozoa, predator instead of grazer, microorganisms rather than microflora and other terms to be used to describe the prey spectrum of protists. We then highlight some dos and don'ts in soil protist ecology including challenges related to interpreting 18S rRNA gene amplicon sequencing data. We caution against the use of standard bioinformatic settings optimized for bacteria and the uncritical reliance on incomplete and partly erroneous reference databases. We also show why causal inferences cannot be drawn from sequence-based correlation analyses or any sampling/monitoring, study in the field without thorough experimental confirmation and sound understanding of the biology of taxa. Together, we envision this work to help non-experts to more easily include protists in their soil ecology analyses and obtain more reliable interpretations from their protist data and other biodiversity data that, in the end, will contribute to a better understanding of soil ecology.}, }
@article {pmid37258870, year = {2023}, author = {Yung, PYM and Tan, SM}, title = {Targeted Enrichment of Low-Abundance and Uncharacterized Taxon Members in Complex Microbial Community with Primer-Free FISH Probes Designed from Next Generation Sequencing Dataset.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {303-315}, pmid = {37258870}, issn = {1940-6029}, mesh = {*High-Throughput Nucleotide Sequencing ; In Situ Hybridization, Fluorescence/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Methods to obtain high-quality assembled genomic information of rare and unclassified member species in complex microbial communities remain a high priority in microbial ecology. Additionally, the supplementation of three-dimensional spatial information that highlights the morphology and spatial interaction would provide additional insights to its ecological role in the community. Fluorescent in-situ hybridization (FISH) coupling with fluorescence-activated cell sorting (FACS) is a powerful tool that enables the detection, visualization, and separation of low-abundance microbial members in samples containing complex microbial compositions. Here, we have described the workflow from designing the appropriate FISH probes from metagenomics or metatranscriptomics datasets to the preparation and treatment of samples to be used in FISH-FACS procedures.}, }
@article {pmid37257612, year = {2023}, author = {Cheng, X and Zeng, Z and Liu, X and Li, L and Wang, H and Zhao, R and Bodelier, PLE and Wang, W and Wang, Y and Tuovinen, OH}, title = {Methanotrophs dominate methanogens and act as a methane sink in a subterranean karst cave.}, journal = {The Science of the total environment}, volume = {892}, number = {}, pages = {164562}, doi = {10.1016/j.scitotenv.2023.164562}, pmid = {37257612}, issn = {1879-1026}, mesh = {*Methane ; Caves/microbiology ; Soil Microbiology ; Soil ; *Methylococcaceae ; }, abstract = {Karst caves are potential sinks of atmospheric methane due to microbial consumption. However, knowledge gaps on methanogens (methane producing microorganisms) and their interaction with methane-oxidizing bacteria (MOB) hinder our further understanding about methane dynamics in karst caves. Here we reported methanogenic community composition and their interaction with MOBs in the Heshang Cave to comprehensively understand methane cycling in subsurface biosphere. MOBs in karst cave were dominated by high-affinity MOB, upland soil cluster (USC), with USCγ pmoA gene abundance within the range of 1.34 × 10[4] to 1.8 × 10[7] copies·g[-1] DW. In contrast, methanogens were dominated by Methanoregula and cluster ZC-I. The mcrA numbers were 7.21 × 10[3] to 8.31 × 10[4] copies·g[-1] DW, 1-3 orders of magnitude lower than those of MOB. The inter-domain network analysis indicated that MOBs and methanogens cooperated more in the interior of the cave. Despite of the higher number of methanogenic nodes in the network, MOB dominated the keystone taxa, suggesting a leading functional role of MOB. MOB in caves showed a comparable with or higher potential methane oxidizing rate (PMOR, 0.63 ng CH4·g[-1] DW·h[-1] in sediment versus 11.02 ng CH4·g[-1] DW·h[-1] in weathered rock) than those in soils, whereas methane produced by methanogens was undetected. Collectively, high absolute abundances of MOB, high PMORs, the dominance of methanotrophic keystone taxa in the inter-domain network confirmed the superiority of MOBs over methanogens in the oligotrophic karst cave, mounting new evidence on caves as an important methane sink in terms of the interaction between methanogens and MOBs.}, }
@article {pmid37257501, year = {2023}, author = {Osorio-Doblado, AM and Feldmann, KP and Lourenco, JM and Stewart, RL and Smith, WB and Tedeschi, LO and Fluharty, FL and Callaway, TR}, title = {Forages and pastures symposium: forage biodegradation: advances in ruminal microbial ecology.}, journal = {Journal of animal science}, volume = {101}, number = {}, pages = {}, pmid = {37257501}, issn = {1525-3163}, mesh = {Animals ; *Ecosystem ; *Digestion ; Rumen/metabolism ; Ruminants ; Diet/veterinary ; Bacteria/metabolism ; Fermentation ; Animal Feed/analysis ; }, abstract = {The rumen microbial ecosystem provides ruminants a selective advantage, the ability to utilize forages, allowing them to flourish worldwide in various environments. For many years, our understanding of the ruminal microbial ecosystem was limited to understanding the microbes (usually only laboratory-amenable bacteria) grown in pure culture, meaning that much of our understanding of ruminal function remained a "black box." However, the ruminal degradation of plant cell walls is performed by a consortium of bacteria, archaea, protozoa, and fungi that produces a wide variety of carbohydrate-active enzymes (CAZymes) that are responsible for the catabolism of cellulose, hemicellulose, and pectin. The past 15 years have seen the development and implementation of numerous next-generation sequencing (NGS) approaches (e.g., pyrosequencing, Illumina, and shotgun sequencing), which have contributed significantly to a greater level of insight regarding the microbial ecology of ruminants fed a variety of forages. There has also been an increase in the utilization of liquid chromatography and mass spectrometry that revolutionized transcriptomic approaches, and further improvements in the measurement of fermentation intermediates and end products have advanced with metabolomics. These advanced NGS techniques along with other analytic approaches, such as metaproteomics, have been utilized to elucidate the specific role of microbial CAZymes in forage degradation. Other methods have provided new insights into dynamic changes in the ruminal microbial population fed different diets and how these changes impact the assortment of products presented to the host animal. As more omics-based data has accumulated on forage-fed ruminants, the sequence of events that occur during fiber colonization by the microbial consortium has become more apparent, with fungal populations and fibrolytic bacterial populations working in conjunction, as well as expanding understanding of the individual microbial contributions to degradation of plant cell walls and polysaccharide components. In the future, the ability to predict microbial population and enzymatic activity and end products will be able to support the development of dynamic predictive models of rumen forage degradation and fermentation. Consequently, it is imperative to understand the rumen's microbial population better to improve fiber degradation in ruminants and, thus, stimulate more sustainable production systems.}, }
@article {pmid37257378, year = {2023}, author = {Sun, W and Jing, Z}, title = {Migration of rare and abundant species, assembly mechanisms, and ecological networks of microbiomes in drinking water treatment plants: Effects of different treatment processes.}, journal = {Journal of hazardous materials}, volume = {457}, number = {}, pages = {131726}, doi = {10.1016/j.jhazmat.2023.131726}, pmid = {37257378}, issn = {1873-3336}, mesh = {*Drinking Water ; Charcoal ; *Water Purification/methods ; *Microbiota ; *Ozone ; }, abstract = {Microorganisms play an important role in the degradation of pollutants. However, they also cause problems in drinking water distribution systems, such as pipe corrosion and biofilm growth. The microbial assembly mechanisms and molecular ecological networks associated with different drinking water treatment processes have not yet been clearly analyzed. Therefore, this study investigated the microbiomes of three processes (coal filtration-activated carbon, ozone-activated carbon and UV, and ozone-activated carbon) during different seasons. The results showed that the microbial composition and diversity among the different processes and during different seasons. Water treatment processes had deterministic effects on the microbial assembly process and significantly changed the composition of rare and abundant species, altering the size and modules of molecular ecology networks. Rare species considered as keystone species play important roles in microbial ecology and microbial community construction. Ozone-activated carbon and UV/chlorination decreased the bacterial concentration, increased the deterministic process of microbial assembly, and significantly reduced the size of the network, which is of great significance to microbial control in drinking water. This research broadens our perspectives on the microbial assembly associated with drinking water treatment processes and contributes to ensuring the safe supply of drinking water.}, }
@article {pmid37253619, year = {2023}, author = {Takahashi, N and Terauchi, Y and Tanaka, T and Yoshimi, A and Yabu, H and Abe, K}, title = {Involvement of ionic interactions in self-assembly and resultant rodlet formation of class I hydrophobin RolA from Aspergillus oryzae.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {87}, number = {8}, pages = {857-864}, doi = {10.1093/bbb/zbad066}, pmid = {37253619}, issn = {1347-6947}, support = {17H03787//Japan Society for the Promotion of Science/ ; }, mesh = {*Fungal Proteins/metabolism ; *Aspergillus oryzae/metabolism ; Polymers/chemistry/metabolism ; Hydrophobic and Hydrophilic Interactions ; }, abstract = {Hydrophobins are small amphiphilic proteins that are conserved in filamentous fungi. They localized on the conidial surface to make it hydrophobic, which contributes to conidial dispersal in the air, and helps fungi to infect plants and mammals and degrade polymers. Hydrophobins self-assemble and undergo structural transition from the amorphous state to the rodlet (rod-like multimeric structure) state. However, it remains unclear whether the amorphous or rodlet state is biologically functional and what external factors regulate state transition. In this study, we analyzed the self-assembly of hydrophobin RolA of Aspergillus oryzae in detail and identified factors regulating this process. Using atomic force microscopy, we observed RolA rodlet formation over time, and determined "rodlet elongation rate" and "rodlet formation frequency." Changes in these kinetic parameters in response to pH and salt concentration suggest that RolA rodlet formation is regulated by the strength of ionic interactions between RolA molecules.}, }
@article {pmid37249591, year = {2023}, author = {Wu-Chuang, A and Hartmann, D and Maitre, A and Mateos-Hernández, L and Frantová, H and Urbanová, V and Obregon, D and Cabezas-Cruz, A and Perner, J}, title = {Variation of bacterial community assembly over developmental stages and midgut of Dermanyssus gallinae.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2400-2413}, pmid = {37249591}, issn = {1432-184X}, support = {205/2018//Programa Nacional de Becas de Postgrado en el Exterior "Don Carlos Antonio L&#xf3;pez"/ ; SGCE - RAPPORT N&#xb0; 0300//Collectivit&#xe9; de Corse/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche/ ; 22-18424M and 22-12648J//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; }, mesh = {Animals ; Female ; Chickens/parasitology ; *Poultry Diseases/parasitology/prevention &amp; control ; *Mites/microbiology ; Life Cycle Stages ; Bacteria/genetics ; *Mite Infestations/parasitology/prevention &amp; control ; }, abstract = {Bacterial microbiota play an important role in the fitness of arthropods, but the bacterial microflora in the parasitic mite Dermanyssus gallinae is only partially explored; there are gaps in our understanding of the microbiota localization and in our knowledge of microbial community assembly. In this work, we have visualized, quantified the abundance, and determined the diversity of bacterial occupancy, not only across developmental stages of D. gallinae, but also in the midgut of micro-dissected female D. gallinae mites. We explored community assembly and the presence of keystone taxa, as well as predicted metabolic functions in the microbiome of the mite. The diversity of the microbiota and the complexity of co-occurrence networks decreased with the progression of the life cycle. However, several bacterial taxa were present in all samples examined, indicating a core symbiotic consortium of bacteria. The relatively higher bacterial abundance in adult females, specifically in their midguts, implicates a function linked to the biology of D. gallinae mites. If such an association proves to be important, the bacterial microflora qualifies itself as an acaricidal or vaccine target against this troublesome pest.}, }
@article {pmid37247701, year = {2023}, author = {Garrido-Benavent, I and de Los Ríos, A and Núñez-Zapata, J and Ortiz-Álvarez, R and Schultz, M and Pérez-Ortega, S}, title = {Ocean crossers: A tale of disjunctions and speciation in the dwarf-fruticose Lichina (lichenized Ascomycota).}, journal = {Molecular phylogenetics and evolution}, volume = {185}, number = {}, pages = {107829}, doi = {10.1016/j.ympev.2023.107829}, pmid = {37247701}, issn = {1095-9513}, mesh = {Phylogeny ; *Ascomycota/genetics ; *Lichens/genetics ; Fossils ; Oceans and Seas ; Phylogeography ; }, abstract = {Lichens thrive in rocky coastal areas in temperate and cold regions of both hemispheres. Species of the genus Lichina, which form characteristic black fruiting thalli associated with cyanobacteria, often create distinguishable bands in the intertidal and supralittoral zones. The present study uses a comprehensive specimen dataset and four gene loci to (1) delineate and discuss species boundaries in this genus, (2) assess evolutionary relationships among species, and (3) infer the most likely causes of their current geographic distribution in the Northern and Southern hemispheres. A dated phylogeny describes the time frame in which extant disjunctions of species and populations were established. The results showed that the genus is integrated by four species, with Lichina pygmaea, L. confinis and the newly described L. canariensis from rocky seashores in the Canary Islands, occurring in the Northern Hemisphere, whereas L. intermedia is restricted to the Southern Hemisphere. Lichina intermedia hosted a much higher intraspecific genetic diversity than the other species, with subclades interpreted as species-level lineages by the different species delimitation approaches. However, a conservative taxonomic approach was adopted. This species showed a striking disjunct distribution between Australasia and southern South America. The timing for the observed interspecific and intraspecific divergences and population disjunctions postdated continental plate movements, suggesting that long-distance dispersal across body waters in the two hemispheres played a major role in shaping the current species distributions. Such ocean crossings were, as in L. canariensis, followed by speciation. New substitution rates for the nrITS of the genus Lichina were inferred using a tree spanning the major Ascomycota lineages calibrated using fossils. In conclusion, this work lays the foundation for a better understanding of the evolution through time and space of maritime lichens.}, }
@article {pmid37247028, year = {2023}, author = {Gao, K and Li, W and Gan, E and Li, J and Jiang, L and Liu, Y}, title = {Impacts of 10 Years of Elevated CO2 and Warming on Soil Fungal Diversity and Network Complexity in a Chinese Paddy Field.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2386-2399}, pmid = {37247028}, issn = {1432-184X}, mesh = {*Ascomycota ; *Basidiomycota ; Carbon Dioxide ; Fungi/genetics ; *Oryza ; Soil/chemistry ; *Soil Microbiology ; China ; }, abstract = {Climatic change conditions (elevated CO2 and warming) have been known to threaten agricultural sustainability and grain yield. Soil fungi play an important role in maintaining agroecosystem functions. However, little is known about the responses of fungal community in paddy field to elevated CO2 and warming. Herein, using internal transcribed spacer (ITS) gene amplicon sequencing and co-occurrence network methods, the responses of soil fungal community to factorial combinations of elevated CO2 (550 ppm), and canopy warming (+2 °C) were explored in an open-air field experiment for 10 years. Elevated CO2 significantly increased the operational taxonomic unit (OTU) richness and Shannon diversity of fungal communities in both rice rhizosphere and bulk soils, whereas the relative abundances of Ascomycota and Basidiomycota were significantly decreased and increased under elevated CO2, respectively. Co-occurrence network analysis showed that elevated CO2, warming, and their combination increased the network complexity and negative correlation of the fungal community in rhizosphere and bulk soils, suggesting that these factors enhanced the competition of microbial species. Warming resulted in a more complex network structure by altering topological roles and increasing the numbers of key fungal nodes. Principal coordinate analysis indicated that rice growth stages rather than elevated CO2 and warming altered soil fungal communities. Specifically, the changes in diversity and network complexity were greater at the heading and ripening stages than at the tillering stage. Furthermore, elevated CO2 and warming significantly increased the relative abundances of pathotrophic fungi and reduced those of symbiotrophic fungi in both rhizosphere and bulk soils. Overall, the results indicate that long-term CO2 exposure and warming enhance the complexity and stability of soil fungal community, potentially threatening crop health and soil functions through adverse effects on fungal community functions.}, }
@article {pmid37242886, year = {2023}, author = {Mattelin, V and Verfaille, L and Kundu, K and De Wildeman, S and Boon, N}, title = {A New Colorimetric Test for Accurate Determination of Plastic Biodegradation.}, journal = {Polymers}, volume = {15}, number = {10}, pages = {}, pmid = {37242886}, issn = {2073-4360}, support = {HBC.2019.2622//Flemish Agency for Innovation &amp; Enterpreneurship (VLAIO)/ ; }, abstract = {As plastic waste is accumulating in both controlled waste management settings and natural settings, much research is devoted to search for solutions, also in the field of biodegradation. However, determining the biodegradability of plastics in natural environments remains a big challenge due to the often very low biodegradation rates. Many standardised test methods for biodegradation in natural environments exist. These are often based on mineralisation rates in controlled conditions and are thus indirect measurements of biodegradation. It is of interest for both researchers and companies to have tests that are more rapid, easier, and more reliable to screen different ecosystems and/or niches for their plastic biodegradation potential. In this study, the goal is to validate a colorimetric test, based on carbon nanodots, to screen biodegradation of different types of plastics in natural environments. After introducing carbon nanodots into the matrix of the target plastic, a fluorescent signal is released upon plastic biodegradation. The in-house-made carbon nanodots were first confirmed regarding their biocompatibility and chemical and photostability. Subsequently, the effectivity of the developed method was evaluated positively by an enzymatic degradation test with polycaprolactone with Candida antarctica lipase B. Finally, validation experiments were performed with enriched microorganisms and real environmental samples (freshwater and seawater), of which the results were compared with parallel, frequently used biodegradation measures such as O2 and CO2, dissolved organic carbon, growth and pH, to assess the reliability of the test. Our results indicate that this colorimetric test is a good alternative to other methods, but a combination of different methods gives the most information. In conclusion, this colorimetric test is a good fit to screen, in high throughput, the depolymerisation of plastics in natural environments and under different conditions in the lab.}, }
@article {pmid37236880, year = {2023}, author = {Malard, LA and Guisan, A}, title = {Into the microbial niche.}, journal = {Trends in ecology &amp; evolution}, volume = {38}, number = {10}, pages = {936-945}, doi = {10.1016/j.tree.2023.04.015}, pmid = {37236880}, issn = {1872-8383}, mesh = {*Ecosystem ; *Metagenomics ; }, abstract = {The environmental niche concept describes the distribution of a taxon in the environment and can be used to understand community dynamics, biological invasions, and the impact of environmental changes. The uses and applications are still restricted in microbial ecology, largely due to the complexity of microbial systems and associated methodological limitations. The development of shotgun metagenomics and metatranscriptomics opens new ways to investigate the microbial niche by focusing on the metabolic niche within the environmental space. Here, we propose the metabolic niche framework, which, by defining the fundamental and realised metabolic niche of microorganisms, has the potential to not only provide novel insights into habitat preferences and the metabolism associated, but also to inform on metabolic plasticity, niche shifts, and microbial invasions.}, }
@article {pmid37236039, year = {2023}, author = {Anderson, AG and Bedford, MR and Parsons, CM}, title = {Effects of adaptation diet and exogenous enzymes on true metabolizable energy and cecal microbial ecology, short-chain fatty acid profile, and enzyme activity in roosters fed barley and rye diets.}, journal = {Poultry science}, volume = {102}, number = {7}, pages = {102768}, pmid = {37236039}, issn = {1525-3171}, mesh = {Animals ; Male ; *Chickens/physiology ; Dietary Supplements ; *Hordeum ; Secale ; Diet/veterinary ; Fatty Acids, Volatile ; Animal Feed/analysis ; Digestion/physiology ; Animal Nutritional Physiological Phenomena ; }, abstract = {Three experiments evaluated effects of adaptation diet and exogenous β-glucanase and xylanase on TMEn of barley and rye. Single Comb White Leghorn roosters were fed adaptation diets based on corn/soybean meal (SBM), barley/SBM with and without β-glucanase, or rye/corn/SBM with and without xylanase for 4 wk. In Experiments 1 and 2, after the adaptation period, TMEn was determined using a 48 h precision-fed rooster assay for 100% barley or 100% rye diets with or without β-glucanase or xylanase, respectively. Experiment 3 consisted only of feeding adaptation diets for 4 wk. Cecal samples were collected at the end of experiments for microbial ecology, short-chain fatty acid (SCFA) profiles, and enzyme activity analyses. In Experiments 1 and 2, β-glucanase increased (P < 0.05) TMEn of barley, and there was no significant effect of adaptation diet on TMEn values. Total cecal Eubacteria and Ruminococcaceae were decreased (P < 0.05) and Escherichia coli were increased (P < 0.05) at the end of the TMEn assay compared with the end of the adaptation period (with no TMEn assay). There was a large decrease (P < 0.05) for most cecal SCFA at the end of the TMEn assay compared with the end of the adaptation period. Both cecal β-glucanase and xylanase activity were increased for birds fed adaptation diets containing the respective enzyme. In Experiment 3, there were no consistent effects of adaptation diet on cecal microbial profiles or SCFA but cecal β-glucanase activity was increased (P < 0.05) by exogenous β-glucanase for barley and cecal xylanase activity was increased (P < 0.05) by exogenous xylanase for rye. Overall, the results indicated that TMEn of barley was increased by exogenous β-glucanase, adaptation diet did not significantly influence the TMEn response to the dietary enzymes, and cecal fermentation (based on cecal SCFA) was greatly reduced by the TMEn assay. Cecal β-glucanase and xylanase activity, however, were often increased by feeding high barley and high rye diets containing exogenous enzymes.}, }
@article {pmid37235689, year = {2023}, author = {Esteves, SM and Jadoul, A and Iacono, F and Schloesser, M and Bosman, B and Carnol, M and Druet, T and Cardol, P and Hanikenne, M}, title = {Natural variation of nutrient homeostasis among laboratory and field strains of Chlamydomonas reinhardtii.}, journal = {Journal of experimental botany}, volume = {74}, number = {17}, pages = {5198-5217}, doi = {10.1093/jxb/erad194}, pmid = {37235689}, issn = {1460-2431}, mesh = {*Chlamydomonas reinhardtii/metabolism ; Photosynthesis/physiology ; *Chlamydomonas/metabolism ; Micronutrients/metabolism ; Homeostasis ; }, abstract = {Natural variation among individuals and populations exists in all species, playing key roles in response to environmental stress and adaptation. Micro- and macronutrients have a wide range of functions in photosynthetic organisms, and mineral nutrition thus plays a sizable role in biomass production. To maintain nutrient concentrations inside the cell within physiological limits and prevent the detrimental effects of deficiency or excess, complex homeostatic networks have evolved in photosynthetic cells. The microalga Chlamydomonas reinhardtii (Chlamydomonas) is a unicellular eukaryotic model for studying such mechanisms. In this work, 24 Chlamydomonas strains, comprising field isolates and laboratory strains, were examined for intraspecific differences in nutrient homeostasis. Growth and mineral content were quantified in mixotrophy, as full nutrition control, and compared with autotrophy and nine deficiency conditions for macronutrients (-Ca, -Mg, -N, -P, and -S) and micronutrients (-Cu, -Fe, -Mn, and -Zn). Growth differences among strains were relatively limited. However, similar growth was accompanied by highly divergent mineral accumulation among strains. The expression of nutrient status marker genes and photosynthesis were scored in pairs of contrasting field strains, revealing distinct transcriptional regulation and nutrient requirements. Leveraging this natural variation should enable a better understanding of nutrient homeostasis in Chlamydomonas.}, }
@article {pmid37235378, year = {2023}, author = {Gomes, TC and Conrado, R and Oliveira, RC and Selari, PJRG and Melo, IS and Araújo, WL and Maria, DA and De Souza, AO}, title = {Effect of Monocerin, a Fungal Secondary Metabolite, on Endothelial Cells.}, journal = {Toxins}, volume = {15}, number = {5}, pages = {}, pmid = {37235378}, issn = {2072-6651}, mesh = {Humans ; Human Umbilical Vein Endothelial Cells ; Cells, Cultured ; *Cellular Senescence ; *Lactones/pharmacology ; Cell Proliferation ; }, abstract = {This study reports the isolation and identification of the endophytic fungus Exserohilum rostratum through molecular and morphological analysis using optical and transmission electron microscopy (TEM), as well as the procurement of its secondary metabolite monocerin, an isocoumarin derivative. Considering the previously observed biological activities of monocerin, this study was performed on human umbilical vein endothelial cells (HUVECs) that are widely used as an in vitro model for several different purposes. Important parameters, such as cell viability, senescence-associated β-galactosidase, cellular proliferation by using 5(6)-carboxyfluorescein diacetate N-succinimidyl ester (CFSE), apoptosis analysis with annexin, cellular morphology through scanning electron microscopy (SEM), and laser confocal analysis were evaluated after exposing the cells to monocerin. After 24 h of exposure to monocerin at 1.25 mM, there was more than 80% of cell viability and a low percentage of cells in the early and late apoptosis and necrosis. Monocerin increased cell proliferation and did not induce cell senescence. Morphological analysis showed cellular integrity. The study demonstrates aspects of the mechanism of action of monocerin on endothelial cell proliferation, suggesting the possibility of its pharmaceutical application, such as in regenerative medicine.}, }
@article {pmid37234538, year = {2023}, author = {Sarrocco, S and Herrera-Estrella, A and Collinge, DB}, title = {Editorial: Plant disease management in the post-genomic era: from functional genomics to genome editing, Volume II.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1203870}, pmid = {37234538}, issn = {1664-302X}, }
@article {pmid37233803, year = {2023}, author = {Leonhardt, F and Keller, A and Arranz Aveces, C and Ernst, R}, title = {From Alien Species to Alien Communities: Host- and Habitat-Associated Microbiomes in an Alien Amphibian.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2373-2385}, pmid = {37233803}, issn = {1432-184X}, mesh = {Animals ; Introduced Species ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Gastrointestinal Microbiome ; Anura ; }, abstract = {Alien species can host diverse microbial communities. These associated microbiomes may be important in the invasion process and their analysis requires a holistic community-based approach. We analysed the skin and gut microbiome of Eleutherodactylus johnstonei from native range populations in St Lucia and exotic range populations in Guadeloupe, Colombia, and European greenhouses along with their respective environmental microbial reservoir through a 16S metabarcoding approach. We show that amphibian-associated and environmental microbial communities can be considered as meta-communities that interact in the assembly process. High proportions of bacteria can disperse between frogs and environment, while respective abundances are rather determined by niche effects driven by the microbial community source and spatial environmental properties. Environmental transmissions appeared to have higher relevance for skin than for gut microbiome composition and variation. We encourage further experimental studies to assess the implications of turnover in amphibian-associated microbial communities and potentially invasive microbiota in the context of invasion success and impacts. Within this novel framework of "nested invasions," (meta-)community ecology thinking can complement and widen the traditional perspective on biological invasions.}, }
@article {pmid37230351, year = {2023}, author = {Bossolani, JW and Leite, MFA and Momesso, L and Ten Berge, H and Bloem, J and Kuramae, EE}, title = {Nitrogen input on organic amendments alters the pattern of soil-microbe-plant co-dependence.}, journal = {The Science of the total environment}, volume = {890}, number = {}, pages = {164347}, doi = {10.1016/j.scitotenv.2023.164347}, pmid = {37230351}, issn = {1879-1026}, mesh = {*Soil/chemistry ; *Nitrogen ; Carbon ; Crops, Agricultural ; Triticum ; Soil Microbiology ; Bacteria ; Fertilizers ; }, abstract = {The challenges of nitrogen (N) management in agricultural fields include minimizing N losses while maximizing profitability and soil health. Crop residues can alter N and carbon (C) cycle processes in the soil and modulate the responses of the subsequent crop and soil- microbe-plant interactions. Here, we aim to understand how organic amendments with low and high C/N ratio, combined or not with mineral N may change soil bacterial community and their activity in the soil. Organic amendments with different C/N ratios were combined or not with N fertilization as follows: i) unamended soil (control), ii) grass clover silage (GC; low C/N ratio), and iii) wheat straw (WS; high C/N ratio). The organic amendments modulated the bacterial community assemblage and increased microbial activity. WS amendment had the strongest effects on hot water extractable carbon, microbial biomass N and soil respiration, which were linked with changes in bacterial community composition compared with GC-amended and unamended soil. By contrast, N transformation processes in the soil were more pronounced in GC-amended and unamended soil than in WS-amended soil. These responses were stronger in the presence of mineral N input. WS amendment induced greater N immobilization in the soil, even with mineral N input, impairing crop development. Interestingly, N input in unamended soil altered the co-dependence between the soil and the bacterial community to favor a new co-dependence among the soil, plant and microbial activity. In GC-amended soil, N fertilization shifted the dependence of the crop plant from the bacterial community to soil characteristics. Finally, the combined N input with WS amendment (organic carbon input) placed microbial activity at the center of the interrelationships between the bacterial community, plant, and soil. This emphasizes the crucial importance of microorganisms in the functioning of agroecosystems. To achieve higher yields in crops managed with various organic amendments, it is essential to incorporate mineral N management practices. This becomes particularly crucial when the soil amendments have a high C/N ratio.}, }
@article {pmid37229861, year = {2023}, author = {Zou, J and Cai, L and Lin, J and Wang, R and Li, J and Jia, M}, title = {Anaerobic fermentation of aerobic granular sludge: Insight into the effect of granule size and sludge structure on hydrolysis and acidification.}, journal = {Journal of environmental management}, volume = {343}, number = {}, pages = {118202}, doi = {10.1016/j.jenvman.2023.118202}, pmid = {37229861}, issn = {1095-8630}, mesh = {Fermentation ; *Sewage/chemistry ; Hydrolysis ; Anaerobiosis ; *Bioreactors ; Bacteria ; Hydrolases ; Fatty Acids, Volatile ; Hydrogen-Ion Concentration ; Waste Disposal, Fluid/methods ; }, abstract = {Aerobic granular sludge (AGS) has different physicochemical properties and microbial communities compared to conventional activated sludge (CAS), which may result in different behaviors during anaerobic fermentation and require further investigation. This study investigated the effect of granule size and sludge structure on the hydrolysis and acidification of AGS. Experimental results show that AGS exhibited significantly higher soluble chemical oxygen demand (SCOD) dissolution and total volatile fatty acids (TVFA) production (330.6-430.3 mg/gVSS and 231.0-312.5 mgCOD/gVSS) compared to conventional activated sludge (CAS) (167.0 mg/gVSS and 133.3 mgCOD/gVSS). This is because AGS (90.6-96.9 mg/gVSS) had higher extracellular polymeric substances (EPS) content than CAS (81.2 mg/gVSS). EPS can not only serve as substrates but also release the trapped hydrolases. Moreover, the relative abundances of hydrolytic/acidogenic bacteria and genes were higher in AGS (0.46%-3.60% and 3.01 × 10[-3]%-4.04 × 10[-3]%) than in CAS (0.30% and 1.23 × 10[-3]%). The optimal granule size for AGS fermentation was found to be 500-1600 μm. The crushing of granule structure promoted the dissolution of small amounts of EPS and the release of some trapped hydrolases, thereby potentially enhancing the enzyme-substrate contacts and bacteria-substrate interactions. Therefore, the highest SCOD dissolution (510.6 mg/gVSS) and TVFA production (352.1 mgCOD/gVSS) from crushed 500-1600 μm AGS were observed. Overall, the findings of this study provide valuable insights into the recovery of organic carbon from AGS via anaerobic fermentation.}, }
@article {pmid37227467, year = {2023}, author = {S Camargo, T and A Nickele, M and Reis Filho, W and do R C Penteado, S and C de Queiroz, E and G Auer, C}, title = {Correction to: Fungal Community Associated with the Leaf-Cutting Ant Acromyrmex crassispinus (Hymenoptera: Formicidae) Colonies: A Search for Potential Biocontrol Agents.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3138}, doi = {10.1007/s00248-023-02247-1}, pmid = {37227467}, issn = {1432-184X}, }
@article {pmid37225998, year = {2023}, author = {Tao, F and Huang, Y and Hungate, BA and Manzoni, S and Frey, SD and Schmidt, MWI and Reichstein, M and Carvalhais, N and Ciais, P and Jiang, L and Lehmann, J and Wang, YP and Houlton, BZ and Ahrens, B and Mishra, U and Hugelius, G and Hocking, TD and Lu, X and Shi, Z and Viatkin, K and Vargas, R and Yigini, Y and Omuto, C and Malik, AA and Peralta, G and Cuevas-Corona, R and Di Paolo, LE and Luotto, I and Liao, C and Liang, YS and Saynes, VS and Huang, X and Luo, Y}, title = {Microbial carbon use efficiency promotes global soil carbon storage.}, journal = {Nature}, volume = {618}, number = {7967}, pages = {981-985}, pmid = {37225998}, issn = {1476-4687}, mesh = {*Carbon/analysis/metabolism ; *Carbon Sequestration ; Climate Change ; *Ecosystem ; Plants ; *Soil/chemistry ; *Soil Microbiology ; Datasets as Topic ; Deep Learning ; }, abstract = {Soils store more carbon than other terrestrial ecosystems[1,2]. How soil organic carbon (SOC) forms and persists remains uncertain[1,3], which makes it challenging to understand how it will respond to climatic change[3,4]. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss[5-7]. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways[4,6,8-11], microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes[12,13]. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved[7,14,15]. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.}, }
@article {pmid37225918, year = {2023}, author = {Elston, KM and Phillips, LE and Leonard, SP and Young, E and Holley, JC and Ahsanullah, T and McReynolds, B and Moran, NA and Barrick, JE}, title = {The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {49}, pmid = {37225918}, issn = {2730-6151}, support = {R35 GM131738/GM/NIGMS NIH HHS/United States ; }, abstract = {Toolkits of plasmids and genetic parts streamline the process of assembling DNA constructs and engineering microbes. Many of these kits were designed with specific industrial or laboratory microbes in mind. For researchers interested in non-model microbial systems, it is often unclear which tools and techniques will function in newly isolated strains. To address this challenge, we designed the Pathfinder toolkit for quickly determining the compatibility of a bacterium with different plasmid components. Pathfinder plasmids combine three different broad-host-range origins of replication with multiple antibiotic resistance cassettes and reporters, so that sets of parts can be rapidly screened through multiplex conjugation. We first tested these plasmids in Escherichia coli, a strain of Sodalis praecaptivus that colonizes insects, and a Rosenbergiella isolate from leafhoppers. Then, we used the Pathfinder plasmids to engineer previously unstudied bacteria from the family Orbaceae that were isolated from several fly species. Engineered Orbaceae strains were able to colonize Drosophila melanogaster and could be visualized in fly guts. Orbaceae are common and abundant in the guts of wild-caught flies but have not been included in laboratory studies of how the Drosophila microbiome affects fly health. Thus, this work provides foundational genetic tools for studying microbial ecology and host-associated microbes, including bacteria that are a key constituent of the gut microbiome of a model insect species.}, }
@article {pmid37225767, year = {2023}, author = {Przybylska, MS and Violle, C and Vile, D and Scheepens, JF and Lacombe, B and Le Roux, X and Perrier, L and Sales-Mabily, L and Laumond, M and Vinyeta, M and Moulin, P and Beurier, G and Rouan, L and Cornet, D and Vasseur, F}, title = {AraDiv: a dataset of functional traits and leaf hyperspectral reflectance of Arabidopsis thaliana.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {314}, pmid = {37225767}, issn = {2052-4463}, support = {ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Adaptation, Physiological ; *Arabidopsis/genetics ; Biological Evolution ; Databases, Factual ; Plant Leaves ; }, abstract = {Data from functional trait databases have been increasingly used to address questions related to plant diversity and trait-environment relationships. However, such databases provide intraspecific data that combine individual records obtained from distinct populations at different sites and, hence, environmental conditions. This prevents distinguishing sources of variation (e.g., genetic-based variation vs. phenotypic plasticity), a necessary condition to test for adaptive processes and other determinants of plant phenotypic diversity. Consequently, individual traits measured under common growing conditions and encompassing within-species variation across the occupied geographic range have the potential to leverage trait databases with valuable data for functional and evolutionary ecology. Here, we recorded 16 functional traits and leaf hyperspectral reflectance (NIRS) data for 721 widely distributed Arabidopsis thaliana natural accessions grown in a common garden experiment. These data records, together with meteorological variables obtained during the experiment, were assembled to create the AraDiv dataset. AraDiv is a comprehensive dataset of A. thaliana's intraspecific variability that can be explored to address questions at the interface of genetics and ecology.}, }
@article {pmid37223788, year = {2023}, author = {Venbrux, M and Crauwels, S and Rediers, H}, title = {Current and emerging trends in techniques for plant pathogen detection.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1120968}, pmid = {37223788}, issn = {1664-462X}, abstract = {Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting in economic and social adversity. The spread of such plant pathogens and the emergence of new diseases is facilitated by human practices such as monoculture farming and global trade. Therefore, the early detection and identification of pathogens is of utmost importance to reduce the associated agricultural losses. In this review, techniques that are currently available to detect plant pathogens are discussed, including culture-based, PCR-based, sequencing-based, and immunology-based techniques. Their working principles are explained, followed by an overview of the main advantages and disadvantages, and examples of their use in plant pathogen detection. In addition to the more conventional and commonly used techniques, we also point to some recent evolutions in the field of plant pathogen detection. The potential use of point-of-care devices, including biosensors, have gained in popularity. These devices can provide fast analysis, are easy to use, and most importantly can be used for on-site diagnosis, allowing the farmers to take rapid disease management decisions.}, }
@article {pmid37222807, year = {2023}, author = {Broman, E and Abdelgadir, M and Bonaglia, S and Forsberg, SC and Wikström, J and Gunnarsson, JS and Nascimento, FJA and Sjöling, S}, title = {Long-Term Pollution Does Not Inhibit Denitrification and DNRA by Adapted Benthic Microbial Communities.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2357-2372}, pmid = {37222807}, issn = {1432-184X}, support = {3150-3.1.1-2017//&#xd6;stersj&#xf6;stiftelsen/ ; 2020-0002//Naturv&#xe5;rdsverket/ ; 1.1-1602-0106//Statens geotekniska institut/ ; }, mesh = {Nitrates ; *Ammonium Compounds ; Denitrification ; Nitrogen ; *Microbiota ; Oxidation-Reduction ; }, abstract = {Denitrification in sediments is a key microbial process that removes excess fixed nitrogen, while dissimilatory nitrate reduction to ammonium (DNRA) converts nitrate to ammonium. Although microorganisms are responsible for essential nitrogen (N) cycling, it is not yet fully understood how these microbially mediated processes respond to toxic hydrophobic organic compounds (HOCs) and metals. In this study, we sampled long-term polluted sediment from the outer harbor of Oskarshamn (Baltic Sea), measured denitrification and DNRA rates, and analyzed taxonomic structure and N-cycling genes of microbial communities using metagenomics. Results showed that denitrification and DNRA rates were within the range of a national reference site and other unpolluted sites in the Baltic Sea, indicating that long-term pollution did not significantly affect these processes. Furthermore, our results indicate an adaptation to metal pollution by the N-cycling microbial community. These findings suggest that denitrification and DNRA rates are affected more by eutrophication and organic enrichment than by historic pollution of metals and organic contaminants.}, }
@article {pmid37222806, year = {2023}, author = {Korpita, TM and Muths, EL and Watry, MK and McKenzie, VJ}, title = {Captivity, Reintroductions, and the Rewilding of Amphibian-associated Bacterial Communities.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2271-2281}, pmid = {37222806}, issn = {1432-184X}, support = {D19ZO-044//Morris Animal Foundation/ ; 2123583//National Science Foundation/ ; }, mesh = {Humans ; Animals ; *Bufonidae/microbiology ; Larva/microbiology ; Bacteria/genetics ; *Microbiota ; Skin/microbiology ; }, abstract = {Many studies have noted differences in microbes associated with animals reared in captivity compared to their wild counterparts, but few studies have examined how microbes change when animals are reintroduced to the wild after captive rearing. As captive assurance populations and reintroduction programs increase, a better understanding of how microbial symbionts respond during animal translocations is critical. We examined changes in microbes associated with boreal toads (Anaxyrus boreas), a threatened amphibian, after reintroduction to the wild following captive rearing. Previous studies demonstrate that developmental life stage is an important factor in amphibian microbiomes. We collected 16S marker-gene sequencing datasets to investigate: (i) comparisons of the skin, mouth, and fecal bacteria of boreal toads across four developmental life stages in captivity and the wild, (ii) tadpole skin bacteria before and after reintroduction to the wild, and (iii) adult skin bacteria during reintroduction to the wild. We demonstrated that differences occur across skin, fecal, and mouth bacterial communities in captive versus wild boreal toads, and that the degree of difference depends on developmental stage. Skin bacterial communities from captive tadpoles were more similar to their wild counterparts than captive post-metamorphic individuals were to their wild counterparts. When captive-reared tadpoles were introduced to a wild site, their skin bacteria changed rapidly to resemble wild tadpoles. Similarly, the skin bacterial communities of reintroduced adult boreal toads also shifted to resemble those of wild toads. Our results indicate that a clear microbial signature of captivity in amphibians does not persist after release into natural habitat.}, }
@article {pmid37222805, year = {2023}, author = {Rodríguez, MF and Gomez, AP and Parra-Giraldo, CM and Ceballos-Garzon, A}, title = {Proteomics and Genetic Approaches Elucidate the Circulation of Low Variability Staphylococcus aureus Strains on Colombian Dairy Farms.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2320-2329}, pmid = {37222805}, issn = {1432-184X}, mesh = {Animals ; Cattle ; Humans ; Female ; Staphylococcus aureus/genetics ; Farms ; Colombia/epidemiology ; Proteomics ; *Mastitis, Bovine/epidemiology ; *Staphylococcal Infections/epidemiology/veterinary ; Milk ; }, abstract = {Staphylococcus aureus is one of the most prevalent pathogens causing bovine mastitis in the world, in part because of its ease of adaptation to various hosts and the environment. This study aimed to determine the prevalence of S. aureus in Colombian dairy farms and its relationship with the causal network of subclinical mastitis. From thirteen dairy farms enrolled, 1288 quarter milk samples (QMS) and 330 teat samples were taken from cows with positive (70.1%) and negative California Mastitis Test (CMT). In addition, 126 samples from the milking parlor environment and 40 from workers (nasal) were collected. On each dairy farm, a survey was conducted, and the milking process was monitored on the day of sampling. S. aureus was identified in 176 samples, i.e., 138 QMS, 20 from teats, 8 from the milking parlor environment, and 10 from workers' nasal swabs. Isolates identified as S. aureus underwent proteomics (clustering of mass spectrum) and molecular (tuf, coa, spa Ig, clfA, and eno genes) analysis. Regarding proteomics results, isolates were distributed into three clusters, each with members from all sources and all farms. Concerning molecular analysis, the virulence-related genes clfA and eno were identified in 41.3% and 37.8% of S. aureus isolates, respectively. We provide evidence on the circulation of S. aureus strains with limited variability among animals, humans, and the environment. The parameters with the lowest compliance in the farms which may be implicated in the transmission of S. aureus are the lack of handwashing and abnormal milk handling.}, }
@article {pmid37222804, year = {2023}, author = {Liu, B and Wang, Y and Zhang, H and Zhou, Y and Zhang, C and Yang, N and Wang, W}, title = {The Variations of Microbial Diversity and Community Structure Along Different Stream Orders in Wuyi Mountains.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2330-2343}, pmid = {37222804}, issn = {1432-184X}, mesh = {*Bacteria/genetics ; Fresh Water/microbiology ; Water/chemistry ; *Microbiota ; Oxygen ; }, abstract = {The surface water is an important habitat for freshwater microorganisms, but there is a lack of understanding of the pattern of microbial diversity and structure in stream continuums of small subtropical forest watersheds. Therefore, this study aimed to understand the variations in microbial diversity and community structure along stream orders (1-5) in the small subtropical forest catchments of the Wuyi Mountains. Using GIS software, 20 streams were chosen and classified into 5 orders. Illumina sequencing was used to analyze the dynamics of microbial communities, along with stream orders and hydro-chemical properties of stream water were also determined. Our results indicated that the bacterial and fungal richness (ACE index) was higher in low-order (1 and 2 orders) streams than in high-order (3, 4, and 5 orders) streams, with the highest value in the order 2 streams (P < 0.05). The water temperature and dissolved oxygen were positively correlated with fungal richness (P < 0.05). The bacterial rare taxa had a significant correlation with the abundance taxa (P < 0.05). The relative abundances of Bacteroidetes, Actinobacteria, and Chytridiomycota microbial phyla were significantly different among different order streams (P < 0.05). Using the neutral community model, we found that the fungal community structure was significantly shaped by hydro-chemical properties, while the bacterial community structure was largely regulated by stochastic processes. Our findings suggest that variations in microbial community structure in subtropical headwaters are largely shaped by the water temperature and dissolved oxygen.}, }
@article {pmid37222803, year = {2023}, author = {Malesevic, M and Stanisavljevic, N and Matijasevic, D and Curcic, J and Tasic, V and Tasic, S and Kojic, M}, title = {Metagenomic Analysis of Bacterial Community and Isolation of Representative Strains from Vranjska Banja Hot Spring, Serbia.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2344-2356}, pmid = {37222803}, issn = {1432-184X}, support = {451-03-47/2023-01/200042//Ministarstvo Prosvete, Nauke i Tehnolo&#x161;kog Razvoja/ ; }, mesh = {*Hot Springs/microbiology ; Serbia ; Phylogeny ; Bacteria ; Metagenome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The hot spring Vranjska Banja is the hottest spring on the Balkan Peninsula with a water temperature of 63-95 °C and a pH value of 7.1, in situ. According to the physicochemical analysis, Vranjska Banja hot spring belongs to the bicarbonated and sulfated hyperthermal waters. The structures of microbial community of this geothermal spring are still largely unexplored. In order to determine and monitor the diversity of microbiota of the Vranjska Banja hot spring, a comprehensive culture-independent metagenomic analysis was conducted in parallel with a culture-dependent approach for the first time. Microbial profiling using amplicon sequencing analysis revealed the presence of phylogenetically novel taxa, ranging from species to phyla. Cultivation-based methods resulted in the isolation of 17 strains belonging to the genera Anoxybacillus, Bacillus, Geobacillus, and Hydrogenophillus. Whole-genome sequencing of five representative strains was then performed. The genomic characterization and OrthoANI analysis revealed that the Vranjska Banja hot spring harbors phylogenetically novel species of the genus Anoxybacillus, proving its uniqueness. Moreover, these isolates contain stress response genes that enable them to survive in the harsh conditions of the hot springs. The results of the in silico analysis show that most of the sequenced strains have the potential to produce thermostable enzymes (proteases, lipases, amylases, phytase, chitinase, and glucanase) and various antimicrobial molecules that can be of great importance for industrial, agricultural, and biotechnological applications. Finally, this study provides a basis for further research and understanding of the metabolic potential of these microorganisms.}, }
@article {pmid37221307, year = {2023}, author = {Djotan, AKG and Matsushita, N and Fukuda, K}, title = {Correction to: Paired root-soil samples and metabarcoding reveal taxon-based colonization strategies in arbuscular mycorrhizal fungi communities in Japanese cedar and cypress stands.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2147-2148}, doi = {10.1007/s00248-023-02246-2}, pmid = {37221307}, issn = {1432-184X}, }
@article {pmid37221014, year = {2023}, author = {Carr, EC and Barton, Q and Grambo, S and Sullivan, M and Renfro, CM and Kuo, A and Pangilinan, J and Lipzen, A and Keymanesh, K and Savage, E and Barry, K and Grigoriev, IV and Riekhof, WR and Harris, SD}, title = {Characterization of a novel polyextremotolerant fungus, Exophiala viscosa, with insights into its melanin regulation and ecological niche.}, journal = {G3 (Bethesda, Md.)}, volume = {13}, number = {8}, pages = {}, pmid = {37221014}, issn = {2160-1836}, mesh = {*Melanins ; *Exophiala/genetics ; Fungi ; Ecosystem ; Soil ; }, abstract = {Black yeasts are polyextremotolerant fungi that contain high amounts of melanin in their cell wall and maintain a primar yeast form. These fungi grow in xeric, nutrient depletes environments which implies that they require highly flexible metabolisms and have been suggested to contain the ability to form lichen-like mutualisms with nearby algae and bacteria. However, the exact ecological niche and interactions between these fungi and their surrounding community are not well understood. We have isolated 2 novel black yeasts from the genus Exophiala that were recovered from dryland biological soil crusts. Despite notable differences in colony and cellular morphology, both fungi appear to be members of the same species, which has been named Exophiala viscosa (i.e. E. viscosa JF 03-3 Goopy and E. viscosa JF 03-4F Slimy). A combination of whole genome sequencing, phenotypic experiments, and melanin regulation experiments have been performed on these isolates to fully characterize these fungi and help decipher their fundamental niche within the biological soil crust consortium. Our results reveal that E. viscosa is capable of utilizing a wide variety of carbon and nitrogen sources potentially derived from symbiotic microbes, can withstand many forms of abiotic stresses, and excretes melanin which can potentially provide ultraviolet resistance to the biological soil crust community. Besides the identification of a novel species within the genus Exophiala, our study also provides new insight into the regulation of melanin production in polyextremotolerant fungi.}, }
@article {pmid37217203, year = {2023}, author = {Dundore-Arias, JP and Michalska-Smith, M and Millican, M and Kinkel, LL}, title = {More Than the Sum of Its Parts: Unlocking the Power of Network Structure for Understanding Organization and Function in Microbiomes.}, journal = {Annual review of phytopathology}, volume = {61}, number = {}, pages = {403-423}, doi = {10.1146/annurev-phyto-021021-041457}, pmid = {37217203}, issn = {1545-2107}, mesh = {*Biological Evolution ; *Microbiota ; Organizations ; Phenotype ; Soil ; }, abstract = {Plant and soil microbiomes are integral to the health and productivity of plants and ecosystems, yet researchers struggle to identify microbiome characteristics important for providing beneficial outcomes. Network analysis offers a shift in analytical framework beyond "who is present" to the organization or patterns of coexistence between microbes within the microbiome. Because microbial phenotypes are often significantly impacted by coexisting populations, patterns of coexistence within microbiomes are likely to be especially important in predicting functional outcomes. Here, we provide an overview of the how and why of network analysis in microbiome research, highlighting the ways in which network analyses have provided novel insights into microbiome organization and functional capacities, the diverse network roles of different microbial populations, and the eco-evolutionary dynamics of plant and soil microbiomes.}, }
@article {pmid37216901, year = {2023}, author = {Cao, Y and Almeida-Silva, F and Zhang, WP and Ding, YM and Bai, D and Bai, WN and Zhang, BW and Van de Peer, Y and Zhang, DY}, title = {Genomic Insights into Adaptation to Karst Limestone and Incipient Speciation in East Asian Platycarya spp. (Juglandaceae).}, journal = {Molecular biology and evolution}, volume = {40}, number = {6}, pages = {}, pmid = {37216901}, issn = {1537-1719}, support = {833522/ERC_/European Research Council/International ; }, mesh = {Asia, Eastern ; Calcium ; *Calcium Carbonate ; Genetic Speciation ; Genomics ; *Juglandaceae/genetics/physiology ; }, abstract = {When challenged by similar environmental conditions, phylogenetically distant taxa often independently evolve similar traits (convergent evolution). Meanwhile, adaptation to extreme habitats might lead to divergence between taxa that are otherwise closely related. These processes have long existed in the conceptual sphere, yet molecular evidence, especially for woody perennials, is scarce. The karst endemic Platycarya longipes and its only congeneric species, Platycarya strobilacea, which is widely distributed in the mountains in East Asia, provide an ideal model for examining the molecular basis of both convergent evolution and speciation. Using chromosome-level genome assemblies of both species, and whole-genome resequencing data from 207 individuals spanning their entire distribution range, we demonstrate that P. longipes and P. strobilacea form two species-specific clades, which diverged around 2.09 million years ago. We find an excess of genomic regions exhibiting extreme interspecific differentiation, potentially due to long-term selection in P. longipes, likely contributing to the incipient speciation of the genus Platycarya. Interestingly, our results unveil underlying karst adaptation in both copies of the calcium influx channel gene TPC1 in P. longipes. TPC1 has previously been identified as a selective target in certain karst-endemic herbs, indicating a convergent adaptation to high calcium stress among karst-endemic species. Our study reveals the genic convergence of TPC1 among karst endemics and the driving forces underneath the incipient speciation of the two Platycarya lineages.}, }
@article {pmid37213502, year = {2023}, author = {Díaz, M and Monfort-Lanzas, P and Quiroz-Moreno, C and Rivadeneira, E and Castillejo, P and Arnau, V and Díaz, W and Agathos, SN and Sangari, FJ and Jarrín-V, P and Molina, CA}, title = {The microbiome of the ice-capped Cayambe Volcanic Complex in Ecuador.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1154815}, pmid = {37213502}, issn = {1664-302X}, abstract = {A major challenge in microbial ecology is to understand the principles and processes by which microbes associate and interact in community assemblages. Microbial communities in mountain glaciers are unique as first colonizers and nutrient enrichment drivers for downstream ecosystems. However, mountain glaciers have been distinctively sensitive to climate perturbations and have suffered a severe retreat over the past 40 years, compelling us to understand glacier ecosystems before their disappearance. This is the first study in an Andean glacier in Ecuador offering insights into the relationship of physicochemical variables and altitude on the diversity and structure of bacterial communities. Our study covered extreme Andean altitudes at the Cayambe Volcanic Complex, from 4,783 to 5,583 masl. Glacier soil and ice samples were used as the source for 16S rRNA gene amplicon libraries. We found (1) effects of altitude on diversity and community structure, (2) the presence of few significantly correlated nutrients to community structure, (3) sharp differences between glacier soil and glacier ice in diversity and community structure, where, as quantified by the Shannon γ-diversity distribution, the meta-community in glacier soil showed more diversity than in glacier ice; this pattern was related to the higher variability of the physicochemical distribution of variables in the former substrate, and (4) significantly abundant genera associated with either high or low altitudes that could serve as biomarkers for studies on climate change. Our results provide the first assessment of these unexplored communities, before their potential disappearance due to glacier retreat and climate change.}, }
@article {pmid37212664, year = {2023}, author = {Wu, SY and Ou, CC and Lee, ML and Hsin, IL and Kang, YT and Jan, MS and Ko, JL}, title = {Polysaccharide of Ganoderma lucidum Ameliorates Cachectic Myopathy Induced by the Combination Cisplatin plus Docetaxel in Mice.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0313022}, pmid = {37212664}, issn = {2165-0497}, mesh = {Mice ; Animals ; Cisplatin/adverse effects ; Cachexia/chemically induced/drug therapy ; Docetaxel/adverse effects ; *Reishi ; Mice, Inbred C57BL ; Muscular Atrophy/chemically induced/drug therapy ; *Muscular Diseases/chemically induced/complications ; *Neoplasms ; Polysaccharides/therapeutic use ; }, abstract = {Cachexia is a lethal muscle-wasting syndrome associated with cancer and chemotherapy use. Mounting evidence suggests a correlation between cachexia and intestinal microbiota, but there is presently no effective treatment for cachexia. Whether the Ganoderma lucidum polysaccharide Liz-H exerts protective effects on cachexia and gut microbiota dysbiosis induced by the combination cisplatin plus docetaxel (cisplatin + docetaxel) was investigated. C57BL/6J mice were intraperitoneally injected with cisplatin + docetaxel, with or without oral administration of Liz-H. Body weight, food consumption, complete blood count, blood biochemistry, and muscle atrophy were measured. Next-generation sequencing was also performed to investigate changes to gut microbial ecology. Liz-H administration alleviated the cisplatin + docetaxel-induced weight loss, muscle atrophy, and neutropenia. Furthermore, upregulation of muscle protein degradation-related genes (MuRF-1 and Atrogin-1) and decline of myogenic factors (MyoD and myogenin) after treatment of cisplatin and docetaxel were prevented by Liz-H. Cisplatin and docetaxel treatment resulted in reducing comparative abundances of Ruminococcaceae and Bacteroides, but Liz-H treatment restored these to normal levels. This study indicates that Liz-H is a good chemoprotective reagent for cisplatin + docetaxel-induced cachexia. IMPORTANCE Cachexia is a multifactorial syndrome driven by metabolic dysregulation, anorexia, systemic inflammation, and insulin resistance. Approximately 80% of patients with advanced cancer have cachexia, and cachexia is the cause of death in 30% of cancer patients. Nutritional supplementation has not been shown to reverse cachexia progression. Thus, developing strategies to prevent and/or reverse cachexia is urgent. Polysaccharide is a major biologically active compound in the fungus Ganoderma lucidum. This study is the first to report that G. lucidum polysaccharides could alleviate chemotherapy-induced cachexia via reducing expression of genes that are known to drive muscle wasting, such as MuRF-1 and Atrogin-1. These results suggest that Liz-H is an effective treatment for cisplatin + docetaxel-induced cachexia.}, }
@article {pmid37211607, year = {2023}, author = {Liu, Y and Wang, H and Qian, X and Gu, J and Chen, W and Shen, X and Tao, S and Jiao, S and Wei, G}, title = {Metagenomics insights into responses of rhizobacteria and their alleviation role in licorice allelopathy.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {109}, pmid = {37211607}, issn = {2049-2618}, mesh = {*Glycyrrhiza/chemistry ; Allelopathy ; Glycyrrhizic Acid ; Metagenomics ; Rhizosphere ; }, abstract = {BACKGROUND: Allelopathy is closely associated with rhizosphere biological processes, and rhizosphere microbial communities are essential for plant development. However, our understanding of rhizobacterial communities under influence of allelochemicals in licorice remains limited. In the present study, the responses and effects of rhizobacterial communities on licorice allelopathy were investigated using a combination of multi-omics sequencing and pot experiments, under allelochemical addition and rhizobacterial inoculation treatments.<br><br>RESULTS: Here, we demonstrated that exogenous glycyrrhizin inhibits licorice development, and reshapes and enriches specific rhizobacteria and corresponding functions related to glycyrrhizin degradation. Moreover, the Novosphingobium genus accounted for a relatively high proportion of the enriched taxa and appeared in metagenomic assembly genomes. We further characterized the different capacities of single and synthetic inoculants to degrade glycyrrhizin and elucidated their distinct potency for alleviating licorice allelopathy. Notably, the single replenished N (Novosphingobium resinovorum) inoculant had the greatest allelopathy alleviation effects in licorice seedlings.<br><br>CONCLUSIONS: Altogether, the findings highlight that exogenous glycyrrhizin simulates the allelopathic autotoxicity effects of licorice, and indigenous single rhizobacteria had greater effects than synthetic inoculants in protecting licorice growth from allelopathy. The results of the present study enhance our understanding of rhizobacterial community dynamics during licorice allelopathy, with potential implications for resolving continuous cropping obstacle in medicinal plant agriculture using rhizobacterial biofertilizers. Video Abstract.}, }
@article {pmid37211183, year = {2023}, author = {Yokoyama, D and Kikuchi, J}, title = {Inferring microbial community assembly in an urban river basin through geo-multi-omics and phylogenetic bin-based null-model analysis of surface water.}, journal = {Environmental research}, volume = {231}, number = {Pt 3}, pages = {116202}, doi = {10.1016/j.envres.2023.116202}, pmid = {37211183}, issn = {1096-0953}, mesh = {Humans ; *Rivers ; Phylogeny ; Multiomics ; *Microbiota ; Stochastic Processes ; }, abstract = {Understanding the community assembly process is a central issue in microbial ecology. In this study, we analyzed the community assembly of particle-associated (PA) and free-living (FL) surface water microbiomes in 54 sites from the headstream to the river mouth of an urban river in Japan, the river basin of which has the highest human population density in the country. Analyses were conducted from two perspectives: (1) analysis of deterministic processes considering only environmental factors using a geo-multi-omics dataset and (2) analysis of deterministic and stochastic processes to estimate the contributions of heterogeneous selection (HeS), homogeneous selection (HoS), dispersal limitation (DL), homogenizing dispersal (HD), and drift (DR) as community assembly processes using a phylogenetic bin-based null model. The variation in microbiomes was successfully explained from a deterministic perspective by environmental factors, such as organic matter-related, nitrogen metabolism, and salinity-related parameters, using multivariate statistical analysis, network analysis, and habitat prediction. In addition, we demonstrated the dominance of stochastic processes (DL, HD, and DR) over deterministic processes (HeS and HoS) in community assembly from both deterministic and stochastic perspectives. Our analysis revealed that as the distance between two sites increased, the effect of HoS sharply decreased while the effect of HeS increased, particularly between upstream and estuary sites, indicating that the salinity gradient could potentially enhance the contribution of HeS to community assembly. Our study highlights the importance of both stochastic and deterministic processes in community assembly of PA and FL surface water microbiomes in urban riverine ecosystems.}, }
@article {pmid37209180, year = {2023}, author = {Kostešić, E and Mitrović, M and Kajan, K and Marković, T and Hausmann, B and Orlić, S and Pjevac, P}, title = {Microbial Diversity and Activity of Biofilms from Geothermal Springs in Croatia.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2305-2319}, pmid = {37209180}, issn = {1432-184X}, mesh = {*Hot Springs/microbiology ; Croatia ; *Cyanobacteria/genetics ; Temperature ; *Chloroflexi ; Biofilms ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Hot spring biofilms are stable, highly complex microbial structures. They form at dynamic redox and light gradients and are composed of microorganisms adapted to the extreme temperatures and fluctuating geochemical conditions of geothermal environments. In Croatia, a large number of poorly investigated geothermal springs host biofilm communities. Here, we investigated the microbial community composition of biofilms collected over several seasons at 12 geothermal springs and wells. We found biofilm microbial communities to be temporally stable and highly dominated by Cyanobacteria in all but one high-temperature sampling site (Bizovac well). Of the physiochemical parameters recorded, temperature had the strongest influence on biofilm microbial community composition. Besides Cyanobacteria, the biofilms were mainly inhabited by Chloroflexota, Gammaproteobacteria, and Bacteroidota. In a series of incubations with Cyanobacteria-dominated biofilms from Tuhelj spring and Chloroflexota- and Pseudomonadota-dominated biofilms from Bizovac well, we stimulated either chemoorganotrophic or chemolithotrophic community members, to determine the fraction of microorganisms dependent on organic carbon (in situ predominantly produced via photosynthesis) versus energy derived from geochemical redox gradients (here simulated by addition of thiosulfate). We found surprisingly similar levels of activity in response to all substrates in these two distinct biofilm communities, and observed microbial community composition and hot spring geochemistry to be poor predictors of microbial activity in the study systems.}, }
@article {pmid37207751, year = {2023}, author = {Jin, Z and Shen, M and Wang, L and Wang, C and Gao, M and Yu, G and Chang, Z and Zhang, X}, title = {Antibacterial and immunoregulatory activity of an antimicrobial peptide hepcidin in loach (Misgurnus anguillicaudatus).}, journal = {International journal of biological macromolecules}, volume = {242}, number = {Pt 2}, pages = {124833}, doi = {10.1016/j.ijbiomac.2023.124833}, pmid = {37207751}, issn = {1879-0003}, mesh = {Animals ; Hepcidins/genetics/metabolism ; Antimicrobial Peptides ; Anti-Bacterial Agents/pharmacology ; Saccharomyces cerevisiae/metabolism ; Gene Expression Regulation ; Amino Acid Sequence ; Fish Proteins/chemistry ; Gram-Negative Bacteria/metabolism ; Gram-Positive Bacteria/metabolism ; *Cypriniformes/genetics ; *Bacterial Infections ; Peptides/metabolism ; Bacteria/metabolism ; Amino Acids/metabolism ; }, abstract = {Antimicrobial peptides (AMPs) are members of humoral immunity and particpate in resisting microbial invasion. In this study, an AMP gene hepcidin was obtained from the oriental loach Misgurnus anguillicaudatus and named Ma-Hep. This Ma-Hep encodes a peptide of 90 amino acids, with a predicted active peptide segment (Ma-sHep) of 25 amino acids at C terminus. Stimulation by a bacterial pathogen Aeromonas hydrophila resulted in significant up-regulation of Ma-Hep transcripts in loach midgut, head kidney, and gill. Ma-Hep and Ma-sHep proteins were expressed in Pichia pastoris and their antibacterial activity was examined. Results showed that Ma-sHep possessed stronger antibacterial activity against various Gram-positive and Gram-negative bacteria, compared to Ma-Hep. Scanning electron microscopy showed that Ma-sHep might kill bacteria by destroying bacterial cell membranes. Moreover, we found that Ma-sHep had an inhibitory effect on blood cell apoptosis induced by A. hydrophila and facilitated the bacterial phagocytosis and clearance in loach. Histopathological analysis indicated Ma-sHep could protect liver and gut of loach from bacterial infection. Ma-sHep has high thermal stability and PH stability, which is conducive to further feed addition. Feed supplemented with Ma-sHep expressing yeast improved the intestinal flora of loach by increasing the dominant bacteria and decreasing the harmful bacteria. Feed supplemented with Ma-sHep expressing yeast also regulated the expression of inflammatory related factors in various tissues of loach and reduced the mortality of loach upon bacterial infection. These findings show that the antibacterial peptide Ma-sHep is involved in the antibacterial defense of loach and can be used as a candidate for new antimicrobial agents in aquaculture.}, }
@article {pmid37206339, year = {2023}, author = {Rasmussen, KL and Stamps, BW and Vanzin, GF and Ulrich, SM and Spear, JR}, title = {Spatial and temporal dynamics at an actively silicifying hydrothermal system.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1172798}, pmid = {37206339}, issn = {1664-302X}, abstract = {Steep Cone Geyser is a unique geothermal feature in Yellowstone National Park (YNP), Wyoming, actively gushing silicon-rich fluids along outflow channels possessing living and actively silicifying microbial biomats. To assess the geomicrobial dynamics occurring temporally and spatially at Steep Cone, samples were collected at discrete locations along one of Steep Cone's outflow channels for both microbial community composition and aqueous geochemistry analysis during field campaigns in 2010, 2018, 2019, and 2020. Geochemical analysis characterized Steep Cone as an oligotrophic, surface boiling, silicious, alkaline-chloride thermal feature with consistent dissolved inorganic carbon and total sulfur concentrations down the outflow channel ranging from 4.59 ± 0.11 to 4.26 ± 0.07 mM and 189.7 ± 7.2 to 204.7 ± 3.55 μM, respectively. Furthermore, geochemistry remained relatively stable temporally with consistently detectable analytes displaying a relative standard deviation <32%. A thermal gradient decrease of ~55°C was observed from the sampled hydrothermal source to the end of the sampled outflow transect (90.34°C ± 3.38 to 35.06°C ± 7.24). The thermal gradient led to temperature-driven divergence and stratification of the microbial community along the outflow channel. The hyperthermophile Thermocrinis dominates the hydrothermal source biofilm community, and the thermophiles Meiothermus and Leptococcus dominate along the outflow before finally giving way to more diverse and even microbial communities at the end of the transect. Beyond the hydrothermal source, phototrophic taxa such as Leptococcus, Chloroflexus, and Chloracidobacterium act as primary producers for the system, supporting heterotrophic growth of taxa such as Raineya, Tepidimonas, and Meiothermus. Community dynamics illustrate large changes yearly driven by abundance shifts of the dominant taxa in the system. Results indicate Steep Cone possesses dynamic outflow microbial communities despite stable geochemistry. These findings improve our understanding of thermal geomicrobiological dynamics and inform how we can interpret the silicified rock record.}, }
@article {pmid37206314, year = {2023}, author = {Van de Walle, A and Kim, M and Alam, MK and Wang, X and Wu, D and Dash, SR and Rabaey, K and Kim, J}, title = {Greywater reuse as a key enabler for improving urban wastewater management.}, journal = {Environmental science and ecotechnology}, volume = {16}, number = {}, pages = {100277}, pmid = {37206314}, issn = {2666-4984}, abstract = {Sustainable water management is essential to guaranteeing access to safe water and addressing the challenges posed by climate change, urbanization, and population growth. In a typical household, greywater, which includes everything but toilet waste, constitutes 50-80% of daily wastewater generation and is characterized by low organic strength and high volume. This can be an issue for large urban wastewater treatment plants designed for high-strength operations. Segregation of greywater at the source for decentralized wastewater treatment is therefore necessary for its proper management using separate treatment strategies. Greywater reuse may thus lead to increased resilience and adaptability of local water systems, reduction in transport costs, and achievement of fit-for-purpose reuse. After covering greywater characteristics, we present an overview of existing and upcoming technologies for greywater treatment. Biological treatment technologies, such as nature-based technologies, biofilm technologies, and membrane bioreactors (MBR), conjugate with physicochemical treatment methods, such as membrane filtration, sorption and ion exchange technologies, and ultraviolet (UV) disinfection, may be able to produce treated water within the allowable parameters for reuse. We also provide a novel way to tackle challenges like the demographic variance of greywater quality, lack of a legal framework for greywater management, monitoring and control systems, and the consumer perspective on greywater reuse. Finally, benefits, such as the potential water and energy savings and sustainable future of greywater reuse in an urban context, are discussed.}, }
@article {pmid37204848, year = {2023}, author = {Rattray, JB and Kramer, PJ and Gurney, J and Thomas, S and Brown, SP}, title = {The dynamic response of quorum sensing to density is robust to signal supplementation and individual signal synthase knockouts.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {5}, pages = {}, pmid = {37204848}, issn = {1465-2080}, support = {R21 AI156817/AI/NIAID NIH HHS/United States ; }, mesh = {*Quorum Sensing/genetics ; *Bacterial Proteins/genetics/metabolism ; Homoserine/metabolism ; Pseudomonas aeruginosa/metabolism ; Dietary Supplements ; }, abstract = {Quorum sensing (QS) is a widespread mechanism of environment sensing and behavioural coordination in bacteria. At its core, QS is based on the production, sensing and response to small signalling molecules. Previous work with Pseudomonas aeruginosa shows that QS can be used to achieve quantitative resolution and deliver a dosed response to the bacteria's density environment, implying a sophisticated mechanism of control. To shed light on how the mechanistic signal components contribute to graded responses to density, we assess the impact of genetic (AHL signal synthase deletion) and/or signal supplementation (exogenous AHL addition) perturbations on lasB reaction-norms to changes in density. Our approach condenses data from 2000 timeseries (over 74 000 individual observations) into a comprehensive view of QS-controlled gene expression across variation in genetic, environmental and signal determinants of lasB expression. We first confirm that deleting either (∆lasI, ∆rhlI) or both (∆lasIrhlI) AHL signal synthase gene attenuates QS response to density. In the ∆rhlI background we show persistent yet attenuated density-dependent lasB expression due to native 3-oxo-C12-HSL signalling. We then test if density-independent quantities of AHL signal (3-oxo-C12-HSL, C4-HSL) added to the WT either flatten or increase responsiveness to density and find that the WT response is robust to all tested concentrations of signal, alone or in combination. We then move to progressively supplementing the genetic knockouts and find that cognate signal supplementation of a single AHL signal (∆lasI +3-oxo-C12-HSL, ∆rhlI +C4HSL) is sufficient to restore the ability to respond in a density-dependent manner to increasing density. We also find that dual signal supplementation of the double AHL synthase knockout restores the ability to produce a graded response to increasing density, despite adding a density-independent amount of signal. Only the addition of high concentrations of both AHLs and PQS can force maximal lasB expression and ablate responsiveness to density. Our results show that density-dependent control of lasB expression is robust to multiple combinations of QS gene deletion and density-independent signal supplementation. Our work develops a modular approach to query the robustness and mechanistic bases of the central environmental sensing phenotype of quorum sensing.}, }
@article {pmid37201636, year = {2023}, author = {He, Y and Xu, M and Lu, S and Zou, W and Wang, Y and Fakhar-E-Alam Kulyar, M and Iqbal, M and Li, K}, title = {Seaweed polysaccharides treatment alleviates injury of inflammatory responses and gut barrier in LPS-induced mice.}, journal = {Microbial pathogenesis}, volume = {180}, number = {}, pages = {106159}, doi = {10.1016/j.micpath.2023.106159}, pmid = {37201636}, issn = {1096-1208}, mesh = {Mice ; Humans ; Animals ; *Lipopolysaccharides/pharmacology ; Dysbiosis/chemically induced/drug therapy ; RNA, Ribosomal, 16S/genetics ; *Seaweed ; Polysaccharides/pharmacology ; Bacteria ; Vegetables ; }, abstract = {Gastrointestinal (GI) disease is a common digestive tract disease effects health of millions of human globally each year, thus the role of intestinal microflora had been emphasized. Seaweed polysaccharides featured a wide range of pharmacological activities, such as antioxidant activity and pharmacological action, but whether they can alleviate the dysbiosis of gut microbial ecology caused by lipopolysaccharide (LPS) exposure has not been well conducted. In this study, we investigated the effects of different concentration of seaweed polysaccharides on LPS-induced intestinal disorder by using hematoxylin and eosin (H&amp;E) staining and 16S rRNA high-throughput sequencing. Histopathological results indicated that the intestinal structure in the LPS-induced group was damaged. Furthermore, LPS exposure not only reduced the intestinal microbial diversity in mice but also induced considerable transformation in its composition, along with significant increase in pathogenic bacteria (Helicobacter, Citrobacter and Mucispirillum) and decrease in beneficial bacteria (Firmicutes, Lactobacillus, Akkermansia and Parabacteroides). Nonetheless, seaweed polysaccharides administration could recover the gut microbial dysbiosis and the loss of gut microbial diversity induced by LPS exposure. In summary, seaweed polysaccharides were effective against LPS-induced intestinal damage in mice via the modulation of intestinal microecology.}, }
@article {pmid37200211, year = {2023}, author = {Pascual, J and Lepleux, C and Methner, A and Spröer, C and Bunk, B and Overmann, J}, title = {Arcobacter roscoffensis sp. nov., a marine bacterium isolated from coastal seawater.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {5}, pages = {}, doi = {10.1099/ijsem.0.005895}, pmid = {37200211}, issn = {1466-5034}, mesh = {*Fatty Acids/chemistry ; Phospholipids/analysis ; *Arcobacter ; RNA, Ribosomal, 16S/genetics ; Base Composition ; Phylogeny ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Bacterial Typing Techniques ; Seawater/microbiology ; }, abstract = {A novel Gram-negative, aerobic, motile, rod-shaped, beige-pigmented bacterium, strain ARW1-2F2[T], was isolated from a seawater sample collected from Roscoff, France. Strain ARW1-2F2[T] was catalase-negative and oxidase-positive, and grew under mesophilic, neutrophilic and halophilic conditions. The 16S rRNA sequences revealed that strain ARW1-2F2[T] was closely related to Arcobacter lekithochrous LFT 1.7[T] and Arcobacter caeni RW17-10[T](95.8 and 95.5 % gene sequence similarity, respectively). The genome of strain ARW1-2F2[T] was sequenced and had a G+C content of 28.7%. Two different measures of genome similarity, average nucleotide identity based on blast and digital DNA-DNA hybridization, indicated that strain ARW1-2F2[T] represents a new Arcobacter species. The predominant fatty acids were C16 : 1 ω7c/C16 : 1 ω6c and C18 : 1 ω7c/C18 : 1 ω6c. The results of a polyphasic analysis supported the description of strain ARW1-2F2[T] as representing a novel species of the genus Arcobacter, for which the name Arcobacter roscoffensis sp. nov. is proposed with the type strain ARW1-2F2[T] (DSM 29169[T]=KCTC 52423[T]).}, }
@article {pmid37199998, year = {2023}, author = {Getz, EW and Lanclos, VC and Kojima, CY and Cheng, C and Henson, MW and Schön, ME and Ettema, TJG and Faircloth, BC and Thrash, JC}, title = {The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct.}, journal = {mSystems}, volume = {8}, number = {3}, pages = {e0017923}, pmid = {37199998}, issn = {2379-5077}, support = {Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation/ ; OCE-1945279, EF-2125191//National Science Foundation/ ; }, mesh = {*Seawater/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Aquatic Organisms ; Bacteria/genetics ; *Alphaproteobacteria ; }, abstract = {Bacterioplankton of the SAR11 clade are the most abundant marine microorganisms and consist of numerous subclades spanning order-level divergence (Pelagibacterales). The assignment of the earliest diverging subclade V (a.k.a. HIMB59) to the Pelagibacterales is highly controversial, with multiple recent phylogenetic studies placing them completely separate from SAR11. Other than through phylogenomics, subclade V has not received detailed examination due to limited genomes from this group. Here, we assessed the ecogenomic characteristics of subclade V to better understand the role of this group in comparison to the Pelagibacterales. We used a new isolate genome, recently released single-amplified genomes and metagenome-assembled genomes, and previously established SAR11 genomes to perform a comprehensive comparative genomics analysis. We paired this analysis with the recruitment of metagenomes spanning the open ocean, coastal, and brackish systems. Phylogenomics, average amino acid identity, and 16S rRNA gene phylogeny indicate that SAR11 subclade V is synonymous with the ubiquitous AEGEAN-169 clade and support the contention that this group represents a taxonomic family. AEGEAN-169 shared many bulk genome qualities with SAR11, such as streamlining and low GC content, but genomes were generally larger. AEGEAN-169 had overlapping distributions with SAR11 but was metabolically distinct from SAR11 in its potential to transport and utilize a broader range of sugars as well as in the transport of trace metals and thiamin. Thus, regardless of the ultimate phylogenetic placement of AEGEAN-169, these organisms have distinct metabolic capacities that likely allow them to differentiate their niche from canonical SAR11 taxa. IMPORTANCE One goal of marine microbiologists is to uncover the roles various microorganisms are playing in biogeochemical cycles. Success in this endeavor relies on differentiating groups of microbes and circumscribing their relationships. An early-diverging group (subclade V) of the most abundant bacterioplankton, SAR11, has recently been proposed as a separate lineage that does not share a most recent common ancestor. But beyond phylogenetics, little has been done to evaluate how these organisms compare with SAR11. Our work leverages dozens of new genomes to demonstrate the similarities and differences between subclade V and SAR11. In our analysis, we also establish that subclade V is synonymous with a group of bacteria established from 16S rRNA gene sequences, AEGEAN-169. Subclade V/AEGEAN-169 has clear metabolic distinctions from SAR11 and their shared traits point to remarkable convergent evolution if they do not share a most recent common ancestor.}, }
@article {pmid37196970, year = {2023}, author = {Farrell, ML and Chueiri, A and O'Connor, L and Duane, S and Maguire, M and Miliotis, G and Cormican, M and Hooban, B and Leonard, A and Gaze, WH and Devane, G and Tuohy, A and Burke, LP and Morris, D}, title = {Assessing the impact of recreational water use on carriage of antimicrobial resistant organisms.}, journal = {The Science of the total environment}, volume = {888}, number = {}, pages = {164201}, doi = {10.1016/j.scitotenv.2023.164201}, pmid = {37196970}, issn = {1879-1026}, mesh = {Adult ; Humans ; *Enterobacteriaceae Infections/epidemiology ; Water ; beta-Lactamases ; Carbapenems ; Feces ; *Gammaproteobacteria ; *Anti-Infective Agents ; Anti-Bacterial Agents ; }, abstract = {Understanding the role of exposure to natural recreational waters in the acquisition and transmission of antimicrobial resistance (AMR) is an area of increasing interest. A point prevalence study was carried out in the island of Ireland to determine the prevalence of colonisation with extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) and carbapenem-resistant Enterobacterales (CRE) in recreational water users (WU) and matched controls. A total of 411 adult participants (199 WU, 212 controls) submitted at least one faecal sample between September 2020 - October 2021. In total, 80 Enterobacterales were isolated from 73 participants. ESBL-PE were detected in 29 (7.1 %) participants (7 WU, 22 controls), and CRE were detected in nine (2.2 %) participants (4 WU, 5 controls). No carbapenemase-producing Enterobacterales (CPE) were detected. WU were significantly less likely to harbour ESBL-PE than controls (risk ratio = 0.34, 95 % CI 0.148 to 0.776, χ[2] 7.37, p = 0.007). This study demonstrates the occurrence of ESBL-PE and CRE in healthy participants in Ireland. Recreational exposure to bathing water in Ireland was associated with a decreased prevalence of colonisation with ESBL-PE and CRE.}, }
@article {pmid37196741, year = {2023}, author = {Lin, B and Tan, B and Zhang, Q and Li, M and Peng, H and Su, J and He, J and Zhang, Y and Liu, X and Wu, N}, title = {Unraveling the nexus of Cr (VI), aniline, and microbial ecology on aniline-degrading biosystem: Removal efficiency, sludge type, microbial ecology.}, journal = {Bioresource technology}, volume = {382}, number = {}, pages = {129185}, doi = {10.1016/j.biortech.2023.129185}, pmid = {37196741}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Denitrification ; Bioreactors/microbiology ; Nitrification ; Aniline Compounds/metabolism ; Nitrogen/metabolism ; }, abstract = {In order to explore the stress principle of Cr (Ⅵ) on aniline biodegradation system, a control group and experimental groups with the concentration of Cr (Ⅵ) at 2, 5, 8 mg/L were set up. The results demonstrated that Cr (Ⅵ) had minimal effects on the degradation efficiency of aniline but significantly inhibited nitrogen removal function. When Cr (Ⅵ) concentration was below 5 mg/L, the nitrification performance recovered spontaneously, while denitrification performance was severely impaired. Furthermore, the secretion of extracellular polymeric substances (EPS) and its fluorescence substance concentration were strongly inhibited with increasing Cr (Ⅵ) concentration. High-throughput sequencing revealed that the experimental groups were enriched with Leucobacter and Cr (Ⅵ)-reducing bacteria, but the abundance of nitrifiers and denitrifiers was significantly decreased compared to the control group. Overall, the effects of Cr (Ⅵ) stress at different concentrations on nitrogen removal performance were more significant than those on aniline degradation.}, }
@article {pmid37196568, year = {2023}, author = {Xu, Y and Teng, Y and Wang, X and Ren, W and Zhao, L and Luo, Y and Christie, P and Greening, C}, title = {Endogenous biohydrogen from a rhizobium-legume association drives microbial biodegradation of polychlorinated biphenyl in contaminated soil.}, journal = {Environment international}, volume = {176}, number = {}, pages = {107962}, doi = {10.1016/j.envint.2023.107962}, pmid = {37196568}, issn = {1873-6750}, mesh = {*Polychlorinated Biphenyls/analysis ; *Rhizobium/metabolism ; *Fabaceae/metabolism ; Ecosystem ; *Soil Pollutants/analysis ; Biodegradation, Environmental ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Endogenous hydrogen (H2) is produced through rhizobium-legume associations in terrestrial ecosystems worldwide through dinitrogen fixation. In turn, this gas may alter rhizosphere microbial community structure and modulate biogeochemical cycles. However, very little is understood about the role that this H2 leaking to the rhizosphere plays in shaping the persistent organic pollutants degrading microbes in contaminated soils. Here, we combined DNA-stable isotope probing (DNA-SIP) with metagenomics to explore how endogenous H2 from the symbiotic rhizobium-alfalfa association drives the microbial biodegradation of tetrachlorobiphenyl PCB 77 in a contaminated soil. The results showed that PCB77 biodegradation efficiency increased significantly in soils treated with endogenous H2. Based on metagenomes of [13]C-enriched DNA fractions, endogenous H2 selected bacteria harboring PCB degradation genes. Functional gene annotation allowed the reconstruction of several complete pathways for PCB catabolism, with different taxa conducting successive metabolic steps of PCB metabolism. The enrichment through endogenous H2 of hydrogenotrophic Pseudomonas and Magnetospirillum encoding biphenyl oxidation genes drove PCB biodegradation. This study proves that endogenous H2 is a significant energy source for active PCB-degrading communities and suggests that elevated H2 can influence the microbial ecology and biogeochemistry of the legume rhizosphere.}, }
@article {pmid37195192, year = {2023}, author = {Wang, J and Pan, Z and Yu, J and Zhang, Z and Li, YZ}, title = {Global assembly of microbial communities.}, journal = {mSystems}, volume = {8}, number = {3}, pages = {e0128922}, pmid = {37195192}, issn = {2379-5077}, support = {32070030//National Natural Science Foundation of China (NSFC)/ ; 2018YFA0900400, 2018YFA0901704//MOST | National Key Research and Development Program of China (NKPs)/ ; ZR2022QC229//Science Foundation for Youths of Shandong Province/ ; 2022M711918//China Postdoctoral Science Foundation/ ; SDCX-ZG-20220201//Postdoctoral Innovation Project of Shandong Province ()/ ; 32201303//National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Bacteria/genetics ; *Microbiota/genetics ; Microbial Interactions ; Genes, Bacterial ; Stochastic Processes ; }, abstract = {Different habitats harbor different microbial communities with elusive assembly mechanisms. This study comprehensively investigated the global assembly mechanisms of microbial communities and effects of community-internal influencing factors using the Earth Microbiome Project (EMP) data set. We found that deterministic and stochastic processes contribute approximately equally to global microbial community assembly, and, specifically, deterministic processes generally play a major role in free-living and plant-associated (but not plant corpus) environments, while stochastic processes are the major contributor in animal-associated environments. In contrast with the assembly of microorganisms, the assembly of functional genes, predicted from PICRUSt, is mainly attributed to deterministic processes in all microbial communities. The sink and source microbial communities are normally assembled using similar mechanisms, and the core microorganisms are specific to different environment types. On a global scale, deterministic processes are positively related to the community alpha diversity, microbial interaction degree and bacterial predatory-specific gene abundance. Our analysis provides a panoramic picture and regularities of global and environment-typical microbial community assemblies. IMPORTANCE With the development of sequencing technologies, the research topic of microbial ecology has evolved from the analysis of community composition to community assembly, including the relative contribution of deterministic and stochastic processes for the formation and maintenance of community diversity. Many studies have reported the microbial assembly mechanisms in various habitats, but the assembly regularities of global microbial communities remain unknown. In this study, we analyzed the EMP data set using a combined pipeline to explore the assembly mechanisms of global microbial communities, microbial sources to construct communities, core microbes in different environment types, and community-internal factors influencing assembly. The results provide a panoramic picture and rules of global and environment-typical microbial community assemblies, which enhances our understandings of the mechanisms globally controlling community diversity and species coexistence.}, }
@article {pmid37193669, year = {2023}, author = {Delbaere, K and Roegiers, I and Bron, A and Durif, C and Van de Wiele, T and Blanquet-Diot, S and Marinelli, L}, title = {The small intestine: dining table of host-microbiota meetings.}, journal = {FEMS microbiology reviews}, volume = {47}, number = {3}, pages = {}, pmid = {37193669}, issn = {1574-6976}, mesh = {*Intestine, Small/microbiology ; *Microbiota ; Diet ; }, abstract = {Growing evidence suggests the importance of the small intestinal bacteria in the diet-host-microbiota dialogue in various facets of health and disease. Yet, this body site is still poorly explored and its ecology and mechanisms of interaction with the host are just starting to be unraveled. In this review, we describe the current knowledge on the small intestinal ecology, its composition and diversity, and how the intestinal bacteria in homeostatic conditions participate in nutrient digestion and absorption. We illustrate the importance of a controlled bacterial density and of the preservation of absorptive surface for the host's nutritional status. In particular, we discuss these aspects of the small intestinal environment in the framework of two disease conditions, namely small intestinal bacterial overgrowth (SIBO) and short bowel syndrome (SBS). We also detail in vivo, ex vivo, and in vitro models developed to simulate the small intestinal environment, some applied for (diet-)host-bacteria interaction studies. Lastly, we highlight recent technological, medical, and scientific advances applicable to investigate this complex and yet understudied body environment to broaden our knowledge in support of further progress in the medical practice, and to proceed towards the integration of the (small)intestinal bacteria in personalized therapeutic approaches.}, }
@article {pmid37191674, year = {2023}, author = {Zhao, J and Fan, D and Guo, W and Wu, J and Zhang, X and Zhuang, X and Kong, W}, title = {Precipitation Drives Soil Protist Diversity and Community Structure in Dry Grasslands.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2293-2304}, pmid = {37191674}, issn = {1432-184X}, support = {41771303//NSFC/ ; }, mesh = {*Ecosystem ; Grassland ; Soil/chemistry ; Biomass ; Plants ; *Microbiota ; Soil Microbiology ; }, abstract = {Protists are essential components of soil microbial communities, mediating nutrient cycling and ecosystem functions in terrestrial ecosystems. However, their distribution patterns and driving factors, particularly, the relative importance of climate, plant and soil factors, remain largely unknown. This limits our understanding of soil protist roles in ecosystem functions and their responses to climate change. This is particularly a concern in dryland ecosystems where soil microbiomes are more important for ecosystem functions because plant diversity and growth are heavily constrained by environmental stresses. Here, we explored protist diversity and their driving factors in grassland soils on the Tibetan Plateau, which is a typical dryland region with yearly low temperatures. Soil protist diversity significantly decreased along the gradient of meadow, steppe, and desert. Soil protist diversity positively correlated with precipitation, plant biomass and soil nutrients, but these correlations were changed by grazing. Structural equation and random forest models demonstrated that precipitation dominated soil protist diversity directly and indirectly by influencing plant and soil factors. Soil protist community structure gradually shifted along meadow, steppe and desert, and was driven more by precipitation than by plant and soil factors. Soil protist community compositions were dominated by Cercozoa, Ciliophora and Chlorophyta. In particular, Ciliophora increased but Chlorophyta decreased in relative abundance along the gradient of meadow, steppe and desert. These results demonstrate that precipitation plays more important roles in driving soil protist diversity and community structure than plant and soil factors, suggesting that future precipitation change profoundly alters soil protist community and functions in dry grasslands.}, }
@article {pmid37190986, year = {2023}, author = {Yang, Y and Suyamud, B and Liang, S and Liang, X and Wan, W and Zhang, W}, title = {Distinct spatiotemporal succession of bacterial generalists and specialists in the lacustrine plastisphere.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {2746-2760}, doi = {10.1111/1462-2920.16400}, pmid = {37190986}, issn = {1462-2920}, support = {[2020SWG04]//Foundation of the State Key Laboratory of Water Resources and Hydropower Engineering Science (Wuhan University), China/ ; E0291P0101//Funding Project of Sino-Africa Joint Research Center, Chinese Academy of Sciences/ ; 32071614//National Natural Science Foundation of China/ ; 42107147//National Natural Science Foundation of China/ ; Y9519802//the Starting Research Fund and Opening Research Fund from Key Laboratory of Aquatic Botany and Watershed Ecology, Chinese Academy of Sciences/ ; E0520202//the Starting Research Fund and Opening Research Fund from Key Laboratory of Aquatic Botany and Watershed Ecology, Chinese Academy of Sciences/ ; }, mesh = {*Ecosystem ; *Plastics ; Bacteria/genetics ; Stochastic Processes ; }, abstract = {The assembly processes of generalists and specialists and their driving mechanisms during spatiotemporal succession is a central issue in microbial ecology but a poorly researched subject in the plastisphere. We investigated the composition variation, spatiotemporal succession, and assembly processes of bacterial generalists and specialists in the plastisphere, including non-biodegradable (NBMPs) and biodegradable microplastics (BMPs). Although the composition of generalists and specialists on NBMPs differed from that of BMPs, colonization time mainly mediated the composition variation. The relative abundance of generalists and the relative contribution of species replacement were initially increased and then decreased with colonization time, while the specialists initially decreased and then increased. Besides, the richness differences also affected the composition variation of generalists and specialists in the plastisphere, and the generalists were more susceptible to richness differences than corresponding specialists. Furthermore, the assembly of generalists in the plastisphere was dominated by deterministic processes, while stochastic processes dominated the assembly of specialists. The network stability test showed that the community stability of generalists on NBMPs and BMPs was lower than corresponding specialists. Our results suggested that different ecological assembly processes shaped the spatiotemporal succession of bacterial generalists and specialists in the plastisphere, but were less influenced by polymer types.}, }
@article {pmid37188915, year = {2023}, author = {Moeller, FU and Herbold, CW and Schintlmeister, A and Mooshammer, M and Motti, C and Glasl, B and Kitzinger, K and Behnam, F and Watzka, M and Schweder, T and Albertsen, M and Richter, A and Webster, NS and Wagner, M}, title = {Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta.}, journal = {The ISME journal}, volume = {17}, number = {8}, pages = {1208-1223}, pmid = {37188915}, issn = {1751-7370}, support = {T 1218/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; *Porifera/microbiology ; Taurine ; Ammonia ; Carbon ; Symbiosis ; Phylogeny ; }, abstract = {Marine sponges are critical components of marine benthic fauna assemblages, where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, diverse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways. By using a combination of metaproteogenomics and laboratory incubations coupled with isotope-based functional assays, we showed that the dominant gammaproteobacterial symbiont, 'Candidatus Taurinisymbion ianthellae', residing in the marine sponge, Ianthella basta, expresses a pathway for the import and dissimilation of taurine, a ubiquitously occurring sulfonate metabolite in marine sponges. 'Candidatus Taurinisymbion ianthellae' incorporates taurine-derived carbon and nitrogen while, at the same time, oxidizing the dissimilated sulfite into sulfate for export. Furthermore, we found that taurine-derived ammonia is exported by the symbiont for immediate oxidation by the dominant ammonia-oxidizing thaumarchaeal symbiont, 'Candidatus Nitrosospongia ianthellae'. Metaproteogenomic analyses also suggest that 'Candidatus Taurinisymbion ianthellae' imports DMSP and possesses both pathways for DMSP demethylation and cleavage, enabling it to use this compound as a carbon and sulfur source for biomass, as well as for energy conservation. These results highlight the important role of biogenic sulfur compounds in the interplay between Ianthella basta and its microbial symbionts.}, }
@article {pmid37188366, year = {2023}, author = {Harder, CB and Hesling, E and Botnen, SS and Lorberau, KE and Dima, B and von Bonsdorff-Salminen, T and Niskanen, T and Jarvis, SG and Ouimette, A and Hester, A and Hobbie, EA and Taylor, AFS and Kauserud, H}, title = {Mycena species can be opportunist-generalist plant root invaders.}, journal = {Environmental microbiology}, volume = {25}, number = {10}, pages = {1875-1893}, doi = {10.1111/1462-2920.16398}, pmid = {37188366}, issn = {1462-2920}, mesh = {*Mycorrhizae ; *Agaricales ; Symbiosis ; Plants/microbiology ; Plant Roots/microbiology ; }, abstract = {Traditional strict separation of fungi into ecological niches as mutualist, parasite or saprotroph is increasingly called into question. Sequences of assumed saprotrophs have been amplified from plant root interiors, and several saprotrophic genera can invade and interact with host plants in laboratory growth experiments. However, it is uncertain if root invasion by saprotrophic fungi is a widespread phenomenon and if laboratory interactions mirror field conditions. Here, we focused on the widespread and speciose saprotrophic genus Mycena and performed (1) a systematic survey of their occurrences (in ITS1/ITS2 datasets) in mycorrhizal roots of 10 plant species, and (2) an analysis of natural abundances of [13] C/[15] N stable isotope signatures of Mycena basidiocarps from five field locations to examine their trophic status. We found that Mycena was the only saprotrophic genus consistently found in 9 out of 10 plant host roots, with no indication that the host roots were senescent or otherwise vulnerable. Furthermore, Mycena basidiocarps displayed isotopic signatures consistent with published [13] C/[15] N profiles of both saprotrophic and mutualistic lifestyles, supporting earlier laboratory-based studies. We argue that Mycena are widespread latent invaders of healthy plant roots and that Mycena species may form a spectrum of interactions besides saprotrophy also in the field.}, }
@article {pmid37187536, year = {2023}, author = {Liao, Q and Ye, Y and Li, Z and Chen, H and Zhuo, L}, title = {Prediction of miRNA-disease associations in microbes based on graph convolutional networks and autoencoders.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1170559}, pmid = {37187536}, issn = {1664-302X}, abstract = {MicroRNAs (miRNAs) are short RNA molecular fragments that regulate gene expression by targeting and inhibiting the expression of specific RNAs. Due to the fact that microRNAs affect many diseases in microbial ecology, it is necessary to predict microRNAs' association with diseases at the microbial level. To this end, we propose a novel model, termed as GCNA-MDA, where dual-autoencoder and graph convolutional network (GCN) are integrated to predict miRNA-disease association. The proposed method leverages autoencoders to extract robust representations of miRNAs and diseases and meantime exploits GCN to capture the topological information of miRNA-disease networks. To alleviate the impact of insufficient information for the original data, the association similarity and feature similarity data are combined to calculate a more complete initial basic vector of nodes. The experimental results on the benchmark datasets demonstrate that compared with the existing representative methods, the proposed method has achieved the superior performance and its precision reaches up to 0.8982. These results demonstrate that the proposed method can serve as a tool for exploring miRNA-disease associations in microbial environments.}, }
@article {pmid37186228, year = {2023}, author = {Woksepp, H and Camara, F and Bonnedahl, J}, title = {High prevalence of blaCTX-M-15 type extended-spectrum beta-lactamases in Gambian hooded vultures (Necrosyrtes monachus): A threatened species with substantial human interaction.}, journal = {MicrobiologyOpen}, volume = {12}, number = {2}, pages = {e1349}, pmid = {37186228}, issn = {2045-8827}, mesh = {Animals ; Humans ; *Escherichia coli ; *Escherichia coli Infections/microbiology ; Endangered Species ; Gambia ; Colistin ; Prevalence ; beta-Lactamases/genetics ; Anti-Bacterial Agents/pharmacology ; Klebsiella pneumoniae/genetics ; Birds ; Microbial Sensitivity Tests ; }, abstract = {One hundred fecal samples from hooded vultures in the Gambia (Banjul area) were investigated for the presence of bacteria with extended-spectrum cephalosporin- (ESBL/AmpC), carbapenemases, and colistin resistance. No Enterobacteriales carrying carbapenemases or resistance against colistin were detected. Fifty-four ESBL-producing Escherichia coli and five ESBL-producing Klebsiella pneumoniae isolates were identified in 52 of the samples, of which 52 E. coli and 4 K. pneumoniae yielded passed sequencing results. Fifty of the E. coli had ESBL phenotype and genotype harboring blaCTX-M genes, of which 88.5% (n = 46) were the blaCTX-M-15 gene, commonly found on the African continent. Furthermore, the genetic context around blaCTX-M-15 was similar between isolates, being colocalized with ISKpn19. In contrast, cgMLST analysis of the E. coli harboring ESBL genes revealed a genetic distribution over a large fraction of the currently known existing E. coli populations in the Gambia. Hooded vultures in the Gambia thus have a high ESBL E. coli-prevalence (>50%) with low diversity regarding key resistance genes. Furthermore, given the urban presence and frequent interactions between hooded vultures and humans, data from this study implies hooded vultures as potential vectors contributing to the further dissemination of antibiotic-resistance genes.}, }
@article {pmid37185621, year = {2023}, author = {Li, J and Liu, T and McIlroy, SJ and Tyson, GW and Guo, J}, title = {Phylogenetic and metabolic diversity of microbial communities performing anaerobic ammonium and methane oxidations under different nitrogen loadings.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {39}, pmid = {37185621}, issn = {2730-6151}, abstract = {The microbial guild coupling anammox and nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) is an innovative process to achieve energy-efficient nitrogen removal with the beneficial use of methane in biogas or in anaerobically treated wastewater. Here, metagenomics and metatranscriptomics were used to reveal the microbial ecology of two biofilm systems, which incorporate anammox and n-DAMO for high-level nitrogen removal in low-strength domestic sewage and high-strength sidestream wastewater, respectively. We find that different nitrogen loadings (i.e., 0.1 vs. 1.0 kg N/m[3]/d) lead to different combinations of anammox bacteria and anaerobic methanotrophs ("Candidatus Methanoperedens" and "Candidatus Methylomirabilis"), which play primary roles for carbon and nitrogen transformations therein. Despite methane being the only exogenous organic carbon supplied, heterotrophic populations (e.g., Verrucomicrobiota and Bacteroidota) co-exist and actively perform partial denitrification or dissimilatory nitrate reduction to ammonium (DNRA), likely using organic intermediates from the breakdown of methane and biomass as carbon sources. More importantly, two novel genomes belonging to "Ca. Methylomirabilis" are recovered, while one surprisingly expresses nitrate reductases, which we designate as "Ca. Methylomirabilis nitratireducens" representing its inferred capability in performing nitrate-dependent anaerobic methane oxidation. This finding not only suggests a previously neglected possibility of "Ca. Methylomirabilis" bacteria in performing methane-dependent nitrate reduction, and also challenges the previous understanding that the methane-dependent complete denitrification from nitrate to dinitrogen gas is carried out by the consortium of bacteria and archaea.}, }
@article {pmid37184385, year = {2023}, author = {Sänger, PA and Knüpfer, M and Kegel, M and Spanier, B and Liebler-Tenorio, EM and Fuchs, TM}, title = {Regulation and Functionality of a Holin/Endolysin Pair Involved in Killing of Galleria mellonella and Caenorhabditis elegans by Yersinia enterocolitica.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {6}, pages = {e0003623}, pmid = {37184385}, issn = {1098-5336}, mesh = {Animals ; Humans ; *Yersinia enterocolitica/genetics ; Caenorhabditis elegans/metabolism ; *Moths/microbiology ; *Bacterial Toxins/metabolism ; Insecta ; *Insecticides/metabolism ; Luciferases ; Bacterial Proteins/genetics/metabolism ; }, abstract = {The insecticidal toxin complex (Tc) proteins are produced by several insect-associated bacteria, including Yersinia enterocolitica strain W22703, which oscillates between two distinct pathogenicity phases in invertebrates and humans. The mechanism by which this high-molecular-weight toxin is released into the extracellular surrounding, however, has not been deciphered. In this study, we investigated the regulation and functionality of a phage-related holin/endolysin (HE) cassette located within the insecticidal pathogenicity island Tc-PAIYe of W22703. Using the Galleria mellonella infection model and luciferase reporter fusions, we revealed that quorum sensing contributes to the insecticidal activity of W22703 upon influencing the transcription of tcaR2, which encodes an activator of the tc and HE genes. In contrast, a lack of the Yersinia modulator, YmoA, stimulated HE gene transcription, and mutant W22703 ΔymoA exhibited a stronger toxicity toward insect larvae than did W22703. A luciferase reporter fusion demonstrated transcriptional activation of the HE cassette in vivo, and a significantly larger extracellular amount of subunit TcaA was found in W22703 ΔymoA relative to its ΔHE mutant. Using competitive growth assays, we demonstrated that at least in vitro, the TcaA release upon HE activity is not mediated by cell lysis of a significant part of the population. Oral infection of Caenorhabditis elegans with a HE deletion mutant attenuated the nematocidal activity of the wild type, similar to the case with a mutant lacking a Tc subunit. We conclude that the dual holin/endolysin cassette of yersiniae is a novel example of a phage-related function adapted for the release of a bacterial toxin. IMPORTANCE Members of the genus Yersinia cause gastroenteritis in humans but also exhibit toxicity toward invertebrates. A virulence factor required for this environmental life cycle stage is the multisubunit toxin complex (Tc), which is distinct from the insecticidal toxin of Bacillus thuringiensis and has the potential to be used in pest control. The mechanism by which this high-molecular-weight Tc is secreted from bacterial cells has not been uncovered. Here, we show that a highly conserved phage-related holin/endolysin pair, which is encoded by the genes holY and elyY located between the Tc subunit genes, is essential for the insecticidal activity of Y. enterocolitica and that its activation increases the amount of Tc subunits in the supernatant. Thus, the dual holY-elyY cassette of Y. enterocolitica constitutes a new example for a type 10 secretion system to release bacterial toxins.}, }
@article {pmid37182790, year = {2023}, author = {Refisch, A and Sen, ZD and Klassert, TE and Busch, A and Besteher, B and Danyeli, LV and Helbing, D and Schulze-Späte, U and Stallmach, A and Bauer, M and Panagiotou, G and Jacobsen, ID and Slevogt, H and Opel, N and Walter, M}, title = {Microbiome and immuno-metabolic dysregulation in patients with major depressive disorder with atypical clinical presentation.}, journal = {Neuropharmacology}, volume = {235}, number = {}, pages = {109568}, doi = {10.1016/j.neuropharm.2023.109568}, pmid = {37182790}, issn = {1873-7064}, mesh = {Humans ; *Depressive Disorder, Major/metabolism ; Brain/metabolism ; *Microbiota ; }, abstract = {Depression is highly prevalent (6% 1-year prevalence) and is the second leading cause of disability worldwide. Available treatment options for depression are far from optimal, with response rates only around 50%. This is most likely related to a heterogeneous clinical presentation of major depression disorder (MDD), suggesting different manifestations of underlying pathophysiological mechanisms. Poorer treatment outcomes to first-line antidepressants were reported in MDD patients endorsing an "atypical" symptom profile that is characterized by preserved reactivity in mood, increased appetite, hypersomnia, a heavy sensation in the limbs, and interpersonal rejection sensitivity. In recent years, evidence has emerged that immunometabolic biological dysregulation is an important underlying pathophysiological mechanism in depression, which maps more consistently to atypical features. In the last few years human microbial residents have emerged as a key influencing variable associated with immunometabolic dysregulations in depression. The microbiome plays a critical role in the training and development of key components of the host's innate and adaptive immune systems, while the immune system orchestrates the maintenance of key features of the host-microbe symbiosis. Moreover, by being a metabolically active ecosystem commensal microbes may have a huge impact on signaling pathways, involved in underlying mechanisms leading to atypical depressive symptoms. In this review, we discuss the interplay between the microbiome and immunometabolic imbalance in the context of atypical depressive symptoms. Although research in this field is in its infancy, targeting biological determinants in more homogeneous clinical presentations of MDD may offer new avenues for the development of novel therapeutic strategies for treatment-resistant depression. This article is part of the Special Issue on "Microbiome &amp; the Brain: Mechanisms &amp; Maladies".}, }
@article {pmid37180236, year = {2023}, author = {Huang, W and Li, S and Li, S and Laanbroek, HJ and Zhang, Q}, title = {Pro- and eukaryotic keystone taxa as potential bio-indicators for the water quality of subtropical Lake Dongqian.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1151768}, pmid = {37180236}, issn = {1664-302X}, abstract = {The microbial community plays an important role in the biogeochemical cycles in water aquatic ecosystems, and it is regulated by environmental variables. However, the relationships between microbial keystone taxa and water variables, which play a pivotal role in aquatic ecosystems, has not been clarified in detail. We analyzed the seasonal variation in microbial communities and co-occurrence network in the representative areas taking Lake Dongqian as an example. Both pro- and eukaryotic community compositions were more affected by seasons than by sites, and the prokaryotes were more strongly impacted by seasons than the eukaryotes. Total nitrogen, pH, temperature, chemical oxygen demand, dissolved oxygen and chlorophyll a significantly affected the prokaryotic community, while the eukaryotic community was significantly influenced by total nitrogen, ammonia, pH, temperature and dissolved oxygen. The eukaryotic network was more complex than that of prokaryotes, whereas the number of eukaryotic keystone taxa was less than that of prokaryotes. The prokaryotic keystone taxa belonged mainly to Alphaproteobacteria, Betaproteobacteria, Actinobacteria and Bacteroidetes. It is noteworthy that some of the keystone taxa involved in nitrogen cycling are significantly related to total nitrogen, ammonia, temperature and chlorophyll a, including Polaromonas, Albidiferax, SM1A02 and Leptolyngbya so on. And the eukaryotic keystone taxa were found in Ascomycota, Choanoflagellida and Heterophryidae. The mutualistic pattern between pro- and eukaryotes was more evident than the competitive pattern. Therefore, it suggests that keystone taxa could be as bio-indicators of aquatic ecosystems.}, }
@article {pmid37178239, year = {2023}, author = {Nandni,  and Rani, S and Chopra, G and Wati, L}, title = {Deciphering the Potential of Sulphur-Oxidizing Bacteria for Sulphate Production Correlating with pH Change.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2282-2292}, pmid = {37178239}, issn = {1432-184X}, mesh = {*Sulfates ; *Bacteria ; Soil ; Soil Microbiology ; Oxidation-Reduction ; Sulfur ; Hydrogen-Ion Concentration ; }, abstract = {Sulphur, available in the form of sulphate, is one of the essential nutrients that is required by plants. Bacteria capable of oxidizing reduced forms of sulphur to sulphate play an important role in sulphur nutrition for plants. The present study was conducted to isolate, screen, and characterize sulphur-oxidizing bacteria from different soil samples collected from mustard rhizosphere and fly ash mixed soil. A total of 33 sulphur-oxidizing bacterial isolates (HMSOB1-33) were retrieved from soil and further screened for sulphur-oxidizing ability. Maximum solubilization index (3.76), pH reduction (3.93), and sulphate production (173.61 µg/ml) were observed for the isolate HMSOB2 which on the basis of 16S rDNA sequencing was identified as Pantoea dispersa with sequence similarity 98.22%. Four other selected bacterial isolates were identified as Bacillus megaterium, Bacillus tropicus, Bacillus velezensis, and Bacillus cereus. Sulphate solubilization index (SSI) correlated positively (r = 0.91) with sulphate production; however, pH showed negative correlation (r = - 0.82) with SSI as well as sulphate production after 120 h of incubation. These promising bacterial isolates could be further explored as bioinoculant after assessing plant growth traits.}, }
@article {pmid37177981, year = {2023}, author = {Bier, RL and Mosher, JJ and Kaplan, LA and Kan, J}, title = {Spatial scale impacts microbial community composition and distribution within and across stream ecosystems in North and Central America.}, journal = {Environmental microbiology}, volume = {25}, number = {10}, pages = {1860-1874}, doi = {10.1111/1462-2920.16396}, pmid = {37177981}, issn = {1462-2920}, mesh = {*Ecosystem ; Bacteria/genetics ; Fresh Water ; Acidobacteria ; *Microbiota ; Central America ; }, abstract = {A mechanistic understanding of factors that structure spatiotemporal community composition is a major challenge in microbial ecology. Our study of microbial communities in the headwaters of three freshwater stream networks showed significant community changes at the small spatial scale of benthic habitats when compared to changes at mid- and large-spatial scales associated with stream order and catchment. Catchment (which included temperate and tropical catchments) had the strongest influence on community composition followed by habitat type (epipsammon or epilithon) and stream orders. Alpha diversity of benthic microbiomes resulted from interactions between catchment, habitat, and canopy. Epilithon contained relatively more Cyanobacteria and algae while Acidobacteria and Actinobacteria proportions were higher in epipsammic habitats. Turnover from replacement created ~60%-95% of beta diversity differences among habitats, stream orders, and catchments. Turnover within a habitat type generally decreased downstream indicating longitudinal linkages in stream networks while between habitat turnover also shaped benthic microbial community assembly. Our study suggests that factors influencing microbial community composition shift in dominance across spatial scales, with habitat dominating locally and catchment dominating globally.}, }
@article {pmid37173204, year = {2023}, author = {Pan, X and Raaijmakers, JM and Carrión, VJ}, title = {Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning.}, journal = {Trends in microbiology}, volume = {31}, number = {9}, pages = {959-971}, doi = {10.1016/j.tim.2023.03.018}, pmid = {37173204}, issn = {1878-4380}, mesh = {Animals ; Humans ; *Ecosystem ; *Bacteroidetes/genetics ; Host Microbial Interactions ; Ecology ; Genome ; Plants ; Soil Microbiology ; }, abstract = {Bacteroidetes are prevalent in soil ecosystems and are associated with various eukaryotic hosts, including plants, animals, and humans. The ubiquity and diversity of Bacteroidetes exemplify their impressive versatility in niche adaptation and genomic plasticity. Over the past decade, a wealth of knowledge has been obtained on the metabolic functions of clinically relevant Bacteroidetes, but much less attention has been given to Bacteroidetes living in close association with plants. To improve our understanding of the functional roles of Bacteroidetes for plants and other hosts, we review the current knowledge of their taxonomy and ecology, in particular their roles in nutrient cycling and host fitness. We highlight their environmental distribution, stress resilience, genomic diversity, and functional importance in diverse ecosystems, including, but not limited to, plant-associated microbiomes.}, }
@article {pmid37173060, year = {2023}, author = {Krebs, NF and Belfort, MB and Meier, PP and Mennella, JA and O'Connor, DL and Taylor, SN and Raiten, DJ}, title = {Infant factors that impact the ecology of human milk secretion and composition-a report from "Breastmilk Ecology: Genesis of Infant Nutrition (BEGIN)" Working Group 3.}, journal = {The American journal of clinical nutrition}, volume = {117 Suppl 1}, number = {Suppl 1}, pages = {S43-S60}, pmid = {37173060}, issn = {1938-3207}, support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {Female ; Infant ; Infant, Newborn ; Humans ; *Milk, Human ; Lactation/physiology ; *Premature Birth ; Breast Feeding ; Infant Nutritional Physiological Phenomena ; }, abstract = {Infants drive many lactation processes and contribute to the changing composition of human milk through multiple mechanisms. This review addresses the major topics of milk removal; chemosensory ecology for the parent-infant dyad; the infant's inputs into the composition of the human milk microbiome; and the impact of disruptions in gestation on the ecology of fetal and infant phenotypes, milk composition, and lactation. Milk removal, which is essential for adequate infant intake and continued milk synthesis through multiple hormonal and autocrine/paracrine mechanisms, should be effective, efficient, and comfortable for both the lactating parent and the infant. All 3 components should be included in the evaluation of milk removal. Breastmilk "bridges" flavor experiences in utero with postweaning foods, and the flavors become familiar and preferred. Infants can detect flavor changes in human milk resulting from parental lifestyle choices, including recreational drug use, and early experiences with the sensory properties of these recreational drugs impact subsequent behavioral responses. Interactions between the infant's own developing microbiome, that of the milk, and the multiple environmental factors that are drivers-both modifiable and nonmodifiable-in the microbial ecology of human milk are explored. Disruptions in gestation, especially preterm birth and fetal growth restriction or excess, impact the milk composition and lactation processes such as the timing of secretory activation, adequacy of milk volume and milk removal, and duration of lactation. Research gaps are identified in each of these areas. To assure a sustained and robust breastfeeding ecology, these myriad infant inputs must be systematically considered.}, }
@article {pmid37169795, year = {2023}, author = {Conners, R and León-Quezada, RI and McLaren, M and Bennett, NJ and Daum, B and Rakonjac, J and Gold, VAM}, title = {Cryo-electron microscopy of the f1 filamentous phage reveals insights into viral infection and assembly.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2724}, pmid = {37169795}, issn = {2041-1723}, support = {BB/R008639/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R000484/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; Cryoelectron Microscopy ; Ecosystem ; *Bacteriophages/genetics ; *Inovirus/genetics ; Bacteria ; *Virus Diseases ; }, abstract = {Phages are viruses that infect bacteria and dominate every ecosystem on our planet. As well as impacting microbial ecology, physiology and evolution, phages are exploited as tools in molecular biology and biotechnology. This is particularly true for the Ff (f1, fd or M13) phages, which represent a widely distributed group of filamentous viruses. Over nearly five decades, Ffs have seen an extraordinary range of applications, yet the complete structure of the phage capsid and consequently the mechanisms of infection and assembly remain largely mysterious. In this work, we use cryo-electron microscopy and a highly efficient system for production of short Ff-derived nanorods to determine a structure of a filamentous virus including the tips. We show that structure combined with mutagenesis can identify phage domains that are important in bacterial attack and for release of new progeny, allowing new models to be proposed for the phage lifecycle.}, }
@article {pmid37166501, year = {2023}, author = {Weber, M and Göpfert, B and von Wezyk, S and Savin-Hoffmeyer, M and Lipski, A}, title = {Correlation between Bacterial Cell Density and Abundance of Antibiotic Resistance on Milking Machine Surfaces Assessed by Cultivation and Direct qPCR Methods.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1676-1685}, pmid = {37166501}, issn = {1432-184X}, support = {41.2015.02//Ministry for Environment, Agriculture, Conservation and Consumer Protection of the State of North Rhine-Westphalia/ ; }, mesh = {Animals ; Cattle ; Female ; RNA, Ribosomal, 16S/genetics ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics ; Tetracycline ; Cloxacillin ; Drug Resistance, Microbial/genetics ; Cell Count ; Genes, Bacterial ; }, abstract = {The relative abundance of antibiotic-resistant bacteria and antibiotic-resistance genes was surveyed for different parts of a milking machine. A cultivation approach based on swab samples showed a highly diverse microbiota, harboring resistances against cloxacillin, ampicillin, penicillin, and tetracycline. This approach demonstrated a substantial cloxacillin resistance of numerous taxa within milking machine microbiota coming along with regular use of cloxacillin for dry-off therapy of dairy cows. For the less abundant tetracycline-resistant bacteria we found a positive correlation between microbial cell density and relative abundance of tetracycline-resistant microorganisms (R[2] = 0.73). This indicated an accelerated dispersion of resistant cells for sampling locations with high cell density. However, the direct quantification of the tetM gene from the swap samples by qPCR showed the reverse relation to bacterial density if normalized against the abundance of 16S rRNA genes (R[2] = 0.88). The abundance of 16S rRNA genes was analyzed by qPCR combined with a propidium monoazide treatment, which eliminates 16S rRNA gene signals in negative controls.}, }
@article {pmid37166500, year = {2023}, author = {Zeng, Z and Yang, Z and Yang, A and Li, Y and Zhang, H}, title = {Genetic Evidence for Colletotrichum gloeosporioides Transmission Between the Invasive Plant Ageratina adenophora and Co-occurring Neighbor Plants.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2192-2201}, pmid = {37166500}, issn = {1432-184X}, support = {2021Z022//Postgraduate Research and Innovation Foundation of Yunnan University/ ; 2022YFF1302402//National key research and development program of China/ ; }, mesh = {*Ageratina/genetics/microbiology ; Introduced Species ; Ecosystem ; *Colletotrichum/genetics ; }, abstract = {To understand the disease-mediated invasion of exotic plants and the potential risk of disease transmission in local ecosystems, it is necessary to characterize population genetic structure and spatio-temporal dynamics of fungal community associated with both invasive and co-occurring plants. In this study, multiple genes were used to characterize the genetic diversity of 165 strains of Colletotrichum gloeosporioides species complex (CGSC) isolated from healthy leaves and symptomatic leaves of invasive plant Ageratina adenophora, as well as symptomatic leaves of its neighbor plants from eleven geographic sites in China. The data showed that these CGSC strains had a high genetic diversity in each geographic site (all Hd > 0.67 and Pi > 0.01). Haplotype diversity and nucleotide diversity varied greatly in individual gene locus: gs had the highest haplotype diversity (Hd = 0.8972), gapdh had the highest nucleotide diversity (Pi = 0.0705), and ITS had the lowest nucleotide diversity (Pi = 0.0074). Haplotypes were not clustered by geographic site, invasive age, or isolation source. AMOVA revealed that the genetic variation was mainly from within-populations, regardless of geographic or isolation origin. Both AMOVA and neutrality tests indicated these CGSC strains occurred gene exchange among geographic populations but did not experience population expansion along with A. adenophora invasion progress. Our data indicated that A. adenophora primarily accumulated these CGSC fungi in the introduced range, suggesting a high frequency of CGSC transmission between A. adenophora and co-occurring neighbor plants. This study is valuable for understanding the disease-mediated plant invasion and the potential risk of disease transmission driven by exotic plants in local ecosystems.}, }
@article {pmid37162342, year = {2023}, author = {Cruz-Paredes, C and Tájmel, D and Rousk, J}, title = {Variation in Temperature Dependences across Europe Reveals the Climate Sensitivity of Soil Microbial Decomposers.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {5}, pages = {e0209022}, pmid = {37162342}, issn = {1098-5336}, mesh = {Temperature ; *Ecosystem ; Soil ; Soil Microbiology ; Climate Change ; Europe ; Carbon ; *Microbiota ; }, abstract = {Temperature is a major determinant of biological process rates, and microorganisms are key regulators of ecosystem carbon (C) dynamics. Temperature controls microbial rates of decomposition, and thus warming can stimulate C loss, creating positive feedback to climate change. If trait distributions that define temperature relationships of microbial communities can adapt to altered temperatures, they could modulate the strength of this feedback, but if this occurs remains unclear. In this study, we sampled soils from a latitudinal climate gradient across Europe. We established the temperature relationships of microbial growth and respiration rates and used these to investigate if and with what strength the community trait distributions for temperature were adapted to their local environment. Additionally, we sequenced bacterial and fungal amplicons to link the variance in community composition to changes in temperature traits. We found that microbial temperature trait distributions varied systematically with climate, suggesting that an increase in mean annual temperature (MAT) of 1°C will result in warm-shifted microbial temperature trait distributions equivalent to an increase in temperature minimum (Tmin) of 0.20°C for bacterial growth, 0.07°C for fungal growth, and 0.10°C for respiration. The temperature traits for bacterial growth were thus more responsive to warming than those for respiration and fungal growth. The microbial community composition also varied with temperature, enabling the interlinkage of taxonomic information with microbial temperature traits. Our work shows that the adaptation of microbial temperature trait distributions to a warming climate will affect the C-climate feedback, emphasizing the need to represent this to capture the microbial feedback to climate change. IMPORTANCE One of the largest uncertainties of global warming is if the microbial decomposer feedback will strengthen or weaken soil C-climate feedback. Despite decades of research effort, the strength of this feedback to warming remains unknown. We here present evidence that microbial temperature relationships vary systematically with environmental temperatures along a climate gradient and use this information to forecast how microbial temperature traits will create feedback between the soil C cycle and climate warming. We show that the current use of a universal temperature sensitivity is insufficient to represent the microbial feedback to climate change and provide new estimates to replace this flawed assumption in Earth system models. We also demonstrate that temperature relationships for rates of microbial growth and respiration are differentially affected by warming, with stronger responses to warming for microbial growth (soil C formation) than for respiration (C loss from soil to atmosphere), which will affect the atmosphere-land C balance.}, }
@article {pmid37161621, year = {2023}, author = {Talukdar, D and Bandopadhyay, P and Ray, Y and Paul, SR and Sarif, J and D'Rozario, R and Lahiri, A and Das, S and Bhowmick, D and Chatterjee, S and Das, B and Ganguly, D}, title = {Association of gut microbial dysbiosis with disease severity, response to therapy and disease outcomes in Indian patients with COVID-19.}, journal = {Gut pathogens}, volume = {15}, number = {1}, pages = {22}, pmid = {37161621}, issn = {1757-4749}, support = {BT/PR38173/MED/97/474/2020//Department of Biotechnology, Ministry of Science and Technology, India/ ; MLP-129//Council of Scientific and Industrial Research, India/ ; }, abstract = {BACKGROUND: Severe coronavirus disease 2019 (COVID-19) is associated with systemic hyper-inflammation. An adaptive interaction between gut microbiota and host immune systems is important for intestinal homeostasis and systemic immune regulation. The association of gut microbial composition and functions with COVID-19 disease severity is sparse, especially in India. We analysed faecal microbial diversity and abundances in a cohort of Indian COVID-19 patients to identify key signatures in the gut microbial ecology in patients with severe COVID-19 disease as well as in response to different therapies. The composition of the gut microbiome was characterized using 16Sr RNA gene sequences of genomic DNA extracted from faecal samples of 52 COVID-19 patients. Metabolic pathways across the groups were predicted using PICRUSt2. All statistical analyses were done using Vegan in the R environment. Plasma cytokine abundance at recruitment was measured in a multiplex assay.<br><br>RESULTS: The gut microbiome composition of mild and severe patients was found to be significantly different. Immunomodulatory commensals, viz. Lachnospiraceae family members and Bifidobacteria producing butyrate and short-chain fatty acids (SCFAs), were under represented in patients with severe COVID-19, with an increased abundance of opportunistic pathogens like Eggerthella. The higher abundance of Lachnoclostridium in severe disease was reduced in response to convalescent plasma therapy. Specific microbial genera showed distinctive trends in enriched metabolic pathways, strong correlations with blood plasma cytokine levels, and associative link to disease outcomes.<br><br>CONCLUSION: Our study indicates that, along with SARS-CoV-2, a dysbiotic gut microbial community may also play an important role in COVID-19 severity through modulation of host immune responses.}, }
@article {pmid37158858, year = {2023}, author = {Bi, S and Lai, H and Guo, D and Yi, H and Li, H and Liu, X and Chen, Q and Chen, J and Zhang, Z and Wei, X and Li, G and Xin, G}, title = {The characteristics of the intestinal bacterial community from Oreochromis mossambicus and its interaction with microbiota from artificial fishery habitats.}, journal = {BMC ecology and evolution}, volume = {23}, number = {1}, pages = {16}, pmid = {37158858}, issn = {2730-7182}, mesh = {Animals ; *Tilapia ; Fisheries ; Fusobacterium ; Fusobacteria ; Firmicutes ; *Microbiota/genetics ; *Verbenaceae ; Water ; }, abstract = {BACKGROUND: Artificial habitats can allow many fish to flock together and interact and have been widely used to restore and protect fishery resources. The piece of research intends to elucidate the relationship of microbial communities between tilapia (Oreochromis mossambicus) intestines and artificial fishery habitats (water and sediments). Hence, 16 S rDNA sequencing technology was used to study the bacterial communities from intestines, water, and sediments.<br><br>RESULTS: The results showed that the tilapia intestines had the lowest richness of Operational Taxonomic Units (OTUs) and the lowest diversity of the bacterial community compared to water and sediments. The intestine, water, and sediment microbial communities shared many OTUs. Overall, 663 shared OTUs were identified from the tilapia intestines (76.20%), the surrounding water (71.14%), and sediment (56.86%) in artificial habitats. However, there were unique OTUs that were detected in different sample types. There were 81, 77 and 112 unique OTUs observed in tilapia intestines, the surrounding water and sediment, respectively. Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, Fusobacteria, and Bacteroidetes were the most common and dominant bacterial phyla between the tilapia intestines and habitats.&#xa0;In the two groups, the microbial communities were similar in the taxonomic composition but different in the abundance of bacterial phyla. Interestingly, Firmicutes increased, while Fusobacteria decreased in artificial habitats. These findings indicated that the artificial habitats had fewer effects on the water environment and indicated that the mode of artificial habitats could have an effect on the enriched bacteria in the tilapia intestines.<br><br>CONCLUSIONS: This study analysed the bacterial communities of artificial habitats from the intestines, water, and sediments, which can explain the relationship between the tilapia intestines and habitats and strengthen the value of ecological services provided by artificial habitats.}, }
@article {pmid37156959, year = {2023}, author = {Banaszkiewicz, S and Tabiś, A and Wałecki, B and Łyżwińska, K and Bystroń, J and Bania, J}, title = {spa Types and Staphylococcal Enterotoxin Production of Staphylococcus aureus Isolated from Wild Boar.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2184-2191}, pmid = {37156959}, issn = {1432-184X}, mesh = {Animals ; Swine ; Humans ; *Staphylococcus aureus/genetics ; Enterotoxins/genetics ; Sus scrofa ; *Staphylococcal Infections/veterinary/epidemiology/microbiology ; }, abstract = {Little is known about the structure of S. aureus population and the enterotoxin gene content in wild boar. In 1025 nasal swabs from wild boars, 121 S. aureus isolates were identified. Staphylococcal enterotoxin (SE) genes were identified in 18 isolates (14.9%). The seb gene was found in 2 S. aureus isolates, sec in 2 isolates, the see and seh genes were found in 4 and 11 isolates, respectively. The production of SEs was evaluated in bacteria grown in microbial broth. Concentration of SEB reached 2.70 µg/ml after 24 h and 4.46 µg/ml at 48 h. SEC was produced at 952.6 ng/ml after 24 h and 7.2 µg/ml at 48 h. SEE reached 124.1 ng/ml after 24 h and 191.6 ng/ml at 48 h of culture. SEH production reached 4.36 µg/ml at 24 h and 5.42 µg/ml at 48 h of culture. Thirty-nine spa types were identified among S. aureus isolates. The most prevalent spa types were t091 and t1181, followed by t4735 and t742, t3380 and t127. Twelve new spa types, i.e., t20572‒t20583 were identified. The wild boar S. aureus population was shown to contain previously identified animal/human-associated spa types and spa types not identified in humans or animals. We also indicate that wildlife animals can be a significant reservoir of see-positive S. aureus.}, }
@article {pmid37155494, year = {2023}, author = {Gomez-Alvarez, V and Siponen, S and Kauppinen, A and Hokajärvi, AM and Tiwari, A and Sarekoski, A and Miettinen, IT and Torvinen, E and Pitkänen, T}, title = {A comparative analysis employing a gene- and genome-centric metagenomic approach reveals changes in composition, function, and activity in waterworks with different treatment processes and source water in Finland.}, journal = {Water research}, volume = {229}, number = {}, pages = {119495}, pmid = {37155494}, issn = {1879-2448}, support = {EPA999999/ImEPA/Intramural EPA/United States ; }, mesh = {Metagenome ; *Drinking Water/microbiology ; Finland ; Bacteria/metabolism ; *Microbiota/genetics ; Archaea/genetics ; *Disinfectants ; Metagenomics ; }, abstract = {The emergence and development of next-generation sequencing technologies (NGS) has made the analysis of the water microbiome in drinking water distribution systems (DWDSs) more accessible and opened new perspectives in microbial ecology studies. The current study focused on the characterization of the water microbiome employing a gene- and genome-centric metagenomic approach to five waterworks in Finland with different raw water sources, treatment methods, and disinfectant. The microbial communities exhibit a distribution pattern of a few dominant taxa and a large representation of low-abundance bacterial species. Changes in the community structure may correspond to the presence or absence and type of disinfectant residual which indicates that these conditions exert selective pressure on the microbial community. The Archaea domain represented a small fraction (up to 2.5%) and seemed to be effectively controlled by the disinfection of water. Their role particularly in non-disinfected DWDS may be more important than previously considered. In general, non-disinfected DWDSs harbor higher microbial richness and maintaining disinfectant residual is significantly important for ensuring low microbial numbers and diversity. Metagenomic binning recovered 139 (138 bacterial and 1 archaeal) metagenome-assembled genomes (MAGs) that had a >50% completeness and <10% contamination consisting of 20 class representatives in 12 phyla. The presence and occurrence of nitrite-oxidizing bacteria (NOB)-like microorganisms have significant implications for nitrogen biotransformation in drinking water systems. The metabolic and functional complexity of the microbiome is evident in DWDSs ecosystems. A comparative analysis found a set of differentially abundant taxonomic groups and functional traits in the active community. The broader set of transcribed genes may indicate an active and diverse community regardless of the treatment methods applied to water. The results indicate a highly dynamic and diverse microbial community and confirm that every DWDS is unique, and the community reflects the selection pressures exerted at the community structure, but also at the levels of functional properties and metabolic potential.}, }
@article {pmid37154919, year = {2023}, author = {Pan, Q and Shikano, I and Liu, TX and Felton, GW}, title = {Helicoverpa zea-Associated Gut Bacteria as Drivers in Shaping Plant Anti-herbivore Defense in Tomato.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2173-2182}, pmid = {37154919}, issn = {1432-184X}, mesh = {Humans ; Animals ; *Solanum lycopersicum ; Zea mays ; Plant Defense Against Herbivory ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Moths ; Larva/microbiology ; Bacteria/genetics ; Enterobacteriaceae ; Herbivory ; }, abstract = {Insect-associated bacteria can mediate the intersection of insect and plant immunity. In this study, we aimed to evaluate the effects of single isolates or communities of gut-associated bacteria of Helicoverpa zea larvae on herbivore-induced defenses in tomato. We first identified bacterial isolates from the regurgitant of field-collected H. zea larvae by using a culture-dependent method and 16S rRNA gene sequencing. We identified 11 isolates belonging to the families Enterobacteriaceae, Streptococcaceae, Yersiniaceae, Erwiniaceae, and unclassified Enterobacterales. Seven different bacterial isolates, namely Enterobacteriaceae-1, Lactococcus sp., Klebsiella sp. 1, Klebsiella sp. 3, Enterobacterales, Enterobacteriaceae-2, and Pantoea sp., were selected based on their phylogenetic relationships to test their impacts on insect-induced plant defenses. We found that the laboratory population of H. zea larvae inoculated with individual isolates did not induce plant anti-herbivore defenses, whereas larvae inoculated with a bacterial community (combination of the 7 bacterial isolates) triggered increased polyphenol oxidase (PPO) activity in tomato, leading to retarded larval development. Additionally, field-collected H. zea larvae with an unaltered bacterial community in their gut stimulated higher plant defenses than the larvae with a reduced gut microbial community. In summary, our findings highlight the importance of the gut microbial community in mediating interactions between herbivores and their host plants.}, }
@article {pmid37150906, year = {2023}, author = {Rasmussen, TS and Mentzel, CMJ and Danielsen, MR and Jakobsen, RR and Zachariassen, LSF and Castro Mejia, JL and Brunse, A and Hansen, LH and Hansen, CHF and Hansen, AK and Nielsen, DS}, title = {Fecal virome transfer improves proliferation of commensal gut Akkermansia muciniphila and unexpectedly enhances the fertility rate in laboratory mice.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2208504}, pmid = {37150906}, issn = {1949-0984}, mesh = {Male ; Feces ; Birth Rate ; *Gastrointestinal Microbiome ; Infant ; Female ; Pregnancy ; Humans ; Animals ; Cell Proliferation ; Verrucomicrobia ; Mice, Inbred C57BL ; Akkermansia ; Virome ; Mice ; }, abstract = {Probiotics are intended to improve gastrointestinal health when consumed. However, the probiotics marketed today only colonize the densely populated gut to a limited extent. Bacteriophages comprise the majority of viruses in the human gut virome and there are strong indications that they play important roles in shaping the gut microbiome. Here, we investigate the use of fecal virome transplantation (FVT, sterile filtrated feces) as a mean to alter the gut microbiome composition to lead the way for persistent colonization of two types of probiotics: Lacticaseibacillus rhamnosus GG (LGG) representing a well-established probiotic and Akkermansia muciniphila (AKM) representing a putative next-generation probiotic. Male and female C57BL/6NTac mice were cohoused in pairs from 4 weeks of age and received the following treatment by oral gavage at week 5 and 6: AKM+FVT, LGG+FVT, probiotic sham (Pro-sham)+FVT, LGG+Saline, AKM+Saline, and control (Pro-sham+Saline). The FVT donor material originated from mice with high relative abundance of A. muciniphila. All animals were terminated at age 9 weeks. The FVT treatment did not increase the relative abundance of the administered LGG or AKM in the recipient mice. Instead FVT significantly (p < 0.05) increased the abundance of naturally occurring A. muciniphila compared to the control. This highlights the potential of propagating the existing commensal "probiotics" that have already permanently colonized the gut. Being co-housed male and female, a fraction of the female mice became pregnant. Unexpectedly, the FVT treated mice were found to have a significantly (p < 0.05) higher fertility rate independent of probiotic administration. These preliminary observations urge for follow-up studies investigating interactions between the gut microbiome and fertility.}, }
@article {pmid37150044, year = {2023}, author = {Hu, D and Li, S and Liu, X and Liu, H and Liu, G}, title = {Kinetic model derivation for design, building and operation of solid waste treatment unit based on system dynamics and computer simulation.}, journal = {Waste management (New York, N.Y.)}, volume = {166}, number = {}, pages = {58-69}, doi = {10.1016/j.wasman.2023.04.037}, pmid = {37150044}, issn = {1879-2456}, mesh = {Solid Waste/analysis ; Computer Simulation ; Conservation of Natural Resources ; Models, Theoretical ; Ecosystem ; *Refuse Disposal ; *Waste Management ; }, abstract = {Solid waste disposal is significantly important to maintaining normal operation of both natural and artificial ecosystems. In this study, a kinetic model of solid waste treatment unit (SWTU) was upfront developed based on microbial ecology, system dynamics, cybernetics and digital simulation, which accurately described the relationships and interactions between solid waste decomposition (SWD) processes and biotic/abiotic factors. Then a specific SWTU prototype was designed and built from this kinetic model. A 370-day experiment demonstrated that SWTU maintained normal operation with robust stability and desired dynamic behaviors, and effectively disposed the solid waste. Therefore, this kinetic model was highly valid due to its high structural and behavioral similarity with the prototype. This research could lay a strong theoretical foundation for further closed-loop control as well as optimization of SWTU, and provide scientific guidance to environmental management as well as sustainable development.}, }
@article {pmid37149807, year = {2023}, author = {Pjevac, P and Bartosik, T and Schneider, S and Eckl-Dorna, J}, title = {Pitfalls in sampling and analyzing low-biomass human nasal microbiome samples.}, journal = {The Journal of allergy and clinical immunology}, volume = {152}, number = {1}, pages = {304}, doi = {10.1016/j.jaci.2023.04.001}, pmid = {37149807}, issn = {1097-6825}, mesh = {Humans ; Biomass ; *Nose ; *Microbiota ; Specimen Handling ; RNA, Ribosomal, 16S ; }, }
@article {pmid37149500, year = {2023}, author = {Kharshandi, F and Kayang, H}, title = {Antagonistic potential of rhizobacterial isolates against fungal pathogens causing rhizome rot in turmeric.}, journal = {Archives of microbiology}, volume = {205}, number = {6}, pages = {221}, pmid = {37149500}, issn = {1432-072X}, support = {(332490, Ref.No:20/12/2015(ii)EU-V))//University Grants Commission, India/ ; }, mesh = {*Rhizome/microbiology ; *Curcuma/microbiology ; Plant Diseases/prevention &amp; control/microbiology ; Antifungal Agents/pharmacology ; Bacteria ; }, abstract = {The study aims to select potent bacterial antagonists to be used as biocontrol agents against rhizome rot disease in turmeric (Curcuma longa L.). A total of 48 bacterial isolates were isolated from the rhizosphere of turmeric. These isolates were screened for their in vitro antagonism against Fusarium solani FS-01 and Pythium aphanidermatum (ITCC 7908). Production of volatile organic compounds and chitinase activity were also performed. Among the tested isolates, two bacterial isolates (IJ2 and IJ10) showed the highest inhibitory activity against these fungal pathogens. GC/MS analysis of the crude extract produced by Pseudomonas sp. IJ2 and B. subtilis IJ10 was found to contain many bioactive compounds with antifungal and antimicrobial activities. The rhizome treatment with these isolates exhibited the lowest percent disease severity with high biocontrol efficacy against the tested pathogens. These isolates with promising antagonistic potential, therefore, can be used as biocontrol agents against rhizome rot in turmeric.}, }
@article {pmid37149269, year = {2023}, author = {Li, Y and Kuramae, EE and Nasir, F and Wang, E and Zhang, Z and Li, J and Yao, Z and Tian, L and Sun, Y and Luo, S and Guo, L and Ren, G and Tian, C}, title = {Addition of cellulose degrading bacterial agents promoting keystone fungal-mediated cellulose degradation during aerobic composting: Construction the complex co-degradation system.}, journal = {Bioresource technology}, volume = {381}, number = {}, pages = {129132}, doi = {10.1016/j.biortech.2023.129132}, pmid = {37149269}, issn = {1873-2976}, mesh = {Animals ; Cattle ; *Cellulose/metabolism ; *Composting ; Agriculture ; Soil ; Bacillus subtilis/metabolism ; Manure/microbiology ; }, abstract = {To excavate a complex co-degradation system for decomposing cellulose more efficiently, cellulose-degrading bacteria, including Bacillus subtilis WF-8, Bacillus licheniformis WF-11, Bacillus Cereus WS-1 and Streptomyces Nogalater WF-10 were added during maize straw and cattle manure aerobic composting. Bacillus and Streptomyces successfully colonized, which improve cellulose degrading ability. Continuous colonization of cellulose-degrading bacteria can promote the fungi to produce more precursors for humus and promote the negative correlation with Ascomycota. In the current study, the addition of cellulose-degrading bacteria has resulted in the rapid development of Mycothermus and Remersonia in the phylum Ascomycota as keystone fungal genera which constitute the foundation of the co-degradation system. Network analysis reveals the complex co-degradation system of efficient cellulose bacteria and mature fungi to treat cellulose in the process of straw aerobic composting mainly related to the influence of total carbon (TC) /total nitrogen (TN) and humic acid (HA)/fulvic acid (FA). This research offers a complex co-degradation system more efficiently to decompose cellulose aiming to maintain the long-term sustainability of agriculture.}, }
@article {pmid37148310, year = {2023}, author = {Burgess, WL and Bishop, CD}, title = {Bacterial Diversity in Egg Capsular Fluid of the Spotted Salamander Ambystoma maculatum Decreases with Embryonic Development.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1789-1798}, pmid = {37148310}, issn = {1432-184X}, support = {RGPIN-2015-05040//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; *Ambystoma ; Capsules ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; Embryonic Development ; }, abstract = {Egg capsules within egg masses of the spotted salamander Ambystoma maculatum host a symbiosis with the unicellular green alga Oophila amblystomatis. However, this alga is not the only microbe to inhabit those capsules, and the significance of these additional taxa for the symbiosis is unknown. Spatial and temporal patterns of bacterial diversity in egg capsules of A. maculatum have recently begun to be characterized, but patterns of bacterial diversity as a function of embryonic development are unknown. We sampled fluid from individual capsules in egg masses over a large range of host embryonic development in 2019 and 2020. We used 16S rRNA gene amplicon sequencing to examine how diversity and relative abundance of bacteria changed with embryonic development. In general, bacterial diversity decreased as embryos developed; significant differences were observed (depending on the metric) by embryonic development, pond, and year, and there were interaction effects. The function of bacteria in what is thought of as a bipartite symbiosis calls for further research.}, }
@article {pmid37148309, year = {2023}, author = {Gazulla, CR and Cabello, AM and Sánchez, P and Gasol, JM and Sánchez, O and Ferrera, I}, title = {A Metagenomic and Amplicon Sequencing Combined Approach Reveals the Best Primers to Study Marine Aerobic Anoxygenic Phototrophs.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2161-2172}, pmid = {37148309}, issn = {1432-184X}, support = {CEX2019-000928-S//Severo Ochoa Centre of Excellence/ ; PID2019-110128RB-I00/AEI/10.13039/501100011033//Agencia Estatal de Investigaci&#xf3;n/ ; }, mesh = {Phylogeny ; Metagenomics ; Bacterial Proteins/genetics ; *Gammaproteobacteria ; *Alphaproteobacteria/genetics ; }, abstract = {Studies based on protein-coding genes are essential to describe the diversity within bacterial functional groups. In the case of aerobic anoxygenic phototrophic (AAP) bacteria, the pufM gene has been established as the genetic marker for this particular functional group, although available primers are known to have amplification biases. We review here the existing primers for pufM gene amplification, design new ones, and evaluate their phylogenetic coverage. We then use samples from contrasting marine environments to evaluate their performance. By comparing the taxonomic composition of communities retrieved with metagenomics and with different amplicon approaches, we show that the commonly used PCR primers are biased towards the Gammaproteobacteria phylum and some Alphaproteobacteria clades. The metagenomic approach, as well as the use of other combinations of the existing and newly designed primers, show that these groups are in fact less abundant than previously observed, and that a great proportion of pufM sequences are affiliated to uncultured representatives, particularly in the open ocean. Altogether, the framework developed here becomes a better alternative for future studies based on the pufM gene and, additionally, serves as a reference for primer evaluation of other functional genes.}, }
@article {pmid37146562, year = {2023}, author = {Todorović, I and Abrouk, D and Kyselková, M and Lavire, C and Rey, M and Raičević, V and Jovičić-Petrović, J and Moënne-Loccoz, Y and Muller, D}, title = {Two novel species isolated from wheat rhizospheres in Serbia: Pseudomonas serbica sp. nov. and Pseudomonas serboccidentalis sp. nov.}, journal = {Systematic and applied microbiology}, volume = {46}, number = {4}, pages = {126425}, doi = {10.1016/j.syapm.2023.126425}, pmid = {37146562}, issn = {1618-0984}, mesh = {*Pseudomonas ; *Triticum/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Serbia ; Rhizosphere ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Bacterial Typing Techniques ; Nucleic Acid Hybridization ; }, abstract = {Pseudomonas strains IT-194P, IT-215P, IT-P366[T] and IT-P374[T] were isolated from the rhizospheres of wheat grown in soils sampled from different fields (some of them known to be disease-suppressive) located near Mionica, Serbia. Phylogenetic analysis of the 16S rRNA genes and of whole genome sequences showed that these strains belong to two potentially new species, one containing strains IT-P366[T] and IT-194P and clustering (whole genome analysis) next to P. umsongensis DSM16611[T], and another species containing strains IT-P374[T] and IT-215P and clustering next to P. koreensis LMG21318[T]. Genome analysis confirmed the proposition of novel species, as ANI was below the threshold of 95% and dDDH below 70% for strains IT-P366[T] (compared with P. umsongensis DSM16611[T]) and IT-P374[T] (compared with P. koreensis LMG21318[T]). Unlike P. umsongensis DSM16611[T], strains of P. serbica can grow on D-mannitol, but not on pectin, D-galacturonic acid, L-galactonic acid lactone and α-hydroxybutyric acid. In contrary to P. koreensis LMG21318[T], strains of P. serboccidentalis can use sucrose, inosine and α-ketoglutaric acid (but not L-histidine) as carbon sources. Altogether, these results indicate the existence of two novel species for which we propose the names Pseudomonas serbica sp. nov., with the type strain IT-P366[T] (=CFBP 9060 [T] = LMG 32732 [T] = EML 1791 [T]) and Pseudomonas serboccidentalis sp. nov., with the type strain IT-P374[T] (=CFBP 9061 [T] = LMG 32734 [T] = EML 1792 [T]). Strains from this study presented a set of phytobeneficial functions modulating plant hormonal balance, plant nutrition and plant protection, suggesting a potential as Plant Growth-Promoting Rhizobacteria (PGPR).}, }
@article {pmid37145936, year = {2023}, author = {Fiskal, A and Shuster, J and Fischer, S and Joshi, P and Raghunatha Reddy, L and Wulf, SE and Kappler, A and Fischer, H and Herrig, I and Meier, J}, title = {Microbially influenced corrosion and rust tubercle formation on sheet piles in freshwater systems.}, journal = {Environmental microbiology}, volume = {25}, number = {10}, pages = {1796-1815}, doi = {10.1111/1462-2920.16393}, pmid = {37145936}, issn = {1462-2920}, mesh = {*Ferric Compounds ; Corrosion ; RNA, Ribosomal, 16S/genetics ; X-Ray Microtomography ; *Bacteria/genetics ; Minerals ; Fresh Water ; Oxidation-Reduction ; }, abstract = {The extent of how complex natural microbial communities contribute to metal corrosion is still not fully resolved, especially not for freshwater environments. In order to elucidate the key processes, we investigated rust tubercles forming massively on sheet piles along the river Havel (Germany) applying a complementary set of techniques. In-situ microsensor profiling revealed steep gradients of O2 , redox potential and pH within the tubercle. Micro-computed tomography and scanning electron microscopy showed a multi-layered inner structure with chambers and channels and various organisms embedded in the mineral matrix. Using Mössbauer spectroscopy we identified typical corrosion products including electrically conductive iron (Fe) minerals. Determination of bacterial gene copy numbers and sequencing of 16S rRNA and 18S rRNA amplicons supported a densely populated tubercle matrix with a phylogenetically and metabolically diverse microbial community. Based on our results and previous models of physic(electro)chemical reactions, we propose here a comprehensive concept of tubercle formation highlighting the crucial reactions and microorganisms involved (such as phototrophs, fermenting bacteria, dissimilatory sulphate and Fe(III) reducers) in metal corrosion in freshwaters.}, }
@article {pmid37142893, year = {2023}, author = {Paul, P and Sarkar, S and Dastidar, DG and Shukla, A and Das, S and Chatterjee, S and Chakraborty, P and Tribedi, P}, title = {1, 4-naphthoquinone efficiently facilitates the disintegration of pre-existing biofilm of Staphylococcus aureus through eDNA intercalation.}, journal = {Folia microbiologica}, volume = {68}, number = {6}, pages = {843-854}, pmid = {37142893}, issn = {1874-9356}, mesh = {Humans ; Staphylococcus aureus/genetics ; Ethidium/pharmacology ; *Naphthoquinones/pharmacology ; DNA/pharmacology ; Biofilms ; *Staphylococcal Infections ; }, abstract = {1, 4-naphthoquinone, a plant-based quinone derivative, has gained much attention for its effectiveness against several biofilm-linked diseases. The biofilm inhibitory effect of 1, 4-naphthoquinone against Staphylococcus aureus has already been reported in our previous study. We observed that the extracellular DNA (eDNA) could play an important role in holding the structural integrity of the biofilm. Hence, in this study, efforts have been directed to examine the possible interactions between 1, 4-naphthoquinone and DNA. An in silico analysis indicated that 1, 4-naphthoquinone could interact with DNA through intercalation. To validate the same, UV-Vis spectrophotometric analysis was performed in which a hypochromic shift was observed when the said molecule was titrated with calf-thymus DNA (CT-DNA). Thermal denaturation studies revealed a change of 8℃ in the melting temperature (Tm) of CT-DNA when complexed with 1, 4-naphthoquinone. The isothermal calorimetric titration (ITC) assay revealed a spontaneous intercalation between CT-DNA and 1, 4-naphthoquinone with a binding constant of 0.95 ± 0.12 × 10[8]. Furthermore, DNA was run through an agarose gel electrophoresis with a fixed concentration of ethidium bromide and increasing concentrations of 1, 4-naphthoquinone. The result showed that the intensity of ethidium bromide-stained DNA got reduced concomitantly with the gradual increase of 1, 4-naphthoquinone suggesting its intercalating nature. To gain further confidence, the pre-existing biofilm was challenged with ethidium bromide wherein we observed that it could also show biofilm disintegration. Therefore, the results suggested that 1, 4-naphthoquinone could exhibit disintegration of the pre-existing biofilm of Staphylococcus aureus through eDNA intercalation.}, }
@article {pmid37142736, year = {2023}, author = {Mukorako, P and St-Pierre, DH and Flamand, N and Biertho, L and Lebel, S and Lemoine, N and Plamondon, J and Roy, MC and Tchernof, A and Varin, TV and Marette, A and Silvestri, C and Di Marzo, V and Richard, D}, title = {Hypoabsorptive surgeries cause limb-dependent changes in the gut endocannabinoidome and microbiome in association with beneficial metabolic effects.}, journal = {International journal of obesity (2005)}, volume = {47}, number = {7}, pages = {630-641}, pmid = {37142736}, issn = {1476-5497}, mesh = {Male ; Rats ; Animals ; Rats, Wistar ; Chromatography, Liquid ; RNA, Ribosomal, 16S ; Tandem Mass Spectrometry ; *Biliopancreatic Diversion/methods ; Duodenum/surgery ; *Gastrointestinal Hormones ; *Gastrointestinal Microbiome ; Gastrectomy ; Tyrosine ; *Obesity, Morbid/surgery ; *Gastric Bypass/methods ; Retrospective Studies ; }, abstract = {OBJECTIVE: To determine whether the metabolic benefits of hypoabsorptive surgeries are associated with changes in the gut endocannabinoidome (eCBome) and microbiome.<br><br>METHODS: Biliopancreatic diversion with duodenal switch (BPD-DS) and single anastomosis duodeno-ileal bypass with sleeve gastrectomy (SADI-S) were performed in diet-induced obese (DIO) male Wistar rats. Control groups fed a high-fat diet (HF) included sham-operated (SHAM HF) and SHAM HF-pair-weighed to BPD-DS (SHAM HF-PW). Body weight, fat mass gain, fecal energy loss, HOMA-IR, and gut-secreted hormone levels were measured. The levels of eCBome lipid mediators and prostaglandins were quantified in different intestinal segments by LC-MS/MS, while expression levels of genes encoding eCBome metabolic enzymes and receptors were determined by RT-qPCR. Metataxonomic (16S rRNA) analysis was performed on residual distal jejunum, proximal jejunum, and ileum contents.<br><br>RESULTS: BPD-DS and SADI-S reduced fat gain and HOMA-IR, while increasing glucagon-like peptide-1 (GLP-1) and peptide tyrosine tyrosine (PYY) levels in HF-fed rats. Both surgeries induced potent limb-dependent alterations in eCBome mediators and in gut microbial ecology. In response to BPD-DS and SADI-S, changes in gut microbiota were significantly correlated with those of eCBome mediators. Principal component analyses revealed connections between PYY, N-oleoylethanolamine (OEA), N-linoleoylethanolamine (LEA), Clostridium, and Enterobacteriaceae_g_2 in the proximal and distal jejunum and in the ileum.<br><br>CONCLUSIONS: BPD-DS and SADI-S caused limb-dependent changes in the gut eCBome and microbiome. The present results indicate that these variables could significantly influence the beneficial metabolic outcome of hypoabsorptive bariatric surgeries.}, }
@article {pmid37138640, year = {2023}, author = {Sorouri, B and Rodriguez, CI and Gaut, BS and Allison, SD}, title = {Variation in Sphingomonas traits across habitats and phylogenetic clades.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1146165}, pmid = {37138640}, issn = {1664-302X}, abstract = {Whether microbes show habitat preferences is a fundamental question in microbial ecology. If different microbial lineages have distinct traits, those lineages may occur more frequently in habitats where their traits are advantageous. Sphingomonas is an ideal bacterial clade in which to investigate how habitat preference relates to traits because these bacteria inhabit diverse environments and hosts. Here we downloaded 440 publicly available Sphingomonas genomes, assigned them to habitats based on isolation source, and examined their phylogenetic relationships. We sought to address whether: (1) there is a relationship between Sphingomonas habitat and phylogeny, and (2) whether there is a phylogenetic correlation between key, genome-based traits and habitat preference. We hypothesized that Sphingomonas strains from similar habitats would cluster together in phylogenetic clades, and key traits that improve fitness in specific environments should correlate with habitat. Genome-based traits were categorized into the Y-A-S trait-based framework for high growth yield, resource acquisition, and stress tolerance. We selected 252 high quality genomes and constructed a phylogenetic tree with 12 well-defined clades based on an alignment of 404 core genes. Sphingomonas strains from the same habitat clustered together within the same clades, and strains within clades shared similar clusters of accessory genes. Additionally, key genome-based trait frequencies varied across habitats. We conclude that Sphingomonas gene content reflects habitat preference. This knowledge of how environment and host relate to phylogeny may also help with future functional predictions about Sphingomonas and facilitate applications in bioremediation.}, }
@article {pmid37138619, year = {2023}, author = {Yin, H and Zhao, M and Pan, G and Zhang, H and Yang, R and Sun, J and Yu, Z and Bai, C and Xue, Y}, title = {Effects of Bacillus subtilis or Lentilactobacillus buchneri on aerobic stability, and the microbial community in aerobic exposure of whole plant corn silage.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1177031}, pmid = {37138619}, issn = {1664-302X}, abstract = {This study aimed to evaluate the effects of Bacillus subtilis or Lentilactobacillus buchneri on the fermentation quality, aerobic stability, and bacterial and fungal communities of whole plant corn silage during aerobic exposure. Whole plant corn was harvested at the wax maturity stage, which chopped to a length of approximately 1 cm, and treated with the following: distilled sterile water control, 2.0 × 10[5] CFU/g of Lentilactobacillus buchneri (LB) or 2.0 × 10[5] CFU/g of Bacillus subtilis (BS) for 42 days silage. Then, the samples were exposed to air (23-28[°]C) after opening and sampled at 0, 18 and 60 h, to investigate fermentation quality, bacterial and fungal communities, and aerobic stability. Inoculation with LB or BS increased the pH value, acetic acid, and ammonia nitrogen content of silage (P < 0.05), but it was still far below the threshold of inferior silage, the yield of ethanol was reduced (P < 0.05), and satisfactory fermentation quality was achieved. With the extension of the aerobic exposure time, inoculation with LB or BS prolonged the aerobic stabilization time of silage, attenuated the trend of pH increase during aerobic exposure, and increased the residues of lactic acid and acetic acid. The bacterial and fungal alpha diversity indices gradually declined, and the relative abundance of Basidiomycota and Kazachstania gradually increased. The relative abundance of Weissella and unclassified_f_Enterobacteria was higher and the relative abundance of Kazachstania was lower after inoculation with BS compared to the CK group. According to the correlation analysis, Bacillus and Kazachstania are bacteria and fungi that are more closely related to aerobic spoilage and inoculation with LB or BS could inhibit spoilage. The FUNGuild predictive analysis indicated that the higher relative abundance of fungal parasite-undefined saprotroph in the LB or BS groups at AS2, may account for its good aerobic stability. In conclusion, silage inoculated with LB or BS had better fermentation quality and improved aerobic stability by effectively inhibiting the microorganisms that induce aerobic spoilage.}, }
@article {pmid37133496, year = {2023}, author = {Donohue, ME and Hert, ZL and Karrick, CE and Rowe, AK and Wright, PC and Randriamanandaza, LJ and Zakamanana, F and Nomenjanahary, ES and Everson, KM and Weisrock, DW}, title = {Lemur Gut Microeukaryotic Community Variation Is Not Associated with Host Phylogeny, Diet, or Habitat.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2149-2160}, pmid = {37133496}, issn = {1432-184X}, mesh = {Animals ; Phylogeny ; *Lemur ; RNA, Ribosomal, 16S/genetics ; Diet/veterinary ; *Microbiota ; }, abstract = {Identifying the major forces driving variation in gut microbiomes enhances our understanding of how and why symbioses between hosts and microbes evolved. Gut prokaryotic community variation is often closely associated with host evolutionary and ecological variables. Whether these same factors drive variation in other microbial taxa occupying the animal gut remains largely untested. Here, we present a one-to-one comparison of gut prokaryotic (16S rRNA metabarcoding) and microeukaryotic (18S rRNA metabarcoding) community patterning among 12 species of wild lemurs. Lemurs were sampled from dry forests and rainforests of southeastern Madagascar and display a range of phylogenetic and ecological niche diversity. We found that while lemur gut prokaryotic community diversity and composition vary with host taxonomy, diet, and habitat, gut microeukaryotic communities have no detectable association with any of these factors. We conclude that gut microeukaryotic community composition is largely random, while gut prokaryotic communities are conserved among host species. It is likely that a greater proportion of gut microeukaryotic communities comprise taxa with commensal, transient, and/or parasitic symbioses compared with gut prokaryotes, many of which form long-term relationships with the host and perform important biological functions. Our study highlights the importance of greater specificity in microbiome research; the gut microbiome contains many "omes" (e.g., prokaryome, eukaryome), each comprising different microbial taxa shaped by unique selective pressures.}, }
@article {pmid37133495, year = {2023}, author = {Saikrishna, K and Talukdar, D and Das, S and Bakshi, S and Chakravarti, P and Jana, P and Karmakar, S and Wig, N and Das, B and Ray, A}, title = {Study on Effects of Probiotics on Gut Microbiome and Clinical Course in Patients with Critical Care Illnesses.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1814-1828}, pmid = {37133495}, issn = {1432-184X}, support = {5/9/1208/2019-Nut, Dt. 16.09.2019//Indian Council of Medical Research/ ; No. BT/PR30159/MED/15/188/2018//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Probiotics/therapeutic use ; Critical Care ; Disease Progression ; }, abstract = {Ventilator-associated pneumonia (VAP) is a nosocomial infection contracted by ventilator patients in which bacteria colonize the upper digestive tract and contaminated secretions are released into the lower airway. This nosocomial infection increases the morbidity and mortality of the patients as well as the cost of treatment. Probiotic formulations have recently been proposed to prevent the colonization of these pathogenic bacteria. In this prospective observational study, we aimed to investigate the effects of probiotics on gut microbiota and their relation to clinical outcomes in mechanically ventilated patients. For this study, 35 patients were recruited (22 probiotic-treated and 13 without probiotic treatment) from a cohort of 169 patients. Patients in the probiotic group were given a dose of 6 capsules of a commercially available probiotic (VSL#3®:112.5 billion CFU/cap) in three divided doses for 10 days. Sampling was carried out after each dose to monitor the temporal change in the gut microbiota composition. To profile the microbiota, we used a 16S rRNA metagenomic approach, and differences among the groups were computed using multivariate statistical analyses. Differences in gut microbial diversity (Bray Curtis and Jaccard distance, p-value > 0.05) between the probiotic-treated group and the control group were not observed. Furthermore, treatment with probiotics resulted in the enrichment of Lactobacillus and Streptococcus in the gut microbiota of the probiotic-treated groups. Our results demonstrated that probiotics might lead to favorable alterations in gut microbiome characteristics. Future studies should focus on the appropriate dosages and frequency of probiotics, which can lead to improved clinical outcomes.}, }
@article {pmid37131715, year = {2023}, author = {Wu, L and Wang, XW and Tao, Z and Wang, T and Zuo, W and Zeng, Y and Liu, YY and Dai, L}, title = {Data-driven prediction of colonization outcomes for complex microbial communities.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.04.19.537502}, pmid = {37131715}, issn = {2692-8205}, abstract = {Complex microbial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the colonization of exogenous species in complex communities remains a fundamental challenge in microbial ecology, mainly due to our limited knowledge of the diverse physical, biochemical, and ecological processes governing microbial dynamics. Here, we proposed a data-driven approach independent of any dynamics model to predict colonization outcomes of exogenous species from the baseline compositions of microbial communities. We systematically validated this approach using synthetic data, finding that machine learning models (including Random Forest and neural ODE) can predict not only the binary colonization outcome but also the post-invasion steady-state abundance of the invading species. Then we conducted colonization experiments for two commensal gut bacteria species Enterococcus faecium and Akkermansia muciniphila in hundreds of human stool-derived in vitro microbial communities, confirming that the data-driven approach can successfully predict the colonization outcomes. Furthermore, we found that while most resident species were predicted to have a weak negative impact on the colonization of exogenous species, strongly interacting species could significantly alter the colonization outcomes, e.g., the presence of Enterococcus faecalis inhibits the invasion of E. faecium . The presented results suggest that the data-driven approach is a powerful tool to inform the ecology and management of complex microbial communities.}, }
@article {pmid37130890, year = {2023}, author = {Onyango, LA and Ngonga, FA and Karanja, EN and Kuja, JO and Boga, HI and Cowan, DA and Mwangi, KW and Maghenda, MW and Marinho Lebre, PBN and Kambura, AK}, title = {The soil microbiomes of forest ecosystems in Kenya: their diversity and environmental drivers.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {7156}, pmid = {37130890}, issn = {2045-2322}, mesh = {Kenya ; *Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; Forests ; Bacteria/genetics ; Archaea/genetics ; *Microbiota/genetics ; Soil Microbiology ; }, abstract = {Soil microbiomes in forest ecosystems act as both nutrient sources and sinks through a range of processes including organic matter decomposition, nutrient cycling, and humic compound incorporation into the soil. Most forest soil microbial diversity studies have been performed in the northern hemisphere, and very little has been done in forests within African continent. This study examined the composition, diversity and distribution of prokaryotes in Kenyan forests top soils using amplicon sequencing of V4-V5 hypervariable region of the 16S rRNA gene. Additionally, soil physicochemical characteristics were measured to identify abiotic drivers of prokaryotic distribution. Different forest soils were found to have statistically distinct microbiome compositions, with Proteobacteria and Crenarchaeota taxa being the most differentially abundant across regions within bacterial and archaeal phyla, respectively. Key bacterial community drivers included pH, Ca, K, Fe, and total N while archaeal diversity was shaped by Na, pH, Ca, total P and total N. To contextualize the prokaryote diversity of Kenyan forest soils on a global scale, the sample set was compared to amplicon data obtained from forest biomes across the globe; displaying them to harbor distinct microbiomes with an over-representation of uncultured taxa such as TK-10 and Ellin6067 genera.}, }
@article {pmid37129484, year = {2023}, author = {Farr, AD and Pesce, D and Das, SG and Zwart, MP and de Visser, JAGM}, title = {The Fitness of Beta-Lactamase Mutants Depends Nonlinearly on Resistance Level at Sublethal Antibiotic Concentrations.}, journal = {mBio}, volume = {14}, number = {3}, pages = {e0009823}, pmid = {37129484}, issn = {2150-7511}, mesh = {*Anti-Bacterial Agents/pharmacology ; *beta-Lactamases/genetics ; Cefotaxime/pharmacology ; Drug Resistance, Microbial/genetics ; Selection, Genetic ; Mutation ; }, abstract = {Adaptive evolutionary processes are constrained by the availability of mutations which cause a fitness benefit and together make up the fitness landscape, which maps genotype space onto fitness under specified conditions. Experimentally derived fitness landscapes have demonstrated a predictability to evolution by identifying limited "mutational routes" that evolution by natural selection may take between low and high-fitness genotypes. However, such studies often utilize indirect measures to determine fitness. We estimated the competitive fitness of mutants relative to all single-mutation neighbors to describe the fitness landscape of three mutations in a β-lactamase enzyme. Fitness assays were performed at sublethal concentrations of the antibiotic cefotaxime in a structured and unstructured environment. In the unstructured environment, the antibiotic selected for higher-resistance types-but with an equivalent fitness for a subset of mutants, despite substantial variation in resistance-resulting in a stratified fitness landscape. In contrast, in a structured environment with a low antibiotic concentration, antibiotic-susceptible genotypes had a relative fitness advantage, which was associated with antibiotic-induced filamentation. These results cast doubt that highly resistant genotypes have a unique selective advantage in environments with subinhibitory concentrations of antibiotics and demonstrate that direct fitness measures are required for meaningful predictions of the accessibility of evolutionary routes. IMPORTANCE The evolution of antibiotic-resistant bacterial populations underpins the ongoing antibiotic resistance crisis. We aim to understand how antibiotic-degrading enzymes can evolve to cause increased resistance, how this process is constrained, and whether it can be predictable. To this end, competition experiments were performed with a combinatorially complete set of mutants of a β-lactamase gene subject to subinhibitory concentrations of the antibiotic cefotaxime. While some mutations confer on their hosts high resistance to cefotaxime, in competition these mutations do not always confer a selective advantage. Specifically, high-resistance mutants had equivalent fitnesses despite different resistance levels and even had selective disadvantages under conditions involving spatial structure. Together, our findings suggest that the relationship between resistance level and fitness at subinhibitory concentrations is complex; predicting the evolution of antibiotic resistance requires knowledge of the conditions that select for resistant genotypes and the selective advantage evolved types have over their predecessors.}, }
@article {pmid37127597, year = {2023}, author = {Mosquera, KD and Nilsson, LKJ and de Oliveira, MR and Rocha, EM and Marinotti, O and Håkansson, S and Tadei, WP and de Souza, AQL and Terenius, O}, title = {Comparative assessment of the bacterial communities associated with Anopheles darlingi immature stages and their breeding sites in the Brazilian Amazon.}, journal = {Parasites &amp; vectors}, volume = {16}, number = {1}, pages = {156}, pmid = {37127597}, issn = {1756-3305}, support = {348-2012-622//Swedish Research Council/ ; }, mesh = {Animals ; *Anopheles/genetics ; *Malaria ; Brazil ; Mosquito Vectors ; RNA, Ribosomal, 16S ; Larva ; *Microbiota ; Bacteria ; Water ; }, abstract = {BACKGROUND: The neotropical anopheline mosquito Anopheles darlingi is a major malaria vector in the Americas. Studies on mosquito-associated microbiota have shown that symbiotic bacteria play a major role in host biology. Mosquitoes acquire and transmit microorganisms over their life cycle. Specifically, the microbiota of immature forms is largely acquired from their aquatic environment. Therefore, our study aimed to describe the microbial communities associated with An. darlingi immature forms and their breeding sites in the Coari municipality, Brazilian Amazon.<br><br>METHODS: Larvae, pupae, and breeding water were collected in two different geographical locations. Samples were submitted for DNA extraction and high-throughput 16S rRNA gene sequencing was conducted. Microbial ecology analyses were performed to explore and compare the bacterial profiles of An. darlingi and their aquatic habitats.<br><br>RESULTS: We found lower richness and diversity in An. darlingi microbiota than in water samples, which suggests that larvae are colonized by a subset of the bacterial community present in their breeding sites. Moreover, the bacterial community composition of the immature mosquitoes and their breeding water differed according to their collection sites, i.e., the microbiota associated with An. darlingi reflected that in the aquatic habitats where they developed. The three most abundant bacterial classes across the An. darlingi samples were Betaproteobacteria, Clostridia, and Gammaproteobacteria, while across the water samples they were Gammaproteobacteria, Bacilli, and Alphaproteobacteria.<br><br>CONCLUSIONS: Our findings reinforce the current evidence that the environment strongly shapes the composition and diversity of mosquito microbiota. A better understanding of mosquito-microbe interactions will contribute to identifying microbial candidates impacting host fitness and disease transmission.}, }
@article {pmid37127168, year = {2023}, author = {Liu, YC and Ramiro-Garcia, J and Paulo, LM and Braguglia, CM and Gagliano, MC and O'Flaherty, V}, title = {Psychrophilic and mesophilic anaerobic treatment of synthetic dairy wastewater with long chain fatty acids: Process performances and microbial community dynamics.}, journal = {Bioresource technology}, volume = {380}, number = {}, pages = {129124}, doi = {10.1016/j.biortech.2023.129124}, pmid = {37127168}, issn = {1873-2976}, mesh = {*Wastewater ; Anaerobiosis ; Sewage/microbiology ; Bioreactors/microbiology ; Fatty Acids ; *Microbiota ; Methane ; }, abstract = {Facilitating the anaerobic degradation of long chain fatty acids (LCFA) is the key to unlock the energy potential of lipids-rich wastewater. In this study, the feasibility of psychrophilic anaerobic treatment of LCFA-containing dairy wastewater was assessed and compared to mesophilic anaerobic treatment. The results showed that psychrophilic treatment at 15 ℃ was feasible for LCFA-containing dairy wastewater, with high removal rates of soluble COD (>90%) and LCFA (∼100%). However, efficient long-term treatment required prior acclimation of the biomass to psychrophilic temperatures. The microbial community analysis revealed that putative syntrophic fatty acid bacteria and Methanocorpusculum played a crucial role in LCFA degradation during both mesophilic and psychrophilic treatments. Additionally, a fungal-bacterial biofilm was found to be important during the psychrophilic treatment. Overall, these findings demonstrate the potential of psychrophilic anaerobic treatment for industrial wastewaters and highlight the importance of understanding the microbial communities involved in the process.}, }
@article {pmid37126126, year = {2023}, author = {Kearns, PJ and Winter, AS and Woodhams, DC and Northup, DE}, title = {The Mycobiome of Bats in the American Southwest Is Structured by Geography, Bat Species, and Behavior.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1565-1574}, pmid = {37126126}, issn = {1432-184X}, support = {P14AC00793//Carlsbad, Caverns National Park (CAVE) Award/ ; P14AC00588//El Malpais National Monument award/ ; P12AC10812//Grand Canyon Parashant National Monument (PARA) Award/ ; TE-EAA-01222014//T and E/ ; 12516000000045//New Mexico Department of Game and Fish/ ; IOS-1845634//National Science Foundation/ ; }, mesh = {Animals ; *Mycobiome ; *Chiroptera/microbiology ; Fungi/genetics ; *Microbiota ; Geography ; }, abstract = {Bats are widespread mammals that play key roles in ecosystems as pollinators and insectivores. However, there is a paucity of information about bat-associated microbes, in particular their fungal communities, despite the important role microbes play in host health and overall host function. The emerging fungal disease, white-nose syndrome, presents a potential challenge to the bat microbiome and understanding healthy bat-associated taxa will provide valuable information about potential microbiome-pathogen interactions. To address this knowledge gap, we collected 174 bat fur/skin swabs from 14 species of bats captured in five locations in New Mexico and Arizona and used high-throughput sequencing of the fungal internal transcribed (ITS) region to characterize bat-associated fungal communities. Our results revealed a highly heterogeneous bat mycobiome that was structured by geography and bat species. Furthermore, our data suggest that bat-associated fungal communities are affected by bat foraging, indicating the bat skin microbiota is dynamic on short time scales. Finally, despite the strong effects of site and species, we found widespread and abundant taxa from several taxonomic groups including the genera Alternaria and Metschnikowia that have the potential to be inhibitory towards fungal and bacterial pathogens.}, }
@article {pmid37125162, year = {2023}, author = {Miao, Y and Colosimo, F and Mouser, PJ and De Long, S and Hanson Rhoades, A}, title = {Editorial: Emerging microbiological processes and tools that shine in pilot- and field-scale environmental engineering applications.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1194772}, doi = {10.3389/fmicb.2023.1194772}, pmid = {37125162}, issn = {1664-302X}, }
@article {pmid37124757, year = {2023}, author = {Esquivel-Hernández, DA and Martínez-López, YE and Sánchez-Castañeda, JP and Neri-Rosario, D and Padrón-Manrique, C and Giron-Villalobos, D and Mendoza-Ortíz, C and Resendis-Antonio, O}, title = {A network perspective on the ecology of gut microbiota and progression of type 2 diabetes: Linkages to keystone taxa in a Mexican cohort.}, journal = {Frontiers in endocrinology}, volume = {14}, number = {}, pages = {1128767}, pmid = {37124757}, issn = {1664-2392}, mesh = {Humans ; *Diabetes Mellitus, Type 2/epidemiology ; *Glucose Intolerance/epidemiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Glucose ; }, abstract = {INTRODUCTION: The human gut microbiota (GM) is a dynamic system which ecological interactions among the community members affect the host metabolism. Understanding the principles that rule the bidirectional communication between GM and its host, is one of the most valuable enterprise for uncovering how bacterial ecology influences the clinical variables in the host.<br><br>METHODS: Here, we used SparCC to infer association networks in 16S rRNA gene amplicon data from the GM of a cohort of Mexican patients with type 2 diabetes (T2D) in different stages: NG (normoglycemic), IFG (impaired fasting glucose), IGT (impaired glucose tolerance), IFG + IGT (impaired fasting glucose plus impaired glucose tolerance), T2D and T2D treated (T2D with a 5-year ongoing treatment).<br><br>RESULTS: By exploring the network topology from the different stages of T2D, we observed that, as the disease progress, the networks lose the association between bacteria. It suggests that the microbial community becomes highly sensitive to perturbations in individuals with T2D. With the purpose to identify those genera that guide this transition, we computationally found keystone taxa (driver nodes) and core genera for a Mexican T2D cohort. Altogether, we suggest a set of genera driving the progress of the T2D in a Mexican cohort, among them Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-010, Ruminococcaceae UCG-002, Ruminococcaceae UCG-005, Alistipes, Anaerostipes, and Terrisporobacter.<br><br>DISCUSSION: Based on a network approach, this study suggests a set of genera that can serve as a potential biomarker to distinguish the distinct degree of advances in T2D for a Mexican cohort of patients. Beyond limiting our conclusion to one population, we present a computational pipeline to link ecological networks and clinical stages in T2D, and desirable aim to advance in the field of precision medicine.}, }
@article {pmid37120943, year = {2023}, author = {Gounari, Z and Bonatsou, S and Ferrocino, I and Cocolin, L and Papadopoulou, OS and Panagou, EZ}, title = {Exploring yeast diversity of dry-salted naturally black olives from Greek retail outlets with culture dependent and independent molecular methods.}, journal = {International journal of food microbiology}, volume = {398}, number = {}, pages = {110226}, doi = {10.1016/j.ijfoodmicro.2023.110226}, pmid = {37120943}, issn = {1879-3460}, mesh = {*Sodium Chloride ; *Olea/chemistry ; Staphylococcus aureus ; Greece ; Food Microbiology ; Yeasts/genetics ; Enterobacteriaceae ; Fermentation ; }, abstract = {In the present study, the physicochemical (pH, water activity, moisture content, salt concentration) classical plate counts (total viable counts, yeasts, lactic acid bacteria, Staphylococcus aureus, Pseudomonas spp., Enterobacteriaceae) and amplicon sequencing of naturally black dry-salted olives obtained from different retail outlets of the Greek market were investigated. According to the results, the values of the physicochemical characteristics presented great variability among the samples. Specifically, pH and water activity (aw) values ranged between 4.0 and 5.0, as well as between 0.58 and 0.91, respectively. Moisture content varied between 17.3 and 56.7 % (g Η2Ο/100 g of olive pulp), whereas salt concentration ranged from 5.26 to 9.15 % (g NaCl/100 g of olive pulp). No lactic acid bacteria, S. aureus, Pseudomonas spp. and Enterobacteriaceae were detected. The mycobiota consisted of yeasts that were further characterized and identified by culture-dependent (rep-PCR, ITS-PCR, and RFLP) and amplicon target sequencing (ATS). Pichia membranifaciens, Candida sorbosivorans, Citeromyces nyonsensis, Candida etchelsii, Wickerhamomyces subpelliculosus, Candida apicola, Wickerhamomyces anomalus, Torulaspora delbrueckii and Candida versatilis were the dominant species according to ITS sequencing (culture-dependent), while ATS revealed the dominance of C. etchelsii, Pichia triangularis, P. membranifaciens, and C. versatilis among samples. The results of this study demonstrated considerable variability in quality attributes among the different commercial samples of dry-salted olives, reflecting a lack of standardization in the processing of this commercial style. However, the majority of the samples were characterized by satisfactory microbiological and hygienic quality and complied with the requirements of the trade standard for table olives of the International Olive Council (IOC) for this processing style in terms of salt concentration. In addition, the diversity of yeast species was elucidated for the first time in commercially available products, increasing our knowledge on the microbial ecology of this traditional food. Further investigation into the technological and multifunctional traits of the dominant yeast species may result in better control during dry-salting and enhance the quality and shelf-life of the final product.}, }
@article {pmid37119999, year = {2023}, author = {Goswami, V and Deepika, S and Diwakar, S and Kothamasi, D}, title = {Arbuscular mycorrhizas amplify the risk of heavy metal transfer to human food chain from fly ash ameliorated agricultural soils.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {329}, number = {}, pages = {121733}, doi = {10.1016/j.envpol.2023.121733}, pmid = {37119999}, issn = {1873-6424}, mesh = {Humans ; *Mycorrhizae/chemistry ; Soil ; Coal Ash/analysis ; Food Chain ; Lead/analysis ; *Metals, Heavy/analysis ; Agriculture ; Plants ; *Environmental Pollutants/analysis ; *Soil Pollutants/analysis ; Plant Roots/chemistry ; }, abstract = {Soil contaminants threaten global food security by posing threats to food safety through food chain pollution. Fly ash is a potential agent of soil contamination that contains heavy metals and hazardous pollutants. However, being rich in macro- and micronutrients that have direct beneficial effects on plant growth, fly ash has been recommended as a low-cost soil ameliorant in agriculture in countries of the Global South. Arbuscular mycorrhizal fungi (AMF), ubiquitous in agricultural soils, enhance efficiency of plant nutrient uptake from soils but can equally increase uptake of toxic pollutants from fly ash ameliorated soils to edible crop tissues. We investigated AMF-mediated amplification of nutrient and heavy metal uptake from fly ash amended soils to shoots, roots and grains of barley. We used a microcosm-based experiment to analyse the impacts of fly ash amendments to soil in concentrations of 0 (control), 15, 30 or 50% respectively, on root colonization by AMF Rhizophagus irregularis and AMF-mediated transfer of N, P and heavy metals: Ni, Co, Pb and Cr to barley tissues. These concentrations of fly ash are equivalent to 0, 137, 275 and 458 t ha[-1] respectively, in soil. Root AMF colonization correlated negatively with fly ash concentration and was not detected at 50% fly ash amendment. Shoots, roots and grains of mycorrhizal barley grown with 15, 30 and 50% fly ash amendments had significantly higher concentrations of Ni, Co, Pb and Cr compared to the control and their respective non-mycorrhizal counterparts. Presence of heavy metals in barley plants grown with fly ash amended soil and their increased AMF-mediated translocation to edible grains may significantly enhance the volume of heavy metals entering the human food chain. We recommend careful assessment of manipulation of agricultural soils with fly ash as heavy metal accumulation in agricultural soils and human tissues may cause irreversible damage.}, }
@article {pmid37117817, year = {2023}, author = {Woo, AYM and Aguilar Ramos, MA and Narayan, R and Richards-Corke, KC and Wang, ML and Sandoval-Espinola, WJ and Balskus, EP}, title = {Targeting the human gut microbiome with small-molecule inhibitors.}, journal = {Nature reviews. Chemistry}, volume = {7}, number = {5}, pages = {319-339}, pmid = {37117817}, issn = {2397-3358}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; }, abstract = {The human gut microbiome is a complex microbial community that is strongly linked to both host health and disease. However, the detailed molecular mechanisms underlying the effects of these microorganisms on host biology remain largely uncharacterized. The development of non-lethal, small-molecule inhibitors that target specific gut microbial activities enables a powerful but underutilized approach to studying the gut microbiome and a promising therapeutic strategy. In this Review, we will discuss the challenges of studying this microbial community, the historic use of small-molecule inhibitors in microbial ecology, and recent applications of this strategy. We also discuss the evidence suggesting that host-targeted drugs can affect the growth and metabolism of gut microbes. Finally, we address the issues of developing and implementing microbiome-targeted small-molecule inhibitors and define important future directions for this research.}, }
@article {pmid37115262, year = {2023}, author = {Camargo, TS and Nickele, MA and Filho, WR and do Rocio Chiarello Penteado, S and de Queiroz, EC and Auer, CG}, title = {Fungal Community Associated with the Leaf-Cutting Ant Acromyrmex crassispinus (Hymenoptera: Formicidae) Colonies: a Search for Potential Biocontrol Agents.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1281-1291}, pmid = {37115262}, issn = {1432-184X}, mesh = {Humans ; Animals ; *Ants/microbiology ; Fungi ; *Mycobiome ; Biological Control Agents ; *Penicillium ; Brazil ; Symbiosis ; }, abstract = {The leaf-cutting ant Acromyrmex crassispinus is considered an important pest in forest plantations in southern Brazil. This work aimed to study the fungal community associated with A. crassispinus colonies, subjected to treatments with subdoses of granulated baits (sulfluramid), which might reduce the ability of the ants to care for their symbiotic fungus and other fungi (maybe biocontrol fungi) would take over, to prospect for potential biological control agents. Samplings of fungus gardens and dead ants allowed the identification of 195 fungal isolates, distributed in 29 families, 36 genera, and 53 species. The most frequent genera were Trichoderma (49.2%), Penicillium (13.8%), Chaetomium (6.2%), and Fusarium (3.6%). This is the first study that conducted a survey of antagonistic and entomopathogenic fungi to A. crassispinus and its symbiotic fungus, reporting for the first time the occurrence of potential biological control agents. Escovopsis weberi, Fusarium oxysporum, Rhizomucor variabilis, Trichoderma atroviride, Trichoderma harzianum, Trichoderma koningiopsis, and Trichoderma spirale are considered some of the potential biocontrol organisms.}, }
@article {pmid37115261, year = {2023}, author = {Djotan, AKG and Matsushita, N and Fukuda, K}, title = {Paired Root-Soil Samples and Metabarcoding Reveal Taxon-Based Colonization Strategies in Arbuscular Mycorrhizal Fungi Communities in Japanese Cedar and Cypress Stands.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2133-2146}, pmid = {37115261}, issn = {1432-184X}, mesh = {*Mycorrhizae/genetics ; *Cryptomeria ; *Cupressus ; Plant Roots/microbiology ; Fungi/genetics ; *Glomeromycota/genetics ; Soil ; Soil Microbiology ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) in the roots and soil surrounding their hosts are typically independently investigated and little is known of the relationships between the communities of the two compartments. We simultaneously collected root and surrounding soil samples from Cryptomeria japonica (Cj) and Chamaecyparis obtusa (Co) at three environmentally different sites. Based on molecular and morphological analyses, we characterized their associated AMF communities. Cj was more densely colonized than Co and that root colonization intensity was significantly correlated with soil AMF diversity. The communities comprised 15 AMF genera dominated by Glomus and Paraglomus and 1443 operational taxonomic units (OTUs) of which 1067 and 1170 were in roots and soil, respectively. AMF communities were significantly different among sites, and the root AMF communities were significantly different from those of soil at each site. The root and soil AMF communities responded differently to soil pH. At the genus level, Glomus and Acaulospora were abundant in roots while Paraglomus and Redeckera were abundant in soil. Our findings suggest that AMF colonizing roots are protected from environmental stresses in soil. However, the root-soil-abundant taxa have adapted to both environments and represent a model AMF symbiont. This evidence of strategic exploitation of the rhizosphere by AMF supports prior hypotheses and provides insights into community ecology.}, }
@article {pmid37114064, year = {2023}, author = {Berman, TS and Weinberg, M and Moreno, KR and Czirják, G&#xc1; and Yovel, Y}, title = {In sickness and in health: the dynamics of the fruit bat gut microbiota under a bacterial antigen challenge and its association with the immune response.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1152107}, pmid = {37114064}, issn = {1664-3224}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Chiroptera/genetics ; RNA, Ribosomal, 16S/genetics ; Haptoglobins ; Bacteria/genetics ; Immunity ; }, abstract = {INTRODUCTION: Interactions between the gut microbiome (GM) and the immune system influence host health and fitness. However, few studies have investigated this link and GM dynamics during disease in wild species. Bats (Mammalia: Chiroptera) have an exceptional ability to cope with intracellular pathogens and a unique GM adapted to powered flight. Yet, the contribution of the GM to bat health, especially immunity, or how it is affected by disease, remains unknown.<br><br>METHODS: Here, we examined the dynamics of the Egyptian fruit bats' (Rousettus aegyptiacus) GM during health and disease. We provoked an inflammatory response in bats using lipopolysaccharides (LPS), an endotoxin of Gram-negative bacteria. We then measured the inflammatory marker haptoglobin, a major acute phase protein in bats, and analyzed the GM (anal swabs) of control and challenged bats using high-throughput 16S rRNA sequencing, before the challenge, 24h and 48h post challenge.<br><br>RESULTS: We revealed that the antigen challenge causes a shift in the composition of the bat GM (e.g., Weissella, Escherichia, Streptococcus). This shift was significantly correlated with haptoglobin concentration, but more strongly with sampling time. Eleven bacterial sequences were correlated with haptoglobin concentration and nine were found to be potential predictors of the strength of the immune response, and implicit of infection severity, notably Weissella and Escherichia. The bat GM showed high resilience, regaining the colony's group GM composition rapidly, as bats resumed foraging and social activities.<br><br>CONCLUSION: Our results demonstrate a tight link between bat immune response and changes in their GM, and emphasize the importance of integrating microbial ecology in ecoimmunological studies of wild species. The resilience of the GM may provide this species with an adaptive advantage to cope with infections and maintain colony health.}, }
@article {pmid37113665, year = {2023}, author = {Crognale, S and Massimi, A and Sbicego, M and Braguglia, CM and Gallipoli, A and Gazzola, G and Gianico, A and Tonanzi, B and Di Pippo, F and Rossetti, S}, title = {Ecology of food waste chain-elongating microbiome.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {11}, number = {}, pages = {1157243}, pmid = {37113665}, issn = {2296-4185}, abstract = {Microbial chain elongation has emerged as a valuable bioprocess for obtaining marketable products, such as medium chain fatty acids usable in several industrial applications, from organic waste. The understanding of the microbiology and microbial ecology in these systems is crucial to apply these microbiomes in reliable production processes controlling microbial pathways to promote favourable metabolic processes, which will in turn increase product specificity and yields. In this research, the dynamics, cooperation/competition and potentialities of bacterial communities involved in the long-term lactate-based chain elongation process from food waste extract were evaluated under different operating conditions by DNA/RNA amplicon sequencing and functional profile prediction. The feeding strategies and the applied organic loading rates strongly affected the microbial community composition. The use of food waste extract promoted the selection of primary fermenters (i.e., Olsenella, Lactobacillus) responsible for the in situ production of electron donors (i.e., lactate). The discontinuous feeding and the organic loading rate 15 gCOD L[-1] d[-1] selected the best performing microbiome in which microbes coexist and cooperate to complete the chain elongation process. Both at DNA and RNA level, this microbiome was composed by the lactate producer Olsenella, the short chain fatty acids producers Anaerostipes, Clostridium sensu stricto 7, C. sensu stricto 12, Corynebacterium, Erysipelotrichaceae UCG-004, F0332, Leuconostoc, and the chain elongator Caproiciproducens. This microbiome also showed the highest predicted abundance of short-chain acyl-CoA dehydrogenase, the functional enzyme responsible for the chain elongation process. The combined approach herein used allowed to study the microbial ecology of chain elongation process from food waste by identifying the main functional groups, establishing the presence of potential biotic interactions within the microbiomes, and predicting metabolic potentialities. This study provided pivotal indications for the selection of high-performance microbiome involved in caproate production from food waste that can serve as a basis for further improving system performance and engineering the process scale-up.}, }
@article {pmid37112890, year = {2023}, author = {Turzynski, V and Griesdorn, L and Moraru, C and Soares, AR and Simon, SA and Stach, TL and Rahlff, J and Esser, SP and Probst, AJ}, title = {Virus-Host Dynamics in Archaeal Groundwater Biofilms and the Associated Bacterial Community Composition.}, journal = {Viruses}, volume = {15}, number = {4}, pages = {}, pmid = {37112890}, issn = {1999-4915}, mesh = {Archaea/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Biofilms ; *Groundwater ; *Viruses/genetics ; }, abstract = {Spatial and temporal distribution of lytic viruses in deep groundwater remains unexplored so far. Here, we tackle this gap of knowledge by studying viral infections of Altivir_1_MSI in biofilms dominated by the uncultivated host Candidatus Altiarchaeum hamiconexum sampled from deep anoxic groundwater over a period of four years. Using virus-targeted direct-geneFISH (virusFISH) whose detection efficiency for individual viral particles was 15%, we show a significant and steady increase of virus infections from 2019 to 2022. Based on fluorescence micrographs of individual biofilm flocks, we determined different stages of viral infections in biofilms for single sampling events, demonstrating the progression of infection of biofilms in deep groundwater. Biofilms associated with many host cells undergoing lysis showed a substantial accumulation of filamentous microbes around infected cells probably feeding off host cell debris. Using 16S rRNA gene sequencing across ten individual biofilm flocks from one sampling event, we determined that the associated bacterial community remains relatively constant and was dominated by sulfate-reducing members affiliated with Desulfobacterota. Given the stability of the virus-host interaction in these deep groundwater samples, we postulate that the uncultivated virus-host system described herein represents a suitable model system for studying deep biosphere virus-host interactions in future research endeavors.}, }
@article {pmid37111201, year = {2023}, author = {Wong, MCS and Zhang, L and Ching, JYL and Mak, JWY and Huang, J and Wang, S and Mok, CKP and Wong, A and Chiu, OL and Fung, YT and Cheong, PK and Tun, HM and Ng, SC and Chan, FKL}, title = {Effects of Gut Microbiome Modulation on Reducing Adverse Health Outcomes among Elderly and Diabetes Patients during the COVID-19 Pandemic: A Randomised, Double-Blind, Placebo-Controlled Trial (IMPACT Study).}, journal = {Nutrients}, volume = {15}, number = {8}, pages = {}, pmid = {37111201}, issn = {2072-6643}, support = {COVID19F07//Food and Health Bureau/ ; }, mesh = {Aged ; Humans ; *COVID-19 ; *Gastrointestinal Microbiome ; Pandemics/prevention &amp; control ; COVID-19 Vaccines ; *Diabetes Mellitus ; Outcome Assessment, Health Care ; Double-Blind Method ; }, abstract = {Gut microbiota is believed to be a major determinant of health outcomes. We hypothesised that a novel oral microbiome formula (SIM01) can reduce the risk of adverse health outcomes in at-risk subjects during the coronavirus disease 2019 (COVID-19) pandemic. In this single-centre, double-blind, randomised, placebo-controlled trial, we recruited subjects aged ≥65 years or with type two diabetes mellitus. Eligible subjects were randomised in a 1:1 ratio to receive three months of SIM01 or placebo (vitamin C) within one week of the first COVID-19 vaccine dose. Both the researchers and participants were blinded to the groups allocated. The rate of adverse health outcomes was significantly lower in the SIM01 group than the placebo at one month (6 [2.9%] vs. 25 [12.6], p < 0.001) and three months (0 vs. 5 [3.1%], p = 0.025). At three months, more subjects who received SIM01 than the placebo reported better sleep quality (53 [41.4%] vs. 22 [19.3%], p < 0.001), improved skin condition (18 [14.1%] vs. 8 [7.0%], p = 0.043), and better mood (27 [21.2%] vs. 13 [11.4%], p = 0.043). Subjects who received SIM01 showed a significant increase in beneficial Bifidobacteria and butyrate-producing bacteria in faecal samples and strengthened the microbial ecology network. SIM01 reduced adverse health outcomes and restored gut dysbiosis in elderly and diabetes patients during the COVID-19 pandemic.}, }
@article {pmid37110442, year = {2023}, author = {Maimone, G and Azzaro, M and Placenti, F and Paranhos, R and Cabral, AS and Decembrini, F and Zaccone, R and Cosenza, A and Rappazzo, AC and Patti, B and Basilone, G and Cuttitta, A and Ferreri, R and Aronica, S and Ferla, R}, title = {A Morphometric Approach to Understand Prokaryoplankton: A Study in the Sicily Channel (Central Mediterranean Sea).}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, pmid = {37110442}, issn = {2076-2607}, abstract = {A new understanding of plankton ecology has been obtained by studying the phenotypic traits of free-living prokaryotes in the Sicily Channel (Central Mediterranean Sea), an area characterised by oligotrophic conditions. During three cruises carried out in July 2012, January 2013 and July 2013, the volume and morphology of prokaryotic cells were assessed microscopically using image analysis in relation to environmental conditions. The study found significant differences in cell morphologies among cruises. The largest cell volumes were observed in the July 2012 cruise (0.170 ± 0.156 µm[3]), and the smallest in the January 2013 cruise (0.060 ± 0.052 µm[3]). Cell volume was negatively limited by nutrients and positively by salinity. Seven cellular morphotypes were observed among which cocci, rods and coccobacilli were the most abundant. Cocci, although they prevailed numerically, always showed the smallest volumes. Elongated shapes were positively related to temperature. Relationships between cell morphologies and environmental drivers indicated a bottom-up control of the prokaryotic community. The morphology/morphometry-based approach is a useful tool for studying the prokaryotic community in microbial ecology and should be widely applied to marine microbial populations in nature.}, }
@article {pmid37110372, year = {2023}, author = {Zhou, T and Zhao, F and Xu, K}, title = {Information Scale Correction for Varying Length Amplicons Improves Eukaryotic Microbiome Data Integration.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, pmid = {37110372}, issn = {2076-2607}, support = {41930533//National Natural Science Foundation of China/ ; 41976099//National Natural Science Foundation of China/ ; XDB42000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2022206//Youth Innovation Promotion Association CAS/ ; }, abstract = {The integration and reanalysis of big data provide valuable insights into microbiome studies. However, the significant difference in information scale between amplicon data poses a key challenge in data analysis. Therefore, reducing batch effects is crucial to enhance data integration for large-scale molecular ecology data. To achieve this, the information scale correction (ISC) step, involving cutting different length amplicons into the same sub-region, is essential. In this study, we used the Hidden Markov model (HMM) method to extract 11 different 18S rRNA gene v4 region amplicon datasets with 578 samples in total. The length of the amplicons ranged from 344 bp to 720 bp, depending on the primer position. By comparing the information scale correction of amplicons with varying lengths, we explored the extent to which the comparability between samples decreases with increasing amplicon length. Our method was shown to be more sensitive than V-Xtractor, the most popular tool for performing ISC. We found that near-scale amplicons exhibited no significant change after ISC, while larger-scale amplicons exhibited significant changes. After the ISC treatment, the similarity among the data sets improved, especially for long amplicons. Therefore, we recommend adding ISC processing when integrating big data, which is crucial for unlocking the full potential of microbial community studies and advancing our knowledge of microbial ecology.}, }
@article {pmid37110315, year = {2023}, author = {Lashani, E and Amoozegar, MA and Turner, RJ and Moghimi, H}, title = {Use of Microbial Consortia in Bioremediation of Metalloid Polluted Environments.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, pmid = {37110315}, issn = {2076-2607}, abstract = {Metalloids are released into the environment due to the erosion of the rocks or anthropogenic activities, causing problems for human health in different world regions. Meanwhile, microorganisms with different mechanisms to tolerate and detoxify metalloid contaminants have an essential role in reducing risks. In this review, we first define metalloids and bioremediation methods and examine the ecology and biodiversity of microorganisms in areas contaminated with these metalloids. Then we studied the genes and proteins involved in the tolerance, transport, uptake, and reduction of these metalloids. Most of these studies focused on a single metalloid and co-contamination of multiple pollutants were poorly discussed in the literature. Furthermore, microbial communication within consortia was rarely explored. Finally, we summarized the microbial relationships between microorganisms in consortia and biofilms to remove one or more contaminants. Therefore, this review article contains valuable information about microbial consortia and their mechanisms in the bioremediation of metalloids.}, }
@article {pmid37110258, year = {2023}, author = {Thomas, P and Knox, OGG and Powell, JR and Sindel, B and Winter, G}, title = {The Hydroponic Rockwool Root Microbiome: Under Control or Underutilised?.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, pmid = {37110258}, issn = {2076-2607}, support = {P2-007//Future Food Systems Cooperative Research Centre (CRC) Ltd., funded under the Australian Commonwealth Government CRC Program/ ; }, abstract = {Land plants have an ancient and intimate relationship with microorganisms, which influences the composition of natural ecosystems and the performance of crops. Plants shape the microbiome around their roots by releasing organic nutrients into the soil. Hydroponic horticulture aims to protect crops from damaging soil-borne pathogens by replacing soil with an artificial growing medium, such as rockwool, an inert material made from molten rock spun into fibres. Microorganisms are generally considered a problem to be managed, to keep the glasshouse clean, but the hydroponic root microbiome assembles soon after planting and flourishes with the crop. Hence, microbe-plant interactions play out in an artificial environment that is quite unlike the soil in which they evolved. Plants in a near-ideal environment have little dependency on microbial partners, but our growing appreciation of the role of microbial communities is revealing opportunities to advance practices, especially in agriculture and human health. Hydroponic systems are especially well-suited to active management of the root microbiome because they allow complete control over the root zone environment; however, they receive much less attention than other host-microbiome interactions. Novel techniques for hydroponic horticulture can be identified by extending our understanding of the microbial ecology of this unique environment.}, }
@article {pmid37108739, year = {2023}, author = {Codoñer-Franch, P and Gombert, M and Martínez-Raga, J and Cenit, MC}, title = {Circadian Disruption and Mental Health: The Chronotherapeutic Potential of Microbiome-Based and Dietary Strategies.}, journal = {International journal of molecular sciences}, volume = {24}, number = {8}, pages = {}, pmid = {37108739}, issn = {1422-0067}, support = {CEX2021-001189-S/MCIN/AEI/10.13039/501100011033//A grant by the Spanish Ministry of Science and Innovation (MCIN/AEI)/ ; }, mesh = {Humans ; *Mental Health ; Drug Chronotherapy ; Diet ; Circadian Rhythm/physiology ; *Gastrointestinal Microbiome ; }, abstract = {Mental illness is alarmingly on the rise, and circadian disruptions linked to a modern lifestyle may largely explain this trend. Impaired circadian rhythms are associated with mental disorders. The evening chronotype, which is linked to circadian misalignment, is a risk factor for severe psychiatric symptoms and psychiatric metabolic comorbidities. Resynchronization of circadian rhythms commonly improves psychiatric symptoms. Furthermore, evidence indicates that preventing circadian misalignment may help reduce the risk of psychiatric disorders and the impact of neuro-immuno-metabolic disturbances in psychiatry. The gut microbiota exhibits diurnal rhythmicity, as largely governed by meal timing, which regulates the host's circadian rhythms. Temporal circadian regulation of feeding has emerged as a promising chronotherapeutic strategy to prevent and/or help with the treatment of mental illnesses, largely through the modulation of gut microbiota. Here, we provide an overview of the link between circadian disruption and mental illness. We summarize the connection between gut microbiota and circadian rhythms, supporting the idea that gut microbiota modulation may aid in preventing circadian misalignment and in the resynchronization of disrupted circadian rhythms. We describe diurnal microbiome rhythmicity and its related factors, highlighting the role of meal timing. Lastly, we emphasize the necessity and rationale for further research to develop effective and safe microbiome and dietary strategies based on chrononutrition to combat mental illness.}, }
@article {pmid37106747, year = {2023}, author = {Ghouili, E and Abid, G and Hogue, R and Jeanne, T and D'Astous-Pagé, J and Sassi, K and Hidri, Y and M'Hamed, HC and Somenahally, A and Xue, Q and Jebara, M and Nefissi Ouertani, R and Riahi, J and de Oliveira, AC and Muhovski, Y}, title = {Date Palm Waste Compost Application Increases Soil Microbial Community Diversity in a Cropping Barley (Hordeum vulgare L.) Field.}, journal = {Biology}, volume = {12}, number = {4}, pages = {}, pmid = {37106747}, issn = {2079-7737}, abstract = {Application of date palm waste compost is quite beneficial in improving soil properties and crop growth. However, the effect of its application on soil microbial communities is less understood. High-throughput sequencing and quantitative real-time PCR (qPCR) were used to evaluate the effect of compost application on the soil microbial composition in a barley field during the tillering, booting and ripening stages. The results showed that compost treatment had the highest bacterial and fungal abundance, and its application significantly altered the richness (Chao1 index) and α-diversity (Shannon index) of fungal and bacterial communities. The dominant bacterial phyla found in the samples were Proteobacteria and Actinobacteria while the dominant fungal orders were Ascomycota and Mortierellomycota. Interestingly, compost enriched the relative abundance of beneficial microorganisms such as Chaetomium, Actinobacteriota, Talaromyces and Mortierella and reduced those of harmful microorganisms such as Alternaria, Aspergillus and Neocosmospora. Functional prediction based on Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed that amplicon sequence variant (ASV) sequences related to energy metabolism, amino acid metabolism and carbohydrate metabolism were associated with compost-treated soil. Based on Fungi Functional Guild (FUNGuild), identified fungi community metabolic functions such as wood saprotroph, pathotroph, symbiotroph and endophyte were associated with compost-treated soil. Overall, compost addition could be considered as a sustainable practice for establishing a healthy soil microbiome and subsequently improving the soil quality and barley crop production.}, }
@article {pmid37103739, year = {2024}, author = {Balakrishnan, K and Krishnaa, D and Balakrishnan, G and Manickam, M and Abdulkader, AM and Dharumadurai, D}, title = {Association of Bacterial Communities with Psychedelic Mushroom and Soil as Revealed in 16S rRNA Gene Sequencing.}, journal = {Applied biochemistry and biotechnology}, volume = {196}, number = {5}, pages = {2566-2590}, pmid = {37103739}, issn = {1559-0291}, mesh = {*Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; *Microbiota/drug effects ; Agaricales/genetics ; Psilocybe ; Rhizosphere ; }, abstract = {Microbial communities' resident in the mushroom fruiting body and the soil around it play critical roles in the growth and propagation of the mushroom. Among the microbial communities associated with psychedelic mushrooms and the rhizosphere soil, bacterial communities are considered vital since their presence greatly influences the health of the mushrooms. The present study aimed at finding the microbiota present in the psychedelic mushroom Psilocybe cubensis and the soil the mushroom inhabits. The study was conducted at two different locations in Kodaikanal, Tamil Nadu, India. The composition and structure of microbial communities in the mushroom fruiting body and the soil were deciphered. The genomes of the microbial communities were directly assessed. High-throughput amplicon sequencing revealed distinct microbial diversity in the mushroom and the related soil. The interaction of environmental and anthropogenic factors appeared to have a significant impact on the mushroom and soil microbiome. The most abundant bacterial genera were Ochrobactrum, Stenotrophomonas, Achromobacter, and Brevundimonas. Thus, the study advances the knowledge of the composition of the microbiome and microbial ecology of a psychedelic mushroom, and paves the way for in-depth investigation of the influence of microbiota on the mushroom, with special emphasis on the impact of bacterial communities on mushroom growth. Further studies are required for a deeper understanding of the microbial communities that influence the growth of P. cubensis mushroom.}, }
@article {pmid37103495, year = {2023}, author = {Towett-Kirui, S and Morrow, JL and Close, S and Royer, JE and Riegler, M}, title = {Bacterial Communities Are Less Diverse in a Strepsipteran Endoparasitoid than in Its Fruit Fly Hosts and Dominated by Wolbachia.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2120-2132}, pmid = {37103495}, issn = {1432-184X}, support = {IC150100026//Australian Research Council (ARC) Industrial Transformation Training Centre (ITTC) Fruit Fly Biosecurity Innovation/ ; }, mesh = {*Wolbachia/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota ; High-Throughput Nucleotide Sequencing ; }, abstract = {Microbiomes play vital roles in insect fitness and health and can be influenced by interactions between insects and their parasites. Many studies investigate the microbiome of free-living insects, whereas microbiomes of endoparasitoids and their interactions with parasitised insects are less explored. Due to their development in the constrained environment within a host, endoparasitoids are expected to have less diverse yet distinct microbiomes. We used high-throughput 16S rRNA gene amplicon sequencing to characterise the bacterial communities of Dipterophagus daci (Strepsiptera) and seven of its tephritid fruit fly host species. Bacterial communities of D. daci were less diverse and contained fewer taxa relative to the bacterial communities of the tephritid hosts. The strepsipteran's microbiome was dominated by Pseudomonadota (formerly Proteobacteria) (> 96%), mainly attributed to the presence of Wolbachia, with few other bacterial community members, indicative of an overall less diverse microbiome in D. daci. In contrast, a dominance of Wolbachia was not found in flies parasitised by early stages of D. daci nor unparasitised flies. Yet, early stages of D. daci parasitisation resulted in structural changes in the bacterial communities of parasitised flies. Furthermore, parasitisation with early stages of D. daci with Wolbachia was associated with a change in the relative abundance of some bacterial taxa relative to parasitisation with early stages of D. daci lacking Wolbachia. Our study is a first comprehensive characterisation of bacterial communities in a Strepsiptera species together with the more diverse bacterial communities of its hosts and reveals effects of concealed stages of parasitisation on host bacterial communities.}, }
@article {pmid37101565, year = {2023}, author = {Mosquera-Romero, S and Ntagia, E and Rousseau, DPL and Esteve-Núñez, A and Prévoteau, A}, title = {Water treatment and reclamation by implementing electrochemical systems with constructed wetlands.}, journal = {Environmental science and ecotechnology}, volume = {16}, number = {}, pages = {100265}, pmid = {37101565}, issn = {2666-4984}, abstract = {Seasonal or permanent water scarcity in off-grid communities can be alleviated by recycling water in decentralized wastewater treatment systems. Nature-based solutions, such as constructed wetlands (CWs), have become popular solutions for sanitation in remote locations. Although typical CWs can efficiently remove solids and organics to meet water reuse standards, polishing remains necessary for other parameters, such as pathogens, nutrients, and recalcitrant pollutants. Different CW designs and CWs coupled with electrochemical technologies have been proposed to improve treatment efficiency. Electrochemical systems (ECs) have been either implemented within the CW bed (ECin-CW) or as a stage in a sequential treatment (CW + EC). A large body of literature has focused on ECin-CW, and multiple scaled-up systems have recently been successfully implemented, primarily to remove recalcitrant organics. Conversely, only a few reports have explored the opportunity to polish CW effluents in a downstream electrochemical module for the electro-oxidation of micropollutants or electro-disinfection of pathogens to meet more stringent water reuse standards. This paper aims to critically review the opportunities, challenges, and future research directions of the different couplings of CW with EC as a decentralized technology for water treatment and recovery.}, }
@article {pmid37101495, year = {2023}, author = {Nakato, GV and Wicker, E and Coutinho, TA and Mahuku, G and Studholme, DJ}, title = {Corrigendum to "A highly specific tool for identification of Xanthomonas vasicola pv. musacearum based on five Xvm-specific coding sequences" [Heliyon 4 (12) (December 2018) Article e01080].}, journal = {Heliyon}, volume = {9}, number = {3}, pages = {e14606}, doi = {10.1016/j.heliyon.2023.e14606}, pmid = {37101495}, issn = {2405-8440}, abstract = {[This corrects the article DOI: 10.1016/j.heliyon.2018.e01080.].}, }
@article {pmid37101136, year = {2023}, author = {Mosquera, KD and Martínez Villegas, LE and Rocha Fernandes, G and Rocha David, M and Maciel-de-Freitas, R and A Moreira, L and Lorenzo, MG}, title = {Egg-laying by female Aedes aegypti shapes the bacterial communities of breeding sites.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {97}, pmid = {37101136}, issn = {1741-7007}, mesh = {Animals ; Humans ; Female ; *Aedes ; Mosquito Vectors ; Water ; Bacteria/genetics ; Oviposition ; Larva ; }, abstract = {BACKGROUND: Aedes aegypti, the main arboviral mosquito vector, is attracted to human dwellings and makes use of human-generated breeding sites. Past research has shown that bacterial communities associated with such sites undergo compositional shifts as larvae develop and that exposure to different bacteria during larval stages can have an impact on mosquito development and life-history traits. Based on these facts, we hypothesized that female Ae. aegypti shape the bacteria communities of breeding sites during oviposition as a form of niche construction to favor offspring fitness.<br><br>RESULTS: To test this hypothesis, we first verified that gravid females can act as mechanical vectors of bacteria. We then elaborated an experimental scheme to test the impact of oviposition on breeding site microbiota. Five different groups of experimental breeding sites were set up with a sterile aqueous solution of larval food, and subsequently exposed to (1) the environment alone, (2) surface-sterilized eggs, (3) unsterilized eggs, (4) a non-egg laying female, or (5) oviposition by a gravid female. The microbiota of these differently treated sites was assessed by amplicon-oriented DNA sequencing once the larvae from the sites with eggs had completed development and formed pupae. Microbial ecology analyses revealed significant differences between the five treatments in terms of diversity. In particular, between-treatment shifts in abundance profiles were detected, showing that females induce a significant decrease in microbial alpha diversity through oviposition. In addition, indicator species analysis pinpointed bacterial taxa with significant predicting values and fidelity coefficients for the samples in which single females laid eggs. Furthermore, we provide evidence regarding how one of these indicator taxa, Elizabethkingia, exerts a positive effect on the development and fitness of mosquito larvae.<br><br>CONCLUSIONS: Ovipositing females impact the composition of the microbial community associated with a breeding site, promoting certain bacterial taxa over those prevailing in the environment. Among these bacteria, we found known mosquito symbionts and showed that they can improve offspring fitness if present in the water where eggs are laid. We deem this oviposition-mediated bacterial community shaping as a form of niche construction initiated by the gravid female.}, }
@article {pmid37100151, year = {2023}, author = {Wang, B and Zhu, C and Hu, Y and Zhang, B and Wang, J}, title = {Dynamics of microbial community composition during degradation of silks in burial environment.}, journal = {The Science of the total environment}, volume = {883}, number = {}, pages = {163694}, doi = {10.1016/j.scitotenv.2023.163694}, pmid = {37100151}, issn = {1879-1026}, mesh = {*Soil Microbiology ; Bacteria/metabolism ; Silk ; *Microbiota/genetics ; Soil/chemistry ; Burial ; }, abstract = {The silk residues in the soil formed the unique niche, termed "silksphere." Here, we proposed a hypothesis that silksphere microbiota have great potential as a biomarker for unraveling the degradation of the ancient silk textiles with great archaeological and conservation values. To test our hypothesis, in this study, we monitored the dynamics of microbial community composition during silk degradation via both indoor soil microcosmos model and outdoor environment with amplicon sequencing against 16S and ITS gene. Microbial community divergence was evaluated with Welch two sample t-test, PCoA, negative binomial generalized log-linear model and clustering, etc. Community assembly mechanisms differences between silksphere and bulk soil microbiota were compared with dissimilarity-overlap curve (DOC) model, Neutral model and Null model. A well-established machine learning algorithm, random forest, was also applied to the screening of potential biomarkers of silk degradation. The results illustrated the ecological and microbial variability during the microbial degradation of silk. Vast majority of microbes populating the silksphere microbiota strongly diverged from those in bulk soil. Certain microbial flora can serve as an indicator of silk degradation, which would lead to a novel perspective to perform identification of archaeological silk residues in the field. To sum up, this study provides a new perspective to perform the identification of archaeological silk residue through the dynamics of microbial communities.}, }
@article {pmid37099394, year = {2023}, author = {McCartney, AL and Hoyles, L}, title = {The role of Klebsiella populations in preterm infants.}, journal = {Biochemical Society transactions}, volume = {51}, number = {2}, pages = {887-896}, pmid = {37099394}, issn = {1470-8752}, mesh = {Infant ; Infant, Newborn ; Humans ; *Infant, Premature ; Retrospective Studies ; Klebsiella ; Feces/microbiology ; *Sepsis/microbiology ; Bacteria ; }, abstract = {The preterm infant microbiota is dominated by Enterobacteriaceae (Escherichia, Klebsiella or Enterobacter spp.), Enterococcus and Staphylococcus spp. Recent work has demonstrated the development of this microbiota is predictable and driven by simple microbe-microbe interactions. Because of their systemic immaturity, including an underdeveloped immune system, preterm infants are susceptible to a range of infections. Numerous retrospective studies have examined the association of the preterm gut microbiota with diseases such as necrotizing enterocolitis (NEC), early-onset sepsis and late-onset sepsis. To date, no single bacterium has been associated with infection in these infants, but a Klebsiella/Enterococcus-dominated faecal microbiota is associated with an increased risk of developing NEC. Staphylococci aid and enterococci inhibit establishment/maintenance of gastrointestinal Klebsiella populations in preterm infants, though the mechanisms underlying these interactions are poorly understood. Klebsiella spp. recovered from healthy and sick preterm infants display similar antimicrobial resistance and virulence profiles, giving no clues as to why some infants develop potentially life-threatening diseases while others do not. The identification of cytotoxin-producing Klebsiella oxytoca sensu lato in the gut microbiota of some preterm infants has led to the suggestion that these bacteria may contribute to NEC in a subset of neonates. This mini review highlights current knowledge on Klebsiella spp. contributing to the preterm gut microbiota and provides insights into areas of research that warrant further attention.}, }
@article {pmid37099156, year = {2023}, author = {Nguyen, PN and Rehan, SM}, title = {Environmental Effects on Bee Microbiota.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1487-1498}, pmid = {37099156}, issn = {1432-184X}, mesh = {Humans ; Animals ; Bees ; *Ecosystem ; Animals, Wild ; Urbanization ; *Microbiota ; Climate ; Agriculture ; Pollination ; }, abstract = {Anthropogenic activities and increased land use, which include industrialization, agriculture and urbanization, directly affect pollinators by changing habitats and floral availability, and indirectly by influencing their microbial composition and diversity. Bees form vital symbioses with their microbiota, relying on microorganisms to perform physiological functions and aid in immunity. As altered environments and climate threaten bees and their microbiota, characterizing the microbiome and its complex relationships with its host offers insights into understanding bee health. This review summarizes the role of sociality in microbiota establishment, as well as examines if such factors result in increased susceptibility to altered microbiota due to environmental changes. We characterize the role of geographic distribution, temperature, precipitation, floral resources, agriculture, and urbanization on bee microbiota. Bee microbiota are affected by altered surroundings regardless of sociality. Solitary bees that predominantly acquire their microbiota through the environment are particularly sensitive to such effects. However, the microbiota of obligately eusocial bees are also impacted by environmental changes despite typically well conserved and socially inherited microbiota. We provide an overview of the role of microbiota in plant-pollinator relationships and how bee microbiota play a larger role in urban ecology, offering microbial connections between animals, humans, and the environment. Understanding bee microbiota presents opportunities for sustainable land use restoration and aiding in wildlife conservation.}, }
@article {pmid37099155, year = {2023}, author = {Wang, B and Qi, M and Ma, Y and Zhang, B and Hu, Y}, title = {Microbiome Diversity and Cellulose Decomposition Processes by Microorganisms on the Ancient Wooden Seawall of Qiantang River of Hangzhou, China.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2109-2119}, pmid = {37099155}, issn = {1432-184X}, mesh = {Humans ; *Cellulose/metabolism ; Rivers ; *Microbiota/genetics ; Fungi/genetics ; Bacteria/genetics ; Wood/microbiology ; }, abstract = {Archaeological wood, also known as wooden cultural relics, refers to ancient wood that has been worked by humans. Further insights into the decomposition mechanism of archaeological wood are needed for its preventive conservation. In this study, we assessed the microbiome diversity and cellulose decomposition processes on a 200-year-old ancient wooden seawall - the Qiantang River of Hangzhou, China. We used high-throughput sequencing (HTS) to deduce the metagenomic functions, particularly the cellulose-decomposing pathway of the microbial communities, through bioinformatical approaches. The predominant cellulose-decomposing microorganisms were then verified with traditional isolation, culture, and identification method. The results showed that the excavation of archaeological wood significantly altered the environment, accelerating the deterioration process of the archaeological wood through the carbohydrate metabolism and the xenobiotic biodegradation and metabolism pathways, under the comprehensive metabolism of complex ecosystem formed by bacteria, archaea, fungi, microfauna, plants, and algae. Bacteroidetes, Proteobacteria, Firmicutes, and Actinobacteria were found to be the predominant source of bacterial cellulose-decomposing enzymes. Accordingly, we suggest relocating the wooden seawall to an indoor environment with controllable conditions to better preserve it. In addition, these results provide further evidence for our viewpoints that HTS techniques, combined with rational bioinformatical data interpretation approaches, can serve as powerful tools for the preventive protection of cultural heritage.}, }
@article {pmid37098915, year = {2023}, author = {Kim, N and Vargas, P and Fortuna, K and Wagemans, J and Rediers, H}, title = {Draft Genome Sequences of 27 Rhizogenic Agrobacterium Biovar 1 Strains, the Causative Agent of Hairy Root Disease.}, journal = {Microbiology resource announcements}, volume = {12}, number = {5}, pages = {e0012423}, pmid = {37098915}, issn = {2576-098X}, support = {HBC.2017.0816//Agentschap Innoveren en Ondernemen (VLAIO)/ ; C14/19/074//KU Leuven (Katholieke Universiteit Leuven)/ ; C3/19/047//KU Leuven (Katholieke Universiteit Leuven)/ ; }, abstract = {Rhizogenic Agrobacterium biovar 1 strains are important plant pathogens that cause hairy root disease in Cucurbitaceae and Solanaceae crops cultivated under hydroponic conditions. In contrast to tumorigenic agrobacteria, only a few genome sequences of rhizogenic agrobacteria are currently available. Here, we report the draft genome sequences of 27 rhizogenic Agrobacterium strains.}, }
@article {pmid37097879, year = {2023}, author = {Stewart, CJ}, title = {2022 Fleming Prize Lecture: diet-microbe-host interaction in early life.}, journal = {Journal of medical microbiology}, volume = {72}, number = {4}, pages = {}, doi = {10.1099/jmm.0.001662}, pmid = {37097879}, issn = {1473-5644}, mesh = {Infant ; Female ; Infant, Newborn ; Humans ; Middle Aged ; *Infant, Premature ; Host Microbial Interactions ; Milk, Human ; *Microbiota ; Diet ; }, abstract = {The last decade has witnessed a meteoric rise in research focused on characterizing the human microbiome and identifying associations with disease risk. The advent of sequencing technology has all but eradicated gel-based fingerprinting approaches for studying microbial ecology, while at the same time traditional microbiological culture is undergoing a renaissance. Although multiplexed high-throughput sequencing is relatively new, the discoveries leading to this are nearly 50 years old, coinciding with the inaugural Microbiology Society Fleming Prize lecture. It was an honour to give the 2022 Fleming Prize lecture and this review will cover the topics from that lecture. The focus will be on the bacterial community in early life, beginning with term infants before moving on to infants delivered prematurely. The review will discuss recent work showing how human milk oligosaccharides (HMOs), an abundant but non-nutritious component of breast milk, can modulate infant microbiome and promote the growth of Bifidobacterium spp. This has important connotations for preterm infants at risk of necrotizing enterocolitis, a devastating intestinal disease representing the leading cause of death and long-term morbidity in this population. With appropriate mechanistic studies, it may be possible to harness the power of breast milk bioactive factors and infant gut microbiome to improve short- and long-term health in infants.}, }
@article {pmid37097592, year = {2023}, author = {Paul, P and Roy, R and Das, S and Sarkar, S and Chatterjee, S and Mallik, M and Shukla, A and Chakraborty, P and Tribedi, P}, title = {The combinatorial applications of 1,4-naphthoquinone and tryptophan inhibit the biofilm formation of Staphylococcus aureus.}, journal = {Folia microbiologica}, volume = {68}, number = {5}, pages = {801-811}, pmid = {37097592}, issn = {1874-9356}, mesh = {Humans ; *Staphylococcus aureus ; Tryptophan/pharmacology ; Extracellular Polymeric Substance Matrix ; Anti-Bacterial Agents/pharmacology ; *Staphylococcal Infections/drug therapy/microbiology ; Biofilms ; Microbial Sensitivity Tests ; }, abstract = {Microorganisms embedded within an extracellular polymeric matrix are known as biofilm. The extensive use of antibiotics to overcome the biofilm-linked challenges has led to the emergence of multidrug-resistant strains. Staphylococcus aureus is one such nosocomial pathogen that is known to cause biofilm-linked infections. Thus, novel strategies have been adopted in this study to inhibit the biofilm formation of S. aureus. Two natural compounds, namely, 1,4-naphthoquinone (a quinone derivative) and tryptophan (aromatic amino acid), have been chosen as they could independently show efficient antibiofilm activity. To enhance the antibiofilm potential, the two compounds were combined and tested against the same organism. Several experiments like crystal violet (CV) assay, protein estimation, extracellular polymeric substance (EPS) extraction, and estimation of metabolic activity confirmed that the combination of the two compounds could significantly inhibit the biofilm formation of S. aureus. To comprehend the underlying mechanism, efforts were further directed to understand whether the two compounds could inhibit biofilm formation by compromising the cell surface hydrophobicity of the bacteria. The results revealed that the cell surface hydrophobicity got reduced by ~ 49% when the compounds were applied together. Thus, the combinations could show enhanced antibiofilm activity by attenuating cell surface hydrophobicity. Further studies revealed that the selected concentrations of the compounds could disintegrate (~ 70%) the pre-existing biofilm of the test bacteria without showing any antimicrobial activity. Hence, the combined application of tryptophan and 1,4-naphthoquinone could be used to inhibit the biofilm threats of S. aureus.}, }
@article {pmid37097162, year = {2023}, author = {Masasa, M and Kushmaro, A and Nguyen, D and Chernova, H and Shashar, N and Guttman, L}, title = {Spatial Succession Underlies Microbial Contribution to Food Digestion in the Gut of an Algivorous Sea Urchin.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0051423}, pmid = {37097162}, issn = {2165-0497}, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics ; *Sea Urchins/genetics ; Seafood ; Digestion ; Sulfates ; }, abstract = {Dietary influence on the microbiome in algivorous sea urchins such as Tripneustes gratilla elatensis suggests a bacterial contribution to the digestion of fiber-rich seaweed. An ecological insight into the spatial arrangement in the gut bacterial community will improve our knowledge of host-microbe relations concerning the involved taxa, their metabolic repertoire, and the niches of activity. Toward this goal, we investigated the bacterial communities in the esophagus, stomach, and intestine of Ulva-fed sea urchins through 16S rRNA amplicon sequencing, followed by the prediction of their functional genes. We revealed communities with distinct features, especially those in the esophagus and intestine. The esophageal community was less diverse and was poor in food digestive or fermentation genes. In contrast, bacteria that can contribute to the digestion of the dietary Ulva were common in the stomach and intestine and consisted of genes for carbohydrate decomposition, fermentation, synthesis of short-chain fatty acids, and various ways of N and S metabolism. Bacteroidetes and Firmicutes were found as the main phyla in the gut and are presumably also necessary in food digestion. The abundant sulfate-reducing bacteria in the stomach and intestine from the genera Desulfotalea, Desulfitispora, and Defluviitalea may aid in removing the excess sulfate from the decomposition of the algal polysaccharides. Although these sea urchins were fed with Ulva, genes for the degradation of polysaccharides of other algae and plants were present in this sea urchin gut microbiome. We conclude that the succession of microbial communities along the gut obtained supports the hypothesis on bacterial contribution to food digestion. IMPORTANCE Alga grazing by the sea urchin Tripneustes gratilla elatensis is vital for nutrient recycling and constructing new reefs. This research was driven by the need to expand the knowledge of bacteria that may aid this host in alga digestion and their phylogeny, roles, and activity niches. We hypothesized alterations in the bacterial compositional structure along the gut and their association with the potential contribution to food digestion. The current spatial insight into the sea urchin's gut microbiome ecology is novel and reveals how distinct bacterial communities are when distant from each other in this organ. It points to keynote bacteria with genes that may aid the host in the digestion of the complex sulfated polysaccharides in dietary Ulva by removing the released sulfates and fermentation to provide energy. The gut bacteria's genomic arsenal may also help to gain energy from diets of other algae and plants.}, }
@article {pmid37093231, year = {2023}, author = {Ichige, R and Urabe, J}, title = {Divergence of the Host-Associated Microbiota with the Genetic Distance of Host Individuals Within a Parthenogenetic Daphnia Species.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2097-2108}, pmid = {37093231}, issn = {1432-184X}, support = {JPMJSP2114//Japan Science and Technology Agency/ ; KAKENHI:20H03315//Japan Society for the Promotion of Science Grant-in-Aid for Scientific Research/ ; }, mesh = {Animals ; *Daphnia/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Genotype ; }, abstract = {The taxonomic composition of the microbiota in the gut and epidermis of animals is known to vary among genetically and physiologically different host individuals within the same species. However, it is not clear whether the taxonomic composition diverges with increasing genetic distance of the host individuals. To unveil this uncertainty, we compared the host-associated microbiota among the genotypes within and between genetically distant lineages of parthenogenetic Daphnia cf. pulex across different physiological states, namely, well-fed, starved, and dead. Metagenomic analysis with 16S rRNA showed that, regardless of the host genotypes, diversity of the host-associated microbiota was high when the host individuals were fed food and gradually decreased when they were starved until they died. However, the difference in the host-associated microbiota, that is, β-diversity, was significant among the genotypes within and between the host lineages when they were fed. Although some bacteria in the microbiota, such as Limnohabitans, Rhodococcus, and Aeromicrobium, were found abundantly and commonly in all host genotypes; others, such as those of Holosoporacea, were found only in the genotypes of a specific lineage. Accordingly, the β-diversity tended to increase with increasing genetic distance of the host individuals. These results support an idea that the host-associated microbiota diverged with genetic divergence in the host species and that at least some bacteria are highly dependent on the genetically specific metabolites produced by the host individuals.}, }
@article {pmid37093057, year = {2023}, author = {Chen, Q and Fan, Y and Zhang, B and Yan, C and Zhang, Q and Ke, Y and Chen, Z and Wang, L and Shi, H and Hu, Y and Huang, Q and Su, J and Xie, C and Zhang, X and Zhou, L and Ren, J and Xu, H}, title = {Capsulized Fecal Microbiota Transplantation Induces Remission in Patients with Ulcerative Colitis by Gut Microbial Colonization and Metabolite Regulation.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0415222}, pmid = {37093057}, issn = {2165-0497}, mesh = {Humans ; Bacteria ; *Colitis, Ulcerative/therapy/microbiology ; *Communicable Diseases ; Fecal Microbiota Transplantation/methods ; Feces/microbiology ; *Gastrointestinal Microbiome ; Treatment Outcome ; }, abstract = {Fecal microbiota transplantation (FMT) can induce clinical remission in ulcerative colitis (UC) patients. Enemas, nasoduodenal tubes, and colonoscopies are the most common routes for FMT administration. However, there is a lack of definitive evidence regarding the effectiveness of capsulized FMT treatment in UC patients. In this study, we administered capsulized FMT to 22 patients with active UC to assess the efficiency of capsulized FMT and determine the specific bacteria and metabolite factors associated with the response to clinical remission. Our results showed that the use of capsulized FMT was successful in the treatment of UC patients. Capsulized FMT induced clinical remission and clinical response in 57.1% (12 of 21) and 76.2% (16 of 21) of UC patients, respectively. Gut bacterial richness was increased after FMT in patients who achieved remission. Patients in remission after FMT exhibited enrichment of Alistipes sp. and Odoribacter splanchnicus, along with increased levels of indolelactic acid. Patients who did not achieve remission exhibited enrichment of Escherichia coli and Klebsiella and increased levels of biosynthesis of 12,13-DiHOME (12,13-dihydroxy-9Z-octadecenoic acid) and lipopolysaccharides. Furthermore, we identified a relationship between specific bacteria and metabolites and the induction of remission in patients. These findings may provide new insights into FMT in UC treatment and provide reference information about therapeutic microbial manipulation of FMT to enhance its effects. (This study has been registered at ClinicalTrails.gov under registration no. NCT03426683). IMPORTANCE Fecal microbiota transplantation has been successfully used in patients. Recently, capsulized FMT was reported to induce a response in patients with UC. However, limited patients were enrolled in such studies, and the functional factors of capsulized FMT have not been reported in the remission of patients with UC. In this study, we prospectively recruited patients with UC to receive capsulized FMT. First, we found that capsulized FMT could induce clinical remission in 57.1% of patients and clinical response in 76.2% after 12 weeks, which was more acceptable. Second, we found a relationship between the decrease of opportunistic pathogen and lipopolysaccharide synthesis in patients in remission after capsulized FMT. We also identified an association between specific bacteria and metabolites and remission induction in patients after capsulized FMT. These findings put forward a possibility for patients to receive FMT at home and provide reference information about therapeutic microbial manipulation of FMT to enhance its effects.}, }
@article {pmid37090461, year = {2023}, author = {Al-Rshaidat, MMD and Al-Sharif, S and Refaei, AA and Shewaikani, N and Alsayed, AR and Rayyan, YM}, title = {Evaluating the clinical application of the immune cells' ratios and inflammatory markers in the diagnosis of inflammatory bowel disease.}, journal = {Pharmacy practice}, volume = {21}, number = {1}, pages = {2755}, pmid = {37090461}, issn = {1885-642X}, abstract = {OBJECTIVE: Inflammatory Bowel Diseases (IBDs) are chronic inflammatory conditions of the gastrointestinal tract, including Crohn's disease (CD) and ulcerative colitis (UC). Developing methods for effective screening and diagnosis is extremely needed. Accordingly, this study aims to evaluate the potential of immune cells ratios in the diagnosis of IBD.<br><br>METHODS: This case-control study includes data from Jordan University Hospital (JUH) medical records for IBD patients with age- and gender-matched healthy controls.<br><br>RESULTS: This study included 46 participants, of which 56.52% had IBD, 54.35% were males, with insignificant differences in sex, age, and body mass index (BMI) between IBD patients and controls (p>0.05). In the CD group, the variables with the highest sensitivity and specificity (HSS) were neutrophil-to-lymphocyte (NLR) (75%, 80%) and platelet-to-lymphocytes (PLR) (75%, 90%), in UC group; mean corpuscular hemoglobin (MCH) (80%, 80%). In CD group, the combinations giving the HSS were PLR+NLR (76%, 90.9%), C-reactive protein (CRP)+PLR (76%, 90.9%), and CRP+NLR (73.07%, 90%). In UC group, the combinations giving the HSS were erythrocyte sedimentation rate (ESR)+PLR (76.9%, 100%), PLR+MCH (74.07%, 100%), PLR+CRP (71.42%, 100%), and PLR+NLR (71.42%, 100%). Regression analysis identified five different combinations of significance in the diagnosis of CD and UC. Higher Youden's index was used and defined the most beneficial clinical combinations as NLR+PLR and CRP+PLR for CD, whereas ESR+PLR for UC.<br><br>CONCLUSION: Implications to our study include the clinical application of immune cell ratios, inflammatory markers, and their different combinations along with patients' history and physical examination findings for easier, faster, and more cost-effective diagnosis of IBDs.}, }
@article {pmid37088849, year = {2023}, author = {Mills, TJT and Nelson, TM and Pearson, LA and Neilan, BA}, title = {Hive Transplantation Has Minimal Impact on the Core Gut Microbiome of the Australian Stingless Bee, Tetragonula carbonaria.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2086-2096}, pmid = {37088849}, issn = {1432-184X}, support = {FF0883440//Australian Research Council/ ; }, mesh = {Bees ; Animals ; *Gastrointestinal Microbiome ; Australia ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Urticaria ; }, abstract = {Bacteria residing in the guts of pollinating insects play a key role in nutrient acquisition, digestion, and resistance to pests and diseases. Imbalances in microbial flora in response to environmental change and stress can therefore impact insect health and resilience. This study is aimed at defining the core gut microbiome of the Australian native stingless bee, Tetragonula carbonaria, and exploring the impact of colony transplantation on gut health. The gut microbiomes of nine forager bees from natural (log) and manufactured (box) hives were examined via 16S rRNA gene amplicon sequencing. Some differences were observed at the ASV level between the microbiomes of log and box hive bees. However, a core microbiome, dominated by Lactobacillus spp., unclassified Acetobacteraceae spp., and Bombella spp., was maintained. Further, the inferred functional potential of the microbiomes was consistent across all individuals. This study highlights that although hive transplantation has an impact on the overall diversity of stingless bee gut microbiomes, it is unlikely to have a significant negative impact on the overall health and resilience of the colony.}, }
@article {pmid37088357, year = {2023}, author = {Selhorst, P and Lequime, S and Dudas, G and Proesmans, S and Lutumba, P and Katshongo, F and Ramadan, K and Micalessi, I and Ahuka-Mundeke, S and Vanlerberghe, V and Van Esbroeck, M and Ariën, KK}, title = {Phylogeographic analysis of dengue virus serotype 1 and cosmopolitan serotype 2 in Africa.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {133}, number = {}, pages = {46-52}, doi = {10.1016/j.ijid.2023.04.391}, pmid = {37088357}, issn = {1878-3511}, mesh = {Humans ; *Dengue Virus/genetics ; *Dengue/epidemiology ; Serogroup ; Phylogeny ; Bayes Theorem ; Africa/epidemiology ; Genotype ; Disease Outbreaks ; Fever/epidemiology ; }, abstract = {OBJECTIVES: The origin and spread of dengue virus (DENV) circulating in Africa remain poorly characterized, with African sequences representing <1% of global sequence data.<br><br>METHODS: Whole genome sequencing was performed on serum samples (n&#xa0;=&#xa0;29) from an undifferentiated fever study in 2016 in the Democratic Republic of Congo (DRC), and from febrile travelers returning from Africa. The evolutionary history of the newly acquired African DENV-1 (n&#xa0;=&#xa0;1) and cosmopolitan genotype DENV-2 (n&#xa0;=&#xa0;18) genomes was reconstructed using a phylogeographic, time-scaled Bayesian analysis on a curated DENV panel including all known African sequences.<br><br>RESULTS: A minimum of 10 and eight introductions could be identified into Africa for DENV-1 and cosmopolitan DENV-2, respectively, almost all originating from Asia. Three introductions were previously unknown. The currently circulating virus comprises mainly the recently introduced clades and one long-established African clade. Robust geographical clustering suggests limited spread of DENV after each introduction. Our data identified the DRC as the source of the 2018 Angolan DENV-2 epidemic, and similarly, the 2013 Angolan DENV-1 outbreak as the origin of our DRC study.<br><br>CONCLUSION: Active genomic surveillance of DENV in Africa at the portals of entry might help early outbreak response and limit sero- and genotype spread and human disease burden.}, }
@article {pmid37086855, year = {2023}, author = {Buivydaitė, &#x17d; and Aryal, L and Corrêa, FB and Chen, T and Langlois, V and Elberg, CL and Netherway, T and Wang, R and Zhao, T and Acharya, B and Emerson, JB and Hillary, L and Khadka, RB and Mason-Jones, K and Sapkota, R and Sutela, S and Trubl, G and White, RA and Winding, A and Carreira, C}, title = {Meeting report: The first soil viral workshop 2022.}, journal = {Virus research}, volume = {331}, number = {}, pages = {199121}, pmid = {37086855}, issn = {1872-7492}, mesh = {Humans ; Ecology ; Food Chain ; Genome, Viral ; *Viruses ; }, abstract = {Soil viral ecology is a growing research field; however, the state of knowledge still lags behind that of aquatic systems. Therefore, to facilitate progress, the first Soil Viral Workshop was held to encourage international scientific discussion and collaboration, suggest guidelines for future research, and establish soil viral research as a concrete research area. The workshop took place at Søminestationen, Denmark, between 15 and 17th of June 2022. The meeting was primarily held in person, but the sessions were also streamed online. The workshop was attended by 23 researchers from ten different countries and from a wide range of subfields and career stages. Eleven talks were presented, followed by discussions revolving around three major topics: viral genomics, virus-host interactions, and viruses in the soil food web. The main take-home messages and suggestions from the discussions are summarized in this report.}, }
@article {pmid37086668, year = {2023}, author = {Wu, K and Atasoy, M and Zweers, H and Rijnaarts, H and Langenhoff, A and Fernandes, TV}, title = {Impact of wastewater characteristics on the removal of organic micropollutants by Chlorella sorokiniana.}, journal = {Journal of hazardous materials}, volume = {453}, number = {}, pages = {131451}, doi = {10.1016/j.jhazmat.2023.131451}, pmid = {37086668}, issn = {1873-3336}, mesh = {Wastewater ; *Chlorella ; Carbon ; Phosphates ; *Microalgae ; Biomass ; Nitrogen ; }, abstract = {Microalgae-based technologies can be used for the removal of organic micropollutants (OMPs) from different types of wastewater. However, the effect of wastewater characteristics on the removal is still poorly understood. In this study, the removal of sixteen OMPs by Chlorella sorokiniana, cultivated in three types of wastewater (anaerobically digested black water (AnBW), municipal wastewater (MW), and secondary clarified effluent (SCE)), were assessed. During batch operational mode, eleven OMPs were removed from AnBW and MW. When switching from batch to continuous mode (0.8 d HRT), the removal of most OMPs from AnBW and MW decreased, suggesting that a longer retention time enhances the removal of some OMPs. Most OMPs were not removed from SCE since poor nutrient availability limited C. sorokiniana growth. Further correlation analyses between wastewater characteristics, biomass and OMPs removal indicated that the wastewater soluble COD and biomass concentration predominantly affected the removal of OMPs. Lastly, carbon uptake rate had a higher effect on the removal of OMPs than nitrogen and phosphate uptake rate. These data will give an insight on the implementation of microalgae-based technologies for the removal of OMPs in wastewater with varying strengths and nutrient availability.}, }
@article {pmid37084659, year = {2023}, author = {Zeng, Z and Yue, W and Kined, C and Wang, P and Liu, R and Liu, J and Chen, X}, title = {Bacillus licheniformis reverses the environmental ceftriaxone sodium-induced gut microbial dysbiosis and intestinal inflammation in mice.}, journal = {Ecotoxicology and environmental safety}, volume = {257}, number = {}, pages = {114890}, doi = {10.1016/j.ecoenv.2023.114890}, pmid = {37084659}, issn = {1090-2414}, mesh = {Humans ; Mice ; Animals ; Ceftriaxone/pharmacology ; *Bacillus licheniformis/genetics ; *Gastrointestinal Microbiome ; Dysbiosis/chemically induced ; RNA, Ribosomal, 16S/genetics ; Caco-2 Cells ; Inflammation/drug therapy ; Bacteria/genetics ; Anti-Bacterial Agents/toxicity ; Firmicutes/genetics ; }, abstract = {Antibiotics used as a common clinical treatment have saved many lives. Widespread use of antibiotic therapy has been known to disrupt the balance of pathogenic bacteria, host-associated microorganisms and environment. However, our understanding of Bacillus licheniformis for health benefits and ability to restore the ceftriaxone sodium-induced gut microbial dysbiosis is severely limited. We used Caco-2 cell, H&amp;E (hematoxylin-eosin staining), RT-PCR and 16S rRNA sequencing techniques to investigate the influence of Bacillus licheniformis on gut microbial dysbiosis and inflammation following ceftriaxone sodium treatment. The results showed that treatment of ceftriaxone sodium in 7 days suppressed the expression of Nf-κB pathway mRNA levels, which caused cytoplasmic vacuolization in intestinal tissues, afterward, the administration of Bacillus licheniformis could effectively restore intestinal morphology and inflammation levels. Moreover, the ceftriaxone sodium treatment entirely affected the intestinal microbial ecology, leading to a decrease in microbial abundance. Firmicutes, Proteobacteria, and Epsilonbacteraeota were the most predominant phyla in each of the four groups. Specifically, the MA group (ceftriaxone sodium treatment) resulted in a significant decrease in the relative abundance of 2 bacterial phyla and 20 bacterial genera compared to the administration of Bacillus licheniformis after ceftriaxone sodium treatment. The supplementation of Bacillus licheniformis could increase the growth of Firmicutes and Lactobacillus and encourage the construction of a more mature and stable microbiome. Furthermore, Bacillus licheniformis could restore the intestinal microbiome disorders and inflammation levels following ceftriaxone sodium treatment.}, }
@article {pmid37082712, year = {2023}, author = {Song, W and Zhang, S and Li, X and Gao, C and Cai, J and Li, Y}, title = {Editorial: Relationship between intestinal microbiome and vasculitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1165730}, pmid = {37082712}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; Dysbiosis ; *Vasculitis ; }, }
@article {pmid37082182, year = {2023}, author = {Zhang, J and Wang, J and Labes, A and Zeng, R}, title = {Editorial: Marine microbial-derived molecules and their potential medical and cosmetic applications, volume II.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1188008}, doi = {10.3389/fmicb.2023.1188008}, pmid = {37082182}, issn = {1664-302X}, }
@article {pmid37081077, year = {2023}, author = {Zorz, J and Li, C and Chakraborty, A and Gittins, DA and Surcon, T and Morrison, N and Bennett, R and MacDonald, A and Hubert, CRJ}, title = {SituSeq: an offline protocol for rapid and remote Nanopore 16S rRNA amplicon sequence analysis.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {33}, pmid = {37081077}, issn = {2730-6151}, abstract = {Microbiome analysis through 16S rRNA gene sequencing is a crucial tool for understanding the microbial ecology of any habitat or ecosystem. However, workflows require large equipment, stable internet, and extensive computing power such that most of the work is performed far away from sample collection in both space and time. Performing amplicon sequencing and analysis at sample collection would have positive implications in many instances including remote fieldwork and point-of-care medical diagnoses. Here we present SituSeq, an offline and portable workflow for the sequencing and analysis of 16S rRNA gene amplicons using Nanopore sequencing and a standard laptop computer. SituSeq was validated by comparing Nanopore 16S rRNA gene amplicons, Illumina 16S rRNA gene amplicons, and Illumina metagenomes, sequenced using the same environmental DNA. Comparisons revealed consistent community composition, ecological trends, and sequence identity across platforms. Correlation between the abundance of taxa in each taxonomic level in Illumina and Nanopore data sets was high (Pearson's r > 0.9), and over 70% of Illumina 16S rRNA gene sequences matched a Nanopore sequence with greater than 97% sequence identity. On board a research vessel on the open ocean, SituSeq was used to analyze amplicon sequences from deep sea sediments less than 2 h after sequencing, and 8 h after sample collection. The rapidly available results informed decisions about subsequent sampling in near real-time while the offshore expedition was still underway. SituSeq is a portable and user-friendly workflow that helps to bring the power of microbial genomics and diagnostics to many more researchers and situations.}, }
@article {pmid37076812, year = {2023}, author = {De Wolfe, TJ and Wright, ES}, title = {Multi-factorial examination of amplicon sequencing workflows from sample preparation to bioinformatic analysis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {107}, pmid = {37076812}, issn = {1471-2180}, support = {T15 LM007059/LM/NLM NIH HHS/United States ; }, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Workflow ; *Microbiota/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: The development of sequencing technologies to evaluate bacterial microbiota composition has allowed new insights into the importance of microbial ecology. However, the variety of methodologies used among amplicon sequencing workflows leads to uncertainty about best practices as well as reproducibility and replicability among microbiome studies. Using a bacterial mock community composed of 37 soil isolates, we performed a comprehensive methodological evaluation of workflows, each with a different combination of methodological factors spanning sample preparation to bioinformatic analysis to define sources of artifacts that affect coverage, accuracy, and biases in the resulting compositional profiles.<br><br>RESULTS: Of the workflows examined, those using the V4-V4 primer set enabled the highest level of concordance between the original mock community and resulting microbiome sequence composition. Use of a high-fidelity polymerase, or a lower-fidelity polymerase with an&#xa0;increased PCR elongation time, limited chimera formation. Bioinformatic pipelines presented a trade-off between the fraction of distinct community members identified (coverage) and fraction of correct sequences (accuracy). DADA2 and QIIME2 assembled V4-V4 reads amplified by Taq polymerase resulted in the highest accuracy (100%) but had a coverage of only 52%. Using mothur to assemble and denoise V4-V4 reads resulted in a coverage of 75%, albeit with marginally lower accuracy (99.5%).<br><br>CONCLUSIONS: Optimization of microbiome workflows is critical for accuracy and to support reproducibility and replicability among microbiome studies. These considerations will help reveal the guiding principles of microbial ecology and impact the translation of microbiome research to human and environmental health.}, }
@article {pmid37075990, year = {2023}, author = {Svigruha, R and Prikler, B and Farkas, A and Ács, A and Fodor, I and Tapolczai, K and Schmidt, J and Bordós, G and Háhn, J and Harkai, P and Kaszab, E and Szoboszlay, S and Pirger, Z}, title = {Presence, variation, and potential ecological impact of microplastics in the largest shallow lake of Central Europe.}, journal = {The Science of the total environment}, volume = {883}, number = {}, pages = {163537}, doi = {10.1016/j.scitotenv.2023.163537}, pmid = {37075990}, issn = {1879-1026}, mesh = {*Microplastics ; Plastics ; Ecosystem ; Progestins ; Lakes/chemistry ; Polyethylene ; *Water Pollutants, Chemical/analysis ; }, abstract = {The presence of microplastics (MPs) in the global ecosystem has generated a rapidly growing concern worldwide. Although their presence in the marine environment has been well-studied, much less data are available on their abundance in freshwaters. MPs alone and in combination with different chemicals has been shown to cause acute and chronic effects on algae and aquatic invertebrate and vertebrate species at different biological levels. However, the combined ecotoxicological effects of MPs with different chemicals on aquatic organisms are still understudied in many species and the reported data are often controversial. In the present study, we investigated, for the first time, the presence of MPs in Lake Balaton, which is the largest shallow lake of Central Europe and an important summer holiday destination. Moreover, we exposed neonates of the well-established ecotoxicological model organism Daphnia magna to different MPs (polystyrene [3 μm] or polyethylene [≤ 100 μm]) alone and in combination with three progestogen compounds (progesterone, drospirenone, levonorgestrel) at an environmentally relevant concentration (10 ng L[-1]) for 21 days. The presence of 7 polymer types of MPs in the size range of 50-100 μm was detected in Lake Balaton. Similarly to the global trends, polypropylene and polyethylene MPs were the most common types of polymer. The calculated polymer-independent average particle number was 5.5 particles m[-3] (size range: 50 μm - 100 μm) which represents the values detected in other European lakes. Our ecotoxicological experiments confirmed that MPs and progestogens can affect D. magna at the behavioral (body size and reproduction) and biochemical (detoxification-related enzyme activity) levels. The joint effects were negligible. The presence of MPs may lead to reduced fitness in the aquatic biota in freshwaters such as Lake Balaton, however, the potential threat of MPs as vectors for progestogens may be limited.}, }
@article {pmid37071646, year = {2023}, author = {Poudel, SK and Padmanabhan, R and Dave, H and Guinta, K and Stevens, T and Sanaka, MR and Chahal, P and Sohal, DPS and Khorana, AA and Eng, C}, title = {Microbiomic profiles of bile in patients with benign and malignant pancreaticobiliary disease.}, journal = {PloS one}, volume = {18}, number = {4}, pages = {e0283021}, pmid = {37071646}, issn = {1932-6203}, mesh = {Humans ; Bile ; RNA, Ribosomal, 16S/genetics ; Cholangiopancreatography, Endoscopic Retrograde ; *Pancreatic Neoplasms/genetics/pathology ; *Cholangiocarcinoma/genetics/pathology ; *Bile Duct Neoplasms/pathology ; Bile Ducts, Intrahepatic/pathology ; Pancreatic Ducts/pathology ; }, abstract = {BACKGROUND: The prognostic and pathophysiologic significance of the biliary microbiota in pancreaticobiliary malignancies is little understood. Our goal was to find malignancy-related microbiomic fingerprints in bile samples taken from patients with benign and malignant pancreaticobiliary diseases.<br><br>METHODS: Bile specimens were collected from consenting patients during routine endoscopic retrograde cholangiopancreatography. We used PowerViral RNA/DNA Isolation kit to extract DNA from bile specimens. The Illumina 16S Metagenomic Sequencing Library Preparation guide was used to amplify the bacterial 16S rRNA gene and create libraries. QIIME (Quantitative Insights Into Microbial Ecology), Bioconductor phyloseq, microbiomeSeq, and mixMC packages were used for post-sequencing analysis.<br><br>RESULTS: Of 46 enrolled patients, 32 patients had pancreatic cancers, 6 had cholangiocarcinoma and 1 had gallbladder cancer. Rest of the patients had benign diseases including gallstones, and acute and chronic pancreatitis. We used multivariate approach in mixMC to classify Operational Taxonomic Units (OTUs). Doing this, we found a predominance of genera Dickeya (p = 0.00008), [Eubacterium] hallii group (p = 0.0004), Bacteroides (p = 0.0006), Faecalibacterium (p = 0.006), Escherichia-Shigella (p = 0.008), and Ruminococcus 1 (p = 0.008) in bile samples from pancreaticobiliary cancers as compared to benign diseases. Additionally, bile samples from patients with pancreatic cancer exhibited a predominance of genus Rothia (p = 0.008) as compared to those with cholangiocarcinoma, whereas bile samples from patients with cholangiocarcinoma exhibited a predominance of genera Akkermansia (p = 0.031) and Achromobacter (p = 0.031) as compared to those with pancreatic cancers.<br><br>CONCLUSIONS: Both benign and malignant pancreaticobiliary diseases have distinct microbiomic fingerprints. The relative abundance of OTUs in bile samples varies between patients with benign and malignant pancreaticobiliary diseases, as well as between cholangiocarcinoma and pancreatic cancer. Our data suggest that either these OTUs play a role in carcinogenesis or that benign disease-specific microenvironmental changes differ from cancer-specific microenvironmental changes, resulting to a clear separation of OTU clusters. We need more research to confirm and expand on our findings.}, }
@article {pmid37070710, year = {2023}, author = {García Mendez, DF and Sanabria, J and Wist, J and Holmes, E}, title = {Effect of Operational Parameters on the Cultivation of the Gut Microbiome in Continuous Bioreactors Inoculated with Feces: A Systematic Review.}, journal = {Journal of agricultural and food chemistry}, volume = {71}, number = {16}, pages = {6213-6225}, pmid = {37070710}, issn = {1520-5118}, mesh = {Humans ; *Gastrointestinal Microbiome ; Feces ; Gastrointestinal Tract ; Bioreactors ; }, abstract = {Since the early 1980s, multiple researchers have contributed to the development of in vitro models of the human gastrointestinal system for the mechanistic interrogation of the gut microbiome ecology. Using a bioreactor for simulating all the features and conditions of the gastrointestinal system is a massive challenge. Some conditions, such as temperature and pH, are readily controlled, but a more challenging feature to simulate is that both may vary in different regions of the gastrointestinal tract. Promising solutions have been developed for simulating other functionalities, such as dialysis capabilities, peristaltic movements, and biofilm growth. This research field is under constant development, and further efforts are needed to drive these models closer to in vivo conditions, thereby increasing their usefulness for studying the gut microbiome impact on human health. Therefore, understanding the influence of key operational parameters is fundamental for the refinement of the current bioreactors and for guiding the development of more complex models. In this review, we performed a systematic search for operational parameters in 229 papers that used continuous bioreactors seeded with human feces. Despite the reporting of operational parameters for the various bioreactor models being variable, as a result of a lack of standardization, the impact of specific operational parameters on gut microbial ecology is discussed, highlighting the advantages and limitations of the current bioreactor systems.}, }
@article {pmid37069235, year = {2023}, author = {Zhang, Y and Liu, T and Li, MM and Hua, ZS and Evans, P and Qu, Y and Tan, S and Zheng, M and Lu, H and Jiao, JY and Lücker, S and Daims, H and Li, WJ and Guo, J}, title = {Hot spring distribution and survival mechanisms of thermophilic comammox Nitrospira.}, journal = {The ISME journal}, volume = {17}, number = {7}, pages = {993-1003}, pmid = {37069235}, issn = {1751-7370}, support = {P 30570/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Ammonia/metabolism ; Ecosystem ; *Hot Springs ; Oxidation-Reduction ; Bacteria/genetics/metabolism ; Nitrification ; *Ammonium Compounds/metabolism ; Nitrates/metabolism ; Phylogeny ; Archaea/genetics ; }, abstract = {The recent discovery of Nitrospira species capable of complete ammonia oxidation (comammox) in non-marine natural and engineered ecosystems under mesothermal conditions has changed our understanding of microbial nitrification. However, little is known about the occurrence of comammox bacteria or their ability to survive in moderately thermal and/or hyperthermal habitats. Here, we report the wide distribution of comammox Nitrospira in five terrestrial hot springs at temperatures ranging from 36 to 80°C and provide metagenome-assembled genomes of 11 new comammox strains. Interestingly, the identification of dissimilatory nitrate reduction to ammonium (DNRA) in thermophilic comammox Nitrospira lineages suggests that they have versatile ecological functions as both sinks and sources of ammonia, in contrast to the described mesophilic comammox lineages, which lack the DNRA pathway. Furthermore, the in situ expression of key genes associated with nitrogen metabolism, thermal adaptation, and oxidative stress confirmed their ability to survive in the studied hot springs and their contribution to nitrification in these environments. Additionally, the smaller genome size and higher GC content, less polar and more charged amino acids in usage profiles, and the expression of a large number of heat shock proteins compared to mesophilic comammox strains presumably confer tolerance to thermal stress. These novel insights into the occurrence, metabolic activity, and adaptation of comammox Nitrospira in thermal habitats further expand our understanding of the global distribution of comammox Nitrospira and have significant implications for how these unique microorganisms have evolved thermal tolerance strategies.}, }
@article {pmid37065146, year = {2023}, author = {Vannier, P and Farrant, GK and Klonowski, A and Gaidos, E and Thorsteinsson, T and Marteinsson, V&#xde;}, title = {Metagenomic analyses of a microbial assemblage in a subglacial lake beneath the Vatnajökull ice cap, Iceland.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1122184}, pmid = {37065146}, issn = {1664-302X}, abstract = {Skaftárkatlar are two subglacial lakes located beneath the Vatnajökull ice cap in Iceland associated with geothermal and volcanic activity. Previous studies of these lakes with ribosomal gene (16S rDNA) tag sequencing revealed a limited diversity of bacteria adapted to cold, dark, and nutrient-poor waters. In this study, we present analyses of metagenomes from the lake which give new insights into its microbial ecology. Analyses of the 16S rDNA genes in the metagenomes confirmed the existence of a low-diversity core microbial assemblage in the lake and insights into the potential metabolisms of the dominant members. Seven taxonomic genera, Sulfuricurvum, Sulfurospirillum, Acetobacterium, Pelobacter/Geobacter, Saccharibacteria, Caldisericum, and an unclassified member of Prolixibacteraceae, comprised more than 98% of the rDNA reads in the library. Functional characterisation of the lake metagenomes revealed complete metabolic pathways for sulphur cycling, nitrogen metabolism, carbon fixation via the reverse Krebs cycle, and acetogenesis. These results show that chemolithoautotrophy constitutes the main metabolism in this subglacial ecosystem. This assemblage and its metabolisms are not reflected in enrichment cultures, demonstrating the importance of in situ investigations of this environment.}, }
@article {pmid37060391, year = {2023}, author = {Adhikari, NP and Adhikari, S}, title = {First report on the bacterial community composition, diversity, and functions in Ramsar site of Central Himalayas, Nepal.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {5}, pages = {573}, pmid = {37060391}, issn = {1573-2959}, mesh = {RNA, Ribosomal, 16S/genetics ; Nepal ; *Environmental Monitoring ; *Bacteria/genetics ; Wetlands ; Water ; }, abstract = {Wetland bacterial communities are highly sensitive to altered hydrology and the associated change in water physicochemical and biological properties leading to shifts in community composition and diversity, hence affecting the ecological roles. However, relevant studies are lacking in the wetlands of central Himalayas Nepal. Thus, we aimed to explore the variation of bacterial communities, diversity, and ecologic functions in the wet and dry periods of a wetland (designed as Ramsar site, Ramsar no 2257) by using 16S rRNA gene-based Illumina MiSeq sequencing. We reported a pronounced variation in water physicochemical and biological properties (temperature, pH, Chla, DOC, and TN), bacterial diversity, and community composition. Bacterial communities in the dry season harbored significantly higher alpha diversity, while significantly higher richness and abundance were reflected in the wet season. Our results uncovered the effect of nutrients on bacterial abundance, richness, and community composition. Fourteen percent of the total OTUs were shared in two hydrological periods, and the largest portion of unique OTUs (58%) was observed in the dry season. Planctomycetes and Bacteroidetes dominated the wet season exclusive OTUs; meanwhile, Actinobacteria dominated the dry season exclusive OTUs. Bacteria in these wetlands exhibited divergent ecological functions during the dry and wet seasons. By disclosing the variation of water bacterial communities in different hydrologic periods and their relationship with environmental factors, this first-hand work in the Ramsar site of Nepal will develop a baseline dataset for the scientific community that will assist in understanding the wetland's microbial ecology and biogeography.}, }
@article {pmid37056166, year = {2023}, author = {Lindsay, RJ and Holder, PJ and Talbot, NJ and Gudelj, I}, title = {Metabolic efficiency reshapes the seminal relationship between pathogen growth rate and virulence.}, journal = {Ecology letters}, volume = {26}, number = {6}, pages = {896-907}, pmid = {37056166}, issn = {1461-0248}, support = {BB/T015985/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Virulence ; *Biological Evolution ; }, abstract = {A cornerstone of classical virulence evolution theories is the assumption that pathogen growth rate is positively correlated with virulence, the amount of damage pathogens inflict on their hosts. Such theories are key for incorporating evolutionary principles into sustainable disease management strategies. Yet, empirical evidence raises doubts over this central assumption underpinning classical theories, thus undermining their generality and predictive power. In this paper, we identify a key component missing from current theories which redefines the growth-virulence relationship in a way that is consistent with data. By modifying the activity of a single metabolic gene, we engineered strains of Magnaporthe oryzae with different nutrient acquisition and growth rates. We conducted in planta infection studies and uncovered an unexpected non-monotonic relationship between growth rate and virulence that is jointly shaped by how growth rate and metabolic efficiency interact. This novel mechanistic framework paves the way for a much-needed new suite of virulence evolution theories.}, }
@article {pmid37055390, year = {2023}, author = {Dudek, NK and Galaz-Montoya, JG and Shi, H and Mayer, M and Danita, C and Celis, AI and Viehboeck, T and Wu, GH and Behr, B and Bulgheresi, S and Huang, KC and Chiu, W and Relman, DA}, title = {Previously uncharacterized rectangular bacterial structures in the dolphin mouth.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2098}, pmid = {37055390}, issn = {2041-1723}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; P41 GM103832/GM/NIGMS NIH HHS/United States ; RM1 GM135102/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; *Neisseriaceae/genetics ; *Bottle-Nosed Dolphin ; Mouth ; Bacterial Structures ; }, abstract = {Much remains to be explored regarding the diversity of uncultured, host-associated microbes. Here, we describe rectangular bacterial structures (RBSs) in the mouths of bottlenose dolphins. DNA staining revealed multiple paired bands within RBSs, suggesting the presence of cells dividing along the longitudinal axis. Cryogenic transmission electron microscopy and tomography showed parallel membrane-bound segments that are likely cells, encapsulated by an S-layer-like periodic surface covering. RBSs displayed unusual pilus-like appendages with bundles of threads splayed at the tips. We present multiple lines of evidence, including genomic DNA sequencing of micromanipulated RBSs, 16S rRNA gene sequencing, and fluorescence in situ hybridization, suggesting that RBSs are bacterial and distinct from the genera Simonsiella and Conchiformibius (family Neisseriaceae), with which they share similar morphology and division patterning. Our findings highlight the diversity of novel microbial forms and lifestyles that await characterization using tools complementary to genomics such as microscopy.}, }
@article {pmid37049481, year = {2023}, author = {Pham, VT and Steinert, RE and Duysburgh, C and Ghyselinck, J and Marzorati, M and Dekker, PJT}, title = {In Vitro Effect of Enzymes and Human Milk Oligosaccharides on FODMAP Digestion and Fecal Microbiota Composition.}, journal = {Nutrients}, volume = {15}, number = {7}, pages = {}, pmid = {37049481}, issn = {2072-6643}, support = {Company funds//DSM/ ; }, mesh = {Humans ; *Irritable Bowel Syndrome ; Ecosystem ; Milk, Human ; Oligosaccharides ; Fatty Acids, Volatile ; *Gastrointestinal Microbiome ; Digestion ; }, abstract = {Fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) cause intestinal discomfort in patients with irritable bowel syndrome (IBS). An enzyme mix (2500 SU invertase, 2400 GalU α-galactosidase, 10,000 ALU β-galactosidase) optimized for FODMAP digestion, and/or human milk oligosaccharides (HMO) (2'-FL, DFL, and LNnT), were evaluated for effects on microbial community activity and composition in short-term colonic incubations using the fecal microbiota of four patients with IBS-D symptoms under the following test conditions: (i) FODMAP, (ii) pre-digested (with enzyme mix) FODMAP, (iii) FODMAP + HMO, and (iv) pre-digested FODMAP + HMO. Pre-digested FODMAP reduced short-chain fatty acid (SCFA) production versus FODMAP; HMO restored this. A 10-day experiment with the simulator of the human intestinal microbial ecosystem (SHIME[®]), using fecal samples from two patients with IBS-D, further evaluated these findings. FODMAP resulted in decreased microbial diversity versus blank. Pre-digestion with the enzyme mix restored microbial diversity, improved FODMAP digestibility, and reduced gas pressure versus undigested FODMAP; however, SCFA production decreased. HMO restored SCFA production along with an increase in gas pressure and increased abundance of Lachnospiraceae. When used in combination, the FODMAP enzyme mix and HMO may resolve FODMAP-related IBS symptoms while maintaining a healthy gut microbiome via prebiotic activity.}, }
@article {pmid37044393, year = {2022}, author = {Datta, R and Maity, P and Bhadury, P and Rizvi, AN and Raghunathan, C}, title = {An Updated Checklist of Free-living Marine Nematodes from Coastal India.}, journal = {Zootaxa}, volume = {5196}, number = {2}, pages = {151-196}, doi = {10.11646/zootaxa.5196.2.1}, pmid = {37044393}, issn = {1175-5334}, mesh = {Animals ; Chromadorea ; Ecosystem ; India ; *Nematoda ; Rhabditoidea ; Checklist ; Aquatic Organisms ; }, abstract = {The present study provides an updated species list of free-living marine nematodes reported from coastal India (Coasts and Islands) based on the thorough consultation of literature published from 1956 to 2022. This exercise resulted in a total of 617 valid species belonging to 266 genera, 48 families, 21 superfamilies and 9 orders. Class Chromadorea comprises 487 species represented by 205 genera, while class Enoplea includes 130 species belonging to 61 genera. The most common family was Xyalidae, with 76 species and the least common families having a single species each were represented by Aegialoalaimidae, Rhadinematidae, Aphanolaimidae, Rhabditidae, Pandolaimidae and Rhabdodemaniidae. The checklist provides a robust framework for the distribution and biogeography of free-living marine nematodes from the Indian waters and could be used to relate with marine ecosystems of other countries.}, }
@article {pmid37044259, year = {2023}, author = {Kim, HS and Keum, HL and Chung, IY and Nattkemper, L and Head, CR and Koh, A and Sul, WJ and Pastar, I and Yosipovitch, G}, title = {Characterization of a Perturbed Skin Microbiome in Prurigo Nodularis and Lichen Simplex Chronicus.}, journal = {The Journal of investigative dermatology}, volume = {143}, number = {10}, pages = {2082-2085.e5}, doi = {10.1016/j.jid.2023.03.1669}, pmid = {37044259}, issn = {1523-1747}, mesh = {Humans ; *Neurodermatitis/diagnosis ; *Prurigo/diagnosis ; Skin ; Diagnosis, Differential ; }, }
@article {pmid37042985, year = {2023}, author = {Zhang, Y and Xia, X and Wan, L and Han, BP and Liu, H and Jing, H}, title = {Microbial Communities Are Shaped by Different Ecological Processes in Subtropical Reservoirs of Different Trophic States.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2073-2085}, pmid = {37042985}, issn = {1432-184X}, mesh = {*Plankton ; *Microbiota ; Eukaryota ; Seasons ; }, abstract = {Understanding microbial community structure and the underlying control mechanisms are fundamental purposes of aquatic ecology. However, little is known about the seasonality and how trophic conditions regulate plankton community in subtropical reservoirs. In this study, we study the prokaryotic and picoeukaryotic communities and their interactions during wet and dry seasons in two subtropical reservoirs: one at oligotrophic state and another at mesotrophic state. Distinct microbial community compositions (prokaryotes and picoeukaryotes) and seasonal variation pattern were detected in the oligotrophic and mesotrophic reservoirs. The interactions between prokaryotic and picoeukaryotic communities were more prevalent in the oligotrophic reservoir, suggesting enhanced top-down control of small eukaryotic grazers on the prokaryotic communities. On the other hand, the microbial community in the mesotrophic reservoir was more influenced by physico-chemical parameters and showed a stronger seasonal variation, which may be the result of distinct nutrient levels in wet and dry seasons, indicating the importance of bottom-up control. Our study contributes to new understandings of the environmental and biological processes that shape the structure and dynamics of the planktonic microbial communities in reservoirs of different trophic states.}, }
@article {pmid37039841, year = {2023}, author = {Del Campo, EM and Gasulla, F and Hell, AF and González-Hourcade, M and Casano, LM}, title = {Comparative Transcriptomic and Proteomic Analyses Provide New Insights into the Tolerance to Cyclic Dehydration in a Lichen Phycobiont.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1725-1739}, pmid = {37039841}, issn = {1432-184X}, mesh = {*Transcriptome ; Dehydration ; *Lichens/physiology ; Proteome/metabolism ; Proteomics ; Desiccation ; }, abstract = {Desiccation tolerance (DT) is relatively frequent in non-vascular plants and green algae. However, it is poorly understood how successive dehydration/rehydration (D/R) cycles shape their transcriptomes and proteomes. Here, we report a comprehensive analysis of adjustments on both transcript and protein profiles in response to successive D/R cycles in Coccomyxa simplex (Csol), isolated from the lichen Solorina saccata. A total of 1833 transcripts and 2332 proteins were differentially abundant as a consequence of D/R; however, only 315 of these transcripts/proteins showed similar trends. Variations in both transcriptomes and proteomes along D/R cycles together with functional analyses revealed an extensive decrease in transcript and protein levels during dehydration, most of them involved in gene expression, metabolism, substance transport, signalling and folding catalysis, among other cellular functions. At the same time, a series of protective transcripts/proteins, such as those related to antioxidant defence, polyol metabolism and autophagy, was upregulated during dehydration. Overall, our results show a transient decrease in most cellular functions as a result of drying and a gradual reactivation of specific cell processes to accommodate the hydration status along successive D/R cycles. This study provides new insights into key mechanisms involved in the DT of Csol and probably other dehydration-tolerant microalgae. In addition, functionally characterising the high number of genes/proteins of unknown functions found in this study may lead to the discovery of new DT mechanisms.}, }
@article {pmid37037922, year = {2023}, author = {Lemke, M and DeSalle, R}, title = {The Role of Microbial Ecology in Restoration Ecology in the Age of Genomics: A Summary of the Microbial Ecology Special Issue.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {1136-1141}, pmid = {37037922}, issn = {1432-184X}, mesh = {*Ecology ; *Genomics ; }, }
@article {pmid37037808, year = {2023}, author = {Song, A and Su, J and Wang, H and Zhang, Z and Zhang, X and Van de Peer, Y and Chen, F and Fang, W and Guan, Z and Zhang, F and Wang, Z and Wang, L and Ding, B and Zhao, S and Ding, L and Liu, Y and Zhou, L and He, J and Jia, D and Zhang, J and Chen, C and Yu, Z and Sun, D and Jiang, J and Chen, S and Chen, F}, title = {Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2021}, pmid = {37037808}, issn = {2041-1723}, mesh = {*Chrysanthemum/genetics ; Phylogeny ; Plant Breeding ; Gene Expression Profiling ; Flowers/genetics ; Chromosomes ; }, abstract = {Chrysanthemum (Chrysanthemum morifolium Ramat.) is a globally important ornamental plant with great economic, cultural, and symbolic value. However, research on chrysanthemum is challenging due to its complex genetic background. Here, we report a near-complete assembly and annotation for C. morifolium comprising 27 pseudochromosomes (8.15 Gb; scaffold N50 of 303.69 Mb). Comparative and evolutionary analyses reveal a whole-genome triplication (WGT) event shared by Chrysanthemum species approximately 6 million years ago (Mya) and the possible lineage-specific polyploidization of C. morifolium approximately 3 Mya. Multilevel evidence suggests that C. morifolium is likely a segmental allopolyploid. Furthermore, a combination of genomics and transcriptomics approaches demonstrate the C. morifolium genome can be used to identify genes underlying key ornamental traits. Phylogenetic analysis of CmCCD4a traces the flower colour breeding history of cultivated chrysanthemum. Genomic resources generated from this study could help to accelerate chrysanthemum genetic improvement.}, }
@article {pmid37032887, year = {2023}, author = {Prendergast, DM and Slowey, R and Burgess, CM and Murphy, D and Johnston, D and Morris, D and O' Doherty, &#xc1; and Moriarty, J and Gutierrez, M}, title = {Characterization of cephalosporin and fluoroquinolone resistant Enterobacterales from Irish farm waste by whole genome sequencing.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1118264}, pmid = {37032887}, issn = {1664-302X}, abstract = {BACKGROUND: The Enterobacterales are a group of Gram-negative bacteria frequently exhibiting extended antimicrobial resistance (AMR) and involved in the transmission of resistance genes to other bacterial species present in the same environment. Due to their impact on human health and the paucity of new antibiotics, the World Health Organization (WHO) categorized carbapenem resistant and ESBL-producing as critical. Enterobacterales are ubiquitous and the role of the environment in the transmission of AMR organisms or antimicrobial resistance genes (ARGs) must be examined in tackling AMR in both humans and animals under the one health approach. Animal manure is recognized as an important source of AMR bacteria entering the environment, in which resistant genes can accumulate.<br><br>METHODS: To gain a better understanding of the dissemination of third generation cephalosporin and fluoroquinolone resistance genes between isolates in the environment, we applied whole genome sequencing (WGS) to Enterobacterales (79 E. coli, 1 Enterobacter cloacae, 1 Klebsiella pneumoniae, and 1 Citrobacter gillenii) isolated from farm effluents in Ireland before (n&#x2009;=&#x2009;72) and after (n&#x2009;=&#x2009;10) treatment by integrated constructed wetlands (ICWs). DNA was extracted using the MagNA Pure 96 system (Roche Diagnostics, Rotkreuz, Switzerland) followed by WGS on a MiSeq platform (Illumina, Eindhoven, Netherlands) using v3 chemistry as 300-cycle paired-end runs. AMR genes and point mutations were identified and compared to the phenotypic results for better understanding of the mechanisms of resistance and resistance transmission.<br><br>RESULTS: A wide variety of cephalosporin and fluoroquinolone resistance genes (mobile genetic elements (MGEs) and chromosomal mutations) were identified among isolates that mostly explained the phenotypic AMR patterns. A total of 31 plasmid replicon types were identified among the 82 isolates, with a subset of them (n&#x2009;=&#x2009;24), identified in E. coli isolates. Five plasmid replicons were confined to the Enterobacter cloacae isolate and two were confined to the Klebsiella pneumoniae isolate. Virulence genes associated with functions including stress, survival, regulation, iron uptake secretion systems, invasion, adherence and toxin production were identified.<br><br>CONCLUSION: Our study showed that antimicrobial resistant organisms (AROs) can persist even following wastewater treatment and could transmit AMR of clinical relevance to the environment and ultimately pose a risk to human or animal health.}, }
@article {pmid37030359, year = {2023}, author = {Yang, X and Duan, P and Hicks, L and Wang, K and Li, D}, title = {Mechanisms underlying the responses of microbial carbon and nitrogen use efficiencies to nitrogen addition are mediated by topography in a subtropical forest.}, journal = {The Science of the total environment}, volume = {880}, number = {}, pages = {163236}, doi = {10.1016/j.scitotenv.2023.163236}, pmid = {37030359}, issn = {1879-1026}, mesh = {*Nitrogen/analysis ; *Carbon ; Forests ; Biomass ; Soil/chemistry ; Phosphorus ; Soil Microbiology ; }, abstract = {Microbial carbon use efficiency (CUE) and nitrogen use efficiency (NUE) are key parameters determining the fate of C and N in soils. Atmospheric N deposition has been found to heavily impact multiple soil C and N transformations, but we lack understanding of the responses of CUE and NUE to N deposition, and it remains uncertain whether responses may be mediated by topography. Here, a N addition experiment with three treatment levels (0, 50 and 100 kg N ha[-1] yr[-1]) was conducted in the valley and on the slope of a subtropical karst forest. Nitrogen addition increased microbial CUE and NUE at both topographic positions, but the underlying mechanisms differed. In the valley, the increase in CUE was associated with an increase in soil fungal richness:biomass and lower litter C:N, whereas on the slope, the response was linked with a reduced ratio of dissolved soil organic C (DOC) to available phosphorus (AVP) which reduced respiration, and increased root N:P stoichiometry. In the valley, the increase in NUE was explained by stimulated microbial N growth relative to gross N mineralization, which was associated with increased ratios of soil total dissolved N:AVP and fungal richness:biomass. In contrast, on the slope, the increase in NUE was attributed to reduced gross N mineralization, linked to increased DOC:AVP. Overall, our results highlight how topography-driven soil substrate availability and microbial properties can regulate microbial CUE and NUE.}, }
@article {pmid37030231, year = {2023}, author = {Liu, H and Jiao, Q and Fan, L and Jiang, Y and Alyemeni, MN and Ahmad, P and Chen, Y and Zhu, M and Liu, H and Zhao, Y and Liu, F and Liu, S and Li, G}, title = {Integrated physio-biochemical and transcriptomic analysis revealed mechanism underlying of Si-mediated alleviation to cadmium toxicity in wheat.}, journal = {Journal of hazardous materials}, volume = {452}, number = {}, pages = {131366}, doi = {10.1016/j.jhazmat.2023.131366}, pmid = {37030231}, issn = {1873-3336}, mesh = {*Cadmium/toxicity/metabolism ; Silicon/pharmacology/chemistry ; Triticum/metabolism ; Transcriptome ; Antioxidants/metabolism ; *Soil Pollutants/toxicity/metabolism ; }, abstract = {Cadmium (Cd) contamination has resulted in serious reduction of crop yields. Silicon (Si), as a beneficial element, regulates plant growth to heavy metal toxicity mainly through reducing metal uptake and protecting plants from oxidative injury. However, the molecular mechanism underlying Si-mediated Cd toxicity in wheat has not been well understood. This study aimed to reveal the beneficial role of Si (1 mM) in alleviating Cd-induced toxicity in wheat (Triticum aestivum) seedlings. The results showed that exogenous supply of Si decreased Cd concentration by 67.45% (root) and 70.34% (shoot), and maintained ionic homeostasis through the function of important transporters, such as Lsi, ZIP, Nramp5 and HIPP. Si ameliorated Cd-induced photosynthetic performance inhibition through up-regulating photosynthesis-related genes and light harvesting-related genes. Si minimized Cd-induced oxidative stress by decreasing MDA contents by 46.62% (leaf) and 75.09% (root), and helped re-establish redox homeostasis by regulating antioxidant enzymes activities, AsA-GSH cycle and expression of relevant genes through signal transduction pathway. The results revealed molecular mechanism of Si-mediated wheat tolerance to Cd toxicity. Si fertilizer is suggested to be applied in Cd contaminated soil for food safety production as a beneficial and eco-friendly element.}, }
@article {pmid37026303, year = {2023}, author = {Pal, S and Vani, G and Donthineni, PR and Basu, S and Arunasri, K}, title = {Tear film microbiome in Sjogren's and non-Sjogren's aqueous deficiency dry eye.}, journal = {Indian journal of ophthalmology}, volume = {71}, number = {4}, pages = {1566-1573}, pmid = {37026303}, issn = {1998-3689}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Dry Eye Syndromes ; *Sjogren's Syndrome/diagnosis/complications ; Tears ; *Microbiota ; Bacteria/genetics ; }, abstract = {PURPOSE: To understand the bacterial microbiome changes associated with Sjogren's syndrome (SS) and non-Sjogren's syndrome (NSS) aqueous-deficient dry eyes compared to healthy eyes.<br><br>METHODS: Bacterial microbiome was generated from the deoxyribonucleic acid of tear film samples in healthy (n = 33), SS (n = 17), and NSS (n = 28) individuals. Sequencing of the V3-V4 region of the 16S rRNA gene was performed on the Illumina HiSeq2500 platform. Quantitative Insights Into Microbial Ecology (QIIME) pipeline was used to assign taxa to sequences. Statistical analysis was performed in R to assess the alpha diversity and beta diversity indices. Significant changes between the healthy, SS, and NSS cohorts were depicted by principal coordinate analysis (PCoA), differential abundance, and network analysis.<br><br>RESULTS: Tear microbiome was generated in healthy, SS, and NSS samples. Phyla Actinobacteria, Firmicutes, and Bacteroidetes showed significant changes in SS and NSS compared to healthy. Genera Lactobacillus and Bacillus were predominantly present in all samples. PCoA and heat map analysis showed distinct clusters for SS and NSS from the healthy cohort. Genera Prevotella, Coriobacteriaceae UCG-003, Enterococcus, Streptomyces, Rhodobacter, Ezakiella, and Microbacterium significantly increased in abundance in SS and NSS compared to a healthy cohort. Bacteria-bacteria interaction in SS, NSS, and healthy cohorts was predicted by CoNet network analysis. This analysis predicted a major hub of interaction for the pro-inflammatory bacterium Prevotella in the SS and NSS cohorts.<br><br>CONCLUSION: The results of the study indicate significant changes in the phyla and genera in SS and NSS compared to healthy. Both discriminative analysis and network analysis indicated a possible association of predominant pro-inflammatory bacteria with SS and NSS.}, }
@article {pmid37024470, year = {2023}, author = {Young, E and Melaugh, G and Allen, RJ}, title = {Active layer dynamics drives a transition to biofilm fingering.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {17}, pmid = {37024470}, issn = {2055-5008}, support = {682237/ERC_/European Research Council/International ; BB/R012415/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biofilms/growth &amp; development ; }, abstract = {The emergence of spatial organisation in biofilm growth is one of the most fundamental topics in biofilm biophysics and microbiology. It has long been known that growing biofilms can adopt smooth or rough interface morphologies, depending on the balance between nutrient supply and microbial growth; this 'fingering' transition has been linked with the average width of the 'active layer' of growing cells at the biofilm interface. Here we use long-time individual-based simulations of growing biofilms to investigate in detail the driving factors behind the biofilm-fingering transition. We show that the transition is associated with dynamical changes in the active layer. Fingering happens when gaps form in the active layer, which can cause local parts of the biofilm interface to pin, or become stationary relative to the moving front. Pinning can be transient or permanent, leading to different biofilm morphologies. By constructing a phase diagram for the transition, we show that the controlling factor is the magnitude of the relative fluctuations in the active layer thickness, rather than the active layer thickness per se. Taken together, our work suggests a central role for active layer dynamics in controlling the pinning of the biofilm interface and hence biofilm morphology.}, }
@article {pmid37024159, year = {2023}, author = {Vikram, S and Ramond, JB and Ortiz, M and Maggs-Kölling, G and Pelser, K and Cowan, DA}, title = {Soil fungal diversity and assembly along a xeric stress gradient in the central Namib Desert.}, journal = {Fungal biology}, volume = {127}, number = {4}, pages = {997-1003}, doi = {10.1016/j.funbio.2023.03.001}, pmid = {37024159}, issn = {1878-6146}, mesh = {*Soil/chemistry ; Bacteria ; Soil Microbiology ; Desert Climate ; *Ascomycota ; }, abstract = {The Namib Desert of south-western Africa is one of the oldest deserts in the world and possesses unique geographical, biological and climatic features. While research through the last decade has generated a comprehensive survey of the prokaryotic communities in Namib Desert soils, little is yet known about the diversity and function of edaphic fungal communities, and even less of their responses to aridity. In this study, we have characterized soil fungal community diversity across the longitudinal xeric gradient across the Namib desert (for convenience, divided into the western fog zone, the central low-rainfall zone and the eastern high-rainfall zone), using internal transcribed sequence (ITS) metabarcoding. Ascomycota, Basidiomycota and Chytridiomycota consistently dominated the Namib Desert edaphic fungal communities and a core mycobiome composed of only 15 taxa, dominated by members of the class Dothideomycetes (Ascomycota), was identified. However, fungal community structures were significantly different in the fog, low-rainfall and high-rainfall zones. Furthermore, Namib Desert gravel plain fungal community assembly was driven by both deterministic and stochastic processes; the latter dominating in the all three xeric zones. We also present data that suggest that the inland limit of fog penetration represents an ecological barrier to fungal dispersal across the Namib Desert.}, }
@article {pmid37020129, year = {2023}, author = {Berman, TS and Izraeli, Y and Lalzar, M and Mozes-Daube, N and Lepetit, D and Tabic, A and Varaldi, J and Zchori-Fein, E}, title = {RNA Viruses Are Prevalent and Active Tenants of the Predatory Mite Phytoseiulus persimilis (Acari: Phytoseiidae).}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2060-2072}, pmid = {37020129}, issn = {1432-184X}, support = {397/21//Israel Science Foundation/ ; }, mesh = {Humans ; Animals ; *Mites ; Pest Control, Biological ; *RNA Viruses/genetics ; Predatory Behavior ; *Tetranychidae ; }, abstract = {Many arthropod species harbor a diverse range of viruses. While much is known about pathogenic viruses of some economically important insects and arthropods involved in disease transmission, viruses associated with mites have rarely been studied. The main objective of this study was to characterize the virome of Phytoseiulus persimilis (Phytoseiidae), a predatory mite commercially used worldwide for the biological control of the key pest Tetranychus urticae (Tetranichidae). A combination of de novo transcriptome assembly and virion sequencing, revealed that RNA viruses are highly prevalent and active tenants of commercial populations of P. persimilis, comprising on average 9% of the mite's total mRNA. Seventeen RNA viruses dominated the mite's virome (i.e., were highly transcribed) with over half (n = 10) belonging to the order Picornavirales, + ssRNA viruses that infect a large range of hosts, including arthropods. Screening of the 17 dominant virus sequences in P. persimilis and T. urticae revealed that three viruses (two Picornavirales of the families Iflaviridae and Dicistroviridae, and one unclassified Riboviria) are unique to P. persimilis and three others (two unclassified Picornavirales and one unclassified Riboviria) are present in both mite species. Most of the sequences were related to viruses previously documented in economically important arthropods, while others have rarely been documented before in arthropods. These findings demonstrate that P. persimilis, like many other arthropods, harbors a diverse RNA virome, which might affect the mite's physiology and consequently its efficiency as a biological control agent.}, }
@article {pmid37017718, year = {2023}, author = {Thompson, CC and Tschoeke, D and Coutinho, FH and Leomil, L and Garcia, GD and Otsuki, K and Turcq, BJ and Moreira, LS and Turcq, PFM and Cordeiro, RC and Asp, NE and Thompson, FL}, title = {Diversity of Microbiomes Across a 13,000-Year-Old Amazon Sediment.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2202-2209}, pmid = {37017718}, issn = {1432-184X}, mesh = {*Microbiota/genetics ; Bacteria ; Metagenome ; Rivers/microbiology ; Lakes/microbiology ; Geologic Sediments/microbiology ; }, abstract = {The microbiome is fundamental for understanding bacterial activities in sediments. However, only a limited number of studies have addressed the microbial diversity of Amazonian sediments. Here, we studied the microbiome of sediments from a 13,000-year BP core retrieved in a floodplain lake in Amazonia using metagenomics and biogeochemistry. Our aim was to evaluate the possible environmental influence over a river to a lake transition using a core sample. To this end, we sampled a core in the Airo Lake, a floodplain lake in the Negro River basin. The Negro River is the largest tributary of the Amazon River. The obtained core was divided into three strata: (i) surface, almost complete separation of the Airo Lake from the Negro River when the environment becomes more lentic with greater deposition of organic matter (black-colored sediment); (ii) transitional environment (reddish brown); and (iii) deep, environment with a tendency for greater past influence of the Negro River (brown color). The deepest sample possibly had the greatest influence of the Negro River as it represented the bottom of this river in the past, while the surface sample is the current Airo Lake bottom. In total, six metagenomes were obtained from the three different depth strata (total number of reads: 10.560.701; sequence length: 538 ± 24, mean ± standard deviation). The older (deeper) sediment strata contained a higher abundance of Burkholderia, Chitinophaga, Mucilaginibacter, and Geobacter, which represented ~ 25% of the metagenomic sequences. On the other hand, the more recent sediment strata had mainly Thermococcus, Termophilum, Sulfolobus, Archaeoglobus, and Methanosarcina (in total 11% of the metagenomic sequences). The sequence data were binned into metagenome-assembled genomes (MAGs). The majority of the obtained MAGs (n = 16) corresponded to unknown taxa, suggesting they may belong to new species. The older strata sediment microbiome was enriched with sulfur cycle genes, TCA cycle, YgfZ, and ATP-dependent proteolysis in bacteria. Meanwhile, serine-glyoxylate cycle, stress response genes, bacterial cell division, cell division-ribosomal stress protein cluster, and oxidative stress increased in the younger strata. Metal resistance and antimicrobial resistance genes were found across the entire core, including genes coding for fluoroquinolones, polymyxin, vancomycin, and multidrug resistance transporters. These findings depict the possible microbial diversity during the depositional past events and provided clues of the past microbial metabolism throughout time.}, }
@article {pmid37010970, year = {2023}, author = {May, AK}, title = {Host Microbiome Threats in the Intensive Care Unit.}, journal = {Surgical infections}, volume = {24}, number = {3}, pages = {276-283}, doi = {10.1089/sur.2023.029}, pmid = {37010970}, issn = {1557-8674}, mesh = {Humans ; *Microbiota ; Anti-Bacterial Agents/therapeutic use ; Intensive Care Units ; Dysbiosis/therapy ; }, abstract = {Human microbiota demonstrate diversity and balance that is adaptive for the host and supports maintaining homeostasis. Although acute illness or injury may derange microbiota diversity and the proportion of potentially pathogenic microbes, that derangement may be further exacerbated by commonly deployed intensive care unit (ICU) therapeutic and practices. These include antibiotic administration, delayed luminal nutrition, acid suppression, and vasopressor infusion. Furthermore, the local ICU microbial ecology, regardless of disinfection practices, shapes the patient's microbiota, especially with the acquisition of multi-drug-resistant pathogens. Current approaches to protect a normal microbiome, or restore a deranged one, are part of a multifaceted approach that may include antibiotic stewardship and infection control practices as microbiome-directed therapeutics emerge.}, }
@article {pmid37010558, year = {2023}, author = {Khatri, S and Chaudhary, P and Shivay, YS and Sharma, S}, title = {Role of Fungi in Imparting General Disease Suppressiveness in Soil from Organic Field.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2047-2059}, pmid = {37010558}, issn = {1432-184X}, support = {fellowship//University Grants Commission/ ; fellowship//University of Queensland - Indian Institute of Technology Delhi Academy of Research/ ; MI02024//IITD-ICAR/ ; MI02535//IITD-TUD/ ; }, mesh = {*Soil ; *Fungi/genetics ; Bacteria ; Agriculture/methods ; Organic Agriculture/methods ; Soil Microbiology ; }, abstract = {Soil microbial communities are key players responsible for imparting suppressive potential to the soil against soil-borne phytopathogens. Fungi have an immense potential to inhibit soil-borne phytopathogens, but the fungal counterpart has been less explored in this context. We assessed the composition of fungal communities in soil under long-term organic and conventional farming practice, and control soil. The disease-suppressive potential of organic field was already established. A comparative analysis of the disease suppressiveness contributed by the fungal component of soil from conventional and organic farms was assessed using dual culture assays. The quantification of biocontrol markers and total fungi was done; the characterization of fungal community was carried out using ITS-based amplicon sequencing. Soil from organic field exhibited higher disease-suppressive potential than that from conventional farming, against the pathogens selected for the study. Higher levels of hydrolytic enzymes such as chitinase and cellulase, and siderophore production were observed in soil from the organic field compared to the conventional field. Differences in community composition were observed under conventional and organic farming, with soil from organic field exhibiting specific enrichment of key biocontrol fungal genera. The fungal alpha diversity was lower in soil from the organic field compared to the conventional field. Our results highlight the role of fungi in contributing to general disease-suppressive ability of the soil against phytopathogens. The identification of fungal taxa specifically associated with organic farming can aid in understanding the mechanism of disease suppression under such a practice, and can be exploited to induce general disease suppressiveness in otherwise conducive soil.}, }
@article {pmid37010433, year = {2023}, author = {Fortuna, KJ and Holtappels, D and Venneman, J and Baeyen, S and Vallino, M and Verwilt, P and Rediers, H and De Coninck, B and Maes, M and Van Vaerenbergh, J and Lavigne, R and Wagemans, J}, title = {Back to the Roots: Agrobacterium-Specific Phages Show Potential to Disinfect Nutrient Solution from Hydroponic Greenhouses.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {4}, pages = {e0021523}, pmid = {37010433}, issn = {1098-5336}, mesh = {*Bacteriophages/genetics ; Agrobacterium ; Hydroponics ; Hydrogen Peroxide/pharmacology ; Mutation ; }, abstract = {Agrobacterium biovar 1 is a soilborne plant pathogen with the ability to colonize the irrigation system of greenhouses, causing hairy root disease (HRD). Currently, management focuses on using hydrogen peroxide to disinfect the nutrient solution, but due to the emergence of resistant strains, its efficacy and sustainability are questioned. Using a relevant collection of pathogenic Agrobacterium biovar 1 strains, OLIVR1 to 6, six phages specific to this pathogen and belonging to three different genera were isolated from Agrobacterium biovar 1-infected greenhouses. All phages were named OLIVR, referring to their location of isolation, Onze-Lieve-Vrouwe-Waver, and were characterized by whole-genome analysis, confirming their strictly lytic lifestyle. They remained stable under greenhouse-relevant conditions. To assess the efficacy of the phages, their ability to disinfect greenhouse nutrient solution inoculated with agrobacteria was tested. Each of the phages infected their host, but their ability to decrease the bacterial concentration differed. For instance, OLIVR1 reduced the bacterial concentration with 4 log units without phage resistance emerging. While OLIVR4 and OLIVR5 were also infectious in nutrient solution, they did not always decrease the bacterial load below the limit of detection, and phage resistance emerged. Finally, the mutations causing phage resistance by receptor modification were identified. For OLIVR4-resistant Agrobacterium isolates, but not for OLIVR5-resistant isolates, motility decreased. Together, these data show the potential of some of these phages as disinfectant of nutrient solution, and they might be a valuable tool to tackle HRD. IMPORTANCE Hairy root disease, caused by rhizogenic Agrobacterium biovar 1 is a rapidly emerging bacterial disease worldwide. It affects tomatoes, cucumbers, eggplant, and bell pepper, causing high yield losses in hydroponic greenhouses. Recent findings suggest that the current management practices, mainly focusing on UV-C and hydrogen peroxide to disinfect contaminated water, have a questionable efficacy. Hence, we investigate the potential of phages as a biological means of preventing this disease. Using a diverse collection of Agrobacterium biovar 1, we isolated three different phage species that together infect 75% of the collection. Since these phages are strictly lytic, while remaining both stable and infectious under greenhouse-relevant conditions, they might be suitable candidates for biological control.}, }
@article {pmid37009161, year = {2023}, author = {Cummings, S and Ardor Bellucci, LM and Seabrook, S and Raineault, NA and McPhail, KL and Thurber, AR}, title = {Variations and gradients between methane seep and off-seep microbial communities in a submarine canyon system in the Northeast Pacific.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15119}, pmid = {37009161}, issn = {2167-8359}, mesh = {*Seawater ; Methane/chemistry ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; *Microbiota/genetics ; }, abstract = {Methane seeps are highly abundant marine habitats that contribute sources of chemosynthetic primary production to marine ecosystems. Seeps also factor into the global budget of methane, a potent greenhouse gas. Because of these factors, methane seeps influence not only local ocean ecology, but also biogeochemical cycles on a greater scale. Methane seeps host specialized microbial communities that vary significantly based on geography, seep gross morphology, biogeochemistry, and a diversity of other ecological factors including cross-domain species interactions. In this study, we collected sediment cores from six seep and non-seep locations from Grays and Quinault Canyons (46-47°N) off Washington State, USA, as well as one non-seep site off the coast of Oregon, USA (45°N) to quantify the scale of seep influence on biodiversity within marine habitats. These samples were profiled using 16S rRNA gene sequencing. Predicted gene functions were generated using the program PICRUSt2, and the community composition and predicted functions were compared among samples. The microbial communities at seeps varied by seep morphology and habitat, whereas the microbial communities at non-seep sites varied by water depth. Microbial community composition and predicted gene function clearly transitioned from on-seep to off-seep in samples collected from transects moving away from seeps, with a clear ecotone and high diversity where methane-fueled habitats transition into the non-seep deep sea. Our work demonstrates the microbial and metabolic sphere of influence that extends outwards from methane seep habitats.}, }
@article {pmid37008301, year = {2022}, author = {Deyaert, S and Moens, F and Pirovano, W and van den Bogert, B and Klaassens, ES and Marzorati, M and Van de Wiele, T and Kleerebezem, M and Van den Abbeele, P}, title = {Development of a reproducible small intestinal microbiota model and its integration into the SHIME[®]-system, a dynamic in vitro gut model.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1054061}, pmid = {37008301}, issn = {1664-302X}, abstract = {The human gastrointestinal tract consists of different regions, each characterized by a distinct physiology, anatomy, and microbial community. While the colonic microbiota has received a lot of attention in recent research projects, little is known about the small intestinal microbiota and its interactions with ingested compounds, primarily due to the inaccessibility of this region in vivo. This study therefore aimed to develop and validate a dynamic, long-term simulation of the ileal microbiota using the SHIME[®]-technology. Essential parameters were identified and optimized from a screening experiment testing different inoculation strategies, nutritional media, and environmental parameters over an 18-day period. Subjecting a synthetic bacterial consortium to the selected conditions resulted in a stable microbiota that was representative in terms of abundance [8.81 ± 0.12 log (cells/ml)], composition and function. Indeed, the observed community mainly consisted of the genera Streptococcus, Veillonella, Enterococcus, Lactobacillus, and Clostridium (qPCR and 16S rRNA gene targeted Illumina sequencing), while nutrient administration boosted lactate production followed by cross-feeding interactions towards acetate and propionate. Furthermore, similarly as in vivo, bile salts were only partially deconjugated and only marginally converted into secondary bile salts. After confirming reproducibility of the small intestinal microbiota model, it was integrated into the established M-SHIME® where it further increased the compositional relevance of the colonic community. This long-term in vitro model provides a representative simulation of the ileal bacterial community, facilitating research of the ileum microbiota dynamics and activity when, for example, supplemented with microbial or diet components. Furthermore, integration of this present in vitro simulation increases the biological relevance of the current M-SHIME® technology.}, }
@article {pmid37002423, year = {2023}, author = {Pushpakumara, BLDU and Tandon, K and Willis, A and Verbruggen, H}, title = {The Bacterial Microbiome of the Coral Skeleton Algal Symbiont Ostreobium Shows Preferential Associations and Signatures of Phylosymbiosis.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2032-2046}, pmid = {37002423}, issn = {1432-184X}, support = {DP200101613//Australian Research Council grant/ ; }, mesh = {Animals ; *Anthozoa/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Chlorophyta ; *Microbiota ; Coral Reefs ; }, abstract = {Ostreobium, the major algal symbiont of the coral skeleton, remains understudied despite extensive research on the coral holobiont. The enclosed nature of the coral skeleton might reduce the dispersal and exposure of residing bacteria to the outside environment, allowing stronger associations with the algae. Here, we describe the bacterial communities associated with cultured strains of 5 Ostreobium clades using 16S rRNA sequencing. We shed light on their likely physical associations by comparative analysis of three datasets generated to capture (1) all algae associated bacteria, (2) enriched tightly attached and potential intracellular bacteria, and (3) bacteria in spent media. Our data showed that while some bacteria may be loosely attached, some tend to be tightly attached or potentially intracellular. Although colonised with diverse bacteria, Ostreobium preferentially associated with 34 bacterial taxa revealing a core microbiome. These bacteria include known nitrogen cyclers, polysaccharide degraders, sulphate reducers, antimicrobial compound producers, methylotrophs, and vitamin B12 producers. By analysing co-occurrence networks of 16S rRNA datasets from Porites lutea and Paragoniastrea australensis skeleton samples, we show that the Ostreobium-bacterial associations present in the cultures are likely to also occur in their natural environment. Finally, our data show significant congruence between the Ostreobium phylogeny and the community composition of its tightly associated microbiome, largely due to the phylosymbiotic signal originating from the core bacterial taxa. This study offers insight into the Ostreobium microbiome and reveals preferential associations that warrant further testing from functional and evolutionary perspectives.}, }
@article {pmid37001600, year = {2023}, author = {Gilles, S and Meinzer, M and Landgraf, M and Kolek, F and von Bargen, S and Pack, K and Charalampopoulos, A and Ranpal, S and Luschkova, D and Traidl-Hoffmann, C and Jochner-Oette, S and Damialis, A and Büttner, C}, title = {Betula pendula trees infected by birch idaeovirus and cherry leaf roll virus: Impacts of urbanisation and NO2 levels.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {327}, number = {}, pages = {121526}, doi = {10.1016/j.envpol.2023.121526}, pmid = {37001600}, issn = {1873-6424}, mesh = {Humans ; *Trees ; Betula ; *Nepovirus ; Urbanization ; Nitrogen Dioxide ; Plants ; }, abstract = {Viruses are frequently a microbial biocontaminant of healthy plants. The occurrence of the infection can be also due to environmental stress, like urbanisation, air pollution and increased air temperature, especially under the ongoing climate change. The aim of the present study was to investigate the hypothesis that worsened air quality and fewer green areas may favour the higher frequency of common viral infections, particularly in a common tree in temperate and continental climates, Betula pendula ROTH. We examined 18 trees, during the years 2015-2017, the same always for each year, in the region of Augsburg, Germany. By specific PCR, the frequency of two viruses, Cherry leaf roll virus (CLRV, genus Nepovirus, family Secoviridae), which is frequent in birch trees, and a novel virus tentatively named birch idaeovirus (BIV), which has been only recently described, were determined in pollen samples. The occurrence of the viruses was examined against the variables of urban index, air pollution (O3 and NO2), air temperature, and tree morphometrics (trunk perimeter, tree height, crown height and diameter). Generalized Non-linear models (binomial logit with backward stepwise removal of independent variables) were employed. During the study period, both CLRV and BIV were distributed widely throughout the investigated birch individuals. CLRV seemed to be rather cosmopolitan and was present independent of any abiotic factor. BIV's occurrence was mostly determined by higher values of the urban index and of NO2. Urban birch trees, located next to high-traffic roads with higher NO2 levels, are more likely to be infected by BIV. Increased environmental stress may lead to more plant viral infections. Here we suggest that this is particularly true for urban spaces, near high-traffic roads, where plants may be more stressed, and we recommend taking mitigation measures for controlling negative human interventions.}, }
@article {pmid37001406, year = {2023}, author = {Vaezzadeh, V and Yi, X and Rais, FR and Bong, CW and Thomes, MW and Lee, CW and Zakaria, MP and Wang, AJ and Zhong, G and Zhang, G}, title = {Corrigendum to "Distribution of black carbon and PAHs in sediments of Peninsular Malaysia" [Mar. Pollut. Bull.172 (2021) 112871].}, journal = {Marine pollution bulletin}, volume = {190}, number = {}, pages = {114797}, doi = {10.1016/j.marpolbul.2023.114797}, pmid = {37001406}, issn = {1879-3363}, }
@article {pmid37001405, year = {2023}, author = {Kundu, K and Van Landuyt, J and Mattelin, V and Martin, B and Neyts, M and Parmentier, K and Boon, N}, title = {Enhanced removal of warfare agent tri-nitro-toluene by a Methylophaga-dominated microbiome.}, journal = {Marine pollution bulletin}, volume = {190}, number = {}, pages = {114866}, doi = {10.1016/j.marpolbul.2023.114866}, pmid = {37001405}, issn = {1879-3363}, mesh = {*Methanol/metabolism ; *Trinitrotoluene/metabolism ; Bacteria/metabolism ; North Sea ; }, abstract = {Historical exposure of the marine environment to 2,4,6-trinitrotoluene (TNT) happened due to the dumping of left-over munitions. Despite significant research on TNT decontamination, the potential of marine microbiome for TNT degradation remains only little explored. In this study, TNT degradation experiments were conducted with sediment located near the World War I munition dumpsite - Paardenmarkt in the Belgian part of North Sea. A slow removal was observed using TNT as sole source of C and N, which could be enhanced by adding methanol. Degradation was reflected in nitro-reduced metabolites and microbial growth. 16S Illumina sequencing analysis revealed several enriched genera that used TNT as a sole source of C and N - Colwellia, Thalossospira, and Methylophaga. Addition of methanol resulted in increased abundance of Methylophaga, which corresponded to the rapid removal of TNT. Methanol enhanced the degradation by providing additional energy and establishing syntrophic association between methanol-utilizing and TNT-utilizing bacteria.}, }
@article {pmid37000232, year = {2023}, author = {Stupar, M and Savković, &#x17d; and Popović, S and Simić, GS and Grbić, ML}, title = {Speleomycology of Air in Stopića Cave (Serbia).}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2021-2031}, pmid = {37000232}, issn = {1432-184X}, mesh = {Animals ; Humans ; *Fungi ; Caves/microbiology ; Serbia ; Pandemics ; *COVID-19 ; Seasons ; Air Microbiology ; Environmental Monitoring/methods ; }, abstract = {Fungi can colonize organic matter present in subterranean sites and have a significant role as dwellers in different microniches of cave habitats. In order to analyze the content of airborne fungal propagules in different parts of "Stopića Cave," a touristic site in Serbia, air sampling was carried out in three seasons during 2020, prior to and during the onset of COVID-19 pandemic. Culturable mycobiota was identified using both microscopic techniques and ITS region/BenA gene barcoding, while multivariate analyses were employed to establish the link between fungal taxa and different environmental factors. The maximal measured fungal propagule concentrations were recorded during spring sampling which were based on fungal propagule concentration categories; the cave environment matches the category V. A total of 29 fungal isolates were identified, while Aspergillus, Cladosporium, Fusarium, Lecanicillium, Mucor, and Penicillium were the most diverse genera. According to the trophic mode, most of the isolated fungal species were pathotrophs (75.86%), but when regarding ecological guilds, the most dominant were undefined saprobes and animal pathogens (41.38% for each). Show caves are especially vulnerable to human impacts, and the fungal propagules' concentration within the caves could be good indices for the level of ecological disturbance.}, }
@article {pmid37000231, year = {2023}, author = {Kurm, V and Visser, J and Schilder, M and Nijhuis, E and Postma, J and Korthals, G}, title = {Soil Suppressiveness Against Pythium ultimum and Rhizoctonia solani in Two Land Management Systems and Eleven Soil Health Treatments.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1709-1724}, pmid = {37000231}, issn = {1432-184X}, support = {KB-33-006//Ministerie van Landbouw, Natuur en Voedselkwaliteit/ ; LWV20042/BO-56-001-061//Ministerie van Landbouw, Natuur en Voedselkwaliteit/ ; }, mesh = {*Soil ; *Pythium ; Conservation of Natural Resources ; Soil Microbiology ; Rhizoctonia ; Plant Diseases/prevention &amp; control/microbiology ; }, abstract = {The soil microbiome is known to be crucial for the control of soil-borne plant diseases. However, there is still little knowledge on how to modify the soil microbiome to induce or increase disease suppressiveness. In the present study, we applied eleven soil health treatments combined with conventional and organic agricultural management in a long-term field experiment. Suppressiveness against Pythium ultimum and Rhizoctonia solani was assessed in bioassays for 2 years. In addition, the microbiome community composition and microbial abundance were determined. We found that while several treatments changed the microbial community composition compared to the control, only a combination treatment of anaerobic soil disinfestation, hair meal, and compost addition resulted in suppressiveness against P. ultimum. Pythium suppressiveness is likely to have been caused by an increased microbial abundance and activity. Moreover, the increased abundance of several bacterial taxa, such as Pseudomonas sp., Chryseobacterium sp., members of the family Chitinophagaceae, and the fungal genus Mortierella sp. and family Trichosporonaceae, was measured. There was no overall difference in suppressiveness between conventional and organic land management. Also, no suppressiveness against R. solani could be detected. Our results indicate that a treatment combining the reduction of microorganisms followed by a recovery phase with high amounts of organic amendments may be more effective in inducing suppressiveness than treatments consisting of only one of these measures.}, }
@article {pmid37000121, year = {2023}, author = {Lopes, LD and Futrell, SL and Wright, EE and Danalatos, GJ and Castellano, MJ and Vyn, TJ and Archontoulis, SV and Schachtman, DP}, title = {Soil depth and geographic distance modulate bacterial β-diversity in deep soil profiles throughout the U.S. Corn Belt.}, journal = {Molecular ecology}, volume = {32}, number = {13}, pages = {3718-3732}, doi = {10.1111/mec.16945}, pmid = {37000121}, issn = {1365-294X}, mesh = {*Soil ; *Zea mays/genetics ; Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; }, abstract = {Understanding how microbial communities are shaped across spatial dimensions is of fundamental importance in microbial ecology. However, most studies on soil biogeography have focused on the topsoil microbiome, while the factors driving the subsoil microbiome distribution are largely unknown. Here we used 16S rRNA amplicon sequencing to analyse the factors underlying the bacterial β-diversity along vertical (0-240 cm of soil depth) and horizontal spatial dimensions (~500,000 km[2]) in the U.S. Corn Belt. With these data we tested whether the horizontal or vertical spatial variation had stronger impacts on the taxonomic (Bray-Curtis) and phylogenetic (weighted Unifrac) β-diversity. Additionally, we assessed whether the distance-decay (horizontal dimension) was greater in the topsoil (0-30 cm) or subsoil (in each 30 cm layer from 30-240 cm) using Mantel tests. The influence of geographic distance versus edaphic variables on the bacterial communities from the different soil layers was also compared. Results indicated that the phylogenetic β-diversity was impacted more by soil depth, while the taxonomic β-diversity changed more between geographic locations. The distance-decay was lower in the topsoil than in all subsoil layers analysed. Moreover, some subsoil layers were influenced more by geographic distance than any edaphic variable, including pH. Although different factors affected the topsoil and subsoil biogeography, niche-based models explained the community assembly of all soil layers. This comprehensive study contributed to elucidating important aspects of soil bacterial biogeography including the major impact of soil depth on the phylogenetic β-diversity, and the greater influence of geographic distance on subsoil than on topsoil bacterial communities in agroecosystems.}, }
@article {pmid36999338, year = {2023}, author = {Garbeva, P and Avalos, M and Ulanova, D and van Wezel, GP and Dickschat, JS}, title = {Volatile sensation: The chemical ecology of the earthy odorant geosmin.}, journal = {Environmental microbiology}, volume = {25}, number = {9}, pages = {1565-1574}, doi = {10.1111/1462-2920.16381}, pmid = {36999338}, issn = {1462-2920}, mesh = {*Odorants/analysis ; *Bacteria/genetics/metabolism ; Naphthols/chemistry/metabolism ; Sensation ; }, abstract = {Geosmin may be the most familiar volatile compound, as it lends the earthy smell to soil. The compound is a member of the largest family of natural products, the terpenoids. The broad distribution of geosmin among bacteria in both terrestrial and aquatic environments suggests that this compound has an important ecological function, for example, as a signal (attractant or repellent) or as a protective specialized metabolite against biotic and abiotic stresses. While geosmin is part of our everyday life, scientists still do not understand the exact biological function of this omnipresent natural product. This minireview summarizes the current general observations regarding geosmin in prokaryotes and introduces new insights into its biosynthesis and regulation, as well as its biological roles in terrestrial and aquatic environments.}, }
@article {pmid36998391, year = {2023}, author = {Rajala, P and Bomberg, M}, title = {Editorial: Geomicrobes: Life in terrestrial deep subsurface, volume II.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1169127}, pmid = {36998391}, issn = {1664-302X}, }
@article {pmid36996916, year = {2023}, author = {Hidalgo, J and Epelde, L and Anza, M and Becerril, JM and Garbisu, C}, title = {Mycoremediation with Agaricus bisporus and Pleurotus ostreatus growth substrates versus phytoremediation with Festuca rubra and Brassica sp. for the recovery of a Pb and γ-HCH contaminated soil.}, journal = {Chemosphere}, volume = {327}, number = {}, pages = {138538}, doi = {10.1016/j.chemosphere.2023.138538}, pmid = {36996916}, issn = {1879-1298}, mesh = {*Pleurotus ; Soil ; Hexachlorocyclohexane ; *Festuca ; Lead ; Biodegradation, Environmental ; *Brassica ; *Agaricus ; }, abstract = {Mycoremediation with mushroom growth substrates can be used for the recovery of mixed contaminated soils due to the benefits derived from the physicochemical characteristics of the substrates, the activity of extracellular enzymes secreted by the fungi, and the presence of the fungal mycelia. The objective of this work was to assess the potential of Agaricus bisporus and Pleurotus ostreatus growth substrates (inoculated mushroom substrates vs. spent mushroom substrates) for the mycoremediation of soils co-contaminated with lead and lindane (γ-HCH). We compared the efficiency of these mycoremediation strategies with the phytoremediation with Brassica spp. Or Festuca rubra plants, in terms of both reduction in contaminant levels and enhancement of soil health. An enhanced soil health was achieved as a result of the application of mycoremediation treatments, compared to phytoremediation and control (untreated) treatments. The application of P. ostreatus inoculated substrate led to the most significant reduction in γ-HCH concentration (up to 88.9% compared to corresponding controls). In the presence of inoculated mushroom substrate, P. ostreatus fruiting bodies extracted more Pb than Brassica spp. Or F. rubra plants. Mycoremediation with P. ostreatus growth substrates appears a promising strategy for the recovery of the health of soils co-contaminated with Pb and γ-HCH.}, }
@article {pmid36991472, year = {2023}, author = {Wang, Y and Jiménez, DJ and Zhang, Z and van Elsas, JD}, title = {Functioning of a tripartite lignocellulolytic microbial consortium cultivated under two shaking conditions: a metatranscriptomic study.}, journal = {Biotechnology for biofuels and bioproducts}, volume = {16}, number = {1}, pages = {54}, pmid = {36991472}, issn = {2731-3654}, abstract = {BACKGROUND: In a previous study, shaking speed was found to be an important factor affecting the population dynamics and lignocellulose-degrading activities of a synthetic lignocellulolytic microbial consortium composed of the bacteria Sphingobacterium paramultivorum w15, Citrobacter freundii so4, and the fungus Coniochaeta sp. 2T2.1. Here, the gene expression profiles of each strain in this consortium were examined after growth at two shaking speeds (180 and 60 rpm) at three time points (1, 5 and 13 days).<br><br>RESULTS: The results indicated that, at 60&#xa0;rpm, C. freundii so4 switched, to a large extent, from aerobic to flexible&#xa0;(aerobic/microaerophilic/anaerobic) metabolism, resulting in continued slow growth till late stage. In addition, Coniochaeta sp. 2T2.1 tended to occur to a larger extent in the hyphal form, with genes encoding adhesion proteins being highly expressed. Much like at 180&#xa0;rpm, at 60&#xa0;rpm, S. paramultivorum w15 and Coniochaeta sp. 2T2.1 were key players in hemicellulose degradation processes, as evidenced from the respective CAZy-specific transcripts. Coniochaeta sp. 2T2.1 exhibited expression of genes encoding arabinoxylan-degrading enzymes (i.e., of CAZy groups GH10, GH11, CE1, CE5 and GH43), whereas, at 180&#xa0;rpm, some of these genes were suppressed at early stages of growth. Moreover, C. freundii so4 stably expressed genes that were predicted to encode proteins with (1) &#x3b2;-xylosidase/&#x3b2;-glucosidase and (2) peptidoglycan/chitinase activities, (3) stress response- and detoxification-related proteins. Finally, S. paramultivorum w15 showed involvement in vitamin B2 generation in the early stages across the two shaking speeds, while this role was taken over by C. freundii so4 at late stage at 60&#xa0;rpm.<br><br>CONCLUSIONS: We provide evidence that S. paramultivorum w15 is involved in the degradation of mainly hemicellulose and in vitamin B2 production, and C. freundii so4 in the degradation of oligosaccharides or sugar dimers, next to detoxification processes. Coniochaeta sp. 2T2.1 was held to be strongly involved in cellulose and xylan (at early stages), next to lignin modification processes (at later stages). The synergism and alternative functional roles presented in this study enhance the eco-enzymological understanding of the degradation of lignocellulose in this tripartite microbial consortium.}, }
@article {pmid36989794, year = {2023}, author = {Goswami, V and Deepika, S and Chandra, R and Babu, CR and Kothamasi, D}, title = {Arbuscular mycorrhizas accelerate the degradation of colour containing organic pollutants present in distillery spent wash leachates.}, journal = {Journal of hazardous materials}, volume = {452}, number = {}, pages = {131291}, doi = {10.1016/j.jhazmat.2023.131291}, pmid = {36989794}, issn = {1873-3336}, mesh = {*Mycorrhizae ; *Environmental Pollutants ; Color ; Oxides ; Esters ; }, abstract = {Distillery spent wash (DSW) from molasses-based distilleries is being used as a low-cost alternative to chemical fertilizers in countries like India and Brazil. However, using DSW as a fertilizer substitute causes organic pollutant leaching, including melanoidins and caramel colourants that turn bodies of water dark brown. This study investigated the arbuscular mycorrhiza (AM) mediated degradation of organic pollutants in DSW. Mycorrhizal and non-mycorrhizal Sorghum bicolor were grown in microcosms for 16 weeks. The plants were fertilized with either raw DSW or Hoagland solution. Leachates draining from the microcosms after fertilization were collected three times in 30-day intervals. Each 30-day collection was preceded by two fertilizations. A gas chromatography-mass spectrometry comparative analyses of raw DSW with leachates of the third collection from mycorrhizal and non-mycorrhizal microcosms was made. Sixty-five and 42 complex organic compounds were detected in raw DSW and leachate collected from the non-mycorrhizal pots respectively. Only 26 compounds were detected in leachate collected from mycorrhizal pots. Absent from leachate of the mycorrhizal pots were: colour-containing organic compounds diacetone alcohol; 3-amino-2-cyano-6-methyl-6,7-dihydrothieno[2,3-b]pyrazine S-oxide; cyclohexane; 1,2-benzenedicarboxylic acid, butyl 8-methylnonyl ester; 2-pyrrolidinone; and acetic acid, dodecyl ester present in raw DSW. The results indicate that AM fungi can degrade organic pollutants in DSW.}, }
@article {pmid36988842, year = {2023}, author = {Messaoudi, Y and Smichi, N and Allaf, T and Besombes, C and Allaf, K and Gargouri, M}, title = {Instant Controlled Pressure-Drop (DIC) for Volatile Compound Extraction and Bioethanol Production from Empty Aleppo Pinecones and Eucalyptus Chips: Process Optimization and Statistical Modeling.}, journal = {Applied biochemistry and biotechnology}, volume = {195}, number = {11}, pages = {7086-7109}, pmid = {36988842}, issn = {1559-0291}, mesh = {*Eucalyptus ; *Oils, Volatile/chemistry ; Fermentation ; }, abstract = {Several plant species contain volatile compounds extracted as "essential oils" through different technologies. After essential oil extraction, the residual solid is a lignocellulosic solid waste. This work proposes the instant controlled pressure-drop (DIC) technology to autovaporize volatile compounds and modify the lignocellulosic matrix. Indeed, DIC technology is a thermomechanical process based on short-time/high-temperature and pressure pretreatment. It enhances the saccharification and fermentation process (SSF) for bioethanol production. A 3-variable design of experiments optimized the DIC processing parameters to reach 100% efficiency (EE) of volatile compound extraction using response surface methodology (RSM). Eucalyptus chips presented 50 volatile identified compounds after 7 min of DIC treatment. 1,8-Cineole, β-phellandrene, aromadendrene, eudesmol, and spathulenol are the most important volatile compounds. The empty Aleppo pinecones delivered 32 volatile compounds in 5 min of DIC treatment, the most important of which were caryophyllene, nortricyclene, verbenol, and camphor. After the autovaporization extraction stage, solid fraction residues were hydrolyzed and fermented in the same stirred bioreactor, using SSF strategy for 72 h at 37 °C. The highest bioethanol yields reached 73.9% and 54.82% (g per 100 g DM) from eucalyptus chip and empty Aleppo pinecone, respectively.}, }
@article {pmid36987547, year = {2023}, author = {Coats, ER and Appel, FJ and Guho, N and Brinkman, CK and Mellin, J}, title = {Interrogating the performance and microbial ecology of an enhanced biological phosphorus removal/post-anoxic denitrification process at bench and pilot scales.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {95}, number = {4}, pages = {e10852}, doi = {10.1002/wer.10852}, pmid = {36987547}, issn = {1554-7531}, support = {2018-67022-27894//National Institute of Food and Agriculture/ ; IDA01720//National Institute of Food and Agriculture/ ; IDA01585//National Institute of Food and Agriculture/ ; CBET-1705728//National Science Foundation/ ; //Sorenson Family Endowment/ ; }, mesh = {*Phosphorus ; *Denitrification ; Bioreactors/microbiology ; Bacteria ; Carbon ; Fatty Acids, Volatile ; Sewage ; }, abstract = {Research focused on interrogating post-anoxic enhanced biological phosphorus removal (EBPR) at bench and pilot scales. Average bench-scale effluent ranged from 0.33 to 1.4 mgP/L, 0.35 to 3.7 mgNH3 -N/L, and 1.1 to 3.9 mgNOx -N/L. Comparatively, the pilot achieved effluent (50th percentile/average) of 0.13/0.2 mgP/L, 9.7/8.2 mgNH3 -N/L, and 0.38/3.3 mgNOx -N/L under dynamic influent and environmental conditions. For EBPR process monitoring, P:C ratio data indicated that 0.2-0.4 molP/molC will result in stable EBPR; relatedly, a target design influent volatile fatty acid (VFA):P ratio would exceed 15 mgCOD/mgP. Post-anoxic EBPR was enriched for Nitrobacter spp. at 1.70%-20.27%, with Parcubacteria also dominating; the former is putatively associated with nitritation and the latter is a putative fermenting heterotrophic organism. Post-anoxic specific denitrification rates (SDNRs) (20°C) ranged from 0.70 to 3.10 mgN/gVSS/h; there was a strong correlation (R[2] = 0.94) between the SDNR and %Parcubacteria for systems operated at a 20-day solids residence time (SRT). These results suggest that carbon substrate potentially generated by this putative fermenter may enhance post-anoxic EBPR. PRACTITIONER POINTS: Post-anoxic EBPR can achieve effluent of <0.2 mgP/L and <12 mgN/L. The P:C and VFA:P ratios can be predictive for EBPR process monitoring. Post-anoxic EBPR was enriched for Nitrobacter spp. over Nitrospira spp. and also for Parcubacteria, which is a putative fermenting heterotrophic organism. Post-anoxic specific denitrification rates (20°C) ranged from 0.70 to 3.10 mgN/gVSS/h. BLASTn analysis of 16S rDNA PAO primer set was shown to be improved to 93.8% for Ca. Accumulibacter phosphatis and 73.2%-94.0% for all potential PAOs.}, }
@article {pmid36985355, year = {2023}, author = {Masigol, H and Grossart, HP and Taheri, SR and Mostowfizadeh-Ghalamfarsa, R and Pourmoghaddam, MJ and Bouket, AC and Khodaparast, SA}, title = {Utilization of Low Molecular Weight Carbon Sources by Fungi and Saprolegniales: Implications for Their Ecology and Taxonomy.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985355}, issn = {2076-2607}, support = {GR1540/23-1//Leibniz-Institute of Freshwater Ecology and Inland Fisheries/ ; No.4728//Deputy of Research and Technology of the University of Guilan/ ; }, abstract = {Contributions of fungal and oomycete communities to freshwater carbon cycling have received increasing attention in the past years. It has been shown that fungi and oomycetes constitute key players in the organic matter cycling of freshwater ecosystems. Therefore, studying their interactions with dissolved organic matter is crucial for understanding the aquatic carbon cycle. Therefore, we studied the consumption rates of various carbon sources using 17 fungal and 8 oomycete strains recovered from various freshwater ecosystems using EcoPlate™ and FF MicroPlate™ approaches. Furthermore, phylogenetic relationships between strains were determined via single and multigene phylogenetic analyses of the internal transcribed spacer regions. Our results indicated that the studied fungal and oomycete strains could be distinguished based on their carbon utilization patterns, as indicated by their phylogenetic distance. Thereby, some carbon sources had a higher discriminative strength to categorize the studied strains and thus were applied in a polyphasic approach. We concluded that studying the catabolic potential enables a better understanding of taxonomic relationships and ecological roles of fungal vs. oomycete strains.}, }
@article {pmid36985156, year = {2023}, author = {Nayduch, D and Neupane, S and Pickens, V and Purvis, T and Olds, C}, title = {House Flies Are Underappreciated Yet Important Reservoirs and Vectors of Microbial Threats to Animal and Human Health.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985156}, issn = {2076-2607}, support = {3020-32000-018-00D//United States Department of Agriculture/ ; }, abstract = {House flies are well recognized as filth-associated organisms and public nuisances. House flies create sanitation issues when they bridge the gap between microbe-rich breeding environments and animal/human habitations. Numerous scientific surveys have demonstrated that house flies harbor bacterial pathogens that pose a threat to humans and animals. More extensive and informative surveys incorporating next-generation sequencing technologies have shown that house fly carriage of pathogens and harmful genetic elements, such as antimicrobial resistance genes, is more widespread and dangerous than previously thought. Further, there is a strong body of research confirming that flies not only harbor but also transmit viable, and presumably infectious, bacterial pathogens. Some pathogens replicate and persist in the fly, permitting prolonged shedding and dissemination. Finally, although the drivers still have yet to be firmly determined, the potential range of dissemination of flies and their associated pathogens can be extensive. Despite this evidence, the house flies' role as reservoirs, disseminators, and true, yet facultative, vectors for pathogens have been greatly underestimated and underappreciated. In this review, we present key studies that bolster the house fly's role both an important player in microbial ecology and population biology and as transmitters of microbial threats to animal and human health.}, }
@article {pmid36983540, year = {2023}, author = {Veas-Mattheos, K and Almendras, K and Pezoa, M and Muster, C and Orlando, J}, title = {High Andean Steppes of Southern Chile Contain Little-Explored Peltigera Lichen Symbionts.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {3}, pages = {}, pmid = {36983540}, issn = {2309-608X}, support = {FONDECYT 1181510//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; ICN2021_002//Millennium Science Initiative/ ; }, abstract = {Peltigera lichens can colonize extreme habitats, such as high-elevation ecosystems, but their biodiversity is still largely unknown in these environments, especially in the southern hemi- sphere. We assessed the genetic diversity of mycobionts and cyanobionts of 60 Peltigera lichens collected in three high Andean steppes of southern Chile using LSU, β-tubulin, COR3 and ITS loci for mycobionts, and SSU and rbcLX loci for cyanobionts. We obtained 240 sequences for the different mycobiont markers and 118 for the cyanobiont markers, including the first report of β-tubulin sequences of P. patagonica through modifying a previously designed primer. Phylogenetic analyses, ITS scrutiny and variability of haplotypes were used to compare the sequences with those previously reported. We found seven mycobiont species and eleven cyanobiont haplotypes, including considerable novel symbionts. This was reflected by ~30% of mycobionts and ~20% of cyanobionts haplotypes that yielded less than 99% BLASTn sequence identity, 15 new sequences of the ITS1-HR, and a putative new Peltigera species associated with 3 Nostoc haplotypes not previously reported. Our results suggest that high Andean steppe ecosystems are habitats of unknown or little-explored lichen species and thus valuable environments to enhance our understanding of global Peltigera biodiversity.}, }
@article {pmid36983467, year = {2023}, author = {Hkiri, N and Olicón-Hernández, DR and Pozo, C and Chouchani, C and Asses, N and Aranda, E}, title = {Simultaneous Heavy Metal-Polycyclic Aromatic Hydrocarbon Removal by Native Tunisian Fungal Species.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {3}, pages = {}, pmid = {36983467}, issn = {2309-608X}, support = {B-RNM-204-UGR20//Regional Government of Andalusia/ ; 20230427//Instituto Polit&#xe9;cnico Nacional. Mexico/ ; }, abstract = {Multi-contamination by organic pollutants and toxic metals is common in anthropogenic and industrial environments. In this study, the five fungal strains Chaetomium jodhpurense (MH667651.1), Chaetomium maderasense (MH665977.1), Paraconiothyrium variabile (MH667653.1), Emmia lacerata, and Phoma betae (MH667655.1), previously isolated in Tunisia, were investigated for the simultaneous removal and detoxification of phenanthrene (PHE) and benzo[a]anthracene (BAA), as well as heavy metals (HMs) (Cu, Zn, Pb and Ag) in Kirk's media. The removal was analysed using HPLC, ultra-high performance liquid chromatography (UHPLC) coupled to a QToF mass spectrometer, transmission electron microscopy, and toxicology was assessed using phytotoxicity (Lepidium sativum seeds) and Microtox[®] (Allivibrio fisherii) assays. The PHE and BAA degradation rates, in free HMs cultures, reached 78.8% and 70.7%, respectively. However, the addition of HMs considerably affected the BAA degradation rate. The highest degradation rates were associated with the significant production of manganese-peroxidase, lignin peroxidase, and unspecific peroxygenase. The Zn and Cu removal efficacy was considerably higher with live cells than dead cells. Transmission electron microscopy confirmed the involvement of both bioaccumulation and biosorption processes in fungal HM removal. The environmental toxicological assays proved that simultaneous PAH and HM removal was accompanied by detoxification. The metabolites produced during co-treatment were not toxic for plant tissues, and the acute toxicity was reduced. The obtained results indicate that the tested fungi can be applied in the remediation of sites simultaneously contaminated with PAHs and HMs.}, }
@article {pmid36979988, year = {2023}, author = {Lindner, C and Looijesteijn, E and Dijck, HV and Bovee-Oudenhoven, I and Heerikhuisen, M and Broek, TJVD and Marzorati, M and Triantis, V and Nauta, A}, title = {Infant Fecal Fermentations with Galacto-Oligosaccharides and 2'-Fucosyllactose Show Differential Bifidobacterium longum Stimulation at Subspecies Level.}, journal = {Children (Basel, Switzerland)}, volume = {10}, number = {3}, pages = {}, pmid = {36979988}, issn = {2227-9067}, support = {none//FrieslandCampina (Netherlands)/ ; }, abstract = {The objective of the current study was to evaluate the potential of 2'-FL and GOS, individually and combined, in beneficially modulating the microbial composition of infant and toddler (12-18 months) feces using the micro-Matrix bioreactor. In addition, the impacts of GOS and 2'-FL, individually and combined, on the outgrowth of fecal bifidobacteria at (sub)species level was investigated using the baby M-SHIME[®] model. For young toddlers, significant increases in the genera Bifidobacterium, Veillonella, and Streptococcus, and decreases in Enterobacteriaceae, Clostridium XIVa, and Roseburia were observed in all supplemented fermentations. In addition, GOS, and combinations of GOS and 2'-FL, increased Collinsella and decreased Salmonella, whereas 2'-FL, and combined GOS and 2'-FL, decreased Dorea. Alpha diversity increased significantly in infants with GOS and/or 2'-FL, as well as the relative abundances of the genera Veillonella and Akkermansia with 2'-FL, and Lactobacillus with GOS. Combinations of GOS and 2'-FL significantly stimulated Veillonella, Lactobacillus, Bifidobacterium, and Streptococcus. In all supplemented fermentations, Proteobacteria decreased, with the most profound decreases accomplished by the combination of GOS and 2'-FL. When zooming in on the different (sub)species of Bifidobacterium, GOS and 2'-FL were shown to be complementary in stimulating breast-fed infant-associated subspecies of Bifidobacterium longum in a dose-dependent manner: GOS stimulated Bifidobacterium longum subsp. longum, whereas 2'-FL supported outgrowth of Bifidobacterium longum subsp. infantis.}, }
@article {pmid36978500, year = {2023}, author = {Peruzzo, A and Vascellari, M and Massaro, A and Mancin, M and Stefani, A and Orsini, M and Danesi, P and Petrin, S and Carminato, A and Santoro, MM and Speranza, R and Losasso, C and Capelli, G}, title = {Giardia duodenalis Colonization Slightly Affects Gut Microbiota and Hematological Parameters in Clinically Healthy Dogs.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {6}, pages = {}, pmid = {36978500}, issn = {2076-2615}, support = {RC-IZSVE 8/2019)//Ministero della Salute/ ; }, abstract = {Giardia duodenalis (Giardia) is a worldwide cause of acute diarrheal disease both in humans and animals. The primary aim of this study was to investigate possible variations in gut microbiota in a population of asymptomatic dogs (n = 31), naturally infected or not by Giardia. Gut microbiota and the hematological, biochemical, and fecal parameters related to intestinal function were investigated. Giardia infection was associated with a significant shift of beta diversity, showing a relevant reduction of Gammaproteobacteria and an increase of Fusobacteria in male-positive dogs if compared with negatives. A significant imbalance of different bacterial taxa, with particular reference to the Erysipelotrichales, Lactobacillales, Clostridiales, and Burkholderiales orders, was observed, with the first two being higher in Giardia-positive dogs. Giardia-positive males displayed significantly higher values of cCRP than negative males as well as positive females, supporting the presence of a pro-inflammatory state. Taken together, these results indicate that the presence of Giardia does not substantially modify the microbial ecology of the intestine nor the hematological markers of disease. Thus treatments against Giardia should be considered with caution in asymptomatic subjects.}, }
@article {pmid36978419, year = {2023}, author = {Perestrelo, S and Amaro, A and Brouwer, MSM and Clemente, L and Ribeiro Duarte, AS and Kaesbohrer, A and Karpíšková, R and Lopez-Chavarrias, V and Morris, D and Prendergast, D and Pista, A and Silveira, L and Skarżyńska, M and Slowey, R and Veldman, KT and Zając, M and Burgess, C and Alvarez, J}, title = {Building an International One Health Strain Level Database to Characterise the Epidemiology of AMR Threats: ESBL-AmpC Producing E. coli as An Example-Challenges and Perspectives.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, pmid = {36978419}, issn = {2079-6382}, support = {773830//European Union's Horizon 2020/ ; }, abstract = {Antimicrobial resistance (AMR) is one of the top public health threats nowadays. Among the most important AMR pathogens, Escherichia coli resistant to extended spectrum cephalosporins (ESC-EC) is a perfect example of the One Health problem due to its global distribution in animal, human, and environmental sources and its resistant phenotype, derived from the carriage of plasmid-borne extended-spectrum and AmpC β-lactamases, which limits the choice of effective antimicrobial therapies. The epidemiology of ESC-EC infection is complex as a result of the multiple possible sources involved in its transmission, and its study would require databases ideally comprising information from animal (livestock, companion, wildlife), human, and environmental sources. Here, we present the steps taken to assemble a database with phenotypic and genetic information on 10,763 ESC-EC isolates retrieved from multiple sources provided by 13 partners located in eight European countries, in the frame of the DiSCoVeR Joint Research project funded by the One Health European Joint Programme (OH-EJP), along with its strengths and limitations. This database represents a first step to help in the assessment of different geographical and temporal trends and transmission dynamics in animals and humans. The work performed highlights aspects that should be considered in future international efforts, such as the one presented here.}, }
@article {pmid36978279, year = {2023}, author = {Horsch, CCA and Antunes, PM and Fahey, C and Grandy, AS and Kallenbach, CM}, title = {Trait-based assembly of arbuscular mycorrhizal fungal communities determines soil carbon formation and retention.}, journal = {The New phytologist}, volume = {239}, number = {1}, pages = {311-324}, doi = {10.1111/nph.18914}, pmid = {36978279}, issn = {1469-8137}, mesh = {*Mycorrhizae ; Soil/chemistry ; Carbon ; *Mycobiome ; *Glomeromycota ; *Sorghum ; Phosphorus ; Soil Microbiology ; Plant Roots/microbiology ; }, abstract = {Fungi are crucial for soil organic carbon (SOC) formation, especially for the more persistent mineral-associated organic C (MAOC) pool. Yet, evidence for this often overlooks arbuscular mycorrhizal fungi (AMF) communities and how their composition and traits impact SOC accumulation. We grew sudangrass with AMF communities representing different traits conserved at the family level: competitors, from the Gigasporaceae family; ruderals, from the Glomeraceae family; or both families combined. We labeled sudangrass with [13] C-CO2 to assess AMF contributions to SOC, impacts on SOC priming, and fungal biomass persistence in MAOC. Single-family AMF communities decreased total SOC by 13.8%, likely due to fungal priming. Despite net SOC losses, all AMF communities contributed fungal C to soil but only the Glomeraceae community initially contributed to MAOC. After a month of decomposition, both the Glomeraceae and mixed-family communities contributed to MAOC formation. Plant phosphorus uptake, but not hyphal chemistry, was positively related to AMF soil C and MAOC accumulation. Arbuscular mycorrhizal fungi contribution to MAOC is dependent on the specific traits of the AMF community and related to phosphorus uptake. These findings provide insight into how variations in AMF community composition and traits, and thus processes like environmental filtering of AMF, may impact SOC accumulation.}, }
@article {pmid36975801, year = {2023}, author = {Carter, KA and Fodor, AA and Balkus, JE and Zhang, A and Serrano, MG and Buck, GA and Engel, SM and Wu, MC and Sun, S}, title = {Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0100322}, pmid = {36975801}, issn = {2379-5077}, support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; R01 MD011504/MD/NIMHD NIH HHS/United States ; T32 AI007140/AI/NIAID NIH HHS/United States ; }, mesh = {Infant, Newborn ; Pregnancy ; Female ; Humans ; Metagenome/genetics ; RNA, Ribosomal, 16S/genetics ; *Premature Birth/genetics ; *Microbiota/genetics ; Vagina/microbiology ; }, abstract = {Several studies have compared metagenome inference performance in different human body sites; however, none specifically reported on the vaginal microbiome. Findings from other body sites cannot easily be generalized to the vaginal microbiome due to unique features of vaginal microbial ecology, and investigators seeking to use metagenome inference in vaginal microbiome research are "flying blind" with respect to potential bias these methods may introduce into analyses. We compared the performance of PICRUSt2 and Tax4Fun2 using paired 16S rRNA gene amplicon sequencing and whole-metagenome sequencing data from vaginal samples from 72 pregnant individuals enrolled in the Pregnancy, Infection, and Nutrition (PIN) cohort. Participants were selected from those with known birth outcomes and adequate 16S rRNA gene amplicon sequencing data in a case-control design. Cases experienced early preterm birth (<32 weeks of gestation), and controls experienced term birth (37 to 41 weeks of gestation). PICRUSt2 and Tax4Fun2 performed modestly overall (median Spearman correlation coefficients between observed and predicted KEGG ortholog [KO] relative abundances of 0.20 and 0.22, respectively). Both methods performed best among Lactobacillus crispatus-dominated vaginal microbiotas (median Spearman correlation coefficients of 0.24 and 0.25, respectively) and worst among Lactobacillus iners-dominated microbiotas (median Spearman correlation coefficients of 0.06 and 0.11, respectively). The same pattern was observed when evaluating correlations between univariable hypothesis test P values generated with observed and predicted metagenome data. Differential metagenome inference performance across vaginal microbiota community types can be considered differential measurement error, which often causes differential misclassification. As such, metagenome inference will introduce hard-to-predict bias (toward or away from the null) in vaginal microbiome research. IMPORTANCE Compared to taxonomic composition, the functional potential within a bacterial community is more relevant to establishing mechanistic understandings and causal relationships between the microbiome and health outcomes. Metagenome inference attempts to bridge the gap between 16S rRNA gene amplicon sequencing and whole-metagenome sequencing by predicting a microbiome's gene content based on its taxonomic composition and annotated genome sequences of its members. Metagenome inference methods have been evaluated primarily among gut samples, where they appear to perform fairly well. Here, we show that metagenome inference performance is markedly worse for the vaginal microbiome and that performance varies across common vaginal microbiome community types. Because these community types are associated with sexual and reproductive outcomes, differential metagenome inference performance will bias vaginal microbiome studies, obscuring relationships of interest. Results from such studies should be interpreted with substantial caution and the understanding that they may over- or underestimate associations with metagenome content.}, }
@article {pmid36973438, year = {2023}, author = {Xu, Z and Chen, J and Li, Y and Shekarriz, E and Wu, W and Chen, B and Liu, H}, title = {High Microeukaryotic Diversity in the Cold-Seep Sediment.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2003-2020}, pmid = {36973438}, issn = {1432-184X}, support = {SMSEGL20SC02//Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; SMSEGL20SC01//Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; PRG-2020-389//Leverhulme Trust Research Project Grant/ ; GML2019ZD0409//Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 16101917//Research Grants Council of Hong Kong/ ; }, mesh = {Animals ; *Ecosystem ; Geologic Sediments/chemistry ; Methane/chemistry ; Biodiversity ; *Dinoflagellida/genetics ; Phylogeny ; }, abstract = {Microeukaryotic diversity, community structure, and their regulating mechanisms remain largely unclear in chemosynthetic ecosystems. Here, using high-throughput sequencing data of 18S rRNA genes, we explored microeukaryotic communities from the Haima cold seep in the northern South China Sea. We compared three distinct habitats: active, less active, and non-seep regions, with vertical layers (0-25 cm) from sediment cores. The results showed that seep regions harbored more abundant and diverse parasitic microeukaryotes (e.g., Apicomplexa and Syndiniales) as indicator species, compared to nearby non-seep region. Microeukaryotic community heterogeneity was larger between habitats than within habitat, and greatly increased when considering molecular phylogeny, suggesting the local diversification in cold-seep sediments. Microeukaryotic α-diversity at cold seeps was positively increased by metazoan richness and dispersal rate of microeukaryotes, while its β-diversity was promoted by heterogeneous selection mainly from metazoan communities (as potential hosts). Their combined effects led to the significant higher γ-diversity (i.e., total diversity in a region) at cold seeps than non-seep regions, suggesting cold-seep sediment as a hotspot for microeukaryotic diversity. Our study highlights the importance of microeukaryotic parasitism in cold-seep sediment and has implications for the roles of cold seep in maintaining and promoting marine biodiversity.}, }
@article {pmid36971795, year = {2023}, author = {Lemke, M and DeSalle, R}, title = {The Role of Microbial Genomics in Restoration Ecology: An Introduction.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {779-780}, doi = {10.1007/s00248-023-02207-9}, pmid = {36971795}, issn = {1432-184X}, mesh = {*Ecology ; *Genomics ; }, }
@article {pmid36970136, year = {2023}, author = {Munley, JA and Nagpal, R and Hanson, NC and Mirzaie, A and Laquian, L and Mohr, AM and Efron, PA and Arnaoutakis, DJ and Cooper, MA}, title = {Chronic mesenteric ischemia-induced intestinal dysbiosis resolved after revascularization.}, journal = {Journal of vascular surgery cases and innovative techniques}, volume = {9}, number = {2}, pages = {101084}, pmid = {36970136}, issn = {2468-4287}, abstract = {OBJECTIVE: Chronic mesenteric ischemia (CMI) is a debilitating condition arising from intestinal malperfusion from mesenteric artery stenosis or occlusion. Mesenteric revascularization has been the standard of care but can result in substantial morbidity and mortality. Most of the perioperative morbidity has been secondary to postoperative multiple organ dysfunction, potentially from ischemia-reperfusion injury. The intestinal microbiome is a dense community of microorganisms in the gastrointestinal tract that help regulate pathways ranging from nutritional metabolism to the immune response. We hypothesized that patients with CMI will have microbiome perturbations that contribute to this inflammatory response and could potentially normalize in the postoperative period.<br><br>METHODS: We performed a prospective study of patients with CMI who had undergone mesenteric bypass and/or stenting from 2019 to 2020. Stool samples were collected at three time points: preoperatively at the clinic, perioperatively within 14&#xa0;days after surgery, and postoperatively at the clinic at >30&#xa0;days after revascularization. Stool samples from healthy controls were used for comparison. The microbiome was measured using 16S rRNA sequencing on an Illumina-MiSeq sequence platform and analyzed using the QIIME2 (quantitative insights into microbial ecology 2)-DADA2 bioinformatics pipeline with the Silva database. Beta-diversity was analyzed using a principal coordinates analysis and permutational analysis of variance. Alpha-diversity (microbial richness and evenness) was compared using the nonparametric Mann-Whitney U test. Microbial taxa unique to CMI patients vs controls were identified using linear discriminatory analysis effect size analysis. P&#xa0;< .05 was considered statistically significant.<br><br>RESULTS: Eight patients with CMI had undergone mesenteric revascularization (25% men; average age, 71&#xa0;years). Nine healthy controls were also analyzed (78% men; average age, 55&#xa0;years). Bacterial alpha-diversity (number of operational taxonomic units) was dramatically reduced preoperatively compared with that of the controls (P&#xa0;= .03). However, revascularization partially restored the species richness and evenness in the perioperative and postoperative phases. Beta-diversity was only different between the perioperative and postoperative groups (P&#xa0;= .03). Further analyses revealed increased abundance of Bacteroidetes and Clostridia taxa preoperatively and perioperatively compared with the controls, which was reduced during the postoperative period.<br><br>CONCLUSIONS: The results from the present study have shown that patients with CMI have intestinal dysbiosis that resolves after revascularization. The intestinal dysbiosis is characterized by the loss of alpha-diversity, which is restored perioperatively and maintained postoperatively. This microbiome restoration demonstrates the importance of intestinal perfusion to sustain gut homeostasis and suggests that microbiome modulation could be a possible intervention to ameliorate acute and subacute postoperative outcomes in these patients.}, }
@article {pmid36964230, year = {2023}, author = {Abdullahi, IN and Juárez-Fernández, G and Höfle, U and Latorre-Fernández, J and Cardona-Cabrera, T and Mínguez-Romero, D and Zarazaga, M and Lozano, C and Torres, C}, title = {Staphylococcus aureus Carriage in the Nasotracheal Cavities of White Stork Nestlings (Ciconia ciconia) in Spain: Genetic Diversity, Resistomes and Virulence Factors.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1993-2002}, pmid = {36964230}, issn = {1432-184X}, support = {Marie Sklodowska-Curie grant agreement N&#xb0; 801586//European Union's H2020 research and innovation programme/ ; PID2019-106158RB-I00//MCIN/ AEI /10.13039/501100011033/ ; SBPLY/19/180501/000325//Regional government of Castilla - La Mancha by the European Union's funds for regional development (FEDER)/ ; }, mesh = {Animals ; Staphylococcus aureus/genetics ; *Methicillin-Resistant Staphylococcus aureus/genetics ; Virulence Factors/genetics ; Clindamycin ; Multilocus Sequence Typing ; Spain/epidemiology ; Ecosystem ; Anti-Bacterial Agents/pharmacology ; Birds ; Genetic Variation ; *Staphylococcal Infections/veterinary/epidemiology ; Microbial Sensitivity Tests ; }, abstract = {The molecular ecology of Staphylococcus aureus in migratory birds (such as white storks) is necessary to understand their relevance in the "One Health" ecosystems. This study determined the nasotracheal carriage rates of S. aureus from white storks in Southern Spain and genetically characterized the within-host diversity. A collection of 67 S. aureus strains, previously obtained from 87 white stork nestlings (52 nasal and 85 tracheal samples) fed by their parents with food foraged in natural and landfill habitats, were tested for their antimicrobial resistance (AMR) phenotypes. Moreover, the AMR genotypes, immune evasion cluster (IEC), virulence genes and the detection of CC398 lineage were studied by PCR. The spa types and multilocus-sequencing-typing (MLST) were also determined by PCR and sequencing. Staphylococcus aureus carriage was found in 31% of storks (36.5%/11.9% in nasal/tracheal samples). All isolates were methicillin-susceptible (MSSA) and 8.8% of them were also susceptible to all tested antibiotics. The AMR phenotype/percentage/genes detected were as follows: penicillin/79.1%/blaZ; erythromycin-clindamycin-inducible/19.1%/ermA, ermT; tetracycline/11.9%/tetK; clindamycin/4.5%/lnuA and ciprofloxacin/4.5%. Twenty-one different spa types, including 2 new ones (t7778-ST15-CC15 and t18009-ST26-CC25), were detected and ascribed to 11 clonal complexes (CCs). MSSA-CC398 (8.2%), MSSA-CC15 (7.1%) and MSSA-ST291 (5.9%) were the most prevalent lineages in storks. Moreover, tst-positive (MSSA-CC22-t223 and MSSA-CC30-t1654), eta-positive (MSSA-CC9-t209) and etb-positive strains (MSSA-CC45-t015) were detected in four storks. The 18.5% of storks harboured distinct MSSA strains (with different lineages and/or AMR genes). Nestlings of storks foraging in landfills (10 CCs) had more diverse S. aureus strains than those of parents foraging in natural habitats (3 CCs). Low level of AMR was demonstrated among S. aureus strains. The predominance of MSSA-CC398 (an emergent clade) and toxigenic MSSA strains in stork nestlings highlight the need for continuous surveillance of S. aureus in wild birds.}, }
@article {pmid36964199, year = {2023}, author = {Kavagutti, VS and Chiriac, MC and Ghai, R and Salcher, MM and Haber, M}, title = {Isolation of phages infecting the abundant freshwater Actinobacteriota order 'Ca. Nanopelagicales'.}, journal = {The ISME journal}, volume = {17}, number = {6}, pages = {943-946}, pmid = {36964199}, issn = {1751-7370}, mesh = {*Bacteriophages ; Bacteria/genetics ; Gene Transfer, Horizontal ; Metagenome ; Fresh Water/microbiology ; Genome, Viral ; Phylogeny ; }, abstract = {Low-GC Actinobacteriota of the order 'Ca. Nanopelagicales' (also known as acI or hgcI clade) are abundant in freshwaters around the globe. Extensive predation pressure by phages has been assumed to be the reason for their high levels of microdiversity. So far, however, only a few metagenome-assembled phages have been proposed to infect them and no phages have been isolated. Taking advantage of recent advances in the cultivation of 'Ca. Nanopelagicales' we isolated a novel species of its genus 'Ca. Planktophila'. Using this isolate as bait, we cultivated the first two phages infecting this abundant bacterial order. Both genomes contained a whiB-like transcription factor and a RNA polymerase sigma-70 factor, which might aid in manipulating their host's metabolism. Both phages encoded a glycosyltransferase and one an anti-restriction protein, potential means to evade degradation of their DNA by nucleases present in the host genome. The two phage genomes shared only 6% of their genome with their closest relatives, with whom they form a previously uncultured family of actinophages within the Caudoviricetes. Read recruitment analyses against globally distributed metagenomes revealed the endemic distribution of this group of phages infecting 'Ca. Nanopelagicales'. The recruitment pattern against metagenomes from the isolation site and the modular distribution of shared genes between the two phages indicate high levels of horizontal gene transfer, likely mirroring the microdiversity of their host in the evolutionary arms race between host and phage.}, }
@article {pmid36963636, year = {2023}, author = {Campos, EVR and Pereira, ADES and Aleksieienko, I and do Carmo, GC and Gohari, G and Santaella, C and Fraceto, LF and Oliveira, HC}, title = {Encapsulated plant growth regulators and associative microorganisms: Nature-based solutions to mitigate the effects of climate change on plants.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {331}, number = {}, pages = {111688}, doi = {10.1016/j.plantsci.2023.111688}, pmid = {36963636}, issn = {1873-2259}, mesh = {*Plant Growth Regulators/metabolism ; *Climate Change ; Ecosystem ; Ultraviolet Rays ; Plants/metabolism ; }, abstract = {Over the past decades, the atmospheric CO2 concentration and global average temperature have been increasing, and this trend is projected to soon become more severe. This scenario of climate change intensifies abiotic stress factors (such as drought, flooding, salinity, and ultraviolet radiation) that threaten forest and associated ecosystems as well as crop production. These factors can negatively affect plant growth and development with a consequent reduction in plant biomass accumulation and yield, in addition to increasing plant susceptibility to biotic stresses. Recently, biostimulants have become a hotspot as an effective and sustainable alternative to alleviate the negative effects of stresses on plants. However, the majority of biostimulants have poor stability under environmental conditions, which leads to premature degradation, shortening their biological activity. To solve these bottlenecks, micro- and nano-based formulations containing biostimulant molecules and/or microorganisms are gaining attention, as they demonstrate several advantages over their conventional formulations. In this review, we focus on the encapsulation of plant growth regulators and plant associative microorganisms as a strategy to boost their application for plant protection against abiotic stresses. We also address the potential limitations and challenges faced for the implementation of this technology, as well as possibilities regarding future research.}, }
@article {pmid36963187, year = {2023}, author = {Wang, B and Xiao, L and Xu, A and Mao, W and Wu, Z and Hicks, LC and Jiang, Y and Xu, J}, title = {Silicon fertilization enhances the resistance of tobacco plants to combined Cd and Pb contamination: Physiological and microbial mechanisms.}, journal = {Ecotoxicology and environmental safety}, volume = {255}, number = {}, pages = {114816}, doi = {10.1016/j.ecoenv.2023.114816}, pmid = {36963187}, issn = {1090-2414}, mesh = {Cadmium/analysis ; Silicon/pharmacology ; Nicotiana/metabolism ; Lead/toxicity ; Fertilizers/analysis ; *Metals, Heavy/metabolism ; Soil/chemistry ; Fertilization ; *Soil Pollutants/analysis ; }, abstract = {Remediation of soil contaminated with cadmium (Cd) and lead (Pb) is critical for tobacco production. Silicon (Si) fertilizer can relieve heavy metal stress and promote plant growth, however, it remains unknown whether fertilization with Si can mitigate the effects of Cd and Pb on tobacco growth and alter microbial community composition in polluted soils. Here we assessed the effect of two organic (OSiFA, OSiFB) and one mineral Si fertilizer (MSiF) on Cd and Pb accumulation in tobacco plants, together with responses in plant biomass, physiological parameters and soil bacterial communities in pot experiments. Results showed that Si fertilizer relieved Cd and Pb stress on tobacco, thereby promoting plant growth: Si fertilizer reduced available Cd and Pb in the soil by 37.3 % and 28.6 %, respectively, and decreased Cd and Pb contents in the plant tissue by 42.0-55.5 % and 17.2-25.6 %, resulting in increased plant biomass by 13.0-30.5 %. Fertilization with Si alleviated oxidative damage by decreasing malondialdehyde content and increasing peroxidase and ascorbate peroxidase content. In addition, Si fertilization increased photosynthesis, chlorophyll and carotenoid content. Microbial community structure was also affected by Si fertilization. Proteobacteria and Actinobacteria were the dominant phylum in the Cd and Pb contaminated soils, but Si fertilization reduced the abundance of Actinobacteria. Si fertilization also altered microbial metabolic pathways associated with heavy metal resistance. Together, our results suggest that both organic and mineral Si fertilizers can promote tobacco growth by relieving plant physiological stress and favoring a heavy metal tolerant soil microbial community.}, }
@article {pmid36960281, year = {2023}, author = {Kapinusova, G and Lopez Marin, MA and Uhlik, O}, title = {Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1089630}, pmid = {36960281}, issn = {1664-302X}, abstract = {In terms of the number and diversity of living units, the prokaryotic empire is the most represented form of life on Earth, and yet it is still to a significant degree shrouded in darkness. This microbial "dark matter" hides a great deal of potential in terms of phylogenetically or metabolically diverse microorganisms, and thus it is important to acquire them in pure culture. However, do we know what microorganisms really need for their growth, and what the obstacles are to the cultivation of previously unidentified taxa? Here we review common and sometimes unexpected requirements of environmental microorganisms, especially soil-harbored bacteria, needed for their replication and cultivation. These requirements include resuscitation stimuli, physical and chemical factors aiding cultivation, growth factors, and co-cultivation in a laboratory and natural microbial neighborhood.}, }
@article {pmid36959175, year = {2023}, author = {Bjerg, JJ and Lustermans, JJM and Marshall, IPG and Mueller, AJ and Brokjær, S and Thorup, CA and Tataru, P and Schmid, M and Wagner, M and Nielsen, LP and Schramm, A}, title = {Cable bacteria with electric connection to oxygen attract flocks of diverse bacteria.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1614}, pmid = {36959175}, issn = {2041-1723}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Oxidation-Reduction ; *Oxygen ; Geologic Sediments/microbiology ; *Deltaproteobacteria ; Bacteria/genetics ; Sulfides ; }, abstract = {Cable bacteria are centimeter-long filamentous bacteria that conduct electrons via internal wires, thus coupling sulfide oxidation in deeper, anoxic sediment with oxygen reduction in surface sediment. This activity induces geochemical changes in the sediment, and other bacterial groups appear to benefit from the electrical connection to oxygen. Here, we report that diverse bacteria swim in a tight flock around the anoxic part of oxygen-respiring cable bacteria and disperse immediately when the connection to oxygen is disrupted (by cutting the cable bacteria with a laser). Raman microscopy shows that flocking bacteria are more oxidized when closer to the cable bacteria, but physical contact seems to be rare and brief, which suggests potential transfer of electrons via unidentified soluble intermediates. Metagenomic analysis indicates that most of the flocking bacteria appear to be aerobes, including organotrophs, sulfide oxidizers, and possibly iron oxidizers, which might transfer electrons to cable bacteria for respiration. The association and close interaction with such diverse partners might explain how oxygen via cable bacteria can affect microbial communities and processes far into anoxic environments.}, }
@article {pmid36958555, year = {2023}, author = {Zhang, X and Chen, L and Wang, Y and Jiang, P and Hu, Y and Ouyang, S and Wu, H and Lei, P and Kuzyakov, Y and Xiang, W}, title = {Plantations thinning: A meta-analysis of consequences for soil properties and microbial functions.}, journal = {The Science of the total environment}, volume = {877}, number = {}, pages = {162894}, doi = {10.1016/j.scitotenv.2023.162894}, pmid = {36958555}, issn = {1879-1026}, mesh = {*Soil/chemistry ; Ecosystem ; Soil Microbiology ; Forests ; Trees ; Biomass ; Nitrogen/analysis ; *Microbiota ; Carbon/analysis ; }, abstract = {Thinning is a widely-used management practice to reduce tree competition and improve wood production and quality in forest plantations. Thinning affects the soil ecosystem by changing the microclimate and plant growth, as well as litter inputs above and belowground, with all the resulting consequences for microbial communities and functions. Although many case studies have been carried out, a comprehensive understanding of the thinning effects on soil properties and microbial communities and functions in plantations remains to be explored. In this study, a meta-analysis was performed on 533 paired observations based on 90 peer-reviewed articles to evaluate the general responses of soil (mainly 0-20 cm depth) physicochemical properties, microbial biomass and community structure, and enzyme activities to thinning. Results showed that thinning increased soil temperature (13 %), moisture (8.0 %), electric conductivity (13 %), and the contents of total nitrogen (TN, 4.1 %), dissolved organic carbon (DOC, 9.7 %), nitrate N (NO3[-]-N, 27 %) and available phosphorous (22 %). For microbial properties, thinning decreased the fungi to bacteria ratio (F:B, -28 %) and the gram-positive bacteria to gram-negative bacteria ratio (G+:G-, -12 %), while increased microbial biomass C (7.1 %), microbial respiration (13 %), and nutrient-cycle related enzyme activities, including phenol oxidase (14 %), cellobiohydrolase (21 %), urease (10 %), and acid phosphatase (9 %). In particular, moderate thinning (30-60 % intensity) has higher conservation benefits for soil C and nutrients than light and heavy intensity, thus being recommended as the optimal thinning activity. This meta-analysis suggests that thinning consistently altered soil properties, shifted microbial community compositions from K- to-r strategist dominance, and stimulated microbial activities. These results are essential for optimizing plantation thinning management and provide evidence for applying the macro-ecology theory to ecosystem disturbance in soil microbial ecology.}, }
@article {pmid36948064, year = {2023}, author = {Goswami, P and Bhadury, P}, title = {First record of an Anthropocene marker plastiglomerate in Andaman Island, India.}, journal = {Marine pollution bulletin}, volume = {190}, number = {}, pages = {114802}, doi = {10.1016/j.marpolbul.2023.114802}, pmid = {36948064}, issn = {1879-3363}, mesh = {Ecosystem ; *Environmental Monitoring ; *Environmental Pollutants ; Environmental Pollution ; India ; *Plastics ; Polyethylene ; Waste Products ; }, abstract = {One of the most significant environmental issues confronting our world is plastic trash, which is of particular concern to the marine environment. The sedimentary record of the planet may likely one day contain a horizon of plastic that can be potentially identified as an Anthropocene marker. Here we report the presence of 'plastiglomerate' from coastal habitats located in the Aves Island, Andaman Sea, India. This novel form of plastic pollution forms with the incineration of plastic litter in the environment and then mixing of organic/inorganic composite materials in the molten plastic matrix. The plastic pollutants were collected from the Aves Island beach during marine litter surveys. Micro-Raman (μ-Raman) spectroscopy was used to evaluate and confirm all putative plastic forms. Plastiglomerates were made of a polyethylene (PE) and polyvinyl chloride (PVC) matrix with inclusions of rock and sand. Therefore, our research offers new insight into the intricate process of plastiglomerates formation.}, }
@article {pmid36947551, year = {2023}, author = {Bourne, ME and Gloder, G and Weldegergis, BT and Slingerland, M and Ceribelli, A and Crauwels, S and Lievens, B and Jacquemyn, H and Dicke, M and Poelman, EH}, title = {Parasitism causes changes in caterpillar odours and associated bacterial communities with consequences for host-location by a hyperparasitoid.}, journal = {PLoS pathogens}, volume = {19}, number = {3}, pages = {e1011262}, pmid = {36947551}, issn = {1553-7374}, mesh = {Animals ; Odorants ; Larva ; *Butterflies/parasitology ; *Wasps/parasitology ; Host-Parasite Interactions ; }, abstract = {Microorganisms living in and on macroorganisms may produce microbial volatile compounds (mVOCs) that characterise organismal odours. The mVOCs might thereby provide a reliable cue to carnivorous enemies in locating their host or prey. Parasitism by parasitoid wasps might alter the microbiome of their caterpillar host, affecting organismal odours and interactions with insects of higher trophic levels such as hyperparasitoids. Hyperparasitoids parasitise larvae or pupae of parasitoids, which are often concealed or inconspicuous. Odours of parasitised caterpillars aid them to locate their host, but the origin of these odours and its relationship to the caterpillar microbiome are unknown. Here, we analysed the odours and microbiome of the large cabbage white caterpillar Pieris brassicae in relation to parasitism by its endoparasitoid Cotesia glomerata. We identified how bacterial presence in and on the caterpillars is correlated with caterpillar odours and tested the attractiveness of parasitised and unparasitised caterpillars to the hyperparasitoid Baryscapus galactopus. We manipulated the presence of the external microbiome and the transient internal microbiome of caterpillars to identify the microbial origin of odours. We found that parasitism by C. glomerata led to the production of five characteristic volatile products and significantly affected the internal and external microbiome of the caterpillar, which were both found to have a significant correlation with caterpillar odours. The preference of the hyperparasitoid was correlated with the presence of the external microbiome. Likely, the changes in external microbiome and body odour after parasitism were driven by the resident internal microbiome of caterpillars, where the bacterium Wolbachia sp. was only present after parasitism. Micro-injection of Wolbachia in unparasitised caterpillars increased hyperparasitoid attraction to the caterpillars compared to untreated caterpillars, while no differences were found compared to parasitised caterpillars. In conclusion, our results indicate that host-parasite interactions can affect multi-trophic interactions and hyperparasitoid olfaction through alterations of the microbiome.}, }
@article {pmid36947169, year = {2023}, author = {Hammerle, F and Quirós-Guerrero, L and Wolfender, JL and Peintner, U and Siewert, B}, title = {Highlighting the Phototherapeutical Potential of Fungal Pigments in Various Fruiting Body Extracts with Informed Feature-Based Molecular Networking.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1972-1992}, pmid = {36947169}, issn = {1432-184X}, support = {P 31915/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Singlet Oxygen/analysis ; *Antineoplastic Agents ; Plant Extracts ; Fruiting Bodies, Fungal/chemistry ; }, abstract = {Fungal pigments are characterized by a diverse set of chemical backbones, some of which present photosensitizer-like structures. From the genus Cortinarius, for example, several biologically active photosensitizers have been identified leading to the hypothesis that photoactivity might be a more general phenomenon in the kingdom Fungi. This paper aims at testing the hypothesis. Forty-eight fruiting body-forming species producing pigments from all four major biosynthetic pathways (i.e., shikimate-chorismate, acetate-malonate, mevalonate, and nitrogen heterocycles) were selected and submitted to a workflow combining in vitro chemical and biological experiments with state-of-the-art metabolomics. Fungal extracts were profiled by high-resolution mass spectrometry and subsequently explored by spectral organization through feature-based molecular networking (FBMN), including advanced metabolite dereplication techniques. Additionally, the photochemical properties (i.e., light-dependent production of singlet oxygen), the phenolic content, and the (photo)cytotoxic activity of the extracts were studied. Different levels of photoactivity were found in species from all four metabolic groups, indicating that light-dependent effects are common among fungal pigments. In particular, extracts containing pigments from the acetate-malonate pathway, e.g., extracts from Bulgaria inquinans, Daldinia concentrica, and Cortinarius spp., were not only efficient producers of singlet oxygen but also exhibited photocytotoxicity against three different cancer cell lines. This study explores the distribution of photobiological traits in fruiting body forming fungi and highlights new sources for phototherapeutics.}, }
@article {pmid36946113, year = {2023}, author = {Kauai, F and Mortier, F and Milosavljevic, S and Van de Peer, Y and Bonte, D}, title = {Neutral processes underlying the macro eco-evolutionary dynamics of mixed-ploidy systems.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {1995}, pages = {20222456}, pmid = {36946113}, issn = {1471-2954}, mesh = {Humans ; *Ploidies ; *Diploidy ; Polyploidy ; Chromosomes ; Reproduction ; }, abstract = {Polyploidy, i.e. the occurrence of multiple sets of chromosomes, is regarded as an important phenomenon in plant ecology and evolution, with all flowering plants likely having a polyploid ancestry. Owing to genome shock, minority cytotype exclusion and reduced fertility, polyploids emerging in diploid populations are expected to face significant challenges to successful establishment. Their establishment and persistence are often explained by possible fitness or niche differences that would relieve the competitive pressure with diploid progenitors. Experimental evidence for such advantages is, however, not unambiguous, and considerable niche overlap exists among most polyploid species and their diploid counterparts. Here, we develop a neutral spatially explicit eco-evolutionary model to understand whether neutral processes can explain the eco-evolutionary patterns of polyploids. We present a general mechanism for polyploid establishment by showing that sexually reproducing organisms assemble in space in an iterative manner, reducing frequency-dependent mating disadvantages and overcoming potential reduced fertility issues. Moreover, we construct a mechanistic theoretical framework that allows us to understand the long-term evolution of mixed-ploidy populations and show that our model is remarkably consistent with recent phylogenomic estimates of species extinctions in the Brassicaceae family.}, }
@article {pmid36946107, year = {2023}, author = {Jones, KR and Hughey, MC and Belden, LK}, title = {Colonization order of bacterial isolates on treefrog embryos impacts microbiome structure in tadpoles.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {1995}, pages = {20230308}, pmid = {36946107}, issn = {1471-2954}, mesh = {Animals ; Larva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Anura/genetics ; Biota ; Bacteria ; }, abstract = {Priority effects, or impacts of colonization order, may have lasting influence on ecological community composition. The embryonic microbiome is subject to stochasticity in colonization order of bacteria. Stochasticity may be especially impactful for embryos developing in bacteria-rich environments, such as the embryos of many amphibians. To determine if priority effects experienced as embryos impacted bacterial community composition in newly hatched tadpoles, we selectively inoculated the embryos of laboratory-raised hourglass treefrogs, Dendropsophus ebraccatus, with bacteria initially isolated from the skin of wild D. ebraccatus adults over 2 days. First, embryos were inoculated with two bacteria in alternating sequences. Next, we evaluated the outcomes of priority effects in an in vitro co-culture assay absent of host factors. We then performed a second embryo experiment, inoculating embryos with one of three bacteria on the first day and a community of five target bacteria on the second. Through 16S rRNA gene amplicon sequencing, we observed relative abundance shifts in tadpole bacteria communities due to priority effects. Our results suggest that the initial bacterial source pools of embryos shape bacterial communities at later life stages; however, the magnitude of those changes is dependent on the host environment and the identity of bacterial colonists.}, }
@article {pmid36945867, year = {2023}, author = {Snyder, GM and Passaretti, CL and Stevens, MP}, title = {Hospital approaches to universal masking after public health "unmasking" guidance.}, journal = {Infection control and hospital epidemiology}, volume = {44}, number = {5}, pages = {845-846}, doi = {10.1017/ice.2023.9}, pmid = {36945867}, issn = {1559-6834}, mesh = {Humans ; *Public Health ; *Hospitals ; }, }
@article {pmid36944303, year = {2023}, author = {Trebuch, LM and Sohier, J and Altenburg, S and Oyserman, BO and Pronk, M and Janssen, M and Vet, LEM and Wijffels, RH and Fernandes, TV}, title = {Enhancing phosphorus removal of photogranules by incorporating polyphosphate accumulating organisms.}, journal = {Water research}, volume = {235}, number = {}, pages = {119748}, doi = {10.1016/j.watres.2023.119748}, pmid = {36944303}, issn = {1879-2448}, mesh = {*Polyphosphates ; *Phosphorus ; Bioreactors ; Sewage ; Photobioreactors ; Carbon ; Nitrogen ; }, abstract = {Photogranules are a novel wastewater treatment technology that can utilize the sun's energy to treat water with lower energy input and have great potential for nutrient recovery applications. They have been proven to efficiently remove nitrogen and carbon but show lower conversion rates for phosphorus compared to established treatment systems, such as aerobic granular sludge. In this study, we successfully introduced polyphosphate accumulating organisms (PAOs) to an established photogranular culture. We operated photobioreactors in sequencing batch mode with six cycles per day and alternating anaerobic (dark) and aerobic (light) phases. We were able to increase phosphorus removal/recovery by 6 times from 5.4 to 30 mg/L/d while maintaining similar nitrogen and carbon removal compared to photogranules without PAOs. To maintain PAOs activity, alternating anaerobic feast and aerobic famine conditions were required. In future applications, where aerobic conditions are dependent on in-situ oxygenation via photosynthesis, the process will rely on sunlight availability. Therefore, we investigated the feasibility of the process under diurnal cycles with a 12-h anaerobic phase during nighttime and six short cycles during the 12 h daytime. The 12-h anaerobic phase had no adverse effect on the PAOs and phototrophs. Due to the extension of one anaerobic phase to 12 h the six aerobic phases were shortened by 47% and consequently decreased the light hours per day. This resulted in a decrease of phototrophs, which reduced nitrogen removal and biomass productivity up to 30%. Finally, we discuss and suggest strategies to apply PAO-enriched photogranules at large-scale.}, }
@article {pmid36943084, year = {2023}, author = {Kop, LFM and Koch, H and Spieck, E and van Alen, T and Cremers, G and Daims, H and Lücker, S}, title = {Complete Genome Sequence of Nitrospina watsonii 347, Isolated from the Black Sea.}, journal = {Microbiology resource announcements}, volume = {12}, number = {4}, pages = {e0007823}, pmid = {36943084}, issn = {2576-098X}, support = {SIAM grant 024.002.002//Dutch Ministry of Education, Culture and Science/ ; VI.Veni.192.086//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; 016.Vidi.189.050//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; }, abstract = {Here, we present the complete genome sequence of Nitrospina watsonii 347, a nitrite-oxidizing bacterium isolated from the Black Sea at a depth of 100 m. The genome has a length of 3,011,914 bp with 2,895 predicted coding sequences. Its predicted metabolism is similar to that of Nitrospina gracilis with differences in defense against reactive oxygen species.}, }
@article {pmid36943059, year = {2023}, author = {Durán-Viseras, A and Sánchez-Porro, C and Viver, T and Konstantinidis, KT and Ventosa, A}, title = {Discovery of the Streamlined Haloarchaeon Halorutilus salinus, Comprising a New Order Widespread in Hypersaline Environments across the World.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0119822}, pmid = {36943059}, issn = {2379-5077}, mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Analysis, DNA ; *Euryarchaeota/genetics ; *Halobacteriales/genetics ; }, abstract = {The class Halobacteria is one of the most diverse groups within the Euryarchaeota phylum, whose members are ubiquitously distributed in hypersaline environments, where they often constitute the major population. Here, we report the discovery and isolation of a new halophilic archaeon, strain F3-133[T] exhibiting ≤86.3% 16S rRNA gene identity to any previously cultivated archaeon, and, thus, representing a new order. Analysis of available 16S rRNA gene amplicon and metagenomic data sets showed that the new isolate represents an abundant group in intermediate-to-high salinity ecosystems and is widely distributed across the world. The isolate presents a streamlined genome, which probably accounts for its ecological success in nature and its fastidious growth in culture. The predominant osmoprotection mechanism appears to be the typical salt-in strategy used by other haloarchaea. Furthermore, the genome contains the complete gene set for nucleotide monophosphate degradation pathway through archaeal RuBisCO, being within the first halophilic archaea representatives reported to code this enzyme. Genomic comparisons with previously described representatives of the phylum Euryarchaeota were consistent with the 16S rRNA gene data in supporting that our isolate represents a novel order within the class Halobacteria for which we propose the names Halorutilales ord. nov., Halorutilaceae fam. nov., Halorutilus gen. nov. and Halorutilus salinus sp. nov. IMPORTANCE The discovery of the new halophilic archaeon, Halorutilus salinus, representing a novel order, family, genus, and species within the class Halobacteria and phylum Euryarchaeota clearly enables insights into the microbial dark matter, expanding the current taxonomical knowledge of this group of archaea. The in-depth comparative genomic analysis performed on this new taxon revealed one of the first known examples of an Halobacteria representative coding the archaeal RuBisCO gene and with a streamlined genome, being ecologically successful in nature and explaining its previous non-isolation. Altogether, this research brings light into the understanding of the physiology of the Halobacteria class members, their ecological distribution, and capacity to thrive in hypersaline environments.}, }
@article {pmid36943046, year = {2023}, author = {Diener, C and Gibbons, SM}, title = {More is Different: Metabolic Modeling of Diverse Microbial Communities.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0127022}, pmid = {36943046}, issn = {2379-5077}, support = {R01 DK133468/DK/NIDDK NIH HHS/United States ; }, mesh = {*Models, Biological ; *Microbial Consortia ; }, abstract = {Microbial consortia drive essential processes, ranging from nitrogen fixation in soils to providing metabolic breakdown products to animal hosts. However, it is challenging to translate the composition of microbial consortia into their emergent functional capacities. Community-scale metabolic models hold the potential to simulate the outputs of complex microbial communities in a given environmental context, but there is currently no consensus for what the fitness function of an entire community should look like in the presence of ecological interactions and whether community-wide growth operates close to a maximum. Transitioning from single-taxon genome-scale metabolic models to multitaxon models implies a growth cone without a well-specified growth rate solution for individual taxa. Here, we argue that dynamic approaches naturally overcome these limitations, but they come at the cost of being computationally expensive. Furthermore, we show how two nondynamic, steady-state approaches approximate dynamic trajectories and pick ecologically relevant solutions from the community growth cone with improved computational scalability.}, }
@article {pmid36941122, year = {2023}, author = {Logroño, W and Kleinsteuber, S and Kretzschmar, J and Harnisch, F and De Vrieze, J and Nikolausz, M}, title = {The microbiology of Power-to-X applications.}, journal = {FEMS microbiology reviews}, volume = {47}, number = {2}, pages = {}, doi = {10.1093/femsre/fuad013}, pmid = {36941122}, issn = {1574-6976}, mesh = {*Electrolysis ; *Hydrogen/metabolism ; }, abstract = {Power-to-X (P2X) technologies will play a more important role in the conversion of electric power to storable energy carriers, commodity chemicals and even food and feed. Among the different P2X technologies, microbial components form cornerstones of individual process steps. This review comprehensively presents the state-of-the-art of different P2X technologies from a microbiological standpoint. We are focusing on microbial conversions of hydrogen from water electrolysis to methane, other chemicals and proteins. We present the microbial toolbox needed to gain access to these products of interest, assess its current status and research needs, and discuss potential future developments that are needed to turn todays P2X concepts into tomorrow's technologies.}, }
@article {pmid36939866, year = {2023}, author = {Malard, LA and Bergk-Pinto, B and Layton, R and Vogel, TM and Larose, C and Pearce, DA}, title = {Snow Microorganisms Colonise Arctic Soils Following Snow Melt.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1661-1675}, pmid = {36939866}, issn = {1432-184X}, support = {675546//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 1192//Institut Polaire Fran&#xe7;ais Paul Emile Victor/ ; }, mesh = {*Soil ; *Ecosystem ; Snow ; Arctic Regions ; }, abstract = {Arctic soils are constantly subjected to microbial invasion from either airborne, marine, or animal sources, which may impact local microbial communities and ecosystem functioning. However, in winter, Arctic soils are isolated from outside sources other than snow, which is the sole source of microorganisms. Successful colonisation of soil by snow microorganisms depends on the ability to survive and compete of both, the invading and resident community. Using shallow shotgun metagenome sequencing and amplicon sequencing, this study monitored snow and soil microbial communities throughout snow melt to investigate the colonisation process of Arctic soils. Microbial colonisation likely occurred as all the characteristics of successful colonisation were observed. The colonising microorganisms originating from the snow were already adapted to the local environmental conditions and were subsequently subjected to many similar conditions in the Arctic soil. Furthermore, competition-related genes (e.g. motility and virulence) increased in snow samples as the snow melted. Overall, one hundred potentially successful colonisers were identified in the soil and, thus, demonstrated the deposition and growth of snow microorganisms in soils during melt.}, }
@article {pmid36934908, year = {2023}, author = {Kalantzis, D and Daskaloudis, I and Lacoere, T and Stasinakis, AS and Lekkas, DF and De Vrieze, J and Fountoulakis, MS}, title = {Granular activated carbon stimulates biogas production in pilot-scale anaerobic digester treating agro-industrial wastewater.}, journal = {Bioresource technology}, volume = {376}, number = {}, pages = {128908}, doi = {10.1016/j.biortech.2023.128908}, pmid = {36934908}, issn = {1873-2976}, mesh = {*Wastewater ; *Charcoal/chemistry ; Waste Disposal, Fluid ; Biofuels ; Anaerobiosis ; Bioreactors ; Methane ; }, abstract = {This work examines the continuous addition (5 g/L) of conductive granular activated carbon (GAC) in an integrated pilot-scale unit containing an anaerobic digester (180 L) and an aerobic submerged membrane bioreactor (1600 L) connected in series for the treatment of agro-industrial wastewater. Biogas production increased by 32 % after the addition of GAC. Methanosaeta was the dominant methanogen in the digester, and its relative abundance increased after the addition of GAC. The final effluent after post-treatment with the aerobic membrane bioreactor had a total solids content <0.01 g/L and a chemical oxygen demand between 120 and 150 mg/L. A simple cost analysis showed that GAC addition is potentially profitable, but alternatives ways of retaining the GAC in the system need to be found. Overall, this study provides useful scientific data for the possible application of GAC in full-scale biogas projects.}, }
@article {pmid36934439, year = {2023}, author = {Runde, J and Veseli, I and Fogarty, EC and Watson, AR and Clayssen, Q and Yosef, M and Shaiber, A and Verma, R and Quince, C and Gerasimidis, K and Rubin, DT and Eren, AM}, title = {Transient Suppression of Bacterial Populations Associated with Gut Health is Critical in Success of Exclusive Enteral Nutrition for Children with Crohn's Disease.}, journal = {Journal of Crohn's &amp; colitis}, volume = {17}, number = {7}, pages = {1103-1113}, doi = {10.1093/ecco-jcc/jjad031}, pmid = {36934439}, issn = {1876-4479}, mesh = {Humans ; *Crohn Disease ; Enteral Nutrition ; Remission Induction ; Bacteria ; *Microbiota ; }, abstract = {BACKGROUND AND AIMS: Exclusive enteral nutrition [EEN] is a dietary intervention to induce clinical remission in children with active luminal Crohn's disease [CD]. While changes in the gut microbial communities have been implicated in achieving this remission, a precise understanding of the role of microbial ecology in the restoration of gut homeostasis is lacking.<br><br>METHODS: Here we reconstructed genomes from the gut metagenomes of 12 paediatric subjects who were sampled before, during and after EEN. We then classified each microbial population into distinct 'phenotypes' or patterns of response based on changes in their relative abundances throughout the therapy on a per-individual basis.<br><br>RESULTS: Our data show that children achieving clinical remission during therapy were enriched with microbial populations that were either suppressed or that demonstrated a transient bloom as a function of EEN. In contrast, this ecosystem-level response was not observed in cases of EEN failure. Further analysis revealed that populations that were suppressed during EEN were significantly more prevalent in healthy children and adults across the globe compared with those that bloomed ephemerally during the therapy.<br><br>CONCLUSIONS: These observations taken together suggest that successful outcomes of EEN are marked by a temporary emergence of microbial populations that are rare in healthy individuals, and a concomitant reduction in microbes that are commonly associated with gut homeostasis. Our work is a first attempt to highlight individual-specific, complex environmental factors that influence microbial response in EEN. This model offers a novel, alternative viewpoint to traditional taxonomic strategies used to characterize associations with health and disease states.}, }
@article {pmid36930295, year = {2023}, author = {Harsonowati, W and Rahayuningsih, S and Yuniarti, E and Susilowati, DN and Manohara, D and Sipriyadi,  and Widyaningsih, S and Akhdiya, A and Suryadi, Y and Tentrem, T}, title = {Bacterial Metal-Scavengers Newly Isolated from Indonesian Gold Mine-Impacted Area: Bacillus altitudinis MIM12 as Novel Tools for Bio-Transformation of Mercury.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1646-1660}, pmid = {36930295}, issn = {1432-184X}, mesh = {Bacillus ; Lead ; *Mercury ; Gold ; Bacteria/genetics ; Cadmium ; Indonesia ; Environmental Monitoring ; }, abstract = {Selikat river, located in the north part of Bengkulu Province, Indonesia, has critical environmental and ecological issues of contamination by mercury due to artisanal small-scale gold mining (ASGM) activities. The present study focused on the identification and bioremediation efficiency of the mercury-resistant bacteria (MRB) isolated from ASGM-impacted areas in Lebong Tambang village, Bengkulu Province, and analyzed their merA gene function in transforming Hg[2+] to Hg[0]. Thirty-four MRB isolates were isolated, and four out of the 34 isolates exhibited not only the highest degree of resistance to Hg (up to 200 ppm) but also to cadmium (Cd), chromium (Cr), copper (Cu), and lead (Pb). Further analysis shows that all four selected isolates harbor a merA operon-encoded mercuric ion (Hg[2+]) reductase enzyme, with the Hg bioremediation efficiency varying from 71.60 to 91.30%. Additionally, the bioremediation efficiency for Cd, Cr, Cu, and Pb ranged from 54.36 to 98.37%. Among the 34, two isolates identified as Bacillus altitudinis possess effective and superior multi-metal degrading capacity up to 91.30% for Hg, 98.07% for Cu, and 54.36% for Cr. A pilot-scale study exhibited significant in situ bioremediation of Hg from gold mine tailings of 82.10 and 95.16% at 4- and 8-day intervals, respectively. Interestingly, translated nucleotide blast against bacteria and Bacilli merA sequence databases suggested that B. altitudinis harbor merA gene is the first case among Bacilli with the possibility exhibits a novel mechanism of bioremediation, considering our new finding. This study is the first to report the structural and functional Hg-resistant bacterial diversity of unexplored ASGM-impacted areas, emphasizing their biotechnological potential as novel tools for the biological transformation and adsorption of mercury and other toxic metals.}, }
@article {pmid36928747, year = {2023}, author = {Zhang, Y and Liu, F and Liang, H and Gao, D}, title = {Correction to: Mediative Mechanism of Freezing/Thawing on Greenhouse Gas Emissions in an Inland Saline Alkaline Wetland: a Metagenomic Analysis.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2210}, doi = {10.1007/s00248-023-02205-x}, pmid = {36928747}, issn = {1432-184X}, }
@article {pmid36927871, year = {2023}, author = {Doulidis, PG and Galler, AI and Hausmann, B and Berry, D and Rodríguez-Rojas, A and Burgener, IA}, title = {Gut microbiome signatures of Yorkshire Terrier enteropathy during disease and remission.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {4337}, pmid = {36927871}, issn = {2045-2322}, support = {898858/MCCC_/Marie Curie/United Kingdom ; }, mesh = {Humans ; Dogs ; Animals ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; *Microbiota ; Bacteroidetes ; }, abstract = {The role of the gut microbiome in developing Inflammatory Bowel Disease (IBD) in humans and dogs has received attention in recent years. Evidence suggests that IBD is associated with alterations in gut microbial composition, but further research is needed in veterinary medicine. The impact of IBD treatment on the gut microbiome needs to be better understood, especially in a breed-specific form of IBD in Yorkshire Terriers known as Yorkshire Terrier Enteropathy (YTE). This study aimed to investigate the difference in gut microbiome composition between YTE dogs during disease and remission and healthy Yorkshire Terriers. Our results showed a significant increase in specific taxa such as Clostridium sensu stricto 1, Escherichia-Shigella, and Streptococcus, and a decrease in Bacteroides, Prevotella, Alloprevotella, and Phascolarctobacterium in YTE dogs compared to healthy controls. No significant difference was found between the microbiome of dogs in remission and those with active disease, suggesting that the gut microbiome is affected beyond clinical recovery.}, }
@article {pmid36926228, year = {2023}, author = {Zayed, N and Figueiredo, J and Van Holm, W and Boon, N and Bernaerts, K and Teughels, W}, title = {Mode of killing determines the necrotrophic response of oral bacteria.}, journal = {Journal of oral microbiology}, volume = {15}, number = {1}, pages = {2184930}, pmid = {36926228}, issn = {2000-2297}, abstract = {BACKGROUND: Bacteria respond to changes in their environment, such as nutrient depletion and antimicrobials exposure. Antimicrobials result not only in bacterial death, but also have a hand in determining species abundances and ecology of the oral biofilms. Proximity of dead bacterial cells to living ones is an important environmental change or stress factor. Dead bacteria represent high concentrations of nutrients, such as proteins, lipids, sugars, and nucleic acids. Living bacteria can use these biomasses as a nutrients source, which is termed necrotrophy.<br><br>AIM: This study investigates the effect of exposing living oral bacteria (planktonic and biofilms) to their dead siblings after being killed by heat or hydrogen peroxide.<br><br>RESULTS: Tested bacterial species showed different responses towards the dead cells, depending on the mode of killing, the nutritional value of the culture media, and the the dead cells density. The multispecies oral biofilms showed different responses towards the supplementation of dead cells during biofilm development, while matured biofilms were more resilient.<br><br>CONCLUSION: This study indicates that dead bacteria resulting from antiseptics use may imbalance the nutrient availability in the oral cavity, resulting in overgrowth of opportunistic species, and hence ecological changes in oral communities, or introducing new bacterial phenotypes.}, }
@article {pmid36925466, year = {2023}, author = {Rachid, CTCC and Balieiro, FC and Peixoto, RS and Fonseca, ES and Jesus, HE and Novotny, EH and Chaer, GM and Santos, FM and Tiedje, JM and Rosado, AS}, title = {Mycobiome structure does not affect field litter decomposition in Eucalyptus and Acacia plantations.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1106422}, pmid = {36925466}, issn = {1664-302X}, abstract = {Mixed tree plantations have been studied because of their potential to improve biomass production, ecosystem diversity, and soil quality. One example is a mixture of Eucalyptus and Acacia trees, which is a promising strategy to improve microbial diversity and nutrient cycling in soil. We examined how a mixture of these species may influence the biochemical attributes and fungal community associated with leaf litter, and the effects on litter decomposition. We studied the litter from pure and mixed plantations, evaluating the effects of plant material and incubation site on the mycobiome and decomposition rate using litterbags incubated in situ. Our central hypothesis was litter fungal community would change according to incubation site, and it would interfere in litter decomposition rate. Both the plant material and the incubation locale significantly affected the litter decomposition. The origin of the litter was the main modulator of the mycobiome, with distinct communities from one plant species to another. The community changed with the incubation time but the incubation site did not influence the mycobiome community. Our data showed that litter and soil did not share the main elements of the community. Contrary to our hypothesis, the microbial community structure and diversity lacked any association with the decomposition rate. The differences in the decomposition pattern are explained basically as a function of the exchange of nitrogen compounds between the litter.}, }
@article {pmid36923055, year = {2023}, author = {Correa, F and Luise, D and Negrini, C and Ruggeri, R and Bosi, P and Trevisi, P}, title = {Effect of two milk supplements and two ways of administration on growth performance, welfare and fecal microbial ecology of suckling piglets.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1050414}, pmid = {36923055}, issn = {2297-1769}, abstract = {INTRODUCTION: The aim of this study was to evaluate the effect of two MS formulas, DanMilk™ (AB Neo, Denmark) (MS1) and Neopigg[®] RescueMilk (Provimi, Netherlands) (MS2) administered manually and to compare two ways of administration (manual vs automatic) of MS1 on growth performance, health, fecal microbial profile, behavior, and skin lesions of piglets during suckling and post-weaning.<br><br>METHODS: Forty litters (528 piglets) were divided into 4 groups: 1) Control group receiving no MS (CON); 2) MS1 administered automatically (A-MS1); 3) MS1 administered manually (Ma-MS1) 4) MS2 administered manually (Ma-MS2). All groups had access to sow milk and creep feed. On day 5 after birth (d0), litters were equalized (13.2 piglets/litter &#xb1; 0.8 SD), thereafter no cross-fostering was allowed. Piglets were weighed at day 5 after birth (d0), at the end of milk supplementation (d14), at weaning (d21 of the trial, 26 days of age) and ten days post-weaning (d31). Piglet welfare was assessed using behavioral and lesion measures at d4 and d10. Feces were collected at d14 and d21.<br><br>RESULTS AND DISCUSSION: During the suckling period, A-MS1 had lowest mortality (p < 0.05), while Ma-MS1 had lower mortality compared with CON and Ma-MS2 (p < 0.05). Negative social behavior at d4, was more frequent in MS groups (A-MS1, Ma-MS1, Ma-MS2) compared to CON group (p = 0.03). Growth performance and lesion prevalence were not affected by MS provision. During lactation, Ma-MS2 group had a higher percentage of piglets not eating during suckling at d18 compared with Ma-MS1 (p = 0.03). MS1 increased microbial diversity compared with CON at d14 (Chao1, p = 0.02; Shannon, p = 0.03) and compared with CON (Shannon, p < 0.05; InvSimpson, p = 0.01) and Ma-MS2 (Chao1, p < 0.05; Shannon, p = 0.05, InvSimpson p = 0.01) at d21. Groups that received MS1 were characterized by genera producing short-chain fatty acids (SCFAs), i.e., Lachnospiraceae (A-MS1) and Oscillospiraceae (Ma-MS1). MS composition and availability can contribute to reduce piglet's mortality during the suckling phase and can also affect intestinal microbiota by favoring the presence of SCFAs producing bacteria.}, }
@article {pmid36920955, year = {2023}, author = {Schada von Borzyskowski, L}, title = {Taking Synthetic Biology to the Seas: From Blue Chassis Organisms to Marine Aquaforming.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {24}, number = {13}, pages = {e202200786}, doi = {10.1002/cbic.202200786}, pmid = {36920955}, issn = {1439-7633}, mesh = {*Synthetic Biology ; Oceans and Seas ; *Bacteria/metabolism ; Biotechnology ; Aquatic Organisms/metabolism ; }, abstract = {Oceans cover 71 % of Earth's surface and are home to hundreds of thousands of species, many of which are microbial. Knowledge about marine microbes has strongly increased in the past decades due to global sampling expeditions, and hundreds of detailed studies on marine microbial ecology, physiology, and biogeochemistry. However, the translation of this knowledge into biotechnological applications or synthetic biology approaches using marine microbes has been limited so far. This review highlights key examples of marine bacteria in synthetic biology and metabolic engineering, and outlines possible future work based on the emerging marine chassis organisms Vibrio natriegens and Halomonas bluephagenesis. Furthermore, the valorization of algal polysaccharides by genetically enhanced microbes is presented as an example of the opportunities and challenges associated with blue biotechnology. Finally, new roles for marine synthetic biology in tackling pressing global challenges, including climate change and marine pollution, are discussed.}, }
@article {pmid36917283, year = {2023}, author = {Anand, U and Pal, T and Yadav, N and Singh, VK and Tripathi, V and Choudhary, KK and Shukla, AK and Sunita, K and Kumar, A and Bontempi, E and Ma, Y and Kolton, M and Singh, AK}, title = {Current Scenario and Future Prospects of Endophytic Microbes: Promising Candidates for Abiotic and Biotic Stress Management for Agricultural and Environmental Sustainability.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1455-1486}, pmid = {36917283}, issn = {1432-184X}, mesh = {*Symbiosis ; *Endophytes/physiology ; Fungi/physiology ; Stress, Physiological ; Plants/microbiology ; Agriculture ; }, abstract = {Globally, substantial research into endophytic microbes is being conducted to increase agricultural and environmental sustainability. Endophytic microbes such as bacteria, actinomycetes, and fungi inhabit ubiquitously within the tissues of all plant species without causing any harm or disease. Endophytes form symbiotic relationships with diverse plant species and can regulate numerous host functions, including resistance to abiotic and biotic stresses, growth and development, and stimulating immune systems. Moreover, plant endophytes play a dominant role in nutrient cycling, biodegradation, and bioremediation, and are widely used in many industries. Endophytes have a stronger predisposition for enhancing mineral and metal solubility by cells through the secretion of organic acids with low molecular weight and metal-specific ligands (such as siderophores) that alter soil pH and boost binding activity. Finally, endophytes synthesize various bioactive compounds with high competence that are promising candidates for new drugs, antibiotics, and medicines. Bioprospecting of endophytic novel secondary metabolites has given momentum to sustainable agriculture for combating environmental stresses. Biotechnological interventions with the aid of endophytes played a pivotal role in crop improvement to mitigate biotic and abiotic stress conditions like drought, salinity, xenobiotic compounds, and heavy metals. Identification of putative genes from endophytes conferring resistance and tolerance to crop diseases, apart from those involved in the accumulation and degradation of contaminants, could open new avenues in agricultural research and development. Furthermore, a detailed molecular and biochemical understanding of endophyte entry and colonization strategy in the host would better help in manipulating crop productivity under changing climatic conditions. Therefore, the present review highlights current research trends based on the SCOPUS database, potential biotechnological interventions of endophytic microorganisms in combating environmental stresses influencing crop productivity, future opportunities of endophytes in improving plant stress tolerance, and their contribution to sustainable remediation of hazardous environmental contaminants.}, }
@article {pmid36916881, year = {2023}, author = {Hadjirin, NF and van Tonder, AJ and Blane, B and Lees, JA and Kumar, N and Delappe, N and Brennan, W and McGrath, E and Parkhill, J and Cormican, M and Peacock, SJ and Ludden, C}, title = {Dissemination of carbapenemase-producing Enterobacterales in Ireland from 2012 to 2017: a retrospective genomic surveillance study.}, journal = {Microbial genomics}, volume = {9}, number = {3}, pages = {}, pmid = {36916881}, issn = {2057-5858}, support = {MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Escherichia coli/genetics ; Ireland/epidemiology ; Retrospective Studies ; *Klebsiella pneumoniae/genetics ; Genomics ; }, abstract = {The spread of carbapenemase-producing Enterobacterales (CPE) is of major public health concern. The transmission dynamics of CPE in hospitals, particularly at the national level, are not well understood. Here, we describe a retrospective nationwide genomic surveillance study of CPE in Ireland between 2012 and 2017. We sequenced 746 national surveillance CPE samples obtained between 2012 and 2017. After clustering the sequences, we used thresholds based on pairwise SNPs, and reported within-host diversity along with epidemiological data to infer recent putative transmissions. All clusters in circulating clones, derived from high-resolution phylogenies, of a species (Klebsiella pneumoniae, Escherichia coli, Klebsiella oxytoca, Enterobacter cloacae, Enterobacter hormaechei and Citrobacter freundii) were individually examined for evidence of transmission. Antimicrobial resistance trends over time were also assessed. We identified 352 putative transmission events in six species including widespread and frequent transmissions in three species. We detected putative outbreaks in 4/6 species with three hospitals experiencing prolonged outbreaks. The bla OXA-48 gene was the main cause of carbapenem resistance in Ireland in almost all species. An expansion in the number of sequence types carrying bla OXA-48 was an additional cause of the increasing prevalence of carbapenemase-producing K. pneumoniae and E. coli.}, }
@article {pmid36916137, year = {2024}, author = {Elhalis, H and Chin, XH and Chow, Y}, title = {Soybean fermentation: Microbial ecology and starter culture technology.}, journal = {Critical reviews in food science and nutrition}, volume = {64}, number = {21}, pages = {7648-7670}, doi = {10.1080/10408398.2023.2188951}, pmid = {36916137}, issn = {1549-7852}, mesh = {*Fermentation ; *Glycine max ; *Soy Foods/microbiology/analysis ; Food Microbiology ; Fungi/metabolism ; Nutritive Value ; Fermented Foods/microbiology ; Food Handling/methods ; }, abstract = {Fermented soybean products, including Soya sauce, Tempeh, Miso, and Natto have been consumed for decades, mainly in Asian countries. Beans are processed using either solid-state fermentation, submerged fermentation, or a sequential of both methods. Traditional ways are still used to conduct the fermentation processes, which, depending on the fermented products, might take a few days or even years to complete. Diverse microorganisms were detected during fermentation in various processes with Bacillus species or filamentous fungi being the two main dominant functional groups. Microbial activities were essential to increase the bean's digestibility, nutritional value, and sensory quality, as well as lower its antinutritive factors. The scientific understanding of fermentation microbial communities, their enzymes, and their metabolic activities, however, still requires further development. The use of a starter culture is crucial, to control the fermentation process and ensure product consistency. A broad understanding of the spontaneous fermentation ecology, biochemistry, and the current starter culture technology is essential to facilitate further improvement and meet the needs of the current extending and sustainable economy. This review covers what is currently known about these aspects and reveals the limited available information, along with the possible directions for future starter culture design in soybean fermentation.}, }
@article {pmid36915862, year = {2023}, author = {Freixa, A and Ortiz-Rivero, J and Sabater, S}, title = {Artificial substrata to assess ecological and ecotoxicological responses in river biofilms: Use and recommendations.}, journal = {MethodsX}, volume = {10}, number = {}, pages = {102089}, pmid = {36915862}, issn = {2215-0161}, abstract = {River biofilms are biological consortia of autotrophs and heterotrophs colonizing most solid surfaces in rivers. Biofilm composition and biomass differ according to the environmental conditions, having different characteristics between systems and even between river habitats. Artificial substrata (AS) are an alternative for in situ or laboratory experiments to handle the natural variability of biofilms. However, specific research goals may require decisions on colonization time or type of substrata. Substrata properties (i.e., texture, roughness, hydrophobicity) and the colonization period and site are selective factors of biofilm characteristics. Here we describe the uses of artificial substrata in the assessment of ecological and ecotoxicological responses and propose a decision tree for the best use of artificial substrata in river biofilm studies. We propose departing from the purpose of the study to define the necessity of obtaining a realistic biofilm community, from which it may be defined the colonization time, the colonization site, and the type of artificial substratum. Having a simple or mature biofilm community should guide our decisions on the colonization time and type of substrata to be selected for the best use of AS in biofilm studies. Tests involving contaminants should avoid adsorbing materials while those ecologically oriented may use any AS mimicking those substrata occurring in the streambed.•We review the utilization of different artificial substrata to colonize biofilm in river ecology and ecotoxicology.•We propose a decision tree to guide on selecting the appropriate artificial substrata and colonization site and duration.•Type of artificial substrata (material, size, shape...) and colonization duration are to be decided according to the specific purpose of the study.}, }
@article {pmid36914121, year = {2023}, author = {Rožman, M and Lekunberri, I and Grgić, I and Borrego, CM and Petrović, M}, title = {Effects of combining flow intermittency and exposure to emerging contaminants on the composition and metabolic response of streambed biofilm bacterial communities.}, journal = {The Science of the total environment}, volume = {877}, number = {}, pages = {162818}, doi = {10.1016/j.scitotenv.2023.162818}, pmid = {36914121}, issn = {1879-1026}, mesh = {*Ecosystem ; *Water Pollutants, Chemical/analysis ; Dissolved Organic Matter ; Bacteria/genetics ; Rivers/chemistry ; Biofilms ; }, abstract = {Freshwater ecosystems are characterised by the co-occurrence of stressors that simultaneously affect the biota. Among these, flow intermittency and chemical pollution severely impair the diversity and functioning of streambed bacterial communities. Using an artificial streams mesocosm facility, this study examined how desiccation and pollution caused by emerging contaminants affect the composition of stream biofilm bacterial communities, their metabolic profiles, and interactions with their environment. Through an integrative analysis of the composition of biofilm communities, characterization of their metabolome and composition of the dissolved organic matter, we found strong genotype-to-phenotype interconnections. The strongest correlation was found between the composition and metabolism of the bacterial community, both of which were influenced by incubation time and desiccation. Unexpectedly, no effect of the emerging contaminants was observed, which was due to the low concentration of the emerging contaminants and the dominant impact of desiccation. However, biofilm bacterial communities modified the chemical composition of their environment under the effect of pollution. Considering the tentatively identified classes of metabolites, we hypothesised that the biofilm response to desiccation was mainly intracellular while the response to chemical pollution was extracellular. The present study demonstrates that metabolite and dissolved organic matter profiling may be effectively integrated with compositional analysis of stream biofilm communities to yield a more complete picture of changes in response to stressors.}, }
@article {pmid36912945, year = {2023}, author = {Bouchachi, N and Obernosterer, I and Carpaneto Bastos, C and Li, F and Scenna, L and Marie, B and Crispi, O and Catala, P and Ortega-Retuerta, E}, title = {Effects of Phosphorus Limitation on the Bioavailability of DOM Released by Marine Heterotrophic Prokaryotes.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1961-1971}, pmid = {36912945}, issn = {1432-184X}, mesh = {*Dissolved Organic Matter ; Biological Availability ; *Phosphorus/analysis ; Bacteria ; Mediterranean Sea ; }, abstract = {Heterotrophic prokaryotes (HP) contribute largely to dissolved organic matter (DOM) processing in the ocean, but they also release diverse organic substances. The bioavailability of DOM released by HP under varying environmental conditions has not been fully elucidated. In this study, we investigated the bioavailability of DOM released by a single bacterial strain (Sphingopyxis alaskensis) and 2 natural HP communities grown under P-replete and P-limited conditions. The released DOM (HP-DOM) was used as a substrate for natural HP communities at a coastal site in the Northwestern Mediterranean Sea. We followed changes in HP growth, enzymatic activity, diversity, and community composition together with the consumption of HP-DOM fluorescence (FDOM). HP-DOM produced under P-replete and P-limited conditions promoted significant growth in all incubations. No clear differences in HP-DOM lability released under P-repletion and P-limitation were evidenced based on the HP growth, and P-limitation was not demonstrated to decrease HP-DOM lability. However, HP-DOM supported the growth of diverse HP communities, and P-driven differences in HP-DOM quality were selected for different indicator taxa in the degrading communities. The humic-like fluorescence, commonly considered recalcitrant, was consumed during the incubations when this peak was initially dominating the FDOM pool, and this consumption coincided with higher alkaline phosphatase activity. Taken together, our findings emphasize that HP-DOM lability is dependent on both DOM quality, which is shaped by P availability, and the composition of the consumer community.}, }
@article {pmid36912675, year = {2023}, author = {Oswin, HP and Haddrell, AE and Hughes, C and Otero-Fernandez, M and Thomas, RJ and Reid, JP}, title = {Oxidative Stress Contributes to Bacterial Airborne Loss of Viability.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0334722}, pmid = {36912675}, issn = {2165-0497}, support = {BB/W00884X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {While the airborne decay of bacterial viability has been observed for decades, an understanding of the mechanisms driving the decay has remained elusive. The airborne transport of bacteria is often a key step in their life cycle and as such, characterizing the mechanisms driving the airborne decay of bacteria is an essential step toward a more complete understanding of microbial ecology. Using the Controlled Electrodynamic Levitation and Extraction of Bioaerosols onto a Substrate (CELEBS), it was possible to systematically evaluate the impact of different physicochemical and environmental parameters on the survival of Escherichia coli in airborne droplets of Luria Bertani broth. Rather than osmotic stress driving the viability loss, as was initially considered, oxidative stress was found to play a key role. As the droplets evaporate and equilibrate with the surrounding environment, the surface-to-volume ratio increases, which in turn increased the formation of reactive oxygen species in the droplet. These reactive oxygen species appear to play a key role in driving the airborne loss of viability of E. coli. IMPORTANCE The airborne transport of bacteria has a wide range of impacts, from disease transmission to cloud formation. By understanding the factors that influence the airborne stability of bacteria, we can better understand these processes. However, while we have known for several decades that airborne bacteria undergo a gradual loss of viability, we have not previously identified the mechanisms driving this process. In this work, we discovered that oxygen surrounding an airborne droplet facilitates the formation of reactive oxygen species within the droplet, which then gradually damage and kill bacteria within the droplet. This discovery indicates that adaptations to help bacteria deal with oxidative stress may also aid their airborne survival and be essential adaptations for bacterial airborne pathogens. Understanding the adaptations bacteria need to survive in airborne droplets could eventually lead to the development of novel antimicrobials designed to inhibit their airborne survival, helping to prevent the transmission of disease.}, }
@article {pmid36911623, year = {2023}, author = {Meng, H and Peng, Y and Li, P and Su, J and Jiang, Y and Fu, X}, title = {Global trends in research of high-throughput sequencing technology associated with chronic wounds from 2002 to 2022: A bibliometric and visualized study.}, journal = {Frontiers in surgery}, volume = {10}, number = {}, pages = {1089203}, pmid = {36911623}, issn = {2296-875X}, abstract = {BACKGROUND: Chronic wounds are a complex medical problem. With the difficulty of skin healing, the microbial ecology of chronic wounds is an essential factor affecting wound healing. High-throughput sequencing (HTS) technology is a vital method to reveal the microbiome diversity and population structure of chronic wounds.<br><br>OBJECTIVE: The aim of this paper was to delineate the scientific output characteristics, research trends, hotspots and frontiers of HTS technologies related to chronic wounds globally over the past 20 years.<br><br>METHODS: We searched the Web of Science Core Collection (WoSCC) database for articles published between 2002 and 2022 and their full record information. The Bibliometrix software package was used to analyze bibliometric indicators and VOSviewer visualization analysis results.<br><br>RESULTS: Ultimately, a total of 449 original articles were reviewed, and the results showed that the number of annual publications (Nps) about HTS associated with chronic wounds has steadily increased over the last 20 years. The United States and China produce the most articles and have the highest H-index, while the United States and England have the largest number of citations (Nc) in this field. The University of California, Wound Repair and Regeneration and National Institutes of Health Nih United States were the most published institutions, journals and fund resources, respectively. The global research could be divided into 3 clusters as follows: microbial infection of chronic wounds, the healing process of wounds and microscopic processes, skin repair mechanism stimulated by antimicrobial peptides and oxidative stress. In recent years, "wound healing", "infections", "expression", "inflammation", "chronic wounds", "identification" and "bacteria" "angiogenesis", "biofilms" and "diabetes" were the most frequently used keywords. In addition, research on "prevalence", "gene expression", "inflammation" and "infection" has recently become a hotspot.<br><br>CONCLUSIONS: This paper compares the research hotspots and directions in this field globally from the perspectives of countries, institutions and authors, analyzes the trend of international cooperation, and reveals the future development direction of the field and research hotspots of great scientific research value. Through this paper, we can further explore the value of HTS technology in chronic wounds to better solve the problem of chronic wounds.}, }
@article {pmid36911268, year = {2023}, author = {Polk, C and Sampson, M and Fairman, RT and DeWitt, ME and Leonard, M and Neelakanta, A and Davidson, L and Roshdy, D and Branner, C and McCurdy, L and Ludden, T and Tapp, H and Passaretti, C}, title = {Evaluation of a health system's implementation of a monkeypox care model under the RE-AIM framework.}, journal = {Therapeutic advances in infectious disease}, volume = {10}, number = {}, pages = {20499361231158463}, pmid = {36911268}, issn = {2049-9361}, abstract = {OBJECTIVE: Emerging infectious diseases challenge healthcare systems to implement new models of care. We aim to evaluate the rapid implementation of a new care model for monkeypox in our health system.<br><br>DESIGN: This is a retrospective case series evaluation under the Reach, Effectiveness, Adoption, Implementation, and Maintenance (RE-AIM) framework of implementation of a testing and care model for monkeypox in a large, integrated health system.<br><br>METHODS: Atrium Health implemented education of providers, testing protocols, and management of potential monkeypox cases using electronic health record (EHR) data capabilities, telehealth, and collaboration between multiple disciplines. The first 4 weeks of care model implementation were evaluated under the RE-AIM framework.<br><br>RESULTS: One hundred fifty-three patients were tested for monkeypox by 117 unique providers at urgent care, emergency departments, and infectious disease clinics in our healthcare system between 18 July 2022 and 14 August 2022. Fifty-eight monkeypox cases were identified, compared with 198 cases in the state during the time period, a disproportionate number compared with the health system service area, and 52 patients were assessed for need for tecovirimat treatment. The number of tests performed and providers sending tests increased during the study period.<br><br>CONCLUSION: Implementation of a dedicated care model leveraging EHR data support, telehealth, and cross-disciplinary collaboration led to more effective identification and management of emerging infectious diseases and is important for public health.<br><br>PLAIN LANGUAGE SUMMARY: Impact of care model implementation on monkeypox New infectious diseases challenge health systems to implement new care practices. Our health system responded to this challenge by implementing a care model for education, testing, and clinical care of monkeypox patients. We analyzed results from implementing the model. We were able to identify a disproportionate number of monkeypox cases compared with the rest of our state by using our model to educate medical providers, encourage testing, and ensure patients had access to best disease care. Implementation of care models for testing and management of new diseases will improve patient care and public health.}, }
@article {pmid36910186, year = {2023}, author = {Niu, T and Xu, Y and Chen, J and Qin, L and Li, Z and Yang, Y and Liang, J}, title = {Bacterial taxonomic and functional profiles from Bohai Sea to northern Yellow Sea.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1139950}, pmid = {36910186}, issn = {1664-302X}, abstract = {Microbial distribution patterns are the result of a combination of biotic and abiotic factors, which are the core issues in microbial ecology research. To better understand the biogeographic pattern of bacteria in water environments from the Bohai Sea to the northern Yellow Sea, the effects of environmental factors, and spatial distance on the structure of bacterial communities in marine water were investigated using high-throughput sequencing technology based on 16S rRNA genes. The results showed that Proteobacteria, Bacteroidetes, Actinobacteri, Desulfobacterota, and Bdellovibrionota were the dominant phyla in the study area. A clear spatial pattern in the bacterial community was observed, and environmental factors, including salinity, nutrient concentration, carbon content, total phosphorus, dissolved oxygen, and seawater turbidity emerged as the central environmental factors regulating the variation in bacterial communities. In addition, the study provides direct evidence of the existence of dispersal limitation in this strongly connected marine ecological system. Therefore, these results revealed that the variation in bacterial community characteristics was attributed to environmental selection, accompanied by the regulation of stochastic diffusion. The network analysis demonstrated a nonrandom co-occurrence pattern in the microbial communities with distinct spatial distribution characteristics. It is implied that the biogeography patterns of bacterial community may also be associated with the characteristics of co-occurrence characterize among bacterial species. Furthermore, the PICRUSt analysis indicated a clear spatial distribution of functional characteristics in bacterial communities. This functional variation was significantly modulated by the environmental characteristics of seawater but uncoupled from the taxonomic characteristics of bacterial communities (e.g., diversity characteristics, community structure, and co-occurrence relationships). Together, this findings represent a significant advance in linking seawater to the mechanisms underlying bacterial biogeographic patterns and community assembly, co-occurrence patterns, and ecological functions, providing new insights for identifying the microbial ecology as well as the biogeochemical cycle in the marine environment.}, }
@article {pmid36906178, year = {2023}, author = {Stanhope, J and Weinstein, P}, title = {Exposure to environmental microbiota may modulate gut microbial ecology and the immune system.}, journal = {Mucosal immunology}, volume = {16}, number = {2}, pages = {99-103}, doi = {10.1016/j.mucimm.2023.03.001}, pmid = {36906178}, issn = {1935-3456}, mesh = {*Gastrointestinal Microbiome ; *Microbiota ; Immune System ; }, }
@article {pmid36906027, year = {2023}, author = {Cahill, N and Hooban, B and Fitzhenry, K and Joyce, A and O'Connor, L and Miliotis, G and McDonagh, F and Burke, L and Chueiri, A and Farrell, ML and Bray, JE and Delappe, N and Brennan, W and Prendergast, D and Gutierrez, M and Burgess, C and Cormican, M and Morris, D}, title = {First reported detection of the mobile colistin resistance genes, mcr-8 and mcr-9, in the Irish environment.}, journal = {The Science of the total environment}, volume = {876}, number = {}, pages = {162649}, doi = {10.1016/j.scitotenv.2023.162649}, pmid = {36906027}, issn = {1879-1026}, mesh = {*Colistin/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Wastewater ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; Klebsiella pneumoniae ; Plasmids ; Microbial Sensitivity Tests ; }, abstract = {The emergence and dissemination of mobile colistin resistance (mcr) genes across the globe poses a significant threat to public health, as colistin remains one of the last line treatment options for multi-drug resistant infections. Environmental samples (157 water and 157 wastewater) were collected in Ireland between 2018 and 2020. Samples collected were assessed for the presence of antimicrobial resistant bacteria using Brilliance ESBL, Brilliance CRE, mSuperCARBA and McConkey agar containing a ciprofloxacin disc. All water and integrated constructed wetland influent and effluent samples were filtered and enriched in buffered peptone water prior to culture, while wastewater samples were cultured directly. Isolates collected were identified via MALDI-TOF, were tested for susceptibility to 16 antimicrobials, including colistin, and subsequently underwent whole genome sequencing. Overall, eight mcr positive Enterobacterales (one mcr-8 and seven mcr-9) were recovered from six samples (freshwater (n = 2), healthcare facility wastewater (n = 2), wastewater treatment plant influent (n = 1) and integrated constructed wetland influent (piggery farm waste) (n = 1)). While the mcr-8 positive K. pneumoniae displayed resistance to colistin, all seven mcr-9 harbouring Enterobacterales remained susceptible. All isolates demonstrated multi-drug resistance and through whole genome sequencing analysis, were found to harbour a wide variety of antimicrobial resistance genes i.e., 30 ± 4.1 (10-61), including the carbapenemases, blaOXA-48 (n = 2) and blaNDM-1 (n = 1), which were harboured by three of the isolates. The mcr genes were located on IncHI2, IncFIIK and IncI1-like plasmids. The findings of this study highlight potential sources and reservoirs of mcr genes in the environment and illustrate the need for further research to gain a better understanding of the role the environment plays in the persistence and dissemination of antimicrobial resistance.}, }
@article {pmid36905734, year = {2023}, author = {Ongena, S and de Walle, AV and Mosquera-Romero, S and Driesen, N and Gutierrez, L and Rabaey, K}, title = {Comparison of MBR and MBBR followed by UV or electrochemical disinfection for decentralized greywater treatment.}, journal = {Water research}, volume = {235}, number = {}, pages = {119818}, doi = {10.1016/j.watres.2023.119818}, pmid = {36905734}, issn = {1879-2448}, mesh = {*Waste Disposal, Fluid/methods ; *Escherichia coli ; Disinfection ; Biofilms ; Bioreactors ; Membranes, Artificial ; }, abstract = {Greywater is an attractive source for water reuse at the household or building level, particularly for non-potable applications. Two greywater treatment approaches are membrane bioreactors (MBR) and moving bed biofilm reactors (MBBR), yet, their performance has not been compared so far within their respective treatment flowsheets, including post-disinfection. Two lab-scale treatment trains were operated on synthetic greywater: a) MBR with either polymeric (chlorinated polyethylene, C-PE, 165 days) or ceramic (silicon carbide, SiC, 199 days) membranes coupled with UV disinfection; and b) single-stage (66 days) or two-stage (124 days) MBBR coupled with an electrochemical cell (EC) for in-situ disinfectant generation. Water quality was constantly monitored, and Escherichia coli log removals were assessed through spike tests. Under low-flux operation of the MBR (<8 L·m [-] [2]·h [-] [1]), the SiC membranes delayed the onset of membrane fouling and needed less frequent cleaning compared to C-PE membranes. Both treatment systems met most water quality requirements for unrestricted greywater reuse, at a 10-fold lower reactor volume for the MBR than the MBBR. However, neither the MBR nor the two-staged MBBR allowed adequate nitrogen removal, and the MBBR did not consistently meet effluent chemical oxygen demand and turbidity requirements. Both EC and UV provided non-detectable E. coli concentrations in the effluent. Although the EC provided residual disinfection, scaling and fouling decreased its energetic and disinfection performance over time, making it less efficient than UV disinfection. Several outlines to improve the performance of both treatment trains and disinfection processes are proposed, thus, allowing a fit-for-use approach that leverages the advantages of the respective treatment trains. Results from this investigation will assist in elucidating the most efficient, robust, and low-maintenance technology and configurations for small-scale greywater treatment for reuse.}, }
@article {pmid36901656, year = {2023}, author = {Song, L}, title = {Toward Understanding Microbial Ecology to Restore a Degraded Ecosystem.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {5}, pages = {}, pmid = {36901656}, issn = {1660-4601}, mesh = {Humans ; *Ecosystem ; *Microbiota ; Fecal Microbiota Transplantation ; }, abstract = {The microbial community plays an important role in maintaining human health, addressing climate change, maintaining environmental quality, etc. High-throughput sequencing leads to the discovery and identification of more microbial community composition and function in diverse ecosystems. Microbiome therapeutics such as fecal microbiota transplantation for human health and bioaugmentation for activated sludge restoration have drawn great attention. However, microbiome therapeutics cannot secure the success of microbiome transplantation. This paper begins with a view on fecal microbiota transplantation and bioaugmentation and is followed by a parallel analysis of these two microbial therapeutic strategies. Accordingly, the microbial ecology mechanisms behind them were discussed. Finally, future research on microbiota transplantation was proposed. Successful application of both microbial therapeutics for human disease and bioremediation for contaminated environments relies on a better understanding of the microbial "entangled bank" and microbial ecology of these environments.}, }
@article {pmid36896143, year = {2023}, author = {Pous, N and Bañeras, L and Corvini, PF and Liu, SJ and Puig, S}, title = {Direct ammonium oxidation to nitrogen gas (Dirammox) in Alcaligenes strain HO-1: The electrode role.}, journal = {Environmental science and ecotechnology}, volume = {15}, number = {}, pages = {100253}, pmid = {36896143}, issn = {2666-4984}, abstract = {It has been recently suggested that Alcaligenes use a previously unknown pathway to convert ammonium into dinitrogen gas (Dirammox) via hydroxylamine (NH2OH). This fact alone already implies a significant decrease in the aeration requirements for the process, but the process would still be dependent on external aeration. This work studied the potential use of a polarised electrode as an electron acceptor for ammonium oxidation using the recently described Alcaligenes strain HO-1 as a model heterotrophic nitrifier. Results indicated that Alcaligenes strain HO-1 requires aeration for metabolism, a requirement that cannot be replaced for a polarised electrode alone. However, concomitant elimination of succinate and ammonium was observed when operating a previously grown Alcaligenes strain HO-1 culture in the presence of a polarised electrode and without aeration. The usage of a polarised electrode together with aeration did not increase the succinate nor the nitrogen removal rates observed with aeration alone. However, current density generation was observed along a feeding batch test representing an electron share of 3% of the ammonium removed in the presence of aeration and 16% without aeration. Additional tests suggested that hydroxylamine oxidation to dinitrogen gas could have a relevant role in the electron discharge onto the anode. Therefore, the presence of a polarised electrode supported the metabolic functions of Alcaligenes strain HO-1 on the simultaneous oxidation of succinate and ammonium.}, }
@article {pmid36884370, year = {2023}, author = {Álvarez-Pérez, S and de Vega, C and Vanoirbeek, K and Tsuji, K and Jacquemyn, H and Fukami, T and Michiels, C and Lievens, B}, title = {Phylogenomic analysis of the genus Rosenbergiella and description of Rosenbergiella gaditana sp. nov., Rosenbergiella metrosideri sp. nov., Rosenbergiella epipactidis subsp. epipactidis subsp. nov., Rosenbergiella epipactidis subsp. californiensis subsp. nov., Rosenbergiella epipactidis subsp. japonicus subsp. nov., Rosenbergiella nectarea subsp. nectarea subsp. nov. and Rosenbergiella nectarea subsp. apis subsp. nov., isolated from floral nectar and insects.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {3}, pages = {}, doi = {10.1099/ijsem.0.005777}, pmid = {36884370}, issn = {1466-5034}, mesh = {*Plant Nectar ; Sequence Analysis, DNA ; Phylogeny ; Nucleic Acid Hybridization ; RNA, Ribosomal, 16S/genetics ; *Fatty Acids/chemistry ; Enterobacteriaceae ; Base Composition ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Animals ; Insecta ; Bees ; }, abstract = {The genus Rosenbergiella is one of the most frequent bacterial inhabitants of flowers and a usual member of the insect microbiota worldwide. To date, there is only one publicly available Rosenbergiella genome, corresponding to the type strain of Rosenbergiella nectarea (8N4[T]), which precludes a detailed analysis of intra-genus phylogenetic relationships. In this study, we obtained draft genomes of the type strains of the other Rosenbergiella species validly published to date (R. australiborealis, R. collisarenosi and R. epipactidis) and 23 additional isolates of flower and insect origin. Isolate S61[T], retrieved from the nectar of an Antirrhinum sp. flower collected in southern Spain, displayed low average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values when compared with other Rosenbergiella members (≤86.5 and ≤29.8 %, respectively). Similarly, isolate JB07[T], which was obtained from the floral nectar of Metrosideros polymorpha plants in Hawaii (USA) had ≤95.7 % ANI and ≤64.1 % isDDH with other Rosenbergiella isolates. Therefore, our results support the description of two new Rosenbergiella species for which we propose the names Rosenbergiella gaditana sp. nov. (type strain: S61[T]=NCCB 100789[T]=DSM 111181[T]) and Rosenbergiella metrosideri sp. nov. (JB07[T]=NCCB 100888[T]=LMG 32616[T]). Additionally, some R. epipactidis and R. nectarea isolates showed isDDH values<79 % with other conspecific isolates, which suggests that these species include subspecies for which we propose the names Rosenbergiella epipactidis subsp. epipactidis subsp. nov. (S256[T]=CECT 8502[T]=LMG 27956[T]), Rosenbergiella epipactidis subsp. californiensis subsp. nov. (FR72[T]=NCCB 100898[T]=LMG 32786[T]), Rosenbergiella epipactidis subsp. japonicus subsp. nov. (K24[T]=NCCB 100924[T]=LMG 32785[T]), Rosenbergiella nectarea subsp. nectarea subsp. nov. (8N4[T] = DSM 24150[T] = LMG 26121[T]) and Rosenbergiella nectarea subsp. apis subsp. nov. (B1A[T]=NCCB 100810[T]= DSM 111763[T]), respectively. Finally, we present the first phylogenomic analysis of the genus Rosenbergiella and update the formal description of the species R. australiborealis, R. collisarenosi, R. epipactidis and R. nectarea based on new genomic and phenotypic information.}, }
@article {pmid36882570, year = {2023}, author = {Bourceau, OM and Ferdelman, T and Lavik, G and Mussmann, M and Kuypers, MMM and Marchant, HK}, title = {Simultaneous sulfate and nitrate reduction in coastal sediments.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {17}, pmid = {36882570}, issn = {2730-6151}, abstract = {The oscillating redox conditions that characterize coastal sandy sediments foster microbial communities capable of respiring oxygen and nitrate simultaneously, thereby increasing the potential for organic matter remineralization, nitrogen (N)-loss and emissions of the greenhouse gas nitrous oxide. It is unknown to what extent these conditions also lead to overlaps between dissimilatory nitrate and sulfate respiration. Here, we show that sulfate and nitrate respiration co-occur in the surface sediments of an intertidal sand flat. Furthermore, we found strong correlations between dissimilatory nitrite reduction to ammonium (DNRA) and sulfate reduction rates. Until now, the nitrogen and sulfur cycles were assumed to be mainly linked in marine sediments by the activity of nitrate-reducing sulfide oxidisers. However, transcriptomic analyses revealed that the functional marker gene for DNRA (nrfA) was more associated with microorganisms known to reduce sulfate rather than oxidise sulfide. Our results suggest that when nitrate is supplied to the sediment community upon tidal inundation, part of the sulfate reducing community may switch respiratory strategy to DNRA. Therefore increases in sulfate reduction rate in-situ may result in enhanced DNRA and reduced denitrification rates. Intriguingly, the shift from denitrification to DNRA did not influence the amount of N2O produced by the denitrifying community. Our results imply that microorganisms classically considered as sulfate reducers control the potential for DNRA within coastal sediments when redox conditions oscillate and therefore retain ammonium that would otherwise be removed by denitrification, exacerbating eutrophication.}, }
@article {pmid36881623, year = {2023}, author = {Rohwer, RR and Hale, RJ and Vander Zanden, MJ and Miller, TR and McMahon, KD}, title = {Species invasions shift microbial phenology in a two-decade freshwater time series.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {11}, pages = {e2211796120}, pmid = {36881623}, issn = {1091-6490}, support = {DBI-2011002//National Science Foundation (NSF)/ ; WIS01516//USDA | National Institute of Food and Agriculture (NIFA)/ ; WIS01789//USDA | National Institute of Food and Agriculture (NIFA)/ ; WIS03004//USDA | National Institute of Food and Agriculture (NIFA)/ ; WIS01912//USDA | National Institute of Food and Agriculture (NIFA)/ ; DEB-9632853//National Science Foundation (NSF)/ ; DEB-0217533//National Science Foundation (NSF)/ ; DEB-0822700//National Science Foundation (NSF)/ ; DEB-1440297//National Science Foundation (NSF)/ ; MCB-9977903//National Science Foundation (NSF)/ ; DEB-0702395//National Science Foundation (NSF)/ ; DEB-1344254//National Science Foundation (NSF)/ ; }, mesh = {Animals ; Time Factors ; *Actinobacteria ; Bacteroidetes ; *Cladocera ; *Dreissena ; Fresh Water ; *Microbiota ; }, abstract = {Invasive species impart abrupt changes on ecosystems, but their impacts on microbial communities are often overlooked. We paired a 20 y freshwater microbial community time series with zooplankton and phytoplankton counts, rich environmental data, and a 6 y cyanotoxin time series. We observed strong microbial phenological patterns that were disrupted by the invasions of spiny water flea (Bythotrephes cederströmii) and zebra mussels (Dreissena polymorpha). First, we detected shifts in Cyanobacteria phenology. After the spiny water flea invasion, Cyanobacteria dominance crept earlier into clearwater; and after the zebra mussel invasion, Cyanobacteria abundance crept even earlier into the diatom-dominated spring. During summer, the spiny water flea invasion sparked a cascade of shifting diversity where zooplankton diversity decreased and Cyanobacteria diversity increased. Second, we detected shifts in cyanotoxin phenology. After the zebra mussel invasion, microcystin increased in early summer and the duration of toxin production increased by over a month. Third, we observed shifts in heterotrophic bacteria phenology. The Bacteroidota phylum and members of the acI Nanopelagicales lineage were differentially more abundant. The proportion of the bacterial community that changed differed by season; spring and clearwater communities changed most following the spiny water flea invasion that lessened clearwater intensity, while summer communities changed least following the zebra mussel invasion despite the shifts in Cyanobacteria diversity and toxicity. A modeling framework identified the invasions as primary drivers of the observed phenological changes. These long-term invasion-mediated shifts in microbial phenology demonstrate the interconnectedness of microbes with the broader food web and their susceptibility to long-term environmental change.}, }
@article {pmid36880579, year = {2023}, author = {Chen, L and Wang, G and Teng, M and Wang, L and Yang, F and Jin, G and Du, H and Xu, Y}, title = {Non-gene-editing microbiome engineering of spontaneous food fermentation microbiota-Limitation control, design control, and integration.}, journal = {Comprehensive reviews in food science and food safety}, volume = {22}, number = {3}, pages = {1902-1932}, doi = {10.1111/1541-4337.13135}, pmid = {36880579}, issn = {1541-4337}, mesh = {Fermentation ; *Microbiota ; Food ; Food Microbiology ; }, abstract = {Non-gene-editing microbiome engineering (NgeME) is the rational design and control of natural microbial consortia to perform desired functions. Traditional NgeME approaches use selected environmental variables to force natural microbial consortia to perform the desired functions. Spontaneous food fermentation, the oldest kind of traditional NgeME, transforms foods into various fermented products using natural microbial networks. In traditional NgeME, spontaneous food fermentation microbiotas (SFFMs) are typically formed and controlled manually by the establishment of limiting factors in small batches with little mechanization. However, limitation control generally leads to trade-offs between efficiency and the quality of fermentation. Modern NgeME approaches based on synthetic microbial ecology have been developed using designed microbial communities to explore assembly mechanisms and target functional enhancement of SFFMs. This has greatly improved our understanding of microbiota control, but such approaches still have shortcomings compared to traditional NgeME. Here, we comprehensively describe research on mechanisms and control strategies for SFFMs based on traditional and modern NgeME. We discuss the ecological and engineering principles of the two approaches to enhance the understanding of how best to control SFFM. We also review recent applied and theoretical research on modern NgeME and propose an integrated in vitro synthetic microbiota model to bridge gaps between limitation control and design control for SFFM.}, }
@article {pmid36880421, year = {2023}, author = {Anand, S and Hallsworth, JE and Timmis, J and Verstraete, W and Casadevall, A and Ramos, JL and Sood, U and Kumar, R and Hira, P and Dogra Rawat, C and Kumar, A and Lal, S and Lal, R and Timmis, K}, title = {Weaponising microbes for peace.}, journal = {Microbial biotechnology}, volume = {16}, number = {6}, pages = {1091-1111}, pmid = {36880421}, issn = {1751-7915}, mesh = {Humans ; *Industrial Microbiology ; *Technology ; }, abstract = {There is much human disadvantage and unmet need in the world, including deficits in basic resources and services considered to be human rights, such as drinking water, sanitation and hygiene, healthy nutrition, access to basic healthcare, and a clean environment. Furthermore, there are substantive asymmetries in the distribution of key resources among peoples. These deficits and asymmetries can lead to local and regional crises among peoples competing for limited resources, which, in turn, can become sources of discontent and conflict. Such conflicts have the potential to escalate into regional wars and even lead to global instability. Ergo: in addition to moral and ethical imperatives to level up, to ensure that all peoples have basic resources and services essential for healthy living and to reduce inequalities, all nations have a self-interest to pursue with determination all available avenues to promote peace through reducing sources of conflicts in the world. Microorganisms and pertinent microbial technologies have unique and exceptional abilities to provide, or contribute to the provision of, basic resources and services that are lacking in many parts of the world, and thereby address key deficits that might constitute sources of conflict. However, the deployment of such technologies to this end is seriously underexploited. Here, we highlight some of the key available and emerging technologies that demand greater consideration and exploitation in endeavours to eliminate unnecessary deprivations, enable healthy lives of all and remove preventable grounds for competition over limited resources that can escalate into conflicts in the world. We exhort central actors: microbiologists, funding agencies and philanthropic organisations, politicians worldwide and international governmental and non-governmental organisations, to engage - in full partnership - with all relevant stakeholders, to 'weaponise' microbes and microbial technologies to fight resource deficits and asymmetries, in particular among the most vulnerable populations, and thereby create humanitarian conditions more conducive to harmony and peace.}, }
@article {pmid36875992, year = {2022}, author = {Tadrent, N and Dedeine, F and Hervé, V}, title = {SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes.}, journal = {F1000Research}, volume = {11}, number = {}, pages = {1522}, pmid = {36875992}, issn = {2046-1402}, mesh = {*Metagenome ; Workflow ; *Software ; Metagenomics/methods ; Computational Biology ; }, abstract = {Background: Over the last decade, we have observed in microbial ecology a transition from gene-centric to genome-centric analyses. Indeed, the advent of metagenomics combined with binning methods, single-cell genome sequencing as well as high-throughput cultivation methods have contributed to the continuing and exponential increase of available prokaryotic genomes, which in turn has favored the exploration of microbial metabolisms. In the case of metagenomics, data processing, from raw reads to genome reconstruction, involves various steps and software which can represent a major technical obstacle. Methods: To overcome this challenge, we developed SnakeMAGs, a simple workflow that can process Illumina data, from raw reads to metagenome-assembled genomes (MAGs) classification and relative abundance estimate. It integrates state-of-the-art bioinformatic tools to sequentially perform: quality control of the reads (illumina-utils, Trimmomatic), host sequence removal (optional step, using Bowtie2), assembly (MEGAHIT), binning (MetaBAT2), quality filtering of the bins (CheckM, GUNC), classification of the MAGs (GTDB-Tk) and estimate of their relative abundance (CoverM). Developed with the popular Snakemake workflow management system, it can be deployed on various architectures, from single to multicore and from workstation to computer clusters and grids. It is also flexible since users can easily change parameters and/or add new rules. Results: Using termite gut metagenomic datasets, we showed that SnakeMAGs is slower but allowed the recovery of more MAGs encompassing more diverse phyla compared to another similar workflow named ATLAS. Importantly, these additional MAGs showed no significant difference compared to the other ones in terms of completeness, contamination, genome size nor relative abundance. Conclusions: Overall, it should make the reconstruction of MAGs more accessible to microbiologists. SnakeMAGs as well as test files and an extended tutorial are available at https://github.com/Nachida08/SnakeMAGs.}, }
@article {pmid36878770, year = {2023}, author = {Lyng, M and Kovács, &#xc1;T}, title = {Frenemies of the soil: Bacillus and Pseudomonas interspecies interactions.}, journal = {Trends in microbiology}, volume = {31}, number = {8}, pages = {845-857}, doi = {10.1016/j.tim.2023.02.003}, pmid = {36878770}, issn = {1878-4380}, mesh = {*Pseudomonas/genetics ; *Bacillus/genetics ; Soil ; Soil Microbiology ; Bacteria ; }, abstract = {Bacillus and Pseudomonas ubiquitously occur in natural environments and are two of the most intensively studied bacterial genera in the soil. They are often coisolated from environmental samples, and as a result, several studies have experimentally cocultured bacilli and pseudomonads to obtain emergent properties. Even so, the general interaction between members of these genera is virtually unknown. In the past decade, data on interspecies interactions between natural isolates of Bacillus and Pseudomonas has become more detailed, and now, molecular studies permit mapping of the mechanisms behind their pairwise ecology. This review addresses the current knowledge about microbe-microbe interactions between strains of Bacillus and Pseudomonas and discusses how we can attempt to generalize the interaction on a taxonomic and molecular level.}, }
@article {pmid36877031, year = {2023}, author = {Barnett, SE and Egan, R and Foster, B and Eloe-Fadrosh, EA and Buckley, DH}, title = {Genomic Features Predict Bacterial Life History Strategies in Soil, as Identified by Metagenomic Stable Isotope Probing.}, journal = {mBio}, volume = {14}, number = {2}, pages = {e0358422}, pmid = {36877031}, issn = {2150-7511}, mesh = {*Life History Traits ; Soil/chemistry ; Soil Microbiology ; Bacteria/genetics/metabolism ; Carbon/metabolism ; Isotopes/metabolism ; Metagenomics ; }, abstract = {Bacteria catalyze the formation and destruction of soil organic matter, but the bacterial dynamics in soil that govern carbon (C) cycling are not well understood. Life history strategies explain the complex dynamics of bacterial populations and activities based on trade-offs in energy allocation to growth, resource acquisition, and survival. Such trade-offs influence the fate of soil C, but their genomic basis remains poorly characterized. We used multisubstrate metagenomic DNA stable isotope probing to link genomic features of bacteria to their C acquisition and growth dynamics. We identify several genomic features associated with patterns of bacterial C acquisition and growth, notably genomic investment in resource acquisition and regulatory flexibility. Moreover, we identify genomic trade-offs defined by numbers of transcription factors, membrane transporters, and secreted products, which match predictions from life history theory. We further show that genomic investment in resource acquisition and regulatory flexibility can predict bacterial ecological strategies in soil. IMPORTANCE Soil microbes are major players in the global carbon cycle, yet we still have little understanding of how the carbon cycle operates in soil communities. A major limitation is that carbon metabolism lacks discrete functional genes that define carbon transformations. Instead, carbon transformations are governed by anabolic processes associated with growth, resource acquisition, and survival. We use metagenomic stable isotope probing to link genome information to microbial growth and carbon assimilation dynamics as they occur in soil. From these data, we identify genomic traits that can predict bacterial ecological strategies which define bacterial interactions with soil carbon.}, }
@article {pmid36876069, year = {2023}, author = {Ge, W and Ren, Y and Dong, C and Shao, Q and Bai, Y and He, Z and Yao, T and Zhang, Y and Zhu, G and Deshmukh, SK and Han, Y}, title = {New perspective: Symbiotic pattern and assembly mechanism of Cantharellus cibarius-associated bacteria.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1074468}, pmid = {36876069}, issn = {1664-302X}, abstract = {Cantharellus cibarius, an ectomycorrhizal fungus belonging to the Basidiomycetes, has significant medicinal and edible value, economic importance, and ecological benefits. However, C. cibarius remains incapable of artificial cultivation, which is thought to be due to the presence of bacteria. Therefore, much research has focused on the relationship between C. cibarius and bacteria, but rare bacteria are frequently overlooked, and symbiotic pattern and assembly mechanism of the bacterial community associated with C. cibarius remain unknown. In this study, the assembly mechanism and driving factors of both abundant and rare bacterial communities of C. cibarius were revealed by the null model. The symbiotic pattern of the bacterial community was examined using a co-occurrence network. Metabolic functions and phenotypes of the abundant and rare bacteria were compared using METAGENassist2, and the impacts of abiotic variables on the diversity of abundant and rare bacteria were examined using partial least squares path modeling. In the fruiting body and mycosphere of C. cibarius, there was a higher proportion of specialist bacteria compared with generalist bacteria. Dispersal limitation dominated the assembly of abundant and rare bacterial communities in the fruiting body and mycosphere. However, pH, 1-octen-3-ol, and total phosphorus of the fruiting body were the main driving factors of bacterial community assembly in the fruiting body, while available nitrogen and total phosphorus of the soil affected the assembly process of the bacterial community in the mycosphere. Furthermore, bacterial co-occurrence patterns in the mycosphere may be more complex compared with those in the fruiting body. Unlike the specific potential functions of abundant bacteria, rare bacteria may provide supplementary or unique metabolic pathways (such as sulfite oxidizer and sulfur reducer) to enhance the ecological function of C. cibarius. Notably, while volatile organic compounds can reduce mycosphere bacterial diversity, they can increase fruiting body bacterial diversity. Findings from this study further, our understanding of C. cibarius-associated microbial ecology.}, }
@article {pmid36876066, year = {2023}, author = {Melcher, M and Hodgskiss, LH and Mardini, MA and Schleper, C and Rittmann, SKR}, title = {Analysis of biomass productivity and physiology of Nitrososphaera viennensis grown in continuous culture.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1076342}, pmid = {36876066}, issn = {1664-302X}, abstract = {Microbial ammonia oxidation is the first and usually rate limiting step in nitrification and is therefore an important step in the global nitrogen cycle. Ammonia-oxidizing archaea (AOA) play an important role in nitrification. Here, we report a comprehensive analysis of biomass productivity and the physiological response of Nitrososphaera viennensis to different ammonium and carbon dioxide (CO2) concentrations aiming to understand the interplay between ammonia oxidation and CO2 fixation of N. viennensis. The experiments were performed in closed batch in serum bottles as well as in batch, fed-batch, and continuous culture in bioreactors. A reduced specific growth rate (μ) of N. viennensis was observed in batch systems in bioreactors. By increasing CO2 gassing μ could be increased to rates comparable to that of closed batch systems. Furthermore, at a high dilution rate (D) in continuous culture (≥ 0.7 of μmax) the biomass to ammonium yield (Y(X/NH3)) increased up to 81.7% compared to batch cultures. In continuous culture, biofilm formation at higher D prevented the determination of D crit. Due to changes in Y(X/NH3) and due to biofilm, nitrite concentration becomes an unreliable proxy for the cell number in continuous cultures at D towards μmax. Furthermore, the obscure nature of the archaeal ammonia oxidation prevents an interpretation in the context of Monod kinetics and thus the determination of K S. Our findings indicate that the physiological response of N. viennensis might be regulated with different enzymatic make-ups, according to the ammonium catalysis rate. We reveal novel insights into the physiology of N. viennensis that are important for biomass production and the biomass yield of AOA. Moreover, our study has implications to the field of archaea biology and microbial ecology by showing that bioprocess technology and quantitative analysis can be applied to decipher environmental factors affecting the physiology and productivity of AOA.}, }
@article {pmid36875535, year = {2022}, author = {Zhang, H and Xing, D and Wu, Y and Jin, R and Liu, D and Deines, P}, title = {Editorial: Microbial ecology and function of the aquatic systems.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1109221}, pmid = {36875535}, issn = {1664-302X}, }
@article {pmid36872509, year = {2023}, author = {Munley, JA and Kelly, LS and Park, G and Gillies, GS and Pons, EE and Kannan, KB and Whitley, EM and Bible, LE and Efron, PA and Nagpal, R and Mohr, AM}, title = {Multicompartmental traumatic injury induces sex-specific alterations in the gut microbiome.}, journal = {The journal of trauma and acute care surgery}, volume = {95}, number = {1}, pages = {30-38}, pmid = {36872509}, issn = {2163-0763}, support = {R01 GM105893/GM/NIGMS NIH HHS/United States ; T32 GM008721/GM/NIGMS NIH HHS/United States ; }, mesh = {Rats ; Animals ; Male ; Female ; *Gastrointestinal Microbiome ; Rats, Sprague-Dawley ; Occludin ; RNA, Ribosomal, 16S ; Lipopolysaccharides ; }, abstract = {BACKGROUND: Previous preclinical studies have demonstrated an altered gut microbiome after traumatic injury; however, the impact of sex on dysbiosis remains unknown. We hypothesized that the "pathobiome" phenotype induced by multicompartmental injuries and chronic stress is host sex specific with unique microbiome signatures.<br><br>METHODS: Male and proestrus female Sprague-Dawley rats (n = 8/group) aged 9 weeks to 11 weeks were subjected to either multicompartmental injury (PT) (lung contusion, hemorrhagic shock, cecectomy, bifemoral pseudofractures), PT plus 2 hours daily chronic restraint stress (PT/CS) or naive controls. Fecal microbiome was measured on Days 0 and 2 using high-throughput 16S rRNA sequencing and Quantitative Insights Into Microbial Ecology bioinformatics analyses. Microbial alpha-diversity was assessed using Chao1 (number of different unique species) and Shannon (species richness and evenness) indices. Beta-diversity was assessed using principle coordinate analysis. Intestinal permeability was evaluated by plasma occludin and lipopolysaccharide binding protein. Histologic evaluation of ileum and colon tissues was scored for injury by a blinded pathologist. Analyses were performed in GraphPad and R, with significance defined as p < 0.05 between males versus females.<br><br>RESULTS: At baseline, females had significantly elevated alpha-diversity (Chao1, Shannon indices) compared with males (p < 0.05) which was no longer present 2 days postinjury in PT and PT/CS. Beta-diversity also differed significantly between males and females after PT (p = 0.01). At Day 2, the microbial composition in PT/CS females was dominated by Bifidobacterium , whereas PT males demonstrated elevated levels of Roseburia (p < 0.01). The PT/CS males had significantly elevated ileum injury scores compared with females (p = 0.0002). Plasma occludin was higher in PT males compared with females (p = 0.004); plasma lipopolysaccharide binding protein was elevated in PT/CS males (p = 0.03).<br><br>CONCLUSION: Multicompartmental trauma induces significant alterations in microbiome diversity and taxa, but these signatures differ by host sex. These findings suggest that sex is an important biological variable that may influence outcomes after severe trauma and critical illness.}, }
@article {pmid36869137, year = {2023}, author = {Rifkin, RF and Vikram, S and Alcorta, J and Ramond, JB and Cowan, DA and Jakobsson, M and Schlebusch, CM and Lombard, M}, title = {Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {240}, pmid = {36869137}, issn = {2399-3642}, support = {NGS-371R-18//National Geographic Society/ ; }, mesh = {Humans ; Child ; *Rickettsia felis ; Africa, Southern ; DNA ; South Africa ; DNA, Ancient ; }, abstract = {The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.}, }
@article {pmid36868548, year = {2023}, author = {Zeng, X and Cao, Y and Wang, L and Wang, M and Wang, Q and Yang, Q}, title = {Viability and transcriptional responses of multidrug resistant E. coli to chromium stress.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {324}, number = {}, pages = {121346}, doi = {10.1016/j.envpol.2023.121346}, pmid = {36868548}, issn = {1873-6424}, mesh = {*Escherichia coli/genetics/metabolism ; *Chromium/toxicity ; Transcriptome ; Reactive Oxygen Species/metabolism ; }, abstract = {The viability of multidrug resistant (MDR) bacteria in environment is critical for the spread of antimicrobial resistance. In this study, two Escherichia coli strains, MDR LM13 and susceptible ATCC25922, were used to elucidate differences in their viability and transcriptional responses to hexavalent chromium (Cr(VI)) stress. The results show that the viability of LM13 was notably higher than that of ATCC25922 under 2-20 mg/L Cr(VI) exposure with bacteriostatic rates of 3.1%-57%, respectively, for LM13 and 0.9%-93.1%, respectively, for ATCC25922. The levels of reactive oxygen species and superoxide dismutase in ATCC25922 were much higher than those in LM13 under Cr(VI) exposure. Additionally, 514 and 765 differentially expressed genes were identified from the transcriptomes of the two strains (log2|FC| > 1, p < 0.05). Among them, 134 up-regulated genes were enriched in LM13 in response to external pressure, but only 48 genes were annotated in ATCC25922. Furthermore, the expression levels of antibiotic resistance genes, insertion sequences, DNA and RNA methyltransferases, and toxin-antitoxin systems were generally higher in LM13 than in ATCC25922. This work shows that MDR LM13 has a stronger viability under Cr(VI) stress, and therefore may promote the dissemination of MDR bacteria in environment.}, }
@article {pmid36866381, year = {2023}, author = {Lin, J and Yu, D and Pan, R and Cai, J and Liu, J and Zhang, L and Wen, X and Peng, X and Cernava, T and Oufensou, S and Migheli, Q and Chen, X and Zhang, X}, title = {Improved YOLOX-Tiny network for detection of tobacco brown spot disease.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1135105}, pmid = {36866381}, issn = {1664-462X}, abstract = {INTRODUCTION: Tobacco brown spot disease caused by Alternaria fungal species is a major threat to tobacco growth and yield. Thus, accurate and rapid detection of tobacco brown spot disease is vital for disease prevention and chemical pesticide inputs.<br><br>METHODS: Here, we propose an improved YOLOX-Tiny network, named YOLO-Tobacco, for the detection of tobacco brown spot disease under open-field scenarios. Aiming to excavate valuable disease features and enhance the integration of different levels of features, thereby improving the ability to detect dense disease spots at different scales, we introduced hierarchical mixed-scale units (HMUs) in the neck network for information interaction and feature refinement between channels. Furthermore, in order to enhance the detection of small disease spots and the robustness of the network, we also introduced convolutional block attention modules (CBAMs) into the neck network.<br><br>RESULTS: As a result, the YOLO-Tobacco network achieved an average precision (AP) of 80.56% on the test set. The AP was 3.22%, 8.99%, and 12.03% higher than that obtained by the classic lightweight detection networks YOLOX-Tiny network, YOLOv5-S network, and YOLOv4-Tiny network, respectively. In addition, the YOLO-Tobacco network also had a fast detection speed of 69 frames per second (FPS).<br><br>DISCUSSION: Therefore, the YOLO-Tobacco network satisfies both the advantages of high detection accuracy and fast detection speed. It will likely have a positive impact on early monitoring, disease control, and quality assessment in diseased tobacco plants.}, }
@article {pmid36864462, year = {2023}, author = {Keuschnig, C and Vogel, TM and Barbaro, E and Spolaor, A and Koziol, K and Björkman, MP and Zdanowicz, C and Gallet, JC and Luks, B and Layton, R and Larose, C}, title = {Selection processes of Arctic seasonal glacier snowpack bacterial communities.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {35}, pmid = {36864462}, issn = {2049-2618}, mesh = {Bayes Theorem ; *Ice Cover ; Seasons ; *Bacteria/genetics ; Biodiversity ; }, abstract = {BACKGROUND: Arctic snowpack microbial communities are continually subject to dynamic chemical and microbial input from the atmosphere. As such, the factors that contribute to structuring their microbial communities are complex and have yet to be completely resolved. These snowpack communities can be used to evaluate whether they fit niche-based or neutral assembly theories.<br><br>METHODS: We sampled snow from 22 glacier sites on 7 glaciers across Svalbard in April during the maximum snow accumulation period and prior to the melt period to evaluate the factors that drive snowpack metataxonomy. These snowpacks were seasonal, accumulating in early winter on bare ice and firn and completely melting out in autumn. Using a Bayesian fitting strategy to evaluate Hubbell's Unified Neutral Theory of Biodiversity at multiple sites, we tested for neutrality and defined immigration rates at different taxonomic levels. Bacterial abundance and diversity were measured and the amount of potential ice-nucleating bacteria was calculated. The chemical composition (anions, cations, organic acids) and particulate impurity load (elemental and organic carbon) of the winter and spring snowpack were also characterized. We used these data in addition to geographical information to assess possible niche-based effects on snow microbial communities using multivariate and variable partitioning analysis.<br><br>RESULTS: While certain taxonomic signals were found to fit the neutral assembly model, clear evidence of niche-based selection was observed at most sites. Inorganic chemistry was not linked directly to diversity, but helped to identify predominant colonization sources and predict microbial abundance, which was tightly linked to sea spray. Organic acids were the most significant predictors of microbial diversity. At low organic acid concentrations, the snow microbial structure represented the seeding community closely, and evolved away from it at higher organic acid concentrations, with concomitant increases in bacterial numbers.<br><br>CONCLUSIONS: These results indicate that environmental selection plays a significant role in structuring snow microbial communities and that future studies should focus on activity and growth. Video Abstract.}, }
@article {pmid36864279, year = {2023}, author = {Ma, X and Ding, J and Ren, H and Xin, Q and Li, Z and Han, L and Liu, D and Zhuo, Z and Liu, C and Ren, Z}, title = {Distinguishable Influence of the Delivery Mode, Feeding Pattern, and Infant Sex on Dynamic Alterations in the Intestinal Microbiota in the First Year of Life.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1799-1813}, pmid = {36864279}, issn = {1432-184X}, support = {2020T130609//China Postdoctoral Science Foundation/ ; 2020T130109ZX//China Postdoctoral Science Foundation/ ; SBGJ2018004//Henan Provincial Medical Science and Technology Project/ ; 2018YFC2000500//National Key Research and Development Program of China/ ; 182102310404//Henan Province Science and Technology Project/ ; 202102310055//Henan Province Science and Technology Project/ ; 21A320055//Key Scientific Research Projects of Higher Education Institutions in Henan Province/ ; 20A320056//and Key Scientific Research Projects of Higher Education Institutions in Henan Province/ ; }, mesh = {Humans ; Infant ; Male ; Female ; Pregnancy ; *Cesarean Section ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Breast Feeding ; Feces/microbiology ; Bacteroidetes/genetics ; Feeding Behavior ; }, abstract = {The delivery mode, the feeding pattern and infant sex significantly influence the development of the infant gut flora. However, the extent to which these factors contribute to the establishment of the gut microbiota at different stages has rarely been studied. The factors that play a dominant role in determining microbial colonization of the infant gut at specific time points are unknown. The purpose of this study was to assess the different contributions of the delivery mode, the feeding pattern and infant sex to the composition of the infant gut microbiome. Here, 213 fecal samples from 55 infants at five ages (0, 1, 3, 6, and 12 months postpartum) were collected, and the composition of the gut microbiota via 16S rRNA sequencing was analyzed. The results showed that the average relative abundances of four genera, Bifidobacterium, Bacteroides, Parabacteroides, and Phascolarctobacterium, were increased in vaginally delivered infants versus cesarean section-delivered infants, while those of ten genera, such as Salmonella and Enterobacter, were reduced. The relative proportions of Anaerococcus and Peptostreptococcaceae were higher in exclusive breastfeeding than in combined feeding, while those of Coriobacteriaceae, Lachnospiraceae and Erysipelotrichaceae were lower. The average relative abundances of two genera, Alistipes and Anaeroglobus, were increased in male infants compared with female infants, whereas those of the phyla Firmicutes and Proteobacteria were reduced. During the first year of life, the average UniFrac distances revealed that the individual difference in the gut microbial composition in vaginally delivered infants was greater than that in cesarean section-delivered infants (P < 0.001) and that infants who received combined feeding had greater individual microbiota differences than exclusively breastfed infants (P < 0.01). The delivery mode, infant sex, and the feeding pattern were the dominant factors determining colonization of the infant gut microbiota at 0 months, from 1 to 6 months, and at 12 months postpartum, respectively. This study demonstrated for the first time that infant sex accounted for the dominant contribution to infant gut microbial development from 1 to 6 months postpartum. More broadly, this study effectively established the extent to which the delivery mode, the feeding pattern and infant sex contribute to the development of the gut microbiota at various time points during the first year of life.}, }
@article {pmid36861302, year = {2023}, author = {Lopes, LD and Futrell, SL and Bergmeyer, E and Hao, J and Schachtman, DP}, title = {Root exudate concentrations of indole-3-acetic acid (IAA) and abscisic acid (ABA) affect maize rhizobacterial communities at specific developmental stages.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {3}, pages = {}, doi = {10.1093/femsec/fiad019}, pmid = {36861302}, issn = {1574-6941}, mesh = {*Abscisic Acid ; *Plant Growth Regulators ; Zea mays ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology ; Bacteria/genetics ; Rhizosphere ; Soil Microbiology ; }, abstract = {Root exudates shape the rhizosphere microbiome, but little is known about the specific compounds in root exudates that are important. Here, we investigated the impacts of the plant-synthesized phytohormones indole-3-acetic acid (IAA) and abscisic acid (ABA) exuded by roots on the maize rhizobacterial communities. To identify maize genotypes that differed in the root exudate concentrations of IAA and ABA, we screened hundreds of inbred lines using a semi-hydroponic system. Twelve genotypes with variable exudate concentrations of IAA and ABA were selected for a replicated field experiment. Bulk soil, rhizosphere, and root endosphere samples were collected at two vegetative and one reproductive maize developmental stage. IAA and ABA concentrations in rhizosphere samples were quantified by liquid chromatography-mass spectrometry. The bacterial communities were analyzed by V4 16S rRNA amplicon sequencing. Results indicated that IAA and ABA concentrations in root exudates significantly affected the rhizobacterial communities at specific developmental stages. ABA impacted the rhizosphere bacterial communities at later developmental stages, whereas IAA affected the rhizobacterial communities at the vegetative stages. This study contributed to our knowledge about the influence that specific root exudate compounds have on the rhizobiome composition, showing that the phytohormones IAA and ABA exuded by roots have a role in the plant-microbiome interactions.}, }
@article {pmid36860022, year = {2023}, author = {Mandal, A and Ghosh, A and Saha, R and Bhadury, P}, title = {Seasonal variability of modern benthic foraminifera assemblages in a mangrove ecosystem from northeast coastal Bay of Bengal.}, journal = {Marine pollution bulletin}, volume = {188}, number = {}, pages = {114679}, doi = {10.1016/j.marpolbul.2023.114679}, pmid = {36860022}, issn = {1879-3363}, mesh = {Humans ; Bays ; Ecosystem ; *Foraminifera ; Seasons ; *Cyclonic Storms ; }, abstract = {Benthic foraminifera assemblages, nutrient dynamics of surface and porewater from 10 intertidal sites spanning over two years (2019-2020) covering two major estuaries in Sundarbans mangrove were evaluated to understand role of seasonal precipitation and primary production (driven by eddy nutrients) with a focus on standing crop. Benthic foraminifera abundance ranged between 280 individuals/10 cc in pre-monsoon (2019), 415 individuals/10 cc in post-monsoon 2019 and 630 individuals/10 cc in post-monsoon (2020). Standing crop was highest in post-monsoon coinciding with eddy nutrients driven stoichiometry and increase in abundance of large diatom cells. Calcareous and agglutinated foraminifer taxa Ammonia sp.1, Quinqueloculina seminulum, Entzia macrescens and Textularia sp. respectively were frequent. Entzia macrescens was found in dense mangrove vegetation sites; exhibited strong relationship with sediment texture and pore water total organic carbon. One of the major findings is mangroves with pneumatophores improves oxygen availability in sediment and leads to an increase in standing crop.}, }
@article {pmid36859706, year = {2023}, author = {Pinheiro, Y and Faria da Mota, F and Peixoto, RS and van Elsas, JD and Lins, U and Mazza Rodrigues, JL and Rosado, AS}, title = {A thermophilic chemolithoautotrophic bacterial consortium suggests a mutual relationship between bacteria in extreme oligotrophic environments.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {230}, pmid = {36859706}, issn = {2399-3642}, support = {BAS/1/1096-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, mesh = {*Actinobacteria ; Carbon ; *Extreme Environments ; *Bacillaceae ; *Alphaproteobacteria ; }, abstract = {A thermophilic, chemolithoautotrophic, and aerobic microbial consortium (termed carbonitroflex) growing in a nutrient-poor medium and an atmosphere containing N2, O2, CO2, and CO is investigated as a model to expand our understanding of extreme biological systems. Here we show that the consortium is dominated by Carbonactinospora thermoautotrophica (strain StC), followed by Sphaerobacter thermophilus, Chelatococcus spp., and Geobacillus spp. Metagenomic analysis of the consortium reveals a mutual relationship among bacteria, with C. thermoautotrophica StC exhibiting carboxydotrophy and carbon-dioxide storage capacity. C. thermoautotrophica StC, Chelatococcus spp., and S. thermophilus harbor genes encoding CO dehydrogenase and formate oxidase. No pure cultures were obtained under the original growth conditions, indicating that a tightly regulated interactive metabolism might be required for group survival and growth in this extreme oligotrophic system. The breadwinner hypothesis is proposed to explain the metabolic flux model and highlight the vital role of C. thermoautotrophica StC (the sole keystone species and primary carbon producer) in the survival of all consortium members. Our data may contribute to the investigation of complex interactions in extreme environments, exemplifying the interconnections and dependency within microbial communities.}, }
@article {pmid36858219, year = {2023}, author = {Ouradou, A and Veillette, M and Bélanger Cayouette, A and Corbin, S and Boulanger, C and Dorner, S and Duchaine, C and Bédard, E}, title = {Effect of odor treatment systems on bioaerosol microbial concentration and diversity from wastewater treatment plants.}, journal = {The Science of the total environment}, volume = {874}, number = {}, pages = {162419}, doi = {10.1016/j.scitotenv.2023.162419}, pmid = {36858219}, issn = {1879-1026}, mesh = {Odorants ; *Legionella ; Bacteria ; *Water Purification/methods ; *Air Pollutants ; Water Microbiology ; }, abstract = {Biofiltration, activated carbon and chemical scrubbing are technologies used for odor control in wastewater treatment plants. These systems may also influence the airborne microbial load in treated air. The study objectives were to 1) evaluate the capacity of three odor control system technologies to reduce the airborne concentration of total bacteria, Legionella, L. pneumophila, non-tuberculous mycobacteria (NTM) and Cladosporium in winter and summer seasons and 2) to describe the microbial ecology of the biofiltration system and evaluate its impact on treated air microbial diversity. A reduction of the total bacterial concentration up to 25 times was observed after odor treatment. Quantification by qPCR revealed the presence of Legionella spp. in all air samples ranging between 26 and 1140 GC/m[3], while L. pneumophila was not detected except for three samples below the limit of quantification. A significant increase of up to 25-fold of Legionella spp. was noticed at the outlet of two of the three treatment systems. NTM were ubiquitously detected before air treatment (up to 2500 GC/m[3]) and were significantly reduced by all 3 systems (up to 13-fold). Cladosporium was measured at low concentrations for each system (< 190 GC/m[3]), with 68 % of the air samples below the limit of detection. Biodiversity results revealed that biofiltration system is an active process that adapts to air pollutants over time. Legionella spp. were detected in significant abundance in the air once treated in winter (up to 27 %). Nevertheless, the abundance of protozoan hosts is low and does not explain the multiplication of Legionella spp. The season remains the most influential factor shaping biodiversity. In summer only, air biofiltration caused a significant enrichment of the biodiversity. Although odor control technologies are not designed for bacterial mitigation, findings from this study suggest their potential to reduce the abundance of some genera harboring pathogenic species.}, }
@article {pmid36858028, year = {2023}, author = {Martins, SJ and Pasche, J and Silva, HAO and Selten, G and Savastano, N and Abreu, LM and Bais, HP and Garrett, KA and Kraisitudomsook, N and Pieterse, CMJ and Cernava, T}, title = {The Use of Synthetic Microbial Communities to Improve Plant Health.}, journal = {Phytopathology}, volume = {113}, number = {8}, pages = {1369-1379}, doi = {10.1094/PHYTO-01-23-0016-IA}, pmid = {36858028}, issn = {0031-949X}, abstract = {Despite the numerous benefits plants receive from probiotics, maintaining consistent results across applications is still a challenge. Cultivation-independent methods associated with reduced sequencing costs have considerably improved the overall understanding of microbial ecology in the plant environment. As a result, now, it is possible to engineer a consortium of microbes aiming for improved plant health. Such synthetic microbial communities (SynComs) contain carefully chosen microbial species to produce the desired microbiome function. Microbial biofilm formation, production of secondary metabolites, and ability to induce plant resistance are some of the microbial traits to consider when designing SynComs. Plant-associated microbial communities are not assembled randomly. Ecological theories suggest that these communities have a defined phylogenetic organization structured by general community assembly rules. Using machine learning, we can study these rules and target microbial functions that generate desired plant phenotypes. Well-structured assemblages are more likely to lead to a stable SynCom that thrives under environmental stressors as compared with the classical selection of single microbial activities or taxonomy. However, ensuring microbial colonization and long-term plant phenotype stability is still one of the challenges to overcome with SynComs, as the synthetic community may change over time with microbial horizontal gene transfer and retained mutations. Here, we explored the advances made in SynCom research regarding plant health, focusing on bacteria, as they are the most dominant microbial form compared with other members of the microbiome and the most commonly found in SynCom studies.}, }
@article {pmid36857007, year = {2023}, author = {Senabio, JA and de Campos Pereira, F and Pietro-Souza, W and Sousa, TF and Silva, GF and Soares, MA}, title = {Enhanced mercury phytoremediation by Pseudomonodictys pantanalensis sp. nov. A73 and Westerdykella aquatica P71.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {54}, number = {2}, pages = {949-964}, pmid = {36857007}, issn = {1678-4405}, support = {.0568258/2014//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Mato Grosso/ ; }, mesh = {*Mercury/metabolism ; Biodegradation, Environmental ; *Ascomycota/metabolism ; Endophytes ; Plant Growth Regulators/metabolism ; *Soil Pollutants/metabolism ; Plant Roots/microbiology ; }, abstract = {Mercury is a non-essential and toxic metal that induces toxicity in most organisms, but endophytic fungi can develop survival strategies to tolerate and respond to metal contaminants and other environmental stressors. The present study demonstrated the potential of mercury-resistant endophytic fungi in phytoremediation. We examined the functional traits involved in plant growth promotion, phytotoxicity mitigation, and mercury phytoremediation in seven fungi strains. The endophytic isolates synthesized the phytohormone indole-3-acetic acid, secreted siderophores, and solubilized phosphate in vitro. Inoculation of maize (Zea mays) plants with endophytes increased plant growth attributes by up to 76.25%. The endophytic fungi stimulated mercury uptake from the substrate and promoted its accumulation in plant tissues (t test, p < 0.05), preferentially in the roots, which thereby mitigated the impacts of metal phytotoxicity. Westerdykella aquatica P71 and the newly identified species Pseudomonodictys pantanalensis nov. A73 were the isolates that presented the best phytoremediation potential. Assembling and annotation of P. pantanalensis A73 and W. aquatica P71 genomes resulted in genome sizes of 45.7 and 31.8 Mb that encoded 17,774 and 11,240 protein-coding genes, respectively. Some clusters of genes detected were involved in the synthesis of secondary metabolites such as dimethylcoprogen (NRPS) and melanin (T1PKS), which are metal chelators with antioxidant activity; mercury resistance (merA and merR1); oxidative stress (PRX1 and TRX1); and plant growth promotion (trpS and iscU). Therefore, both fungi species are potential tools for the bioremediation of mercury-contaminated soils due to their ability to reduce phytotoxicity and assist phytoremediation.}, }
@article {pmid36855215, year = {2023}, author = {Hernandez-Becerra, N and Cliffe, L and Xiu, W and Boothman, C and Lloyd, JR and Nixon, SL}, title = {New microbiological insights from the Bowland shale highlight heterogeneity of the hydraulically fractured shale microbiome.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {14}, pmid = {36855215}, issn = {2524-6372}, support = {2018-000061-02EXTF-00218//Mexican National Council for Science and Technology/ ; NE/R013462/1//NERC/ ; }, abstract = {BACKGROUND: Hydraulically fractured shales offer a window into the deep biosphere, where hydraulic fracturing creates new microbial ecosystems kilometers beneath the surface of the Earth. Studying the microbial communities from flowback fluids that are assumed to inhabit these environments provides insights into their ecophysiology, and in particular their ability to survive in these extreme environments as well as their influence on site operation e.g. via problematic biofouling processes and/or biocorrosion. Over the past decade, research on fractured shale microbiology has focused on wells in North America, with a few additional reported studies conducted in China. To extend the knowledge in this area, we characterized the geochemistry and microbial ecology of two exploratory shale gas wells in the Bowland Shale, UK. We then employed a meta-analysis approach to compare geochemical and 16S rRNA gene sequencing data from our study site with previously published research from geographically distinct formations spanning China, Canada and the USA.<br><br>RESULTS: Our findings revealed that fluids recovered from exploratory wells in the Bowland are characterized by moderate salinity and high microbial diversity. The microbial community was dominated by lineages known to degrade hydrocarbons, including members of Shewanellaceae, Marinobacteraceae, Halomonadaceae and Pseudomonadaceae. Moreover, UK fractured shale communities lacked the usually dominant Halanaerobium lineages. From our meta-analysis, we infer that chloride concentrations play a dominant role in controlling microbial community composition. Spatio-temporal trends were also apparent, with different shale formations giving rise to communities of distinct diversity and composition.<br><br>CONCLUSIONS: These findings highlight an unexpected level of compositional heterogeneity across fractured shale formations, which is not only relevant to inform management practices but also provides insight into the ability of diverse microbial consortia to tolerate the extreme conditions characteristic of the engineered deep subsurface.}, }
@article {pmid36851794, year = {2023}, author = {Dart, E and Fuhrman, JA and Ahlgren, NA}, title = {Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics.}, journal = {Viruses}, volume = {15}, number = {2}, pages = {}, pmid = {36851794}, issn = {1999-4915}, support = {1R01GM120624-01A1/NH/NIH HHS/United States ; }, mesh = {*Bacteriophages/genetics ; Host Specificity ; Metagenome ; Pacific Ocean ; Seasons ; *Synechococcus ; }, abstract = {Cyanophages exert important top-down controls on their cyanobacteria hosts; however, concurrent analysis of both phage and host populations is needed to better assess phage-host interaction models. We analyzed picocyanobacteria Prochlorococcus and Synechococcus and T4-like cyanophage communities in Pacific Ocean surface waters using five years of monthly viral and cellular fraction metagenomes. Cyanophage communities contained thousands of mostly low-abundance (<2% relative abundance) species with varying temporal dynamics, categorized as seasonally recurring or non-seasonal and occurring persistently, occasionally, or sporadically (detected in ≥85%, 15-85%, or <15% of samples, respectively). Viromes contained mostly seasonal and persistent phages (~40% each), while cellular fraction metagenomes had mostly sporadic species (~50%), reflecting that these sample sets capture different steps of the infection cycle-virions from prior infections or within currently infected cells, respectively. Two groups of seasonal phages correlated to Synechococcus or Prochlorococcus were abundant in spring/summer or fall/winter, respectively. Cyanophages likely have a strong influence on the host community structure, as their communities explained up to 32% of host community variation. These results support how both seasonally recurrent and apparent stochastic processes, likely determined by host availability and different host-range strategies among phages, are critical to phage-host interactions and dynamics, consistent with both the Kill-the-Winner and the Bank models.}, }
@article {pmid36849610, year = {2023}, author = {Spescha, A and Zwyssig, M and Hess Hermida, M and Moix, A and Bruno, P and Enkerli, J and Campos-Herrera, R and Grabenweger, G and Maurhofer, M}, title = {When Competitors Join Forces: Consortia of Entomopathogenic Microorganisms Increase Killing Speed and Mortality in Leaf- and Root-Feeding Insect Hosts.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1947-1960}, pmid = {36849610}, issn = {1432-184X}, mesh = {Animals ; Reproducibility of Results ; *Pest Control, Biological ; Insecta ; Larva/microbiology ; *Rhabditida/microbiology ; Plant Leaves ; }, abstract = {Combining different biocontrol agents (BCA) is an approach to increase efficacy and reliability of biological control. If several BCA are applied together, they have to be compatible and ideally work together. We studied the interaction of a previously selected BCA consortium of entomopathogenic pseudomonads (Pseudomonas chlororaphis), nematodes (Steinernema feltiae associated with Xenorhabdus bovienii), and fungi (Metarhizium brunneum). We monitored the infection course in a leaf- (Pieris brassicae) and a root-feeding (Diabrotica balteata) pest insect after simultaneous application of the three BCA as well as their interactions inside the larvae in a laboratory setting. The triple combination caused the highest mortality and increased killing speed compared to single applications against both pests. Improved efficacy against P. brassicae was mainly caused by the pseudomonad-nematode combination, whereas the nematode-fungus combination accelerated killing of D. balteata. Co-monitoring of the three BCA and the nematode-associated Xenorhabdus symbionts revealed that the four organisms are able to co-infect the same larva. However, with advancing decay of the cadaver there is increasing competition and cadaver colonization is clearly dominated by the pseudomonads, which are known for their high competitivity in the plant rhizosphere. Altogether, the combination of the three BCA increased killing efficacy against a Coleopteran and a Lepidopteran pest which indicates that this consortium could be applied successfully against a variety of insect pests.}, }
@article {pmid36847986, year = {2023}, author = {Rawat, J and Kumar, V and Ahlawat, P and Tripathi, LK and Tomar, R and Kumar, R and Dholpuria, S and Gupta, PK}, title = {Current Trends on the Effects of Metal-Based Nanoparticles on Microbial Ecology.}, journal = {Applied biochemistry and biotechnology}, volume = {195}, number = {10}, pages = {6168-6182}, pmid = {36847986}, issn = {1559-0291}, mesh = {Animals ; Ecosystem ; *Metal Nanoparticles/toxicity ; *Nanoparticles ; Soil ; Agriculture ; *Soil Pollutants ; }, abstract = {The growing field of nanotechnology and its many applications have led to the irregular release of nanoparticles (NPs), with unintended effects on the environment and continued contamination of water bodies. Metallic NPs are used more frequently in extreme environmental conditions due to their higher efficiency, which attracts more attention in various applications. Due to improper pre-treatment of biosolids, inefficient wastewater treatment practices, and other unregulated agricultural practices continue to contaminate the environment. In particular, the uncontrolled use of NPs in various industrial applications has led to damage to the microbial flora and caused irreplaceable damage to animals and plants. This study focuses on the effect of different doses, types, and compositions of NP on the ecosystem. The review also mentions the impact of various metallic NPs on microbial ecology, their interactions with microorganisms, ecotoxicity studies, and dosage evaluation of the NPs, mainly focused on the review article. However, further research is still needed to understand the complexity of interactions between NPs and microbes in soil and aquatic ecosystems.}, }
@article {pmid36844628, year = {2023}, author = {Morales-Rodríguez, M and Paniagua-García, L and Narayanan, J and Zamudio-Meza, H and Moreno-Torres, RV and Cortés-González, CC and Juanico-Lorán, JA and Martínez-Pérez, B and Fernández-Retana, J}, title = {Insulin‑like growth factor axis: A potential nanotherapy target for resistant cervical cancer tumors (Review).}, journal = {Oncology letters}, volume = {25}, number = {3}, pages = {128}, pmid = {36844628}, issn = {1792-1082}, abstract = {Cervical cancer is among the most frequently occurring neoplasms worldwide, and it particularly affects individuals in developing countries. Factors such as the low quality of screening tests, the high incidence of locally advanced cancer stages and the intrinsic resistance of certain tumors are the main causes of failure in the treatment of this neoplasm. Due to advances in the understanding of carcinogenic mechanisms and bioengineering research, advanced biological nanomaterials have been manufactured. The insulin-like growth factor (IGF) system comprises multiple growth factor receptors, including IGF receptor 1. These receptors are activated by binding to their respective growth factor ligands, IGF-1 and IGF-2, and insulin, and play an important role in the development, maintenance, progression, survival and treatment resistance of cervical cancer. In the present review, the role of the IGF system in cervical cancer and three nanotechnological applications that use elements of this system are described, namely Trap decoys, magnetic iron oxide nanoparticles and protein nanotubes. Their use in the treatment of resistant cervical cancer tumors is also discussed.}, }
@article {pmid36841075, year = {2023}, author = {Parente, E and Zotta, T and Giavalisco, M and Ricciardi, A}, title = {Metataxonomic insights in the distribution of Lactobacillaceae in foods and food environments.}, journal = {International journal of food microbiology}, volume = {391-393}, number = {}, pages = {110124}, doi = {10.1016/j.ijfoodmicro.2023.110124}, pmid = {36841075}, issn = {1879-3460}, mesh = {Humans ; Animals ; *Lactobacillaceae/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; *Bacteria/genetics ; }, abstract = {Members of the family Lactobacillaceae, which now includes species formerly belonging to the genera Lactobacillus and Pediococcus, but also Leuconostocaceae, are of foremost importance in food fermentations and spoilage, but also as components of animal and human microbiota and as potentially pathogenic microorganisms. Knowledge of the ecological distribution of a given species and genus is important, among other things, for the inclusion in lists of microorganisms with a Qualified Presumption of Safety or with beneficial use. The objective of this work is to use the data in FoodMicrobionet database to obtain quantitative insights (in terms of both abundance and prevalence) on the distribution of these bacteria in foods and food environments. We first explored the reliability of taxonomic assignments using the SILVA v138.1 reference database with full length and partial sequences of the 16S rRNA gene for type strain sequences. Full length 16S rRNA gene sequences allow a reasonably good classification at the genus and species level in phylogenetic trees but shorter sequences (V1-V3, V3-V4, V4) perform much worse, with type strains of many species sharing identical V4 and V3-V4 sequences. Taxonomic assignment at the genus level of 16S rRNA genes sequences and the SILVA v138.1 reference database can be done for almost all genera of the family Lactobacillaceae with a high degree of confidence for full length sequences, and with a satisfactory level of accuracy for the V1-V3 regions. Results for the V3-V4 and V4 region are still acceptable but significantly worse. Taxonomic assignment at the species level for sequences for the V1-V3, V3-V4, V4 regions of the 16S rRNA gene of members of the family Lactobacillaceae is hardly possible and, even for full length sequences, and only 49.9 % of the type strain sequences can be unambiguously assigned to species. We then used the FoodMicrobionet database to evaluate the prevalence and abundance of Lactobacillaceae in food samples and in food related environments. Generalist and specialist genera were clearly evident. The ecological distribution of several genera was confirmed and insights on the distribution and potential origin of rare genera (Dellaglioa, Holzapfelia, Schleiferilactobacillus) were obtained. We also found that combining Amplicon Sequence Variants from different studies is indeed possible, but provides little additional information, even when strict criteria are used for the filtering of sequences.}, }
@article {pmid36838501, year = {2023}, author = {Bai, S and Zhang, J and Qi, X and Zeng, J and Wu, S and Peng, X}, title = {Changes of In Situ Prokaryotic and Eukaryotic Communities in the Upper Sanya River to the Sea over a Nine-Hour Period.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838501}, issn = {2076-2607}, abstract = {The transition areas of riverine, estuarine, and marine environments are particularly valuable for the research of microbial ecology, biogeochemical processes, and other physical-chemical studies. Although a large number of microbial-related studies have been conducted within such systems, the vast majority of sampling have been conducted over a large span of time and distance, which may lead to separate batches of samples receiving interference from different factors, thus increasing or decreasing the variability between samples to some extent. In this study, a new in situ filtration system was used to collect membrane samples from six different sampling sites along the Sanya River, from upstream freshwater to the sea, over a nine-hour period. We used high-throughput sequencing of 16S and 18S rRNA genes to analyze the diversity and composition of prokaryotic and eukaryotic communities. The results showed that the structures of these communities varied according to the different sampling sites. The α-diversity of the prokaryotic and eukaryotic communities both decreased gradually along the downstream course. The structural composition of prokaryotic and eukaryotic communities changed continuously with the direction of river flow; for example, the relative abundances of Rhodobacteraceae and Flavobacteriaceae increased with distance downstream, while Sporichthyaceae and Comamonadaceae decreased. Some prokaryotic taxa, such as Phycisphaeraceae and Chromobacteriaceae, were present nearly exclusively in pure freshwater environments, while some additional prokaryotic taxa, including the SAR86 clade, Clade I, AEGEAN-169 marine group, and Actinomarinaceae, were barely present in pure freshwater environments. The eukaryotic communities were mainly composed of the Chlorellales X, Chlamydomonadales X, Sphaeropleales X, Trebouxiophyceae XX, Annelida XX, and Heteroconchia. The prokaryotic and eukaryotic communities were split into abundant, common, and rare communities for NCM analysis, respectively, and the results showed that assembly of the rare community assembly was more impacted by stochastic processes and less restricted by species dispersal than that of abundant and common microbial communities for both prokaryotes and eukaryotes. Overall, this study provides a valuable reference and new perspectives on microbial ecology during the transition from freshwater rivers to estuaries and the sea.}, }
@article {pmid36838461, year = {2023}, author = {Zhao, RZ and Zhang, WJ and Zhao, ZF and Qiu, XC}, title = {Determinants and Assembly Mechanism of Bacterial Community Structure in Ningxia Section of the Yellow River.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838461}, issn = {2076-2607}, support = {NXYLXK2021A03//Ningxia University first-class discipline (water conservancy engineering) construction subsidy project/ ; 2019BFG02014//Key Research and Development Plan (key project) of Ningxia Hui Autonomous Region/ ; 2020AAC03280//Natural Science Foundation of Ningxia Province/ ; }, abstract = {The Yellow River is a valuable resource in the Ningxia Hui Autonomous Region and plays a vital role in local human activities and biodiversity. Bacteria are a crucial component of river ecosystems, but the driving factors and assembly mechanisms of bacterial community structure in this region remain unclear. Herein, we documented the bacterial community composition, determinants, co-occurrence pattern, and assembly mechanism for surface water and sediment. In comparison to sediment, the bacterioplankton community showed significant seasonal variation, as well as less diversity and abundance. The network topology parameters indicated that the sediment bacterial network was more stable than water, but the bacterioplankton network had higher connectivity. In this lotic ecosystem, CODMn, Chl a, and pH affected the structure of the bacterioplankton community, while TP was the primary factor influencing the structure of the sediment bacterial community. The combined results of the neutral community model and the phylogenetic null model indicate that Bacterial communities in both habitats were mainly affected by stochastic processes, with ecological processes dominated by ecological drift for bacterioplankton and dispersal limitation for sediment bacteria. These results provide essential insights into future research on microbial ecology, environmental monitoring, and classified management in the Ningxia section of the Yellow River.}, }
@article {pmid36838363, year = {2023}, author = {Zwarycz, AS and Whitworth, DE}, title = {Myxobacterial Predation: A Standardised Lawn Predation Assay Highlights Strains with Unusually Efficient Predatory Activity.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838363}, issn = {2076-2607}, abstract = {Myxobacteria prey upon a broad range of microorganisms. Lawn assays are commonly used to quantify myxobacterial predation-myxobacterial suspensions are spotted onto prey lawns, and monitored via spot expansion. The diversity in motility behaviours of myxobacterial strains and differing assay protocols in myxobacteriology laboratories led us to develop a highly-specified assay, which was applied to 28 myxobacterial strains preying on seven phytopathogenic prey species. Generally, prey organisms showed no qualitative differences in their susceptibility/resistance to myxobacterial predation. For most myxobacteria, prey did not stimulate, and in ~50% of cases actively hindered colony expansion. Only ~25% of predator/prey strain combinations exhibited greater colony expansion than in the absence of nutrients. The activity of predatory strains against different prey correlated, implying effective predators may have relatively non-specific predation mechanisms (e.g., broad specificity proteases/lipases), but no correlation was observed between predatory activity and phylogeny. Predation on dead (but intact) or lysed prey cells gave greater colony expansion than on live prey. Occasional strains grew substantially faster on dead compared to lysed cells, or vice-versa. Such differences in accessing nutrients from live, dead and lysed cells indicates there are strain-specific differences in the efficiencies/machineries of prey killing and nutrient acquisition, which has important implications for the ecology of myxobacterial predators and their prey.}, }
@article {pmid36838349, year = {2023}, author = {Pradeep Ram, AS and Sime-Ngando, T}, title = {Differential Effects of Viruses on the Growth Efficiency of Freshwater Bacterioplankton in Eutrophic Relative to Non-Eutrophic Lakes.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838349}, issn = {2076-2607}, abstract = {In aquatic environments, the consensus of viral impact on bacterial carbon metabolism with the nutrient environment as an important axis is limited. Henceforth, we explored the viral regulation of carbon-based bacterial growth efficiency (BGE) in a set of freshwater systems from French Massif Central, which were broadly classified based on two trophic statuses: eutrophic and non-eutrophic lakes. Comparative analysis showed that microbial abundances (viruses and bacteria) were 3-fold higher in eutrophic compared with non-eutrophic lakes, and so were bacterial production and viral lytic infection. The observed variability in BGE (10-60%) was explained by the uncoupling between bacterial respiration and production. Viruses through selective lysis of susceptible host communities had an antagonistic impact on BGE in the eutrophic lakes, whereas the release of substrates via viral shunt exerted a synergistic influence on the carbon metabolism of non-targeted host populations in non-eutrophic lakes. The decisive effect of the two individual processes (i.e., lysis and substrate release) on BGE was supported by regressions of bacterial abundance as a function of bacterial production, which is considered as a proxy of top-down processes. The role of viruses through their negative impact via mortality and positive impact via substrate supply can eventually have implications on carbon transfer through bacterioplankton in freshwaters.}, }
@article {pmid36836352, year = {2023}, author = {Adedayo, AA and Babalola, OO}, title = {Fungi That Promote Plant Growth in the Rhizosphere Boost Crop Growth.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {2}, pages = {}, pmid = {36836352}, issn = {2309-608X}, support = {UID132595//The National Research Foundation of South Africa grant/ ; }, abstract = {The fungi species dwelling in the rhizosphere of crop plants, revealing functions that endeavor sustainability of the plants, are commonly referred to as 'plant-growth-promoting fungi' (PGPF). They are biotic inducers that provide benefits and carry out important functions in agricultural sustainability. The problem encountered in the agricultural system nowadays is how to meet population demand based on crop yield and protection without putting the environment and human and animal health at risk based on crop production. PGPF including Trichoderma spp., Gliocladium virens, Penicillium digitatum, Aspergillus flavus, Actinomucor elegans, Podospora bulbillosa, Arbuscular mycorrhizal fungi, etc., have proven their ecofriendly nature to ameliorate the production of crops by improving the growth of the shoots and roots of crop plants, the germination of seeds, the production of chlorophyll for photosynthesis, and the abundant production of crops. PGPF's potential mode of action is as follows: the mineralization of the major and minor elements required to support plants' growth and productivity. In addition, PGPF produce phytohormones, induced resistance, and defense-related enzymes to inhibit or eradicate the invasion of pathogenic microbes, in other words, to help the plants while encountering stress. This review portrays the potential of PGPF as an effective bioagent to facilitate and promote crop production, plant growth, resistance to disease invasion, and various abiotic stresses.}, }
@article {pmid36836247, year = {2023}, author = {Wang, J and Qin, S and Fan, R and Peng, Q and Hu, X and Yang, L and Liu, Z and Baccelli, I and Migheli, Q and Berg, G and Chen, X and Cernava, T}, title = {Plant Growth Promotion and Biocontrol of Leaf Blight Caused by Nigrospora sphaerica on Passion Fruit by Endophytic Bacillus subtilis Strain GUCC4.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {2}, pages = {}, pmid = {36836247}, issn = {2309-608X}, support = {2021YFE0107700//National Key research and Development of China/ ; Guike AA21196003//Science and Technology Base &amp; Talent Project of Guangxi Province/ ; 2019-1410;2021-229;HZJD[2022]001//Guizhou Provincial Science and Technology Program/ ; KY2021-026//Outstanding Young Scientist Program of Guizhou Province/ ; 2022-36-Z01-KF12//Guangxi Key Laboratory of Rice Genetics and Breeding Opening Research Project/ ; 111 Program; D20023//Guizhou University Cultivation Project 2019-04 and Program for Introducing Talents to Chinese Universities/ ; }, abstract = {Passion fruit (Passiflora edulis Sims) is widely cultivated in tropic and sub-tropic regions for the production of fruit, flowers, cosmetics, and for pharmacological applications. Its high economic, nutritional, and medical values elicit the market demand, and the growing areas are rapidly increasing. Leaf blight caused by Nigrospora sphaerica is a new and emerging disease of passion fruit in Guizhou, in southwest China, where the unique karst mountainous landscape and climate conditions are considered potential areas of expansion for passion fruit production. Bacillus species are the most common biocontrol and plant-growth-promotion bacteria (PGPB) resources in agricultural systems. However, little is known about the endophytic existence of Bacillus spp. in the passion fruit phyllosphere as well as their potential as biocontrol agents and PGPB. In this study, 44 endophytic strains were isolated from 15 healthy passion fruit leaves, obtained from Guangxi province, China. Through purification and molecular identification, 42 of the isolates were ascribed to Bacillus species. Their inhibitory activity against N. sphaerica was tested in vitro. Eleven endophytic Bacillus spp. strains inhibited the pathogen by >65%. All of them produced biocontrol- and plant-growth-promotion-related metabolites, including indole-3-acetic acid (IAA), protease, cellulase, phosphatase, and solubilized phosphate. Furthermore, the plant growth promotion traits of the above 11 endophytic Bacillus strains were tested on passion fruit seedlings. One isolate, coded B. subtilis GUCC4, significantly increased passion fruit stem diameter, plant height, leaf length, leaf surface, fresh weight, and dry weight. In addition, B. subtilis GUCC4 reduced the proline content, which indicated its potential to positively regulate passion fruit biochemical properties and resulted in plant growth promotion effects. Finally, the biocontrol efficiencies of B. subtilis GUCC4 against N. sphaerica were determined in vivo under greenhouse conditions. Similarly to the fungicide mancozeb and to a commercial B. subtilis-based biofungicide, B. subtilis GUCC4 significantly reduced disease severity. These results suggest that B. subtilis GUCC4 has great potential as a biological control agent and as PGPB on passion fruit.}, }
@article {pmid36835503, year = {2023}, author = {Alsayed, AR and Abed, A and Khader, HA and Al-Shdifat, LMH and Hasoun, L and Al-Rshaidat, MMD and Alkhatib, M and Zihlif, M}, title = {Molecular Accounting and Profiling of Human Respiratory Microbial Communities: Toward Precision Medicine by Targeting the Respiratory Microbiome for Disease Diagnosis and Treatment.}, journal = {International journal of molecular sciences}, volume = {24}, number = {4}, pages = {}, pmid = {36835503}, issn = {1422-0067}, mesh = {Humans ; *Precision Medicine ; Prospective Studies ; Lung/microbiology ; *Microbiota/genetics ; Bacteria/genetics ; }, abstract = {The wide diversity of microbiota at the genera and species levels across sites and individuals is related to various causes and the observed differences between individuals. Efforts are underway to further understand and characterize the human-associated microbiota and its microbiome. Using 16S rDNA as a genetic marker for bacterial identification improved the detection and profiling of qualitative and quantitative changes within a bacterial population. In this light, this review provides a comprehensive overview of the basic concepts and clinical applications of the respiratory microbiome, alongside an in-depth explanation of the molecular targets and the potential relationship between the respiratory microbiome and respiratory disease pathogenesis. The paucity of robust evidence supporting the correlation between the respiratory microbiome and disease pathogenesis is currently the main challenge for not considering the microbiome as a novel druggable target for therapeutic intervention. Therefore, further studies are needed, especially prospective studies, to identify other drivers of microbiome diversity and to better understand the changes in the lung microbiome along with the potential association with disease and medications. Thus, finding a therapeutic target and unfolding its clinical significance would be crucial.}, }
@article {pmid36834682, year = {2023}, author = {Deng, Q and Liu, H and Lu, Q and Gangurde, SS and Du, P and Li, H and Li, S and Liu, H and Wang, R and Huang, L and Chen, R and Fan, C and Liang, X and Chen, X and Hong, Y}, title = {Silicon Application for the Modulation of Rhizosphere Soil Bacterial Community Structures and Metabolite Profiles in Peanut under Ralstonia solanacearum Inoculation.}, journal = {International journal of molecular sciences}, volume = {24}, number = {4}, pages = {}, pmid = {36834682}, issn = {1422-0067}, support = {2020B020219003 and 2022B0202060004//Guangdong Provincial Key Research and Development Program-Modern Seed Industry/ ; CARS-13//China Agriculture Research System of MOF and MARA/ ; 32001442 and 32172051//National Natural Science Foundation of China/ ; 2021M700895//China Postdoctoral Science Foundation/ ; 2020A1515010021 and 2021A1515010811//Guangdong Basic and Applied Basic Research Foundation/ ; 20200503//Guangdong Provincial Department of Science and Technology Project- International Scientific and Technological Cooperation/ ; 2019KJ136-02//Technology Special Fund of Guangdong Province Agriculture and Rural Affairs Department/ ; 202201010281//Guangzhou Basic and Applied Basic Research Foundation/ ; 202104TD//Agricultural Competitive Industry Discipline Team Building Project of Guangdong Academy of Agricultural Sciences/ ; R2020PY-JX004, R2020PY-JG005 and R2021PY-QY003//Special Fund for Scientific Innovation Strategy-Construction of High Level Academy of Agriculture Science/ ; 202101//Foundation of Director of Crop Research Institute of Guangdong Academy of Agriculture Sciences/ ; 202201//Open Fund of Guangdong Provincial Key Laboratory of Crop Genetic Improvement/ ; 2021A0505030047//Science and Technology Planning Project of Guangdong Province/ ; 20171BBF60036//Jiangxi Provincial Key R&amp;D Program Project/ ; }, mesh = {*Arachis/genetics ; *Ralstonia solanacearum/metabolism ; Silicon/metabolism ; Soil/chemistry ; Rhizosphere ; Bacteria/metabolism ; Plant Diseases/microbiology ; }, abstract = {Silicon (Si) has been shown to promote peanut growth and yield, but whether Si can enhance the resistance against peanut bacterial wilt (PBW) caused by Ralstonia solanacearum, identified as a soil-borne pathogen, is still unclear. A question regarding whether Si enhances the resistance of PBW is still unclear. Here, an in vitro R. solanacearum inoculation experiment was conducted to study the effects of Si application on the disease severity and phenotype of peanuts, as well as the microbial ecology of the rhizosphere. Results revealed that Si treatment significantly reduced the disease rate, with a decrement PBW severity of 37.50% as compared to non-Si treatment. The soil available Si (ASi) significantly increased by 13.62-44.87%, and catalase activity improved by 3.01-3.10%, which displayed obvious discrimination between non-Si and Si treatments. Furthermore, the rhizosphere soil bacterial community structures and metabolite profiles dramatically changed under Si treatment. Three significantly changed bacterial taxa were observed, which showed significant abundance under Si treatment, whereas the genus Ralstonia genus was significantly suppressed by Si. Similarly, nine differential metabolites were identified to involve into unsaturated fatty acids via a biosynthesis pathway. Significant correlations were also displayed between soil physiochemical properties and enzymes, the bacterial community, and the differential metabolites by pairwise comparisons. Overall, this study reports that Si application mediated the evolution of soil physicochemical properties, the bacterial community, and metabolite profiles in the soil rhizosphere, which significantly affects the colonization of the Ralstonia genus and provides a new theoretical basis for Si application in PBW prevention.}, }
@article {pmid36834619, year = {2023}, author = {Cruz-Rubio, JM and Riva, A and Cybulska, J and Zdunek, A and Berry, D and Loeppert, R and Viernstein, H and Praznik, W and Maghuly, F}, title = {Neutral and Pectic Heteropolysaccharides Isolated from Opuntia joconostle Mucilage: Composition, Molecular Dimensions and Prebiotic Potential.}, journal = {International journal of molecular sciences}, volume = {24}, number = {4}, pages = {}, pmid = {36834619}, issn = {1422-0067}, support = {Scholarship 440539//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; }, mesh = {*Opuntia/chemistry ; Prebiotics ; Plant Breeding ; Polysaccharides/chemistry ; Galactans ; }, abstract = {Opuntia joconostle is a semi-wild cactus cultivated for its fruit. However, the cladodes are often discarded, wasting the potentially useful mucilage in them. The mucilage is composed primarily of heteropolysaccharides, characterized by their molar mass distribution, monosaccharide composition, structural features (by vibrational spectroscopy, FT IR, and atomic force microscopy, AFM), and fermentability by known saccharolytic commensal members of the gut microbiota. After fractionation with ion exchange chromatography, four polysaccharides were found: one neutral (composed mainly of galactose, arabinose, and xylose) and three acidic, with a galacturonic acid content from 10 to 35%mol. Their average molar masses ranged from 1.8 × 10[5] to 2.8 × 10[5] g·mol[-1]. Distinct structural features such as galactan, arabinan, xylan, and galacturonan motifs were present in the FT IR spectra. The intra- and intermolecular interactions of the polysaccharides, and their effect on the aggregation behavior, were shown by AFM. The composition and structural features of these polysaccharides were reflected in their prebiotic potential. Lactobacilli and Bifidobacteria were not able to utilize them, whereas members of Bacteroidetes showed utilization capacity. The obtained data suggest a high economic potential for this Opuntia species, with potential uses such as animal feed in arid areas, precise prebiotic, and symbiotic formulations, or as the carbon skeleton source in a green refinery. Our methodology can be used to evaluate the saccharides as the phenotype of interest, helping to guide the breeding strategy.}, }
@article {pmid36826588, year = {2023}, author = {Morris, N and Alldred, M and Zarnoch, C and Alter, SE}, title = {Estuarine Sediment Microbiomes from a Chronosequence of Restored Urban Salt Marshes.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {916-930}, pmid = {36826588}, issn = {1432-184X}, mesh = {*Wetlands ; Ecosystem ; RNA, Ribosomal, 16S/genetics/metabolism ; Geologic Sediments/microbiology ; *Microbiota ; Bacteria ; Nitrogen/metabolism ; Carbon/metabolism ; }, abstract = {Salt marshes play an important role in the global nutrient cycle. The sediments in these systems harbor diverse and complex bacterial communities possessing metabolic capacities that provide ecosystem services such as nutrient cycling and removal. On the East Coast of the USA, salt marshes have been experiencing degradation due to anthropogenic stressors. Salt marsh islands within Jamaica Bay, New York City (USA), are surrounded by a large highly urbanized watershed and have declined in area. Restoration efforts have been enacted to reduce further loss, but little is known about how microbial communities develop following restoration activities, or how processes such as nitrogen cycling are impacted. Sediment samples were collected at two sampling depths from five salt marsh islands to characterize the bacterial communities found in marsh sediment including a post-restoration chronosequence of 3-12 years. We used 16s rRNA amplicon sequencing to define alpha and beta diversity, taxonomic composition, and predicted metabolic profile of each sediment sample. We found significant differences in alpha diversity between sampling depths, and significant differences in beta diversity, taxonomic composition, and predicted metabolic capacity among the five sampling locations. The youngest restored site and the degraded natural sampling site exhibited the most distinct communities among the five sites. Our findings suggest that while the salt marsh islands are located in close proximity to each other, they harbor distinct bacterial communities that can be correlated with post-restoration age, marsh health, and other environmental factors such as availability of organic carbon. IMPORTANCE: Salt marshes play a critical role in the global nutrient cycle due to sediment bacteria and their metabolic capacities. Many East Coast salt marshes have experienced significant degradation over recent decades, thought largely to be due to anthropogenic stressors such as nitrogen loading, urban development, and sea-level rise. Salt marsh islands in Jamaica Bay (Queens/Brooklyn NY) are exposed to high water column nitrogen due to wastewater effluent. Several receding marsh islands have been subjected to restoration efforts to mitigate this loss. Little is known about the effect marsh restoration has on bacterial communities, their metabolic capacity, or how they develop post-restoration. Here, we describe the bacterial communities found in marsh islands including a post-restoration chronosequence of 3-12 years and one degraded marsh island that remains unrestored. We found distinct communities at marsh sites, despite their geographic proximity. Differences in diversity and community composition were consistent with changes in organic carbon availability that occur during marsh development, and may result in differences in ecosystem function among sites.}, }
@article {pmid36826587, year = {2023}, author = {Lemke, M and DeSalle, R}, title = {The Next Generation of Microbial Ecology and Its Importance in Environmental Sustainability.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {781-795}, pmid = {36826587}, issn = {1432-184X}, mesh = {*Ecology ; Genomics ; *Microbiota ; Genome, Bacterial ; }, abstract = {Collectively, we have been reviewers for microbial ecology, genetics and genomics studies that include environmental DNA (eDNA), microbiome studies, and whole bacterial genome biology for Microbial Ecology and other journals for about three decades. Here, we wish to point out trends and point to areas of study that readers, especially those moving into the next generation of microbial ecology research, might learn and consider. In this communication, we are not saying the work currently being accomplished in microbial ecology and restoration biology is inadequate. What we are saying is that a significant milestone in microbial ecology has been reached, and approaches that may have been overlooked or were unable to be completed before should be reconsidered in moving forward into a new more ecological era where restoration of the ecological trajectory of systems has become critical. It is our hope that this introduction, along with the papers that make up this special issue, will address the sense of immediacy and focus needed to move into the next generation of microbial ecology study.}, }
@article {pmid36825884, year = {2023}, author = {Thiele, S and Vader, A and Øvreås, L}, title = {The mystery of the ice cold rose-Microbiome of an Arctic winter frost flower.}, journal = {MicrobiologyOpen}, volume = {12}, number = {1}, pages = {e1345}, pmid = {36825884}, issn = {2045-8827}, mesh = {RNA, Ribosomal, 16S/genetics ; Arctic Regions ; *Bacteria ; *Microbiota ; Archaea/genetics ; Flowers ; Ice Cover/microbiology ; }, abstract = {Under very cold conditions, delicate ice-crystal structures called frost flowers emerge on the surface of newly formed sea ice. These understudied, ephemeral structures include saline brine, organic material, inorganic nutrients, and bacterial and archaeal communities in their brine channels. Hitherto, only a few frost flowers have been studied during spring and these have been reported to be dominated by Rhizobia or members of the SAR11 clade. Here we report on the microbiome of frost flowers sampled during the winter and polar night in the Barents Sea. There was a distinct difference in community profile between the extracted DNA and RNA, but both were dominated by members of the SAR11 clade (78% relative abundance and 41.5% relative activity). The data further suggested the abundance and activity of Cand. Nitrosopumilus, Nitrospinia, and Nitrosomonas. Combined with the inference of marker genes based on the 16S rRNA gene data, this indicates that sulfur and nitrogen cycling are likely the major metabolism in these ephemeral structures.}, }
@article {pmid36825091, year = {2023}, author = {Bogdan, DF and Baricz, AI and Chiciudean, I and Bulzu, PA and Cristea, A and Năstase-Bucur, R and Levei, EA and Cadar, O and Sitar, C and Banciu, HL and Moldovan, OT}, title = {Diversity, distribution and organic substrates preferences of microbial communities of a low anthropic activity cave in North-Western Romania.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {962452}, pmid = {36825091}, issn = {1664-302X}, abstract = {INTRODUCTION: Karst caves are characterized by relatively constant temperature, lack of light, high humidity, and low nutrients availability. The diversity and functionality of the microorganisms dwelling in caves micro-habitats are yet underexplored. Therefore, in-depth investigations of these ecosystems aid in enlarging our understanding of the microbial interactions and microbially driven biogeochemical cycles. Here, we aimed at evaluating the diversity, abundance, distribution, and organic substrate preferences of microbial communities from Peștera cu Apă din Valea Leșului (Leșu Cave) located in the Apuseni Mountains (North-Western Romania).<br><br>MATERIALS AND METHODS: To achieve this goal, we employed 16S rRNA gene amplicon sequencing and community-level physiological profiling (CLPP) paralleled by the assessment of environmental parameters of cave sediments and water.<br><br>RESULTS AND DISCUSSION: Pseudomonadota (synonym Proteobacteria) was the most prevalent phylum detected across all samples whereas the abundance detected at order level varied among sites and between water and sediment samples. Despite the general similarity at the phylum-level in Le&#x219;u Cave across the sampled area, the results obtained in this study suggest that specific sites drive bacterial community at the order-level, perhaps sustaining the enrichment of unique bacterial populations due to microenvironmental conditions. For most of the dominant orders the distribution pattern showed a positive correlation with C-sources such as putrescine, &#x3b3;-amino butyric acid, and D-malic acid, while particular cases were positively correlated with polymers (Tween 40, Tween 80 and &#x3b1;-cyclodextrin), carbohydrates (&#x3b1;-D-lactose, i-erythritol, D-mannitol) and most of the carboxylic and ketonic acids. Physicochemical analysis reveals that sediments are geochemically distinct, with increased concentration of Ca, Fe, Al, Mg, Na and K, whereas water showed low nitrate concentration. Our PCA indicated the clustering of different dominant orders with Mg, As, P, Fe, and Cr. This information serves as a starting point for further studies in elucidating the links between the taxonomic and functional diversity of subterranean microbial communities.}, }
@article {pmid36823577, year = {2023}, author = {Shao, K and Zhang, L and Ba, T and Chao, J and Gao, G}, title = {Bacterial community composition of the sediment in Sayram Lake, an alpine lake in the arid northwest of China.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {47}, pmid = {36823577}, issn = {1471-2180}, mesh = {*Lakes/microbiology ; Geologic Sediments/microbiology ; Bacteria/genetics ; *Microbiota ; China ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Sediment bacterial communities play a critical role in biogeochemical cycling in alpine lake ecosystems. However, little is known about the sediment microbial communities in these lakes. In this study, the bacterial community composition (BCC) and their relationships with environmental factors of the sediment in Sayram Lake, the largest alpine and cold-water inland lake, China was analyzed using Illumina MiSeq sequencing. In total, we obtained 618,271 high quality sequences. The results showed that the bacterial communities with 30 phyla and 546 genera, were spread out among the 5 furface sediment samples, respectively. The communities were dominated by Proteobacteria, Acidobacteria, Planctomycetes, Gemmatimonadetes, Chloroflexi, Actinobacteria, Verrucomicrobia and Bacteroidetes, accounting for 48.15 ± 8.10%, 11.23 ± 3.10%, 8.42 ± 2.15%, 8.37 ± 2.26%, 7.40 ± 3.05%, 5.62 ± 1.25%, 4.18 ± 2.12% and 2.24 ± 1.10% of the total reads, respectively. At the genus level, the communities were dominated by Aquabacterium, Pseudomonas, Woeseia, MND1, Ignavibacterium and Truepera, accounting for 7.89% ± 8.24%, 2.32% ± 1.05%, 2.14% ± 0.94%, 2% ± 1.22%, 0.94% ± 0.14% and 0.80% ± 0.14% of the total reads, respectively. Statistical analyses showed the similarity of the sediment bacterial communities at our field sites was considerably low, far below 35%, and total organic carbon (TOC) was the dominant environmental factor affecting the spatial changes of BCC in the sediment. Thus, this study greatly improving our understanding of the microbial ecology of alpine lake in the arid and semi-arid ecosystems today so seriously threatened.}, }
@article {pmid36822952, year = {2023}, author = {Pilosof, S}, title = {Conceptualizing microbe-plasmid communities as complex adaptive systems.}, journal = {Trends in microbiology}, volume = {31}, number = {7}, pages = {672-680}, doi = {10.1016/j.tim.2023.01.007}, pmid = {36822952}, issn = {1878-4380}, mesh = {*Ecology ; *Microbiota ; Plasmids/genetics ; Microbial Interactions ; }, abstract = {Plasmids shape microbial communities' diversity, structure, and function. Nevertheless, we lack a mechanistic understanding of how community structure and dynamics emerge from local microbe-plasmid interactions and coevolution. Addressing this gap is challenging because multiple processes operate simultaneously at multiple levels of organization. For example, immunity operates between a plasmid and a cell, but incompatibility mechanisms regulate coexistence between plasmids. Conceptualizing microbe-plasmid communities as complex adaptive systems is a promising approach to overcoming these challenges. I illustrate how agent-based evolutionary modeling, extended by network analysis, can be used to quantify the relative importance of local processes governing community dynamics. These theoretical developments can advance our understanding of plasmid ecology and evolution, especially when combined with empirical data.}, }
@article {pmid36821051, year = {2023}, author = {Karnachuk, OV and Panova, IA and Rusanov, II and Schetinina, L and Lepokurova, OY and Domrocheva, EV and Kadnikov, VV and Avakyan, MR and Lukina, AP and Glukhova, LB and Pimenov, NV and Ravin, NV}, title = {Coexistence of Psychrophilic, Mesophilic, and Thermophilic Sulfate-Reducing Bacteria in a Deep Subsurface Aquifer Associated with Coal-Bed Methane Production.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1934-1946}, pmid = {36821051}, issn = {1432-184X}, support = {21-14-00114//Russian Science Foundation/ ; 22-14-00178//Russian Science Foundation/ ; }, mesh = {Bacteria ; Coal/microbiology ; RNA, Ribosomal, 16S/genetics ; *Desulfovibrio/genetics ; Water ; Methane ; *Groundwater ; Sulfates ; }, abstract = {The microbial community of subsurface environments remains understudied due to limited access to deep strata and aquifers. Coal-bed methane (CBM) production is associated with a large number of wells pumping water out of coal seams. CBM wells provide access to deep biotopes associated with coal-bed water. Temperature is one of the key constraints for the distribution and activity of subsurface microorganisms, including sulfate-reducing prokaryotes (SRP). The 16S rRNA gene amplicon sequencing coupled with in situ sulfate reduction rate (SRR) measurements with a radioactive tracer and cultivation at various temperatures revealed that the SRP community of the coal bed water of the Kuzbass coal basin is characterized by an overlapping mesophilic-psychrophilic boundary. The genus Desulfovibrio comprised a significant share of the SRP community. The D. psychrotolerans strain 1203, which has a growth optimum below 20 °C, dominated the cultivated SRP. SRR in coal bed water varied from 0.154 ± 0.07 to 2.04 ± 0.048 nmol S cm[-3] day[-1]. Despite the ambient water temperature of ~ 10-20 °C, an active thermophilic SRP community occurred in the fracture water, which reduced sulfate with the rate of 0.159 ± 0.023 to 0.198 ± 0.007 nmol S cm[-3] day[-1] at 55 °C. A novel moderately thermophilic "Desulforudis audaxviator"-clade SRP has been isolated in pure culture from the coal-bed water.}, }
@article {pmid36820832, year = {2023}, author = {Rosas-Salazar, C and Kimura, KS and Shilts, MH and Strickland, BA and Freeman, MH and Wessinger, BC and Gupta, V and Brown, HM and Boone, HH and Rajagopala, SV and Turner, JH and Das, SR}, title = {Upper respiratory tract microbiota dynamics following COVID-19 in adults.}, journal = {Microbial genomics}, volume = {9}, number = {2}, pages = {}, pmid = {36820832}, issn = {2057-5858}, support = {R21 AI154016/AI/NIAID NIH HHS/United States ; R21 AI149262/AI/NIAID NIH HHS/United States ; R21 AI142321/AI/NIAID NIH HHS/United States ; R01 HL146401/HL/NHLBI NIH HHS/United States ; K23 HL148638/HL/NHLBI NIH HHS/United States ; UL1 RR024975/RR/NCRR NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; P30 EY008126/EY/NEI NIH HHS/United States ; G20 RR030956/RR/NCRR NIH HHS/United States ; }, mesh = {Humans ; Adult ; Middle Aged ; *COVID-19 ; SARS-CoV-2 ; *Microbiota ; Respiratory System ; }, abstract = {To date, little is known about the effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the coronavirus disease 2019 (COVID-19) pandemic, on the upper respiratory tract (URT) microbiota over time. To fill this knowledge gap, we used 16S ribosomal RNA gene sequencing to characterize the URT microbiota in 48 adults, including (1) 24 participants with mild-to-moderate COVID-19 who had serial mid-turbinate swabs collected up to 21 days after enrolment and (2) 24 asymptomatic, uninfected controls who had mid-turbinate swabs collected at enrolment only. To compare the URT microbiota between groups in a comprehensive manner, different types of statistical analyses that are frequently employed in microbial ecology were used, including ⍺-diversity, β-diversity and differential abundance analyses. Final statistical models included age, sex and the presence of at least one comorbidity as covariates. The median age of all participants was 34.00 (interquartile range=28.75-46.50) years. In comparison to samples from controls, those from participants with COVID-19 had a lower observed species index at day 21 (linear regression coefficient=-13.30; 95 % CI=-21.72 to -4.88; q=0.02). In addition, the Jaccard index was significantly different between samples from participants with COVID-19 and those from controls at all study time points (PERMANOVA q<0.05 for all comparisons). The abundance of three amplicon sequence variants (ASVs) (one Corynebacterium ASV, Frederiksenia canicola, and one Lactobacillus ASV) were decreased in samples from participants with COVID-19 at all seven study time points, whereas the abundance of one ASV (from the family Neisseriaceae) was increased in samples from participants with COVID-19 at five (71.43 %) of the seven study time points. Our results suggest that mild-to-moderate COVID-19 can lead to alterations of the URT microbiota that persist for several weeks after the initial infection.}, }
@article {pmid36819055, year = {2023}, author = {Ugwuanyi, IR and Fogel, ML and Bowden, R and Steele, A and De Natale, G and Troise, C and Somma, R and Piochi, M and Mormone, A and Glamoclija, M}, title = {Comparative metagenomics at Solfatara and Pisciarelli hydrothermal systems in Italy reveal that ecological differences across substrates are not ubiquitous.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1066406}, pmid = {36819055}, issn = {1664-302X}, abstract = {INTRODUCTION: Continental hydrothermal systems (CHSs) are geochemically complex, and they support microbial communities that vary across substrates. However, our understanding of these variations across the complete range of substrates in CHS is limited because many previous studies have focused predominantly on aqueous settings.<br><br>METHODS: Here we used metagenomes in the context of their environmental geochemistry to investigate the ecology of different substrates (i.e., water, mud and fumarolic deposits) from Solfatara and Pisciarelli.<br><br>RESULTS AND DISCUSSION: Results indicate that both locations are lithologically similar with distinct fluid geochemistry. In particular, all substrates from Solfatara have similar chemistry whereas Pisciarelli substrates have varying chemistry; with water and mud from bubbling pools exhibiting high SO4 [2-] and NH4 [+] concentrations. Species alpha diversity was found to be different between locations but not across substrates, and pH was shown to be the most important driver of both diversity and microbial community composition. Based on cluster analysis, microbial community structure differed significantly between Pisciarelli substrates but not between Solfatara substrates. Pisciarelli mud pools, were dominated by (hyper)thermophilic archaea, and on average, bacteria dominated Pisciarelli fumarolic deposits and all investigated Solfatara environments. Carbon fixation and sulfur oxidation were the most important metabolic pathways fueled by volcanic outgassing at both locations. Together, results demonstrate that ecological differences across substrates are not a widespread phenomenon but specific to the system. Therefore, this study demonstrates the importance of analyzing different substrates of a CHS to understand the full range of microbial ecology to avoid biased ecological assessments.}, }
@article {pmid36818730, year = {2023}, author = {Noordijk, B and Nijland, R and Carrion, VJ and Raaijmakers, JM and de Ridder, D and de Lannoy, C}, title = {baseLess: lightweight detection of sequences in raw MinION data.}, journal = {Bioinformatics advances}, volume = {3}, number = {1}, pages = {vbad017}, pmid = {36818730}, issn = {2635-0041}, abstract = {SUMMARY: With its candybar form factor and low initial investment cost, the MinION brought affordable portable nucleic acid analysis within reach. However, translating the electrical signal it outputs into a sequence of bases still requires mid-tier computer hardware, which remains a caveat when aiming for deployment of many devices at once or usage in remote areas. For applications focusing on detection of a target sequence, such as infectious disease monitoring or species identification, the computational cost of analysis may be reduced by directly detecting the target sequence in the electrical signal instead. Here, we present baseLess, a computational tool that enables such target-detection-only analysis. BaseLess makes use of an array of small neural networks, each of which efficiently detects a fixed-size subsequence of the target sequence directly from the electrical signal. We show that baseLess can accurately determine the identity of reads between three closely related fish species and can classify sequences in mixtures of 20 bacterial species, on an inexpensive single-board computer.<br><br>baseLess and all code used in data preparation and validation are available on Github at https://github.com/cvdelannoy/baseLess, under an MIT license. Used validation data and scripts can be found at https://doi.org/10.4121/20261392, under an MIT license.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.}, }
@article {pmid36817258, year = {2022}, author = {Castro, AE and De Ungria, MCA}, title = {Methods used in microbial forensics and epidemiological investigations for stronger health systems.}, journal = {Forensic sciences research}, volume = {7}, number = {4}, pages = {650-661}, pmid = {36817258}, issn = {2471-1411}, abstract = {This review discusses microbial forensics as an emerging science that finds application in protecting human health. It is important to distinguish naturally acquired infections from those caused by the intentional release of microorganisms to the environment. This information is crucial in formulating procedures against the spread of infectious diseases and prosecuting persons who may be involved in acts of biocrime, bioterrorism, or biowarfare. A comparison between epidemiological investigations and microbial forensic investigations is provided. In addition, a discussion on how microbial forensics strengthens health systems is included in this review. Microbial forensic investigations and epidemiologic examinations employ similar concepts and involve identifying and characterising the microbe of interest. Both fields require formulating an appropriate case definition, determining a pathogen's mode of transmission, and identifying the source(s) of infection. However, the two subdisciplines differ in their objectives. An epidemiological investigation aims to identify the pathogen's source to prevent the spread of the disease. Microbial forensics focuses on source-tracking to facilitate the prosecution of persons responsible for the spread of a pathogen. Both fields use molecular techniques in analysing and comparing DNA, gene products, and biomolecules to identify and characterise the microorganisms of interest. We included case studies to show methods used in microbial forensic investigations, a brief discussion of the public significance of microbial forensic systems, and a roadmap for establishing a system at a national level. This system is expected to strengthen a country's capacity to respond to public health emergencies. Several factors must be considered in establishing national microbial forensic systems. First is the inherent ubiquity, diversity, and adaptability of microorganisms that warrants the use of robust and accurate molecular typing systems. Second, the availability of facilities and scientists who have been trained in epidemiology, molecular biology, bioinformatics, and data analytics. Human resources and infrastructure are critical requirements because formulating strategies and allocating resources in times of infectious disease outbreaks must be data-driven. Establishing and maintaining a national microbial forensic system to strengthen capacities in conducting forensic and epidemiological investigations should be prioritised by all countries, accompanied by a national policy that sets the legislative framework and provides for the system's financial requirements.}, }
@article {pmid36815773, year = {2023}, author = {Nestor, E and Toledano, G and Friedman, J}, title = {Interactions between Culturable Bacteria Are Predicted by Individual Species' Growth.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0083622}, pmid = {36815773}, issn = {2379-5077}, mesh = {*Bacteria/genetics ; Microbial Consortia ; Microbial Interactions ; *Microbiota/genetics ; }, abstract = {Predicting interspecies interactions is a key challenge in microbial ecology given that interactions shape the composition and functioning of microbial communities. However, predicting microbial interactions is challenging because they can vary considerably depending on species' metabolic capabilities and environmental conditions. Here, we employ machine learning models to predict pairwise interactions between culturable bacteria based on their phylogeny, monoculture growth capabilities, and interactions with other species. We trained our models on one of the largest available pairwise interactions data set containing over 7,500 interactions between 20 species from two taxonomic groups that were cocultured in 40 different carbon environments. Our models accurately predicted both the sign (accuracy of 88%) and the strength of effects (R[2] of 0.87) species had on each other's growth. Encouragingly, predictions with comparable accuracy could be made even when not relying on information about interactions with other species, which are often hard to measure. However, species' monoculture growth was essential to the model, as predictions based solely on species' phylogeny and inferred metabolic capabilities were significantly less accurate. These results bring us one step closer to a predictive understanding of microbial communities, which is essential for engineering beneficial microbial consortia. IMPORTANCE In order to understand the function and structure of microbial communities, one must know all pairwise interactions that occur between the different species within the community, as these interactions shape the community's structure and functioning. However, measuring all pairwise interactions can be an extremely difficult task especially when dealing with big complex communities. Because of that, predicting interspecies interactions is a key challenge in microbial ecology. Here, we use machine learning models in order to accurately predict the type and strength of interactions. We trained our models on one of the largest available pairwise interactions data set, containing over 7,500 interactions between 20 different species that were cocultured in 40 different environments. Our results show that, in general, accurate predictions can be made, and that the ability of each species to grow on its own in the given environment contributes the most to predictions. Being able to predict microbial interactions would put us one step closer to predicting the functionality of microbial communities and to rationally microbiome engineering.}, }
@article {pmid36814573, year = {2023}, author = {Cheng, X and Xiang, X and Yun, Y and Wang, W and Wang, H and Bodelier, PLE}, title = {Archaea and their interactions with bacteria in a karst ecosystem.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1068595}, pmid = {36814573}, issn = {1664-302X}, abstract = {Karst ecosystems are widely distributed around the world, accounting for 15-20% of the global land area. However, knowledge on microbial ecology of these systems does not match with their global importance. To close this knowledge gap, we sampled three niches including weathered rock, sediment, and drip water inside the Heshang Cave and three types of soils overlying the cave (forest soil, farmland soil, and pristine karst soil). All these samples were subjected to high-throughput sequencing of V4-V5 region of 16S rRNA gene and analyzed with multivariate statistical analysis. Overall, archaeal communities were dominated by Thaumarchaeota, whereas Actinobacteria dominated bacterial communities. Thermoplasmata, Nitrosopumilaceae, Aenigmarchaeales, Crossiella, Acidothermus, and Solirubrobacter were the important predictor groups inside the Heshang Cave, which were correlated to NH4 [+] availability. In contrast, Candidatus Nitrososphaera, Candidatus Nitrocosmicus, Thaumarchaeota Group 1.1c, and Pseudonocardiaceae were the predictors outside the cave, whose distribution was correlated with pH, Ca[2+], and NO2 [-]. Tighter network structures were found in archaeal communities than those of bacteria, whereas the topological properties of bacterial networks were more similar to those of total prokaryotic networks. Both chemolithoautotrophic archaea (Candidatus Methanoperedens and Nitrosopumilaceae) and bacteria (subgroup 7 of Acidobacteria and Rokubacteriales) were the dominant keystone taxa within the co-occurrence networks, potentially playing fundamental roles in obtaining energy under oligotrophic conditions and thus maintaining the stability of the cave ecosystem. To be noted, all the keystone taxa of karst ecosystems were related to nitrogen cycling, which needs further investigation, particularly the role of archaea. The predicted ecological functions in karst soils mainly related to carbohydrate metabolism, biotin metabolism, and synthesis of fatty acid. Our results offer new insights into archaeal ecology, their potential functions, and archaeal interactions with bacteria, which enhance our understanding about the microbial dark matter in the subsurface karst ecosystems.}, }
@article {pmid36813568, year = {2023}, author = {Gonzalez-Garcia, L and Guevara-Barrientos, D and Lozano-Arce, D and Gil, J and Díaz-Riaño, J and Duarte, E and Andrade, G and Bojacá, JC and Hoyos-Sanchez, MC and Chavarro, C and Guayazan, N and Chica, LA and Buitrago Acosta, MC and Bautista, E and Trujillo, M and Duitama, J}, title = {New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads.}, journal = {Life science alliance}, volume = {6}, number = {5}, pages = {}, pmid = {36813568}, issn = {2575-1077}, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Algorithms ; Sequence Analysis, DNA/methods ; Genome ; Software ; }, abstract = {Building de novo genome assemblies for complex genomes is possible thanks to long-read DNA sequencing technologies. However, maximizing the quality of assemblies based on long reads is a challenging task that requires the development of specialized data analysis techniques. We present new algorithms for assembling long DNA sequencing reads from haploid and diploid organisms. The assembly algorithm builds an undirected graph with two vertices for each read based on minimizers selected by a hash function derived from the k-mer distribution. Statistics collected during the graph construction are used as features to build layout paths by selecting edges, ranked by a likelihood function. For diploid samples, we integrated a reimplementation of the ReFHap algorithm to perform molecular phasing. We ran the implemented algorithms on PacBio HiFi and Nanopore sequencing data taken from haploid and diploid samples of different species. Our algorithms showed competitive accuracy and computational efficiency, compared with other currently used software. We expect that this new development will be useful for researchers building genome assemblies for different species.}, }
@article {pmid36813189, year = {2023}, author = {Zhu, X and Guo, Z and Wang, N and Liu, J and Zuo, Y and Li, K and Song, C and Song, Y and Gong, C and Xu, X and Yuan, F and Zhang, L}, title = {Environmental stress stimulates microbial activities as indicated by cyclopropane fatty acid enhancement.}, journal = {The Science of the total environment}, volume = {873}, number = {}, pages = {162338}, doi = {10.1016/j.scitotenv.2023.162338}, pmid = {36813189}, issn = {1879-1026}, mesh = {*Fatty Acids ; *Soil Microbiology ; Soil/chemistry ; Wetlands ; China ; }, abstract = {Soil microbial responses to environmental stress remain a critical question in microbial ecology. The content of cyclopropane fatty acid (CFA) in cytomembrane has been widely used to evaluate environmental stress on microorganisms. Here, we used CFA to investigate the ecological suitability of microbial communities and found a stimulating impact of CFA on microbial activities during wetland reclamation in Sanjiang Plain, Northeastern China. The seasonality of environmental stress resulted in the fluctuation of CFA content in the soil, which suppressed microbial activities due to nutrient loss upon wetland reclamation. After land conversion, the aggravation of temperature stress to microbes increased the CFA content by 5 % (autumn) to 163 % (winter), which led to the suppression of microbial activities by 7 %-47 %. By contrast, the warmer soil temperature and permeability decreased the CFA content by 3 % to 41 % and consequently aggravated the microbial reduction by 15 %-72 % in spring and summer. Complex microbial communities of 1300 CFA-produced species were identified using a sequencing approach, suggesting that soil nutrients dominated the differentiation in these microbial community structures. Further analysis with structural equation modeling highlighted the important function of CFA content to environmental stress and the stimulating influence of CFA induced by environmental stress on microbial activities. Our study shows the biological mechanisms of seasonal CFA content for microbial adaption to environmental stress under wetland reclamation. It advances our knowledge of microbial physiology affecting soil element cycling caused by anthropogenic activities.}, }
@article {pmid36811710, year = {2023}, author = {Akter, S and Wos-Oxley, ML and Catalano, SR and Hassan, MM and Li, X and Qin, JG and Oxley, AP}, title = {Host Species and Environment Shape the Gut Microbiota of Cohabiting Marine Bivalves.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1755-1772}, pmid = {36811710}, issn = {1432-184X}, support = {2014/027//Fisheries Research and Development Corporation/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Mytilus/microbiology ; Bacteria/genetics ; *Crassostrea/microbiology ; }, abstract = {Pacific oysters (Crassostrea gigas) and Mediterranean mussels (Mytilus galloprovincialis) are commercially important marine bivalves that frequently coexist and have overlapping feeding ecologies. Like other invertebrates, their gut microbiota is thought to play an important role in supporting their health and nutrition. Yet, little is known regarding the role of the host and environment in driving these communities. Here, bacterial assemblages were surveyed from seawater and gut aspirates of farmed C. gigas and co-occurring wild M. galloprovincialis in summer and winter using Illumina 16S rRNA gene sequencing. Unlike seawater, which was dominated by Pseudomonadata, bivalve samples largely consisted of Mycoplasmatota (Mollicutes) and accounted for >50% of the total OTU abundance. Despite large numbers of common (core) bacterial taxa, bivalve-specific species (OTUs) were also evident and predominantly associated with Mycoplasmataceae (notably Mycoplasma). An increase in diversity (though with varied taxonomic evenness) was observed in winter for both bivalves and was associated with changes in the abundance of core and bivalve-specific taxa, including several representing host-associated and environmental (free-living or particle-diet associated) organisms. Our findings highlight the contribution of the environment and the host in defining the composition of the gut microbiota in cohabiting, intergeneric bivalve populations.}, }
@article {pmid36810880, year = {2023}, author = {Varliero, G and Lebre, PH and Stevens, MI and Czechowski, P and Makhalanyane, T and Cowan, DA}, title = {The use of different 16S rRNA gene variable regions in biogeographical studies.}, journal = {Environmental microbiology reports}, volume = {15}, number = {3}, pages = {216-228}, pmid = {36810880}, issn = {1758-2229}, mesh = {RNA, Ribosomal, 16S/genetics ; Phylogeny ; Genes, rRNA ; Sequence Analysis, DNA ; *Bacteria/genetics ; }, abstract = {16S rRNA gene amplicon sequencing is routinely used in environmental surveys to identify microbial diversity and composition of the samples of interest. The dominant sequencing technology of the past decade (Illumina) is based on the sequencing of 16S rRNA hypervariable regions. Online sequence data repositories, which represent an invaluable resource for investigating microbial distributional patterns across spatial, environmental or temporal scales, contain amplicon datasets from diverse 16S rRNA gene variable regions. However, the utility of these sequence datasets is potentially reduced by the use of different 16S rRNA gene amplified regions. By comparing 10 Antarctic soil samples sequenced for five different 16S rRNA amplicons, we explore whether sequence data derived from diverse 16S rRNA variable regions can be validly used as a resource for biogeographical studies. Patterns of shared and unique taxa differed among samples as a result of variable taxonomic resolutions of the assessed 16S rRNA variable regions. However, our analyses also suggest that the use of multi-primer datasets for biogeographical studies of the domain Bacteria is a valid approach to explore bacterial biogeographical patterns due to the preservation of bacterial taxonomic and diversity patterns across different variable region datasets. We deem composite datasets useful for biogeographical studies.}, }
@article {pmid36810610, year = {2023}, author = {Muro, T and Hikida, H and Fujii, T and Kiuchi, T and Katsuma, S}, title = {Two Complete Genomes of Male-Killing Wolbachia Infecting Ostrinia Moth Species Illuminate Their Evolutionary Dynamics and Association with Hosts.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1740-1754}, pmid = {36810610}, issn = {1432-184X}, support = {17H06431//Japan Society for the Promotion of Science/ ; 22H00366//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; Male ; *Moths/genetics ; *Wolbachia/genetics ; Phylogeny ; Sex Ratio ; Genomics ; }, abstract = {Wolbachia is an extremely widespread intracellular symbiont which causes reproductive manipulation on various arthropod hosts. Male progenies are killed in Wolbachia-infected lineages of the Japanese Ostrinia moth population. While the mechanism of male killing and the evolutionary interaction between host and symbiont are significant concerns for this system, the absence of Wolbachia genomic information has limited approaches to these issues. We determined the complete genome sequences of wFur and wSca, the male-killing Wolbachia of Ostrinia furnacalis and Ostrinia scapulalis. The two genomes shared an extremely high degree of homology, with over 95% of the predicted protein sequences being identical. A comparison of these two genomes revealed nearly minimal genome evolution, with a strong emphasis on the frequent genome rearrangements and the rapid evolution of ankyrin repeat-containing proteins. Additionally, we determined the mitochondrial genomes of both species' infected lineages and performed phylogenetic analyses to deduce the evolutionary dynamics of Wolbachia infection in the Ostrinia clade. According to the inferred phylogenetic relationship, two possible scenarios were proposed: (1) Wolbachia infection was established in the Ostrinia clade prior to the speciation of related species such as O. furnacalis and O. scapulalis, or (2) Wolbachia infection in these species was introgressively transferred from a currently unidentified relative. Simultaneously, the relatively high homology of mitochondrial genomes suggested recent Wolbachia introgression between infected Ostrinia species. The findings of this study collectively shed light on the host-symbiont interaction from an evolutionary standpoint.}, }
@article {pmid36810576, year = {2023}, author = {Klawonn, I and Van den Wyngaert, S and Iversen, MH and Walles, TJW and Flintrop, CM and Cisternas-Novoa, C and Nejstgaard, JC and Kagami, M and Grossart, HP}, title = {Fungal parasitism on diatoms alters formation and bio-physical properties of sinking aggregates.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {206}, pmid = {36810576}, issn = {2399-3642}, support = {3332/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Diatoms ; Phytoplankton ; Food Chain ; Bacteria ; Fresh Water/microbiology ; }, abstract = {Phytoplankton forms the base of aquatic food webs and element cycling in diverse aquatic systems. The fate of phytoplankton-derived organic matter, however, often remains unresolved as it is controlled by complex, interlinked remineralization and sedimentation processes. We here investigate a rarely considered control mechanism on sinking organic matter fluxes: fungal parasites infecting phytoplankton. We demonstrate that bacterial colonization is promoted 3.5-fold on fungal-infected phytoplankton cells in comparison to non-infected cells in a cultured model pathosystem (diatom Synedra, fungal microparasite Zygophlyctis, and co-growing bacteria), and even ≥17-fold in field-sampled populations (Planktothrix, Synedra, and Fragilaria). Additional data obtained using the Synedra-Zygophlyctis model system reveals that fungal infections reduce the formation of aggregates. Moreover, carbon respiration is 2-fold higher and settling velocities are 11-48% lower for similar-sized fungal-infected vs. non-infected aggregates. Our data imply that parasites can effectively control the fate of phytoplankton-derived organic matter on a single-cell to single-aggregate scale, potentially enhancing remineralization and reducing sedimentation in freshwater and coastal systems.}, }
@article {pmid36809975, year = {2023}, author = {Bovio-Winkler, P and Guerrero, LD and Erijman, L and Oyarzúa, P and Suárez-Ojeda, ME and Cabezas, A and Etchebehere, C}, title = {Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {45}, pmid = {36809975}, issn = {1471-2180}, mesh = {*Sewage ; *Chloroflexi/genetics/metabolism ; Ecosystem ; In Situ Hybridization, Fluorescence ; Anaerobic Ammonia Oxidation ; Bioreactors ; Anaerobiosis ; Nitrogen/metabolism ; Oxidation-Reduction ; }, abstract = {BACKGROUND: The phylum Chloroflexi is highly abundant in a wide variety of wastewater treatment bioreactors. It has been suggested that they play relevant roles in these ecosystems, particularly in degrading carbon compounds and on structuring flocs or granules. Nevertheless, their function is not yet well understood as most species have not been isolated in axenic cultures. Here we used a metagenomic approach to investigate Chloroflexi diversity and their metabolic potential in three environmentally different bioreactors: a methanogenic full-scale reactor, a full-scale activated sludge reactor and a lab scale anammox reactor.<br><br>RESULTS: Differential coverage binning approach was used to assemble the genomes of 17 new Chloroflexi species, two of which are proposed as new Candidatus genus. In addition, we recovered the first representative genome belonging to the genus 'Ca. Villigracilis'. Even though samples analyzed were collected from bioreactors operating under different environmental conditions, the assembled genomes share several metabolic features: anaerobic metabolism, fermentative pathways and several genes coding for hydrolytic enzymes. Interestingly, genome analysis from the anammox reactor indicated a putative role of Chloroflexi in nitrogen conversion. Genes related to adhesiveness and exopolysaccharides production were also detected. Complementing sequencing analysis, filamentous morphology was detected by Fluorescent in situ hybridization.<br><br>CONCLUSION: Our results suggest that Chloroflexi participate in organic matter degradation, nitrogen removal and biofilm aggregation, playing different roles according to the environmental conditions.}, }
@article {pmid36809072, year = {2023}, author = {Yuan, S and Friman, VP and Balcazar, JL and Zheng, X and Ye, M and Sun, M and Hu, F}, title = {Viral and Bacterial Communities Collaborate through Complementary Assembly Processes in Soil to Survive Organochlorine Contamination.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {3}, pages = {e0181022}, pmid = {36809072}, issn = {1098-5336}, mesh = {Soil ; Bacteria ; *Microbiota ; Soil Microbiology ; *Viruses ; *Pesticides/metabolism ; *Hydrocarbons, Chlorinated/metabolism ; }, abstract = {The ecological drivers that direct the assembly of viral and host bacterial communities are largely unknown, even though viral-encoded accessory genes help host bacteria survive in polluted environments. To understand the ecological mechanism(s) of viruses and hosts synergistically surviving under organochlorine pesticide (OCP) stress, we investigated the community assembly processes of viruses and bacteria at the taxon and functional gene levels in clean and OCP-contaminated soils in China using a combination of metagenomics/viromics and bioinformatics approaches. We observed a decreased richness of bacterial taxa and functional genes but an increased richness of viral taxa and auxiliary metabolic genes (AMGs) in OCP-contaminated soils (from 0 to 2,617.6 mg · kg[-1]). In OCP-contaminated soils, the assembly of bacterial taxa and genes was dominated by a deterministic process, of which the relative significance was 93.0% and 88.7%, respectively. In contrast, the assembly of viral taxa and AMGs was driven by a stochastic process, which contributed 83.1% and 69.2%, respectively. The virus-host prediction analysis, which indicated Siphoviridae was linked to 75.0% of bacterial phyla, and the higher migration rate of viral taxa and AMGs in OCP-contaminated soil suggested that viruses show promise for the dissemination of functional genes among bacterial communities. Taken together, the results of this study indicated that the stochastic assembly processes of viral taxa and AMGs facilitated bacterial resistance to OCP stress in soils. Moreover, our findings provide a novel avenue for understanding the synergistic interactions between viruses and bacteria from the perspective of microbial ecology, highlighting the significance of viruses in mediating bioremediation of contaminated soils. IMPORTANCE The interaction between viral communities and microbial hosts has been studied extensively, and the viral community affects host community metabolic function through AMGs. Microbial community assembly is the process by which species colonize and interact to establish and maintain communities. This is the first study that aimed to understand the assembly process of bacterial and viral communities under OCP stress. The findings of this study provide information about microbial community responses to OCP stress and reveal the collaborative interactions between viral and bacterial communities to resist pollutant stress. Thereby, we highlight the importance of viruses in soil bioremediation from the perspective of community assembly.}, }
@article {pmid36808010, year = {2023}, author = {Khodse, VB and Amberkar, U and Khandeparker, R and Ramaiah, N}, title = {Variability of biochemical compounds in surface sediments along the eastern margin of the Arabian Sea.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {3}, pages = {414}, pmid = {36808010}, issn = {1573-2959}, mesh = {*Galactose ; *Mannose ; Arabinose ; Ribose ; Fucose ; Rhamnose ; Environmental Monitoring ; Hexoses ; Glucose ; Uronic Acids ; Geologic Sediments/analysis ; }, abstract = {Different fractions of organic matter in surface sediments from three transects along the eastern margin of the Arabian Sea (AS) were quantified to determine the sources of organic matter, and also to study its impact on microbial community structure. From the extensive analyses of different biochemical parameters, it was evident that the distribution of total carbohydrate (TCHO), total neutral carbohydrate (TNCHO), proteins, lipids, and uronic acids (URA) concentrations and yield (% TCHO-C/TOC) are affected by organic matter (OM) sources and microbial degradation of sedimentary OM. Monosaccharide compositions from surface sediment was quantified to assess the sources and diagenetic fate of carbohydrates, suggesting that the deoxysugars (rhamnose plus fucose) had significant inverse relationship (r = 0.928, n = 13, p < 0.001) with hexoses (mannose plus galactose plus glucose) and positive relationship (r = 0.828, n = 13, p < 0.001) with pentoses (ribose plus arabinose plus xylose). This shows that marine microorganisms are the source of carbohydrates and there is no influence of terrestrial OM along the eastern margin of AS. During the degradation of algal material, the hexoses seem to be preferentially used by heterotrophic organisms in this region. Arabinose plus galactose (glucose free wt %) values between 28 and 64 wt% indicate that OM was derived from phytoplankton, zooplankton, and non-woody tissues. In the principal component analysis, rhamnose, fucose, and ribose form one cluster of positive loadings while glucose, galactose, and mannose form another cluster of negative loadings which suggest that during OM sinking process, hexoses were removed resulting in increase in bacterial biomass and microbial sugars. Results indicate sediment OM to be derived from marine microbial source along the eastern margin of AS.}, }
@article {pmid36806012, year = {2023}, author = {Janakiev, T and Milošević, &#x110; and Petrović, M and Miljković, J and Stanković, N and Zdravković, DS and Dimkić, I}, title = {Chironomus riparius Larval Gut Bacteriobiota and Its Potential in Microplastic Degradation.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1909-1922}, pmid = {36806012}, issn = {1432-184X}, support = {451-03-68/2022-14/200178//Ministarstvo Prosvete, Nauke i Tehnolo&#x161;kog Razvoja/ ; 101072777//Integrated Cross-Sectoral Solutions to Micro- and Nanoplastic Pollution in Soil and Groundwater Ecosystem - Plastic Underground HORIZON - MSCA - 2021- DN (2022-2026)/ ; }, mesh = {Plastics ; Nylons ; *Microplastics ; Polyvinyl Chloride ; Bacteria ; Ecosystem ; Animals ; Bacillus ; Larva ; Polyethylenes ; *Chironomidae ; }, abstract = {Chironomus riparius are sediment-dwelling invertebrates in freshwater ecosystems and are used as indicators of environmental pollution. Their habitat is threatened by high levels of contaminants such as microplastics and organic matter. A promising strategy for the eco-friendly degradation of pollutants is the use of bacteria and their enzymatic activity. The aim of this study was to characterize for the first time bacteriobiota associated with the gut of C. riparius larvae from nature and laboratory samples, to compare it with sediment and food as potential sources of gut microbiota, and to assess its ability to degrade cellulose, proteins, and three different types of microplastics (polyethylene, polyvinyl chloride, and polyamide). The metabarcoding approach highlighted Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteriota as most abundant in both gut samples. Culturable microbiota analysis revealed Metabacillus idriensis, Peribacillus simplex, Neobacillus cucumis, Bacillus thuringiensis/toyonensis, and Fictibacillus phosphorivorans as five common species for nature and laboratory samples. Two P. simplex and one P. frigoritolerans isolates showed the ability for intensive growth on polyethylene, polyvinyl chloride, and polyamide. Both cellulolytic and proteolytic activity was observed for Paenibacillus xylanexedens and P. amylolyticus isolates. The characterized strains are promising candidates for the development of environmentally friendly strategies to degrade organic pollution and microplastics in freshwater ecosystems.}, }
@article {pmid36805785, year = {2023}, author = {Capri, FC and Prazzi, E and Casamento, G and Gambino, D and Cassata, G and Alduina, R}, title = {Correlation Between Microbial Community and Hatching Failure in Loggerhead Sea Turtle Caretta caretta.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1923-1933}, pmid = {36805785}, issn = {1432-184X}, mesh = {Animals ; *Turtles ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Ecology ; Bacteria/genetics ; }, abstract = {Microbial communities provide essential information about host ecology and could be helpful as a tool to improve species conservation efforts. However, microbes can also infect and compromise the host development process and viability. Caretta caretta is the most widespread marine turtle species in the Mediterranean basin and is the only species of sea turtle nesting along the Italian coasts. Little is known about the microbiota composition of the nest of sea turtles and its correlation with hatching failures. In this study, the microbial composition of two nests of C. caretta featuring different rates of hatching success from a nesting beach in Lampedusa (Italy) was analyzed and compared. The bacterial community was determined using culture-dependent methods and next-generation sequencing based on 16S rRNA gene metabarcoding analysis. Our results showed five dominant bacterial phyla (Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, and Firmicutes) and indicated different bacterial families (Pseudomonadaceae and Brucellaceae) as likely causes of hatching failures. Besides, our findings demonstrated the nests' active role in modulating the sand's bacterial communities. This study suggests microbiological analysis could be a valuable tool in monitoring nests to take preventive actions and reduce hatching failures.}, }
@article {pmid36805022, year = {2023}, author = {Kodera, SM and Sharma, A and Martino, C and Dsouza, M and Grippo, M and Lutz, HL and Knight, R and Gilbert, JA and Negri, C and Allard, SM}, title = {Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {10}, pmid = {36805022}, issn = {2524-6372}, abstract = {BACKGROUND: Microorganisms such as coliform-forming bacteria are commonly used to assess freshwater quality for drinking and recreational use. However, such organisms do not exist in isolation; they exist within the context of dynamic, interactive microbial communities which vary through space and time. Elucidating spatiotemporal microbial dynamics is imperative for discriminating robust community changes from ephemeral ecological trends, and for improving our overall understanding of the relationship between microbial communities and ecosystem health. We conducted a seven-year (2013-2019) microbial time-series investigation in the Chicago Area Waterways (CAWS): an urban river system which, in 2016, experienced substantial upgrades to disinfection processes at two wastewater reclamation plants (WRPs) that discharge into the CAWS and improved stormwater capture, to improve river water quality and reduce flooding. Using culture-independent and culture-dependent approaches, we compared CAWS microbial ecology before and after the intervention.<br><br>RESULTS: Examinations of time-resolved beta distances between WRP-adjacent sites showed that community similarity measures were often consistent with the spatial orientation of site locations to one another and to the WRP outfalls. Fecal coliform results suggested that upgrades reduced coliform-associated bacteria in the effluent and the downstream river community. However, examinations of whole community changes through time suggest that the upgrades did little to affect overall riverine community dynamics, which instead were overwhelmingly driven by yearly patterns consistent with seasonality.<br><br>CONCLUSIONS: This study presents a systematic effort to combine 16S rRNA gene amplicon sequencing with traditional culture-based methods to evaluate the influence of treatment innovations and systems upgrades on the microbiome of the Chicago Area Waterway System, representing the longest and most comprehensive characterization of the microbiome of an urban waterway yet attempted. We found that the systems upgrades were successful in improving specific water quality measures immediately downstream of wastewater outflows. Additionally, we found that the implementation of the water quality improvement measures to the river system did not disrupt the overall dynamics of the downstream microbial community, which remained heavily influenced by seasonal trends. Such results emphasize the dynamic nature of microbiomes in open environmental systems such as the CAWS, but also suggest that the seasonal oscillations remain consistent even when perturbed.}, }
@article {pmid36803622, year = {2023}, author = {Ceron-Chafla, P and de Vrieze, J and Rabaey, K and van Lier, JB and Lindeboom, REF}, title = {Steering the product spectrum in high-pressure anaerobic processes: CO2 partial pressure as a novel tool in biorefinery concepts.}, journal = {Biotechnology for biofuels and bioproducts}, volume = {16}, number = {1}, pages = {27}, pmid = {36803622}, issn = {2731-3654}, support = {676070//Horizon 2020 Framework Programme/ ; }, abstract = {BACKGROUND: Elevated CO2 partial pressure (pCO2) has been proposed as a potential steering parameter for selective carboxylate production in mixed culture fermentation. It is anticipated that intermediate product spectrum and production rates, as well as changes in the microbial community, are (in)directly influenced by elevated pCO2. However, it remains unclear how pCO2 interacts with other operational conditions, namely substrate specificity, substrate-to-biomass (S/X) ratio and the presence of an additional electron donor, and what effect pCO2 has on the exact composition of fermentation products. Here, we investigated possible steering effects of elevated pCO2 combined with (1) mixed substrate (glycerol/glucose) provision; (2) subsequent increments in substrate concentration to increase the S/X ratio; and (3) formate as an additional electron donor.<br><br>RESULTS: Metabolite predominance, e.g., propionate vs. butyrate/acetate, and cell density, depended on interaction effects between pCO2-S/X ratio and pCO2-formate. Individual substrate consumption rates were negatively impacted by the interaction effect between pCO2-S/X ratio and were not re-established after lowering the S/X ratio and adding formate. The product spectrum was influenced by the microbial community composition, which in turn, was modified by substrate type and the interaction effect between pCO2-formate. High propionate and butyrate levels strongly correlated with Negativicutes and Clostridia predominance, respectively. After subsequent pressurized fermentation phases, the interaction effect between pCO2-formate enabled a shift from propionate towards succinate production when mixed substrate was provided.<br><br>CONCLUSIONS: Overall, interaction effects between elevated pCO2, substrate specificity, high S/X ratio and availability of reducing equivalents from formate, rather than an isolated pCO2 effect, modified the proportionality of propionate, butyrate and acetate in pressurized mixed substrate fermentations at the expense of reduced consumption rates and increased lag-phases. The interaction effect between elevated pCO2 and formate was beneficial for succinate production and biomass growth with a glycerol/glucose mixture as the substrate. The positive effect may be attributed to the availability of extra reducing equivalents, likely enhanced carbon fixating activity and hindered propionate conversion due to increased concentration of undissociated carboxylic acids.}, }
@article {pmid36802019, year = {2023}, author = {Ortiz-Rivero, J and Garrido-Benavent, I and Heiðmarsson, S and de Los Ríos, A}, title = {Moss and Liverwort Covers Structure Soil Bacterial and Fungal Communities Differently in the Icelandic Highlands.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1893-1908}, pmid = {36802019}, issn = {1432-184X}, mesh = {*Hepatophyta ; Iceland ; Soil ; *Mycobiome ; *Bryophyta ; Bacteria/genetics ; *Microbiota ; Soil Microbiology ; }, abstract = {Cryptogamic covers extend over vast polar tundra regions and their main components, e.g., bryophytes and lichens, are frequently the first visible colonizers of deglaciated areas. To understand their role in polar soil development, we analyzed how cryptogamic covers dominated by different bryophyte lineages (mosses and liverworts) influence the diversity and composition of edaphic bacterial and fungal communities as well as the abiotic attributes of underlying soils in the southern part of the Highlands of Iceland. For comparison, the same traits were examined in soils devoid of bryophyte covers. We measured an increase in soil C, N, and organic matter contents coupled with a lower pH in association with bryophyte cover establishment. However, liverwort covers showed noticeably higher C and N contents than moss covers. Significant changes in diversity and composition of bacterial and fungal communities were revealed between (a) bare and bryophyte-covered soils, (b) bryophyte covers and the underlying soils, and (c) moss and liverworts covers. These differences were more obvious for fungi than bacteria, and involved different lineages of saprotrophic and symbiotic fungi, which suggests a certain specificity of microbial taxa to particular bryophyte groups. In addition, differences observed in the spatial structure of the two bryophyte covers may be also responsible for the detected differences in microbial community diversity and composition. Altogether, our findings indicate that soil microbial communities and abiotic attributes are ultimately affected by the composition of the most conspicuous elements of cryptogamic covers in polar regions, which is of great value to predict the biotic responses of these ecosystems to future climate change.}, }
@article {pmid36801973, year = {2023}, author = {Morgan-Lang, C and Hallam, SJ}, title = {A Guide to Gene-Centric Analysis Using TreeSAPP.}, journal = {Current protocols}, volume = {3}, number = {2}, pages = {e671}, doi = {10.1002/cpz1.671}, pmid = {36801973}, issn = {2691-1299}, support = {//Natural Sciences and Engineering Research Council/ ; //Genome Canada/ ; //Genome British Columbia/ ; //the Digital Research Alliance of Canada/ ; //the G. Unger Vetlesen and Ambrose Monell Foundations/ ; //the U.S. Department of Energy (DOE) Joint Genome Institute (JGI)/ ; //and the Facilities Integrating Collaborations for User Science (FICUS)/ ; }, mesh = {*Software ; Phylogeny ; *Algorithms ; Metagenomics/methods ; Sequence Alignment ; }, abstract = {Gene-centric analysis is commonly used to chart the structure, function, and activity of microbial communities in natural and engineered environments. A common approach is to create custom ad hoc reference marker gene sets, but these come with the typical disadvantages of inaccuracy and limited utility beyond assigning query sequences taxonomic labels. The Tree-based Sensitive and Accurate Phylogenetic Profiler (TreeSAPP) software package standardizes analysis of phylogenetic and functional marker genes and improves predictive performance using a classification algorithm that leverages information-rich reference packages consisting of a multiple sequence alignment, a profile hidden Markov model, taxonomic lineage information, and a phylogenetic tree. Here, we provide a set of protocols that link the various analysis modules in TreeSAPP into a coherent process that both informs and directs the user experience. This workflow, initiated from a collection of candidate reference sequences, progresses through construction and refinement of a reference package to marker identification and normalized relative abundance calculations for homologous sequences in metagenomic and metatranscriptomic datasets. The alpha subunit of methyl-coenzyme M reductase (McrA) involved in biological methane cycling is presented as a use case given its dual role as a phylogenetic and functional marker gene driving an ecologically relevant process. These protocols fill several gaps in prior TreeSAPP documentation and provide best practices for reference package construction and refinement, including manual curation steps from trusted sources in support of reproducible gene-centric analysis. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Creating reference packages Support Protocol 1: Installing TreeSAPP Support Protocol 2: Annotating traits within a phylogenetic context Basic Protocol 2: Updating reference packages Basic Protocol 3: Calculating relative abundance of genes in metagenomic and metatranscriptomic datasets.}, }
@article {pmid36801035, year = {2023}, author = {Law, CKY and Kundu, K and Bonin, L and Peñacoba-Antona, L and Bolea-Fernandez, E and Vanhaecke, F and Rabaey, K and Esteve-Núñez, A and De Gusseme, B and Boon, N}, title = {Electrochemically assisted production of biogenic palladium nanoparticles for the catalytic removal of micropollutants in wastewater treatment plants effluent.}, journal = {Journal of environmental sciences (China)}, volume = {128}, number = {}, pages = {203-212}, doi = {10.1016/j.jes.2022.08.018}, pmid = {36801035}, issn = {1001-0742}, mesh = {Wastewater ; Palladium/chemistry ; *Metal Nanoparticles ; *Water Purification ; *Water Pollutants, Chemical/metabolism ; }, abstract = {Biogenic palladium nanoparticles (bio-Pd NPs) are used for the reductive transformation and/or dehalogenation of persistent micropollutants. In this work, H2 (electron donor) was produced in situ by an electrochemical cell, permitting steered production of differently sized bio-Pd NPs. The catalytic activity was first assessed by the degradation of methyl orange. The NPs showing the highest catalytic activity were selected for the removal of micropollutants from secondary treated municipal wastewater. The synthesis at different H2 flow rates (0.310 L/hr or 0.646 L/hr) influenced the bio-Pd NPs size. The NPs produced over 6 hr at a low H2 flow rate had a larger size (D50 = 39.0 nm) than those produced in 3 hr at a high H2 flow rate (D50 = 23.2 nm). Removal of 92.1% and 44.3% of methyl orange was obtained after 30 min for the NPs with sizes of 39.0 nm and 23.2 nm, respectively. Bio-Pd NPs of 39.0 nm were used to treat micropollutants present in secondary treated municipal wastewater at concentrations ranging from µg/L to ng/L. Effective removal of 8 compounds was observed: ibuprofen (69.5%) < sulfamethoxazole (80.6%) < naproxen (81.4%) < furosemide (89.7%) < citalopram (91.7%) < diclofenac (91.9%) < atorvastatin (> 94.3%) < lorazepam (97.2%). Removal of fluorinated antibiotics occurred at > 90% efficiency. Overall, these data indicate that the size, and thus the catalytic activity of the NPs can be steered and that the removal of challenging micropollutants at environmentally relevant concentrations can be achieved through the use of bio-Pd NPs.}, }
@article {pmid36799977, year = {2023}, author = {Zhao, H and Yang, S and Qin, X and Huang, J and Huang, H and Li, W and Jiang, G and Tang, J and Dong, K and Li, N}, title = {Disentangling the Ecological Processes and Driving Forces Shaping the Seasonal Pattern of Halobacteriovorax Communities in a Subtropical Estuary.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1881-1892}, pmid = {36799977}, issn = {1432-184X}, mesh = {*Ecosystem ; Seasons ; *Estuaries ; Phylogeny ; Proteobacteria ; }, abstract = {Halobacteriovorax are predatory bacteria that have a significant ecological role in marine environments. However, understanding of dynamics of populations, driving forces, and community composition of Halobacteriovorax groups in natural marine environments is still limited. Here, we used high-throughput sequencing to study the underlying mechanisms governing the diversity and assembly of the Halobacteriovorax community at spatiotemporal scales in a subtropical estuary. Phylogenetic analysis showed that 10 of 15 known Halobacteriovorax clusters were found in the studied estuary. Halobacteriovorax α-diversity and β-diversity exhibited significant seasonal variation. Variation partitioning analysis showed that the effect of nutrients was greater than that of other measured water properties on Halobacteriovorax community distribution. The results of Spearman's and Mantel's tests indicated that the trophic pollutants dissolved inorganic phosphorus (DIP) and NH4[+]-N in the estuary were the key factors that significantly affected Halobacteriovorax species and community diversity. In addition, this work indicated that the biological stoichiometry (especially N/P) of nutrients exerted a significant influence on the Halobacteriovorax community. Furthermore, we found that both deterministic and stochastic processes contributed to the turnover of Halobacteriovorax communities, and environmental filtering dominated the assembly of estuarine Halobacteriovorax communities. Overall, we provide new insights into the mechanisms in the generation and maintenance of the Halobacteriovorax community in marine environments.}, }
@article {pmid36799146, year = {2023}, author = {Gsell, AS and Biere, A and de Boer, W and de Bruijn, I and Eichhorn, G and Frenken, T and Geisen, S and van der Jeugd, H and Mason-Jones, K and Meisner, A and Thakur, MP and van Donk, E and Zwart, MP and Van de Waal, DB}, title = {Environmental refuges from disease in host-parasite interactions under global change.}, journal = {Ecology}, volume = {104}, number = {4}, pages = {e4001}, doi = {10.1002/ecy.4001}, pmid = {36799146}, issn = {1939-9170}, mesh = {Animals ; *Host-Parasite Interactions/physiology ; *Parasites ; Temperature ; Acclimatization ; Adaptation, Physiological ; Climate Change ; }, abstract = {The physiological performance of organisms depends on their environmental context, resulting in performance-response curves along environmental gradients. Parasite performance-response curves are generally expected to be broader than those of their hosts due to shorter generation times and hence faster adaptation. However, certain environmental conditions may limit parasite performance more than that of the host, thereby providing an environmental refuge from disease. Thermal disease refuges have been extensively studied in response to climate warming, but other environmental factors may also provide environmental disease refuges which, in turn, respond to global change. Here, we (1) showcase laboratory and natural examples of refuges from parasites along various environmental gradients, and (2) provide hypotheses on how global environmental change may affect these refuges. We strive to synthesize knowledge on potential environmental disease refuges along different environmental gradients including salinity and nutrients, in both natural and food-production systems. Although scaling up from single host-parasite relationships along one environmental gradient to their interaction outcome in the full complexity of natural environments remains difficult, integrating host and parasite performance-response can serve to formulate testable hypotheses about the variability in parasitism outcomes and the occurrence of environmental disease refuges under current and future environmental conditions.}, }
@article {pmid36796331, year = {2023}, author = {Sanchez, A and Bajic, D and Diaz-Colunga, J and Skwara, A and Vila, JCC and Kuehn, S}, title = {The community-function landscape of microbial consortia.}, journal = {Cell systems}, volume = {14}, number = {2}, pages = {122-134}, doi = {10.1016/j.cels.2022.12.011}, pmid = {36796331}, issn = {2405-4720}, mesh = {*Microbial Consortia/genetics ; *Microbiota/genetics ; Ecology ; }, abstract = {Quantitatively linking the composition and function of microbial communities is a major aspiration of microbial ecology. Microbial community functions emerge from a complex web of molecular interactions between cells, which give rise to population-level interactions among strains and species. Incorporating this complexity into predictive models is highly challenging. Inspired by a similar problem in genetics of predicting quantitative phenotypes from genotypes, an ecological community-function (or structure-function) landscape could be defined that maps community composition and function. In this piece, we present an overview of our current understanding of these community landscapes, their uses, limitations, and open questions. We argue that exploiting the parallels between both landscapes could bring powerful predictive methodologies from evolution and genetics into ecology, providing a boost to our ability to engineer and optimize microbial consortia.}, }
@article {pmid36792869, year = {2023}, author = {Tai, JB and Ferrell, MJ and Yan, J and Waters, CM}, title = {New Insights into Vibrio cholerae Biofilms from Molecular Biophysics to Microbial Ecology.}, journal = {Advances in experimental medicine and biology}, volume = {1404}, number = {}, pages = {17-39}, pmid = {36792869}, issn = {0065-2598}, support = {DP2 GM146253/GM/NIGMS NIH HHS/United States ; R01 AI158433/AI/NIAID NIH HHS/United States ; R35 GM139537/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Vibrio cholerae ; *Cholera/epidemiology/microbiology ; Pandemics ; *COVID-19 ; Biofilms ; }, abstract = {With the discovery that 48% of cholera infections in rural Bangladesh villages could be prevented by simple filtration of unpurified waters and the detection of Vibrio cholerae aggregates in stools from cholera patients it was realized V. cholerae biofilms had a central function in cholera pathogenesis. We are currently in the seventh cholera pandemic, caused by O1 serotypes of the El Tor biotypes strains, which initiated in 1961. It is estimated that V. cholerae annually causes millions of infections and over 100,000 deaths. Given the continued emergence of cholera in areas that lack access to clean water, such as Haiti after the 2010 earthquake or the ongoing Yemen civil war, increasing our understanding of cholera disease remains a worldwide public health priority. The surveillance and treatment of cholera is also affected as the world is impacted by the COVID-19 pandemic, raising significant concerns in Africa. In addition to the importance of biofilm formation in its life cycle, V. cholerae has become a key model system for understanding bacterial signal transduction networks that regulate biofilm formation and discovering fundamental principles about bacterial surface attachment and biofilm maturation. This chapter will highlight recent insights into V. cholerae biofilms including their structure, ecological role in environmental survival and infection, regulatory systems that control them, and biomechanical insights into the nature of V. cholerae biofilms.}, }
@article {pmid36790500, year = {2023}, author = {Elsherbini, J and Corzett, C and Ravaglioli, C and Tamburello, L and Polz, M and Bulleri, F}, title = {Epilithic Bacterial Assemblages on Subtidal Rocky Reefs: Variation Among Alternative Habitats at Ambient and Enhanced Nutrient Levels.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1552-1564}, pmid = {36790500}, issn = {1432-184X}, mesh = {Animals ; *Ecosystem ; *Forests ; Nutrients ; Sea Urchins ; Coral Reefs ; }, abstract = {Temperate rocky reefs often support mosaics of alternative habitats such as macroalgal forests, algal turfs and sea urchin barrens. Although the composition of epilithic microbial biofilms (EMBs) is recognized as a major determinant of macroalgal recruitment, their role in regulating the stability of alternative habitats on temperate rocky reefs remains unexplored. On shallow rocky reefs of the Island of Capraia (NW Mediterranean), we compared EMB structure among canopy stands formed by the fucoid Ericaria brachycarpa, algal turfs, and urchin barrens under ambient versus experimentally enhanced nutrient levels. The three habitats shared a core microbial community consisting of 21.6 and 25.3% of total ASVs under ambient and enhanced nutrient conditions, respectively. Although Gammaproteobacteria, Alphaproteobacteria and Flavobacteriia were the most abundant classes across habitats, multivariate analyses at the ASV level showed marked differences in EMB composition among habitats. Enhancing nutrient level had no significant effect on EMBs, although it increased their similarity between macroalgal canopy and turf habitats. At both ambient and enriched nutrient levels, ASVs mostly belonging to Proteobacteria and Bacteroidetes were more abundant in EMBs from macroalgal canopies than barrens. In contrast, ASVs belonging to the phylum of Proteobacteria and, in particular, to the families of Rhodobacteraceae and Flavobacteriaceae at ambient nutrient levels and of Rhodobacteraceae and Bacteriovoracaceae at enhanced nutrient levels were more abundant in turf than canopy habitats. Our results show that primary surfaces from alternative habitats that form mosaics on shallow rocky reefs in oligotrophic areas host distinct microbial communities that are, to some extent, resistant to moderate nutrient enhancement. Understanding the role of EMBs in generating reinforcing feedback under different nutrient loading regimes appears crucial to advance our understanding of the mechanisms underpinning the stability of habitats alternative to macroalgal forests as well as their role in regulating reverse shifts.}, }
@article {pmid36788337, year = {2023}, author = {Bayer, N and Hausmann, B and Pandey, RV and Deckert, F and Gail, LM and Strobl, J and Pjevac, P and Krall, C and Unterluggauer, L and Redl, A and Bachmayr, V and Kleissl, L and Nehr, M and Kirkegaard, R and Makristathis, A and Watzenboeck, ML and Nica, R and Staud, C and Hammerl, L and Wohlfarth, P and Ecker, RC and Knapp, S and Rabitsch, W and Berry, D and Stary, G}, title = {Correction: Disturbances in microbial skin recolonization and cutaneous immune response following allogeneic stem cell transfer.}, journal = {Leukemia}, volume = {37}, number = {3}, pages = {724}, doi = {10.1038/s41375-023-01839-7}, pmid = {36788337}, issn = {1476-5551}, }
@article {pmid36786580, year = {2023}, author = {Gittins, DA and Bhatnagar, S and Hubert, CRJ}, title = {Environmental Selection and Biogeography Shape the Microbiome of Subsurface Petroleum Reservoirs.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0088422}, pmid = {36786580}, issn = {2379-5077}, mesh = {*Petroleum/metabolism ; RNA, Ribosomal, 16S/genetics ; Oil and Gas Fields ; *Microbiota/genetics ; Carbon ; }, abstract = {Petroleum reservoirs within the deep biosphere are extreme environments inhabited by diverse microbial communities and represent biogeochemical hot spots in the subsurface. Despite the ecological and industrial importance of oil reservoir microbiomes, systematic study of core microbial taxa and their associated genomic attributes spanning different environmental conditions is limited. Here, we compile and compare 343 16S rRNA gene amplicon libraries and 25 shotgun metagenomic libraries from oil reservoirs in different parts of the world to test for the presence of core taxa and functions. These oil reservoir libraries do not share any core taxa at the species, genus, family, or order levels, and Gammaproteobacteria was the only taxonomic class detected in all samples. Instead, taxonomic composition varies among reservoirs with different physicochemical characteristics and with geographic distance highlighting environmental selection and biogeography in these deep biosphere habitats. Gene-centric metagenomic analysis reveals a functional core of metabolic pathways including carbon acquisition and energy-yielding strategies consistent with biogeochemical cycling in other subsurface environments. Genes for anaerobic hydrocarbon degradation are observed in a subset of the samples and are therefore not considered to represent core functions in oil reservoirs despite hydrocarbons representing an abundant source of carbon in these deep biosphere settings. Overall, this work reveals common and divergent features of oil reservoir microbiomes that are shaped by and responsive to environmental factors, highlighting controls on subsurface microbial community assembly. IMPORTANCE This comprehensive analysis showcases how environmental selection and geographic distance influence the microbiome of subsurface petroleum reservoirs. We reveal substantial differences in the taxonomy of the inhabiting microbes but shared metabolic function between reservoirs with different in situ temperatures and between reservoirs separated by large distances. The study helps understand and advance the field of deep biosphere science by providing an ecological framework and footing for geologists, chemists, and microbiologists studying these habitats to elucidate major controls on deep biosphere microbial ecology.}, }
@article {pmid36786571, year = {2023}, author = {Ji, M and Fan, X and Cornell, CR and Zhang, Y and Yuan, MM and Tian, Z and Sun, K and Gao, R and Liu, Y and Zhou, J}, title = {Tundra Soil Viruses Mediate Responses of Microbial Communities to Climate Warming.}, journal = {mBio}, volume = {14}, number = {2}, pages = {e0300922}, pmid = {36786571}, issn = {2150-7511}, mesh = {Soil/chemistry ; Biodiversity ; Temperature ; Tundra ; *Microbiota/physiology ; Climate Change ; *Viruses/metabolism ; Soil Microbiology ; Carbon/metabolism ; }, abstract = {The rise of global temperature causes the degradation of the substantial reserves of carbon (C) stored in tundra soils, in which microbial processes play critical roles. Viruses are known to influence the soil C cycle by encoding auxiliary metabolic genes and infecting key microorganisms, but their regulation of microbial communities under climate warming remains unexplored. In this study, we evaluated the responses of viral communities for about 5 years of experimental warming at two depths (15 to 25 cm and 45 to 55 cm) in the Alaskan permafrost region. Our results showed that the viral community and functional gene composition and abundances (including viral functional genes related to replication, structure, infection, and lysis) were significantly influenced by environmental conditions such as total nitrogen (N), total C, and soil thawing duration. Although long-term warming did not impact the viral community composition at the two depths, some glycoside hydrolases encoded by viruses were more abundant at both depths of the warmed plots. With the continuous reduction of total C, viruses may alleviate methane release by altering infection strategies on methanogens. Importantly, viruses can adopt lysogenic and lytic lifestyles to manipulate microbial communities at different soil depths, respectively, which could be one of the major factors causing the differences in microbial responses to warming. This study provides a new ecological perspective on how viruses regulate the responses of microbes to warming at community and functional scales. IMPORTANCE Permafrost thawing causes microbial release of greenhouse gases, exacerbating climate warming. Some previous studies examined the responses of the microbial communities and functions to warming in permafrost region, but the roles of viruses in mediating the responses of microbial communities to warming are poorly understood. This study revealed that warming induced changes in some viral functional classes and in the virus/microbe ratios for specific lineages, which might influence the entire microbial community. Furthermore, differences in viral communities and functions, along with soil depths, are important factors influencing microbial responses to warming. Collectively, our study revealed the regulation of microbial communities by viruses and demonstrated the importance of viruses in the microbial ecology research.}, }
@article {pmid36786067, year = {2023}, author = {Caroli, AP and Mansoldo, FRP and Cardoso, VS and Lage, CLS and Carmo, FL and Supuran, CT and Beatriz Vermelho, A}, title = {Are patents important indicators of innovation for Chagas disease treatment?.}, journal = {Expert opinion on therapeutic patents}, volume = {33}, number = {3}, pages = {193-209}, doi = {10.1080/13543776.2023.2176219}, pmid = {36786067}, issn = {1744-7674}, mesh = {Humans ; *Trypanosoma cruzi ; Patents as Topic ; *Chagas Disease/drug therapy/epidemiology/parasitology ; Drug Delivery Systems ; *Trypanocidal Agents/pharmacology/therapeutic use ; }, abstract = {INTRODUCTION: Chagas disease is a neglected, endemic disease in 21 countries, spreading to non-endemic countries too. Like other neglected diseases affecting primarily low- and middle-income countries, low investment and the absence of new chemical entities from the industry occurred. Increased knowledge about the parasite, drug targets, and vector control has been observed, but this was not translated into new drugs. The partnerships of pharmaceutical companies with academies and consolidated networks to increment the new drugs and treatment research in Chagas disease are shown. The current review analyzes in detail the patents dealing with compounds candidates for new drugs and treatment. The patent search was performed using Orbit Intelligence® software in the 2001-2021 period.<br><br>AREAS COVERED: The author focused specifically on patents for the treatment, the new candidates disclosed in the patents, and the barriers to innovation.<br><br>EXPERT OPINION: Patents in Chagas disease have been increasing in the last years, although they do not bring new compounds to an effective treatment.}, }
@article {pmid36781140, year = {2023}, author = {Vos, M and Hering, D and Gessner, MO and Leese, F and Schäfer, RB and Tollrian, R and Boenigk, J and Haase, P and Meckenstock, R and Baikova, D and Bayat, H and Beermann, A and Beisser, D and Beszteri, B and Birk, S and Boden, L and Brauer, V and Brauns, M and Buchner, D and Burfeid-Castellanos, A and David, G and Deep, A and Doliwa, A and Dunthorn, M and Enß, J and Escobar-Sierra, C and Feld, CK and Fohrer, N and Grabner, D and Hadziomerovic, U and Jähnig, SC and Jochmann, M and Khaliq, S and Kiesel, J and Kuppels, A and Lampert, KP and Le, TTY and Lorenz, AW and Madariaga, GM and Meyer, B and Pantel, JH and Pimentel, IM and Mayombo, NS and Nguyen, HH and Peters, K and Pfeifer, SM and Prati, S and Probst, AJ and Reiner, D and Rolauffs, P and Schlenker, A and Schmidt, TC and Shah, M and Sieber, G and Stach, TL and Tielke, AK and Vermiert, AM and Weiss, M and Weitere, M and Sures, B}, title = {The Asymmetric Response Concept explains ecological consequences of multiple stressor exposure and release.}, journal = {The Science of the total environment}, volume = {872}, number = {}, pages = {162196}, doi = {10.1016/j.scitotenv.2023.162196}, pmid = {36781140}, issn = {1879-1026}, mesh = {*Ecosystem ; *Rivers ; }, abstract = {Our capacity to predict trajectories of ecosystem degradation and recovery is limited, especially when impairments are caused by multiple stressors. Recovery may be fast or slow and either complete or partial, sometimes result in novel ecosystem states or even fail completely. Here, we introduce the Asymmetric Response Concept (ARC) that provides a basis for exploring and predicting the pace and magnitude of ecological responses to, and release from, multiple stressors. The ARC holds that three key mechanisms govern population, community and ecosystem trajectories. Stress tolerance is the main mechanism determining responses to increasing stressor intensity, whereas dispersal and biotic interactions predominantly govern responses to the release from stressors. The shifting importance of these mechanisms creates asymmetries between the ecological trajectories that follow increasing and decreasing stressor intensities. This recognition helps to understand multiple stressor impacts and to predict which measures will restore communities that are resistant to restoration.}, }
@article {pmid36775167, year = {2023}, author = {Archer, SDJ and Lee, KC and Caruso, T and Alcami, A and Araya, JG and Cary, SC and Cowan, DA and Etchebehere, C and Gantsetseg, B and Gomez-Silva, B and Hartery, S and Hogg, ID and Kansour, MK and Lawrence, T and Lee, CK and Lee, PKH and Leopold, M and Leung, MHY and Maki, T and McKay, CP and Al Mailem, DM and Ramond, JB and Rastrojo, A and Šantl-Temkiv, T and Sun, HJ and Tong, X and Vandenbrink, B and Warren-Rhodes, KA and Pointing, SB}, title = {Contribution of soil bacteria to the atmosphere across biomes.}, journal = {The Science of the total environment}, volume = {871}, number = {}, pages = {162137}, doi = {10.1016/j.scitotenv.2023.162137}, pmid = {36775167}, issn = {1879-1026}, mesh = {*Ecosystem ; Soil ; Bacteria ; Atmosphere ; *Microbiota ; Temperature ; Soil Microbiology ; }, abstract = {The dispersion of microorganisms through the atmosphere is a continual and essential process that underpins biogeography and ecosystem development and function. Despite the ubiquity of atmospheric microorganisms globally, specific knowledge of the determinants of atmospheric microbial diversity at any given location remains unresolved. Here we describe bacterial diversity in the atmospheric boundary layer and underlying soil at twelve globally distributed locations encompassing all major biomes, and characterise the contribution of local and distant soils to the observed atmospheric community. Across biomes the diversity of bacteria in the atmosphere was negatively correlated with mean annual precipitation but positively correlated to mean annual temperature. We identified distinct non-randomly assembled atmosphere and soil communities from each location, and some broad trends persisted across biomes including the enrichment of desiccation and UV tolerant taxa in the atmospheric community. Source tracking revealed that local soils were more influential than distant soil sources in determining observed diversity in the atmosphere, with more emissive semi-arid and arid biomes contributing most to signatures from distant soil. Our findings highlight complexities in the atmospheric microbiota that are relevant to understanding regional and global ecosystem connectivity.}, }
@article {pmid36775144, year = {2023}, author = {Liu, L and Zhu, L and Yan, R and Yang, Y and Adams, JM and Liu, J}, title = {Abundant bacterial subcommunity is structured by a stochastic process in an agricultural system with P fertilizer inputs.}, journal = {The Science of the total environment}, volume = {871}, number = {}, pages = {162178}, doi = {10.1016/j.scitotenv.2023.162178}, pmid = {36775144}, issn = {1879-1026}, mesh = {*Ecosystem ; *Fertilizers ; Soil Microbiology ; Soil ; Bacteria ; Stochastic Processes ; }, abstract = {Soil microorganisms play an important role in agroecosystems and are related to ecosystem functioning. Nevertheless, little is understood about their community assembly and the major factors regulating stochastic and deterministic processes, particularly with respect to the comparison of abundant and rare bacterial subcommunities in agricultural systems. Here, we investigated the assembly of abundant and rare bacterial subcommunities in fields with different crops (maize and wheat) and phosphorus (P) fertilizer input at three different growth stages on the Loess Plateau. The high-throughput sequencing dataset was assessed using null and neutral community models. We found that abundant bacteria was governed by the stochastic process of homogenizing dispersal, but rare bacterial subcommunity was predominant by deterministic processes in maize and wheat fields due to broader niche breadths of abundant species. Soil nitrogen (N) and P also determined the assembly of abundant and rare soil subcommunities. The relative abundance and composition of the abundant and rare bacterial subcommunities were also influenced by soil nutrients (soil available P (AP) and NO3[-]-N) and agricultural practices (P fertilization and crop cultivation). In addition, the abundant bacterial community was more susceptible to P fertilizer input than that of the rare bacteria, and a higher relative abundance of abundant bacteria was observed in the P70 treatment both in maize and wheat soils. The microbial co-occurrence network analysis indicated that the maize field and low nutrient treatment exhibited stronger associations and that the abundant bacteria showed fewer interconnections. This study provides new insights toward understanding the mechanisms for the assembly of abundant and rare bacterial taxa in dryland cropping systems, enhancing our understanding of ecosystem diversity theory in microbial ecology.}, }
@article {pmid36773920, year = {2023}, author = {Pico-Tomàs, A and Mejías-Molina, C and Zammit, I and Rusiñol, M and Bofill-Mas, S and Borrego, CM and Corominas, L}, title = {Surveillance of SARS-CoV-2 in sewage from buildings housing residents with different vulnerability levels.}, journal = {The Science of the total environment}, volume = {872}, number = {}, pages = {162116}, pmid = {36773920}, issn = {1879-1026}, mesh = {Aged ; Humans ; *Sewage ; Wastewater ; SARS-CoV-2 ; Housing ; *COVID-19/epidemiology ; }, abstract = {During the last three years, various restrictions have been set up to limit the transmission of the Coronavirus Disease (COVID-19). While these rules apply at a large scale (e.g., country-wide level) human-to-human transmission of the virus that causes COVID-19, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), occurs at a small scale. Different preventive policies and testing protocols were implemented in buildings where COVID-19 poses a threat (e.g., elderly residences) or constitutes a disruptive force (e.g., schools). In this study, we sampled sewage from different buildings (a school, a university campus, a university residence, and an elderly residence) that host residents of different levels of vulnerability. Our main goal was to assess the agreement between the SARS-CoV-2 concentration in wastewater and the policies applied in these buildings. All buildings were sampled using passive samplers while 24 h composite samples were also collected from the elderly residence. Results showed that passive samplers performed comparably well to composite samples while being cost-effective to keep track of COVID-19 prevalence. In the elderly residence, the comparison of sampling protocols (passive vs. active) combined with the strict clinical testing allowed us to compare the sensitivities of the two methods. Active sampling was more sensitive than passive sampling, as the former was able to detect a COVID-19 prevalence of 0.4 %, compared to a prevalence of 2.2 % for passive sampling. The number of COVID-19-positive individuals was tracked clinically in all the monitored buildings. More frequent detection of SARS-CoV-2 in wastewater was observed in residential buildings than in non-residential buildings using passive samplers. In all buildings, sewage surveillance can be used to complement COVID-19 clinical testing regimes, as the detection of SARS-CoV-2 in wastewater remained positive even when no COVID-19-positive individuals were reported. Passive sampling is useful for building managers to adapt their COVID-19 mitigation policies.}, }
@article {pmid36773636, year = {2023}, author = {Honeyman, AS and Merl, T and Spear, JR and Koren, K}, title = {Optode-based chemical imaging of laboratory burned soil reveals millimeter-scale heterogeneous biogeochemical responses.}, journal = {Environmental research}, volume = {224}, number = {}, pages = {115469}, doi = {10.1016/j.envres.2023.115469}, pmid = {36773636}, issn = {1096-0953}, mesh = {*Soil/chemistry ; *Bacteria/metabolism ; Archaea/genetics ; Water ; RNA/metabolism ; Soil Microbiology ; }, abstract = {Soil spatial responses to fire are unclear. Using optical chemical sensing with planar 'optodes', pH and dissolved O2 concentration were tracked spatially with a resolution of 360 μm per pixel for 72 h after burning soil in the laboratory with a butane torch (∼1300 °C) and then sprinkling water to simulate a postfire moisture event. Imaging data from planar optodes correlated with microbial activity (quantified via RNA transcripts). Post-fire and post-wetting, soil pH increased throughout the entire ∼13 cm × 17 cm × 20 cm rectangular cuboid of sandy loam soil. Dissolved O2 concentrations were not impacted until the application of water postfire. pH and dissolved O2 both negatively correlated (p < 0.05) with relative transcript expression for galactose metabolism, the degradation of aromatic compounds, sulfur metabolism, and narH. Additionally, dissolved O2 negatively correlated (p < 0.05) with the relative activity of carbon fixation pathways in Bacteria and Archaea, amoA/amoB, narG, nirK, and nosZ. nifH was not detected in any samples. Only amoB and amoC correlated with depth in soil (p < 0.05). Results demonstrate that postfire soils are spatially complex on a mm scale and that using optode-based chemical imaging as a chemical navigator for RNA transcript sampling is effective.}, }
@article {pmid36771744, year = {2023}, author = {Vasilchenko, AV and Poshvina, DV and Semenov, MV and Timofeev, VN and Iashnikov, AV and Stepanov, AA and Pervushina, AN and Vasilchenko, AS}, title = {Triazoles and Strobilurin Mixture Affects Soil Microbial Community and Incidences of Wheat Diseases.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, pmid = {36771744}, issn = {2223-7747}, support = {075-15-2021-1345 unique identifier RF----193021X0012//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Pesticides are widely used in agriculture as a pest control strategy. Despite the benefits of pesticides on crop yields, the persistence of chemical residues in soil has an unintended impact on non-targeted microorganisms. In the present study, we evaluated the potential adverse effects of a mixture of fungicides (difenoconazole, epoxiconazole, and kresoxim-methyl) on soil fungal and bacterial communities, as well as the manifestation of wheat diseases. In the fungicide-treated soil, the Shannon indices of both fungal and bacterial communities decreased, whereas the Chao1 indices did not differ compared to the control soil. Among bacterial taxa, the relative abundances of Arthrobacter and Sphingomonas increased in fungicide-treated soil due to their ability to utilize fungicides and other toxic compounds. Rhizopus and plant-beneficial Chaetomium were the dominant fungal genera, with their prevalence increasing by 2-4 times in the fungicide-treated soil. The genus Fusarium, which includes phytopathogenic species, which are notably responsible for root rot, was the most abundant taxon in each of the two conditions but its relative abundance was two times lower in fungicide-treated soils, consistent with a lower level of disease incidence in plants. The prediction of metabolic pathways revealed that the soil bacterial community had a high potential for degrading various pollutants, and the soil fungal community was in a state of recovery after the application of quinone outside inhibitor (QoI) fungicides. Fungicide-treated soil was characterized by an increase in soil microbial carbon, compared with the control soil. Collectively, the obtained results suggest that the application of difenoconazole, epoxiconazole, and kresoxim-methyl is an effective approach for pest control that does not pose a hazard for the soil ecosystem in the short term. However, it is necessary to carry out additional sampling to take into account the spatio-temporal impact of this fungicide mixture on the functional properties of the soil.}, }
@article {pmid36766201, year = {2023}, author = {Mudoor Sooresh, M and Willing, BP and Bourrie, BCT}, title = {Opportunities and Challenges of Understanding Community Assembly in Spontaneous Food Fermentation.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, pmid = {36766201}, issn = {2304-8158}, support = {202102309//Alberta Innovates/ ; ALLRP-556600-20//Natural Sciences and Engineering Research Council/ ; }, abstract = {Spontaneous fermentations that do not rely on backslopping or industrial starter cultures were especially important to the early development of society and are still practiced around the world today. While current literature on spontaneous fermentations is observational and descriptive, it is important to understand the underlying mechanism of microbial community assembly and how this correlates with changes observed in microbial succession, composition, interaction, and metabolite production. Spontaneous food and beverage fermentations are home to autochthonous bacteria and fungi that are naturally inoculated from raw materials, environment, and equipment. This review discusses the factors that play an important role in microbial community assembly, particularly focusing on commonly reported yeasts and bacteria isolated from spontaneously fermenting food and beverages, and how this affects the fermentation dynamics. A wide range of studies have been conducted in spontaneously fermented foods that highlight some of the mechanisms that are involved in microbial interactions, niche adaptation, and lifestyle of these microorganisms. Moreover, we will also highlight how controlled culture experiments provide greater insight into understanding microbial interactions, a modest attempt in decoding the complexity of spontaneous fermentations. Further research using specific in vitro microbial models to understand the role of core microbiota are needed to fill the knowledge gap that currently exists in understanding how the phenotypic and genotypic expression of these microorganisms aid in their successful adaptation and shape fermentation outcomes. Furthermore, there is still a vast opportunity to understand strain level implications on community assembly. Translating these findings will also help in improving other fermentation systems to help gain more control over the fermentation process and maintain consistent and superior product quality.}, }
@article {pmid36765824, year = {2023}, author = {Pandey, H and Tang, DWT and Wong, SH and Lal, D}, title = {Gut Microbiota in Colorectal Cancer: Biological Role and Therapeutic Opportunities.}, journal = {Cancers}, volume = {15}, number = {3}, pages = {}, pmid = {36765824}, issn = {2072-6694}, support = {021337-00001//NTU Start Up Grant and Wang Lee Wah Memorial Fund/ ; }, abstract = {Colorectal cancer (CRC) is the second-leading cause of cancer-related deaths worldwide. While CRC is thought to be an interplay between genetic and environmental factors, several lines of evidence suggest the involvement of gut microbiota in promoting inflammation and tumor progression. Gut microbiota refer to the ~40 trillion microorganisms that inhabit the human gut. Advances in next-generation sequencing technologies and metagenomics have provided new insights into the gut microbial ecology and have helped in linking gut microbiota to CRC. Many studies carried out in humans and animal models have emphasized the role of certain gut bacteria, such as Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and colibactin-producing Escherichia coli, in the onset and progression of CRC. Metagenomic studies have opened up new avenues for the application of gut microbiota in the diagnosis, prevention, and treatment of CRC. This review article summarizes the role of gut microbiota in CRC development and its use as a biomarker to predict the disease and its potential therapeutic applications.}, }
@article {pmid36765150, year = {2023}, author = {Xu, G and Zhao, X and Zhao, S and Rogers, MJ and He, J}, title = {Salinity determines performance, functional populations, and microbial ecology in consortia attenuating organohalide pollutants.}, journal = {The ISME journal}, volume = {17}, number = {5}, pages = {660-670}, pmid = {36765150}, issn = {1751-7370}, mesh = {*Chloroflexi/genetics ; *Environmental Pollutants ; Salinity ; *Polychlorinated Biphenyls/analysis/chemistry ; Biodegradation, Environmental ; *Microbiota ; Physical Functional Performance ; }, abstract = {Organohalide pollutants are prevalent in coastal regions due to extensive intervention by anthropogenic activities, threatening public health and ecosystems. Gradients in salinity are a natural feature of coasts, but their impacts on the environmental fate of organohalides and the underlying microbial communities remain poorly understood. Here we report the effects of salinity on microbial reductive dechlorination of tetrachloroethene (PCE) and polychlorinated biphenyls (PCBs) in consortia derived from distinct environments (freshwater and marine sediments). Marine-derived microcosms exhibited higher halotolerance during PCE and PCB dechlorination, and a halotolerant dechlorinating culture was enriched from these microcosms. The organohalide-respiring bacteria (OHRB) responsible for PCE and PCB dechlorination in marine microcosms shifted from Dehalococcoides to Dehalobium when salinity increased. Broadly, lower microbial diversity, simpler co-occurrence networks, and more deterministic microbial community assemblages were observed under higher salinity. Separately, we observed that inhibition of dechlorination by high salinity could be attributed to suppressed viability of Dehalococcoides rather than reduced provision of substrates by syntrophic microorganisms. Additionally, the high activity of PCE dechlorinating reductive dehalogenases (RDases) in in vitro tests under high salinity suggests that high salinity likely disrupted cellular components other than RDases in Dehalococcoides. Genomic analyses indicated that the capability of Dehalobium to perform dehalogenation under high salinity was likely owing to the presence of genes associated with halotolerance in its genomes. Collectively, these mechanistic and ecological insights contribute to understanding the fate and bioremediation of organohalide pollutants in environments with changing salinity.}, }
@article {pmid36764950, year = {2023}, author = {Kim, C and Staver, LW and Chen, X and Bulseco, A and Cornwell, JC and Malkin, SY}, title = {Microbial Community Succession Along a Chronosequence in Constructed Salt Marsh Soils.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {931-950}, pmid = {36764950}, issn = {1432-184X}, mesh = {*Wetlands ; Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Methane ; }, abstract = {In this study, we examined the succession of soil microbial communities across a chronosequence of newly constructed salt marshes constructed primarily of fine-grained dredge material, using 16S rRNA amplicon sequences. Alpha diversity in the subsurface horizons was initially low and increased to reference levels within 3 years of marsh construction, while alpha diversity in the newly accumulating organic matter-rich surface soils was initially high and remained unchanged. Microbial community succession was fastest in the surface horizon (~ 24 years to reference equivalency) and became progressively slower with depth in the subsurface horizons (~ 30-67 years). Random forest linear regression analysis was used to identify important taxa driving the trajectories toward reference conditions. In the parent material, putative sulfate-reducers (Desulfobacterota), methanogens (Crenarchaeota, especially Methanosaeta), and fermenters (Chloroflexi and Clostridia) increased over time, suggesting an enrichment of these metabolisms over time, similar to natural marshes. Concurrently in the surface soils, the relative abundances of putative methane-, methyl-, and sulfide oxidizers, especially among Gammaproteobacteria, increased over time, suggesting the co-development of sulfide and methane removal metabolisms in marsh soils. Finally, we observed that the surface soil communities at one of the marshes did not follow the trajectory of the others, exhibiting a greater relative abundance of anaerobic taxa. Uniquely in this dataset, this marsh was developing signs of excessive inundation stress in terms of vegetation coverage and soil geochemistry. Therefore, we suggest that soil microbial community structure may be effective bioindicators of salt marsh inundation and are worthy of further targeted investigation.}, }
@article {pmid36763113, year = {2023}, author = {Mason, ARG and Cavagnaro, TR and Guerin, GR and Lowe, AJ}, title = {Soil Bacterial Assemblage Across a Production Landscape: Agriculture Increases Diversity While Revegetation Recovers Community Composition.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {1098-1112}, pmid = {36763113}, issn = {1432-184X}, mesh = {*Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; *Agriculture ; Bacteria/genetics ; Plants ; Soil Microbiology ; }, abstract = {Aboveground ecological impacts associated with agricultural land use change are evident as natural plant communities are replaced with managed production systems. These impacts have been extensively studied, unlike those belowground, which remain poorly understood. Soil bacteria are good candidates to monitor belowground ecological dynamics due to their prevalence within the soil system and ability to survive under harsh and changing conditions. Here, we use soil physicochemical assessment and 16S rRNA gene sequencing to investigate the soil physical and bacterial assemblage changes across a mixed-use agricultural landscape. We assess soil from remnant vegetation (Eucalyptus mallee), new and old vineyards, old pasture, and recently revegetated areas. Elevated concentrations of nitrogen (NO3[-]) and plant-available (Colwell) phosphorus were identified in the managed vineyard systems, highlighting the impact of agricultural inputs on soil nutrition. Alpha diversity comparison revealed a significant difference between the remnant mallee vegetation and the vineyard systems, with vineyards supporting highest bacterial diversity. Bacterial community composition of recently revegetated areas was similar to remnant vegetation systems, suggesting that bacterial communities can respond quickly to aboveground changes, and that actions taken to restore native plant communities may also act to recover natural microbial communities, with implications for soil and plant health. Findings here suggest that agriculture may disrupt the correlation between above- and belowground diversities by altering the natural processes that otherwise govern this relationship (e.g. disturbance, plant production, diversity of inputs), leading to the promotion of belowground microbial diversity in agricultural systems.}, }
@article {pmid36758734, year = {2023}, author = {Wu, X and Chen, S and Yan, Q and Yu, F and Shao, H and Zheng, X and Zhang, X}, title = {Gpr35 shapes gut microbial ecology to modulate hepatic steatosis.}, journal = {Pharmacological research}, volume = {189}, number = {}, pages = {106690}, doi = {10.1016/j.phrs.2023.106690}, pmid = {36758734}, issn = {1096-1186}, mesh = {Mice ; Animals ; *Gastrointestinal Microbiome/genetics ; *Fatty Liver/metabolism ; Receptors, G-Protein-Coupled/metabolism ; Obesity/metabolism ; Diet, High-Fat ; Mice, Inbred C57BL ; Liver/metabolism ; }, abstract = {The gut microbiome is closely shaped by host genetic and dietary factors to regulate metabolic health and disease. However, the signaling mechanisms underlying such interactions have been largely unclear. Here we identify G protein-coupled receptor 35 (Gpr35) as a regulator of gut microbial ecology and the susceptibility to obesity and hepatic steatosis in mice. Both global and intestinal epithelia specific ablation of Gpr35 aggravated high-fat diet (HFD)-induced metabolic disturbance and hepatic steatosis in mice. Gpr35 deficiency induced a remarkable loss of goblet cells and an extensive remodeling of the gut microbiome, featuring enrichment of the Bacteroides and Ruminococcus genera. Antibiotics treatment and co-housing alleviated the metabolic disturbance markers in Gpr35 deficient mice. Spatiotemporal profiling and mono-colonization screening revealed that Ruminococcus gnavus synergized with HFD to promote hepatic steatosis possibly via tryptophan and phenylalanine pathway metabolites. Our results provide mechanistic insights into a genetic-diet-microbe interplay that dictates susceptibility to metabolic disorder.}, }
@article {pmid36758644, year = {2023}, author = {Xie, Y and Jia, M and De Wilde, F and Daeninck, K and De Clippeleir, H and Verstraete, W and Vlaeminck, SE}, title = {Feasibility of packed-bed trickling filters for partial nitritation/anammox: Effects of carrier material, bottom ventilation openings, hydraulic loading rate and free ammonia.}, journal = {Bioresource technology}, volume = {373}, number = {}, pages = {128713}, doi = {10.1016/j.biortech.2023.128713}, pmid = {36758644}, issn = {1873-2976}, mesh = {*Ammonia ; Anaerobic Ammonia Oxidation ; Feasibility Studies ; Bioreactors ; Nitrogen ; Oxidation-Reduction ; *Ammonium Compounds ; }, abstract = {This study pioneers the feasibility of cost-effective partial nitritation/anammox (PN/A) in packed-bed trickling filters (TFs). Three parallel TFs tested different carrier materials, the presence or absence of bottom ventilation openings, hydraulic loading rates (HLR, 0.4-2.2 m[3] m[-2] h[-1]), and free ammonia (FA) levels on synthetic medium. The inexpensive Argex expanded clay was recommended due to the similar nitrogen removal rates as commercially used plastics. Top-only ventilation at an optimum HLR of 1.8 m[3] m[-2] h[-1] could remove approximately 60% of the total nitrogen load (i.e., 300 mg N L[-1] d[-1], 30 °C) and achieve relatively low NO3[-]-N accumulation (13%). Likely FA levels of around 1.3-3.2 mg N L[-1] suppressed nitratation. Most of the total nitrogen removal took place in the upper third of the reactor, where anammox activity was highest. Provided further optimizations, the results demonstrated TFs are suitable for low-energy shortcut nitrogen removal.}, }
@article {pmid36758435, year = {2023}, author = {Liu, J and Xu, G and Zhao, S and Chen, C and Rogers, MJ and He, J}, title = {Mechanistic and microbial ecological insights into the impacts of micro- and nano- plastics on microbial reductive dehalogenation of organohalide pollutants.}, journal = {Journal of hazardous materials}, volume = {448}, number = {}, pages = {130895}, doi = {10.1016/j.jhazmat.2023.130895}, pmid = {36758435}, issn = {1873-3336}, mesh = {*Environmental Pollutants ; Microplastics/toxicity ; Plastics ; Ecosystem ; Biodegradation, Environmental ; }, abstract = {Micro- and nano-plastics are prevalent in diverse ecosystems, but their impacts on biotransformation of organohalide pollutants and underpinning microbial communities remain poorly understood. Here we investigated the influence of micro- and nano-plastics on microbial reductive dehalogenation at strain and community levels. Generally, microplastics including polyethylene (PE), polystyrene (PS), polylactic acid (PLA), and a weathered microplastic mixture increased dehalogenation rate by 10 - 217% in both the Dehalococcoides isolate and enrichment culture, whereas the effects of polyvinyl chloride (PVC) and a defined microplastic mixture depended on their concentrations and cultures. Contrarily, nano-PS (80 nm) consistently inhibited dehalogenation due to increased production of reactive oxygen species. Nevertheless, the enrichment culture showed higher tolerance to nano-PS inhibition, implying crucial roles of non-dehalogenating populations in ameliorating nanoplastic inhibition. The variation in dehalogenation activity was linked to altered organohalide-respiring bacteria (OHRB) growth and reductive dehalogenase (RDase) gene transcription. Moreover, microplastics changed the community structure and benefited the enrichment of OHRB, favoring the proliferation of Dehalogenimonas. More broadly, the assembly of microbial communities on plastic biofilms was more deterministic than that in the planktonic cells, with more complex co-occurrence networks in the former. Collectively, these findings contribute to better understanding the fate of organohalides in changing environments with increasing plastic pollution.}, }
@article {pmid36757423, year = {2023}, author = {Moreno, IJ and Brahamsha, B and Donia, MS and Palenik, B}, title = {Diverse Microbial Hot Spring Mat Communities at Black Canyon of the Colorado River.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1534-1551}, pmid = {36757423}, issn = {1432-184X}, mesh = {Humans ; *Hot Springs/microbiology ; RNA, Ribosomal, 16S/genetics ; Colorado ; Rivers ; Biodiversity ; *Cyanobacteria/genetics ; *Microbiota/genetics ; Phylogeny ; }, abstract = {The thermophilic microbial mat communities at hot springs in the Black Canyon of the Colorado River, thought to harbor the protistan human pathogen Naegleria fowleri, were surveyed using both culture-independent and -dependent methods to further understand the ecology of these hot spring microbiomes. Originating from Lake Mead source water, seven spring sites were sampled, varying in temperature from 25 to 55 °C. Amplicon-based high-throughput sequencing of twelve samples using 16S rRNA primers (hypervariable V4 region) revealed that most mats are dominated by cyanobacterial taxa, some but not all similar to those dominating the mats at other studied hot spring systems. 18S rRNA amplicon sequencing (V9 region) demonstrated a diverse community of protists and other eukaryotes including a highly abundant amoebal sequence related to Echinamoeba thermarum. Additional taxonomic and diversity metric analyses using near full-length 16S and 18S rRNA gene sequencing allowed a higher sequence-based resolution of the community. The mat sequence data suggest a major diversification of the cyanobacterial orders Leptolyngbyales, as well as microdiversity among several cyanobacterial taxa. Cyanobacterial isolates included some representatives of ecologically abundant taxa. A Spearman correlation analysis of short-read amplicon sequencing data supported the co-occurrences of populations of cyanobacteria, chloroflexi, and bacteroidetes providing evidence of common microbial co-occurrences across the Black Canyon hot springs.}, }
@article {pmid36755119, year = {2023}, author = {Fairén, AG and Rodríguez, N and Sánchez-García, L and Rojas, P and Uceda, ER and Carrizo, D and Amils, R and Sanz, JL}, title = {Ecological successions throughout the desiccation of Tirez lagoon (Spain) as an astrobiological time-analog for wet-to-dry transitions on Mars.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {1423}, pmid = {36755119}, issn = {2045-2322}, support = {818602/ERC_/European Research Council/International ; }, mesh = {*Extraterrestrial Environment ; Desiccation ; Spain ; *Mars ; Water ; }, abstract = {Tirez was a small and seasonal endorheic athalassohaline lagoon that was located in central Spain. In recent years, the lagoon has totally dried out, offering for the first time the opportunity to analyze its desiccation process as a "time-analog" to similar events occurred in paleolakes with varying salinity during the wet-to-dry transition on early Mars. On the martian cratered highlands, an early period of water ponding within enclosed basins evolved to a complete desiccation of the lakes, leading to deposition of evaporitic sequences during the Noachian and into the Late Hesperian. As Tirez also underwent a process of desiccation, here we describe (i) the microbial ecology of Tirez when the lagoon was still active 20 years ago, with prokaryotes adapted to extreme saline conditions; (ii) the composition of the microbial community in the dried lake sediments today, in many case groups that thrive in sediments of extreme environments; and (iii) the molecular and isotopic analysis of the lipid biomarkers that can be recovered from the sediments today. We discuss the implications of these results to better understanding the ecology of possible Martian microbial communities during the wet-to-dry transition at the end of the Hesperian, and how they may inform about research strategies to search for possible biomarkers in Mars after all the water was lost.}, }
@article {pmid36754866, year = {2023}, author = {Martiarena, MJS and Deveau, A and Montoya, QV and Flórez, LV and Rodrigues, A}, title = {The Hyphosphere of Leaf-Cutting Ant Cultivars Is Enriched with Helper Bacteria.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1773-1788}, pmid = {36754866}, issn = {1432-184X}, mesh = {Animals ; *Ants/microbiology ; Bacteria ; Hyphae ; *Actinobacteria ; Cellulose ; Symbiosis ; }, abstract = {Bacteria can live in a variety of interkingdom communities playing key ecological roles. The microbiome of leaf-cutting attine ant colonies are a remarkable example of such communities, as they support ants' metabolic processes and the maintenance of ant-fungus gardens. Studies on this topic have explored the bacterial community of the whole fungus garden, without discerning bacterial groups associated with the nutrient storage structures (gongylidia) of ant fungal cultivars. Here we studied bacteria isolated from the surface of gongylidia in the cultivars of Atta sexdens and Acromyrmex coronatus, to assess whether the bacterial community influences the biology of the fungus. A total of 10 bacterial strains were isolated from gongylidia (Bacillus sp., Lysinibacillus sp., Niallia sp., Staphylococcus sp., Paenibacillus sp., Pantoea sp., Staphylococcus sp., and one Actinobacteria). Some bacterial isolates increased gongylidia production and fungal biomass while others had inhibitory effects. Eight bacterial strains were confirmed to form biofilm-like structures on the fungal cultivar hyphae. They also showed auxiliary metabolic functions useful for the development of the fungal garden such as phosphate solubilization, siderophore production, cellulose and chitin degradation, and antifungal activity against antagonists of the fungal cultivar. Bacteria-bacteria interaction assays revealed heterogeneous behaviors including synergism and competition, which might contribute to regulate the community structure inside the garden. Our results suggest that bacteria and the ant fungal cultivar interact directly, across a continuum of positive and negative interactions within the community. These complex relationships could ultimately contribute to the stability of the ant-fungus mutualism.}, }
@article {pmid36752910, year = {2023}, author = {Campos, MA and Zhang, Q and Acuña, JJ and Rilling, JI and Ruiz, T and Carrazana, E and Reyno, C and Hollenback, A and Gray, K and Jaisi, DP and Ogram, A and Bai, J and Zhang, L and Xiao, R and Elias, M and Sadowsky, MJ and Hu, J and Jorquera, MA}, title = {Structure and Functional Properties of Bacterial Communities in Surface Sediments of the Recently Declared Nutrient-Saturated Lake Villarrica in Southern Chile.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1513-1533}, pmid = {36752910}, issn = {1432-184X}, support = {NSFC19001//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; REDES190079//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; }, mesh = {Humans ; *Lakes/microbiology ; Chile ; *Bacteria/genetics ; Proteobacteria/genetics ; Genes, Bacterial ; Bacteroidetes/genetics ; Geologic Sediments/microbiology ; }, abstract = {Lake Villarrica, one of Chile's main freshwater water bodies, was recently declared a nutrient-saturated lake due to increased phosphorus (P) and nitrogen (N) levels. Although a decontamination plan based on environmental parameters is being established, it does not consider microbial parameters. Here, we conducted high-throughput DNA sequencing and quantitative polymerase chain reaction (qPCR) analyses to reveal the structure and functional properties of bacterial communities in surface sediments collected from sites with contrasting anthropogenic pressures in Lake Villarrica. Alpha diversity revealed an elevated bacterial richness and diversity in the more anthropogenized sediments. The phylum Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria dominated the community. The principal coordinate analysis (PCoA) and redundancy analysis (RDA) showed significant differences in bacterial communities of sampling sites. Predicted functional analysis showed that N cycling functions (e.g., nitrification and denitrification) were significant. The microbial co-occurrence networks analysis suggested Chitinophagaceae, Caldilineaceae, Planctomycetaceae, and Phycisphaerae families as keystone taxa. Bacterial functional genes related to P (phoC, phoD, and phoX) and N (nifH and nosZ) cycling were detected in all samples by qPCR. In addition, an RDA related to N and P cycling revealed that physicochemical properties and functional genes were positively correlated with several nitrite-oxidizing, ammonia-oxidizing, and N-fixing bacterial genera. Finally, denitrifying gene (nosZ) was the most significant factor influencing the topological characteristics of co-occurrence networks and bacterial interactions. Our results represent one of a few approaches to elucidate the structure and role of bacterial communities in Chilean lake sediments, which might be helpful in conservation and decontamination plans.}, }
@article {pmid36752639, year = {2023}, author = {Mukherjee, S and Bhadury, P and Mitra, S and Naha, S and Saha, B and Dutta, S and Basu, S}, title = {Hypervirulent Klebsiella pneumoniae Causing Neonatal Bloodstream Infections: Emergence of NDM-1-Producing Hypervirulent ST11-K2 and ST15-K54 Strains Possessing pLVPK-Associated Markers.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0412122}, pmid = {36752639}, issn = {2165-0497}, abstract = {Klebsiella pneumoniae is a major cause of neonatal sepsis. Hypervirulent Klebsiella pneumoniae (hvKP) that cause invasive infections and/or carbapenem-resistant hvKP (CR-hvKP) limit therapeutic options. Such strains causing neonatal sepsis have rarely been studied. Characterization of neonatal septicemic hvKP/CR-hvKP strains in terms of resistance and virulence was carried out. Antibiotic susceptibility, molecular characterization, evaluation of clonality, in vitro virulence, and transmissibility of carbapenemase genes were evaluated. Whole-genome sequencing (WGS) and mouse lethality assays were performed on strains harboring pLVPK-associated markers. About one-fourth (26%, 28/107) of the studied strains, leading to mortality in 39% (11/28) of the infected neonates, were categorized as hvKP. hvKP-K2 was the prevalent pathotype (64.2%, 18/28), but K54 and K57 were also identified. Most strains were clonally diverse belonging to 12 sequence types, of which ST14 was most common. Majority of hvKPs possessed virulence determinants, strong biofilm-forming, and high serum resistance ability. Nine hvKPs were carbapenem-resistant, harboring blaNDM-1/blaNDM-5 on conjugative plasmids of different replicon types. Two NDM-1-producing high-risk clones, ST11 and ST15, had pLVPK-associated markers (rmpA, rmpA2, iroBCDEN, iucABCDiutA, and peg-344), of which one co-transferred the markers along with blaNDM-1. The 2 strains revealed high inter-genomic resemblance with the other hvKP reference genomes, and were lethal in mouse model. To the best of our knowledge, this study is the first to report on the NDM-1-producing hvKP ST11-K2 and ST15-K54 strains causing fatal neonatal sepsis. The presence of pLVPK-associated markers and blaNDM-1 in high-risk clones, and the co-transmission of these genes via conjugation calls for surveillance of these strains. IMPORTANCE Klebsiella pneumoniae is a leading cause of sepsis in newborns and adults. Among the 2 major pathotypes of K. pneumoniae, classical (cKP) and hypervirulent (hvKP), hvKP causes community-acquired severe fatal invasive infections in even healthy individuals, as it possesses several virulence factors. The lack of comprehensive studies on neonatal septicemic hvKPs prompted this work. Nearly 26% diverse hvKP strains were recovered possessing several resistance and virulence determinants. The majority of them exhibited strong biofilm-forming and high serum resistance ability. Nine of these strains were also carbapenem (last-resort antibiotic)-resistant, of which 2 high-risk clones (ST11-K2 and ST15-K54) harbored markers (pLVPK) noted for their virulence, and were lethal in the mouse model. Genome-level characterization of the high-risk clones showed resemblance with the other hvKP reference genomes. The presence of transmissible carbapenem-resistant gene, blaNDM, along with pLVPK-markers calls for vigilance, as most clinical microbiology laboratories do not test for them.}, }
@article {pmid36752053, year = {2023}, author = {Táncsics, A and Banerjee, S and Soares, A and Bedics, A and Kriszt, B}, title = {Combined Omics Approach Reveals Key Differences between Aerobic and Microaerobic Xylene-Degrading Enrichment Bacterial Communities: Rhodoferax─A Hitherto Unknown Player Emerges from the Microbial Dark Matter.}, journal = {Environmental science &amp; technology}, volume = {57}, number = {7}, pages = {2846-2855}, doi = {10.1021/acs.est.2c09283}, pmid = {36752053}, issn = {1520-5851}, mesh = {Xylenes/analysis/metabolism ; Phylogeny ; *Hydrocarbons, Aromatic/metabolism ; Bacteria/genetics ; *Dioxygenases/genetics/metabolism ; Biodegradation, Environmental ; }, abstract = {Among monoaromatic hydrocarbons, xylenes, especially the ortho and para isomers, are the least biodegradable compounds in oxygen-limited subsurface environments. Although much knowledge has been gained regarding the anaerobic degradation of xylene isomers in the past 2 decades, the diversity of those bacteria which are able to degrade them under microaerobic conditions is still unknown. To overcome this limitation, aerobic and microaerobic xylene-degrading enrichment cultures were established using groundwater taken from a xylene-contaminated site, and the associated bacterial communities were investigated using a polyphasic approach. Our results show that the xylene-degrading bacterial communities were distinctly different between aerobic and microaerobic enrichment conditions. Although members of the genus Pseudomonas were the most dominant in both types of enrichments, the Rhodoferax and Azovibrio lineages were only abundant under microaerobic conditions, while Sphingobium entirely replaced them under aerobic conditions. Analysis of a metagenome-assembled genome of a Rhodoferax-related bacterium revealed aromatic hydrocarbon-degrading ability by identifying two catechol 2,3-dioxygenases in the genome. Moreover, phylogenetic analysis indicated that both enzymes belonged to a newly defined subfamily of type I.2 extradiol dioxygenases (EDOs). Aerobic and microaerobic xylene-degradation experiments were conducted on strains Sphingobium sp. AS12 and Pseudomonas sp. MAP12, isolated from the aerobic and microaerobic enrichments, respectively. The obtained results, together with the whole-genome sequence data of the strains, confirmed the observation that members of the genus Sphingobium are excellent aromatic hydrocarbon degraders but effective only under clear aerobic conditions. Overall, it was concluded that the observed differences between the bacterial communities of aerobic and microaerobic xylene-degrading enrichments were driven primarily by (i) the method of aromatic ring activation (monooxygenation vs dioxygenation), (ii) the type of EDO enzymes, and (iii) the ability of degraders to respire utilizing nitrate.}, }
@article {pmid36750476, year = {2023}, author = {Nicolosi, G and Gonzalez-Pimentel, JL and Piano, E and Isaia, M and Miller, AZ}, title = {First Insights into the Bacterial Diversity of Mount Etna Volcanic Caves.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1632-1645}, pmid = {36750476}, issn = {1432-184X}, support = {PID2019-108672RJ-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; RYC2019-026885-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PTDC/CTA-AMB/0608/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; CEECIND/01147/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PIE_20214AT021//Consejo Superior de Investigaciones Cient&#xed;ficas/ ; }, mesh = {*Caves/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Biodiversity ; *Microbiota ; Phylogeny ; }, abstract = {While microbial communities in limestone caves across the world are relatively understood, knowledge of the microbial composition in lava tubes is lagging behind. These caves are found in volcanic regions worldwide and are typically lined with multicolored microbial mats on their walls and ceilings. The Mount Etna (Sicily, S-Italy) represents one of the most active volcanos in the world. Due to its outstanding biodiversity and geological features, it was declared Natural Heritage of Humanity by the UNESCO in 2013. Despite the presence of more than 200 basaltic lava tubes, the microbial diversity of these hypogean systems has never been investigated so far. Here, we investigated bacterial communities in four lava tubes of Mount Etna volcano. Field emission scanning electron microscopy (FESEM) was carried out for the morphological characterization and detection of microbial features. We documented an abundant presence of microbial cells with different morphotypes including rod-shaped, filamentous, and coccoidal cells with surface appendages, resembling actinobacteria reported in other lava tubes across the world. Based on 16S rRNA gene analysis, the colored microbial mats collected were mostly composed of bacteria belonging to the phyla Actinomycetota, Pseudomonadota, Acidobacteriota, Chloroflexota, and Cyanobacteria. At the genus level, the analysis revealed a dominance of the genus Crossiella, which is actively involved in biomineralization processes, followed by Pseudomonas, Bacillus, Chujaibacter, and Sphingomonas. The presence of these taxa is associated with the carbon, nitrogen, and ammonia cycles, and some are possibly related to the anthropic disturbance of these caves. This study provides the first insight into the microbial diversity of the Etna volcano lava tubes, and expands on previous research on microbiology of volcanic caves across the world.}, }
@article {pmid36749701, year = {2023}, author = {Girolamini, L and Pascale, MR and Salaris, S and Mazzotta, M and Orsini, M and Grottola, A and Zini, N and Cristino, S}, title = {Corrigendum: Legionella bononiensis sp. nov., isolated from a hotel water distribution system in northern Italy.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {2}, pages = {}, doi = {10.1099/ijsem.0.005710}, pmid = {36749701}, issn = {1466-5034}, }
@article {pmid36749697, year = {2023}, author = {Pradel, N and Fardeau, ML and Bunk, B and Spröer, C and Boedeker, C and Wolf, J and Neumann-Schaal, M and Pester, M and Spring, S}, title = {Aminithiophilus ramosus gen. nov., sp. nov., a sulphur-reducing bacterium isolated from a pyrite-forming enrichment culture, and taxonomic revision of the family Synergistaceae.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {2}, pages = {}, doi = {10.1099/ijsem.0.005691}, pmid = {36749697}, issn = {1466-5034}, mesh = {*Fatty Acids/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Base Composition ; Sequence Analysis, DNA ; *Bacteria/genetics ; Sewage/microbiology ; Sulfides ; Phospholipids/chemistry ; }, abstract = {A novel sulphur-reducing bacterium was isolated from a pyrite-forming enrichment culture inoculated with sewage sludge from a wastewater treatment plant. Based on phylogenetic data, strain J.5.4.2-T.3.5.2[T] could be affiliated with the phylum Synergistota. Among type strains of species with validly published names, the highest 16S rRNA gene sequence identity value was found with Aminiphilus circumscriptus ILE-2[T] (89.2 %). Cells of the new isolate were Gram-negative, non-spore-forming, straight to slightly curved rods with tapered ends. Motility was conferred by lateral flagella. True branching of cells was frequently observed. The strain had a strictly anaerobic, asaccharolytic, fermentative metabolism with peptides and amino acids as preferred substrates. Sulphur was required as an external electron acceptor during fermentative growth and was reduced to sulphide, whereas it was dispensable during syntrophic growth with a Methanospirillum species. Major fermentation products were acetate and propionate. The cellular fatty acid composition was dominated by unsaturated and branched fatty acids, especially iso-C15 : 0. Its major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and distinct unidentified polar lipids. Respiratory lipoquinones were not detected. Based on the obtained data we propose the novel species and genus Aminithiophilus ramosus, represented by the type strain J.5.4.2-T.3.5.2[T] (=DSM 107166[T]=NBRC 114655[T]) and the novel family Aminithiophilaceae fam. nov. to accommodate the genus Aminithiophilus. In addition, we suggest reclassifying certain members of the Synergistaceae into new families to comply with current standards for the classification of higher taxa. Based on phylogenomic data, the novel families Acetomicrobiaceae fam. nov., Aminiphilaceae fam. nov., Aminobacteriaceae fam. nov., Dethiosulfovibrionaceae fam. nov. and Thermovirgaceae fam. nov. are proposed.}, }
@article {pmid36748549, year = {2023}, author = {Soares, A and Edwards, A and An, D and Bagnoud, A and Bradley, J and Barnhart, E and Bomberg, M and Budwill, K and Caffrey, SM and Fields, M and Gralnick, J and Kadnikov, V and Momper, L and Osburn, M and Mu, A and Moreau, JW and Moser, D and Purkamo, L and Rassner, SM and Sheik, CS and Sherwood Lollar, B and Toner, BM and Voordouw, G and Wouters, K and Mitchell, AC}, title = {A global perspective on bacterial diversity in the terrestrial deep subsurface.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {1}, pages = {}, pmid = {36748549}, issn = {1465-2080}, mesh = {Water Microbiology ; Bacteria/genetics ; *Microbiota/genetics ; Biomass ; Metagenomics ; *Gammaproteobacteria ; RNA, Ribosomal, 16S ; }, abstract = {While recent efforts to catalogue Earth's microbial diversity have focused upon surface and marine habitats, 12-20 % of Earth's biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8 % in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. An in silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.}, }
@article {pmid36747985, year = {2023}, author = {Green, GBH and DePaola, A and Linville, JG and Morrow, CD and Bej, AK}, title = {High-throughput amplicon sequencing datasets of coastal sediments from three locations of the Gulf of Mexico, USA.}, journal = {Data in brief}, volume = {47}, number = {}, pages = {108895}, pmid = {36747985}, issn = {2352-3409}, support = {P30 AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR000165/TR/NCATS NIH HHS/United States ; }, abstract = {We present high-throughput amplicon sequence (HTS) datasets of the purified microbial metacommunity DNA of coastal surface sediments from Portersville Bay (PVB) (n = 3), Bayou La Batre (BLB) (n = 3), and Mobile Bay (MOB) (n = 3) of the U.S. Gulf of Mexico (U.S. Gulf Coast). The PVB samples were collected from the oyster aquaculture Shellevator™ system; the BLB samples were from locations on the shoreline adjacent to wild oysters attached to rocks and likely polluted from sewage and possibly chemical contamination from boats, shipyards, and seafood processing facilities; and MOB samples were adjacent to aquaculture oysters in bottom cages. The amplicons of the V4 hypervariable segment of the 16S rRNA gene from each sample were sequenced on an Illumina MiSeq to generate these HTS datasets. The raw sequences were quality-checked, demultiplexed into FASTQ files, denoised using DADA2, and subsampled. Then, the FASTA formatted sequences were assigned the taxonomic ids to amplicon sequence variants (ASVs) against the silva-138-99-nb-classifier using the Quantitative Insights Into Microbial Ecology (QIIME2 v2022.2). The applicability of the HTS datasets was confirmed by microbial taxa analysis at the phylum level using the "qiime taxa collapse" command. All HTS datasets are available through the BioSample Submission Portal under the BioProject ID PRJNA876773 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA876773).}, }
@article {pmid36746236, year = {2023}, author = {Zhang, L and Hu, C and Zhang, Z and Liu, R and Liu, G and Xue, D and Wang, Z and Wu, C and Wu, X and She, J and Shi, F}, title = {Association between prior appendectomy and the risk and course of Crohn's disease: A systematic review and meta-analysis.}, journal = {Clinics and research in hepatology and gastroenterology}, volume = {47}, number = {3}, pages = {102090}, doi = {10.1016/j.clinre.2023.102090}, pmid = {36746236}, issn = {2210-741X}, mesh = {Humans ; *Crohn Disease ; Appendectomy ; Cohort Studies ; *Appendix ; Case-Control Studies ; }, abstract = {BACKGROUND AND AIMS: The appendix has an important immune function in both health and disease, and appendectomy may influence microbial ecology and immune function. This meta-analysis aims to assess the association between appendectomy and the risk and course of Crohn's disease (CD).<br><br>METHODS: PubMed, EMBASE, and the Cochrane Library were used to identify all studies published until June 2022. Data from studies evaluating the association between appendectomy and CD were reviewed.<br><br>RESULTS: A total of 28 studies were included in the final analysis, comprising 22 case-control and 6 cohort studies. A positive relationship between prior appendectomy and the risk of developing CD was observed in both case-control studies (odds ratio [OR]: 1.59, 95% confidence interval [CI]: 1.22-2.08) and cohort studies (relative risk [RR]: 2.28, 95% CI: 1.66-3.14). The elevated risk of CD persisted 5 years post-appendectomy (RR&#xa0;=&#xa0;1.24, 95% CI: 1.12-1.36). The risk of developing CD was similarly elevated regardless of the presence (RR&#xa0;=&#xa0;1.64, 95% CI: 1.17-2.31) or absence (RR&#xa0;=&#xa0;2.77, 95% CI: 1.84-4.16) of appendicitis in patients. Moreover, significant differences were found in the proportion of terminal ileum lesions (OR&#xa0;=&#xa0;1.63; 95% CI: 1.38-1.93) and colon lesions (OR&#xa0;=&#xa0;0.70; 95% CI: 0.5-0.84) between CD patients with appendectomy and those without appendectomy.<br><br>CONCLUSIONS: The risk of developing CD following an appendectomy is significant and persists 5 years postoperatively. Moreover, the elevated risk of CD may mainly occur in the terminal ileum.}, }
@article {pmid36744882, year = {2023}, author = {Liu, X and Lyu, L and Li, J and Sen, B and Bai, M and Stajich, JE and Collier, JL and Wang, G}, title = {Comparative Genomic Analyses of Cellulolytic Machinery Reveal Two Nutritional Strategies of Marine Labyrinthulomycetes Protists.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0424722}, pmid = {36744882}, issn = {2165-0497}, abstract = {Labyrinthulomycetes are a group of ubiquitous and diverse unicellular Stramenopiles and have long been known for their vital role in ocean carbon cycling. However, their ecological function from the perspective of organic matter degradation remains poorly understood. This study reports high-quality genomes of two newly isolated Labyrinthulomycetes strains, namely, Botryochytrium sp. strain S-28 and Oblongichytrium sp. strain S-429, and provides molecular analysis of their ecological functions using comparative genomics and a biochemical assay. Our results suggest that Labyrinthulomycetes may occupy multiple ecological niches in marine ecosystems because of the significant differences in gene function among different genera. Certain strains could degrade wheat bran independently by secreting cellulase. The key glycoside hydrolase families (GH1, GH5, and GH9) related to cellulase and the functional domains of carbohydrate-active enzymes (CAZymes) were more enriched in their genomes. This group can actively participate in marine biochemical cycles as decomposers. In contrast, other strains that could not produce cellulase may thrive as "leftover scavengers" and act as a source of nutrients to the higher-trophic-level plankton. In addition, our findings emphasize the dual roles of endoglucanase, acting as both exo- and endoglucanases, in the process of cellulose degradation. Using genomic, biochemical, and phylogenetic analyses, our study provides a broader insight into the nutritional patterns and ecological functions of Labyrinthulomycetes. IMPORTANCE Unicellular heterotrophic eukaryotes are an important component of marine ecosystems. However, their ecological functions and modes of nutrition remain largely unknown. Our current understanding of marine microbial ecology is incomplete without integrating these heterotrophic microeukaryotes into the food web models. This study focuses on the unicellular fungus-like protists Labyrinthulomycetes and provides two high-quality genomes of cellulase-producing Labyrinthulomycetes. Our study uncovers the basis of their cellulase production by deciphering the results of genomic, biochemical, and phylogenetic analyses. This study instigates a further investigation of the molecular mechanism of organic matter utilization by Labyrinthulomycetes in the world's oceans.}, }
@article {pmid36744088, year = {2023}, author = {Wang, D and Tang, G and Yu, J and Li, Y and Wang, Y and Chen, L and Lei, X and Cao, Y and Yao, J}, title = {Litter size influences rumen microbiota and fermentation efficiency, thus determining host early growth in goats.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1098813}, pmid = {36744088}, issn = {1664-302X}, abstract = {INTRODUCTION: Multiple litters are accompanied by low birth weight, low survival rates, and growth rates in goats during early life. Regulating rumen microbiota structure can indirectly or directly affect host metabolism and animal growth. However, the relationship between high litter size and rumen microbiome, rumen fermentation, and growth performance in goat kids is unclear.<br><br>METHODS: In the present study, thirty 6-month-old, female goats were investigated, of which 10 goats were randomly chosen from single, twin and triplet goats respectively, and their birth weight was recorded. From birth, all goats were subjected to the same feed and management practices. Individual weaning and youth body weight were measured, and the rumen fluid samples were collected to characterize the bacterial communities and to determine the ruminal volatile fatty acids (VFA), free amino acids (AA), and free fatty acids (FA) concentration of those young goats.<br><br>RESULTS AND DISCUSSION: Compared with the single and twin goats, triplet goats have lower weaning and youth body weight and average daily gain (ADG). Ruminal propionate, butyrate, and total VFA were decreased in triplet goats. Meanwhile, ruminal AA, such as branched chain amino acids (BCAA), essential amino acids (EAA), unsaturated fatty acids (UFA), and monounsaturated fatty acids (MUFA) were decreased, while saturated fatty acids (SFA) and odd and branched chain fatty acids (OBCFA) were increased in triplet goats. Our results also revealed that litter size significantly affected the rumen bacterial communities, and triplet goats had a lower the Firmicutes: Bacteroidota ratio, the abundance of Firmicutes phylum, Rikenellaceae family, and Rikenellaceae RC9 gut group, and had a higher proportion of Prevotellaceae family, and several genera of Prevotellaceae, such as Prevotella, and unclassified f Prevotellaceae. Furthermore, Spearman's correlation network analysis showed that the changes in the rumen bacteria were associated with changes in rumen metabolites. In conclusion, this study revealed that high litter size could bring disturbances to the microbial communities and decrease the rumen fermentation efficiency and growth performance, which can be utilized to better understand variation in microbial ecology that will improve growth performance in triplet goats.}, }
@article {pmid36741554, year = {2022}, author = {Lombard, L and van Doorn, R and Groenewald, JZ and Tessema, T and Kuramae, EE and Etolo, DW and Raaijmakers, JM and Crous, PW}, title = {Fusarium diversity associated with the Sorghum-Striga interaction in Ethiopia.}, journal = {Fungal systematics and evolution}, volume = {10}, number = {}, pages = {177-215}, pmid = {36741554}, issn = {2589-3831}, abstract = {Sorghum production is seriously threatened by the root parasitic weeds (RPWs) Striga hermonthica and Striga asiatica in sub-Saharan Africa. Research has shown that Striga control depends on eliminating its seed reserves in soil. Several species of the genus Fusarium (Nectriaceae, Hypocreales), which have been isolated from diseased Striga plants have proven to be highly pathogenic to all developmental stages of these RPWs. In the present study 439 isolates of Fusarium spp. were found associated with soils from Sorghum growing fields, Sorghum rhizosphere, or as endophytes with Sorghum roots and seeds, or as endophytes of Striga stems and seeds. Based on multi-locus phylogenies of combinations of CaM, tef1, rpb1 and rpb2 alignments, and morphological characteristics, 42 species were identified, including three species that are newly described, namely F. extenuatum and F. tangerinum from Sorghum soils, and F. pentaseptatum from seed of Striga hermonthica. Using a previously published AFLP-derived marker that is specific to detect isolates of F. oxysporum f.sp. strigae, an effective soil-borne biocontrol agent against Striga, we also detected the gene in several other Fusarium species. As these isolates were all associated with the Striga/Sorghum pathosystem, the possibility of horizontal gene transfer among these fusaria will be of interest to further investigate in future. Citation: Lombard L, van Doorn R, Groenewald JZ, Tessema T, Kuramae EE, Etolo DW, Raaijmakers JM, Crous PW (2022). Fusarium diversity associated with the Sorghum-Striga interaction in Ethiopia. Fungal Systematics and Evolution 10: 177-215. doi: 10.3114/fuse.2022.10.08.}, }
@article {pmid36739987, year = {2023}, author = {Liu, Q and Zhu, J and Wang, L and Wang, X and Huang, Z and Zhao, F and Zou, J and Liu, Y and Ma, J}, title = {Interpreting the degradation mechanism of triclosan in microbial fuel cell by combining analysis microbiome community and degradation pathway.}, journal = {Chemosphere}, volume = {321}, number = {}, pages = {137983}, doi = {10.1016/j.chemosphere.2023.137983}, pmid = {36739987}, issn = {1879-1298}, mesh = {*Triclosan/metabolism ; *Bioelectric Energy Sources ; Biodegradation, Environmental ; Bacteria/metabolism ; *Microbiota ; }, abstract = {Microbes play a dominant role for the transformation of organic contaminants in the environment, while a significant gap exists in understanding the degradation mechanism and the function of different species. Herein, the possible bio-degradation of triclosan in microbial fuel cell was explored, with the investigation of degradation kinetics, microbial community, and possible degradation products. 5 mg/L of triclosan could be degraded within 3 days, and an intermediate degradation product (2,4-dichlorophen) could be further degraded in system. 32 kinds of dominant bacteria (relative intensity >0.5%) were identified in the biofilm, and 10 possible degradation products were identified. By analyzing the possible involved bioreactions (including decarboxylation, dehalogenation, dioxygenation, hydrolysis, hydroxylation, and ring-cleavage) of the dominant bacteria and possible degradation pathway of triclosan based on the identified products, biodegradation mechanism and function of the bacteria involved in the degradation of triclosan was clarified simultaneously. This study provides useful information for further interpreting the degradation mechanism of organic pollutants in mixed flora by combining analysis microbiome community and degradation pathway.}, }
@article {pmid36739716, year = {2023}, author = {Doni, L and Oliveri, C and Lasa, A and Di Cesare, A and Petrin, S and Martinez-Urtaza, J and Coman, F and Richardson, A and Vezzulli, L}, title = {Large-scale impact of the 2016 Marine Heatwave on the plankton-associated microbial communities of the Great Barrier Reef (Australia).}, journal = {Marine pollution bulletin}, volume = {188}, number = {}, pages = {114685}, doi = {10.1016/j.marpolbul.2023.114685}, pmid = {36739716}, issn = {1879-3363}, mesh = {Animals ; Ecosystem ; Coral Reefs ; Plankton ; RNA, Ribosomal, 16S ; *Anthozoa ; Australia ; Bacteria/genetics ; *Microbiota ; }, abstract = {The Great Barrier Reef (GBR) is the world's largest coral ecosystem and is threatened by climate change. This study investigated the impact of the 2016 Marine Heatwave (MHW) on plankton associated microbial communities along a ∼800 km transect in the GBR. 16S rRNA gene metabarcoding of archived plankton samples collected from November 2014 to August 2016 in this region showed a significant increase in Planctomycetes and bacteria belonging to the genus Vibrio and Synechococcus during and after the heatwave. Notably, Droplet Digital PCR and targeted metagenomic analysis applied on samples collected four months after the MHW event revealed the presence of several potential pathogenic Vibrio species previously associated with diseases in aquatic animals. Overall, the 2016 MHW significantly impacted the surface picoplankton community and fostered the spread of potentially pathogenic bacteria across the GBR providing an additional threat for marine biodiversity in this area.}, }
@article {pmid36737902, year = {2023}, author = {Cabezas-Terán, K and Grootaert, C and Ortiz, J and Donoso, S and Ruales, J and Van Bockstaele, F and Van Camp, J and Van de Wiele, T}, title = {In vitro bioaccessibility and uptake of β-carotene from encapsulated carotenoids from mango by-products in a coupled gastrointestinal digestion/Caco-2 cell model.}, journal = {Food research international (Ottawa, Ont.)}, volume = {164}, number = {}, pages = {112301}, doi = {10.1016/j.foodres.2022.112301}, pmid = {36737902}, issn = {1873-7145}, mesh = {Animals ; Humans ; *beta Carotene/metabolism ; Carotenoids/metabolism ; Caco-2 Cells ; *Mangifera/metabolism ; Provitamins ; Inulin ; Birds/metabolism ; Digestion ; }, abstract = {β-carotene is a carotenoid with provitamin A activity and other health benefits, which needs to become bioavailable upon oral intake to exert its biological activity. A better understanding of its behaviour and stability in the gastrointestinal tract and means to increase its bioavailability are highly needed. Using an in vitro gastrointestinal digestion method coupled to an intestinal cell model, we explored the stability, gastrointestinal bioaccessibility and cellular uptake of β-carotene from microparticles containing carotenoid extracts derived from mango by-products. Three types of microparticles were tested: one with the carotenoid extract as such, one with added inulin and one with added fructooligosaccharides. Overall, β-carotene was relatively stable during the in vitro digestion, as total recoveries were above 68 %. Prebiotics in the encapsulating material, especially inulin, enhanced the bioaccessibility of β-carotene almost 2-fold compared to microparticles without prebiotics. Likewise, β-carotene bioaccessibility increased proportionally with bile salt concentrations during digestion. Yet, a bile salts level above 10 mM did not contribute markedly to β-carotene bioaccessibility of prebiotic containing microparticles. Cellular uptake experiments with non-filtered gastrointestinal digests yielded higher absolute levels of β-carotene taken up in the epithelial cells as compared to uptake assays with filtered digests. However, the proportional uptake of β-carotene was higher for filtered digests (24 - 31 %) than for non-filtered digests (2 - 8 %). Matrix-dependent carotenoid uptake was only visible in the unfiltered medium, thereby pointing to possible other cellular transport mechanisms of non-micellarized carotenoids, besides the concentration effect. Regardless of a filtration step, inulin-amended microparticles consistently resulted in a higher β-carotene uptake than regular microparticles or FOS-amended microparticles. In conclusion, encapsulation of carotenoid extracts from mango by-products displayed chemical stability and release of a bioaccessible β-carotene fraction upon gastrointestinal digestion. This indicates the potential of the microparticles to be incorporated into functional foods with provitamin A activity.}, }
@article {pmid36737826, year = {2023}, author = {Forgie, AJ and Pepin, DM and Ju, T and Tollenaar, S and Sergi, CM and Gruenheid, S and Willing, BP}, title = {Over supplementation with vitamin B12 alters microbe-host interactions in the gut leading to accelerated Citrobacter rodentium colonization and pathogenesis in mice.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {21}, pmid = {36737826}, issn = {2049-2618}, mesh = {Humans ; Animals ; Mice ; *Vitamin B 12/pharmacology ; *Citrobacter rodentium ; Host Microbial Interactions ; Colon ; Dietary Supplements ; }, abstract = {BACKGROUND: Vitamin B12 supplements typically contain doses that far exceed the recommended daily amount, and high exposures are generally considered safe. Competitive and syntrophic interactions for B12 exist between microbes in the gut. Yet, to what extent excessive levels contribute to the activities of the gut microbiota remains unclear. The objective of this study was to evaluate the effect of B12 on microbial ecology using a B12 supplemented mouse model with Citrobacter rodentium, a mouse-specific pathogen. Mice were fed a standard chow diet and received either water or water supplemented with B12 (cyanocobalamin: ~120 μg/day), which equates to approximately 25 mg in humans. Infection severity was determined by body weight, pathogen load, and histopathologic scoring. Host biomarkers of inflammation were assessed in the colon before and after the pathogen challenge.<br><br>RESULTS: Cyanocobalamin supplementation enhanced pathogen colonization at day 1 (P < 0.05) and day 3 (P < 0.01) postinfection. The impact of B12 on gut microbial communities, although minor, was distinct and attributed to the changes in the Lachnospiraceae populations and reduced alpha diversity. Cyanocobalamin treatment disrupted the activity of the low-abundance community members of the gut microbiota. It enhanced the amount of interleukin-12 p40 subunit protein (IL12/23p40; P < 0.001) and interleukin-17a (IL-17A; P < 0.05) in the colon of na&#xef;ve mice. This immune phenotype was microbe dependent, and the response varied based on the baseline microbiota. The cecal metatranscriptome revealed that excessive cyanocobalamin decreased the expression of glucose utilizing genes by C. rodentium, a metabolic attribute previously associated with pathogen virulence.<br><br>CONCLUSIONS: Oral vitamin B12 supplementation promoted C. rodentium colonization in mice by altering the activities of the Lachnospiraceae populations in the gut. A lower abundance of select Lachnospiraceae species correlated to higher p40 subunit levels, while the detection of Parasutterella exacerbated inflammatory markers in the colon of na&#xef;ve mice. The B12-induced change in gut ecology enhanced the ability of C. rodentium colonization by impacting key microbe-host interactions that help with pathogen exclusion. This research provides insight into how B12 impacts the gut microbiota and highlights potential consequences of disrupting microbial B12 competition/sharing through over-supplementation. Video Abstract.}, }
@article {pmid36736839, year = {2023}, author = {Zhao, L and Dou, Q and Chen, S and Wang, Y and Yang, Q and Chen, W and Zhang, H and Du, Y and Xie, M}, title = {Adsorption abilities and mechanisms of Lactobacillus on various nanoplastics.}, journal = {Chemosphere}, volume = {320}, number = {}, pages = {138038}, doi = {10.1016/j.chemosphere.2023.138038}, pmid = {36736839}, issn = {1879-1298}, mesh = {Humans ; *Microplastics/chemistry ; Lactobacillus ; Adsorption ; Polypropylenes/chemistry ; Polyethylene/chemistry ; *Water Pollutants, Chemical/analysis ; Plastics/chemistry ; }, abstract = {As a new type of pollutants, nanoplastics (NPs), which are easily ingested by humans from food wraps, salt, drinking water, have been widely detected in various water environments, and are a threat to human health. It is therefore urgent to develop an efficient method to remove NPs from the diet or relief its harm. In the present study, the possibility of a well-known human probiotic, lactic acid bacteria (LAB), was evaluated to remove NPs from food as an absorbent. The results indicated that LAB from infant feces could efficiently absorb three types NPs, i.e. polypropylene (PP), polyethylene (PE), and polyvinyl chloride (PVC) with the adsorption rates of PP > PE > PVC (PP 78.57%, PE 71.59%, PVC 66.57%) and the Nile red-stained NPs being aggregated on the surfaces of Lactobacillus cells. The smaller the particle size, the stronger the ability of NP adsorption on the cell surface. The hydrophobicity of NPs and bacterial cells affected the adsorption process. The measurement of adsorption rates of different cell components indicated that the overall adsorption effect of cell was better than that of individual cell component. The results of molecular dynamics analysis revealed that adsorption was mainly caused by electrostatic interactions, van der Waals forces, and hydrogen bonds. The hydrophobic interaction was also involved in adsorption process. Overall, this research may provide new information for developing new strategies for NPs removal in intestinal environment.}, }
@article {pmid36735066, year = {2023}, author = {Modenutti, B and Martyniuk, N and Bastidas Navarro, M and Balseiro, E}, title = {Glacial Influence Affects Modularity in Bacterial Community Structure in Three Deep Andean North-Patagonian Lakes.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1869-1880}, pmid = {36735066}, issn = {1432-184X}, mesh = {*Lakes/microbiology ; *Bacteria/genetics ; Ice Cover/microbiology ; Argentina ; }, abstract = {We analyze the bacteria community composition and the ecological processes structuring these communities in three deep lakes that receive meltwater from the glaciers of Mount Tronador (North-Patagonia, Argentina). Lakes differ in their glacial connectivity and in their turbidity due to glacial particles. Lake Ventisquero Negro is a recently formed proglacial lake and it is still in contact with the glacier. Lakes Mascardi and Frías lost their glacial connectivity during the Pleistocene-Holocene transition. Total dissolved solid concentration has a significant contribution to the environmental gradient determining the segregation of the three lakes. The newly formed lake Ventisquero Negro conformed a particular bacterial community that seemed to be more related to the microorganisms coming from glacier melting than to the other lakes of the basin. The net relatedness index (NRI) showed that the bacterial community of lake Ventisquero Negro is determined by environmental filtering, while in the other lakes, species interaction would be a more important driver. The co-occurrence network analysis showed an increase in modularity and in the number of modules when comparing Lake Ventisquero Negro with the two large glacier-fed lakes suggesting an increase in heterogeneity. At the same time, the presence of modules with phototrophic bacteria (Cyanobium strains) in lakes Frías and Mascardi would reflect the increase of this functional photosynthetic association. Overall, our results showed that the reduction in ice masses in Patagonia will affect downstream large deep Piedmont lakes losing the glacial influence in their bacterial communities.}, }
@article {pmid36735065, year = {2023}, author = {Graham, EB and Knelman, JE}, title = {Implications of Soil Microbial Community Assembly for Ecosystem Restoration: Patterns, Process, and Potential.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {809-819}, pmid = {36735065}, issn = {1432-184X}, mesh = {*Ecosystem ; Soil/chemistry ; Ecology ; Soil Microbiology ; *Microbiota ; }, abstract = {While it is now widely accepted that microorganisms provide essential functions in restoration ecology, the nature of relationships between microbial community assembly and ecosystem recovery remains unclear. There has been a longstanding challenge to decipher whether microorganisms facilitate or simply follow ecosystem recovery, and evidence for each is mixed at best. We propose that understanding microbial community assembly processes is critical to understanding the role of microorganisms during ecosystem restoration and thus optimizing management strategies. We examine how the connection between environment, community structure, and function is fundamentally underpinned by the processes governing community assembly of these microbial communities. We review important factors to consider in evaluating microbial community structure in the context of ecosystem recovery as revealed in studies of microbial succession: (1) variation in community assembly processes, (2) linkages to ecosystem function, and (3) measurable microbial community attributes. We seek to empower restoration ecology with microbial assembly and successional understandings that can generate actionable insights and vital contexts for ecosystem restoration efforts.}, }
@article {pmid36735064, year = {2023}, author = {Tessler, M and Cunningham, SW and Ingala, MR and Warring, SD and Brugler, MR}, title = {An Environmental DNA Primer for Microbial and Restoration Ecology.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {796-808}, pmid = {36735064}, issn = {1432-184X}, mesh = {*DNA, Environmental/genetics ; DNA Primers ; DNA Barcoding, Taxonomic/methods ; Ecology ; DNA/genetics ; Environmental Monitoring ; Biodiversity ; }, abstract = {Environmental DNA (eDNA) sequencing-DNA collected from the environment from living cells or shed DNA-was first developed for working with microbes and has greatly benefitted microbial ecologists for decades since. These tools have only become increasingly powerful with the advent of metabarcoding and metagenomics. Most new studies that examine diverse assemblages of bacteria, archaea, protists, fungi, and viruses lean heavily into eDNA using these newer technologies, as the necessary sequencing technology and bioinformatic tools have become increasingly affordable and user friendly. However, eDNA methods are rapidly evolving, and sometimes it can feel overwhelming to simply keep up with the basics. In this review, we provide a starting point for microbial ecologists who are new to DNA-based methods by detailing the eDNA methods that are most pertinent, including study design, sample collection and storage, selecting the right sequencing technology, lab protocols, equipment, and a few bioinformatic tools. Furthermore, we focus on how eDNA work can benefit restoration and what modifications are needed when working in this subfield.}, }
@article {pmid36734313, year = {2023}, author = {Hassan, MM and van Vliet, AHM and Higgins, O and Burke, LP and Chueiri, A and O'Connor, L and Morris, D and Smith, TJ and La Ragione, RM}, title = {Rapid culture-independent loop-mediated isothermal amplification detection of antimicrobial resistance markers from environmental water samples.}, journal = {Microbial biotechnology}, volume = {16}, number = {5}, pages = {977-989}, pmid = {36734313}, issn = {1751-7915}, mesh = {Sensitivity and Specificity ; Water ; Escherichia coli ; *Escherichia coli Proteins ; Animals ; Molecular Diagnostic Techniques ; Nucleic Acid Amplification Techniques/methods ; Drug Resistance, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Humans ; }, abstract = {Environmental water is considered one of the main vehicles for the transmission of antimicrobial resistance (AMR), posing an increasing threat to humans and animals health. Continuous efforts are being made to eliminate AMR; however, the detection of AMR pathogens from water samples often requires at least one culture step, which is time-consuming and can limit sensitivity. In this study, we employed comparative genomics to identify the prevalence of AMR genes within among: Escherichia coli, Klebsiella, Salmonella enterica and Acinetobacter, using publicly available genomes. The mcr-1, blaKPC (KPC-1 to KPC-4 alleles), blaOXA-48, blaOXA-23 and blaVIM (VIM-1 and VIM-2 alleles) genes are of great medical and veterinary significance, thus were selected as targets for the development of isothermal loop-mediated amplification (LAMP) detection assays. We also developed a rapid and sensitive sample preparation method for an integrated culture-independent LAMP-based detection from water samples. The developed assays successfully detected the five AMR gene markers from pond water within 1 h and were 100% sensitive and specific with a detection limit of 0.0625 μg/mL and 10 cfu/mL for genomic DNA and spiked bacterial cells, respectively. The integrated detection can be easily implemented in resource-limited areas to enhance One Health AMR surveillances and improve diagnostics.}, }
@article {pmid36728429, year = {2023}, author = {Graffius, S and Garzón, JFG and Zehl, M and Pjevac, P and Kirkegaard, R and Flieder, M and Loy, A and Rattei, T and Ostrovsky, A and Zotchev, SB}, title = {Secondary Metabolite Production Potential in a Microbiome of the Freshwater Sponge Spongilla lacustris.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0435322}, pmid = {36728429}, issn = {2165-0497}, abstract = {Marine and freshwater sponges harbor diverse communities of bacteria with vast potential to produce secondary metabolites that may play an important role in protecting the host from predators and infections. In this work, we initially used cultivation and metagenomics to investigate the microbial community of the freshwater sponge Spongilla lacustris collected in an Austrian lake. Representatives of 41 bacterial genera were isolated from the sponge sample and classified according to their 16S rRNA gene sequences. The genomes of 33 representative isolates and the 20 recovered metagenome-assembled genomes (MAGs) contained in total 306 secondary metabolite biosynthesis gene clusters (BGCs). Comparative 16S rRNA gene and genome analyses showed very little taxon overlap between the recovered isolates and the sponge community as revealed by cultivation-independent methods. Both culture-independent and -dependent analyses suggested high biosynthetic potential of the S. lacustris microbiome, which was confirmed experimentally even at the subspecies level for two Streptomyces isolates. To our knowledge, this is the most thorough description of the secondary metabolite production potential of a freshwater sponge microbiome to date. IMPORTANCE A large body of research is dedicated to marine sponges, filter-feeding animals harboring rich bacterial microbiomes believed to play an important role in protecting the host from predators and infections. Freshwater sponges have received so far much less attention with respect to their microbiomes, members of which may produce bioactive secondary metabolites with potential to be developed into drugs to treat a variety of diseases. In this work, we investigated the potential of bacteria associated with the freshwater sponge Spongilla lacustris to biosynthesize diverse secondary metabolites. Using culture-dependent and -independent methods, we discovered over 300 biosynthetic gene clusters in sponge-associated bacteria and proved production of several compounds by selected isolates using genome mining. Our results illustrate the importance of a complex approach when dealing with microbiomes of multicellular organisms that may contain producers of medically important secondary metabolites.}, }
@article {pmid36725750, year = {2023}, author = {Tessler, M and David, FJ and Cunningham, SW and Herstoff, EM}, title = {Rewilding in Miniature: Suburban Meadows Can Improve Soil Microbial Biodiversity and Soil Health.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {1077-1086}, pmid = {36725750}, issn = {1432-184X}, mesh = {Humans ; *Soil/chemistry ; *Grassland ; Soil Microbiology ; Biodiversity ; Ecosystem ; Bacteria/genetics ; }, abstract = {Lawns are a ubiquitous, human-made environment created for human enjoyment, leisure, and aesthetics. While net positive for carbon storage, lawns can have negative environmental impacts. Lawns require frequent mowing, which produces high levels of CO2 pollution and kills off native plants. Lawn fertilizing creates its own environmental pollution. One (presumed) ecologically-friendly alternative to lawns is restoration, or rewilding, of these spaces as meadows, which need less maintenance (e.g., infrequent mowing). However, little work has compared lawns against small-scale meadows for biodiversity outside of pollinator studies. Here, we tested the hypotheses that compared to lawns, meadows have (1) unique and higher levels of soil microbial biodiversity and (2) different soil physical and chemical characteristics. We conducted bacterial (16S) and fungal (ITS2) metabarcoding, and found that both bacteria and fungi are indeed more diverse in meadows (significantly so for bacteria). Species composition between meadows and lawns was significantly different for both types of microbes, including higher levels of mycorrhizal fungi in meadows. We also found that chemistry (e.g., potassium and metrics relating to pH) differed significantly between lawns and meadows and was more optimal for plant growth in the meadows. We believe these differences are caused by the different organisms dwelling in these habitats. In summary, these findings point to notable-positive-shifts in microbial and chemical compositions within meadows, further indicating that meadow restoration benefits biodiversity and soil health.}, }
@article {pmid36725749, year = {2023}, author = {Sullivan, TJ and Roberts, H and Bultman, TL}, title = {Genetic Covariation Between the Vertically Transmitted Endophyte Epichloë canadensis and Its Host Canada Wildrye.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1686-1695}, pmid = {36725749}, issn = {1432-184X}, mesh = {Endophytes/genetics ; Symbiosis ; *Epichloe/genetics ; Poaceae/microbiology ; *Elymus/genetics/microbiology ; }, abstract = {Symbiotic mutualisms are thought to be stabilized by correlations between the interacting genotypes which may be strengthened via vertical transmission and/or reduced genetic variability within each species. Vertical transmission, however, may weaken interactions over time as the endosymbionts would acquire mutations that could not be purged. Additionally, temporal variation in a conditional mutualism could create genetic variation and increased variation in the interaction outcome. In this study, we assessed genetic variation in both members of a symbiosis, the endosymbiotic fungal endophyte Epichloë canadensis and its grass host Canada wildrye (Elymus canadensis). Both species exhibited comparable levels of diversity, mostly within populations rather than between. There were significant differences between populations, although not in the same pattern for the two species, and the differences were not correlated with geographic distance for either species. Interindividual genetic distance matrices for the two species were significantly correlated, although all combinations of discriminant analysis of principle components (DAPC) defined multilocus genotype groups were found suggesting that strict genotype matching is not necessary. Variation in interaction outcome is common in grass/endophyte interactions, and our results suggest that the accumulation of mutations overtime combined with temporal variation in selection pressures increasing genetic variation in the symbiosis may be the cause.}, }
@article {pmid36725211, year = {2023}, author = {Hernández-Gómez, O and Hua, J}, title = {From the organismal to biosphere levels: environmental impacts on the amphibian microbiota.}, journal = {FEMS microbiology reviews}, volume = {47}, number = {1}, pages = {}, doi = {10.1093/femsre/fuad002}, pmid = {36725211}, issn = {1574-6976}, mesh = {Animals ; *Ecosystem ; *Microbiota ; Amphibians ; Phylogeny ; }, abstract = {This review summarizes the role of environmental factors on amphibian microbiotas at the organismal, population, community, ecosystem, and biosphere levels. At the organismal-level, tissue source, disease status, and experimental manipulations were the strongest predictors of variation in amphibian microbiotas. At the population-level, habitat quality, disease status, and ancestry were commonly documented as drivers of microbiota turnover. At the community-level, studies focused on how species' niche influence microbiota structure and function. At the ecosystem-level, abiotic and biotic reservoirs were important contributors to microbiota structure. At the biosphere-level, databases, sample banks, and seminatural experiments were commonly used to describe microbiota assembly mechanisms among temperate and tropical amphibians. Collectively, our review demonstrates that environmental factors can influence microbiotas through diverse mechanisms at all biological scales. Importantly, while environmental mechanisms occurring at each of the different scales can interact to shape microbiotas, the past 10 years of research have mostly been characterized by targeted approaches at individual scales. Looking forward, efforts considering how environmental factors at multiple organizational levels interact to shape microbiota diversity and function are paramount. Generating opportunities for meaningful cross-disciplinary interactions and supporting infrastructure for research that spans biological scales are imperative to addressing this gap.}, }
@article {pmid36723682, year = {2023}, author = {Bulannga, RB and Schmidt, S}, title = {Two Predators, One Prey - the Interaction Between Bacteriophage, Bacterivorous Ciliates, and Escherichia coli.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1620-1631}, pmid = {36723682}, issn = {1432-184X}, support = {132700//NRF/ ; }, mesh = {*Bacteriophages ; Escherichia coli ; *Ciliophora ; *Tetrahymena ; *Paramecium ; Bacteria ; }, abstract = {Bacterivorous ciliates and lytic bacteriophages are two major predators in aquatic environments, competing for the same type of prey. This study investigated the possible interaction of these different microorganisms and their influence on the activity of each other. Therefore, two bacterivorous ciliates, Paramecium sp. RB1 and Tetrahymena sp. RB2, were used as representative ciliates; a T4-like Escherichia coli targeting lytic bacteriophage as a model virus; and E. coli ATCC 25922 as a susceptible bacterial host and prey. The growth of the two ciliates with E. coli ATCC 25922 as prey was affected by the presence of phage particles. The grazing activity of the two ciliates resulted in more than a 99% reduction of the phage titer and bacterial cell numbers. However, viable phage particles were recovered from individual washed cells of the two ciliates after membrane filtration. Therefore, ciliates such as Paramecium sp. RB1 and Tetrahymena sp. RB2 can remove bacteriophages present in natural and artificial waters by ingesting the viral particles and eliminating bacterial host cells required for viral replication. The ingestion of phage particles may marginally contribute to the nutrient supply of the ciliates. However, the interaction of phage particles with ciliate cells may contribute to the transmission of bacteriophages in aquatic environments.}, }
@article {pmid36723077, year = {2023}, author = {Lennon, JT and Frost, SDW and Nguyen, NK and Peralta, AL and Place, AR and Treseder, KK}, title = {Microbiology and Climate Change: a Transdisciplinary Imperative.}, journal = {mBio}, volume = {14}, number = {1}, pages = {e0333522}, pmid = {36723077}, issn = {2150-7511}, mesh = {*Climate Change ; *Policy ; Technology ; }, abstract = {Climate change is a complex problem involving nonlinearities and feedback that operate across scales. No single discipline or way of thinking can effectively address the climate crisis. Teams of natural scientists, social scientists, engineers, economists, and policymakers must work together to understand, predict, and mitigate the rapidly accelerating impacts of climate change. Transdisciplinary approaches are urgently needed to address the role that microorganisms play in climate change. Here, we demonstrate with case studies how diverse teams and perspectives provide climate-change insight related to the range expansion of emerging fungal pathogens, technological solutions for harmful cyanobacterial blooms, and the prediction of disease-causing microorganisms and their vector populations using massive networks of monitoring stations. To serve as valuable members of a transdisciplinary climate research team, microbiologists must reach beyond the boundaries of their immediate areas of scientific expertise and engage in efforts to build open-minded teams aimed at scalable technologies and adoptable policies.}, }
@article {pmid36722970, year = {2023}, author = {Melnik, AV and Callewaert, C and Dorrestein, K and Broadhead, R and Minich, JJ and Ernst, M and Humphrey, G and Ackermann, G and Gathercole, R and Aksenov, AA and Knight, R and Dorrestein, PC}, title = {The Molecular Effect of Wearing Silver-Threaded Clothing on the Human Skin.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0092222}, pmid = {36722970}, issn = {2379-5077}, support = {P41 GM103484/GM/NIGMS NIH HHS/United States ; R01 GM107550/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Female ; Silver/analysis ; Clothing ; Skin/chemistry ; Textiles ; *Microbiota ; Bacteria/genetics ; *Propionibacteriaceae ; }, abstract = {With growing awareness that what we put in and on our bodies affects our health and wellbeing, little is still known about the impact of textiles on the human skin. Athletic wear often uses silver threading to improve hygiene, but little is known about its effect on the body's largest organ. In this study, we investigated the impact of such clothing on the skin's chemistry and microbiome. Samples were collected from different body sites of a dozen volunteers over the course of 12 weeks. The changes induced by the antibacterial clothing were specific for individuals, but more so defined by gender and body site. Unexpectedly, the microbial biomass on skin increased in the majority of the volunteers when wearing silver-threaded T-shirts. Although the most abundant taxa remained unaffected, silver caused an increase in diversity and richness of low-abundant bacteria and a decrease in chemical diversity. Both effects were mainly observed for women. The hallmark of the induced changes was an increase in the abundance of various monounsaturated fatty acids (MUFAs), especially in the upper back. Several microbe-metabolite associations were uncovered, including Cutibacterium, detected in the upper back area, which was correlated with the distribution of MUFAs, and Anaerococcus spp. found in the underarms, which were associated with a series of different bile acids. Overall, these findings point to a notable impact of the silver-threaded material on the skin microbiome and chemistry. We observed that relatively subtle changes in the microbiome result in pronounced shifts in molecular composition. IMPORTANCE The impact of silver-threaded material on human skin chemistry and microbiome is largely unknown. Although the most abundant taxa remained unaffected, silver caused an increase in diversity and richness of low-abundant bacteria and a decrease in chemical diversity. The major change was an increase in the abundance of various monounsaturated fatty acids that were also correlated with Cutibacterium. Additionally, Anaerococcus spp., found in the underarms, were associated with different bile acids in the armpit samples. Overall, the impact of the silver-threaded clothing was gender and body site specific.}, }
@article {pmid36721064, year = {2023}, author = {van Kasteren, S and Rozen, DE}, title = {Using click chemistry to study microbial ecology and evolution.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {9}, pmid = {36721064}, issn = {2730-6151}, abstract = {Technological advances have largely driven the revolution in our understanding of the structure and function of microbial communities. Culturing, long the primary tool to probe microbial life, was supplanted by sequencing and other -omics approaches, which allowed detailed quantitative insights into species composition, metabolic potential, transcriptional activity, secretory responses and more. Although the ability to characterize "who's there" has never been easier or cheaper, it remains technically challenging and expensive to understand what the diverse species and strains that comprise microbial communities are doing in situ, and how these behaviors change through time. Our aim in this brief review is to introduce a developing toolkit based on click chemistry that can accelerate and reduce the expense of functional analyses of the ecology and evolution of microbial communities. After first outlining the history of technological development in this field, we will discuss key applications to date using diverse labels, including BONCAT, and then end with a selective (biased) view of areas where click-chemistry and BONCAT-based approaches stand to have a significant impact on our understanding of microbial communities.}, }
@article {pmid36720878, year = {2023}, author = {Vincent, F and Gralka, M and Schleyer, G and Schatz, D and Cabrera-Brufau, M and Kuhlisch, C and Sichert, A and Vidal-Melgosa, S and Mayers, K and Barak-Gavish, N and Flores, JM and Masdeu-Navarro, M and Egge, JK and Larsen, A and Hehemann, JH and Marrasé, C and Simó, R and Cordero, OX and Vardi, A}, title = {Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {510}, pmid = {36720878}, issn = {2041-1723}, mesh = {Humans ; *Eukaryota ; Eukaryotic Cells ; Bacteria ; Carbon ; *Virus Diseases ; }, abstract = {Algal blooms are hotspots of marine primary production and play central roles in microbial ecology and global elemental cycling. Upon demise of the bloom, organic carbon is partly respired and partly transferred to either higher trophic levels, bacterial biomass production or sinking. Viral infection can lead to bloom termination, but its impact on the fate of carbon remains largely unquantified. Here, we characterize the interplay between viral infection and the composition of a bloom-associated microbiome and consequently the evolving biogeochemical landscape, by conducting a large-scale mesocosm experiment where we monitor seven induced coccolithophore blooms. The blooms show different degrees of viral infection and reveal that only high levels of viral infection are followed by significant shifts in the composition of free-living bacterial and eukaryotic assemblages. Intriguingly, upon viral infection the biomass of eukaryotic heterotrophs (thraustochytrids) rivals that of bacteria as potential recyclers of organic matter. By combining modeling and quantification of active viral infection at a single-cell resolution, we estimate that viral infection causes a 2-4 fold increase in per-cell rates of extracellular carbon release in the form of acidic polysaccharides and particulate inorganic carbon, two major contributors to carbon sinking into the deep ocean. These results reveal the impact of viral infection on the fate of carbon through microbial recyclers of organic matter in large-scale coccolithophore blooms.}, }
@article {pmid36719456, year = {2023}, author = {Lin, Z and Zheng, X and Chen, J}, title = {Deciphering pH-dependent microbial taxa and functional gene co-occurrence in the coral Galaxea fascicularis.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1856-1868}, pmid = {36719456}, issn = {1432-184X}, mesh = {Animals ; *Anthozoa/microbiology ; Seawater/microbiology ; Hydrogen-Ion Concentration ; Bacteria/genetics ; *Microbiota/genetics ; Carbon ; Coral Reefs ; }, abstract = {How the coral microbiome responds to oceanic pH changes due to anthropogenic climate change, including ocean acidification and deliberate artificial alkalization, remains an open question. Here, we applied a 16S profile and GeoChip approach to microbial taxonomic and gene functional landscapes in the coral Galaxea fascicularis under three pH levels (7.85, 8.15, and 8.45) and tested the influence of pH changes on the cell growth of several coral-associated strains and bacterial populations. Statistical analysis of GeoChip-based data suggested that both ocean acidification and alkalization destabilized functional cores related to aromatic degradation, carbon degradation, carbon fixation, stress response, and antibiotic biosynthesis in the microbiome, which are related to holobiont carbon cycling and health. The taxonomic analysis revealed that bacterial species richness was not significantly different among the three pH treatments, but the community compositions were significantly distinct. Acute seawater alkalization leads to an increase in pathogens as well as a stronger taxonomic shift than acidification, which is worth considering when using artificial ocean alkalization to protect coral ecosystems from ocean acidification. In addition, our co-occurrence network analysis reflected microbial community and functional shifts in response to pH change cues, which will further help to understand the functional ecological role of the microbiome in coral resilience.}, }
@article {pmid36717392, year = {2023}, author = {Pavlova, ON and Tupikin, AE and Chernitsyna, SM and Bukin, YS and Lomakina, AV and Pogodaeva, TV and Nikonova, AA and Bukin, SV and Zemskaya, TI and Kabilov, MR}, title = {Description and Genomic Analysis of the First Facultatively Lithoautotrophic, Thermophilic Bacteria of the Genus Thermaerobacter Isolated from Low-temperature Sediments of Lake Baikal.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1604-1619}, pmid = {36717392}, issn = {1432-184X}, support = {0279-2021-0006//Ministry of Science and Higher Education of the Russian Federation/ ; 22-14-00084//Russian Science Foundation/ ; }, mesh = {Temperature ; *Lakes/analysis ; Sequence Analysis, DNA ; *Bacteria, Aerobic/genetics ; Genomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics/analysis ; Bacterial Typing Techniques ; }, abstract = {Members of the genus Thermaerobacter belong to the phylum Firmicutes and all isolates characterised to date are strictly aerobic and thermophilic. They were isolated from a mud sample of the Challenger Deep in the Mariana Trench, hydrothermal vents, and silt compost. A novel thermophilic, facultatively lithoautotrophic bacteria of the genus Thermaerobacter, strain PB12/4term (=VKM B-3151[T]), with a metabolism that is uncharacteristic of the type species, was isolated from low-temperature surface sediments near the Posolsk Bank methane seep, Lake Baikal, Russia. The new strain grows with molecular hydrogen as electron donor, elemental sulfur, and thiosulfate as electron acceptors, and CO2/[Formula: see text] as carbon source. The genome of strain PB12/4term consists of one chromosome with a total length of 2.820.915 bp and the G+C content of the genomic DNA was 72.2%. The phylogenomic reconstruction based on 120 conserved bacterial single-copy proteins revealed that strain PB12/4term belongs to the genus Thermaerobacter within in the class Thermaerobacteria, phylum Firmicutes_E. The strain PB12/4term is closely related to Thermaerobacter subterraneus DSM 13965 (ANI=95.08%, AF=0.91) and Thermaerobacter marianensis DSM 12885 (ANI=84.98%, AF=0.77). Genomic and experimental data confirm the ability of the Thermaerobacter PB12/4term pure culture to facultatively lithotrophic growth, which is provided by the presence of [NiFe]hydrogenase enzymes that are absent in T. marianensis DSM 12885 and T. subterraneus DSM 13965. The data obtained on the physiological and biochemical differences of strain PB12/4term provide a deeper insight into the species diversity and functional activity of the genus Thermaerobacter.}, }
@article {pmid36717391, year = {2023}, author = {Ma, W and Lin, L and Peng, Q}, title = {Origin, Selection, and Succession of Coastal Intertidal Zone-Derived Bacterial Communities Associated with the Degradation of Various Lignocellulose Substrates.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1589-1603}, pmid = {36717391}, issn = {1432-184X}, support = {91951116//National Natural Science Foundation of China/ ; 2019YFA0606704//Key Technologies Research and Development Program of Anhui Province/ ; }, mesh = {*Lignin/metabolism ; Ecosystem ; Bacteria/metabolism ; Microbial Consortia ; *Oryza/metabolism ; }, abstract = {Terrestrial microbial consortia were reported to play fundamental roles in the global carbon cycle and renewable energy production through the breakdown of complex organic carbon. However, we have a poor understanding of how biotic/abiotic factors combine to influence consortia assembly and lignocellulose degradation in aquatic ecosystems. In this study, we used 96 in situ lignocellulose enriched, coastal intertidal zone-derived bacterial consortia as the initial inoculating consortia and developed 384 cultured consortia under different lignocellulose substrates (aspen, pine, rice straw, and purified Norway spruce lignin) with gradients of salinity and temperature. As coastal consortia, salinity was the strongest driver for assembly, followed by Norway spruce lignin, temperature, and aspen. Moreover, a conceptual model was proposed to demonstrate different succession dynamics between consortia under herbaceous and woody lignocelluloses. The succession of consortium under Norway spruce lignin is greatly related with abiotic factors, while its substrate degradation is mostly correlated with biotic factors. A discrepant pattern was observed in the consortium under rice straw. Finally, we developed four groups of versatile, yet specific consortia. Our study not only reveals that coastal intertidal wetlands are important natural resources to enrich lignocellulolytic degrading consortia but also provides insights into the succession and ecological function of coastal consortium.}, }
@article {pmid36716515, year = {2023}, author = {Pateraki, C and Magdalinou, E and Skliros, D and Flemetakis, E and Rabaey, K and Koutinas, A}, title = {Transcriptional regulation in key metabolic pathways of Actinobacillus succinogenes in the presence of electricity.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {151}, number = {}, pages = {108376}, doi = {10.1016/j.bioelechem.2023.108376}, pmid = {36716515}, issn = {1878-562X}, mesh = {Fermentation ; *Actinobacillus/genetics/metabolism ; Metabolic Networks and Pathways ; Electricity ; }, abstract = {The potential of renewable energy application via direct electrode interaction for the production of bio-based chemicals is a promising technology. The utilization of extracellular energy in pure culture fermentations aims in intracellular redox balance regulation in order to improve fermentation efficiency. This work evaluates the impact of a bioelectrochemical system in succinic acid fermentation and the metabolic response of Actinobacillus succinogenes. The metabolic pathway regulation of A. succinogenes was evaluated via RNA expression of the key enzymes that participate in TCA cycle, pyruvate metabolism and oxidative phosphorylation. The genes that were significantly overexpressed in BES compared to non-BES were phosphoenolpyruvate carboxykinase (0.4-fold change), inorganic pyrophosphatase (2.3-fold change) and hydrogenase (2.2-fold change) and the genes that were significantly underexpressed were fumarase (-0.94-fold change), pyruvate kinase (-6.9-fold change), all subunits of fumarate reductase (-2.1 to -1.17-fold change), cytochromes I and II (-1.25 and -1.02-fold change, respectively) and two C4-carboxylic acid transporters.}, }
@article {pmid36713329, year = {2022}, author = {Gusareva, ES and Gaultier, NE and Uchida, A and Premkrishnan, BNV and Heinle, CE and Phung, WJ and Wong, A and Lau, KJX and Yap, ZH and Koh, Y and Ang, PN and Putra, A and Panicker, D and Lee, JGH and Neves, LC and Drautz-Moses, DI and Schuster, SC}, title = {Short-range contributions of local sources to ambient air.}, journal = {PNAS nexus}, volume = {1}, number = {2}, pages = {pgac043}, pmid = {36713329}, issn = {2752-6542}, abstract = {Recent developments in aerobiology have enabled the investigation of airborne biomass with high temporal and taxonomic resolution. In this study, we assess the contributions of local sources to ambient air within a 160,000 m[2] tropical avian park (AP). We sequenced and analyzed 120 air samples from seven locations situated 160 to 400 m apart, representing distinct microhabitats. Each microhabitat contained a characteristic air microbiome, defined by the abundance and richness of its airborne microbial community members, supported by both, PCoA and Random Forest analysis. Each outdoor microhabitat contained 1% to 18.6% location-specific taxa, while a core microbiome of 27.1% of the total taxa was shared. To identify and assess local sources, we compared the AP dataset with a DVE reference dataset from a location 2 km away, collected during a year-round sampling campaign. Intersection of data from the two sites demonstrated 61.6% of airborne species originated from local sources of the AP, 34.5% from ambient air background, and only 3.9% of species were specific to the DVE reference site. In-depth taxonomic analysis demonstrated association of bacteria-dominated air microbiomes with indoor spaces, while fungi-dominated airborne microbial biomass was predominant in outdoor settings with ample vegetation. The approach presented here demonstrates an ability to identify local source contributions against an ambient air background, despite the prevailing mixing of air masses caused by atmospheric turbulences.}, }
@article {pmid36713171, year = {2022}, author = {Zhang, X and Wang, Y and Xu, Y and Babalola, BJ and Xiang, S and Ma, J and Su, Y and Fan, Y}, title = {Stochastic processes dominate community assembly of ectomycorrhizal fungi associated with Picea crassifolia in the Helan Mountains, China.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1061819}, pmid = {36713171}, issn = {1664-302X}, abstract = {INTRODUCTION: Understanding the underlying mechanisms of microbial community assembly is a fundamental topic in microbial ecology. As an integral part of soil organisms, ectomycorrhizal (EM) fungi play vital roles in ecosystems. Picea crassifolia is an important pine species in the Helan Mountains in Inner Mongolia, China, with high ecological and economic values. However, studies of EM fungal diversity and mechanisms underlying community assembly on this pine species are limited.<br><br>METHODS: In this study, we investigated EM fungal communities associated with P. crassifolia from 45 root samples across three sites in the Helan Mountains using Illumina Miseq sequencing of the fungal rDNA ITS2 region.<br><br>RESULTS: A total of 166 EM fungal OTUs belonging to 24 lineages were identified, of which Sebacina and Tomentella-Thelephora were the most dominant lineages. Ordination analysis revealed that EM fungal communities were significantly different among the three sites. Site/fungus preference analysis showed that some abundant EM fungal OTUs preferred specific sites. Ecological process analysis implied that dispersal limitation and ecological drift in stochastic processes dominantly determined the community assembly of EM fungi.<br><br>DISCUSSION: Our study indicates that P. crassifolia harbors a high EM fungal diversity and highlights the important role of the stochastic process in driving community assembly of mutualistic fungi associated with a single plant species in a semi-arid forest in northwest China.}, }
@article {pmid36713170, year = {2022}, author = {Lin, J and Li, G and Sun, L and Wang, S and Meng, X and Sun, L and Yuan, L and Xu, L}, title = {Varieties and ensiling: Impact on chemical composition, fermentation quality and bacterial community of alfalfa.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1091491}, pmid = {36713170}, issn = {1664-302X}, abstract = {INTRODUCTION: Six species of alfalfa commonly found in northern China were collected in the present study.<br><br>METHODS: The chemical composition and epiphytic microbial communities during the ensiling were analyzed; and their effects on fermentation quality and silage bacterial communities were assessed. The effects of physicochemical characteristics of alfalfa on the bacterial community were also investigated in terms of nutritional sources of microbial growth and reproduction.<br><br>RESULTS AND DISCUSSION: The results showed that the chemical composition was significantly different in various alfalfa varieties, yet, the dominant genera attached to each variety of alfalfa was similar, except for pantoea (p<0.05). After ensiling, both the fermentation quality and microbial community changed obviously (p<0.05). Specifically, ZM2 had lower pH and ammonia nitrogen (NH3-N) content but higher LA content than other varieties of alfalfa silage. Beneficial bacteria such as Lentilactobacillus and Lactiplantibacillus were predominant in ZM2, which accounted for the higher fermentation quality. Significant correlations between the chemical composition of silage, fermentation quality and bacterial communities composition were observed. Moreover, variations in bacteria community structure during the fermentation of alfalfa were mainly influenced by water-soluble carbohydrates (36.79%) and dry matter (21.77%).<br><br>CONCLUSION: In conclusion, this study revealed the influence of chemical composition on microbial community and fermentation quality, laying the groundwork for future studies on high-quality silage.}, }
@article {pmid36709487, year = {2023}, author = {Stahl, LM and Olson, JB}, title = {Investigating the interactive effects of temperature, pH, and salinity on Naegleria fowleri persistence.}, journal = {The Journal of eukaryotic microbiology}, volume = {70}, number = {3}, pages = {e12964}, doi = {10.1111/jeu.12964}, pmid = {36709487}, issn = {1550-7408}, mesh = {Humans ; *Naegleria fowleri ; Temperature ; Salinity ; Sodium Chloride ; *Amebiasis ; Water ; Hydrogen-Ion Concentration ; *Central Nervous System Protozoal Infections ; }, abstract = {Naegleria fowleri causes primary amoebic meningoencephalitis, a deadly infection that occurs when free-living amoebae enter the nose via freshwater and travel to the brain. N. fowleri naturally thrives in freshwater and soil and is thought to be associated with elevated water temperatures. While environmental and laboratory studies have sought to identify what environmental factors influence its presence, many questions remain. This study investigated the interactive effects of temperature, pH, and salinity on N. fowleri in deionized and environmental waters. Three temperatures (15, 25, 35°C), pH values (6.5, 7.5, 8.5), and salinity concentrations (0.5%, 1.5%, 2.5% NaCl) were used to evaluate the growth of N. fowleri via ATP luminescent assays. Results indicated N. fowleri grew best at 25°C, and multiple interactive effects occurred between abiotic factors. Interactions varied slightly by water type but were largely driven by temperature and salinity. Lower temperature increased N. fowleri persistence at higher salinity levels, while low salinity (0.5% NaCl) supported N. fowleri growth at all temperatures. This research provided an experimental approach to assess interactive effects influencing the persistence of N. fowleri. As climate change impacts water temperatures and conditions, understanding the microbial ecology of N. fowleri will be needed minimize pathogen exposure.}, }
@article {pmid36709366, year = {2023}, author = {Song, W and Qin, Z and Hu, X and Han, H and Li, A and Zhou, X and Li, Y and Li, R}, title = {Using Bayesian networks with Tabu-search algorithm to explore risk factors for hyperhomocysteinemia.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {1610}, pmid = {36709366}, issn = {2045-2322}, mesh = {Humans ; *Hyperhomocysteinemia ; Bayes Theorem ; Risk Factors ; Smoking ; Algorithms ; Homocysteine ; }, abstract = {Hyperhomocysteinemia (HHcy) is a condition closely associated with cardiovascular and cerebrovascular diseases. Detecting its risk factors and taking some relevant interventions still represent the top priority to lower its prevalence. Yet, in discussing risk factors, Logistic regression model is usually adopted but accompanied by some defects. In this study, a Tabu Search-based BNs was first constructed for HHcy and its risk factors, and the conditional probability between nodes was calculated using Maximum Likelihood Estimation. Besides, we tried to compare its performance with Hill Climbing-based BNs and Logistic regression model in risk factor detection and discuss its prospect in clinical practice. Our study found that Age, sex, α1-microgloblobumin to creatinine ratio, fasting plasma glucose, diet and systolic blood pressure represent direct risk factors for HHcy, and smoking, glycosylated hemoglobin and BMI constitute indirect risk factors for HHcy. Besides, the performance of Tabu Search-based BNs is better than Hill Climbing-based BNs. Accordingly, BNs with Tabu Search algorithm could be a supplement for Logistic regression, allowing for exploring the complex network relationship and the overall linkage between HHcy and its risk factors. Besides, Bayesian reasoning allows for risk prediction of HHcy, which is more reasonable in clinical practice and thus should be promoted.}, }
@article {pmid36708393, year = {2023}, author = {Kļaviņa, D and Lione, G and Kenigsvalde, K and Pellicciaro, M and Muižnieks, I and Silbauma, L and Jansons, J and Gaitnieks, T and Gonthier, P}, title = {Host-associated Intraspecific Phenotypic Variation in the Saprobic Fungus Phlebiopsis gigantea.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1847-1855}, pmid = {36708393}, issn = {1432-184X}, support = {1.1.1.1/20/A/095//European Regional Development Fund/ ; 5-5.9.1_007q_101_21_79//JSC Latvian State Forests/ ; }, mesh = {Fungi ; *Polyporales ; *Pinus sylvestris/microbiology ; *Abies ; Biological Variation, Population ; *Picea/microbiology ; }, abstract = {Whether intraspecific phenotypic variation in saprobic fungi may be driven by the host of origin has received little attention. We addressed this issue by testing hypotheses using the model system Phlebiopsis gigantea, a wood destroying fungus associated with Picea abies and Pinus sylvestris, among others, and widely employed in practical forestry as a biological control agent. By examining approximately 60 sympatric P. gigantea isolates from both P. abies and P. sylvestris, we showed that the former grew in vitro significantly (P < 0.05) slower than the latter (average 5.56 mm/day vs. 6.84) while producing 1.8-fold significantly higher number of mitospores. An overall significant trade-off between these two phenotypic traits was detected, in particular for isolates originating from P. abies. Comparative inoculation experiments of a subsample of isolates and the assessment of mycelial growth in logs of both hosts allowed to reject the hypothesis that isolates are equally fit in terms of growth rate in wood of both hosts regardless of the host of origin. Tree models revealed that the growth rate of isolates was associated not only with the wood species in which the isolates were inoculated (P < 0.001), P. sylvestris being more rapidly colonized than P. abies, but also with the host of origin of isolates (P < 0.001). Results showed that P. gigantea isolates originating from different hosts differ phenotypically in terms of some key phenotypic traits demonstrating that a host-driven intraspecific phenotypic variation may occur in saprobic fungi.}, }
@article {pmid36708392, year = {2023}, author = {Figueiredo, MA and da Silva, TH and Pinto, OHB and Leite, MGP and de Oliveira, FS and Messias, MCTB and Rosa, LH and Câmara, PEAS and Lopes, FAC and Kozovits, AR}, title = {Metabarcoding of Soil Fungal Communities in Rupestrian Grassland Areas Preserved and Degraded by Mining: Implications for Restoration.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {1045-1055}, pmid = {36708392}, issn = {1432-184X}, mesh = {*Mycobiome ; Grassland ; Soil ; Ecosystem ; Biodiversity ; Fungi/genetics ; Soil Microbiology ; }, abstract = {Rupestrian grasslands are vegetation complexes of the Cerrado biome (Brazilian savanna), exhibiting simultaneously great biodiversity and important open-pit mining areas. There is a strong demand for the conservation of remaining areas and restoration of degraded. This study evaluated, using next-generation sequencing, the diversity and ecological aspects of soil fungal communities in ferruginous rupestrian grassland areas preserved and degraded by bauxite mining in Brazil. In the preserved and degraded area, respectively, 565 and 478 amplicon sequence variants (ASVs) were detected. Basidiomycota and Ascomycota comprised nearly 72% of the DNA, but Ascomycota showed greater abundance than Basidiomycota in the degraded area (64% and 10%, respectively). In the preserved area, taxa of different hierarchical levels (Agaromycetes, Agaricales, Mortierelaceae, and Mortierella) associated with symbiosis and decomposition were predominant. However, taxa that colonize environments under extreme conditions and pathogens (Dothideomycetes, Pleoporales, Pleosporaceae, and Curvularia) prevailed in the degraded area. The degradation reduced the diversity, and modified the composition of taxa and predominant ecological functions in the community. The lack of fungi that facilitate plant establishment and development in the degraded area suggests the importance of seeking the restoration of this community to ensure the success of the ecological restoration of the environment. The topsoil of preserved area can be a source of inocula of several groups of fungi important for the restoration process but which occur in low abundance or are absent in the degraded area.}, }
@article {pmid36707764, year = {2023}, author = {Pantoja-Feliciano, IG and Karl, JP and Perisin, M and Doherty, LA and McClung, HL and Armstrong, NJ and Renberg, R and Racicot, K and Branck, T and Arcidiacono, S and Soares, JW}, title = {In vitro gut microbiome response to carbohydrate supplementation is acutely affected by a sudden change in diet.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {32}, pmid = {36707764}, issn = {1471-2180}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Diet ; Feces/microbiology ; Carbohydrates ; Starch/metabolism ; Dietary Supplements ; }, abstract = {BACKGROUND: Interactions between diet, stress and the gut microbiome are of interest as a means to modulate health and performance. Here, in vitro fermentation was used to explore the effects of a sudden change in diet, 21 days sole sustenance on the Meal, Ready-to-Eat (MRE) U.S. military combat ration, on inter-species competition and functional potential of the human gut microbiota. Human fecal samples collected before and after MRE intervention or consuming a habitual diet (HAB) were introduced to nutrient-rich media supplemented with starch for in vitro fermentation under ascending colon conditions. 16S rRNA amplicon and Whole-metagenome sequencing (WMS) were used to measure community composition and functional potential. Specific statistical analyses were implemented to detect changes in relative abundance from taxa, genes and pathways.<br><br>RESULTS: Differential changes in relative abundance of 11 taxa, Dorea, Lachnospira, Bacteroides fragilis, Akkermansia muciniphila, Bifidobacterium adolescentis, Betaproteobacteria, Enterobacteriaceae, Bacteroides egerthii, Ruminococcus bromii, Prevotella, and Slackia, and nine Carbohydrate-Active Enzymes, specifically GH13_14, over the 24&#xa0;h fermentation were observed as a function of the diet intervention and correlated to specific taxa of interest.<br><br>CONCLUSIONS: These findings suggest that consuming MRE for 21&#xa0;days acutely effects changes in gut microbiota structure in response to carbohydrate but may induce alterations in metabolic capacity. Additionally, these findings demonstrate the potential of starch as a candidate supplemental strategy to functionally modulate specific gut commensals during stress-induced states.}, }
@article {pmid36706488, year = {2023}, author = {Veloso, S and Amouroux, D and Lanceleur, L and Cagnon, C and Monperrus, M and Deborde, J and Laureau, CC and Duran, R}, title = {Keystone microbial taxa organize micropollutant-related modules shaping the microbial community structure in estuarine sediments.}, journal = {Journal of hazardous materials}, volume = {448}, number = {}, pages = {130858}, doi = {10.1016/j.jhazmat.2023.130858}, pmid = {36706488}, issn = {1873-3336}, mesh = {*Geologic Sediments/chemistry ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Rivers/microbiology ; Metals/toxicity ; Estuaries ; Pharmaceutical Preparations ; }, abstract = {The fluctuation of environmental conditions drives the structure of microbial communities in estuaries, highly dynamic ecosystems. Microorganisms inhabiting estuarine sediments play a key role in ecosystem functioning. They are well adapted to the changing conditions, also threatened by the presence of pollutants. In order to determine the environmental characteristics driving the organization of the microbial assemblages, we conducted a seasonal survey along the Adour Estuary (Bay of Biscay, France) using 16S rRNA gene Illumina sequencing. Microbial diversity data were combined with a set of chemical analyses targeting metals and pharmaceuticals. Microbial communities were largely dominated by Proteobacteria (41 %) and Bacteroidota (32 %), showing a strong organization according to season, with an important shift in winter. The composition of microbial communities showed spatial distribution according to three main areas (upstream, middle, and downstream estuary) revealing the influence of the Adour River. Further analyses indicated that the microbial community was influenced by biogeochemical parameters (Corg/Norg and δ[13]C) and micropollutants, including metals (As, Cu, Mn, Sn, Ti, and Zn) and pharmaceuticals (norfloxacin, oxolinic acid and trimethoprim). Network analysis revealed specific modules, organized around keystone taxa, linked to a pollutant type, providing information of paramount importance to understand the microbial ecology in estuarine ecosystems.}, }
@article {pmid36705425, year = {2023}, author = {Birzle, C and Schrader, H and Blutke, A and Ferling, H and Scholz-Göppel, K and Wanke, R and Schwaiger, J}, title = {Detection of Diclofenac-Induced Alterations in Rainbow Trout (Oncorhynchus mykiss) Using Quantitative Stereological Methods.}, journal = {Environmental toxicology and chemistry}, volume = {42}, number = {4}, pages = {859-872}, doi = {10.1002/etc.5573}, pmid = {36705425}, issn = {1552-8618}, support = {76e0100000123//Bavarian State Ministry for the Environment and Health (STMUV), Munich/ ; }, mesh = {Male ; Animals ; Diclofenac/toxicity ; *Oncorhynchus mykiss ; Reproducibility of Results ; Anti-Inflammatory Agents, Non-Steroidal/toxicity ; Kidney ; *Water Pollutants, Chemical/analysis ; Gills ; }, abstract = {In 2013, the nonsteroidal anti-inflammatory drug diclofenac (DCF) was included in the watch list for emerging pollutants under the European Union Water Framework Directive. Frequently, monitoring data revealed DCF concentrations in surface waters exceeding the proposed environmental quality standards of 0.04 µg L[-1] and 0.126 µg L[-1] . In recent literature, the possible effects of DCF on fish are discussed controversially. To contribute to a realistic risk assessment of DCF, a 28-day exposure experiment was carried on rainbow trout (Oncorhynchus mykiss). To warrant reliability of data, experiments were conducted considering the Criteria for Reporting and Evaluating Ecotoxicity Data. The test concentrations of DCF used (0.1, 0.5, 1, 5, 25, and 100 µg L[-1]) also included environmentally relevant concentrations. The lowest-observed-effect concentration (LOEC) for a significant decrease in the plasma concentrations of the DCF biomarker prostaglandin E2 was 0.5 µg L[-1] (male fish). For objective evaluation of relevant histomorphological parameters of gills and trunk kidneys, unbiased quantitative stereological methods were applied. In the gills, significant increases in the thickness of the secondary lamella and in the true harmonic mean of barrier thickness in secondary lamellae were present at DCF concentrations of 25 µg L[-1] and 100 µg L[-1] . In the trunk kidneys, the absolute and relative volumes of nephrons were significantly decreased, paralleled by a significant increase of the volume of the interstitial renal tissue. With regard to quantitative histomorphological alterations in the trunk kidney, the observed LOEC was 0.5 µg L[-1] . The quantitative histomorphological analyses that were conducted allow identification and objective quantification of even subtle but significant morphological effects and thus provide an important contribution for the comparability of study results for the determination of no-observed-effect concentrations (NOEC). Environ Toxicol Chem 2023;42:859-872. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.}, }
@article {pmid36702929, year = {2023}, author = {Li, T and Wang, X and Wang, X and Huang, J and Shen, L}, title = {Mechanisms Driving the Distribution and Activity of Mineralization and Nitrification in the Reservoir Riparian Zone.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1829-1846}, pmid = {36702929}, issn = {1432-184X}, support = {KZ201810028047//Beijing Natural Science Fund-Beijing Municipal Education Commission jointly funded key projects/ ; 41271495//National Natural Science Foundation of China/ ; }, mesh = {*Nitrification ; Ammonia ; Oxidation-Reduction ; Soil Microbiology ; Archaea/genetics ; *Microbiota ; Nitrogen ; Soil/chemistry ; Phylogeny ; }, abstract = {The riparian zone ecosystems have greater energy flow and elemental cycling than adjacent terrestrial and aquatic ecosystems. Mineralization and nitrification are important initiating processes in the nitrogen cycle, but their distribution and activity under different environmental conditions in the riparian zone and the driving mechanisms are still not clear. We investigated the effects of environmental and microbial factors on mineralization and nitrification activities by analyzing the community of alkaline (apr) and neutral (npr) metallopeptidase, ammonia-oxidizing archaea (AOA), and bacteria (AOB) in soils and sediments under different land-use types in the riparian zone of Miyun Reservoir, as well as measuring potential nitrogen mineralization and ammonia oxidation rates (AOR). The results showed that the mineralization and nitrification activities of soils were greater than those of sediments. AOA and AOB dominate the ammonia oxidation activity of soil and sediment, respectively. NH4[+] content was a key factor influencing the ecological niche differentiation between AOA and AOB. The high carbon and nitrogen content of the woodland significantly increased mineralization and nitrification activity. Microbial communities were significantly clustered in the woodland. The land-use type, not the flooding condition, determined the distribution of microbial community structure. The diversity of npr was significantly correlated with potential N mineralization rates, while the transcript abundance of AOA was significantly correlated with ammonia oxidation rates. Our study suggests that environmental changes regulate the distribution and activity of mineralization and nitrification processes in the reservoir riparian zone by affecting the transcript abundance, diversity and community structure of the microbial functional genes.}, }
@article {pmid36701921, year = {2023}, author = {Onyango, SO and Beerens, K and Li, Q and Van Camp, J and Desmet, T and Van de Wiele, T}, title = {Glycosidic linkage of rare and new-to-nature disaccharides reshapes gut microbiota in vitro.}, journal = {Food chemistry}, volume = {411}, number = {}, pages = {135440}, doi = {10.1016/j.foodchem.2023.135440}, pmid = {36701921}, issn = {1873-7072}, mesh = {*Trehalose ; *Gastrointestinal Microbiome ; Glycosides ; RNA, Ribosomal, 16S ; Disaccharides/pharmacology ; Bacteria/genetics ; Glucosides ; }, abstract = {The impact of glycosidic linkage of seven rare and new-to-nature disaccharides on gut bacteria was assessed in vitro. The community shift of the inocula from four donors in response to 1 % (w/v) disaccharide supplementation was captured by sequencing the 16S rRNA gene. A significant loss of bacterial alpha diversity, short lag time, low pH, and high total short-chain fatty acid displayed a faster fermentation of trehalose(Glc-α1,1α-Glc) and fibrulose(fructan, DP2-10). Bacteroides reduced in relative abundance under disaccharide supplementation suggesting a loss in complex carbohydrates metabolizing capacity. Fibrulose and l-arabinose glucoside(Glc-α1,3-l-Ara) significantly stimulated bifidobacteria but was suppressed with trehalose, ribose glucoside(Glc-α1,2-Rib), and 4'-epitrehalose(Glc-α1,1α-Gal) supplementation. Albeit insignificant, bifidobacteria increased with 4'-epikojibiose(Glc-α1,2-Gal), nigerose(Glc-α1,3-Glc), and kojibiose(Glc-α1,2-Glc). Prior conditioning of inoculum in kojibiose medium profoundly induced bifidobacteria by 44 % and 55 % upon reinoculation into kojibiose and fibrulose-supplemented media respectively. This study has demonstrated the importance of the disaccharide structure-function relationship in driving the gut bacterial community.}, }
@article {pmid36700533, year = {2023}, author = {Palau, J and Trueba-Santiso, A and Yu, R and Mortan, SH and Shouakar-Stash, O and Freedman, DL and Wasmund, K and Hunkeler, D and Marco-Urrea, E and Rosell, M}, title = {Dual C-Br Isotope Fractionation Indicates Distinct Reductive Dehalogenation Mechanisms of 1,2-Dibromoethane in Dehalococcoides- and Dehalogenimonas-Containing Cultures.}, journal = {Environmental science &amp; technology}, volume = {57}, number = {5}, pages = {1949-1958}, pmid = {36700533}, issn = {1520-5851}, mesh = {Carbon Isotopes/analysis/metabolism ; *Dehalococcoides/metabolism ; *Ethylene Dibromide ; Organic Chemicals ; Biodegradation, Environmental ; Chemical Fractionation ; }, abstract = {Brominated organic compounds such as 1,2-dibromoethane (1,2-DBA) are highly toxic groundwater contaminants. Multi-element compound-specific isotope analysis bears the potential to elucidate the biodegradation pathways of 1,2-DBA in the environment, which is crucial information to assess its fate in contaminated sites. This study investigates for the first time dual C-Br isotope fractionation during in vivo biodegradation of 1,2-DBA by two anaerobic enrichment cultures containing organohalide-respiring bacteria (i.e., either Dehalococcoides or Dehalogenimonas). Different εbulk[C] values (-1.8 ± 0.2 and -19.2 ± 3.5‰, respectively) were obtained, whereas their respective εbulk[Br] values were lower and similar to each other (-1.22 ± 0.08 and -1.2 ± 0.5‰), leading to distinctly different trends (ΛC-Br = Δδ[13]C/Δδ[81]Br ≈ εbulk[C]/εbulk[Br]) in a dual C-Br isotope plot (1.4 ± 0.2 and 12 ± 4, respectively). These results suggest the occurrence of different underlying reaction mechanisms during enzymatic 1,2-DBA transformation, that is, concerted dihaloelimination and nucleophilic substitution (SN2-reaction). The strongly pathway-dependent ΛC-Br values illustrate the potential of this approach to elucidate the reaction mechanism of 1,2-DBA in the field and to select appropriate εbulk[C] values for quantification of biodegradation. The results of this study provide valuable information for future biodegradation studies of 1,2-DBA in contaminated sites.}, }
@article {pmid36700061, year = {2023}, author = {Sathiananthamoorthy, S and Florman, K and Richard, D and Cheng, KK and Torri, V and McCaig, F and Harber, M and Rohn, JL}, title = {Application of Various Techniques to Gain Insights Into the Complex Urinary Tract Microbial Communities of Renal Transplant Recipients.}, journal = {Transplantation direct}, volume = {9}, number = {2}, pages = {e1418}, pmid = {36700061}, issn = {2373-8731}, abstract = {UNLABELLED: Urinary tract infections (UTIs) are prevalent in renal transplant (RTX) recipients and associated with worse outcomes. Early detection by sensitive diagnostic tests and appropriate treatment strategies in this cohort is therefore crucial, but evidence has shown that current methods may miss genuine infections. Research has shed light on the urinary tract microbial ecology of healthy individuals and nontransplant patients with UTI, but information on the RTx cohort is scant. We conducted a cross-sectional study to (i) compare the gold standard diagnostic culture with alternative techniques and (ii) characterize RTx patient urinary microbial communities.<br><br>METHODS: Midstream urine specimens were collected from 51 RTx patients attending a renal transplant clinic and 27 asymptomatic controls. Urinary microscopy, dipstick, and routine culture were performed. To improve sensitivity of microbial detection, we cultured the urinary cell sediment and performed 16S rRNA gene sequencing on urine. Uroplakin-positive urothelial cells shed in urine were analyzed by immunofluorescence staining for any bacterial association.<br><br>RESULTS: Sediment culture and 16S rRNA sequencing confirmed detection deficiencies of diagnostic culture and revealed differences in the urobiomes of RTx patients and controls. Specifically, Gardnerella, Escherichia, and Lactobacillus were most abundant in patients, whereas Lactobacillus, Streptococcus, and Gardnerella were most abundant in controls. The application of both culture and sequencing provided a more nuanced view of the urinary microbial communities.<br><br>CONCLUSIONS: This study provides insight into the potential problems of diagnostic culture within RTx patients and sheds light on their urinary microbial inhabitants. Further work may identify key microbial signatures and facilitate the development of better tools for UTI detection within this cohort, which could allow targeted intervention before an infection leads to serious consequences. http://links.lww.com/TXD/A479.}, }
@article {pmid36699726, year = {2022}, author = {Shen, Y and Yu, F and Qiu, L and Gao, M and Xu, P and Zhang, L and Liao, X and Wang, M and Hu, X and Sun, Y and Pan, Y}, title = {Ecological influence by colonization of fluoride-resistant Streptococcus mutans in oral biofilm.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1106392}, pmid = {36699726}, issn = {2235-2988}, mesh = {Humans ; *Streptococcus mutans ; Fluorides/pharmacology ; In Situ Hybridization, Fluorescence ; *Dental Caries ; RNA, Ribosomal, 16S/genetics ; Biofilms ; }, abstract = {BACKGROUND: Dental caries is one of the oldest and most common infections in humans. Improved oral hygiene practices and the presence of fluoride in dentifrices and mouth rinses have greatly reduced the prevalence of dental caries. However, increased fluoride resistance in microbial communities is concerning. Here, we studied the effect of fluoride-resistant Streptococcus mutans (S. mutans) on oral microbial ecology and compare it with wild-type S. mutans in vitro.<br><br>METHODS: Biofilm was evaluated for its polysaccharide content, scanning electron microscopy (SEM) imaging, acid-producing ability, and related lactic dehydrogenase (LDH), arginine deiminase (ADS), and urease enzymatic activity determination. Fluorescence in situ hybridization (FISH) and quantitative real-time polymerase chain reaction (qRT-PCR) were used to evaluate the S. mutans ratio within the biofilm. It was followed by 16S rRNA sequencing to define the oral microbial community.<br><br>RESULTS: Fluoride-resistant S. mutans produced increased polysaccharides in presence of NaF (P < 0.05). The enzymatic activities related to both acid and base generation were less affected by the fluoride. In presence of 275 ppm NaF, the pH in the fluoride-resistant strain sample was lower than the wild type. We observed that with the biofilm development and accumulative fluoride concentration, the fluoride-resistant strain had positive relationships with other bacteria within the oral microbial community, which enhanced its colonization and survival. Compared to the wild type, fluoride-resistant strain significantly increased the diversity and difference of oral microbial community at the initial stage of biofilm formation (4 and 24 h) and at a low fluoride environment (0 and 275 ppm NaF) (P < 0.05). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that fluoride-resistant strain enhanced the metabolic pathways and glucose transfer.<br><br>CONCLUSIONS: Fluoride-resistant S. mutans affected the microecological balance of oral biofilm and its cariogenic properties in vitro, indicating its negative impact on fluoride's caries prevention effect.}, }
@article {pmid36699674, year = {2022}, author = {Siddiqui, JA and Fan, R and Naz, H and Bamisile, BS and Hafeez, M and Ghani, MI and Wei, Y and Xu, Y and Chen, X}, title = {Insights into insecticide-resistance mechanisms in invasive species: Challenges and control strategies.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {1112278}, pmid = {36699674}, issn = {1664-042X}, abstract = {Threatening the global community is a wide variety of potential threats, most notably invasive pest species. Invasive pest species are non-native organisms that humans have either accidentally or intentionally spread to new regions. One of the most effective and first lines of control strategies for controlling pests is the application of insecticides. These toxic chemicals are employed to get rid of pests, but they pose great risks to people, animals, and plants. Pesticides are heavily used in managing invasive pests in the current era. Due to the overuse of synthetic chemicals, numerous invasive species have already developed resistance. The resistance development is the main reason for the failure to manage the invasive species. Developing pesticide resistance management techniques necessitates a thorough understanding of the mechanisms through which insects acquire insecticide resistance. Insects use a variety of behavioral, biochemical, physiological, genetic, and metabolic methods to deal with toxic chemicals, which can lead to resistance through continuous overexpression of detoxifying enzymes. An overabundance of enzymes causes metabolic resistance, detoxifying pesticides and rendering them ineffective against pests. A key factor in the development of metabolic resistance is the amplification of certain metabolic enzymes, specifically esterases, Glutathione S-transferase, Cytochromes p450 monooxygenase, and hydrolyses. Additionally, insect guts offer unique habitats for microbial colonization, and gut bacteria may serve their hosts a variety of useful services. Most importantly, the detoxification of insecticides leads to resistance development. The complete knowledge of invasive pest species and their mechanisms of resistance development could be very helpful in coping with the challenges and effectively developing effective strategies for the control of invasive species. Integrated Pest Management is particularly effective at lowering the risk of chemical and environmental contaminants and the resulting health issues, and it may also offer the most effective ways to control insect pests.}, }
@article {pmid36698845, year = {2022}, author = {Song, W and Liu, Y and Qiu, L and Qing, J and Li, A and Zhao, Y and Li, Y and Li, R and Zhou, X}, title = {Machine learning-based warning model for chronic kidney disease in individuals over 40 years old in underprivileged areas, Shanxi Province.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {930541}, pmid = {36698845}, issn = {2296-858X}, abstract = {INTRODUCTION: Chronic kidney disease (CKD) is a progressive disease with high incidence but early imperceptible symptoms. Since China's rural areas are subject to inadequate medical check-ups and single disease screening programme, it could easily translate into end-stage renal failure. This study aimed to construct an early warning model for CKD tailored to impoverished areas by employing machine learning (ML) algorithms with easily accessible parameters from ten rural areas in Shanxi Province, thereby, promoting a forward shift of treatment time and improving patients' quality of life.<br><br>METHODS: From April to November 2019, CKD opportunistic screening was carried out in 10 rural areas in Shanxi Province. First, general information, physical examination data, blood and urine specimens were collected from 13,550 subjects. Afterward, feature selection of explanatory variables was performed using LASSO regression, and target datasets were balanced using the SMOTE (synthetic minority over-sampling technique) algorithm, i.e., albuminuria-to-creatinine ratio (ACR) and &#x3b1;1-microglobulin-to-creatinine ratio (MCR). Next, Bagging, Random Forest (RF) and eXtreme Gradient Boosting (XGBoost) were employed for classification of ACR outcomes and MCR outcomes, respectively.<br><br>RESULTS: 12,330 rural residents were included in this study, with 20 explanatory variables. The cases with increased ACR and increased MCR represented 1,587 (12.8%) and 1,456 (11.8%), respectively. After conducting LASSO, 14 and 15 explanatory variables remained in these two datasets, respectively. Bagging, RF, and XGBoost performed well in classification, with the AUC reaching 0.74, 0.87, 0.87, 0.89 for ACR outcomes and 0.75, 0.88, 0.89, 0.90 for MCR outcomes. The five variables contributing most to the classification of ACR outcomes and MCR outcomes constituted SBP, TG, TC, and Hcy, DBP and age, TG, SBP, Hcy and FPG, respectively. Overall, the machine learning algorithms could emerge as a warning model for CKD.<br><br>CONCLUSION: ML algorithms in conjunction with rural accessible indexes boast good performance in classification, which allows for an early warning model for CKD. This model could help achieve large-scale population screening for CKD in poverty-stricken areas and should be promoted to improve the quality of life and reduce the mortality rate.}, }
@article {pmid36697862, year = {2023}, author = {Kennedy, KM and de Goffau, MC and Perez-Muñoz, ME and Arrieta, MC and Bäckhed, F and Bork, P and Braun, T and Bushman, FD and Dore, J and de Vos, WM and Earl, AM and Eisen, JA and Elovitz, MA and Ganal-Vonarburg, SC and Gänzle, MG and Garrett, WS and Hall, LJ and Hornef, MW and Huttenhower, C and Konnikova, L and Lebeer, S and Macpherson, AJ and Massey, RC and McHardy, AC and Koren, O and Lawley, TD and Ley, RE and O'Mahony, L and O'Toole, PW and Pamer, EG and Parkhill, J and Raes, J and Rattei, T and Salonen, A and Segal, E and Segata, N and Shanahan, F and Sloboda, DM and Smith, GCS and Sokol, H and Spector, TD and Surette, MG and Tannock, GW and Walker, AW and Yassour, M and Walter, J}, title = {Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies.}, journal = {Nature}, volume = {613}, number = {7945}, pages = {639-649}, pmid = {36697862}, issn = {1476-4687}, support = {MR/K021133/1/MRC_/Medical Research Council/United Kingdom ; BBS/E/F/00044409/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 HD102318/HD/NICHD NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; R01 AI139240/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; 100974/C/13/Z/WT_/Wellcome Trust/United Kingdom ; 220876/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; R01 CA219871/CA/NCI NIH HHS/United States ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 NR014784/NR/NINR NIH HHS/United States ; R01 AI120489/AI/NIAID NIH HHS/United States ; R01 HD098867/HD/NICHD NIH HHS/United States ; R33 HL137063/HL/NHLBI NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Female ; Humans ; Pregnancy ; Amniotic Fluid/immunology/microbiology ; *Biomass ; Mammals ; *Microbiota/genetics ; Placenta/immunology/microbiology ; *Fetus/immunology/microbiology ; *DNA Contamination ; Reproducibility of Results ; }, abstract = {Whether the human fetus and the prenatal intrauterine environment (amniotic fluid and placenta) are stably colonized by microbial communities in a healthy pregnancy remains a subject of debate. Here we evaluate recent studies that characterized microbial populations in human fetuses from the perspectives of reproductive biology, microbial ecology, bioinformatics, immunology, clinical microbiology and gnotobiology, and assess possible mechanisms by which the fetus might interact with microorganisms. Our analysis indicates that the detected microbial signals are likely the result of contamination during the clinical procedures to obtain fetal samples or during DNA extraction and DNA sequencing. Furthermore, the existence of live and replicating microbial populations in healthy fetal tissues is not compatible with fundamental concepts of immunology, clinical microbiology and the derivation of germ-free mammals. These conclusions are important to our understanding of human immune development and illustrate common pitfalls in the microbial analyses of many other low-biomass environments. The pursuit of a fetal microbiome serves as a cautionary example of the challenges of sequence-based microbiome studies when biomass is low or absent, and emphasizes the need for a trans-disciplinary approach that goes beyond contamination controls by also incorporating biological, ecological and mechanistic concepts.}, }
@article {pmid36697746, year = {2023}, author = {Yan, Y and Lin, T and Xie, W and Zhang, D and Jiang, Z and Han, Q and Zhu, X and Zhang, H}, title = {Contrasting Mechanisms Determine the Microeukaryotic and Syndiniales Community Assembly in a Eutrophic bay.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1575-1588}, pmid = {36697746}, issn = {1432-184X}, support = {42076158//National Natural Science Foundation of China/ ; 42076156//National Natural Science Foundation of China/ ; LY22D060002//Zhejiang Provincial Natural Science Foundation of China/ ; 2021YFC3101702//National Key Research and Development Program of China/ ; SJLY2020005//Fundamental Research Funds for the Provincial Universities of Zhejiang/ ; SOEDZZ2202//Project of State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography/ ; }, mesh = {Ecosystem ; Bays ; *Dinoflagellida/genetics ; *Diatoms/genetics ; RNA, Ribosomal, 18S/genetics ; Seasons ; }, abstract = {Syndiniales is a diverse parasitic group, increasingly gaining attention owing to its high taxonomic diversity in marine ecosystems and inhibitory effects on the dinoflagellate blooms. However, their seasonal dynamics, host interactions, and mechanisms of community assembly are largely unknown, particularly in eutrophic waters. Here, using 18S rRNA gene amplicon sequencing, we intended to elucidate the interactions between Syndiniales and microeukaryotes, as well as community assembly processes in a eutrophic bay. The results showed that Syndiniales group II was dominating throughout the year, with substantially higher abundance in the winter and spring, whereas Syndiniales group I was more abundant in the summer and autumn. Temperature and Dinoflagellata were the most important abiotic and biotic factors driving variations of the Syndiniales community, respectively. The assembly processes of microeukaryotes and Syndiniales were completely different, with the former being controlled by a balance between homogeneous selection and drift and the latter being solely governed by drift. Network analysis revealed that Syndiniales group II had the largest number of interactions with microeukaryotes, and they primarily associated with Dinoflagellata in the winter, while interactions with Chlorophyta and Bacillariophyta increased dramatically in summer and autumn. These findings provide significant insights in understanding the interactions and assembly processes of Syndiniales throughout the year, which is critical in revealing the roles of single-celled parasites in driving protist dynamics in eutrophic waters.}, }
@article {pmid36697704, year = {2023}, author = {Jentzsch, L and Grossart, HP and Plewe, S and Schulze-Makuch, D and Goldhammer, T}, title = {Response of cyanobacterial mats to ambient phosphate fluctuations: phosphorus cycling, polyphosphate accumulation and stoichiometric flexibility.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {6}, pmid = {36697704}, issn = {2730-6151}, abstract = {Cyanobacterial mats inhabit a variety of aquatic habitats, including the most extreme environments on Earth. They can thrive in a wide range of phosphorus (P) levels and are thus important players for ecosystem primary production and P cycling at the sediment-water interface. Polyphosphate (polyP), the major microbial P storage molecule, is assigned a critical role in compensating for phosphate fluctuations in planktonic cyanobacteria, but little is known about potentially analogous mechanisms of mat-forming cyanobacteria. To investigate acclimation strategies of cyanobacterial mats to fluctuating phosphate concentrations, laboratory batch experiments were conducted, in which the cosmopolitan mat-forming, marine cyanobacterium Sodalinema stali was exposed to low dissolved P concentrations, followed by a P pulse. Our results show that the cyanobacteria dynamically adjusted cellular P content to ambient phosphate concentrations and that they had accumulated polyP during periods of high phosphate availability, which was subsequently recycled to sustain growth during phosphate scarcity. However, following the depletion of dispensable cellular P sources, including polyP, we observed a reallocation of P contained in DNA into polyP, accompanied by increasing alkaline phosphatase activity. This suggests a change of the metabolic focus from growth towards maintenance and the attempt to acquire organic P, which would be naturally contained in the sediment. P overplus uptake following a simulated P pulse further suggests that Sodalinema-dominated mats exhibit elaborated mechanisms to cope with severe P fluctuations to overcome unfavourable environmental conditions, and potentially modulate critical P fluxes in the aquatic cycle.}, }
@article {pmid36696803, year = {2023}, author = {Huang, X and Chen, Q and Fan, Y and Yang, R and Gong, G and Yan, C and Song, Y and Zhang, B and Xi, S and Huang, Y and Xu, H}, title = {Fructooligosaccharides attenuate non-alcoholic fatty liver disease by remodeling gut microbiota and association with lipid metabolism.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {159}, number = {}, pages = {114300}, doi = {10.1016/j.biopha.2023.114300}, pmid = {36696803}, issn = {1950-6007}, mesh = {Mice ; Animals ; *Non-alcoholic Fatty Liver Disease/metabolism ; Lipid Metabolism ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Liver ; Diet, High-Fat/adverse effects ; Choline/metabolism/pharmacology/therapeutic use ; Methionine/metabolism ; }, abstract = {BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is a common liver disease highly associated with metabolic diseases and gut dysbiosis. Several clinical trials have confirmed that fructooligosaccharides (FOSs) are a viable alternative treatment for NAFLD. However, the mechanisms underlying the activities of FOSs remain unclear.<br><br>METHODS: In this study, the effects of FOSs were investigated with the use of two C57BL/6&#xa0;J mouse models of NAFLD induced by a high-fat, high-cholesterol (HFHC) diet and a methionine- and choline-deficient (MCD) diet, respectively. The measured metabolic parameters included body, fat, and liver weights; and blood glucose, glucose tolerance, and serum levels of glutamate transaminase, aspartate transaminase, and triglycerides. Liver tissues were collected for histological analysis. In addition, 16&#xa0;S rRNA sequencing was conducted to investigate the effects of FOSs on the composition of the gut microbiota of mice in the HFHC and MCD groups and treated with FOSs.<br><br>RESULTS: FOS treatment attenuated severe metabolic changes and hepatic steatosis caused by the HFHC and MCD diets. In addition, FOSs remodeled the structure of gut microbiota in mice fed the HFHC and MCD diets, as demonstrated by increased abundances of Bacteroidetes (phylum level), Klebsiella variicola, Lactobacillus gasseri, and Clostridium perfringens (species level); and decreased abundances of Verrucomicrobia (phylum level) and the Fissicatena group (genus level). Moreover, the expression levels of genes associated with lipid metabolism and inflammation (i.e., ACC1, PPAR&#x3b3;, CD36, MTTP, APOC3, IL-6, and IL-1&#x3b2;) were down-regulated after FOS treatment.<br><br>CONCLUSION: FOSs alleviated the pathological phenotype of NAFLD via remodeling of the gut microbiota composition and decreasing hepatic lipid metabolism, suggesting that FOSs as functional dietary supplements can potentially reduce the risk of NAFLD.}, }
@article {pmid36695828, year = {2023}, author = {Hilderbrand, RH and Bambakidis, T and Crump, BC}, title = {The Roles of Microbes in Stream Restorations.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {853-861}, pmid = {36695828}, issn = {1432-184X}, mesh = {Animals ; *Ecosystem ; Rivers ; Fishes ; Biomass ; *Microbiota ; Biofilms ; }, abstract = {The goods and services provided by riverine systems are critical to humanity, and our reliance increases with our growing population and demands. As our activities expand, these systems continue to degrade throughout the world even as we try to restore them, and many efforts have not met expectations. One way to increase restoration effectiveness could be to explicitly design restorations to promote microbial communities, which are responsible for much of the organic matter breakdown, nutrient removal or transformation, pollutant removal, and biomass production in river ecosystems. In this paper, we discuss several design concepts that purposefully create conditions for these various microbial goods and services, and allow microbes to act as ecological restoration engineers. Focusing on microbial diversity and function could improve restoration effectiveness and overall ecosystem resilience to the stressors that caused the need for the restoration. Advances in next-generation sequencing now allow the use of microbial 'omics techniques (e.g., metagenomics, metatranscriptomics) to assess stream ecological conditions in similar fashion to fish and benthic macroinvertebrates. Using representative microbial communities from stream sediments, biofilms, and the water column may greatly advance assessment capabilities. Microbes can assess restorations and ecosystem function where animals may not currently be present, and thus may serve as diagnostics for the suitability of animal reintroductions. Emerging applications such as ecological metatranscriptomics may further advance our understanding of the roles of specific restoration designs towards ecological services as well as assess restoration effectiveness.}, }
@article {pmid36695592, year = {2023}, author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Site Specialization of Human Oral Veillonella Species.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0404222}, pmid = {36695592}, issn = {2165-0497}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Veillonella/genetics ; Mouth/microbiology ; Tongue/microbiology ; Palatine Tonsil ; *Microbiota ; }, abstract = {Veillonella species are abundant members of the human oral microbiome with multiple interspecies commensal relationships. Examining the distribution patterns of Veillonella species across the oral cavity is fundamental to understanding their oral ecology. In this study, we used a combination of pangenomic analysis and oral metagenomic information to clarify Veillonella taxonomy and to test the site specialist hypothesis for the Veillonella genus, which contends that most oral bacterial species are adapted to live at specific oral sites. Using isolate genome sequences combined with shotgun metagenomic sequence data, we showed that Veillonella species have clear, differential site specificity: Veillonella parvula showed strong preference for supra- and subgingival plaque, while closely related V. dispar, as well as more distantly related V. atypica, preferred the tongue dorsum, tonsils, throat, and hard palate. In addition, the provisionally named Veillonella sp. Human Microbial Taxon 780 showed strong site specificity for keratinized gingiva. Using comparative genomic analysis, we identified genes associated with thiamine biosynthesis and the reductive pentose phosphate cycle that may enable Veillonella species to occupy their respective habitats. IMPORTANCE Understanding the microbial ecology of the mouth is fundamental for understanding human physiology. In this study, metapangenomics demonstrated that different Veillonella species have clear ecological preferences in the oral cavity of healthy humans, validating the site specialist hypothesis. Furthermore, the gene pool of different Veillonella species was found to be reflective of their ecology, illuminating the potential role of vitamins and carbohydrates in determining Veillonella distribution patterns and interspecies interactions.}, }
@article {pmid36694586, year = {2022}, author = {Thirumala, M and Sai Krishna, E and Sindhu Priya, P and Vishnuvardhan Reddy, S}, title = {Characterization of a novel Fluoride resistant bacterial isolate and its capability of Fluoride bioremediation.}, journal = {AIMS microbiology}, volume = {8}, number = {4}, pages = {470-483}, pmid = {36694586}, issn = {2471-1888}, abstract = {A Gram positive rod shaped bacterium designated as isolate H1 with Fluoride resistance up to 4 g/L sodium fluoride (NaF) in LB (Luria-Bertani) agar was isolated from a ground water sample of Narketpally area, Nalgonda district, Telangana, India. The colonies of isolate H1 were off white in color. Growth patterns of isolate H1 were observed at two different concentrations, 100 and 250 ppm, of NaF and also without NaF in the medium. In cases where NaF was present in the media, the lag phases of the growth curves were extended when compared to the absence of NaF. Optimum pH required for the organism's growth was 8. Isolate H1 required a temperature of 37 °C with 150 rpm and 2% NaCl for its optimal growth in the medium without NaF. Meanwhile, isolate H1 could thrive in a diverse pH range, i.e., pH 5-10, and at an NaCl concentration of up to 11% in the medium with NaF. Based on morphological, biochemical and molecular characterization, isolate H1 was identified as belonging to the genus Bacillus. It showed 98.47% 16S rDNA gene sequence similarity with Bacillus australimaris NH71_1[T]. Isolate H1 showed high fluoride removals of 22.5% and 38.2% with 100 and 250 mg/L of NaF in the LB broth when incubated at pH 8 and a temperature of 37 °C with 150 rpm for 3 day. Hence, this organism could be a promising isolate to apply for defluoridation of ground water in fluoride contaminthe ated areas.}, }
@article {pmid36694253, year = {2023}, author = {Uiterwijk, M and Vojta, L and Šprem, N and Beck, A and Jurković, D and Kik, M and Duscher, GG and Hodžić, A and Reljić, S and Sprong, H and Beck, R}, title = {Diversity of Hepatozoon species in wild mammals and ticks in Europe.}, journal = {Parasites &amp; vectors}, volume = {16}, number = {1}, pages = {27}, pmid = {36694253}, issn = {1756-3305}, mesh = {Dogs ; Animals ; *Wolves ; *Coccidiosis/epidemiology/veterinary/parasitology ; *Eucoccidiida/genetics ; *Ixodes/parasitology ; *Ixodidae/parasitology ; Foxes/parasitology ; Europe/epidemiology ; Rodentia ; *Mustelidae ; Animals, Domestic ; }, abstract = {BACKGROUND: Hepatozoon spp. are tick-borne parasites causing subclinical to clinical disease in wild and domestic animals. Aim of this study was to determine Hepatozoon prevalence and species distribution among wild mammals and ticks in Europe.<br><br>METHODS: Samples of wild mammals and ticks, originating from Austria, Bosnia and Herzegovina, Croatia, Belgium and the Netherlands, were tested with PCR to amplify a&#x2009;~&#x2009;670-bp fragment of the small subunit ribosomal RNA gene.<br><br>RESULTS: Of the 2801 mammal samples that were used for this study, 370 (13.2%) tested positive. Hepatozoon canis was detected in samples of 178 animals (3 Artiodactyla, 173 Carnivora, 1 Eulipotyphia, 1 Lagomorpha), H. martis in 125 (3 Artiodactyla, 122 Carnivora), H. sciuri in 13 (all Rodentia), Hepatozoon sp. in 47 (among which Hepatozoon sp. Vole isolate, all Rodentia) and H. ayorgbor in 4 (all Rodentia). Regarding origin, 2.9% (6/208) tested positive from Austria, 2.8% (1/36) from Bosnia and Herzegovina, 14.6% (173/1186) from Croatia and 13.9% (190/1371) from Belgium/the Netherlands. Of the 754 ticks collected, 0.0% (0/35) Hyalomma sp., 16.0% (4/25) Dermacentor spp., 0.0% (0/23) Haemaphysalis spp., 5.3% (24/50) Ixodes and 1.4% (3/221) Rhipicephalus spp. tested positive for Hepatozoon (4.2%; 32/754), most often H. canis (n&#x2009;=&#x2009;22).<br><br>CONCLUSIONS: Hepatozoon canis is most present in mammals (especially in Carnivora such as gray wolves and golden jackals) and ticks, followed by H. martis, which was found merely in stone martens and pine martens. None of the rodent-associated Hepatozoon spp. were detected in the ticks, suggesting the possible implication of other arthropod species or non-vectorial routes in the transmission cycle of the hemoprotozoans in rodents. Our findings of H. canis in ticks other than R. sanguineus add to the observation that other ticks are also involved in the life cycle of Hepatozoon. Now that presence of Hepatozoon has been demonstrated in red foxes, gray wolves, mustelids and rodents from the Netherlands and/or Belgium, veterinary clinicians should be aware of the possibility of spill-over to domestic animals, such as dogs.}, }
@article {pmid36694053, year = {2023}, author = {Arroyo, MC and Laurie, I and Rotsaert, C and Marzorati, M and Risso, D and Karnik, K}, title = {Age-Dependent Prebiotic Effects of Soluble Corn Fiber in M-SHIME[®] Gut Microbial Ecosystems.}, journal = {Plant foods for human nutrition (Dordrecht, Netherlands)}, volume = {78}, number = {1}, pages = {213-220}, pmid = {36694053}, issn = {1573-9104}, support = {PO 4500037596//Tate &amp; Lyle PLC/ ; }, mesh = {Humans ; Prebiotics/analysis ; Zea mays ; *Gastrointestinal Microbiome ; Lipopolysaccharides/pharmacology ; Caco-2 Cells ; Fatty Acids, Volatile/metabolism ; *Microbiota ; }, abstract = {Soluble corn fiber (SCF) has demonstrated prebiotic effects in clinical studies. Using an in vitro mucosal simulator of the human intestinal microbial ecosystem (M-SHIME[®]) model, the effects of SCF treatment on colonic microbiota composition and metabolic activity and on host-microbiome interactions were evaluated using fecal samples from healthy donors of different ages (baby [≤ 2 years], n = 4; adult [18-45 years], n = 2; elderly [70 years], n = 1). During the 3-week treatment period, M-SHIME[®] systems were supplemented with SCF daily (baby, 1.5, 3, or 4.5 g/d; adult, 3 or 8.5 g/d; and elderly, 8.5 g/d). M-SHIME[®] supernatants were evaluated for their effect on the intestinal epithelial cell barrier and inflammatory responses in lipopolysaccharide. (LPS)-stimulated cells. Additionally, short-chain fatty acid (SCFA) production and microbial community composition were assessed. In the baby and adult models, M-SHIME[®] supernatants from SCF treated vessels protected Caco-2 membrane integrity from LPS-induced damage. SCF treatment resulted in the expansion of Bacteroidetes, Firmicutes, and Bifidobacterial, as well as increased SCFA production in all age groups. SCF tended to have the greatest effect on propionate production. These findings demonstrate the prebiotic potential of SCF in babies, adults, and the elderly and provide insight into the mechanisms behind the observed prebiotic effects.}, }
@article {pmid36687598, year = {2022}, author = {Midani, FS and David, LA}, title = {Tracking defined microbial communities by multicolor flow cytometry reveals tradeoffs between productivity and diversity.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {910390}, pmid = {36687598}, issn = {1664-302X}, support = {R01 DK116187/DK/NIDDK NIH HHS/United States ; T32 DK007664/DK/NIDDK NIH HHS/United States ; }, abstract = {Cross feeding between microbes is ubiquitous, but its impact on the diversity and productivity of microbial communities is incompletely understood. A reductionist approach using simple microbial communities has the potential to detect cross feeding interactions and their impact on ecosystem properties. However, quantifying abundance of more than two microbes in a community in a high throughput fashion requires rapid, inexpensive assays. Here, we show that multicolor flow cytometry combined with a machine learning-based classifier can rapidly quantify species abundances in simple, synthetic microbial communities. Our approach measures community structure over time and detects the exchange of metabolites in a four-member community of fluorescent Bacteroides species. Notably, we quantified species abundances in co-cultures and detected evidence of cooperation in polysaccharide processing and competition for monosaccharide utilization. We also observed that co-culturing on simple sugars, but not complex sugars, reduced microbial productivity, although less productive communities maintained higher community diversity. In summary, our multicolor flow cytometric approach presents an economical, tractable model system for microbial ecology using well-studied human bacteria. It can be extended to include additional species, evaluate more complex environments, and assay response of communities to a variety of disturbances.}, }
@article {pmid36684671, year = {2023}, author = {Huang, F and Zhu, C and Huang, M and Song, X and Peng, A}, title = {The root enrichment of bacteria is consistent across different stress-resistant plant species.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e14683}, pmid = {36684671}, issn = {2167-8359}, mesh = {*Microbiota ; Soil Microbiology ; Phylogeny ; Plant Roots/microbiology ; Plants ; *Burkholderia ; }, abstract = {Bacteria, inhabiting around and in plant roots, confer many beneficial traits to promote plant growth and health. The secretion of root exudates modulates the nutritional state of the rhizosphere and root area, further selecting specific bacteria taxa and shaping the bacteria communities. Many studies of the rhizosphere effects have demonstrated that selection by the plant rhizosphere consistently enriches a set of bacteria taxa, and this is conserved across different plant species. Root selection effects are considered to be stronger than the rhizosphere selection effects, yet studies are limited. Here, we focus on the root selection effects across a group of 11 stress-resistant plant species. We found that the root selection consistently reduced the alpha diversity (represented by total number of observed species, Shannon's diversity, and phylogenetic diversity) and altered the structure and composition of bacteria communities. Furthermore, root selection tended to enrich for clusters of bacteria genera including Pantoea, Akkermansia, Blautia, Acinetobacter, Burkholderia-Paraburkholderia, Novosphingobium, Massilia, Pseudomonas, Chryseobacterium, and Stenotrophomonas. Our study offers some basic knowledge for understanding the microbial ecology of the plant root, and suggests that several bacteria genera are of interest for future studies.}, }
@article {pmid36683960, year = {2023}, author = {Li, Y and Deng, X and Zhang, N and Shen, Z and Li, R and Shen, Q and Salles, JF}, title = {Rhizosphere suppression hinders antibiotic resistance gene (ARG) spread under bacterial invasion.}, journal = {One health (Amsterdam, Netherlands)}, volume = {16}, number = {}, pages = {100481}, pmid = {36683960}, issn = {2352-7714}, abstract = {The rhizosphere is an extremely important component of the "one health" scenario by linking the soil microbiome and plants, in which the potential enrichment of antibiotic resistance genes (ARGs) might ultimately flow into the human food chain. Despite the increased occurrence of soil-borne diseases, which can lead to increased use of pesticides and antibiotic-producing biocontrol agents, the understanding of the dynamics of ARG spread in the rhizosphere is largely overlooked. Here, tomato seedlings grown in soils conducive and suppressive to the pathogen Ralstonia solanacearum were selected as a model to investigate ARG spread in the rhizosphere with and without pathogen invasion. Metagenomics data revealed that R. solanacearum invasion increased the density of ARGs and mobile genetic elements (MGEs). Although we found ARGs originating from human pathogenic bacteria in both soils, the enrichment was alleviated in the suppressive soil. In summary, the suppressive soil hindered ARG spread through pathogen suppression and had a lower number of taxa carrying antibiotic resistance.}, }
@article {pmid36683707, year = {2022}, author = {Chen, Q and Fan, Y and Zhang, B and Yan, C and Chen, Z and Wang, L and Hu, Y and Huang, Q and Su, J and Ren, J and Xu, H}, title = {Specific fungi associated with response to capsulized fecal microbiota transplantation in patients with active ulcerative colitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1086885}, pmid = {36683707}, issn = {2235-2988}, mesh = {Humans ; *Colitis, Ulcerative/therapy ; *Fecal Microbiota Transplantation/adverse effects ; Feces/microbiology ; Fungi/genetics ; Remission Induction ; Treatment Outcome ; }, abstract = {OBJECTIVE: Fecal microbiota transplantation (FMT) is a novel microbial treatment for patients with ulcerative colitis (UC). In this study, we performed a clinical trial of capsulized FMT in UC patients to determine the association between the gut fungal community and capsulized FMT outcomes.<br><br>DESIGN: This study recruited patients with active UC (N = 22) and healthy individuals (donor, N = 9) according to the criteria. The patients received capsulized FMT three times a week. Patient stool samples were collected before (week 0) and after FMT follow-up visits at weeks 1, 4, and 12. Fungal communities were analysed using shotgun metagenomic sequencing.<br><br>RESULTS: According to metagenomic analysis, fungal community evenness index was greater in samples collected from patients, and the overall fungal community was clustered among the samples collected from donors. The dominant fungi in fecal samples collected from donors and patients were Ascomycota and Basidiomycota. However, capsulized FMT ameliorated microbial fungal diversity and altered fungal composition, based on metagenomic analysis of fecal samples collected before and during follow-up visits after capsulized FMT. Fungal diversity decreased in samples collected from patients who achieved remission after capsulized FMT, similar to samples collected from donors. Patients achieving remission after capsulized FMT had specific enrichment of Kazachstania naganishii, Pyricularia grisea, Lachancea thermotolerans, and Schizosaccharomyces pombe compared with patients who did not achieve remission. In addition, the relative abundance of P. grisea was higher in remission fecal samples during the follow-up visit. Meanwhile, decreased levels of pathobionts, such as Candida and Debaryomyces hansenii, were associated with remission in patients receiving capsulized FMT.<br><br>CONCLUSION: In the metagenomic analysis of fecal samples from donors and patients with UC receiving capsulized FMT, shifts in gut fungal diversity and composition were associated with capsulized FMT and validated in patients with active UC. We also identified the specific fungi associated with the induction of remission. ClinicalTrails.gov (NCT03426683).}, }
@article {pmid36683444, year = {2023}, author = {Gegenbauer, C and Bellaire, A and Schintlmeister, A and Schmid, MC and Kubicek, M and Voglmayr, H and Zotz, G and Richter, A and Mayer, VE}, title = {Exo- and endophytic fungi enable rapid transfer of nutrients from ant waste to orchid tissue.}, journal = {The New phytologist}, volume = {238}, number = {5}, pages = {2210-2223}, pmid = {36683444}, issn = {1469-8137}, mesh = {Animals ; *Ants ; Nitrogen/metabolism ; Fungi/metabolism ; *Ascomycota/metabolism ; *Orchidaceae ; *Hypocreales ; Nutrients ; }, abstract = {The epiphytic orchid Caularthron bilamellatum sacrifices its water storage tissue for nutrients from the waste of ants lodging inside its hollow pseudobulb. Here, we investigate whether fungi are involved in the rapid translocation of nutrients. Uptake was analysed with a [15] N labelling experiment, subsequent isotope ratio mass spectrometry (IRMS) and secondary ion mass spectrometry (ToF-SIMS and NanoSIMS). We encountered two hyphae types: a thick melanized type assigned to 'black fungi' (Chaetothyriales, Cladosporiales, and Mycosphaerellales) in ant waste, and a thin endophytic type belonging to Hypocreales. In few cell layers, both hyphae types co-occurred. [15] N accumulation in both hyphae types was conspicuous, while for translocation to the vessels only Hypocreales were involved. There is evidence that the occurrence of the two hyphae types results in a synergism in terms of nutrient uptake. Our study provides the first evidence that a pseudobulb (=stem)-born endophytic network of Hypocreales is involved in the rapid translocation of nitrogen from insect-derived waste to the vegetative and reproductive tissue of the host orchid. For C. bilamellatum that has no contact with the soil, ant waste in the hollow pseudobulbs serves as equivalent to soil in terms of nutrient sources.}, }
@article {pmid36683151, year = {2023}, author = {Vallier, M and Suwandi, A and Ehrhardt, K and Belheouane, M and Berry, D and Čepić, A and Galeev, A and Johnsen, JM and Grassl, GA and Baines, JF}, title = {Pathometagenomics reveals susceptibility to intestinal infection by Morganella to be mediated by the blood group-related B4galnt2 gene in wild mice.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2164448}, pmid = {36683151}, issn = {1949-0984}, mesh = {Humans ; Mice ; Animals ; Morganella ; *Blood Group Antigens ; RNA, Ribosomal, 16S ; *Gastrointestinal Microbiome ; Genotype ; }, abstract = {Infectious disease is widely considered to be a major driver of evolution. A preponderance of signatures of balancing selection at blood group-related genes is thought to be driven by inherent trade-offs in susceptibility to disease. B4galnt2 is subject to long-term balancing selection in house mice, where two divergent allele classes direct alternative tissue-specific expression of a glycosyltransferase in the intestine versus blood vessels. The blood vessel allele class leads to prolonged bleeding times similar to von Willebrand disease in humans, yet has been maintained for millions of years. Based on in vivo functional studies in inbred lab strains, it is hypothesized that the cost of prolonged bleeding times may be offset by an evolutionary trade-off involving susceptibility to a yet unknown pathogen(s). To identify candidate pathogens for which resistance could be mediated by B4galnt2 genotype, we here employed a novel "pathometagenomic" approach in a wild mouse population, which combines bacterial 16S rRNA gene-based community profiling with histopathology of gut tissue. Through subsequent isolation, genome sequencing and controlled experiments in lab mice, we show that the presence of the blood vessel allele is associated with resistance to a newly identified subspecies of Morganella morganii, a clinically important opportunistic pathogen. Given the increasing importance of zoonotic events, the approach outlined here may find useful application in the detection of emerging diseases in wild animal populations.}, }
@article {pmid36681674, year = {2023}, author = {Van Holm, W and Carvalho, R and Delanghe, L and Eilers, T and Zayed, N and Mermans, F and Bernaerts, K and Boon, N and Claes, I and Lebeer, S and Teughels, W}, title = {Antimicrobial potential of known and novel probiotics on in vitro periodontitis biofilms.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {3}, pmid = {36681674}, issn = {2055-5008}, support = {G091218N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G091218N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G091218N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; C24/17/086//KU Leuven (Katholieke Universiteit Leuven)/ ; C24/17/086//KU Leuven (Katholieke Universiteit Leuven)/ ; HBC.2020.2873//Agentschap Innoveren en Ondernemen (Flanders Innovation &amp; Entrepreneurship)/ ; Lacto-Be 26850//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; Lacto-Be 26850//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {Humans ; *Periodontitis/drug therapy ; Lactobacillus/physiology ; Biofilms ; *Anti-Infective Agents/pharmacology ; *Probiotics/pharmacology ; }, abstract = {Several oral diseases are characterized by a shift within the oral microbiome towards a pathogenic, dysbiotic composition. Broad-spectrum antimicrobials are often part of patient care. However, because of the rising antibiotic resistance, alternatives are increasingly desirable. Alternatively, supplying beneficial species through probiotics is increasingly showing favorable results. Unfortunately, these probiotics are rarely evaluated comparatively. In this study, the in vitro effects of three known and three novel Lactobacillus strains, together with four novel Streptococcus salivarius strains were comparatively evaluated for antagonistic effects on proximal agar growth, antimicrobial properties of probiotic supernatant and the probiotic's effects on in vitro periodontal biofilms. Strain-specific effects were observed as differences in efficacy between genera and differences within genera. While some of the Lactobacillus candidates were able to reduce the periodontal pathobiont A. actinomycetemcomitans, the S. salivarius strains were not. However, the S. salivarius strains were more effective against periodontal pathobionts P. intermedia, P. gingivalis, and F. nucleatum. Vexingly, most of the Lactobacillus strains also negatively affected the prevalence of commensal species within the biofilms, while this was lower for S. salivarius strains. Both within lactobacilli and streptococci, some strains showed significantly more inhibition of the pathobionts, indicating the importance of proper strain selection. Additionally, some species showed reductions in non-target species, which can result in unexpected and unexplored effects on the whole microbiome.}, }
@article {pmid36677477, year = {2023}, author = {Neidhöfer, C and Sib, E and Benhsain, AH and Mutschnik-Raab, C and Schwabe, A and Wollkopf, A and Wetzig, N and Sieber, MA and Thiele, R and Döhla, M and Engelhart, S and Mutters, NT and Parčina, M}, title = {Examining Different Analysis Protocols Targeting Hospital Sanitary Facility Microbiomes.}, journal = {Microorganisms}, volume = {11}, number = {1}, pages = {}, pmid = {36677477}, issn = {2076-2607}, abstract = {Indoor spaces exhibit microbial compositions that are distinctly dissimilar from one another and from outdoor spaces. Unique in this regard, and a topic that has only recently come into focus, is the microbiome of hospitals. While the benefits of knowing exactly which microorganisms propagate how and where in hospitals are undoubtedly beneficial for preventing hospital-acquired infections, there are, to date, no standardized procedures on how to best study the hospital microbiome. Our study aimed to investigate the microbiome of hospital sanitary facilities, outlining the extent to which hospital microbiome analyses differ according to sample-preparation protocol. For this purpose, fifty samples were collected from two separate hospitals-from three wards and one hospital laboratory-using two different storage media from which DNA was extracted using two different extraction kits and sequenced with two different primer pairs (V1-V2 and V3-V4). There were no observable differences between the sample-preservation media, small differences in detected taxa between the DNA extraction kits (mainly concerning Propionibacteriaceae), and large differences in detected taxa between the two primer pairs V1-V2 and V3-V4. This analysis also showed that microbial occurrences and compositions can vary greatly from toilets to sinks to showers and across wards and hospitals. In surgical wards, patient toilets appeared to be characterized by lower species richness and diversity than staff toilets. Which sampling sites are the best for which assessments should be analyzed in more depth. The fact that the sample processing methods we investigated (apart from the choice of primers) seem to have changed the results only slightly suggests that comparing hospital microbiome studies is a realistic option. The observed differences in species richness and diversity between patient and staff toilets should be further investigated, as these, if confirmed, could be a result of excreted antimicrobials.}, }
@article {pmid36677425, year = {2023}, author = {Shedleur-Bourguignon, F and Duchemin, T and P Thériault, W and Longpré, J and Thibodeau, A and Hocine, MN and Fravalo, P}, title = {Distinct Microbiotas Are Associated with Different Production Lines in the Cutting Room of a Swine Slaughterhouse.}, journal = {Microorganisms}, volume = {11}, number = {1}, pages = {}, pmid = {36677425}, issn = {2076-2607}, support = {RDCPJ 520873-17//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {The microorganisms found on fresh, raw meat cuts at a slaughterhouse can influence the meat's safety and spoilage patterns along further stages of processing. However, little is known about the general microbial ecology of the production environment of slaughterhouses. We used 16s rRNA sequencing and diversity analysis to characterize the microbiota heterogeneity on conveyor belt surfaces in the cutting room of a swine slaughterhouse from different production lines (each associated with a particular piece/cut of meat). Variation of the microbiota over a period of time (six visits) was also evaluated. Significant differences of alpha and beta diversity were found between the different visits and between the different production lines. Bacterial genera indicative of each visit and production line were also identified. We then created random forest models that, based on the microbiota of each sample, allowed us to predict with 94% accuracy to which visit a sample belonged and to predict with 88% accuracy from which production line it was taken. Our results suggest a possible influence of meat cut on processing surface microbiotas, which could lead to better prevention, surveillance, and control of microbial contamination of meat during processing.}, }
@article {pmid36671807, year = {2023}, author = {Kropochev, AI and Lashin, SA and Matushkin, YG and Klimenko, AI}, title = {Trait-Based Method of Quantitative Assessment of Ecological Functional Groups in the Human Intestinal Microbiome.}, journal = {Biology}, volume = {12}, number = {1}, pages = {}, pmid = {36671807}, issn = {2079-7737}, support = {No. &#x41c;&#x41a;-3363.2022.1.4.//Russian presidential grant for support of young scientists/ ; }, abstract = {We propose the trait-based method for quantifying the activity of functional groups in the human gut microbiome based on metatranscriptomic data. It allows one to assess structural changes in the microbial community comprised of the following functional groups: butyrate-producers, acetogens, sulfate-reducers, and mucin-decomposing bacteria. It is another way to perform a functional analysis of metatranscriptomic data by focusing on the ecological level of the community under study. To develop the method, we used published data obtained in a carefully controlled environment and from a synthetic microbial community, where the problem of ambiguity between functionality and taxonomy is absent. The developed method was validated using RNA-seq data and sequencing data of the 16S rRNA amplicon on a simplified community. Consequently, the successful verification provides prospects for the application of this method for analyzing natural communities of the human intestinal microbiota.}, }
@article {pmid36662284, year = {2023}, author = {He, T and Zhang, X and Du, J and Gilliam, FS and Yang, S and Tian, M and Zhang, C and Zhou, Y}, title = {Arbuscular Mycorrhizal Fungi Shift Soil Bacterial Community Composition and Reduce Soil Ammonia Volatilization and Nitrous Oxide Emissions.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {951-964}, pmid = {36662284}, issn = {1432-184X}, support = {No. 182300410013//Natural Science Foundation of Henan Province of China/ ; No. 30500712//Science and Technology Innovation Fund of Henan Agricultural University/ ; No. 2018YFD0200605//National Key Research and Development Program of China/ ; }, mesh = {*Soil ; Nitrous Oxide ; Ammonia/analysis ; *Mycorrhizae/chemistry ; Volatilization ; Nitrogen ; Fertilizers/analysis ; Agriculture ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) establish mutualistic relationships with the majority of terrestrial plants, increasing plant uptake of soil nitrogen (N) in exchange for photosynthates. And may influence soil ammonia (NH3) volatilization and nitrous oxide (N2O) emissions directly by improving plant N uptake, and/or indirectly by modifying soil bacterial community composition for the soil C availability increasing. However, the effects of AMF on soil NH3 volatilization and N2O emissions and their underlying mechanisms remain unclear. We carried out two independent experiments using contrasting methods, one with a compartmental box device (in 2016) and the other with growth pot experiment (in 2020) to examine functional relationships between AMF and soil NH3 volatilization and N2O emissions under varying N input. The presence of AMF significantly reduced soil NH3 volatilization and N2O emissions while enhancing plant biomass and plant N acquisition, and reducing soil NH4[+] and NO3[-], even with high N input. The presence of AMF also significantly reduced the relative abundance within the bacterial orders Sphingomonadales and Rhizobiales. Sphingomonadales correlated significantly and positively with soil NH3 volatilization in 2016 and N2O emissions, whereas Rhizobiales correlated positively with soil N2O emissions. High N input significantly increased soil NH3 volatilization and N2O emissions with increasing relative abundance of Sphingomonadales and Rhizobiales. These findings demonstrate the contribution of AMF in regulating NH3 and N2O emission by improving plant N uptake and altering soil bacterial communities. They also suggest that altering the rhizosphere microbiome might offer additional potential for restoration of N-enriched agroecosystems.}, }
@article {pmid36656658, year = {2023}, author = {Zhang, S and Van Haesebroeck, J and Yang, Q and Defoirdt, T}, title = {Indole-3-acetic acid increases the survival of brine shrimp challenged with vibrios belonging to the Harveyi clade.}, journal = {Journal of fish diseases}, volume = {46}, number = {5}, pages = {477-486}, doi = {10.1111/jfd.13759}, pmid = {36656658}, issn = {1365-2761}, support = {//Bijzonder Onderzoeksfonds UGent/ ; //China Scholarship Council/ ; //Scientific Research Fund of Flanders/ ; }, mesh = {Animals ; *Artemia/microbiology ; *Indoleacetic Acids/pharmacology ; Larva ; *Vibrio parahaemolyticus/drug effects/physiology ; }, abstract = {Vibrios belonging to the Harveyi clade (including closely related species such as Vibrio campbellii, Vibrio harveyi and Vibrio parahaemolyticus) are important pathogens of aquatic organisms. In this study, we investigated the use of indole-3-acetic acid to control disease caused by Harveyi clade vibrios. Indole-3-acetic acid, which can be produced by various seaweeds and microalgae, was added to the rearing water of brine shrimp larvae challenged with 12 different Harveyi clade Vibrio strains. Indole-3-acetic acid significantly decreased the virulence of 10 of the strains without any effect on their growth. The latter is important as it will minimize the selective pressure for resistance development. The survival rate of brine shrimp larvae increased from 1.2-fold to 4.8-fold upon treatment with 400 μM indole-3-acetic acid. Additionally, indole-3-acetic acid significantly decreased the swimming motility in 10 of the strains and biofilm formation in eight of the strains. The mRNA levels of the pirA and pirB toxin genes were decreased to 46% and 42% by indole-3-acetic acid in the AHPND-causing strain V. parahaemolyticus M0904. Hence, our data demonstrate that indole-3-acetic acid has the potential to be an effective virulence inhibitor to control infections in aquaculture.}, }
@article {pmid36654062, year = {2022}, author = {Song, W and Qiu, L and Qing, J and Zhi, W and Zha, Z and Hu, X and Qin, Z and Gong, H and Li, Y}, title = {Using Bayesian network model with MMHC algorithm to detect risk factors for stroke.}, journal = {Mathematical biosciences and engineering : MBE}, volume = {19}, number = {12}, pages = {13660-13674}, doi = {10.3934/mbe.2022637}, pmid = {36654062}, issn = {1551-0018}, mesh = {Humans ; Bayes Theorem ; *Algorithms ; *Stroke/epidemiology ; Risk Factors ; Logistic Models ; }, abstract = {Stroke is a major chronic non-communicable disease with high incidence, high mortality, and high recurrence. To comprehensively digest its risk factors and take some relevant measures to lower its prevalence is of great significance. This study aimed to employ Bayesian Network (BN) model with Max-Min Hill-Climbing (MMHC) algorithm to explore the risk factors for stroke. From April 2019 to November 2019, Shanxi Provincial People's Hospital conducted opportunistic screening for stroke in ten rural areas in Shanxi Province. First, we employed propensity score matching (PSM) for class balancing for stroke. Afterwards, we used Chi-square testing and Logistic regression model to conduct a preliminary analysis of risk factors for stroke. Statistically significant variables were incorporated into BN model construction. BN structure learning was achieved using MMHC algorithm, and its parameter learning was achieved with Maximum Likelihood Estimation. After PSM, 748 non-stroke cases and 748 stroke cases were included in this study. BN was built with 10 nodes and 12 directed edges. The results suggested that age, fasting plasma glucose, systolic blood pressure, and family history of stroke constitute direct risk factors for stroke, whereas sex, educational levels, high density lipoprotein cholesterol, diastolic blood pressure, and urinary albumin-to-creatinine ratio represent indirect risk factors for stroke. BN model with MMHC algorithm not only allows for a complicated network relationship between risk factors and stroke, but also could achieve stroke risk prediction through Bayesian reasoning, outshining traditional Logistic regression model. This study suggests that BN model boasts great prospects in risk factor detection for stroke.}, }
@article {pmid36652878, year = {2023}, author = {Lin, Q and De Vrieze, J and Li, L and Fang, X and Li, X}, title = {Interconnected versus unconnected microorganisms: Does it matter in anaerobic digestion functioning.}, journal = {Journal of environmental management}, volume = {331}, number = {}, pages = {117307}, doi = {10.1016/j.jenvman.2023.117307}, pmid = {36652878}, issn = {1095-8630}, mesh = {Animals ; Swine ; Anaerobiosis ; Phylogeny ; *Manure ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Methane ; Bioreactors ; Biofuels ; }, abstract = {Microorganisms in anaerobic digestion (AD) are essential for wastes/pollutants treatment and energy recovery. Due to microbial enormous diversity, developing effective perspectives to understand microbial roles therein is urgent. This study conducted AD of swine manure, used an ensemble-based network analysis to distinguish interconnected, unconnected, copresence (positively interconnected) and mutual-exclusion (negatively interconnected) microorganisms within microbial communities, and explored their importance towards AD performances, using amplicon sequencing of 16S rRNA and 16S rRNA gene. Our analyses revealed greater importance of interconnected than unconnected microorganisms towards CH4 production and AD multifunctionality, which was attributed to higher niche breadth, deterministic community assembly, community stability and phylogenetic conservatism. The diversity was higher in unconnected than interconnected microorganisms, but was not linked to AD performances. Compared to copresence microorganisms, mutual-exclusion microorganisms showed greater and equal importance towards CH4 production and AD multifunctionality, which was attributed to their roles in stabilizing microbial communities. The increased feedstock biodegradability, by replacing part of manure with fructose or apple waste, hardly affected the relative importance of interconnected versus unconnected microorganisms towards CH4 production or AD multifunctionality. Our findings develop a new framework to understand microbial roles, and have important implications in targeted manipulation of critical microorganisms in waste-treatment systems.}, }
@article {pmid36651641, year = {2023}, author = {Daebeler, A and Güell-Bujons, Q and Mooshammer, M and Zechmeister, T and Herbold, CW and Richter, A and Wagner, M and Daims, H}, title = {Rapid nitrification involving comammox and canonical Nitrospira at extreme pH in saline-alkaline lakes.}, journal = {Environmental microbiology}, volume = {25}, number = {5}, pages = {1055-1067}, pmid = {36651641}, issn = {1462-2920}, support = {P 30570/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Lakes ; *Nitrites ; Nitrates ; Ammonia ; Nitrification ; Bacteria/genetics ; Archaea/genetics ; Hydrogen-Ion Concentration ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Nitrite-oxidizing bacteria (NOB) catalyse the second nitrification step and are the main biological source of nitrate. The most diverse and widespread NOB genus is Nitrospira, which also contains complete ammonia oxidizers (comammox) that oxidize ammonia to nitrate. To date, little is known about the occurrence and biology of comammox and canonical nitrite oxidizing Nitrospira in extremely alkaline environments. Here, we studied the seasonal distribution and diversity, and the effect of short-term pH changes on comammox and canonical Nitrospira in sediments of two saline, highly alkaline lakes. We identified diverse canonical and comammox Nitrospira clade A-like phylotypes as the only detectable NOB during more than a year, suggesting their major importance for nitrification in these habitats. Gross nitrification rates measured in microcosm incubations were highest at pH 10 and considerably faster than reported for other natural, aquatic environments. Nitrification could be attributed to canonical and comammox Nitrospira and to Nitrososphaerales ammonia-oxidizing archaea. Furthermore, our data suggested that comammox Nitrospira contributed to ammonia oxidation at an extremely alkaline pH of 11. These results identify saline, highly alkaline lake sediments as environments of uniquely strong nitrification with novel comammox Nitrospira as key microbial players.}, }
@article {pmid36648219, year = {2023}, author = {Jiang, C and Zeng, H}, title = {Unique Habitat of Karst Tiankengs Changes the Taxonomy and Potential Metabolism of Soil Microbial Communities.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0231622}, pmid = {36648219}, issn = {2165-0497}, mesh = {Humans ; *Ecosystem ; Soil/chemistry ; Soil Microbiology ; Biodiversity ; *Microbiota ; Bacteria/genetics ; }, abstract = {Microbial communities in karst ecosystems have been extensively studied. However, in a class of deep-lying habitats with unique climates (karst tiankeng), the structure and ecological functions of microorganisms receive little attention, which is essential for understanding the biogeochemistry of karst tiankeng. Herein, microorganisms from inside (ITK) and outside (OTK) karst tiankengs were analyzed by high-throughput sequencing and multivariate statistical analysis. The results showed that the structure and function of soil bacterial communities inside and outside karst tiankengs were significantly different. The ITK microbial communities presented significantly higher Shannon diversity due to the abundant nutrients in karst tiankeng soil. Random molecular ecological network analysis revealed that the ITK network was simpler and more vulnerable and may be susceptible to environmental changes. More positive links within the network indicate that microorganisms adapt to the karst tiankeng through synergies. The keystones in karst tiankeng were mainly involved in the decomposition of soil organic matter and carbon/nitrogen cycles. Although soil total phosphorus and available potassium regulate microbial community structure variation, dispersal limitation is the predominant ecological process within the microbial community in karst tiankeng. In addition, the functional profiles of the microbial communities reveal that some human diseases (such as infectious diseases) exist in OTK. Collectively, these findings have enhanced our understanding of microbial interactions, ecological functions, and community composition processes in karst tiankeng ecosystems. IMPORTANCE Constrained by the trapped terrain, a unique ecosystem has formed in karst tiankeng. Soil microorganisms are essential for the formation and maintenance of ecosystems, but soil microbial ecology research in karst tiankeng is still lacking. In this study, representative habitats inside and outside karst tiankeng were selected to study the taxonomy and potential metabolism of soil microbial communities. The results show that the unique habitat of karst tiankeng reshapes the composition, structure, and function of soil microbial communities. Our results contribute to enhancing our understanding of sustainable recovery strategies in fragile ecosystems and understanding the biodiversity value of karst tiankeng under climate change.}, }
@article {pmid36646914, year = {2023}, author = {Gruppuso, L and Receveur, JP and Fenoglio, S and Bona, F and Benbow, ME}, title = {Hidden Decomposers: the Role of Bacteria and Fungi in Recently Intermittent Alpine Streams Heterotrophic Pathways.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1499-1512}, pmid = {36646914}, issn = {1432-184X}, mesh = {*Rivers/microbiology ; Biodegradation, Environmental ; *Fungi/genetics/metabolism ; Bacteria/genetics/metabolism ; Plant Leaves/microbiology ; Ecosystem ; }, abstract = {The frequency of flow intermittency and drying events in Alpine rivers is expected to increase due to climate change. These events can have significant consequences for stream ecological communities, though the effects of reduced flow conditions on microbial communities of decomposing allochthonous leaf material require additional research. In this study, we investigated the bacterial and fungal communities associated with the decomposition of two common species of leaf litter, chestnut (Castanea sativa), and oak (Quercus robur). A sampling of experimentally placed leaf bags occurred over six collection dates (up to 126 days after placement) at seven stream sites in the Western Italian Alps with historically different flow conditions. Leaf-associated bacterial and fungal communities were identified using amplicon-based, high-throughput sequencing. Chestnut and oak leaf material harbored distinct bacterial and fungal communities, with a number of taxonomic groups differing in abundance, though bacterial community structure converged later in decomposition. Historical flow conditions (intermittent vs perennial rivers) and observed conditions (normal flow, low flow, ongoing drying event) had weaker effects on bacterial and fungal communities compared to leaf type and collection date (i.e., length of decomposition). Our findings highlight the importance of leaf characteristics (e.g., C:N ratios, recalcitrance) to the in-stream conditioning of leaf litter and a need for additional investigations of drying events in Alpine streams. This study provides new information on the microbial role in leaf litter decomposition with expected flow changes associated with a global change scenario.}, }
@article {pmid36646913, year = {2023}, author = {Maucourt, F and Cébron, A and Budzinski, H and Le Menach, K and Peluhet, L and Czarnes, S and Melayah, D and Chapulliot, D and Vallon, L and Plassart, G and Hugoni, M and Fraissinet-Tachet, L}, title = {Prokaryotic, Microeukaryotic, and Fungal Composition in a Long-Term Polychlorinated Biphenyl-Contaminated Brownfield.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1696-1708}, pmid = {36646913}, issn = {1432-184X}, mesh = {*Polychlorinated Biphenyls/analysis/chemistry/metabolism ; *Soil Pollutants/analysis ; Biodegradation, Environmental ; Soil Microbiology ; Bacteria/genetics/metabolism ; Soil/chemistry ; }, abstract = {Polychlorinated biphenyls (PCBs) are recognized as persistent organic pollutants and accumulate in organisms, soils, waters, and sediments, causing major health and ecological perturbations. Literature reported PCB bio-transformation by fungi and bacteria in vitro, but data about the in situ impact of those compounds on microbial communities remained scarce while being useful to guide biotransformation assays. The present work investigated for the first time microbial diversity from the three-domains-of-life in a long-term contaminated brownfield (a former factory land). Soil samples were ranked according to their PCB concentrations, and a significant increase in abundance was shown according to increased concentrations. Microbial communities structure showed a segregation from the least to the most PCB-polluted samples. Among the identified microorganisms, Bacteria belonging to Gammaproteobacteria class, as well as Fungi affiliated to Saccharomycetes class or Pleurotaceae family, including some species known to transform some PCBs were abundantly retrieved in the highly polluted soil samples.}, }
@article {pmid36645380, year = {2023}, author = {Mynard, P and Algar, AC and Lancaster, LT and Bocedi, G and Fahri, F and Gubry-Rangin, C and Lupiyaningdyah, P and Nangoy, M and Osborne, OG and Papadopulos, AST and Sudiana, IM and Juliandi, B and Travis, JMJ and Herrera-Alsina, L}, title = {Impact of Phylogenetic Tree Completeness and Mis-specification of Sampling Fractions on Trait Dependent Diversification Models.}, journal = {Systematic biology}, volume = {72}, number = {1}, pages = {106-119}, pmid = {36645380}, issn = {1076-836X}, mesh = {Phylogeny ; Phenotype ; *Genetic Speciation ; }, abstract = {Understanding the origins of diversity and the factors that drive some clades to be more diverse than others are important issues in evolutionary biology. Sophisticated SSE (state-dependent speciation and extinction) models provide insights into the association between diversification rates and the evolution of a trait. The empirical data used in SSE models and other methods is normally imperfect, yet little is known about how this can affect these models. Here, we evaluate the impact of common phylogenetic issues on inferences drawn from SSE models. Using simulated phylogenetic trees and trait information, we fitted SSE models to determine the effects of sampling fraction (phylogenetic tree completeness) and sampling fraction mis-specification on model selection and parameter estimation (speciation, extinction, and transition rates) under two sampling regimes (random and taxonomically biased). As expected, we found that both model selection and parameter estimate accuracies are reduced at lower sampling fractions (i.e., low tree completeness). Furthermore, when sampling of the tree is imbalanced across sub-clades and tree completeness is ≤ 60%, rates of false positives increase and parameter estimates are less accurate, compared to when sampling is random. Thus, when applying SSE methods to empirical datasets, there are increased risks of false inferences of trait dependent diversification when some sub-clades are heavily under-sampled. Mis-specifying the sampling fraction severely affected the accuracy of parameter estimates: parameter values were over-estimated when the sampling fraction was specified as lower than its true value, and under-estimated when the sampling fraction was specified as higher than its true value. Our results suggest that it is better to cautiously under-estimate sampling efforts, as false positives increased when the sampling fraction was over-estimated. We encourage SSE studies where the sampling fraction can be reasonably estimated and provide recommended best practices for SSE modeling. [Trait dependent diversification; SSE models; phylogenetic tree completeness; sampling fraction.].}, }
@article {pmid36644938, year = {2023}, author = {van Neerbos, FAC and Dewitte, P and Wäckers, F and Wenseleers, T and Jacquemyn, H and Lievens, B}, title = {Bacterial volatiles elicit differential olfactory responses in insect species from the same and different trophic levels.}, journal = {Insect science}, volume = {30}, number = {5}, pages = {1464-1480}, doi = {10.1111/1744-7917.13176}, pmid = {36644938}, issn = {1744-7917}, abstract = {Insect communities consist of species from several trophic levels that have to forage for suitable resources among and within larger patches of nonresources. To locate their resources, insects use diverse stimuli, including olfactory, visual, acoustic, tactile and gustatory cues. While most research has focused on cues derived from plants and other insects, there is mounting evidence that insects also respond to volatile organic compounds (VOCs) emitted by microorganisms. However, to date little is known about how the olfactory response of insects within and across different trophic levels is affected by bacterial VOCs. In this study, we used Y-tube bioassays and chemical analysis of VOCs to assess how VOCs emitted by bacteria affect the olfactory response of insects of the same and different trophic levels. Experiments were performed using two aphid species (Amphorophora idaei Börner and Myzus persicae var. nicotianae Blackman), three primary parasitoid species (Aphidius colemani Viereck, A. ervi Haliday, and A. matricariae Viereck), and two hyperparasitoid species (Asaphes suspensus Nees and Dendrocerus aphidum Rondani). Olfactory responses were evaluated for three bacterial strains (Bacillus pumilus ST18.16/133, Curtobacterium sp. ST18.16/085, and Staphylococcus saprophyticus ST18.16/160) that were isolated from the habitat of the insects. Results revealed that insects from all trophic levels responded to bacterial volatiles, but olfactory responses varied between and within trophic levels. All bacteria produced the same set of volatile compounds, but often in different relative concentrations. For 11 of these volatiles we found contrasting correlations between their concentration and the behavior of the primary parasitoids and hyperparasitoids. Furthermore, olfactometer experiments on three of these compounds confirmed the contrasting olfactory responses of primary parasitoids and hyperparasitoids. The potential of these findings for the development of novel semiochemical-based strategies to improve biological aphid control has been discussed.}, }
@article {pmid36644338, year = {2022}, author = {Romano, F and Symiakaki, K and Pitta, P}, title = {Sex in the wild: repeated observations of planktonic ciliate conjugation from field samples.}, journal = {Journal of plankton research}, volume = {44}, number = {2}, pages = {333-336}, pmid = {36644338}, issn = {0142-7873}, abstract = {Ciliate conjugation is considered a rare event to encounter in the field and it is mostly reported from cultures. In this work, we describe a synchronized conjugation event of planktonic ciliates that was discovered twice; in September 2019, at two different locations in the Cretan Sea, Eastern Mediterranean, and in October 2020. In 2019, first, at 2 m depth of the coastal station POSEIDON-HCB, in samples fixed with acid Lugol and formaldehyde, we found 340 and 200 mating pairs L[-1]of different ciliate species, respectively; and second, at the Heraklion port, we found 220 mating pairs L[-1] of Strombidinopsis sp. and 1960 mating pairs L[-1] of Strombidium sp. At the Heraklion port visited again in 2020, we found 800 mating pairs L[-1] of Strombidinopsis sp. and 200 mating pairs L[-1] of Strombidium sp. Since detailed descriptions of conjugation in pelagic oligotrich ciliates are missing, our observations indicate that ciliate conjugation could be a frequent and periodic phenomenon, under specific conditions.}, }
@article {pmid36643595, year = {2023}, author = {Villa, F and Wu, YL and Zerboni, A and Cappitelli, F}, title = {Corrigendum: In Living Color: Pigment-Based Microbial Ecology At the Mineral-Air Interface.}, journal = {Bioscience}, volume = {73}, number = {1}, pages = {69}, doi = {10.1093/biosci/biac109}, pmid = {36643595}, issn = {0006-3568}, abstract = {[This corrects the article DOI: 10.1093/biosci/biac091.].}, }
@article {pmid36640506, year = {2023}, author = {Lamprea Pineda, PA and Demeestere, K and Toledo, M and Boon, N and Van Langenhove, H and Walgraeve, C}, title = {Long-term biofiltration of gaseous N,N-dimethylformamide: Operational performance and microbial diversity analysis at different conditions.}, journal = {Journal of hazardous materials}, volume = {447}, number = {}, pages = {130767}, doi = {10.1016/j.jhazmat.2023.130767}, pmid = {36640506}, issn = {1873-3336}, mesh = {*Gases/analysis ; Dimethylformamide ; *Air Pollutants/analysis ; Temperature ; Filtration/methods ; Biodegradation, Environmental ; }, abstract = {N,N-Dimethylformamide (DMF) is an organic solvent produced in large quantities worldwide. It is considered as a hazardous air pollutant and its emission should be controlled. However, only a limited number of studies have been performed on the removal of gaseous DMF by biological technologies. In this paper, we evaluate the removal of DMF under mesophilic and thermophilic conditions in a lab-scale biofilter for 472 days. The results show that, at ambient temperature, the biofilter achieved an average removal efficiency (RE) of 99.7 ± 0.3 % at Inlet Loads (ILs) up to 297 ± 52 g DFM m[-3] h[-1] (Empty Bed Residence Time (EBRTs) of 10.7 s). However, a decrease in EBRT (6.4 s) led to an unstable outlet concentration and, thus, to a drop in the biofilter performance (average RE: 90 ± 9 %). Moreover, an increase in temperature up to 65 °C led to a gradual decrease in RE (till 91 ± 7 %). Microbial analysis indicates that once the microorganisms encountered DMF, Rhizobiaceae dominated followed by Alcaligenaceae. Afterwards, a strong decrease in Rhizobiaceae was observed at every increase in temperature, and at 65 °C, the taxa were more heterogeneous. Overall, our experimental results indicate that biofiltration is a promising technique to remove DMF from waste gas streams.}, }
@article {pmid36639537, year = {2023}, author = {Osvatic, JT and Yuen, B and Kunert, M and Wilkins, L and Hausmann, B and Girguis, P and Lundin, K and Taylor, J and Jospin, G and Petersen, JM}, title = {Gene loss and symbiont switching during adaptation to the deep sea in a globally distributed symbiosis.}, journal = {The ISME journal}, volume = {17}, number = {3}, pages = {453-466}, pmid = {36639537}, issn = {1751-7370}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Phylogeny ; *Symbiosis/genetics ; Adaptation, Physiological ; Biological Evolution ; Bacteria/genetics ; Water ; *Hydrothermal Vents ; }, abstract = {Chemosynthetic symbioses between bacteria and invertebrates occur worldwide from coastal sediments to the deep sea. Most host groups are restricted to either shallow or deep waters. In contrast, Lucinidae, the most species-rich family of chemosymbiotic invertebrates, has both shallow- and deep-sea representatives. Multiple lucinid species have independently colonized the deep sea, which provides a unique framework for understanding the role microbial symbionts play in evolutionary transitions between shallow and deep waters. Lucinids acquire their symbionts from their surroundings during early development, which may allow them to flexibly acquire symbionts that are adapted to local environments. Via metagenomic analyses of museum and other samples collected over decades, we investigated the biodiversity and metabolic capabilities of the symbionts of 22 mostly deep-water lucinid species. We aimed to test the theory that the symbiont played a role in adaptation to life in deep-sea habitats. We identified 16 symbiont species, mostly within the previously described genus Ca. Thiodiazotropha. Most genomic functions were shared by both shallow-water and deep-sea Ca. Thiodiazotropha, though nitrogen fixation was exclusive to shallow-water species. We discovered multiple cases of symbiont switching near deep-sea hydrothermal vents and cold seeps, where distantly related hosts convergently acquired novel symbionts from a different bacterial order. Finally, analyses of selection revealed consistently stronger purifying selection on symbiont genomes in two extreme habitats - hydrothermal vents and an oxygen-minimum zone. Our findings reveal that shifts in symbiont metabolic capability and, in some cases, acquisition of a novel symbiont accompanied adaptation of lucinids to challenging deep-sea habitats.}, }
@article {pmid36635570, year = {2023}, author = {Strachan, CR and Yu, XA and Neubauer, V and Mueller, AJ and Wagner, M and Zebeli, Q and Selberherr, E and Polz, MF}, title = {Differential carbon utilization enables co-existence of recently speciated Campylobacteraceae in the cow rumen epithelial microbiome.}, journal = {Nature microbiology}, volume = {8}, number = {2}, pages = {309-320}, pmid = {36635570}, issn = {2058-5276}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Female ; Cattle ; Animals ; *Rumen/metabolism ; *Microbiota/genetics ; Genome ; Acetates/metabolism ; }, abstract = {The activities of different microbes in the cow rumen have been shown to modulate the host's ability to utilize plant biomass, while the host-rumen interface has received little attention. As datasets collected worldwide have pointed to Campylobacteraceae as particularly abundant members of the rumen epithelial microbiome, we targeted this group in a subset of seven cows with meta- and isolate genome analysis. We show that the dominant Campylobacteraceae lineage has recently speciated into two populations that were structured by genome-wide selective sweeps followed by population-specific gene import and recombination. These processes led to differences in gene expression and enzyme domain composition that correspond to the ability to utilize acetate, the main carbon source for the host, at the cost of inhibition by propionate. This trade-off in competitive ability further manifests itself in differential dynamics of the two populations in vivo. By exploring population-level adaptations that otherwise remain cryptic in culture-independent analyses, our results highlight how recent evolutionary dynamics can shape key functional roles in the rumen microbiome.}, }
@article {pmid36635489, year = {2023}, author = {Wang, J and Raza, W and Jiang, G and Yi, Z and Fields, B and Greenrod, S and Friman, VP and Jousset, A and Shen, Q and Wei, Z}, title = {Bacterial volatile organic compounds attenuate pathogen virulence via evolutionary trade-offs.}, journal = {The ISME journal}, volume = {17}, number = {3}, pages = {443-452}, pmid = {36635489}, issn = {1751-7370}, support = {BB/T010606/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Volatile Organic Compounds/pharmacology ; Virulence/genetics ; *Bacillus ; Adaptation, Physiological ; Soil ; *Ralstonia solanacearum/genetics ; Plant Diseases/microbiology ; }, abstract = {Volatile organic compounds (VOCs) produced by soil bacteria have been shown to exert plant pathogen biocontrol potential owing to their strong antimicrobial activity. While the impact of VOCs on soil microbial ecology is well established, their effect on plant pathogen evolution is yet poorly understood. Here we experimentally investigated how plant-pathogenic Ralstonia solanacearum bacterium adapts to VOC-mixture produced by a biocontrol Bacillus amyloliquefaciens T-5 bacterium and how these adaptations might affect its virulence. We found that VOC selection led to a clear increase in VOC-tolerance, which was accompanied with cross-tolerance to several antibiotics commonly produced by soil bacteria. The increasing VOC-tolerance led to trade-offs with R. solanacearum virulence, resulting in almost complete loss of pathogenicity in planta. At the genetic level, these phenotypic changes were associated with parallel mutations in genes encoding lipopolysaccharide O-antigen (wecA) and type-4 pilus biosynthesis (pilM), which both have been linked with outer membrane permeability to antimicrobials and plant pathogen virulence. Reverse genetic engineering revealed that both mutations were important, with pilM having a relatively larger negative effect on the virulence, while wecA having a relatively larger effect on increased antimicrobial tolerance. Together, our results suggest that microbial VOCs are important drivers of bacterial evolution and could potentially be used in biocontrol to select for less virulent pathogens via evolutionary trade-offs.}, }
@article {pmid36631688, year = {2023}, author = {Rasmussen, TS and Koefoed, AK and Deng, L and Muhammed, MK and Rousseau, GM and Kot, W and Sprotte, S and Neve, H and Franz, CMAP and Hansen, AK and Vogensen, FK and Moineau, S and Nielsen, DS}, title = {CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice.}, journal = {The ISME journal}, volume = {17}, number = {3}, pages = {432-442}, pmid = {36631688}, issn = {1751-7370}, support = {//CIHR/Canada ; }, mesh = {Animals ; Mice ; *Bacteriophages/genetics ; CRISPR-Cas Systems ; Bacteria/genetics ; Base Sequence ; Plasmids ; }, abstract = {Many bacteria and archaea harbor the adaptive CRISPR-Cas system, which stores small nucleotide fragments from previous invasions of nucleic acids via viruses or plasmids. This molecular archive blocks further invaders carrying identical or similar nucleotide sequences. However, few of these systems have been confirmed experimentally to be active in gut bacteria. Here, we demonstrate experimentally that the type I-C CRISPR-Cas system of the prevalent gut bacterium Eggerthella lenta can specifically target and cleave foreign DNA in vitro by using a plasmid transformation assay. We also show that the CRISPR-Cas system acquires new immunities (spacers) from the genome of a virulent E. lenta phage using traditional phage assays in vitro but also in vivo using gnotobiotic (GB) mice. Both high phage titer and an increased number of spacer acquisition events were observed when E. lenta was exposed to a low multiplicity of infection in vitro, and three phage genes were found to contain protospacer hotspots. Fewer new spacer acquisitions were detected in vivo than in vitro. Longitudinal analysis of phage-bacteria interactions showed sustained coexistence in the gut of GB mice, with phage abundance being approximately one log higher than the bacteria. Our findings show that while the type I-C CRISPR-Cas system is active in vitro and in vivo, a highly virulent phage in vitro was still able to co-exist with its bacterial host in vivo. Taken altogether, our results suggest that the CRISPR-Cas defense system of E. lenta provides only partial immunity in the gut.}, }
@article {pmid36631293, year = {2023}, author = {Mason, AR and Taylor, LS and DeBruyn, JM}, title = {Microbial ecology of vertebrate decomposition in terrestrial ecosystems.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {2}, pages = {}, doi = {10.1093/femsec/fiad006}, pmid = {36631293}, issn = {1574-6941}, mesh = {Animals ; Humans ; *Ecosystem ; Vertebrates/metabolism ; Ecology ; Soil Microbiology ; Soil ; *Microbiota ; Mammals ; }, abstract = {Vertebrate decomposition results in an ephemeral disturbance of the surrounding environment. Microbial decomposers are recognized as key players in the breakdown of complex organic compounds, controlling carbon and nutrient fate in the ecosystem and potentially serving as indicators of time since death for forensic applications. As a result, there has been increasing attention on documenting the microbial communities associated with vertebrate decomposition, or the 'necrobiome'. These necrobiome studies differ in the vertebrate species, microhabitats (e.g. skin vs. soil), and geographic locations studied, but many are narrowly focused on the forensic application of microbial data, missing the larger opportunity to understand the ecology of these communities. To further our understanding of microbial dynamics during vertebrate decomposition and identify knowledge gaps, there is a need to assess the current works from an ecological systems perspective. In this review, we examine recent work pertaining to microbial community dynamics and succession during vertebrate (human and other mammals) decomposition in terrestrial ecosystems, through the lens of a microbial succession ecological framework. From this perspective, we describe three major microbial microhabitats (internal, external, and soil) in terms of their unique successional trajectories and identify three major knowledge gaps that remain to be addressed.}, }
@article {pmid36629441, year = {2023}, author = {Šigutová, H and Šigut, M and Pyszko, P and Kostovčík, M and Kolařík, M and Drozd, P}, title = {Seasonal Shifts in Bacterial and Fungal Microbiomes of Leaves and Associated Leaf-Mining Larvae Reveal Persistence of Core Taxa Regardless of Diet.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0316022}, pmid = {36629441}, issn = {2165-0497}, mesh = {Animals ; *Mycobiome ; Larva ; Seasons ; Bacteria/genetics ; Diet ; }, abstract = {Microorganisms are key mediators of interactions between insect herbivores and their host plants. Despite a substantial interest in studying various aspects of these interactions, temporal variations in microbiomes of woody plants and their consumers remain understudied. In this study, we investigated shifts in the microbiomes of leaf-mining larvae (Insecta: Lepidoptera) and their host trees over one growing season in a deciduous temperate forest. We used 16S and ITS2 rRNA gene metabarcoding to profile the bacterial and fungal microbiomes of leaves and larvae. We found pronounced shifts in the leaf and larval microbiota composition and richness as the season progressed, and bacteria and fungi showed consistent patterns. The quantitative similarity between leaf and larval microbiota was very low for bacteria (~9%) and decreased throughout the season, whereas fungal similarity increased and was relatively high (~27%). In both leaves and larvae, seasonality, along with host taxonomy, was the most important factor shaping microbial communities. We identified frequently occurring microbial taxa with significant seasonal trends, including those more prevalent in larvae (Streptococcus, Candida sake, Debaryomyces prosopidis, and Neoascochyta europaea), more prevalent in leaves (Erwinia, Seimatosporium quercinum, Curvibasidium cygneicollum, Curtobacterium, Ceramothyrium carniolicum, and Mycosphaerelloides madeirae), and frequent in both leaves and larvae (bacterial strain P3OB-42, Methylobacterium/Methylorubrum, Bacillus, Acinetobacter, Cutibacterium, and Botrytis cinerea). Our results highlight the importance of considering seasonality when studying the interactions between plants, herbivorous insects, and their respective microbiomes, and illustrate a range of microbial taxa persistent in larvae, regardless of their occurrence in the diet. IMPORTANCE Leaf miners are endophagous insect herbivores that feed on plant tissues and develop and live enclosed between the epidermis layers of a single leaf for their entire life cycle. Such close association is a precondition for the evolution of more intimate host-microbe relationships than those found in free-feeding herbivores. Simultaneous comparison of bacterial and fungal microbiomes of leaves and their tightly linked consumers over time represents an interesting study system that could fundamentally contribute to the ongoing debate on the microbial residence of insect gut. Furthermore, leaf miners are ideal model organisms for interpreting the ecological and evolutionary roles of microbiota in host plant specialization. In this study, the larvae harbored specific microbial communities consisting of core microbiome members. Observed patterns suggest that microbes, especially bacteria, may play more important roles in the caterpillar holobiont than generally presumed.}, }
@article {pmid36629429, year = {2023}, author = {Dragone, NB and Whittaker, K and Lord, OM and Burke, EA and Dufel, H and Hite, E and Miller, F and Page, G and Slayback, D and Fierer, N}, title = {The Early Microbial Colonizers of a Short-Lived Volcanic Island in the Kingdom of Tonga.}, journal = {mBio}, volume = {14}, number = {1}, pages = {e0331322}, pmid = {36629429}, issn = {2150-7511}, mesh = {Tonga ; *Cyanobacteria/metabolism ; Volcanic Eruptions/analysis ; Sulfur/metabolism ; }, abstract = {The island of Hunga Tonga Hunga Ha'apai (HTHH) in the Kingdom of Tonga was formed by Surtseyan eruptions and persisted for 7 years before being obliterated by a massive volcanic eruption on 15 January 2022. Before it was destroyed, HTHH was an unparalleled natural laboratory to study primary succession on a newly formed landmass. We characterized the microbial communities found on the surface sediments of HTHH using a combination of quantitative PCR, marker gene sequencing, and shotgun metagenomic analyses. Contrary to expectations, photosynthetic cyanobacteria were not detected in these sediments, even though they are typically dominant in the earliest stages of primary succession in other terrestrial environments. Instead, our results suggest that the early sediment communities were composed of a diverse array of bacterial taxa, including trace gas oxidizers, anoxygenic photosynthesizers, and chemolithotrophs capable of metabolizing inorganic sulfur, with these bacteria likely sourced from nearby active geothermal environments. While the destruction of HTHH makes it impossible to revisit the site to conduct in situ metabolic measurements or observe how the microbial communities might have continued to change over time, our results do suggest that the early microbial colonizers have unique origins and metabolic capabilities. IMPORTANCE The volcanic island of Hunga Tonga Hunga Ha'apai in the Kingdom of Tonga represents a very rare example of new island formation and thus a unique opportunity to study how organisms colonize a new landmass. We found that the island was colonized by diverse microbial communities shortly after its formation in 2015, with these microbes likely originating from nearby geothermal environments. Primary succession in this system was distinct from that typically observed in other terrestrial environments, with the early microbial colonizers relying on unique metabolic strategies to survive on the surface of this newly formed island, including the capacity to generate energy via sulfur and trace gas metabolism.}, }
@article {pmid36623784, year = {2023}, author = {Anedda, E and Farrell, ML and Morris, D and Burgess, CM}, title = {Evaluating the impact of heavy metals on antimicrobial resistance in the primary food production environment: A scoping review.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {320}, number = {}, pages = {121035}, doi = {10.1016/j.envpol.2023.121035}, pmid = {36623784}, issn = {1873-6424}, mesh = {*Anti-Bacterial Agents/toxicity/analysis ; Manure/analysis ; Drug Resistance, Bacterial/genetics ; *Metals, Heavy/toxicity/analysis ; Copper/analysis ; Genes, Bacterial ; Soil ; }, abstract = {Heavy metals are naturally occurring environmental compounds, which can influence antimicrobial resistance (AMR) dissemination. However, there is limited information on how heavy metals may act as a selective pressure on AMR in the primary food production environment. This review aims to examine the literature on this topic in order to identify knowledge gaps. A total of 73 studies, which met pre-established criteria, were included. These investigations were undertaken between 2008 and 2021, with a significant increase in the last three years. The majority of studies included were undertaken in China. Soil, water and manure were the most common samples analysed, and the sampling locations varied from areas with a natural presence of heavy metals, areas intentionally amended with heavy metals or manure, to areas close to industrial activity or mines. Fifty-four per cent of the investigations focused on the analysis of four or more heavy metals, and copper and zinc were the metals most frequently analysed (n = 59, n = 49, respectively). The findings of this review highlight a link between heavy metals and AMR in the primary food production environment. Heavy metals impacted the abundance and dissemination of mobile genetic elements (MGEs) and antimicrobial resistance genes (ARGs), with MGEs also observed as playing a key role in the spread of ARGs and metal resistance genes (MRGs). Harmonization of methodologies used in future studies would increase the opportunity for comparison between studies. Further research is also required to broaden the availability of data at a global level.}, }
@article {pmid36621691, year = {2023}, author = {Cui, H and Xu, R and Yu, Z and Meng, F}, title = {Phylogenetic group-based assembly and co-occurrence pattern of the microbial community in full-scale wastewater treatment plants during the Chinese spring festival.}, journal = {Chemosphere}, volume = {316}, number = {}, pages = {137775}, doi = {10.1016/j.chemosphere.2023.137775}, pmid = {36621691}, issn = {1879-1298}, mesh = {Sewage ; Phylogeny ; Holidays ; Bioreactors ; *Microbiota ; *Gammaproteobacteria ; *Water Purification ; }, abstract = {The quality and quantity of domestic sewage discharge vary significantly during the Chinese Spring Festival due to the huge population shift. The dynamics of microbial community traits during the Spring Festival, particularly the phylogenetic group-based assembly and co-occurrence patterns, are however little understood. Here, influent and activated sludge samples from 2 full-scale wastewater treatment plants were collected bi-daily throughout a 20-day Spring Festival period and subjected to high-throughput Illumina-MiSeq sequencing. The findings revealed that the microbial communities in the activated sludge displayed a comparatively stable pattern, and that the influent communities experienced significant temporal fluctuations in terms of diversity and composition. The characterization by "Infer Community Assembly Mechanisms by Phylogenetic-bin based null model" demonstrated that for Competibacter glycogen-accumulating organisms, the assembly mechanism shifted from deterministic process (HoS = 69.5%) before the Spring Festival to stochastic process (DR = 65.9%) after the Spring Festival. The network analysis revealed that the network structure of sludge communities was more stable before the Spring Festival than that after the Spring Festival. Additionally, sludge communities had no keystone species in common with the influent before the Spring Festival, while the sludge and influent communities shared two keystone taxa after the Spring Festival (Sebaldella and Candidatus Competibacter). This study would deepen our understanding of the microbial ecology in biological wastewater treatment systems, which also aids in managing wastewater treatment plants.}, }
@article {pmid36615993, year = {2022}, author = {Mosquera-Romero, S and Anaya-Garzon, J and Garcia-Timermans, C and Van Dorpe, J and Hoorens, A and Commenges-Bernole, N and Verbeken, K and Rabaey, K and Varia, J}, title = {Combined Gold Recovery and Nanoparticle Synthesis in Microbial Systems Using Fractional Factorial Design.}, journal = {Nanomaterials (Basel, Switzerland)}, volume = {13}, number = {1}, pages = {}, pmid = {36615993}, issn = {2079-4991}, abstract = {Green synthesis of gold nanoparticles (AuNPs) using microorganisms has been generally studied aiming for high-yield production and morphologies appropriated for various applications, such as bioremediation, (bio)sensors, and (bio)catalysis. Numerous approaches showed the individual effect of factors influencing the synthesis of AuNPs with limited analysis of the governing factors enhancing the production and desired quality of the precipitates. This study proposes a fractional-factorial design to investigate the simultaneous influence of seven environmental factors (cell concentration, temperature, anoxic/oxic conditions, pH, gold concentration, electron donor type, and bacterial species) on the recovery yield and synthesis of targeted AuNPs. Various sizes and morphologies of the AuNPs were obtained by varying the environmental factors studied. The factors with significant effects (i.e., 0.2 mM Au and pH 5) were selected according to statistical analysis for optimal removal of 88.2 ± 3.5% of gold and with the production of valuable 50 nm AuNPs, which are known for their enhanced sensitivity. Implications of the cytochrome-C on the bacterial mechanisms and the provision of electron donors via an electrochemical system are further discussed. This study helps develop gold recovery and nanoparticle synthesis methods, focusing on the determining factor(s) for efficient, low-cost, green synthesis of valuable materials.}, }
@article {pmid36611775, year = {2022}, author = {Imperatore, R and Fronte, B and Scicchitano, D and Orso, G and Marchese, M and Mero, S and Licitra, R and Coccia, E and Candela, M and Paolucci, M}, title = {Dietary Supplementation with a Blend of Hydrolyzable and Condensed Tannins Ameliorates Diet-Induced Intestinal Inflammation in Zebrafish (Danio rerio).}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {1}, pages = {}, pmid = {36611775}, issn = {2076-2615}, abstract = {The current study evaluated the effects of hydrolyzable and condensed tannins from chestnut and quebracho wood, respectively (TSP, Silvafeed[®]), on zebrafish with intestinal inflammation induced by a plant-based diet (basal diet). Four experimental diets were prepared as follows: the basal diet + 0 TSP, the basal diet + TSP at 0.9 g/kg of feed, the basal diet + TSP at 1.7 g/kg of feed, and the basal diet + TSP at 3.4 g/kg of feed. Eighty-four zebrafish (Danio rerio) were fed for 12 days with the experimental diets. In zebrafish fed the basal diet, intestine integrity appeared to be altered, with damaged intestinal villi, high immunoexpression of tumor necrosis factor-α (TNFα) and cyclooxygenase 2 (COX2), and high expression of the cox2, interleukin 1 (il-1b), interleukin 8 (cxcl8-l1), and tnfα genes. The tannin treatment partially restored intestinal morphology and downregulated the expression of cytokines. The best activity was detected with 1.7 and 3.4 g/kg of feed. In the guts of all groups, Proteobacteria, Fusobacteria, Firmicutes, and Bacteroidetes were the most represented phyla. The most represented genera were Plesiomonas and Sphingomonas, belonging to the Proteobacteria phylum; Cetobacterium, belonging to the Fusobacteria phylum; and Lactobacillus, belonging to the Firmicutes phylum. No significant differences were detected among groups, except for a slight decrease in the Fusobacteria phylum and slight increases in the Shewanella and Bacteroides genera with TSP. In conclusion, these results suggest that tannins can improve the zebrafish intestinal inflammation caused by a terrestrial-plant-based diet in a dose-dependent manner.}, }
@article {pmid36610634, year = {2023}, author = {Li, C and Liu, C and Liu, J and Feng, C}, title = {Insight into the temporal dynamics of microbial succession and ecology mechanisms in biological activated carbon tanks.}, journal = {The Science of the total environment}, volume = {866}, number = {}, pages = {161366}, doi = {10.1016/j.scitotenv.2022.161366}, pmid = {36610634}, issn = {1879-1026}, mesh = {*Charcoal/chemistry ; *Microbiota ; Microbial Consortia ; Biodiversity ; China ; }, abstract = {Biological activated carbon (BAC) has long been applied in China to guarantee water quality and to achieve drinking water regulations. However, a knowledge gap remains regarding the temporal dynamics of microbial communities, particularly microbe-based assembly and co-occurrence patterns. Accordingly, this study investigated the evolution of BAC microbial communities using a pilot-scale system and examined by multivariate ecological combined with high-throughput Illumina sequencing and statistical methods. The results showed that BAC microbial diversity reached its peak in 2 years and declined thereafter. Microbial communities composition was accompanied by significant temporal evolution in the BAC biofilm. Deterministic processes gained in importance along with time, especially homogeneous selection which contributed 59.09 %-75.63 % to the community assembly in 8-yr, 9-yr, and 10-yr BAC. According to co-occurrence network analysis, microbial networks have more unstable structures over time, as evidenced by higher modularity, heightened connectivity, and fewer keystones. Moreover, the interaction between microbial taxa tended to have a higher proportion of competitive relationships during the operation of the BAC tank, ranging from 13.51 % to 76.35 %. Based on these dynamic ecological processes, microbial community succession in BAC biofilm might undergo four phases: community establishment (Years 0-2); community stability (Years 2-5); community quasi-degradation (Years 5-8); community degradation (Years 8-10). The performance of BAC was greatly influenced by community development, and contaminant removal gradually decreased as community succession proceeded. These results add to our knowledge of microbial ecology and provide the basis for further research into microbial communities' regulation strategies in BAC tanks.}, }
@article {pmid36602317, year = {2023}, author = {An, XL and Xu, JX and Xu, MR and Zhao, CX and Li, H and Zhu, YG and Su, JQ}, title = {Dynamics of Microbial Community and Potential Microbial Pollutants in Shopping Malls.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0057622}, pmid = {36602317}, issn = {2379-5077}, mesh = {Humans ; *Environmental Pollutants ; *Microbiota/genetics ; Soil ; Public Health ; Built Environment ; }, abstract = {Shopping malls offer various niches for microbial populations, potentially serving as sources and reservoirs for the spread of microorganisms of public health concern. However, knowledge about the microbiome and the distribution of human pathogens in malls is largely unknown. Here, we examine the microbial community dynamics and genotypes of potential pathogens from floor and escalator surfaces in shopping malls and adjacent road dusts and greenbelt soils. The distribution pattern of microbial communities is driven primarily by habitats and seasons. A significant enrichment of human-associated microbiota in the indoor environment indicates that human interactions with surfaces might be another strong driver for mall microbiomes. Neutral community models suggest that the microbial community assembly is strongly driven by stochastic processes. Distinct performances of microbial taxonomic signatures for environmental classifications indicate the consistent differences of microbial communities of different seasons/habitats and the strong anthropogenic effect on homogenizing microbial communities of shopping malls. Indoor environments harbored higher concentrations of human pathogens than outdoor samples, also carrying a high proportion of antimicrobial resistance-associated multidrug efflux genes and virulence genes. These findings enhanced the understanding of the microbiome in the built environment and the interactions between humans and the built environment, providing a basis for tracking biothreats and communicable diseases and developing sophisticated early warning systems. IMPORTANCE Shopping malls are distinct microbial environments which can facilitate a constant transmission of microorganisms of public health concern between humans and the built environment or between human and human. Despite extensive investigation of the natural environmental microbiome, no comprehensive profile of microbial ecology has been reported in malls. Characterizing microbial distribution, potential pathogens, and antimicrobial resistance will enhance our understanding of how these microbial communities are formed, maintained, and transferred and help establish a baseline for biosurveillance of potential public health threats in malls.}, }
@article {pmid36596939, year = {2023}, author = {Lemberger, U and Pjevac, P and Hausmann, B and Berry, D and Moser, D and Jahrreis, V and Özsoy, M and Shariat, SF and Veser, J}, title = {The microbiome of kidney stones and urine of patients with nephrolithiasis.}, journal = {Urolithiasis}, volume = {51}, number = {1}, pages = {27}, pmid = {36596939}, issn = {2194-7236}, mesh = {Humans ; *Metabolic Syndrome ; RNA, Ribosomal, 16S/genetics ; *Kidney Calculi/diagnosis ; *Nephrolithiasis/urine ; *Microbiota ; Bacteria ; }, abstract = {The incidence of nephrolithiasis is rising worldwide. Although it is a multifactorial disease, lifestyle plays a major role in its etiology. Another considerable factor could be an aberrant microbiome. In our observational single-center study, we aimed to investigate the composition of bacteria in kidney stones and urine focusing on patients with features of metabolic syndrome. Catheterized urine and kidney stones were collected prospectively from 100 consecutive patients undergoing endoscopic nephrolithotomy between 2020 and 2021 at our clinic. Microbiome composition was analyzed via 16S rRNA gene amplicon sequencing. Detection of bacteria was successful in 24% of the analyzed kidney stones. These patients had a prolonged length of stay compared to patients without verifiable bacteria in their stones (2.9 vs 1.5 days). Patients with features of metabolic syndrome were characterized by kidney stones colonized with classical gastrointestinal bacteria and displayed a significant enrichment of Enterococcaceae and Enterobacteriaceae. Stones of patients without features of metabolic syndrome characterized by Ureaplasma and Staphylococcaceae. Patients with bacteria in their kidney stones exhibit a longer length of stay, possibly due to more complex care. Patients presenting with features of metabolic syndrome displayed a distinct stone microbiome compared to metabolically fit patients. Understanding the role of bacteria in stone formation could enable targeted therapy, prevention of post-operative complications and new therapeutic strategies.}, }
@article {pmid36592956, year = {2023}, author = {Martiniuk, JT and Hamilton, J and Dodsworth, T and Measday, V}, title = {Grape-associated fungal community patterns persist from berry to wine on a fine geographical scale.}, journal = {FEMS yeast research}, volume = {23}, number = {}, pages = {}, pmid = {36592956}, issn = {1567-1364}, mesh = {*Vitis/microbiology ; *Wine/microbiology ; *Mycobiome ; Fruit ; Geography ; Fermentation ; }, abstract = {Wine grape fungal community composition is influenced by abiotic factors including geography and vintage. Compositional differences may correlate with different wine metabolite composition and sensory profiles, suggesting a microbial role in the shaping of a wine's terroir, or regional character. While grape and wine-associated fungal community composition has been studied extensively at a regional and sub-regional scale, it has not been explored in detail on fine geographical scales over multiple harvests. Over two years, we examined the fungal communities on Vitis Vinifera cv. Pinot noir grape berry surfaces, in crushed grapes, and in lab spontaneous fermentations from three vineyards within a < 1 km radius in Canada's Okanagan Valley wine region. We also evaluated the effect of winery environment exposure on fungal community composition by sampling grapes crushed and fermented in the winery at commercial scale. Spatiotemporal community structure was evident among grape berry surface, crushed grape and fermentation samples, with each vineyard exhibiting a distinct fungal community signature. Crushed grape fungal populations were richer in fermentative yeast species compared to grape berry surface fungal populations. Our study suggests that, as on a regional level, fungal populations may contribute to fine-scale -terroir,' with significant implications for single-vineyard wines.}, }
@article {pmid36592918, year = {2023}, author = {Burke, LP and Chique, C and Fitzhenry, K and Chueiri, A and O'Connor, L and Hooban, B and Cahill, N and Brosnan, E and Olaore, L and Sullivan, E and Reilly, L and Morris, D and Hynds, P and O'Dwyer, J}, title = {Characterization of Shiga toxin-producing Escherichia coli presence, serogroups and risk factors from private groundwater sources in western Ireland.}, journal = {The Science of the total environment}, volume = {866}, number = {}, pages = {161302}, doi = {10.1016/j.scitotenv.2022.161302}, pmid = {36592918}, issn = {1879-1026}, mesh = {Animals ; Sheep ; *Shiga-Toxigenic Escherichia coli ; Serogroup ; Ireland/epidemiology ; *Escherichia coli Proteins/genetics ; Risk Factors ; Feces ; }, abstract = {Over recent years, Ireland has reported the highest crude incidence rates of Shiga toxin-producing Escherichia coli (STEC) enteritis in Europe. Unregulated private groundwater sources have emerged as an important potential transmission route for STEC, with up to 750,000 Irish residents reliant on these sources for domestic waters. This study aimed to investigate the prevalence and serogroup profile of STEC contamination from domestic private wells in western Ireland. Fifty-two groundwater sources were analysed during two sampling campaigns in the autumn (September/October) of 2019 (n = 21) and 2021 (n = 31). Untreated groundwater samples (30 L) were collected and analysed using the "CapE" (capture, amplify, extract) method. Extracted DNA was tested using multiplex real-time PCR for Shiga toxin stx1 and/or stx2 and eae genes. STEC positive DNA samples were tested for clinically relevant serogroups by real-time PCR. Data relating to 27 potential groundwater contamination risk factors were geospatially linked to each well and assessed for association with E. coli, stx1 and/or stx2 and eae presence/absence. Overall, 20/52 wells (38.4 %) were positive for E. coli (median concentration 8.5 MPN/100 mL as assessed by Colilert-18 method). Stx1 and/or stx2 was detected in 10/52 (19.2 %) wells overall and 8/20 E. coli positive wells, equating to a STEC to "generic" E. coli detection ratio of 40 %. Six of these wells (30 %) were also positive for eae. One or more serogroup-specific gene targets were identified in all but one stx1 and/or stx2 positive sample, with O145 (n = 6), O157 (n = 5) and O103 (n = 4) most prevalent. STEC presence was significantly associated with decreasing well depth (U = -2.243; p = 0.024) and increasing 30-day mean antecedent rainfall (U = 2.126; p = 0.034). Serogroup O104 was associated with increased sheep density (U = 2.089; p = 0.044) and detection of stx1 and/or stx2 + eae with increased septic tank density (U = 2.246 p = 0.023). Findings indicate high detection rates of clinically relevant STEC in E. coli contaminated groundwater sources in Ireland.}, }
@article {pmid36590596, year = {2022}, author = {Hu, X and Fan, R and Song, W and Qing, J and Yan, X and Li, Y and Duan, Q and Li, Y}, title = {Landscape of intestinal microbiota in patients with IgA nephropathy, IgA vasculitis and Kawasaki disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1061629}, pmid = {36590596}, issn = {2235-2988}, mesh = {Humans ; *Glomerulonephritis, IGA ; *Mucocutaneous Lymph Node Syndrome/complications/diagnosis ; *Gastrointestinal Microbiome ; *IgA Vasculitis ; *Vasculitis/diagnosis/genetics ; Immunoglobulin A ; }, abstract = {OBJECTIVE: To explore the common differential flora of IgAN, Kawasaki disease and IgA vasculitis by screening and analyzing the differential intestinal flora between the three disease groups of IgAN, Kawasaki disease and IgA vasculitis and their healthy controls.<br><br>METHODS: Papers on 16srRNA sequencing-related intestinal flora of IgAN, Kawasaki disease and IgA vasculitis were searched in databases, the literature was systematically collated and analysed, the original data was download from the relevant databases, and then the operational taxonomic unit and species classification analysis were performed. Besides, Alpha diversity analysis and Beta diversity analysis were performed to screen for IgAN, Kawasaki disease and I1gA vasculitis groups and finally compare the common intestinal differential flora among the three groups.<br><br>RESULTS: Among the common differential flora screened, Lachnospiracea_incertae_sedis was lower in both the IgAN and Kawasaki disease groups than in the respective healthy controls; Coprococcus was low in the IgAN group but high in the IgA vasculitis group. Fusicatenibacter was lower in both the Kawasaki disease and IgA vasculitis groups than in their respective healthy controls, and Intestinibacter was low in the Kawasaki disease group, but its expression was high in the IgA vasculitis group.<br><br>CONCLUSION: The dysbiosis of the intestinal flora in the three groups of patients with IgAN, Kawasaki disease and IgA vasculitis, its effect on the immunity of the organism and its role in the development of each disease group remain unclear, and the presence of their common differential flora may further provide new ideas for the association of the pathogenesis of the three diseases.}, }
@article {pmid36590430, year = {2022}, author = {Krohn, C and Khudur, L and Dias, DA and van den Akker, B and Rees, CA and Crosbie, ND and Surapaneni, A and O'Carroll, DM and Stuetz, RM and Batstone, DJ and Ball, AS}, title = {The role of microbial ecology in improving the performance of anaerobic digestion of sewage sludge.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1079136}, pmid = {36590430}, issn = {1664-302X}, abstract = {The use of next-generation diagnostic tools to optimise the anaerobic digestion of municipal sewage sludge has the potential to increase renewable natural gas recovery, improve the reuse of biosolid fertilisers and help operators expand circular economies globally. This review aims to provide perspectives on the role of microbial ecology in improving digester performance in wastewater treatment plants, highlighting that a systems biology approach is fundamental for monitoring mesophilic anaerobic sewage sludge in continuously stirred reactor tanks. We further highlight the potential applications arising from investigations into sludge ecology. The principal limitation for improvements in methane recoveries or in process stability of anaerobic digestion, especially after pre-treatment or during co-digestion, are ecological knowledge gaps related to the front-end metabolism (hydrolysis and fermentation). Operational problems such as stable biological foaming are a key problem, for which ecological markers are a suitable approach. However, no biomarkers exist yet to assist in monitoring and management of clade-specific foaming potentials along with other risks, such as pollutants and pathogens. Fundamental ecological principles apply to anaerobic digestion, which presents opportunities to predict and manipulate reactor functions. The path ahead for mapping ecological markers on process endpoints and risk factors of anaerobic digestion will involve numerical ecology, an expanding field that employs metrics derived from alpha, beta, phylogenetic, taxonomic, and functional diversity, as well as from phenotypes or life strategies derived from genetic potentials. In contrast to addressing operational issues (as noted above), which are effectively addressed by whole population or individual biomarkers, broad improvement and optimisation of function will require enhancement of hydrolysis and acidogenic processes. This will require a discovery-based approach, which will involve integrative research involving the proteome and metabolome. This will utilise, but overcome current limitations of DNA-centric approaches, and likely have broad application outside the specific field of anaerobic digestion.}, }
@article {pmid36587901, year = {2023}, author = {Lietaer, L and Pascottini, OB and Lacoere, T and Kerckhof, FM and Martens, A and Van de Wiele, T and Opsomer, G}, title = {Studying the pre-implantation uterine microbiota in cattle using transabdominal laparoscopic low-volume lavage: Aiming for zero-contamination.}, journal = {Journal of microbiological methods}, volume = {205}, number = {}, pages = {106664}, doi = {10.1016/j.mimet.2022.106664}, pmid = {36587901}, issn = {1872-8359}, mesh = {Pregnancy ; Cattle ; Animals ; Female ; *Therapeutic Irrigation ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; *Microbiota/genetics ; DNA/genetics ; Bacteria/genetics ; DNA, Bacterial/genetics ; }, abstract = {Recent studies have suggested that bacteria associated with the female reproductive tract - the uterine microbiota - may be important for reproductive health and pregnancy success. Therefore, uterine microbiome research gained much interest in the last few years. However, it is challenging to study late postpartum uterine samples, since they hold a low microbial biomass. Next-generation sequencing techniques are very sensitive for microbial identification, but they cannot make a distinction between actual microbiota and contaminant bacteria or their DNA. Our aim was to test a new method to sample the bovine uterine lumen in vivo, while minimizing the risk of cross-contamination. In order to evaluate this method, we performed a descriptive assessment of the microbial composition of the obtained samples. Transabdominal, laparoscopic sampling of the uterine lumen was conducted in five Holstein-Friesian cows. Uterine fluid from the uterine horns was collected by low-volume lavage. DNA from the samples was extracted using two different DNA extraction methods, and negative controls (sampling blank controls and DNA extraction blank controls) were included. Bacteria were identified using 16S rRNA gene amplicon sequencing. In this proof-of-concept study, no evidence for authentically present uterine microbiota could be found. During laparoscopic sampling, some practical challenges were encountered, and the reliability of low-volume-lavage for the collection of a low microbial biomass could be questioned. By comparing two DNA extraction methods, a significant contamination background could be noticed originating from the DNA extraction kits.}, }
@article {pmid36586465, year = {2023}, author = {McDonagh, F and Singh, NK and Venkateswaran, K and Lonappan, AM and Hallahan, B and Tuohy, A and Burke, L and Kovarova, A and Miliotis, G}, title = {First complete genome of a multidrug-resistant strain of the novel human pathogen Kalamiella piersonii (GABEKP28) identified in human saliva.}, journal = {Journal of global antimicrobial resistance}, volume = {32}, number = {}, pages = {31-34}, doi = {10.1016/j.jgar.2022.12.003}, pmid = {36586465}, issn = {2213-7173}, mesh = {Humans ; *Saliva ; *Genome, Bacterial ; Whole Genome Sequencing ; Plasmids/genetics ; Virulence ; Virulence Factors/genetics ; }, abstract = {OBJECTIVES: Kalamiella piersonii is a newly identified bacterial species, first isolated from surfaces of the International Space Station (ISS). It also appears as a novel human pathogen reported to be implicated in bacteremia and kidney stone disease. Here, we report the first complete genome of a multidrug-resistant strain of K. piersonii (GABEKP28), isolated from the saliva of a patient with treatment-resistant schizophrenia (TRS), to determine the mobile genetic elements (MGEs), antibiotic resistance genes (ARGs), and virulence factors (VFs) harboured by such a strain of this novel species.<br><br>METHODS: Whole-genome sequencing was performed using DNABSEQ (PE150) and Nanopore MinION platforms. Hybrid assembly was conducted using Unicycler v0.5.0. Genome assembly quality was verified using QUAST v5.0.2. The assembly was annotated using PROKKA v1.14.5. ARGs and VFs were identified using Abricate v1.0.0.<br><br>RESULTS: K. piersonii strain GABEKP28 was classified as multidrug-resistant while also carrying plasmidic genetic determinants associated with a hypervirulent phenotype. The complete genome size is 3 881 479 bp and has a guanine-cytosine content of 57.76% while it encodes for 3 525 chromosome coding sequences. The strain was also identified to carry three plasmids of 513 647 bp, 261 771 bp, and 106 029 bp, respectively.<br><br>CONCLUSIONS: K.piersonii GABEKP28 is the first complete genome of this species to be submitted to GenBank and only the second to be sequenced from a human host. The whole-genome sequencing data with multiple plasmids, ARGs, and VFs will aid in understanding the pathogenicity, evolution, and phylogeny of this novel opportunistic pathogen.}, }
@article {pmid36585490, year = {2023}, author = {Zhao, J and Wang, Z and Li, C and Shi, T and Liang, Y and Jiao, N and Zhang, Y}, title = {Significant Differences in Planktonic Virus Communities Between "Cellular Fraction" (0.22 ~ 3.0 µm) and "Viral Fraction" (&lt; 0.22 μm) in the Ocean.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {825-842}, pmid = {36585490}, issn = {1432-184X}, support = {41876174//National Natural Science Foundation of China/ ; }, mesh = {Plankton/genetics ; *Viruses/genetics ; *Bacteriophages ; Seawater ; Genome, Viral ; Oceans and Seas ; Metagenome ; Metagenomics ; }, abstract = {Compared to free-living viruses (< 0.22 m) in the ocean, planktonic viruses in the "cellular fraction" (0.22 ~ 3.0 μm) are now far less well understood, and the differences between them remain largely unexplored. Here, we revealed that even in the same seawater samples, the "cellular fraction" comprised significantly distinct virus communities from the free virioplankton, with only 13.87% overlap in viral contigs at the species level. Compared to the viral genomes deposited in NCBI RefSeq database, 99% of the assembled viral genomes in the "cellular fraction" represented novel genera. Notably, the assembled (near-) complete viral genomes within the "cellular fraction" were significantly larger than that in the "viral fraction," and the "cellular fraction" contained three times more species of giant viruses or jumbo phages with genomes > 200 kb than the "viral fraction." The longest complete genomes of jumbo phage (~ 252 kb) and giant virus (~ 716 kb) were both detected only in the "cellular fraction." Moreover, a relatively higher proportion of proviruses were predicted within the "cellular fraction" than "viral fraction." Besides the substantial divergence in viral community structure, the different fractions also contained their unique viral auxiliary metabolic genes; e.g., those potentially participating in inorganic carbon fixation in deep sea were detected only in the "cellular-fraction" viromes. In addition, there was a considerable divergence in the community structure of both "cellular fraction" and "viral fraction" viromes between the surface and deep-sea habitats, suggesting that they might have similar environmental adaptation properties. The findings deepen our understanding of the complexity of viral community structure and function in the ocean.}, }
@article {pmid36585489, year = {2023}, author = {Zhang, Y and Liu, F and Liang, H and Gao, D}, title = {Mediative Mechanism of Freezing/Thawing on Greenhouse Gas Emissions in an Inland Saline-Alkaline Wetland: a Metagenomic Analysis.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {985-996}, pmid = {36585489}, issn = {1432-184X}, support = {31470543//National Natural Science Foundation of China/ ; }, mesh = {*Greenhouse Gases ; Wetlands ; Freezing ; Carbon Dioxide ; Nitrous Oxide ; Carbon ; Methane/analysis ; Soil ; }, abstract = {Inland saline-alkaline wetlands distributed in the mid-high latitude have repeatedly experienced freezing and thawing. However, the response of greenhouse gas (GHG) emission and microbially-mediated carbon and nitrogen cycle to freezing and thawing remains unclear. We monitored the GHG flux in an inland saline-alkaline wetland and found that, compared with the growth period, the average CO2 flux decreased from 171.99 to 76.61-80.71 mg/(m[2]‧h), the average CH4 flux decreased from 10.72 to 1.96-3.94 mg/(m[2]‧h), and the average N2O flux decreased from 56.17 to - 27.14 to - 20.70 μg/(m[2]‧h). Freezing and thawing significantly decreased the relative abundance of functional genes involved in carbon and nitrogen cycles. The aceticlastic methanogenic pathway was the main methanogenic pathway, whereas the Candidatus Methylomirabilis oxyfera was the most abundant methane oxidizer in the wetland. Ammonia-oxidizing archaea and denitrifier belonging to proteobacteria was the major microbial N2O source, while bacteria within clade II nosZ was the major microbial N2O sink. Freezing and thawing reduced the relative abundance of these genes, leading to a decrease in GHG flux.}, }
@article {pmid36584949, year = {2023}, author = {Fraser, MW and Martin, BC and Wong, HL and Burns, BP and Kendrick, GA}, title = {Sulfide intrusion in a habitat forming seagrass can be predicted from relative abundance of sulfur cycling genes in sediments.}, journal = {The Science of the total environment}, volume = {864}, number = {}, pages = {161144}, doi = {10.1016/j.scitotenv.2022.161144}, pmid = {36584949}, issn = {1879-1026}, mesh = {*Geologic Sediments ; Ecosystem ; Sulfides ; Sulfur ; Australia ; *Microbiota ; }, abstract = {Sulfide intrusion from sediments is an increasingly recognized contributor to seagrass declines globally, yet the relationship between sediment microorganisms and sulfide intrusion has received little attention. Here, we use metagenomic sequencing and stable isotope ([34]S) analysis to examine this relationship in Cockburn Sound, Australia, a seagrass-dominated embayment with a gradient of sulfide stress and seagrass declines. There was a significant positive relationship between sulfide intrusion into seagrasses and sulfate reduction genes in sediment microbial communities, which was greatest at sites with long term seagrass declines. This is the first demonstration of a significant link between sulfur cycling genes present in seagrass sediments and sulfide intrusion in a habitat-forming seagrass that is experiencing long-term shoot density decline. Given that microorganisms respond rapidly to environmental change, the quantitative links established in this study can be used as a potential management tool to enable the prediction of sulfide stress on large habitat forming seagrasses; a global issue expected to worsen with climate change.}, }
@article {pmid36584719, year = {2023}, author = {Andrzejak, T and Raje, H and LaFleur, G and Willis, J and Boopathy, R}, title = {Water quality and antibiotic resistance in the recreational waters.}, journal = {Bioresource technology}, volume = {370}, number = {}, pages = {128546}, doi = {10.1016/j.biortech.2022.128546}, pmid = {36584719}, issn = {1873-2976}, mesh = {*Water Quality ; *Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The overuse and improper disposal of antibiotics results in antibiotic resistance. This raises concern over the presence of antibiotic resistant bacteria (ARB) in waterways and pose health risks of antibiotic resistant infections to water recreationists. The purpose of this study was to monitor water quality, microbial ecology, and antibiotic resistance in water and biofilm on submerged plastics at two public boat launches in southeastern Louisiana. Water and biofilm samples were collected once a month, in triplicate, from two public boat launches in Louisiana, USA for a year. Water quality metrics included nitrate, ammonia, sulfate, phosphate, and organic carbon. Water samples were tested for total and fecal coliform abundance and the presence of ARB. Out of 131 bacterial isolates studied from these two sites, 86% of them tested positive for antibiotic resistance with multi-drug resistance. Antibiotic resistance genes (ARGs) for sulfonamide (sul2), bacitracin (bacA) and ampicillin (ampA) were identified in bacterial isolates from water and biofilm samples at both sites. Molecular genetic diversity analysis identified distinct taxonomic diversity differences in biofilm bacteria compared to the planktonic bacteria in the surrounding water. Biofilm samples showed increased diversity at the phylum, genus, and species levels.}, }
@article {pmid36583056, year = {2022}, author = {Doster, E and Pinnell, LJ and Noyes, NR and Parker, JK and Anderson, CA and Booker, CW and Hannon, SJ and McAllister, TA and Gow, SP and Belk, KE and Morley, PS}, title = {Evaluating the effects of antimicrobial drug use on the ecology of antimicrobial resistance and microbial community structure in beef feedlot cattle.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {970358}, pmid = {36583056}, issn = {1664-302X}, abstract = {INTRODUCTION: Use of antimicrobial drugs (AMDs) in food producing animals has received increasing scrutiny because of concerns about antimicrobial resistance (AMR) that might affect consumers. Previously, investigations regarding AMR have focused largely on phenotypes of selected pathogens and indicator bacteria, such as Salmonella enterica or Escherichia coli. However, genes conferring AMR are known to be distributed and shared throughout microbial communities. The objectives of this study were to employ target-enriched metagenomic sequencing and 16S rRNA gene amplicon sequencing to investigate the effects of AMD use, in the context of other management and environmental factors, on the resistome and microbiome in beef feedlot cattle.<br><br>METHODS: This study leveraged samples collected during a previous longitudinal study of cattle at beef feedlots in Canada. This included fecal samples collected from randomly selected individual cattle, as well as composite-fecal samples from randomly selected pens of cattle. All AMD use was recorded and characterized across different drug classes using animal defined daily dose (ADD) metrics.<br><br>RESULTS: Overall, fecal resistome composition was dominated by genes conferring resistance to tetracycline and macrolide-lincosamide-streptogramin (MLS) drug classes. The diversity of bacterial phyla was greater early in the feeding period and decreased over time in the feedlot. This decrease in diversity occurred concurrently as the microbiome represented in different individuals and different pens shifted toward a similar composition dominated by Proteobacteria and Firmicutes. Some antimicrobial drug exposures in individuals and groups were associated with explaining a statistically significant proportion of the variance in the resistome, but the amount of variance explained by these important factors was very small (<0.6% variance each), and smaller than associations with other factors measured in this study such as time and feedlot ID. Time in the feedlot was associated with greater changes in the resistome for both individual animals and composite pen-floor samples, although the proportion of the variance associated with this factor was small (2.4% and 1.2%, respectively).<br><br>DISCUSSION: Results of this study are consistent with other investigations showing that, compared to other factors, AMD exposures did not have strong effects on antimicrobial resistance or the fecal microbial ecology of beef cattle.}, }
@article {pmid36583045, year = {2022}, author = {Puig, S and Bañeras, L and Heijne, AT and Paquete, CM}, title = {Editorial: Latest breakthroughs in microbial electrochemistry research.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1100272}, doi = {10.3389/fmicb.2022.1100272}, pmid = {36583045}, issn = {1664-302X}, }
@article {pmid36579161, year = {2022}, author = {Metcalf, CJE and Tepekule, B and Bruijning, M and Koskella, B}, title = {Hosts, microbiomes, and the evolution of critical windows.}, journal = {Evolution letters}, volume = {6}, number = {6}, pages = {412-425}, pmid = {36579161}, issn = {2056-3744}, abstract = {The absence of microbial exposure early in life leaves individuals vulnerable to immune overreaction later in life, manifesting as immunopathology, autoimmunity, or allergies. A key factor is thought to be a "critical window" during which the host's immune system can "learn" tolerance, and beyond which learning is no longer possible. Animal models indicate that many mechanisms have evolved to enable critical windows, and that their time limits are distinct and consistent. Such a variety of mechanisms, and precision in their manifestation suggest the outcome of strong evolutionary selection. To strengthen our understanding of critical windows, we explore their underlying evolutionary ecology using models encompassing demographic and epidemiological transitions, identifying the length of the critical window that would maximize fitness in different environments. We characterize how direct effects of microbes on host mortality, but also indirect effects via microbial ecology, will drive the optimal length of the critical window. We find that indirect effects such as magnitude of transmission, duration of infection, rates of reinfection, vertical transmission, host demography, and seasonality in transmission all have the effect of redistributing the timing and/or likelihood of encounters with microbial taxa across age, and thus increasing or decreasing the optimal length of the critical window. Declining microbial population abundance and diversity are predicted to result in increases in immune dysfunction later in life. We also make predictions for the length of the critical window across different taxa and environments. Overall, our modeling efforts demonstrate how critical windows will be impacted over evolution as a function of both host-microbiome/pathogen interactions and dispersal, raising central questions about potential mismatches between these evolved systems and the current loss of microbial diversity and/or increases in infectious disease.}, }
@article {pmid36578577, year = {2022}, author = {Hsu, PL and Di, HJ and Cameron, K and Podolyan, A and Chau, H and Luo, J and Miller, B and Carrick, S and Johnstone, P and Ferguson, S and Wei, W and Shen, J and Zhang, L and Liu, H and Zhao, T and Wei, W and Ding, W and Pan, H and Liu, Y and Li, B}, title = {Comammox Nitrospira Clade B is the most abundant complete ammonia oxidizer in a dairy pasture soil and inhibited by dicyandiamide and high ammonium concentrations.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1048735}, pmid = {36578577}, issn = {1664-302X}, abstract = {The recent discovery of comammox Nitrospira, a complete ammonia oxidizer, capable of completing the nitrification on their own has presented tremendous challenges to our understanding of the nitrification process. There are two divergent clades of comammox Nitrospira, Clade A and B. However, their population abundance, community structure and role in ammonia and nitrite oxidation are poorly understood. We conducted a 94-day microcosm study using a grazed dairy pasture soil amended with urea fertilizers, synthetic cow urine, and the nitrification inhibitor, dicyandiamide (DCD), to investigate the growth and community structure of comammox Nitrospira spp. We discovered that comammox Nitrospira Clade B was two orders of magnitude more abundant than Clade A in this fertile dairy pasture soil and the most abundant subcluster was a distinctive phylogenetic uncultured subcluster Clade B2. We found that comammox Nitrospira Clade B might not play a major role in nitrite oxidation compared to the role of canonical Nitrospira nitrite-oxidizers, however, comammox Nitrospira Clade B is active in nitrification and the growth of comammox Nitrospira Clade B was inhibited by a high ammonium concentration (700 kg synthetic urine-N ha[-1]) and the nitrification inhibitor DCD. We concluded that comammox Nitrospira Clade B: (1) was the most abundant comammox in the dairy pasture soil; (2) had a low tolerance to ammonium and can be inhibited by DCD; and (3) was not the dominant nitrite-oxidizer in the soil. This is the first study discovering a new subcluster of comammox Nitrospira Clade B2 from an agricultural soil.}, }
@article {pmid36578575, year = {2022}, author = {Coutinho, TA and Jacques, MA and Jones, J}, title = {Editorial: Emergence and re-emergence of plant diseases caused by Xanthomonas species.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1081601}, pmid = {36578575}, issn = {1664-302X}, }
@article {pmid36578568, year = {2022}, author = {Dirren-Pitsch, G and Bühler, D and Salcher, MM and Bassin, B and Le Moigne, A and Schuler, M and Pernthaler, J and Posch, T}, title = {FISHing for ciliates: Catalyzed reporter deposition fluorescence in situ hybridization for the detection of planktonic freshwater ciliates.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1070232}, pmid = {36578568}, issn = {1664-302X}, abstract = {Planktonic ciliate species form multiple trophic guilds and are central components of freshwater food webs. Progress in molecular analytical tools has opened new insight into ciliate assemblages. However, high and variable 18S rDNA copy numbers, typical for ciliates, make reliable quantification by amplicon sequencing extremely difficult. For an exact determination of abundances, the classical morphology-based quantitative protargol staining is still the method of choice. Morphotype analyses, however, are time consuming and need specific taxonomic expertise. Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) may represent a promising tool for the analysis of planktonic ciliates by combining molecular identification with microscopic quantification. We tested the applicability of CARD-FISH using nine cultured ciliate species. Eight species- and three genus-specific oligonucleotide probes were designed based on their 18S rRNA genes. The CARD-FISH protocol was adapted and the specificity of probes was established. We subsequently examined the precision of quantitation by CARD-FISH on single cultures and mock assemblages. Successful tests on lake water samples proved that planktonic ciliates could be identified and quantified in field samples by CARD-FISH. Double hybridizations allowed studying interspecific predator prey interactions between two ciliate species. In summary, we demonstrate that CARD-FISH with species-specific probes can facilitate studies on the population dynamics of closely related, small sized or cryptic species at high sampling frequencies.}, }
@article {pmid36578531, year = {2023}, author = {Lasa, AV and Guevara, M&#xc1; and Villadas, PJ and Fernández-González, AJ and Cervera, MT and Fernández-López, M}, title = {Bacteriome dataset from the rhizosphere of trees in a Pinus pinaster and Pinus halepensis dominated forest subjected to drought conditions.}, journal = {Data in brief}, volume = {46}, number = {}, pages = {108805}, pmid = {36578531}, issn = {2352-3409}, abstract = {The Mediterranean basin is drastically affected by intense and frequent droughts, which jeopardize the diversity and survival of its forest, for example, Pinus pinaster forests. The dynamics of the bacterial communities inhabiting the rhizosphere of Pinus pinaster and other plants from a pine dominated forest under contrasting hydric conditions was monitored. The forest was located in Sierra de Oria (southeast Spain), and it was mainly composed by P. pinaster, P. halepensis, woody shrub species and herbaceous plants. 18 trees visually belonging to P. pinaster located along the perimeter and across the forest were selected for the analysis. All the trees were separated at least 50 m each other. Although all of them belonged to P. pinaster morphologically according to visual identification, the genotyping of the roots confirmed that they corresponded to P. pinaster, P. halepensis, and other plant species different from genus Pinus, although in the last case it was not possible to identify the plant species. At a distance less than 50 cm from the trunk, the litter and topsoil were removed, and the soil closely attached to non-suberified roots (rhizosphere soil) was collected (depth of 5-25 cm). Sampling was carried out in two seasons with contrasting temperature and rainfall patterns: on July 18, 2017 (summer) and April 24, 2018 (spring). After rhizosphere soil DNA and RNA extraction (and cDNA synthesis), a metabarcoding approach was followed by sequencing the V3-V4 hypervariable regions of the 16S rRNA gene and its derived transcripts by Illumina MiSeq platform. Sequencing reads were bioinformatically processed; specifically, they were filtered, trimmed, clustered into ASV (Amplicon Sequence Variants), and taxonomically identified. As a result, a total of 1,123,209 and 1,089,359 quality sequences were obtained from DNA and RNA-derived libraries, which resulted in 5,241 and 5,231 ASVs, respectively. Total communities (DNA) were mainly dominated by phyla Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia and Bacteroidetes in summer and spring, while potentially active populations (RNA libraries) were rich in Proteobacteria, Acidobacteria, Candidate division WPS-1, Actinobacteria and Verrucomicrobia both in summer and spring. On the other hand, DNA libraries were mainly dominated by genera Sphingomonas and acidobacterial groups Gp4 and Gp6, while potentially active bacteria (RNA) were rich in acidobacterial Gp3, Gp4, Gp6 and Phenylobacterium, although their relative abundance depended on the considered season. This dataset can provide valuable information about bacterial candidates which could be used as bioindicators of drought conditions. In addition to shifts in the bacterial relative abundance due to seasonal changes, the ratio RNA-based cDNA:DNA could be calculated as proxy of the potential activity of bacterial taxa. Moreover, these data could aid in developing bioformulations based on microorganisms which could be resistant to desiccation and involved in the drought resistance mechanisms of the host plant.}, }
@article {pmid36577993, year = {2022}, author = {Qi, Q and Wang, L and Gebremedhin, MA and Li, S and Wang, X and Shen, J and Zhu, Y and Andegiorgish, AK and Cheng, Y and Shi, L and Zhou, J and Yang, Y and Kang, Y and Yang, W and Zhu, Z and Zeng, L}, title = {The impact of early-life antibiotics and probiotics on gut microbial ecology and infant health outcomes: a Pregnancy and Birth Cohort in Northwest China (PBCC) study protocol.}, journal = {BMC pediatrics}, volume = {22}, number = {1}, pages = {738}, pmid = {36577993}, issn = {1471-2431}, support = {81872633//National Natural Science Foundation of China/ ; 2017YFC0907200//National Key Research and Development Program of China/ ; 2017YFC0907201//National Key Research and Development Program of China/ ; 2020JM-077//Natural Science Basic Research Plan of the Shaanxi Province/ ; 202006280219//China Scholarship Council/ ; }, mesh = {Infant ; Infant, Newborn ; Humans ; Female ; Pregnancy ; Child, Preschool ; Anti-Bacterial Agents/therapeutic use ; *Gastrointestinal Microbiome ; Infant Health ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Birth Cohort ; Cohort Studies ; *Probiotics/therapeutic use ; }, abstract = {BACKGROUND: Unreasonable use of antibiotics and probiotics can alter the gut ecology, leading to antibiotic resistance and suboptimal health outcomes during early life. Our study aims are to clarify the association among antibiotic and probiotic exposure in early life, the microecology of the gut microbiota, and the development of antibiotic resistance; to investigate the long-term impact of antibiotics and probiotics on the health outcomes of infants and young children; and to provide a theoretical basis for the rational use of antibiotics and probiotics from a life course perspective.<br><br>METHODS: The study is a prospective, longitudinal birth cohort study conducted in Shaanxi Province, China from 2018 to 2024. A total of 3,000 eligible mother-child pairs will be enrolled from rural, suburban, and urban areas. The recruitment of the participants begins at pregnancy, and the newborns will be followed up for 2&#xa0;years at successive timepoints: within 3&#xa0;days after birth, 42&#xa0;days after birth, and at 3, 6, 12, 18, and 24&#xa0;months of age. Sociodemographic data, environmental exposures, dietary patterns, psychological conditions, and medical and drug histories are collected. Cognitive and behavioural development among infants and young children and questionnaires on antibiotic knowledge and behaviour among caregivers will be collected at 12 and 24&#xa0;months of age. The faecal samples are collected and analysed by 16S rRNA high-throughput sequencing and quantitative PCR (qPCR) for antibiotic resistance genes.<br><br>DISCUSSION: The findings will inform antibiotic and probiotic use for pregnant women and infants and contribute to establishing rational use strategies of antibiotics and probiotics for paediatricians, health practitioners, and drug administration policy-makers.<br><br>TRIAL REGISTRATION: The study was registered on the Chinese Clinical Trial Registry (ChiCTR) platform, http://www.chictr.org.cn (Record ID: ChiCTR2100047531, June 20, 2021).}, }
@article {pmid36576521, year = {2023}, author = {Westreich, LR and Westreich, ST and Tobin, PC}, title = {Bacterial and Fungal Symbionts in Pollen Provisions of a Native Solitary Bee in Urban and Rural Environments.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1416-1427}, pmid = {36576521}, issn = {1432-184X}, support = {1012774//USDA-NIFA McIntire Stennis Cooperative Forestry Program/ ; }, mesh = {Bees ; Animals ; *Bacteria/genetics ; Seasons ; *Pollen ; Washington ; }, abstract = {Among insects, symbionts such as bacteria and fungi can be linked to their physiology and immature development, and in some cases are part of a defense system against parasites and diseases. Current bacterial and fungal symbiont associations in solitary bees are understudied, especially in the Pacific Northwest region of the USA. We collected pollen provisions from the native spring-foraging solitary bee, Osmia lignaria Say, across two distinct foraging periods over 2 years at 22 sites along an urban-to-rural gradient in western Washington. We then used next-generation sequencing to identify bacterial and fungi within pollen provisions and assessed the effect of their richness and diversity on O. lignaria larval development success and adult emergence. We detected a significantly positive relationship between bacterial diversity in pollen with O. lignaria larval developmental success, and higher bacterial richness and diversity during the later foraging period. Fungal generic richness and diversity decreased with increasing plant richness. Although neither was associated with O. lignaria developmental success, we did detect Ascosphaera spp. known to be pathogenic to O. lignaria and other bee species. Neither bacterial or fungal richness or diversity was affected by site type when classified as urban or rural. This study provides new information on bacterial and fungal symbionts present in pollen provisions of a native solitary bee when foraging across urban and rural areas of the Pacific Northwest.}, }
@article {pmid36575570, year = {2023}, author = {Zhou, J and Song, W and Tu, Q}, title = {To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {1}, pages = {}, doi = {10.1093/bib/bbac594}, pmid = {36575570}, issn = {1477-4054}, support = {ZR2020YQ21//National Natural Science Foundation of China/ ; 2019YFA0606700//National Key Research and Development Program of China/ ; }, mesh = {*Metagenome ; *Metagenomics ; High-Throughput Nucleotide Sequencing ; }, abstract = {High-throughput profiling of microbial functional traits involved in various biogeochemical cycling pathways using shotgun metagenomic sequencing has been routinely applied in microbial ecology and environmental science. Multiple bioinformatics data processing approaches are available, including assembly-based (single-sample assembly and multi-sample assembly) and read-based (merged reads and raw data). However, it remains not clear how these different approaches may differ in data analyses and affect result interpretation. In this study, using two typical shotgun metagenome datasets recovered from geographically distant coastal sediments, the performance of different data processing approaches was comparatively investigated from both technical and biological/ecological perspectives. Microbially mediated biogeochemical cycling pathways, including nitrogen cycling, sulfur cycling and B12 biosynthesis, were analyzed. As a result, multi-sample assembly provided the most amount of usable information for targeted functional traits, at a high cost of computational resources and running time. Single-sample assembly and read-based analysis were comparable in obtaining usable information, but the former was much more time- and resource-consuming. Critically, different approaches introduced much stronger variations in microbial profiles than biological differences. However, community-level differences between the two sampling sites could be consistently observed despite the approaches being used. In choosing an appropriate approach, researchers shall balance the trade-offs between multiple factors, including the scientific question, the amount of usable information, computational resources and time cost. This study is expected to provide valuable technical insights and guidelines for the various approaches used for metagenomic data analysis.}, }
@article {pmid36575453, year = {2022}, author = {Barone, M and Garelli, S and Rampelli, S and Agostini, A and Matysik, S and D'Amico, F and Krautbauer, S and Mazza, R and Salituro, N and Fanelli, F and Iozzo, P and Sanz, Y and Candela, M and Brigidi, P and Pagotto, U and Turroni, S}, title = {Multi-omics gut microbiome signatures in obese women: role of diet and uncontrolled eating behavior.}, journal = {BMC medicine}, volume = {20}, number = {1}, pages = {500}, pmid = {36575453}, issn = {1741-7015}, support = {613979//Seventh Framework Programme/ ; 245009//Seventh Framework Programme/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Multiomics ; Obesity/genetics ; Diet ; Feeding Behavior/physiology ; Feces/microbiology ; }, abstract = {BACKGROUND: Obesity and related co-morbidities represent a major health challenge nowadays, with a rapidly increasing incidence worldwide. The gut microbiome has recently emerged as a key modifier of human health that can affect the development and progression of obesity, largely due to its involvement in the regulation of food intake and metabolism. However, there are still few studies that have in-depth explored the functionality of the human gut microbiome in obesity and even fewer that have examined its relationship to eating behaviors.<br><br>METHODS: In an attempt to advance our knowledge of the gut-microbiome-brain axis in the obese phenotype, we thoroughly characterized the gut microbiome signatures of obesity in a well-phenotyped Italian female cohort from the NeuroFAST and MyNewGut EU FP7 projects. Fecal samples were collected from 63 overweight/obese and 37 normal-weight women and analyzed via a multi-omics approach combining 16S rRNA amplicon sequencing, metagenomics, metatranscriptomics, and lipidomics. Associations with anthropometric, clinical, biochemical, and nutritional data were then sought, with particular attention to cognitive and behavioral domains of eating.<br><br>RESULTS: We identified four compositional clusters of the gut microbiome in our cohort that, although not distinctly associated with weight status, correlated differently with eating habits and behaviors. These clusters also differed in functional features, i.e., transcriptional activity and fecal metabolites. In particular, obese women with uncontrolled eating behavior were mostly characterized by low-diversity microbial steady states, with few and poorly interconnected species (e.g., Ruminococcus torques and Bifidobacterium spp.), which exhibited low transcriptional activity, especially of genes involved in secondary bile acid biosynthesis and neuroendocrine signaling (i.e., production of neurotransmitters, indoles and ligands for cannabinoid receptors). Consistently, high amounts of primary bile acids as well as sterols were found in their feces.<br><br>CONCLUSIONS: By finding peculiar gut microbiome profiles associated with eating patterns, we laid the foundation for elucidating gut-brain axis communication in the obese phenotype. Subject to confirmation of the hypotheses herein generated, our work could help guide the design of microbiome-based precision interventions, aimed at rewiring microbial networks to support a healthy diet-microbiome-gut-brain axis, thus counteracting obesity and related complications.}, }
@article {pmid36574886, year = {2023}, author = {Lee, M and Yoo, K and Kim, H and Song, KG and Kim, D and Tiedje, JM and Lee, PH and Park, J}, title = {Metatranscriptional characterization of metabolic dynamics in anaerobic membrane bioreactor producing methane from low-strength wastewater.}, journal = {Bioresource technology}, volume = {370}, number = {}, pages = {128532}, doi = {10.1016/j.biortech.2022.128532}, pmid = {36574886}, issn = {1873-2976}, mesh = {*Wastewater ; Waste Disposal, Fluid/methods ; Anaerobiosis ; Methane/metabolism ; Bioreactors/microbiology ; *Euryarchaeota/metabolism ; Membranes, Artificial ; }, abstract = {An anaerobic membrane bioreactor (AnMBR) with media is an emerging carbon-neutral biotechnology for low-strength wastewater (LSWW) treatment and methane recovery. Understanding metabolic dynamics among methanogens and syntrophic bacteria is important in optimizing the design and operation of AnMBR. However, little is known about it, especially in media-attached microbial communities. This study explored metabolic dynamics to compare media-attached and suspended conditions. Accordingly, metagenomes and metatranscriptomes from AnMBRs with polymeric media and fed with different influent concentrations (350 and 700 mg-COD/L) were analyzed. Metabolic dynamics were profoundly influenced by the different growth habitats and influent conditions, although the applied influent concentrations are within the range of typical LSWW. Metabolic dynamics prediction results suggest that media-attached-growth habitats may have provided a more favorable microenvironment for methanogens to grow and produce methane, especially under low influent conditions. These findings provide significant implications for optimizing floating media design and operation of AnMBR-producing methane from LSWW.}, }
@article {pmid36574041, year = {2023}, author = {Lozano, IL and González-Olalla, JM and Medina-Sánchez, JM}, title = {New Insights for the Renewed Phytoplankton-Bacteria Coupling Concept: the Role of the Trophic Web.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {810-824}, pmid = {36574041}, issn = {1432-184X}, support = {B-RNM-310-UGR20//Consejer&#xed;a de Transformaci&#xf3;n Econ&#xf3;mica, Industria, Conocimiento y Universidades/ ; PID2020-118872RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; LifeWatch-2019-10-UGR-01//FEDER Funds/ ; }, mesh = {*Phytoplankton/metabolism ; *Ecosystem ; Bacteria/metabolism ; Carbon/metabolism ; }, abstract = {It is widely accepted that in many aquatic ecosystems bacterioplankton is dependent on and regulated by organic carbon supplied by phytoplankton, leading to coupled algae-bacteria relationship. In this study, an in-depth analysis of this relationship has been carried out by combining two approaches: (i) a correlation analyses between heterotrophic bacterial production (BP) vs. primary production (PP) or algal excretion of organic carbon (EOC), (ii) the balance between bacterial carbon demands (BCD) and the supply of C as EOC, measured as BCD:EOC ratio. During the study period (2013-2016), the algae-bacteria relationship was constantly changing from a coupling in 2013, uncoupling in 2014 and 2015, and an incipient return to coupling (in 2016). Our results show that top-down control (bacterivory) by algal mixotrophy acts as a decoupling force since it provides a fresh C source different to algal EOC to satisfy bacterial carbon demands. Notably, a relationship between the BCD:EOC ratio and the ecosystem metabolic balance (Primary production (PP): respiration (R)) was found, suggesting that PP:R may be a good predictor of the algae-bacteria coupling. This analysis, including the comparison between basal and potential ecosystem metabolic balance, can be a tool to improve knowledge on the interaction between both biotics compartments, which the traditional analyses on coupling may not capture.}, }
@article {pmid36571608, year = {2023}, author = {la Rosa, GM and García-Oliva, F and Ovando-Vázquez, C and Celis-García, LB and López-Reyes, L and López-Lozano, NE}, title = {Amino Acids in the Root Exudates of Agave lechuguilla Torr. Favor the Recruitment and Enzymatic Activity of Nutrient-Improvement Rhizobacteria.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1176-1188}, pmid = {36571608}, issn = {1432-184X}, support = {Basic Science 254406//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; }, mesh = {*Agave ; Amino Acids ; Plant Roots/microbiology ; Bacteria ; Rhizosphere ; *Alphaproteobacteria ; *Microbiota ; Plants/microbiology ; Exudates and Transudates ; Nutrients ; Arginine ; Phosphorus ; Soil Microbiology ; }, abstract = {Agave lechuguilla is a widely distributed plant in arid ecosystems. It has been suggested that its microbiome is partially responsible for its great adaptability to the oligotrophic environments of the Chihuahuan Desert. To lead the recruitment of beneficial rhizobacteria, the root exudates are essential; however, the amino acids contained within these compounds had been largely overlooked. Thus, we investigated how the variations of amino acids in the rhizosphere at different growth stages of A. lechuguilla affect the rhizobacterial community composition, its functions, and activity of the beneficial bacteria. In this regard, it was found that arginine and tyrosine were related to the composition of the rhizobacterial community associated to A. lechuguilla, where the most abundant genera were from the phylum Proteobacteria and Bacteroidetes. Moreover, Firmicutes was largely represented by Bacillus in the phosphorus-mineralizing bacteria community, which may indicate its great distribution and versatility in the harsh environments of the Chihuahuan Desert. In contrast, we found a high proportion of Unknown taxa of nitrogen-fixing bacteria, reflecting the enormous diversity in the rhizosphere of these types of plants that remains to be explored. This work also reports the influence of micronutrients and the amino acids methionine and arginine over the increased activity of the nitrogen-fixing and phosphorus-mineralizing bacteria in the rhizosphere of lechuguillas. In addition, the results highlight the multiple beneficial functions present in the microbiome that could help the host to tolerate arid conditions and improve nutrient availability.}, }
@article {pmid36569156, year = {2022}, author = {Meller, S and Al Khatri, MSA and Alhammadi, HK and Álvarez, G and Alvergnat, G and Alves, LC and Callewaert, C and Caraguel, CGB and Carancci, P and Chaber, AL and Charalambous, M and Desquilbet, L and Ebbers, H and Ebbers, J and Grandjean, D and Guest, C and Guyot, H and Hielm-Björkman, A and Hopkins, A and Kreienbrock, L and Logan, JG and Lorenzo, H and Maia, RCC and Mancilla-Tapia, JM and Mardones, FO and Mutesa, L and Nsanzimana, S and Otto, CM and Salgado-Caxito, M and de Los Santos, F and da Silva, JES and Schalke, E and Schoneberg, C and Soares, AF and Twele, F and Vidal-Martínez, VM and Zapata, A and Zimin-Veselkoff, N and Volk, HA}, title = {Expert considerations and consensus for using dogs to detect human SARS-CoV-2-infections.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {1015620}, pmid = {36569156}, issn = {2296-858X}, }
@article {pmid36565551, year = {2023}, author = {Li, Q and Stautemas, J and Omondi Onyango, S and De Mey, M and Duchi, D and Tuenter, E and Hermans, N and Calders, P and Van de Wiele, T}, title = {Human gut microbiota stratified by (+)-catechin metabolism dynamics reveals colon region-dependent metabolic profile.}, journal = {Food chemistry}, volume = {408}, number = {}, pages = {135203}, doi = {10.1016/j.foodchem.2022.135203}, pmid = {36565551}, issn = {1873-7072}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Catechin/metabolism ; Colon/microbiology ; *Microbiota ; Bacteria/genetics/metabolism ; Metabolome ; }, abstract = {Catechins have proven to have several health benefits, yet a huge interindividual variability occurs. The metabolic potency of the colonic microbiota towards catechin is a key determinant of this variability. Microbiota from two donors - previously characterized as a fast and a slow converter- were incubated with (+)-catechin in vitro. The robustness of in vitro metabolic profiles was verified by well-fitted human trials. The colon region-dependent and donor-dependent patterns were reflected in both metabolic features and colonic microbiota composition. Upstream and downstream metabolites were mainly detected in the proximal and distal colons, respectively, and were considered important explanatory variables for microbiota clustering in the corresponding colon regions. Higher abundances of two catechin-metabolizing bacteria, Eggerthella and Flavonifractor were found in the distal colon compared to the proximal colon and in slow converter than fast converter. Additionally, these two bacteria were enriched in treatment samples compared to sham treatment samples.}, }
@article {pmid36564013, year = {2023}, author = {Kreth, J and Merritt, J}, title = {Illuminating the oral microbiome and its host interactions: tools and approaches for molecular ecological studies.}, journal = {FEMS microbiology reviews}, volume = {47}, number = {1}, pages = {}, pmid = {36564013}, issn = {1574-6976}, support = {R01 DE022083/DE/NIDCR NIH HHS/United States ; R01 DE029492/DE/NIDCR NIH HHS/United States ; R21 DE029612/DE/NIDCR NIH HHS/United States ; R35 DE028252/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; Biofilms ; }, abstract = {A more comprehensive understanding of oral diseases like caries and periodontitis is dependent on an intimate understanding of the microbial ecological processes that are responsible for disease development. With this review, we provide a comprehensive overview of relevant molecular ecology techniques that have played critical roles in the current understanding of human oral biofilm development, interspecies interactions, and microbiome biogeography. The primary focus is on relevant technologies and examples available in the oral microbiology literature. However, most, if not all, of the described technologies should be readily adaptable for studies of microbiomes from other mucosal sites in the body. Therefore, this review is intended to serve as a reference guide used by microbiome researchers as they inevitably transition into molecular mechanistic studies of the many significant phenotypes observed clinically.}, }
@article {pmid36563760, year = {2023}, author = {Xie, L and Li, W and Pang, X and Liu, Q and Yin, C}, title = {Soil properties and root traits are important factors driving rhizosphere soil bacterial and fungal community variations in alpine Rhododendron nitidulum shrub ecosystems along an altitudinal gradient.}, journal = {The Science of the total environment}, volume = {864}, number = {}, pages = {161048}, doi = {10.1016/j.scitotenv.2022.161048}, pmid = {36563760}, issn = {1879-1026}, mesh = {*Mycobiome ; Rhizosphere ; Soil/chemistry ; *Rhododendron ; Soil Microbiology ; Fungi ; Bacteria ; *Microbiota ; }, abstract = {Both soil properties and plant root traits are pivotal factors affecting microbial communities. However, there is still limited information about their importance in shaping rhizosphere soil microbial communities, particularly in less-studied alpine shrub ecosystems. To investigate the effects of altitude (3300, 3600, 3900, and 4200 m) on the diversity and composition of rhizosphere soil bacterial and fungal communities, as well as the factors shaping rhizosphere soil microbial communities, we conducted this study in alpine Rhododendron nitidulum shrub ecosystems from the Zheduo mountain of the eastern Tibetan Plateau. Results demonstrated that bacterial community diversity and richness decreased to the lowest value at 3600 m and then increased at higher altitudes compared with 3300 m; whereas fungal richness at 3300 m was much lower than at other altitudes, and was closely related to soil properties and root traits. The composition of rhizosphere soil bacterial and fungal communities at the low altitude (3300 m) was different from that at high altitudes. Permutational multivariate analysis of variance and redundancy analysis indicated that soil properties (soil water content, pH, NO3[-]-N, and available phosphorus) and root traits (surface area, and maximum depth) were the major factors explaining the variations of rhizosphere soil bacterial and fungal communities. Specific bacterial and fungal taxa along altitudes were identified. The bacterial taxa Planctomycetota was dominant at 3300 and 3600 m with low soil nutrient availability and high root surface area, whereas the fungal taxa Mortierellomycota was abundant at 3900 and 4200 m with high soil nutrient availability and low root surface area. These results suggested that different soil microbes can respond differently to altitude. This study provides a novel insight into factors driving rhizosphere soil bacterial and fungal community variations, which could improve our understanding of microbial ecology in alpine R. nitidulum shrub ecosystems along altitude.}, }
@article {pmid36562630, year = {2023}, author = {Larrouy, JL and Dhami, MK and Jones, EE and Ridgway, HJ}, title = {Physiological stage drives fungal community dynamics and diversity in Leptospermum scoparium (mānuka) flowers.}, journal = {Environmental microbiology}, volume = {25}, number = {3}, pages = {766-771}, doi = {10.1111/1462-2920.16324}, pmid = {36562630}, issn = {1462-2920}, mesh = {Leptospermum ; *Mycobiome ; Flowers/microbiology ; Plant Nectar ; *Microbiota ; Pollination ; }, abstract = {Flowers are an important niche for microbes, and microbes in turn influence plant fitness. As flower morphology and biology change rapidly over time, dynamic niches for microbes are formed and lost. Floral physiology at each life stage can therefore influence arrival, persistence and loss of microbial species; however, this remains little understood despite its potential consequences for host reproductive success. Through internal transcribed spacer 1 (ITS1) community profiling, we characterized the effect of transitioning through five floral stages of mānuka (Leptospermum scoparium), from immature bud to spent flower, and subsequent allocation to seed, on the flower-inhabiting fungal community. We found nectar-consuming yeasts from Aureobasidium and Vishniacozyma genera and functionally diverse filamentous fungi from the Cladosporium genus dominated the anthosphere. The candidate core microbiota persisted across this dynamic niche despite high microbial turnover, as observed in shifts in community composition and diversity as flowers matured and senesced. The results demonstrated that floral stages are strong drivers of anthosphere fungal community assembly and dynamics. This study represents the first detailed exploration of fungi through floral development, building on fundamental knowledge in microbial ecology of healthy flowers.}, }
@article {pmid36560818, year = {2022}, author = {Budzyńska, D and Zwart, MP and Hasiów-Jaroszewska, B}, title = {Defective RNA Particles of Plant Viruses-Origin, Structure and Role in Pathogenesis.}, journal = {Viruses}, volume = {14}, number = {12}, pages = {}, pmid = {36560818}, issn = {1999-4915}, mesh = {Animals ; Humans ; RNA, Viral/genetics ; *Plant Viruses/genetics ; *RNA Viruses/genetics ; RNA, Satellite ; Virus Replication ; Defective Viruses/genetics ; }, abstract = {The genomes of RNA viruses may be monopartite or multipartite, and sub-genomic particles such as defective RNAs (D RNAs) or satellite RNAs (satRNAs) can be associated with some of them. D RNAs are small, deletion mutants of a virus that have lost essential functions for independent replication, encapsidation and/or movement. D RNAs are common elements associated with human and animal viruses, and they have been described for numerous plant viruses so far. Over 30 years of studies on D RNAs allow for some general conclusions to be drawn. First, the essential condition for D RNA formation is prolonged passaging of the virus at a high cellular multiplicity of infection (MOI) in one host. Second, recombination plays crucial roles in D RNA formation. Moreover, during virus propagation, D RNAs evolve, and the composition of the particle depends on, e.g., host plant, virus isolate or number of passages. Defective RNAs are often engaged in transient interactions with full-length viruses-they can modulate accumulation, infection dynamics and virulence, and are widely used, i.e., as a tool for research on cis-acting elements crucial for viral replication. Nevertheless, many questions regarding the generation and role of D RNAs in pathogenesis remain open. In this review, we summarise the knowledge about D RNAs of plant viruses obtained so far.}, }
@article {pmid36557627, year = {2022}, author = {Tao, L and Chai, J and Liu, H and Huang, W and Zou, Y and Wu, M and Peng, B and Wang, Q and Tang, K}, title = {Characterization and Dynamics of the Gut Microbiota in Rice Fishes at Different Developmental Stages in Rice-Fish Coculture Systems.}, journal = {Microorganisms}, volume = {10}, number = {12}, pages = {}, pmid = {36557627}, issn = {2076-2607}, support = {2022NSFSC1711//Natural Science Foundation of Sichuan Province, China/ ; 341965//Starting Research Funding from Sichuan Normal University/ ; SYJS2021030//Experimental Technology Funding from Sichuan Normal University/ ; }, abstract = {The rice-fish system (RFS), a traditional coculture farming model, was selected as a "globally important agricultural heritage system." Host-associated microbiota play important roles in development, metabolism, physiology, and immune function. However, studies on the gut microbiota of aquatic animals in the RFS are scarce, especially the lack of baseline knowledge of the dynamics of gut microbial communities in rice fish during different developmental stages. In this study, we characterized the microbial composition, community structure, and functions of several sympatric aquatic animals (common carp (Cyprinus carpio), crucian carp (Carassius carassius), and black-spotted frogs (Pelophylax nigromaculatus)), and the environment (water) in the RFS using 16S rRNA gene sequencing. Moreover, we investigated stage-specific signatures in the gut microbiota of common carp throughout the three developmental stages (juvenile, sub-adult, and adult). Our results indicated that the Fusobacteriota, Proteobacteria, and Firmicutes were dominant gut microbial phyla in rice fish. The differences in gut microbial compositions and community structure between the three aquatic species were observed. Although no significant differences in alpha diversity were observed across the three developmental stages, the microbial composition and community structure varied with development in common carp in the RFS, with an increase in the relative abundance of Firmicutes in sub-adults and a shift in the functional features of the community. This study sheds light on the gut microbiota of aquatic animals in the RFS. It deepens our understanding of the dynamics of gut microflora during common carp development, which may help improve aquaculture strategies in the RFS.}, }
@article {pmid36557593, year = {2022}, author = {Delgadillo-Ordoñez, N and Raimundo, I and Barno, AR and Osman, EO and Villela, H and Bennett-Smith, M and Voolstra, CR and Benzoni, F and Peixoto, RS}, title = {Red Sea Atlas of Coral-Associated Bacteria Highlights Common Microbiome Members and Their Distribution across Environmental Gradients-A Systematic Review.}, journal = {Microorganisms}, volume = {10}, number = {12}, pages = {}, pmid = {36557593}, issn = {2076-2607}, support = {BAS/1/1095-01-01 and FCC/1/1973-51-01//King Abdullah University of Science and Technology/ ; }, abstract = {The Red Sea is a suitable model for studying coral reefs under climate change due to its strong environmental gradient that provides a window into future global warming scenarios. For instance, corals in the southern Red Sea thrive at temperatures predicted to occur at the end of the century in other biogeographic regions. Corals in the Red Sea thrive under contrasting thermal and environmental regimes along their latitudinal gradient. Because microbial communities associated with corals contribute to host physiology, we conducted a systematic review of the known diversity of Red Sea coral-associated bacteria, considering geographic location and host species. Our assessment comprises 54 studies of 67 coral host species employing cultivation-dependent and cultivation-independent techniques. Most studies have been conducted in the central and northern Red Sea, while the southern and western regions remain largely unexplored. Our data also show that, despite the high diversity of corals in the Red Sea, the most studied corals were Pocillopora verrucosa, Dipsastraea spp., Pleuractis granulosa, and Stylophora pistillata. Microbial diversity was dominated by bacteria from the class Gammaproteobacteria, while the most frequently occurring bacterial families included Rhodobacteraceae and Vibrionaceae. We also identified bacterial families exclusively associated with each of the studied coral orders: Scleractinia (n = 125), Alcyonacea (n = 7), and Capitata (n = 2). This review encompasses 20 years of research in the Red Sea, providing a baseline compendium for coral-associated bacterial diversity.}, }
@article {pmid36554499, year = {2022}, author = {Dania, MI and Faraji, B and Wachira, J}, title = {Micronutrient Biosynthesis Potential of Spontaneous Grain Fermentation Microbiomes.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {24}, pages = {}, pmid = {36554499}, issn = {1660-4601}, support = {U54 MD013376/MD/NIMHD NIH HHS/United States ; UL1 GM118973/GM/NIGMS NIH HHS/United States ; 5UL1GM118973/GM/NIGMS NIH HHS/United States ; 5U54MD013376/NH/NIH HHS/United States ; }, mesh = {Humans ; Fermentation ; Micronutrients/metabolism ; Phylogeny ; Bacteria ; *Microbiota ; Edible Grain ; *Trace Elements/metabolism ; }, abstract = {Fermented foods play an important role in the human diet and particularly so in under-resourced environments where cold preservation is not attainable due to irregular supply of electricity. Fermented foods are reported to support gut health by contributing probiotics. The purpose of this study was to investigate the microbial diversity and metabolic potential of spontaneous millet fermentation. The literature in the field was reviewed and analyses were conducted on publicly available Sequence Read Archive (SRA) datasets. Quality analysis was performed with FastQC, and operational taxonomic units (OTUs) were generated using Quantitative Insights Into Microbial Ecology (QIIME2) and Divisive Amplicon Denoising Algorithm (DADA2) pipelines with Greengenes as the reference database. Metagenomics and pathways analysis were performed with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2). Statistical analysis and visualization were accomplished with Statistical Analysis of Metagenomic Profiles (STAMP). At the family taxonomic level, there were differences in the relative abundances of the dominant taxa of bacteria that are involved in the spontaneous fermentation of millet namely Lactobacillaceae, Burkholderiaceae, Streptococcaceae, Leuconostocaceae, and Acetobacteraceae. Clostridiaceae was the dominant family in one dataset. The incidence of Lactobacillaceae and Bifidobacteriaceae suggest the probiotic characteristics of fermented millet. The datasets were collected with fermentations that were mediated by autochthonous microorganisms and the presence of some potential pathogens such as Enterobacteriaceae, Clostridiaceae, Aeromonadaceae, Microbacteiaceae, Pseudomonadaceae, and Neisseriaceae which suggest the need for standardization of fermentation approaches. The genomes show the potential to synthesize metabolites such as essential amino acids and vitamins, suggesting that the respective fermented foods can be further optimized to enhance nutritional benefits.}, }
@article {pmid36549925, year = {2023}, author = {Hodžić, A and Alić, A}, title = {Hepatozoon silvestris: an emerging feline vector-borne pathogen in Europe?.}, journal = {Trends in parasitology}, volume = {39}, number = {3}, pages = {163-166}, doi = {10.1016/j.pt.2022.12.001}, pmid = {36549925}, issn = {1471-5007}, mesh = {Cats ; Animals ; *Eucoccidiida/genetics ; *Coccidiosis/epidemiology/veterinary/parasitology ; Europe/epidemiology ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Hepatozoon silvestris (Adeleorina: Hepatozoidae) is a recently described agent of feline hepatozoonosis. Although possibly emerging in Europe, this apicomplexan parasite is still largely unknown. Here, we provide insight into our current knowledge of the parasite's distribution, biology, and pathogenesis of the associated disease.}, }
@article {pmid36549441, year = {2023}, author = {Bilbija, B and Spitzweg, C and Papoušek, I and Fritz, U and Földvári, G and Mullett, M and Ihlow, F and Sprong, H and Civáňová Křížová, K and Anisimov, N and Belova, OA and Bonnet, SI and Bychkova, E and Czułowska, A and Duscher, GG and Fonville, M and Kahl, O and Karbowiak, G and Kholodilov, IS and Kiewra, D and Krčmar, S and Kumisbek, G and Livanova, N and Majláth, I and Manfredi, MT and Mihalca, AD and Miró, G and Moutailler, S and Nebogatkin, IV and Tomanović, S and Vatansever, Z and Yakovich, M and Zanzani, S and Široký, P}, title = {Dermacentor reticulatus - a tick on its way from glacial refugia to a panmictic Eurasian population.}, journal = {International journal for parasitology}, volume = {53}, number = {2}, pages = {91-101}, doi = {10.1016/j.ijpara.2022.11.002}, pmid = {36549441}, issn = {1879-0135}, mesh = {Dogs ; Animals ; *Dermacentor/genetics ; Phylogeny ; Bayes Theorem ; Refugium ; *Rhipicephalus sanguineus ; }, abstract = {The ornate dog tick (Dermacentor reticulatus) shows a recently expanding geographic distribution. Knowledge on its intraspecific variability, population structure, rate of genetic diversity and divergence, including its evolution and geographic distribution, is crucial to understand its dispersal capacity. All such information would help to evaluate the potential risk of future spread of associated pathogens of medical and veterinary concern. A set of 865 D. reticulatus ticks was collected from 65 localities across 21 countries, from Portugal in the west to Kazakhstan and southern Russia in the east. Cluster analyses of 16 microsatellite loci were combined with nuclear (ITS2, 18S) and mitochondrial (12S, 16S, COI) sequence data to uncover the ticks' population structures and geographical patterns. Approximate Bayesian computation was applied to model evolutionary relationships among the found clusters. Low variability and a weak phylogenetic signal showing an east-west cline were detected both for mitochondrial and nuclear sequence markers. Microsatellite analyses revealed three genetic clusters, where the eastern and western cluster gradient was supplemented by a third, northern cluster. Alternative scenarios could explain such a tripartite population structure by independent formation of clusters in separate refugia, limited gene flow connected with isolation by distance causing a "bipolar pattern", and the northern cluster deriving from admixture between the eastern and western populations. The best supported demographic scenario of this tick species indicates that the northern cluster derived from admixture between the eastern and western populations 441 (median) to 224 (mode) generations ago, suggesting a possible link with the end of the Little Ice Age in Europe.}, }
@article {pmid36548240, year = {2022}, author = {Lee, JR and Terauds, A and Carwardine, J and Shaw, JD and Fuller, RA and Possingham, HP and Chown, SL and Convey, P and Gilbert, N and Hughes, KA and McIvor, E and Robinson, SA and Ropert-Coudert, Y and Bergstrom, DM and Biersma, EM and Christian, C and Cowan, DA and Frenot, Y and Jenouvrier, S and Kelley, L and Lee, MJ and Lynch, HJ and Njåstad, B and Quesada, A and Roura, RM and Shaw, EA and Stanwell-Smith, D and Tsujimoto, M and Wall, DH and Wilmotte, A and Chadès, I}, title = {Threat management priorities for conserving Antarctic biodiversity.}, journal = {PLoS biology}, volume = {20}, number = {12}, pages = {e3001921}, pmid = {36548240}, issn = {1545-7885}, mesh = {Animals ; Humans ; *Conservation of Natural Resources ; Antarctic Regions ; Biodiversity ; Introduced Species ; *Spheniscidae ; Climate Change ; Ecosystem ; }, abstract = {Antarctic terrestrial biodiversity faces multiple threats, from invasive species to climate change. Yet no large-scale assessments of threat management strategies exist. Applying a structured participatory approach, we demonstrate that existing conservation efforts are insufficient in a changing world, estimating that 65% (at best 37%, at worst 97%) of native terrestrial taxa and land-associated seabirds are likely to decline by 2100 under current trajectories. Emperor penguins are identified as the most vulnerable taxon, followed by other seabirds and dry soil nematodes. We find that implementing 10 key threat management strategies in parallel, at an estimated present-day equivalent annual cost of US$23 million, could benefit up to 84% of Antarctic taxa. Climate change is identified as the most pervasive threat to Antarctic biodiversity and influencing global policy to effectively limit climate change is the most beneficial conservation strategy. However, minimising impacts of human activities and improved planning and management of new infrastructure projects are cost-effective and will help to minimise regional threats. Simultaneous global and regional efforts are critical to secure Antarctic biodiversity for future generations.}, }
@article {pmid36545206, year = {2022}, author = {Molina, V and Lavergne, C and Eissler, Y and Junier, P}, title = {Editorial: Microbial ecology and ecosystems from a Southern perspective.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1098400}, pmid = {36545206}, issn = {1664-302X}, }
@article {pmid36542127, year = {2023}, author = {Davis, TS and Stewart, JE and Clark, C and Van Buiten, C}, title = {Nutritional Profile and Ecological Interactions of Yeast Symbionts Associated with North American Spruce Beetle (Dendroctonus rufipennis).}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1268-1280}, pmid = {36542127}, issn = {1432-184X}, support = {2046109//Division of Integrative Organismal Systems/ ; }, mesh = {*Picea ; Saccharomycetales ; *Ophiostomatales ; Yeasts ; *Coleoptera/microbiology ; North America ; *Phenylethyl Alcohol ; Symbiosis ; Animals ; }, abstract = {To better understand functional ecology of bark beetle-microbial symbioses, we characterized yeast associates of North American spruce beetle (Dendroctous rufipennis Kirby) across populations. Seven yeast species were detected; Wickerhamomyces canadensis (Wickerham) Kurtzman et al. (Sachharomycetales: Saccharomycetaceae) was the most common (74% of isolates) and found in all populations. Isolates of W. canadensis were subsequently tested for competitive interactions with symbiotic (Leptographium abietinum, = Grosmannia abietina) and pathogenic (Beauvaria bassiana) filamentous fungi, and isolates were nutritionally profiled (protein and P content). Exposure to yeast headspace emissions had isolate-dependent effects on colony growth of symbiotic and pathogenic fungi; most isolates of W. canadensis slightly inhibited growth rates of symbiotic (L. abietinum, mean effect: - 4%) and entomopathogenic (B. bassiana, mean effect: - 6%) fungi. However, overall variation was high (range: - 35.4 to + 88.6%) and some yeasts enhanced growth of filamentous fungi whereas others were consistently inhibitory. The volatile 2-phenylethanol was produced by W. canadensis and synthetic 2-phenylethanol reduced growth rates of both L. abietinum and B. bassiana by 36% on average. Mean protein and P content of Wickerhamomyces canadensis cultures were 0.8% and 7.2%, respectively, but isolates varied in nutritional content and protein content was similar to that of host tree phloem. We conclude that W. canadensis is a primary yeast symbiont of D. rufipennis in the Rocky Mountains and emits volatiles that can affect growth of associated microbes. Wickerhamomyces canadensis isolates vary substantially in limiting nutrients (protein and P), but concentrations are less than reported for the symbiotic filamentous fungus L. abietinum.}, }
@article {pmid36542126, year = {2023}, author = {Wicaksono, WA and Buko, A and Kusstatscher, P and Cernava, T and Sinkkonen, A and Laitinen, OH and Virtanen, SM and Hyöty, H and Berg, G}, title = {Impact of Cultivation and Origin on the Fruit Microbiome of Apples and Blueberries and Implications for the Exposome.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {973-984}, pmid = {36542126}, issn = {1432-184X}, support = {874864//Horizon 2020 Framework Programme/ ; }, mesh = {Humans ; Fruit/microbiology ; *Malus ; *Blueberry Plants/chemistry ; *Exposome ; *Microbiota ; }, abstract = {Vegetables and fruits are a crucial part of the planetary health diet, directly affecting human health and the gut microbiome. The objective of our study was to understand the variability of the fruit (apple and blueberry) microbiome in the frame of the exposome concept. The study covered two fruit-bearing woody species, apple and blueberry, two countries of origin (Austria and Finland), and two fruit production methods (naturally grown and horticultural). Microbial abundance, diversity, and community structures were significantly different for apples and blueberries and strongly influenced by the growing system (naturally grown or horticultural) and country of origin (Austria or Finland). Our results indicated that bacterial communities are more responsive towards these factors than fungal communities. We found that fruits grown in the wild and within home gardens generally carry a higher microbial diversity, while commercial horticulture homogenized the microbiome independent of the country of origin. This can be explained by horticultural management, including pesticide use and post-harvest treatments. Specific taxonomic indicators were identified for each group, i.e., for horticultural apples: Pseudomonas, Ralstonia, and Stenotrophomonas. Interestingly, Ralstonia was also found to be enriched in horticultural blueberries in comparison to such that were home and wildly grown. Our study showed that the origin of fruits can strongly influence the diversity and composition of their microbiome, which means that we are exposed to different microorganisms by eating fruits from different origins. Thus, the fruit microbiome needs to be considered an important but relatively unexplored external exposomic factor.}, }
@article {pmid36539202, year = {2023}, author = {Almeida-Silva, F and Zhao, T and Ullrich, KK and Schranz, ME and Van de Peer, Y}, title = {syntenet: an R/Bioconductor package for the inference and analysis of synteny networks.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {1}, pages = {}, pmid = {36539202}, issn = {1367-4811}, support = {833522//European Research Council/International ; 833522//European Union's Horizon 2020 Research and Innovation Program/ ; }, mesh = {Synteny ; Phylogeny ; *Software ; *Genome ; }, abstract = {SUMMARY: Interpreting and visualizing synteny relationships across several genomes is a challenging task. We previously proposed a network-based approach for better visualization and interpretation of large-scale microsynteny analyses. Here, we present syntenet, an R package to infer and analyze synteny networks from whole-genome protein sequence data. The package offers a simple and complete framework, including data preprocessing, synteny detection and network inference, network clustering and phylogenomic profiling, and microsynteny-based phylogeny inference. Graphical functions are also available to create publication-ready plots. Synteny networks inferred with syntenet can highlight taxon-specific gene clusters that likely contributed to the evolution of important traits, and microsynteny-based phylogenies can help resolve phylogenetic relationships under debate.<br><br>syntenet is available on Bioconductor (https://bioconductor.org/packages/syntenet), and the source code is available on a GitHub repository (https://github.com/almeidasilvaf/syntenet).<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid36538089, year = {2023}, author = {Moukarzel, R and Ridgway, HJ and Waller, L and Guerin-Laguette, A and Cripps-Guazzone, N and Jones, EE}, title = {Soil Arbuscular Mycorrhizal Fungal Communities Differentially Affect Growth and Nutrient Uptake by Grapevine Rootstocks.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1035-1049}, pmid = {36538089}, issn = {1432-184X}, support = {Strategic Science Investment Fund//New Zealand Institute for Plant and Food Research Limited/ ; Project P/471778/08//New Zealand Institute for Plant and Food Research Limited/ ; }, mesh = {*Mycorrhizae ; Ecosystem ; Soil ; *Mycobiome ; Crops, Agricultural ; Nutrients ; Soil Microbiology ; Plant Roots/microbiology ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) deliver potentially significant services in sustainable agricultural ecosystems, yet we still lack evidence showing how AMF abundance and/or community composition can benefit crops. In this study, we manipulated AMF communities in grapevine rootstock and measured plant growth and physiological responses. Glasshouse experiments were set up to determine the interaction between rootstock variety and different AMF communities, using AMF communities originating under their own (i.e., "home") soil and other rootstocks' (i.e., "away") soil. The results revealed that specific AMF communities had differential effects on grapevine rootstock growth and nutrient uptake. It was demonstrated that a rootstock generally performed better in the presence of its own AMF community. This study also showed that AMF spore diversity and the relative abundance of certain species is an important factor as, when present in equal abundance, competition between species was indicated to occur, resulting in a reduction in the positive growth outcomes. Moreover, there was a significant difference between the communities with some AMF communities increasing plant growth and nutrient uptake compared with others. The outcomes also demonstrated that some AMF communities indirectly influenced the chlorophyll content in grapevine leaves through the increase of specific nutrients such as K, Mn, and Zn. The findings also indicated that some AMF species may deliver particular benefits to grapevine plants. This work has provided an improved understanding of community level AMF-grapevine interaction and delivered an increased knowledge of the ecosystem services they provide which will benefit the wine growers and the viticulture industry.}, }
@article {pmid36537799, year = {2023}, author = {Tyc, O and Kulkarni, P and Ossowicki, A and Tracanna, V and Medema, MH and van Baarlen, P and van IJcken, WFJ and Verhoeven, KJF and Garbeva, P}, title = {Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0057422}, pmid = {36537799}, issn = {2379-5077}, mesh = {*Soil ; Metabolome ; Symbiosis ; *Comamonadaceae ; }, abstract = {Microbial community analysis of aquatic environments showed that an important component of its microbial diversity consists of bacteria with cell sizes of ~0.1 μm. Such small bacteria can show genomic reductions and metabolic dependencies with other bacteria. However, so far, no study has investigated if such bacteria exist in terrestrial environments like soil. Here, we isolated soil bacteria that passed through a 0.1-μm filter. The complete genome of one of the isolates was sequenced and the bacterium was identified as Hylemonella gracilis. A set of coculture assays with phylogenetically distant soil bacteria with different cell and genome sizes was performed. The coculture assays revealed that H. gracilis grows better when interacting with other soil bacteria like Paenibacillus sp. AD87 and Serratia plymuthica. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct cell-cell contact. Our study indicates that in soil there are bacteria that can pass through a 0.1-μm filter. These bacteria may have been overlooked in previous research on soil microbial communities. Such small bacteria, exemplified here by H. gracilis, can induce transcriptional and metabolomic changes in other bacteria upon their interactions in soil. In vitro, the studied interspecific interactions allowed utilization of growth substrates that could not be utilized by monocultures, suggesting that biochemical interactions between substantially different sized soil bacteria may contribute to the symbiosis of soil bacterial communities. IMPORTANCE Analysis of aquatic microbial communities revealed that parts of its diversity consist of bacteria with cell sizes of ~0.1 μm. Such bacteria can show genomic reductions and metabolic dependencies with other bacteria. So far, no study investigated if such bacteria exist in terrestrial environments such as soil. Here, we show that such bacteria also exist in soil. The isolated bacteria were identified as Hylemonella gracilis. Coculture assays with phylogenetically different soil bacteria revealed that H. gracilis grows better when cocultured with other soil bacteria. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct contact. Our study revealed that bacteria are present in soil that can pass through 0.1-μm filters. Such bacteria may have been overlooked in previous research on soil microbial communities and may contribute to the symbiosis of soil bacterial communities.}, }
@article {pmid36534053, year = {2023}, author = {Amaneesh, C and Anna Balan, S and Silpa, PS and Kim, JW and Greeshma, K and Aswathi Mohan, A and Robert Antony, A and Grossart, HP and Kim, HS and Ramanan, R}, title = {Gross Negligence: Impacts of Microplastics and Plastic Leachates on Phytoplankton Community and Ecosystem Dynamics.}, journal = {Environmental science &amp; technology}, volume = {57}, number = {1}, pages = {5-24}, doi = {10.1021/acs.est.2c05817}, pmid = {36534053}, issn = {1520-5851}, mesh = {Animals ; Humans ; *Ecosystem ; *Plastics/analysis ; Microplastics/toxicity ; Phytoplankton ; Aquatic Organisms ; }, abstract = {Plastic debris is an established environmental menace affecting aquatic systems globally. Recently, microplastics (MP) and plastic leachates (PL) have been detected in vital human organs, the vascular system, and in vitro animal studies positing severe health hazards. MP and PL have been found in every conceivable aquatic ecosystem─from open oceans and deep sea floors to supposedly pristine glacier lakes and snow covered mountain catchment sites. Many studies have documented the MP and PL impacts on a variety of aquatic organisms, whereby some exclusively focus on aquatic microorganisms. Yet, the specific MP and PL impacts on primary producers have not been systematically analyzed. Therefore, this review focuses on the threats posed by MP, PL, and associated chemicals on phytoplankton, their comprehensive impacts at organismal, community, and ecosystem scales, and their endogenous amelioration. Studies on MP- and PL-impacted individual phytoplankton species reveal the production of reactive oxygen species, lipid peroxidation, physical damage of thylakoids, and other physiological and metabolic changes, followed by homo- and heteroaggregations, ultimately eventuating in decreased photosynthesis and primary productivity. Likewise, analyses of the microbial community in the plastisphere show a radically different profile compared to the surrounding planktonic diversity. The plastisphere also enriches multidrug-resistant bacteria, cyanotoxins, and pollutants, accelerating microbial succession, changing the microbiome, and thus, affecting phytoplankton diversity and evolution. These impacts on cellular and community scales manifest in changed ecosystem dynamics with widespread bottom-up and top-down effects on aquatic biodiversity and food web interactions. These adverse effects─through altered nutrient cycling─have "knock-on" impacts on biogeochemical cycles and greenhouse gases. Consequently, these impacts affect provisioning and regulating ecosystem services. Our citation network analyses (CNA) further demonstrate dire effects of MP and PL on all trophic levels, thereby unsettling ecosystem stability and services. CNA points to several emerging nodes indicating combined toxicity of MP, PL, and their associated hazards on phytoplankton. Taken together, our study shows that ecotoxicity of plastic particles and their leachates have placed primary producers and some aquatic ecosystems in peril.}, }
@article {pmid36533929, year = {2023}, author = {Rojas, CA and Holekamp, KE and Viladomat Jasso, M and Souza, V and Eisen, JA and Theis, KR}, title = {Taxonomic, Genomic, and Functional Variation in the Gut Microbiomes of Wild Spotted Hyenas Across 2 Decades of Study.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0096522}, pmid = {36533929}, issn = {2379-5077}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Hyaenidae/genetics ; RNA, Ribosomal, 16S/genetics ; *Carnivora/genetics ; Metagenomics ; }, abstract = {The gut microbiome provides vital functions for mammalian hosts, yet research on its variability and function across adult life spans and multiple generations is limited in large mammalian carnivores. Here, we used 16S rRNA gene and metagenomic high-throughput sequencing to profile the bacterial taxonomic composition, genomic diversity, and metabolic function of fecal samples collected from 12 wild spotted hyenas (Crocuta crocuta) residing in the Masai Mara National Reserve, Kenya, over a 23-year period spanning three generations. The metagenomic data came from four of these hyenas and spanned two 2-year periods. With these data, we determined the extent to which host factors predicted variation in the gut microbiome and identified the core microbes present in the guts of hyenas. We also investigated novel genomic diversity in the mammalian gut by reporting the first metagenome-assembled genomes (MAGs) for hyenas. We found that gut microbiome taxonomic composition varied temporally, but despite this, a core set of 14 bacterial genera were identified. The strongest predictors of the microbiome were host identity and age, suggesting that hyenas possess individualized microbiomes and that these may change with age during adulthood. The gut microbiome functional profiles of the four adult hyenas were also individual specific and were associated with prey abundance, indicating that the functions of the gut microbiome vary with host diet. We recovered 149 high-quality MAGs from the hyenas' guts; some MAGs were classified as taxa previously reported for other carnivores, but many were novel and lacked species-level matches to genomes in existing reference databases. IMPORTANCE There is a gap in knowledge regarding the genomic diversity and variation of the gut microbiome across a host's life span and across multiple generations of hosts in wild mammals. Using two types of sequencing approaches, we found that although gut microbiomes were individualized and temporally variable among hyenas, they correlated similarly to large-scale changes in the ecological conditions experienced by their hosts. We also recovered 149 high-quality MAGs from the hyena gut, greatly expanding the microbial genome repertoire known for hyenas, carnivores, and wild mammals in general. Some MAGs came from genera abundant in the gastrointestinal tracts of canid species and other carnivores, but over 80% of MAGs were novel and from species not previously represented in genome databases. Collectively, our novel body of work illustrates the importance of surveying the gut microbiome of nonmodel wild hosts, using multiple sequencing methods and computational approaches and at distinct scales of analysis.}, }
@article {pmid36533921, year = {2023}, author = {Graf, F and Zehentner, B and Fellner, L and Scherer, S and Neuhaus, K}, title = {Three Novel Antisense Overlapping Genes in E. coli O157:H7 EDL933.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0235122}, pmid = {36533921}, issn = {2165-0497}, mesh = {*Escherichia coli O157/genetics/metabolism ; *Escherichia coli Proteins/genetics ; Base Sequence ; Genes, Overlapping ; Ribosome Profiling ; }, abstract = {The abundance of long overlapping genes in prokaryotic genomes is likely to be significantly underestimated. To date, only a few examples of such genes are fully established. Using RNA sequencing and ribosome profiling, we found expression of novel overlapping open reading frames in Escherichia coli O157:H7 EDL933 (EHEC). Indeed, the overlapping candidate genes are equipped with typical structural elements required for transcription and translation, i.e., promoters, transcription start sites, as well as terminators, all of which were experimentally verified. Translationally arrested mutants, unable to produce the overlapping encoded protein, were found to have a growth disadvantage when grown competitively against the wild type. Thus, the phenotypes found imply biological functionality of the genes at the level of proteins produced. The addition of 3 more examples of prokaryotic overlapping genes to the currently limited, yet constantly growing pool of such genes emphasizes the underestimated coding capacity of bacterial genomes. IMPORTANCE The abundance of long overlapping genes in prokaryotic genomes is likely to be significantly underestimated, since such genes are not allowed in genome annotations. However, ribosome profiling catches mRNA in the moment of being template for protein production. Using this technique and subsequent experiments, we verified 3 novel overlapping genes encoded in antisense of known genes. This adds more examples of prokaryotic overlapping genes to the currently limited, yet constantly growing pool of such genes.}, }
@article {pmid36533904, year = {2023}, author = {Timmis, K and Berry, D and Bonfante, P and Coleman, M and Cunliffe, M and Danchin, A and Galperin, M and Huang, W and Lopez, P and Stewart, F and Wood, T}, title = {Juan Luis Ramos: An exceptional Editor of Environmental Microbiology.}, journal = {Environmental microbiology}, volume = {25}, number = {3}, pages = {595-596}, doi = {10.1111/1462-2920.16315}, pmid = {36533904}, issn = {1462-2920}, }
@article {pmid36530964, year = {2022}, author = {Inomura, K and Deutsch, C and Jahn, O and Dutkiewicz, S and Follows, MJ}, title = {Global patterns in marine organic matter stoichiometry driven by phytoplankton ecophysiology.}, journal = {Nature geoscience}, volume = {15}, number = {12}, pages = {1034-1040}, pmid = {36530964}, issn = {1752-0894}, abstract = {The proportion of major elements in marine organic matter links cellular processes to global nutrient, oxygen and carbon cycles. Differences in the C:N:P ratios of organic matter have been observed between ocean biomes, but these patterns have yet to be quantified from the underlying small-scale physiological and ecological processes. Here we use an ecosystem model that includes adaptive resource allocation within and between ecologically distinct plankton size classes to attribute the causes of global patterns in the C:N:P ratios. We find that patterns of N:C variation are largely driven by common physiological adjustment strategies across all phytoplankton, while patterns of N:P are driven by ecological selection for taxonomic groups with different phosphorus storage capacities. Although N:C varies widely due to cellular adjustment to light and nutrients, its latitudinal gradient is modest because of depth-dependent trade-offs between nutrient and light availability. Strong latitudinal variation in N:P reflects an ecological balance favouring small plankton with lower P storage capacity in the subtropics, and larger eukaryotes with a higher cellular P storage capacity in nutrient-rich high latitudes. A weaker N:P difference between southern and northern hemispheres, and between the Atlantic and Pacific oceans, reflects differences in phosphate available for cellular storage. Despite simulating only two phytoplankton size classes, the emergent global variability of elemental ratios resembles that of all measured species, suggesting that the range of growth conditions and ecological selection sustain the observed diversity of stoichiometry among phytoplankton.}, }
@article {pmid36530180, year = {2023}, author = {Messadi, N and Mechmeche, M and Setti, K and Tizemmour, Z and Hamdi, M and Kachouri, F}, title = {Optimization of Extraction Parameters and Characterization of Tunisian Date Extract: A Scientific Approach Toward Their Utilization.}, journal = {Sugar tech : an international journal of sugar crops &amp; related industries}, volume = {25}, number = {2}, pages = {460-472}, pmid = {36530180}, issn = {0972-1525}, abstract = {UNLABELLED: The response surface methodology (RSM) was used in order to select the extraction conditions of extract from Kentichi date powder; a by-product of the date-processing process. Powder/solvent ratio, extraction temperature, and extraction time all had an impact on sugar yield, and these model factors have quadratic effects influencing sugar yield. Optimal extraction was obtained with 300 g/L powder/solvent ratio, 32.7 °C extraction temperature, and 2.1 h extraction time. Under these conditions, Kentichi date powder's (KDP) sugar yield was 77.1%, which was close to the predicted value of the model (80.50%). The results of Kentichi date powder extract (KDPE) showed that the total sugar content is 160.09 g/L. However, the protein content is 10.31 g/L with a majority of the essential amino acids (essentially glutamic acid (28.39 mg/L) and aspartic acid (9.65 mg/L)). The determination of antioxidant activity of KDPE showed a high activity (DPPH IC50 = 4.8 mg/mL, ABTS IC50 = 3 mg/mL, FRAP = 4.70 μmol AAE/mL and, TAA = 18.04 μmol Fe(II)/mL). The results show also that the freeze-drying technique has a lot of potential for producing powder from KDPE with many desirable properties. The findings indicate that KDPE with a high nutritional value could be used as a component for the formulation of functional foods.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12355-022-01223-2.}, }
@article {pmid36529834, year = {2023}, author = {Kormas, K and Nikouli, E and Kousteni, V and Damalas, D}, title = {Midgut Bacterial Microbiota of 12 Fish Species from a Marine Protected Area in the Aegean Sea (Greece).}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1405-1415}, pmid = {36529834}, issn = {1432-184X}, mesh = {Animals ; Greece ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Fishes ; }, abstract = {Fish microbiome science is progressing fast, but it is biased toward farmed or laboratory fish species against natural fish populations, which remain considerably underinvestigated. We analyzed the midgut bacterial microbiota of 45 specimens of 12 fish species collected from the Gyaros Island marine protected area (Aegean Sea, Greece). The species belong to seven taxonomic families and are either herbivores or omnivores. Mucosa midgut bacterial diversity was assessed by amplicon metabarcoding of the 16S rRNA V3-V4 gene region. A total of 854 operational taxonomic units (OTUs) were identified. In each fish species, between 2 and 18 OTUs dominated with cumulative relative abundance ≥ 70%. Most of the dominating bacterial taxa have been reported to occur both in wild and farmed fish populations. The midgut bacterial communities were different among the 12 fish species, except for Pagrus pagrus and Pagellus erythrinus, which belong to the Sparidae family. No differentiation of the midgut bacterial microbiota was found based on feeding habits, i.e., omnivorous vs. carnivorous. Comparing wild and farmed P. pagrus midgut bacterial microbiota revealed considerable variation between them. Our results expand the gut microbiota of wild fish and support the host species effect as the more likely factor shaping intestinal bacterial microbiota.}, }
@article {pmid36528730, year = {2023}, author = {Bizic, M and Brad, T and Ionescu, D and Barbu-Tudoran, L and Zoccarato, L and Aerts, JW and Contarini, PE and Gros, O and Volland, JM and Popa, R and Ody, J and Vellone, D and Flot, JF and Tighe, S and Sarbu, SM}, title = {Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species.}, journal = {The ISME journal}, volume = {17}, number = {3}, pages = {340-353}, pmid = {36528730}, issn = {1751-7370}, mesh = {*Caves/chemistry ; Sulfur/metabolism ; *Epsilonproteobacteria/metabolism ; Romania ; Phylogeny ; }, abstract = {Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O2 (~7%). The cave's surface-water microbial community is dominated by bacteria we identified as Thiovulum. We show that this strain, and others from subsurface environments, are phylogenetically distinct from marine Thiovulum. We assembled a closed genome of the Movile strain and confirmed its metabolism using RNAseq. We compared the genome of this strain and one we assembled from public data from the sulfidic Frasassi caves to four marine genomes, including Candidatus Thiovulum karukerense and Ca. T. imperiosus, whose genomes we sequenced. Despite great spatial and temporal separation, the genomes of the Movile and Frasassi Thiovulum were highly similar, differing greatly from the very diverse marine strains. We concluded that cave Thiovulum represent a new species, named here Candidatus Thiovulum stygium. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O2 and NO3[-] as electron acceptors, the latter likely via dissimilatory nitrate reduction to ammonia. Thus, Thiovulum is likely important to both S and N cycles in sulfidic caves. Electron microscopy analysis suggests that at least some of the short peritrichous structures typical of Thiovulum are type IV pili, for which genes were found in all strains. These pili may play a role in veil formation, by connecting adjacent cells, and in the motility of these exceptionally fast swimmers.}, }
@article {pmid36528203, year = {2023}, author = {Jaiswal, S and Singh, DK and Shukla, P}, title = {Degradation effectiveness of hexachlorohexane (ϒ-HCH) by bacterial isolate Bacillus cereus SJPS-2, its gene annotation for bioremediation and comparison with Pseudomonas putida KT2440.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {318}, number = {}, pages = {120867}, doi = {10.1016/j.envpol.2022.120867}, pmid = {36528203}, issn = {1873-6424}, mesh = {*Hexachlorocyclohexane/metabolism ; Biodegradation, Environmental ; *Pseudomonas putida/genetics ; Bacillus cereus/genetics ; Molecular Sequence Annotation ; }, abstract = {The contamination of Hexachlorohexane (Lindane) in soil and water has toxic effects due to its persistent nature. In our study, an indigenous HCH (gamma isomer) degrading bacterium viz Bacillus cereus SJPS-2 was isolated from Yamuna river water using enrichment culture method. The growth curve indicated that Bacillus cereus SJPS-2 was able to degrade ϒ-HCH effectively with 80.98% degradation. Further, process was improved by using immobilization using alginate beads which showed enhanced degradation (89.34%). Interestingly, in presence of fructose, the ϒ-HCH degradation was up to 79.24% with exponential growth curve whereas the degradation was only 5.61% in presence of glucose revealing diauxic growth curve. Furthermore, The FTIR results confirmed the potential lindane degradation capability of Bacillus cereus SJPS-2 and the bonds were recorded at wavelengths viz. 2900-2500 cm-[1], 3300-2800 cm-[1] and 785-540 cm-[1]. Similarity, the GC studies also reconfirmed the degradation potential with retention time (RT) of ethyl acetate and lindane was 2.12 and 11.0 respectively. Further, we studied the metabolic pathway involved for lindane utilization in Bacillus cereus using KEGG-KASS and functional gene annotation through Rapid Annotation using Subsystems Technology (RAST) resulted in the annotation of the lin genes (lin A, lin B, lin C, lin X, lin D, lin E) and respective encoding enzymes. The comparative ϒ-HCH degradation potential of B. cereus and P. putida KT2440 was also evaluated. The island viewer showed the different colors on circular genome indicate the coordinates of genomic islands resulted with some common genomic islands (GEIs) between both bacteria indicating the possibility of horizontal gene transfer at contaminated site or natural environment. These genomic islands (GEIs) contribute in the rearrangement genetic material or to evolve bacteria in stress conditions, as a result the metabolic pathways evolve by formation of catabolic genes. This study establishes the potential of Bacillus cereus SJPS-2 for effectual ϒ-HCH degradation.}, }
@article {pmid36524228, year = {2022}, author = {Othieno, J and Njagi, O and Masika, S and Apamaku, M and Tenge, E and Mwasa, B and Kimondo, P and Gardner, E and Von Dobschuetz, S and Muriira, J and Adul, B and Mwongela, L and Hambe, HA and Nyariki, T and Fasina, FO}, title = {Knowledge, attitudes, and practices on camel respiratory diseases and conditions in Garissa and Isiolo, Kenya.}, journal = {Frontiers in veterinary science}, volume = {9}, number = {}, pages = {1022146}, pmid = {36524228}, issn = {2297-1769}, abstract = {BACKGROUND: Livestock farmers' attitudes, practices, and behaviors are major factors in infection prevention and control of animal diseases. Kenya has the fourth largest global camel population, and the industry has grown over the last two decades, transforming beyond the traditional camel-keeping areas to include peri-urban camel trade and value chain growth. The dromedary camel is resilient, and it is a preferred species in the arid and semi-arid areas (ASALs) of Kenya. However, it still faces many health and production challenges; to identify infection drivers and risky behaviors for camel respiratory illnesses and conditions in Kenya, we conducted a knowledge, attitudes, and practices (KAP) survey.<br><br>METHOD: Using a set of tools (questionnaires, key informant interviews, and focus group discussions), we interviewed camel owners, herders, agro-veterinary outlets, and other relevant value chain stakeholders in Garissa and Isiolo counties (n = 85). Data were analyzed using descriptive and analytic statistics.<br><br>RESULTS: Most camel owners/herders are male and most are relatively uneducated (85.5%). The camels were used primarily for milk and meat production, income generation, and transport. Larger herd sizes (>30 camels) and owner/herder's lack of formal education are risk factors for owner-reported respiratory illnesses in camels. Major clinical signs of respiratory conditions were coughing (85.7%), nasal discharge (59.7%), and fever (23.4%). Diseases, lack of feeds, theft, and marketing challenges are the major constraints to camel production in Kenya. Owners-herders use drugs indiscriminately and this may contribute to antimicrobial resistance challenges.<br><br>CONCLUSION: Practitioners in the camel value chain want more commitment from the government and animal health officials on support services and access to veterinary services. Watering points, grazing areas, and marketing points are the primary areas for congregating camels and have a significant potential for disease spread. Kenya camels have a massive capacity for rural and ASALs' livelihoods transformation but the identified health challenges, and other issues must be addressed. Further studies on the Kenyan camels' respiratory microbial ecology are important to understand microbial risks and reduce the burden of zoonotic infections. Intensification of risk communication and community engagement, and messaging targeted at behavior change interventions should be directed at camel value chain actors.}, }
@article {pmid36523823, year = {2022}, author = {Bernasconi, R and Lund, MA and Blanchette, ML}, title = {Non-charismatic waterbodies and ecosystem disservices: Mine pit lakes are underrepresented in the literature.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1063594}, pmid = {36523823}, issn = {1664-302X}, abstract = {Pit lakes are one of the greatest legacies of open-cut mining. Despite the potential hazards of these lakes, they represent newly formed ecosystems with great scientific and ecological potential. Although thousands of pit lakes occur on every inhabited continent, with more being created, the microbial ecology of pit lakes is relatively under-researched. We evaluated the current state of microbial research in pit lakes by performing a Web of Science search and creating a literature database. Study lakes were categorized according to location and water quality (pH and conductivity) which is a key community and environmental concern. Research technology employed in the study was also categorized. We compared research effort in lakes, rivers, and streams which are the more "charismatic" inland aquatic ecosystems. Pit lake publications on microbes from 1987 to 2022 (n = 128) were underrepresented in the literature relative to rivers and streams (n = 321) and natural lakes (n = 948). Of the 128 pit lake publications, 28 were within the field of geochemistry using indirect measures of microbial activity. Most pit lake microbial research was conducted in a few acidic lakes in Germany due to social pressure for remediation and government initiative. Relatively few studies have capitalized on emerging technology. Pit lake microbial research likely lags other more charismatic ecosystems given that they are viewed as performing "ecosystem disservices," but this is socially complex and requires further research. Improving understanding of microbial dynamics in pit lakes will allow scientists to deliver safer pit lakes to communities.}, }
@article {pmid36523636, year = {2022}, author = {Morales, C and Rojas, G and Rebolledo, C and Rojas-Herrera, M and Arias-Carrasco, R and Cuadros-Orellana, S and Maracaja-Coutinho, V and Saavedra, K and Leal, P and Lanas, F and Salazar, LA and Saavedra, N}, title = {Characterization of microbial communities from gut microbiota of hypercholesterolemic and control subjects.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {943609}, pmid = {36523636}, issn = {2235-2988}, mesh = {Adult ; Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Microbiota ; Cholesterol ; }, abstract = {INTRODUCTION: In recent years, several studies have evidenced the importance of the microbiome to host physiology as metabolism regulator, along with its potential role in triggering various diseases. In this study, we analyzed the gut microbiota in hypercholesterolemic (cases) and normocholesterolemic (controls) individuals to identify characteristic microbial signature for each condition.<br><br>METHODS: Stool samples were obtained from 57 adult volunteers (27 hypercholesterolemic and 30 controls). The taxonomic profiling of microbial communities was performed using high-throughput sequencing of 16S rRNA V3-V4 amplicons, followed by data analysis using Quantitative Insights Into Microbial Ecology 2 (QIIME2) and linear discriminant analysis (LDA) effect size (LEfSe).<br><br>RESULTS: Significant differences were observed in weight, height, body mass index (BMI) and serum levels of triglycerides, total cholesterol and low-density lipoprotein cholesterol (LDL-C) between the groups (p<0.05). LEfSe showed differentially abundant prokaryotic taxa (&#x3b1;=0.05, LDA score > 2.0) in the group of hypercholesterolemic individuals (Methanosphaera, Rothia, Chromatiales, Clostridiales, Bacillaceae and Coriobacteriaceae) and controls (Faecalibacterium, Victivallis and Selenomonas) at various taxonomic levels. In addition, through the application of Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2), the predominance of pathways related to biosynthesis in hypercholesterolemic patients was established, compared to controls in which degradation pathways were predominant. Finally, in the analysis of co-occurrence networks, it was possible to identify associations between the microorganisms present in both studied groups.<br><br>CONCLUSION: Our results point out to unique microbial signatures, which likely play a role on the cholesterol metabolism in the studied population.}, }
@article {pmid36523515, year = {2022}, author = {Thongthaisong, P and Kasada, M and Grossart, HP and Wollrab, S}, title = {Critical role of parasite-mediated energy pathway on community response to nutrient enrichment.}, journal = {Ecology and evolution}, volume = {12}, number = {12}, pages = {e9622}, pmid = {36523515}, issn = {2045-7758}, abstract = {Parasites form an integral part of food webs, however, they are often ignored in classic food web theory or limited to the investigation of trophic transmission pathways. Specifically, direct consumption of parasites by nonhost predators is rarely considered, while it can contribute substantially to energy flow in food webs. In aquatic systems, chytrids constitute a major group of fungal parasites whose free-living infective stages (zoospores) form a highly nutritional food source to zooplankton. Thereby, the consumption of zoospores can create an energy pathway from otherwise inedible phytoplankton to zooplankton ("mycoloop"). This parasite-mediated energy pathway might be of special importance during phytoplankton blooms dominated by inedible or toxic primary producers like cyanobacteria, which are on the rise with eutrophication and global warming. We theoretically investigated community dynamics and energy transfer in a food web consisting of an edible nonhost and an inedible host phytoplankton species, a parasitic fungus, and a zooplankton species grazing on edible phytoplankton and fungi. Food web dynamics were investigated along a nutrient gradient contrasting nonadaptive zooplankton species representative for filter feeders like cladocerans and zooplankton with the ability to actively adapt their feeding preferences like many copepod species. Overall, the importance of the mycoloop for zooplankton increases with nutrient availability. This increase is smooth for nonadaptive consumers. For adaptive consumers, we observe an abrupt shift from an almost exclusive preference for edible phytoplankton at low nutrient levels to a strong preference for parasitic fungi at high nutrient levels. The model predicts that parasitic fungi could contribute up to 50% of the zooplankton diet in nutrient-rich environments, which agrees with empirical observations on zooplankton gut content from eutrophic systems during blooms of inedible diatoms or cyanobacteria. Our findings highlight the role of parasite-mediated energy pathways for predictions of energy flow and community composition under current and future environmental change.}, }
@article {pmid36523400, year = {2022}, author = {Upadhyay, V and Suryawanshi, R and Tasoff, P and McCavitt-Malvido, M and Kumar, GR and Murray, VW and Noecker, C and Bisanz, JE and Hswen, Y and Ha, C and Sreekumar, B and Chen, IP and Lynch, SV and Ott, M and Lee, S and Turnbaugh, PJ}, title = {Mild SARS-CoV-2 infection results in long-lasting microbiota instability.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2022.12.07.519508}, pmid = {36523400}, issn = {2692-8205}, support = {T32 AI060537/AI/NIAID NIH HHS/United States ; }, abstract = {UNLABELLED: Viruses targeting mammalian cells can indirectly alter the gut microbiota, potentially compounding their phenotypic effects. Multiple studies have observed a disrupted gut microbiota in severe cases of SARS-CoV-2 infection that require hospitalization. Yet, despite demographic shifts in disease severity resulting in a large and continuing burden of non-hospitalized infections, we still know very little about the impact of mild SARS-CoV-2 infection on the gut microbiota in the outpatient setting. To address this knowledge gap, we longitudinally sampled 14 SARS-CoV-2 positive subjects who remained outpatient and 4 household controls. SARS-CoV-2 cases exhibited a significantly less stable gut microbiota relative to controls, as long as 154 days after their positive test. These results were confirmed and extended in the K18-hACE2 mouse model, which is susceptible to SARS-CoV-2 infection. All of the tested SARS-CoV-2 variants significantly disrupted the mouse gut microbiota, including USA-WA1/2020 (the original variant detected in the United States), Delta, and Omicron. Surprisingly, despite the fact that the Omicron variant caused the least severe symptoms in mice, it destabilized the gut microbiota and led to a significant depletion in Akkermansia muciniphila . Furthermore, exposure of wild-type C57BL/6J mice to SARS-CoV-2 disrupted the gut microbiota in the absence of severe lung pathology.<br><br>IMPORTANCE: Taken together, our results demonstrate that even mild cases of SARS-CoV-2 can disrupt gut microbial ecology. Our findings in non-hospitalized individuals are consistent with studies of hospitalized patients, in that reproducible shifts in gut microbial taxonomic abundance in response to SARS-CoV-2 have been difficult to identify. Instead, we report a long-lasting instability in the gut microbiota. Surprisingly, our mouse experiments revealed an impact of the Omicron variant, despite producing the least severe symptoms in genetically susceptible mice, suggesting that despite the continued evolution of SARS-CoV-2 it has retained its ability to perturb the intestinal mucosa. These results will hopefully renew efforts to study the mechanisms through which Omicron and future SARS-CoV-2 variants alter gastrointestinal physiology, while also considering the potentially broad consequences of SARS-CoV-2-induced microbiota instability for host health and disease.}, }
@article {pmid36521745, year = {2023}, author = {Araujo, ASF and Jia, X and Miranda, ARL and Pereira, APA and Melo, VMM and Rocha, SMB and Costa, RM and Saraiva, TCDS and Mendes, LW and Salles, JF}, title = {Changes in the bacterial rare biosphere after permanent application of composted tannery sludge in a tropical soil.}, journal = {Chemosphere}, volume = {313}, number = {}, pages = {137487}, doi = {10.1016/j.chemosphere.2022.137487}, pmid = {36521745}, issn = {1879-1298}, mesh = {*Soil/chemistry ; Sewage/chemistry ; Soil Microbiology ; Bacteria/genetics ; *Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {Composted tannery sludge (CTS) promotes shifts in soil chemical properties, affecting microbial communities. Although the effect of CTS application on the bacterial community has been studied, it is unclear whether this impact discriminates between the dominant and rare species. This present study investigated how the dominant and rare bacterial communities respond over time to different concentrations of CTS application (0, 2.5, 5, 10, and 20 tons/ha) for 180 days. The richness of operational taxonomic units (OTU) was 30-fold higher in the rare than in the dominant biosphere. While some phyla shifted their relative abundance differently in the dominant and rare biosphere, some genera increased their relative abundance under higher CTS concentrations, such as Nocardioides (∼100%), Rubrobacter (∼300%), and Nordella (∼400%). Undominated processes largely governed the dominant biosphere (76.97%), followed by homogeneous (12.51%) and variable (8.03%) selection, and to a lesser extent, the dispersal limitation (2.48%). The rare biosphere was driven by the CTS application as evidenced by the exclusively homogeneous selection (100%). This study showed that the rare biosphere was more sensitive to changes in soil chemical parameters due to CTS application, which evidences the importance explore this portion of the bacterial community for its biotechnological use in contaminated soils.}, }
@article {pmid36520668, year = {2022}, author = {Ibberson, CB and Barraza, JP and Holmes, AL and Cao, P and Whiteley, M}, title = {Precise spatial structure impacts antimicrobial susceptibility of S. aureus in polymicrobial wound infections.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {51}, pages = {e2212340119}, pmid = {36520668}, issn = {1091-6490}, support = {K22 AI155927/AI/NIAID NIH HHS/United States ; R01 GM116547/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Mice ; Animals ; Staphylococcus aureus ; *Methicillin-Resistant Staphylococcus aureus ; Pseudomonas aeruginosa ; *Wound Infection/drug therapy ; *Staphylococcal Infections/drug therapy ; Anti-Bacterial Agents/pharmacology ; *Coinfection ; *Pseudomonas Infections/drug therapy ; Biofilms ; }, abstract = {A hallmark of microbial ecology is that interactions between members of a community shape community function. This includes microbial communities in human infections, such as chronic wounds, where interactions can result in more severe diseases. Staphylococcus aureus is the most common organism isolated from human chronic wound infections and has been shown to have both cooperative and competitive interactions with Pseudomonas aeruginosa. Still, despite considerable study, most interactions between these microbes have been characterized using in vitro well-mixed systems, which do not recapitulate the infection environment. Here, we characterized interactions between S. aureus and P. aeruginosa in chronic murine wounds, focusing on the role that both macro- and micro-scale spatial structures play in disease. We discovered that S. aureus and P. aeruginosa coexist at high cell densities in murine wounds. High-resolution imaging revealed that these microbes establish a patchy distribution, only occupying 5 to 25% of the wound volume. Using a quantitative framework, we identified a precise spatial structure at both the macro (mm)- and micro (µm)-scales, which was largely mediated by P. aeruginosa production of the antimicrobial 2-heptyl-4-hydroxyquinoline N-oxide, while the antimicrobial pyocyanin had no impact. Finally, we discovered that this precise spatial structure enhances S. aureus tolerance to aminoglycoside antibiotics but not vancomycin. Our results provide mechanistic insights into the biogeography of S. aureus and P. aeruginosa coinfected wounds and implicate spatial structure as a key determinant of antimicrobial tolerance in wound infections.}, }
@article {pmid36520387, year = {2023}, author = {Melayah, D and Bontemps, Z and Bruto, M and Nguyen, A and Oger, P and Hugoni, M}, title = {Metabarcoding of the Three Domains of Life in Aquatic Saline Ecosystems.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2605}, number = {}, pages = {17-35}, pmid = {36520387}, issn = {1940-6029}, mesh = {*Ecosystem ; *Archaea/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Biodiversity ; }, abstract = {High-throughput amplicon sequencing, known as metabarcoding, is a powerful technique to decipher exhaustive microbial diversity considering specific gene markers. While most of the studies investigating ecosystem functioning through microbial diversity targeted only one domain of life, either bacteria, or archaea or microeukaryotes, the remaining challenge in microbial ecology is to uncover the integrated view of microbial diversity occurring in ecosystems. Indeed, interactions occurring between the different microbial counterparts are now recognized having a great impact on stability and resilience of ecosystems. Here, we summarize protocols describing sampling, molecular, and simultaneous metabarcoding of bacteria, archaea, and microeukaryotes, as well as a bioinformatic pipeline allowing the study of exhaustive microbial diversity in natural aquatic saline samples.}, }
@article {pmid36520176, year = {2023}, author = {Martínez-Yáñez, MG and Silva-Ortega, CO and Hernández-Aranda, VA and Vallejo-Pérez, MR and Alcalá-Briseño, R and Vega-Manriquez, DX and Aguilar-Benítez, G and Jarquin-Gálvez, R and Lara-Ávila, JP}, title = {Analysis of Bacterial Microbiota of Aerated Compost Teas and Effect on Tomato Growth.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {959-972}, pmid = {36520176}, issn = {1432-184X}, support = {236066//CONACYT-SEP/ ; 806623//CONACYT/ ; }, mesh = {*Solanum lycopersicum ; *Composting ; Soil/chemistry ; Bacteria ; *Microbiota ; Nitrogen ; Soil Microbiology ; }, abstract = {Mature composts and their water-based extracts, known as aerated compost teas (ACTs), are biofertilizers that share bioactive effects like soil restoration and plant health promotion, widely used for sustainable agriculture. Bioactive effects of compost and ACTs could be associated with their physicochemical and biological characteristics, like carbon/nitrogen (C/N) ratio and microbiota structure respectively. In our study, we elaborated ACTs using mature homemade compost, wheat bran, and grass clippings, following the C/N ratio criteria. Irrigation of tomato plantlets with ACT whose C/N ratio was close to the expected C/N ratio for mature compost evidenced plant growth promotion. Exploring the bacterial microbiota of elaborated ACTs and origin compost revealed significant structural differences, including phyla involved in N mineralization and free-living N-fixing bacteria. Therefore, ACTs harbor diverse bacterial microbiota involved in the N cycle, which would enrich plant and soil bacterial communities at the taxonomic and functional levels. Furthermore, ACTs are considered a part of agroecological and circular economy approaches.}, }
@article {pmid36519160, year = {2022}, author = {Frąc, M and Hannula, ES and Bełka, M and Salles, JF and Jedryczka, M}, title = {Soil mycobiome in sustainable agriculture.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1033824}, pmid = {36519160}, issn = {1664-302X}, abstract = {The soil microbiome contributes to several ecosystem processes. It plays a key role in sustainable agriculture, horticulture and forestry. In contrast to the vast number of studies focusing on soil bacteria, the amount of research concerning soil fungal communities is limited. This is despite the fact that fungi play a crucial role in the cycling of matter and energy on Earth. Fungi constitute a significant part of the pathobiome of plants. Moreover, many of them are indispensable to plant health. This group includes mycorrhizal fungi, superparasites of pathogens, and generalists; they stabilize the soil mycobiome and play a key role in biogeochemical cycles. Several fungal species also contribute to soil bioremediation through their uptake of high amounts of contaminants from the environment. Moreover, fungal mycelia stretch below the ground like blood vessels in the human body, transferring water and nutrients to and from various plants. Recent advances in high-throughput sequencing combined with bioinformatic tools have facilitated detailed studies of the soil mycobiome. This review discusses the beneficial effects of soil mycobiomes and their interactions with other microbes and hosts in both healthy and unhealthy ecosystems. It may be argued that studying the soil mycobiome in such a fashion is an essential step in promoting sustainable and regenerative agriculture.}, }
@article {pmid36518175, year = {2022}, author = {Tang, Q and Huang, J and Zhang, S and Qin, H and Dong, Y and Wang, C and Li, D and Zhou, R}, title = {Characterizing the correlation between species/strain-specific starter with community assembly and metabolic regulation in Xiaoqu Pei.}, journal = {Current research in microbial sciences}, volume = {3}, number = {}, pages = {100170}, pmid = {36518175}, issn = {2666-5174}, abstract = {Studying the correlation between microbiome metabolism and flavor of fermented foods has garnered significant attention recently. Understanding the contribution of metabolic regulation and environmental stress to microecosystems is essential for exploring the mechanisms of action of traditional fermented foods. Here, the interaction between microbial communities was investigated using a Xiaoqu fermentation system, processed as "simulative microecosystems," in which starters were composed of Rhizopus-specific species/strains, Meyerozyma guilliermondii, and Bacillus licheniformis. The differences between community succession and metabolites were also explored. The results indicated that Rhizopus species/strain specificity affected starch hydrolyzation, resulting in a remarkable difference in the type and content of organic acids. This further suggested that the differences in nutrient abundance and organic acids influenced the colonization of microorganisms in the fermentation system, thereby influencing the succession of their communities. The fungi in the community predominantly originated from starters, whereas the bacteria were derived from both the environment and starter. Environmentally colonized microbes were the major contributors to the co-occurrence network and were strongly correlated with network. Regional characteristics of fermented foods were closely related to environmental microbes. These results contribute to the understanding of microbial assembly and flavor metabolism in fermented foods and provide strategies for quality regulation.}, }
@article {pmid36516408, year = {2023}, author = {Kasanke, CP and Zhao, Q and Alfaro, T and Walter, CA and Hobbie, SE and Cheeke, TE and Hofmockel, KS}, title = {Grassland ecosystem type drives AM fungal diversity and functional guild distribution in North American grasslands.}, journal = {Molecular ecology}, volume = {32}, number = {5}, pages = {1133-1148}, doi = {10.1111/mec.16823}, pmid = {36516408}, issn = {1365-294X}, support = {NSF-DEB-1042132//National Science Foundation/ ; NSF-DEB-1234162//National Science Foundation/ ; NSF-DEB-1556418//National Science Foundation/ ; NSF-DEB-1831944//National Science Foundation/ ; }, mesh = {*Mycorrhizae ; Ecosystem ; Grassland ; Soil Microbiology ; Soil/chemistry ; Plants/microbiology ; North America ; Plant Roots/microbiology ; Fungi/genetics ; }, abstract = {Nutrient exchange forms the basis of the ancient symbiotic relationship that occurs between most land plants and arbuscular mycorrhizal (AM) fungi. Plants provide carbon (C) to AM fungi and fungi provide the plant with nutrients such as nitrogen (N) and phosphorous (P). Nutrient addition can alter this symbiotic coupling in key ways, such as reducing AM fungal root colonization and changing the AM fungal community composition. However, environmental parameters that differentiate ecosystems and drive plant distribution patterns (e.g., pH, moisture), are also known to impact AM fungal communities. Identifying the relative contribution of environmental factors impacting AM fungal distribution patterns is important for predicting biogeochemical cycling patterns and plant-microbe relationships across ecosystems. To evaluate the relative impacts of local environmental conditions and long-term nutrient addition on AM fungal abundance and composition across grasslands, we studied experimental plots amended for 10 years with N, P, or N and P fertilizer in different grassland ecosystem types, including tallgrass prairie, montane, shortgrass prairie, and desert grasslands. Contrary to our hypothesis, we found ecosystem type, not nutrient treatment, was the main driver of AM fungal root colonization, diversity, and community composition, even when accounting for site-specific nutrient limitations. We identified several important environmental drivers of grassland ecosystem AM fungal distribution patterns, including aridity, mean annual temperature, root moisture, and soil pH. This work provides empirical evidence for niche partitioning strategies of AM fungal functional guilds and emphasizes the importance of long-term, large scale research projects to provide ecologically relevant context to nutrient addition studies.}, }
@article {pmid36516248, year = {2022}, author = {Diaz-Tang, G and Meneses, EM and Patel, K and Mirkin, S and García-Diéguez, L and Pajon, C and Barraza, I and Patel, V and Ghali, H and Tracey, AP and Blanar, CA and Lopatkin, AJ and Smith, RP}, title = {Growth productivity as a determinant of the inoculum effect for bactericidal antibiotics.}, journal = {Science advances}, volume = {8}, number = {50}, pages = {eadd0924}, pmid = {36516248}, issn = {2375-2548}, support = {R15 AI159902/AI/NIAID NIH HHS/United States ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Bacteria ; }, abstract = {Understanding the mechanisms by which populations of bacteria resist antibiotics has implications in evolution, microbial ecology, and public health. The inoculum effect (IE), where antibiotic efficacy declines as the density of a bacterial population increases, has been observed for multiple bacterial species and antibiotics. Several mechanisms to account for IE have been proposed, but most lack experimental evidence or cannot explain IE for multiple antibiotics. We show that growth productivity, the combined effect of growth and metabolism, can account for IE for multiple bactericidal antibiotics and bacterial species. Guided by flux balance analysis and whole-genome modeling, we show that the carbon source supplied in the growth medium determines growth productivity. If growth productivity is sufficiently high, IE is eliminated. Our results may lead to approaches to reduce IE in the clinic, help standardize the analysis of antibiotics, and further our understanding of how bacteria evolve resistance.}, }
@article {pmid36516075, year = {2023}, author = {Hu, A and Meng, F and Tanentzap, AJ and Jang, KS and Wang, J}, title = {Dark Matter Enhances Interactions within Both Microbes and Dissolved Organic Matter under Global Change.}, journal = {Environmental science &amp; technology}, volume = {57}, number = {1}, pages = {761-769}, doi = {10.1021/acs.est.2c05052}, pmid = {36516075}, issn = {1520-5851}, mesh = {*Ecosystem ; *Dissolved Organic Matter ; Bacteria/metabolism ; Climate ; China ; }, abstract = {There are vast but uncharacterized microbial taxa and chemical metabolites (that is, dark matter) across the Earth's ecosystems. A lack of knowledge about dark matter hinders a complete understanding of microbial ecology and biogeochemical cycles. Here, we examine sediment bacteria and dissolved organic matter (DOM) in 300 microcosms along experimental global change gradients in subtropical and subarctic climate zones of China and Norway, respectively. We develop an indicator to quantify the importance of dark matter by comparing co-occurrence network patterns with and without dark matter in bacterial or DOM assemblages. In both climate zones, dark matter constitutes approximately 30-56% of bacterial taxa and DOM metabolites and changes connectivity within bacterial and DOM assemblages by between -15.5 and +61.8%. Dark matter is generally more important for changing network connectivity within DOM assemblages than those of microbes, especially in the subtropical zone. However, the importance of dark matter along global change gradients is strongly correlated between bacteria and DOM and consistently increased toward higher primary productivity because of increasing temperatures and nutrient enrichment. Our findings highlight the importance of microbial and chemical dark matter for changing biogeochemical interactions under global change.}, }
@article {pmid36511762, year = {2023}, author = {Leite, MFA and Liu, B and Gómez Cardozo, E and Silva, HRE and Luz, RL and Muchavisoy, KHM and Moraes, FHR and Rousseau, GX and Kowalchuk, G and Gehring, C and Kuramae, EE}, title = {Microbiome resilience of Amazonian forests: Agroforest divergence to bacteria and secondary forest succession convergence to fungi.}, journal = {Global change biology}, volume = {29}, number = {5}, pages = {1314-1327}, pmid = {36511762}, issn = {1365-2486}, support = {A080/2013//Brazilian Council of Higher Education/ ; }, mesh = {*Ecosystem ; Forests ; Soil ; *Microbiota ; Fungi ; Bacteria ; Soil Microbiology ; }, abstract = {An alarming and increasing deforestation rate threatens Amazon tropical ecosystems and subsequent degradation due to frequent fires. Agroforestry systems (AFS) may offer a sustainable alternative, reportedly mimicking the plant-soil interactions of the natural mature forest (MF). However, the role of microbial community in tropical AFS remains largely unknown. This knowledge is crucial for evaluating the sustainability of AFS and practices given the key role of microbes in the aboveground-belowground interactions. The current study, by comparing different AFS and successions of secondary and MFs, showed that AFS fostered distinct groups of bacterial community, diverging from the MFs, likely a result of management practices while secondary forests converged to the same soil microbiome found in the MF, by favoring the same groups of fungi. Model simulations reveal that AFS would require profound changes in aboveground biomass and in soil factors to reach the same microbiome found in MFs. In summary, AFS practices did not result in ecosystems mimicking natural forest plant-soil interactions but rather reshaped the ecosystem to a completely different relation between aboveground biomass, soil abiotic properties, and the soil microbiome.}, }
@article {pmid36511717, year = {2023}, author = {Chen, Y and Lyu, Y and Zhang, J and Li, Q and Lyu, L and Zhou, Y and Kong, J and Zeng, X and Zhang, S and Li, J}, title = {Riddles of Lost City: Chemotrophic Prokaryotes Drives Carbon, Sulfur, and Nitrogen Cycling at an Extinct Cold Seep, South China Sea.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0333822}, pmid = {36511717}, issn = {2165-0497}, mesh = {*Geologic Sediments/microbiology ; *Ecosystem ; Carbon/metabolism ; Methane/metabolism ; Archaea/metabolism ; Bacteria/genetics/metabolism ; Hydrocarbons/metabolism ; Proteobacteria/metabolism ; Sulfur/metabolism ; Nitrogen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Deep-sea cold seeps are one of the most productive ecosystems that sustained by hydrocarbons carried by the fluid. Once the seep fluid ceases, the thriving autotrophic communities die out, terming as the extinct seep. But heterotrophic fauna can still survive even for thousands of years. The critical role of prokaryotes in active seeps are well defined, but their functions in extinct seeps are poorly understood to date. Here, we clarified the diversity, taxonomic specificity, interspecies correlation, and metabolic profiles of sediment prokaryotes at an extinct seep site of Haima cold seep, South China Sea. Alpha diversity of archaea significantly increased, while that of bacteria remained unchanged in extinct seep compared to active seep. However, archaea composition did not differ significantly at extinct seep from active or nonseep sites based on weighted-unifrac dissimilarity, while bacteria composition exhibited significant difference. Distribution of archaea and bacteria showed clear specificity to extinct seeps, indicating the unique life strategies here. Prokaryotes might live chemolithoautotrophically on cycling of inorganic carbon, sulfur, and nitrogen, or chemoorganotrophically on recycling of hydrocarbons. Notably, many of the extinct seep specific species and networked keystone lineages are classified as Proteobacteria. Regarding the functional diversity and metabolic flexibility of this clade, Proteobacteria is supposed to integrate the geochemical cycles and play a critical role in energy and resource supplement for microbiome in extinct seep. Collectively, our findings shed lights on the microbial ecology and functional diversity in extinct seeps, providing new understanding of biogeochemical cycling after fluid cessation. IMPORTANCE This research paper uncovered the potential mechanisms for microbiota mediated geochemical cycling in extinct cold seep, advancing our understanding in deep sea microbiology ecology.}, }
@article {pmid36511696, year = {2023}, author = {Higgins, O and Chueiri, A and O'Connor, L and Lahiff, S and Burke, L and Morris, D and Pfeifer, NM and Santamarina, BG and Berens, C and Menge, C and Caniça, M and Manageiro, V and Kisand, V and Hassan, MM and Gardner, B and van Vliet, AHM and La Ragione, RM and Gonzalez-Zorn, B and Smith, TJ}, title = {Portable Differential Detection of CTX-M ESBL Gene Variants, blaCTX-M-1 and blaCTX-M-15, from Escherichia coli Isolates and Animal Fecal Samples Using Loop-Primer Endonuclease Cleavage Loop-Mediated Isothermal Amplification.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0331622}, pmid = {36511696}, issn = {2165-0497}, mesh = {*Escherichia coli ; DNA ; beta-Lactamases/genetics ; Swine ; Humans ; *Escherichia coli Infections/diagnosis/veterinary/epidemiology ; Enterobacteriaceae/genetics ; Animals ; Molecular Diagnostic Techniques ; Anti-Bacterial Agents ; Nucleic Acid Amplification Techniques ; }, abstract = {Cefotaximase-Munich (CTX-M) extended-spectrum beta-lactamase (ESBL) enzymes produced by Enterobacteriaceae confer resistance to clinically relevant third-generation cephalosporins. CTX-M group 1 variants, CTX-M-1 and CTX-M-15, are the leading ESBL-producing Enterobacteriaceae associated with animal and human infection, respectively, and are an increasing antimicrobial resistance (AMR) global health concern. The blaCTX-M-1 and blaCTX-M-15 genes encoding these variants have an approximate nucleotide sequence similarity of 98.7%, making effective differential diagnostic monitoring difficult. Loop-primer endonuclease cleavage loop-mediated isothermal amplification (LEC-LAMP) enables rapid real-time multiplex pathogen detection with single-base specificity and portable on-site testing. We have developed an internally controlled multiplex CTX-M-1/15 LEC-LAMP assay for the differential detection of blaCTX-M-1 and blaCTX-M-15. Assay analytical specificity was established using a panel of human, animal, and environmental Escherichia coli isolates positive for blaCTX-M-1 (n = 18), blaCTX-M-15 (n = 35), and other closely related blaCTX-Ms (n = 38) from Ireland, Germany, and Portugal, with analytical sensitivity determined using probit regression analysis. Animal fecal sample testing using the CTX-M-1/15 LEC-LAMP assay in combination with a rapid DNA extraction protocol was carried out on porcine fecal samples previously confirmed to be PCR-positive for E. coli blaCTX-M. Portable instrumentation was used to further analyze each fecal sample and demonstrate the on-site testing capabilities of the LEC-LAMP assay with the rapid DNA extraction protocol. The CTX-M-1/15 LEC-LAMP assay demonstrated complete analytical specificity for the differential detection of both variants with sensitive low-level detection of 8.5 and 9.8 copies per reaction for blaCTX-M-1 and blaCTX-M-15, respectively, and E. coli blaCTX-M-1 was identified in all blaCTX-M positive porcine fecal samples tested. IMPORTANCE CTX-M ESBL-producing E. coli is an increasing AMR public health issue with the transmission between animals and humans via zoonotic pathogens now a major area of interest. Accurate and timely identification of ESBL-expressing E. coli CTX-M variants is essential for disease monitoring, targeted antibiotic treatment and infection control. This study details the first report of portable diagnostics technology for the rapid differential detection of CTX-M AMR markers blaCTX-M-1 and blaCTX-M-15, facilitating improved identification and surveillance of these closely related variants. Further application of this portable internally controlled multiplex CTX-M-1/15 LEC-LAMP assay will provide new information on the transmission and prevalence of these CTX-M ESBL alleles. Furthermore, this transferable diagnostic technology can be applied to other new and emerging relevant AMR markers of interest providing more efficient and specific portable pathogen detection for improved epidemiological surveillance.}, }
@article {pmid36511682, year = {2023}, author = {Teng, W and Liao, B and Chen, M and Shu, W}, title = {Genomic Legacies of Ancient Adaptation Illuminate GC-Content Evolution in Bacteria.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0214522}, pmid = {36511682}, issn = {2165-0497}, mesh = {Phylogeny ; Base Composition ; *Bacteria/genetics ; Mutation ; *Genomics ; Evolution, Molecular ; }, abstract = {Bacterial evolution is characterized by strong purifying selection as well as rapid adaptive evolution in changing environments. In this context, the genomic GC content (genomic GC) varies greatly but presents some level of phylogenetic stability, making it challenging to explain based on current hypotheses. To illuminate the evolutionary mechanisms of the genomic GC, we analyzed the base composition and functional inventory of 11,083 representative genomes. A phylogenetically constrained bimodal distribution of the genomic GC, which mainly originated from parallel divergences in the early evolution, was demonstrated. Such variation of the genomic GC can be well explained by DNA replication and repair (DRR), in which multiple pathways correlate with the genomic GC. Furthermore, the biased conservation of various stress-related genes, especially the DRR-related ones, implies distinct adaptive processes in the ancestral lineages of high- or low-GC clades which are likely induced by major environmental changes. Our findings support that the mutational biases resulting from these legacies of ancient adaptation have changed the course of adaptive evolution and generated great variation in the genomic GC. This highlights the importance of indirect effects of natural selection, which indicates a new model for bacterial evolution. IMPORTANCE GC content has been shown to be an important factor in microbial ecology and evolution, and the genomic GC of bacteria can be characterized by great intergenomic heterogeneity, high intragenomic homogeneity, and strong phylogenetic inertia, as well as being associated with the environment. Current hypotheses concerning direct selection or mutational biases cannot well explain these features simultaneously. Our findings of the genomic GC showing that ancient adaptations have transformed the DRR system and that the resulting mutational biases further contributed to a bimodal distribution of it offer a more reasonable scenario for the mechanism. This would imply that, when thinking about the evolution of life, diverse processes of adaptation exist, and combined effects of natural selection should be considered.}, }
@article {pmid36510309, year = {2022}, author = {Boekhorst, J and Venlet, N and Procházková, N and Hansen, ML and Lieberoth, CB and Bahl, MI and Lauritzen, L and Pedersen, O and Licht, TR and Kleerebezem, M and Roager, HM}, title = {Stool energy density is positively correlated to intestinal transit time and related to microbial enterotypes.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {223}, pmid = {36510309}, issn = {2049-2618}, mesh = {Adult ; Humans ; Feces/microbiology ; *Gastrointestinal Microbiome ; Bacteroides ; Prevotella ; *Microbiota ; }, abstract = {BACKGROUND: It has been hypothesised that the gut microbiota causally affects obesity via its capacity to extract energy from the diet. Yet, evidence elucidating the role of particular human microbial community structures and determinants of microbiota-dependent energy harvest is lacking.<br><br>RESULTS: Here, we investigated whether energy extraction from the diet in 85 overweight adults, estimated by dry stool energy density, was associated with intestinal transit time and variations in microbial community diversity and overall structure stratified as enterotypes. We hypothesised that a slower intestinal transit would allow for more energy extraction. However, opposite of what we expected, the stool energy density was positively associated with intestinal transit time. Stratifications into enterotypes showed that individuals with a Bacteroides enterotype (B-type) had significantly lower stool energy density, shorter intestinal transit times, and lower alpha-diversity compared to individuals with a Ruminococcaceae enterotype (R-type). The Prevotella (P-type) individuals appeared in between the B- and R-type. The differences in stool energy density between enterotypes were not explained by differences in habitual diet, intake of dietary fibre or faecal bacterial cell counts. However, the R-type individuals showed higher urinary and faecal levels of microbial-derived proteolytic metabolites compared to the B-type, suggesting increased colonic proteolysis in the R-type individuals. This could imply a less effective colonic energy extraction in the R-type individuals compared to the B-type individuals. Notably, the R-type had significantly lower body weight compared to the B-type.<br><br>CONCLUSIONS: Our findings suggest that gut microbial energy harvest is diversified among individuals by intestinal transit time and associated gut microbiome ecosystem variations. A better understanding of these associations could support the development of personalised nutrition and improved weight-loss strategies. Video Abstract.}, }
@article {pmid36509943, year = {2023}, author = {Li, W and Ma, ZS}, title = {The Upper Respiratory Tract Microbiome Network Impacted by SARS-CoV-2.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1428-1437}, pmid = {36509943}, issn = {1432-184X}, mesh = {Animals ; Humans ; SARS-CoV-2/genetics ; *COVID-19 ; *Chiroptera ; *Microbiota/genetics ; Bacteria/genetics ; Respiratory System ; }, abstract = {The microbiome of upper respiratory tract (URT) acts as a gatekeeper to respiratory health of the host. However, little is still known about the impacts of SARS-CoV-2 infection on the microbial species composition and co-occurrence correlations of the URT microbiome, especially the relationships between SARS-CoV-2 and other microbes. Here, we characterized the URT microbiome based on RNA metagenomic-sequencing datasets from 1737 nasopharyngeal samples collected from COVID-19 patients. The URT-microbiome network consisting of bacteria, archaea, and RNA viruses was built and analyzed from aspects of core/periphery species, cluster composition, and balance between positive and negative interactions. It is discovered that the URT microbiome in the COVID-19 patients is enriched with Enterobacteriaceae, a gut associated family containing many pathogens. These pathogens formed a dense cooperative guild that seemed to suppress beneficial microbes collectively. Besides bacteria and archaea, 72 eukaryotic RNA viruses were identified in the URT microbiome of COVID-19 patients. Only five of these viruses were present in more than 10% of all samples, including SARS-CoV-2 and a bat coronavirus (i.e., BatCoV BM48-31) not detected in humans by routine means. SARS-CoV-2 was inhibited by a cooperative alliance of 89 species, but seems to cooperate with BatCoV BM48-31 given their statistically significant, positive correlations. The presence of cooperative bat-coronavirus partner of SARS-CoV-2 (BatCoV BM48-31), which was previously discovered in bat but not in humans to the best of our knowledge, is puzzling and deserves further investigation given their obvious implications. Possible microbial translocation mechanism from gut to URT also deserves future studies.}, }
@article {pmid36506396, year = {2022}, author = {Daba, G and Berecha, G and Lievens, B and Hundera, K and Helsen, K and Honnay, O}, title = {Contrasting coffee leaf rust epidemics between forest coffee and semi-forest coffee agroforestry systems in SW-Ethiopia.}, journal = {Heliyon}, volume = {8}, number = {12}, pages = {e11892}, pmid = {36506396}, issn = {2405-8440}, abstract = {Ethiopian Arabica coffee is produced in different agroforestry systems which differ in forest management intensity. In forest coffee systems (FC), coffee shrubs grow naturally in the understory of Afromontane forests with little human intervention, whereas in semi-forest coffee systems (SFC) thinning of the canopy and removal of the understory is applied. Coffee leaf rust (CLR) disease is a growing concern for coffee agroforestry, but to what extent infection pressure is affected by management intensity is poorly known. Here we assessed CLR infection through time across FC and SFC systems in SW-Ethiopia. CLR infection was significantly higher for SFC, with a gradual reduction of this difference during the beginning of dry season (November) through main rainy season of (July). Our findings also demonstrated that CLR infections were significantly lower in the FC system as compared to SFC system in both years 2015/16 and 2020/21. The higher CLR infection was partly explained by lower crown cover and higher human impact. We expect that reduced wind speed and droplet penetration under closed canopies and reduced human-facilitated spore dispersal are the dominating mechanisms behind lower CLR infection in FC systems, yet lower coffee density in FC may also play a role. Overall, our results indicate that although higher management intensity still generally results in higher total yields per hectare, proportionally larger losses due to CLR infection can be expected. Therefore, introducing more coffee genetic diversity, screening resistant coffee varieties and increasing canopy cover in the SFC will mitigate the CLR disease pressure and guarantee the sustainability of higher yields of the system in the future. Also, lower yields in the FC will be rewarded through providing price premiums so that farmers instantly get a higher price for their lower yield, guaranteeing livelihoods.}, }
@article {pmid36504693, year = {2022}, author = {Amano, C and Zhao, Z and Sintes, E and Reinthaler, T and Stefanschitz, J and Kisadur, M and Utsumi, M and Herndl, GJ}, title = {Limited carbon cycling due to high-pressure effects on the deep-sea microbiome.}, journal = {Nature geoscience}, volume = {15}, number = {12}, pages = {1041-1047}, pmid = {36504693}, issn = {1752-0894}, support = {I 486/FWF_/Austrian Science Fund FWF/Austria ; P 28781/FWF_/Austrian Science Fund FWF/Austria ; P 35587/FWF_/Austrian Science Fund FWF/Austria ; Z 194/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Deep-sea microbial communities are exposed to high-pressure conditions, which has a variable impact on prokaryotes depending on whether they are piezophilic (that is, pressure-loving), piezotolerant or piezosensitive. While it has been suggested that elevated pressures lead to higher community-level metabolic rates, the response of these deep-sea microbial communities to the high-pressure conditions of the deep sea is poorly understood. Based on microbial activity measurements in the major oceanic basins using an in situ microbial incubator, we show that the bulk heterotrophic activity of prokaryotic communities becomes increasingly inhibited at higher hydrostatic pressure. At 4,000 m depth, the bulk heterotrophic prokaryotic activity under in situ hydrostatic pressure was about one-third of that measured in the same community at atmospheric pressure conditions. In the bathypelagic zone-between 1,000 and 4,000 m depth-~85% of the prokaryotic community was piezotolerant and ~5% of the prokaryotic community was piezophilic. Despite piezosensitive-like prokaryotes comprising only ~10% (mainly members of Bacteroidetes, Alteromonas) of the deep-sea prokaryotic community, the more than 100-fold metabolic activity increase of these piezosensitive prokaryotes upon depressurization leads to high apparent bulk metabolic activity. Overall, the heterotrophic prokaryotic activity in the deep sea is likely to be substantially lower than hitherto assumed, with major impacts on the oceanic carbon cycling.}, }
@article {pmid36503688, year = {2022}, author = {Delgado-Baquerizo, M and Hu, HW and Maestre, FT and Guerra, CA and Eisenhauer, N and Eldridge, DJ and Zhu, YG and Chen, QL and Trivedi, P and Du, S and Makhalanyane, TP and Verma, JP and Gozalo, B and Ochoa, V and Asensio, S and Wang, L and Zaady, E and Illán, JG and Siebe, C and Grebenc, T and Zhou, X and Liu, YR and Bamigboye, AR and Blanco-Pastor, JL and Duran, J and Rodríguez, A and Mamet, S and Alfaro, F and Abades, S and Teixido, AL and Peñaloza-Bojacá, GF and Molina-Montenegro, MA and Torres-Díaz, C and Perez, C and Gallardo, A and García-Velázquez, L and Hayes, PE and Neuhauser, S and He, JZ}, title = {The global distribution and environmental drivers of the soil antibiotic resistome.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {219}, pmid = {36503688}, issn = {2049-2618}, support = {Y 801/FWF_/Austrian Science Fund FWF/Austria ; CLIMIFUN//Horizon 2020/ ; MUSGONET LRA17\1193//British Ecological Society/ ; DP210100332//Australian Research Council/ ; }, mesh = {Humans ; *Soil ; *Anti-Bacterial Agents/pharmacology ; Ecology ; Phenotype ; }, abstract = {BACKGROUND: Little is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earth's largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and global patterns remain poorly described. Here, we analyzed 285 ARGs in soils from 1012 sites across all continents and created the first global atlas with the distributions of topsoil ARGs.<br><br>RESULTS: We show that ARGs peaked in high latitude cold and boreal forests. Climatic seasonality and mobile genetic elements, associated with the transmission of antibiotic resistance, were also key drivers of their global distribution. Dominant ARGs were mainly related to multidrug resistance genes and efflux pump machineries. We further pinpointed the global hotspots of the diversity and proportions of soil ARGs.<br><br>CONCLUSIONS: Together, our work provides the foundation for a better understanding of the ecology and global distribution of the environmental soil antibiotic resistome. Video Abstract.}, }
@article {pmid36503639, year = {2023}, author = {Hodžić, A and Dheilly, NM and Cabezas-Cruz, A and Berry, D}, title = {The helminth holobiont: a multidimensional host-parasite-microbiota interaction.}, journal = {Trends in parasitology}, volume = {39}, number = {2}, pages = {91-100}, doi = {10.1016/j.pt.2022.11.012}, pmid = {36503639}, issn = {1471-5007}, mesh = {Animals ; Humans ; *Parasites ; *Helminths/genetics ; *Microbiota ; *Helminthiasis/parasitology ; *Gastrointestinal Microbiome ; }, abstract = {Gastrointestinal helminths have developed multiple mechanisms by which they manipulate the host microbiome to make a favorable environment for their long-term survival. While the impact of helminth infections on vertebrate host immunity and its gut microbiota is relatively well studied, little is known about the structure and functioning of microbial populations supported by metazoan parasites. Here we argue that an integrated understanding of the helminth-associated microbiome and its role in the host disease pathogenesis may facilitate the discovery of specific microbial and/or genetic patterns critical for parasite biology and subsequently pave the way for the development of alternative control strategies against parasites and parasitic disease.}, }
@article {pmid36502425, year = {2023}, author = {Ye, F and Sun, Z and Moore, SS and Wu, J and Hong, Y and Wang, Y}, title = {Discrepant Effects of Flooding on Assembly Processes of Abundant and Rare Communities in Riparian Soils.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1164-1175}, pmid = {36502425}, issn = {1432-184X}, support = {51908145//National Natural Science Foundation of China/ ; 41977153//National Natural Science Foundation of China/ ; 2022A1515010828//Natural Science Foundation of Guangdong Province/ ; }, mesh = {*Ecosystem ; Soil ; Soil Microbiology ; Bacteria/genetics ; Archaea ; *Microbiota ; Carbon ; }, abstract = {Numerous rare species coexist with a few abundant species in microbial communities and together play an essential role in riparian ecosystems. Relatively little is understood, however, about the nature of assembly processes of these communities and how they respond to a fluctuating environment. In this study, drivers controlling the assembly of abundant and rare subcommunities for bacteria and archaea in a riparian zone were determined, and their resulting patterns on these processes were analyzed. Abundant and rare bacteria and archaea showed a consistent variation in the community structure along the riparian elevation gradient, which was closely associated with flooding frequency. The community assembly of abundant bacteria was not affected by any measured environmental variables, while soil moisture and ratio of submerged time to exposed time were the two most decisive factors determining rare bacterial community. Assembly of abundant archaeal community was also determined by these two factors, whereas rare archaea was significantly associated with soil carbon-nitrogen ratio and total carbon content. The assembly process of abundant and rare bacterial subcommunities was driven respectively by dispersal limitation and variable selection. Undominated processes and dispersal limitation dominated the assembly of abundant archaea, whereas homogeneous selection primarily driven rare archaea. Flooding may therefore play a crucial role in determining the community assembly processes by imposing disturbances and shaping soil niches. Overall, this study reveals the assembly patterns of abundant and rare communities in the riparian zone and provides further insight into the importance of their respective roles in maintaining a stable ecosystem during times of environmental perturbations.}, }
@article {pmid36500505, year = {2022}, author = {Ben Rejeb, I and Charfi, I and Baraketi, S and Hached, H and Gargouri, M}, title = {Bread Surplus: A Cumulative Waste or a Staple Material for High-Value Products?.}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {23}, pages = {}, pmid = {36500505}, issn = {1420-3049}, mesh = {*Refuse Disposal ; Bread/analysis ; Recycling/methods ; Food Handling ; Waste Disposal Facilities ; Waste Products/analysis ; }, abstract = {Food waste has been widely valorized in the past years in order to develop eco-friendly materials. Among others, bread waste is currently of increasing interest, as it is considered a huge global issue with serious environmental impacts and significant economic losses that have become even greater in the post-pandemic years due to an increase in cereal prices, which has led to higher production costs and bread prices. Owing to its richness in polysaccharides, bread waste has been previously studied for its physico-chemical characteristics and its numerous biotechnological applications. The present review highlights the re-use of bread waste and its valorization as a valuable resource by making value-added products through numerous technological processes to increase efficiency at all stages. Many research studies reporting several transformation methods of surplus bread into ethanol, lactic acid, succinic acid, biohydrogen, hydroxymethylfurfural, proteins and pigments, glucose-fructose syrup, aroma compounds, and enzymes are widely discussed. The wide variety of suggested applications for recycling bread waste provides significant insights into the role of technology development in potentially maximizing resource recovery and consequently contributing to environmental performance by reducing the amount of bread waste in landfills.}, }
@article {pmid36500302, year = {2022}, author = {Kuttithodi, AM and Nikhitha, D and Jacob, J and Narayanankutty, A and Mathews, M and Olatunji, OJ and Rajagopal, R and Alfarhan, A and Barcelo, D}, title = {Antioxidant, Antimicrobial, Cytotoxicity, and Larvicidal Activities of Selected Synthetic Bis-Chalcones.}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {23}, pages = {}, pmid = {36500302}, issn = {1420-3049}, mesh = {Animals ; Antioxidants/pharmacology/chemistry ; Microbial Sensitivity Tests ; *Chalcones/pharmacology ; Anthocyanins ; Plant Extracts/chemistry ; *Anti-Infective Agents/pharmacology ; Anti-Bacterial Agents/pharmacology/chemistry ; Escherichia coli ; }, abstract = {Plants are known to have numerous phytochemicals and other secondary metabolites with numerous pharmacological and biological properties. Among the various compounds, polyphenols, flavonoids, anthocyanins, alkaloids, and terpenoids are the predominant ones that have been explored for their biological potential. Among these, chalcones and bis-chalcones are less explored for their biological potential under in vitro experiments, cell culture models, and animal studies. In the present study, we evaluated six synthetic bis-chalcones that were different in terms of their aromatic cores, functional group substitution, and position of substitutions. The results indicated a strong antioxidant property in terms of DPPH and ABTS radical-scavenging potentials and ferric-reducing properties. In addition, compounds 1, 2, and 4 exhibited strong antibacterial activities against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Salmonella enteritidis. The disc diffusion assay values were indicative of the antibacterial properties of these compounds. Overall, the study indicated the antioxidant and antimicrobial properties of the compounds. Our preliminary studies point to the potential of this class of compounds for further in vivo investigation.}, }
@article {pmid36495359, year = {2023}, author = {Liu, W and Qiu, K and Xie, Y and Huang, Y and Wang, R and Li, H and Meng, W and He, Y and Li, Y and Li, H and Zhao, P and Yang, Y}, title = {High-Throughput Absolute Quantification Sequencing Reveals that a Combination of Leguminous Shrubs Is Effective in Driving Soil Bacterial Diversity During the Process of Desertification Reversal.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1145-1163}, pmid = {36495359}, issn = {1432-184X}, support = {2019BEB04011//Ningxia Key Research and Development Project/ ; [2019] 160//Ningxia High-Level Talent Innovation Program/ ; 42001095//National Natural Science Foundation of China/ ; 2020AAC03273//Ningxia Natural Science Foundation/ ; }, mesh = {*Ecosystem ; Soil/chemistry ; *Fabaceae ; RNA, Ribosomal, 16S/genetics ; Carbon/analysis ; Conservation of Natural Resources ; Bacteria/genetics ; China ; Phosphorus/analysis ; Potassium/analysis ; Soil Microbiology ; }, abstract = {Desertification leads to the extreme fragility of ecosystems and seriously threatens ecosystem functioning in desert areas. The planting of xerophytes, especially leguminous shrubs, is an effective and common means to reverse desertification. Soil microorganisms play a crucial role in nutrient cycling and energy flow in ecosystems. However, the effects of introducing leguminous shrubs on soil microbial diversity and the relevant mechanisms are not clear. Here, we employed the high-throughput absolute quantification 16S rRNA sequencing method to analyze the diversity of soil bacteria in sand-fixing areas of mixed shrublands with three combinations of shrubs, i.e., C. korshinskii × Corethrodendron scoparium (CaKCoS), C. korshinskii × Calligonum mongolicum (CaKCaM), and C. scoparium × C. mongolicum (CoSCaM), in the south of the Mu Us Sandy Land, China. This area suffered from moving dunes 20 years ago, but after introducing these shrubs to fix the dunes, the ecosystem was restored. Additionally, the effects of soil physicochemical properties on soil bacterial composition and diversity were analyzed with redundancy analysis (RDA) and structural equation modeling (SEM). It was found that the Shannon index of soil bacteria in CaKCoS was significantly higher than that in CaKCaM and CoSCaM, and the abundance of the dominant phyla, including Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Planctomycetes, Thaumarchaeota, Armatimonadetes, candidate_division_WPS-1, and Nitrospirae, increased significantly in CaKCoS and CaKCaM compared to that in CoSCaM. RDA showed that the majority of soil properties, such as total nitrogen (TN), available potassium (AK), N:P ratio, soil moisture (SM), and available phosphorus (AP), were important soil environmental factors affecting the abundance of the dominant phyla, and RDA1 and RDA2 accounted for 56.66% and 2.35% of the total variation, respectively. SEM showed that the soil bacterial α-diversity was positively affected by the soil organic carbon (SOC), N:P ratio, and total phosphorus (TP). Moreover, CaKCoS had higher SM, total carbon (TC), total potassium (TK), and AP than CaKCaM and CoSCaM. Collectively, these results highlight a conceptual framework in which the combination of leguminous shrubs can effectively drive soil bacterial diversity by improving soil physicochemical properties and maintaining ecosystem functioning during desertification reversal.}, }
@article {pmid36482478, year = {2022}, author = {Hodžić, A and Alić, A and Spahić, A and Harl, J and Beck, R}, title = {Genetic diversity of Echinococcus granulosus sensu lato from animals and humans in Bosnia and Herzegovina.}, journal = {Parasites &amp; vectors}, volume = {15}, number = {1}, pages = {457}, pmid = {36482478}, issn = {1756-3305}, mesh = {Humans ; Sheep ; Cattle ; Animals ; Swine ; *Echinococcus granulosus ; *Echinococcus/genetics ; *Echinococcosis/veterinary ; Genotype ; Genetic Variation ; *Cysts ; }, abstract = {BACKGROUND: Cystic echinococcosis (CE) is recognized as one of the most prevalent zoonotic diseases in Bosnia and Herzegovina. However, no systemic investigation of the genetic diversity of Echinococcus granulosus sensu lato circulating among animals and humans in the country has been performed to date.<br><br>METHODS: In this preliminary study, we analysed one cyst each from 36 sheep, 27 cattle, 27 pigs, 11 wild boars and 16 human patients for amplification and partial sequencing of the adenosine triphosphate 6 (atp6) and cytochrome c oxidase 1 (cox1) genes. The host species, fertility rate and organ cyst location were recorded for each subject involved in the study.<br><br>RESULTS: Overall, the atp6 gene was successfully amplified and sequenced from 110 samples, while 96 of the PCRs for cox1 were positive. Three zoonotic genotypes of E. granulosus sensu stricto (G1 and G3) and Echinococcus canadensis (G7) were identified in our isolates based on analyses of the atp6 gene. These genotypes were represented by 11 different genetic variants (haplotypes), six of which were identified for the first time in the present study.<br><br>CONCLUSIONS: This study demonstrates, for the first time, that CE in Bosnia and Herzegovina is predominantly caused by E. granulosus sensu stricto and E. canadensis clusters, which exhibited a lower genetic diversity compared to isolates from other European countries. Further molecular studies employing other mitochondrial and nuclear genes are required to better understand the transmission cycles of E. granulosus sensu stricto among intermediate and definitive hosts in the country.}, }
@article {pmid36480164, year = {2023}, author = {Engelberts, JP and Robbins, SJ and Herbold, CW and Moeller, FU and Jehmlich, N and Laffy, PW and Wagner, M and Webster, NS}, title = {Metabolic reconstruction of the near complete microbiome of the model sponge Ianthella basta.}, journal = {Environmental microbiology}, volume = {25}, number = {3}, pages = {646-660}, pmid = {36480164}, issn = {1462-2920}, support = {294343/ERC_/European Research Council/International ; }, mesh = {Animals ; *Porifera/microbiology ; Phylogeny ; Archaea/metabolism ; *Microbiota ; Symbiosis/physiology ; }, abstract = {Many marine sponges host highly diverse microbiomes that contribute to various aspects of host health. Although the putative function of individual groups of sponge symbionts has been increasingly described, the extreme diversity has generally precluded in-depth characterization of entire microbiomes, including identification of syntrophic partnerships. The Indo-Pacific sponge Ianthella basta is emerging as a model organism for symbiosis research, hosting only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium and a range of other low abundance or transitory taxa. Here, we retrieved metagenome assembled genomes (MAGs) representing >90% of I. basta's microbial community, facilitating the metabolic reconstruction of the sponge's near complete microbiome. Through this analysis, we identified metabolic complementarity between microbes, including vitamin sharing, described the importance of low abundance symbionts, and characterized a novel microbe-host attachment mechanism in the Alphaproteobacterium. We further identified putative viral sequences, highlighting the role viruses can play in maintaining symbioses in I. basta through the horizontal transfer of eukaryotic-like proteins, and complemented this data with metaproteomics to identify active metabolic pathways in bacteria, archaea, and viruses. This data provide the framework to adopt I. basta as a model organism for studying host-microbe interactions and provide a basis for in-depth physiological experiments.}, }
@article {pmid36480133, year = {2023}, author = {Eck, M and Schwab, ST and Nelson, TF and Wurst, K and Iberl, S and Schleheck, D and Link, C and Battagliarin, G and Mecking, S}, title = {Biodegradable High-Density Polyethylene-like Material.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {62}, number = {6}, pages = {e202213438}, pmid = {36480133}, issn = {1521-3773}, mesh = {*Polyethylene ; Biodegradation, Environmental ; *Polyesters/chemistry ; Hydrolysis ; }, abstract = {We report a novel polyester material generated from readily available biobased 1,18-octadecanedicarboxylic acid and ethylene glycol possesses a polyethylene-like solid-state structure and also tensile properties similar to high density polyethylene (HDPE). Despite its crystallinity, high melting point (Tm =96 °C) and hydrophobic nature, polyester-2,18 is subject to rapid and complete hydrolytic degradation in in vitro assays with isolated naturally occurring enzymes. Under industrial composting conditions (ISO standard 14855-1) the material is biodegraded with mineralization above 95 % within two months. Reference studies with polyester-18,18 (Tm =99 °C) reveal a strong impact of the nature of the diol repeating unit on degradation rates, possibly related to the density of ester groups in the amorphous phase. Depolymerization by methanolysis indicates suitability for closed-loop recycling.}, }
@article {pmid36479626, year = {2022}, author = {Geerinck, MWJ and Van Hee, S and Gloder, G and Crauwels, S and Colazza, S and Jacquemyn, H and Cusumano, A and Lievens, B}, title = {Diversity and composition of the microbiome associated with eggs of the Southern green stinkbug, Nezara viridula (Hemiptera: Pentatomidae).}, journal = {MicrobiologyOpen}, volume = {11}, number = {6}, pages = {e1337}, pmid = {36479626}, issn = {2045-8827}, mesh = {Animals ; *Hemiptera ; Belgium ; Italy ; *Microbiota ; }, abstract = {Although microbial communities of insects from larval to adult stage have been increasingly investigated in recent years, little is still known about the diversity and composition of egg-associated microbiomes. In this study, we used high-throughput amplicon sequencing and quantitative PCR to get a better understanding of the microbiome of insect eggs and how they are established using the Southern green stinkbug Nezara viridula (L.) (Hemiptera: Pentatomidae) as a study object. First, to determine the bacterial community composition, egg masses from two natural populations in Belgium and Italy were examined. Subsequently, microbial community establishment was assessed by studying stinkbug eggs of different ages obtained from laboratory strains (unlaid eggs collected from the ovaries, eggs less than 24 h old, and eggs collected 4 days after oviposition). Both the external and internal egg-associated microbiomes were analyzed by investigating egg washes and surface-sterilized washed eggs, respectively. Eggs from the ovaries were completely devoid of bacteria, indicating that egg-associated bacteria were deposited on the eggs during or after oviposition. The bacterial diversity of deposited eggs was very low, with on average 6.1 zero-radius operational taxonomic units (zOTUs) in the external microbiome and 1.2 zOTUs in internal samples of egg masses collected from the field. Bacterial community composition and density did not change significantly over time, suggesting limited bacterial growth. A Pantoea-like symbiont previously found in the midgut of N. viridula was found in every sample and generally occurred at high relative and absolute densities, especially in the internal egg samples. Additionally, some eggs harbored a Sodalis symbiont, which has previously been found in the abdomen of several insects, but so far not in N. viridula populations. We conclude that the egg-associated bacterial microbiome of N. viridula is species-poor and dominated by a few symbionts, particularly the species-specific obligate Pantoea-like symbiont.}, }
@article {pmid36478428, year = {2022}, author = {Lee, JS and Lee, SM and Son, HS and Yoon, YN and Shin, JE and Sul, WJ and Yu, DA and Choe, YB and Lee, YW}, title = {Analysis of the Microbiome of the Ear Canal in Normal Individuals and Patients with Chronic Otitis Externa.}, journal = {Annals of dermatology}, volume = {34}, number = {6}, pages = {461-471}, pmid = {36478428}, issn = {2005-3894}, support = {//Konkuk University/Korea ; }, abstract = {BACKGROUND: Recently, microbiome research has been actively conducted for various skin areas. However, no study has yet compared the microbiome of bacteria and fungi in the ear canal of healthy individuals and patients with chronic otitis externa in Korea.<br><br>OBJECTIVE: This study aimed to investigate the difference in the distribution of fungal and bacterial microbial communities in ear canal samples of healthy individuals and patients with chronic otitis externa.<br><br>METHODS: In 24 patients with bilateral chronic otitis externa and 24 healthy controls, cotton swabs were used to obtain samples from the bilateral ear canal. To characterize the fungal and bacterial communities, we sequenced and analyzed the 16S rRNA V4-V5 and ITS1 regions using Quantitative Insights into Microbial Ecology 2, respectively.<br><br>RESULTS: The alpha diversity analysis for bacteria and fungi confirmed that both richness and evenness decreased in the patient group. The beta diversity analysis for bacteria confirmed that these parameters differed between the control and patient groups. The beta diversity analysis for fungi showed no difference between the groups.<br><br>CONCLUSION: We observed different skin microbiomes in the patients with chronic otitis externa compared with those in the healthy individuals.}, }
@article {pmid36478022, year = {2023}, author = {Watson, M and May, G and Bushley, KE}, title = {Sources of Fungal Symbionts in the Microbiome of a Mobile Insect Host, Spodoptera frugiperda.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {900-913}, pmid = {36478022}, issn = {1432-184X}, support = {Natural History Award//Bell Museum of Natural History, University of Minnesota/ ; }, mesh = {Animals ; Spodoptera/microbiology ; *Insecta ; Plants ; Larva ; *Microbiota ; }, abstract = {The sources of fungal symbionts of insects are not well understood, yet the acquisition and assembly of fungal communities in mobile insect hosts have important implications for the ecology of migratory insects and their plant hosts. To determine potential sources of fungi associated with the fall armyworm (Spodoptera frugiperda), we characterized the fungal communities associated with four different ecological compartments (insects, infested leaves, uninfested leaves, and soil) and estimated the contributions of each of these potential sources to the insect's fungal microbiome. Results show that insect fungal community composition was distinct from and more varied than the composition of fungal communities in the environment of those insects (plants and soil). Among the sources evaluated, on average we found a surprisingly large apparent contribution from other congeneric S. frugiperda insect larvae (ca. 25%) compared to the contribution from soil or plant sources (< 5%). However, a large proportion of the insect microbiome could not be attributed to the sampled sources and was instead attributed to unknown sources (ca. 50%). Surprisingly, we found little evidence for exchange of fungal taxa, with the exception of a Fusarium oxysporum and a Cladosporium sp. OTU, between larvae and the infested leaves on which they fed. Together, our results suggest that mobile insects such as S. frugiperda obtain their fungal symbionts from a variety of sources, not limited to plants and soil, but including conspecific insects and other unsampled environmental sources, and that transmission among insects may play an important role in acquisition of fungal symbionts.}, }
@article {pmid36475832, year = {2023}, author = {Jens, JN and Breiner, DJ and Neve, RL and Fiebig, MM and Phelan, VV}, title = {MBRA-2: a Modified Chemostat System to Culture Biofilms.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0292822}, pmid = {36475832}, issn = {2165-0497}, support = {R35 GM128690/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biofilms ; Culture Media ; *Microbiota ; Bioreactors ; Pseudomonas aeruginosa ; Plankton ; }, abstract = {Culture-dependent approaches for investigating microbial ecology aim to model the nutrient content of specific environments by simplifying the system for high-resolution molecular analysis. These in vitro systems are enticing due to their increased throughput compared to animal models, flexibility in modulating nutrient content and community composition, scaling of culture volume to isolate biological molecules, and control of environmental parameters, such as temperature, humidity, and nutrient flow. However, different devices are used to investigate homogenous, planktonic microbial communities and heterogeneous biofilms. Here, we present the minibioreactor array 2 (MBRA-2) with media rails, a benchtop multireactor system derived from the MBRA system that enables researchers to use the same system to grow planktonic and biofilm cultures. We simplified flow through the system and reduced contamination, leakage, and time required for array assembly by designing and implementing a reusable media rail to replace the branched tubing traditionally used to convey media through chemostat arrays. Additionally, we altered the structure of the six-bioreactor strip to incorporate a removable lid to provide easy access to the bioreactor wells, enabling biofilm recovery and thorough cleaning for reuse. Using Pseudomonas aeruginosa, a model biofilm-producing organism, we show that the technical improvements of the MBRA-2 for biofilms growth does not disrupt the function of the bioreactor array. IMPORTANCE The MBRA-2 with media rails provides an accessible system for investigators to culture heterogenous, suspended biofilms under constant flow.}, }
@article {pmid36475750, year = {2023}, author = {Wollein Waldetoft, K and Sundius, S and Kuske, R and Brown, SP}, title = {Defining the Benefits of Antibiotic Resistance in Commensals and the Scope for Resistance Optimization.}, journal = {mBio}, volume = {14}, number = {1}, pages = {e0134922}, pmid = {36475750}, issn = {2150-7511}, support = {R01 DE020100/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Bacteria ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Symbiosis ; *Microbiota ; Drug Resistance, Bacterial ; }, abstract = {Antibiotic resistance is a major medical and public health challenge, characterized by global increases in the prevalence of resistant strains. The conventional view is that all antibiotic resistance is problematic, even when not in pathogens. Resistance in commensal bacteria poses risks, as resistant organisms can provide a reservoir of resistance genes that can be horizontally transferred to pathogens or may themselves cause opportunistic infections in the future. While these risks are real, we propose that commensal resistance can also generate benefits during antibiotic treatment of human infection, by promoting continued ecological suppression of pathogens. To define and illustrate this alternative conceptual perspective, we use a two-species mathematical model to identify the necessary and sufficient ecological conditions for beneficial resistance. We show that the benefits are limited to species (or strain) interactions where commensals suppress pathogen growth and are maximized when commensals compete with, rather than prey on or otherwise exploit pathogens. By identifying benefits of commensal resistance, we propose that rather than strictly minimizing all resistance, resistance management may be better viewed as an optimization problem. We discuss implications in two applied contexts: bystander (nontarget) selection within commensal microbiomes and pathogen treatment given polymicrobial infections. IMPORTANCE Antibiotic resistance is commonly viewed as universally costly, regardless of which bacterial cells express resistance. Here, we derive an opposing logic, where resistance in commensal bacteria can lead to reductions in pathogen density and improved outcomes on both the patient and public health scales. We use a mathematical model of commensal-pathogen interactions to define the necessary and sufficient conditions for beneficial resistance, highlighting the importance of reciprocal ecological inhibition to maximize the benefits of resistance. More broadly, we argue that determining the benefits as well as the costs of resistances in human microbiomes can transform resistance management from a minimization to an optimization problem. We discuss applied contexts and close with a review of key resistance optimization dimensions, including the magnitude, spectrum, and mechanism of resistance.}, }
@article {pmid36472419, year = {2022}, author = {Coker, J and Zhalnina, K and Marotz, C and Thiruppathy, D and Tjuanta, M and D'Elia, G and Hailu, R and Mahosky, T and Rowan, M and Northen, TR and Zengler, K}, title = {A Reproducible and Tunable Synthetic Soil Microbial Community Provides New Insights into Microbial Ecology.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0095122}, pmid = {36472419}, issn = {2379-5077}, support = {T32 GM007198/GM/NIGMS NIH HHS/United States ; }, mesh = {*Soil ; Reproducibility of Results ; Soil Microbiology ; Plant Roots ; *Microbiota ; Plants/microbiology ; }, abstract = {Microbial soil communities form commensal relationships with plants to promote the growth of both parties. The optimization of plant-microbe interactions to advance sustainable agriculture is an important field in agricultural research. However, investigation in this field is hindered by a lack of model microbial community systems and efficient approaches for building these communities. Two key challenges in developing standardized model communities are maintaining community diversity over time and storing/resuscitating these communities after cryopreservation, especially considering the different growth rates of organisms. Here, a model synthetic community (SynCom) of 16 soil microorganisms commonly found in the rhizosphere of diverse plant species, isolated from soil surrounding a single switchgrass plant, has been developed and optimized for in vitro experiments. The model soil community grows reproducibly between replicates and experiments, with a high community α-diversity being achieved through growth in low-nutrient media and through the adjustment of the starting composition ratios for the growth of individual organisms. The community can additionally be cryopreserved with glycerol, allowing for easy replication and dissemination of this in vitro system. Furthermore, the SynCom also grows reproducibly in fabricated ecosystem devices (EcoFABs), demonstrating the application of this community to an existing in vitro plant-microbe system. EcoFABs allow reproducible research in model plant systems, offering the precise control of environmental conditions and the easy measurement of plant microbe metrics. Our results demonstrate the generation of a stable and diverse microbial SynCom for the rhizosphere that can be used with EcoFAB devices and can be shared between research groups for maximum reproducibility. IMPORTANCE Microbes associate with plants in distinct soil communities to the benefit of both the soil microbes and the plants. Interactions between plants and these microbes can improve plant growth and health and are therefore a field of study in sustainable agricultural research. In this study, a model community of 16 soil bacteria has been developed to further the reproducible study of plant-soil microbe interactions. The preservation of the microbial community has been optimized for dissemination to other research settings. Overall, this work will advance soil microbe research through the optimization of a robust, reproducible model community.}, }
@article {pmid36471016, year = {2023}, author = {Wang, YJ and He, XH and Meng, LL and Zou, YN and Wu, QS}, title = {Extraradical Mycorrhizal Hyphae Promote Soil Carbon Sequestration through Difficultly Extractable Glomalin-Related Soil Protein in Response to Soil Water Stress.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1023-1034}, pmid = {36471016}, issn = {1432-184X}, support = {32272643//National Natural Science Foundation of China/ ; 31372017//National Natural Science Foundation of China/ ; T201604//Plan in Scientific and Technological Innovation Team of Outstanding Young Scientists, Hubei Provincial Department of Education, China/ ; }, mesh = {*Mycorrhizae ; Soil/chemistry ; Hyphae ; Carbon Sequestration ; Carbon/metabolism ; Dehydration/metabolism ; Fungal Proteins/metabolism ; Glycoproteins/metabolism ; }, abstract = {Soil water stress (WS) affects the decomposition of soil organic carbon (SOC) and carbon (C) emissions. Glomalin, released by arbuscular mycorrhizal fungi into soil that has been defined as glomalin-related soil protein (GRSP), is an important pool of SOC, with hydrophobic characteristics. We hypothesized that mycorrhizal fungi have a positive effect on SOC pools under soil WS for C sequestration in GRSP secreted by extraradical mycorrhizal hyphae. A microsystem was used to establish a root chamber (co-existence of roots and extraradical mycorrhizal hyphae) and a hyphal chamber (the presence of extraradical mycorrhizal hyphae) to study changes in plant growth, leaf water potential, soil aggregate stability, SOC, GRSP, C concentrations in GRSP (CGRSP), and the contribution of CGRSP to SOC after inoculating Rhizophagus intraradices with trifoliate orange (Poncirus trifoliata) in the root chamber under adequate water (AW) and WS. Inoculation with R. intraradices alleviated negative effects on leaf water potential and plant growth after 7 weeks of WS. Soil WS decreased SOC and mean weight diameter (MWD), while AMF inoculation led to an increase in SOC and MWD in both chambers, with the most prominent increase in the hyphal chamber under WS. The C concentration in easily extractable GRSP (EE-GRSP) and difficultly extractable GRSP (DE-GRSP) was 7.32 - 12.57 and 24.90 - 32.60 mg C/g GRSP, respectively. WS reduced CGRSP, while AMF mitigated the reduction. Extraradical mycorrhizal hyphae increased GRSP production and CGRSP, along with a more prominent increase in DE-GRSP under WS than under AW. Extraradical mycorrhizal hyphae increased the contribution of CDE-GRSP to SOC only under WS. CEE-GRSP and CDE-GRSP were significantly positively correlated with SOC and MWD. It is concluded that extraradical mycorrhizal hyphae prominently promoted C sequestration of recalcitrant DE-GRSP under soil WS, thus contributing more organic C accumulation and preservation in aggregates and soil C pool.}, }
@article {pmid36468868, year = {2023}, author = {Zeng, L and Walker, AR and Burne, RA and Taylor, ZA}, title = {Glucose Phosphotransferase System Modulates Pyruvate Metabolism, Bacterial Fitness, and Microbial Ecology in Oral Streptococci.}, journal = {Journal of bacteriology}, volume = {205}, number = {1}, pages = {e0035222}, pmid = {36468868}, issn = {1098-5530}, support = {R01 DE012236/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Hydrogen Peroxide/metabolism ; Glucose/metabolism ; *Dental Caries ; Streptococcus mutans/genetics ; Lactic Acid/metabolism ; Acids/metabolism ; Pyruvates/metabolism ; Biofilms ; }, abstract = {Spontaneous mutants with defects in the primary glucose phosphotransferase permease (manLMNO) of Streptococcus sanguinis SK36 showed enhanced fitness at low pH. Transcriptomics and metabolomics with a manL deletion mutant (SK36/manL) revealed redirection of pyruvate to production of acetate and formate, rather than lactate. These observations were consistent with measurements of decreased lactic acid accumulation and increased excretion of acetate, formate, pyruvate, and H2O2. Genes showing increased expression in SK36/manL included those encoding carbohydrate transporters, extracellular glycosidases, intracellular polysaccharide metabolism, and arginine deiminase and pathways for metabolism of acetoin, ethanolamine, ascorbate, and formate, along with genes required for membrane biosynthesis and adhesion. Streptococcus mutans UA159 persisted much better in biofilm cocultures with SK36/manL than with SK36, an effect that was further enhanced by culturing the biofilms anaerobically but dampened by adding arginine to the medium. We posited that the enhanced persistence of S. mutans with SK36/manL was in part due to excess excretion of pyruvate by the latter, as addition of pyruvate to S. mutans-S. sanguinis cocultures increased the proportions of UA159 in the biofilms. Reducing the buffer capacity or increasing the concentration of glucose benefited UA159 when cocultured with SK36, but not with SK36/manL, likely due to the altered metabolism and enhanced acid tolerance of the mutant. When manL was deleted in S. mutans or Streptococcus gordonii, the mutants presented altered fitness characteristics. Our study demonstrated that phosphotransferase system (PTS)-dependent modulation of central metabolism can profoundly affect streptococcal fitness and metabolic interactions, revealing another dimension in commensal-pathogen relationships influencing dental caries development. IMPORTANCE Dental caries is underpinned by a dysbiotic microbiome and increased acid production. As beneficial bacteria that can antagonize oral pathobionts, oral streptococci such as S. sanguinis and S. gordonii can ferment many carbohydrates, despite their relative sensitivity to low pH. We characterized the molecular basis for why mutants of glucose transporter ManLMNO of S. sanguinis showed enhanced production of hydrogen peroxide and ammonia and improved persistence under acidic conditions. A metabolic shift involving more than 300 genes required for carbohydrate transport, energy production, and envelope biogenesis was observed. Significantly, manL mutants engineered in three different oral streptococci displayed altered capacities for acid production and interspecies antagonism, highlighting the potential for targeting the glucose-PTS to modulate the pathogenicity of oral biofilms.}, }
@article {pmid36468853, year = {2022}, author = {Zhang, B and Zhao, C and Zhang, X and Li, X and Zhang, Y and Liu, X and Yin, J and Li, X and Wang, J and Wang, S}, title = {An Elemental Diet Enriched in Amino Acids Alters the Gut Microbial Community and Prevents Colonic Mucus Degradation in Mice with Colitis.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0088322}, pmid = {36468853}, issn = {2379-5077}, mesh = {Mice ; Humans ; Animals ; Amino Acids/adverse effects ; Expectorants/adverse effects ; *Colitis/chemically induced ; *Microbiota ; Bacteria ; Mucus/metabolism ; }, abstract = {The role of dietary amino acids or intact proteins in the progression of colitis remains controversial, and the mechanism involving gut microbes is unclear. Here, we investigated the effects of an elemental diet (ED) enriched in amino acids and a polymeric diet enriched in intact protein on the pathogenesis of dextran sulfate sodium (DSS)-induced colitis in mice. Our results showed that the ED induced remission of colitis in mice. Notably, ED treatment reduced the abundance of the mucolytic bacteria Akkermansia and Bacteroides, which was attributed to decreased colonic protein fermentation. Consistently, the activities of mucolytic enzymes were decreased, leading to protection against mucus layer degradation and microbial invasion. Fecal microbiota transplantation from ED-fed mice reshaped microbial ecology and alleviated intestinal inflammation in recipient mice. The ED failed to induce remission of colitis in pseudogermfree mice. Together, our results demonstrate the critical role of the gut microbiota in the prevention of colitis by an ED. IMPORTANCE The prevalence of inflammatory bowel disease is rapidly increasing and has become a global burden. Several specific amino acids have been shown to benefit mucosal healing and colitis remission. However, the role of amino acids or intact proteins in diets and enteral nutrition formulas is controversial, and the mechanisms involving gut microbes remain unclear. In this study, we investigated the effects of an elemental diet (ED) enriched in amino acids and a polymeric diet enriched in intact protein on the pathogenesis of colitis in mice. The underlying mechanisms were explored by utilizing fecal microbiota transplantation and pseudogermfree mice. ED treatment reduced the abundance of mucolytic bacteria, thereby protecting the mucus layer from microbial invasion and degradation. For the first time, we convincingly demonstrated the critical role of gut microbiota in the effects of the ED. This study may provide new insights into the gut microbiota-diet interaction and its role in human health.}, }
@article {pmid36466646, year = {2022}, author = {Twing, KI and Ward, LM and Kane, ZK and Sanders, A and Price, RE and Pendleton, HL and Giovannelli, D and Brazelton, WJ and McGlynn, SE}, title = {Microbial ecology of a shallow alkaline hydrothermal vent: Strýtan Hydrothermal Field, Eyjafördur, northern Iceland.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {960335}, pmid = {36466646}, issn = {1664-302X}, abstract = {Strýtan Hydrothermal Field (SHF) is a submarine system located in Eyjafördur in northern Iceland composed of two main vents: Big Strýtan and Arnarnesstrýtan. The vents are shallow, ranging from 16 to 70 m water depth, and vent high pH (up to 10.2), moderate temperature (T max ∼70°C), anoxic, fresh fluids elevated in dissolved silica, with slightly elevated concentrations of hydrogen and methane. In contrast to other alkaline hydrothermal vents, SHF is unique because it is hosted in basalt and therefore the high pH is not created by serpentinization. While previous studies have assessed the geology and geochemistry of this site, the microbial diversity of SHF has not been explored in detail. Here we present a microbial diversity survey of the actively venting fluids and chimneys from Big Strýtan and Arnarnesstrýtan, using 16S rRNA gene amplicon sequencing. Community members from the vent fluids are mostly aerobic heterotrophic bacteria; however, within the chimneys oxic, low oxygen, and anoxic habitats could be distinguished, where taxa putatively capable of acetogenesis, sulfur-cycling, and hydrogen metabolism were observed. Very few archaea were observed in the samples. The inhabitants of SHF are more similar to terrestrial hot spring samples than other marine sites. It has been hypothesized that life on Earth (and elsewhere in the solar system) could have originated in an alkaline hydrothermal system, however all other studied alkaline submarine hydrothermal systems to date are fueled by serpentinization. SHF adds to our understandings of hydrothermal vents in relationship to microbial diversity, evolution, and possibly the origin of life.}, }
@article {pmid36465136, year = {2022}, author = {Simmonds, EG and Adjei, KP and Andersen, CW and Hetle Aspheim, JC and Battistin, C and Bulso, N and Christensen, HM and Cretois, B and Cubero, R and Davidovich, IA and Dickel, L and Dunn, B and Dunn-Sigouin, E and Dyrstad, K and Einum, S and Giglio, D and Gjerløw, H and Godefroidt, A and González-Gil, R and Gonzalo Cogno, S and Große, F and Halloran, P and Jensen, MF and Kennedy, JJ and Langsæther, PE and Laverick, JH and Lederberger, D and Li, C and Mandeville, EG and Mandeville, C and Moe, E and Navarro Schröder, T and Nunan, D and Sicacha-Parada, J and Simpson, MR and Skarstein, ES and Spensberger, C and Stevens, R and Subramanian, AC and Svendsen, L and Theisen, OM and Watret, C and O'Hara, RB}, title = {Insights into the quantification and reporting of model-related uncertainty across different disciplines.}, journal = {iScience}, volume = {25}, number = {12}, pages = {105512}, pmid = {36465136}, issn = {2589-0042}, abstract = {Quantifying uncertainty associated with our models is the only way we can express how much we know about any phenomenon. Incomplete consideration of model-based uncertainties can lead to overstated conclusions with real-world impacts in diverse spheres, including conservation, epidemiology, climate science, and policy. Despite these potentially damaging consequences, we still know little about how different fields quantify and report uncertainty. We introduce the "sources of uncertainty" framework, using it to conduct a systematic audit of model-related uncertainty quantification from seven scientific fields, spanning the biological, physical, and political sciences. Our interdisciplinary audit shows no field fully considers all possible sources of uncertainty, but each has its own best practices alongside shared outstanding challenges. We make ten easy-to-implement recommendations to improve the consistency, completeness, and clarity of reporting on model-related uncertainty. These recommendations serve as a guide to best practices across scientific fields and expand our toolbox for high-quality research.}, }
@article {pmid36463738, year = {2023}, author = {Li, J and Yu, S and Liu, Q and Wang, D and Yang, L and Wang, J and Zuo, R}, title = {Screening of hazardous groundwater pollutants responsible for microbial ecological consequences by integrated nontargeted analysis and high-throughput sequencing technologies.}, journal = {Journal of hazardous materials}, volume = {445}, number = {}, pages = {130516}, doi = {10.1016/j.jhazmat.2022.130516}, pmid = {36463738}, issn = {1873-3336}, mesh = {*Environmental Pollutants/analysis ; *Groundwater/chemistry ; *Microbiota ; Beijing ; High-Throughput Nucleotide Sequencing ; *Water Pollutants, Chemical/toxicity/analysis ; Environmental Monitoring ; }, abstract = {Organic contaminants, especially hydrophobic organic contaminants (HOCs), pose potential ecological threats even at environmental concentrations. Characterization of HOC profiles and identification of key environmental stressors are vital but still challenging in groundwater quality management. In this study, a strategy for identifying the key environmental stressors among HOCs in groundwater based on integrated chemical monitoring technologies and microbial ecology analysis methods was proposed and applied to typical groundwater samples. Specifically, the characteristics of HOCs were systematically analyzed based on nontargeted and targeted approaches, and microbial community assembly and specific biomarker analysis were combined to determine the major ecological processes and key environmental stressors. The results showed that a total of 234 HOCs were detected in groundwater collected from Tongzhou, Beijing; among them, phthalate esters (PAEs) were screened out as key environmental stressors, considering that they made relatively higher microbial ecology contributions. Furthermore, their influences on the structure and function of the groundwater microbial community were evaluated by adopting high-throughput sequencing and bioinformatics analysis technologies. These findings confirmed PAEs as vital determinants driving microbial assembly, shifting community structure, and regulating community function in groundwater; in addition, the findings validated the feasibility and suitability of the proposed strategy.}, }
@article {pmid36460563, year = {2023}, author = {Sutherland, WJ and Bennett, C and Brotherton, PNM and Butterworth, HM and Clout, MN and Côté, IM and Dinsdale, J and Esmail, N and Fleishman, E and Gaston, KJ and Herbert-Read, JE and Hughes, A and Kaartokallio, H and Le Roux, X and Lickorish, FA and Matcham, W and Noor, N and Palardy, JE and Pearce-Higgins, JW and Peck, LS and Pettorelli, N and Pretty, J and Scobey, R and Spalding, MD and Tonneijck, FH and Tubbs, N and Watson, JEM and Wentworth, JE and Wilson, JD and Thornton, A}, title = {A global biological conservation horizon scan of issues for 2023.}, journal = {Trends in ecology &amp; evolution}, volume = {38}, number = {1}, pages = {96-107}, doi = {10.1016/j.tree.2022.10.005}, pmid = {36460563}, issn = {1872-8383}, mesh = {*Ecosystem ; *Conservation of Natural Resources ; Biodiversity ; Forecasting ; Fisheries ; }, abstract = {We present the results of our 14th horizon scan of issues we expect to influence biological conservation in the future. From an initial set of 102 topics, our global panel of 30 scientists and practitioners identified 15 issues we consider most urgent for societies worldwide to address. Issues are novel within biological conservation or represent a substantial positive or negative step change at global or regional scales. Issues such as submerged artificial light fisheries and accelerating upper ocean currents could have profound negative impacts on marine or coastal ecosystems. We also identified potentially positive technological advances, including energy production and storage, improved fertilisation methods, and expansion of biodegradable materials. If effectively managed, these technologies could realise future benefits for biological diversity.}, }
@article {pmid36460187, year = {2023}, author = {Liu, X and Zhang, J and Si, J and Li, P and Gao, H and Li, W and Chen, Y}, title = {What happens to gut microorganisms and potential repair mechanisms when meet heavy metal(loid)s.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {317}, number = {}, pages = {120780}, doi = {10.1016/j.envpol.2022.120780}, pmid = {36460187}, issn = {1873-6424}, mesh = {Humans ; *Metals, Heavy/toxicity/analysis ; *Arsenic/analysis ; Chromium ; Cadmium ; *Metalloids ; Risk Assessment ; *Soil Pollutants/analysis ; Environmental Monitoring ; China ; Soil ; }, abstract = {Heavy metal (loid) pollution is a significant threat to human health, as the intake of heavy metal (loid)s can cause disturbances in intestinal microbial ecology and metabolic disorders, leading to intestinal and systemic diseases. Therefore, it is important to understand the effects of heavy metal (loid)s on intestinal microorganisms and the necessary approaches to restore them after damage. This review provides a summary of the effects of common toxic elements, such as lead (Pb), cadmium (Cd), chromium (Cr), and metalloid arsenic (As), on the microbial community and structure, metabolic pathways and metabolites, and intestinal morphology and structure. The effects of heavy metal (loid)s on metabolism are focused on energy, nitrogen, and short-chain fatty acid metabolism. We also discussed the main solutions for recovery of intestinal microorganisms from the effects of heavy metal (loid)s, namely the supplementation of probiotics, recombinant bacteria with metal resistance, and the non-toxic transformation of heavy metal (loid) ions by their own intestinal flora. This article provides insight into the toxic effects of heavy metals and As on gut microorganisms and hosts and provides additional therapeutic options to mitigate the damage caused by these toxic elements.}, }
@article {pmid36460149, year = {2023}, author = {Araujo, ASF and Miranda, ARL and Pereira, APA and de Melo, WJ and Melo, VMM and Ventura, SH and Brito Junior, ES and de Medeiros, EV and Araujo, FF and Mendes, LW}, title = {Microbial communities in the rhizosphere of maize and cowpea respond differently to chromium contamination.}, journal = {Chemosphere}, volume = {313}, number = {}, pages = {137417}, doi = {10.1016/j.chemosphere.2022.137417}, pmid = {36460149}, issn = {1879-1298}, mesh = {Chromium/analysis ; Rhizosphere ; Zea mays ; *Vigna ; Soil Microbiology ; Bacteria ; *Microbiota ; Soil ; Firmicutes ; *Soil Pollutants/analysis ; }, abstract = {Chromium (Cr) contamination can affect microorganisms in the soil, but the response of the microbial community in the rhizosphere of plants grown in Cr-contaminated soils is poorly understood. Therefore, this study assessed the microbial community, by amplicon sequencing, in the rhizosphere of maize and cowpea growing in uncontaminated (∼6.0 mg kg[-1] Cr) and Cr-contaminated soils (∼250 mg kg[-1] Cr). Comparing Cr-contaminated and uncontaminated soils, the microbial community in the maize rhizosphere clustered separately, while the microbial community in the cowpea rhizosphere did not present clear clustering. The microbial richness ranged from ∼5000 (rhizosphere in Cr-contaminated soil) to ∼8000 OTUs (in uncontaminated soil). In the comparison of specific bacterial groups in the rhizosphere of maize, Firmicutes were enriched in Cr-contaminated soil, including Bacilli, Bacillales, and Paenibacillus. Cowpea rhizosphere showed a higher abundance of six microbial groups in Cr-contaminated soil, highlighting Rhizobiales, Pedomicrobium, and Gemmatimonadetes. The microbial community in both rhizospheres presented a similar proportion of specialists comparing uncontaminated (2.2 and 3.4% in the rhizosphere of maize and cowpea, respectively) and Cr-contaminated soils (1.8 and 3.2% in the rhizosphere of maize and cowpea, respectively). This study showed that each plant species drove differently the microbial community in the rhizosphere, with an important effect of Cr-contamination on the microbial community assembly.}, }
@article {pmid36455460, year = {2023}, author = {Rothman, JA and Saghir, A and Chung, SA and Boyajian, N and Dinh, T and Kim, J and Oval, J and Sharavanan, V and York, C and Zimmer-Faust, AG and Langlois, K and Steele, JA and Griffith, JF and Whiteson, KL}, title = {Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread transcription of antibiotic resistance genes.}, journal = {Water research}, volume = {229}, number = {}, pages = {119421}, doi = {10.1016/j.watres.2022.119421}, pmid = {36455460}, issn = {1879-2448}, mesh = {Humans ; *Wastewater ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Sewage/microbiology ; Bacteria/genetics ; RNA ; Genes, Bacterial ; }, abstract = {Municipal wastewater provides a representative sample of human fecal waste across a catchment area and contains a wide diversity of microbes. Sequencing wastewater samples provides information about human-associated and medically important microbial populations, and may be useful to assay disease prevalence and antimicrobial resistance (AMR). Here, we present a study in which we used untargeted metatranscriptomic sequencing on RNA extracted from 275 sewage influent samples obtained from eight wastewater treatment plants (WTPs) representing approximately 16 million people in Southern California between August 2020 - August 2021. We characterized bacterial and viral transcripts, assessed metabolic pathway activity, and identified over 2,000 AMR genes/variants across all samples. Because we did not deplete ribosomal RNA, we have a unique window into AMR carried as ribosomal mutants. We show that AMR diversity varied between WTPs (as measured through PERMANOVA, P < 0.001) and that the relative abundance of many individual AMR genes/variants increased over time (as measured with MaAsLin2, Padj < 0.05). Similarly, we detected transcripts mapping to human pathogenic bacteria and viruses suggesting RNA sequencing is a powerful tool for wastewater-based epidemiology and that there are geographical signatures to microbial transcription. We captured the transcription of gene pathways common to bacterial cell processes, including central carbon metabolism, nucleotide synthesis/salvage, and amino acid biosynthesis. We also posit that due to the ubiquity of many viruses and bacteria in wastewater, new biological targets for microbial water quality assessment can be developed. To the best of our knowledge, our study provides the most complete longitudinal metatranscriptomic analysis of a large population's wastewater to date and demonstrates our ability to monitor the presence and activity of microbes in complex samples. By sequencing RNA, we can track the relative abundance of expressed AMR genes/variants and metabolic pathways, increasing our understanding of AMR activity across large human populations and sewer sheds.}, }
@article {pmid36452921, year = {2022}, author = {Xu, H and Wu, N and Na, N and Sun, L and Zhao, Y and Ding, H and Fang, Y and Wang, T and Xue, Y and Zhong, J}, title = {Fermentation weight loss, fermentation quality, and bacterial community of ensiling of sweet sorghum with lactic acid bacteria at different silo densities.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1013913}, pmid = {36452921}, issn = {1664-302X}, abstract = {Sweet sorghum is an important forage in arid and semi-arid climatic regions. This study aimed to reveal the fermentation weight loss (FWL), fermentation quality, and bacterial community of ensiling of sweet sorghum with lactic acid bacteria LAB; (Lactiplantibacillus plantarum and Lentilactobacillus buchneri) at different silo densities. For this study, sweet sorghum was harvested at the first spikelet of inflorescence stage and ensiled without or with LAB (CK or L) in polyethylene laboratory-scale silos (diameter, 20 cm; height, 30 cm) at densities of 650 (CK_650 and L_650), 700 (CK_700 and L_700), and 750 kg/m[3] (CK_750 and L_750), respectively. The FWL, fermentation quality, microbial counts, and bacterial community of the silage were assessed after 100 days of ensiling. L_750 had a lower FWL than CK_650, _700, and _750 after 100 days of ensiling (P < 0.005), and the FWL was affected by silo density and inoculating LAB (P < 0.005). All silages had low pH (<4.0) and ammonia nitrogen content (<50 g/kg total nitrogen) and did not contain propionic and butyric acids; moreover, inoculating LAB increased lactic and acetic acids (P < 0.005). Bacterial communities in inoculated and uninoculated silages were clustered together, respectively, and clearly separated from each other. The total abundance of Lactiplantibacillus and Lentilactobacillus in fresh forage was <1%. Lactiplantibacillus had the highest abundance in all silages (from 71.39 to 93.27%), followed by Lentilactobacillus (from 3.59 to 27.63%). Inoculating LAB increased the abundance of Lentilactobacillus in each silo density (P < 0.005) and decreased Lactiplantibacillus in the silage in densities of 700 and 750 kg/m[3] (P < 0.005); moreover, increasing silo density decreased Lactiplantibacillus abundance and increased Lentilactobacillus abundance in inoculated silages (P < 0.005). Overall, sweet sorghum silage showed satisfactory fermentation quality, with a density of no <650 kg/m[3], and inoculating LAB improved fermentation quality and reduced FWL. Lactiplantibacillus and Lentilactobacillus presented as minor taxa in fresh sweet sorghum and dominated the bacterial community of all silages. Inoculating LAB was the main factor affecting the bacterial community of sweet sorghum silage. Moreover, inoculating LAB and increasing silo density can contribute to the decreasing Lactiplantibacillus abundance and increasing Lentilactobacillus abundance.}, }
@article {pmid36451971, year = {2022}, author = {Villa, F and Wu, YL and Zerboni, A and Cappitelli, F}, title = {In Living Color: Pigment-Based Microbial Ecology At the Mineral-Air Interface.}, journal = {Bioscience}, volume = {72}, number = {12}, pages = {1156-1175}, pmid = {36451971}, issn = {0006-3568}, abstract = {Pigment-based color is one of the most important phenotypic traits of biofilms at the mineral-air interface (subaerial biofilms, SABs), because it reflects the physiology of the microbial community. Because color is the hallmark of all SABs, we argue that pigment-based color could convey the mechanisms that drive microbial adaptation and coexistence across different terrestrial environments and link phenotypic traits to community fitness and ecological dynamics. Within this framework, we present the most relevant microbial pigments at the mineral-air interface and discuss some of the evolutionary landscapes that necessitate pigments as adaptive strategies for resource allocation and survivability. We report several pigment features that reflect SAB communities' structure and function, as well as pigment ecology in the context of microbial life-history strategies and coexistence theory. Finally, we conclude the study of pigment-based ecology by presenting its potential application and some of the key challenges in the research.}, }
@article {pmid36449026, year = {2023}, author = {Badger Hanson, E and Docherty, KM}, title = {Mini-review: Current and Future Perspectives on Microbially Focused Restoration Strategies in Tallgrass Prairies.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {1087-1097}, pmid = {36449026}, issn = {1432-184X}, support = {Graduate College//Western Michigan University/ ; Doctoral Fellowship//Western Michigan University/ ; Graduate Student Research Grant//Western Michigan University/ ; }, mesh = {*Ecosystem ; *Grassland ; Soil Microbiology ; Soil ; Carbon/metabolism ; }, abstract = {Ecosystem restoration is a critical conservation strategy, especially for increasing resilience and resistance to climate change. Current restoration efforts that convert reclaimed agricultural land to native tallgrass prairies typically focus on aboveground communities, but it can take decades to restore soil microbial biodiversity and function using these strategies, if they recover at all. This incomplete restoration can have detrimental impacts on longer-term restoration goals, such as supporting late-successional plant species and facilitating soil carbon sequestration. Soil microorganisms are key components in determining the fate of organic material that enters the soil. They mediate decomposition rates and contribute to plant-microbe-soil interactions, produce microbial biomass, necromass, and metabolic products, and physically protect soil carbon through aggregation. Interactions with plants and controls over soil carbon vary widely depending on the specific microbial taxa present, their physiology, their functional capabilities, and their responses to environmental stressors. Thus, the ability for new restorations, prairie conservation corridors, and prairies planted in marginal lands to act as carbon sinks and help balance greenhouse gas emissions can depend on the success of microbial restoration. Next-generation sequencing approaches can support novel methods for evaluating existing restoration practices and developing microbially focused management strategies. This review summarizes the growing body of literature describing microbially focused tallgrass prairie restoration and considers when and how integrating next-generation sequencing approaches into management efforts can be beneficial. We provide a roadmap for future restoration efforts where microbial ecologists, restoration ecologists, and land managers can work together to meet their goals to promote climate-ready restored ecosystems.}, }
@article {pmid36445401, year = {2023}, author = {Bates, KA and Friesen, J and Loyau, A and Butler, H and Vredenburg, VT and Laufer, J and Chatzinotas, A and Schmeller, DS}, title = {Environmental and Anthropogenic Factors Shape the Skin Bacterial Communities of a Semi-Arid Amphibian Species.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1393-1404}, pmid = {36445401}, issn = {1432-184X}, support = {ANR-15-MASC-0001-P3//Belmont Forum/ ; Junior Research Fellowship//St. Hilda's College, University of Oxford/ ; }, mesh = {Animals ; Anthropogenic Effects ; *Chytridiomycota ; Bufonidae ; Skin/microbiology ; Bacteria/genetics ; *Ranavirus ; }, abstract = {The amphibian skin microbiome is important in maintaining host health, but is vulnerable to perturbation from changes in biotic and abiotic conditions. Anthropogenic habitat disturbance and emerging infectious diseases are both potential disrupters of the skin microbiome, in addition to being major drivers of amphibian decline globally. We investigated how host environment (hydrology, habitat disturbance), pathogen presence, and host biology (life stage) impact the skin microbiome of wild Dhofar toads (Duttaphrynus dhufarensis) in Oman. We detected ranavirus (but not Batrachochytrium dendrobatidis) across all sampling sites, constituting the first report of this pathogen in Oman, with reduced prevalence in disturbed sites. We show that skin microbiome beta diversity is driven by host life stage, water source, and habitat disturbance, but not ranavirus infection. Finally, although trends in bacterial diversity and differential abundance were evident in disturbed versus undisturbed sites, bacterial co-occurrence patterns determined through network analyses revealed high site specificity. Our results therefore provide support for amphibian skin microbiome diversity and taxa abundance being associated with habitat disturbance, with bacterial co-occurrence (and likely broader aspects of microbial community ecology) being largely site specific.}, }
@article {pmid36445161, year = {2022}, author = {Sylvain, F&#xc9; and Leroux, N and Normandeau, &#xc9; and Holland, A and Bouslama, S and Mercier, PL and Luis Val, A and Derome, N}, title = {Genomic and Environmental Factors Shape the Active Gill Bacterial Community of an Amazonian Teleost Holobiont.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0206422}, pmid = {36445161}, issn = {2165-0497}, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Gills/chemistry/microbiology ; Fishes/genetics/microbiology ; *Microbiota/physiology ; Water ; Genomics ; Bacteria/genetics ; }, abstract = {Fish bacterial communities provide functions critical for their host's survival in contrasting environments. These communities are sensitive to environmental-specific factors (i.e., physicochemical parameters, bacterioplankton), and host-specific factors (i.e., host genetic background). The relative contribution of these factors shaping Amazonian fish bacterial communities is largely unknown. Here, we investigated this topic by analyzing the gill bacterial communities of 240 wild flag cichlids (Mesonauta festivus) from 4 different populations (genetic clusters) distributed across 12 sites in 2 contrasting water types (ion-poor/acidic black water and ion-rich/circumneutral white water). Transcriptionally active gill bacterial communities were characterized by a 16S rRNA metabarcoding approach carried on RNA extractions. They were analyzed using comprehensive data sets from the hosts genetic background (Genotyping-By-Sequencing), the bacterioplankton (16S rRNA) and a set of 34 environmental parameters. Results show that the taxonomic structure of 16S rRNA gene transcripts libraries were significantly different between the 4 genetic clusters and also between the 2 water types. However, results suggest that the contribution of the host's genetic background was relatively weak in comparison to the environment-related factors in structuring the relative abundance of different active gill bacteria species. This finding was also confirmed by a mixed-effects modeling analysis, which indicated that the dissimilarity between the taxonomic structure of bacterioplanktonic communities possessed the best explicative power regarding the dissimilarity between gill bacterial communities' structure, while pairwise fixation indexes (FST) from the hosts' genetic data only had a weak explicative power. We discuss these results in terms of bacterial community assembly processes and flag cichlid fish ecology. IMPORTANCE Host-associated microbial communities respond to factors specific to the host physiology, genetic backgrounds, and life history. However, these communities also show different degrees of sensitivity to environment-dependent factors, such as abiotic physico-chemical parameters and ecological interactions. The relative importance of host- versus environment-associated factors in shaping teleost bacterial communities is still understudied and is paramount for their conservation and aquaculture. Here, we studied the relative importance of host- and environment-associated factors structuring teleost bacterial communities using gill samples from a wild Amazonian teleost model (Mesonauta festivus) sampled in contrasting habitats along a 1500 km section of the Amazonian basin, thus ensuring high genetic diversity. Results showed that the contribution of the host's genetic background was weak compared to environment-related bacterioplanktonic communities in shaping gill bacterial assemblages, thereby suggesting that our understanding of teleost microbiome assembly could benefit from further studies focused on the ecological interplay between host-associated and free-living communities.}, }
@article {pmid36445112, year = {2022}, author = {Sánchez-Navarro, R and Nuhamunada, M and Mohite, OS and Wasmund, K and Albertsen, M and Gram, L and Nielsen, PH and Weber, T and Singleton, CM}, title = {Long-Read Metagenome-Assembled Genomes Improve Identification of Novel Complete Biosynthetic Gene Clusters in a Complex Microbial Activated Sludge Ecosystem.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0063222}, pmid = {36445112}, issn = {2379-5077}, mesh = {*Metagenome/genetics ; Sewage ; Multigene Family/genetics ; *Microbiota/genetics ; Genome, Bacterial/genetics ; }, abstract = {Microorganisms produce a wide variety of secondary/specialized metabolites (SMs), the majority of which are yet to be discovered. These natural products play multiple roles in microbiomes and are important for microbial competition, communication, and success in the environment. SMs have been our major source of antibiotics and are used in a range of biotechnological applications. In silico mining for biosynthetic gene clusters (BGCs) encoding the production of SMs is commonly used to assess the genetic potential of organisms. However, as BGCs span tens to over 200 kb, identifying complete BGCs requires genome data that has minimal assembly gaps within the BGCs, a prerequisite that was previously only met by individually sequenced genomes. Here, we assess the performance of the currently available genome mining platform antiSMASH on 1,080 high-quality metagenome-assembled bacterial genomes (HQ MAGs) previously produced from wastewater treatment plants (WWTPs) using a combination of long-read (Oxford Nanopore) and short-read (Illumina) sequencing technologies. More than 4,200 different BGCs were identified, with 88% of these being complete. Sequence similarity clustering of the BGCs implies that the majority of this biosynthetic potential likely encodes novel compounds, and few BGCs are shared between genera. We identify BGCs in abundant and functionally relevant genera in WWTPs, suggesting a role of secondary metabolism in this ecosystem. We find that the assembly of HQ MAGs using long-read sequencing is vital to explore the genetic potential for SM production among the uncultured members of microbial communities. IMPORTANCE Cataloguing secondary metabolite (SM) potential using genome mining of metagenomic data has become the method of choice in bioprospecting for novel compounds. However, accurate biosynthetic gene cluster (BGC) detection requires unfragmented genomic assemblies, which have been technically difficult to obtain from metagenomes until very recently with new long-read technologies. Here, we determined the biosynthetic potential of activated sludge (AS), the microbial community used in resource recovery and wastewater treatment, by mining high-quality metagenome-assembled genomes generated from long-read data. We found over 4,000 BGCs, including BGCs in abundant process-critical bacteria, with no similarity to the BGCs of characterized products. We show how long-read MAGs are required to confidently assemble complete BGCs, and we determined that the AS BGCs from different studies have very little overlap, suggesting that AS is a rich source of biosynthetic potential and new bioactive compounds.}, }
@article {pmid36444830, year = {2022}, author = {Russo, V and Ancora, M and Gatta, V and Orsini, M and Prencipe, G and Peserico, A and Colosimo, A and El Khatib, M and Mauro, A and Di Berardino, C and Scialabba, S and Tiboni, GM and Marcacci, M and Cammà, C and Barboni, B}, title = {Profiling of mitochondrial heteroplasmy in single human oocytes by next-generation sequencing.}, journal = {Molecular reproduction and development}, volume = {89}, number = {12}, pages = {646-654}, doi = {10.1002/mrd.23655}, pmid = {36444830}, issn = {1098-2795}, mesh = {Humans ; *Heteroplasmy ; *Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Oocytes/metabolism ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Mitochondrial DNA (mtDNA) plays a crucial role in the development of a competent oocyte. Indeed, mtDNA alterations may predispose to chromosome nondisjunction, resulting in infertility due to a reduced vitality and quality of oocytes and embryos. In this methods paper, the multiple displacement amplification approach was applied in combination with next-generation sequencing (NGS) to amplify and sequence, in single-end, the entire mtDNA of single human oocytes to directly construct genomic NGS libraries, and subsequently, to highlight and quantify the mutations they presented. The bioinformatic workflow was carried out with a specific ad hoc developed in-house software. This approach proved to be sensitive and specific, also highlighting the mutations present in heteroplasmy, showing deletion, insertion or substitution mutations in the genes involved in the respiratory chain, even if the found variants were benign or of uncertain meaning. The analysis of mtDNA mutations in the oocyte could provide a better understanding of specific genetic abnormalities and of their possible effect on oocyte developmental competence. This study shows how this approach, based on a massive parallel sequencing of clonally amplified DNA molecules, allows to sequence the entire mitochondrial genome of single oocytes in a short time and with a single analytical run and to verify mtDNA mutations.}, }
@article {pmid36443470, year = {2022}, author = {Jang, H and Koh, H and Gu, W and Kang, B}, title = {Integrative web cloud computing and analytics using MiPair for design-based comparative analysis with paired microbiome data.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {20465}, pmid = {36443470}, issn = {2045-2322}, mesh = {Humans ; Cloud Computing ; *Microbiota ; *Gastrointestinal Microbiome ; Mouth ; Skin ; }, abstract = {Pairing (or blocking) is a design technique that is widely used in comparative microbiome studies to efficiently control for the effects of potential confounders (e.g., genetic, environmental, or behavioral factors). Some typical paired (block) designs for human microbiome studies are repeated measures designs that profile each subject's microbiome twice (or more than twice) (1) for pre and post treatments to see the effects of a treatment on microbiome, or (2) for different organs of the body (e.g., gut, mouth, skin) to see the disparity in microbiome between (or across) body sites. Researchers have developed a sheer number of web-based tools for user-friendly microbiome data processing and analytics, though there is no web-based tool currently available for such paired microbiome studies. In this paper, we thus introduce an integrative web-based tool, named MiPair, for design-based comparative analysis with paired microbiome data. MiPair is a user-friendly web cloud service that is built with step-by-step data processing and analytic procedures for comparative analysis between (or across) groups or between baseline and other groups. MiPair employs parametric and non-parametric tests for complete or incomplete block designs to perform comparative analyses with respect to microbial ecology (alpha- and beta-diversity) and taxonomy (e.g., phylum, class, order, family, genus, species). We demonstrate its usage through an example clinical trial on the effects of antibiotics on gut microbiome. MiPair is an open-source software that can be run on our web server (http://mipair.micloud.kr) or on user's computer (https://github.com/yj7599/mipairgit).}, }
@article {pmid36442715, year = {2023}, author = {Islam, T and Albracht-Schulte, K and Ramalingam, L and Schlabritz-Lutsevich, N and Park, OH and Zabet-Moghaddam, M and Kalupahana, NS and Moustaid-Moussa, N}, title = {Anti-inflammatory mechanisms of polyphenols in adipose tissue: role of gut microbiota, intestinal barrier integrity and zinc homeostasis.}, journal = {The Journal of nutritional biochemistry}, volume = {115}, number = {}, pages = {109242}, doi = {10.1016/j.jnutbio.2022.109242}, pmid = {36442715}, issn = {1873-4847}, mesh = {Humans ; *Gastrointestinal Microbiome ; Polyphenols/pharmacology ; Lipopolysaccharides/pharmacology ; Anthocyanins/pharmacology ; Obesity/microbiology ; Inflammation/drug therapy ; Anti-Inflammatory Agents/pharmacology ; Homeostasis ; Zinc/pharmacology ; Dysbiosis/microbiology ; }, abstract = {Obesity is associated with an imbalance of micro-and macro-nutrients, gut dysbiosis, and a "leaky" gut phenomenon. Polyphenols, such as curcumin, resveratrol, and anthocyanins may alleviate the systemic effects of obesity, potentially by improving gut microbiota, intestinal barrier integrity (IBI), and zinc homeostasis. The essential micronutrient zinc plays a crucial role in the regulation of enzymatic processes, including inflammation, maintenance of the microbial ecology, and intestinal barrier integrity. In this review, we focus on IBI- which prevents intestinal lipopolysaccharide (LPS) leakage - as a critical player in polyphenol-mediated protective effects against obesity-associated white adipose tissue (WAT) inflammation. This occurs through mechanisms that block the movement of the bacterial endotoxin LPS across the gut barrier. Available research suggests that polyphenols reduce WAT and systemic inflammation via crosstalk with inflammatory NF-κB, the mammalian target of rapamycin (mTOR) signaling and zinc homeostasis.}, }
@article {pmid36442312, year = {2023}, author = {Zhong, X and Yu, S and Xu, H}, title = {Colonization dynamics in body-size spectrum of protozoan periphytons for marine bioassessment using two modified sampling systems.}, journal = {Marine pollution bulletin}, volume = {186}, number = {}, pages = {114382}, doi = {10.1016/j.marpolbul.2022.114382}, pmid = {36442312}, issn = {1879-3363}, mesh = {Ecosystem ; Biodiversity ; *Periphyton ; Environmental Monitoring/methods ; *Ciliophora ; China ; }, abstract = {The body-size spectrum of microperiphytons has been proved to be a powerful tool for bioassessment. To explore colonization dynamics in body-size spectrum of periphytic protozoa in two modified sampling systems of both glass slide (mGS) and polyurethane foam unit (mPFU), a 28-day colonization survey was conducted in coastal waters of the Yellow Sea, China. A total of 7 body-size ranks were identified from 62 species, with 7 ranks (60 species) in the mGS and 6 ranks (37 species) in the mPFU system. The stable pattern with similar body-size spectra was found earlier in the mGS system than mPFU system during the colonization period. Both the trajectory and bootstrapped average analyses revealed that the colonization dynamics were significantly different in the body-size spectrum between the two methods. Based on our data, it suggests that the mGS system might be a better choice than the mPFU system for bioassessment in marine ecosystems.}, }
@article {pmid36441249, year = {2023}, author = {Scherer, BP and Mast, A}, title = {Red Mangrove Propagule Bacterial Communities Vary With Geographic, But Not Genetic Distance.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1010-1022}, pmid = {36441249}, issn = {1432-184X}, mesh = {Humans ; *Rhizophoraceae/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Florida ; }, abstract = {Bacterial communities associated with plant propagules remain understudied, despite the opportunities that propagules represent as dispersal vectors for bacteria to new sites. These communities may be the product of a combination of environmental influence and inheritance from parent to offspring. The relative role of these mechanisms could have significant implications for our understanding of plant-microbe interactions. We studied the correlates of microbiome community similarities across an invasion front of red mangroves (Rhizophora mangle L.) in Florida, where the species is expanding northward. We collected georeferenced propagule samples from 110 individuals of red mangroves across 11 populations in Florida and used 16S rRNA gene (iTag) sequencing to describe their bacterial communities. We found no core community of bacterial amplicon sequence variants (ASVs) across the Florida range of red mangroves, though there were some ASVs shared among individuals within most populations. Populations differed significantly as measured by Bray-Curtis dissimilarity, but not Unifrac distance. We generated data from 6 microsatellite loci from 60 individuals across 9 of the 11 populations. Geographic distance was correlated with beta diversity, but genetic distance was not. We conclude that red mangrove propagule bacterial communities are likely influenced more by local environmental acquisition than by inheritance.}, }
@article {pmid36440485, year = {2022}, author = {Alsayed, AR and Al-Dulaimi, A and Alkhatib, M and Al Maqbali, M and Al-Najjar, MAA and Al-Rshaidat, MMD}, title = {A comprehensive clinical guide for Pneumocystis jirovecii pneumonia: a missing therapeutic target in HIV-uninfected patients.}, journal = {Expert review of respiratory medicine}, volume = {16}, number = {11-12}, pages = {1167-1190}, doi = {10.1080/17476348.2022.2152332}, pmid = {36440485}, issn = {1747-6356}, mesh = {Humans ; *Pneumonia, Pneumocystis/complications/diagnosis/drug therapy ; *COVID-19/complications ; *Pneumocystis carinii ; Immunocompromised Host ; *HIV Infections/complications ; }, abstract = {INTRODUCTION: Pneumocystis jirovecii is an opportunistic, human-specific fungus that causes Pneumocystis pneumonia (PCP). PCP symptoms are nonspecific. A patient with P. jirovecii and another lung infection faces a diagnostic challenge. It may be difficult to determine which of these agents is responsible for the clinical symptoms, preventing effective treatment. Diagnostic and treatment efforts have been made more difficult by the rising frequency with which coronavirus 2019 (COVID-19) and PCP co-occur.<br><br>AREAS COVERED: Herein, we provide a comprehensive review of clinical and pharmacological recommendations along with a literature review of PCP in immunocompromised patients focusing on HIV-uninfected patients.<br><br>EXPERT OPINION: PCP may be masked by identifying co-existing pathogens that are not necessarily responsible for the observed infection. Patients with severe form COVID-19 should be examined for underlying immunodeficiency, and co-infections must be considered as co-infection with P. jirovecii may worsen COVID-19's severity and fatality. PCP should be investigated in patients with PCP risk factors who come with pneumonia and suggestive radiographic symptoms but have not previously received PCP prophylaxis. PCP prophylaxis should be explored in individuals with various conditions that impair the immune system, depending on their PCP risk.}, }
@article {pmid36439796, year = {2022}, author = {Bandini, F and Vaccari, F and Soldano, M and Piccinini, S and Misci, C and Bellotti, G and Taskin, E and Cocconcelli, PS and Puglisi, E}, title = {Rigid bioplastics shape the microbial communities involved in the treatment of the organic fraction of municipal solid waste.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1035561}, pmid = {36439796}, issn = {1664-302X}, abstract = {While bioplastics are gaining wide interest in replacing conventional plastics, it is necessary to understand whether the treatment of the organic fraction of municipal solid waste (OFMSW) as an end-of-life option is compatible with their biodegradation and their possible role in shaping the microbial communities involved in the processes. In the present work, we assessed the microbiological impact of rigid polylactic acid (PLA) and starch-based bioplastics (SBB) spoons on the thermophilic anaerobic digestion and the aerobic composting of OFMSW under real plant conditions. In order to thoroughly evaluate the effect of PLA and SBB on the bacterial, archaeal, and fungal communities during the process, high-throughput sequencing (HTS) technology was carried out. The results suggest that bioplastics shape the communities' structure, especially in the aerobic phase. Distinctive bacterial and fungal sequences were found for SBB compared to the positive control, which showed a more limited diversity. Mucor racemosus was especially abundant in composts from bioplastics' treatment, whereas Penicillium roqueforti was found only in compost from PLA and Thermomyces lanuginosus in that from SBB. This work shed a light on the microbial communities involved in the OFMSW treatment with and without the presence of bioplastics, using a new approach to evaluate this end-of-life option.}, }
@article {pmid36436634, year = {2023}, author = {Sakarika, M and Regueira, A and Rabaey, K and Ganigué, R}, title = {Thermophilic caproic acid production from grass juice by sugar-based chain elongation.}, journal = {The Science of the total environment}, volume = {860}, number = {}, pages = {160501}, doi = {10.1016/j.scitotenv.2022.160501}, pmid = {36436634}, issn = {1879-1026}, mesh = {*Caproates ; Fermentation ; *Bioreactors ; Sugars ; Carbohydrates ; Carboxylic Acids ; Glucose ; }, abstract = {Medium chain carboxylic acids (MCCA) such as caproic acid have a plethora of applications, ranging from food additives to bioplastics. MCCA can be produced via microbial chain elongation using waste and side-streams as substrates, a process that can be more sustainable than conventional production routes. Most chain elongation studies have focused on mesophilic conditions, with only two recent studies hinting at the possibility of thermophilic chain elongation, but a systematic study of its mechanisms is lacking. Here, we investigated thermophilic chain elongation from grass juice, to understand the effect of key operational parameters (pH, temperature, substrate) on the process performance and to establish the key microbial genera and their role in the system. The genus Caproiciproducens was identified as responsible for thermophilic chain elongation, and caproic acid production was most favorable at pH 6.0 and 50 °C among the conditions tested, reaching an average concentration of 3.4 g/L. Batch experiments showed that the substrate for caproic acid production were glucose and xylose, while lactic acid led to the production of only butyric acid. Fed-batch experiments showed that substrate availability and the presence of caproic acid in the system play a major role in shaping the profile of thermophilic chain elongation. The increase of the total sugar concentration by glucose addition (without changing the organic load) during continuous operation led to a microbial community dominated (75 %) by Caproiciproducens and increased by 76 % the final average caproic acid concentration to 6.0 g/L (13 gCOD/L) which represented 32 % (g/g) of the total carboxylic acids. The highest concentration achieved was 7.2 g/L (day 197) which is the highest concentration reported under thermophilic conditions thus far. The results of this work pave the way to the potential development of thermophilic systems for upgrading various underexplored abundant and cheap sugar-rich side-streams to caproic acid.}, }
@article {pmid36436244, year = {2023}, author = {Sun, W and Qian, X and Wang, X and Gu, J}, title = {Residual enrofloxacin in cattle manure increased persistence and dissemination risk of antibiotic resistance genes during anaerobic digestion.}, journal = {Journal of environmental management}, volume = {326}, number = {Pt B}, pages = {116864}, doi = {10.1016/j.jenvman.2022.116864}, pmid = {36436244}, issn = {1095-8630}, mesh = {Cattle ; Animals ; *Manure/analysis ; *Anti-Bacterial Agents/pharmacology/metabolism ; Enrofloxacin/pharmacology ; Anaerobiosis ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; }, abstract = {Anaerobic digestion is a common approach to dispose and recycle livestock manures, and the agricultural application of anaerobic digestives represents an important pathway of spreading antibiotic resistance genes (ARGs) from livestock manures to soils. Enrofloxacin is a clinically important fluoroquinolone antibiotic with high residual concentrations in livestock manure, and propagation of fluoroquinolone resistance genes poses a huge risk to public health. Compared with other antibiotics, enrofloxacin is relatively durable in anaerobic digestion system. However, its effect on the persistence of ARGs during anaerobic digestion and its mechanism are not clear. In this study, we investigated effects of 0, 4, and 8 mg/L enrofloxacin on the abundance, persistence, and transferring risk of five plasmid-mediated fluroquinolone ARGs and five typic clinically important non-fluoroquinolone ARGs during cattle manure digestion. The responses of integrons and microbial communities to enrofloxacin were assessed to uncover the underlying mechanisms. All the ten detected ARGs were highly persistent in anaerobic digestion, among them seven ARGs increased over 8.2 times after digestion. Network analysis revealed that the potential hosts of ARGs were critical functional taxa during anaerobic digestion, which can explain the high persistence of ARGs. Residual enrofloxacin significantly increased the abundance of aac(6')-ib-cr, sul1, intI1, and intI2 throughout the digestion, but had no impact on the other ARGs, demonstrating its role in facilitating horizontal gene transfer of the plasmid-mediated aac(6')-ib-cr. The influence of enrofloxacin on microbial communities disappeared at the end of digestion, but the ARG profiles remained distinctive between the enrofloxacin treatments and the control, suggesting the high persistence of enrofloxacin induced ARGs. Our results suggested the high persistence of ARGs in anaerobic digestion system, and highlighted the role of residual enrofloxacin in livestock manure in increasing dissemination risk of fluroquinolone resistance genes.}, }
@article {pmid36434466, year = {2023}, author = {Hietaranta, E and Juottonen, H and Kytöviita, MM}, title = {Honeybees affect floral microbiome composition in a central food source for wild pollinators in boreal ecosystems.}, journal = {Oecologia}, volume = {201}, number = {1}, pages = {59-72}, pmid = {36434466}, issn = {1432-1939}, mesh = {Bees ; Animals ; *Pollination ; Insecta ; Plants ; Pollen ; *Microbiota ; Flowers ; }, abstract = {Basic knowledge on dispersal of microbes in pollinator networks is essential for plant, insect, and microbial ecology. Thorough understanding of the ecological consequences of honeybee farming on these complex plant-pollinator-microbe interactions is a prerequisite for sustainable honeybee keeping. Most research on plant-pollinator-microbe interactions have focused on temperate agricultural systems. Therefore, information on a wild plant that is a seasonal bottleneck for pollinators in cold climate such as Salix phylicifolia is of specific importance. We investigated how floral visitation by insects influences the community structure of bacteria and fungi in Salix phylicifolia inflorescences under natural conditions. Insect visitors were experimentally excluded with net bags. We analyzed the microbiome and measured pollen removal in open and bagged inflorescences in sites where honeybees were foraging and in sites without honeybees. Site and plant individual explained most of the variation in floral microbial communities. Insect visitation and honeybees had a smaller but significant effect on the community composition of microbes. Honeybees had a specific effect on the inflorescence microbiome and, e.g., increased the relative abundance of operational taxonomic units (OTUs) from the bacterial order Lactobacillales. Site had a significant effect on the amount of pollen removed from inflorescences but this was not due to honeybees. Insect visitors increased bacterial and especially fungal OTU richness in the inflorescences. Pollinator visits explained 38% variation in fungal richness, but only 10% in bacterial richness. Our work shows that honeybee farming affects the floral microbiome in a wild plant in rural boreal ecosystems.}, }
@article {pmid36434303, year = {2023}, author = {Querejeta, M and Hervé, V and Perdereau, E and Marchal, L and Herniou, EA and Boyer, S and Giron, D}, title = {Changes in Bacterial Community Structure Across the Different Life Stages of Black Soldier Fly (Hermetia illucens).}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1254-1267}, pmid = {36434303}, issn = {1432-184X}, support = {EX004527//Conseil R&#xe9;gional du Centre-Val de Loire/ ; EX011185//European Regional Development Fund/ ; AYUD/2021/58607//Fundaci&#xf3;n para el Fomento en Asturias de la Investigaci&#xf3;n Cient&#xed;fica Aplicada y la Tecnolog&#xed;a/ ; }, mesh = {Animals ; *Diptera/microbiology ; Larva/microbiology ; Digestion ; Pupa ; *Microbiota ; Bacteria/genetics ; }, abstract = {The digestive capacity of organic compounds by the black soldier fly (BSF, Hermetia illucens, Diptera: Stratiomyidae, Linnaeus, 1758) is known to rely on complex larva-microbiota interactions. Although insect development is known to be a driver of changes of bacterial communities, the fluctuations along BSF life cycle in terms of composition and diversity of bacterial communities are still unknown. In this work, we used a metabarcoding approach to explore the differences in bacterial diversity along all four BSF developmental stages: eggs, larvae, pupae, and adult. We detected not only significant differences in bacterial community composition and species richness along the development of BSF, but also nine prevalent amplicon single variants (ASVs) forming the core microbiota. Out of the 2010 ASVs identified, 160 were significantly more abundant in one of the life stages. Moreover, using PICRUSt2, we inferred 27 potential metabolic pathways differentially used among the BSF life cycle. This distribution of metabolic pathways was congruent with the bacterial taxonomic distribution among life stages, demonstrating that the functional requirements of each phase of development are drivers of bacterial composition and diversity. This study provides a better understanding of the different metabolic processes occurring during BSF development and their links to changes in bacterial taxa. This information has important implications for improving bio-waste processing in such an economically important insect species.}, }
@article {pmid36432829, year = {2022}, author = {May-Mutul, CG and López-Garrido, MA and O'Connor-Sánchez, A and Peña-Ramírez, YJ and Labrín-Sotomayor, NY and Estrada-Medina, H and Ferrer, MM}, title = {Hidden Tenants: Microbiota of the Rhizosphere and Phyllosphere of Cordia dodecandra Trees in Mayan Forests and Homegardens.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {22}, pages = {}, pmid = {36432829}, issn = {2223-7747}, support = {CB 2017-2018 A1S30471//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Honors-thesis-grants 31490//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Honors-thesis-grants 31430//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; }, abstract = {During domestication, the selection of cultivated plants often reduces microbiota diversity compared with their wild ancestors. Microbiota in compartments such as the phyllosphere or rhizosphere can promote fruit tree health, growth, and development. Cordia dodecandra is a deciduous tree used by Maya people for its fruit and wood, growing, to date, in remnant forest fragments and homegardens (traditional agroforestry systems) in Yucatán. In this work, we evaluated the microbiota's alpha and beta diversity per compartment (phyllosphere and rhizosphere) and per population (forest and homegarden) in the Northeast and Southwest Yucatán regions. Eight composite DNA samples (per compartment/population/region combination) were amplified for 16S-RNA (bacteria) and ITS1-2 (fungi) and sequenced by Illumina MiSeq. Bioinformatic analyses were performed with QIIME and phyloseq. For bacteria and fungi, from 107,947 and 128,786 assembled sequences, 618 and 1092 operating taxonomic units (OTUs) were assigned, respectively. The alpha diversity of bacteria and fungi was highly variable among samples and was similar among compartments and populations. A significant species turnover among populations and regions was observed in the rhizosphere. The core microbiota from the phyllosphere was similar among populations and regions. Forests and homegarden populations are reservoirs of the C. dodecandra phyllosphere core microbiome and significant rhizosphere biodiversity.}, }
@article {pmid36431270, year = {2022}, author = {Cheng, T and Zhi, H and Liu, Y and Zhang, S and Song, Z and Li, Y}, title = {Dual Anti-Glomerular Basement Membrane and Anti-Neutrophil Cytoplasmic Antibodies-Positive Rapidly Progressive Glomerulonephritis with Rheumatoid Arthritis and Sjogren's Syndrome: A Case Report and Literature Review.}, journal = {Journal of clinical medicine}, volume = {11}, number = {22}, pages = {}, pmid = {36431270}, issn = {2077-0383}, support = {82170716//National Natural Science Foundation of China/ ; }, abstract = {Rapidly progressive glomerulonephritis (RPGN) is a life-threatening disease characterized by rapid progressive deterioration of renal function and extensive formation of crescents. Some antibodies tend to be positive, such as a perinuclear anti-neutrophil cytoplasmic antibody (p-ANCA) and anti-glomerular basement membrane (anti-GBM) antibodies, in most patients with the disease. However, cases of double positivity for the above antibodies are considered to be rare. In addition, both rheumatoid arthritis (RA) and Sjogren's syndrome (SS) are deemed to be independent immune disorders that can cause renal impairment. Nevertheless, the association between RPGN and these two diseases has not been elucidated in previous studies. Here, we provide a case of RPGN with the concurrence of RA and SS characterized by double positivity in anti-GBM antibodies and p-ANCA. After aggressive treatment with cyclophosphamide, glucocorticoids, and plasma exchange, the patient improved significantly. Despite the malignant event of arteriovenous fistula rupture and bleeding during treatment, the patient survived with renal function recovery for the rest of the follow-up period.}, }
@article {pmid36431177, year = {2022}, author = {Zhi, W and Yuan, X and Song, W and Jin, G and Li, Y}, title = {Fecal Microbiota Transplantation May Represent a Good Approach for Patients with Focal Segmental Glomerulosclerosis: A Brief Report.}, journal = {Journal of clinical medicine}, volume = {11}, number = {22}, pages = {}, pmid = {36431177}, issn = {2077-0383}, support = {82170716//National Natural Science Foundation of China, Gut microbiota promotes IgAN through CASP-1/IL-1&#x3b2;-driven increased intestinal permeability/ ; }, abstract = {This is the first report of fecal microbiota transplantation (FMT) in patients with chronic kidney disease. The patient was subjected to focal segmental glomerulosclerosis (FSGS), with onset in April 2021. The main manifestation featured abnormal renal function and no proteinuria at the level of nephrotic syndrome. In May 2021, she showed biopsy-proven FSGS and was treated with glucocorticoid. However, after glucocorticoid reduction, the patient's serum creatinine increased again, so she adjusted the dosage and continued use until now. In April 2022, the patient was prescribed the FMT capsules. After FMT, the renal function remained stable, urinary protein decreased, reaching the clinical standard of complete remission, and there was no recurrence after glucocorticoid reduction. Furthermore, the patient showed significantly decreased hyperlipidemia, triglyceride (TG) and cholesterol (CHO) after FMT. During FMT, the level of cytokines fluctuated slightly, but returned to the pre-transplantation level after three months. From this, we conclude that FMT is a potential adjuvant therapy for FSGS, and patients can benefit from improving renal function and dyslipidemia.}, }
@article {pmid36430059, year = {2022}, author = {Savadova-Ratkus, K and Mazur-Marzec, H and Karosienė, J and Sivonen, K and Suurnäkki, S and Kasperovičienė, J and Paškauskas, R and Koreivienė, J}, title = {Cyanobacteria and Their Metabolites in Mono- and Polidominant Shallow Eutrophic Temperate Lakes.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {22}, pages = {}, pmid = {36430059}, issn = {1660-4601}, mesh = {*Lakes ; Ecosystem ; *Cyanobacteria ; Biota ; Biomass ; }, abstract = {Monodominant (one species dominates) or polidominant (multiple species dominate) cyanobacterial blooms are pronounced in productive freshwater ecosystems and pose a potential threat to the biota due to the synthesis of toxins. Seasonal changes in cyanobacteria species and cyanometabolites composition were studied in two shallow temperate eutrophic lakes. Data on cyanobacteria biomass and diversity of dominant species in the lakes were combined with chemical and molecular analyses of fifteen potentially toxin-producing cyanobacteria species (248 isolates from the lakes). Anatoxin-a, saxitoxin, microcystins and other non-ribosomal peptides formed the diverse profiles in monodominant (Planktothrix agardhii) and polidominant (Aphanizomenon gracile, Limnothrix spp. and Planktolyngbya limnetica) lakes. However, the harmfulness of the blooms depended on the ability of the dominant species to synthesize cyanometabolites. It was confirmed that P. agardhii produced a greater amount and diverse range of MCs and other NRPs. In the polidominant lake, isolates of the co-dominant A. gracile, L. planctonica and P. limnetica synthesized no or only small amounts of cyanometabolites. In general, the profile of cyanometabolites was greater in cyanobacteria isolates than in environmental samples, indicating a high potential for toxic cyanobacteria bloom.}, }
@article {pmid36427812, year = {2023}, author = {Ramsperger, AFRM and Bergamaschi, E and Panizzolo, M and Fenoglio, I and Barbero, F and Peters, R and Undas, A and Purker, S and Giese, B and Lalyer, CR and Tamargo, A and Moreno-Arribas, MV and Grossart, HP and Kühnel, D and Dietrich, J and Paulsen, F and Afanou, AK and Zienolddiny-Narui, S and Eriksen Hammer, S and Kringlen Ervik, T and Graff, P and Brinchmann, BC and Nordby, KC and Wallin, H and Nassi, M and Benetti, F and Zanella, M and Brehm, J and Kress, H and Löder, MGJ and Laforsch, C}, title = {Nano- and microplastics: a comprehensive review on their exposure routes, translocation, and fate in humans.}, journal = {NanoImpact}, volume = {29}, number = {}, pages = {100441}, doi = {10.1016/j.impact.2022.100441}, pmid = {36427812}, issn = {2452-0748}, mesh = {Humans ; *Microplastics/metabolism ; *Plastics/metabolism ; Ecosystem ; Gastrointestinal Tract/metabolism ; Respiratory System/metabolism ; }, abstract = {Contamination of the environment with nano-and microplastic particles (NMPs) and its putative adverse effects on organisms, ecosystems, and human health is gaining increasing scientific and public attention. Various studies show that NMPs occur abundantly within the environment, leading to a high likelihood of human exposure to NMPs. Here, different exposure scenarios can occur. The most notable exposure routes of NMPs into the human body are via the airways and gastrointestinal tract (GIT) through inhalation or ingestion, but also via the skin due to the use of personal care products (PCPs) containing NMPs. Once NMPs have entered the human body, it is possible that they are translocated from the exposed organ to other body compartments. In our review article, we combine the current knowledge on the (1) exposure routes of NMPs to humans with the basic understanding of the potential (2) translocation mechanisms into human tissues and, consequently, their (3) fate within the human body. Regarding the (1) exposure routes, we reviewed the current knowledge on the occurrence of NMPs in food, beverages, personal care products and the air (focusing on indoors and workplaces) and found that the studies suggest an abundant presence of MPs within the exposure scenarios. The overall abundance of MPs in exposure matrices relevant to humans highlights the importance of understanding whether NMPs have the potential for tissue translocation. Therefore, we describe the current knowledge on the potential (2) translocation pathways of NMPs from the skin, GIT and respiratory systems to other body compartments. Here, particular attention was paid to how likely NMPs can translocate from the primary exposed organs to secondary organs due to naturally occurring defence mechanisms against tissue translocation. Based on the current understanding, we conclude that a dermal translocation of NMPs is rather unlikely. In contrast, small MPs and NPs can generally translocate from the GIT and respiratory system to other tissues. Thus, we reviewed the existing literature on the (3) fate of NMPs within the human body. Based on the current knowledge of the contamination of human exposure routes and the potential translocation mechanisms, we critically discuss the size of the detected particles reported in the fate studies. In some cases, the particles detected in human tissue samples exceed the size of a particle to overcome biological barriers allowing particle translocation into tissues. Therefore, we emphasize the importance of critically reading and discussing the presented results of NMP in human tissue samples.}, }
@article {pmid36424853, year = {2023}, author = {Chang, J and Duong, TA and Schoeman, C and Ma, X and Roodt, D and Barker, N and Li, Z and Van de Peer, Y and Mizrachi, E}, title = {The genome of the king protea, Protea cynaroides.}, journal = {The Plant journal : for cell and molecular biology}, volume = {113}, number = {2}, pages = {262-276}, pmid = {36424853}, issn = {1365-313X}, support = {833522/ERC_/European Research Council/International ; }, mesh = {*Proteaceae/genetics ; Ecosystem ; Genomics ; South Africa ; Soil ; }, abstract = {The king protea (Protea cynaroides), an early-diverging eudicot, is the most iconic species from the Megadiverse Cape Floristic Region, and the national flower of South Africa. Perhaps best known for its iconic flower head, Protea is a key genus for the South African horticulture industry and cut-flower market. Ecologically, the genus and the family Proteaceae are important models for radiation and adaptation, particularly to soils with limited phosphorus bio-availability. Here, we present a high-quality chromosome-scale assembly of the P. cynaroides genome as the first representative of the fynbos biome. We reveal an ancestral whole-genome duplication event that occurred in the Proteaceae around the late Cretaceous that preceded the divergence of all crown groups within the family and its extant diversity in all Southern continents. The relatively stable genome structure of P. cynaroides is invaluable for comparative studies and for unveiling paleopolyploidy in other groups, such as the distantly related sister group Ranunculales. Comparative genomics in sequenced genomes of the Proteales shows loss of key arbuscular mycorrhizal symbiosis genes likely ancestral to the family, and possibly the order. The P. cynaroides genome empowers new research in plant diversification, horticulture and adaptation, particularly to nutrient-poor soils.}, }
@article {pmid36423548, year = {2023}, author = {Wu, D and Zhao, J and Su, Y and Yang, M and Dolfing, J and Graham, DW and Yang, K and Xie, B}, title = {Explaining the resistomes in a megacity's water supply catchment: Roles of microbial assembly-dominant taxa, niched environments and pathogenic bacteria.}, journal = {Water research}, volume = {228}, number = {Pt A}, pages = {119359}, doi = {10.1016/j.watres.2022.119359}, pmid = {36423548}, issn = {1879-2448}, support = {MR/P028195/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Drinking Water ; China ; Water Supply ; Bacteria/genetics ; Anti-Bacterial Agents ; }, abstract = {Antibiotic resistance genes (ARGs) in drinking water sources suggest the possible presence of resistant microorganisms that jeopardize human health. However, explanations for the presence of specific ARGs in situ are largely unknown, especially how their prevalence is affected by local microbial ecology, taxa assembly and community-wide gene transfer. Here, we characterized resistomes and bacterial communities in the Taipu River catchment, which feeds a key drinking water reservoir to a global megacity, Shanghai. Overall, ARG abundances decreased significantly as the river flowed downstream towards the reservoir (P < 0.01), whereas the waterborne bacteria assembled deterministically (|βNRI| > 2.0) as a function of temperature and dissolved oxygen conditions with the assembly-dominant taxa (e.g. Ilumatobacteraceae and Cyanobiaceae) defining local resistomes (P < 0.01, Cohen's D = 4.22). Bacterial hosts of intragenomic ARGs stayed at the same level across the catchment (60 ∼ 70 genome copies per million reads). Among them, the putative resistant pathogens (e.g. Burkholderiaceae) carried mixtures of ARGs that exhibited high transmission probability (transfer counts = 126, P < 0.001), especially with the microbial assembly-dominant taxa. These putative resistant pathogens had densities ranging form 3.0 to 4.0 × 10[6] cell/L, which was more pronouncedly affected by resistome and microbial assembly structures than environmental factors (SEM, std-coeff β = 0.62 vs. 0.12). This work shows that microbial assembly and resistant pathogens play predominant roles in prevelance and dissemination of resistomes in receiving water, which deserves greater attention in devisng control strategies for reducing in-situ ARGs and resistant strains in a catchment.}, }
@article {pmid36423338, year = {2022}, author = {Abera, S and Shimels, M and Tessema, T and Raaijmakers, JM and Dini-Andreote, F}, title = {Back to the roots: defining the core microbiome of Sorghum bicolor in agricultural field soils from the centre of origin.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {12}, pages = {}, doi = {10.1093/femsec/fiac136}, pmid = {36423338}, issn = {1574-6941}, mesh = {Humans ; *Sorghum ; Soil ; Plant Roots ; *Microbiota/genetics ; Rhizosphere ; Edible Grain ; }, abstract = {Sorghum is a major staple crop in sub-Saharan Africa with yields severely impacted by biotic and abiotic factors. Here, we analysed the taxonomic diversity and biogeographical distribution of bacterial taxa of 48 agricultural fields along a transect of approximately 2000 km across the Ethiopian sorghum belt, the centre of origin of sorghum. The ultimate goal is to identify-yet-unexplored-beneficial plant-microbe associations. Based on bulk soil bacterial communities and DArT-SNP analyses of 59 sorghum accessions, we selected three microbiologically distinct field soils and 12 sorghum genotypes, including commercial varieties, wild relatives, and farmer-preferred landraces. The results showed a core rhizosphere microbiome of 2125 amplicon sequence variants (ASVs), belonging to eight bacterial families consistently found across the three soil types and the 12 sorghum genotypes. Integration of the rhizosphere bacterial community analysis with DArT-SNP sorghum genotyping revealed the association of differentially abundant ASVs with sorghum genotypic traits, including the distinct recruitment of Pseudomonadaceae by the stay-green, drought-tolerant, and wild sorghum genotypes. Collectively, these results provide new insights into the core and accessory bacterial taxa in the sorghum rhizosphere in the centre of origin, setting a baseline for targeted isolation and functional characterization of putative beneficial rhizobacteria.}, }
@article {pmid36422381, year = {2022}, author = {Cantillo-González, A and Anguita, J and Rojas, C and Vargas, IT}, title = {Winogradsky Bioelectrochemical System as a Novel Strategy to Enrich Electrochemically Active Microorganisms from Arsenic-Rich Sediments.}, journal = {Micromachines}, volume = {13}, number = {11}, pages = {}, pmid = {36422381}, issn = {2072-666X}, support = {FONDECYT 1201134//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; FONDAP 15110020//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; }, abstract = {Bioelectrochemical systems (BESs) have been extensively studied for treatment and remediation. However, BESs have the potential to be used for the enrichment of microorganisms that could replace their natural electron donor or acceptor for an electrode. In this study, Winogradsky BES columns with As-rich sediments extracted from an Andean watershed were used as a strategy to enrich lithotrophic electrochemically active microorganisms (EAMs) on electrodes (i.e., cathodes). After 15 months, Winogradsky BESs registered power densities up to 650 μWcm[-2]. Scanning electron microscopy and linear sweep voltammetry confirmed microbial growth and electrochemical activity on cathodes. Pyrosequencing evidenced differences in bacterial composition between sediments from the field and cathodic biofilms. Six EAMs from genera Herbaspirillum, Ancylobacter, Rhodococcus, Methylobacterium, Sphingomonas, and Pseudomonas were isolated from cathodes using a lithoautotrophic As oxidizers culture medium. These results suggest that the tested Winogradsky BES columns result in an enrichment of electrochemically active As-oxidizing microorganisms. A bioelectrochemical boost of centenarian enrichment approaches, such as the Winogradsky column, represents a promising strategy for prospecting new EAMs linked with the biogeochemical cycles of different metals and metalloids.}, }
@article {pmid36421212, year = {2022}, author = {Stoll, ML and Wang, J and Kau, CH and Pierce, MK and Morrow, CD and Geurs, NC}, title = {Pro-Inflammatory Oral Microbiota in Juvenile Spondyloarthritis: A Pilot Study.}, journal = {Children (Basel, Switzerland)}, volume = {9}, number = {11}, pages = {}, pmid = {36421212}, issn = {2227-9067}, support = {P30 AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR000165/TR/NCATS NIH HHS/United States ; P30Ar050948/NH/NIH HHS/United States ; UL1TR000165/NH/NIH HHS/United States ; }, abstract = {The role of the microbiota in the pathogenesis of arthritis is gaining increasing attention. While multiple studies have queried the intestinal microbiota, very few have analyzed the contents of the oral microbiota. In this pilot study, we obtained salivary and sub-gingival specimens from a cohort of six healthy controls and five children with well-controlled spondyloarthritis (SpA) and performed 16S sequencing on bacteria obtained from both habitats. The Quantitative Insight into Microbial Ecology tool suite was used to generate operational taxonomic units, Phyloseq was used for diversity analyses, and DeSeq2 was used to compare abundances while adjusting for multiple comparisons. A repeat specimen was obtained from one subject during a flare. Clustering based upon diagnosis was observed from both habitats, with decreased alpha diversity seen within the plaque obtained from the patients vs. controls. Among the differentially abundant taxa were statistically significantly increased plaque Fusobacterium and salivary Rothia mucilaginosa among the patients compared to the controls. Additionally, the abundance of plaque Fusobacterium increased in one patient at the time of a flare. Our data suggest that the oral cavity may harbor bacteria involved in the pathogenesis of spondyloarthritis; additional studies are warranted.}, }
@article {pmid36419905, year = {2023}, author = {Zhang, X and Arbour, T and Zhang, D and Wei, S and Rabaey, K}, title = {Microbial electrosynthesis of acetate from CO2 under hypersaline conditions.}, journal = {Environmental science and ecotechnology}, volume = {13}, number = {}, pages = {100211}, pmid = {36419905}, issn = {2666-4984}, abstract = {Microbial electrosynthesis (MES) enables the bioproduction of multicarbon compounds from CO2 using electricity as the driver. Although high salinity can improve the energetic performance of bioelectrochemical systems, acetogenic processes under elevated salinity are poorly known. Here MES under 35-60 g L[-1] salinity was evaluated. Acetate production in two-chamber MES systems at 35 g L[-1] salinity (seawater composition) gradually decreased within 60 days, both under -1.2 V cathode potential (vs. Ag/AgCl) and -1.56 A m[-2] reductive current. Carbonate precipitation on cathodes (mostly CaCO3) likely declined the production through inhibiting CO2 supply, the direct electrode contact for acetogens and H2 production. Upon decreasing Ca[2+] and Mg[2+] levels in three-chamber reactors, acetate was stably produced over 137 days along with a low cathode apparent resistance at 1.9 ± 0.6 mΩ m[2] and an average production rate at 3.80 ± 0.21 g m[-2] d[-1]. Increasing the salinity step-wise from 35 to 60 g L[-1] gave the most efficient acetate production at 40 g L[-1] salinity with average rates of acetate production and CO2 consumption at 4.56 ± 3.09 and 7.02 ± 4.75 g m[-2] d[-1], respectively. The instantaneous coulombic efficiency for VFA averaged 55.1 ± 31.4%. Acetate production dropped at higher salinity likely due to the inhibited CO2 dissolution and acetogenic metabolism. Acetobacterium up to 78% was enriched on cathodes as the main acetogen at 35 g L[-1]. Under high-salinity selection, 96.5% Acetobacterium dominated on the cathode along with 34.0% Sphaerochaeta in catholyte. This research provides a first proof of concept that MES starting from CO2 reduction can be achieved at elevated salinity.}, }
@article {pmid36419170, year = {2022}, author = {Chang, J and Tian, L and Leite, MFA and Sun, Y and Shi, S and Xu, S and Wang, J and Chen, H and Chen, D and Zhang, J and Tian, C and Kuramae, EE}, title = {Nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the wild rice Oryza rufipogon core rhizomicrobiome.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {196}, pmid = {36419170}, issn = {2049-2618}, mesh = {*Oryza/microbiology ; Nitrogen ; Carbon ; Manganese ; Iron ; Bacteria/genetics ; Soil ; }, abstract = {BACKGROUND: The assembly of the rhizomicrobiome, i.e., the microbiome in the soil adhering to the root, is influenced by soil conditions. Here, we investigated the core rhizomicrobiome of a wild plant species transplanted to an identical soil type with small differences in chemical factors and the impact of these soil chemistry differences on the core microbiome after long-term cultivation. We sampled three natural reserve populations of wild rice (i.e., in situ) and three populations of transplanted in situ wild rice grown ex situ for more than 40 years to determine the core wild rice rhizomicrobiome.<br><br>RESULTS: Generalized joint attribute modeling (GJAM) identified a total of 44 amplicon sequence variants (ASVs) composing the core wild rice rhizomicrobiome, including 35 bacterial ASVs belonging to the phyla Actinobacteria, Chloroflexi, Firmicutes, and Nitrospirae and 9 fungal ASVs belonging to the phyla Ascomycota, Basidiomycota, and Rozellomycota. Nine core bacterial ASVs belonging to the genera Haliangium, Anaeromyxobacter, Bradyrhizobium, and Bacillus were more abundant in the rhizosphere of ex situ wild rice than in the rhizosphere of in situ wild rice. The main ecological functions of the core microbiome were nitrogen fixation, manganese oxidation, aerobic chemoheterotrophy, chemoheterotrophy, and iron respiration, suggesting roles of the core rhizomicrobiome in improving nutrient resource acquisition for rice growth. The function of the core rhizosphere bacterial community was significantly (p < 0.05) shaped by electrical conductivity, total nitrogen, and available phosphorus present in the soil adhering to the roots.<br><br>CONCLUSION: We discovered that nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the core rhizomicrobiome of the wild rice Oryza rufipogon. Our findings suggest that further potential utilization of the core rhizomicrobiome should consider the effects of soil properties on the abundances of different genera. Video Abstract.}, }
@article {pmid36415023, year = {2022}, author = {Baumgartner, M and Zirnbauer, R and Schlager, S and Mertens, D and Gasche, N and Sladek, B and Herbold, C and Bochkareva, O and Emelianenko, V and Vogelsang, H and Lang, M and Klotz, A and Moik, B and Makristathis, A and Berry, D and Dabsch, S and Khare, V and Gasche, C}, title = {Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2143218}, pmid = {36415023}, issn = {1949-0984}, mesh = {Humans ; *Enteropathogenic Escherichia coli/genetics ; *Colitis, Ulcerative ; *Escherichia coli Infections ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases ; }, abstract = {With increasing urbanization and industrialization, the prevalence of inflammatory bowel diseases (IBDs) has steadily been rising over the past two decades. IBD involves flares of gastrointestinal (GI) inflammation accompanied by microbiota perturbations. However, microbial mechanisms that trigger such flares remain elusive. Here, we analyzed the association of the emerging pathogen atypical enteropathogenic E. coli (aEPEC) with IBD disease activity. The presence of diarrheagenic E. coli was assessed in stool samples from 630 IBD patients and 234 age- and sex-matched controls without GI symptoms. Microbiota was analyzed with 16S ribosomal RNA gene amplicon sequencing, and 57 clinical aEPEC isolates were subjected to whole-genome sequencing and in vitro pathogenicity experiments including biofilm formation, epithelial barrier function and the ability to induce pro-inflammatory signaling. The presence of aEPEC correlated with laboratory, clinical and endoscopic disease activity in ulcerative colitis (UC), as well as microbiota dysbiosis. In vitro, aEPEC strains induce epithelial p21-activated kinases, disrupt the epithelial barrier and display potent biofilm formation. The effector proteins espV and espG2 distinguish aEPEC cultured from UC and Crohn's disease patients, respectively. EspV-positive aEPEC harbor more virulence factors and have a higher pro-inflammatory potential, which is counteracted by 5-ASA. aEPEC may tip a fragile immune-microbiota homeostasis and thereby contribute to flares in UC. aEPEC isolates from UC patients display properties to disrupt the epithelial barrier and to induce pro-inflammatory signaling in vitro.}, }
@article {pmid36413896, year = {2023}, author = {Mijnendonckx, K and Rogiers, T and Giménez Del Rey, FJ and Merroun, ML and Williamson, A and Ali, MM and Charlier, D and Leys, N and Boon, N and Van Houdt, R}, title = {PrsQ2, a small periplasmic protein involved in increased uranium resistance in the bacterium Cupriavidus metallidurans.}, journal = {Journal of hazardous materials}, volume = {444}, number = {Pt A}, pages = {130410}, doi = {10.1016/j.jhazmat.2022.130410}, pmid = {36413896}, issn = {1873-3336}, mesh = {*Uranium/toxicity ; *Cupriavidus/genetics ; Uranyl Nitrate ; Acclimatization ; }, abstract = {Uranium contamination is a widespread problem caused by natural and anthropogenic activities. Although microorganisms thrive in uranium-contaminated environments, little is known about the actual molecular mechanisms mediating uranium resistance. Here, we investigated the resistance mechanisms driving the adaptation of Cupriavidus metallidurans NA4 to toxic uranium concentrations. We selected a spontaneous mutant able to grow in the presence of 1 mM uranyl nitrate compared to 250 µM for the parental strain. The increased uranium resistance was acquired via the formation of periplasmic uranium-phosphate precipitates facilitated by the increased expression of a genus-specific small periplasmic protein, PrsQ2, regulated as non-cognate target of the CzcS2-CzcR2 two-component system. This study shows that bacteria can adapt to toxic uranium concentrations and explicates the complete genetic circuit behind the adaptation.}, }
@article {pmid36413834, year = {2023}, author = {Páez-Watson, T and van Loosdrecht, MCM and Wahl, SA}, title = {Predicting the impact of temperature on metabolic fluxes using resource allocation modelling: Application to polyphosphate accumulating organisms.}, journal = {Water research}, volume = {228}, number = {Pt A}, pages = {119365}, doi = {10.1016/j.watres.2022.119365}, pmid = {36413834}, issn = {1879-2448}, mesh = {Temperature ; *Polyphosphates ; *Resource Allocation ; Biomass ; Sewage ; }, abstract = {The understanding of microbial communities and the biological regulation of its members is crucial for implementation of novel technologies using microbial ecology. One poorly understood metabolic principle of microbial communities is resource allocation and biosynthesis. Resource allocation theory in polyphosphate accumulating organisms (PAOs) is limited as a result of their slow imposed growth rate (typical sludge retention times of at least 4 days) and limitations to quantify changes in biomass components over a 6 hours cycle (less than 10% of their growth). As a result, there is no direct evidence supporting that biosynthesis is an exclusive aerobic process in PAOs that alternate continuously between anaerobic and aerobic phases. Here, we apply resource allocation metabolic flux analysis to study the optimal phenotype of PAOs over a temperature range of 4 °C to 20 °C. The model applied in this research allowed to identify optimal metabolic strategies in a core metabolic model with limited constraints based on biological principles. The addition of a constraint limiting biomass synthesis to be an exclusive aerobic process changed the metabolic behaviour and improved the predictability of the model over the studied temperature range by closing the gap between prediction and experimental findings. The results validate the assumption of limited anaerobic biosynthesis in PAOs, specifically "Candidatus Accumulibacter" related species. Interestingly, the predicted growth yield was lower, suggesting that there are mechanistic barriers for anaerobic growth not yet understood nor reflected in the current models of PAOs. Moreover, we identified strategies of resource allocation applied by PAOs at different temperatures as a result of the decreased catalytic efficiencies of their biochemical reactions. Understanding resource allocation is paramount in the study of PAOs and their currently unknown complex metabolic regulation, and metabolic modelling based on biological first principles provides a useful tool to develop a mechanistic understanding.}, }
@article {pmid36410318, year = {2023}, author = {Kelly, LC and Rivett, DW and Pakostova, E and Creer, S and Cotterell, T and Johnson, DB}, title = {Mineralogy affects prokaryotic community composition in an acidic metal mine.}, journal = {Microbiological research}, volume = {266}, number = {}, pages = {127257}, doi = {10.1016/j.micres.2022.127257}, pmid = {36410318}, issn = {1618-0623}, mesh = {*Archaea ; Acids/metabolism ; Bacteria ; *Microbiota ; Sulfides/metabolism ; Minerals/metabolism ; }, abstract = {The microbial ecology of acidic mine and sulfide cave ecosystems is well characterised with respect to aquatic communities, typically revealing low taxonomic complexity and dominance by a relatively limited number of cosmopolitan acidophilic bacterial and archaeal taxa. Whilst pH, temperature, and geochemistry are recognised drivers of diversity in these ecosystems, the specific question of a possible influence of substratum mineralogy on microbial community composition remains unanswered. Here we address this void, using 81 subterranean mineral samples from a low temperature abandoned, acidic, sulfide ore mine system at Mynydd Parys (Parys Mountain in English), Wales, UK. Four primary and 15 secondary minerals were identified via x-ray diffraction, each sample containing a maximum of five and an average of two minerals. The mineralogy of primary (e.g. pyrite and quartz) and secondary (e.g. melanterite and pisanite) minerals was significantly correlated with prokaryotic community structure at multiple taxonomic levels, implying that the mineralosphere effect reported in less extreme terrestrial environments is also implicated in driving prokaryotic community composition in extremely acidic, base metal-bearing sulfide mineralisation at Mynydd Parys. Twenty phyla were identified, nine of which were abundant (mean relative abundance >1%). While taxa characteristic of acidic mines were detected, for example Leptospirillum (phylum Nitrospirae), Acidithiobacillus (phylum Proteobacteria), Sulfobacillus (phylum Firmicutes) and Ferroplasma (phylum Euryarchaeota), their abundance in individual samples was highly variable. Indeed, in the majority of the 81 samples investigated the abundance of these and other typical acidic mine taxa was low, with 25% of samples devoid of sequences from recognised acidic mine taxa. Most notable amongst the bacterial taxa not previously reported in such environments were the recently cultivated Muribaculaceae family (phylum Bacteroidetes), which often dominated Mynydd Parys samples regardless of their mineralogical content. Our results pose further questions regarding the mechanisms by which taxa not previously reported in such extreme environments appear to survive in Mynydd Parys, opening up research pathways for exploring the biodiversity drivers underlying microbial community composition and function in extremely acidic mine environments.}, }
@article {pmid36409329, year = {2023}, author = {Changey, F and Aissaoui, G and Plain, C and Ranger, J and Legout, A and Zeller, B and Epron, D and Lerch, TZ}, title = {Prolonged Effect of Forest Soil Compaction on Methanogen and Methanotroph Seasonal Dynamics.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1447-1452}, pmid = {36409329}, issn = {1432-184X}, support = {12-60-C0057//ADEME- REACTIF program/ ; }, mesh = {*Soil ; Seasons ; Bacteria/genetics ; Oxidation-Reduction ; *Euryarchaeota ; Forests ; Methane ; Soil Microbiology ; }, abstract = {Methane (CH4) oxidation by methanotrophic bacteria in forest soils is the largest biological sink for this greenhouse gas on earth. However, the compaction of forest soils by logging traffic has previously been shown to reduce the potential rate of CH4 uptake. This change could be due to not only a decrease of methanotrophs but also an increase in methanogen activity. In this study, we investigated whether the decrease in CH4 uptake by forest soils, subjected to compaction by heavy machinery 7 years earlier, can be explained by quantitative and qualitative changes in methanogenic and methanotrophic communities. We measured the functional gene abundance and polymorphism of CH4 microbial oxidizers (pmoA) and producers (mcrA) at different depths and during different seasons. Our results revealed that the soil compaction effect on the abundance of both genes depended on season and soil depth, contrary to the effect on gene polymorphism. Bacterial pmoA abundance was significantly lower in the compacted soil than in the controls across all seasons, except in winter in the 0-10 cm depth interval and in summer in the 10-20 cm depth interval. In contrast, archaeal mcrA abundance was higher in compacted than control soil in winter and autumn in the two soil depths investigated. This study shows the usefulness of using pmoA and mcrA genes simultaneously in order to better understand the spatial and temporal variations of soil CH4 fluxes and the potential effect of physical disturbances.}, }
@article {pmid36407791, year = {2022}, author = {Rawat, D and Sharma, U and Poria, P and Finlan, A and Parker, B and Sharma, RS and Mishra, V}, title = {Iron-dependent mutualism between Chlorella sorokiniana and Ralstonia pickettii forms the basis for a sustainable bioremediation system.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {83}, pmid = {36407791}, issn = {2730-6151}, support = {2021_BPS_0039//British Phycological Society (BPS)/ ; 345775672//Newton Fund/ ; }, abstract = {Phototrophic communities of autotrophic microalgae and heterotrophic bacteria perform complex tasks of nutrient acquisition and tackling environmental stress but remain underexplored as a basis for the bioremediation of emerging pollutants. In industrial monoculture designs, poor iron uptake by microalgae limits their productivity and biotechnological efficacy. Iron supplementation is expensive and ineffective because iron remains insoluble in an aqueous medium and is biologically unavailable. However, microalgae develop complex interkingdom associations with siderophore-producing bacteria that help solubilize iron and increase its bioavailability. Using dye degradation as a model, we combined environmental isolations and synthetic ecology as a workflow to design a simplified microbial community based on iron and carbon exchange. We established a mutualism between the previously non-associated alga Chlorella sorokiniana and siderophore-producing bacterium Ralstonia pickettii. Siderophore-mediated increase in iron bioavailability alleviated Fe stress for algae and increased the reductive iron uptake mechanism and bioremediation potential. In exchange, C. sorokiniana produced galactose, glucose, and mannose as major extracellular monosaccharides, supporting bacterial growth. We propose that extracellular iron reduction by ferrireductase is crucial for azoreductase-mediated dye degradation in microalgae. These results demonstrate that iron bioavailability, often overlooked in cultivation, governs microalgal growth, enzymatic processes, and bioremediation potential. Our results suggest that phototrophic communities with an active association for iron and carbon exchange have the potential to overcome challenges associated with micronutrient availability, while scaling up bioremediation designs.}, }
@article {pmid36406446, year = {2022}, author = {Guo, R and Ma, X and Zhang, J and Liu, C and Thu, CA and Win, TN and Aung, NL and Win, HS and Naing, S and Li, H and Zhou, F and Wang, P}, title = {Microbial community structures and important taxa across oxygen gradients in the Andaman Sea and eastern Bay of Bengal epipelagic waters.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1041521}, pmid = {36406446}, issn = {1664-302X}, abstract = {In oceanic oxygen minimum zones (OMZs), the abundances of aerobic organisms significantly decrease and energy shifts from higher trophic levels to microorganisms, while the microbial communities become critical drivers of marine biogeochemical cycling activities. However, little is known of the microbial ecology of the Andaman Sea and eastern Bay of Bengal (BoB) OMZs. In the present study, a total of 131 samples which from the Andaman Sea and eastern BoB epipelagic waters were analyzed. The microbial community distribution patterns across oxygen gradients, including oxygenic zones (OZs, dissolved oxygen [DO] ≥ 2 mg/L), oxygen limited zones (OLZs, 0.7 mg/L < DO < 2 mg/L), and OMZs (DO ≤ 0.7 mg/L), were investigated. Mantel tests and Spearman's correlation analysis revealed that DO was the most important driver of microbial community structures among several environmental factors. Microbial diversity, richness, and evenness were highest in the OLZs and lowest in the OZs. The microbial community compositions of OZ and OMZ waters were significantly different. Random forest analysis revealed 24 bioindicator taxa that differentiated OZ, OLZ, and OMZ water communities. These bioindicator taxa included Burkholderiaceae, HOC36, SAR11 Clade IV, Thioglobaceae, Nitrospinaceae, SAR86, and UBA10353. Further, co-occurrence network analysis revealed that SAR202, AEGEAN-169, UBA10353, SAR406, and Rhodobacteraceae were keystone taxa among the entire interaction network of the microbial communities. Functional prediction further indicated that the relative abundances of microbial populations involved in nitrogen and sulfur cycling were higher in OMZs. Several microbial taxa, including the Thioglobaceae, Nitrospinaceae, SAR202, SAR406, WPS-2, UBA10353, and Woeseiaceae, may be involved in nitrogen and/or sulfur cycling, while also contributing to oxygen consumption in these waters. This study consequently provides new insights into the microbial community structures and potentially important taxa that contribute to oxygen consumption in the Andaman Sea and eastern BoB OMZ.}, }
@article {pmid36401317, year = {2022}, author = {Nata'ala, MK and Avila Santos, AP and Coelho Kasmanas, J and Bartholomäus, A and Saraiva, JP and Godinho Silva, S and Keller-Costa, T and Costa, R and Gomes, NCM and Ponce de Leon Ferreira de Carvalho, AC and Stadler, PF and Sipoli Sanches, D and Nunes da Rocha, U}, title = {MarineMetagenomeDB: a public repository for curated and standardized metadata for marine metagenomes.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {57}, pmid = {36401317}, issn = {2524-6372}, support = {VH-NG-1248 Micro 'Big Data'//Hemlholtz Association/ ; 460129525//Deutsche Forschungsgemeinschaft/ ; 91759074//Petroleum Trust Development Fund, Nigeria/ ; 91759074//Deutscher Akademischer Austauschdienst/ ; }, abstract = {BACKGROUND: Metagenomics is an expanding field within microbial ecology, microbiology, and related disciplines. The number of metagenomes deposited in major public repositories such as Sequence Read Archive (SRA) and Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST) is rising exponentially. However, data mining and interpretation can be challenging due to mis-annotated and misleading metadata entries. In this study, we describe the Marine Metagenome Metadata Database (MarineMetagenomeDB) to help researchers identify marine metagenomes of interest for re-analysis and meta-analysis. To this end, we have manually curated the associated metadata of several thousands of microbial metagenomes currently deposited at SRA and MG-RAST.<br><br>RESULTS: In total, 125 terms were curated according to 17 different classes (e.g., biome, material, oceanic zone, geographic feature&#xa0;and oceanographic phenomena). Other standardized features include sample attributes (e.g., salinity, depth), sample location (e.g., latitude, longitude), and sequencing features (e.g., sequencing platform, sequence count). MarineMetagenomeDB version 1.0 contains 11,449 marine metagenomes from SRA and MG-RAST distributed across all oceans and several seas. Most samples were sequenced using Illumina sequencing technology (84.33%). More than 55% of the samples were collected from the Pacific and the Atlantic Oceans. About 40% of the samples had their biomes assigned as 'ocean'. The 'Quick Search' and 'Advanced Search' tabs allow users to use different filters to select samples of interest dynamically in the web app. The interactive map allows the visualization of samples based on their location on the world map. The web app is also equipped with a novel download tool (on both Windows and Linux operating systems), that allows easy download of raw sequence data of selected samples from their respective repositories. As a use case, we demonstrated how to use the&#xa0;MarineMetagenomeDB web app to select estuarine metagenomes for&#xa0;potential large-scale microbial biogeography studies.<br><br>CONCLUSION: The MarineMetagenomeDB is a powerful resource for non-bioinformaticians to find marine metagenome samples with curated metadata and stimulate meta-studies involving marine microbiomes. Our user-friendly web app is publicly available at https://webapp.ufz.de/marmdb/ .}, }
@article {pmid36400616, year = {2023}, author = {Secchi, G and Amalfitano, N and Carafa, I and Franciosi, E and Gallo, L and Schiavon, S and Sturaro, E and Tagliapietra, F and Bittante, G}, title = {Milk metagenomics and cheese-making properties as affected by indoor farming and summer highland grazing.}, journal = {Journal of dairy science}, volume = {106}, number = {1}, pages = {96-116}, doi = {10.3168/jds.2022-22449}, pmid = {36400616}, issn = {1525-3198}, mesh = {Female ; Humans ; Cattle ; Animals ; *Cheese/analysis ; Milk ; Farms ; Metagenomics ; Agriculture ; }, abstract = {The study of the complex relationships between milk metagenomics and milk composition and cheese-making efficiency as affected by indoor farming and summer highland grazing was the aim of the present work. The experimental design considered monthly sampling (over 5 mo) of the milk produced by 12 Brown Swiss cows divided into 2 groups: the first remained on a lowland indoor farm from June to October, and the second was moved to highland pastures in July and then returned to the lowland farm in September. The resulting 60 milk samples (2 kg each) were used to analyze milk composition, milk coagulation, curd firming, and syneresis processes, and to make individual model cheeses to measure cheese yields and nutrient recoveries in the cheese. After DNA extraction and Illumina Miseq sequencing, milk microbiota amplicons were also processed by means of an open-source pipeline called Quantitative Insights Into Microbial Ecology (Qiime2, version 2018.2; https://qiime2.org). Out of a total of 44 taxa analyzed, 13 bacterial taxa were considered important for the dairy industry (lactic acid bacteria, LAB, 5 taxa; and spoilage bacteria, 4) and for human (other probiotics, 2) and animal health (pathogenic bacteria, 2). The results revealed the transhumant group of cows transferred to summer highland pastures showed an increase in almost all the LAB taxa, bifidobacteria, and propionibacteria, and a reduction in spoilage taxa. All the metagenomic changes disappeared when the transhumant cows were moved back to the permanent indoor farm. The relationships between 17 microbial traits and 30 compositional and technological milk traits were investigated through analysis of correlation and latent explanatory factor analysis. Eight latent factors were identified, explaining 75.3% of the total variance, 2 of which were mainly based on microbial traits: pro-dairy bacteria (14% of total variance, improving during summer pasturing) and pathogenic bacteria (6.0% of total variance). Some bacterial traits contributed to other compositional-technological latent factors (gelation, udder health, and caseins).}, }
@article {pmid36399842, year = {2022}, author = {Li, Y and Ling, J and Xue, J and Huang, J and Zhou, X and Wang, F and Hou, W and Zhao, J and Xu, Y}, title = {Acute stress of the typical disinfectant glutaraldehyde-didecyldimethylammonium bromide (GD) on sludge microecology in livestock wastewater treatment plants: Effect and its mechanisms.}, journal = {Water research}, volume = {227}, number = {}, pages = {119342}, doi = {10.1016/j.watres.2022.119342}, pmid = {36399842}, issn = {1879-2448}, mesh = {Swine ; Animals ; Sewage ; *Disinfectants/pharmacology ; Glutaral/pharmacology ; Livestock ; *African Swine Fever ; Reactive Oxygen Species ; *COVID-19 ; *Water Purification ; Nitrogen ; }, abstract = {Glutaraldehyde and didecyldimethylammonium bromide (GD) is a disinfectant widely used to prevent African swine fever (ASF) in livestock farms. However, the effect of residual GD on the activated sludge microbial ecology of receiving wastewater treatment plants (WWTPs) remains largely unknown. In this study, seven simulated systems were established to research the effects of GD on WWTPs and reveal the underlying mechanisms of microecological responses to GD at different concentrations. Both the nitrogen and carbon removal rates decreased with increasing GD concentrations, and nitrogen metabolism was inhibited more obviously, but the inhibition weakened with increasing stress duration. Microorganisms activated their SoxRS systems to promote ATP synthesis and electron transfer to support the hydrolysis and efflux of GD by producing a small number of ROS when exposed to GD at less than 1 mg/L. The overproduction of ROS led to a decrease of antioxidant and nitrogen removal enzyme activities, and upregulation of the porin gene increased the risk of GD entering the intracellular space upon exposure to GD at concentrations higher than 1 mg/L. Some denitrifiers survived via resistance and their basic capabilities of sugar metabolism and nitrogen assimilation. Notably, low concentrations of disinfectants could promote vertical and horizontal transfer of multiple resistance genes, especially aminoglycosides, among microorganisms, which might increase not only the adaptation capability of denitrifiers but also the risk to ecological systems. Therefore, the risks of disinfectants targeting ASF on ecology and health as well as the effects of disinfectant residuals from the COVID-19 epidemic should receive more attention.}, }
@article {pmid36399746, year = {2022}, author = {Sinclair, P and Brackley, CA and Carballo-Pacheco, M and Allen, RJ}, title = {Model for Quorum-Sensing Mediated Stochastic Biofilm Nucleation.}, journal = {Physical review letters}, volume = {129}, number = {19}, pages = {198102}, doi = {10.1103/PhysRevLett.129.198102}, pmid = {36399746}, issn = {1079-7114}, mesh = {*Quorum Sensing ; *Biofilms ; Bacteria ; }, abstract = {Surface-attached bacterial biofilms cause disease and industrial biofouling, as well as being widespread in the natural environment. Density-dependent quorum sensing is one of the mechanisms implicated in biofilm initiation. Here we present and analyze a model for quorum-sensing triggered biofilm initiation. In our model, individual, planktonic bacteria adhere to a surface, proliferate, and undergo a collective transition to a biofilm phenotype. This model predicts a stochastic transition between a loosely attached, finite layer of bacteria near the surface and a growing biofilm. The transition is governed by two key parameters: the collective transition density relative to the carrying capacity and the immigration rate relative to the detachment rate. Biofilm initiation is complex, but our model suggests that stochastic nucleation phenomena may be relevant.}, }
@article {pmid36399658, year = {2022}, author = {Simmer, RA and Schnoor, JL}, title = {Phytoremediation, Bioaugmentation, and the Plant Microbiome.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {23}, pages = {16602-16610}, pmid = {36399658}, issn = {1520-5851}, support = {P30 ES005605/ES/NIEHS NIH HHS/United States ; }, mesh = {Biodegradation, Environmental ; *Soil Pollutants/metabolism ; Plants/metabolism ; Soil ; *Microbiota ; }, abstract = {Understanding plant biology and related microbial ecology as a means to phytoremediate soil and groundwater contamination has broadened and advanced the field of environmental engineering and science over the past 30 years. Using plants to transform and degrade xenobiotic organic pollutants delivers new methods for environmental restoration. Manipulations of the plant microbiome through bioaugmentation, endophytes, adding various growth factors, genetic modification, and/or selecting the microbial community via insertion of probiotics or phages for gene transfer are future areas of research to further expand this green, cost-effective, aesthetically pleasing technology─phytoremediation.}, }
@article {pmid36399496, year = {2023}, author = {Terlouw, BR and Blin, K and Navarro-Muñoz, JC and Avalon, NE and Chevrette, MG and Egbert, S and Lee, S and Meijer, D and Recchia, MJJ and Reitz, ZL and van Santen, JA and Selem-Mojica, N and Tørring, T and Zaroubi, L and Alanjary, M and Aleti, G and Aguilar, C and Al-Salihi, SAA and Augustijn, HE and Avelar-Rivas, JA and Avitia-Domínguez, LA and Barona-Gómez, F and Bernaldo-Agüero, J and Bielinski, VA and Biermann, F and Booth, TJ and Carrion Bravo, VJ and Castelo-Branco, R and Chagas, FO and Cruz-Morales, P and Du, C and Duncan, KR and Gavriilidou, A and Gayrard, D and Gutiérrez-García, K and Haslinger, K and Helfrich, EJN and van der Hooft, JJJ and Jati, AP and Kalkreuter, E and Kalyvas, N and Kang, KB and Kautsar, S and Kim, W and Kunjapur, AM and Li, YX and Lin, GM and Loureiro, C and Louwen, JJR and Louwen, NLL and Lund, G and Parra, J and Philmus, B and Pourmohsenin, B and Pronk, LJU and Rego, A and Rex, DAB and Robinson, S and Rosas-Becerra, LR and Roxborough, ET and Schorn, MA and Scobie, DJ and Singh, KS and Sokolova, N and Tang, X and Udwary, D and Vigneshwari, A and Vind, K and Vromans, SPJM and Waschulin, V and Williams, SE and Winter, JM and Witte, TE and Xie, H and Yang, D and Yu, J and Zdouc, M and Zhong, Z and Collemare, J and Linington, RG and Weber, T and Medema, MH}, title = {MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D603-D610}, pmid = {36399496}, issn = {1362-4962}, support = {F32 AT011475/AT/NCCIH NIH HHS/United States ; F32 GM134688/GM/NIGMS NIH HHS/United States ; R01 AI155694/AI/NIAID NIH HHS/United States ; U24 AT010811/AT/NCCIH NIH HHS/United States ; }, mesh = {*Genomics ; *Genome ; Multigene Family ; Biosynthetic Pathways/genetics ; }, abstract = {With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.}, }
@article {pmid36399337, year = {2023}, author = {Janssen, K and Krasenbrink, J and Strangfeld, S and Kroheck, S and Josten, M and Engeser, M and Bierbaum, G}, title = {Elucidation of the Bridging Pattern of the Lantibiotic Pseudomycoicidin.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {24}, number = {2}, pages = {e202200540}, pmid = {36399337}, issn = {1439-7633}, mesh = {*Bacteriocins/chemistry ; *Methicillin-Resistant Staphylococcus aureus ; Amino Acid Sequence ; Anti-Bacterial Agents/pharmacology/chemistry ; Sulfides ; Disulfides ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {Lantibiotics are post-translationally modified antibiotic peptides with lanthionine thioether bridges that represent potential alternatives to conventional antibiotics. The lantibiotic pseudomycoicidin is produced by Bacillus pseudomycoides DSM 12442 and is effective against many Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus. While prior work demonstrated that pseudomycoicidin possesses one disulfide bridge and four thioether bridges, the ring topology has so far remained unclear. Here, we analyzed several pseudomycoicidin analogues that are affected in ring formation via MALDI-TOF-MS and tandem mass spectrometry with regard to their dehydration and fragmentation patterns, respectively. As a result, we propose a bridging pattern involving Thr8 and Cys13, Thr10 and Cys16, Ser18 and Cys21, and Ser20 and Cys26, thus, forming two double ring systems. Additionally, we localized the disulfide bridge to connect Cys3 and Cys7 and, therefore, fully elucidated the bridging pattern of pseudomycoicidin.}, }
@article {pmid36396943, year = {2022}, author = {Minich, JJ and Härer, A and Vechinski, J and Frable, BW and Skelton, ZR and Kunselman, E and Shane, MA and Perry, DS and Gonzalez, A and McDonald, D and Knight, R and Michael, TP and Allen, EE}, title = {Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6978}, pmid = {36396943}, issn = {2041-1723}, support = {T32 GM139790/GM/NIGMS NIH HHS/United States ; P01 ES021921/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Biomass ; *Fishes ; Ecology ; *Microbiota ; Gills ; Vertebrates ; Mammals ; }, abstract = {Fish are the most diverse and widely distributed vertebrates, yet little is known about the microbial ecology of fishes nor the biological and environmental factors that influence fish microbiota. To identify factors that explain microbial diversity patterns in a geographical subset of marine fish, we analyzed the microbiota (gill tissue, skin mucus, midgut digesta and hindgut digesta) from 101 species of Southern California marine fishes, spanning 22 orders, 55 families and 83 genera, representing ~25% of local marine fish diversity. We compare alpha, beta and gamma diversity while establishing a method to estimate microbial biomass associated with these host surfaces. We show that body site is the strongest driver of microbial diversity while microbial biomass and diversity is lowest in the gill of larger, pelagic fishes. Patterns of phylosymbiosis are observed across the gill, skin and hindgut. In a quantitative synthesis of vertebrate hindguts (569 species), we also show that mammals have the highest gamma diversity when controlling for host species number while fishes have the highest percent of unique microbial taxa. The composite dataset will be useful to vertebrate microbiota researchers and fish biologists interested in microbial ecology, with applications in aquaculture and fisheries management.}, }
@article {pmid36388928, year = {2022}, author = {Plunder, S and Burkard, M and Lauer, UM and Venturelli, S and Marongiu, L}, title = {Determination of phage load and administration time in simulated occurrences of antibacterial treatments.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {1040457}, pmid = {36388928}, issn = {2296-858X}, abstract = {The use of phages as antibacterials is becoming more and more common in Western countries. However, a successful phage-derived antibacterial treatment needs to account for additional features such as the loss of infective virions and the multiplication of the hosts. The parameters critical inoculation size (V F) and failure threshold time (T F) have been introduced to assure that the viral dose (V ϕ) and administration time (T ϕ) would lead to the extinction of the targeted bacteria. The problem with the definition of V F and T F is that they are non-linear equations with two unknowns; thus, obtaining their explicit values is cumbersome and not unique. The current study used machine learning to determine V F and T F for an effective antibacterial treatment. Within these ranges, a Pareto optimal solution of a multi-criterial optimization problem (MCOP) provided a pair of V ϕ and T ϕ to facilitate the user's work. The algorithm was tested on a series of in silico microbial consortia that described the outgrowth of a species at high cell density by another species initially present at low concentration. The results demonstrated that the MCOP-derived pairs of V ϕ and T ϕ could effectively wipe out the bacterial target within the context of the simulation. The present study also introduced the concept of mediated phage therapy, where targeting booster bacteria might decrease the virulence of a pathogen immune to phagial infection and highlighted the importance of microbial competition in attaining a successful antibacterial treatment. In summary, the present work developed a novel method for investigating phage/bacteria interactions that can help increase the effectiveness of the application of phages as antibacterials and ease the work of microbiologists.}, }
@article {pmid36386706, year = {2022}, author = {Zhao, M and Zhang, H and Pan, G and Yin, H and Sun, J and Yu, Z and Bai, C and Xue, Y}, title = {Effect of exogenous microorganisms on the fermentation quality, nitrate degradation and bacterial community of sorghum-sudangrass silage.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1052837}, pmid = {36386706}, issn = {1664-302X}, abstract = {This study aims to investigate the effects of adding Lactobacillus buchneri (LB), Lactobacillus brevis (LBR) and Bacillus subtilis (BS) on the fermentation quality, nitrate degradation and bacterial community of sorghum-sudangrass silage. The results showed that the addition of LB significantly increased the pH and acetic acid content (p < 0.05), but high-quality silage was obtained. The addition of LBR and BS improved the fermentation quality of sorghum-sudangrass silage. The use of additives reduced the nitrate content in sorghum-sudangrass silage. The LB group increased the release of N2O at 3-7 days of ensiling (p < 0.05), and LBR and BS increased the release of N2O at 1-40 days of ensiling (p < 0.05). On the first day of ensiling, all silages were dominated by Weisslla, over 3 days of ensiling all silages were dominated by Lactobacillus. Acinetobacter, Serratia, Aquabacterium, and unclassified_f_enterobacteriaceae showed significant negative correlations with nitrate degradation during sorghum-sudangrass ensiling (p < 0.05). The BS and LBR groups increased the metabolic abundance of denitrification, dissimilatory nitrate reduction, and assimilatory nitrate reduction (p < 0.05). Overall, the additive ensures the fermentation quality of sorghum-sudangrass silage and promotes the degradation of nitrate by altering the bacterial community.}, }
@article {pmid36386657, year = {2022}, author = {Liu, J and Wang, X and Liu, J and Liu, X and Zhang, XH and Liu, J}, title = {Comparison of assembly process and co-occurrence pattern between planktonic and benthic microbial communities in the Bohai Sea.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1003623}, pmid = {36386657}, issn = {1664-302X}, abstract = {Unraveling the mechanisms structuring microbial community is a central goal in microbial ecology, but a detailed understanding of how community assembly processes relate to living habitats is still lacking. Here, via 16S rRNA gene amplicon sequencing, we investigated the assembly process of microbial communities in different habitats [water verse sediment, free-living (FL) verse particle-associated (PA)] and their impacts on the inter-taxa association patterns in the coastal Bohai Sea, China. The results showed clear differences in the composition and diversity of microbial communities among habitats, with greater dissimilarities between water column and sediment than between FL and PA communities. The microbial community assembly was dominated by dispersal limitation, ecological drift, and homogeneous selection, but their relative importance varied in different habitats. The planktonic communities were mainly shaped by dispersal limitation and ecological drift, whereas homogeneous selection played a more important role in structuring the benthic communities. Furthermore, the assembly mechanisms differed between FL and PA communities, especially in the bottom water with a greater effect of ecological drift and dispersal limitation on the FL and PA fractions, respectively. Linking assembly process to co-occurrence pattern showed that the relative contribution of deterministic processes (mainly homogeneous selection) increased under closer co-occurrence relationships. By contrast, stochastic processes exerted a higher effect when there were less inter-taxa connections. Overall, our findings demonstrate contrasting ecological processes underpinning microbial community distribution in different habitats including different lifestyles, which indicate complex microbial dynamic patterns in coastal systems with high anthropogenic perturbations.}, }
@article {pmid36386638, year = {2022}, author = {Djeni, TN and Keisam, S and Kouame, KH and Assohoun-Djeni, CN and Ake, FDM and Amoikon, LST and Tuikhar, N and Labala, RK and Dje, MK and Jeyaram, K}, title = {Dynamics of microbial populations and metabolites of fermenting saps throughout tapping process of ron and oil palm trees in Côte d'Ivoire.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {954917}, pmid = {36386638}, issn = {1664-302X}, abstract = {Palm wine fermentation is a complex microbial process that evolves with tapping times. The dynamics in microbiota and metabolites throughout palm wine tapping days is still not established, which are critical for the distinctive characteristics of palm wine taste and quality, and thus the mastery of the daily quality fluctuation during tapping. We analyzed the changes in microbial community structure by amplicon sequencing of bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) region, and metabolite profile changes using mass spectrometry in palm wine collected over 25-30 days tapping of ron (Borassus aethiopum) and oil palms (Elaeis guineensis) from Côte d'Ivoire. The stage-wise collected palm wine samples showed distinct changes in microbial diversity and pH, supporting microbial community dynamics during palm wine tapping. Results highlighted the dominance of Saccharomyces cerevisiae in early stages and the emergence of non-Saccharomyces yeasts, particularly Hanseniaspora spp. in the later stages of oil palm wine tapping, vice versa in the case of ron palm wine tapping, with a unique presence of Saccharomycodes in the later stages (15-30 days). Fructophilic lactic acid bacteria (FLAB), mainly Fructobacillus and Leuconostoc, encountered in both types of palm wine tapping showed a decline at later stages of oil palm wine tapping. In this type of palm wine, acetic acid bacteria with genera Acetobacter and Glucanoacetobacter, by surpassing Lactobacillus in the last stage become dominant, whereas Lactobacillus remained dominant in ron palm wine throughout tapping days. The decline in the relative abundance of gevotroline and essential amino acids during the later stages of palm wine tapping (15-25 days) supports the difference in the health benefits of the palm wine obtained from different days of tapping, indicating that early stages of tapping is more nutritional and healthy than the later stages. The microbial dynamics may be a potential indicator of metabolite changes during palm sap fermentation, thus contributing to establish particular features of palm wines in different stages of tapping. This understanding of microbial ecology and chemical composition changes during palm wine tapping can be used as biomarkers to assess palm wine's quality and help to design an optimum starter culture.}, }
@article {pmid36385637, year = {2023}, author = {Natalini, JG and Singh, S and Segal, LN}, title = {The dynamic lung microbiome in health and disease.}, journal = {Nature reviews. Microbiology}, volume = {21}, number = {4}, pages = {222-235}, pmid = {36385637}, issn = {1740-1534}, support = {R37 CA244775/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Lung/microbiology ; *Microbiota ; Bacteria ; }, abstract = {New methods and technologies within the field of lung biology are beginning to shed new light into the microbial world of the respiratory tract. Long considered to be a sterile environment, it is now clear that the human lungs are frequently exposed to live microbes and their by-products. The nature of the lung microbiome is quite distinct from other microbial communities inhabiting our bodies such as those in the gut. Notably, the microbiome of the lung exhibits a low biomass and is dominated by dynamic fluxes of microbial immigration and clearance, resulting in a bacterial burden and microbiome composition that is fluid in nature rather than fixed. As our understanding of the microbial ecology of the lung improves, it is becoming increasingly apparent that certain disease states can disrupt the microbial-host interface and ultimately affect disease pathogenesis. In this Review, we provide an overview of lower airway microbial dynamics in health and disease and discuss future work that is required to uncover novel therapeutic targets to improve lung health.}, }
@article {pmid36384808, year = {2022}, author = {Park, J and Davis, K and Lajoie, G and Parfrey, LW}, title = {Alternative approaches to identify core bacteria in Fucus distichus microbiome and assess their distribution and host-specificity.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {55}, pmid = {36384808}, issn = {2524-6372}, support = {2021-03160//NSERC Discovery/ ; }, abstract = {BACKGROUND: Identifying meaningful ecological associations between host and components of the microbiome is challenging. This is especially true for hosts such as marine macroalgae where the taxonomic composition of the microbiome is highly diverse and variable in space and time. Identifying core taxa is one way forward but there are many methods and thresholds in use. This study leverages a large dataset of microbial communities associated with the widespread brown macroalga, Fucus distichus, across sites and years on one island in British Columbia, Canada. We compare three different methodological approaches to identify core taxa at the amplicon sequence variant (ASV) level from this dataset: (1) frequency analysis of taxa on F. distichus performed over the whole dataset, (2) indicator species analysis (IndVal) over the whole dataset that identifies frequent taxa that are enriched on F. distichus in comparison to the local environment, and (3) a two-step IndVal method that identifies taxa that are consistently enriched on F. distichus across sites and time points. We then investigated a F. distichus time-series dataset to see if those core taxa are seasonally consistent on another remote island in British Columbia, Canada. We then evaluate host-specificity of the identified F. distichus core ASVs using comparative data from 32 other macroalgal species sampled at one of the sites.<br><br>RESULTS: We show that a handful of core ASVs are consistently identified by both frequency analysis and IndVal approaches with alternative definitions, although no ASVs were always present on F. distichus and IndVal identified a diverse array of F. distichus indicator taxa across sites on Calvert Island in multiple years. Frequency analysis captured a broader suit of taxa, while IndVal was better at identifying host-specific microbes. Finally, two-step IndVal identified hundreds of indicator ASVs for particular sites/timepoints but only 12 that were indicators in a majority (>&#x2009;6 out of 11) of sites/timepoints. Ten of these ASVs were also indicators on Quadra Island, 250&#xa0;km away. Many F. distichus-core ASVs are generally found on multiple macroalgal species, while a few ASVs are highly specific to F. distichus.<br><br>CONCLUSIONS: Different methodological approaches with variable set thresholds influence core identification, but a handful of core taxa are apparently identifiable as they are widespread and temporally associated with F. distichus and enriched in comparison to the environment. Moreover, we show that many of these core ASVs of F. distichus are found on multiple macroalgal hosts, indicating that most occupy a macroalgal generalist niche rather than forming highly specialized associations with F. distichus. Further studies should test whether macroalgal generalists or specialists are more likely to engage in biologically important exchanges with host.}, }
@article {pmid36383236, year = {2023}, author = {Peralta-Maraver, I and Rutere, C and Horn, MA and Reche, I and Behrends, V and Reiss, J and Robertson, AL}, title = {Correction to: Intermediate levels of predation and nutrient enrichment enhance the activity of ibuprofen degrading bacteria.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1442}, doi = {10.1007/s00248-022-02145-y}, pmid = {36383236}, issn = {1432-184X}, }
@article {pmid36378688, year = {2022}, author = {Bermúdez-Méndez, E and Bronsvoort, KF and Zwart, MP and van de Water, S and Cárdenas-Rey, I and Vloet, RPM and Koenraadt, CJM and Pijlman, GP and Kortekaas, J and Wichgers Schreur, PJ}, title = {Incomplete bunyavirus particles can cooperatively support virus infection and spread.}, journal = {PLoS biology}, volume = {20}, number = {11}, pages = {e3001870}, pmid = {36378688}, issn = {1545-7885}, mesh = {Animals ; Humans ; *Rift Valley fever virus/genetics ; *Orthobunyavirus ; *Rift Valley Fever/genetics/metabolism ; *Virus Diseases ; Virion/metabolism ; *Culicidae ; *Arboviruses ; Mammals ; }, abstract = {Bunyaviruses lack a specific mechanism to ensure the incorporation of a complete set of genome segments into each virion, explaining the generation of incomplete virus particles lacking one or more genome segments. Such incomplete virus particles, which may represent the majority of particles produced, are generally considered to interfere with virus infection and spread. Using the three-segmented arthropod-borne Rift Valley fever virus as a model bunyavirus, we here show that two distinct incomplete virus particle populations unable to spread autonomously are able to efficiently complement each other in both mammalian and insect cells following co-infection. We further show that complementing incomplete virus particles can co-infect mosquitoes, resulting in the reconstitution of infectious virus that is able to disseminate to the mosquito salivary glands. Computational models of infection dynamics predict that incomplete virus particles can positively impact virus spread over a wide range of conditions, with the strongest effect at intermediate multiplicities of infection. Our findings suggest that incomplete particles may play a significant role in within-host spread and between-host transmission, reminiscent of the infection cycle of multipartite viruses.}, }
@article {pmid36378579, year = {2023}, author = {Matassa, S and Boeckx, P and Boere, J and Erisman, JW and Guo, M and Manzo, R and Meerburg, F and Papirio, S and Pikaar, I and Rabaey, K and Rousseau, D and Schnoor, J and Smith, P and Smolders, E and Wuertz, S and Verstraete, W}, title = {How can we possibly resolve the planet's nitrogen dilemma?.}, journal = {Microbial biotechnology}, volume = {16}, number = {1}, pages = {15-27}, pmid = {36378579}, issn = {1751-7915}, mesh = {Animals ; *Nitrogen/analysis ; *Fertilizers/analysis ; Planets ; Soil ; Fossil Fuels ; Agriculture ; }, abstract = {Nitrogen is the most crucial element in the production of nutritious feeds and foods. The production of reactive nitrogen by means of fossil fuel has thus far been able to guarantee the protein supply for the world population. Yet, the production and massive use of fertilizer nitrogen constitute a major threat in terms of environmental health and sustainability. It is crucial to promote consumer acceptance and awareness towards proteins produced by highly effective microorganisms, and their potential to replace proteins obtained with poor nitrogen efficiencies from plants and animals. The fact that reactive fertilizer nitrogen, produced by the Haber Bosch process, consumes a significant amount of fossil fuel worldwide is of concern. Moreover, recently, the prices of fossil fuels have increased the cost of reactive nitrogen by a factor of 3 to 5 times, while international policies are fostering the transition towards a more sustainable agro-ecology by reducing mineral fertilizers inputs and increasing organic farming. The combination of these pressures and challenges opens opportunities to use the reactive nitrogen nutrient more carefully. Time has come to effectively recover used nitrogen from secondary resources and to upgrade it to a legal status of fertilizer. Organic nitrogen is a slow-release fertilizer, it has a factor of 2.5 or higher economic value per unit nitrogen as fertilizer and thus adequate technologies to produce it, for instance by implementing photobiological processes, are promising. Finally, it appears wise to start the integration in our overall feed and food supply chains of the exceptional potential of biological nitrogen fixation. Nitrogen produced by the nitrogenase enzyme, either in the soil or in novel biotechnology reactor systems, deserves to have a 'renaissance' in the context of planetary governance in general and the increasing number of people who desire to be fed in a sustainable way in particular.}, }
@article {pmid36374338, year = {2023}, author = {Yan, Y and Xie, Y and Zhang, J and Li, R and Ali, A and Cai, Z and Huang, X and Liu, L}, title = {Effects of Reductive Soil Disinfestation Combined with Liquid-Readily Decomposable Compounds and Solid Plant Residues on the Bacterial Community and Functional Composition.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1132-1144}, pmid = {36374338}, issn = {1432-184X}, support = {32160748//National Natural Science Foundation of China/ ; }, mesh = {*Soil/chemistry ; Bacteria/genetics ; *Microbiota ; Soil Microbiology ; }, abstract = {Reductive soil disinfestation (RSD) incorporated with sole plant residues or liquid-readily decomposable compounds is an effective management strategy to improve soil health. However, the synthetic effects of RSD incorporated with liquid-readily decomposable compounds and solid plant residues on soil ecosystem services remain unclear. Field experiments were carried out to investigate the effects of untreated soil (CK), RSD incorporated with sawdust (SA), molasses (MO), and their combinations (SA + MO) on the bacterial community and functional composition. The results showed that RSD treatments significantly altered soil bacterial community structure compared to CK treatment. The bacterial community structure and composition in MO and SA + MO treatments were clustered compared to SA treatment. This was mainly attributed to the readily decomposable carbon sources in molasses having a stronger driving force to reshape the soil microbial community during the RSD process. Furthermore, the functional compositions, such as the disinfestation efficiency of F. oxysporum (96.4 - 99.1%), abundances of nitrogen functional genes, soil metabolic activity, and functional diversity, were significantly increased in all of the RSD treatments. The highest disinfestation efficiency and abundances of denitrification (nirS and nrfA) and nitrogen fixation (nifH) genes were observed in SA + MO treatment. Specifically, SA + MO treatment enriched more abundant beneficial genera, e.g., Oxobacter, Paenibacillus, Cohnella, Rummeliibacillus, and Streptomyces, which were significantly and positively linked to disinfestation efficiency, soil metabolic activity, and denitrification processes. Our results indicated that combining RSD practices with liquid-readily decomposable compounds and solid plant residues could effectively improve soil microbial community and functional composition.}, }
@article {pmid36374046, year = {2022}, author = {Agarwal, V and Inomura, K and Mouw, CB}, title = {Quantitative Analysis of the Trade-Offs of Colony Formation for Trichodesmium.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0202522}, pmid = {36374046}, issn = {2165-0497}, mesh = {*Trichodesmium/metabolism ; Nitrogen Fixation ; Nitrogen Cycle ; Nitrogen/metabolism ; Carbon/metabolism ; }, abstract = {There is considerable debate about the benefits and trade-offs for colony formation in a major marine nitrogen fixer, Trichodesmium. To quantitatively analyze the trade-offs, we developed a metabolic model based on carbon fluxes to compare the performance of Trichodesmium colonies and free trichomes under different scenarios. Despite reported reductions in carbon fixation and nitrogen fixation rates for colonies relative to free trichomes, we found that model colonies can outperform individual cells in several cases. The formation of colonies can be advantageous when respiration rates account for a high proportion of the carbon fixation rate. Negative external influence on vital rates, such as mortality due to predation or micronutrient limitations, can also create a net benefit for colony formation relative to individual cells. In contrast, free trichomes also outcompete colonies in many scenarios, such as when respiration rates are equal for both colonies and individual cells or when there is a net positive external influence on rate processes (i.e., optimal environmental conditions regarding light and temperature or high nutrient availability). For both colonies and free trichomes, an increase in carbon fixation relative to nitrogen fixation rates would increase their relative competitiveness. These findings suggest that the formation of colonies in Trichodesmium might be linked to specific environmental and ecological circumstances. Our results provide a road map for empirical studies and models to evaluate the conditions under which colony formation in marine phytoplankton can be sustained in the natural environment. IMPORTANCE Trichodesmium is a marine filamentous cyanobacterium that fixes nitrogen and is an important contributor to the global nitrogen cycle. In the natural environment, Trichodesmium can exist as individual cells (trichomes) or as colonies (puffs and tufts). In this paper, we try to answer a longstanding question in marine microbial ecology: how does colony formation benefit the survival of Trichodesmium? To answer this question, we developed a carbon flux model that utilizes existing published rates to evaluate whether and when colony formation can be sustained. Enhanced respiration rates, influential external factors such as environmental conditions and ecological interactions, and variable carbon and nitrogen fixation rates can all create scenarios for colony formation to be a viable strategy. Our results show that colony formation is an ecologically beneficial strategy under specific conditions, enabling Trichodesmium to be a globally significant organism.}, }
@article {pmid36373138, year = {2022}, author = {Hillary, LS and Adriaenssens, EM and Jones, DL and McDonald, JE}, title = {RNA-viromics reveals diverse communities of soil RNA viruses with the potential to affect grassland ecosystems across multiple trophic levels.}, journal = {ISME communications}, volume = {2}, number = {}, pages = {34}, pmid = {36373138}, issn = {2730-6151}, support = {BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {The distribution and diversity of RNA viruses in soil ecosystems are largely unknown, despite their significant impact on public health, ecosystem functions, and food security. Here, we characterise soil RNA viral communities along an altitudinal productivity gradient of peat, managed grassland and coastal soils. We identified 3462 viral contigs in RNA viromes from purified virus-like-particles in five soil-types and assessed their spatial distribution, phylogenetic diversity and potential host ranges. Soil types exhibited minimal similarity in viral community composition, but with >10-fold more viral contigs shared between managed grassland soils when compared with peat or coastal soils. Phylogenetic analyses predicted soil RNA viral communities are formed from viruses of bacteria, plants, fungi, vertebrates and invertebrates, with only 12% of viral contigs belonging to the bacteria-infecting Leviviricetes class. 11% of viral contigs were found to be most closely related to members of the Ourmiavirus genus, suggesting that members of this clade of plant viruses may be far more widely distributed and diverse than previously thought. These results contrast with soil DNA viromes which are typically dominated by bacteriophages. RNA viral communities, therefore, have the potential to exert influence on inter-kingdom interactions across terrestrial biomes.}, }
@article {pmid36372840, year = {2023}, author = {Ye, G and Chen, J and Yang, P and Hu, HW and He, ZY and Wang, D and Cao, D and Zhang, W and Wu, B and Wu, Y and Wei, X and Lin, Y}, title = {Non-native Plant Species Invasion Increases the Importance of Deterministic Processes in Fungal Community Assembly in a Coastal Wetland.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1120-1131}, pmid = {36372840}, issn = {1432-184X}, support = {42077041//National Natural Science Foundation of China/ ; 2021J011038//Natural Science Foundation of Fujian Province/ ; }, mesh = {*Wetlands ; *Mycobiome ; Introduced Species ; Plants ; Poaceae/physiology ; Soil/chemistry ; Fungi/genetics ; Soil Microbiology ; China ; }, abstract = {Fungal communities are essential to the maintenance of soil multifunctionality. Plant invasion represents a growing challenge for the conservation of soil biodiversity across the globe, but the impact of non-native species invasion on fungal diversity, community structure, and assembly processes remains largely unknown. Here, we examined the diversity, community composition, functional guilds, and assembly process of fungi at three soil depths underneath a native species, three non-native species, and a bare tidal flat from a coastal wetland. Plant species was more important than soil depth in regulating the diversity, community structure, and functional groups of fungi. Non-native species, especially Spartina alterniflora, increased fungal diversity, altered fungal community structure, and increased the relative abundance of saprotrophic and pathogenic fungi in coastal wetland soils. Stochastic processes played a predominant role in driving fungal community assembly, explaining more than 70% of the relative contributions. However, compared to a native species, non-native species, especially S. alterniflora, reduced the relative influence of stochastic processes in fungal community assembly. Collectively, our results provide novel evidence that non-native species can increase fungal diversity, the relative abundance of saprotrophic and pathogenic fungi, and deterministic processes in the assembly of fungi in coastal wetlands, which can expand our knowledge of the dynamics of fungal communities in subtropical coastal wetlands.}, }
@article {pmid36370453, year = {2022}, author = {Alfradique Monteiro, D and Fazolato, CSB and Martins, LF and Tavora Coelho da Costa Rachid, C}, title = {The bacteriome of the halophyte Atriplex nummularia (old man saltbush) in salt-affected soils - an ecological model.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {12}, pages = {}, doi = {10.1093/femsec/fiac135}, pmid = {36370453}, issn = {1574-6941}, mesh = {Humans ; Male ; *Atriplex/genetics ; Salt-Tolerant Plants/microbiology ; Soil ; RNA, Ribosomal, 16S/genetics ; Sodium Chloride ; Bacteria/genetics ; Plant Roots/microbiology ; Soil Microbiology ; }, abstract = {Halophytes, plants capable of growing under saline conditions, are an important source of bacteria with biotechnological potential for plant growth under extreme conditions. In this study, we evaluated the halophyte Atriplex nummularia bacteriome assemblage from three different salinized sites in northeastern Brazil with different edaphoclimatic characteristics, understanding the participation of the plant in the assembly of its microbiome. We sampled 30 specimens, from which the leaves, roots, and rhizospheric soil were subjected to 16S rRNA gene sequencing, bringing forth patterns of alpha and beta diversity, taxonomical composition, co-occurrence network, and the core microbiome of each compartment. Overall, this species harbors a very restricted set of endophytic microbes, and communities showed an increasing gradient of complexity (soil > root > leaf), reflecting a change in the main selective pressure being active over the microbial community. Although the leaf bacteriome was influenced basically by host factors, the soil community was modulated by the environment, and the root bacteriome was structured by both factors. These results help us understand how plant-microbe interactions occur in saline environments. As these plants shelter microbes that potentially alleviate abiotic stresses, we discuss how culture-independent methods could contribute to the prospection of plant growth promoting bacteria in plants.}, }
@article {pmid36369598, year = {2023}, author = {Havenga, M and Halleen, F and Baloyi, A and Bester, M and Linde, CC and Mostert, L}, title = {Predominant Clonal Reproduction with Infrequent Genetic Recombination of Phaeoacremonium minimum in Western Cape Vineyards.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {887-899}, pmid = {36369598}, issn = {1432-184X}, mesh = {*Reproduction ; *Genetics, Population ; Farms ; Recombination, Genetic ; Microsatellite Repeats ; Ascomycota ; Genotype ; Genetic Variation ; }, abstract = {Phaeoacremonium minimum is an important esca and Petri disease pathogen that causes dieback of grapevines in South Africa. Little is known regarding the reproductive strategy of the pathogen. Sexual reproduction could lead to a better adaptation of the pathogen to disease management strategies by combining alleles through recombination. The study aimed to investigate the genetic diversity and recombination potential of eight populations in the Western Cape, from six commercial vineyards and two nursery rootstock mother blocks. This was achieved by developing and applying nine polymorphic microsatellites and mating-type-specific markers. Thirty-seven genotypes were identified from 295 isolates. Populations were characterised by the same dominant genotype (MLG20 occurring 65.43%), low genotypic diversity (H) and high numbers of clones (81.36% of dataset). However, genotypes from the same sampling sites were not closely related based on a minimum spanning network and had high molecular variation within populations (94%), suggesting that multiple introductions of different genotypes occurred over time. Significant linkage disequilibrium among loci (r̅d) further indicated a dominant asexual cycle, even though perithecia have been observed in these four populations. The two rootstock mother blocks had unique genotypes and genotypes shared with the vineyard populations. Propagation material obtained from infected rootstock mother blocks could lead to the spread of more genotypes to newly established vineyards. Based on our results, it is important to determine the health status of rootstock mother blocks. Management strategies must focus on reducing aerial inoculum to prevent repeated infections and further spread of P. minimum genotypes.}, }
@article {pmid36368693, year = {2022}, author = {Poppeliers, SWM and Hefting, M and Dorrepaal, E and Weedon, JT}, title = {Functional microbial ecology in arctic soils: the need for a year-round perspective.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {12}, pages = {}, pmid = {36368693}, issn = {1574-6941}, mesh = {*Soil ; Arctic Regions ; Climate Change ; Carbon Cycle ; *Microbiota ; }, abstract = {The microbial ecology of arctic and sub-arctic soils is an important aspect of the global carbon cycle, due to the sensitivity of the large soil carbon stocks to ongoing climate warming. These regions are characterized by strong climatic seasonality, but the emphasis of most studies on the short vegetation growing season could potentially limit our ability to predict year-round ecosystem functions. We compiled a database of studies from arctic, subarctic, and boreal environments that include sampling of microbial community and functions outside the growing season. We found that for studies comparing across seasons, in most environments, microbial biomass and community composition vary intra-annually, with the spring thaw period often identified by researchers as the most dynamic time of year. This seasonality of microbial communities will have consequences for predictions of ecosystem function under climate change if it results in: seasonality in process kinetics of microbe-mediated functions; intra-annual variation in the importance of different (a)biotic drivers; and/or potential temporal asynchrony between climate change-related perturbations and their corresponding effects. Future research should focus on (i) sampling throughout the entire year; (ii) linking these multi-season measures of microbial community composition with corresponding functional or physiological measurements to elucidate the temporal dynamics of the links between them; and (iii) identifying dominant biotic and abiotic drivers of intra-annual variation in different ecological contexts.}, }
@article {pmid36368382, year = {2023}, author = {Monahan, C and Morris, D and Nag, R and Cummins, E}, title = {Risk ranking of macrolide antibiotics - Release levels, resistance formation potential and ecological risk.}, journal = {The Science of the total environment}, volume = {859}, number = {Pt 2}, pages = {160022}, doi = {10.1016/j.scitotenv.2022.160022}, pmid = {36368382}, issn = {1879-1026}, mesh = {Humans ; *Anti-Bacterial Agents/toxicity ; *Macrolides/toxicity ; Azithromycin/toxicity ; Clarithromycin ; Erythromycin ; }, abstract = {Antibiotic resistance (AR) development in natural water bodies is a significant source of concern. Macrolide antibiotics in particular have been identified as pollutants of concern for AR development throughout the literature, as well as by state and international authorities. This study utilises a probabilistic model to examine the risk of AR development arising from human-use macrolide residues, utilising administration rates from Ireland as a case study. Stages modelled included level of administration, excretion, degradation in wastewater, removal in wastewater treatment, assuming conventional activated sludge (CAS) treatment, and dilution. Release estimates per day, as well as risk quotient values for antibiotic resistance development and ecological impact, are generated for erythromycin, clarithromycin, and azithromycin. In the modelled scenario in which conventional activated sludge treatment is utilised in wastewater treatment, this model ranks risk of resistance development for each antibiotic in the order clarithromycin > azithromycin > erythromycin, with mean risk quotient values of 0.50, 0.34 and 0.12, respectively. A membrane bioreactor scenario was also modelled, which reduced risk quotient values for all three macrolides by at least 50 %. Risk of ecological impact for each antibiotic was also examined, by comparing environmental concentrations predicted to safety limits based on toxicity data for cyanobacteria and other organisms from the literature, with azithromycin being identified as the macrolide of highest risk. This study compares and quantifies the risk of resistance development and ecological impact for a high-risk antibiotic group in the Irish context, and demonstrates the potential for risk reduction achieved by adoption of alternative (e.g. membrane bioreactor) technology.}, }
@article {pmid36368371, year = {2023}, author = {Kumar, A and Ajay, A and Dasgupta, B and Bhadury, P and Sanyal, P}, title = {Deciphering the nitrate sources and processes in the Ganga river using dual isotopes of nitrate and Bayesian mixing model.}, journal = {Environmental research}, volume = {216}, number = {Pt 4}, pages = {114744}, doi = {10.1016/j.envres.2022.114744}, pmid = {36368371}, issn = {1096-0953}, mesh = {*Rivers ; Nitrates/analysis ; Environmental Monitoring ; Bayes Theorem ; *Water Pollutants, Chemical/analysis ; Nitrogen Isotopes/analysis ; Fertilizers/analysis ; China ; }, abstract = {The dual isotopes of dissolved NO3- (n = 43) has been used to delineate the nitrate sources and N-cycling processes in the Ganga river. The proportional contribution of nitrate from different sources has been estimated using the Bayesian mixing model. The seasonal NO3- concentration in the lower stretch of the river Ganga varied between 4.1 and 64.1 μM with higher concentration during monsoon and post-monsoon season and lower concentration during the pre-monsoon and winter season. The temporal variation in the isotopic values ranged between +0.0 and +9.6‰ for δ[15]NNO3- and -1.2 to +11.0‰ for δ[18]ONO3-. The spatial NO3- concentration during the post-monsoon season varied between 23.2 and 57.7 μM, with higher values from the middle and lower values from the lower stretch of the river Ganga. The isotopic ratio during the post-monsoon season varied between -1.0 and +11.3‰ for δ[15]NNO3- and -4.6 to +5.2‰ for δ[18]ONO3-. The temporal dataset from the lower stretch of the river Ganga showed the dominance of nitrate derived from the nitrification of soil organic matter (SOM) (average ∼53.4%). The nitrate contribution from synthetic fertilizers was observed to be higher during the post-monsoon season (34.7 ± 23.4%) compared to that in the monsoon (25.5 ± 19.5%) and pre-monsoon (22.2 ± 19.6%) season. No significant seasonal variations were observed in the nitrate input from manure/sewage (∼13.9%). Spatial samples collected during the post-monsoon season showed higher contribution of synthetic fertilizer in the lower stretch (34.6 ± 22.7%) compared to the middle stretch (21.1 ± 18.2%), which indicates greater influence of the agricultural activity in the lower stretch. The dual isotope study of dissolved NO3- established that the nitrate in the Ganga river water is mostly derived from the nitrification of incoming organic compounds and is subsequently removed via assimilatory nitrate uptake. The study also emphasises significant nitrification and assimilatory nitrate removal processes operating in the mixing zone of the Ganga river and Hooghly estuary.}, }
@article {pmid36365043, year = {2022}, author = {Han, H and Saed, YA and Song, W and Wang, M and Li, Y}, title = {Prevalence of Non-SARS-CoV-2 Respiratory Pathogens and Co-Infection with SARS-CoV-2 in the Early Stage of COVID-19 Epidemic.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {11}, pages = {}, pmid = {36365043}, issn = {2076-0817}, abstract = {BACKGROUND: This study aims to reflect the prevalence of non-SARS-CoV-2 respiratory pathogens and co-infection with SARS-CoV-2 in the early stage of the COVID-19 epidemic, considering SARS-CoV-2 broke out during influenza season and its symptoms resemble those of influenza.<br><br>METHODS: A total of 685 nucleic acid samples of respiratory pathogens were collected from 1 November 2019 to 20 January 2020 and were detected by the 13 Respiratory Pathogen Multiplex Detection Kit and Novel Coronavirus (2019-nCoV) Nucleic Acid Diagnostic Kit.<br><br>RESULTS: In Wuhan, human rhinovirus was the most frequent infectious pathogen in November (31.5%) and human respiratory syncytial virus appeared the most in December and January (37.1%, 8.6%, respectively). Detection of SARS-CoV-2 first appeared from January 1 to January 10. Generally, 115 patients of 616 patients (18.7%) from Wuhan were infected with SARS-CoV-2, and only two children were co-infected with other respiratory pathogens. In Taiyuan, influenza A virus was detected most frequently in December and January (30.3%, 12%, respectively) without infection of SARS-CoV-2.<br><br>CONCLUSIONS: Some cases diagnosed with influenza before routine nucleic acid testing of SARS-CoV-2 were attributed to COVID-19. Co-infection between SARS-CoV-2 and other non-SARS-CoV-2 respiratory pathogens existed in the early stage of COVID-19 epidemic.}, }
@article {pmid36364003, year = {2022}, author = {Jivkova, D and Sathiyanarayanan, G and Harir, M and Hertkorn, N and Schmitt-Kopplin, P and Sanhaji, G and Fochesato, S and Berthomieu, C and Heyraud, A and Achouak, W and Santaella, C and Heulin, T}, title = {Production and Characterization of a Novel Exopolysaccharide from Ramlibacter tataouinensis.}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {21}, pages = {}, pmid = {36364003}, issn = {1420-3049}, mesh = {Humans ; Gas Chromatography-Mass Spectrometry ; *Comamonadaceae ; Rhamnose ; *Cysts ; Polysaccharides, Bacterial/chemistry ; }, abstract = {The current study examines the desiccation-resistant Ramlibacter tataouinensis TTB310[T] as a model organism for the production of novel exopolysaccharides and their structural features. This bacterium is able to produce dividing forms of cysts which synthesize cell-bound exopolysaccharide. Initial experiments were conducted on the enrichment of cyst biomass for exopolysaccharide production under batch-fed conditions in a pilot-scale bioreactor, with lactate as the source of carbon and energy. The optimized medium produced significant quantities of exopolysaccharide in a single growth phase, since the production of exopolysaccharide took place during the division of the cysts. The exopolysaccharide layer was extracted from the cysts using a modified trichloroacetic acid method. The biochemical characterization of purified exopolysaccharide was performed by gas chromatography, ultrahigh-resolution mass spectrometry, nuclear magnetic resonance, and Fourier-transform infrared spectrometry. The repeating unit of exopolysaccharide was a decasaccharide consisting of ribose, glucose, rhamnose, galactose, mannose, and glucuronic acid with the ratio 3:2:2:1:1:1, and additional substituents such as acetyl, succinyl, and methyl moieties were also observed as a part of the exopolysaccharide structure. This study contributes to a fundamental understanding of the novel structural features of exopolysaccharide from a dividing form of cysts, and, further, results can be used to study its rheological properties for various industrial applications.}, }
@article {pmid36363794, year = {2022}, author = {Zaitseva, S and Badmaev, N and Kozyreva, L and Dambaev, V and Barkhutova, D}, title = {Microbial Community in the Permafrost Thaw Gradient in the South of the Vitim Plateau (Buryatia, Russia).}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36363794}, issn = {2076-2607}, support = {19-29-05250//Russian Foundation for Basic Research/ ; }, abstract = {Soil microbial communities play key roles in biogeochemical cycles and greenhouse gas formation during the decomposition of the released organic matter in the thawing permafrost. The aim of our research was to assess the taxonomic prokaryotic diversity in soil-ecological niches of the Darkhituy-Khaimisan transect during the initial period of soil thawing. We investigated changes in the microbial communities present in the active layer of four sites representing distinct habitats (larch forest, birch forest, meadow steppe and thermokarst lake). We explore the relationship between the biogeochemical differences among habitats and the active layer microbial community via a spatial (across habitats, and with depth through the active layer) community survey using high-throughput Illumina sequencing. Microbial communities showed significant differences between active and frozen layers and across ecosystem types, including a high relative abundance of Alphaproteobacteria, Firmicutes, Crenarchaeota, Bacteroidota and Gemmatimonadota in the active layer and a high relative abundance of Actinobacteriota and Desulfobacterota in the frozen layer. Soil pH, temperature and moisture were the most significant parameters underlying the variations in the microbial community composition. CCA suggested that the differing environmental conditions between the four soil habitats had strong influences on microbial distribution and diversity and further explained the variability of soil microbial community structures.}, }
@article {pmid36363713, year = {2022}, author = {Hurtado-McCormick, V and Trevathan-Tackett, SM and Bowen, JL and Connolly, RM and Duarte, CM and Macreadie, PI}, title = {Pathways for Understanding Blue Carbon Microbiomes with Amplicon Sequencing.}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36363713}, issn = {2076-2607}, support = {DP200100575//Australian Research Council/ ; DE210101029//Australian Research Council/ ; DEB2203322//National Science Foundation/ ; }, abstract = {The capacity of Blue Carbon Ecosystems to act as carbon sinks is strongly influenced by the metabolism of soil-associated microbes, which ultimately determine how much carbon is accumulated or returned to the atmosphere. The rapid evolution of sequencing technologies has facilitated the generation of tremendous amounts of data on what taxa comprise belowground microbial assemblages, largely available as isolated datasets, offering an opportunity for synthesis research that informs progress on understanding Blue Carbon microbiomes. We identified questions that can be addressed with a synthesis approach, including the high variability across datasets, space, and time due to differing sampling techniques, ecosystem or vegetation specificity, and the relationship between microbiome community and edaphic properties, particularly soil carbon. To address these questions, we collated 34 16S rRNA amplicon sequencing datasets, including bulk soil or rhizosphere from seagrass, mangroves, and saltmarshes within publicly available repositories. We identified technical and theoretical challenges that precluded a synthesis of multiple studies with currently available data, and opportunities for addressing the knowledge gaps within Blue Carbon microbial ecology going forward. Here, we provide a standardisation toolbox that supports enacting tasks for the acquisition, management, and integration of Blue Carbon-associated sequencing data and metadata to potentially elucidate novel mechanisms behind Blue Carbon dynamics.}, }
@article {pmid36360970, year = {2022}, author = {Sousa, V and Spratt, D and Davrandi, M and Mardas, N and Beltrán, V and Donos, N}, title = {Oral Microcosm Biofilms Grown under Conditions Progressing from Peri-Implant Health, Peri-Implant Mucositis, and Peri-Implantitis.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {21}, pages = {}, pmid = {36360970}, issn = {1660-4601}, support = {/DH_/Department of Health/United Kingdom ; }, mesh = {Humans ; *Peri-Implantitis/microbiology ; RNA, Ribosomal, 16S/genetics ; *Mucositis ; Biofilms ; *Microbiota/genetics ; Bacteria/genetics ; }, abstract = {Peri-implantitis is a disease influenced by dysbiotic microbial communities that play a role in the short- and long-term outcomes of its clinical treatment. The ecological triggers that establish the progression from peri-implant mucositis to peri-implantitis remain unknown. This investigation describes the development of a novel in vitro microcosm biofilm model. Biofilms were grown over 30 days over machined titanium discs in a constant depth film fermentor (CDFF), which was inoculated (I) with pooled human saliva. Following longitudinal biofilm sampling across peri-implant health (PH), peri-implant mucositis (PM), and peri-implantitis (PI) conditions, the characterisation of the biofilms was performed. The biofilm analyses included imaging by confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM), selective and non-selective culture media of viable biofilms, and 16S rRNA gene amplification and sequencing. Bacterial qualitative shifts were observed by CLSM and SEM across conditions, which were defined by characteristic phenotypes. A total of 9 phyla, 83 genera, and 156 species were identified throughout the experiment. The phyla Proteobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Actinobacteria showed the highest prevalence in PI conditions. This novel in vitro microcosm model provides a high-throughput alternative for growing microcosm biofilms resembling an in vitro progression from PH-PM-PI conditions.}, }
@article {pmid36358990, year = {2022}, author = {Scott, E and De Paepe, K and Van de Wiele, T}, title = {Postbiotics and Their Health Modulatory Biomolecules.}, journal = {Biomolecules}, volume = {12}, number = {11}, pages = {}, pmid = {36358990}, issn = {2218-273X}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Probiotics ; Fatty Acids, Volatile ; Vitamins ; Inflammation ; }, abstract = {Postbiotics are a new category of biotics that have the potential to confer health benefits but, unlike probiotics, do not require living cells to induce health effects and thus are not subject to the food safety requirements that apply to live microorganisms. Postbiotics are defined as a "preparation of inanimate microorganisms and/or their components that confers a health benefit on the host". Postbiotic components include short-chain fatty acids, exopolysaccharides, vitamins, teichoic acids, bacteriocins, enzymes and peptides in a non-purified inactivated cell preparation. While research into postbiotics is in its infancy, there is increasing evidence that postbiotics have the potential to modulate human health. Specifically, a number of postbiotics have been shown to improve gut health by strengthening the gut barrier, reducing inflammation and promoting antimicrobial activity against gut pathogens. Additionally, research is being conducted into the potential application of postbiotics to other areas of the body, including the skin, vagina and oral cavity. The purpose of this review is to set out the current research on postbiotics, demonstrate how postbiotics are currently used in commercial products and identify a number of knowledge gaps where further research is needed to identify the potential for future applications of postbiotics.}, }
@article {pmid36358119, year = {2022}, author = {Calatayud, M and Duysburgh, C and Van den Abbeele, P and Franckenstein, D and Kuchina-Koch, A and Marzorati, M}, title = {Long-Term Lactulose Administration Improves Dysbiosis Induced by Antibiotic and C. difficile in the PathoGut[TM] SHIME Model.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {11}, pages = {}, pmid = {36358119}, issn = {2079-6382}, abstract = {Clostridioides difficile infection (CDI) is the leading cause of antibiotic-associated diarrhea and an important nosocomial infection with different severity degrees. Disruption of the gut microbiota by broad-spectrum antibiotics creates a proper environment for C. difficile colonization, proliferation, and clinical disease onset. Restoration of the gut microbial ecosystem through prebiotic interventions can constitute an effective complementary treatment of CDI. Using an adapted simulator of the human gut microbial ecosystem, the PathoGut[TM] SHIME, the effect of different long-term and repeated dose lactulose treatments was tested on C. difficile germination and growth in antibiotic-induced dysbiotic gut microbiota environments. The results showed that lactulose reduced the growth of viable C. difficile cells following clindamycin treatment, shifted the antibiotic-induced dysbiotic microbial community, and stimulated the production of health-promoting metabolites (especially butyrate). Recovery of the gut microenvironment by long-term lactulose administration following CDI was also linked to lactate production, decrease in pH and modulation of bile salt metabolism. At a structural level, lactulose showed a significant bifidogenic potential and restored key commensal members of the gut ecosystem such as Lactobacillaceae, Veillonellaceae and Lachnospiraceae. These results support further human intervention studies aiming to validate the in vitro beneficial effects of lactulose on gut microbiome recovery during antibiotic exposure and CDI.}, }
@article {pmid36356812, year = {2023}, author = {Kim, M and Cui, F}, title = {Identification of bacterial communities in conventional wastewater treatment sludge to inform inoculation of the anammox process.}, journal = {Chemosphere}, volume = {311}, number = {Pt 2}, pages = {137167}, doi = {10.1016/j.chemosphere.2022.137167}, pmid = {36356812}, issn = {1879-1298}, mesh = {*Wastewater ; Sewage/microbiology ; Denitrification ; Anaerobic Ammonia Oxidation ; Bioreactors/microbiology ; Oxidation-Reduction ; Anaerobiosis ; Bacteria/genetics ; Nitrogen ; *Water Purification ; }, abstract = {This study uses 16 S rRNA gene pyrosequencing for the identification of a vast number of wastewater bacterial communities to investigate the evolution of bacterial communities in the Anammox process. Four lab-scale Anammox reactors inoculated with different conventional wastewater treatment sludge (activated sludge, livestock wastewater treatment sludge, denitrification sludge, and anaerobic digestion sludge) were operated under identical operating conditions for more than 400 days. The phylum Planctomycetes was present in all seeds of conventional sludge with a relative abundance of 1-3%. In particular, the known Anammox bacteria Candidatus Brocadia was found in the seed of the denitrification sludge. The reactor inoculated with denitrification sludge demonstrated the most effective nitrogen removal of ∼80% with successful cultivation of Anammox bacteria. This study found that the performance of the Anammox process is related to the presence of Nitrospira genus (nitrite-oxidizing bacteria) and that symbiotic association with other functional groups can lead to nitrogen removal. The outcomes of this study can provide vital insight into the study of microbial ecology for the cultivation of Anammox bacteria.}, }
@article {pmid36355167, year = {2022}, author = {Yoon, KH and Indong, RA and Lee, JI}, title = {Making "Sense" of Ecology from a Genetic Perspective: Caenorhabditis elegans, Microbes and Behavior.}, journal = {Metabolites}, volume = {12}, number = {11}, pages = {}, pmid = {36355167}, issn = {2218-1989}, support = {2021R1A2C101178312//National Research Foundation of Korea/ ; 2019R1C1C1008708//National Research Foundation of Korea/ ; }, abstract = {Our knowledge of animal and behavior in the natural ecology is based on over a century's worth of valuable field studies. In this post-genome era, however, we recognize that genes are the underpinning of ecological interactions between two organisms. Understanding how genes contribute to animal ecology, which is essentially the intersection of two genomes, is a tremendous challenge. The bacterivorous nematode Caenorhabditis elegans, one of the most well-known genetic animal model experimental systems, experiences a complex microbial world in its natural habitat, providing us with a window into the interplay of genes and molecules that result in an animal-microbial ecology. In this review, we will discuss C. elegans natural ecology, how the worm uses its sensory system to detect the microbes and metabolites that it encounters, and then discuss some of the fascinating ecological dances, including behaviors, that have evolved between the nematode and the microbes in its environment.}, }
@article {pmid36354324, year = {2022}, author = {Saati-Santamaría, Z and Baroncelli, R and Rivas, R and García-Fraile, P}, title = {Comparative Genomics of the Genus Pseudomonas Reveals Host- and Environment-Specific Evolution.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0237022}, pmid = {36354324}, issn = {2165-0497}, mesh = {Animals ; *Ecosystem ; Phylogeny ; *Pseudomonas/genetics ; Genomics ; Adaptation, Physiological/genetics ; }, abstract = {Each Earth ecosystem has unique microbial communities. Pseudomonas bacteria have evolved to occupy a plethora of different ecological niches, including living hosts, such as animals and plants. Many genes necessary for the Pseudomonas-niche interaction and their encoded functions remain unknown. Here, we describe a comparative genomic study of 3,274 genomes with 19,056,667 protein-coding sequences from Pseudomonas strains isolated from diverse environments. We detected functional divergence of Pseudomonas that depends on the niche. Each group of strains from a certain environment harbored a distinctive set of metabolic pathways or functions. The horizontal transfer of genes, which mainly proceeded between closely related taxa, was dependent on the isolation source. Finally, we detected thousands of undescribed proteins and functions associated with each Pseudomonas lifestyle. This research represents an effort to reveal the mechanisms underlying the ecology, pathogenicity, and evolution of Pseudomonas, and it will enable clinical, ecological, and biotechnological advances. IMPORTANCE Microbes play important roles in the health of living beings and in the environment. The knowledge of these functions may be useful for the development of new clinical and biotechnological applications and the restoration and preservation of natural ecosystems. However, most mechanisms implicated in the interaction of microbes with the environment remain poorly understood; thus, this field of research is very important. Here, we try to understand the mechanisms that facilitate the differential adaptation of Pseudomonas-a large and ubiquitous bacterial genus-to the environment. We analyzed more than 3,000 Pseudomonas genomes and searched for genetic patterns that can be related with their coevolution with different hosts (animals, plants, or fungi) and environments. Our results revealed that thousands of genes and genetic features are associated with each niche. Our data may be useful to develop new technical and theoretical advances in the fields of ecology, health, and industry.}, }
@article {pmid36352414, year = {2022}, author = {Pitiriga, V and Bakalis, J and Theodoridou, K and Kanellopoulos, P and Saroglou, G and Tsakris, A}, title = {Lower risk of bloodstream infections for peripherally inserted central catheters compared to central venous catheters in critically ill patients.}, journal = {Antimicrobial resistance and infection control}, volume = {11}, number = {1}, pages = {137}, pmid = {36352414}, issn = {2047-2994}, mesh = {Adult ; Humans ; *Central Venous Catheters/adverse effects ; *Catheter-Related Infections/epidemiology/etiology ; *Catheterization, Central Venous/adverse effects ; Retrospective Studies ; Critical Illness ; Risk Factors ; *Sepsis/epidemiology ; }, abstract = {BACKGROUND: Peripherally inserted central venous catheters (PICCs) serve as an alternative to short-term central venous catheters (CVCs) for providing intravenous access in hospitalized patients. Although a number of studies suggest that PICCs are associated with a lower risk of central line-associated bloodstream infections (CLABSIs) than CVCs, recent data concerning specific patient groups support the contrary. In this regard, we are comparing CVC- and PICC-related CLABSI rates developed in a selected group of critically ill inpatients and evaluating the CLABSI microbiological distribution.<br><br>METHODS: The study was conducted at a tertiary care hospital in Greece between May 2017 and May 2019. We performed a two-year retrospective analysis of the data collected from medical records of consecutive adult patients who underwent PICC or CVC placement.<br><br>RESULTS: A total of 1187 CVCs placed for 9774 catheter-days and 639 PICCs placed for 11,110 catheter-days, were reported and analyzed during the study period. Among CVCs, a total of 59 (4.9%) CLABSIs were identified, while among PICCs, 18 (2.8%) cases presented CLABSI (p&#x2009;=&#x2009;0.029). The CLABSI incidence rate per 1,000 catheter-days was 6.03 for CVC group and 1.62 for PICC group (p&#x2009;<&#x2009;0.001). The CLABSI rate due to multidrug-resistant organisms (MDROs) among the two groups was 3.17 in CVC group and 0.36 in PICC group (p&#x2009;<&#x2009;0.001). Within CLABSI-CVC group, the most common microorganism detected was MDR Acinetobacter baumannii (27.1%) followed by MDR Klebsiella pneumoniae (22%). In CLABSI-PICC group, the predominant microorganism was Candida spp. (33.3%) followed by non-MDR gram-negative pathogens (22.2%).<br><br>CONCLUSIONS: PICC lines were associated with significantly lower CLABSI rates comparing to CVC although they were in place longer than CVC lines. Given their longer time to the development of infection, PICCs may be a safer alternative for prolonged inpatient IV access. The high prevalence of CLABSI-MDROs depicts the local microbial ecology, emphasizing the need of&#xa0;public health awareness.}, }
@article {pmid36352137, year = {2023}, author = {Graber, LC and Ramalho, MO and Powell, S and Moreau, CS}, title = {Identifying the Role of Elevation, Geography, and Species Identity in Structuring Turtle Ant (Cephalotes Latreille, 1802) Bacterial Communities.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1240-1253}, pmid = {36352137}, issn = {1432-184X}, support = {DEB 1442256//National Science Foundation/ ; DEB 1900357//National Science Foundation/ ; }, mesh = {Animals ; *Ants/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Geography ; *Microbiota ; Bacteria/genetics ; }, abstract = {Bacterial communities in animals are often necessary for hosts to survive, particularly for hosts with nutrient-limited diets. The composition, abundance, and richness of these bacterial communities may be shaped by host identity and external ecological factors. The turtle ants (genus Cephalotes) are predominantly herbivorous and known to rely on bacterial communities to enrich their diet. Cephalotes have a broad Neotropical distribution, with high diversity in the South American Cerrado, a geologically and biologically diverse savanna. Using 16S rRNA amplicon sequencing, we examined the bacterial communities of forty-one Cephalotes samples of sixteen different species collected from multiple locations across two sites in the Cerrado (MG, Brazil) and compared the bacterial communities according to elevation, locality, species, and species group, defined by host phylogeny. Beta diversity of bacterial communities differed with respect to all categories but particularly strongly when compared by geographic location, species, and species group. Differences seen in species and species groups can be partially explained by the high abundance of Mesorhizobium in Cephalotes pusillus and Cephalotes depressus species groups, when compared to other clades via the Analysis of Composition of Microbiome (ANCOM). Though the Cephalotes bacterial community is highly conserved, results from this study indicate that multiple external factors can affect and change bacterial community composition and abundance.}, }
@article {pmid36350347, year = {2023}, author = {Ayilara, MS and Adeleke, BS and Babalola, OO}, title = {Correction to: Bioprospecting and Challenges of Plant Microbiome Research for Sustainable Agriculture, a Review on Soybean Endophytic Bacteria.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1454}, doi = {10.1007/s00248-022-02141-2}, pmid = {36350347}, issn = {1432-184X}, }
@article {pmid36350260, year = {2022}, author = {Collin, B and Auffan, M and Doelsch, E and Proux, O and Kieffer, I and Ortet, P and Santaella, C}, title = {Bacterial Metabolites and Particle Size Determine Cerium Oxide Nanomaterial Biotransformation.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {23}, pages = {16838-16847}, doi = {10.1021/acs.est.2c05280}, pmid = {36350260}, issn = {1520-5851}, mesh = {Particle Size ; *Cerium/chemistry ; Soil/chemistry ; *Metal Nanoparticles/chemistry ; Bacteria ; *Nanostructures ; }, abstract = {Soil is a major receptor of manufactured nanomaterials (NMs) following unintentional releases or intentional uses. Ceria NMs have been shown to undergo biotransformation in plant and soil organisms with a partial Ce(IV) reduction into Ce(III), but the influence of environmentally widespread soil bacteria is poorly understood. We used high-energy resolution fluorescence-detected X-ray absorption spectroscopy (HERFD-XAS) with an unprecedented detection limit to assess Ce speciation in a model soil bacterium (Pseudomonas brassicacearum) exposed to CeO2 NMs of different sizes and shapes. The findings revealed that the CeO2 NM's size drives the biotransformation process. No biotransformation was observed for the 31 nm CeO2 NMs, contrary to 7 and 4 nm CeO2 NMs, with a Ce reduction of 64 ± 14% and 70 ± 15%, respectively. This major reduction appeared quickly, from the early exponential bacterial growth phase. Environmentally relevant organic acid metabolites secreted by Pseudomonas, especially in the rhizosphere, were investigated. The 2-keto-gluconic and citric acid metabolites alone were able to induce a significant reduction in 4 nm CeO2 NMs. The high biotransformation measured for <7 nm NMs would affect the fate of Ce in the soil and biota.}, }
@article {pmid36349406, year = {2023}, author = {Chen, H and Fang, Y and Zwaenepoel, A and Huang, S and Van de Peer, Y and Li, Z}, title = {Revisiting ancient polyploidy in leptosporangiate ferns.}, journal = {The New phytologist}, volume = {237}, number = {4}, pages = {1405-1417}, pmid = {36349406}, issn = {1469-8137}, support = {833522//European Research Council/International ; }, mesh = {*Ferns/genetics ; Phylogeny ; Gene Duplication ; Genome Size ; Polyploidy ; Evolution, Molecular ; Genome, Plant ; }, abstract = {Ferns, and particularly homosporous ferns, have long been assumed to have experienced recurrent whole-genome duplication (WGD) events because of their substantially large genome sizes, surprisingly high chromosome numbers, and high degrees of polyploidy among many extant members. As the number of sequenced fern genomes is limited, recent studies have employed transcriptome data to find evidence for WGDs in ferns. However, they have reached conflicting results concerning the occurrence of ancient polyploidy, for instance, in the lineage of leptosporangiate ferns. Because identifying WGDs in a phylogenetic context is the foremost step in studying the contribution of ancient polyploidy to evolution, we here revisited earlier identified WGDs in leptosporangiate ferns, mainly the core leptosporangiate ferns, by building KS -age distributions and applying substitution rate corrections and by conducting statistical gene tree-species tree reconciliation analyses. Our integrative analyses not only identified four ancient WGDs in the sampled core leptosporangiate ferns but also identified false positives and false negatives for WGDs that recent studies have reported earlier. In conclusion, we underscore the significance of substitution rate corrections and uncertainties in gene tree-species tree reconciliations in calling WGD events and advance an exemplar workflow to overcome such often-overlooked issues.}, }
@article {pmid36346444, year = {2023}, author = {Palmer, B and Lawson, D and Lipson, DA}, title = {Years After a Fire, Biocrust Microbial Communities are Similar to Unburned Communities in a Coastal Grassland.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {1028-1044}, pmid = {36346444}, issn = {1432-184X}, mesh = {Ecosystem ; Grassland ; *Microbiota ; *Fires ; Bacteria/genetics ; Chlorophyll ; Soil ; }, abstract = {Microbial communities are integral for ecosystem processes and their taxonomic composition and function may be altered by a disturbance such as fire. Biocrusts are composed of macroscopic and microscopic organisms and are important for a variety of ecosystem functions, such as nutrient cycling and erosion control. We sought to understand if biocrust community composition and function were altered 1 year after a prescribed fire and 6 years after a wildfire in a coastal California grassland on San Clemente Island. We used shotgun metagenomic sequencing and measurements of chlorophyll content, exopolysaccharide production related to soil stability, and nitrogen fixation. There were no differences in the community composition between unburned samples and the samples burned in the prescribed fire and wildfire. Chlorophyll content differed between the prescribed fire and the controls; however, there were no measured differences in exopolysaccharide production, and nitrogen fixation. However, the wildfire and their respective unburned samples had different functions based on the gene annotations. We compiled one Actinobacteria metagenome-assembled genome from the shotgun sequences which had genes for oxidative and heat stress tolerance. These results suggest that the biocrust community can reach a community composition and function similar to the unburned biocrusts within a year after a prescribed burn and 6 years after a wildfire. However, legacy effects of the wildfire may present themselves in the differences between functional gene sequences. Due to their ability to match the undisturbed community composition and function within years and without intervention, future restoration work should consider the biocrusts in their restoration plans as they may provide valuable ecosystem functions after a disturbance.}, }
@article {pmid36345526, year = {2022}, author = {DeWitt, ME and Polk, C and Williamson, J and Shetty, AK and Passaretti, CL and McNeil, CJ and Fairman, RT and Sampson, MM and Dalton, C and Sanders, JW}, title = {Global monkeypox case hospitalisation rates: A rapid systematic review and meta-analysis.}, journal = {EClinicalMedicine}, volume = {54}, number = {}, pages = {101710}, pmid = {36345526}, issn = {2589-5370}, abstract = {BACKGROUND: Estimates of the case hospitalization rate and case fatality rate when hospital care is available for monkeypox (MPX) infections have not been well defined. This rapid systematic review and meta-analysis aimed to estimate the case hospitalisation rate and case fatality rate where hospital care is available.<br><br>METHODS: We systematically searched PubMed, Embase, the Lancet Preprints, and MedRxiv for studies published between Jan 1, 1950 and Aug 2, 2022. We included documents which contained both the number of cases and associated hospitalisations of MPX infections. From eligible studies we extracted the country, the year of the study, the study design type, the clade of MPX, the participant characteristics, transmission type, any treatments used, number of cases (including suspected, probable, or laboratory confirmed diagnosis), number of hospitalizations, hospitalized patient outcomes, and case definition. Case hospitalization rate (CHR) was defined as the proportion of cases that were admitted to hospital care while case fatality rate (CFR) was defined as the proportion of cases that died. CHR and CFR were analysed in a fully Bayesian meta-analytic framework using random effects models, including sub-group analysis with heterogeneity assessed using I[2].<br><br>FINDINGS: Of the 259 unique documents identified, 19 studies were eligible for inclusion. Included studies represented 7553 reported cases among which there were 555 hospitalizations. Of the 7540 cases for which outcomes were available, there were 15 recorded deaths. The median age of cases was 35 years (interquartile range 28-38, n&#xa0;=&#xa0;2010) and primarily male (7339/7489, 98%) in studies where age or sex were available. Combined CHR was estimated to be 14.1% (95% credible interval, 7.5-25.0, I[2] 97.4%), with a high degree of heterogeneity. Further analysis by outbreak period indicates CHRs of 49.8% (28.2-74.0, I[2] 81.4%), 21.7% (7.2-52.1, I[2] 57.7%), and 5.8% (3.2-9.4, I[2] 92.4%) during the pre-2017, 2017-2021, and 2022 outbreaks, respectively, again with high levels of heterogeneity. CFR was estimated to be 0.03% (0.0-0.44, I[2] 99.9%), with evidence of large heterogeneity between the studies.<br><br>INTERPRETATION: There is limited data for MPX hospitalization rates in countries where MPX has been traditionally non-endemic until the current outbreak. Due to substantial heterogeneity, caution is needed when interpreting these findings. Health care organizations should be cognizant of the potential increase in healthcare utilization. Rapid identification of infection and use of appropriate therapies such as antivirals play a role reducing the CHR and associated CFR.<br><br>FUNDING: None.}, }
@article {pmid36345334, year = {2022}, author = {Verbeelen, T and Van Houdt, R and Leys, N and Ganigué, R and Mastroleo, F}, title = {Optimization of RNA extraction for bacterial whole transcriptome studies of low-biomass samples.}, journal = {iScience}, volume = {25}, number = {11}, pages = {105311}, pmid = {36345334}, issn = {2589-0042}, abstract = {We developed a procedure for extracting maximal amounts of high-quality RNA from low-biomass producing (autotrophic) bacteria for experiments where sample volume is limited. Large amounts of high-quality RNA for downstream analyses cannot be obtained using larger quantities of culture volume. The performance of standard commercial silica-column based kit protocols and these procedures amended by ultrasonication or enzymatic lysis were assessed. The ammonium-oxidizing Nitrosomonas europaea and nitrite-oxidizing Nitrobacter winogradskyi were used as model organisms for optimization of the RNA isolation protocol. Enzymatic lysis through lysozyme digestion generated high-quality, high-yield RNA samples. Subsequent RNA-seq analysis resulted in qualitative data for both strains. The RNA extraction procedure is suitable for experiments with volume and/or biomass limitations, e.g., as encountered during space flight experiments. Furthermore, it will also result in higher RNA yields for whole transcriptome experiments where sample volume and/or biomass was increased to compensate the low-biomass characteristic of autotrophs.}, }
@article {pmid36344828, year = {2023}, author = {Bringhurst, B and Allert, M and Greenwold, M and Kellner, K and Seal, JN}, title = {Environments and Hosts Structure the Bacterial Microbiomes of Fungus-Gardening Ants and their Symbiotic Fungus Gardens.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1374-1392}, pmid = {36344828}, issn = {1432-184X}, support = {IOS-1552822//Directorate for Biological Sciences/ ; DEB-1354629//Directorate for Biological Sciences/ ; }, mesh = {Animals ; Gardens ; Gardening ; *Ants/microbiology ; Fungi/genetics ; Symbiosis/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria/genetics ; Phylogeny ; }, abstract = {The fungus gardening-ant system is considered a complex, multi-tiered symbiosis, as it is composed of ants, their fungus, and microorganisms associated with either ants or fungus. We examine the bacterial microbiome of Trachymyrmex septentrionalis and Mycetomoellerius turrifex ants and their symbiotic fungus gardens, using 16S rRNA Illumina sequencing, over a region spanning approximately 350 km (east and central Texas). Typically, microorganisms can be acquired from a parent colony (vertical transmission) or from the environment (horizontal transmission). Because the symbiosis is characterized by co-dispersal of the ants and fungus, elements of both ant and fungus garden microbiome could be characterized by vertical transmission. The goals of this study were to explore how both the ant and fungus garden bacterial microbiome are acquired. The main findings were that different mechanisms appear to explain the structure the microbiomes of ants and their symbiotic fungus gardens. Ant associated microbiomes had a strong host ant signature, which could be indicative of vertical inheritance of the ant associated bacterial microbiome or an unknown mechanism of active uptake or screening. On the other hand, the bacterial microbiome of the fungus garden was more complex in that some bacterial taxa appear to be structured by the ant host species, whereas others by fungal lineage or the environment (geographic region). Thus bacteria in fungus gardens appear to be acquired both horizontally and vertically.}, }
@article {pmid36342171, year = {2022}, author = {Jin, H and Li, X and Wang, H and Cápiro, NL and Li, X and Löffler, FE and Yan, J and Yang, Y}, title = {Anaerobic Biohydrogenation of Isoprene by Acetobacterium wieringae Strain Y.}, journal = {mBio}, volume = {13}, number = {6}, pages = {e0208622}, pmid = {36342171}, issn = {2150-7511}, mesh = {*Acetobacterium/genetics/metabolism ; Anaerobiosis ; Proteomics ; Oxidoreductases/metabolism ; }, abstract = {Isoprene is a ubiquitously distributed, biogenic, and climate-active organic compound. Microbial isoprene degradation in oxic environments is fairly well understood; however, studies exploring anaerobic isoprene metabolism remain scarce, with no isolates for study available. Here, we obtained an acetogenic isolate, designated Acetobacterium wieringae strain Y, which hydrogenated isoprene to a mixture of methyl-1-butenes at an overall rate of 288.8 ± 20.9 μM day[-1] with concomitant acetate production at a rate of 478.4 ± 5.6 μM day[-1]. Physiological characterization demonstrated that isoprene was not utilized in a respiratory process; rather, isoprene promoted acetogenesis kinetically. Bioinformatic analysis and proteomics experiments revealed the expression of candidate ene-reductases responsible for isoprene biohydrogenation. Notably, the addition of isoprene to strain Y cultures stimulated the expression of proteins associated with the Wood-Ljungdahl pathway, indicating unresolved impacts of isoprene on carbon cycling and microbial ecology in anoxic environments (e.g., promoting CO2 plus H2 reductive acetogenesis while inhibiting methanogenesis). Our new findings advance understanding of microbial transformation of isoprene under anoxic conditions and suggest that anoxic environments are isoprene sinks. IMPORTANCE Isoprene is the most abundant, biologically generated, volatile organic compound on Earth, with estimated emissions in the same magnitude as methane. Nonetheless, a comprehensive knowledge of isoprene turnover in the environment is lacking, impacting global isoprene flux models and our understanding of the environmental fate and longevity of isoprene. A critical knowledge gap that has remained largely unexplored until recently is the microbiology and associated molecular mechanisms involved in the anaerobic biotransformation of isoprene. By integrating culture-dependent approaches with omics techniques, we isolated an acetogen, Acetobacterium wieringae strain Y, capable of anaerobic biohydrogenation of isoprene. We obtained the complete genome of strain Y, and proteomic experiments identified candidate ene-reductases for catalyzing the asymmetric reduction of the electronically activated carbon-carbon double bond of isoprene. We also demonstrated that isoprene biohydrogenation stimulates the expression of Wood-Ljungdahl pathway enzymes. This study emphasizes the ecological roles of specialized Acetobacterium on the natural cycling of isoprene in anoxic environments and the potential effects of isoprene biohydrogenation on acetogens and methanogens, which have implications for global climate change and bioenergy production.}, }
@article {pmid36338036, year = {2022}, author = {Kraemer, SA and Barbosa da Costa, N and Oliva, A and Huot, Y and Walsh, DA}, title = {A resistome survey across hundreds of freshwater bacterial communities reveals the impacts of veterinary and human antibiotics use.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {995418}, pmid = {36338036}, issn = {1664-302X}, abstract = {Our decreasing ability to fight bacterial infections is a major health concern. It is arising due to the evolution of antimicrobial resistance (AMR) in response to the mis- and overuse of antibiotics in both human and veterinary medicine. Lakes integrate watershed processes and thus may act as receptors and reservoirs of antibiotic resistance genes (ARGs) introduced into the watershed by human activities. The resistome - the diversity of ARGs - under varying anthropogenic watershed pressures has been previously studied either focused on few select genes or few lakes. Here, we link the resistome of ~350 lakes sampled across Canada to human watershed activity, trophic status, as well as point sources of ARG pollution including wastewater treatment plants and hospitals in the watershed. A high percentage of the resistance genes detected was either unimpacted by human activity or highly prevalent in pristine lakes, highlighting the role of AMR in microbial ecology in aquatic systems, as well as a pool of genes available for potential horizontal gene transfer to pathogenic species. Nonetheless, watershed agricultural and pasture area significantly impacted the resistome. Moreover, the number of hospitals and the population density in a watershed, the volume of wastewater entering the lake, as well as the fraction of manure applied in the watershed as fertilizer significantly impacted ARG diversity. Together, these findings indicate that lake resistomes are regularly stocked with resistance genes evolved in the context of both veterinary and human antibiotics use and represent reservoirs of ARGs that require further monitoring.}, }
@article {pmid36334202, year = {2023}, author = {Tian, L and Wang, L and Zhang, X and Huang, X and Wang, F and Zhu, S and Li, X and Guan, Y}, title = {Multi-omics analysis on seasonal variations of the biofilm microbial community in a full-scale pre-denitrification biofilter.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {9}, pages = {24284-24298}, pmid = {36334202}, issn = {1614-7499}, support = {21-1-4-sf-11-nsh//science and technology program for public wellbeing of qingdao/ ; }, mesh = {*Denitrification ; Bioreactors/microbiology ; Seasons ; Multiomics ; Proteomics ; *Microbiota ; Biofilms ; Nitrogen ; }, abstract = {The seasonal variations of biofilm communities in a municipal wastewater treatment plant were investigated using multi-omics techniques. The abundance of the main phyla of microorganisms varied with summer (July 2019) and winter (January 2019) samples considerably, the Bacteroidetes enriched in winter and Chloroflexi in summer. The results of metaproteomic and metagenomic showed that most of the functional microorganisms belonged to the Betaproteobacteria class, and the enrichment of Flavobacteria class in winter guaranteed the stability of denitrification performance to some extent. Seasonal variations affected the proteomic expression profiling, a total of 2835 differentially expressed proteins identified were significantly enriched in quorum sensing, two-component system, ribosome, benzoate degradation, butanoate metabolism, tricarboxylic acid cycle (TCA cycle), and cysteine and methionine metabolism pathways. With the expression of nitrogen metabolic proteins decreases in winter, the overall expression of denitrification-related enzymes in winter was much lower than that in summer, the nitrogen metabolism pathway varied significantly. Seasonal variations also induced the alteration of the biofilm metabolite profile; a total of 66 differential metabolites, 8 potential biomarkers, and 8 perturbed metabolic pathways such as TCA cycle were detected. It was found that most of the perturbed pathways are directly related to nitrogen metabolism, and several amino acids and organic acids associated with the TCA cycle were significantly perturbed, the accumulation of TCA cycle intermediates, ornithine, and L-histidine in winter might be conducive to resisting cold temperatures. Furthermore, the correlation between biofilm microbial communities and metabolites was identified by the combined analysis of metabolomic and metaproteomic. The differences of microbial community structure, function, and metabolism between winter and summer in a full-scale pre-denitrification biofilter were revealed for the first time, strengthening our understanding of the microbial ecology of biofilm communities.}, }
@article {pmid36334118, year = {2023}, author = {Stouvenakers, G and Massart, S and Jijakli, MH}, title = {First Study Case of Microbial Biocontrol Agents Isolated from Aquaponics Through the Mining of High-Throughput Sequencing Data to Control Pythium aphanidermatum on Lettuce.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1107-1119}, pmid = {36334118}, issn = {1432-184X}, mesh = {Animals ; *Fungicides, Industrial ; *Pythium ; Lactuca ; Pest Control, Biological ; Plant Diseases/prevention &amp; control/microbiology ; Water ; High-Throughput Nucleotide Sequencing ; }, abstract = {Aquaponics is defined as a sustainable and integrated system that combines fish aquaculture and hydroponic plant production in the same recirculated water loop. A recent study using high-throughput sequencing (HTS) technologies highlighted that microbial communities from an aquaponic system could control one of the most problematic pathogens in soilless lettuce culture, namely, Pythium aphanidermatum. Therefore, this study aims at isolating the microorganisms responsible for this biocontrol action. Based on the most promising genera identified by HTS, an innovative strategy for isolating and testing original biocontrol agents from aquaponic water was designed to control P. aphanidermatum. Eighty-two bacterial strains and 18 fungal strains were isolated, identified by Sanger sequencing, and screened in vivo to control damping-off of lettuce seeds caused by P. aphanidermatum. Out of these 100 isolates, the eight most efficacious ones were selected and further tested individually to control root rot disease caused by the same pathogen at a later stage of lettuce growth. Strains SHb30 (Sphingobium xenophagum), G2 (Aspergillus flavus), and Chito13 (Mycolicibacterium fortuitum) decreased seed damping-off at a better rate than a propamocarb fungicide and a Pseudomonas chlororaphis registered biocontrol agent did. In root rot bioassays, lettuce mortality was prevented by applying strains G2 and Chito13, which were at least as efficacious as the fungicide or biopesticide controls. Lettuce disease symptoms and mortality were eradicated by strain SHb30 in the first bioassay, but not in the second one. These results show that aquaponic systems are promising sources of original biocontrol agents, and that HTS-guided strategies could represent interesting approaches to identify new biocontrol agents.}, }
@article {pmid36333944, year = {2022}, author = {Zhang, S and Yang, Q and Defoirdt, T}, title = {Indole analogues decreasing the virulence of Vibrio campbellii towards brine shrimp larvae.}, journal = {Microbial biotechnology}, volume = {15}, number = {12}, pages = {2917-2928}, pmid = {36333944}, issn = {1751-7915}, support = {//China Scholarship Council/ ; 1500219N//Scientific Research Fund of Flanders/ ; //Special Research Fund of Ghent University/ ; }, mesh = {Animals ; *Artemia/microbiology ; Larva/microbiology ; *Vibrio ; }, abstract = {Indole signalling has been proposed as a potential target for the development of novel virulence inhibitors to control bacterial infections. However, the major structural features of indole analogues that govern antivirulence activity remain unexplored. Therefore, we investigated the impact of 26 indole analogues on indole-regulated virulence phenotypes in Vibrio campbellii and on the virulence of the bacterium in a gnotobiotic brine shrimp model. The results demonstrated that 10 indole analogues significantly increased the fluorescence of indole reporter strain Vibrio cholerae S9149, 21 of them decreased the swimming motility of V. campbellii, and 13 of them significantly decreased the biofilm formation of V. campbellii. Further, we found that 1-methylindole, indene, 2,3-benzofuran, thianaphthene, indole-3-acetonitrile, methyl indole-3-carboxylate, 3-methylindole, and indole-2-carboxaldehyde exhibited a significant protective effect on brine shrimp larvae against V. campbellii infection, resulting in survival rates of challenged brine shrimp above 80%. The highest survival of shrimp larvae (98%) was obtained with indole-3-acetonitrile, even at a relatively low concentration of 20 μM. Importantly, the indole analogues did not affect bacterial growth, both in vitro and in vivo. These results indicate the potential of indole analogues in applications aiming at the protection of shrimp from vibriosis.}, }
@article {pmid36333915, year = {2023}, author = {Berry, O and Briand, E and Bagot, A and Chaigné, M and Meslet-Cladière, L and Wang, J and Grovel, O and Jansen, JJ and Ruiz, N and du Pont, TR and Pouchus, YF and Hess, P and Bertrand, S}, title = {Deciphering interactions between the marine dinoflagellate Prorocentrum lima and the fungus Aspergillus pseudoglaucus.}, journal = {Environmental microbiology}, volume = {25}, number = {2}, pages = {250-267}, pmid = {36333915}, issn = {1462-2920}, mesh = {Marine Toxins ; *Dinoflagellida/metabolism ; Aspergillus ; Chromatography, High Pressure Liquid/methods ; *Microalgae/metabolism ; }, abstract = {The comprehension of microbial interactions is one of the key challenges in marine microbial ecology. This study focused on exploring chemical interactions between the toxic dinoflagellate Prorocentrum lima and a filamentous fungal species, Aspergillus pseudoglaucus, which has been isolated from the microalgal culture. Such interspecies interactions are expected to occur even though they were rarely studied. Here, a co-culture system was designed in a dedicated microscale marine-like condition. This system allowed to explore microalgal-fungal physical and metabolic interactions in presence and absence of the bacterial consortium. Microscopic observation showed an unusual physical contact between the fungal mycelium and dinoflagellate cells. To delineate specialized metabolome alterations during microalgal-fungal co-culture metabolomes were monitored by high-performance liquid chromatography coupled to high-resolution mass spectrometry. In-depth multivariate statistical analysis using dedicated approaches highlighted (1) the metabolic alterations associated with microalgal-fungal co-culture, and (2) the impact of associated bacteria in microalgal metabolome response to fungal interaction. Unfortunately, only a very low number of highlighted features were fully characterized. However, an up-regulation of the dinoflagellate toxins okadaic acid and dinophysistoxin 1 was observed during co-culture in supernatants. Such results highlight the importance to consider microalgal-fungal interactions in the study of parameters regulating toxin production.}, }
@article {pmid36333353, year = {2022}, author = {Barret, M and Gandois, L and Thalasso, F and Martinez Cruz, K and Sepulveda Jauregui, A and Lavergne, C and Teisserenc, R and Aguilar, P and Gerardo Nieto, O and Etchebehere, C and Martins Dellagnezze, B and Bovio Winkler, P and Fochesatto, GJ and Tananaev, N and Svenning, MM and Seppey, C and Tveit, A and Chamy, R and Astorga España, MS and Mansilla, A and Van de Putte, A and Sweetlove, M and Murray, AE and Cabrol, L}, title = {A combined microbial and biogeochemical dataset from high-latitude ecosystems with respect to methane cycle.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {674}, pmid = {36333353}, issn = {2052-4463}, mesh = {Carbon Dioxide/analysis ; *Greenhouse Gases ; Methane/analysis ; *Microbiota ; Soil ; Wetlands ; }, abstract = {High latitudes are experiencing intense ecosystem changes with climate warming. The underlying methane (CH4) cycling dynamics remain unresolved, despite its crucial climatic feedback. Atmospheric CH4 emissions are heterogeneous, resulting from local geochemical drivers, global climatic factors, and microbial production/consumption balance. Holistic studies are mandatory to capture CH4 cycling complexity. Here, we report a large set of integrated microbial and biogeochemical data from 387 samples, using a concerted sampling strategy and experimental protocols. The study followed international standards to ensure inter-comparisons of data amongst three high-latitude regions: Alaska, Siberia, and Patagonia. The dataset encompasses different representative environmental features (e.g. lake, wetland, tundra, forest soil) of these high-latitude sites and their respective heterogeneity (e.g. characteristic microtopographic patterns). The data included physicochemical parameters, greenhouse gas concentrations and emissions, organic matter characterization, trace elements and nutrients, isotopes, microbial quantification and composition. This dataset addresses the need for a robust physicochemical framework to conduct and contextualize future research on the interactions between climate change, biogeochemical cycles and microbial communities at high-latitudes.}, }
@article {pmid36332310, year = {2023}, author = {Daille, LK and Aguirre, J and Anguita, J and Galarce, C and Caro-Lara, L and Armijo, F and Vargas, IT and Pizarro, G and Walczak, M and De la Iglesia, R}, title = {When material science meets microbial ecology: Bacterial community selection on stainless steels in natural seawater.}, journal = {Colloids and surfaces. B, Biointerfaces}, volume = {221}, number = {}, pages = {112955}, doi = {10.1016/j.colsurfb.2022.112955}, pmid = {36332310}, issn = {1873-4367}, mesh = {Humans ; *Steel ; *Stainless Steel ; Materials Science ; Corrosion ; Seawater/microbiology ; Biofilms ; Bacteria ; Oxides ; }, abstract = {The passive film depends on the alloy's composition and the exposure conditions. How the surface composition affects the selection of microbial biofilms though, has not been fully elucidated or incorporated into the analysis of corrosive biofilms. The degradation of stainless steel (SS) exposed to natural seawater was studied to understand how the oxide layer composition of SS could affect the selection and variability of the bacterial community. To accomplish this goal, austenitic and superferritic SS grades were exposed to natural seawater on the central coast of Chile. The deterioration of steel and qualitative description of biofilm formation was monitored at different exposure periods. Biofilms were evaluated based on massive sequencing analysis of the bacterial community and subsequent ecological studies. The results revealed that variability of the calculated corrosion rate correlated with the similarity of the bacterial community within samples from each SS and its corrosion inferred capacity. The associated bacterial families showed a higher representation in SSs with a more significant increase in the Fe/Cr ratio over the exposure time. These findings revealed that iron content in the oxide layer represents a key feature of the surface composition for selecting bacterial assemblages in marine environments.}, }
@article {pmid36332298, year = {2022}, author = {Lin, Q and De Vrieze, J and Fang, X and Li, L and Li, X}, title = {Microbial life strategy with high rRNA operon copy number facilitates the energy and nutrient flux in anaerobic digestion.}, journal = {Water research}, volume = {226}, number = {}, pages = {119307}, doi = {10.1016/j.watres.2022.119307}, pmid = {36332298}, issn = {1879-2448}, mesh = {Swine ; Animals ; *rRNA Operon ; RNA, Ribosomal, 16S/genetics ; *Manure ; Anaerobiosis ; DNA Copy Number Variations ; Nutrients ; Bioreactors ; Methane ; }, abstract = {Microbial life strategy, reflected by rRNA operon (rrn) copy number, determines microbial ecological roles. However, the relationship between microbial life strategy and the energy and nutrient flux in anaerobic digestion (AD) remains elusive. This study investigated microbial rrn copy number and expression ratio using amplicon sequencing of 16S rRNA gene and 16S rRNA, and monitored CH4 daily production to approximate the status of energy and nutrient flux in semi-continuous AD. A significantly positive correlation between the mean rrn copy number of microbial communities in digestate and CH4 daily production was detected in the control treatment fed swine manure. The reduced feedstock complexity, by replacing parts of swine manure with fructose or apple waste, weakened the correlation. When feedstock complexity was increased again, the correlation was strengthened again. Similar results were detected in mean rrn expression ratio of microbial communities. The responses of mean rrn copy number and expression ratio of communities to feedstock addition differed between the reduced feedstock complexity and the control treatment, as well as between in digestate and in straw. Our findings reveal a novel relationship between microbial community life strategy and the energy and nutrient flux, and the roles of feedstock characteristics therein in AD.}, }
@article {pmid36331579, year = {2023}, author = {Cortés-Pérez, S and Ferrera-Cerrato, R and Rodríguez-Zaragoza, S and Alarcón, A}, title = {Short-Term Evaluation of the Spatial Distribution of Trophic Groups of Amoebae in the Rhizosphere of Zea mays Inoculated with Rhizophagus intraradices.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {997-1009}, pmid = {36331579}, issn = {1432-184X}, mesh = {*Amoeba ; Seedlings ; Bacteria ; Fungi ; *Mycorrhizae ; Plant Roots/microbiology ; Soil ; Ecosystem ; Zea mays/microbiology ; Rhizosphere ; }, abstract = {Primary production in terrestrial ecosystems is sustained by plants, microbiota, and fungi, which are the major organic matter providers in the root zone, setting in motion the soil food webs. Predators like soil amoebae voraciously feed on bacteria, fungi, and microbial eukaryotes releasing the nutrients sequestered in their biomass. Early food web setting up is crucial for seedling nutrition and its further development after establishment. Mycorrhizal fungi are more than phosphorus providers, and we wonder what their role is in structuring the predators' trophic groups in the root zone. We evaluated the effect of Rhizophagus intraradices inoculated in Zea mays (mycorrhizosphere), on the structuration of amoebae trophic groups along vertical and horizontal (3, 6, and 9 cm) soil distribution when compared to un-inoculated plants, after 20 days in microcosms. Amoebae species richness was highest in non-mycorrhizal seedlings in the root zone at 6- to 9-cm depth, and 3 cm away from plants. More bacterial species are needed when plants are devoid of mycorrhiza, and their influence is constrained 3 cm away from roots. Higher diversity of trophic groups was recorded at mycorrhizal seedlings and at the compartment influenced by the mycelium at 6- to 9-cm depth. The highest bacterivorous diversity, higher number of rare species and protozoa-eating amoebae, and the absence of fungivorous group recorded at the mycorrhizosphere of Z. mays, indicate that the community was very different from the non-mycorrhizal plants. We conclude that the arbuscular mycorrhizal fungus exerts significant changes on the community of trophic groups of amoebae.}, }
@article {pmid36331034, year = {2022}, author = {Schrad, N and Pensky, J and Gorski, G and Beganskas, S and Fisher, AT and Saltikov, C}, title = {Soil characteristics and redox properties of infiltrating water are determinants of microbial communities at managed aquifer recharge sites.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {12}, pages = {}, doi = {10.1093/femsec/fiac130}, pmid = {36331034}, issn = {1574-6941}, mesh = {Soil/chemistry ; *Groundwater/chemistry ; *Microbiota ; Carbon/analysis ; Oxidation-Reduction ; Soil Microbiology ; }, abstract = {In this study, we conducted a meta-analysis of soil microbial communities at three, pilot-scale field sites simulating shallow infiltration for managed aquifer recharge (MAR). We evaluated shifts in microbial communities after infiltration across site location, through different soils, with and without carbon-rich amendments added to test plots. Our meta-analysis aims to enable more effective MAR basin design by identifying potentially important interactions between soil physical-geochemical parameters and microbial communities across several geographically separate MAR basins. We hypothesized infiltration and carbon amendments would lead to common changes in subsurface microbial communities at multiple field sites but instead found distinct differences. Sites with coarser (mainly sandy) soil had large changes in diversity and taxa abundance, while sites with finer soils had fewer significant changes in genera, despite having the greatest increase in nitrogen cycling. Below test plots amended with a carbon-rich permeable reactive barrier, we observed more nitrate removal and a decrease in genera capable of nitrification. Multivariate statistics determined that the soil texture (a proxy for numerous soil characteristics) was the main determinant of whether the microbial community composition changed because of infiltration. These results suggest that microbial communities in sandy soil with carbon-rich amendments are most impacted by infiltration. Soil composition is a critical parameter that links between microbial communities and nutrient cycling during infiltration and could influence the citing and operation of MAR to benefit water quality and supply.}, }
@article {pmid36330300, year = {2022}, author = {Klein, M and Stewart, JD and Porter, SS and Weedon, JT and Kiers, ET}, title = {Evolution of manipulative microbial behaviors in the rhizosphere.}, journal = {Evolutionary applications}, volume = {15}, number = {10}, pages = {1521-1536}, pmid = {36330300}, issn = {1752-4571}, abstract = {The rhizosphere has been called "one of the most complex ecosystems on earth" because it is a hotspot for interactions among millions of microbial cells. Many of these are microbes are also participating in a dynamic interplay with host plant tissues, signaling pathways, and metabolites. Historically, breeders have employed a plant-centric perspective when trying to harness the potential of microbiome-derived benefits to improve productivity and resilience of economically important plants. This is potentially problematic because: (i) the evolution of the microbes themselves is often ignored, and (ii) it assumes that the fitness of interacting plants and microbes is strictly aligned. In contrast, a microbe-centric perspective recognizes that putatively beneficial microbes are still under selection to increase their own fitness, even if there are costs to the host. This can lead to the evolution of sophisticated, potentially subtle, ways for microbes to manipulate the phenotype of their hosts, as well as other microbes in the rhizosphere. We illustrate this idea with a review of cases where rhizosphere microbes have been demonstrated to directly manipulate host root growth, architecture and exudation, host nutrient uptake systems, and host immunity and defense. We also discuss indirect effects, whereby fitness outcomes for the plant are a consequence of ecological interactions between rhizosphere microbes. If these consequences are positive for the plant, they can potentially be misconstrued as traits that have evolved to promote host growth, even if they are a result of selection for unrelated functions. The ubiquity of both direct microbial manipulation of hosts and context-dependent, variable indirect effects leads us to argue that an evolutionary perspective on rhizosphere microbial ecology will become increasingly important as we continue to engineer microbial communities for crop production.}, }
@article {pmid36329848, year = {2022}, author = {Xu, H and Xue, Y and Na, N and Wu, N and Zhao, Y and Sun, L and Qili, M and Wang, T and Zhong, J}, title = {Fermentation quality, bacterial community, and aerobic stability of ensiling Leymus chinensis with lactic acid bacteria or/and water after long-term storage.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {959018}, pmid = {36329848}, issn = {1664-302X}, abstract = {Leymus chinensis is a major forage resource for herbivores on typical steppe and meadow steppes in Northern China. This study aimed to reveal the fermentation quality, bacterial community, and aerobic stability of L. chinensis silage treated with lactic acid bacteria or/and water after long-term storage. Leymus chinensis was harvested at the heading stage and ensiled with lactic acid bacteria [LAB, 2.00 ml/kg fresh weight (FW) of LAB, L], water (100 ml/kg FW of distilled water, W), or a combination of both [2.00 ml/kg fresh weight (FW) of LAB and 100 ml/kg FW of distilled water, LW] in polyethylene laboratory-scale silos (diameter, 20 cm; height, 30 cm) at a density of 650 kg/m[3]. As a control silage (CK), untreated L. chinensis silage was also assessed. The samples were taken at 0 day of opening after 300 days of ensiling (CK_0d, L_0d, W_0d, and LW_0d) and at 10 days of opening (CK_10d, L_10d, W_10d, and LW_10d). The fermentation quality, microbial counts, bacterial community, and aerobic stability of the silage were assessed. The CK_0d contained higher pH and aerobic bacteria count, and lower LA and BC concentrations than L_0d, W_0d, and LW_0d (p < 0.05), and the LAB and yeasts were only detected in CK at 0 day of opening. Lactobacillus had the most abundance among bacterial genera in all silages at 0 day of opening. Just CK had 2°C above the ambient temperature during aerobic exposure (at 224 h). During aerobic exposure, the pH and microbial counts in CK increased (p < 0.05), and Lactobacillus in L and LW had decreasing abundance (p < 0.05). The CK_10d had higher pH and microbial counts, and lower lactic acid and buffering capacity than L_10d, W_10d, and LW_10d (p < 0.05). At 10 days of opening, the coliforms and yeasts were just detected in CK, and Lactobacillus also had the most abundance among bacterial genera in all silages at 10 days of opening. Overall, inoculating LAB and adding water improved the fermentation quality and the aerobic exposure of L. chinensis silage after long-term storage. The activities of coliforms and yeasts during aerobic exposure contributed to the aerobic deterioration of L. chinensis silage without any treating. Lactobacillus dominated the bacterial communities of all silage at 0 and 10 days of opening. During aerobic exposure, the abundance of Lactobacillus reduced in L. chinensis silage treated with LAB or water.}, }
@article {pmid36329282, year = {2023}, author = {Fang, FZ and Chen, SL and Gui, HY and Li, ZJ and Zhang, XF}, title = {Long-Read Sequencing Analysis Revealed the Impact of Forest Conversion on Soil Fungal Diversity in Limu Mountain, Hainan.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {872-886}, pmid = {36329282}, issn = {1432-184X}, mesh = {Animals ; *Ecosystem ; *Soil/chemistry ; Fungi/genetics ; Soil Microbiology ; Forests ; }, abstract = {Soil fungi are essential to soil microorganisms that play an important role in the ecosystem's soil carbon cycle and mineral nutrient transformation. Understanding the structural characteristics and diversity of soil fungal communities helps understand the health of forest ecosystems. The transition from tropical rainforest to artificial forest greatly impacts the composition and diversity of fungal communities. Hainan Limushan tropical rainforest National Park has a large area of artificial forests. Ecologists have conducted in-depth studies on the succession of animals and plants to regenerate tropical rainforests. There are few reports on the diversity of soil fungi and its influencing factors in the succession of tropical rainforests in Limu Mountain. In this study, 44 soil samples from five different stands were collected in the tropical rainforest of Limushan, Hainan. High-throughput sequencing of rDNA in its region was used to analyze fungal communities and study their α and β diversity. Analysis of variance and multiple regression models was used to analyze soil variables and fungal functional groups to determine the effects of interaction between fungi and environmental factors. A total of 273,996 reads and 1290 operational taxonomic units (OTUs) were obtained, belonging to 418 species, 325 genera, 159 families, eight phyla, 30 classes, and 73 orders. The results showed that the composition of soil fungal communities in the five stands was similar, with ascomycetes accounting for 70.5% and basidiomycetes accounting for 14.7%. α and β diversity analysis showed that soil fungi in Limushan tropical rainforest had high abundance and diversity. Multiple regression analysis between soil variables and functional groups showed that organic matter, TN, TP, TK, and AK were excellent predictors for soil fungi. TP was the strongest predictor in all functional groups except soil saprotroph. Organic matter and total nitrogen were the strongest predictors of soil rot. The transformation from tropical rainforest to artificial forest in Limushan did not change the soil fungal community structure, but the richness and diversity of soil fungi changed. The forest transformation did not lead to decreased soil fungal abundance and diversity. Different vegetation types and soil properties affect the diversity of soil fungal communities. We found that Caribbean pine plantations can improve soil fungal diversity, while long-term Eucalyptus spp. plantations may reduce soil fungal diversity.}, }
@article {pmid36329197, year = {2022}, author = {van Spanning, RJM and Guan, Q and Melkonian, C and Gallant, J and Polerecky, L and Flot, JF and Brandt, BW and Braster, M and Iturbe Espinoza, P and Aerts, JW and Meima-Franke, MM and Piersma, SR and Bunduc, CM and Ummels, R and Pain, A and Fleming, EJ and van der Wel, NN and Gherman, VD and Sarbu, SM and Bodelier, PLE and Bitter, W}, title = {Methanotrophy by a Mycobacterium species that dominates a cave microbial ecosystem.}, journal = {Nature microbiology}, volume = {7}, number = {12}, pages = {2089-2100}, pmid = {36329197}, issn = {2058-5276}, mesh = {*Ecosystem ; Proteomics ; Phylogeny ; Methane/metabolism ; *Mycobacterium/genetics ; }, abstract = {So far, only members of the bacterial phyla Proteobacteria and Verrucomicrobia are known to grow methanotrophically under aerobic conditions. Here we report that this metabolic trait is also observed within the Actinobacteria. We enriched and cultivated a methanotrophic Mycobacterium from an extremely acidic biofilm growing on a cave wall at a gaseous chemocline interface between volcanic gases and the Earth's atmosphere. This Mycobacterium, for which we propose the name Candidatus Mycobacterium methanotrophicum, is closely related to well-known obligate pathogens such as M. tuberculosis and M. leprae. Genomic and proteomic analyses revealed that Candidatus M. methanotrophicum expresses a full suite of enzymes required for aerobic growth on methane, including a soluble methane monooxygenase that catalyses the hydroxylation of methane to methanol and enzymes involved in formaldehyde fixation via the ribulose monophosphate pathway. Growth experiments combined with stable isotope probing using [13]C-labelled methane confirmed that Candidatus M. methanotrophicum can grow on methane as a sole carbon and energy source. A broader survey based on 16S metabarcoding suggests that species closely related to Candidatus M. methanotrophicum may be abundant in low-pH, high-methane environments.}, }
@article {pmid36329192, year = {2022}, author = {Slack, E and Diard, M}, title = {Resistance is futile? Mucosal immune mechanisms in the context of microbial ecology and evolution.}, journal = {Mucosal immunology}, volume = {15}, number = {6}, pages = {1188-1198}, pmid = {36329192}, issn = {1935-3456}, mesh = {Animals ; Humans ; Immunoglobulin A, Secretory ; Mucous Membrane ; *Gastrointestinal Microbiome ; Bacteria ; *Vaccines ; Inflammation ; Intestinal Mucosa ; Mammals ; }, abstract = {In the beginning it was simple: we injected a protein antigen and studied the immune responses against the purified protein. This elegant toolbox uncovered thousands of mechanisms via which immune cells are activated. However, when we consider immune responses against real infectious threats, this elegant simplification misses half of the story: the infectious agents are typically evolving orders-of-magnitude faster than we are. Nowhere is this more pronounced than in the mammalian large intestine. A bacterium representing only 0.1% of the human gut microbiota will have a population size of 10[9] clones, each actively replicating. Moreover, the evolutionary pressure from other microbes is at least as profound as direct effects of the immune system. Therefore, to really understand intestinal immune mechanisms, we need to understand both the host response and how rapid microbial evolution alters the apparent outcome of the response. In this review we use the examples of intestinal inflammation and secretory immunoglobulin A (SIgA) to highlight what is already known (Fig. 1). Further, we will explore how these interactions can inform immunotherapy and prophylaxis. This has major implications for how we design effective mucosal vaccines against increasingly drug-resistant bacterial pathogens Fig. 1 THE IMMUNE RESPONSE SHAPES THE FITNESS LANDSCAPE IN THE GASTRO-INTESTINAL TRACT.: The red arrows depict possible evolutionary paths of a novel colonizer along adaptive peaks in the intestinal fitness landscapes that change with the status of the host immune system. The flat surfaces represent the non-null fitness baselines (values x or y) at which a bacterium can establish at minimum carrying capacity. a In the healthy gut, metabolic competence, resistance to aggressions by competitors and predators, swift adaptation to rapid fluctuations as well as surviving acidic pH and the flow of the intestinal content, represent potent selective pressures and as many opportunities for bacteria to increase fitness by phenotypic or genetic variations. b When pathogens trigger acute inflammation, bacteria must adapt to iron starvation, killing by immune cells and antimicrobial peptides, and oxidative stress, while new metabolic opportunities emerge. c When high-affinity SIgA are produced against a bacterium, e.g., after oral vaccination, escape of SIgA by altering or losing surface epitopes becomes crucial for maximum fitness. However, escaping polyvalent SIgA responses after vaccination with "evolutionary trap" vaccines leads to evolutionary trade-offs: A fitness maximum is reached in the vaccinated host gut that represents a major disadvantage for transmission into naïve hosts (fitness diminished below x) (d).}, }
@article {pmid36328255, year = {2023}, author = {Abdullah Al, M and Wang, W and Jin, L and Chen, H and Xue, Y and Jeppesen, E and Majaneva, M and Xu, H and Yang, J}, title = {Planktonic ciliate community driven by environmental variables and cyanobacterial blooms: A 9-year study in two subtropical reservoirs.}, journal = {The Science of the total environment}, volume = {858}, number = {Pt 2}, pages = {159866}, doi = {10.1016/j.scitotenv.2022.159866}, pmid = {36328255}, issn = {1879-1026}, mesh = {*Ciliophora/classification/physiology ; *Cyanobacteria/physiology ; *Ecosystem ; Eutrophication ; Lakes/microbiology/parasitology ; Phylogeny ; Plankton/classification/physiology ; Biodiversity ; Population Dynamics ; }, abstract = {It is well-established that environmental variability and cyanobacterial blooms have major effects on the assembly and functioning of bacterial communities in both marine and freshwater habitats. It remains unclear, however, how the ciliate community responds to such changes over the long-term, particularly in subtropical lake and reservoir ecosystems. We analysed 9-year planktonic ciliate data series from the surface water of two subtropical reservoirs to elucidate the role of cyanobacterial bloom and environmental variabilities on the ciliate temporal dynamics. We identified five distinct periods of cyanobacterial succession in both reservoirs. Using multiple time-scale analyses, we found that the interannual variability of ciliate communities was more strongly related to cyanobacterial blooms than to other environmental variables or to seasonality. Moreover, the percentage of species turnover across cyanobacterial bloom and non-bloom periods increased significantly with time over the 9-year period. Phylogenetic analyses further indicated that 84 %-86 % of ciliate community turnover was governed by stochastic dispersal limitation or undominated processes, suggesting that the ciliate communities in subtropical reservoirs were mainly controlled by neutral processes. However, short-term blooms increased the selection pressure and drove 30 %-53 % of the ciliate community turnover. We found that the ciliate community composition was influenced by environmental conditions with nutrients, cyanobacterial biomass and microzooplankton having direct and/or indirect significant effects on the ciliate taxonomic or functional community dynamics. Our results provide new insights into the long-term temporal dynamics of planktonic ciliate communities under cyanobacterial bloom disturbance.}, }
@article {pmid36327936, year = {2022}, author = {Wong, YY and Lee, CW and Chai, SCY and Lim, JH and Bong, CW and Sim, EUH and Narayanan, K and Hii, YS and Wang, AJ}, title = {Distribution of faecal indicator bacteria in tropical waters of Peninsular Malaysia and their decay rates in tropical seawater.}, journal = {Marine pollution bulletin}, volume = {185}, number = {Pt A}, pages = {114297}, doi = {10.1016/j.marpolbul.2022.114297}, pmid = {36327936}, issn = {1879-3363}, mesh = {*Escherichia coli/physiology ; Malaysia ; *Seawater/microbiology ; Feces/microbiology ; Bacteria ; Water Microbiology ; }, abstract = {We investigated the appropriateness of faecal indicator bacteria in tropical waters. We compared total coliform (undetectable to 7.2 × 10[5] cfu 100 mL[-1]), faecal coliform (undetectable to 6.1 × 10[5] cfu 100 mL[-1]) and enterococci (undetectable to 3.1 × 10[4] cfu 100 mL[-1]) distribution in Peninsular Malaysia. Faecal indicator bacteria was highest in freshwater, and lowest in seawater (q > 4.18, p < 0.01). We also measured the decay rates of Escherichia coli and Enterococcus faecium in microcosms. In seawater, average decay rate for E. coli was 0.084 ± 0.029 h[-1], and higher than E. faecium (0.048 ± 0.024 h[-1]) (t = 2.527, p < 0.05). Grazing accounted for 54 % of both E. coli and E. faecium decay. E. coli decayed in the <0.02 μm seawater fraction (0.023 ± 0.012 h[-1]) but E. faecium sometimes grew. Seawater warming further uncoupled the response from both E. coli and E. faecium as E. faecium grew and E. coli decayed with warming. Our results suggested that the prevalence of faecal indicator bacteria in tropical waters was not due to faecal pollution alone, and this will have serious implications towards the use of these faecal indicator bacteria.}, }
@article {pmid36327839, year = {2023}, author = {Moreira, VA and Cravo-Laureau, C and de Carvalho, ACB and Baldy, A and Bidone, ED and Sabadini-Santos, E and Duran, R}, title = {Microbial indicators along a metallic contamination gradient in tropical coastal sediments.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt B}, pages = {130244}, doi = {10.1016/j.jhazmat.2022.130244}, pmid = {36327839}, issn = {1873-3336}, mesh = {Geologic Sediments ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria/genetics ; Brazil ; Environmental Monitoring ; *Water Pollutants, Chemical/analysis ; *Metals, Heavy/analysis ; }, abstract = {The structure and diversity of microbial community inhabiting coastal sediments reflect the exposition to contaminants. Aiming to assess the changes in the microbiota from Sepetiba Bay (SB, Brazil) sediments, correlations between the 16S rRNA gene data (V4-V5 region), metal contamination factors (CF), and the ecological risk classification provided by the Quality Ratio (QR) index were considered. The results show that microbial diversity differs significantly between the less (SB external sector) and the most (SB internal sector) polluted sectors. Also, differences in the microbial community structure regarding the ecological risk classifications validated the QR index as a reliable tool to report the SB chronic contamination. Microbial indicator genera resistant to metals (Desulfatiglans, SEEP-SRB1, Spirochaeta 2, among others) presented mainly anaerobic metabolisms. These genera are related to the sulfate reducing and methanogenic metabolisms probably participating in the natural attenuation processes but also associated with greenhouse gas emissions. In contrast, microbial indicator genera sensitive to metals (Rubripirellula, Blastopirellula, Aquibacter, among others) presented mainly aerobic metabolisms. It is suggested that future works should investigate the metabolic functions to evaluate the influence of metallic contaminants on microbial community inhabiting SB sediment.}, }
@article {pmid36326874, year = {2023}, author = {Chen, T and Zhao, M and Tang, X and Wang, W and Zhang, M and Tang, J and Wang, W and Wei, W and Ma, B and Zou, Y and Zhang, N and Mi, J and Wang, Y and Liao, X and Wu, Y}, title = {Serious Risk of Tigecycline Resistance in Escherichia coli Isolated from Swine Manure.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {947-958}, pmid = {36326874}, issn = {1432-184X}, mesh = {Humans ; Swine ; Animals ; Tigecycline/pharmacology ; *Escherichia coli/genetics ; *Manure/microbiology ; Doxycycline ; Anti-Bacterial Agents/pharmacology ; Tetracycline ; Microbial Sensitivity Tests ; }, abstract = {The emergence of the plasmid-mediated tigecycline resistance gene tetX family in pig farms has attracted worldwide attention. The use of tetracycline antibiotics in pig farms has a facilitating effect on the prevalence of the tetX family, but the relationship among its presence, expression, and resistance phenotype in resistant bacteria is unknown. In this study, the presence and expression characteristics of tetracycline resistance genes (TRGs) in 89 strains of doxycycline-resistant E. coli (DRE) isolated from pig manure samples from 20 pig farms under low concentrations of doxycycline stress (2 μg/mL) were analyzed. The detection rate of tetO was 96.63%, which is higher than those of other TRGs, such as tetA (94.38%), tetX (76.40%), tetB (73.03%), and tet(X4) (69.66%). At least three TRG types were present in DRE strains, which thus showed extensive resistance to tetracycline antibiotics, and 37% of these strains were resistant to tigecycline. In the presence of a low concentration of doxycycline, tetA played an important role, and the expression and existence ratio of TRGs indicated low expression of TRGs. Furthermore, the doxycycline resistance of DRE was jointly determined by the total absolute abundance of TRGs, and the absolute abundance of tetX and tet(X4) was significantly positively associated with tigecycline resistance in DRE (P < 0.05). Overall, DRE isolated from swine manure is an important reservoir of the tetX family, which suggests that DRE in swine manure has a high risk of tigecycline resistance, poses a potential threat to human health, and should be of public concern.}, }
@article {pmid36326287, year = {2022}, author = {Bandekar, M and Abdolahpur Monikh, F and Kekäläinen, J and Tahvanainen, T and Kortet, R and Zhang, P and Guo, Z and Akkanen, J and Leskinen, JTT and Gomez-Gonzalez, MA and Krishna Darbha, G and Grossart, HP and Valsami-Jones, E and Kukkonen, JVK}, title = {Submicron Plastic Adsorption by Peat, Accumulation in Sphagnum Mosses and Influence on Bacterial Communities in Peatland Ecosystems.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {22}, pages = {15661-15671}, pmid = {36326287}, issn = {1520-5851}, mesh = {*Sphagnopsida/chemistry/microbiology ; Soil/chemistry ; Adsorption ; Plastics ; Bacteria ; *Microbiota ; }, abstract = {The smallest fraction of plastic pollution, submicron plastics (SMPs <1 μm) are expected to be ubiquitous in the environment. No information is available about SMPs in peatlands, which have a key role in sequestering carbon in terrestrial ecosystems. It is unknown how these plastic particles might behave and interact with (micro)organisms in these ecosystems. Here, we show that the chemical composition of polystyrene (PS) and poly(vinyl chloride) (PVC)-SMPs influenced their adsorption to peat. Consequently, this influenced the accumualtion of SMPs by Sphagnum moss and the composition and diversity of the microbial communities in peatland. Natural organic matter (NOM), which adsorbs from the surrounding water to the surface of SMPs, decreased the adsorption of the particles to peat and their accumulation by Sphagnum moss. However, the presence of NOM on SMPs significantly altered the bacterial community structure compared to SMPs without NOM. Our findings show that peatland ecosystems can potentially adsorb plastic particles. This can not only impact mosses themselves but also change the local microbial communities.}, }
@article {pmid36324386, year = {2022}, author = {Li, Y and Xin, X and Song, W and Zhang, X and Chen, S and Wang, Q and Li, A and Li, Y}, title = {VHL syndrome without clear family history: A rare case report and literature review of Chinese patients.}, journal = {Frontiers in neurology}, volume = {13}, number = {}, pages = {951054}, pmid = {36324386}, issn = {1664-2295}, abstract = {OBJECTIVE: To analyze the clinical manifestations and imaging features of a hospitalized patient with intermittent headache who was finally diagnosed with von Hippel-Lindau (VHL) syndrome and to perform whole-exon gene detection to improve the understanding of the diagnosis and treatment strategies of the disease.<br><br>METHODS: A case of suspected VHL syndrome in Shanxi Provincial People's Hospital was analyzed. Proband DNA was also extracted for whole exome sequencing and screened for causative mutation sites, which were validated by Sanger sequencing. The literature about VHL gene mutations in Chinese patients in the past 10 years were also reviewed.<br><br>RESULTS: There is a heterozygous mutation site c.499C > G on the VHL gene on the short arm of chromosome 3 of the patient, which is a missense mutation. The mutation results in the substitution of arginine with glycine at amino acid 167 of the encoded protein, which may be primarily responsible for the disease in the patient with VHL syndrome. However, the mutation did not occur in other family members.<br><br>CONCLUSION: Early recognition and treatment of VHL syndrome can be available with genetic testing technology. Strengthening the understanding of this complex genetic disease and improving the diagnostic rate of VHL syndrome are helpful for the precise treatment of patients with this disease, which may help prolong the survival time of patients to a certain extent and improve their quality of life.}, }
@article {pmid36323973, year = {2023}, author = {Ma, Y and Li, P and Zhong, H and He, M and Wang, B and Mou, X and Wu, L}, title = {The Ecological Differentiation of Particle-Attached and Free-Living Bacterial Communities in a Seasonal Flooding Lake-the Poyang Lake.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {795-809}, pmid = {36323973}, issn = {1432-184X}, support = {31660027//National Natural Science Foundation of China/ ; 31971470//National Natural Science Foundation of China/ ; 31560143//National Natural Science Foundation of China/ ; 2017ZX07301002-05//Collaborative Innovation Center for Water Treatment Technology and Materials/ ; 20202BAB203025//Natural Science Foundation of Jiangxi Province/ ; 20192ACB20021//Natural Science Foundation of Jiangxi Province/ ; }, mesh = {*Lakes/microbiology ; Seasons ; *Bacteria/genetics/metabolism ; Bacteroidetes ; China ; Water/metabolism ; }, abstract = {Particle-attached (PA) and free-living (FL) bacterial communities play essential roles in the biogeochemical cycling of essential nutrients in aquatic environments. However, little is known about the factors that drive the differentiation of bacterial lifestyles, especially in flooding lake systems. Here we assessed the compositional and functional similarities between the FL and PA bacterial fractions in a typical flooding lake-the Poyang Lake (PYL) of China. The results revealed that PA communities had significantly different compositions and functions from FL communities in every hydrological period, and the diversity of both PA and FL communities was affected mainly by the water regime rather than bacterial lifestyles. PA communities were more diverse and enriched with Proteobacteria and Bacteroidetes, while FL communities had more Actinobacteria. There was a higher abundance of photosynthetic and nitrogen-cycling bacterial groups in PA communities, but a higher abundance of members involved in hydrocarbon degradation, aromatic hydrocarbon degradation, and methylotrophy in FL communities. Water properties (e.g., temperature, pH, total phosphorus) significantly regulated the lifestyle variations of PA and FL bacteria in PYL. Collectively, our results have demonstrated a clear ecological differentiation of PA and FL bacterial communities in flooding lakes, suggesting that the connectivity between FL and PA bacterial fractions is water property-related rather than water regime-related.}, }
@article {pmid36322177, year = {2023}, author = {Stupar, M and Savković, &#x17d; and Breka, K and Stamenković, S and Krizmanić, I and Vukojević, J and Grbić, ML}, title = {A Variety of Fungal Species on the Green Frogs' Skin (Pelophylax esculentus complex) in South Banat.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {859-871}, pmid = {36322177}, issn = {1432-184X}, mesh = {Animals ; Rana esculenta ; *Rana clamitans ; Ranidae/microbiology ; Anura ; Skin/microbiology ; }, abstract = {In the last several decades, amphibian populations have been declining worldwide. Many factors have been linked to global amphibian decline, including habitat destruction, pollution, introduced species, global environmental changes, and emerging infectious diseases. Recent studies of amphibian skin infections were mainly focused on the presence of chytridiomycosis, neglecting other members of the frogs' skin communities. The diversity pattern of fungal dwellers on the skin of green frogs (Pelophylax esculentus complex) was investigated. A total of 100 adults were sampled from three localities in South Banat (northern Serbia) over three consecutive years and detected fungal dwellers were identified using light microscopy and ITS and BenA gene sequencing. Structures belonging to fungi and fungus-like organisms including a variety of spores and different mycelia types were documented in the biofilm formed on amphibian skin, and are classified into 10 groups. In total, 42 fungal isolates were identified to species, section, or genus level. The difference in mycobiota composition between sampling points (localities and green frog taxa) was documented. The highest number of fungal structures and isolates was recorded on the hybrid taxon P. esculentus and locality Stevanove ravnice. Parental species showed a markedly lower diversity than the hybrid taxon and were more similar in diversity patterns and were placed in the same homogenous group. The locality Stevanove ravnice exhibited more pronounced differences in diversity pattern than the other two localities and was placed in a distinct and separate homogenous group. Among the fungal isolates, the highest isolation frequency was documented for Alternaria alternata, Aspergillus sp. sect. Nigri, Epicoccum nigrum, Fusarium proliferatum, and Trichoderma atroviride. Among the documented species, dematiaceous fungi, causative agents of chromomycosis in amphibians, were also recorded in this research with high isolation frequency. Also, some rare fungal species such as Quambalaria cyanescens and Pseudoteniolina globosa are documented for the first time in this research as microbial inhabitants of amphibian skin.}, }
@article {pmid36321898, year = {2022}, author = {Spencer-Williams, I and Balangoda, A and Dabundo, R and Elliott, E and Haig, SJ}, title = {Exploring the Impacts of Full-Scale Distribution System Orthophosphate Corrosion Control Implementation on the Microbial Ecology of Hydrologically Connected Urban Streams.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0215822}, pmid = {36321898}, issn = {2165-0497}, mesh = {*Rivers/microbiology ; Lead/chemistry ; Phosphates ; *Drinking Water ; Corrosion ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Many cities across the nation are plagued by lead contamination in drinking water. As such, many drinking water utilities have undertaken lead service line (LSL) replacement to prevent further lead contamination. However, given the urgency of lead mitigation, and the socioeconomic challenges associated with LSL replacement, cities have used phosphate-based corrosion inhibitors (i.e., orthophosphate) alongside LSL replacement. While necessary to ensure public health protection from lead contamination, the addition of orthophosphate into an aging and leaking drinking water system may increase the concentration of phosphate leaching into urban streams characterized by century-old failing water infrastructure. Such increases in phosphate availability may cascade into nutrient and microbial community composition shifts. The purpose of this study was to determine how this occurs and to understand whether full-scale distribution system orthophosphate addition impacts the microbial ecology of urban streams. Through monthly collection of water samples from five urban streams before and after orthophosphate addition, significant changes in microbial community composition (16S rRNA amplicon sequencing) and in the relative abundance of typical freshwater taxa were observed. In addition, key microbial phosphorus and nitrogen metabolism genes (e.g., two component regulatory systems) were predicted to change via BugBase. No significant differences in the absolute abundances of total bacteria, Cyanobacteria, and "Candidatus Accumulibacter" were observed. Overall, the findings from this study provide further evidence that urban streams are compromised by unintentional hydrologic connections with drinking water infrastructure. Moreover, our results suggest that infiltration of phosphate-based corrosion inhibitors can impact urban streams and have important, as-yet-overlooked impacts on urban stream microbial communities. IMPORTANCE Elevated lead levels in drinking water supplies are a public health risk. As such, it is imperative for cities to urgently address lead contamination from aging drinking water supplies by way of lead service line replacements and corrosion control methods. However, when applying corrosion control methods, it is also important to consider the chemical and microbiological effects that can occur in natural settings, given that our water infrastructure is aging and more prone to leaks and breaks. Here, we examine the impacts on the microbial ecology of five urban stream systems before and after full-scale distribution system orthophosphate addition. Overall, the results suggest that infiltration of corrosion inhibitors may impact microbial communities; however, future work should be done to ascertain the true impact to protect both public and environmental health.}, }
@article {pmid36320358, year = {2022}, author = {Simões, ACP and Fernandes, RP and Barreto, MS and Marques da Costa, GB and de Godoy, MG and Freire, DMG and Pereira, N}, title = {Growth of Methylobacterium organophilum in Methanol for the Simultaneous Production of Single-Cell Protein and Metabolites of Interest.}, journal = {Food technology and biotechnology}, volume = {60}, number = {3}, pages = {338-349}, pmid = {36320358}, issn = {1330-9862}, abstract = {RESEARCH BACKGROUND: This study aims to monitor the growth of the methylotrophic bacteria Methylobacterium organophilum in a culture medium with methanol as a carbon source and to verify the production of unicellular proteins and other biomolecules, such as carotenoids, exopolysaccharides and polyhydroxyalkanoates, making them more attractive as animal feed.<br><br>EXPERIMENTAL APPROACH: Bacterial growth was studied in shake flasks using different carbon/nitrogen (C:N) ratios to determine their best ratio for achieving the highest volumetric productivity of cells and substrate consumption rate. This optimal parameter was further used in a fed-batch operating bioreactor system to define the kinetic profile of cell growth. Methanol consumption was measured by HPLC analysis and the extracted pigments were analyzed by liquid chromatography/mass spectrometry. Chemical composition and rheological properties of the produced exopolysaccharides were also determined.<br><br>RESULTS AND CONCLUSIONS: The best experimental parameters were verified using an initial methanol concentration of 7 g/L in the culture medium. The same initial substrate concentration was used in the fed-batch operation and after 60 h of cultivation 5 g/L of biomass were obtained. The accumulation of carotenoids associated with cell growth was monitored, reaching a concentration of 1.6 mg/L at the end of the process. These pigments were then analyzed and characterized as a set of xanthophylls (oxidized carotenoids). In addition, two other product types were identified during the fed-batch operation: exopolysaccharides, which reached a concentration of 8.9 g/L at the end of the cultivation, and an intracellular granular structure that was detected by transmission electron microscopy (TEM), suggesting the accumulation of polyhydroxyalkanoate (PHA), most likely polyhydroxybutyrate.<br><br>Methylobacterium organophilum demonstrated a unique ability to produce compounds of commercial interest. The distinct metabolic diversity of this bacterium makes room for its use in biorefineries.}, }
@article {pmid36319743, year = {2023}, author = {Ayilara, MS and Adeleke, BS and Babalola, OO}, title = {Bioprospecting and Challenges of Plant Microbiome Research for Sustainable Agriculture, a Review on Soybean Endophytic Bacteria.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {1113-1135}, pmid = {36319743}, issn = {1432-184X}, support = {123634//National Research Foundation/ ; 132595//National Research Foundation/ ; }, mesh = {*Glycine max/microbiology ; Bioprospecting ; Bacteria/genetics/metabolism ; Agriculture ; *Microbiota ; Soil ; Crops, Agricultural ; Soil Microbiology ; }, abstract = {This review evaluates oilseed crop soybean endophytic bacteria, their prospects, and challenges for sustainable agriculture. Soybean is one of the most important oilseed crops with about 20-25% protein content and 20% edible oil production. The ability of soybean root-associated microbes to restore soil nutrients enhances crop yield. Naturally, the soybean root endosphere harbors root nodule bacteria, and endophytic bacteria, which help increase the nitrogen pool and reclamation of another nutrient loss in the soil for plant nutrition. Endophytic bacteria can sustain plant growth and health by exhibiting antibiosis against phytopathogens, production of enzymes, phytohormone biosynthesis, organic acids, and secondary metabolite secretions. Considerable effort in the agricultural industry is focused on multifunctional concepts and bioprospecting on the use of bioinput from endophytic microbes to ensure a stable ecosystem. Bioprospecting in the case of this review is a systemic overview of the biorational approach to harness beneficial plant-associated microbes to ensure food security in the future. Progress in this endeavor is limited by available techniques. The use of molecular techniques in unraveling the functions of soybean endophytic bacteria can explore their use in integrated organic farming. Our review brings to light the endophytic microbial dynamics of soybeans and current status of plant microbiome research for sustainable agriculture.}, }
@article {pmid36318280, year = {2023}, author = {Hill, AJ and Grisnik, M and Walker, DM}, title = {Bacterial Skin Assemblages of Sympatric Salamanders Are Primarily Shaped by Host Genus.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1364-1373}, pmid = {36318280}, issn = {1432-184X}, mesh = {Animals ; *Caudata/microbiology ; RNA, Ribosomal, 16S/genetics ; *Skin/microbiology ; Animals, Wild ; Bacteria/genetics ; }, abstract = {Bacterial assemblages on the skins of amphibians are known to influence pathogen resistance and other important physiological functions in the host. Host-specific factors and the environment play significant roles in structuring skin assemblages. This study used high-throughput 16S rRNA sequencing and multivariate analyses to examine differences in skin-bacterial assemblages from 246 salamanders belonging to three genera in the lungless family Plethodontidae along multiple spatial gradients. Composition and α- and β-diversity of bacterial assemblages were defined, indicator species were identified for each host group, and the relative influences of host- versus environment-specific ecological factors were evaluated. At the broadest spatial scale, host genus, host species, and sampling site were predictive of skin assemblage structure, but host genus and species were more influential after controlling for the marginal effects of site, as well as nestedness of site. Furthermore, assemblage similarity within each host genus did not change with increasing geographic distance. At the smallest spatial scale, site-specific climate analyses revealed different relationships to climatic variables for each of the three genera, and these relationships were determined by host ecomode. Variation in bacterial assemblages of terrestrial hosts correlated with landscape-level climatic variability, and this pattern decayed with increasing water dependence of the host. Results from this study highlight host-specific considerations for researchers studying wildlife diseases in co-occurring, yet ecologically divergent, species.}, }
@article {pmid36317499, year = {2022}, author = {Bachimanchi, H and Midtvedt, B and Midtvedt, D and Selander, E and Volpe, G}, title = {Microplankton life histories revealed by holographic microscopy and deep learning.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36317499}, issn = {2050-084X}, support = {677511/ERC_/European Research Council/International ; }, mesh = {Animals ; *Phytoplankton ; *Deep Learning ; Microscopy ; Zooplankton ; Oceans and Seas ; Seawater ; }, abstract = {The marine microbial food web plays a central role in the global carbon cycle. However, our mechanistic understanding of the ocean is biased toward its larger constituents, while rates and biomass fluxes in the microbial food web are mainly inferred from indirect measurements and ensemble averages. Yet, resolution at the level of the individual microplankton is required to advance our understanding of the microbial food web. Here, we demonstrate that, by combining holographic microscopy with deep learning, we can follow microplanktons throughout their lifespan, continuously measuring their three-dimensional position and dry mass. The deep-learning algorithms circumvent the computationally intensive processing of holographic data and allow rapid measurements over extended time periods. This permits us to reliably estimate growth rates, both in terms of dry mass increase and cell divisions, as well as to measure trophic interactions between species such as predation events. The individual resolution provides information about selectivity, individual feeding rates, and handling times for individual microplanktons. The method is particularly useful to detail the rates and routes of organic matter transfer in micro-zooplankton, the most important and least known group of primary consumers in the oceans. Studying individual interactions in idealized small systems provides insights that help us understand microbial food webs and ultimately larger-scale processes. We exemplify this by detailed descriptions of micro-zooplankton feeding events, cell divisions, and long-term monitoring of single cells from division to division.}, }
@article {pmid36316374, year = {2022}, author = {Noiset, P and Cabirol, N and Rojas-Oropeza, M and Warrit, N and Nkoba, K and Vereecken, NJ}, title = {Honey compositional convergence and the parallel domestication of social bees.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {18280}, pmid = {36316374}, issn = {2045-2322}, support = {T.0255.20//Fonds De La Recherche Scientifique - FNRS/ ; }, mesh = {Bees ; Animals ; *Honey/analysis ; Domestication ; Magnetic Resonance Spectroscopy ; Thailand ; Mexico ; }, abstract = {Honey collection evolved from simple honey hunting to the parallel and independent domestication of different species of bees in various parts of the world. In this study, we investigate the extent to which the composition of Apis and stingless bee honeys has been a driver in the selection of different bee species for domestication in Mesoamerica (Mexico) and Asia (Thailand) using a sampling design that combines peak honey profiling by H1 NMR spectroscopy with the collection of honeys from domesticated and undomesticated bee species. Our results show that, independently of the region of the world considered, domesticated stingless bees produce honey whose compositional profiles differ from those of the non-domesticated species and exhibit more similarities towards honeys produced by the domesticated Apis species. Our results provide evidence for the first time that the search for natural sweeteners in the environment by our ancestors led to the parallel and independent domestication of social bees producing honeys with similar compositional profiles.}, }
@article {pmid36314760, year = {2022}, author = {Florent, P and Cauchie, HM and Herold, M and Ogorzaly, L}, title = {Bacteriophages pass through candle-shaped porous ceramic filters: Application for the collection of viruses in soil water.}, journal = {MicrobiologyOpen}, volume = {11}, number = {5}, pages = {e1314}, pmid = {36314760}, issn = {2045-8827}, mesh = {*Bacteriophages/genetics ; Soil ; Porosity ; Water ; *Viruses ; Ceramics ; }, abstract = {Despite the ubiquity of viruses in soils, their diversity in soil water has not been explored, mainly due to the difficulty of collecting them. In hydrology, soil water is usually collected using porous candles. This study proposes using these porous candles as a new tool for sampling viruses in soil water to analyze their passage through the ceramic part of the candles. The recovery of the viruses was determined after filtration under laboratory conditions using three model bacteriophages (MS2, ΦX174, and Φ6) and Escherichia coli, at neutral and acidic pH. Then, a field experiment was carried out where soil water filtration and viral identification by metagenomic shotgun were performed. At neutral pH, all bacteriophages tested successfully passed through the porous candles during the filtration process, with reductions of 0.02 log, 0.16 log, and 0.55 log for MS2 ΦX174 and Φ6, respectively. At pH 4.4, the passage of MS2 was not affected while ΦX174 underwent a slight reduction in recovery, probably caused by adsorption onto the filter material. Regarding the application of the porous candles in the field, the results obtained allowed the successful recovery of viruses, exposing porous candles as a new method suitable for the collection of viruses from soil water in the context of the study of viral communities.}, }
@article {pmid36314757, year = {2022}, author = {Brauer, A and Bengtsson, MM}, title = {DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes.}, journal = {MicrobiologyOpen}, volume = {11}, number = {5}, pages = {e1323}, pmid = {36314757}, issn = {2045-8827}, mesh = {*Eukaryota/genetics ; Archaea/genetics ; Bacteria/genetics ; *Microbiota/genetics ; DNA/genetics ; }, abstract = {DNA extraction and preservation bias is a recurring topic in DNA sequencing-based microbial ecology. The different methodologies can lead to distinct outcomes, which has been demonstrated especially in studies investigating prokaryotic community composition. Eukaryotic microbes are ubiquitous, diverse, and increasingly a subject of investigation in addition to bacteria and archaea. However, little is known about how the choice of DNA preservation and extraction methodology impacts perceived eukaryotic community composition. In this study, we compared the effect of two DNA preservation methods and six DNA extraction methods on the community profiles of both eukaryotes and prokaryotes in phototrophic biofilms on seagrass (Zostera marina) leaves from the Baltic Sea. We found that, whereas both DNA preservation and extraction method caused significant bias in perceived community composition for both eukaryotes and prokaryotes, extraction bias was more pronounced for eukaryotes than for prokaryotes. In particular, soft-bodied and hard-shelled eukaryotes like nematodes and diatoms, respectively, were differentially abundant depending on the extraction method. We conclude that careful consideration of DNA preservation and extraction methodology is crucial to achieving representative community profiles of eukaryotes in marine biofilms and likely all other habitats containing diverse eukaryotic microbial communities.}, }
@article {pmid36314752, year = {2022}, author = {Orsini, M and Ianni, A and Zinzula, L}, title = {Brucella ceti and Brucella pinnipedialis genome characterization unveils genetic features that highlight their zoonotic potential.}, journal = {MicrobiologyOpen}, volume = {11}, number = {5}, pages = {e1329}, pmid = {36314752}, issn = {2045-8827}, mesh = {Animals ; Humans ; *Brucella/genetics ; *Brucellosis/microbiology ; *Caniformia/microbiology ; Cetacea/microbiology ; }, abstract = {The Gram-negative bacteria Brucella ceti and Brucella pinnipedialis circulate in marine environments primarily infecting marine mammals, where they cause an often-fatal disease named brucellosis. The increase of brucellosis among several species of cetaceans and pinnipeds, together with the report of sporadic human infections, raises concerns about the zoonotic potential of these pathogens on a large scale and may pose a threat to coastal communities worldwide. Therefore, the characterization of the B. ceti and B. pinnipedialis genetic features is a priority to better understand the pathological factors that may impact global health. Moreover, an in-depth functional analysis of the B. ceti and B. pinnipedialis genome in the context of virulence and pathogenesis was not undertaken so far. Within this picture, here we present the comparative whole-genome characterization of all B. ceti and B. pinnipedialis genomes available in public resources, uncovering a collection of genetic tools possessed by these aquatic bacterial species compared to their zoonotic terrestrial relatives. We show that B. ceti and B. pinnipedialis genomes display a wide host-range infection capability and a polyphyletic phylogeny within the genus, showing a genomic structure that fits the canonical definition of closeness. Functional genome annotation led to identifying genes related to several pathways involved in mechanisms of infection, others conferring pan-susceptibility to antimicrobials and a set of virulence genes that highlight the similarity of B. ceti and B. pinnipedialis genotypes to those of Brucella spp. displaying human-infecting phenotypes.}, }
@article {pmid36312987, year = {2022}, author = {Ma, K and Tu, Q}, title = {Random sampling associated with microbial profiling leads to overestimated stochasticity inference in community assembly.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1011269}, pmid = {36312987}, issn = {1664-302X}, abstract = {Revealing the mechanisms governing the complex community assembly over space and time is a central issue in ecology. Null models have been developed to quantitatively disentangle the relative importance of deterministic vs. stochastic processes in structuring the compositional variations of biological communities. Similar approaches have been recently extended to the field of microbial ecology. However, the profiling of highly diverse biological communities (e.g., microbial communities) is severely influenced by random sampling issues, leading to undersampled community profiles and overestimated β-diversity, which may further affect stochasticity inference in community assembly. By implementing simulated datasets, this study demonstrate that microbial stochasticity inference is also affected due to random sampling issues associated with microbial profiling. The effects on microbial stochasticity inference for the whole community and the abundant subcommunities were different using different randomization methods in generating null communities. The stochasticity of rare subcommunities, however, was persistently overestimated irrespective of which randomization method was used. Comparatively, the stochastic ratio approach was more sensitive to random sampling issues, whereas the Raup-Crick metric was more affected by randomization methods. As more studies begin to focus on the mechanisms governing abundant and rare subcommunities, we urge cautions be taken for microbial stochasticity inference based on β-diversity, especially for rare subcommunities. Randomization methods to generate null communities shall also be carefully selected. When necessary, the cutoff used for judging the relative importance of deterministic vs. stochastic processes shall be redefined.}, }
@article {pmid36312976, year = {2022}, author = {Quagliariello, A and Ramiro, RS and Couce, A and Martino, ME}, title = {Editorial: Integrating multi-scale approaches for predicting microbiome ecology and evolution.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1045045}, pmid = {36312976}, issn = {1664-302X}, }
@article {pmid36309426, year = {2023}, author = {Jääskeläinen, E and Säde, E and Rönkkö, T and Hultman, J and Johansson, P and Riekkola, ML and Björkroth, J}, title = {Marination increased tyramine levels in rainbow trout fillet strips packaged under modified atmosphere.}, journal = {Food microbiology}, volume = {109}, number = {}, pages = {104099}, doi = {10.1016/j.fm.2022.104099}, pmid = {36309426}, issn = {1095-9998}, mesh = {Animals ; *Oncorhynchus mykiss ; Tyramine ; Meat/microbiology ; Atmosphere ; }, abstract = {Marinades are increasingly used to manufacture raw fish products. In corresponding meats, marinating is known to have a major effect on the composition of the microbiome, but the effect of marinating on fish is not known as well. This knowledge gap prompted our study of the microbial ecology and amine formation in marinated and unmarinated modified atmosphere commercially packaged rainbow trout fillet strips. According to our findings, marination increased the maximum concentrations (7-8 log CFU/g) of psychrotrophic bacteria by one logarithmic unit and led to 5 times higher average tyramine concentrations than the corresponding unmarinated product. Instead, trimethylamine concentrations were 30 times higher in the unmarinated product than those in the marinated one. According to the 16 S rRNA sequence analyses, lactic acid bacteria (LAB) predominated in the marinated strips one day after the use-by date, whereas in the unmarinated strips Fusobacteriaceae and LAB were the dominating taxa. Based on the culture-dependent analysis, Latilactobacillus fuchuensis was the prevailing LAB in both products. Since the subset of L. fuchuensis strains tested was able to produce tyramine in vitro, we hypothesise that the use of the acidic marinade activated the production of tyrosine-decarboxylating enzymes in L. fuchuensis and led to the increased tyramine concentrations.}, }
@article {pmid36307735, year = {2023}, author = {Hladnik, M and Unković, N and Janakiev, T and Grbić, ML and Arbeiter, AB and Stanković, S and Janaćković, P and Gavrilović, M and Rančić, D and Bandelj, D and Dimkić, I}, title = {An Insight into an Olive Scab on the "Istrska Belica" Variety: Host-Pathogen Interactions and Phyllosphere Mycobiome.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1343-1363}, pmid = {36307735}, issn = {1432-184X}, support = {451-03-68/2022-14/200178//Ministarstvo Prosvete, Nauke i Tehnolo&#x161;kog Razvoja/ ; P1-0386//Javna Agencija za Raziskovalno Dejavnost RS/ ; SLO-SRB-2018/19-OAN//Bilateral scientific - research cooperation between SRB and RS/ ; }, mesh = {*Olea/microbiology ; *Mycobiome ; *Ascomycota ; *Basidiomycota ; Host-Pathogen Interactions ; }, abstract = {The olive tree is one of the most important agricultural plants, affected by several pests and diseases that cause a severe decline in health status leading to crop losses. Olive leaf spot disease caused by the fungus Venturia oleaginea can result in complete tree defoliation and consequently lower yield. The aim of the study was to obtain new knowledge related to plant-pathogen interaction, reveal mechanisms of plant defense against the pathogen, and characterize fungal phyllosphere communities on infected and symptomless leaves that could contribute to the development of new plant breeding strategies and identification of novel biocontrol agents. The highly susceptible olive variety "Istrska Belica"' was selected for a detailed evaluation. Microscopy analyses led to the observation of raphides in the mesophyll and parenchyma cells of infected leaves and gave new insight into the complex V. oleaginea pathogenesis. Culturable and total phyllosphere mycobiota, obtained via metabarcoding approach, highlighted Didymella, Aureobasidium, Cladosporium, and Alternaria species as overlapping between infected and symptomless leaves. Only Venturia and Erythrobasidium in infected and Cladosporium in symptomless samples with higher abundance showed statistically significant differences. Based on the ecological role of identified taxa, it can be suggested that Cladosporium species might have potential antagonistic effects on V. oleaginea.}, }
@article {pmid36306091, year = {2023}, author = {Jameson, E and Taubert, M and Angel, R and Coyotzi, S and Chen, Y and Eyice, &#xd6; and Schäfer, H and Murrell, JC and Neufeld, JD and Dumont, MG}, title = {DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {261-282}, pmid = {36306091}, issn = {1940-6029}, mesh = {RNA, Ribosomal, 16S/genetics/chemistry ; Carbon Isotopes/chemistry ; Isotope Labeling/methods ; *DNA/chemistry ; *Proteins/chemistry ; Biomarkers ; RNA, Messenger ; }, abstract = {Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of [13]C, [18]O, or [15]N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labelled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labelled populations by targeted gene analysis. Such approaches usually involved fingerprint-based analyses or sequencing clone libraries containing 16S rRNA genes or functional marker gene amplicons. Although molecular fingerprinting remains a valuable approach for rapid confirmation of isotope labelling, recent advances in sequencing technology mean that it is possible to obtain affordable and comprehensive amplicon profiles, or even metagenomes and metatranscriptomes from SIP experiments. Not only can the abundance of microbial groups be inferred from metagenomes, but researchers can bin, assemble, and explore individual genomes to build hypotheses about the metabolic capabilities of labelled microorganisms. Analysis of labelled mRNA is a more recent advance that can provide independent metatranscriptome-based analysis of active microorganisms. The power of metatranscriptomics is that mRNA abundance often correlates closely with the corresponding activity of encoded enzymes, thus providing insight into microbial metabolism at the time of sampling. Together, these advances have improved the sensitivity of SIP methods and allowed using labelled substrates at environmentally relevant concentrations. Particularly as methods improve and costs continue to drop, we expect that the integration of SIP with multiple omics-based methods will become prevalent components of microbial ecology studies, leading to further breakthroughs in our understanding of novel microbial populations and elucidation of the metabolic function of complex microbial communities. In this chapter, we provide protocols for obtaining labelled DNA, RNA, and proteins that can be used for downstream omics-based analyses.}, }
@article {pmid36305941, year = {2023}, author = {Costas-Selas, C and Martínez-García, S and Logares, R and Hernández-Ruiz, M and Teira, E}, title = {Role of Bacterial Community Composition as a Driver of the Small-Sized Phytoplankton Community Structure in a Productive Coastal System.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {777-794}, pmid = {36305941}, issn = {1432-184X}, support = {EM2013/023//Xunta de Galicia/ ; ED481A-2019/290//Xunta de Galicia/ ; ED431I 2020/03//Xunta de Galicia/ ; CTM2017-83362-R//Ministerio de Econom&#xed;a y Competitividad/ ; PID2019-110011RB-C33)//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {Humans ; *Phytoplankton ; *Plankton ; Bacteria ; Seasons ; Eukaryota ; }, abstract = {We present here the first detailed description of the seasonal patterns in bacterial community composition (BCC) in shelf waters off the Ría de Vigo (Spain), based on monthly samplings during 2 years. Moreover, we studied the relationship between bacterial and small-sized eukaryotic community composition to identify potential biotic interactions among components of these two communities. Bacterial operational taxonomic unit (OTU) richness and diversity systematically peaked in autumn-winter, likely related to low resource availability during this period. BCC showed seasonal and vertical patterns, with Rhodobacteraceae and Flavobacteriaceae families dominating in surface waters, and SAR11 clade dominating at the base of the photic zone (30 m depth). BCC variability was significantly explained by environmental variables (e.g., temperature of water, solar radiation, or dissolved organic matter). Interestingly, a strong and significant correlation was found between BCC and small-sized eukaryotic community composition (ECC), which suggests that biotic interactions may play a major role as structuring factors of the microbial plankton in this productive area. In addition, co-occurrence network analyses revealed strong and significant, mostly positive, associations between bacteria and small-sized phytoplankton. Positive associations likely result from mutualistic relationships (e.g., between Dinophyceae and Rhodobacteraceae), while some negative correlations suggest antagonistic interactions (e.g., between Pseudo-nitzchia sp. and SAR11). These results support the key role of biotic interactions as structuring factors of the small-sized eukaryotic community, mostly driven by positive associations between small-sized phytoplankton and bacteria.}, }
@article {pmid36304282, year = {2022}, author = {Saenz, C and Nigro, E and Gunalan, V and Arumugam, M}, title = {MIntO: A Modular and Scalable Pipeline For Microbiome Metagenomic and Metatranscriptomic Data Integration.}, journal = {Frontiers in bioinformatics}, volume = {2}, number = {}, pages = {846922}, pmid = {36304282}, issn = {2673-7647}, abstract = {Omics technologies have revolutionized microbiome research allowing the characterization of complex microbial communities in different biomes without requiring their cultivation. As a consequence, there has been a great increase in the generation of omics data from metagenomes and metatranscriptomes. However, pre-processing and analysis of these data have been limited by the availability of computational resources, bioinformatics expertise and standardized computational workflows to obtain consistent results that are comparable across different studies. Here, we introduce MIntO (Microbiome Integrated meta-Omics), a highly versatile pipeline that integrates metagenomic and metatranscriptomic data in a scalable way. The distinctive feature of this pipeline is the computation of gene expression profile through integrating metagenomic and metatranscriptomic data taking into account the community turnover and gene expression variations to disentangle the mechanisms that shape the metatranscriptome across time and between conditions. The modular design of MIntO enables users to run the pipeline using three available modes based on the input data and the experimental design, including de novo assembly leading to metagenome-assembled genomes. The integrated pipeline will be relevant to provide unique biochemical insights into microbial ecology by linking functions to retrieved genomes and to examine gene expression variation. Functional characterization of community members will be crucial to increase our knowledge of the microbiome's contribution to human health and environment. MIntO v1.0.1 is available at https://github.com/arumugamlab/MIntO.}, }
@article {pmid36304272, year = {2022}, author = {Karaoz, U and Brodie, EL}, title = {microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes.}, journal = {Frontiers in bioinformatics}, volume = {2}, number = {}, pages = {918853}, pmid = {36304272}, issn = {2673-7647}, abstract = {Remote sensing approaches have revolutionized the study of macroorganisms, allowing theories of population and community ecology to be tested across increasingly larger scales without much compromise in resolution of biological complexity. In microbial ecology, our remote window into the ecology of microorganisms is through the lens of genome sequencing. For microbial organisms, recent evidence from genomes recovered from metagenomic samples corroborate a highly complex view of their metabolic diversity and other associated traits which map into high physiological complexity. Regardless, during the first decades of this omics era, microbial ecological research has primarily focused on taxa and functional genes as ecological units, favoring breadth of coverage over resolution of biological complexity manifested as physiological diversity. Recently, the rate at which provisional draft genomes are generated has increased substantially, giving new insights into ecological processes and interactions. From a genotype perspective, the wide availability of genome-centric data requires new data synthesis approaches that place organismal genomes center stage in the study of environmental roles and functional performance. Extraction of ecologically relevant traits from microbial genomes will be essential to the future of microbial ecological research. Here, we present microTrait, a computational pipeline that infers and distills ecologically relevant traits from microbial genome sequences. microTrait maps a genome sequence into a trait space, including discrete and continuous traits, as well as simple and composite. Traits are inferred from genes and pathways representing energetic, resource acquisition, and stress tolerance mechanisms, while genome-wide signatures are used to infer composite, or life history, traits of microorganisms. This approach is extensible to any microbial habitat, although we provide initial examples of this approach with reference to soil microbiomes.}, }
@article {pmid36303775, year = {2021}, author = {Hu, B and Canon, S and Eloe-Fadrosh, EA and Anubhav,  and Babinski, M and Corilo, Y and Davenport, K and Duncan, WD and Fagnan, K and Flynn, M and Foster, B and Hays, D and Huntemann, M and Jackson, EKP and Kelliher, J and Li, PE and Lo, CC and Mans, D and McCue, LA and Mouncey, N and Mungall, CJ and Piehowski, PD and Purvine, SO and Smith, M and Varghese, NJ and Winston, D and Xu, Y and Chain, PSG}, title = {Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale.}, journal = {Frontiers in bioinformatics}, volume = {1}, number = {}, pages = {826370}, pmid = {36303775}, issn = {2673-7647}, abstract = {The nascent field of microbiome science is transitioning from a descriptive approach of cataloging taxa and functions present in an environment to applying multi-omics methods to investigate microbiome dynamics and function. A large number of new tools and algorithms have been designed and used for very specific purposes on samples collected by individual investigators or groups. While these developments have been quite instructive, the ability to compare microbiome data generated by many groups of researchers is impeded by the lack of standardized application of bioinformatics methods. Additionally, there are few examples of broad bioinformatics workflows that can process metagenome, metatranscriptome, metaproteome and metabolomic data at scale, and no central hub that allows processing, or provides varied omics data that are findable, accessible, interoperable and reusable (FAIR). Here, we review some of the challenges that exist in analyzing omics data within the microbiome research sphere, and provide context on how the National Microbiome Data Collaborative has adopted a standardized and open access approach to address such challenges.}, }
@article {pmid36303759, year = {2021}, author = {Giulia, A and Anna, S and Antonia, B and Dario, P and Maurizio, C}, title = {Extending Association Rule Mining to Microbiome Pattern Analysis: Tools and Guidelines to Support Real Applications.}, journal = {Frontiers in bioinformatics}, volume = {1}, number = {}, pages = {794547}, pmid = {36303759}, issn = {2673-7647}, abstract = {Boosted by the exponential growth of microbiome-based studies, analyzing microbiome patterns is now a hot-topic, finding different fields of application. In particular, the use of machine learning techniques is increasing in microbiome studies, providing deep insights into microbial community composition. In this context, in order to investigate microbial patterns from 16S rRNA metabarcoding data, we explored the effectiveness of Association Rule Mining (ARM) technique, a supervised-machine learning procedure, to extract patterns (in this work, intended as groups of species or taxa) from microbiome data. ARM can generate huge amounts of data, making spurious information removal and visualizing results challenging. Our work sheds light on the strengths and weaknesses of pattern mining strategy into the study of microbial patterns, in particular from 16S rRNA microbiome datasets, applying ARM on real case studies and providing guidelines for future usage. Our results highlighted issues related to the type of input and the use of metadata in microbial pattern extraction, identifying the key steps that must be considered to apply ARM consciously on 16S rRNA microbiome data. To promote the use of ARM and the visualization of microbiome patterns, specifically, we developed microFIM (microbial Frequent Itemset Mining), a versatile Python tool that facilitates the use of ARM integrating common microbiome outputs, such as taxa tables. microFIM implements interest measures to remove spurious information and merges the results of ARM analysis with the common microbiome outputs, providing similar microbiome strategies that help scientists to integrate ARM in microbiome applications. With this work, we aimed at creating a bridge between microbial ecology researchers and ARM technique, making researchers aware about the strength and weaknesses of association rule mining approach.}, }
@article {pmid36303234, year = {2022}, author = {Yin, G and Chen, F and Chen, G and Yang, X and Huang, Q and Chen, L and Chen, M and Zhang, W and Ou, M and Cao, M and Lin, H and Chen, M and Xu, H and Ren, J and Chen, Y and Chen, Z}, title = {Alterations of bacteriome, mycobiome and metabolome characteristics in PCOS patients with normal/overweight individuals.}, journal = {Journal of ovarian research}, volume = {15}, number = {1}, pages = {117}, pmid = {36303234}, issn = {1757-2215}, support = {81200619//National Natural Science Foundation of China/ ; 81900541//National Natural Science Foundation of China/ ; A2020390//Medical Scientific Research Foundation of Guangdong Province of China/ ; 210715106900958//Guangdong Provincial Science and Technology Special Fund/ ; }, mesh = {Humans ; Female ; *Polycystic Ovary Syndrome ; *Mycobiome ; Overweight/complications ; RNA, Ribosomal, 16S ; Metabolome ; Bacteria/genetics ; }, abstract = {To characterize the gut bacteriome, mycobiome and serum metabolome profiles in polycystic ovary syndrome (PCOS) patients with normal/overweight individuals and evaluate a potential microbiota-related diagnostic method development for PCOS, 16S rRNA and ITS2 gene sequencing using 88 fecal samples and 87 metabolome analysis from serum samples are conducted and PCOS classifiers based on multiomics markers are constructed. There are significant bacterial, fungal community and metabolite differences among PCOS patients and healthy volunteers with normal/overweight individuals. Healthy individuals with overweight/obesity display less abnormal metabolism than PCOS patients and uniquely higher abundance of the fungal genus Mortierella. Nine bacterial genera, 4 predicted pathways, 11 fungal genera and top 30 metabolites are screened out which distinguish PCOS from healthy controls, with AUCs of 0.84, 0.64, 0.85 and 1, respectively. The metabolite-derived model is more accurate than the microbe-based model in discriminating normal BMI PCOS (PCOS-LB) from normal BMI healthy (Healthy-LB), PCOS-HB from Healthy-HB. Featured bacteria, fungi, predicted pathways and serum metabolites display higher associations with free androgen index (FAI) in the cooccurrence network. In conclusion, our data reveal that hyperandrogenemia plays a central role in the dysbiosis of intestinal microecology and the change in metabolic status in patients with PCOS and that its effect exceeds the role of BMI. Healthy women with high BMI showed unique microbiota and metabolic features.The priority of predictive models in discriminating PCOS from healthy status in this study were serum metabolites, fungal taxa and bacterial taxa.}, }
@article {pmid36303146, year = {2022}, author = {Xu, X and Dodd, AN}, title = {Is there crosstalk between circadian clocks in plants and the rhizomicrobiome?.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {241}, pmid = {36303146}, issn = {1741-7007}, support = {BBS/E/J/000PR9788/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Rhizosphere ; *Circadian Clocks ; Circadian Rhythm ; Soil Microbiology ; *Microbiota ; Plants/microbiology ; *Arabidopsis ; Soil ; }, abstract = {Circadian clocks occur across the kingdoms of life, including some fungi and bacteria present in the root-associated soil known as the rhizosphere. Recent work from Amy Newman and colleagues, published in BMC Biology, has discovered that the circadian clock in Arabidopsis plants affects the rhythmicity of rhizosphere microbial communities This brings into play the exciting question of whether there is a bidirectional rhythmic interaction between plants and their rhizomicrobiome. Here, we discuss how the findings of Newman et al. suggest that soil microbiomes can have both self-sustained and plant-imposed rhythmicity, and the challenges of plant-microbiome circadian clock research.}, }
@article {pmid36301703, year = {2022}, author = {Xiang, L and Harindintwali, JD and Wang, F and Redmile-Gordon, M and Chang, SX and Fu, Y and He, C and Muhoza, B and Brahushi, F and Bolan, N and Jiang, X and Ok, YS and Rinklebe, J and Schaeffer, A and Zhu, YG and Tiedje, JM and Xing, B}, title = {Integrating Biochar, Bacteria, and Plants for Sustainable Remediation of Soils Contaminated with Organic Pollutants.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {23}, pages = {16546-16566}, pmid = {36301703}, issn = {1520-5851}, mesh = {Humans ; Soil/chemistry ; *Soil Pollutants/analysis ; *Environmental Pollutants ; Ecosystem ; Biodegradation, Environmental ; Plants ; Bacteria ; }, abstract = {The contamination of soil with organic pollutants has been accelerated by agricultural and industrial development and poses a major threat to global ecosystems and human health. Various chemical and physical techniques have been developed to remediate soils contaminated with organic pollutants, but challenges related to cost, efficacy, and toxic byproducts often limit their sustainability. Fortunately, phytoremediation, achieved through the use of plants and associated microbiomes, has shown great promise for tackling environmental pollution; this technology has been tested both in the laboratory and in the field. Plant-microbe interactions further promote the efficacy of phytoremediation, with plant growth-promoting bacteria (PGPB) often used to assist the remediation of organic pollutants. However, the efficiency of microbe-assisted phytoremediation can be impeded by (i) high concentrations of secondary toxins, (ii) the absence of a suitable sink for these toxins, (iii) nutrient limitations, (iv) the lack of continued release of microbial inocula, and (v) the lack of shelter or porous habitats for planktonic organisms. In this regard, biochar affords unparalleled positive attributes that make it a suitable bacterial carrier and soil health enhancer. We propose that several barriers can be overcome by integrating plants, PGPB, and biochar for the remediation of organic pollutants in soil. Here, we explore the mechanisms by which biochar and PGPB can assist plants in the remediation of organic pollutants in soils, and thereby improve soil health. We analyze the cost-effectiveness, feasibility, life cycle, and practicality of this integration for sustainable restoration and management of soil.}, }
@article {pmid36301451, year = {2022}, author = {Woo, C and Bhuiyan, MIU and Kim, D and Kumari, P and Lee, SK and Park, JY and Dong, K and Lee, K and Yamamoto, N}, title = {DNA metabarcoding-based study on bacteria and fungi associated with house dust mites (Dermatophagoides spp.) in settled house dust.}, journal = {Experimental &amp; applied acarology}, volume = {88}, number = {3-4}, pages = {329-347}, pmid = {36301451}, issn = {1572-9702}, mesh = {Animals ; Humans ; *Pyroglyphidae ; *Dust ; DNA Barcoding, Taxonomic ; Ecosystem ; RNA, Ribosomal, 16S ; Bacteria/genetics ; }, abstract = {House dust mites (HDMs) including Dermatophagoides spp. are an important cause of respiratory allergies. However, their relationship with microorganisms in house dust has not been fully elucidated. Here, we characterized bacteria and fungi associated with HDMs in house dust samples collected in 107 homes in Korea by using DNA barcode sequencing of bacterial 16S rRNA gene, fungal internal transcribed spacer 2 (ITS2) region, and arthropod cytochrome c oxidase I (COI) gene. Our inter-kingdom co-occurrence network analysis and/or indicator species analysis identified that HDMs were positively related with a xerophilic fungus Wallemia, mycoparasitic fungi such as Cystobasidium, and some human skin-related bacterial and fungal genera, and they were negatively related with the hygrophilous fungus Cephalotrichum. Overall, our study has succeeded in adding novel insights into HDM-related bacteria and fungi in the house dust ecosystem, and in confirming the historically recognized fact that HDMs are associated with xerophilic fungi such as Wallemia. Understanding the microbial ecology in house dust is thought to be important for elucidating the etiology of human diseases including allergies, and our study revealed baseline information of house dust ecology in relation to HDMs. The findings could be useful from a perspective of human health.}, }
@article {pmid36300970, year = {2022}, author = {Deng, Y and Mauri, M and Vallet, M and Staudinger, M and Allen, RJ and Pohnert, G}, title = {Dynamic Diatom-Bacteria Consortia in Synthetic Plankton Communities.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {22}, pages = {e0161922}, pmid = {36300970}, issn = {1098-5336}, mesh = {*Diatoms ; Plankton ; Phytoplankton ; *Flavobacteriaceae ; Ecosystem ; *Microalgae/microbiology ; }, abstract = {Microalgae that form phytoplankton live and die in a complex microbial consortium in which they co-exist with bacteria and other microorganisms. The dynamics of species succession in the plankton depends on the interplay of these partners. Bacteria utilize substrates produced by the phototrophic algae, while algal growth can be supported by bacterial exudates. Bacteria might also use chemical mediators with algicidal properties to attack algae. To elucidate whether specific bacteria play universal or context-specific roles in the interaction with phytoplankton, we investigated the effect of cocultured bacteria on the growth of 8 microalgae. An interaction matrix revealed that the function of a given bacterium is highly dependent on the cocultured partner. We observed no universally algicidal or universally growth-promoting bacteria. The activity of bacteria can even change during the aging of an algal culture from inhibitory to stimulatory or vice versa. We further established a synthetic phytoplankton/bacteria community with the centric diatom, Coscinodiscus radiatus, and 4 phylogenetically distinctive bacterial isolates, Mameliella sp., Roseovarius sp., Croceibacter sp., and Marinobacter sp. Supported by a Lotka-Volterra model, we show that interactions within the consortium are specific and that the sum of the pairwise interactions can explain algal and bacterial growth in the community. No synergistic effects between bacteria in the presence of the diatom was observed. Our survey documents highly species-specific interactions that are dependent on algal fitness, bacterial metabolism, and community composition. This species specificity may underly the high complexity of the multi-species plankton communities observed in nature. IMPORTANCE The marine food web is fueled by phototrophic phytoplankton. These algae are central primary producers responsible for the fixation of ca. 40% of the global CO2. Phytoplankton always co-occur with a diverse bacterial community in nature. This diversity suggests the existence of ecological niches for the associated bacteria. We show that the interaction between algae and bacteria is highly species-specific. Furthermore, both, the fitness stage of the algae and the community composition are relevant in determining the effect of bacteria on algal growth. We conclude that bacteria should not be sorted into algicidal or growth supporting categories; instead, a context-specific function of the bacteria in the plankton must be considered. This functional diversity of single players within a consortium may underly the observed diversity in the plankton.}, }
@article {pmid36296484, year = {2022}, author = {Gao, J and Wang, M and Huang, W and You, Y and Zhan, J}, title = {Indigenous Saccharomyces cerevisiae Could Better Adapt to the Physicochemical Conditions and Natural Microbial Ecology of Prince Grape Must Compared with Commercial Saccharomyces cerevisiae FX10.}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {20}, pages = {}, pmid = {36296484}, issn = {1420-3049}, support = {201905410610663//Screening, Identification and Development of Wild Saccharomyces cerevisiae/ ; }, mesh = {Saccharomyces cerevisiae ; *Vitis/chemistry ; Glycerol ; *Wine/analysis ; Fermentation ; }, abstract = {Indigenous Saccharomyces cerevisiae, as a new and useful tool, can be used in fermentation to enhance the aroma characteristic qualities of the wine-production region. In this study, we used indigenous S. cerevisiae L59 and commercial S. cerevisiae FX10 to ferment Prince (a new hybrid variety from Lion Winery) wine, detected the basic physicochemical parameters and the dynamic changes of fungal communities during fermentation, and analyzed the correlations between fungal communities and volatile compounds. The results showed that the indigenous S. cerevisiae L59 could quickly adapt to the specific physicochemical conditions and microbial ecology of the grape must, showing a strong potential for winemaking. Compared with commercial S. cerevisiae FX10, the wine fermented by indigenous S. cerevisiae L59 contained more glycerol and less organic acids, contributing to a rounder taste. The results of volatile compounds indicated that the indigenous S. cerevisiae L59 had a positive effect on adding rosy, honey, pineapple and other sweet aroma characteristics to the wine. Overall, the study we performed showed that selection of indigenous S. cerevisiae from the wine-producing region as a starter for wine fermentation is conducive to improving the aroma profile of wine and preserving the aroma of the grape variety.}, }
@article {pmid36296348, year = {2022}, author = {Lorenzi, AS and Bonatelli, ML and Chia, MA and Peressim, L and Quecine, MC}, title = {Opposite Sides of Pantoea agglomerans and Its Associated Commercial Outlook.}, journal = {Microorganisms}, volume = {10}, number = {10}, pages = {}, pmid = {36296348}, issn = {2076-2607}, abstract = {Multifaceted microorganisms such as the bacterium Pantoea colonize a wide range of habitats and can exhibit both beneficial and harmful behaviors, which provide new insights into microbial ecology. In the agricultural context, several strains of Pantoea spp. can promote plant growth through direct or indirect mechanisms. Members of this genus contribute to plant growth mainly by increasing the supply of nitrogen, solubilizing ammonia and inorganic phosphate, and producing phytohormones (e.g., auxins). Several other studies have shown the potential of strains of Pantoea spp. to induce systemic resistance and protection against pests and pathogenic microorganisms in cultivated plants. Strains of the species Pantoea agglomerans deserve attention as a pest and phytopathogen control agent. Several of them also possess a biotechnological potential for therapeutic purposes (e.g., immunomodulators) and are implicated in human infections. Thus, the differentiation between the harmful and beneficial strains of P. agglomerans is mandatory to apply this bacterium safely as a biofertilizer or biocontroller. This review specifically evaluates the potential of the strain-associated features of P. agglomerans for bioprospecting and agricultural applications through its biological versatility as well as clarifying its potential animal and human health risks from a genomic point of view.}, }
@article {pmid36296237, year = {2022}, author = {Trego, A and Keating, C and Nzeteu, C and Graham, A and O'Flaherty, V and Ijaz, UZ}, title = {Beyond Basic Diversity Estimates-Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data.}, journal = {Microorganisms}, volume = {10}, number = {10}, pages = {}, pmid = {36296237}, issn = {2076-2607}, support = {NE/L011956/1//Natural Environment Research Council/ ; EP/P029329/1//Engineering and Physical Sciences Research Council/ ; EP/V030515/1//Engineering and Physical Sciences Research Council/ ; TC/2014/0016//Enterprise Ireland/ ; 14/IA/2371/SFI_/Science Foundation Ireland/Ireland ; 16/RC/3889/SFI_/Science Foundation Ireland/Ireland ; }, abstract = {Understanding microbial ecology through amplifying short read regions, typically 16S rRNA for prokaryotic species or 18S rRNA for eukaryotic species, remains a popular, economical choice. These methods provide relative abundances of key microbial taxa, which, depending on the experimental design, can be used to infer mechanistic ecological underpinnings. In this review, we discuss recent advancements in in situ analytical tools that have the power to elucidate ecological phenomena, unveil the metabolic potential of microbial communities, identify complex multidimensional interactions between species, and compare stability and complexity under different conditions. Additionally, we highlight methods that incorporate various modalities and additional information, which in combination with abundance data, can help us understand how microbial communities respond to change in a typical ecosystem. Whilst the field of microbial informatics continues to progress substantially, our emphasis is on popular methods that are applicable to a broad range of study designs. The application of these methods can increase our mechanistic understanding of the ongoing dynamics of complex microbial communities.}, }
@article {pmid36296177, year = {2022}, author = {Leite, MFA and van den Broek, SWEB and Kuramae, EE}, title = {Current Challenges and Pitfalls in Soil Metagenomics.}, journal = {Microorganisms}, volume = {10}, number = {10}, pages = {}, pmid = {36296177}, issn = {2076-2607}, abstract = {Soil microbial communities are essential components of agroecological ecosystems that influence soil fertility, nutrient turnover, and plant productivity. Metagenomics data are increasingly easy to obtain, but studies of soil metagenomics face three key challenges: (1) accounting for soil physicochemical properties; (2) incorporating untreated controls; and (3) sharing data. Accounting for soil physicochemical properties is crucial for better understanding the changes in soil microbial community composition, mechanisms, and abundance. Untreated controls provide a good baseline to measure changes in soil microbial communities and separate treatment effects from random effects. Sharing data increases reproducibility and enables meta-analyses, which are important for investigating overall effects. To overcome these challenges, we suggest establishing standard guidelines for the design of experiments for studying soil metagenomics. Addressing these challenges will promote a better understanding of soil microbial community composition and function, which we can exploit to enhance soil quality, health, and fertility.}, }
@article {pmid36292810, year = {2022}, author = {Ghosh, S and Namin, SM and Jung, C}, title = {Differential Bacterial Community of Bee Bread and Bee Pollen Revealed by 16s rRNA High-Throughput Sequencing.}, journal = {Insects}, volume = {13}, number = {10}, pages = {}, pmid = {36292810}, issn = {2075-4450}, support = {NRF- 2018R1A6A1A03024862//National Research Foundation of Korea/ ; 20211362A00-2123-BD01//Korean forest service/ ; }, abstract = {We investigated the bacterial community of bee bread and bee pollen samples using an approach through 16 s rRNA high-throughput sequencing. The results revealed a higher bacterial diversity in bee bread than in bee pollen as depicted in taxonomic profiling, as well as diversity indices such as the Shannon diversity index (3.7 to 4.8 for bee bread and 1.1 to 1.7 for bee pollen samples) and Simpson’s index (>0.9 for bee bread and 0.4−0.5 for bee pollen). Principal component analysis showed a distinct difference in bacterial communities. The higher bacterial diversity in the bee bread than bee pollen could presumably be due to factors such as storage period, processing of food, fermentation, and high sugar environment. However, no effect of the feed (rapeseed or oak pollen patties or even natural inflow) was indicated on the bacterial composition of bee bread, presumably because of the lack of restriction of foraged pollen inflow in the hive. The diverse bacterial profile of the bee bread could contribute to the nutritional provisioning as well as enhance the detoxification process; however, a thorough investigation of the functional role of individual bacteria genera remains a task for future studies.}, }
@article {pmid36286524, year = {2022}, author = {Akob, DM and Sutton, JM and Bushman, TJ and Baesman, SM and Klein, E and Shrestha, Y and Andrews, R and Fierst, JL and Kolton, M and Gushgari-Doyle, S and Oremland, RS and Freeman, JL}, title = {Acetylenotrophic and Diazotrophic Bradyrhizobium sp. Strain I71 from TCE-Contaminated Soils.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {22}, pages = {e0121922}, pmid = {36286524}, issn = {1098-5336}, mesh = {*Bradyrhizobium ; *Trichloroethylene/metabolism ; Nitrogen Fixation/genetics ; Soil/chemistry ; Acetylene/metabolism ; Phylogeny ; Symbiosis ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; }, abstract = {Acetylene (C2H2) is a molecule rarely found in nature, with very few known natural sources, but acetylenotrophic microorganisms can use acetylene as their primary carbon and energy source. As of 2018 there were 15 known strains of aerobic and anaerobic acetylenotrophs; however, we hypothesize there may yet be unrecognized diversity of acetylenotrophs in nature. This study expands the known diversity of acetylenotrophs by isolating the aerobic acetylenotroph, Bradyrhizobium sp. strain I71, from trichloroethylene (TCE)-contaminated soils. Strain I71 is a member of the class Alphaproteobacteria and exhibits acetylenotrophic and diazotrophic activities, the only two enzymatic reactions known to transform acetylene. This unique capability in the isolated strain may increase the genus' economic impact beyond agriculture as acetylenotrophy is closely linked to bioremediation of chlorinated contaminants. Computational analyses indicate that the Bradyrhizobium sp. strain I71 genome contains 522 unique genes compared to close relatives. Moreover, applying a novel hidden Markov model of known acetylene hydratase (AH) enzymes identified a putative AH enzyme. Protein annotation with I-TASSER software predicted the AH from the microbe Syntrophotalea acetylenica as the closest structural and functional analog. Furthermore, the putative AH was flanked by horizontal gene transfer (HGT) elements, like that of AH in anaerobic acetylenotrophs, suggesting an unknown source of acetylene or acetylenic substrate in the environment that is selecting for the presence of AH. IMPORTANCE The isolation of Bradyrhizobium strain I71 expands the distribution of acetylene-consuming microbes to include a group of economically important microorganisms. Members of Bradyrhizobium are well studied for their abilities to improve plant health and increase crop yields by providing bioavailable nitrogen. Additionally, acetylene-consuming microbes have been shown to work in tandem with other microbes to degrade soil contaminants. Based on genome, cultivation, and protein prediction analysis, the ability to consume acetylene is likely not widespread within the genus Bradyrhizobium. These findings suggest that the suite of phenotypic capabilities of strain I71 may be unique and make it a good candidate for further study in several research avenues.}, }
@article {pmid36286523, year = {2022}, author = {Van Peteghem, L and Sakarika, M and Matassa, S and Rabaey, K}, title = {The Role of Microorganisms and Carbon-to-Nitrogen Ratios for Microbial Protein Production from Bioethanol.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {22}, pages = {e0118822}, pmid = {36286523}, issn = {1098-5336}, mesh = {Humans ; *Nitrogen ; *Carbon ; Biomass ; Ethanol/metabolism ; Yeasts/metabolism ; Fermentation ; Biofuels ; }, abstract = {With industrial agriculture increasingly challenging our ecological limits, alternative food production routes such as microbial protein (MP) production are receiving renewed interest. Among the multiple substrates so far evaluated for MP production, renewable bioethanol (EtOH) is still underexplored. Therefore, the present study investigated the cultivation of five microorganisms (2 bacteria, 3 yeasts) under carbon (C), nitrogen (N), and dual C-N-limiting conditions (molar C/N ratios of 5, 60, and 20, respectively) to evaluate the production (specific growth rate, protein and biomass yield, production cost) as well as the nutritional characteristics (protein and carbohydrate content, amino acid [AA] profile) of MP production from bioethanol. Under C-limiting conditions, all the selected microorganisms showed a favorable AA profile for human nutrition (average AA score of 1.5 or higher), with a negative correlation between protein content and growth rate. Maximal biomass yields were achieved under conditions where no extracellular acetate was produced. Cyberlindnera saturnus and Wickerhamomyces anomalus displayed remarkably high biomass yields (0.40 to 0.82 g cell dry weight [CDW]/g EtOHconsumed), which was reflected in the lowest estimated biomass production costs when cultivated with a C/N ratio of 20. Finally, when the production cost was evaluated on a protein basis, Corynebacterium glutamicum grown under C-limiting conditions showed the most promising economic outlook. IMPORTANCE The global protein demand is rapidly increasing at rates that cannot be sustained, with projections showing 78% increased global protein needs by 2050 (361 compared to 202 million tonprotein/year in 2017). In the absence of dedicated mitigation strategies, the environmental effects of our current food production system (relying on agriculture) are expected to surpass the planetary boundaries-the safe operating space for humanity-by 2050. Here, we illustrate the potential of bioethanol-renewable ethanol produced from side streams-as a main resource for the production of microbial protein, a radically different food production strategy in comparison to traditional agriculture, with the potential to be more sustainable. This study unravels the kinetic, productive, and nutritional potential for microbial protein production from bioethanol using the bacteria Methylorubrum extorquens and Corynebacterium glutamicum and the yeasts Wickerhamomyces anomalus, Cyberlindnera saturnus, and Metschnikowia pulcherrima, setting the scene for microbial protein production from renewable ethanol.}, }
@article {pmid36282736, year = {2022}, author = {Sarkar, A and Prescott, SM and Dutra, S and Yoo, JY and Gordon, J and Shaffer, E and McSkimming, D and Groer, ME}, title = {Relationships of the very low birth weight infant microbiome with neurodevelopment at 2 and 4 years of age.}, journal = {Developmental psychobiology}, volume = {64}, number = {7}, pages = {e22317}, pmid = {36282736}, issn = {1098-2302}, support = {R01 HD086805/HD/NICHD NIH HHS/United States ; R01 NR015446/NR/NINR NIH HHS/United States ; R21 NR013094/NR/NINR NIH HHS/United States ; }, mesh = {Infant, Newborn ; Infant ; Adult ; Humans ; Child, Preschool ; *Infant, Very Low Birth Weight ; Intensive Care Units, Neonatal ; Gestational Age ; Birth Weight ; *Microbiota ; Anti-Bacterial Agents ; }, abstract = {Very low birth weight (VLBW) infants (<1500 g) are at risk for poor neurodevelopmental outcomes depending on gestational age (GA), birth weight (BW), and morbidity in early life. The contribution of the gut microbiome is not well understood. Stool samples were collected weekly in the neonatal intensive care unit (NICU) from 24 VLBW infants for 6 weeks after admission and then again at 2 and 4 years of age. The Battelle Development Inventory-2 Screening Test (BDI-2 ST) was administered at 2- and 4-year time points. VLBW infants had dysbiotic microbiota in the NICU that progressed for most to an adult-type microbiota by 4 years of age. The BDI-2 ST results at age of 2 years triggered referral for further testing in 14 toddlers (70%), and by 4 years of age only seven of these 14 continued to require referral. Both NICU infant stool diversity and particular microbial amplicon sequence variants were associated with BDI-2 ST subscales, particularly for cognition, adaptive, and communication subscales, when controlled for GA, BW, and antibiotic exposure. Network analysis of the NICU infant stool microbial ecology showed differences in children needing neurodevelopmental referral. The results of this preliminary study indicate that the neonatal gut microbiome plays a role in early cognitive and behavioral neurodevelopment.}, }
@article {pmid36282286, year = {2023}, author = {Ortiz, WE and Carlos-Shanley, C and Huertas, M}, title = {Impact of Sublethal Concentrations of Nitrite on Goldfish (Carassius auratus) Microbiomes.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1331-1342}, pmid = {36282286}, issn = {1432-184X}, mesh = {Animals ; *Goldfish ; *Nitrites ; Aquaculture ; Gills/microbiology ; Water ; }, abstract = {Elevated concentrations of nitrite are toxic to fish and can cause a myriad of well documented issues. However, the effects of sublethal concentrations of nitrite on fish health, and specifically, fish tissue microbiomes have not been studied. To test the effects of nitrite exposure, goldfish were exposed to sublethal concentrations of nitrite, 0.0 mM, 0.1 mM, and 1.0 mM, for 2 months. The bacteria in the nose, skin, gills, and water were then extracted and sequenced to identify changes to the microbial composition. The water microbiome was not significantly changed by the added nitrite; however, each of the tissue microbiomes was changed by at least one of the treatments. The skin and gill microbiomes were significantly different between the control and 1.0 mM treatment and the nose microbiome showed significant changes between the control and both the 0.1 mM and 1.0 mM treatments. Thus, sublethal concentrations of nitrite in the environment caused a shift in the fish tissue microbiomes independently of the water microbiome. These changes could lead to an increased chance of infection, disrupt organ systems, and raise the mortality rate of fish. In systems with high nitrite concentrations, like intensive aquaculture setups or polluted areas, the effects of nitrite on the microbiomes could negatively affect fish populations.}, }
@article {pmid37091220, year = {2022}, author = {Obase, K}, title = {Morphological characteristics of ectomycorrhizas formed by in vitro synthesis between conifer seedlings and Tuber mycelial strains of the Puberulum clade isolated in Japan.}, journal = {Mycoscience}, volume = {63}, number = {1}, pages = {39-44}, pmid = {37091220}, issn = {1340-3540}, abstract = {Seedlings of Pinus densiflora and Abies sachalinensis were inoculated with Tuber mycelial strains of the Puberulum clade in vitro to examine the morphological characteristics of their ectomycorrhizas. Axenically germinated seedlings were inoculated with the mycelia of five taxa from the Puberulum clade and grown in glass jars for 4 mo in an illuminated incubator. The seedlings were successfully colonized by the inoculated Tuber strains, as confirmed by the nuclear ribosomal internal transcribed spacer barcoding of the synthesized ectomycorrhizas. The ectomycorrhizas were characterized by a pale yellow to brown color, short needle-shaped cystidia, and net-like hyphal arrangement, and epidermoid cells on the mantle surface; notably, these features are similar to the ectomycorrhizas of various Puberulum clade members. As the ectomycorrhizas of different Tuber species are indistinguishable by morphological characters, molecular techniques are necessary to identify ectomycorrhizas formed by Tuber species within the Puberulum clade.}, }
@article {pmid37744128, year = {2021}, author = {Otto, EC and Held, BW and Gould, TJ and Blanchette, RA}, title = {Fungal Diversity in Multiple Post-harvest Aged Red Pine Stumps and Their Potential Influence on Heterobasidion Root Rot in Managed Stands Across Minnesota.}, journal = {Frontiers in fungal biology}, volume = {2}, number = {}, pages = {782181}, pmid = {37744128}, issn = {2673-6128}, abstract = {Thinning operations that occur in managed red pine (Pinus resinosa) stands, create tree stumps that can serve as a habitat for fungi, especially Heterobasidion irregulare, the cause of a serious root disease. Different fungi can colonize stumps early and the community of fungi can change over time as initial fungal species become replaced. Samples were collected from both the native and non-native range of red pine from stumps that were cut at different time periods. Stumps that were harvested at 0-1, 2-3, 5-6, and 10-12 years before sampling were used to provide data on the diversity of fungi that colonize tree stumps and how these communities can change over time as well as how they influence colonization of H. irregulare. Traditional culturing methods and Illumina MiSeq sequencing were used to identify the fungi in the samples. Of particular interest was Phlebiopsis gigantea, which can colonize cut stumps and prevent H. irregulare from becoming established. Overall, P. gigantea was the most abundant fungus isolated and sequenced via Illumina MiSeq. Results show that Phlebiopsis gigantea was isolated from 90% of all stumps sampled for sites harvested within 3 years of sampling in the native range of red pine compared to 33% in the non-native range. For Illumina MiSeq, 5,940 total amplicon sequence variants (ASVs) were detected. P. gigantea represented 14% of the total reads and composed 19% of the reads in the native range and 8% in non-native range of red pine. Furthermore, P. gigantea represented 38% of the reads for stumps that were harvested within 3 years of sampling in the native range of red pine compared to 14% in the non-native range. These results help demonstrate that a higher amount of P. gigantea is present in the native range of red pine and could be acting as a native biological control agent. Additional fungi, including Resinicium bicolor, Hypochnicium cremicolor, Leptographium spp., and others identified at different cutting times are also discussed. Finally, different diversity indices revealed similar, but slightly higher diversity for southern sites via Shannon and Simpson Diversity indices. Beta diversity demonstrated a similar species composition in stumps harvested at different times with these stumps being grouped together based on harvesting years.}, }
@article {pmid36765158, year = {2021}, author = {Nuccio, EE and Nguyen, NH and Nunes da Rocha, U and Mayali, X and Bougoure, J and Weber, PK and Brodie, E and Firestone, M and Pett-Ridge, J}, title = {Community RNA-Seq: multi-kingdom responses to living versus decaying roots in soil.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {72}, pmid = {36765158}, issn = {2730-6151}, support = {SCW1711//DOE | SC | Biological and Environmental Research (BER)/ ; DE-SC0010570//DOE | SC | Biological and Environmental Research (BER)/ ; DE-SC0016247//DOE | SC | Biological and Environmental Research (BER)/ ; DE-SC0020163//DOE | SC | Biological and Environmental Research (BER)/ ; SCW1421//DOE | SC | Biological and Environmental Research (BER)/ ; SCW1589//DOE | SC | Biological and Environmental Research (BER)/ ; SCW1678//DOE | SC | Biological and Environmental Research (BER)/ ; }, abstract = {Roots are a primary source of organic carbon input in most soils. The consumption of living and detrital root inputs involves multi-trophic processes and multiple kingdoms of microbial life, but typical microbial ecology studies focus on only one or two major lineages. We used Illumina shotgun RNA sequencing to conduct PCR-independent SSU rRNA community analysis ("community RNA-Seq") and simultaneously assess the bacteria, archaea, fungi, and microfauna surrounding both living and decomposing roots of the annual grass, Avena fatua. Plants were grown in [13]CO2-labeled microcosms amended with [15]N-root litter to identify the preferences of rhizosphere organisms for root exudates ([13]C) versus decaying root biomass ([15]N) using NanoSIMS microarray imaging (Chip-SIP). When litter was available, rhizosphere and bulk soil had significantly more Amoebozoa, which are potentially important yet often overlooked top-down drivers of detritusphere community dynamics and nutrient cycling. Bulk soil containing litter was depleted in Actinobacteria but had significantly more Bacteroidetes and Proteobacteria. While Actinobacteria were abundant in the rhizosphere, Chip-SIP showed Actinobacteria preferentially incorporated litter relative to root exudates, indicating this group's more prominent role in detritus elemental cycling in the rhizosphere. Our results emphasize that decomposition is a multi-trophic process involving complex interactions, and our methodology can be used to track the trajectory of carbon through multi-kingdom soil food webs.}, }
@article {pmid37693795, year = {2021}, author = {Crous, PW and Osieck, ER and Jurjević, &#x17d; and Boers, J and van Iperen, AL and Starink-Willemse, M and Dima, B and Balashov, S and Bulgakov, TS and Johnston, PR and Morozova, OV and Pinruan, U and Sommai, S and Alvarado, P and Decock, CA and Lebel, T and McMullan-Fisher, S and Moreno, G and Shivas, RG and Zhao, L and Abdollahzadeh, J and Abrinbana, M and Ageev, DV and Akhmetova, G and Alexandrova, AV and Altés, A and Amaral, AGG and Angelini, C and Antonín, V and Arenas, F and Asselman, P and Badali, F and Baghela, A and Bañares, A and Barreto, RW and Baseia, IG and Bellanger, JM and Berraf-Tebbal, A and Biketova, AY and Bukharova, NV and Burgess, TI and Cabero, J and Câmara, MPS and Cano-Lira, JF and Ceryngier, P and Chávez, R and Cowan, DA and de Lima, AF and Oliveira, RL and Denman, S and Dang, QN and Dovana, F and Duarte, IG and Eichmeier, A and Erhard, A and Esteve-Raventós, F and Fellin, A and Ferisin, G and Ferreira, RJ and Ferrer, A and Finy, P and Gaya, E and Geering, ADW and Gil-Durán, C and Glässnerová, K and Glushakova, AM and Gramaje, D and Guard, FE and Guarnizo, AL and Haelewaters, D and Halling, RE and Hill, R and Hirooka, Y and Hubka, V and Iliushin, VA and Ivanova, DD and Ivanushkina, NE and Jangsantear, P and Justo, A and Kachalkin, AV and Kato, S and Khamsuntorn, P and Kirtsideli, IY and Knapp, DG and Kochkina, GA and Koukol, O and Kovács, GM and Kruse, J and Kumar, TKA and Kušan, I and Læssøe, T and Larsson, E and Lebeuf, R and Levicán, G and Loizides, M and Marinho, P and Luangsa-Ard, JJ and Lukina, EG and Magaña-Dueñas, V and Maggs-Kölling, G and Malysheva, EF and Malysheva, VF and Martín, B and Martín, MP and Matočec, N and McTaggart, AR and Mehrabi-Koushki, M and Mešić, A and Miller, AN and Mironova, P and Moreau, PA and Morte, A and Müller, K and Nagy, LG and Nanu, S and Navarro-Ródenas, A and Nel, WJ and Nguyen, TH and Nóbrega, TF and Noordeloos, ME and Olariaga, I and Overton, BE and Ozerskaya, SM and Palani, P and Pancorbo, F and Papp, V and Pawłowska, J and Pham, TQ and Phosri, C and Popov, ES and Portugal, A and Pošta, A and Reschke, K and Reul, M and Ricci, GM and Rodríguez, A and Romanowski, J and Ruchikachorn, N and Saar, I and Safi, A and Sakolrak, B and Salzmann, F and Sandoval-Denis, M and Sangwichein, E and Sanhueza, L and Sato, T and Sastoque, A and Senn-Irlet, B and Shibata, A and Siepe, K and Somrithipol, S and Spetik, M and Sridhar, P and Stchigel, AM and Stuskova, K and Suwannasai, N and Tan, YP and Thangavel, R and Tiago, I and Tiwari, S and Tkalčec, Z and Tomashevskaya, MA and Tonegawa, C and Tran, HX and Tran, NT and Trovão, J and Trubitsyn, VE and Van Wyk, J and Vieira, WAS and Vila, J and Visagie, CM and Vizzini, A and Volobuev, SV and Vu, DT and Wangsawat, N and Yaguchi, T and Ercole, E and Ferreira, BW and de Souza, AP and Vieira, BS and Groenewald, JZ}, title = {Fungal Planet description sheets: 1284-1382.}, journal = {Persoonia}, volume = {47}, number = {}, pages = {178-374}, pmid = {37693795}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Antartica, Cladosporium austrolitorale from coastal sea sand. Australia, Austroboletus yourkae on soil, Crepidotus innuopurpureus on dead wood, Curvularia stenotaphri from roots and leaves of Stenotaphrum secundatum and Thecaphora stajsicii from capsules of Oxalis radicosa. Belgium, Paraxerochrysium coryli (incl. Paraxerochrysium gen. nov.) from Corylus avellana. Brazil, Calvatia nordestina on soil, Didymella tabebuiicola from leaf spots on Tabebuia aurea, Fusarium subflagellisporum from hypertrophied floral and vegetative branches of Mangifera indica and Microdochium maculosum from living leaves of Digitaria insularis. Canada, Cuphophyllus bondii from a grassland. Croatia, Mollisia inferiseptata from a rotten Laurus nobilis trunk. Cyprus, Amanita exilis on calcareous soil. Czech Republic, Cytospora hippophaicola from wood of symptomatic Vaccinium corymbosum. Denmark, Lasiosphaeria deviata on pieces of wood and herbaceous debris. Dominican Republic, Calocybella goethei among grass on a lawn. France (Corsica), Inocybe corsica on wet ground. France (French Guiana), Trechispora patawaensis on decayed branch of unknown angiosperm tree and Trechispora subregularis on decayed log of unknown angiosperm tree. Germany, Paramicrothecium sambuci (incl. Paramicrothecium gen. nov.) on dead stems of Sambucus nigra. India, Aureobasidium microtermitis from the gut of a Microtermes sp. termite, Laccaria diospyricola on soil and Phylloporia tamilnadensis on branches of Catunaregam spinosa. Iran, Pythium serotinoosporum from soil under Prunus dulcis. Italy, Pluteus brunneovenosus on twigs of broadleaved trees on the ground. Japan, Heterophoma rehmanniae on leaves of Rehmannia glutinosa f. hueichingensis. Kazakhstan, Murispora kazachstanica from healthy roots of Triticum aestivum. Namibia, Caespitomonium euphorbiae (incl. Caespitomonium gen. nov.) from stems of an Euphorbia sp. Netherlands, Alfaria junci, Myrmecridium junci, Myrmecridium juncicola, Myrmecridium juncigenum, Ophioceras junci, Paradinemasporium junci (incl. Paradinemasporium gen. nov.), Phialoseptomonium junci, Sporidesmiella juncicola, Xenopyricularia junci and Zaanenomyces quadripartis (incl. Zaanenomyces gen. nov.), from dead culms of Juncus effusus, Cylindromonium everniae and Rhodoveronaea everniae from Evernia prunastri, Cyphellophora sambuci and Myrmecridium sambuci from Sambucus nigra, Kiflimonium junci, Sarocladium junci, Zaanenomyces moderatricis-academiae and Zaanenomyces versatilis from dead culms of Juncus inflexus, Microcera physciae from Physcia tenella, Myrmecridium dactylidis from dead culms of Dactylis glomerata, Neochalara spiraeae and Sporidesmium spiraeae from leaves of Spiraea japonica, Neofabraea salicina from Salix sp., Paradissoconium narthecii (incl. Paradissoconium gen. nov.) from dead leaves of Narthecium ossifragum, Polyscytalum vaccinii from Vaccinium myrtillus, Pseudosoloacrosporiella cryptomeriae (incl. Pseudosoloacrosporiella gen. nov.) from leaves of Cryptomeria japonica, Ramularia pararhabdospora from Plantago lanceolata, Sporidesmiella pini from needles of Pinus sylvestris and Xenoacrodontium juglandis (incl. Xenoacrodontium gen. nov. and Xenoacrodontiaceae fam. nov.) from Juglans regia. New Zealand, Cryptometrion metrosideri from twigs of Metrosideros sp., Coccomyces pycnophyllocladi from dead leaves of Phyllocladus alpinus, Hypoderma aliforme from fallen leaves Fuscopora solandri and Hypoderma subiculatum from dead leaves Phormium tenax. Norway, Neodevriesia kalakoutskii from permafrost and Variabilispora viridis from driftwood of Picea abies. Portugal, Entomortierella hereditatis from a biofilm covering a deteriorated limestone wall. Russia, Colpoma junipericola from needles of Juniperus sabina, Entoloma cinnamomeum on soil in grasslands, Entoloma verae on soil in grasslands, Hyphodermella pallidostraminea on a dry dead branch of Actinidia sp., Lepiota sayanensis on litter in a mixed forest, Papiliotrema horticola from Malus communis, Paramacroventuria ribis (incl. Paramacroventuria gen. nov.) from leaves of Ribes aureum and Paramyrothecium lathyri from leaves of Lathyrus tuberosus. South Africa, Harzia combreti from leaf litter of Combretum collinum ssp. sulvense, Penicillium xyleborini from Xyleborinus saxesenii, Phaeoisaria dalbergiae from bark of Dalbergia armata, Protocreopsis euphorbiae from leaf litter of Euphorbia ingens and Roigiella syzygii from twigs of Syzygium chordatum. Spain, Genea zamorana on sandy soil, Gymnopus nigrescens on Scleropodium touretii, Hesperomyces parexochomi on Parexochomus quadriplagiatus, Paraphoma variabilis from dung, Phaeococcomyces kinklidomatophilus from a blackened metal railing of an industrial warehouse and Tuber suaveolens in soil under Quercus faginea. Svalbard and Jan Mayen, Inocybe nivea associated with Salix polaris. Thailand, Biscogniauxia whalleyi on corticated wood. UK, Parasitella quercicola from Quercus robur. USA, Aspergillus arizonicus from indoor air in a hospital, Caeliomyces tampanus (incl. Caeliomyces gen. nov.) from office dust, Cippumomyces mortalis (incl. Cippumomyces gen. nov.) from a tombstone, Cylindrium desperesense from air in a store, Tetracoccosporium pseudoaerium from air sample in house, Toxicocladosporium glendoranum from air in a brick room, Toxicocladosporium losalamitosense from air in a classroom, Valsonectria portsmouthensis from air in men's locker room and Varicosporellopsis americana from sludge in a water reservoir. Vietnam, Entoloma kovalenkoi on rotten wood, Fusarium chuoi inside seed of Musa itinerans, Micropsalliota albofelina on soil in tropical evergreen mixed forests and Phytophthora docyniae from soil and roots of Docynia indica. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Osieck ER, Jurjević Ž, et al. 2021. Fungal Planet description sheets: 1284-1382. Persoonia 47: 178-374. https://doi.org/10.3767/persoonia.2021.47.06.}, }
@article {pmid37744139, year = {2021}, author = {Yoshimi, A and Hagiwara, D and Ono, M and Fukuma, Y and Midorikawa, Y and Furukawa, K and Fujioka, T and Mizutani, O and Sato, N and Miyazawa, K and Maruyama, JI and Marui, J and Yamagata, Y and Nakajima, T and Tanaka, C and Abe, K}, title = {Downregulation of the ypdA Gene Encoding an Intermediate of His-Asp Phosphorelay Signaling in Aspergillus nidulans Induces the Same Cellular Effects as the Phenylpyrrole Fungicide Fludioxonil.}, journal = {Frontiers in fungal biology}, volume = {2}, number = {}, pages = {675459}, pmid = {37744139}, issn = {2673-6128}, abstract = {Many eukaryotic histidine-to-aspartate (His-Asp) phosphorelay systems consist of three types of signal transducers: a His-kinase (HK), a response regulator (RR), and a histidine-containing phosphotransfer intermediate (HPt). In general, the HPt acts as an intermediate between the HK and the RR and is indispensable for inducing appropriate responses to environmental stresses. In a previous study, we attempted but were unable to obtain deletion mutants of the ypdA gene in order to characterize its function in the filamentous fungus Aspergillus nidulans. In the present study, we constructed the CypdA strain in which ypdA expression is conditionally regulated by the A. nidulans alcA promoter. We constructed CypdA strains with RR gene disruptions (CypdA-sskAΔ, CypdA-srrAΔ, and CypdA-sskAΔsrrAΔ). Suppression of YpdA induced by ypdA downregulation activated the downstream HogA mitogen-activated protein kinase cascade. YpdA suppression caused severe growth defects and abnormal hyphae, with features such as enhanced septation, a decrease in number of nuclei, nuclear fragmentation, and hypertrophy of vacuoles, both regulated in an SskA-dependent manner. Fludioxonil treatment caused the same cellular responses as ypdA suppression. The growth-inhibitory effects of fludioxonil and the lethality caused by ypdA downregulation may be caused by the same or similar mechanisms and to be dependent on both the SskA and SrrA pathways.}, }
@article {pmid36398283, year = {2021}, author = {Jeganathan, P and Holmes, SP}, title = {A Statistical Perspective on the Challenges in Molecular Microbial Biology.}, journal = {Journal of agricultural, biological, and environmental statistics}, volume = {26}, number = {2}, pages = {131-160}, pmid = {36398283}, issn = {1085-7117}, support = {R01 AI112401/AI/NIAID NIH HHS/United States ; }, abstract = {High throughput sequencing (HTS)-based technology enables identifying and quantifying non-culturable microbial organisms in all environments. Microbial sequences have enhanced our understanding of the human microbiome, the soil and plant environment, and the marine environment. All molecular microbial data pose statistical challenges due to contamination sequences from reagents, batch effects, unequal sampling, and undetected taxa. Technical biases and heteroscedasticity have the strongest effects, but different strains across subjects and environments also make direct differential abundance testing unwieldy. We provide an introduction to a few statistical tools that can overcome some of these difficulties and demonstrate those tools on an example. We show how standard statistical methods, such as simple hierarchical mixture and topic models, can facilitate inferences on latent microbial communities. We also review some nonparametric Bayesian approaches that combine visualization and uncertainty quantification. The intersection of molecular microbial biology and statistics is an exciting new venue. Finally, we list some of the important open problems that would benefit from more careful statistical method development.}, }
@article {pmid37089255, year = {2021}, author = {Obase, K and Yamanaka, S and Kinoshita, A and Tamai, Y and Yamanaka, T}, title = {Phylogenetic placements and cultural characteristics of Tuber species isolated from ectomycorrhizas.}, journal = {Mycoscience}, volume = {62}, number = {2}, pages = {124-131}, pmid = {37089255}, issn = {1340-3540}, abstract = {Pure cultures of Tuber were isolated from ectomycorrhizal root tips in Abies sachalinensis plantations in Hokkaido, Japan. Their phylogenetic relationships as well as vegetative hyphal characteristics on culture media were reported. Phylogenetic analysis based on the internal transcribed spacer within ribosomal DNA settled well-supported eight lineages within Puberulum, Latisporum, and Maculatum clades in Tuber. Three and one lineages were grouped with undescribed species of Puberulum clade in Japan and that of the Latisporum group in China, respectively. Two lineages were closely associated to but distinct from an undescribed species of Puberulum clade in Japan. One lineage did not group with any sequences in the International Nucleotide Sequence Database (INSD), proposing a new taxon in the Latisporum group. One lineage was grouped with T. foetidum in Maculatum clade. All strains in each lineage displayed yellowish white, thin, filamentous colonies on Melin-Norkrans agar medium. Various differences in morphological characteristics of hyphae on pure cultures of various strains were noted, but they were frequently uncommon among strains of the same taxa. Isolation from ectomycorrhizal root tips can be among the effective ways to acquire pure cultures of Tuber strains.}, }
@article {pmid36590333, year = {2021}, author = {Koshy-Chenthittayil, S and Mendes, P and Laubenbacher, R}, title = {Optimization of Agent-Based Models Through Coarse-Graining: A Case Study in Microbial Ecology.}, journal = {Letters in biomathematics}, volume = {8}, number = {1}, pages = {167-178}, pmid = {36590333}, issn = {2373-7867}, support = {R01 AI135128/AI/NIAID NIH HHS/United States ; R01 GM127909/GM/NIGMS NIH HHS/United States ; U01 EB024501/EB/NIBIB NIH HHS/United States ; }, abstract = {Optimization and control are important objectives across biology and biomedicine, and mathematical models are a key enabling technology. This paper reports a computational study of model-based multi-objective optimization in the setting of microbial ecology, using agent-based models. This modeling framework is well-suited to the field, but is not amenable to standard control-theoretic approaches. Furthermore, due to computational complexity, simulation-based optimization approaches are often challenging to implement. This paper presents the results of an approach that combines control-dependent coarse-graining with Pareto optimization, applied to two models of multi-species bacterial biofilms. It shows that this approach can be successful for models whose computational complexity prevents effective simulation-based optimization.}, }
@article {pmid37333959, year = {2020}, author = {Zeibich, L and Guhl, J and Drake, HL}, title = {Impact of water content and dietary organic carbon richness on gut bacteria in the earthworm Lumbricus terrestris.}, journal = {FEMS microbes}, volume = {1}, number = {1}, pages = {xtaa002}, pmid = {37333959}, issn = {2633-6685}, abstract = {Many higher and lower animal gut ecosystems have complex resident microbial communities. In contrast, ingested soil is the primary source of the gut microbial diversity of earthworms, invertebrates of fundamental importance to the terrestrial biosphere. Earthworms also harbor a few endemic bacteria including Tenericutes-affiliated Candidatus Lumbricincola of unknown function. Gut microbes are subject to nutrient fluctuations due to dilution effects during gut passage, the nutrient richness of the anoxic gut, and dietary organic carbon, factors that could alter their activity/detection. This study's objective was to assess the potential impact of these factors on the occurrence and activity of ingested and endemic bacteria in gut content of Lumbricus terrestris. Fermentation product profiles of anoxic undiluted and diluted gut content treatments were similar, suggesting that experimental increase in water content and nutrient dilution had marginal impact on fermentation. However, 16S ribosomal Ribonucleic Acid (16S rRNA) sequence abundances indicated that stimulated bacterial taxa were not identical in undiluted and diluted treatments, with dominate potentially functionally redundant phylotypes being affiliated to the Firmicutes, Fusobacteria and Proteobacteria. Although the earthworm-associated Tenericutes were not stimulated in these treatments, the occurrence of three Tenericutes-affiliated phylotypes varied with the organic carbon richness of the earthworm diet, with two phylotypes being associated with high organic carbon richness. 16S rRNA sequence abundances indicated that other dominant gut taxa also varied with dietary organic carbon richness. These findings illustrate that functionally redundant ingested bacteria and earthworm-associated Tenericutes might be influenced by nutrient fluctuations in the gut and organic carbon richness of the earthworm diet.}, }
@article {pmid37128070, year = {2020}, author = {Vandeweyer, D and Lievens, B and Van Campenhout, L}, title = {Identification of bacterial endospores and targeted detection of foodborne viruses in industrially reared insects for food.}, journal = {Nature food}, volume = {1}, number = {8}, pages = {511-516}, pmid = {37128070}, issn = {2662-1355}, support = {141129//Agentschap Innoveren en Ondernemen (Flanders Innovation &amp; Entrepreneurship)/ ; PDM/18/159//KU Leuven (Katholieke Universiteit Leuven)/ ; }, abstract = {With edible insects being increasingly produced, food safety authorities have called for the determination of microbiological challenges posed to human health. Here, we find that the bacterial endospore fraction in industrially reared mealworm and cricket samples is largely comprised of Bacillus cereus group members that can pose insect or human health risks. Hepatitis A virus, hepatitis E virus and norovirus genogroup II were not detected in the sample collection, indicating a low food safety risk from these viral pathogens.}, }
@article {pmid36659680, year = {2019}, author = {Zheng, BX and Zhao, Y and Bi, QF and Zhou, GW and Wang, HJ and Hao, XL and Ding, K}, title = {How to disentangle microbially functional complexity: an insight from the network analysis of C, N, P and S cycling genes.}, journal = {Science bulletin}, volume = {64}, number = {16}, pages = {1129-1131}, doi = {10.1016/j.scib.2019.06.011}, pmid = {36659680}, issn = {2095-9281}, }
@article {pmid36280326, year = {2022}, author = {Narendrakumar, L and Ray, A}, title = {Respiratory tract microbiome and pneumonia.}, journal = {Progress in molecular biology and translational science}, volume = {192}, number = {1}, pages = {97-124}, doi = {10.1016/bs.pmbts.2022.07.002}, pmid = {36280326}, issn = {1878-0814}, mesh = {Humans ; *Microbiota ; Dysbiosis ; *Pneumonia ; *Respiratory Tract Infections/microbiology ; Lung ; }, abstract = {The respiratory system, like the gut, harbors a vast variety of microorganisms which include bacteria, viruses and fungi. The advent of next generation sequencing and multi-omic approaches has revealed the diversity and functional significances of microorganisms in the respiratory health. It has been identified that there has been a co-evolution of indigenous respiratory microbiota and the human immune system. However, an immune response is usually generated when the homeostasis of the microbiota is disturbed. The respiratory microbiome has been identified to be important in shaping the respiratory immunity. Gut microbiota and oral microbiota are also known to be pivotal in shaping the immune system of the respiratory tract and influence its microbial dynamics. Proteobacteria, Firmicutes, and Bacteroidetes have been identified to be predominant in the respiratory system. While, Streptococcus, Prevotella, Fusobacteria, and Veillonella forms the major part, potential pathogens, such as Haemophilus and Neisseria, also form a small fraction of the healthy lung microbiome. Dysbiosis of respiratory microbiome can lead to increased colonization of opportunistic pathogens that can lead to respiratory infections such as pneumonia. This chapter describes the microbial diversity of respiratory system and the role of respiratory microbiome during respiratory infections like pneumonia. The chapter also discusses few strategies that have been proved effective in preventing pneumonia.}, }
@article {pmid36275752, year = {2022}, author = {Xin, X and Wang, Q and Qing, J and Song, W and Gui, Y and Li, X and Li, Y}, title = {Th17 cells in primary Sjögren's syndrome negatively correlate with increased Roseburia and Coprococcus.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {974648}, pmid = {36275752}, issn = {1664-3224}, mesh = {Humans ; *Th17 Cells ; RNA, Ribosomal, 16S/genetics ; *Sjogren's Syndrome ; Galactose ; Peptidoglycan ; Bacteria/genetics ; Inflammation/complications ; Pyrimidines ; Amino Acids ; Glyoxylates ; Glucuronates ; Pentoses ; Butyrates ; }, abstract = {BACKGROUND: Dysbiosis of the gut microbiota is closely related to chronic systemic inflammation and autoimmunity, playing an essential role in the pathogenesis of primary Sjögren's syndrome (pSS). Abnormalities in the proportions of blood T lymphocyte subtype, that is Th17/Treg, were detected in pSS patients. We aimed to determine the associations between gut microbiota and Th17/Treg in pSS.<br><br>METHOD: 98 pSS patients and 105 healthy controls (NC) were enrolled between Dec 1, 2018, and Aug 31, 2019. The baseline information and clinical parameters on pSS patients and healthy controls were collected. 16S rRNA sequencing was performed to characterize the gut microbiome and identify gut microbes that are differentially abundant between patients and healthy controls. Lastly, associations between relative abundances of specific bacterial taxa in the gut and clinical outcome parameters were evaluated.<br><br>RESULTS: Patients with pSS show decreased gut microbial diversity and richness, decreased abundance of butyrate producing bacteria, such as Roseburia and Coprococcus, and increased abundance of other taxa, such as Eubacterium rectale and Roseburia inulinivorans. These bacteria are enriched with functions related to glycolytic and lipogenic, energy, substance, galactose, pentose metabolism pathways and glucuronate interconversions, decreased with functions related to peptidoglycan biosynthesis, pyrimidine metabolism pathways. An integrative analysis identified pSS-related specific bacterial taxa in the gut, for which the abundance of Eubacterium rectale is negatively correlated with Th17/Treg. Furthermore, the pathways of biosynthesis of secondary metabolites, biosynthesis of amino acids, peptidoglycan biosynthesis and pyrimidine, galactose, pentose, microbial metabolism in diverse environments, glyoxylate and dicarboxylate metabolism are associated with Treg or Th17/Treg.<br><br>CONCLUSIONS: Primary Sj&#xf6;gren's syndrome could lead to decreased gut microbial diversity and richness of intestinal flora in patients. The proportions of Th17 and Treg cells induced by microbiota were predictive pSS manifestations and accounted for the pSS severity.}, }
@article {pmid36274442, year = {2022}, author = {Tims, S and Marsaux, C and Pinto, A and Daly, A and Karall, D and Kuhn, M and Santra, S and Roeselers, G and Knol, J and MacDonald, A and Scholl-Bürgi, S}, title = {Altered gut microbiome diversity and function in patients with propionic acidemia.}, journal = {Molecular genetics and metabolism}, volume = {137}, number = {3}, pages = {308-322}, doi = {10.1016/j.ymgme.2022.09.012}, pmid = {36274442}, issn = {1096-7206}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Propionic Acidemia ; Propionates ; Feces/microbiology ; Butyrates ; }, abstract = {Propionic acidemia (PA) is an inherited metabolic disorder of propionate metabolism, where the gut microbiota may play a role in pathophysiology and therefore, represent a relevant therapeutic target. Little is known about the gut microbiota composition and activity in patients with PA. Although clinical practice varies between metabolic treatment centers, management of PA requires combined dietary and pharmaceutical treatments, both known to affect the gut microbiota. This study aimed to characterize the gut microbiota and its metabolites in fecal samples of patients with PA compared with healthy controls from the same household. Eight patients (aged 3-14y) and 8 controls (4-31y) were recruited from Center 1 (UK) and 7 patients (11-33y) and 6 controls (15-54y) from Center 2 (Austria). Stool samples were collected 4 times over 3 months, alongside data on dietary intakes and medication usage. Several microbial taxa differed between patients with PA and controls, particularly for Center 1, e.g., Proteobacteria levels were increased, whereas butyrate-producing genera, such as Roseburia and Faecalibacterium, were decreased. Most measured microbial metabolites were lower in patients with PA, and butyrate was particularly depleted in patients from Center 1. Furthermore, microbiota profile of these patients showed the lowest compositional and functional diversity, and lowest stability over 3 months. As the first study to map the gut microbiota of patients with PA, this work represents an important step forward for developing new therapeutic strategies to further improve PA clinical status. New dietary strategies should consider microbial propionate production as well as butyrate production and microbiota stability.}, }
@article {pmid36270682, year = {2022}, author = {Ahrodia, T and Das, S and Bakshi, S and Das, B}, title = {Structure, functions, and diversity of the healthy human microbiome.}, journal = {Progress in molecular biology and translational science}, volume = {191}, number = {1}, pages = {53-82}, doi = {10.1016/bs.pmbts.2022.07.003}, pmid = {36270682}, issn = {1878-0814}, mesh = {Humans ; *Microbiota ; Bacteria/genetics ; Metagenome ; *Gastrointestinal Microbiome ; Archaea ; }, abstract = {Taxonomic composition and functional potency of microbes associated with different parts of the human body have largely been explored by culture-independent metagenome sequencing. The diverse microbiota living throughout the human body is made up of thousands of microbial taxa from all three domains of life: Archaea, Bacteria, and Eukarya. Microbial load and functional potency in different body sites are well distinct and have minimal resemblance at higher taxonomic levels between the two habitats. The highest microbial load, diversity, and functional potency including biosynthesis of essential nutrients, chemical modifications of dietary components, and sources of immunomodulatory molecules, are found in the gut microbiome. However, the inter-individual diversity and dynamics of the human microbiome in a given body habitat vary greatly over time. Both environmental factors and host genetics contribute significantly to shaping microbial community structure and its stability. A basic understanding of native microbial compositions and their functional potency and stability in different parts of healthy humans living across geography will help us to identify disease-specific microbiota and develop potential microbiome-based therapeutics. Here, we updated our current understanding of the diversity, dynamics, and functional potency of microbiomes associated with different parts of the human body.}, }
@article {pmid36270678, year = {2022}, author = {Purohit, A and Alam, MJ and Kandiyal, B and Shalimar,  and Das, B and Banerjee, SK}, title = {Gut microbiome and non-alcoholic fatty liver disease.}, journal = {Progress in molecular biology and translational science}, volume = {191}, number = {1}, pages = {187-206}, doi = {10.1016/bs.pmbts.2022.07.004}, pmid = {36270678}, issn = {1878-0814}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Non-alcoholic Fatty Liver Disease/therapy/complications/microbiology ; Prebiotics ; Dysbiosis ; Fecal Microbiota Transplantation ; *Probiotics/therapeutic use ; }, abstract = {The human gastrointestinal tract (GIT) contains a dynamic and diverse collection of bacteria, archaea, and fungi termed the "gut microbiome." The gut microbiome has a major impact on the host during homeostasis and disease. The connection between both the host and the microbiome is complex, although its manipulation may assist prevent or treating a multitude of morbidities. These microorganisms play a critical role in the host's energy metabolism and homeostasis. According to new research, the microbes in the gastrointestinal tract play a substantial role in host health, and alterations in its composition and function might lead to the emergence of metabolic disorders like non-alcoholic fatty liver disease (NAFLD). The resilience of the GIT microbial ecology and its tolerance to perturbation are robust but not ideal. Several factors may disrupt the GIT microbiome's homeostasis leading to dysbiosis, characterized by an imbalanced equilibrium and perturbations in gut homeostasis. Irritable bowel disease (IBD), malnutrition, and metabolic disorders, such as NAFLD, have been associated with the dysbiotic gut microbiome. Recent evidence suggests that utilizing medications, prebiotics, probiotics, and fecal microbiota transplantation (FMT) to manipulate the microbiome could be a viable method for treating NAFLD.}, }
@article {pmid36270674, year = {2022}, author = {Das, B}, title = {An introduction to human microbiome.}, journal = {Progress in molecular biology and translational science}, volume = {191}, number = {1}, pages = {1-28}, doi = {10.1016/bs.pmbts.2022.06.026}, pmid = {36270674}, issn = {1878-0814}, mesh = {Humans ; *Microbiota ; Dysbiosis ; Bacteria ; Archaea ; Host Microbial Interactions ; }, abstract = {The microbiome is an assemblage of a complex community of microbes (bacteria, archaea, fungi, algae, protists, and viruses) and their biomolecules occupying a well-defined habitat in or on a living or non-living object. All the environmentally exposed surfaces of the human body are colonized with trillions of microbes from all three major domains of life, including bacteria, archea, and microscopic eukarya. However, the richness, abundance, and functional potency of microbial taxa living in different parts of the human body are distinct. The Presence of common microbial taxa in different body habitats is also very rare. With the recent development of next generation sequencing technologies, it has been established that the indigenous microbial community in the human body and their functional attributes within a given body habitat vary over time, between ethnic groups and health status of the host. Perturbation of homeostasis in community structures or functions due to any extrinsic factors can alter mutualistic host-microbe interactions and may lead to disease. In addition, the dysbiotic state of the microbiome can also affect the efficacy of therapeutics, prolong treatment duration and lead to undesired treatment outcomes. In this chapter, structure, functions, diversity and dynamics of human microbiome in health and diseases, factors that alter microbial composition, interactions between microbial taxa and xenobiotics, and therapeutic efficacy of drugs in dysbiotic conditions are highlighted.}, }
@article {pmid36270377, year = {2023}, author = {Evariste, L and Mouchet, F and Pinelli, E and Flahaut, E and Gauthier, L and Barret, M}, title = {Gut microbiota impairment following graphene oxide exposure is associated to physiological alterations in Xenopus laevis tadpoles.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 2}, pages = {159515}, doi = {10.1016/j.scitotenv.2022.159515}, pmid = {36270377}, issn = {1879-1026}, mesh = {Animals ; *Gastrointestinal Microbiome ; Larva ; *Graphite/toxicity ; Xenopus laevis ; *Microbiota ; Bacteria/genetics ; }, abstract = {Graphene-based nanomaterials such as graphene oxide (GO) possess unique properties triggering high expectations for the development of technological applications. Thus, GO is likely to be released in aquatic ecosystems. It is essential to evaluate its ecotoxicological potential to ensure a safe use of these nanomaterials. In amphibians, previous studies highlighted X. laevis tadpole growth inhibitions together with metabolic disturbances and genotoxic effects following GO exposure. As GO is known to exert bactericidal effects whereas the gut microbiota constitutes a compartment involved in host homeostasis regulation, it is important to determine if this microbial compartment constitutes a toxicological pathway involved in known GO-induced host physiological impairments. This study investigates the potential link between gut microbial communities and host physiological alterations. For this purpose, X. laevis tadpoles were exposed during 12 days to GO. Growth rate was monitored every 2 days and genotoxicity was assessed through enumeration of micronucleated erythrocytes. Genomic DNA was also extracted from the whole intestine to quantify gut bacteria and to analyze the community composition. GO exposure led to a dose dependent growth inhibition and genotoxic effects were detected following exposure to low doses. A transient decrease of the total bacteria was noticed with a persistent shift in the gut microbiota structure in exposed animals. Genotoxic effects were associated to gut microbiota remodeling characterized by an increase of the relative abundance of Bacteroides fragilis. The growth inhibitory effects would be associated to a shift in the Firmicutes/Bacteroidetes ratio while metagenome inference suggested changes in metabolic pathways and upregulation of detoxification processes. This work indicates that the gut microbiota compartment is a biological compartment of interest as it is integrative of host physiological alterations and should be considered for ecotoxicological studies as structural or functional impairments could lead to later life host fitness loss.}, }
@article {pmid36270363, year = {2023}, author = {Regueira, A and Turunen, R and Vuoristo, KS and Carballa, M and Lema, JM and Uusitalo, J and Mauricio-Iglesias, M}, title = {Model-aided targeted volatile fatty acid production from food waste using a defined co-culture microbial community.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 2}, pages = {159521}, doi = {10.1016/j.scitotenv.2022.159521}, pmid = {36270363}, issn = {1879-1026}, mesh = {Food ; Caproates ; Coculture Techniques ; *Refuse Disposal ; Fatty Acids, Volatile ; Butyrates ; *Microbiota ; Carbon ; Bioreactors ; Fermentation ; Hydrogen-Ion Concentration ; }, abstract = {The production of volatile fatty acids (VFA) is gaining momentum due to their central role in the emerging carboxylate platform. Particularly, the production of the longest VFA (from butyrate to caproate) is desired due to their increased economic value and easier downstream processing. While the use of undefined microbial cultures is usually preferred with organic waste streams, the use of defined microbial co-culture processes could tackle some of their drawbacks such as poor control over the process outcome, which often leads to low selectivity for the desired products. However, the extensive experimentation needed to design a co-culture system hinders the use of this technology. In this work, a workflow based on the combined use of mathematical models and wet experimentation is proposed to accelerate the design of novel bioprocesses. In particular, a co-culture consisting of Pediococcus pentosaceus and Megaphaera cerevisiae is used to target the production of high-value odd- and even‑carbon VFA. An unstructured kinetic model was developed, calibrated and used to design experiments with the goal of increasing the selectivity for the desired VFA, which were experimentally validated. In the case of even‑carbon VFA, the experimental validation showed an increase of 38 % in caproate yield and, in the case of enhanced odd‑carbon VFA experiments, the yield of butyrate and caproate diminished by 62 % and 94 %, respectively, while propionate became one of the main end products and valerate yield value increased from 0.007 to 0.085 gvalearte per gconsumed sugar. The workflow followed in this work proved to be a sound tool for bioprocess design due to its capacity to explore and design new experiments in silico in a fast way and ability to quickly adapt to new scenarios.}, }
@article {pmid36267243, year = {2022}, author = {Huang, W and Zhu, L and Song, W and Zhang, M and Teng, L and Wu, M}, title = {Crosstalk between the Gut and Brain in Ischemic Stroke: Mechanistic Insights and Therapeutic Options.}, journal = {Mediators of inflammation}, volume = {2022}, number = {}, pages = {6508046}, pmid = {36267243}, issn = {1466-1861}, mesh = {Humans ; Prebiotics ; *Ischemic Stroke ; Fecal Microbiota Transplantation ; *Probiotics/therapeutic use ; Brain/metabolism ; *Stroke/therapy/metabolism ; }, abstract = {There has been a significant amount of interest in the past two decades in the study of the evolution of the gut microbiota, its internal and external impacts on the gut, and risk factors for cerebrovascular disorders such as cerebral ischemic stroke. The network of bidirectional communication between gut microorganisms and their host is known as the microbiota-gut-brain axis (MGBA). There is mounting evidence that maintaining gut microbiota homeostasis can frequently enhance the effectiveness of ischemic stroke treatment by modulating immune, metabolic, and inflammatory responses through MGBA. To effectively monitor and cure ischemic stroke, restoring a healthy microbial ecology in the gut may be a critical therapeutic focus. This review highlights mechanistic insights on the MGBA in disease pathophysiology. This review summarizes the role of MGBA signaling in the development of stroke risk factors such as aging, hypertension, obesity, diabetes, and atherosclerosis, as well as changes in the microbiota in experimental or clinical populations. In addition, this review also examines dietary changes, the administration of probiotics and prebiotics, and fecal microbiota transplantation as treatment options for ischemic stroke as potential health benefits. It will become more apparent how the MGBA affects human health and disease with continuing advancements in this emerging field of biomedical sciences.}, }
@article {pmid36267180, year = {2022}, author = {Wang, M and Tu, Q}, title = {Effective data filtering is prerequisite for robust microbial association network construction.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1016947}, pmid = {36267180}, issn = {1664-302X}, abstract = {Microorganisms do not exist as individual population in the environment. Rather, they form complex assemblages that perform essential ecosystem functions and maintain ecosystem stability. Besides the diversity and composition of microbial communities, deciphering their potential interactions in the form of association networks has attracted many microbiologists and ecologists. Much effort has been made toward the methodological development for constructing microbial association networks. However, microbial profiles suffer dramatically from zero values, which hamper accurate association network construction. In this study, we investigated the effects of zero-value issues associated with microbial association network construction. Using the TARA Oceans microbial profile as an example, different zero-value-treatment approaches were comparatively investigated using different correlation methods. The results suggested dramatic variations of correlation coefficient values for differently treated microbial profiles. Most specifically, correlation coefficients among less frequent microbial taxa were more affected, whichever method was used. Negative correlation coefficients were more problematic and sensitive to network construction, as many of them were inferred from low-overlapped microbial taxa. Consequently, microbial association networks were greatly differed. Among various approaches, we recommend sequential calculation of correlation coefficients for microbial taxa pairs by excluding paired zero values. Filling missing values with pseudo-values is not recommended. As microbial association network analyses have become a widely used technique in the field of microbial ecology and environmental science, we urge cautions be made to critically consider the zero-value issues in microbial data.}, }
@article {pmid36266277, year = {2022}, author = {Sauvaitre, T and Van Landuyt, J and Durif, C and Roussel, C and Sivignon, A and Chalancon, S and Uriot, O and Van Herreweghen, F and Van de Wiele, T and Etienne-Mesmin, L and Blanquet-Diot, S}, title = {Role of mucus-bacteria interactions in Enterotoxigenic Escherichia coli (ETEC) H10407 virulence and interplay with human microbiome.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {86}, pmid = {36266277}, issn = {2055-5008}, mesh = {Humans ; *Enterotoxigenic Escherichia coli/physiology ; Interleukin-8/genetics ; Virulence ; Diarrhea ; Caco-2 Cells ; *Escherichia coli Infections/microbiology ; Travel ; *Microbiota ; Bacteria ; Mucus ; Mucins ; }, abstract = {The intestinal mucus layer has a dual role in human health constituting a well-known microbial niche that supports gut microbiota maintenance but also acting as a physical barrier against enteric pathogens. Enterotoxigenic Escherichia coli (ETEC), the major agent responsible for traveler's diarrhea, is able to bind and degrade intestinal mucins, representing an important but understudied virulent trait of the pathogen. Using a set of complementary in vitro approaches simulating the human digestive environment, this study aimed to describe how the mucus microenvironment could shape different aspects of the human ETEC strain H10407 pathophysiology, namely its survival, adhesion, virulence gene expression, interleukin-8 induction and interactions with human fecal microbiota. Using the TNO gastrointestinal model (TIM-1) simulating the physicochemical conditions of the human upper gastrointestinal (GI) tract, we reported that mucus secretion and physical surface sustained ETEC survival, probably by helping it to face GI stresses. When integrating the host part in Caco2/HT29-MTX co-culture model, we demonstrated that mucus secreting-cells favored ETEC adhesion and virulence gene expression, but did not impede ETEC Interleukin-8 (IL-8) induction. Furthermore, we proved that mucosal surface did not favor ETEC colonization in a complex gut microbial background simulated in batch fecal experiments. However, the mucus-specific microbiota was widely modified upon the ETEC challenge suggesting its role in the pathogen infectious cycle. Using multi-targeted in vitro approaches, this study supports the major role played by mucus in ETEC pathophysiology, opening avenues in the design of new treatment strategies.}, }
@article {pmid36265143, year = {2023}, author = {Zhu 朱墨, M and Duan, X and Cai, P and Qiu, Z and Li 李正男, Z}, title = {Genome Sequence Resource of Trichothecium roseum (ZM-Tr2021), the Causal Agent of Postharvest Pink Rot.}, journal = {Plant disease}, volume = {107}, number = {1}, pages = {205-209}, doi = {10.1094/PDIS-03-22-0655-A}, pmid = {36265143}, issn = {0191-2917}, mesh = {*Hypocreales ; *Ascomycota/genetics ; }, }
@article {pmid36262799, year = {2022}, author = {Faust, V and van Alen, TA and Op den Camp, HJM and Vlaeminck, SE and Ganigué, R and Boon, N and Udert, KM}, title = {Ammonia oxidation by novel "Candidatus Nitrosacidococcus urinae" is sensitive to process disturbances at low pH and to iron limitation at neutral pH.}, journal = {Water research X}, volume = {17}, number = {}, pages = {100157}, pmid = {36262799}, issn = {2589-9147}, abstract = {Acid-tolerant ammonia-oxidizing bacteria (AOB) can open the door to new applications, such as partial nitritation at low pH. However, they can also be problematic because chemical nitrite oxidation occurs at low pH, leading to the release of harmful nitrogen oxide gases. In this publication, the role of acid-tolerant AOB in urine treatment was explored. On the one hand, the technical feasibility of ammonia oxidation under acidic conditions for source-separated urine with total nitrogen concentrations up to 3.5 g-N L[-1] was investigated. On the other hand, the abundance and growth of acid-tolerant AOB at more neutral pH was explored. Under acidic conditions (pH of 5), ammonia oxidation rates of 500 mg-N L[-1] d[-1] and 10 g-N g-VSS[-1] d[-1] were observed, despite high concentrations of 15 mg-N L[-1] of the AOB-inhibiting compound nitrous acid and low concentration of 0.04 mg-N L[-1] of the substrate ammonia. However, ammonia oxidation under acidic conditions was very sensitive to process disturbances. Even short periods of less than 12 h without oxygen or without influent resulted in a complete cessation of ammonia oxidation with a recovery time of up to two months, which is a problem for low maintenance applications such as decentralized treatment. Furthermore, undesirable nitrogen losses of about 10% were observed. Under acidic conditions, a novel AOB strain was enriched with a relative abundance of up to 80%, for which the name "Candidatus (Ca.) Nitrosacidococcus urinae" is proposed. While Nitrosacidococcus members were present only to a small extent (0.004%) in urine nitrification reactors operated at pH values between 5.8 and 7, acid-tolerant AOB were always enriched during long periods without influent, resulting in an uncontrolled drop in pH to as low as 2.5. Long-term experiments at different pH values showed that the activity of "Ca. Nitrosacidococcus urinae" decreased strongly at a pH of 7, where they were also outcompeted by the acid-sensitive AOB Nitrosomonas halophila. The experiment results showed that the decreased activity of "Ca. Nitrosacidococcus urinae" correlated with the limited availability of dissolved iron at neutral pH.}, }
@article {pmid36261994, year = {2022}, author = {De La Fuente, MJ and De la Iglesia, R and Farias, L and Glasner, B and Torres-Rojas, F and Muñoz, D and Daims, H and Lukumbuzya, M and Vargas, IT}, title = {Enhanced nitrogen and carbon removal in natural seawater by electrochemical enrichment in a bioelectrochemical reactor.}, journal = {Journal of environmental management}, volume = {323}, number = {}, pages = {116294}, doi = {10.1016/j.jenvman.2022.116294}, pmid = {36261994}, issn = {1095-8630}, mesh = {Nitrogen/chemistry ; Denitrification ; Nitrification ; Wastewater ; Carbon ; Nitrates ; Bioreactors ; RNA, Ribosomal, 16S ; Nitrites ; *Graphite ; In Situ Hybridization, Fluorescence ; *Ammonium Compounds ; Seawater ; }, abstract = {Municipal and industrial wastewater discharges in coastal and marine environments are of major concern due to their high carbon and nitrogen loads and the resulted phenomenon of eutrophication. Bioelectrochemical reactors (BERs) for simultaneous nitrogen and carbon removal have gained attention owing to their cost efficiency and versatility, as well as the possibility of electrochemical enrich specific groups. This study presented a scalable two-chamber BERs using graphite granules as electrode material. BERs were inoculated and operated for 37 days using natural seawater with high concentrations of ammonium and acetate. The BERs demonstrated a maximum current density of 0.9 A m[-3] and removal rates of 7.5 mg NH4[+]-N L[-1] d[-1] and 99.5 mg L[-1] d[-1] for total organic carbon (TOC). Removals observed for NH4[+]-N and TOC were 96.2% and 68.7%, respectively. The results of nutrient removal (i.e., ammonium, nitrate, nitrite and TOC) and microbial characterization (i.e., next-generation sequencing of the 16S rRNA gene and fluorescence in situ hybridization) showed that BERs operated with a poised cathode at -260 mV (vs. Ag/AgCl) significantly enriched nitrifying microorganisms in the anode and denitrifying microorganisms and planctomycetes in the cathode. Interestingly, the electrochemical enrichment did not increase the total number of microorganisms in the formed biofilms but controlled their composition. Thus, this work shows the first successful attempt to electrochemically enrich marine nitrifying and denitrifying microorganisms and presents a technique to accelerate the start-up process of BERs to remove dissolved inorganic nitrogen and total organic carbon from seawater.}, }
@article {pmid36259773, year = {2022}, author = {Eliades, SJ and Colston, TJ and Siler, CD}, title = {Gut microbial ecology of Philippine gekkonids: ecoevolutionary effects on microbiome compositions.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {12}, pages = {}, pmid = {36259773}, issn = {1574-6941}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; Philippines ; *Microbiota/genetics ; Symbiosis ; }, abstract = {Given the rapidly changing landscapes of habitats across the globe, a sound understanding of host-associated microbial communities and the ecoevolutionary forces that shape them is needed to assess general organismal adaptability. Knowledge of the symbiotic endogenous microbiomes of most reptilian species worldwide remains limited. We sampled gut microbiomes of geckos spanning nine species and four genera in the Philippines to (i) provide baseline data on gut microbiota in these host species, (ii) test for significant associations between host phylogenetic relationships and observed microbial assemblages, potentially indicative of phylosymbiosis, and (iii) identify correlations between multiple ecoevolutionary factors (e.g. species identity, habitat tendencies, range extents, and maximum body sizes) and gut microbiomes in Philippine gekkonids. We recovered no significant association between interspecific host genetic distances and observed gut microbiomes, providing limited evidence for phylosymbiosis in this group. Philippine gekkonid microbiomes were associated most heavily with host species identity, though marked variation among conspecifics at distinct sampling sites indicates that host locality influences gut microbiomes as well. Interestingly, individuals grouped as widespread and microendemic regardless of host species identity displayed significant differences in alpha and beta diversity metrics examined, likely driven by differences in rare OTU presence between groups. These results provide much needed insight in host-associated microbiomes in wild reptiles and the ecoevolutionary forces that structure such communities.}, }
@article {pmid36259715, year = {2022}, author = {Conacher, CG and Naidoo-Blassoples, RK and Rossouw, D and Bauer, FF}, title = {A Transcriptomic Analysis of Higher-Order Ecological Interactions in a Eukaryotic Model Microbial Ecosystem.}, journal = {mSphere}, volume = {7}, number = {6}, pages = {e0043622}, pmid = {36259715}, issn = {2379-5042}, mesh = {*Saccharomyces cerevisiae/genetics/metabolism ; *Wine ; Ecosystem ; Transcriptome ; Gene Expression Profiling ; }, abstract = {Nonlinear ecological interactions within microbial ecosystems and their contribution to ecosystem functioning remain largely unexplored. Higher-order interactions, or interactions in systems comprised of more than two members that cannot be explained by cumulative pairwise interactions, are particularly understudied, especially in eukaryotic microorganisms. The wine fermentation ecosystem presents an ideal model to study yeast ecosystem establishment and functioning. Some pairwise ecological interactions between wine yeast species have been characterized, but very little is known about how more complex, multispecies systems function. Here, we evaluated nonlinear ecosystem properties by determining the transcriptomic response of Saccharomyces cerevisiae to pairwise versus tri-species culture. The transcriptome revealed that genes expressed during pairwise coculture were enriched in the tri-species data set but also that just under half of the data set comprised unique genes attributed to a higher-order response. Through interactive protein-association network visualizations, a holistic cell-wide view of the gene expression data was generated, which highlighted known stress response and metabolic adaptation mechanisms which were specifically activated during tri-species growth. Further, extracellular metabolite data corroborated that the observed differences were a result of a biotic stress response. This provides exciting new evidence showing the presence of higher-order interactions within a model microbial ecosystem. IMPORTANCE Higher-order interactions are one of the major blind spots in our understanding of microbial ecosystems. These systems remain largely unpredictable and are characterized by nonlinear dynamics, in particular when the system is comprised of more than two entities. By evaluating the transcriptomic response of S. cerevisiae to an increase in culture complexity from a single species to two- and three-species systems, we were able to confirm the presence of a unique response in the more complex setting that could not be explained by the responses observed at the pairwise level. This is the first data set that provides molecular targets for further analysis to explain unpredictable ecosystem dynamics in yeast.}, }
@article {pmid36258041, year = {2023}, author = {Wang, J and Shi, X and Tan, Y and Wang, L and Zhang, G}, title = {Elevated O3 Exerts Stronger Effects than Elevated CO2 on the Functional Guilds of Fungi, but Collectively Increase the Structural Complexity of Fungi in a Paddy Soil.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1096-1106}, pmid = {36258041}, issn = {1432-184X}, support = {42077209//National Natural Science Foundation of China/ ; 32071631//National Natural Science Foundation of China/ ; 41907022//National Natural Science Foundation of China/ ; 31901165//National Natural Science Foundation of China/ ; 2020J01186//Natural Science Foundation of Fujian Province/ ; 2020J01138//Natural Science Foundation of Fujian Province/ ; }, mesh = {*Soil ; Carbon Dioxide ; Biomass ; Fungi/genetics ; Carbon ; Soil Microbiology ; *Ozone/pharmacology ; }, abstract = {Global climate change is characterized by altered global atmospheric composition, including elevated CO2 and O3, with important consequences on soil fungal communities. However, the function and community composition of soil fungi in response to elevated CO2 together with elevated O3 in paddy soils remain largely unknown. Here we used twelve open-top chamber facilities (OTCs) to evaluate the interactive effect of CO2 (+ 200 ppm) and O3 (+ 40 ppb) on the diversity, gene abundance, community structure, and functional composition of soil fungi during the growing seasons of two rice cultivars (Japonica, Wuyujing 3 vs. Nangeng 5055) in a Chinese paddy soil. Elevated CO2 and O3 showed no individual or combined effect on the gene abundance or relative abundance of soil fungi, but increased structural complexity of soil fungal communities, indicating that elevated CO2 and/or O3 promoted the competition of species-species interactions. When averaged both cultivars, elevated CO2 showed no individual effect on the diversity or abundance of functional guilds of soil fungi. By contrast, elevated O3 significantly reduced the relative abundance and diversity of symbiotrophic fungi by an average of 47.2% and 39.1%, respectively. Notably, elevated O3 exerts stronger effects on the functional processes of fungal communities than elevated CO2. The structural equation model revealed that elevated CO2 and/or O3 indirectly affected the functional composition of soil fungi through community structure and diversity of soil fungi. Root C/N and soil environmental parameters were identified as the top direct predictors for the community structure of soil fungi. Furthermore, significant correlations were identified between saprotrophic fungi and root biomass, symbiotrophic fungi and root carbon, the pathotroph-symbiotroph and soil pH, as well as pathotroph-saprotroph-symbiotroph and soil microbial biomass carbon. These results suggest that climatic factors substantially affected the functional processes of soil fungal, and threatened soil function and food production, highlighting the detrimental impacts of high O3 on the function composition of soil biota.}, }
@article {pmid36257429, year = {2023}, author = {Chen, H and Liu, K and Yang, E and Chen, J and Gu, Y and Wu, S and Yang, M and Wang, H and Wang, D and Li, H}, title = {A critical review on microbial ecology in the novel biological nitrogen removal process: Dynamic balance of complex functional microbes for nitrogen removal.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 2}, pages = {159462}, doi = {10.1016/j.scitotenv.2022.159462}, pmid = {36257429}, issn = {1879-1026}, mesh = {*Nitrogen ; *Denitrification ; Acyl-Butyrolactones ; Quorum Sensing ; Bacteria ; }, abstract = {The novel biological nitrogen removal process has been extensively studied for its high nitrogen removal efficiency, energy efficiency, and greenness. A successful novel biological nitrogen removal process has a stable microecological equilibrium and benign interactions between the various functional bacteria. However, changes in the external environment can easily disrupt the dynamic balance of the microecology and affect the activity of functional bacteria in the novel biological nitrogen removal process. Therefore, this review focuses on the microecology in existing the novel biological nitrogen removal process, including the growth characteristics of functional microorganisms and their interactions, together with the effects of different influencing factors on the evolution of microbial communities. This provides ideas for achieving a stable dynamic balance of the microecology in a novel biological nitrogen removal process. Furthermore, to investigate deeply the mechanisms of microbial interactions in novel biological nitrogen removal process, this review also focuses on the influence of quorum sensing (QS) systems on nitrogen removal microbes, regulated by which bacteria secrete acyl homoserine lactones (AHLs) as signaling molecules to regulate microbial ecology in the novel biological nitrogen removal process. However, the mechanisms of action of AHLs on the regulation of functional bacteria have not been fully determined and the composition of QS system circuits requires further investigation. Meanwhile, it is necessary to further apply molecular analysis techniques and the theory of systems ecology in the future to enhance the exploration of microbial species and ecological niches, providing a deeper scientific basis for the development of a novel biological nitrogen removal process.}, }
@article {pmid36257158, year = {2022}, author = {Yang, Y and Lu, Z and Azari, M and Kartal, B and Du, H and Cai, M and Herbold, CW and Ding, X and Denecke, M and Li, X and Li, M and Gu, JD}, title = {Discovery of a new genus of anaerobic ammonium oxidizing bacteria with a mechanism for oxygen tolerance.}, journal = {Water research}, volume = {226}, number = {}, pages = {119165}, doi = {10.1016/j.watres.2022.119165}, pmid = {36257158}, issn = {1879-2448}, mesh = {*Ammonium Compounds/metabolism ; Anaerobiosis ; Catalase ; Nitrates/metabolism ; Oxygen/metabolism ; Bacteria, Anaerobic/genetics/metabolism ; Oxidation-Reduction ; Bacteria/metabolism ; }, abstract = {In the past 20 years, there has been a major stride in understanding the core mechanism of anaerobic ammonium-oxidizing (anammox) bacteria, but there are still several discussion points on their survival strategies. Here, we discovered a new genus of anammox bacteria in a full-scale wastewater-treating biofilm system, tentatively named "Candidatus Loosdrechtia aerotolerans". Next to genes of all core anammox metabolisms, it encoded and transcribed genes involved in the dissimilatory nitrate reduction to ammonium (DNRA), which coupled to oxidation of small organic acids, could be used to replenish ammonium and sustain their metabolism. Surprisingly, it uniquely harbored a new ferredoxin-dependent nitrate reductase, which has not yet been found in any other anammox genome and might confer a selective advantage to it in nitrate assimilation. Similar to many other microorganisms, superoxide dismutase and catalase related to oxidative stress resistance were encoded and transcribed by "Ca. Loosdrechtia aerotolerans". Interestingly, bilirubin oxidase (BOD), likely involved in oxygen resistance of anammox bacteria under fluctuating oxygen concentrations, was identified in "Ca. Loosdrechtia aerotolerans" and four Ca. Brocadia genomes, and its activity was demonstrated using purified heterologously expressed proteins. A following survey of oxygen-active proteins in anammox bacteria revealed the presence of other previously undetected oxygen defense systems. The novel cbb3-type cytochrome c oxidase and bifunctional catalase-peroxidase may confer a selective advantage to Ca. Kuenenia and Ca. Scalindua that face frequent changes in oxygen concentrations. The discovery of this new genus significantly broadens our understanding of the ecophysiology of anammox bacteria. Furthermore, the diverse oxygen tolerance strategies employed by distinct anammox bacteria advance our understanding of their niche adaptability and provide valuable insight for the operation of anammox-based wastewater treatment systems.}, }
@article {pmid36255374, year = {2022}, author = {Castillo, DJ and Dithugoe, CD and Bezuidt, OK and Makhalanyane, TP}, title = {Microbial ecology of the Southern Ocean.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {11}, pages = {}, doi = {10.1093/femsec/fiac123}, pmid = {36255374}, issn = {1574-6941}, mesh = {*Ecosystem ; Seawater/microbiology ; Phytoplankton ; Carbon Cycle ; *Microbiota ; Oceans and Seas ; }, abstract = {The Southern Ocean (SO) distributes climate signals and nutrients worldwide, playing a pivotal role in global carbon sequestration. Microbial communities are essential mediators of primary productivity and carbon sequestration, yet we lack a comprehensive understanding of microbial diversity and functionality in the SO. Here, we examine contemporary studies in this unique polar system, focusing on prokaryotic communities and their relationships with other trophic levels (i.e. phytoplankton and viruses). Strong seasonal variations and the characteristic features of this ocean are directly linked to community composition and ecosystem functions. Specifically, we discuss characteristics of SO microbial communities and emphasise differences from the Arctic Ocean microbiome. We highlight the importance of abundant bacteria in recycling photosynthetically derived organic matter. These heterotrophs appear to control carbon flux to higher trophic levels when light and iron availability favour primary production in spring and summer. Conversely, during winter, evidence suggests that chemolithoautotrophs contribute to prokaryotic production in Antarctic waters. We conclude by reviewing the effects of climate change on marine microbiota in the SO.}, }
@article {pmid36252671, year = {2023}, author = {Wang, Z and Li, K and Shen, X and Yan, F and Zhao, X and Xin, Y and Ji, L and Xiang, Q and Xu, X and Li, D and Ran, J and Xu, X and Chen, Q}, title = {Soil nitrogen substances and denitrifying communities regulate the anaerobic oxidation of methane in wetlands of Yellow River Delta, China.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 2}, pages = {159439}, doi = {10.1016/j.scitotenv.2022.159439}, pmid = {36252671}, issn = {1879-1026}, mesh = {*Methane ; *Wetlands ; Nitrogen ; Anaerobiosis ; Soil ; Rivers ; Oxidation-Reduction ; }, abstract = {Anaerobic oxidation of methane (AOM) in wetland soils is widely recognized as a key sink for the greenhouse gas methane (CH4). The occurrence of this reaction is influenced by several factors, but the exact process and related mechanism of this reaction remain unclear, due to the complex interactions between multiple influencing factors in nature. Therefore, we investigated how environmental and microbial factors affect AOM in wetlands using laboratory incubation methods combined with molecular biology techniques. The results showed that wetland AOM was associated with a variety of environmental factors and microbial factors. The environmental factors include such as vegetation, depth, hydrogen ion concentration (pH), oxidation-reduction potential (ORP), electrical conductivity (EC), total nitrogen (TN), nitrate (NO3[-]), sulfate (SO4[2-]), and nitrous oxide (N2O) flux, among them, soil N substances (TN, NO3[-], N2O) have essential regulatory roles in the AOM process, while NO3[-] and N2O may be the key electron acceptors driving the AOM process under the coexistence of multiple electron acceptors. Moreover, denitrification communities (narG, nirS, nirK, nosZI, nosZII) and anaerobic methanotrophic (ANME-2d) were identified as important functional microorganisms affecting the AOM process, which is largely regulated by the former. In the environmental context of growing global anthropogenic N inputs to wetlands, these findings imply that N cycle-mediated AOM processes are a more important CH4 sink for controlling global climate change. This studying contributes to the knowledge and prediction of wetland CH4 biogeochemical cycling and provides a microbial ecology viewpoint on the AOM response to global environmental change.}, }
@article {pmid36252516, year = {2022}, author = {Calatayud, M and Xiong, C and Selma-Royo, M and van de Wiele, T}, title = {Arsenolipids reduce butyrate levels and influence human gut microbiota in a donor-dependent way.}, journal = {Ecotoxicology and environmental safety}, volume = {246}, number = {}, pages = {114175}, doi = {10.1016/j.ecoenv.2022.114175}, pmid = {36252516}, issn = {1090-2414}, support = {I 2412/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Butyrates/pharmacology ; *Arsenic/toxicity ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; }, abstract = {Arsenolipids are organic arsenic species with variable toxicity. Accurate assessment of the risks derived from arsenic-contaminated seafood intake requires studying the interplay between arsenolipids and the human gut microbiota. This research used the in vitro mucosal simulator of the human intestinal microbial ecosystem (M-SHIME) to assess the effect of defined chemical standards of arsenolipids (AsFA 362 and AsHC 332) on a simulated healthy human gut microbiota (n = 4). Microbial-derived metabolites were quantified by gas chromatography and microbiota structure was characterized by 16S rRNA gene sequencing. A specific reduction in butyrate production (control=5.28 ± 0.3 mM; AsFAs=4.56 ± 0.4 mM; AsHC 332=4.4 ± 0.6 mM, n = 4 donors), concomitant with a reduction in the abundance of Lachnospiraceae UCG-004 group and the Faecalibacterium genus was observed, albeit in a donor-dependent manner. Furthermore, an increase in Escherichia/Shigella, Proteobacteria and Fusobacterium abundance was observed after arsenolipid treatments, depending on individual microbiota background. These alterations in microbial functionality and microbial community structure suggest a detrimental effect of arsenolipids intake towards the commensal gut microbiome, and consequently, on human health.}, }
@article {pmid36251278, year = {2022}, author = {Ross, DE and Lipus, D and Gulliver, D}, title = {Predominance of Methanomicrobiales and diverse hydrocarbon-degrading taxa in the Appalachian coalbed biosphere revealed through metagenomics and genome-resolved metabolisms.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {5984-5997}, doi = {10.1111/1462-2920.16251}, pmid = {36251278}, issn = {1462-2920}, mesh = {*Methanomicrobiales/metabolism ; *Metagenomics ; Metagenome ; Hydrocarbons/metabolism ; Methane/metabolism ; Bacteria ; }, abstract = {Coalbed deposits are a unique subsurface environment and represent an underutilized resource for methane generation. Microbial communities extant in coalbed deposits are responsible for key subsurface biogeochemical cycling and could be utilized to enhance methane production in areas where existing gas wells have depleted methane stores, or in coalbeds that are unmined, or conversely be utilized for mitigation of methane release. Here we utilize metagenomics and metagenome-assembled genomes (MAGs) to identify extant microbial lineages and genome-resolved microbial metabolisms of coalbed produced water, which has not yet been explored in the Appalachian Basin (AppB). Our analyses resulted in the recovery of over 40 MAGs from 8 coalbed methane wells. The most commonly identified taxa among samples were hydrogenotrophic methanogens from the order Methanomicrobiales and these dominant MAGs were highly similar to one another. Conversely, low-abundance coalbed bacterial populations were taxonomically and functionally diverse, mostly belonging to a variety of Proteobacteria classes, and encoding various hydrocarbon solubilization and degradation pathways. The data presented herein provides novel insights into AppB coalbed microbial ecology, and our findings provide new perspectives on underrepresented Methanocalculus species and low-relative abundance bacterial assemblages in coalbed environments, and their potential roles in stimulation or mitigation of methane release.}, }
@article {pmid36246995, year = {2022}, author = {Mörkl, S and Oberascher, A and Tatschl, JM and Lackner, S and Bastiaanssen, TFS and Butler, MI and Moser, M and Frühwirth, M and Mangge, H and Cryan, JF and Dinan, TG and Holasek, SJ}, title = {Cardiac vagal activity is associated with gut-microbiome patterns in women-An exploratory pilot study.}, journal = {Dialogues in clinical neuroscience}, volume = {24}, number = {1}, pages = {1-9}, pmid = {36246995}, issn = {1958-5969}, mesh = {Female ; *Gastrointestinal Microbiome/physiology ; Humans ; Interleukin-6 ; *Microbiota ; Pilot Projects ; }, abstract = {INTRODUCTION: A functional reciprocity between the gut microbiome and vagal nerve activity has been suggested, however, human studies addressing this phenomenon are limited.<br><br>METHODS: Twenty-four-hour cardiac vagal activity (CVA) was assessed from 73 female participants (aged 24.5&#x2009;&#xb1;&#x2009;4.3&#x2009;years). Additionally, stool samples were subjected to 16SrRNA gene analysis (V1-V2). Quantitative Insights Into Microbial Ecology (QIIME) was used to analyse microbiome data. Additionally, inflammatory parameters (such as CRP and IL-6) were derived from serum samples.<br><br>RESULTS: Daytime CVA correlated significantly with gut microbiota diversity (r sp&#x2009;=&#x2009;0.254, p&#x2009;=&#x2009;0.030), CRP (r sp&#x2009;=&#x2009;-0.348, p&#x2009;=&#x2009;0.003), and IL-6 (r sp&#x2009;=&#x2009;-0.320, p&#x2009;=&#x2009;0.006). When the group was divided at the median of 24&#x2009;h CVA (Mdn = 1.322), the following features were more abundant in the high CVA group: Clostridia (Linear discriminant analysis effect size (LDA)&#x2009;=&#x2009;4.195, p&#x2009;=&#x2009;0.029), Clostridiales (LDA = 4.195, p&#x2009;=&#x2009;0.029), Lachnospira (LDA = 3.489, p&#x2009;=&#x2009;0.004), Ruminococcaceae (LDA = 4.073, p&#x2009;=&#x2009;0.010), Faecalibacterium (LDA = 3.982, p&#x2009;=&#x2009;0.042), Lactobacillales (LDA = 3.317, p&#x2009;=&#x2009;0.029), Bacilli (LDA = 3.294, p&#x2009;=&#x2009;0.0350), Streptococcaceae (LDA = 3.353, p&#x2009;=&#x2009;0.006), Streptococcus (LDA = 3.332, p&#x2009;=&#x2009;0.011). Based on Dirichlet multinomial mixtures two enterotypes could be detected, which differed significantly in CVA, age, BMI, CRP, IL-6, and diversity.<br><br>CONCLUSIONS: As an indicator of gut-brain communication, gut microbiome analysis could be extended by measurements of CVA to enhance our understanding of signalling via microbiota-gut-brain-axis and its alterations through psychobiotics.}, }
@article {pmid36243459, year = {2022}, author = {Pinnell, LJ and Morley, PS}, title = {The Microbial Ecology of Liver Abscesses in Cattle.}, journal = {The Veterinary clinics of North America. Food animal practice}, volume = {38}, number = {3}, pages = {367-381}, doi = {10.1016/j.cvfa.2022.08.004}, pmid = {36243459}, issn = {1558-4240}, mesh = {Animals ; Bacteroidetes/genetics ; Cattle ; *Cattle Diseases ; Humans ; *Liver Abscess/veterinary ; *Microbiota/genetics ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Emerging evidence regarding the microbiome of liver abscesses (LAs) and the gastrointestinal tract of cattle suggests that a reexamination of the etiopathogenesis of LAs is warranted. Microbiome studies using 16S rRNA gene sequencing have demonstrated that LAs are highly polymicrobial, and hundreds of bacterial taxa are typically found in these lesions at slaughter. Fusobacteria and Bacteroidetes are equally dominant phyla within LAs, followed by Proteobacteria. The gut-liver axis (ie, bidirectional crosstalk between the gut and liver) is linked with a variety of liver diseases in humans, and investigation of host-microbiome interactions in cattle may lead to improved methods of prevention.}, }
@article {pmid36242623, year = {2023}, author = {Li, W and Li, X and Wang, W and Zhang, S and Cui, J and Peng, Y and Zhao, Y}, title = {Impact of Sulfoxaflor Exposure on Bacterial Community and Developmental Performance of the Predatory Ladybeetle Propylea japonica.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1226-1239}, pmid = {36242623}, issn = {1432-184X}, mesh = {Animals ; *Insecticides/pharmacology ; Ecosystem ; *Coleoptera ; Larva ; Bacteria/genetics ; }, abstract = {Insects maintain a vast number of symbiotic bacteria, and these symbionts play key roles in the hosts' life processes. Propylea japonica (Coleoptera: Coccinellidae) is an abundant and widespread ladybeetle in agricultural fields in Asia. Both larvae and adults of P. japonica are likely to be exposed to insecticide residue in the field during their predatory activity. Sulfoxaflor is a highly powerful insecticide that has strong efficacy in controlling sap-sucking pests. To date, there have been several studies on the acute and long-term toxicity of sulfoxaflor to insects, but few studies have reported the impact of sulfoxaflor on the predators' micro-ecosystems. This study was to determine the impact of sulfoxaflor on the symbiotic bacteria and developmental performance of P. japonica. In the present study, two concentrations (1 mg/L and 5 mg/L) and two exposure periods (1 day and 5 days) were set for P. japonica under sulfoxaflor exposure. The survival rate, developmental duration, pupation rate, emergence rate, and body weight of P. japonica were examined. Moreover, the bacterial community of P. japonica was investigated by high-throughput 16S ribosomal RNA gene sequencing. Our results indicated that bacterial community of P. japonica was mainly composed of Staphylococcus, Pantoea, Acinetobacter, Rhodococcus, and Ralstonia at the genus level. The bacterial community of P. japonica in 1 mg/L and 5 mg/L sulfoxaflor groups was significantly altered on day 1, compared with that in control group. The results also showed that the larval duration was significantly prolonged but the pupal duration was significantly shortened in both sulfoxaflor groups. Meanwhile, the pupation and emergence rate was not significantly changed, but the body weights of adults were significantly decreased in both sulfoxaflor groups. Our study will provide a new perspective for evaluating the safety of pesticides to beneficial arthropods.}, }
@article {pmid36239777, year = {2023}, author = {Tian, C and Lv, Y and Yang, Z and Zhang, R and Zhu, Z and Ma, H and Li, J and Zhang, Y}, title = {Microbial Community Structure and Metabolic Potential at the Initial Stage of Soil Development of the Glacial Forefields in Svalbard.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {933-946}, pmid = {36239777}, issn = {1432-184X}, support = {41676177//National Natural Science Foundation of China/ ; 41921006//National Natural Science Foundation of China/ ; 41676175//National Natural Science Foundation of China/ ; 41676188//National Natural Science Foundation of China/ ; SL2020MS022//Oceanic Interdisciplinary Program of Shanghai Jiao Tong University/ ; 21TQ1400201//Shanghai Pilot Program for Basic Research of Shanghai Jiao Tong University/ ; }, mesh = {*Soil/chemistry ; Svalbard ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota/genetics ; Ice Cover/microbiology ; Soil Microbiology ; }, abstract = {Microbial communities have been identified as the primary inhabitants of Arctic forefields. However, the metabolic potential of microbial communities in these newly exposed soils remains underexplored due to limited access. Here, we sampled the very edge of the glacial forefield in Svalbard and performed the 16S rRNA genes and metagenomic analysis to illustrate the ecosystem characteristics. Burkholderiales and Micrococcales were the dominant bacterial groups at the initial stage of soil development of glacial forefields. 214 metagenome-assembled genomes were recovered from glacier forefield microbiome datasets, including only 2 belonging to archaea. Analysis of these metagenome-assembled genomes revealed that 41% of assembled genomes had the genetic potential to use nitrate and nitrite as electron acceptors. Metabolic pathway reconstruction for these microbes suggested versatility for sulfide and thiosulfate oxidation, H2 and CO utilization, and CO2 fixation. Our results indicate the importance of anaerobic processes in elemental cycling in the glacial forefields. Besides, a range of genes related to adaption to low temperature and other stresses were detected, which revealed the presence of diverse mechanisms of adaption to the extreme environment of Svalbard. This research provides ecological insight into the initial stage of the soil developed during the retreating of glaciers.}, }
@article {pmid36239764, year = {2022}, author = {Nissen, L and Aniballi, C and Casciano, F and Elmi, A and Ventrella, D and Zannoni, A and Gianotti, A and Bacci, ML}, title = {Maternal amoxicillin affects piglets colon microbiota: microbial ecology and metabolomics in a gut model.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {22}, pages = {7595-7614}, pmid = {36239764}, issn = {1432-0614}, mesh = {Animals ; Swine ; Female ; *Gastrointestinal Microbiome ; Amoxicillin/pharmacology ; Colon ; *Microbiota ; Metabolomics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The first weeks of life represent a crucial stage for microbial colonization of the piglets' gastrointestinal tract. Newborns' microbiota is unstable and easily subject to changes under stimuli or insults. Nonetheless, the administration of antibiotics to the sow is still considered as common practice in intensive farming for pathological conditions in the postpartum. Therefore, transfer of antibiotic residues through milk may occurs, affecting the piglets' colon microbiota. In this study, we aimed to extend the knowledge on antibiotic transfer through milk, employing an in vitro dedicated piglet colon model (MICODE-Multi Unit In vitro Colon Model). The authors' focus was set on the shifts of the piglets' microbiota composition microbiomics (16S r-DNA MiSeq and qPCR-quantitative polymerase chain reaction) and on the production of microbial metabolites (SPME GC/MS-solid phase micro-extraction gas chromatography/mass spectrometry) in response to milk with different concentrations of amoxicillin. The results showed an effective influence of amoxicillin in piglets' microbiota and metabolites production; however, without altering the overall biodiversity. The scenario is that of a limitation of pathogens and opportunistic taxa, e.g., Staphylococcaceae and Enterobacteriaceae, but also a limitation of commensal dominant Lactobacillaceae, a reduction in commensal Ruminococcaceae and a depletion in beneficial Bifidobactericeae. Lastly, an incremental growth of resistant species, such as Enterococcaceae or Clostridiaceae, was observed. To the authors' knowledge, this study is the first evaluating the impact of antibiotic residues towards the piglets' colon microbiota in an in vitro model, opening the way to include such approach in a pipeline of experiments where a reduced number of animals for testing is employed. KEY POINTS: • Piglet colon model to study antibiotic transfer through milk. • MICODE resulted a robust and versatile in vitro gut model. • Towards the "3Rs" Principles to replace, reduce and refine the use of animals used for scientific purposes (Directive 2010/63/UE).}, }
@article {pmid36238597, year = {2022}, author = {Sinclair, P and Longyear, J and Reynolds, K and Finnie, AA and Brackley, CA and Carballo-Pacheco, M and Allen, RJ}, title = {A computational model for microbial colonization of an antifouling surface.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {920014}, pmid = {36238597}, issn = {1664-302X}, abstract = {Biofouling of marine surfaces such as ship hulls is a major industrial problem. Antifouling (AF) paints delay the onset of biofouling by releasing biocidal chemicals. We present a computational model for microbial colonization of a biocide-releasing AF surface. Our model accounts for random arrival from the ocean of microorganisms with different biocide resistance levels, biocide-dependent proliferation or killing, and a transition to a biofilm state. Our computer simulations support a picture in which biocide-resistant microorganisms initially form a loosely attached layer that eventually transitions to a growing biofilm. Once the growing biofilm is established, immigrating microorganisms are shielded from the biocide, allowing more biocide-susceptible strains to proliferate. In our model, colonization of the AF surface is highly stochastic. The waiting time before the biofilm establishes is exponentially distributed, suggesting a Poisson process. The waiting time depends exponentially on both the concentration of biocide at the surface and the rate of arrival of resistant microorganisms from the ocean. Taken together our results suggest that biofouling of AF surfaces may be intrinsically stochastic and hence unpredictable, but immigration of more biocide-resistant species, as well as the biological transition to biofilm physiology, may be important factors controlling the time to biofilm establishment.}, }
@article {pmid36229976, year = {2022}, author = {De Spiegeleer, A and Wynendaele, E and Descamps, A and Debunne, N and Braeckman, BP and De Mey, M and Coudenys, J and Crombez, L and Verbeke, F and Janssens, Y and Janky, R and Goossens, E and Vlaeminck, C and Duchi, D and Andries, V and Dumas, E and Petrovic, M and Van de Wiele, T and Knappe, D and Hoffmann, R and Mouly, V and Bigot, A and Vereecke, L and Van Immerseel, F and Van Den Noortgate, N and De Spiegeleer, B and Elewaut, D}, title = {The bacterial quorum sensing peptide iAM373 is a novel inducer of sarcopenia.}, journal = {Clinical and translational medicine}, volume = {12}, number = {10}, pages = {e1053}, pmid = {36229976}, issn = {2001-1326}, support = {P40 OD010440/OD/NIH HHS/United States ; }, mesh = {Bacteria ; Humans ; Oligopeptides ; Peptides ; *Quorum Sensing ; *Sarcopenia ; }, }
@article {pmid36224329, year = {2022}, author = {Bayer, N and Hausmann, B and Pandey, RV and Deckert, F and Gail, LM and Strobl, J and Pjevac, P and Krall, C and Unterluggauer, L and Redl, A and Bachmayr, V and Kleissl, L and Nehr, M and Kirkegaard, R and Makristathis, A and Watzenboeck, ML and Nica, R and Staud, C and Hammerl, L and Wohlfarth, P and Ecker, RC and Knapp, S and Rabitsch, W and Berry, D and Stary, G}, title = {Disturbances in microbial skin recolonization and cutaneous immune response following allogeneic stem cell transfer.}, journal = {Leukemia}, volume = {36}, number = {11}, pages = {2705-2714}, pmid = {36224329}, issn = {1476-5551}, support = {P 31494/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Graft vs Host Disease/etiology ; *Gastrointestinal Microbiome ; Immunity ; }, abstract = {The composition of the gut microbiome influences the clinical course after allogeneic hematopoietic stem cell transplantation (HSCT), but little is known about the relevance of skin microorganisms. In a single-center, observational study, we recruited a cohort of 50 patients before undergoing conditioning treatment and took both stool and skin samples up to one year after HSCT. We could confirm intestinal dysbiosis following HSCT and report that the skin microbiome is likewise perturbed in HSCT-recipients. Overall bacterial colonization of the skin was decreased after conditioning. Particularly patients that developed acute skin graft-versus-host disease (aGVHD) presented with an overabundance of Staphylococcus spp. In addition, a loss in alpha diversity was indicative of aGVHD development already before disease onset and correlated with disease severity. Further, co-localization of CD45[+] leukocytes and staphylococci was observed in the skin of aGVHD patients even before disease development and paralleled with upregulated genes required for antigen-presentation in mononuclear phagocytes. Overall, our data reveal disturbances of the skin microbiome as well as cutaneous immune response in HSCT recipients with changes associated with cutaneous aGVHD.}, }
@article {pmid36224114, year = {2023}, author = {Rohrbach, S and Gkoutselis, G and Hink, L and Weig, AR and Obst, M and Diekmann, A and Ho, A and Rambold, G and Horn, MA}, title = {Microplastic polymer properties as deterministic factors driving terrestrial plastisphere microbiome assembly and succession in the field.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {2681-2697}, doi = {10.1111/1462-2920.16234}, pmid = {36224114}, issn = {1462-2920}, support = {SFB1357-391977956//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Plastics ; Microplastics ; Polymers ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Soil ; }, abstract = {Environmental microplastic (MP) is ubiquitous in aquatic and terrestrial ecosystems providing artificial habitats for microbes. Mechanisms of MP colonization, MP polymer impacts, and effects on soil microbiomes are largely unknown in terrestrial systems. Therefore, we experimentally tested the hypothesis that MP polymer type is an important deterministic factor affecting MP community assembly by incubating common MP polymer types in situ in landfill soil for 14 months. 16S rRNA gene amplicon sequencing indicated that MP polymers have specific impacts on plastisphere microbiomes, which are subsets of the soil microbiome. Chloroflexota, Gammaproteobacteria, certain Nitrososphaerota, and Nanoarchaeota explained differences among MP polymers and time points. Plastisphere microbial community composition derived from different MP diverged over time and was enriched in potential pathogens. PICRUSt predictions of pathway abundances and quantitative PCR of functional marker genes indicated that MP polymers exerted an ambivalent effect on genetic potentials of biogeochemical cycles. Overall, the data indicate that (i) polymer type as deterministic factor rather than stochastic factors drives plastisphere community assembly, (ii) MP impacts greenhouse gas metabolism, xenobiotic degradation and pathogen distribution, and (iii) MP serves as an ideal model system for studying fundamental questions in microbial ecology such as community assembly mechanisms in terrestrial environments.}, }
@article {pmid36216061, year = {2023}, author = {Sabba, F and Farmer, M and Jia, Z and Di Capua, F and Dunlap, P and Barnard, J and Qin, CD and Kozak, JA and Wells, G and Downing, L}, title = {Impact of operational strategies on a sidestream enhanced biological phosphorus removal (S2EBPR) reactor in a carbon limited wastewater plant.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 1}, pages = {159280}, doi = {10.1016/j.scitotenv.2022.159280}, pmid = {36216061}, issn = {1879-1026}, mesh = {*Wastewater ; *Phosphorus ; Carbon ; Bioreactors ; Sewage ; }, abstract = {Water resource recovery facilities are faced with stringent effluent phosphorus limits to reduce nutrient pollution. Enhanced biological phosphorus removal (EBPR) is the most common biological route to remove phosphorus; however, many facilities struggle to achieve consistent performance due to limited carbon availability in the influent wastewater. A promising process to improve carbon availability is through return activated sludge (RAS) fermentation via sidestream EBPR (S2EBPR). In this study, a full-scale S2EBPR pilot was operated with a sidestream plus carbon configuration (SSRC) at a carbon-limited facility. A model based on the pilot test was developed and calibrated in the SUMO platform and used to explore routes for improving orthophosphate (OP) effluent compliance. Modeling results showed that RAS diversion by itself was not sufficient to drive OP removal to permit limits of 1 mg L[-1], therefore, other strategies were evaluated. Supplemental carbon addition of MicroC® at 1.90 L min[-1] and controlling the phosphorus concentration below 3.5 mgP L[-1] in the primary effluent (PE) proved to be valid supplemental strategies to achieve OP removal below 1 mg L[-1] most of the time. In particular, the proposed supplemental carbon flow rate would result in an improvement of the rbCOD:P ratio from 17:1 to 26:1. The synergistic approach of RAS diversion and supplemental carbon addition increased the polyphosphate accumulating organisms (PAO) population while minimizing the supplemental carbon needed to achieve consistent phosphorus removal. Overall, this pilot and modeling study shows that joint strategies, including RAS diversion, carbon addition and PE control, can be effective to achieve optimal control of OP effluent.}, }
@article {pmid36215761, year = {2022}, author = {Uroosa,  and Kazmi, SSUH and Warren, A and Zhong, X and Xu, H}, title = {Effects of nitrofurazone on ecosystem function in marine environments: A case study on microbial fauna.}, journal = {Marine pollution bulletin}, volume = {184}, number = {}, pages = {114216}, doi = {10.1016/j.marpolbul.2022.114216}, pmid = {36215761}, issn = {1879-3363}, mesh = {*Ecosystem ; Nitrofurazone/toxicity ; Environmental Monitoring ; *Ciliophora ; Anti-Bacterial Agents ; }, abstract = {To evaluate the effects of nitrofurazone on functional processes in marine ecosystems, periphytic protozoan communities were exposed to different concentrations of the antibiotic for a 10-day duration. Species trait distributions in the tested communities were observed during exposure to five concentrations of nitrofurazone. A fuzzy coding system with seven traits and seventeen categories was used to summarize the changes in functional patterns of the test organisms. Nitrofurazone had a significant influence on the function process of the periphytic ciliate communities. Bacterivores with flattened bodies were sensitive to the toxicant whereas sessile and cylindrical raptors showed a high tolerance to nitrofurazone, invariably dominating communities exposed to high concentrations. Bootstrapped-average analysis demonstrated a significant change in functional patterns at highest nitrofurazone concentrations (8 mg l[-1]). Based on these findings, it is suggested that nitrofurazone may negatively influence ecosystem function in marine environments.}, }
@article {pmid36215464, year = {2022}, author = {Chevrette, MG and Thomas, CS and Hurley, A and Rosario-Meléndez, N and Sankaran, K and Tu, Y and Hall, A and Magesh, S and Handelsman, J}, title = {Microbiome composition modulates secondary metabolism in a multispecies bacterial community.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {42}, pages = {e2212930119}, pmid = {36215464}, issn = {1091-6490}, support = {T32 GM135066/GM/NIGMS NIH HHS/United States ; S10 RR029531/RR/NCRR NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents ; Benzamides ; Humans ; *Microbiota ; Secondary Metabolism ; *Siderophores/genetics/metabolism ; }, abstract = {Bacterial secondary metabolites are a major source of antibiotics and other bioactive compounds. In microbial communities, these molecules can mediate interspecies interactions and responses to environmental change. Despite the importance of secondary metabolites in human health and microbial ecology, little is known about their roles and regulation in the context of multispecies communities. In a simplified model of the rhizosphere composed of Bacillus cereus, Flavobacterium johnsoniae, and Pseudomonas koreensis, we show that the dynamics of secondary metabolism depend on community species composition and interspecies interactions. Comparative metatranscriptomics and metametabolomics reveal that the abundance of transcripts of biosynthetic gene clusters (BGCs) and metabolomic molecular features differ between monocultures or dual cultures and a tripartite community. In both two- and three-member cocultures, P. koreensis modified expression of BGCs for zwittermicin, petrobactin, and other secondary metabolites in B. cereus and F. johnsoniae, whereas the BGC transcriptional response to the community in P. koreensis itself was minimal. Pairwise and tripartite cocultures with P. koreensis displayed unique molecular features that appear to be derivatives of lokisin, suggesting metabolic handoffs between species. Deleting the BGC for koreenceine, another P. koreensis metabolite, altered transcript and metabolite profiles across the community, including substantial up-regulation of the petrobactin and bacillibactin BGCs in B. cereus, suggesting that koreenceine represses siderophore production. Results from this model community show that bacterial BGC expression and chemical output depend on the identity and biosynthetic capacity of coculture partners, suggesting community composition and microbiome interactions may shape the regulation of secondary metabolism in nature.}, }
@article {pmid36214570, year = {2022}, author = {Utter, DR and Cavanaugh, CM and Borisy, GG}, title = {Genome-Centric Dynamics Shape the Diversity of Oral Bacterial Populations.}, journal = {mBio}, volume = {13}, number = {6}, pages = {e0241422}, pmid = {36214570}, issn = {2150-7511}, support = {R01 DE030136/DE/NIDCR NIH HHS/United States ; UL1 TR001102/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/genetics ; Bacteria/genetics ; Metagenome ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; }, abstract = {Two major viewpoints have been put forward for how microbial populations change, differing in whether adaptation is driven principally by gene-centric or genome-centric processes. Longitudinal sampling at microbially relevant timescales, i.e., days to weeks, is critical for distinguishing these mechanisms. Because of its significance for both microbial ecology and human health and its accessibility and high level of curation, we used the oral microbiota to study bacterial intrapopulation genome dynamics. Metagenomes were generated by shotgun sequencing of total community DNA from the healthy tongues of 17 volunteers at four to seven time points obtained over intervals of days to weeks. We obtained 390 high-quality metagenome-assembled genomes (MAGs) defining population genomes from 55 genera. The vast majority of genes in each MAG were tightly linked over the 2-week sampling window, indicating that the majority of the population's genomes were temporally stable at the MAG level. MAG-defined populations were composed of up to 5 strains, as determined by single-nucleotide-variant frequencies. Although most were stable over time, individual strains carrying over 100 distinct genes that rose from low abundance to dominance in a population over a period of days were detected. These results indicate a genome-wide as opposed to a gene-level process of population change. We infer that genome-wide selection of ecotypes is the dominant mode of adaptation in the oral populations over short timescales. IMPORTANCE The oral microbiome represents a microbial community of critical relevance to human health. Recent studies have documented the diversity and dynamics of different bacteria to reveal a rich, stable ecosystem characterized by strain-level dynamics. However, bacterial populations and their genomes are neither monolithic nor static; their genomes are constantly evolving to lose, gain, or alter their functional potential. To better understand how microbial genomes change in complex communities, we used culture-independent approaches to reconstruct the genomes (MAGs) for bacterial populations that approximated different species, in 17 healthy donors' mouths over a 2-week window. Our results underscored the importance of strain-level dynamics, which agrees with and expands on the conclusions of previous research. Altogether, these observations reveal patterns of genomic dynamics among strains of oral bacteria occurring over a matter of days.}, }
@article {pmid36213689, year = {2022}, author = {He, KJ and Zhang, YF and Liang, LY and Cheng, XS and Gong, G and Ouyang, XM and Lin, Y and Guleng, B}, title = {ncRNAs-mediated high expression of TICRR promotes tumor cell proliferation and migration and is correlated with poor prognosis and tumor immune infiltration of hepatocellular carcinoma.}, journal = {Molecular therapy. Nucleic acids}, volume = {30}, number = {}, pages = {80-94}, pmid = {36213689}, issn = {2162-2531}, abstract = {TICRR is a regulatory factor of DNA replication with ToPBP1 interaction. At present, the underlying function and mechanisms of TICRR remain unclear in LIHC. Our objective was to assess the function and prognosis of TICRR in LIHC. We conducted a differential expression analysis, GO/KEGG, and GSEA enrichment analysis of TICRR in LIHC. We also carried out the gene frequency and SCNA of TICRR. We found that TICRR could serve as an independent prognostic marker in LIHC by univariate and multivariate analysis. In addition, we observed that TICRR was related to immune infiltration, and TICRR had positive correlation with PD1/PD-L1 and CTLA-4 in LIHC. The hsa-miR-126-3p/IPO9-AS1 may be the candidate ncRNAs to regulate the expression of TICRR. The high rate of SCNV of TICRR might have critical effect on the function of CTL cells in LIHC. We further demonstrate through a series of experiments that TICRR facilitated the proliferation and metastasis of liver cancer cells in vitro. Altogether, TICRR might be a potential biomarker and therapeutic target in LIHC.}, }
@article {pmid36213308, year = {2022}, author = {Vinyard, JR and Faciola, AP}, title = {Unraveling the pros and cons of various in vitro methodologies for ruminant nutrition: a review.}, journal = {Translational animal science}, volume = {6}, number = {4}, pages = {txac130}, pmid = {36213308}, issn = {2573-2102}, abstract = {To decrease the time and cost of experiments as well as the use of animals in nutrition research, in vitro methodologies have become more commonplace in the field of ruminant nutrition. Therefore, the objectives of this review are 1) to describe the development of different in vitro methodologies, 2) to discuss the application, utilization, and advantages of in vitro methodologies, 3) to discuss shortcomings of in vitro methodologies, and 4) to describe the potential developments that may be able to improve in vitro methods. Having been used for decades, some in vitro methodologies such as pure, batch, and continuous cultures have been very well documented and utilized to investigate a wide array of different aspects of nutrition, including the effects of different dietary compositions, individual fermentation end products, and impacts on the microbiome of the rumen. However, both batch and pure cultures can result in a build-up of end products that may inhibit fermentation, as they culture ruminal contents or defined strains of bacteria, respectfully. Continuous culture; however, allows for the removal of end products but, similar to pure and batch cultures, is applicable only to ruminal fermentation and cannot provide information regarding intestinal digestion and bioavailability. This information for in vitro can only be provided using an assay designed for total tract digestibility, which is the three-step procedure (TSP). The TSP may be improved by coupling it with cell culture to investigate the absorption of nutrients in both the ruminal and intestinal phases of the methodology; however, the TSP needs further development to investigate all nutrients and the methodologies available for cell culture are still relatively new to ruminant nutrition. Therefore, while in vitro methodologies provide useful data in the field of ruminant nutrition without the continuous use of animals, there is still much work to be done to improve the methodologies to further apply them.}, }
@article {pmid36208750, year = {2023}, author = {Gros, M and Mas-Pla, J and Sànchez-Melsió, A and Čelić, M and Castaño, M and Rodríguez-Mozaz, S and Borrego, CM and Balcázar, JL and Petrović, M}, title = {Antibiotics, antibiotic resistance and associated risk in natural springs from an agroecosystem environment.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 1}, pages = {159202}, doi = {10.1016/j.scitotenv.2022.159202}, pmid = {36208750}, issn = {1879-1026}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/analysis ; Escherichia coli/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Tetracyclines/analysis ; *Natural Springs ; Sulfonamides ; Water ; China ; }, abstract = {This study investigates the occurrence, transport, and risks associated to antibiotic residues, antibiotic resistance genes (ARGs) and antibiotic resistant Escherichia coli (AR-E. coli) in eleven natural springs in an agroecosystem environment with intense livestock production, where groundwater nitrate concentration usually sets above 50 mg L[-1]. Out of 23 multiple-class antibiotics monitored, tetracycline and sulfonamide residues were the most ubiquitous, and they were detected at concentrations ranging from ng L[-1] to μg L[-1]. Five ARGs were monitored, conferring resistance to the antibiotic classes of major use in livestock production. Thus, genes conferring resistance to sulfonamides (sul1 and sul2) and tetracyclines (tetW) as well as a gene proxy for anthropogenic pollution (intI1) were present in most springs. sul1 was the most abundant, with absolute concentrations ranging from 4 × 10[2] to 5.6 × 10[6] gene copies L[-1] water. AR-E. coli showing resistance to sulfonamides and tetracyclines was also detected, with a prevalence up to approximately 40 % in some sites but with poor correlations with the concentration of antibiotic residues and ARGs. The occurrence of antibiotics, ARGs and AR-E. coli was characterized by large seasonal variations which were mostly associated to both hydrological factors and reactive transport processes. Finally, a risk assessment approach pointed out towards low risk for both the groundwater environment and human health, when spring water is used for direct human consumption, associated with the occurrence of antibiotics, ARGs and AR-E. coli. However, long-term effects cannot be neglected, and proper actions must be taken to preserve groundwater quality.}, }
@article {pmid36207335, year = {2022}, author = {Tao, J and Wang, W and Weissman, JL and Zhang, Y and Chen, S and Zhu, Y and Zhang, C and Hou, S}, title = {Size-fractionated microbiome observed during an eight-month long sampling in Jiaozhou Bay and the Yellow Sea.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {605}, pmid = {36207335}, issn = {2052-4463}, support = {Nos. 42141003//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Bays/microbiology ; China ; Genome, Microbial ; Metagenome ; *Microbiota ; Oceans and Seas ; }, abstract = {Jiaozhou Bay is a typical semi-enclosed bay with a temperate climate imposed by strong anthropogenic influence. To investigate microbial biodiversity and ecosystem services in this highly dynamic coastal environment, we conducted a monthly microbial survey spanning eight months at two stations in the bay and the open Yellow Sea starting in April 2015. This report provides a comprehensive inventory of amplicon sequences and environmental microbial genomes from this survey. In total, 2,543 amplicon sequence variants were obtained with monthly relative abundance profiles in three size fractions (>2.7 μm, 2.7-0.7 μm, and 0.7-0.22 μm). Shotgun metagenomes yielded 915 high-quality metagenome-assembled genomes with ≥50% completeness and ≤5% contamination. These environmental genomes comprise 27 bacterial and 5 archaeal phyla. We expect this comprehensive dataset will facilitate a better understanding of coastal microbial ecology.}, }
@article {pmid36206900, year = {2023}, author = {Sauter, D and Steuer, A and Wasmund, K and Hausmann, B and Szewzyk, U and Sperlich, A and Gnirss, R and Cooper, M and Wintgens, T}, title = {Microbial communities and processes in biofilters for post-treatment of ozonated wastewater treatment plant effluent.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 2}, pages = {159265}, doi = {10.1016/j.scitotenv.2022.159265}, pmid = {36206900}, issn = {1879-1026}, mesh = {Filtration/methods ; RNA, Ribosomal, 16S ; *Water Purification/methods ; Charcoal ; *Microbiota ; Coal ; *Water Pollutants, Chemical ; }, abstract = {Ozonation is an established solution for organic micropollutant (OMP) abatement in tertiary wastewater treatment. Biofiltration is the most common process for the biological post-treatment step, which is generally required to remove undesired oxidation products from the reaction of ozone with water matrix compounds. This study comparatively investigates the effect of filter media on the removal of organic contaminants and on biofilm properties for biologically activated carbon (BAC) and anthracite biofilters. Biofilms were analysed in two pilot-scale filters that have been operated for >50,000 bed volumes as post-treatment for ozonated wastewater treatment plant effluent. In parallel, the removal performance of bulk organics and OMP, including differentiation of adsorption and biotransformation through sodium azide inhibition, were carried out in bench-scale filter columns filled with material from the pilot filters. The use of BAC instead of anthracite resulted in an improved removal of organic bulk parameters, dissolved oxygen, and OMP. The OMP removal observed in the BAC filter but not in the anthracite filter was based on adsorption for most of the investigated compounds. For valsartan, however, biotransformation was found to be the dominant pathway, indicating that conditions for biotransformation of certain OMP are better on BAC than on anthracite. Adenosine triphosphate analyses in the media-attached biofilms of the pilot filters showed that biomass concentrations in the BAC filter were significantly higher than in the anthracite filter. The microbial communities (16S rRNA gene sequencing) appeared to be similar with respect to the types of organisms occurring on both filter materials. Alpha diversity also exhibited little variation between filter media. Beta diversity analysis, however, revealed that filter media and bed depth substantially influenced the biofilm composition. In practice, the impact of filter media on biofilm properties and biotransformation processes should be considered for the design of biofilters.}, }
@article {pmid36205738, year = {2023}, author = {Quero, GM and Piredda, R and Basili, M and Maricchiolo, G and Mirto, S and Manini, E and Seyfarth, AM and Candela, M and Luna, GM}, title = {Host-associated and Environmental Microbiomes in an Open-Sea Mediterranean Gilthead Sea Bream Fish Farm.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1319-1330}, pmid = {36205738}, issn = {1432-184X}, mesh = {Animals ; *Sea Bream ; Fisheries ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Aquaculture ; }, abstract = {Gilthead seabream is among the most important farmed fish species in the Mediterranean Sea. Several approaches are currently applied to assure a lower impact of diseases and higher productivity, including the exploration of the fish microbiome and its manipulation as a sustainable alternative to improve aquaculture practices. Here, using 16S rRNA gene high-throughput sequencing, we explored the microbiome of farmed seabream to assess similarities and differences among microbial assemblages associated to different tissues and compare them with those in the surrounding environment. Seabream had distinct associated microbiomes according to the tissue and compared to the marine environment. The gut hosted the most diverse microbiome; different sets of dominant ASVs characterized the environmental and fish samples. The similarity between fish and environmental microbiomes was higher in seawater than sediment (up to 7.8 times), and the highest similarity (3.9%) was observed between gill and seawater, suggesting that gills are more closely interacting with the environment. We finally analyzed the potential connections occurring among microbiomes. These connections were relatively low among the host's tissues and, in particular, between the gut and the others fish-related microbiomes; other tissues, including skin and gills, were found to be the most connected microbiomes. Our results suggest that, in mariculture, seabream microbiomes reflect only partially those in their surrounding environment and that the host is the primary driver shaping the seabream microbiome. These data provide a step forward to understand the role of the microbiome in farmed fish and farming environments, useful to enhance disease control, fish health, and environmental sustainability.}, }
@article {pmid36205737, year = {2023}, author = {Feng, SW and Lu, JL and Liang, JL and Wu, ZH and Yi, X and Wen, P and Li, FL and Liao, B and Jia, P and Shu, WS and Li, JT}, title = {Functional Guilds, Community Assembly, and Co-occurrence Patterns of Fungi in Metalliferous Mine Tailings Ponds in Mainland China.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {843-858}, pmid = {36205737}, issn = {1432-184X}, support = {42077117//National Natural Science Foundation of China/ ; 42177009//National Natural Science Foundation of China/ ; 41622106//National Natural Science Foundation of China/ ; 2019B110207001//Key-Area Research and Development Program of Guangdong Province/ ; 2021B1515120039//Guangdong Basic and Applied Basic Research Foundation/ ; 2020A1515010937//Natural Science Foundation of Guangdong Province of China/ ; }, mesh = {*Ponds ; *Soil Microbiology ; China ; Soil ; Fungi/genetics ; }, abstract = {Metalliferous mine tailings ponds are generally characterized by low levels of nutrient elements, sustained acidic conditions, and high contents of toxic metals. They represent one kind of extreme environments that are believed to resemble the Earth's early environmental conditions. There is increasing evidence that the diversity of fungi inhabiting mine tailings ponds is much higher than previously thought. However, little is known about functional guilds, community assembly, and co-occurrence patterns of fungi in such habitats. As a first attempt to address this critical knowledge gap, we employed high-throughput sequencing to characterize fungal communities in 33 mine tailings ponds distributed across 18 provinces of mainland China. A total of 5842 fungal phylotypes were identified, with saprotrophic fungi being the major functional guild. The predictors of fungal diversity in whole community and sub-communities differed considerably. Community assembly of the whole fungal community and individual functional guilds were primarily governed by stochastic processes. Total soil nitrogen and total phosphorus mediated the balance between stochastic and deterministic processes of the fungal community assembly. Co-occurrence network analysis uncovered a high modularity of the whole fungal community. The observed main modules largely consisted of saprotrophic fungi as well as various phylotypes that could not be assigned to known functional guilds. The richness of core fungal phylotypes, occupying vital positions in co-occurrence network, was positively correlated with edaphic properties such as soil enzyme activity. This indicates the important roles of core fungal phylotypes in soil organic matter decomposition and nutrient cycling. These findings improve our understanding of fungal ecology of extreme environments.}, }
@article {pmid36204622, year = {2022}, author = {Banerjee, S and Bedics, A and Tóth, E and Kriszt, B and Soares, AR and Bóka, K and Táncsics, A}, title = {Isolation of Pseudomonas aromaticivorans sp. nov from a hydrocarbon-contaminated groundwater capable of degrading benzene-, toluene-, m- and p-xylene under microaerobic conditions.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {929128}, pmid = {36204622}, issn = {1664-302X}, abstract = {Members of the genus Pseudomonas are known to be widespread in hydrocarbon contaminated environments because of their remarkable ability to degrade a variety of petroleum hydrocarbons, including BTEX (benzene, toluene, ethylbenzene and xylene) compounds. During an enrichment investigation which aimed to study microaerobic xylene degradation in a legacy petroleum hydrocarbon-contaminated groundwater, a novel Gram-stain-negative, aerobic, motile and rod-shaped bacterial strain, designated as MAP12[T] was isolated. It was capable of degrading benzene, toluene, meta- and para- xylene effectively under both aerobic and microaerobic conditions. The 16S rRNA gene sequence analysis revealed that strain MAP12[T] belongs to the genus Pseudomonas, with the highest 16S rRNA gene similarity to Pseudomonas linyingensis LYBRD3-7 [T] (98.42%), followed by Pseudomonas sagittaria JCM 18195 [T] (98.29%) and Pseudomonas alcaliphila JCM 10630 [T] (98.08%). Phylogenomic tree constructed using a concatenated alignment of 92 core genes indicated that strain MAP12[T] is distinct from any known Pseudomonas species. The draft genome sequence of strain MAP12[T] is 4.36 Mb long, and the G+C content of MAP12[T] genome is 65.8%. Orthologous average nucleotide identity (OrthoANI) and digital DNA-DNA hybridization (dDDH) analyses confirmed that strain MAP12[T] is distinctly separated from its closest neighbors (OrthoANI < 89 %; dDDH < 36%). Though several members of the genus Pseudomonas are well known for their aerobic BTEX degradation capability, this is the first report of a novel Pseudomonas species capable of degrading xylene under microaerobic conditions. By applying genome-resolved metagenomics, we were able to partially reconstruct the genome of strain MAP12 [T] from metagenomics sequence data and showed that strain MAP12 [T] was an abundant member of the xylene-degrading bacterial community under microaerobic conditions. Strain MAP12[T] contains ubiquinone 9 (Q9) as the major respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine as major polar lipids. The major cellular fatty acids of strain MAP12[T] are summed feature 3 (C16:1ω6c and/or C16:1ω7c), C16:0 and summed feature 8 (C18:1ω6c and/or C18:1ω7c). The results of this polyphasic study support that strain MAP12[T] represents a novel species of the genus Pseudomonas, hence the name of Pseudomonas aromaticivorans sp. nov. is proposed for this strain considering its aromatic hydrocarbon degradation capability. The type strain is MAP12[T] (=LMG 32466, =NCAIM B.02668).}, }
@article {pmid36204070, year = {2022}, author = {Zhang, H and Ma, Y and Shao, J and Di, R and Zhu, F and Yang, Z and Sun, J and Zhang, X and Zheng, C}, title = {Changes in soil bacterial community and functions by substituting chemical fertilizer with biogas slurry in an apple orchard.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1013184}, pmid = {36204070}, issn = {1664-462X}, abstract = {Growing concerns about the negative environmental effects of excessive chemical fertilizer input in fruit production have resulted in many attempts looking for adequate substitution. Biogas slurry as a representative organic fertilizer has the potential to replace chemical fertilizer for improvement of sustainability. However, it is still poorly known how biogas slurry applications may affect the composition of soil microbiome. Here, we investigated different substitution rates of chemical fertilizer with biogas slurry treatment (the control with no fertilizer and biogas slurry, CK; 100% chemical fertilizer, CF; biogas slurry replacing 50% of chemical fertilizer, CBS; and biogas slurry replacing 100% of chemical fertilizer, BS) in an apple orchard. Soil bacterial community and functional structure among treatments were determined using Illumina sequencing technology coupled with Functional Annotation of Prokaryotic Taxonomy (FAPROTAX) analysis. Leaf nutrient contents, apple fruit and soil parameters were used to assess plant and soil quality. Results showed that most of fruit parameters and soil properties were significantly varied in the four treatments. CBS treatment increased the contents of soil organic matter, alkali nitrogen and available potassium average by 49.8%, 40.7% and 27.9%, respectively. Treatments with biogas slurry application increased the single fruit weight, fresh weight, and dry weight of apple fruit average by 15.6%, 18.8% and 17.8, respectively. Soil bacterial community dominance and composition were significantly influenced by substituting of chemical fertilizer with biogas slurry. Biogas slurry application enhanced the relative abundance of some beneficial taxa (e.g. Acidobacteria Gp5 and Gp7, Parasegetibacter) and functional groups related to carbon and nitrogen cycling such as chemoheterotrophy, cellulolysis, and nitrogen fixation. Soil available phosphorus and potassium, pH and electrical conductivity were identified having a high potential for regulating soil bacterial specific taxa and functional groups. This study showed that the proper ratio application (50%: 50%) of biogas slurry with chemical fertilizer could regulate soil bacterial composition and functional structure via changes in soil nutrients. The variations of bacterial community could potentially take significant ecological roles in maintaining apple plant growth, soil fertility and functionality.}, }
@article {pmid36203239, year = {2023}, author = {Munley, JA and Kelly, LS and Pons, EE and Kannan, KB and Coldwell, PS and Whitley, EM and Gillies, GS and Efron, PA and Nagpal, R and Mohr, AM}, title = {Multicompartmental traumatic injury and the microbiome: Shift to a pathobiome.}, journal = {The journal of trauma and acute care surgery}, volume = {94}, number = {1}, pages = {15-22}, pmid = {36203239}, issn = {2163-0763}, support = {R01 GM105893/GM/NIGMS NIH HHS/United States ; T32 GM008721/GM/NIGMS NIH HHS/United States ; }, mesh = {Rats ; Animals ; Male ; Rats, Sprague-Dawley ; Critical Illness ; Occludin ; RNA, Ribosomal, 16S ; *Multiple Trauma ; *Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: Previous animal models have demonstrated altered gut microbiome after mild traumatic injury; however, the impact of injury severity and critical illness is unknown. We hypothesized that a rodent model of severe multicompartmental injuries and chronic stress would demonstrate microbiome alterations toward a "pathobiome" characterized by an overabundance of pathogenic organisms, which would persist 1 week after injury.<br><br>METHODS: Male Sprague-Dawley rats (n = 8 per group) were subjected to either multiple injuries (PT) (lung contusion, hemorrhagic shock, cecectomy, and bifemoral pseudofractures), PT plus daily chronic restraint stress for 2 hours (PT/CS), or naive controls. Fecal microbiome was measured on days 0, 3, and 7 using high-throughput 16S rRNA sequencing and Quantitative Insights Into Microbial Ecology 2 bioinformatics analysis. Microbial &#x3b1; diversity was assessed using Chao1 and Shannon indices, and &#x3b2; diversity with principle coordinate analysis. Intestinal permeability was evaluated by plasma occludin; ileum and descending colon tissues were reviewed for injury. Analyses were performed in GraphPad (GraphPad Software, La Jolla, CA) and R (R Foundation for Statistical Computing, Vienna, Austria), with significance defined as p < 0.05.<br><br>RESULTS: There were significant alterations in &#x3b2; diversity at day 3 and between all groups. By day 3, both PT and PT/CS demonstrated significantly depleted bacterial diversity (Chao1) (p = 0.01 and p = 0.001, respectively) versus naive, which persisted up to day 7 in PT/CS only (p = 0.001). Anaerostipes and Rothia dominated PT and Lactobacillus bloomed in PT/CS cohorts by day 7. Plasma occludin was significantly elevated in PT/CS compared with naive (p = 0.04), and descending colon of both PT and PT/CS showed significantly higher injury compared with naive (p = 0.005, p = 0.006).<br><br>CONCLUSIONS: Multiple injuries with and without chronic stress induces significant alterations in microbiome diversity and composition within 3 days; these changes are more prominent and persist for 1 week postinjury with stress. This rapid and persistent transition to a "pathobiome" phenotype represents a critical phenomenon that may influence outcomes after severe trauma and critical illness.}, }
@article {pmid36202959, year = {2022}, author = {Guerrero-Latorre, L and Collado, N and Abasolo, N and Anzaldi, G and Bofill-Mas, S and Bosch, A and Bosch, L and Busquets, S and Caimari, A and Canela, N and Carcereny, A and Chacón, C and Ciruela, P and Corbella, I and Domingo, X and Escoté, X and Espiñeira, Y and Forés, E and Gandullo-Sarró, I and Garcia-Pedemonte, D and Girones, R and Guix, S and Hundesa, A and Itarte, M and Mariné-Casadó, R and Martínez, A and Martínez-Puchol, S and Mas-Capdevila, A and Mejías-Molina, C and Rafa, MMI and Munné, A and Pintó, RM and Pueyo-Ros, J and Robusté-Cartró, J and Rusiñol, M and Sanfeliu, R and Teichenné, J and Torrell, H and Corominas, L and Borrego, CM}, title = {The Catalan Surveillance Network of SARS-CoV-2 in Sewage: design, implementation, and performance.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {16704}, pmid = {36202959}, issn = {2045-2322}, mesh = {*COVID-19/epidemiology ; Humans ; Pandemics ; RNA, Viral ; *SARS-CoV-2 ; Sewage ; Wastewater ; Wastewater-Based Epidemiological Monitoring ; }, abstract = {Wastewater-based epidemiology has shown to be an efficient tool to track the circulation of SARS-CoV-2 in communities assisted by wastewater treatment plants (WWTPs). The challenge comes when this approach is employed to help Health authorities in their decision-making. Here, we describe the roadmap for the design and deployment of SARSAIGUA, the Catalan Surveillance Network of SARS-CoV-2 in Sewage. The network monitors, weekly or biweekly, 56 WWTPs evenly distributed across the territory and serving 6 M inhabitants (80% of the Catalan population). Each week, samples from 45 WWTPs are collected, analyzed, results reported to Health authorities, and finally published within less than 72 h in an online dashboard (https://sarsaigua.icra.cat). After 20 months of monitoring (July 20-March 22), the standardized viral load (gene copies/day) in all the WWTPs monitored fairly matched the cumulative number of COVID-19 cases along the successive pandemic waves, showing a good fit with the diagnosed cases in the served municipalities (Spearman Rho = 0.69). Here we describe the roadmap of the design and deployment of SARSAIGUA while providing several open-access tools for the management and visualization of the surveillance data.}, }
@article {pmid36202936, year = {2022}, author = {Fournier, E and Denis, S and Dominicis, A and Van de Wiele, T and Alric, M and Mercier-Bonin, M and Etienne-Mesmin, L and Blanquet-Diot, S}, title = {A child is not an adult: development of a new in vitro model of the toddler colon.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {21}, pages = {7315-7336}, pmid = {36202936}, issn = {1432-0614}, mesh = {Adult ; Infant ; Humans ; Child, Preschool ; Child ; *Propionates ; Colon ; Fatty Acids, Volatile ; Feces ; *Microbiota ; Butyrates ; Methane ; }, abstract = {Early life is a critical period where gut ecosystem and functions are being established with significant impact on health. For regulatory, technical, and cost reasons, in vitro gut models can be used as a relevant alternative to in vivo assays. An exhaustive literature review was conducted to adapt the Mucosal Artificial Colon (M-ARCOL) to specific physicochemical (pH, transit time, and nutritional composition of ileal effluents) and microbial parameters from toddlers in the age range of 6 months-3 years, resulting in the Tm-ARCOL. In vitro fermentations were performed to validate this newly developed colonic model compared to in vivo toddler data. Results were also compared to those obtained with the classical adult configuration. Fecal samples from 5 toddlers and 4 adults were used to inoculate bioreactors, and continuous fermentations were performed for 8 days. Gut microbiota structure (lumen and mucus-associated microbiota) and functions (gas and short-chain fatty acids) were monitored. Clearly distinct microbial signatures were obtained between the two in vitro conditions, with lower α-diversity indices and higher abundances of infant-related microbial populations (e.g., Bifidobacteriaceae, Enterobacteriaceae) in toddler versus adult conditions. In accordance with in vivo data, methane was found only in adult bioreactors, while higher percentage of acetate but lower proportions of propionate and butyrate was measured in toddlers compared to adults. This new in vitro model will provide a powerful platform for gut microbiome mechanistic studies in a pediatric context, both in nutritional- (e.g., nutrients, probiotics, prebiotics) and health-related (e.g., drugs, enteric pathogens) studies. KEY POINTS: • Development of a novel in vitro colonic model recapitulating the toddler environment. • Specific toddler versus adult digestive conditions are preserved in vitro. • The new model provides a powerful platform for microbiome mechanistic studies.}, }
@article {pmid36202391, year = {2023}, author = {Haskell-Ramsay, CF and Dodd, FL and Smith, D and Cuthbertson, L and Nelson, A and Lodge, JK and Jackson, PA}, title = {Mixed Tree Nuts, Cognition, and Gut Microbiota: A 4-Week, Placebo-Controlled, Randomized Crossover Trial in Healthy Nonelderly Adults.}, journal = {The Journal of nutrition}, volume = {152}, number = {12}, pages = {2778-2788}, pmid = {36202391}, issn = {1541-6100}, mesh = {Humans ; Aged ; *Gastrointestinal Microbiome ; Cross-Over Studies ; Cognition ; *Cognitive Dysfunction ; Bacteria/genetics ; }, abstract = {BACKGROUND: Beneficial effects of nut supplementation on cognitive function have previously been demonstrated in young and older adults. Alterations to gut microbiota have also been shown following tree nut consumption. However, no data exists on the effects of nuts on cognition and intestinal microbial communities assessed within the same study.<br><br>OBJECTIVES: The study aimed to examine the effects of daily consumption of tree nuts for 4 wk on cognitive function (primary outcome), mood, metabolomics, and gut microbial species (secondary outcomes) in healthy, nonelderly adults.<br><br>METHODS: This randomized, placebo-controlled, double-blind, counterbalanced crossover study assessed the effects of 4 wk of supplementation with 30&#xa0;g/d mixed tree nuts versus placebo on cognition and mood in 79 healthy adults aged 18-49 y. Metabolic responses, gut bacterial community structure, and the potential for these to impact cognition were explored using a multi-omic approach. Bacterial community analysis was conducted in Quantitative Insights Into Microbial Ecology 2 (QIIME2).<br><br>RESULTS: Mixed model analysis indicated that nut consumption led to significant improvements to accuracy (placebo M&#xa0;=&#xa0;92.2%&#xa0;compared with NUTS M&#xa0;=&#xa0;94.5%; P&#xa0;=&#xa0;0.019) and speed of response (placebo M&#xa0;=&#xa0;788&#xa0;ms compared with NUTS M&#xa0;=&#xa0;757&#xa0;ms; P&#xa0;=&#xa0;0.004) on a picture recognition task. No significant changes to bacterial community &#x3b1; or &#x3b2; diversity were observed when comparing nut consumption to the placebo arm. However, an unclassified Lachnospiraceae amplicon sequence variant (ASV) was significantly enriched in participants when supplemented with nuts (P&#xa0;=&#xa0;0.015). No correlations were observed between the changes to picture recognition and the changes to the unclassified Lachnospiraceae ASV. There were no significant changes to the urinary metabolome.<br><br>CONCLUSIONS: These findings indicate a positive effect of nut on cognition following only 4 wk of consumption in a healthy nonelderly sample, as well as upregulation of a microbial taxa associated with gut health. The effects appear to be independent of one another, but further exploration is required in those experiencing cognitive decline and/or gut dysbiosis.}, }
@article {pmid36198042, year = {2022}, author = {Yan, C and Kwek, E and Ding, HF and He, Z and Ma, KY and Zhu, H and Chen, ZY}, title = {Dietary Oxidized Cholesterol Aggravates Chemically Induced Murine Colon Inflammation and Alters Gut Microbial Ecology.}, journal = {Journal of agricultural and food chemistry}, volume = {70}, number = {41}, pages = {13289-13301}, doi = {10.1021/acs.jafc.2c05001}, pmid = {36198042}, issn = {1520-5118}, mesh = {Mice ; Humans ; Animals ; *Gastrointestinal Microbiome ; Dextran Sulfate/adverse effects ; Cholesterol, Dietary ; Mice, Inbred C57BL ; *Colitis/chemically induced/microbiology ; Colon/microbiology ; Fatty Acids, Volatile/pharmacology ; Inflammation ; Disease Models, Animal ; }, abstract = {Western diet with a higher intake of fat and cholesterol has been claimed as an intestinal inflammation trigger. Human diet contains both cholesterol and oxidized cholesterol. Oxidized cholesterol has been claimed to be associated with various inflammation diseases, but its effects on colitis and gut microbiome remain largely unknown. The present study was the first time to investigate the effect of the oxidized cholesterol on gut microbiota and dextran sodium sulfate-induced colitis using mice as a model. The results showed that oxidized cholesterol promoted colitis by exacerbating bleeding, body weight decrease, colon shortening, gut barrier damage, oxidative stress, and gut inflammation, whereas non-oxidized cholesterol had no effect. Meanwhile, oxidized cholesterol could adversely modulate the gut microbiota by increasing the relative abundance of pro-inflammatory bacteria (including Escherichia-Shigella and Bacteroides) and decreasing that of beneficial bacteria (Lachnospiraceae_NK4A136_group and Odoribacter). In addition, oxidized cholesterol significantly reduced the production of fecal short-chain fatty acids in colitis mice. It was concluded that oxidized cholesterol was a potential dietary factor of gut dysbiosis.}, }
@article {pmid36197502, year = {2023}, author = {Pin Viso, ND and Rizzo, PF and Young, BJ and Gabioud, E and Bres, P and Riera, NI and Merino, L and Farber, MD and Crespo, DC}, title = {The Use of Raw Poultry Waste as Soil Amendment Under Field Conditions Caused a Loss of Bacterial Genetic Diversity Together with an Increment of Eutrophic Risk and Phytotoxic Effects.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1082-1095}, pmid = {36197502}, issn = {1432-184X}, support = {PIUNAHUR5-04//UNaHur/ ; }, mesh = {Animals ; *Soil/chemistry ; *Poultry ; Manure ; Fertilizers ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Genetic Variation ; }, abstract = {Poultry waste has been used as fertilizer to avoid soil degradation caused by the long-term application of chemical fertilizer. However, few studies have evaluated field conditions where livestock wastes have been used for extended periods of time. In this study, physicochemical parameters, metabarcoding of the 16S rRNA gene, and ecotoxicity indexes were used for the characterization of chicken manure and poultry litter to examine the effect of their application to agricultural soils for 10 years. Poultry wastes showed high concentrations of nutrients and increased electrical conductivity leading to phytotoxic effects on seeds. The bacterial communities were dominated by typical members of the gastrointestinal tract, noting the presence of pathogenic bacteria. Soils subjected to poultry manure applications showed statistically higher values of total and extractable phosphorous, increasing the risk of eutrophication. Moreover, while the soil bacterial community remained dominated by the ones related to the biogeochemical cycles of nutrients and plant growth promotion, losses of alpha diversity were observed on treated soils. Altogether, our work would contribute to understand the effects of common local agricultural practices and support the adoption of the waste treatment process in compliance with environmental sustainability guidelines.}, }
@article {pmid36196151, year = {2022}, author = {Zhang, YW and Cao, MM and Li, YJ and Lu, PP and Dai, GC and Zhang, M and Wang, H and Rui, YF}, title = {Fecal microbiota transplantation ameliorates bone loss in mice with ovariectomy-induced osteoporosis via modulating gut microbiota and metabolic function.}, journal = {Journal of orthopaedic translation}, volume = {37}, number = {}, pages = {46-60}, pmid = {36196151}, issn = {2214-031X}, abstract = {BACKGROUND: Osteoporosis (OP) is a systemic metabolic bone disease characterized by decreased bone mass and destruction of bone microstructure, which tends to result in enhanced bone fragility and related fractures. The postmenopausal osteoporosis (PMOP) has a relatively high proportion, and numerous studies reveal that estrogen-deficiency is related to the imbalance of gut microbiota (GM), impaired intestinal mucosal barrier function and enhanced inflammatory reactivity. However, the underlying mechanisms remain unclear and the existing interventions are also scarce.<br><br>METHODS: In this study, we established a mouse model induced by ovariectomy (OVX) and conducted fecal microbiota transplantation (FMT) by gavage every day for 8 weeks. Subsequently, the bone mass and microarchitecture of mice were evaluated by the micro computed tomography (Micro-CT). The intestinal permeability, pro-osteoclastogenic cytokines expression, osteogenic and osteoclastic activities were detected by the immunohistological analysis, histological examination, enzyme-linked immunosorbent assay (ELISA) and western blot analysis accordingly. Additionally, the composition and abundance of GM were assessed by 16S rRNA sequencing and the fecal short chain fatty acids (SCFAs) level was measured by metabolomics.<br><br>RESULTS: Our results demonstrated that FMT inhibited the excessive osteoclastogenesis and prevented the OVX-induced bone loss. Specifically, compared with the OVX group, FMT enhanced the expressions of tight junction proteins (zonula occludens protein 1 (ZO-1) and Occludin) and suppressed the release of pro-osteoclastogenic cytokines (tumor necrosis factor-&#x3b1; (TNF-&#x3b1;) and interleukin-1&#x3b2; (IL-1&#x3b2;)). Furthermore, FMT also optimized the composition and abundance of GM, and increased the fecal SCFAs level (mainly acetic acid and propionic acid).<br><br>CONCLUSIONS: Collectively, based on GM-bone axis, FMT prevented the OVX-induced bone loss by correcting the imbalance of GM, improving the SCFAs level, optimizing the intestinal permeability and suppressing the release of pro-osteoclastogenic cytokines, which may be an alternative option to serve as a promising candidate for the prevention and treatment of PMOP in the future.<br><br>This study indicates the ingenious involvement of GM-bone axis in PMOP and the role of FMT in reshaping the status of GM and ameliorating the bone loss in OVX-induced mice. FMT might serve as a promising candidate for the prevention and treatment of PMOP in the future.}, }
@article {pmid36196117, year = {2022}, author = {Dong, H and Huang, L and Zhao, L and Zeng, Q and Liu, X and Sheng, Y and Shi, L and Wu, G and Jiang, H and Li, F and Zhang, L and Guo, D and Li, G and Hou, W and Chen, H}, title = {A critical review of mineral-microbe interaction and co-evolution: mechanisms and applications.}, journal = {National science review}, volume = {9}, number = {10}, pages = {nwac128}, pmid = {36196117}, issn = {2053-714X}, abstract = {Mineral-microbe interactions play important roles in environmental change, biogeochemical cycling of elements and formation of ore deposits. Minerals provide both beneficial (physical and chemical protection, nutrients, and energy) and detrimental (toxic substances and oxidative pressure) effects to microbes, resulting in mineral-specific microbial colonization. Microbes impact dissolution, transformation and precipitation of minerals through their activity, resulting in either genetically controlled or metabolism-induced biomineralization. Through these interactions, minerals and microbes co-evolve through Earth history. Mineral-microbe interactions typically occur at microscopic scale but the effect is often manifested at global scale. Despite advances achieved through decades of research, major questions remain. Four areas are identified for future research: integrating mineral and microbial ecology, establishing mineral biosignatures, linking laboratory mechanistic investigation to field observation, and manipulating mineral-microbe interactions for the benefit of humankind.}, }
@article {pmid36194291, year = {2023}, author = {Lomelí-Ortega, CO and Barajas-Sandoval, DR and Martínez-Villalobos, JM and Jaramillo, CR and Chávez, EM and Gómez-Gil, B and Balcázar, JL and Quiroz-Guzmán, E}, title = {A Broad-Host-Range Phage Cocktail Selectively and Effectively Eliminates Vibrio Species from Shrimp Aquaculture Environment.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1443-1446}, pmid = {36194291}, issn = {1432-184X}, support = {Aquaculture program//Centro de Investigaciones Biol&#xf3;gicas del Noroeste/ ; }, mesh = {Animals ; *Bacteriophages ; *Vibrio ; *Penaeidae/microbiology ; Aquaculture ; }, abstract = {The protective effects of a phage cocktail composed of vB_Vc_SrVc2 and vB_Vc_SrVc9 were tested in Pacific white shrimp (Litopenaeus vannamei) postlarvae, which were originally isolated from diseased shrimps and selected due to their broad-host-range properties against several pathogenic Vibsrio species. We used culture-dependent and culture-independent approaches to explore its effect on bacterial communities associated with shrimp postlarvae. Both methods revealed that the levels of Vibrio species were significantly reduced after phage cocktail administration. Phage-treated shrimp also exhibisuppted lesser damage and higher lipid accumulation in B cells of the hepatopancreas, as revealed by histopathological examination. Taken together, this study provides clear evidence that phage therapy can selectively and effectively reduce Vibrio species, thereby providing an environmentally safe alternative to the prophylactic use of antibiotics in shrimp aquaculture.}, }
@article {pmid36194136, year = {2022}, author = {Fang, Y and Stanford, K and Yang, X}, title = {Lactic Acid Resistance and Population Structure of Escherichia coli from Meat Processing Environment.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0135222}, pmid = {36194136}, issn = {2165-0497}, mesh = {Cattle ; Animals ; Escherichia coli ; Lactic Acid ; Phylogeny ; Meat ; Anti-Bacterial Agents/pharmacology ; Food Handling ; *Anti-Infective Agents/pharmacology ; *Disinfectants/pharmacology ; Sugar Acids/analysis/pharmacology ; Colony Count, Microbial ; Food Microbiology ; Food Contamination/analysis ; }, abstract = {To explore the effect of beef processing on Escherichia coli populations in relation to lactic acid resistance, this study investigated the links among acid response, phylogenetic structure, genome diversity, and genotypes associated with acid resistance of meat plant E. coli. Generic E. coli isolates (n = 700) were from carcasses, fabrication equipment, and beef products. Acid treatment was carried out in Luria-Bertani broth containing 5.5% lactic acid (pH 2.9). Log reductions of E. coli ranged from <0.5 to >5 log CFU/mL (median: 1.37 log). No difference in lactic acid resistance was observed between E. coli populations recovered before and after a processing step or antimicrobial interventions. E. coli from the preintervention carcasses were slightly more resistant than E. coli isolated from equipment, differing by <0.5 log unit. Acid-resistant E. coli (log reduction <1, n = 45) had a higher prevalence of genes related to energy metabolism (ydj, xap, ato) and oxidative stress (fec, ymjC) than the less resistant E. coli (log reduction >1, n = 133). The ydj and ato operons were abundant in E. coli from preintervention carcasses. In contrast, fec genes were abundant in E. coli from equipment surfaces. The preintervention E. coli contained phylogroups A and B1 in relatively equal proportions. Phylogroup B1 predominated (95%) in the population from equipment. Of note, E. coli collected after sanitation shared either the antigens of O8 or H21. Additionally, genome diversity decreased after chilling and equipment sanitation. Overall, beef processing did not select for E. coli resistant to lactic acid but shaped the population structure. IMPORTANCE Antimicrobial interventions have significantly reduced the microbial loads on carcasses/meat products; however, the wide use of chemical and physical biocides has raised concerns over their potential for selecting resistant populations in the beef processing environment. Phenotyping of acid resistance and whole-genome analysis described in this study demonstrated beef processing practices led to differences in acid resistance, genotype, and population structure between carcass- and equipment-associated E. coli but did not select for the acid-resistant population. Results indicate that genes coding for the metabolism of long-chain sugar acids (ydj) and short-chain fatty acids (ato) were more prevalent in carcass-associated than equipment-associated E. coli. These results suggest E. coli from carcasses and equipment surfaces have been exposed to different selective pressures. The findings improve our understanding of the microbial ecology of E. coli in food processing environments and in general.}, }
@article {pmid36192537, year = {2022}, author = {Zaremba, M and Dakineviciene, D and Golovinas, E and Zagorskaitė, E and Stankunas, E and Lopatina, A and Sorek, R and Manakova, E and Ruksenaite, A and Silanskas, A and Asmontas, S and Grybauskas, A and Tylenyte, U and Jurgelaitis, E and Grigaitis, R and Timinskas, K and Venclovas, &#x10c; and Siksnys, V}, title = {Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD[+] depletion.}, journal = {Nature microbiology}, volume = {7}, number = {11}, pages = {1857-1869}, pmid = {36192537}, issn = {2058-5276}, mesh = {*NAD/genetics/metabolism ; Prokaryotic Cells/metabolism ; Argonaute Proteins/genetics ; DNA/metabolism ; *Bacteriophages/genetics/metabolism ; Interspersed Repetitive Sequences ; }, abstract = {Argonaute (Ago) proteins are found in all three domains of life. The so-called long Agos are composed of four major domains (N, PAZ, MID and PIWI) and contribute to RNA silencing in eukaryotes (eAgos) or defence against invading mobile genetic elements in prokaryotes (pAgos). The majority (~60%) of pAgos identified bioinformatically are shorter (comprising only MID and PIWI domains) and are typically associated with Sir2, Mrr or TIR domain-containing proteins. The cellular function and mechanism of short pAgos remain enigmatic. Here we show that Geobacter sulfurreducens short pAgo and the NAD[+]-bound Sir2 protein form a stable heterodimeric complex. The GsSir2/Ago complex presumably recognizes invading plasmid or phage DNA and activates the Sir2 subunit, which triggers endogenous NAD[+] depletion and cell death, and prevents the propagation of invading DNA. We reconstituted NAD[+] depletion activity in vitro and showed that activated GsSir2/Ago complex functions as a NADase that hydrolyses NAD[+] to ADPR. Thus, short Sir2-associated pAgos provide defence against phages and plasmids, underscoring the diversity of mechanisms of prokaryotic Agos.}, }
@article {pmid36192536, year = {2022}, author = {Garb, J and Lopatina, A and Bernheim, A and Zaremba, M and Siksnys, V and Melamed, S and Leavitt, A and Millman, A and Amitai, G and Sorek, R}, title = {Multiple phage resistance systems inhibit infection via SIR2-dependent NAD[+] depletion.}, journal = {Nature microbiology}, volume = {7}, number = {11}, pages = {1849-1856}, pmid = {36192536}, issn = {2058-5276}, mesh = {*NAD/metabolism ; Silent Information Regulator Proteins, Saccharomyces cerevisiae/genetics/metabolism ; Sirtuin 2/genetics ; *Bacteriophages/genetics/metabolism ; NAD+ Nucleosidase ; }, abstract = {Defence-associated sirtuins (DSRs) comprise a family of proteins that defend bacteria from phage infection via an unknown mechanism. These proteins are common in bacteria and harbour an N-terminal sirtuin (SIR2) domain. In this study we report that DSR proteins degrade nicotinamide adenine dinucleotide (NAD[+]) during infection, depleting the cell of this essential molecule and aborting phage propagation. Our data show that one of these proteins, DSR2, directly identifies phage tail tube proteins and then becomes an active NADase in Bacillus subtilis. Using a phage mating methodology that promotes genetic exchange between pairs of DSR2-sensitive and DSR2-resistant phages, we further show that some phages express anti-DSR2 proteins that bind and repress DSR2. Finally, we demonstrate that the SIR2 domain serves as an effector NADase in a diverse set of phage defence systems outside the DSR family. Our results establish the general role of SIR2 domains in bacterial immunity against phages.}, }
@article {pmid36190138, year = {2022}, author = {Weissman, JL and Peras, M and Barnum, TP and Fuhrman, JA}, title = {Benchmarking Community-Wide Estimates of Growth Potential from Metagenomes Using Codon Usage Statistics.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0074522}, pmid = {36190138}, issn = {2379-5077}, mesh = {Humans ; *Metagenome/genetics ; Benchmarking ; Codon Usage ; *Microbiota/genetics ; }, abstract = {Trait inference from mixed-species assemblages is a central problem in microbial ecology. Frequently, sequencing information from an environment is available, but phenotypic measurements from individual community members are not. With the increasing availability of molecular data for microbial communities, bioinformatic approaches that map metagenome to (meta)phenotype are needed. Recently, we developed a tool, gRodon, that enables the prediction of the maximum growth rate of an organism from genomic data on the basis of codon usage patterns. Our work and that of other groups suggest that such predictors can be applied to mixed-species communities in order to derive estimates of the average community-wide maximum growth rate. Here, we present an improved maximum growth rate predictor designed for metagenomes that corrects a persistent GC bias in the original gRodon model for metagenomic prediction. We benchmark this predictor with simulated metagenomic data sets to show that it has superior performance on mixed-species communities relative to earlier models. We go on to provide guidance on data preprocessing and show that calling genes from assembled contigs rather than directly from reads dramatically improves performance. Finally, we apply our predictor to large-scale metagenomic data sets from marine and human microbiomes to illustrate how community-wide growth prediction can be a powerful approach for hypothesis generation. Altogether, we provide an updated tool with clear guidelines for users about the uses and pitfalls of metagenomic prediction of the average community-wide maximal growth rate. IMPORTANCE Microbes dominate nearly every known habitat, and therefore tools to survey the structure and function of natural microbial communities are much needed. Metagenomics, in which the DNA content of an entire community of organisms is sequenced all at once, allows us to probe the genetic diversity contained in a habitat. Yet, mapping metagenomic information to the actual traits of community members is a difficult and largely unsolved problem. Here, we present and validate a tool that allows users to predict the average maximum growth rate of a microbial community directly from metagenomic data. Maximum growth rate is a fundamental characteristic of microbial species that can give us a great deal of insight into their ecological role, and by applying our community-level predictor to large-scale metagenomic data sets from marine and human-associated microbiomes, we show how community-wide growth prediction can be a powerful approach for hypothesis generation.}, }
@article {pmid36189957, year = {2022}, author = {Hunter, BT and Flury, JD and Cocioba, SS and Cope-Arguello, ML and Helms, JM and García, KH and Dominguez, G and Taniguchi, DA and Becket, E}, title = {Engineering an incubation environment that mimics in situ conditions for in vitro coastal microbiome studies.}, journal = {BioTechniques}, volume = {73}, number = {4}, pages = {183-191}, pmid = {36189957}, issn = {1940-9818}, support = {R15 ES033027/ES/NIEHS NIH HHS/United States ; R25 GM066341/GM/NIGMS NIH HHS/United States ; }, mesh = {*Microbiota/genetics ; Temperature ; }, abstract = {Coastal environments are dynamic and can vary widely on short- or long-term scales depending on location and weather. Incubation equipment that reflects these changes through programmable gradient light and temperature cycles would permit more precise in vitro coastal microbiome studies. Here we present an open-source incubation environment that mimics in situ conditions for in vitro coastal microbiome studies using a modified shaking water bath that has fully customizable temperature and light gradients that can also mimic real-time field conditions. We compared coastal microbial community profiles incubated in situ and in our build mimicking field conditions over 48 h. Analyses of congruence indicated significant overlap (p > 0.2) between microbial communities incubated in situ and in vitro at each time point.}, }
@article {pmid36189437, year = {2022}, author = {Moussa, DG and Sharma, AK and Mansour, TA and Witthuhn, B and Perdigão, J and Rudney, JD and Aparicio, C and Gomez, A}, title = {Functional signatures of ex-vivo dental caries onset.}, journal = {Journal of oral microbiology}, volume = {14}, number = {1}, pages = {2123624}, pmid = {36189437}, issn = {2000-2297}, support = {R01 DE026117/DE/NIDCR NIH HHS/United States ; R90 DE023058/DE/NIDCR NIH HHS/United States ; }, abstract = {BACKGROUND: The etiology of dental caries remains poorly understood. With the advent of next-generation sequencing, a number of studies have focused on the microbial ecology of the disease. However, taxonomic associations with caries have not been consistent. Researchers have also pursued function-centric studies of the caries microbial communities aiming to identify consistently conserved functional pathways. A major question is whether changes in microbiome are a cause or a consequence of the disease. Thus, there is a critical need to define conserved functional signatures at the onset of dental caries.<br><br>METHODS: Since it is unethical to induce carious lesions clinically, we developed an innovative longitudinal ex-vivo model integrated with the advanced non-invasive multiphoton second harmonic generation bioimaging to spot the very early signs of dental caries, combined with 16S rRNA short amplicon sequencing and liquid chromatography-mass spectrometry-based targeted metabolomics.<br><br>FINDINGS: For the first time, we induced longitudinally monitored caries lesions validated with the scanning electron microscope. Consequently, we spotted the caries onset and, associated with it, distinguished five differentiating metabolites - Lactate, Pyruvate, Dihydroxyacetone phosphate, Glyceraldehyde 3-phosphate (upregulated) and Fumarate (downregulated). Those metabolites co-occurred with certain bacterial taxa; Streptococcus, Veillonella, Actinomyces, Porphyromonas, Fusobacterium, and Granulicatella, regardless of the abundance of other taxa.<br><br>INTERPRETATION: These findings are crucial for understanding the etiology and dynamics of dental caries, and devising targeted interventions to prevent disease progression.}, }
@article {pmid36188424, year = {2022}, author = {Geldenhuys, J and Redelinghuys, MJ and Lombaard, HA and Ehlers, MM and Cowan, D and Kock, MM}, title = {Diversity of the gut, vaginal and oral microbiome among pregnant women in South Africa with and without pre-eclampsia.}, journal = {Frontiers in global women's health}, volume = {3}, number = {}, pages = {810673}, pmid = {36188424}, issn = {2673-5059}, abstract = {BACKGROUND: Changes in microbial communities are a known characteristic of various inflammatory diseases and have been linked to adverse pregnancy outcomes, such as preterm birth. However, there is a paucity of information regarding the taxonomic composition and/or diversity of microbial communities in pre-eclampsia. The aim of this study was to determine the diversity of the gut, vaginal and oral microbiome in a cohort of South African pregnant women with and without pre-eclampsia. The diversity of the gut, vaginal and oral microbiome was determined by targeted next generation sequencing (NGS) of the V3 and V4 region of the 16S rRNA gene on the Illumina MiSeq platform.<br><br>RESULTS: In this study population, pre-eclampsia was associated with a significantly higher alpha diversity (P = 0.0472; indicated by the Shannon index) in the vaginal microbiome accompanied with a significant reduction in Lactobacillus spp. (P = 0.0275), compared to normotensive pregnant women. Lactobacillus iners was identified as the predominant species of the vaginal microbiome in both cohorts. High inter-individual variation in alpha diversity was observed in the gut and oral microbiome in both cohorts. Although differences in the relative abundance of bacteria at all phylogenetic levels were observed, overall microbial composition of the gut, oral and vaginal microbiome was not significantly different in the pre-eclampsia cohort compared to the normotensive cohort.<br><br>CONCLUSION: Collectively, a reduction of Lactobacillus spp., and predominance of L. iners in pregnant women with pre-eclampsia could suggest an unstable vaginal microbiome that might predispose pregnant women to develop pre-eclampsia. The lack of significant structural changes in the gut, oral and vaginal microbiome does not suggest that the characterized communities play a role in pre-eclampsia, but could indicate a characteristic unique to the study population. The current study provided novel information on the diversity of the gut, oral and vaginal microbiome among pregnant women in South Africa with and without pre-eclampsia. The current study provides a baseline for further investigations on the potential role of microbial communities in pre-eclampsia.}, }
@article {pmid36187988, year = {2022}, author = {Zufiaurre, A and Felip, M and Camarero, L and Sala-Faig, M and Juhanson, J and Bonilla-Rosso, G and Hallin, S and Catalan, J}, title = {Bacterioplankton seasonality in deep high-mountain lakes.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {935378}, pmid = {36187988}, issn = {1664-302X}, abstract = {Due to global warming, shorter ice cover duration might drastically affect the ecology of lakes currently undergoing seasonal surface freezing. High-mountain lakes show snow-rich ice covers that determine contrasting conditions between ice-off and ice-on periods. We characterized the bacterioplankton seasonality in a deep high-mountain lake ice-covered for half a year. The lake shows a rich core bacterioplankton community consisting of three components: (i) an assemblage stable throughout the year, dominated by Actinobacteria, resistant to all environmental conditions; (ii) an ice-on-resilient assemblage dominating during the ice-covered period, which is more diverse than the other components and includes a high abundance of Verrucomicrobia; the deep hypolimnion constitutes a refuge for many of the typical under-ice taxa, many of which recover quickly during autumn mixing; and (iii) an ice-off-resilient assemblage, which members peak in summer in epilimnetic waters when the rest decline, characterized by a dominance of Flavobacterium, and Limnohabitans. The rich core community and low random elements compared to other relatively small cold lakes can be attributed to its simple hydrological network in a poorly-vegetated catchment, the long water-residence time (ca. 4 years), and the long ice-cover duration; features common to many headwater deep high-mountain lakes.}, }
@article {pmid36187961, year = {2022}, author = {Yang, X and Yu, X and He, Q and Deng, T and Guan, X and Lian, Y and Xu, K and Shu, L and Wang, C and Yan, Q and Yang, Y and Wu, B and He, Z}, title = {Niche differentiation among comammox (Nitrospira inopinata) and other metabolically distinct nitrifiers.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {956860}, pmid = {36187961}, issn = {1664-302X}, abstract = {Due to global change, increasing nutrient input to ecosystems dramatically affects the nitrogen cycle, especially the nitrification process. Nitrifiers including ammonia-oxidizing archaea (AOAs), ammonia-oxidizing bacteria (AOBs), nitrite-oxidizing bacteria (NOBs), and recently discovered complete ammonia oxidizers (comammoxs) perform nitrification individually or in a community. However, much remains to be learned about their niche differentiation, coexistence, and interactions among those metabolically distinct nitrifiers. Here, we used synthetic microbial ecology approaches to construct synthetic nitrifying communities (SNCs) with different combinations of Nitrospira inopinata as comammox, Nitrososphaera gargensis as AOA, Nitrosomonas communis as AOB, and Nitrospira moscoviensis as NOB. Our results showed that niche differentiation and potential interactions among those metabolically distinct nitrifiers were determined by their kinetic characteristics. The dominant species shifted from N. inopinata to N. communis in the N4 community (with all four types of nitrifiers) as ammonium concentrations increased, which could be well explained by the kinetic difference in ammonia affinity, specific growth rate, and substrate tolerance of nitrifiers in the SNCs. In addition, a conceptual model was developed to infer niche differentiation and possible interactions among the four types of nitrifiers. This study advances our understanding of niche differentiation and provides new strategies to further study their interactions among the four types of nitrifiers.}, }
@article {pmid36187958, year = {2022}, author = {Li, Y and Zhang, Y and Xue, S}, title = {pH mediated assemblage of carbon, nitrogen, and sulfur related microbial communities in petroleum reservoirs.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {952285}, pmid = {36187958}, issn = {1664-302X}, abstract = {Microorganisms are the core drivers of biogeochemistry processes in petroleum reservoirs and have been widely used to enhance petroleum recovery. However, systematic information about the microbial communities related to the C-N-S cycle in petroleum reservoirs under different pH conditions remains poorly understood. In this study, 16S rRNA gene data from 133 petroleum samples were collected, and 756 C-N-S related genera were detected. The Chao1 richness and Shannon diversity indices for the C-N-S-related microbial communities showed significant differences among different pH conditions and at the lowest levels in acidic conditions with pH values of 4.5-6.5. In addition, pH was the most important factor influencing the C-N-S related microbial communities and contributed to 17.95% of the variation in the methanogenesis community. A total of 55 functional genera were influenced by pH, which accounted for 42.08% of the C-N-S related genera. Among them, the genera Pseudomonas and Arcobacter were the highest and were concentrated in acidic conditions with pH values of 4.5-6.5. In parallel, 56 predicted C-N-S related genes were examined, and pH affected 16 of these genes, including putative chitinase, mcrA, mtrB, cysH, narGHIVYZ, nirK, nirB, nifA, sat, aprAB, and dsrAB. Furthermore, the co-occurrence networks of the C-N-S related microbial communities distinctly varied among the different pH conditions. The acidic environment exhibited the lowest complex network with the lowest keystone taxa number, and Escherichia-Shigella was the only keystone group that existed in all three networks. In summary, this study strengthened our knowledge regarding the C-N-S related microbial communities in petroleum reservoirs under different pH conditions, which is of great significance for understanding the microbial ecology and geochemical cycle of petroleum reservoirs.}, }
@article {pmid36185017, year = {2022}, author = {Zhang, Y and Xue, S and Chang, X and Li, Y and Yue, X}, title = {Nutrients Changed the Assembly Processes of Profuse and Rare Microbial Communities in Coals.}, journal = {Polish journal of microbiology}, volume = {71}, number = {3}, pages = {359-370}, pmid = {36185017}, issn = {2544-4646}, mesh = {*Coal ; Firmicutes/genetics ; Methane ; *Microbiota ; Nutrients ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Nutrient stimulation is considered effective for improving biogenic coalbed methane production potential. However, our knowledge of the microbial assembly process for profuse and rare microbial communities in coals under nutrient stimulation is still limited. This study collected 16S rRNA gene data from 59 microbial communities in coals for a meta-analysis. Among these communities, 116 genera were identified as profuse taxa, and the remaining 1,637 genera were identified as rare taxa. Nutrient stimulation increased the Chao1 richness of profuse and rare genera and changed the compositions of profuse and rare genera based on nonmetric multidimensional scaling with Bray-Curtis dissimilarities. In addition, many profuse and rare genera belonging to Proteobacteria and Acidobacteria were reduced, whereas those belonging to Euryarchaeota and Firmicutes were increased under nutrient stimulation. Concomitantly, the microbial co-occurrence relationship network was also altered by nutrient addition, and many rare genera mainly belonging to Firmicutes, Bacteroides, and Euryarchaeota also comprised the key microorganisms. In addition, the compositions of most of the profuse and rare genera in communities were driven by stochastic processes, and nutrient stimulation increased the relative contribution of dispersal limitation for both profuse and rare microbial community assemblages and that of variable selection for rare microbial community assemblages. In summary, this study strengthened our knowledge regarding the mechanistic responses of coal microbial diversity and community composition to nutrient stimulation, which are of great importance for understanding the microbial ecology of coals and the sustainability of methane production stimulated by nutrients.}, }
@article {pmid36182151, year = {2023}, author = {Wang, C and Yao, Z and Zhan, P and Yi, X and Chen, J and Xiong, J}, title = {Significant tipping points of sediment microeukaryotes forewarn increasing antibiotic pollution.}, journal = {Journal of environmental sciences (China)}, volume = {124}, number = {}, pages = {429-439}, doi = {10.1016/j.jes.2021.10.031}, pmid = {36182151}, issn = {1001-0742}, mesh = {*Ammonium Compounds ; *Anti-Bacterial Agents ; Environmental Biomarkers ; Phosphates ; Tetracyclines ; Wastewater ; }, abstract = {Antibiotic pollution imposes urgent threats to public health and microbial-mediated ecological processes. Existing studies have primarily focused on bacterial responses to antibiotic pollution, but they ignored the microeukaryotic counterpart, though microeukaryotes are functionally important (e.g., predators and saprophytes) in microbial ecology. Herein, we explored how the assembly of sediment microeukaryotes was affected by increasing antibiotic pollution at the inlet (control) and across the outlet sites along a shrimp wastewater discharge channel. The structures of sediment microeukaryotic community were substantially altered by the increasing nutrient and antibiotic pollutions, which were primarily controlled by the direct effects of phosphate and ammonium (-0.645 and 0.507, respectively). In addition, tetracyclines exerted a large effect (0.209), including direct effect (0.326) and indirect effect (-0.117), on the microeukaryotic assembly. On the contrary, the fungal subcommunity was relatively resistant to antibiotic pollution. Segmented analysis depicted nonlinear responses of microeukaryotic genera to the antibiotic pollution gradient, as supported by the significant tipping points. We screened 30 antibiotic concentration-discriminatory taxa of microeukaryotes, which can quantitatively and accurately predict (98.7% accuracy) the in-situ antibiotic concentration. Sediment microeukaryotic (except fungal) community is sensitive to antibiotic pollution, and the identified bioindicators could be used for antibiotic pollution diagnosis.}, }
@article {pmid36181942, year = {2022}, author = {Shen, Z and Xie, G and Zhang, Y and Yu, B and Shao, K and Gao, G and Tang, X}, title = {Similar assembly mechanisms but distinct co-occurrence patterns of free-living vs. particle-attached bacterial communities across different habitats and seasons in shallow, eutrophic Lake Taihu.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {314}, number = {}, pages = {120305}, doi = {10.1016/j.envpol.2022.120305}, pmid = {36181942}, issn = {1873-6424}, mesh = {*Lakes/microbiology ; *Ecosystem ; RNA, Ribosomal, 16S/genetics ; Seasons ; Bacteria/genetics ; Phosphorus ; Nitrogen ; Methane ; Carbon ; }, abstract = {Eutrophication due to nitrogen and phosphorus input is an increasing problem in lake ecosystems. Free-living (FL) and particle-attached (PA) bacterial communities play a primary role in mediating biogeochemical processes in these lakes and in responding to eutrophication. However, knowledge of factors governing function, assembly mechanisms, and co-occurrence patterns of these communities remain poorly understood and are key challenges in microbial ecology. To address this knowledge gap, we collected 96 samples from Lake Taihu across four seasons and investigated the bacterial community using 16S rRNA gene sequencing. Our results demonstrate that the α-diversity, β-diversity, community composition, and functional composition of FL and PA bacterial communities exhibited differing spatiotemporal dynamics. FL and PA bacterial communities displayed similar distance-decay relationships across seasons. Deterministic processes (i.e., environmental filtering and species interaction) were the primary factors shaping community assembly in both FL and PA bacteria. Similar environmental factors shaped bacterial community structure while different environmental factors drove bacterial functional composition. Habitat filtering influenced enrichment of bacteria within specific functional groups. Among them, the FL bacterial community appeared to play a critical role in methane-utilization, whereas the PA bacteria contributed more to biogeochemical cycling of carbon. FL and PA bacterial communities exhibited distinct co-occurrence pattern across different seasons. In the FL network, Methylotenera and Methylophilaceae were identified as keystone taxa, while Burkholderiaceae and the hgcI clade were keystone taxa in the PA network. The PA bacterial community appeared to possess greater stability in the face of environmental change than did FL counterparts. These results broaden our knowledge of the driving factors, co-occurrence patterns, and assembly processes in FL and PA bacterial communities in eutrophic ecosystems and provide improved insight into the underlying mechanisms responsible for these results.}, }
@article {pmid36180800, year = {2023}, author = {Uroosa,  and Kazmi, SSUH and Rahman, MS and Xu, H}, title = {Can functional units of periphytic protozoan communities be used to evaluate the effects of harmful algal blooms on ecological quality in marine ecosystems?.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {6}, pages = {16408-16417}, pmid = {36180800}, issn = {1614-7499}, mesh = {*Ecosystem ; Harmful Algal Bloom ; *Dinoflagellida ; }, abstract = {Based on biological traits, the ecological quality status under the pressure of two harmful algal bloom (HAB) species was evaluated using functional units (FUs) of periphytic protozoan communities. Five treatments with different concentrations of Alexandrium tamarense and Gymnodinium catenatum, i.e., 10[0], 10[2], 10[3], 10[4], and 10[5] cells ml[-1], were used. A total of 20 FUs were identified from 25 test protozoan species. Among these FUs, vagile algivores with large sizes showed a decreasing trend (i.e., in diversity and abundance) with increasing concentrations of algae, while vagile bacterivores and non-selectives with small sizes dominated at concentrations of 10[4] cells ml[-1] of both algal species. Ellipse tests on pair-wise functional distinctness indices revealed a significant departure of test protozoan communities from an expected functional distinctness breadth when algal concentrations exceeded 10[4] cells ml[-1]. Based on these findings, it was concluded that FUs of periphytic protozoa may be a useful tool for evaluating the effects of HABs on ecological quality status in marine ecosystems.}, }
@article {pmid36180621, year = {2023}, author = {Signorini, M and Midolo, G and Cesco, S and Mimmo, T and Borruso, L}, title = {A Matter of Metals: Copper but Not Cadmium Affects the Microbial Alpha-Diversity of Soils and Sediments - a Meta-analysis.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1071-1081}, pmid = {36180621}, issn = {1432-184X}, support = {TN200V//Libera Universit&#xe0; di Bolzano/ ; }, mesh = {Copper/analysis ; Cadmium ; Soil ; *Soil Pollutants/analysis ; Soil Microbiology ; *Metals, Heavy/analysis ; Bacteria/genetics ; }, abstract = {Heavy metal (HM) accumulation in soil affects plants and soil fauna, yet the effect on microbial alpha-diversity remains unclear, mainly due to the absence of dedicated research synthesis (e.g. meta-analysis). Here, we report the first meta-analysis of the response of soil microbial alpha-diversity to the experimental addition of cadmium (Cd) and copper (Cu). We considered studies conducted between 2013 and 2022 using DNA metabarcoding of bacterial and fungal communities to overcome limitations of other cultivation- and electrophoresis-based techniques. Fungi were discarded due to the limited study number (i.e. 6 studies). Bacterial studies resulted in 66 independent experiments reported in 32 primary papers from four continents. We found a negative dose-dependent response for Cu but not for Cd for bacterial alpha-diversity in the environments, only for Cu additions exceeding 29.6 mg kg[-1] (first loss of - 0.06% at 30 mg kg[-1]). The maximal loss of bacterial alpha-diversity registered was 13.89% at 3837 mg kg[-1]. Our results first highlight that bacterial communities behave differently to soil pollution depending on the metal. Secondly, our study suggests that even extreme doses of Cu do not cause a dramatic loss in alpha-diversity, highlighting how the behaviour of bacterial communities diverges from soil macro-organisms.}, }
@article {pmid36179845, year = {2023}, author = {Dziurzynski, M and Gorecki, A and Pawlowska, J and Istel, L and Decewicz, P and Golec, P and Styczynski, M and Poszytek, K and Rokowska, A and Gorniak, D and Dziewit, L}, title = {Revealing the diversity of bacteria and fungi in the active layer of permafrost at Spitsbergen island (Arctic) - Combining classical microbiology and metabarcoding for ecological and bioprospecting exploration.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 2}, pages = {159072}, doi = {10.1016/j.scitotenv.2022.159072}, pmid = {36179845}, issn = {1879-1026}, mesh = {*Bioprospecting ; Soil Microbiology ; *Permafrost ; Ecosystem ; Biodiversity ; Svalbard ; Bacteria/genetics ; Soil ; Fungi/genetics ; Arctic Regions ; }, abstract = {Arctic soils are constantly subjected to extreme environmental conditions such as low humidity, strong winds, high salinity, freeze-thaw cycles, UV exposition, and low nutrient availability, therefore, they have developed unique microbial ecosystems. These environments provide excellent opportunities to study microbial ecology and evolution within pristine (i.e. with limited anthropogenic influence) regions since the High Arctic is still considered one of the wildest and least explored environments on the planet. This environment is also of interest for the screening and recovery of unique microbial strains suitable for various biotechnological applications. In this study, a combination of culture-depended and culture-independent approaches was used to determine the cultivation bias in studies of the diversity of cold-active microorganisms. Cultivation bias is a reduction in recovered diversity, introduced when applying a classical culturing technique. Six different soil types, collected in the vicinity of the Polish Polar Station Hornsund (Spitsbergen, Norway), were tested. It was revealed that the used media allowed recovery of only 6.37 % of bacterial and 20 % of fungal genera when compared with a culture-independent approach. Moreover, it was shown that a combination of R2A and Marine Broth media recovered as much as 93.6 % of all cultivable bacterial genera detected in this study. Based on these results, a novel protocol for genome-guided bioprospecting, combining a culture-dependent approach, metabarcoding, next-generation sequencing, and genomic data reuse was developed. With this methodology, 14 psychrotolerant, multi-metal-resistant strains, including the highly promising Rhodococcus spp., were obtained. These strains, besides increased metal tolerance, have a petroleum hydrocarbon utilization capacity, and thus may be good candidates for future bioremediation technologies, also suited to permanently cold regions.}, }
@article {pmid36179842, year = {2023}, author = {Romans-Casas, M and Perona-Vico, E and Dessì, P and Bañeras, L and Balaguer, MD and Puig, S}, title = {Boosting ethanol production rates from carbon dioxide in MES cells under optimal solventogenic conditions.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 1}, pages = {159124}, doi = {10.1016/j.scitotenv.2022.159124}, pmid = {36179842}, issn = {1879-1026}, mesh = {*Carbon Dioxide ; *Ethanol ; Biofuels ; Electricity ; Acetic Acid ; Electrodes ; }, abstract = {Microbial Electrosynthesis (MES) has been widely applied for acetic acid (HA) production from CO2 and electricity. Ethanol (EtOH) has a higher market value than HA, and wide application in industry and as a biofuel. However, it has only been obtained sporadically and at low concentrations, probably due to sub-optimal operating conditions. This study aimed at enhancing EtOH productivity in MES cells by jointly optimising key operation parameters, including pH, H2 and CO2 partial pressure (pH2 and pCO2), and HA concentration, to promote solventogenesis. Two H-type cells were operated in fed-batch mode at -0.8 V vs. SHE with CO2 as the sole carbon source. A mixed culture, enriched with Clostridium ljungdahlii was used as the biocatalyst. The combination of low pH (<4.5) and pCO2 (<0.3 atm), along with high HA concentration (about 6 g L[-1]) and pH2 (>3 atm), were mandatory conditions for maintaining an efficient solventogenic culture, dominated by Clostridium sp., capable of high-rate EtOH production. The maximum EtOH production rate was 10.95 g m[-2] d[-1], and a concentration of 5.28 g L[-1] was achieved. Up to 30 % of the electrons and 15.2 % of the carbon provided were directed towards EtOH production, and 28.1 kWh were required for the synthesis of 1 kg of EtOH from CO2. These results highlight that strict conditions are required for a continuous, reliable, EtOH production in MES cells. Future investigation should focus on improving cell configuration to achieve EtOH production at higher current densities while minimizing the electric energy input.}, }
@article {pmid36178538, year = {2023}, author = {Ishigami, K and Jang, S and Itoh, H and Kikuchi, Y}, title = {Obligate Gut Symbiotic Association with Caballeronia in the Mulberry Seed Bug Paradieuches dissimilis (Lygaeoidea: Rhyparochromidae).}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1307-1318}, pmid = {36178538}, issn = {1432-184X}, support = {21F21090//Japan Society for the Promotion of Science/ ; 20H03303//Ministry of Education, Culture, Sports, Science and Technology (MEXT) KAKENHI/ ; }, mesh = {Humans ; Animals ; Adult ; *Morus ; Symbiosis ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Heteroptera/genetics/microbiology ; *Burkholderiaceae ; Insecta ; Bacteria ; }, abstract = {Many insects possess symbiotic bacteria in their bodies, and microbial symbionts play pivotal metabolic roles for their hosts. Members of the heteropteran superfamilies Coreoidea and Lygaeoidea stinkbugs harbor symbionts of the genus Caballeronia in their intestinal tracts. Compared with symbiotic associations in Coreoidea, those in Lygaeoidea insects are still less understood. Here, we investigated a symbiotic relationship involving the mulberry seed bug Paradieuches dissimilis (Lygaeoidea: Rhyparochromidae) using histological observations, cultivation of the symbiont, 16S rRNA gene amplicon sequencing, and infection testing of cultured symbionts. Histological observations and cultivation revealed that P. dissimilis harbors Caballeronia symbionts in the crypts of its posterior midgut. 16S rRNA gene amplicon sequencing of field-collected P. dissimilis confirmed that the genus Caballeronia is dominant in the midgut of natural populations of P. dissimilis. In addition, PCR diagnostics showed that the eggs were free of symbiotic bacteria, and hatchlings horizontally acquired the symbionts from ambient soil. Infection and rearing experiments revealed that symbiont-free aposymbiotic individuals had abnormal body color, small body size, and, strikingly, a low survival rate, wherein no individuals reached adulthood, indicating an obligate cooperative mutualism between the mulberry seed bug and Caballeronia symbionts.}, }
@article {pmid36175476, year = {2022}, author = {Gan, L and Zheng, J and Xu, WH and Lin, J and Liu, J and Zhang, Y and Wu, Z and Lv, Z and Jia, Y and Guo, Q and Chen, S and Liu, C and Defoirdt, T and Qin, Q and Liu, Y}, title = {Deciphering the virulent Vibrio harveyi causing spoilage in muscle of aquatic crustacean Litopenaeus vannamei.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {16296}, pmid = {36175476}, issn = {2045-2322}, mesh = {Animals ; Humans ; Lithium ; Muscle Fibers, Skeletal ; *Penaeidae ; Seafood ; *Vibrio ; *Vibrio cholerae ; }, abstract = {The muscle of aquatic crustaceans is perishable and susceptible to environmental contamination. Vibrio harveyi is a widely occurring pathogen in aquatic animals. Here, bath treatment with a virulent V. harveyi strain (which was added directly in the rearing water to imitate environmental contamination) isolated from the muscle of the whiteleg shrimp, Litopenaeus vannamei, caused the muscle of Li. vannamei to display a whitish-opaque appearance due to microscopic changes including muscle lysis, muscle fiber damage and microbial colonization. When administered orally by incorporating this isolate in feed (which is an imitation of infection via natural route), rather than direct invasion followed by colonization in the muscle, this isolate indirectly stimulated severe muscle necrosis in Li. vannamei via steering the enrichment of two important (human) pathogens, V. cholerae and V. vulnificus, and one environmental bacterium Pseudomonas oleovorans, based on the meta-taxonomic analyses. In addition to the scientifically proven viral diseases, our research proved that bacterial agents are also capable of causing muscle spoilage in crustaceans via changing the microbial composition, and that the crustaceans might be exploited as the wide-spectrum sensitive bio-detector to indicate the extent of microbial contamination.}, }
@article {pmid36173731, year = {2022}, author = {Girolamini, L and Pascale, MR and Salaris, S and Mazzotta, M and Orsini, M and Grottola, A and Zini, N and Cristino, S}, title = {Legionella bononiensis sp. nov., isolated from a hotel water distribution system in northern Italy.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {72}, number = {9}, pages = {}, doi = {10.1099/ijsem.0.005512}, pmid = {36173731}, issn = {1466-5034}, mesh = {Agar ; Bacterial Typing Techniques ; Base Composition ; Catalase/genetics ; Charcoal ; Ciprofloxacin ; Cycloheximide ; Cysteine/genetics ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Gelatinases/genetics ; Glycine/genetics ; Hippurates ; *Legionella ; Nucleotides ; Phylogeny ; Polymyxin B/analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Vancomycin ; Water ; }, abstract = {Legionella-like isolates, strains 27fs60, 30fs61 and 30cs62[T], were isolated from a hotel water distribution system in the Emilia-Romagna region, Italy. Isolates were Gram- and Ziehl Neelsen-stain-negative, rod-shaped, with transitory flagella presence and able to grow at 32-37 °C (with an optimum at 32 °C) on buffered charcoal-yeast extract agar with l-cysteine, glycine-vancomycin-polymyxin B-cycloheximide agar and Wadowsky-Yee medium agar. The strains showed positive reactions for oxidase, hippurate and gelatinase and a weakly positive reaction for catalase. Based on the EUCAST cut-off, strain 30cs62[T] was resistant to ciprofloxacin (5 mg l[-1]). The mip and rpoB gene sequences of the three strains showed close matches to those of Legionella quateirensis ATCC 49507[T] with similarity values of 98.2 and 94.5 %, respectively. Whole genome sequencing of the three strains was performed, resulting in G+C contents of 39.0, 39.1 and 39.0 mol%, respectively. The identity percentage measured by average nucleotide identity between the three strains and their respective closest strains were: 91.32 % L. quateirensis NCTC 12376[T], 91.45 % L. quateirensis ATCC 49507[T] and 91.45 % L. quateirensis ATCC 49507[T], respectively. The digital DNA-DNA hybridization analysis demonstrated how the isolates were separated from the most related phylogenetic Legionella species (L. quateirensis ATCC 49507[T], ≤40.10 % DNA-DNA relatedness). The concatenated phylogenetic tree based on 16S rRNA, mip, rpoB and rnpB genes, shows a close relationship with L. quateirensis ATCC 49507[T]. The results obtained confirm the status of an independent species. The name proposed for this species is Legionella bononiensis sp. nov. with 30cs62[T] (=ATCC TSD-262[T]=DSM 112526[T]) as the type strain.}, }
@article {pmid36173132, year = {2022}, author = {Izcue, J and Palacios-García, I and Rojas Traverso, F and Koller, M and Parada, FJ}, title = {Perspectives on Inequity and Health Disparities in Chile and Their Relationship to Microbial Ecology.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0149621}, pmid = {36173132}, issn = {2379-5077}, mesh = {Humans ; Chile/epidemiology ; *COVID-19/epidemiology ; Income ; *Pandemics ; }, abstract = {Among countries in the Organisation for Economic Cooperation and Development (OECD), Chile stands out as having important inequalities in income distribution, dietary quality, access to urban green spaces, and health outcomes. People in lower socioeconomic groups consistently show higher rates of noncommunicable chronic diseases and are being hit the hardest by the COVID-19 pandemic. These chronic conditions are increasingly considered to be shaped, or affected by, the human gut microbiome. Moreover, inequity as an overarching concept might also be associated with microbial patterns and if so, this may represent a novel pathway through which to address health and other disparities. Focusing on the case of Chile, our goal is to contribute to a critical discussion and motivate researchers and policymakers to consider the role of the microbiome in social equity in future endeavors.}, }
@article {pmid36172557, year = {2022}, author = {Li, J and Yu, X and Shan, Q and Shi, Z and Li, J and Zhao, X and Chang, C and Yu, J}, title = {Integrated volatile metabolomic and transcriptomic analysis provides insights into the regulation of floral scents between two contrasting varieties of Lonicera japonica.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {989036}, pmid = {36172557}, issn = {1664-462X}, abstract = {Lonicera japonica Thunb., belonging to the Caprifoliaceae family, is an important traditional Chinese medicinal plant. The L. japonica flower (LJF) is widely used in medicine, cosmetics, drinks, and food due to its medicinal and sweet-smelling properties. Considerable efforts have been devoted to investigating the pharmacological activities of LJF; however, the regulatory mechanism of the floral scents remains unknown. We previously selected and bred an elite variety of L. japonica var. chinensis Thunb. called 'Yujin2', which has a strong aroma and is used in functional drinks and cosmetics. In order to reveal the regulatory mechanism of the floral scents of LJF, volatile metabolomic and transcriptomic analyses of the LJF at the silver flowering stage of 'Yujin2' (strong aroma) and 'Fengjin1' (bland odor) were performed. Our results revealed that a total of 153 metabolites and 9,523 genes were differentially regulated in LJF between 'Yujin2' and 'Fengjin1'. The integrated analysis of omics data indicated that the biosynthetic pathways of terpenoids (i.e., monoterpenoids, including geraniol and alpha-terpineol; sesquiterpenoids, including farnesol, farnesal, and alpha-farnesene; triterpenoid squalene), tryptophan and its derivatives (methyl anthranilate), and fatty acid derivatives, were major contributors to the stronger aroma of 'Yujin2' compared to 'Fengjin1'. Moreover, several genes involved in the terpenoid biosynthetic pathway were characterized using quantitative real-time PCR. These results provide insights into the metabolic mechanisms and molecular basis of floral scents in LJF, enabling future screening of genes related to the floral scent regulation, such as alpha-terpineol synthase, geranylgeranyl diphosphate synthase, farnesyl pyrophosphate synthase, anthranilate synthase, as well as transcription factors such as MYB, WRKY, and LFY. The knowledge from this study will facilitate the breeding of quality-improved and more fragrant variety of L. japonica for ornamental purpose and functional beverages and cosmetics.}, }
@article {pmid36171563, year = {2022}, author = {Junghare, M and Frey, J and Naji, KM and Spiteller, D and Vaaje-Kolstad, G and Schink, B}, title = {Isophthalate:coenzyme A ligase initiates anaerobic degradation of xenobiotic isophthalate.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {227}, pmid = {36171563}, issn = {1471-2180}, mesh = {Acetyl Coenzyme A/metabolism ; Adenosine Monophosphate/metabolism ; Adenosine Triphosphate/metabolism ; Anaerobiosis ; Base Composition ; Benzoates/metabolism ; Carbon ; Carcinogens ; Coenzyme A/metabolism ; Coenzyme A Ligases ; *Diphosphates ; *Environmental Pollutants ; Escherichia coli/metabolism ; Glutarates ; Hydroxybenzoates ; Mutagens ; Oxygen ; Phenylacetates/metabolism ; Phthalic Acids ; Phylogeny ; Plastics ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; Sulfur ; Xenobiotics ; }, abstract = {BACKGROUND: Environmental contamination from synthetic plastics and their additives is a widespread problem. Phthalate esters are a class of refractory synthetic organic compounds which are widely used in plastics, coatings, and for several industrial applications such as packaging, pharmaceuticals, and/or paints. They are released into the environment during production, use and disposal, and some of them are potential mutagens and carcinogens. Isophthalate (1,3-benzenedicarboxylic acid) is a synthetic chemical that is globally produced at a million-ton scale for industrial applications and is considered a priority pollutant. Here we describe the biochemical characterization of an enzyme involved in anaerobic degradation of isophthalate by the syntrophically fermenting bacterium Syntrophorhabdus aromaticivorans strain UI that activate isophthalate to isophthalyl-CoA followed by its decarboxylation to benzoyl-CoA.<br><br>RESULTS: Isophthalate:Coenzyme A ligase (IPCL, AMP-forming) that activates isophthalate to isophthalyl-CoA was heterologously expressed in E. coli (49.6&#x2009;kDa) for biochemical characterization. IPCL is homologous to phenylacetate-CoA ligase that belongs to the family of ligases that form carbon-sulfur bonds. In the presence of coenzyme A, Mg[2+] and ATP, IPCL converts isophthalate to isophthalyl-CoA, AMP and pyrophosphate (PPi). The enzyme was specifically induced after anaerobic growth of S. aromaticivorans in a medium containing isophthalate as the sole carbon source. Therefore, IPCL exhibited high substrate specificity and affinity towards isophthalate. Only substrates that are structurally related to isophthalate, such as glutarate and 3-hydroxybenzoate, could be partially converted to the respective coenzyme A esters. Notably, no activity could be measured with substrates such as phthalate, terephthalate&#xa0;and benzoate. Acetyl-CoA or succinyl-CoA did not serve as CoA donors. The enzyme has a theoretical pI of 6.8 and exhibited optimal activity between&#xa0;pH 7.0 to 7.5. The optimal temperature was between 25&#x2009;&#xb0;C and 37&#x2009;&#xb0;C. Denaturation temperature (Tm) of IPCL was found to be at about&#xa0;63&#x2009;&#xb0;C. The apparent KM values for isophthalate, CoA, and ATP were 409&#x2009;&#x3bc;M, 642&#x2009;&#x3bc;M, and 3580&#x2009;&#x3bc;M, respectively. Although S. aromaticivorans is a strictly anaerobic bacterium, the enzyme was found to be&#xa0;oxygen-insensitive and catalysed isophthalyl-CoA formation under both anoxic and oxic conditions.<br><br>CONCLUSION: We have successfully cloned&#xa0;the ipcl gene, expressed and characterized the corresponding IPCL&#xa0;enzyme, which plays a key role in isophthalate activation that initiates its activation and&#xa0;further degradation by S. aromaticivorans. Its biochemical characterization represents an important step in the elucidation of the complete degradation pathway of isophthalate.}, }
@article {pmid36170274, year = {2022}, author = {Mohammed, A and Hu, J and Murugesan, R and Cheng, HW}, title = {Effects of a synbiotic as an antibiotic alternative on behavior, production performance, cecal microbial ecology, and jejunal histomorphology of broiler chickens under heat stress.}, journal = {PloS one}, volume = {17}, number = {9}, pages = {e0274179}, pmid = {36170274}, issn = {1932-6203}, mesh = {Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Anti-Bacterial Agents/pharmacology ; Chickens ; Diet/veterinary ; Dietary Supplements ; Escherichia coli ; *Escherichia coli Infections ; *Heat Stress Disorders ; Heat-Shock Response ; Male ; *Synbiotics ; }, abstract = {The aim of this study was to examine if synbiotics present similar efficiency to a common antibiotic used in poultry production under heat stress (HS) conditions. Two hundred and forty-one-day-old male Ross 708 broiler chicks were distributed among 3 treatments with 8 pens per treatment of 80 birds each for a 42-day trial. From day 15, birds were heat stressed (32°C for 9 h daily, HS) and fed the basal diet (CONT), the basal diet mixed with an antibiotic (Bactiracin Methylene Disalicylate) (0.05 g/kg of feed, BMD) or a synbiotic (0.5 g/kg of feed, SYN). The treatment effects on bird behavior, production performance, jejunal histomorphology, and cecal microbial ecology were examined. Behavioral observation was recorded by using instantaneous scan sampling technique. Production parameters were measured on day 14, 28, and 42. Cecal microbial populations of Escherichia coli and Lactobacilli and jejunal histomorphological parameters were measured at day 42. The results showed that, SYN birds exhibited more feeding and preening but less drinking and panting behaviors compared with both BMD and CONT birds (P < 0.05). The SYN birds also had higher body weight (BW) at both day 28 and 42 compared to CONT birds (P < 0.05). At the end of the experiment, the counts of Escherichia coli of SYN birds were at the similar levels of BMD but were lower than that of CONT birds (P < 0.05); while there were no treatment effects on the populations of Lactobacilli (P > 0.05). In addition, SYN birds had greater villus height compared with both CONT and BMD birds (P < 0.05). These findings suggest that the dietary synbiotic supplement has significant performance and welfare benefits, with the potential to be used as an alternative to antibiotics for poultry meat production, especially during hot seasons.}, }
@article {pmid36167684, year = {2022}, author = {Seong, HJ and Roux, S and Hwang, CY and Sul, WJ}, title = {Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {157}, pmid = {36167684}, issn = {2049-2618}, mesh = {*Bacteriophages/genetics ; DNA ; DNA Methylation/genetics ; Metagenome/genetics ; Metagenomics ; Methyltransferases/genetics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life.<br><br>RESULTS: We reconstructed 15,056 viral, 252 prokaryotic, 56 giant viral, and 6 eukaryotic metagenome-assembled genomes from northwest Pacific Ocean seawater samples using short- and long-read sequencing approaches. These metagenome-derived genomes mostly represented novel taxa, and recruited a majority of reads. Thanks to single-molecule real-time (SMRT) sequencing technology, base modification could also be detected for these genomes. This showed that DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark.<br><br>CONCLUSIONS: Overall, this study elucidates that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome. Video Abstract.}, }
@article {pmid36166154, year = {2023}, author = {Duarte, IO and Hissa, DC and Quintela, BCSF and Rabelo, MC and Oliveira, FADS and Lima, NCB and Melo, VMM}, title = {Genomic Analysis of Surfactant-Producing Bacillus vallismortis TIM68: First Glimpse at Species Pangenome and Prediction of New Plipastatin-Like Lipopeptide.}, journal = {Applied biochemistry and biotechnology}, volume = {195}, number = {2}, pages = {753-771}, pmid = {36166154}, issn = {1559-0291}, support = {312462/2017-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {*Lipopeptides/pharmacology ; Surface-Active Agents/pharmacology/chemistry ; *Bacillus/genetics ; Genomics ; }, abstract = {Surfactants are applied in several industrial processes when the modification of interface activity and the stability of colloidal systems are required. Lipopeptides are a class of microbial biosurfactants produced by species of the Bacillus genus. The present study aimed at assembling and analyzing the genome of a new Bacillus vallismortis strain, TIM68, that was shown to produce surfactant lipopeptides. The draft genome was also screened for common virulence factors and antibiotics resistance genes to investigate the strain biosafety. Comparative genomics analyses, i.e., synteny, average nucleotide identity (ANI), and pangenome, were also carried out using strain TIM68 and publicly available B. vallismortis complete and partial genomes. Three peptide synthetase operons were found in TIM68 genome, and they were surfactin A, mojavensin, and a novel plipastatin-like lipopeptide named vallisin. No virulence factors that render pathogenicity to the strain have been identified, but a region of prophage, that may contain unknown pathogenic factors, has been predicted. The pangenome of the species was characterized as closed, with 57% of genes integrating the core genome. The results obtained here on the genetic potential of TIM68 strain should contribute to its exploration in biotechnological applications.}, }
@article {pmid36166070, year = {2023}, author = {Alcantara, DMC and Ikeda, P and Souza, CS and de Mello, VVC and Torres, JM and Lourenço, EC and Bassini-Silva, R and Herrera, HM and Machado, RZ and Barros-Battesti, DM and Graciolli, G and André, MR}, title = {Multilayer Networks Assisting to Untangle Direct and Indirect Pathogen Transmission in Bats.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1292-1306}, pmid = {36166070}, issn = {1432-184X}, support = {2018/02753-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/14124-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 59/300.187/2016//Funda&#xe7;&#xe3;o de Apoio ao Desenvolvimento do Ensino, Ci&#xea;ncia e Tecnologia do Estado de Mato Grosso do Sul/ ; 302420/2017-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 303802/2021-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 308768/2017-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; E-26/202.158/2015//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; RED-00253-16//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; }, mesh = {Animals ; *Chiroptera/microbiology ; Brazil ; *Mites ; }, abstract = {The importance of species that connect the different types of interactions is becoming increasingly recognized, and this role may be related to specific attributes of these species. Multilayer networks have two or more layers, which represent different types of interactions, for example, between different parasites and hosts that are nonetheless connected. The understanding of the ecological relationship between bats, ectoparasites, and vector-borne bacteria could shed some light on the complex transmission cycles of these pathogens. In this study, we investigated a multilayer network in Brazil formed by interactions between bat-bacteria, bat-ectoparasite, and ectoparasite-bacteria, and asked how these interactions overlap considering different groups and transmission modes. The multilayer network was composed of 31 nodes (12 bat species, 14 ectoparasite species, and five bacteria genera) and 334 links, distributed over three layers. The multilayer network has low modularity and shows a core-periphery organization, that is, composed of a few generalist species with many interactions and many specialist species participating in few interactions in the multilayer network. The three layers were needed to accurately describe the multilayer structure, while aggregation leads to loss of information. Our findings also demonstrated that the multilayer network is influenced by a specific set of species that can easily be connected to the behavior, life cycle, and type of existing interactions of these species. Four bat species (Artibeus lituratus, A. planirostris, Phyllostomus discolor, and Platyrrhinus lineatus), one ectoparasite species (Steatonyssus) and three bacteria genera (Ehrlichia, hemotropic Mycoplasma and Neorickettsia) are the most important species for the multilayer network structure. Finally, our study brings an ecological perspective under a multilayer network approach on the interactions between bats, ectoparasites, and pathogens. By using a multilayer approach (different types of interactions), it was possible to better understand these different ecological interactions and how they affect each other, advancing our knowledge on the role of bats and ectoparasites as potential pathogen vectors and reservoirs, as well as the modes of transmission of these pathogens.}, }
@article {pmid36164984, year = {2022}, author = {Li, HB and Xu, ML and Xu, XD and Tang, YY and Jiang, HL and Li, L and Xia, WJ and Cui, N and Bai, J and Dai, ZM and Han, B and Li, Y and Peng, B and Dong, YY and Aryal, S and Manandhar, I and Eladawi, MA and Shukla, R and Kang, YM and Joe, B and Yang, T}, title = {Faecalibacterium prausnitzii Attenuates CKD via Butyrate-Renal GPR43 Axis.}, journal = {Circulation research}, volume = {131}, number = {9}, pages = {e120-e134}, pmid = {36164984}, issn = {1524-4571}, support = {R01 HL143082/HL/NHLBI NIH HHS/United States ; R21 AG079357/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Butyrates/pharmacology/therapeutic use ; Disease Models, Animal ; *Faecalibacterium prausnitzii ; Inflammation ; Kidney/physiology ; Receptors, G-Protein-Coupled/genetics ; *Renal Insufficiency, Chronic ; }, abstract = {BACKGROUND: Despite available clinical management strategies, chronic kidney disease (CKD) is associated with severe morbidity and mortality worldwide, which beckons new solutions. Host-microbial interactions with a depletion of Faecalibacterium prausnitzii in CKD are reported. However, the mechanisms about if and how F prausnitzii can be used as a probiotic to treat CKD remains unknown.<br><br>METHODS: We evaluated the microbial compositions in 2 independent CKD populations for any potential probiotic. Next, we investigated if supplementation of such probiotic in a mouse CKD model can restore gut-renal homeostasis as monitored by its effects on suppression on renal inflammation, improvement in gut permeability and renal function. Last, we investigated the molecular mechanisms underlying the probiotic-induced beneficial outcomes.<br><br>RESULTS: We observed significant depletion of Faecalibacterium in the patients with CKD in both Western (n=283) and Eastern populations (n=75). Supplementation of F prausnitzii to CKD mice reduced renal dysfunction, renal inflammation, and lowered the serum levels of various uremic toxins. These are coupled with improved gut microbial ecology and intestinal integrity. Moreover, we demonstrated that the beneficial effects in kidney induced by F prausnitzii-derived butyrate were through the GPR (G protein-coupled receptor)-43.<br><br>CONCLUSIONS: Using a mouse CKD model, we uncovered a novel beneficial role of F prausnitzii in the restoration of renal function in CKD, which is, at least in part, attributed to the butyrate-mediated GPR-43 signaling in the kidney. Our study provides the necessary foundation to harness the therapeutic potential of F prausnitzii for ameliorating CKD.}, }
@article {pmid36163700, year = {2023}, author = {Orsi, WD}, title = {Quantitative microbial ecology: Future challenges and opportunities.}, journal = {Environmental microbiology}, volume = {25}, number = {1}, pages = {91-96}, doi = {10.1111/1462-2920.16204}, pmid = {36163700}, issn = {1462-2920}, mesh = {*Ecology ; *Ecosystem ; }, }
@article {pmid36161873, year = {2024}, author = {Orner, KD and Deleu, E and Rabaey, K and Nelson, KL}, title = {Accelerating urea hydrolysis in fresh urine by modifying operating conditions of a sequencing batch reactor.}, journal = {Environmental technology}, volume = {45}, number = {5}, pages = {845-853}, doi = {10.1080/09593330.2022.2129456}, pmid = {36161873}, issn = {1479-487X}, mesh = {*Urea ; Hydrolysis ; *Urease ; Soil ; Nitrogen/analysis ; Bioreactors ; }, abstract = {A number of existing and emerging technologies can recover nitrogen from urine. A preliminary step in many nitrogen recovery processes is hydrolyzing urea to ammonium, a biologically-mediated process that can take days to weeks without intervention. The ability to achieve urea hydrolysis quickly and reliably would increase the feasibility of decentralized nitrogen recovery, especially where space and treatment time are constrained. The goal of this research was to determine whether urea hydrolysis could be accelerated by providing an inoculum containing microorganisms likely to have urease activity (feces or soil), providing a carrier to support attached growth (plastic carriers, granular activated carbon, or no carrier), and modifying the hydraulic retention time (HRT; 1.3, 2, and 4 days) and feeding frequency (Δt = 4, 24 h). Inoculated reactors achieved significantly more urea hydrolysis, and reactors inoculated with soil were able to sustain higher urea hydrolysis rates over time than those inoculated with feces. The mean zero-order rate constants (mM/hr) for reactors with a soil inoculum (15.1) were about three times higher than that of reactors with an inoculum of feces (4.9). A reactor with GAC and an inoculum of soil fed daily with fresh urine achieved greater than 90% hydrolysis with an HRT of 2 days; results suggest the HRT could be reduced to 16 h without reducing performance. No significant benefit was provided by increasing the frequency of feedings for the same HRT, likely because urease enzymes were saturated and operating at maximum hydrolysis rates during most of the reaction period.}, }
@article {pmid36161499, year = {2023}, author = {Alonso-Reyes, DG and Galván, FS and Irazoqui, JM and Amadio, A and Tschoeke, D and Thompson, F and Albarracín, VH and Farias, ME}, title = {Dissecting Light Sensing and Metabolic Pathways on the Millimeter Scale in High-Altitude Modern Stromatolites.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {914-932}, pmid = {36161499}, issn = {1432-184X}, support = {2019-03216//PICT RAICES/ ; G603//PIUNT/ ; }, mesh = {*Altitude ; *Cyanobacteria/genetics/metabolism ; Photosynthesis ; Light ; Lakes/microbiology ; }, abstract = {Modern non-lithifying stromatolites on the shore of the volcanic lake Socompa (SST) in the Puna are affected by several extreme conditions. The present study assesses for the first time light utilization and functional metabolic stratification of SST on a millimeter scale through shotgun metagenomics. In addition, a scanning-electron-microscopy approach was used to explore the community. The analysis on SST unveiled the profile of a photosynthetic mat, with cyanobacteria not directly exposed to light, but placed just below a high-UV-resistant community. Calvin-Benson and 3-hydroxypropinate cycles for carbon fixation were abundant in upper, oxic layers, while the Wood-Ljungdahl pathway was dominant in the deeper anoxic strata. The high abundance of genes for UV-screening and oxidant-quenching pigments and CPF (photoreactivation) in the UV-stressed layers could indicate that the zone itself works as a UV shield. There is a remarkable density of sequences associated with photoreceptors in the first two layers. Also, genetic evidence of photosynthesis split in eukaryotic (layer 1) and prokaryotic (layer 2). Photoheterotrophic bacteria, aerobic photoautotrophic bacteria, and anaerobic photoautotrophic bacteria coexist by selectively absorbing different parts of the light spectrum (blue, red, and IR respectively) at different positions of the mat. Genes for oxygen, nitrogen, and sulfur metabolism account for the microelectrode chemical data and pigment measurements performed in previous publications. We also provide here an explanation for the vertical microbial mobility within the SST described previously. Finally, our study points to SST as ideal modern analogues of ancient ST.}, }
@article {pmid36160194, year = {2022}, author = {Guajardo-Leiva, S and Alarcón, J and Gutzwiller, F and Gallardo-Cerda, J and Acuña-Rodríguez, IS and Molina-Montenegro, M and Crandall, KA and Pérez-Losada, M and Castro-Nallar, E}, title = {Source and acquisition of rhizosphere microbes in Antarctic vascular plants.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {916210}, pmid = {36160194}, issn = {1664-302X}, abstract = {Rhizosphere microbial communities exert critical roles in plant health, nutrient cycling, and soil fertility. Despite the essential functions conferred by microbes, the source and acquisition of the rhizosphere are not entirely clear. Therefore, we investigated microbial community diversity and potential source using the only two native Antarctic plants, Deschampsia antarctica (Da) and Colobanthus quitensis (Cq), as models. We interrogated rhizosphere and bulk soil microbiomes at six locations in the Byers Peninsula, Livingston Island, Antarctica, both individual plant species and their association (Da.Cq). Our results show that host plant species influenced the richness and diversity of bacterial communities in the rhizosphere. Here, the Da rhizosphere showed the lowest richness and diversity of bacteria compared to Cq and Da.Cq rhizospheres. In contrast, for rhizosphere fungal communities, plant species only influenced diversity, whereas the rhizosphere of Da exhibited higher fungal diversity than the Cq rhizosphere. Also, we found that environmental geographic pressures (i.e., sampling site, latitude, and altitude) and, to a lesser extent, biotic factors (i.e., plant species) determined the species turnover between microbial communities. Moreover, our analysis shows that the sources of the bacterial communities in the rhizosphere were local soils that contributed to homogenizing the community composition of the different plant species growing in the same sampling site. In contrast, the sources of rhizosphere fungi were local (for Da and Da.Cq) and distant soils (for Cq). Here, the host plant species have a specific effect in acquiring fungal communities to the rhizosphere. However, the contribution of unknown sources to the fungal rhizosphere (especially in Da and Da.Cq) indicates the existence of relevant stochastic processes in acquiring these microbes. Our study shows that rhizosphere microbial communities differ in their composition and diversity. These differences are explained mainly by the microbial composition of the soils that harbor them, acting together with plant species-specific effects. Both plant species acquire bacteria from local soils to form part of their rhizosphere. Seemingly, the acquisition process is more complex for fungi. We identified a significant contribution from unknown fungal sources due to stochastic processes and known sources from soils across the Byers Peninsula.}, }
@article {pmid36159733, year = {2022}, author = {Van de Walle, A and Torfs, E and Gaublomme, D and Rabaey, K}, title = {In silico assessment of household level closed water cycles: Towards extreme decentralization.}, journal = {Environmental science and ecotechnology}, volume = {10}, number = {}, pages = {100148}, pmid = {36159733}, issn = {2666-4984}, abstract = {Water management in most of the developed world is currently practiced in a highly centralized manner, leading to major infrastructure and energy costs to transport water. To decrease the impacts of water scarcity and climate change, the decentralization of water can increase local robustness. In extremis, decentralization can involve building or house level water supply and treatment. Here, we constructed a MATLAB/Simulink model for two decentralized water management configurations at the household level, assuming the socio-environmental setting of Flanders, Belgium. Independence from the potable water grid and sewer system was pursued through rainwater harvesting, reuse of wastewater streams fit-for-purpose, and discharge via infiltration. The mass balance for water was calculated over the system boundaries showing high potential for independence from the grid with a reasonable treatment train and storage options. Next, the risk of contaminant accumulation within the circular system was assessed, showing a key limitation on decentralized system performance necessitating a system purge. Up to 59% of system rainwater usage was due to the replacement of this purge. Employing treatment units with high (95%) contaminant rejection efficiencies eliminated contaminant accumulation issues. The raw model output was quantitatively assessed by constructing four newly proposed key performance indicators (KPIs), quantifying system independence, circularity, drought tolerance and local water body recharge, which allowed for facilitated system comparison and communication to stakeholders. A sensitivity analysis was performed in which the effect of input parameter variability and uncertainty on system performance was quantified. The sensitivity analysis showed the importance of water recovery and contaminant removal efficiencies of the applied treatment technologies on system performance when contaminant accumulation in the system forms an issue. In systems not severely affected by pollutant accumulation, parameters such as inhabitant number and roof surface had the largest effect. As a whole, this work shows the potential of extreme decentralization of water systems and addresses the obstacle towards implementation formed by the accumulation of contaminants due to system circularity. Additionally, this study provides a framework for operational and technological decision support of decentralized household-scale water systems and, by extension, for future water policy-making.}, }
@article {pmid36158753, year = {2022}, author = {Ostermeyer, P and Van Landuyt, J and Bonin, L and Folens, K and Williamson, A and Hennebel, T and Rabaey, K}, title = {High rate production of concentrated sulfides from metal bearing wastewater in an expanded bed hydrogenotrophic sulfate reducing bioreactor.}, journal = {Environmental science and ecotechnology}, volume = {11}, number = {}, pages = {100173}, pmid = {36158753}, issn = {2666-4984}, abstract = {Metallurgical wastewaters contain high concentrations of sulfate, up to 15 g L[-1]. Sulfate-reducing bioreactors are employed to treat these wastewaters, reducing sulfates to sulfides which subsequently co-precipitate metals. Sulfate loading and reduction rates are typically restricted by the total H2S concentration. Sulfide stripping, sulfide precipitation and dilution are the main strategies employed to minimize inhibition by H2S, but can be adversely compromised by suboptimal sulfate reduction, clogging and additional energy costs. Here, metallurgical wastewater was treated for over 250 days using two hydrogenotrophic granular activated carbon expanded bed bioreactors without additional removal of sulfides. H2S toxicity was minimized by operating at pH 8 ± 0.15, resulting in an average sulfate removal of 7.08 ± 0.08 g L[-1], sulfide concentrations of 2.1 ± 0.2 g L[-1] and peaks up to 2.3 ± 0.2 g L[-1]. A sulfate reduction rate of 20.6 ± 0.9 g L[-1] d[-1] was achieved, with maxima up to 27.2 g L[-1] d[-1], which is among the highest reported considering a literature review of 39 studies. The rates reported here are 6-8 times higher than those reported for other reactors without active sulfide removal and the only reported for expanded bed sulfate-reducing bioreactors using H2. By increasing the influent sulfate concentration and maintaining high sulfide concentrations, sulfate reducers were promoted while fermenters and methanogens were suppressed. Industrial wastewater containing 4.4 g L[-1] sulfate, 0.036 g L[-1] nitrate and various metals (As, Fe, Tl, Zn, Ni, Sb, Co and Cd) was successfully treated with all metal(loid)s, nitrates and sulfates removed below discharge limits.}, }
@article {pmid36154441, year = {2022}, author = {Zhang, S and Yang, Q and Defoirdt, T}, title = {Halogenated Indoles Decrease the Virulence of Vibrio campbellii in a Gnotobiotic Brine Shrimp Model.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0268922}, pmid = {36154441}, issn = {2165-0497}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Artemia/microbiology ; Germ-Free Life ; Indoles/pharmacology ; Peptide Hydrolases/pharmacology ; *Vibrio ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Indole signaling is viewed as a potential target for antivirulence therapy against antibiotic-resistant pathogens because of its link with the production of virulence factors. This study examined the antimicrobial and antivirulence properties of 44 indoles toward Vibrio campbellii. Based on the results, 17 halogenated indole analogues were selected, as they significantly improved the survival of brine shrimp larvae challenged with V. campbellii. Specifically, 6-bromoindole, 7-bromoindole, 4-fluoroindole, 5-iodoindole, and 7-iodoindole showed a high protective effect, improving the survival of brine shrimp to over 80% even at a low concentration of 10 μM. To explore the impact of selected indole analogues on bacterial virulence phenotypes, swimming motility, biofilm formation, protease activity, and hemolytic activity of V. campbellii were determined. The results showed that all of the 17 selected indole analogues decreased swimming motility at both 10 μM and 100 μM. Most of the indole analogues decreased biofilm formation at a concentration of 100 μM. In contrast, only a slightly decreased protease activity and no effect on hemolytic activity were observed at both concentrations. To our knowledge, this is the first study of the structure-activity relation of halogenated indole analogues with respect to virulence inhibition of a pathogenic bacterium in an in vivo host model system, and the results demonstrate the potential of these compounds in applications aiming at the protection of shrimp from vibriosis, a major disease in aquaculture. IMPORTANCE Bacterial diseases are a major problem in the aquaculture industry. In order to counter this problem, farmers have been using antibiotics, and this has led to the evolution and spread of antibiotic resistance. In order for the aquaculture industry to further grow in a sustainable way, novel and sustainable methods to control diseases are needed. We previously reported that indole signaling is a valid target for the development of novel therapies to control disease caused by Vibrio campbellii and related bacteria, which are among the major bacterial pathogens in aquaculture. In the present study, we identified indole analogues that are more potent in protecting brine shrimp (a model organism for shrimp) from V. campbellii. To our knowledge, this is the first study of the structure-activity relation of halogenated indole analogues with respect to virulence inhibition of a pathogenic bacterium in an in vivo host model system.}, }
@article {pmid36153325, year = {2022}, author = {Zhu, H and Xu, L and Luan, G and Zhan, T and Kang, Z and Li, C and Lu, X and Zhang, X and Zhu, Z and Zhang, Y and Li, Y}, title = {A miniaturized bionic ocean-battery mimicking the structure of marine microbial ecosystems.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5608}, pmid = {36153325}, issn = {2041-1723}, mesh = {*Bioelectric Energy Sources ; Bionics ; Hydrogels ; *Microbiota ; Oceans and Seas ; }, abstract = {Marine microbial ecosystems can be viewed as a huge ocean-battery charged by solar energy. It provides a model for fabricating bio-solar cell, a bioelectrochemical system that converts light into electricity. Here, we fabricate a bio-solar cell consisting of a four-species microbial community by mimicking the ecological structure of marine microbial ecosystems. We demonstrate such ecological structure consisting of primary producer, primary degrader, and ultimate consumers is essential for achieving high power density and stability. Furthermore, the four-species microbial community is assembled into a spatial-temporally compacted cell using conductive hydrogel as a sediment-like anaerobic matrix, forming a miniaturized bionic ocean-battery. This battery directly converts light into electricity with a maximum power of 380 μW and stably operates for over one month. Reproducing the photoelectric conversion function of marine microbial ecosystems in this bionic battery overcomes the sluggish and network-like electron transfer, showing the biotechnological potential of synthetic microbial ecology.}, }
@article {pmid36152855, year = {2023}, author = {Zhang, X and Shen, M and Wang, C and Gao, M and Wang, L and Jin, Z and Xia, X}, title = {Impact of aluminum exposure on oxidative stress, intestinal changes and immune responses in red swamp crayfish (Procambarus clarkii).}, journal = {The Science of the total environment}, volume = {855}, number = {}, pages = {158902}, doi = {10.1016/j.scitotenv.2022.158902}, pmid = {36152855}, issn = {1879-1026}, mesh = {Animals ; *Astacoidea ; *Aluminum/toxicity ; Hemocytes ; Oxidative Stress ; Immunity ; }, abstract = {Aluminum (Al) is an abundant metal that has been classified as a threatening pollutant due to indiscriminate use and anthropogenic activities. This study aimed to evaluate the impacts of Al on crayfish (Procambarus clarkii), including biochemical change, histological alteration, gut microbial community diversification, and immune changes. The bioaccumulation of Al was detected in the hemolymph and intestine of crayfish after Al exposure at different time points. Results showed that Al exposure significantly induced oxidative stress and caused pathohistological changes on intestinal barrier structures in crayfish. It was found that the intestinal microbiota was affected by retained Al and the intestinal community diversity was changed after Al treated in the crayfish. Furthermore, Al exposure affected the immunity in crayfish, by altering the expression of a set of immune-related genes, as well as reducing the phenoloxidase and lysozyme activities. Moreover, Al exposure promoted hemocytes apoptosis and impaired hemophagocytic capacity against Vibro parahamolyticus, resulting in higher mortality of crayfish upon bacterial infection. Taken these results together, we conclude that excessive Al exposure caused adverse effects on multiple biological processes of crayfish and Al pollution is a potential threat to crayfish culture.}, }
@article {pmid36152034, year = {2023}, author = {Weingarten, EA and Jackson, CR}, title = {Microbial Composition of Freshwater Marsh Sediment Responds more Strongly to Microcosm Seawater Addition than Simulated Nitrate or Phosphate Eutrophication.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1060-1070}, pmid = {36152034}, issn = {1432-184X}, mesh = {*Wetlands ; *Nitrates ; Phosphates ; Fresh Water ; Seawater ; Eutrophication ; }, abstract = {As sea level rise impacts coastal wetlands, saltmarsh will overtake coastal freshwater marsh in many areas, but changes in the sediment microbiome in response to saltwater intrusion are difficult to predict. Coastal freshwater marsh sediment was exposed to ambient, brackish, and saline conditions as well as to elevated nitrate and phosphate to model the combined stresses of saltwater intrusion and coastal eutrophication. Initially, sediment prokaryotic composition was similar to prior studies of freshwater marsh but diverged over time, reflecting the magnitude of increase in saltwater. There was no observed effect of nutrient amendment, potentially ranking seawater intrusion as a higher-importance compositional driver. Although the previously described loss of methanogenic populations and promotion of sulfate reducers in response to saltwater exposure was observed, taxonomic distribution was not similar to typical meso-polyhaline wetlands. Without colonization by marine taxa, such a community may be short-lived naturally, ultimately equilibrating with more common saltmarsh species. However, the recapitulation of salinity concentration by freshwater sediment microbial composition demonstrates the overwhelming nature of saltwater intrusion relative to other drivers like eutrophication.}, }
@article {pmid36151709, year = {2022}, author = {Prosser, JI}, title = {How and why in microbial ecology: An appeal for scientific aims, questions, hypotheses and theories.}, journal = {Environmental microbiology}, volume = {24}, number = {11}, pages = {4973-4980}, doi = {10.1111/1462-2920.16221}, pmid = {36151709}, issn = {1462-2920}, mesh = {*Ecology ; *Environmental Microbiology ; }, abstract = {This article precedes a series of articles on the important questions, hypotheses and theories in microbial ecology. It considers why, as scientists, we ask questions and propose hypotheses and what makes them important, good or significant. Emphasis is placed on 'scientific' questions, the need for scientific aims and on possible reasons for, and inadequacy of aim-less studies and question free studies. Current global issues surrounding the climate crisis, pandemics and antibiotic resistance focus attention on science and scientists. They exemplify the urgent need for greater understanding of the interactions between microbes and their biological and physicochemical environments, that is, of microbial ecology. They also provide examples of reaction against science and scientists and highlight why we must be clear regarding what defines (good) science, its power and limitations, and ensure that this is communicated to stakeholders and the general public.}, }
@article {pmid36151339, year = {2023}, author = {Zhou, X and Lee, J and Yun, J and Kim, J and Yang, Y and Kang, H}, title = {Distinct Nitrification Rates and Nitrifiers in Needleleaf and Evergreen Broadleaf Forest Soils.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1050-1059}, pmid = {36151339}, issn = {1432-184X}, mesh = {*Soil/chemistry ; *Nitrification ; Ecosystem ; Ammonia ; Phylogeny ; Oxidation-Reduction ; Soil Microbiology ; Archaea ; Forests ; }, abstract = {Research on niche specialization in the microbial communities of ammonia oxidizers is important for assessing the consequences of vegetation shift on nitrogen (N) cycling. In this study, soils were sampled from three tree stands (needleleaf, mixed, and evergreen broadleaf) from the Hannam experimental forest in South Korea in spring (May 2019), summer (August 2019), autumn (November 2019), and winter (January 2020). Quantitative polymerase chain reaction (qPCR) and high-throughput sequencing were used to measure the abundance and community structure of various nitrifiers: ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) as well as complete ammonia oxidizers (comammox). Nitrification rates and total ammonia oxidizer abundance were significantly higher in needleleaf forest soil than those in other forest stands, and they were lowest in evergreen broadleaf forest soil. Comammox clade B was most abundant in needleleaf and evergreen broadleaf forest soils, while AOA were significantly more abundant in mixed forest soil. The abundances of comammox clade B and AOA were negatively correlated with dissolved organic carbon. Phylogenetic analysis showed that NT-alpha and NS-gamma-2.3.2 were the most abundant AOA lineages in all the samples. The seasonal of AOA, AOB, and comammox varied with the sites, suggesting the need to examine the combinations of environmental factors when considering the effects of seasonal changes in the environment. Overall, the results suggest that potential vegetation shifts in forest ecosystems might affect nitrification activities by regulating the abundance and community structure of ammonia oxidizers.}, }
@article {pmid36150718, year = {2022}, author = {Kritzberg, E and Bååth, E}, title = {Seasonal variation in temperature sensitivity of bacterial growth in a temperate soil and lake.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {10}, pages = {}, pmid = {36150718}, issn = {1574-6941}, mesh = {Bacteria/metabolism ; *Lakes ; Seasons ; *Soil ; Temperature ; Water/metabolism ; }, abstract = {Faster bacterial biomass turnover is expected in water compared to soil, which would result in more rapid community adaption to changing environmental conditions, including temperature. Bacterial community adaptation for growth is therefore predicted to have larger seasonal amplitudes in lakes than in soil. To test this prediction, we compared the seasonal variation in temperature adaptation of bacterial community growth in a soil and lake in Southern Sweden (Tin situ 0-20°C, mean 10°C) during 1.5 years, based on monthly samplings including two winters and summers. An indicator of community adaptation, minimum temperature for growth (Tmin), was calculated from bacterial growth measurements (Leu incorporation) using the Ratkowsky model. The seasonal variation in Tmin (sinusoidal function, R2 = 0.71) was most pronounced for the lake bacterial community, with an amplitude for Tmin of 3.0°C (-4.5 to -10.5°C) compared to 0.6°C (-7 to -8°C) for the soil. Thus, Tmin in water increased by 0.32°C/degree change of Tin situ. Similar differences were also found when comparing four lakes and soils in the winter and summer (amplitudes 2.9°C and 0.9°C for lakes and soils, respectively). Thus, seasonal variation in temperature adaptation has to be taken into account in lakes, while for soils a constant Tmin can be used.}, }
@article {pmid36150364, year = {2022}, author = {Mitrović, M and Kostešić, E and Marković, T and Selak, L and Hausmann, B and Pjevac, P and Orlić, S}, title = {Microbial community composition and hydrochemistry of underexplored geothermal waters in Croatia.}, journal = {Systematic and applied microbiology}, volume = {45}, number = {6}, pages = {126359}, doi = {10.1016/j.syapm.2022.126359}, pmid = {36150364}, issn = {1618-0984}, mesh = {RNA, Ribosomal, 16S/genetics ; Ammonia/metabolism ; Croatia ; Phylogeny ; *Hot Springs/microbiology ; Archaea ; *Microbiota/genetics ; Bacteria/genetics ; }, abstract = {In Croatia, a variety of geothermal springs with a wide temperature range and varied hydrochemical conditions exist, and they may harbor different niches for the distribution of microbial communities. In this study, 19 different sites, mainly located in central and eastern Croatia, were selected for primary characterization of spring hydrochemistry and microbial community composition. Using 16S rRNA gene amplicon sequencing, it was found that the bacterial communities that dominated most geothermal waters were related to Proteobacteria and Campylobacteria, while most archaeal sequences were related to Crenarchaeota. At the genus level, the prokaryotic community was highly site-specific and was often dominated by a single genus, including sites dominated by Hydrogenophilus, Sulfuricurvum, Sulfurovum, Thiofaba and Nitrospira, while the most abundant archaeal genera were affiliated to the ammonia-oxidizing archaea, Candidatus Nitrosotenuis and Candidatus Nitrososphaera. Whereas the microbial communities were overall highly location-specific, temperature, pH, ammonia, nitrate, total nitrogen, sulfate and hydrogen sulfide, as well as dissolved organic and inorganic carbon, were the abiotic factors that significantly affected microbial community composition. Furthermore, an aquifer-type effect was observed in the community composition, but there was no pronounced seasonal variability for geothermal spring communities (i.e. the community structure was mainly stable during the three seasons sampled). These results surprisingly pointed to stable and geographically unique microbial communities that were adapted to different geothermal water environments throughout Croatia. Knowing which microbial communities are present in these extreme habitats is essential for future research. They will allow us to explore further the microbial metabolisms prevailing at these geothermal sites that have high potential for biotechnological uses, as well as the establishment of the links between microbial community structure and the physicochemical environment of geothermal waters.}, }
@article {pmid36145836, year = {2022}, author = {Vidal, C and González, F and Santander, C and Pérez, R and Gallardo, V and Santos, C and Aponte, H and Ruiz, A and Cornejo, P}, title = {Management of Rhizosphere Microbiota and Plant Production under Drought Stress: A Comprehensive Review.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {18}, pages = {}, pmid = {36145836}, issn = {2223-7747}, support = {ANID/FONDECYT/1210964//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; ANID/FONDAP/15130015//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; InES19-FRO19001//Ministry of Education/ ; FONDECYT1210964//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; ANID/FONDAP/15130015//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; InES19.FRO19001//Ministry of Education/ ; }, abstract = {Drought generates a complex scenario worldwide in which agriculture should urgently be reframed from an integrative point of view. It includes the search for new water resources and the use of tolerant crops and genotypes, improved irrigation systems, and other less explored alternatives that are very important, such as biotechnological tools that may increase the water use efficiency. Currently, a large body of evidence highlights the role of specific strains in the main microbial rhizosphere groups (arbuscular mycorrhizal fungi, yeasts, and bacteria) on increasing the drought tolerance of their host plants through diverse plant growth-promoting (PGP) characteristics. With this background, it is possible to suggest that the joint use of distinct PGP microbes could produce positive interactions or additive beneficial effects on their host plants if their co-inoculation does not generate antagonistic responses. To date, such effects have only been partially analyzed by using single omics tools, such as genomics, metabolomics, or proteomics. However, there is a gap of information in the use of multi-omics approaches to detect interactions between PGP and host plants. This approach must be the next scale-jump in the study of the interaction of soil-plant-microorganism. In this review, we analyzed the constraints posed by drought in the framework of an increasing global demand for plant production, integrating the important role played by the rhizosphere biota as a PGP agent. Using multi-omics approaches to understand in depth the processes that occur in plants in the presence of microorganisms can allow us to modulate their combined use and drive it to increase crop yields, improving production processes to attend the growing global demand for food.}, }
@article {pmid36145178, year = {2022}, author = {Overbeeke, A and Lang, M and Hausmann, B and Watzka, M and Nikolov, G and Schwarz, J and Kohl, G and De Paepe, K and Eislmayr, K and Decker, T and Richter, A and Berry, D}, title = {Impaired Mucosal Homeostasis in Short-Term Fiber Deprivation Is Due to Reduced Mucus Production Rather Than Overgrowth of Mucus-Degrading Bacteria.}, journal = {Nutrients}, volume = {14}, number = {18}, pages = {}, pmid = {36145178}, issn = {2072-6643}, support = {LS18-053//Vienna Science and Technology Fund/ ; P27831-B28//FWF Austrian Science Fund/ ; 741623/ERC_/European Research Council/International ; MAINTAIN DOC 69//FWF Austrian Science Fund/ ; P 27831/FWF_/Austrian Science Fund FWF/Austria ; W 1261/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria ; Butyrates/metabolism ; *Dietary Fiber/metabolism ; Homeostasis ; Intestinal Mucosa/metabolism ; *Mucus/metabolism ; }, abstract = {The gut mucosal environment is key in host health; protecting against pathogens and providing a niche for beneficial bacteria, thereby facilitating a mutualistic balance between host and microbiome. Lack of dietary fiber results in erosion of the mucosal layer, suggested to be a result of increased mucus-degrading gut bacteria. This study aimed to use quantitative analyses to investigate the diet-induced imbalance of mucosal homeostasis. Seven days of fiber-deficiency affected intestinal anatomy and physiology, seen by reduced intestinal length and loss of the colonic crypt-structure. Moreover, the mucus layer was diminished, muc2 expression decreased, and impaired mucus secretion was detected by stable isotope probing. Quantitative microbiome profiling of the gut microbiota showed a diet-induced reduction in bacterial load and decreased diversity across the intestinal tract, including taxa with fiber-degrading and butyrate-producing capabilities. Most importantly, there was little change in the absolute abundance of known mucus-degrading bacteria, although, due to the general loss of taxa, relative abundance would erroneously indicate an increase in mucus degraders. These findings underscore the importance of using quantitative methods in microbiome research, suggesting erosion of the mucus layer during fiber deprivation is due to diminished mucus production rather than overgrowth of mucus degraders.}, }
@article {pmid36144291, year = {2022}, author = {Kuzyk, SB and Ma, X and Yurkov, V}, title = {Seasonal Dynamics of Lake Winnipeg's Microbial Communities Reveal Aerobic Anoxygenic Phototrophic Populations Coincide with Sunlight Availability.}, journal = {Microorganisms}, volume = {10}, number = {9}, pages = {}, pmid = {36144291}, issn = {2076-2607}, support = {5492-2018//Natural Sciences and Engineering Research Council/ ; }, abstract = {In this first comprehensive study of Lake Winnipeg's microbial communities, limnetic and littoral euphotic zones were examined during each season from 2016 through 2020. Classical cultivation and modern high-throughput sequencing techniques provided quantification and identification of key phototrophic populations, including aerobic anoxygenic phototrophs (AAP). Annual dynamics found total heterotrophs reached 4.23 × 10[6] CFU/g in littoral sands, and 7.69 × 10[4] CFU/mL in summer littoral waters on oligotrophic media, higher counts than for copiotrophic compositions. Limnetic numbers inversely dipped to 4.34 × 10[3] CFU/mL midsummer. Cultured AAP did not follow heterotrophic trends, instead peaking during the spring in both littoral and limnetic waters as 19.1 and 4.7% of total copiotrophs, or 3.9 and 4.9% of oligotrophs, decreasing till autumn each year. Complementary observations came from environmental 16S V4 rRNA gene analysis, as AAP made up 1.49 and 1.02% of the littoral and limnetic sequenced communities in the spring, declining with seasonal progression. Spatial and temporal fluctuations of microbes compared to environmental factors exposed photosynthetic populations to independently and regularly fluctuate in the ecosystem. Oxygenic phototrophic numbers expectantly matched the midsummer peak of Chl a and b, oxygenic photosynthesis related carbon fixation, and water temperature. Independently, AAP particularly colonized spring littoral areas more than limnetic, and directly corresponded to habitat conditions that specifically promoted growth: the requirement of light and organic material.}, }
@article {pmid36143410, year = {2022}, author = {Johnston-Monje, D and Gutiérrez, JP and Becerra Lopez-Lavalle, LA}, title = {Stochastic Inoculum, Biotic Filtering and Species-Specific Seed Transmission Shape the Rare Microbiome of Plants.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {9}, pages = {}, pmid = {36143410}, issn = {2075-1729}, abstract = {A plant's health and productivity is influenced by its associated microbes. Although the common/core microbiome is often thought to be the most influential, significant numbers of rare or uncommon microbes (e.g., specialized endosymbionts) may also play an important role in the health and productivity of certain plants in certain environments. To help identify rare/specialized bacteria and fungi in the most important angiosperm plants, we contrasted microbiomes of the seeds, spermospheres, shoots, roots and rhizospheres of Arabidopsis, Brachypodium, maize, wheat, sugarcane, rice, tomato, coffee, common bean, cassava, soybean, switchgrass, sunflower, Brachiaria, barley, sorghum and pea. Plants were grown inside sealed jars on sterile sand or farm soil. Seeds and spermospheres contained some uncommon bacteria and many fungi, suggesting at least some of the rare microbiome is vertically transmitted. About 95% and 86% of fungal and bacterial diversity inside plants was uncommon; however, judging by read abundance, uncommon fungal cells are about half of the mycobiome, while uncommon bacterial cells make up less than 11% of the microbiome. Uncommon-seed-transmitted microbiomes consisted mostly of Proteobacteria, Firmicutes, Bacteriodetes, Ascomycetes and Basidiomycetes, which most heavily colonized shoots, to a lesser extent roots, and least of all, rhizospheres. Soil served as a more diverse source of rare microbes than seeds, replacing or excluding the majority of the uncommon-seed-transmitted microbiome. With the rarest microbes, their colonization pattern could either be the result of stringent biotic filtering by most plants, or uneven/stochastic inoculum distribution in seeds or soil. Several strong plant-microbe associations were observed, such as seed transmission to shoots, roots and/or rhizospheres of Sarocladium zeae (maize), Penicillium (pea and Phaseolus), and Curvularia (sugarcane), while robust bacterial colonization from cassava field soil occurred with the cyanobacteria Leptolyngbya into Arabidopsis and Panicum roots, and Streptomyces into cassava roots. Some abundant microbes such as Sakaguchia in rice shoots or Vermispora in Arabidopsis roots appeared in no other samples, suggesting that they were infrequent, stochastically deposited propagules from either soil or seed (impossible to know based on the available data). Future experiments with culturing and cross-inoculation of these microbes between plants may help us better understand host preferences and their role in plant productivity, perhaps leading to their use in crop microbiome engineering and enhancement of agricultural production.}, }
@article {pmid36139115, year = {2022}, author = {Qing, J and Zheng, F and Zhi, H and Yaigoub, H and Tirichen, H and Li, Y and Zhao, J and Qiang, Y and Li, Y}, title = {Identification of Unique Genetic Biomarkers of Various Subtypes of Glomerulonephritis Using Machine Learning and Deep Learning.}, journal = {Biomolecules}, volume = {12}, number = {9}, pages = {}, pmid = {36139115}, issn = {2218-273X}, mesh = {Biomarkers/analysis ; *Deep Learning ; *Glomerulonephritis/genetics/metabolism ; Humans ; Kidney Glomerulus/chemistry/metabolism/pathology ; Macrophages/metabolism ; }, abstract = {(1) Objective: Identification of potential genetic biomarkers for various glomerulonephritis (GN) subtypes and discovering the molecular mechanisms of GN. (2) Methods: four microarray datasets of GN were downloaded from Gene Expression Omnibus (GEO) database and merged to obtain the gene expression profiles of eight GN subtypes. Then, differentially expressed immune-related genes (DIRGs) were identified to explore the molecular mechanisms of GN, and single-sample gene set enrichment analysis (ssGSEA) was performed to discover the abnormal inflammation in GN. In addition, a nomogram model was generated using the R package "glmnet", and the calibration curve was plotted to evaluate the predictive power of the nomogram model. Finally, deep learning (DL) based on a multilayer perceptron (MLP) network was performed to explore the characteristic genes for GN. (3) Results: we screened out 274 common up-regulated or down-regulated DIRGs in the glomeruli and tubulointerstitium. These DIRGs are mainly involved in T-cell differentiation, the RAS signaling pathway, and the MAPK signaling pathway. ssGSEA indicates that there is a significant increase in DC (dendritic cells) and macrophages, and a significant decrease in neutrophils and NKT cells in glomeruli, while monocytes and NK cells are increased in tubulointerstitium. A nomogram model was constructed to predict GN based on 7 DIRGs, and 20 DIRGs of each subtype of GN in glomeruli and tubulointerstitium were selected as characteristic genes. (4) Conclusions: this study reveals that the DIRGs are closely related to the pathogenesis of GN and could serve as genetic biomarkers in GN. DL further identified the characteristic genes that are essential to define the pathogenesis of GN and develop targeted therapies for eight GN subtypes.}, }
@article {pmid36138209, year = {2023}, author = {Liu, Q and Zhang, H and Huang, X}, title = {Strong Linkage Between Symbiotic Bacterial Community and Host Age and Morph in a Hemipteran Social Insect.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1213-1225}, pmid = {36138209}, issn = {1432-184X}, support = {31970446//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Female ; Biological Evolution ; *Aphids/microbiology ; Insecta ; Symbiosis/physiology ; *Buchnera/genetics ; }, abstract = {The relationships between symbionts and insects are complex, and symbionts usually have diverse ecological and evolutionary effects on their hosts. The phloem sap-sucking aphids are good models to study the interactions between insects and symbiotic microorganisms. Although aphids usually exhibit remarkable life cycle complexity, most previous studies on symbiotic diversity sampled only apterous viviparous adult females or very few morphs. In this study, high-throughput 16S rDNA amplicon sequencing was used to assess the symbiotic bacterial communities of eleven morphs or developmental stages of the social aphid Pseudoregma bambucicola. We found there were significant differences in bacterial composition in response to different morphs and developmental stages, and for the first time, we revealed male aphids hosted very different symbiotic composition featured with low abundance of dominant symbionts but high diversity of total symbionts. The relative abundance of Pectobacterium showed relatively stable across different types of samples, while that of Wolbachia fluctuated greatly, indicating the former may have a consistent function in this species and the latter may provide specific function for certain morphs or developmental stages. Our study presents new evidence of complexity of symbiotic associations and indicates strong linkage between symbiotic bacterial community and host age and morph.}, }
@article {pmid36138151, year = {2022}, author = {Simpson, RC and Shanahan, ER and Batten, M and Reijers, ILM and Read, M and Silva, IP and Versluis, JM and Ribeiro, R and Angelatos, AS and Tan, J and Adhikari, C and Menzies, AM and Saw, RPM and Gonzalez, M and Shannon, KF and Spillane, AJ and Velickovic, R and Lazar, AJ and Damania, AV and Mishra, AK and Chelvanambi, M and Banerjee, A and Ajami, NJ and Wargo, JA and Macia, L and Holmes, AJ and Wilmott, JS and Blank, CU and Scolyer, RA and Long, GV}, title = {Diet-driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome.}, journal = {Nature medicine}, volume = {28}, number = {11}, pages = {2344-2352}, pmid = {36138151}, issn = {1546-170X}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Prospective Studies ; Immunotherapy/adverse effects ; *Melanoma/therapy ; Diet ; }, abstract = {The gut microbiota shapes the response to immune checkpoint inhibitors (ICIs) in cancer, however dietary and geographic influences have not been well-studied in prospective trials. To address this, we prospectively profiled baseline gut (fecal) microbiota signatures and dietary patterns of 103 trial patients from Australia and the Netherlands treated with neoadjuvant ICIs for high risk resectable metastatic melanoma and performed an integrated analysis with data from 115 patients with melanoma treated with ICIs in the United States. We observed geographically distinct microbial signatures of response and immune-related adverse events (irAEs). Overall, response rates were higher in Ruminococcaceae-dominated microbiomes than in Bacteroidaceae-dominated microbiomes. Poor response was associated with lower fiber and omega 3 fatty acid consumption and elevated levels of C-reactive protein in the peripheral circulation at baseline. Together, these data provide insight into the relevance of native gut microbiota signatures, dietary intake and systemic inflammation in shaping the response to and toxicity from ICIs, prompting the need for further studies in this area.}, }
@article {pmid36135386, year = {2022}, author = {Mason, AR and McKee-Zech, HS and Hoeland, KM and Davis, MC and Campagna, SR and Steadman, DW and DeBruyn, JM}, title = {Body Mass Index (BMI) Impacts Soil Chemical and Microbial Response to Human Decomposition.}, journal = {mSphere}, volume = {7}, number = {5}, pages = {e0032522}, pmid = {36135386}, issn = {2379-5042}, support = {I01 BX000180/BX/BLRD VA/United States ; }, mesh = {Humans ; *Soil/chemistry ; *Soil Microbiology ; Body Mass Index ; Bacteria ; Cadaver ; }, abstract = {Microorganisms are key decomposers of vertebrate mortalities, breaking down body tissues and impacting decomposition progress. During human decomposition, both extrinsic environmental factors and intrinsic cadaver-related factors have the potential to impact microbial decomposers either directly or indirectly via altered physical or chemical conditions. While extrinsic factors (e.g., temperature, humidity) explain some variation in microbial response during human decomposition in terrestrial settings, recent work has noted that even under the same environmental conditions, individuals can have different decomposition patterns, highlighting the potential for intrinsic factors to impact microbial decomposers. The goal of this study was to investigate the effects of several intrinsic factors (age, sex, diseases at time of death, and body mass index [BMI]) on chemical and microbial changes in decomposition-impacted soils. In a field study conducted at the University of Tennessee Anthropology Research Facility, soils were collected from the decomposition-impacted area surrounding 19 deceased human individuals through the end of active decomposition. Soil physicochemical parameters were measured, and microbial (bacterial and fungal) communities were assessed via amplicon sequencing. BMI was shown to explain some variation in soil pH and microbial response to human decomposition. Hierarchical linear mixed (HLM) effects models revealed that BMI category significantly explained variation in pH response within decomposition-impacted soils over time (HLM F = 9.647; P < 0.001). Additionally, the relative abundance of soil Saccharomycetes in decomposition soils under underweight donors displayed little to no changes (mean maximum change in relative abundance, +6.6%), while all other BMI categories displayed an increased relative abundance of these organisms over time (normal, +50.6%; overweight, +64.4%; and obese, +64.6%) (HLM F = 3.441; P = 0.11). Together, these results reveal intrinsic factors influencing decomposition patterns, especially within the soil environment, and suggest BMI is an important factor for controlling decomposition processes. IMPORTANCE This work begins to address questions about interindividual variation in vertebrate decomposition attributed to intrinsic factors, that is, properties of the carcass or cadaver itself. Most research on factors affecting decomposition has focused on the extrinsic environment, such as temperature or humidity. While these extrinsic factors do explain some variation in decomposition patterns, interindividual variability is still observed. Understanding how intrinsic factors influence microbial decomposers will help reveal the ecological impacts of decomposition. This work also has forensic applications, as soil chemical and biological changes have been suggested as indicators of postmortem interval. We reveal factors that explain variation in the decomposition environment that should be considered in these estimates. This is particularly important as we consider the implications of variations in human populations due to diet, age, BMI, disease, toxicological loading, etc. on forensic investigations dealing with decomposing remains.}, }
@article {pmid36133177, year = {2022}, author = {Villegas-Plazas, M and Villamil, L and Martínez-Silva, MA and González-Jiménez, T and Salazar, M and Güiza, L and Mendoza, M and Junca, H}, title = {Microbiome composition and autochthonous probiotics from contrasting probiosis/dysbiosis states in cobia (Rachycentron canadum) fish epitheliocystis.}, journal = {Access microbiology}, volume = {4}, number = {8}, pages = {acmi000405}, pmid = {36133177}, issn = {2516-8290}, abstract = {Microbiome components and bacterial isolates related to healthy and epitheliocystis states in aquaculture cycles of cobia fish were studied. We detected well-defined 16S rRNA amplicon gene sequence variants showing differential abundance in healthy or diseased cycles. Isolation trials were performed, and experimental tests were used to determine probiotic potential of the bacterial strains obtained from water, tissues or live food used in this aquaculture model. The taxonomic affiliation of these strains was cross-compared against microbiome components, finding that some of them had close or identical affiliation to the abundant types found in healthy cycles. Strains belonging to the groups already identified as predominant by culture-independent means were screened as potential probiotics based on desirable activities such as antagonism and antibiosis against marine pathogenic bacteria, quorum quenching, bile acid resistance, antibiotic sensitivity and enzymatic activities for improved nutrient digestion. We have also found that in the tracking of microbiome composition across different developmental stages of cobia, healthy cycles exhibited a consistent high relative abundance of a Mesobacillus sp., while in the diseased cycle the emergence of a Vibrio sp. was observed. Our study suggests that epithelocystis in cobia is associated with a displacement of a symbiotic microbiome community linked to the increase frequency of Vibrio species.}, }
@article {pmid36133174, year = {2022}, author = {Beirne, C and McCann, E and McDowell, A and Miliotis, G}, title = {Genetic determinants of antimicrobial resistance in three multi-drug resistant strains of Cutibacterium acnes isolated from patients with acne: a predictive in silico study.}, journal = {Access microbiology}, volume = {4}, number = {8}, pages = {acmi000404}, pmid = {36133174}, issn = {2516-8290}, abstract = {OBJECTIVES: Using available whole genome data, the objective of this in silico study was to identify genetic mechanisms that could explain the antimicrobial resistance profile of three multi-drug resistant (MDR) strains (CA17, CA51, CA39) of the skin bacterium Cutibacterium acnes previously recovered from patients with acne. In particular, we were interested in detecting novel genetic determinants associated with resistance to fluoroquinolone and macrolide antibiotics that could then be confirmed experimentally.<br><br>METHODS: A range of open source bioinformatics tools were used to 'mine' genetic determinants of antimicrobial resistance and plasmid borne contigs, and to characterise the phylogenetic diversity of the MDR strains.<br><br>RESULTS: As probable mechanisms of resistance to fluoroquinolones, we identified a previously described resistance associated allelic variant of the gyrA gene with a 'deleterious' S101L mutation in type IA1 strains CA51 (ST1) and CA39 (ST1), as well as a novel E761R 'deleterious' mutation in the type II strain CA17 (ST153). A distinct genomic sequence of the efflux protein YfmO which is potentially associated with resistance to MLSB antibiotics was also present in CA17; homologues in CA51, CA39, and other strains of Cutibacterium acnes , were also found but differed in amino acid content. Strikingly, in CA17 we also identified a circular 2.7&#x2009;kb non-conjugative plasmid (designated pCA17) that closely resembled a 4.8&#x2009;kb plasmid (pYU39) from the MDR Salmonella enterica strain YU39.<br><br>CONCLUSIONS: This study has provided a detailed explanation of potential genetic determinants for MDR in the Cutibacterium acnes strains CA17, CA39 and CA51. Further laboratory investigations will be required to validate these in silico results, especially in relation to pCA17.}, }
@article {pmid36132223, year = {2022}, author = {Yanez-Montalvo, A and Aguila, B and Gómez-Acata, ES and Guerrero-Jacinto, M and Oseguera, LA and Falcón, LI and Alcocer, J}, title = {Shifts in water column microbial composition associated to lakes with different trophic conditions: "Lagunas de Montebello" National Park, Chiapas, México.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13999}, pmid = {36132223}, issn = {2167-8359}, mesh = {*Lakes/analysis ; Ecosystem ; Chlorophyll A ; Mexico ; RNA, Ribosomal, 16S/genetics ; Parks, Recreational ; *Cyanobacteria/genetics ; }, abstract = {Eutrophication is a global problem causing the reduction of water quality and the loss of ecosystem goods and services. The lakes of the "Lagunas de Montebello" National Park (LMNP), Chiapas, Mexico, not only represent unique and beautiful natural scenic sites in southern Mexico but are also a national protected area and RAMSAR site. Unfortunately, some of these lakes started showing eutrophication signs since 2003. Anthropogenic activities (e.g., land-use change from forested to agricultural and urban development) are leading to water quality and trophic state alterations of the lakes of the LMNP. This study shows the results of a coupled limnological characterization and high-throughput sequencing of the V4 hypervariable region of the 16S rRNA gene to analyze the microbial composition of the water column in a set of oligotrophic and eutrophic lakes. Chlorophyll a (Chl-a) was the main environmental parameter correlated with the trophic conditions of the lakes. Although the microbial diversity was similar, the microbial composition changed significantly from oligo to eutrophic lakes. Proteobacteria, Firmicutes, and Cyanobacteria were the main components of oligotrophic lakes, and Cyanobacteria, Proteobacteria, and Bacteroidetes of eutrophic lakes. While Acinetobacter (Proteobacteria) and Cyanobium (a unicellular cyanobacterium) dominated in oligotrophic lakes, the filamentous, bloom-forming, and toxin-producing cyanobacteria Planktothrix was the dominant genus in eutrophic lakes. High-throughput sequencing allowed the detection of changes in the composition of the microbial component in oligotrophic lakes, suggesting a shift towards eutrophication, highlighting the relevance of sensitive monitoring protocols of these ecosystems to implement remediation programs for eutrophicated lakes and conservation strategies for those yet pristine.}, }
@article {pmid36130296, year = {2022}, author = {Kerr, BJ and Trachsel, JM and Bearson, BL and Loving, CL and Bearson, SMD and Byrne, KA and Pearce, SC and Ramirez, SM and Gabler, NK and Schweer, WP and Helm, ET and De Mille, CM}, title = {Evaluation of digestively resistant or soluble fibers, short- and medium-chain fatty acids, trace minerals, and antibiotics in nonchallenged nursery pigs on performance, digestibility, and intestinal integrity.}, journal = {Journal of animal science}, volume = {100}, number = {11}, pages = {}, pmid = {36130296}, issn = {1525-3163}, mesh = {Swine ; Animals ; *Animal Nutritional Physiological Phenomena ; Animal Feed/analysis ; Digestion ; *Trace Elements/pharmacology ; Anti-Bacterial Agents/pharmacology ; Diet/veterinary ; Zea mays ; Fatty Acids, Volatile/pharmacology ; Starch/pharmacology ; Butyrates/pharmacology ; }, abstract = {Three experiments (EXP) were conducted to determine the effect of feed additives on performance, intestinal integrity, gastrointestinal volatile fatty acids (VFA), and energy and nutrient digestion in nonchallenged nursery pigs. In EXP 1, 480 pigs (6.36-kg body weight, BW) were placed into 96 pens with 5 pigs/pen, and allotted to 1 of 10 dietary treatments: 1) negative control containing no feed additive (NC), 2) NC + 44 mg chlortetracycline and 38.5 mg tiamulin/kg diet (CTsb), 3) NC + 5% resistant potato starch (RSpo), 4) NC + 5% soluble corn fiber (SCF), 5) NC + 5% sugar beet pulp (SBP), 6) NC + 0.30% fatty acid mix (FAM), 7) NC + 0.10% phytogenic blend of essential oils and flavoring compounds (PHY), 8) NC + 50 mg Cu and 1,600 mg zinc oxide/kg diet (CuZn), 9) NC + 5% resistant corn starch (RScn), and 10) NC + 0.05% β-glucan (BG) for 28 d. There was no impact of dietary treatment on BW gain or feed intake (P ≥ 0.22). Pigs fed diets containing SCF, CTsb, and RSpo resulted in microbial community differences compared to pigs fed the NC (P < 0.05). In EXP 2, 48 barrows (12.8 kg BW) were selected at the end of EXP 1 and fed the same dietary treatments they had previously received: 1) NC, 2) NC + 5% RScn, 3) NC + 5% SCF, and 4) NC + FAM for 8 d. There was no effect of feeding diets containing RScn, SCF, or FAM on in vivo intestinal permeability (P ≤ 0.21). Ileal or colon pH, concentrations of VFA did not differ due to dietary treatment (P ≥ 0.36), but pigs fed diets containing FAM resulted in a greater butyric acid concentration in the cecum compared to pigs fed the NC (P ≤ 0.05). In EXP 3, 156 pigs (6.11 kg BW) were placed into 52 pens with 3 pigs/pen and allotted to 1 of 4 dietary treatments arranged in a factorial manner: 1) NC, 2) NC + 5% RSpo, 3) NC + 0.30% FAM, and 4) NC + 5% RSpo + 0.30% FAM for 24 d. Feeding pigs diets containing RSpo did not affect BW gain (P = 0.91) while pigs fed diets containing FAM grew improved BW gain (P = 0.09). Colonic butyric acid concentrations were greater in pigs fed diets containing RSpo (P = 0.03), while pigs fed diets containing FAM exhibited reduced total VFA concentrations (P = 0.11). The results indicate that supplementing diets with digestively resistant but fermentable fibers, short- and medium-chain fatty acids, or antibiotics do not have a consistent effect, positive or negative, on markers of intestinal integrity or barrier function, intestinal VFA patterns, ATTD of energy and nutrients, or on pig performance.}, }
@article {pmid36128567, year = {2022}, author = {El Amrani, B}, title = {Aspects of the rhizospheric microbiota and their interactions with the soil ecosystem.}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {26}, number = {5}, pages = {442-448}, doi = {10.18699/VJGB-22-54}, pmid = {36128567}, issn = {2500-0462}, abstract = {Soil microbial communities play a key role in the evolution of the rhizosphere. In addition, proper exploration of these microbial resources represents a promising strategy that guarantees the health and sustainability of all ecosystems connected to the ground. Under the inf luence of environmental conditions, microbial communities can change compositions in terms of abundance and diversity. Beyond the descriptive level, the current orientation of microbial ecology is to link these structures to the functioning of ecosystems; specif ically, to understand the effect of environmental factors on the functional structure of microbial communities in ecosystems. This review focuses on the main interactions between the indigenous soil microf lora and the major constituents of the rhizosphere to understand, on the one hand, how microbial biodiversity can improve plant growth and maintain homeostasis of the rhizospheric ecosystem, on the other hand, how the maintenance and enrichment of plant biodiversity can contribute to the conservation of soil microbial diversity; knowing that these microorganisms are also controlled by the abiotic properties of the soil. Overall, understanding the dynamics of the rhizosphere microbiome is essential for developing innovative strategies in the f ield of protecting and maintaining the proper functioning of the soil ecosystem.}, }
@article {pmid36128049, year = {2022}, author = {Külekci, B and Schwarz, S and Brait, N and Perkmann-Nagele, N and Jaksch, P and Hoetzenecker, K and Puchhammer-Stöckl, E and Goerzer, I}, title = {Human cytomegalovirus strain diversity and dynamics reveal the donor lung as a major contributor after transplantation.}, journal = {Virus evolution}, volume = {8}, number = {2}, pages = {veac076}, pmid = {36128049}, issn = {2057-1577}, support = {P 31503/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Mixed human cytomegalovirus (HCMV) strain infections are frequent in lung transplant recipients (LTRs). To date, the influence of the donor (D) and recipient (R) HCMV serostatus on intra-host HCMV strain composition and viral population dynamics after transplantation is only poorly understood. Here, we investigated ten pre-transplant lungs from HCMV-seropositive donors and 163 sequential HCMV-DNA-positive plasma and bronchoalveolar lavage samples from fifty LTRs with multiviremic episodes post-transplantation. The study cohort included D+R+ (38 per cent), D+R- (36 per cent), and D-R+ (26 per cent) patients. All samples were subjected to quantitative genotyping by short amplicon deep sequencing, and twenty-four of them were additionally PacBio long-read sequenced for genotype linkages. We find that D+R+ patients show a significantly elevated intra-host strain diversity compared to D+R- and D-R+ patients (P = 0.0089). Both D+ patient groups display significantly higher viral population dynamics than D- patients (P = 0.0061). Five out of ten pre-transplant donor lungs were HCMV DNA positive, whereof three multiple HCMV strains were detected, indicating that multi-strain transmission via lung transplantation is likely. Using long reads, we show that intra-host haplotypes can share distinctly linked genotypes, which limits overall intra-host diversity in mixed infections. Together, our findings demonstrate donor-derived strains as the main source of increased HCMV strain diversity and dynamics post-transplantation. These results foster strategies to mitigate the potential transmission of the donor strain reservoir to the allograft, such as ex vivo delivery of HCMV-selective immunotoxins prior to transplantation to reduce latent HCMV.}, }
@article {pmid36126627, year = {2022}, author = {Xu, G and He, J}, title = {Resilience of organohalide-detoxifying microbial community to oxygen stress in sewage sludge.}, journal = {Water research}, volume = {224}, number = {}, pages = {119055}, doi = {10.1016/j.watres.2022.119055}, pmid = {36126627}, issn = {1879-2448}, mesh = {Bacteria/chemistry ; Biodegradation, Environmental ; *Chloroflexi/genetics ; *Environmental Pollutants ; Halogenated Diphenyl Ethers ; Humans ; *Microbiota ; Oxygen ; Sewage ; *Tetrachloroethylene ; }, abstract = {Organohalide pollutants are prevalent in the environment, causing harms to wildlife and human. Organohalide-respiring bacteria (OHRB) could detoxify these pollutants in anaerobic environments, but the most competent OHRB (i.e., Dehalococcoides) is susceptible to oxygen. This study reports exceptional resistance and resilience of sewage sludge microbial communities to oxygen stress for attenuation of structurally distinct organohalide pollutants, including tetrachloroethene, tetrabromobisphenol A, and polybrominated diphenyl ethers. The dehalogenation rate constant of these organohalide pollutants in oxygen-exposed sludge microcosms was maintained as 74-120% as that in the control without oxygen exposure. Subsequent top-down experiments clarified that sludge flocs and non-OHRB contributed to alleviating oxygen stress on OHRB. In the dehalogenating microcosms, multiple OHRB (Dehahlococcoides, Dehalogenimonas, and Sulfurospirillum) harboring distinct reductive dehalogenase genes (pceA, pteA, tceA, vcrA, and bdeA) collaborated to detoxify organohalide pollutants but responded differentially to oxygen stress. Comprehensive microbial community analyses (taxonomy, diversity, and structure) demonstrated certain resilience of the sludge-derived dehalogenating microbial communities to oxygen stress. Additionally, microbial co-occurrence networks were intensified by oxygen stress in most microcosms, as a possible stress mitigation strategy. Altogether the mechanistic and ecological findings in this study contribute to remediation of organohalide-contaminated sites encountering oxygen disturbance.}, }
@article {pmid36123806, year = {2022}, author = {Zhang, Y and Yang, X and Van de Peer, Y and Chen, J and Marchal, K and Shi, T}, title = {Evolution of isoform-level gene expression patterns across tissues during lotus species divergence.}, journal = {The Plant journal : for cell and molecular biology}, volume = {112}, number = {3}, pages = {830-846}, pmid = {36123806}, issn = {1365-313X}, support = {833522/ERC_/European Research Council/International ; }, mesh = {*Lotus/genetics ; Gene Duplication ; Genes, Duplicate ; Protein Isoforms/genetics ; *Arabidopsis/genetics ; *Nelumbo/genetics ; Gene Expression ; Evolution, Molecular ; }, abstract = {Both gene duplication and alternative splicing (AS) drive the functional diversity of gene products in plants, yet the relative contributions of the two key mechanisms to the evolution of gene function are largely unclear. Here, we studied AS in two closely related lotus plants, Nelumbo lutea and Nelumbo nucifera, and the outgroup Arabidopsis thaliana, for both single-copy and duplicated genes. We show that most splicing events evolved rapidly between orthologs and that the origin of lineage-specific splice variants or isoforms contributed to gene functional changes during species divergence within Nelumbo. Single-copy genes contain more isoforms, have more AS events conserved across species, and show more complex tissue-dependent expression patterns than their duplicated counterparts. This suggests that expression divergence through isoforms is a mechanism to extend the expression breadth of genes with low copy numbers. As compared to isoforms of local, small-scale duplicates, isoforms of whole-genome duplicates are less conserved and display a less conserved tissue bias, pointing towards their contribution to subfunctionalization. Through comparative analysis of isoform expression networks, we identified orthologous genes of which the expression of at least some of their isoforms displays a conserved tissue bias across species, indicating a strong selection pressure for maintaining a stable expression pattern of these isoforms. Overall, our study shows that both AS and gene duplication contributed to the diversity of gene function during the evolution of lotus.}, }
@article {pmid36123554, year = {2023}, author = {Xu, MP and Zhi, RC and Jian, JN and Feng, YZ and Han, XH and Zhang, W}, title = {Changes in Soil Organic C Fractions and C Pool Stability Are Mediated by C-Degrading Enzymes in Litter Decomposition of Robinia pseudoacacia Plantations.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1189-1199}, pmid = {36123554}, issn = {1432-184X}, mesh = {*Soil/chemistry ; Ecosystem ; *Robinia ; Carbon/metabolism ; Lignin/metabolism ; Cellulose/metabolism ; Hydrolases/metabolism ; Soil Microbiology ; Oxidoreductases ; Forests ; China ; }, abstract = {Litter decomposition is the main source of soil organic carbon (SOC) pool, regarding as an important part of terrestrial ecosystem C dynamics. The turnover of SOC is mainly regulated by extracellular enzymes secreted by microorganisms. However, the response mechanism of soil C-degrading enzymes and SOC in litter decomposition remains unclear. To clarify how SOC fraction dynamics respond to C-degrading enzymes in litter decomposition, we used field experiments to collect leaf litter and SOC fractions from the underlying layer in Robinia pseudoacacia plantations on the Loess Plateau. Our results showed that SOC, easily oxidizable organic C, dissolved organic C, and microbial biomass C increased significantly during the decomposition process. Litter decomposition significantly decreased soil hydrolase activity, but slightly increased oxidase activity. Correlation analysis results showed that SOC fractions were significantly positively correlated with the litter mass, lignin, soil moisture, and oxidase activity, but significantly negatively correlated with cellulose content and soil pH. Partial least squares path models revealed that soil C-degrading enzymes can directly or indirectly affect the changes of soil C fractions. The most direct factors affecting the SOC fractions of topsoil during litter decomposition were litter lignin and cellulose degradation, soil pH, and C-degrading enzymes. Furthermore, regression analysis showed that the decrease of SOC stability in litter decomposition was closely related to the decrease of soil hydrolase to oxidase ratio. These results highlighted that litter degradation-induced changes in C-degrading enzyme activity significantly affected SOC fractions. Furthermore, the distribution of soil hydrolases and oxidases affected the stability of SOC during litter decomposition. These findings provided a theoretical framework for a more comprehensive understanding of C turnover and stabilization mechanisms between plant and soil.}, }
@article {pmid36123442, year = {2022}, author = {Hedlund, BP and Chuvochina, M and Hugenholtz, P and Konstantinidis, KT and Murray, AE and Palmer, M and Parks, DH and Probst, AJ and Reysenbach, AL and Rodriguez-R, LM and Rossello-Mora, R and Sutcliffe, IC and Venter, SN and Whitman, WB}, title = {SeqCode: a nomenclatural code for prokaryotes described from sequence data.}, journal = {Nature microbiology}, volume = {7}, number = {10}, pages = {1702-1708}, pmid = {36123442}, issn = {2058-5276}, mesh = {*Metagenome ; *Prokaryotic Cells ; }, abstract = {Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry (https://seqco.de/), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.}, }
@article {pmid36122204, year = {2022}, author = {Peng, R and Xu, Y and Tian, S and Unver, T and Liu, Z and Zhou, Z and Cai, X and Wang, K and Wei, Y and Liu, Y and Wang, H and Hu, G and Zhang, Z and Grover, CE and Hou, Y and Wang, Y and Li, P and Wang, T and Lu, Q and Wang, Y and Conover, JL and Ghazal, H and Wang, Q and Zhang, B and Van Montagu, M and Van de Peer, Y and Wendel, JF and Liu, F}, title = {Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {39}, pages = {e2208496119}, pmid = {36122204}, issn = {1091-6490}, mesh = {Cotton Fiber ; *Evolution, Molecular ; Genetic Variation/genetics ; *Genome, Plant/genetics ; *Gossypium/classification/genetics ; Isomerases/genetics/metabolism ; Tetraploidy ; }, abstract = {Allotetraploid cotton (Gossypium) species represents a model system for the study of plant polyploidy, molecular evolution, and domestication. Here, chromosome-scale genome sequences were obtained and assembled for two recently described wild species of tetraploid cotton, Gossypium ekmanianum [(AD)6, Ge] and Gossypium stephensii [(AD)7, Gs], and one early form of domesticated Gossypium hirsutum, race punctatum [(AD)1, Ghp]. Based on phylogenomic analysis, we provide a dated whole-genome level perspective for the evolution of the tetraploid Gossypium clade and resolved the evolutionary relationships of Gs, Ge, and domesticated G. hirsutum. We describe genomic structural variation that arose during Gossypium evolution and describe its correlates-including phenotypic differentiation, genetic isolation, and genetic convergence-that contributed to cotton biodiversity and cotton domestication. Presence/absence variation is prominent in causing cotton genomic structural variations. A presence/absence variation-derived gene encoding a phosphopeptide-binding protein is implicated in increasing fiber length during cotton domestication. The relatively unimproved Ghp offers the potential for gene discovery related to adaptation to environmental challenges. Expanded gene families enoyl-CoA δ isomerase 3 and RAP2-7 may have contributed to abiotic stress tolerance, possibly by targeting plant hormone-associated biochemical pathways. Our results generate a genomic context for a better understanding of cotton evolution and for agriculture.}, }
@article {pmid36118848, year = {2022}, author = {Rabapane, KJ and Ijoma, GN and Matambo, TS}, title = {Insufficiency in functional genomics studies, data, and applications: A case study of bio-prospecting research in ruminant microbiome.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {946449}, pmid = {36118848}, issn = {1664-8021}, abstract = {Over the last two decades, biotechnology has advanced at a rapid pace, propelled by the incorporation of bio-products into various aspects of pharmaceuticals, industry, and the environment. These developments have sparked interest in the bioprospecting of microorganisms and their products in a variety of niche environments. Furthermore, the use of omics technologies has greatly aided our analyses of environmental samples by elucidating the microbial ecological framework, biochemical pathways, and bio-products. However, the more often overemphasis on taxonomic identification in most research publications, as well as the data associated with such studies, is detrimental to immediate industrial and commercial applications. This review identifies several factors that contribute to the complexity of sequence data analysis as potential barriers to the pragmatic application of functional genomics, utilizing recent research on ruminants to demonstrate these limitations in the hopes of broadening our horizons and drawing attention to this gap in bioprospecting studies for other niche environments as well. The review also aims to emphasize the importance of routinely incorporating functional genomics into environmental metagenomics analyses in order to improve solutions that drive rapid industrial biocatalysis developments from derived outputs with the aim of achieving potential benefits in energy-use reduction and environmental considerations for current and future applications.}, }
@article {pmid36113308, year = {2022}, author = {Alves, KJ and Pylro, VS and Nakayama, CR and Vital, VG and Taketani, RG and Santos, DG and Rodrigues, JLM and Tsai, SM and Andreote, FD}, title = {Methanogenic communities and methane emissions from enrichments of Brazilian Amazonia soils under land-use change.}, journal = {Microbiological research}, volume = {265}, number = {}, pages = {127178}, doi = {10.1016/j.micres.2022.127178}, pmid = {36113308}, issn = {1618-0623}, mesh = {Archaea ; Bacteria ; Brazil ; *Euryarchaeota/genetics ; *Greenhouse Gases/analysis/metabolism ; Methane ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Amazonian forest conversion into agricultural and livestock areas is considered one of the activities that contribute most to the emission of greenhouse gases, including methane. Biogenic methane production is mainly performed by methanogenic Archaea, which underscores the importance of understanding the drivers shaping microbial communities involved in the methane cycling and changes in methane metabolism. Here, we aimed to investigate the composition and structure of bacterial and archaeal communities in tropical soils in response to land-use changes, emphasizing the methanogenic communities. We collected soil samples from primary forest, pasture, and secondary forest of the Amazonian region and used a strategy based on the enrichment of the methanogenic community with three different methanogenic substrates followed by measurements of methane emission, quantification of mcrA gene copies by qPCR, and total 16 S rRNA gene sequencing (metataxonomics). We observed variations in the structure of bacterial and archaeal communities of soils under different uses. The richness of methanogenic communities was higher in pasture than forest soils and this richness remained during the incubation period, and as a consequence, the enrichment induced earlier methane emission in pastures-derived samples. Furthermore, pastures enrichments exhibited methanogenic archaea networks more complex than primary and secondary forests. In conclusion, pastures harbor a richer and more responsive methanogenic community than forest samples, suggesting that conversion of forest areas to pasture may boost methane emission.}, }
@article {pmid36112603, year = {2022}, author = {Miller, JC and Satheesh Babu, AK and Petersen, C and Wankhade, UD and Robeson, MS and Putich, MN and Mueller, JE and O'Farrell, AS and Cho, JM and Chintapalli, SV and Jalili, T and Symons, JD and Anandh Babu, PV}, title = {Gut Microbes Are Associated with the Vascular Beneficial Effects of Dietary Strawberry on Metabolic Syndrome-Induced Vascular Inflammation.}, journal = {Molecular nutrition &amp; food research}, volume = {66}, number = {22}, pages = {e2200112}, pmid = {36112603}, issn = {1613-4133}, support = {R03 AG052848/AG/NIA NIH HHS/United States ; R01 AT010247/AT/NCCIH NIH HHS/United States ; R01 HL141540/HL/NHLBI NIH HHS/United States ; P30 DK020579/DK/NIDDK NIH HHS/United States ; R03AGO52848/HL/NHLBI NIH HHS/United States ; }, mesh = {Male ; Mice ; Animals ; *Fragaria/chemistry ; *Metabolic Syndrome/etiology/drug therapy ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; Inflammation ; }, abstract = {SCOPE: Metabolic syndrome (MetS) alters the gut microbial ecology and increases the risk of cardiovascular disease. This study investigates whether strawberry consumption reduces vascular complications in an animal model of MetS and identifies whether this effect is associated with changes in the composition of gut microbes.<br><br>METHODS AND RESULTS: Seven-week-old male mice consume diets with 10% (C) or 60% kcal from fat (high-fat diet fed mice; HF) for 12 weeks and subgroups are fed a 2.35% freeze-dried strawberry supplemented diet (C+SB or HF+SB). This nutritional dose is equivalent to &#x2248;160 g of strawberry. After 12 weeks treatment, vascular inflammation is enhanced in HF versus C mice as shown by an increased monocyte binding to vasculature, elevated serum chemokines, and increased mRNA expression of inflammatory molecules. However, strawberry supplementation suppresses vascular inflammation in HF+SB versus HF mice. Metabolic variables, blood pressure, and indices of vascular function were similar among the groups. Further, the abundance of opportunistic microbe is decreased in HF+SB. Importantly, circulating chemokines are positively associated with opportunistic microbes and negatively associated with the commensal microbes (Bifidobacterium and Facalibaculum).<br><br>CONCLUSION: Dietary strawberry decreases the abundance of opportunistic microbe and this is associated with a decrease in vascular inflammation resulting from MetS.}, }
@article {pmid36112501, year = {2023}, author = {Abdel-Rahman, LIH and Morgan, XC}, title = {Searching for a Consensus Among Inflammatory Bowel Disease Studies: A Systematic Meta-Analysis.}, journal = {Inflammatory bowel diseases}, volume = {29}, number = {1}, pages = {125-139}, pmid = {36112501}, issn = {1536-4844}, mesh = {Humans ; *Colitis, Ulcerative/pathology ; Consensus ; *Inflammatory Bowel Diseases ; *Crohn Disease/pathology ; Feces ; }, abstract = {BACKGROUND: Numerous studies have examined the gut microbial ecology of patients with Crohn's disease (CD) and ulcerative colitis, but inflammatory bowel disease-associated taxa and ecological effect sizes are not consistent between studies.<br><br>METHODS: We systematically searched PubMed and Google Scholar and performed a meta-analysis of 13 studies to analyze how variables such as sample type (stool, biopsy, and lavage) affect results in inflammatory bowel disease gut microbiome studies, using uniform bioinformatic methods for all primary data.<br><br>RESULTS: Reduced alpha diversity was a consistent feature of both CD and ulcerative colitis but was more pronounced in CD. Disease contributed significantly variation in beta diversity in most studies, but effect size varied, and the effect of sample type was greater than the effect of disease. Fusobacterium was the genus most consistently associated with CD, but disease-associated genera were mostly inconsistent between studies. Stool studies had lower heterogeneity than biopsy studies, especially for CD.<br><br>CONCLUSIONS: Our results indicate that sample type variation is an important contributor to study variability that should be carefully considered during study design, and stool is likely superior to biopsy for CD studies due to its lower heterogeneity.}, }
@article {pmid36112189, year = {2023}, author = {Peralta-Maraver, I and Rutere, C and Horn, MA and Reche, I and Behrends, V and Reiss, J and Robertson, AL}, title = {Intermediate Levels of Predation and Nutrient Enrichment Enhance the Activity of Ibuprofen-Degrading Bacteria.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1438-1441}, pmid = {36112189}, issn = {1432-184X}, support = {641939//Horizon 2020 Framework Programme/ ; }, mesh = {Animals ; *Ecosystem ; *Food Chain ; Ibuprofen/metabolism ; Predatory Behavior ; Bacteria/metabolism ; }, abstract = {Water is the most indispensable natural resource; yet, organic pollution of freshwater sources is widespread. In recent years, there has been increasing concern over the vast array of emerging organic contaminants (EOCs) in the effluent of wastewater treatment plants (WWTPs). Several of these EOCs are degraded within the pore space of riverbeds by active microbial consortia. However, the mechanisms behind this ecosystem service are largely unknown. Here, we report how phosphate concentration and predator-prey interactions drive the capacity of bacteria to process a model EOC (ibuprofen). The presence of phosphate had a significant positive effect on the population growth rate of an ibuprofen-degrading strain. Thus, when phosphate was present, ibuprofen removal efficiency increased. Moreover, low and medium levels of predation, by a ciliated protozoan, stimulated bacterial population growth. This unimodal effect of predation was lost under high phosphate concentration, resulting in the flattening of the relationships between predator density and population growth of ibuprofen degraders. Our results suggest that moderate nutrient and predation levels promote the growth rate of bacterial degraders and, consequently, the self-purifying capability of the system. These findings enhance our understanding of the mechanisms by which riverbed communities drive the processing of EOCs.}, }
@article {pmid36111808, year = {2022}, author = {Marzorati, M and Bubeck, S and Bayne, T and Krishnan, K and Giusto, M}, title = {Effects of combined prebiotic, probiotic, IgG and amino acid supplementation on the gut microbiome of patients with inflammatory bowel disease.}, journal = {Future microbiology}, volume = {17}, number = {}, pages = {1307-1324}, doi = {10.2217/fmb-2022-0066}, pmid = {36111808}, issn = {1746-0921}, mesh = {Amino Acids ; Caco-2 Cells ; Dietary Supplements ; Fatty Acids, Volatile/pharmacology ; Flavonoids ; *Gastrointestinal Microbiome ; Humans ; Immunoglobulin G ; *Inflammatory Bowel Diseases/drug therapy ; Interleukin-10 ; Interleukin-6 ; Prebiotics ; *Probiotics/pharmacology ; }, abstract = {Background: The effects of the Total Gut Restoration (TGR) system supplementation on the gut microbiome were evaluated. Materials &amp; methods: A mucosal in vitro simulation of the human gastrointestinal tract (M-SHIME[®]) system was inoculated with fecal samples from patients with inflammatory bowel disease. Chambers were supplemented for 5 days with the TGR system (five probiotic Bacillus strains, prebiotic mixture, immunoglobulin concentrate, amino acids and prebiotic flavonoids). Results: Compared with unsupplemented controls, supplementation was associated with a significant increase in short-chain fatty acid production, and changes to the microbiome were observed. Supernatants from supplemented chambers improved intestinal barrier function, increased IL-6 and IL-10 production and decreased MCP1 production versus control in Caco-2/THP1 coculture. Conclusion: Daily TGR supplementation facilitated changes to the gut microbiome of patients with inflammatory bowel disease.}, }
@article {pmid36110415, year = {2022}, author = {Song, W and Gong, H and Wang, Q and Zhang, L and Qiu, L and Hu, X and Han, H and Li, Y and Li, R and Li, Y}, title = {Using Bayesian networks with Max-Min Hill-Climbing algorithm to detect factors related to multimorbidity.}, journal = {Frontiers in cardiovascular medicine}, volume = {9}, number = {}, pages = {984883}, pmid = {36110415}, issn = {2297-055X}, abstract = {OBJECTIVES: Multimorbidity (MMD) is a medical condition that is linked with high prevalence and closely related to many adverse health outcomes and expensive medical costs. The present study aimed to construct Bayesian networks (BNs) with Max-Min Hill-Climbing algorithm (MMHC) algorithm to explore the network relationship between MMD and its related factors. We also aimed to compare the performance of BNs with traditional multivariate logistic regression model.<br><br>METHODS: The data was downloaded from the Online Open Database of CHARLS 2018, a population-based longitudinal survey. In this study, we included 10 variables from data on demographic background, health status and functioning, and lifestyle. Missing value imputation was first performed using Random Forest. Afterward, the variables were included into logistic regression model construction and BNs model construction. The structural learning of BNs was achieved using MMHC algorithm and the parameter learning was conducted using maximum likelihood estimation.<br><br>RESULTS: Among 19,752 individuals (9,313 men and 10,439 women) aged 64.73 &#xb1; 10.32 years, there are 9,129 ones without MMD (46.2%) and 10,623 ones with MMD (53.8%). Logistic regression model suggests that physical activity, sex, age, sleep duration, nap, smoking, and alcohol consumption are associated with MMD (P < 0.05). BNs, by establishing a complicated network relationship, reveals that age, sleep duration, and physical activity have a direct connection with MMD. It also shows that education levels are indirectly connected to MMD through sleep duration and residence is indirectly linked to MMD through sleep duration.<br><br>CONCLUSION: BNs could graphically reveal the complex network relationship between MMD and its related factors, outperforming traditional logistic regression model. Besides, BNs allows for risk reasoning for MMD through Bayesian reasoning, which is more consistent with clinical practice and thus holds some application prospects.}, }
@article {pmid36108399, year = {2022}, author = {Sun, H and Xia, J and Wu, B and Ren, H and Zhang, X and Ye, L}, title = {Aerobic starvation treatment of activated sludge enhances the degradation efficiency of refractory organic compounds.}, journal = {Water research}, volume = {224}, number = {}, pages = {119069}, doi = {10.1016/j.watres.2022.119069}, pmid = {36108399}, issn = {1879-2448}, mesh = {Benzhydryl Compounds ; Bioreactors/microbiology ; Fluorocarbons ; Gabapentin ; Humans ; Phenols ; RNA, Ribosomal, 16S/genetics ; *Sewage/chemistry ; *Wastewater ; }, abstract = {Many refractory organic compounds (ROCs) in wastewater are toxic to human and aquatic organisms. Here, we reported an aerobic starvation approach to improve the degradation efficiencies of ROCs in activated sludge systems. The highest degradation rates of bisphenol AF (BPAF) (11.4 mg/g VSS · h) and gabapentin (GBP) (8.9 mg/g VSS · h) were achieved on the second day of the starvation process. While, the degradation rate of bisphenol A (BPA) on the 43rd day reached the maximum value of 0.8 mg/g VSS ·h, which was significantly higher than that of the seeding sludge (0.01 mg/g VSS · h). To investigate the mechanisms of this finding, we applied magnetic-nanoparticle mediated isolation, 16S rRNA gene sequencing, metagenomic sequencing and metatranscriptomic sequencing to analyze the microbial community structures and functions during the starvation process. The results showed that the increase of the BPA degradation ability was caused by the increase of the relative abundance of BPA degrading bacteria (Sphingomonas, Achromobacter, etc.), while, the enhancement of BPAF and GBP degradation was attributed to the increase of the expression of ROC degrading genes. Overall, these results improve our understanding of the microbial ecology of starved activated sludge and provide useful information for the future development of ROC removal technologies.}, }
@article {pmid36106503, year = {2023}, author = {Law, CKY and Bolea-Fernandez, E and Liu, T and Bonin, L and Wallaert, E and Verbeken, K and De Gusseme, B and Vanhaecke, F and Boon, N}, title = {The influence of H2 partial pressure on biogenic palladium nanoparticle production assessed by single-cell ICP-mass spectrometry.}, journal = {Microbial biotechnology}, volume = {16}, number = {5}, pages = {901-914}, pmid = {36106503}, issn = {1751-7915}, mesh = {*Metal Nanoparticles ; Palladium ; Partial Pressure ; Mass Spectrometry/methods ; Spectrum Analysis ; }, abstract = {The production of biogenic palladium nanoparticles (bio-Pd NPs) is widely studied due to their high catalytic activity, which depends on the size of nanoparticles (NPs). Smaller NPs (here defined as <100 nm) are more efficient due to their higher surface/volume ratio. In this work, inductively coupled plasma-mass spectrometry (ICP-MS), flow cytometry (FCM) and transmission electron microscopy (TEM) were combined to obtain insight into the formation of these bio-Pd NPs. The precipitation of bio-Pd NPs was evaluated on a cell-per-cell basis using single-cell ICP-MS (SC-ICP-MS) combined with TEM images to assess how homogenously the particles were distributed over the cells. The results provided by SC-ICP-MS were consistent with those provided by "bulk" ICP-MS analysis and FCM. It was observed that heterogeneity in the distribution of palladium over an entire cell population is strongly dependent on the Pd[2+] concentration, biomass and partial H2 pressure. The latter three parameters affected the particle size, ranging from 15.6 to 560 nm, and exerted a significant impact on the production of the bio-Pd NPs. The TEM combined with SC-ICP-MS revealed that the mass distribution for bacteria with high Pd content (144 fg Pd cell[-1]) indicated the presence of a large number of very small NPs (D50 = 15.6 nm). These results were obtained at high cell density (1 × 10[5] ± 3 × 10[4] cells μl[-1]) and H2 partial pressure (180 ml H2). In contrast, very large particles (D50 = 560 nm) were observed at low cell density (3 × 10[4] ± 10 × 10[2] cells μl[-1]) and H2 partial pressure (10-100 ml H2). The influence of the H2 partial pressure on the nanoparticle size and the possibility of size-tuned nanoparticles are presented.}, }
@article {pmid36106339, year = {2022}, author = {Van Wyk, JC and Sewell, BT and Danson, MJ and Tsekoa, TL and Sayed, MF and Cowan, DA}, title = {Engineering enhanced thermostability into the Geobacillus pallidus nitrile hydratase.}, journal = {Current research in structural biology}, volume = {4}, number = {}, pages = {256-270}, pmid = {36106339}, issn = {2665-928X}, abstract = {Nitrile hydratases (NHases) are important biocatalysts for the enzymatic conversion of nitriles to industrially-important amides such as acrylamide and nicotinamide. Although thermostability in this enzyme class is generally low, there is not sufficient understanding of its basis for rational enzyme design. The gene expressing the Co-type NHase from the moderate thermophile, Geobacillus pallidus RAPc8 (NRRL B-59396), was subjected to random mutagenesis. Four mutants were selected that were 3 to 15-fold more thermostable than the wild-type NHase, resulting in a 3.4-7.6 kJ/mol increase in the activation energy of thermal inactivation at 63 °C. High resolution X-ray crystal structures (1.15-1.80 Å) were obtained of the wild-type and four mutant enzymes. Mutant 9E, with a resolution of 1.15 Å, is the highest resolution crystal structure obtained for a nitrile hydratase to date. Structural comparisons between the wild-type and mutant enzymes illustrated the importance of salt bridges and hydrogen bonds in enhancing NHase thermostability. These additional interactions variously improved thermostability by increased intra- and inter-subunit interactions, preventing cooperative unfolding of α-helices and stabilising loop regions. Some hydrogen bonds were mediated via a water molecule, specifically highlighting the significance of structured water molecules in protein thermostability. Although knowledge of the mutant structures makes it possible to rationalize their behaviour, it would have been challenging to predict in advance that these mutants would be stabilising.}, }
@article {pmid36102128, year = {2023}, author = {Sampson, MM and Polk, CM and Fairman, RT and DeWitt, ME and Leonard, MK and Davidson, L and McCurdy, L and Passaretti, CL}, title = {Monkeypox testing delays: The need for drastic expansion of education and testing for monkeypox virus.}, journal = {Infection control and hospital epidemiology}, volume = {44}, number = {2}, pages = {348-349}, doi = {10.1017/ice.2022.237}, pmid = {36102128}, issn = {1559-6834}, mesh = {Humans ; *Monkeypox virus ; *Mpox, Monkeypox ; Educational Status ; }, }
@article {pmid36100598, year = {2022}, author = {Metz, S and Huber, P and Mateus-Barros, E and Junger, PC and de Melo, M and Bagatini, IL and Izaguirre, I and Câmara Dos Reis, M and Llames, ME and Accattatis, V and Quiroga, MV and Devercelli, M and Schiaffino, MR and Niño-García, JP and Bastidas Navarro, M and Modenutti, B and Vieira, H and Saraceno, M and Sabio Y García, CA and Pereira, E and González-Revello, A and Piccini, C and Unrein, F and Alonso, C and Sarmento, H}, title = {A georeferenced rRNA amplicon database of aquatic microbiomes from South America.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {565}, pmid = {36100598}, issn = {2052-4463}, mesh = {Bacteria/genetics ; Databases, Genetic ; High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; South America ; Water Microbiology ; }, abstract = {The biogeography of bacterial communities is a key topic in Microbial Ecology. Regarding continental water, most studies are carried out in the northern hemisphere, leaving a gap on microorganism's diversity patterns on a global scale. South America harbours approximately one third of the world's total freshwater resources, and is one of these understudied regions. To fill this gap, we compiled 16S rRNA amplicon sequencing data of microbial communities across South America continental water ecosystems, presenting the first database µSudAqua[db]. The database contains over 866 georeferenced samples from 9 different ecoregions with contextual environmental information. For its integration and validation we constructed a curated database (µSudAqua[db.sp]) using samples sequenced by Illumina MiSeq platform with commonly used prokaryote universal primers. This comprised ~60% of the total georeferenced samples of the µSudAqua[db]. This compilation was carried out in the scope of the µSudAqua collaborative network and represents one of the most complete databases of continental water microbial communities from South America.}, }
@article {pmid36100325, year = {2022}, author = {Xu, Q and Vandenkoornhuyse, P and Li, L and Guo, J and Zhu, C and Guo, S and Ling, N and Shen, Q}, title = {Microbial generalists and specialists differently contribute to the community diversity in farmland soils.}, journal = {Journal of advanced research}, volume = {40}, number = {}, pages = {17-27}, pmid = {36100325}, issn = {2090-1224}, mesh = {Bacteria ; *Ecosystem ; Farms ; *Soil ; Soil Microbiology ; }, abstract = {INTRODUCTION: Microbial generalists and specialists are thought to have distinct impacts on community dynamics, while there have been limited efforts to estimate their contribution to microbial diversity.<br><br>OBJECTIVES: We aimed to resolve this research gap in microbial ecology to strengthen our understanding of the biogeography of microbial diversity, with implications for global-scale biodiversity mapping.<br><br>METHODS: Herein, we identified the ecological characteristics of microbial generalists and specialists across over 3,000 farmland soil samples from eleven countries that encompassed seven climate types.<br><br>RESULTS: Considering the distinct distributions of generalists and specialists in degree of connexions, betweenness and as key species in network topology, both generalists and specialists contributed to species interactions, though through different modalities. A stronger signature of deterministic processes in specialists indicated their lower tolerance to environment fluctuations. Generalists, in contrast, were more characterized by stochastic processes with higher diversification and transition rates that suggested more important roles in maintaining community stability when exposed to environmental disturbances. The relationship between latitude and diversity combining with distance-decay effects showed that generalists dampened microbial biogeographical patterns, with contrasting impacts by specialists.<br><br>CONCLUSION: By demonstrating the ecological characteristics of microbial generalists and specialists, this study deepens our understanding of microbial diversity and highlights the need to impart systematic distinctions among different categories of species when modelling and predicting the fate of ecosystems in the face of global climate change, rather than assuming that species are functionally equivalent.}, }
@article {pmid36098749, year = {2023}, author = {Angelella, G and Nalam, V and Nachappa, P and White, J and Kaplan, I}, title = {Correction to: Endosymbionts Differentially Alter Exploratory Probing Behavior of a Nonpersistent Plant Virus Vector.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1453}, doi = {10.1007/s00248-022-02107-4}, pmid = {36098749}, issn = {1432-184X}, }
@article {pmid36094300, year = {2022}, author = {Brugiroux, S and Berry, D and Ring, D and Barnich, N and Daims, H and Stecher, B}, title = {Specific Localization and Quantification of the Oligo-Mouse-Microbiota (OMM[12]) by Fluorescence In Situ Hybridization (FISH).}, journal = {Current protocols}, volume = {2}, number = {9}, pages = {e548}, doi = {10.1002/cpz1.548}, pmid = {36094300}, issn = {2691-1299}, mesh = {Animals ; In Situ Hybridization, Fluorescence/methods ; Mice ; *Microbiota ; Oligonucleotide Probes ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The oligo-mouse-microbiota (OMM[12]) is a widely used syncom that colonizes gnotobiotic mice in a stable manner. It provides several fundamental functions to its murine host, including colonization resistance against enteric pathogens. Here, we designed and validated specific fluorescence in situ hybridization (FISH) probes to detect and quantify OMM[12] strains on intestinal tissue cross sections. 16S rRNA-specific probes were designed, and specificity was validated on fixed pure cultures. A hybridization protocol was optimized for sensitive detection of the individual bacterial cells in cryosections. Using this method, we showed that the intestinal mucosal niche of Akkermansia muciniphila can be influenced by global gut microbial community context. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Localization and quantification of OMM[12] single strains in mouse cecum cross section Support Protocol: Establishment of specific FISH probe set for OMM[12] syncom.}, }
@article {pmid36087683, year = {2022}, author = {Yaigoub, H and Fath, N and Tirichen, H and Wu, C and Li, R and Li, Y}, title = {Bidirectional crosstalk between dysbiotic gut microbiota and systemic lupus erythematosus: What is new in therapeutic approaches?.}, journal = {Clinical immunology (Orlando, Fla.)}, volume = {244}, number = {}, pages = {109109}, doi = {10.1016/j.clim.2022.109109}, pmid = {36087683}, issn = {1521-7035}, mesh = {*Autoimmune Diseases ; Autoimmunity ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; *Lupus Erythematosus, Systemic ; *Microbiota ; }, abstract = {Systemic lupus erythematosus is an autoimmune disease characterized by chronic inflammation and multiple organs damage. Its pathogenesis is complex and involves multiple factors including gut microbiota. Accumulating evidence indicates the interaction of microbial communities with the host immune system to maintain a state of homeostasis. Imbalances within the gut microbial composition and function may contribute to the development of many autoimmune diseases including SLE. In this review, we aim to highlight the dysregulation of commensal bacteria and their metabolites in the gastrointestinal tract and the resulting autoimmune responses in lupus and to decrypt the cross-link between the altered gut microbiota and the immune system in the SLE condition. We also provide new insights into targeting gut microbiota as a promising therapeutic approach to treat and manage SLE.}, }
@article {pmid36084824, year = {2022}, author = {Van Winckel, T and Ngo, N and Sturm, B and Al-Omari, A and Wett, B and Bott, C and Vlaeminck, SE and De Clippeleir, H}, title = {Enhancing bioflocculation in high-rate activated sludge improves effluent quality yet increases sensitivity to surface overflow rate.}, journal = {Chemosphere}, volume = {308}, number = {Pt 2}, pages = {136294}, doi = {10.1016/j.chemosphere.2022.136294}, pmid = {36084824}, issn = {1879-1298}, mesh = {Flocculation ; *Sewage ; *Waste Disposal, Fluid/methods ; }, abstract = {High-rate activated sludge (HRAS) relies on good bioflocculation and subsequent solid-liquid separation to maximize the capture of organics. However, full-scale applications often suffer from poor and unpredictable effluent suspended solids (ESS). While the biological aspects of bioflocculation are thoroughly investigated, the effects of fines (settling velocity < 0.6 m[3]/m[2]/h), shear and surface overflow rate (SOR) are unclear. This work tackled the impact of fines, shear, and SOR on the ESS in absence of settleable influent solids. This was assessed on a full-scale HRAS step-feed (SF) and pilot-scale HRAS contact-stabilization (CS) configuration using batch settling tests, controlled clarifier experiments, and continuous operation of reactors. Fines contributed up to 25% of the ESS in the full-scale SF configuration. ESS decreased up to 30 mg TSS/L when bioflocculation was enhanced with the CS configuration. The feast-famine regime applied in CS promoted the production of high-quality extracellular polymeric substances (EPS). However, this resulted in a narrow and unfavorable settling velocity distribution, with 50% ± 5% of the sludge mass settling between 0.6 and 1.5 m[3]/m[2]/h, thus increasing sensitivity towards SOR changes. A low shear environment (20 s[-1]) before the clarifier for at least one min was enough to ensure the best possible settling velocity distribution, regardless of prior shear conditions. Overall, this paper provides a more complete view on the drivers of ESS in HRAS systems, creating the foundation for the design of effective HRAS clarifiers. Tangible recommendations are given on how to manage fines and establish the optimal settling velocity of the sludge.}, }
@article {pmid36083443, year = {2022}, author = {Fournier, GP and Parsons, CW and Cutts, EM and Tamre, E}, title = {Standard Candles for Dating Microbial Lineages.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2569}, number = {}, pages = {41-74}, pmid = {36083443}, issn = {1940-6029}, mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Eukaryotic Cells ; Evolution, Molecular ; *Fossils ; Phylogeny ; Plants/genetics ; }, abstract = {Molecular clock analyses are challenging for microbial phylogenies, due to a lack of fossil calibrations that can reliably provide absolute time constraints. An alternative source of temporal constraints for microbial groups is provided by the inheritance of proteins that are specific for the utilization of eukaryote-derived substrates, which have often been dispersed across the Tree of Life via horizontal gene transfer. In particular, animal, algal, and plant-derived substrates are often produced by groups with more precisely known divergence times, providing an older-bound on their availability within microbial environments. Therefore, these ages can serve as "standard candles" for dating microbial groups across the Tree of Life, expanding the reach of informative molecular clock investigations. Here, we formally develop the concept of substrate standard candles and describe how they can be propagated and applied using both microbial species trees and individual gene family phylogenies. We also provide detailed evaluations of several candidate standard candles and discuss their suitability in light of their often complex evolutionary and metabolic histories.}, }
@article {pmid36081452, year = {2022}, author = {Duan, Q and Tian, L and Feng, J and Ping, X and Li, L and Yaigoub, H and Li, R and Li, Y}, title = {Trametenolic Acid Ameliorates the Progression of Diabetic Nephropathy in db/db Mice via Nrf2/HO-1 and NF-κB-Mediated Pathways.}, journal = {Journal of immunology research}, volume = {2022}, number = {}, pages = {6151847}, pmid = {36081452}, issn = {2314-7156}, mesh = {Albumins/metabolism ; Animals ; Antioxidants/metabolism ; Body Weight ; *Diabetes Mellitus ; *Diabetic Nephropathies/drug therapy ; Glutathione/metabolism ; Heme Oxygenase-1/metabolism ; Interleukin-6/metabolism ; Mice ; NF-E2-Related Factor 2/metabolism ; NF-kappa B/metabolism ; Oxidative Stress ; Superoxide Dismutase/metabolism ; *Triterpenes/therapeutic use ; Tumor Necrosis Factor-alpha/metabolism ; }, abstract = {Diabetic nephropathy (DN) is a fatal complication of diabetes and the main cause of end-stage renal disease. Due to the suboptimal effects of current treatments, there is an urgent need to develop new therapeutic strategies for DN. Trametenolic acid (TA), a lanostane-type tetracyclic triterpenoid, is one of the main active ingredients extracted from the natural product Inonotus obliquus. Our study was aimed at clarifying the potential protective effects of TA on DN and its underlying mechanism. In this research, C57BLKS/db (db/db) mice were used as the spontaneous DN model, and TA (10 mg/kg/d) was intraperitoneally injected for 4 consecutive weeks. Ratio of right kidney weight/body weight was calculated, and the contents of serum creatinine (Scr), blood urea nitrogen (BUN), and urine albumin were detected. The activities of superoxide dismutase (SOD) and catalase (CAT) and the contents of reductive glutathione (GSH) and malondialdehyde (MDA) were measured. The histopathological changes of renal tissues were observed by hematoxylin and eosin (HE), periodic acid-Schiff (PAS), and Masson staining. The protein expressions of nuclear factor erythroid 2-related factor 2 (Nrf2), heme oxygenase-1 (HO-1), NAD(P)H:quinone oxidoreductase-1 (NQO-1), nuclear factor kappa B (NF-κB), proinflammation cytokine tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), interleukin-1β (IL-1β), Nephrin, and Podocin were detected by western blot assay. Immunohistochemistry was utilized to detect expressions of collagen III (COL-III) and fibronectin (FN). Our results showed that TA administration significantly reduced the ratio of right kidney weight/body weight, BUN, Scr, and urine albumin levels and alleviated the histopathological changes of DN mice. Moreover, TA administration remarkably increased GSH content and SOD and CAT activities and decreased MDA content. Western blot assay demonstrated that TA activated Nrf2 signaling and increased the expression of downstream antioxidant enzymes HO-1 and NQO-1. Further studies illustrated that NF-κB signaling was inhibited, and downstream proinflammation cytokine expressions of TNF-α, IL-6, and IL-1β were also downregulated. In addition, we also found that TA administration significantly increased the expression of nephrin and podocin proteins and reduced the protein expression of COL-III and FN. These findings suggested that TA exhibited a renoprotective effect by ameliorating oxidative stress and inflammation via Nrf2/HO-1 and NF-κB signaling pathways.}, }
@article {pmid36078654, year = {2022}, author = {Zou, J and Yang, J and He, H and Wang, X and Mei, R and Cai, L and Li, J}, title = {Effect of Seed Sludge Type on Aerobic Granulation, Pollutant Removal and Microbial Community in a Sequencing Batch Reactor Treating Real Textile Wastewater.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {17}, pages = {}, pmid = {36078654}, issn = {1660-4601}, mesh = {Aerobiosis ; Bioreactors/microbiology ; *Environmental Pollutants ; *Microbiota ; Nitrogen ; Sewage/microbiology ; Textiles ; Waste Disposal, Fluid/methods ; Wastewater ; }, abstract = {The aerobic granulation, pollutant removal, and microbial community in real textile wastewater (TWW) treatment were compared using conventional activated sludge (CAS) and preformed aerobic granular sludge (AGS) in synthetic wastewater as seed in two reactors, reactor-1 (R1) and reactor-2 (R2), respectively. The results showed that complete granulation was achieved in R1 (sludge volume index at 5 min (SVI5) and 30 min (SVI30): 19.4 mL/g; granule size: 210 μm) within 65 days, while it only required 28 days in R2 (SVI5 and SVI30: 27.3 mL/g; granule size: 496 μm). The removal of COD, NH4[+]-N and TN in R1 (49.8%, 98.8%, and 41.6%) and R2 (53.6%, 96.9%, and 40.8%) were comparable in 100% real TWW treatment, but stable performance was achieved much faster in R2. The real TWW had an inhibitory effect on heterotrophic bacteria activity, but it had no inhibition on ammonia-oxidizing bacteria activity. AGS with a larger particle size had a higher microbial tolerance to real TWW. Furthermore, filamentous Thiothrix in the AGS in R2 disappeared when treating real TWW, leading to the improvement of sludge settleability. Thus, seeding preformed AGS is suggested as a rapid start-up method for a robust AGS system in treating real TWW.}, }
@article {pmid36077481, year = {2022}, author = {Villalba, LA and Kasada, M and Zoccarato, L and Wollrab, S and Grossart, HP}, title = {Differing Escape Responses of the Marine Bacterium Marinobacter adhaerens in the Presence of Planktonic vs. Surface-Associated Protist Grazers.}, journal = {International journal of molecular sciences}, volume = {23}, number = {17}, pages = {}, pmid = {36077481}, issn = {1422-0067}, support = {not asigned yet//Leibniz Association/ ; }, mesh = {Bacteria ; Ecosystem ; Humans ; Marinobacter ; *Plankton ; *Stramenopiles ; Water ; }, abstract = {Protist grazing pressure plays a major role in controlling aquatic bacterial populations, affecting energy flow through the microbial loop and biogeochemical cycles. Predator-escape mechanisms might play a crucial role in energy flow through the microbial loop, but are yet understudied. For example, some bacteria can use planktonic as well as surface-associated habitats, providing a potential escape mechanism to habitat-specific grazers. We investigated the escape response of the marine bacterium Marinobacter adhaerens in the presence of either planktonic (nanoflagellate: Cafeteria roenbergensis) or surface-associated (amoeba: Vannella anglica) protist predators, following population dynamics over time. In the presence of V. anglica, M. adhaerens cell density increased in the water, but decreased on solid surfaces, indicating an escape response towards the planktonic habitat. In contrast, the planktonic predator C. roenbergensis induced bacterial escape to the surface habitat. While C. roenbergensis cell numbers dropped substantially after a sharp initial increase, V. anglica exhibited a slow, but constant growth throughout the entire experiment. In the presence of C. roenbergensis, M. adhaerens rapidly formed cell clumps in the water habitat, which likely prevented consumption of the planktonic M. adhaerens by the flagellate, resulting in a strong decline in the predator population. Our results indicate an active escape of M. adhaerens via phenotypic plasticity (i.e., behavioral and morphological changes) against predator ingestion. This study highlights the potentially important role of behavioral escape mechanisms for community composition and energy flow in pelagic environments, especially with globally rising particle loads in aquatic systems through human activities and extreme weather events.}, }
@article {pmid36076760, year = {2022}, author = {Mutalub, YB and Abdulwahab, M and Mohammed, A and Yahkub, AM and Al-Mhanna, SB and Yusof, W and Tang, SP and Rasool, AHG and Mokhtar, SS}, title = {Gut Microbiota Modulation as a Novel Therapeutic Strategy in Cardiometabolic Diseases.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {17}, pages = {}, pmid = {36076760}, issn = {2304-8158}, support = {1001/PPSP/8012346//Universiti Sains Malaysia/ ; }, abstract = {The human gut harbors microbial ecology that is in a symbiotic relationship with its host and has a vital function in keeping host homeostasis. Inimical alterations in the composition of gut microbiota, known as gut dysbiosis, have been associated with cardiometabolic diseases. Studies have revealed the variation in gut microbiota composition in healthy individuals as compared to the composition of those with cardiometabolic diseases. Perturbation of host-microbial interaction attenuates physiological processes and may incite several cardiometabolic disease pathways. This imbalance contributes to cardiometabolic diseases via metabolism-independent and metabolite-dependent pathways. The aim of this review was to elucidate studies that have demonstrated the complex relationship between the intestinal microbiota as well as their metabolites and the development/progression of cardiometabolic diseases. Furthermore, we systematically itemized the potential therapeutic approaches for cardiometabolic diseases that target gut microbiota and/or their metabolites by following the pathophysiological pathways of disease development. These approaches include the use of diet, prebiotics, and probiotics. With the exposition of the link between gut microbiota and cardiometabolic diseases, the human gut microbiota therefore becomes a potential therapeutic target in the development of novel cardiometabolic agents.}, }
@article {pmid36076344, year = {2023}, author = {Xu, H and Qian, Y and Jia, S and Shi, Z and Zhong, Q}, title = {Comparative analysis of subgingival microbiota in patients with mild, moderate, and severe chronic periodontitis.}, journal = {Oral diseases}, volume = {29}, number = {7}, pages = {2865-2877}, doi = {10.1111/odi.14373}, pmid = {36076344}, issn = {1601-0825}, support = {20184Y0244//Shanghai Municipal Health and Family Planning Commission/ ; }, mesh = {Humans ; *Chronic Periodontitis/therapy ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Gingival Crevicular Fluid ; *Microbiota/genetics ; }, abstract = {In this study, we explored the suspected pathogens of chronic periodontitis at different stages of occurrence and development. We collected 100 gingival crevicular fluid samples, 27, 27, and 26 from patients with mild, moderate, and severe chronic periodontitis, respectively, and 20 from healthy individuals. Pathogens were detected using a 16S rRNA metagenomic approach. Quantitative Insights in Microbial Ecology, Mothur, and other software were used to analyze the original data, draw relative abundance histograms and heat maps, and calculate flora abundance and diversity indexes. We identified 429 operational taxonomic units, covering 13 phyla, 20 classes, 32 orders, 66 families, and 123 genera from the four groups of samples. Each group showed microbial diversity, and the number of new species of bacterial flora in the gingival crevicular fluid samples gradually increased from the healthy to the severe chronic periodontitis group. There was a significant difference in the relative abundance of the core flora at the phylum, class, order, family, and genus classification levels. Our data indicated a certain correlation between the changes in the subgingival microbial structure and the occurrence and development of chronic periodontitis, which might be able to provide a reference for the diagnosis, treatment and prevention of chronic periodontitis.}, }
@article {pmid36075785, year = {2023}, author = {Martín-Rodríguez, AJ}, title = {Respiration-induced biofilm formation as a driver for bacterial niche colonization.}, journal = {Trends in microbiology}, volume = {31}, number = {2}, pages = {120-134}, doi = {10.1016/j.tim.2022.08.007}, pmid = {36075785}, issn = {1878-4380}, mesh = {*Biofilms ; Oxidation-Reduction ; *Bacteria/metabolism ; Oxygen/metabolism ; Respiration ; }, abstract = {Depending on their physiology and metabolism, bacteria can carry out diverse redox processes for energy acquisition, which facilitates adaptation to environmental or host-associated niches. Of these processes, respiration, using oxygen or alternative terminal electron acceptors, is energetically the most favorable in heterotrophic bacteria. The biofilm lifestyle, a coordinated multicellular behavior, is ubiquitous in bacteria and is regulated by a variety of intrinsic and extrinsic cues. Respiration of distinct electron acceptors has been shown to induce biofilm formation or dispersal. The notion of biofilm formation regulation by electron acceptor availability and respiration has often been considered species-specific. However, recent evidence suggests that this phenomenon can be strain-specific, even in strains sharing the same functional respiratory pathways, thereby implying subtle regulatory mechanisms. On this basis, I argue that induction of biofilm formation by sensing and respiration of electron acceptors might direct subgroups of redox-specialized strains to occupy certain niches. A palette of respiration and electron-transfer-mediated microbial social interactions within biofilms may broaden ecological opportunities. The strain specificity of this phenomenon represents an important opportunity to identify key molecular mechanisms and their ecophysiological significance, which in turn may lay the ground for applications in areas ranging from biotechnology to the prevention of antimicrobial resistance.}, }
@article {pmid36075698, year = {2022}, author = {Van Holm, W and Verspecht, T and Carvalho, R and Bernaerts, K and Boon, N and Zayed, N and Teughels, W}, title = {Glycerol strengthens probiotic effect of Limosilactobacillus reuteri in oral biofilms: A synergistic synbiotic approach.}, journal = {Molecular oral microbiology}, volume = {37}, number = {6}, pages = {266-275}, doi = {10.1111/omi.12386}, pmid = {36075698}, issn = {2041-1014}, mesh = {Humans ; *Limosilactobacillus reuteri/metabolism ; Glycerol/pharmacology/metabolism ; *Synbiotics ; *Probiotics/pharmacology ; Biofilms ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; }, abstract = {Both in vitro and in vivo studies have shown that the probiotic Limosilactobacillus reuteri can improve oral health. Limosilactobacillus reuteri species are known to produce the antimicrobial "reuterin" from glycerol. In order to further increase its antimicrobial activity, this study evaluated the effect of the combined use of glycerol and Limosilactobacillus reuteri (ATCC PTA 5289) in view of using a synergistic synbiotic over a probiotic. An antagonistic agar growth and a multispecies biofilm model showed that the antimicrobial potential of the probiotic was significantly enhanced against periodontal pathobionts and anaerobic commensals when supplemented with glycerol. Synbiotic biofilms also showed a significant reduction in inflammatory expression of human oral keratinocytes (HOK-18A), but only when the keratinocytes were preincubated with the probiotic. Probiotic preincubation of keratinocytes or probiotic and synbiotic treatment of biofilms alone was insufficient to significantly reduce inflammatory expression. Overall, this study shows that combining glycerol with the probiotic L. reuteri into a synergistic synbiotic can greatly improve the effectiveness of the latter.}, }
@article {pmid36073497, year = {2022}, author = {Lammers, A and Nazipi, S and Zweers, H and Bilde, T and Schramm, A and Garbeva, P and Lalk, M}, title = {Antimicrobial volatiles emitted by members of the nest microbiome of social spiders.}, journal = {FEMS microbiology letters}, volume = {369}, number = {1}, pages = {}, doi = {10.1093/femsle/fnac088}, pmid = {36073497}, issn = {1574-6968}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Antifungal Agents/pharmacology ; *Microbiota ; *Spiders ; *Streptomyces ; }, abstract = {Microbes produce and respond to a range of structurally and functionally diverse volatiles. Many microbial volatiles have antimicrobial properties. Since volatiles can diffuse through complex 3D systems like spider nests, they are promising pathogen protection for social arthropods. Here, we analyzed the volatilomes of five nest microbiome members of the Namibian, social spider Stegodyphus dumicola, namely the bacteria Massilia sp. IC2-278, Massilia sp. IC2-477, Sphingomonas sp. IC-11, Streptomyces sp. IC-207, and the fungus Aureobasidium sp. CE_32, and tested their antimicrobial activity against two putative spider pathogens, namely Bacillus thuringiensis and Purpureocillium lilacinum. Most nest microbiome members released volatilomes with antibacterial and/or antifungal activities under in vitro conditions. The analysis of their volatilomes using GC/Q-TOF revealed that they include numerous antimicrobial volatiles. We tested the antimicrobial activity of five pure volatile compounds found in the volatilomes and revealed that all of them were antibacterial and/or antifungal. We could not identify the same antimicrobial volatiles as in a previous in situ study, but our results indicate that social spider-associated microorganisms as a source of antimicrobial volatiles are important for pathogen inhibition. Additionally, we showed the influence of the volatilomes on the antibiotic sensitivity of B. thuringiensis offering novel approaches to counter antibiotic resistance.}, }
@article {pmid36073311, year = {2022}, author = {McLean, AR and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Site-tropism of streptococci in the oral microbiome.}, journal = {Molecular oral microbiology}, volume = {37}, number = {6}, pages = {229-243}, pmid = {36073311}, issn = {2041-1014}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE027958/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Streptococcus/genetics ; *Microbiota/genetics ; Metagenome ; Bacteria/genetics ; Mouth/microbiology ; Tropism ; Phylogeny ; }, abstract = {A detailed understanding of where bacteria localize is necessary to advance microbial ecology and microbiome-based therapeutics. The site-specialist hypothesis predicts that most microbes in the human oral cavity have a primary habitat type within the mouth where they are most abundant. We asked whether this hypothesis accurately describes the distribution of the members of the genus Streptococcus, a clinically relevant taxon that dominates most oral sites. Prior analysis of 16S rRNA gene sequencing data indicated that some oral Streptococcus clades are site-specialists while others may be generalists. However, within complex microbial populations composed of numerous closely related species and strains, such as the oral streptococci, genome-scale analysis is necessary to provide the resolution to discriminate closely related taxa with distinct functional roles. Here, we assess whether individual species within this genus are specialists using publicly available genomic sequence data that provide species-level resolution. We chose a set of high-quality representative genomes for human oral Streptococcus species. Onto these genomes, we mapped shotgun metagenomic sequencing reads from supragingival plaque, tongue dorsum, and other sites in the oral cavity. We found that every abundant Streptococcus species in the healthy human oral cavity showed strong site-tropism and that even closely related species such as S. mitis, S. oralis, and S. infantis specialized in different sites. These findings indicate that closely related bacteria can have distinct habitat distributions in the absence of dispersal limitation and under similar environmental conditions and immune regimes. Substantial overlap between the core genes of these three species suggests that site-specialization is determined by subtle differences in genomic content.}, }
@article {pmid36069784, year = {2022}, author = {Hahn, MW and Pitt, A and Schmidt, J and Koll, U and Wolf, J and Whitman, WB and Bodelier, PLE and Neumann-Schaal, M}, title = {Zwartia hollandica gen. nov., sp. nov., Jezberella montanilacus gen. nov., sp. nov. and Sheuella amnicola gen. nov., comb. nov., representing the environmental GKS98 (betIII) cluster.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {72}, number = {9}, pages = {}, doi = {10.1099/ijsem.0.005513}, pmid = {36069784}, issn = {1466-5034}, mesh = {*Alcaligenaceae/genetics ; Animals ; Bacteria/genetics ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; *Gastropoda ; Lakes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {We present two strains affiliated with the GKS98 cluster. This phylogenetically defined cluster is representing abundant, mainly uncultured freshwater bacteria, which were observed by many cultivation-independent studies on the diversity of bacteria in various freshwater lakes and streams. Bacteria affiliated with the GKS98 cluster were detected by cultivation-independent methods in freshwater systems located in Europe, Asia, Africa and the Americas. The two strains, LF4-65[T] (=CCUG 56422[T]=DSM 107630[T]) and MWH-P2sevCIIIb[T] (=CCUG 56420[T]=DSM 107629[T]), are aerobic chemoorganotrophs, both with genome sizes of 3.2 Mbp and G+C values of 52.4 and 51.0 mol%, respectively. Phylogenomic analyses based on concatenated amino acid sequences of 120 proteins suggest an affiliation of the two strains with the family Alcaligenaceae and revealed Orrella amnicola and Orrella marina (= Algicoccus marinus) as being the closest related, previously described species. However, the calculated phylogenomic trees clearly suggest that the current genus Orrella represents a polyphyletic taxon. Based on the branching order in the phylogenomic trees, as well as the revealed phylogenetic distances and chemotaxonomic traits, we propose to establish the new genus Zwartia gen. nov. and the new species Z. hollandica sp. nov. to harbour strain LF4-65[T] and the new genus Jezberella gen. nov. and the new species J. montanilacus sp. nov. to harbour strain MWH-P2sevCIIIb[T]. Furthermore, we propose the reclassification of the species Orrella amnicola in the new genus Sheuella gen. nov. The new genera Zwartia, Jezberella and Sheuella together represent taxonomically the GKS98 cluster.}, }
@article {pmid36069437, year = {2022}, author = {Eddie, BJ and Bird, LJ and Pelikan, C and Mussmann, M and Martínez-Pérez, C and Pinamang, P and Malanoski, AP and Glaven, SM}, title = {Conservation of Energetic Pathways for Electroautotrophy in the Uncultivated Candidate Order Tenderiales.}, journal = {mSphere}, volume = {7}, number = {5}, pages = {e0022322}, pmid = {36069437}, issn = {2379-5042}, support = {P 31010/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Carbon Dioxide/metabolism ; *Chromatiaceae ; Sulfur ; Iron/metabolism ; Cytochromes ; Oxidoreductases ; Heme ; }, abstract = {Electromicrobiology can be used to understand extracellular electron uptake in previously undescribed chemolithotrophs. Enrichment and characterization of the uncultivated electroautotroph "Candidatus Tenderia electrophaga" using electromicrobiology led to the designation of the order Tenderiales. Representative Tenderiales metagenome-assembled genomes (MAGs) have been identified in a number of environmental surveys, yet a comprehensive characterization of conserved genes for extracellular electron uptake has thus far not been conducted. Using comparative genomics, we identified conserved orthologous genes within the Tenderiales and nearest-neighbor orders important for extracellular electron uptake based on a previously proposed pathway from "Ca. Tenderia electrophaga." The Tenderiales contained a conserved cluster we designated uetABCDEFGHIJ, which encodes proteins containing features that would enable transport of extracellular electrons to cytoplasmic membrane-bound energy-transducing complexes such as two conserved cytochrome cbb3 oxidases. For example, UetJ is predicted to be an extracellular undecaheme c-type cytochrome that forms a heme wire. We also identified clusters of genes predicted to facilitate assembly and maturation of electron transport proteins, as well as cellular attachment to surfaces. Autotrophy among the Tenderiales is supported by the presence of carbon fixation and stress response pathways that could allow cellular growth by extracellular electron uptake. Key differences between the Tenderiales and other known neutrophilic iron oxidizers were revealed, including very few Cyc2 genes in the Tenderiales. Our results reveal a possible conserved pathway for extracellular electron uptake and suggest that the Tenderiales have an ecological role in coupling metal or mineral redox chemistry and the carbon cycle in marine and brackish sediments. IMPORTANCE Chemolithotrophic bacteria capable of extracellular electron uptake to drive energy metabolism and CO2 fixation are known as electroautotrophs. The recently described order Tenderiales contains the uncultivated electroautotroph "Ca. Tenderia electrophaga." The "Ca. Tenderia electrophaga" genome contains genes proposed to make up a previously undescribed extracellular electron uptake pathway. Here, we use comparative genomics to show that this pathway is well conserved among Tenderiales spp. recovered by metagenome-assembled genomes. This conservation extends to near neighbors of the Tenderiales but not to other well-studied chemolithotrophs, including iron and sulfur oxidizers, indicating that these genes may be useful markers of growth using insoluble extracellular electron donors. Our findings suggest that extracellular electron uptake and electroautotrophy may be pervasive among the Tenderiales, and the geographic locations from which metagenome-assembled genomes were recovered offer clues to their natural ecological niche.}, }
@article {pmid36068360, year = {2023}, author = {Xie, Z and Xu, G and Miao, F and Kong, H and Hu, M and Wang, Y}, title = {Predator Presence Alters Intestinal Microbiota in Mussel.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1200-1212}, pmid = {36068360}, issn = {1432-184X}, support = {31872587//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Mytilus ; *Brachyura ; Biodiversity ; }, abstract = {Intestinal microbes are essential participants in host vital activities. The composition of the microbiota is closely related to the environmental factors. Predator presence may impact on intestinal microbiota of prey. In the present study, stone crab Charybdis japonica was used as potential predator, an external stress on mussel Mytilus coruscus, to investigate the intestinal microbiota alteration in M. coruscus. We set up two forms of predator presence including free crab and trapped crab, with a blank treatment without crab. The composition of intestinal microbiota in mussels among different treatments showed significant differences by 16S rRNA techniques. The biodiversity increased with trapped crab presence, but decreased with free crab presence. Neisseria, the most abundant genus, fell with the presence of crabs. Besides, the Arcobacter, a kind of pathogenic bacteria, increased with free crab presence. Regarding PICRUTs analysis, Environmental Information Processing, Genetic Information Processing and Metabolism showed differences in crab presence treatments compared with the blank, with a bit higher in the presence of free crab than trapped crab. In conclusion, trapped crab effects activated the metabolism and immunity of the intestinal flora, but free crabs made mussels more susceptible to disease and mortality, corresponding to the decreased biodiversity and the increased Arcobacter in their intestine.}, }
@article {pmid36067300, year = {2022}, author = {Saunders, JK and McIlvin, MR and Dupont, CL and Kaul, D and Moran, DM and Horner, T and Laperriere, SM and Webb, EA and Bosak, T and Santoro, AE and Saito, MA}, title = {Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {37}, pages = {e2200014119}, pmid = {36067300}, issn = {1091-6490}, support = {R01 GM135709/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaea/classification/enzymology ; *Archaeal Proteins/analysis ; Bacteria/classification/enzymology ; *Bacterial Proteins/analysis ; Biodiversity ; *Microbiota ; *Nitrification ; Nitrite Reductases/metabolism ; Pacific Ocean ; Proteomics/methods ; *Seawater/microbiology ; }, abstract = {Enzymes catalyze key reactions within Earth's life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO2, NO, methanethiol, and methylamines were most abundant in the upwelling region. We identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.}, }
@article {pmid36067150, year = {2022}, author = {Wilberts, L and Vuts, J and Caulfield, JC and Thomas, G and Birkett, MA and Herrera-Malaver, B and Verstrepen, KJ and Sobhy, IS and Jacquemyn, H and Lievens, B}, title = {Impact of endophytic colonization by entomopathogenic fungi on the behavior and life history of the tobacco peach aphid Myzus persicae var. nicotianae.}, journal = {PloS one}, volume = {17}, number = {9}, pages = {e0273791}, pmid = {36067150}, issn = {1932-6203}, mesh = {Animals ; *Aphids/physiology ; *Beauveria/physiology ; *Capsicum ; Insecta ; Nicotiana ; }, abstract = {Entomopathogenic fungi can adopt an endophytic lifestyle and provide protection against insect herbivores and plant pathogens. So far, most studies have focused on Beauveria bassiana to increase plant resistance against abiotic and biotic stresses, while only little is known for other entomopathogenic fungi. In this study, we investigated whether root inoculation of sweet pepper (Capsicum annuum L.) by the entomopathogenic fungi Akanthomyces muscarius ARSEF 5128 and B. bassiana ARSEF 3097 can improve resistance against the tobacco peach aphid Myzus persicae var. nicotianae. First, dual-choice experiments were performed to test the hypothesis that the fungi deter aphids via modifying plant volatile profiles. Next, we tested the hypothesis that endophytic colonization negatively affects aphid life history traits, such as fecundity, development and mortality rate. Aphids were significantly attracted to the odor of plants inoculated with A. muscarius over non-inoculated plants. Plants inoculated with A. muscarius emitted significantly higher amounts of β-pinene than non-inoculated plants, and significantly higher amounts of indole than B. bassiana-inoculated and non-inoculated plants. Inoculation with the fungal strains also caused significantly higher emission of terpinolene. Further, both aphid longevity and fecundity were significantly reduced by 18% and 10%, respectively, when feeding on plants inoculated with A. muscarius, although intrinsic rate of population increase did not differ between inoculated and non-inoculated plants. Sweet pepper plants inoculated with B. bassiana ARSEF 3097 did not elicit a significant behavioral response nor affected the investigated life history traits. We conclude that endophytic colonization by entomopathogenic fungi has the potential to alter olfactory behavior and performance of M. persicae var. nicotianae, but effects are small and depend on the fungal strain used.}, }
@article {pmid36065063, year = {2022}, author = {Nottingham, AT and Scott, JJ and Saltonstall, K and Broders, K and Montero-Sanchez, M and Püspök, J and Bååth, E and Meir, P}, title = {Microbial diversity declines in warmed tropical soil and respiration rise exceed predictions as communities adapt.}, journal = {Nature microbiology}, volume = {7}, number = {10}, pages = {1650-1660}, pmid = {36065063}, issn = {2058-5276}, mesh = {Carbon ; Carbon Dioxide/metabolism ; Respiration ; *Soil ; *Soil Microbiology ; }, abstract = {Perturbation of soil microbial communities by rising temperatures could have important consequences for biodiversity and future climate, particularly in tropical forests where high biological diversity coincides with a vast store of soil carbon. We carried out a 2-year in situ soil warming experiment in a tropical forest in Panama and found large changes in the soil microbial community and its growth sensitivity, which did not fully explain observed large increases in CO2 emission. Microbial diversity, especially of bacteria, declined markedly with 3 to 8 °C warming, demonstrating a breakdown in the positive temperature-diversity relationship observed elsewhere. The microbial community composition shifted with warming, with many taxa no longer detected and others enriched, including thermophilic taxa. This community shift resulted in community adaptation of growth to warmer temperatures, which we used to predict changes in soil CO2 emissions. However, the in situ CO2 emissions exceeded our model predictions threefold, potentially driven by abiotic acceleration of enzymatic activity. Our results suggest that warming of tropical forests will have rapid, detrimental consequences both for soil microbial biodiversity and future climate.}, }
@article {pmid36064650, year = {2022}, author = {Morillo-Lopez, V and Sjaarda, A and Islam, I and Borisy, GG and Mark Welch, JL}, title = {Corncob structures in dental plaque reveal microhabitat taxon specificity.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {145}, pmid = {36064650}, issn = {2049-2618}, support = {R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE027958/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Biofilms ; *Dental Plaque ; Humans ; In Situ Hybridization, Fluorescence/methods ; Mouth/microbiology ; Streptococcus ; *Zea mays ; }, abstract = {BACKGROUND: The human mouth is a natural laboratory for studying how bacterial communities differ across habitats. Different bacteria colonize different surfaces in the mouth-teeth, tongue dorsum, and keratinized and non-keratinized epithelia-despite the short physical distance between these habitats and their connection through saliva. We sought to determine whether more tightly defined microhabitats might have more tightly defined sets of resident bacteria. A microhabitat may be characterized, for example, as the space adjacent to a particular species of bacterium. Corncob structures of dental plaque, consisting of coccoid bacteria bound to filaments of Corynebacterium cells, present an opportunity to analyze the community structure of one such well-defined microhabitat within a complex natural biofilm. Here, we investigate by fluorescence in situ hybridization and spectral imaging the composition of the cocci decorating the filaments.<br><br>RESULTS: The range of taxa observed in corncobs was limited to a small subset of the taxa present in dental plaque. Among four major groups of dental plaque streptococci, two were the major constituents of corncobs, including one that was the most abundant Streptococcus species in corncobs despite being relatively rare in dental plaque overall. Images showed both Streptococcus types in corncobs in all individual donors, suggesting that the taxa have different ecological roles or that mechanisms exist for stabilizing the persistence of functionally redundant taxa in the population. Direct taxon-taxon interactions were observed not only between the Streptococcus cells and the central corncob filament but also between Streptococcus cells and the limited subset of other plaque bacteria detected in the corncobs, indicating species ensembles involving these taxa as well.<br><br>CONCLUSIONS: The spatial organization we observed in corncobs suggests that each of the microbial participants can interact with multiple, albeit limited, potential partners, a feature that may encourage the long-term stability of the community. Additionally, our results suggest the general principle that a precisely defined microhabitat will be inhabited by a small and well-defined set of microbial taxa. Thus, our results are important for understanding the structure and organizing principles of natural biofilms and lay the groundwork for future work to modulate and control biofilms for human health. Video Abstract.}, }
@article {pmid36063938, year = {2023}, author = {Navarrete, AA and Aburto, F and González-Rocha, G and Guzmán, CM and Schmidt, R and Scow, K}, title = {Anthropogenic degradation alter surface soil biogeochemical pools and microbial communities in an Andean temperate forest.}, journal = {The Science of the total environment}, volume = {854}, number = {}, pages = {158508}, doi = {10.1016/j.scitotenv.2022.158508}, pmid = {36063938}, issn = {1879-1026}, mesh = {Soil/chemistry ; Forests ; Bacteria ; *Ascomycota ; *Microbiota ; Soil Microbiology ; }, abstract = {Soil microbial communities regulate a myriad of critical biogeochemical functions in forest ecosystems. Anthropogenic disturbances in natural forests could drive major shifts in plant and microbial communities resulting in substantial biogeochemical alterations. We evaluated the effect of anthropogenic disturbances in the soils of Andean temperate forests with different levels of degradation: i) mature forest (MF), ii) secondary forest (SF), iii) degraded forest (DF), and iv) deforested site converted into a prairie (DP). We quantified total soil carbon, nitrogen and phosphorous (TC, TN, and TP), and available nutrient stocks. The soil microbial community structure (i.e., composition, diversity, and abundance) was assessed under each condition from amplicon sequence variants (ASVs) obtained via NGS-Illumina sequencing and subsequent microbiome analysis. There were no significant differences in TC, TN, and TP across the forested states (MF, SF, DF). The deforested site condition presented significantly higher soil TC, TN, and TP and the lowest C:N, C:P, and N:P ratios. The DP soil microbiome was significantly more diverse in bacteria (D' = 0.47 ± 0.04); and fungi (H' = 5.11 ± 0.33). The bacterial microbiome was dominated by Proteobacteria (45.35 ± 0.89 %), Acidobacteria (20.73 ± 1.48 %), Actinobacteria (12.59 ± 0.34 %), and Bacteroidetes (7.32 ± 0.36 %) phyla in all sites. The soil fungal community was dominated by the phyla Ascomycota (42.11 ± 0.95 %), Mortierellomycota (28.74 ± 2.25 %), Basidiomycota (24.61 ± 0.52), and Mucoromycota (2.06 ± 0.43 %). Yet, there were significant differences at the genus level across conditions. Forest to prairie conversion facilitated the introduction of exotic bacterial and fungal taxa associated with agricultural activities and livestock grazing (∼50 % of DP core microbiome composed of unique ASVs). For example, the ammonia-oxidizing bacteria community emerged as a dominant group in the DP soils, along with a reduction in the ectomycorrhizal fungi community. The surface soil microbial community was surprisingly resistant to forest degradation and did not show a clear succession along the degradation gradient, but it was strongly altered after deforestation.}, }
@article {pmid36063436, year = {2022}, author = {Li, Y and Bletsa, M and Zisi, Z and Boonen, I and Gryseels, S and Kafetzopoulou, L and Webster, JP and Catalano, S and Pybus, OG and Van de Perre, F and Li, H and Li, Y and Li, Y and Abramov, A and Lymberakis, P and Lemey, P and Lequime, S}, title = {Endogenous Viral Elements in Shrew Genomes Provide Insights into Pestivirus Ancient History.}, journal = {Molecular biology and evolution}, volume = {39}, number = {10}, pages = {}, pmid = {36063436}, issn = {1537-1719}, mesh = {Animals ; Evolution, Molecular ; Genome, Viral ; Humans ; *Pestivirus/genetics ; Phylogeny ; Shrews/genetics ; *Viruses/genetics ; *Zika Virus/genetics ; *Zika Virus Infection ; }, abstract = {As viral genomic imprints in host genomes, endogenous viral elements (EVEs) shed light on the deep evolutionary history of viruses, ancestral host ranges, and ancient viral-host interactions. In addition, they may provide crucial information for calibrating viral evolutionary timescales. In this study, we conducted a comprehensive in silico screening of a large data set of available mammalian genomes for EVEs deriving from members of the viral family Flaviviridae, an important group of viruses including well-known human pathogens, such as Zika, dengue, or hepatitis C viruses. We identified two novel pestivirus-like EVEs in the reference genome of the Indochinese shrew (Crocidura indochinensis). Homologs of these novel EVEs were subsequently detected in vivo by molecular detection and sequencing in 27 shrew species, including 26 species representing a wide distribution within the Crocidurinae subfamily and one in the Soricinae subfamily on different continents. Based on this wide distribution, we estimate that the integration event occurred before the last common ancestor of the subfamily, about 10.8 million years ago, attesting to an ancient origin of pestiviruses and Flaviviridae in general. Moreover, we provide the first description of Flaviviridae-derived EVEs in mammals even though the family encompasses numerous mammal-infecting members. This also suggests that shrews were past and perhaps also current natural reservoirs of pestiviruses. Taken together, our results expand the current known Pestivirus host range and provide novel insight into the ancient evolutionary history of pestiviruses and the Flaviviridae family in general.}, }
@article {pmid36061686, year = {2022}, author = {Liu, B and Chen, J and Li, Y}, title = {Keystone Microorganisms Regulate the Methanogenic Potential in Coals with Different Coal Ranks.}, journal = {ACS omega}, volume = {7}, number = {34}, pages = {29901-29908}, pmid = {36061686}, issn = {2470-1343}, abstract = {Microorganisms are the core drivers of coal biogeochemistry and are closely related to the formation of coalbed methane. However, it remains poorly understood about the network relationship and stability of microbial communities in coals with different ranks. In this study, a high-throughput sequencing data set was analyzed to understand the microbial co-occurrence network in coals with different ranks including anthracite, medium-volatile bituminous, and high-volatile bituminous. The results showed similar topological properties for the microbial networks among coals with different ranks, but a great difference was found in the microbial composition in different large modules among coals with different ranks, and these three networks had three, four, and four large modules with seven, nine, and nine phyla, respectively. Among these networks, a total of 46 keystone taxa were identified in large modules, and these keystone taxa were different in coals with different ranks. Bacteria dominated the keystone taxa in the microbial network, and these bacterial keystone taxa mainly belonged to phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Besides, the removal of the key microbial data could reduce the community stability of microbial communities in bituminous coals. A partial least-squares path model further showed that these bacterial keystone taxa indirectly affected methanogenic potential by maintaining the microbial community stability and bacterial diversity. In summary, these results showed that keystone taxa played an important role in determining the community diversity, maintaining the microbial community stability, and controlling the methanogenic potential, which is of great significance for understanding the microbial ecology and the geochemical cycle of coal seams.}, }
@article {pmid36061525, year = {2022}, author = {von Hoermann, C and Weithmann, S and Sikorski, J and Nevo, O and Szpila, K and Grzywacz, A and Grunwald, JE and Reckel, F and Overmann, J and Steiger, S and Ayasse, M}, title = {Linking bacteria, volatiles and insects on carrion: the role of temporal and spatial factors regulating inter-kingdom communication via volatiles.}, journal = {Royal Society open science}, volume = {9}, number = {8}, pages = {220555}, pmid = {36061525}, issn = {2054-5703}, abstract = {Multi-kingdom community complexity and the chemically mediated dynamics between bacteria and insects have recently received increased attention in carrion research. However, the strength of these inter-kingdom interactions and the factors that regulate them are poorly studied. We used 75 piglet cadavers across three forest regions to survey the relationship between three actors (epinecrotic bacteria, volatile organic compounds (VOCs) and flies) during the first 4 days of decomposition and the factors that regulate this interdependence. The results showed a dynamic bacterial change during decomposition (temperature-time index) and across the forest management gradient, but not between regions. Similarly, VOC emission was dynamic across a temperature-time index and the forest management gradient but did not differ between regions. However, fly occurrence was dynamic across both space and time. The strong interdependence between the three actors was mainly regulated by the temperature-time index and the study regions, thereby revealing regulation at temporal and spatial scales. Additionally, the actor interdependence was stable across a gradient of forest management intensity. By combining different actors of decomposition, we have expanded our knowledge of the holistic mechanisms regulating carrion community dynamics and inter-kingdom interactions, an important precondition for better describing food web dynamics and entire ecosystem functions.}, }
@article {pmid36061322, year = {2022}, author = {Jones, PA and Frischer, D and Mueller, S and Le, T and Schwanes, A and Govindaraju, A and Shalvarjian, K and Leducq, JB and Marx, CJ and Martinez-Gomez, NC and Lee, JA}, title = {Methylothon: a Versatile Course-Based High School Research Experience in Microbiology and Bioinformatics with Pink Bacteria.}, journal = {Journal of microbiology &amp; biology education}, volume = {23}, number = {2}, pages = {}, pmid = {36061322}, issn = {1935-7877}, support = {T32 GM132022/GM/NIGMS NIH HHS/United States ; }, abstract = {Methylothon is an inquiry-based high school learning module in microbial ecology, molecular biology, and bioinformatics that centers around pink-pigmented plant-associated methylotrophic bacteria. Here, we present an overview of the module's learning goals, describe course resources (available for public use at http://methylothon.com), and relate lessons learned from adapting Methylothon for remote learning during the pandemic in spring of 2021. This curriculum description is intended not only for instructors but also for microbial ecology researchers with an interest in conducting K-12 outreach. The original in-person version of the module allows students to isolate their own strains of methylotrophic bacteria from plants they sample from the environment, to identify these using PCR, sequencing, and phylogenetic analysis, and to contribute their strains to original research in a university lab. The adapted version strengthens the focus on bioinformatics and increases its flexibility and accessibility by making the lab portion optional and adopting free web-based tools. Student feedback and graded assignments from spring 2021 revealed that the lesson was especially effective at introducing the concepts of BLAST and phylogenetic trees and that students valued and felt inspired by the opportunity to conduct hands-on work and to participate in community science.}, }
@article {pmid36059518, year = {2022}, author = {Qing, J and Hu, X and Li, C and Song, W and Tirichen, H and Yaigoub, H and Li, Y}, title = {Fucose as a potential therapeutic molecule against the immune-mediated inflammation in IgA nepharopathy: An unrevealed link.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {929138}, pmid = {36059518}, issn = {1664-3224}, mesh = {Fucose ; *Gene Expression Profiling ; *Glomerulonephritis, IGA/drug therapy/genetics/metabolism ; Humans ; Immunoglobulin A/genetics ; Inflammation/genetics ; }, abstract = {BACKGROUND: IgA nephropathy (IgAN) is an autoimmune disease that affects people of any age and is an important cause of end-stage renal disease. However, the pathogenesis and pathophysiology of IgAN is not clear. This article aimed to explore the immune-mediated inflammation and genetic mechanisms in IgAN.<br><br>METHODS: The transcriptome sequencing data of IgAN glomeruli in the Gene Expression Omnibus database were downloaded.&#xa0;Single-sample gene set enrichment analysis was used to estimate the immune microenvironment of the merged microarray data and GSE141295. IgAN samples were divided into two clusters by cluster analysis. "limma" and "DEseq2" package in R were used to identify differentially expressed genes (DEGs). The weighted gene co-expression network analysis (WGCNA) was used to identify the co-expression modules related to inflammation in IgAN. R software package "clusterProfiler" was used for enrichment analysis, whereas Short Time-Series Expression Miner (STEM) analysis was used to identify the trend of gene expression. Machine-learn (ML) was performed using the shiny app. Finally, Drug Signatures Database (DSigDB) was used to identify potential molecules for treating IgAN.<br><br>RESULTS: The infiltration of macrophages in IgAN glomeruli was increased, whereas CD4+ T cells, especially inducedregulatory T cells (iTregs) were decreased. A total of 1,104 common DEGs were identified from the merged data and GSE141295. Brown module was identified to have the highest inflammatory correlation with IgAN using WGCNA, and 15 hub genes were screened from this module. Among these 15 hub genes, 14 increased with the severity of IgAN inflammation based on STEM analysis. Neural network (nnet) is considered as the best model to predict the severity of IgAN. Fucose identified from DSigDB has a potential biological activity to treat IgAN.<br><br>CONCLUSION: The increase of macrophages and the decrease of iTregs in glomeruli represent the immune-mediated inflammation of IgAN, and fucose may be a potential therapeutic molecule against IgAN because it affects genes involved in the severe inflammation of IgAN.}, }
@article {pmid36056428, year = {2022}, author = {Ma, X and Wang, T and Shi, Z and Chiariello, NR and Docherty, K and Field, CB and Gutknecht, J and Gao, Q and Gu, Y and Guo, X and Hungate, BA and Lei, J and Niboyet, A and Le Roux, X and Yuan, M and Yuan, T and Zhou, J and Yang, Y}, title = {Correction: Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {144}, pmid = {36056428}, issn = {2049-2618}, }
@article {pmid36056039, year = {2022}, author = {Arandia-Gorostidi, N and Berthelot, H and Calabrese, F and Stryhanyuk, H and Klawonn, I and Iversen, M and Nahar, N and Grossart, HP and Ploug, H and Musat, N}, title = {Efficient carbon and nitrogen transfer from marine diatom aggregates to colonizing bacterial groups.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {14949}, pmid = {36056039}, issn = {2045-2322}, mesh = {Bacteria/metabolism ; Biomass ; Carbon/metabolism ; *Diatoms/metabolism ; Nitrogen/metabolism ; }, abstract = {Bacterial degradation of sinking diatom aggregates is key for the availability of organic matter in the deep-ocean. Yet, little is known about the impact of aggregate colonization by different bacterial taxa on organic carbon and nutrient cycling within aggregates. Here, we tracked the carbon (C) and nitrogen (N) transfer from the diatom Leptocylindrus danicus to different environmental bacterial groups using a combination of [13]C and [15]N isotope incubation (incubated for 72 h), CARD-FISH and nanoSIMS single-cell analysis. Pseudoalteromonas bacterial group was the first colonizing diatom-aggregates, succeeded by the Alteromonas group. Within aggregates, diatom-attached bacteria were considerably more enriched in [13]C and [15]N than non-attached bacteria. Isotopic mass balance budget indicates that both groups showed comparable levels of diatom C in their biomass, accounting for 19 ± 7% and 15 ± 11%, respectively. In contrast to C, bacteria of the Alteromonas groups showed significantly higher levels of N derived from diatoms (77 ± 28%) than Pseudoalteromonas (47 ± 17%), suggesting a competitive advantage for Alteromonas in the N-limiting environments of the deep-sea. Our results imply that bacterial succession within diatom aggregates may largely impact taxa-specific C and N uptake, which may have important consequences for the quantity and quality of organic matter exported to the deep ocean.}, }
@article {pmid36054689, year = {2022}, author = {Calvo-Martin, E and Teira, E and Álvarez-Salgado, XA and Rocha, C and Jiang, S and Justel-Díez, M and Ibánhez, JSP}, title = {On the hidden diversity and niche specialization of the microbial realm of subterranean estuaries.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {5859-5881}, pmid = {36054689}, issn = {1462-2920}, mesh = {*Estuaries ; RNA, Ribosomal, 16S/genetics ; Archaea/genetics ; *Groundwater ; Oxygen ; }, abstract = {Subterranean estuaries (STEs) modulate the chemical composition of continental groundwater before it reaches the coast, but their microbial community is poorly known. Here, we explored the microbial ecology of two neighbouring, yet contrasting STEs (Panxón and Ladeira STEs; Ría de Vigo, NW Iberian Peninsula). We investigated microbial composition (16S rRNA gene sequencing), abundance, heterotrophic production and their geochemical drivers. A total of 10,150 OTUs and 59 phyla were retrieved from porewater sampled during four surveys covering each STE seepage face. In both STEs, we find a very diverse microbial community composed by abundant cosmopolitans and locally restricted rare taxa. Porewater oxygen and dissolved organic matter are the main environmental predictors of microbial community composition. More importantly, the high variety of benthic microbiota links to biogeochemical processes of different elements in STEs. The oxygen-rich Panxón beach showed strong associations of the ammonium oxidizing archaea Nitrosopumilales with the heterotrophic community, thus acting as a net source of nitrogen to the coast. On the other hand, the prevailing anoxic conditions of Ladeira beach promoted the dominance of anaerobic heterotrophs related to the degradation of complex and aromatic compounds, such as Dehalococcoidia and Desulfatiglans, and the co-occurrence of methane oxidizers and methanogens.}, }
@article {pmid36054683, year = {2023}, author = {Fan, L and Chen, J and Pan, L and Xin, X and Geng, B and Yang, L and Wang, Q and Ma, W and Lou, Y and Bian, J and Cui, X and Li, J and Wang, L and Chen, Z and Wang, W and Cui, C and Li, S and Gao, Q and Song, Q and Deng, Y and Fan, J and Yu, J and Zhang, H and Li, Y and Cai, J}, title = {Alterations of Gut Microbiome, Metabolome, and Lipidome in Takayasu Arteritis.}, journal = {Arthritis &amp; rheumatology (Hoboken, N.J.)}, volume = {75}, number = {2}, pages = {266-278}, doi = {10.1002/art.42331}, pmid = {36054683}, issn = {2326-5205}, mesh = {Humans ; *Takayasu Arteritis/drug therapy ; *Gastrointestinal Microbiome/genetics ; Lipidomics ; Inflammation ; Metabolome ; *Behcet Syndrome ; *Cardiovascular Diseases ; }, abstract = {OBJECTIVE: Mounting evidence has linked microbiome and metabolome to systemic autoimmunity and cardiovascular diseases (CVDs). Takayasu arteritis (TAK) is a rare disease that shares features of immune-related inflammatory diseases and CVDs, about which there is relatively limited information. This study was undertaken to characterize gut microbial dysbiosis and its crosstalk with phenotypes in TAK.<br><br>METHODS: To address the discriminatory signatures, we performed shotgun sequencing of fecal metagenome across a discovery cohort (n&#xa0;=&#xa0;97) and an independent validation cohort (n&#xa0;=&#xa0;75) including TAK patients, healthy controls, and controls with Beh&#xe7;et's disease (BD). Interrogation of untargeted metabolomics and lipidomics profiling of plasma and fecal samples were also used to refine features mediating associations between microorganisms and TAK phenotypes.<br><br>RESULTS: A combined model of bacterial species, including unclassified Escherichia, Veillonella parvula, Streptococcus parasanguinis, Dorea formicigenerans, Bifidobacterium adolescentis, Lachnospiraceae bacterium 7 1 58FAA, Escherichia coli, Streptococcus salivarius, Klebsiella pneumoniae, Bifidobacterium longum, and Lachnospiraceae Bacterium 5 1 63FAA, distinguished TAK patients from controls with areas under the curve (AUCs) of 87.8%, 85.9%, 81.1%, and 71.1% in training, test, and validation sets including healthy or BD controls, respectively. Diagnostic species were directly or indirectly (via metabolites or lipids) correlated with TAK phenotypes of vascular involvement, inflammation, discharge medication, and prognosis. External validation against publicly metagenomic studies (n&#xa0;=&#xa0;184) on hypertension, atrial fibrillation, and healthy controls, confirmed the diagnostic accuracy of the model for TAK.<br><br>CONCLUSION: This study first identifies the discriminatory gut microbes in TAK. Dysbiotic microbes are also linked to TAK phenotypes directly or indirectly via metabolic and lipid modules. Further explorations of the microbiome-metagenome interface in TAK subtype prediction and pathogenesis are suggested.}, }
@article {pmid36053304, year = {2023}, author = {Trumhová, K and Klimešová, V and Pichrtová, M}, title = {Seasonal Dynamics of Zygnema (Zygnematophyceae) Mats from the Austrian Alps.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {763-776}, pmid = {36053304}, issn = {1432-184X}, support = {980518//Univerzita Karlova v Praze/ ; 204069//Univerzita Karlova v Praze/ ; }, mesh = {Seasons ; *Ecosystem ; Phylogeny ; Austria ; *Streptophyta ; Water ; }, abstract = {Filamentous green algae of the genus Zygnema are an essential part of hydro-terrestrial ecosystems. Despite several studies on their resistance to natural stresses, little is known about the composition of their assemblages and the changes they undergo over time. Two sites at altitudes above 2200 m a.s.l. in the Austrian Alps were selected for a 2-year observation period and sampled five times. Molecular phylogenetic analysis of the 152 isolated strains of Zygnema sp. was performed based on the rbcL and trnG sequences. Seven genotypes were found at these sites during the samplings, but their proportion varied throughout the seasons. The site with a more stable water regime also had a more stable representation of genotypes, in contrast to the site with fluctuating water availability. The mats formed resistant pre-akinetes at the end of the season with reduced photosynthetic activity. Contrary to expectations, the mats were not exposed to extremely cold temperatures in winter due to snow cover. Some genotypes have been previously observed at this site, indicating that the population composition is stable. This work highlights the importance of resistant pre-akinetes in surviving winter conditions, the ability of algae to re-establish mats, and the need to address the hidden diversity of the genus Zygnema.}, }
@article {pmid36050462, year = {2022}, author = {Fang, Y and Qin, X and Liao, Q and Du, R and Luo, X and Zhou, Q and Li, Z and Chen, H and Jin, W and Yuan, Y and Sun, P and Zhang, R and Zhang, J and Wang, L and Cheng, S and Yang, X and Yan, Y and Zhang, X and Zhang, Z and Bai, S and Van de Peer, Y and Lucas, WJ and Huang, S and Yan, J}, title = {The genome of homosporous maidenhair fern sheds light on the euphyllophyte evolution and defences.}, journal = {Nature plants}, volume = {8}, number = {9}, pages = {1024-1037}, pmid = {36050462}, issn = {2055-0278}, support = {833522//European Research Council/International ; }, mesh = {*Adiantum/genetics ; *Ferns/genetics ; Genome, Plant ; Phylogeny ; }, abstract = {Euphyllophytes encompass almost all extant plants, including two sister clades, ferns and seed plants. Decoding genomes of ferns is the key to deep insight into the origin of euphyllophytes and the evolution of seed plants. Here we report a chromosome-level genome assembly of Adiantum capillus-veneris L., a model homosporous fern. This fern genome comprises 30 pseudochromosomes with a size of 4.8-gigabase and a contig N50 length of 16.22 Mb. Gene co-expression network analysis uncovered that homospore development in ferns has relatively high genetic similarities with that of the pollen in seed plants. Analysing fern defence response expands understanding of evolution and diversity in endogenous bioactive jasmonates in plants. Moreover, comparing fern genomes with those of other land plants reveals changes in gene families important for the evolutionary novelties within the euphyllophyte clade. These results lay a foundation for studies on fern genome evolution and function, as well as the origin and evolution of euphyllophytes.}, }
@article {pmid36049255, year = {2022}, author = {Whitman, WB and Chuvochina, M and Hedlund, BP and Hugenholtz, P and Konstantinidis, KT and Murray, AE and Palmer, M and Parks, DH and Probst, AJ and Reysenbach, AL and Rodriguez-R, LM and Rossello-Mora, R and Sutcliffe, I and Venter, SN}, title = {Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type.}, journal = {Systematic and applied microbiology}, volume = {45}, number = {5}, pages = {126305}, pmid = {36049255}, issn = {1618-0984}, support = {P20 GM103440/GM/NIGMS NIH HHS/United States ; }, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Base Sequence ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.}, }
@article {pmid36048618, year = {2022}, author = {Li, G and Wu, C and Wang, D and Srinivasan, V and Kaeli, DR and Dy, JG and Gu, AZ}, title = {Machine Learning-Based Determination of Sampling Depth for Complex Environmental Systems: Case Study with Single-Cell Raman Spectroscopy Data in EBPR Systems.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {18}, pages = {13473-13484}, doi = {10.1021/acs.est.1c08768}, pmid = {36048618}, issn = {1520-5851}, mesh = {*Biological Products ; Humans ; Machine Learning ; *Phosphorus/chemistry ; Polyphosphates ; Sewage ; Spectrum Analysis, Raman ; }, abstract = {Rapid progress in various advanced analytical methods, such as single-cell technologies, enable unprecedented and deeper understanding of microbial ecology beyond the resolution of conventional approaches. A major application challenge exists in the determination of sufficient sample size without sufficient prior knowledge of the community complexity and, the need to balance between statistical power and limited time or resources. This hinders the desired standardization and wider application of these technologies. Here, we proposed, tested and validated a computational sampling size assessment protocol taking advantage of a metric, named kernel divergence. This metric has two advantages: First, it directly compares data set-wise distributional differences with no requirements on human intervention or prior knowledge-based preclassification. Second, minimal assumptions in distribution and sample space are made in data processing to enhance its application domain. This enables test-verified appropriate handling of data sets with both linear and nonlinear relationships. The model was then validated in a case study with Single-cell Raman Spectroscopy (SCRS) phenotyping data sets from eight different enhanced biological phosphorus removal (EBPR) activated sludge communities located across North America. The model allows the determination of sufficient sampling size for any targeted or customized information capture capacity or resolution level. Promised by its flexibility and minimal restriction of input data types, the proposed method is expected to be a standardized approach for sampling size optimization, enabling more comparable and reproducible experiments and analysis on complex environmental samples. Finally, these advantages enable the extension of the capability to other single-cell technologies or environmental applications with data sets exhibiting continuous features.}, }
@article {pmid36048179, year = {2023}, author = {Cook, K and Taylor, AD and Sharma, J and Taylor, DL}, title = {Inter-annual Persistence of Canopy Fungi Driven by Abundance Despite High Spatial Turnover.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {261-270}, pmid = {36048179}, issn = {1432-184X}, support = {DEB-1355155//National Science Foundation/ ; }, mesh = {*Ecosystem ; Fungi ; Trees/microbiology ; Rainforest ; *Mycobiome ; Soil Microbiology ; Biodiversity ; }, abstract = {While it is now well established that fungal community composition varies spatially at a variety of scales, temporal turnover of fungi is less well understood. Here we studied inter-annual community compositional changes of fungi in a rainforest tree canopy environment. We tracked fungal community shifts over 3 years in three substrate types (live bryophytes, dead bryophytes, and host tree bark) and compared these changes to amounts of community turnover seen at small spatial scales in the same system. The effect of substrate type on fungal community composition was stronger than that of sampling year, which was very small but significant. Although levels of temporal turnover varied among substrates, with greater turnover in live bryophytes than other substrates, the amount of turnover from year to year was comparable to what is seen at spatial distances between 5 and 9 cm for the same substrate. Stability of communities was largely driven by a few fungi with high relative abundances. A majority of fungal occurrences were at low relative abundances (≤ 0.1%). These fungi tended to be short lived and persisted to following years ≤ 50% of the time, depending on substrate. Their presence and persistence are likely impacted by stochastic processes like dispersal limitation and disturbance. Most samples contained only one or a few fungi at high relative abundance (≥ 10%) that persisted half or more of the time. These more abundant and persistent fungi are expected to have sustained functional interactions within the canopy ecosystem.}, }
@article {pmid36047700, year = {2022}, author = {Versluis, DM and Schoemaker, R and Looijesteijn, E and Muysken, D and Jeurink, PV and Paques, M and Geurts, JMW and Merks, RMH}, title = {A Multiscale Spatiotemporal Model Including a Switch from Aerobic to Anaerobic Metabolism Reproduces Succession in the Early Infant Gut Microbiota.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0044622}, pmid = {36047700}, issn = {2379-5077}, mesh = {Infant ; Humans ; Infant, Newborn ; *Gastrointestinal Microbiome ; Anaerobiosis ; Lactose/metabolism ; Bifidobacterium ; *Microbiota ; Bacteria ; Enterobacteriaceae ; }, abstract = {The human intestinal microbiota starts to form immediately after birth and is important for the health of the host. During the first days, facultatively anaerobic bacterial species generally dominate, such as Enterobacteriaceae. These are succeeded by strictly anaerobic species, particularly Bifidobacterium species. An early transition to Bifidobacterium species is associated with health benefits; for example, Bifidobacterium species repress growth of pathogenic competitors and modulate the immune response. Succession to Bifidobacterium is thought to be due to consumption of intracolonic oxygen present in newborns by facultative anaerobes, including Enterobacteriaceae. To study if oxygen depletion suffices for the transition to Bifidobacterium species, here we introduced a multiscale mathematical model that considers metabolism, spatial bacterial population dynamics, and cross-feeding. Using publicly available metabolic network data from the AGORA collection, the model simulates ab initio the competition of strictly and facultatively anaerobic species in a gut-like environment under the influence of lactose and oxygen. The model predicts that individual differences in intracolonic oxygen in newborn infants can explain the observed individual variation in succession to anaerobic species, in particular Bifidobacterium species. Bifidobacterium species became dominant in the model by their use of the bifid shunt, which allows Bifidobacterium to switch to suboptimal yield metabolism with fast growth at high lactose concentrations, as predicted here using flux balance analysis. The computational model thus allows us to test the internal plausibility of hypotheses for bacterial colonization and succession in the infant colon. IMPORTANCE The composition of the infant microbiota has a great impact on infant health, but its controlling factors are still incompletely understood. The frequently dominant anaerobic Bifidobacterium species benefit health, e.g., they can keep harmful competitors under control and modulate the intestinal immune response. Controlling factors could include nutritional composition and intestinal mucus composition, as well as environmental factors, such as antibiotics. We introduce a modeling framework of a metabolically realistic intestinal microbial ecology in which hypothetical scenarios can be tested and compared. We present simulations that suggest that greater levels of intraintestinal oxygenation more strongly delay the dominance of Bifidobacterium species, explaining the observed variety of microbial composition and demonstrating the use of the model for hypothesis generation. The framework allowed us to test a variety of controlling factors, including intestinal mixing and transit time. Future versions will also include detailed modeling of oligosaccharide and mucin metabolism.}, }
@article {pmid36044056, year = {2023}, author = {Li, W and Xie, L and Zhao, C and Hu, X and Yin, C}, title = {Nitrogen Fertilization Increases Soil Microbial Biomass and Alters Microbial Composition Especially Under Low Soil Water Availability.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {536-548}, pmid = {36044056}, issn = {1432-184X}, mesh = {*Soil/chemistry ; Biomass ; *Carbon/chemistry ; Nitrogen/analysis ; Water ; Soil Microbiology ; Fertilization ; }, abstract = {Soil microbial biomass and composition are affected by resource supply and water availability. However, the response of soil microbial communities to nitrogen fertilization under different water availability conditions is unclear. Therefore, this study conducted a 6-year pot experiment comprising five watering regimes (40%, 50%, 60%, 80%, and 100% of field capacity (FC)) and three nitrogen fertilization levels (NH4NO3 solution; 0 [N0], 20 [N1], and 40 [N2] g N m[-2] year[-1]) to investigate soil microbial biomass, composition, and properties. The results indicated that soil microbial biomass and composition were more strongly affected by nitrogen fertilization compared with water regime. Nitrogen fertilization increased soil microbial biomass and altered soil microbial community composition, especially under low soil water availability. Soil microbial biomass was positively linearly associated with soil water regimes under N0, whereas it responded polynomially to soil water regimes under N1 and N2. The maximal soil microbial biomass was observed at FC80 for N1 and FC60 for N2. Furthermore, the biomass of soil microbial groups with high nitrogen and carbon acquisition ability as well as the enzyme activities of carbon and nitrogen cycling (β-1,4-glucosidase and β-1,4-N-acetyl-glucosaminidase, respectively) were stimulated by nitrogen fertilization. Soil microbial biomass was affected directly by nitrogen fertilization and indirectly by nitrogen and water regimes, via altering soil pH, dissolved inorganic nitrogen (NH4[+]-N and NO3[-]-N) concentration, and soil organic carbon concentration. This study provides new insights into the effect of interaction between soil nitrogen and water availabilities on soil microbial biomass, composition, and its underlying mechanism.}, }
@article {pmid36041615, year = {2022}, author = {Leistenschneider, C and Le Bohec, C and Eisen, O and Houstin, A and Neff, S and Primpke, S and Zitterbart, DP and Burkhardt-Holm, P and Gerdts, G}, title = {No evidence of microplastic ingestion in emperor penguin chicks (Aptenodytes forsteri) from the Atka Bay colony (Dronning Maud Land, Antarctica).}, journal = {The Science of the total environment}, volume = {851}, number = {Pt 2}, pages = {158314}, doi = {10.1016/j.scitotenv.2022.158314}, pmid = {36041615}, issn = {1879-1026}, mesh = {Animals ; Humans ; *Spheniscidae ; Microplastics ; Antarctic Regions ; Plastics ; Ecosystem ; Bays ; Eating ; }, abstract = {Microplastic (<5 mm; MP) pollution has been an emerging threat for marine ecosystems around the globe with increasing evidence that even the world's most remote areas, including Antarctica, are no longer unaffected. Few studies however, have examined MP in Antarctic biota, and especially those from Antarctic regions with low human activity, meaning little is known about the extent to which biota are affected. The aim of this study was to investigate, for the first time, the occurrence of MP in the emperor penguin (Aptenodytes forsteri), the only penguin species breeding around Antarctica during the austral winter, and an endemic apex predator in the Southern Ocean. To assess MP ingestion, the gizzards of 41 emperor penguin chicks from Atka Bay colony (Dronning Maud Land, Antarctica), were dissected and analyzed for MP >500 μm using Attenuated Total Reflection Fourier-transform Infrared (ATR-FTIR) spectroscopy. A total of 85 putative particles, mostly in the shape of fibers (65.9 %), were sorted. However, none of the particles were identified as MP applying state-of-the-art methodology. Sorted fibers were further evidenced to originate from contamination during sample processing and analyses. We find that MP concentrations in the local food web of the Weddell Sea and Dronning Maud Land coastal and marginal sea-ice regions; the feeding grounds to chick-rearing emperor penguin adults, are currently at such low levels that no detectable biomagnification is occurring via trophic transfer. Being in contrast to MP studies on other Antarctic and sub-Antarctic penguin species, our comparative discussion including these studies, highlights the importance for standardized procedures for sampling, sample processing and analyses to obtain comparable results. We further discuss other stomach contents and their potential role for MP detection, as well as providing a baseline for the long-term monitoring of MP in apex predator species from this region.}, }
@article {pmid36040152, year = {2022}, author = {He, J and Shen, X and Zhang, N and Sun, C and Shao, Y}, title = {Smartphones as an Ecological Niche of Microorganisms: Microbial Activities, Assembly, and Opportunistic Pathogens.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0150822}, pmid = {36040152}, issn = {2165-0497}, mesh = {Humans ; RNA, Ribosomal, 16S ; Smartphone ; Phylogeny ; Pandemics ; *COVID-19 ; *Microbiota ; Bacteria/genetics ; Adenosine Triphosphate ; }, abstract = {Smartphone usage and contact frequency are unprecedentedly high in this era, and they affect humans mentally and physically. However, the characteristics of the microorganisms associated with smartphones and smartphone hygiene habits remain unclear. In this study, using various culture-independent techniques, including high-throughput sequencing, real-time quantitative PCR (RT-qPCR), the ATP bioluminescence system, and electron microscopy, we investigated the structure, assembly, quantity, and dynamic metabolic activity of the bacterial community on smartphone surfaces and the user's dominant and nondominant hands. We found that smartphone microbiotas are more similar to the nondominant hand microbiotas than the dominant hand microbiotas and show significantly decreased phylogenetic diversity and stronger deterministic processes than the hand microbiota. Significant interindividual microbiota differences were observed, contributing to an average owner identification accuracy of 70.6% using smartphone microbiota. Furthermore, it is estimated that approximately 1.75 × 10[6] bacteria (2.24 × 10[4]/cm[2]) exist on the touchscreen of a single smartphone, and microbial activities remain stable for at least 48 h. Scanning electron microscopy detected large fragments harboring microorganisms, suggesting that smartphone microbiotas live on the secreta or other substances, e.g., human cell debris and food debris. Fortunately, simple smartphone cleaning/hygiene could significantly reduce the bacterial load. Taken together, our results demonstrate that smartphone surfaces not only are a reservoir of microbes but also provide an ecological niche in which microbiotas, particularly opportunistic pathogens, can survive, be active, and even grow. IMPORTANCE Currently, people spend an average of 4.2 h per day on their smartphones. Due to the COVID-19 pandemic, this figure may still be increasing. The high frequency of smartphone usage may allow microbes, particularly pathogens, to attach to-and even survive on-phone surfaces, potentially causing adverse effects on humans. We employed various culture-independent techniques in this study to evaluate the microbiological features and hygiene of smartphones, including community assembly, bacterial load, and activity. Our data showed that deterministic processes drive smartphone microbiota assembly and that approximately 1.75 × 10[6] bacteria exist on a single smartphone touchscreen, with activities being stable for at least 48 h. Fortunately, simple smartphone cleaning/hygiene could significantly reduce the bacterial load. This work expands our understanding of the microbial ecology of smartphone surfaces and might facilitate the development of electronic device cleaning/hygiene guidelines to support public health.}, }
@article {pmid36037277, year = {2022}, author = {Carregosa, D and Pinto, C and Ávila-Gálvez, M&#xc1; and Bastos, P and Berry, D and Santos, CN}, title = {A look beyond dietary (poly)phenols: The low molecular weight phenolic metabolites and their concentrations in human circulation.}, journal = {Comprehensive reviews in food science and food safety}, volume = {21}, number = {5}, pages = {3931-3962}, doi = {10.1111/1541-4337.13006}, pmid = {36037277}, issn = {1541-4337}, mesh = {*Diet ; Flavonoids/metabolism ; Fruit ; Humans ; Molecular Weight ; *Phenols ; }, abstract = {A large number of epidemiological studies have shown that consumption of fruits, vegetables, and beverages rich in (poly)phenols promote numerous health benefits from cardiovascular to neurological diseases. Evidence on (poly)phenols has been applied mainly to flavonoids, yet the role of phenolic acids has been largely overlooked. Such phenolics present in food combine with those resulting from gut microbiota catabolism of flavonoids and chlorogenic acids and those produced by endogenous pathways, resulting in large concentrations of low molecular weight phenolic metabolites in human circulation. Independently of the origin, in human intervention studies using diets rich in (poly)phenols, a total of 137 low molecular weight phenolic metabolites have been detected and quantified in human circulation with largely unknown biological function. In this review, we will pinpoint two main aspects of the low molecular weight phenolic metabolites: (i) the microbiota responsible for their generation, and (ii) the analysis (quali- and quantitative) in human circulation and their respective pharmacokinetics. In doing so, we aim to drive scientific advances regarding the ubiquitous roles of low molecular weight phenolic metabolites using physiologically relevant concentrations and under (patho)physiologically relevant conditions in humans.}, }
@article {pmid36034889, year = {2022}, author = {He, KJ and Dong, JH and Ouyang, XM and Huo, YN and Cheng, XS and Lin, Y and Li, Y and Gong, G and Liu, J and Ren, JL and Guleng, B}, title = {Glycerol monolaurate ameliorates DSS-induced acute colitis by inhibiting infiltration of Th17, neutrophils, macrophages and altering the gut microbiota.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {911315}, pmid = {36034889}, issn = {2296-861X}, abstract = {BACKGROUND AND AIMS: Inflammatory bowel disease (IBD) places a heavy medical burden on countries and families due to repeated and prolonged attacks, and the incidence and prevalence of IBD are increasing worldwide. Therefore, finding an effective treatment is a matter of great urgency. Glycerol monolaurate (GML), which has a twelve-carbon chain, is a compound naturally found in human breast milk. Some studies have shown that GML has antibacterial and anti-inflammatory effects. However, the specific mechanism of action remains unclear.<br><br>METHODS: Acute colitis was established in mice using 3% DSS, and glycerol monolaurate (500 mg&#xb7;kg-[1]) was administered for two weeks. QPCR and western blotting were performed to examine the inflammatory status. Mice described were subjected to flow cytometry analysis for immune cell activation.<br><br>RESULTS: GML treated alleviated macroscopic symptoms such as shortened colons, increased spleen weight, and caused weight loss in mice with DSS-induced colitis. In addition, GML decreased the expression of pro-inflammatory factors (NF-&#x3b1;, IL-1&#x3b2; and IL-1&#x3b1;) and increased the expression of anti-inflammatory factors (IL-10 and TGF-&#x3b2;). GML inhibited the activation of the MAPK and NF-&#x3ba;B signalling pathways, improved tissue damage, and increased the expression of intestinal tight junction proteins. In addition, LPMCs extracted from intestinal tissue via flow cytometry showed that GML treatment led to a decrease of Th17 cells, Neutrophils and Macrophages. 16S rDNA sequencing showed that GML increased the abundance of commensal bacterium such as Akkermansia and Lactobacillus murinus.<br><br>CONCLUSIONS: We showed that oral administration of GML ameliorated DSS-induced colitis by inhibiting infiltration of Th17 cells, Neutrophils, and Macrophages, protecting the intestinal mucosal barrier and altered the abundance of commensal bacterium. This study provides new insights into the biological function and therapeutic potential of GML in the treatment of IBD.}, }
@article {pmid36030743, year = {2022}, author = {Chen, W and Wei, J and Su, Z and Wu, L and Liu, M and Huang, X and Yao, P and Wen, D}, title = {Deterministic mechanisms drive bacterial communities assembly in industrial wastewater treatment system.}, journal = {Environment international}, volume = {168}, number = {}, pages = {107486}, doi = {10.1016/j.envint.2022.107486}, pmid = {36030743}, issn = {1873-6750}, mesh = {Wastewater ; Sewage/chemistry ; Bacteria ; *Microbiota ; *Water Purification ; }, abstract = {Microbial communities are responsible for biological treatment of many industrial wastewater, but our knowledge of their diversity, assembly patterns, and function is still poor. Here, we analyzed the bacterial communities of wastewater and activated sludge samples taken from 11 full-scale industrial wastewater treatment plants (IWWTPs) characterized by the same process design but different wastewater types and WWTP compartments. We found significantly different diversity and compositions of bacterial assemblages among distinct wastewater types and IWWTPs compartments. IWWTPs bacterial communities exhibited a clear species abundance distribution. The dispersal-driven process was weak in shaping IWWTP communities. Meanwhile, environmental and operating conditions were important factors in regulating the structure of the activated sludge community and pollutants removal, indicating that bacterial community was largely driven by deterministic mechanisms. The core microbial community in IWWTPs was different from that in municipal wastewater treatment plants (MWWTPs), and many taxa (e.g. the genus Citreitalea) rarely were detected before, indicating IWWTPs harbored unique core bacterial communities. Furthermore, we found that bacterial community compositions were strongly linked to activated sludge function. These findings are important to both microbial ecologists and environmental engineers, who may optimize the operation strategies jointly for maintaining biodiversity, which in turn may promote a more stable performance of the IWWTP. Overall, our study enhances the mechanistic understanding of the IWWTP microbial community diversity, assembly patterns, and function, and provides important implications for microbial ecology and wastewater treatment processes.}, }
@article {pmid36030426, year = {2022}, author = {Barman, D and Dkhar, MS}, title = {Characterization and purification of esterase from Cellulomonas fimi DB19 isolated from Zanthoxylum armatum with its possible role in diesel biodegradation.}, journal = {Archives of microbiology}, volume = {204}, number = {9}, pages = {580}, pmid = {36030426}, issn = {1432-072X}, mesh = {Azo Compounds ; Cellulomonas ; Enzyme Stability ; *Esterases ; Hydrogen Peroxide ; Hydrogen-Ion Concentration ; Temperature ; *Zanthoxylum ; }, abstract = {Endophytic bacteria inhabit all or part of their life cycle within the tissues of healthy plants, without causing any apparent symptoms of disease. They are treasure trove of several hydrolytic enzymes with distinct characteristics. Esterase is one of such enzymes and this study aims to characterize esterase produced by endophytic actinobacteria Cellulomonas fimi DB19 isolated from Zanthoxylum armatum with its capacity to degrade diesel oil. The enzyme was purified with purification fold 8.22 and specific activity 124.72 U/mg with 16.43% recovery. The purified enzyme showed a single protein band on SDS-PAGE having molecular mass of approximately 39 kDa. The Km and Vmax value for p-nitrophenyl acetate were 2.23 mM and 22.04 U/mL, respectively. The enzyme was stable in the pH range 6-9 with its optimal activity at pH 8.0. The enzyme was stable at 40 °C and retained more than 80% activity after incubation for two h. The enzyme activity was positively influenced in the presence of Na[+], Ba[2+], Ca[2+], and negatively by Mn[2+], and Mg[2+]. The EDTA and PMSF inhibited the enzyme activity and retained its activity in the presence of SDS, H2O2, β-mercaptoethanol, and organic solvents. Application of the isolate in degradation of diesel showed that its growth and degradation capacity enhanced in media supplemented with 0.2-4% of diesel oil with maximum at 3% of diesel oil. Furthermore, esterase activity was greater in media containing diesel than control which is suggesting the plausible role of esterase produced by Cellulomonas fimi DB19 in the degradation of diesel oil.}, }
@article {pmid36029817, year = {2022}, author = {Wang, P and Cao, J and Mao, L and Zhu, L and Zhang, Y and Zhang, L and Jiang, H and Zheng, Y and Liu, X}, title = {Effect of H3PO4-modified biochar on the fate of atrazine and remediation of bacterial community in atrazine-contaminated soil.}, journal = {The Science of the total environment}, volume = {851}, number = {Pt 2}, pages = {158278}, doi = {10.1016/j.scitotenv.2022.158278}, pmid = {36029817}, issn = {1879-1026}, mesh = {*Atrazine/analysis ; *Soil Pollutants/analysis ; Adsorption ; Charcoal/chemistry ; Soil/chemistry ; Bacteria ; *Pesticides ; Phosphorus ; *Environmental Restoration and Remediation ; }, abstract = {The application of chemically modified biochar is a promising strategy for the remediation of contaminated (e.g., pesticides) soil. In this study, H3PO4 was used to modify peanut shell to improve the remediation performance of biochar. Surface area (980.19 m[2]/g), pore volume (0.12 cm[3]/g), and the functional groups (OH, CO, and phosphorus-containing groups) on the biochar were increased by H3PO4 treatment. The sorption experimental data were well fitted by Freundlich model, while the sorption affinity (Kf) of H3PO4 modified biochar (PBC) for atrazine was 128 times greater than that of the untreated biochar (BC) in the aquatic systems. The Kf values of PBC-amended soil to atrazine were increased by 13.57 times than that of single soil. The strong sorption of PBC on atrazine delayed the degradation of atrazine in soil, and the residual percentage of atrazine in soil and soil-PBC mixture were 4.90% and 71.44% at the end of 60-day incubation, with the degradation half-life increased from 13.3 to 121.6 d. The analysis of high-throughput sequencing results showed that atrazine reduced the diversity of soil microbial community, but the abundance of microorganisms with degradation function increased and became dominant species. The addition of PBC in soil accelerated the microbial remediation of atrazine stress, which may promote the soil nitrogen cycle. Therefore, amendment of atrazine contaminated soil with PBC can reduce the environmental risk of atrazine and benefit the soil microbial ecology.}, }
@article {pmid36028909, year = {2022}, author = {Somerville, V and Schowing, T and Chabas, H and Schmidt, RS and von Ah, U and Bruggmann, R and Engel, P}, title = {Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {137}, pmid = {36028909}, issn = {2049-2618}, mesh = {Bacteria ; *Bacteriophages ; *Cheese ; Genome, Bacterial ; Metagenome ; }, abstract = {BACKGROUND: Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such diversity is maintained because the effective immune system of a bacterial species is the one distributed across all strains present in the community. However, only few studies have analyzed the distribution of bacterial defense systems at the community-level, mostly focusing on CRISPR and comparing samples from complex environments. Here, we studied 2778 bacterial genomes and 188 metagenomes from cheese-associated communities, which are dominated by a few bacterial taxa and occur in relatively stable environments.<br><br>RESULTS: We corroborate previous laboratory findings that in cheese-associated communities nearly identical strains contain diverse and highly variable arsenals of innate and adaptive (i.e., CRISPR-Cas) immunity systems suggesting rapid turnover. CRISPR spacer abundance correlated with the abundance of matching target sequences across the metagenomes providing evidence that the identified defense repertoires are functional and under selection. While these characteristics align with the pan-immunity model, the detected CRISPR spacers only covered a subset of the phages previously identified in cheese, providing evidence that CRISPR does not enable complete immunity against all phages, and that the innate immune mechanisms may have complementary roles.<br><br>CONCLUSIONS: Our findings show that the evolution of bacterial defense mechanisms is a highly dynamic process and highlight that experimentally tractable, low complexity communities such as those found in cheese, can help to understand ecological and molecular processes underlying phage-defense system relationships. These findings can have implications for the design of robust synthetic communities used in biotechnology and the food industry. Video Abstract.}, }
@article {pmid36016781, year = {2022}, author = {Zhimo, VY and Kumar, A and Biasi, A and Abdelfattah, A and Sharma, VK and Salim, S and Feygenberg, O and Bartuv, R and Freilich, S and Whitehead, SR and Wisniewski, M and Droby, S}, title = {Assembly and dynamics of the apple carposphere microbiome during fruit development and storage.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {928888}, pmid = {36016781}, issn = {1664-302X}, abstract = {Microbial communities associated with fruit can contribute to quality and pathogen resistance, but little is known about their assembly and dynamics during fruit development and storage. Three apple cultivars growing under the same environmental conditions were utilized to examine the apple carposphere microbiome composition and structure at different developmental stages and storage. There was a significant effect (Adonis, p ≤ 0.001) of fruit genotype and its developmental stages and storage times on the fruit surface microbial assemblage and a strong temporal microbial community succession was detected (Mantel test: R ≤ 0.5, p = 0.001) in both bacterial and fungal communities. A set of 15 bacterial and 35 fungal core successional taxa and members exhibiting differential abundances at different fruit stages were identified. For the first time, we show the existence of underlying universal dynamics in the assembly of fruit-associated microbiomes. We also provide evidence of strong microbial cross-domain associations and uncover potential microbe-microbe correlations in the apple carposphere. Together our findings shed light on how the fruit carposphere assemble and change over time, and provide new insights into fruit microbial ecology.}, }
@article {pmid36014090, year = {2022}, author = {Schultz, J and Parise, MTD and Parise, D and Medeiros, LG and Sousa, TJ and Kato, RB and Uetanabaro, APT and Araújo, F and Ramos, RTJ and de Castro Soares, S and Brenig, B and de Carvalho Azevedo, VA and Góes-Neto, A and Rosado, AS}, title = {Unraveling the Genomic Potential of the Thermophilic Bacterium Anoxybacillus flavithermus from an Antarctic Geothermal Environment.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, pmid = {36014090}, issn = {2076-2607}, support = {Baseline Grant//King Abdullah University of Science and Technology/ ; }, abstract = {Antarctica is a mosaic of extremes. It harbors active polar volcanoes, such as Deception Island, a marine stratovolcano having notable temperature gradients over very short distances, with the temperature reaching up to 100 °C near the fumaroles and subzero temperatures being noted in the glaciers. From the sediments of Deception Island, we isolated representatives of the genus Anoxybacillus, a widely spread genus that is mainly encountered in thermophilic environments. However, the phylogeny of this genus and its adaptive mechanisms in the geothermal sites of cold environments remain unknown. To the best of our knowledge, this is the first study to unravel the genomic features and provide insights into the phylogenomics and metabolic potential of members of the genus Anoxybacillus inhabiting the Antarctic thermophilic ecosystem. Here, we report the genome sequencing data of seven A. flavithermus strains isolated from two geothermal sites on Deception Island, Antarctic Peninsula. Their genomes were approximately 3.0 Mb in size, had a G + C ratio of 42%, and were predicted to encode 3500 proteins on average. We observed that the strains were phylogenomically closest to each other (Average Nucleotide Identity (ANI) > 98%) and to A. flavithermus (ANI 95%). In silico genomic analysis revealed 15 resistance and metabolic islands, as well as genes related to genome stabilization, DNA repair systems against UV radiation threats, temperature adaptation, heat- and cold-shock proteins (Csps), and resistance to alkaline conditions. Remarkably, glycosyl hydrolase enzyme-encoding genes, secondary metabolites, and prophage sequences were predicted, revealing metabolic and cellular capabilities for potential biotechnological applications.}, }
@article {pmid36014036, year = {2022}, author = {Thiele, S and Storesund, JE and Fernández-Méndez, M and Assmy, P and Øvreås, L}, title = {A Winter-to-Summer Transition of Bacterial and Archaeal Communities in Arctic Sea Ice.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, pmid = {36014036}, issn = {2076-2607}, support = {U17 CE002015/CE/NCIPC CDC HHS/United States ; }, abstract = {The Arctic is warming 2-3 times faster than the global average, leading to a decrease in Arctic sea ice extent, thickness, and associated changes in sea ice structure. These changes impact sea ice habitat properties and the ice-associated ecosystems. Sea-ice algal blooms provide various algal-derived carbon sources for the bacterial and archaeal communities within the sea ice. Here, we detail the transition of these communities from winter through spring to early summer during the Norwegian young sea ICE (N-ICE2015) expedition. The winter community was dominated by the archaeon Candidatus Nitrosopumilus and bacteria belonging to the Gammaproteobacteria (Colwellia, Kangiellaceae, and Nitrinocolaceae), indicating that nitrogen-based metabolisms, particularly ammonia oxidation to nitrite by Cand. Nitrosopumilus was prevalent. At the onset of the vernal sea-ice algae bloom, the community shifted to the dominance of Gammaproteobacteria (Kangiellaceae, Nitrinocolaceae) and Bacteroidia (Polaribacter), while Cand. Nitrosopumilus almost disappeared. The bioinformatically predicted carbohydrate-active enzymes increased during spring and summer, indicating that sea-ice algae-derived carbon sources are a strong driver of bacterial and archaeal community succession in Arctic sea ice during the change of seasons. This implies a succession from a nitrogen metabolism-based winter community to an algal-derived carbon metabolism-based spring/ summer community.}, }
@article {pmid36014023, year = {2022}, author = {Ouwerkerk, JP and Tytgat, HLP and Elzinga, J and Koehorst, J and Van den Abbeele, P and Henrissat, B and Gueimonde, M and Cani, PD and Van de Wiele, T and Belzer, C and de Vos, WM}, title = {Comparative Genomics and Physiology of Akkermansia muciniphila Isolates from Human Intestine Reveal Specialized Mucosal Adaptation.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, pmid = {36014023}, issn = {2076-2607}, support = {BOF12-GOA-008//Ghent University/ ; Advanced Grand 250172 - Microbes Inside/ERC_/European Research Council/International ; Spinoza Award Willem M. de Vos/NWO_/Dutch Research Council/Netherlands ; SIAM Gravity Grant 024.002.002/NWO_/Dutch Research Council/Netherlands ; FRFS-WELBIO: WELBIO-CR-2022A-02//Fund for Scientific Research/ ; }, abstract = {Akkermansia muciniphila is a champion of mucin degradation in the human gastrointestinal tract. Here, we report the isolation of six novel strains from healthy human donors and their genomic, proteomic and physiological characterization in comparison to the type-strains A. muciniphila MucT and A. glycaniphila PytT. Complete genome sequencing revealed that, despite their large genomic similarity (>97.6%), the novel isolates clustered into two distinct subspecies of A. muciniphila: Amuc1, which includes the type-strain MucT, and AmucU, a cluster of unassigned strains that have not yet been well characterized. CRISPR analysis showed all strains to be unique and confirmed that single healthy subjects can carry more than one A. muciniphila strain. Mucin degradation pathways were strongly conserved amongst all isolates, illustrating the exemplary niche adaptation of A. muciniphila to the mucin interface. This was confirmed by analysis of the predicted glycoside hydrolase profiles and supported by comparing the proteomes of A. muciniphila strain H2, belonging to the AmucU cluster, to MucT and A. glycaniphila PytT (including 610 and 727 proteins, respectively). While some intrinsic resistance was observed among the A. muciniphila straind, none of these seem to pose strain-specific risks in terms of their antibiotic resistance patterns nor a significant risk for the horizontal transfer of antibiotic resistance determinants, opening the way to apply the type-strain MucT or these new A. muciniphila strains as next generation beneficial microbes.}, }
@article {pmid36009876, year = {2022}, author = {Nakatani, H and Yamada, N and Hashimoto, N and Okazaki, F and Arakawa, T and Tamaru, Y and Hori, K}, title = {Perturbation by Antimicrobial Bacteria of the Epidermal Bacterial Flora of Rainbow Trout in Flow-Through Aquaculture.}, journal = {Biology}, volume = {11}, number = {8}, pages = {}, pmid = {36009876}, issn = {2079-7737}, support = {JPMJMI18CF//Japan Science and Technology Agency/ ; JP 20H02539//Japan Society for the Promotion of Science/ ; }, abstract = {The bacterial flora of the epidermal mucus of fish is closely associated with the host's health and susceptibility to pathogenic infections. In this study, we analyzed the epidermal mucus bacteria of rainbow trout (Oncorhynchus mykiss) reared in flow-through aquaculture under environmental perturbations. Over ~2 years, the bacteria present in the skin mucus and water were analyzed based on the 16S rDNA sequences. The composition of the mucus bacterial community showed significant monthly fluctuations, with frequent changes in the dominant bacterial species. Analysis of the beta- and alpha-diversity of the mucus bacterial flora showed the fluctuations of the composition of the flora were caused by the genera Pseudomonas, Yersinia, and Flavobacterium, and some species of Pseudomonas and Yersinia in the mucus were identified as antimicrobial bacteria. Examination of the antimicrobial bacteria in the lab aquarium showed that the natural presence of antimicrobial bacteria in the mucus and water, or the purposeful addition of them to the rearing water, caused a transition in the mucus bacteria community composition. These results demonstrate that specific antimicrobial bacteria in the water or in epidermal mucus comprise one of the causes of changes in fish epidermal mucus microflora.}, }
@article {pmid36008420, year = {2022}, author = {Weyhenmeyer, GA and Obertegger, U and Rudebeck, H and Jakobsson, E and Jansen, J and Zdorovennova, G and Bansal, S and Block, BD and Carey, CC and Doubek, JP and Dugan, H and Erina, O and Fedorova, I and Fischer, JM and Grinberga, L and Grossart, HP and Kangur, K and Knoll, LB and Laas, A and Lepori, F and Meier, J and Palshin, N and Peternell, M and Pulkkanen, M and Rusak, JA and Sharma, S and Wain, D and Zdorovennov, R}, title = {Towards critical white ice conditions in lakes under global warming.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {4974}, pmid = {36008420}, issn = {2041-1723}, mesh = {Global Warming ; Humans ; *Ice ; Ice Cover ; *Lakes ; Seasons ; Temperature ; }, abstract = {The quality of lake ice is of uppermost importance for ice safety and under-ice ecology, but its temporal and spatial variability is largely unknown. Here we conducted a coordinated lake ice quality sampling campaign across the Northern Hemisphere during one of the warmest winters since 1880 and show that lake ice during 2020/2021 commonly consisted of unstable white ice, at times contributing up to 100% to the total ice thickness. We observed that white ice increased over the winter season, becoming thickest and constituting the largest proportion of the ice layer towards the end of the ice cover season when fatal winter drownings occur most often and light limits the growth and reproduction of primary producers. We attribute the dominance of white ice before ice-off to air temperatures varying around the freezing point, a condition which occurs more frequently during warmer winters. Thus, under continued global warming, the prevalence of white ice is likely to substantially increase during the critical period before ice-off, for which we adjusted commonly used equations for human ice safety and light transmittance through ice.}, }
@article {pmid36005399, year = {2022}, author = {Pacheco, AR and Pauvert, C and Kishore, D and Segrè, D}, title = {Toward FAIR Representations of Microbial Interactions.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0065922}, pmid = {36005399}, issn = {2379-5077}, support = {R21 CA260382/CA/NCI NIH HHS/United States ; UH2 AG064704/AG/NIA NIH HHS/United States ; R21CA260382//NIH, National Cancer Institute/ ; UH2AG064704//HHS | NIH | National Institute on Aging (NIA)/ ; }, mesh = {*Microbial Interactions ; *Microbiota ; }, abstract = {Despite an ever-growing number of data sets that catalog and characterize interactions between microbes in different environments and conditions, many of these data are neither easily accessible nor intercompatible. These limitations present a major challenge to microbiome research by hindering the streamlined drawing of inferences across studies. Here, we propose guiding principles to make microbial interaction data more findable, accessible, interoperable, and reusable (FAIR). We outline specific use cases for interaction data that span the diverse space of microbiome research, and discuss the untapped potential for new insights that can be fulfilled through broader integration of microbial interaction data. These include, among others, the design of intercompatible synthetic communities for environmental, industrial, or medical applications, and the inference of novel interactions from disparate studies. Lastly, we envision potential trajectories for the deployment of FAIR microbial interaction data based on existing resources, reporting standards, and current momentum within the community.}, }
@article {pmid36005392, year = {2022}, author = {Richter, I and Radosa, S and Cseresnyés, Z and Ferling, I and Büttner, H and Niehs, SP and Gerst, R and Scherlach, K and Figge, MT and Hillmann, F and Hertweck, C}, title = {Toxin-Producing Endosymbionts Shield Pathogenic Fungus against Micropredators.}, journal = {mBio}, volume = {13}, number = {5}, pages = {e0144022}, pmid = {36005392}, issn = {2150-7511}, support = {P40 OD010440/OD/NIH HHS/United States ; }, mesh = {Animals ; *Burkholderia/metabolism ; *Antimitotic Agents/metabolism ; Macrolides ; Symbiosis ; *Oryza/microbiology ; *Toxins, Biological ; Seedlings ; Soil ; }, abstract = {The fungus Rhizopus microsporus harbors a bacterial endosymbiont (Mycetohabitans rhizoxinica) for the production of the antimitotic toxin rhizoxin. Although rhizoxin is the causative agent of rice seedling blight, the toxinogenic bacterial-fungal alliance is, not restricted to the plant disease. It has been detected in numerous environmental isolates from geographically distinct sites covering all five continents, thus raising questions regarding the ecological role of rhizoxin beyond rice seedling blight. Here, we show that rhizoxin serves the fungal host in fending off protozoan and metazoan predators. Fluorescence microscopy and coculture experiments with the fungivorous amoeba Protostelium aurantium revealed that ingestion of R. microsporus spores is toxic to P. aurantium. This amoebicidal effect is caused by the dominant bacterial rhizoxin congener rhizoxin S2, which is also lethal toward the model nematode Caenorhabditis elegans. By combining stereomicroscopy, automated image analysis, and quantification of nematode movement, we show that the fungivorous nematode Aphelenchus avenae actively feeds on R. microsporus that is lacking endosymbionts, whereas worms coincubated with symbiotic R. microsporus are significantly less lively. This study uncovers an unexpected ecological role of rhizoxin as shield against micropredators. This finding suggests that predators may function as an evolutionary driving force to maintain toxin-producing endosymbionts in nonpathogenic fungi. IMPORTANCE The soil community is a complex system characterized by predator-prey interactions. Fungi have developed effective strategies to defend themselves against predators. Understanding these strategies is of critical importance for ecology, medicine, and biotechnology. In this study, we shed light on the defense mechanisms of the phytopathogenic Rhizopus-Mycetohabitans symbiosis that has spread worldwide. We report an unexpected role of rhizoxin, a secondary metabolite produced by the bacterium M. rhizoxinica residing within the hyphae of R. microsporus. We show that this bacterial secondary metabolite is utilized by the fungal host to successfully fend off fungivorous protozoan and metazoan predators and thus identified a fundamentally new function of this infamous cytotoxic compound. This endosymbiont-dependent predator defense illustrates an unusual strategy employed by fungi that has broader implications, since it may serve as a model for understanding how animal predation acts as an evolutionary driving force to maintain endosymbionts in nonpathogenic fungi.}, }
@article {pmid36002667, year = {2023}, author = {Lopes, RB and Faria, M and Souza, DA and Sosa-Gómez, DR}, title = {Potential Impact of Chemical Fungicides on the Efficacy of Metarhizium rileyi and the Occurrence of Pandora gammae on Caterpillars in Soybean Crops.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {647-657}, pmid = {36002667}, issn = {1432-184X}, support = {20.19.02.007.00.00//Embrapa Recursos Gen&#xe9;ticos e Biotecnologia/ ; PQ 309070/2020-1//National Council for Scientific and Technological Development (CNPq - BR)/ ; }, mesh = {Animals ; Glycine max ; *Moths ; *Metarhizium ; Larva/microbiology ; Crops, Agricultural ; *Fungicides, Industrial/pharmacology ; }, abstract = {Entomopathogenic fungi may play a crucial role in the regulation of caterpillar populations in soybean crops, either through natural occurrences or applied as mycopesticides. In the present work, we reported the naturally occurring entomopathogenic fungus Pandora gammae attacking the caterpillar Chrysodeixis includens, with infection rates in field trials ran in two consecutive years in the 10-35% range. As many chemicals are potentially harmful to entomopathogenic fungi, this work aimed to investigate the potential impact of two chemical fungicides (azoxystrobin + benzovindiflupyr and trifloxistrobina + prothioconazole) used to control soybean rust (Phakopsora pachyrhizi) on the natural occurrence of P. gammae and Metarhizium rileyi, as well as the efficacy of the latter fungus applied as different formulations against the soybean caterpillars Anticarsia gemmatalis and C. includens. Under laboratory conditions, fungicides used at field-recommended rates had a considerable negative impact on the germinability of M. riley on the medium surface, and all tested formulations did not protect conidia from damage by these chemicals. This harmful effect also impacted host infectivity, as the larval mortality owing to this fungus was reduced by 30-40% compared to that of the fungicide-free treatments. In field trials conducted in two subsequent years, unformulated and formulated M. rileyi conidia applied to soybean plants produced primary infection sites in caterpillar populations after a single spray. Spraying unformulated or formulated M. rileyi conidia following fungicide application on plants did not affect host infection rates over time. Moreover, the use of M. rileyi-based formulations or chemical fungicide did not interfere with the natural infection rates by P. gammae on its host, C. includens. Although a higher degree of exposure to non-selective fungicides can negatively affect fungal entomopathogens, a single foliar application of fungicides may be harmless to both M. rileyi and P. gammae in soybean fields. Additionally, this work showed that naturally occurring wasps and tachnids also play an important role in the regulation of A. gemmatalis and, notably, C. includens, with parasitism rates above 40-50% in some cases.}, }
@article {pmid36001047, year = {2023}, author = {Shaffer, M and Thurimella, K and Sterrett, JD and Lozupone, CA}, title = {SCNIC: Sparse correlation network investigation for compositional data.}, journal = {Molecular ecology resources}, volume = {23}, number = {1}, pages = {312-325}, pmid = {36001047}, issn = {1755-0998}, support = {T15 LM009451/LM/NLM NIH HHS/United States ; 4 T15 LM009451-10//U.S. National Library of Medicine/ ; //National Science Foundation/ ; }, mesh = {*Software ; Algorithms ; *Microbiota ; }, abstract = {Microbiome studies are often limited by a lack of statistical power due to small sample sizes and a large number of features. This problem is exacerbated in correlative studies of multi-omic datasets. Statistical power can be increased by finding and summarizing modules of correlated observations, which is one dimensionality reduction method. Additionally, modules provide biological insight as correlated groups of microbes can have relationships among themselves. To address these challenges, we developed SCNIC: Sparse Cooccurrence Network Investigation for compositional data. SCNIC is open-source software that can generate correlation networks and detect and summarize modules of highly correlated features. Modules can be formed using either the Louvain Modularity Maximization (LMM) algorithm or a Shared Minimum Distance algorithm (SMD) that we newly describe here and relate to LMM using simulated data. We applied SCNIC to two published datasets and we achieved increased statistical power and identified microbes that not only differed across groups, but also correlated strongly with each other, suggesting shared environmental drivers or cooperative relationships among them. SCNIC provides an easy way to generate correlation networks, identify modules of correlated features and summarize them for downstream statistical analysis. Although SCNIC was designed considering properties of microbiome data, such as compositionality and sparsity, it can be applied to a variety of data types including metabolomics data and used to integrate multiple data types. SCNIC allows for the identification of functional microbial relationships at scale while increasing statistical power through feature reduction.}, }
@article {pmid35998537, year = {2022}, author = {Qin, Z and Zhao, Z and Xia, L and Ohore, OE}, title = {Unraveling the ecological mechanisms of bacterial succession in epiphytic biofilms on Vallisneria natans and Hydrilla verticillata during bioremediation of phenanthrene and pyrene polluted wetland.}, journal = {Journal of environmental management}, volume = {321}, number = {}, pages = {115986}, doi = {10.1016/j.jenvman.2022.115986}, pmid = {35998537}, issn = {1095-8630}, mesh = {Bacteria/genetics ; Biodegradation, Environmental ; Biofilms ; Ecosystem ; *Hydrocharitaceae ; *Phenanthrenes ; *Polycyclic Aromatic Hydrocarbons ; Pyrenes ; Wetlands ; }, abstract = {In wetland ecosystem, the microbial succession in epiphytic biofilms of submerged macrophytes remains to be fully elucidated, especially submerged macrophytes used to remediate organic pollutants contaminated sediment. Herein, 16 S rRNA gene sequencing was used to investigate the bacterial dynamics and ecological processes in the biofilms of two typical submerged macrophytes (Vallisneria natans and Hydrilla verticillata) settled in sediment polluted by polycyclic aromatic hydrocarbons (PAHs) at two growth periods. The results presented that the variations of bacterial community in the biofilms were influenced by attached surfaces (explanation ratio: 17.30%), incubation time (32.30%) and environmental factors (39.10%). Bacterial community assembly was mainly driven by dispersal limitation which triggered more positive co-occurrence associations in microbial networks, maintaining ecological stability in the process of bioremediation of PAHs. Additionally, the functional redundancy strength of bacterial community was more affected by attached surface than incubation time. The structural equation model illustrated that community assembly drove β-diversity and explained a part of ecological functions. Environmental factors, community assembly, and β-diversity jointly affected microbial networks. Overall, our study offers new insights into the microbial ecology in biofilms attached on the submerged macrophytes settled in PAH-polluted sediment, providing important information for deeply understanding submerged macrophyte-biofilm complex and promoting sustainable phytoremediation in shallow lacustrine and marshy ecosystems.}, }
@article {pmid35997797, year = {2023}, author = {Javal, M and Terblanche, JS and Benoit, L and Conlong, DE and Lloyd, JR and Smit, C and Chapuis, MP}, title = {Does Host Plant Drive Variation in Microbial Gut Communities in a Recently Shifted Pest?.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {636-646}, pmid = {35997797}, issn = {1432-184X}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Microbiota ; Larva/microbiology ; *Coleoptera/microbiology ; Bacteria/genetics ; Plants ; }, abstract = {Biotic interactions can modulate the responses of organisms to environmental stresses, including diet changes. Gut microbes have substantial effects on diverse ecological and evolutionary traits of their hosts, and microbial communities can be highly dynamic within and between individuals in space and time. Modulations of the gut microbiome composition and their potential role in the success of a species to maintain itself in a new environment have been poorly studied to date. Here we examine this question in a large wood-boring beetle Cacosceles newmannii (Cerambycidae), that was recently found thriving on a newly colonized host plant. Using 16S metabarcoding, we assessed the gut bacterial community composition of larvae collected in an infested field and in "common garden" conditions, fed under laboratory-controlled conditions on four either suspected or known hosts (sugarcane, tea tree, wattle, and eucalyptus). We analysed microbiome variation (i.e. diversity and differentiation), measured fitness-related larval growth, and studied host plant lignin and cellulose contents, since their degradation is especially challenging for wood-boring insects. We show that sugarcane seems to be a much more favourable host for larval growth. Bacterial diversity level was the highest in field-collected larvae, whereas lab-reared larvae fed on sugarcane showed a relatively low level of diversity but very specific bacterial variants. Bacterial communities were mainly dominated by Proteobacteria, but were significantly different between sugarcane-fed lab-reared larvae and any other hosts or field-collected larvae. We identified changes in the gut microbiome associated with different hosts over a short time frame, which support the hypothesis of a role of the microbiome in host switches.}, }
@article {pmid35997493, year = {2022}, author = {Floudas, D and Gentile, L and Andersson, E and Kanellopoulos, SG and Tunlid, A and Persson, P and Olsson, U}, title = {X-Ray Scattering Reveals Two Mechanisms of Cellulose Microfibril Degradation by Filamentous Fungi.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {17}, pages = {e0099522}, pmid = {35997493}, issn = {1098-5336}, mesh = {*Agaricales/metabolism ; *Basidiomycota/metabolism ; Cellulose/metabolism ; Fungi/metabolism ; Lignin/metabolism ; Microfibrils/metabolism ; Wood/microbiology ; X-Rays ; }, abstract = {Mushroom-forming fungi (Agaricomycetes) employ enzymatic and nonenzymatic cellulose degradation mechanisms, the latter presumably relying on Fenton-generated radicals. The effects of the two mechanisms on the cellulose microfibrils structure remain poorly understood. We examined cellulose degradation caused by litter decomposers and wood decomposers, including brown-rot and white-rot fungi and one fungus with uncertain wood decay type, by combining small- and wide-angle X-ray scattering. We also examined the effects of commercial enzymes and Fenton-generated radicals on cellulose using the same method. We detected two main degradation or modification mechanisms. The first characterized the mechanism used by most fungi and resembled enzymatic cellulose degradation, causing simultaneous microfibril thinning and decreased crystalline cellulose. The second mechanism was detected in one brown-rot fungus and one litter decomposer and was characterized by patchy amorphogenesis of crystalline cellulose without substantial thinning of the fibers. This pattern did not resemble the effect of Fenton-generated radicals, suggesting a more complex mechanism is involved in the destruction of cellulose crystallinity by fungi. Furthermore, our results showed a mismatch between decay classifications and cellulose degradation patterns and that even within litter decomposers two degradation mechanisms were found, suggesting higher functional diversity under current ecological classifications of fungi. IMPORTANCE Cellulose degradation by fungi plays a fundamental role in terrestrial carbon cycling, but the mechanisms by which fungi cope with the crystallinity of cellulose are not fully understood. We used X-ray scattering to analyze how fungi, a commercial enzyme mix, and a Fenton reaction-generated radical alter the crystalline structure of cellulose. Our data revealed two mechanisms involved in crystalline cellulose degradation by fungi: one that results in the thinning of the cellulose fibers, resembling the enzymatic degradation of cellulose, and one that involves amorphogenesis of crystalline cellulose by yet-unknown pathways, resulting in a patchy-like degradation pattern. These results pave the way to a deeper understanding of cellulose degradation and the development of novel ways to utilize crystalline cellulose.}, }
@article {pmid35997077, year = {2022}, author = {Cho, GY and Whang, KS}, title = {Aquibacillus saliphilus sp. nov., a moderately halophilic bacterium isolated from a grey saltern.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {72}, number = {8}, pages = {}, doi = {10.1099/ijsem.0.005496}, pmid = {35997077}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; *Fatty Acids/chemistry ; Phospholipids/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Sequence Analysis, DNA ; }, abstract = {A novel moderately halophilic bacterium, designated strain KHM2[T], was isolated from the sediment of a grey solar saltern located on Sinui Island, Shinan, Republic of Korea. Cells were rod-shaped, endospore-forming, Gram-stain-positive, motile and facultative anaerobic. Strain KHM2[T] performed anaerobic respiration using nitrates and did not produce glucose acids, indicating the absence of fermentation. Strain KHM2[T] grew at 10-45 °C (optimum, 37 °C), pH 6.0-10.0 (optimum, pH 8.0) and with 1.0-20.0 % (w/v) NaCl (optimum, 10.0%). Based on 16S rRNA gene sequence similarity and chemotaxonomic properties, strain KHM2[T] was assigned to the genus Aquibacillus, with high 16S rRNA gene sequence similarity to Aquibacillus halophilus B6B[T] (98.2%) and less than 96.8 % similarity to the other recognized members of the genus Aquibacillus. The polar lipid profile consisted of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and one unidentified phospholipid (PL). Major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The average nucleotide identity and digital DNA-DNA hybridization values of strain KHM2[T] with A. halophilus B6B[T] were 77.6 and 22.0 %, respectively. Based on the results of polyphasic analysis, strain KHM2[T] is proposed to represent a bacterial species within the genus Aquibacillus with the name Aquibacillus saliphilus sp. nov. The type strain is KHM2[T] (=KACC 19068[T]=NBRC 112577[T]).}, }
@article {pmid35996183, year = {2022}, author = {Cowan, DA and Lebre, PH and Amon, C and Becker, RW and Boga, HI and Boulangé, A and Chiyaka, TL and Coetzee, T and de Jager, PC and Dikinya, O and Eckardt, F and Greve, M and Harris, MA and Hopkins, DW and Houngnandan, HB and Houngnandan, P and Jordaan, K and Kaimoyo, E and Kambura, AK and Kamgan-Nkuekam, G and Makhalanyane, TP and Maggs-Kölling, G and Marais, E and Mondlane, H and Nghalipo, E and Olivier, BW and Ortiz, M and Pertierra, LR and Ramond, JB and Seely, M and Sithole-Niang, I and Valverde, A and Varliero, G and Vikram, S and Wall, DH and Zeze, A}, title = {Biogeographical survey of soil microbiomes across sub-Saharan Africa: structure, drivers, and predicted climate-driven changes.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {131}, pmid = {35996183}, issn = {2049-2618}, mesh = {Biodiversity ; Desert Climate ; Ecosystem ; *Microbiota/genetics ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {BACKGROUND: Top-soil microbiomes make a vital contribution to the Earth's ecology and harbor an extraordinarily high biodiversity. They are also key players in many ecosystem services, particularly in arid regions of the globe such as the African continent. While several recent studies have documented patterns in global soil microbial ecology, these are largely biased towards widely studied regions and rely on models to interpolate the microbial diversity of other regions where there is low data coverage. This is the case for sub-Saharan Africa, where the number of regional microbial studies is very low in comparison to other continents.<br><br>RESULTS: The aim of this study was to conduct an extensive biogeographical survey of sub-Saharan Africa's top-soil microbiomes, with a specific focus on investigating the environmental drivers of microbial ecology across the region. In this study, we sampled 810 sample sites across 9 sub-Saharan African countries and used taxonomic barcoding to profile the microbial ecology of these regions. Our results showed that the sub-Saharan nations included in the study harbor qualitatively distinguishable soil microbiomes. In addition, using soil chemistry and climatic data extracted from the same sites, we demonstrated that the top-soil microbiome is shaped by a broad range of environmental factors, most notably pH, precipitation, and temperature. Through the use of structural equation modeling, we also developed a model to predict how soil microbial biodiversity in sub-Saharan Africa might be affected by future climate change scenarios. This model predicted that the soil microbial biodiversity of countries such as Kenya will be negatively affected by increased temperatures and decreased precipitation, while the fungal biodiversity of Benin will benefit from the increase in annual precipitation.<br><br>CONCLUSION: This study represents the most extensive biogeographical survey of sub-Saharan top-soil microbiomes to date. Importantly, this study has allowed us to identify countries in sub-Saharan Africa that might be particularly vulnerable to losses in soil microbial ecology and productivity due to climate change. Considering the reliance of many economies in the region on rain-fed agriculture, this study provides crucial information to support conservation efforts in the countries that will be most heavily impacted by climate change. Video Abstract.}, }
@article {pmid35995772, year = {2022}, author = {Nyongesa, S and Weber, PM and Bernet, &#xc8; and Pulido, F and Nieves, C and Nieckarz, M and Delaby, M and Viehboeck, T and Krause, N and Rivera-Millot, A and Nakamura, A and Vischer, NOE and vanNieuwenhze, M and Brun, YV and Cava, F and Bulgheresi, S and Veyrier, FJ}, title = {Evolution of longitudinal division in multicellular bacteria of the Neisseriaceae family.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {4853}, pmid = {35995772}, issn = {2041-1723}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; P 28593/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Biological Evolution ; *Cell Division ; Cell Wall/metabolism ; Mammals/microbiology ; *Neisseriaceae/cytology ; Peptidoglycan/metabolism ; }, abstract = {Rod-shaped bacteria typically elongate and divide by transverse fission. However, several bacterial species can form rod-shaped cells that divide longitudinally. Here, we study the evolution of cell shape and division mode within the family Neisseriaceae, which includes Gram-negative coccoid and rod-shaped species. In particular, bacteria of the genera Alysiella, Simonsiella and Conchiformibius, which can be found in the oral cavity of mammals, are multicellular and divide longitudinally. We use comparative genomics and ultrastructural microscopy to infer that longitudinal division within Neisseriaceae evolved from a rod-shaped ancestor. In multicellular longitudinally-dividing species, neighbouring cells within multicellular filaments are attached by their lateral peptidoglycan. In these bacteria, peptidoglycan insertion does not appear concentric, i.e. from the cell periphery to its centre, but as a medial sheet guillotining each cell. Finally, we identify genes and alleles associated with multicellularity and longitudinal division, including the acquisition of amidase-encoding gene amiC2, and amino acid changes in proteins including MreB and FtsA. Introduction of amiC2 and allelic substitution of mreB in a rod-shaped species that divides by transverse fission results in shorter cells with longer septa. Our work sheds light on the evolution of multicellularity and longitudinal division in bacteria, and suggests that members of the Neisseriaceae family may be good models to study these processes due to their morphological plasticity and genetic tractability.}, }
@article {pmid35993706, year = {2022}, author = {Kojima, CY and Getz, EW and Thrash, JC}, title = {RRAP: RPKM Recruitment Analysis Pipeline.}, journal = {Microbiology resource announcements}, volume = {11}, number = {9}, pages = {e0064422}, pmid = {35993706}, issn = {2576-098X}, support = {OCE-1747681//National Science Foundation (NSF)/ ; OCE-1945279//National Science Foundation (NSF)/ ; Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation (SF)/ ; }, abstract = {A common method for quantifying microbial abundances in situ is through metagenomic read recruitment to genomes and normalizing read counts as reads per kilobase (of genome) per million (bases of recruited sequences) (RPKM). We created RRAP (RPKM Recruitment Analysis Pipeline), a wrapper that automates this process using Bowtie2 and SAMtools.}, }
@article {pmid35992701, year = {2022}, author = {Nimonkar, YS and Godambe, T and Kulkarni, A and Patel, T and Paul, D and Paul, D and Rale, V and Prakash, O}, title = {Oligotrophy vs. copiotrophy in an alkaline and saline habitat of Lonar Lake.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {939984}, pmid = {35992701}, issn = {1664-302X}, abstract = {We reported our comparative observations on oligotrophs vs. copiotrophs from a hyper-alkaline and hypersaline habitat, Lonar Lake, situated in the Buldhana district of Maharashtra, India. Cell numbers of oligotrophic and copiotrophic microbes from the sediment were enumerated by the three-tube most probable number (MPN) method using an array of nutrient-rich and oligotrophic (≈10-20 mg carbon L[-1]) media offering simulated natural conditions of pH and salinity. A total of 50 strains from 15 different genera and 30 different species were isolated from the highest positive dilutions of MPN to identify the taxa of oligotrophs and copiotrophic microorganisms dominating in Lonar Lake. We did not get any true oligotrophs due to their adaptation to higher carbon levels during the isolation procedure. On the contrary, several true copiotrophs, which could not adapt and survive on a low-carbon medium, were isolated. It is also observed that changes in medium composition and nutrient level altered the selection of organisms from the same sample. Our data indicate that copiotrophic microorganisms dominate the eutrophic Lonar Lake, which is also supported by the past metagenomics studies from the same site. We also reported that quick depletion of carbon from oligotrophic medium worked as a limiting factor, inducing cell death after 2-3 generations and preventing the development of visible colonies on plates and sufficient optical density in liquid medium. Therefore, a long-term supply of low levels of carbon, followed by isolation on enriched media, can serve as a good strategy in isolation of novel taxa of microorganism, with industrial or environmental importance.}, }
@article {pmid35992662, year = {2022}, author = {Tang, X and Yangjing, G and Zhuoma, G and Guo, X and Cao, P and Yi, B and Wang, W and Ji, D and Pasquali, M and Baccelli, I and Migheli, Q and Chen, X and Cernava, T}, title = {Biological characterization and in vitro fungicide screenings of a new causal agent of wheat Fusarium head blight in Tibet, China.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {941734}, pmid = {35992662}, issn = {1664-302X}, abstract = {Wheat (Triticum aestivum L.) is an important cereal crop, widely grown throughout the temperate zones, and also suitable for cultivation at higher elevations. Fusarium head blight (FHB) is a highly destructive disease of wheat throughout the globe. In July 2020, serious wheat FHB symptoms were observed in open fields located in Linzhi City, southeast of Tibet, China. The causal agent was identified as Fusarium avenaceum (Fr.) Sacc. by amplification and sequencing of the internal transcribed spacer (ITS) region, translation elongation factor 1-alpha (EF-1α) gene, and RNA polymerase II subunit (RPB-2) gene, as well as by morphological characterization. Koch's postulates were confirmed by a pathogenicity test on healthy spikes, including re-isolation and identification. To our knowledge, this is the first report of F. avenaceum causing FHB on wheat in Tibet, China. Moreover, to determine pathogen characteristics that may be useful for future disease management, the utilization of different carbon and nitrogen resources, temperature, light, and ultraviolet (UV) irradiation on mycelium growth and conidia germination were studied. Soluble starch and peptone were the best carbon, and nitrogen source for the pathogen respectively. The optimal temperatures for the pathogen's mycelium growth and conidia germination were 15-20°C, matching the average temperature during the growing season in Linzhi (Tibet). Meanwhile, alternating 8-h light and 16-h dark was shown to be conducive to mycelia growth, and complete darkness facilitated conidia germination. In addition, UV Irradiation of 48 MJ/cm[2], approximately 100 times of the local condition, did not inhibit the germination of conidia. Furthermore, in vitro screening of effective fungicides was conducted. Among the seven tested pesticides, carbendazim showed the best inhibition rate, with an EC50 (concentration for 50% of maximal effect) value of 2.1 mg/L. Propiconazole also showed sufficient inhibitory effects against F. avenaceum, with an EC50 value of 2.6 mg/L. The study provides insights into the newly identified causal agent of wheat FHB in Tibet, China, as well as first pathogen characteristics and promising candidate substances for its management.}, }
@article {pmid35987172, year = {2022}, author = {Silva, DFD and Moreira, JV and Sousa, LIS and Santana, MC and Mota, JCA and Queiroz, ADS and Nascimento, &#xcd;VD and Silva, AMM and Araújo, ASF and Melo, VMM and Medeiros, &#xc9;V and Cardoso, EJBN and Pereira, APA}, title = {Arbuscular mycorrhizal fungi community in soils under desertification and restoration in the Brazilian semiarid.}, journal = {Microbiological research}, volume = {264}, number = {}, pages = {127161}, doi = {10.1016/j.micres.2022.127161}, pmid = {35987172}, issn = {1618-0623}, mesh = {Brazil ; Conservation of Natural Resources ; Fungi ; *Glomeromycota ; Humans ; *Mycorrhizae ; Plant Roots/microbiology ; Soil/chemistry ; Soil Microbiology ; Spores, Fungal ; }, abstract = {Soil desertification has a significant social, economic, and environmental impact worldwide. Mycorrhizal diversity remains poorly understood in semiarid regions impacted by desertification, especially in Brazilian drylands. More importantly, positive impacts of grazing exclusion on mycorrhizal communities are still incipient. Here, we hypothesized that overgrazing changes the structure of Arbuscular Mycorrhizal Fungi (AMF) community compared to native areas and, grazing exclusion is effective to restore the AMF community. Thus, we analyzed the status of AMF community in soils under desertification (overgrazing) and restoration (twenty-years of grazing exclusion) in the Brazilian semiarid. AMF-spores were extracted via humid decantation methodology, morphologically classified, and alpha diversity metrics were calculated. Soil samples were chemically, and physically characterized and multivariate statistical analyses were applied to verify the impact of soil degradation and restoration on AMF-community. Briefly, native, and restored areas presented higher contents of organic matter, phosphorus, microbial carbon, and β-glucosidase activity. However, degraded soil showed higher Al[3+], Na[+,] and bulk soil density values. The abundance of AMF spores was higher in restored soil, followed by degraded and native vegetation, and Shannon's diversity index was significantly higher in restored soils, followed by native vegetation. AMF-spores were classified into four families (Gigasporaceae > Acaulosporaceae > Glomeraceae > Ambisporaceae). Ambisporaceae was closed correlated with degraded soil, mainly with Al[3+], Na[+], and bulk soil density properties. On the other hand, Acaulosporaceae and Glomeraceae were positively correlated with native vegetation and restored soil, respectively, thereby improving Shannon index, richness, enzyme activity, and soil respiration. Thus, grazing exclusion, in long term, can be a good strategy to restore AMF-diversity in soils in the Brazilian semiarid.}, }
@article {pmid35987022, year = {2022}, author = {Mian, G and Belfiore, N and Musetti, R and Tomasi, D and Cantone, P and Lovat, L and Lupinelli, S and Iacumin, L and Celotti, E and Golinelli, F}, title = {Effect of a triacontanol-rich biostimulant on the ripening dynamic and wine must technological parameters in Vitis vinifera cv. 'Ribolla Gialla'.}, journal = {Plant physiology and biochemistry : PPB}, volume = {188}, number = {}, pages = {60-69}, doi = {10.1016/j.plaphy.2022.07.032}, pmid = {35987022}, issn = {1873-2690}, mesh = {Crops, Agricultural ; Fatty Alcohols ; Fruit/metabolism ; *Vitis/metabolism ; *Wine/analysis ; }, abstract = {Biostimulants are organic compounds which can influence the biochemical activity of the whole plant. Lately, great attention has been focused on the possibility of using these stimulants in the viticulture sector. Due to this, the aim of this work was to investigate the foliar application of a biostimulant made by Fabaceae tissue, rich in amino acids and peptides along with the high presence of natural triacontanol (C30H62O) (>6 mg kg[-1]), previously reported in many crops as chemicals able to stimulate different yield components, the technological composition of musts still having an effect on some of the microbial population of different fruits/crops. Hence, this research was conducted during the growing seasons 2020 and 2021 in a commercial vineyard of the 'Ribolla Gialla' grapevine (Vitis vinifera, L.), in the Friuli Venezia Giulia Region (North-Eastern Italy), in order to understand the effect on this woody perennial crop not yet investigated. After a two-year-study, a physiological response occurred, as ripening and veraision were brought forward in the treated plants as well as the harvest time, having higher enological parameters (sugars, total titrable acidity and citric acid content) than the non-treated at every stage. Thus, grapes in the treated plants reached a full technological maturity earlier than the non-treated, in both study years. There was a positive effect on must microbial ecology important for winemaking, hence, the biostimulant have promoted the growth of the microbial community on berry skin translating into what found in the must.}, }
@article {pmid35982656, year = {2022}, author = {Rothman, JA and Saghir, A and Chung, SA and Boyajian, N and Dinh, T and Kim, J and Oval, J and Sharavanan, V and York, C and Zimmer-Faust, AG and Langlois, K and Steele, JA and Griffith, JF and Whiteson, KL}, title = {Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread transcription of antibiotic resistance genes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {35982656}, issn = {2692-8205}, support = {P30 CA062203/CA/NCI NIH HHS/United States ; S10 OD010794/OD/NIH HHS/United States ; S10 OD021718/OD/NIH HHS/United States ; S10 RR025496/RR/NCRR NIH HHS/United States ; }, abstract = {Municipal wastewater provides a representative sample of human fecal waste across a catchment area and contains a wide diversity of microbes. Sequencing wastewater samples provides information about human-associated and medically-important microbial populations, and may be useful to assay disease prevalence and antimicrobial resistance (AMR). Here, we present a study in which we used untargeted metatranscriptomic sequencing on RNA extracted from 275 sewage influent samples obtained from eight wastewater treatment plants (WTPs) representing approximately 16 million people in Southern California between August 2020 - August 2021. We characterized bacterial and viral transcripts, assessed metabolic pathway activity, and identified over 2,000 AMR genes/variants across all samples. Because we did not deplete ribosomal RNA, we have a unique window into AMR carried as ribosomal mutants. We show that AMR diversity varied between WTPs and that the relative abundance of many individual AMR genes/variants increased over time and may be connected to antibiotic use during the COVID-19 pandemic. Similarly, we detected transcripts mapping to human pathogenic bacteria and viruses suggesting RNA sequencing is a powerful tool for wastewater-based epidemiology and that there are geographical signatures to microbial transcription. We captured the transcription of gene pathways common to bacterial cell processes, including central carbon metabolism, nucleotide synthesis/salvage, and amino acid biosynthesis. We also posit that due to the ubiquity of many viruses and bacteria in wastewater, new biological targets for microbial water quality assessment can be developed. To the best of our knowledge, our study provides the most complete longitudinal metatranscriptomic analysis of a large population's wastewater to date and demonstrates our ability to monitor the presence and activity of microbes in complex samples. By sequencing RNA, we can track the relative abundance of expressed AMR genes/variants and metabolic pathways, increasing our understanding of AMR activity across large human populations and sewer sheds.}, }
@article {pmid35980043, year = {2022}, author = {Belk, AD and Frazier, AN and Fuerniss, LK and Delmore, R and Belk, K and Borlee, B and Geornaras, I and Martin, JN and Metcalf, JL}, title = {A Pilot Study: the Development of a Facility-Associated Microbiome and Its Association with the Presence of Listeria Spp. in One Small Meat Processing Facility.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0204522}, pmid = {35980043}, issn = {2165-0497}, mesh = {Humans ; *Listeria/genetics ; Pilot Projects ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Meat ; *Microbiota/genetics ; Food Contamination/analysis ; }, abstract = {Microbial communities which persist in food processing facilities may have a detrimental impact on food safety and spoilage. In meat processing, Listeria monocytogenes is an organism of concern due to its ability to cause significant human illnesses and persist in refrigerated environments. The microbial ecology of Listeria spp. in small meat processing facilities has not been well characterized. Therefore, we collected samples from a newly constructed meat processing facility as an opportunity to investigate several research objectives: (i) to determine whether a stable, consistent microbiome develops in a small meat processing facility during the first 18 months of operation, (ii) to evaluate the environmental factors that drive microbial community formation, and (iii) to elucidate the relationship between microbial communities and the presence of Listeria species. We evaluated microbiomes using 16S rRNA gene sequencing and Listeria presence using quantitative PCR. We demonstrated that microbial communities differentiate by the functional room type, which is representative of several environmental differences such as temperature, sources of microbes, and activity. Temperature was an especially important factor; in rooms with low temperatures, communities were dominated by psychotrophs, especially Pseudomonas, while warmer rooms supported greater diversity. A stable core community formed in facility drains, indicating that mechanisms which cause persistence are present in the communities. The overall presence of Listeria in the facility was low but could be tied to specific organisms within a room, and the species of Listeria could be stratified by room function. IMPORTANCE This study provides critical knowledge to improve meat safety and quality from small meat processing facilities. Principally, it demonstrates the importance of facility design and room condition to the development of important microbial communities; temperature, sanitation regimen, and physical barriers all influence the ability of microorganisms to join the stable core community. It also demonstrates a relationship between the microbial community and Listeria presence in the facility, showing the importance of managing facility sanitation plans for not only pathogens, but also the general facility microbiome.}, }
@article {pmid35979497, year = {2022}, author = {Monteiro, GGTN and Barros, DJ and Gabriel, GVM and Venturini, AM and Veloso, TGR and Vazquez, GH and Oliveira, LC and Neu, V and Bodelier, PLE and Mansano, CFM and Tsai, SM and Navarrete, AA}, title = {Molecular evidence for stimulation of methane oxidation in Amazonian floodplains by ammonia-oxidizing communities.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {913453}, pmid = {35979497}, issn = {1664-302X}, abstract = {Ammonia oxidation is the rate-limiting first step of nitrification and a key process in the nitrogen cycle that results in the formation of nitrite (NO2 [-]), which can be further oxidized to nitrate (NO3 [-]). In the Amazonian floodplains, soils are subjected to extended seasons of flooding during the rainy season, in which they can become anoxic and produce a significant amount of methane (CH4). Various microorganisms in this anoxic environment can couple the reduction of different ions, such as NO2 [-] and NO3 [-], with the oxidation of CH4 for energy production and effectively link the carbon and nitrogen cycle. Here, we addressed the composition of ammonium (NH4 [+]) and NO3 [-]-and NO2 [-]-dependent CH4-oxidizing microbial communities in an Amazonian floodplain. In addition, we analyzed the influence of environmental and geochemical factors on these microbial communities. Soil samples were collected from different layers of forest and agroforest land-use systems during the flood and non-flood seasons in the floodplain of the Tocantins River, and next-generation sequencing of archaeal and bacterial 16S rRNA amplicons was performed, coupled with chemical characterization of the soils. We found that ammonia-oxidizing archaea (AOA) were more abundant than ammonia-oxidizing bacteria (AOB) during both flood and non-flood seasons. Nitrogen-dependent anaerobic methane oxidizers (N-DAMO) from both the archaeal and bacterial domains were also found in both seasons, with higher abundance in the flood season. The different seasons, land uses, and depths analyzed had a significant influence on the soil chemical factors and also affected the abundance and composition of AOA, AOB, and N-DAMO. During the flood season, there was a significant correlation between ammonia oxidizers and N-DAMO, indicating the possible role of these oxidizers in providing oxidized nitrogen species for methanotrophy under anaerobic conditions, which is essential for nitrogen removal in these soils.}, }
@article {pmid35978986, year = {2022}, author = {Crous, PW and Sandoval-Denis, M and Costa, MM and Groenewald, JZ and van Iperen, AL and Starink-Willemse, M and Hernández-Restrepo, M and Kandemir, H and Ulaszewski, B and de Boer, W and Abdel-Azeem, AM and Abdollahzadeh, J and Akulov, A and Bakhshi, M and Bezerra, JDP and Bhunjun, CS and Câmara, MPS and Chaverri, P and Vieira, WAS and Decock, CA and Gaya, E and Gené, J and Guarro, J and Gramaje, D and Grube, M and Gupta, VK and Guarnaccia, V and Hill, R and Hirooka, Y and Hyde, KD and Jayawardena, RS and Jeewon, R and Jurjević, &#x17d; and Korsten, L and Lamprecht, SC and Lombard, L and Maharachchikumbura, SSN and Polizzi, G and Rajeshkumar, KC and Salgado-Salazar, C and Shang, QJ and Shivas, RG and Summerbell, RC and Sun, GY and Swart, WJ and Tan, YP and Vizzini, A and Xia, JW and Zare, R and González, CD and Iturriaga, T and Savary, O and Coton, M and Coton, E and Jany, JL and Liu, C and Zeng, ZQ and Zhuang, WY and Yu, ZH and Thines, M}, title = {Fusarium and allied fusarioid taxa (FUSA). 1.}, journal = {Fungal systematics and evolution}, volume = {9}, number = {}, pages = {161-200}, pmid = {35978986}, issn = {2589-3831}, abstract = {Seven Fusarium species complexes are treated, namely F. aywerte species complex (FASC) (two species), F. buharicum species complex (FBSC) (five species), F. burgessii species complex (FBURSC) (three species), F. camptoceras species complex (FCAMSC) (three species), F. chlamydosporum species complex (FCSC) (eight species), F. citricola species complex (FCCSC) (five species) and the F. concolor species complex (FCOSC) (four species). New species include Fusicolla elongata from soil (Zimbabwe), and Neocosmospora geoasparagicola from soil associated with Asparagus officinalis (Netherlands). New combinations include Neocosmospora akasia, N. awan, N. drepaniformis, N. duplosperma, N. geoasparagicola, N. mekan, N. papillata, N. variasi and N. warna. Newly validated taxa include Longinectria gen. nov., L. lagenoides, L. verticilliforme, Fusicolla gigas and Fusicolla guangxiensis. Furthermore, Fusarium rosicola is reduced to synonymy under N. brevis. Finally, the genome assemblies of Fusarium secorum (CBS 175.32), Microcera coccophila (CBS 310.34), Rectifusarium robinianum (CBS 430.91), Rugonectria rugulosa (CBS 126565), and Thelonectria blattea (CBS 952.68) are also announced here. Citation: Crous PW, Sandoval-Denis M, Costa MM, Groenewald JZ, van Iperen AL, Starink-Willemse M, Hernández-Restrepo M, Kandemir H, Ulaszewski B, de Boer W, Abdel-Azeem AM, Abdollahzadeh J, Akulov A, Bakhshi M, Bezerra JDP, Bhunjun CS, Câmara MPS, Chaverri P, Vieira WAS, Decock CA, Gaya E, Gené J, Guarro J, Gramaje D, Grube M, Gupta VK, Guarnaccia V, Hill R, Hirooka Y, Hyde KD, Jayawardena RS, Jeewon R, Jurjević Ž, Korsten L, Lamprecht SC, Lombard L, Maharachchikumbura SSN, Polizzi G, Rajeshkumar KC, Salgado-Salazar C, Shang Q-J, Shivas RG, Summerbell RC, Sun GY, Swart WJ, Tan YP, Vizzini A, Xia JW, Zare R, González CD, Iturriaga T, Savary O, Coton M, Coton E, Jany J-L, Liu C, Zeng Z-Q, Zhuang W-Y, Yu Z-H, Thines M (2022). Fusarium and allied fusarioid taxa (FUSA). 1. Fungal Systematics and Evolution 9: 161-200. doi: 10.3114/fuse.2022.09.08.}, }
@article {pmid35978183, year = {2023}, author = {Tong, CY and Derek, CJC}, title = {Novel Extrapolymeric Substances Biocoating on Polyvinylidene Fluoride Membrane for Enhanced Attached Growth of Navicula incerta.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {549-562}, pmid = {35978183}, issn = {1432-184X}, support = {RUI/8014065//Universiti Sains Malaysia/ ; }, mesh = {*Biofilms ; Polyvinyls/metabolism ; Extracellular Polymeric Substance Matrix ; Polysaccharides/metabolism ; *Microalgae/metabolism ; }, abstract = {Cell adhesion is always the first step in biofilm development. With the emergence of attached cultivation systems, this study aims to promote a cost-effective approach for sustainable cultivation of microalgae, Navicula incerta, by pre-coating the main substrates, commercial polyvinylidene fluoride (PVDF) membranes with its own washed algal cells and self-produced soluble extracellular polymeric substances (EPS) for strengthened biofilm development. The effects of pH value (6 to 9), cell suspension volume (10 to 30 mL), and EPS volume (10 to 50 mL) were statistically optimized by means of response surface methodology toolkit. Model outputs revealed good agreement with cell adhesion data variation less than 1% at optimized pre-coating conditions (7.20 pH, 30 mL cell suspension volume, and 50 mL EPS volume). Throughout long-term biofilm cultivation, results demonstrated that EPS pre-coating substantially improved the attached microalgae density by as high as 271% than pristine PVDF due to rougher surface and the presence of sticky exopolymer particles. Nutrients absorbed via the available EPS coating from the bulk medium made the immobilized cells to release less polysaccharides on an average of 30% less than uncoated PVDF. This work suggests that adhesive polymer binders derived from organic sources can be effectively integrated into the development of high-performance novel materials as biocoating for immobilized microalgae cultivation.}, }
@article {pmid35977570, year = {2022}, author = {Read-Daily, B and Ben Maamar, S and Sabba, F and Green, S and Nerenberg, R}, title = {Effect of nitrous oxide (N2O) on the structure and function of nitrogen-oxide reducing microbial communities.}, journal = {Chemosphere}, volume = {307}, number = {Pt 3}, pages = {135819}, doi = {10.1016/j.chemosphere.2022.135819}, pmid = {35977570}, issn = {1879-1298}, mesh = {Bacteria/genetics/metabolism ; Denitrification ; *Greenhouse Gases/analysis ; *Microbiota ; Nitrates/chemistry ; Nitrites/metabolism ; Nitrogen/analysis ; Nitrogen Dioxide/analysis ; Nitrous Oxide/analysis ; Sewage/chemistry ; }, abstract = {Nitrous oxide (N2O) is a potent greenhouse gas that can be produced by nitrifying and denitrifying bacteria. Yet the effects of N2O on microbial communities is not well understood. We used batch tests to explore the effects of N2O on mixed denitrifying communities. Batch tests were carried out with acetate as the electron donor and with the following electron acceptors: nitrate (NO3[-]), nitrite (NO2[-]), N2O, NO3[-] + N2O, and NO2[-] + N2O. Activated sludge from a municipal wastewater treatment plant was used as the inoculum. The bacteria grew readily with N2O as the sole acceptor. When N2O was provided along with NO3[-] or NO2[-], it was used concurrently and resulted in higher growth rates than the same acceptors without added N2O. The microbial communities resulting from N2O addition were significantly different at the genus level from those with just NO3[-] or NO2[-]. Tests with N2O as the sole added acceptor revealed a reduced diversity. Analysis of inferred gene content using PICRUSt2 indicated a greater abundance of genera with a complete denitrification pathway when growing on N2O or NO2[-], relative to all other tests. This suggests that specific N2O reduction rates are high, and that N2O alone selects for a low-diversity, fully denitrifying community. When N2O is present with NO2[-] or NO3[-], the microbial communities were more diverse and did not select exclusively for full denitrifiers. N2O alone appears to select for a "generalist" community with full denitrification pathways and lower diversity. In terms of denitrification genes, the combination of acceptors with N2O appeared to increase the number of microbes carrying nirK, while fully denitrifying bacteria appear more likely to carry nirS. Lastly, all the taxa in NO2[-] and N2O samples were predicted to harbor nosZ. This suggests the potential for reduced N2O emissions in denitrifying systems.}, }
@article {pmid35977400, year = {2022}, author = {IJdema, F and De Smet, J and Crauwels, S and Lievens, B and Van Campenhout, L}, title = {Meta-analysis of larvae of the black soldier fly (Hermetia illucens) microbiota based on 16S rRNA gene amplicon sequencing.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {9}, pages = {}, pmid = {35977400}, issn = {1574-6941}, mesh = {Animals ; Bacteria/genetics ; *Diptera/microbiology ; Genes, rRNA ; Larva/microbiology ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Black soldier fly larvae (BSFL) belong to the most widely reared insects as an alternative protein source at industrial scale. Bacteria in the larval gut can provide benefits for the animal, though some bacteria can also be pathogenic for the insect. Accurate characterization of the BSFL microbiota is important for the production of BSFL in terms of yield and microbiological safety. In this study, 16S ribosomal RNA gene sequence data sets from 11 studies were re-analysed to gain better insights in the BSFL gut microbiota, potential factors that influence their composition, and differences between the gut and the whole larvae microbiota. A core gut microbiota was found consisting of members of Enterococcus, Klebsiella, Morganella, Providencia, and Scrofimicrobium. Further, the factors 'Study', 'Age' and 'Feed' (i.e. rearing substrate of the larvae) significantly affected the microbiota gut composition. When compared to whole larvae, a significantly lower diversity was found for gut samples, suggesting that the larvae harboured additional microbes on their cuticle or in the insect body. Universal choices in insect sample type, primer selection and bio-informatics analysis pipeline can strengthen future meta-analyses and improve our understanding of the BSFL gut microbiota towards the optimization of insect rearing conditions and substrates.}, }
@article {pmid35975997, year = {2022}, author = {Lensink, MJ and Li, Y and Lequime, S}, title = {Aquatic Flaviviruses.}, journal = {Journal of virology}, volume = {96}, number = {17}, pages = {e0043922}, pmid = {35975997}, issn = {1098-5514}, mesh = {Animals ; Aquaculture ; *Aquatic Organisms/isolation &amp; purification/virology ; Biological Evolution ; Fishes/virology ; *Flavivirus/isolation &amp; purification ; *Flavivirus Infections/virology ; Humans ; }, abstract = {Flaviviruses are positive-sense single-stranded RNA viruses, including some well-known human pathogens such as Zika, dengue, and yellow fever viruses, which are primarily associated with mosquito and tick vectors. The vast majority of flavivirus research has focused on terrestrial environments; however, recent findings indicate that a range of flaviviruses are also present in aquatic environments, both marine and freshwater. These flaviviruses are found in various hosts, including fish, crustaceans, molluscs, and echinoderms. Although the effects of aquatic flaviviruses on the hosts they infect are not all known, some have been detected in farmed species and may have detrimental effects on the aquaculture industry. Exploration of the evolutionary history through the discovery of the Wenzhou shark flavivirus in both a shark and crab host is of particular interest since the potential dual-host nature of this virus may indicate that the invertebrate-vertebrate relationship seen in other flaviviruses may have a more profound evolutionary root than previously expected. Potential endogenous viral elements and the range of novel aquatic flaviviruses discovered thus shed light on virus origins and evolutionary history and may indicate that, like terrestrial life, the origins of flaviviruses may lie in aquatic environments.}, }
@article {pmid35971012, year = {2023}, author = {Giongo, A and Dos Anjos Borges, LG and Simão, TLL and Eizirik, E and Utz, LRP}, title = {Structure and Dynamics of Periphyton in a Neotropical Freshwater Lake, with Emphasis on Ciliates and Their Relationships with Bacterial Taxa.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {187-199}, pmid = {35971012}, issn = {1432-184X}, support = {476310/2011-3//CNPq/ ; 001//Capes/ ; }, mesh = {Lakes ; Ecosystem ; *Periphyton ; *Ciliophora/genetics ; *Oligohymenophorea/genetics ; }, abstract = {Periphyton communities in freshwater systems play an essential role in biogeochemical processes, but knowledge of their structure and dynamics lags far behind other environments. We used eDNA metabarcoding of 16S and 18S rRNA markers to investigate the formation and establishment of a periphytic community, in addition to a morphology-based approach for peritrich ciliate determinations, its most abundant group. We sampled two nearby sites within a large Neotropical lake at four time points, aiming to assess whether periphyton establishment can be replicated on this local scale. Producers and denitrifiers were abundant in the community, illustrating the relevant role of biofilms in freshwater nutrient recycling. Among microeukaryotes, peritrich ciliates dominated the community, with genera Epistylis and Vorticella being the most abundant and showing a clear succession at both sites. Other ciliates were morphologically identified and, in some cases, their occurrence was strongly related to bacterial abundance. The structure of both prokaryotic and eukaryotic components of periphyton was not different, while the turnover dynamics differed between the two sites, in spite of their adjacent locations and similar abiotic properties. This indicates that the establishment of these communities can vary even on a local scale within a lake ecosystem.}, }
@article {pmid35969955, year = {2022}, author = {Yin, W and Zhang, B and Zhang, H and Zhang, D and Leiviskä, T}, title = {Vertically co-distributed vanadium and microplastics drive distinct microbial community composition and assembly in soil.}, journal = {Journal of hazardous materials}, volume = {440}, number = {}, pages = {129700}, doi = {10.1016/j.jhazmat.2022.129700}, pmid = {35969955}, issn = {1873-3336}, mesh = {*Microbiota ; Microplastics ; Plastics ; *Soil/chemistry ; Soil Microbiology ; Vanadium ; }, abstract = {Vanadium (V) and microplastics in soils draw increasing attention considering their significant threats to ecosystems. However, little is known about the vertical co-distribution of V and microplastics in soil profile and their combined effects on microbial community dynamics and assembly. This study investigated the spatial distribution of V and microplastics in the soils at a V smelting site and the associated microbial community characteristics along the vertical gradient. Both V and microplastics were found in the 50 cm soil profile with average concentrations of 203.5 ± 314.4 mg/kg and 165.1 ± 124.8 item/kg, respectively. Topsoil (0-20 cm) and subsoil (20-50 cm) displayed distinct microbial community compositions. Metal-tolerant (e.g., Spirochaeta, Rubellimicrobium) and organic-degrading (e.g., Bradyrhizobium, Pseudolabrys) taxa as biomarkers were more abundant in the topsoil layer. V and microplastics directly affected the microbial structure in the topsoil and had indirect influences in the subsoil, with direct impacts from organic matter. In topsoil, deterministic processes were more prevalent for community assembly, whereas stochastic processes governed the subsoil. The interspecific relationship was closer in topsoil with greater network complexity and higher modularity. These findings promote the understanding of distinct heterogeneity of microbial communities jointly driven by V and microplastics in soil environment.}, }
@article {pmid35968126, year = {2022}, author = {Naqqash, T and Malik, KA and Imran, A and Hameed, S and Shahid, M and Hanif, MK and Majeed, A and Iqbal, MJ and Qaisrani, MM and van Elsas, JD}, title = {Inoculation With Azospirillum spp. Acts as the Liming Source for Improving Growth and Nitrogen Use Efficiency of Potato.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {929114}, pmid = {35968126}, issn = {1664-462X}, abstract = {Nitrogen (N) is one of the limiting factors for plant growth, and it is mainly supplied exogenously by fertilizer application. It is well documented that diazotrophic rhizobacteria improve plant growth by fixing atmospheric N in the soil. The present study investigates the nitrogen-fixing potential of two Azospirillum spp. strains using the [15]N isotope-dilution method. The two diazotrophic strains (TN03 and TN09) native to the rhizosphere of potato belong to the genus Azospirillum (16S rRNA gene accession numbers LN833443 and LN833448, respectively). Both strains were able to grow on an N-free medium with N-fixation potential (138-143 nmol mg[-1] protein h[-1]) and contained the nifH gene. Strain TN03 showed highest indole acetic acid (IAA) production (30.43 μg/mL), while TN09 showed highest phosphate solubilization activity (249.38 μg/mL) while both diazotrophs showed the production of organic acids. A [15]N dilution experiment was conducted with different fertilizer inputs to evaluate the N-fixing potential of both diazotrophs in pots. The results showed that plant growth parameters and N contents increased significantly by the inoculations. Moreover, reduced [15]N enrichment was found compared to uninoculated controls that received similar N fertilizer levels. This validates the occurrence of N-fixation through isotopic dilution. Strain TN09 showed higher N-fixing potential than TN03 and the uninoculated controls. Inoculation with either strain also showed a remarkable increase in plant growth under field conditions. Thus, there were remarkable increases in N use efficiency, N uptake and N utilization levels. Confocal laser scanning and transmission electron microscopy showed that TN03 is an ectophyte, i.e., present outside root cells or within the grooves of root hairs, while TN09 is an endophyte, i.e., present within root cells, forming a strong association withroot it. This study confirms that diazotrophic Azospirillum spp. added to potato systems can improve plant growth and N use efficiency, opening avenues for improvement of potato crop growth with reduced input of N fertilizer.}, }
@article {pmid35966858, year = {2022}, author = {Song, W and Zhou, X and Duan, Q and Wang, Q and Li, Y and Li, A and Zhou, W and Sun, L and Qiu, L and Li, R and Li, Y}, title = {Using random forest algorithm for glomerular and tubular injury diagnosis.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {911737}, pmid = {35966858}, issn = {2296-858X}, abstract = {OBJECTIVES: Chronic kidney disease (CKD) is a common chronic condition with high incidence and insidious onset. Glomerular injury (GI) and tubular injury (TI) represent early manifestations of CKD and could indicate the risk of its development. In this study, we aimed to classify GI and TI using three machine learning algorithms to promote their early diagnosis and slow the progression of CKD.<br><br>METHODS: Demographic information, physical examination, blood, and morning urine samples were first collected from 13,550 subjects in 10 counties in Shanxi province for classification of GI and TI. Besides, LASSO regression was employed for feature selection of explanatory variables, and the SMOTE (synthetic minority over-sampling technique) algorithm was used to balance target datasets, i.e., GI and TI. Afterward, Random Forest (RF), Naive Bayes (NB), and logistic regression (LR) were constructed to achieve classification of GI and TI, respectively.<br><br>RESULTS: A total of 12,330 participants enrolled in this study, with 20 explanatory variables. The number of patients with GI, and TI were 1,587 (12.8%) and 1,456 (11.8%), respectively. After feature selection by LASSO, 14 and 15 explanatory variables remained in these two datasets. Besides, after SMOTE, the number of patients and normal ones were 6,165, 6,165 for GI, and 6,165, 6,164 for TI, respectively. RF outperformed NB and LR in terms of accuracy (78.14, 80.49%), sensitivity (82.00, 84.60%), specificity (74.29, 76.09%), and AUC (0.868, 0.885) for both GI and TI; the four variables contributing most to the classification of GI and TI represented SBP, DBP, sex, age and age, SBP, FPG, and GHb, respectively.<br><br>CONCLUSION: RF boasts good performance in classifying GI and TI, which allows for early auxiliary diagnosis of GI and TI, thus facilitating to help alleviate the progression of CKD, and enjoying great prospects in clinical practice.}, }
@article {pmid35966660, year = {2022}, author = {Young, E and Allen, RJ}, title = {Lineage dynamics in growing biofilms: Spatial patterns of standing vs. de novo diversity.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {915095}, pmid = {35966660}, issn = {1664-302X}, support = {682237/ERC_/European Research Council/International ; }, abstract = {Microbial biofilms show high phenotypic and genetic diversity, yet the mechanisms underlying diversity generation and maintenance remain unclear. Here, we investigate how spatial patterns of growth activity within a biofilm lead to spatial patterns of genetic diversity. Using individual-based computer simulations, we show that the active layer of growing cells at the biofilm interface controls the distribution of lineages within the biofilm, and therefore the patterns of standing and de novo diversity. Comparing biofilms of equal size, those with a thick active layer retain more standing diversity, while de novo diversity is more evenly distributed within the biofilm. In contrast, equal-sized biofilms with a thin active layer retain less standing diversity, and their de novo diversity is concentrated at the top of the biofilm, and in fewer lineages. In the context of antimicrobial resistance, biofilms with a thin active layer may be more prone to generate lineages with multiple resistance mutations, and to seed new resistant biofilms via sloughing of resistant cells from the upper layers. Our study reveals fundamental "baseline" mechanisms underlying the patterning of diversity within biofilms.}, }
@article {pmid35965269, year = {2023}, author = {Lima, LFO and Alker, AT and Papudeshi, B and Morris, MM and Edwards, RA and de Putron, SJ and Dinsdale, EA}, title = {Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {392-407}, pmid = {35965269}, issn = {1432-184X}, mesh = {Animals ; *Anthozoa/microbiology ; Ecosystem ; Metagenome ; Coral Reefs ; Bacteria/genetics/metabolism ; *Microbiota/genetics ; Seawater/microbiology ; }, abstract = {The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes, as it constitutes the direct interface between the coral host and the environment. Here, we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. The analysis was conducted using metagenomes and metagenome-assembled genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs. The microbial community structure in the coral SML varied according to the local environment, both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and those that are related to higher levels of microbial activity, competition, and stress response. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome, potentially increasing holobiont resilience to environmental changes and disease.}, }
@article {pmid35962889, year = {2022}, author = {Oliveira, MET and Paulino, GVB and Dos Santos Júnior, ED and da Silva Oliveira, FA and Melo, VMM and Ursulino, JS and de Aquino, TM and Shetty, AK and Landell, MF and Gitaí, DLG}, title = {Multi-omic Analysis of the Gut Microbiome in Rats with Lithium-Pilocarpine-Induced Temporal Lobe Epilepsy.}, journal = {Molecular neurobiology}, volume = {59}, number = {10}, pages = {6429-6446}, pmid = {35962889}, issn = {1559-1182}, support = {311553/2018-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 313769/2018-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 312889/2021-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 315895/2021-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Animals ; *Epilepsy/metabolism ; *Epilepsy, Temporal Lobe/metabolism ; *Gastrointestinal Microbiome ; Lithium ; Pilocarpine ; Rats ; }, abstract = {Evidence supports that the gut microbiota and bacteria-dependent metabolites influence the maintenance of epileptic brain activity. However, the alterations in the gut microbiota between epileptic versus healthy individuals are poorly understood. We used a multi-omic approach to evaluate the changes in the composition of gut metagenome as well in the fecal metabolomic profile in rats before and after being submitted to status epilepticus (SE)-induced temporal lobe epilepsy (TLE). The 16S ribosomal RNA (rRNA) sequencing of fecal samples coupled to bioinformatic analysis revealed taxonomic, compositional, and functional shifts in epileptic rats. The species richness (Chao1 index) was significantly lower in the post-TLE group, and the β-diversity analysis revealed clustering separated from the pre-TLE group. The taxonomic abundance analysis showed a significant increase of phylum Desulfobacterota and a decrease of Patescibacteria in the post-TLE group. The DESEq2 and LEfSe analysis resulted in 18 genera significantly enriched between post-TLE and pre-TLE groups at the genus level. We observed that epileptic rats present a peculiar metabolic phenotype, including a lower concentration of D-glucose and L-lactic acid and a higher concentration of L-glutamic acid and glycine. The microbiota-host metabolic correlation analysis showed that the genera differentially abundant in post-TLE rats are associated with the altered metabolites, especially the proinflammatory Desulfovibrio and Marvinbryantia, which were enriched in epileptic animals and positively correlated with these excitatory neurotransmitters and carbohydrate metabolites. Therefore, our data revealed a correlation between dysbacteriosis in epileptic animals and fecal metabolites that are known to be relevant for maintaining epileptic brain activity by enhancing chronic inflammation, an excitatory-inhibitory imbalance, and/or a metabolic disturbance. These data are promising and suggest that targeting the gut microbiota could provide a novel avenue for preventing and treating acquired epilepsy. However, the causal relationship between these microbial/metabolite components and the SRS occurrence still needs further exploration.}, }
@article {pmid35962839, year = {2023}, author = {Gadoin, E and Desnues, C and d'Orbcastel, ER and Bouvier, T and Auguet, JC and Dagorn, L and Moroh, JL and Adingra, A and Bettarel, Y}, title = {Fishing for the Microbiome of Tropical Tuna.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {742-755}, pmid = {35962839}, issn = {1432-184X}, mesh = {Animals ; *Tuna/microbiology ; Hunting ; Histamine ; Bacteria/genetics ; *Microbiota ; }, abstract = {Although tunas represent a significant part of the global fish economy and a major nutritional resource worldwide, their microbiome still remains poorly documented. Here, we conducted an analysis of the taxonomic composition of the bacterial communities inhabiting the gut, skin, and liver of two most consumed tropical tuna species (skipjack and yellowfin), from individuals caught in the Atlantic and Indian oceans. We hypothesized that each organ harbors a specific microbial assemblage whose composition might vary according to different biotic (sex, species) and/or abiotic (environmental) factors. Our results revealed that the composition of the tuna microbiome was totally independent of fish sex, regardless of the species and ocean considered. Instead, the main determinants of observed diversity were (i) tuna species for the gut and (ii) sampling site for the skin mucus layer and (iii) a combination of both parameters for the liver. Interestingly, 4.5% of all amplicon sequence variants (ASV) were shared by the three organs, highlighting the presence of a core-microbiota whose most abundant representatives belonged to the genera Mycoplasma, Cutibacterium, and Photobacterium. Our study also revealed the presence of a unique and diversified bacterial assemblage within the tuna liver, comprising a substantial proportion of potential histamine-producing bacteria, well known for their pathogenicity and their contribution to fish poisoning cases. These results indicate that this organ is an unexplored microbial niche whose role in the health of both the host and consumers remains to be elucidated.}, }
@article {pmid35962280, year = {2023}, author = {Bizarria, R and de Castro Pietrobon, T and Rodrigues, A}, title = {Uncovering the Yeast Communities in Fungus-Growing Ant Colonies.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {624-635}, pmid = {35962280}, issn = {1432-184X}, support = {2019/03746-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2019/24412-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 305269/2018-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 142396/2019-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {*Fungi ; Yeasts/genetics ; Ecology ; *Ascomycota ; Gardening ; Gardens ; Symbiosis ; Phylogeny ; }, abstract = {Yeast-insect interactions are compelling models to study the evolution, ecology, and diversification of yeasts. Fungus-growing (attine) ants are prominent insects in the Neotropics that evolved an ancient fungiculture of basidiomycete fungi over 55-65 million years, supplying an environment for a hidden yeast diversity. Here we assessed the yeast diversity in the attine ant environment by thoroughly sampling fungus gardens across four out of five ant fungiculture systems: Acromyrmex coronatus and Mycetomoellerius tucumanus standing for leaf-cutting and higher-attine fungicultures, respectively; Apterostigma sp., Mycetophylax sp., and Mycocepurus goeldii as ants from the lower-attine fungiculture. Among the fungus gardens of all fungus-growing ants examined, we found taxonomically unique and diverse microbial yeast communities across the different fungicultures. Ascomycete yeasts were the core taxa in fungus garden samples, with Saccharomycetales as the most frequent order. The genera Aureobasidium, Candida, Papiliotrema, Starmerella, and Sugiyamaella had the highest incidence in fungus gardens. Despite the expected similarity within the same fungiculture system, colonies of the same ant species differed in community structure. Among Saccharomycotina yeasts, few were distinguishable as killer yeasts, with a classical inhibition pattern for the killer phenotype, differing from earlier observations in this environment, which should be further investigated. Yeast mycobiome in fungus gardens is distinct between colonies of the same fungiculture and each ant colony harbors a distinguished and unique yeast community. Fungus gardens of attine ants are emergent environments to study the diversity and ecology of yeasts associated with insects.}, }
@article {pmid35960845, year = {2022}, author = {Amend, AS and Swift, SOI and Darcy, JL and Belcaid, M and Nelson, CE and Buchanan, J and Cetraro, N and Fraiola, KMS and Frank, K and Kajihara, K and McDermot, TG and McFall-Ngai, M and Medeiros, M and Mora, C and Nakayama, KK and Nguyen, NH and Rollins, RL and Sadowski, P and Sparagon, W and Téfit, MA and Yew, JY and Yogi, D and Hynson, NA}, title = {A ridge-to-reef ecosystem microbial census reveals environmental reservoirs for animal and plant microbiomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {33}, pages = {e2204146119}, pmid = {35960845}, issn = {1091-6490}, support = {P20 GM125508/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria ; *Ecosystem ; *Microbiota ; *Plants/microbiology ; }, abstract = {Microbes are found in nearly every habitat and organism on the planet, where they are critical to host health, fitness, and metabolism. In most organisms, few microbes are inherited at birth; instead, acquiring microbiomes generally involves complicated interactions between the environment, hosts, and symbionts. Despite the criticality of microbiome acquisition, we know little about where hosts' microbes reside when not in or on hosts of interest. Because microbes span a continuum ranging from generalists associating with multiple hosts and habitats to specialists with narrower host ranges, identifying potential sources of microbial diversity that can contribute to the microbiomes of unrelated hosts is a gap in our understanding of microbiome assembly. Microbial dispersal attenuates with distance, so identifying sources and sinks requires data from microbiomes that are contemporary and near enough for potential microbial transmission. Here, we characterize microbiomes across adjacent terrestrial and aquatic hosts and habitats throughout an entire watershed, showing that the most species-poor microbiomes are partial subsets of the most species-rich and that microbiomes of plants and animals are nested within those of their environments. Furthermore, we show that the host and habitat range of a microbe within a single ecosystem predicts its global distribution, a relationship with implications for global microbial assembly processes. Thus, the tendency for microbes to occupy multiple habitats and unrelated hosts enables persistent microbiomes, even when host populations are disjunct. Our whole-watershed census demonstrates how a nested distribution of microbes, following the trophic hierarchies of hosts, can shape microbial acquisition.}, }
@article {pmid35960594, year = {2022}, author = {Koistinen, VM and Hedberg, M and Shi, L and Johansson, A and Savolainen, O and Lehtonen, M and Aura, AM and Hanhineva, K and Landberg, R}, title = {Metabolite Pattern Derived from Lactiplantibacillus plantarum-Fermented Rye Foods and In Vitro Gut Fermentation Synergistically Inhibits Bacterial Growth.}, journal = {Molecular nutrition &amp; food research}, volume = {66}, number = {21}, pages = {e2101096}, pmid = {35960594}, issn = {1613-4133}, mesh = {Humans ; Secale/chemistry ; Bread/analysis/microbiology ; Fermentation ; Triticum/chemistry ; *Fermented Foods ; Lactobacillaceae ; *Lactobacillales ; Food Microbiology ; }, abstract = {SCOPE: Fermentation improves many food characteristics using microbes, such as lactic acid bacteria (LAB). Recent studies suggest fermentation may also enhance the health properties, but mechanistic evidence is lacking. The study aims to identify a metabolite pattern reproducibly produced during sourdough and in vitro colonic fermentation of various whole-grain rye products and how it affects the growth of bacterial species of potential importance to health and disease.<br><br>METHODS AND RESULTS: The study uses Lactiplantibacillus plantarum DSMZ 13890 strain, previously shown to favor rye as its substrate. Using LC-MS metabolomics, the study finds seven microbial metabolites commonly produced during the fermentations, including dihydroferulic acid, dihydrocaffeic acid, and five amino acid metabolites, and stronger inhibition is achieved when exposing the bacteria to a mixture of the metabolites in vitro compared to individual compound exposures.<br><br>CONCLUSION: The study suggests that metabolites produced by LAB may synergistically modulate the local microbial ecology, such as in the gut. This could provide new hypotheses on how fermented foods influence human health via diet-microbiota interactions.}, }
@article {pmid35959366, year = {2022}, author = {Lopez, LR and Ahn, JH and Alves, T and Arthur, JC}, title = {Microenvironmental Factors that Shape Bacterial Metabolites in Inflammatory Bowel Disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {934619}, pmid = {35959366}, issn = {2235-2988}, support = {P40 OD010995/OD/NIH HHS/United States ; R01 DK124617/DK/NIDDK NIH HHS/United States ; R21 AI159786/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria ; Dysbiosis/microbiology ; Enterobacteriaceae ; Fibrosis ; *Gastrointestinal Microbiome ; Humans ; Inflammation/microbiology ; *Inflammatory Bowel Diseases/microbiology ; }, abstract = {Inflammatory bowel disease (IBD) is a significant global health problem that involves chronic intestinal inflammation and can involve severe comorbidities, including intestinal fibrosis and inflammation-associated colorectal cancer (CRC). Disease-associated alterations to the intestinal microbiota often include fecal enrichment of Enterobacteriaceae, which are strongly implicated in IBD development. This dysbiosis of intestinal flora accompanies changes in microbial metabolites, shaping host:microbe interactions and disease risk. While there have been numerous studies linking specific bacterial taxa with IBD development, our understanding of microbial function in the context of IBD is limited. Several classes of microbial metabolites have been directly implicated in IBD disease progression, including bacterial siderophores and genotoxins. Yet, our microbiota still harbors thousands of uncharacterized microbial products. In-depth discovery and characterization of disease-associated microbial metabolites is necessary to target these products in IBD treatment strategies. Towards improving our understanding of microbiota metabolites in IBD, it is important to recognize how host relevant factors influence microbiota function. For example, changes in host inflammation status, metal availability, interbacterial community structure, and xenobiotics all play an important role in shaping gut microbial ecology. In this minireview, we outline how each of these factors influences gut microbial function, with a specific focus on IBD-associated Enterobacteriaceae metabolites. Importantly, we discuss how altering the intestinal microenvironment could improve the treatment of intestinal inflammation and associated disorders, like intestinal fibrosis and CRC.}, }
@article {pmid35954765, year = {2022}, author = {Kuczewski, E and Henaff, L and Regard, A and Argaud, L and Lukaszewicz, AC and Rimmelé, T and Cassier, P and Fredenucci, I and Loeffert-Frémiot, S and Khanafer, N and Vanhems, P}, title = {Bacterial Cross-Transmission between Inanimate Surfaces and Patients in Intensive Care Units under Real-World Conditions: A Repeated Cross-Sectional Study.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {15}, pages = {}, pmid = {35954765}, issn = {1660-4601}, mesh = {*Acinetobacter baumannii ; Bacteria ; *Cross Infection/epidemiology/microbiology ; Cross-Sectional Studies ; Humans ; Intensive Care Units ; }, abstract = {Background/Objectives: Contaminated surfaces play an important role in the nosocomial infection of patients in intensive care units (ICUs). This study, conducted in two ICUs at Edouard Herriot Hospital (Lyon, France), aimed to describe rooms' microbial ecology and explore the potential link between environmental contamination and patients' colonization and/or infection. Methods: Environmental samples were realized once monthly from January 2020 to December 2021 on surfaces close to the patient (bedrails, bedside table, and dedicated stethoscope) and healthcare workers' high-touch surfaces, which were distant from the patient (computer, worktop/nurse cart, washbasin, and hydro-alcoholic solution/soap dispenser). Environmental bacteria were compared to the cultures of the patients hospitalized in the sampled room over a period of ± 10 days from the environmental sampling. Results: Overall, 137 samples were collected: 90.7% of the samples close to patients, and 87.9% of the distant ones were positives. Overall, 223 bacteria were isolated, mainly: Enterococcus faecalis (15.7%), Pantoea agglomerans (8.1%), Enterobacter cloacae/asburiae (6.3%), Bacillus cereus and other Bacillus spp (6.3%), Enterococcusfaecium (5.8%), Stenotrophomonas maltophilia (5.4%), and Acinetobacter baumannii (4.9%). Throughout the study, 142 patients were included, of which, n = 67 (47.2%) were infected or colonized by at least one bacterium. In fourteen cases, the same bacterial species were found both in environment and patient samples, with the suspicion of a cross-contamination between the patient-environment (n = 10) and environment-patient (n = 4). Conclusions: In this work, we found a high level of bacterial contamination on ICU rooms' surfaces and described several cases of potential cross-contamination between environment and patients in real-world conditions.}, }
@article {pmid35953677, year = {2023}, author = {Grisnik, M and Grinath, JB and Munafo, JP and Walker, DM}, title = {Functional Redundancy in Bat Microbial Assemblage in the Presence of the White Nose Pathogen.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {713-726}, pmid = {35953677}, issn = {1432-184X}, support = {1016031//National Institute of Food and Agriculture/ ; 32801-00803//Tennessee Wildlife Resources Agency/ ; }, mesh = {Animals ; *Chiroptera/microbiology ; Nose/microbiology ; Antifungal Agents ; Skin/microbiology ; Bacteria/genetics ; }, abstract = {Understanding how host-associated microbial assemblages respond to pathogen invasion has implications for host health. Until recently, most investigations have focused on understanding the taxonomic composition of these assemblages. However, recent studies have suggested that microbial assemblage taxonomic composition is decoupled from its function, with assemblages being taxonomically varied but functionally constrained. The objective of this investigation was to understand how the Tri-colored bat, Perimyotis subflavus cutaneous microbial assemblage responds to fungal pathogen invasion within a functional context. We hypothesized that at a broad scale (e.g., KEGG pathways), there will be no difference in the functional assemblages between the white nose pathogen, Pseudogymnoascus destructans, positive and negative bats; and this pattern will be driven by the functional redundancy of bacterial taxa. At finer scales (e.g., gene models), we postulate differences in function attributed to interactions between bacteria and P. destructans, resulting in the production of antifungal metabolites. To test this, we used a combination of shotgun metagenomic and amplicon sequencing to characterize the bat cutaneous microbial assemblage in the presence/absence of P. destructans. Results showed that while there was a shift in taxonomic assemblage composition between P. destructans positive and negative bats, there was little overall difference in microbial function. Functional redundancy across bacterial taxa was clear at a broad-scale; however, both redundancy and variation in bacterial capability related to defense against pathogens was evident at finer scales. While functionality of the microbial assemblage was largely conserved in relation to P. destructans, the roles of particular functional pathways in resistance to fungal pathogens require further attention.}, }
@article {pmid35948833, year = {2023}, author = {Díaz-Pérez, SP and Solis, CS and López-Bucio, JS and Valdez Alarcón, JJ and Villegas, J and Reyes-De la Cruz, H and Campos-Garcia, J}, title = {Pathogenesis in Pseudomonas aeruginosa PAO1 Biofilm-Associated Is Dependent on the Pyoverdine and Pyocyanin Siderophores by Quorum Sensing Modulation.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {727-741}, pmid = {35948833}, issn = {1432-184X}, support = {256119//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 2.14//Universidad Michoacana de San Nicol&#xe1;s de Hidalgo/ ; }, mesh = {Humans ; Animals ; *Quorum Sensing ; *Siderophores ; Pseudomonas aeruginosa/genetics ; Pyocyanine ; Biofilms ; Virulence Factors/genetics ; Phenazines ; Bacterial Proteins/genetics ; }, abstract = {Pseudomonas aeruginosa is an opportunistic pathogenic bacterium for humans, animals, and plants, through producing different molecular factors such as biofilm, siderophores, and other virulence factors which favor bacterial establishment and infection in the host. In P. aeruginosa PAO1, the production of these factors is regulated by the bacterial quorum sensing (QS) mechanisms. From them, siderophores are involved in iron acquisition, transport, and homeostasis. They are also considered some of the main virulence factors in P. aeruginosa; however, detailed mechanisms to induce bacterial pathogenesis are poorly understood. In this work, through reverse genetics, we evaluated the function of bacterial pathogenesis in the pvd cluster genes, which are required for synthesizing the siderophore pyoverdine (PVD). Single pvdI, pvdJ, pvdL, and double mutant strains were analyzed, and contrary to expected, the pvdL and pvdI mutations increased the concentration of PVD and other phenazines, such as pyocyanin (PYO) and phenazine-1-carboxylic acid (PCA) and also an increased biofilm production and morphology depending on the autoinducer 2-alkyl-4-quinolone (PQS) and the QS molecules acyl-homoserine lactones. Consequently, in the in vivo pathogenicity model of Caenorhabditis elegans, the mutations in pvdI, pvdJ, and pvdL increased the survival of the worms exposed to supernatants or biofilms of the bacterial cultures. However, the double mutant pvdI/pvdJ increased its toxicity in agreeing with the biofilm production, PVD, PYO, and PCA. The findings indicate that the mutations in pvd genes encode non-ribosomal peptide synthetases impacted the biofilm's structure, but suppressively also of the phenazines, confirming that the siderophores contribute to the bacterial establishment and pathogenicity of P. aeruginosa PAO1.}, }
@article {pmid35948832, year = {2023}, author = {Ali, A and Elrys, AS and Liu, L and Xia, Q and Wang, B and Li, Y and Dan, X and Iqbal, M and Zhao, J and Huang, X and Cai, Z}, title = {Deciphering the Synergies of Reductive Soil Disinfestation Combined with Biochar and Antagonistic Microbial Inoculation in Cucumber Fusarium Wilt Suppression Through Rhizosphere Microbiota Structure.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {980-997}, pmid = {35948832}, issn = {1432-184X}, support = {42090060//National Natural Science Foundation of China/ ; U21A20226//National Natural Science Foundation of China/ ; 2021 M691622//Postdoctoral Research Foundation of China/ ; }, mesh = {*Fusarium ; *Cucumis sativus ; Soil/chemistry ; Carbon ; Rhizosphere ; *Microbiota ; Bacteria ; *Bacillus ; Soil Microbiology ; Plant Diseases/prevention &amp; control/microbiology ; }, abstract = {Application of reductive soil disinfestation (RSD), biochar, and antagonistic microbes have become increasingly popular strategies in a microbiome-based approach to control soil-borne diseases. The combined effect of these remediation methods on the suppression of cucumber Fusarium wilt associated with microbiota reconstruction, however, is still unknown. In this study, we applied RSD treatment together with biochar and microbial application of Trichoderma and Bacillus spp. in Fusarium-diseased cucumbers to investigate their effects on wilt suppression, soil chemical changes, microbial abundances, and the rhizosphere communities. The results showed that initial RSD treatment followed by biochar amendment (RSD-BC) and combined applications of microbial inoculation and biochar (RSD-SQR-T37-BC) decreased nitrate concentration and raised soil pH, soil organic carbon (SOC), and ammonium in the treated soils. Under RSD, the applications of Bacillus (RSD-SQR), Trichoderma (RSD-T37), and biochar (RSD-BC) suppressed wilt incidence by 26.8%, 37.5%, and 32.5%, respectively, compared to non-RSD treatments. Moreover, RSD-SQR-T37-BC and RSD-T37 caused greater suppressiveness of Fusarium wilt and F. oxysporum by 57.0 and 33.5%, respectively. Rhizosphere beta diversity and alpha diversity revealed a difference between RSD-treated and non-RSD microbial groups. The significant increase in the abundance, richness, and diversity of bacteria, and the decrease in the abundance and diversity of fungi under RSD-induced treatments attributed to the general suppression. Identified bacterial (Bacillus, Pseudoxanthomonas, Flavobacterium, Flavisolibacter, and Arthrobacter) and fungal (Trichoderma, Chaetomium, Cladosporium, Psathyrella, and Westerdykella) genera were likely the potential antagonists of specific disease suppression for their significant increase of abundances under RSD-treated soils and high relative importance in linear models. This study infers that the RSD treatment induces potential synergies with biochar amendment and microbial applications, resulting in enhanced general-to-specific suppression mechanisms by changing the microbial community composition in the cucumber rhizosphere.}, }
@article {pmid35948105, year = {2022}, author = {Han, T and Wang, K and Rushimisha, IE and Ye, H and Sun, Y and Zhao, L and Weng, L and Li, Y and Li, X}, title = {Influence of biocurrent self-generated by indigenous microorganisms on soil quality.}, journal = {Chemosphere}, volume = {307}, number = {Pt 3}, pages = {135864}, doi = {10.1016/j.chemosphere.2022.135864}, pmid = {35948105}, issn = {1879-1298}, mesh = {Nitrogen ; Phosphorus ; Potassium ; *Soil/chemistry ; *Soil Microbiology ; Water ; }, abstract = {The redox process driven by anaerobic respiration is a link between matter conversion and energy exchange in soil biogeochemistry. Microbial extracellular electron transfer forming biocurrents is a force in element cycling and community living in soil. However, the effect of indigenous microorganisms generating biocurrents on soil quality is unclear. We found that soil biocurrent showed little adverse influence on soil pH, cation exchange capacity, and available nitrogen, phosphorus and potassium and deblocked sequestered organic matter (29%). In addition, the bioelectric field derived from biocurrent obviously forced the migration of mineral elements, which was a supplement to the theory of water-salt transport, providing a new perspective on element transport. Moreover, the soil biocurrent directly regulated the availability of Ca and Fe (increase of 7-fold), indicating that electron transfer plays an important role in weathering and mineralization and thus pedogenesis. From a microbial ecology point of view, the soil bacterial richness and diversity were perfectly restored to their original state when the biocurrent stopped; including bacterial functions; although a temporary enrichment of certain species was observed. The above results provide new insights into the interactions between electron transfer and soil quality and confirm the safety of soil bioelectrochemical technology.}, }
@article {pmid35944516, year = {2023}, author = {Goldman, AD and Kaçar, B}, title = {Very early evolution from the perspective of microbial ecology.}, journal = {Environmental microbiology}, volume = {25}, number = {1}, pages = {5-10}, doi = {10.1111/1462-2920.16144}, pmid = {35944516}, issn = {1462-2920}, mesh = {*Evolution, Molecular ; Genome ; Ecology ; Gene Transfer, Horizontal ; *Microbiota ; Phylogeny ; Biological Evolution ; }, abstract = {The universal ancestor at the root of the species tree of life depicts a population of organisms with a surprising degree of complexity, posessing genomes and translation systems much like that of microbial life today. As the first life forms were most likely to have been simple replicators, considerable evolutionary change must have taken place prior to the last universal common ancestor. It is often assumed that the lack of earlier branches on the tree of life is due to a prevalence of random horizontal gene transfer that obscured the delineations between lineages and hindered their divergence. Therefore, principles of microbial evolution and ecology may give us some insight into these early stages in the history of life. Here, we synthesize the current understanding of organismal and genome evolution from the perspective of microbial ecology and apply these evolutionary principles to the earliest stages of life on Earth. We focus especially on broad evolutionary modes pertaining to horizontal gene transfer, pangenome structure, and microbial mat communities.}, }
@article {pmid35943262, year = {2022}, author = {Laanbroek, HJ and Cassman, NA and Keijzer, RM and Kuramae, EE}, title = {The Stochastic Assembly of Nitrobacter winogradskyi-Selected Microbiomes with Heterotrophs from Sewage Sludge or Grassland Soil.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {17}, pages = {e0078322}, pmid = {35943262}, issn = {1098-5336}, mesh = {Bacteria/genetics ; Bioreactors/microbiology ; Carbon ; Grassland ; *Microbiota ; Nitrification ; Nitrites ; Nitrobacter/genetics ; Nitrogen ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; *Sewage/microbiology ; Soil ; }, abstract = {Chemolitho-autotrophic microorganisms like the nitrite-oxidizing Nitrobacter winogradskyi create an environment for heterotrophic microorganisms that profit from the production of organic compounds. It was hypothesized that the assembly of a community of heterotrophic microorganisms around N. winogradskyi depends on the ecosystem from which the heterotrophs are picked. To test this hypothesis, pure cultures of N. winogradskyi were grown in continuously nitrite-fed bioreactors in a mineral medium free of added organic carbon that had been inoculated with diluted sewage sludge or with a suspension from a grassland soil. Samples for chemical and 16S rRNA gene amplicon analyses were taken after each volume change in the bioreactor. At the end of the enrichment runs, samples for shotgun metagenomics were also collected. Already after two volume changes, the transformations in community structure became less dynamic. The enrichment of heterotrophs from both sewage and soil was highly stochastic and yielded different dominant genera in most of the enrichment runs that were independent of the origin of the inoculum. Hence, the hypothesis had to be refuted. Notwithstanding the large variation in taxonomic community structure among the enrichments, the functional compositions of the communities were statistically not different between soil- and sludge-based enrichments. IMPORTANCE In the process of aerobic nitrification, nitrite-oxidizing bacteria together with ammonia-oxidizing microorganisms convert mineral nitrogen from its most reduced appearance, i.e., ammonium, into its most oxidized form, i.e., nitrate. Because the form of mineral nitrogen has large environmental implications, nitrite-oxidizing bacteria such as Nitrobacter winogradskyi play a central role in the global biogeochemical nitrogen cycle. In addition to this central role, the autotrophic nitrite-oxidizing bacteria also play a fundamental role in the global carbon cycle. They form the basis of heterotrophic food webs, in which the assimilated carbon is recycled. Little is known about the heterotrophic microorganisms that participate in these food webs, let alone their assembly in different ecosystems. This study showed that the assembly of microbial food webs by N. winogradskyi was a highly stochastic process and independent of the origin of the heterotrophic microorganisms, but the functional characteristics of the different food webs were similar.}, }
@article {pmid35942165, year = {2022}, author = {Abid, L and Smiri, M and Federici, E and Lievens, B and Manai, M and Yan, Y and Sadfi-Zouaoui, N}, title = {Diversity of rhizospheric and endophytic bacteria isolated from dried fruit of Ficus carica.}, journal = {Saudi journal of biological sciences}, volume = {29}, number = {9}, pages = {103398}, pmid = {35942165}, issn = {1319-562X}, abstract = {There is currently an increasing demand for the characterization of endophytic bacteria isolated from different parts of plants (rhizosphere, roots, fruit, leaf) in order to improve the organic agriculture practices. The current research was performed to identify both rhizospheric bacteria isolated from the rhizosphere of Ficus carica in three different sites in the north of Tunisia and endophytic bacteria isolated from dried figs. We then characterized them for a diversity of plant growth-promoting (PGP) activities. A collection of 120 isolates from rhizospheric soil and 9 isolates from dried figs was obtained and purified. 16SrDNA gene amplification of rhizospheric bacteria revealed significant diversity and allowed for the assigning of the isolates to 6 phyla: Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Representative strains of the collection (90 strains) were tested for numerous PGP activities and resistance to abiotic stresses. The most common PGP trait for all bacteria from the three regions was siderophore production (62%), followed by cellulase (38%), then protease activity (37%), then by lipases activity (17%) and lastly by solubilization of phosphates (9%). Twenty -three strains that showed most PGP traits were selected, 8 strains presented 12 or more, and 15 strains displayed between 7 and 11 of 17 PGP activities. The majority of the isolates manifested a possible adaptation to abiotic stress and unfavorable environments. PCR-DGGE analysis of soil rhizosphere of the three sites allowed also for the acquisition of a Cluster analysis of rhizospheric bacterial communities. Our current study identified and characterized for the first time in Tunisia rhizospheric and endophytic bacteria from dried fruit of Ficus carica.}, }
@article {pmid35941249, year = {2023}, author = {de La Harpe, M and Gütlin, A and Chiang, C and Dietemann, V and Dainat, B}, title = {Influence of Honey bee Nutritive Jelly Type and Dilution on its Bactericidal Effect on Melissococcus plutonius, the Etiological Agent of European Foulbrood.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {617-623}, pmid = {35941249}, issn = {1432-184X}, mesh = {Bees ; Animals ; Larva/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Enterococcaceae ; Bacteria ; }, abstract = {To defend themselves against pathogenic microorganisms, honey bees resort to social immunity mechanisms, such as the secretion of antibiotic compounds in the jelly they feed to their larvae. Whereas the bactericidal activity of jelly fed to queen larvae is well studied, little is known about the bioactivity of compositionally different jelly fed to worker larvae. However, the numerous worker larvae are likely to drive the spread of the microorganism and influence its virulence and pathogenesis. Diluted jelly or extracts are mostly used for jelly bioactivity tests, which may bias the evaluation of the pathogen's resistance and virulence. Here, we compared the bactericidal effect of pure and diluted jellies destined for queen and worker larvae on Melissococcus plutonius, the etiological agent of the European foulbrood (EFB) disease of honey bees, and on a secondary invader bacteria, Enterococcus faecalis. We tested three strains of M. plutonius with varying virulence to investigate the association between resistance to antibacterial compounds and virulence. The resistance of the bacteria varied but was not strictly correlated with their virulence and was lower in pure than in diluted jelly. Resistance differed according to whether the jelly was destined for queen or worker larvae, with some strains being more resistant to queen jelly and others to worker jelly. Our results provide a biologically realistic assessment of host defenses via nutritive jelly and contribute to a better understanding of the ecology of M. plutonius and of secondary invaders bacteria in the honey bee colony environment, thus shedding light on the selective forces affecting their virulence and on their role in EFB pathogenesis.}, }
@article {pmid35940746, year = {2022}, author = {Xian, S and Zhong, H and Yi, B and Liu, X and Shen, G and Li, M and Zhang, Z and Luo, Q and Li, S and Zhou, M and Xu, F and Chen, A}, title = {Identification of pellicle formation related microorganisms in traditional Sichuan paocai through metagenomic sequence and the effects of Baijiu/Salt on pellicle and volatile components.}, journal = {Food research international (Ottawa, Ont.)}, volume = {159}, number = {}, pages = {111130}, doi = {10.1016/j.foodres.2022.111130}, pmid = {35940746}, issn = {1873-7145}, mesh = {Fermentation ; *Lactobacillus/metabolism ; Metagenome ; Metagenomics ; Pichia ; *Saccharomycetales ; }, abstract = {The occurrence of pellicle on the surface of paocai brine is a common undesirable phenomenon during the multi-rounds of paocai fermentation, which is mainly caused by the growth of microorganisms related to pellicle formation. But the detailed information on these microorganisms and volatile components produced by them, as well as the changes of the microorganisms during the process of paocai recovery, are still rare in the literature. Therefore, the purpose of this study was (1) to analyze the pellicle formation related microorganisms by comparing the differential microorganisms in initial brine and the brine when pellicle occurred through metagenomic sequencing technology, (2) to explore the changes of microorganisms in the fermentation system after addition Baijiu and/or salt, and (3) to further detect the VOCs in paocai samples by gas chromatography-mass spectrometry (GC-MS). The relationship between VOCs and the selected marker microorganisms was also determined. The results showed that the diversity of fungi was increased when pellicle formed, the pellicle formation related microorganisms mainly belonged to six genus, including Kazachstania, Lactobacillus, Pichia, Candida, Lachancea, and Saccharomyces. Apart from the unknown function and basic life activities of microorganisms, the metabolic activities of these pellicle formation related microorganisms were mainly carbohydrate transport and metabolism, and amino acid transport and metabolism. The growth of pellicle formation related microorganisms could be inhibited by adding Baijiu (1.5% v/v), but the addition of salt (7% salt (w/v) did not promote this inhibitory effect. Through PCA analysis, it was found that the VOCs of paocai were significantly affected by adding Baijiu and Baijiu and salt. The undesirable smell at the beginning of pellicle formation may be related to Propanoic acid, hexyl ester, 1,3-Dimethyl-1-cyclohexene, Oxime-, methoxy-phenyl- and Phenylethyl Alcohol.}, }
@article {pmid35940271, year = {2022}, author = {Selak, L and Marković, T and Pjevac, P and Orlić, S}, title = {Microbial marker for seawater intrusion in a coastal Mediterranean shallow Lake, Lake Vrana, Croatia.}, journal = {The Science of the total environment}, volume = {849}, number = {}, pages = {157859}, doi = {10.1016/j.scitotenv.2022.157859}, pmid = {35940271}, issn = {1879-1026}, mesh = {Croatia ; *Ecosystem ; *Lakes ; RNA, Ribosomal, 16S ; Salinity ; Seawater ; Sulfates ; Sulfur ; Water ; }, abstract = {Climate change-induced rising sea levels and prolonged dry periods impose a global threat to the freshwater scarcity on the coastline: salinization. Lake Vrana is the largest surface freshwater resource in mid-Dalmatia, while the local springs are heavily used in agriculture. The karstified carbonate ridge that separates this shallow lake from the Adriatic Sea enables seawater intrusion if the lakes' precipitation-evaporation balance is disturbed. In this study, the impact of anthropogenic activities and drought exuberated salinization on microbial communities was tracked in Lake Vrana and its inlets, using 16S rRNA gene sequencing. The lack of precipitation and high water temperatures in summer months introduced an imbalance in the water regime of the lake, allowing for seawater intrusion, mainly via the karst conduit Jugovir. The determined microbial community spatial differences in the lake itself and the main drainage canals were driven by salinity, drought, and nutrient loading. Particle-associated and free-living microorganisms both strongly responded to the ecosystem perturbations, and their co-occurrence was driven by the salinization event. Notably, a bloom of halotolerant taxa, predominant the sulfur-oxidizing genus Sulfurovum, emerged with increased salinity and sulfate concentrations, having the potential to be used as an indicator for salinization of shallow coastal lakes. Following summer salinization, lake water column homogenization took from a couple of weeks up to a few months, while the entire system displayed increased salinity despite increased precipitation. This study represents a valuable contribution to understanding the impact of the Freshwater Salinization Syndrome on Mediterranean lakes' microbial communities and the ecosystem resilience.}, }
@article {pmid35940233, year = {2022}, author = {Fox, A and Widmer, F and Lüscher, A}, title = {Soil microbial community structures are shaped by agricultural systems revealing little temporal variation.}, journal = {Environmental research}, volume = {214}, number = {Pt 3}, pages = {113915}, pmid = {35940233}, issn = {1096-0953}, mesh = {Agriculture ; Bacteria ; Fungi ; *Microbiota ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {Many studies in soil microbial ecology are undertaken with a single sampling event, with the influence of temporal progression rarely being considered. Under field conditions, soil samples were taken from different agricultural systems; a sown grassland to maize rotation (MC), an intensively managed permanent grassland (INT), as well as extensively managed permanent grasslands with high (EXT_HP), low to sufficient (EXT_LP) and deficient available P (EXT_DP), six times throughout the 2017 growing season. Thus, this study aimed to determine if any differences in soil microbiome structures between both sharply contrasting (MC - INT - EXT), slightly differing (EXT_HP - EXT_DP) and quite similar (EXT_HP - EXT_LP and EXT_LP - EXT_DP) agricultural systems persist through changing growth conditions within the growing season. For both fungal and bacterial community structure, the influence of agricultural system (CV = 0.256, P < 0.001 and CV = 0.145, P < 0.01, respectively) was much greater than that of temporal progression (√CV = 0.065 and 0.042, respectively, both P < 0.001). Importantly, nearly all agricultural systems persistently harbored significantly distinct fungal community structures across each of the six sampling events (all at least P < 0.05). There were not as many pairwise differences in bacterial community structure between the agricultural systems, but some did persist (MC and EXT_HP ∼ EXT_DP, all P < 0.001). Additionally, persistent indicator fungal OTUs (IndVal >0.7, P ≤ 0.05) associated to each agricultural system (except EXT_LP) were found in each of the six sampling events. These results highlight the temporal stability of pairwise differences in soil microbiome structures between established agricultural systems through changing plant growth conditions, even between those with a comparable management regime. This is a highly relevant finding in informing the sampling strategy of studies in soil microbial ecology as well as for designing efficient soil biodiversity monitoring systems.}, }
@article {pmid35938717, year = {2022}, author = {Okazaki, Y and Nakano, SI and Toyoda, A and Tamaki, H}, title = {Long-Read-Resolved, Ecosystem-Wide Exploration of Nucleotide and Structural Microdiversity of Lake Bacterioplankton Genomes.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0043322}, pmid = {35938717}, issn = {2379-5077}, mesh = {*Lakes/microbiology ; Ecosystem ; Nucleotides ; Metagenome ; Bacteria/genetics ; *Bacteriophages/genetics ; }, abstract = {Reconstruction of metagenome-assembled genomes (MAGs) has become a fundamental approach in microbial ecology. However, a MAG is hardly complete and overlooks genomic microdiversity because metagenomic assembly fails to resolve microvariants among closely related genotypes. Aiming at understanding the universal factors that drive or constrain prokaryotic genome diversification, we performed an ecosystem-wide high-resolution metagenomic exploration of microdiversity by combining spatiotemporal (2 depths × 12 months) sampling from a pelagic freshwater system, high-quality MAG reconstruction using long- and short-read metagenomic sequences, and profiling of single nucleotide variants (SNVs) and structural variants (SVs) through mapping of short and long reads to the MAGs, respectively. We reconstructed 575 MAGs, including 29 circular assemblies, providing high-quality reference genomes of freshwater bacterioplankton. Read mapping against these MAGs identified 100 to 101,781 SNVs/Mb and 0 to 305 insertions, 0 to 467 deletions, 0 to 41 duplications, and 0 to 6 inversions for each MAG. Nonsynonymous SNVs were accumulated in genes potentially involved in cell surface structural modification to evade phage recognition. Most (80.2%) deletions overlapped with a gene coding region, and genes of prokaryotic defense systems were most frequently (>8% of the genes) overlapped with a deletion. Some such deletions exhibited a monthly shift in their allele frequency, suggesting a rapid turnover of genotypes in response to phage predation. MAGs with extremely low microdiversity were either rare or opportunistic bloomers, suggesting that population persistency is key to their genomic diversification. The results concluded that prokaryotic genomic diversification is driven primarily by viral load and constrained by a population bottleneck. IMPORTANCE Identifying intraspecies genomic diversity (microdiversity) is crucial to understanding microbial ecology and evolution. However, microdiversity among environmental assemblages is not well investigated, because most microbes are difficult to culture. In this study, we performed cultivation-independent exploration of bacterial genomic microdiversity in a lake ecosystem using a combination of short- and long-read metagenomic analyses. The results revealed the broad spectrum of genomic microdiversity among the diverse bacterial species in the ecosystem, which has been overlooked by conventional approaches. Our ecosystem-wide exploration further allowed comparative analysis among the genomes and genes and revealed factors behind microbial genomic diversification, namely, that diversification is driven primarily by resistance against viral infection and constrained by the population size.}, }
@article {pmid35937361, year = {2022}, author = {Cardini, U and Marín-Guirao, L and Montilla, LM and Marzocchi, U and Chiavarini, S and Rimauro, J and Quero, GM and Petersen, JM and Procaccini, G}, title = {Nested interactions between chemosynthetic lucinid bivalves and seagrass promote ecosystem functioning in contaminated sediments.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {918675}, pmid = {35937361}, issn = {1664-462X}, abstract = {In seagrass sediments, lucinid bivalves and their chemoautotrophic bacterial symbionts consume H2S, relying indirectly on the plant productivity for the presence of the reduced chemical. Additionally, the role of lucinid bivalves in N provisioning to the plant (through N2 fixation by the symbionts) was hypothesized. Thus, lucinids may contribute to sediment detoxification and plant fitness. Seagrasses are subject to ever-increasing human pressure in coastal environments. Here, disentangling nested interactions between chemosynthetic lucinid bivalves and seagrass exposed to pollution may help to understand seagrass ecosystem dynamics and to develop successful seagrass restoration programs that consider the roles of animal-microbe symbioses. We evaluated the capacity of lucinid bivalves (Loripes orbiculatus) to promote nutrient cycling and seagrass (Cymodocea nodosa) growth during a 6-week mesocosm experiment. A fully crossed design was used to test for the effect of sediment contamination (metals, nutrients, and hydrocarbons) on plant and bivalve (alone or interacting) fitness, assessed by mortality, growth, and photosynthetic efficiency, and for the effect of their nested interaction on sediment biogeochemistry. Plants performed better in the contaminated sediment, where a larger pool of dissolved nitrogen combined with the presence of other trace elements allowed for an improved photosynthetic efficiency. In fact, pore water nitrogen accumulated during the experiment in the controls, while it was consumed in the contaminated sediment. This trend was accentuated when lucinids were present. Concurrently, the interaction between clams and plants benefitted both organisms and promoted plant growth irrespective of the sediment type. In particular, the interaction with lucinid clams resulted in higher aboveground biomass of C. nodosa in terms of leaf growth, leaf surface, and leaf biomass. Our results consolidate the notion that nested interactions involving animal-microbe associations promote ecosystem functioning, and potentially help designing unconventional seagrass restoration strategies that exploit chemosynthetic symbioses.}, }
@article {pmid35937348, year = {2022}, author = {Zhu, M and Liu, Y and Cai, P and Duan, X and Sang, S and Qiu, Z}, title = {Jasmonic acid pretreatment improves salt tolerance of wheat by regulating hormones biosynthesis and antioxidant capacity.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {968477}, pmid = {35937348}, issn = {1664-462X}, abstract = {Salt stress is a severe environmental factor that detrimentally affects wheat growth and production worldwide. Previous studies illustrate that exogenous jasmonic acid (JA) significantly improved salt tolerance in plants. However, little is known about the underlying molecular mechanisms of JA induced physiochemical changes in wheat seedlings under salt stress conditions. In this study, biophysiochemical and transcriptome analysis was conducted to explore the mechanisms of exogenous JA induced salt tolerance in wheat. Exogenous JA increased salt tolerance of wheat seedlings by alleviating membrane lipid oxidation, improving root morphology, enhancing the contents of ABA, JA and SA and increasing relative water content. In the RNA-seq profiles, we identified a total of 54,263 unigenes and 1,407 unigenes showed differentially expressed patterns in JA pretreated wheat seedlings exposed to salt stress comparing to those with salt stress alone. Subsequently, gene ontology (GO) and KEGG pathway enrichment analysis characterized that DEGs involved in linoleic acid metabolism and plant hormone signal transduction pathways were up-regulated predominantly in JA pretreated wheat seedlings exposed to salt stress. We noticed that genes that involved in antioxidative defense system and that encoding transcription factors were mainly up- or down-regulated. Moreover, SOD, POD, CAT and APX activities were increased in JA pretreated wheat seedlings exposed to salt stress, which is in accordance with the transcript profiles of the relevant genes. Taken together, our results demonstrate that the genes and enzymes involved in physiological and biochemical processes of antioxidant system, plant hormones and transcriptional regulation contributed to JA-mediated enhancement of salt tolerance in wheat. These findings will facilitate the elucidation of the potential molecular mechanisms associated with JA-dependent amelioration of salt stress in wheat and lay theoretical foundations for future studies concerning the improvement of plant tolerance to abiotic environmental stresses.}, }
@article {pmid35935241, year = {2022}, author = {Bergmann, GE and Leveau, JHJ}, title = {A metacommunity ecology approach to understanding microbial community assembly in developing plant seeds.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {877519}, pmid = {35935241}, issn = {1664-302X}, abstract = {Microorganisms have the potential to affect plant seed germination and seedling fitness, ultimately impacting plant health and community dynamics. Because seed-associated microbiota are highly variable across individual plants, plant species, and environments, it is challenging to identify the dominant processes that underlie the assembly, composition, and influence of these communities. We propose here that metacommunity ecology provides a conceptually useful framework for studying the microbiota of developing seeds, by the application of metacommunity principles of filtering, species interactions, and dispersal at multiple scales. Many studies in seed microbial ecology already describe individual assembly processes in a pattern-based manner, such as correlating seed microbiome composition with genotype or tracking diversity metrics across treatments in dispersal limitation experiments. But we see a lot of opportunities to examine understudied aspects of seed microbiology, including trait-based research on mechanisms of filtering and dispersal at the micro-scale, the use of pollination exclusion experiments in macro-scale seed studies, and an in-depth evaluation of how these processes interact via priority effect experiments and joint species distribution modeling.}, }
@article {pmid35933499, year = {2022}, author = {Ray, AE and Zaugg, J and Benaud, N and Chelliah, DS and Bay, S and Wong, HL and Leung, PM and Ji, M and Terauds, A and Montgomery, K and Greening, C and Cowan, DA and Kong, W and Williams, TJ and Hugenholtz, P and Ferrari, BC}, title = {Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts.}, journal = {The ISME journal}, volume = {16}, number = {11}, pages = {2547-2560}, pmid = {35933499}, issn = {1751-7370}, support = {FT170100341//Department of Education and Training | Australian Research Council (ARC)/ ; APP5191146//Department of Health | National Health and Medical Research Council (NHMRC)/ ; }, mesh = {Carbon Cycle ; *Hydrogenase/genetics ; Ribulose-Bisphosphate Carboxylase ; Soil/chemistry ; Soil Microbiology ; Verrucomicrobia ; }, abstract = {Cold desert soil microbiomes thrive despite severe moisture and nutrient limitations. In Eastern Antarctic soils, bacterial primary production is supported by trace gas oxidation and the light-independent RuBisCO form IE. This study aims to determine if atmospheric chemosynthesis is widespread within Antarctic, Arctic and Tibetan cold deserts, to identify the breadth of trace gas chemosynthetic taxa and to further characterize the genetic determinants of this process. H2 oxidation was ubiquitous, far exceeding rates reported to fulfill the maintenance needs of similarly structured edaphic microbiomes. Atmospheric chemosynthesis occurred globally, contributing significantly (p < 0.05) to carbon fixation in Antarctica and the high Arctic. Taxonomic and functional analyses were performed upon 18 cold desert metagenomes, 230 dereplicated medium-to-high-quality derived metagenome-assembled genomes (MAGs) and an additional 24,080 publicly available genomes. Hydrogenotrophic and carboxydotrophic growth markers were widespread. RuBisCO IE was discovered to co-occur alongside trace gas oxidation enzymes in representative Chloroflexota, Firmicutes, Deinococcota and Verrucomicrobiota genomes. We identify a novel group of high-affinity [NiFe]-hydrogenases, group 1m, through phylogenetics, gene structure analysis and homology modeling, and reveal substantial genetic diversity within RuBisCO form IE (rbcL1E), and high-affinity 1h and 1l [NiFe]-hydrogenase groups. We conclude that atmospheric chemosynthesis is a globally-distributed phenomenon, extending throughout cold deserts, with significant implications for the global carbon cycle and bacterial survival within environmental reservoirs.}, }
@article {pmid35933411, year = {2022}, author = {Zhang, H and Wang, M and Wang, H and Chen, H and Cao, L and Zhong, Z and Lian, C and Zhou, L and Li, C}, title = {Metagenome sequencing and 768 microbial genomes from cold seep in South China Sea.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {480}, pmid = {35933411}, issn = {2052-4463}, support = {42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42076091//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42076091//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Archaea/genetics ; Bacteria/genetics ; *Genome, Microbial ; Geologic Sediments/microbiology ; *Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Cold seep microbial communities are fascinating ecosystems on Earth which provide unique models for understanding the living strategies in deep-sea distinct environments. In this study, 23 metagenomes were generated from samples collected in the Site-F cold seep field in South China Sea, including the sea water closely above the invertebrate communities, the cold seep fluids, the fluids under the invertebrate communities and the sediment column around the seep vent. By binning tools, we retrieved a total of 768 metagenome assembled genome (MAGs) that were estimated to be >60% complete. Of the MAGs, 61 were estimated to be >90% complete, while an additional 105 were >80% complete. Phylogenomic analysis revealed 597 bacterial and 171 archaeal MAGs, of which nearly all were distantly related to known cultivated isolates. In the 768 MAGs, the abundant Bacteria in phylum level included Proteobacteria, Desulfobacterota, Bacteroidota, Patescibacteria and Chloroflexota, while the abundant Archaea included Asgardarchaeota, Thermoplasmatota, and Thermoproteota. These results provide a dataset available for further interrogation of deep-sea microbial ecology.}, }
@article {pmid35933162, year = {2022}, author = {Kumar, S and Kumar, V and Ambika, AAA and Nag, D and Kumar, V and Darnal, S and Thakur, V and Patial, V and Singh, D}, title = {Microbial pigments: Learning from Himalayan perspective to industrial applications.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {49}, number = {5}, pages = {}, pmid = {35933162}, issn = {1476-5535}, abstract = {Pigments are an essential part of life on earth, ranging from microbes to plants and humans. The physiological and environmental cues induce microbes to produce a broad spectrum of pigments, giving them adaptation and survival advantages. Microbial pigments are of great interest due to their natural origin, diverse biological activities, and wide applications in the food, pharmaceutical, cosmetics, and textile industries. Despite noticeable research on pigment-producing microbes, commercial successes are scarce, primarily from higher, remote, and inaccessible Himalayan niches. Therefore, substantial bioprospection integrated with advanced biotechnological strategies is required to commercialize microbial pigments successfully. The current review elaborates on pigment-producing microbes from a Himalayan perspective, offering tremendous opportunities for industrial applications. Additionally, it illustrates the ecological significance of microbial pigments and emphasizes the current status and prospects of microbial pigments production above the test tube scale.}, }
@article {pmid35932316, year = {2023}, author = {Pedrolo, AM and Matteoli, FP and Soares, CRFS and Arisi, ACM}, title = {Comparative Genomics Reveal the High Conservation and Scarce Distribution of Nitrogen Fixation nif Genes in the Plant-Associated Genus Herbaspirillum.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {563-574}, pmid = {35932316}, issn = {1432-184X}, mesh = {*Herbaspirillum/genetics/metabolism ; Nitrogen Fixation/genetics ; Phylogeny ; Genomics ; }, abstract = {The genus Herbaspirillum gained the spotlight due to the several reports of diazotrophic strains and promising results in plant-growth field assays. However, as diversity exploration of Herbaspirillum species gained momentum, it became clearer that the plant beneficial lifestyle was not the only form of ecological interaction in this genus, due to reports of phytopathogenesis and nosocomial infections. Here we performed a deep search across all publicly available Herbaspirillum genomes. Using a robust core genome phylogeny, we have found that all described species are well delineated, being the only exception H. aquaticum and H. huttiense clade. We also uncovered that the nif genes are only highly prevalent in H. rubrisubalbicans; however, irrespective to the species, all nif genes share the same gene arrangement with high protein identity, and are present in only two main types, in inverted strands. By means of a NifHDKENB phylogenetic tree, we have further revealed that the Herbaspirillum nif sequences may have been acquired from the same last common ancestor belonging to the Nitrosomonadales order.}, }
@article {pmid35931774, year = {2023}, author = {Gómez-Molina, E and Sánchez, S and Puig-Pey, M and García-Barreda, S}, title = {Intraspecific Competition Results in Reduced Evenness of Tuber melanosporum Mating-Type Abundance from the Nursery Stage.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {253-260}, pmid = {35931774}, issn = {1432-184X}, support = {Collaboration agreement for the operation of CIET//Diputaci&#xf3;n de Huesca/ ; }, mesh = {*Ascomycota/genetics ; *Mycorrhizae ; Reproduction ; Seedlings/microbiology ; *Quercus/microbiology ; }, abstract = {The highly prized black truffle is a fungus mostly harvested in orchards planted with mycorrhizal seedlings. It is an obligatory outcrossing fungus with a single MAT locus containing two alternative mating-type idiomorphs. In the orchards, at the mycorrhizal level, these mating types are frequently spatially segregated. Some studies found that this segregation was pronounced from the nursery stage, whereas others did not find such a marked segregation. Besides, information on the host tree species and nursery conditions used in Spain, one of the main truffle-producing countries, are very scarce. In this study, we investigated the temporal dynamics of mating types in nursery seedlings of Quercus ilex and Quercus faginea, as well as the influence of cultural conditions in the nursery. Our results indicated that at the plant level, there was a trend for one of the mating types to dominate over the other from the first to the second year in the nursery, in both host species and both nursery conditions tested. However, this segregation process was not so sharp as previously reported. Our results support the hypothesis that intraspecific competition results in reduced evenness of mating-type abundance from the nursery stage, although almost all seedlings maintained both mating types and, at the seedling batch scale, the occurrence of both mating types was roughly balanced.}, }
@article {pmid35930073, year = {2023}, author = {Morales-Poole, JR and de Vega, C and Tsuji, K and Jacquemyn, H and Junker, RR and Herrera, CM and Michiels, C and Lievens, B and Álvarez-Pérez, S}, title = {Sugar Concentration, Nitrogen Availability, and Phylogenetic Factors Determine the Ability of Acinetobacter spp. and Rosenbergiella spp. to Grow in Floral Nectar.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {377-391}, pmid = {35930073}, issn = {1432-184X}, support = {742964//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; RYC2018-023847-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; DFG//Deutsche Forschungsgemeinschaft/ ; JU2856/2-2//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Bees ; Animals ; *Plant Nectar/analysis/chemistry/physiology ; Phylogeny ; *Sugars/analysis ; Carbohydrates/analysis ; Flowers/microbiology ; Glucose ; Sucrose/analysis ; Fructose/analysis ; Enterobacteriaceae/genetics ; }, abstract = {The floral nectar of angiosperms harbors a variety of microorganisms that depend predominantly on animal visitors for their dispersal. Although some members of the genus Acinetobacter and all currently known species of Rosenbergiella are thought to be adapted to thrive in nectar, there is limited information about the response of these bacteria to variation in the chemical characteristics of floral nectar. We investigated the growth performance of a diverse collection of Acinetobacter (n = 43) and Rosenbergiella (n = 45) isolates obtained from floral nectar and the digestive tract of flower-visiting bees in a set of 12 artificial nectars differing in sugar content (15% w/v or 50% w/v), nitrogen content (3.48/1.67 ppm or 348/167 ppm of total nitrogen/amino nitrogen), and sugar composition (only sucrose, 1/3 sucrose + 1/3 glucose + 1/3 fructose, or 1/2 glucose + 1/2 fructose). Growth was only observed in four of the 12 artificial nectars. Those containing elevated sugar concentration (50% w/v) and low nitrogen content (3.48/1.67 ppm) were limiting for bacterial growth. Furthermore, phylogenetic analyses revealed that the ability of the bacteria to grow in different types of nectar is highly conserved between closely related isolates and genotypes, but this conservatism rapidly vanishes deeper in phylogeny. Overall, these results demonstrate that the ability of Acinetobacter spp. and Rosenbergiella spp. to grow in floral nectar largely depends on nectar chemistry and bacterial phylogeny.}, }
@article {pmid35929359, year = {2022}, author = {Mandal, S and Kundu, S and Uddin, MR and Das, P and Paul, P and Roy, P and Tribedi, P and Sahoo, P}, title = {Identification of a novel quinoline-based UV-protective pigment from a psychrotrophic Arctic bacterium.}, journal = {Journal of applied microbiology}, volume = {133}, number = {5}, pages = {3059-3068}, doi = {10.1111/jam.15760}, pmid = {35929359}, issn = {1365-2672}, mesh = {RNA, Ribosomal, 16S/genetics ; Sodium Chloride ; Methanol ; Acetone ; Bacteria/genetics ; *Anti-Infective Agents ; *Quinolines/pharmacology ; Soil ; Phylogeny ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Arctic Regions ; Bacterial Typing Techniques ; }, abstract = {AIMS: Psychrotrophs are extremophilic microorganisms that grow optimally in low temperature having many unique bioactive molecules of biotechnological applications. In this study, we characterized a pigment from an arctic bacterium with protective activity towards UV exposure.<br><br>METHODS AND RESULTS: The present research reports isolation and characterization of a psychrotrophic bacteria, RSAP2, from the soil sample of NyAlesund (78&#xb0;56"N, 11&#xb0;54"E), Svalbard, Norway. The strain showed closest 16S rRNA gene sequence similarity (99.9%) with Kocuria indica NIO-1021. RSAP2 is a Gram-positive, coccoid aerobe which produces a yellow pigment. The optimal parameters for pigment production while grown in LB medium were 3% (w/v) NaCl and 4&#x2009;days of incubation of the culture at 20&#xb0;C and pH&#xa0;9 with shaking (180&#x2009;rpm). The pigment was extracted in methanol and acetone (2:1) and further purified through column chromatography. It was characterized by mass spectrometry, UV-visible, fluorescence, IR, [1] H NMR, [13] C NMR spectroscopy and CHNS/O analysis. The pigment has a molecular weight of about 258 daltons and the molecular formula was determined as C15 H18 N2 O2 and is a quinoline derivative. We show that the pigment can protect Escherichia coli against UV-mediated mutagenesis. We further demonstrate that the pigment displays a significant antimicrobial effect and in sublethal concentrations it impairs biofilm formation ability of the model organism Staphylococcus aureus.<br><br>CONCLUSIONS: The pigment of a psychrotrophic Arctic bacterium, most likely a strain of K. indica, was purified and its chemical structure was determined. The quinoline-based pigment has the ability to protect live cells from UV induced damage.<br><br>Analysis and characterization of this newly isolated quinoline-based pigment is a potential candidate for future application in skin care products.}, }
@article {pmid35927589, year = {2023}, author = {Zhu, W and Zhu, M and Liu, X and Xia, J and Yin, H and Li, X}, title = {Different Responses of Bacteria and Microeukaryote to Assembly Processes and Co-occurrence Pattern in the Coastal Upwelling.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {174-186}, pmid = {35927589}, issn = {1432-184X}, support = {42076108//the National Natural Science Foundation of China/ ; 42161144006 or 3511/21//the National Natural Science Foundation of China/ ; 2021RC169//the Natural Science Foundation of Hainan Province/ ; ZDYF2020177//the Hainan Provincial Key Research and Development Program/ ; KYQD(ZR)1805//the Foundation of Hainan University/ ; }, mesh = {*Bacteria/genetics ; *Microbiota ; Phylogeny ; Eukaryota ; }, abstract = {Upwelling may generate unique hydrological and environmental heterogeneity, leading to enhanced diffusion to reshape microbial communities. However, it remains largely unknown how different microbial taxa respond to highly complex and dynamic upwelling systems. In the present study, geographic patterns and co-occurrence network of different microbial communities in response to upwelling were examined. Our results showed that coastal upwelling shaped prokaryotic and eukaryotic microbial community and decreased their diversity. In addition, bacteria and microeukaryote had similar biogeographical patterns with distinct assembly mechanisms. The impact of stochastic processes on bacteria was significantly stronger compared with microeukaryote in upwelling. Lower network complexity but more frequent interaction was found in upwelling microbial co-occurrence. However, the upwelling environment increased the robustness and modularity of bacterial network, while eukaryotic network was just the opposite. Co-occurrence networks of bacteria and microeukaryote showed significant distance-decay patterns, while the bacterial network had a stronger spatial variation. Temperature and salinity were the strongest environmental factors affecting microbial coexistence, whereas the topological characteristics of bacterial and eukaryotic networks had different responses to the upwelling environment. These findings expanded our understanding of biogeographic patterns of microbial community and ecological network and the underlying mechanisms of different microbial taxa in upwelling.}, }
@article {pmid35927588, year = {2023}, author = {He, D and Guo, Z and Shen, W and Ren, L and Sun, D and Yao, Q and Zhu, H}, title = {Fungal Communities Are More Sensitive to the Simulated Environmental Changes than Bacterial Communities in a Subtropical Forest: the Single and Interactive Effects of Nitrogen Addition and Precipitation Seasonality Change.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {521-535}, pmid = {35927588}, issn = {1432-184X}, mesh = {Ecosystem ; *Mycobiome ; Nitrogen/analysis ; Forests ; Bacteria/genetics ; *Microbiota ; Soil/chemistry ; China ; Soil Microbiology ; Fungi/genetics ; }, abstract = {Increased nitrogen deposition (N factor) and changes in precipitation patterns (W factor) can greatly impact soil microbial communities in tropical/subtropical forests. Although knowledge about the effects of a single factor on soil microbial communities is growing rapidly, little is understood about the interactive effects of these two environmental change factors. In this study, we investigated the responses of soil bacterial and fungal communities to the short-term simulated environmental changes (nitrogen addition, precipitation seasonality change, and their combination) in a subtropical forest in South China. The interaction between N and W factors was detected significant for affecting some soil physicochemical properties (such as pH, soil water, and NO3[-] contents). Fungi were more susceptible to treatment than bacteria in a variety of community traits (alpha, beta diversity, and network topological features). The N and W factors act antagonistically to affect fungal alpha diversity, and the interaction effect was detected significant for the dry season. The topological features of the meta-community (containing both bacteria and fungi) network overrode the alpha and beta diversity of bacterial or fungal communities in explaining the variation of soil enzyme activities. The associations between Ascomycota fungi and Gammaproteobacteria or Alphaproteobacteria might be important in mediating the inter-kingdom interactions. In summary, our results suggested that fungal communities were more sensitive to N and W factors (and their interaction) than bacterial communities, and the treatments' effects were more prominent in the dry season, which may have great consequences in soil processes and ecosystem functions in subtropical forests.}, }
@article {pmid35925231, year = {2023}, author = {Chinta, YD and Araki, H}, title = {Cover Crop Amendments and Lettuce Plant Growth Stages Alter Rhizobacterial Properties and Roles in Plant Performance.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {446-459}, pmid = {35925231}, issn = {1432-184X}, support = {18H02310//japan society for the promotion of science/ ; }, mesh = {*Lactuca/genetics/microbiology ; RNA, Ribosomal, 16S/genetics/metabolism ; *Soil/chemistry ; Bacteria/genetics ; Plant Development ; Soil Microbiology ; Rhizosphere ; Plant Roots/microbiology ; }, abstract = {Lettuce plants respond differently to cover crop amendments by altering their biomass and nitrogen uptake (Nup) at different plant growth stages. Nonetheless, plant-microbe interactions involved in the alterations are scarcely studied. This study elucidated how the properties of the soil microbial community inhabiting the rhizosphere associated with lettuce (Lactuca sativa L. var. crispa "Red fire") change during plant growth stages. Lettuce plants were cultivated in control soil and soil with rye, hairy vetch (HV), and rye plus HV (rye + HV) cover crop amendments. Rhizosphere soil samples were collected at the mid-growth and mature stages of plant development. DNA was extracted from the soil, and the 16S rRNA region was amplified using polymerase chain reaction to analyze bacterial genes and community structures and functions. Cover crop amendments and plant growth stages increased or decreased the relative abundances of bacterial taxa at the genus level. Plant maturity decreased 16S rRNA gene expression and the number of bacterial operational taxonomic units in all treatments. The unique, core, and shared taxa with low relative abundances may be associated with improved lettuce Nup and lettuce shoot and root biomass at each plant growth stage under different cover crop amendments based on multivariate analysis between plant indicators and bacterial genera groups. This study revealed the importance of bacterial groups with low relative abundance in plant-microbe interactions; such bacteria may promote the cover crop application for high lettuce productivity.}, }
@article {pmid35925016, year = {2022}, author = {Cheng, X and Wang, H and Zeng, Z and Li, L and Zhao, R and Bodelier, PLE and Wang, Y and Liu, X and Su, C and Liu, S}, title = {Niche differentiation of atmospheric methane-oxidizing bacteria and their community assembly in subsurface karst caves.}, journal = {Environmental microbiology reports}, volume = {14}, number = {6}, pages = {886-896}, doi = {10.1111/1758-2229.13112}, pmid = {35925016}, issn = {1758-2229}, mesh = {*Methylococcaceae ; Ecosystem ; Soil Microbiology ; Soil ; Methane ; Oxidation-Reduction ; }, abstract = {Karst caves are recently proposed as atmospheric methane sinks in terrestrial ecosystems. Despite of the detection of atmospheric methane-oxidizing bacteria (atmMOB) in caves, we still know little about their ecology and potential ability of methane oxidation in this ecosystem. To understand atmMOB ecology and their potential in methane consumption, we collected weathered rocks and sediments from three different caves in southwestern China. We determined the potential methane oxidization rates in the range of 1.25 ± 0.08 to 1.87 ± 0.41 ng CH4 g[-1] DW h[-1] , which are comparable to those reported in forest and grassland soils. Results showed that alkaline oligotrophic caves harbour high numbers of atmMOB, particularly upland soil cluster (USC), which significantly correlated with temperature, CH4 and CO2 concentrations. The absolute abundance of USCγ was higher than that of USCα. USCγ-OPS (open patch soil) and USCγ-SS (subsurface soil) dominated in most samples, whereas USCα-BFS (boreal forest soil) only predominated in the sediments near cave entrances, indicating niche differentiation of atmMOB in caves. Overwhelming dominance of homogenous selection in community assembly resulted in convergence of atmMOB communities. Collectively, our results demonstrated the niche differentiation of USC in subsurface alkaline caves and their non-negligible methane-oxidizing potential, providing brand-new knowledge about atmMOB ecology in subsurface biosphere.}, }
@article {pmid35924847, year = {2022}, author = {Gude, S and Pherribo, GJ and Taga, ME}, title = {A Salvaging Strategy Enables Stable Metabolite Provisioning among Free-Living Bacteria.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0028822}, pmid = {35924847}, issn = {2379-5077}, support = {R01 GM114535/GM/NIGMS NIH HHS/United States ; R35 GM139633/GM/NIGMS NIH HHS/United States ; }, mesh = {*Vitamin B 12 ; *Cobamides ; Bacteria/metabolism ; Escherichia coli/metabolism ; Vitamins/metabolism ; }, abstract = {All organisms rely on complex metabolites such as amino acids, nucleotides, and cofactors for essential metabolic processes. Some microbes synthesize these fundamental ingredients of life de novo, while others rely on uptake to fulfill their metabolic needs. Although certain metabolic processes are inherently "leaky," the mechanisms enabling stable metabolite provisioning among microbes in the absence of a host remain largely unclear. In particular, how can metabolite provisioning among free-living bacteria be maintained under the evolutionary pressure to economize resources? Salvaging, the process of "recycling and reusing," can be a metabolically efficient route to obtain access to required resources. Here, we show experimentally how precursor salvaging in engineered Escherichia coli populations can lead to stable, long-term metabolite provisioning. We find that salvaged cobamides (vitamin B12 and related enzyme cofactors) are readily made available to nonproducing population members, yet salvagers are strongly protected from overexploitation. We also describe a previously unnoted benefit of precursor salvaging, namely, the removal of the nonfunctional, proliferation-inhibiting precursor. As long as compatible precursors are present, any microbe possessing the terminal steps of a biosynthetic process can, in principle, forgo de novo biosynthesis in favor of salvaging. Consequently, precursor salvaging likely represents a potent, yet overlooked, alternative to de novo biosynthesis for the acquisition and provisioning of metabolites in free-living bacterial populations. IMPORTANCE Recycling gives new life to old things. Bacteria have the ability to recycle and reuse complex molecules they encounter in their environment to fulfill their basic metabolic needs in a resource-efficient way. By studying the salvaging (recycling and reusing) of vitamin B12 precursors, we found that metabolite salvaging can benefit others and provide stability to a bacterial community at the same time. Salvagers of vitamin B12 precursors freely share the result of their labor yet cannot be outcompeted by freeloaders, likely because salvagers retain preferential access to the salvaging products. Thus, salvaging may represent an effective, yet overlooked, mechanism of acquiring and provisioning nutrients in microbial populations.}, }
@article {pmid35920032, year = {2022}, author = {Heinz, J and Doellinger, J and Maus, D and Schneider, A and Lasch, P and Grossart, HP and Schulze-Makuch, D}, title = {Perchlorate-specific proteomic stress responses of Debaryomyces hansenii could enable microbial survival in Martian brines.}, journal = {Environmental microbiology}, volume = {24}, number = {11}, pages = {5051-5065}, doi = {10.1111/1462-2920.16152}, pmid = {35920032}, issn = {1462-2920}, mesh = {Perchlorates/metabolism ; Extraterrestrial Environment ; *Debaryomyces ; Proteomics ; *Mars ; }, abstract = {If life exists on Mars, it would face several challenges including the presence of perchlorates, which destabilize biomacromolecules by inducing chaotropic stress. However, little is known about perchlorate toxicity for microorganisms on the cellular level. Here, we present the first proteomic investigation on the perchlorate-specific stress responses of the halotolerant yeast Debaryomyces hansenii and compare these to generally known salt stress adaptations. We found that the responses to NaCl and NaClO4 -induced stresses share many common metabolic features, for example, signalling pathways, elevated energy metabolism, or osmolyte biosynthesis. Nevertheless, several new perchlorate-specific stress responses could be identified, such as protein glycosylation and cell wall remodulations, presumably in order to stabilize protein structures and the cell envelope. These stress responses would also be relevant for putative life on Mars, which-given the environmental conditions-likely developed chaotropic defence strategies such as stabilized confirmations of biomacromolecules or the formation of cell clusters.}, }
@article {pmid35918440, year = {2023}, author = {Wu, Q and Ji, M and Yu, S and Li, J and Wu, X and Ju, X and Liu, B and Zhang, X}, title = {Distinct Denitrifying Phenotypes of Predominant Bacteria Modulate Nitrous Oxide Metabolism in Two Typical Cropland Soils.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {509-520}, pmid = {35918440}, issn = {1432-184X}, support = {31971526//National Natural Science Foundation of China/ ; 31861133018//National Natural Science Foundation of China/ ; XDB40020204//Chinese Academy of Sciences/ ; 2017YFD0200102//Key Technologies Research and Development Program/ ; }, mesh = {*Soil ; *Nitrous Oxide ; Denitrification ; Soil Microbiology ; Bacteria/genetics ; Carbon ; Nitrogen ; Crops, Agricultural ; }, abstract = {Denitrifying nitrous oxide (N2O) emissions in agroecosystems result from variations in microbial composition and soil properties. However, the microbial mechanisms of differential N2O emissions in agricultural soils are less understood. In this study, microcosm experiments using two main types of Chinese cropland soil were conducted with different supplements of nitrate and glucose to simulate the varying nitrogen and carbon conditions. The results show that N2O accumulation in black soil (BF) was significantly higher than that in fluvo-aquic soil (FF) independent of nitrogen and carbon. The abundance of most denitrifying genes was significantly higher in FF, but the ratios of genes responsible for N2O production (nirS and nirK) to the gene responsible for N2O reduction (nosZ) did not significantly differ between the two soils. However, the soils showed obvious discrepancies in denitrifying bacterial communities, with a higher abundance of N2O-generating bacteria in BF and a higher abundance of N2O-reducing bacteria in FF. High accumulation of N2O was verified by the bacterial isolates of Rhodanobacter predominated in BF due to a lack of N2O reduction capacity. The dominance of Castellaniella and others in FF led to a rapid reduction in N2O and thus less N2O accumulation, as demonstrated when the corresponding isolate was inoculated into the studied soils. Therefore, the different phenotypes of N2O metabolism of the distinct denitrifiers predominantly colonized the two soils, causing differing N2O accumulation. This knowledge would help to develop a strategy for mitigating N2O emissions in agricultural soils by regulating the phenotypes of N2O metabolism.}, }
@article {pmid35918056, year = {2023}, author = {Santos Correa, S and Schultz, J and Lauersen, KJ and Soares Rosado, A}, title = {Natural carbon fixation and advances in synthetic engineering for redesigning and creating new fixation pathways.}, journal = {Journal of advanced research}, volume = {47}, number = {}, pages = {75-92}, pmid = {35918056}, issn = {2090-1224}, mesh = {*Photosynthesis ; *Carbon Dioxide/metabolism ; Bacteria/genetics/metabolism ; Archaea/genetics/metabolism ; Carbon Cycle ; Plants/metabolism ; }, abstract = {BACKGROUND: Autotrophic carbon fixation is the primary route through which organic carbon enters the biosphere, and it is a key step in the biogeochemical carbon cycle. The Calvin-Benson-Bassham pathway, which is predominantly found in plants, algae, and some bacteria (mainly cyanobacteria), was previously considered to be the sole carbon-fixation pathway. However, the discovery of a new carbon-fixation pathway in sulfurous green bacteria almost two decades ago encouraged further research on previously overlooked ancient carbon-fixation pathways in taxonomically and phylogenetically distinct microorganisms.<br><br>AIM OF REVIEW: In this review, we summarize the six known natural carbon-fixation pathways and outline the newly proposed additions to this list. We also discuss the recent achievements in synthetic carbon fixation and the importance of the metabolism of thermophilic microorganisms in this field.<br><br>Currently, at least six carbon-fixation routes have been confirmed in Bacteria and Archaea. Other possible candidate routes have also been suggested on the basis of emerging "omics" data analyses, expanding our knowledge and stimulating discussions on the importance of these pathways in the way organisms acquire carbon. Notably, the currently known natural fixation routes cannot balance the excessive anthropogenic carbon emissions in a highly unbalanced global carbon cycle. Therefore, significant efforts have also been made to improve the existing carbon-fixation pathways and/or design new efficient in vitro and in vivo synthetic pathways.}, }
@article {pmid35916938, year = {2023}, author = {Tang, Y and Wang, S and Jin, X and Zhou, D and Lin, Q and Liu, Z and Zhang, X and Dumont, HJ}, title = {Extensive Carbon Contribution of Inundated Terrestrial Plants to Zooplankton Biomass in a Eutrophic Lake.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {163-173}, pmid = {35916938}, issn = {1432-184X}, support = {32071566//National Natural Science Foundation of China/ ; 2022A1515011074//Natural Science Foundation of Guangdong Province/ ; }, mesh = {Humans ; Animals ; *Zooplankton ; Carbon/metabolism ; Lakes ; Ecosystem ; Biomass ; Food Chain ; Phytoplankton/metabolism ; *Cyanobacteria/metabolism ; }, abstract = {Organic carbon derived from terrestrial plants contributes to aquatic consumers, e.g., zooplankton in lakes. The degree of the contribution depends on the availability of terrestrial organic carbon in lake organic pool and the transfer efficiency of the carbon. Terrestrial organic carbon is poor-quality food for zooplankton with a mismatch of nutrition content and was incorporated to zooplankton with much lower efficiency than phytoplankton. Contributions of terrestrial carbon to zooplankton generally decrease with an increase in phytoplankton production, indicating a preferential incorporation of phytoplankton in previous investigations. However, in eutrophic lakes, the dominating cyanobacteria were of poor quality and incorporated to consumers inefficiently too. In that case, zooplankton in eutrophic wetlands, where cyanobacteria dominate the phytoplankton production and massive terrestrial plants are inundated, may not preferentially incorporate poor food-quality phytoplankton resource to their biomass. Therefore, we hypothesize that carbon contributions of terrestrial vegetation to zooplankton and to lake particulate organic pool should be similar in such aquatic ecosystems. We tested this hypothesis by sampling zooplankton and carbon sources in Ming Lake (Jinan University Campus, southern China) which was overgrown by terrestrial plants after drying and re-flooded. After 60 days of observations at weekly (or biweekly) intervals, applying stable carbon ([13]C), nitrogen ([15] N), and hydrogen ([2]H) isotopic analysis and a stable isotope mixing model, we estimated the occurrence of extensive carbon contribution (≥ 50%) of flooded terrestrial plants to cladocerans and copepods. Contribution of inundated terrestrial plants to cladocerans was similar to that to lake particulate organic pool. Thus, our study quantified the role of terrestrial carbon in eutrophic wetlands, enhancing our understanding of cross-ecosystem interactions in food webs with an emphasis on the resource quality.}, }
@article {pmid35916937, year = {2023}, author = {Pellegrinetti, TA and Cotta, SR and Sarmento, H and Costa, JS and Delbaje, E and Montes, CR and Camargo, PB and Barbiero, L and Rezende-Filho, AT and Fiore, MF}, title = {Bacterial Communities Along Environmental Gradients in Tropical Soda Lakes.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {892-903}, pmid = {35916937}, issn = {1432-184X}, support = {2016/14227-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {*Lakes/chemistry/microbiology ; Brazil ; Eutrophication ; *Cyanobacteria/growth &amp; development/isolation &amp; purification ; Metagenomics ; }, abstract = {Soda lake environments are known to be variable and can have distinct differences according to geographical location. In this study, we investigated the effects of different environmental conditions of six adjacent soda lakes in the Pantanal biome (Mato Grosso do Sul state, Brazil) on bacterial communities and their functioning using a metagenomic approach combined with flow cytometry and chemical analyses. Ordination analysis using flow cytometry and water chemistry data from two sampling periods (wet and dry) clustered soda lakes into three different profiles: eutrophic turbid (ET), oligotrophic turbid (OT), and clear vegetated oligotrophic (CVO). Analysis of bacterial community composition and functioning corroborated this ordination; the exception was one ET lake, which was similar to one OT lake during the wet season, indicating drastic shifts between seasons. Microbial abundance and diversity increased during the dry period, along with a considerable number of limnological variables, all indicative of a strong effect of the precipitation-evaporation balance in these systems. Cyanobacteria were associated with high electric conductivity, pH, and nutrient availability, whereas Actinobacteria, Alphaproteobacteria, and Betaproteobacteria were correlated with landscape morphology variability (surface water, surface perimeter, and lake volume) and with lower salinity and pH levels. Stress response metabolism was enhanced in OT and ET lakes and underrepresented in CVO lakes. The microbiome dataset of this study can serve as a baseline for restoring impacted soda lakes. Altogether, the results of this study demonstrate the sensitivity of tropical soda lakes to climate change, as slight changes in hydrological regimes might produce drastic shifts in community diversity.}, }
@article {pmid35915645, year = {2022}, author = {Mitiku, G and Rybka, D and Klein-Gunnewiek, P and Tessema, T and Raaijmakers, JM and Etalo, DW}, title = {Molecular detection and quantification of the Striga seedbank in agricultural soils.}, journal = {Weed research}, volume = {62}, number = {3}, pages = {181-191}, pmid = {35915645}, issn = {0043-1737}, abstract = {Striga hermonthica (Del.) Benth is a devastating parasitic weed in Sub-Saharan Africa (SSA) and its soil seedbank is the major factor contributing to its prevalence and persistence. To date, there is a little information on the Striga seedbank density in agricultural fields in SSA due to the lack of reliable detection and quantification methods. We developed a high-throughput method that combines density- and size-based separation techniques with quantitative polymerase chain reaction (qPCR)-based detection of Striga seeds in soil. The method was optimised and validated by introducing increasing numbers of Striga seeds in two physicochemically different Striga-free agricultural soils. The results showed that as little as one seed of S. hermonthica per 150 g of soil could be detected. This technique was subsequently tested on soil samples of 48 sorghum fields from different agro-ecological zones in Ethiopia to map the geospatial distribution of the Striga seedbank along a trajectory of more than 1500 km. Considerable variation in Striga seed densities was observed. Striga seeds were detectable in 75% of the field soils with densities up to 86 seeds per 150 g of soil. The Striga seed density in soil and the number of emerged Striga plants in the field showed a non-linear relationship. In conclusion, the method developed allows for accurate mapping of the Striga seedbank in physicochemically diverse SSA field soils and can be used to assess the impact of management strategies on Striga seedbank dynamics.}, }
@article {pmid35914169, year = {2022}, author = {Gwak, JH and Awala, SI and Nguyen, NL and Yu, WJ and Yang, HY and von Bergen, M and Jehmlich, N and Kits, KD and Loy, A and Dunfield, PF and Dahl, C and Hyun, JH and Rhee, SK}, title = {Sulfur and methane oxidation by a single microorganism.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {32}, pages = {e2114799119}, pmid = {35914169}, issn = {1091-6490}, mesh = {*Bacteria/metabolism ; *Methane/metabolism ; Oxidation-Reduction ; Proteomics ; *Sulfur/metabolism ; Thiosulfates/metabolism ; }, abstract = {Natural and anthropogenic wetlands are major sources of the atmospheric greenhouse gas methane. Methane emissions from wetlands are mitigated by methanotrophic bacteria at the oxic-anoxic interface, a zone of intense redox cycling of carbon, sulfur, and nitrogen compounds. Here, we report on the isolation of an aerobic methanotrophic bacterium, 'Methylovirgula thiovorans' strain HY1, which possesses metabolic capabilities never before found in any methanotroph. Most notably, strain HY1 is the first bacterium shown to aerobically oxidize both methane and reduced sulfur compounds for growth. Genomic and proteomic analyses showed that soluble methane monooxygenase and XoxF-type alcohol dehydrogenases are responsible for methane and methanol oxidation, respectively. Various pathways for respiratory sulfur oxidation were present, including the Sox-rDsr pathway and the S4I system. Strain HY1 employed the Calvin-Benson-Bassham cycle for CO2 fixation during chemolithoautotrophic growth on reduced sulfur compounds. Proteomic and microrespirometry analyses showed that the metabolic pathways for methane and thiosulfate oxidation were induced in the presence of the respective substrates. Methane and thiosulfate could therefore be independently or simultaneously oxidized. The discovery of this versatile bacterium demonstrates that methanotrophy and thiotrophy are compatible in a single microorganism and underpins the intimate interactions of methane and sulfur cycles in oxic-anoxic interface environments.}, }
@article {pmid35913610, year = {2023}, author = {Cusumano, A and Bella, P and Peri, E and Rostás, M and Guarino, S and Lievens, B and Colazza, S}, title = {Nectar-Inhabiting Bacteria Affect Olfactory Responses of an Insect Parasitoid by Altering Nectar Odors.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {364-376}, pmid = {35913610}, issn = {1432-184X}, support = {FFR_D13-2018/2021//Universit&#xe0; degli Studi di Palermo/ ; }, mesh = {Animals ; *Plant Nectar ; *Odorants ; Insecta ; Flowers ; Bacteria ; Pollination ; }, abstract = {Floral nectar is ubiquitously colonized by a variety of microorganisms among which yeasts and bacteria are the most common. Microorganisms inhabiting floral nectar can alter several nectar traits, including nectar odor by producing microbial volatile organic compounds (mVOCs). Evidence showing that mVOCs can affect the foraging behavior of insect pollinators is increasing in the literature, whereas the role of mVOCs in altering the foraging behavior of third-trophic level organisms such as insect parasitoids is largely overlooked. Parasitoids are frequent visitors of flowers and are well known to feed on nectar. In this study, we isolated bacteria inhabiting floral nectar of buckwheat, Fagopyrum esculentum (Polygonales: Polygonaceae), to test the hypothesis that nectar bacteria affect the foraging behavior of the egg parasitoid Trissolcus basalis (Hymenoptera: Scelionidae) via changes in odors of nectar. In behavioral assays, we found that T. basalis wasps are attracted toward nectar fermented by 4 out of the 14 bacterial strains isolated, which belong to Staphylococcus epidermidis, Terrabacillus saccharophilus (both Firmicutes), Pantoea sp. (Proteobacteria), and Curtobacterium sp. (Actinobacteria). Results of chemical investigations revealed significant differences in the volatile blend composition of nectars fermented by the bacterial isolates. Our results indicate that nectar-inhabiting bacteria play an important role in the interactions between flowering plants and foraging parasitoids. These results are also relevant from an applied perspective as flowering resources, such as buckwheat, are largely used in agriculture to promote conservation biological control of insect pests.}, }
@article {pmid35913161, year = {2022}, author = {Lesniak, NA and Tomkovich, S and Henry, A and Taylor, A and Colovas, J and Bishop, L and McBride, K and Schloss, PD}, title = {Diluted Fecal Community Transplant Restores Clostridioides difficile Colonization Resistance to Antibiotic-Perturbed Murine Communities.}, journal = {mBio}, volume = {13}, number = {4}, pages = {e0136422}, pmid = {35913161}, issn = {2150-7511}, support = {U19 AI090871/AI/NIAID NIH HHS/United States ; R01 GM099514/GM/NIGMS NIH HHS/United States ; T32 AI007528/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/genetics ; Cefoperazone/pharmacology ; Clindamycin/pharmacology/therapeutic use ; Clostridioides ; *Clostridioides difficile ; *Clostridium Infections/microbiology/prevention &amp; control ; Disease Susceptibility ; Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome ; Male ; Mice ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S/genetics ; Streptomycin/pharmacology/therapeutic use ; }, abstract = {Fecal communities transplanted into individuals can eliminate recurrent Clostridioides difficile infection (CDI) with high efficacy. However, this treatment is only used once CDI becomes resistant to antibiotics or has recurred multiple times. We sought to investigate whether a fecal community transplant (FCT) pretreatment could be used to prevent CDI altogether. We treated male C57BL/6 mice with either clindamycin, cefoperazone, or streptomycin and then inoculated them with the microbial community from untreated mice before challenge with C. difficile. We measured colonization and sequenced the V4 region of the 16S rRNA gene to understand the dynamics of the murine fecal community in response to the FCT and C. difficile challenge. Clindamycin-treated mice became colonized with C. difficile but cleared it naturally and did not benefit from the FCT. Cefoperazone-treated mice became colonized by C. difficile, but the FCT enabled clearance of C. difficile. In streptomycin-treated mice, the FCT was able to prevent C. difficile from colonizing. We then diluted the FCT and repeated the experiments. Cefoperazone-treated mice no longer cleared C. difficile. However, streptomycin-treated mice colonized with 1:10[2] dilutions resisted C. difficile colonization. Streptomycin-treated mice that received an FCT diluted 1:10[3] became colonized with C. difficile but later cleared the infection. In streptomycin-treated mice, inhibition of C. difficile was associated with increased relative abundance of a group of bacteria related to Porphyromonadaceae and Lachnospiraceae. These data demonstrate that C. difficile colonization resistance can be restored to a susceptible community with an FCT as long as it complements the missing populations. IMPORTANCE Antibiotic use, ubiquitous with the health care environment, is a major risk factor for Clostridioides difficile infection (CDI), the most common nosocomial infection. When C. difficile becomes resistant to antibiotics, a fecal microbiota transplant from a healthy individual can effectively restore the gut bacterial community and eliminate the infection. While this relationship between the gut bacteria and CDI is well established, there are no therapies to treat a perturbed gut community to prevent CDI. This study explored the potential of restoring colonization resistance to antibiotic-induced susceptible gut communities. We described the effect that gut bacterial community variation has on the effectiveness of a fecal community transplant for inhibiting CDI. These data demonstrated that communities susceptible to CDI can be supplemented with fecal communities but that the effectiveness depended on the structure of the community following the perturbation. Thus, a reduced bacterial community may be able to recover colonization resistance in patients treated with antibiotics.}, }
@article {pmid35909604, year = {2022}, author = {Jepsen, T and Jensen, B and Jørgensen, NOG}, title = {Volatiles produced by Streptomyces spp. delay rot in apples caused by Colletotrichum acutatum.}, journal = {Current research in microbial sciences}, volume = {3}, number = {}, pages = {100121}, pmid = {35909604}, issn = {2666-5174}, abstract = {Volatile organic compounds (VOCs) produced by microorganisms may prevent postharvest rot in fruits. Here, it was examined if VOCs from different species of Streptomyces can control infection in apples caused by the fungal pathogen Colletotrichum acutatum. Incubation of C. acutatum-infected apples in semi-closed boxes with actively growing strains of three Streptomyces (S. coelicolor, S. diastatochromogenes and Streptomyces strain 2R) showed that VOCs reduced rot areas of the apples by 45-66% after 8 days and 39-57% after 10 days, relative to infected apples incubated without Streptomyces. No differences in inhibition among the three strains were seen. In contrast, a mutant strain of Streptomyces that lacks major genes involved in biosynthesis of secondary metabolites, did not reduce development of rot in the apples. Furthermore, Streptomyces VOCs reduced radial hyphal growth of C. acutatum on agar. Several of the VOCs produced by three Streptomyces strains have previously shown fungicidal properties. Although the specific VOCs being active in inhibition of C. acutatum remain to be determined, VOCs may have a great potential as biofumigants to minimize postharvest diseases in fruits.}, }
@article {pmid35903477, year = {2022}, author = {Olmo, R and Wetzels, SU and Armanhi, JSL and Arruda, P and Berg, G and Cernava, T and Cotter, PD and Araujo, SC and de Souza, RSC and Ferrocino, I and Frisvad, JC and Georgalaki, M and Hansen, HH and Kazou, M and Kiran, GS and Kostic, T and Krauss-Etschmann, S and Kriaa, A and Lange, L and Maguin, E and Mitter, B and Nielsen, MO and Olivares, M and Quijada, NM and Romaní-Pérez, M and Sanz, Y and Schloter, M and Schmitt-Kopplin, P and Seaton, SC and Selvin, J and Sessitsch, A and Wang, M and Zwirzitz, B and Selberherr, E and Wagner, M}, title = {Microbiome Research as an Effective Driver of Success Stories in Agrifood Systems - A Selection of Case Studies.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {834622}, pmid = {35903477}, issn = {1664-302X}, abstract = {Increasing knowledge of the microbiome has led to significant advancements in the agrifood system. Case studies based on microbiome applications have been reported worldwide and, in this review, we have selected 14 success stories that showcase the importance of microbiome research in advancing the agrifood system. The selected case studies describe products, methodologies, applications, tools, and processes that created an economic and societal impact. Additionally, they cover a broad range of fields within the agrifood chain: the management of diseases and putative pathogens; the use of microorganism as soil fertilizers and plant strengtheners; the investigation of the microbial dynamics occurring during food fermentation; the presence of microorganisms and/or genes associated with hazards for animal and human health (e.g., mycotoxins, spoilage agents, or pathogens) in feeds, foods, and their processing environments; applications to improve HACCP systems; and the identification of novel probiotics and prebiotics to improve the animal gut microbiome or to prevent chronic non-communicable diseases in humans (e.g., obesity complications). The microbiomes of soil, plants, and animals are pivotal for ensuring human and environmental health and this review highlights the impact that microbiome applications have with this regard.}, }
@article {pmid35902889, year = {2022}, author = {Ma, X and Wang, T and Shi, Z and Chiariello, NR and Docherty, K and Field, CB and Gutknecht, J and Gao, Q and Gu, Y and Guo, X and Hungate, BA and Lei, J and Niboyet, A and Le Roux, X and Yuan, M and Yuan, T and Zhou, J and Yang, Y}, title = {Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {112}, pmid = {35902889}, issn = {2049-2618}, mesh = {Carbon ; Ecosystem ; *Microbiota/genetics ; Nitrogen/metabolism ; *Soil ; Soil Microbiology ; }, abstract = {BACKGROUND: Anthropogenic activities have increased the inputs of atmospheric reactive nitrogen (N) into terrestrial ecosystems, affecting soil carbon stability and microbial communities. Previous studies have primarily examined the effects of nitrogen deposition on microbial taxonomy, enzymatic activities, and functional processes. Here, we examined various functional traits of soil microbial communities and how these traits are interrelated in a Mediterranean-type grassland administrated with 14 years of 7 g m[-2] year[-1] of N amendment, based on estimated atmospheric N deposition in areas within California, USA, by the end of the twenty-first century.<br><br>RESULTS: Soil microbial communities were significantly altered by N deposition. Consistent with higher aboveground plant biomass and litter, fast-growing bacteria, assessed by abundance-weighted average rRNA operon copy number, were favored in N deposited soils. The relative abundances of genes associated with labile carbon (C) degradation (e.g., amyA and cda) were also increased. In contrast, the relative abundances of functional genes associated with the degradation of more recalcitrant C (e.g., mannanase and chitinase) were either unchanged or decreased. Compared with the ambient control, N deposition significantly reduced network complexity, such as average degree and connectedness. The network for N deposited samples contained only genes associated with C degradation, suggesting that C degradation genes became more intensely connected under N deposition.<br><br>CONCLUSIONS: We propose a conceptual model to summarize the mechanisms of how changes in above- and belowground ecosystems by long-term N deposition collectively lead to more soil C accumulation. Video Abstract.}, }
@article {pmid35896536, year = {2022}, author = {Lin, C and Peñaranda, JSD and Dendooven, J and Detavernier, C and Schaubroeck, D and Boon, N and Baets, R and Le Thomas, N}, title = {UV photonic integrated circuits for far-field structured illumination autofluorescence microscopy.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {4360}, pmid = {35896536}, issn = {2041-1723}, mesh = {Light ; *Lighting ; *Microscopy/methods ; Photons ; }, abstract = {Ultra-violet (UV) light has still a limited scope in optical microscopy despite its potential advantages over visible light in terms of optical resolution and of interaction with a wide variety of biological molecules. The main challenge is to control in a robust, compact and cost-effective way UV light beams at the level of a single optical spatial mode and concomitantly to minimize the light propagation loss. To tackle this challenge, we present here photonic integrated circuits made of aluminum oxide thin layers that are compatible with both UV light and high-volume manufacturing. These photonic circuits designed at a wavelength of 360 nm enable super-resolved structured illumination microscopy with conventional wide-field microscopes and without modifying the usual protocol for handling the object to be imaged. As a biological application, we show that our UV photonic chips enable to image the autofluorescence of yeast cells and reveal features unresolved with standard wide-field microscopy.}, }
@article {pmid35893569, year = {2022}, author = {Mugani, R and Khalloufi, FE and Redouane, EM and Haida, M and Zerrifi, SEA and Campos, A and Kasada, M and Woodhouse, J and Grossart, HP and Vasconcelos, V and Oudra, B}, title = {Bacterioplankton Associated with Toxic Cyanobacteria Promote Pisum sativum (Pea) Growth and Nutritional Value through Positive Interactions.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, pmid = {35893569}, issn = {2076-2607}, support = {823860//European Commission/ ; }, abstract = {Research on Plant Growth-Promoting Bacteria (PGPB) has focused much more on rhizospheric bacteria. However, PGPB associated with toxic cyanobacterial bloom (TCB) could enter the rhizosphere through irrigation water, helping plants such as Pisum sativum L. (pea) overcome oxidative stress induced by microcystin (MC) and improve plant growth and nutritional value. This study aimed to isolate bacteria associated with toxic cyanobacteria, test PGPB properties, and inoculate them as a consortium to pea seedlings irrigated with MC to investigate their role in plant protection as well as in improving growth and nutritional value. Two bacterioplankton isolates and one rhizosphere isolate were isolated and purified on a mineral salt medium supplemented with 1000 μg/L MC and identified via their 16S rRNA gene. The mixed strains were inoculated to pea seedlings in pots irrigated with 0, 50, and 100 μg/L MC. We measured the morphological and physiological parameters of pea plants at maturity and evaluated the efficiency of the plant’s enzymatic and non-enzymatic antioxidant responses to assess the role and contribution of PGPB. Both bacterioplankton isolates were identified as Starkeya sp., and the rhizobacterium was identified as Brevundimonas aurantiaca. MC addition significantly (p < 0.05) reduced all the growth parameters of the pea, i.e., total chlorophyll content, leaf quantum yield, stomatal conductance, carotenoids, and polyphenol contents, in an MC concentration-dependent manner, while bacterial presence positively affected all the measured parameters. In the MC treatment, the levels of the pea’s antioxidant traits, including SOD, CAT, POD, PPO, GST, and ascorbic acid, were increased in the sterile pots. In contrast, these levels were reduced with double and triple PGPB addition. Additionally, nutritional values such as sugars, proteins, and minerals (Ca and K) in pea fruits were reduced under MC exposure but increased with PGPB addition. Overall, in the presence of MC, PGPB seem to positively interact with pea plants and thus may constitute a natural alternative for soil fertilization when irrigated with cyanotoxin-contaminated water, increasing the yield and nutritional value of crops.}, }
@article {pmid35892285, year = {2023}, author = {von Gastrow, L and Michel, E and Legrand, J and Amelot, R and Segond, D and Guezenec, S and Rué, O and Chable, V and Goldringer, I and Dousset, X and Serpolay-Bessoni, E and Taupier-Letage, B and Vindras-Fouillet, C and Onno, B and Valence, F and Sicard, D}, title = {Microbial community dispersal from wheat grains to sourdoughs: A contribution of participatory research.}, journal = {Molecular ecology}, volume = {32}, number = {10}, pages = {2413-2427}, doi = {10.1111/mec.16630}, pmid = {35892285}, issn = {1365-294X}, mesh = {Humans ; *Triticum/microbiology ; Community-Based Participatory Research ; Fermentation ; Food Microbiology ; *Microbiota/genetics ; Bacteria/genetics ; Yeasts/genetics ; Bread/analysis/microbiology ; }, abstract = {Understanding microbial dispersal is critical to understand the dynamics and evolution of microbial communities. However, microbial dispersal is difficult to study because of uncertainty about their vectors of migration. This applies to both microbial communities in natural and human-associated environments. Here, we studied microbial dispersal along the sourdoughs bread-making chain using a participatory research approach. Sourdough is a naturally fermented mixture of flour and water. It hosts a community of bacteria and yeasts whose origins are only partially known. We analysed the potential of wheat grains and flour to serve as an inoculum for sourdough microbial communities using 16S rDNA and ITS1 metabarcoding. First, in an experiment involving farmers, a miller and bakers, we followed the microbiota from grains to newly initiated and propagated sourdoughs. Second, we compared the microbiota of 46 sourdough samples collected everywhere in France, and of the flour used for their back-slopping. The core microbiota detected on the seeds, in the flour and in the sourdough was composed mainly of microbes known to be associated with plants and not living in sourdoughs. No sourdough yeast species were detected on grains and flours. Sourdough lactic acid bacteria were rarely found in flour. When they were, they did not have the same amplicon sequence variant (ASV) as found in the corresponding sourdough. However, the low sequencing depth for bacteria in flour did not allow us to draw definitive conclusion. Thus, our results showed that sourdough yeasts did not come from flour, and suggest that neither do sourdough LAB.}, }
@article {pmid35890046, year = {2022}, author = {Orsini, M and Petrin, S and Corrò, M and Baggio, G and Spagnolo, E and Losasso, C}, title = {Anthroponotic-Based Transfer of Staphylococcus to Dog: A Case Study.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {7}, pages = {}, pmid = {35890046}, issn = {2076-0817}, support = {RC IZSVE 16/18//Ministero della Salute/ ; }, abstract = {Although usually harmless, Staphylococcus spp. can cause nosocomial and community-onset skin and soft tissue infections in both humans and animals; thus, it is considered a significant burden for healthcare systems worldwide. Companion animals have been identified as potential reservoirs of pathogenic Staphylococcus with specific reference to Methicillin Resistant Staphylococcus aureus (MRSA). In this study, we investigated the circulation and the genetic relationships of a collection of Staphylococcus spp. isolates in a family composed of four adults (a mother, father, grandmother, and grandfather), one child, and a dog, which were sampled over three years. The routes of transmission among humans and between humans and the dog werelyzed. The results displayed the circulation of many Staphylococcus lineages, belonging to different species and sequence types (ST) and being related to both human and pet origins. However, among the observed host-switch events, one of them clearly underpinnthroponotic route from a human to a dog. This suggests that companion animals can potentially have a role as a carrier of Staphylococcus, thus posing a serious concern about MRSA spreading within human and animal microbial communities.}, }
@article {pmid35889095, year = {2022}, author = {Melo-Bolívar, JF and Ruiz Pardo, RY and Junca, H and Sidjabat, HE and Cano-Lozano, JA and Villamil Díaz, LM}, title = {Competitive Exclusion Bacterial Culture Derived from the Gut Microbiome of Nile Tilapia (Oreochromis niloticus) as a Resource to Efficiently Recover Probiotic Strains: Taxonomic, Genomic, and Functional Proof of Concept.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889095}, issn = {2076-2607}, support = {ING181-2016//Universidad de La Sabana/ ; INGPHD-6-2017//Universidad de La Sabana/ ; INGPHD-9-2019//Universidad de La Sabana/ ; 808-2018-contract CT 329-2019//MINCIENCIAS- Patrimonio Aut&#xf3;nomo Fondo Nacional de Financiamiento para la Ciencia, la Tecnolog&#xed;a y la Innovaci&#xf3;n Francisco Jos&#xe9; de Caldas/ ; 727-2015, contract CT 122-2017//MINCIENCIAS/ ; }, abstract = {This study aims to mine a previously developed continuous-flow competitive exclusion culture (CFCEC) originating from the Tilapia gut microbiome as a rational and efficient autochthonous probiotic strain recovery source. Three isolated strains were tested on their adaptability to host gastrointestinal conditions, their antibacterial activities against aquaculture bacterial pathogens, and their antibiotic susceptibility patterns. Their genomes were fully sequenced, assembled, annotated, and relevant functions inferred, such as those related to pinpointed probiotic activities and phylogenomic comparative analyses to the closer reported strains/species relatives. The strains are possible candidates of novel genus/species taxa inside Lactococcus spp. and Priestia spp. (previously known as Bacillus spp.) These results were consistent with reports on strains inside these phyla exhibiting probiotic features, and the strains we found are expanding their known diversity. Furthermore, their pangenomes showed that these bacteria have indeed a set of so far uncharacterized genes that may play a role in the antagonism to competing strains or specific symbiotic adaptations to the fish host. In conclusion, CFCEC proved to effectively allow the enrichment and further pure culture isolation of strains with probiotic potential.}, }
@article {pmid35886559, year = {2022}, author = {Shen, W and Long, Y and Qiu, Z and Gao, N and Masuda, Y and Itoh, H and Ohba, H and Shiratori, Y and Rajasekar, A and Senoo, K}, title = {Investigation of Rice Yields and Critical N Losses from Paddy Soil under Different N Fertilization Rates with Iron Application.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {14}, pages = {}, pmid = {35886559}, issn = {1660-4601}, mesh = {Agriculture ; Fertilization ; Fertilizers/analysis ; Iron ; Nitrogen/analysis ; Nitrous Oxide/analysis ; *Oryza/chemistry ; Powders ; *Soil/chemistry ; Urea ; }, abstract = {The application of iron powder stimulated the growth of iron-reducing bacteria as a respiratory substrate and enhanced their nitrogen (N)-fixing activity in flooded paddy soils. High N fertilization (urea) in the flooded paddy soils has caused adverse environmental impacts such as ammonia (NH3) volatilization, nitrous oxide (N2O) emissions, and nitrate (NO3[-]) leaching. This study aims to investigate the effects of N fertilization rates in combination with an iron amendment on rice yields and N losses from flooded paddy fields. We performed a 2-year field plot experiment with traditional rice-wheat rotation in China's Yangtze River Delta. The investigation consisted of seven treatments, including 100%, 80%, 60%, and 0% of the conventional N (urea and commercial organic manure) fertilization rate, and 80%, 60%, and 0% of the conventional N with the iron powder (≥99% purity) amendment. The rice yields decreased with a reduction in the conventional N fertilization rate, whereas they were comparable after the iron application under the 80% and 60% conventional N rate. The critical N losses, including NH3 volatilization, N2O emissions, and NO3[-] and NH4[+] leaching, generally decreased with a reduction in the conventional N fertilization rate. These N losses were significantly greater after the iron amendment compared with the non-amended treatments under the 80% and 60% conventional N fertilization rate in the first rice-growing season. However, it was comparable between the iron-amended and the non-amended treatments in the second season. Furthermore, NO3[-] leaching was the most significant N loss throughout the two rice seasons, followed by NH3 volatilization. The iron amendment significantly increased soil Fe[2+] content compared with the non-amended treatments irrespective of N fertilization, suggesting the reduction of amended iron by iron-reducing bacteria and their simultaneous N fixation. A combination of the iron application with 60-80% of the conventional N fertilization rate could maintain rice yields similar to the conventional N fertilization rate while reducing the critical N losses in the flooded paddy field tested in this study. Our study leads to the establishment of novel and practical rice cultivation, which is a step towards the development of green agriculture.}, }
@article {pmid35884216, year = {2022}, author = {Duysburgh, C and Van den Abbeele, P and Franckenstein, D and Westphal, M and Kuchinka-Koch, A and Marzorati, M}, title = {Co-Administration of Lactulose Crystals with Amoxicillin Followed by Prolonged Lactulose Treatment Promotes Recovery of the Human Gut Microbiome In Vitro.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {7}, pages = {}, pmid = {35884216}, issn = {2079-6382}, abstract = {The validated SHIME model was used to assess the effect of repeated administration of two different lactulose dosages (5 g/d and 10 g/d) on the human gut microbiome during and following amoxicillin-clavulanic acid treatment. First, antibiotic treatment strongly decreased Bifidobacteriaceae levels from 54.4% to 0.6% and from 23.8% to 2.3% in the simulated proximal and distal colon, respectively, coinciding with a marked reduction in butyrate concentrations. Treatment with lactulose enhanced acetate and lactate levels during antibiotic treatment, likely through lactulose fermentation by Lachnospiraceae and Lactobacillaceae. One week after cessation of antibiotic treatment, Bifidobacteriaceae levels re-increased to 20.4% and 7.6% in the proximal and distal colon of the 5 g lactulose/d co-administered unit, as compared with 1.0% and 2.2% in the antibiotic-treated unit, and were even further stimulated upon extension of lactulose administration. Marked butyrogenic effects were observed upon prolonged lactulose supplementation, suggesting the establishment of cross-feeding interactions between Bifidobacteriaceae and butyrate producers. Furthermore, a limited Enterobacteriaceae outgrowth following antibiotic treatment was observed upon dosing with 10 g lactulose/d, indicating inhibition of pathogenic colonization by lactulose following antibiotic therapy. Overall, lactulose seems to be an interesting candidate for limiting the detrimental effects of amoxicillin-clavulanic acid on the human gut microbiome, though further studies are warranted to confirm these findings.}, }
@article {pmid35883112, year = {2022}, author = {Romo Bechara, N and Wasserberg, G and Raymann, K}, title = {Microbial ecology of sand fly breeding sites: aging and larval conditioning alter the bacterial community composition of rearing substrates.}, journal = {Parasites &amp; vectors}, volume = {15}, number = {1}, pages = {265}, pmid = {35883112}, issn = {1756-3305}, support = {R01 AI123327/AI/NIAID NIH HHS/United States ; R01AI123327//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Animals ; Bacteria/genetics ; Breeding ; Female ; Larva ; Mosquito Vectors ; *Phlebotomus/genetics ; *Psychodidae/genetics ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Sand flies vector several human pathogens, including Leishmania species, which cause leishmaniases. A leishmaniasis vaccine does not yet exist, so the most common prevention strategies involve personal protection and insecticide spraying. However, insecticides can impact non-target organisms and are becoming less effective because of the evolution of resistance. An alternative control strategy is the attract-and-kill approach, where the vector is lured to a lethal trap, ideally located in oviposition sites that will attract gravid females. Oviposition traps containing attractive microbes have proven successful for the control of some mosquito populations but have not been developed for sand flies. Gravid female sand flies lay their eggs in decomposing organic matter on which the larvae feed and develop. Studies have demonstrated that gravid females are particularly attracted to larval conditioned (containing eggs and larvae) and aged rearing substrates. An isolate-based study has provided some evidence that bacteria play a role in the attraction of sand flies to conditioned substrates. However, the overall bacterial community structure of conditioned and aged substrates and how they change over time has not been investigated.<br><br>METHODS: The goal of this study was to characterize the bacterial communities of rearing and oviposition substrates that have been shown to vary in attractiveness to gravid sand flies in previous behavioral studies. Using 16S rRNA amplicon sequencing we determined the bacterial composition in fresh, aged, and larval-conditioned substrates at four time points representing the main life-cycle stages of developing sand flies. We compared the diversity, presence, and abundance of taxa across substrate types and time points in order to identify how aging and larval-conditioning impact bacterial community structure.<br><br>RESULTS: We found that the bacterial communities significantly change within and between substrates over time. We also identified bacteria that might be responsible for attraction to conditioned and aged substrates, which could be potential candidates for the development of attract-and-kill strategies for sand flies.<br><br>CONCLUSION: This study demonstrated that both aging and larval conditioning induce shifts in the bacterial communities of sand fly oviposition and rearing substrates, which may explain the previously observed preference of gravid female sand flies to substrates containing second/third-instar larvae (conditioned) and substrates aged the same amount of time without larvae (aged).}, }
@article {pmid35882347, year = {2022}, author = {Aziz, A and Rameez, H and Sengar, A and Sharma, D and Farooqi, IH and Basheer, F}, title = {Biogas production and nutrients removal from slaughterhouse wastewater using integrated anaerobic and aerobic granular intermittent SBRs - Bioreactors stability and microbial dynamics.}, journal = {The Science of the total environment}, volume = {848}, number = {}, pages = {157575}, doi = {10.1016/j.scitotenv.2022.157575}, pmid = {35882347}, issn = {1879-1026}, mesh = {Abattoirs ; Ammonia ; Anaerobiosis ; Bacteria ; Biofuels ; Bioreactors ; Carbon ; *Environmental Pollutants ; Nitrites ; Nutrients ; Waste Disposal, Fluid/methods ; *Wastewater/microbiology ; }, abstract = {Slaughterhouse wastewater (SWW) was effectively treated in sequential anaerobic and aerobic granular intermittent sequencing batch reactors (ASBR+ISBR) for 665 days at different HRTs (48 h, 32 h, 24 h, and 12 h). The ASBR was stable at each HRT but performed relatively well at 12 h (OLR - 7.8-9.8 kg COD/m[3]-d) in terms of pollutants removal and biogas production than previously conducted research. The average biogas production was about 17.3 L/day having 70-76 % of CH4 which could subsidize around 52 % of electricity demand while saving 103 US dollars/day if installed at full scale. In the case of post aerobic granular ISBR, carbon and nutrients removal (N&amp;P) was achieved by enriching granules (1.7-2.2 mm) at low DO (0.5-0.8 mg/L) via the nitrite pathway. The ISBR was also well stable at 12 h HRT (average OLR of 2.1 kg COD/m[3]-d) and met the effluent discharge guidelines recommended by the Central Pollution Control Board of India. During steady-state conditions (12 h HRT), the average removal efficiencies for COD, TSS, O&amp;G, TN, and PO4-P were 98.8 %, 96.4 %, 98.7 %, 93.4 %, and 86.6 % respectively from combined ASBR and ISBR. The microbial analysis confirmed Euryarchaeota, Proteobacteria, Firmicutes, Chloroflexi, Bacteroidetes, Planctomycetes, and Synergistetes as the dominant phyla in ASBR. Methanosaeta (21.56 %) and Methanosarcina (6.48 %) were the prevailing methanogens for CH4 production. The leading phyla observed in ISBR were Bacteroidetes, Proteobacteria, Firmicutes, Armatimonadetes, Verrucomicrobia, Chloroflexi, and Planctomycetes. Heterotrophic AOB (Thauera, Xanthomonadaceae, Pseudomonas, Sphingomonadaceae, and Rhodococcus) were mainly detected in the system for ammonia oxidation besides common autotrophic AOB. Similarly, a known PAO (Accumulibacter) was not identified but other PAO (Rhodocyclaceae, Dechloromonas, Pseudomonas, Flavobacteriaceae, and Sphingobacteriaceae) were prevalent inside aerobic granular ISBR that contributed to both carbon and nutrients removal. The results obtained would help implement the investigated reactor configurations at the pilot and full scale for SWW treatment.}, }
@article {pmid35882195, year = {2022}, author = {Lyng, M and Kovács, &#xc1;T}, title = {Microbial ecology: Metabolic heterogeneity and the division of labor in multicellular structures.}, journal = {Current biology : CB}, volume = {32}, number = {14}, pages = {R771-R774}, doi = {10.1016/j.cub.2022.06.008}, pmid = {35882195}, issn = {1879-0445}, abstract = {Many bacterial species are capable of differentiating to create phenotypic heterogeneity. Using the aggregate-forming marine bacterium Vibrio splendidus, a new study reveals how this organism differentiates to form spherical structures with a motile, carbon-storing core and a non-motile shell.}, }
@article {pmid35881247, year = {2023}, author = {King, NG and Smale, DA and Thorpe, JM and McKeown, NJ and Andrews, AJ and Browne, R and Malham, SK}, title = {Core Community Persistence Despite Dynamic Spatiotemporal Responses in the Associated Bacterial Communities of Farmed Pacific Oysters.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {154-162}, pmid = {35881247}, issn = {1432-184X}, support = {MR/S032827/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Crassostrea/microbiology ; Temperature ; Bacteria/genetics ; Seasons ; Seawater/microbiology ; }, abstract = {A breakdown in host-bacteria relationships has been associated with the progression of a number of marine diseases and subsequent mortality events. For the Pacific oyster, Crassostrea gigas, summer mortality syndrome (SMS) is one of the biggest constraints to the growth of the sector and is set to expand into temperate systems as ocean temperatures rise. Currently, a lack of understanding of natural spatiotemporal dynamics of the host-bacteria relationship limits our ability to develop microbially based monitoring approaches. Here, we characterised the associated bacterial community of C. gigas, at two Irish oyster farms, unaffected by SMS, over the course of a year. We found C. gigas harboured spatiotemporally variable bacterial communities that were distinct from bacterioplankton in surrounding seawater. Whilst the majority of bacteria-oyster associations were transient and highly variable, we observed clear patterns of stability in the form of a small core consisting of six persistent amplicon sequence variants (ASVs). This core made up a disproportionately large contribution to sample abundance (34 ± 0.14%), despite representing only 0.034% of species richness across the study, and has been associated with healthy oysters in other systems. Overall, our study demonstrates the consistent features of oyster bacterial communities across spatial and temporal scales and provides an ecologically meaningful baseline to track environmental change.}, }
@article {pmid35880896, year = {2022}, author = {Sun, Y and Shi, J and Wang, X and Ding, C and Wang, J}, title = {Deciphering the Mechanisms Shaping the Plastisphere Microbiota in Soil.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0035222}, pmid = {35880896}, issn = {2379-5077}, mesh = {*Microplastics ; Plastics ; Soil ; Soil Microbiology ; Polyesters ; *Microbiota/genetics ; Polyethylene ; }, abstract = {The gradual accumulation of microplastics has aroused increasing concern for the unique niche, termed "plastisphere." As research so far has focused on their characteristics in aquatic ecosystems, our understanding of the colonization and assembly of the attached bacterial communities on microplastics in soil ecosystems remains poor. Here, we aimed to characterize the plastisphere microbiomes of two types of microplastics (polylactic acid [PLA] and polyethylene [PE]) differing in their biodegradability in two different soils. After incubation for 60 days, considerably lower alpha diversity of bacterial community was observed on the microplastic surfaces, and prominent divergences occurred in the microbial community compositions between the plastisphere and the bulk soil. The temperature, rather than polymer type, significantly induced the differences between the plastisphere communities. The rRNA gene operon (rrn) copy numbers were significantly higher in the PLA plastisphere, suggesting potential degradation. The co-occurrence network analysis showed that the PE plastisphere exhibited greater network complexity and stronger stability than those in the PLA plastisphere. The stochasticity ratio indicated the remarkable importance of stochastic process on community assembly in PE and PLA plastispheres, while the null model analysis showed the nonnegligible roles of deterministic processes in shaping the plastisphere communities. Higher contributions of homogenous selection in the PLA plastisphere were observed in comparison with the PE plastisphere, which could probably be attributed to the selective pressure induced by microplastic degradation. Our findings enhance our mechanistic understanding of the diversity patterns and assembly processes of plastisphere in soil environments and have important implications for microbial ecology and microplastic risk assessment. IMPORTANCE The increasing pervasive microplastic pollution is creating a new environmental compartment, termed plastisphere. Even though there was conclusive information characterizing the plastisphere, the underlying mechanisms shaping the bacterial communities in the plastisphere in the soil remain unclear. Therefore, we incubated two types of microplastics (PE and PLA) in two different soils and explored the differences between plastisphere and bulk soil communities. Additionally, the co-occurrence network and the assembly processes of plastisphere were subjected to further analysis. Our results highlight the importance of selective recruitment of microplastics and contribute to the understanding of the diversity patterns and assembly processes of plastisphere in soil environments.}, }
@article {pmid35880097, year = {2022}, author = {Strik, DPBTB and Ganigué, R and Angenent, LT}, title = {Editorial: Microbial Chain Elongation- Close the Carbon Loop by Connecting-Communities.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {894490}, pmid = {35880097}, issn = {2296-4185}, }
@article {pmid35878855, year = {2022}, author = {Camacho-Sanchez, M and Camacho, M and Redondo-Gómez, S and Mateos-Naranjo, E}, title = {Bacterial assemblage in Mediterranean salt marshes: Disentangling the relative importance of seasonality, zonation and halophytes.}, journal = {The Science of the total environment}, volume = {846}, number = {}, pages = {157514}, doi = {10.1016/j.scitotenv.2022.157514}, pmid = {35878855}, issn = {1879-1026}, mesh = {Bacteria ; *Chenopodiaceae ; Phylogeny ; Rhizosphere ; *Salt-Tolerant Plants/microbiology ; Soil ; Soil Microbiology ; Wetlands ; }, abstract = {Salt marshes gather a high diversity of prokaryotes across their environmental gradients. Most of this diversity and the factors determining their community assemblage are unknown. We massively sequenced a portion of the 16S gene to characterize the diversity of prokaryotes in soils from a salt marsh in Río Piedras, Southern Spain. We sampled in the four seasons, and in five plots dominated by a different halophyte (Spartina maritima, S. densiflora, Salicornia ramosissima, Arthrocaulon macrostachyum and Atriplex portulacoides) growing under different environmental conditions and representing different stages in the marsh ecological succession. Soil was sampled in their rhizosphere and adjacent bulk soil. We report the effects of different factors explaining prokaryotic beta diversity in the marsh: zonation (50 %), seasonality (14 %), and halophyte rhizosphere (7 %). Proteobacteria and Bacteroidota were the most abundant phyla. Firmicutes had a peak in winter and Desulfobacterota with other bacteria involved in sulfur cycling were abundant in the low marsh plots from S. maritima. Alpha diversity was highest in spring and decreased in winter. We detected a marked phylogenetic turnover between seasons and in rhizospheric soil respect to adjacent bulk soil for most pairwise comparisons. The effect of halophyte on its rhizosphere was species-specific, being S. maritima the species with more differentiated taxa between rhizosphere versus surrounding bulk soil. Our work highlights how the complex interaction between marsh zonation, seasonality and rhizosphere, onsets processes structuring bacterial community assemblage in salt marsh soils.}, }
@article {pmid35876854, year = {2023}, author = {Perliński, P and Mudryk, ZJ and Zdanowicz, M and Kubera, &#x141;}, title = {Abundance of Live and Dead Bacteriopsammon Inhabiting Sandy Ecosystems of Recreational Marine Beaches of the Southern Baltic Sea.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {350-363}, pmid = {35876854}, issn = {1432-184X}, mesh = {*Sand ; *Ecosystem ; Bathing Beaches ; Seawater ; Bacteria ; Environmental Monitoring ; }, abstract = {The study was carried out on four non-tidal sandy marine beaches located on the Polish part of the southern Baltic Sea coast. We applied a LIVE/DEAD™ BacLight™ Bacterial Viability Kit (Invitrogen™) method to determine the abundance of live and dead bacteriopsammon. Live psammon bacteria cells constituted 31-53% of the total number of bacteria inhabiting sand of the studied beaches. Abundance of live and dead psammon bacteria generally differed along the horizontal profile in all beaches. The maximum density of bacteria was noted in the dune and the middle part of the beach (dry zones) and the minimum in wet zones, i.e., under seawater surface and at the swash zone. Generally along the vertical profile, the highest numbers of two studied bacterial groups were noted in the surface sand layer, while with increasing sediment depth their numbers significantly decreased. The abundance of live and dead bacteria showed a distinct seasonal variation.}, }
@article {pmid35873980, year = {2022}, author = {Gouka, L and Vogels, C and Hansen, LH and Raaijmakers, JM and Cordovez, V}, title = {Genetic, Phenotypic and Metabolic Diversity of Yeasts From Wheat Flag Leaves.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {908628}, pmid = {35873980}, issn = {1664-462X}, abstract = {The phyllosphere, the aboveground part of a plant, is a harsh environment with diverse abiotic and biotic stresses, including oscillating nutrient availability and temperature as well as exposure to UV radiation. Microbial colonization of this dynamic environment requires specific adaptive traits, including tolerance to fluctuating temperatures, the production of secondary metabolites and pigments to successfully compete with other microorganisms and to withstand abiotic stresses. Here, we isolated 175 yeasts, comprising 15 different genera, from the wheat flag leaf and characterized a selection of these for various adaptive traits such as substrate utilization, tolerance to different temperatures, biofilm formation, and antagonism toward the fungal leaf pathogen Fusarium graminearum. Collectively our results revealed that the wheat flag leaf is a rich resource of taxonomically and phenotypically diverse yeast genera that exhibit various traits that can contribute to survival in the harsh phyllosphere environment.}, }
@article {pmid35872283, year = {2022}, author = {Macêdo, WV and Poulsen, JS and Zaiat, M and Nielsen, JL}, title = {Proteogenomics identification of TBBPA degraders in anaerobic bioreactor.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {310}, number = {}, pages = {119786}, doi = {10.1016/j.envpol.2022.119786}, pmid = {35872283}, issn = {1873-6424}, mesh = {Anaerobiosis ; Biodegradation, Environmental ; Bioreactors ; Ecosystem ; Isotopes ; *Polybrominated Biphenyls ; *Proteogenomics ; }, abstract = {Tetrabromobisphenol A (TBBPA) is the most used flame retardant worldwide and has become a threat to aquatic ecosystems. Previous research into the degradation of this micropollutant in anaerobic bioreactors has suggested several identities of putative TBBPA degraders. However, the organisms actively degrading TBBPA under in situ conditions have so far not been identified. Protein-stable isotope probing (protein-SIP) has become a cutting-edge technique in microbial ecology for enabling the link between identity and function under in situ conditions. Therefore, it was hypothesized that combining protein-based stable isotope probing with metagenomics could be used to identify and provide genomic insight into the TBBPA-degrading organisms. The identified [13]C-labelled peptides were found to belong to organisms affiliated to Phytobacter, Clostridium, Sporolactobacillus, and Klebsilla genera. The functional classification of identified labelled peptides revealed that TBBPA is not only transformed by cometabolic reactions, but also assimilated into the biomass. By application of the proteogenomics with labelled micropollutants (protein-SIP) and metagenome-assembled genomes, it was possible to extend the current perspective of the diversity of TBBPA degraders in wastewater and predict putative TBBPA degradation pathways. The study provides a link to the active TBBPA degraders and which organisms to favor for optimized biodegradation.}, }
@article {pmid35870225, year = {2022}, author = {Collinge, DB and Jensen, B and Jørgensen, HJ}, title = {Fungal endophytes in plants and their relationship to plant disease.}, journal = {Current opinion in microbiology}, volume = {69}, number = {}, pages = {102177}, doi = {10.1016/j.mib.2022.102177}, pmid = {35870225}, issn = {1879-0364}, mesh = {*Endophytes/genetics ; *Fungi/genetics/metabolism ; Plant Diseases ; Plant Growth Regulators/metabolism ; Plants/microbiology ; }, abstract = {The enigmatic endophytic fungi are beginning to reveal their secrets. Like pathogens, they can manipulate the host for their own benefit to create their own optimal habitat. Some endophytic manipulations induce resistance or otherwise outcompete pathogens and can thus be exploited for biological control. Like pathogens and other symbionts, endophytes produce effector proteins and other molecules, ranging from specialised metabolites, phytohormones and microRNAs, to manipulate their hosts and other microorganisms they meet. There is a continuum from endophyte to pathogen: some organisms can infest or cause disease in some hosts, but not in others. Molecular genetics approaches coupled with functional characterisation have demonstrated their worth for understanding the biological phenomena underlying endophytic fungal interactions.}, }
@article {pmid35869999, year = {2023}, author = {Pant, A and Maiti, TK and Mahajan, D and Das, B}, title = {Human Gut Microbiota and Drug Metabolism.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {97-111}, pmid = {35869999}, issn = {1432-184X}, support = {DST/INSPIRE/04/2020/001246//Department of Science and Technology, Government of India/ ; THSTI Intramural//Department of Biotechnology, Government of India/ ; 2021//Department of Biotechnology, Government of India/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Microbiota/physiology ; Xenobiotics/metabolism/pharmacology ; }, abstract = {The efficacy of drugs widely varies in individuals, and the gut microbiota plays an important role in this variability. The commensal microbiota living in the human gut encodes several enzymes that chemically modify systemic and orally administered drugs, and such modifications can lead to activation, inactivation, toxification, altered stability, poor bioavailability, and rapid excretion. Our knowledge of the role of the human gut microbiome in therapeutic outcomes continues to evolve. Recent studies suggest the existence of complex interactions between microbial functions and therapeutic drugs across the human body. Therapeutic drugs or xenobiotics can influence the composition of the gut microbiome and the microbial encoded functions. Both these deviations can alter the chemical transformations of the drugs and hence treatment outcomes. In this review, we provide an overview of (i) the genetic ecology of microbially encoded functions linked with xenobiotic degradation; (ii) the effect of drugs on the composition and function of the gut microbiome; and (iii) the importance of the gut microbiota in drug metabolism.}, }
@article {pmid35869965, year = {2022}, author = {West, JR and Whitman, T}, title = {Disturbance by soil mixing decreases microbial richness and supports homogenizing community assembly processes.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {9}, pages = {}, pmid = {35869965}, issn = {1574-6941}, mesh = {Bacteria ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; *Soil ; *Soil Microbiology ; }, abstract = {The spatial heterogeneity of soil's microhabitats warrants the study of ecological patterns and community assembly processes in the context of physical disturbance that disrupts the inherent spatial isolation of soil microhabitats and microbial communities. By mixing soil at various frequencies in a 16-week lab incubation, we explored the effects of physical disturbance on soil bacterial richness, community composition, and community assembly processes. We hypothesized that well-mixed soil would harbor a less rich microbial community, with community assembly marked by homogenizing dispersal and homogeneous selection. Using 16S rRNA gene sequencing, we inferred community assembly processes, estimated richness and differential abundance, and calculated compositional dissimilarity. Findings supported our hypotheses, with > 20% decrease in soil bacterial richness in well-mixed soil. Soil mixing caused communities to diverge from unmixed controls (Bray-Curtis dissimilarity; 0.75 vs. 0.25), while reducing within-group heterogeneity. Our results imply that the vast diversity observed in soil may be supported by spatial heterogeneity and isolation of microbial communities, and also provide insight into the effects of physical disturbance and community coalescence events. By isolating and better understanding the effects of spatial heterogeneity and disconnectivity on soil microbial communities, we can better extrapolate how anthropogenic disturbances may affect broad soil functions.}, }
@article {pmid35869541, year = {2022}, author = {Palomo, A and Azevedo, D and Touceda-Suárez, M and Domingo-Félez, C and Mutlu, AG and Dechesne, A and Wang, Y and Zhang, T and Smets, BF}, title = {Efficient management of the nitritation-anammox microbiome through intermittent aeration: absence of the NOB guild and expansion and diversity of the NOx reducing guild suggests a highly reticulated nitrogen cycle.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {39}, pmid = {35869541}, issn = {2524-6372}, support = {REA 607492//FP7 People: Marie-Curie Actions/ ; REA 607492//FP7 People: Marie-Curie Actions/ ; Expa-N 13391//Villlum Fonden/ ; Expa-N 13391//Villlum Fonden/ ; }, abstract = {Obtaining efficient autotrophic ammonia removal (aka partial nitritation-anammox, or PNA) requires a balanced microbiome with abundant aerobic and anaerobic ammonia oxidizing bacteria and scarce nitrite oxidizing bacteria. Here, we analyzed the microbiome of an efficient PNA process that was obtained by sequential feeding and periodic aeration. The genomes of the dominant community members were inferred from metagenomes obtained over a 6 month period. Three Brocadia spp. genomes and three Nitrosomonas spp. genomes dominated the autotrophic community; no NOB genomes were retrieved. Two of the Brocadia spp. genomes lacked the genomic potential for nitrite reduction. A diverse set of heterotrophic genomes was retrieved, each with genomic potential for only a fraction of the denitrification pathway. A mutual dependency in amino acid and vitamin synthesis was noted between autotrophic and heterotrophic community members. Our analysis suggests a highly-reticulated nitrogen cycle in the examined PNA microbiome with nitric oxide exchange between the heterotrophs and the anammox guild.}, }
@article {pmid35867140, year = {2023}, author = {López-Hernández, J and García-Cárdenas, E and López-Bucio, JS and Jiménez-Vázquez, KR and de la Cruz, HR and Ferrera-Rodríguez, O and Santos-Rodríguez, DL and Ortiz-Castro, R and López-Bucio, J}, title = {Screening of Phosphate Solubilization Identifies Six Pseudomonas Species with Contrasting Phytostimulation Properties in Arabidopsis Seedlings.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {431-445}, pmid = {35867140}, issn = {1432-184X}, support = {A1-S-34768//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; }, mesh = {*Arabidopsis/genetics/metabolism ; Pseudomonas/genetics ; Seedlings ; Phosphates/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; Plant Roots/microbiology ; Indoleacetic Acids/metabolism ; Bacteria/genetics ; }, abstract = {The interaction of plants with bacteria and the long-term success of their adaptation to challenging environments depend upon critical traits that include nutrient solubilization, remodeling of root architecture, and modulation of host hormonal status. To examine whether bacterial promotion of phosphate solubilization, root branching and the host auxin response may account for plant growth, we isolated and characterized ten bacterial strains based on their high capability to solubilize calcium phosphate. All strains could be grouped into six Pseudomonas species, namely P. brassicae, P. baetica, P. laurylsulfatiphila, P. chlororaphis, P. lurida, and P. extremorientalis via 16S rRNA molecular analyses. A Solibacillus isronensis strain was also identified, which remained neutral when interacting with Arabidopsis roots, and thus could be used as inoculation control. The interaction of Arabidopsis seedlings with bacterial streaks from pure cultures in vitro indicated that their phytostimulation properties largely differ, since P. brassicae and P. laurylsulfatiphila strongly increased shoot and root biomass, whereas the other species did not. Most bacterial isolates, except P. chlororaphis promoted lateral root formation, and P. lurida and P. chlororaphis strongly enhanced expression of the auxin-inducible gene construct DR5:GUS in roots, but the most bioactive probiotic bacterium P. brassicae could not enhance the auxin response. Inoculation with P. brassicae and P. lurida improved shoot and root growth in medium supplemented with calcium phosphate as the sole Pi source. Collectively, our data indicate the differential responses of Arabidopsis seedlings to inoculation with several Pseudomonas species and highlight the potential of P. brassicae to manage phosphate nutrition and plant growth in a more eco-friendly manner.}, }
@article {pmid35867139, year = {2023}, author = {Birnbaum, C and Wood, J and Lilleskov, E and Lamit, LJ and Shannon, J and Brewer, M and Grover, S}, title = {Degradation Reduces Microbial Richness and Alters Microbial Functions in an Australian Peatland.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {875-891}, pmid = {35867139}, issn = {1432-184X}, support = {DEB-1 146 149//National Science Foundation/ ; ID 1445//U.S. Department of Energy/ ; SLaM/2020/118//Australian Centre for International Agricultural Research/ ; }, mesh = {Australia ; Carbon/metabolism ; *Ecosystem ; Manganese ; *Microbiota ; Nitrogen/analysis ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Peatland ecosystems cover only 3% of the world's land area; however, they store one-third of the global soil carbon (C). Microbial communities are the main drivers of C decomposition in peatlands, yet we have limited knowledge of their structure and function. While the microbial communities in the Northern Hemisphere peatlands are well documented, we have limited understanding of microbial community composition and function in the Southern Hemisphere peatlands, especially in Australia. We investigated the vertical stratification of prokaryote and fungal communities from Wellington Plains peatland in the Australian Alps. Within the peatland complex, bog peat was sampled from the intact peatland and dried peat from the degraded peatland along a vertical soil depth gradient (i.e., acrotelm, mesotelm, and catotelm). We analyzed the prokaryote and fungal community structure, predicted functional profiles of prokaryotes using PICRUSt, and assigned soil fungal guilds using FUNGuild. We found that the structure and function of prokaryotes were vertically stratified in the intact bog. Soil carbon, manganese, nitrogen, lead, and sodium content best explained the prokaryote composition. Prokaryote richness was significantly higher in the intact bog acrotelm compared to degraded bog acrotelm. Fungal composition remained similar across the soil depth gradient; however, there was a considerable increase in saprotroph abundance and decrease in endophyte abundance along the vertical soil depth gradient. The abundance of saprotrophs and plant pathogens was two-fold higher in the degraded bog acrotelm. Soil manganese and nitrogen content, electrical conductivity, and water table level (cm) best explained the fungal composition. Our results demonstrate that both fungal and prokaryote communities are shaped by soil abiotic factors and that peatland degradation reduces microbial richness and alters microbial functions. Thus, current and future changes to the environmental conditions in these peatlands may lead to altered microbial community structures and associated functions which may have implications for broader ecosystem function changes in peatlands.}, }
@article {pmid35867138, year = {2023}, author = {Mathur, V and Ulanova, D}, title = {Microbial Metabolites Beneficial to Plant Hosts Across Ecosystems.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {25-48}, pmid = {35867138}, issn = {1432-184X}, support = {ECR/2017/001466//SERB (Ministry of S&amp;T, Govt. of India)/ ; Four dimensions Kuroshio Marine Science (4D-KMS) Project//Ministry of Education, Culture, Sports, Science and Technology, Japan/ ; }, mesh = {*Ecosystem ; *Plants/metabolism ; Adaptation, Physiological ; Symbiosis ; Environmental Pollution ; }, abstract = {Plants are intimately connected with their associated microorganisms. Chemical interactions via natural products between plants and their microbial symbionts form an important aspect in host health and development, both in aquatic and terrestrial ecosystems. These interactions range from negative to beneficial for microbial symbionts as well as their hosts. Symbiotic microbes synchronize their metabolism with their hosts, thus suggesting a possible coevolution among them. Metabolites, synthesized from plants and microbes due to their association and coaction, supplement the already present metabolites, thus promoting plant growth, maintaining physiological status, and countering various biotic and abiotic stress factors. However, environmental changes, such as pollution and temperature variations, as well as anthropogenic-induced monoculture settings, have a significant influence on plant-associated microbial community and its interaction with the host. In this review, we put the prominent microbial metabolites participating in plant-microbe interactions in the natural terrestrial and aquatic ecosystems in a single perspective and have discussed commonalities and differences in these interactions for adaptation to surrounding environment and how environmental changes can alter the same. We also present the status and further possibilities of employing chemical interactions for environment remediation. Our review thus underlines the importance of ecosystem-driven functional adaptations of plant-microbe interactions in natural and anthropogenically influenced ecosystems and their possible applications.}, }
@article {pmid35866234, year = {2022}, author = {Mahmud, MR and Akter, S and Tamanna, SK and Mazumder, L and Esti, IZ and Banerjee, S and Akter, S and Hasan, MR and Acharjee, M and Hossain, MS and Pirttilä, AM}, title = {Impact of gut microbiome on skin health: gut-skin axis observed through the lenses of therapeutics and skin diseases.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2096995}, pmid = {35866234}, issn = {1949-0984}, mesh = {Dysbiosis/therapy ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Prebiotics ; *Probiotics/therapeutic use ; Skin ; *Skin Diseases/therapy ; }, abstract = {The human intestine hosts diverse microbial communities that play a significant role in maintaining gut-skin homeostasis. When the relationship between gut microbiome and the immune system is impaired, subsequent effects can be triggered on the skin, potentially promoting the development of skin diseases. The mechanisms through which the gut microbiome affects skin health are still unclear. Enhancing our understanding on the connection between skin and gut microbiome is needed to find novel ways to treat human skin disorders. In this review, we systematically evaluate current data regarding microbial ecology of healthy skin and gut, diet, pre- and probiotics, and antibiotics, on gut microbiome and their effects on skin health. We discuss potential mechanisms of the gut-skin axis and the link between the gut and skin-associated diseases, such as psoriasis, atopic dermatitis, acne vulgaris, rosacea, alopecia areata, and hidradenitis suppurativa. This review will increase our understanding of the impacts of gut microbiome on skin conditions to aid in finding new medications for skin-associated diseases.}, }
@article {pmid35864173, year = {2023}, author = {Tian, C and Pang, J and Bu, C and Wu, S and Bai, H and Li, Y and Guo, Q and Siddique, KHM}, title = {The Microbiomes in Lichen and Moss Biocrust Contribute Differently to Carbon and Nitrogen Cycles in Arid Ecosystems.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {497-508}, pmid = {35864173}, issn = {1432-184X}, support = {2016YFE0203400//National Key Research and Development Program of China/ ; 2017YFC0504703//National Key Research and Development Program of China/ ; 41971131//National Natural Scientific Foundation of China/ ; }, mesh = {Ecosystem ; *Lichens ; Carbon ; Nitrates ; Soil/chemistry ; *Bryophyta ; Nitrogen Fixation ; *Microbiota ; Soil Microbiology ; Nitrogen/chemistry ; }, abstract = {Biological soil crusts (biocrusts) are distributed in arid and semiarid regions across the globe. Microorganisms are an essential component in biocrusts. They add and accelerate critical biochemical processes. However, little is known about the functional genes and metabolic processes of microbiomes in lichen and moss biocrust. This study used shotgun metagenomic sequencing to compare the microbiomes of lichen-dominated and moss-dominated biocrust and reveal the microbial genes and metabolic pathways involved in carbon and nitrogen cycling. The results showed that Actinobacteria, Bacteroidetes, and Acidobacteria were more abundant in moss biocrust than lichen biocrust, while Proteobacteria and Cyanobacteria were more abundant in lichen biocrust than moss biocrust. The relative abundance of carbohydrate-active enzymes and enzymes associated with carbon and nitrogen metabolism differed significantly between microbiomes of the two biocrust types. However, in the microbial communities of both biocrust types, respiration pathways dominated over carbon fixation pathways. The genes encoding carbon monoxide dehydrogenase were more abundant than those encoding ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo) involved in carbon fixation. Similarly, metabolic N-pathway diversity was dominated by nitrogen reduction, followed by denitrification, with nitrogen fixation the lowest proportion. Gene diversity involved in N cycling differed between the microbiomes of the two biocrust types. Assimilatory nitrate reduction genes had higher relative abundance in lichen biocrust, whereas dissimilatory nitrate reduction genes had higher relative abundance in moss biocrust. As dissolved organic carbon and soil organic carbon are considered the main drivers of the community structure in the microbiome of biocrust, these results indicate that biocrust type has a pivotal role in microbial diversity and related biogeochemical cycling.}, }
@article {pmid35863929, year = {2022}, author = {Ouamba, AJK and Gagnon, M and LaPointe, G and Chouinard, PY and Roy, D}, title = {Graduate Student Literature Review: Farm management practices: Potential microbial sources that determine the microbiota of raw bovine milk.}, journal = {Journal of dairy science}, volume = {105}, number = {9}, pages = {7276-7287}, doi = {10.3168/jds.2021-21758}, pmid = {35863929}, issn = {1525-3198}, mesh = {Animals ; Bacteria ; Cattle ; *Dairying/methods ; Farms ; Female ; Humans ; Lactation ; *Microbiota ; Milk/microbiology ; Students ; }, abstract = {Environmental and herd-associated factors such as geographical location, climatic conditions, forage types, bedding, soil, animal genetics, herd size, housing, lactation stage, and udder health are exploited by farmers to dictate specific management strategies that ensure dairy operation profitability and enhance the sustainability of milk production. Along with milking routines, milking systems, and storage conditions, these farming practices greatly influence the microbiota of raw milk, as evidenced by several recent studies. During the past few years, the increased interest in high-throughput sequencing technologies combined with culture-dependent methods to investigate dairy microbial ecology has improved our understanding of raw milk community dynamics throughout storage and processing. However, knowledge is still lacking on the niche-specific communities in the farm environment, and on the factors that determine bacteria transfer to the raw milk. This review summarizes findings from the past 2 decades regarding the effects of farm management practices on the diversity of bacterial species that determine the microbiological quality of raw cow milk.}, }
@article {pmid35862964, year = {2022}, author = {Zhang, Q and Zou, X and Wu, S and Wu, N and Chen, X and Zhou, W}, title = {Effects of Pyroligneous Acid on Diversity and Dynamics of Antibiotic Resistance Genes in Alfalfa Silage.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0155422}, pmid = {35862964}, issn = {2165-0497}, mesh = {Ammonia ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Fermentation ; Humans ; Lactobacillus/genetics ; *Medicago sativa/chemistry/microbiology ; *Silage/analysis/microbiology ; Terpenes ; Tetracyclines ; }, abstract = {Antibiotic resistance genes (ARGs) are recognized as contaminants due to their potential risk for human and environment. The aim of the present study is to investigate the effects of pyroligneous acid (PA), a waste of biochar production, on fermentation characteristics, diversity, and dynamics of ARGs during ensiling of alfalfa using metagenomic analysis. The results indicated that PA decreased (P < 0.05) dry matter loss, pH value, gas production, coliform bacteria count, protease activity, and nonprotein-N, ammonia-N, and butyric acid contents and increased (P < 0.05) lactic acid content during ensiling. During fermentation, Bacteria, Firmicutes, and Lactobacillus were the most abundant at kingdom, phylum, and genus levels, respectively. Pyroligneous acid reduced the relative abundance of Bacteria and Firmicutes and increased that of Lactobacillus. The detected ARGs belonged to 36 drug classes, including mainly macrolides, tetracycline, lincosamides, and phenicol. These types of ARGs decreased during fermentation and were further reduced by PA. These types of ARGs were positively correlated (P < 0.05) with fermentation parameters like pH value and ammonia-N content and with bacterial communities. At the genus level, the top several drug classes, including macrolide, tetracycline, lincosamide, phenicol, oxazolidinone, streptogramin, pleuromutilin, and glycopeptide, were positively correlated with Staphylococcus, Streptococcus, Listeria, Bacillus, Klebsiella, Clostridium, and Enterobacter, the potential hosts of ARGs. Overall, ARGs in alfalfa silage were abundant and were influenced by the fermentation parameters and microbial community composition. Ensiling could be a feasible way to mitigate ARGs in forages. The addition of PA could not only improve fermentation quality but also reduce ARG pollution of alfalfa silage. IMPORTANCE Antibiotic resistance genes (ARGs) are considered environmental pollutants posing a potential human health risk. Silage is an important and traditional feed, mainly for ruminants. ARGs in silages might influence the diversity and distribution of ARGs in animal intestinal and feces and then the manure and the manured soil. However, the diversity and dynamics of ARGs in silage during fermentation are still unknown. We ensiled alfalfa, one of the most widely used forages, with or without pyroligneous acid (PA), which was proved to have the ability to reduce ARGs in soils. The results showed that ARGs in alfalfa silage were abundant and were influenced by the fermentation parameters and microbial community. The majority of ARGs in alfalfa silage reduced during fermentation. The addition of PA could improve silage quality and reduce ARG pollution in alfalfa silage. This study can provide useful information for understanding and controlling ARG pollution in animal production.}, }
@article {pmid35862940, year = {2022}, author = {Molina-Santiago, C and Pearson, JR and Berlanga-Clavero, MV and Pérez-Lorente, AI and de Vicente, A and Romero, D}, title = {A Noninvasive Method for Time-Lapse Imaging of Microbial Interactions and Colony Dynamics.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0093922}, pmid = {35862940}, issn = {2165-0497}, mesh = {Bacteria ; Biofilms ; *Microbial Interactions ; *Microbiota ; Time-Lapse Imaging ; }, abstract = {Complex interactions between microbial populations can greatly affect the overall properties of a microbial community, sometimes leading to cooperation and mutually beneficial coexistence, or competition and the death or displacement of organisms or subpopulations. Interactions between different biofilm populations are highly relevant in diverse scientific areas, from antimicrobial resistance to microbial ecology. The utilization of modern microscopic techniques has provided a new and interesting insight into how bacteria interact at the cellular level to form and maintain microbial biofilms. However, our ability to follow complex intraspecies and interspecies interactions in vivo at the microscopic level has remained somewhat limited. Here, we detailed BacLive, a novel noninvasive method for tracking bacterial growth and biofilm dynamics using high-resolution fluorescence microscopy and an associated ImageJ processing macro (https://github.com/BacLive) for easier data handling and image analysis. Finally, we provided examples of how BacLive can be used in the analysis of complex bacterial communities. IMPORTANCE Communication and interactions between single cells are continuously defining the structure and composition of microbial communities temporally and spatially. Methods routinely used to study these communities at the cellular level rely on sample manipulation which makes microscopic time-lapse experiments impossible. BacLive was conceived as a method for the noninvasive study of the formation and development of bacterial communities, such as biofilms, and the formation dynamics of specialized subpopulations in time-lapse experiments at a colony level. In addition, we developed a tool to simplify the processing and analysis of the data generated by this method.}, }
@article {pmid35862824, year = {2022}, author = {Schultz, J and Modolon, F and Rosado, AS and Voolstra, CR and Sweet, M and Peixoto, RS}, title = {Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0036722}, pmid = {35862824}, issn = {2379-5077}, mesh = {Animals ; *Anthozoa ; Bacteria/genetics ; *Microbiota/genetics ; Metagenome ; Biotechnology ; }, abstract = {The vast majority of environmental microbes have not yet been cultured, and most of the knowledge on coral-associated microbes (CAMs) has been generated from amplicon sequencing and metagenomes. However, exploring cultured CAMs is key for a detailed and comprehensive characterization of the roles of these microbes in shaping coral health and, ultimately, for their biotechnological use as, for example, coral probiotics and other natural products. Here, the strategies and technologies that have been used to access cultured CAMs are presented, while advantages and disadvantages associated with each of these strategies are discussed. We highlight the existing gaps and potential improvements in culture-dependent methodologies, indicating several possible alternatives (including culturomics and in situ diffusion devices) that could be applied to retrieve the CAM "dark matter" (i.e., the currently undescribed CAMs). This study provides the most comprehensive synthesis of the methodologies used to recover the cultured coral microbiome to date and draws suggestions for the development of the next generation of CAM culturomics.}, }
@article {pmid35862808, year = {2022}, author = {Dove, NC and Carrell, AA and Engle, NL and Klingeman, DM and Rodriguez, M and Wahl, T and Tschaplinski, TJ and Muchero, W and Schadt, CW and Cregger, MA}, title = {Relationships between Sphaerulina musiva Infection and the Populus Microbiome and Metabolome.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0012022}, pmid = {35862808}, issn = {2379-5077}, mesh = {*Populus/genetics ; *Ascomycota/genetics ; *Microbiota/genetics ; Trees/microbiology ; Metabolome ; }, abstract = {Pathogenic fungal infections in plants may, in some cases, lead to downstream systematic impacts on the plant metabolome and microbiome that may either alleviate or exacerbate the effects of the fungal pathogen. While Sphaerulina musiva is a well-characterized fungal pathogen which infects Populus tree species, an important wood fiber and biofuel feedstock, little is known about its systematic effects on the metabolome and microbiome of Populus. Here, we investigated the metabolome of Populus trichocarpa and Populus deltoides leaves and roots and the microbiome of the leaf and root endospheres, phylloplane, and rhizosphere to understand the systematic impacts of S. musiva abundance and infection on Populus species in a common garden field setting. We found that S. musiva is indeed present in both P. deltoides and P. trichocarpa, but S. musiva abundance was not statistically related to stem canker onset. We also found that the leaf and root metabolomes significantly differ between the two Populus species and that certain leaf metabolites, particularly the phenolic glycosides salirepin and salireposide, are diminished in canker-infected P. trichocarpa trees compared to their uninfected counterparts. Furthermore, we found significant associations between the metabolome, S. musiva abundance, and microbiome composition and α-diversity, particularly in P. trichocarpa leaves. Our results show that S. musiva colonizes both resistant and susceptible hosts and that the effects of S. musiva on susceptible trees are not confined to the site of canker infection. IMPORTANCE Poplar (Populus spp.) trees are ecologically and economically important trees throughout North America. However, many western North American poplar plantations are at risk due to the introduction of the nonnative fungal pathogen Sphaerulina musiva, which causes leaf spot and cankers, limiting their production. To better understand the interactions among the pathogen S. musiva, the poplar metabolome, and the poplar microbiome, we collected leaf, root, and rhizosphere samples from poplar trees consisting of 10 genotypes and two species with differential resistance to S. musiva in a common garden experiment. Here, we outline the nuanced relationships between the poplar metabolome, microbiome, and S. musiva, showing that S. musiva may affect poplar trees in tissues distal to the site of infection (i.e., stem). Our research contributes to improving the fundamental understanding of S. musiva and Populus sp. ecology and the utility of a holobiont approach in understanding plant disease.}, }
@article {pmid35862804, year = {2022}, author = {Green, EA and Klassen, JL}, title = {Trachymyrmex septentrionalis Ant Microbiome Assembly Is Unique to Individual Colonies and Castes.}, journal = {mSphere}, volume = {7}, number = {4}, pages = {e0098921}, pmid = {35862804}, issn = {2379-5042}, mesh = {Animals ; Female ; Male ; *Ants/microbiology ; Fungi ; Larva ; *Microbiota ; United States ; }, abstract = {Within social insect colonies, microbiomes often differ between castes due to their different functional roles and between colony locations. Trachymyrmex septentrionalis fungus-growing ants form colonies throughout the eastern United States and northern Mexico that include workers, female and male alates (unmated reproductive castes), larvae, and pupae. How T. septentrionalis microbiomes vary across this geographic range and between castes is unknown. Our sampling of individual ants from colonies across the eastern United States revealed a conserved T. septentrionalis worker ant microbiome and revealed that worker ant microbiomes are more conserved within colonies than between them. A deeper sampling of individual ants from two colonies that included all available castes (pupae, larvae, workers, and female and male alates), from both before and after adaptation to controlled laboratory conditions, revealed that ant microbiomes from each colony, caste, and rearing condition were typically conserved within but not between each sampling category. Tenericute bacterial symbionts were especially abundant in these ant microbiomes and varied widely in abundance between sampling categories. This study demonstrates how individual insect colonies primarily drive the composition of their microbiomes and shows that these microbiomes are further modified by developmental differences between insect castes and the different environmental conditions experienced by each colony. IMPORTANCE This study investigates microbiome assembly in the fungus-growing ant Trachymyrmex septentrionalis, showing how colony, caste, and lab adaptation influence the microbiome and revealing unique patterns of mollicute symbiont abundance. We find that ant microbiomes differ strongly between colonies but less so within colonies. Microbiomes of different castes and following lab adaptation also differ in a colony-specific manner. This study advances our understanding of the nature of individuality in social insect microbiomes and cautions against the common practice of only sampling a limited number of populations to understand microbiome diversity and function.}, }
@article {pmid35862792, year = {2022}, author = {Wale, N}, title = {mSphere of Influence: There's More to (a Pathogen's) Life than Growing Fast.}, journal = {mSphere}, volume = {7}, number = {4}, pages = {e0027722}, pmid = {35862792}, issn = {2379-5042}, mesh = {*Virulence ; }, abstract = {Nina Wale works in the field of infectious disease evolution and ecology. In this mSphere of Influence article, she reflects on how the paper by Roller and Schmidt, "The physiology and ecological implications of efficient growth" (B. R. Roller and T. M. Schmidt, ISME J 9:1481-1487, 2015, https://doi.org/10.1038/ismej.2014.235) broadened her thinking about how microbes acquire and allocate resources and, in so doing, set her research on pathogen virulence evolution in a new direction.}, }
@article {pmid35862730, year = {2022}, author = {Smith, DJ and Kharbush, JJ and Kersten, RD and Dick, GJ}, title = {Uptake of Phytoplankton-Derived Carbon and Cobalamins by Novel Acidobacteria Genera in Microcystis Blooms Inferred from Metagenomic and Metatranscriptomic Evidence.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {14}, pages = {e0180321}, pmid = {35862730}, issn = {1098-5336}, mesh = {Acidobacteria/metabolism ; Amino Acids/metabolism ; Carbon/metabolism ; *Cyanobacteria/genetics ; Ecosystem ; Hydrogen Peroxide/metabolism ; Lakes/microbiology ; *Microcystis/genetics/metabolism ; Nitrogen/metabolism ; Phytoplankton/metabolism ; Vitamin B 12/metabolism ; }, abstract = {Interactions between bacteria and phytoplankton can influence primary production, community composition, and algal bloom development. However, these interactions are poorly described for many consortia, particularly for freshwater bloom-forming cyanobacteria. Here, we assessed the gene content and expression of two uncultivated Acidobacteria from Lake Erie Microcystis blooms. These organisms were targeted because they were previously identified as important catalase producers in Microcystis blooms, suggesting that they protect Microcystis from H2O2. Metatranscriptomics revealed that both Acidobacteria transcribed genes for uptake of organic compounds that are known cyanobacterial products and exudates, including lactate, glycolate, amino acids, peptides, and cobalamins. Expressed genes for amino acid metabolism and peptide transport and degradation suggest that use of amino acids and peptides by Acidobacteria may regenerate nitrogen for cyanobacteria and other organisms. The Acidobacteria genomes lacked genes for biosynthesis of cobalamins but expressed genes for its transport and remodeling. This indicates that the Acidobacteria obtained cobalamins externally, potentially from Microcystis, which has a complete gene repertoire for pseudocobalamin biosynthesis; expressed them in field samples; and produced pseudocobalamin in axenic culture. Both Acidobacteria were detected in Microcystis blooms worldwide. Together, the data support the hypotheses that uncultured and previously unidentified Acidobacteria taxa exchange metabolites with phytoplankton during harmful cyanobacterial blooms and influence nitrogen available to phytoplankton. Thus, novel Acidobacteria may play a role in cyanobacterial physiology and bloom development. IMPORTANCE Interactions between heterotrophic bacteria and phytoplankton influence competition and successions between phytoplankton taxa, thereby influencing ecosystem-wide processes such as carbon cycling and algal bloom development. The cyanobacterium Microcystis forms harmful blooms in freshwaters worldwide and grows in buoyant colonies that harbor other bacteria in their phycospheres. Bacteria in the phycosphere and in the surrounding community likely influence Microcystis physiology and ecology and thus the development of freshwater harmful cyanobacterial blooms. However, the impacts and mechanisms of interaction between bacteria and Microcystis are not fully understood. This study explores the mechanisms of interaction between Microcystis and uncultured members of its phycosphere in situ with population genome resolution to investigate the cooccurrence of Microcystis and freshwater Acidobacteria in blooms worldwide.}, }
@article {pmid35859070, year = {2023}, author = {Ienes-Lima, J and Prichula, J and Abadie, M and Borges-Martins, M and Frazzon, APG}, title = {First Report of Culturable Skin Bacteria in Melanophryniscus admirabilis (Admirable Redbelly Toad).}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {756-761}, pmid = {35859070}, issn = {1432-184X}, support = {#305495/2018-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico do Brasil/ ; #309769/2020-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; PROAP//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {Animals ; *Chytridiomycota ; Bufonidae ; Forests ; Bacteria ; Skin/microbiology ; }, abstract = {Melanophryniscus admirabilis is a small toad, critically endangered with a microendemic distribution in the Atlantic Forest in southern Brazil. The amphibian skin microbiome is considered one of the first lines of defense against pathogenic infections, such as Batrachochytrium dendrobatidis (Bd). The knowledge of skin amphibian microbiomes is important to numerous fields, including species conservation, detection, and quantification of environmental changes and stressors. In the present study, we investigated, for the first time, cultivable bacteria in the skin of wild M. admirabilis, and detected Bd fungus by nested polymerase chain reaction (PCR) technique. Skin swab samples were collected from 15 wild M. admirabilis, and the isolation of bacteria was performed by means of different culture strategies. A total of 62 bacterial isolates being Bacillus (n = 22; 34.48%), Citrobacter (n = 10; 16.13%), and Serratia (n = 12; 19.35%) were more frequently isolated genera. Interestingly, all skin samples tested were Bd negative. Some bacterial genera identified in our study might be acting in a synergic relationship and protecting them against the Bd fungus. In addition, these bacteria may play an essential role in maintaining this species in an environment modulated by anthropic actions. This first report of skin cultivable bacteria from M. admirabilis natural population improves our knowledge of skin amphibian microbiomes, contributing to a better understanding of their ecology and how this species has survived in an environment modulated by anthropic action.}, }
@article {pmid35859069, year = {2023}, author = {Alvarenga, DO and Elmdam, IV and Timm, AB and Rousk, K}, title = {Chemical Stimulation of Heterocyte Differentiation by the Feather Moss Hylocomium splendens: a Potential New Step in Plant-Cyanobacteria Symbioses.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {419-430}, pmid = {35859069}, issn = {1432-184X}, support = {7027-00011B//Danmarks Frie Forskningsfond/ ; }, mesh = {Ecosystem ; Stimulation, Chemical ; Nitrogen Fixation/physiology ; *Bryophyta/physiology ; *Bryopsida/metabolism/microbiology ; *Cyanobacteria/metabolism ; Nitrogenase/metabolism ; Plant Extracts ; }, abstract = {Cyanobacteria associated with mosses play a key role in the nitrogen (N) cycle in unpolluted ecosystems. Mosses have been found to release molecules that induce morphophysiological changes in epiphytic cyanobionts. Nevertheless, the extent of moss influence on these microorganisms remains unknown. To evaluate how mosses or their metabolites influence N2 fixation rates by cyanobacteria, we assessed the nitrogenase activity, heterocyte frequency and biomass of a cyanobacterial strain isolated from the feather moss Hylocomium splendens and a non-symbiotic strain when they were either growing by themselves, together with H. splendens or exposed to H. splendens water, acetone, ethanol, or isopropanol extracts. The same cyanobacterial strains were added to another moss (Taxiphyllum barbieri) and a liverwort (Monosolenium tenerum) to assess if these bryophytes affect N2 fixation differently. Although no significant increases in nitrogenase activity by the cyanobacteria were observed when in contact with H. splendens shoots, both the symbiotic and non-symbiotic cyanobacteria increased nitrogenase activity as well as heterocyte frequency significantly upon exposure to H. splendens ethanol extracts. Contact with T. barbieri shoots, on the other hand, did lead to increases in nitrogenase activity, indicating low host-specificity to cyanobacterial activity. These findings suggest that H. splendens produces heterocyte-differentiating factors (HDFs) that are capable of stimulating cyanobacterial N2 fixation regardless of symbiotic competency. Based on previous knowledge about the chemical ecology and dynamics of moss-cyanobacteria interactions, we speculate that HDF expression by the host takes place in a hypothetical new step occurring after plant colonization and the repression of hormogonia.}, }
@article {pmid35858363, year = {2022}, author = {Miller, SD}, title = {Boat encounter with the 2019 Java bioluminescent milky sea: Views from on-deck confirm satellite detection.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {29}, pages = {e2207612119}, pmid = {35858363}, issn = {1091-6490}, mesh = {*Bacteria ; Indonesia ; Luminescence ; Oceans and Seas ; *Satellite Imagery ; *Seawater/microbiology ; *Ships ; }, abstract = {"Milky seas" are massive swaths of uniformly and steadily glowing ocean seen at night. The phenomenon is thought to be caused by luminous bacteria, but details of milky sea composition, structure, cause, and implications in nature remain largely uncertain. Between late July and early September 2019, specialized low-light satellite sensors detected a possible bioluminescent milky sea south of Java, Indonesia, spanning >100,000 km[2]. Upon learning of these findings, crew members of the yacht Ganesha reached out to confirm and share details of their personal encounter with this same event. Here, we document Ganesha's experience as recalled by the crew, compare their course to satellite data, and assess their photography of this milky sea.}, }
@article {pmid35857039, year = {2023}, author = {Matsumura, E and Morinaga, K and Fukuda, K}, title = {Host Specificity and Seasonal Variation in the Colonization of Tubakia sensu lato Associated with Evergreen Oak Species in Eastern Japan.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {240-252}, pmid = {35857039}, issn = {1432-184X}, support = {JP16H06737//Japan Society for the Promotion of Science/ ; }, mesh = {*Quercus/microbiology ; Seasons ; Host Specificity ; Japan ; *Ascomycota ; Endophytes ; }, abstract = {Foliar fungal endophytes are ubiquitous and hyperdiverse, and tend to be host-specific among dominant forest tree species. The fungal genus Tubakia sensu lato is comprised of foliar pathogens and endophytes that exhibit host preference for Quercus and other Fagaceae species. To clarify interspecific differences in ecological characteristics among Tubakia species, we examined the endophyte communities of seven evergreen Quercus spp. at three sites in eastern Japan during summer and winter. Host tree species was the most significant factor affecting endophyte community composition. Tubakia species found at the study sites were divided into five specialists and three generalists according to their relative abundance in each host species and their host ranges. Specialists were dominant on their own host in summer, and their abundance declined in winter. To test the hypothesis that generalists are more widely adapted to their environment than specialists, we compared their spore germination rates at different temperatures. Spores of generalist Tubakia species were more tolerant of colder temperatures than were spores of specialist Tubakia species, supporting our hypothesis. Seasonal and site variations among Tubakia species were also consistent with our hypothesis. Host identity and ecology were significantly associated with endophyte community structure.}, }
@article {pmid35856685, year = {2022}, author = {Forchielli, E and Sher, D and Segrè, D}, title = {Metabolic Phenotyping of Marine Heterotrophs on Refactored Media Reveals Diverse Metabolic Adaptations and Lifestyle Strategies.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0007022}, pmid = {35856685}, issn = {2379-5077}, mesh = {*Seawater/chemistry ; Phylogeny ; Oceans and Seas ; Bacteria/genetics ; *Microbiota/genetics ; Phytoplankton/genetics ; Carbon/metabolism ; }, abstract = {Microbial communities, through their metabolism, drive carbon cycling in marine environments. These complex communities are composed of many different microorganisms including heterotrophic bacteria, each with its own nutritional needs and metabolic capabilities. Yet, models of ecosystem processes typically treat heterotrophic bacteria as a "black box," which does not resolve metabolic heterogeneity nor address ecologically important processes such as the successive modification of different types of organic matter. Here we directly address the heterogeneity of metabolism by characterizing the carbon source utilization preferences of 63 heterotrophic bacteria representative of several major marine clades. By systematically growing these bacteria on 10 media containing specific subsets of carbon sources found in marine biomass, we obtained a phenotypic fingerprint that we used to explore the relationship between metabolic preferences and phylogenetic or genomic features. At the class level, these bacteria display broadly conserved patterns of preference for different carbon sources. Despite these broad taxonomic trends, growth profiles correlate poorly with phylogenetic distance or genome-wide gene content. However, metabolic preferences are strongly predicted by a handful of key enzymes that preferentially belong to a few enriched metabolic pathways, such as those involved in glyoxylate metabolism and biofilm formation. We find that enriched pathways point to enzymes directly involved in the metabolism of the corresponding carbon source and suggest potential associations between metabolic preferences and other ecologically relevant traits. The availability of systematic phenotypes across multiple synthetic media constitutes a valuable resource for future quantitative modeling efforts and systematic studies of interspecies interactions. IMPORTANCE Half of the Earth's annual primary production is carried out by phytoplankton in the surface ocean. However, this metabolic activity is heavily impacted by heterotrophic bacteria, which dominate the transformation of organic matter released from phytoplankton. Here, we characterize the diversity of metabolic preferences across many representative heterotrophs by systematically growing them on different fractions of dissolved organic carbon. Our analysis suggests that different clades of bacteria have substantially distinct preferences for specific carbon sources, in a way that cannot be simply mapped onto phylogeny. These preferences are associated with the presence of specific genes and pathways, reflecting an association between metabolic capabilities and ecological lifestyles. In addition to helping understand the importance of heterotrophs under different conditions, the phenotypic fingerprint we obtained can help build higher resolution quantitative models of global microbial activity and biogeochemical cycles in the oceans.}, }
@article {pmid35856563, year = {2022}, author = {Lesniak, NA and Schubert, AM and Flynn, KJ and Leslie, JL and Sinani, H and Bergin, IL and Young, VB and Schloss, PD}, title = {The Gut Bacterial Community Potentiates Clostridioides difficile Infection Severity.}, journal = {mBio}, volume = {13}, number = {4}, pages = {e0118322}, pmid = {35856563}, issn = {2150-7511}, support = {T32 AI007528/AI/NIAID NIH HHS/United States ; U19 AI090871/AI/NIAID NIH HHS/United States ; R01 GM099514/GM/NIGMS NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; U2C DK110768/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; Bile Acids and Salts ; *Clostridioides difficile ; *Clostridium Infections/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Mice ; }, abstract = {The severity of Clostridioides difficile infections (CDI) has increased over the last few decades. Patient age, white blood cell count, and creatinine levels as well as C. difficile ribotype and toxin genes have been associated with disease severity. However, it is unclear whether specific members of the gut microbiota are associated with variations in disease severity. The gut microbiota is known to interact with C. difficile during infection. Perturbations to the gut microbiota are necessary for C. difficile to colonize the gut. The gut microbiota can inhibit C. difficile colonization through bile acid metabolism, nutrient consumption, and bacteriocin production. Here, we sought to demonstrate that members of the gut bacterial communities can also contribute to disease severity. We derived diverse gut communities by colonizing germfree mice with different human fecal communities. The mice were then infected with a single C. difficile ribotype 027 clinical isolate, which resulted in moribundity and histopathologic differences. The variation in severity was associated with the human fecal community that the mice received. Generally, bacterial populations with pathogenic potential, such as Enterococcus, Helicobacter, and Klebsiella, were associated with more-severe outcomes. Bacterial groups associated with fiber degradation and bile acid metabolism, such as Anaerotignum, Blautia, Lactonifactor, and Monoglobus, were associated with less-severe outcomes. These data indicate that, in addition to the host and C. difficile subtype, populations of gut bacteria can influence CDI disease severity. IMPORTANCE Clostridioides difficile colonization can be asymptomatic or develop into an infection ranging in severity from mild diarrhea to toxic megacolon, sepsis, and death. Models that predict severity and guide treatment decisions are based on clinical factors and C. difficile characteristics. Although the gut microbiome plays a role in protecting against CDI, its effect on CDI disease severity is unclear and has not been incorporated into disease severity models. We demonstrated that variation in the microbiome of mice colonized with human feces yielded a range of disease outcomes. These results revealed groups of bacteria associated with both severe and mild C. difficile infection outcomes. Gut bacterial community data from patients with CDI could improve our ability to identify patients at risk of developing more severe disease and improve interventions that target C. difficile and the gut bacteria to reduce host damage.}, }
@article {pmid35852610, year = {2022}, author = {Kankonkar, HT and Khandeparker, RS}, title = {Microplastics a Novel Substratum for Polyhydroxyalkanoate (PHA)-Producing Bacteria in Aquatic Environments.}, journal = {Current microbiology}, volume = {79}, number = {9}, pages = {258}, pmid = {35852610}, issn = {1432-0991}, mesh = {*Bacillus/genetics/metabolism ; Bacteria/genetics/metabolism ; Carbon/metabolism ; Microplastics ; Plastics/metabolism ; *Polyhydroxyalkanoates ; }, abstract = {Polyhydroxyalkanoates (PHA) being biological polymers have attracted great attention. PHA have similar properties to that of synthetic plastic and are biodegradable. To discourage plastic pollution in the environment alternative solutions to the plastic pollution has to be readily available. High cost in production of PHA limits the production of these polymers at industrial scale. Bacteria are screened for PHA from diverse niches to meet the current requirements of cheap PHA production at industrial level. The microbial biofilm formed on the surface of microplastic could be a potential source in providing bacteria of economic importance. This paper is an attempt to search microplastic niche for potential PHA producers. PHA production variation was observed with different parameters such as type of carbon source, nitrogen source concentration and also time of incubation. Bacillus sp. CM27 showed maximum PHA yield up to 32.1% among other isolates at 48 h with 2% glucose as carbon source. Optimization of media leads to increase in PHA yield (37.69%) of CDW in Bacillus sp. CM27. Amino acid sequence of Bacillus sp.CM27 showed the presence of PhaC box with sequence, G-Y-C-M-G-G having cysteine in the middle of the box. The extracted polymer was confirmed by FTIR spectroscopy.}, }
@article {pmid35849862, year = {2022}, author = {Vaezzadeh, V and Thomes, MW and Kunisue, T and Tue, NM and Zhang, G and Zakaria, MP and Affendi, YA and Yap, FC and Chew, LL and Teoh, HW and Lee, CW and Bong, CW}, title = {Corrigendum to "Examination of barnacles' potential to be used as bioindicators of persistent organic pollutants in coastal ecosystem: A Malaysia case study" [Chemosphere 263 (2021) 128272].}, journal = {Chemosphere}, volume = {307}, number = {Pt 1}, pages = {135742}, doi = {10.1016/j.chemosphere.2022.135742}, pmid = {35849862}, issn = {1879-1298}, }
@article {pmid35845424, year = {2022}, author = {Hessler, T and Harrison, STL and Huddy, RJ}, title = {Integrated Kinetic Modelling and Microbial Profiling Provide Insights Into Biological Sulfate-Reducing Reactor Design and Operation.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {897094}, pmid = {35845424}, issn = {2296-4185}, abstract = {Biological sulfate reduction (BSR) is an attractive approach for the bioremediation of sulfate-rich wastewater streams. Many sulfate-reducing microorganisms (SRM), which facilitate this process, have been well-studied in pure culture. However, the role of individual members of microbial communities within BSR bioreactors remains understudied. In this study we investigated the performance of two up-flow anaerobic packed bed reactors (UAPBRs) supplemented primarily with acetate and with lactate, respectively, during a hydraulic retention time (HRT) study set up to remediate sulfate-rich synthetic wastewater over the course of 1,000 + days. Plug-flow hydrodynamics led to a continuum of changing volumetric sulfate reduction rates (VSRRs), available electron donors, degrees of biomass retention and compositions of microbial communities throughout these reactors. Microbial communities throughout the successive zones of the reactors were resolved using 16S rRNA gene amplicon sequencing which allowed the association of features of performance with discrete microorganisms. The acetate UAPBR achieved a maximum VSRR of 23.2 mg.L[-1]. h[-1] at a one-day HRT and a maximum sulfate conversion of the 1 g/L sulfate of 96% at a four-day HRT. The sulfate reduction reactions in this reactor could be described with a reaction order of 2.9, an important observation for optimisation and future scale-up. The lactate UAPBR achieved a 96% sulfate conversion at one-day HRT, corresponding with a VSRR of 40.1 mg.L[-1]. h[-1]. Lactate was supplied in this reactor at relatively low concentrations necessitating the subsequent use of propionate and acetate, by-products of lactate fermentation with acetate also a by-product of incomplete lactate oxidation, to achieve competitive performance. The consumption of these electron donors could be associated with specific SRM localised within biofilms of discrete zones. The sulfate reduction rates in the lactate UAPBR could be modelled as first-order reactions, indicating effective rates were conferred by these propionate- and acetate-oxidising SRM. Our results demonstrate how acetate, a low-cost substrate, can be used effectively despite low associated SRM growth rates, and that lactate, a more expensive substrate, can be used sparingly to achieve high VSRR and sulfate conversions. We further identified the preferred environment of additional microorganisms to inform how these microorganisms could be enriched or diminished in BSR reactors.}, }
@article {pmid35844603, year = {2022}, author = {Zhang, Q and Chen, Q and Yan, C and Niu, C and Zhou, J and Liu, J and Song, Y and Zhou, F and Fan, Y and Ren, J and Xu, H and Zhang, B}, title = {The Absence of STING Ameliorates Non-Alcoholic Fatty Liver Disease and Reforms Gut Bacterial Community.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {931176}, pmid = {35844603}, issn = {1664-3224}, mesh = {Animals ; Bacteria ; CD8-Positive T-Lymphocytes/metabolism ; Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Inflammation ; Mice ; Mice, Inbred C57BL ; *Non-alcoholic Fatty Liver Disease/etiology/metabolism ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD) is one of the primary causes of cirrhosis and a major risk factor for hepatocellular carcinoma and liver-related death. It has been correlated with changes in the gut microbiota, which promote its development by regulating insulin resistance, bile acid and choline metabolism, and inflammation. Recent studies suggested a controversial role of the stimulator of interferon genes (STING) in the development of NAFLD. Here, we showed that as an immune regulator, STING aggravates the progression of NAFLD in diet-induced mice and correlated it with the changes in hepatic lipid metabolism and gut microbiota diversity. After feeding wild-type (WT) and STING deletion mice with a normal control diet (NCD) or a high-fat diet (HFD), the STING deletion mice showed decreased lipid accumulation and liver inflammation compared with WT mice fed the same diet. In addition, STING specifically produced this hepatoprotective effect by inhibiting the activation of CD8[+] T cells. The gut microbiota analysis revealed significant differences in intestinal bacteria between STING deletion mice and WT mice under the same diet and environmental conditions; moreover, differential bacterial genera were associated with altered metabolic phenotypes and involved in related metabolic pathways. Overall, our findings reveal the important regulatory role that STING plays in the progression of NAFLD. In addition, the change in intestinal microbiota diversity may be the contributing factor.}, }
@article {pmid35842525, year = {2023}, author = {Kou, Y and Li, C and Tu, B and Li, J and Li, X}, title = {The Responses of Ammonia-Oxidizing Microorganisms to Different Environmental Factors Determine Their Elevational Distribution and Assembly Patterns.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {485-496}, pmid = {35842525}, issn = {1432-184X}, support = {32171550//the National Natural Science Foundation of China/ ; 31870473//the National Natural Science Foundation of China/ ; XDA20020401//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2021371//the Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; 2019QZKK0600//the Second Tibetan Plateau Scientic Expedition and Research Program/ ; Sino BON//China Biodiversity Observation Networks/ ; }, mesh = {*Bacteria/genetics ; Ammonia ; Soil Microbiology ; Oxidation-Reduction ; Archaea/genetics ; Soil ; Nitrification ; *Betaproteobacteria ; Phylogeny ; }, abstract = {The assembly mechanisms shaping the elevational patterns of diversity and community structure in ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are not well understood. We investigated the diversities, co-occurrence network patterns, key drivers, and potential activities of AOA and AOB communities along a large altitudinal gradient. The α-diversity of the AOA communities exhibited a monotonically decreasing pattern with increasing elevation, whereas a sinusoidal pattern was observed for the AOB communities. The mean annual temperature was the single factor that most strongly influenced the α-diversity of the AOA communities; however, the interactions of plant richness, soil conductivity, and total nitrogen made comparable contributions to the α-diversity of the AOB communities. Moreover, the β-diversities of the AOA and AOB communities were divided into two distinct clusters by elevation, i.e., low- (1800-2600 m) and high-altitude (2800-4100 m) sections. These patterns were attributed mainly to the soil pH, followed by variations in plant richness along the altitudinal gradient. In addition, the AOB communities were more important to the soil nitrification potential in the low-altitude section, whereas the AOA communities contributed more to the soil nitrification potential in the high-altitude section. Overall, this study revealed the key factors shaping the elevational patterns of ammonia-oxidizing communities and might predict the consequences of changes in ammonia-oxidizing communities.}, }
@article {pmid35842340, year = {2022}, author = {Gouka, L and Raaijmakers, JM and Cordovez, V}, title = {Ecology and functional potential of phyllosphere yeasts.}, journal = {Trends in plant science}, volume = {27}, number = {11}, pages = {1109-1123}, doi = {10.1016/j.tplants.2022.06.007}, pmid = {35842340}, issn = {1878-4372}, mesh = {Bacteria ; *Ecology ; Fungi ; Plant Leaves ; Plants/microbiology ; *Yeasts/genetics ; }, abstract = {The phyllosphere (i.e., the aerial parts of plants) harbors a rich microbial life, including bacteria, fungi, viruses, and yeasts. Current knowledge of yeasts stems primarily from industrial and medical research on Saccharomyces cerevisiae and Candida albicans, both of which can be found on plant tissues. For most other yeasts found in the phyllosphere, little is known about their ecology and functions. Here, we explore the diversity, dynamics, interactions, and genomics of yeasts associated with plant leaves and how tools and approaches developed for model yeasts can be adopted to disentangle the ecology and natural functions of phyllosphere yeasts. A first genomic survey exemplifies that we have only scratched the surface of the largely unexplored functional potential of phyllosphere yeasts.}, }
@article {pmid35840683, year = {2023}, author = {Hubert, J and Nesvorna, M and Bostlova, M and Sopko, B and Green, SJ and Phillips, TW}, title = {The Effect of Residual Pesticide Application on Microbiomes of the Storage Mite Tyrophagus putrescentiae.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1527-1540}, pmid = {35840683}, issn = {1432-184X}, support = {21-337-J//Kansas State Research and Extension/ ; LTAUSA19012//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; }, mesh = {Animals ; *Acaridae/microbiology ; *Pesticides/pharmacology ; *Pesticide Residues/pharmacology ; *Microbiota ; *Mites/microbiology ; *Bacillus/genetics ; *Bartonella ; *Pyrethrins/pharmacology ; }, abstract = {Arthropods can host well-developed microbial communities, and such microbes can degrade pesticides and confer tolerance to most types of pests. Two cultures of the stored-product mite Tyrophagus putrescentiae, one with a symbiotic microbiome containing Wolbachia and the other without Wolbachia, were compared on pesticide residue (organophosphate: pirimiphos-methyl and pyrethroid: deltamethrin, deltamethrin + piperonyl butoxide)-containing diets. The microbiomes from mite bodies, mite feces and debris from the spent mite diet were analyzed using barcode sequencing. Pesticide tolerance was different among mite cultures and organophosphate and pyrethroid pesticides. The pesticide residues influenced the microbiome composition in both cultures but without any remarkable trend for mite cultures with and without Wolbachia. The most influenced bacterial taxa were Bartonella-like and Bacillus for both cultures and Wolbachia for the culture containing this symbiont. However, there was no direct evidence of any effect of Wolbachia on pesticide tolerance. The high pesticide concentration residues in diets reduced Wolbachia, Bartonella-like and Bacillus in mites of the symbiotic culture. This effect was low for Bartonella-like and Bacillus in the asymbiotic microbiome culture. The results showed that the microbiomes of mites are affected by pesticide residues in the diets, but the effect is not systemic. No actual detoxification effect by the microbiome was observed for the tested pesticides.}, }
@article {pmid35840682, year = {2023}, author = {Williams, A and Birt, HWG and Raghavendra, A and Dennis, PG}, title = {Cropping System Diversification Influences Soil Microbial Diversity in Subtropical Dryland Farming Systems.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1473-1484}, pmid = {35840682}, issn = {1432-184X}, mesh = {*Soil ; *Carbon ; Soil Microbiology ; Phylogeny ; Agriculture/methods ; Nitrogen ; }, abstract = {Conventional dryland cropping systems are characterised by low crop diversity and frequent fallows. This has significant impacts on soil microbes that underpin soil function. Diversifying crop rotations can potentially counter these effects; however, limited data exists on the impacts of diversified crop rotations on soil microbes in drylands. Using phylogenetic marker gene sequencing, we characterised soil microbial diversity in conventional and diversified dryland crop rotations in subtropical Australia. This included winter and summer dominant rotations. Conventional systems were cereal-dominant with a crop-fallow rotation. Diversified systems included greater crop diversity, double crops, cover crops, and a multi-year ley pasture. In summer rotations with increased crop diversity and cover crops, bacterial and fungal richness increased, and distinct communities were formed compared to fallow land. Often, these community shifts were associated with greater soil organic carbon (SOC) and nitrogen. All winter rotations had distinct fungal communities and ley pasture resulted in greater fungal diversity compared to other rotations. No effects of the winter rotations were evident on bacterial communities. Our results show that diversification of dryland crop rotations leads to significant shifts in soil microbial communities in both winter and summer cropping systems. Both summer and winter rotations incorporating cover crops and ley pasture had greater soil respiration and nitrogen, indicating increases in soil fertility. These rotations may offer an alternative to conventional crop-fallow rotations to counter ongoing declines in soil health.}, }
@article {pmid35839698, year = {2022}, author = {Babaahmadifooladia, M and da Silva Junior, EC and Van de Wiele, T and Du Laing, G and Jacxsens, L}, title = {Probabilistic chronic dietary exposure assessment adjusted for bioaccessible fraction to metals by consumption of seaweed and derived foods.}, journal = {Food chemistry}, volume = {395}, number = {}, pages = {133588}, doi = {10.1016/j.foodchem.2022.133588}, pmid = {35839698}, issn = {1873-7072}, mesh = {Cadmium ; Dietary Exposure ; Lead ; *Mercury ; *Metals, Heavy/analysis ; Risk Assessment ; *Seaweed ; Vegetables ; }, abstract = {The chronic exposure to heavy elements, i.e. Ni, As, Cd, Hg and Pb the evaluation of toxicological risk through intake of raw or seaweed based foods for Belgian consumers is presented in this study. The bioaccessible fraction, obtained for different metals, were used to refine the exposure values to avoid overestimation in the reported exposures. The decrease in the exposure values was higher for As with average bioaccessible fraction of 56.8% followed by Pb, Cd, Ni and Hg. The pure seaweeds show more approximation or exceeding of toxicological limits compared to the composite foodstuffs. For all elements (except Hg), toxicological limits are approached at the maximum exposure situation due to consumption of certain seaweed-based foods. Further, the study demonstrates that the introduction of innovative foods on an emerging market may result in potential health issues due to the shift in consumption patterns as the increased consumption of seaweed and their derivatives in Europe.}, }
@article {pmid35838347, year = {2022}, author = {Rijkers, R and Rousk, J and Aerts, R and Sigurdsson, BD and Weedon, JT}, title = {Optimal growth temperature of Arctic soil bacterial communities increases under experimental warming.}, journal = {Global change biology}, volume = {28}, number = {20}, pages = {6050-6064}, pmid = {35838347}, issn = {1365-2486}, mesh = {Arctic Regions ; Bacteria/genetics ; *Carbon/chemistry ; Climate Change ; *Soil/chemistry ; Soil Microbiology ; Temperature ; }, abstract = {Future climate warming in the Arctic will likely increase the vulnerability of soil carbon stocks to microbial decomposition. However, it remains uncertain to what extent decomposition rates will change in a warmer Arctic, because extended soil warming could induce temperature adaptation of bacterial communities. Here we show that experimental warming induces shifts in the temperature-growth relationships of bacterial communities, which is driven by community turnover and is common across a diverse set of 8 (sub) Arctic soils. The optimal growth temperature (Topt) of the soil bacterial communities increased 0.27 ± 0.039 (SE) and 0.07 ± 0.028°C per °C of warming over a 0-30°C gradient, depending on the sampling moment. We identify a potential role for substrate depletion and time-lag effects as drivers of temperature adaption in soil bacterial communities, which possibly explain discrepancies between earlier incubation and field studies. The changes in Topt were accompanied by species-level shifts in bacterial community composition, which were mostly soil specific. Despite the clear physiological responses to warming, there was no evidence for a common set of temperature-responsive bacterial amplicon sequence variants. This implies that community composition data without accompanying physiological measurements may have limited utility for the identification of (potential) temperature adaption of soil bacterial communities in the Arctic. Since bacterial communities in Arctic soils are likely to adapt to increasing soil temperature under future climate change, this adaptation to higher temperature should be implemented in soil organic carbon modeling for accurate predictions of the dynamics of Arctic soil carbon stocks.}, }
@article {pmid35836424, year = {2022}, author = {Muster, C and Leiva, D and Morales, C and Grafe, M and Schloter, M and Carú, M and Orlando, J}, title = {Peltigera frigida Lichens and Their Substrates Reduce the Influence of Forest Cover Change on Phosphate Solubilizing Bacteria.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {843490}, pmid = {35836424}, issn = {1664-302X}, abstract = {Phosphorus (P) is one of the most critical macronutrients in forest ecosystems. More than 70 years ago, some Chilean Patagonian temperate forests suffered wildfires and the subsequent afforestation with foreign tree species such as pines. Since soil P turnover is interlinked with the tree cover, this could influence soil P content and bioavailability. Next to soil microorganisms, which are key players in P transformation processes, a vital component of Patagonian temperate forest are lichens, which represent microbial hotspots for bacterial diversity. In the present study, we explored the impact of forest cover on the abundance of phosphate solubilizing bacteria (PSB) from three microenvironments of the forest floor: Peltigera frigida lichen thallus, their underlying substrates, and the forest soil without lichen cover. We expected that the abundance of PSB in the forest soil would be strongly affected by the tree cover composition since the aboveground vegetation influences the edaphic properties; but, as P. frigida has a specific bacterial community, lichens would mitigate this impact. Our study includes five sites representing a gradient in tree cover types, from a mature forest dominated by the native species Nothofagus pumilio, to native second-growth forests with a gradual increase in the presence of Pinus contorta in the last sites. In each site, we measured edaphic parameters, P fractions, and the bacterial potential to solubilize phosphate by quantifying five specific marker genes by qPCR. The results show higher soluble P, labile mineral P, and organic matter in the soils of the sites with a higher abundance of P. contorta, while most of the molecular markers were less abundant in the soils of these sites. Contrarily, the abundance of the molecular markers in lichens and substrates was less affected by the tree cover type. Therefore, the bacterial potential to solubilize phosphate is more affected by the edaphic factors and tree cover type in soils than in substrates and thalli of P. frigida lichens. Altogether, these results indicate that the microenvironments of lichens and their substrates could act as an environmental buffer reducing the influence of forest cover composition on bacteria involved in P turnover.}, }
@article {pmid35835965, year = {2023}, author = {Larsen, S and Albanese, D and Stegen, J and Franceschi, P and Coller, E and Zanzotti, R and Ioriatti, C and Stefani, E and Pindo, M and Cestaro, A and Donati, C}, title = {Distinct and Temporally Stable Assembly Mechanisms Shape Bacterial and Fungal Communities in Vineyard Soils.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {337-349}, pmid = {35835965}, issn = {1432-184X}, mesh = {*Mycobiome ; Soil Microbiology ; Soil ; Fungi/genetics ; *Microbiota ; Bacteria/genetics ; }, abstract = {Microbial communities in agricultural soils are fundamental for plant growth and in vineyard ecosystems contribute to defining regional wine quality. Managing soil microbes towards beneficial outcomes requires knowledge of how community assembly processes vary across taxonomic groups, spatial scales, and through time. However, our understanding of microbial assembly remains limited. To quantify the contributions of stochastic and deterministic processes to bacterial and fungal assembly across spatial scales and through time, we used 16 s rRNA gene and ITS sequencing in the soil of an emblematic wine-growing region of Italy.Combining null- and neutral-modelling, we found that assembly processes were consistent through time, but bacteria and fungi were governed by different processes. At the within-vineyard scale, deterministic selection and homogenising dispersal dominated bacterial assembly, while neither selection nor dispersal had clear influence over fungal assembly. At the among-vineyard scale, the influence of dispersal limitation increased for both taxonomic groups, but its contribution was much larger for fungal communities. These null-model-based inferences were supported by neutral modelling, which estimated a dispersal rate almost two orders-of-magnitude lower for fungi than bacteria.This indicates that while stochastic processes are important for fungal assembly, bacteria were more influenced by deterministic selection imposed by the biotic and/or abiotic environment. Managing microbes in vineyard soils could thus benefit from strategies that account for dispersal limitation of fungi and the importance of environmental conditions for bacteria. Our results are consistent with theoretical expectations whereby larger individual size and smaller populations can lead to higher levels of stochasticity.}, }
@article {pmid35834007, year = {2022}, author = {Mańkowska, K and Marchelek-Myśliwiec, M and Kochan, P and Kosik-Bogacka, D and Konopka, T and Grygorcewicz, B and Roszkowska, P and Cecerska-Heryć, E and Siennicka, A and Konopka, J and Dołęgowska, B}, title = {Microbiota in sports.}, journal = {Archives of microbiology}, volume = {204}, number = {8}, pages = {485}, pmid = {35834007}, issn = {1432-072X}, mesh = {Bacteria/genetics ; Bifidobacterium ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Lactobacillus ; *Microbiota ; *Probiotics ; }, abstract = {The influence of microbiota on the human body is currently the subject of many studies. The composition of bacteria colonizing the gastrointestinal tract varies depending on genetic make-up, lifestyle, use of antibiotics or the presence of diseases. The diet is also important in the species diversity of the microbiota. This study is an analysis of the relationships between physical activity, diet, and the microbiota of the gastrointestinal tract in athletes. This review shows the differences in the microbial composition in various sports disciplines, the influence of probiotics on the microbiome, the consequence of which may be achieved even better sports results. Physical activity increases the number of bacteria, mainly of the Clostridiales order and the genus: Lactobacillus, Prevotella, Bacteroides, and Veillonella, and their number varies depending on the sports discipline. These bacteria are present in athletes in sports that require a high VO2 max. The players' diet also influences the composition of the microbiota. A diet rich in dietary fiber increases the amount of Lactobacillus or Bifidobacterium bacteria, probiotic microorganisms, which indicates the need to supplement the diet with probiotic preparations. It is impossible to suggest an unambiguous answer to how the microbiota of the gastrointestinal tract changes in athletes and requires further analyzes.}, }
@article {pmid35831642, year = {2023}, author = {Kluting, K and Strid, Y and Six, D and Rosling, A}, title = {Forest Fire Influence on Tomicus piniperda-Associated Fungal Communities and Phloem Nutrient Availability of Colonized Pinus sylvestris.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {224-239}, pmid = {35831642}, issn = {1432-184X}, support = {2014-458//Svenska Forskningsr&#xe5;det Formas/ ; SSWF 17-1-Chdre//Stiftelsen Stina Werners Fond/ ; }, mesh = {Animals ; *Pinus sylvestris ; *Mycobiome ; *Wildfires ; Phloem ; *Weevils ; *Coleoptera/microbiology ; *Pinus/microbiology ; Fungi/genetics ; Trees ; }, abstract = {Forest fire is known to positively affect bark beetle populations by providing fire-damaged trees with impaired defenses for infestation. Tomicus piniperda, the common pine shoot beetle, breeds and lays eggs under the bark of stressed pine trees and is considered a serious forest pest within its native range. Wood-colonizing fungi have been hypothesized to improve substrate quality and detoxify tree defensive chemistry to indirectly facilitate tree colonization by beetles. While some bark beetle species form symbiotic associations with fungi and actively vector their partners when colonizing new trees, T. piniperda does not have mycangia or body hairs for specific vectoring of fungi. To explore the T. piniperda-associated fungal community for signs of specific association, we used ITS metabarcoding to separately characterize fungal communities associated with surface and gut of male and female beetles. We also characterized the temporal changes in fungal community and nutrient status of pine phloem with and without beetle galleries. Sampling was performed 2 years after a natural forest fire and included both burnt and unburnt sites. In our study system, we find that forest fire significantly impacts the fungal community composition associated with T. piniperda and that fire may also indirectly change nutrient availability in phloem to beetle galleries. We conclude that T. piniperda can vector fungi to newly colonized trees but the absence of positive effects on substrate quality and minimal effects of sex indicate that vectoring of associated fungal communities is not a strategy associated with the T. piniperda life cycle.}, }
@article {pmid35822810, year = {2022}, author = {Senn, S and Pangell, K and Bowerman, AL}, title = {Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxia.}, journal = {Biotech (Basel (Switzerland))}, volume = {11}, number = {1}, pages = {}, pmid = {35822810}, issn = {2673-6284}, abstract = {The purpose of this paper is to elucidate the roles that microbes may be playing in the rootzone of the medicinal plant Daturainoxia. We hypothesized that the microbes associated with the Datura rootzone would be significantly different than the similar surrounding fields in composition and function. We also hypothesized that rhizospheric and endophytic microbes would be associated with similar metabolic functions to the plant rootzone they inhabited. The methods employed were microbial barcoding, tests of essential oils against antibiotic resistant bacteria and other soil bacterial isolates, 16S Next Generation Sequencing (NGS) metabarcoding, and Whole Genome Shotgun (WGS) taxonomic and functional analyses. A few of the main bacterial genera of interest that were differentially abundant in the Datura root microbiome were Flavobacterium (p = 0.007), Chitinophaga (p = 0.0007), Pedobacter (p = 6 × 10[-5]), Bradyhizobium (p = 1 × 10[-8]), and Paenibacillus (p = 1.46 × 10[-6]). There was significant evidence that the microbes associated with the Datura rootzone had elevated function related to bacterial chalcone synthase (p = 1.49 × 10[-3]) and permease genes (p < 0.003). There was some evidence that microbial functions in the Datura rootzone provided precursors to important plant bioactive molecules or were beneficial to plant growth. This is important because these compounds are phyto-protective antioxidants and are precursors to many aromatic bioactive compounds that are relevant to human health. In the context of known interactions, and current results, plants and microbes influence the flavonoid biosynthetic pathways of one other, in terms of the regulation of the phenylpropanoid pathway. This is the first study to focus on the microbial ecology of the Datura rootzone. There are possible biopharmaceutical and agricultural applications of the natural interplay that was discovered during this study of the Datura inoxia rhizosphere.}, }
@article {pmid35822787, year = {2022}, author = {Khoo, C and Duysburgh, C and Marzorati, M and Van den Abbeele, P and Zhang, D}, title = {A Freeze-Dried Cranberry Powder Consistently Enhances SCFA Production and Lowers Abundance of Opportunistic Pathogens In Vitro.}, journal = {Biotech (Basel (Switzerland))}, volume = {11}, number = {2}, pages = {}, pmid = {35822787}, issn = {2673-6284}, abstract = {The American cranberry, Vaccinium macrocarpon, contains fibers and (poly)phenols that could exert health-promoting effects through modulation of gut microbiota. This study aimed to investigate how a freeze-dried whole cranberry powder (FCP) modulated metabolite production and microbial composition using both a 48-h incubation strategy and a long-term human gut simulator study with the M-SHIME (Mucosal Simulator of the Human Intestinal Microbial Ecosystem). FCP was repeatedly administered over three weeks. The studies included five and three study subjects, respectively. In both models, FCP significantly increased levels of health-related short-chain fatty acids (SCFA: acetate, propionate and butyrate), while decreased levels of branched-chain fatty acids (markers of proteolytic fermentation). Interestingly, FCP consistently increased luminal Bacteroidetes abundances in the proximal colon of the M-SHIME (+17.5 ± 9.3%) at the expense of Proteobacteria (-10.2 ± 1.5%). At family level, this was due to the stimulation of Bacteroidaceae and Prevotellaceae and a decrease of Pseudomonodaceae and Enterobacteriaceae. Despite of interpersonal differences, FCP also increased the abundance of families of known butyrate producers. Overall, FCP displayed an interesting prebiotic potential in vitro given its selective utilization by host microorganisms and potential health-related effects on inhibition of pathogens and selective stimulation of beneficial metabolites.}, }
@article {pmid35821127, year = {2023}, author = {Roy, J and Reichel, R and Brüggemann, N and Rillig, MC}, title = {Functional, not Taxonomic, Composition of Soil Fungi Reestablishes to Pre-mining Initial State After 52 Years of Recultivation.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {213-223}, pmid = {35821127}, issn = {1432-184X}, mesh = {Agriculture ; *Ecosystem ; *Fungi/classification/genetics/metabolism ; Plants/microbiology ; Soil/chemistry ; *Soil Microbiology ; *Environmental Restoration and Remediation ; Introns/genetics ; Mining ; Biodiversity ; }, abstract = {Open-cast mining leads to the loss of naturally developed soils and their ecosystem functions and services. Soil restoration after mining aims to restore the agricultural productivity in which the functions of the fungal community play a crucial role. Whether fungi reach a comparable functional state as in the soil before mining within half a century of recultivation is still unanswered. Here, we characterised the soil fungal community using ITS amplicon Illumina sequencing across a 52-year chronosequence of agricultural recultivation after open-cast mining in northern Europe. Both taxonomic and functional community composition showed profound shifts over time, which could be attributed to the changes in nutrient status, especially phosphorus availability. However, taxonomic composition did not reach the pre-mining state, whereas functional composition did. Importantly, we identified a positive development of arbuscular mycorrhizal root fungal symbionts after the initial three years of alfalfa cultivation, followed by a decline after conversion to conventional farming, with arbuscular mycorrhizal fungi being replaced by soil saprobes. We conclude that appropriate agricultural management can steer the fungal community to its functional pre-mining state despite stochasticity in the reestablishment of soil fungal communities. Nonetheless, conventional agricultural management results in the loss of plant symbionts, favouring non-symbiotic fungi.}, }
@article {pmid35819480, year = {2023}, author = {Alberoni, D and Di Gioia, D and Baffoni, L}, title = {Alterations in the Microbiota of Caged Honeybees in the Presence of Nosema ceranae Infection and Related Changes in Functionality.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {601-616}, pmid = {35819480}, issn = {1432-184X}, mesh = {Bees ; Animals ; *Gastrointestinal Microbiome ; *Nosema ; Bacteria/genetics ; *Neisseriaceae ; }, abstract = {Several studies have outlined that changes in the honeybee gut microbial composition may impair important metabolic functions supporting the honeybees' life. Gut dysbiosis may be caused by diseases like Nosema ceranae or by other anthropic, environmental or experimental stressors. The present work contributes to increasing knowledge on the dynamics of the gut microbiome acquisition in caged honeybees, an experimental condition frequently adopted by researchers, with or without infection with N. ceranae, and fed with a bacterial mixture to control N. ceranae development. Changes of the gut microbiota were elucidated comparing microbial profile of caged and open-field reared honeybees. The absolute abundance of the major gut microbial taxa was studied with both NGS and qPCR approaches, whereas changes in the functionality were based on RAST annotations and manually curated. In general, all caged honeybees showed important changes in the gut microbiota, with [Formula: see text]-proteobacteria (Frischella, Gilliamella and Snodgrassella) lacking in all caged experimental groups. Caged honeybees infected with N. ceranae showed also a strong colonization of environmental taxa like Citrobacter, Cosenzaea and Morganella, as well as possibly pathogenic bacteria such as Serratia. The colonization of Serratia did not occur in presence of the bacterial mixture. The functionality prediction revealed that environmental bacteria or the supplemented bacterial mixture increased the metabolic potential of the honeybee gut microbiome compared to field and caged controls.}, }
@article {pmid35818766, year = {2022}, author = {Sánchez-Suárez, J and Díaz, L and Junca, H and Garcia-Bonilla, E and Villamil, L}, title = {Microbiome composition of the marine sponge Cliona varians at the neotropical southern Caribbean Sea displays a predominant core of Rhizobiales and Nitrosopumilaceae.}, journal = {Journal of applied microbiology}, volume = {133}, number = {3}, pages = {2027-2038}, doi = {10.1111/jam.15714}, pmid = {35818766}, issn = {1365-2672}, support = {80740-168-2019//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n (Minciencias)/ ; ING-175-2016//Universidad de La Sabana/ ; }, mesh = {Animals ; Archaea ; Caribbean Region ; Hydrogen-Ion Concentration ; *Microbiota/genetics ; *Porifera/microbiology ; Seawater/microbiology ; }, abstract = {AIMS: This work aims to characterize the microbial diversity of the encrusting sponge Cliona varians, a pore-forming and coral reef bioeroding marine sponge of emerging spread related to ocean acidification.<br><br>METHODS AND RESULTS: We analysed the microbiome composition by 16S V4 amplicon next-generation sequencing in a community of the bioeroding coral reef encrusting/excavating marine sponge Cliona varians thriving at the Southern Caribbean Sea. About 87.21% and 6.76% of the sequences retrieved were assigned to the domain Bacteria and Archaea. The most predominant operational taxonomic units were classified as members of the order Rhizobiales and family Nitrosopumilaceae, representing members of not yet characterized genera. Features found strictly conserved in the strain/genomic representatives reported in those microbial taxa are nitrogen fixation and transformation.<br><br>CONCLUSION: Our results suggest, in accordance with recent results, that these microbiome members and associated functions could be contributing to the biological fitness of the sponge to be able to colonize and bioerode in environments with low access and scarce availability of nitrogen sources.<br><br>Coral reefs bioresources such as sponge holobionts are intriguing and complex ecosystem units. This study contributes to the knowledge of how C. varians microbiota is composed or shaped, which is crucial to understand its ecological functions.}, }
@article {pmid35818006, year = {2022}, author = {Mesa, V}, title = {Rhizosphere and Endosphere Bacterial Communities Survey by Metagenomics Approach.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2512}, number = {}, pages = {181-197}, doi = {10.1007/978-1-0716-2429-6_11}, pmid = {35818006}, issn = {1940-6029}, mesh = {Bacteria/genetics ; *Metagenomics ; Plant Roots/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil Microbiology ; }, abstract = {The diversity of microbes associated with plant roots is in the order of tens of thousands of species. It is estimated that only 0.1-1.0% of the living bacteria present in soils can be cultured under standard conditions. The microbial marker-gene sequence data and the next-generation sequencing technologies have enabled systemic studies of root-associated microbiomes. Molecular techniques can be used to generate comprehensive taxonomic profiles of the microorganisms present in roots. The aim of this chapter is to provide a standard method for the obtention of rhizosphere and endosphere fractions, and a generic workflow of the Quantitative Insights Into Microbial Ecology version 2 (QIIME2) software to analysis of 16S rRNA marker-gene.}, }
@article {pmid35817179, year = {2022}, author = {Liu, Y and Xi, Y and Xie, T and Liu, H and Su, Z and Huang, Y and Xu, W and Wang, D and Zhang, C and Li, X}, title = {Enhanced removal of diclofenac via coupling Pd catalytic and microbial processes in a H2-based membrane biofilm reactor: Performance, mechanism and biofilm microbial ecology.}, journal = {Chemosphere}, volume = {307}, number = {Pt 1}, pages = {135597}, doi = {10.1016/j.chemosphere.2022.135597}, pmid = {35817179}, issn = {1879-1298}, mesh = {Biofilms ; *Bioreactors ; Catalysis ; *Diclofenac ; Humans ; Membranes ; }, abstract = {Diclofenac (DCF) is a most widely used anti-inflammatory drug, which has attracted worldwide attention given its low biodegradability and ecological damage, especially toxic effects on mammals including humans. In this study, a H2-based membrane biofilm reactor (H2-MBfR) was constructed with well-dispersed Pd nanoparticles generated in situ. The Pd-MBfR was applied for catalytic reductive dechlorination of DCF. In batch tests, DCF concentration had significantly effect on the rate and extent DCF removal, and NO3[-] had negative impact on DCF reductive dechlorination. Over 67% removal of 0.5 mg/L DCF and 99% removal of 10 mg/L NO3[-]-N were achieved in 90 min, and the highest removal of 97% was obtained at 0.5 mg/L DCF in the absence of NO3[-]. Over 78 days of continuous operation, the highest steady-state removal flux of DCF was 0.0097 g/m[2]/d. LC-MS analysis indicated that the major product was 2-anilinephenylacetic acid (APA). Dechlorination was the main removal process of DCF mainly owing to the catalytic reduction by PdNPs, microbial reduction, and the synergistic reduction of microbial and PdNPs catalysis using direct delivery of H2. Moreover, DCF reductive Dechlorination shifted the microbial community in the biofilms and Sporomusa was responsible for DCF degradation. In summary, this work expands a remarkable feasibility of sustainable catalytic removal of DCF.}, }
@article {pmid35817167, year = {2022}, author = {Khan, MA and Singh, D and Arif, A and Sodhi, KK and Singh, DK and Islam, SN and Ahmad, A and Akhtar, K and Siddique, HR}, title = {Protective effect of green synthesized Selenium Nanoparticles against Doxorubicin induced multiple adverse effects in Swiss albino mice.}, journal = {Life sciences}, volume = {305}, number = {}, pages = {120792}, doi = {10.1016/j.lfs.2022.120792}, pmid = {35817167}, issn = {1879-0631}, mesh = {Animals ; Antibiotics, Antineoplastic/therapeutic use ; Antioxidants/metabolism ; Cardiotoxicity/etiology ; Chromatography, Liquid ; Doxorubicin/toxicity ; Humans ; Mice ; *Nanoparticles ; Proto-Oncogene Proteins c-bcl-2 ; Reactive Oxygen Species ; *Selenium/pharmacology ; Tandem Mass Spectrometry ; }, abstract = {AIMS: Doxorubicin (DOX) is a widely used drug against multiple cancers. However, its clinical Use is often restricted due to multiple adverse effects. Recently, Selenium Nanoparticles (SeNPs) are gaining attention due to their low toxicity and higher biocompatibility, making them attractive nanoparticles (NPs) in medical and pharmaceutical sciences. Therefore, the current study aimed to assess if our biosynthesized SeNP from the endophytic fungus Fusarium oxysporum conjugated with DOX could alleviate the DOX-induced adverse effects.<br><br>MAIN METHODS: For this purpose, we investigated various genotoxic, biochemical, histopathological, and immunohistochemical parameters and finally analyzed the metabolite profile by LC-MS/MS.<br><br>KEY FINDINGS: We observed that DOX causes an increase in reactive oxygen and nitrogen species (ROS, RNS), 8-OHdG, and malondialdehyde (MDA), decreases antioxidant defense systems and reduces BCL-2 expression in cardiac tissue. In addition, a significant increase in DNA damage and alteration in the cytoarchitecture of the liver, kidney, and heart tissues was observed by Comet Tail Length and histopathological studies, respectively. Interestingly, the DOX-SeNP conjugate reduced ROS/RNS, 8-OHdG, and MDA levels in the liver, kidney, and heart tissues. It also restored the antioxidant enzymes and cytoarchitectures of the examined tissues, reduced genotoxicity, and increased the BCL-2 levels. Finally, metabolic profiling showed that DOX reduced the number of cardioprotective metabolites, which DOX-SeNP restored.<br><br>SIGNIFICANCE: Collectively, the present results describe the protective effect of DOX-conjugated SeNP against DOX-induced toxicities. In conclusion, DOX-SeNP conjugate might be better for treating patients receiving DOX alone. However, it warrants further thorough investigation.}, }
@article {pmid35811862, year = {2022}, author = {Li, Y and Liu, B and Chen, J and Yue, X}, title = {Carbon-Nitrogen-Sulfur-Related Microbial Taxa and Genes Maintained the Stability of Microbial Communities in Coals.}, journal = {ACS omega}, volume = {7}, number = {26}, pages = {22671-22681}, pmid = {35811862}, issn = {2470-1343}, abstract = {Coal microbes are the predominant form of life in the subsurface ecosystem, which play a vital role in biogeochemical cycles. However, the systematic information about carbon-nitrogen-sulfur (C-N-S)-related microbial communities in coal seams is limited. In this study, 16S rRNA gene data from a total of 93 microbial communities in coals were collected for meta-analysis. The results showed that 718 functional genera were related to the C-N-S cycle, wherein N2 fixation, denitrification, and C degradation groups dominated in relative abundance, Chao1 richness, Shannon diversity, and niche width. Genus Pseudomonas having the most C-N-S-related functions showed the highest relative abundance, and genus Herbaspirillum with a higher abundance participated in C degradation, CH4 oxidation, N2 fixation, ammoxidation, and denitrification. Such Herbaspirillum was a core genus in the co-occurrence network of microbial prokaryotes and showed higher levels in weight degree, betweenness centrality, and eigenvector centrality. In addition, most of the methanogens could fix N2 and dominated in the N2 fixation groups. Among them, genera Methanoculleus and Methanosaeta showed higher levels in the betweenness centrality index. In addition, the genus Clostridium was linked to the methanogenesis co-occurrence network module. In parallel, the S reduction gene was present in the highest total relative abundance of genes, followed by the C degradation and the denitrification genes, and S genes (especially cys genes) were the main genes linked to the co-occurrence network of the C-N-S-related genes. In summary, this study strengthened our knowledge regarding the C-N-S-related coal microbial communities, which is of great significance in understanding the microbial ecology and geochemical cycle of coals.}, }
@article {pmid35809121, year = {2023}, author = {Carvalho, MJ and S Oliveira, AL and Santos Pedrosa, S and Pintado, M and Pinto-Ribeiro, I and Madureira, AR}, title = {Skin Microbiota and the Cosmetic Industry.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {86-96}, pmid = {35809121}, issn = {1432-184X}, support = {027578//Fundo Europeu de Desenvolvimento Regional (FEDER)/ ; 01-0247//Programa Operacional Competitividade e Internacionaliza&#xe7;&#xe3;o (POCI)/ ; UID/Multi/50016/2019//Fundo Regional para a Ci&#xea;ncia e Tecnologia/ ; }, mesh = {Humans ; *Cosmetics/pharmacology ; Homeostasis ; *Microbiota/drug effects ; *Skin/microbiology ; *Host Microbial Interactions/drug effects ; Industry/standards/trends ; }, abstract = {Skin harbors an important microbial ecosystem - the skin microbiota that is in homeostasis with its host and is beneficial for human health. Cosmetic products have the potential to interfere with this microbial community; therefore their impact should be assessed. The aim of this review is to highlight the importance of skin microbiota in the cosmetic industry. Several studies determined that cosmetic ingredients have the potential to disrupt the skin microbiota equilibrium leading to the development of skin diseases and dysregulation of immune response. These studies led their investigation by using different methodologies and models, concluding that methods must be chosen according to the aim of the study, the skin site to be evaluated, and the target population of the cosmetics. Overall, it is crucial to test the impact of cosmetics in the skin microbiota and to stablish standard procedures, as well as specific criteria that allow to classify a cosmetic product as skin microbiota friendly.}, }
@article {pmid35804731, year = {2022}, author = {Clodoveo, ML and Muraglia, M and Crupi, P and Hbaieb, RH and De Santis, S and Desantis, A and Corbo, F}, title = {The Tower of Babel of Pharma-Food Study on Extra Virgin Olive Oil Polyphenols.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {13}, pages = {}, pmid = {35804731}, issn = {2304-8158}, abstract = {Much research has been conducted to reveal the functional properties of extra virgin olive oil polyphenols on human health once EVOO is consumed regularly as part of a balanced diet, as in the Mediterranean lifestyle. Despite the huge variety of research conducted, only one effect of EVOO polyphenols has been formally approved by EFSA as a health claim. This is probably because EFSA's scientific opinion is entrusted to scientific expertise about food and medical sciences, which adopt very different investigative methods and experimental languages, generating a gap in the scientific communication that is essential for the enhancement of the potentially useful effects of EVOO polyphenols on health. Through the model of the Tower of Babel, we propose a challenge for science communication, capable of disrupting the barriers between different scientific areas and building bridges through transparent data analysis from the different investigative methodologies at each stage of health benefits assessment. The goal of this work is the strategic, distinctive, and cost-effective integration of interdisciplinary experiences and technologies into a highly harmonious workflow, organized to build a factual understanding that translates, because of trade, into health benefits for buyers, promoting EVOOs as having certified health benefits, not just as condiments.}, }
@article {pmid35802409, year = {2022}, author = {Edwards, A and Soares, A and Debbonaire, A and Edwards Rassner, SM}, title = {Before you go: a packing list for portable DNA sequencing of microbiomes and metagenomes.}, journal = {Microbiology (Reading, England)}, volume = {168}, number = {7}, pages = {}, doi = {10.1099/mic.0.001220}, pmid = {35802409}, issn = {1465-2080}, mesh = {High-Throughput Nucleotide Sequencing ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; }, }
@article {pmid35802173, year = {2023}, author = {Rocha, FP and Ronque, MUV and Lyra, ML and Bacci, M and Oliveira, PS}, title = {Habitat and Host Species Drive the Structure of Bacterial Communities of Two Neotropical Trap-Jaw Odontomachus Ants : Habitat and Host Species Drive the Structure of Bacterial Communities of Two Neotropical Trap-Jaw Odontomachus Ants.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {699-712}, pmid = {35802173}, issn = {1432-184X}, support = {Finance Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 2017/26162-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/04824-9//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2014/23141-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/16645-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 163546/2020-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 441036/2016-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 307541/2018-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 306115/2013-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 302219/2017-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 303730/2021-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Animals ; *Ants ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Brazil ; Bacteria/genetics ; }, abstract = {Ants have long been known for their associations with other taxa, including macroscopic fungi and symbiotic bacteria. Recently, many ant species have had the composition and function of their bacterial communities investigated. Due to its behavioral and ecological diversity, the subfamily Ponerinae deserves more attention regarding its associated microbiota. Here, we used the V4 region of the 16S rRNA gene to characterize the bacterial communities of Odontomachus chelifer (ground-nesting) and Odontomachus hastatus (arboreal), two ponerine trap-jaw species commonly found in the Brazilian savanna ("Cerrado") and Atlantic rainforest. We investigated habitat effects (O. chelifer in the Cerrado and the Atlantic rainforest) and species-specific effects (both species in the Atlantic rainforest) on the bacterial communities' structure (composition and abundance) in two different body parts: cuticle and gaster. Bacterial communities differed in all populations studied. Cuticular communities were more diverse, while gaster communities presented variants common to other ants, including Wolbachia and Candidatus Tokpelaia hoelldoblerii. Odontomachus chelifer populations presented different communities in both body parts, highlighting the influence of habitat type. In the Atlantic rainforest, the outcome depended on the body part targeted. Cuticular communities were similar between species, reinforcing the habitat effect on bacterial communities, which are mainly composed of environmentally acquired taxa. Gaster communities, however, differed between the two Odontomachus species, suggesting species-specific effects and selective filters. Unclassified Firmicutes and uncultured Rhizobiales variants are the main components accounting for the observed differences. Our study indicates that both host species and habitat act synergistically, but to different degrees, to shape the bacterial communities in these Odontomachus species.}, }
@article {pmid35802172, year = {2023}, author = {Mejia, MP and Rojas, CA and Curd, E and Renshaw, MA and Edalati, K and Shih, B and Vincent, N and Lin, M and Nguyen, PH and Wayne, R and Jessup, K and Parker, SS}, title = {Soil Microbial Community Composition and Tolerance to Contaminants in an Urban Brownfield Site.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {998-1012}, pmid = {35802172}, issn = {1432-184X}, support = {CA-16-376437//Office of the President, University of California/ ; 443952-SR-69085//La Kretz and Stunt Ranch Reserve Grant/ ; }, mesh = {Soil/chemistry ; *Volatile Organic Compounds/metabolism ; *Soil Pollutants/analysis ; *Metals, Heavy/metabolism ; Bacteria ; *Microbiota ; *Petroleum ; *Environmental Pollutants ; Cobalt/metabolism ; Soil Microbiology ; RNA, Ribosomal, 16S/genetics/metabolism ; Biodegradation, Environmental ; }, abstract = {Brownfields are unused sites that contain hazardous substances due to previous commercial or industrial use. The sites are inhospitable for many organisms, but some fungi and microbes can tolerate and thrive in the nutrient-depleted and contaminated soils. However, few studies have characterized the impacts of long-term contamination on soil microbiome composition and diversity at brownfields. This study focuses on an urban brownfield-a former rail yard in Los Angeles that is contaminated with heavy metals, volatile organic compounds, and petroleum-derived pollutants. We anticipate that heavy metals and organic pollutants will shape soil microbiome diversity and that several candidate fungi and bacteria will be tolerant to the contaminants. We sequence three gene markers (16S ribosomal RNA, 18S ribosomal RNA, and the fungal internal transcribed spacer (FITS)) in 55 soil samples collected at five depths to (1) profile the composition of the soil microbiome across depths; (2) determine the extent to which hazardous chemicals predict microbiome variation; and (3) identify microbial taxonomic groups that may metabolize these contaminants. Detected contaminants in the samples included heavy metals, petroleum hydrocarbons, polycyclic aromatic hydrocarbons, and volatile organic compounds. Bacterial, eukaryotic, and fungal communities all varied with depth and with concentrations of arsenic, chromium, cobalt, and lead. 18S rRNA microbiome richness and fungal richness were positively correlated with lead and cobalt levels, respectively. Furthermore, bacterial Paenibacillus and Iamia, eukaryotic Actinochloris, and fungal Alternaria were enriched in contaminated soils compared to uncontaminated soils and represent taxa of interest for future bioremediation research. Based on our results, we recommend incorporating DNA-based multi-marker microbial community profiling at multiple sites and depths in brownfield site assessment standard methods and restoration.}, }
@article {pmid35799308, year = {2023}, author = {Holderman, NR and Ferrer-González, FX and Glushka, J and Moran, MA and Edison, AS}, title = {Dissolved organic metabolite extraction from high-salt media.}, journal = {NMR in biomedicine}, volume = {36}, number = {4}, pages = {e4797}, doi = {10.1002/nbm.4797}, pmid = {35799308}, issn = {1099-1492}, support = {S10 OD021623/OD/NIH HHS/United States ; }, mesh = {*Seawater/chemistry/microbiology ; *Phytoplankton/metabolism ; Bacteria/metabolism ; Organic Chemicals/metabolism ; Water/metabolism ; }, abstract = {We describe considerations and strategies for developing a nuclear magnetic resonance (NMR) sample preparation method to extract low molecular weight metabolites from high-salt spent media in a model coculture system of phytoplankton and marine bacteria. Phytoplankton perform half the carbon fixation and oxygen generation on Earth. A substantial fraction of fixed carbon becomes part of a metabolite pool of small molecules known as dissolved organic matter (DOM), which are taken up by marine bacteria proximate to phytoplankton. There is an urgent need to elucidate these metabolic exchanges due to widespread anthropogenic transformations on the chemical, phenotypic, and species composition of seawater. These changes are increasing water temperature and the amount of CO2 absorbed by the ocean at energetic costs to marine microorganisms. Little is known about the metabolite-mediated, structured interactions occurring between phytoplankton and associated marine bacteria, in part because of challenges in studying high-salt solutions on various analytical platforms. NMR analysis is problematic due to the high-salt content of both natural seawater and culture media for marine microbes. High-salt concentration degrades the performance of the radio frequency coil, reduces the efficiency of some pulse sequences, limits signal-to-noise, and prolongs experimental time. The method described herein can reproducibly extract low molecular weight DOM from small-volume, high-salt cultures. It is a promising tool for elucidating metabolic flux between marine microorganisms and facilitates genetic screens of mutant microorganisms.}, }
@article {pmid35795698, year = {2022}, author = {Salerno, B and Cornaggia, M and Sabatino, R and Di Cesare, A and Furlan, M and Barco, L and Orsini, M and Cordioli, B and Mantovani, C and Bano, L and Losasso, C}, title = {Calves as Main Reservoir of Antibiotic Resistance Genes in Dairy Farms.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {918658}, pmid = {35795698}, issn = {2296-2565}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Cattle ; Drug Resistance, Microbial/genetics ; Farms ; *Genes, Bacterial ; Penicillins/pharmacology ; }, abstract = {A side effect of antibiotic usage is the emergence and dissemination of antibiotic resistance genes (ARGs) within microbial communities. The spread of ARGs among pathogens has emerged as a public health concern. While the distribution of ARGs is documented on a global level, their routes of transmission have not been clarified yet; for example, it is not clear whether and to what extent the emergence of ARGs originates in farms, following the selective pressure exerted by antibiotic usage in animal husbandry, and if they can spread into the environment. Here we address this cutting edge issue by combining data regarding antimicrobial usage and quantitative data from selected ARGs (blaTEM, blaCTXM, ermB, vanA, qnrS, tetA, sul2, and mcr-1) encoding for resistance to penicillins, macrolides-lincosamides-streptogramins, glycopeptides, quinolones, tetracyclines, sulfonamides, and colistin at the farm level. Results suggest that dairy farms could be considered a hotspot of ARGs, comprising those classified as the highest risk for human health and that a correlation existed between the usage of penicillins and blaTEM abundances, meaning that, although the antibiotic administration is not exclusive, it remains a certain cause of the ARGs' selection and spread in farms. Furthermore, this study identified the role of calves as the main source of ARGs spread in dairy farms, claiming the need for targeted actions in this productive category to decrease the load of ARGs along the production chain.}, }
@article {pmid35788867, year = {2023}, author = {Kim, SB and Lyou, ES and Kim, MS and Lee, TK}, title = {Bacterial Resuscitation from Starvation-Induced Dormancy Results in Phenotypic Diversity Coupled with Translational Activity Depending on Carbon Substrate Availability.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {325-336}, pmid = {35788867}, issn = {1432-184X}, support = {2020R1C1C1006249//National Research Foundation of Korea/ ; }, mesh = {Animals ; Cattle ; *Carbon/metabolism ; Phenotype ; *Bacteria/genetics/metabolism ; Adaptation, Physiological ; }, abstract = {Dormancy is a survival strategy of stressed bacteria inhabiting a various environment. Frequent dormant-active transitions owing to environmental changes play an important role in functional redundancy. However, a proper understanding of the phenotypic changes in bacteria during these transitions remains to be clarified. In this study, orthogonal approaches, such as electron microscopy, flow cytometry, and Raman spectroscopy, which can evaluate phenotypic heterogeneity at the single-cell level, were used to observe morphological and molecular phenotypic changes in resuscitated cells, and RNA sequencing (RNASeq) was used to determine the genetic characteristics associated with phenotypes. Within 12 h of the resuscitation process, morphological (cell size and shape) and physiological (growth and viability) characteristics as well as molecular phenotypes (cellular components) were found to be recovered to the extent that they were similar to those in active cells. The recovery rate and detailed phenotypic properties of the resuscitated cells differed significantly depending on the type or concentration of carbon sources. RNASeq analysis revealed that genes related to translation were significantly upregulated under all resuscitation conditions. The simpler the carbon source (e.g., glucose), the higher the expression of genes involved in cellular repair, and the more complex the carbon source (e.g., beef extract), the higher the expression of genes associated with increased energy production associated with cellular aerobic respiration. This study of phenotypic plasticity of resuscitated cells provides fundamental insight into understanding the adaptive fine-tuning of the microbiome in response to environmental changes and the functional redundancy resulting from phenotype heterogeneity.}, }
@article {pmid35788422, year = {2023}, author = {Baubin, C and Ran, N and Siebner, H and Gillor, O}, title = {Divergence of Biocrust Active Bacterial Communities in the Negev Desert During a Hydration-Desiccation Cycle.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {474-484}, pmid = {35788422}, issn = {1432-184X}, support = {993/11//Israeli Science Academy/ ; }, mesh = {*Ecosystem ; Desiccation ; Desert Climate ; *Cyanobacteria/physiology ; Chlorophyll ; Soil ; Soil Microbiology ; }, abstract = {Rain events in arid environments are highly unpredictable and intersperse extended periods of drought. Therefore, tracking changes in desert soil bacterial communities during rain events, in the field, was seldom attempted. Here, we assessed rain-mediated dynamics of active bacterial communities in the Negev Desert biological soil crust (biocrust). Biocrust samples were collected during, and after a medium rainfall and dry soil was used as a control; we evaluated the changes in active bacterial composition, potential function, potential photosynthetic activity, and extracellular polysaccharide (EPS) production. We hypothesized that rain would activate the biocrust phototrophs (mainly Cyanobacteria), while desiccation would inhibit their activity. In contrast, the biocrust Actinobacteria would decline during rewetting and revive with desiccation. Our results showed that hydration increased chlorophyll content and EPS production. As expected, biocrust rewetting activated Cyanobacteria, which replaced the former dominant Actinobacteria, boosting potential autotrophic functions. However, desiccation of the biocrust did not immediately change the bacterial composition or potential function and was followed by a delayed decrease in chlorophyll and EPS levels. This dramatic shift in the community upon rewetting led to modifications in ecosystem services. We propose that following a rain event, the response of the active bacterial community lagged behind the biocrust water content due to the production of EPS which delayed desiccation and temporarily sustained the biocrust community activity.}, }
@article {pmid35785246, year = {2022}, author = {Jiang, X and Wang, L}, title = {Grassland-based ruminant farming systems in China: Potential, challenges and a way forward.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {10}, number = {}, pages = {243-248}, pmid = {35785246}, issn = {2405-6383}, abstract = {With an increasing demand for high-quality, eco-friendly food products and growing concerns over ecological conservation, the development of ecology-based alternatives for ruminant production in China is urgently needed. This review discusses the capabilities for integrating grassland grazing into existing livestock farming systems to meet the contemporary human needs for high-quality foods and ecologically stable environments. Additionally, this review provides a critical analysis of the challenges and future directions associated with grassland-based ruminant farming systems. Integrating nutritional manipulation with grazing manipulation is critical for improving the productivity of grassland-based ecosystems and natural ecological functions. Biodiversity is the primary determinant of grassland ecosystem functions, while the composition and function of rumen microbiomes determine ruminant production performance. Future studies should focus on the following aspects: 1) how livestock grazing regulates grassland biodiversity and the mechanisms of grassland biodiversity maintenance, offering an important scientific basis for guiding grazing manipulation practices, including grazing intensity, livestock types, and grazing management practices; to 2) characterize the microbial ecology within the rumen of grazing ruminants to offer clarified instruction for the nutritional manipulation of grazing ruminants. Our recommendation includes creating a transdisciplinary system that integrates ecology, animal nutrition, and animal behavior to develop grassland-based ruminant farming systems sustainably, thereby achieving high-quality animal production and environmentally sustainable goals.}, }
@article {pmid35783424, year = {2022}, author = {O'Brien, J and McParland, EL and Bramucci, AR and Ostrowski, M and Siboni, N and Ingleton, T and Brown, MV and Levine, NM and Laverock, B and Petrou, K and Seymour, J}, title = {The Microbiological Drivers of Temporally Dynamic Dimethylsulfoniopropionate Cycling Processes in Australian Coastal Shelf Waters.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {894026}, pmid = {35783424}, issn = {1664-302X}, abstract = {The organic sulfur compounds dimethylsulfoniopropionate (DMSP) and dimethyl sulfoxide (DMSO) play major roles in the marine microbial food web and have substantial climatic importance as sources and sinks of dimethyl sulfide (DMS). Seasonal shifts in the abundance and diversity of the phytoplankton and bacteria that cycle DMSP are likely to impact marine DMS (O) (P) concentrations, but the dynamic nature of these microbial interactions is still poorly resolved. Here, we examined the relationships between microbial community dynamics with DMS (O) (P) concentrations during a 2-year oceanographic time series conducted on the east Australian coast. Heterogenous temporal patterns were apparent in chlorophyll a (chl a) and DMSP concentrations, but the relationship between these parameters varied over time, suggesting the phytoplankton and bacterial community composition were affecting the net DMSP concentrations through differential DMSP production and degradation. Significant increases in DMSP were regularly measured in spring blooms dominated by predicted high DMSP-producing lineages of phytoplankton (Heterocapsa, Prorocentrum, Alexandrium, and Micromonas), while spring blooms that were dominated by predicted low DMSP-producing phytoplankton (Thalassiosira) demonstrated negligible increases in DMSP concentrations. During elevated DMSP concentrations, a significant increase in the relative abundance of the key copiotrophic bacterial lineage Rhodobacterales was accompanied by a three-fold increase in the gene, encoding the first step of DMSP demethylation (dmdA). Significant temporal shifts in DMS concentrations were measured and were significantly correlated with both fractions (0.2-2 μm and >2 μm) of microbial DMSP lyase activity. Seasonal increases of the bacterial DMSP biosynthesis gene (dsyB) and the bacterial DMS oxidation gene (tmm) occurred during the spring-summer and coincided with peaks in DMSP and DMSO concentration, respectively. These findings, along with significant positive relationships between dsyB gene abundance and DMSP, and tmm gene abundance with DMSO, reinforce the significant role planktonic bacteria play in producing DMSP and DMSO in ocean surface waters. Our results highlight the highly dynamic nature and myriad of microbial interactions that govern sulfur cycling in coastal shelf waters and further underpin the importance of microbial ecology in mediating important marine biogeochemical processes.}, }
@article {pmid35783390, year = {2022}, author = {Sanchez-Cid, C and Keuschnig, C and Torzewski, K and Stachnik, &#x141; and Kępski, D and Luks, B and Nawrot, A and Niedzielski, P and Vogel, TM and Larose, C}, title = {Environmental and Anthropogenic Factors Shape the Snow Microbiome and Antibiotic Resistome.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {918622}, pmid = {35783390}, issn = {1664-302X}, abstract = {Winter tourism can generate environmental pollution and affect microbial ecology in mountain ecosystems. This could stimulate the development of antibiotic resistance in snow and its dissemination through the atmosphere and through snow melting. Despite these potential impacts, the effect of winter tourism on the snow antibiotic resistome remains to be elucidated. In this study, snow samples subjected to different levels of anthropogenic activities and surrounding forest were obtained from the Sudety Mountains in Poland to evaluate the impact of winter tourism on snow bacteria using a metagenomic approach. Bacterial community composition was determined by the sequencing of the V3-V4 hypervariable region of the 16S rRNA gene and the composition of the antibiotic resistome was explored by metagenomic sequencing. Whereas environmental factors were the main drivers of bacterial community and antibiotic resistome composition in snow, winter tourism affected resistome composition in sites with similar environmental conditions. Several antibiotic resistance genes (ARGs) showed a higher abundance in sites subjected to human activities. This is the first study to show that anthropogenic activities may influence the antibiotic resistome in alpine snow. Our results highlight the need to survey antibiotic resistance development in anthropogenically polluted sites.}, }
@article {pmid35780192, year = {2023}, author = {Borsanelli, AC and Athayde, FRF and Saraiva, JR and Riggio, MP and Dutra, IS}, title = {Dysbiosis and Predicted Functions of the Dental Biofilm of Dairy Goats with Periodontitis.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {687-698}, pmid = {35780192}, issn = {1432-184X}, support = {4-299//United States Agency for International Development/ ; }, mesh = {Animals ; Dysbiosis/veterinary ; *Periodontitis/veterinary/microbiology ; Bacteria/genetics ; *Microbiota/genetics ; Biofilms ; }, abstract = {Periodontitis is a polymicrobial biofilm-induced inflammatory disease associated with a dysbiotic microbial community and severely affects the health and welfare of animals. However, little is known regarding the dental microbiota associated with this disease in goats. In this study, we used high-throughput sequencing, network analysis, and predicted functions to investigate the microbiota of clinically healthy goats and those with periodontitis and identify possible pathogens and proteins associated with the disease. Dental microbiomes of goats with periodontitis were richer, and network analyses showed that the number of negative interactions was higher in the networks of animals with periodontitis. Based on the interrelationships, Porphyromonas, Fusobacterium, and Prevotella were suggested to play an important role in the dental microbiota associated with goat periodontitis. Protein families linked to translation, cytoplasmatic translation, and rRNA processing were more abundant in the dental microbiota of goats with periodontitis. In conclusion, the dental biofilm microbiota associated with goat periodontitis seems to be dysbiotic and has significant antagonistic interactions, which discriminate healthy animals from diseased animals and highlight the importance of key bacteria. Thus, these novel findings contribute to the evolution of knowledge regarding the etiopathogenesis of goat periodontitis and possibly to the development of periodontitis control measures.}, }
@article {pmid35778570, year = {2022}, author = {Lee, HJ and Whang, KS}, title = {Roseomonas rosulenta sp. nov., isolated from rice paddy soil.}, journal = {Archives of microbiology}, volume = {204}, number = {7}, pages = {445}, pmid = {35778570}, issn = {1432-072X}, mesh = {Bacterial Typing Techniques ; DNA, Bacterial/genetics ; *Methylobacteriaceae ; *Oryza/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil ; }, abstract = {Three bacterial isolates, Gram-stain-negative, non-motile, coccobacilli-shaped bacteria, strains OP-27[T], OP-5 and OP-30, were isolated from rice paddy soil. Phylogenetic analyses based on 16S rRNA gene sequences revealed that three isolates belonged to the genus Roseomonas, showing the highest sequence similarities to Roseomonas sediminicola FW-3[T] (98.1%) and Roseomonas lacus TH-G33[T] (98.0%). The genome size of strain OP-27[T] was 5.2 Mb in a single contig with DNA G+C content of 71.2%. The genome included 5164 predicted protein-coding genes, as well as 48 tRNA, 4 rRNA and 4 mRNA genes. The average nucleotide identity value between strain OP-27[T] and type strains of related species of the genus Roseomonas were 81.1-83.1%, and the digital DNA-DNA hybridization values of strain OP-27[T] and the related strains were 24.6-26.8%, respectively. The DNA-DNA hybridization values between strains OP-27[T], OP-5 and OP-30 were 84-100% and its closest relative, Roseomonas sediminicola KACC 16616[T] was 21.1%. The major fatty acids were C18:1 ω7c, C18:1 2-OH and C16:0 and predominant quinone was Q-10. Based on its distinctive phenotypic, phylogenetic, and chemotaxonomic characteristics, the three strains are considered to represent novel species of the genus Roseomonas, for which the name Roseomonas rosulenta sp. nov. is proposed. The type strain is OP-27[T] (=KACC 21501[T]= NBRC 114497[T]).}, }
@article {pmid35777363, year = {2022}, author = {Schwartzman, JA and Ebrahimi, A and Chadwick, G and Sato, Y and Roller, BRK and Orphan, VJ and Cordero, OX}, title = {Bacterial growth in multicellular aggregates leads to the emergence of complex life cycles.}, journal = {Current biology : CB}, volume = {32}, number = {14}, pages = {3059-3069.e7}, pmid = {35777363}, issn = {1879-0445}, support = {R25 GM067110/GM/NIGMS NIH HHS/United States ; }, mesh = {*Alginates/metabolism ; Animals ; Carbon ; Humans ; *Life Cycle Stages ; }, abstract = {Facultative multicellular behaviors expand the metabolic capacity and physiological resilience of bacteria. Despite their ubiquity in nature, we lack an understanding of how these behaviors emerge from cellular-scale phenomena. Here, we show how the coupling between growth and resource gradient formation leads to the emergence of multicellular lifecycles in a marine bacterium. Under otherwise carbon-limited growth conditions, Vibrio splendidus 12B01 forms clonal multicellular groups to collectively harvest carbon from soluble polymers of the brown-algal polysaccharide alginate. As they grow, groups phenotypically differentiate into two spatially distinct sub-populations: a static "shell" surrounding a motile, carbon-storing "core." Differentiation of these two sub-populations coincides with the formation of a gradient in nitrogen-source availability within clusters. Additionally, we find that populations of cells containing a high proportion of carbon-storing individuals propagate and form new clusters more readily on alginate than do populations with few carbon-storing cells. Together, these results suggest that local metabolic activity and differential partitioning of resources leads to the emergence of reproductive cycles in a facultatively multicellular bacterium.}, }
@article {pmid35776963, year = {2022}, author = {Viitamäki, S and Pessi, IS and Virkkala, AM and Niittynen, P and Kemppinen, J and Eronen-Rasimus, E and Luoto, M and Hultman, J}, title = {The activity and functions of soil microbial communities in the Finnish sub-Arctic vary across vegetation types.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {8}, pages = {}, pmid = {35776963}, issn = {1574-6941}, mesh = {Arctic Regions ; Bacteria/genetics ; Carbon/analysis ; Finland ; *Microbiota ; Plants ; *Soil/chemistry ; Soil Microbiology ; Tundra ; }, abstract = {Due to climate change, increased microbial activity in high-latitude soils may lead to higher greenhouse gas (GHG) emissions. However, microbial GHG production and consumption mechanisms in tundra soils are not thoroughly understood. To investigate how the diversity and functional potential of bacterial and archaeal communities vary across vegetation types and soil layers, we analyzed 116 soil metatranscriptomes from 73 sites in the Finnish sub-Arctic. Meadow soils were characterized by higher pH and lower soil organic matter (SOM) and carbon/nitrogen ratio. By contrast, dwarf shrub-dominated ecosystems had higher SOM and lower pH. Although Actinobacteria, Acidobacteria, Alphaproteobacteria and Planctomycetes were dominant in all communities, there were significant differences at the genus level between vegetation types; plant polymer-degrading groups were more active in shrub-dominated soils than in meadows. Given that climate-change scenarios predict the expansion of shrubs at high latitudes, our results indicate that tundra soil microbial communities harbor potential decomposers of increased plant litter, which may affect the rate of carbon turnover in tundra soils. Additionally, transcripts of methanotrophs were detected in the mineral layer of all soils, which may moderate methane fluxes. This study provides new insights into possible shifts in tundra microbial diversity and activity due to climate change.}, }
@article {pmid35775832, year = {2022}, author = {Muurinen, J and Muziasari, WI and Hultman, J and Pärnänen, K and Narita, V and Lyra, C and Fadlillah, LN and Rizki, LP and Nurmi, W and Tiedje, JM and Dwiprahasto, I and Hadi, P and Virta, MPJ}, title = {Antibiotic Resistomes and Microbiomes in the Surface Water along the Code River in Indonesia Reflect Drainage Basin Anthropogenic Activities.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {21}, pages = {14994-15006}, pmid = {35775832}, issn = {1520-5851}, mesh = {Humans ; *Rivers/microbiology ; Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; Genes, Bacterial ; Water ; Indonesia ; Anthropogenic Effects ; *Microbiota ; Bacteria/genetics ; }, abstract = {Water and sanitation are important factors in the emergence of antimicrobial resistance in low- and middle-income countries. Drug residues, metals, and various wastes foster the spread of antibiotic resistance genes (ARGs) with the help of mobile genetic elements (MGEs), and therefore, rivers receiving contaminants and effluents from multiple sources are of special interest. We followed both the microbiome and resistome of the Code River in Indonesia from its pristine origin at the Merapi volcano through rural and then city areas to the coast of the Indian Ocean. We used a SmartChip quantitative PCR with 382 primer pairs for profiling the resistome and MGEs and 16S rRNA gene amplicon sequencing to analyze the bacterial communities. The community structure explained the resistome composition in rural areas, while the city sampling sites had lower bacterial diversity and more ARGs, which correlated with MGEs, suggesting increased mobility potential in response to pressures from human activities. Importantly, the vast majority of ARGs and MGEs were no longer detectable in marine waters at the ocean entrance. Our work provides information on the impact of different influents on river health as well as sheds light on how land use contributes to the river resistome and microbiome.}, }
@article {pmid35771243, year = {2022}, author = {Bai, X and Dinkla, IJT and Muyzer, G}, title = {Microbial ecology of biofiltration used for producing safe drinking water.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {13-16}, pages = {4813-4829}, pmid = {35771243}, issn = {1432-0614}, support = {17840//NWO-TTW/ ; }, mesh = {Charcoal ; *Drinking Water ; Filtration ; Organic Chemicals ; Sand ; *Water Pollutants, Chemical ; *Water Purification ; }, abstract = {Biofiltration is a water purification technology playing a pivotal role in producing safe drinking water. This technology attracts many interests worldwide due to its advantages, such as no addition of chemicals, a low energy input, and a high removal efficiency of organic compounds, undesirable taste and odours, and pathogens. The current review describes the microbial ecology of three biofiltration processes that are routinely used in drinking water treatment plants, i.e. (i) rapid sand filtration (RSF), (ii) granular activated carbon filtration (GACF), and (iii) slow sand filtration (SSF). We summarised and compared the characteristics, removal performance, and corresponding (newly revealed) mechanisms of the three biofiltration processes. Specifically, the microbial ecology of the different biofilter processes and the role of microbial communities in removing nutrients, organic compounds, and pathogens were reviewed. Finally, we highlight the limitations and challenges in the study of biofiltration in drinking water production, and propose future perspectives for obtaining a comprehensive understanding of the microbial ecology of biofiltration, which is needed to promote and optimise its further application. KEY POINTS: • Biofilters are composed of complex microbiomes, primarily shaped by water quality. • Conventional biofilters contribute to address safety challenges in drinking water. • Studies may underestimate the active/functional role of microbiomes in biofilters.}, }
@article {pmid35770362, year = {2022}, author = {Sridhar, B and Wilhelm, RC and Debenport, SJ and Fahey, TJ and Buckley, DH and Goodale, CL}, title = {Microbial community shifts correspond with suppression of decomposition 25 years after liming of acidic forest soils.}, journal = {Global change biology}, volume = {28}, number = {18}, pages = {5399-5415}, doi = {10.1111/gcb.16321}, pmid = {35770362}, issn = {1365-2486}, mesh = {Bacteria/metabolism ; Carbon/metabolism ; Forests ; Fungi/metabolism ; *Microbiota ; *Mycorrhizae/metabolism ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Microbial community structure and function regularly covary with soil pH, yet effects of these interactions on soil carbon are rarely tested experimentally within natural ecosystems. We investigated the enduring (25 year) impacts of liming on microbial community structure and decomposition at an acidic northern hardwood forest, where experimental liming increased pH one unit and surprisingly doubled the organic carbon stocks of the forest floor. We show that this increase in carbon storage corresponded with restructuring of the bacterial and fungal communities that drive decomposition. In the Oe horizon, liming reduced the activities of five extracellular enzymes that mediate decomposition, while the Oa horizon showed an especially large (64%) reduction in the activity of a sixth, peroxidase, which is an oxidative enzyme central to lignocellulose degradation. Decreased enzyme activities corresponded with loss of microbial taxa important for lignocellulose decay, including large reductions in the dominant ectomycorrhizal genera Russula and Cenococcum, saprotrophic and wood decaying fungi, and Actinobacteria (Thermomonosporaceae). These results demonstrate the importance of pH as a dominant regulator of microbial community structure and illustrate how changes to this structure can produce large, otherwise unexpected increases in carbon storage in forest soils.}, }
@article {pmid35770167, year = {2022}, author = {Girolamini, L and Pascale, MR and Mazzotta, M and Spiteri, S and Marino, F and Salaris, S and Grottola, A and Orsini, M and Cristino, S}, title = {Combining Traditional and Molecular Techniques Supports the Discovery of a Novel Legionella Species During Environmental Surveillance in a Healthcare Facility.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {900936}, pmid = {35770167}, issn = {1664-302X}, abstract = {Legionella surveillance plays a significant role not only to prevent the risk of infection but also to study the ecology of isolates, their characteristics, and how their prevalence changes in the environment. The difficulty in Legionella isolation, identification, and typing results in a low notification rate; therefore, human infection is still underestimated. In addition, during Legionella surveillance, the special attention given to Legionella pneumophila leads to an underestimation of the prevalence and risk of infection for other species. This study describes the workflow performed during environmental Legionella surveillance that resulted in the isolation of two strains, named 8cVS16 and 9fVS26, associated with the genus Legionella. Traditional and novel approaches such as standard culture technique, MALDI-TOF MS, gene sequencing, and whole-genome sequencing (WGS) analysis were combined to demonstrate that isolates belong to a novel species. The strain characteristics, the differences between macrophage infectivity potential (mip), RNA polymerase β subunit (rpoB), and reference gene sequences, the average nucleotide identity (ANI) of 90.4%, and the DNA-DNA digital hybridization (dDDH) analysis of 43% demonstrate that these isolates belong to a new Legionella species. The finding suggests that, during the culture technique, special attention should be paid to the characteristics of the isolates that are less associated with the Legionella genus in order to investigate the differences found using more sensitive methods. The characterization of the two newly discovered isolates based on morphological, biochemical, and microscopic characteristics is currently underway and will be described in another future study.}, }
@article {pmid35770161, year = {2022}, author = {Pan, Y and Li, G and Su, L and Zheng, P and Wang, Y and Shen, Z and Chen, Z and Han, Q and Gong, J}, title = {Seagrass Colonization Alters Diversity, Abundance, Taxonomic, and Functional Community Structure of Benthic Microbial Eukaryotes.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {901741}, pmid = {35770161}, issn = {1664-302X}, abstract = {Seagrass form high productive ecosystems in coastal environments. However, the effects of these coastal plants on the structure and function of the belowground eukaryotic microbiome remain elusive. In this study, we characterized the community of microbial eukaryotes (microeukaryotes) in both vegetated and unvegetated sediments using 18S rRNA gene amplicon sequencing and quantitative PCR. Analysis of sequencing data showed that the eelgrass (Zostera marina) colonization decreased the alpha diversity indices of benthic microeukaryotes. Apicomplexa represented an average of 83% of reads across all samples, with a higher proportion at the vegetated sites. The taxonomic community structure was significantly different between these two types of sediments, for which the concentration of NH 4 + in sediment porewater and salinity could account. Phylogenetic analyses of long 18S rRNA genes (around 1,030 bp) indicated these apicomplexan parasites are closely related to gregarine Lecudina polymorpha. Determination of 18S rRNA gene abundances provided evidence that the eelgrass markedly promoted the biomass of the gregarine and all microeukaryotes in the seagrass-colonized sediments and confirmed that the gregarine was hosted by a polychaete species. Significantly higher gene abundances of heterotrophs and mixotrophs were found at the vegetated sites, which could be explained by the finer sediments and short supply of dissolved inorganic nitrogen, respectively. The pigmented protists were more abundant in 18S rRNA gene copies at the lower and higher pH levels than at the intermediate. Nevertheless, the fractions of heterotrophs and phototrophs in the community were significantly related to porewater N:P ratio. These results indicate that seagrass colonization significantly induces an increase in overall biomass and a decrease in diversity of benthic microeukaryotes, making them more heterotrophic. This study also highlights that the hotspot of eukaryotic parasites could be linked with the high productivity of a natural ecosystem.}, }
@article {pmid35769467, year = {2022}, author = {Qing, J and Li, C and Hu, X and Song, W and Tirichen, H and Yaigoub, H and Li, Y}, title = {Differentiation of T Helper 17 Cells May Mediate the Abnormal Humoral Immunity in IgA Nephropathy and Inflammatory Bowel Disease Based on Shared Genetic Effects.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {916934}, pmid = {35769467}, issn = {1664-3224}, mesh = {Biomarkers/metabolism ; Cell Differentiation/immunology ; *Glomerulonephritis, IGA/immunology ; Humans ; Immunity, Humoral ; *Inflammatory Bowel Diseases/genetics/immunology ; *MicroRNAs/genetics ; *Th17 Cells/cytology/immunology ; }, abstract = {BACKGROUND: IgA nephropathy (IgAN) is the most frequent glomerulonephritis in inflammatory bowel disease (IBD). However, the inter-relational mechanisms between them are still unclear. This study aimed to explore the shared gene effects and potential immune mechanisms in IgAN and IBD.<br><br>METHODS: The microarray data of IgAN and IBD in the Gene Expression Omnibus (GEO) database were downloaded. The differential expression analysis was used to identify the shared differentially expressed genes (SDEGs). Besides, the shared transcription factors (TFs) and microRNAs (miRNAs) in IgAN and IBD were screened using humanTFDB, HMDD, ENCODE, JASPAR, and ChEA databases. Moreover, weighted gene co-expression network analysis (WGCNA) was used to identify the shared immune-related genes (SIRGs) related to IgAN and IBD, and R software package org.hs.eg.db (Version3.1.0) were used to identify common immune pathways in IgAN and IBD.<br><br>RESULTS: In this study, 64 SDEGs and 28 SIRGs were identified, and the area under the receiver operating characteristic curve (ROC) of 64 SDEGs was calculated and two genes (MVP, PDXK) with high area under the curve (AUC) in both IgAN and IBD were screened out as potential diagnostic biomarkers. We then screened 3 shared TFs (SRY, MEF2D and SREBF1) and 3 miRNAs (hsa-miR-146, hsa-miR-21 and hsa-miR-320), and further found that the immune pathways of 64SDEGs, 28SIRGs and 3miRNAs were mainly including B cell receptor signaling pathway, Fc&#x3b3;R-mediated phagocytosis, IL-17 signaling pathway, toll-like receptor signaling pathway, TNF signaling pathway, TRP channels, T cell receptor signaling pathway, Th17 cell differentiation, and cytokine-cytokine receptor interaction.<br><br>CONCLUSION: Our work revealed the differentiation of Th17 cells may mediate the abnormal humoral immunity in IgAN and IBD patients and identified novel gene candidates that could be used as biomarkers or potential therapeutic targets.}, }
@article {pmid35768458, year = {2022}, author = {Catania, T and Li, Y and Winzer, T and Harvey, D and Meade, F and Caridi, A and Leech, A and Larson, TR and Ning, Z and Chang, J and Van de Peer, Y and Graham, IA}, title = {Author Correction: A functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3755}, doi = {10.1038/s41467-022-31568-x}, pmid = {35768458}, issn = {2041-1723}, }
@article {pmid35768269, year = {2022}, author = {Yin, H and Huang, J and Hu, M}, title = {Moderate-Intensity Exercise Improves Endothelial Function by Altering Gut Microbiome Composition in Rats Fed a High-Fat Diet.}, journal = {Journal of Nippon Medical School = Nippon Ika Daigaku zasshi}, volume = {89}, number = {3}, pages = {316-327}, doi = {10.1272/jnms.JNMS.2022_89-307}, pmid = {35768269}, issn = {1347-3409}, mesh = {Animals ; *Diet, High-Fat/adverse effects ; Endothelium/metabolism ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred C57BL ; Obesity/etiology/metabolism/therapy ; RNA, Ribosomal, 16S/genetics ; Rats ; Vascular Endothelial Growth Factor A ; }, abstract = {BACKGROUND: Obesity changes gut microbial ecology and is related to endothelial dysfunction. Although the correlation between gut microbial ecology and endothelial dysfunction has been studied in obese persons, the underlying mechanisms by which exercise enhances endothelial function in this group remain unclear. This study investigated whether exercise improves endothelial function and alters gut microbiome composition in rats fed a high-fat diet (HFD).<br><br>METHODS: Obesity was induced by an HFD for 11 weeks. Whole-body composition and endothelium-dependent relaxation of mesenteric arteries were measured. Blood biochemical tests were performed, and gut microbiomes were characterized by 16S rRNA gene sequencing on an Illumina HiSeq platform.<br><br>RESULTS: Exercise training for 8 weeks improved body composition in HFD-fed rats. Furthermore, compared with the untrained/HFD group, aerobic exercise significantly increased acetylcholine-induced, endothelium-dependent relaxation in mesenteric arteries (P < 0.05) and circulating vascular endothelial growth factor levels (P < 0.01) and decreased circulating C-reactive protein levels (P < 0.05). In addition, exercise and HFD resulted in alterations in the composition of the gut microbiome; exercise reduced the relative abundance of Clostridiales and Romboutsia. Moreover, 12 species of bacteria, including Romboutsia, were significantly associated with parameters of endothelial function in the overall sample.<br><br>CONCLUSIONS: These results suggest that aerobic exercise enhances endothelial function in HFD-fed rats by altering the composition of the gut microbiota. These findings provide new insights on the application of physical exercise for improving endothelial function in obese persons.}, }
@article {pmid35764676, year = {2022}, author = {Van den Wyngaert, S and Ganzert, L and Seto, K and Rojas-Jimenez, K and Agha, R and Berger, SA and Woodhouse, J and Padisak, J and Wurzbacher, C and Kagami, M and Grossart, HP}, title = {Seasonality of parasitic and saprotrophic zoosporic fungi: linking sequence data to ecological traits.}, journal = {The ISME journal}, volume = {16}, number = {9}, pages = {2242-2254}, pmid = {35764676}, issn = {1751-7370}, support = {WY175/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; AG 284/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; WU 890/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; GR1540/30-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Animals ; *Chytridiomycota/genetics ; *Diatoms/genetics/microbiology ; Fungi/genetics ; Lakes/microbiology ; *Parasites ; Phytoplankton/microbiology ; }, abstract = {Zoosporic fungi of the phylum Chytridiomycota (chytrids) regularly dominate pelagic fungal communities in freshwater and marine environments. Their lifestyles range from obligate parasites to saprophytes. Yet, linking the scarce available sequence data to specific ecological traits or their host ranges constitutes currently a major challenge. We combined 28 S rRNA gene amplicon sequencing with targeted isolation and sequencing approaches, along with cross-infection assays and analysis of chytrid infection prevalence to obtain new insights into chytrid diversity, ecology, and seasonal dynamics in a temperate lake. Parasitic phytoplankton-chytrid and saprotrophic pollen-chytrid interactions made up the majority of zoosporic fungal reads. We explicitly demonstrate the recurrent dominance of parasitic chytrids during frequent diatom blooms and saprotrophic chytrids during pollen rains. Distinct temporal dynamics of diatom-specific parasitic clades suggest mechanisms of coexistence based on niche differentiation and competitive strategies. The molecular and ecological information on chytrids generated in this study will aid further exploration of their spatial and temporal distribution patterns worldwide. To fully exploit the power of environmental sequencing for studies on chytrid ecology and evolution, we emphasize the need to intensify current isolation efforts of chytrids and integrate taxonomic and autecological data into long-term studies and experiments.}, }
@article {pmid35762794, year = {2022}, author = {Roguet, A and Newton, RJ and Eren, AM and McLellan, SL}, title = {Guts of the Urban Ecosystem: Microbial Ecology of Sewer Infrastructure.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0011822}, pmid = {35762794}, issn = {2379-5077}, support = {R01 AI091829/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Anti-Bacterial Agents ; Bacteria/genetics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; United States ; *Wastewater ; }, abstract = {Microbes have inhabited the oceans and soils for millions of years and are uniquely adapted to their habitat. In contrast, sewer infrastructure in modern cities dates back only ~150 years. Sewer pipes transport human waste and provide a view into public health, but the resident organisms that likely modulate these features are relatively unexplored. Here, we show that the bacterial assemblages sequenced from untreated wastewater in 71 U.S. cities were highly coherent at a fine sequence level, suggesting that urban infrastructure separated by great spatial distances can give rise to strikingly similar communities. Within the overall microbial community structure, temperature had a discernible impact on the distribution patterns of closely related amplicon sequence variants, resulting in warm and cold ecotypes. Two bacterial genera were dominant in most cities regardless of their size or geographic location; on average, Arcobacter accounted for 11% and Acinetobacter 10% of the entire community. Metagenomic analysis of six cities revealed these highly abundant resident organisms carry clinically important antibiotic resistant genes blaCTX-M, blaOXA, and blaTEM. In contrast, human fecal bacteria account for only ~13% of the community; therefore, antibiotic resistance gene inputs from human sources to the sewer system could be comparatively small, which will impact measurement capabilities when monitoring human populations using wastewater. With growing awareness of the metabolic potential of microbes within these vast networks of pipes and the ability to examine the health of human populations, it is timely to increase our understanding of the ecology of these systems. IMPORTANCE Sewer infrastructure is a relatively new habitat comprised of thousands of kilometers of pipes beneath cities. These wastewater conveyance systems contain large reservoirs of microbial biomass with a wide range of metabolic potential and are significant reservoirs of antibiotic resistant organisms; however, we lack an adequate understanding of the ecology or activity of these communities beyond wastewater treatment plants. The striking coherence of the sewer microbiome across the United States demonstrates that the sewer environment is highly selective for a particular microbial community composition. Therefore, results from more in-depth studies or proven engineering controls in one system could be extrapolated more broadly. Understanding the complex ecology of sewer infrastructure is critical for not only improving our ability to treat human waste and increasing the sustainability of our cities but also to create scalable and effective sewage microbial observatories, which are inevitable investments of the future to monitor health in human populations.}, }
@article {pmid35761925, year = {2022}, author = {Modin, O and Fuad, N and Abadikhah, M and I'Ons, D and Ossiansson, E and Gustavsson, DJI and Edefell, E and Suarez, C and Persson, F and Wilén, BM}, title = {A relationship between phages and organic carbon in wastewater treatment plant effluents.}, journal = {Water research X}, volume = {16}, number = {}, pages = {100146}, pmid = {35761925}, issn = {2589-9147}, abstract = {With stringent effluent requirements and the implementation of new processes for micropollutant removal, it is increasingly important for wastewater treatment plants (WWTPs) to understand the factors affecting effluent quality. Phages (viruses infecting prokaryotes) are abundant in the biological treatment processes. They can contribute to organic carbon in the treated effluent both because they are organic in nature and occur in the effluent and because they cause lysis of microorganisms. Today very little is known about the effects of phages on effluent quality. The goal of this study was, therefore, to determine the relationship between phages and organic carbon in WWTP effluents. We also examined the diversity, taxonomy, and host-association of DNA phages using metagenomics. Effluent samples were collected from four WWTPs treating municipal wastewater. Significant differences in both organic carbon and virus-like particle concentrations were observed between the plants and there was a linear relationship between the two parameters. The phage communities were diverse with many members being taxonomically unclassified. Putative hosts were dominated by bacteria known to be abundant in activated sludge systems such as Comamonadaceae. The composition of phages differed between the WWTPs, suggesting that local conditions shape the communities. Overall, our findings suggest that the abundance and composition of phages are related to effluent quality. Thus, there is a need for further research clarifying the association between phage dynamics and WWTP function.}, }
@article {pmid35761577, year = {2022}, author = {Kothe, CI and Mohellibi, N and Renault, P}, title = {Revealing the microbial heritage of traditional Brazilian cheeses through metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {157}, number = {}, pages = {111265}, doi = {10.1016/j.foodres.2022.111265}, pmid = {35761577}, issn = {1873-7145}, mesh = {Animals ; Biodiversity ; Brazil ; *Cheese/analysis ; Food Microbiology ; *Lactobacillales/genetics ; *Lactococcus lactis/genetics ; Metagenomics ; Streptococcus thermophilus/genetics ; Yeasts ; }, abstract = {Brazilian artisanal cheeses date from the first Portuguese settlers and evolved via local factors, resulting in unique products that are now part of the patrimony and identity of different Brazilian regions. In this study, we combined several culture-independent approaches, including 16S/ITS metagenetics, assembly- and deep profiling-metagenomics to characterize the originality of the microbiota of five varieties of Brazilian artisanal cheeses from the South and Southeast regions of Brazil. Their core microbiota contained mainly lactic acid bacteria (LAB), of which Lactococcus lactis subsp. lactis was the most frequent, followed by Streptococcus thermophilus in the South region. Moreover, several samples from the Southeast region contained, as dominant LAB, two other food Streptococci belonging to a new species of the salivarius group and S. infantarius. Rinds of samples from the Southeast region were dominated by the halotolerant bacterium Corynebacterium variabile, and the yeasts Diutina catenulata, followed by Debaryomyces hansenii and Kodamaea ohmeri. Rinds from the South region contained mainly LAB due to their short ripening time, and the predominant yeast was D. hansenii. Phylogenomic analysis based on L. lactis metagenome-assembled genomes (MAGs) showed that most Brazilian strains are closely related and form a different clade from those whose genomes are available at this time, indicating that they belong to a specific group. Lastly, functional analysis showed that S. infantarius acquired a ∼ 26 kb DNA fragment from S. thermophilus starter strains that carry the LacSZ system, allowing fast lactose assimilation, an adaptation advantage for growth in milk. Finally, our study identified several areas of concern, such as the presence of somatic cell DNA and high levels of antibiotic resistance genes in several cheese microbiota, suggesting that milk from diseased animals may still be used occasionally. Overall, the data from this study highlight the potential value of the traditional and artisanal cheese production network in Brazil, and provide a metagenomic-based scheme to help manage this resource safely.}, }
@article {pmid35761554, year = {2022}, author = {Sequino, G and Valentino, V and Villani, F and De Filippis, F}, title = {Omics-based monitoring of microbial dynamics across the food chain for the improvement of food safety and quality.}, journal = {Food research international (Ottawa, Ont.)}, volume = {157}, number = {}, pages = {111242}, doi = {10.1016/j.foodres.2022.111242}, pmid = {35761554}, issn = {1873-7145}, mesh = {*Food Chain ; Food Safety ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {The diffusion of high-throughput sequencing has dramatically changed the study of food microbial ecology. Amplicon-based description of the microbial community may be routinary implemented in the food industry to understand how the processing parameters and the raw material quality may affect the microbial community of the final product, as well as how the community changes during the shelf-life. In addition, application of shotgun metagenomics may represent an invaluable resource to understand the functional potential of the microbial community, identifying the presence of spoilage-associated activities or genes related to pathogenesis. Finally, retrieving Metagenome-Assembled Genomes (MAGs) of relevant species may be useful for strain-tracking along the food chain and in case of food poisoning outbreaks. This review gives an overview of the possible applications of sequencing-based approaches in the study of food microbial ecology, highlighting limitations that still prevent the spreading of these techniques to the food industry.}, }
@article {pmid35761415, year = {2022}, author = {Liu, Y and Yang, M and Tang, L and Wang, F and Huang, S and Liu, S and Lei, Y and Wang, S and Xie, Z and Wang, W and Zhao, X and Tang, B and Yang, S}, title = {TLR4 regulates RORγt[+] regulatory T-cell responses and susceptibility to colon inflammation through interaction with Akkermansia muciniphila.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {98}, pmid = {35761415}, issn = {2049-2618}, mesh = {*Akkermansia ; Animals ; *Colitis/immunology ; Colon ; Dextran Sulfate/adverse effects ; Inflammation ; Mice ; Mice, Inbred C57BL ; Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; *T-Lymphocytes, Regulatory/immunology ; *Toll-Like Receptor 4/genetics ; }, abstract = {BACKGROUND: Well-balanced interactions between gut microbiota and the immune system are essential to prevent chronic intestinal inflammation, as observed in inflammatory bowel diseases (IBD). Toll-like receptor 4 (TLR4) functions as a sensor mediating the crosstalk between the intestinal commensal microbiome and host immunity, but the influence of TLR4 on the shaping of intestinal microbiota and immune responses during colon inflammation remains poorly characterized. We investigated whether the different susceptibilities to colitis between wild-type (WT) and TLR4[-/-] mice were gut microbiota-dependent and aimed to identify the potential immunity modulation mechanism.<br><br>METHODS: We performed antibiotic depletion of the microbiota, cohousing experiments, and faecal microbiota transplantation (FMT) in WT and TLR4[-/-] mice to assess the influence of TLR4 on intestinal microbial ecology. 16S rRNA sequencing was performed to dissect microbial discrepancies, and dysbiosis-associated immune perturbation was investigated by flow cytometry. Akkermansia muciniphila (A. muciniphila)-mediated immune modulation was confirmed through the T-cell transfer colitis model and bone marrow chimaera construction.<br><br>RESULTS: TLR4[-/-] mice experienced enhanced susceptibility to DSS-induced colitis. 16S rRNA sequencing showed notable discrepancy in the gut microbiota between WT and TLR4[-/-] mice. In particular, A. muciniphila contributed most to distinguishing the two groups. The T-cell transfer colitis model and bone marrow transplantation (BMT) consistently demonstrated that A. muciniphila ameliorated colitis by upregulating ROR&#x3b3;t[+] Treg cell-mediated immune responses. Mucosal biopsies from human manifested parallel outcomes with colon tissue from WT mice, as evidenced by the positive correlation between TLR4 expression and intestinal A. muciniphila colonization during homeostasis.<br><br>CONCLUSIONS: Our results demonstrate a novel protective role of TLR4 against intestinal inflammation, wherein it can modulate A. muciniphila-associated immune responses. These findings provide a new perspective on host-commensal symbiosis, which may be beneficial for developing potential therapeutic strategies. Video abstract.}, }
@article {pmid35760840, year = {2022}, author = {Piel, D and Bruto, M and Labreuche, Y and Blanquart, F and Goudenège, D and Barcia-Cruz, R and Chenivesse, S and Le Panse, S and James, A and Dubert, J and Petton, B and Lieberman, E and Wegner, KM and Hussain, FA and Kauffman, KM and Polz, MF and Bikard, D and Gandon, S and Rocha, EPC and Le Roux, F}, title = {Phage-host coevolution in natural populations.}, journal = {Nature microbiology}, volume = {7}, number = {7}, pages = {1075-1086}, pmid = {35760840}, issn = {2058-5276}, mesh = {*Bacteriophages/genetics ; Host Specificity ; }, abstract = {Coevolution between bacteriophages (phages) and their bacterial hosts occurs through changes in resistance and counter-resistance mechanisms. To assess phage-host evolution in wild populations, we isolated 195 Vibrio crassostreae strains and 243 vibriophages during a 5-month time series from an oyster farm and combined these isolates with existing V. crassostreae and phage isolates. Cross-infection studies of 81,926 host-phage pairs delineated a modular network where phages are best at infecting co-occurring hosts, indicating local adaptation. Successful propagation of phage is restricted by the ability to adsorb to closely related bacteria and further constrained by strain-specific defence systems. These defences are highly diverse and predominantly located on mobile genetic elements, and multiple defences are active within a single genome. We further show that epigenetic and genomic modifications enable phage to adapt to bacterial defences and alter host range. Our findings reveal that the evolution of bacterial defences and phage counter-defences is underpinned by frequent genetic exchanges with, and between, mobile genetic elements.}, }
@article {pmid35754723, year = {2022}, author = {Waring, B and Gee, A and Liang, G and Adkins, S}, title = {A quantitative analysis of microbial community structure-function relationships in plant litter decay.}, journal = {iScience}, volume = {25}, number = {7}, pages = {104523}, pmid = {35754723}, issn = {2589-0042}, abstract = {Soil microbes play a central role in ecosystem element cycling. Yet a central question in microbial ecology remains unanswered: to what extent does the taxonomic composition of soil microbial communities mediate biogeochemical process rates? In this quantitative review, we explore the mechanisms that lead to variation in the strength of microbial community structure-function relationships over space and time. To evaluate these mechanisms, we conduct a meta-analysis of studies that have monitored the decomposition of sterilized plant litter inoculated with different microbial assemblages. We find that the influence of microbial community composition on litter decay is pervasive and strong, rivalling in magnitude the influence of litter chemistry on decomposition. However, no single environmental or experimental attribute was correlated with variation in the inoculum effect. These results emphasize the need to better understand ecological dynamics within microbial communities, particularly emergent features such as cross-feeding networks, to improve predictions of soil biogeochemical function.}, }
@article {pmid35753302, year = {2022}, author = {Zhang, K and Hu, J and Yang, S and Xu, W and Wang, Z and Zhuang, P and Grossart, HP and Luo, Z}, title = {Biodegradation of polyester polyurethane by the marine fungus Cladosporium halotolerans 6UPA1.}, journal = {Journal of hazardous materials}, volume = {437}, number = {}, pages = {129406}, doi = {10.1016/j.jhazmat.2022.129406}, pmid = {35753302}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; Carbon/metabolism ; Cladosporium ; Esterases/metabolism ; Fungi/metabolism ; Lipase ; *Polyesters/chemistry ; *Polyurethanes/chemistry ; Soil Microbiology ; }, abstract = {Lack of degradability and the accumulation of polymeric wastes increase the risk for the health of the environment. Recently, recycling of polymeric waste materials becomes increasingly important as raw materials for polymer synthesis are in short supply due to the rise in price and supply chain disruptions. As an important polymer, polyurethane (PU) is widely used in modern life, therefore, PU biodegradation is desirable to avoid its accumulation in the environment. In this study, we isolated a fungal strain Cladosporium halotolerans from the deep sea which can grow in mineral medium with a polyester PU (Impranil DLN) as a sole carbon source. Further, we demonstrate that it can degrade up to 80% of Impranil PU after 3 days of incubation at 28 ℃ by breaking the carbonyl groups (1732 cm[-1]) and C-N-H bonds (1532 cm[-1] and 1247 cm[-1]) as confirmed by Fourier-transform infrared (FTIR) spectroscopy analysis. Gas chromatography-mass spectrometry (GC-MS) analysis revealed polyols and alkanes as PU degradation intermediates, indicating the hydrolysis of ester and urethane bonds. Esterase and urease activities were detected in 7 days-old cultures with PU as a carbon source. Transcriptome analysis showed a number of extracellular protein genes coding for enzymes such as cutinase, lipase, peroxidase and hydrophobic surface binding proteins A (HsbA) were expressed when cultivated on Impranil PU. The yeast two-hybrid assay revealed that the hydrophobic surface binding protein ChHsbA1 directly interacts with inducible esterases, ChLip1 (lipase) and ChCut1 (cutinase). Further, the KEGG pathway for "fatty acid degradation" was significantly enriched in Impranil PU inducible genes, indicating that the fungus may use the degradation intermediates to generate energy via this pathway. Taken together, our data indicates secretion of both esterase and hydrophobic surface binding proteins by C. halotolerans plays an important role in Impranil PU absorption and subsequent degradation. Our study provides a mechanistic insight into Impranil PU biodegradation by deep sea fungi and provides the basis for future development of biotechnological PU recycling.}, }
@article {pmid35752808, year = {2022}, author = {Wang, Q and Chen, Y and Yang, Q and Zhao, J and Feng, L and Wang, M}, title = {SR5AL serves as a key regulatory gene in lycopene biosynthesis by Blakeslea trispora.}, journal = {Microbial cell factories}, volume = {21}, number = {1}, pages = {126}, pmid = {35752808}, issn = {1475-2859}, support = {21A180014//Key Scientific Research Project of Colleges and Universities in Henan Province/ ; 212102110322//Science and Technology Department of Henan Province/ ; }, mesh = {Genes, Regulator ; Lycopene/metabolism ; *Mucorales/genetics/metabolism ; Oxidoreductases/metabolism ; }, abstract = {BACKGROUND: Trisporic acids are considered to be key regulators of carotenoid biosynthesis and sexual reproduction in zygomycetes, but the mechanisms underlying this regulation have not been fully elucidated.<br><br>RESULTS: In this study, the relationships between trisporic acids and lycopene synthesis were investigated in Blakeslea trispora. The lycopene concentration in single fermentation by the (-) strain with the addition of 24&#xa0;&#x3bc;g/L trisporic acids was slightly higher than that observed in mated fermentation. After transcriptomic analysis, a steroid 5&#x3b1;-reductase-like gene, known as SR5AL in B. trispora, was first reported. 5&#x3b1;-Reductase inhibitors reduced lycopene biosynthesis and downregulated the expression of sex determination and carotenoid biosynthesis genes. Overexpression of the SR5AL gene upregulated these genes, regardless of whether trisporic acids were added.<br><br>CONCLUSION: These findings indicated that the SR5AL gene is a key gene associated with the response to trisporic acids.}, }
@article {pmid35752802, year = {2022}, author = {Darcy, JL and Amend, AS and Swift, SOI and Sommers, PS and Lozupone, CA}, title = {specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {34}, pmid = {35752802}, issn = {2524-6372}, support = {5 T15 LM009451-12/NH/NIH HHS/United States ; 1255972//National Science Foundation/ ; }, abstract = {BACKGROUND: Understanding the factors that influence microbes' environmental distributions is important for determining drivers of microbial community composition. These include environmental variables like temperature and pH, and higher-dimensional variables like geographic distance and host species phylogeny. In microbial ecology, "specificity" is often described in the context of symbiotic or host parasitic interactions, but specificity can be more broadly used to describe the extent to which a species occupies a narrower range of an environmental variable than expected by chance. Using a standardization we describe here, Rao's (Theor Popul Biol, 1982. https://doi.org/10.1016/0040-5809(82)90004-1, Sankhya A, 2010. https://doi.org/10.1007/s13171-010-0016-3) Quadratic Entropy can be conveniently applied to calculate specificity of a feature, such as a species, to many different environmental variables.<br><br>RESULTS: We present our R package specificity for performing the above analyses, and apply it to four real-life microbial data sets to demonstrate its application. We found that many fungi within the leaves of native Hawaiian plants had strong specificity to rainfall and elevation, even though these variables showed minimal importance in a previous analysis of fungal beta-diversity. In Antarctic cryoconite holes, our tool revealed that many bacteria have specificity to co-occurring algal community composition. Similarly, in the human gut microbiome, many bacteria showed specificity to the composition of bile acids. Finally, our analysis of the Earth Microbiome Project data set showed that most bacteria show strong ontological specificity to sample type. Our software performed as expected on synthetic data as well.<br><br>CONCLUSIONS: specificity is well-suited to analysis of microbiome data, both in synthetic test cases, and across multiple environment types and experimental designs. The analysis and software we present here can reveal patterns in microbial taxa that may not be evident from a community-level perspective. These insights can also be visualized and interactively shared among researchers using specificity's companion package, specificity.shiny.}, }
@article {pmid35752717, year = {2022}, author = {Leung, PM and Daebeler, A and Chiri, E and Hanchapola, I and Gillett, DL and Schittenhelm, RB and Daims, H and Greening, C}, title = {A nitrite-oxidising bacterium constitutively consumes atmospheric hydrogen.}, journal = {The ISME journal}, volume = {16}, number = {9}, pages = {2213-2219}, pmid = {35752717}, issn = {1751-7370}, support = {P 30570/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Ammonia/metabolism ; Bacteria ; *Hydrogen/metabolism ; Nitrification ; *Nitrites/metabolism ; Oxidation-Reduction ; Proteomics ; }, abstract = {Chemolithoautotrophic nitrite-oxidising bacteria (NOB) of the genus Nitrospira contribute to nitrification in diverse natural environments and engineered systems. Nitrospira are thought to be well-adapted to substrate limitation owing to their high affinity for nitrite and capacity to use alternative energy sources. Here, we demonstrate that the canonical nitrite oxidiser Nitrospira moscoviensis oxidises hydrogen (H2) below atmospheric levels using a high-affinity group 2a nickel-iron hydrogenase [Km(app) = 32 nM]. Atmospheric H2 oxidation occurred under both nitrite-replete and nitrite-deplete conditions, suggesting low-potential electrons derived from H2 oxidation promote nitrite-dependent growth and enable survival during nitrite limitation. Proteomic analyses confirmed the hydrogenase was abundant under both conditions and indicated extensive metabolic changes occur to reduce energy expenditure and growth under nitrite-deplete conditions. Thermodynamic modelling revealed that H2 oxidation theoretically generates higher power yield than nitrite oxidation at low substrate concentrations and significantly contributes to growth at elevated nitrite concentrations. Collectively, this study suggests atmospheric H2 oxidation enhances the growth and survival of NOB amid variability of nitrite supply, extends the phenomenon of atmospheric H2 oxidation to an eighth phylum (Nitrospirota), and reveals unexpected new links between the global hydrogen and nitrogen cycles. Long classified as obligate nitrite oxidisers, our findings suggest H2 may primarily support growth and survival of certain NOB in natural environments.}, }
@article {pmid35751580, year = {2022}, author = {Akritidou, T and Smet, C and Akkermans, S and Tonti, M and Williams, J and Van de Wiele, T and Van Impe, JFM}, title = {A protocol for the cultivation and monitoring of ileal gut microbiota surrogates.}, journal = {Journal of applied microbiology}, volume = {133}, number = {3}, pages = {1919-1939}, doi = {10.1111/jam.15684}, pmid = {35751580}, issn = {1365-2672}, support = {1224620N//Fonds Wetenschappelijk Onderzoek/ ; G062519N//Fonds Wetenschappelijk Onderzoek/ ; C24/18/046//KU Leuven/ ; }, mesh = {Bacteria/genetics ; *Gastrointestinal Microbiome ; Ileum/microbiology ; Intestine, Small ; *Microbiota ; }, abstract = {AIMS: This research aimed to develop and validate a cultivation and monitoring protocol that is suitable for a surrogate microbial community that accounts for the gut microbiota of the ileum of the small intestine.<br><br>METHODS AND RESULTS: Five bacterial species have been selected as representatives of the ileal gut microbiota and a general anaerobic medium (MS-BHI, as minimally supplemented brain heart infusion) has been constructed and validated against BCCM/LGM recommended and commercial media. Moreover, appropriate selective/differential media have been investigated for monitoring each ileal gut microbiota surrogate. Results showed that MS-BHI was highly efficient in displaying individual and collective behaviour of the ileal gut microbiota species, when compared with other types of media. Likewise, the selective/differential media managed to identify and describe the behaviour of their targeted species.<br><br>CONCLUSIONS: MS-BHI renders a highly efficient, inexpensive and easy-to-prepare cultivation and enumeration alternative for the surrogate ileal microbiota species. Additionally, the selective/differential media can identify and quantify the bacteria of the surrogate ileal microbial community.<br><br>The selected gut microbiota species can represent an in vitro ileal community, forming the basis for future studies on small intestinal microbiota. MS-BHI and the proposed monitoring protocol can be used as a standard for gut microbiota studies that utilize conventional microbiological techniques.}, }
@article {pmid35751418, year = {2022}, author = {Jeon, JS and Rybka, D and Carreno-Quintero, N and De Vos, R and Raaijmakers, JM and Etalo, DW}, title = {Metabolic signatures of rhizobacteria-induced plant growth promotion.}, journal = {Plant, cell &amp; environment}, volume = {45}, number = {10}, pages = {3086-3099}, doi = {10.1111/pce.14385}, pmid = {35751418}, issn = {1365-3040}, mesh = {*Arabidopsis/genetics ; Flavonoids/metabolism ; Herbivory ; Plant Development ; Plant Roots/microbiology ; Plant Shoots ; }, abstract = {Various root-colonizing bacterial species can promote plant growth and trigger systemic resistance against aboveground leaf pathogens and herbivore insects. To date, the underlying metabolic signatures of these rhizobacteria-induced plant phenotypes are poorly understood. To identify core metabolic pathways that are targeted by growth-promoting rhizobacteria, we used combinations of three plant species and three rhizobacterial species and interrogated plant shoot chemistry by untargeted metabolomics. A substantial part (50%-64%) of the metabolites detected in plant shoot tissue was differentially affected by the rhizobacteria. Among others, the phenylpropanoid pathway was targeted by the rhizobacteria in each of the three plant species. Differential regulation of the various branches of the phenylpropanoid pathways showed an association with either plant growth promotion or growth reduction. Overall, suppression of flavonoid biosynthesis was associated with growth promotion, while growth reduction showed elevated levels of flavonoids. Subsequent assays with 12 Arabidopsis flavonoid biosynthetic mutants revealed that the proanthocyanidin branch plays an essential role in rhizobacteria-mediated growth promotion. Our study also showed that a number of pharmaceutically and nutritionally relevant metabolites in the plant shoot were significantly increased by rhizobacterial treatment, providing new avenues to use rhizobacteria to tilt plant metabolism towards the biosynthesis of valuable natural plant products.}, }
@article {pmid35750182, year = {2022}, author = {Mishra, S and Wang, W and Xia, S and Lin, L and Yang, X}, title = {Spatial pattern of functional genes abundance reveals the importance of PhoD gene harboring bacterial community for maintaining plant growth in the tropical forest of Southwestern China.}, journal = {The Science of the total environment}, volume = {842}, number = {}, pages = {156863}, doi = {10.1016/j.scitotenv.2022.156863}, pmid = {35750182}, issn = {1879-1026}, mesh = {Bacteria/genetics ; China ; Ecosystem ; Forests ; Humans ; *Microbiota ; Phosphorus/analysis ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The concept of microbial functional genes has added a new dimension to microbial ecology research by improving the model of microbial community-ecosystem functions relationship. However, our knowledge vis-à-vis fine-scale spatial distribution pattern of functional genes and their probable impact on plant community in the hyper-diverse tropical forest ecosystem is very limited. Here, we investigated the spatial pattern of functional genes abundance (NirK, AOA, AOB, and PhoD), identified key influencing factors, and distinguished the key functional group supporting the plant community in a tropical rainforest located in Xishuangbanna. In total, 200 soil samples and vegetation data of ~4800 individuals of plants across a 1 ha study area were collected. Our results detected higher spatial variability with a maximum magnitude of abundance for PhoD gene (4.53 × 10[7] copies) followed by NirK (2.71 × 10[6] copies), AOA (1.97 × 10[6] copies), and AOB (7.38 × 10[4] copies). A strong spatial dependence was observed for PhoD and NirK over the distance of 17 and 18 m, respectively. Interestingly, the N:P stoichiometry played a critical role in structuring the spatial pattern of the most abundant PhoD gene. The significant positive and negative relationship of PhoD with N:P ratio and available phosphorus, respectively, indicated that the P-limiting environment was a driving factor for recruitment of PhoD gene community. The structural equation modeling ascertained the direct positive impact of PhoD on plant biomass and high demand of available P by plants suggesting that the organic phosphorus mineralization process is essential to maintain plant productivity by re-establishing the availability of the most limiting P nutrient. Our preliminary study improves our understanding of how microbial functional genes-environment associations could be used for monitoring soil health and its overall impact on ecosystem multifunctionality. Finally, we intend to conduct the study at a large spatial scale for achieving a holistic view.}, }
@article {pmid35749983, year = {2022}, author = {Chavez-Rico, VS and Bodelier, PLE and van Eekert, M and Sechi, V and Veeken, A and Buisman, C}, title = {Producing organic amendments: Physicochemical changes in biowaste used in anaerobic digestion, composting, and fermentation.}, journal = {Waste management (New York, N.Y.)}, volume = {149}, number = {}, pages = {177-185}, doi = {10.1016/j.wasman.2022.06.005}, pmid = {35749983}, issn = {1879-2456}, mesh = {Anaerobiosis ; Carbon ; *Composting/methods ; Fermentation ; Soil/chemistry ; }, abstract = {Organic amendments (OAs) produced via composting, anaerobic digestion, or lactic acid fermentation, can be used to replenish soil carbon. Not all OAs production technologies preserve C and nutrients in the same way. In this study, we compared the influence of these technologies (i.e., treatments) on C and nutrient preservation and OAs chemical composition after production. We produced compost, digestate, and lactic-acid fermentation product using the same biowaste-resembling model substrate using three reactors under laboratory conditions. We compared the chemical conversions and end-products using mass balances over C, N, and P. Overall results show that losses are minimal under reducing production conditions. Fermentation and digestion conserved 99% and 64% of C; and 93% and 100% of N, respectively. While compost conservation of nutrients was limited to 25% of C and 38% of N. Digestate had the highest concentrations of C, N, and P in the water-soluble phase, enabling their accessibility for soil microbes. Concentrations in the fermentation product were one order of magnitude lower but still higher than in compost. The treatments also influence the final availability of C, N, and P, which could potentially improve the fertilising and soil-improving properties of produced OAs. Our results show that under reducing conditions, losses of C, N, and P can be decreased while increasing OAs applications in terms of sources for soil-microbial development.}, }
@article {pmid35749381, year = {2022}, author = {Favila, N and Madrigal-Trejo, D and Legorreta, D and Sánchez-Pérez, J and Espinosa-Asuar, L and Eguiarte, LE and Souza, V}, title = {MicNet toolbox: Visualizing and unraveling a microbial network.}, journal = {PloS one}, volume = {17}, number = {6}, pages = {e0259756}, pmid = {35749381}, issn = {1932-6203}, mesh = {Cluster Analysis ; Computational Biology/methods ; Microbial Consortia ; *Microbiota ; *Software ; }, abstract = {Applications of network theory to microbial ecology are an emerging and promising approach to understanding both global and local patterns in the structure and interplay of these microbial communities. In this paper, we present an open-source python toolbox which consists of two modules: on one hand, we introduce a visualization module that incorporates the use of UMAP, a dimensionality reduction technique that focuses on local patterns, and HDBSCAN, a clustering technique based on density; on the other hand, we have included a module that runs an enhanced version of the SparCC code, sustaining larger datasets than before, and we couple the resulting networks with network theory analyses to describe the resulting co-occurrence networks, including several novel analyses, such as structural balance metrics and a proposal to discover the underlying topology of a co-occurrence network. We validated the proposed toolbox on 1) a simple and well described biological network of kombucha, consisting of 48 ASVs, and 2) we validate the improvements of our new version of SparCC. Finally, we showcase the use of the MicNet toolbox on a large dataset from Archean Domes, consisting of more than 2,000 ASVs. Our toolbox is freely available as a github repository (https://github.com/Labevo/MicNetToolbox), and it is accompanied by a web dashboard (http://micnetapplb-1212130533.us-east-1.elb.amazonaws.com) that can be used in a simple and straightforward manner with relative abundance data. This easy-to-use implementation is aimed to microbial ecologists with little to no experience in programming, while the most experienced bioinformatics will also be able to manipulate the source code's functions with ease.}, }
@article {pmid35746816, year = {2022}, author = {Aguirre Sourrouille, Z and Schwarzer, S and Lequime, S and Oksanen, HM and Quax, TEF}, title = {The Viral Susceptibility of the Haloferax Species.}, journal = {Viruses}, volume = {14}, number = {6}, pages = {}, pmid = {35746816}, issn = {1999-4915}, mesh = {Archaea ; DNA Viruses ; Genomics ; *Haloferax/genetics ; Host Specificity ; }, abstract = {Viruses can infect members of all three domains of life. However, little is known about viruses infecting archaea and the mechanisms that determine their host interactions are poorly understood. Investigations of molecular mechanisms of viral infection rely on genetically accessible virus-host model systems. Euryarchaea belonging to the genus Haloferax are interesting models, as a reliable genetic system and versatile microscopy methods are available. However, only one virus infecting the Haloferax species is currently available. In this study, we tested ~100 haloarchaeal virus isolates for their infectivity on 14 Haloferax strains. From this, we identified 10 virus isolates in total capable of infecting Haloferax strains, which represented myovirus or siphovirus morphotypes. Surprisingly, the only susceptible strain of all 14 tested was Haloferax gibbonsii LR2-5, which serves as an auspicious host for all of these 10 viruses. By applying comparative genomics, we shed light on factors determining the host range of haloarchaeal viruses on Haloferax. We anticipate our study to be a starting point in the study of haloarchaeal virus-host interactions.}, }
@article {pmid35745275, year = {2022}, author = {Natividad, JM and Marsaux, B and Rodenas, CLG and Rytz, A and Vandevijver, G and Marzorati, M and Van den Abbeele, P and Calatayud, M and Rochat, F}, title = {Human Milk Oligosaccharides and Lactose Differentially Affect Infant Gut Microbiota and Intestinal Barrier In Vitro.}, journal = {Nutrients}, volume = {14}, number = {12}, pages = {}, pmid = {35745275}, issn = {2072-6643}, support = {NA//Nestl&#xe9; Research, Soci&#xe9;t&#xe9; des Produits Nestl&#xe9;/ ; 812969//European Union's Horizon 2020 research and innovation program/ ; }, mesh = {Caco-2 Cells ; Ecosystem ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant Formula ; Lactose/metabolism/pharmacology ; *Milk, Human/metabolism ; Oligosaccharides/metabolism ; }, abstract = {BACKGROUND: The infant gut microbiota establishes during a critical window of opportunity when metabolic and immune functions are highly susceptible to environmental changes, such as diet. Human milk oligosaccharides (HMOs) for instance are suggested to be beneficial for infant health and gut microbiota. Infant formulas supplemented with the HMOs 2'-fucosyllactose (2'-FL) and lacto-N-neotetraose (LNnT) reduce infant morbidity and medication use and promote beneficial bacteria in the infant gut ecosystem. To further improve infant formula and achieve closer proximity to human milk composition, more complex HMO mixtures could be added. However, we currently lack knowledge about their effects on infants' gut ecosystems.<br><br>METHOD: We assessed the effect of lactose, 2'-FL, 2'-FL + LNnT, and a mixture of six HMOs (HMO6: consisting of 2'-FL, LNnT, difucosyllactose, lacto-N-tetraose, 3'- and 6'-sialyllactose) on infant gut microbiota and intestinal barrier integrity using a combination of in vitro models to mimic the microbial ecosystem (baby M-SHIME[&#xae;]) and the intestinal epithelium (Caco-2/HT29-MTX co-culture).<br><br>RESULTS: All the tested products had bifidogenic potential and increased SCFA levels; however, only the HMOs' fermented media protected against inflammatory intestinal barrier disruption. 2'-FL/LNnT and HMO6 promoted the highest diversification of OTUs within the Bifidobactericeae family, whereas beneficial butyrate-producers were specifically enriched by HMO6.<br><br>CONCLUSION: These results suggest that increased complexity in HMO mixture composition may benefit the infant gut ecosystem, promoting different bifidobacterial communities and protecting the gut barrier against pro-inflammatory imbalances.}, }
@article {pmid35744740, year = {2022}, author = {Kozień, &#x141; and Gallienne, E and Martin, O and Front, S and Strus, M and Heczko, P}, title = {PDIA, an Iminosugar Compound with a Wide Biofilm Inhibitory Spectrum Covering Both Gram-Positive and Gram-Negative Human Bacterial Pathogens.}, journal = {Microorganisms}, volume = {10}, number = {6}, pages = {}, pmid = {35744740}, issn = {2076-2607}, support = {2018/31/B/NZ6/02443//National Science Center/ ; N N401 547040//National Science Center/ ; }, abstract = {Many difficult-to-treat human infections related to catheters and other indwelling devices are caused by bacteria residing in biofilms. One of the key properties of microorganisms residing in a biofilm is decreased susceptibility towards antimicrobial agents. Therefore, many different approaches have been researched to destroy or inhibit biofilm production by bacteria. Different iminosugars (IS) were reported to inhibit biofilm formation in S. mutans, S. aureus, and P. aeruginosa. The aim of this study was to look for a spectrum of the activity in one of these IS. The iminosugar PDIA beta-1-C-propyl-1,4-dideoxy-1,4-imino-L-arabinitol was tested in vitro at the same concentration against 30 different strains of the most important Gram-negative and Gram-positive human pathogens looking for their biofilm production and viability at different time intervals. It appeared that PDIA inhibited biofilm production of Enterobacter spp., P. aeruginosa, Enterococcus spp. and S. aureus in 8 h, and Klebsiella spp., Acinetobacter spp. and S.epidermidis in 24 h. PDIA caused no growth inhibition of the tested bacteria at a concentration of 0.9 mM. Our results indicate a broad-spectrum biofilm inhibitory activity of PDIA. which may be the basis for future application studies that will help in control of the associated device and biofilm-related infections caused by a wide spectrum of the causative agents.}, }
@article {pmid35744736, year = {2022}, author = {Shi, Z and Kong, Q and Li, X and Xu, W and Mao, C and Wang, Y and Song, W and Huang, J}, title = {The Effects of DNA Extraction Kits and Primers on Prokaryotic and Eukaryotic Microbial Community in Freshwater Sediments.}, journal = {Microorganisms}, volume = {10}, number = {6}, pages = {}, pmid = {35744736}, issn = {2076-2607}, support = {2018YFD0900701//the National Key Research and Development Program of China/ ; 31801984, 32030015//National Natural Science Foundation of China/ ; 2019333//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; }, abstract = {DNA based sequencing technology has revolutionized the field of microbial ecology and environmental studies. However, biases can be introduced at all experimental steps and, thus, affect the interpretation of microbial community. So far, previous studies on the biases introduced from the key steps of DNA extraction and primer sets mainly focused on the bacterial communities in soil or sediment samples, while little is known about the effect on the eukaryotic microbial communities. Here, we studied the effects of three different DNA extraction kits on both prokaryotic and micro-eukaryotic communities by 16S and 18S rRNA gene amplicon sequencing, and further disentangled the influence of primer choice on the micro-eukaryotic communities. Our results showed that the FastDNA SPIN Kit for Soil and DNeasy PowerSoil Kit produced much higher DNA yield with good reproducibility, and observed more eukaryotic OTUs compared to the MinkaGene DNA extraction kit, but all three kits exhibited comparable ability in recovering bacterial alpha diversity. Of the two primer sets, both targeting the V4 region of the 18S rRNA gene, the TAR primer set detected higher number of unique OTUs than the EK primer set, while the EK primer set resulted in longer amplicons and better reproducibility between replicates. Based on our findings, we recommend using the DNeasy PowerSoil Kit with the EK primer set to capture the abundant micro-eukaryotic taxa from freshwater sediment samples. If a more complete picture of the eukaryotic microbial community is desired, the TAR primer set in combination with the FastDNA SPIN Kit is more efficient in this study.}, }
@article {pmid35744686, year = {2022}, author = {Hossain, KS and Amarasena, S and Mayengbam, S}, title = {B Vitamins and Their Roles in Gut Health.}, journal = {Microorganisms}, volume = {10}, number = {6}, pages = {}, pmid = {35744686}, issn = {2076-2607}, support = {Funding no. 20210719//Memorial University of Newfoundland/ ; }, abstract = {B vitamins act as coenzymes in a myriad of cellular reactions. These include energy production, methyl donor generation, neurotransmitter synthesis, and immune functions. Due to the ubiquitous roles of these vitamins, their deficiencies significantly affect the host's metabolism. Recently, novel roles of B vitamins in the homeostasis of gut microbial ecology and intestinal health continue to be unravelled. This review focuses on the functional roles and biosynthesis of B vitamins and how these vitamins influence the growth and proliferation of the gut microbiota. We have identified the gut bacteria that can produce vitamins, and their biosynthetic mechanisms are presented. The effects of B vitamin deficiencies on intestinal morphology, inflammation, and its effects on intestinal disorders are also discussed.}, }
@article {pmid35744611, year = {2022}, author = {Costa, OYA and de Hollander, M and Kuramae, EE and Bodelier, PLE}, title = {PhyloFunDB: A Pipeline to Create and Update Functional Gene Taxonomic Databases.}, journal = {Microorganisms}, volume = {10}, number = {6}, pages = {}, pmid = {35744611}, issn = {2076-2607}, abstract = {The increase in sequencing capacity has amplified the number of taxonomically unclassified sequences in most databases. The classification of such sequences demands phylogenetic tree construction and comparison to currently classified sequences, a process that demands the processing of large amounts of data and use of several different software. Here, we present PhyloFunDB, a pipeline for extracting, processing, and inferring phylogenetic trees from specific functional genes. The goal of our work is to decrease processing time and facilitate the grouping of sequences that can be used for improved taxonomic classification of functional gene datasets.}, }
@article {pmid35741397, year = {2022}, author = {Micci, A and Zhang, Q and Chang, X and Kingsley, K and Park, L and Chiaranunt, P and Strickland, R and Velazquez, F and Lindert, S and Elmore, M and Vines, PL and Crane, S and Irizarry, I and Kowalski, KP and Johnston-Monje, D and White, JF}, title = {Histochemical Evidence for Nitrogen-Transfer Endosymbiosis in Non-Photosynthetic Cells of Leaves and Inflorescence Bracts of Angiosperms.}, journal = {Biology}, volume = {11}, number = {6}, pages = {}, pmid = {35741397}, issn = {2079-7737}, abstract = {We used light and confocal microscopy to visualize bacteria in leaf and bract cells of more than 30 species in 18 families of seed plants. Through histochemical analysis, we detected hormones (including ethylene and nitric oxide), superoxide, and nitrogenous chemicals (including nitric oxide and nitrate) around bacteria within plant cells. Bacteria were observed in epidermal cells, various filamentous and glandular trichomes, and other non-photosynthetic cells. Most notably, bacteria showing nitrate formation based on histochemical staining were present in glandular trichomes of some dicots (e.g., Humulus lupulus and Cannabis sativa). Glandular trichome chemistry is hypothesized to function to scavenge oxygen around bacteria and reduce oxidative damage to intracellular bacterial cells. Experiments to assess the differential absorption of isotopic nitrogen into plants suggest the assimilation of nitrogen into actively growing tissues of plants, where bacteria are most active and carbohydrates are more available. The leaf and bract cell endosymbiosis types outlined in this paper have not been previously reported and may be important in facilitating plant growth, development, oxidative stress resistance, and nutrient absorption into plants. It is unknown whether leaf and bract cell endosymbioses are significant in increasing the nitrogen content of plants. From the experiments that we conducted, it is impossible to know whether plant trichomes evolved specifically as organs for nitrogen fixation or if, instead, trichomes are structures in which bacteria easily colonize and where some casual nitrogen transfer may occur between bacteria and plant cells. It is likely that the endosymbioses seen in leaves and bracts are less efficient than those of root nodules of legumes in similar plants. However, the presence of endosymbioses that yield nitrate in plants could confer a reduced need for soil nitrogen and constitute increased nitrogen-use efficiency, even if the actual amount of nitrogen transferred to plant cells is small. More research is needed to evaluate the importance of nitrogen transfer within leaf and bract cells of plants.}, }
@article {pmid35739682, year = {2022}, author = {Wang, C and Wang, L and Ok, YS and Tsang, DCW and Hou, D}, title = {Soil plastisphere: Exploration methods, influencing factors, and ecological insights.}, journal = {Journal of hazardous materials}, volume = {430}, number = {}, pages = {128503}, doi = {10.1016/j.jhazmat.2022.128503}, pmid = {35739682}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; Ecosystem ; Microplastics ; *Plastics ; *Soil/chemistry ; }, abstract = {Microplastic (MP), an emerging contaminant, is globally prevalent and poses potential environmental threats and ecological risks to both aquatic and terrestrial ecosystems. When MPs enter into natural environments, they may serve as artificial substrates for microbial colonization and plastisphere formation, providing new ecological niches for microorganisms. Recent studies of the plastisphere have focused on aquatic ecosystems. However, our understanding of the soil plastisphere e.g. its formation process, microbial ecology, co-transport of organic pollutants and heavy metals, and effects on biogeochemical processes is still very limited. This review summarizes latest methods used to explore the soil plastisphere, assesses the factors influencing the microbial ecology of the soil plastisphere, and sheds light on potential ecological risks caused by the soil plastisphere. The formation and succession of soil plastisphere communities can be driven by MP characteristics and soil environmental factors. The soil plastisphere may affect a series of ecological processes, especially the co-transport of environmental contaminants, biodegradation of MPs, and soil carbon cycling. We aim to narrow the knowledge gap between the soil and aquatic plastisphere, and provide valuable guidance for future research on the soil plastisphere in MP-contaminated soils.}, }
@article {pmid35739580, year = {2022}, author = {Dey, S and Rout, AK and Behera, BK and Ghosh, K}, title = {Plastisphere community assemblage of aquatic environment: plastic-microbe interaction, role in degradation and characterization technologies.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {32}, pmid = {35739580}, issn = {2524-6372}, abstract = {It is undeniable that plastics are ubiquitous and a threat to global ecosystems. Plastic waste is transformed into microplastics (MPs) through physical and chemical disruption processes within the aquatic environment. MPs are detected in almost every environment due to their worldwide transportability through ocean currents or wind, which allows them to reach even the most remote regions of our planet. MPs colonized by biofilm-forming microbial communities are known as the ''plastisphere". The revelation that this unique substrate can aid microbial dispersal has piqued interest in the ground of microbial ecology. MPs have synergetic effects on the development, transportation, persistence, and ecology of microorganisms. This review summarizes the studies of plastisphere in recent years and the microbial community assemblage (viz. autotrophs, heterotrophs, predators, and pathogens). We also discussed plastic-microbe interactions and the potential sources of plastic degrading microorganisms. Finally, it also focuses on current technologies used to characterize those microbial inhabitants and recommendations for further research.}, }
@article {pmid35739325, year = {2023}, author = {Legeay, J and Hijri, M}, title = {A Comprehensive Insight of Current and Future Challenges in Large-Scale Soil Microbiome Analyses.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {75-85}, pmid = {35739325}, issn = {1432-184X}, mesh = {*Soil ; *Microbiota ; Geography ; Soil Microbiology ; }, abstract = {In the last decade, various large-scale projects describing soil microbial diversity across large geographical gradients have been undertaken. However, many questions remain unanswered about the best ways to conduct these studies. In this review, we present an overview of the experience gathered during these projects, and of the challenges that future projects will face, such as standardization of protocols and results, considering the temporal variation of microbiomes, and the legal constraints limiting such studies. We also present the arguments for and against the exhaustive description of soil microbiomes. Finally, we look at future developments of soil microbiome studies, notably emphasizing the important role of cultivation techniques.}, }
@article {pmid35738377, year = {2022}, author = {Merino, N and Jackson, TR and Campbell, JH and Kersting, AB and Sackett, J and Fisher, JC and Bruckner, JC and Zavarin, M and Hamilton-Brehm, SD and Moser, DP}, title = {Subsurface microbial communities as a tool for characterizing regional-scale groundwater flow.}, journal = {The Science of the total environment}, volume = {842}, number = {}, pages = {156768}, doi = {10.1016/j.scitotenv.2022.156768}, pmid = {35738377}, issn = {1879-1026}, mesh = {Geology ; *Groundwater/chemistry ; Hydrology ; *Microbiota ; Nevada ; }, abstract = {Subsurface microbial community distribution patterns are influenced by biogeochemical and groundwater fluxes and may inform hydraulic connections along groundwater-flow paths. This study examined the regional-scale microbial community of the Death Valley Regional Flow System and evaluated whether subsurface communities can be used to identify groundwater-flow paths between recharge and discharge areas. Samples were collected from 36 sites in three groundwater basins: Pahute Mesa-Oasis Valley (PMOV), Ash Meadows (AM), and Alkali Flat-Furnace Creek Ranch (AFFCR). Microbial diversity within and between communities varied by location, and communities were separated into two overall groups that affiliated with the AM and PMOV/AFFCR basins. Network analysis revealed patterns between clusters of common microbes that represented groundwaters with similar geochemical conditions and largely corroborated hydraulic connections between recharge and discharge areas. Null model analyses identified deterministic and stochastic ecological processes contributing to microbial community assemblages. Most communities were more different than expected and governed by dispersal limitation, geochemical differences, or undominating processes. However, certain communities from sites located within or near the Nevada National Security Site were more similar than expected and dominated by homogeneous dispersal or selection. Overall, the (dis)similarities between the microbial communities of DVRFS recharge and discharge areas supported previously documented hydraulic connections between: (1) Spring Mountains and Ash Meadows; (2) Frenchman and Yucca Flat and Amargosa Desert; and (3) Amargosa Desert and Death Valley. However, only a portion of the flow path between Pahute Mesa and Oasis Valley could be supported by microbial community analyses, likely due to well-associated artifacts in samples from the two Oasis Valley sites. This study demonstrates the utility of combining microbial data with hydrologic, geologic, and water-chemistry information to comprehensively characterize groundwater systems, highlighting both strengths and limitations of this approach.}, }
@article {pmid35730934, year = {2022}, author = {Morris, MM and Kimbrel, JA and Geng, H and Tran-Gyamfi, MB and Yu, ET and Sale, KL and Lane, TW and Mayali, X}, title = {Bacterial Community Assembly, Succession, and Metabolic Function during Outdoor Cultivation of Microchloropsis salina.}, journal = {mSphere}, volume = {7}, number = {4}, pages = {e0023122}, pmid = {35730934}, issn = {2379-5042}, mesh = {*Biofuels ; Biomass ; Metagenome ; *Microbiota ; Symbiosis ; }, abstract = {Outdoor cultivation of microalgae has promising potential for renewable bioenergy, but there is a knowledge gap on the structure and function of the algal microbiome that coinhabits these ecosystems. Here, we describe the assembly mechanisms, taxonomic structure, and metabolic potential of bacteria associated with Microchloropsis salina cultivated outdoors. Open mesocosms were inoculated with algal cultures that were either free of bacteria or coincubated with one of two different strains of alga-associated bacteria and were sampled across five time points taken over multiple harvesting rounds of a 40-day experiment. Using quantitative analyses of metagenome-assembled genomes (MAGs), we tracked bacterial community compositional abundance and taxon-specific functional capacity involved in algal-bacterial interactions. One of the inoculated bacteria (Alteromonas sp.) persisted and dispersed across mesocosms, whereas the other inoculated strain (Phaeobacter gallaeciensis) disappeared by day 17 while a taxonomically similar but functionally distinct Phaeobacter strain became established. The inoculated strains were less abundant than 6 numerically dominant newly recruited taxa with functional capacities for mutualistic or saprophytic lifestyles, suggesting a generalist approach to persistence. This includes a highly abundant unclassified Rhodobacteraceae species that fluctuated between 25% and 77% of the total community. Overall, we did not find evidence for priority effects exerted by the distinct inoculum conditions; all mesocosms converged with similar microbial community compositions by the end of the experiment. Instead, we infer that the 15 total populations were retained due to host selection, as they showed high metabolic potential for algal-bacterial interactions such as recycling alga-produced carbon and nitrogen and production of vitamins and secondary metabolites associated with algal growth and senescence, including B vitamins, tropodithietic acid, and roseobacticides. IMPORTANCE Bacteria proliferate in nutrient-rich aquatic environments, including engineered algal biofuel systems, where they remineralize photosynthates, exchange secondary metabolites with algae, and can influence system output of biomass or oil. Despite this, knowledge on the microbial ecology of algal cultivation systems is lacking, and the subject is worthy of investigation. Here, we used metagenomics to characterize the metabolic capacities of the predominant bacteria associated with the biofuel-relevant microalga Microchloropsis salina and to predict testable metabolic interactions between algae and manipulated communities of bacteria. We identified a previously undescribed and uncultivated organism that dominated the community. Collectively, the microbial community may interact with the alga in cultivation via exchange of secondary metabolites which could affect algal success, which we demonstrate as a possible outcome from controlled experiments with metabolically analogous isolates. These findings address the scalability of lab-based algal-bacterial interactions through to cultivation systems and more broadly provide a framework for empirical testing of genome-based metabolic predictions.}, }
@article {pmid35729185, year = {2022}, author = {Beterams, A and Calatayud Arroyo, M and De Paepe, K and De Craemer, AS and Elewaut, D and Venken, K and Van de Wiele, T}, title = {In vitro triple coculture with gut microbiota from spondyloarthritis patients is characterized by inter-individual differences in inflammatory responses.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {10475}, pmid = {35729185}, issn = {2045-2322}, mesh = {Coculture Techniques ; *Gastrointestinal Microbiome ; Humans ; Individuality ; Phylogeny ; *Spondylarthritis ; }, abstract = {Spondyloarthritis is a group of chronic inflammatory diseases that primarily affects axial or peripheral joints and is frequently associated with inflammation at non-articular sites. The disease is multifactorial, involving genetics, immunity and environmental factors, including the gut microbiota. In vivo, microbiome contributions are difficult to assess due to the multifactorial disease complexity. In a proof-of-concept approach, we therefore used a triple coculture model of immune-like, goblet and epithelial cells to investigate whether we could detect a differential impact from spondyloarthritis- vs. healthy-derived gut microbiota on host cell response. Despite their phylogenetic resemblance, flow cytometry-based phenotypic clustering revealed human-derived gut microbiota from healthy origin to cluster together and apart from spondyloarthritis donors. At host level, mucus production was higher upon exposure to healthy microbiota. Pro-inflammatory cytokine responses displayed more inter-individual variability in spondyloarthritis than in healthy donors. Interestingly, the high dominance in the initial sample of one patient of Prevotella, a genus previously linked to spondyloarthritis, resulted in the most differential host response upon 16 h host-microbe coincubation. While future research should further focus on inter-individual variability by using gut microbiota from a large cohort of patients, this study underscores the importance of the gut microbiota during the SpA disease course.}, }
@article {pmid35726107, year = {2022}, author = {Khuntia, HK and Paliwal, A and Kumar, DR and Chanakya, HN}, title = {Review on solid-state anaerobic digestion of lignocellulosic biomass and organic solid waste.}, journal = {Environmental monitoring and assessment}, volume = {194}, number = {7}, pages = {514}, pmid = {35726107}, issn = {1573-2959}, mesh = {Anaerobiosis ; Biofuels/analysis ; Biomass ; Bioreactors ; Environmental Monitoring ; Lignin ; Methane ; *Refuse Disposal/methods ; *Solid Waste/analysis ; }, abstract = {Sustainable management of organic solid wastes especially the municipal solid waste (MSW) is essential for the realization of various sustainable development goals (SDGs). Resource recovery centric waste processing technologies generate valorizable products to meet the operations and maintenance (O&amp;M) costs while reducing the GHG emissions. Solid-state anaerobic digestion (SSAD) of organic solid wastes is a biomethanation process performed at a relatively higher total solids (TS) loading in the range of 10-45%. SSAD overcomes various limitations posed by conventional anaerobic slurry digesters such as higher degradable matter per unit volume of the bioreactor resulting in a smaller footprint, low freshwater consumption, low wastewater generation, simple upstream and downstream processes, relatively lower operation, and maintenance costs. This review elucidates the recent developments and critical assessment of different aspects of SSAD, such as bioreactor design, operational strategy, process performances, mass balance, microbial ecology, applications, and mathematical models. A critical assessment revealed that the operating scale of SSAD varies between 1000 and 100,000 ts/year at organic loading rate (OLR) of 2-15 g volatile solids (VS)/L·day. The SSAD experiences process failures due to the formation of volatile fatty acids (VFAs), biogas pockets and clogging of the digestate outlet. Acclimatization of microbes accelerates the startup phase, steady-state performances, and the enrichment of syntrophic microbes with 10-50 times greater population of cellulolytic and xylanolytic microbes in thermophilic SSAD over mesophilic SSAD. Experimental limitations in the accurate determination of rate constants and the oversimplification of biochemical reactions result in an inaccurate prediction by the models.}, }
@article {pmid35724776, year = {2022}, author = {Chang, J and van Veen, JA and Tian, C and Kuramae, EE}, title = {A review on the impact of domestication of the rhizosphere of grain crops and a perspective on the potential role of the rhizosphere microbial community for sustainable rice crop production.}, journal = {The Science of the total environment}, volume = {842}, number = {}, pages = {156706}, doi = {10.1016/j.scitotenv.2022.156706}, pmid = {35724776}, issn = {1879-1026}, mesh = {Crop Production ; Crops, Agricultural/microbiology ; Domestication ; Edible Grain ; *Microbiota ; *Mycorrhizae ; *Oryza/microbiology ; Plant Roots/microbiology ; Rhizosphere ; Soil Microbiology ; }, abstract = {The rhizosphere-associated microbiome impacts plant performance and tolerance to abiotic and biotic stresses. Despite increasing recognition of the enormous functional role of the rhizomicrobiome on the survival of wild plant species growing under harsh environmental conditions, such as nutrient, water, temperature, and pathogen stresses, the utilization of the rhizosphere microbial community in domesticated rice production systems has been limited. Better insight into how this role of the rhizomicrobiome for the performance and survival of wild plants has been changed during domestication and development of present domesticated crops, may help to assess the potential of the rhizomicrobial community to improve the sustainable production of these crops. Here, we review the current knowledge of the effect of domestication on the microbial rhizosphere community of rice and other crops by comparing its diversity, structure, and function in wild versus domesticated species. We also examine the existing information on the impact of the plant on their physico-chemical environment. We propose that a holobiont approach should be explored in future studies by combining detailed analysis of the dynamics of the physicochemical microenvironment surrounding roots to systematically investigate the microenvironment-plant-rhizomicrobe interactions during rice domestication, and suggest focusing on the use of beneficial microbes (arbuscular mycorrhizal fungi and Nitrogen fixers), denitrifiers and methane consumers to improve the sustainable production of rice.}, }
@article {pmid35722352, year = {2022}, author = {Paddock, KJ and Finke, DL and Kim, KS and Sappington, TW and Hibbard, BE}, title = {Patterns of Microbiome Composition Vary Across Spatial Scales in a Specialist Insect.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {898744}, pmid = {35722352}, issn = {1664-302X}, abstract = {Microbial communities associated with animals vary based on both intrinsic and extrinsic factors. Of many possible determinants affecting microbiome composition, host phylogeny, host diet, and local environment are the most important. How these factors interact across spatial scales is not well understood. Here, we seek to identify the main influences on microbiome composition in a specialist insect, the western corn rootworm (WCR; Diabrotica virgifera virgifera), by analyzing the bacterial communities of adults collected from their obligate host plant, corn (Zea mays), across several geographic locations and comparing the patterns in communities to its congeneric species, the northern corn rootworm (NCR; Diabrotica barberi). We found that bacterial communities of WCR and NCR shared a portion of their bacterial communities even when collected from disparate locations. However, within each species, the location of collection significantly influenced the composition of their microbiome. Correlations of geographic distance between sites with WCR bacterial community composition revealed different patterns at different spatial scales. Community similarity decreased with increased geographic distance at smaller spatial scales (~25 km between the nearest sites). At broad spatial scales (>200 km), community composition was not correlated with distances between sites, but instead reflected the historical invasion path of WCR across the United States. These results suggest bacterial communities are structured directly by dispersal dynamics at small, regional spatial scales, while landscape-level genetic or environmental differences may drive community composition across broad spatial scales in this specialist insect.}, }
@article {pmid35722289, year = {2022}, author = {Rocha, ADL and Ferrari, RG and Pereira, WE and de Lima, LA and Givisiez, PEN and Moreno-Switt, AI and Toro, M and Delgado-Suárez, EJ and Meng, J and de Oliveira, CJB}, title = {Revisiting the Biological Behavior of Salmonella enterica in Hydric Resources: A Meta-Analysis Study Addressing the Critical Role of Environmental Water on Food Safety and Public Health.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {802625}, pmid = {35722289}, issn = {1664-302X}, support = {U01 FD001418/FD/FDA HHS/United States ; }, abstract = {The increasing number of studies reporting the presence of Salmonella in environmental water sources suggests that it is beyond incidental findings originated from sparse fecal contamination events. However, there is no consensus on the occurrence of Salmonella as its relative serovar representation across non-recycled water sources. We conducted a meta-analysis of proportions by fitting a random-effects model using the restricted maximum-likelihood estimator to obtain the weighted average proportion and between-study variance associated with the occurrence of Salmonella in water sources. Moreover, meta-regression and non-parametric supervised machine learning method were performed to predict the effect of moderators on the frequency of Salmonella in non-recycled water sources. Three sequential steps (identification of information sources, screening and eligibility) were performed to obtain a preliminary selection from identified abstracts and article titles. Questions related to the frequency of Salmonella in aquatic environments, as well as putative differences in the relative frequencies of the reported Salmonella serovars and the role of potential variable moderators (sample source, country, and sample volume) were formulated according to the population, intervention, comparison, and outcome method (PICO). The results were reported according to the Preferred Reporting Items for Systematic Review and Meta-Analyzes statement (PRISMA). A total of 26 eligible papers reporting 148 different Salmonella serovars were retrieved. According to our model, the Salmonella frequency in non-recycled water sources was 0.19 [CI: 0.14; 0.25]. The source of water was identified as the most import variable affecting the frequency of Salmonella, estimated as 0.31 and 0.17% for surface and groundwater, respectively. There was a higher frequency of Salmonella in countries with lower human development index (HDI). Small volume samples of surface water resulted in lower detectable Salmonella frequencies both in high and low HDI regions. Relative frequencies of the 148 serovars were significantly affected only by HDI and volume. Considering that serovars representation can also be affected by water sample volume, efforts toward the standardization of water samplings for monitoring purposes should be considered. Further approaches such as metagenomics could provide more comprehensive insights about the microbial ecology of fresh water and its importance for the quality and safety of agricultural products.}, }
@article {pmid35722279, year = {2022}, author = {Egenriether, S and Sanford, R and Yang, WH and Kent, AD}, title = {Nitrogen Cycling Microbial Diversity and Operational Taxonomic Unit Clustering: When to Prioritize Accuracy Over Speed.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {730340}, pmid = {35722279}, issn = {1664-302X}, abstract = {BACKGROUND: Assessments of the soil microbiome provide valuable insight to ecosystem function due to the integral role microorganisms play in biogeochemical cycling of carbon and nutrients. For example, treatment effects on nitrogen cycling functional groups are often presented alongside one another to demonstrate how agricultural management practices affect various nitrogen cycling processes. However, the functional groups commonly evaluated in nitrogen cycling microbiome studies range from phylogenetically narrow (e.g., N-fixation, nitrification) to broad [e.g., denitrification, dissimilatory nitrate reduction to ammonium (DNRA)]. The bioinformatics methods used in such studies were developed for 16S rRNA gene sequence data, and how these tools perform across functional genes of different phylogenetic diversity has not been established. For example, an OTU clustering method that can accurately characterize sequences harboring comparatively little diversity may not accurately resolve the diversity within a gene comprised of a large number of clades. This study uses two nitrogen cycling genes, nifH, a gene which segregates into only three distinct clades, and nrfA, a gene which is comprised of at least eighteen clades, to investigate differences which may arise when using heuristic OTU clustering (abundance-based greedy clustering, AGC) vs. true hierarchical OTU clustering (Matthews Correlation Coefficient optimizing algorithm, Opti-MCC). Detection of treatment differences for each gene were evaluated to demonstrate how conclusions drawn from a given dataset may differ depending on clustering method used.<br><br>RESULTS: The heuristic and hierarchical methods performed comparably for the more conserved gene, nifH. The hierarchical method outperformed the heuristic method for the more diverse gene, nrfA; this included both the ability to detect treatment differences using PERMANOVA, as well as higher resolution in taxonomic classification. The difference in performance between the two methods may be traced to the AGC method's preferential assignment of sequences to the most abundant OTUs: when analysis was limited to only the largest 100 OTUs, results from the AGC-assembled OTU table more closely resembled those of the Opti-MCC OTU table. Additionally, both AGC and Opti-MCC OTU tables detected comparable treatment differences using the rank-based ANOSIM test. This demonstrates that treatment differences were preserved using both clustering methods but were structured differently within the OTU tables produced using each method.<br><br>CONCLUSION: For questions which can be answered using tests agnostic to clustering method (e.g., ANOSIM), or for genes of relatively low phylogenetic diversity (e.g., nifH), most upstream processing methods should lead to similar conclusions from downstream analyses. For studies involving more diverse genes, however, care should be exercised to choose methods that ensure accurate clustering for all genes. This will mitigate the risk of introducing Type II errors by allowing for detection of comparable treatment differences for all genes assessed, rather than disproportionately detecting treatment differences in only low-diversity genes.}, }
@article {pmid35720594, year = {2022}, author = {Kong, Z and Liu, H}, title = {Modification of Rhizosphere Microbial Communities: A Possible Mechanism of Plant Growth Promoting Rhizobacteria Enhancing Plant Growth and Fitness.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {920813}, pmid = {35720594}, issn = {1664-462X}, abstract = {Plant beneficial bacteria, defined as plant growth-promoting rhizobacteria (PGPR), play a crucial role in plants' growth, stress tolerance and disease prevention. In association with the rhizosphere of plants, PGPR facilitate plant growth and development either directly or indirectly through multiple mechanisms, including increasing available mineral nutrients, moderating phytohormone levels and acting as biocontrol agents of phytopathogens. It is generally accepted that the effectiveness of PGPR inoculants is associated with their ability to colonize, survive and persist, as well as the complex network of interactions in the rhizosphere. Despite the promising plant growth promotion results commonly reported and mostly attributed to phytohormones or other organic compounds produced by PGPR inoculants, little information is available on the potential mechanisms underlying such positive effects via modifying rhizosphere microbial community and soil functionality. In this review, we overviewed the effects of PGPR inoculants on rhizosphere microbial ecology and soil function, hypothesizing that PGPR may indirectly promote plant growth and health via modifying the composition and functioning of rhizosphere microbial community, and highlighting the further directions for investigating the role of PGPR in rhizosphere from an ecological perspective.}, }
@article {pmid35717339, year = {2022}, author = {Grote, M}, title = {Microbes before microbiology: Christian Gottfried Ehrenberg and Berlin's infusoria.}, journal = {Endeavour}, volume = {46}, number = {1-2}, pages = {100815}, doi = {10.1016/j.endeavour.2022.100815}, pmid = {35717339}, issn = {1873-1929}, mesh = {*Bacteria ; Berlin ; Christianity ; *Historiography ; }, abstract = {Naturalist Christian Gottfried Ehrenberg pioneered research on living and fossil infusoria (including protists and bacteria) since the 1830s by collecting samples from all over the world, thus describing numerous microbes and discussing their effects for the planet and for humankind. This article introduces Ehrenberg as a natural historian of microbes and situates his work in the nineteenth century life sciences with respect to debates about cell theory, evolution, and concepts of disease. I argue that in spite of occurring before these major conceptual innovations of the life sciences, Ehrenberg's work on the diversity of microbes found in earth or air is more exciting than historiography has made it appear so far, especially in light of today's ecological microbiology.}, }
@article {pmid35714745, year = {2022}, author = {DeVilbiss, SE and Steele, MK and Brown, BL and Badgley, BD}, title = {Stream bacterial diversity peaks at intermediate freshwater salinity and varies by salt type.}, journal = {The Science of the total environment}, volume = {840}, number = {}, pages = {156690}, doi = {10.1016/j.scitotenv.2022.156690}, pmid = {35714745}, issn = {1879-1026}, mesh = {Bacteria ; Chlorides/chemistry ; Fresh Water/chemistry ; *Rivers/chemistry ; *Salinity ; Salts ; Sodium Chloride ; }, abstract = {Anthropogenic freshwater salinization is an emerging and widespread water quality stressor that increases salt concentrations of freshwater, where specific upland land-uses produce distinct ionic profiles. In-situ studies find salinization in disturbed landscapes is correlated with declines in stream bacterial diversity, but cannot isolate the effects of salinization from multiple co-occurring stressors. By manipulating salt concentration and type in controlled microcosm studies, we identified direct and complex effects of freshwater salinization on bacterial diversity in the absence of other stressors common in field studies using chloride salts. Changes in both salt concentration and cation produced distinct bacterial communities. Bacterial richness, or the total number of amplicon sequence variants (ASVs) detected, increased at conductivities as low as 350 μS cm[-1], which is opposite the observations from field studies. Richness remained elevated at conductivities as high as 1500 μS cm[-1] in communities exposed to a mixture of Ca, Mg, and K chloride salts, but decreased in communities exposed to NaCl, revealing a classic subsidy-stress response. Exposure to different chloride salts at the same conductivity resulted in distinct bacterial community structure, further supporting that salt type modulates responses of bacterial communities to freshwater salinization. Community variability peaked at 125-350 μS cm[-1] and was more similar at lower and upper conductivities suggesting possible shifts in deterministic vs. stochastic assembly mechanisms across freshwater salinity gradients. Based on these results, we hypothesize that modest freshwater salinization (125-350 μS cm[-1]) lessens hypo-osmotic stress, reducing the importance of salinity as an environmental filter at intermediate freshwater ranges but effects of higher salinities at the upper freshwater range differ based on salt type. Our results also support previous findings that ~300 μS cm[-1] is a biological effect concentration and effective salt management strategies may need to consider variable effects of different salt types associated with land-use.}, }
@article {pmid35714546, year = {2022}, author = {Kazmi, SSUH and Uroosa,  and Warren, A and Zhong, X and Xu, H}, title = {Corrigendum to "Insights into the ecotoxicity of nitrofurazone in marine ecosystems based on body-size spectra of periphytic ciliates" [Mar. Pollut. Bull. 174 (2022) 113217 1-8].}, journal = {Marine pollution bulletin}, volume = {181}, number = {}, pages = {113841}, doi = {10.1016/j.marpolbul.2022.113841}, pmid = {35714546}, issn = {1879-3363}, }
@article {pmid35713683, year = {2023}, author = {Lau, NS and Ting, SY and Sam, KK and M, J and Wong, SC and Wu, X and Waiho, K and Fazhan, H and Shu-Chien, AC}, title = {Correction to: Comparative Analyses of Scylla olivacea Gut Microbiota Composition and Function Suggest the Capacity for Polyunsaturated Fatty Acid Biosynthesis.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {589}, doi = {10.1007/s00248-022-02059-9}, pmid = {35713683}, issn = {1432-184X}, }
@article {pmid35713682, year = {2023}, author = {Sandy, M and Bui, TI and Abá, KS and Ruiz, N and Paszalek, J and Connor, EW and Hawkes, CV}, title = {Plant Host Traits Mediated by Foliar Fungal Symbionts and Secondary Metabolites.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {408-418}, pmid = {35713682}, issn = {1432-184X}, support = {2017-67013-29207//National Institute of Food and Agriculture/ ; HATCH accesssion no 1018688//National Institute of Food and Agriculture/ ; }, mesh = {*Endophytes/physiology ; Plants ; Phenotype ; Biomass ; Plant Physiological Phenomena ; *Panicum/microbiology ; Fungi/genetics ; }, abstract = {Fungal symbionts living inside plant leaves ("endophytes") can vary from beneficial to parasitic, but the mechanisms by which the fungi affect the plant host phenotype remain poorly understood. Chemical interactions are likely the proximal mechanism of interaction between foliar endophytes and the plant, as individual fungal strains are often exploited for their diverse secondary metabolite production. Here, we go beyond single strains to examine commonalities in how 16 fungal endophytes shift plant phenotypic traits such as growth and physiology, and how those relate to plant metabolomics profiles. We inoculated individual fungi on switchgrass, Panicum virgatum L. This created a limited range of plant growth and physiology (2-370% of fungus-free controls on average), but effects of most fungi overlapped, indicating functional similarities in unstressed conditions. Overall plant metabolomics profiles included almost 2000 metabolites, which were broadly correlated with plant traits across all the fungal treatments. Terpenoid-rich samples were associated with larger, more physiologically active plants and phenolic-rich samples were associated with smaller, less active plants. Only 47 metabolites were enriched in plants inoculated with fungi relative to fungus-free controls, and of these, Lasso regression identified 12 metabolites that explained from 14 to 43% of plant trait variation. Fungal long-chain fatty acids and sterol precursors were positively associated with plant photosynthesis, conductance, and shoot biomass, but negatively associated with survival. The phytohormone gibberellin, in contrast, was negatively associated with plant physiology and biomass. These results can inform ongoing efforts to develop metabolites as crop management tools, either by direct application or via breeding, by identifying how associations with more beneficial components of the microbiome may be affected.}, }
@article {pmid35712047, year = {2022}, author = {Guseva, K and Darcy, S and Simon, E and Alteio, LV and Montesinos-Navarro, A and Kaiser, C}, title = {From diversity to complexity: Microbial networks in soils.}, journal = {Soil biology &amp; biochemistry}, volume = {169}, number = {}, pages = {108604}, pmid = {35712047}, issn = {0038-0717}, abstract = {Network analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research. Analysing microbial networks in soils opens a window to a better understanding of the complexity of microbial communities. However, this approach is unfortunately often used to draw conclusions which are far beyond the scientific evidence it can provide, which has damaged its reputation for soil microbial analysis. In this Perspectives Paper, we would like to sharpen the view for the real potential of microbial co-occurrence analysis in soils, and at the same time raise awareness regarding its limitations and the many ways how it can be misused or misinterpreted.}, }
@article {pmid35711777, year = {2022}, author = {Jiang, Y and Luo, J and Huang, D and Liu, Y and Li, DD}, title = {Machine Learning Advances in Microbiology: A Review of Methods and Applications.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {925454}, pmid = {35711777}, issn = {1664-302X}, abstract = {Microorganisms play an important role in natural material and elemental cycles. Many common and general biology research techniques rely on microorganisms. Machine learning has been gradually integrated with multiple fields of study. Machine learning, including deep learning, aims to use mathematical insights to optimize variational functions to aid microbiology using various types of available data to help humans organize and apply collective knowledge of various research objects in a systematic and scaled manner. Classification and prediction have become the main achievements in the development of microbial community research in the direction of computational biology. This review summarizes the application and development of machine learning and deep learning in the field of microbiology and shows and compares the advantages and disadvantages of different algorithm tools in four fields: microbiome and taxonomy, microbial ecology, pathogen and epidemiology, and drug discovery.}, }
@article {pmid35711776, year = {2022}, author = {You, J and Zhang, H and Zhu, H and Xue, Y and Cai, Y and Zhang, G}, title = {Microbial Community, Fermentation Quality, and in vitro Degradability of Ensiling Caragana With Lactic Acid Bacteria and Rice Bran.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {804429}, pmid = {35711776}, issn = {1664-302X}, abstract = {This study aimed to assess the effects of microbial inoculants and growth stage on fermentation quality, microbial community, and in vitro degradability of Caragana silage from different varieties. Caragana intermedia (CI) and Caragana korshinskii (CK) harvested at the budding (BU) and blooming (BL) stages were used as raw materials to prepare silage, respectively. The silages at each growth stage were treated for ensiling alone (control), with 5% rice bran (RB), a combination of RB with commercial Lactobacillus plantarum (RB + LP), and a combination of RB with a selected strain Lactobacillus plantarum L694 (RB + L694). The results showed that the crude protein (CP) content of CI was higher than that of CK, and delay in harvest resulted in greater CP content in Caragana at BL stage. After 60 days of fermentation, the concentrations of lactic acid (LA) in the RB + L694 treatments were higher than those in control treatments (p < 0.05), while the pH, concentrations of NH3-N, neutral detergent fiber with the addition of α-amylase (aNDF) were lower than those in control treatments (p < 0.05). RB + L694 treatments could decrease acid detergent fiber (ADF) content except in CIBL. In CK silages, adding RB + L694 could reduce bacterial diversity and richness (p < 0.05). Compared with the control, RB + L694 treatment contained higher Lactobacillus and Enterobacter (p < 0.05). In vitro NDF and DM degradability (IVNDFD and IVDMD) was mostly affected by growth period, and additive RB + l694 treatment had higher IVDMD and lower IVNDFD than other treatments (p < 0.05). Consequently, the varieties, growth stages, and additives could influence the fermentation process, while the blooming stage should be selected in both Caragana. Furthermore, the results showed that RB and L. plantarum could exert a positive effect on fermentation quality of Caragana silage by shifting bacterial community composition, and RB + L694 treatments outperformed other additives.}, }
@article {pmid35711751, year = {2022}, author = {Bannon, C and Rapp, I and Bertrand, EM}, title = {Community Interaction Co-limitation: Nutrient Limitation in a Marine Microbial Community Context.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {846890}, pmid = {35711751}, issn = {1664-302X}, abstract = {The simultaneous limitation of productivity by two or more nutrients, commonly referred to as nutrient co-limitation, affects microbial communities throughout the marine environment and is of profound importance because of its impacts on various biogeochemical cycles. Multiple types of co-limitation have been described, enabling distinctions based on the hypothesized mechanisms of co-limitation at a biochemical level. These definitions usually pertain to individuals and do not explicitly, or even implicitly, consider complex ecological dynamics found within a microbial community. However, limiting and co-limiting nutrients can be produced in situ by a subset of microbial community members, suggesting that interactions within communities can underpin co-limitation. To address this, we propose a new category of nutrient co-limitation, community interaction co-limitation (CIC). During CIC, one part of the community is limited by one nutrient, which results in the insufficient production or transformation of a biologically produced nutrient that is required by another part of the community, often primary producers. Using cobalamin (vitamin B12) and nitrogen fixation as our models, we outline three different ways CIC can arise based on current literature and discuss CIC's role in biogeochemical cycles. Accounting for the inherent and complex roles microbial community interactions play in generating this type of co-limitation requires an expanded toolset - beyond the traditional approaches used to identify and study other types of co-limitation. We propose incorporating processes and theories well-known in microbial ecology and evolution to provide meaningful insight into the controls of community-based feedback loops and mechanisms that give rise to CIC in the environment. Finally, we highlight the data gaps that limit our understanding of CIC mechanisms and suggest methods to overcome these and further identify causes and consequences of CIC. By providing this framework for understanding and identifying CIC, we enable systematic examination of the impacts this co-limitation can have on current and future marine biogeochemical processes.}, }
@article {pmid35710629, year = {2022}, author = {Oyserman, BO and Flores, SS and Griffioen, T and Pan, X and van der Wijk, E and Pronk, L and Lokhorst, W and Nurfikari, A and Paulson, JN and Movassagh, M and Stopnisek, N and Kupczok, A and Cordovez, V and Carrión, VJ and Ligterink, W and Snoek, BL and Medema, MH and Raaijmakers, JM}, title = {Disentangling the genetic basis of rhizosphere microbiome assembly in tomato.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3228}, pmid = {35710629}, issn = {2041-1723}, support = {U01 GM110706/GM/NIGMS NIH HHS/United States ; }, mesh = {Iron/metabolism ; *Solanum lycopersicum/metabolism ; *Microbiota/genetics ; Plant Breeding ; Plants/metabolism ; Rhizosphere ; }, abstract = {Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, we map the molecular features of the rhizosphere microbiome as quantitative traits of a diverse hybrid population of wild and domesticated tomato. Gene content analysis of prioritized tomato quantitative trait loci suggests a genetic basis for differential recruitment of various rhizobacterial lineages, including a Streptomyces-associated 6.31 Mbp region harboring tomato domestication sweeps and encoding, among others, the iron regulator FIT and the water channel aquaporin SlTIP2.3. Within metagenome-assembled genomes of root-associated Streptomyces and Cellvibrio, we identify bacterial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associates with specific tomato QTLs. By integrating 'microbiomics' and quantitative plant genetics, we pinpoint putative plant and reciprocal rhizobacterial traits underlying microbiome assembly, thereby providing a first step towards plant-microbiome breeding programs.}, }
@article {pmid35710200, year = {2022}, author = {Antosiak, A and Šulčius, S and Malec, P and Tokodi, N and Łobodzińska, A and Dziga, D}, title = {Cyanophage infections reduce photosynthetic activity and expression of CO2 fixation genes in the freshwater bloom-forming cyanobacterium Aphanizomenon flos-aquae.}, journal = {Harmful algae}, volume = {116}, number = {}, pages = {102215}, doi = {10.1016/j.hal.2022.102215}, pmid = {35710200}, issn = {1878-1470}, mesh = {Aphanizomenon ; Carbon ; *Carbon Dioxide ; *Cyanobacteria ; DNA Replication ; DNA, Viral ; Ecosystem ; Fresh Water ; Photosynthesis ; Virus Replication ; }, abstract = {Cyanobacteria play a significant role in ecosystem functioning as photosynthetic and CO2 fixing microorganisms. Whether and to what extent cyanophages alter these carbon and energy cycles in their cyanobacterial hosts is still poorly understood. In this study, we investigated changes in photosynthetic activity (PSII), expression of genes associated with the light phase of photosynthesis (psbA, petA, ndhK) and carbon metabolism (rbcL, zwf) as well as intracellular ATP and NADHP concentrations in freshwater bloom-forming filamentous cyanobacterium Aphanizomenon flos-aquae infected by cyanophage vB_AphaS-CL131. We found that PSII activity and expression level of rbcL genes, indicating potential for CO2 fixation, had decreased in response to cyanophage adsorption and DNA injection. During the period of viral DNA replication and assembly, PSII performance and gene expression remained at this decreased level and did not change significantly, indicating lack of transcriptional shutdown by the cyanophage. Combined, these observations suggest that although there is little to no interference between cyanophage DNA replication, host transcription and cellular metabolism, A. flos-aquae underwent a physiological state-shift toward lower efficiency of carbon and energy cycling. This further suggest potential cascading effect for co-occurring non-infected members of the microbial community.}, }
@article {pmid35706139, year = {2022}, author = {Purkamo, L and Ó Dochartaigh, B and MacDonald, A and Cousins, C}, title = {Following the flow-Microbial ecology in surface- and groundwaters in the glacial forefield of a rapidly retreating glacier in Iceland.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {5840-5858}, pmid = {35706139}, issn = {1462-2920}, mesh = {Ice Cover/microbiology ; Iceland ; Rivers ; *Microbiota ; *Groundwater ; }, abstract = {The retreat of glaciers in response to climate change has major impacts on the hydrology and ecosystems of glacier forefield catchments. Microbes are key players in ecosystem functionality, supporting the supply of ecosystem services that glacier systems provide. The interaction between surface and groundwaters in glacier forefields has only recently gained much attention, and how these interactions influence the microbiology is still unclear. Here, we identify the microbial communities in groundwater from shallow (<15 m deep) boreholes in a glacial forefield floodplain ('sandur') aquifer at different distances from the rapidly retreating Virkisjökull glacier, Iceland, and with varying hydraulic connectivity with the glacial meltwater river that flows over the sandur. Groundwater communities are shown to differ from those in nearby glacial and non-glacial surface water communities. Groundwater-meltwater interactions and groundwater flow dynamics affect the microbial community structure, leading to different microbial communities at different sampling points in the glacier forefield. Groundwater communities differ from those in nearby glacial and non-glacial surface waters. Functional potential for microbial nitrogen and methane cycling was detected, although the functional gene copy numbers of specific groups were low.}, }
@article {pmid35705745, year = {2023}, author = {Song, L and Wang, Y and Zhang, R and Yang, S}, title = {Microbial Mediation of Carbon, Nitrogen, and Sulfur Cycles During Solid Waste Decomposition.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {311-324}, pmid = {35705745}, issn = {1432-184X}, support = {52000016//National Natural Science Foundation of China/ ; 51578642//National Natural Science Foundation of China/ ; }, mesh = {*Solid Waste/analysis ; Nitrogen/analysis ; Carbon ; RNA, Ribosomal, 16S/genetics ; Carbon Dioxide ; Bacteria/genetics ; Archaea/genetics ; *Microbiota ; Sulfur ; Waste Disposal Facilities ; }, abstract = {Landfills are a unique "terrestrial ecosystem" and serve as a significant carbon sink. Microorganisms convert biodegradable substances in municipal solid waste (MSW) to CH4, CO2, and microbial biomass, consisting of the carbon cycling in landfills. Microbial-mediated N and S cycles are also the important biogeochemical process during MSW decomposition, resulting in N2O and H2S emission, respectively. Meanwhile, microbial-mediated N and S cycles affect carbon cycling. How microbial community structure and function respond to C, N, and S cycling during solid waste decomposition, however, are not well-characterized. Here, we show the response of bacterial and archaeal community structure and functions to C, N, and S cycling during solid waste decomposition in a long-term (265 days) operation laboratory-scale bioreactor through 16S rRNA-based pyrosequencing and metagenomics analysis. Bacterial and archaeal community composition varied during solid waste decomposition. Aerobic respiration was the main pathway for CO2 emission, while anaerobic C fixation was the main pathway in carbon fixation. Methanogenesis and denitrification increased during solid waste decomposition, suggesting increasing CH4 and N2O emission. In contract, fermentation decreased along solid waste decomposition. Interestingly, Clostridiales were abundant and showed potential for several pathways in C, N, and S cycling. Archaea were involved in many pathways of C and N cycles. There is a shift between bacteria and archaea involvement in N2 fixation along solid waste decomposition that bacteria Clostridiales and Bacteroidales were initially dominant and then Methanosarcinales increased and became dominant in methanogenic phase. These results provide extensive microbial mediation of C, N, and S cycling profiles during solid waste decomposition.}, }
@article {pmid35705744, year = {2023}, author = {García-Sánchez, JC and Arredondo-Centeno, J and Segovia-Ramírez, MG and Tenorio Olvera, AM and Parra-Olea, G and Vredenburg, VT and Rovito, SM}, title = {Factors Influencing Bacterial and Fungal Skin Communities of Montane Salamanders of Central Mexico.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {670-686}, pmid = {35705744}, issn = {1432-184X}, support = {221614//Conacyt/ ; 2015-01-721//Conacyt/ ; 1633948//National Science Foundation/ ; }, mesh = {Animals ; *Caudata/microbiology ; *Mycobiome ; Mexico ; Phylogeny ; Amphibians/microbiology ; Bacteria/genetics ; Skin/microbiology ; }, abstract = {Host microbial communities are increasingly seen as an important component of host health. In amphibians, the first land vertebrates that are threatened by a fungal skin disease globally, our understanding of the factors influencing the microbiome of amphibian skin remains incomplete because recent studies have focused almost exclusively on bacteria, and little information exists on fungal communities associated with wild amphibian species. In this study, we describe the effects of host phylogeny, climate, geographic distance, and infection with a fungal pathogen on the composition and structure of bacterial and fungal communities in seven tropical salamander species that occur in the Trans-Mexican Volcanic Belt of Central Mexico. We find that host phylogenetic relatedness is correlated with bacterial community composition while a composite climatic variable of temperature seasonality and precipitation is significantly associated with fungal community composition. We also estimated co-occurrence networks for bacterial and fungal taxa and found differences in the degree of connectivity and the distribution of negative associations between the two networks. Our results suggest that different factors may be responsible for structuring the bacterial and fungal communities of amphibian skin and that the inclusion of fungi in future studies could shed light on important functional interactions within the microbiome.}, }
@article {pmid35703548, year = {2022}, author = {Honeyman, AS and Fegel, TS and Peel, HF and Masters, NA and Vuono, DC and Kleiber, W and Rhoades, CC and Spear, JR}, title = {Statistical Learning and Uncommon Soil Microbiota Explain Biogeochemical Responses after Wildfire.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {13}, pages = {e0034322}, pmid = {35703548}, issn = {1098-5336}, mesh = {*Fires ; *Microbiota ; Soil ; Water Quality ; *Wildfires ; }, abstract = {Wildfires are a perennial event globally, and the biogeochemical underpinnings of soil responses at relevant spatial and temporal scales are unclear. Soil biogeochemical processes regulate plant growth and nutrient losses that affect water quality, yet the response of soil after variable intensity fire is difficult to explain and predict. To address this issue, we examined two wildfires in Colorado, United States, across the first and second postfire years and leveraged statistical learning (SL) to predict and explain biogeochemical responses. We found that SL predicts biogeochemical responses in soil after wildfire with surprising accuracy. Of the 13 biogeochemical analytes analyzed in this study, 9 are best explained with a hybrid microbiome + biogeochemical SL model. Biogeochemical-only models best explain 3 features, and 1 feature is explained equally well with the hybrid and biogeochemical-only models. In some cases, microbiome-only SL models are also effective (such as predicting NH4[+]). Whenever a microbiome component is employed, selected features always involve uncommon soil microbiota (i.e., the "rare biosphere" [existing at <1% mean relative abundance]). Here, we demonstrate that SL paired with DNA sequence and biogeochemical data predicts environmental features in postfire soils, although this approach could likely be applied to any biogeochemical system. IMPORTANCE Soil biogeochemical processes are critical to plant growth and water quality and are substantially disturbed by wildfire. However, soil responses to fire are difficult to predict. To address this issue, we developed a large environmental data set that tracks postfire changes in soil and used statistical learning (SL) to build models that exploit complex data to make predictions about biogeochemical responses. Here, we show that SL depends upon uncommon microbiota in soil (the "rare biosphere") to make surprisingly accurate predictions about soil biogeochemical responses to wildfire. Using SL to explain variation in a natively chaotic environmental system is mechanism independent. Likely, the approach that we describe for combining SL with microbiome and biogeochemical parameters has practical applications across a range of issues in the environmental sciences where predicting responses would be useful.}, }
@article {pmid35701635, year = {2023}, author = {Vignale, FA and Bernal Rey, D and Pardo, AM and Almasqué, FJ and Ibarra, JG and Fernández Do Porto, D and Turjanski, AG and López, NI and Helman, RJM and Raiger Iustman, LJ}, title = {Spatial and Seasonal Variations in the Bacterial Community of an Anthropogenic Impacted Urban Stream.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {862-874}, pmid = {35701635}, issn = {1432-184X}, support = {PUE2016 22920160100064CO//conicet/ ; 20020170200338BA//Secretar&#xed;a de Ciencia y T&#xe9;cnica, Universidad de Buenos Aires/ ; 20020170100310BA//Secretar&#xed;a de Ciencia y T&#xe9;cnica, Universidad de Buenos Aires/ ; }, mesh = {Humans ; *Rivers/microbiology ; Seasons ; RNA, Ribosomal, 16S/genetics ; *Anthropogenic Effects ; Bacteria/genetics ; }, abstract = {Environmental changes and human activities can alter the structure and diversity of aquatic microbial communities. In this work, we analyzed the bacterial community dynamics of an urban stream to understand how these factors affect the composition of river microbial communities. Samples were taken from a stream situated in Buenos Aires, Argentina, which flows through residential, peri-urban horticultural, and industrial areas. For sampling, two stations were selected: one influenced by a series of industrial waste treatment plants and horticultural farms (PL), and the other influenced by residential areas (R). Microbial communities were analyzed by sequence analysis of 16S rRNA gene amplicons along an annual cycle. PL samples showed high nutrient content compared with R samples. The diversity and richness of the R site were more affected by seasonality than those of the PL site. At the amplicon sequence variants level, beta diversity analysis showed a differentiation between cool-season (fall and winter) and warm-season (spring and summer) samples, as well as between PL and R sites. This demonstrated that there is spatial and temporal heterogeneity in the composition of the bacterial community, which should be considered if a bioremediation strategy is applied. The taxonomic composition analysis also revealed a differential seasonal cycle of phototrophs and chemoheterotrophs between the sampling sites, as well as different taxa associated with each sampling site. This analysis, combined with a comparative analysis of global rivers, allowed us to determine the genera Arcobacter, Simplicispira, Vogesella, and Sphingomonas as potential bioindicators of anthropogenic disturbance.}, }
@article {pmid35700773, year = {2022}, author = {Chen, H and Pan, Y and Zhou, Q and Liang, C and Wong, CC and Zhou, Y and Huang, D and Liu, W and Zhai, J and Gou, H and Su, H and Zhang, X and Xu, H and Wang, Y and Kang, W and Kei Wu, WK and Yu, J}, title = {METTL3 Inhibits Antitumor Immunity by Targeting m[6]A-BHLHE41-CXCL1/CXCR2 Axis to Promote Colorectal Cancer.}, journal = {Gastroenterology}, volume = {163}, number = {4}, pages = {891-907}, doi = {10.1053/j.gastro.2022.06.024}, pmid = {35700773}, issn = {1528-0012}, mesh = {Animals ; Basic Helix-Loop-Helix Transcription Factors ; *CD8-Positive T-Lymphocytes/metabolism ; Cell Line, Tumor ; Chemokine CXCL1 ; *Colorectal Neoplasms/pathology ; Cytokines/metabolism ; Humans ; Methyltransferases/genetics/metabolism ; Mice ; Mice, Knockout ; Phenylurea Compounds ; Receptors, Interleukin-8B/genetics/metabolism ; Triazoles ; RNA, Guide, CRISPR-Cas Systems ; }, abstract = {BACKGROUND &amp; AIMS: N[6]-Methyladenosine (m[6]A) is the most prevalent RNA modification and recognized as an important epitranscriptomic mechanism in colorectal cancer (CRC). We aimed to exploit whether and how tumor-intrinsic m[6]A modification driven by methyltransferase like 3 (METTL3) can dictate the immune landscape of CRC.<br><br>METHODS: Mettl3 knockout mice, CD34[+] humanized mice, and different syngeneic mice models were used. Immune cell composition and cytokine level were analyzed by flow cytometry and Cytokine 23-Plex immunoassay, respectively. M[6]A sequencing and RNA sequencing were performed to identify downstream targets and pathways of METTL3. Human CRC specimens (n&#xa0;= 176) were used to evaluate correlation between METTL3 expression and myeloid-derived suppressor cell (MDSC) infiltration.<br><br>RESULTS: We demonstrated that silencing of METTL3 in CRC cells reduced MDSC accumulation to sustain activation and proliferation of CD4[+] and CD8[+] T cells, and eventually suppressed CRC in Apc[Min/+]Mettl3[+/-] mice, CD34[+] humanized mice, and syngeneic mice models. Mechanistically, METTL3 activated the m[6]A-BHLHE41-CXCL1 axis by analysis of m[6]A sequencing, RNA sequencing, and cytokine arrays. METTL3 promoted BHLHE41 expression in an m[6]A-dependent manner, which subsequently induced CXCL1 transcription to enhance MDSC migration in&#xa0;vitro. However, the effect was negligible on BHLHE41 depletion, CXCL1 protein or CXCR2 inhibitor SB265610 administration, inferring that METTL3 promotes MDSC migration via BHLHE41-CXCL1/CXCR2. Consistently, depletion of MDSCs by anti-Gr1 antibody or SB265610 blocked the tumor-promoting effect of METTL3 in&#xa0;vivo. Importantly, targeting METTL3 by METTL3-single guide RNA or specific inhibitor potentiated the effect of anti-programmed cell death protein 1 (anti-PD1) treatment.<br><br>CONCLUSIONS: Our study identifies METTL3 as a potential therapeutic target for CRC immunotherapy whose inhibition reverses immune suppression through the m[6]A-BHLHE41-CXCL1 axis. METTL3 inhibition plus anti-PD1 treatment shows promising antitumor efficacy against CRC.}, }
@article {pmid35700135, year = {2022}, author = {Deng, Z and Hou, K and Valencak, TG and Luo, XM and Liu, J and Wang, H}, title = {AI-2/LuxS Quorum Sensing System Promotes Biofilm Formation of Lactobacillus rhamnosus GG and Enhances the Resistance to Enterotoxigenic Escherichia coli in Germ-Free Zebrafish.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0061022}, pmid = {35700135}, issn = {2165-0497}, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Biofilms ; Carbon-Sulfur Lyases/genetics/metabolism ; *Enterotoxigenic Escherichia coli/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Inflammation ; *Lacticaseibacillus rhamnosus/metabolism ; Quorum Sensing ; Zebrafish/metabolism ; }, abstract = {The LuxS enzyme plays a key role in both quorum sensing (QS) and the regulation of bacterial growth. It catalyzes the production of autoinducer-2 (AI-2) signaling molecule, which is a component of the methyl cycle and methionine metabolism. This study aimed at investigating the differences between the Lactobacillus rhamnosus GG (LGG) wild-type strain (WT) and its luxS mutant (ΔluxS) during biofilm formation and when resisting to inflammation caused by Enterotoxigenic Escherichia coli (ETEC) in germ-free zebrafish. Our results suggest that in the absence of luxS when LGG was knocked out, biofilm formation, extracellular polysaccharide secretion and adhesion were all compromised. Addition of synthetic AI-2 indeed rescued, at least partially, the deficiencies observed in the mutant strain. The colonizing and immunomodulatory function in WT versus ΔluxS mutants were further studied in a germ-free zebrafish model. The concentration of AI-2 signaling molecules decreased sharply in zebrafish infected with the ΔluxS. At the same time, compared with the ΔluxS, the wild-type strain could colonize the germ-free zebrafish more effectively. Our transcriptome results suggest that genes involved in immunity, signal transduction, and cell adhesion were downregulated in zebrafish infected with ΔluxS and WT. In the WT, the immune system of germ-free zebrafish was activated more effectively through the MAPK and NF-κB pathway, and its ability to fight the infection against ETEC was increased. Together, our results demonstrate that the AI-2/LuxS system plays an important role in biofilm formation to improve LGG and alleviate inflammation caused by ETEC in germ-free zebrafish. IMPORTANCE Lactobacillus rhamnosus GG is a widely used probiotic to improve host intestinal health, promote growth, reduce diarrhea, and modulate immunity. In recent years, the bacterial quorum sensing system has attracted much attention; however, there has not been much research on the effect of the LuxS/AI-2 quorum sensing system of Lactobacillus on bacteriostasis, microbial ecology balance, and immune regulation in intestine. In this study, we used germ-free zebrafish as an animal model to compare the differences between wild-type and luxS mutant strains. We showed how AI-2/LuxS QS affects the release of AI-2 and how QS regulates the colonization, EPS synthesis and biofilm formation of LGG. This study provides an idea for the targeted regulation of animal intestinal health with probiotics by controlling bacteria quorum sensing system.}, }
@article {pmid35697795, year = {2022}, author = {Wu, L and Zhang, Y and Guo, X and Ning, D and Zhou, X and Feng, J and Yuan, MM and Liu, S and Guo, J and Gao, Z and Ma, J and Kuang, J and Jian, S and Han, S and Yang, Z and Ouyang, Y and Fu, Y and Xiao, N and Liu, X and Wu, L and Zhou, A and Yang, Y and Tiedje, JM and Zhou, J}, title = {Reduction of microbial diversity in grassland soil is driven by long-term climate warming.}, journal = {Nature microbiology}, volume = {7}, number = {7}, pages = {1054-1062}, pmid = {35697795}, issn = {2058-5276}, mesh = {Bacteria ; Biodiversity ; Ecosystem ; *Grassland ; *Soil ; Soil Microbiology ; }, abstract = {Anthropogenic climate change threatens ecosystem functioning. Soil biodiversity is essential for maintaining the health of terrestrial systems, but how climate change affects the richness and abundance of soil microbial communities remains unresolved. We examined the effects of warming, altered precipitation and annual biomass removal on grassland soil bacterial, fungal and protistan communities over 7 years to determine how these representative climate changes impact microbial biodiversity and ecosystem functioning. We show that experimental warming and the concomitant reductions in soil moisture play a predominant role in shaping microbial biodiversity by decreasing the richness of bacteria (9.6%), fungi (14.5%) and protists (7.5%). Our results also show positive associations between microbial biodiversity and ecosystem functional processes, such as gross primary productivity and microbial biomass. We conclude that the detrimental effects of biodiversity loss might be more severe in a warmer world.}, }
@article {pmid35697683, year = {2022}, author = {Paredes, GF and Viehboeck, T and Markert, S and Mausz, MA and Sato, Y and Liebeke, M and König, L and Bulgheresi, S}, title = {Differential regulation of degradation and immune pathways underlies adaptation of the ectosymbiotic nematode Laxus oneistus to oxic-anoxic interfaces.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9725}, pmid = {35697683}, issn = {2045-2322}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; P 28743/FWF_/Austrian Science Fund FWF/Austria ; P28743-B22/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Chromadorea ; *Chromatiaceae ; Hypoxia ; *Nematoda/microbiology ; Oxygen/metabolism ; Sand ; Sulfides ; Sulfur/metabolism ; }, abstract = {Eukaryotes may experience oxygen deprivation under both physiological and pathological conditions. Because oxygen shortage leads to a reduction in cellular energy production, all eukaryotes studied so far conserve energy by suppressing their metabolism. However, the molecular physiology of animals that naturally and repeatedly experience anoxia is underexplored. One such animal is the marine nematode Laxus oneistus. It thrives, invariably coated by its sulfur-oxidizing symbiont Candidatus Thiosymbion oneisti, in anoxic sulfidic or hypoxic sand. Here, transcriptomics and proteomics showed that, whether in anoxia or not, L. oneistus mostly expressed genes involved in ubiquitination, energy generation, oxidative stress response, immune response, development, and translation. Importantly, ubiquitination genes were also highly expressed when the nematode was subjected to anoxic sulfidic conditions, together with genes involved in autophagy, detoxification and ribosome biogenesis. We hypothesize that these degradation pathways were induced to recycle damaged cellular components (mitochondria) and misfolded proteins into nutrients. Remarkably, when L. oneistus was subjected to anoxic sulfidic conditions, lectin and mucin genes were also upregulated, potentially to promote the attachment of its thiotrophic symbiont. Furthermore, the nematode appeared to survive oxygen deprivation by using an alternative electron carrier (rhodoquinone) and acceptor (fumarate), to rewire the electron transfer chain. On the other hand, under hypoxia, genes involved in costly processes (e.g., amino acid biosynthesis, development, feeding, mating) were upregulated, together with the worm's Toll-like innate immunity pathway and several immune effectors (e.g., bactericidal/permeability-increasing proteins, fungicides). In conclusion, we hypothesize that, in anoxic sulfidic sand, L. oneistus upregulates degradation processes, rewires the oxidative phosphorylation and reinforces its coat of bacterial sulfur-oxidizers. In upper sand layers, instead, it appears to produce broad-range antimicrobials and to exploit oxygen for biosynthesis and development.}, }
@article {pmid35697586, year = {2022}, author = {Ayeni, KI and Berry, D and Wisgrill, L and Warth, B and Ezekiel, CN}, title = {Early-life chemical exposome and gut microbiome development: African research perspectives within a global environmental health context.}, journal = {Trends in microbiology}, volume = {30}, number = {11}, pages = {1084-1100}, doi = {10.1016/j.tim.2022.05.008}, pmid = {35697586}, issn = {1878-4380}, mesh = {Adult ; Dysbiosis/chemically induced ; Environmental Health ; *Exposome ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; *Metals, Heavy ; *Mycotoxins ; *Pesticide Residues ; Xenobiotics ; }, abstract = {The gut microbiome of neonates, infants, and toddlers (NITs) is very dynamic, and only begins to stabilize towards the third year of life. Within this period, exposure to xenobiotics may perturb the gut environment, thereby driving or contributing to microbial dysbiosis, which may negatively impact health into adulthood. Despite exposure of NITs globally, but especially in Africa, to copious amounts and types of xenobiotics - such as mycotoxins, pesticide residues, and heavy metals - little is known about their influence on the early-life microbiome or their effects on acute or long-term health. Within the African context, the influence of fermented foods, herbal mixtures, and the delivery environment on the early-life microbiome are often neglected, despite being potentially important factors that influence the microbiome. Consequently, data on in-depth understanding of the microbiome-exposome interactions is lacking in African cohorts. Collecting and evaluating such data is important because exposome-induced gut dysbiosis could potentially favor disease progression.}, }
@article {pmid35696896, year = {2022}, author = {Kazmi, SSUH and Uroosa,  and Xu, H and Xuexi, T}, title = {Corrigendum to "An approach to determining the nitrofurazone-induced toxic dynamics for ecotoxicity assessment using protozoan periphytons in marine ecosystems" [Mar. Pollut. Bull. 175 (2022) 113329 1-7].}, journal = {Marine pollution bulletin}, volume = {180}, number = {}, pages = {113836}, doi = {10.1016/j.marpolbul.2022.113836}, pmid = {35696896}, issn = {1879-3363}, }
@article {pmid35695510, year = {2022}, author = {Maciá-Vicente, JG and Bai, B and Qi, R and Ploch, S and Breider, F and Thines, M}, title = {Nutrient Availability Does Not Affect Community Assembly in Root-Associated Fungi but Determines Fungal Effects on Plant Growth.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0030422}, pmid = {35695510}, issn = {2379-5077}, mesh = {Plant Roots ; Symbiosis ; *Arabidopsis ; *Mycorrhizae/physiology ; Plants ; *Microbiota ; Nutrients ; }, abstract = {Nonmycorrhizal root-colonizing fungi are key determinants of plant growth, driving processes ranging from pathogenesis to stress alleviation. Evidence suggests that they might also facilitate host access to soil nutrients in a mycorrhiza-like manner, but the extent of their direct contribution to plant nutrition is unknown. To study how widespread such capacity is across root-colonizing fungi, we surveyed soils in nutrient-limiting habitats using plant baits to look for fungal community changes in response to nutrient conditions. We established a fungal culture collection and used Arabidopsis thaliana inoculation bioassays to assess the ability of fungi to facilitate host's growth in the presence of organic nutrients unavailable to plants. Plant baits captured a representation of fungal communities extant in natural habitats and showed that nutrient limitation has little influence on community assembly. Arabidopsis thaliana inoculated with 31 phylogenetically diverse fungi exhibited a consistent fungus-driven growth promotion when supplied with organic nutrients compared to untreated plants. However, direct phosphorus measurement and RNA-seq data did not support enhanced nutrient uptake but rather that growth effects may result from changes in the plant's immune response to colonization. The widespread and consistent host responses to fungal colonization suggest that distinct, locally adapted nonmycorrhizal fungi affect plant performance across habitats. IMPORTANCE Recent studies have shown that root-associated fungi that do not engage in classical mycorrhizal associations can facilitate the hosts' access to nutrients in a mycorrhiza-like manner. However, the generality of this capacity remains to be tested. Root-associated fungi are frequently deemed major determinants of plant diversity and performance, but in the vast majority of cases their ecological roles in nature remain unknown. Assessing how these plant symbionts affect plant productivity, diversity, and fitness is important to understanding how plant communities function. Recent years have seen important advances in the understanding of the main drivers of the diversity and structure of plant microbiomes, but a major challenge is still linking community properties with function. This study contributes to the understanding of the cryptic function of root-associated fungi by testing their ability to participate in a specific process: nutrient acquisition by plants.}, }
@article {pmid35694162, year = {2022}, author = {Karl, CM and Vidakovic, A and Pjevac, P and Hausmann, B and Schleining, G and Ley, JP and Berry, D and Hans, J and Wendelin, M and König, J and Somoza, V and Lieder, B}, title = {Individual Sweet Taste Perception Influences Salivary Characteristics After Orosensory Stimulation With Sucrose and Noncaloric Sweeteners.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {831726}, pmid = {35694162}, issn = {2296-861X}, abstract = {Emerging evidence points to a major role of salivary flow and viscoelastic properties in taste perception and mouthfeel. It has been proposed that sweet-tasting compounds influence salivary characteristics. However, whether perceived differences in the sensory properties of structurally diverse sweet-tasting compounds contribute to salivary flow and saliva viscoelasticity as part of mouthfeel and overall sweet taste perception remains to be clarified. In this study, we hypothesized that the sensory diversity of sweeteners would differentially change salivary characteristics in response to oral sweet taste stimulation. Therefore, we investigated salivary flow and saliva viscoelasticity from 21 healthy test subjects after orosensory stimulation with sucrose, rebaudioside M (RebM), sucralose, and neohesperidin dihydrochalcone (NHDC) in a crossover design and considered the basal level of selected influencing factors, including the basal oral microbiome. All test compounds enhanced the salivary flow rate by up to 1.51 ± 0.12 g/min for RebM compared to 1.10 ± 0.09 g/min for water within the 1st min after stimulation. The increase in flow rate was moderately correlated with the individually perceived sweet taste (r = 0.3, p < 0.01) but did not differ between the test compounds. The complex viscosity of saliva was not affected by the test compounds, but the analysis of covariance showed that it was associated (p < 0.05) with mucin 5B (Muc5B) concentration. The oral microbiome was of typical composition and diversity but was strongly individual-dependent (permutational analysis of variance (PERMANOVA): R [2] = 0.76, p < 0.001) and was not associated with changes in salivary characteristics. In conclusion, this study indicates an impact of individual sweet taste impressions on the flow rate without measurable changes in the complex viscosity of saliva, which may contribute to the overall taste perception and mouthfeel of sweet-tasting compounds.}, }
@article {pmid35691180, year = {2022}, author = {Kazmi, SSUH and Uroosa,  and Xu, H and Warren, A}, title = {Corrigendum to "A community-based approach to analyzing the ecotoxicity of nitrofurazone using periphytic protozoa" [Mar. Pollut. Bull. 175 (2022) 113165 1-6].}, journal = {Marine pollution bulletin}, volume = {180}, number = {}, pages = {113837}, doi = {10.1016/j.marpolbul.2022.113837}, pmid = {35691180}, issn = {1879-3363}, }
@article {pmid35689685, year = {2023}, author = {Mills, JG and Selway, CA and Thomas, T and Weyrich, LS and Lowe, AJ}, title = {Schoolyard Biodiversity Determines Short-Term Recovery of Disturbed Skin Microbiota in Children.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {658-669}, pmid = {35689685}, issn = {1432-184X}, mesh = {Humans ; Child ; *Microbiota ; Biodiversity ; Forests ; Skin ; }, abstract = {Creating biodiverse urban habitat has been proposed, with growing empirical support, as an intervention for increasing human microbial diversity and reducing associated diseases. However, ecological understanding of urban biodiversity interventions on human skin microbiota remains limited. Here, we experimentally test the hypotheses that disturbed skin microbiota recover better in outdoor schoolyard environments and that greater biodiversity provides a greater response. Repeating the experiment three times, we disturbed skin microbiota of fifty-seven healthy 10-to-11-year-old students with a skin swab (i.e., cleaning), then exposed them to one school environment-either a 'classroom' (n = 20), 'sports field' (n = 14), or biodiverse 'forest' (n = 23)-for 45 min. Another skin swab followed the exposure to compare 'before' and 'after' microbial communities. After 45 min, the disturbance immediately followed by outdoor exposure, especially the 'forest', had an enriching and diversifying effect on skin microbiota, while 'classroom' exposure homogenised inter-personal variability. Each effect compounded over consecutive days indicating longer-term exposure outcomes. The experimental disturbance also reduced the core skin microbiota, and only outdoor environments were able to replenish lost species richness to core membership (n species > 50% prevalent). Overall, we find that environmental setting, especially including biodiversity, is important in human microbiota recovery periods and that the outdoors provide resilience to skin communities. This work also has implications for the inclusion of short periods of outside or forest exposure in school scheduling. Future investigations of the health impacts of permanent urban biodiversity interventions are needed.}, }
@article {pmid35687346, year = {2023}, author = {Morata, A and Arroyo, T and Bañuelos, MA and Blanco, P and Briones, A and Cantoral, JM and Castrillo, D and Cordero-Bueso, G and Del Fresno, JM and Escott, C and Escribano-Viana, R and Fernández-González, M and Ferrer, S and García, M and González, C and Gutiérrez, AR and Loira, I and Malfeito-Ferreira, M and Martínez, A and Pardo, I and Ramírez, M and Ruiz-Muñoz, M and Santamaría, P and Suárez-Lepe, JA and Vilela, A and Capozzi, V}, title = {Wine yeast selection in the Iberian Peninsula: Saccharomyces and non-Saccharomyces as drivers of innovation in Spanish and Portuguese wine industries.}, journal = {Critical reviews in food science and nutrition}, volume = {63}, number = {31}, pages = {10899-10927}, doi = {10.1080/10408398.2022.2083574}, pmid = {35687346}, issn = {1549-7852}, mesh = {Saccharomyces cerevisiae ; *Wine/analysis ; Portugal ; Fermentation ; Biotechnology ; *Vitis ; }, abstract = {Yeast selection for the wine industry in Spain started in 1950 for the understanding of the microbial ecology, and for the selection of optimal strains to improve the performance of alcoholic fermentation and the overall wine quality. This process has been strongly developed over the last 30 years, firstly on Saccharomyces cerevisiae, and, lately, with intense activity on non-Saccharomyces. Several thousand yeast strains have been isolated, identified and tested to select those with better performance and/or specific technological properties. The present review proposes a global survey of this massive ex-situ preservation of eukaryotic microorganisms, a reservoir of biotechnological solutions for the wine sector, overviewing relevant screenings that led to the selection of strains from 12 genera and 22 species of oenological significance. In the first part, the attention goes to the selection programmes related to relevant wine-producing areas (i.e. Douro, Extremadura, Galicia, La Mancha and Uclés, Ribera del Duero, Rioja, Sherry area, and Valencia). In the second part, the focus shifted on specific non-Saccharomyces genera/species selected from different Spanish and Portuguese regions, exploited to enhance particular attributes of the wines. A fil rouge of the dissertation is the design of tailored biotechnological solutions for wines typical of given geographic areas.}, }
@article {pmid35685924, year = {2022}, author = {Barcoto, MO and Rodrigues, A}, title = {Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {812143}, pmid = {35685924}, issn = {1664-302X}, abstract = {Anthropogenic activities have extensively transformed the biosphere by extracting and disposing of resources, crossing boundaries of planetary threat while causing a global crisis of waste overload. Despite fundamental differences regarding structure and recalcitrance, lignocellulose and plastic polymers share physical-chemical properties to some extent, that include carbon skeletons with similar chemical bonds, hydrophobic properties, amorphous and crystalline regions. Microbial strategies for metabolizing recalcitrant polymers have been selected and optimized through evolution, thus understanding natural processes for lignocellulose modification could aid the challenge of dealing with the recalcitrant human-made polymers spread worldwide. We propose to look for inspiration in the charismatic fungal-growing insects to understand multipartite degradation of plant polymers. Independently evolved in diverse insect lineages, fungiculture embraces passive or active fungal cultivation for food, protection, and structural purposes. We consider there is much to learn from these symbioses, in special from the community-level degradation of recalcitrant biomass and defensive metabolites. Microbial plant-degrading systems at the core of insect fungicultures could be promising candidates for degrading synthetic plastics. Here, we first compare the degradation of lignocellulose and plastic polymers, with emphasis in the overlapping microbial players and enzymatic activities between these processes. Second, we review the literature on diverse insect fungiculture systems, focusing on features that, while supporting insects' ecology and evolution, could also be applied in biotechnological processes. Third, taking lessons from these microbial communities, we suggest multidisciplinary strategies to identify microbial degraders, degrading enzymes and pathways, as well as microbial interactions and interdependencies. Spanning from multiomics to spectroscopy, microscopy, stable isotopes probing, enrichment microcosmos, and synthetic communities, these strategies would allow for a systemic understanding of the fungiculture ecology, driving to application possibilities. Detailing how the metabolic landscape is entangled to achieve ecological success could inspire sustainable efforts for mitigating the current environmental crisis.}, }
@article {pmid35681050, year = {2022}, author = {Andreu-Sánchez, S and Aubert, G and Ripoll-Cladellas, A and Henkelman, S and Zhernakova, DV and Sinha, T and Kurilshikov, A and Cenit, MC and Jan Bonder, M and Franke, L and Wijmenga, C and Fu, J and van der Wijst, MGP and Melé, M and Lansdorp, P and Zhernakova, A}, title = {Genetic, parental and lifestyle factors influence telomere length.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {565}, pmid = {35681050}, issn = {2399-3642}, mesh = {*Aging/genetics ; Epigenesis, Genetic ; Female ; Humans ; Life Style ; Parents ; Pregnancy ; *Telomere/genetics ; }, abstract = {The average length of telomere repeats (TL) declines with age and is considered to be a marker of biological ageing. Here, we measured TL in six blood cell types from 1046 individuals using the clinically validated Flow-FISH method. We identified remarkable cell-type-specific variations in TL. Host genetics, environmental, parental and intrinsic factors such as sex, parental age, and smoking are associated to variations in TL. By analysing the genome-wide methylation patterns, we identified that the association of maternal, but not paternal, age to TL is mediated by epigenetics. Single-cell RNA-sequencing data for 62 participants revealed differential gene expression in T-cells. Genes negatively associated with TL were enriched for pathways related to translation and nonsense-mediated decay. Altogether, this study addresses cell-type-specific differences in telomere biology and its relation to cell-type-specific gene expression and highlights how perinatal factors play a role in determining TL, on top of genetics and lifestyle.}, }
@article {pmid35680917, year = {2022}, author = {Willson, AM and Trugman, AT and Powers, JS and Smith-Martin, CM and Medvigy, D}, title = {Climate and hydraulic traits interact to set thresholds for liana viability.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3332}, pmid = {35680917}, issn = {2041-1723}, mesh = {*Ecosystem ; Forests ; Plants ; Trees ; *Tropical Climate ; }, abstract = {Lianas, or woody vines, and trees dominate the canopy of tropical forests and comprise the majority of tropical aboveground carbon storage. These growth forms respond differently to contemporary variation in climate and resource availability, but their responses to future climate change are poorly understood because there are very few predictive ecosystem models representing lianas. We compile a database of liana functional traits (846 species) and use it to parameterize a mechanistic model of liana-tree competition. The substantial difference between liana and tree hydraulic conductivity represents a critical source of inter-growth form variation. Here, we show that lianas are many times more sensitive to drying atmospheric conditions than trees as a result of this trait difference. Further, we use our competition model and projections of tropical hydroclimate based on Representative Concentration Pathway 4.5 to show that lianas are more susceptible to reaching a hydraulic threshold for viability by 2100.}, }
@article {pmid35680131, year = {2022}, author = {Kim, HJ and Kim, JH and Han, SA and Kim, W}, title = {Compositional Alterations of the Nasal Microbiome and Staphylococcus aureus-Characterized Dysbiosis in the Nasal Mucosa of Patients With Allergic Rhinitis.}, journal = {Clinical and experimental otorhinolaryngology}, volume = {15}, number = {4}, pages = {335-345}, pmid = {35680131}, issn = {1976-8710}, support = {//National Research Foundation of Korea/ ; 2016R1D1A1B01- 014116//Ministry of Education/ ; 2019M3C9A6091945//Ministry of Education/ ; HI20C0546//Ministry of Health &amp; Welfare of the Republic of Korea/ ; }, abstract = {OBJECTIVES: Host-microbial commensalism can shape the innate immune response in the nasal mucosa, and the microbial characteristics of nasal mucus directly impact the mechanisms of the initial allergic responses in the nasal epithelium. We sought to determine alterations of the microbial composition in the nasal mucus of patients with allergic rhinitis (AR) and to elucidate the interplay between dysbiosis of the nasal microbiome and allergic inflammation.<br><br>METHODS: In total, 364,923 high-quality bacterial 16S ribosomal RNA-encoding gene sequence reads from 104 middle turbinate mucosa samples from healthy participants and patients with AR were obtained and analyzed using the Quantitative Insights into Microbial Ecology pipeline.<br><br>RESULTS: We analyzed the microbiota in samples of nasal mucus from patients with AR (n=42) and clinically healthy participants (n=30). The Proteobacteria (Ralstonia genus) and Actinobacteria (Propionibacterium genus) phyla were predominant in the nasal mucus of healthy subjects, whereas the Firmicutes (Staphylococcus genus) phylum was significantly abundant in the nasal mucus of patients with AR. In particular, the Ralstonia genus was significantly dominant in the clinically healthy subjects. Additional pyrosequencing data from 32 subjects (healthy participants: n=15, AR patients: n=17) revealed a greater abundance of Staphylococcus epidermidis, Corynebacterium accolens, and Nocardia coeliaca, accounting for 41.55% of mapped sequences in the nasal mucus of healthy participants. Dysbiosis of the nasal microbiome was more pronounced in patients with AR, and Staphylococcus aureus exhibited the greatest abundance (37.69%) in their nasal mucus, in association with a positive response to house dust mites and patients' age and height.<br><br>CONCLUSION: This study revealed alterations in the nasal microbiome in the nasal mucus of patients with AR at the levels of microbial genera and species. S. aureus-dominant dysbiosis was distinctive in the nasal mucus of patients with AR, suggesting a role of host-microbial commensalism in allergic inflammation.}, }
@article {pmid35679938, year = {2022}, author = {Wu, K and Tizzani, R and Zweers, H and Rijnaarts, H and Langenhoff, A and Fernandes, TV}, title = {Removal processes of individual and a mixture of organic micropollutants in the presence of Scenedesmus obliquus.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 4}, pages = {156526}, doi = {10.1016/j.scitotenv.2022.156526}, pmid = {35679938}, issn = {1879-1026}, mesh = {Carbamazepine ; *Chlorophyceae ; Clarithromycin ; Diclofenac ; Metoprolol ; *Microalgae ; *Scenedesmus ; Wastewater ; *Water Pollutants, Chemical/analysis ; }, abstract = {Organic micropollutants (OMPs) need to be removed from wastewater as they can negatively affect aquatic organisms. It has been demonstrated that microalgae-based technologies are efficient in removing OMPs from wastewater. In this study, the removal processes and kinetics of six persistent OMPs (diclofenac, clarithromycin, benzotriazole, metoprolol, carbamazepine and mecoprop) were studied during cultivation of Scenedesmus obliquus in batch mode. These OMPs were added as individual compounds and in a mixture. Short experiments (8 days) were performed to avoid masking of OMP removal processes by light and nutrient limitation. The results show that diclofenac, clarithromycin, and benzotriazole were mainly removed by photodegradation (diclofenac), biodegradation (benzotriazole), or a combination of these two processes (clarithromycin). Peroxidase was involved in intracellular and extracellular biodegradation when benzotriazole was present as individual compound. Carbamazepine, metoprolol and mecoprop showed no biodegradation or photodegradation, and neglectable removal (<5%) by bioadsorption and bioaccumulation. Using an OMP mixture had an adverse effect on the photodegradation of clarithromycin and diclofenac, with reduced first-order kinetic constants compared to the individual compounds. Benzotriazole biodegradation was inhibited by the presence of the OMP mixture. This indicates that the presence of OMPs inhibits the photodegradation and biodegradation of some individual OMPs. These results will improve our understanding of removal processes of individual and mixtures of OMPs by microalgae-based technologies for wastewater treatment.}, }
@article {pmid35677244, year = {2022}, author = {Ahmad, M and Imtiaz, M and Shoib Nawaz, M and Mubeen, F and Imran, A}, title = {What Did We Learn From Current Progress in Heat Stress Tolerance in Plants? Can Microbes Be a Solution?.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {794782}, pmid = {35677244}, issn = {1664-462X}, abstract = {Temperature is a significant parameter in agriculture since it controls seed germination and plant growth. Global warming has resulted in an irregular rise in temperature posing a serious threat to the agricultural production around the world. A slight increase in temperature acts as stress and exert an overall negative impact on different developmental stages including plant phenology, development, cellular activities, gene expression, anatomical features, the functional and structural orientation of leaves, twigs, roots, and shoots. These impacts ultimately decrease the biomass, affect reproductive process, decrease flowering and fruiting and significant yield losses. Plants have inherent mechanisms to cope with different stressors including heat which may vary depending upon the type of plant species, duration and degree of the heat stress. Plants initially adapt avoidance and then tolerance strategies to combat heat stress. The tolerance pathway involves ion transporter, osmoprotectants, antioxidants, heat shock protein which help the plants to survive under heat stress. To develop heat-tolerant plants using above-mentioned strategies requires a lot of time, expertise, and resources. On contrary, plant growth-promoting rhizobacteria (PGPRs) is a cost-effective, time-saving, and user-friendly approach to support and enhance agricultural production under a range of environmental conditions including stresses. PGPR produce and regulate various phytohormones, enzymes, and metabolites that help plant to maintain growth under heat stress. They form biofilm, decrease abscisic acid, stimulate root development, enhance heat shock proteins, deamination of ACC enzyme, and nutrient availability especially nitrogen and phosphorous. Despite extensive work done on plant heat stress tolerance in general, very few comprehensive reviews are available on the subject especially the role of microbes for plant heat tolerance. This article reviews the current studies on the retaliation, adaptation, and tolerance to heat stress at the cellular, organellar, and whole plant levels, explains different approaches, and sheds light on how microbes can help to induce heat stress tolerance in plants.}, }
@article {pmid35677075, year = {2022}, author = {Lai, P and Nguyen, L and Okin, D and Drew, D and Battista, V and Jesudasen, S and Kuntz, T and Bhosle, A and Thompson, K and Reinicke, T and Lo, CH and Woo, J and Caraballo, A and Berra, L and Vieira, J and Huang, CY and Adhikari, UD and Kim, M and Sui, HY and Magicheva-Gupta, M and McIver, L and Goldberg, M and Kwon, D and Huttenhower, C and Chan, A}, title = {Metagenomic assessment of gut microbial communities and risk of severe COVID-19.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {35677075}, issn = {2693-5015}, support = {K01 DK120742/DK/NIDDK NIH HHS/United States ; K23 DK125838/DK/NIDDK NIH HHS/United States ; T32 HL116275/HL/NHLBI NIH HHS/United States ; UL1 TR002541/TR/NCATS NIH HHS/United States ; }, abstract = {The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure. We profiled 127 hospitalized patients with COVID-19 (n=79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites. 48 species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or "long COVID", suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with predicting whether stool was obtained from patients with severe vs. moderate COVID-19. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease. Here, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to validate these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention.}, }
@article {pmid35676296, year = {2022}, author = {Suarez, C and Sedlacek, CJ and Gustavsson, DJI and Eiler, A and Modin, O and Hermansson, M and Persson, F}, title = {Disturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {47}, pmid = {35676296}, issn = {2055-5008}, mesh = {Anaerobic Ammonia Oxidation ; Bacteria/genetics ; Biofilms ; Bioreactors/microbiology ; *Microbiota ; *Nitrites ; }, abstract = {The resistance and resilience provided by functional redundancy, a common feature of microbial communities, is not always advantageous. An example is nitrite oxidation in partial nitritation-anammox (PNA) reactors designed for nitrogen removal in wastewater treatment, where suppression of nitrite oxidizers like Nitrospira is sought. In these ecosystems, biofilms provide microhabitats with oxygen gradients, allowing the coexistence of aerobic and anaerobic bacteria. We designed a disturbance experiment where PNA biofilms, treating water from a high-rate activated sludge process, were constantly or intermittently exposed to anaerobic sidestream wastewater, which has been proposed to inhibit nitrite oxidizers. With increasing sidestream exposure we observed decreased abundance, alpha-diversity, functional versatility, and hence functional redundancy, among Nitrospira in the PNA biofilms, while the opposite patterns were observed for anammox bacteria within Brocadia. At the same time, species turnover was observed for aerobic ammonia-oxidizing Nitrosomonas populations. The different exposure regimens were associated with metagenomic assembled genomes of Nitrosomonas, Nitrospira, and Brocadia, encoding genes related to N-cycling, substrate usage, and osmotic stress response, possibly explaining the three different patterns by niche differentiation. These findings imply that disturbances can be used to manage the functional redundancy of biofilm microbiomes in a desirable direction, which should be considered when designing operational strategies for wastewater treatment.}, }
@article {pmid35675172, year = {2022}, author = {Jammer, A and Akhtar, SS and Amby, DB and Pandey, C and Mekureyaw, MF and Bak, F and Roth, PM and Roitsch, T}, title = {Enzyme activity profiling for physiological phenotyping within functional phenomics: plant growth and stress responses.}, journal = {Journal of experimental botany}, volume = {73}, number = {15}, pages = {5170-5198}, doi = {10.1093/jxb/erac215}, pmid = {35675172}, issn = {1460-2431}, support = {//Ministry of Education, Youth and Sports of Czech/ ; //NordForsk/ ; //Innovation Fund Denmark/ ; //Novo Nordisk Fonden/ ; }, mesh = {Crops, Agricultural/genetics ; *Phenomics ; Phenotype ; *Plant Breeding ; Plant Development/genetics ; Stress, Physiological/genetics ; }, abstract = {High-throughput profiling of key enzyme activities of carbon, nitrogen, and antioxidant metabolism is emerging as a valuable approach to integrate cell physiological phenotyping into a holistic functional phenomics approach. However, the analyses of the large datasets generated by this method represent a bottleneck, often keeping researchers from exploiting the full potential of their studies. We address these limitations through the exemplary application of a set of data evaluation and visualization tools within a case study. This includes the introduction of multivariate statistical analyses that can easily be implemented in similar studies, allowing researchers to extract more valuable information to identify enzymatic biosignatures. Through a literature meta-analysis, we demonstrate how enzyme activity profiling has already provided functional information on the mechanisms regulating plant development and response mechanisms to abiotic stress and pathogen attack. The high robustness of the distinct enzymatic biosignatures observed during developmental processes and under stress conditions underpins the enormous potential of enzyme activity profiling for future applications in both basic and applied research. Enzyme activity profiling will complement molecular -omics approaches to contribute to the mechanistic understanding required to narrow the genotype-to-phenotype knowledge gap and to identify predictive biomarkers for plant breeding to develop climate-resilient crops.}, }
@article {pmid35672295, year = {2022}, author = {Catania, T and Li, Y and Winzer, T and Harvey, D and Meade, F and Caridi, A and Leech, A and Larson, TR and Ning, Z and Chang, J and Van de Peer, Y and Graham, IA}, title = {A functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3150}, pmid = {35672295}, issn = {2041-1723}, support = {BB/K018809/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Alkaloids/metabolism ; *Benzylisoquinolines/metabolism ; Gene Fusion ; *Morphinans/metabolism ; *Papaver/genetics/metabolism ; Plant Proteins/genetics/metabolism ; }, abstract = {The STORR gene fusion event is considered essential for the evolution of the promorphinan/morphinan subclass of benzylisoquinoline alkaloids (BIAs) in opium poppy as the resulting bi-modular protein performs the isomerization of (S)- to (R)-reticuline essential for their biosynthesis. Here, we show that of the 12 Papaver species analysed those containing the STORR gene fusion also contain promorphinans/morphinans with one important exception. P. californicum encodes a functionally conserved STORR but does not produce promorphinans/morphinans. We also show that the gene fusion event occurred only once, between 16.8-24.1 million years ago before the separation of P. californicum from other Clade 2 Papaver species. The most abundant BIA in P. californicum is (R)-glaucine, a member of the aporphine subclass of BIAs, raising the possibility that STORR, once evolved, contributes to the biosynthesis of more than just the promorphinan/morphinan subclass of BIAs in the Papaveraceae.}, }
@article {pmid35669957, year = {2022}, author = {Adedayo, AA and Babalola, OO and Prigent-Combaret, C and Cruz, C and Stefan, M and Kutu, F and Glick, BR}, title = {The application of plant growth-promoting rhizobacteria in Solanum lycopersicum production in the agricultural system: a review.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13405}, pmid = {35669957}, issn = {2167-8359}, mesh = {Humans ; Animals ; *Solanum lycopersicum ; Agriculture ; Plant Development ; Plants/microbiology ; Bacteria ; Soil/chemistry ; *Alphaproteobacteria ; }, abstract = {Food safety is a significant challenge worldwide, from plantation to cultivation, especially for perishable products such as tomatoes. New eco-friendly strategies are needed, and beneficial microorganisms might be a sustainable solution. This study demonstrates bacteria activity in the tomato plant rhizosphere. Further, it investigates the rhizobacteria's structure, function, and diversity in soil. Rhizobacteria that promote the growth and development of tomato plants are referred to as plant growth-promoting bacteria (PGPR). They form a series of associations with plants and other organisms in the soil through a mutualistic relationship where both parties benefit from living together. It implies the antagonistic activities of the rhizobacteria to deter pathogens from invading tomato plants through their roots. Some PGPR are regarded as biological control agents that hinder the development of spoilage organisms and can act as an alternative for agricultural chemicals that may be detrimental to the health of humans, animals, and some of the beneficial microbes in the rhizosphere soil. These bacteria also help tomato plants acquire essential nutrients like potassium (K), magnesium (Mg), phosphorus (P), and nitrogen (N). Some rhizobacteria may offer a solution to low tomato production and help tackle food insecurity and farming problems. In this review, an overview of soil-inhabiting rhizobacteria focused on improving the sustainable production of Solanum lycopersicum.}, }
@article {pmid35669004, year = {2022}, author = {Green, GBH and Williams, MB and Chehade, SB and Morrow, CD and Watts, SA and Bej, AK}, title = {High-throughput amplicon sequencing datasets of the metacommunity DNA of the gut microbiota of Zebrafish Danio rerio fed diets with differential quantities of protein and fat contents.}, journal = {Data in brief}, volume = {42}, number = {}, pages = {108313}, pmid = {35669004}, issn = {2352-3409}, support = {P30 AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR000165/TR/NCATS NIH HHS/United States ; }, abstract = {In this paper, we present high-throughput amplicon sequence (HTS) datasets of the gut microbiota of male and female Zebrafish Danio rerio fed diets consisting of sub-optimal and above-optimal quantities of proteins and fats. The HTS datasets were generated using an Illumina MiSeq targeting the V4 hypervariable segment of the 16S rRNA gene. The raw sequence reads were quality checked, demultiplexed into FASTQ files, denoised using DADA2 (q2-dada2 denoise-paired), and subsampled. Taxonomic ids were then assigned to amplicon sequence variants (ASVs) against the silva-138-99-nb-classifier for taxonomic output using the Quantitative Insights Into Microbial Ecology (QIIME2 v2021.4). The resultant taxa list was generated at the phylum level to confirm the applicability of the HTS dataset using the "qiime taxa collapse" command. These HTS datasets of the metagenome can be accessed through the BioSample Submission Portal (https://www.ncbi.nlm.nih.gov/bioproject/) under the BioProject IDs PRJNA772302 and PRJNA772305.}, }
@article {pmid35668112, year = {2022}, author = {Berlanga-Clavero, MV and Molina-Santiago, C and Caraballo-Rodríguez, AM and Petras, D and Díaz-Martínez, L and Pérez-García, A and de Vicente, A and Carrión, VJ and Dorrestein, PC and Romero, D}, title = {Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon.}, journal = {Nature microbiology}, volume = {7}, number = {7}, pages = {1001-1015}, pmid = {35668112}, issn = {2058-5276}, support = {R01 GM107550/GM/NIGMS NIH HHS/United States ; P41 GM103484/GM/NIGMS NIH HHS/United States ; DP2 GM137413/GM/NIGMS NIH HHS/United States ; R03 CA211211/CA/NCI NIH HHS/United States ; }, mesh = {*Bacillus subtilis/metabolism ; *Cucurbitaceae/microbiology ; Extracellular Polymeric Substance Matrix ; Lipid Droplets ; Seeds/microbiology ; }, abstract = {Beneficial microorganisms are used to stimulate the germination of seeds; however, their growth-promoting mechanisms remain largely unexplored. Bacillus subtilis is commonly found in association with different plant organs, providing protection against pathogens or stimulating plant growth. We report that application of B. subtilis to melon seeds results in genetic and physiological responses in seeds that alter the metabolic and developmental status in 5-d and 1-month-old plants upon germination. We analysed mutants in different components of the extracellular matrix of B. subtilis biofilms in interaction with seeds and found cooperation in bacterial colonization of seed storage tissues and growth promotion. Combining confocal microscopy with fluorogenic probes, we found that two specific components of the extracellular matrix, amyloid protein TasA and fengycin, differentially increased the concentrations of reactive oxygen species inside seeds. Further, using electron and fluorescence microscopy and metabolomics, we showed that both TasA and fengycin targeted the oil bodies in the seed endosperm, resulting in specific changes in lipid metabolism and accumulation of glutathione-related molecules. In turn, this results in two different plant growth developmental programmes: TasA and fengycin stimulate the development of radicles, and fengycin alone stimulate the growth of adult plants and resistance in the phylloplane to the fungus Botrytis cinerea. Understanding mechanisms of bacterial growth promotion will enable the design of bespoke growth promotion strains.}, }
@article {pmid35667433, year = {2022}, author = {Van Le, A and Straub, D and Planer-Friedrich, B and Hug, SJ and Kleindienst, S and Kappler, A}, title = {Microbial communities contribute to the elimination of As, Fe, Mn, and NH4[+] from groundwater in household sand filters.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 4}, pages = {156496}, doi = {10.1016/j.scitotenv.2022.156496}, pmid = {35667433}, issn = {1879-1026}, mesh = {*Ammonium Compounds ; *Arsenic ; Ferrous Compounds ; *Groundwater/microbiology ; Manganese ; *Microbiota ; Oxidation-Reduction ; }, abstract = {Household sand filters (SFs) are widely applied to remove iron (Fe), manganese (Mn), arsenic (As), and ammonium (NH4[+]) from groundwater in the Red River delta, Vietnam. Processes in the filters probably include a combination of biotic and abiotic reactions. However, there is limited information on the microbial communities treating varied groundwater compositions and on whether biological oxidation of Fe(II), Mn(II), As(III), and NH4[+] contributes to the overall performance of SFs. We therefore analyzed the removal efficiencies, as well as the microbial communities and their potential activities, of SFs fed by groundwater with varying compositions from low (3.3 μg L[-1]) to high (600 μg L[-1]) As concentrations. The results revealed that Fe(II)-, Mn(II)-, NH4[+]-, and NO2[-]-oxidizing microorganisms were prevalent and contributed to the performance of SFs. Additionally, groundwater composition was responsible for the differences among the present microbial communities. We found i) microaerophilic Fe(II) oxidation by Sideroxydans in all SFs, with the highest abundance in SFs fed by low-As and high-Fe groundwater, ii) Hyphomicropbiaceae as the main Mn(II)-oxidizers in all SFs, iii) As sequestration on formed Fe and Mn (oxyhydr)oxide minerals, iv) nitrification by ammonium-oxidizing archaea (AOA) followed by nitrite-oxidizing bacteria (NOB), and v) unexpectedly, the presence of a substantial amount of methane monooxygenase genes (pmoA), suggesting microbial methane oxidation taking place in SFs. Overall, our study revealed diverse microbial communities in SFs used for purifying arsenic-contaminated groundwater, and our data indicate an important contribution of microbial activities to the key functional processes in SFs.}, }
@article {pmid35666722, year = {2022}, author = {Boezen, D and Ali, G and Wang, M and Wang, X and van der Werf, W and Vlak, JM and Zwart, MP}, title = {Empirical estimates of the mutation rate for an alphabaculovirus.}, journal = {PLoS genetics}, volume = {18}, number = {6}, pages = {e1009806}, pmid = {35666722}, issn = {1553-7404}, mesh = {Animals ; Mutation ; Mutation Rate ; *Nucleopolyhedroviruses/genetics ; Spodoptera ; }, abstract = {Mutation rates are of key importance for understanding evolutionary processes and predicting their outcomes. Empirical mutation rate estimates are available for a number of RNA viruses, but few are available for DNA viruses, which tend to have larger genomes. Whilst some viruses have very high mutation rates, lower mutation rates are expected for viruses with large genomes to ensure genome integrity. Alphabaculoviruses are insect viruses with large genomes and often have high levels of polymorphism, suggesting high mutation rates despite evidence of proofreading activity by the replication machinery. Here, we report an empirical estimate of the mutation rate per base per strand copying (s/n/r) of Autographa californica multiple nucleopolyhedrovirus (AcMNPV). To avoid biases due to selection, we analyzed mutations that occurred in a stable, non-functional genomic insert after five serial passages in Spodoptera exigua larvae. Our results highlight that viral demography and the stringency of mutation calling affect mutation rate estimates, and that using a population genetic simulation model to make inferences can mitigate the impact of these processes on estimates of mutation rate. We estimated a mutation rate of μ = 1×10-7 s/n/r when applying the most stringent criteria for mutation calling, and estimates of up to μ = 5×10-7 s/n/r when relaxing these criteria. The rates at which different classes of mutations accumulate provide good evidence for neutrality of mutations occurring within the inserted region. We therefore present a robust approach for mutation rate estimation for viruses with stable genomes, and strong evidence of a much lower alphabaculovirus mutation rate than supposed based on the high levels of polymorphism observed.}, }
@article {pmid35665438, year = {2022}, author = {Sun, J and Li, S and Fan, C and Cui, K and Tan, H and Qiao, L and Lu, L}, title = {N-Acetylglucosamine Promotes Tomato Plant Growth by Shaping the Community Structure and Metabolism of the Rhizosphere Microbiome.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0035822}, pmid = {35665438}, issn = {2165-0497}, mesh = {Acetylglucosamine ; Chitin ; *Solanum lycopersicum/microbiology ; *Microbiota/physiology ; Plant Roots/microbiology ; Plants ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Communication between plants and microorganisms is vital because it influences their growth, development, defense, propagation, and metabolism in achieving maximal fitness. N-acetylglucosamine (N-GlcNAc), the building block of bacterial and fungal cell walls, was first reported to promote tomato plant growth via stimulation of microorganisms typically known to dominate the tomato root rhizosphere, such as members of Proteobacteria and Actinobacteria. Using KEGG pathway analysis of the rhizosphere microbial operational taxonomic units, the streptomycin biosynthesis pathway was enriched in the presence of N-GlcNAc. The biosynthesis of 3-hydroxy-2-butanone (acetoin) and 2,3-butanediol, two foremost types of plant growth promotion-related volatile organic compounds, were activated in both Bacillus subtilis and Streptomyces thermocarboxydus strains when they were cocultured with N-GlcNAc. In addition, the application of N-GlcNAc increased indole-3-acetic acid production in a dose-dependent manner in strains of Bacillus cereus, Proteus mirabilis, Pseudomonas putida, and S. thermocarboxydus that were isolated from an N-GlcNAc-treated tomato rhizosphere. Overall, this study found that N-GlcNAc could function as microbial signaling molecules to shape the community structure and metabolism of the rhizosphere microbiome, thereby regulating plant growth and development and preventing plant disease through complementary plant-microbe interactions. IMPORTANCE While the benefits of using plant growth-promoting rhizobacteria (PGPRs) to enhance crop production have been recognized and studied extensively under laboratory conditions, the success of their application in the field varies immensely. More fundamentally explicit processes of positive, plant-PGPRs interactions are needed. The utilization of organic amendments, such as chitin and its derivatives, is one of the most economical and practical options for improving soil and substrate quality as well as plant growth and resilience. In this study, we observed that the chitin monomer N-GlcNAc, a key microbial signaling molecule produced through interactions between chitin, soil microbes, and the plants, positively shaped the community structure and metabolism of the rhizosphere microbiome of tomatoes. Our findings also provide a new direction for enhancing the benefits and stability of PGPRs in the field.}, }
@article {pmid35662397, year = {2022}, author = {Yu, Y and van der Zwaag, M and Wedman, JJ and Permentier, H and Plomp, N and Jia, X and Kanon, B and Eggens-Meijer, E and Buist, G and Harmsen, H and Kok, J and Salles, JF and Wertheim, B and Hayflick, SJ and Strauss, E and Grzeschik, NA and Schepers, H and Sibon, OCM}, title = {Coenzyme A precursors flow from mother to zygote and from microbiome to host.}, journal = {Molecular cell}, volume = {82}, number = {14}, pages = {2650-2665.e12}, doi = {10.1016/j.molcel.2022.05.006}, pmid = {35662397}, issn = {1097-4164}, mesh = {Animals ; *Coenzyme A/genetics/metabolism ; Drosophila/metabolism ; Female ; Humans ; *Microbiota ; Mothers ; Phosphotransferases (Alcohol Group Acceptor)/metabolism ; Zygote/metabolism ; }, abstract = {Coenzyme A (CoA) is essential for metabolism and protein acetylation. Current knowledge holds that each cell obtains CoA exclusively through biosynthesis via the canonical five-step pathway, starting with pantothenate uptake. However, recent studies have suggested the presence of additional CoA-generating mechanisms, indicating a more complex system for CoA homeostasis. Here, we uncovered pathways for CoA generation through inter-organismal flows of CoA precursors. Using traceable compounds and fruit flies with a genetic block in CoA biosynthesis, we demonstrate that progeny survive embryonal and early larval development by obtaining CoA precursors from maternal sources. Later in life, the microbiome can provide the essential CoA building blocks to the host, enabling continuation of normal development. A flow of stable, long-lasting CoA precursors between living organisms is revealed. This indicates the presence of complex strategies to maintain CoA homeostasis.}, }
@article {pmid35661942, year = {2022}, author = {Schmid, K and Reis-Filho, JA and Loiola, M and Harvey, ES and de Kikuchi, RKP and Giarrizzo, T}, title = {Habitat-specific fish fauna responses to different management regimes in the largest coral reef complex in the South Atlantic.}, journal = {Marine environmental research}, volume = {178}, number = {}, pages = {105661}, doi = {10.1016/j.marenvres.2022.105661}, pmid = {35661942}, issn = {1879-0291}, mesh = {Animals ; Biodiversity ; Conservation of Natural Resources ; *Coral Reefs ; Ecosystem ; Fishes ; *Sharks ; }, abstract = {While marine protected areas (MPAs) are increasing worldwide, it is still needed to assess the effectiveness of those already consolidated. Methods and ecological assessments to understanding integrated and habitat-specific management regimes are still scarce and insufficient for policy implications and biodiversity conservation. Through Baited Remote Underwater Video (BRUV), we used fish assemblages as proxy of ecological and managerial status in two reef habitat types along three protection levels at Abrolhos Bank - the largest and most biodiverse coral reef complex of the South Atlantic. We found completely distinct responses in the fish fauna between the top (shallow) and bottom (deep) habitats of the unique "chapeirões" pinnacle reef formations. In the most protected zone (no-take), higher richness and abundance of commercial fish and more diverse trophic structure was observed. Particularly, large (sharks and groupers) and small carnivores (snappers) were more abundant and distributed more homogeneously over both reef habitats in the strictly enforced no-take zone. Abundance of these top-predators decreased from the low enforcement no-take zone to the multiple use area, where they were often absent while their typical preys (primary and secondary consumers) were thriving, notably in the top habitats. These outcomes highlight the importance to focus investigations not selectively on a single habitat type or depth zone in order to properly assess MPA effectiveness. Consequently, the monitoring and protection of fish species supported by marine spatial planning may benefit from an improved understanding of ecological functioning provided by MPA performance.}, }
@article {pmid35660593, year = {2022}, author = {Pensky, J and Fisher, AT and Gorski, G and Schrad, N and Dailey, H and Beganskas, S and Saltikov, C}, title = {Enhanced cycling of nitrogen and metals during rapid infiltration: Implications for managed recharge.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 4}, pages = {156439}, doi = {10.1016/j.scitotenv.2022.156439}, pmid = {35660593}, issn = {1879-1026}, mesh = {Carbon ; *Groundwater ; Humans ; Metals ; Nitrates/analysis ; Nitrogen ; Soil ; *Water Pollutants, Chemical/metabolism ; }, abstract = {We present results from a series of plot-scale field experiments to quantify physical infiltration dynamics and the influence of adding a carbon-rich, permeable reactive barrier (PRB) for the cycling of nitrogen and associated trace metals during rapid infiltration for managed aquifer recharge (MAR). Recent studies suggest that adding a bio-available carbon source to soils can enhance denitrification rates and associated N load reduction during moderate-to-rapid infiltration (≤1 m/day). We examined the potential for N removal during faster infiltration (>1 m/day), through coarse and carbon-poor soils, and how adding a carbon-rich PRB (wood chips) affects subsurface redox conditions and trace metal mobilization. During rapid infiltration, plots amended with a carbon-rich PRB generally demonstrated modest increases in subsurface loads of dissolved organic carbon, nitrite, manganese and iron, decreases in loads of nitrate and ammonium, and variable changes in arsenic. These trends differed considerably from those seen during infiltration through native soil without a carbon-rich PRB. Use of a carbon-rich soil amendment increased the fraction of dissolved N species that was removed at equivalent inflowing N loads. There is evidence that N removal took place primarily via denitrification. Shifts in microbial ecology following infiltration in all of the plots included increases in the relative abundances of microbes in the families Comamonadaceae, Pseudomonadaceae, Methylophilaceae, Rhodocyclaceae and Sphingomonadaceae, all of which contain genera capable of carrying out denitrification. These results, in combination with studies that have tested other soil types, flow rates, and system scales, show how water quality can be improved during infiltration for managed recharge, even during rapid infiltration, with a carbon-rich soil amendment.}, }
@article {pmid35659305, year = {2022}, author = {Chiriac, MC and Bulzu, PA and Andrei, AS and Okazaki, Y and Nakano, SI and Haber, M and Kavagutti, VS and Layoun, P and Ghai, R and Salcher, MM}, title = {Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {84}, pmid = {35659305}, issn = {2049-2618}, mesh = {Animals ; Bacteria ; In Situ Hybridization, Fluorescence ; Lakes/microbiology ; *Metagenome/genetics ; *Metagenomics ; Phylogeny ; }, abstract = {BACKGROUND: The increased use of metagenomics and single-cell genomics led to the discovery of organisms from phyla with no cultivated representatives and proposed new microbial lineages such as the candidate phyla radiation (CPR or Patescibacteria). These bacteria have peculiar ribosomal structures, reduced metabolic capacities, small genome, and cell sizes, and a general host-associated lifestyle was proposed for the radiation. So far, most CPR genomes were obtained from groundwaters; however, their diversity, abundance, and role in surface freshwaters is largely unexplored. Here, we attempt to close these knowledge gaps by deep metagenomic sequencing of 119 samples of 17 different freshwater lakes located in Europe and Asia. Moreover, we applied Fluorescence in situ Hybridization followed by Catalyzed Reporter Deposition (CARD-FISH) for a first visualization of distinct CPR lineages in freshwater samples.<br><br>RESULTS: A total of 174 dereplicated metagenome-assembled genomes (MAGs) of diverse CPR lineages were recovered from the investigated lakes, with a higher prevalence from hypolimnion samples (162 MAGs). They have reduced genomes (median size 1 Mbp) and were generally found in low abundances (0.02-14.36 coverage/Gb) and with estimated slow replication rates. The analysis of genomic traits and CARD-FISH results showed that the radiation is an eclectic group in terms of metabolic capabilities and potential lifestyles, ranging from what appear to be free-living lineages to host- or particle-associated groups. Although some complexes of the electron transport chain were present in the CPR MAGs, together with ion-pumping rhodopsins and heliorhodopsins, we believe that they most probably adopt a fermentative metabolism. Terminal oxidases might function in O2 scavenging, while heliorhodopsins could be involved in mitigation against oxidative stress.<br><br>CONCLUSIONS: A high diversity of CPR MAGs was recovered, and distinct CPR lineages did not seem to be limited to lakes with specific trophic states. Their reduced metabolic capacities resemble the ones described for genomes in groundwater and animal-associated samples, apart from Gracilibacteria that possesses more complete metabolic pathways. Even though this radiation is mostly host-associated, we also observed organisms from different clades (ABY1, Paceibacteria, Saccharimonadia) that appear to be unattached to any other organisms or were associated with 'lake snow' particles (ABY1, Gracilibacteria), suggesting a broad range of potential life-strategies in this phylum. Video Abstract.}, }
@article {pmid35657425, year = {2023}, author = {Meena, M and Yadav, G and Sonigra, P and Nagda, A and Mehta, T and Swapnil, P and Harish,  and Marwal, A and Kumar, S}, title = {Multifarious Responses of Forest Soil Microbial Community Toward Climate Change.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {49-74}, pmid = {35657425}, issn = {1432-184X}, mesh = {*Ecosystem ; Climate Change ; Soil/chemistry ; Forests ; *Microbiota ; Nitrogen/analysis ; Soil Microbiology ; Carbon ; }, abstract = {Forest soils are a pressing subject of worldwide research owing to the several roles of forests such as carbon sinks. Currently, the living soil ecosystem has become dreadful as a consequence of several anthropogenic activities including climate change. Climate change continues to transform the living soil ecosystem as well as the soil microbiome of planet Earth. The majority of studies have aimed to decipher the role of forest soil bacteria and fungi to understand and predict the impact of climate change on soil microbiome community structure and their ecosystem in the environment. In forest soils, microorganisms live in diverse habitats with specific behavior, comprising bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are influenced by biotic interactions and nutrient accessibility. Soil microbiome also drives multiple crucial steps in the nutrient biogeochemical cycles (carbon, nitrogen, phosphorous, and sulfur cycles). Soil microbes help in the nitrogen cycle through nitrogen fixation during the nitrogen cycle and maintain the concentration of nitrogen in the atmosphere. Soil microorganisms in forest soils respond to various effects of climate change, for instance, global warming, elevated level of CO2, drought, anthropogenic nitrogen deposition, increased precipitation, and flood. As the major burning issue of the globe, researchers are facing the major challenges to study soil microbiome. This review sheds light on the current scenario of knowledge about the effect of climate change on living soil ecosystems in various climate-sensitive soil ecosystems and the consequences for vegetation-soil-climate feedbacks.}, }
@article {pmid35655857, year = {2022}, author = {Wang, Y and Tian, L and Sun, L and Zhou, W and Zhi, W and Qing, J and Abdi Saed, Y and Dong, L and Zhang, X and Li, Y}, title = {Gut Microbes in Immunoglobulin A Nephropathy and Their Potential Therapeutic Applications.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {823267}, pmid = {35655857}, issn = {2296-858X}, abstract = {Microbial ecosystem consists of a complex community of bacterial interactions and its host microenvironment (tissue, cell, metabolite). Because the interaction between gut microbiota and host involves many diseases and seriously affects human health, the study of the interaction mechanism between gut microbiota and host has attracted great attention. The gut microbiome is made up of 100 trillion bacteria that have both beneficial and adverse effects on human health. The development of IgA Nephropathy results in changes in the intestinal microbial ecosystem that affect host physiology and health. Similarly, changes in intestinal microbiota also affect the development of IgA Nephropathy. Thus, the gut microbiome represents a novel therapeutic target for improving the outcome of IgA Nephropathy, including hematuria symptoms and disease progression. In this review, we summarize the effect of intestinal microbiota on IgA Nephropathy in recent years and it has been clarified that the intestinal microbiota has a great influence on the pathogenesis and treatment of IgA Nephropathy.}, }
@article {pmid35655089, year = {2022}, author = {Morelli, G and Patuzzi, I and Losasso, C and Ricci, A and Contiero, B and Andrighetto, I and Ricci, R}, title = {Characterization of intestinal microbiota in normal weight and overweight Border Collie and Labrador Retriever dogs.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9199}, pmid = {35655089}, issn = {2045-2322}, mesh = {Animals ; Bacteria/genetics ; Dogs ; Feces/microbiology ; Firmicutes/genetics ; *Gastrointestinal Microbiome/genetics ; Mice ; Obesity/microbiology ; Overweight/veterinary ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Obesity in dogs is an emerging issue that affects canine health and well-being. Its development is ascribed to several factors, including genetic predisposition and dietary management, and recent evidence suggests that intestinal microbiota may be involved as well. Previous works have shown obesity to be linked to significant changes in gut microbiota composition in humans and mice, but only limited information is available on the role played by canine gut microbiota. The aim of this exploratory study was to investigate whether composition of canine faecal microbiota may be influenced by overweight condition and breed. All the enrolled companion dogs were young adults, intact, healthy, and fed commercial extruded pet food; none had received antibiotics, probiotics or immunosuppressant drugs in the previous six months. Labrador Retriever (LR) and Border Collie (BC) were chosen as reference breeds and Body Condition Score (BCS) on a 9-point scale as reference method for evaluating body fat. The faecal microbial communities of 15 lean (BCS 4-5/9; 7 LRs and 8 BCs) and 14 overweight (BCS > 5/9; 8 LRs and 6 BCs) family dogs were analysed using 16S rRNA gene sequencing. Moreover, for each dog, the daily intake of energy (kcal/d) and dietary macronutrients (g/d) were calculated according to an accurate feeding history collection. Firmicutes and Bacteroidetes resulted the predominant phyla (51.5 ± 10.0% and 33.4 ± 8.5%, respectively) in all dogs. Bioinformatic and statistical analysis revealed that no bacterial taxon differed significantly based on body condition, except for genus Allisonella (p < 0.05); BC gut microbiota was richer (p < 0.05) in bacteria belonging to phyla Actinobacteria (family Coriobacteriaceae in particular) and Firmicutes (Allobaculum and Roseburia genera). No remarkable differences were recorded either for diversity indices (i.e., alpha diversity, p > 0.10) or for divergence within the sample set (i.e., beta diversity, p > 0.05). PERMANOVA tests performed on single factors demonstrated the tendency of dietary protein to influence the recruited dogs' microbiota beta-diversity at amplicon sequence variant level (p = 0.08). In conclusion, the faecal microbiota of dogs involved in this exploratory study showed no major variations based on body condition. However, our findings suggested that certain bacterial taxa previously acknowledged in obesity-related studies may be detected in dissimilar amounts depending on canine breed.}, }
@article {pmid35655088, year = {2022}, author = {de la Fuente Cantó, C and Diouf, MN and Ndour, PMS and Debieu, M and Grondin, A and Passot, S and Champion, A and Barrachina, C and Pratlong, M and Gantet, P and Assigbetsé, K and Kane, N and Cubry, P and Diedhiou, AG and Heulin, T and Achouak, W and Vigouroux, Y and Cournac, L and Laplaze, L}, title = {Genetic control of rhizosheath formation in pearl millet.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9205}, pmid = {35655088}, issn = {2045-2322}, mesh = {Genome-Wide Association Study ; *Pennisetum/genetics ; Quantitative Trait Loci ; Rhizosphere ; Soil/chemistry ; }, abstract = {The rhizosheath, the layer of soil that adheres strongly to roots, influences water and nutrients acquisition. Pearl millet is a cereal crop that plays a major role for food security in arid regions of sub-Saharan Africa and India. We previously showed that root-adhering soil mass is a heritable trait in pearl millet and that it correlates with changes in rhizosphere microbiota structure and functions. Here, we studied the correlation between root-adhering soil mass and root hair development, root architecture, and symbiosis with arbuscular mycorrhizal fungi and we analysed the genetic control of this trait using genome wide association (GWAS) combined with bulk segregant analysis and gene expression studies. Root-adhering soil mass was weakly correlated only to root hairs traits in pearl millet. Twelve QTLs for rhizosheath formation were identified by GWAS. Bulk segregant analysis on a biparental population validated five of these QTLs. Combining genetics with a comparison of global gene expression in the root tip of contrasted inbred lines revealed candidate genes that might control rhizosheath formation in pearl millet. Our study indicates that rhizosheath formation is under complex genetic control in pearl millet and suggests that it is mainly regulated by root exudation.}, }
@article {pmid35654854, year = {2023}, author = {Monroy, S and Larrañaga, A and Martínez, A and Pérez, J and Molinero, J and Basaguren, A and Pozo, J}, title = {Temperature Sensitivity of Microbial Litter Decomposition in Freshwaters: Role of Leaf Litter Quality and Environmental Characteristics.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {839-852}, pmid = {35654854}, issn = {1432-184X}, support = {CGL2010-22129-C04-01//Ministry of Science and Innovation of the Spanish Government/ ; BES-2012-060743//Spanish Ministry of Economy and Competitiveness/ ; DOKBERRI 2018 I//UPV/EHU/ ; }, mesh = {Temperature ; *Ecosystem ; Biomass ; Plant Leaves/microbiology ; *Alnus/microbiology ; Fresh Water ; }, abstract = {Ongoing global warming is expected to alter temperature-dependent processes. Nevertheless, how co-occurring local drivers will influence temperature sensitivity of plant litter decomposition in lotic ecosystems remains uncertain. Here, we examined the temperature sensitivity of microbial-mediated decomposition, microbial respiration, fungal biomass and leaf nutrients of two plant species varying in litter quality. We also assessed whether the type of microbial community and stream water characteristics influence such responses to temperature. We incubated alder (Alnus glutinosa) and eucalypt (Eucalyptus globulus) litter discs in three streams differing in autumn-winter water temperature (range 4.6-8.9 °C). Simultaneously, in laboratory microcosms, litter discs microbially conditioned in these streams were incubated at 5, 10 and 15 °C with water from the conditioning stream and with a water control from an additional stream. Both in the field and in the laboratory, higher temperatures enhanced litter decomposition rates, except for eucalypt in the field. Leaf quality modified the response of decomposition to temperature in the field, with eucalypt leaf litter showing a lower increase, whereas it did not in the laboratory. The origin of microbial community only affected the decomposition rates in the laboratory, but it did not modify the response to temperature. Water quality only defined the phosphorus content of the leaf litter or the fungal biomass, but it did not modify the response to temperature. Our results suggest that the acceleration in decomposition by global warming will be shaped by local factors, mainly by leaf litter quality, in headwater streams.}, }
@article {pmid35652980, year = {2022}, author = {Behairi, S and Baha, N and Barakat, M and Ortet, P and Achouak, W and Heulin, T and Kaci, Y}, title = {Bacterial diversity and community structure in the rhizosphere of the halophyte Halocnemum strobilaceum in an Algerian arid saline soil.}, journal = {Extremophiles : life under extreme conditions}, volume = {26}, number = {2}, pages = {18}, pmid = {35652980}, issn = {1433-4909}, support = {14MDU907//French-Algerian Hubert Curien Partnership Program (PHC) TASSILI/ ; }, mesh = {Algeria ; Bacteria ; *Microbiota ; *Rhizosphere ; Salt-Tolerant Plants/microbiology ; Sodium Chloride ; Soil ; Soil Microbiology ; }, abstract = {Hypersaline ecosystems host a particular microbiota, which can be specifically recruited by halophytes. In order to broaden our knowledge of hypersaline ecosystems, an in natura study was conducted on the microbiota associated with the halophyte Halocnemum strobilaceum from alkaline-saline arid soil in Algeria. We collected and identified a total of 414 strains isolated from root tissues (RT), root-adhering soil (RAS), non-adhering rhizospheric soil (NARS) and bulk soil (BS) using different NaCl concentrations. Our data showed that halophilic and halotolerant bacterial isolates in BS and the rhizosphere belonged to 32 genera distributed in Proteobacteria (49%), Firmicutes (36%), Actinobacteria (14%) and Bacteroidetes (1%). Bacterial population size and species diversity were greatly increased in the rhizosphere (factor 100). The reservoir of diversity in BS was dominated by the genera Bacillus and Halomonas. Bacillus/Halomonas ratio decreased with the proximity to the roots from 2.2 in BS to 0.3 at the root surface. Salt screening of the strains showed that species belonging to nine genera were able to grow up to 5.1 M NaCl. Thus, we found that H. strobilaceum exerted a strong effect on the diversity of the recruited microbiota with an affinity strongly attributed to the genus Halomonas.}, }
@article {pmid35652935, year = {2022}, author = {Lürling, M and Mucci, M and Douglas, GB}, title = {Response to "Risk of Collapse in Water Quality in the Guandu River (Rio de Janeiro, Brazil)" by Bacha et al., Published Online 23 August 2021, Microbial Ecology, 10.1007/s00248-021-01,839-z.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {14-19}, pmid = {35652935}, issn = {1432-184X}, mesh = {Brazil ; Environmental Monitoring ; *Rivers ; *Water Pollutants, Chemical/analysis ; Water Quality ; }, }
@article {pmid35652664, year = {2022}, author = {Smercina, DN and Kim, YM and Lipton, MS and Velickovic, D and Hofmockel, KS}, title = {Bulk and Spatially Resolved Extracellular Metabolome of Free-Living Nitrogen Fixation.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {12}, pages = {e0050522}, pmid = {35652664}, issn = {1098-5336}, mesh = {Bacteria/metabolism ; *Ecosystem ; Metabolome ; Nitrogen/metabolism ; *Nitrogen Fixation ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Soil nitrogen (N) transformations constrain terrestrial net primary productivity and are driven by the activity of soil microorganisms. Free-living N fixation (FLNF) is an important soil N transformation and key N input to terrestrial systems, but the forms of N contributed to soil by FLNF are poorly understood. To address this knowledge gap, a focus on microorganisms and microbial scale processes is needed that links N-fixing bacteria and their contributed N sources to FLNF process rates. However, studying the activity of soil microorganisms in situ poses inherent challenges, including differences in sampling scale between microorganism and process rates, which can be addressed with culture-based studies and an emphasis on microbial-scale measurements. Culture conditions can differ significantly from soil conditions, so it also important that such studies include multiple culture conditions like liquid and solid media as proxies for soil environments like soil pore water and soil aggregate surfaces. Here we characterized extracellular N-containing metabolites produced by two common, diazotrophic soil bacteria in liquid and solid media, with or without N, across two sampling scales (bulk via GC-MS and spatially resolved via MALDI mass spec imaging). We found extracellular production of inorganic and organic N during FLNF, indicating terrestrial N contributions from FLNF occur in multiple forms not only as ammonium as previously thought. Extracellular metabolite profiles differed between liquid and solid media supporting previous work indicating environmental structure influences microbial function. Metabolite profiles also differed between sampling scales underscoring the need to quantify microbial scale conditions to accurately interpret microbial function. IMPORTANCE Free-living nitrogen-fixing bacteria contribute significantly to terrestrial nitrogen availability; however, the forms of nitrogen contributed by this process are poorly understood. This is in part because of inherent challenges to studying soil microorganisms in situ, such as vast differences in scale between microorganism and ecosystem and complexities of the soil system (e.g., opacity, chemical complexity). Thus, upscaling important ecosystem processes driven by soil microorganisms, like free-living nitrogen fixation, requires microbial-scale measurements in controlled systems. Our work generated bulk and spatially resolved measurements of nitrogen released during free-living nitrogen fixation under two contrasting growth conditions analogous to soil pores and aggregates. This work allowed us to determine that diverse forms of nitrogen are likely contributed to terrestrial systems by free-living nitrogen bacteria. We also demonstrated that microbial habitat (e.g., liquid versus solid media) alters microbial activity and that measurement of microbial activity is altered by sampling scale (e.g., bulk versus spatially resolved) highlighting the critical importance of quantifying microbial-scale processes to upscaling of ecosystem function.}, }
@article {pmid35651031, year = {2022}, author = {Huang, R and Shen, L and Yu, H and Jiang, J and Qin, Y and Liu, Y and Zhang, J and Song, Y}, title = {Evaluation of rain-shelter cultivation mode effects on microbial diversity during Cabernet Sauvignon (Vitis vinifera L.) maturation in Jingyang, Shaanxi, China.}, journal = {Food research international (Ottawa, Ont.)}, volume = {156}, number = {}, pages = {111165}, doi = {10.1016/j.foodres.2022.111165}, pmid = {35651031}, issn = {1873-7145}, mesh = {Bacteria/classification ; China ; Fruit/chemistry/microbiology ; Fungi/classification ; *Microbiota ; *Rain ; *Vitis/chemistry/microbiology ; *Wine/analysis/microbiology ; }, abstract = {Rainfall particularly under continental climates with monsoonal tendency impacts the vineyard microbial niches during grapevine growth. With microbial community shifts, vine traits (grape flavor and yield) cultivated/protected under rain-shelter may ultimately be altered. Such cultivation may influence microflora dynamics via meteorological parameter variations, however this is unclear yet. Here, we used Cabernet Sauvignon, a prevalent red cultivar among wine growing regions, to evaluate the effects of the rain-shelter cultivation on the microorganism diversity. We found that average air temperature under rain-shelter conditions was 2-3 °C higher than the non-covered group, while air humidity the maximum reduction was 5.79% (p < 0.05). After grape setting stage, similar trends were observed on soil temperature (increased) and humidity (lowered) under the treatments (p < 0.05). UV and precipitation of rain-shelter treatment were less by a total of 72% and 96%, respectively (p < 0.05). The rain-shelter management presented lower fungal and bacterial OTUs. The fungal alpha diversity on leaves and branches under rain-shelter was lower (p < 0.05) than the control as the grape ripeness, with Ascomycota, Mycosphaerella and Cladosporium as the principal fungi. Our results revealed that the fungal microbiota patterns were differentiated by the cultivations from setting stage to the entire véraison and then tended to be similar at harvesting. Only branch fungal patterns were observed asymmetrically at all stages. Meanwhile, bacterial diversity and distribution varied on colonization locations where Proteobacteria and Actinobacteria were the primary bacteria phyla. Bacterial community structures overlapped at harvest, while the differences were observed between two cultivations at other stages, excluding grape berry. The rain-shelter cultivation reduced the abundance of Alternaria and Colletotrichum that may adversely affect grapevine health. Multivariate statistical analysis suggested that the effect of vineyard microclimate on microbiota distribution and succession were influenced by cultivation modes and grapevine developmental stages. This research provides evidence to address the dynamics of microbial ecology from vineyard to grape under rain-shelter cultivation, and its benefits as a sustainable vineyard management.}, }
@article {pmid35650293, year = {2023}, author = {Ren, Z and Ma, K and Jia, X and Wang, Q and Zhang, C and Li, X}, title = {Metagenomics Unveils Microbial Diversity and Their Biogeochemical Roles in Water and Sediment of Thermokarst Lakes in the Yellow River Source Area.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {904-915}, pmid = {35650293}, issn = {1432-184X}, mesh = {*Lakes/microbiology ; *Metagenomics ; Water ; Rivers ; Nitrogen ; Sulfates ; }, abstract = {Thermokarst lakes have long been recognized as biogeochemical hotspots, especially as sources of greenhouse gases. On the Qinghai-Tibet Plateau, thermokarst lakes are experiencing extensive changes due to faster warming. For a deep understanding of internal lake biogeochemical processes, we applied metagenomic analyses to investigate the microbial diversity and their biogeochemical roles in sediment and water of thermokarst lakes in the Yellow River Source Area (YRSA). Sediment microbial communities (SMCs) had lower species and gene richness than water microbial communities (WMCs). Bacteria were the most abundant component in both SMCs and WMCs with significantly different abundant genera. The functional analyses showed that both SMCs and WMCs had low potential in methanogenesis but strong in aerobic respiration, nitrogen assimilation, exopolyphosphatase, glycerophosphodiester phosphodiesterases, and polyphosphate kinase. Moreover, SMCs were enriched in genes involved in anaerobic carbon fixation, aerobic carbon fixation, fermentation, most nitrogen metabolism pathways, dissimilatory sulfate reduction, sulfide oxidation, polysulfide reduction, 2-phosphonopropionate transporter, and phosphate regulation. WMCs were enriched in genes involved in assimilatory sulfate reduction, sulfur mineralization, phosphonoacetate hydrolase, and phosphonate transport. Functional potentials suggest the differences of greenhouse gas emission, nutrient cycling, and living strategies between SMCs and WMCs. This study provides insight into the main biogeochemical processes and their properties in thermokarst lakes in YRSA, improving our understanding of the roles and fates of these lakes in a warming world.}, }
@article {pmid35648155, year = {2023}, author = {Ma, M and Chen, X and Li, S and Luo, J and Han, R and Xu, L}, title = {Composition and Diversity of Gut Bacterial Community in Different Life Stages of a Leaf Beetle Gastrolina depressa.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {590-600}, pmid = {35648155}, issn = {1432-184X}, mesh = {Animals ; *Coleoptera ; *Gastrointestinal Microbiome ; Larva/microbiology ; Bacteria/genetics ; Life Cycle Stages ; }, abstract = {Insect gut bacteria have a significant impact on host biology, which has a favorable or negative impact on insect fitness. The walnut leaf beetle (Gastrolina depressa) is a notorious pest in China, causing severe damage to Juglandaceae trees including Juglans regia and Pterocarya rhoifolia. To date, however, we know surprisingly little about the gut microbiota of G. depressa. This study used a high-throughput sequencing platform to investigate the gut bacterial community of G. depressa throughout its life cycle, including the 1st, 2nd, and 3rd instar larvae, as well as male, female, and pre-pregnant female adults. Our results showed that the diversity of the gut bacterial community in larvae was generally higher than that in adults, and young larvae (1st and 2nd larvae) possessed the most diversified and abundant community. Principal coordinate analysis results showed that the gut microbiota of adults cluster together, which is independent of the 1st and 2nd instar larvae. The main phyla were Proteobacteria and Firmicutes in the microbial community of G. depressa, while the dominant genera were Enterobacter, Rosenbergiella, Erwinia, Pseudomonas, and Lactococcus. The gut bacteria of G. depressa were mostly enriched in metabolic pathways (carbohydrate metabolism and amino acid metabolism) as revealed by functional prediction. This study contributes to a better knowledge of G. depressa's gut microbiota and its potential interactions with the host insect, facilitating the development of a microbial-based pest management strategy.}, }
@article {pmid35648154, year = {2023}, author = {Doniger, T and Kerfahi, D and Wachtel, C and Marais, E and Maggs-Kölling, G and Sherman, C and Adams, JM and Steinberger, Y}, title = {Plant Gender Affects Soil Fungal Microbiota Associated with Welwitschia mirabilis, an Unusual Desert Gymnosperm.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {200-212}, pmid = {35648154}, issn = {1432-184X}, mesh = {*Mycobiome ; Cycadopsida ; *Mirabilis ; Soil/chemistry ; Plants/microbiology ; *Ascomycota ; Soil Microbiology ; }, abstract = {In a recent study, we found a distinct soil bacterial community associated with male and female plants of the desert gymnosperm Welwitschia mirabilis. In this subsequent study, we also found that the soil fungal community associated with Welwitschia differs between male and female plants, and between unvegetated areas and the soil under plants. Site location, pH, and soil moisture also had an important influence on the composition of the fungal community. A number of Ascomycota and Chytrid species were found to be distinct indicators of male and female plants, respectively, but there was no overall difference at the phylum level or in terms of diversity. The unvegetated areas between plants also differed in terms of several Ascomycota OTUs. Network connectivity of the fungal communities was found to be higher under both male and female Welwitschia plants than in unvegetated control areas. As with the bacterial community, it is unclear what processes produce the gender-distinct fungal community, and also the more general plant-associated community, and also what the effects on the biology of the plants are. One possibility behind the gender-related difference in fungal community is that there are differences in the production of pollen or nectar between the two plant genders, affecting the below-ground soil community.}, }
@article {pmid35647000, year = {2022}, author = {Zhi, W and Song, W and Abdi Saed, Y and Wang, Y and Li, Y}, title = {Fecal Capsule as a Therapeutic Strategy in IgA Nephropathy: A Brief Report.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {914250}, pmid = {35647000}, issn = {2296-858X}, abstract = {In this brief report, we reported an IgA nephropathy (IgAN) patient who presented in November 2020 with an acute exacerbation with massive proteinuria and diarrhea. He had the earliest onset in 2018 when his IgAN was diagnosed by renal biopsy. He has been treated with active ACEI/ARB drugs for more than 90 days, intermittent steroid therapy, combined with anti-infective therapy. Although his acute symptoms resolved with each episode, he became increasingly severe as the interval between episodes shortened. Accordingly, the immunosuppressive drugs were administered under the KDIGO guidelines and related guidelines. However, the patient and his family refused this treatment. We pondered over the possible pathogenesis of IgAN, and after a full discussion with the patient and his family, FMT was administered to him after obtaining his informed consent. During the FMT procedure, one healthy volunteer (the doctor himself) also took the FMT capsules. In the end, the patient's urine protein dropped significantly and even turned negative after treatment. Neither the patient nor the healthy volunteer experienced any serious adverse effects during the use of the capsules and the subsequent 6-month follow-up period. We also used metagenomic sequencing to analyze the intestinal flora of patients before and after treatment, and a gradual increase stood out in the abundance of the patient's intestinal flora after drug administration.}, }
@article {pmid35646730, year = {2022}, author = {Yang, I and Claussen, H and Arthur, RA and Hertzberg, VS and Geurs, N and Corwin, EJ and Dunlop, AL}, title = {Subgingival Microbiome in Pregnancy and a Potential Relationship to Early Term Birth.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {873683}, pmid = {35646730}, issn = {2235-2988}, support = {K01 NR016971/NR/NINR NIH HHS/United States ; R01 NR014800/NR/NINR NIH HHS/United States ; }, mesh = {Female ; Humans ; Infant, Newborn ; *Microbiota ; *Periodontal Diseases ; Porphyromonas gingivalis/genetics ; Pregnancy ; *Premature Birth ; RNA, Ribosomal, 16S/genetics ; Term Birth ; }, abstract = {BACKGROUND: Periodontal disease in pregnancy is considered a risk factor for adverse birth outcomes. Periodontal disease has a microbial etiology, however, the current state of knowledge about the subgingival microbiome in pregnancy is not well understood.<br><br>OBJECTIVE: To characterize the structure and diversity of the subgingival microbiome in early and late pregnancy and explore relationships between the subgingival microbiome and preterm birth among pregnant Black women.<br><br>METHODS: This longitudinal descriptive study used 16S rRNA sequencing to profile the subgingival microbiome of 59 Black women and describe microbial ecology using alpha and beta diversity metrics. We also compared microbiome features across early (8-14 weeks) and late (24-30 weeks) gestation overall and according to gestational age at birth outcomes (spontaneous preterm, spontaneous early term, full term).<br><br>RESULTS: In this sample of Black pregnant women, the top twenty bacterial taxa represented in the subgingival microbiome included a spectrum representative of various stages of biofilm progression leading to periodontal disease, including known periopathogens Porphyromonas gingivalis and Tannerella forsythia. Other organisms associated with periodontal disease reflected in the subgingival microbiome included several Prevotella spp., and Campylobacter spp. Measures of alpha or beta diversity did not distinguish the subgingival microbiome of women according to early/late gestation or full term/spontaneous preterm birth; however, alpha diversity differences in late pregnancy between women who spontaneously delivered early term and women who delivered full term were identified. Several taxa were also identified as being differentially abundant according to early/late gestation, and full term/spontaneous early term births.<br><br>CONCLUSIONS: Although the composition of the subgingival microbiome is shifted toward complexes associated with periodontal disease, the diversity of the microbiome remains stable throughout pregnancy. Several taxa were identified as being associated with spontaneous early term birth. Two, in particular, are promising targets of further investigation. Depletion of the oral commensal Lautropia mirabilis in early pregnancy and elevated levels of Prevotella melaninogenica in late pregnancy were both associated with spontaneous early term birth.}, }
@article {pmid35644105, year = {2022}, author = {Bossaert, S and Kocijan, T and Winne, V and Schlich, J and Herrera-Malaver, B and Verstrepen, KJ and Van Opstaele, F and De Rouck, G and Crauwels, S and Lievens, B}, title = {Beer ethanol and iso-α-acid level affect microbial community establishment and beer chemistry throughout wood maturation of beer.}, journal = {International journal of food microbiology}, volume = {374}, number = {}, pages = {109724}, doi = {10.1016/j.ijfoodmicro.2022.109724}, pmid = {35644105}, issn = {1879-3460}, mesh = {*Beer/microbiology ; Ethanol ; Fermentation ; *Microbiota ; Saccharomyces cerevisiae ; Wood ; }, abstract = {Sour beers produced by barrel-aging of conventionally fermented beers are becoming increasingly popular. However, as the intricate interactions between the wood, the microbes and the beer are still unclear, wood maturation often leads to inconsistent end products with undesired sensory properties. Previous research on industrial barrel-aging of beer suggests that beer parameters like the ethanol content and bitterness play an important role in the microbial community composition and beer chemistry, but their exact impact still remains to be investigated. In this study, an experimentally tractable lab-scale system based on an in-vitro community of four key bacteria (Acetobacter malorum, Gluconobacter oxydans, Lactobacillus brevis and Pediococcus damnosus) and four key yeasts (Brettanomyces bruxellensis, Candida friedrichii, Pichia membranifaciens and Saccharomyces cerevisiae) that are consistently associated with barrel-aging of beer, was used to test the hypotheses that beer ethanol and bitterness impact microbial community composition and beer chemistry. Experiments were performed using different levels of ethanol (5.2 v/v%, 8 v/v% and 11 v/v%) and bitterness (13 ppm, 35 ppm and 170 ppm iso-α-acids), and beers were matured for 60 days. Samples were taken after 0, 10, 20, 30 and 60 days to monitor population densities and beer chemistry. Results revealed that all treatments and the maturation time significantly affected the microbial community composition and beer chemistry. More specifically, the ethanol treatments obstructed growth of L. brevis and G. oxydans and delayed fungal growth. The iso-α-acid treatments hindered growth of L. brevis and stimulated growth of P. membranifaciens, while the other strains remained unaffected. Beer chemistry was found to be affected by higher ethanol levels, which led to an increased extraction of wood-derived compounds. Furthermore, the distinct microbial communities also induced changes in the chemical composition of the beer samples, leading to concentration differences in beer- and wood-derived compounds like 4-ethyl guaiacol, 4-ethyl phenol, cis-oak lactone, vanillin, furfural and 5-hydroxymethyl furfural. Altogether, our results indicate that wood-aging of beer is affected by biotic and abiotic parameters, influencing the quality of the final product. Additionally, this work provides a new, cost-effective approach to study the production of barrel-aged beers based on a simplified microbial community model.}, }
@article {pmid35644095, year = {2022}, author = {Cao, Y and Zhao, J and Wang, Q and Bai, S and Yang, Q and Wei, Y and Wang, R}, title = {Industrial aerobic composting and the addition of microbial agents largely reduce the risks of heavy metal and ARG transfer through livestock manure.}, journal = {Ecotoxicology and environmental safety}, volume = {239}, number = {}, pages = {113694}, doi = {10.1016/j.ecoenv.2022.113694}, pmid = {35644095}, issn = {1090-2414}, mesh = {Animals ; Anti-Bacterial Agents ; *Composting/methods ; Genes, Bacterial ; Livestock ; Manure/microbiology ; *Metals, Heavy/toxicity ; }, abstract = {Composting is an effective and necessary modality in the recycling of agricultural wastes such as livestock manure, furfural, and straw. However, the risks of heavy metals (HMs) and antibiotic resistance genes (ARGs) during industrial-scale composting process have not been adequately assessed, especially with the addition of bacterial agents. In this study, changes in HMs toxicity, ARGs propagation and microbial community structure during industrial-scale aerobic composting of livestock manure were firstly investigated with various substrates addition. Moreover, the effect of the addition of bacterial agents (Bacillus strains) was evaluated. The results showed that industrial aerobic composting process could immobilize various HMs with different extents and significantly reduce the levels of ARGs such as intl1 and oqxB genes. The addition of Bacillus strains could further reduce the levels of most detected ARGs and the bioavailability of Cu and Cr, and the relative abundance of ereA and tetA was undetectable in some materials. After composting, the main bacterial community structures were similar among different substrates irrespective of bacterial agents and indicated that the composting process was the main driver for their change. This study provides a scientific reference for the safe reuse of livestock manure.}, }
@article {pmid35643931, year = {2022}, author = {Ueckermann, V and Lebre, P and Geldenhuys, J and Hoosien, E and Cowan, D and van Rensburg, LJ and Ehlers, M}, title = {The lung microbiome in HIV-positive patients with active pulmonary tuberculosis.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {8975}, pmid = {35643931}, issn = {2045-2322}, mesh = {*Coinfection/complications ; *HIV Infections/complications ; *HIV Seropositivity/complications ; Humans ; Lung ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Tuberculosis, Pulmonary/microbiology ; }, abstract = {Tuberculosis poses one of the greatest infectious disease threats of our time, especially when associated with human immunodeficiency virus (HIV) infection. Very little data is available on the lung microbiome in pulmonary tuberculosis (PTB) in HIV-positive patients. Three patient cohorts were studied: (i) HIV-positive with no respiratory disease (control cohort), (ii) HIV-positive with pneumonia and (iii) HIV-positive with PTB. Sputum specimens were collected in all patients and where possible a paired BALF was collected. DNA extraction was performed using the QIAamp DNA mini kit (QIAGEN, Germany) and extracted DNA specimens were sent to Inqaba Biotechnical Industries (Pty) Ltd for 16S rRNA gene sequence analysis using the Illumina platform (Illumina Inc, USA). Data analysis was performed using QIMME II and R Studio version 3.6.2 (2020). The lung microbiomes of patients with PTB, in the context of HIV co-infection, were dominated by Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Loss of biodiversity and dysbiosis was found in these patients when compared to the HIV-positive control cohort. Microbial community structure was also distinct from the control cohort, with the dominance of genera such as Achromobacter, Mycobacterium, Acinetobacter, Stenotrophomonas and Pseudomonas in those patients with PTB. This is the first study to describe the lung microbiome in patients with HIV and PTB co-infection and to compare findings with an HIV-positive control cohort. The lung microbiomes of patients with HIV and PTB were distinct from the HIV-positive control cohort without PTB, with an associated loss of microbial diversity.}, }
@article {pmid35643312, year = {2022}, author = {Chen, X and Chen, J and Yu, X and Sanganyado, E and Wang, L and Li, P and Liu, W}, title = {Effects of norfloxacin, copper, and their interactions on microbial communities in estuarine sediment.}, journal = {Environmental research}, volume = {212}, number = {Pt D}, pages = {113506}, doi = {10.1016/j.envres.2022.113506}, pmid = {35643312}, issn = {1096-0953}, mesh = {Bacteria ; *Copper/toxicity ; Estuaries ; Geologic Sediments ; *Microbiota ; Norfloxacin ; }, abstract = {The discharge of antibiotics and metals in estuaries is of great concern since they threaten microbial communities that are critical for maintaining ecosystem function. To understand single and combined effects of norfloxacin (0-20 μg g[-1]) and copper (40 μg g[-1]) on microbial ecology in estuaries, we evaluated changes in bacteria population, inhibition rates, and microbial composition in estuarine sediments over a 28-day period. Bacteria population significantly decreased following single and combined exposure to norfloxacin and copper throughout the incubation period, except on Day 28 in treatments exposed to copper, 20 μg g[-1] norfloxacin, or both. These three treatment groups had lower Shannon diversity and Simpson's indices on Day 28 than other treatments and the controls suggesting recovery in bacteria population did not correspond with recovery in richness and evenness. Furthermore, functional predictions revealed that the effect of time and contaminants were significantly different on some microbial community functions on Day 28, especially the combination of Cu and high concentration NFX, including aerobic chemoheterotrophy, methanol oxidation and methylotrophy. Thus, norfloxacin and copper had significant adverse effects on microbial communities in estuarine sediments; however, the combined effects were variable and depended on exposure duration and antibiotic concentration.}, }
@article {pmid35643062, year = {2022}, author = {Reinl, KL and Harris, TD and Elfferich, I and Coker, A and Zhan, Q and De Senerpont Domis, LN and Morales-Williams, AM and Bhattacharya, R and Grossart, HP and North, RL and Sweetman, JN}, title = {The role of organic nutrients in structuring freshwater phytoplankton communities in a rapidly changing world.}, journal = {Water research}, volume = {219}, number = {}, pages = {118573}, doi = {10.1016/j.watres.2022.118573}, pmid = {35643062}, issn = {1879-2448}, mesh = {*Eutrophication ; Fresh Water ; Lakes ; Nitrogen ; Nutrients ; Phosphorus ; *Phytoplankton/physiology ; }, abstract = {Carbon, nitrogen, and phosphorus are critical macroelements in freshwater systems. Historically, researchers and managers have focused on inorganic forms, based on the premise that the organic pool was not available for direct uptake by phytoplankton. We now know that phytoplankton can tap the organic nutrient pool through a number of mechanisms including direct uptake, enzymatic hydrolysis, mixotrophy, and through symbiotic relationships with microbial communities. In this review, we explore these mechanisms considering current and projected future anthropogenically-driven changes to freshwater systems. In particular, we focus on how naturally- and anthropogenically- derived organic nutrients can influence phytoplankton community structure. We also synthesize knowledge gaps regarding phytoplankton physiology and the potential challenges of nutrient management in an organically dynamic and anthropogenically modified world. Our review provides a basis for exploring these topics and suggests several avenues for future work on the relation between organic nutrients and eutrophication and their ecological implications in freshwater systems.}, }
@article {pmid35643037, year = {2022}, author = {Arora, K and Carafa, I and Fava, F and Tuohy, KM and Nikoloudaki, O and Gobbetti, M and Cagno, RD}, title = {Sourdough performances of the golden cereal Tritordeum: Dynamics of microbial ecology, biochemical and nutritional features.}, journal = {International journal of food microbiology}, volume = {374}, number = {}, pages = {109725}, doi = {10.1016/j.ijfoodmicro.2022.109725}, pmid = {35643037}, issn = {1879-3460}, mesh = {Bread/microbiology ; *Edible Grain/microbiology ; Fermentation ; Flour/microbiology ; Food Microbiology ; Lactobacillaceae ; *Lactobacillales ; Saccharomyces cerevisiae ; Weissella ; }, abstract = {The novel cereal 'Tritordeum' was employed in sourdough fermentation for bread making using a traditional backslopping procedure over 10 days. Culture-dependent and culture-independent approaches were used to characterize microbial ecology during sourdough preparation and propagation. Sourdough reached the highest microbial diversity after three days of propagation. Microbial diversity decreased as sourdough reached maturity (day 5). Microbiota dominance shifted from Weissella to Lactiplantibacillus genera after 5 days of propagation. Lactic acid bacteria (LAB) showed a constant increase throughout the propagations starting from 3.9 ± 0.24 log CFU g[-1] on day 0 up to 8.0 ± 0.39 log CFU g[-1] on day 5. Weissella confusa/cibaria and Weissella paramesenteroides were the most prevalent LAB species until day 5 of propagation, while Lactiplantibacillus plantarum was the most prevalent thereafter. Yeasts were present in low cell density (2.0 ± 0.11 log CFU g[-1]) until the fourth backslopping (day 4) and then gradually increased until day 10 (5.0 ± 0.29 log CFU g[-1]), with Saccharomyces cerevisiae being the most prevalent and dominant species. Lactic and acetic acid concentrations increased throughout Tritordeum sourdough propagations, indicative of a proportional decrease of fermentation quotient (lactic acid/acetic acid) from 13.54 ± 1.29 to 4.08 ± 0.15. Utilization of glucose, fructose and sucrose was observed, followed a progressive increase in mannitol concentrations beginning from day 4. The nutritional potential (total phenol content, antioxidant activity, dietary fiber content and total free amino acids) remained elevated during sourdough propagations. Antinutritional factors (phytic acid and raffinose) were reduced to minimal concentrations by day 10. Finally, texture analysis of Tritordeum sourdough bread was demonstrated to have better cohesiveness, resilience and firmness compared to baker's yeast bread, confirming its potential to improve functionality and use in sourdough biotechnology.}, }
@article {pmid35642946, year = {2022}, author = {Ginnan, NA and De Anda, NI and Campos Freitas Vieira, F and Rolshausen, PE and Roper, MC}, title = {Microbial Turnover and Dispersal Events Occur in Synchrony with Plant Phenology in the Perennial Evergreen Tree Crop Citrus sinensis.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0034322}, pmid = {35642946}, issn = {2150-7511}, mesh = {Aged ; Bacteria/genetics ; *Citrus sinensis ; Humans ; *Microbiota ; Phylogeny ; Plants ; }, abstract = {Emerging research indicates that plant-associated microbes can alter plant developmental timing. However, it is unclear if host phenology affects microbial community assembly. Microbiome studies in annual or deciduous perennial plants face challenges in separating effects of tissue age from phenological driven effects on the microbiome. In contrast, evergreen perennial trees, like Citrus sinensis, retain leaves for years, allowing for uniform sampling of similarly aged leaves from the same developmental cohort. This aids in separating phenological effects on the microbiome from impacts due to annual leaf maturation/senescence. Here, we used this system to test the hypothesis that host phenology acts as a driver of microbiome composition. Citrus sinensis leaves and roots were sampled during seven phenological stages. Using amplicon-based sequencing, followed by diversity, phylogenetic, differential abundance, and network analyses, we examined changes in bacterial and fungal communities. Host phenological stage is the main determinant of microbiome composition, particularly within the foliar bacteriome. Microbial enrichment/depletion patterns suggest that microbial turnover and dispersal were driving these shifts. Moreover, a subset of community shifts were phylogenetically conserved across bacterial clades, suggesting that inherited traits contribute to microbe-microbe and/or plant-microbe interactions during specific phenophases. Plant phenology influences microbial community composition. These findings enhance understanding of microbiome assembly and identify microbes that potentially influence plant development and reproduction. IMPORTANCE Research at the forefront of plant microbiome studies indicates that plant-associated microbes can alter the timing of plant development (phenology). However, it is unclear if host phenological stage affects microbial community assembly. Microbiome studies in annual or deciduous perennial plants can face difficulty in separating effects of tissue age from phenological driven effects on the microbiome. Evergreen perennial plants, like sweet orange, maintain mature leaves for multiple years, allowing for uniform sampling of similarly aged tissue across host reproductive stages. Using this system, multiyear sampling, and high-throughput sequencing, we identified plant phenology as a major driver of microbiome composition, particularly within the leaf-associated bacterial communities. Distinct changes in microbial patterns suggest that microbial turnover and dispersal are mechanisms driving these community shifts. Additionally, closely related bacteria have similar abundance patterns across plant stages, indicating that inherited microbial traits may influence how bacteria respond to host developmental changes. Overall, this study illustrates that plant phenology does indeed govern microbiome seasonal shifts and identifies microbial candidates that may affect plant reproduction and development.}, }
@article {pmid35641581, year = {2023}, author = {Hu, S and He, R and Zeng, J and Zhao, D and Wang, S and He, F and Yu, Z and Wu, QL}, title = {Lower Compositional Variation and Higher Network Complexity of Rhizosphere Bacterial Community in Constructed Wetland Compared to Natural Wetland.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {965-979}, pmid = {35641581}, issn = {1432-184X}, support = {2021NIGLAS-CJH01//Project of Young Scientist Group of NIGLAS/ ; QYZDJ-SSW-DQC030//Key Research Program of Frontier Science, CAS/ ; U2040201//National Natural Science Foundation of China/ ; 32022050//National Natural Science Foundation of China/ ; 31730013//National Natural Science Foundation of China/ ; 31971478//National Natural Science Foundation of China/ ; 32171563//National Natural Science Foundation of China/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; }, mesh = {*Wetlands ; Rhizosphere ; RNA, Ribosomal, 16S/genetics/metabolism ; Bacteria ; *Microbiota ; Soil Microbiology ; }, abstract = {Macrophyte rhizosphere microbes, as crucial components of the wetland ecosystem, play an important role in maintaining the function and stability of natural and constructed wetlands. Distinct environmental conditions and management practices between natural and constructed wetlands would affect macrophytes rhizosphere microbial communities and their associated functions. Nevertheless, the understanding of the diversity, composition, and co-occurrence patterns of the rhizosphere bacterial communities in natural and constructed wetlands remains unclear. Here, we used 16S rRNA gene high-throughput sequencing to characterize the bacterial community of the rhizosphere and bulk sediments of macrophyte Phragmites australis in representative natural and constructed wetlands. We observed higher alpha diversity of the bacterial community in the constructed wetland than that of the natural wetland. Additionally, the similarity of bacterial community composition between rhizosphere and bulk sediments in the constructed wetland was increased compared to that of the natural wetland. We also found that plants recruit specific taxa with adaptive functions in the rhizosphere of different wetland types. Rhizosphere samples of the natural wetland significantly enriched the functional bacterial groups that mainly related to nutrient cycling and plant-growth-promoting, while those of the constructed wetland-enriched bacterial taxa with potentials for biodegradation. Co-occurrence network analysis showed that the interactions among rhizosphere bacterial taxa in the constructed wetland were more complex than those of the natural wetland. This study broadens our understanding of the distinct selection processes of the macrophytes rhizosphere-associated microbes and the co-occurrence network patterns in different wetland types. Furthermore, our findings emphasize the importance of plant-microbe interactions in wetlands and further suggest P. australis rhizosphere enriched diverse functional bacteria that might enhance the wetland performance through biodegradation, nutrient cycling, and supporting plant growth.}, }
@article {pmid35640890, year = {2022}, author = {Sadiq, FA and Hansen, MF and Burmølle, M and Heyndrickx, M and Flint, S and Lu, W and Chen, W and Zhang, H}, title = {Trans-kingdom interactions in mixed biofilm communities.}, journal = {FEMS microbiology reviews}, volume = {46}, number = {5}, pages = {}, doi = {10.1093/femsre/fuac024}, pmid = {35640890}, issn = {1574-6976}, mesh = {*Archaea/physiology ; Bacteria/metabolism ; *Biofilms ; Ecosystem ; Plants ; Quorum Sensing ; }, abstract = {The microbial world represents a phenomenal diversity of microorganisms from different kingdoms of life, which occupy an impressive set of ecological niches. Most, if not all, microorganisms once colonize a surface develop architecturally complex surface-adhered communities, which we refer to as biofilms. They are embedded in polymeric structural scaffolds and serve as a dynamic milieu for intercellular communication through physical and chemical signalling. Deciphering microbial ecology of biofilms in various natural or engineered settings has revealed coexistence of microorganisms from all domains of life, including Bacteria, Archaea, and Eukarya. The coexistence of these dynamic microbes is not arbitrary, as a highly coordinated architectural setup and physiological complexity show ecological interdependence and myriads of underlying interactions. In this review, we describe how species from different kingdoms interact in biofilms and discuss the functional consequences of such interactions. We highlight metabolic advances of collaboration among species from different kingdoms, and advocate that these interactions are of great importance and need to be addressed in future research. Since trans-kingdom biofilms impact diverse contexts, ranging from complicated infections to efficient growth of plants, future knowledge within this field will be beneficial for medical microbiology, biotechnology, and our general understanding of microbial life in nature.}, }
@article {pmid35640512, year = {2022}, author = {Piras, F and Nakhla, G and Murgolo, S and De Ceglie, C and Mascolo, G and Bell, K and Jeanne, T and Mele, G and Santoro, D}, title = {Optimal integration of vacuum UV with granular biofiltration for advanced wastewater treatment: Impact of process sequence on CECs removal and microbial ecology.}, journal = {Water research}, volume = {220}, number = {}, pages = {118638}, doi = {10.1016/j.watres.2022.118638}, pmid = {35640512}, issn = {1879-2448}, mesh = {Charcoal/chemistry ; Oxidation-Reduction ; Ultraviolet Rays ; Vacuum ; Wastewater/chemistry ; *Water Pollutants, Chemical/chemistry ; *Water Purification ; *Zeolites ; }, abstract = {This study explored process synergies attainable by integrating a vacuum ultraviolet-based advanced oxidation process with biofiltration. A comparison using granular activated carbon or granular zeolite as filtration media were examined in context of advanced wastewater treatment for potable reuse. Six biofiltration columns, three with granular activated carbon and three with granular zeolite, were operated in parallel and batch-fed daily with nitrified secondary effluent. After achieving a pseudo-steady state through the filter columns, vacuum ultraviolet treatment was applied as pre-treatment or as post-treatment, at two different applied energies (i.e., VUV-E1=1 kWh/m[3] and VUV-E10=10 kWh/m[3]). Once granular activated carbon had transitioned to biologically activated carbon, as determined based on soluble chemical oxygen demand removal, adsorption was still observed as the main mechanism for contaminants of emerging concern and nitrate removal. Vacuum ultraviolet pre-treatment markedly improved contaminants of emerging concern removal through the integrated system, achieving 40% at VUV-E1 and 90% at VUV-E10. When applied as post-treatment to zeolite column effluents, VUV-E1 and VUV-E10 further increased contaminants of emerging concern removal by 20% and 90%, respectively. In the zeolite system, vacuum ultraviolet pre-treatment also increased soluble chemical oxygen demand removal efficiency, indicating that higher energy vacuum ultraviolet increased biodegradability. Total prokaryotes were two-fold more abundant in biologically activated carbon than in zeolite, with vacuum ultraviolet pretreatment markedly affecting microbial diversity, both in terms of richness and composition. Media type only marginally affected microbial richness in the biofilters but showed a marked impact on structural composition. No clear relationship between compositional structure and depth was observed.}, }
@article {pmid35638872, year = {2022}, author = {Jonassen, KR and Ormåsen, I and Duffner, C and Hvidsten, TR and Bakken, LR and Vick, SHW}, title = {A Dual Enrichment Strategy Provides Soil- and Digestate-Competent Nitrous Oxide-Respiring Bacteria for Mitigating Climate Forcing in Agriculture.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0078822}, pmid = {35638872}, issn = {2150-7511}, mesh = {Agriculture ; Bacteria/genetics/metabolism ; Denitrification ; Fertilizers/analysis ; *Nitrous Oxide/metabolism ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {Manipulating soil metabolism through heavy inoculation with microbes is feasible if organic wastes can be utilized as the substrate for growth and vector as a fertilizer. This, however, requires organisms active in both digestate and soil (generalists). Here, we present a dual enrichment strategy to enrich and isolate such generalists among N2O-respiring bacteria (NRB) in soil and digestates, to be used as an inoculum for strengthening the N2O-reduction capacity of soils. The enrichment strategy utilizes sequential batch enrichment cultures alternating between sterilized digestate and soil as substrates, with each batch initiated with limited O2 and unlimited N2O. The cultures were monitored for gas kinetics and community composition. As predicted by a Lotka-Volterra competition model, cluster analysis identified generalist operational taxonomic units (OTUs) which became dominant, digestate/soil-specialists which did not, and a majority that were gradually diluted out. We isolated several NRBs circumscribed by generalist OTUs. Their denitrification genes and phenotypes predicted a variable capacity to act as N2O-sinks, while all genomes predicted broad catabolic capacity. The latter contrasts with previous attempts to enrich NRB by anaerobic incubation of unsterilized digestate only, which selected for organisms with a catabolic capacity limited to fermentation products. The two isolates with the most promising characteristics as N2O sinks were a Pseudomonas sp. with a full-fledged denitrification-pathway and a Cloacibacterium sp. carrying only N2O reductase (clade II), and soil experiments confirmed their capacity to reduce N2O-emissions from soil. The successful enrichment of NRB with broad catabolic spectra suggests that the concept of dual enrichment should also be applicable for enrichment of generalists with traits other than N2O reduction. IMPORTANCE N2O emissions from farmed soils are a major source of climate forcing. Here, denitrifying bacteria act as both source and sink for N2O, determined by regulatory traits or the absence of genes coding for the enzymes producing or reducing N2O. One approach to reducing emissions is to amend large numbers of N2O-reducing bacteria (NRB) to soil. This was shown to be feasible by growing NRB to high densities in organic wastes and then applying them as fertilizers. The effect on N2O emissions, however, was transient because the isolated NRBs were unsuited to soil. Here, we have developed an enrichment strategy selecting for organisms with generalist lifestyles, tolerant of rapid environmental changes. This was used to isolate robust NRBs that grow both in digestate and when amended to soils. This strategy opens an avenue for obtaining not just robust NRBs to reduce N2O emissions, but any organism destined for application to complex environments.}, }
@article {pmid35638840, year = {2022}, author = {Zhang, S and Xia, X and Wang, J and Li, X and Xin, Y and Bao, J and Han, L and Qin, W and Yang, Z}, title = {Biogeographic Patterns and Elevational Differentiation of Sedimentary Bacterial Communities across River Systems in China.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {12}, pages = {e0059722}, pmid = {35638840}, issn = {1098-5336}, mesh = {Bacteria/genetics ; Biodiversity ; China ; *Ecosystem ; *Rivers/microbiology ; }, abstract = {Bacterial biodiversity is tightly correlated with ecological functions of natural systems, and bacterial rare and abundant subcommunities make distinct contributions to ecosystem functioning. However, the biogeographic pattern and elevational differentiation of sedimentary bacterial diversity have rarely been studied in cross-river systems at a continental scale. This study analyzed the biogeographic patterns and elevational differentiations of the entire, abundant, and rare bacterial (sub)communities as well as the underlying mechanisms across nine rivers that span distinct geographic regions and large elevational gradients in China. We found that bacterial rare and abundant subcommunities shared similar biogeographic patterns and both demonstrated strong distance-decay relationships, despite their distinct community compositions. However, both null model and variation partitioning analysis results showed that while environmental selection governed rare subcommunity assemblies (contribution: 51.9%), dispersal limitation (62.7%) controlled the assembly of abundant subcommunities. The disparity was associated with the broader threshold width of abundant taxa to water temperature and pH variations than rare taxa. Elevation-induced bacterial composition variations were more evident than latitude-induced ones. Some specific operational taxonomic units (OTUs), representing 16.4% of the total sequences, much preferentially and even exclusively lived in high-elevation or low-elevation habitats and demonstrated some adaptations to local conditions. Greater positive: negative link ratios in bacterial co-occurrence networks of low elevations than high elevations (P < 0.05) partly resulted from their harboring higher organic carbon: nitrogen ratios. Together, this study draws a biogeographic picture of sedimentary bacterial communities in a continental-scale riverine system and highlights the importance of incorporating elevation-associated patterns of microbial diversity into riverine microbial ecology studies. IMPORTANCE Bacterial diversity is tightly correlated with the nutrient cycling of river systems. However, previous studies on bacterial diversity are mainly constrained to one single river system, although microbial biogeography and its drivers exhibit strong spatial scale dependence. Moreover, elevational differentiations of bacterial communities across river systems have also rarely been studied. Bacterial rare and abundant subcommunities make distinct contributions to ecosystem functioning, and they share similar biogeographic patterns in some environments but not in others. Therefore, we explored the biogeography of the entire, abundant, and rare (sub)communities in nine rivers that cover a wide space range and large elevational gradient in China. Our results revealed that bacterial rare and abundant subcommunities shared similar biogeographic patterns but their assembly mechanisms were much different in these rivers. Moreover, bacterial communities showed evident differentiations between high elevations and low elevations. These findings will facilitate a better understanding of bacterial diversity features in river systems.}, }
@article {pmid35633375, year = {2023}, author = {Araujo, ASF and de Araujo Pereira, AP and Melo, VMM and de Medeiros, EV and Mendes, LW}, title = {Environmental DNA Sequencing to Monitor Restoration Practices on Soil Bacterial and Archaeal Communities in Soils Under Desertification in the Brazilian Semiarid.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {1072-1076}, pmid = {35633375}, issn = {1432-184X}, mesh = {Humans ; *Archaea/genetics ; Soil/chemistry ; *DNA, Environmental ; Conservation of Natural Resources ; Brazil ; Soil Microbiology ; Bacteria/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Soils from Brazilian semiarid regions are highly vulnerable to desertification due to their geology, climate, human actions, and intensive land use that contribute to desertification. Therefore, areas under desertification have increased in the Brazilian semiarid region and it has negatively changed the soil bacterial and archaeal communities and their functionality. On the other hand, although restoration strategies are expensive and there are few soils restoration programs, some practices have been applied to restore these soils under desertification. For instance, conservationist practices and grazing exclusion have been strategically implemented, and they created a new altered soil condition for soil microbial communities, boosting soil microbial diversity. Here, we discuss the potential of these restoration strategies to recover the richness and diversity of soil bacterial and archaeal communities that were described through environmental DNA (eDNA) sequencing of soil samples. eDNA sequencing results show that areas where restoration strategies have been applied in regions under desertification in the Brazilian semiarid have increased species richness, diversity, and structure of the bacterial and archaeal community. In addition, network connectivity and functionality of the soil microorganisms have been improved over time. Altogether, we show that management strategies for soil restoration have positive effects on soil microbial communities and these effects can be monitored using the eDNA sequencing approach.}, }
@article {pmid35633186, year = {2022}, author = {Ravegnini, G and Fosso, B and Ricci, R and Gorini, F and Turroni, S and Serrano, C and Pilco-Janeta, DF and Zhang, Q and Zanotti, F and De Robertis, M and Nannini, M and Pantaleo, MA and Hrelia, P and Angelini, S}, title = {Analysis of microbiome in gastrointestinal stromal tumors: Looking for different players in tumorigenesis and novel therapeutic options.}, journal = {Cancer science}, volume = {113}, number = {8}, pages = {2590-2599}, pmid = {35633186}, issn = {1349-7006}, support = {//FG and FZ were supported by the Fondazione Cassa di Risparmio di Bologna (CARISBO)/ ; }, mesh = {Cell Transformation, Neoplastic ; *Gastrointestinal Neoplasms/genetics ; *Gastrointestinal Stromal Tumors/genetics/pathology ; Humans ; *Microbiota ; Mutation ; Proto-Oncogene Proteins c-kit/genetics ; }, abstract = {Preclinical forms of gastrointestinal stromal tumor (GIST), small asymptomatic lesions, called microGIST, are detected in approximately 30% of the general population. Gastrointestinal stromal tumor driver mutation can be already detected in microGISTs, even if they do not progress into malignant cancer; these mutations are necessary, but insufficient events to foster tumor progression. Here we profiled the tissue microbiota of 60 gastrointestinal specimens in three different patient cohorts-micro, low-risk, and high-risk or metastatic GIST-exploring the compositional structure, predicted function, and microbial networks, with the aim of providing a complete overview of microbial ecology in GIST and its preclinical form. Comparing microGISTs and GISTs, both weighted and unweighted UniFrac and Bray-Curtis dissimilarities showed significant community-level separation between them and a pronounced difference in Proteobacteria, Firmicutes, and Bacteroidota was observed. Through the LEfSe tool, potential microbial biomarkers associated with a specific type of lesion were identified. In particular, GIST samples were significantly enriched in the phylum Proteobacteria compared to microGISTs. Several pathways involved in sugar metabolism were also highlighted in GISTs; this was expected as cancer usually displays high aerobic glycolysis in place of oxidative phosphorylation and rise of glucose flux to promote anabolic request. Our results highlight that specific differences do exist in the tissue microbiome community between GIST and benign lesions and that microbiome restructuration can drive the carcinogenesis process.}, }
@article {pmid35631287, year = {2022}, author = {Sauvaitre, T and Van Herreweghen, F and Delbaere, K and Durif, C and Van Landuyt, J and Fadhlaoui, K and Huille, S and Chaucheyras-Durand, F and Etienne-Mesmin, L and Blanquet-Diot, S and Van de Wiele, T}, title = {Lentils and Yeast Fibers: A New Strategy to Mitigate Enterotoxigenic Escherichia coli (ETEC) Strain H10407 Virulence?.}, journal = {Nutrients}, volume = {14}, number = {10}, pages = {}, pmid = {35631287}, issn = {2072-6643}, mesh = {Caco-2 Cells ; Diarrhea ; Dietary Fiber/pharmacology ; *Enterotoxigenic Escherichia coli ; *Escherichia coli Infections/prevention &amp; control ; Humans ; *Lens Plant ; Plant Extracts ; Saccharomyces cerevisiae ; Travel ; Virulence ; }, abstract = {Dietary fibers exhibit well-known beneficial effects on human health, but their anti-infectious properties against enteric pathogens have been poorly investigated. Enterotoxigenic Escherichia coli (ETEC) is a major food-borne pathogen that causes acute traveler's diarrhea. Its virulence traits mainly rely on adhesion to an epithelial surface, mucus degradation, and the secretion of two enterotoxins associated with intestinal inflammation. With the increasing burden of antibiotic resistance worldwide, there is an imperious need to develop novel alternative strategies to control ETEC infections. This study aimed to investigate, using complementary in vitro approaches, the inhibitory potential of two dietary-fiber-containing products (a lentil extract and yeast cell walls) against the human ETEC reference strain H10407. We showed that the lentil extract decreased toxin production in a dose-dependent manner, reduced pro-inflammatory interleukin-8 production, and modulated mucus-related gene induction in ETEC-infected mucus-secreting intestinal cells. We also report that the yeast product reduced ETEC adhesion to mucin and Caco-2/HT29-MTX cells. Both fiber-containing products strengthened intestinal barrier function and modulated toxin-related gene expression. In a complex human gut microbial background, both products did not elicit a significant effect on ETEC colonization. These pioneering data demonstrate the promising role of dietary fibers in controlling different stages of the ETEC infection process.}, }
@article {pmid35630477, year = {2022}, author = {Johnson, MS and Burns, BP and Herdean, A and Angeloski, A and Ralph, P and Morris, T and Kindler, G and Wong, HL and Kuzhiumparambil, U and Sedger, LM and Larkum, AWD}, title = {A Cyanobacteria Enriched Layer of Shark Bay Stromatolites Reveals a New Acaryochloris Strain Living in Near Infrared Light.}, journal = {Microorganisms}, volume = {10}, number = {5}, pages = {}, pmid = {35630477}, issn = {2076-2607}, abstract = {The genus Acaryochloris is unique among phototrophic organisms due to the dominance of chlorophyll d in its photosynthetic reaction centres and light-harvesting proteins. This allows Acaryochloris to capture light energy for photosynthesis over an extended spectrum of up to ~760 nm in the near infra-red (NIR) spectrum. Acaryochloris sp. has been reported in a variety of ecological niches, ranging from polar to tropical shallow aquatic sites. Here, we report a new Acarychloris strain isolated from an NIR-enriched stratified microbial layer 4-6 mm under the surface of stromatolite mats located in the Hamelin Pool of Shark Bay, Western Australia. Pigment analysis by spectrometry/fluorometry, flow cytometry and spectral confocal microscopy identifies unique patterns in pigment content that likely reflect niche adaption. For example, unlike the original A. marina species (type strain MBIC11017), this new strain, Acarychloris LARK001, shows little change in the chlorophyll d/a ratio in response to changes in light wavelength, displays a different Fv/Fm response and lacks detectable levels of phycocyanin. Indeed, 16S rRNA analysis supports the identity of the A. marina LARK001 strain as close to but distinct from from the A. marina HICR111A strain first isolated from Heron Island and previously found on the Great Barrier Reef under coral rubble on the reef flat. Taken together, A. marina LARK001 is a new cyanobacterial strain adapted to the stromatolite mats in Shark Bay.}, }
@article {pmid35630422, year = {2022}, author = {Scoma, A and Khor, WC and Coma, M and Heyer, R and Props, R and Bouts, T and Benndorf, D and Li, D and Zhang, H and Rabaey, K}, title = {Lignocellulose Fermentation Products Generated by Giant Panda Gut Microbiomes Depend Ultimately on pH Rather than Portion of Bamboo: A Preliminary Study.}, journal = {Microorganisms}, volume = {10}, number = {5}, pages = {}, pmid = {35630422}, issn = {2076-2607}, abstract = {Giant pandas feed almost exclusively on bamboo but miss lignocellulose-degrading genes. Their gut microbiome may contribute to their nutrition; however, the limited access to pandas makes experimentation difficult. In vitro incubation of dung samples is used to infer gut microbiome activity. In pandas, such tests indicated that green leaves are largely fermented to ethanol at neutral pH and yellow pith to lactate at acidic pH. Pandas may feed on either green leaves or yellow pith within the same day, and it is unclear how pH, dung sample, fermentation products and supplied bamboo relate to one another. Additionally, the gut microbiome contribution to solid bamboo digestion must be appropriately assessed. Here, gut microbiomes derived from dung samples with mixed colors were used to ferment green leaves, also by artificially adjusting the initial pH. Gut microbiomes digestion of solid lignocellulose accounted for 30-40% of the detected final fermentation products. At pH 6.5, mixed-color dung samples had the same fermentation profile as green dung samples (mainly alcohols), while adjusting the initial pH to 4.5 resulted in the profile of yellow dung samples (mainly lactate). Metaproteomics confirmed that gut microbiomes attacked hemicellulose, and that the panda's alpha amylase was the predominant enzyme (up to 75%).}, }
@article {pmid35630387, year = {2022}, author = {Smercina, D and Zambare, N and Hofmockel, K and Sadler, N and Bredeweg, EL and Nicora, C and Markillie, LM and Aufrecht, J}, title = {Synthetic Soil Aggregates: Bioprinted Habitats for High-Throughput Microbial Metaphenomics.}, journal = {Microorganisms}, volume = {10}, number = {5}, pages = {}, pmid = {35630387}, issn = {2076-2607}, abstract = {The dynamics of microbial processes are difficult to study in natural soil, owing to the small spatial scales on which microorganisms operate and to the opacity and chemical complexity of the soil habitat. To circumvent these challenges, we have created a 3D-bioprinted habitat that mimics aspects of natural soil aggregates while providing a chemically defined and translucent alternative culturing method for soil microorganisms. Our Synthetic Soil Aggregates (SSAs) retain the porosity, permeability, and patchy resource distribution of natural soil aggregates-parameters that are expected to influence emergent microbial community interactions. We demonstrate the printability and viability of several different microorganisms within SSAs and show how the SSAs can be integrated into a multi-omics workflow for single SSA resolution genomics, metabolomics, proteomics, lipidomics, and biogeochemical assays. We study the impact of the structured habitat on the distribution of a model co-culture microbial community and find that it is significantly different from the spatial organization of the same community in liquid culture, indicating a potential for SSAs to reproduce naturally occurring emergent community phenotypes. The SSAs have the potential as a tool to help researchers quantify microbial scale processes in situ and achieve high-resolution data from the interplay between environmental properties and microbial ecology.}, }
@article {pmid35628778, year = {2022}, author = {Tao, S and Zhang, Y and Tian, C and Duplessis, S and Zhang, N}, title = {Elevated Ozone Concentration and Nitrogen Addition Increase Poplar Rust Severity by Shifting the Phyllosphere Microbial Community.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {5}, pages = {}, pmid = {35628778}, issn = {2309-608X}, support = {2021ZY02//Fundamental Research Funds for the Central Universities/ ; 2021M690418//China Postdoctoral Science Foundation/ ; }, abstract = {Tropospheric ozone and nitrogen deposition are two major environmental pollutants. A great deal of research has focused on the negative impacts of elevated O3 and the complementary effect of soil N addition on the physiological properties of trees. However, it has been overlooked how elevated O3 and N addition affect tree immunity in face of pathogen infection, as well as of the important roles of phyllosphere microbiome community in host-pathogen-environment interplay. Here, we examined the effects of elevated O3 and soil N addition on poplar leaf rust [Melampsora larici-populina] severity of two susceptible hybrid poplars [clone '107': Populus euramericana cv. '74/76'; clone '546': P. deltoides Í P. cathayana] in Free-Air-Controlled-Environment plots, in addition, the link between Mlp-susceptibility and changes in microbial community was determined using Miseq amplicon sequencing. Rust severity of clone '107' significantly increased under elevated O3 or N addition only; however, the negative impact of elevated O3 could be significantly mitigated when accompanied by N addition, likewise, this trade-off was reflected in its phyllosphere microbial α-diversity responding to elevated O3 and N addition. However, rust severity of clone '546' did not differ significantly in the cases of elevated O3 and N addition. Mlp infection altered microbial community composition and increased its sensitivity to elevated O3, as determined by the markedly different abundance of taxa. Elevated O3 and N addition reduced the complexity of microbial community, which may explain the increased severity of poplar rust. These findings suggest that poplars require a changing phyllosphere microbial associations to optimize plant immunity in response to environmental changes.}, }
@article {pmid35624481, year = {2022}, author = {Tian, Z and Pu, H and Cai, D and Luo, G and Zhao, L and Li, K and Zou, J and Zhao, X and Yu, M and Wu, Y and Yang, T and Guo, P and Hu, X}, title = {Characterization of the bacterial microbiota in different gut and oral compartments of splendid japalure (Japalura sensu lato).}, journal = {BMC veterinary research}, volume = {18}, number = {1}, pages = {205}, pmid = {35624481}, issn = {1746-6148}, support = {2019QD09//Doctor Launch Project of Yibin University/ ; 2019QD10//Doctor Launch Project of Yibin University/ ; XDA 20050201//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2019QZKK05010105//Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; }, mesh = {Animals ; Bacteria/genetics ; Bacteroidetes/genetics ; Feces/microbiology ; Firmicutes/genetics ; *Lizards ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Gut and oral microbes form complex communities and play key roles in co-evolution with their hosts. However, little is understood about the bacterial community in lizards.<br><br>RESULTS: In this study, we investigated the gut and oral bacterial communities in Japalura sensu lato from Sichuan Province, China, using 16S rRNA gene sequencing. Results showed that Bacteroidota (36.5%) and Firmicutes (32.8%) were the main phyla in the gut, while Proteobacteria, Bacteroidota, Firmicutes, and Actinobacteriota were the dominant phyla in the oral cavity. 16&#xa0;S rRNA sequencing analysis of fecal samples showed that: (1) Bacteroidota was the most abundant in Japalura sensu lato, which was different from the bacterial community of insectivorous animals; (2) Bacteroidota, Firmicutes, Actinobacteriota, Fusobacteriota, and Cyanobacteria were the most abundant phylum in Japalura sensu lato. (3) Proteobacteria was the dominant phylum in Japalura sensu lato and other domestic insectivorous lizards (Shinisaurus crocodilurus, Phrynocephalus vlangalii, and Takydromus septentrionalis); (4) Comparing with the bacterial community of Shinisaurus crocodilurus, Phrynocephalus vlangalii, Takydromus septentrionalis, Liolaemus parvus, L. ruibali, and Phymaturus williamsi, Desulfobacterota was uniquely present in the gut of Japalura sensu lato. 16&#xa0;S rRNA sequencing of oral samples showed that Chloroflexi and Deinococcota phyla were enriched in the oral cavity, which may have a significant influence on living in extreme environments.<br><br>CONCLUSIONS: Thus, based on 16&#xa0;S rRNA sequencing analysis of the community composition of the gut and oral microbiomes, this study firstly represents a foundation for understanding the gut and oral microbial ecology of Japalura sensu lato, and constitutes a detail account of the diversity of the microbiota inhabiting the gut and oral cavity of Japalura sensu lato. Further researches will continue to reveal how gut and oral microbial communities may be impacting the ecology and evolution of lizards.}, }
@article {pmid35624343, year = {2023}, author = {Vázquez, V and León, P and Gordillo, FJL and Jiménez, C and Concepción, I and Mackenzie, K and Bresnan, E and Segovia, M}, title = {High-CO2 Levels Rather than Acidification Restrict Emiliania huxleyi Growth and Performance.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {127-143}, pmid = {35624343}, issn = {1432-184X}, support = {FC14-RNM-27//Universidad de M&#xe1;laga/ ; }, mesh = {*Seawater ; *Haptophyta/physiology ; Carbon Dioxide/metabolism ; Hydrogen-Ion Concentration ; Photosynthesis ; }, abstract = {The coccolithophore Emiliania huxleyi shows a variety of responses to ocean acidification (OA) and to high-CO2 concentrations, but there is still controversy on differentiating between these two factors when using different strains and culture methods. A heavily calcified type A strain isolated from the Norwegian Sea was selected and batch cultured in order to understand whether acclimation to OA was mediated mainly by CO2 or H[+], and how it impacted cell growth performance, calcification, and physiological stress management. Emiliania huxleyi responded differently to each acidification method. CO2-enriched aeration (1200 µatm, pH 7.62) induced a negative effect on the cells when compared to acidification caused by decreasing pH alone (pH 7.60). The growth rates of the coccolithophore were more negatively affected by high pCO2 than by low pH without CO2 enrichment with respect to the control (400 µatm, pH 8.1). High CO2 also affected cell viability and promoted the accumulation of reactive oxygen species (ROS), which was not observed under low pH. This suggests a possible metabolic imbalance induced by high CO2 alone. In contrast, the affinity for carbon uptake was negatively affected by both low pH and high CO2. Photochemistry was only marginally affected by either acidification method when analysed by PAM fluorometry. The POC and PIC cellular quotas and the PIC:POC ratio shifted along the different phases of the cultures; consequently, calcification did not follow the same pattern observed in cell stress and growth performance. Specifically, acidification by HCl addition caused a higher proportion of severely deformed coccoliths, than CO2 enrichment. These results highlight the capacity of CO2 rather than acidification itself to generate metabolic stress, not reducing calcification.}, }
@article {pmid35622094, year = {2023}, author = {Zhang, Z and Zhao, H and Mou, S and Nair, S and Zhao, J and Jiao, N and Zhang, Y}, title = {Phage Infection Benefits Marine Diatom Phaeodactylum tricornutum by Regulating the Associated Bacterial Community.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {144-153}, pmid = {35622094}, issn = {1432-184X}, support = {2020YFA0608304//National Key Research and Development Programs of China/ ; }, mesh = {*Diatoms/physiology ; *Bacteriophages ; Bacteria ; Aquatic Organisms ; }, abstract = {The interaction between marine phyto- and bacterioplankton is regulated by multiple environmental and biological factors. Among them, phages as the major regulators of bacterial mortality are considered to have important impacts on algae-associated bacteria and algae-bacteria relationship. However, little is currently known about the actual impact of phages from this perspective. Here, we revealed that phage infection improved the maximum quantum efficiency of photosystem II of Phaeodactylum tricornutum by regulating the associated bacterial community. Specifically, phage infection weakened bacterial abundance and eliminated their negative effects on the diatom. Unexpectedly, the structure of the bacterial community co-cultured with the diatom was not significantly affected, likely because the shaping effect of the diatom on the bacterial community structure can far outcompete or mask the impact of phage infection. Our results established a link between algae, bacteria, and phages, suggesting that phage infection benefits the diatom by regulating the associated bacterial community.}, }
@article {pmid35620054, year = {2022}, author = {Yaigoub, H and Tirichen, H and Xin, X and Shi, S and Wu, C and Li, R and Li, Y}, title = {Isolation of Viable Single Cells With High Yield and Purity Using a Small Amount of Human Kidney Tissue Biopsy.}, journal = {Frontiers in cell and developmental biology}, volume = {10}, number = {}, pages = {822275}, pmid = {35620054}, issn = {2296-634X}, abstract = {Objective: Establishment of an efficient method of preparing human kidney single cell suspension, using a very small amount of tissue puncture. Methods: Samples of human kidney tissue puncture were cut into pieces, and then 80 μL of the digestive enzyme were added to each punctured tissue to induce enzymatic digestion. The enzyme combination is composed of collagenases, DNase and hyaluronidase and the sample was incubated 20 min at 37°C. The obtained cell suspension was filtered through a 70 μm cell strainer, centrifuged at 300 g for 5 min and the supernatant was removed, then the pellet was resuspended in 3 ml of DMEM (Dulbecco's Modified Eagle's Medium). Cell suspension was sorted and purified by flow sorting to remove dead cells and obtain a cell suspension with higher viability rate. Results: We found that 1) diverse single cells of human kidney can be obtained by the digestive enzyme, as observed under the light microscope, with different sizes, normal cell morphology and good dispersion. 2) (2-3) × 10[6] single cells can be extracted from one fresh punctured kidney tissue of about 10 mg, with a cell viability rate of more than 80%. Conclusion: In this work we generated a comprehensive and high-resolution single-cell method, which is simple and efficient for preparing single cell suspension from a minimal amount of human kidney tissue. This method can facilitate the study of renal cell biology and the pathogenesis of kidney diseases.}, }
@article {pmid35618944, year = {2023}, author = {Lau, NS and Ting, SY and Sam, KK and M, J and Wong, SC and Wu, X and Waiho, K and Fazhan, H and Shu-Chien, AC}, title = {Comparative Analyses of Scylla olivacea Gut Microbiota Composition and Function Suggest the Capacity for Polyunsaturated Fatty Acid Biosynthesis.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {575-588}, pmid = {35618944}, issn = {1432-184X}, mesh = {Animals ; *Brachyura ; *Gastrointestinal Microbiome ; Fatty Acids, Unsaturated/metabolism ; Diet ; Lipid Metabolism ; }, abstract = {Although numerous studies in aquatic organisms have linked lipid metabolism with intestinal bacterial structure, the possibility of the gut microbiota participating in the biosynthesis of beneficial long-chain polyunsaturated fatty acid (LC-PUFA) remains vague. We profiled the gut microbiota of the mud crab Scylla olivacea fed with either a LC-PUFA rich (FO) or a LC-PUFA-poor but C18-PUFA substrate-rich (LOCO) diet. Additionally, a diet with a similar profile as LOCO but with the inclusion of an antibiotic, oxolinic acid (LOCOAB), was also used to further demarcate the possibility of LC-PUFA biosynthesis in gut microbiota. Compared to diet FO treatment, crabs fed diet LOCO contained a higher proportion of Proteobacteria, notably two known taxonomy groups with PUFA biosynthesis capacity, Vibrio and Shewanella. Annotation of metagenomic datasets also revealed enrichment in the KEGG pathway of unsaturated fatty acid biosynthesis and polyketide synthase-like system sequences with this diet. Intriguingly, diet LOCOAB impeded the presence of Vibrio and Shewanella and with it, the function of unsaturated fatty acid biosynthesis. However, there was an increase in the function of short-chain fatty acid production, accompanied by a shift towards the abundance of phyla Bacteroidota and Spirochaetota. Collectively, these results exemplified bacterial communities and their corresponding PUFA biosynthesis pathways in the microbiota of an aquatic crustacean species.}, }
@article {pmid35617903, year = {2022}, author = {Xiong, C and Calatayud, M and van de Wiele, T and Francesconi, K}, title = {Gut microbiota metabolize arsenolipids in a donor dependent way.}, journal = {Ecotoxicology and environmental safety}, volume = {239}, number = {}, pages = {113662}, doi = {10.1016/j.ecoenv.2022.113662}, pmid = {35617903}, issn = {1090-2414}, support = {I 2412/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Arsenic/analysis ; *Arsenicals/chemistry ; Chromatography, High Pressure Liquid/methods ; Ecosystem ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {Understanding the interplay between the gut microbiome and arsenolipids can help us manage the potential health risk of consuming seafood, but little is known about the bioconversion fate of arsenolipids in the gastrointestinal tract. We use an in vitro mucosal simulator of the human intestinal microbial ecosystem (M-SHIME) to mimic the digestive tract of four healthy donors during exposure to two arsenolipids (an arsenic fatty acid AsFA 362 or an arsenic hydrocarbon AsHC 332). The metabolites were analyzed by HPLC-mass spectrometry. The human gut bacteria accumulated arsenolipids in a donor-dependent way, with higher retention of AsHC 332. Colonic microbiota partly transformed both arsenolipids to their thioxo analogs, while AsFA 362 was additionally transformed into arsenic-containing fatty esters, arsenic-containing fatty alcohols, and arsenic-containing sterols. There was no significant difference in water-soluble arsenicals between arsenolipid treatments. The study shows that arsenolipids can be quickly biotransformed into several lipid-soluble arsenicals of unknown toxicity, which cannot be excluded when considering potential implications on human health.}, }
@article {pmid35615500, year = {2022}, author = {Laber, CP and Pontiller, B and Bunse, C and Osbeck, CMG and Pérez-Martínez, C and Di Leo, D and Lundin, D and Legrand, C and Pinhassi, J and Farnelid, H}, title = {Seasonal and Spatial Variations in Synechococcus Abundance and Diversity Throughout the Gullmar Fjord, Swedish Skagerrak.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {828459}, pmid = {35615500}, issn = {1664-302X}, abstract = {The picophytoplankton Synechococcus is a globally abundant autotroph that contributes significantly to primary production in the oceans and coastal areas. These cyanobacteria constitute a diverse genus of organisms that have developed independent niche spaces throughout aquatic environments. Here, we use the 16S V3-V4 rRNA gene region and flow cytometry to explore the diversity of Synechococcus within the picophytoplankton community in the Gullmar Fjord, on the west coast of Sweden. We conducted a station-based 1-year time series and two transect studies of the fjord. Our analysis revealed that within the large number of Synechococcus amplicon sequence variants (ASVs; 239 in total), prevalent ASVs phylogenetically clustered with clade representatives in both marine subcluster 5.1 and 5.2. The near-surface composition of ASVs shifted from spring to summer, when a 5.1 subcluster dominated community developed along with elevated Synechococcus abundances up to 9.3 × 10[4] cells ml[-1]. This seasonal dominance by subcluster 5.1 was observed over the length of the fjord (25 km), where shifts in community composition were associated with increasing depth. Unexpectedly, the community shift was not associated with changes in salinity. Synechococcus abundance dynamics also differed from that of the photosynthetic picoeukaryote community. These results highlight how seasonal variations in environmental conditions influence the dynamics of Synechococcus clades in a high latitude threshold fjord.}, }
@article {pmid35610383, year = {2023}, author = {Pierangeli, GMF and Domingues, MR and Choueri, RB and Hanisch, WS and Gregoracci, GB and Benassi, RF}, title = {Spatial Variation and Environmental Parameters Affecting the Abundant and Rare Communities of Bacteria and Archaea in the Sediments of Tropical Urban Reservoirs.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {297-310}, pmid = {35610383}, issn = {1432-184X}, mesh = {*Archaea/genetics ; *Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Water Quality ; }, abstract = {Microbial communities in freshwater sediments play an important role in organic matter remineralization, contributing to biogeochemical cycles, nutrient release, and greenhouse gases emissions. Bacterial and archaeal communities might show spatial or seasonal patterns and were shown to be influenced by distinct environmental parameters and anthropogenic activities, including pollution and damming. Here, we determined the spatial variation and the environmental variables influencing the abundant and rare bacterial and archaeal communities in the sediments of eutrophic-hypereutrophic reservoirs from a tropical urban area in Brazil. The most abundant microbes included mainly Anaerolineae and Deltaproteobacteria genera from the Bacteria domain, and Methanomicrobia genera from the Archaea domain. Microbial communities differed spatially in each reservoir, reflecting the establishment of specific environmental conditions. Locations with better or worst water quality, or close to a dam, showed more distinct microbial communities. Besides the water column depth, microbial communities were affected by some pollution indicators, including total phosphorus, orthophosphate, electrical conductivity, and biochemical oxygen demand. Distinct proportions of variation were explained by spatial and environmental parameters for each microbial community. Furthermore, spatial variations in environmental parameters affecting these communities, especially the most distinct ones, contributed to microbial variations mediated by spatial and environmental properties together. Finally, our study showed that different pressures in each reservoir affected the sediment microbiota, promoting different responses and possible adaptations of abundant and rare bacterial and archaeal communities.}, }
@article {pmid35610382, year = {2023}, author = {Dhar, K and Panneerselvan, L and Subashchandrabose, SR and Venkateswarlu, K and Megharaj, M}, title = {Anaerobic Degradation of Naphthalene and Pyrene by Sulfate-Reducing Cultures Enriched from Former Manufactured Gas Plant Soil.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {271-281}, pmid = {35610382}, issn = {1432-184X}, support = {RTP scholarship//University of Newcastle/ ; }, mesh = {Anaerobiosis ; *Sulfates/metabolism ; Naphthalenes/metabolism ; *Polycyclic Aromatic Hydrocarbons/metabolism ; Pyrenes ; Biodegradation, Environmental ; }, abstract = {Biodegradation of polycyclic aromatic hydrocarbons (PAHs) under completely anaerobic sulfate-reducing conditions is an energetically challenging process. To date, anaerobic degradations of only two-ringed naphthalene and three-ringed phenanthrene by sediment-free and enriched sulfate-reducing bacteria have been reported. In this study, sulfate-reducing enrichment cultures capable of degrading naphthalene and four-ringed PAH, pyrene, were enriched from a contaminated former gas plant site soil. Bacterial community composition analysis revealed that a naphthalene-degrading enrichment culture, MMNap, was dominated (84.90%) by a Gram-positive endospore-forming member of the genus Desulfotomaculum with minor contribution (8.60%) from a member of Clostridium. The pyrene-degrading enrichment, MMPyr, was dominated (97.40%) by a species of Desulfotomaculum. The sequences representing the Desulfotomaculum phylotypes shared 98.80% similarity to each other. After 150 days of incubation, MMNap degraded 195 µM naphthalene with simultaneous reduction of sulfate and accumulation of sulfide. Similarly, MMPyr degraded 114 µM pyrene during 180 days of incubation with nearly stochiometric sulfate consumption and sulfide accumulation. In both cases, the addition of sulfate reduction inhibitor, molybdate (20 mM), resulted in complete cessation of the substrate utilization and sulfate reduction that clearly indicated the major role of the sulfate-reducing Desulfotomaculum in biodegradation of the two PAHs. This study is the first report on anaerobic pyrene degradation by a matrix-free, strictly anaerobic, and sulfate-reducing enrichment culture.}, }
@article {pmid35609949, year = {2022}, author = {De Wit, G and Svet, L and Lories, B and Steenackers, HP}, title = {Microbial Interspecies Interactions and Their Impact on the Emergence and Spread of Antimicrobial Resistance.}, journal = {Annual review of microbiology}, volume = {76}, number = {}, pages = {179-192}, doi = {10.1146/annurev-micro-041320-031627}, pmid = {35609949}, issn = {1545-3251}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Drug Resistance, Bacterial ; Microbial Interactions ; }, abstract = {Bacteria are social organisms that commonly live in dense communities surrounded by a multitude of other species. The competitive and cooperative interactions between these species not only shape the bacterial communities but also influence their susceptibility to antimicrobials. While several studies have shown that mixed-species communities are more tolerant toward antimicrobials than their monospecies counterparts, only limited empirical data are currently available on how interspecies interactions influence resistance development. We here propose a theoretic framework outlining the potential impact of interspecies social behavior on different aspects of resistance development. We identify factors by which interspecies interactions might influence resistance evolution and distinguish between their effect on (a) the emergence of a resistant mutant and (b) the spread of this resistance throughout the population. Our analysis indicates that considering the social life of bacteria is imperative to the rational design of more effective antibiotic treatment strategies with a minimal hazard for resistance development.}, }
@article {pmid35608637, year = {2023}, author = {Perini, L and Gostinčar, C and Likar, M and Frisvad, JC and Kostanjšek, R and Nicholes, M and Williamson, C and Anesio, AM and Zalar, P and Gunde-Cimerman, N}, title = {Interactions of Fungi and Algae from the Greenland Ice Sheet.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {282-296}, pmid = {35608637}, issn = {1432-184X}, support = {675546//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; NE/M021025/1//Natural Environment Research Council/ ; 856416//H2020 European Research Council/ ; P1-0170//Javna Agencija za Raziskovalno Dejavnost RS/ ; P1-0198//Javna Agencija za Raziskovalno Dejavnost RS/ ; J4-2549//Javna Agencija za Raziskovalno Dejavnost RS/ ; DNRF137//Danmarks Grundforskningsfond/ ; 2871//Agilent Foundation/ ; }, mesh = {*Ice Cover/microbiology ; Greenland ; Benzocycloheptenes ; *Streptophyta ; Fungi ; }, abstract = {Heavily pigmented glacier ice algae Ancylonema nordenskiöldii and Ancylonema alaskanum (Zygnematophyceae, Streptophyta) reduce the bare ice albedo of the Greenland Ice Sheet, amplifying melt from the largest cryospheric contributor to eustatic sea-level rise. Little information is available about glacier ice algae interactions with other microbial communities within the surface ice environment, including fungi, which may be important for sustaining algal bloom development. To address this substantial knowledge gap and investigate the nature of algal-fungal interactions, an ex situ co-cultivation experiment with two species of fungi, recently isolated from the surface of the Greenland Ice Sheet (here proposed new species Penicillium anthracinoglaciei Perini, Frisvad and Zalar, Mycobank (MB 835602), and Articulospora sp.), and the mixed microbial community dominated by glacier ice algae was performed. The utilization of the dark pigment purpurogallin carboxylic acid-6-O-β-D-glucopyranoside (C18H18O12) by the two fungi was also evaluated in a separate experiment. P. anthracinoglaciei was capable of utilizing and converting the pigment to purpurogallin carboxylic acid, possibly using the sugar moiety as a nutrient source. Furthermore, after 3 weeks of incubation in the presence of P. anthracinoglaciei, a significantly slower decline in the maximum quantum efficiency (Fv/Fm, inverse proxy of algal stress) in glacier ice algae, compared to other treatments, was evident, suggesting a positive relationship between these species. Articulospora sp. did uptake the glycosylated purpurogallin, but did not seem to be involved in its conversion to aglycone derivative. At the end of the incubation experiments and, in conjunction with increased algal mortality, we detected a substantially increasing presence of the zoosporic fungi Chytridiomycota suggesting an important role for them as decomposers or parasites of glacier ice algae.}, }
@article {pmid35607968, year = {2022}, author = {Semler, AC and Fortney, JL and Fulweiler, RW and Dekas, AE}, title = {Cold Seeps on the Passive Northern U.S. Atlantic Margin Host Globally Representative Members of the Seep Microbiome with Locally Dominant Strains of Archaea.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {11}, pages = {e0046822}, pmid = {35607968}, issn = {1098-5336}, mesh = {*Archaea/metabolism ; Geologic Sediments/microbiology ; Methane/metabolism ; Methanosarcinales/genetics ; *Microbiota ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Seawater/microbiology ; }, abstract = {Marine cold seeps are natural sites of methane emission and harbor distinct microbial communities capable of oxidizing methane. The majority of known cold seeps are on tectonically active continental margins, but recent discoveries have revealed abundant seeps on passive margins as well, including on the U.S. Atlantic Margin (USAM). We sampled in and around four USAM seeps and combined pore water geochemistry measurements with amplicon sequencing of 16S rRNA and mcrA (DNA and RNA) to investigate the microbial communities present, their assembly processes, and how they compare to communities at previously studied sites. We found that the USAM seeps contained communities consistent with the canonical seep microbiome at the class and order levels but differed markedly at the sequence variant level, especially within the anaerobic methanotrophic (ANME) archaea. The ANME populations were highly uneven, with just a few dominant mcrA sequence variants at each seep. Interestingly, the USAM seeps did not form a distinct phylogenetic cluster when compared with other previously described seeps around the world. Consistent with this, we found only a very weak (though statistically significant) distance-decay trend in seep community similarity across a global data set. Ecological assembly indices suggest that the USAM seep communities were assembled primarily deterministically, in contrast to the surrounding nonseep sediments, where stochastic processes dominated. Together, our results suggest that the primary driver of seep microbial community composition is local geochemistry-specifically methane, sulfide, nitrate, acetate, and ammonium concentrations-rather than the geologic context, the composition of nearby seeps, or random events of dispersal. IMPORTANCE Cold seeps are now known to be widespread features of passive continental margins, including the northern U.S. Atlantic Margin (USAM). Methane seepage is expected to intensify at these relatively shallow seeps as bottom waters warm and underlying methane hydrates dissociate. While methanotrophic microbial communities might reduce or prevent methane release, microbial communities on passive margins have rarely been characterized. In this study, we investigated the Bacteria and Archaea at four cold seeps on the northern USAM and found that despite being colocated on the same continental slope, the communities significantly differ by site at the sequence variant level, particularly methane-cycling community members. Differentiation by site was not observed in similarly spaced background sediments, raising interesting questions about the dispersal pathways of cold seep microorganisms. Understanding the genetic makeup of these discrete seafloor ecosystems and how their microbial communities develop will be increasingly important as the climate changes.}, }
@article {pmid35604764, year = {2022}, author = {Benítez-Páez, A and Hartstra, AV and Nieuwdorp, M and Sanz, Y}, title = {Species- and strain-level assessment using rrn long-amplicons suggests donor's influence on gut microbial transference via fecal transplants in metabolic syndrome subjects.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2078621}, pmid = {35604764}, issn = {1949-0984}, mesh = {Bacteria/genetics ; *Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; Humans ; *Metabolic Syndrome/microbiology/physiopathology/therapy ; Nucleotides ; }, abstract = {Fecal microbiota transplantation (FMT) is currently used for treating Clostridium difficile infection and explored for other clinical applications in experimental trials. However, the effectiveness of this therapy could vary, and partly depend on the donor's bacterial species engraftment, whose evaluation is challenging because there are no cost-effective strategies for accurately tracking the microbe transference. In this regard, the precise identification of bacterial species inhabiting the human gut is essential to define their role in human health unambiguously. We used Nanopore-based device to sequence bacterial rrn operons (16S-ITS-23S) and to reveal species-level abundance changes in the human gut microbiota of a FMT trial. By assessing the donor and recipient microbiota before and after FMT, we further evaluated whether this molecular approach reveals strain-level genetic variation to demonstrate microbe transfer and engraftment. Strict control over sequencing data quality and major microbiota covariates was critical for accurately estimating the changes in gut microbial species abundance in the recipients after FMT. We detected strain-level variation via single-nucleotide variants (SNVs) at rrn regions in a species-specific manner. We showed that it was possible to explore successfully the donor-bacterial strain (e.g., Parabacteroides merdae) engraftment in recipients of the FMT by assessing the nucleotide frequencies at rrn-associated SNVs. Our findings indicate that the engraftment of donors' microbiota is to some extent correlated with the improvement of metabolic health in recipients and that parameters such as the baseline gut microbiota configuration, sex, and age of donors should be considered to ensure the success of FMT in humans. The study was prospectively registered at the Dutch Trial registry - NTR4488 (https://www.trialregister.nl/trial/4488).}, }
@article {pmid35604433, year = {2023}, author = {Fang, J and Jiang, W and Meng, S and He, W and Wang, G and Guo, E and Yan, Y}, title = {Polychaete Bioturbation Alters the Taxonomic Structure, Co-occurrence Network, and Functional Groups of Bacterial Communities in the Intertidal Flat.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {112-126}, pmid = {35604433}, issn = {1432-184X}, support = {41876185//National Natural Science Foundation of China/ ; 2020TD50//Central Public-interest Scientific Institution Basal Research Fund/ ; ZR2020QC046//Shandong Province Natural Science Foundation/ ; 2018YFJH0703//Key Projects of Science and Technology Innovation of Shandong Province/ ; }, mesh = {Humans ; Animals ; Bacteria/genetics ; *Polychaeta ; *Environmental Restoration and Remediation ; *Microbiota ; Bacteroidetes ; Geologic Sediments/microbiology ; }, abstract = {Polychaetes are important benthic macrofauna that lives in sediments, usually in intertidal flats with high organic content and high sulfide. It has been suggested that polychaete bioturbation could perform environmental remediation. During the process, the microbial community plays important roles. Here, we used high-throughput sequencing technology to study the bioturbation effects on the bacterial community in the polychaete (Perinereis aibuhitensis) burrows at different tidal positions in intertidal flat. The results showed that the bacterial communities were dramatically influenced by the polychaete bioturbation. The ACE, Chao, and Shannon indices of the polychaete burrows increased in summer. Dominant phyla in the polychaete burrows were Proteobacteria, Campilobacterota, Desulfobacterota, Chloroflexi, and Bacteroidota, and the dominant bacterial families were Sulfurvaceae, Flavobacteriaceae, Rhodobacteraceae, Woeseiaceae, Desulfobulbaceae, and Sulfurimonadaceae. Results of linear discriminant analysis effect size (LEfSe) showed that groups that include organic matter degraders, such as Bacteroidota, Flavobacteriaceae, Rhodobacteraceae, Woeseiaceae, and groups that include sulfur oxidizers, such as Campilobacterota, Sulfurovaceae, Rhodobacteraceae, Desulfobulbaceae, and Sulfurimonadaceae, were significantly increased due to the polychaete bioturbation. The polychaete bioturbation reduced the complexity of the bacterial co-occurrence network while increased its modularity and homogeneity. The polychaete bioturbation also changed the functional groups, which significantly enhanced in functional groups of aerobic nitrite oxidation, nitration, dark thiosulfate oxidation, dark sulfur oxidation, and dark sulfite oxidation, while nitrogen respiration and nitrate respiration decreased. These results provide insight into the impact of bacterial communities under the intertidal polychaete bioturbation.}, }
@article {pmid35604432, year = {2023}, author = {Salazar, B and Ortiz, A and Keswani, C and Minkina, T and Mandzhieva, S and Pratap Singh, S and Rekadwad, B and Borriss, R and Jain, A and Singh, HB and Sansinenea, E}, title = {Bacillus spp. as Bio-factories for Antifungal Secondary Metabolites: Innovation Beyond Whole Organism Formulations.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {1-24}, pmid = {35604432}, issn = {1432-184X}, support = {LabNOTs-21-01AB//Ministry of Science and Higher Education of the Russian Federationt/ ; }, mesh = {Humans ; Agriculture/methods/trends ; *Antifungal Agents/metabolism ; *Bacillus/genetics/metabolism ; Fungicides, Industrial/metabolism ; *Plant Diseases/prevention &amp; control/microbiology ; *Industrial Microbiology ; Crops, Agricultural/microbiology ; *Pest Control, Biological/methods/trends ; Multigene Family/genetics ; }, abstract = {Several fungi act as parasites for crops causing huge annual crop losses at both pre- and post-harvest stages. For years, chemical fungicides were the solution; however, their wide use has caused environmental contamination and human health problems. For this reason, the use of biofungicides has been in practice as a green solution against fungal phytopathogens. In the context of a more sustainable agriculture, microbial biofungicides have the largest share among the commercial biocontrol products that are available in the market. Precisely, the genus Bacillus has been largely studied for the management of plant pathogenic fungi because they offer a chemically diverse arsenal of antifungal secondary metabolites, which have spawned a heightened industrial engrossment of it as a biopesticide. In this sense, it is indispensable to know the wide arsenal that Bacillus genus has to apply these products for sustainable agriculture. Having this idea in our minds, in this review, secondary metabolites from Bacillus having antifungal activity are chemically and structurally described giving details of their action against several phytopathogens. Knowing the current status of Bacillus secreted antifungals is the base for the goal to apply these in agriculture and it is addressed in depth in the second part of this review.}, }
@article {pmid35602031, year = {2022}, author = {Schultz, J and Argentino, ICV and Kallies, R and Nunes da Rocha, U and Rosado, AS}, title = {Polyphasic Analysis Reveals Potential Petroleum Hydrocarbon Degradation and Biosurfactant Production by Rare Biosphere Thermophilic Bacteria From Deception Island, an Active Antarctic Volcano.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {885557}, pmid = {35602031}, issn = {1664-302X}, abstract = {Extreme temperature gradients in polar volcanoes are capable of selecting different types of extremophiles. Deception Island is a marine stratovolcano located in maritime Antarctica. The volcano has pronounced temperature gradients over very short distances, from as high as 100°C in the fumaroles to subzero next to the glaciers. These characteristics make Deception a promising source of a variety of bioproducts for use in different biotechnological areas. In this study, we isolated thermophilic bacteria from sediments in fumaroles at two geothermal sites on Deception Island with temperatures between 50 and 100°C, to evaluate the potential capacity of these bacteria to degrade petroleum hydrocarbons and produce biosurfactants under thermophilic conditions. We isolated 126 thermophilic bacterial strains and identified them molecularly as members of genera Geobacillus, Anoxybacillus, and Brevibacillus (all in phylum Firmicutes). Seventy-six strains grew in a culture medium supplemented with crude oil as the only carbon source, and 30 of them showed particularly good results for oil degradation. Of 50 strains tested for biosurfactant production, 13 showed good results, with an emulsification index of 50% or higher of a petroleum hydrocarbon source (crude oil and diesel), emulsification stability at 100°C, and positive results in drop-collapse, oil spreading, and hemolytic activity tests. Four of these isolates showed great capability of degrade crude oil: FB2_38 (Geobacillus), FB3_54 (Geobacillus), FB4_88 (Anoxybacillus), and WB1_122 (Geobacillus). Genomic analysis of the oil-degrading and biosurfactant-producer strain FB4_88 identified it as Anoxybacillus flavithermus, with a high genetic and functional diversity potential for biotechnological applications. These initial culturomic and genomic data suggest that thermophilic bacteria from this Antarctic volcano have potential applications in the petroleum industry, for bioremediation in extreme environments and for microbial enhanced oil recovery (MEOR) in reservoirs. In addition, recovery of small-subunit rRNA from metagenomes of Deception Island showed that Firmicutes is not among the dominant phyla, indicating that these low-abundance microorganisms may be important for hydrocarbon degradation and biosurfactant production in the Deception Island volcanic sediments.}, }
@article {pmid35601228, year = {2022}, author = {Okeke, ES and Olovo, CV and Nkwoemeka, NE and Okoye, CO and Nwankwo, CEI and Onu, CJ}, title = {Microbial ecology and evolution is key to pandemics: using the coronavirus model to mitigate future public health challenges.}, journal = {Heliyon}, volume = {8}, number = {5}, pages = {e09449}, pmid = {35601228}, issn = {2405-8440}, abstract = {Pandemics are global challenges that lead to total disruption of human activities. From the inception of human existence, all pandemics have resulted in loss of human lives. The coronavirus disease caused by SAR-CoV-2 began in China and is now at the global scale with an increase in mortality and morbidity. Numerous anthropogenic activities have been implicated in the emergence and severity of pandemics, including COVID-19. These activities cause changes in microbial ecology, leading to evolution due to mutation and recombination. This review hypothesized that an understanding of these anthropogenic activities would explain the dynamics of pandemics. The recent coronavirus model was used to study issues leading to microbial evolution, towards preventing future pandemics. Our review highlighted anthropogenic activities, including deforestation, mining activities, waste treatment, burning of fossil fuel, as well as international travels as drivers of microbial evolution leading to pandemics. Furthermore, human-animal interaction has also been implicated in pandemic incidents. Our study recommends substantial control of such anthropogenic activities as having been highlighted as ways to reduce the frequency of mutation, reduce pathogenic reservoirs, and the emergence of infectious diseases.}, }
@article {pmid35598673, year = {2022}, author = {Abel, SM and Primpke, S and Wu, F and Brandt, A and Gerdts, G}, title = {Human footprints at hadal depths: interlayer and intralayer comparison of sediment cores from the Kuril Kamchatka trench.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 2}, pages = {156035}, doi = {10.1016/j.scitotenv.2022.156035}, pmid = {35598673}, issn = {1879-1026}, mesh = {Ecosystem ; Environmental Pollution ; Humans ; *Microplastics ; Pacific Ocean ; *Plastics ; }, abstract = {Microplastic (MP) pollution affects almost all ecosystems on Earth. Given the increasing plastic production worldwide and the durability of these polymers, concerns arise about the fate of this material in the environment. A candidate to consider as a depositional final sink of MP is the sea floor and its deepest representatives, hadal trenches, as ultimate sinks. In this study, 13 sediment samples were collected with a multiple-corer at depths between 5740 and 9450 m from the Kuril Kamchatka trench (KKT), in the Northwest (NW) Pacific Ocean. These samples were analysed for MP presence in the upper sediment layer, by slicing the first 5 cm of sediment cores into 1 cm horizontal layers. These were compared against each other and between the sampling areas, in order to achieve a detailed picture of the depositional system of the trench and small-scale perturbations such as bioturbation. The analyses revealed the presence of 215 to 1596 MP particles per kg [-1] sediment (dry weight), with a polymer composition represented by 14 polymer types and the prevalence of particles smaller than 25 μm. A heterogeneous microplastic distribution through the sediment column and different microplastic concentration and polymer types among sampling stations located in different areas of the trench reflects the dynamics of this environment and the numerous forces that drive the deposition processes and the in situ recast of this pollutant at the trench floor.}, }
@article {pmid35598661, year = {2022}, author = {Müller, V and Chavez-Capilla, T and Feldmann, J and Mestrot, A}, title = {Increasing temperature and flooding enhance arsenic release and biotransformations in Swiss soils.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 1}, pages = {156049}, doi = {10.1016/j.scitotenv.2022.156049}, pmid = {35598661}, issn = {1879-1026}, mesh = {*Arsenic/analysis ; Biotransformation ; Soil ; *Soil Pollutants/analysis ; Switzerland ; Temperature ; }, abstract = {Reductive dissolution is one of the main causes for arsenic (As) mobilisation in flooded soils while biomethylation and biovolatilisation are two microbial mechanisms that greatly influence the mobility and toxicity of As. Climate change results in more extreme weather events such as flooding and higher temperatures, potentially leading to an increase in As release and biotransformations. Here, we investigated the effects of flooding and temperature on As release, biomethylation and biovolatilisation from As-rich soils with different pH and source of As (one acidic and anthropogenic (Salanfe) and one neutral and geogenic (Liesberg)). Flooded soils incubated at 23 °C for two weeks showed a ~ 3-fold (Liesberg site) and ~ 7-fold (Salanfe site) increase in the total As concentration of soil solution compared to those incubated at 18 °C. Methyl- and thio-As species were found in the acidic soil and soil solution. High temperatures enhanced thiolation and methylation although inorganic As was predominant. We also show that volatile As fluxes increased more than 4-fold between treatments, from 18 ± 5 ng/kg/d at 18 °C to 75 ± 6 ng/kg/d at 23 °C from Salanfe soil. Our results suggest that high As soils with acidic pH can become an important source of As to the surrounding environment according to realistic climatic scenarios, and that biovolatilisation is very sensitive to increases in temperature. This study provides new data and further justifies further investigations into climate-induced changes on As release and speciation and its links to important factors such as microbial ecology and sulfate or iron biogeochemistry. SYNOPSIS: In the studied Swiss soils, elevated temperature increases arsenic mobility through volatilisation and methylation.}, }
@article {pmid35597889, year = {2022}, author = {Ghuneim, LJ and Raghuvanshi, R and Neugebauer, KA and Guzior, DV and Christian, MH and Schena, B and Feiner, JM and Castillo-Bahena, A and Mielke, J and McClelland, M and Conrad, D and Klapper, I and Zhang, T and Quinn, RA}, title = {Complex and unexpected outcomes of antibiotic therapy against a polymicrobial infection.}, journal = {The ISME journal}, volume = {16}, number = {9}, pages = {2065-2075}, pmid = {35597889}, issn = {1751-7370}, support = {R01 AI145925/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; *Coinfection/drug therapy ; *Cystic Fibrosis/drug therapy/microbiology ; Humans ; Metagenome ; Sputum/microbiology ; }, abstract = {Antibiotics are our primary approach to treating complex infections, yet we have a poor understanding of how these drugs affect microbial communities. To better understand antimicrobial effects on host-associated microbial communities we treated cultured sputum microbiomes from people with cystic fibrosis (pwCF, n = 24) with 11 different antibiotics, supported by theoretical and mathematical modeling-based predictions in a mucus-plugged bronchiole microcosm. Treatment outcomes we identified in vitro that were predicted in silico were: 1) community death, 2) community resistance, 3) pathogen killing, and 4) fermenter killing. However, two outcomes that were not predicted when antibiotics were applied were 5) community profile shifts with little change in total bacterial load (TBL), and 6) increases in TBL. The latter outcome was observed in 17.8% of samples with a TBL increase of greater than 20% and 6.8% of samples with an increase greater than 40%, demonstrating significant increases in community carrying capacity in the presence of an antibiotic. An iteration of the mathematical model showed that TBL increase was due to antibiotic-mediated release of pH-dependent inhibition of pathogens by anaerobe fermentation. These dynamics were verified in vitro when killing of fermenters resulted in a higher community carrying capacity compared to a no antibiotic control. Metagenomic sequencing of sputum samples during antibiotic therapy revealed similar dynamics in clinical samples. This study shows that the complex microbial ecology dictates the outcomes of antibiotic therapy against a polymicrobial infection.}, }
@article {pmid35596751, year = {2023}, author = {Yu, X and Zhang, Y and Shen, M and Dong, S and Zhang, F and Gao, Q and He, P and Shen, G and Yang, J and Wang, Z and Bo, G}, title = {Soil Conditioner Affects Tobacco Rhizosphere Soil Microecology.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {460-473}, pmid = {35596751}, issn = {1432-184X}, support = {027Y2021-011//Hubei tobacco company/ ; 201903//Qingdao (Shandong Province) Tobacco Company/ ; 6651117005, 6651121004//Qingdao Agricultural University/ ; }, mesh = {*Soil/chemistry ; *Fertilizers/analysis ; Nicotiana ; Rhizosphere ; Soil Microbiology ; }, abstract = {Reasonable fertilization management can increase nutrient content and enzyme activity in rhizosphere soil, and even increase soil microbial richness. However, different fertilizers could raise distinct influences on the soil properties, including soil environmental factors (physicochemical properties and enzymatic activities) and microbial community. Here, the effects of two soil amendments (microbial fertilizer and woody peat) on environmental factors and microbial community structure in tobacco rhizosphere soil were evaluated, with the correlations between microbes and environmental factors explored. As the results, microbial fertilizer could effectively alleviate soil acidification, increase available potassium and organic matter contents in soil, and was also beneficial to increase nitrate reductase activity in rhizosphere soil. Fertilizers cause changes in the abundance of certain microbes in the soil. Besides, it was shown that the candidate phyla Gal15, Acidobacterota, Latescibacterota, Mortierellommycota, Basidiomycota, and Rozellomycota in tobacco rhizosphere soil had significant correlation with soil environmental factors. Through the functional analysis of these populations, it can be deduced that the changes in the abundance of certain microorganisms may be an important reason for the differences in environmental factors. All these indicated that the differences of environmental factors in different treatments are closely related to the abundance of some special soil microorganisms. Studying the life activities of these microbes would provide good guidance for exploring the interaction among crops, soil, and microorganisms and improving crop yields.}, }
@article {pmid35596750, year = {2023}, author = {Arnolds, KL and Yamada, E and Neff, CP and Schneider, JM and Palmer, BE and Lozupone, CA}, title = {Disruption of Genes Encoding Putative Zwitterionic Capsular Polysaccharides of Diverse Intestinal Bacteroides Reduces the Induction of Host Anti-Inflammatory Factors.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1620-1629}, pmid = {35596750}, issn = {1432-184X}, support = {R01 DK104047/DK/NIDDK NIH HHS/United States ; T32 AI007405/AI/NIAID NIH HHS/United States ; T32 AI007405/NH/NIH HHS/United States ; }, mesh = {Humans ; *Interleukin-10/genetics ; *Leukocytes, Mononuclear ; Polysaccharides, Bacterial ; Bacteroides fragilis/genetics ; Anti-Inflammatory Agents ; Bacteria ; }, abstract = {Bacterial zwitterionic capsular polysaccharides (ZPS), such as polysaccharide A (PSA) of the intestinal commensal Bacteroides fragilis, have been shown to modulate T cells, including inducing anti-inflammatory IL-10-secreting T regulatory cells (Tregs). We previously used a genomic screen to identify diverse host-associated bacteria with the predicted genetic capacity to produce ZPSs related to PSA of B. fragilis and hypothesized that genetic disruption (KO) of a key functional gene within these operons would reduce the anti-inflammatory activity of these bacteria. We found that ZPS-KO bacteria in two common gut commensals, Bacteroides uniformis and Bacteroides cellulosilyticus, had a reduced ability to induce Tregs and IL-10 in stimulations of human peripheral blood mononuclear cells (PBMCs). Additionally, we found that macrophage stimulated with either wildtype B. fragilis or B. uniformis produced significantly more IL-10 than KOs, indicating a potentially novel function of ZPS of shifting the cytokine response in macrophages to a more anti-inflammatory state. These findings support the hypothesis that these related ZPS may represent a shared strategy to modulate host immune responses.}, }
@article {pmid35595468, year = {2022}, author = {Rotoni, C and Leite, MFA and Pijl, A and Kuramae, EE}, title = {Rhizosphere microbiome response to host genetic variability: a trade-off between bacterial and fungal community assembly.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {6}, pages = {}, doi = {10.1093/femsec/fiac061}, pmid = {35595468}, issn = {1574-6941}, mesh = {Bacteria/genetics ; Fungi ; *Microbiota/genetics ; *Mycobiome/genetics ; Plant Roots/microbiology ; Plants ; Rhizosphere ; Soil Microbiology ; }, abstract = {Rhizosphere microbial community composition is strongly influenced by plant species and cultivar. However, our understanding of the impact of plant cultivar genetic variability on microbial assembly composition remains limited. Here, we took advantage of vegetatively propagated chrysanthemum (Chrysanthemum indicum L.) as a plant model and induced roots in five commercial cultivars: Barolo, Chic, Chic 45, Chic Cream and Haydar. We observed strong rhizosphere selection for the bacterial community but weaker selection for the fungal community. The genetic distance between cultivars explained 42.83% of the total dissimilarity between the bacteria selected by the different cultivars. By contrast, rhizosphere fungal selection was not significantly linked to plant genetic dissimilarity. Each chrysanthemum cultivar selected unique bacterial and fungal genera in the rhizosphere. We also observed a trade-off in the rhizosphere selection of bacteria and fungi in which the cultivar with the strongest selection of fungal communities showed the weakest bacterial selection. Finally, bacterial and fungal family taxonomic groups consistently selected by all cultivars were identified (bacteria Chitinophagaceae, Beijerinckiaceae and Acidobacteriaceae, and fungi Pseudeurotiaceae and Chrysozymaceae). Taken together, our findings suggest that chrysanthemum cultivars select distinct rhizosphere microbiomes and share a common core of microbes partially explained by the genetic dissimilarity between cultivars.}, }
@article {pmid35590462, year = {2022}, author = {Blakney, AJC and Bainard, LD and St-Arnaud, M and Hijri, M}, title = {Brassicaceae host plants mask the feedback from the previous year's soil history on bacterial communities, except when they experience drought.}, journal = {Environmental microbiology}, volume = {24}, number = {8}, pages = {3529-3548}, doi = {10.1111/1462-2920.16046}, pmid = {35590462}, issn = {1462-2920}, mesh = {Bacteria/genetics ; *Brassica napus ; Droughts ; Feedback ; Plant Roots/microbiology ; Plants/microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {Soil history operates through time to influence the structure and biodiversity of soil bacterial communities. Examining how different soil histories endure will help clarify the rules of bacterial community assembly. In this study, we established three different soil histories in field trials; the following year these plots were planted with five different Brassicaceae species. We hypothesized that the previously established soil histories would continue to structure the subsequent Brassicaceae bacterial root and rhizosphere communities. We used a MiSeq 16S rRNA metabarcoding strategy to determine the impact of different soil histories on the structure and biodiversity of the bacterial root and rhizosphere communities from the five different Brassicaceae host plants. We found that the Brassicaceae hosts were consistently significant factors in structuring the bacterial communities. Four host plants (Sinapis alba, Brassica napus, B. juncea, B. carinata) formed similar bacterial communities, regardless of different soil histories. Camelina sativa host plants structured phylogenetically distinct bacterial communities compared to the other hosts, particularly in their roots. Soil history established the previous year was only a significant factor for bacterial community structure when the feedback of the Brassicaceae host plants was weakened, potentially due to limited soil moisture during a dry year. Understanding how soil history is involved in the structure and biodiversity of bacterial communities through time is a limitation in microbial ecology and is required for employing microbiome technologies in improving agricultural systems.}, }
@article {pmid35589992, year = {2023}, author = {King, NG and Moore, PJ and Thorpe, JM and Smale, DA}, title = {Consistency and Variation in the Kelp Microbiota: Patterns of Bacterial Community Structure Across Spatial Scales.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1265-1275}, pmid = {35589992}, issn = {1432-184X}, support = {MR/S032827/1/MRC_/Medical Research Council/United Kingdom ; MR/S032827/1//UKRI/ ; NE/S011692/1//Natural Environment Research Council/ ; }, mesh = {Humans ; *Kelp/microbiology ; Ecosystem ; *Laminaria/microbiology ; Forests ; Bacteria/genetics ; *Microbiota ; }, abstract = {Kelp species are distributed along ~ 25% of the world's coastlines and the forests they form represent some of the world's most productive and diverse ecosystems. Like other marine habitat-formers, the associated microbial community is fundamental for host and, in turn, wider ecosystem functioning. Given there are thousands of bacteria-host associations, determining which relationships are important remains a major challenge. We characterised the associated bacteria of two habitat-forming kelp species, Laminaria hyperborea and Saccharina latissima, from eight sites across a range of spatial scales (10 s of metres to 100 s of km) in the northeast Atlantic. We found no difference in diversity or community structure between the two kelps, but there was evidence of regional structuring (across 100 s km) and considerable variation between individuals (10 s of metres). Within sites, individuals shared few amplicon sequence variants (ASVs) and supported a very small proportion of diversity found across the wider study area. However, consistent characteristics between individuals were observed with individual host communities containing a small conserved "core" (8-11 ASVs comprising 25 and 32% of sample abundances for L. hyperborea and S. latissima, respectively). At a coarser taxonomic resolution, communities were dominated by four classes (Planctomycetes, Gammaproteobacteria, Alphaproteobacteria and Bacteroidia) that made up ~ 84% of sample abundances. Remaining taxa (47 classes) made up very little contribution to overall abundance but the majority of taxonomic diversity. Overall, our study demonstrates the consistent features of kelp bacterial communities across large spatial scales and environmental gradients and provides an ecologically meaningful baseline to track environmental change.}, }
@article {pmid35587374, year = {2022}, author = {Kohl, KD and Dieppa-Colón, E and Goyco-Blas, J and Peralta-Martínez, K and Scafidi, L and Shah, S and Zawacki, E and Barts, N and Ahn, Y and Hedayati, S and Secor, SM and Rowe, MP}, title = {Gut Microbial Ecology of Five Species of Sympatric Desert Rodents in Relation to Herbivorous and Insectivorous Feeding Strategies.}, journal = {Integrative and comparative biology}, volume = {62}, number = {2}, pages = {237-251}, doi = {10.1093/icb/icac045}, pmid = {35587374}, issn = {1557-7023}, support = {IOS-1942587//National Science Foundation/ ; }, mesh = {Animals ; Chitin ; Dipodomys ; *Gastrointestinal Microbiome ; Herbivory ; *Microbiota ; Peromyscus ; Rodentia ; }, abstract = {The gut microbial communities of mammals provide numerous benefits to their hosts. However, given the recent development of the microbiome field, we still lack a thorough understanding of the variety of ecological and evolutionary factors that structure these communities across species. Metabarcoding is a powerful technique that allows for multiple microbial ecology questions to be investigated simultaneously. Here, we employed DNA metabarcoding techniques, predictive metagenomics, and culture-dependent techniques to inventory the gut microbial communities of several species of rodent collected from the same environment that employ different natural feeding strategies [granivorous pocket mice (Chaetodipus penicillatus); granivorous kangaroo rats (Dipodomys merriami); herbivorous woodrats (Neotoma albigula); omnivorous cactus mice (Peromyscus eremicus); and insectivorous grasshopper mice (Onychomys torridus)]. Of particular interest were shifts in gut microbial communities in rodent species with herbivorous and insectivorous diets, given the high amounts of indigestible fibers and chitinous exoskeleton in these diets, respectively. We found that herbivorous woodrats harbored the greatest microbial diversity. Granivorous pocket mice and kangaroo rats had the highest abundances of the genus Ruminococcus and highest predicted abundances of genes related to the digestion of fiber, representing potential adaptations in these species to the fiber content of seeds and the limitations to digestion given their small body size. Insectivorous grasshopper mice exhibited the greatest inter-individual variation in the membership of their microbiomes, and also exhibited the highest predicted abundances of chitin-degrading genes. Culture-based approaches identified 178 microbial isolates (primarily Bacillus and Enterococcus), with some capable of degrading cellulose and chitin. We observed several instances of strain-level diversity in these metabolic capabilities across isolates, somewhat highlighting the limitations and hidden diversity underlying DNA metabarcoding techniques. However, these methods offer power in allowing the investigation of several questions concurrently, thus enhancing our understanding of gut microbial ecology.}, }
@article {pmid35586862, year = {2022}, author = {Raglin, SS and Kent, AD and Ngumbi, EN}, title = {Herbivory Protection via Volatile Organic Compounds Is Influenced by Maize Genotype, Not Bacillus altitudinis-Enriched Bacterial Communities.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {826635}, pmid = {35586862}, issn = {1664-302X}, abstract = {Belowground, plants interact with beneficial soil microbes such as plant growth-promoting rhizobacteria (PGPR). PGPR are rhizosphere bacteria that colonize roots and elicit beneficial effects in plants such as improved plant growth, pathogen resistance, abiotic stress tolerance, and herbivore protection. Treatment of plants with PGPR has been shown to trigger the emission of volatile organic compounds (VOCs). Volatile emissions can also be triggered by herbivory, termed herbivore-induced plant volatiles (HIPV), with important ramifications for chemical-mediated plant and insect interactions. Much of our current understanding of PGPR and herbivore-induced volatiles is based on studies using one plant genotype, yet domestication and modern breeding has led to the development of diverse germplasm with altered phenotypes and chemistry. In this study, we investigated if volatile emissions triggered by PGPR colonization and herbivory varies by maize genotype and microbial community assemblages. Six maize genotypes representing three decades of crop breeding and two heterotic groups were used, with four microbiome treatments: live or sterilized soil, with or without a Bacillus inoculant. Soil sterilization was used to delay microbiome establishment, resulting in low-diversity treatments. At planting, maize seeds were inoculated with PGPR Bacillus altitudinis AP-283 and grown under greenhouse conditions. Four weeks post planting, plants were subjected to feeding by third instar Helicoverpa zea (Lepidoptera: Noctuidae) larvae. Volatiles were collected using solid phase microextraction and analyzed with gas chromatography-mass spectrometry. Illumina NovaSeq 16S rRNA amplicon sequencing was carried out to characterize the rhizosphere microbiome. Maize genotype significantly influenced total volatile emissions, and relative abundance of volatile classes. We did not document a strong influence of microbe treatment on plant VOC emissions. However, inoculating plants with PGPR improved plant growth under sterile conditions. Taken together, our results suggest that genotypic variation is the dominant driver in HIPV composition and individual HIPV abundances, and any bacterial-mediated benefit is genotype and HIPV-specific. Therefore, understanding the interplay of these factors is necessary to fully harness microbially-mediated benefits and improve agricultural sustainability.}, }
@article {pmid35584587, year = {2022}, author = {Kuroda, K and Narihiro, T and Shinshima, F and Yoshida, M and Yamaguchi, H and Kurashita, H and Nakahara, N and Nobu, MK and Noguchi, TQP and Yamauchi, M and Yamada, M}, title = {High-rate cotreatment of purified terephthalate and dimethyl terephthalate manufacturing wastewater by a mesophilic upflow anaerobic sludge blanket reactor and the microbial ecology relevant to aromatic compound degradation.}, journal = {Water research}, volume = {219}, number = {}, pages = {118581}, doi = {10.1016/j.watres.2022.118581}, pmid = {35584587}, issn = {1879-2448}, mesh = {Anaerobiosis ; Benzoates ; Bioreactors ; Phthalic Acids ; RNA, Ribosomal, 16S/genetics ; *Sewage ; Waste Disposal, Fluid ; *Wastewater ; }, abstract = {Polyethylene terephthalate (PET) is produced worldwide, mainly as material for plastic drink bottles. PET is produced by polymerization of purified terephthalate (PTA) or dimethyl terephthalate (DMT) with ethylene glycol. During the synthetic manufacturing processes of PTA and DMT, high organic loading wastewater is produced, which is typically treated separately by anaerobic wastewater treatment technologies. Given the high demand for PET, manufacturing plants are expanding globally, which will result in an increase in the amounts of PTA and DMT wastewater in need of treatment. In terms of effective treatment, the cotreatment of PTA and DMT wastewater has several advantages, including lower area and energy requirements. In this study, we examined the performance of an upflow anaerobic sludge blanket (UASB) reactor in cotreating PTA and DMT wastewater with high organic loading, evaluating its removal characteristics after 518 days of continuous operation. In addition, we performed a microbiome analysis of the UASB granular sludge to uncover the microbial interactions and metabolic functions within the reactor. By continuous operation, we achieved an organic removal rate of 6.6 kg m[-3] day[-1]. In addition, we confirmed that aromatic compounds in the complex wastewater from the PTA and DMT manufacturing processes are biodegradable in the following order: benzoate > orthophthalate > terephthalate > isophthalate > p-toluic acid. 16S rRNA gene-based network analysis shows that anaerobic Woesearchaeales belonging to phylum Nanoarchaeota has a positive correlation with Methanoregula, Candidatus Methanofastidiosum, and Methanosarcina, suggesting a symbiotic relationship with methanogens in granular sludge. Shotgun metagenomic analysis revealed that terephthalate, isophthalate/orthophthalate, and benzoate were degraded by different members of Pelotomaculaceae and Syntrophorhabdaceae. According to the genomic information, we propose two new possible routes for orthophthalate degradation by the Syntrophorhabdaceae organism.}, }
@article {pmid35583791, year = {2022}, author = {Pavan, S and Prabhu, AN and Prasad Gorthi, S and Das, B and Mutreja, A and Shetty, V and Ramamurthy, T and Ballal, M}, title = {Exploring the multifactorial aspects of Gut Microbiome in Parkinson's Disease.}, journal = {Folia microbiologica}, volume = {67}, number = {5}, pages = {693-706}, pmid = {35583791}, issn = {1874-9356}, mesh = {Antiparkinson Agents ; Brain ; *Gastrointestinal Microbiome/physiology ; Humans ; *Parkinson Disease/therapy ; alpha-Synuclein/metabolism ; }, abstract = {Advanced research in health science has broadened our view in approaching and understanding the pathophysiology of diseases and has also revolutionised diagnosis and treatment. Ever since the establishment of Braak's hypothesis in the propagation of alpha-synuclein from the distant olfactory and enteric nervous system towards the brain in Parkinson's Disease (PD), studies have explored and revealed the involvement of altered gut microbiota in PD. This review recapitulates the gut microbiome associated with PD severity, duration, motor and non-motor symptoms, and antiparkinsonian treatment from recent literature. Gut microbial signatures in PD are potential predictors of the disease and are speculated to be used in early diagnosis and treatment. In brief, the review also emphasises on implications of the prebiotic, probiotic, faecal microbiota transplantation, and dietary interventions as alternative treatments in modulating the disease symptoms in PD.}, }
@article {pmid35583685, year = {2023}, author = {Wu, MH and Li, T and Zhang, GS and Wu, FS and Chen, T and Zhang, BL and Wu, XK and Liu, GX and Zhang, KC and Zhang, W}, title = {Seasonal Variation of Hypolithic Microbiomes in the Gobi Desert : Seasonal Variation of Hypolithic Microbiomes in the Gobi Desert.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1382-1395}, pmid = {35583685}, issn = {1432-184X}, support = {31870479//National Natural Science Foundation of China/ ; 2019YFE0121100//National Key R&amp;D Program of China/ ; 20YF3WA007//Scientific Project of Gansu Province, China/ ; 20JR5RA548//Scientific Project of Gansu Province, China/ ; }, mesh = {Seasons ; Desert Climate ; *Cyanobacteria/genetics ; Temperature ; *Microbiota ; Soil Microbiology ; }, abstract = {Understanding how microbial communities adapt to environmental stresses is critical for interpreting ecological patterns and microbial diversity. In the case of the Gobi Desert, little is known on the environmental factors that explain hypolithic colonization under quartz stones. By analyzing nine hypolithic communities across an arid gradient and the effects of the season of the year in the Hexi Corridor of this desert, we found a significant decrease in hypolithic colonization rates (from 47.24 to 15.73%) with the increasing drought gradient and found two distinct communities in Hot and Cold samples, which survived or proliferated after a hot or a cold period. While Cold communities showed a greater species diversity and a predominance of Cyanobacteria, Hot communities showed a predominance of members of the Proteobacteria and the Firmicutes. In comparison, Cold communities also possessed stronger functions in the photosynthesis and carbon metabolism. Based on the findings of this study, we proposed that the hypolithic communities of the Hexi Corridor of the Gobi Desert might follow a seasonal developmental cycle in which temperature play an important role. Thus after a critical thermal threshold is crossed, heterotrophic microorganisms predominate in the hot period, while Cyanobacteria predominate in the cold period.}, }
@article {pmid35581504, year = {2023}, author = {Wan, L and Caruso, G and Cao, X and Song, C and Maimone, G and Rappazzo, AC and Laganà, P and Zhou, Y}, title = {Microbial Response to Coastal-Offshore Gradients in Taiwan Straits: Community Metabolism and Total Prokaryotic Abundance as Potential Proxies.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1253-1264}, pmid = {35581504}, issn = {1432-184X}, support = {2016YFE0202100.//Ministry of Science and Technology of the People's Republic of China/ ; }, mesh = {*Ecosystem ; Taiwan ; *Estuaries ; Rivers ; China ; Environmental Monitoring ; Carbon ; }, abstract = {Located between the South and the East China Sea, the Taiwan Straits (TWS) are a marine shelf-channel area, with unique hydrological and geomorphological features affected by rivers inflow and with recent algal blooms with red tide events. This study aimed at assessing microbial distribution and function and their modulation in response to environmental gradients. Surface (0.5 m) water samples from 16 stations along five north to south transects were collected; total prokaryotic abundance by epifluorescence microscope and carbon substrate utilization patterns by Biolog Ecoplates were estimated. Spatially, a patchy microbial distribution was found, with the highest microbial metabolic levels and prokaryotic abundance in the TWS area between Minjiang River estuary and Pingtan Island, and progressive decreases towards offshore stations. Complex carbon sources and carbohydrates were preferentially metabolized. This study provides a snapshot of the microbial abundance and activity in TWS as a model site of aquatic ecosystems impacted from land inputs; obtained data highlights that microbial metabolism is more sensitive than abundance to environmental changes.}, }
@article {pmid35581020, year = {2022}, author = {Xie, J and Li, Q and Haesebrouck, F and Van Hoecke, L and Vandenbroucke, RE}, title = {The tremendous biomedical potential of bacterial extracellular vesicles.}, journal = {Trends in biotechnology}, volume = {40}, number = {10}, pages = {1173-1194}, doi = {10.1016/j.tibtech.2022.03.005}, pmid = {35581020}, issn = {1879-3096}, mesh = {Bacteria ; *Cancer Vaccines ; *Extracellular Vesicles ; Host Microbial Interactions ; Lipids ; }, abstract = {Bacterial extracellular vesicles (bEVs) are nano-sized, lipid membrane-delimited particles filled with bacteria-derived components. They have important roles in the physiology and pathogenesis of bacteria, and in bacteria-bacteria and bacteria-host interactions. Interestingly, recent advances in biotechnology have made it possible to engineer the bEV surface and decorate it with diverse biomolecules and nanoparticles (NPs). bEVs have been the focus of significant interest in a range of biomedical fields and are being evaluated as vaccines, cancer immunotherapy agents, and drug delivery vehicles. However, significant hurdles in terms of their safety, efficacy, and mass production need to be addressed to enable their full clinical potential. Here, we review recent advances and remaining obstacles regarding the use of bEVs in different biomedical applications and discuss paths toward clinical translation.}, }
@article {pmid35577973, year = {2022}, author = {Mangola, SM and Lund, JR and Schnorr, SL and Crittenden, AN}, title = {Ethical microbiome research with Indigenous communities.}, journal = {Nature microbiology}, volume = {7}, number = {6}, pages = {749-756}, pmid = {35577973}, issn = {2058-5276}, support = {RM1 HG009042/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; }, abstract = {Human-microbiome interactions have been associated with evolutionary, cultural and environmental processes. With clinical applications of microbiome research now feasible, it is crucial that the science conducted, particularly among Indigenous communities, adheres to principles of inclusion. This necessitates a transdisciplinary dialogue to decide how biological samples are collected and who benefits from the research and any derived products. As a group of scholars working at the interface of biological and social science, we offer a candid discussion of the lessons learned from our own research and introduce one approach to carry out ethical microbiome research with Indigenous communities.}, }
@article {pmid35576038, year = {2022}, author = {Kuzikova, I and Andronov, E and Zaytseva, T and Metelkova, L and Zhakovskaya, Z and Medvedeva, N}, title = {A microcosm approach for evaluating the microbial nonylphenol and butyltin biodegradation and bacterial community shifts in co-contaminated bottom sediments from the Gulf of Finland, the Baltic Sea.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {46}, pages = {69849-69860}, pmid = {35576038}, issn = {1614-7499}, mesh = {*Alphaproteobacteria/metabolism ; Bacteria/metabolism ; Biodegradation, Environmental ; Ecosystem ; Finland ; Geologic Sediments/chemistry ; Phenols ; *Water Pollutants, Chemical/analysis ; }, abstract = {Pollution of aquatic ecosystems with nonylphenol (NP) and butyltins (BuTs) is of great concern due to their effects on endocrine activity, toxicity to aquatic organisms, and extended persistence in sediments. The impact of contamination with NP and/or BuTs on the microbial community structure in marine sediments was investigated using microcosms and high-throughput sequencing. Sediment microcosms with NP (300 mg/kg) and/or BuTs (95 mg/kg) were constructed. Complete removal of monobutyltin (MBT) occurred in the microcosms after 240 days of incubation, while a residual NP rate was 40%. The content of toxic tributyltin (TBT) and dibutyltin (DBT) in the sediments did not change notably. Co-contamination of the sediments with NP and BuTs did not affect the processes of their degradation. The pollutants in the microcosms could have been biodegraded by autochthonous microorganisms. Significantly different and less diverse bacterial communities were observed in the contaminated sediments compared to non-contaminated control. Firmicutes and Gammaproteobacteria dominated in the NP treatment, Actinobacteria and Alphaproteobacteria in the BuT treatment, and Gammaproteobacteria, Alphaproteobacteria, Firmicutes, and Acidobacteria in the NP-BuT mixture treatment. The prevalence of microorganisms from the bacterial genera Halothiobacillus, Geothrix, Methanosarcina, Dyella, Parvibaculum, Pseudomonas, Proteiniclasticum, and bacteria affiliated with the order Rhizobiales may indicate their role in biodegradation of NP and BuTs in the co-contaminated sediments. This study can provide some new insights towards NP and BuT biodegradation and microbial ecology in NP-BuT co-contaminated environment.}, }
@article {pmid35575806, year = {2023}, author = {Patil, JS and Sathish, K}, title = {Responses of Phytoplankton Benthic Propagules to Macronutrient Enrichment and Varying Light Intensities: Elucidation from Monsoon-Influenced Mandovi and Zuari Riverine System : Responses of Phytoplankton Benthic Propagules to Macronutrient Enrichment and Varying Light Intensities: Elucidation from Monsoon-Influenced Mandovi and Zuari Riverine System.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1367-1381}, pmid = {35575806}, issn = {1432-184X}, support = {//science and engineering research board/ ; }, mesh = {*Phytoplankton ; Nitrates ; Seawater ; Rivers ; Fresh Water ; *Diatoms ; India ; Seasons ; Environmental Monitoring/methods ; Estuaries ; }, abstract = {The ecological importance of phytoplankton-benthic-propagules (PBP) from coastal sediments, except tropical monsoon-influenced rivers and estuaries, is well documented. PBP in such systems is often transported from upstream (near freshwater) to downstream (estuary) through freshwater discharges during monsoon and thereby experiences higher salinities (>30 PSU) and nutrients with varying light conditions due to reducing discharges during the monsoon-break/withdrawal-phase. However, the PBP responses (germination and subsequent growth) to such changes are unknown and are examined here at ~35 PSU salinity. For the study, macronutrients (nitrate, phosphate, silicate, and nitrate+phosphate+silicate) and light intensities were considered to assess the response of PBP representing estuarine, brackish, and near freshwater locations of monsoon-influenced Mandovi and Zuari rivers (Goa, India). Diatoms dominated the viable PBP community, but the maximum growth and sustained photosynthetic activity were observed when all macronutrients were supplied than individually. Here, variable fluorescence technique utility in PBP resurrection (detection of viability and responses) was also explored. The PBP growth was similar for macronutrients but increased with light intensity indicating a longer growth response during monsoon. For PBP (germination and photosynthetic activity), light intensities drive the rate of improvement/development, whereas the nutrients are essential for maintaining vegetative growth upon germination in the region. The PBP dominance of common planktonic species (Skeletonema and Thalassiosira) along the river also signifies the role of seawater intrusion (up to upstream locations) in distribution. Skeletonema and Thalassiosira, which contribute significantly to the total community, are light-sensitive with a similar response and cause single species blooms during monsoon and non-monsoon, respectively, depending on the species' tolerance to salinity.}, }
@article {pmid35575486, year = {2022}, author = {Peruzzo, A and Losasso, C and Di Castri, A and Drigo, I and Bano, L and Orsini, M}, title = {Genome Sequence of Campylobacter Strain 19-13652, Isolated from Breeding Pheasants.}, journal = {Microbiology resource announcements}, volume = {11}, number = {6}, pages = {e0118421}, pmid = {35575486}, issn = {2576-098X}, support = {IZS VE 03/18 RC//Ministero della Salute (Ministry of Health, Italy)/ ; }, abstract = {We report the whole-genome sequence of a Campylobacter strain that was isolated from breeding pheasants presenting "bulgy eyes" in Italy. Traditional molecular typing methods did not return any reliable result. Whole-genome sequencing and sequence comparison with known genomes did not meet the criteria for assignment to an existing species.}, }
@article {pmid35573175, year = {2022}, author = {Ghosh, A and Saha, R and Bhadury, P}, title = {Metagenomic insights into surface water microbial communities of a South Asian mangrove ecosystem.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13169}, pmid = {35573175}, issn = {2167-8359}, mesh = {*Water ; Wetlands ; *Microbiota/genetics ; Metagenome/genetics ; Bacteria/genetics ; Firmicutes/genetics ; }, abstract = {Estuaries are one of the most productive ecosystems and their productivity is maintained by resident microbial communities. Recent alterations driven by climate change have further escalated these stressors leading to the propagation of traits such as antibiotic resistance and heavy metal resistance in microbial communities. Surface water samples from eleven stations along the Thakuran and Matla estuaries of the Sundarbans Biosphere Reserve (SBR) of Sundarbans mangrove located in South Asia were sampled in monsoon (June) 2019 to elucidate resident microbial communities based on Nanopore sequencing. Metagenomic analyses revealed the widespread dominance of Proteobacteria across all the stations along with a high abundance of Firmicutes. Other phyla, including Euryarchaeota, Thaumarchaeota, Actinobacteria, Bacteroidetes and Cyanobacteria showed site-specific trends in abundance. Further taxonomic affiliations showed Gammaproteobacteria and Alphaproteobacteria to be dominant classes with high abundances of Bacilli in SBR_Stn58 and SBR_Stn113. Among the eukaryotic communities, the most abundant classes included Prasinophyceae, Saccharyomycetes and Sardariomycetes. Functional annotation showed metabolic activities such as carbohydrate, amino acid, nitrogen and phosphorus metabolisms to be uniformly distributed across all the studied stations. Pathways such as stress response, sulphur metabolism and motility-associated genes appeared in low abundances in SBR. Functional traits such as antibiotic resistance showed overwhelming dominance of genes involved in multidrug resistance along with widespread resistance towards commonly used antibiotics including Tetracycline, glycopeptide and aminoglycoside. Metal resistance genes including arsenic, nickel and copper were found in comparable abundances across the studied stations. The prevalence of ARG and MRG might indicate presence of pollutants and hint toward deteriorating ecosystem health status of Sundarbans mangrove.}, }
@article {pmid35572632, year = {2022}, author = {Aponte, H and Galindo-Castañeda, T and Yáñez, C and Hartmann, M and Rojas, C}, title = {Microbial Community-Level Physiological Profiles and Genetic Prokaryotic Structure of Burned Soils Under Mediterranean Sclerophyll Forests in Central Chile.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {824813}, pmid = {35572632}, issn = {1664-302X}, abstract = {Forest fires alter soil microbial communities that are essential to support ecosystem recovery following land burning. These alterations have different responses according to soil abiotic pre- and post-fire conditions and fire severity, among others, and tend to decrease along vegetation recovery over time. Thus, understanding the effects of fires on microbial soil communities is critical to evaluate ecosystem resilience and restoration strategies in fire-prone ecosystems. We studied the state of community-level physiological profiles (CLPPs) and the prokaryotic community structure of rhizosphere and bulk soils from two fire-affected sclerophyll forests (one surveyed 17 months and the other 33 months after fire occurrence) in the Mediterranean climate zone of central Chile. Increases in catabolic activity (by average well color development of CLPPs), especially in the rhizosphere as compared with the bulk soil, were observed in the most recently affected site only. Legacy of land burning was still clearly shaping soil prokaryote community structure, as shown by quantitative PCR (qPCR) and Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene, particularly in the most recent fire-affected site. The qPCR copy numbers and alpha diversity indexes (Shannon and Pielou's evenness) of sequencing data decreased in burned soils at both locations. Beta diversity analyses showed dissimilarity of prokaryote communities at both study sites according to fire occurrence, and NO3 [-] was the common variable explaining community changes for both of them. Acidobacteria and Rokubacteria phyla significantly decreased in burned soils at both locations, while Firmicutes and Actinobacteria increased. These findings provide a better understanding of the resilience of soil prokaryote communities and their physiological conditions in Mediterranean forests of central Chile following different time periods after fire, conditions that likely influence the ecological processes taking place during recovery of fire-affected ecosystems.}, }
@article {pmid35569711, year = {2022}, author = {Matassa, S and Pelagalli, V and Papirio, S and Zamalloa, C and Verstraete, W and Esposito, G and Pirozzi, F}, title = {Direct nitrogen stripping and upcycling from anaerobic digestate during conversion of cheese whey into single cell protein.}, journal = {Bioresource technology}, volume = {358}, number = {}, pages = {127308}, doi = {10.1016/j.biortech.2022.127308}, pmid = {35569711}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Cheese ; Dietary Proteins ; *Nitrogen/analysis ; Whey/chemistry ; Whey Proteins ; }, abstract = {The environmental impact of the dairy industry is heavily influenced by the overproduction of nitrogen- and carbon-rich effluents. The present study proposes an innovative process to recover waste contaminated nitrogen from anaerobic digestate while treating excess cheese whey (CW) and producing high-quality, clean single cell protein (SCP). By relying on direct aeration stripping techniques, employing an airflow subsequently used in the aerobic cheese whey fermentation step, the investigated process was able to strip 41-80% of the total ammonium nitrogen (N-NH4[+]) from liquid digestate. The stripped ammonia gas (NH3) was completely recovered as N-NH4[+] in the acidic CW, and further upcycled into SCP having a total protein content of 74.7% and a balanced amino acids profile. A preliminary techno-economic analysis revealed the potential to directly recover and upcycle nitrogen into SCP at costs (4.3-6.3 €·kgN[-1]) and energetic inputs (90-132 MJ·kgN[-1]) matching those of conventional feed and nitrogen management processes.}, }
@article {pmid35569666, year = {2022}, author = {Li, K and Bi, Q and Liu, X and Wang, H and Sun, C and Zhu, Y and Lin, X}, title = {Unveiling the role of dissolved organic matter on phosphorus sorption and availability in a 5-year manure amended paddy soil.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 1}, pages = {155892}, doi = {10.1016/j.scitotenv.2022.155892}, pmid = {35569666}, issn = {1879-1026}, mesh = {Animals ; Dissolved Organic Matter ; Fertilizers/analysis ; *Manure/analysis ; Phosphorus/analysis ; *Soil/chemistry ; Swine ; }, abstract = {Dissolved organic matter (DOM) is an active component of organic manure that is widely used in agroecosystems to increase nutrient availability and consequently enhance crop yields. However, the ways in which soil DOM characteristics are influenced by organic manure and how it contributes to crop yield and soil P availability remains unclear. Here, we conducted a 5-year field experiment and demonstrated that partial replacement of chemical P fertilizer with swine manure could maintain high rice yield and soil available P levels and increase P fertilizer use efficiency (PUE) in comparison to chemical fertilization, even when the total P input was reduced. This suggests that organic manure application can significantly mobilize soil P and increase P availability. Structural equation modeling analysis indicated that the soil pH and humification degree of DOM, rather than DOM content, directly decreased maximum P adsorption capacity. The combined results of the optical spectroscopy and ultrahigh-resolution mass spectroscopy obtained from the laboratory validation experiment based on the DOM-removed soil demonstrated that manure-derived DOM competing with P for adsorption was one of the main reasons for the increase in soil P availability and that the effective DOM components were N-containing lignins, tannins, and condensed polycyclic aromatics with higher O/C and lower H/C ratios. Overall, our results provide solid evidence that soil DOM characteristics are influenced by manure application and facilitate soil P availability, which could help guide the sustainable P management and manure application in agroecosystems.}, }
@article {pmid35569105, year = {2022}, author = {Deng, X and Zhang, N and Li, Y and Zhu, C and Qu, B and Liu, H and Li, R and Bai, Y and Shen, Q and Falcao Salles, J}, title = {Bio-organic soil amendment promotes the suppression of Ralstonia solanacearum by inducing changes in the functionality and composition of rhizosphere bacterial communities.}, journal = {The New phytologist}, volume = {235}, number = {4}, pages = {1558-1574}, doi = {10.1111/nph.18221}, pmid = {35569105}, issn = {1469-8137}, mesh = {Bacteria/genetics ; Fertilizers ; Plant Diseases/microbiology ; *Ralstonia solanacearum ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Stimulating the development of soil suppressiveness against certain pathogens represents a sustainable solution toward reducing pesticide use in agriculture. However, understanding the dynamics of suppressiveness and the mechanisms leading to pathogen control remain largely elusive. Here, we investigated the mechanisms used by the rhizosphere microbiome induces bacterial wilt disease suppression in a long-term field experiment where continuous application of bio-organic fertilizers (BFs) triggered disease suppressiveness when compared to chemical fertilizer application. We further demonstrated in a glasshouse experiment that the suppressiveness of the rhizosphere bacterial communities was triggered mainly by changes in community composition rather than only by the abundance of the introduced biocontrol strain. Metagenomics approaches revealed that members of the families Sphingomonadaceae and Xanthomonadaceae with the ability to produce secondary metabolites were enriched in the BF plant rhizosphere but only upon pathogen invasion. We experimentally validated this observation by inoculating bacterial isolates belonging to the families Sphingomonadaceae and Xanthomonadaceae into conducive soil, which led to a significant reduction in pathogen abundance and increase in nonribosomal peptide synthetase gene abundance. We conclude that priming of the soil microbiome with BF amendment fostered reactive bacterial communities in the rhizosphere of tomato plants in response to biotic disturbance.}, }
@article {pmid35567250, year = {2022}, author = {Dranseikienė, D and Balčiūnaitė-Murzienė, G and Karosienė, J and Morudov, D and Juodžiukynienė, N and Hudz, N and Gerbutavičienė, RJ and Savickienė, N}, title = {Cyano-Phycocyanin: Mechanisms of Action on Human Skin and Future Perspectives in Medicine.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {9}, pages = {}, pmid = {35567250}, issn = {2223-7747}, abstract = {Cyano-phycocyanin is one of the active pigments of the blue-green algae and is usually isolated from the filamentous cyanobacteria Arthrospira platensis Gomont (Spirulina). Due to its multiple physiological functions and non-toxicity, cyano-phycocyanin may be a potential substance for the topical treatment of various skin diseases. Considering that the conventional medicine faces drug resistance, insufficient efficacy and side effects, the plant origin compounds can act as an alternative option. Thus, the aim of this paper was to review the wound healing, antimicrobial, antioxidative, anti-inflammatory, antimelanogenic and anticancer properties and mechanisms of cyano-phycocyanin topical activities on human skin. Moreover, possible applications and biotechnological requirements for pharmaceutical forms of cyano-phycocyanin for the treatment of various skin diseases are discussed in this review.}, }
@article {pmid35567212, year = {2022}, author = {Li, Y and Wang, C and Ge, L and Hu, C and Wu, G and Sun, Y and Song, L and Wu, X and Pan, A and Xu, Q and Shi, J and Liang, J and Li, P}, title = {Environmental Behaviors of Bacillus thuringiensis (Bt) Insecticidal Proteins and Their Effects on Microbial Ecology.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {9}, pages = {}, pmid = {35567212}, issn = {2223-7747}, abstract = {Bt proteins are crystal proteins produced by Bacillus thuringiensis (Bt) in the early stage of spore formation that exhibit highly specific insecticidal activities. The application of Bt proteins primarily includes Bt transgenic plants and Bt biopesticides. Transgenic crops with insect resistance (via Bt)/herbicide tolerance comprise the largest global area of agricultural planting. After artificial modification, Bt insecticidal proteins expressed from Bt can be released into soils through root exudates, pollen, and plant residues. In addition, the construction of Bt recombinant engineered strains through genetic engineering has become a major focus of Bt biopesticides, and the expressed Bt proteins will also remain in soil environments. Bt proteins expressed and released by Bt transgenic plants and Bt recombinant strains are structurally and functionally quite different from Bt prototoxins naturally expressed by B. thuringiensis in soils. The former can thus be regarded as an environmentally exogenous substance with insecticidal toxicity that may have potential ecological risks. Consequently, biosafety evaluations must be conducted before field tests and production of Bt plants or recombinant strains. This review summarizes the adsorption, retention, and degradation behavior of Bt insecticidal proteins in soils, in addition to their impacts on soil physical and chemical properties along with soil microbial diversity. The review provides a scientific framework for evaluating the environmental biosafety of Bt transgenic plants, Bt transgenic microorganisms, and their expression products. In addition, prospective research targets, research methods, and evaluation methods are highlighted based on current research of Bt proteins.}, }
@article {pmid35562794, year = {2022}, author = {Deehan, EC and Zhang, Z and Riva, A and Armet, AM and Perez-Muñoz, ME and Nguyen, NK and Krysa, JA and Seethaler, B and Zhao, YY and Cole, J and Li, F and Hausmann, B and Spittler, A and Nazare, JA and Delzenne, NM and Curtis, JM and Wismer, WV and Proctor, SD and Bakal, JA and Bischoff, SC and Knights, D and Field, CJ and Berry, D and Prado, CM and Walter, J}, title = {Elucidating the role of the gut microbiota in the physiological effects of dietary fiber.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {77}, pmid = {35562794}, issn = {2049-2618}, support = {RN-298871-372173//CIHR/Canada ; }, mesh = {Adult ; Bacteria ; Bile Acids and Salts/analysis ; Biomarkers/analysis ; Dietary Fiber ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/physiology ; Humans ; Leukocyte L1 Antigen Complex/analysis/pharmacology ; Male ; Obesity/microbiology ; }, abstract = {BACKGROUND: Dietary fiber is an integral part of a healthy diet, but questions remain about the mechanisms that underlie effects and the causal contributions of the gut microbiota. Here, we performed a 6-week exploratory trial in adults with excess weight (BMI: 25-35 kg/m[2]) to compare the effects of a high-dose (females: 25 g/day; males: 35 g/day) supplement of fermentable corn bran arabinoxylan (AX; n = 15) with that of microbiota-non-accessible microcrystalline cellulose (MCC; n = 16). Obesity-related surrogate endpoints and biomarkers of host-microbiome interactions implicated in the pathophysiology of obesity (trimethylamine N-oxide, gut hormones, cytokines, and measures of intestinal barrier integrity) were assessed. We then determined whether clinical outcomes could be predicted by fecal microbiota features or mechanistic biomarkers.<br><br>RESULTS: AX enhanced satiety after a meal and decreased homeostatic model assessment of insulin resistance (HOMA-IR), while MCC reduced tumor necrosis factor-&#x3b1; and fecal calprotectin. Machine learning models determined that effects on satiety could be predicted by fecal bacterial taxa that utilized AX, as identified by bioorthogonal non-canonical amino acid tagging. Reductions in HOMA-IR and calprotectin were associated with shifts in fecal bile acids, but correlations were negative, suggesting that the benefits of fiber may not be mediated by their effects on bile acid pools. Biomarkers of host-microbiome interactions often linked to bacterial metabolites derived from fiber fermentation (short-chain fatty acids) were not affected by AX supplementation when compared to non-accessible MCC.<br><br>CONCLUSION: This study demonstrates the efficacy of purified dietary fibers when used as supplements and suggests that satietogenic effects of AX may be linked to bacterial taxa that ferment the fiber or utilize breakdown products. Other effects are likely microbiome independent. The findings provide a basis for fiber-type specific therapeutic applications and their personalization.<br><br>TRIAL REGISTRATION: Clinicaltrials.gov, NCT02322112 , registered on July 3, 2015. Video Abstract.}, }
@article {pmid35562600, year = {2023}, author = {Greene, LK and McKenney, EA and Gasper, W and Wrampelmeier, C and Hayer, S and Ehmke, EE and Clayton, JB}, title = {Gut Site and Gut Morphology Predict Microbiome Structure and Function in Ecologically Diverse Lemurs.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1608-1619}, pmid = {35562600}, issn = {1432-184X}, support = {PRFB 1906416//Directorate for Biological Sciences/ ; }, mesh = {Animals ; *Lemur ; Retrospective Studies ; *Lemuridae ; *Microbiota ; *Strepsirhini ; }, abstract = {Most studies of wildlife gut microbiotas understandably rely on feces to approximate consortia along the gastrointestinal tract. We therefore compared microbiome structure and predicted metagenomic function in stomach, small intestinal, cecal, and colonic samples from 52 lemurs harvested during routine necropsies. The lemurs represent seven genera (Cheirogaleus, Daubentonia, Varecia, Hapalemur, Eulemur, Lemur, Propithecus) characterized by diverse feeding ecologies and gut morphologies. In particular, the hosts variably depend on fibrous foodstuffs and show correlative morphological complexity in their large intestines. Across host lineages, microbiome diversity, variability, membership, and function differed between the upper and lower gut, reflecting regional tradeoffs in available nutrients. These patterns related minimally to total gut length but were modulated by fermentation capacity (i.e., the ratio of small to large intestinal length). Irrespective of feeding strategy, host genera with limited fermentation capacity harbored more homogenized microbiome diversity along the gut, whereas those with expanded fermentation capacity harbored cecal and colonic microbiomes with greater diversity and abundant fermentative Ruminococcaceae taxa. While highlighting the value of curated sample repositories for retrospective comparisons, our results confirm that the need to survive on fibrous foods, either routinely or in hypervariable environments, can shape the morphological and microbial features of the lower gut.}, }
@article {pmid35562021, year = {2022}, author = {Mariën, Q and Ulčar, B and Verleyen, J and Vanthuyne, B and Ganigué, R}, title = {High-rate conversion of lactic acid-rich streams to caproic acid in a fermentative granular system.}, journal = {Bioresource technology}, volume = {355}, number = {}, pages = {127250}, doi = {10.1016/j.biortech.2022.127250}, pmid = {35562021}, issn = {1873-2976}, mesh = {Acetic Acid ; *Bioreactors ; Caproates ; Carbohydrates ; Glucose ; *Lactic Acid ; Rivers ; Sewage/chemistry ; }, abstract = {Lactic acid-driven chain elongation enables upgrading low-value organic streams into caproic acid. Recently, volumetric production rates over 0.5 g L[-1] h[-1]have been reported for carbohydrate-rich streams in expanded granular sludge bed (EGSB) reactors. However, many target streams contain mixtures of carbohydrates and lactic acid, and little is known about their impact on product profile and microbial ecology, or the importance of carbohydrates as substrate to achieve high rates. This manuscript investigated varying glucose-to-lactate ratios and observed that decreasing glucose-content eliminated odd-chain by-products, while glucose omission required acetic acid addition to support lactic acid conversion. Decreasing the glucose-content fed resulted in decreasing amounts of granular biomass, with the disappearance of granules when no glucose was fed. Lowering the HRT to 0.3 days while feeding only lactic and acetic acid likely triggered re-granulation, enabling the highest lactic acid-driven caproic acid production rates reported thus far at 16.4 ± 1.7 g L[-1] d[-1].}, }
@article {pmid35556154, year = {2023}, author = {Billet, L and Pesce, S and Martin-Laurent, F and Devers-Lamrani, M}, title = {Experimental Evidence for Manure-Borne Bacteria Invasion in Soil During a Coalescent Event: Influence of the Antibiotic Sulfamethazine.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1463-1472}, pmid = {35556154}, issn = {1432-184X}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Sulfamethazine ; Manure/microbiology ; Soil ; Soil Microbiology ; Bacteria/genetics ; }, abstract = {The fertilization of agricultural soil by organic amendment that may contain antibiotics, like manure, can transfer bacterial pathogens and antibiotic-resistant bacteria to soil communities. However, the invasion by manure-borne bacteria in amended soil remains poorly understood. We hypothesized that this kind of process is both influenced by the soil properties (and those of its microbial communities) and by the presence of contaminants such as antibiotics used in veterinary care. To test that, we performed a microcosm experiment in which four different soils were amended or not with manure at an agronomical dose and exposed or not to the antibiotic sulfamethazine (SMZ). After 1 month of incubation, the diversity, structure, and composition of bacterial communities of the soils were assessed by 16S rDNA sequencing. The invasion of manure-borne bacteria was still perceptible 1 month after the soil amendment. The results obtained with the soil already amended in situ with manure 6 months prior to the experiment suggest that some of the bacterial invaders were established in the community over the long term. Even if differences were observed between soils, the invasion was mainly attributable to some of the most abundant OTUs of manure (mainly Firmicutes). SMZ exposure had a limited influence on soil microorganisms but our results suggest that this kind of contaminant can enhance the invasion ability of some manure-borne invaders.}, }
@article {pmid35552795, year = {2023}, author = {Newcombe, G and Marlin, M and Barge, E and Heitmann, S and Ridout, M and Busby, PE}, title = {Plant Seeds Commonly Host Bacillus spp., Potential Antagonists of Phytopathogens.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1356-1366}, pmid = {35552795}, issn = {1432-184X}, support = {1314095//National Science Foundation/ ; 16.67//National Science Foundation/ ; }, mesh = {Humans ; *Bacillus ; Seeds/microbiology ; Fungi ; Bacteria ; Plants ; *Ascomycota ; }, abstract = {In agriculture, horticulture and plantation forestry, Bacillus species are the most commonly applied antagonists and biopesticides, targeting plant pathogens and insect pests, respectively. Bacillus isolates are also used as bacterial plant biostimulants, or BPBs. Such useful isolates of Bacillus are typically sourced from soil. Here, we show that Bacillus - and other antagonistic microbes - can be sourced from a broad range of plant seeds. We found that culturable Bacillus isolates are common in the seeds of 98 plant species representing 39 families (i.e., 87% of the commonly cultured bacteria belonged to Bacillales). We also found that 83% of the commonly cultured fungi from the seeds of the 98 plant species belonged to just three orders of fungi-Pleosporales, Hypocreales and Eurotiales-that are also associated with antagonism. Furthermore, we confirmed antagonism potential in agaro with seed isolates of Bacillus from Pinus monticola as a representative case. Eight isolates each of seed Bacillus, seed fungi, and foliar fungi, all from P. monticola, were paired in a total of 384 possible pair-wise interactions (with seed and foliar fungi as the targets). Seed Bacillus spp. were the strongest antagonists of the seed and foliar fungi, with a mean interaction strength 2.8 times greater than seed fungi (all either Eurotiales or Hypocreales) and 3.2 times greater than needle fungi. Overall, our study demonstrates that seeds host a taxonomically narrow group of culturable, antagonistic bacteria and fungi.}, }
@article {pmid35552794, year = {2023}, author = {Chauvet, M and Monjot, A and Moné, A and Lepère, C}, title = {Single Cell Analysis Reveals a New Microsporidia-Host Association in a Freshwater Lake.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1630-1633}, pmid = {35552794}, issn = {1432-184X}, mesh = {*Microsporidia/physiology ; Lakes/parasitology ; Ecosystem ; Food Chain ; Single-Cell Analysis ; }, abstract = {Microsporidia are a large group of obligate intracellular eukaryotic parasites. Recent studies suggest that their diversity can be huge in freshwater lake ecosystems especially in the < 150-µm size fraction. However, little is known about their hosts and therefore their impact on the trophic food web functioning. In this study, single cell analysis and fluorescence microscopy were used to detect new host-parasite association within rotifer communities in lake Aydat (France). Our analysis showed the existence of a potential new species belonging to the Crispospora genus able of infecting the rotifer Kellicottia with a high prevalence (42.5%) suggesting that Microsporidia could have a great impact on the rotifer populations' regulation in lakes.}, }
@article {pmid35550672, year = {2022}, author = {Samara, J and Moossavi, S and Alshaikh, B and Ortega, VA and Pettersen, VK and Ferdous, T and Hoops, SL and Soraisham, A and Vayalumkal, J and Dersch-Mills, D and Gerber, JS and Mukhopadhyay, S and Puopolo, K and Tompkins, TA and Knights, D and Walter, J and Amin, H and Arrieta, MC}, title = {Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants.}, journal = {Cell host &amp; microbe}, volume = {30}, number = {5}, pages = {696-711.e5}, doi = {10.1016/j.chom.2022.04.005}, pmid = {35550672}, issn = {1934-6069}, mesh = {Bifidobacterium ; Ecosystem ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Extremely Premature ; Infant, Newborn ; Inflammation ; *Probiotics ; }, abstract = {Probiotics are increasingly administered to premature infants to prevent necrotizing enterocolitis and neonatal sepsis. However, their effects on gut microbiome assembly and immunity are poorly understood. Using a randomized intervention trial in extremely premature infants, we tested the effects of a probiotic product containing four strains of Bifidobacterium species autochthonous to the infant gut and one Lacticaseibacillus strain on the compositional and functional trajectory of microbiome. Daily administration of the mixture accelerated the transition into a mature, term-like microbiome with higher stability and species interconnectivity. Besides infant age, Bifidobacterium strains and stool metabolites were the best predictors of microbiome maturation, and structural equation modeling confirmed probiotics as a major determinant for the trajectory of microbiome assembly. Bifidobacterium-driven microbiome maturation was also linked to an anti-inflammatory intestinal immune milieu. This demonstrates that Bifidobacterium strains are ecosystem engineers that lead to an acceleration of microbiome maturation and immunological consequences in extremely premature infants.}, }
@article {pmid35550507, year = {2022}, author = {Jamnik, T and Flasch, M and Braun, D and Fareed, Y and Wasinger, D and Seki, D and Berry, D and Berger, A and Wisgrill, L and Warth, B}, title = {Next-generation biomonitoring of the early-life chemical exposome in neonatal and infant development.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {2653}, pmid = {35550507}, issn = {2041-1723}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Biological Monitoring ; Child ; Child Development ; *Exposome ; Female ; Humans ; Infant ; Infant, Newborn ; Tandem Mass Spectrometry/methods ; Xenobiotics/toxicity ; }, abstract = {Exposure to synthetic and natural chemicals is a major environmental risk factor in the etiology of many chronic diseases. Investigating complex co-exposures is necessary for a holistic assessment in exposome-wide association studies. In this work, a sensitive liquid chromatography-tandem mass spectrometry approach was developed and validated. The assay enables the analysis of more than 80 highly-diverse xenobiotics in urine, serum/plasma, and breast milk; with detection limits generally in the pg-ng mL[-1] range. In plasma of extremely-premature infants, 27 xenobiotics are identified; including contamination with plasticizers, perfluorinated alkylated substances and parabens. In breast milk samples collected longitudinally over the first 211 days post-partum, 29 analytes are detected, including pyrrolizidine- and tropane alkaloids which have not been identified in this matrix before. A preliminary estimation of daily toxicant intake via breast milk is conducted. In conclusion, we observe significant early-life co-exposure to multiple toxicants, and demonstrate the method's applicability for large-scale exposomics-type cohort studies.}, }
@article {pmid35549250, year = {2022}, author = {Xu, G and Ng, HL and Chen, C and Zhao, S and He, J}, title = {Efficient and Complete Detoxification of Polybrominated Diphenyl Ethers in Sediments Achieved by Bioaugmentation with Dehalococcoides and Microbial Ecological Insights.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {12}, pages = {8008-8019}, doi = {10.1021/acs.est.2c00914}, pmid = {35549250}, issn = {1520-5851}, mesh = {Biodegradation, Environmental ; Dehalococcoides ; *Environmental Pollutants ; Geologic Sediments/chemistry ; Halogenated Diphenyl Ethers ; *Tetrachloroethylene ; *Water Pollutants, Chemical ; }, abstract = {Polybrominated diphenyl ethers (PBDEs) are prevalent environmental pollutants, but bioremediation of PBDEs remains to be reported. Here we report accelerated remediation of a penta-BDE mixture in sediments by bioaugmentation with Dehalococcoides mccartyi strains CG1 and TZ50. Bioaugmentation with different amounts of each Dehalococcoides strain enhanced debromination of penta-BDEs compared with the controls. The sediment microcosm spiked with 6.8 × 10[6] cells/mL strain CG1 showed the highest penta-BDEs removal (89.9 ± 7.3%) to diphenyl ether within 60 days. Interestingly, co-contaminant tetrachloroethene (PCE) improved bioaugmentation performance, resulting in faster and more extensive penta-BDEs debromination using less bioinoculants, which was also completely dechlorinated to ethene by introducing D. mccartyi strain 11a. The better bioaugmentation performance in sediments with PCE could be attributed to the boosted growth of the augmented Dehalococcoides and capability of the PCE-induced reductive dehalogenases to debrominate penta-BDEs. Finally, ecological analyses showed that bioaugmentation resulted in more deterministic microbial communities, where the augmented Dehalococcoides established linkages with indigenous microorganisms but without causing obvious alterations of the overall community diversity and structure. Collectively, this study demonstrates that bioaugmentation with Dehalococcoides is a feasible strategy to completely remove PBDEs in sediments.}, }
@article {pmid35547145, year = {2022}, author = {McElhinney, JMWR and Catacutan, MK and Mawart, A and Hasan, A and Dias, J}, title = {Interfacing Machine Learning and Microbial Omics: A Promising Means to Address Environmental Challenges.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {851450}, pmid = {35547145}, issn = {1664-302X}, abstract = {Microbial communities are ubiquitous and carry an exceptionally broad metabolic capability. Upon environmental perturbation, microbes are also amongst the first natural responsive elements with perturbation-specific cues and markers. These communities are thereby uniquely positioned to inform on the status of environmental conditions. The advent of microbial omics has led to an unprecedented volume of complex microbiological data sets. Importantly, these data sets are rich in biological information with potential for predictive environmental classification and forecasting. However, the patterns in this information are often hidden amongst the inherent complexity of the data. There has been a continued rise in the development and adoption of machine learning (ML) and deep learning architectures for solving research challenges of this sort. Indeed, the interface between molecular microbial ecology and artificial intelligence (AI) appears to show considerable potential for significantly advancing environmental monitoring and management practices through their application. Here, we provide a primer for ML, highlight the notion of retaining biological sample information for supervised ML, discuss workflow considerations, and review the state of the art of the exciting, yet nascent, interdisciplinary field of ML-driven microbial ecology. Current limitations in this sphere of research are also addressed to frame a forward-looking perspective toward the realization of what we anticipate will become a pivotal toolkit for addressing environmental monitoring and management challenges in the years ahead.}, }
@article {pmid35543735, year = {2023}, author = {Merlin, BL and Moraes, GJ and Cônsoli, FL}, title = {The Microbiota of a Mite Prey-Predator System on Different Host Plants Are Characterized by Dysbiosis and Potential Functional Redundancy.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1590-1607}, pmid = {35543735}, issn = {1432-184X}, support = {2018/24768-9//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/12004-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {Animals ; Female ; *Dysbiosis ; RNA, Ribosomal, 16S/genetics ; Reproduction ; Life Cycle Stages ; Predatory Behavior/physiology ; *Tetranychidae/physiology ; Pest Control, Biological ; }, abstract = {Microbiota has diverse roles in the life cycles of their hosts, affecting their growth, development, behavior, and reproduction. Changes in physiological conditions of the host can also impact the assemblage of host-associated microorganisms. However, little is known of the effects of host plant-prey-predatory mite interactions on mite microbiota. We compared the microbial communities of eggs and adult females of the two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae), and of adult females of the predatory mite Neoseiulus californicus (McGregor) (Acari: Phytoseiidae) on four different host plants (cotton, maize, pinto bean, and tomato) by metabarcoding sequencing of the V3-V4 region of the 16S ribosomal RNA gene (16S rRNA), using the Illumina MiSeq platform. Only the egg microbiota of T. urticae was affected by the host plant. The microbiota of the predatory mite N. californicus was very different from that of its prey, and the predator microbiota was unaffected by the different host plant-prey systems tested. Only the microbiota of the eggs of T. urticae carried Serratia as a high fidelity-biomarker, but their low abundance in T. urticae adult females suggests that the association between Serratia and T. urticae is accidental. Biomarker bacteria were also detected in the microbiota of adult females of T. urticae and N. californicus, with different biomarkers in each host plant species. The microbiota associated with eggs and adult females of T. urticae and adult females of N. californicus differed in their functional potential contributions to the host mite.}, }
@article {pmid35538057, year = {2022}, author = {Patrono, LV and Vrancken, B and Budt, M and Düx, A and Lequime, S and Boral, S and Gilbert, MTP and Gogarten, JF and Hoffmann, L and Horst, D and Merkel, K and Morens, D and Prepoint, B and Schlotterbeck, J and Schuenemann, VJ and Suchard, MA and Taubenberger, JK and Tenkhoff, L and Urban, C and Widulin, N and Winter, E and Worobey, M and Schnalke, T and Wolff, T and Lemey, P and Calvignac-Spencer, S}, title = {Archival influenza virus genomes from Europe reveal genomic variability during the 1918 pandemic.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {2314}, pmid = {35538057}, issn = {2041-1723}, support = {R01 HG006139/HG/NHGRI NIH HHS/United States ; 206298/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Genome, Viral/genetics ; Genomics ; Humans ; *Influenza A Virus, H1N1 Subtype/genetics ; *Influenza A virus/genetics ; *Influenza, Human/epidemiology/genetics ; }, abstract = {The 1918 influenza pandemic was the deadliest respiratory pandemic of the 20th century and determined the genomic make-up of subsequent human influenza A viruses (IAV). Here, we analyze both the first 1918 IAV genomes from Europe and the first from samples prior to the autumn peak. 1918 IAV genomic diversity is consistent with a combination of local transmission and long-distance dispersal events. Comparison of genomes before and during the pandemic peak shows variation at two sites in the nucleoprotein gene associated with resistance to host antiviral response, pointing at a possible adaptation of 1918 IAV to humans. Finally, local molecular clock modeling suggests a pure pandemic descent of seasonal H1N1 IAV as an alternative to the hypothesis of origination through an intrasubtype reassortment.}, }
@article {pmid35537512, year = {2022}, author = {Cui, G and Liu, Z and Xu, W and Gao, Y and Yang, S and Grossart, HP and Li, M and Luo, Z}, title = {Metagenomic exploration of antibiotic resistance genes and their hosts in aquaculture waters of the semi-closed Dongshan Bay (China).}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 1}, pages = {155784}, doi = {10.1016/j.scitotenv.2022.155784}, pmid = {35537512}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Aquaculture ; Bays ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; *Metagenome ; beta-Lactamases/genetics ; }, abstract = {In marine environments, increasing occurrence and numbers of microbial Antibiotic Resistance Gene (ARG) subtypes, especially of new beta-lactamases, have received lots of attention in recent years. Updated databases with novel developed tools provide new opportunities to obtain more comprehensive ARG profiles as well as ARG-carrying hosts. Yet, ARGs in human-associated marine aquaculture environments, e.g. in China, remains largely unknown. Using metagenomic data, we revealed high numbers of Multi-drug Resistance, beta-lactamase and aminoglycoside genes throughout the year. Thereby, Alpha- and Gamma-proteobacteria were assigned to the majority of beta-lactamase-carrying hosts. From Metagenome-assembled genomes, three blaF-like beta-lactamases (91.7-94.7% identity with beta-lactamase from Mycobacterium fortuitum (blaF)) were exclusively observed in an unclassified Mycobacterium genus. Notably, other new beta-lactamases, VMB-1-like (n = 3) (58.5-67.4% identity to Vibrio metallo-beta-lactamase 1 (VMB-1)), were found in Gammaproteobacteria. Additionally, 175 Multi-drug Resistant Organisms possessed at least 3 ARG subtypes, and seven of the potentially pathogenic genera (n = 17) were assigned to Gammaproteobacteria. These results, together with high-risk ARGs (e.g. tetM, dfrA14 and dfrA17), provide hosts and new beta-lactamases of ARGs in Chinese coastal aquaculture.}, }
@article {pmid35537509, year = {2022}, author = {Xu, N and Zhang, Z and Shen, Y and Zhang, Q and Liu, Z and Yu, Y and Wang, Y and Lei, C and Ke, M and Qiu, D and Lu, T and Chen, Y and Xiong, J and Qian, H}, title = {Compare the performance of multiple binary classification models in microbial high-throughput sequencing datasets.}, journal = {The Science of the total environment}, volume = {837}, number = {}, pages = {155807}, doi = {10.1016/j.scitotenv.2022.155807}, pmid = {35537509}, issn = {1879-1026}, mesh = {Algorithms ; *Artificial Intelligence ; High-Throughput Nucleotide Sequencing ; Machine Learning ; *Neural Networks, Computer ; Support Vector Machine ; }, abstract = {The development of machine learning and deep learning provided solutions for predicting microbiota response on environmental change based on microbial high-throughput sequencing. However, there were few studies specifically clarifying the performance and practical of two types of binary classification models to find a better algorithm for the microbiota data analysis. Here, for the first time, we evaluated the performance, accuracy and running time of the binary classification models built by three machine learning methods - random forest (RF), support vector machine (SVM), logistic regression (LR), and one deep learning method - back propagation neural network (BPNN). The built models were based on the microbiota datasets that removed low-quality variables and solved the class imbalance problem. Additionally, we optimized the models by tuning. Our study demonstrated that dataset pre-processing was a necessary process for model construction. Among these 4 binary classification models, BPNN and RF were the most suitable methods for constructing microbiota binary classification models. Using these 4 models to predict multiple microbial datasets, BPNN showed the highest accuracy and the most robust performance, while the RF method was ranked second. We also constructed the optimal models by adjusting the epochs of BPNN and the n_estimators of RF for six times. The evaluation related to performances of models provided a road map for the application of artificial intelligence to assess microbial ecology.}, }
@article {pmid35534014, year = {2022}, author = {Knapp, BD and Huang, KC}, title = {The Effects of Temperature on Cellular Physiology.}, journal = {Annual review of biophysics}, volume = {51}, number = {}, pages = {499-526}, doi = {10.1146/annurev-biophys-112221-074832}, pmid = {35534014}, issn = {1936-1238}, support = {RM1 GM135102/GM/NIGMS NIH HHS/United States ; }, mesh = {Cell Physiological Phenomena ; *Ecosystem ; *Global Warming ; Humans ; Temperature ; }, abstract = {Temperature impacts biological systems across all length and timescales. Cells and the enzymes that comprise them respond to temperature fluctuations on short timescales, and temperature can affect protein folding, the molecular composition of cells, and volume expansion. Entire ecosystems exhibit temperature-dependent behaviors, and global warming threatens to disrupt thermal homeostasis in microbes that are important for human and planetary health. Intriguingly, the growth rate of most species follows the Arrhenius law of equilibrium thermodynamics, with an activation energy similar to that of individual enzymes but with maximal growth rates and over temperature ranges that are species specific. In this review, we discuss how the temperature dependence of critical cellular processes, such as the central dogma and membrane fluidity, contributes to the temperature dependence of growth. We conclude with a discussion of adaptation to temperature shifts and the effects of temperature on evolution and on the properties of microbial ecosystems.}, }
@article {pmid35533832, year = {2022}, author = {Lu, S and Zhang, W and Li, X and Xian, J and Hu, Y and Zhou, Y}, title = {Skin bacterial richness and diversity in intensive care unit patients with severe pneumonia.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {121}, number = {}, pages = {75-84}, doi = {10.1016/j.ijid.2022.05.006}, pmid = {35533832}, issn = {1878-3511}, mesh = {Bacteria/genetics ; Humans ; Intensive Care Units ; *Microbiota ; *Pneumonia/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVES: Patients with severe pneumonia admitted to the intensive care unit (ICU) have a high risk of mortality, and the microbiome is likely to affect the outcome of such patients. However, the composition of the skin microbiota of ICU patients with severe pneumonia remains unclear. In this study, on the basis of 16S ribosomal ribonucleic acid sequencing, we explored the difference in skin bacterial richness and diversity between the ICU patient group (PG) with severe pneumonia and the healthy control group (CG).<br><br>METHODS: The diversity index and taxonomic distribution of skin bacteria were analyzed using the Quantitative Insights Into Microbial Ecology (QIIME) bioinformatics pipeline. Blood, endotracheal aspirate, and bronchoalveolar lavage fluid samples were collected from the same PG subjects for culture.<br><br>RESULTS: Compared with the CG, the diversity of skin bacteria in the PG decreased significantly. Staphylococcus, Acinetobacter, Stenotrophomonas, Enterococcus, Halomonas, and Brevibacillus were differentially abundant in the PG, and most of these bacteria were also identified in the cultures of upper respiratory tract samples of the same PG.<br><br>CONCLUSION: We provide evidence that healthcare-associated infection in ICU patients with severe pneumonia is strongly associated with skin microbiota, which necessitates the prevention and control of skin bacterial pathogens for these patients.}, }
@article {pmid35532036, year = {2023}, author = {Van Bonn, W and Oliaro, FJ and Pinnell, LJ}, title = {Ultraviolet light alters experimental aquarium water microbial communities.}, journal = {Zoo biology}, volume = {42}, number = {1}, pages = {133-141}, doi = {10.1002/zoo.21701}, pmid = {35532036}, issn = {1098-2361}, mesh = {Animals ; *Water ; Ultraviolet Rays ; Carbon Dioxide ; Animals, Zoo ; Bacteria ; *Microbiota ; }, abstract = {The effect of ultraviolet (UV) light exposure, alone and in combination with CO2 exposure, on the water microbial community composition was tested in replicate experimental aquaria using source water from an established Amazon-themed exhibit housing mixed species of fishes. Total bacterial abundance, α-diversity metrics, and β-diversity metrics were determined 3 weeks and 1 week before, and weekly during 8 weeks of continuous treatment. The UV treatment significantly lowered the overall bacterial abundance while CO2 treatment had no effect. However, the UV exposure effect was variable across phyla. Some phyla were decreased while others were increased, including some of potential clinical significance. At the genus level, there were no significant differences in the relative abundance of Mycobacteria between treatments and an increase in the relative abundance of Aeromonas spp. with UV light treatment. Further work is needed to determine if the observed effects are dose-dependent or if different exposure doses produce different results.}, }
@article {pmid35531295, year = {2022}, author = {Na, N and Qili, M and Wu, N and Sun, L and Xu, H and Zhao, Y and Wei, X and Xue, Y and Tao, Y}, title = {Bacterial Community and Fermentation Quality of Ensiling Alfalfa With Commercial Lactic Acid Bacterial Additives.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {836899}, pmid = {35531295}, issn = {1664-302X}, abstract = {The aim of this study was to determine the effects of six common commercial lactic acid bacteria (LAB) additives [A1, Lactobacillus plantarum, L. buchneri, and Enterococcus faecalis; A2, L. plantarum and L. casei; A3, L. plantarum and L. buchneri; A4, L. plantarum, L. buchneri, L. casei, and Pediococcus acidilactici; A5, L. plantarum (producing feruloyl esterase); and A6, L. buchneri, P. acidilactici, β-glucanase, and xylanase] on the bacterial community and fermentation quality of alfalfa silage. Alfalfa was harvested at the squaring stage, wilted in the field for 24 h, and ensiled without any additives (Control) or with A1, A2, A3, A4, A5, or A6. Microbial counts, bacterial community, fermentation parameters, and nutritional composition were determined after ensiling for 90 days. The total abundance of LAB genera on alfalfa pre-ensiling was 0.38% in bacterial community. The abundances of Lactobacillus, Enterococcus, and Pediococcus in the Control silage were 42.18, 40.18, and 8.09% of abundance, respectively. The abundances of Lactobacillus in A1-, A2-, A3-, A4-, and A5-treatments were 89.32, 92.93, 92.87, 81.12, and 80.44%, respectively. The abundances of Pediococcus and Lactobacillus in A6-treatment were 70.14 and 24.86%, respectively. Compared with Control silage, LAB-treated silage had lower pH and less ammonia nitrogen and water-soluble carbohydrates concentrations (p < 0.05). Further, the A5- and A6-treatments contained lower neutral detergent fiber, acid detergent fiber, and hemicellulose than other treatments (p < 0.05). Overall, LAB genera were presented as minor taxa in alfalfa pre-ensiling and as dominant taxa in alfalfa silage. Adding LAB additives improved the fermentation quality and altered the bacterial community of alfalfa silage. The main bacterial genera in Control silage were Lactobacillus, Enterococcus, and Pediococcus. Lactobacillus dominated the bacterial communities of A1-, A2-, A3-, A4-, and A5-treatments, while Pediococcus and Lactobacillus were dominant bacterial genera in A6-treatment. Inoculating A5 and A6 degraded the fiber in alfalfa silage. It is necessary to ensile alfalfa with LAB inoculants.}, }
@article {pmid35529946, year = {2022}, author = {Franzino, T and Boubakri, H and Cernava, T and Abrouk, D and Achouak, W and Reverchon, S and Nasser, W and Haichar, FEZ}, title = {Implications of carbon catabolite repression for plant-microbe interactions.}, journal = {Plant communications}, volume = {3}, number = {2}, pages = {100272}, pmid = {35529946}, issn = {2590-3462}, mesh = {Bacteria/metabolism ; Carbon/metabolism ; *Catabolite Repression/genetics ; Fungi/metabolism ; }, abstract = {Carbon catabolite repression (CCR) plays a key role in many physiological and adaptive responses in a broad range of microorganisms that are commonly associated with eukaryotic hosts. When a mixture of different carbon sources is available, CCR, a global regulatory mechanism, inhibits the expression and activity of cellular processes associated with utilization of secondary carbon sources in the presence of the preferred carbon source. CCR is known to be executed by completely different mechanisms in different bacteria, yeast, and fungi. In addition to regulating catabolic genes, CCR also appears to play a key role in the expression of genes involved in plant-microbe interactions. Here, we present a detailed overview of CCR mechanisms in various bacteria. We highlight the role of CCR in beneficial as well as deleterious plant-microbe interactions based on the available literature. In addition, we explore the global distribution of known regulatory mechanisms within bacterial genomes retrieved from public repositories and within metatranscriptomes obtained from different plant rhizospheres. By integrating the available literature and performing targeted meta-analyses, we argue that CCR-regulated substrate use preferences of microorganisms should be considered an important trait involved in prevailing plant-microbe interactions.}, }
@article {pmid35528619, year = {2022}, author = {Qing, JB and Song, WZ and Li, CQ and Li, YF}, title = {The Diagnostic and Predictive Significance of Immune-Related Genes and Immune Characteristics in the Occurrence and Progression of IgA Nephropathy.}, journal = {Journal of immunology research}, volume = {2022}, number = {}, pages = {9284204}, pmid = {35528619}, issn = {2314-7156}, mesh = {Female ; *Glomerulonephritis, IGA/diagnosis/genetics ; Humans ; Inflammation/pathology ; Kidney Glomerulus/pathology ; Macrophages/pathology ; Male ; RNA, Messenger/genetics ; }, abstract = {OBJECTIVE: To investigate the potential diagnostic and predictive significance of immune-related genes in IgA nephropathy (IgAN) and discover the abnormal glomerular inflammation in IgAN.<br><br>METHODS: GSE116626 was used as a training set to identify different immune-related genes (DIRGs) and establish machine learning models for the diagnosis of IgAN; then, a nomogram model was generated based on GSE116626, and GSE115857 was used as a test set to evaluate its clinical value. Short Time-Series Expression Miner (STEM) analysis was also performed to explore the changing trend of DIRGs with the progression of IgAN lesions. GSE141344 was used with DIRGs to establish the ceRNA network associated with IgAN progression. Finally, ssGSEA analysis was performed on the GSE141295 dataset to discover the abnormal inflammation in IgAN.<br><br>RESULTS: Machine learning (ML) performed excellently in diagnosing IgAN using six DIRGs. A nomogram model was constructed to predict IgAN based on the six DIRGs. Three trends related to IgAN lesions were identified using STEM analysis. A ceRNA network associated with IgAN progression which contained 8 miRNAs, 14 lncRNAs, and 3 mRNAs was established. A higher macrophage ratio and lower CD4+ T cell ratio in IgAN compared to controls were observed, and the correlation between macrophages and monocytes in the glomeruli of IgAN patients was inverse compared to controls.<br><br>CONCLUSION: This study reveals the diagnostic and predictive significance of DIRGs in IgAN and finds that the imbalance between macrophages and CD4+ immune cells may be an important pathomechanism of IgAN. These results provide potential directions for the treatment and prevention of IgAN.}, }
@article {pmid35526797, year = {2022}, author = {Zhang, X and Jin, Z and Shen, M and Chang, Z and Yu, G and Wang, L and Xia, X}, title = {Accumulation of polyethylene microplastics induces oxidative stress, microbiome dysbiosis and immunoregulation in crayfish.}, journal = {Fish &amp; shellfish immunology}, volume = {125}, number = {}, pages = {276-284}, doi = {10.1016/j.fsi.2022.05.005}, pmid = {35526797}, issn = {1095-9947}, mesh = {Animals ; Astacoidea/genetics ; Dysbiosis ; Hydrogen Peroxide/metabolism ; *Microbiota ; Microplastics ; Oxidative Stress ; Plastics ; Polyethylene ; *Water Pollutants, Chemical/toxicity ; }, abstract = {Microplastics have become a worldwide pollutant, widely discovered in soil, air and aquatic environment. Microplastics have been found in habitats where crayfish (Procambarus clarkii) cultivated, but the impact of microplastics on crayfish remains unclear. In this study, after 21-day dietary exposure, polyethylene (PE) particles were found to accumulate in intestine, hepatopancreas, gills and hemolymph of crayfish. Furthermore, PE particles can still be detected in these tissues after a 7-day depuration in clean water. PE retained in these tissues caused oxidative stress responses, as indicated by the change of oxidative-stress-related index, such as the increase of H2O2 level and SOD activity. PE exposure also caused hemocytic encapsulation in crayfish hepatopancreas and increase of mucus secretion in intestine. Moreover, PE exposure affected the microbiota balance in crayfish, by reducing the total microbiota abundance and altering the proportions of many bacterial families. Interestingly, results showed that PE exposure led to of lower numbers of hemocytes and declination of phenoloxidase activity. Finally, PE exposure induced the expression of immune-related genes, including transcription factors and antimicrobial peptides. Taken these together, we conclude that PE microplastics exert considerable toxic effects on crayfish and are a potential threat to crayfish aquaculture and consumption. This study provides basic toxicological data toward quantifying and illuminating the impact of PE microplastics on freshwater animals.}, }
@article {pmid35525854, year = {2023}, author = {da Silva, JL and Mendes, LW and Rocha, SMB and Antunes, JEL and Oliveira, LMS and Melo, VMM and Oliveira, FAS and Pereira, APA and Costa, GDN and da Silva, VB and Gomes, RLF and de Alcantara Neto, F and Lopes, ACA and Araujo, ASF}, title = {Domestication of Lima Bean (Phaseolus lunatus) Changes the Microbial Communities in the Rhizosphere.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1423-1433}, pmid = {35525854}, issn = {1432-184X}, mesh = {*Phaseolus/genetics/microbiology ; Plant Roots/microbiology ; Rhizosphere ; Domestication ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Proteobacteria/genetics ; Plants ; Acidobacteria/genetics ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Plants modulate the soil microbiota and select a specific microbial community in the rhizosphere. However, plant domestication reduces genetic diversity, changes plant physiology, and could have an impact on the associated microbiome assembly. Here, we used 16S rRNA gene sequencing to assess the microbial community in the bulk soil and rhizosphere of wild, semi-domesticated, and domesticated genotypes of lima bean (Phaseolus lunatus), to investigate the effect of plant domestication on microbial community assembly. In general, rhizosphere communities were more diverse than bulk soil, but no differences were found among genotypes. Our results showed that the microbial community's structure was different from wild and semi-domesticated as compared to domesticated genotypes. The community similarity decreased 57.67% from wild to domesticated genotypes. In general, the most abundant phyla were Actinobacteria (21.9%), Proteobacteria (20.7%), Acidobacteria (14%), and Firmicutes (9.7%). Comparing the different genotypes, the analysis showed that Firmicutes (Bacillus) was abundant in the rhizosphere of the wild genotypes, while Acidobacteria dominated semi-domesticated plants, and Proteobacteria (including rhizobia) was enriched in domesticated P. lunatus rhizosphere. The domestication process also affected the microbial community network, in which the complexity of connections decreased from wild to domesticated genotypes in the rhizosphere. Together, our work showed that the domestication of P. lunatus shaped rhizosphere microbial communities from taxonomic to a functional level, changing the abundance of specific microbial groups and decreasing the complexity of interactions among them.}, }
@article {pmid35525510, year = {2022}, author = {Zhang, Z and Wang, Y and Chen, B and Lei, C and Yu, Y and Xu, N and Zhang, Q and Wang, T and Gao, W and Lu, T and Gillings, M and Qian, H}, title = {Xenobiotic pollution affects transcription of antibiotic resistance and virulence factors in aquatic microcosms.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {306}, number = {}, pages = {119396}, doi = {10.1016/j.envpol.2022.119396}, pmid = {35525510}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents/toxicity ; Ciprofloxacin ; Drug Resistance, Microbial/genetics ; Ecosystem ; Genes, Bacterial ; Humans ; *Virulence Factors/genetics ; *Xenobiotics/toxicity ; }, abstract = {Antibiotic resistance genes (ARGs) and virulence factors (VFs) are critical threats to human health. Their abundance in aquatic ecosystems is maintained and enhanced via selection driven by environmental xenobiotics. However, their activity and expression in these environments under xenobiotic stress remains unknown. Here ARG and VF expression profiles were examined in aquatic microcosms under ciprofloxacin, glyphosate and sertraline hydrochloride treatment. Ciprofloxacin increased total expression of ARGs, particularly multidrug resistance genes. Total expression of ARGs and VFs decreased significantly under glyphosate and sertraline treatments. However, in opportunistic human pathogens, these agents increased expression of both ARGs and VFs. Xenobiotic pollutants, such as the compounds we tested here, have the potential to disrupt microbial ecology, promote resistance, and increase risk to human health. This study systematically evaluated the effects of environmental xenobiotics on transcription of ARGs and VFs, both of which have direct relevance to human health. Transcription of such genes has been overlooked in previous studies.}, }
@article {pmid35524818, year = {2023}, author = {Palacios, OA and Espinoza-Hicks, JC and Camacho-Dávila, AA and López, BR and de-Bashan, LE}, title = {Differences in Exudates Between Strains of Chlorella sorokiniana Affect the Interaction with the Microalga Growth-Promoting Bacteria Azospirillum brasilense : Differences in Exudates Between Strains of Chlorella sorokiniana Affect the Interaction with the Microalga Growth-Promoting Bacteria Azospirillum brasilense.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1412-1422}, pmid = {35524818}, issn = {1432-184X}, support = {284562//CONACYT/ ; }, mesh = {*Chlorella ; *Azospirillum brasilense ; *Microalgae ; Symbiosis ; Exudates and Transudates ; }, abstract = {The microalga Chlorella sorokiniana and the microalgae growth-promoting bacteria (MGPB) Azospirillum brasilense have a mutualistic interaction that can begin within the first hours of co-incubation; however, the metabolites participating in this initial interaction are not yet identified. Nuclear magnetic resonance (NMR) was used in the present study to characterize the metabolites exuded by two strains of C. sorokiniana (UTEX 2714 and UTEX 2805) and A. brasilense Cd when grown together in an oligotrophic medium. Lactate and myo-inositol were identified as carbon metabolites exuded by the two strains of C. sorokiniana; however, only the UTEX 2714 strain exuded glycerol as the main carbon compound. In turn, A. brasilense exuded uracil when grown on the exudates of either microalga, and both microalga strains were able to utilize uracil as a nitrogen source. Interestingly, although the total carbohydrate content was higher in exudates from C. sorokiniana UTEX 2805 than from C. sorokiniana UTEX 2714, the growth of A. brasilense was greater in the exudates from the UTEX 2714 strain. These results highlight the fact that in the exuded carbon compounds differ between strains of the same species of microalgae and suggest that the type, rather than the quantity, of carbon source is more important for sustaining the growth of the partner bacteria.}, }
@article {pmid35522265, year = {2023}, author = {Sun, Y and Shi, X and He, LY and Xing, Y and Guo, QF and Xiu, ZL and Dong, YS}, title = {Biosynthetic Profile in the Co-culture of Aspergillus sydowii and Bacillus subtilis to Produce Novel Benzoic Derivatives.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1288-1299}, pmid = {35522265}, issn = {1432-184X}, support = {2019-ZD-0143//Natural Science Foundation of Liaoning Province/ ; 202110401131YY//Science and Technology Development Program of Jilin Province of China/ ; }, mesh = {*Bacillus subtilis/genetics ; Coculture Techniques ; *Ecosystem ; Benzoic Acid ; }, abstract = {Microbial co-culture simulates the natural ecosystem through the combination of artificial microbes. This approach has been widely applied in the study of activating silent genes to reveal novel secondary metabolites. However, there are still challenges in determining the biosynthetic pathways. In this study, the effects of microbial co-culture on the morphology of the microbes were verified by the morphological observation. Subsequently, through the strategy combining substrate feeding, stable isotope labeling, and gene expression analysis, the biosynthetic pathways of five benzoic acid derivatives N1-N4 and N7 were demonstrated: the secondary metabolite 10-deoxygerfelin of A. sydowii acted as an inducer to induce B. subtilis to produce benzoic acid, which was further converted into 3-OH-benzoic acid by A. sydowii. Subsequently, A. sydowii used 3-OH-benzoic acid as the substrate to synthesize the new compound N2, and then N1, N3, N4, and N7 were biosynthesized upon the upregulation of hydrolase, hydroxylase, and acyltransferase during co-culture. The plate zone analysis suggested that the biosynthesis of the newly induced compounds N1-N4 was mainly attributed to A. sydowii, and both A. sydowii and B. subtilis were indispensable for the biosynthesis of N7. This study provides an important basis for a better understanding of the interactions among microorganisms, providing new ideas for studying the biosynthetic pathways of the newly induced secondary metabolites in co-culture.}, }
@article {pmid35513592, year = {2023}, author = {Haag, KL and Caesar, L and da Silveira Regueira-Neto, M and de Sousa, DR and Montenegro Marcelino, V and de Queiroz Balbino, V and Torres Carvalho, A}, title = {Temporal Changes in Gut Microbiota Composition and Pollen Diet Associated with Colony Weakness of a Stingless Bee.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1514-1526}, pmid = {35513592}, issn = {1432-184X}, support = {PQG 19/2551-0001860-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio Grande do Sul/ ; Associa&#xe7;&#xe3;o ABELHA #400597/2018-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; PQ #302121/2017-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Bees ; Animals ; *Gastrointestinal Microbiome ; Diet ; Bacteria/genetics ; Pollen ; Pollination ; }, abstract = {Compared to honeybees and bumblebees, the effect of diet on the gut microbiome of Neotropical corbiculate bees such as Melipona spp. is largely unknown. These bees have been managed for centuries, but recently an annual disease is affecting M. quadrifasciata, an endangered species kept exclusively by management in Southern Brazil. Here we report the results of a longitudinal metabarcoding study involving the period of M. quadrifasciata colony weakness, designed to monitor the gut microbiota and diet changes preceding an outbreak. We found increasing amounts of bacteria associated to the gut of forager bees 2 months before the first symptoms have been recorded. Simultaneously, forager bees showed decreasing body weight. The accelerated growth of gut-associated bacteria was uneven among taxa, with Bifidobacteriaceae dominating, and Lactobacillaceae decreasing in relative abundance within the bacterial community. Dominant fungi such as Candida and Starmerella also decreased in numbers, and the stingless bee obligate symbiont Zygosaccharomyces showed the lowest relative abundance during the outbreak period. Such changes were associated with pronounced diet shifts, i.e., the rise of Eucalyptus spp. pollen amount in forager bees' guts. Furthermore, there was a negative correlation between the amount of Eucalyptus pollen in diets and the abundance of some bacterial taxa in the gut-associated microbiota. We conclude that diet and subsequent interactions with the gut microbiome are key environmental components of the annual disease and propose the use of diet supplementation as means to sustain the activity of stingless bee keeping as well as native bee pollination services.}, }
@article {pmid35513142, year = {2022}, author = {Bulgarelli, RG and Leite, MFA and de Hollander, M and Mazzafera, P and Andrade, SAL and Kuramae, EE}, title = {Eucalypt species drive rhizosphere bacterial and fungal community assembly but soil phosphorus availability rearranges the microbiome.}, journal = {The Science of the total environment}, volume = {836}, number = {}, pages = {155667}, doi = {10.1016/j.scitotenv.2022.155667}, pmid = {35513142}, issn = {1879-1026}, mesh = {Bacteria ; Fungi ; *Microbiota/physiology ; *Mycobiome ; Phosphorus ; Plant Roots/microbiology ; Plants ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Soil phosphorus (P) availability may limit plant growth and alter root-soil interactions and rhizosphere microbial community composition. The composition of the rhizosphere microbial community can also be shaped by plant genotype. In this study, we examined the rhizosphere microbial communities of young plants of 24 species of eucalypts (22 Eucalyptus and two Corymbia species) under low or sufficient soil P availability. The taxonomic diversity of the rhizosphere bacterial and fungal communities was assessed by 16S and 18S rRNA gene amplicon sequencing. The taxonomic modifications in response to low P availability were evaluated by principal component analysis, and co-inertia analysis was performed to identify associations between bacterial and fungal community structures and parameters related to plant growth and nutritional status under low and sufficient soil P availability. The sequencing results showed that while both soil P availability and eucalypt species influenced the microbial community assembly, eucalypt species was the stronger determinant. However, when the plants are subjected to low P-availability, the rhizosphere selection became strongest. In response to low P, the bacterial and fungal communities in the rhizosphere of some species showed significant changes, whereas in others remained relatively constant under low and sufficient P. Co-inertia analyses revealed a significant co-dependence between plant nutrient contents and bacterial and fungal community composition only under sufficient P. By contrast, under low P, bacterial community composition was related to plant biomass production. In conclusion, our study shows that eucalypt species identity was the main factor modulating rhizosphere microbial community composition; significant shifts due to P availability were observed only for some eucalypt species.}, }
@article {pmid35507445, year = {2022}, author = {Bloxham, B and Lee, H and Gore, J}, title = {Diauxic lags explain unexpected coexistence in multi-resource environments.}, journal = {Molecular systems biology}, volume = {18}, number = {5}, pages = {e10630}, pmid = {35507445}, issn = {1744-4292}, support = {R01 GM102311/GM/NIGMS NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; *Ecosystem ; Models, Biological ; }, abstract = {How the coexistence of species is affected by the presence of multiple resources is a major question in microbial ecology. We experimentally demonstrate that differences in diauxic lags, which occur as species deplete their own environments and adapt their metabolisms, allow slow-growing microbes to stably coexist with faster-growing species in multi-resource environments despite being excluded in single-resource environments. In our focal example, an Acinetobacter species (Aci2) competitively excludes Pseudomonas aurantiaca (Pa) on alanine and on glutamate. However, they coexist on the combination of both resources. Experiments reveal that Aci2 grows faster but Pa has shorter diauxic lags. We establish a tradeoff between Aci2's fast growth and Pa's short lags as their mechanism for coexistence. We model this tradeoff to accurately predict how environmental changes affect community composition. We extend our work by surveying a large set of competitions and observe coexistence nearly four times as frequently when the slow-grower is the fast-switcher. Our work illustrates a simple mechanism, based entirely on supplied-resource growth dynamics, for the emergence of multi-resource coexistence.}, }
@article {pmid35507048, year = {2023}, author = {McLain, NK and Gomez, MY and Gachomo, EW}, title = {Acetaminophen Levels Found in Recycled Wastewater Alter Soil Microbial Community Structure and Functional Diversity.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1448-1462}, pmid = {35507048}, issn = {1432-184X}, support = {1018746//National Institute of Food and Agriculture, Multistate Research Fund ,/ ; }, mesh = {*Wastewater ; Soil/chemistry ; Acetaminophen/metabolism ; Agricultural Irrigation/methods ; Bacteria/genetics ; Crops, Agricultural ; *Microbiota ; Carboxylic Acids/metabolism ; Soil Microbiology ; }, abstract = {The practice of using recycled wastewater (RWW) has been successfully adopted to address the growing demand for clean water. However, chemicals of emerging concern (CECs) including pharmaceutical products remain in the RWW even after additional cleaning. When RWW is used to irrigate crops or landscapes, these chemicals can enter these and adjacent environments. Unfortunately, the overall composition and concentrations of CECs found in different RWW sources vary, and even the same source can vary over time. Therefore, we selected one compound that is found frequently and in high concentrations in many RWW sources, acetaminophen (APAP), to use for our study. Using greenhouse grown eggplants treated with APAP concentrations within the ranges found in RWW effluents, we investigated the short-term impacts of APAP on the soil bacterial population under agricultural settings. Using Illumina sequencing-based approaches, we showed that APAP has the potential to cause shifts in the microbial community most likely by positively selecting for bacteria that are capable of metabolizing the breakdown products of APAP such as glycosides and carboxylic acids. Community-level physiological profiles of carbon metabolism were evaluated using Biolog EcoPlate as a proxy for community functions. The Biolog plates indicated that the metabolism of amines, amino acids, carbohydrates, carboxylic acids, and polymers was significantly higher in the presence of APAP. Abundance of microorganisms of importance to plant health and productivity was altered by APAP. Our results indicate that the soil microbial community and functions could be altered by APAP at concentrations found in RWW. Our findings contribute to the knowledge base needed to guide policies regulating RWW reuse in agriculture and also highlight the need to further investigate the effects of CECs found in RWW on soil microbiomes.}, }
@article {pmid35504465, year = {2022}, author = {Li, H and Miller, T and Lu, J and Goel, R}, title = {Nitrogen fixation contribution to nitrogen cycling during cyanobacterial blooms in Utah Lake.}, journal = {Chemosphere}, volume = {302}, number = {}, pages = {134784}, pmid = {35504465}, issn = {1879-1298}, support = {EPA999999/ImEPA/Intramural EPA/United States ; }, mesh = {*Cyanobacteria/genetics/metabolism ; Ecosystem ; Eutrophication ; *Lakes/microbiology ; Nitrates ; Nitrogen/analysis ; Nitrogen Fixation ; Utah ; }, abstract = {Nitrogen (N) cycling is an essential process in lake systems and N-fixation is an important component of it. Recent studies have also found that nitrate reduction through heterotrophic denitrification in lake systems did not prevent harmful cyanobacterial blooms, but instead, may have favored the dominance of N2-fixing cyanobacteria. The overall objective of this study was to estimate nitrogen fixation rates and the expressions of associated nitrogenase (nif gene) functional gene at several sites at different occasions in freshwater Utah Lake. For comparison purposes, one time sampling was also conducted in the brackish Farmington Bay of Great Salt Lake (GSL). The microbial ecology of the top 20-cm of surface water was investigated to assess the dominant cyanobacterial communities and N-related metabolisms. Our study revealed that Dolichospermum and Nodularia were potential N2-fixers for Utah Lake and brackish Farmington Bay, respectively. The in situ N2-fixation rates were 0-0.73 nmol N hr[-1]L[-1] for Utah Lake and 0-0.85 nmol N hr[-1]L[-1] for Farmington Bay, and these rates positively correlated with the abundance and expressions of the nif gene. In addition, nitrate reduction was measured in sediment (0.002-0.094 mg N VSS[-1] hr[-1]). Significantly positive correlations were found among amoA, nirS and nirK abundance (R = 0.56-0.87, p < 0.05, Spearman) in both lakes. An exception was the lower nirK gene abundance detected at one site in Farmington Bay where high ammonium retentions were also detected. Based on a mass balance approach, we concluded that the amount of inorganic N loss through denitrification still exceeded the N input by N2-fixation, much like in most lakes, rivers, and marine ecosystems. This indicates that N cycling processes such as denitrification mediated by heterotrophic bacteria contributes to N-export from the lakes resulting in N limitations.}, }
@article {pmid35504213, year = {2022}, author = {Lee, M and Liang, G and Holland, SI and O'Farrell, C and Osborne, K and Manefield, MJ}, title = {Dehalobium species implicated in 2,3,7,8-tetrachlorodibenzo-p-dioxin dechlorination in the contaminated sediments of Sydney Harbour Estuary.}, journal = {Marine pollution bulletin}, volume = {179}, number = {}, pages = {113690}, doi = {10.1016/j.marpolbul.2022.113690}, pmid = {35504213}, issn = {1879-3363}, mesh = {Bays ; *Benzofurans/analysis ; Dibenzofurans, Polychlorinated/analysis ; *Dioxins/analysis ; Estuaries ; *Polychlorinated Dibenzodioxins/analysis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Polychlorinated dibenzo-p-dioxins and furans (PCDD/F) are some of the most environmentally recalcitrant and toxic compounds. They occur naturally and as by-products of anthropogenic activity. Sydney Harbour Estuary (Sydney, Australia), is heavily contaminated with PCDD/F. Analysis of sediment cores revealed that the contamination source area in Homebush Bay continues to have one of the highest levels of PCDD/F contamination in the world (5207 pg WHO-TEQ g[-1]) with >50% of the toxicity attributed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD), the most toxic PCDD/F congener. Comparison of congener profiles at the contamination source area with surrounding bays and historical data provided evidence for the attenuation of 2,3,7,8-TCDD and other congeners at the source area. This finding was supported by the detection of di-, mono- and unchlorinated dibenzo-p-dioxin. Microbial community analysis of sediments by 16S rRNA amplicon sequencing revealed an abundance of lineages from the class Dehalococcoidia (up to 15% of the community), including the genus Dehalobium (up to 0.5%). Anaerobic seawater enrichment cultures using perchloroethene as more biologically available growth substrate enriched the Dehalobium population by more than six-fold. The enrichment culture then proved capable of reductively dechlorinating 2,3,7,8-TCDD to 2,3,7-TriCDD and octachlorodibenzo-p-dibenzodioxin (OCDD) to hepta and hexa congeners. This work is the first to show microbial reductive dehalogenation of 2,3,7,8-TCDD with a bacterium from outside the Dehalococcoides genus, and one of only a few that demonstrates PCDD/F dechlorination in a marine environment.}, }
@article {pmid35503575, year = {2023}, author = {Dick, JM and Tan, J}, title = {Chemical Links Between Redox Conditions and Estimated Community Proteomes from 16S rRNA and Reference Protein Sequences.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1338-1355}, pmid = {35503575}, issn = {1432-184X}, mesh = {RNA, Ribosomal, 16S/genetics ; *Proteome ; *Microbiota/genetics ; Metagenome ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Environmental influences on community structure are often assessed through multivariate analyses in order to relate microbial abundances to separately measured physicochemical variables. However, genes and proteins are themselves chemical entities; in combination with genome databases, differences in microbial abundances directly encode for chemical variability. We predicted that the carbon oxidation state of estimated community proteomes, obtained by combining taxonomic abundances from published 16S rRNA gene sequencing datasets with reference microbial proteomes from the NCBI Reference Sequence (RefSeq) database, would reflect environmental oxidation-reduction conditions. Analysis of multiple datasets confirms the geobiochemical predictions for environmental redox gradients in hydrothermal systems, stratified lakes and marine environments, and shale gas wells. The geobiochemical signal is largest for the steep redox gradients associated with hydrothermal systems and between injected water and produced fluids from shale gas wells, demonstrating that microbial community composition can be a chemical proxy for environmental redox gradients. Although estimates of oxidation state from 16S amplicon and metagenomic sequences are correlated, the 16S-based estimates show stronger associations with redox gradients in some environments.}, }
@article {pmid35502577, year = {2022}, author = {Laveilhé, A and Fochesato, S and Lalaouna, D and Heulin, T and Achouak, W}, title = {Phytobeneficial traits of rhizobacteria under the control of multiple molecular dialogues.}, journal = {Microbial biotechnology}, volume = {15}, number = {7}, pages = {2083-2096}, pmid = {35502577}, issn = {1751-7915}, mesh = {*Alphaproteobacteria ; Bacteria/genetics ; Fungi ; Iron ; Plant Diseases/microbiology/prevention &amp; control ; Rhizosphere ; *Soil Microbiology ; }, abstract = {Pseudomonads play crucial roles in plant growth promotion and control of plant diseases. However, under natural conditions, other microorganisms competing for the same nutrient resources in the rhizosphere may exert negative control over their phytobeneficial characteristics. We assessed the expression of phytobeneficial genes involved in biocontrol, biostimulation and iron regulation such as, phlD, hcnA, acdS, and iron-small regulatory RNAs prrF1 and prrF2 in Pseudomonas brassicacearum co-cultivated with three phytopathogenic fungi, and two rhizobacteria in the presence or absence of Brassica napus, and in relation to iron availability. We found that the antifungal activity of P. brassicacearum depends mostly on the production of DAPG and not on HCN whose production is suppressed by fungi. We have also shown that the two-competing bacterial strains modulate the plant growth promotion activity of P. brassicacearum by modifying the expression of phlD, hcnA and acdS according to iron availability. Overall, it allows us to better understand the complexity of the multiple molecular dialogues that take place underground between microorganisms and between plants and its rhizosphere microbiota and to show that synergy in favour of phytobeneficial gene expression may exist between different bacterial species.}, }
@article {pmid35502341, year = {2022}, author = {Qing, J and Song, W and Tian, L and Samuel, SB and Li, Y}, title = {Potential Small Molecules for Therapy of Lupus Nephritis Based on Genetic Effect and Immune Infiltration.}, journal = {BioMed research international}, volume = {2022}, number = {}, pages = {2259164}, pmid = {35502341}, issn = {2314-6141}, mesh = {Computational Biology ; Female ; Gene Expression ; Genes, Regulator ; Humans ; *Lupus Erythematosus, Systemic/genetics ; *Lupus Nephritis/drug therapy/genetics ; Male ; Membrane Proteins/genetics ; RNA-Binding Proteins/genetics ; }, abstract = {Lupus nephritis (LN) is the most common and significant complication of systemic lupus erythematosus (SLE) due to its poor prognosis and mortality rates in SLE patients. There is a critical need for new drugs as the pathogenesis of LN remains to be elucidated and immunosuppressive therapy comes with many deficiencies. In this study, 23 hub genes (IFI6, PLSCR1, XAF1, IFI16, IFI44, MX1, IFI44L, IFIT3, IFIT2, IFI27, DDX58, EIF2AK2, IFITM1, RTP4, IFITM3, TRIM22, PARP12, IFIH1, OAS1, HERC6, RSAD2, DDX60, and MX2) were identified through bioinformatics and network analysis and are closely related to interferon production and function. Interestingly, immune cell infiltration analysis and correlation analysis demonstrate a positive correlation between the expression of 23 hub genes and monocyte infiltration in glomeruli and M2 macrophage infiltration in the tubulointerstitium of LN patients. Additionally, the CTD database, DsigDB database, and DREIMT database were used to explore the bridging role of genes in chemicals and LN as well as the potential influence of these chemicals on immune cells. After comparison and discussion, six small molecules (Acetohexamide, Suloctidil, Terfenadine, Prochlorperazine, Mefloquine, and Triprolidine) were selected for their potential ability in treating lupus nephritis.}, }
@article {pmid35501499, year = {2023}, author = {Liu, Y and Zhang, B and Zhang, Y and Shen, Y and Cheng, C and Yuan, W and Guo, P}, title = {Organic Matter Decomposition in River Ecosystems: Microbial Interactions Influenced by Total Nitrogen and Temperature in River Water.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1236-1252}, pmid = {35501499}, issn = {1432-184X}, support = {2018ZX07111005//the National Science and Technology Major Project of the Ministry of Science and Technology of China/ ; 20200801071GH//the Science and Technology Development Program of Jilin Province/ ; }, mesh = {*Ecosystem ; *Rivers/microbiology ; Nitrogen ; Temperature ; Bacteria/genetics ; Microbial Interactions ; Water ; }, abstract = {Microbes contribute to the organic matter decomposition (OMD) in river ecosystems. This study considers two aspects of OMD in river ecosystems which have not been examined in scientific studies previously, and these are the microbial interactions in OMD and the influence of environmental factors on microbial interactions. Cotton strip (CS), as a substitute for organic matter, was introduced to Luanhe River Basin in China. The results of CS assay, microbial sequencing, and redundancy analysis (RDA) showed that CS selectively enriched bacterial and fungal groups related to cellulose decomposition, achieving cotton strip decomposition (CSD). Bacterial phylum Proteobacteria and fungal phyla Rozellomycota and Ascomycota were the dominant groups associated with CSD. Network analysis and Mantel test results indicated that bacteria and fungi on CS cooperatively formed an interaction network to achieve the CSD. In the network, modules 2 and 4 were significantly positively associated with CSD, which were considered as the key modules in this study. The key modules were mainly composed of phyla Proteobacteria and Ascomycota, indicating that microbes in key modules were the effective decomposers of CS. Although keystone taxa were not directly associated with CSD, they may regulate the genera in key modules to achieve the CSD, since some keystone taxa were linked with the microbial genera associated with CSD in the key modules. Total nitrogen (TN) and temperature in water were the dominant environmental factors positively influenced CSD. The key modules 2 and 4 were positively influenced by water temperature and TN in water, respectively, and two keystone taxa were positively associated with TN. This profoundly revealed that water temperature and TN influenced the OMD through acting on the keystone taxa and key modules in microbial interactions. The research findings help us to understand the microbial interactions influenced by environmental factors in OMD in river ecosystems.}, }
@article {pmid35501031, year = {2022}, author = {Gómez-Muñoz, B and Efthymiou, A and Dubey, M and Sølve, J and Nicolaisen, M and Jensen, DF and Nybroe, O and Larsen, J}, title = {Cellulose amendment promotes P solubilization by Penicillium aculeatum in non-sterilized soil.}, journal = {Fungal biology}, volume = {126}, number = {5}, pages = {356-365}, doi = {10.1016/j.funbio.2022.03.003}, pmid = {35501031}, issn = {1878-6146}, mesh = {Cellulose ; Sewage ; *Soil ; Soil Microbiology ; Sterilization ; *Talaromyces ; }, abstract = {Successful application of microbial biofertilizers, such as phosphorus (P) solubilizing fungi to agroecosystems, is constrained from the lack of knowledge about their ecology; for example in terms of how they respond to an external input of carbon (C) to get established in the soil. In two soil incubation experiments we examined the performance of the P solubilizing fungus Penicillium aculeatum in non-sterile and semi-sterile (γ-irradiated) soil with different C and P sources. Results from the first experiment with C sources showed that starch and cellulose generally improved P solubilization by P. aculeatum measured as water extractable P (Pwep), though only significantly in non-sterile soil. This coincided with an increased population density of P. aculeatum measured with a hygromycin B resistant strain of this fungus. Soil respiration used to measure soil microbial activity was overall much higher in treatments with C compounds than without C in both non-sterile and semi-sterile soil. However, soil respiration was highest with cellulose in semi-sterile soil, especially in combination with P. aculeatum. Hence, for the second experiment with P sources (tricalcium phosphate (TCP) and sewage sludge ash) cellulose was used as a C source for P. aculeatum growth in all treatments. Main results showed that P. aculeatum in combination with cellulose soil amendment increased soil Pwep independent of soil sterilization and P source treatments. Soil resin P (Pres) and microbial P (Pmic), which represents stocks of potentially plant available P, were also affected from P. aculeatum inoculation. Increased soil Pres from TCP and sewage sludge ash was observed with P. aculeatum independent of soil type. On the other hand soil Pmic was higher after P. aculeatum inoculation only in semi-sterile soil. Population density of P. aculeatum measured with qPCR was maintained or increased in non-sterile and semi-sterile soil, respectively, compared to the original inoculum load of P. aculeatum. In conclusion, our results underline the importance of C source addition for P. aculeatum if used as a biofertilizer. For this, cellulose seems to be a promising option promoting P. aculeatum growth and P solubilization also in non-sterilized soil.}, }
@article {pmid35499645, year = {2023}, author = {Anderson, KE and Ricigliano, VA and Copeland, DC and Mott, BM and Maes, P}, title = {Social Interaction is Unnecessary for Hindgut Microbiome Transmission in Honey Bees: The Effect of Diet and Social Exposure on Tissue-Specific Microbiome Assembly.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1498-1513}, pmid = {35499645}, issn = {1432-184X}, support = {2022-21000-021-00D//Agricultural Research Service/ ; }, mesh = {Bees ; Animals ; Social Interaction ; *Microbiota ; *Gastrointestinal Microbiome ; Bacteria/genetics ; Diet ; }, abstract = {Honey bees are a model for host-microbial interactions with experimental designs evolving towards conventionalized worker bees. Research on gut microbiome transmission and assembly has examined only a fraction of factors associated with the colony and hive environment. Here, we studied the effects of diet and social isolation on tissue-specific bacterial and fungal colonization of the midgut and two key hindgut regions. We found that both treatment factors significantly influenced early hindgut colonization explaining similar proportions of microbiome variation. In agreement with previous work, social interaction with older workers was unnecessary for core hindgut bacterial transmission. Exposure to natural eclosion and fresh stored pollen resulted in gut bacterial communities that were taxonomically and structurally equivalent to those produced in the natural colony setting. Stressed diets of no pollen or autoclaved pollen in social isolation resulted in decreased fungal abundance and bacterial diversity, and atypical microbiome structure and tissue-specific variation of functionally important core bacteria. Without exposure to the active hive environment, the abundance and strain diversity of keystone ileum species Gilliamella apicola was markedly reduced. These changes were associated with significantly larger ileum microbiotas suggesting that extended exposure to the active hive environment plays an antibiotic role in hindgut microbiome establishment. We conclude that core hindgut microbiome transmission is facultative horizontal with 5 of 6 core hindgut species readily acquired from the built hive structure and natural diet. Our findings contribute novel insights into factors influencing assembly and maintenance of honey bee gut microbiota and facilitate future experimental designs.}, }
@article {pmid35499337, year = {2022}, author = {Stapelfeldt, HRD and Barnes, SJ and Henson, MW and Thrash, JC}, title = {Draft Genome Sequence of the Marine Flavobacteriaceae sp. Strain LSUCC0859.}, journal = {Microbiology resource announcements}, volume = {11}, number = {5}, pages = {e0018622}, pmid = {35499337}, issn = {2576-098X}, support = {LEQSF[2014-2017]-RDA-06//Louisiana Board of Regents (Board of Regents)/ ; Gulf Research Program Early Career Research Fellowship//National Academies of Sciences, Engineering, and Medicine (NASEM)/ ; Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation (SF)/ ; }, abstract = {A new marine Flavobacteriaceae sp. strain, LSUCC0859, was isolated off the coast of Louisiana with artificial seawater via high-throughput dilution-to-extinction (DTE) cultivation. The 2,168,862-bp genome sequence provides opportunities to investigate the biology of a poorly understood lineage within the Bacteroidetes.}, }
@article {pmid35499326, year = {2022}, author = {Rahlff, J and Bornemann, TLV and Lopatina, A and Severinov, K and Probst, AJ}, title = {Host-Associated Phages Disperse across the Extraterrestrial Analogue Antarctica.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {10}, pages = {e0031522}, pmid = {35499326}, issn = {1098-5336}, mesh = {Antarctic Regions ; *Bacteriophages/genetics ; Ecosystem ; Metagenomics ; Prophages/genetics ; }, abstract = {Extreme Antarctic conditions provide one of the closest analogues of extraterrestrial environments. Since air and snow samples, especially from polar regions, yield DNA amounts in the lower picogram range, binning of prokaryotic genomes is challenging and renders studying the dispersal of biological entities across these environments difficult. Here, we hypothesized that dispersal of host-associated bacteriophages (adsorbed, replicating, or prophages) across the Antarctic continent can be tracked via their genetic signatures, aiding our understanding of virus and host dispersal across long distances. Phage genome fragments (PGFs) reconstructed from surface snow metagenomes of three Antarctic stations were assigned to four host genomes, mainly Betaproteobacteria, including Ralstonia spp. We reconstructed the complete genome of a temperate phage with nearly complete alignment to a prophage in the reference genome of Ralstonia pickettii 12D. PGFs from different stations were related to each other at the genus level and matched similar hosts. Metagenomic read mapping and nucleotide polymorphism analysis revealed a wide dispersal of highly identical PGFs, 13 of which were detected in seawater from the Western Antarctic Peninsula at a distance of 5,338 km from the snow sampling stations. Our results suggest that host-associated phages, especially of Ralstonia sp., disperse over long distances despite the harsh conditions of the Antarctic continent. Given that 14 phages associated with two R. pickettii draft genomes isolated from space equipment were identified, we conclude that Ralstonia phages are ideal mobile genetic elements to track dispersal and contamination in ecosystems relevant for astrobiology. IMPORTANCE Host-associated phages of the bacterium Ralstonia identified in snow samples can be used to track microbial dispersal over thousands of kilometers across the Antarctic continent, which functions as an extraterrestrial analogue because of its harsh environmental conditions. Due to the presence of these bacteria carrying genome-integrated prophages on space-related equipment and the potential for dispersal of host-associated phages demonstrated here, our work has implications for planetary protection, a discipline in astrobiology interested in preventing contamination of celestial bodies with alien biomolecules or forms of life.}, }
@article {pmid35496989, year = {2022}, author = {Di Martino, P}, title = {Antimicrobial agents and microbial ecology.}, journal = {AIMS microbiology}, volume = {8}, number = {1}, pages = {1-4}, pmid = {35496989}, issn = {2471-1888}, abstract = {Antimicrobials are therapeutic substances used to prevent or treat infections. Disinfectants are antimicrobial agents applied to non-living surfaces. Every year, several thousand tonnes of antimicrobials and their by-products are released into the environment and in particular into the aquatic environment. This type of xenobiotic has ecological consequences in the natural environment but also in technological environments such as wastewater treatment plants and methane fermentation sewage sludge treatment plants. The constant exposure of microbial communities not only to high concentrations but also to sub-inhibitory concentrations of antibiotics is a key element in the development of antibiotic resistance in aquatic environments and in soils. The future of antimicrobials lies in the development of biosourced or bioinspired molecules. The observation and deciphering of interactions between living organisms is the key to this development.}, }
@article {pmid35495730, year = {2022}, author = {Nagar, S and Talwar, C and Motelica-Heino, M and Richnow, HH and Shakarad, M and Lal, R and Negi, RK}, title = {Microbial Ecology of Sulfur Biogeochemical Cycling at a Mesothermal Hot Spring Atop Northern Himalayas, India.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {848010}, pmid = {35495730}, issn = {1664-302X}, abstract = {Sulfur related prokaryotes residing in hot spring present good opportunity for exploring the limitless possibilities of integral ecosystem processes. Metagenomic analysis further expands the phylogenetic breadth of these extraordinary sulfur (S) metabolizing microorganisms as well as their complex metabolic networks and syntrophic interactions in environmental biosystems. Through this study, we explored and expanded the microbial genetic repertoire with focus on S cycling genes through metagenomic analysis of S contaminated hot spring, located at the Northern Himalayas. The analysis revealed rich diversity of microbial consortia with established roles in S cycling such as Pseudomonas, Thioalkalivibrio, Desulfovibrio, and Desulfobulbaceae (Proteobacteria). The major gene families inferred to be abundant across microbial mat, sediment, and water were assigned to Proteobacteria as reflected from the reads per kilobase (RPKs) categorized into translation and ribosomal structure and biogenesis. An analysis of sequence similarity showed conserved pattern of both dsrAB genes (n = 178) retrieved from all metagenomes while other S disproportionation proteins were diverged due to different structural and chemical substrates. The diversity of S oxidizing bacteria (SOB) and sulfate reducing bacteria (SRB) with conserved (r)dsrAB suggests for it to be an important adaptation for microbial fitness at this site. Here, (i) the oxidative and reductive dsr evolutionary time-scale phylogeny proved that the earliest (but not the first) dsrAB proteins belong to anaerobic Thiobacillus with other (rdsr) oxidizers, also we confirm that (ii) SRBs belongs to δ-Proteobacteria occurring independent lateral gene transfer (LGT) of dsr genes to different and few novel lineages. Further, the structural prediction of unassigned DsrAB proteins confirmed their relatedness with species of Desulfovibrio (TM score = 0.86, 0.98, 0.96) and Archaeoglobus fulgidus (TM score = 0.97, 0.98). We proposed that the genetic repertoire might provide the basis of studying time-scale evolution and horizontal gene transfer of these genes in biogeochemical S cycling.}, }
@article {pmid35495644, year = {2022}, author = {Rangel, F and Enes, P and Gasco, L and Gai, F and Hausmann, B and Berry, D and Oliva-Teles, A and Serra, CR and Pereira, FC}, title = {Differential Modulation of the European Sea Bass Gut Microbiota by Distinct Insect Meals.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {831034}, pmid = {35495644}, issn = {1664-302X}, support = {ZK 57/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {The aquaculture industry is one of the fastest-growing sectors in animal food production. However, farming of carnivorous fish strongly relies on the use of wild fish-based meals, a practice that is environmentally and economically unsustainable. Insect-based diets constitute a strong candidate for fishmeal substitution, due to their high nutritional value and low environmental footprint. Nevertheless, data on the impact of insect meal (IM) on the gut microbiome of farmed fish are so far inconclusive, and very scarce in what concerns modulation of microbial-mediated functions. Here we use high-throughput 16S rRNA gene amplicon sequencing and quantitative PCR to evaluate the impact of different IMs on the composition and chitinolytic potential of the European sea bass gut digesta- and mucosa-associated communities. Our results show that insect-based diets of distinct origins differently impact the gut microbiota of the European sea bass (Dicentrarchus labrax). We detected clear modulatory effects of IM on the gut microbiota, which were more pronounced in the digesta, where communities differed considerably among the diets tested. Major community shifts were associated with the use of black soldier fly larvae (Hermetia illucens, HM) and pupal exuviae (HEM) feeds and were characterized by an increase in the relative abundance of the Firmicutes families Bacillaceae, Enterococcaceae, and Lachnospiraceae and the Actinobacteria family Actinomycetaceae, which all include taxa considered beneficial for fish health. Modulation of the digesta community by HEM was characterized by a sharp increase in Paenibacillus and a decrease of several Gammaproteobacteria and Bacteroidota members. In turn, a mealworm larvae-based diet (Tenebrio molitor, TM) had only a modest impact on microbiota composition. Further, using quantitative PCR, we demonstrate that shifts induced by HEM were accompanied by an increase in copy number of chitinase ChiA-encoding genes, predominantly originating from Paenibacillus species with effective chitinolytic activity. Our study reveals an HEM-driven increase in chitin-degrading taxa and associated chitinolytic activity, uncovering potential benefits of adopting exuviae-supplemented diets, a waste product of insect rearing, as a functional ingredient.}, }
@article {pmid35494622, year = {2022}, author = {Guéneau, V and Plateau-Gonthier, J and Arnaud, L and Piard, JC and Castex, M and Briandet, R}, title = {Positive biofilms to guide surface microbial ecology in livestock buildings.}, journal = {Biofilm}, volume = {4}, number = {}, pages = {100075}, pmid = {35494622}, issn = {2590-2075}, abstract = {The increase in human consumption of animal proteins implies changes in the management of meat production. This is followed by increasingly restrictive regulations on antimicrobial products such as chemical biocides and antibiotics, used in particular to control pathogens that can spread zoonotic diseases. Aligned with the One Health concept, alternative biological solutions are under development and are starting to be used in animal production. Beneficial bacteria able to form positive biofilms and guide surface microbial ecology to limit microbial pathogen settlement are promising tools that could complement existing biosecurity practices to maintain the hygiene of livestock buildings. Although the benefits of positive biofilms have already been documented, the associated fundamental mechanisms and the rationale of the microbial composition of these new products are still sparce. This review provides an overview of the envisioned modes of action of positive biofilms used on livestock building surfaces and the resulting criteria for the selection of the appropriate microorganisms for this specific application. Limits and advantages of this biosecurity approach are discussed as well as the impact of such practices along the food chain, from farm to fork.}, }
@article {pmid35493735, year = {2022}, author = {Kumar, D and Sharma, SR and Adegoke, A and Kennedy, A and Tuten, HC and Li, AY and Karim, S}, title = {Recently Evolved Francisella-Like Endosymbiont Outcompetes an Ancient and Evolutionarily Associated Coxiella-Like Endosymbiont in the Lone Star Tick (Amblyomma americanum) Linked to the Alpha-Gal Syndrome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {787209}, pmid = {35493735}, issn = {2235-2988}, support = {P20 GM103476/GM/NIGMS NIH HHS/United States ; }, mesh = {Amblyomma ; Animals ; Bacteria ; Coxiella ; *Food Hypersensitivity ; *Francisella/genetics ; Humans ; *Ticks/microbiology ; United States ; }, abstract = {BACKGROUND: Ticks are hematophagous arthropods that transmit various bacterial, viral, and protozoan pathogens of public health significance. The lone star tick (Amblyomma americanum) is an aggressive human-biting tick that transmits bacterial and viral pathogens, and its bites are suspected of eliciting the alpha-gal syndrome, a newly emerged delayed hypersensitivity following consumption of red meat in the United States. While ongoing studies have attempted to investigate the contribution of different tick-inherent factors to the induction of alpha-gal syndrome, an otherwise understudied aspect is the contribution of the tick microbiome and specifically obligate endosymbionts to the establishment of the alpha-gal syndrome in humans.<br><br>MATERIALS AND METHODS: Here we utilized a high-throughput metagenomic sequencing approach to cataloging the entire microbial communities residing within different developmental stages and tissues of unfed and blood-fed ticks from laboratory-maintained ticks and three new geographical locations in the United States. The Quantitative Insights Into Microbial Ecology (QIIME2) pipeline was used to perform data analysis and taxonomic classification. Moreover, using a SparCC (Sparse Correlations for Compositional data) network construction model, we investigated potential interactions between members of the microbial communities from laboratory-maintained and field-collected ticks.<br><br>RESULTS: Overall, Francisellaceae was the most dominant bacteria identified in the microbiome of both laboratory-raised and field-collected Am. americanum across all tissues and developmental stages. Likewise, microbial diversity was seen to be significantly higher in field-collected ticks compared with laboratory-maintained ticks as seen with a higher number of both Operational Taxonomic Units and measures of species richness. Several potential positive and negative correlations were identified from our network analysis. We observed a strong positive correlation between Francisellaceae, Rickettsiaceae, and Midichloriaceae in both developmental stages and tissues from laboratory-maintained ticks, whereas ovarian tissues had a strong positive correlation of bacteria in the family Xanthobacteraceae and Rhizobiaceae. A negative interaction was observed between Coxiellaceae and Francisellaceae in Illinois, and all the bacteria detected from ticks from Delaware were negatively correlated.<br><br>CONCLUSION: This study is the first to catalog the microbiome of Am. americanum throughout its developmental stages and different tissue niches and report the potential replacement of Coxiellaceae by Francisellaceae across developmental stages and tissues tested except in ovarian tissues. These unique and significant findings advance our knowledge and open a new avenue of research to further understand the role of tick microbiome in tick-borne diseases and develop a holistic strategy to control alpha-gal syndrome.}, }
@article {pmid35491817, year = {2022}, author = {Zhang, M and Whiteley, M and Lewin, GR}, title = {Polymicrobial Interactions of Oral Microbiota: a Historical Review and Current Perspective.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0023522}, pmid = {35491817}, issn = {2150-7511}, support = {F32 DE027281/DE/NIDCR NIH HHS/United States ; K99 DE031018/DE/NIDCR NIH HHS/United States ; R01 DE020100/DE/NIDCR NIH HHS/United States ; R01 DE023193/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; Microbial Interactions ; *Microbiota ; Models, Biological ; Mouth ; *Periodontitis ; }, abstract = {The oral microbiota is enormously diverse, with over 700 microbial species identified across individuals that play a vital role in the health of our mouth and our overall well-being. In addition, as oral diseases such as caries (cavities) and periodontitis (gum disease) are mediated through interspecies microbial interactions, this community serves as an important model system to study the complexity and dynamics of polymicrobial interactions. Here, we review historical and recent progress in our understanding of the oral microbiome, highlighting how oral microbiome research has significantly contributed to our understanding of microbial communities, with broad implications in polymicrobial diseases and across microbial community ecology. Further, we explore innovations and challenges associated with analyzing polymicrobial systems and suggest future directions of study. Finally, we provide a conceptual framework to systematically study microbial interactions within complex communities, not limited to the oral microbiota.}, }
@article {pmid35486140, year = {2023}, author = {Rajarajan, A and Wolinska, J and Walser, JC and Dennis, SR and Spaak, P}, title = {Host-Associated Bacterial Communities Vary Between Daphnia galeata Genotypes but Not by Host Genetic Distance.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1578-1589}, pmid = {35486140}, issn = {1432-184X}, support = {310030 L 166628//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; WO 1587/6-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; *Daphnia/genetics/microbiology ; *Bacteria/genetics ; Genotype ; Lakes ; }, abstract = {Host genotype may shape host-associated bacterial communities (commonly referred to as microbiomes). We sought to determine (a) whether bacterial communities vary among host genotypes in the water flea Daphnia galeata and (b) if this difference is driven by the genetic distance between host genotypes, by using D. galeata genotypes hatched from sediments of different time periods. We used 16S amplicon sequencing to profile the gut and body bacterial communities of eight D. galeata genotypes hatched from resting eggs; these were isolated from two distinct sediment layers (dating to 1989 and 2009) of a single sediment core of the lake Greifensee, and maintained in a common garden in laboratory cultures for 5 years. In general, bacterial community composition varied in both the Daphnia guts and bodies; but not between genotypes from different sediment layers. Specifically, genetic distances between host genotypes did not correlate with beta diversity of bacterial communities in Daphnia guts and bodies. Our results indicate that Daphnia bacterial community structure is to some extent determined by a host genetic component, but that genetic distances between hosts do not correlate with diverging bacterial communities.}, }
@article {pmid35486139, year = {2022}, author = {Bacha, L and de Rezende, CE and Cosenza, C and Ottoni, A and Thompson, C and Thompson, F}, title = {Letter to Microbial Ecology.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {11-13}, pmid = {35486139}, issn = {1432-184X}, mesh = {*Ecology ; }, }
@article {pmid35484416, year = {2023}, author = {Câmara, PEAS and Bones, FLV and Lopes, FAC and Oliveira, FS and Barreto, CC and Knop Henriques, D and Campos, LP and Carvalho-Silva, M and Convey, P and Rosa, LH}, title = {DNA Metabarcoding Reveals Cryptic Diversity in Forest Soils on the Isolated Brazilian Trindade Island, South Atlantic.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {1056-1071}, pmid = {35484416}, issn = {1432-184X}, mesh = {Animals ; Humans ; Child, Preschool ; *DNA Barcoding, Taxonomic ; *Soil ; Brazil ; Eukaryota ; Forests ; Biodiversity ; Bacteria ; Archaea ; Fungi ; Plants ; }, abstract = {Located 1140 km from the South American coastline in the South Atlantic Ocean and with an age of 4 million years, Trindade Island is the most recent volcanic component of Brazilian territory. Its original native vegetation has been severely damaged by human influence, in particular through the introduction of exotic grazing animals such as goats. However, since the complete eradication of goats and other feral animals in the late 1990s, the island's vegetation has been recovering, and even some endemic species that had been considered extinct have been rediscovered. In this study, we set out to characterize the contemporary cryptic diversity in soils of the recovering native forest of Trindade Island using metabarcoding by high throughput sequencing (HTS). The sequence diversity obtained was dominated by microorganisms, including three domains (Bacteria, Archaea, and Eukarya) and five kingdoms (Fungi, Metazoa, Protozoa, Chromista, and Viridiplantae). Bacteria were represented by 20 phyla and 116 taxa, with Archaea by only one taxon. Fungi were represented by seven phyla and 250 taxa, Viridiplantae by five phyla and six taxa, Protozoa by five phyla and six taxa, Metazoa by three phyla and four taxa and Chromista by two phyla and two taxa. Even after the considerable anthropogenic impacts and devastation of the island's natural forest, our sequence data reveal the presence of a rich and complex diversity of microorganisms, invertebrates, and plants and provide important baseline biodiversity information that will contribute to ecological restoration efforts on the island.}, }
@article {pmid35482603, year = {2022}, author = {Carrizo, D and Vignale, FA and Sánchez-García, L and Farías, ME}, title = {Ecological variability based on lipid biomarkers in astrobiologically interesting wetlands from the Argentinian central Andes.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {5}, pages = {}, doi = {10.1093/femsec/fiac049}, pmid = {35482603}, issn = {1574-6941}, support = {MDM-2017-0737//INTA/ ; MDM-2017-0737//CSIC/ ; 2015/3825//Fund for Scientific and Technological Research/ ; }, mesh = {Archaea/genetics/metabolism ; Biomarkers/metabolism ; Carbon/metabolism ; *Cyanobacteria/metabolism ; Geologic Sediments/microbiology ; Lipids ; Sulfates/metabolism ; *Wetlands ; }, abstract = {Andean wetlands hold extremophilic communities adapted to live in harsh conditions. Here, we investigated the microbial ecology of three high-altitude hypersaline ponds from La Puna region (Argentina) showing an increasing extent of desiccation by analyzing their lipid sedimentary record. We recreated the microbial community structure and the carbon metabolisms in each lacustrine system based on the molecular distribution of lipid biomarkers and their compound-specific carbon and hydrogen isotopic signatures. We detected lipid compounds considered to be biomarkers of cyanobacteria, sulfate-reducing bacteria, purple sulfur bacteria, and archaea in the three Andean ponds, as well as diatoms in the intermediate salinity system. The relative abundance of purple sulfur and sulfate-reducing bacteria decreased with salinity, whereas cyanobacteria and archaea decreased their relative abundance in the mid-saline pond to increase it again and became both prevailing at the highest salinity. Carbon fixation in the three ponds was driven by a combination of the reductive tricarboxylic acid cycle, the reductive pentose phosphate cycle, and the reductive acetyl-CoA pathway. This work is the first to describe molecular and isotopic lipid fingerprints in wetlands from the central Andean Puna, and serves as a basis for further biogeochemical studies in the area.}, }
@article {pmid35482107, year = {2023}, author = {Alemany, I and Pérez-Cembranos, A and Pérez-Mellado, V and Castro, JA and Picornell, A and Ramon, C and Jurado-Rivera, JA}, title = {Faecal Microbiota Divergence in Allopatric Populations of Podarcis lilfordi and P. pityusensis, Two Lizard Species Endemic to the Balearic Islands.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1564-1577}, pmid = {35482107}, issn = {1432-184X}, support = {CGL2015-68139-C2-1-P//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; FPI-CAIB 2017//Conselleria d'Educaci&#xf3;, Investigaci&#xf3;, Cultura i Esport/ ; }, mesh = {Animals ; *Lizards/microbiology ; Spain ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Feces ; }, abstract = {Gut microbial communities provide essential functions to their hosts and are known to influence both their ecology and evolution. However, our knowledge of these complex associations is still very limited in reptiles. Here we report the 16S rRNA gene faecal microbiota profiles of two lizard species endemic to the Balearic archipelago (Podarcis lilfordi and P. pityusensis), encompassing their allopatric range of distribution through a noninvasive sampling, as an alternative to previous studies that implied killing specimens of these IUCN endangered and near-threatened species, respectively. Both lizard species showed a faecal microbiome composition consistent with their omnivorous trophic ecology, with a high representation of cellulolytic bacteria taxa. We also identified species-specific core microbiota signatures and retrieved lizard species, islet ascription, and seasonality as the main factors in explaining bacterial community composition. The different Balearic Podarcis populations are characterised by harbouring a high proportion of unique bacterial taxa, thus reinforcing their view as unique and divergent evolutionary entities.}, }
@article {pmid35479639, year = {2022}, author = {Xing, L and Zhi, Q and Hu, X and Liu, L and Xu, H and Zhou, T and Yin, H and Yi, Z and Li, J}, title = {Influence of Association Network Properties and Ecological Assembly of the Foliar Fugal Community on Crop Quality.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {783923}, pmid = {35479639}, issn = {1664-302X}, abstract = {Revealing community assembly and their impacts on ecosystem service is a core issue in microbial ecology. However, what ecological factors play dominant roles in phyllosphere fungal community assembly and how they link to crop quality are largely unknown. Here, we applied internal transcriptional spacer high-throughput sequencing to investigate foliar fungal community assembly across three cultivars of a Solanaceae crop (tobacco) and two planting regions with different climatic conditions. Network analyses were used to reveal the pattern in foliar fungal co-occurrence, and phylogenetic null model analysis was used to elucidate the ecological assembly of foliar fungal communities. We found that the sensory quality of crop leaves and the composition of foliar fungal community varied significantly across planting regions and cultivars. In Guangcun (GC), a region with relatively high humidity and low precipitation, there was a higher diversity and more unique fungal species than the region of Wuzhishan (WZS). Further, we found that the association network of foliar fungal communities in GC was more complex than that in WZS, and the network properties were closely related to the sensory quality of crop. Finally, the results of the phylogenetic analyses show that the stochastic processes played important roles in the foliar fungal community assembly, and their relative importance was significantly correlated with the sensory quality of crop leaves, which implies that ecological assembly processes could affect crop quality. Taken together, our results highlight that climatic conditions, and plant cultivars play key roles in the assembly of foliar fungal communities and crop quality, which enhances our understanding of the connections between the phyllosphere microbiome and ecosystem services, especially in agricultural production.}, }
@article {pmid35478286, year = {2022}, author = {Clough, SE and Jousset, A and Elphinstone, JG and Friman, VP}, title = {Combining in vitro and in vivo screening to identify efficient Pseudomonas biocontrol strains against the phytopathogenic bacterium Ralstonia solanacearum.}, journal = {MicrobiologyOpen}, volume = {11}, number = {2}, pages = {e1283}, pmid = {35478286}, issn = {2045-8827}, mesh = {Anti-Bacterial Agents/pharmacology ; Antibiosis ; *Solanum lycopersicum/microbiology ; Plant Diseases/microbiology/prevention &amp; control ; Pseudomonas/genetics ; *Ralstonia solanacearum ; }, abstract = {Although plant pathogens are traditionally controlled using synthetic agrochemicals, the availability of commercial bactericides is still limited. One potential control strategy could be the use of plant growth-promoting bacteria (PGPB) to suppress pathogens via resource competition or the production of antimicrobial compounds. This study aimed to conduct in vitro and in vivo screening of eight Pseudomonas strains against Ralstonia solanacearum (the causative agent of bacterial wilt) and to investigate underlying mechanisms of potential pathogen suppression. We found that inhibitory effects were Pseudomonas strain-specific, with strain CHA0 showing the highest pathogen suppression. Genomic screening identified 2,4-diacetylphloroglucinol, pyoluteorin, and orfamides A and B secondary metabolite clusters in the genomes of the most inhibitory strains, which were investigated further. Although all these compounds suppressed R. solanacearum growth, only orfamide A was produced in the growth media based on mass spectrometry. Moreover, orfamide variants extracted from Pseudomonas cultures showed high pathogen suppression. Using the "Micro-Tom" tomato cultivar, it was found that CHA0 could reduce bacterial wilt disease incidence with one of the two tested pathogen strains. Together, these findings suggest that a better understanding of Pseudomonas-Ralstonia interactions in the rhizosphere is required to successfully translate in vitro findings into agricultural applications.}, }
@article {pmid35476456, year = {2022}, author = {Alvarado, V and Hsu, SC and Wu, Z and Zhuang, H and Lee, PH and Guest, JS}, title = {Roadmap from Microbial Communities to Individuality Modeling for Anaerobic Digestion of Sewage Sludge.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {10}, pages = {6596-6607}, doi = {10.1021/acs.est.1c05258}, pmid = {35476456}, issn = {1520-5851}, mesh = {Acetates ; Anaerobiosis ; Bioreactors/microbiology ; Hydrogen ; Methane ; *Microbiota ; *Sewage/chemistry ; }, abstract = {Biological models describing anaerobic digestion (AD) of sewage sludge have been widely applied to test various control and operation strategies. Anaerobic digestion model 1 (ADM1) provides a generic platform that includes the main processes of AD, excluding homoacetogenesis and the microbial structure. Homoacetogenic bacteria have been identified as important competitors for hydrogen consumption and acetate production. Although recent advances in meta-omics techniques have improved our characterization of AD microbial communities, conventional models treat functional groups as homogeneous and overlook the physiology and behavior of microbial individuality, limiting insights into mechanisms governing process performance. A novel microbial individuality model (MIM) that integrates kinetics, energetics, and agent-based modeling to describe a microbiome's behavior as heterogenic populations, including homoacetogenesis, was developed. The MIM was validated with two datasets from previous studies through daily biogas production, methane content, compound concentrations, and microbial relative abundance changes. The MIM identified the emergence of Methanosaeta at low concentrations of acetate. Moreover, this simulation supports experimental studies confirming that the overlooked homoacetogenesis is an important hydrogen sink in AD. Validated MIMs are expected to provide insights into syntrophic and competitive interactions among microbiomes in AD systems while testing different operational parameters in a virtual environment. The MIM offers a methodological framework to other biological treatment systems and their microbial community dynamics.}, }
@article {pmid35476217, year = {2022}, author = {Xu, Z and Li, Z and Ren, F and Gao, R and Wang, Z and Zhang, J and Zhao, T and Ma, X and Pu, X and Xin, T and Rombauts, S and Sun, W and Van de Peer, Y and Chen, S and Song, J}, title = {The genome of Corydalis reveals the evolution of benzylisoquinoline alkaloid biosynthesis in Ranunculales.}, journal = {The Plant journal : for cell and molecular biology}, volume = {111}, number = {1}, pages = {217-230}, pmid = {35476217}, issn = {1365-313X}, support = {833522/ERC_/European Research Council/International ; }, mesh = {*Alkaloids/genetics/metabolism ; *Benzylisoquinolines/metabolism ; *Corydalis/genetics/metabolism ; Evolution, Molecular ; *Papaveraceae/genetics/metabolism ; Phylogeny ; Ranunculales ; }, abstract = {Species belonging to the order Ranunculales have attracted much attention because of their phylogenetic position as a sister group to all other eudicot lineages and their ability to produce unique yet diverse benzylisoquinoline alkaloids (BIAs). The Papaveraceae family in Ranunculales is often used as a model system for studying BIA biosynthesis. Here, we report the chromosome-level genome assembly of Corydalis tomentella, a species of Fumarioideae, one of the two subfamilies of Papaveraceae. Based on comparisons of sequenced Ranunculalean species, we present clear evidence of a shared whole-genome duplication (WGD) event that has occurred before the divergence of Ranunculales but after its divergence from other eudicot lineages. The C. tomentella genome enabled us to integrate isotopic labeling and comparative genomics to reconstruct the BIA biosynthetic pathway for both sanguinarine biosynthesis shared by papaveraceous species and the cavidine biosynthesis that is specific to Corydalis. Also, our comparative analysis revealed that gene duplications, especially tandem gene duplications, underlie the diversification of BIA biosynthetic pathways in Ranunculales. In particular, tandemly duplicated berberine bridge enzyme-like genes appear to be involved in cavidine biosynthesis. In conclusion, our study of the C. tomentella genome provides important insights into the occurrence of WGDs during the early evolution of eudicots, as well as into the evolution of BIA biosynthesis in Ranunculales.}, }
@article {pmid35474408, year = {2022}, author = {Znidersic, E and Watson, DM}, title = {Acoustic restoration: Using soundscapes to benchmark and fast-track recovery of ecological communities.}, journal = {Ecology letters}, volume = {25}, number = {7}, pages = {1597-1603}, pmid = {35474408}, issn = {1461-0248}, support = {//Charles Sturt University/ ; }, mesh = {*Acoustics ; Animals ; Biota ; Ecosystem ; }, abstract = {We introduce a new approach-acoustic restoration-focusing on the applied utility of soundscapes for restoration, recognising the rich ecological and social values they encapsulate. Broadcasting soundscapes in disturbed areas can accelerate recolonisation of animals and the microbes and propagules they carry; long duration recordings are also ideal sources of data for benchmarking restoration initiatives and evocative engagement tools.}, }
@article {pmid35473973, year = {2022}, author = {S R, S and H P, S and Prakash, I and Khan, M and H N, PK and Om, H and Basavaraj, K and Murthy, PS}, title = {Microbial ecology and functional coffee fermentation dynamics with Pichia kudriavzevii.}, journal = {Food microbiology}, volume = {105}, number = {}, pages = {104012}, doi = {10.1016/j.fm.2022.104012}, pmid = {35473973}, issn = {1095-9998}, mesh = {*Coffee/chemistry ; Fermentation ; Flavoring Agents/metabolism ; *Pichia/metabolism ; Sugars ; }, abstract = {Specialty coffee can be developed by the application of explicit microorganisms or starters to obtain desired fermentation. In the present study, natural fermentation (NF) of Arabica coffee was carried out spontaneously, the other set was inoculated with Pichia kudriavzevii (Y) starter culture (isolated, identified and mass cultured). The effect of microbial fermentation, metagenomics, production of functional metabolites, volatiles and their sensorial aspects were studied. The bioprocess illustrated cohesive interface of coffee nutrients and microbial communities like Mycobacterium, Acinetobacter, Gordonia, etc., in NF, Lactobacillus and Leuconostoc were prevailing in Y. The Pichia and Rhodotorula dominated in both the groups. The bioactivity of bacteria and fungi induced complex changes in physicochemical features like pH (4.2-5.2), Brix° (9.5-3.0), and metabolic transition in sugar (3.0-0.7%), alcohol (1.4-2.7%), organic acids modulating flavour precursors and organoleptics in the final brew. In the roasted bean, Y exhibited higher sugar (42%), protein (25%), polyphenol (3.5%), CGA (2.5%), caffeine (17.2%), and trigonelline (2.8%) than NF. The volatile profile exhibited increased flavour molecules like furans, ketones, and pyrazines in Y, besides lactone complexes. The organoleptics in Y were highlighted with honey, malt and berry notes. P. kudriavzevii coffee fermentation could be beneficial in specialty coffee production and enhancement of distinct characteristic flavours.}, }
@article {pmid35473303, year = {2022}, author = {Seki, D and Schauberger, C and Hausmann, B and Berger, A and Wisgrill, L and Berry, D}, title = {Individuality of the Extremely Premature Infant Gut Microbiota Is Driven by Ecological Drift.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0016322}, pmid = {35473303}, issn = {2379-5077}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; P 27831/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Infant, Newborn ; Infant ; Female ; Humans ; *Gastrointestinal Microbiome/genetics ; Infant, Extremely Premature ; RNA, Ribosomal, 16S/genetics ; Individuality ; Feces ; }, abstract = {The initial contact between humans and their colonizing gut microbiota after birth is thought to have expansive and long-lasting consequences for physiology and health. Premature infants are at high risk of suffering from lifelong impairments, due in part to aberrant development of gut microbiota that can contribute to early-life infections and inflammation. Despite their importance to health, the ecological assembly and succession processes governing gut microbiome composition in premature infants remained incompletely understood. Here, we quantified these ecological processes in a spatiotemporally resolved 16S rRNA gene amplicon sequencing data set of 60 extremely premature neonates using an established mathematical framework. We found that gut colonization during the first months of life is predominantly stochastic, whereby interindividual diversification of microbiota is driven by ecological drift. Dispersal limitations are initially small but have increasing influence at later stages of succession. Furthermore, we find similar trends in a cohort of 32 healthy term-born infants. These results suggest that the uniqueness of individual gut microbiota of extremely premature infants is largely due to stochastic assembly. IMPORTANCE Our knowledge concerning the initial gut microbiome assembly in human neonates is limited, and scientific progression in this interdisciplinary field is hindered due to the individuality in composition of gut microbiota. Our study addresses the ecological processes that result in the observed individuality of microbes in the gastrointestinal tract between extremely premature and term-born infants. We find that initial assembly is mainly driven by neutral ecological processes. Interestingly, while this progression is predominantly random, limitations to the dispersal of microbiota between infants become increasingly important with age and are concomitant features of gut microbiome stability. This indicates that while we cannot predict gut microbiota assembly due to its random nature, we can expect the establishment of certain ecological features that are highly relevant for neonatal health.}, }
@article {pmid35468931, year = {2022}, author = {Jangid, A and Fukuda, S and Suzuki, Y and Taylor, TD and Ohno, H and Prakash, T}, title = {Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6748}, pmid = {35468931}, issn = {2045-2322}, mesh = {Animals ; Cellulose/pharmacology ; Diet ; Dietary Fiber/pharmacology ; Edible Grain ; Lactobacillus/genetics ; *Metagenome ; Metagenomics ; Mice ; *Prebiotics ; }, abstract = {In the present study, we elucidated the effect of grain-based (GB) diet containing both soluble and insoluble fibers and purified ingredients-based (PIB) diet containing only insoluble fiber, namely cellulose on mice gut microbiome using whole shotgun based metagenomic sequencing. Although the fiber content in both diet types is the same (5%) the presence of soluble fiber only in the GB diet differentiates it from the PIB diet. The taxonomic analysis of sequenced reads reveals a significantly higher enrichment of probiotic Lactobacilli in the GB group as compared to the PIB group. Further, the enhancement of energy expensive cellular processes namely, cell cycle control, cell division, chromosome partitioning, and transcription is observed in the GB group which could be due to the metabolization of the soluble fiber for faster energy production. In contrast, a higher abundance of cellulolytic bacterial community namely, the members of family Lachnospiraceae and Ruminococcaceae and the metabolism functions are found in the PIB group. The PIB group shows a significant increase in host-derived oligosaccharide metabolism functions indicating that they might first target the host-derived oligosaccharides and self-stored glycogen in addition to utilising the available cellulose. In addition to the beneficial microbial community variations, both the groups also exhibited an increased abundance of opportunistic pathobionts which could be due to an overall low amount of fiber in the diet. Furthermore, backtracing analysis identified probiotic members of Lactobacillus, viz., L. crispatus ST1, L. fermentum CECT 5716, L. gasseri ATCC 33323, L. johnsonii NCC 533 and L. reuteri 100-23 in the GB group, while Bilophila wadsworthia 3_1_6, Desulfovibrio piger ATCC 29098, Clostridium symbiosum WAL-14163, and Ruminococcaceae bacterium D16 in the PIB group. These data suggest that Lactobacilli, a probiotic community of microorganisms, are the predominant functional contributors in the gut of GB diet-fed mice, whereas pathobionts too coexisted with commensals in the gut microbiome of the PIB group. Thus at 5% fiber, GB modifies the gut microbial ecology more effectively than PIB and the inclusion of soluble fiber in the GB diet may be one of the primary factors responsible for this impact.}, }
@article {pmid35464965, year = {2022}, author = {Petrin, S and Mancin, M and Losasso, C and Deotto, S and Olsen, JE and Barco, L}, title = {Effect of pH and Salinity on the Ability of Salmonella Serotypes to Form Biofilm.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {821679}, pmid = {35464965}, issn = {1664-302X}, abstract = {Salmonella is a major cause of food-borne infections in Europe, and the majority of human infections are caused by only a few serotypes, among them are Salmonella enterica subsp. enterica serotype Enteritidis (hereafter Salmonella Enteritidis), Salmonella Typhimurium, and the monophasic variant of S. Typhimurium. The reason for this is not fully understood, but could include virulence factors as well as increased ability to transfer via the external environment. Formation of biofilm is considered an adaptation strategy used by bacteria to overcome environmental stresses. In order to assess the capability of different Salmonella serotypes to produce biofilm and establish whether this is affected by pH and salinity, 88 Salmonella isolates collected from animal, food, and human sources and belonging to 15 serotypes, including those most frequently responsible for human infections, were tested. Strains were grown in tryptic soy broth (TSB), TSB with 4% NaCl pH 4.5, TSB with 10% NaCl pH 4.5, TSB with 4% NaCl pH 7, or TSB with 10% NaCl pH 7, and biofilm production was assessed after 24 h at 37°C using crystal violet staining. A linear mixed effect model was applied to compare results from the different experimental conditions. Among the tested serotypes, S. Dublin showed the greatest ability to form biofilm even at pH 4.5, which inhibited biofilm production in the other tested serotypes. Salmonella Senftenberg and the monophasic variant of S. Typhimurium showed the highest biofilm production in TSB with 10% NaCl pH 7. In general, pH had a high influence on the ability to form biofilm, and most of the tested strains were not able to produce biofilm at pH 4.5. In contrast, salinity only had a limited influence on biofilm production. In general, serotypes causing the highest number of human infections showed a limited ability to produce biofilm in the tested conditions, indicating that biofilm formation is not a crucial factor in the success of these clones.}, }
@article {pmid35464964, year = {2022}, author = {Haber, M and Roth Rosenberg, D and Lalzar, M and Burgsdorf, I and Saurav, K and Lionheart, R and Lehahn, Y and Aharonovich, D and Gómez-Consarnau, L and Sher, D and Krom, MD and Steindler, L}, title = {Spatiotemporal Variation of Microbial Communities in the Ultra-Oligotrophic Eastern Mediterranean Sea.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {867694}, pmid = {35464964}, issn = {1664-302X}, abstract = {Marine microbial communities vary seasonally and spatially, but these two factors are rarely addressed together. In this study, the temporal and spatial patterns of the bacterial and archaeal community were studied along a coast-to-offshore transect in the Eastern Mediterranean Sea (EMS) over six cruises, in three seasons of 2 consecutive years. Amplicon sequencing of 16S rRNA genes and transcripts was performed to determine presence and activity, respectively. The ultra-oligotrophic status of the Southeastern Mediterranean Sea was reflected in the microbial community composition dominated by oligotrophic bacterial groups such as SAR11, even at the most coastal station sampled, throughout the year. Seasons significantly affected the microbial communities, explaining more than half of the observed variability. However, the same few taxa dominated the community over the 2-year sampling period, varying only in their degree of dominance. While there was no overall effect of station location on the microbial community, the most coastal site (16 km offshore) differed significantly in community structure and activity from the three further offshore stations in early winter and summer. Our data on the microbial community compositions and their seasonality support previous notions that the EMS behaves like an oceanic gyre.}, }
@article {pmid35464924, year = {2022}, author = {Wetherington, MT and Nagy, K and Dér, L and Noorlag, J and Galajda, P and Keymer, JE}, title = {Variance in Landscape Connectivity Shifts Microbial Population Scaling.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {831790}, pmid = {35464924}, issn = {1664-302X}, abstract = {Understanding mechanisms shaping distributions and interactions of soil microbes is essential for determining their impact on large scale ecosystem services, such as carbon sequestration, climate regulation, waste decomposition, and nutrient cycling. As the functional unit of soil ecosystems, we focus our attention on the spatial structure of soil macroaggregates. Emulating this complex physico-chemical environment as a patchy habitat landscape we investigate on-chip the effect of changing the connectivity features of this landscape as Escherichia coli forms a metapopulation. We analyze the distributions of E. coli occupancy using Taylor's law, an empirical law in ecology which asserts that the fluctuations in populations is a power law function of the mean. We provide experimental evidence that bacterial metapopulations in patchy habitat landscapes on microchips follow this law. Furthermore, we find that increased variance of patch-corridor connectivity leads to a qualitative transition in the fluctuation scaling. We discuss these results in the context of the spatial ecology of microbes in soil.}, }
@article {pmid35464923, year = {2022}, author = {Riemann, L and Rahav, E and Passow, U and Grossart, HP and de Beer, D and Klawonn, I and Eichner, M and Benavides, M and Bar-Zeev, E}, title = {Planktonic Aggregates as Hotspots for Heterotrophic Diazotrophy: The Plot Thickens.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {875050}, pmid = {35464923}, issn = {1664-302X}, abstract = {Biological dinitrogen (N2) fixation is performed solely by specialized bacteria and archaea termed diazotrophs, introducing new reactive nitrogen into aquatic environments. Conventionally, phototrophic cyanobacteria are considered the major diazotrophs in aquatic environments. However, accumulating evidence indicates that diverse non-cyanobacterial diazotrophs (NCDs) inhabit a wide range of aquatic ecosystems, including temperate and polar latitudes, coastal environments and the deep ocean. NCDs are thus suspected to impact global nitrogen cycling decisively, yet their ecological and quantitative importance remain unknown. Here we review recent molecular and biogeochemical evidence demonstrating that pelagic NCDs inhabit and thrive especially on aggregates in diverse aquatic ecosystems. Aggregates are characterized by reduced-oxygen microzones, high C:N ratio (above Redfield) and high availability of labile carbon as compared to the ambient water. We argue that planktonic aggregates are important loci for energetically-expensive N2 fixation by NCDs and propose a conceptual framework for aggregate-associated N2 fixation. Future studies on aggregate-associated diazotrophy, using novel methodological approaches, are encouraged to address the ecological relevance of NCDs for nitrogen cycling in aquatic environments.}, }
@article {pmid35462258, year = {2022}, author = {Garrido-Baserba, M and Barnosell, I and Molinos-Senante, M and Sedlak, DL and Rabaey, K and Schraa, O and Verdaguer, M and Rosso, D and Poch, M}, title = {The third route: A techno-economic evaluation of extreme water and wastewater decentralization.}, journal = {Water research}, volume = {218}, number = {}, pages = {118408}, doi = {10.1016/j.watres.2022.118408}, pmid = {35462258}, issn = {1879-2448}, mesh = {*Drinking Water ; Humans ; Politics ; Sewage ; *Wastewater ; Water Supply ; }, abstract = {Water systems need to become more locally robust and sustainable in view of increased population demands and supply uncertainties. Decentralized treatment is often assumed to have the potential to improve the technical, environmental, and economic performance of current technologies. The techno-economic feasibility of implementing independent building-scale decentralized systems combining rainwater harvesting, potable water production, and wastewater treatment and recycling was assessed for six main types of buildings ranging from single-family dwellings to high-rise buildings. Five different treatment layouts were evaluated under five different climatic conditions for each type of building. The layouts considered varying levels of source separation (i.e., black, grey, yellow, brown, and combined wastewater) using the corresponding toilet types (vacuum, urine-diverting, and conventional) and the appropriate pipes and pumping requirements. Our results indicate that the proposed layouts could satisfy 100% of the water demand for the three smallest buildings in all but the aridest climate conditions. For the three larger buildings, rainwater would offset annual water needs by approximately 74 to 100%. A comprehensive economic analysis considering CapEx and OpEx indicated that the cost of installing on-site water harvesting and recycling systems would increase the overall construction cost of multi-family buildings by around 6% and single-family dwellings by about 12%, with relatively low space requirements. For buildings or combined water systems with more than 300 people, the estimated total price of on-site water provision (including harvesting, treatment, recycling, and monitoring) ranged from $1.5/m[3] to $2.7/m,[3] which is considerably less than the typical tariffs collected by utilities in the United States and Western Europe. Where buildings can avoid the need to connect to centralized supplies for potable water and sewage disposal, water costs could be even lower. Urine-diversion has the potential to yield the least expensive solution but is the least well developed and had higher uncertainty in the cost analysis. More mature layouts (e.g., membrane bioreactors) exhibited less cost uncertainty and were economically competitive. Our analysis indicates that existing technologies can be used to create economically viable systems that greatly reduce demands on centralized utilities and, under some conditions, eliminate the need for centralized water supply or sewage collection.}, }
@article {pmid35460373, year = {2023}, author = {Balbuena, S and Castelli, L and Zunino, P and Antúnez, K}, title = {Effect of Chronic Exposure to Sublethal Doses of Imidacloprid and Nosema ceranae on Immunity, Gut Microbiota, and Survival of Africanized Honey Bees.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1485-1497}, pmid = {35460373}, issn = {1432-184X}, support = {ANII-FCE_1_2017_1_135810//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n/ ; POS_NAC_2018_1_151557//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n/ ; For Women in Science//Fondation L'Or&#xe9;al/ ; }, mesh = {Bees ; Animals ; *Gastrointestinal Microbiome ; Neonicotinoids/toxicity ; *Pesticides/pharmacology ; *Nosema/physiology ; }, abstract = {Large-scale honey bee colony losses reported around the world have been associated with intoxication with pesticides, as with the presence of pests and pathogens. Among pesticides, neonicotinoid insecticides are the biggest threat. Due to their extensive use, they can be found in all agricultural environments, including soil, water, and air, are persistent in the environment, and are highly toxic for honey bees. In addition, infection by different pests and pathogens can act synergistically, weakening bees. In this study, we investigated the effects of chronic exposure to sublethal doses of imidacloprid alone or combined with the microsporidia Nosema ceranae on the immune response, deformed wing virus infection (DWV), gut microbiota, and survival of Africanized honey bees. We found that imidacloprid affected the expression of some genes associated with immunity generating an altered physiological state, although it did not favor DWV or N. ceranae infection. The pesticide alone did not affect honey bee gut microbiota, as previously suggested, but when administered to N. ceranae infected bees, it generated significant changes. Finally, both stress factors caused high mortality rates. Those results illustrate the negative impact of imidacloprid alone or combined with N. ceranae on Africanized honey bees and are useful to understand colony losses in Latin America.}, }
@article {pmid35460372, year = {2023}, author = {Mascuch, SJ and Demko, A and Viulu, S and Ginigini, J and Soapi, K and Jensen, P and Kubanek, J}, title = {Antibiotic Activity Altered by Competitive Interactions Between Two Coral Reef-Associated Bacteria.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1226-1235}, pmid = {35460372}, issn = {1432-184X}, support = {U19 TW007401/TW/FIC NIH HHS/United States ; U19 TW007401/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Humans ; Coral Reefs ; Anti-Bacterial Agents/pharmacology ; *Anthozoa/microbiology ; *Streptomyces ; Diketopiperazines ; }, abstract = {Microbes produce natural products that mediate interactions with each other and with their environments, representing a potential source of antibiotics for human use. The biosynthesis of some antibiotics whose constitutive production otherwise remains low has been shown to be induced by competing microbes. Competition among macroorganism hosts may further influence the metabolic outputs of members of their microbiomes, especially near host surfaces where hosts and microbial symbionts come into close contact. At multiple field sites in Fiji, we collected matched samples of corals and algae that were freestanding or in physical contact with each other, cultivated bacteria from their surfaces, and explored growth-inhibitory activities of these bacteria against marine and human pathogens. In the course of the investigation, an interaction was discovered between two coral-associated actinomycetes in which an Agrococcus sp. interfered with the antibiotic output of a Streptomyces sp. Several diketopiperazines identified from the antibiotic-producing bacterium could not, on their own, account for the antibiotic activity indicating that other, as yet unidentified molecule(s) or molecular blends, possibly including diketopiperazines, are likely involved. This observation highlights the complex molecular dynamics at play among microbiome constituents. The mechanisms through which microbial interactions impact the biological activities of specialized metabolites deserve further attention considering the ecological and commercial importance of bacterial natural products.}, }
@article {pmid35460285, year = {2022}, author = {Bartha, L and Mandáková, T and Kovařík, A and Bulzu, PA and Rodde, N and Mahelka, V and Lysak, MA and Fustier, MA and Šafář, J and Cápal, P and Keresztes, L and Banciu, HL}, title = {Intact ribosomal DNA arrays of Potentilla origin detected in Erythronium nucleus suggest recent eudicot-to-monocot horizontal transfer.}, journal = {The New phytologist}, volume = {235}, number = {3}, pages = {1246-1259}, doi = {10.1111/nph.18171}, pmid = {35460285}, issn = {1469-8137}, mesh = {DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; In Situ Hybridization, Fluorescence ; *Liliaceae ; Phylogeny ; *Potentilla/genetics ; }, abstract = {During our initial phylogenetic study of the monocot genus Erythronium (Liliaceae), we observed peculiar eudicot-type internal transcribed spacer (ITS) sequences in a dataset derived from genomic DNA of Erythronium dens-canis. This raised the possibility of horizontal transfer of a eudicot alien ribosomal DNA (rDNA) into the Erythronium genome. In this work we aimed to support this hypothesis by carrying out genomic, molecular, and cytogenetic analyses. Genome skimming coupled by PacBio HiFi sequencing of a bacterial artificial chromosome clone derived from flow-sorted nuclei was used to characterise the alien 45S rDNA. Integration of alien rDNA in the recipient genome was further proved by Southern blotting and fluorescence in situ hybridization using specific probes. Alien rDNA, nested among Potentilla species in phylogenetic analysis, likely entered the Erythronium lineage in the common ancestor of E. dens-canis and E. caucasicum. Transferred eudicot-type rDNA preserved its tandemly arrayed feature on a single chromosome and was found to be transcribed in the monocot host, albeit much less efficiently than the native counterpart. This study adds a new example to the rarely documented nuclear-to-nuclear jumps of DNA between eudicots and monocots while holding the scientific community continually in suspense about the mode of DNA transfer.}, }
@article {pmid35458219, year = {2022}, author = {Franck, M and de Toro-Martín, J and V Varin, T and Garneau, V and Pilon, G and Roy, D and Couture, P and Couillard, C and Marette, A and Vohl, MC}, title = {Gut Microbial Signatures of Distinct Trimethylamine N-Oxide Response to Raspberry Consumption.}, journal = {Nutrients}, volume = {14}, number = {8}, pages = {}, pmid = {35458219}, issn = {2072-6643}, support = {MRT-168045//CIHR/ ; not applicable//WA Red Raspberry Commission (WRRC)/ ; }, mesh = {Bacteria ; *Gastrointestinal Microbiome ; Humans ; Methylamines ; *Rubus/metabolism ; }, abstract = {The aim of this exploratory study was to evaluate the gut microbial signatures of distinct trimethylamine N-oxide (TMAO) responses following raspberry consumption. Investigations were carried out in 24 subjects at risk of developing metabolic syndrome who received 280 g/day of frozen raspberries for 8 weeks. Blood and stool samples were collected at weeks 0 and 8. Inter-individual variability in plasma TMAO levels was analyzed, 7 subjects were excluded due to noninformative signals and 17 subjects were kept for analysis and further stratified according to their TMAO response. Whole-metagenome shotgun sequencing analysis was used to determine the impact of raspberry consumption on gut microbial composition. Before the intervention, the relative abundance of Actinobacteriota was significantly higher in participants whose TMAO levels increased after the intervention (p = 0.03). The delta TMAO (absolute differences of baseline and week 8 levels) was positively associated with the abundance of gut bacteria such as Bilophila wadsworthia (p = 0.02; r[2] = 0.37), from the genus Granulicatella (p = 0.03; r[2] = 0.48) or the Erysipelotrichia class (p = 0.03; r[2] = 0.45). Changes in the gut microbial ecology induced by raspberry consumption over an 8-week period presumably impacted quaternary amines-utilizing activity and thus plasma TMAO levels.}, }
@article {pmid35456812, year = {2022}, author = {Van den Abbeele, P and Ghyselinck, J and Marzorati, M and Koch, AM and Lambert, W and Michiels, J and Chalvon-Demersay, T}, title = {The Effect of Amino Acids on Production of SCFA and bCFA by Members of the Porcine Colonic Microbiota.}, journal = {Microorganisms}, volume = {10}, number = {4}, pages = {}, pmid = {35456812}, issn = {2076-2607}, abstract = {Functional amino acids supplementation to farm animals is considered to not only be beneficial by regulating intestinal barrier, oxidative stress, and immunity, but potentially also by impacting the gut microbiota. The impact of amino acids on a piglet-derived colonic microbiota was evaluated using a 48-h in vitro batch incubation strategy. The combination of 16S rRNA gene profiling with flow cytometry demonstrated that specific microbial taxa were involved in the fermentation of each of the amino acids resulting in the production of specific metabolites. Branched chain amino acids (leucine, isoleucine, valine) strongly increased branched-chain fatty acids (+23.0 mM) and valerate levels (+3.0 mM), coincided with a marked increase of Peptostreptococcaceae. Further, glutamine and glutamate specifically stimulated acetate (~20 mM) and butyrate (~10 mM) production, relating to a stimulation of a range of families containing known butyrate-producing species (Ruminococcaceae, Oscillospiraceae, and Christensenellaceae). Finally, while tryptophan was only fermented to a minor extent, arginine and lysine specifically increased propionate levels (~2 mM), likely produced by Muribaculaceae members. Overall, amino acids were thus shown to be selectively utilized by microbes originating from the porcine colonic microbiota, resulting in the production of health-related short-chain fatty acids, thus confirming the prebiotic potential of specific functional amino acids.}, }
@article {pmid35456724, year = {2022}, author = {Guo, Z and Bao, Y and Liu, J}, title = {Environmental Difference and Spatial Distance Affect the Fidelity of Variation Source of Microbial Community Structure in Air-Dried Soils.}, journal = {Microorganisms}, volume = {10}, number = {4}, pages = {}, pmid = {35456724}, issn = {2076-2607}, abstract = {Air-dried soil archives are important for microbial ecology research, although the process of air-drying preservation inevitably destroys the original microbial information in soils. Only upon fully understanding the limitations of air-dried soil can it play a greater role. The value of air-dried soil depends on the fidelity of microbial community structure information in the air-dried soil relative to that in fresh soil. To evaluate this, high-throughput sequencing was applied to investigate the microbial community of fresh soils and 227 days air-dried archives from typical farmland under a large spatial scale, and PERMANOVA was used to analyze the explanation proportion (EP) of the spatial factor on the microbial community structure in any paired-fresh or air-dried soils. The results show that for any paired soils, the value of EP ranged from 42.4% to 97.9% (p < 0.001). Importantly, taking fresh soil as a reference, the value of EP declined in air-dried soils (effect size r = 0.79, p < 0.001). Furthermore, the standardized difference in EP between fresh and air-dried soil (NDEP) was used to characterize the fidelity of variance source of microbial community structure in air-dried soils, and correlation tests showed that NDEP was negatively correlated with spatial distance (r = −0.21, p < 0.01) and with environmental difference (r = −0.37, p < 0.001). Further analyses show that larger NDEP was observed at a spatial distance <25 km or an environmental difference <0.58. Variance partitioning analysis showed that 28.0% of the variation in NDEP could be explained, with environmental difference constituting 14.0% and the interaction between the environmental difference and spatial distance constituting the remaining 14.0%. Soil texture was the most important factor for predicting NDEP, followed by soil pH and annual average temperature. This study not only emphasizes the possible decline in EP when using air-dried soils to reveal microbial community patterns, but also implies that air-dried soil is more suitable for addressing scientific questions under a large spatial scale or environmental differences.}, }
@article {pmid35454671, year = {2022}, author = {Li, Q and Li, L and Li, Q and Wang, J and Nie, S and Xie, M}, title = {Influence of Natural Polysaccharides on Intestinal Microbiota in Inflammatory Bowel Diseases: An Overview.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {8}, pages = {}, pmid = {35454671}, issn = {2304-8158}, support = {20212BCD42016//Key Laboratory of Bioactive Polysaccharides Program of Jiangxi Province/ ; 20212AAF01005//Key Technology Project in Jiangxi Province/ ; 20212BAB215036//Natural Science Foundation of Jiangxi Province/ ; }, abstract = {The incidence of inflammatory bowel disease (IBD) has increased in recent years. Considering the potential side effects of conventional drugs, safe and efficient treatment methods for IBD are required urgently. Natural polysaccharides (NPs) have attracted considerable attention as potential therapeutic agents for IBD owing to their high efficiency, low toxicity, and wide range of biological activities. Intestinal microbiota and their fermentative products, mainly short-chain fatty acids (SCFAs), are thought to mediate the effect of NPs in IBDs. This review explores the beneficial effects of NPs on IBD, with a special focus on the role of intestinal microbes. Intestinal microbiota exert alleviation effects via various mechanisms, such as increasing the intestinal immunity, anti-inflammatory activities, and intestinal barrier protection via microbiota-dependent and microbiota-independent strategies. The aim of this paper was to document evidence of NP-intestinal microbiota-associated IBD prevention, which would be helpful for guidance in the treatment and management of IBD.}, }
@article {pmid35453798, year = {2022}, author = {Malfertheiner, L and Martínez-Pérez, C and Zhao, Z and Herndl, GJ and Baltar, F}, title = {Phylogeny and Metabolic Potential of the Candidate Phylum SAR324.}, journal = {Biology}, volume = {11}, number = {4}, pages = {}, pmid = {35453798}, issn = {2079-7737}, support = {P 35248/FWF_/Austrian Science Fund FWF/Austria ; P 28781/FWF_/Austrian Science Fund FWF/Austria ; TAI 534/FWF_/Austrian Science Fund FWF/Austria ; P 23234/FWF_/Austrian Science Fund FWF/Austria ; I 486/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {The bacterial SAR324 cluster is ubiquitous and abundant in the ocean, especially around hydrothermal vents and in the deep sea, where it can account for up to 30% of the whole bacterial community. According to a new taxonomy generated using multiple universal protein-coding genes (instead of the previously used 16S rRNA single gene marker), the former Deltaproteobacteria cluster SAR324 has been classified since 2018 as its own phylum. Yet, very little is known about its phylogeny and metabolic potential. We downloaded all publicly available SAR324 genomes (65) from all natural environments and reconstructed 18 new genomes using publicly available oceanic metagenomic data and unpublished data from the waters underneath the Ross Ice Shelf. We calculated a global SAR324 phylogenetic tree and identified six clusters (namely 1A, 1B, 2A, 2B, 2C and 2D) within this clade. Genome annotation and metatranscriptome read mapping showed that SAR324 clades possess a flexible array of genes suited for survival in various environments. Clades 2A and 2C are mostly present in the surface mesopelagic layers of global oceans, while clade 2D dominates in deeper regions. Our results show that SAR324 has a very versatile and broad metabolic potential, including many heterotrophic, but also autotrophic pathways. While one surface water associated clade (2A) seems to use proteorhodopsin to gain energy from solar radiation, some deep-sea genomes from clade 2D contain the complete Calvin-Benson-Bassham cycle gene repertoire to fix carbon. This, in addition to a variety of other genes and pathways for both oxic (e.g., dimethylsulfoniopropionate degradation) and anoxic (e.g., dissimilatory sulfate reduction, anaerobic benzoate degradation) conditions, can help explain the ubiquitous presence of SAR324 in aquatic habitats.}, }
@article {pmid35453791, year = {2022}, author = {Liu, Z and Wang, J and Meng, D and Li, L and Liu, X and Gu, Y and Yan, Q and Jiang, C and Yin, H}, title = {The Self-Organization of Marine Microbial Networks under Evolutionary and Ecological Processes: Observations and Modeling.}, journal = {Biology}, volume = {11}, number = {4}, pages = {}, pmid = {35453791}, issn = {2079-7737}, support = {41877345//National Nature Science Foundation of China/ ; 91851206//National Nature Science Foundation of China/ ; QYZDBSSW-DQC043//Key Research Program of Frontier Sciences of the Chinese Academy of Sciences/ ; }, abstract = {Evolutionary and ecological processes are primary drivers of ecological network constrictions. However, the ways that these processes underpin self-organization and modularity in networks are poorly understood. Here, we performed network analyses to explore the evolutionary and ecological effects on global marine microbial co-occurrence networks across multiple network levels, including those of nodes, motifs, modules and whole networks. We found that both direct and indirect species interactions were evolutionarily and ecologically constrained across at least four network levels. Compared to ecological processes, evolutionary processes generally showed stronger long-lasting effects on indirect interactions and dominated the network assembly of particle-associated communities in spatially homogeneous environments. Regarding the large network path distance, the contributions of either processes to species interactions generally decrease and almost disappear when network path distance is larger than six. Accordingly, we developed a novel mathematical model based on scale-free networks by considering the joint effects of evolutionary and ecological processes. We simulated the self-organization of microbial co-occurrence networks and found that long-lasting effects increased network stability via decreasing link gain or loss. Overall, these results revealed that evolutionary and ecological processes played key roles in the self-organization and modularization of microbial co-occurrence networks.}, }
@article {pmid35449401, year = {2022}, author = {Li, MH and Liu, KW and Li, Z and Lu, HC and Ye, QL and Zhang, D and Wang, JY and Li, YF and Zhong, ZM and Liu, X and Yu, X and Liu, DK and Tu, XD and Liu, B and Hao, Y and Liao, XY and Jiang, YT and Sun, WH and Chen, J and Chen, YQ and Ai, Y and Zhai, JW and Wu, SS and Zhou, Z and Hsiao, YY and Wu, WL and Chen, YY and Lin, YF and Hsu, JL and Li, CY and Wang, ZW and Zhao, X and Zhong, WY and Ma, XK and Ma, L and Huang, J and Chen, GZ and Huang, MZ and Huang, L and Peng, DH and Luo, YB and Zou, SQ and Chen, SP and Lan, S and Tsai, WC and Van de Peer, Y and Liu, ZJ}, title = {Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy.}, journal = {Nature plants}, volume = {8}, number = {4}, pages = {373-388}, pmid = {35449401}, issn = {2055-0278}, mesh = {*Mycorrhizae/genetics ; *Orchidaceae/genetics/metabolism/microbiology ; Symbiosis ; Trehalase/metabolism ; Trehalose/metabolism ; }, abstract = {To improve our understanding of the origin and evolution of mycoheterotrophic plants, we here present the chromosome-scale genome assemblies of two sibling orchid species: partially mycoheterotrophic Platanthera zijinensis and holomycoheterotrophic Platanthera guangdongensis. Comparative analysis shows that mycoheterotrophy is associated with increased substitution rates and gene loss, and the deletion of most photoreceptor genes and auxin transporter genes might be linked to the unique phenotypes of fully mycoheterotrophic orchids. Conversely, trehalase genes that catalyse the conversion of trehalose into glucose have expanded in most sequenced orchids, in line with the fact that the germination of orchid non-endosperm seeds needs carbohydrates from fungi during the protocorm stage. We further show that the mature plant of P. guangdongensis, different from photosynthetic orchids, keeps expressing trehalase genes to hijack trehalose from fungi. Therefore, we propose that mycoheterotrophy in mature orchids is a continuation of the protocorm stage by sustaining the expression of trehalase genes. Our results shed light on the molecular mechanism underlying initial, partial and full mycoheterotrophy.}, }
@article {pmid35448576, year = {2022}, author = {Rojas, EC and Jensen, B and Jørgensen, HJL and Latz, MAC and Esteban, P and Collinge, DB}, title = {The Fungal Endophyte Penicillium olsonii ML37 Reduces Fusarium Head Blight by Local Induced Resistance in Wheat Spikes.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {4}, pages = {}, pmid = {35448576}, issn = {2309-608X}, abstract = {The fungal endophyte Penicillium olsonii ML37 is a biocontrol agent of Fusarium head blight in wheat (caused by Fusarium graminearum), which has shown a limited direct inhibition of fungal growth in vitro. We used RNA-seq and LC-MS/MS analyses to elucidate metabolic interactions of the three-way system Penicillium-wheat-Fusarium in greenhouse experiments. We demonstrated that P. olsonii ML37 colonises wheat spikes and transiently activates plant defence mechanisms, as pretreated spikes show a faster and stronger expression of the defence metabolism during the first 24 h after pathogen inoculation. This effect was transient and the expression of the same genes was lower in the pathogen-infected spikes than in those infected by P. olsonii alone. This response to the endophyte includes the transcriptional activation of several WRKY transcription factors. This early activation is associated with a reduction in FHB symptoms and significantly lower levels of the F. graminearum metabolites 15-acetyl-DON and culmorin. An increase in the Penicillium-associated metabolite asperphanamate confirms colonisation by the endophyte. Our results suggest that the mode of action used by P. olsonii ML37 is via a local defence activation in wheat spikes, and that this fungus has potential as a novel biological alternative in wheat disease control.}, }
@article {pmid35447706, year = {2022}, author = {Jeske, JT and Gallert, C}, title = {Microbiome Analysis via OTU and ASV-Based Pipelines-A Comparative Interpretation of Ecological Data in WWTP Systems.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {9}, number = {4}, pages = {}, pmid = {35447706}, issn = {2306-5354}, support = {02WCL1469A-J//German Federal Ministry of Education and Research/ ; }, abstract = {Linking community composition and ecosystem function via the cultivation-independent analysis of marker genes, e.g., the 16S rRNA gene, is a staple of microbial ecology and dependent disciplines. The certainty of results, independent of the bioinformatic handling, is imperative for any advances made within the field. In this work, thermophilic anaerobic co-digestion experimental data, together with primary and waste-activated sludge prokaryotic community data, were analyzed with two pipelines that apply different principles when dealing with technical, sequencing, and PCR biases. One pipeline (VSEARCH) employs clustering methods, generating individual operational taxonomic units (OTUs), while the other (DADA2) is based on sequencing error correction algorithms and generates exact amplicon sequence variants (ASVs). The outcomes of both pipelines were compared within the framework of ecological-driven data analysis. Both pipelines provided comparable results that would generally allow for the same interpretations. Yet, the two approaches also delivered community compositions that differed between 6.75% and 10.81% between pipelines. Inconsistencies were also observed linked to biologically driven variability in the samples, which affected the two pipelines differently. These pipeline-dependent differences in taxonomic assignment could lead to different conclusions and interfere with any downstream analysis made for such mis- or not-identified species, e.g., network analysis or predictions of their respective ecosystem service.}, }
@article {pmid35447252, year = {2022}, author = {Kelly, MR and Whitworth, P and Jamieson, A and Burgess, JG}, title = {Bacterial colonisation of plastic in the Rockall Trough, North-East Atlantic: An improved understanding of the deep-sea plastisphere.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {305}, number = {}, pages = {119314}, doi = {10.1016/j.envpol.2022.119314}, pmid = {35447252}, issn = {1873-6424}, mesh = {Bacteria/genetics ; Environmental Pollution ; *Microbiota/genetics ; *Plastics ; RNA, Ribosomal, 16S ; }, abstract = {Plastic pollution has now been found within multiple ecosystems across the globe. Characterisation of microbial assemblages associated with marine plastic, or the so-called 'plastisphere', has focused predominantly on plastic in the epipelagic zone. Whether this community includes taxa that are consistently enriched on plastic compared to surrounding non plastic surfaces is unresolved, as are the ecological implications. The deep sea is likely a final sink for most of the plastic entering the ocean, yet there is limited information on microbial colonisation of plastic at depth. The aim of this study was to investigate deep-sea microbial communities associated with polystyrene (PS) and polyurethane (PU) with Bath stone used as a control. The substrates (n = 15) were deployed in the Rockall Trough (Atlantic), and recovered 420 days later from a depth of 1796 m. To characterise the bacterial communities, 16S rRNA genes were sequenced using the Illumina MiSeq platform. A dominant core microbiome (taxa shared across all substrates) comprised 8% of total ASVs (amplicon sequence variant) and accounted for 92% of the total community reads. This suggests that many commonly reported members of the plastisphere are simply opportunistic which freely colonise any hard surface. Transiently associated species consisted of approximately 7% of the total community. Thirty genera were enriched on plastic (P < 0.05), representing 1% of the total community. The discovery of novel deep-sea enriched taxa included Aurantivirga, Algivirga, IheB3-7, Spirosoma, HTCC5015, Ekhidna and Calorithrix on PS and Candidatus Obscuribacter, Haloferula, Marine Methylotrophic Group 3, Aliivibrio, Tibeticola and Dethiosulfatarculus on PU. This small fraction of the microbiome include taxa with unique metabolic abilities and show how bacterial communities can be shaped by plastic pollution at depth. This study outlines a novel approach in categorising the plastisphere to elucidate the ecological implications of enriched taxa that show an affinity for colonising plastic.}, }
@article {pmid35446625, year = {2022}, author = {Li, S and Abdulkadir, N and Schattenberg, F and Nunes da Rocha, U and Grimm, V and Müller, S and Liu, Z}, title = {Stabilizing microbial communities by looped mass transfer.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {17}, pages = {e2117814119}, pmid = {35446625}, issn = {1091-6490}, mesh = {Biotechnology ; Ecology ; *Microbiota ; }, abstract = {Building and changing a microbiome at will and maintaining it over hundreds of generations has so far proven challenging. Despite best efforts, complex microbiomes appear to be susceptible to large stochastic fluctuations. Current capabilities to assemble and control stable complex microbiomes are limited. Here, we propose a looped mass transfer design that stabilizes microbiomes over long periods of time. Five local microbiomes were continuously grown in parallel for over 114 generations and connected by a loop to a regional pool. Mass transfer rates were altered and microbiome dynamics were monitored using quantitative high-throughput flow cytometry and taxonomic sequencing of whole communities and sorted subcommunities. Increased mass transfer rates reduced local and temporal variation in microbiome assembly, did not affect functions, and overcame stochasticity, with all microbiomes exhibiting high constancy and increasing resistance. Mass transfer synchronized the structures of the five local microbiomes and nestedness of certain cell types was eminent. Mass transfer increased cell number and thus decreased net growth rates μ′. Subsets of cells that did not show net growth μ′SCx were rescued by the regional pool R and thus remained part of the microbiome. The loop in mass transfer ensured the survival of cells that would otherwise go extinct, even if they did not grow in all local microbiomes or grew more slowly than the actual dilution rate D would allow. The rescue effect, known from metacommunity theory, was the main stabilizing mechanism leading to synchrony and survival of subcommunities, despite differences in cell physiological properties, including growth rates.}, }
@article {pmid35443156, year = {2022}, author = {Özçam, M and Oh, JH and Tocmo, R and Acharya, D and Zhang, S and Astmann, TJ and Heggen, M and Ruiz-Ramírez, S and Li, F and Cheng, CC and Vivas, E and Rey, FE and Claesen, J and Bugni, TS and Walter, J and van Pijkeren, JP}, title = {A secondary metabolite drives intraspecies antagonism in a gut symbiont that is inhibited by cell-wall acetylation.}, journal = {Cell host &amp; microbe}, volume = {30}, number = {6}, pages = {824-835.e6}, doi = {10.1016/j.chom.2022.03.033}, pmid = {35443156}, issn = {1934-6069}, mesh = {Acetylation ; Animals ; Gastrointestinal Tract/metabolism ; Germ-Free Life ; Mammals/genetics ; Mice ; *Multigene Family ; *Polyketide Synthases/genetics/metabolism ; }, abstract = {The mammalian microbiome encodes numerous secondary metabolite biosynthetic gene clusters; yet, their role in microbe-microbe interactions is unclear. Here, we characterized two polyketide synthase gene clusters (fun and pks) in the gut symbiont Limosilactobacillus reuteri. The pks, but not the fun, cluster encodes antimicrobial activity. Forty-one of 51 L. reuteri strains tested are sensitive to Pks products; this finding was independent of strains' host origin. Sensitivity to Pks was also established in intraspecies competition experiments in gnotobiotic mice. Comparative genome analyses between Pks-resistant and -sensitive strains identified an acyltransferase gene (act) unique to Pks-resistant strains. Subsequent cell-wall analysis of wild-type and act mutant strains showed that Act acetylates cell-wall components, providing resistance to Pks-mediated killing. Additionally, pks mutants lost their competitive advantage, while act mutants lost their Pks resistance in in vivo competition assays. These findings provide insight into how closely related gut symbionts can compete and co-exist in the gastrointestinal tract.}, }
@article {pmid35442877, year = {2022}, author = {Khanal, M and Timilsina, S and Bhatta, BP and Bophela, K and Coutinho, T and Cochran, K and Malla, S}, title = {Pseudomonas uvaldensis sp. nov., a bacterial pathogen causing onion bulb rot.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {72}, number = {4}, pages = {}, doi = {10.1099/ijsem.0.005311}, pmid = {35442877}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; *Genes, Bacterial ; *Onions/microbiology ; Phylogeny ; Pseudomonas ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {A Gram-stain-negative, aerobic and non-spore-forming bacterial strain, designated 20TX0172[T], was isolated from a rotting onion bulb in Texas, USA. The results of phylogenetic analysis based on the 16S rRNA sequence indicated that the novel strain represented a member of the genus Pseudomonas and had the greatest sequence similarities with Pseudomonas kilonensis 520-20[T] (99.3 %), Pseudomonas corrugata CFBP 2431[T] (99.2 %), and Pseudomonas viciae 11K1[T] (99.2 %) but the 16S rRNA phylogenetic tree displayed a monophyletic clade with Pseudomonas mediterranea CFBP 5447[T]. In the phylogenetic trees based on sequences of four housekeeping genes (gap1, gltA, gyrB and rpoD), the novel strain formed a separate branch, indicating that the strain was distinct phylogenetically from known species of the genus Pseudomonas. The genome-sequence-derived average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the novel isolate and P. mediterranea DSM 16733[T] were 86.7 and 32.7 %, respectively. These values were below the accepted species cutoff threshold of 96 % ANI and 70 % dDDH, affirming that the strain represented a novel species. The genome size of the novel species was 5.98 Mbp with a DNA G+C content of 60.8 mol%. On the basis of phenotypic and genotypic characteristics, strain 20TX0172[T] represents a novel species of the genus Pseudomonas. The name Pseudomonas uvaldensis sp. nov. is proposed. The type strain is 20TX0172[T] (=NCIMB 15426[T]=CIP 112022[T]).}, }
@article {pmid35439561, year = {2022}, author = {Fernando Herrera Adarme, O and Eduardo Lobo Baêta, B and Cardoso Torres, M and Camilo Otalora Tapiero, F and Vinicius Alves Gurgel, L and de Queiroz Silva, S and Francisco de Aquino, S}, title = {Biogas production by anaerobic co-digestion of sugarcane biorefinery byproducts: Comparative analyses of performance and microbial community in novel single-and two-stage systems.}, journal = {Bioresource technology}, volume = {354}, number = {}, pages = {127185}, doi = {10.1016/j.biortech.2022.127185}, pmid = {35439561}, issn = {1873-2976}, mesh = {Anaerobiosis ; Biofuels ; Bioreactors ; Cellulose ; Digestion ; Edible Grain ; Methane ; *Microbiota ; *Saccharum ; Sewage/chemistry ; }, abstract = {Anaerobic co-digestion (AcD) of sugarcane biorefinery byproducts (hemicelluloses hydrolysate (HH), vinasse, yeast extract and sugarcane bagasse fly ashes was evaluated using new anaerobic reactors fed with organic loading rates (OLR) from 0.9 to 10.8 gCODL[-1]d[-1]. The best results were obtained in a two-stage system when the OLR was 5.65 gCODL[-1]d[-1], leading to a total chemical oxygen demand (COD) removal of 87.6 % and methane yield of 243NmLCH4gCODr[-1]. Microbial community analyses of sludge from both systems (one and two-stages) revealed structural changes and relationship among the main genus found (Clostridium (62.8%), Bacteroides(11.3 %), Desulfovibrio (19.1 %), Lactobacillus(67.7 %), Lactococcus (22.5%), Longilinea (78%), Methanosaeta (19.2 %) and Syntrophus (18.9 %)) with processes performance, kinetic and hydrodynamic parameters. Moreover, biomass granulation was observed in the novel structured anaerobic reactor operated at single stage due to sugarcane bagasse fly ash addition.}, }
@article {pmid35438534, year = {2022}, author = {Tiedje, JM and Bruns, MA and Casadevall, A and Criddle, CS and Eloe-Fadrosh, E and Karl, DM and Nguyen, NK and Zhou, J}, title = {Microbes and Climate Change: a Research Prospectus for the Future.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0080022}, pmid = {35438534}, issn = {2150-7511}, mesh = {Animals ; Carbon Dioxide ; *Climate Change ; Ecosystem ; *Greenhouse Gases ; Methane ; Nitrous Oxide ; }, abstract = {Climate change is the most serious challenge facing humanity. Microbes produce and consume three major greenhouse gases-carbon dioxide, methane, and nitrous oxide-and some microbes cause human, animal, and plant diseases that can be exacerbated by climate change. Hence, microbial research is needed to help ameliorate the warming trajectory and cascading effects resulting from heat, drought, and severe storms. We present a brief summary of what is known about microbial responses to climate change in three major ecosystems: terrestrial, ocean, and urban. We also offer suggestions for new research directions to reduce microbial greenhouse gases and mitigate the pathogenic impacts of microbes. These include performing more controlled studies on the climate impact on microbial processes, system interdependencies, and responses to human interventions, using microbes and their carbon and nitrogen transformations for useful stable products, improving microbial process data for climate models, and taking the One Health approach to study microbes and climate change.}, }
@article {pmid35437690, year = {2023}, author = {Li, H and Li, Z and Tang, Q and Li, R and Lu, L}, title = {Local-Scale Damming Impact on the Planktonic Bacterial and Eukaryotic Assemblages in the upper Yangtze River.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1323-1337}, pmid = {35437690}, issn = {1432-184X}, support = {51861125204//National Natural Science Foundation of China/ ; 52039006//National Natural Science Foundation of China/ ; cstc2020jscx-msxmX0121//Chongqing Science and Technology Commission/ ; cstc2020jcyj-jqX0010//Chongqing Science and Technology Commission/ ; }, mesh = {*Ecosystem ; *Eukaryota ; Plankton ; Rivers/microbiology ; Bacteria/genetics ; }, abstract = {Dam construction and impoundment cause discontinuities in the natural biophysical gradients in rivers. These discontinuities may alter distinctive habitats and different microbial community assembly mechanisms upstream and downstream of dams, which reflect the potential impacts of damming on riverine aquatic ecosystems. In this study, we investigated the planktonic microbial assemblages of three large dams in the upper Yangtze River by using high-throughput sequencing. The results revealed that the alpha diversity indexes increased downstream of the dams. In addition, more eukaryotic ASVs solely occurred downstream of the dams, which indicated that a large proportion of eukaryotes appeared downstream of the dams. The nonmetric multidimensional scaling analysis indicated that there was no obvious geographic clustering of the planktonic microbial assemblages among the different locations or among the different dams. However, the dam barriers changed dam-related variables (maximum dam height and water level) and local environmental variables (water temperature, DOC, etc.) that could possibly affect the assembly of the planktonic microbial communities that are closest to the dams. A co-occurrence network analysis demonstrated that the keystone taxa of the planktonic bacteria and eukaryotes decreased downstream of the dams. In particular, the keystone taxa of the eukaryotes disappeared downstream of the dams. The robustness analysis indicated that the natural connectivity of the microbial networks decreased more rapidly upstream of the dams, and the downstream eukaryotic network was more stable. In conclusion, damming has a greater impact on planktonic eukaryotes than on bacteria in near-dam areas, and planktonic microbial assemblages were more susceptible to the environmental changes. Our study provides a better understanding of the ecological effects of river damming.}, }
@article {pmid35433514, year = {2022}, author = {Franklin, S and Aitken, SL and Shi, Y and Sahasrabhojane, PV and Robinson, S and Peterson, CB and Daver, N and Ajami, NA and Kontoyiannis, DP and Shelburne, SA and Galloway-Peña, J}, title = {Oral and Stool Microbiome Coalescence and Its Association With Antibiotic Exposure in Acute Leukemia Patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {848580}, pmid = {35433514}, issn = {2235-2988}, support = {K01 AI143881/AI/NIAID NIH HHS/United States ; P30 CA016672/CA/NCI NIH HHS/United States ; T32 CA096520/CA/NCI NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Leukemia, Myeloid, Acute/complications/drug therapy ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Failure to maintain segregation of oral and gut microbial communities has been linked to several diseases. We sought to characterize oral-fecal microbiome community coalescence, ectopic extension of oral bacteria, clinical variables contributing to this phenomenon, and associated infectious consequences by analyzing the 16S rRNA V4 sequences of longitudinal fecal (n=551) and oral (n=737) samples from 97 patients with acute myeloid leukemia (AML) receiving induction chemotherapy (IC). Clustering observed in permutation based multivariate analysis of variance (PERMANOVA) of Bray-Curtis dissimilarity and PCoA plot of UniFrac distances between intra-patient longitudinal oral-stool sample pairs suggested potential oral-stool microbial community coalescence. Bray-Curtis dissimilarities and UniFrac distances were used to create an objective definition of microbial community coalescence. We determined that only 23 of the 92 patients exhibited oral-stool community coalescence. This was validated through a linear mixed model which determined that patients who experienced coalescence had an increased proportion of shared to unique OTUs between their oral-stool sample pairs over time compared to non-coalesced patients. Evaluation of longitudinal microbial characteristics revealed that patients who experienced coalescence had increased stool abundance of Streptococcus and Stenotrophomonas compared to non-coalesced patients. When treated as a time-varying covariate, each additional day of linezolid (HR 1.15, 95% CI 1.06 - 1.24, P <0.001), meropenem (HR 1.13, 95% CI 1.05 - 1.21, P = 0.001), metronidazole (HR 1.13, 95% CI 1.05 - 1.21, P = 0.001), and cefepime (HR 1.10, 95% CI 1.01 - 1.18, P = 0.021) increased the hazard of oral-stool microbial community coalescence. Levofloxacin receipt was associated with a lower risk of microbiome community coalescence (HR 0.75, 95% CI 0.61 - 0.93, P = 0.009). By the time of neutrophil recovery, the relative abundance of Bacteroidia (P<0.001), Fusobacteria (P=0.012), and Clostridia (P=0.013) in the stool were significantly lower in patients with oral-gut community coalescence. Exhibiting oral-stool community coalescence was associated with the occurrence of infections prior to neutrophil recovery (P=0.002), as well as infections during the 90 days post neutrophil recovery (P=0.027). This work elucidates specific antimicrobial effects on microbial ecology and furthers the understanding of oral/intestinal microbial biogeography and its implications for adverse clinical outcomes.}, }
@article {pmid35432228, year = {2022}, author = {Cerbin, S and Pérez, G and Rybak, M and Wejnerowski, &#x141; and Konowalczyk, A and Helmsing, N and Naus-Wiezer, S and Meima-Franke, M and Pytlak, &#x141; and Raaijmakers, C and Nowak, W and Bodelier, PLE}, title = {Methane-Derived Carbon as a Driver for Cyanobacterial Growth.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {837198}, pmid = {35432228}, issn = {1664-302X}, abstract = {Methane, a potent greenhouse gas produced in freshwater ecosystems, can be used by methane-oxidizing bacteria (MOB) and can therefore subsidize the pelagic food web with energy and carbon. Consortia of MOB and photoautotrophs have been described in aquatic ecosystems and MOB can benefit from photoautotrophs which produce oxygen, thereby enhancing CH4 oxidation. Methane oxidation can account for accumulation of inorganic carbon (i.e., CO2) and the release of exometabolites that may both be important factors influencing the structure of phytoplankton communities. The consortium of MOB and phototroph has been mainly studied for methane-removing biotechnologies, but there is still little information on the role of these interactions in freshwater ecosystems especially in the context of cyanobacterial growth and bloom development. We hypothesized that MOB could be an alternative C source to support cyanobacterial growth in freshwater systems. We detected low δ[13]C values in cyanobacterial blooms (the lowest detected value -59.97‰ for Planktothrix rubescens) what could be the result of the use of methane-derived carbon by cyanobacteria and/or MOB attached to their cells. We further proved the presence of metabolically active MOB on cyanobacterial filaments using the fluorescein isothiocyanate (FITC) based activity assay. The PCR results also proved the presence of the pmoA gene in several non-axenic cultures of cyanobacteria. Finally, experiments comprising the co-culture of the cyanobacterium Aphanizomenon gracile with the methanotroph Methylosinus sporium proved that cyanobacterial growth was significantly improved in the presence of MOB, presumably through utilizing CO2 released by MOB. On the other hand, [13]C-CH4 labeled incubations showed the uptake and assimilation of MOB-derived metabolites by the cyanobacterium. We also observed a higher growth of MOB in the presence of cyanobacteria under a higher irradiance regime, then when grown alone, underpinning the bidirectional influence with as of yet unknown environmental consequences.}, }
@article {pmid35428940, year = {2022}, author = {Ganorkar, R and Jadeja, NB and Shanware, A and Ingle, AB}, title = {Characterisation of novel microbial strains Proteus mirabilis and Bordetella avium for heavy metal bioremediation and dye degradation.}, journal = {Archives of microbiology}, volume = {204}, number = {5}, pages = {262}, pmid = {35428940}, issn = {1432-072X}, mesh = {Azo Compounds ; Biodegradation, Environmental ; *Bordetella avium ; *Metals, Heavy/analysis ; Phylogeny ; Proteus mirabilis/genetics ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; Tungsten ; }, abstract = {The entitled study focuses on exploring the microbial diversity and its applicability in the remediation of metal contaminated soil using microbes, which is a reliable and cost effective technique. Tungsten enriched soil of Kuhi-Agargaon-Khobna region (Nagpur, India) were analysed by XRF method to detect heavy metals. The traditional microbiological techniques were used to isolate tungsten tolerant microbes. Applicability of these microbes in bioremediation and Azo dye degradation was mainly studied. The two novel bacterial strains, Proteus mirabilis (RS2K) and Bordetella avium (RS3K), were isolated and identified to show the tolerance to tungsten, using 16S rDNA and phylogenetic analysis. These novel strains have also shown the tolerance to other metallic salts viz., (sodium) tungsten, tungstic acid, ammonium metaparatungstate, mercuric chloride, cobalt chloride and azo dye. These microbes were found to accumulate tungsten intracellularly as confirmed through ICP-MS and SEM-EDS analyses. Microbes exhibited well-equipped cellular mechanisms for metal tolerance to survive in heavy metal-laden ecology. Current study contains substantial potential in bioleaching of heavy metals and green mining along with Nano bioremediation for heavy metal pollution.}, }
@article {pmid35427643, year = {2022}, author = {Steinbauer, P and Monje, FJ and Kothgassner, O and Goreis, A and Eva, C and Wildner, B and Schned, H and Deindl, P and Seki, D and Berger, A and Olischar, M and Giordano, V}, title = {The consequences of neonatal pain, stress and opiate administration in animal models: An extensive meta-analysis concerning neuronal cell death, motor and behavioral outcomes.}, journal = {Neuroscience and biobehavioral reviews}, volume = {137}, number = {}, pages = {104661}, doi = {10.1016/j.neubiorev.2022.104661}, pmid = {35427643}, issn = {1873-7528}, mesh = {*Analgesics, Opioid/administration &amp; dosage ; Animals ; Animals, Newborn ; Anxiety ; *Cell Death ; Depression ; Movement ; *Neurons/cytology ; *Pain ; }, abstract = {This systematic review and meta-analysis aimed to investigate the association of neonatal exposure to pain, stress, opiate administration alone, as well as opiate administration prior to a painful procedure on neuronal cell death, motor, and behavioral outcomes in rodents. In total, 36 studies investigating the effect of pain (n = 18), stress (n = 15), opiate administration (n = 13), as well as opiate administration prior to a painful event (n = 7) in rodents were included in our meta-analysis. The results showed a large effect of pain (g = 1.37, 95% CI 1.00-1.74, p < .001) on neuronal cell death. Moreover, higher number of neonatal pain events were significantly associated with increased neuronal cell death, increased anxiety (b = -1.18, SE = 0.43, p = .006), and depressant-like behavior (b = 1.74, SE = 0.51, p = .027) in rodents. Both opiates and pain had no impact on motor function (g = 0.26, 95% CI 0.18-0.70, p = .248).}, }
@article {pmid35426077, year = {2023}, author = {Oliveira, NC and Rodrigues, PAP and Cônsoli, FL}, title = {Host-Adapted Strains of Spodoptera frugiperda Hold and Share a Core Microbial Community Across the Western Hemisphere.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1552-1563}, pmid = {35426077}, issn = {1432-184X}, support = {2011/50877-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/24377-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 462140-2014/8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 403851/2013-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Animals ; Spodoptera ; *Zea mays ; Larva ; *Gastrointestinal Microbiome ; Colombia ; }, abstract = {The fall armyworm Spodoptera frugiperda is an important polyphagous agricultural pest in the Western Hemisphere and currently invasive to countries of the Eastern Hemisphere. This species has two host-adapted strains named "rice" and "corn" strains. Our goal was to identify the occurrence of core members in the gut bacterial community of fall armyworm larvae from distinct geographical distribution and/or host strain. We used next-generation sequencing to identify the microbial communities of S. frugiperda from corn fields in Brazil, Colombia, Mexico, Panama, Paraguay, and Peru, and rice fields from Panama. The larval gut microbiota of S. frugiperda larvae did not differ between the host strains nor was it affected by the geographical distribution of the populations investigated. Our findings provide additional support for Enterococcus and Pseudomonas as core members of the bacterial community associated with the larval gut of S. frugiperda, regardless of the site of collection or strain. Further investigations are required for a deeper understanding of the nature of this relationship.}, }
@article {pmid35420423, year = {2022}, author = {Li, Q and Van Herreweghen, F and Onyango, SO and De Mey, M and Van de Wiele, T}, title = {In Vitro Microbial Metabolism of (+)-Catechin Reveals Fast and Slow Converters with Individual-Specific Microbial and Metabolite Markers.}, journal = {Journal of agricultural and food chemistry}, volume = {70}, number = {34}, pages = {10405-10416}, doi = {10.1021/acs.jafc.2c00551}, pmid = {35420423}, issn = {1520-5118}, mesh = {*Catechin/metabolism ; Fatty Acids, Volatile ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; }, abstract = {The bioavailability of catechin highly relies on gut microbiota which may determine its metabolic profile, resulting in different health outcomes. Here, we investigated in vitro (+)-catechin metabolism by human microbial communities. There were substantial interindividual differences in the metabolic profiles of (+)-catechin, with 5-(3',4'-dihydroxyphenyl)-γ-valerolactone being the major contributor. Furthermore, the microbial metabolic rate of catechin enabled stratification of 12 participants (fast, medium, and slow converters), despite the interference from the strong intrinsic interindividual variability in fecal microbiota. Correlations were established between this stratified population and microbiota features, such as ecosystem diversity. Additionally, fast converters had significantly higher prevalences of amplicon sequence variants (ASVs) with potential capacity of C-ring cleavage (ASV233_Eggerthella and ASV402_Eubacterium), B-ring dihydroxylation (ASV402_Eubacterium), and short-chain fatty acid (SCFA)-producing ASVs. In conclusion, metabolic-capability-based stratification allows us to uncover differences in microbial composition between fast and slow converters, which could help to elucidate interindividual variabilities in the health benefits of catechins.}, }
@article {pmid35420314, year = {2023}, author = {Fan, X and Chen, H and Yan, G and Ye, M and Yin, C and Li, T and Wakelin, SA and Liang, Y}, title = {Niche Differentiation Among Canonical Nitrifiers and N2O Reducers Is Linked to Varying Effects of Nitrification Inhibitors DCD and DMPP in Two Arable Soils.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1434-1447}, pmid = {35420314}, issn = {1432-184X}, support = {2017YFD0200707//National Key Research and Development Programs of China/ ; 42007083//National Natural Science Foundation of China/ ; 2020M671736//China Postdoctoral Science Foundation/ ; }, mesh = {*Soil/chemistry ; Nitrification ; Dimethylphenylpiperazinium Iodide/pharmacology ; Phosphates ; Ammonia ; Soil Microbiology ; Archaea ; Bacteria ; *Betaproteobacteria ; Oxidation-Reduction ; }, abstract = {The efficacy of nitrification inhibitors (NIs) dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP) varies with soil types. Understanding the microbial mechanisms for this variation may lead to better modelling of NI efficacy and therefore on-farm adoption. This study addressed the response patterns of mineral nitrogen, nitrous oxide (N2O) emission, abundances of N-cycling functional guilds and soil microbiota characteristics, in relation to urea application with or without DCD or DMPP in two arable soils (an alkaline and an acid soil). The inhibition of nitrification rate and N2O emission by NI application occurred by suppressing ammonia-oxidizing bacteria (AOB) abundances and increasing the abundances of nosZI-N2O reducers; however, abundances of ammonia-oxidizing archaea (AOA) were also stimulated with NIs-added in these two arable soils. DMPP generally had stronger inhibition efficiency than DCD, and both NIs' addition decreased Nitrobacter, while increased Nitrospira abundance only in alkaline soil. N2O emissions were positively correlated with AOB and negatively correlated with nosZI in both soils and AOA only in acid soil. Moreover, N2O emissions were also positively correlated with nirK-type denitrifiers in alkaline soil, and clade A comammox in acid soil. Amendment with DCD or DMPP altered soil microbiota community structure, but had minor effect on community composition. These results highlight a crucial role of the niche differentiation among canonical ammonia oxidizers (AOA/AOB), Nitrobacter and Nitrospira, as well as nosZI- and nosZII-N2O reducers in determining the varying efficacies of DCD and DMPP in different arable soils.}, }
@article {pmid35419656, year = {2023}, author = {Xu, F and Zhu, L and Wang, J and Xue, Y and Liu, K and Zhang, F and Zhang, T}, title = {Nonpoint Source Pollution (NPSP) Induces Structural and Functional Variation in the Fungal Community of Sediments in the Jialing River, China.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1308-1322}, pmid = {35419656}, issn = {1432-184X}, support = {19E061//Science Research Program of China West Normal University/ ; CJZDZYJ47//Environmental Protection Research Program of the Yangtze River/ ; 41907132//National Science Foundation of China/ ; }, mesh = {Humans ; Rivers/microbiology ; *Mycobiome ; *Non-Point Source Pollution ; Ecosystem ; Geologic Sediments/microbiology ; China ; *Basidiomycota/genetics ; *Ascomycota/genetics ; }, abstract = {Nonpoint source pollution (NPSP) from human production and life activities causes severe destruction in river basin environments. In this study, three types of sediment samples (A, NPSP tributary samples; B, non-NPSP mainstream samples; C, NPSP mainstream samples) were collected at the estuary of the NPSP tributaries of the Jialing River. High-throughput sequencing of the fungal-specific internal transcribed spacer (ITS) gene region was used to identify fungal taxa. The impact of NPSP on the aquatic environment of the Jialing River was revealed by analysing the community structure, community diversity, and functions of sediment fungi. The results showed that the dominant phylum of sediment fungi was Rozellomycota, followed by Ascomycota and Basidiomycota (relative abundance > 5%). NPSP caused a significant increase in the relative abundances of Exosporium, Phialosimplex, Candida, Inocybe, Tausonia, and Slooffia, and caused a significant decrease in the relative abundances of Cercospora, Cladosporium, Dokmaia, Setophaeosphaeria, Paraphoma, Neosetophoma, Periconia, Plectosphaerella, Claviceps, Botrytis, and Papiliotrema. These fungal communities therefore have a certain indicator role. In addition, NPSP caused significant changes in the physicochemical properties of Jialing River sediments, such as pH and available nitrogen (AN), which significantly increased the species richness of fungi and caused significant changes in the fungal community β-diversity (P < 0.05). pH, total phosphorus (TP), and AN were the main environmental factors affecting fungal communities in sediments of Jialing River. The functions of sediment fungi mainly involved three types of nutrient metabolism (symbiotrophic, pathotrophic, and saprotrophic) and 75 metabolic circulation pathways. NPSP significantly improved the pentose phosphate pathway, pentose phosphate pathway, and fatty acid beta-oxidation V metabolic circulation pathway functions (P < 0.05) and inhibited the chitin degradation to ethanol, super pathway of heme biosynthesis from glycine, and adenine and adenosine salvage III metabolic circulation pathway functions (P < 0.05). Hence, NPSP causes changes in the community structure and functions of sediment fungi in Jialing River and has adversely affected for the stability of the Jialing River Basin ecosystem.}, }
@article {pmid35416682, year = {2022}, author = {Wu, J and Jiang, X and Yang, Q and Zhang, Y and Wang, C and Huang, R}, title = {Inhibition of Streptococcus mutans Biofilm Formation by the Joint Action of Oxyresveratrol and Lactobacillus casei.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {9}, pages = {e0243621}, pmid = {35416682}, issn = {1098-5336}, mesh = {Biofilms ; *Dental Caries ; *Dental Plaque ; Glucans ; Humans ; *Lacticaseibacillus casei ; Plant Extracts ; Polyphenols/pharmacology ; Stilbenes ; Streptococcus mutans/genetics ; Water/pharmacology ; }, abstract = {Microbial dysbiosis in dental plaque contributes to the occurrence of dental caries, to which Streptococcus mutans is a major contributor. Lactobacillus casei can be used as probiotic therapy to treat caries by replacing S. mutans within the dental plaque. However, the effects of probiotic treatment are not always stable. Oxyresveratrol (ORV), a plant-derived polyphenol, displays opposite effects in that it inhibits cariogenic and promotes commensal bacteria. Thus, the objectives of this study are to investigate the effects of ORV on bacterial proportions in S. mutans-L. casei biofilm and to elucidate how ORV weakens the competitiveness of S. mutans. Quantitative real-time PCR confirms a decreased S. mutans-L. casei ratio in dual-species biofilm by action of ORV. The culture supernatant of L. casei after being incubated with ORV (ORVLC) is prepared to explore the joint action of ORV and L. casei. ORVLC displays the strongest anti-biofilm effect against S. mutans when compared with the effects of L. casei supernatant or ORV alone. As a result of this treatment, both exopolysaccharides and bacteria contents in the biofilm are greatly reduced. The biofilm is transformed from water-insoluble glucan-dominant to water-soluble glucan-dominant by ORVLC through the modulation of the glycometabolism-related genes of S. mutans. As for the interactions between ORV and L. casei, ORV promotes L. casei to produce acetic acid, which provides L. casei with a competitive advantage against S. mutans. Taken together, ORV may be very suitable as an adjuvant medicine for probiotic therapy in the control of dental caries. IMPORTANCE The homeostatic imbalance in dental plaque associated with a sharp increase in the number of cariogenic bacteria such as Streptococcus mutans is critical for the occurrence and development of caries. Probiotic therapy can restore ecological balance by replacing cariogenic pathogens with probiotics. The current study innovatively finds that oxyresveratrol, a natural polyphenol, can provide probiotic Lactobacillus casei with competitive dominance in its dual-species biofilm with S. mutans. The joint action of oxyresveratrol and L. casei strongly inhibits the biofilm formation of S. mutans. Additionally, oxyresveratrol promotes L. casei to produce acetic acid, which facilitates L. casei to compete with S. mutans. Through the effects of these two mechanisms, oxyresveratrol leads to a significantly decreased S. mutans-L. casei ratio in their dual-species biofilm. Thus, oxyresveratrol is speculated to be an ideal medicine for the prevention and treatment of caries by regulating oral flora balance.}, }
@article {pmid35415771, year = {2023}, author = {Graça, D and Fernandes, I and Cássio, F and Pascoal, C}, title = {Eco-physiological Responses of Aquatic Fungi to Three Global Change Stressors Highlight the Importance of Intraspecific Trait Variability.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1215-1225}, pmid = {35415771}, issn = {1432-184X}, support = {PTDC/CTA-AMB/31245/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/140761/2018//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04050/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {Phylogeny ; *Mitosporic Fungi/physiology ; Rivers/microbiology ; Fresh Water ; Phenotype ; Plant Leaves/microbiology ; Fungi/genetics ; Ecosystem ; }, abstract = {Anthropogenic change at a global scale is affecting life on Earth with impacts on freshwaters. Aquatic hyphomycetes are fungi that drive organic matter decomposition in freshwaters and mediate energy transfer to higher trophic levels. Intraspecific trait variability affects ecological processes and can account for species adaptations to environmental change. To ascertain how aquatic hyphomycetes respond to global change related stressors, we selected 20 strains (7 species), based on their co-occurrence in streams and phylogenetic relatedness. We measured fungal growth rates at different temperatures (7 levels), nutrient concentrations (6 levels) and medium moisture (6 levels). Our results indicate that all stressors affected fungal growth, and responses to nutrient enrichment and moisture were strain specific. Fungal responses to the stressors were not explained by their phylogenetic relatedness. In the absence of stressors, interspecific diversity best explained the variance in fungal traits, while the increase in the stress gradient increased the importance of intraspecific diversity.}, }
@article {pmid35414897, year = {2022}, author = {Suleiman, M and Pennekamp, F and Choffat, Y and Petchey, OL}, title = {Contrasting resistance and resilience to light variation of the coupled oxic and anoxic components of an experimental microbial ecosystem.}, journal = {Ecology and evolution}, volume = {12}, number = {4}, pages = {e8793}, pmid = {35414897}, issn = {2045-7758}, abstract = {Understanding how microbial communities of aquatic ecosystems respond to environmental change remains a critical challenge in microbial ecology. In this study, we used light-dependent oxic-anoxic micro-ecosystems to understand how the functioning and diversity of aerobic and anaerobic lake analog communities are affected by a pulse light deprivation. Continuous measurements of oxygen concentration were made and a time series of full-length 16S rRNA sequencing was used to quantify changes in alpha- and beta diversity. In the upper oxic layer, oxygen concentration decreased significantly under light reduction, but showed resilience in daily mean, minimum, and maximum after light conditions were restored to control level. Only the amplitude of diurnal fluctuations in oxygen concentrations did not recover fully, and instead tended to remain lower in treated ecosystems. Alpha diversity of the upper oxic layer communities showed a delayed increase after light conditions were restored, and was not resilient in the longer term. In contrast, alpha diversity of the anoxic lower layer communities increased during the light reduction, but was resilient in the longer term. Community composition changed significantly during light reduction, and showed resilience in the oxic layer and lack of resilience in the anoxic layer. Alpha diversity and the amplitude of daily oxygen fluctuations within and among treatments were strongly correlated, suggesting that higher diversity could lead to less variable oxygen concentrations, or vice versa. Our experiment showed that light deprivation induces multifaceted responses of community function (oxygen respiration) and structure, hence focusing on a single stability component could potentially be misleading.}, }
@article {pmid35412096, year = {2022}, author = {Passarini, MRZ and Ottoni, JR and Costa, PEDS and Hissa, DC and Falcão, RM and Melo, VMM and Balbino, VQ and Mendonça, LAR and Lima, MGS and Coutinho, HDM and Verde, LCL}, title = {Fungal community diversity of heavy metal contaminated soils revealed by metagenomics.}, journal = {Archives of microbiology}, volume = {204}, number = {5}, pages = {255}, pmid = {35412096}, issn = {1432-072X}, support = {DCR-0024-01438.01.00/12//funcap/ ; }, mesh = {Biodegradation, Environmental ; Metagenomics ; *Metals, Heavy/metabolism ; *Mycobiome ; Soil ; Soil Microbiology ; *Soil Pollutants/metabolism ; }, abstract = {The inappropriate disposal of toxic compounds generated by industrial activity has been impacting the environment considerably. Microbial communities inhabiting contaminated sites may represent interesting ecological alternatives for the decontamination of environments. The present work aimed to investigate the fungal diversity and its functionality contained in stream sediments with industrial waste contaminated with heavy metals by using metagenomic approach. A total of 12 fungal orders were retrieved from datasets and, at phylum level, Ascomycota was the most abundant, followed by Basidiomycota, Chytridiomycota and Blastocladiomycota. Higher abundance of sequences was encountered within the less contaminated site, while the lower abundance was found in the sample with the higher contamination with lead. Gene sequences related to DNA repair and heavy metals biosorption processes were found in the four samples analyzed. The genera Aspergillus and Chaetomium, and Saccharomycetales order were highly present within all samples, showing their potential to be used for bioremediation studies. The present work demonstrated the importance of using the metagenomic approach to understand the dynamics and the possible metabolic pathways associated with fungal communities related to environmental samples containing heavy metals, as well as evidenced the importance of improving culturomics techniques for isolating strains with potential application in bioremediation processes of environments contaminated with heavy metals.}, }
@article {pmid35411306, year = {2022}, author = {Bibbal, D and Ruiz, P and Sapountzis, P and Mazuy-Cruchaudet, C and Loukiadis, E and Auvray, F and Forano, E and Brugère, H}, title = {Persistent Circulation of Enterohemorrhagic Escherichia coli (EHEC) O157:H7 in Cattle Farms: Characterization of Enterohemorrhagic Escherichia coli O157:H7 Strains and Fecal Microbial Communities of Bovine Shedders and Non-shedders.}, journal = {Frontiers in veterinary science}, volume = {9}, number = {}, pages = {852475}, pmid = {35411306}, issn = {2297-1769}, abstract = {Cattle are carriers, without clinical manifestations, of enterohemorrhagic Escherichia coli (EHEC) O157:H7 responsible for life-threatening infections in humans. A better identification of factors playing a role in maintaining persistence of such strains in cattle is required to develop more effective control measures. Hence, we conducted a study to identify farms with a persistent circulation of EHEC O157:H7. The EHEC O157:H7 herd status of 13 farms, which had previously provided bovine EHEC O157:H7 carriers at slaughter was investigated. Two farms were still housing positive young bulls, and this was true over a 1-year period. Only one fecal sample could be considered from a supershedder, and 60% of the carriers shed concentrations below 10 MPN/g. Moreover, EHEC O157:H7 represented minor subpopulations of E. coli. PFGE analysis of the EHEC O157:H7 strains showed that persistent circulation was due either to the persistence of a few predominant strains or to the repeated exposure of cattle to various strains. Finally, we compared fecal microbial communities of shedders (S) (n = 24) and non-shedders (NS) (n = 28), including 43 young bulls and nine cows, from one farm. Regarding alpha diversity, no significant difference between S vs. NS young bulls (n = 43) was observed. At the genus level, we identified 10 amplicon sequence variant (ASV) indicators of the S or NS groups. The bacterial indicators of S belonged to the family XIII UCG-001, Slackia, and Campylobacter genera, and Ruminococcaceae NK4A21A, Lachnospiraceae-UGC-010, and Lachnospiraceae-GCA-900066575 groups. The NS group indicator ASVs were affiliated to Pirellulaceae-1088-a5 gut group, Anaerovibrio, Victivallis, and Sellimonas genera. In conclusion, the characteristics enhancing the persistence of some predominant strains observed here should be explored further, and studies focused on mechanisms of competition among E. coli strains are also needed.}, }
@article {pmid35406804, year = {2022}, author = {Chidambaram, SB and Rathipriya, AG and Mahalakshmi, AM and Sharma, S and Hediyal, TA and Ray, B and Sunanda, T and Rungratanawanich, W and Kashyap, RS and Qoronfleh, MW and Essa, MM and Song, BJ and Monaghan, TM}, title = {The Influence of Gut Dysbiosis in the Pathogenesis and Management of Ischemic Stroke.}, journal = {Cells}, volume = {11}, number = {7}, pages = {}, pmid = {35406804}, issn = {2073-4409}, mesh = {Dysbiosis/complications ; Fatty Acids, Volatile ; *Gastrointestinal Microbiome/physiology ; Humans ; *Ischemic Stroke ; *Stroke/etiology/therapy ; }, abstract = {Recent research on the gut microbiome has revealed the influence of gut microbiota (GM) on ischemic stroke pathogenesis and treatment outcomes. Alterations in the diversity, abundance, and functions of the gut microbiome, termed gut dysbiosis, results in dysregulated gut-brain signaling, which induces intestinal barrier changes, endotoxemia, systemic inflammation, and infection, affecting post-stroke outcomes. Gut-brain interactions are bidirectional, and the signals from the gut to the brain are mediated by microbially derived metabolites, such as trimethylamine N-oxide (TMAO) and short-chain fatty acids (SCFAs); bacterial components, such as lipopolysaccharide (LPS); immune cells, such as T helper cells; and bacterial translocation via hormonal, immune, and neural pathways. Ischemic stroke affects gut microbial composition via neural and hypothalamic-pituitary-adrenal (HPA) pathways, which can contribute to post-stroke outcomes. Experimental and clinical studies have demonstrated that the restoration of the gut microbiome usually improves stroke treatment outcomes by regulating metabolic, immune, and inflammatory responses via the gut-brain axis (GBA). Therefore, restoring healthy microbial ecology in the gut may be a key therapeutic target for the effective management and treatment of ischemic stroke.}, }
@article {pmid35404785, year = {2022}, author = {Ho, PY and Good, BH and Huang, KC}, title = {Competition for fluctuating resources reproduces statistics of species abundance over time across wide-ranging microbiotas.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35404785}, issn = {2050-084X}, support = {F32 GM143859/GM/NIGMS NIH HHS/United States ; RM1 GM135102/GM/NIGMS NIH HHS/United States ; R01 AI147023/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Microbiota ; *Models, Biological ; }, abstract = {Across diverse microbiotas, species abundances vary in time with distinctive statistical behaviors that appear to generalize across hosts, but the origins and implications of these patterns remain unclear. Here, we show that many of these macroecological patterns can be quantitatively recapitulated by a simple class of consumer-resource models, in which the metabolic capabilities of different species are randomly drawn from a common statistical distribution. Our model parametrizes the consumer-resource properties of a community using only a small number of global parameters, including the total number of resources, typical resource fluctuations over time, and the average overlap in resource-consumption profiles across species. We show that variation in these macroscopic parameters strongly affects the time series statistics generated by the model, and we identify specific sets of global parameters that can recapitulate macroecological patterns across wide-ranging microbiotas, including the human gut, saliva, and vagina, as well as mouse gut and rice, without needing to specify microscopic details of resource consumption. These findings suggest that resource competition may be a dominant driver of community dynamics. Our work unifies numerous time series patterns under a simple model, and provides an accessible framework to infer macroscopic parameters of effective resource competition from longitudinal studies of microbial communities.}, }
@article {pmid35403892, year = {2023}, author = {Marozzi, G and Benucci, GMN and Turchetti, B and Massaccesi, L and Baciarelli Falini, L and Bonito, G and Buzzini, P and Agnelli, A and Donnini, D and Albertini, E}, title = {Correction to: Fungal and Bacterial Diversity in the Tuber magnatum Ecosystem and Microbiome.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {522}, doi = {10.1007/s00248-022-02010-y}, pmid = {35403892}, issn = {1432-184X}, }
@article {pmid35403856, year = {2022}, author = {Yang, S and Li, L and Peng, X and Zhang, R and Song, L}, title = {Eukaryotic community composition and dynamics during solid waste decomposition.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {8}, pages = {3307-3317}, pmid = {35403856}, issn = {1432-0614}, mesh = {Archaea/genetics ; Bioreactors ; Eukaryota ; *Euryarchaeota/genetics ; Methane ; *Refuse Disposal ; Solid Waste/analysis ; Waste Disposal Facilities ; }, abstract = {Consortia of microbial community are involved in organic waste decomposition in municipal solid waste (MSW) landfill via competition, syntropy, and predation. Bacterial and archaeal community structure and function have been extensively studied in this process, whereas the eukaryotic community structure and function are largely unidentified. This gap stands for one of the fundamental researches of microbial ecology, that is, "what is the importance of variation in eukaryotic community structure and function to solid waste decomposition? The main idea of this work is to characterize changes in eukaryotic community composition and the associated driver during solid waste decomposition. Using high throughput sequencing targeting 18S rRNA genes, community composition and dynamics of eukaryotic during solid wasted decomposition were studied, as well as the differences with solid waste and leachate physiochemical parameters. Concomitant to the expected changes in physiochemical factors, eukaryotic community composition and diversity changed along solid waste decomposition indicated by aerobic phase (AP), anaerobic acid phase (ACP), and methanogenic phase (MP) and the structure was shaped by the nutrients (BOD5, total phosphorus, and nitrate) in leachate. Ascomycota, the predominant eukaryote, showed significant (p < 0.05) different structure among AP, ACP, and MP in phylum, genera, and species levels. Abundant Freshwater Opisthokonta was present in MP, suggesting a methane carbon cycling via grazing methane oxidation microorganism. Amoebozoa, Alveolata, Rhizaria, and Stramenopiles showed successional pattern during solid waste decomposition, indicating a short food chain establishment. Characterization on eukaryotic community composition and dynamics during solid waste decomposition are crucial for understanding of microbial consortia ecological function on solid waste decomposition and are also helpful for MSW management.Key points• Abundant Ascomycota significantly differed at AP, ACP, and MP.• Eukaryotic succession indicated a short food chain establishment.• Entire eukaryotic community structure was associated to nutrients in leachate.}, }
@article {pmid35402312, year = {2022}, author = {Nardos, R and Leung, ET and Dahl, EM and Davin, S and Asquith, M and Gregory, WT and Karstens, L}, title = {Network-Based Differences in the Vaginal and Bladder Microbial Communities Between Women With and Without Urgency Urinary Incontinence.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {759156}, pmid = {35402312}, issn = {2235-2988}, support = {K01 DK116706/DK/NIDDK NIH HHS/United States ; T15 LM007088/LM/NLM NIH HHS/United States ; K12 HD043488/HD/NICHD NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Female ; Humans ; Lactobacillus/genetics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Urinary Bladder/microbiology ; *Urinary Incontinence/microbiology ; Vagina/microbiology ; }, abstract = {BACKGROUND: Little is known about the relationship of proximal urogenital microbiomes in the bladder and the vagina and how this contributes to bladder health. In this study, we use a microbial ecology and network framework to understand the dynamics of interactions/co-occurrences of bacteria in the bladder and vagina in women with and without urgency urinary incontinence (UUI).<br><br>METHODS: We collected vaginal swabs and catheterized urine specimens from 20 women with UUI (cases) and 30 women without UUI (controls). We sequenced the V4 region of the bacterial 16S rRNA gene and evaluated using alpha and beta diversity metrics. We used microbial network analysis to detect interactions in the microbiome and the betweenness centrality measure to identify central bacteria in the microbial network. Bacteria exhibiting maximum betweenness centrality are considered central to the microbe-wide networks and likely maintain the overall microbial network structure.<br><br>RESULTS: There were no significant differences in the vaginal or bladder microbiomes between cases and controls using alpha and beta diversity. Silhouette metric analysis identified two distinct microbiome clusters in both the bladder and vagina. One cluster was dominated by Lactobacillus genus while the other was more diverse. Network-based analyses demonstrated that vaginal and bladder microbial networks were different between cases and controls. In the vagina, there were similar numbers of genera and subgroup clusters in each network for cases and controls. However, cases tend to have more unique bacterial co-occurrences. While Bacteroides and Lactobacillus were the central bacteria with the highest betweenness centrality in controls, Aerococcus had the highest centrality in cases and correlated with bacteria commonly associated with bacterial vaginosis. In the bladder, cases have less than half as many network clusters compared to controls. Lactobacillus was the central bacteria in both groups but associated with several known uropathogens in cases. The number of shared bacterial genera between the bladder and the vagina differed between cases and controls, with cases having larger overlap (43%) compared to controls (29%).<br><br>CONCLUSION: Our study shows overlaps in microbial communities of bladder and vagina, with higher overlap in cases. We also identified differences in the bacteria that are central to the overall community structure.}, }
@article {pmid35396623, year = {2023}, author = {Koide, RT}, title = {On Holobionts, Holospecies, and Holoniches: the Role of Microbial Symbioses in Ecology and Evolution.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1143-1149}, pmid = {35396623}, issn = {1432-184X}, mesh = {Phylogeny ; *Symbiosis ; *Adaptation, Physiological ; Eukaryota ; Biological Evolution ; }, abstract = {My goal in writing this is to increase awareness of the roles played by microbial symbionts in eukaryote ecology and evolution. Most eukaryotes host one or more species of symbiotic microorganisms, including prokaryotes and fungi. Many of these have profound impacts on the biology of their hosts. For example, microbial symbionts may expand the niches of their hosts, cause rapid adaptation of the host to the environment and re-adaptation to novel conditions via symbiont swapping, facilitate speciation, and fundamentally alter our concept of the species. In some cases, microbial symbionts and multicellular eukaryote hosts have a mutual dependency, which has obvious conservation implications. Hopefully, this contribution will stimulate a reevaluation of important ecological and evolutionary concepts including niche, adaptation, the species, speciation, and conservation of multicellular eukaryotes.}, }
@article {pmid35395701, year = {2023}, author = {van der Loos, LM and D'hondt, S and Engelen, AH and Pavia, H and Toth, GB and Willems, A and Weinberger, F and De Clerck, O and Steinhagen, S}, title = {Salinity and host drive Ulva-associated bacterial communities across the Atlantic-Baltic Sea gradient.}, journal = {Molecular ecology}, volume = {32}, number = {23}, pages = {6260-6277}, doi = {10.1111/mec.16462}, pmid = {35395701}, issn = {1365-294X}, support = {UIDB/04326/2020//Portugese nation fund from Foundation for Science and Technology/ ; 3F020119//Fonds Wetenschappelijk Onderzoek/ ; 2020-03119//Formas national research program for food/ ; FWO project I001621N//European Marine Biological Resource Centre Belgium/ ; }, mesh = {Humans ; *Ulva/genetics ; Salinity ; Bacteria/genetics ; Baltic States ; Seawater/microbiology ; }, abstract = {The green seaweed Ulva is a model system to study seaweed-bacteria interactions, but the impact of environmental drivers on the dynamics of these interactions is little understood. In this study, we investigated the stability and variability of the seaweed-associated bacteria across the Atlantic-Baltic Sea salinity gradient. We characterized the bacterial communities of 15 Ulva sensu lato species along 2,000 km of coastline in a total of 481 samples. Our results demonstrate that the Ulva-associated bacterial composition was strongly structured by both salinity and host species (together explaining between 34% and 91% of the variation in the abundance of the different bacterial genera). The largest shift in the bacterial consortia coincided with the horohalinicum (5-8 PSU, known as the transition zone from freshwater to marine conditions). Low-salinity communities especially contained high relative abundances of Luteolibacter, Cyanobium, Pirellula, Lacihabitans and an uncultured Spirosomaceae, whereas high-salinity communities were predominantly enriched in Litorimonas, Leucothrix, Sulfurovum, Algibacter and Dokdonia. We identified a small taxonomic core community (consisting of Paracoccus, Sulfitobacter and an uncultured Rhodobacteraceae), which together contributed to 14% of the reads per sample, on average. Additional core taxa followed a gradient model, as more core taxa were shared between neighbouring salinity ranges than between ranges at opposite ends of the Atlantic-Baltic Sea gradient. Our results contradict earlier statements that Ulva-associated bacterial communities are taxonomically highly variable across individuals and largely stochastically defined. Characteristic bacterial communities associated with distinct salinity regions may therefore facilitate the host's adaptation across the environmental gradient.}, }
@article {pmid35394422, year = {2022}, author = {Meyer, BH and Adam, PS and Wagstaff, BA and Kolyfetis, GE and Probst, AJ and Albers, SV and Dorfmueller, HC}, title = {Agl24 is an ancient archaeal homolog of the eukaryotic N-glycan chitobiose synthesis enzymes.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35394422}, issn = {2050-084X}, support = {109357/Z/15/Z//The Wellcome Trust and Royal Society Grant/ ; /WT_/Wellcome Trust/United Kingdom ; 105606/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Archaea/genetics ; Disaccharides ; *Eukaryota ; Phylogeny ; Polysaccharides ; }, abstract = {Protein N-glycosylation is a post-translational modification found in organisms of all domains of life. The crenarchaeal N-glycosylation begins with the synthesis of a lipid-linked chitobiose core structure, identical to that in Eukaryotes, although the enzyme catalyzing this reaction remains unknown. Here, we report the identification of a thermostable archaeal β-1,4-N-acetylglucosaminyltransferase, named archaeal glycosylation enzyme 24 (Agl24), responsible for the synthesis of the N-glycan chitobiose core. Biochemical characterization confirmed its function as an inverting β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol glycosyltransferase. Substitution of a conserved histidine residue, found also in the eukaryotic and bacterial homologs, demonstrated its functional importance for Agl24. Furthermore, bioinformatics and structural modeling revealed similarities of Agl24 to the eukaryotic Alg14/13 and a distant relation to the bacterial MurG, which are catalyzing the same or a similar reaction, respectively. Phylogenetic analysis of Alg14/13 homologs indicates that they are ancient in Eukaryotes, either as a lateral transfer or inherited through eukaryogenesis.}, }
@article {pmid35389344, year = {2022}, author = {Villanueva, EMF and Lim, PK and Lim, JJJ and Lim, SC and Lau, PY and Koh, KTS and Tan, E and Kairon, RS and See, WA and Liao, JX and Hee, KM and Vijay, V and Maitra, I and Boon, CJ and Fo, K and Wang, YT and Jaya, R and Hew, LA and Lim, YY and Lee, WQ and Lee, ZQ and Foo, H and Dos Santos, AL and Mutwil, M}, title = {Protist.guru: A Comparative Transcriptomics Database for Protists.}, journal = {Journal of molecular biology}, volume = {434}, number = {11}, pages = {167502}, doi = {10.1016/j.jmb.2022.167502}, pmid = {35389344}, issn = {1089-8638}, mesh = {*Databases, Genetic ; *Eukaryota/genetics ; Gene Expression Profiling ; Sequence Analysis, DNA ; *Transcriptome/genetics ; }, abstract = {During the last few decades, the study of microbial ecology has been enabled by molecular and genomic data. DNA sequencing has revealed the surprising extent of microbial diversity and how microbial processes run global ecosystems. However, significant gaps in our understanding of the microbial world remain, and one example is that microbial eukaryotes, or protists, are still largely neglected. To address this gap, we used gene expression data from 17 protist species to create protist.guru: an online database equipped with tools for identifying co-expressed genes, gene families, and co-expression clusters enriched for specific biological functions. Here, we show how our database can be used to reveal genes involved in essential pathways, such as the synthesis of secondary carotenoids in Haematococcus lacustris. We expect protist.guru to serve as a valuable resource for protistologists, as well as a catalyst for discoveries and new insights into the biological processes of microbial eukaryotes. AVAILABILITY: The database and co-expression networks are freely available from http://protist.guru/. The expression matrices and sample annotations are found in the supplementary data.}, }
@article {pmid35389249, year = {2022}, author = {Ramond, JB and Jordaan, K and Díez, B and Heinzelmann, SM and Cowan, DA}, title = {Microbial Biogeochemical Cycling of Nitrogen in Arid Ecosystems.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {86}, number = {2}, pages = {e0010921}, pmid = {35389249}, issn = {1098-5557}, mesh = {*Ecosystem ; *Microbiota ; Nitrification ; Nitrogen ; Nitrogen Cycle ; Plants ; Soil ; Soil Microbiology ; }, abstract = {Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N2O), a potent greenhouse gas.}, }
@article {pmid35389085, year = {2023}, author = {Steinigeweg, C and Alkassab, AT and Erler, S and Beims, H and Wirtz, IP and Richter, D and Pistorius, J}, title = {Impact of a Microbial Pest Control Product Containing Bacillus thuringiensis on Brood Development and Gut Microbiota of Apis mellifera Worker Honey Bees.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1300-1307}, pmid = {35389085}, issn = {1432-184X}, mesh = {Bees ; Animals ; *Gastrointestinal Microbiome ; *Bacillus thuringiensis ; Lactobacillus ; Bifidobacterium ; }, abstract = {To avoid potential adverse side effects of chemical plant protection products, microbial pest control products (MPCP) are commonly applied as biological alternatives. This study aimed to evaluate the biosafety of a MPCP with the active organism Bacillus thuringiensis ssp. aizawai (strain: ABTS-1857). An in-hive feeding experiment was performed under field-realistic conditions to examine the effect of B. thuringiensis (B. t.) on brood development and the bacterial abundance of the core gut microbiome (Bifidobacterium asteroids, Gilliamella apicola, the group of Lactobacillus and Snodgrasella alvi) in Apis mellifera worker bees. We detected a higher brood termination rate and a non-successful development into worker bees of treated colonies compared to those of the controls. For the gut microbiome, all tested core members showed a significantly lower normalized abundance in bees of the treated colonies than in those of the controls; thus, a general response of the gut microbiome may be assumed. Consequently, colony exposure to B. t. strain ABTS-1857 had a negative effect on brood development under field-realistic conditions and caused dysbiosis of the gut microbiome. Further studies with B. t.-based products, after field-realistic application in bee attractive crops, are needed to evaluate the potential risk of these MPCPs on honey bees.}, }
@article {pmid35388893, year = {2022}, author = {Águila, B and Yanez-Montalvo, A and Mercado-Juárez, RA and Montejano, GA and Becerra-Absalón, I and Falcón, LI}, title = {Microbialites show a distinct cyanobacterial phylogenetic structure and functional redundancy in Bacalar lagoon and Cenote Azul sinkhole, Yucatan Peninsula, Mexico.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {5}, pages = {}, doi = {10.1093/femsec/fiac039}, pmid = {35388893}, issn = {1574-6941}, support = {IN207220//UNAM/ ; //Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; }, mesh = {*Cyanobacteria/genetics ; Metagenomics ; Mexico ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Cyanobacterial components of microbialites from two geographically close systems, the Bacalar lagoon (BL) and the Cenote Azul sinkhole (CA) in Quintana Roo, Mexico, were characterized. BL and CA systems were studied along a longitudinal gradient (north to south) and a depth gradient (5-30 m), respectively. Microscopic observations, 16S rRNA amplicon sequencing, and shotgun metagenomics were used to characterize Cyanobacteria. Both systems showed similar metabolic/functional profiles but harbored completely different cyanobacterial taxa. BL was dominated by Nostocales, including a population of previously undescribed Chakia sp., while CA was dominated by an unknown taxon of Chroococcales, comprising 70% of relative abundance through all depths. Interestingly, cyanobacterial assemblages in microbialites exhibited phylogenetic overdispersion in most of the BL sites, while CA sites exhibited phylogenetic clustering, these differences were attributed to depth/light conditions and possibly different times of geological formation for BL and CA systems.}, }
@article {pmid35388110, year = {2022}, author = {Zhang, S and Yang, Q and Fu, S and Janssen, CR and Eggermont, M and Defoirdt, T}, title = {Indole decreases the virulence of the bivalve model pathogens Vibrio tasmaniensis LGP32 and Vibrio crassostreae J2-9.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {5749}, pmid = {35388110}, issn = {2045-2322}, mesh = {Animals ; *Bivalvia ; Indoles ; *Vibrio/genetics ; Virulence/genetics ; }, abstract = {Indole signaling plays an important role in bacterial pathogenesis. In this study, the impact of indole on biofilm formation, swimming and swarming motility were explored in Vibrio tasmaniensis LGP32 and Vibrio crassostreae J2-9, two model pathogens of bivalves. The results showed that indole decreased swimming and swarming motility in both strains, and decreased biofilm formation in V. crassostreae J2-9. Furthermore, indole affected a large number of genes at RNA level, including genes related to metabolism, ABC transporters, flagellar assembly, chemotaxis, and response regulators. Finally, the bacterial virulence towards mussel larvae was decreased by pretreatment with indole in both V. tasmaniensis LGP32 and V. crassostreae J2-9. After 5 days, the survival rate of mussel larvae increased 2.4-fold and 2.8-fold in mussel larvae challenged with V. tasmaniensis LGP32 pretreated with 200 µM and 500 µM indole, respectively. The survival rate of mussel larvae increased 1.5-fold and 1.9-fold in mussel larvae challenged with V. crassostreae J2-9 pretreated with 200 µM and 500 µM indole, respectively. These data indicate that indole has a significant impact on the virulence of V. tasmaniensis LGP32 and V. crassostreae J2-9, and indole signaling could be a promising target for antivirulence therapy.}, }
@article {pmid35388078, year = {2022}, author = {Wahl, A and Huptas, C and Neuhaus, K}, title = {Comparison of rRNA depletion methods for efficient bacterial mRNA sequencing.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {5765}, pmid = {35388078}, issn = {2045-2322}, mesh = {Bacteria/genetics ; *Escherichia coli/genetics ; High-Throughput Nucleotide Sequencing ; RNA ; RNA, Messenger/genetics ; *RNA, Ribosomal/genetics ; Sequence Analysis, RNA/methods ; }, abstract = {Current methods of high-throughput RNA sequencing of prokaryotes, including transcriptome analysis or ribosomal profiling, need deep sequencing to achieve sufficient numbers of effective reads (e.g., mapping to mRNA) in order to also find weakly expressed genetic elements. The fraction of high-quality reads mapping to coding RNAs (i.e., mRNA) is mainly influenced by the large content of rRNA and, to a lesser extent, tRNA in total RNA. Thus, depletion of rRNA increases coverage and thus sequencing costs. RiboZero, a depletion kit based on probe hybridisation and rRNA-removal was found to be most efficient in the past, but it was discontinued in 2018. To facilitate comparability with previous experiments and to help choose adequate replacements, we compare three commercially available rRNA depletion kits also based on hybridization and magnetic beads, i.e., riboPOOLs, RiboMinus and MICROBExpress, with the former RiboZero. Additionally, we constructed biotinylated probes for magnetic bead capture and rRNA depletion in this study. Based on E. coli, we found similar efficiencies in rRNA depletion for riboPOOLs and the self-made depletion method; both comparable to the former RiboZero, followed by RiboMinus, succeeded by MICROBExpress. Further, our in-house protocol allows customized species-specific rRNA or even tRNA depletion or depletion of other RNA targets. Both, the self-made biotinylated probes and riboPOOLs, were most successful in reducing the rRNA content and thereby increasing sequencing depth concerning mRNA reads. Additionally, the number of reads matching to weakly expressed genes are increased. In conclusion, the self-made specific biotinylated probes and riboPOOLs are an adequate replacement for the former RiboZero. Both are very efficient in depleting rRNAs, increasing mRNA reads and thus sequencing efficiency.}, }
@article {pmid35388041, year = {2022}, author = {Dwużnik-Szarek, D and Mierzejewska, EJ and Kiewra, D and Czułowska, A and Robak, A and Bajer, A}, title = {Update on prevalence of Babesia canis and Rickettsia spp. in adult and juvenile Dermacentor reticulatus ticks in the area of Poland (2016-2018).}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {5755}, pmid = {35388041}, issn = {2045-2322}, mesh = {Animals ; *Babesia/genetics ; *Dermacentor/microbiology ; *Dog Diseases/epidemiology ; Dogs ; Nymph ; Poland/epidemiology ; Prevalence ; *Rhipicephalus sanguineus ; *Rickettsia/genetics ; }, abstract = {Ornate dog tick, Dermacentor reticulatus is an important vector of Babesia canis, and Rickettsia spp. and other pathogens of veterinary and public health interest. The current study is the first to investigate the long-term changes in prevalence of these pathogens in expanding tick populations in Central Europe. Molecular techniques (PCR, sequencing) were applied for the detection of pathogen DNA in adult (n = 2497) and juvenile ticks (1096 larvae and 410 nymphs). DNA of Rickettsia spp. was identified in 35% of adults and 12.6% of juvenile ticks. DNA of B. canis was detected in 3% of adult ticks and only in ticks from the Eastern region (regional prevalence 6%). As previously, no B. canis-positive ticks were found in Western Poland, including ticks from Wrocław area (n = 298). DNA of B. canis was identified in 0.33% of juvenile ticks (in 3 pools of larvae and 2 nymphs) from the Eastern region. In the current study we confirmed high occurrence of R. raoultii in adults ticks from all four zones and relatively high prevalence of B. canis in the Eastern population of D. reticulatus, corresponding well with high incidence of canine babesiosis in this area of Poland. Finally, we confirmed R. raoultii and B. canis infection in all life stages of D. reticulatus ticks.}, }
@article {pmid35385973, year = {2023}, author = {Alba, C and Sansano-Maestre, J and Cid Vázquez, MD and Martínez-Herrero, MDC and Garijo-Toledo, MM and Azami-Conesa, I and Moraleda Fernández, V and Gómez-Muñoz, MT and Rodríguez, JM}, title = {Captive Breeding and Trichomonas gallinae Alter the Oral Microbiome of Bonelli's Eagle Chicks.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1541-1551}, pmid = {35385973}, issn = {1432-184X}, support = {Grant PR26/16-20328//Santander-UCM/ ; LIFE12 NAT/ES/000701-Integral recovery of Bonelli's eagle population in Spain//LIFE programme/ ; ACIF/2013/055//Conselleria d'Educaci&#xf3;, Investigaci&#xf3;, Cultura i Esport/ ; }, mesh = {Animals ; Humans ; *Trichomonas ; *Eagles ; Europe ; }, abstract = {Bonelli's eagle (Aquila fasciata) is an endangered raptor species in Europe, and trichomonosis is one of the menaces affecting chicks at nest. In this paper, we attempt to describe the oral microbiome of Bonelli's eagle nestlings and evaluate the influence of several factors, such as captivity breeding, Trichomonas gallinae infection, and the presence of lesions at the oropharynx. The core oral microbiome of Bonelli's eagle is composed of Firmicutes, Bacteroidota, Fusobacteria and Proteobacteria as the most abundant phyla, and Megamonas and Bacteroides as the most abundant genera. None of the factors analysed showed a significant influence on alfa diversity, but beta diversity was affected for some of them. Captivity breeding exerted a high influence on the composition of the oral microbiome, with significant differences in the four most abundant phyla, with a relative increase of Proteobacteria and a decrease of the other three phyla in comparison with chicks bred at nest. Some genera were more abundant in captivity bred chicks, such as Escherichia-Shigella, Enterococcus, Lactobacillus, Corynebacterium, Clostridium and Staphylococcus, while Bacteroides, Oceanivirga, Peptostreptococcus, Gemella, Veillonella, Mycoplasma, Suttonella, Alloscardovia, Varibaculum and Campylobacter were more abundant in nest raised chicks. T. gallinae infection slightly influenced the composition of the microbiome, but chicks displaying trichomonosis lesions had a higher relative abundance of Bacteroides and Gemella, being the last one an opportunistic pathogen of abscess complications in humans. Raptor's microbiomes are scarcely studied. This is the first study on the factors that influence the oral microbiome of Bonelli's eagle.}, }
@article {pmid35384214, year = {2022}, author = {Régimbeau, A and Budinich, M and Larhlimi, A and Pierella Karlusich, JJ and Aumont, O and Memery, L and Bowler, C and Eveillard, D}, title = {Contribution of genome-scale metabolic modelling to niche theory.}, journal = {Ecology letters}, volume = {25}, number = {6}, pages = {1352-1364}, pmid = {35384214}, issn = {1461-0248}, support = {//Fonds Fran&#xe7;ais pour l'Environnement Mondial/ ; 80 PRIME//Centre National de la Recherche Scientifique/ ; ANR-10-LABX-54//MEMO LIFE/ ; ANR-19-CE20-0020//BrownCut/ ; ANR-11-IDEX-0001-02//Universit&#xe9; de Recherche Paris Sciences et Lettres/ ; 835067//H2020 Environment/ ; 862923//H2020 Environment/ ; ANR-10-INBS-09-08//OCEANOMICS/ ; ANR-10-INBS-09-08//FRANCE GENOMIQUE/ ; }, mesh = {*Ecosystem ; Phenotype ; }, abstract = {Standard niche modelling is based on probabilistic inference from organismal occurrence data but does not benefit yet from genome-scale descriptions of these organisms. This study overcomes this shortcoming by proposing a new conceptual niche that resumes the whole metabolic capabilities of an organism. The so-called metabolic niche resumes well-known traits such as nutrient needs and their dependencies for survival. Despite the computational challenge, its implementation allows the detection of traits and the formal comparison of niches of different organisms, emphasising that the presence-absence of functional genes is not enough to approximate the phenotype. Further statistical exploration of an organism's niche sheds light on genes essential for the metabolic niche and their role in understanding various biological experiments, such as transcriptomics, paving the way for incorporating better genome-scale description in ecological studies.}, }
@article {pmid35379841, year = {2022}, author = {Saeed, M and Rais, M and Akram, A and Williams, MR and Kellner, KF and Hashsham, SA and Davis, DR}, title = {Development and validation of an eDNA protocol for monitoring endemic Asian spiny frogs in the Himalayan region of Pakistan.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {5624}, pmid = {35379841}, issn = {2045-2322}, mesh = {Altitude ; Animals ; DNA, Environmental/*analysis/genetics ; Ecosystem ; Models, Biological ; Pakistan ; Ranidae/genetics/*physiology ; Species Specificity ; }, abstract = {Wildlife monitoring programs are instrumental for the assessment of species, habitat status, and for the management of factors affecting them. This is particularly important for species found in freshwater ecosystems, such as amphibians, as they have higher estimated extinction rates than terrestrial species. We developed and validated two species-specific environmental DNA (eDNA) protocols and applied them in the field to detect the Hazara Torrent Frog (Allopaa hazarensis) and Murree Hills Frog (Nanorana vicina). Additionally, we compared eDNA surveys with visual encounter surveys and estimated site occupancy. eDNA surveys resulted in higher occurrence probabilities for both A. hazarensis and N. vicina than for visual encounter surveys. Detection probability using eDNA was greater for both species, particularly for A. hazarensis. The top-ranked detection model for visual encounter surveys included effects of both year and temperature on both species, and the top-ranked occupancy model included effects of elevation and year. The top-ranked detection model for eDNA data was the null model, and the top-ranked occupancy model included effects of elevation, year, and wetland type. To our knowledge, this is the first time an eDNA survey has been used to monitor amphibian species in the Himalayan region.}, }
@article {pmid35378966, year = {2022}, author = {Liu, X and Lu, S and Shao, Y and Zhang, D and Tu, J and Chen, J}, title = {Disorders of gut microbiota in children with Tetralogy of Fallot.}, journal = {Translational pediatrics}, volume = {11}, number = {3}, pages = {385-395}, pmid = {35378966}, issn = {2224-4344}, abstract = {BACKGROUND: Gut microbiota plays an important role in cardiovascular health and disease, including congenital heart disease (CHD). Tetralogy of Fallot (TOF) is the most common form of cyanotic CHD characterized by systemic chronic hypoxia and sustained pressure overload of the right ventricle. It is well-known that hypoxia and pressure overload can affect gut microbiota. However, the effects of TOF on the gut microbiota remain little understood. This study explored the profile of the gut microbiota in children with unrepaired TOF.<br><br>METHODS: A total of 12 pediatric patients diagnosed with TOF and 9 healthy age- and gender-matched children were enrolled in this study. Fecal samples were collected from every participant and subjected to 16S rDNA gene sequencing. The raw sequencing data were processed using the Quantitative Insights Into Microbial Ecology pipeline.<br><br>RESULTS: A comparison of the gut microbiota revealed that pediatric patients with TOF had developed dysbiosis as reflected by the altered taxonomic composition and impaired functional profile. A total of 14 indicative bacterial genera were identified as differential biomarkers capable of distinguishing between healthy children and TOF patients. Furthermore, functional annotations revealed that the gut microbiota in TOF patients was characterized by increased levels of inflammatory, oxidative, and immune responses, and decreased activities of adaptation, synthesis, and metabolism.<br><br>CONCLUSIONS: Pediatric patients with unrepaired TOF have intestinal dysbacteriosis that is characterized by altered taxonomic composition and impaired functional profile. These findings suggested that the interplay between gut microbiota and the host may be dysregulated in patients with TOF.}, }
@article {pmid35378620, year = {2023}, author = {Kerfahi, D and Harvey, BP and Kim, H and Yang, Y and Adams, JM and Hall-Spencer, JM}, title = {Whole community and functional gene changes of biofilms on marine plastic debris in response to ocean acidification.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1202-1214}, pmid = {35378620}, issn = {1432-184X}, mesh = {Humans ; *Seawater ; Plastics ; Hydrogen-Ion Concentration ; Ocean Acidification ; Carbon Dioxide ; Biofilms ; *Diatoms/genetics ; }, abstract = {Plastics are accumulating in the world's oceans, while ocean waters are becoming acidified by increased CO2. We compared metagenome of biofilms on tethered plastic bottles in subtidal waters off Japan naturally enriched in CO2, compared to normal ambient CO2 levels. Extending from an earlier amplicon study of bacteria, we used metagenomics to provide direct insights into changes in the full range of functional genes and the entire taxonomic tree of life in the context of the changing plastisphere. We found changes in the taxonomic community composition of all branches of life. This included a large increase in diatom relative abundance across the treatments but a decrease in diatom diversity. Network complexity among families decreased with acidification, showing overall simplification of biofilm integration. With acidification, there was decreased prevalence of genes associated with cell-cell interactions and antibiotic resistance, decreased detoxification genes, and increased stress tolerance genes. There were few nutrient cycling gene changes, suggesting that the role of plastisphere biofilms in nutrient processes within an acidified ocean may not change greatly. Our results suggest that as ocean CO2 increases, the plastisphere will undergo broad-ranging changes in both functional and taxonomic composition, especially the ecologically important diatom group, with possible wider implications for ocean ecology.}, }
@article {pmid35377164, year = {2022}, author = {Gorski, L and Cooley, MB and Oryang, D and Carychao, D and Nguyen, K and Luo, Y and Weinstein, L and Brown, E and Allard, M and Mandrell, RE and Chen, Y}, title = {Prevalence and Clonal Diversity of over 1,200 Listeria monocytogenes Isolates Collected from Public Access Waters near Produce Production Areas on the Central California Coast during 2011 to 2016.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {8}, pages = {e0035722}, pmid = {35377164}, issn = {1098-5336}, mesh = {Humans ; *Listeria monocytogenes ; *Listeriosis/epidemiology ; Multilocus Sequence Typing ; Prevalence ; Virulence Factors/genetics ; }, abstract = {A 5-year survey of public access surface waters in an agricultural region of the Central California Coast was done to assess the prevalence of the foodborne pathogen Listeria monocytogenes. In nature, L. monocytogenes lives as a saprophyte in soil and water, which are reservoirs for contamination of preharvest produce. Moore swabs were deployed biweekly in lakes, ponds, streams, and rivers during 2011 to 2016. L. monocytogenes was recovered in 1,224 of 2,922 samples, resulting in 41.9% prevalence. Multiple subtypes were isolated from 97 samples, resulting in 1,323 L. monocytogenes isolates. Prevalence was higher in winter and spring and after rain events in some waterways. Over 84% of the isolates were serotype 4b. Whole-genome sequencing was done on 1,248 isolates, and in silico multilocus sequence typing revealed 74 different sequence types (STs) and 39 clonal complexes (CCs). The clones most isolated, CC639, CC183, and CC1, made up 27%, 19%, and 13%, respectively, of the sequenced isolates. Other types were CC663, CC6, CC842, CC4, CC2, CC5, and CC217. All sequenced isolates contained intact copies of core L. monocytogenes virulence genes, and pathogenicity islands LIPI-3 and LIPI-4 were identified in 73% and 63%, respectively, of the sequenced isolates. The virulence factor internalin A was predicted to be intact in all but four isolates, while genes important for sanitizer and heavy metal resistance were found in <5% of the isolates. These waters are not used for crop irrigation directly, but they are available to wildlife and can flood fields during heavy rains. IMPORTANCE Listeria monocytogenes serotype 4b and 1/2a strains are implicated in most listeriosis, and hypervirulent listeriosis stems from strains containing pathogenicity islands LIPI-3 and LIPI-4. The waters and sediments in the Central California Coast agricultural region contain widespread and diverse L. monocytogenes populations, and all the isolates contain intact virulence genes. Emerging clones CC183 and CC639 were the most abundant clones, and major clones CC1, CC4, and CC6 were well represented. CC183 was responsible for three produce-related outbreaks in the last 7 years. Most of the isolates in the survey differ from those of lesser virulence that are often isolated from foods and food processing plants because they contain genes encoding an intact virulence factor, internalin A, and most did not contain genes for sanitizer and heavy metal resistance. This isolate collection is important for understanding L. monocytogenes populations in agricultural and natural regions.}, }
@article {pmid35372103, year = {2022}, author = {Halaweish, HF and Boatman, S and Staley, C}, title = {Encapsulated Fecal Microbiota Transplantation: Development, Efficacy, and Clinical Application.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {826114}, pmid = {35372103}, issn = {2235-2988}, mesh = {*Clostridioides difficile ; *Clostridium Infections/therapy ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; }, abstract = {Fecal microbiota transplantation (FMT) has been established as a highly restorative therapeutic approach for treating recurrent Clostridioides difficile infection (rCDI). Recently, the use of capsule-based fecal microbiota transplantation (cFMT) has been shown to be a clinically effective approach to restore intestinal microbiota composition. This convenient, oral delivery provides an easy route of administration and a newfound flexibility for clinicians and patients. In this review, we discuss the development of cFMT, paying particular attention to lyophilized cFMT products. We review the available published clinical studies comparing cFMT with lower endoscopic FMT (eFMT) or placebo. We further discuss the pharmacokinetics of FMT, which should be understood in a framework of microbial ecology that considers the complex and dynamic interactions of gut microbiota with host factors and other microorganisms. Promisingly, the results of multiple trials investigating cFMT vs. eFMT in rCDI show cFMT to be as effective as eFMT at preventing rCDI. However, its efficacy in non-rCDI conditions, including obesity and metabolic syndrome, inflammatory bowel disease, HIV, and neurologic conditions, is less clear and more research is needed in these areas. Standardization of formulation, dose, and timing of administration to ensure optimal microbiota engraftment and clinical response is also a challenge to be addressed. Overall, cFMT is a practical method for fecal microbiota transplantation, with similar efficacy to eFMT in the resolution of rCDI, that holds therapeutic potential in a variety of other diseases.}, }
@article {pmid35370685, year = {2022}, author = {Spisni, E and Turroni, S and Alvisi, P and Spigarelli, R and Azzinnari, D and Ayala, D and Imbesi, V and Valerii, MC}, title = {Nutraceuticals in the Modulation of the Intestinal Microbiota: Current Status and Future Directions.}, journal = {Frontiers in pharmacology}, volume = {13}, number = {}, pages = {841782}, pmid = {35370685}, issn = {1663-9812}, abstract = {Pharmaceutical interest in the human intestinal microbiota has increased considerably, because of the increasing number of studies linking the human intestinal microbial ecology to an increasing number of non-communicable diseases. Many efforts at modulating the gut microbiota have been made using probiotics, prebiotics and recently postbiotics. However, there are other, still little-explored opportunities from a pharmaceutical point of view, which appear promising to obtain modifications of the microbiota structure and functions. This review summarizes all in vitro, in vivo and clinical studies demonstrating the possibility to positively modulate the intestinal microbiota by using probiotics, prebiotics, postbiotics, essential oils, fungus and officinal plants. For the future, clinical studies investigating the ability to impact the intestinal microbiota especially by using fungus, officinal and aromatic plants or their extracts are required. This knowledge could lead to effective microbiome modulations that might support the pharmacological therapy of most non-communicable diseases in a near future.}, }
@article {pmid35370677, year = {2022}, author = {Liu, L and Lu, Y and Xu, C and Chen, H and Wang, X and Wang, Y and Cai, B and Li, B and Verstrepen, L and Ghyselinck, J and Marzorati, M and Yao, Q}, title = {The Modulation of Chaihu Shugan Formula on Microbiota Composition in the Simulator of the Human Intestinal Microbial Ecosystem Technology Platform and its Influence on Gut Barrier and Intestinal Immunity in Caco-2/THP1-Blue™ Cell Co-Culture Model.}, journal = {Frontiers in pharmacology}, volume = {13}, number = {}, pages = {820543}, pmid = {35370677}, issn = {1663-9812}, abstract = {The traditional Chinese medicine (TCM)-Chaihu Shugan Formula (CSF), consisting of several Chinese botanical drugs like Bupleurum, is derived from the ancient Chinese pharmacopeia. It has been used for more than thousands of years in various suboptimal health statuses and diseases induced by chronic stress based on empirical therapy. Recent studies confirm the role of CSF in the development of many diseases, including depression, stress-induced hepatic injury and tumors. However, little has been known about the mechanisms behind the health effects of CSF. Here, we investigate the influence of CSF on the modulation of the simulated colonic microbiota of five healthy donors, gut barrier integrity, and intestinal immunity by combining the simulator of the human intestinal microbial ecosystem (SHIME[®]) technology platform with co-culture of intestinal and immune cells. This approach revealed that CSF stimulated the production of SCFA (acetate, propionate and butyrate) across donors while significantly lowering the production of branched SCFA (bSCFA). In terms of community composition, CSF stimulated a broad spectrum of health-related Bifidobacterium species, which are potent acetate and lactate producers. At the same time, it lowered the abundance of opportunistic pathogenic Escherichia coli. Later, we explore the effect of colonic fermentation of CSF on the gut barrier and intestinal immunity in the Caco-2/THP1-blue™ cell co-culture model. Based on the study using SHIME technology platform, CSF showed protective effects on inflammation-induced intestinal epithelial barrier disruption in all donors. Also, the treatment of CSF showed pronounced anti-inflammatory properties by strongly inducing anti-inflammatory cytokines IL-6 and IL-10 and reducing pro-inflammatory cytokine TNF-α. These findings demonstrate a significant modulatory effect of CSF on intestinal gut microbiota. CSF-microbial fermentation products improved the gut barrier and controlled intestinal inflammation.}, }
@article {pmid35367883, year = {2022}, author = {Zhu, M and Duan, X and Zeng, Q and Liu, Y and Qiu, Z}, title = {He-Ne laser irradiation ameliorates cadmium toxicity in wheat by modulating cadmium accumulation, nutrient uptake and antioxidant defense system.}, journal = {Ecotoxicology and environmental safety}, volume = {236}, number = {}, pages = {113477}, doi = {10.1016/j.ecoenv.2022.113477}, pmid = {35367883}, issn = {1090-2414}, mesh = {*Antioxidants/metabolism ; *Cadmium/metabolism/toxicity ; Chlorophyll/metabolism ; Glutathione/metabolism ; Glutathione Reductase/metabolism ; Hydrogen Peroxide/metabolism ; Lasers ; Nutrients ; Oxidative Stress ; Plant Breeding ; Seedlings/metabolism ; Superoxide Dismutase/metabolism ; Triticum/metabolism ; }, abstract = {Cadmium (Cd) is one of the most hazardous heavy metals that negatively affect the growth and yield of wheat. He-Ne laser irradiation is known to ameliorate cadmium (Cd) stress in wheat. However, the underlying mechanism of He-Ne laser irradiation on protecting wheat against Cd stress is not well recognized. In present study, Cd-treated wheat showed significant reduction in growth, root morphology and total chlorophyll content, but notably increase of Cd accumulation in both roots and shoots. However, He-Ne laser irradiation dramatically reduced concentrations of malondialdehyde (MDA) and hydrogen peroxide (H2O2), and increased total chlorophyll content and activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX) in roots of wheat plants under Cd stress. Further, He-Ne laser irradiation significantly upregulated the transcripts of TaGR (glutathione reductase) and TaGST (glutathione-S-transferase) genes along with the increased activities of GR and GST and glutathione (GSH) concentration in roots of wheat seedlings under Cd stress. In addition, He-Ne laser irradiation enhanced the uptake of mineral elements (N, P, Mg, Fe, Zn and Cu), and significantly decreased Cd uptake and transport mainly through down-regulating the expressions of Cd transport genes (TaHMA2 and TaHMA3) in roots of wheat seedlings under Cd stress. Overall, these findings suggested that He-Ne laser irradiation alleviated the adverse effects of Cd on wheat growth by enhancing antioxidant defense system, improving mineral nutrient status, and decreasing the Cd uptake and transport. This study provides new insights into the roles of He-Ne laser irradiation in the amelioration of Cd stress in wheat and indicates the potential application of this irradiation in crop breeding and growth under Cd stress conditions.}, }
@article {pmid35367386, year = {2022}, author = {de Lapena, SAB and Terra-Garcia, M and Ward, RADC and Rossoni, RD and Melo, VMM and Junqueira, JC}, title = {Enhancing effect of chitosan on methylene blue-mediated photodynamic therapy against C. albicans: A study in planktonic growth, biofilms, and persister cells.}, journal = {Photodiagnosis and photodynamic therapy}, volume = {38}, number = {}, pages = {102837}, doi = {10.1016/j.pdpdt.2022.102837}, pmid = {35367386}, issn = {1873-1597}, mesh = {Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Biofilms ; Candida ; Candida albicans ; *Chitosan/pharmacology ; Fluconazole/pharmacology ; Methylene Blue/pharmacology ; *Photochemotherapy/methods ; Photosensitizing Agents/pharmacology ; Plankton ; }, abstract = {Chitosan (CS) is a natural polymer extracted from the exoskeleton of crustaceans. Due to its cationic structure, CS has been studied as a possible enhancer of antimicrobial photodynamic therapy (aPDT). The objective was to evaluate the association of CS with methylene blue (MB)-mediated aPDT on Candida albicans, investigating its effects on planktonic growth, biofilms, and cells persistent to fluconazole. The ability of CS to interfere with MB absorption by Candida cells was also evaluated. For the assays, planktonic cells of C. albicans were cultivated for 24 h, and the biofilms were formed for 48 h. For the induction of persister cells, C. albicans was cultivated with high concentration of fluconazole for 48 h. Treatments were performed with MB, CS or MB+CS, followed by irradiation with LED (660 nm). As results, aPDT with MB (300 µm) reduced the planktonic cells by 1.6 log10 CFU, while the MB+CS association led to a reduction of 4.8 log10 CFU. For aPDT in biofilms, there was a microbial reduction of 2.9 log10 CFU for the treatment with MB (600 µm) and 5.3 log10 CFU for MB+CS. In relation to persister cells, the fungal reductions were 0.4 log10 CFU for MB and 1.5 log10 CFU for MB+CS. In the absorption assays, the penetration of MB into Candida cells was increased in the presence of CS. It was concluded that CS enhanced the antimicrobial activity of aPDT in planktonic growth, biofilms, and persister cells of C. albicans, probably by facilitating the penetration of MB into fungal cells.}, }
@article {pmid35366684, year = {2023}, author = {Bashir, A and Ahmad, T and Farooq, S and Lone, WI and Manzoor, MM and Nalli, Y and Sultan, P and Chaubey, A and Ali, A and Riyaz-Ul-Hassan, S}, title = {A Secondary Metabolite of Cercospora sp., Associated with Rosa damascena Mill., Inhibits Proliferation, Biofilm Production, Ergosterol Synthesis and Other Virulence Factors in Candida albicans.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1276-1287}, pmid = {35366684}, issn = {1432-184X}, mesh = {*Candida albicans/metabolism ; Virulence Factors/metabolism ; *Rosa/metabolism ; Cercospora/metabolism ; Molecular Docking Simulation ; Phylogeny ; Biofilms ; Ergosterol/metabolism ; Cell Proliferation ; Antifungal Agents/pharmacology/metabolism ; Microbial Sensitivity Tests ; }, abstract = {Here we describe the antimicrobial potential of secondary metabolites, fulvic acid (F.A.) and anhydrofulvic acid (AFA), produced by RDE147, an endophyte of Rosa damascena Mill. The endophyte was identified as Cercospora piaropi by ITS and β-tubulin-based phylogenetic analyses, while chemoprofiling of the endophyte by column chromatography and spectroscopy yielded two pure compounds, F.A. and AFA. The compounds demonstrated different antimicrobial profiles, with AFA suppressing the growth of C. albicans at 7.3 µg ml[-1] IC50. Further studies revealed that AFA strongly restricted the biofilm production and hyphae formation in C. albicans by down-regulating several biofilm and morphogenesis-related genes. The time-kill assays confirmed the fungicidal activity of AFA against C. albicans, killing 83.6% of the pathogen cells in 24 h at the MIC concentration, and the post-antibiotic effect (PAE) experiments established the suppression of C. albicans growth for extended time periods. The compound acted synergistically with amphotericin B and nystatin and reduced ergosterol biosynthesis by the pathogen, confirmed by ergosterol estimation and comparative expression profiling of selected genes and molecular docking of AFA with C. albicans squalene epoxidase. AFA also suppressed the expression of several other virulence genes of the fungal pathogen. The study determines the anti-C. albicans potential of AFA and its impact on the biology of the pathogen. It also indicates that Cercospora species may yield potential bioactive molecules, especially fulvic acid derivatives. However, it is imperative to conduct in vivo studies to explore this molecule's therapeutic potential further.}, }
@article {pmid35366074, year = {2023}, author = {Li, W and Zhou, Z and Li, H and Wang, S and Ren, L and Hu, J and Liu, Q and Wu, C and Tang, C and Hu, F and Zeng, L and Zhao, R and Tao, M and Zhang, C and Qin, Q and Liu, S}, title = {Successional Changes of Microbial Communities and Host-Microbiota Interactions Contribute to Dietary Adaptation in Allodiploid Hybrid Fish.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1190-1201}, pmid = {35366074}, issn = {1432-184X}, support = {NT2021008//the Laboratory of Lingnan Modern Agriculture Project/ ; 21B0053//the Research Foundation of Education Bureau of Hunan Province/ ; U19A2040//National Natural Science Foundation of China/ ; 31730098//National Natural Science Foundation of China/ ; 31802287//National Natural Science Foundation of China/ ; CARS-45//Earmarked Fund for China Agriculture Research System/ ; }, mesh = {Animals ; *Microbiota ; Fishes/microbiology ; Diet/veterinary ; *Gastrointestinal Microbiome ; Bacteria/genetics ; }, abstract = {Host-microbiota interactions play critical roles in host development, immunity, metabolism, and behavior. However, information regarding host-microbiota interactions is limited in fishes due to their complex living environment. In the present study, an allodiploid hybrid fish derived from herbivorous Megalobrama amblycephala (♀) × carnivorous Culter alburnus (♂) was used to investigate the successional changes of the microbial communities and host-microbiota interactions during herbivorous and carnivorous dietary adaptations. The growth level was not significantly different in any developmental stage between the two diet groups of fish. The diversity and composition of the dominant microbial communities showed similar successional patterns in the early developmental stages, but significantly changed during the two dietary adaptations. A large number of bacterial communities coexisted in all developmental stages, whereas the abundance of some genera associated with metabolism, including Acinetobacter, Gemmobacter, Microbacterium, Vibrio, and Aeromonas, was higher in either diet groups of fish. Moreover, the abundance of phylum Firmicutes, Actinobacteria, and Chloroflexi was positively correlated with the host growth level. In addition, Spearman's correlation analysis revealed that the differentially expressed homologous genes in the intestine associated with cell growth, immunity, and metabolism were related to the dominant gut microbiota. Our results present evidence that host genetics-gut microbiota interactions contribute to dietary adaptation in hybrid fish, which also provides basic data for understanding the diversity of dietary adaptations and evolution in fish.}, }
@article {pmid35365572, year = {2023}, author = {Effenberger, M and Widjaja, AA and Grabherr, F and Schaefer, B and Grander, C and Mayr, L and Schwaerzler, J and Enrich, B and Moser, P and Fink, J and Pedrini, A and Jaschke, N and Kirchmair, A and Pfister, A and Hausmann, B and Bale, R and Putzer, D and Zoller, H and Schafer, S and Pjevac, P and Trajanoski, Z and Oberhuber, G and Adolph, T and Cook, S and Tilg, H}, title = {Interleukin-11 drives human and mouse alcohol-related liver disease.}, journal = {Gut}, volume = {72}, number = {1}, pages = {168-179}, doi = {10.1136/gutjnl-2021-326076}, pmid = {35365572}, issn = {1468-3288}, support = {MC_U120085815/MRC_/Medical Research Council/United Kingdom ; P 29379/FWF_/Austrian Science Fund FWF/Austria ; P 33070/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Humans ; Mice ; Animals ; Interleukin-11/metabolism ; *Liver Diseases, Alcoholic/metabolism ; Liver/metabolism ; *Hepatitis, Alcoholic/metabolism ; Ethanol/toxicity/metabolism ; Hepatocytes/metabolism ; Inflammation/metabolism ; Liver Cirrhosis/pathology ; Mice, Inbred C57BL ; }, abstract = {OBJECTIVE: Alcoholic hepatitis (AH) reflects acute exacerbation of alcoholic liver disease (ALD) and is a growing healthcare burden worldwide. Interleukin-11 (IL-11) is a profibrotic, proinflammatory cytokine with increasingly recognised toxicities in parenchymal and epithelial cells. We explored IL-11 serum levels and their prognostic value in patients suffering from AH and cirrhosis of various aetiology and experimental ALD.<br><br>DESIGN: IL-11 serum concentration and tissue expression was determined in a cohort comprising 50 patients with AH, 110 patients with cirrhosis and 19 healthy volunteers. Findings were replicated in an independent patient cohort (n=186). Primary human hepatocytes exposed to ethanol were studied in vitro. Ethanol-fed wildtype mice were treated with a neutralising murine IL-11 receptor-antibody (anti-IL11RA) and examined for severity signs and markers of ALD.<br><br>RESULTS: IL-11 serum concentration and hepatic expression increased with severity of liver disease, mostly pronounced in AH. In a multivariate Cox-regression, a serum level above 6.4 pg/mL was a model of end-stage liver disease independent risk factor for transplant-free survival in patients with compensated and decompensated cirrhosis. In mice, severity of alcohol-induced liver inflammation correlated with enhanced hepatic IL-11 and IL11RA expression. In vitro and in vivo, anti-IL11RA reduced pathogenic signalling pathways (extracellular signal-regulated kinases, c-Jun N-terminal kinase, NADPH oxidase 4) and protected hepatocytes and murine livers from ethanol-induced inflammation and injury.<br><br>CONCLUSION: Pathogenic IL-11 signalling in hepatocytes plays a crucial role in the pathogenesis of ALD and could serve as an independent prognostic factor for transplant-free survival. Blocking IL-11 signalling might be a therapeutic option in human ALD, particularly AH.}, }
@article {pmid35364696, year = {2023}, author = {Liu, N and Hu, H and Ma, W and Deng, Y and Dimitrov, D and Wang, Q and Shrestha, N and Su, X and Feng, K and Liu, Y and Hao, B and Zhang, X and Feng, X and Wang, Z}, title = {Relationships Between Soil Microbial Diversities Across an Aridity Gradient in Temperate Grasslands : Soil Microbial Diversity Relationships.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {1013-1027}, pmid = {35364696}, issn = {1432-184X}, support = {2017YFA0605101//national key research development program of china/ ; XDB31000000//the Strategic Priority Research Program of Chinese Academy of Sciences/ ; 32125026//the National Natural Science Foundation of China/ ; 31988102//the National Natural Science Foundation of China/ ; LESP201702//the Youth Fund of Ministry of Education Laboratory for Earth Surface Processes of Peking University/ ; }, mesh = {*Grassland ; *Soil/chemistry ; Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Fungi/genetics ; Bacteria/genetics ; Archaea/genetics ; }, abstract = {Soil microbes assemble in highly complex and diverse microbial communities, and microbial diversity patterns and their drivers have been studied extensively. However, diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between microbial functional groups in arid regions remain poorly understood. Here we assessed the relationships between the diversity and abundance of bacteria, fungi, and archaea and explored how environmental factors influence these relationships. We sampled soil along a 1500-km-long aridity gradient in temperate grasslands of Inner Mongolia (China) and sequenced the 16S rRNA gene of bacteria and archaea and the ITS2 gene of fungi. The diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between different microbial functional groups were evaluated using α-diversity and co-occurrence networks based on microbial abundance. Our results indicate insignificant correlations among the diversity patterns of bacterial, fungal, and archaeal domains using α-diversity but mostly positive correlations among diversity patterns of microbial functional groups based on α-diversity and co-occurrence networks along the aridity gradient. These results suggest that studying microbial diversity patterns from the perspective of functional groups and co-occurrence networks can provide additional insights on patterns that cannot be accessed using only overall microbial α-diversity. Increase in aridity weakens the diversity correlations between bacteria and fungi and between bacterial and archaeal functional groups, but strengthens the positive diversity correlations between bacterial functional groups and between fungal functional groups and the negative diversity correlations between bacterial and fungal functional groups. These variations of the diversity correlations are associated with the different responses of microbes to environmental factors, especially aridity. Our findings demonstrate the complex responses of microbial community structure to environmental conditions (especially aridity) and suggest that understanding diversity correlations and co-occurrence patterns between soil microbial groups is essential for predicting changes in microbial communities under future climate change in arid regions.}, }
@article {pmid35363772, year = {2022}, author = {Zaoli, S and Grilli, J}, title = {The stochastic logistic model with correlated carrying capacities reproduces beta-diversity metrics of microbial communities.}, journal = {PLoS computational biology}, volume = {18}, number = {4}, pages = {e1010043}, pmid = {35363772}, issn = {1553-7358}, mesh = {Biodiversity ; *Conservation of Natural Resources ; Logistic Models ; *Microbiota ; }, abstract = {The large taxonomic variability of microbial community composition is a consequence of the combination of environmental variability, mediated through ecological interactions, and stochasticity. Most of the analysis aiming to infer the biological factors determining this difference in community structure start by quantifying how much communities are similar in their composition, trough beta-diversity metrics. The central role that these metrics play in microbial ecology does not parallel with a quantitative understanding of their relationships and statistical properties. In particular, we lack a framework that reproduces the empirical statistical properties of beta-diversity metrics. Here we take a macroecological approach and introduce a model to reproduce the statistical properties of community similarity. The model is based on the statistical properties of individual communities and on a single tunable parameter, the correlation of species' carrying capacities across communities, which sets the difference of two communities. The model reproduces quantitatively the empirical values of several commonly-used beta-diversity metrics, as well as the relationships between them. In particular, this modeling framework naturally reproduces the negative correlation between overlap and dissimilarity, which has been observed in both empirical and experimental communities and previously related to the existence of universal features of community dynamics. In this framework, such correlation naturally emerges due to the effect of random sampling.}, }
@article {pmid35362197, year = {2022}, author = {Lal, R and Singh, BK and Sar, P and Phale, P}, title = {The assessment of microbial ecology: a special emphasis on the Indian scenario.}, journal = {Environmental microbiology reports}, volume = {14}, number = {3}, pages = {325-329}, doi = {10.1111/1758-2229.13067}, pmid = {35362197}, issn = {1758-2229}, mesh = {Ecology ; *Microbiota ; }, }
@article {pmid35361906, year = {2022}, author = {Zhang, C and Merana, GR and Harris-Tryon, T and Scharschmidt, TC}, title = {Skin immunity: dissecting the complex biology of our body's outer barrier.}, journal = {Mucosal immunology}, volume = {15}, number = {4}, pages = {551-561}, pmid = {35361906}, issn = {1935-3456}, support = {K08 AR076459/AR/NIAMS NIH HHS/United States ; DP2 AI144968/AI/NIAID NIH HHS/United States ; }, mesh = {Biology ; Immunity, Innate ; *Mucous Membrane ; *Symbiosis ; }, abstract = {Our skin contributes critically to health via its role as a barrier tissue, carefully regulating passage of key substrates while also providing defense against exogenous threats. Immunological processes are integral to almost every skin function and paramount to our ability to live symbiotically with skin commensal microbes and other environmental stimuli. While many parallels can be drawn to immunobiology at other mucosal sites, skin immunity demonstrates unique features that relate to its distinct topography, chemical composition and microbial ecology. Here we provide an overview of skin as an immune organ, with reference to the broader context of mucosal immunology. We review paradigms of innate as well as adaptive immune function and highlight how skin-specific structures such as hair follicles and sebaceous glands interact and contribute to these processes. Finally, we highlight for the mucosal immunology community a few emerging areas of interest for the skin immunity field moving forward.}, }
@article {pmid35361625, year = {2022}, author = {Lee, TJ and Liu, YC and Liu, WA and Lin, YF and Lee, HH and Ke, HM and Huang, JP and Lu, MJ and Hsieh, CL and Chung, KF and Liti, G and Tsai, IJ}, title = {Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages.}, journal = {Genome research}, volume = {32}, number = {5}, pages = {864-877}, pmid = {35361625}, issn = {1549-5469}, mesh = {Asia ; *Biodiversity ; Humans ; Phylogeny ; *Saccharomyces cerevisiae/genetics ; Taiwan ; Whole Genome Sequencing ; }, abstract = {The ecology and genetic diversity of the model yeast Saccharomyces cerevisiae before human domestication remain poorly understood. Taiwan is regarded as part of this yeast's geographic birthplace, where the most divergent natural lineage was discovered. Here, we extensively sampled the broadleaf forests across this continental island to probe the ancestral species' diversity. We found that S. cerevisiae is distributed ubiquitously at low abundance in the forests. Whole-genome sequencing of 121 isolates revealed nine distinct lineages that diverged from Asian lineages during the Pleistocene, when a transient continental shelf land bridge connected Taiwan to other major landmasses. Three lineages are endemic to Taiwan and six are widespread in Asia, making this region a focal biodiversity hotspot. Both ancient and recent admixture events were detected between the natural lineages, and a genetic ancestry component associated with isolates from fruits was detected in most admixed isolates. Collectively, Taiwanese isolates harbor genetic diversity comparable to that of the whole Asia continent, and different lineages have coexisted at a fine spatial scale even on the same tree. Patterns of variations within each lineage revealed that S. cerevisiae is highly clonal and predominantly reproduces asexually in nature. We identified different selection patterns shaping the coding sequences of natural lineages and found fewer gene family expansion and contractions that contrast with domesticated lineages. This study establishes that S. cerevisiae has rich natural diversity sheltered from human influences, making it a powerful model system in microbial ecology.}, }
@article {pmid35360922, year = {2022}, author = {Kaiser, T and Jahansouz, C and Staley, C}, title = {Network-based approaches for the investigation of microbial community structure and function using metagenomics-based data.}, journal = {Future microbiology}, volume = {17}, number = {}, pages = {621-631}, doi = {10.2217/fmb-2021-0219}, pmid = {35360922}, issn = {1746-0921}, mesh = {Host Microbial Interactions ; *Metagenomics/methods ; *Microbiota ; }, abstract = {Network-based approaches offer a powerful framework to evaluate microbial community organization and function as it relates to a variety of environmental processes. Emerging studies are exploring network theory as a method for data integration that is likely to be critical for the integration of 'omics' data using systems biology approaches. Intricacies of network theory and methodological and computational complexities in network construction, however, impede the use of these tools for translational science. We provide a perspective on the methods of network construction, interpretation and emerging uses for these techniques in understanding host-microbiota interactions.}, }
@article {pmid35359714, year = {2022}, author = {Rogiers, T and Van Houdt, R and Williamson, A and Leys, N and Boon, N and Mijnendonckx, K}, title = {Molecular Mechanisms Underlying Bacterial Uranium Resistance.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {822197}, pmid = {35359714}, issn = {1664-302X}, abstract = {Environmental uranium pollution due to industries producing naturally occurring radioactive material or nuclear accidents and releases is a global concern. Uranium is hazardous for ecosystems as well as for humans when accumulated through the food chain, through contaminated groundwater and potable water sources, or through inhalation. In particular, uranium pollution pressures microbial communities, which are essential for healthy ecosystems. In turn, microorganisms can influence the mobility and toxicity of uranium through processes like biosorption, bioreduction, biomineralization, and bioaccumulation. These processes were characterized by studying the interaction of different bacteria with uranium. However, most studies unraveling the underlying molecular mechanisms originate from the last decade. Molecular mechanisms help to understand how bacteria interact with radionuclides in the environment. Furthermore, knowledge on these underlying mechanisms could be exploited to improve bioremediation technologies. Here, we review the current knowledge on bacterial uranium resistance and how this could be used for bioremediation applications.}, }
@article {pmid35358890, year = {2022}, author = {Gui, Y and Sun, Z and Kazmi, SSUH and Rahman, MS and Xu, H}, title = {Insights for monitoring surveys into influence of tidal events on protozoan periphyton fauna along the tidelines of Yellow Sea, Northern China.}, journal = {Marine pollution bulletin}, volume = {178}, number = {}, pages = {113586}, doi = {10.1016/j.marpolbul.2022.113586}, pmid = {35358890}, issn = {1879-3363}, mesh = {Biodiversity ; *Ciliophora ; Ecosystem ; Environmental Monitoring ; *Periphyton ; Surveys and Questionnaires ; }, abstract = {To explore the influence of tidal events on protozoan periphyton fauna along tidelines, a 1-month baseline survey for bioassessment was conducted in an intertidal zone of the Yellow Sea, Northern China. A total of 27 protozoans species were identified among five sampling sites along five tidelines (sites A-E). The periphytic protozoans showed a significant variation in species distribution and community pattern along five tidelines. Species richness decreased from the high tideline (site A) and reached the minimum value at the middle tideline (site C), followed by an increase up to the low tideline (site E). Individual abundances peaked at site C and leveled off at the other four tidelines. Species richness, evenness, and diversity showed low value at site C compared with those at the other four sites. These findings suggest that periphytic protozoan fauna was shaped by tidal events along the tidelines of marine ecosystems.}, }
@article {pmid35358518, year = {2022}, author = {Shahbaz, M and Bengtson, P and Mertes, JR and Kulessa, B and Kljun, N}, title = {Spatial heterogeneity of soil carbon exchanges and their drivers in a boreal forest.}, journal = {The Science of the total environment}, volume = {831}, number = {}, pages = {154876}, doi = {10.1016/j.scitotenv.2022.154876}, pmid = {35358518}, issn = {1879-1026}, mesh = {Carbon ; Carbon Dioxide/analysis ; Forests ; Methane ; *Soil ; *Taiga ; }, abstract = {Boreal forests have a large impact on the global greenhouse gas balance and their soils constitute an important carbon (C) reservoir. Mature boreal forests are typically a net CO2 sink, but there are also examples of boreal forests that are persistent CO2 sources. The reasons remain often unknown, presumably due to a lack of understanding of how biotic and abiotic drivers interact to determine the microbial respiration of soil organic matter (SOM). This study aimed at identifying the main drivers of microbial SOM respiration and CO2 and CH4 soil chamber-fluxes within dry and wet sampling areas at the mature boreal forest of Norunda, Sweden, a persistent net CO2 source. The spatial heterogeneity of the drivers was assessed with a geostatistical approach combined with stepwise multiple regression. We found that heterotrophic soil respiration increased with SOM content and nitrogen (N) availability, while the SOM reactivity, i.e., SOM specific respiration, was determined by soil moisture and N availability. The latter suggests that microbial activity was N rather than C limited and that microbial N mining might be driving old-SOM decomposition, which was observed through a positive correlation between soil respiration and its δ[13]C values. SOM specific heterotrophic respiration was lower in wet than in dry areas, while no such dependencies were found for chamber-based soil CO2 fluxes, implying that oxygen depletion resulted in lower SOM reactivity. The chamber-based soil CH4 flux differed significantly between the wet and dry areas. In the wet area, we observed net CH4 emission that was positively related to soil moisture and NH4[+]-N content. Taken together, our findings suggest that N availability has a strong regulatory effect on soil CO2 and CH4 emissions at Norunda, and that microbial decomposition of old-SOM to release bioavailable N might be partly responsible for the net CO2 emission at the site.}, }
@article {pmid35357520, year = {2023}, author = {Castillo-Esparza, JF and Mora-Velasco, KA and Rosas-Saito, GH and Rodríguez-Haas, B and Sánchez-Rangel, D and Ibarra-Juárez, LA and Ortiz-Castro, R}, title = {Microorganisms Associated with the Ambrosial Beetle Xyleborus affinis with Plant Growth-Promotion Activity in Arabidopsis Seedlings and Antifungal Activity Against Phytopathogenic Fungus Fusarium sp. INECOL_BM-06.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1396-1411}, pmid = {35357520}, issn = {1432-184X}, support = {PDCPN-2015-882//CONACYT/ ; FORDECYT-PRONACES 292399//CONACYT/ ; }, mesh = {Animals ; *Fusarium ; Antifungal Agents/metabolism ; Seedlings/microbiology ; *Coleoptera ; *Arabidopsis/microbiology ; *Weevils/microbiology ; Insecta ; Plant Diseases/microbiology ; }, abstract = {Plants interact with a great diversity of microorganisms or insects throughout their life cycle in the environment. Plant and insect interactions are common; besides, a great variety of microorganisms associated with insects can induce pathogenic damage in the host, as mutualist phytopathogenic fungus. However, there are other microorganisms present in the insect-fungal association, whose biological/ecological activities and functions during plant interaction are unknown. In the present work evaluated, the role of microorganisms associated with Xyleborus affinis, an important beetle species within the Xyleborini tribe, is characterized by attacking many plant species, some of which are of agricultural and forestry importance. We isolated six strains of microorganisms associated with X. affinis shown as plant growth-promoting activity and altered the root system architecture independent of auxin-signaling pathway in Arabidopsis seedlings and antifungal activity against the phytopathogenic fungus Fusarium sp. INECOL_BM-06. In addition, evaluating the tripartite interaction plant-microorganism-fungus, interestingly, we found that microorganisms can induce protection against the phytopathogenic fungus Fusarium sp. INECOL_BM-06 involving the jasmonic acid-signaling pathway and independent of salicylic acid-signaling pathway. Our results showed the important role of this microorganisms during the plant- and insect-microorganism interactions, and the biological potential use of these microorganisms as novel agents of biological control in the crops of agricultural and forestry is important.}, }
@article {pmid35357187, year = {2022}, author = {Holohan, BC and Duarte, MS and Szabo-Corbacho, MA and Cavaleiro, AJ and Salvador, AF and Pereira, MA and Ziels, RM and Frijters, CTMJ and Pacheco-Ruiz, S and Carballa, M and Sousa, DZ and Stams, AJM and O'Flaherty, V and van Lier, JB and Alves, MM}, title = {Principles, Advances, and Perspectives of Anaerobic Digestion of Lipids.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {8}, pages = {4749-4775}, doi = {10.1021/acs.est.1c08722}, pmid = {35357187}, issn = {1520-5851}, mesh = {Anaerobiosis ; Bioreactors ; Lipids ; Methane/metabolism ; *Sewage ; *Waste Disposal, Fluid ; Wastewater ; }, abstract = {Several problems associated with the presence of lipids in wastewater treatment plants are usually overcome by removing them ahead of the biological treatment. However, because of their high energy content, waste lipids are interesting yet challenging pollutants in anaerobic wastewater treatment and codigestion processes. The maximal amount of waste lipids that can be sustainably accommodated, and effectively converted to methane in anaerobic reactors, is limited by several problems including adsorption, sludge flotation, washout, and inhibition. These difficulties can be circumvented by appropriate feeding, mixing, and solids separation strategies, provided by suitable reactor technology and operation. In recent years, membrane bioreactors and flotation-based bioreactors have been developed to treat lipid-rich wastewater. In parallel, the increasing knowledge on the diversity of complex microbial communities in anaerobic sludge, and on interspecies microbial interactions, contributed to extend the knowledge and to understand more precisely the limits and constraints influencing the anaerobic biodegradation of lipids in anaerobic reactors. This critical review discusses the most important principles underpinning the degradation process and recent key discoveries and outlines the current knowledge coupling fundamental and applied aspects. A critical assessment of knowledge gaps in the field is also presented by integrating sectorial perspectives of academic researchers and of prominent developers of anaerobic technology.}, }
@article {pmid35355087, year = {2023}, author = {Zhang, W and Wan, W and Liu, X and Yang, Y and Liu, M}, title = {Stronger Geographic Limitations Shape a Rapid Turnover and Potentially Highly Connected Network of Core Bacteria on Microplastics.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1179-1189}, pmid = {35355087}, issn = {1432-184X}, support = {32071614//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Microplastics ; Plastics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Soil ; Water ; *Microbiota ; }, abstract = {Core microbiota is shared microbial taxa within the same habitat, which is important for understanding the stable and consistent components of the complex microbial assembly. However, information on the microplastic core bacteria from the river ecosystems is poor. Here, we investigated the composition and function of microplastic core bacteria from the Three Gorges Reservoir area along the approximate 662 km of the Yangtze River via full-length 16S rRNA gene sequencing, compared with those in water, sediment, and soil. The results showed that the spatial turnover of bacterial communities in four habitats supported deterministic processes dominated by niche differentiation, which shaped their core bacteria. The composition and function of microplastic core bacteria were significantly different from those in the other three habitats. Rhodobacteraceae was the main component of microplastic core bacteria, while the main component of core bacteria in water, sediment, and soil were Burkholderiaceae (21.90%), Burkholderiaceae (5.01%), Nitrosomonadaceae (4.61%), respectively. Furthermore, microplastic core bacteria had stronger geographic limitations along the Yangtze River in the Three Gorges Reservoir area. Stronger geographic limitations shaped the rapid community turnover and a potentially more connected network for the microplastic core bacteria than water, sediment, and soil. More importantly, microplastic core bacteria had strong potential functions of drug resistance and could cause risks to ecosystems and human health. Microplastic core bacteria were mainly influenced by sediment core bacteria, although the bacteria colonizing on microplastics could be from all the contact environments and original sources. These findings provide important insights into the composition, function, and association of microplastic core bacteria with their surrounding environment.}, }
@article {pmid35355086, year = {2023}, author = {Li, S and Peng, H and Shi, X and Gu, Q and Shen, Z and Wang, M}, title = {Significant Effects of Associated Microorganisms on the Community of Photosynthetic Picoeukaryotes.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1164-1178}, pmid = {35355086}, issn = {1432-184X}, support = {31800388//National Natural Science Foundation of China/ ; 32071573//National Natural Science Foundation of China/ ; }, mesh = {*Chlorophyta ; RNA, Ribosomal, 16S/genetics ; *Diatoms ; Photosynthesis ; *Stramenopiles/genetics ; Bacteria/genetics ; }, abstract = {Photosynthetic picoeukaryotes (PPEs) form associations with other microorganisms. However, whether and how the associated microbes affect PPE communities remain unknown. We used flow cytometric cell sorting combined with parallel high-throughput sequencing of the 18S and 16S rRNA genes to simultaneously investigate PPEs and their associated microbial communities in the Yangtze-connected Lake Dongting. The lake harbors a great diversity of PPEs. PPE communities exhibited significant temporal rather than spatial variations. Two distinct PPE taxa affiliated with Discostella nipponica and Poterioochromonas malhamensis were dominant during winter/spring and summer, respectively. Parallel high-throughput sequencing revealed a great diversity of associated bacteria and non-pigmented eukaryotes (NPEs) in PPEs sorts. Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria among the associated bacteria and fungi among the associated NPEs were dominant. PPEs were more apparently associated with bacteria than with NPEs. The co-occurrence network of PPEs and associated microbes formed five major modules, which exhibited distinct temporal patterns, being specific to a certain period. Variations in PPEs communities were significantly correlated with both environmental factors and associated microbial communities. In variation partitioning analysis, the associated bacteria explained the greatest variations in PPE communities, and associated bacteria and NPEs co-explained a large portion of environmental effects on PPE communities. Our results highlight the significance of associated microbes in shaping PPE communities.}, }
@article {pmid35353006, year = {2022}, author = {Emmons, AL and Mundorff, AZ and Hoeland, KM and Davoren, J and Keenan, SW and Carter, DO and Campagna, SR and DeBruyn, JM}, title = {Postmortem Skeletal Microbial Community Composition and Function in Buried Human Remains.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0004122}, pmid = {35353006}, issn = {2379-5077}, mesh = {Humans ; *Body Remains ; RNA, Ribosomal, 16S/analysis ; *Microbiota/genetics ; DNA ; Soil ; }, abstract = {Bones and teeth can provide a lasting resource to identify human remains following decomposition. Bone can support dynamic communities of micro- and macroscopic scavengers and incidental taxa, which influence the preservation of bone over time. Previously we identified key microbial taxa associated with survivability of DNA in bones of surface-decomposed human remains, observing high intra- and interindividual variation. Here we characterized the postmortem bone microbiome of skeletal remains in a multi-individual burial to better understand subsurface bone colonization and preservation. To understand microbial community origins and assembly, 16S rRNA amplicon sequences from 256 bone and 27 soil samples were compared to bone from individuals who decomposed on the ground surface, and human gut sequences from the American Gut Project. Untargeted metabolomics was applied to a subset of 41 bone samples from buried remains to examine potential microbe-metabolite interactions and infer differences related to community functionality. Results show that postmortem bone microbial communities are distinct from those of the oxic surface soils and the human gut. Microbial communities from surface-deposited bone and shallow buried bone were more similar to those from soils, while bones recovered from saturated areas deeper in the grave showed increased similarity with human gut samples with higher representation of anaerobic taxa, suggesting that the depositional environment affected the established bone microbiome. Correlations between metabolites and microbes indicate that phosphate solubilization is likely an important mechanism of microbially mediated skeletal degradation. This research expands our knowledge of microbial bone colonizers, including colonizers important in a burial environment. IMPORTANCE Understanding the microbes that colonize and degrade bone has important implications for preservation of skeletal elements and identification of unknown human remains. Current research on the postmortem bone microbiome is limited and largely focuses on archaeological or marine contexts. Our research expands our understanding of bone microbiomes in buried remains by characterizing the taxonomic and metabolic diversity of microbes that are colonizing bone after a 4-year postmortem burial interval and examines the potential impact of microbial colonization on human skeletal DNA preservation. Our results indicate that the postmortem bone microbiome is distinct from the human gut and soil. Evidence from combined metabolomic and amplicon sequencing analysis suggests that Pseudomonas and phosphate solubilization likely play a role in skeletal degradation. This work provides important insight into the types and activities of microbes controlling the preservation of buried skeletal remains.}, }
@article {pmid35352861, year = {2022}, author = {Rousk, J and C Brangarí, A}, title = {Do the respiration pulses induced by drying-rewetting matter for the soil-atmosphere carbon balance?.}, journal = {Global change biology}, volume = {28}, number = {11}, pages = {3486-3488}, pmid = {35352861}, issn = {1365-2486}, mesh = {Atmosphere ; Carbon ; Climate Change ; *Ecosystem ; Respiration ; *Soil ; Soil Microbiology ; }, abstract = {We show that the explosive microbial and biogeochemical dynamics triggered by rewetting dry soil in laboratory experiments also has relevance in intact ecosystems. This highlights an opportunity to use predictions derived from laboratory studies to provide targets in ecosystem-scale biogeochemical studies.}, }
@article {pmid35352237, year = {2022}, author = {Vissenaekens, H and Grootaert, C and Raes, K and De Munck, J and Smagghe, G and Boon, N and Van Camp, J}, title = {Quercetin Mitigates Endothelial Activation in a Novel Intestinal-Endothelial-Monocyte/Macrophage Coculture Setup.}, journal = {Inflammation}, volume = {45}, number = {4}, pages = {1600-1611}, pmid = {35352237}, issn = {1573-2576}, support = {1S18417N//FWO-Vlaanderen/ ; }, mesh = {*Atherosclerosis/drug therapy/metabolism ; Cell Adhesion ; Coculture Techniques ; Endothelial Cells/metabolism ; Endothelium, Vascular/metabolism ; Humans ; Intercellular Adhesion Molecule-1/metabolism ; Lipopolysaccharides/metabolism/pharmacology ; Macrophages/metabolism ; Monocytes/metabolism ; *Quercetin/pharmacology ; Tumor Necrosis Factor-alpha/metabolism ; }, abstract = {Atherosclerosis initiation is associated with a pro-inflammatory state of the endothelium. Quercetin is a flavonoid abundantly present in plant-based foods, with a possible impact on cardiovascular health. In this study, the effects of quercetin on lipopolysaccharide (LPS)-mediated endothelial inflammation and monocyte adhesion and migration, which are initial steps of the atherogenic process, are studied. Novel in vitro multicellular models simulating the intestinal-endothelial-monocytes/macrophages axis allowed to combine relevant intestinal flavonoid absorption, metabolism and efflux, and the consequent bioactivity towards peripheral endothelial cells. In this triple coculture, quercetin exposure decreased monocyte adhesion to and macrophage migration through an LPS-stressed endothelium, and this was associated with significantly lower levels of soluble vascular cell adhesion molecule-1 (sVCAM-1). Furthermore, quercetin decreased the pro-inflammatory cell environment upon LPS-induced endothelial activation, in terms of tumor necrosis factor- α (TNF-α), interleukin-6 (IL-6), interleukin-8 (IL-8), and sVCAM-1 expression. These findings highlight a mode-of-action by which quercetin may positively impact the initial states of atherosclerosis under more physiologically relevant conditions in terms of quercetin concentrations, metabolites, and intercellular crosstalk.}, }
@article {pmid35350577, year = {2022}, author = {Song, H and Xiao, K and Chen, Z and Long, Q}, title = {Analysis of Conjunctival Sac Microbiome in Dry Eye Patients With and Without Sjögren's Syndrome.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {841112}, pmid = {35350577}, issn = {2296-858X}, abstract = {PURPOSE: To analyze the conjunctival sac microbial communities in patients with Sjögren's syndrome-associated dry eyes (SSDE) and non-Sjögren's syndrome-associated dry eyes (NSSDE), compared with normal controls (NC).<br><br>METHODS: Conjunctival sac swab samples from 23 eyes of SSDE, 36 eyes of NSSDE, and 39 eyes of NC were collected. The V3-V4 region of the 16S ribosomal RNA (rRNA) gene high-throughput sequencing was performed on an Illumina MiSeq platform and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Alpha diversity was employed to analyze microbiome diversity through Chao1 and Shannon indexes. Beta diversity was demonstrated by the principal coordinates analysis (PCoA) and Partial Least Squares Discrimination Analysis (PLS-DA). The relative abundance was bioinformatically analyzed at the phylum and genus levels.<br><br>RESULTS: The alpha diversity was lower in patients with dry eye disease (Shannon index: NC vs. SSDE: P = 0.020, NC vs. NSSDE: P = 0.029). The beta diversity showed divergent microbiome composition in different groups (NC vs. SSDE: P = 0.001, NC vs. NSSDE: P = 0.001, NSSDE vs. SSDE: P = 0.005). The top 5 abundant phyla were Firmicutes, Proteobacteria, Actinobacteriota, Bacteroidota, and Cyanobacteria in all three groups. The top five abundant genera included Acinetobacter, Staphylococcus, Bacillus, Corynebacterium, and Clostridium_sensu_stricto_1. The relative microbiome abundance was different between groups. The Firmicutes/Bacteroidetes (F/B) ratio was 6.42, 7.31, and 9.71 in the NC, NSSDE, and SSDE groups, respectively (NC vs. SSDE: P = 0.038, NC vs. NSSDE: P = 0.991, SSDE vs. NSSDE: P = 0.048).<br><br>CONCLUSION: The diversity of conjunctival sac microbiome in patients with NSSDE and SSDE was diminished compared with NC. The main microbiome at the phylum and genus level were similar between groups, but the relative abundance had variations. The Firmicutes/Bacteroidetes ratio was higher in the SSDE group.}, }
@article {pmid35348389, year = {2022}, author = {Jiménez, RR and Carfagno, A and Linhoff, L and Gratwicke, B and Woodhams, DC and Chafran, LS and Bletz, MC and Bishop, B and Muletz-Wolz, CR}, title = {Inhibitory Bacterial Diversity and Mucosome Function Differentiate Susceptibility of Appalachian Salamanders to Chytrid Fungal Infection.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {8}, pages = {e0181821}, pmid = {35348389}, issn = {1098-5336}, mesh = {Animals ; Bacteria/genetics ; *Chytridiomycota/genetics ; *Mycoses/microbiology/veterinary ; RNA, Ribosomal, 16S/genetics ; Caudata/microbiology ; }, abstract = {Mucosal defenses are crucial in animals for protection against pathogens and predators. Host defense peptides (antimicrobial peptides, AMPs) as well as skin-associated microbes are key components of mucosal immunity, particularly in amphibians. We integrate microbiology, molecular biology, network-thinking, and proteomics to understand how host and microbially derived products on amphibian skin (referred to as the mucosome) serve as pathogen defenses. We studied defense mechanisms against chytrid pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), in four salamander species with different Batrachochytrium susceptibilities. Bd infection was quantified using qPCR, mucosome function (i.e., ability to kill Bd or Bsal zoospores in vitro), skin bacterial communities using 16S rRNA gene amplicon sequencing, and the role of Bd-inhibitory bacteria in microbial networks across all species. We explored the presence of candidate-AMPs in eastern newts and red-backed salamanders. Eastern newts had the highest Bd prevalence and mucosome function, while red-back salamanders had the lowest Bd prevalence and mucosome function, and two-lined salamanders and seal salamanders were intermediates. Salamanders with highest Bd infection intensity showed greater mucosome function. Bd infection prevalence significantly decreased as putative Bd-inhibitory bacterial richness and relative abundance increased on hosts. In co-occurrence networks, some putative Bd-inhibitory bacteria were found as hub-taxa, with red-backs having the highest proportion of protective hubs and positive associations related to putative Bd-inhibitory hub bacteria. We found more AMP candidates on salamanders with lower Bd susceptibility. These findings suggest that salamanders possess distinct innate mechanisms that affect chytrid fungi. IMPORTANCE How host mucosal defenses interact, and influence disease outcome is critical in understanding host defenses against pathogens. A more detailed understanding is needed of the interactions between the host and the functioning of its mucosal defenses in pathogen defense. This study investigates the variability of chytrid susceptibility in salamanders and the innate defenses each species possesses to mediate pathogens, thus advancing the knowledge toward a deeper understanding of the microbial ecology of skin-associated bacteria and contributing to the development of bioaugmentation strategies to mediate pathogen infection and disease. This study improves the understanding of complex immune defense mechanisms in salamanders and highlights the potential role of the mucosome to reduce the probability of Bd disease development and that putative protective bacteria may reduce likelihood of Bd infecting skin.}, }
@article {pmid35347426, year = {2022}, author = {Dyczko, D and Kiewra, D and Kolanek, A and Błażej, P}, title = {The influence of local environmental factors in southwestern Poland on the abundance of Ixodes ricinus and prevalence of infection with Borrelia burgdorferi s.l. and B. miyamotoi.}, journal = {Parasitology research}, volume = {121}, number = {6}, pages = {1575-1585}, pmid = {35347426}, issn = {1432-1955}, mesh = {Animals ; *Borrelia/genetics ; *Borrelia burgdorferi/genetics ; Female ; *Ixodes/microbiology ; *Lyme Disease/epidemiology/microbiology ; Male ; Poland/epidemiology ; Prevalence ; }, abstract = {Ticks are important ectoparasites and vectors of pathogens that cause disease in humans and animals. The natural habitat of Ixodes ricinus ticks is forests, which are convenient habitats to search for hosts, including reservoir hosts, and therefore can be an important habitat source of tick-borne pathogens. The aim of the study was to assess the usefulness of detailed forest habitat-type maps to estimate the tick-borne risk at a local scale (Lower Silesia, SW Poland). For the purposes of estimating tick abundance, we used the land cover maps available from the Forest Data Bank. For I. ricinus collection, nine sites located in three forest habitat types were chosen: broadleaf forest, mixed broadleaf and coniferous forest and coniferous forest. Ticks were collected once a month from April to June 2018 and 2019 using the standard flagging method. At each of the nine sites, ticks were collected in four plots, of 100 m[2] each. Tick abundance was analysed using general linear mixed models (GLMM). A total of 2196 (10.1/100 m[2]) ticks were collected, including 2093 Ixodes ricinus (95.3%; 9.6/100 m[2]), 46 Dermacentor reticulatus (2.1%; 0.2/100 m[2]) and 57 Haemaphysalis concinna (2.6%; 0.3/100 m[2]). Among the collected I. ricinus were 589 larvae (28.1%; 2.7/100 m[2]), 1261 nymphs (60.3%; 5.8/100 m[2]), 128 females (6.1%; 0.6/100 m[2]) and 115 males (5.5%; 0.5/100 m[2]). We found a highly significant effect of forest habitat type on the density of ticks for broadleaf forest (coefficient = 1.87267, p-value = 2.79e - 07). Additionally, a significant influence of air temperature and relative humidity on the abundance of ticks was observed. During spring, the peak activity of I. ricinus was recorded in May and June. For DNA amplification of Borrelia burgdorferi s.l., a nested PCR method was used. Out of 494 I. ricinus, 83 (16.8%) were positive for Borrelia spp. The RFLP method showed the occurrence of five species including four belonging to the B. burgdorferi s.l. complex: B. afzelii (30.1%), B. garinii (38.6%), B. valaisiana (2.4%) and B. lusitaniae (18.1%). Furthermore, B. miyamotoi (9.6%), a species belonging to bacteria that cause relapsing fever as well as co-infection of B. miyamotoi/B.lusitaniae (1.2%) were found. The differences in the infection level of Borrelia spp. between broadleaf forest and mixed broadleaf and coniferous forest were statistically significant.}, }
@article {pmid35347370, year = {2023}, author = {Vipindas, PV and Venkatachalam, S and Jabir, T and Yang, EJ and Cho, KH and Jung, J and Lee, Y and Krishnan, KP}, title = {Water Mass Controlled Vertical Stratification of Bacterial and Archaeal Communities in the Western Arctic Ocean During Summer Sea-Ice Melting.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1150-1163}, pmid = {35347370}, issn = {1432-184X}, mesh = {*Archaea/genetics ; *Water ; Bacteria/genetics ; Seawater/microbiology ; Chlorophyll ; Oceans and Seas ; Arctic Regions ; }, abstract = {The environmental variations and their interactions with the biosphere are vital in the Arctic Ocean during the summer sea-ice melting period in the current scenario of climate change. Hence, we analysed the vertical distribution of bacterial and archaeal communities in the western Arctic Ocean from sea surface melt-ponds to deep water up to a 3040 m depth. The distribution of microbial communities showed a clear stratification with significant differences among different water depths, and the water masses in the Arctic Ocean - surface mixed layer, Atlantic water mass and deep Arctic water - appeared as a major factor explaining their distribution in the water column. A total of 34 bacterial phyla were detected in the seawater and 10 bacterial phyla in melt-ponds. Proteobacteria was the dominant phyla in the seawater irrespective of depth, whereas Bacteroidota was the dominant phyla in the melt-ponds. A fast expectation-maximization microbial source tracking analysis revealed that only limited dispersion of the bacterial community was possible across the stratified water column. The surface water mass contributed 21% of the microbial community to the deep chlorophyll maximum (DCM), while the DCM waters contributed only 3% of the microbial communities to the deeper water masses. Atlantic water mass contributed 37% to the microbial community of the deep Arctic water. Oligotrophic heterotrophic bacteria were dominant in the melt-ponds and surface waters, whereas chemoautotrophic and mixotrophic bacterial and archaeal communities were abundant in deeper waters. Chlorophyll and ammonium were the major environmental factors that determined the surface microbial communities, whereas inorganic nutrient concentrations controlled the deep-water communities.}, }
@article {pmid35347228, year = {2022}, author = {Zoccarato, L and Sher, D and Miki, T and Segrè, D and Grossart, HP}, title = {A comparative whole-genome approach identifies bacterial traits for marine microbial interactions.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {276}, pmid = {35347228}, issn = {2399-3642}, support = {RGB 0020/2016//Human Frontier Science Program (HFSP)/ ; }, mesh = {*Bacteria/metabolism ; Ecology ; Microbial Interactions ; *Microbiota/genetics ; Phytoplankton/genetics ; }, abstract = {Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities. We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10% of genomes), phytohormones (3-8%) and different B vitamins (57-70%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions. Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics.}, }
@article {pmid35346496, year = {2022}, author = {Dittoe, DK and Olson, EG and Ricke, SC}, title = {Impact of the gastrointestinal microbiome and fermentation metabolites on broiler performance.}, journal = {Poultry science}, volume = {101}, number = {5}, pages = {101786}, pmid = {35346496}, issn = {1525-3171}, mesh = {Animal Feed/analysis ; Animals ; Chickens ; Diet/veterinary ; Fermentation ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/metabolism ; *Microbiota ; }, abstract = {Optimal broiler performance is dependent on several factors such as bird genetics, environment management, and nutrition. The gastrointestinal tract microbial ecology and metabolic activities have long been considered factors contributing to broiler performance responses. However, until recently, it was difficult to define the impact of the gastrointestinal microorganisms on the broiler host. With advances in microbiome sequencing technology, there has been a rapid increase in data generated using both experimental and commercial broiler operations. As the gastrointestinal microbiome data becomes more in-depth, opportunities to link microbiota composition to broiler performance metrics such as broiler growth rate and feed conversion efficiency have emerged. In parallel, with the increased understanding of the microbiota, there has been a shift to modulate the microbiome in order to alter metabolic patterns such as fermentation products. In this review, fermentation pathways and metabolites and the relationship with the microbiome will be discussed. Additionally, this review will connect these patterns and interpretations with current broiler performance data and the potential future directions these relationships could take the broiler industry.}, }
@article {pmid35346495, year = {2022}, author = {Ricke, SC and Dittoe, DK and Olson, EG}, title = {Microbiome applications for laying hen performance and egg production.}, journal = {Poultry science}, volume = {101}, number = {5}, pages = {101784}, pmid = {35346495}, issn = {1525-3171}, mesh = {Animals ; *Chickens ; Female ; Housing, Animal ; *Microbiota ; Reproduction ; }, abstract = {Management of laying hens has undergone considerable changes in the commercial egg industry. Shifting commercial production from cage-based systems to cage-free has impacted the housing environment and created issues not previously encountered. Sources of microorganisms that become established in the early stages of layer chick development may originate from the hen and depend on the microbial ecology of the reproductive tract. Development of the layer hen GIT microbiota appears to occur in stages as the bird matures. Several factors can impact the development of the layer hen GIT, including pathogens, environment, and feed additives such as antibiotics. In this review, the current status of the laying hen GIT microbial consortia and factors that impact the development and function of these respective microbial populations will be discussed, as well as future research directions.}, }
@article {pmid35346494, year = {2022}, author = {Olson, EG and Dittoe, DK and Jendza, JA and Stock, DA and Ricke, SC}, title = {Application of microbial analyses to feeds and potential implications for poultry nutrition.}, journal = {Poultry science}, volume = {101}, number = {5}, pages = {101789}, pmid = {35346494}, issn = {1525-3171}, mesh = {Animal Feed/analysis ; Animals ; Chickens ; *Gastrointestinal Microbiome ; Gastrointestinal Tract ; *Microbiota ; Poultry ; }, abstract = {Poultry nutrition and feed manufacturing are interrelated for a variety of reasons. Diet formulation is essential for optimizing bird growth and feed conversion, but compositional differences and the presence of certain feed additives can alter the gastrointestinal microbial composition and functionality. Not only does dietary composition and digestibility influence poultry performance, but specific physical characteristics such as feed particle size and thermal treatments can impact the avian gastrointestinal tract (GIT) microbiota. Poultry feeds also have a characteristic microbial ecology consisting of pathogenic and nonpathogenic microorganisms. Some feed-borne pathogens such as Salmonella are well studied and linked with the colonization of birds consuming the feed. However, much less is known about the nonpathogenic feed microbiome and what impact that might have on the bird's GIT. This review discusses the potential interaction between poultry feed and the GIT microbiome, microbial ecology of feed, application of microbiome analyses to feed, and approaches for communicating these complex data sets to the poultry industry.}, }
@article {pmid35346493, year = {2022}, author = {Ricke, SC and Dittoe, DK and Brown, JA and Thompson, DR}, title = {Practical opportunities for microbiome analyses and bioinformatics in poultry processing.}, journal = {Poultry science}, volume = {101}, number = {5}, pages = {101787}, pmid = {35346493}, issn = {1525-3171}, mesh = {Animals ; Chickens/genetics/microbiology ; Computational Biology ; Food Microbiology ; *Microbiota ; *Poultry/microbiology ; }, abstract = {Poultry processing is undergoing changes both in operations as well as microbial methodologies. Traditionally, microbial data has been gathered through a series of culturing methods using liquid media and plating for isolation and enumeration. Both foodborne pathogens and nonpathogenic bacterial populations are estimated to assess food safety risks as well as the potential for spoilage. Bacterial loads from carcasses are important for estimating processing control and the effectiveness of antimicrobial applications. However, these culture-based approaches may only provide part of the microbial ecology landscape associated with chicken carcasses and the subsequent changes that occur in these populations during processing. Newer molecular-based approaches, such as 16S sequencing of the microbiota, offer a means to retrieve a more comprehensive microbial compositional profile. However, such approaches also result in large data sets which must be analyzed and interpreted. As more data is generated, this will require not only bioinformatic programs to process the data but appropriate educational forums to present the processed data to a broad audience.}, }
@article {pmid35343797, year = {2022}, author = {Busby, TJ and Miller, CR and Moran, NA and Van Leuven, JT}, title = {Global Composition of the Bacteriophage Community in Honey Bees.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0119521}, pmid = {35343797}, issn = {2379-5077}, support = {P20 GM104420/GM/NIGMS NIH HHS/United States ; }, mesh = {Bees ; Animals ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics ; Bacteria/genetics ; *Microbiota ; Plants ; }, abstract = {The microbial communities in animal digestive systems are critical for host development and health. They stimulate the immune system during development, synthesize important chemical compounds like hormones, aid in digestion, competitively exclude pathogens, etc. Compared to the bacterial and fungal components of the microbiome, we know little about the temporal and spatial dynamics of bacteriophage communities in animal digestive systems. Recently, the bacteriophages of the honey bee gut were characterized in two European bee populations. Most of the bacteriophages described in these two reports were novel, harbored many metabolic genes in their genomes, and had a community structure that suggests coevolution with their bacterial hosts. To describe the conservation of bacteriophages in bees and begin to understand their role in the bee microbiome, we sequenced the virome of Apis mellifera from Austin, TX, and compared bacteriophage compositions among three locations around the world. We found that most bacteriophages from Austin are novel, sharing no sequence similarity with anything in public repositories. However, many bacteriophages are shared among the three bee viromes, indicating specialization of bacteriophages in the bee gut. Our study, along with the two previous bee virome studies, shows that the bee gut bacteriophage community is simple compared to that of many animals, consisting of several hundred types of bacteriophages that primarily infect four of the dominant bacterial phylotypes in the bee gut. IMPORTANCE Viruses that infect bacteria (bacteriophages) are abundant in the microbial communities that live on and in plants and animals. However, our knowledge of the structure, dynamics, and function of these viral communities lags far behind our knowledge of their bacterial hosts. We sequenced the first bacteriophage community of honey bees from the United States and compared the U.S. honey bee bacteriophage community to those of samples from Europe. Our work is an important characterization of an economically critical insect species and shows how bacteriophage communities can contain highly conserved individuals and be highly variable in composition across a wide geographic range.}, }
@article {pmid35343791, year = {2022}, author = {Zhu, YX and Chang, YW and Wen, T and Yang, R and Wang, YC and Wang, XY and Lu, MX and Du, YZ}, title = {Species Identity Dominates over Environment in Driving Bacterial Community Assembly in Wild Invasive Leaf Miners.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0026622}, pmid = {35343791}, issn = {2165-0497}, mesh = {Animals ; *Bacteria/genetics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Soil ; Soil Microbiology ; }, abstract = {The microbiota of invasive animal species may be pivotal to their adaptation and spread, yet the processes driving the assembly and potential sources of host-microbiota remain poorly understood. Here, we characterized microbiota of four Liriomyza leaf miner fly species totaling 310 individuals across 43 geographical populations in China and assessed whether the microbiota of the wild leaf miner was acquired from the soil microbiota or the host plant microbiota, using high-throughput 16S rRNA sequencing. Bacterial communities differed significantly among four leaf miner species but did not mirror host phylogeny. Microbiota diversity in the native L. chinensis was significantly higher than in three invasive leaf miners (i.e., L. trifolii, L. huidobrensis, and L. sativae), yet the microbial community of the invasive species exhibited a more connected and complex network structure. Structural equation models revealed that host species identity was more important than environmental factors (e.g., geography, climate, or plants) in shaping microbiota composition. Using neutral and null model analyses, we found that deterministic processes like variable selection played a primary role in driving microbial community assembly, with some influence by stochastic processes like drift. The relative degree of these processes governing microbiota was likely correlated with host species but independent of either geographical or climatic factors. Finally, source tracking analysis showed that leaf miners might acquire microbes from their host plant rather than the soil. Our results provide a robust assessment of the ecological processes governing bacterial community assembly and potential sources of microbes in invasive leaf miners. IMPORTANCE The invasion of foreign species, including leaf miners, is a major threat to world biota. Host-associated microbiota may facilitate host adaption and expansion in a variety of ways. Thus, understanding the processes that drive leaf miner microbiota assembly is imperative for better management of invasive species. However, how microbial communities assemble during the leaf miner invasions and how predictable the processes remain unexplored. This work quantitatively deciphers the relative importance of deterministic process and stochastic process in governing the assembly of four leaf miner microbiotas and identifies potential sources of leaf miner-colonizing microbes from the soil-plant-leaf miner continuum. Our study provides new insights into the mechanisms underlying the drive of leaf miner microbiota assembly.}, }
@article {pmid35340445, year = {2022}, author = {Parks, ST and Taylor, C}, title = {Development of a Remote, Course-Based Undergraduate Experience to Facilitate In Silico Study of Microbial Metabolic Pathways.}, journal = {Journal of microbiology &amp; biology education}, volume = {23}, number = {1}, pages = {}, pmid = {35340445}, issn = {1935-7877}, abstract = {Course-based undergraduate research experiences (CUREs) often occur in a physical lab space, but they can also be offered remotely while maintaining course expectations and providing opportunity for authentic student engagement in research. Using a novel framework, remote Microbial Ecology CURE students used microbes isolated via antimicrobial-challenged Winogradsky columns to investigate phylogeny and metabolism through a hypothesis-driven meta-analysis (MA). Students used 16S rRNA and key metabolic enzymes to compare phylogeny; enzymes were modeled and evaluated for putative conserved domains, culminating in primer design and analysis. Using in silico tools facilitated student development of bioinformatics skills. The MA was subdivided into discrete sections in order to (i) provide a timeline for students to remain on schedule throughout a remote-learning lab experience, (ii) encourage feedback throughout the project, and (iii) facilitate student understanding of the experimental design. MA deliverables were designed to be specific figures with individual titles, legends, and analyses to enable their feedback for subsequent presentations. The six key formative deliverables included a word cloud (used to develop the works cited list and hypothesis), a 16S rRNA phylogenetic tree, an annotated metabolic pathway and three-dimensional model of the key metabolic enzyme, a phylogenetic tree based on the key metabolic enzyme, design and analysis of a primer set for the key metabolic enzyme, and a summative poster and graphical abstract. The MA project yielded poster presentations at virtual conferences, lab presentations, and written reports. Using the hypothesis-based MA model encouraged an authentic research experience, enabling students to develop, discuss, and progress in meaningful experiments.}, }
@article {pmid35338380, year = {2023}, author = {Yuan, B and Guo, M and Wu, W and Zhou, X and Li, M and Xie, S}, title = {Spatial and Seasonal Patterns of Sediment Bacterial Communities in Large River Cascade Reservoirs: Drivers, Assembly Processes, and Co-occurrence Relationship.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {586-603}, pmid = {35338380}, issn = {1432-184X}, support = {91747206//national natural science foundation of china/ ; 42107493//National Natural Science Foundation of China/ ; }, mesh = {*Rivers/microbiology ; *Ecosystem ; Seasons ; Bacteria ; Fresh Water ; China ; }, abstract = {Sediment bacteria play an irreplaceable role in promoting the function and biogeochemical cycle of the freshwater ecosystem; however, little is known about their biogeographical patterns and community assembly mechanisms in large river suffering from cascade development. Here, we investigated the spatiotemporal distribution patterns of bacterial communities employing next-generation sequencing analysis and multivariate statistical analyses from the Lancang River cascade reservoirs during summer and winter. We found that sediment bacterial composition has a significant seasonal turnover due to the modification of cascade reservoirs operation mode, and the spatial consistency of biogeographical models (including distance-decay relationship and covariation of community composition with geographical distance) also has subtle changes. The linear regression between the dissimilarity of bacterial communities in sediments, geographical and environmental distance showed that the synergistic effects of geographical and environmental factors explained the influence on bacterial communities. Furthermore, the environmental difference explained little variations (19.40%) in community structure, implying the homogeneity of environmental conditions across the cascade reservoirs of Lancang River. From the quantification of the ecological process, the homogeneous selection was recognized as the dominating factor of bacterial community assembly. The co-occurrence topological network analyses showed that the key genera were more important than the most connected genera. In general, the assembly of bacterial communities in sediment of cascade reservoirs was mediated by both deterministic and stochastic processes and is always dominated by homogeneous selection with the seasonal switching, but the effects of dispersal limitation and ecological drift cannot be ignored.}, }
@article {pmid35337832, year = {2022}, author = {Venturini, AM and Dias, NMS and Gontijo, JB and Yoshiura, CA and Paula, FS and Meyer, KM and Nakamura, FM and da França, AG and Borges, CD and Barlow, J and Berenguer, E and Nüsslein, K and Rodrigues, JLM and Bohannan, BJM and Tsai, SM}, title = {Increased soil moisture intensifies the impacts of forest-to-pasture conversion on methane emissions and methane-cycling communities in the Eastern Amazon.}, journal = {Environmental research}, volume = {212}, number = {Pt A}, pages = {113139}, doi = {10.1016/j.envres.2022.113139}, pmid = {35337832}, issn = {1096-0953}, mesh = {Climate ; Forests ; *Methane/analysis ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {Climatic changes are altering precipitation patterns in the Amazon and may influence soil methane (CH4) fluxes due to the differential responses of methanogenic and methanotrophic microorganisms. However, it remains unclear if these climate feedbacks can amplify land-use-related impacts on the CH4 cycle. To better predict the responses of soil CH4-cycling microorganisms and emissions under altered moisture levels in the Eastern Brazilian Amazon, we performed a 30-day microcosm experiment manipulating the moisture content (original moisture; 60%, 80%, and 100% of field capacity - FC) of forest and pasture soils. Gas samples were collected periodically for gas chromatography analysis, and methanogenic archaeal and methanotrophic bacterial communities were assessed using quantitative PCR and metagenomics. Positive and negative daily CH4 fluxes were observed for forest and pasture, indicating that these soils can act as both CH4 sources and sinks. Cumulative emissions and the abundance of methanogenesis-related genes and taxonomic groups were affected by land use, moisture, and their interaction. Pasture soils at 100% FC had the highest abundance of methanogens and CH4 emissions, 22 times higher than forest soils under the same treatment. Higher ratios of methanogens to methanotrophs were found in pasture than in forest soils, even at field capacity conditions. Land use and moisture were significant factors influencing the composition of methanogenic and methanotrophic communities. The diversity and evenness of methanogens did not change throughout the experiment. In contrast, methanotrophs exhibited the highest diversity and evenness in pasture soils at 100% FC. Taken together, our results suggest that increased moisture exacerbates soil CH4 emissions and microbial responses driven by land-use change in the Amazon. This is the first report on the microbial CH4 cycle in Amazonian upland soils that combined one-month gas measurements with advanced molecular methods.}, }
@article {pmid35335680, year = {2022}, author = {Morris, CE and Ramirez, N and Berge, O and Lacroix, C and Monteil, C and Chandeysson, C and Guilbaud, C and Blischke, A and Sigurbjörnsdóttir, MA and Vilhelmsson, O&#xde;}, title = {Pseudomonas syringae on Plants in Iceland Has Likely Evolved for Several Million Years Outside the Reach of Processes That Mix This Bacterial Complex across Earth's Temperate Zones.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {3}, pages = {}, pmid = {35335680}, issn = {2076-0817}, abstract = {Here we report, for the first time, the occurrence of the bacteria from the species complex Pseudomonas syringae in Iceland. We isolated this bacterium from 35 of the 38 samples of angiosperms, moss, ferns and leaf litter collected across the island from five habitat categories (boreal heath, forest, subalpine and glacial scrub, grazed pasture, lava field). The culturable populations of P. syringae on these plants varied in size across 6 orders of magnitude, were as dense as 10[7] cfu g[-1] and were composed of strains in phylogroups 1, 2, 4, 6, 7, 10 and 13. P. syringae densities were significantly greatest on monocots compared to those on dicots and mosses and were about two orders of magnitude greater in grazed pastures compared to all other habitats. The phylogenetic diversity of 609 strains of P. syringae from Iceland was compared to that of 933 reference strains of P. syringae from crops and environmental reservoirs collected from 27 other countries based on a 343 bp sequence of the citrate synthase (cts) housekeeping gene. Whereas there were examples of identical cts sequences across multiple countries and continents among the reference strains indicating mixing among these countries and continents, the Icelandic strains grouped into monophyletic lineages that were unique compared to all of the reference strains. Based on estimates of the time of divergence of the Icelandic genetic lineages of P. syringae, the geological, botanical and land use history of Iceland, and atmospheric circulation patterns, we propose scenarios whereby it would be feasible for P. syringae to have evolved outside the reach of processes that tend to mix this bacterial complex across the planet elsewhere.}, }
@article {pmid35335670, year = {2022}, author = {Chitlapilly Dass, S and Wang, R}, title = {Biofilm through the Looking Glass: A Microbial Food Safety Perspective.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {3}, pages = {}, pmid = {35335670}, issn = {2076-0817}, support = {USDA-NIFA 2020-67017-30776.//United States Department of Agriculture/ ; }, abstract = {Food-processing facilities harbor a wide diversity of microorganisms that persist and interact in multispecies biofilms, which could provide an ecological niche for pathogens to better colonize and gain tolerance against sanitization. Biofilm formation by foodborne pathogens is a serious threat to food safety and public health. Biofilms are formed in an environment through synergistic interactions within the microbial community through mutual adaptive response to their long-term coexistence. Mixed-species biofilms are more tolerant to sanitizers than single-species biofilms or their planktonic equivalents. Hence, there is a need to explore how multispecies biofilms help in protecting the foodborne pathogen from common sanitizers and disseminate biofilm cells from hotspots and contaminate food products. This knowledge will help in designing microbial interventions to mitigate foodborne pathogens in the processing environment. As the global need for safe, high-quality, and nutritious food increases, it is vital to study foodborne pathogen behavior and engineer new interventions that safeguard food from contamination with pathogens. This review focuses on the potential food safety issues associated with biofilms in the food-processing environment.}, }
@article {pmid35333990, year = {2022}, author = {Sugiyama, N and Uehara, O and Morikawa, T and Paudel, D and Ebata, K and Hiraki, D and Harada, F and Yoshida, K and Kato, S and Nagasawa, T and Miura, H and Abiko, Y and Furuichi, Y}, title = {Gut flora alterations due to lipopolysaccharide derived from Porphyromonas gingivalis.}, journal = {Odontology}, volume = {110}, number = {4}, pages = {673-681}, pmid = {35333990}, issn = {1618-1255}, support = {20H03867//Grant-in-Aid for Scientific Research (B)/ ; }, mesh = {Animals ; Dysbiosis ; *Gastrointestinal Microbiome ; Interleukin-6 ; Lipopolysaccharides/pharmacology ; Mice ; Mice, Inbred C57BL ; *Porphyromonas gingivalis ; RNA, Ribosomal, 16S ; Tumor Necrosis Factor-alpha ; }, abstract = {Gut dysbiosis induces 'leaky gut,' a condition associated with diabetes, NASH, and various auto-immune diseases. Porphyromonas gingivalis is a periodontopathic bacterium which causes periodontal tissue breakdown, and often enters the systemic blood flow. Oral administration of P. gingivalis induced gut dysbiosis in mice model, but no systemic administration of P. gingivalis has been reported thus far. In the present study, we investigated the effect of P. gingivalis-derived lipopolysaccharide (Pg-LPS) on the intestinal flora of our established mouse model. Eight-week-old C57BL/6J mice were intraperitoneally administered Pg-LPS. Three months later, DNA was extracted from stool, and RNA from the small and large intestines. After euthanizing the mice, pathological sections of the intestinal tract were prepared and stained with hematoxylin and eosin (H&amp;E). Tumor necrosis factor alpha (TNF-α), interleukin (IL)-1β, and IL-6 expression levels were evaluated using quantitative PCR. 16S rRNA gene PCR amplicon analysis data were acquired using NGS. Microbial diversity and composition were analyzed using Quantitative Insights into Microbial Ecology 2. Furthermore, alterations in microbial function were performed by PICRUSt2. No significant inflammatory changes were observed in the H&amp;E. No significant differences in the mRNA levels of IL-1β, IL-6, and TNF-α were observed between the groups. Pg-LPS administration decreased the abundance of Allobacterium in the gut. A predictive metagenomic analysis by PICRUSt2 and STAMP showed that 47 pathways increased and 17 pathways decreased after Pg-LPS administration. Systemic application of periodontal pathogens may cause changes in the intestinal flora which may affect the physiological functions of the intestinal tract.}, }
@article {pmid35333950, year = {2023}, author = {Angra, V and Sehgal, R and Gupta, R}, title = {Trends in PHA Production by Microbially Diverse and Functionally Distinct Communities.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {572-585}, pmid = {35333950}, issn = {1432-184X}, support = {09/237(0168)/2018-EMR-I//Council&#xa0;of&#xa0;Scientific and Industrial Research, India/ ; }, mesh = {Biopolymers ; *Polyhydroxyalkanoates ; Plastics ; Plants ; *Petroleum ; }, abstract = {Along with the wide applications of conventional plastics, they have a large number of disadvantages like their non-biodegradable nature, dependency on fossil fuels and the release of large amounts of toxic materials in the environment. Therefore, to resolve these problems, a number of bioplastics are studied, out of which polyhydroxyalkanoates are considered as the best alternatives. Polyhydroxyalkanoates (PHAs) are produced by microorganisms as intracellular granules during stressful conditions. Though a wide range of organisms can naturally produce PHAs, only a few of them can be used for commercial production. Therefore, more diverse organisms that accumulate a considerable amount of PHAs and also reduce the production cost need to be exploited. Transgenic plants, recombinant bacteria, algae and extremophiles are some diverse organisms that produce a high amount of PHAs at a low cost. So, if potential organisms are used for PHA production, bioplastics will be able to completely replace petroleum-based polymers. Therefore, our review mainly focuses on production of PHAs using potential organisms so that amount of PHAs produced is high and cost-effective which would further help in the commercialization of PHAs.}, }
@article {pmid35332832, year = {2022}, author = {Crits-Christoph, A and Hallowell, HA and Koutouvalis, K and Suez, J}, title = {Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2055944}, pmid = {35332832}, issn = {1949-0984}, support = {DP5 OD029603/OD/NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Genes, Bacterial ; Humans ; Metagenomics ; *Microbiota/genetics ; }, abstract = {A global rise in antimicrobial resistance among pathogenic bacteria has proved to be a major public health threat, with the rate of multidrug-resistant bacterial infections increasing over time. The gut microbiome has been studied as a reservoir of antibiotic resistance genes (ARGs) that can be transferred to bacterial pathogens via horizontal gene transfer (HGT) of conjugative plasmids and mobile genetic elements (the gut resistome). Advances in metagenomic sequencing have facilitated the identification of resistome modulators, including live microbial therapeutics such as probiotics and fecal microbiome transplantation that can either expand or reduce the abundances of ARG-carrying bacteria in the gut. While many different gut microbes encode for ARGs, they are not uniformly distributed across, or transmitted by, various members of the microbiome, and not all are of equal clinical relevance. Both experimental and theoretical approaches in microbial ecology have been applied to understand differing frequencies of ARG horizontal transfer between commensal microbes as well as between commensals and pathogens. In this commentary, we assess the evidence for the role of commensal gut microbes in encoding antimicrobial resistance genes, the degree to which they are shared both with other commensals and with pathogens, and the host and environmental factors that can impact resistome dynamics. We further discuss novel sequencing-based approaches for identifying ARGs and predicting future transfer events of clinically relevant ARGs from commensals to pathogens.}, }
@article {pmid35332366, year = {2023}, author = {Xiang, X and Wang, H and Man, B and Xu, Y and Gong, L and Tian, W and Yang, H}, title = {Diverse Bathyarchaeotal Lineages Dominate Archaeal Communities in the Acidic Dajiuhu Peatland, Central China.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {557-571}, pmid = {35332366}, issn = {1432-184X}, support = {41572325//National Natural Science Foundation of China/ ; CUGQY1922//Fundamental Research Funds for the Central Universities, China University of Geosciences (Wuhan)/ ; 2021F10//Open Research Fund of Hubei Key Laboratory of Critical Zone Evolution, China University of Geosciences, Wuhan, China/ ; }, mesh = {*Archaea ; *Ecosystem ; Geologic Sediments/chemistry ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Soil ; China ; DNA, Archaeal/genetics ; Phylogeny ; }, abstract = {Bathyarchaeota are believed to have roles in the carbon cycle in marine systems. However, the ecological knowledge of Bathyarchaeota is limited in peatland ecosystems. Here, we investigated the vertical distribution of Bathyarchaeota community structure using quantitative PCR and high-throughput sequencing technology of ribosomal 16S rRNA gene integrated with detailed chemical profiling in the Dajiuhu Peatland, central China. Eight archaeal phyla were observed in peat samples, which mainly composed of Bathyarchaeota with a mean relative abundance about 88%, followed by Thaumarchaeota (9%). Bathyarchaeota were further split into 17 subgroups, and some subgroups showed habitat specificity to peat horizons with distinct lithological and physicochemical properties, for example, Bathy-6 and Bathy-15 had preference for the acrotelm, Bathy-5b, Bathy-16, and Bathy-19 were enriched in the catotelm, Bathy-5a, Bathy-8, and Bathy-11 were specific for the clay horizon. This spatial distribution pattern of archaeal communities along peat profile was mainly influenced by water content as indicated by RDA ordination and permutational MANOVA, whereas organic matter content exclusively affected Bathyarchaeota distribution along the peat profile significantly. The abundance of archaeal 16S rRNA genes ranged from 10[5] to 10[7] copies per gram dry sediment, and the highest archaeal biomass was observed in the periodically oxic mesotelm horizon with more dynamic archaeal interaction relationship as indicated by the network analysis. Bathyarchaeota dominated the archaeal interaction network with 82% nodes, 96% edges, and 71% keystone species. Our results provide an overview of the archaeal population, community structure, and relationship with environmental factors that affect the vertical distribution of archaeal communities and emphasize the ecology of bathyarchaeotal lineages in terrestrial peatland ecosystems.}, }
@article {pmid35331758, year = {2022}, author = {Fang, W and Lin, M and Shi, J and Liang, Z and Tu, X and He, Z and Qiu, R and Wang, S}, title = {Organic carbon and eukaryotic predation synergistically change resistance and resilience of aquatic microbial communities.}, journal = {The Science of the total environment}, volume = {830}, number = {}, pages = {154386}, doi = {10.1016/j.scitotenv.2022.154386}, pmid = {35331758}, issn = {1879-1026}, mesh = {Animals ; *Carbon ; Eukaryota ; *Microbiota ; Predatory Behavior ; Rivers ; Water ; }, abstract = {With rapid global urbanization, anthropogenic activities alter aquatic biota in urban rivers through inputs of dissolved organic carbon (DOC) and nutrients. Microorganisms-mediated global element cycles provide functions in maintaining microbial ecology stability. The DOC (bottom-up control) and microbial predation (top-down control) may synergistically drive the competition and evolution of aquatic microbial communities, as well as their resistance and resilience, for which experimental evidences remain scarce. In this study, laboratory sediment-water column experiments were employed to mimic the organic carbon-driven water blackening and odorization process in urban rivers and to elucidate the impact of DOC on microbial ecology stability. Results showed that low (25-75 mg/L) and high DOC (100-150 mg/L) changed the aquatic microbial community assemblies in different patterns: (1) the low DOC enriched K-selection microorganisms (e.g., C39, Tolumonas and CR08G) with low biomass and low resilience, as well as high resistance to perturbations in changing microbial community assemblies; (2) the high DOC was associated with r-selection microorganisms (e.g., PSB-M-3 and Clostridium) with high biomass and improved resilience, together with low resistance detrimental to microbial ecology stability. Overall, this study provided new insight into the impact of DOC on aquatic microbial community stability, which may help guide sustainable urban river management.}, }
@article {pmid35330304, year = {2022}, author = {Fatemi, S and Haelewaters, D and Urbina, H and Brown, S and Houston, ML and Aime, MC}, title = {Sporobolomyces lactucae sp. nov. (Pucciniomycotina, Microbotryomycetes, Sporidiobolales): An Abundant Component of Romaine Lettuce Phylloplanes.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {3}, pages = {}, pmid = {35330304}, issn = {2309-608X}, support = {8072-42000-077-00D//Agricultural Research Service/ ; 1010662//National Institute of Food and Agriculture/ ; }, abstract = {Shifts in food microbiomes may impact the establishment of human pathogens, such as virulent lineages of Escherichia coli, and thus are important to investigate. Foods that are often consumed raw, such as lettuce, are particularly susceptible to such outbreaks. We have previously found that an undescribed Sporobolomyces yeast is an abundant component of the mycobiome of commercial romaine lettuce (Lactuca sativa). Here, we formally describe this species as Sporobolomyces lactucae sp. nov. (Pucciniomycotina, Microbotryomycetes, and Sporidiobolales). We isolated multiple strains of this yeast from commercial romaine lettuce purchased from supermarkets in Illinois and Indiana; additional isolates were obtained from various plant phylloplanes in California. S. lactucae is a red-pigmented species that is similar in appearance to other members of the genus Sporobolomyces. However, it can be differentiated by its ability to assimilate glucuronate and D-glucosamine. Gene genealogical concordance supports S. lactucae as a new species. The phylogenetic reconstruction of a four-locus dataset, comprising the internal transcribed spacer and large ribosomal subunit D1/D2 domain of the ribosomal RNA gene, translation elongation factor 1-α, and cytochrome B, places S. lactucae as a sister to the S. roseus clade. Sporobolomyces lactucae is one of the most common fungi in the lettuce microbiome.}, }
@article {pmid35322937, year = {2022}, author = {Timmis, K and Ramos, JL and Verstraete, W}, title = {Microbial biotechnology to assure national security of supplies of essential resources: energy, food and water, medical reagents, waste disposal and a circular economy.}, journal = {Microbial biotechnology}, volume = {15}, number = {4}, pages = {1021-1025}, pmid = {35322937}, issn = {1751-7915}, mesh = {Biotechnology ; Food ; Indicators and Reagents ; *Refuse Disposal ; Security Measures ; *Waste Management ; Wastewater ; Water ; }, abstract = {The core responsibility of governments is the security of their citizens, and this means inter alia protecting their safety, nutrition and health. Microbiology and microbial biotechnology have key roles to play in improving supply security of essential resources. In this paper, we discuss the urgent need to fully and immediately exploit existing microbial biotechnologies to maximize supply security of energy, food and medical supplies, and of waste management, and to invest in new research specifically targetting supply security of essential resources.}, }
@article {pmid35320603, year = {2022}, author = {Kohler, TJ and Fodelianakis, S and Michoud, G and Ezzat, L and Bourquin, M and Peter, H and Busi, SB and Pramateftaki, P and Deluigi, N and Styllas, M and Tolosano, M and de Staercke, V and Schön, M and Brandani, J and Marasco, R and Daffonchio, D and Wilmes, P and Battin, TJ}, title = {Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function.}, journal = {Global change biology}, volume = {28}, number = {12}, pages = {3846-3859}, pmid = {35320603}, issn = {1365-2486}, mesh = {Bacteria/genetics ; Climate Change ; Ecosystem ; *Ice Cover/microbiology ; *Microbiota ; Phylogeny ; Water ; }, abstract = {The shrinking of glaciers is among the most iconic consequences of climate change. Despite this, the downstream consequences for ecosystem processes and related microbiome structure and function remain poorly understood. Here, using a space-for-time substitution approach across 101 glacier-fed streams (GFSs) from six major regions worldwide, we investigated how glacier shrinkage is likely to impact the organic matter (OM) decomposition rates of benthic biofilms. To do this, we measured the activities of five common extracellular enzymes and estimated decomposition rates by using enzyme allocation equations based on stoichiometry. We found decomposition rates to average 0.0129 (% d[-1]), and that decreases in glacier influence (estimated by percent glacier catchment coverage, turbidity, and a glacier index) accelerates decomposition rates. To explore mechanisms behind these relationships, we further compared decomposition rates with biofilm and stream water characteristics. We found that chlorophyll-a, temperature, and stream water N:P together explained 61% of the variability in decomposition. Algal biomass, which is also increasing with glacier shrinkage, showed a particularly strong relationship with decomposition, likely indicating their importance in contributing labile organic compounds to these carbon-poor habitats. We also found high relative abundances of chytrid fungi in GFS sediments, which putatively parasitize these algae, promoting decomposition through a fungal shunt. Exploring the biofilm microbiome, we then sought to identify bacterial phylogenetic clades significantly associated with decomposition, and found numerous positively (e.g., Saprospiraceae) and negatively (e.g., Nitrospira) related clades. Lastly, using metagenomics, we found evidence of different bacterial classes possessing different proportions of EEA-encoding genes, potentially informing some of the microbial associations with decomposition rates. Our results, therefore, present new mechanistic insights into OM decomposition in GFSs by demonstrating that an algal-based "green food web" is likely to increase in importance in the future and will promote important biogeochemical shifts in these streams as glaciers vanish.}, }
@article {pmid35316575, year = {2022}, author = {Timmis, K and Verstraete, W}, title = {Multiple intertwined crises facing humanity necessitate a European Environmental Research Organization.}, journal = {Microbial biotechnology}, volume = {15}, number = {4}, pages = {1031-1034}, pmid = {35316575}, issn = {1751-7915}, abstract = {The planet is experiencing all manner of environmental crises, and crises that have their origins in the environment, including global warming, pollution of the air, soil, marine systems and freshwater, loss of habitats and species extinctions, transmission of deadly animal infections to humans, the spread of antimicrobial resistance, to name just a few. Planetary boundaries are being successively breached. Devising and implementing optimal solution and mitigation strategies urgently requires the best possible scientific brains to be harnessed and focused on environmental crises. It is imperative to establish authoritative leadership and the intellectual and organisational framework for this: a European Environmental Research Organisation, modelled on the European Molecular Biology Organisation (EMBO) and Laboratory (EMBL), whose mission is to carry out pioneering research on environmental crisis‐relevant topics, communicate its findings and recommendations to governments, their agencies, the general public, business and other stakeholders, and create outstanding research leaders to populate the best institutions worldwide – a global network of top scientists working together to understand the causes and nature of crises and to devise effective solutions.}, }
@article {pmid35316402, year = {2022}, author = {Tiwari, N and Bansal, M and Santhiya, D and Sharma, JG}, title = {Insights into microbial diversity on plastisphere by multi-omics.}, journal = {Archives of microbiology}, volume = {204}, number = {4}, pages = {216}, pmid = {35316402}, issn = {1432-072X}, mesh = {Biodegradation, Environmental ; *Ecosystem ; High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; Plastics ; }, abstract = {Plastic pollution is a major concern in marine environment as it takes many years to degrade and is one of the greatest threats to marine life. Plastic surface, referred to as plastisphere, provides habitat for growth and proliferation of various microorganisms. The discovery of these microbes is necessary to identify significant genes, enzymes and bioactive compounds that could help in bioremediation and other commercial applications. Conventional culture techniques have been successful in identifying few microbes from these habitats, leaving majority of them yet to be explored. As such, to recognize the vivid genetic diversity of microbes residing in plastisphere, their structure and corresponding ecological roles within the ecosystem, an emerging technique, called metagenomics has been explored. The technique is expected to provide hitherto unknown information on microbes from the plastisphere. Metagenomics along with next generation sequencing provides comprehensive knowledge on microbes residing in plastisphere that identifies novel microbes for plastic bioremediation, bioactive compounds and other potential benefits. The following review summarizes the efficiency of metagenomics and next generation sequencing technology over conventionally used methods for culturing microbes. It attempts to illustrate the workflow mechanism of metagenomics to elucidate diverse microbial profiles. Further, importance of integrated multi-omics techniques has been highlighted in discovering microbial ecology residing on plastisphere for wider applications.}, }
@article {pmid35316343, year = {2023}, author = {Dallas, JW and Warne, RW}, title = {Captivity and Animal Microbiomes: Potential Roles of Microbiota for Influencing Animal Conservation.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {820-838}, pmid = {35316343}, issn = {1432-184X}, mesh = {Animals ; *Microbiota ; Biodiversity ; Diet ; Bacteria/genetics ; Skin/microbiology ; }, abstract = {During the ongoing biodiversity crisis, captive conservation and breeding programs offer a refuge for species to persist and provide source populations for reintroduction efforts. Unfortunately, captive animals are at a higher disease risk and reintroduction efforts remain largely unsuccessful. One potential factor in these outcomes is the host microbiota which includes a large diversity and abundance of bacteria, fungi, and viruses that play an essential role in host physiology. Relative to wild populations, the generalized pattern of gut and skin microbiomes in captivity are reduced alpha diversity and they exhibit a significant shift in community composition and/or structure which often correlates with various physiological maladies. Many conditions of captivity (antibiotic exposure, altered diet composition, homogenous environment, increased stress, and altered intraspecific interactions) likely lead to changes in the host-associated microbiome. To minimize the problems arising from captivity, efforts can be taken to manipulate microbial diversity and composition to be comparable with wild populations through methods such as increasing dietary diversity, exposure to natural environmental reservoirs, or probiotics. For individuals destined for reintroduction, these strategies can prime the microbiota to buffer against novel pathogens and changes in diet and improve reintroduction success. The microbiome is a critical component of animal physiology and its role in species conservation should be expanded and included in the repertoire of future management practices.}, }
@article {pmid35316342, year = {2023}, author = {Zhao, X and Fan, X and Gong, Z and Gao, X and Wang, Y and Ni, B}, title = {The Toxic Effects of Cu and CuO Nanoparticles on Euplotes aediculatus.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {544-556}, pmid = {35316342}, issn = {1432-184X}, support = {31672249//national natural science foundation of china/ ; }, mesh = {*Euplotes ; *Metal Nanoparticles/toxicity ; *Nanoparticles ; Copper ; Oxidative Stress ; }, abstract = {The single-celled eukaryote Euplotes aediculatus was chosen to test and compare the toxic effects of Cu and CuO nanoparticles (NPs). The antioxidant enzymatic activity, morphological changes, and functional groups on the membrane were determined using spectrophotometry, microscopy, and Fourier transform infrared spectroscopy after NPs treatment. The toxicity of the NPs to cells was dose-dependent, and the 24 h-LC50 values of the CuNPs and CuONPs were 0.46 µg/L and 1.24 × 10[3] µg/L, respectively. These NPs increased the activities of superoxide dismutase, glutathione peroxidase, and catalase and destroyed the cell structure; moreover, the CuNPs were more toxic than the CuONPs. In addition to the higher enzymatic activity, CuNPs also caused nucleoli disappearance, chromatin condensation, and mitochondrial and pellicle damage. The oxidization of the functional groups of the membrane (PO2 - , C-O-C, and δ(COH) of carbohydrates) also confirmed the severe damage caused by CuNPs. Our study showed that oxidative stress and organelle destruction played important roles in the toxic effects of these NPs on this protozoan. Compared with other aquatic organisms, E. aediculatus can be considered a potential indicator at the preliminary stage of environmental pollution.}, }
@article {pmid35316093, year = {2022}, author = {Kherfi-Nacer, A and Yan, Z and Bouherama, A and Schmitz, L and Amrane, SO and Franken, C and Schneijderberg, M and Cheng, X and Amrani, S and Geurts, R and Bisseling, T}, title = {High Salt Levels Reduced Dissimilarities in Root-Associated Microbiomes of Two Barley Genotypes.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {35}, number = {7}, pages = {592-603}, doi = {10.1094/MPMI-12-21-0294-FI}, pmid = {35316093}, issn = {0894-0282}, mesh = {Bacteria/genetics ; Genotype ; *Hordeum/genetics/metabolism ; *Microbiota ; Plant Roots/microbiology ; Salt Tolerance ; Soil ; }, abstract = {Plants harbor in and at their roots bacterial microbiomes that contribute to their health and fitness. The microbiome composition is controlled by the environment and plant genotype. Previously, it was shown that the plant genotype-dependent dissimilarity of root microbiome composition of different species becomes smaller under drought stress. However, it remains unknown whether this reduced plant genotype-dependent effect is a specific response to drought stress or a more generic response to abiotic stress. To test this, we studied the effect of salt stress on two distinct barley (Hordeum vulgare L.) genotypes: the reference cultivar Golden Promise and the Algerian landrace AB. As inoculum, we used soil from salinized and degraded farmland on which barley was cultivated. Controlled laboratory experiments showed that plants inoculated with this soil displayed growth stimulation under high salt stress (200 mM) in a plant genotype-independent manner, whereas the landrace AB also showed significant growth stimulation at low salt concentrations. Subsequent analysis of the root microbiomes revealed a reduced dissimilarity of the bacterial communities of the two barley genotypes in response to high salt, especially in the endophytic compartment. High salt level did not reduce α-diversity (richness) in the endophytic compartment of both plant genotypes but was associated with an increased number of shared strains that respond positively to high salt. Among these, Pseudomonas spp. were most abundant. These findings suggest that the plant genotype-dependent microbiome composition is altered generically by abiotic stress.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.}, }
@article {pmid35314061, year = {2022}, author = {Girardi, NS and Sosa, AL and Etcheverry, MG and Passone, MA}, title = {In vitro characterization bioassays of the nematophagous fungus Purpureocillium lilacinum: Evaluation on growth, extracellular enzymes, mycotoxins and survival in the surrounding agroecosystem of tomato.}, journal = {Fungal biology}, volume = {126}, number = {4}, pages = {300-307}, doi = {10.1016/j.funbio.2022.02.001}, pmid = {35314061}, issn = {1878-6146}, mesh = {Animals ; Biological Assay ; Dehydration ; *Hypocreales ; *Solanum lycopersicum ; *Mycotoxins ; *Nematoda ; }, abstract = {The effects of water stress and temperature on in vitro growth and enzymatic activity of Purpureocillium lilacinum (Sordariomycetes, Hypocreales, Ophiocordycipitaceae) isolates with demonstrated capacity to control Nacobbus aberrans (Secernentea, Tylenchida, Pratylenchidae) were evaluated in this study. Also, saprophytic and endophytic colonization in tomato plants were determined. P. lilacinum was able to grow under the evaluated levels of osmotic and matric stress, but the increase in water stress caused reductions in radial growth rates. Moreover, the fungal isolates produced chitinases, proteases, and leucinostatins under inductive conditions. The nematophagous fungi were able to develop saprophytically (10[4] CFU g[-1] of soil). Meanwhile, only P. lilacinum SR38 demonstrated endophytic capacity. The results suggest that P. lilacinum can be effectively applied as biocontrol agents of phytoparasitic nematodes in tomatoes under variable agroecological conditions.}, }
@article {pmid35313934, year = {2022}, author = {Merino, I and de la Fuente, A and Domínguez-Gil, M and Eiros, JM and Tedim, AP and Bermejo-Martín, JF}, title = {Digital PCR applications for the diagnosis and management of infection in critical care medicine.}, journal = {Critical care (London, England)}, volume = {26}, number = {1}, pages = {63}, pmid = {35313934}, issn = {1466-609X}, support = {PI19/00590//Instituto de Salud Carlos III/ ; CD18/00123//Instituto de Salud Carlos III/ ; CM18/00157//Instituto de Salud Carlos III/ ; FI20/00278//Instituto de Salud Carlos III/ ; APT//European Society of Clinical Microbiology and Infectious Diseases/ ; }, mesh = {*COVID-19/diagnosis ; Critical Care ; Humans ; Real-Time Polymerase Chain Reaction/methods ; Reproducibility of Results ; }, abstract = {Infection (either community acquired or nosocomial) is a major cause of morbidity and mortality in critical care medicine. Sepsis is present in up to 30% of all ICU patients. A large fraction of sepsis cases is driven by severe community acquired pneumonia (sCAP), which incidence has dramatically increased during COVID-19 pandemics. A frequent complication of ICU patients is ventilator associated pneumonia (VAP), which affects 10-25% of all ventilated patients, and bloodstream infections (BSIs), affecting about 10% of patients. Management of these severe infections poses several challenges, including early diagnosis, severity stratification, prognosis assessment or treatment guidance. Digital PCR (dPCR) is a next-generation PCR method that offers a number of technical advantages to face these challenges: it is less affected than real time PCR by the presence of PCR inhibitors leading to higher sensitivity. In addition, dPCR offers high reproducibility, and provides absolute quantification without the need for a standard curve. In this article we reviewed the existing evidence on the applications of dPCR to the management of infection in critical care medicine. We included thirty-two articles involving critically ill patients. Twenty-three articles focused on the amplification of microbial genes: (1) four articles approached bacterial identification in blood or plasma; (2) one article used dPCR for fungal identification in blood; (3) another article focused on bacterial and fungal identification in other clinical samples; (4) three articles used dPCR for viral identification; (5) twelve articles quantified microbial burden by dPCR to assess severity, prognosis and treatment guidance; (6) two articles used dPCR to determine microbial ecology in ICU patients. The remaining nine articles used dPCR to profile host responses to infection, two of them for severity stratification in sepsis, four focused to improve diagnosis of this disease, one for detecting sCAP, one for detecting VAP, and finally one aimed to predict progression of COVID-19. This review evidences the potential of dPCR as a useful tool that could contribute to improve the detection and clinical management of infection in critical care medicine.}, }
@article {pmid35312808, year = {2023}, author = {Caballero, JRI and Lalande, BM and Hanna, JW and Klopfenstein, NB and Kim, MS and Stewart, JE}, title = {Genomic Comparisons of Two Armillaria Species with Different Ecological Behaviors and Their Associated Soil Microbial Communities.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {708-729}, pmid = {35312808}, issn = {1432-184X}, mesh = {*Armillaria/genetics ; Soil ; Trees ; Forests ; *Tracheophyta ; *Pinus ; Genomics ; }, abstract = {Armillaria species show considerable variation in ecological roles and virulence, from mycorrhizae and saprophytes to important root pathogens of trees and horticultural crops. We studied two Armillaria species that can be found in coniferous forests of northwestern USA and southwestern Canada. Armillaria altimontana not only is considered as a weak, opportunistic pathogen of coniferous trees, but it also appears to exhibit in situ biological control against A. solidipes, formerly North American A. ostoyae, which is considered a virulent pathogen of coniferous trees. Here, we describe their genome assemblies and present a functional annotation of the predicted genes and proteins for the two Armillaria species that exhibit contrasting ecological roles. In addition, the soil microbial communities were examined in association with the two Armillaria species within a 45-year-old plantation of western white pine (Pinus monticola) in northern Idaho, USA, where A. altimontana was associated with improved tree growth and survival, while A. solidipes was associated with reduced growth and survival. The results from this study reveal a high similarity between the genomes of the beneficial/non-pathogenic A. altimontana and pathogenic A. solidipes; however, many relatively small differences in gene content were identified that could contribute to differences in ecological lifestyles and interactions with woody hosts and soil microbial communities.}, }
@article {pmid35312065, year = {2022}, author = {Ceron-Chafla, P and García-Timermans, C and de Vrieze, J and Ganigué, R and Boon, N and Rabaey, K and van Lier, JB and Lindeboom, REF}, title = {Pre-incubation conditions determine the fermentation pattern and microbial community structure in fermenters at mild hydrostatic pressure.}, journal = {Biotechnology and bioengineering}, volume = {119}, number = {7}, pages = {1792-1807}, pmid = {35312065}, issn = {1097-0290}, mesh = {Fermentation ; Geologic Sediments ; Hydrostatic Pressure ; *Microbiota ; Temperature ; }, abstract = {Fermentation at elevated hydrostatic pressure is a novel strategy targeting product selectivity. However, the role of inoculum history and cross-resistance, that is, acquired tolerance from incubation under distinctive environmental stress, remains unclear in high-pressure operation. In our here presented work, we studied fermentation and microbial community responses of halotolerant marine sediment inoculum (MSI) and anaerobic digester inoculum (ADI), pre-incubated in serum bottles at different temperatures and subsequently exposed to mild hydrostatic pressure (MHP; < 10 MPa) in stainless steel reactors. Results showed that MHP effects on microbial growth, activity, and community structure were strongly temperature-dependent. At moderate temperature (20°C), biomass yield and fermentation were not limited by MHP; suggesting a cross-resistance effect from incubation temperature and halotolerance. Low temperatures (10°C) and MHP imposed kinetic and bioenergetic limitations, constraining growth and product formation. Fermentation remained favorable in MSI at 28°C and ADI at 37°C, despite reduced biomass yield resulting from maintenance and decay proportionally increasing with temperature. Microbial community structure was modified by temperature during the enrichment, and slight differences observed after MHP-exposure did not compromise functionality. Results showed that the relation incubation temperature-halotolerance proved to be a modifier of microbial responses to MHP and could be potentially exploited in fermentations to modulate product/biomass ratio.}, }
@article {pmid35311515, year = {2022}, author = {Linney, MD and Eppley, JM and Romano, AE and Luo, E and DeLong, EF and Karl, DM}, title = {Microbial Sources of Exocellular DNA in the Ocean.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {7}, pages = {e0209321}, pmid = {35311515}, issn = {1098-5336}, mesh = {*Alphaproteobacteria/genetics ; Bacteria/genetics ; DNA ; *Prochlorococcus/genetics ; Seawater/microbiology ; *Viruses/genetics ; Water ; }, abstract = {Exocellular DNA is operationally defined as the fraction of the total DNA pool that passes through a membrane filter (0.1 μm). It is composed of DNA-containing vesicles, viruses, and free DNA and is ubiquitous in all aquatic systems, although the sources, sinks, and ecological consequences are largely unknown. Using a method that provides separation of these three fractions, we compared open ocean depth profiles of DNA associated with each fraction. Pelagibacter-like DNA dominated the vesicle fractions for all samples examined over a depth range of 75 to 500 m. Viral DNA consisted predominantly of myovirus-like and podovirus-like DNA and contained the highest proportion of unannotated sequences. Euphotic zone free DNA (75 to 125 m) contained primarily bacterial and viral sequences, with bacteria dominating samples from the mesopelagic zone (500 to 1,000 m). A high proportion of mesopelagic zone free DNA sequences appeared to originate from surface waters, including a large amount of DNA contributed by high-light Prochlorococcus ecotypes. Throughout the water column, but especially in the mesopelagic zone, the composition of free DNA sequences was not always reflective of cooccurring microbial communities that inhabit the same sampling depth. These results reveal the composition of free DNA in different regions of the water column (euphotic and mesopelagic zones), with implications for dissolved organic matter cycling and export (by way of sinking particles and/or migratory zooplankton) as a delivery mechanism. IMPORTANCE With advances in metagenomic sequencing, the microbial composition of diverse environmental systems has been investigated, providing new perspectives on potential ecological dynamics and dimensions for experimental investigations. Here, we characterized exocellular free DNA via metagenomics, using a newly developed method that separates free DNA from cells, viruses, and vesicles, and facilitated the independent characterization of each fraction. The fate of this free DNA has both ecological consequences as a nutrient (N and P) source and potential evolutionary consequences as a source of genetic transformation. Here, we document different microbial sources of free DNA at the surface (0 to 200 m) versus depths of 250 to 1,000 m, suggesting that distinct free DNA production mechanisms may be present throughout the oligotrophic water column. Examining microbial processes through the lens of exocellular DNA provides insights into the production of labile dissolved organic matter (i.e., free DNA) at the surface (likely by viral lysis) and processes that influence the fate of sinking, surface-derived organic matter.}, }
@article {pmid35309262, year = {2022}, author = {Amit,  and Jamwal, R and Kumari, S and Kelly, S and Cannavan, A and Singh, DK}, title = {Assessment of geographical origin of virgin coconut oil using inductively coupled plasma mass spectrometry along with multivariate chemometrics.}, journal = {Current research in food science}, volume = {5}, number = {}, pages = {545-552}, pmid = {35309262}, issn = {2665-9271}, abstract = {Recently, Virgin coconut oil (VCO) has emerged as one of the most favorable edible oils because of its application in cooking, frying as well as additive used in food, pharmaceuticals, and cosmetic goods. These qualities have established VCO in high consumer demand and there is a great need of establishing a reliable method for the identification of its geographical origin. Through this present study, for the first time, it has been established that Inductively Coupled Plasma-Mass-Spectrometry (ICP-MS) combined with multivariate chemometrics can be used for the identification of the geographical origin of the VCO samples of various provinces. Principal Component Analysis (PCA), and Linear Discriminant Analysis (LDA) were able to differentiate and classify the VCO samples of different geographical origins. Further, calibration models (Principal Component Regression and Partial Least Square Regression) were developed on the calibration dataset of the elemental concentration obtained from the ICP-MS analysis. An external dataset was used to develop the prediction model to predict the geographical origin of an unknown sample. Both PCR and PLS-R models were successfully able to predict the geographical origin with a high R[2] value (0.999) and low RMSEP value 0.074 and 0.075% v/v of prediction respectively. In conclusion, ICP-MS combined with regression modelling can be used as an excellent tool for the identification of the geographical origin of the VCO samples of various provinces. This whole technique is the most suitable as it has high sensitivity as well as provides easy multi-metal analysis for a single sample of edible oil.}, }
@article {pmid35306576, year = {2023}, author = {Hanashiro, FTT and De Meester, L and Vanhamel, M and Mukherjee, S and Gianuca, AT and Verbeek, L and van den Berg, E and Souffreau, C}, title = {Bacterioplankton Assembly Along a Eutrophication Gradient Is Mainly Structured by Environmental Filtering, Including Indirect Effects of Phytoplankton Composition.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {400-410}, pmid = {35306576}, issn = {1432-184X}, support = {PF/2010/07//KU Leuven Research Fund Excellence Center/ ; 245968/2012-1//Science Without Borders/ ; }, mesh = {Animals ; *Phytoplankton ; *Ecosystem ; Aquatic Organisms ; Eutrophication ; Zooplankton ; Lakes/microbiology ; }, abstract = {Biotic interactions are suggested to be key factors structuring bacterioplankton community assembly but are rarely included in metacommunity studies. Eutrophication of ponds and lakes provides a useful opportunity to evaluate how bacterioplankton assembly is affected by specific environmental conditions, especially also by biotic interactions with other trophic levels such as phytoplankton and zooplankton. Here, we evaluated the importance of deterministic and stochastic processes on bacterioplankton community assembly in 35 shallow ponds along a eutrophication gradient in Belgium and assessed the direct and indirect effects of phytoplankton and zooplankton community variation on bacterioplankton assembly through a path analysis and network analysis. Environmental filtering by abiotic factors (suspended matter concentration and pH) explained the largest part of the bacterioplankton community variation. Phytoplankton community structure affected bacterioplankton structure through its effect on variation in chlorophyll-a and suspended matter concentration. Bacterioplankton communities were also spatially structured through pH. Overall, our results indicate that environmental variation is a key component driving bacterioplankton assembly along a eutrophication gradient and that indirect biotic interactions can also be important in explaining bacterioplankton community composition. Furthermore, eutrophication led to divergence in community structure and more eutrophic ponds had a higher diversity of bacteria.}, }
@article {pmid35305980, year = {2022}, author = {Kim, SJ and Kang, S and Xu, H and Bhaskar, P and Chenoli, S}, title = {Special issue: AFoPS on climate and life in poles.}, journal = {Environmental research}, volume = {211}, number = {}, pages = {113125}, doi = {10.1016/j.envres.2022.113125}, pmid = {35305980}, issn = {1096-0953}, mesh = {*Climate ; *Climate Change ; }, }
@article {pmid35302890, year = {2022}, author = {Koldaeva, A and Tsai, HF and Shen, AQ and Pigolotti, S}, title = {Population genetics in microchannels.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {12}, pages = {e2120821119}, pmid = {35302890}, issn = {1091-6490}, mesh = {*Escherichia coli/genetics ; *Genetics, Population ; Soil ; }, abstract = {SignificanceMany microbial populations proliferate in small channels. In such environments, reproducing cells organize in parallel lanes. Reproducing cells shift these lanes, potentially expelling other cells from the channel. In this paper, we combine theory and experiments to understand how these dynamics affects the diversity of a microbial population. We theoretically predict that genetic diversity is quickly lost along lanes of cells. Our experiments confirm that a population of proliferating Escherichia coli in a microchannel organizes into lanes of genetically identical cells within a few generations. Our findings elucidate the effect of lane formation on populations evolution, with potential applications ranging from microbial ecology in soil to dynamics of epithelial tissues in higher organisms.}, }
@article {pmid35300488, year = {2022}, author = {Frey, B and Varliero, G and Qi, W and Stierli, B and Walthert, L and Brunner, I}, title = {Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {828977}, pmid = {35300488}, issn = {1664-302X}, abstract = {Soil microorganisms such as Bacteria and Archaea play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of soil metagenomes to a depth of 1.5 m in Swiss forests of European beech and oak species on calcareous bedrock. We explored the functional genetic potential of soil microorganisms with the aim to disentangle the effects of tree genus and soil depth on the genetic repertoire, and to gain insight into the microbial C and N cycling. The relative abundance of reads assigned to taxa at the domain level indicated a 5-10 times greater abundance of Archaea in the deep soil, while Bacteria showed no change with soil depth. In the deep soil there was an overrepresentation of genes for carbohydrate-active enzymes, which are involved in the catalyzation of the transfer of oligosaccharides, as well as in the binding of carbohydrates such as chitin or cellulose. In addition, N-cycling genes (NCyc) involved in the degradation and synthesis of N compounds, in nitrification and denitrification, and in nitrate reduction were overrepresented in the deep soil. Consequently, our results indicate that N-transformation in the deep soil is affected by soil depth and that N is used not only for assimilation but also for energy conservation, thus indicating conditions of low oxygen in the deep soil. Using shotgun metagenomics, our study provides initial findings on soil microorganisms and their functional genetic potential, and how this may change depending on soil properties, which shift with increasing soil depth. Thus, our data provide novel, deeper insight into the "dark matter" of the soil.}, }
@article {pmid35298685, year = {2023}, author = {Zhang, Z and Han, P and Zheng, Y and Jiao, S and Dong, H and Liang, X and Gao, D and Niu, Y and Yin, G and Liu, M and Hou, L}, title = {Spatiotemporal Dynamics of Bacterial Taxonomic and Functional Profiles in Estuarine Intertidal Soils of China Coastal Zone.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {383-399}, pmid = {35298685}, issn = {1432-184X}, support = {41725002//China National Funds for Distinguished Young Scientists/ ; }, mesh = {*Soil ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; Wetlands ; Bacteria ; China ; }, abstract = {Bacteria play an important role in regulating carbon (C), nitrogen (N), and sulfur (S) in estuarine intertidal wetlands. To gain insights into the ecological and metabolic modes possessed by bacteria in estuarine intertidal wetlands, a total of 78 surface soil samples were collected from China's coastal intertidal wetlands to examine the spatial and seasonal variations of bacterial taxonomic composition, assembly processes, and ecological system functions through shotgun metagenomic and 16S rRNA gene sequencing. Obvious spatiotemporal dynamic patterns in the bacterial community structure were identified, with more pronounced seasonal rather than spatial variations. Dispersion limitation was observed to act as a critical factor affecting community assembly, explaining approximately half of the total variation in the bacterial community. Functional bacterial community structure exhibited a more significant latitudinal change than seasonal variability, highlighting that functional stability of the bacterial communities differed with their taxonomic variability. Identification of biogeochemically related links between C, N, and S cycles in the soils showed the adaptive routed metabolism of the bacterial communities and the strong interactions between coupled metabolic pathways. Our study broadens the insights into the taxonomic and functional profiles of bacteria in China's estuarine intertidal soils and helps us understand the effects exerted by environmental factors on the ecological health and microbial diversity of estuarine intertidal flats.}, }
@article {pmid35295290, year = {2022}, author = {Zioutis, C and Seki, D and Bauchinger, F and Herbold, C and Berger, A and Wisgrill, L and Berry, D}, title = {Ecological Processes Shaping Microbiomes of Extremely Low Birthweight Infants.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {812136}, pmid = {35295290}, issn = {1664-302X}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; P 27831/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {The human microbiome has been implicated in affecting health outcomes in premature infants, but the ecological processes governing early life microbiome assembly remain poorly understood. Here, we investigated microbial community assembly and dynamics in extremely low birth weight infants (ELBWI) over the first 2 weeks of life. We profiled the gut, oral cavity and skin microbiomes over time using 16S rRNA gene amplicon sequencing and evaluated the ecological forces shaping these microbiomes. Though microbiomes at all three body sites were characterized by compositional instability over time and had low body-site specificity (PERMANOVA, r [2] = 0.09, p = 0.001), they could nonetheless be clustered into four discrete community states. Despite the volatility of these communities, deterministic assembly processes were detectable in this period of initial microbial colonization. To further explore these deterministic dynamics, we developed a probabilistic approach in which we modeled microbiome state transitions in each ELBWI as a Markov process, or a "memoryless" shift, from one community state to another. This analysis revealed that microbiomes from different body sites had distinctive dynamics as well as characteristic equilibrium frequencies. Time-resolved microbiome sampling of premature infants may help to refine and inform clinical practices. Additionally, this work provides an analysis framework for microbial community dynamics based on Markov modeling that can facilitate new insights, not only into neonatal microbiomes but also other human-associated or environmental microbiomes.}, }
@article {pmid35294588, year = {2022}, author = {Guarin, TC and Li, L and Pagilla, KR}, title = {Microbial community characterization in advanced water reclamation for potable reuse.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {7}, pages = {2763-2773}, pmid = {35294588}, issn = {1432-0614}, mesh = {Bacteria/genetics ; *Drinking Water/microbiology ; *Microbiota ; *Ozone ; RNA, Ribosomal, 16S/genetics ; *Water Purification ; }, abstract = {This study investigated the microbial community structure and composition across two treatment steps used in advanced water reclamation for potable reuse applications, namely Coagulation/Flocculation/Clarification/Granular Media Filtration (CFCGMF) and Ozone-Biological Activated Carbon filtration (O3/BAC). The study examined the richness, variations, and similarities of the microorganisms involved at each treatment step to better understand the role of ecology and the dynamics on unit process performance and the microbial community developed within it. The bacterial microbiomes at each treatment step were independently characterized using 16S metagenomic sequencing. Combining both treatment steps, a total of 3801 species were detected. From the total species detected, 38% and 98% were identified at CFCGMF and O3/BAC, respectively. The most abundant phyla were Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes in both treatment steps. The identified species were classified based on their preferences to free-living style (59%) vs attached-living style (22%) showing a relatively low richness in the BAC media, but higher diversities. At the taxonomic class level, Betaproteobacteria was the predominant in both system processes. Additionally, a list of eight genera were identified as potential bacterial pathogens present in both process effluents. They are Aeromonas, Clostridium, Enterobacter, Escherichia, Flavobacterium, Legionella, Mycobacterium, and Pseudomonas. CFCGMF effluent yielded less pathogenic bacteria than both the ozone and BAC filter effluent from the O3/BAC process unit; their relative abundance accounted for about 2% and 8% for CFCGMF and O3/BAC, respectively. Detailed studies to characterize the microbial communities are crucial in interpreting the mechanisms and synergies between processes performance and microorganisms by identifying the needs and best practices to ensure public health protection. Key points • Microbial communities of two treatment processes are characterized using 16S rRNA sequencing. • Organisms that can tolerate ozone and form biofilms define microbial community in subsequent biofilters. • In relatively low abundances, potential pathogenic bacteria are detected in the treated water.}, }
@article {pmid35292274, year = {2022}, author = {Chai, G and Wang, D and Shan, J and Jiang, C and Yang, Z and Liu, E and Meng, H and Wang, H and Wang, Z and Qin, L and Xi, J and Ma, Y and Li, H and Qian, Y and Li, J and Lin, Y}, title = {Accumulation of high-molecular-weight polycyclic aromatic hydrocarbon impacted the performance and microbial ecology of bioretention systems.}, journal = {Chemosphere}, volume = {298}, number = {}, pages = {134314}, doi = {10.1016/j.chemosphere.2022.134314}, pmid = {35292274}, issn = {1879-1298}, mesh = {Biological Oxygen Demand Analysis ; *Environmental Pollutants ; Nitrogen/analysis ; *Polycyclic Aromatic Hydrocarbons/analysis ; Soil ; *Soil Pollutants ; }, abstract = {Bioretention has been considered as an effective management practice for urban stormwater in the removal of pollutants including polycyclic aromatic hydrocarbons (PAHs). However, the accumulation of high-molecular-weight (HMW) PAHs in bioretention systems and their potential impact on the pollutants removal performance and microbial ecology are still not fully understood. In this study, comparisons of treatment effectiveness, enzyme activity and microbial community in bioretention systems with different types of media amendments were carried out at different spiking levels of pyrene (PYR). The results showed that the removal efficiencies of chemical oxygen demand (COD) and total nitrogen in the bioretention systems were negatively impacted by the PYR levels. The relative activities of soil dehydrogenase and urease were increasingly inhibited by the elevated PYR level, indicating the declining microbial activity regarding organic matter decomposition. The spiking of PYR negatively affected microbial diversity, and distinct time- and influent-dependent changes in microbial communities were observed. The relative abundance of PAH-degrading microorganisms increased in PYR-spiked systems, while the abundance of nitrifiers decreased. The addition of media amendments was beneficial for the enrichment of microorganisms that are more resistant to PYR-related stress, therefore elevating the COD concentration removal rate by ∼50%. This study gives new insight into the multifaceted impacts of HMW PAH accumulation on microbial fingerprinting and enzyme activities, which may provide guidance on better stormwater management practices via bioretention in terms of improved system longevity and performance.}, }
@article {pmid35290040, year = {2022}, author = {Patzner, MS and Kainz, N and Lundin, E and Barczok, M and Smith, C and Herndon, E and Kinsman-Costello, L and Fischer, S and Straub, D and Kleindienst, S and Kappler, A and Bryce, C}, title = {Seasonal Fluctuations in Iron Cycling in Thawing Permafrost Peatlands.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {7}, pages = {4620-4631}, pmid = {35290040}, issn = {1520-5851}, mesh = {Ferric Compounds/metabolism ; Iron/metabolism ; Oxidation-Reduction ; *Permafrost ; Seasons ; Soil ; }, abstract = {In permafrost peatlands, up to 20% of total organic carbon (OC) is bound to reactive iron (Fe) minerals in the active layer overlying intact permafrost, potentially protecting OC from microbial degradation and transformation into greenhouse gases (GHG) such as CO2 and CH4. During the summer, shifts in runoff and soil moisture influence redox conditions and therefore the balance of Fe oxidation and reduction. Whether reactive iron minerals could act as a stable sink for carbon or whether they are continuously dissolved and reprecipitated during redox shifts remains unknown. We deployed bags of synthetic ferrihydrite (FH)-coated sand in the active layer along a permafrost thaw gradient in Stordalen mire (Abisko, Sweden) over the summer (June to September) to capture changes in redox conditions and quantify the formation and dissolution of reactive Fe(III) (oxyhydr)oxides. We found that the bags accumulated Fe(III) under constant oxic conditions in areas overlying intact permafrost over the full summer season. In contrast, in fully thawed areas, conditions were continuously anoxic, and by late summer, 50.4 ± 12.8% of the original Fe(III) (oxyhydr)oxides were lost via dissolution. Periodic redox shifts (from 0 to +300 mV) were observed over the summer season in the partially thawed areas. This resulted in the dissolution and loss of 47.2 ± 20.3% of initial Fe(III) (oxyhydr)oxides when conditions are wetter and more reduced, and new formation of Fe(III) minerals (33.7 ± 8.6% gain in comparison to initial Fe) in the late summer under more dry and oxic conditions, which also led to the sequestration of Fe-bound organic carbon. Our data suggest that there is seasonal turnover of iron minerals in partially thawed permafrost peatlands, but that a fraction of the Fe pool remains stable even under continuously anoxic conditions.}, }
@article {pmid35287817, year = {2022}, author = {Mota-Gutierrez, J and Lis, L and Lasagabaster, A and Nafarrate, I and Ferrocino, I and Cocolin, L and Rantsiou, K}, title = {Campylobacter spp. prevalence and mitigation strategies in the broiler production chain.}, journal = {Food microbiology}, volume = {104}, number = {}, pages = {103998}, doi = {10.1016/j.fm.2022.103998}, pmid = {35287817}, issn = {1095-9998}, mesh = {Abattoirs ; Animals ; *Campylobacter ; *Chickens/microbiology ; Meat/microbiology ; Prevalence ; }, abstract = {This study aims to discuss the microbial ecology of the broiler gut environment, Campylobacter prevalence across the broiler production chain with a follow-up focus on a possible mitigation strategy, based on the use of bacteriophages. Scientific literature published from the last two decades was reviewed and data were collected to establish the ranges of Campylobacter loads from different samples. Results showed that the pathogen load in the sample is likely to increase from the different stages of the production chain. Contamination of water and feed represents the most notable source of contamination during the primary production, while cross-contamination of broiler carcasses, skin, and meat occurs during the slaughter, dressing, and processing via machinery, work surfaces, water, and air partially due to the leaking of contaminated feces from visceral rupture. Knowledge gaps were identified and included: a lack of studies detecting Campylobacter in broilers in most of the European countries over the last decade and a low number of studies determining the bacterial load in crates used to transport broilers to the slaughterhouse. Determining the prevalence of Campylobacter in the broiler industry will enable us to set critical control points to produce broiler flocks and meat products with a low risk of Campylobacter contamination.}, }
@article {pmid35286940, year = {2022}, author = {Safi, LSL and Tang, KW and Carnegie, RB}, title = {Investigating the epibiotic peritrich Zoothamnium intermedium Precht, 1935: Seasonality and distribution of its relationships with copepods in Chesapeake Bay (USA).}, journal = {European journal of protistology}, volume = {84}, number = {}, pages = {125880}, doi = {10.1016/j.ejop.2022.125880}, pmid = {35286940}, issn = {1618-0429}, mesh = {Animals ; Bays ; *Ciliophora ; *Copepoda ; *Oligohymenophorea ; Plankton ; Water ; }, abstract = {Zoothamnium intermedium is an obligate epibiont ciliate and has been found in a diverse array of hosts and environments. Different studies have reported conflicting distribution patterns and host preferences, even though studies in Chesapeake Bay have suggested that the ciliate has a strong host specificity for two calanoid copepod species. We examined the life cycle, host preferences, and ecological conditions conducive to Z. intermedium presence on copepods in Chesapeake Bay, the largest estuary in North America. The York River tributary was sampled biweekly from fall 2014 through summer 2015 for plankton, peritrichs and bacteria in the water column. Bacterial abundance in the water column peaked in fall and late spring, coinciding with increased abundance and species richness of non-epibiont peritrichs. Among the plankton, only the calanoid copepods Acartia tonsa and Centropages hamatus were colonized by Z. intermedium. The peritrich epibiont displayed higher colonization rates on C. hamatus even when A. tonsa was far more abundant. Multivariate correlation analysis of infestation prevalence on A. tonsa showed a strong correlation with dissolved oxygen, salinity and water temperature. Such correlations, along with differences in host species biology, might be driving the seasonality of this epibiotic relationship.}, }
@article {pmid35286131, year = {2022}, author = {Huang, K and Sun, X and Zou, Y and Li, H and Xu, P and Zhang, W and Zhang, Y and Li, H and Sun, H and Wang, W and Pang, M and Luo, J}, title = {Comparison of the Endophytic Bacterial Microbiota of Asymptomatic and Symptomatic Ginger Rhizomes During the Activation of Adventitious Bud Development.}, journal = {Plant disease}, volume = {106}, number = {9}, pages = {2470-2479}, doi = {10.1094/PDIS-09-21-2069-RE}, pmid = {35286131}, issn = {0191-2917}, mesh = {Bacteria/genetics ; *Zingiber officinale/chemistry/genetics/microbiology ; *Microbiota ; Plant Extracts ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bacterial infections are the cause of rhizome rot in ginger (Zingiber officinale). Key members of the endophytic microbial community in ginger rhizomes have not been identified, and their impact on the decay of rhizomes during the activation of adventitious bud development has not been investigated. High-throughput, 16S rRNA amplicon sequencing and inoculation experiments were used to analyze the microbial diversity, community structure and composition, and pathogenicity of isolated bacteria. Our results indicated that the composition of the endophytic microbiota underwent a shift during the progression of rhizome rot disease. Enterobacteriaceae, Lachnospiraceae, and the bacterial genera Clostridium, Bacteroides, Acrobacter, Dysgonomonas, Anaerosinus, Pectobacterium, and Lactococcus were relatively abundant in the bacterial community of rhizomes exhibiting bacterial decay symptoms but were also present in asymptomatic rhizomes. The presence of Enterobacteriaceae and Pseudomonadaceae were positively correlated (ρ = 0.83) at the beginning of the sampling period in the symptomatic group, while a positive correlation (ρ = 0.89) was only observed after 20 days in the asymptomatic group. These data indicate that the co-occurrence of Enterobacteriaceae and Pseudomonadaceae may be associated with the development of ginger rot. Bacterial taxa isolated from ginger rhizomes, such as Enterobacter cloacae, E. hormaechei, and Pseudomonas putida, induced obvious rot symptoms when they were inoculated on ginger rhizomes. Notably, antibiotic-producing bacterial taxa in the Streptococcaceae and Flavobacteriaceae were also relatively abundant in rhizomes with rot and appeared to be linked to the onset of rhizome rot disease. Our results provide important information on the establishment and management of disease in ginger rhizomes.}, }
@article {pmid35285907, year = {2022}, author = {Nunes, I and Hansen, V and Bak, F and Bonnichsen, L and Su, J and Hao, X and Raymond, NS and Nicolaisen, MH and Jensen, LS and Nybroe, O}, title = {Succession of the wheat seed-associated microbiome as affected by soil fertility level and introduction of Penicillium and Bacillus inoculants in the field.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {3}, pages = {}, pmid = {35285907}, issn = {1574-6941}, mesh = {*Bacillus/genetics/metabolism ; Fertilizers/analysis ; *Microbiota ; *Penicillium/metabolism ; Phosphorus/metabolism ; Seeds ; Soil ; Soil Microbiology ; Triticum/microbiology ; }, abstract = {During germination, the seed releases nutrient-rich exudates into the spermosphere, thereby fostering competition between resident microorganisms. However, insight into the composition and temporal dynamics of seed-associated bacterial communities under field conditions is currently lacking. This field study determined the temporal changes from 11 to 31 days after sowing in the composition of seed-associated bacterial communities of winter wheat as affected by long-term soil fertilization history, and by introduction of the plant growth-promoting microbial inoculants Penicillium bilaiae and Bacillus simplex. The temporal dynamics were the most important factor affecting the composition of the seed-associated communities. An increase in the relative abundance of genes involved in organic nitrogen metabolism (ureC and gdhA), and in ammonium oxidation (amoA), suggested increased mineralization of plant-derived nitrogen compounds over time. Dynamics of the phosphorus cycling genes ppt, ppx and cphy indicated inorganic phosphorus and polyphosphate cycling, as well as phytate hydrolysis by the seed-associated bacteria early after germination. Later, an increase in genes for utilization of organic phosphorus sources (phoD, phoX and phnK) indicated phosphorus limitation. The results indicate that community temporal dynamics are partly driven by changed availability of major nutrients, and reveal no functional consequences of the added inoculants during seed germination.}, }
@article {pmid35285696, year = {2022}, author = {Song, W and Liu, J and Qin, W and Huang, J and Yu, X and Xu, M and Stahl, D and Jiao, N and Zhou, J and Tu, Q}, title = {Functional Traits Resolve Mechanisms Governing the Assembly and Distribution of Nitrogen-Cycling Microbial Communities in the Global Ocean.}, journal = {mBio}, volume = {13}, number = {2}, pages = {e0383221}, pmid = {35285696}, issn = {2150-7511}, support = {2019YFA0606700//National Key Research and Development Program of China/ ; 2020YFA0607600//National Key Research and Development Program of China/ ; 2017YFA0604300//National Key Research and Development Program of China/ ; 31971446//National Natural Science Foundation of China (NSFC)/ ; 92051110//National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Metagenome ; *Microbiota ; *Nitrogen ; Nitrogen Cycle ; Oceans and Seas ; }, abstract = {Microorganisms drive much of the marine nitrogen (N) cycle, which jointly controls the primary production in the global ocean. However, our understanding of the microbial communities driving the global ocean N cycle remains fragmented. Focusing on "who is doing what, where, and how?", this study draws a clear picture describing the global biogeography of marine N-cycling microbial communities by utilizing the Tara Oceans shotgun metagenomes. The marine N-cycling communities are highly variable taxonomically but relatively even at the functional trait level, showing clear functional redundancy properties. The functional traits and taxonomic groups are shaped by the same set of geo-environmental factors, among which, depth is the major factor impacting marine N-cycling communities, differentiating mesopelagic from epipelagic communities. Latitudinal diversity gradients and distance-decay relationships are observed for taxonomic groups, but rarely or weakly for functional traits. The composition of functional traits is strongly deterministic as revealed by null model analysis, while a higher degree of stochasticity is observed for taxonomic composition. Integrating multiple lines of evidence, in addition to drawing a biogeographic picture of marine N-cycling communities, this study also demonstrated an essential microbial ecological theory-determinism governs the assembly of microbial communities performing essential biogeochemical processes; the environment selects functional traits rather than taxonomic groups; functional redundancy underlies stochastic taxonomic community assembly. IMPORTANCE A critical question in microbial ecology is how the complex microbial communities are formed in natural ecosystems with the existence of thousands different species, thereby performing essential ecosystem functions and maintaining ecosystem stability. Previous studies disentangling the community assembly mechanisms mainly focus on microbial taxa, ignoring the functional traits they carry. By anchoring microbial functional traits and their carrying taxonomic groups involved in nitrogen cycling processes, this study demonstrated an important mechanism associated with the complex microbial community assembly. Evidence shows that the environment selects functional traits rather than taxonomic groups, and functional redundancy underlies stochastic taxonomic community assembly. This study is expected to provide valuable mechanistic insights into the complex microbial community assembly in both natural and artificial ecosystems.}, }
@article {pmid35284961, year = {2023}, author = {Almeida, EL and Ribiere, C and Frei, W and Kenny, D and Coffey, MF and O'Toole, PW}, title = {Geographical and Seasonal Analysis of the Honeybee Microbiome.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {765-778}, pmid = {35284961}, issn = {1432-184X}, support = {12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Bees ; Animals ; Seasons ; *Microbiota ; Larva ; Bacteria ; Ireland ; }, abstract = {We previously showed that colonies of thriving and non-thriving honeybees co-located in a single geographically isolated apiary harboured strikingly different microbiomes when sampled at a single time point in the honey season. Here, we profiled the microbiome in returning forager bees from 10 to 12 hives in each of 6 apiaries across the southern half of Ireland, at early, middle, and late time points in the 2019 honey production season. Despite the wide range of geographical locations and forage available, apiary site was not the strongest determinant of the honeybee microbiome. However, there was clear clustering of the honeybee microbiome by time point across all apiaries, independent of which apiary was sampled. The clustering of microbiome by time was weaker although still significant in three of the apiaries, which may be connected to their geographic location and other external factors. The potential forage effect was strongest at the second timepoint (June-July) when the apiaries also displayed greatest difference in microbiome diversity. We identified bacteria in the forager bee microbiome that correlated with hive health as measured by counts of larvae, bees, and honey production. These findings support the hypothesis that the global honeybee microbiome and its constituent species support thriving hives.}, }
@article {pmid35282279, year = {2022}, author = {Amillano-Cisneros, JM and Hernández-Rosas, PT and Gomez-Gil, B and Navarrete-Ramírez, P and Ríos-Durán, MG and Martínez-Chávez, CC and Johnston-Monje, D and Martínez-Palacios, CA and Raggi, L}, title = {Loss of gut microbial diversity in the cultured, agastric fish, Mexican pike silverside (Chirostoma estor: Atherinopsidae).}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13052}, pmid = {35282279}, issn = {2167-8359}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Esocidae/genetics ; RNA, Ribosomal, 16S/genetics ; Fishes/genetics ; Bacteria/genetics ; }, abstract = {Teleost fish are the most diverse group of extant vertebrates and have varied digestive anatomical structures and strategies, suggesting they also possess an array of different host-microbiota interactions. Differences in fish gut microbiota have been shown to affect host development, the process of gut colonization, and the outcomes of gene-environment or immune system-microbiota interactions. There is generally a lack of studies on the digestive mechanisms and microbiota of agastric short-intestine fish however, meaning that we do not understand how changes in gut microbial diversity might influence the health of these types of fish. To help fill these gaps in knowledge, we decided to study the Mexican pike silverside (Chirostoma estor) which has a simplified alimentary canal (agastric, short-intestine, 0.7 gut relative length) to observe the diversity and metabolic potential of its intestinal microbiota. We characterized gut microbial populations using high-throughput sequencing of the V3 region in bacterial 16S rRNA genes while searching for population shifts resulting associated with fish development in different environments and cultivation methods. Microbiota samples were taken from the digesta, anterior and posterior intestine (the three different intestinal components) of fish that grew wild in a lake, that were cultivated in indoor tanks, or that were raised in outdoor ponds. Gut microbial diversity was significantly higher in wild fish than in cultivated fish, suggesting a loss of diversity when fish are raised in controlled environments. The most abundant phyla observed in these experiments were Firmicutes and Proteobacteria, particularly of the genera Mycoplasma, Staphylococcus, Spiroplasma, and Aeromonas. Of the 14,161 OTUs observed in this experiment, 133 were found in all groups, and 17 of these, belonging to Acinetobacter, Aeromonas, Pseudomonas, and Spiroplasma genera, were found in all samples suggesting the existence of a core C. estor microbiome. Functional metagenomic prediction of bacterial ecological functions using PICRUSt2 suggested that different intestinal components select for functionally distinct microbial populations with variation in pathways related to the metabolism of amino acids, vitamins, cofactors, and energy. Our results provide, for the first time, information on the bacterial populations present in an agastric, short-gut teleost with commercial potential and show that controlled cultivation of this fish reduces the diversity of its intestinal microbiota.}, }
@article {pmid35281910, year = {2022}, author = {Zou, C and Chen, Y and Li, H and Li, W and Wei, J and Li, Z and Wang, X and Chen, T and Huang, H}, title = {Engineered Bacteria EcN-MT Alleviate Liver Injury in Cadmium-Exposed Mice via its Probiotics Characteristics and Expressing of Metallothionein.}, journal = {Frontiers in pharmacology}, volume = {13}, number = {}, pages = {857869}, pmid = {35281910}, issn = {1663-9812}, abstract = {Cadmium (Cd) exposure is a widespread problem in many parts of the world, but effective means to treat Cd exposure is still lacking. Hence, an engineered strain expressing metallothionein (MT) named Escherichia coli Nissle 1917 (EcN)-MT was constructed, and its potential in the treatment of Cd exposure was evaluated. The in vitro studies showed that metallothionein expressed by EcN-MT could significantly bind Cd. Further, the in vivo results indicated that EcN-MT strain could reduce 26.3% Cd in the liver and increase 24.7% Cd in the feces, which greatly decreased malondialdehyde (MDA) levels and increased catalase (CAT), glutathione (GSH), and superoxide dismutase (SOD) levels in liver, and reduced the expression of toll-like receptor4 (TLR4), nuclear factor-κB (NF-κB), the myeloid differentiation factor 88 (Myd88) andincreased B-cell lymphoma 2 (Bcl-2)/Bcl-2-Associated X (Bax). Moreover, high throughput sequencing results indicated that EcN-MT strain greatly enhanced the beneficial bacteria of Ruminococcaceae, Lactobacillaceae, Akkermansia, Muribaculaceae, Lachnospiraceae, Dubosiella and restored the disturbed microbial ecology to the normal level. Therefore, the high Cd binding capacity of the expressed metallothionein, together with the beneficial characteristics of the host bacteria EcN, makes EcN-MT a sound reagent for the treatment of subchronic Cd exposure-induced liver injury.}, }
@article {pmid35279466, year = {2022}, author = {Huang, YM and Jakus, N and Straub, D and Konstantinidis, KT and Blackwell, N and Kappler, A and Kleindienst, S}, title = {'Candidatus ferrigenium straubiae' sp. nov., 'Candidatus ferrigenium bremense' sp. nov., 'Candidatus ferrigenium altingense' sp. nov., are autotrophic Fe(II)-oxidizing bacteria of the family Gallionellaceae.}, journal = {Systematic and applied microbiology}, volume = {45}, number = {3}, pages = {126306}, doi = {10.1016/j.syapm.2022.126306}, pmid = {35279466}, issn = {1618-0984}, mesh = {Bacteria/genetics ; Carbon Cycle ; Ecosystem ; Ferrous Compounds/metabolism ; *Gallionellaceae/genetics/metabolism ; Nitrates/metabolism ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Iron(II) [Fe(II)] oxidation coupled to denitrification is recognized as an environmentally important process in many ecosystems. However, the Fe(II)-oxidizing bacteria (FeOB) dominating autotrophic nitrate-reducing Fe(II)-oxidizing enrichment cultures, affiliated with the family Gallionellaceae, remain poorly taxonomically defined due to lack of representative isolates. We describe the taxonomic classification of three novel FeOB based on metagenome-assembled genomes (MAGs) acquired from the autotrophic nitrate-reducing enrichment cultures KS, BP and AG. Phylogenetic analysis of nearly full-length 16S rRNA gene sequences demonstrated that these three FeOB were most closely affiliated to the genera Ferrigenium, Sideroxydans and Gallionella, with up to 96.5%, 95.4% and 96.2% 16S rRNA gene sequence identities to representative isolates of these genera, respectively. In addition, average amino acid identities (AAI) of the genomes compared to the most closely related genera revealed highest AAI with Ferrigenium kumadai An22 (76.35-76.74%), suggesting that the three FeOB are members of this genus. Phylogenetic analysis of conserved functional genes further supported that these FeOB represent three novel species of the genus Ferrigenium. Moreover, the three novel FeOB likely have characteristic features, performing partial denitrification coupled to Fe(II) oxidation and carbon fixation. Scanning electron microscopy of the enrichment cultures showed slightly curved rod-shaped cells, ranging from 0.2-0.7 μm in width and 0.5-2.3 μm in length. Based on the phylogenetic, genomic and physiological characteristics, we propose that these FeOB represent three novel species, 'Candidatus Ferrigenium straubiae' sp. nov., 'Candidatus Ferrigenium bremense' sp. nov. and 'Candidatus Ferrigenium altingense' sp. nov. that might have unique metabolic features among the genus Ferrigenium.}, }
@article {pmid35278970, year = {2022}, author = {Yao, X and Liu, Y and Liu, X and Qiao, Z and Sun, S and Li, X and Wang, J and Zhang, F and Jiang, X}, title = {Effects of thifluzamide on soil fungal microbial ecology.}, journal = {Journal of hazardous materials}, volume = {431}, number = {}, pages = {128626}, doi = {10.1016/j.jhazmat.2022.128626}, pmid = {35278970}, issn = {1873-3336}, mesh = {Anilides ; Fungi ; *Mycobiome ; *Soil/chemistry ; Soil Microbiology ; Thiazoles ; }, abstract = {Thifluzamide, a succinate dehydrogenase inhibitor fungicide, has been used extensively for many diseases control and has the risk of accumulation in soil ecology. In order to study the ecotoxicity of thifluzamide to soil fungal communities, typical corn field soils in north (Tai'an) and south (Guoyang) China were treated with thifluzamide (0, 0.1, 1.0 and 10.0 mg/kg) and incubated for 60 days. Thifluzamide exposure promoted soil basal respiration, and significantly reduced the number of soil culturable fungi and the abundance of soil fungi (RT-qPCR) in middle and late treatment period (15, 30, 60 days). Illumina Mi-Seq sequencing revealed that thifluzamide could reduce fungal alpha diversity (Sobs, Shannon, Simpson indexes) and change fungal community structure. FUN Guild analysis showed that the relative abundance of Undefined Saprotroph increased after the thifluzamide treatment, whereas that of Plant Pathogen decreased, and we concluded that exposure to thifluzamide could change the function of soil fungi. This study evaluated the soil ecological risk caused by thifluzamide's release into soil, providing a basis for its rational application.}, }
@article {pmid35278563, year = {2022}, author = {Hooban, B and Fitzhenry, K and O'Connor, L and Miliotis, G and Joyce, A and Chueiri, A and Farrell, ML and DeLappe, N and Tuohy, A and Cormican, M and Morris, D}, title = {A Longitudinal Survey of Antibiotic-Resistant Enterobacterales in the Irish Environment, 2019-2020.}, journal = {The Science of the total environment}, volume = {828}, number = {}, pages = {154488}, doi = {10.1016/j.scitotenv.2022.154488}, pmid = {35278563}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; *Escherichia coli/genetics ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Sewage ; Water ; beta-Lactamases/genetics ; }, abstract = {The natural environment represents a complex reservoir of antibiotic-resistant bacteria as a consequence of different wastewater discharges including anthropogenic and agricultural. Therefore, the aim of this study was to examine sewage and waters across Ireland for the presence of antibiotic-resistant Enterobacterales. Samples were collected from the West, East and South of Ireland. Two periods of sampling took place between July 2019 and November 2020, during which 118 water (30 L) and 36 sewage samples (200 mL) were collected. Waters were filtered using the CapE method, followed by enrichment and culturing. Sewage samples were directly cultured on selective agars. Isolates were identified by MALDI-TOF and antibiotic susceptibility testing was performed in accordance with EUCAST criteria. Selected isolates were examined for blaCTX-M, blaVIM, blaIMP, blaOXA-48, blaNDM, and blaKPC by real time PCR and whole genome sequencing (n = 146). A total of 419 Enterobacterales (348 water, 71 sewage) were isolated from all samples. Hospital sewage isolates displayed the highest percentage resistance to many beta-lactam and aminoglycoside antibiotics. Extended-spectrum beta-lactamase-producers were identified in 78% of water and 50% of sewage samples. One or more carbapenemase-producing Enterobacterales were identified at 23 individual sampling sites (18 water, 5 sewage). This included the detection of blaOXA-48 (n = 18), blaNDM (n = 14), blaKPC (n = 4) and blaOXA-484 (n = 1). All NDM-producing isolates harbored the ble-MBL bleomycin resistance gene. Commonly detected sequence types included Klebsiella ST323, ST17, and ST405 as well as E. coli ST131, ST38 and ST10. Core genome MLST comparisons detected identical E. coli isolates from wastewater treatment plant (WWTP) influent and nursing home sewage, and the surrounding waters. Similarly, one Klebsiella pneumoniae isolated from WWTP influent and the surrounding estuarine water were identical. These results highlight the need for regular monitoring of the aquatic environment for the presence of antibiotic-resistant organisms to adequately inform public health policies.}, }
@article {pmid35276108, year = {2022}, author = {Wu, Y and Liu, X and Dong, Q and Xiao, M and Li, B and Topalović, O and Tao, Q and Tang, X and Huang, R and Chen, G and Li, H and Chen, Y and Feng, Y and Wang, C}, title = {Remediation of petroleum hydrocarbons-contaminated soil: Analysis based on Chinese patents.}, journal = {Chemosphere}, volume = {297}, number = {}, pages = {134173}, doi = {10.1016/j.chemosphere.2022.134173}, pmid = {35276108}, issn = {1879-1298}, mesh = {Bacteria/metabolism ; Biodegradation, Environmental ; China ; Hydrocarbons/metabolism ; *Petroleum/analysis ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {Increasing soil petroleum hydrocarbons (PHs) pollution have caused world-wide concerns. The removal of PHs from soils mainly involves physical, chemical, biological processes and their combinations. To date, most reviews in this field based on research articles, but limited papers focused on the integration of remediation technologies from the perspective of patents. In this study, 20-years Chinese patents related to the remediation of soil PHs were comprehensively analyzed. It showed an increasing number of patent applications and the patents' quantity were positively correlated with Chinese GDP over the years, suggesting the more the economy developed the more environmental problems and corresponding solutions emerged. In addition, chemical technologies were mostly used in a combination to achieve faster and better effects, while the physical technologies were often used alone due to high costs. In all PHs remediation techniques, bacteria-based bioremediation was the most used from 2000 to 2019. Bacillus spp. and Pseudomonas spp. were the most used bacteria for PHs treatment because these taxa were widely harboring functions such as biosurfactant production and hydrocarbon degradation. The future research on joint technologies combining microbial and physicochemical ones for better remediation effect and application are highly encouraged.}, }
@article {pmid35275230, year = {2023}, author = {Pereira, A and Soares, MC and Santos, T and Poças, A and Pérez-Losada, M and Apprill, A and Sikkel, PC and Xavier, R}, title = {Reef Location and Client Diversity Influence the Skin Microbiome of the Caribbean Cleaner Goby Elacatinus evelynae.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {372-382}, pmid = {35275230}, issn = {1432-184X}, support = {OCE-2023420//National Science Foundation/ ; OCE-2022955//National Science Foundation/ ; OCE-1536794//National Science Foundation/ ; PTDC/BIA-MIC/27995/2017 POCI-01-0145- FEDER-027995//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; IF/00359/2015//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2020.00854.CEECIND//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {Animals ; RNA, Ribosomal, 16S ; *Perciformes ; Fishes/microbiology ; Coral Reefs ; *Microbiota ; Caribbean Region ; Bacteria ; }, abstract = {Fish-associated microorganisms are known to be affected by the environment and other external factors, such as microbial transfer between interacting partners. One of the most iconic mutualistic interactions on coral reefs is the cleaning interactions between cleaner fishes and their clients, during which direct physical contact occurs. Here, we characterized the skin bacteria of the Caribbean cleaner sharknose goby, Elacatinus evelynae, in four coral reefs of the US Virgin Islands using sequencing of the V4 region of the 16S rRNA gene. We specifically tested the relationship between gobies' level of interaction with clients and skin microbiota diversity and composition. Our results showed differences in microbial alpha- and beta-diversity in the skin of gobies from different reef habitats and high inter-individual variation in microbiota diversity and structure. Overall, the results showed that fish-to-fish direct contact and specifically, access to a diverse clientele, influences the bacterial diversity and structure of cleaner gobies' skin. Because of their frequent contact with clients, and therefore, high potential for microbial exchange, cleaner fish may serve as models in future studies aiming to understand the role of social microbial transfer in reef fish communities.}, }
@article {pmid35273366, year = {2022}, author = {Mongelli, V and Lequime, S and Kousathanas, A and Gausson, V and Blanc, H and Nigg, J and Quintana-Murci, L and Elena, SF and Saleh, MC}, title = {Innate immune pathways act synergistically to constrain RNA virus evolution in Drosophila melanogaster.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {5}, pages = {565-578}, pmid = {35273366}, issn = {2397-334X}, support = {615220/ERC_/European Research Council/International ; }, mesh = {Animals ; Antiviral Agents/metabolism ; Dicistroviridae ; *Drosophila Proteins/genetics ; Drosophila melanogaster/genetics ; Immunity, Innate ; *RNA Viruses/metabolism ; }, abstract = {Host-pathogen interactions impose recurrent selective pressures that lead to constant adaptation and counter-adaptation in both competing species. Here, we sought to study this evolutionary arms-race and assessed the impact of the innate immune system on viral population diversity and evolution, using Drosophila melanogaster as model host and its natural pathogen Drosophila C virus (DCV). We isogenized eight fly genotypes generating animals defective for RNAi, Imd and Toll innate immune pathways as well as pathogen-sensing and gut renewal pathways. Wild-type or mutant flies were then orally infected with DCV and the virus was serially passaged ten times via reinfection in naive flies. Viral population diversity was studied after each viral passage by high-throughput sequencing and infection phenotypes were assessed at the beginning and at the end of the evolution experiment. We found that the absence of any of the various immune pathways studied increased viral genetic diversity while attenuating virulence. Strikingly, these effects were observed in a range of host factors described as having mainly antiviral or antibacterial functions. Together, our results indicate that the innate immune system as a whole and not specific antiviral defence pathways in isolation, generally constrains viral diversity and evolution.}, }
@article {pmid35270157, year = {2022}, author = {Madriz-Ordeñana, K and Pazarlar, S and Jørgensen, HJL and Nielsen, TK and Zhang, Y and Nielsen, KL and Hansen, LH and Thordal-Christensen, H}, title = {The Bacillus cereus Strain EC9 Primes the Plant Immune System for Superior Biocontrol of Fusarium oxysporum.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {5}, pages = {}, pmid = {35270157}, issn = {2223-7747}, support = {34009-16-1068//Green Development and Demonstration Programme (GUDP) of the Ministry of Environment and Food of Denmark/ ; }, abstract = {Antibiosis is a key feature widely exploited to develop biofungicides based on the ability of biological control agents (BCAs) to produce fungitoxic compounds. A less recognised attribute of plant-associated beneficial microorganisms is their ability to stimulate the plant immune system, which may provide long-term, systemic self-protection against different types of pathogens. By using conventional antifungal in vitro screening coupled with in planta assays, we found antifungal and non-antifungal Bacillus strains that protected the ornamental plant Kalanchoe against the soil-borne pathogen Fusarium oxysporum in experimental and commercial production settings. Further examination of one antifungal and one non-antifungal strain indicated that high protection efficacy in planta did not correlate with antifungal activity in vitro. Whole-genome sequencing showed that the non-antifungal strain EC9 lacked the biosynthetic gene clusters associated with typical antimicrobial compounds. Instead, this bacterium triggers the expression of marker genes for the jasmonic and salicylic acid defence pathways, but only after pathogen challenge, indicating that this strain may protect Kalanchoe plants by priming immunity. We suggest that the stimulation of the plant immune system is a promising mode of action of BCAs for the development of novel biological crop protection products.}, }
@article {pmid35268714, year = {2022}, author = {Lee Díaz, AS and Rizaludin, MS and Zweers, H and Raaijmakers, JM and Garbeva, P}, title = {Exploring the Volatiles Released from Roots of Wild and Domesticated Tomato Plants under Insect Attack.}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {5}, pages = {}, pmid = {35268714}, issn = {1420-3049}, support = {765290//European Commission/ ; 024.004.14/NWO_/Dutch Research Council/Netherlands ; }, mesh = {Animals ; Herbivory ; *Solanum lycopersicum/genetics ; *Solanum ; Spodoptera ; *Volatile Organic Compounds ; }, abstract = {Plants produce volatile organic compounds that are important in communication and defense. While studies have largely focused on volatiles emitted from aboveground plant parts upon exposure to biotic or abiotic stresses, volatile emissions from roots upon aboveground stress are less studied. Here, we investigated if tomato plants under insect herbivore attack exhibited a different root volatilome than non-stressed plants, and whether this was influenced by the plant's genetic background. To this end, we analyzed one domesticated and one wild tomato species, i.e., Solanum lycopersicum cv Moneymaker and Solanum pimpinellifolium, respectively, exposed to leaf herbivory by the insect Spodoptera exigua. Root volatiles were trapped with two sorbent materials, HiSorb and PDMS, at 24 h after exposure to insect stress. Our results revealed that differences in root volatilome were species-, stress-, and material-dependent. Upon leaf herbivory, the domesticated and wild tomato species showed different root volatile profiles. The wild species presented the largest change in root volatile compounds with an overall reduction in monoterpene emission under stress. Similarly, the domesticated species presented a slight reduction in monoterpene emission and an increased production of fatty-acid-derived volatiles under stress. Volatile profiles differed between the two sorbent materials, and both were required to obtain a more comprehensive characterization of the root volatilome. Collectively, these results provide a strong basis to further unravel the impact of herbivory stress on systemic volatile emissions.}, }
@article {pmid35266794, year = {2022}, author = {Monsees, I and Turzynski, V and Esser, SP and Soares, A and Timmermann, LI and Weidenbach, K and Banas, J and Kloster, M and Beszteri, B and Schmitz, RA and Probst, AJ}, title = {Erratum for Monsees et al., "Label-Free Raman Microspectroscopy for Identifying Prokaryotic Virocells".}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0016222}, doi = {10.1128/msystems.00162-22}, pmid = {35266794}, issn = {2379-5077}, }
@article {pmid35266047, year = {2022}, author = {Proenca, AM and Oliveira, MM and Neves, PFR and Giongo, A and de Oliveira, RR and Ott, CT and Marconatto, L and de Barros Neto, HMC and Ketzer, JMM and Medina-Silva, R}, title = {Genomic, biochemical, and phylogenetic evaluation of bacteria isolated from deep-sea sediment harboring methane hydrates.}, journal = {Archives of microbiology}, volume = {204}, number = {4}, pages = {205}, pmid = {35266047}, issn = {1432-072X}, mesh = {*Bacteria ; Genomics ; Geologic Sediments/microbiology ; *Methane/metabolism ; Phylogeny ; }, abstract = {Over half of the organic carbon on Earth's surface is trapped in marine sediment as methane hydrates. Ocean warming causes hydrate dissociation and methane leakage to the water column, rendering the characterization of microbes from hydrate depositions a pressing matter. Through genomic, phylogenetic, and biochemical assays, we characterize the first microorganisms isolated from the Rio Grande Cone (Brazil), reservoir responsible for massive methane releases to the water column. From sediment harboring rich benthic communities, we obtained 43 strains of Brevibacillus sp., Paenibacillus sp. and groups of Bacillus sp. Methane-enriched samples yielded strains of the Pseudomonas fluorescens complex, exhibiting fluorescent siderophore production and broad multi-carbon catabolism. Genomic characterization of a novel Pseudomonas sp. strain indicated 32 genes not identified in the closest related type-species, including proteins involved with mercury resistance. Our results provide phylogenetic and genomic insights on the first bacterial isolates retrieved from a poorly explored region of the South Atlantic Ocean.}, }
@article {pmid35265531, year = {2022}, author = {Yang, S and Lyu, X and Zhang, J and Shui, Y and Yang, R and Xu, X}, title = {The Application of Small Molecules to the Control of Typical Species Associated With Oral Infectious Diseases.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {816386}, pmid = {35265531}, issn = {2235-2988}, mesh = {*Communicable Diseases ; *Dental Caries/prevention &amp; control ; Dysbiosis ; Humans ; *Microbiota ; Virulence ; }, abstract = {Oral microbial dysbiosis is the major causative factor for common oral infectious diseases including dental caries and periodontal diseases. Interventions that can lessen the microbial virulence and reconstitute microbial ecology have drawn increasing attention in the development of novel therapeutics for oral diseases. Antimicrobial small molecules are a series of natural or synthetic bioactive compounds that have shown inhibitory effect on oral microbiota associated with oral infectious diseases. Novel small molecules, which can either selectively inhibit keystone microbes that drive dysbiosis of oral microbiota or inhibit the key virulence of the microbial community without necessarily killing the microbes, are promising for the ecological management of oral diseases. Here we discussed the research progress in the development of antimicrobial small molecules and delivery systems, with a particular focus on their antimicrobial activity against typical species associated with oral infectious diseases and the underlying mechanisms.}, }
@article {pmid35264931, year = {2022}, author = {Muedra, V and Rodilla, V and Llansola, M and Agustí, A and Pla, C and Canto, A and Hernández-Rabaza, V}, title = {Potential Neuroprotective Role of Sugammadex: A Clinical Study on Cognitive Function Assessment in an Enhanced Recovery After Cardiac Surgery Approach and an Experimental Study.}, journal = {Frontiers in cellular neuroscience}, volume = {16}, number = {}, pages = {789796}, pmid = {35264931}, issn = {1662-5102}, abstract = {BACKGROUND: Postoperative cognitive dysfunction affects the quality of recovery, particularly affecting the elderly, and poses a burden on the health system. We hypothesize that the use of sugammadex (SG) could optimize the quality of postoperative cognitive function and overall recovery through a neuroprotective effect.<br><br>METHODS: A pilot observational study on patients undergoing cardiac surgery with enhanced recovery after cardiac surgery (ERACS) approach, was designed to compare SG-treated (n = 14) vs. neostigmine (NG)-treated (n = 7) patients. The Postoperative Quality Recovery Scale (PQRS) was used at different times to evaluate cognitive function and overall recovery of the patients. An online survey among anesthesiologists on SG use was also performed. Additionally, an animal model study was designed to explore the effects of SG on the hippocampus.<br><br>RESULTS: Sugammadex (SG) was associated with favorable postoperative recovery in cognitive domains particularly 30 days after surgery in patients undergoing aortic valve replacement by cardiopulmonary bypass and the ERACS approach; however, it failed to demonstrate a short-term decrease in length of intensive care unit (ICU) and hospital stay. The survey information indicated a positive appreciation of SG recovery properties. SG reverts postoperative memory deficit and induces the expression of anti-inflammatory microglial markers.<br><br>CONCLUSION: The results show a postoperative cognitive improvement by SG treatment in patients undergoing aortic valve replacement procedure by the ERACS approach. Additionally, experimental data from an animal model of mild surgery confirm the cognitive effect of SG and suggest a potential effect over glia cells as an underlying mechanism.}, }
@article {pmid35264088, year = {2022}, author = {Rana, D and Salave, S and Perla, A and Nadkarni, A and Kolhe, S and Jindal, AB and Mandoli, A and Dwivedi, P and Benival, D}, title = {Bugs as Drugs: Understanding the Linkage between Gut Microbiota and Cancer Treatment.}, journal = {Current drug targets}, volume = {23}, number = {9}, pages = {869-888}, doi = {10.2174/1389450123666220309101345}, pmid = {35264088}, issn = {1873-5592}, mesh = {Carcinogenesis ; Diet ; Dysbiosis/therapy ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; }, abstract = {The commensal microbiota is known to regulate host physiology. Dysbiosis or compromised resilience in the microbial ecology is related to the impending risk of cancer. A potential link between cancer and microbiota is indicated by a lot of evidence. The current review explores in detail the various links leading to and /or facilitating oncogenesis, providing sound reasoning or a basis for its utilization as potential therapeutic targets. The present review emphasizes the existing knowledge of the microbiome in cancer and further elaborates on the factors, like genetic modifications, effects of dietary components, and environmental agents, that are considered to assess the direct and indirect effect of microbes in the process of oncogenesis and on the host's health. Strategies modulating the microbiome and novel biotherapeutics are also discussed. Pharmacomicrobiomics is one such niche accounting for the interplay between the microbiome, xenobiotic, and host responses, which is also looked upon. The literature search strategy for this review was conducted by following the methodology of the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA). The method includes the collection of data from different search engines, like PubMed, ScienceDirect, SciFinder, etc., to get coverage of relevant literature for accumulating appropriate information regarding microbiome, cancer, and their linkages. These considerations are made to expand the existing literature on the role of gut microbiota in the host's health, the interaction between host and microbiota, and the reciprocal relationship between the microbiome and modified neoplastic cells. Potential therapeutic implications of cancer microbiomes that are yet unexplored and have rich therapeutic dividends improving human health are discussed in detail in this review.}, }
@article {pmid35261753, year = {2022}, author = {Stelzer, JAA and Mesman, JP and Gsell, AS and de Senerpont Domis, LN and Visser, PM and Adrian, R and Ibelings, BW}, title = {Phytoplankton responses to repeated pulse perturbations imposed on a trend of increasing eutrophication.}, journal = {Ecology and evolution}, volume = {12}, number = {3}, pages = {e8675}, pmid = {35261753}, issn = {2045-7758}, abstract = {While eutrophication remains one of the main pressures acting on freshwater ecosystems, the prevalence of anthropogenic and nature-induced stochastic pulse perturbations is predicted to increase due to climate change. Despite all our knowledge on the effects of eutrophication and stochastic events operating in isolation, we know little about how eutrophication may affect the response and recovery of aquatic ecosystems to pulse perturbations. There are multiple ways in which eutrophication and pulse perturbations may interact to induce potentially synergic changes in the system, for instance, by increasing the amount of nutrients released after a pulse perturbation. Here, we performed a controlled press and pulse perturbation experiment using mesocosms filled with natural lake water to address how eutrophication modulates the phytoplankton response to sequential mortality pulse perturbations; and what is the combined effect of press and pulse perturbations on the resistance and resilience of the phytoplankton community. Our experiment showed that eutrophication increased the absolute scale of the chlorophyll-a response to pulse perturbations but did not change the proportion of the response relative to its pre-event condition (resistance). Moreover, the capacity of the community to recover from pulse perturbations was significantly affected by the cumulative effect of sequential pulse perturbations but not by eutrophication itself. By the end of the experiment, some mesocosms could not recover from pulse perturbations, irrespective of the trophic state induced by the press perturbation. While not resisting or recovering any less from pulse perturbations, phytoplankton communities from eutrophying systems showed chlorophyll-a levels much higher than non-eutrophying ones. This implies that the higher absolute response to stochastic pulse perturbations in a eutrophying system may increase the already significant risks for water quality (e.g., algal blooms in drinking water supplies), even if the relative scale of the response to pulse perturbations between eutrophying and non-eutrophying systems remains the same.}, }
@article {pmid35261041, year = {2022}, author = {Lousada, MB and Lachnit, T and Edelkamp, J and Paus, R and Bosch, TCG}, title = {Hydra and the hair follicle - An unconventional comparative biology approach to exploring the human holobiont.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {44}, number = {5}, pages = {e2100233}, doi = {10.1002/bies.202100233}, pmid = {35261041}, issn = {1521-1878}, mesh = {Animals ; Biology ; Hair Follicle ; Humans ; *Hydra/physiology ; Microbial Interactions ; *Microbiota/physiology ; }, abstract = {The microbiome of human hair follicles (HFs) has emerged as an important player in different HF and skin pathologies, yet awaits in-depth exploration. This raises questions regarding the tightly linked interactions between host environment, nutrient dependency of host-associated microbes, microbial metabolism, microbe-microbe interactions and host immunity. The use of simple model systems facilitates addressing generally important questions and testing overarching, therapeutically relevant principles that likely transcend obvious interspecies differences. Here, we evaluate the potential of the freshwater polyp Hydra, to dissect fundamental principles of microbiome regulation by the host, that is the human HF. In particular, we focus on therapeutically targetable host-microbiome interactions, such as nutrient dependency, microbial interactions and host defence. Offering a new lens into the study of HF - microbiota interactions, we argue that general principles of how Hydra manages its microbiota can inform the development of novel, microbiome-targeting therapeutic interventions in human skin disease.}, }
@article {pmid35260198, year = {2022}, author = {Xie, Y and Sun, H and Xue, M and Liu, J}, title = {Metagenomics reveals differences in microbial composition and metabolic functions in the rumen of dairy cows with different residual feed intake.}, journal = {Animal microbiome}, volume = {4}, number = {1}, pages = {19}, pmid = {35260198}, issn = {2524-4671}, support = {31872380//National Natural Science Foundation of China/ ; CARS-36//Agriculture Research System of China/ ; }, abstract = {BACKGROUND: Rumen microbial composition and functions have vital roles in feed digestion and fermentation and are linked to feed efficiency in cattle. This study selected Holstein cows, which are high in both milk protein content and milk yield, to analyse the relationship between the rumen microbiota and residual feed intake (RFI). Eighteen multiparous lactating cows were divided into low RFI (LRFI, high efficiency, n = 9) and high RFI (HRFI, low efficiency, n = 9) groups to investigate the differences in microbial composition and functions.<br><br>RESULTS: The relative abundances of butyrate producers, including the Clostridium, Butyrivibrio, Eubacterium and Blautia genera, were higher in HRFI cows than in LRFI cows (P&#x2009;<&#x2009;0.05). Four carbohydrate metabolic pathways (glycolysis/gluconeogenesis, pentose phosphate pathway, fructose and mannose metabolism, and butanoate metabolism) and one energy metabolism pathway (methane metabolism), were more abundant in HRFI animals (P&#x2009;<&#x2009;0.05). Quorum sensing and DNA replication pathways were more abundant in HRFI cows. For CAZyme profiles, 14 out of 19 genes encoding carbohydrates-deconstructing enzymes were more abundant in HRFI cows (P&#x2009;<&#x2009;0.05). Seven Lachnospiraceae species associated with carbohydrate metabolism and quorum sensing may contribute to the difference in feed efficiency. Moreover, the LRFI cows had lower abundances of Methanosphaera (P&#x2009;<&#x2009;0.01), Methanobrevibacter ruminantium (P&#x2009;=&#x2009;0.09) and methanogenesis functions (P&#x2009;=&#x2009;0.04).<br><br>CONCLUSIONS: The rumen microbiota of low-efficiency cows has stronger abilities to degrade carbohydrates and produce methane, and quorum sensing pathways could also be associated with differences in feed efficiency. This study provides a deeper understanding of the microbial ecology of dairy cows with different feed efficiencies and highlights the possibility of modulating the rumen microbiome or microbial functions to improve the feed efficiency of dairy cows.}, }
@article {pmid35256948, year = {2022}, author = {Little, M and Dutta, M and Li, H and Matson, A and Shi, X and Mascarinas, G and Molla, B and Weigel, K and Gu, H and Mani, S and Cui, JY}, title = {Understanding the physiological functions of the host xenobiotic-sensing nuclear receptors PXR and CAR on the gut microbiome using genetically modified mice.}, journal = {Acta pharmaceutica Sinica. B}, volume = {12}, number = {2}, pages = {801-820}, pmid = {35256948}, issn = {2211-3835}, support = {P50 HD103524/HD/NICHD NIH HHS/United States ; R01 ES031098/ES/NIEHS NIH HHS/United States ; R01 ES030197/ES/NIEHS NIH HHS/United States ; R01 GM111381/GM/NIGMS NIH HHS/United States ; P30 ES007033/ES/NIEHS NIH HHS/United States ; R25 ES025503/ES/NIEHS NIH HHS/United States ; R01 CA222469/CA/NCI NIH HHS/United States ; R01 GM057001/GM/NIGMS NIH HHS/United States ; R01 ES025708/ES/NIEHS NIH HHS/United States ; P01 HL029019/HL/NHLBI NIH HHS/United States ; }, abstract = {Pharmacological activation of the xenobiotic-sensing nuclear receptors pregnane X receptor (PXR) and constitutive androstane receptor (CAR) is well-known to increase drug metabolism and reduce inflammation. Little is known regarding their physiological functions on the gut microbiome. In this study, we discovered bivalent hormetic functions of PXR/CAR modulating the richness of the gut microbiome using genetically engineered mice. The absence of PXR or CAR increased microbial richness, and absence of both receptors synergistically increased microbial richness. PXR and CAR deficiency increased the pro-inflammatory bacteria Helicobacteraceae and Helicobacter. Deficiency in both PXR and CAR increased the relative abundance of Lactobacillus, which has bile salt hydrolase activity, corresponding to decreased primary taurine-conjugated bile acids (BAs) in feces, which may lead to higher internal burden of taurine and unconjugated BAs, both of which are linked to inflammation, oxidative stress, and cytotoxicity. The basal effect of PXR/CAR on the gut microbiome was distinct from pharmacological and toxicological activation of these receptors. Common PXR/CAR-targeted bacteria were identified, the majority of which were suppressed by these receptors. hPXR-TG mice had a distinct microbial profile as compared to wild-type mice. This study is the first to unveil the basal functions of PXR and CAR on the gut microbiome.}, }
@article {pmid35254501, year = {2023}, author = {Wang, T and Kuang, B and Ni, Z and Guo, B and Li, Y and Zhu, G}, title = {Stimulating Anaerobic Degradation of Butyrate via Syntrophomonas wolfei and Geobacter sulfurreducens: Characteristics and Mechanism.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {535-543}, pmid = {35254501}, issn = {1432-184X}, support = {52070176//the National Natural Science Foundation of China/ ; 21876167//the National Natural Science Foundation of China/ ; 51678553//the National Natural Science Foundation of China/ ; }, mesh = {Anaerobiosis ; Electron Transport ; *Geobacter ; Butyric Acid ; }, abstract = {Anaerobic digestion (AD) has been widely applied for the degradation of organic wastewater due to its advantages of high-load operation and energy recovery. However, some challenges, such as low treatment capacity and instability caused by the accumulation of volatile fatty acids, limit its further application. Here, S. wolfei and G. sulfurreducens were initially co-cultured in the anaerobic anode of bio-electrochemical system for degrading butyric acid. Butyrate degradation characteristics in different conditions were quantitatively described. Moreover, G. sulfurreducens simultaneously strengthened the consumption of H2 and acetic acid via direct interspecies electron transfer, thereby strengthening the degradation of butyric acid via a co-metabolic process. During butyrate degradation, the co-culture of S. wolfei and G. sulfurreducens showed more advantages than that of S. wolfei and methanogens. This present study provides a new perspective of butyrate metabolism, which was independent of methanogens in an AD process.}, }
@article {pmid35254236, year = {2022}, author = {Tomasch, J and Ringel, V and Wang, H and Freese, HM and Bartling, P and Brinkmann, H and Vollmers, J and Jarek, M and Wagner-Döbler, I and Petersen, J}, title = {Fatal affairs - conjugational transfer of a dinoflagellate-killing plasmid between marine Rhodobacterales.}, journal = {Microbial genomics}, volume = {8}, number = {3}, pages = {}, pmid = {35254236}, issn = {2057-5858}, mesh = {*Dinoflagellida/genetics ; Plasmids/genetics ; Replicon ; Rhodobacteraceae ; *Roseobacter/genetics ; }, abstract = {The roseobacter group of marine bacteria is characterized by a mosaic distribution of ecologically important phenotypes. These are often encoded on mobile extrachromosomal replicons. So far, conjugation had only been experimentally proven between the two model organisms Phaeobacter inhibens and Dinoroseobacter shibae. Here, we show that two large natural RepABC-type plasmids from D. shibae can be transferred into representatives of all known major Rhodobacterales lineages. Complete genome sequencing of the newly established Phaeobacter inhibens transconjugants confirmed their genomic integrity. The conjugated plasmids were stably maintained as single copy number replicons in the genuine as well as the new host. Co-cultivation of Phaeobacter inhibens and the transconjugants with the dinoflagellate Prorocentrum minimum demonstrated that Phaeobacter inhibens is a probiotic strain that improves the yield and stability of the dinoflagellate culture. The transconjugant carrying the 191 kb plasmid, but not the 126 kb sister plasmid, killed the dinoflagellate in co-culture.}, }
@article {pmid35250945, year = {2022}, author = {Bai, C and Pan, G and Leng, R and Ni, W and Yang, J and Sun, J and Yu, Z and Liu, Z and Xue, Y}, title = {Effect of Ensiling Density and Storage Temperature on Fermentation Quality, Bacterial Community, and Nitrate Concentration of Sorghum-Sudangrass Silage.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {828320}, pmid = {35250945}, issn = {1664-302X}, abstract = {This study aimed to evaluate the fermentation quality, bacterial community, and nitrate content of sorghum-sudangrass silage with two ensiling densities [550 kg fresh weight (FW)/m[3] (low density, LD) and 650 kg FW/m[3] (high density, HD)] stored at two temperatures [10°C (low temperature, LT) and 25°C (normal temperature, NT)] for 60 days. The fermentation parameters, microbial counts, bacterial community, nutritional composition, and nitrate and nitrite levels were assessed. The pH and ammonia nitrogen (N) in all silages were below 4.0 and 80 g/kg total N, respectively. Compared with LT treatments, NT treatments had lower pH and lactic acid (LA) bacteria and yeasts counts and contained higher LA and LA/acetic acid (LA/AA) (p < 0.05). The LT-LD contained more ammonia-N than LT-HD (p < 0.05) and had higher nitrate and lower nitrate degradation than other treatments (p < 0.05). Lactobacillus was the most dominant genus with all treatments (57.2-66.9%). The LA, LA/AA, and abundances of Pantoea, Pseudomonas, and Enterobacter in the silage negatively correlated with nitrate concentration and positively correlated with nitrate degradation (p < 0.05). Moreover, pH and ammonia-N were positively correlated with nitrate concentration and negatively correlated with nitrate degradation (p < 0.05). Overall, all silage had satisfactory fermentation quality, and the silage with HD and NT had better fermentation quality and higher nitrate degradation. The bacterial communities in all silages were dominated by Lactobacillus. The nitrate degradation during the fermentation process might be related to the fermentation quality and the activity of Pantoea, Pseudomonas, and Enterobacter in silage.}, }
@article {pmid35248630, year = {2022}, author = {Obieze, CC and Wani, GA and Shah, MA and Reshi, ZA and Comeau, AM and Khasa, DP}, title = {Anthropogenic activities and geographic locations regulate microbial diversity, community assembly and species sorting in Canadian and Indian freshwater lakes.}, journal = {The Science of the total environment}, volume = {826}, number = {}, pages = {154292}, doi = {10.1016/j.scitotenv.2022.154292}, pmid = {35248630}, issn = {1879-1026}, mesh = {Anthropogenic Effects ; Bacteria ; Canada ; Humans ; *Lakes/chemistry ; *Microbiota ; }, abstract = {Freshwater lakes are important reservoirs and sources of drinking water globally. However, the microbiota, which supports the functionality of these ecosystems is threatened by the influx of nutrients, heavy metals and other toxic chemical substances from anthropogenic activities. The influence of these factors on the diversity, assembly mechanisms and co-occurrence patterns of bacterial communities in freshwater lakes is not clearly understood. Hence, samples were collected from six different impacted lakes in Canada and India and examined by 454-pyrosequencing technology. The trophic status of these lakes was determined using specific chemical parameters. Our results revealed that bacterial diversity and community composition was altered by both the lake water chemistry and geographic distance. Anthropogenic activities pervasively influenced species distribution. Dispersal limitation (32.3%), homogenous selection (31.8%) and drift (20%) accounted for the largest proportions of the bacterial community assembly mechanisms. Homogenous selection increased in lakes with higher nutrient concentration, while stochasticity reduced. Community functional profiles revealed that deterministic processes dominated the assembly mechanisms of phylotypes with higher potential for biodegradation, while stochasticity dominated the assembly of phylotypes with potential for antimicrobial resistance. Bacteroidota (44%) and Proteobacteria (34%) were the most abundant phyla. Co-occurrence network analysis revealed that complexity increased in more impacted lakes, while competition and the nature of anthropogenic activity contributed to species sorting. Overall, this study demonstrates that bacterial community changes in freshwater lakes are linked to anthropogenic activities, with corresponding consequences on the distribution of phylotypes of environmental and human health interest.}, }
@article {pmid35248491, year = {2022}, author = {Barragán-Fonseca, KY and Nurfikari, A and van de Zande, EM and Wantulla, M and van Loon, JJA and de Boer, W and Dicke, M}, title = {Insect frass and exuviae to promote plant growth and health.}, journal = {Trends in plant science}, volume = {27}, number = {7}, pages = {646-654}, doi = {10.1016/j.tplants.2022.01.007}, pmid = {35248491}, issn = {1878-4372}, mesh = {Animals ; *Insecta ; *Plant Development ; Plants ; Soil ; Soil Microbiology ; }, abstract = {Beneficial soil microorganisms can contribute to biocontrol of plant pests and diseases, induce systemic resistance (ISR) against attackers, and enhance crop yield. Using organic soil amendments has been suggested to stimulate the abundance and/or activity of beneficial indigenous microbes in the soil. Residual streams from insect farming (frass and exuviae) contain chitin and other compounds that may stimulate beneficial soil microbes that have ISR and biocontrol activity. Additionally, changes in plant phenotype that are induced by beneficial microorganisms may directly influence plant-pollinator interactions, thus affecting plant reproduction. We explore the potential of insect residual streams derived from the production of insects as food and feed to promote plant growth and health, as well as their potential benefits for sustainable agriculture.}, }
@article {pmid35247805, year = {2022}, author = {Song, S and Gui, Y and Rahman, MS and Xu, H}, title = {Use of protozoan periphytons for evaluating of environmental heterogeneity in intertidal zones of marine ecosystems.}, journal = {Marine pollution bulletin}, volume = {177}, number = {}, pages = {113498}, doi = {10.1016/j.marpolbul.2022.113498}, pmid = {35247805}, issn = {1879-3363}, mesh = {Biodiversity ; *Ciliophora ; Ecosystem ; Environmental Monitoring ; *Periphyton ; }, abstract = {As an important biological indicator, multivariate dispersion in homogeneity of an observed community is a useful parameter for bioassessment of environmental heterogeneity. To identify the influence of tidal events on homogeneity of protozoan periphyton fauna from the highest tideline to the lowest, a 1-month baseline survey was carried out along five tidelines (sites A-E) in an intertidal zone of the Yellow Sea, northern China. There was a significant influence of tidal events on the homogeneity in both compositional and community structure among five tidelines. The β-diversity measures generally decreased from the highest tideline to the lowest. The biodiversity indices of the protozoans dropped sharply from the highest to the middle tidelines, followed by an increase until to the lowest tideline. These findings suggest that the homogeneity of protozoan periphyton in both species composition and relative abundance was significantly shaped by the environmental heterogeneity in intertidal zones of marine ecosystems.}, }
@article {pmid35246698, year = {2023}, author = {Fuster, M and Billard, H and Bronner, G and Sime-Ngando, T and Colombet, J}, title = {Occurrence and Seasonal Dynamics of ALNs in Freshwater Lakes Are Influenced by Their Biological Environment.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {523-534}, pmid = {35246698}, issn = {1432-184X}, mesh = {*Lakes ; *Ecosystem ; Seasons ; Prokaryotic Cells ; }, abstract = {Aster-like nanoparticles (ALNs) are femtoentities, recently discovered in different aquatic environments, whose intrinsic nature and ecological features remain to be determined. In this study, we investigate the in situ temporal dynamics of ALNs during 1 year in 3 different lakes, in relation to the physico-chemical and biological environment. ALN abundances in investigated lakes showed a marked seasonal dynamic (from no detectable to 4.28 ± 0.75 × 10[6] ALNs mL[-1]), with characteristic peaks in spring. We recorded a correlation between ALNs and some prokaryotic phyla suggesting a broad and non-specific relationship. From their seasonal dynamics and potential link with prokaryotes, we conclude that ALNs represent an important ecological actor in the functioning of aquatic ecosystems.}, }
@article {pmid35243218, year = {2022}, author = {Liu, X and Le Roux, X and Salles, JF}, title = {The legacy of microbial inoculants in agroecosystems and potential for tackling climate change challenges.}, journal = {iScience}, volume = {25}, number = {3}, pages = {103821}, pmid = {35243218}, issn = {2589-0042}, abstract = {Microbial inoculations contribute to reducing agricultural systems' environmental footprint by supporting sustainable production and regulating climate change. However, the indirect and cascading effects of microbial inoculants through the reshaping of soil microbiome are largely overlooked. By discussing the underlying mechanisms of plant- and soil-based microbial inoculants, we suggest that a key challenge in microbial inoculation is to understand their legacy on indigenous microbial communities and the corresponding impacts on agroecosystem functions and services relevant to climate change. We explain how these legacy effects on the soil microbiome can be understood by building on the mechanisms driving microbial invasions and placing inoculation into the context of ecological succession and community assembly. Overall, we advocate that generalizing field trials to systematically test inoculants' effectiveness and developing knowledge anchored in the scientific field of biological/microbial invasion are two essential requirements for applying microbial inoculants in agricultural ecosystems to tackle climate change challenges.}, }
@article {pmid35242754, year = {2021}, author = {Kuchenbuch, A and Frank, R and Ramos, JV and Jahnke, HG and Harnisch, F}, title = {Electrochemical Microwell Plate to Study Electroactive Microorganisms in Parallel and Real-Time.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {9}, number = {}, pages = {821734}, pmid = {35242754}, issn = {2296-4185}, abstract = {Microbial resource mining of electroactive microorganism (EAM) is currently methodically hampered due to unavailable electrochemical screening tools. Here, we introduce an electrochemical microwell plate (ec-MP) composed of a 96 electrochemical deepwell plate and a recently developed 96-channel multipotentiostat. Using the ec-MP we investigated the electrochemical and metabolic properties of the EAM models Shewanella oneidensis and Geobacter sulfurreducens with acetate and lactate as electron donor combined with an individual genetic analysis of each well. Electrochemical cultivation of pure cultures achieved maximum current densities (j max) and coulombic efficiencies (CE) that were well in line with literature data. The co-cultivation of S. oneidensis and G. sulfurreducens led to an increased current density of j max of 88.57 ± 14.04 µA cm[-2] (lactate) and j max of 99.36 ± 19.12 µA cm[-2] (lactate and acetate). Further, a decreased time period of reaching j max and biphasic current production was revealed and the microbial electrochemical performance could be linked to the shift in the relative abundance.}, }
@article {pmid35242286, year = {2022}, author = {Blakeley-Ruiz, JA and Kleiner, M}, title = {Considerations for constructing a protein sequence database for metaproteomics.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {937-952}, pmid = {35242286}, issn = {2001-0370}, support = {R35 GM138362/GM/NIGMS NIH HHS/United States ; T32 DK007737/DK/NIDDK NIH HHS/United States ; }, abstract = {Mass spectrometry-based metaproteomics has emerged as a prominent technique for interrogating the functions of specific organisms in microbial communities, in addition to total community function. Identifying proteins by mass spectrometry requires matching mass spectra of fragmented peptide ions to a database of protein sequences corresponding to the proteins in the sample. This sequence database determines which protein sequences can be identified from the measurement, and as such the taxonomic and functional information that can be inferred from a metaproteomics measurement. Thus, the construction of the protein sequence database directly impacts the outcome of any metaproteomics study. Several factors, such as source of sequence information and database curation, need to be considered during database construction to maximize accurate protein identifications traceable to the species of origin. In this review, we provide an overview of existing strategies for database construction and the relevant studies that have sought to test and validate these strategies. Based on this review of the literature and our experience we provide a decision tree and best practices for choosing and implementing database construction strategies.}, }
@article {pmid35241676, year = {2022}, author = {Lapidot, Y and Reshef, L and Maya, M and Cohen, D and Gophna, U and Muhsen, K}, title = {Socioeconomic disparities and household crowding in association with the fecal microbiome of school-age children.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {10}, pmid = {35241676}, issn = {2055-5008}, mesh = {Child ; *Crowding ; Family Characteristics ; Humans ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The development of the gut microbiome occurs mainly during the first years of life; however, little is known on the role of environmental and socioeconomic exposures, particularly within the household, in shaping the microbial ecology through childhood. We characterized differences in the gut microbiome of school-age healthy children, in association with socioeconomic disparities and household crowding. Stool samples were analyzed from 176 Israeli Arab children aged six to nine years from three villages of different socioeconomic status (SES). Sociodemographic data were collected through interviews with the mothers. We used 16 S rRNA gene sequencing to characterize the gut microbiome, including an inferred analysis of metabolic pathways. Differential analysis was performed using the analysis of the composition of microbiomes (ANCOM), with adjustment for covariates. An analysis of inferred metagenome functions was performed implementing PICRUSt2. Gut microbiome composition differed across the villages, with the largest difference attributed to socioeconomic disparities, with household crowding index being a significant explanatory variable. Living in a low SES village and high household crowding were associated with increased bacterial richness and compositional differences, including an over-representation of Prevotella copri and depleted Bifidobacterium. Secondary bile acid synthesis, d-glutamine and d-glutamate metabolism and Biotin metabolism were decreased in the lower SES village. In summary, residential SES is a strong determinant of the gut microbiome in healthy school-age children, mediated by household crowding and characterized by increased bacterial richness and substantial taxonomic and metabolic differences. Further research is necessary to explore possible implications of SES-related microbiome differences on children's health and development.}, }
@article {pmid35241064, year = {2022}, author = {Uehara, O and Abiko, Y and Nagasawa, T and Morikawa, T and Hiraki, D and Harada, F and Kawano, Y and Toraya, S and Matsuoka, H and Paudel, D and Shimizu, S and Yoshida, K and Asaka, M and Furuichi, Y and Miura, H}, title = {Alterations in the oral microbiome of individuals with a healthy oral environment following COVID-19 vaccination.}, journal = {BMC oral health}, volume = {22}, number = {1}, pages = {50}, pmid = {35241064}, issn = {1472-6831}, support = {21-6-14//the 8020 Promotion Foundation/ ; 21-6-14//the 8020 Promotion Foundation/ ; 21-6-14//the 8020 Promotion Foundation/ ; 21-6-14//the 8020 Promotion Foundation/ ; }, mesh = {*COVID-19/prevention &amp; control ; COVID-19 Vaccines ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; SARS-CoV-2 ; Vaccination ; Vaccines, Synthetic ; mRNA Vaccines ; }, abstract = {BACKGROUND: Several reports suggest that the microbiome of the digestive system affects vaccine efficacy and that the severity of coronavirus disease (COVID-19) is associated with decreased diversity of the oral and/or intestinal microbiome. The present study examined the effects of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mRNA vaccine on the oral microbiome.<br><br>METHODS: Forty healthy Japanese oral healthcare personnel were recruited, and unstimulated saliva was collected before vaccination, after the 1st vaccination, and after the 2nd vaccination. Genomic DNA was extracted from saliva samples, and PCR amplicons of the 16S rRNA gene were analyzed using next-generation sequencing. Microbial diversity and composition were analyzed using Quantitative Insights into Microbial Ecology 2. In addition, alterations in microbial function were assessed using PICRUSt2.<br><br>RESULTS: SARS-CoV-2 mRNA vaccination significantly increased oral bacterial diversity and significantly decreased the proportion of the genus Bacteroides.<br><br>CONCLUSIONS: The SARS-CoV-2 mRNA vaccine alters the oral microbiome; accordingly, vaccination might have beneficial effects on oral health.}, }
@article {pmid35237932, year = {2022}, author = {Kumar, M and Sodhi, KK and Singh, DK}, title = {Draft genome of Serratia sp. R1 gives an insight into the antibiotic resistant genes against multiple antibiotics.}, journal = {Molecular biology reports}, volume = {49}, number = {6}, pages = {4479-4484}, pmid = {35237932}, issn = {1573-4978}, support = {NASF/CA-6030/2017-18//Indian Agricultural Research Institute/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; Cephalosporins/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Genome, Bacterial/genetics ; Humans ; Infant, Newborn ; Macrolides/pharmacology ; *Metals, Heavy ; Serratia/genetics ; }, abstract = {BACKGROUND: Serratia is a pathogenic bacterium, commonly associated with neonatal intensive care units, and harbors antibiotic-resistant genes against multiple antibiotics e.g., resistance against penams, aminoglycosides, tetracyclines, cephalosporins, and macrolides. In the long-term contaminated habitat, the bacterial communities carry both antibiotic and metal resistance genes. This draft genome sequencing aimed to explore the alarming level of ARGs in the environment, additionally heavy metal-resistant genes were also explored in the draft genome.<br><br>METHODS: Whole-genome sequencing was used to investigate ARGs in Serratia sp. R1. The bacteria were sequenced using Illumina Nova seq sequencer and subjected to genome annotation. The bacterial genome was explored for antibiotic- and metal-resistant genes.<br><br>RESULTS: Sequencing resulted in 8.4&#xa0;Mb genome and a total of 4411 functional genes were characterized in the draft genome. Genes resistant to Beta-lactams, cephalosporins, macrolides, fluoroquinolones, and tetracycline are present in the draft genome. Multiple metal-resistant genes are also present in the sequenced genome.<br><br>CONCLUSION: The genes and proteins providing heavy metal and antibiotic resistance may be used in the bioremediation of environmental antibiotic residues to prevent the spread of antibiotic resistance. The current study can help us to adopt suitable mitigation measures against the multidrug-resistant Serratia.}, }
@article {pmid35237850, year = {2023}, author = {Giorgio, M and Niccolò, BGM and Benedetta, T and Luisa, M and Leonardo, BF and Gregory, B and Pietro, B and Alberto, A and Domizia, D and Emidio, A}, title = {Fungal and Bacterial Diversity in the Tuber magnatum Ecosystem and Microbiome.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {508-521}, pmid = {35237850}, issn = {1432-184X}, support = {1946445//National Science Foundation/ ; }, mesh = {*Microbiota ; *Ascomycota/chemistry ; Soil ; *Rhizobiaceae ; }, abstract = {Fungi belonging to the genus Tuber produce edible ascocarps known as truffles. Tuber magnatum Picco may be the most appreciated truffle species given its peculiar aroma. While its life cycle is not yet fully elucidated, some studies demonstrated an active role of microorganisms. The main goal of this study was to determine how the T. magnatum microbiome varies across space and time. To address this, we characterized microbial communities associated with T. magnatum through high-throughput amplicon sequencing of internal transcribed spacer (ITS) and 16S rDNAs in three productive natural sites in Italy across 2 years. At each site, four truffles were sampled as well as the soil underneath and at 40, 100, and 200 cm from the harvesting points, to assess for microbial variation between substrates, years, and sites. A statistically significant site-related effect on microbial communities was identified, whereas only the prokaryotic community was significantly affected by the distance of soil from the truffle. Significant differences between sampling years were also found, demonstrating a possible relation among rainfall precipitation and Firmicutes and Actinobacteria. Thirty-six bacterial OTUs in truffles and 11 bacterial OTUs in soils beneath truffles were identified as indicator taxa. As shown for other truffle species, the dominance of Bradyrhizobium, Rhizobium, and Ensifer spp. within the truffle fruiting body suggests an evolutionary adaptation of this microorganism to the genus Tuber. The present work offers novel and relevant insights into the microbial ecology of T. magnatum ecosystems and fruiting bodies. The function and role of these bacteria in the truffle microbiome and life cycle are in need of further investigation.}, }
@article {pmid35236879, year = {2022}, author = {de Albuquerque, TM and Mendes, LW and Rocha, SMB and Antunes, JEL and Oliveira, LMS and Melo, VMM and Oliveira, FAS and Pereira, APA and da Silva, VB and Gomes, RLF and de Alcantara Neto, F and Lopes, ACA and de Moura Rocha, M and Araujo, ASF}, title = {Genetically related genotypes of cowpea present similar bacterial community in the rhizosphere.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {3472}, pmid = {35236879}, issn = {2045-2322}, mesh = {Bacteria/genetics ; Genotype ; Plant Breeding ; Plant Roots/microbiology ; Plants/genetics ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil Microbiology ; *Vigna/genetics/microbiology ; }, abstract = {Plant breeding reduces the genetic diversity of plants and could influence the composition, structure, and diversity of the rhizosphere microbiome, selecting more homogeneous and specialized microbes. In this study, we used 16S rRNA sequencing to assess the bacterial community in the rhizosphere of different lines and modern cowpea cultivars, to investigate the effect of cowpea breeding on bacterial community assembly. Thus, two African lines (IT85F-2687 and IT82D-60) and two Brazilian cultivars (BRS-Guariba and BRS-Tumucumaque) of cowpea were assessed to verify if the generation advance and genetic breeding influence the bacterial community in the rhizosphere. No significant differences were found in the structure, richness, and diversity of bacterial community structure between the rhizosphere of the different cowpea genotypes, and only slight differences were found at the OTU level. The complexity of the co-occurrence network decreased from African lines to Brazilian cultivars. Regarding functional prediction, the core functions were significantly altered according to the genotypes. In general, African lines presented a more abundance of groups related to chemoheterotrophy, while the rhizosphere of the modern cultivars decreased functions related to cellulolysis. This study showed that the genetic breeding process affects the dynamics of the rhizosphere community, decreasing the complexity of interaction in one cultivar. As these cowpea genotypes are genetically related, it could suggest a new hypothesis of how genetic breeding of similar genotypes could influence the rhizosphere microbiome.}, }
@article {pmid35234997, year = {2023}, author = {Ribeiro, B and Padua, A and Oliveira, BFR and Puccinelli, G and da Costa Fernandes, F and Laport, MS and Klautau, M}, title = {Uncovering the Microbial Diversity of Two Exotic Calcareous Sponges.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {737-746}, pmid = {35234997}, issn = {1432-184X}, mesh = {Animals ; Ecology ; *Microbiota ; Nitrogen Cycle ; Calcium Carbonate ; *Porifera ; Phylogeny ; }, abstract = {Sponges-associated microorganisms play important roles in their health and ecology; consequently, they may be crucial in the successful adaptation of exotic species to novel environments. However, few studies have focused on the microbial diversity of exotic sponges, especially those with calcium carbonate spicules (class Calcarea). Therefore, this is the first in situ characterization of the microbiota of the exotic calcareous sponges Sycettusa hastifera and Paraleucilla magna. Our results suggest that S. hastifera has a more stable microbiota than P. magna, as there were no differences in its beta diversity among sampling sites. Conversely, P. magna showed significant differences in its microbial communities, perhaps related to its adhesion to artificial substrate and/or shellfish mariculture activities. Each sponge species presented a single dominant proteobacterial OTU potentially active in the nitrogen cycle, which could help sponge detoxification, especially in polluted areas where exotic species usually establish. Our results show the importance of assessing the microbial diversity to unveil host-microorganism relationships and suggest that these associated nitrogen-cycling microorganisms could favor the success of exotic sponges in new environments.}, }
@article {pmid35234496, year = {2022}, author = {Smets, W and Spada, LM and Gandolfi, I and Wuyts, K and Legein, M and Muyshondt, B and Samson, R and Franzetti, A and Lebeer, S}, title = {Bacterial Succession and Community Dynamics of the Emerging Leaf Phyllosphere in Spring.}, journal = {Microbiology spectrum}, volume = {10}, number = {2}, pages = {e0242021}, pmid = {35234496}, issn = {2165-0497}, mesh = {Bacteria ; *Biodiversity ; Humans ; *Microbiota ; Plant Leaves/microbiology ; Plants ; Trees/microbiology ; }, abstract = {Every year, deciduous trees shed their leaves, and when new leaves emerge next spring, they establish a characteristic bacterial leaf community. In this exploratory study, we assessed the bacterial phyllosphere (aboveground plant surfaces) of eight London plane trees (Platanus × acerifolia) in Antwerp and Milan by sampling weekly during leaf emergence and expansion. We sampled the surfaces of different tree compartments: leaves, leaf buds, branches, and trunk, for up to 6 weeks. Phyllosphere community composition was most strongly determined by tree compartment. Only the communities on the emerging leaves showed changing dynamics over time. The rate of change in the leaf phyllosphere composition, expressed as the beta dissimilarity between consecutive time points, was very high following leaf emergence, with decreasing speed over time, indicating that these communities stabilize over time. We also identified cooccurring groups of bacteria associated with potential stages of ecological succession on the leaves and accordingly named them general cluster, early cluster, middle cluster, and late cluster. Taxa of the general cluster were not only more abundant than the others on leaves, but they were also widespread on other tree compartments. The late cluster was most pronounced in trees surrounded by trafficked urban land use. This study mainly generates hypotheses on the ecological succession on the emerging leaves of deciduous trees in urban environments and contributes to understanding the development of the tree leaf phyllosphere in spring. IMPORTANCE Improving our understanding of phyllosphere ecology is key in successfully applying bacterial biological agents or modulating the leaf microbiome in order to achieve valuable ecosystem services, such as plant protection, plant growth, air purification, and developing a healthy human immune system. Modulation of the phyllosphere microbiome in the field works only with variable success. To improve the impact of our applications in the field, a better understanding of the ecological principles governing phyllosphere dynamics is required. This exploratory study demonstrates how the combination of different analyses of a chronosequence of bacterial communities can provide new ecological insights. With a limited number of sampled trees, we demonstrated different indications of ecological succession of bacterial communities in the leaves and observed a potential impact of intensely trafficked land use becoming apparent in the leaf bacterial communities approximately 3 weeks after leaf emergence, consisting of a separate stage in community development.}, }
@article {pmid35232471, year = {2022}, author = {France, MT and Fu, L and Rutt, L and Yang, H and Humphrys, MS and Narina, S and Gajer, PM and Ma, B and Forney, LJ and Ravel, J}, title = {Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {66}, pmid = {35232471}, issn = {1474-760X}, support = {UH2 AI083264/AI/NIAID NIH HHS/United States ; R01 NR015495/NR/NINR NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Female ; Humans ; Lactobacillus/genetics ; *Microbiota/genetics ; Mucins ; RNA, Ribosomal, 16S/genetics ; *Vagina/microbiology ; }, abstract = {BACKGROUND: Vaginal bacterial communities dominated by Lactobacillus species are associated with a reduced risk of various adverse health outcomes. However, somewhat unexpectedly, many healthy women have microbiota that are not dominated by lactobacilli. To determine the factors that drive vaginal community composition we characterized the genetic composition and transcriptional activities of vaginal microbiota in healthy women.<br><br>RESULTS: We demonstrate that the abundance of a species is not always indicative of its transcriptional activity and that impending changes in community composition can be predicted from metatranscriptomic data. Functional comparisons highlight differences in the metabolic activities of these communities, notably in their degradation of host produced mucin but not glycogen. Degradation of mucin by communities not dominated by Lactobacillus may play a role in their association with adverse health outcomes. Finally, we show that the transcriptional activities of L. crispatus, L. iners, and Gardnerella vaginalis vary with the taxonomic composition of the communities in which they reside. Notably, L. iners and G. vaginalis both demonstrate lower expression of their cholesterol-dependent cytolysins when co-resident with Lactobacillus spp. and higher expression when co-resident with other facultative and obligate anaerobes. The pathogenic potential of these species may depend on the communities in which they reside and thus could be modulated by interventional strategies.<br><br>CONCLUSIONS: Our results provide insight to the functional ecology of the vaginal microbiota, demonstrate the diagnostic potential of metatranscriptomic data, and reveal strategies for the management of these ecosystems.}, }
@article {pmid35229646, year = {2022}, author = {Wang, X and Teng, Y and Ren, W and Li, Y and Yang, T and Chen, Y and Zhao, L and Zhang, H and Kuramae, EE}, title = {Variations of Bacterial and Diazotrophic Community Assemblies throughout the Soil Profile in Distinct Paddy Soil Types and Their Contributions to Soil Functionality.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0104721}, pmid = {35229646}, issn = {2379-5077}, mesh = {*Soil/chemistry ; Bacteria ; *Microbiota ; Iron ; Nitrogen ; }, abstract = {Soil microbiota plays fundamental roles in maintaining ecosystem functions and services, including biogeochemical processes and plant productivity. Despite the ubiquity of soil microorganisms from the topsoil to deeper layers, their vertical distribution and contribution to element cycling in subsoils remain poorly understood. Here, nine soil profiles (0 to 135 cm) were collected at the local scale (within 300 km) from two canonical paddy soil types (Fe-accumuli and Hapli stagnic anthrosols), representing redoximorphic and oxidative soil types, respectively. Variations with depth in edaphic characteristics and soil bacterial and diazotrophic community assemblies and their associations with element cycling were explored. The results revealed that nitrogen and iron status were the most distinguishing edaphic characteristics of the two soil types throughout the soil profile. The acidic Fe-accumuli stagnic anthrosols were characterized by lower concentrations of free iron oxides and total iron in topsoil and ammonia in deeper layers compared with the Hapli stagnic anthrosols. The bacterial and diazotrophic community assemblies were mainly shaped by soil depth, followed by soil type. Random forest analysis revealed that nitrogen and iron cycling were strongly correlated in Fe-accumuli stagnic anthrosol, whereas in Hapli soil, available sulfur was the most important variable predicting both nitrogen and iron cycling. The distinctive biogeochemical processes could be explained by the differences in enrichment of microbial taxa between the two soil types. The main discriminant clades were the iron-oxidizing denitrifier Rhodanobacter, Actinobacteria, and diazotrophic taxa (iron-reducing Geobacter, Nitrospirillum, and Burkholderia) in Fe-accumuli stagnic anthrosol and the sulfur-reducing diazotroph Desulfobacca in Hapli stagnic anthrosol. IMPORTANCE Rice paddy ecosystems support nearly half of the global population and harbor remarkably diverse microbiomes and functions in a variety of soil types. Diazotrophs provide significant bioavailable nitrogen in paddy soil, priming nitrogen transformation and other biogeochemical processes. This study provides a novel perspective on the vertical distribution of bacterial and diazotrophic communities in two hydragric anthrosols. Microbiome analysis revealed divergent biogeochemical processes in the two paddy soil types, with a dominance of nitrogen-iron cycling processes in Fe-accumuli stagnic anthrosol and sulfur-nitrogen-iron coupling in Hapli stagnic anthrosol. This study advances our understanding of the multiple significant roles played by soil microorganisms, especially diazotrophs, in biogeochemical element cycles, which have important ecological and biogeochemical ramifications.}, }
@article {pmid35229433, year = {2022}, author = {Yang, S and Poorter, L and Kuramae, EE and Sass-Klaassen, U and Leite, MFA and Costa, OYA and Kowalchuk, GA and Cornelissen, JHC and van Hal, J and Goudzwaard, L and Hefting, MM and van Logtestijn, RSP and Sterck, FJ}, title = {Stem traits, compartments and tree species affect fungal communities on decaying wood.}, journal = {Environmental microbiology}, volume = {24}, number = {8}, pages = {3625-3639}, pmid = {35229433}, issn = {1462-2920}, mesh = {Biodiversity ; Forests ; Fungi/genetics ; *Mycobiome/genetics ; *Trees/microbiology ; Wood/microbiology ; }, abstract = {Dead wood quantity and quality is important for forest biodiversity, by determining wood-inhabiting fungal assemblages. We therefore evaluated how fungal communities were regulated by stem traits and compartments (i.e. bark, outer- and inner wood) of 14 common temperate tree species. Fresh logs were incubated in a common garden experiment in a forest site in the Netherlands. After 1 and 4 years of decay, the fungal composition of different compartments was assessed using Internal Transcribed Spacer amplicon sequencing. We found that fungal alpha diversity differed significantly across tree species and stem compartments, with bark showing significantly higher fungal diversity than wood. Gymnosperms and Angiosperms hold different fungal communities, and distinct fungi were found between inner wood and other compartments. Stem traits showed significant afterlife effects on fungal communities; traits associated with accessibility (e.g. conduit diameter), stem chemistry (e.g. C, N, lignin) and physical defence (e.g. density) were important factors shaping fungal community structure in decaying stems. Overall, stem traits vary substantially across stem compartments and tree species, thus regulating fungal communities and the long-term carbon dynamics of dead trees.}, }
@article {pmid35229200, year = {2023}, author = {Sapkota, R and Jørgensen, LN and Boeglin, L and Nicolaisen, M}, title = {Fungal Communities of Spring Barley from Seedling Emergence to Harvest During a Severe Puccinia hordei Epidemic.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {617-627}, pmid = {35229200}, issn = {1432-184X}, support = {6111-00065B//Danmarks Frie Forskningsfond/ ; }, mesh = {*Mycobiome ; *Hordeum ; Fungi ; Seedlings ; Seasons ; *Ascomycota ; Soil Microbiology ; }, abstract = {All plant tissues from leaves, stems, and roots are hosting a wide diversity of fungal species. Our understanding of the assembly of this diversity of fungi during the plant growth cycle is limited. Here, we characterized the mycobiome of three spring barley cultivars grown in Zealand, Denmark, at weekly intervals during a growth season from seedling emergence to senescence and seed maturity. A notable proportion of members of the fungal communities were shared among different plant organs, but community dynamics were tissue-specific. A severe attack of Puccinia hordei occurring during the vegetative stage had profound effects on the mycobiome, and P. hordei biomass displaced that of other taxa. Plant tissue type was the most important factor determining the mycobiome, but also plant age was contributing significantly. Using a random forest model, we found that specific members of the mycobiome were responding differently to plant age, for instance, Olpidium and Articulospora in roots, Dioszegia and Sporobolomyces in leaves, Pyrenophora in stems, and Epicoccum in heads. A co-occurrence network analysis revealed complex interactions among fungal OTUs, and network connectivity was changing as per plant growth stage and plant tissue type. This study contributes to the understanding of assembly of fungal communities in cereals by providing a detailed description of fungal communities associated with barley. This knowledge will be vital for microbiome assisted plant health management and our study will serve as an important baseline for future efforts to harness microbiota in cereal health.}, }
@article {pmid35228910, year = {2022}, author = {Eisenhofer, R and D'Agnese, E and Taggart, D and Carver, S and Penrose, B}, title = {Microbial biogeography of the wombat gastrointestinal tract.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e12982}, pmid = {35228910}, issn = {2167-8359}, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Tract ; Feces/chemistry ; *Marsupialia ; Colon ; }, abstract = {Most herbivorous mammals have symbiotic microbes living in their gastrointestinal tracts that help with harvesting energy from recalcitrant plant fibre. The bulk of research into these microorganisms has focused on samples collected from faeces, representing the distal region of the gastrointestinal (GI) tract. However, the GI tract in herbivorous mammals is typically long and complex, containing different regions with distinct physico-chemical properties that can structure resident microbial communities. Little work has been done to document GI microbial communities of herbivorous animals at these sites. In this study, we use 16S rRNA gene sequencing to characterize the microbial biogeography along the GI tract in two species of wombats. Specifically, we survey the microbes along four major gut regions (stomach, small intestine, proximal colon, distal colon) in a single bare-nosed wombat (Vombatus ursinus) and a single southern hairy-nosed wombat (Lasiorhinus latifrons). Our preliminary results show that GI microbial communities of wombats are structured by GI region. For both wombat individuals, we observed a trend of increasing microbial diversity from stomach to distal colon. The microbial composition in the first proximal colon region was more similar between wombat species than the corresponding distal colon region in the same species. We found several microbial genera that were differentially abundant between the first proximal colon (putative site for primary plant fermentation) and distal colon regions (which resemble faecal samples). Surprisingly, only 10.6% (98) and 18.8% (206) of amplicon sequence variants (ASVs) were shared between the first proximal colon region and the distal colon region for the bare-nosed and southern hairy-nosed wombat, respectively. These results suggest that microbial communities in the first proximal colon region-the putative site of primary plant fermentation in wombats-are distinct from the distal colon, and that faecal samples may have limitations in capturing the diversity of these communities. While faeces are still a valuable and effective means of characterising the distal colon microbiota, future work seeking to better understand how GI microbiota impact the energy economy of wombats (and potentially other hindgut-fermenting mammals) may need to take gut biogeography into account.}, }
@article {pmid35227678, year = {2022}, author = {Chu, Y and Zhao, Z and Cai, L and Zhang, G}, title = {Viral diversity and biogeochemical potential revealed in different prawn-culture sediments by virus-enriched metagenome analysis.}, journal = {Environmental research}, volume = {210}, number = {}, pages = {112901}, doi = {10.1016/j.envres.2022.112901}, pmid = {35227678}, issn = {1096-0953}, mesh = {Ecosystem ; Geologic Sediments ; *Metagenome ; Metagenomics ; Phylogeny ; *Viruses/genetics ; }, abstract = {As the most numerous biological entities on Earth, viruses affect the microbial dynamics, metabolism and biogeochemical cycles in the aquatic ecosystems. Viral diversity and functions in ocean have been relatively well studied, but our understanding of viruses in mariculture systems is limited. To fill this knowledge gap, we studied viral diversity and potential biogeochemical impacts of sediments from four different prawn-mariculture ecosystems (mono-culture of prawn and poly-culture of prawn with jellyfish, sea cucumber, and clam) using a metagenomic approach with prior virus-like particles (VLPs) separation. We found that the order Caudovirales was the predominant viral category and accounted for the most volume (78.39% of classified viruses). Sediment viruses were verified to have a high diversity by using the construct phylogenetic tree of terL gene, with three potential novel clades being identified. Meanwhile, compared with viruses inhabiting other ecosystems based on gene-sharing network, our results revealed that mariculture sediments harbored considerable unexplored viral diversity and that maricultural species were potentially important drivers of the viral community structure. Notably, viral auxiliary metabolic genes were identified and suggested that viruses influence carbon and sulfur cycling, as well as cofactors/vitamins and amino acid metabolism, which indirectly participate in biogeochemical cycling. Overall, our findings revealed the genomic diversity and ecological function of viral communities in prawn mariculture sediments, and suggested the role of viruses in microbial ecology and biogeochemistry.}, }
@article {pmid35222324, year = {2022}, author = {Marois, C and Girard, C and Klanten, Y and Vincent, WF and Culley, AI and Antoniades, D}, title = {Local Habitat Filtering Shapes Microbial Community Structure in Four Closely Spaced Lakes in the High Arctic.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {779505}, pmid = {35222324}, issn = {1664-302X}, abstract = {Arctic lakes are experiencing increasingly shorter periods of ice cover due to accelerated warming at northern high latitudes. Given the control of ice cover thickness and duration over many limnological processes, these changes will have pervasive effects. However, due to their remote and extreme locations even first-order data on lake ecology is lacking for many ecosystems. The aim of this study was to characterize and compare the microbial communities of four closely spaced lakes in Stuckberry Valley (northern Ellesmere Island, Canadian Arctic Archipelago), in the coastal margin zone of the Last Ice Area, that differed in their physicochemical, morphological and catchment characteristics. We performed high-throughput amplicon sequencing of the V4 16S rRNA gene to provide inter- and intra-lake comparisons. Two deep (>25 m) and mostly oxygenated lakes showed highly similar community assemblages that were distinct from those of two shallower lakes (<10 m) with anoxic bottom waters. Proteobacteria, Verrucomicrobia, and Planctomycetes were the major phyla present in the four water bodies. One deep lake contained elevated proportions of Cyanobacteria and Thaumarchaeota that distinguished it from the others, while the shallow lakes had abundant communities of predatory bacteria, as well as microbes in their bottom waters that contribute to sulfur and methane cycles. Despite their proximity, our data suggest that local habitat filtering is the primary determinant of microbial diversity in these systems. This study provides the first detailed examination of the microbial assemblages of the Stuckberry lakes system, resulting in new insights into the microbial ecology of the High Arctic.}, }
@article {pmid35218016, year = {2022}, author = {Kajihara, KT and Egan, CP and Swift, SOI and Wall, CB and Muir, CD and Hynson, NA}, title = {Core arbuscular mycorrhizal fungi are predicted by their high abundance-occupancy relationship while host-specific taxa are rare and geographically structured.}, journal = {The New phytologist}, volume = {234}, number = {4}, pages = {1464-1476}, doi = {10.1111/nph.18058}, pmid = {35218016}, issn = {1469-8137}, mesh = {Forests ; Fungi ; *Mycobiome ; *Mycorrhizae ; Plant Roots/microbiology ; Soil ; Soil Microbiology ; }, abstract = {Habitat restoration may depend on the recovery of plant microbial symbionts such as arbuscular mycorrhizal (AM) fungi, but this requires a better understanding of the rules that govern their community assembly. We examined the interactions of soil and host-associated AM fungal communities between remnant and restored patches of subtropical montane forests. While AM fungal richness did not differ between habitat types, community membership did and was influenced by geography, habitat and host. These differences were largely driven by rare host-specific AM fungi that displayed near-complete turnover between forest types, while core AM fungal taxa were highly abundant and ubiquitous. The bipartite networks in the remnant forest were more specialized and hosts more specific than in the restored forest. Host-associated AM fungal communities nested within soil communities in both habitats, but only significantly so in the restored forest. Our results provide evidence that restored and remnant forests harbour the same core fungal symbionts, while rare host-specific taxa differ, and that geography, host identity and taxonomic resolution strongly affect the observed distribution patterns of these fungi. We suggest that host-specific interactions with AM fungi, as well as spatial processes, should be explicitly considered to effectively re-establish target host and symbiont communities.}, }
@article {pmid35217776, year = {2022}, author = {Singleton, CM and Petriglieri, F and Wasmund, K and Nierychlo, M and Kondrotaite, Z and Petersen, JF and Peces, M and Dueholm, MS and Wagner, M and Nielsen, PH}, title = {The novel genus, 'Candidatus Phosphoribacter', previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in EBPR wastewater treatment plants worldwide.}, journal = {The ISME journal}, volume = {16}, number = {6}, pages = {1605-1616}, pmid = {35217776}, issn = {1751-7370}, support = {16578//Villum Fonden (Villum Foundation)/ ; }, mesh = {*Actinomycetales/genetics/metabolism ; Bioreactors ; Phosphorus/metabolism ; Polyphosphates/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; Sewage/microbiology ; Wastewater ; *Water Purification ; }, abstract = {The bacterial genus Tetrasphaera encompasses abundant polyphosphate accumulating organisms (PAOs) that are responsible for enhanced biological phosphorus removal (EBPR) in wastewater treatment plants. Recent analyses of genomes from pure cultures revealed that 16S rRNA genes cannot resolve the lineage, and that Tetrasphaera spp. are from several different genera within the Dermatophilaceae. Here, we examine 14 recently recovered high-quality metagenome-assembled genomes from wastewater treatment plants containing full-length 16S rRNA genes identified as Tetrasphaera, 11 of which belong to the uncultured Tetrasphaera clade 3. We find that this clade represents two distinct genera, named here Ca. Phosphoribacter and Ca. Lutibacillus, and reveal that the widely used model organism Tetrasphaera elongata is less relevant for physiological predictions of this uncultured group. Ca. Phosphoribacter incorporates species diversity unresolved at the 16S rRNA gene level, with the two most abundant and often co-occurring species encoding identical V1-V3 16S rRNA gene amplicon sequence variants but different metabolic capabilities, and possibly, niches. Both Ca. P. hodrii and Ca. P. baldrii were visualised using fluorescence in situ hybridisation (FISH), and PAO capabilities were confirmed with FISH-Raman microspectroscopy and phosphate cycling experiments. Ca. Phosphoribacter represents the most abundant former Tetrasphaera lineage and PAO in EPBR systems in Denmark and globally.}, }
@article {pmid35215763, year = {2022}, author = {Farooq, T and Hussain, MD and Shakeel, MT and Tariqjaveed, M and Aslam, MN and Naqvi, SAH and Amjad, R and Tang, Y and She, X and He, Z}, title = {Deploying Viruses against Phytobacteria: Potential Use of Phage Cocktails as a Multifaceted Approach to Combat Resistant Bacterial Plant Pathogens.}, journal = {Viruses}, volume = {14}, number = {2}, pages = {}, pmid = {35215763}, issn = {1999-4915}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*virology ; Bacteriophages/*physiology ; Biological Control Agents/*pharmacology ; Disease Resistance ; Host-Pathogen Interactions ; *Phage Therapy ; Plant Diseases/microbiology/*prevention &amp; control ; Plants/immunology/*microbiology ; }, abstract = {Plants in nature are under the persistent intimidation of severe microbial diseases, threatening a sustainable food production system. Plant-bacterial pathogens are a major concern in the contemporary era, resulting in reduced plant growth and productivity. Plant antibiotics and chemical-based bactericides have been extensively used to evade plant bacterial diseases. To counteract this pressure, bacteria have evolved an array of resistance mechanisms, including innate and adaptive immune systems. The emergence of resistant bacteria and detrimental consequences of antimicrobial compounds on the environment and human health, accentuates the development of an alternative disease evacuation strategy. The phage cocktail therapy is a multidimensional approach effectively employed for the biocontrol of diverse resistant bacterial infections without affecting the fauna and flora. Phages engage a diverse set of counter defense strategies to undermine wide-ranging anti-phage defense mechanisms of bacterial pathogens. Microbial ecology, evolution, and dynamics of the interactions between phage and plant-bacterial pathogens lead to the engineering of robust phage cocktail therapeutics for the mitigation of devastating phytobacterial diseases. In this review, we highlight the concrete and fundamental determinants in the development and application of phage cocktails and their underlying mechanism, combating resistant plant-bacterial pathogens. Additionally, we provide recent advances in the use of phage cocktail therapy against phytobacteria for the biocontrol of devastating plant diseases.}, }
@article {pmid35215209, year = {2022}, author = {Sueiro, RA and Leiro, JM and Blanco-Abad, V and Raaijmakers, J and de Bruijn, I and Dirks, RPH and Lamas, J}, title = {Plant- and Bacteria-Derived Compounds with Anti-Philasterides dicentrarchi Activity.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {2}, pages = {}, pmid = {35215209}, issn = {2076-0817}, support = {ParaFishControl 634429//European Commission/ ; AGL2017-83577-R//Ministry of Economy, Industry and Competitiveness/ ; ED431C2017/31//Xunta de Galicia/ ; }, abstract = {Philasterides dicentrarchi is a scuticociliate that causes high mortalities in farmed fish. Although vaccination is an effective method to prevent scuticociliatosis caused by the homologous serotype, a universal vaccine has not been developed yet. Many compounds have been shown to be toxic to this ciliate species; moreover, most of them are toxic to aquatic life and cannot be used to prevent the disease. We have evaluated the toxicity to P. dicentrarchi of several compounds of natural origin to be used to reduce parasite levels in the seawater. Ciliates were exposed to several compound concentrations, and the mortality was determined at several incubation times. Tomatine, plumbagin and 2',4'-dihydroxychalcone displayed the highest anticiliate activity, with a dose-dependent response. The effects of these compounds on the EPC cell line were also evaluated, finding that 2',4'-dihydroxychalcone displayed the lowest toxicity to fish cells. At 7.54 μM, 2',4'-dihydroxychalcone inhibited 50% parasite growth but only killed about 10% of EPC cells after 24 h incubation. Finally, we evaluated the toxicity of Pseudomonas H6 surfactant (PS) to P. dicentrarchi, finding that PS was toxic to the ciliate but showed lower toxicity to EPC cells. At a concentration of 7.8 μg/mL (LC50 for the ciliate after 3 h incubation), PS killed 14.9% of EPC cells. We conclude that 2',4'-dihydroxychalcone, and PS could be used to reduce parasite levels in seawater, thus decreasing the risk of scuticociliatosis infection in cultured fish.}, }
@article {pmid35208741, year = {2022}, author = {Šimunović, K and Stefanic, P and Klančnik, A and Erega, A and Mandic Mulec, I and Smole Možina, S}, title = {Bacillus subtilis PS-216 Antagonistic Activities against Campylobacter jejuni NCTC 11168 Are Modulated by Temperature, Oxygen, and Growth Medium.}, journal = {Microorganisms}, volume = {10}, number = {2}, pages = {}, pmid = {35208741}, issn = {2076-2607}, support = {J4-7637//Slovenian Research Agency/ ; J4-2542//Slovenian Research Agency/ ; P4-0116//Slovenian Research Agency/ ; }, abstract = {As the incidence of Campylobacter jejuni and campylobacteriosis grows, so does the need for a better understanding and control of this pathogen. We studied the interactions of C. jejuni NCTC 11168 and a potential probiotic, Bacillus subtilis PS-216, in cocultures at different starting ratios and temperatures (20 °C, 37 °C, 42 °C), under different atmospheres (aerobic, microaerobic), and in different growth media (Mueller-Hinton, chicken litter medium, chicken intestinal-content medium). Under microaerobic conditions, B. subtilis effectively inhibited the growth of C. jejuni at 42 °C (log reduction, 4.19), even when C. jejuni counts surpassed B. subtilis by 1000-fold in the starting inoculum. This inhibition was weaker at 37 °C (log reduction, 1.63), while no impact on CFUs was noted at 20 °C, which is a temperature nonpermissive of C. jejuni growth. Under aerobic conditions, B. subtilis supported C. jejuni survival. B. subtilis PS-216 inhibited the growth of C. jejuni in sterile chicken litter (4.07 log reduction) and in sterile intestinal content (2.26 log reduction). In nonsterile intestinal content, B. subtilis PS-216 was able to grow, to a lesser extent, compared to Mueller-Hinton media, still showing potential as a chicken probiotic that could be integrated into the chicken intestinal microbiota. This study showed the strong influence of environmental parameters on the variability of C. jejuni and B. subtilis interactions. Furthermore, B. subtilis PS-216 antagonism was strongest against C. jejuni NCTC 11168 under conditions that might represent conditions in the chicken environment (42 °C, microaerobic atmosphere, chicken litter medium).}, }
@article {pmid35202888, year = {2022}, author = {Yu, J and Ma, X and Wang, L and Dong, N and Wang, K and You, Q and Xu, Y and Wang, C and Dong, Z and Shi, Z and Dai, S and Bai, L and Song, CP}, title = {Arabidopsis CAP1 mediates ammonium-regulated root hair growth by influencing vesicle trafficking and the cytoskeletal arrangement in root hair cells.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {49}, number = {10}, pages = {986-989}, doi = {10.1016/j.jgg.2022.02.005}, pmid = {35202888}, issn = {1673-8527}, mesh = {*Arabidopsis/genetics ; *Ammonium Compounds ; *Arabidopsis Proteins/genetics ; Plant Roots/genetics ; }, }
@article {pmid35198897, year = {2022}, author = {Kreitmeier, M and Ardern, Z and Abele, M and Ludwig, C and Scherer, S and Neuhaus, K}, title = {Spotlight on alternative frame coding: Two long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection.}, journal = {iScience}, volume = {25}, number = {2}, pages = {103844}, pmid = {35198897}, issn = {2589-0042}, abstract = {The existence of overlapping genes (OLGs) with significant coding overlaps revolutionizes our understanding of genomic complexity. We report two exceptionally long (957 nt and 1536 nt), evolutionarily novel, translated antisense open reading frames (ORFs) embedded within annotated genes in the pathogenic Gram-negative bacterium Pseudomonas aeruginosa. Both OLG pairs show sequence features consistent with being genes and transcriptional signals in RNA sequencing. Translation of both OLGs was confirmed by ribosome profiling and mass spectrometry. Quantitative proteomics of samples taken during different phases of growth revealed regulation of protein abundances, implying biological functionality. Both OLGs are taxonomically restricted, and likely arose by overprinting within the genus. Evidence for purifying selection further supports functionality. The OLGs reported here, designated olg1 and olg2, are the longest yet proposed in prokaryotes and are among the best attested in terms of translation and evolutionary constraint. These results highlight a potentially large unexplored dimension of prokaryotic genomes.}, }
@article {pmid35197480, year = {2022}, author = {Xia, L and Miao, Y and Cao, A and Liu, Y and Liu, Z and Sun, X and Xue, Y and Xu, Z and Xun, W and Shen, Q and Zhang, N and Zhang, R}, title = {Biosynthetic gene cluster profiling predicts the positive association between antagonism and phylogeny in Bacillus.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {1023}, pmid = {35197480}, issn = {2041-1723}, mesh = {Anti-Bacterial Agents/pharmacology ; *Bacillus/genetics ; Biosynthetic Pathways/genetics ; Multigene Family ; Phylogeny ; }, abstract = {Understanding the driving forces and intrinsic mechanisms of microbial competition is a fundamental question in microbial ecology. Despite the well-established negative correlation between exploitation competition and phylogenetic distance, the process of interference competition that is exemplified by antagonism remains controversial. Here, we studied the genus Bacillus, a commonly recognized producer of multifarious antibiotics, to explore the role of phylogenetic patterns of biosynthetic gene clusters (BGCs) in mediating the relationship between antagonism and phylogeny. Comparative genomic analysis revealed a positive association between BGC distance and phylogenetic distance. Antagonistic tests demonstrated that the inhibition phenotype positively correlated with both phylogenetic and predicted BGC distance, especially for antagonistic strains possessing abundant BGCs. Mutant-based verification showed that the antagonism was dependent on the BGCs that specifically harbored by the antagonistic strain. These findings highlight that BGC-phylogeny coherence regulates the positive correlation between congeneric antagonism and phylogenetic distance, which deepens our understanding of the driving force and intrinsic mechanism of microbial interactions.}, }
@article {pmid35196931, year = {2022}, author = {Rosier, BT and Takahashi, N and Zaura, E and Krom, BP and MartÍnez-Espinosa, RM and van Breda, SGJ and Marsh, PD and Mira, A}, title = {The Importance of Nitrate Reduction for Oral Health.}, journal = {Journal of dental research}, volume = {101}, number = {8}, pages = {887-897}, doi = {10.1177/00220345221080982}, pmid = {35196931}, issn = {1544-0591}, mesh = {Bacteria ; *Dental Caries/prevention &amp; control ; *Halitosis ; Humans ; Nitrates ; Nitric Oxide ; Nitrites ; Oral Health ; *Periodontal Diseases/prevention &amp; control ; Saliva/microbiology ; }, abstract = {Salivary glands concentrate plasma nitrate into saliva, leading to high nitrate concentrations that can reach the millimolar range after a nitrate-rich vegetable meal. Whereas human cells cannot reduce nitrate to nitrite effectively, certain oral bacteria can. This leads to an increase in systemic nitrite that can improve conditions such as hypertension and diabetes through nitric oxide availability. Apart from systemic benefits, it has been proposed that microbial nitrate reduction can also promote oral health. In this review, we discuss evidence associating dietary nitrate with oral health. Oral bacteria can reduce nitrite to nitric oxide, a free radical with antimicrobial properties capable of inhibiting sensitive species such as anaerobes involved in periodontal diseases. Nitrate has also been shown to increase resilience against salivary acidification in vivo and in vitro, thus preventing caries development. One potential mechanism is proton consumption during denitrification and/or bacterial reduction of nitrite to ammonium. Additionally, lactic acid (organic acid involved in oral acidification) and hydrogen sulfide (volatile compound involved in halitosis) can act as electron donors for these processes. The nitrate-reducing bacteria Rothia and Neisseria are consistently found at higher levels in individuals free of oral disease (vs. individuals with caries, periodontitis, and/or halitosis) and increase when nitrate is consumed in clinical studies. Preliminary in vitro and clinical evidence show that bacteria normally associated with disease, such as Veillonella (caries) and Prevotella (periodontal diseases and halitosis), decrease in the presence of nitrate. We propose nitrate as an ecologic factor stimulating eubiosis (i.e., an increase in health-associated species and functions). Finally, we discuss the preventive and therapeutic potential, as well as safety issues, related to the use of nitrate. In vivo evidence is limited; therefore, robust clinical studies are required to confirm the potential benefits of nitrate reduction on oral health.}, }
@article {pmid35196816, year = {2022}, author = {Ogundero, A and Vignola, M and Connelly, S and Sloan, WT}, title = {Validating Flow Cytometry as a Method for Quantifying Bdellovibrio Predatory Bacteria and Its Prey for Microbial Ecology.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0103321}, pmid = {35196816}, issn = {2165-0497}, mesh = {Bdellovibrio bacteriovorus/*physiology ; Biofilms ; Flow Cytometry/*methods ; Pseudomonas/*metabolism ; }, abstract = {Bdellovibrio bacteriovorus is a predatory, Gram-negative bacteria that feeds on many pathogenic bacteria and has been investigated as a possible solution for mitigating biofilms in different fields. The application depends on more fundamental ecological studies into the dynamics between Bdellovibrio and their prey. To do so requires an accurate, reliable, and, preferably rapid, way of enumerating the cells. Flow cytometry (FCM) is potentially a rapid, accurate, and inexpensive tool for this, but it has yet to be validated in the enumeration of Bdellovibrio. In this study, we developed a protocol to measure the number of Bdellovibrio in samples of various densities using FCM and compared the results with those of other methods: optical density (OD), PFU assay (PFU), and quantitative PCR (qPCR). We observed a strong correlation between values obtained using FCM and PFU (ρ = 0.923) and FCM and qPCR (ρ = 0.987). Compared to optical density there was a much weaker correlation (ρ = 0.784), which was to be expected given the well-documented uncertainty in converting optical density (OD) to cell numbers. The FCM protocol was further validated by demonstrating its ability to distinguish and count mixed populations of Bdellovibrio and the prey Pseudomonas. Thus, the accuracy of FCM as well as its speed and reproducibility make it a suitable alternative for measuring Bdellovibrio cell numbers, especially where many samples are required to capture the dynamics of predator-prey interactions. IMPORTANCE The rise of antibiotic resistance and the unwanted growth of bacteria is a universally growing problem. Predatory bacteria can be used as a biological alternative to antibiotics because they grow by feeding on other bacteria. To apply this effectively requires further study and a deeper understanding of the forces that drive a prey population to elimination. Initially, such studies require more reliable methods to count these cells. Flow cytometry (FCM) is potentially a rapid, accurate, and inexpensive tool for this, but it has yet to be validated for predatory bacteria. This study develops a protocol to count the predatory bacteria Bdellovibrio bacteriovorus and its Pseudomonas prey using FCM and compare the results with those of other methods, demonstrating its ability for studies into B. bacteriovorus predation dynamics. This could lead to the use of B. bacteriovorus for killing bacterial biofilms in fields, such as drinking water and agriculture.}, }
@article {pmid35196810, year = {2022}, author = {Rodrigues, C and Hauser, K and Cahill, N and Ligowska-Marzęta, M and Centorotola, G and Cornacchia, A and Garcia Fierro, R and Haenni, M and Nielsen, EM and Piveteau, P and Barbier, E and Morris, D and Pomilio, F and Brisse, S}, title = {High Prevalence of Klebsiella pneumoniae in European Food Products: a Multicentric Study Comparing Culture and Molecular Detection Methods.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0237621}, pmid = {35196810}, issn = {2165-0497}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Chickens ; Drug Resistance, Multiple, Bacterial ; Europe/epidemiology ; Food Contamination/analysis/*statistics &amp; numerical data ; Foodborne Diseases/microbiology ; Genetic Variation ; Genotype ; Humans ; Klebsiella Infections/epidemiology/microbiology ; Klebsiella pneumoniae/classification/drug effects/genetics/*isolation &amp; purification ; Meat/microbiology ; Microbial Sensitivity Tests ; Phylogeny ; Prevalence ; Salads/microbiology ; beta-Lactamases/genetics/metabolism ; }, abstract = {The Klebsiella pneumoniae species complex (KpSC) is a leading cause of multidrug-resistant human infections. To better understand the potential contribution of food as a vehicle of KpSC, we conducted a multicentric study to define an optimal culture method for its recovery from food matrices and to characterize food isolates phenotypically and genotypically. Chicken meat (n = 160) and salad (n = 145) samples were collected in five European countries and screened for the presence of KpSC using culture-based and zur-khe intergenic region (ZKIR) quantitative PCR (qPCR) methods. Enrichment using buffered peptone water followed by streaking on Simmons citrate agar with inositol (44°C for 48 h) was defined as the most suitable selective culture method for KpSC recovery. A high prevalence of KpSC was found in chicken meat (60% and 52% by ZKIR qPCR and the culture approach, respectively) and salad (30% and 21%, respectively) samples. Genomic analyses revealed high genetic diversity with the dominance of phylogroups Kp1 (91%) and Kp3 (6%). A total of 82% of isolates presented a natural antimicrobial susceptibility phenotype and genotype, with only four CTX-M-15-producing isolates detected. Notably, identical genotypes were found across samples-same food type and same country (15 cases), different food types and same country (1), and same food type and two countries (1)-suggesting high rates of transmission of KpSC within the food sector. Our study provides a novel isolation strategy for KpSC from food matrices and reinforces the view of food as a potential source of KpSC colonization in humans. IMPORTANCE Bacteria of the Klebsiella pneumoniae species complex (KpSC) are ubiquitous, and K. pneumoniae is a leading cause of antibiotic-resistant infections in humans. Despite the urgent public health threat represented by K. pneumoniae, there is a lack of knowledge of the contribution of food sources to colonization and subsequent infection in humans. This is partly due to the absence of standardized methods for characterizing the presence of KpSC in food matrices. Our multicentric study provides and implements a novel isolation strategy for KpSC from food matrices and shows that KpSC members are highly prevalent in salads and chicken meat, reinforcing the view of food as a potential source of KpSC colonization in humans. Despite the large genetic diversity and the low levels of resistance detected, the occurrence of identical genotypes across samples suggests high rates of transmission of KpSC within the food sector, which need to be further explored to define possible control strategies.}, }
@article {pmid35195737, year = {2023}, author = {Zhao, H and Brearley, FQ and Huang, L and Tang, J and Xu, Q and Li, X and Huang, Y and Zou, S and Chen, X and Hou, W and Pan, L and Dong, K and Jiang, G and Li, N}, title = {Abundant and Rare Taxa of Planktonic Fungal Community Exhibit Distinct Assembly Patterns Along Coastal Eutrophication Gradient.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {495-507}, pmid = {35195737}, issn = {1432-184X}, support = {41966005//National Natural Science Foundation of China/ ; U20A2087//National Natural Science Foundation of China/ ; 2018GXNSFDA281006//Natural Science Foundation of Guangxi Province/ ; 2017GXNSFBA198009//Natural Science Foundation of Guangxi Province/ ; 6020303891251//the "One Hundred Talents" Project of Guangxi/ ; MED202014//the Open Research Fund Program of Key Laboratory of Marine Ecosystem Dynamics, MNR/ ; 2017YJ23003//Foundation of Guangxi Academy of Sciences/ ; 2021KY0391//Basic scientific research capacity improvement project of young and middle-aged teachers in colleges and universities, Guangxi/ ; AD20238059//Research on quantitative remote sensing technology for tropical vegetation and International Joint Laboratory of Ecological &amp; Remote Sensing/ ; }, mesh = {Plankton ; *Mycobiome ; Eutrophication ; *Microbiota ; Nitrogen ; }, abstract = {Revealing planktonic fungal ecology under coastal eutrophication is crucial to our understanding of microbial community shift in marine pollution background. We investigated the diversity, putative interspecies interactions, assembly processes and environmental responses of abundant and rare planktonic fungal communities along a eutrophication gradient present in the Beibu Gulf. The results showed that Dothideomycetes and Agaricomycetes were the predominant classes of abundant and rare fungi, respectively. We found that eutrophication significantly altered the planktonic fungal communities and affected the abundant taxa more than the rare taxa. The abundant and rare taxa were keystone members in the co-occurrence networks, and their interaction was enhanced with increasing nutrient concentrations. Stochastic processes dominated the community assembly of both abundant and rare planktonic fungi across the eutrophication gradient. Heterogeneous selection affected abundant taxa more than rare taxa, whereas homogenizing dispersal had a greater influence on rare taxa. Influences of environmental factors involving selection processes were detected, we found that abundant fungi were mainly influenced by carbon compounds, whereas rare taxa were simultaneously affected by carbon, nitrogen and phosphorus compounds in the Beibu Gulf. Overall, these findings highlight the distinct ecological adaptations of abundant and rare fungal communities to marine eutrophication.}, }
@article {pmid35195736, year = {2023}, author = {Rangamaran, VR and Sankara Subramanian, SH and Balachandran, KRS and Gopal, D}, title = {Vertical Microbial Profiling of Arabian Sea Oxygen Minimal Zone Reveals Complex Bacterial Communities and Distinct Functional Implications.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {357-371}, pmid = {35195736}, issn = {1432-184X}, mesh = {*Seawater/microbiology ; *Oxygen/metabolism ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Bacteria ; Water/metabolism ; Nitrogen/metabolism ; }, abstract = {Arabian Sea harbours one of the largest oxygen minimal zones (OMZs) among the global oceans wherein biogeochemical cycles are regulated through dominant and complex microbial processes. The present study investigated the bacterial communities at various depths of the Arabian Sea OMZ using high-throughput sequencing of the v3-v4 hyper variable region of 16S rRNA gene. A total of 10 samples which included water samples from 8 different depths and 2 sediment samples were analyzed in this study. About 2.7 million sequences were obtained from all the samples. The sequence analysis revealed high bacterial diversity at deep waters and sediment samples and comparatively less species richness at the core OMZ depths. Number of OTUs ranged from 114 to 14441.Taxonomic assignments of the obtained OTUs showed dominant presence of Proteobacteria, Bacteriodetes, and Chloroflexi across all the samples. The identified OTUs were further affiliated to the phyla Marinimicrobia, Colwellia, Nitrospina, Tepidicaulis, Shewanella, Pseudoalteromonas, Woeseia at various depths along the water column. Correlation with abiotic factors suggested distinct variation in bacterial community composition with change in depth and dissolved oxygen (DO) levels. Predictive functional annotation based on bacterial phylotypes suggested presence of active nitrogen, sulphur, carbon, and methane metabolic cycles along the vertical transect of the studied region. Presence of nitrogen reduction bacterial group below the core OMZ depths may potentially provide insight into the expansion of OMZ region in Arabian Sea. Functional profiling further revealed presence of genes related to xenobiotic degradation in the water and sediment samples indicating a potential hotspot for bio-prospection.}, }
@article {pmid35194659, year = {2023}, author = {Chen, J and Deng, Y and Yu, X and Wu, G and Gao, Y and Ren, A}, title = {Epichloë Endophyte Infection Changes the Root Endosphere Microbial Community Composition of Leymus Chinensis Under Both Potted and Field Growth Conditions.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {604-616}, pmid = {35194659}, issn = {1432-184X}, support = {31971425//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Endophytes ; *Epichloe ; Poaceae/microbiology ; *Microbiota ; Bacteria ; Rhizosphere ; Plants/microbiology ; Soil ; Plant Roots/microbiology ; Soil Microbiology ; }, abstract = {Epichloë endophytes can not only affect the growth and resistance of the host plant but also change the biotic and abiotic properties of the soil where the host is situated. Here, we used endophyte-infected (EI) and endophyte-free (EF) Leymus chinensis as plant materials, to study the microbial diversity and composition in the host root endosphere and rhizosphere soil under both pot and field conditions. The results showed that endophyte infection did not affect the diversity of either bacteria or fungi in the root zone. There were significant differences in both bacterial and fungal communities between the root endosphere and the rhizosphere, and between the field and the pot, while endophytes only affected root endosphere microbial communities. The bacterial families affected by endophyte infection changed from 29.07% under field conditions to 40% under pot conditions. In contrast, the fungal families affected by endophyte infection were maintained at nearly 50% under both field and pot conditions. That is to say, bacterial communities in the root endosphere were more strongly affected by environmental conditions, and in comparison, the fungal communities were more strongly affected by species specificity. Endophytes significantly affected the fungal community composition of the host root endosphere in both potted and field plants, only the effect was more obvious in potted plants. Endophyte infection increased the abundance of three fungal families (Thelebolaceae, Herpotrichiellaceae and Trimorphomycetaceae) under both field and potted conditions. In potted plants, endophytes also altered the dominant fungi from pathogenic Pleosporales to saprophytic Chaetomiaceae. Endophyte infection increased the relative abundance of arbuscular mycorrhizal fungi and saprophytic fungi, especially under potted conditions.Overall, endophytes significantly affected the fungal community composition of the host root endosphere in both potted and field plants. Endophytes had a greater impact on root endosphere microorganisms than the rhizosphere, a greater impact on fungal communities than bacteria, and a greater impact on root endosphere microorganisms under potted conditions than at field sites.}, }
@article {pmid35192040, year = {2023}, author = {Detcharoen, M and Nilsai, A}, title = {Low Endosymbiont Incidence in Drosophila Species Across Peninsula Thailand.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {730-736}, pmid = {35192040}, issn = {1432-184X}, support = {SCI6404008S//Faculty of Science, Prince of Songkla University/ ; }, mesh = {Animals ; Male ; Drosophila ; Incidence ; Thailand ; Symbiosis ; Bacteroidetes ; *Wolbachia ; *Spiroplasma ; *Rickettsia ; }, abstract = {Arthropods are known to harbor several endosymbionts, such as Cardinium, Rickettsia, Spiroplasma, and Wolbachia. Wolbachia, for example, are the most widespread known endosymbionts in the world, which are found in about half of all arthropod species. To increase their transmission, these endosymbionts must manipulate their hosts in several ways such as cytoplasmic incompatibility and male killing. In tropical regions, endosymbiont diversity has not been studied exhaustively. Here, we checked four endosymbionts, including Cardinium, Rickettsia, Spiroplasma, and Wolbachia, in eleven Drosophila species found in Thai Peninsula. The Wolbachia strain wRi-like was found in all populations of Drosophila ananassae and Drosophila simulans. Furthermore, we found two new strains, wMalA and wMalB, in two populations of Drosophila malerkotliana. Besides Wolbachia, we did not find any of the above endosymbionts in all fly species. This work reveals the hidden diversity of endosymbionts in Drosophila and is the first exhaustive study on Drosophila in the region.}, }
@article {pmid35190857, year = {2023}, author = {Elmi, F and Etemadifar, Z and Emtiazi, G}, title = {Biosynthesis of Calcite Nanocrystal by a Novel Polyextremophile Bhargavaea cecembensis-Related Strain Isolated from Sandy Soil.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {698-707}, pmid = {35190857}, issn = {1432-184X}, mesh = {*Sand ; Soil ; Calcium Carbonate/chemistry ; Urease ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Nanoparticles ; Chemical Precipitation ; }, abstract = {Urease-producing bacteria are abundant in soils, which can precipitate calcium carbonate nanocrystals by enzymatic hydrolysis of urea in the presence of calcium ions. This process is known as microbially induced calcium carbonate precipitation (MICP), and it has received much attention in recent years as an eco-friendly technology. Therefore, the purpose of the present study was to isolate local extremophile bacterial strains capable of producing calcium carbonate. Among a total of 44 isolated urease-producing strains from sandy soils, one strain with a high level of urease activity (8.16 U/ml) and production of a large amount of calcium carbonate (410 mg/100 ml) was selected for further investigation. 16S rRNA gene sequencing showed that this strain had 99.66% sequence identity to Bhargavaea cecembensis. The SEM-EDX and XRD analyses indicated that irregular vaterite and aggregated nanocalcite were the dominant polymorphs produced by this strain. The size of these nanocalcite crystals ranged between 25 and 42 nm. The selected strain showed high levels of tolerance to different conditions of temperature, pH, and salinity. This strain grows at high temperatures up to 50 °C, alkaline pH (9-11), and high concentrations of NaCl (20-25% w/v). Flow cytometry analysis demonstrated 96% cell viability of the isolated strain after desiccation stress. Bhargavaea was first reported in 2009 as a new genus, and it belongs to the Firmicutes. So far, there has been no report on its MICP potential. The present study is the first one to report nanocrystal calcium carbonate precipitation in polyextremophile Bhargavaea cecembensis, which makes it a suitable candidate for bio-cementation under extreme circumstances.}, }
@article {pmid35188073, year = {2022}, author = {Ou, Y and Belzer, C and Smidt, H and de Weerth, C}, title = {Development of the gut microbiota in healthy children in the first ten years of life: associations with internalizing and externalizing behavior.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2038853}, pmid = {35188073}, issn = {1949-0984}, mesh = {Bifidobacterium/genetics ; Child ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Longitudinal Studies ; *Microbiota ; Prevotella ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Increasing evidence indicates that psychopathological disorders are associated with the gut microbiota. However, data are largely lacking from long-term longitudinal birth cohorts, especially those comprising low-risk healthy individuals. Therefore, this study aims to describe gut microbiota development in healthy children from birth till age 10 years, as well as to investigate potential associations with internalizing and externalizing behavior.<br><br>RESULTS: Fecal microbial composition of participants in an ongoing longitudinal study (N =&#xa0;193) was analyzed at 1, 3 and 4 months, and 6 and 10 years of age by 16S ribosomal RNA gene sequencing. Based on these data, three clusters were identified in infancy, two of which were predominated by Bifidobacterium. In childhood, four clusters were observed, two of which increased in prevalence with age. One of the childhood clusters, similar to an enterotype, was highly enriched in genus-level taxon Prevotella_9. Breastfeeding had marked associations with microbiota composition up till age 10, implying an extended role in shaping gut microbial ecology. Microbial clusters were not associated with behavior. However, Prevotella_9 in childhood was positively related to mother-reported externalizing behavior at age 10; this was validated in child reports.<br><br>CONCLUSIONS: This study validated previous findings on Bifidobacterium-enriched and -depleted clusters in infancy. Importantly, it also mapped continued development of gut microbiota in middle childhood. Novel associations between gut microbial composition in the first 10 years of life (especially Prevotella_9), and externalizing behavior at age 10 were found. Replications in other cohorts, as well as follow-up assessments, will help determine the significance of these findings.}, }
@article {pmid35185949, year = {2021}, author = {Matiz-Ceron, L and Reyes, A and Anzola, J}, title = {Taxonomical Evaluation of Plant Chloroplastic Markers by Bayesian Classifier.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {782663}, pmid = {35185949}, issn = {1664-462X}, abstract = {DNA barcodes are standardized sequences that range between 400 and 800 bp, vary at different taxonomic levels, and make it possible to assign sequences to species that have been previously taxonomically characterized. Several DNA barcodes have been postulated for plants, nonetheless, their classification potential has not been evaluated for metabarcoding, and as a result, it would appear as none of them excels above the others in this area. One tool that has been widely used and served as a baseline when evaluating new approaches is Naïve Bayesian Classifiers (NBC). The present study aims at evaluating the classification power of several plant chloroplast genetic markers that have been proposed as barcodes (trnL, rpoB, rbcL, matK, psbA-trnH, and psbK) using an NBC. We performed the classification at different taxonomic levels, and identified problematic genera when resolution was desired. We propose matK and trnL as potential candidate markers with resolution up to genus level. Some problematic genera within certain families could lead to the misclassification no matter which marker is used (i.e., Aegilops, Gueldenstaedtia, Helianthus, Oryza, Shorea, Thysananthus, and Triticum). Finally, we suggest recommendations for the taxonomic identification of plants in samples with potential mixtures.}, }
@article {pmid35185839, year = {2022}, author = {Sikorski, J and Baumgartner, V and Birkhofer, K and Boeddinghaus, RS and Bunk, B and Fischer, M and Fösel, BU and Friedrich, MW and Göker, M and Hölzel, N and Huang, S and Huber, KJ and Kandeler, E and Klaus, VH and Kleinebecker, T and Marhan, S and von Mering, C and Oelmann, Y and Prati, D and Regan, KM and Richter-Heitmann, T and Rodrigues, JFM and Schmitt, B and Schöning, I and Schrumpf, M and Schurig, E and Solly, EF and Wolters, V and Overmann, J}, title = {The Evolution of Ecological Diversity in Acidobacteria.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {715637}, pmid = {35185839}, issn = {1664-302X}, abstract = {Acidobacteria occur in a large variety of ecosystems worldwide and are particularly abundant and highly diverse in soils. In spite of their diversity, only few species have been characterized to date which makes Acidobacteria one of the most poorly understood phyla among the domain Bacteria. We used a culture-independent niche modeling approach to elucidate ecological adaptations and their evolution for 4,154 operational taxonomic units (OTUs) of Acidobacteria across 150 different, comprehensively characterized grassland soils in Germany. Using the relative abundances of their 16S rRNA gene transcripts, the responses of active OTUs along gradients of 41 environmental variables were modeled using hierarchical logistic regression (HOF), which allowed to determine values for optimum activity for each variable (niche optima). By linking 16S rRNA transcripts to the phylogeny of full 16S rRNA gene sequences, we could trace the evolution of the different ecological adaptations during the diversification of Acidobacteria. This approach revealed a pronounced ecological diversification even among acidobacterial sister clades. Although the evolution of habitat adaptation was mainly cladogenic, it was disrupted by recurrent events of convergent evolution that resulted in frequent habitat switching within individual clades. Our findings indicate that the high diversity of soil acidobacterial communities is largely sustained by differential habitat adaptation even at the level of closely related species. A comparison of niche optima of individual OTUs with the phenotypic properties of their cultivated representatives showed that our niche modeling approach (1) correctly predicts those physiological properties that have been determined for cultivated species of Acidobacteria but (2) also provides ample information on ecological adaptations that cannot be inferred from standard taxonomic descriptions of bacterial isolates. These novel information on specific adaptations of not-yet-cultivated Acidobacteria can therefore guide future cultivation trials and likely will increase their cultivation success.}, }
@article {pmid35185836, year = {2021}, author = {Unzueta-Martínez, A and Welch, H and Bowen, JL}, title = {Determining the Composition of Resident and Transient Members of the Oyster Microbiome.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {828692}, pmid = {35185836}, issn = {1664-302X}, abstract = {To better understand how complex microbial communities become assembled on eukaryotic hosts, it is essential to disentangle the balance between stochastic and deterministic processes that drive their assembly. Deterministic processes can create consistent patterns of microbiome membership that result in persistent resident communities, while stochastic processes can result in random fluctuation of microbiome members that are transient with regard to their association to the host. We sampled oyster reefs from six different populations across the east coast of the United States. At each site we collected gill tissues for microbial community analysis and additionally collected and shipped live oysters to Northeastern University where they were held in a common garden experiment. We then examined the microbiome shifts in gill tissues weekly for 6 weeks using 16S rRNA gene amplicon sequencing. We found a strong population-specific signal in the microbial community composition of field-sampled oysters. Surprisingly, the oysters sampled during the common garden experiment maintained compositionally distinct gill-associated microbial communities that reflected their wild population of origin, even after rearing them in a common garden for several weeks. This indicates that oyster gill-associated microbiota are predominantly composed of resident microbes specific to host population, rather than being a reflection of their immediate biotic and abiotic surroundings. However, certain bacterial taxa tended to appear more frequently on individuals from different populations than on individuals from the same population, indicating that there is a small portion of the gill microbiome that is transient and is readily exchanged with the environmental pool of microbes. Regardless, the majority of gill-associated microbes were resident members that were specific to each oyster population, suggesting that there are strong deterministic factors that govern a large portion of the gill microbiome. A small portion of the microbial communities, however, was transient and moved among oyster populations, indicating that stochastic assembly also contributes to the oyster gill microbiome. Our results are relevant to the oyster aquaculture industry and oyster conservation efforts because resident members of the oyster microbiome may represent microbes that are important to oyster health and some of these key members vary depending on oyster population.}, }
@article {pmid35181861, year = {2022}, author = {Hu, X and Peng, K and Chen, Y and Chen, X and Liu, S and Zhao, Y and Wu, Y and Xu, Z}, title = {Effect of g-C3N4 on biodiversity and structure of bacterial community in sediment of Xiangjiang River under tetracycline pressure.}, journal = {Ecotoxicology (London, England)}, volume = {31}, number = {3}, pages = {503-515}, doi = {10.1007/s10646-022-02525-7}, pmid = {35181861}, issn = {1573-3017}, support = {19A509//Science and Technology Innovative Research Team in Higher Educational Institutions of Hunan Province/ ; 201801//Key Projects of National Forestry and Grassland Bureau/ ; 31971462//National Aerospace Science Foundation of China/ ; 2021JJ31138//Natural Science Foundation of Hunan Province/ ; }, mesh = {Anti-Bacterial Agents/toxicity ; *Bacteria ; Biodiversity ; Geologic Sediments/chemistry ; *Rivers/chemistry ; Tetracyclines ; }, abstract = {Photocatalysts have been widely prepared and used in wastewater treatment. Although the influence of photocatalyst application on survival and activity of organisms has been examined, its impact on composition and diversity of microbial community is not fully understood. In this study, the impact of photocatalyst g-C3N4 (Graphitic carbon nitride) on microbial communities in riverbed sediments polluted by antibiotic tetracycline (TC) was investigated. The sediment samples collected from the Xiangjiang River of China were exposed to different concentrations of TC, g-C3N4 and TC/g-C3N4 and the bacterial community were analyzed by Illumina sequencing. The results showed that the dominant bacterial phyla were Acidobacteriota, Proteobacteria, Actinobacteriota, and Chloroflexi in the study site. When compared to the control treatments, the application of TC, g-C3N4 and TC/g-C3N4 exhibited distinguishable effects on bacterial community structure in sediments. The presence of TC had greater influence on bacterial composition, while g-C3N4 and TC/g-C3N4 had less influence on bacteria. The diversity and richness of microorganisms in sediment increased under g-C3N4 application and reached the highest values when g-C3N4 was 75 mg/kg. The photocatalyst g-C3N4 restored bacterial community diversity affected by TC, reduced the TC residues in aquatic environment, and eliminated the side effects of TC application in sediments. Our study indicated that g-C3N4 was an environmentally friendly photocatalyst with lightly negative effects on microbial community in riverbed sediments, and could be used for effective remediation of TC-contaminated environments.}, }
@article {pmid35181077, year = {2022}, author = {Xie, Z and Bai, Y and Chen, G and Dong, W and Peng, Y and Xu, W and Sun, Y and Zeng, X and Liu, Z}, title = {Immunomodulatory activity of polysaccharides from the mycelium of Aspergillus cristatus, isolated from Fuzhuan brick tea, associated with the regulation of intestinal barrier function and gut microbiota.}, journal = {Food research international (Ottawa, Ont.)}, volume = {152}, number = {}, pages = {110901}, doi = {10.1016/j.foodres.2021.110901}, pmid = {35181077}, issn = {1873-7145}, mesh = {Animals ; Aspergillus ; *Gastrointestinal Microbiome ; Immunity ; Mice ; Mycelium/metabolism ; Polysaccharides/pharmacology ; Tea/metabolism ; }, abstract = {Aspergillus cristatus is the dominant fungus involved in the fermentation of Fuzhuan brick tea (FBT). The intracellular polysaccharides (IPSs) from A. cristatus (MK346334, NCBI), isolated from FBT, exhibited immunomodulatory activity in vitro while the effects in vivo on immune system and gut microbiota remain unclear. In this study, IPSs and the purified fraction (IPSs-2) from IPSs were prepared and their immunomodulatory activities were investigated with cyclophosphamide (Cy)-induced immunosuppressive mice. As results, IPSs strengthened the immune function, manifesting in the improvement of body weight, daily intake, immune organ indices, cytokines and immunoglobulin. Meanwhile, IPSs attenuated Cy-induced intestinal barrier injury and promoted the expression of tight junction proteins and mucin, reinforcing the intestinal barrier function. Moreover, IPSs not only promoted the production of short-chain fatty acids and the expression of G protein-coupled receptor (GPR), but also balanced dysbiosis of gut microbiota through elevating the growth of beneficial bacteria while reducing pathobionts to maintain the homeostasis of the microbial ecology. These results suggested that IPSs exerted immunomodulatory activity linking with the restoration of intestinal barrier function and regulation of gut microbiota, which contributes to the development of novel probiotics and effective immunomodulators for strengthening host immunity and gut health.}, }
@article {pmid35181074, year = {2022}, author = {Young Kim, S and Ban, GH and Won Hong, Y and Ji Jang, M and Ae Kim, S}, title = {Microbiome shifts in sprouts (alfalfa, radish, and rapeseed) during production from seed to sprout using 16S rRNA microbiome sequencing.}, journal = {Food research international (Ottawa, Ont.)}, volume = {152}, number = {}, pages = {110896}, doi = {10.1016/j.foodres.2021.110896}, pmid = {35181074}, issn = {1873-7145}, mesh = {*Brassica napus ; Colony Count, Microbial ; Food Microbiology ; Humans ; Medicago sativa ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Raphanus ; Seeds ; }, abstract = {Sprouts harbor high levels of bacteria and have been implicated in massive outbreaks of foodborne illnesses. The elucidation of microbial profiles in sprouts is important; however, little is known about the changes in the microbial composition during production. The present study aimed to define the microbial ecology of sprouts during the stages of production using 16S rRNA metagenome sequencing and culture-dependent methods. Samples of three types of sprouts (alfalfa, radish, and rapeseed) were collected from each stage of production (seed, soaking, germination 1 (Germ 1), germination 2 (Germ 2), sprouting, unwashed, and washed sprouts; n = 105) and subjected to microbiome analyses as well as quantitative and qualitative analyses. Aerobic plate count (APC) and coliforms levels significantly increased within one day (Germ 1) by 3.9-4.4 and 4.2-5.2 log CFU/g, respectively, and levels up to 8.0-9.0 and 6.9-9.0 log CFU/g, respectively, were recorded at the final stage. During production, the microbial communities in alfalfa sprouts simplified into Enterobacteriaceae (80.97-99.29%), whereas the radish and rapeseed sprouts were dominated by microbial communities belonging to two families, the Enterobacteriaceae (radish: 32-43.4%, rapeseed: 24.11-38.39%) and Pseudomonadaceae (radish: 30.53-46.45%, rapeseed: 41.51-57.34%). This suggests that the sprout manufacturing conditions could promote the growth of particular bacterium. Alpha diversity analysis revealed a diverse bacterial community structure in the seeds; however, the diversity sharply declined until Germ 1 and recovered during the production steps thereafter. Beta diversity results suggested that the pattern of microbial composition, and the major shifts in composition, differed by seed type. Significant changes in the bacterial community were observed during the soaking (alfalfa), Germ 1 (radish), and Germ 2 (rapeseed) stages. The present study is the first fundamental report to investigate microbial changes by during the various stages of the sprouting process. The results highlight the potential risk of sprouts regarding foodborne illness and facilitate the determination of effective intervention points during sprout production.}, }
@article {pmid35179631, year = {2023}, author = {Mitbavkar, S and D'souza, S}, title = {Seasonal Dynamics of Photosynthetic Picoeukaryotes in a Monsoon-Influenced Tropical Bay: a Flow Cytometric and Chemotaxonomic Approach.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {341-356}, pmid = {35179631}, issn = {1432-184X}, mesh = {Seasons ; Flow Cytometry ; *Bays ; *Phytoplankton ; Photosynthesis ; Biomass ; }, abstract = {The composition and ecology of photosynthetic picoeukaryotes (PPE) are essential for understanding microbial food web functioning. We hypothesize that the simultaneous use of flow cytometry (FCM) and high-performance liquid chromatography (HPLC) tools will aid in discerning the dominant PPE groups contributing to abundance and biomass under prevailing environmental conditions. The PPE seasonal community abundance and pigment biomass were investigated from a southwest monsoon-influenced tropical bay from June 2015 to May 2016. A size-fractionated (<3 µm) approach using FCM and HPLC revealed five and six PPE groups, respectively. Picocryptophytes dominated the PPE biomass under varied environmental conditions, whereas picodiatoms contributed substantially, being abundant under turbulent, low-temperature, nutrient (NO3[-], SiO4[4-])-enriched conditions. The picochlorophytes dominated the community numerically. The relatively higher abundance and biomass of picoprasinophytes and a positive correlation with NO3[-] and NH4[+] imply proliferation under higher nutrient concentrations. The least contributors to biomass were dinoflagellates and picoprymnesiophytes. The relatively larger cell size of picocryptophytes and picodiatoms resulted in higher cumulative biomass, signifying their role in the microbial food web. Our study proposes incorporation of additional indicator pigments in algorithms used to estimate coastal picophytoplankton contribution to total phytoplankton biomass to avoid discrepancies.}, }
@article {pmid35179276, year = {2022}, author = {Yemmen, C and Gargouri, M}, title = {Potential hazards associated with the consumption of Scombridae fish: Infection and toxicity from raw material and processing.}, journal = {Journal of applied microbiology}, volume = {132}, number = {6}, pages = {4077-4096}, doi = {10.1111/jam.15499}, pmid = {35179276}, issn = {1365-2672}, mesh = {Animals ; Fishes ; *Food Contamination/analysis ; *Metals, Heavy/toxicity ; Seafood ; Tuna/microbiology ; }, abstract = {Scombridae fish (tuna, bonito and mackerel) have significant ecological and economic values. They are very appreciated by consumers worldwide for their high-quality flesh and for their high nutritional value. However, consumption of Scombridae fish is potentially hazardous. Indeed, several cases of infections and toxicity linked to the consumption of Scombridae fish as raw, or processed food products have been reported worldwide. In this review, we presented the most common health risks associated with Scombridae fish consumption. Diseases associated with the consumption of these fish are generally infectious or toxic and are caused by biological hazards, such as bacteria, viruses, parasites or chemicals hazards that enter the body through contaminated fish (polycyclic aromatic hydrocarbons, histamine) or by physical contaminants, such as heavy metals. The risks of contamination exist throughout the food chain, from primary production to the preparation of products for consumption.}, }
@article {pmid35176463, year = {2022}, author = {Van Peteghem, L and Sakarika, M and Matassa, S and Pikaar, I and Ganigué, R and Rabaey, K}, title = {Towards new carbon-neutral food systems: Combining carbon capture and utilization with microbial protein production.}, journal = {Bioresource technology}, volume = {349}, number = {}, pages = {126853}, doi = {10.1016/j.biortech.2022.126853}, pmid = {35176463}, issn = {1873-2976}, mesh = {*Carbon ; Carbon Dioxide ; *Carbon Footprint ; }, abstract = {Alternative protein sources such as microbial protein (MP) are currently considered to alleviate the burden that food production exerts on the environment. Even though MP production is highly efficient in land and nutrient utilization, their carbon footprint should be improved. Here we propose the use of CCU as a driver for heterotrophic MP production. By comparing different MP production routes starting from liquid substrates derived from CO2 (i.e., formate, acetate, methanol, and ethanol) and their respective metabolic pathways, the potential of this concept as a carbon-neutral food or feed production process was estimated. Acetate and ethanol appear to be the most beneficial substrates for the integrated CCU-to-MP process in terms of electricity demand (acetate: 25 - 54 kWh/kgproduct, ethanol: 28 - 56 kWh/kgproduct). Moreover, recycling CO2 enables a carbon-negative protein production process by 2030 (considering the projected CO2 emissions from electricity in the EU: 0.096 kgCO2-eq/kWh) for formate, acetate, and ethanol (-1.1 up to 13 kgCO2-eq/kgproduct).}, }
@article {pmid35176304, year = {2022}, author = {Li, JL and Duan, L and Wu, Y and Ahmad, M and Yin, LZ and Luo, XQ and Wang, X and Fang, BZ and Li, SH and Huang, LN and Wu, JX and Mou, XZ and Wang, P and Li, WJ}, title = {Unraveling microbe-mediated degradation of lignin and lignin-derived aromatic fragments in the Pearl River Estuary sediments.}, journal = {Chemosphere}, volume = {296}, number = {}, pages = {133995}, doi = {10.1016/j.chemosphere.2022.133995}, pmid = {35176304}, issn = {1879-1298}, mesh = {Archaea/genetics ; Bacteria/genetics ; Carbon/analysis ; China ; *Estuaries ; Geologic Sediments/microbiology ; Lignin ; *Rivers/microbiology ; }, abstract = {Estuaries are one of the most crucial areas for the transformation and burial of terrestrial organic carbon (TerrOC), playing an important role in the global carbon cycle. While the transformation and degradation of TerrOC are mainly driven by microorganisms, the specific taxa and degradation processes involved remain largely unknown in estuaries. We collected surface sediments from 14 stations along the longitudinal section of the Pearl River Estuary (PRE), P. R. China. By combining analytical chemistry, metagenomics, and bioinformatics methods, we analyzed composition, source and degradation pathways of lignin/lignin-derived aromatic fragments and their potential decomposers in these samples. A diversity of bacterial and archaeal taxa, mostly those from Proteobacteria (Deltaproteobacteria, Gammaproteobacteria etc.), including some lineages (e.g., Nitrospria, Polyangia, Tectomicrobia_uc) not previously implicated in lignin degradation, were identified as potential polymeric lignin or its aromatic fragments degraders. The abundance of lignin degradation pathways genes exhibited distinct spatial distribution patterns with the area adjacent to the outlet of Modaomen as a potential degradation hot zone and the Syringyl lignin fragments, 3,4-PDOG, and 4,5-PDOG pathways as the primary potential lignin aromatic fragments degradation processes. Notably, the abundance of ferulic acid metabolic pathway genes exhibited significant correlations with degree of lignin oxidation and demethylation/demethoxylization and vegetation source. Additionally, the abundance of 2,3-PDOG degradation pathways genes also showed a positive significant correlation with degree of lignin oxidation. Our study provides a meaningful insight into the microbial ecology of TerrOC degradation in the estuary.}, }
@article {pmid35173689, year = {2021}, author = {Monteiro, MR and Marshall, AJ and Hawes, I and Lee, CK and McDonald, IR and Cary, SC}, title = {Geochemically Defined Space-for-Time Transects Successfully Capture Microbial Dynamics Along Lacustrine Chronosequences in a Polar Desert.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {783767}, pmid = {35173689}, issn = {1664-302X}, abstract = {The space-for-time substitution approach provides a valuable empirical assessment to infer temporal effects of disturbance from spatial gradients. Applied to predict the response of different ecosystems under current climate change scenarios, it remains poorly tested in microbial ecology studies, partly due to the trophic complexity of the ecosystems typically studied. The McMurdo Dry Valleys (MDV) of Antarctica represent a trophically simple polar desert projected to experience drastic changes in water availability under current climate change scenarios. We used this ideal model system to develop and validate a microbial space-for-time sampling approach, using the variation of geochemical profiles that follow alterations in water availability and reflect past changes in the system. Our framework measured soil electrical conductivity, pH, and water activity in situ to geochemically define 17 space-for-time transects from the shores of four dynamic and two static Dry Valley lakes. We identified microbial taxa that are consistently responsive to changes in wetness in the soils and reliably associated with long-term dry or wet edaphic conditions. Comparisons between transects defined at static (open-basin) and dynamic (closed-basin) lakes highlighted the capacity for geochemically defined space-for-time gradients to identify lasting deterministic impacts of historical changes in water presence on the structure and diversity of extant microbial communities. We highlight the potential for geochemically defined space-for-time transects to resolve legacy impacts of environmental change when used in conjunction with static and dynamic scenarios, and to inform future environmental scenarios through changes in the microbial community structure, composition, and diversity.}, }
@article {pmid35172890, year = {2022}, author = {Zhou, Z and Tran, PQ and Breister, AM and Liu, Y and Kieft, K and Cowley, ES and Karaoz, U and Anantharaman, K}, title = {METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {33}, pmid = {35172890}, issn = {2049-2618}, support = {T15 LM007359/LM/NLM NIH HHS/United States ; T32 GM140935/GM/NIGMS NIH HHS/United States ; }, mesh = {*Genome, Microbial ; Humans ; Lakes ; Metagenome/genetics ; Metagenomics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling.<br><br>RESULTS: We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric "MW-score" (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~&#x2009;3 h with 40 CPU threads to process ~&#x2009;100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~&#x2009;45 min, while it takes ~&#x2009;5 h to complete hmmsearch for ~&#x2009;3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut.<br><br>CONCLUSION: METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3&#xa0;at https://github.com/AnantharamanLab/METABOLIC . Video abstract.}, }
@article {pmid35171088, year = {2022}, author = {Lee, HJ and Whang, KS}, title = {Roseomonas rubea sp. nov., isolated from rice paddy soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {72}, number = {2}, pages = {}, doi = {10.1099/ijsem.0.005251}, pmid = {35171088}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; *Methylobacteriaceae/classification/isolation &amp; purification ; *Oryza ; Phospholipids/chemistry ; *Phylogeny ; Pigmentation ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Ubiquinone/analogs &amp; derivatives/chemistry ; }, abstract = {Three pale-red-pigmented, Gram-stain-negative, coccobacilli-shaped, motile and strictly aerobic bacteria, strains MO17[T], MO41 and NPKOSM1, were isolated from rice paddy soil. Colonies were circular with entire edges, convex and pale red. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains MO17[T], MO41 and NPKOSM1 belonged to the genus Roseomonas and were closely related to Roseomonas sediminicola FW-3[T] (98.2 %), Roseomonas oryzicola YC6724[T] (98.0 %), Roseomonas soli 5N26[T] (98.0 %), Roseomonas eburnea BUT-5[T] (97.8 %), Roseomonas alkaliterrae YIM 78007[T] (97.7 %), Roseomonas lacus TH-G33[T] (97.6 %) and Roseomonas terrae DS-48[T] (96.8 %). The DNA-DNA hybridization values between strains MO17[T], MO41 and NPKOSM1 were 84-92 %, and the values between the three strains and their close phylogenetic relatives were also below 70 %. The major cellular fatty acids were C18 : 1 ω7c, C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2OH). The predominant respiratory quinone was identified as Q-10. The polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified aminophospholipid and two unknown phospholipids. Based on their distinctive phenotypic, phylogenetic and chemotaxonomic characteristics, the three strains are considered to represent novel species of the genus Roseomonas for which the name Roseomonas rubea sp. nov. is proposed. The type strain is MO17[T] (=KACC 19933[T]=NBRC 114495[T]).}, }
@article {pmid35171049, year = {2022}, author = {Yu, T and Cheng, L and Liu, Q and Wang, S and Zhou, Y and Zhong, H and Tang, M and Nian, H and Lian, T}, title = {Effects of Waterlogging on Soybean Rhizosphere Bacterial Community Using V4, LoopSeq, and PacBio 16S rRNA Sequence.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0201121}, pmid = {35171049}, issn = {2165-0497}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics/physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; Glycine max/growth &amp; development/*microbiology ; }, abstract = {Waterlogging causes a significant reduction in soil oxygen levels, which in turn negatively affects soil nutrient use efficiency and crop yields. Rhizosphere microbes can help plants to better use nutrients and thus better adapt to this stress, while it is not clear how the plant-associated microbes respond to waterlogging stress. There are also few reports on whether this response is influenced by different sequencing methods and by different soils. In this study, using partial 16S rRNA sequencing targeting the V4 region and two full-length 16S rRNA sequencing approaches targeting the V1 to V9 regions, the effects of waterlogging on soybean rhizosphere bacterial structure in two types of soil were examined. Our results showed that, compared with the partial 16S sequencing, full-length sequencing, both LoopSeq and Pacific Bioscience (PacBio) 16S sequencing, had a higher resolution. On both types of soil, all the sequencing methods showed that waterlogging significantly affected the bacterial community structure of the soybean rhizosphere and increased the relative abundance of Geobacter. Furthermore, modular analysis of the cooccurrence network showed that waterlogging increased the relative abundance of some microorganisms related to nitrogen cycling when using V4 sequencing and increased the microorganisms related to phosphorus cycling when using LoopSeq and PacBio 16S sequencing methods. Core microorganism analysis further revealed that the enriched members of different species might play a central role in maintaining the stability of bacterial community structure and ecological functions. Together, our study explored the role of microorganisms enriched at the rhizosphere under waterlogging in assisting soybeans to resist stress. Furthermore, compared to partial and PacBio 16S sequencing, LoopSeq offers improved accuracy and reduced sequencing prices, respectively, and enables accurate species-level and strain identification from complex environmental microbiome samples. IMPORTANCE Soybeans are important oil-bearing crops, and waterlogging has caused substantial decreases in soybean production all over the world. The microbes associated with the host have shown the ability to promote plant growth, nutrient absorption, and abiotic resistance. High-throughput sequencing of partial 16S rRNA is the most commonly used method to analyze the microbial community. However, partial sequencing cannot provide correct classification information below the genus level, which greatly limits our research on microbial ecology. In this study, the effects of waterlogging on soybean rhizosphere microbial structure in two soil types were explored using partial 16S rRNA and full-length 16S gene sequencing by LoopSeq and Pacific Bioscience (PacBio). The results showed that full-length sequencing had higher classification resolution than partial sequencing. Three sequencing methods all indicated that rhizosphere bacterial community structure was significantly impacted by waterlogging, and the relative abundance of Geobacter was increased in the rhizosphere in both soil types after suffering waterlogging. Moreover, the core microorganisms obtained by different sequencing methods all contain species related to nitrogen cycling. Together, our study not only explored the role of microorganisms enriched at the rhizosphere level under waterlogging in assisting soybean to resist stress but also showed that LoopSeq sequencing is a less expensive and more convenient method for full-length sequencing by comparing different sequencing methods.}, }
@article {pmid35166563, year = {2022}, author = {Pudlo, NA and Urs, K and Crawford, R and Pirani, A and Atherly, T and Jimenez, R and Terrapon, N and Henrissat, B and Peterson, D and Ziemer, C and Snitkin, E and Martens, EC}, title = {Phenotypic and Genomic Diversification in Complex Carbohydrate-Degrading Human Gut Bacteria.}, journal = {mSystems}, volume = {7}, number = {1}, pages = {e0094721}, pmid = {35166563}, issn = {2379-5077}, support = {K01 DK084214/DK/NIDDK NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; R01 DK118024/DK/NIDDK NIH HHS/United States ; R01 DK125445/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Polysaccharides/chemistry ; Bacteria/metabolism ; Dietary Carbohydrates/metabolism ; *Microbiota ; Dietary Fiber/metabolism ; Genomics ; Mucins/metabolism ; }, abstract = {Symbiotic bacteria are responsible for the majority of complex carbohydrate digestion in the human colon. Since the identities and amounts of dietary polysaccharides directly impact the gut microbiota, determining which microorganisms consume specific nutrients is central for defining the relationship between diet and gut microbial ecology. Using a custom phenotyping array, we determined carbohydrate utilization profiles for 354 members of the Bacteroidetes, a dominant saccharolytic phylum. There was wide variation in the numbers and types of substrates degraded by individual bacteria, but phenotype-based clustering grouped members of the same species indicating that each species performs characteristic roles. The ability to utilize dietary polysaccharides and endogenous mucin glycans was negatively correlated, suggesting exclusion between these niches. By analyzing related Bacteroides ovatus/Bacteroides xylanisolvens strains that vary in their ability to utilize mucin glycans, we addressed whether gene clusters that confer this complex, multilocus trait are being gained or lost in individual strains. Pangenome reconstruction of these strains revealed a remarkably mosaic architecture in which genes involved in polysaccharide metabolism are highly variable and bioinformatics data provide evidence of interspecies gene transfer that might explain this genomic heterogeneity. Global transcriptomic analyses suggest that the ability to utilize mucin has been lost in some lineages of B. ovatus and B. xylanisolvens, which harbor residual gene clusters that are involved in mucin utilization by strains that still actively express this phenotype. Our data provide insight into the breadth and complexity of carbohydrate metabolism in the microbiome and the underlying genomic events that shape these behaviors. IMPORTANCE Nonharmful bacteria are the primary microbial symbionts that inhabit the human gastrointestinal tract. These bacteria play many beneficial roles and in some cases can modify disease states, making it important to understand which nutrients sustain specific lineages. This knowledge will in turn lead to strategies to intentionally manipulate the gut microbial ecosystem. We designed a scalable, high-throughput platform for measuring the ability of gut bacteria to utilize polysaccharides, of which many are derived from dietary fiber sources that can be manipulated easily. Our results provide paths to expand phenotypic surveys of more diverse gut bacteria to understand their functions and also to leverage dietary fibers to alter the physiology of the gut microbial community.}, }
@article {pmid35166561, year = {2022}, author = {Monsees, I and Turzynski, V and Esser, SP and Soares, A and Timmermann, LI and Weidenbach, K and Banas, J and Kloster, M and Beszteri, B and Schmitz, RA and Probst, AJ}, title = {Label-Free Raman Microspectroscopy for Identifying Prokaryotic Virocells.}, journal = {mSystems}, volume = {7}, number = {1}, pages = {e0150521}, pmid = {35166561}, issn = {2379-5077}, mesh = {*Prokaryotic Cells ; Anti-Bacterial Agents ; Ecosystem ; Gram-Negative Bacteria ; Archaea ; *Bacteriophages ; Bacillus subtilis ; }, abstract = {Raman microspectroscopy has been used to thoroughly assess growth dynamics and heterogeneity of prokaryotic cells, yet little is known about how the chemistry of individual cells changes during infection with virulent viruses, resulting in so-called virocells. Here, we investigate biochemical changes of bacterial and archaeal cells of three different species in laboratory cultures before and after addition of their respective viruses using single-cell Raman microspectroscopy. By applying multivariate statistics, we identified significant differences in the spectra of single cells with/without addition of virulent dsRNA phage (phi6) for Pseudomonas syringae. A general ratio of wavenumbers that contributed the greatest differences in the recorded spectra was defined as an indicator for virocells. Based on reference spectra, this difference is likely attributable to an increase in nucleic acid versus protein ratio of virocells. This method also proved successful for identification of Bacillus subtilis cells infected with the double-stranded DNA (dsDNA) phage phi29, displaying a decrease in respective ratio, but failed for archaeal virocells (Methanosarcina mazei with the dsDNA methanosarcina spherical virus) due to autofluorescence. Multivariate and univariate analyses suggest that Raman spectral data of infected cells can also be used to explore the complex biology behind viral infections of bacteria. Using this method, we confirmed the previously described two-stage infection of P. syringae's phi6 and that infection of B. subtilis with phi29 results in a stress response within single cells. We conclude that Raman microspectroscopy is a promising tool for chemical identification of Gram-positive and Gram-negative virocells undergoing infection with virulent DNA or RNA viruses. IMPORTANCE Viruses are highly diverse biological entities shaping many ecosystems across Earth. However, understanding the infection of individual microbial cells and the related biochemical changes remains limited. Using Raman microspectroscopy in conjunction with univariate and multivariate statistics, we established a marker for identification of infected Gram-positive and Gram-negative bacteria. This nondestructive, label-free analytical method at single-cell resolution paves the way for future studies geared towards analyzing virus-host systems of prokaryotes to further understand the complex chemistry and function of virocells.}, }
@article {pmid35159609, year = {2022}, author = {Tsigkrimani, M and Panagiotarea, K and Paramithiotis, S and Bosnea, L and Pappa, E and Drosinos, EH and Skandamis, PN and Mataragas, M}, title = {Microbial Ecology of Sheep Milk, Artisanal Feta, and Kefalograviera Cheeses. Part II: Technological, Safety, and Probiotic Attributes of Lactic Acid Bacteria Isolates.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {3}, pages = {}, pmid = {35159609}, issn = {2304-8158}, support = {T1EDK-02087//European Union and Greek national funds/ ; }, abstract = {The aim of the present study was to examine 189 LAB strains belonging to the species Enterococcus faecium, E. faecalis, Lactococcus lactis, Pediococcus pentosaceus, Leuconostoc mesenteroides, Lactiplantibacillus pentosus, Latilactobacillus curvatus, Lp. plantarum, Levilactobacillus brevis, and Weissella paramesenteroides isolated form sheep milk, Feta and Kefalograviera cheeses at different ripening stages, for their technological compatibility with dairy products manufacturing, their activities that may compromise safety of the dairy products as well as their capacity to survive in the human gastrointestinal tract. For that purpose, milk acidification and coagulation capacity, caseinolytic, lipolytic, hemolytic, gelatinolytic, and bile salt hydrolase activity, production of exopolysaccharides, antimicrobial compounds, and biogenic amines, as well as acid and bile salt tolerance and antibiotic susceptibility were examined. The faster acidifying strains were Lc. lactis DRD 2658 and P. pentosaceus DRD 2657 that reduced the pH value of skim milk, within 6 h to 5.97 and 5.92, respectively. Strains able to perform weak caseinolysis were detected in all species assessed. On the contrary, lipolytic activity, production of exopolysaccharides, amino acid decarboxylation, hemolytic, gelatinase, and bile salt hydrolase activity were not detected. Variable susceptibility to the antibiotics examined was detected among LAB strains. However, in the majority of the cases, resistance was evident. None of the strains assessed, managed to survive to exposure at pH value 1. On the contrary, 25.9 and 88.9% of the strains survived after exposure at pH values 2 and 3, respectively; the reduction of the population was larger in the first case. The strains survived well after exposure to bile salts. The strain-dependent character of the properties examined was verified. Many strains, belonging to different species, have presented very interesting properties; however, further examination is needed before their potential use as starter or adjunct cultures.}, }
@article {pmid35157872, year = {2022}, author = {Sperlea, T and Schenk, JP and Dreßler, H and Beisser, D and Hattab, G and Boenigk, J and Heider, D}, title = {The relationship between land cover and microbial community composition in European lakes.}, journal = {The Science of the total environment}, volume = {825}, number = {}, pages = {153732}, doi = {10.1016/j.scitotenv.2022.153732}, pmid = {35157872}, issn = {1879-1026}, mesh = {Environmental Biomarkers ; *Lakes ; *Microbiota ; Water Quality ; }, abstract = {Microbes are essential for element cycling and ecosystem functioning. However, many questions central to understanding the role of microbes in ecology are still open. Here, we analyze the relationship between lake microbiomes and the lakes' land cover. By applying machine learning methods, we quantify the covariance between land cover categories and the microbial community composition recorded in the largest amplicon sequencing dataset of European lakes available to date. Our results show that the aggregation of environmental features or microbial taxa before analysis can obscure ecologically relevant patterns. We observe a comparatively high covariation of the lakes' microbial community with herbaceous and open spaces surrounding the lake; nevertheless, the microbial covariation with land cover categories is generally lower than the covariation with physico-chemical parameters. Combining land cover and physico-chemical bioindicators identified from the same amplicon sequencing dataset, we develop analytical data structures that facilitate insights into the ecology of the lake microbiome. Among these, a list of the environmental parameters sorted by the number of microbial bioindicators we have identified for them points towards apparent environmental drivers of the lake microbial community composition, such as the altitude, conductivity, and area covered herbaceous vegetation surrounding the lake. Furthermore, the response map, a similarity matrix calculated from the Jaccard similarity of the environmental parameters' lists of bioindicators, allows us to study the ecosystem's structure from the standpoint of the microbiome. More specifically, we identify multiple clusters of highly similar and possibly functionally linked ecological parameters, including one that highlights the importance of the calcium-bicarbonate equilibrium for lake ecology. Taken together, we demonstrate the use of machine learning approaches in studying the interplay between microbial diversity and environmental factors and introduce novel approaches to integrate environmental molecular diversity into monitoring and water quality assessments.}, }
@article {pmid35157108, year = {2023}, author = {Mo, S and He, S and Sang, Y and Li, J and Kashif, M and Zhang, Z and Su, G and Jiang, C}, title = {Integration of Microbial Transformation Mechanism of Polyphosphate Accumulation and Sulfur Cycle in Subtropical Marine Mangrove Ecosystems with Spartina alterniflora Invasion.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {478-494}, pmid = {35157108}, issn = {1432-184X}, support = {31760437//National Natural Science Foundation of China/ ; GUIKEZY21195021//Funding Project of Chinese Central Government Guiding to the Guangxi Local Science and Technology Development/ ; 2019GXNSFFA245011//Natural Science Fund for Distinguished Young Scholars of Guangxi Zhuang Autonomous Region of China/ ; AD20297142//China-ASEAN International Innovative Center for Health Industry of Traditional Chinese Medicine/ ; 2022KA02//Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University/ ; YCBZ2021012//Innovation Project of Guangxi Graduate Education/ ; YCSW2021064//Innovation Project of Guangxi Graduate Education/ ; }, mesh = {*Wetlands ; Polyphosphates/analysis/metabolism ; Phylogeny ; Introduced Species ; Nitrogen/metabolism ; Phosphorus/metabolism ; Poaceae ; *Microbiota ; Sulfur/metabolism ; Sulfates/metabolism ; China ; }, abstract = {Excessive phosphorus can lead to eutrophication in marine and coastal ecosystems. Sulfur metabolism-associated microorganisms stimulate biological phosphorous removal. However, the integrating co-biotransformation mechanism of phosphorus and sulfur in subtropical marine mangrove ecosystems with Spartina alterniflora invasion is poorly understood. In this study, an ecological model of the coupling biotransformation of sulfur and phosphorus is constructed using metagenomic analysis and quantitative polymerase chain reaction strategies. Phylogenetic analysis profiling, a distinctive microbiome with high frequencies of Gammaproteobacteria and Deltaproteobacteria, appears to be an adaptive characteristic of microbial structures in subtropical mangrove ecosystems. Functional analysis reveals that the levels of sulfate reduction, sulfur oxidation, and poly-phosphate (Poly-P) aggregation decrease with increasing depth. However, at depths of 25-50 cm in the mangrove ecosystems with S. alterniflora invasion, the abundance of sulfate reduction genes, sulfur oxidation genes, and polyphosphate kinase (ppk) significantly increased. A strong positive correlation was found among ppk, sulfate reduction, sulfur oxidation, and sulfur metabolizing microorganisms, and the content of sulfide was significantly and positively correlated with the abundance of ppk. Further microbial identification suggested that Desulfobacterales, Anaerolineales, and Chromatiales potentially drove the coupling biotransformation of phosphorus and sulfur cycling. In particular, Desulfobacterales exhibited dominance in the microbial community structure. Our findings provided insights into the simultaneous co-biotransformation of phosphorus and sulfur bioconversions in subtropical marine mangrove ecosystems with S. alterniflora invasion.}, }
@article {pmid35154025, year = {2021}, author = {DeWolf, EI and Calder, WJ and Harrison, JG and Randolph, GD and Noren, BE and Weinig, C}, title = {Aquatic Macrophytes Are Associated With Variation in Biogeochemistry and Bacterial Assemblages of Mountain Lakes.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {777084}, pmid = {35154025}, issn = {1664-302X}, abstract = {In aquatic systems, microbes likely play critical roles in biogeochemical cycling and ecosystem processes, but much remains to be learned regarding microbial biogeography and ecology. The microbial ecology of mountain lakes is particularly understudied. We hypothesized that microbial distribution among lakes is shaped, in part, by aquatic plant communities and the biogeochemistry of the lake. Specifically, we investigated the associations of yellow water lilies (Nuphar polysepala) with the biogeochemistry and microbial assemblages within mountain lakes at two scales: within a single lake and among lakes within a mountain range. We first compared the biogeochemistry of lakes without water lilies to those colonized to varying degrees by water lilies. Lakes with >10% of the surface occupied by water lilies had lower pH and higher dissolved organic carbon than those without water lilies and had a different microbial composition. Notably, cyanobacteria were negatively associated with water lily presence, a result consistent with the past observation that macrophytes outcompete phytoplankton and can suppress cyanobacterial and algal blooms. To examine the influence of macrophytes on microbial distribution within a lake, we characterized microbial assemblages present on abaxial and adaxial water lily leaf surfaces and in the water column. Microbial diversity and composition varied among all three habitats, with the highest diversity of microbes observed on the adaxial side of leaves. Overall, this study suggests that water lilies influence the biogeochemistry and microbiology of mountains lakes.}, }
@article {pmid35151004, year = {2022}, author = {Mekureyaw, MF and Pandey, C and Hennessy, RC and Nicolaisen, MH and Liu, F and Nybroe, O and Roitsch, T}, title = {The cytokinin-producing plant beneficial bacterium Pseudomonas fluorescens G20-18 primes tomato (Solanum lycopersicum) for enhanced drought stress responses.}, journal = {Journal of plant physiology}, volume = {270}, number = {}, pages = {153629}, doi = {10.1016/j.jplph.2022.153629}, pmid = {35151004}, issn = {1618-1328}, abstract = {Plant growth-promoting rhizobacteria (PGPR) are known for exerting beneficial effects on plant growth and tolerance to plant pathogens. However, their specific role in mediating protection against abiotic stress remains underexplored. The aim of this study was to characterise the ability of the cytokinin-producing beneficial bacterium Pseudomonas fluorescens G20-18 to enhance tomato growth and boost tolerance to drought stress. Tomato seedlings were root inoculated and their growth and physiological and molecular responses assessed under well-watered conditions and also in response to progressive drought stress and a subsequent recovery period. Root inoculation with G20-18 had a significant positive impact on tomato growth. Furthermore, G20-18 inoculated and drought-stressed plants showed higher leaf chlorophyll and abscisic acid (ABA) content and stomatal closure than non-inoculated controls. Root inoculation also increased the activity of different carbohydrate metabolism enzymes, which are important for root and leaf growth and development in drought stressed plants. A significant increase in the activity of different antioxidant enzymes and total antioxidant capacity correlated with elevated levels of relevant secondary metabolites, such as phenolics, anthocyanins and flavonoids. RNA sequencing revealed distinct qualitative and quantitative differences in gene regulation in response to G20-18. Notably, the number of genes differentially regulated in response to G20-18 was approximately sevenfold higher during drought stress, indicating that root inoculation with the bacteria primed the plants for a much stronger transcriptionally regulated systemic drought stress response. The regulated genes are related to phenylalanine metabolism and other key processes linked to plant growth, development and drought stress resilience. A role of the ability of G20-18 to produce the plant hormone cytokinin for interaction with tomato was established by the cytokinin-deficient biosynthesis mutants CNT1 and CNT2. In comparison with G20-18, the inoculation of plants with CNT1 resulted in a reduced number of differentially regulated genes. The relative change was most prominent under well-watered conditions with a 85 % reduction, corresponding to 462 genes. However, under drought conditions the absolute number of differentially regulated genes was reduced by even 2219 in response to the CNT1 mutant. The relevance of the ability of G20-18 to produce cytokinins for interaction with plants was also evident from differences in growth and specific cell and ecophysiological parameters in response to CNT1 and CNT2. These findings provide novel insights about G20-18's ability to improve drought stress responses and the role of interkingdom signalling by bacterial-derived cytokinins, and contribute to enhance the robustness of the practical application of these microorganisms to improve crop resilience in agricultural production.}, }
@article {pmid35150249, year = {2022}, author = {Qi, Y and Ossowicki, A and Yergeau, &#xc9; and Vigani, G and Geissen, V and Garbeva, P}, title = {Plastic mulch film residues in agriculture: impact on soil suppressiveness, plant growth, and microbial communities.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {2}, pages = {}, doi = {10.1093/femsec/fiac017}, pmid = {35150249}, issn = {1574-6941}, mesh = {Agriculture ; *Ascomycota ; *Microbiota ; Plastics ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Plastic mulch film residues have been accumulating in agricultural soils for decades, but so far, little is known about its consequences on soil microbial communities and functions. Here, we tested the effects of plastic residues of low-density polyethylene and biodegradable mulch films on soil suppressiveness and microbial community composition. We investigated how plastic residues in a Fusarium culmorum suppressive soil affect the level of disease suppressiveness, plant biomass, nutrient status, and microbial communities in rhizosphere using a controlled pot experiment. The addition of 1% plastic residues to the suppressive soil did not affect the level of suppression and the disease symptoms index. However, we did find that plant biomasses decreased, and that plant nutrient status changed in the presence of plastic residues. No significant changes in bacterial and fungal rhizosphere communities were observed. Nonetheless, bacterial and fungal communities closely attached to the plastisphere were very different from the rhizosphere communities with overrepresentation of potential plant pathogens. The plastisphere revealed a high abundance of specific bacterial phyla (Actinobacteria, Bacteroidetes, and Proteobacteria) and fungal genera (Rhizoctonia and Arthrobotrys). Our work revealed new insights and raises emerging questions for further studies on the impact of microplastics on the agroecosystems.}, }
@article {pmid35149704, year = {2022}, author = {Ling, N and Wang, T and Kuzyakov, Y}, title = {Rhizosphere bacteriome structure and functions.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {836}, pmid = {35149704}, issn = {2041-1723}, mesh = {Antitoxins ; Bacteria/*classification/genetics ; *Bacterial Physiological Phenomena ; Bacteroidetes ; Biodiversity ; Microbiota/genetics ; Proteobacteria ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil ; *Soil Microbiology ; }, abstract = {Microbial composition and functions in the rhizosphere-an important microbial hotspot-are among the most fascinating yet elusive topics in microbial ecology. We used 557 pairs of published 16S rDNA amplicon sequences from the bulk soils and rhizosphere in different ecosystems around the world to generalize bacterial characteristics with respect to community diversity, composition, and functions. The rhizosphere selects microorganisms from bulk soil to function as a seed bank, reducing microbial diversity. The rhizosphere is enriched in Bacteroidetes, Proteobacteria, and other copiotrophs. Highly modular but unstable bacterial networks in the rhizosphere (common for r-strategists) reflect the interactions and adaptations of microorganisms to dynamic conditions. Dormancy strategies in the rhizosphere are dominated by toxin-antitoxin systems, while sporulation is common in bulk soils. Functional predictions showed that genes involved in organic compound conversion, nitrogen fixation, and denitrification were strongly enriched in the rhizosphere (11-182%), while genes involved in nitrification were strongly depleted.}, }
@article {pmid35148097, year = {2022}, author = {Kundu, K and Melsbach, A and Heckel, B and Schneidemann, S and Kanapathi, D and Marozava, S and Merl-Pham, J and Elsner, M}, title = {Linking Increased Isotope Fractionation at Low Concentrations to Enzyme Activity Regulation: 4-Cl Phenol Degradation by Arthrobacter chlorophenolicus A6.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {5}, pages = {3021-3032}, pmid = {35148097}, issn = {1520-5851}, mesh = {*Arthrobacter ; *Atrazine ; Biodegradation, Environmental ; Carbon Isotopes/metabolism ; Chemical Fractionation ; Isotopes ; Micrococcaceae ; Phenol ; }, abstract = {Slow microbial degradation of organic trace chemicals ("micropollutants") has been attributed to either downregulation of enzymatic turnover or rate-limiting substrate supply at low concentrations. In previous biodegradation studies, a drastic decrease in isotope fractionation of atrazine revealed a transition from rate-limiting enzyme turnover to membrane permeation as a bottleneck when concentrations fell below the Monod constant of microbial growth. With degradation of the pollutant 4-chlorophenol (4-CP) by Arthrobacter chlorophenolicus A6, this study targeted a bacterium which adapts its enzyme activity to concentrations. Unlike with atrazine degradation, isotope fractionation of 4-CP increased at lower concentrations, from ε(C) = -1.0 ± 0.5‰ in chemostats (D = 0.090 h[-1], 88 mg L[-1]) and ε(C) = -2.1 ± 0.5‰ in batch (c0 = 220 mg L[-1]) to ε(C) = -4.1 ± 0.2‰ in chemostats at 90 μg L[-1]. Surprisingly, fatty acid composition indicated increased cell wall permeability at high concentrations, while proteomics revealed that catabolic enzymes (CphCI and CphCII) were differentially expressed at D = 0.090 h[-1]. These observations support regulation on the enzyme activity level─through either a metabolic shift between catabolic pathways or decreased enzymatic turnover at low concentrations─and, hence, reveal an alternative end-member scenario for bacterial adaptation at low concentrations. Including more degrader strains into this multidisciplinary analytical approach offers the perspective to build a knowledge base on bottlenecks of bioremediation at low concentrations that considers bacterial adaptation.}, }
@article {pmid35146791, year = {2022}, author = {Mozzachiodi, S and Bai, FY and Baldrian, P and Bell, G and Boundy-Mills, K and Buzzini, P and Čadež, N and Cubillos, FA and Dashko, S and Dimitrov, R and Fisher, KJ and Gibson, B and Gouliamova, D and Greig, D and Heistinger, L and Hittinger, CT and Jecmenica, M and Koufopanou, V and Landry, CR and Mašínová, T and Naumova, ES and Opulente, D and Peña, JJ and Petrovič, U and Tsai, IJ and Turchetti, B and Villarreal, P and Yurkov, A and Liti, G and Boynton, P}, title = {Yeasts from temperate forests.}, journal = {Yeast (Chichester, England)}, volume = {39}, number = {1-2}, pages = {4-24}, doi = {10.1002/yea.3699}, pmid = {35146791}, issn = {1097-0061}, mesh = {Biodiversity ; *Ecosystem ; Forests ; *Trees ; Yeasts/genetics ; }, abstract = {Yeasts are ubiquitous in temperate forests. While this broad habitat is well-defined, the yeasts inhabiting it and their life cycles, niches, and contributions to ecosystem functioning are less understood. Yeasts are present on nearly all sampled substrates in temperate forests worldwide. They associate with soils, macroorganisms, and other habitats and no doubt contribute to broader ecosystem-wide processes. Researchers have gathered information leading to hypotheses about yeasts' niches and their life cycles based on physiological observations in the laboratory as well as genomic analyses, but the challenge remains to test these hypotheses in the forests themselves. Here, we summarize the habitat and global patterns of yeast diversity, give some information on a handful of well-studied temperate forest yeast genera, discuss the various strategies to isolate forest yeasts, and explain temperate forest yeasts' contributions to biotechnology. We close with a summary of the many future directions and outstanding questions facing researchers in temperate forest yeast ecology. Yeasts present an exciting opportunity to better understand the hidden world of microbial ecology in this threatened and global habitat.}, }
@article {pmid35146390, year = {2022}, author = {Kodera, SM and Das, P and Gilbert, JA and Lutz, HL}, title = {Conceptual strategies for characterizing interactions in microbial communities.}, journal = {iScience}, volume = {25}, number = {2}, pages = {103775}, pmid = {35146390}, issn = {2589-0042}, abstract = {Understanding the sets of inter- and intraspecies interactions in microbial communities is a fundamental goal of microbial ecology. However, the study and quantification of microbial interactions pose several challenges owing to their complexity, dynamic nature, and the sheer number of unique interactions within a typical community. To overcome such challenges, microbial ecologists must rely on various approaches to distill the system of study to a functional and conceptualizable level, allowing for a practical understanding of microbial interactions in both simplified and complex systems. This review broadly addresses the role of several conceptual approaches available for the microbial ecologist's arsenal, examines specific tools used to accomplish such approaches, and describes how the assumptions, expectations, and philosophies underlying these tools change across scales of complexity.}, }
@article {pmid35145031, year = {2022}, author = {Karita, Y and Limmer, DT and Hallatschek, O}, title = {Scale-dependent tipping points of bacterial colonization resistance.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {7}, pages = {}, pmid = {35145031}, issn = {1091-6490}, support = {R01 GM115851/GM/NIGMS NIH HHS/United States ; S10 OD023532/OD/NIH HHS/United States ; }, mesh = {Acetobacter/drug effects/*physiology ; Anti-Bacterial Agents/pharmacology ; Bacteriological Techniques ; Drug Resistance, Bacterial ; *Lab-On-A-Chip Devices ; Tetracycline/pharmacology ; }, abstract = {Bacteria are efficient colonizers of a wide range of secluded microhabitats, such as soil pores, skin follicles, or intestinal crypts. How the structural diversity of these habitats modulates microbial self-organization remains poorly understood, in part because of the difficulty to precisely manipulate the physical structure of microbial environments. Using a microfluidic device to grow bacteria in crypt-like incubation chambers of systematically varied lengths, we show that small variations in the physical structure of the microhabitat can drastically alter bacterial colonization success and resistance against invaders. Small crypts are uncolonizable; intermediately sized crypts can stably support dilute populations, while beyond a second critical length scale, populations phase separate into a dilute region and a jammed region. The jammed state is characterized by extreme colonization resistance, even if the resident strain is suppressed by an antibiotic. Combined with a flexible biophysical model, we demonstrate that colonization resistance and associated priority effects can be explained by a crowding-induced phase transition, which results from a competition between proliferation and density-dependent cell leakage. The emerging sensitivity to scale underscores the need to control for scale in microbial ecology experiments. Systematic flow-adjustable length-scale variations may serve as a promising strategy to elucidate further scale-sensitive tipping points and to rationally modulate the stability and resilience of microbial colonizers.}, }
@article {pmid35145022, year = {2022}, author = {Lambert, BS and Groussman, RD and Schatz, MJ and Coesel, SN and Durham, BP and Alverson, AJ and White, AE and Armbrust, EV}, title = {The dynamic trophic architecture of open-ocean protist communities revealed through machine-guided metatranscriptomics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {7}, pages = {}, pmid = {35145022}, issn = {1091-6490}, mesh = {Eukaryota/genetics/*physiology ; *Food Chain ; Gene Expression Profiling ; *Machine Learning ; *Models, Biological ; Oceans and Seas ; Plankton/genetics/*physiology ; }, abstract = {Intricate networks of single-celled eukaryotes (protists) dominate carbon flow in the ocean. Their growth, demise, and interactions with other microorganisms drive the fluxes of biogeochemical elements through marine ecosystems. Mixotrophic protists are capable of both photosynthesis and ingestion of prey and are dominant components of open-ocean planktonic communities. Yet the role of mixotrophs in elemental cycling is obscured by their capacity to act as primary producers or heterotrophic consumers depending on factors that remain largely uncharacterized. Here, we develop and apply a machine learning model that predicts the in situ trophic mode of aquatic protists based on their patterns of gene expression. This approach leverages a public collection of protist transcriptomes as a training set to identify a subset of gene families whose transcriptional profiles predict trophic mode. We applied our model to nearly 100 metatranscriptomes obtained during two oceanographic cruises in the North Pacific and found community-level and population-specific evidence that abundant open-ocean mixotrophic populations shift their predominant mode of nutrient and carbon acquisition in response to natural gradients in nutrient supply and sea surface temperature. Metatranscriptomic data from ship-board incubation experiments revealed that abundant mixotrophic prymnesiophytes from the oligotrophic North Pacific subtropical gyre rapidly remodeled their transcriptome to enhance photosynthesis when supplied with limiting nutrients. Coupling this approach with experiments designed to reveal the mechanisms driving mixotroph physiology provides an avenue toward understanding the ecology of mixotrophy in the natural environment.}, }
@article {pmid35142544, year = {2022}, author = {Girolamini, L and Salaris, S and Orsini, M and Pascale, MR and Mazzotta, M and Grottola, A and Cristino, S}, title = {Draft Genome Sequence of Legionella Species Isolated from Drinking Water in an Italian Industry.}, journal = {Microbiology resource announcements}, volume = {11}, number = {2}, pages = {e0115221}, pmid = {35142544}, issn = {2576-098X}, abstract = {We report the draft genome sequences of an environmental Legionella strain isolated from an industrial water distribution system in Italy. Macrophage infectivity potentiator (mip) and β-subunit of RNA polymerase (rpoB) genes were used to perform the species identification. Whole-genome sequencing (WGS) and average nucleotide identity (ANI) identified the isolate as belonging to a presumptive novel Legionella species, with a genome length of 3,281,851 bp.}, }
@article {pmid35140699, year = {2021}, author = {Taketani, RG and Dini-Andreote, F and Beier, S and Fernandez, C}, title = {Editorial: Advancements in the Understanding of Anthropogenic Impacts on the Microbial Ecology and Function of Aquatic Environments.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {820697}, pmid = {35140699}, issn = {1664-302X}, }
@article {pmid35139898, year = {2022}, author = {Qu, J and Cai, Z and Duan, X and Zhang, H and Cheng, H and Han, S and Yu, K and Jiang, Z and Zhang, Y and Liu, Y and Bai, F and Liu, Y and Liu, L and Yang, L}, title = {Pseudomonas aeruginosa modulates alginate biosynthesis and type VI secretion system in two critically ill COVID-19 patients.}, journal = {Cell &amp; bioscience}, volume = {12}, number = {1}, pages = {14}, pmid = {35139898}, issn = {2045-3701}, support = {2020B1515020003//Guangdong Natural Science Foundation for Distinguished Young Scholar/ ; JCYJ20190809144005609//Science and Technology Program of Shenzhen/ ; 2020A1515010586//Guangdong Basic and Applied Basic Research Foundation/ ; 2020B1111170014//Guangdong Province Science and Technology Project/ ; ZDSYS20200811144002008//Shenzhen Innovation Committee of Science and Technology/ ; KQTD20200909113758004//Shenzhen Science and Technology Program/ ; }, abstract = {BACKGROUND: COVID-19 pneumonia has caused huge impact on the health of infected patients and associated with high morbidity and mortality. Shift in the lung microbial ecology upon such viral infection often worsens the disease and increases host susceptibility to superinfections. Bacterial superinfection contributes to the aggravation of COVID-19 and poses a great challenge to clinical treatments. An in-depth investigation on superinfecting bacteria in COVID-19 patients might facilitate understanding of lung microenvironment post virus infections and superinfection mechanism.<br><br>RESULTS: We analyzed the adaptation of two pairs of P. aeruginosa strains with the same MLST type isolated from two critical COVID-19 patients by combining sequencing analysis and phenotypic assays. Both P. aeruginosa strains were found to turn on alginate biosynthesis and attenuate type VI secretion system (T6SS) during short-term colonization in the COVID-19 patients, which results in excessive biofilm formation and virulence reduction-two distinct markers for chronic infections. The macrophage cytotoxicity test and intracellular reactive oxygen species measurement confirmed that the adapted P. aeruginosa strains reduced their virulence towards host cells and are better to escape from host immune clearance than their ancestors.<br><br>CONCLUSION: Our study suggests that SARS-CoV-2 infection can create a lung environment that allow rapid adaptive evolution of bacterial pathogens with genetic traits suitable for chronic infections.}, }
@article {pmid35138931, year = {2022}, author = {Bjorndahl, P and Bielawski, JP and Liu, L and Zhou, W and Gu, H}, title = {Novel Application of Survival Models for Predicting Microbial Community Transitions with Variable Selection for Environmental DNA.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {6}, pages = {e0214621}, pmid = {35138931}, issn = {1098-5336}, mesh = {*Cyanobacteria/genetics ; *DNA, Environmental ; Harmful Algal Bloom ; *Microbiota ; Seasons ; }, abstract = {Survival analysis is a prolific statistical tool in medicine for inferring risk and time to disease-related events. However, it is underutilized in microbiome research to predict microbial community-mediated events, partly due to the sparsity and high-dimensional nature of the data. We advance the application of Cox proportional hazards (Cox PH) survival models to environmental DNA (eDNA) data with feature selection suitable for filtering irrelevant and redundant taxonomic variables. Selection methods are compared in terms of false positives, sensitivity, and survival estimation accuracy in simulation and in a real data setting to forecast harmful cyanobacterial blooms. A novel extension of a method for selecting microbial biomarkers with survival data (SuRFCox) reliably outperforms other methods. We determine that Cox PH models with SuRFCox-selected predictors are more robust to varied signal, noise, and data correlation structure. SuRFCox also yields the most accurate and consistent prediction of blooms according to cross-validated testing by year over eight different bloom seasons. Identification of common biomarkers among validated survival forecasts over changing conditions has clear biological significance. Survival models with such biomarkers inform risk assessment and provide insight into the causes of critical community transitions. IMPORTANCE In this paper, we report on a novel approach of selecting microorganisms for model-based prediction of the time to critical microbially modulated events (e.g., harmful algal blooms, clinical outcomes, community shifts, etc.). Our novel method for identifying biomarkers from large, dynamic communities of microbes has broad utility to environmental and ecological impact risk assessment and public health. Results will also promote theoretical and practical advancements relevant to the biology of specific organisms. To address the unique challenge posed by diverse environmental conditions and sparse microbes, we developed a novel method of selecting predictors for modeling time-to-event data. Competing methods for selecting predictors are rigorously compared to determine which is the most accurate and generalizable. Model forecasts are applied to show suitable predictors can precisely quantify the risk over time of biological events like harmful cyanobacterial blooms.}, }
@article {pmid35138927, year = {2022}, author = {Perry, EK and Newman, DK}, title = {Prevalence and Correlates of Phenazine Resistance in Culturable Bacteria from a Dryland Wheat Field.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {6}, pages = {e0232021}, pmid = {35138927}, issn = {1098-5336}, support = {R01 AI127850/AI/NIAID NIH HHS/United States ; 1R01AI127850-01A1//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {Bacteria/metabolism ; *Phenazines/metabolism ; Prevalence ; *Triticum/microbiology ; }, abstract = {Phenazines are a class of bacterially produced redox-active natural antibiotics that have demonstrated potential as a sustainable alternative to traditional pesticides for the biocontrol of fungal crop diseases. However, the prevalence of bacterial resistance to agriculturally relevant phenazines is poorly understood, limiting both the understanding of how these molecules might shape rhizosphere bacterial communities and the ability to perform a risk assessment for off-target effects. Here, we describe profiles of susceptibility to the antifungal agent phenazine-1-carboxylic acid (PCA) across more than 100 bacterial strains isolated from a wheat field where PCA producers are indigenous and abundant. We found that Gram-positive bacteria are typically more sensitive to PCA than Gram-negative bacteria, and there was significant variability in susceptibility both within and across phyla. Phenazine-resistant strains were more likely to be isolated from the wheat rhizosphere, where PCA producers were also more abundant, compared to bulk soil. Furthermore, PCA toxicity was pH-dependent for most susceptible strains and broadly correlated with PCA reduction rates, suggesting that uptake and redox-cycling were important determinants of phenazine toxicity. Our results shed light on which classes of bacteria are most likely to be susceptible to phenazine toxicity in acidic or neutral soils. In addition, the taxonomic and phenotypic diversity of our strain collection represents a valuable resource for future studies on the role of natural antibiotics in shaping wheat rhizosphere communities. IMPORTANCE Microbial communities contribute to crop health in important ways. For example, phenazine metabolites are a class of redox-active molecules made by diverse soil bacteria that underpin the biocontrol of diseases of wheat and other crops. Their physiological functions are nuanced. In some contexts, they are toxic. In others, they are beneficial. While much is known about phenazine production and the effect of phenazines on producing strains, our ability to predict how phenazines might shape the composition of environmental microbial communities is poorly constrained. In addition, phenazine prevalence in the rhizosphere has been predicted to increase in arid soils as the climate changes, providing an impetus for further study. As a step toward gaining a predictive understanding of phenazine-linked microbial ecology, we document the effects of phenazines on diverse bacteria that were coisolated from a wheat rhizosphere and identify conditions and phenotypes that correlate with how a strain will respond to phenazines.}, }
@article {pmid35138381, year = {2022}, author = {Smakman, F and Hall, AR}, title = {Exposure to lysed bacteria can promote or inhibit growth of neighboring live bacteria depending on local abiotic conditions.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {2}, pages = {}, pmid = {35138381}, issn = {1574-6941}, mesh = {*Bacteria/genetics ; *Escherichia coli ; Nutrients ; }, abstract = {Microbial death is extremely common in nature, yet the ecological role of dead bacteria is unclear. Dead cells are assumed to provide nutrients to surrounding microbes, but may also affect them in other ways. We found that adding lysate prepared from dead bacteria to cultures of Escherichia coli in nutrient-rich conditions suppressed their final population density. This is in stark contrast with the notion that the primary role of dead cells is nutritional, although we also observed this type of effect when we added dead bacteria to cultures that were not supplied with other nutrients. We only observed the growth-suppressive effect of our dead-bacteria treatment after they had undergone significant lysis, suggesting a key role for cellular contents released during lysis. Transcriptomic analysis indicated changes in gene expression in response to dead cells in growing populations, particularly in genes involved in motility. This was supported by experiments with genetic knockouts and copy-number manipulation. Because lysis is commonplace in natural and clinical settings, the growth-suppressive effect of dead cells we describe here may be a widespread and previously unrecognized constraint on bacterial population growth.}, }
@article {pmid35137064, year = {2022}, author = {Šantl-Temkiv, T and Amato, P and Casamayor, EO and Lee, PKH and Pointing, SB}, title = {Microbial ecology of the atmosphere.}, journal = {FEMS microbiology reviews}, volume = {46}, number = {4}, pages = {}, pmid = {35137064}, issn = {1574-6976}, mesh = {*Atmosphere/chemistry ; Metagenomics ; *Microbiota ; }, abstract = {The atmosphere connects habitats across multiple spatial scales via airborne dispersal of microbial cells, propagules and biomolecules. Atmospheric microorganisms have been implicated in a variety of biochemical and biophysical transformations. Here, we review ecological aspects of airborne microorganisms with respect to their dispersal, activity and contribution to climatic processes. Latest studies utilizing metagenomic approaches demonstrate that airborne microbial communities exhibit pronounced biogeography, driven by a combination of biotic and abiotic factors. We quantify distributions and fluxes of microbial cells between surface habitats and the atmosphere and place special emphasis on long-range pathogen dispersal. Recent advances have established that these processes may be relevant for macroecological outcomes in terrestrial and marine habitats. We evaluate the potential biological transformation of atmospheric volatile organic compounds and other substrates by airborne microorganisms and discuss clouds as hotspots of microbial metabolic activity in the atmosphere. Furthermore, we emphasize the role of microorganisms as ice nucleating particles and their relevance for the water cycle via formation of clouds and precipitation. Finally, potential impacts of anthropogenic forcing on the natural atmospheric microbiota via emission of particulate matter, greenhouse gases and microorganisms are discussed.}, }
@article {pmid35137050, year = {2022}, author = {Kim, B and Westerhuis, JA and Smilde, AK and Floková, K and Suleiman, AKA and Kuramae, EE and Bouwmeester, HJ and Zancarini, A}, title = {Effect of strigolactones on recruitment of the rice root-associated microbiome.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {2}, pages = {}, pmid = {35137050}, issn = {1574-6941}, mesh = {Lactones/analysis/chemistry/pharmacology ; *Microbiota ; *Mycorrhizae ; *Oryza ; Plant Roots/chemistry ; Rhizosphere ; Symbiosis ; }, abstract = {Strigolactones are endogenous plant hormones regulating plant development and are exuded into the rhizosphere when plants experience nutrient deficiency. There, they promote the mutualistic association of plants with arbuscular mycorrhizal fungi that help the plant with the uptake of nutrients from the soil. This shows that plants actively establish-through the exudation of strigolactones-mutualistic interactions with microbes to overcome inadequate nutrition. The signaling function of strigolactones could possibly extend to other microbial partners, but the effect of strigolactones on the global root and rhizosphere microbiome remains poorly understood. Therefore, we analyzed the bacterial and fungal microbial communities of 16 rice genotypes differing in their root strigolactone exudation. Using multivariate analyses, distinctive differences in the microbiome composition were uncovered depending on strigolactone exudation. Moreover, the results of regression modeling showed that structural differences in the exuded strigolactones affected different sets of microbes. In particular, orobanchol was linked to the relative abundance of Burkholderia-Caballeronia-Paraburkholderia and Acidobacteria that potentially solubilize phosphate, while 4-deoxyorobanchol was associated with the genera Dyella and Umbelopsis. With this research, we provide new insight into the role of strigolactones in the interplay between plants and microbes in the rhizosphere.}, }
@article {pmid35135844, year = {2022}, author = {Sanz, Y and Olivares, M}, title = {Tiny contributors to severe obesity inside the gut.}, journal = {Gut}, volume = {71}, number = {12}, pages = {2376-2378}, pmid = {35135844}, issn = {1468-3288}, mesh = {Humans ; *Obesity, Morbid/complications ; Prebiotics ; Obesity/complications ; }, }
@article {pmid35134909, year = {2022}, author = {Foster-Nyarko, E and Pallen, MJ}, title = {The microbial ecology of Escherichia coli in the vertebrate gut.}, journal = {FEMS microbiology reviews}, volume = {46}, number = {3}, pages = {}, pmid = {35134909}, issn = {1574-6976}, mesh = {Animals ; Bacteria ; *Escherichia coli ; *Escherichia coli Infections/microbiology ; Symbiosis ; Vertebrates ; }, abstract = {Escherichia coli has a rich history as biology's 'rock star', driving advances across many fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a versatile pathogen commonly associated with intestinal and extraintestinal infections and antimicrobial resistance-including large foodborne outbreaks such as the one that swept across Europe in 2011, killing 54 individuals and causing approximately 4000 infections and 900 cases of haemolytic uraemic syndrome. Given that most E. coli are harmless gut colonizers, an important ecological question plaguing microbiologists is what makes E. coli an occasionally devastating pathogen? To address this question requires an enhanced understanding of the ecology of the organism as a commensal. Here, we review how our knowledge of the ecology and within-host diversity of this organism in the vertebrate gut has progressed in the 137 years since E. coli was first described. We also review current approaches to the study of within-host bacterial diversity. In closing, we discuss some of the outstanding questions yet to be addressed and prospects for future research.}, }
@article {pmid35134450, year = {2022}, author = {Weis, S and Jacksch, S and Welkerling, M and Schmidt, MS and Egert, M}, title = {Do it yourself! - Initial experiences with self-synthesized CsTFA for RNA-SIP analyses.}, journal = {Journal of microbiological methods}, volume = {194}, number = {}, pages = {106432}, doi = {10.1016/j.mimet.2022.106432}, pmid = {35134450}, issn = {1872-8359}, mesh = {Carbon Isotopes/chemistry ; Centrifugation, Density Gradient/methods ; Centrifugation, Isopycnic/methods ; Isotope Labeling/methods ; *Isotopes ; *RNA, Bacterial/genetics ; Trifluoroacetic Acid ; }, abstract = {Cesium trifluoroacetate (CsTFA) is a gradient medium for isopycnic centrifugation in RNA-based Stable Isotope Probing (RNA-SIP), an important means to link the structure and function of microbial communities. We report a protocol to easily synthesize CsTFA from cesium carbonate (Cs2CO3) and trifluoroacetic acid (TFA) and show that self-synthesized CsTFA performs similarly to commercial CsTFA in the separation of isotopically labelled and unlabelled bacterial RNA.}, }
@article {pmid35134272, year = {2022}, author = {Dar, MA and Xie, R and Pandit, RS and Danso, B and Dong, C and Sun, J}, title = {Exploring the region-wise diversity and functions of symbiotic bacteria in the gut system of wood-feeding termite, Coptotermes formosanus, toward the degradation of cellulose, hemicellulose, and organic dyes.}, journal = {Insect science}, volume = {29}, number = {5}, pages = {1414-1432}, doi = {10.1111/1744-7917.13012}, pmid = {35134272}, issn = {1744-7917}, mesh = {Animals ; Bacteria ; Cellulose/metabolism ; Coloring Agents/metabolism ; *Isoptera/microbiology ; Polysaccharides ; Symbiosis ; Wood/metabolism ; Xylans/metabolism ; }, abstract = {The wood-feeding termite Coptotermes formosanus represents a unique and impressive system for lignocellulose degradation. The highly efficient digestion of lignocellulose is achieved through symbiosis with gut symbionts like bacteria. Despite extensive research during the last three decades, diversity of bacterial symbionts residing in individual gut regions of the termite and their associated functions is still lacking. To this end, cellulose, xylan, and dye-decolorization bacteria residing in foregut, midgut, and hindgut regions of C. formosanus were enlisted by using enrichment and culture-dependent molecular methods. A total of 87 bacterial strains were successfully isolated from different gut regions of C. formosanus which belonged to 27 different species of 10 genera, majorly affiliated with Proteobacteria (80%) and Firmicutes (18.3%). Among the gut regions, 37.9% of the total bacterial isolates were observed in the hindgut that demonstrated predominance of cellulolytic bacteria (47.6%). The majority of the xylanolytic and dye-decolorization bacteria (50%) were obtained from the foregut and midgut, respectively. Actinobacteria represented by Dietza sp. was observed in the hindgut only. Based on species richness, the highest diversity was observed in midgut and hindgut regions each of which harbored seven unique bacterial species. The members of Enterobacter, Klebsiella, and Pseudomonas were common among the gut regions. The lignocellulolytic activities of the selected potential bacteria signpost their assistance to the host for lignocellulose digestion. The overall results indicate that C. formosanus harbors diverse communities of lignocellulolytic bacteria in different regions of the gut system. These observations will significantly advance our understanding of the termite-bacteria symbiosis and their microbial ecology uniquely existed in different gut regions of C. formosanus, which may further shed a light on its potential values at termite-modeled biotechnology.}, }
@article {pmid35133186, year = {2022}, author = {Pan, H and Gao, H and Peng, Z and Chen, B and Chen, S and Liu, Y and Gu, J and Wei, X and Chen, W and Wei, G and Jiao, S}, title = {Aridity Threshold Induces Abrupt Change of Soil Abundant and Rare Bacterial Biogeography in Dryland Ecosystems.}, journal = {mSystems}, volume = {7}, number = {1}, pages = {e0130921}, pmid = {35133186}, issn = {2379-5077}, mesh = {*Soil ; Phylogeny ; Soil Microbiology ; Bacteria ; *Microbiota ; }, abstract = {Aridity, which is increasing worldwide due to climate change, affects the biodiversity and functions of dryland ecosystems. Whether aridification leads to gradual (or abrupt) and systemic (or specific) changes in the biogeography of abundant and rare microbial species is largely unknown. Here, we investigated stress-adaptive changes (aridity-driven, ranging from 0.65 to 0.94) and biogeographic patterns of abundant and rare bacterial communities in different habitats, including agricultural field, forest, wetland, grassland, and desert, in desert oasis transition zones in northern China. We observed abrupt changes at the breakpoint of aridity values (0.92), characterized by diversity (α-diversity and β-diversity), species coexistence, community assembly processes, and phylogenetic niche conservatism. Specifically, when aridity was <0.92, increasing aridity led to more deterministic assembly and species coexistences for the abundant subcommunity, whereas the reverse was observed for the rare subcommunity. The phylogenetic niche conservatism for both subcommunities increased slowly with aridity. When aridity was >0.92, the systemic responses of abundant and rare taxa changed dramatically in a consistent direction, such that both subcommunities rapidly tended to have a more deterministic assembly, species coexistence, and stronger phylogenetic niche conservatism with increasing aridity. In addition, the change rates of abundant taxa were higher than those of rare taxa, indicating the more sensitive responses of abundant taxa along aridity variation. This finding has important implications for understanding the impact of aridity on the structure and function of abundant and rare soil taxa and how diversity maintenance is associated with soil microbiota responding to global change. The abrupt threshold of soil bacteria found can be used for buffering and for building effective adaptation and mitigation measures aimed at maintaining the capacity of drylands for basic ecosystem functioning. IMPORTANCE Aridity, which is increasing worldwide due to climate change, affects the biodiversity and functions of dryland ecosystems. We provided the first statistical evidence for abrupt changes of species coexistence, ecological processes, and niche conservation of abundant and rare soil bacteria triggered by diversity to abrupt increases in aridity. The abrupt threshold of soil bacterial community response to aridity is spatially heterogeneous at the local scale and should be specified according to local conditions for buffering and for building effective adaptation and mitigation measures aimed at maintaining the capacity of drylands for basic ecosystem functioning.}, }
@article {pmid35131944, year = {2022}, author = {Drautz-Moses, DI and Luhung, I and Gusareva, ES and Kee, C and Gaultier, NE and Premkrishnan, BNV and Lee, CF and Leong, ST and Park, C and Yap, ZH and Heinle, CE and Lau, KJX and Purbojati, RW and Lim, SBY and Lim, YH and Kutmutia, SK and Aung, NW and Oliveira, EL and Ng, SG and Dacanay, J and Ang, PN and Spence, S and Phung, WJ and Wong, A and Kennedy, RJ and Kalsi, N and Sasi, SP and Chandrasekaran, L and Uchida, A and Junqueira, ACM and Kim, HL and Hankers, R and Feuerle, T and Corsmeier, U and Schuster, SC}, title = {Vertical stratification of the air microbiome in the lower troposphere.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {7}, pages = {}, pmid = {35131944}, issn = {1091-6490}, mesh = {Aerosols ; *Air Microbiology ; Altitude ; Atmosphere ; Bacteria/*classification/*isolation &amp; purification ; Humans ; }, abstract = {The troposphere constitutes the final frontier of global ecosystem research due to technical challenges arising from its size, low biomass, and gaseous state. Using a vertical testing array comprising a meteorological tower and a research aircraft, we conducted synchronized measurements of meteorological parameters and airborne biomass (n = 480) in the vertical air column up to 3,500 m. The taxonomic analysis of metagenomic data revealed differing patterns of airborne microbial community composition with respect to time of day and height above ground. The temporal and spatial resolution of our study demonstrated that the diel cycle of airborne microorganisms is a ground-based phenomenon that is entirely absent at heights >1,000 m. In an integrated analysis combining meteorological and biological data, we demonstrate that atmospheric turbulence, identified by potential temperature and high-frequency three-component wind measurements, is the key driver of bioaerosol dynamics in the lower troposphere. Multivariate regression analysis shows that at least 50% of identified airborne microbial taxa (n = ∼10,000) are associated with either ground or height, allowing for an understanding of dispersal patterns of microbial taxa in the vertical air column. Due to the interconnectedness of atmospheric turbulence and temperature, the dynamics of microbial dispersal are likely to be impacted by rising global temperatures, thereby also affecting ecosystems on the planetary surface.}, }
@article {pmid35131464, year = {2022}, author = {Blansaer, N and Alloul, A and Verstraete, W and Vlaeminck, SE and Smets, BF}, title = {Aggregation of purple bacteria in an upflow photobioreactor to facilitate solid/liquid separation: Impact of organic loading rate, hydraulic retention time and water composition.}, journal = {Bioresource technology}, volume = {348}, number = {}, pages = {126806}, doi = {10.1016/j.biortech.2022.126806}, pmid = {35131464}, issn = {1873-2976}, mesh = {Biological Oxygen Demand Analysis ; Bioreactors ; *Photobioreactors/microbiology ; *Proteobacteria ; Sewage/chemistry ; Waste Disposal, Fluid/methods ; Wastewater/chemistry ; Water ; }, abstract = {Purple non-sulfur bacteria (PNSB) form an interesting group of microbes for resource recovery from wastewater. Solid/liquid separation is key for biomass and value-added products recovery, yet insights into PNSB aggregation are thus far limited. This study explored the effects of organic loading rate (OLR), hydraulic retention time (HRT) and water composition on the aggregation of Rhodobacter capsulatus in an anaerobic upflow photobioreactor. Between 2.0 and 14.6 gCOD/(L.d), the optimal OLR for aggregation was 6.1 gCOD/(L.d), resulting in a sedimentation flux of 5.9 kgTSS/(m[2].h). With HRT tested between 0.04 and 1.00 d, disaggregation occurred at the relatively long HRT (1 d), possibly due to accumulation of thus far unidentified heat-labile metabolites. Chemical oxygen demand (COD) to nitrogen ratios (6-35 gCOD/gN) and the nitrogen source (ammonium vs. glutamate) also impacted aggregation, highlighting the importance of the type of wastewater and its pre-treatment. These novel insights to improve purple biomass separation pave the way for cost-efficient PNSB applications.}, }
@article {pmid35130833, year = {2022}, author = {Baruzzo, G and Patuzzi, I and Di Camillo, B}, title = {Beware to ignore the rare: how imputing zero-values can improve the quality of 16S rRNA gene studies results.}, journal = {BMC bioinformatics}, volume = {22}, number = {Suppl 15}, pages = {618}, pmid = {35130833}, issn = {1471-2105}, support = {PROACTIVE 2017 - C92F17003530005//Department of Information Engineering, University of Padova/ ; }, mesh = {*Bacteria/genetics ; *Data Analysis ; Genes, rRNA ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: 16S rRNA-gene sequencing is a valuable approach to characterize the taxonomic content of the whole bacterial population inhabiting a metabolic and spatial niche, providing an important opportunity to study bacteria and their role in many health and environmental mechanisms. The analysis of data produced by amplicon sequencing, however, brings very specific methodological issues that need to be properly addressed to obtain reliable biological conclusions. Among these, 16S count data tend to be very sparse, with many null values reflecting species that are present but got unobserved due to the multiplexing constraints. However, current data workflows do not consider a step in which the information about unobserved species is recovered.<br><br>RESULTS: In this work, we evaluate for the first time the effects of introducing in the 16S data workflow a new preprocessing step, zero-imputation, to recover this lost information. Due to the lack of published zero-imputation methods specifically designed for 16S count data, we considered a set of zero-imputation strategies available for other frameworks, and benchmarked them using in silico 16S count data reflecting different experimental designs. Additionally, we assessed the effect of combining zero-imputation and normalization, i.e. the only preprocessing step in current 16S workflow. Overall, we benchmarked 35 16S preprocessing pipelines assessing their ability to handle data sparsity, identify species presence/absence, recovery sample proportional abundance distributions, and improve typical downstream analyses such as computation of alpha and beta diversity indices and differential abundance analysis.<br><br>CONCLUSIONS: The results clearly show that 16S data analysis greatly benefits from a properly-performed zero-imputation step, despite the choice of the right zero-imputation method having a pivotal role. In addition, we identify a set of best-performing pipelines that could be a valuable indication for data analysts.}, }
@article {pmid35130830, year = {2022}, author = {Dreier, M and Meola, M and Berthoud, H and Shani, N and Wechsler, D and Junier, P}, title = {High-throughput qPCR and 16S rRNA gene amplicon sequencing as complementary methods for the investigation of the cheese microbiota.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {48}, pmid = {35130830}, issn = {1471-2180}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Cheese/*microbiology ; Computational Biology ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/*methods ; High-Throughput Screening Assays/methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; Real-Time Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Next-generation sequencing (NGS) methods and especially 16S rRNA gene amplicon sequencing have become indispensable tools in microbial ecology. While they have opened up new possibilities for studying microbial communities, they also have one drawback, namely providing only relative abundances and thus compositional data. Quantitative PCR (qPCR) has been used for years for the quantification of bacteria. However, this method requires the development of specific primers and has a low throughput. The constraint of low throughput has recently been overcome by the development of high-throughput qPCR (HT-qPCR), which allows for the simultaneous detection of the most prevalent bacteria in moderately complex systems, such as cheese and other fermented dairy foods. In the present study, the performance of the two approaches, NGS and HT-qPCR, was compared by analyzing the same DNA samples from 21 Raclette du Valais protected designation of origin (PDO) cheeses. Based on the results obtained, the differences, accuracy, and usefulness of the two approaches were studied in detail.<br><br>RESULTS: The results obtained using NGS (non-targeted) and HT-qPCR (targeted) show considerable agreement in determining the microbial composition of the cheese DNA samples studied, albeit the fundamentally different nature of these two approaches. A few inconsistencies in species detection were observed, particularly for less abundant ones. The detailed comparison of the results for 15 bacterial species/groups measured by both methods revealed a considerable bias for certain bacterial species in the measurements of the amplicon sequencing approach. We identified as probable origin to this PCR bias due to primer mismatches, variations in the number of copies for the 16S rRNA gene, and bias introduced in the bioinformatics analysis.<br><br>CONCLUSION: As the normalized microbial composition results of NGS and HT-qPCR agreed for most of the 21 cheese samples analyzed, both methods can be considered as complementary and reliable for studying the microbial composition of cheese. Their combined application proved to be very helpful in identifying potential biases and overcoming methodological limitations in the quantitative analysis of the cheese microbiota.}, }
@article {pmid35129649, year = {2023}, author = {Doane, MP and Johnson, CJ and Johri, S and Kerr, EN and Morris, MM and Desantiago, R and Turnlund, AC and Goodman, A and Mora, M and Lima, LFO and Nosal, AP and Dinsdale, EA}, title = {The Epidermal Microbiome Within an Aggregation of Leopard Sharks (Triakis semifasciata) Has Taxonomic Flexibility with Gene Functional Stability Across Three Time-points.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {747-764}, pmid = {35129649}, issn = {1432-184X}, support = {1330800//National Science Foundation/ ; 1323809//National Science Foundation/ ; }, mesh = {Animals ; *Sharks ; Epidermis ; *Microbiota ; }, abstract = {The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein-rich mucus that collectively, influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbiome of the Triakis semifasciata (leopard shark) at three time-points collected across 4 years to identify links between microbial groups and host metabolism. Our aims include (1) describing the variation of microbiome taxa over time and identifying recurrent microbiome members (present across all time-points); (2) investigating the relationship between the recurrent and flexible taxa (those which are not found consistently across time-points); (3) describing the functional compositions of the microbiome which may suggest links with the host metabolism; and (4) identifying whether metabolic processes are shared across microbial genera or are unique to specific taxa. Microbial members of the microbiome showed high similarity between all individuals (Bray-Curtis similarity index = 82.7, where 0 = no overlap, 100 = total overlap) with the relative abundance of those members varying across sampling time-points, suggesting flexibility of taxa in the microbiome. One hundred and eighty-eight genera were identified as recurrent, including Pseudomonas, Erythrobacter, Alcanivorax, Marinobacter, and Sphingopxis being consistently abundant across time-points, while Limnobacter and Xyella exhibited switching patterns with high relative abundance in 2013, Sphingobium and Sphingomona in 2015, and Altermonas, Leeuwenhoekiella, Gramella, and Maribacter in 2017. Of the 188 genera identified as recurrent, the top 19 relatively abundant genera formed three recurrent groups. The microbiome also displayed high functional similarity between individuals (Bray-Curtis similarity index = 97.6) with gene function composition remaining consistent across all time-points. These results show that while the presence of microbial genera exhibits consistency across time-points, their abundances do fluctuate. Microbial functions however remain stable across time-points; thus, we suggest the leopard shark microbiomes exhibit functional redundancy. We show coexistence of microbes hosted in elasmobranch microbiomes that encode genes involved in utilizing nitrogen, but not fixing nitrogen, degrading urea, and resistant to heavy metal.}, }
@article {pmid35128002, year = {2022}, author = {Costa, DPD and Araujo, ASF and Pereira, APA and Mendes, LW and França, RFD and Silva, TDGED and Oliveira, JB and Araujo, JS and Duda, GP and Menezes, RSC and Medeiros, EV}, title = {Dataset for effects of the transition from dry forest to pasture on diversity and structure of bacterial communities in Northeastern Brazil.}, journal = {Data in brief}, volume = {41}, number = {}, pages = {107842}, pmid = {35128002}, issn = {2352-3409}, abstract = {The data included in this article supplement the research article titled "Forest-to-pasture conversion modifies the soil bacterial community in Brazilian dry forest Caatinga (manuscript ID: STOTEN-D-21-19067R1)". This data article included the analysis of 18 chemical variables in 36 composite samples (included 4 replicates) of soils from the Microregion of Garanhuns (Northeast Brazil) and also partial 16S rRNA gene sequences from genomic DNA extracted from 27 of these samples (included 3 best quality replicates) for paired-end sequencing (up to 2 × 300 bp) in Illumina MiSeq platform (NCBI - BioProject accession: PRJNA753707). Soils were collected in August 2018 in a tropical subhumid region from the Brazilian Caatinga, along with 27 composite samples from the aboveground part of pastures to determine nutritional quality based on leaf N content. The analysis of variance (ANOVA) and post-hoc tests of environmental data and the main alpha-diversity indices based on linear mixed models (LMM) were represented in the tables. In this case, the collection region (C1 - Brejão, C2 - Garanhuns, and C3 - São João) was the random-effect variable and adjacent habitats formed by a forest (FO) and two pastures (PA and PB succeeded by this forest) composed the fixed-effect variable (land cover), both nested within C. In addition, a table with similarity percentages breakdown (SIMPER) was also shown, a procedure to assess the average percent contribution of individual phyla and bacterial classes. The figures showed the details of the study location, sampling procedure, vegetation status through the Normalized Difference Vegetation Index (NDVI), in addition to the general abundance and composition of the main bacterial phyla.}, }
@article {pmid35126404, year = {2021}, author = {Li, H and Wang, N and Ding, J and Liu, Y and Ding, X and Wei, Y and Li, J and Ding, GC}, title = {Spatial Distribution of the Pepper Blight (Phytophthora capsici) Suppressive Microbiome in the Rhizosphere.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {748542}, pmid = {35126404}, issn = {1664-462X}, abstract = {The properties of plant rhizosphere are dynamic and heterogeneous, serving as different habitat filters for or against certain microorganisms. Herein, we studied the spatial distribution of bacterial communities in the rhizosphere of pepper plants treated with a disease-suppressive or non-suppressive soil. The bacterial richness was significantly (p < 0.05) higher in plants treated with the disease-suppressive soil than in those treated with the non-suppressive soil. Bacterial richness and evenness greatly differed between root parts, with decrease from the upper taproot to the upper fibrous root, the lower taproot, and the lower fibrous root. As expected, the bacterial community in the rhizosphere differed between suppressive and non-suppressive soil. However, the spatial variation (36%) of the bacterial community in the rhizosphere was much greater than that explained by soils (10%). Taxa such as subgroups of Acidobacteria, Nitrosospira, and Nitrospira were known to be selectively enriched in the upper taproot. In vitro Bacillus antagonists against Phytophthora capsici were also preferentially colonized in the taproot, while the genera such as Clostridium, Rhizobium, Azotobacter, Hydrogenophaga, and Magnetospirillum were enriched in the lower taproot or fibrous root. In conclusion, the spatial distribution of bacterial taxa and antagonists in the rhizosphere of pepper sheds light on our understanding of microbial ecology in the rhizosphere.}, }
@article {pmid35125827, year = {2022}, author = {Hillestad, EMR and van der Meeren, A and Nagaraja, BH and Bjørsvik, BR and Haleem, N and Benitez-Paez, A and Sanz, Y and Hausken, T and Lied, GA and Lundervold, A and Berentsen, B}, title = {Gut bless you: The microbiota-gut-brain axis in irritable bowel syndrome.}, journal = {World journal of gastroenterology}, volume = {28}, number = {4}, pages = {412-431}, pmid = {35125827}, issn = {2219-2840}, mesh = {Brain-Gut Axis ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Humans ; *Irritable Bowel Syndrome/therapy ; *Microbiota ; }, abstract = {Irritable bowel syndrome (IBS) is a common clinical label for medically unexplained gastrointestinal symptoms, recently described as a disturbance of the microbiota-gut-brain axis. Despite decades of research, the pathophysiology of this highly heterogeneous disorder remains elusive. However, a dramatic change in the understanding of the underlying pathophysiological mechanisms surfaced when the importance of gut microbiota protruded the scientific picture. Are we getting any closer to understanding IBS' etiology, or are we drowning in unspecific, conflicting data because we possess limited tools to unravel the cluster of secrets our gut microbiota is concealing? In this comprehensive review we are discussing some of the major important features of IBS and their interaction with gut microbiota, clinical microbiota-altering treatment such as the low FODMAP diet and fecal microbiota transplantation, neuroimaging and methods in microbiota analyses, and current and future challenges with big data analysis in IBS.}, }
@article {pmid35124727, year = {2023}, author = {Tanunchai, B and Ji, L and Schroeter, SA and Wahdan, SFM and Hossen, S and Delelegn, Y and Buscot, F and Lehnert, AS and Alves, EG and Hilke, I and Gleixner, G and Schulze, ED and Noll, M and Purahong, W}, title = {FungalTraits vs. FUNGuild: Comparison of Ecological Functional Assignments of Leaf- and Needle-Associated Fungi Across 12 Temperate Tree Species.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {411-428}, pmid = {35124727}, issn = {1432-184X}, mesh = {*Trees/microbiology ; Fungi ; *Mycobiome ; Plant Leaves/microbiology ; }, abstract = {Recently, a new annotation tool "FungalTraits" was created based on the previous FUNGuild and Fun[Fun] databases, which has attracted high attention in the scientific community. These databases were widely used to gain more information from fungal sequencing datasets by assigning fungal functional traits. More than 1500 publications so far employed FUNGuild and the aim of this study is to compare this successful database with the recent FungalTraits database. Quality and quantity of the assignment by FUNGuild and FungalTraits to a fungal internal transcribed spacer (ITS)-based amplicon sequencing dataset on amplicon sequence variants (ASVs) were addressed. Sequencing dataset was derived from leaves and needles of 12 temperate broadleaved and coniferous tree species. We found that FungalTraits assigned more functional traits than FUNGuild, and especially the coverage of saprotrophs, plant pathogens, and endophytes was higher while lichenized fungi revealed similar findings. Moreover, ASVs derived from leaves and needles of each tree species were better assigned to all available fungal traits as well as to saprotrophs by FungalTraits compared to FUNGuild in particular for broadleaved tree species. Assigned ASV richness as well as fungal functional community composition was higher and more diverse after analyses with FungalTraits compared to FUNGuild. Moreover, datasets of both databases showed similar effect of environmental factors for saprotrophs but for endophytes, unidentical patterns of significant corresponding factors were obtained. As a conclusion, FungalTraits is superior to FUNGuild in assigning a higher quantity and quality of ASVs as well as a higher frequency of significant correlations with environmental factors.}, }
@article {pmid35118509, year = {2023}, author = {Zhou, J and Kong, Y and Wu, M and Shu, F and Wang, H and Ma, S and Li, Y and Jeppesen, E}, title = {Effects of Nitrogen Input on Community Structure of the Denitrifying Bacteria with Nitrous Oxide Reductase Gene (nosZ I): a Long-Term Pond Experiment.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {454-464}, pmid = {35118509}, issn = {1432-184X}, mesh = {*Ponds ; *Ecosystem ; Nitrogen ; Denitrification ; Bacteria/genetics ; Nitrous Oxide ; Soil Microbiology ; }, abstract = {Excessive nitrogen (N) input is an important factor influencing aquatic ecosystems and has received increasing public attention in the past decades. It remains unclear how N input affects the denitrifying bacterial communities that play a key role in regulating N cycles in various ecosystems. To test our hypothesis-that the abundance and biodiversity of denitrifying bacterial communities decrease with increasing N-we compared the abundance and composition of denitrifying bacteria having nitrous oxide reductase gene (nosZ I) from sediments (0-20 cm) in five experimental ponds with different nitrogen fertilization treatment (TN10, TN20, TN30, TN40, TN50) using quantitative PCR and pyrosequencing techniques. We found that (1) N addition significantly decreased nosZ I gene abundance, (2) the Invsimpson and Shannon indices (reflecting biodiversity) first increased significantly along with the increasing N loading in TN10-TN40 followed by a decrease in TN50, (3) the beta diversity of the nosZ I denitrifier was clustered into three groups along the TN concentration levels: Cluster I (TN50), Cluster II (TN40), and Cluster III (TN10-TN30), (4) the proportions of Alphaproteobacteria and Betaproteobacteria in the high-N treatment (TN50) were significantly lower than in the lower N treatments (TN10-TN30). (5) The TN concentration was the most important factor driving the alteration of denitrifying bacteria assemblages. Our findings shed new light on the response of denitrification-related bacteria to long-term N loading at pond scale and on the response of denitrifying microorganisms to N pollution.}, }
@article {pmid35114951, year = {2022}, author = {Bi, S and Lai, H and Guo, D and Liu, X and Wang, G and Chen, X and Liu, S and Yi, H and Su, Y and Li, G}, title = {Spatio-temporal variation of bacterioplankton community structure in the Pearl River: impacts of artificial fishery habitat and physicochemical factors.}, journal = {BMC ecology and evolution}, volume = {22}, number = {1}, pages = {10}, pmid = {35114951}, issn = {2730-7182}, mesh = {Aquatic Organisms ; *Cyanobacteria/genetics ; Ecosystem ; Fisheries ; Follow-Up Studies ; RNA, Ribosomal, 16S/genetics ; *Rivers/chemistry ; Water ; }, abstract = {BACKGROUND: Artificial fishery habitat has been widely used in fishery resource protection and water habitat restoration. Although the bacterioplankton plays an important ecological role in fisheries ecosystems, the effect of artificial fishery habitat on bacterioplankton is not clear. In this study, high-throughput sequencing based on the 16S rRNA gene was carried out to study the characteristics of bacterioplankton community structure in artificial fishery habitat and to determine the principal environmental factors that shaped the composition, structure and function of bacterioplankton communities in an unfed aquaculture system.<br><br>RESULTS: The results indicated that the most dominant phyla were Proteobacteria (Alphaproteobacteria and Gammaproteobacteria), Actinobacteria, Cyanobacteria, and Bacteroidetes, which accounted for 28.61%, 28.37%, 19.79%, and 10.25% of the total abundance, respectively. The factors that cause the differences in bacterioplankton community were mainly manifested in three aspects, including the diversity of the community, the role of artificial fishery habitat, and the change of environmental factors. The alpha diversity analysis showed that the diversity and richness index of the bacterioplankton communities were the highest in summer, which indicated that the seasonal variation characteristics had a great influence on it. The CCA analysis identified that the dissolved oxygen, temperature, and ammonium salt were the dominant environmental factors in an unfed aquaculture system. The LEfSe analysis founded 37 indicator species in artificial structure areas (AS group), only 9 kinds existing in the control areas of the open-water group (CW group). Meanwhile, the KEGG function prediction analysis showed that the genes which were related to metabolism in group AS were significantly enhanced.<br><br>CONCLUSIONS: This study can provide reference value for the effect of artificial habitat on bacterioplankton community and provide fundamental information for the follow-up study of ecological benefits of artificial fishery habitat. It may be contributed to apply artificial fishery habitat in more rivers.}, }
@article {pmid35114015, year = {2022}, author = {Angulo, V and Beriot, N and Garcia-Hernandez, E and Li, E and Masteling, R and Lau, JA}, title = {Plant-microbe eco-evolutionary dynamics in a changing world.}, journal = {The New phytologist}, volume = {234}, number = {6}, pages = {1919-1928}, doi = {10.1111/nph.18015}, pmid = {35114015}, issn = {1469-8137}, mesh = {*Biological Evolution ; *Microbiota ; Plants ; }, abstract = {Both plants and their associated microbiomes can respond strongly to anthropogenic environmental changes. These responses can be both ecological (e.g. a global change affecting plant demography or microbial community composition) and evolutionary (e.g. a global change altering natural selection on plant or microbial populations). As a result, global changes can catalyse eco-evolutionary feedbacks. Here, we take a plant-focused perspective to discuss how microbes mediate plant ecological responses to global change and how these ecological effects can influence plant evolutionary response to global change. We argue that the strong and functionally important relationships between plants and their associated microbes are particularly likely to result in eco-evolutionary feedbacks when perturbed by global changes and discuss how improved understanding of plant-microbe eco-evolutionary dynamics could inform conservation or even agriculture.}, }
@article {pmid35113183, year = {2023}, author = {Dong, X and Lan, H and Huang, L and Zhang, H and Lin, X and Weng, S and Peng, Y and Lin, J and Wang, JH and Peng, J and Yang, Y}, title = {Metagenomic Views of Microbial Communities in Sand Sediments Associated with Coral Reefs.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {465-477}, pmid = {35113183}, issn = {1432-184X}, mesh = {Animals ; Coral Reefs ; Ecosystem ; Sand ; Metagenomics ; Bacteria/genetics ; *Microbiota ; Proteobacteria ; *Anthozoa/microbiology ; }, abstract = {Reef sediments, the home for microbes with high abundances, provide an important source of carbonates and nutrients for the growth and maintenance of coral reefs. However, there is a lack of systematic research on the composition of microbial community in sediments of different geographic sites and their potential effect on nutrient recycling and health of the coral reef ecosystem. In combination of biogeochemical measurements with gene- and genome-centric metagenomics, we assessed microbial community compositions and functional diversity, as well as profiles of antibiotic resistance genes in surface sediments of 16 coral reef sites at different depths from the Xisha islands in the South China Sea. Reef sediment microbiomes are diverse and novel at lower taxonomic ranks, dominated by Proteobacteria and Planctomycetota. Most reef sediment bacteria potentially participate in biogeochemical cycling via oxidizing various organic and inorganic compounds as energy sources. High abundances of Proteobacteria (mostly Rhizobiales and Woeseiales) are metabolically flexible and contain rhodopsin genes. Various classes of antibiotic resistance genes, hosted by diverse bacterial lineages, were identified to confer resistance to multidrug, aminoglycoside, and other antibiotics. Overall, our findings expanded the understanding of reef sediment microbial ecology and provided insights for their link to the coral reef ecosystem health.}, }
@article {pmid35112152, year = {2023}, author = {LeBlanc, N}, title = {Green Manures Alter Taxonomic and Functional Characteristics of Soil Bacterial Communities.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {684-697}, pmid = {35112152}, issn = {1432-184X}, support = {2038-22000-016-000-D//USDA-ARS/ ; 2038-22430-003-000-D//USDA-ARS/ ; }, mesh = {*Soil ; Manure ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria ; Plants ; Soil Microbiology ; }, abstract = {Incorporation of plant biomass into soil as green manures can reduce soilborne diseases and improve crop and soil health in agricultural ecosystems. Soil microbial communities can mediate beneficial effects of these amendments, but their response to different types of green manures is poorly understood. This study tested the effect of green manures from broccoli, marigold, and sudangrass on taxonomic and functional characteristics of soil bacterial communities. Green manures were amended to field soil and maintained in microcosms artificially infested with the soilborne plant pathogen Verticillium dahliae. Lettuce seedlings were transplanted into green manure amended and fallow soil and maintained under growth chamber conditions for 12 weeks. Bacterial communities in bulk and rhizosphere soils were characterized using nanopore sequencing of 16S rRNA and shotgun metagenome libraries. Under microcosm conditions, all green manures reduced the abundance of the soilborne plant pathogen V. dahliae and altered the taxonomic composition of bacterial communities. Twelve weeks following amendment, green manures had differential effects on lettuce yield as well as the taxonomic diversity and composition of soil bacterial communities. In addition, multiple green manures increased the abundance of bacterial functional traits in rhizosphere soil related to iron and polysaccharide acquisition and decreased the abundance of functional traits related to bacterial protein secretion systems. This study demonstrates green manures alter the taxonomic composition and functional traits in soil bacterial communities suggesting these changes may impact beneficial effects of green manures on plant and soil health.}, }
@article {pmid35112151, year = {2023}, author = {Mishra, A and Singh, L and Singh, D}, title = {Unboxing the black box-one step forward to understand the soil microbiome: A systematic review.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {669-683}, pmid = {35112151}, issn = {1432-184X}, mesh = {*Ecosystem ; Soil/chemistry ; Soil Microbiology ; Biodiversity ; *Microbiota ; Climate Change ; }, abstract = {Soil is one of the most important assets of the planet Earth, responsible for maintaining the biodiversity and managing the ecosystem services for both managed and natural ecosystems. It encompasses large proportion of microscopic biodiversity, including prokaryotes and the microscopic eukaryotes. Soil microbiome is critical in managing the soil functions, but their activities have diminutive recognition in few systems like desert land and forest ecosystems. Soil microbiome is highly dependent on abiotic and biotic factors like pH, carbon content, soil structure, texture, and vegetation, but it can notably vary with ecosystems and the respective inhabitants. Thus, unboxing this black box is essential to comprehend the basic components adding to the soil systems and supported ecosystem services. Recent advancements in the field of molecular microbial ecology have delivered commanding tools to examine this genetic trove of soil biodiversity. Objective of this review is to provide a critical evaluation of the work on the soil microbiome, especially since the advent of the NGS techniques. The review also focuses on advances in our understanding of soil communities, their interactions, and functional capabilities along with understanding their role in maneuvering the biogeochemical cycle while underlining and tapping the unprecedented metagenomics data to infer the ecological attributes of yet undiscovered soil microbiome. This review focuses key research directions that could shape the future of basic and applied research into the soil microbiome. This review has led us to understand that it is difficult to generalize that soil microbiome plays a substantiated role in shaping the soil networks and it is indeed a vital resource for sustaining the ecosystem functioning. Exploring soil microbiome will help in unlocking their roles in various soil network. It could be resourceful in exploring and forecasting its impacts on soil systems and for dealing with alleviating problems like rapid climate change.}, }
@article {pmid35108090, year = {2022}, author = {Choi, O and Cho, J and Kang, B and Lee, Y and Kim, J}, title = {Negatively Regulated Aerobactin and Desferrioxamine E by Fur in Pantoea ananatis Are Required for Full Siderophore Production and Antibacterial Activity, but Not for Virulence.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {6}, pages = {e0240521}, pmid = {35108090}, issn = {1098-5336}, mesh = {Anti-Bacterial Agents/metabolism/pharmacology ; Humans ; Hydroxamic Acids ; Lactams ; *Pantoea/genetics/metabolism ; *Siderophores/metabolism ; Virulence ; }, abstract = {Pantoea ananatis is an emerging plant pathogen that causes disease in economically important crops such as rice, corn, onion, melon, and pineapple, and it also infects humans and insects. In this study, we identified biosynthetic gene clusters of aerobactin and desferrioxamine E (DFO-E) siderophores by using the complete genome of P. ananatis PA13 isolated from rice sheath rot. P. ananatis PA13 exhibited the strongest antibacterial activity against Erwinia amylovora and Yersinia enterocolitica (Enterobacterales). Mutants of aerobactin or DFO-E maintained antibacterial activity against E. amylovora and Y. enterocolitica, as well as in a siderophore activity assay. However, double aerobactin and DFO-E gene deletion mutants completely lost siderophore and antibacterial activity. These results reveal that both siderophore biosynthetic gene clusters are essential for siderophore production and antibacterial activity in P. ananatis PA13. A ferric uptake regulator protein (Fur) mutant exhibited a significant increase in siderophore production, and a Fur-overexpressing strain completely lost antibacterial activity. Expression of the iucA, dfoJ, and foxA genes was significantly increased in the Δfur mutant background, and expression of these genes returned to wild-type levels after fur compensation. These results indicate that Fur negatively regulates aerobactin and DFO-E siderophores. However, siderophore production was not required for P. ananatis virulence in plants, but it appears to be involved in the microbial ecology surrounding the plant environment. This study is the first to report the regulation and functional characteristics of siderophore biosynthetic genes in P. ananatis. IMPORTANCE Pantoea ananatis is a bacterium that causes diseases in several economically important crops, as well as in insects and humans. This bacterium has been studied extensively as a potentially dangerous pathogen due to its saprophytic ability. Recently, the types, biosynthetic gene clusters, and origin of the siderophores in the Pantoea genus were determined by using genome comparative analyses. However, few genetic studies have investigated the characteristics and functions of siderophores in P. ananatis. The results of this study revealed that the production of aerobactin and desferrioxamine E in the rice pathogen P. ananatis PA13 is negatively regulated by Fur and that these siderophores are essential for antibacterial activity against Erwinia amylovora and Yersinia enterocolitica (Enterobacterales). However, siderophore production was not required for P. ananatis virulence in plants, but it appears to be involved in the microbial ecology surrounding the plant environment.}, }
@article {pmid35107341, year = {2022}, author = {Sovacool, KL and Westcott, SL and Mumphrey, MB and Dotson, GA and Schloss, PD}, title = {OptiFit: an Improved Method for Fitting Amplicon Sequences to Existing OTUs.}, journal = {mSphere}, volume = {7}, number = {1}, pages = {e0091621}, pmid = {35107341}, issn = {2379-5042}, support = {R01 CA215574/CA/NCI NIH HHS/United States ; T32 HG000040/HG/NHGRI NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; T32 GM070449/GM/NIGMS NIH HHS/United States ; T32 CA140044/CA/NCI NIH HHS/United States ; }, mesh = {Cluster Analysis ; *Metagenomics/methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Assigning amplicon sequences to operational taxonomic units (OTUs) is an important step in characterizing microbial communities across large data sets. A notable difference between de novo clustering and database-dependent reference clustering methods is that OTU assignments from de novo methods may change when new sequences are added. However, one may wish to incorporate new samples to previously clustered data sets without clustering all sequences again, such as when comparing across data sets or deploying machine learning models. Existing reference-based methods produce consistent OTUs but only consider the similarity of each query sequence to a single reference sequence in an OTU, resulting in assignments that are worse than those generated by de novo methods. To provide an efficient method to fit sequences to existing OTUs, we developed the OptiFit algorithm. Inspired by the de novo OptiClust algorithm, OptiFit considers the similarity of all pairs of reference and query sequences to produce OTUs of the best possible quality. We tested OptiFit using four data sets with two strategies: (i) clustering to a reference database and (ii) splitting the data set into a reference and query set, clustering the references using OptiClust, and then clustering the queries to the references. The result is an improved implementation of reference-based clustering. OptiFit produces OTUs of a quality similar to that of OptiClust at faster speeds when using the split data set strategy. OptiFit provides a suitable option for users requiring consistent OTU assignments at the same quality as afforded by de novo clustering methods. IMPORTANCE Advancements in DNA sequencing technology have allowed researchers to affordably generate millions of sequence reads from microorganisms in diverse environments. Efficient and robust software tools are needed to assign microbial sequences into taxonomic groups for characterization and comparison of communities. The OptiClust algorithm produces high-quality groups by comparing sequences to each other, but the assignments can change when new sequences are added to a data set, making it difficult to compare different studies. Other approaches assign sequences to groups by comparing them to sequences in a reference database to produce consistent assignments, but the quality of the groups produced is reduced compared to that with OptiClust. We developed OptiFit, a new reference-based algorithm that produces consistent yet high-quality assignments like OptiClust. OptiFit allows researchers to compare microbial communities across different studies or add new data to existing studies without sacrificing the quality of the group assignments.}, }
@article {pmid35107340, year = {2022}, author = {Baumann, KBL and Thoma, R and Callbeck, CM and Niederdorfer, R and Schubert, CJ and Müller, B and Lever, MA and Bürgmann, H}, title = {Microbial Nitrogen Transformation Potential in Sediments of Two Contrasting Lakes Is Spatially Structured but Seasonally Stable.}, journal = {mSphere}, volume = {7}, number = {1}, pages = {e0101321}, pmid = {35107340}, issn = {2379-5042}, mesh = {Eutrophication ; *Lakes/microbiology ; *Microbiota ; Nitrates/analysis ; Nitrogen ; }, abstract = {The nitrogen (N) cycle is of global importance, as N is an essential element and a limiting nutrient in terrestrial and aquatic ecosystems. Excessive anthropogenic N fertilizer usage threatens sensitive downstream aquatic ecosystems. Although freshwater lake sediments remove N through various microbially mediated processes, few studies have investigated the microbial communities involved. In an integrated biogeochemical and microbiological study on a eutrophic and oligotrophic lake, we estimated N removal rates from pore water concentration gradients in sediments. Simultaneously, the abundance of different microbial N transformation genes was investigated using metagenomics on a seasonal and spatial scale. We observed that contrasting nutrient concentrations in sediments were associated with distinct microbial community compositions and significant differences in abundances of various N transformation genes. For both characteristics, we observed a more pronounced spatial than seasonal variability within each lake. The eutrophic Lake Baldegg showed a higher denitrification potential with higher nosZ gene (N2O reductase) abundances and higher nirS:nirK (nitrite reductase) ratios, indicating a greater capacity for complete denitrification. Correspondingly, this lake had a higher N removal efficiency. The oligotrophic Lake Sarnen, in contrast, had a higher potential for nitrification. Specifically, it harbored a high abundance of Nitrospira, including some with the potential for comammox. Our results demonstrate that knowledge of the genomic N transformation potential is important for interpreting N process rates and understanding how the lacustrine sedimentary N cycle responds to variations in trophic conditions. IMPORTANCE Anthropogenic nitrogen (N) inputs can lead to eutrophication in surface waters, especially in N-limited coastal ecosystems. Lakes effectively remove reactive N by transforming it to N2 through microbial denitrification or anammox. The rates and distributions of these microbial processes are affected by factors such as the amount and quality of settling organic material and nitrate concentrations. However, the microbial communities mediating these N transformation processes in freshwater lake sediments remain largely unknown. We provide the first seasonally and spatially resolved metagenomic analysis of the N cycle in sediments of two lakes with different trophic states. We show that lakes with different trophic states select for distinct communities of N-cycling microorganisms with contrasting functional potentials for N transformation.}, }
@article {pmid35106901, year = {2022}, author = {Herms, CH and Hennessy, RC and Bak, F and Dresbøll, DB and Nicolaisen, MH}, title = {Back to our roots: exploring the role of root morphology as a mediator of beneficial plant-microbe interactions.}, journal = {Environmental microbiology}, volume = {24}, number = {8}, pages = {3264-3272}, pmid = {35106901}, issn = {1462-2920}, mesh = {*Microbiota ; Plant Roots/microbiology ; Plants/microbiology ; Rhizosphere ; *Soil Microbiology ; }, abstract = {Plant breeding for belowground traits that have a positive impact on the rhizosphere microbiome is a promising strategy to sustainably improve crop yields. Root architecture and morphology are understudied plant breeding targets despite their potential to significantly shape microbial community structure and function in the rhizosphere. In this review, we explore the relationship between various root architectural and morphological traits and rhizosphere interactions, focusing on the potential of root diameter to impact the rhizosphere microbiome structure and function while discussing the potential biological and ecological mechanisms underpinning this process. In addition, we propose three future research avenues to drive this research area in an effort to unravel the effect of belowground traits on rhizosphere microbiology. This knowledge will pave the way for new plant breeding strategies that can be exploited for sustainable and high-yielding crop cultivars.}, }
@article {pmid35106579, year = {2022}, author = {Weinroth, MD and Belk, AD and Dean, C and Noyes, N and Dittoe, DK and Rothrock, MJ and Ricke, SC and Myer, PR and Henniger, MT and Ramírez, GA and Oakley, BB and Summers, KL and Miles, AM and Ault-Seay, TB and Yu, Z and Metcalf, JL and Wells, JE}, title = {Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies.}, journal = {Journal of animal science}, volume = {100}, number = {2}, pages = {}, pmid = {35106579}, issn = {1525-3163}, mesh = {Animals ; Genes, rRNA ; High-Throughput Nucleotide Sequencing/veterinary ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/veterinary ; }, abstract = {Microbiome studies in animal science using 16S rRNA gene sequencing have become increasingly common in recent years as sequencing costs continue to fall and bioinformatic tools become more powerful and user-friendly. The combination of molecular biology, microbiology, microbial ecology, computer science, and bioinformatics-in addition to the traditional considerations when conducting an animal science study-makes microbiome studies sometimes intimidating due to the intersection of different fields. The objective of this review is to serve as a jumping-off point for those animal scientists less familiar with 16S rRNA gene sequencing and analyses and to bring up common issues and concerns that arise when planning an animal microbiome study from design through analysis. This review includes an overview of 16S rRNA gene sequencing, its advantages, and its limitations; experimental design considerations such as study design, sample size, sample pooling, and sample locations; wet lab considerations such as field handing, microbial cell lysis, low biomass samples, library preparation, and sequencing controls; and computational considerations such as identification of contamination, accounting for uneven sequencing depth, constructing diversity metrics, assigning taxonomy, differential abundance testing, and, finally, data availability. In addition to general considerations, we highlight some special considerations by species and sample type.}, }
@article {pmid35106548, year = {2022}, author = {Nerva, L and Garcia, JF and Favaretto, F and Giudice, G and Moffa, L and Sandrini, M and Cantu, D and Zanzotto, A and Gardiman, M and Velasco, R and Gambino, G and Chitarra, W}, title = {The hidden world within plants: metatranscriptomics unveils the complexity of wood microbiomes.}, journal = {Journal of experimental botany}, volume = {73}, number = {8}, pages = {2682-2697}, doi = {10.1093/jxb/erac032}, pmid = {35106548}, issn = {1460-2431}, support = {C94E19000770008//Italian Ministry for Agriculture and Forestry/ ; }, mesh = {Bacteria/genetics ; *Endophytes ; *Microbiota ; Plants ; Wood ; }, abstract = {The importance of plants as complex entities influenced by genomes of the associated microorganisms is now seen as a new source of variability for a more sustainable agriculture, also in the light of ongoing climate change. For this reason, we investigated through metatranscriptomics whether the taxa profile and behaviour of microbial communities associated with the wood of 20-year-old grapevine plants are influenced by the health status of the host. We report for the first time a metatranscriptome from a complex tissue in a real environment, highlighting that this approach is able to define the microbial community better than referenced transcriptomic approaches. In parallel, the use of total RNA enabled the identification of bacterial taxa in healthy samples that, once isolated from the original wood tissue, displayed potential biocontrol activities against a wood-degrading fungal taxon. Furthermore, we revealed an unprecedented high number of new viral entities (~120 new viral species among 180 identified) associated with a single and limited environment and with potential impact on the whole holobiont. Taken together, our results suggest a complex multitrophic interaction in which the viral community also plays a crucial role in raising new ecological questions for the exploitation of microbial-assisted sustainable agriculture.}, }
@article {pmid35102425, year = {2023}, author = {McBride, SG and Osburn, ED and Lucas, JM and Simpson, JS and Brown, T and Barrett, JE and Strickland, MS}, title = {Volatile and Dissolved Organic Carbon Sources Have Distinct Effects on Microbial Activity, Nitrogen Content, and Bacterial Communities in Soil.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {659-668}, pmid = {35102425}, issn = {1432-184X}, support = {1023307//National Institute of Food and Agriculture/ ; 1556753//Directorate for Biological Sciences/ ; }, mesh = {*Soil/chemistry ; Dissolved Organic Matter ; Nitrogen/analysis ; Carbon ; Soil Microbiology ; Bacteria ; Proteobacteria ; *Microbiota ; Water ; }, abstract = {Variation in microbial use of soil carbon compounds is a major driver of biogeochemical processes and microbial community composition. Available carbon substrates in soil include both low molecular weight-dissolved organic carbon (LMW-DOC) and volatile organic compounds (VOCs). To compare the effects of LMW-DOC and VOCs on soil chemistry and microbial communities under different moisture regimes, we performed a microcosm experiment with five levels of soil water content (ranging from 25 to 70% water-holding capacity) and five levels of carbon amendment: a no carbon control, two dissolved compounds (glucose and oxalate), and two volatile compounds (methanol and α-pinene). Microbial activity was measured throughout as soil respiration; at the end of the experiment, we measured extractable soil organic carbon and total extractable nitrogen and characterized prokaryotic communities using amplicon sequencing. All C amendments increased microbial activity, and all except oxalate decreased total extractable nitrogen. Likewise, individual phyla responded to specific C amendments-e.g., Proteobacteria increased under addition of glucose, and both VOCs. Further, we observed an interaction between moisture and C amendment, where both VOC treatments had higher microbial activity than LMW-DOC treatments and controls at low moisture. Across moisture and C treatments, we identified that Chloroflexi, Nitrospirae, Proteobacteria, and Verrucomicrobia were strong predictors of microbial activity, while Actinobacteria, Bacteroidetes, and Thaumarcheota strongly predicted soil extractable nitrogen. These results indicate that the type of labile C source available to soil prokaryotes can influence both microbial diversity and ecosystem function and that VOCs may drive microbial functions and composition under low moisture conditions.}, }
@article {pmid35102262, year = {2022}, author = {Bretzke, K and Preusser, F and Jasim, S and Miller, C and Preston, G and Raith, K and Underdown, SJ and Parton, A and Parker, AG}, title = {Multiple phases of human occupation in Southeast Arabia between 210,000 and 120,000 years ago.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {1600}, pmid = {35102262}, issn = {2045-2322}, abstract = {Changing climatic conditions are thought to be a major control of human presence in Arabia during the Paleolithic. Whilst the Pleistocene archaeological record shows that periods of increased monsoon rainfall attracted human occupation and led to increased population densities, the impact of arid conditions on human populations in Arabia remains largely speculative. Here, we present data from Jebel Faya in Southeast (SE) Arabia, which document four periods of human occupation between c. 210,000 and 120,000 years ago. The Jebel Faya record indicates that human occupation of SE Arabia was more regular and not exclusively linked to major humid periods. Our data show that brief phases of increased rainfall additionally enabled human settlement in the Faya region. These results imply that the mosaic environments in SE Arabia have likely formed a population refugia at the end of the Middle and the beginning of the Late Pleistocene.}, }
@article {pmid35098423, year = {2022}, author = {Ben Rejeb, I and Khemir, H and Messaoudi, Y and Miled, N and Gargouri, M}, title = {Optimization of Enzymatic Degreasing of Sheep Leather for an Efficient Approach and Leather Quality Improvement Using Fractional Experimental Design.}, journal = {Applied biochemistry and biotechnology}, volume = {194}, number = {5}, pages = {2251-2268}, pmid = {35098423}, issn = {1559-0291}, mesh = {Animals ; Hydrolysis ; Lipase ; *Quality Improvement ; *Research Design ; Sheep ; Skin/chemistry ; }, abstract = {Leather industry is making significant contributions to economic development. However, it is notably leading to a serious environmental pollution. Recently, the enzyme technology developments offer new opportunities for enzymatic application in leather making. In the present investigation, microbial lipases were studied and used in degreasing process of sheep leathers. In order to optimize degreasing efficiency, a fractional experimental design with four parameters (enzyme source, processing stage, lipase amount, and degreasing duration) was used. Lipases A from Aspergillus niger, F from Rhizopus oryzae, R from Penicillium roqueforti, and AY from Candida rugosa were selected for leather degreasing. Enzymatic treatment of sheep skin was carried out during two stages of beamhouse operations: deliming-bating and pickling. Obtained results showed that enzymatic degreasing efficiency is higher than those obtained with the conventional process. Lipase F from Rhizopus oryzae demonstrated the most interesting hydrolysis with yields of 58.3% and 37.2% for delimed and pickled skins, respectively. An enzymatic degreasing process on pickled leather using 0.125% (w/v) of lipase F during 3.5 h is the most promising for an industrial application with a 76.03 of degreasing efficiency. Results of the physico-mechanical tests of leathers having undergone enzymatic treatment complied with industry requirement. The enzymatic treatment may be carried out in the same conditions as employed in leather manufacturing process. Results suggested that the enzymatic degreasing improves the leather quality and reduces the use of chemical compounds and surfactant.}, }
@article {pmid35098330, year = {2023}, author = {Shen, LD and Geng, CY and Ren, BJ and Jin, JH and Huang, HC and Liu, X and Yang, WT and Yang, YL and Liu, JQ and Tian, MH}, title = {Detection and Quantification of Candidatus Methanoperedens-Like Archaea in Freshwater Wetland Soils.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {441-453}, pmid = {35098330}, issn = {1432-184X}, support = {41977037//National Natural Science Foundation of China/ ; BK20190092//Natural Science Foundation of Jiangsu Province/ ; }, mesh = {*Archaea/genetics ; *Wetlands ; Nitrates ; Soil ; Phylogeny ; Oxidation-Reduction ; Fresh Water ; Methane ; Water ; Iron ; Anaerobiosis ; }, abstract = {Candidatus Methanoperedens-like archaea, which can use multiple electron acceptors (nitrate, iron, manganese, and sulfate) for anaerobic methane oxidation, could play an important role in reducing methane emissions from freshwater wetlands. Currently, very little is known about the distribution and community composition of Methanoperedens-like archaea in freshwater wetlands, particularly based on their alpha subunit of methyl-coenzyme M reductase (mcrA) genes. Here, the community composition, diversity, and abundance of Methanoperedens-like archaea were investigated in a freshwater wetland through high-throughput sequencing and quantitative PCR on their mcrA genes. A large number of Methanoperedens-like mcrA gene sequences (119,250) were recovered, and a total of 31 operational taxonomic units (OTUs) were generated based on 95% sequence similarity cut-off. The majority of Methanoperedens-like sequences can be grouped into three distinct clusters that were closely associated with the known Methanoperedens species which can couple anaerobic methane oxidation to nitrate or iron reduction. The community composition of Methanoperedens-like archaea differed significantly among different sampling sites, and their mcrA gene abundance was 1.49 × 10[6] ~ 4.62 × 10[6] copies g[-1] dry soil in the examined wetland. In addition, the community composition of Methanoperedens-like archaea was significantly affected by the soil water content, and the archaeal abundance was significantly positively correlated with the water content. Our results suggest that the mcrA gene is a good biomarker for detection and quantification of Methanoperedens-like archaea, and provide new insights into the distribution and environmental regulation of these archaea in freshwater wetlands.}, }
@article {pmid35095807, year = {2021}, author = {Anagnostopoulos, DA and Tsaltas, D}, title = {Current Status, Recent Advances, and Main Challenges on Table Olive Fermentation: The Present Meets the Future.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {797295}, pmid = {35095807}, issn = {1664-302X}, abstract = {Table olives are among the most well-known fermented foods, being a vital part of the Mediterranean pyramid diet. They constitute a noteworthy economic factor for the producing countries since both their production and consumption are exponentially increasing year by year, worldwide. Despite its significance, olive's processing is still craft based, not changed since antiquity, leading to the production of an unstable final product with potential risk concerns, especially related to deterioration. However, based on industrial needs and market demands for reproducible, safe, and healthy products, the modernization of olive fermentation processing is the most important challenge of the current decade. In this sense, the reduction of sodium content and more importantly the use of suitable starter cultures, exhibiting both technological and potential probiotic features, to drive the process may extremely contribute to this need. Prior, to achieve in this effort, the full understanding of table olive microbial ecology during fermentation, including an in-depth determination of microbiota presence and/or dominance and its functionality (genes responsible for metabolite production) that shape the sensorial characteristics of the final product, is a pre-requisite. The advent of meta-omics technology could provide a thorough study of this complex ecosystem, opening in parallel new insights in the field, such as the concept of microbial terroir. Herein, we provide an updated overview in the field of olive fermentation, pointing out some important challenges/perspectives that could be the key to the olive sector's advancement and modernization.}, }
@article {pmid35094098, year = {2023}, author = {Song, H and Lee, K and Hwang, I and Yang, E and Ha, J and Kim, W and Park, S and Cho, H and Choe, JC and Lee, SI and Jablonski, P}, title = {Dynamics of Bacterial Communities on Eggshells and on Nest Materials During Incubation in the Oriental Tit (Parus minor).}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {429-440}, pmid = {35094098}, issn = {1432-184X}, support = {3344-20180017//National Research Foundation of Korea/ ; 2-2019-1273-001-3//National Research Foundation of Korea/ ; 2021010026//Daegu Gyeongbuk Institute of Science and Technology/ ; 5253-20180100//the BK21 Korea/ ; 21A20131212006//the BK21 Korea/ ; }, mesh = {Animals ; *Egg Shell/microbiology ; Phylogeny ; *Bacteria ; Birds/microbiology ; Skin ; }, abstract = {Eggshell bacterial communities may affect hatching success and nestling's condition. Nest materials are in direct contact with the eggshells, but the relationships with the eggshell microbiome during incubation have not been fully elucidated. Here, we characterize eggshell and nest material bacterial communities and their changes during incubation in the Oriental Tit (Parus minor). Bacterial communities on the nest material were relatively stable and remained distinct from the eggshell communities and had higher diversity and greater phylogenetic clustering than the eggshell communities from the same nest, resulting in lower phylogenetic turnover rate of nest material microbiome during incubation than expected by chance. While the species diversity of both communities did not change during incubation, we found significantly greater changes in the structure of bacterial communities on the eggshell than on the nest material. However, eggshell microbiome remained distinct from nest material microbiome, suggesting independent dynamics of the two microbiomes during incubation. We detected an increase in the relative abundance of several bacterial taxa on the eggshell that likely come from the bird's skin, feathers, cloaca/intestine, or uropygial secretion which suggests some exchange of bacteria between the incubating bird and the eggshell. Furthermore, incubation appeared to promote the abundance of antibiotic producing taxa on the eggshell, which may hypothetically inhibit growth of many bacteria including pathogenic ones. Our results suggest that the future studies should focus on simultaneous monitoring of absolute abundance as well as relative abundance in communities on eggshells, nest materials, and the incubating bird's body.}, }
@article {pmid35094062, year = {2022}, author = {Berg, JS and Ahmerkamp, S and Pjevac, P and Hausmann, B and Milucka, J and Kuypers, MMM}, title = {How low can they go? Aerobic respiration by microorganisms under apparent anoxia.}, journal = {FEMS microbiology reviews}, volume = {46}, number = {3}, pages = {}, pmid = {35094062}, issn = {1574-6976}, mesh = {*Ecosystem ; Humans ; Hypoxia ; *Oxygen/metabolism ; Respiration ; }, abstract = {Oxygen (O2) is the ultimate oxidant on Earth and its respiration confers such an energetic advantage that microorganisms have evolved the capacity to scavenge O2 down to nanomolar concentrations. The respiration of O2 at extremely low levels is proving to be common to diverse microbial taxa, including organisms formerly considered strict anaerobes. Motivated by recent advances in O2 sensing and DNA/RNA sequencing technologies, we performed a systematic review of environmental metatranscriptomes revealing that microbial respiration of O2 at nanomolar concentrations is ubiquitous and drives microbial activity in seemingly anoxic aquatic habitats. These habitats were key to the early evolution of life and are projected to become more prevalent in the near future due to anthropogenic-driven environmental change. Here, we summarize our current understanding of aerobic microbial respiration under apparent anoxia, including novel processes, their underlying biochemical pathways, the involved microorganisms, and their environmental importance and evolutionary origin.}, }
@article {pmid35093783, year = {2022}, author = {Zhong, X and Yu, S and Xu, H and Kim, S}, title = {Can tidal events influence analysis on colonization dynamics in body-size spectrum of periphytic ciliates for marine bioassessment?.}, journal = {Marine pollution bulletin}, volume = {175}, number = {}, pages = {113342}, doi = {10.1016/j.marpolbul.2022.113342}, pmid = {35093783}, issn = {1879-3363}, mesh = {Body Size ; *Ciliophora ; Cluster Analysis ; *Ecosystem ; Environmental Monitoring/methods ; }, abstract = {The tidal influence on body-size spectrum of the protozoan periphytons was explored by using the conventional slide system (CS) and the polyurethane foam enveloped slide system (PFES) in coastal waters during a 1-month study. During the colonization process, clear temporal patterns of the body-size spectrum were observed using the two sampling methods. In terms of relative species number and frequency of occurrence, the rank S4 represented a more stable temporal variability in the PFES system than the CS system during the colonization. Additionally, the small forms (e.g., S1, S2, and S3) were more abundant in the PFES system. The clustering and bootstrapped average analyses demonstrated differences in body-size spectrum of protozoans between the two sampling systems. Our results imply that the body-size spectrum of protozoan periphytons may be impacted by tidal events during colonization process in marine waters.}, }
@article {pmid35092770, year = {2022}, author = {Baril, X and Durand, AA and Srei, N and Lamothe, S and Provost, C and Martineau, C and Dunfield, K and Constant, P}, title = {The biological sink of atmospheric H2 is more sensitive to spatial variation of microbial diversity than N2O and CO2 emissions in a winter cover crop field trial.}, journal = {The Science of the total environment}, volume = {821}, number = {}, pages = {153420}, doi = {10.1016/j.scitotenv.2022.153420}, pmid = {35092770}, issn = {1879-1026}, mesh = {*Carbon Dioxide/analysis ; *Microbiota ; Nitrous Oxide/analysis ; RNA, Ribosomal, 16S ; Seasons ; Soil ; }, abstract = {The integration of winter cover crop (WCC) in culture rotations promotes multiple ecosystem services, but concomitant microbial diversity and functioning responses in soil have received less attention. A field trial was established to test the hypothesis that enhanced crop diversity with the integration of WCC in a conventional maize-soy rotation promotes microbial diversity and the biological sink of H2 in soil, while reducing N2O emissions to the atmosphere. Vicia villosa (hairy vetch), Avena sativa (oat), and Raphanus sativus (Daikon radish) were cultivated alone or in combinations and flux measurements were performed throughout two subsequent growing seasons. Soil acted as a net sink for H2 and as a net source for CO2 and N2O. CO2 flux was the most sensitive to WCC whereas a significant spatial variation was observed for H2 flux with soil uptake rates observed in the most productive area two-fold greater than the baseline level. Sequencing and quantification of taxonomic and functional genes were integrated to explain variation in trace gas fluxes with compositional changes in soil microbial communities. Fungal communities were the most sensitive to WCC, but neither community abundance nor beta diversity were found to be indicative of fluxes. The alpha diversity of taxonomic and functional genes, expressed as the number of effective species, was integrated into composite variables extracted from multivariate analyses. Only the composite variable computed with the inverse Simpson's index displayed a reproducible pattern throughout both growing seasons, with functional genes and bacterial 16S rRNA gene defining the two most contrasting gradients. The composite variable was decoupled from WCC treatment and explained 19-20% spatial variation of H2 fluxes. The coupling of composite alpha diversity metrics derived from multiple genes with soil processes warrants further investigations to implement novel indicators of soil health in response to changing management practices at the local scale.}, }
@article {pmid35091250, year = {2022}, author = {Sharma, N and Kumari, R and Thakur, M and Rai, AK and Singh, SP}, title = {Molecular dissemination of emerging antibiotic, biocide, and metal co-resistomes in the Himalayan hot springs.}, journal = {Journal of environmental management}, volume = {307}, number = {}, pages = {114569}, doi = {10.1016/j.jenvman.2022.114569}, pmid = {35091250}, issn = {1095-8630}, mesh = {Anti-Bacterial Agents ; *Disinfectants ; *Hot Springs ; Humans ; Metagenomics ; *Metals, Heavy ; }, abstract = {Growing resistance among microbial communities against antimicrobial compounds, especially antibiotics, is a significant threat to living beings. With increasing antibiotic resistance in human pathogens, it is necessary to examine the habitats having community interests. In the present study, a metagenomic approach has been employed to understand the causes, dissemination, and effects of antibiotic, metal, and biocide resistomes on the microbial ecology of three hot springs, Borong, Lingdem, and Yumthang, located at different altitudes of the Sikkim Himalaya. The taxonomic assessment of these hot springs depicted the predominance of mesophilic organisms, mainly belonging to the phylum Proteobacteria. The enriched microbial metabolism assosiated with energy, cellular processes, adaptation to diverse environments, and defence were deciphered in the metagenomes. The genes representing resistance to semisynthetic antibiotics, e.g., aminoglycosides, fluoroquinolones, fosfomycin, vancomycin, trimethoprim, tetracycline, streptomycin, beta-lactams, multidrug resistance, and biocides such as triclosan, hydrogen peroxide, acriflavin, were abundantly present. Various genes attributing resistance to copper, arsenic, iron, and mercury in metal resistome were detected. Relative abundance, correlation, and genome mapping of metagenome-assembled genomes indicated the co-evolution of antibiotic and metal resistance in predicted novel species belonging to Vogesella, Thiobacillus, and Tepidimona genera. The metagenomic findings were further validated with isolation of microbial cultures, exhibiting resistance against antibiotics and heavy metals, from the hot spring water samples. The study furthers our understanding about the molecular basis of co-resistomes in the ceological niches and their possible impact on the environment.}, }
@article {pmid35090934, year = {2022}, author = {Amaral, RR and Braga, T and Siqueira, JF and Rôças, IN and da Costa Rachid, CTC and Oliveira, AGG and de Souza Côrtes, MI and Love, RM}, title = {Root Canal Microbiome Associated With Asymptomatic Apical Periodontitis as Determined by High-Throughput Sequencing.}, journal = {Journal of endodontics}, volume = {48}, number = {4}, pages = {487-495}, doi = {10.1016/j.joen.2022.01.012}, pmid = {35090934}, issn = {1878-3554}, mesh = {Dental Pulp Cavity/microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota/genetics ; *Periapical Periodontitis/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {INTRODUCTION: Advanced DNA sequencing technology allows more detailed analysis and description of the endodontic microbiome. This study used the MiSeq high-throughput sequencing platform (Illumina, San Diego, CA) to describe the endodontic microbiome of teeth with primary asymptomatic apical periodontitis with no sinus tract.<br><br>METHODS: Root canal samples from 25 patients were prepared for DNA sequencing analysis. Bacterial diversity of the microbiome was identified and compared between cases and according to the size of the related apical periodontitis lesions. Statistical analyses of the operational taxonomic unit distribution was performed using principal component analysis with the Bray-Curtis distance and a principal coordinate analysis, 2-way permutational multivariate analysis of variance. The chi-square or Fisher exact test was used to evaluate the prevalence of different operational taxonomic units related to small and large apical periodontitis lesions.<br><br>RESULTS: Although there was a very high bacterial diversity in the microbiome of teeth with asymptomatic apical periodontitis, 4 phyla dominated the microbiome: Firmicutes (27%), Bacteroidetes (21%), Proteobacteria (21%), and Actinobacteria (12%). There was high variability in species composition between root canal samples with no common species pattern for the cases. Large lesions showed a higher number of species but did not significantly differ from small lesions in bacterial diversity indexes. Bacteroidaceae [G-1] bacterium HMT 272, a previously uncultivated but still unnamed and uncharacterized taxon, was the most prevalent and abundant phylotype.<br><br>CONCLUSIONS: High-throughput sequencing technology confirmed the complexity of the endodontic microbiome and revealed that microbial heterogeneity is a feature between cases. This indicates that various microbial combinations of the endodontic microbiome are able to illicit periapical inflammatory diseases.}, }
@article {pmid35089393, year = {2023}, author = {Deng, J and Zhou, W and Dai, L and Yuan, Q and Zhou, L and Qi, L and Yu, D}, title = {The Effects of Shrub Removal on Soil Microbial Communities in Primary Forest, Secondary Forest and Plantation Forest on Changbai Mountain.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {642-658}, pmid = {35089393}, issn = {1432-184X}, mesh = {*Soil ; Forests ; Betula ; *Microbiota ; Bacteria ; China ; }, abstract = {Shrub removal is a common management method in forest ecosystems, but comparatively little is known regarding the effects of shrub removal on soil microbial communities among primary forest, secondary forest, and plantation forests in temperate forests, which limits our accurate assessment of sustainable management of understory vegetation removal. Given this, we used a long-term operation experiment across a contrasting mixed broadleaved-Pinus koraiensis forest, Betula platyphylla forest, and Larix gmelinii plantation forest to explore the variations of soil properties and microbial community after 5 years of shrub removal on Changbai Mountain, as well as the contribution of the soil properties and understory plant diversity to the soil microbial community. The results demonstrated that shrub removal could significantly alter soil SWC and TN, TP, and AP contents of the L. gmelinii, as well as N/P of B. platyphylla. Moreover, shrub removal also clearly improved soil bacterial Pielou_e index and Simpson index of mixed broadleaved-P. koraiensis and soil bacterial Simpson index of L. gmelinii, and decreased soil fungal Pielou_e index and Shannon index of L. gmelinii and soil bacterial Pielou_e index and soil fungal Shannon index of B. platyphylla. Identically, shrub removal notably altered the soil bacterial community composition. Soil characteristics and understory plant diversity accounted for 48.02% and 26.88%, and 45.88% and 27.57% of the variance in the bacterial and fungal community composition, respectively. This study aimed to provide an important scientific basis for the restoration and sustainable management of temperate forests in the Changbai Mountain region.}, }
@article {pmid35085485, year = {2022}, author = {Gowda, K and Ping, D and Mani, M and Kuehn, S}, title = {Genomic structure predicts metabolite dynamics in microbial communities.}, journal = {Cell}, volume = {185}, number = {3}, pages = {530-546.e25}, doi = {10.1016/j.cell.2021.12.036}, pmid = {35085485}, issn = {1097-4172}, mesh = {Biomass ; Denitrification ; Genome ; *Genomics ; *Metabolomics ; Microbiota/*genetics ; Models, Biological ; Nitrates/metabolism ; Nitrites/metabolism ; Phenotype ; Regression Analysis ; Reproducibility of Results ; }, abstract = {The metabolic activities of microbial communities play a defining role in the evolution and persistence of life on Earth, driving redox reactions that give rise to global biogeochemical cycles. Community metabolism emerges from a hierarchy of processes, including gene expression, ecological interactions, and environmental factors. In wild communities, gene content is correlated with environmental context, but predicting metabolite dynamics from genomes remains elusive. Here, we show, for the process of denitrification, that metabolite dynamics of a community are predictable from the genes each member of the community possesses. A simple linear regression reveals a sparse and generalizable mapping from gene content to metabolite dynamics for genomically diverse bacteria. A consumer-resource model correctly predicts community metabolite dynamics from single-strain phenotypes. Our results demonstrate that the conserved impacts of metabolic genes can predict community metabolite dynamics, enabling the prediction of metabolite dynamics from metagenomes, designing denitrifying communities, and discovering how genome evolution impacts metabolism.}, }
@article {pmid35083529, year = {2023}, author = {Tian, Q and Jiang, Q and Huang, L and Li, D and Lin, Q and Tang, Z and Liu, F}, title = {Vertical Distribution of Soil Bacterial Communities in Different Forest Types Along an Elevation Gradient.}, journal = {Microbial ecology}, volume = {85}, number = {2}, pages = {628-641}, pmid = {35083529}, issn = {1432-184X}, support = {31700462//national natural science foundation of china/ ; 31870465//national natural science foundation of china/ ; 2020338//youth innovation promotion association of the chinese academy of sciences/ ; }, mesh = {*Soil ; Soil Microbiology ; Forests ; Bacteria ; *Chloroflexi ; }, abstract = {Microorganisms inhabit the entire soil profile and play important roles in nutrient cycling and soil formation. Recent studies have found that soil bacterial diversity and composition differ significantly among soil layers. However, little is known about the vertical variation in soil bacterial communities and how it may change along an elevation gradient. In this study, we collected soil samples from 5 forest types along an elevation gradient in Taibai Mountain to characterize the bacterial communities and their vertical patterns and variations across soil profiles. The richness and Shannon index of soil bacterial communities decreased from surface soils to deep soils in three forest types, and were comparable among soil layers in the other two forests at the medium elevation. The composition of soil bacterial communities differed significantly between soil layers in all forest types, and was primarily affected by soil C availability. Oligotrophic members of the bacterial taxa, such as Chloroflexi, Gemmatimonadetes, Nitrospirae, and AD3, were more abundant in the deep layers. The assembly of soil bacterial communities within each soil profile was mainly governed by deterministic processes based on environmental heterogeneity. The vertical variations in soil bacterial communities differed among forest types, and the soil bacterial communities in the Betula albo-sinensis forest at the medium elevation had the lowest vertical variation. The vertical variation was negatively correlated with mean annual precipitation (MAP), weighted rock content, and weighted sand particle content in soils, among which MAP had the highest explanatory power. These results indicated that the vertical mobilization of microbes with preferential and matrix flows likely enhanced bacterial homogeneity. Overall, our results suggest that the vertical variations in soil bacterial communities differ along the elevation gradient and potentially affect soil biological processes across soil profiles.}, }
@article {pmid35082431, year = {2022}, author = {Dede, B and Hansen, CT and Neuholz, R and Schnetger, B and Kleint, C and Walker, S and Bach, W and Amann, R and Meyerdierks, A}, title = {Niche differentiation of sulfur-oxidizing bacteria (SUP05) in submarine hydrothermal plumes.}, journal = {The ISME journal}, volume = {16}, number = {6}, pages = {1479-1490}, pmid = {35082431}, issn = {1751-7370}, support = {03G0253//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; }, mesh = {Bacteria ; *Hydrothermal Vents/microbiology ; In Situ Hybridization, Fluorescence ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Seawater/microbiology ; Sulfur/metabolism ; }, abstract = {Hydrothermal plumes transport reduced chemical species and metals into the open ocean. Despite their considerable spatial scale and impact on biogeochemical cycles, niche differentiation of abundant microbial clades is poorly understood. Here, we analyzed the microbial ecology of two bathy- (Brothers volcano; BrV-cone and northwest caldera; NWC) and a mesopelagic (Macauley volcano; McV) plumes on the Kermadec intra-oceanic arc in the South Pacific Ocean. The microbial community structure, determined by a combination of 16S rRNA gene, fluorescence in situ hybridization and metagenome analysis, was similar to the communities observed in other sulfur-rich plumes. This includes a dominance of the vent characteristic SUP05 clade (up to 22% in McV and 51% in BrV). In each of the three plumes analyzed, the community was dominated by a different yet uncultivated chemoautotrophic SUP05 species, here, provisionally named, Candidatus Thioglobus vadi (McV), Candidatus Thioglobus vulcanius (BrV-cone) and Candidatus Thioglobus plumae (BrV-NWC). Statistical analyses, genomic potential and mRNA expression profiles suggested a SUP05 niche partitioning based on sulfide and iron concentration as well as water depth. A fourth SUP05 species was present at low frequency throughout investigated plume samples and may be capable of heterotrophic or mixotrophic growth. Taken together, we propose that small variations in environmental parameters and depth drive SUP05 niche partitioning in hydrothermal plumes.}, }
@article {pmid35081826, year = {2022}, author = {Morou-Bermúdez, E and Torres-Colón, JE and Bermúdez, NS and Patel, RP and Joshipura, KJ}, title = {Pathways Linking Oral Bacteria, Nitric Oxide Metabolism, and Health.}, journal = {Journal of dental research}, volume = {101}, number = {6}, pages = {623-631}, pmid = {35081826}, issn = {1544-0591}, support = {R01 DE028195/DE/NIDCR NIH HHS/United States ; }, mesh = {*Ammonium Compounds ; Bacteria/metabolism ; *Cardiovascular Diseases ; Humans ; *Microbiota ; Nitrates/metabolism ; Nitric Oxide/metabolism ; Nitrites/metabolism ; }, abstract = {Nitrate-reducing oral bacteria have gained a lot of interest due to their involvement in nitric oxide (NO) synthesis and its important cardiometabolic outcomes. Consortia of nitrate-metabolizing oral bacteria associated with cardiometabolic health and cognitive function have been recently identified. Longitudinal studies and clinical trials have shown that chronic mouthwash use is associated with increased blood pressure and increased risk for prediabetes/diabetes and hypertension. Concurrently, recent studies are beginning to shed some light on the complexity of nitrate reduction pathways of oral bacteria, such as dissimilatory nitrate reduction to ammonium (DNRA), which converts nitrite into ammonium, and denitrification, which converts nitrite to NO, nitrous oxide, and dinitrogen. These pathways can affect the composition and metabolism of the oral microbiome; consequently, salivary nitrate and nitrite metabolism have been proposed as targets for probiotics and oral health. These pathways could also affect systemic NO levels because NO generated through denitrification can be oxidized back to nitrite in the saliva, thus facilitating flux along the NO3[-]-NO2[-]-NO pathway, while DNRA converts nitrite to ammonium, leading to reduced NO. It is, therefore, important to understand which pathway predominates under different oral environmental conditions, since the clinical consequences could be different for oral and systemic health. Recent studies show that oral hygiene measures such as tongue cleaning and dietary nitrate are likely to favor denitrifying bacteria such as Neisseria, which are linked with better cardiometabolic health. A vast body of literature demonstrates that redox potential, carbon-to-nitrate ratio, and nitrate-to-nitrite ratio are key environmental drivers of the competing denitrification and DNRA pathways in various natural and artificial ecosystems. Based on this information, a novel behavioral and microbial model for nitric oxide metabolism and health is proposed, which links lifestyle factors with oral and systemic health through NO metabolism.}, }
@article {pmid35078415, year = {2022}, author = {Duthoo, E and De Reu, K and Leroy, F and Weckx, S and Heyndrickx, M and Rasschaert, G}, title = {To culture or not to culture: careful assessment of metabarcoding data is necessary when evaluating the microbiota of a modified-atmosphere-packaged vegetarian meat alternative throughout its shelf-life period.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {34}, pmid = {35078415}, issn = {1471-2180}, mesh = {Atmosphere ; Bacteria/classification/genetics/*growth &amp; development/isolation &amp; purification ; Colony Count, Microbial ; DNA Barcoding, Taxonomic/*methods/*standards/statistics &amp; numerical data ; Food Microbiology/*methods/standards ; Food Packaging/methods/standards ; Food Storage/methods/*standards/statistics &amp; numerical data ; Meat Products/classification/*microbiology ; RNA, Ribosomal, 16S/genetics ; Refrigeration ; *Vegetarians ; }, abstract = {BACKGROUND: As the increased consumption of ready-to-eat meat alternatives is a fairly recent trend, little is known about the composition and dynamics of the microbiota present on such products. Such information is nonetheless valuable in view of spoilage and food safety prevention. Even though refrigeration and modified-atmosphere-packaging (MAP) can extend the shelf-life period, microbial spoilage can still occur in these products. In the present study, the microbiota of a vegetarian alternative to poultry-based charcuterie was investigated during storage, contrasting the use of a culture-dependent method to a culture-independent metagenetic method.<br><br>RESULTS: The former revealed that lactic acid bacteria (LAB) were the most abundant microbial group, specifically at the end of the shelf-life period, whereby Latilactobacillus sakei was the most abundant species. Metabarcoding analysis, in contrast, revealed that DNA of Xanthomonas was most prominently present, which likely was an artifact due to the presence of xanthan gum as an ingredient, followed by Streptococcus and Weissella.<br><br>CONCLUSIONS: Taken together, these results indicated that Lb. sakei was likely the most prominent specific spoilage organisms (SSO) and, additionally, that the use of metagenetic analysis needs to be interpreted with care in this specific type of product. In order to improve the performance of metagenetics in food samples with a high DNA matrix but a low bacterial DNA load, selective depletion techniques for matrix DNA could be explored.}, }
@article {pmid35077695, year = {2022}, author = {Glass, NL and Rico-Ramírez, AM}, title = {Microbial ecology: Fungal foes and friends.}, journal = {Current biology : CB}, volume = {32}, number = {2}, pages = {R84-R86}, doi = {10.1016/j.cub.2021.12.030}, pmid = {35077695}, issn = {1879-0445}, mesh = {Bacteria ; Friends ; *Fungi ; Humans ; Phenazines ; Soil ; *Soil Microbiology ; }, abstract = {A tripartite interaction between soil fungi, soil bacteria that produce phenazines that are toxic to the fungi, and a second bacterium that sequesters and detoxifies phenazines illustrates the complexity of antagonistic and mutualistic bacterial-fungal interactions.}, }
@article {pmid35076268, year = {2022}, author = {Perez-Lamarque, B and Krehenwinkel, H and Gillespie, RG and Morlon, H}, title = {Limited Evidence for Microbial Transmission in the Phylosymbiosis between Hawaiian Spiders and Their Microbiota.}, journal = {mSystems}, volume = {7}, number = {1}, pages = {e0110421}, pmid = {35076268}, issn = {2379-5077}, mesh = {Animals ; Phylogeny ; Hawaii ; *Spiders ; *Microbiota ; Infectious Disease Transmission, Vertical ; }, abstract = {The degree of similarity between the microbiotas of host species often mirrors the phylogenetic proximity of the hosts. This pattern, referred to as phylosymbiosis, is widespread in animals and plants. While phylosymbiosis was initially interpreted as the signal of symbiotic transmission and coevolution between microbes and their hosts, it is now recognized that similar patterns can emerge even if the microbes are environmentally acquired. Distinguishing between these two scenarios, however, remains challenging. We recently developed HOME (host-microbiota evolution), a cophylogenetic model designed to detect vertically transmitted microbes and host switches from amplicon sequencing data. Here, we applied HOME to the microbiotas of Hawaiian spiders of the genus Ariamnes, which experienced a recent radiation on the archipelago. We demonstrate that although Hawaiian Ariamnes spiders display a significant phylosymbiosis, there is little evidence of microbial vertical transmission. Next, we performed simulations to validate the absence of transmitted microbes in Ariamnes spiders. We show that this is not due to a lack of detection power because of the low number of segregating sites or an effect of phylogenetically driven or geographically driven host switches. Ariamnes spiders and their associated microbes therefore provide an example of a pattern of phylosymbiosis likely emerging from processes other than vertical transmission. IMPORTANCE How host-associated microbiotas assemble and evolve is one of the outstanding questions of microbial ecology. Studies aiming at answering this question have repeatedly found a pattern of "phylosymbiosis," that is, a phylogenetic signal in the composition of host-associated microbiotas. While phylosymbiosis was often interpreted as evidence for vertical transmission and host-microbiota coevolution, simulations have now shown that it can emerge from other processes, including host filtering of environmentally acquired microbes. However, distinguishing the processes driving phylosymbiosis in nature remains challenging. We recently developed a cophylogenetic method that can detect vertical transmission. Here, we applied this method to the microbiotas of recently diverged spiders from the Hawaiian archipelago, which display a clear phylosymbiosis pattern. We found that none of the bacterial operational taxonomic units is vertically transmitted. We show with simulations that this result is not due to methodological artifacts. Thus, we provide a striking empirical example of phylosymbiosis emerging from processes other than vertical transmission.}, }
@article {pmid35074976, year = {2022}, author = {Roy, P and Sarma, A and Kataki, AC and Rai, AK and Chattopadhyay, I}, title = {Salivary microbial dysbiosis may predict lung adenocarcinoma: A pilot study.}, journal = {Indian journal of pathology &amp; microbiology}, volume = {65}, number = {1}, pages = {123-128}, doi = {10.4103/IJPM.IJPM_1111_20}, pmid = {35074976}, issn = {0974-5130}, mesh = {Adenocarcinoma of Lung/*diagnosis/etiology ; Bacteria/classification/*genetics/isolation &amp; purification ; Biomarkers, Tumor/analysis ; DNA, Bacterial/*genetics ; Dysbiosis/etiology/*microbiology ; Female ; Humans ; India ; Male ; Microbiota/genetics ; Middle Aged ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; }, abstract = {BACKGROUND: Adenocarcinoma is a more common type of Non-small cell lung cancer (NSCLC). Lung cancer showed a statistically significant increment in the Kamrup Urban district of Assam, Tripura, Sikkim, and Manipur of India. The goal of our pilot study is to identify non-invasive microbial biomarkers to detect lung adenocarcinoma (LAC).<br><br>MATERIAL AND METHODS: DNA extraction from saliva samples of five LAC patients and five healthy controls was performed by Qiagen DNeasy blood and tissue kit using Lysozyme (3mg/ml) treatment. 16S rRNA genes of distinct regions (V3-V4) were amplified from saliva DNA by PCR. Paired-end sequencing targeting the V3-V4 region of the 16S rRNA gene has been performed on the Illumina MiSeq platform. Raw sequences were analyzed using the QIIME(Quantitative Insights Into Microbial Ecology) software package.<br><br>RESULTS: Our preliminary results showed that Rothia mucilaginosa, Veillonella dispar, Prevotella melaninogenica, Prevotella pallens, Prevotella copri, Haemophilus parainfluenzae, Neisseria bacilliformis and Aggregatibacter segnis were significantly elevated in saliva of LAC which may serve as potential non-invasive biomarkers for LAC detection. Functional prediction analysis showed that bacterial genes involved in glycosyltransferase, peptidases, amino sugar, and nucleotide sugar metabolism, starch and sucrose metabolism were significantly enriched in LAC.<br><br>CONCLUSION: These salivary bacteria may contribute to the development of LAC by increasing expression of glycosyltransferase and peptidases. However to understand their role in pathobiology, studies are required to perform in large cohort.}, }
@article {pmid35074363, year = {2022}, author = {Fu, S and Wang, Q and Wang, R and Zhang, Y and Lan, R and He, F and Yang, Q}, title = {Horizontal transfer of antibiotic resistance genes within the bacterial communities in aquacultural environment.}, journal = {The Science of the total environment}, volume = {820}, number = {}, pages = {153286}, doi = {10.1016/j.scitotenv.2022.153286}, pmid = {35074363}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Aquaculture ; *Drug Resistance, Bacterial/genetics ; Enterobacter/genetics ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Genome, Bacterial ; Providencia/genetics ; RNA, Ribosomal, 16S ; Shewanella/genetics ; *Vibrio parahaemolyticus/genetics ; }, abstract = {Very little is known about how microbiome interactions shape the horizontal transfer of antibiotic resistance genes in aquacultural environment. To this end, we first conducted 16S rRNA gene amplicon sequencing to monitor the dynamics of bacterial community compositions in one shrimp farm from 2019 to 2020. Next, co-occurrence analysis was then conducted to reveal the interactions network between Vibrio spp. and other species. Subsequently, 21 V. parahaemolyticus isolates and 15 related bacterial species were selected for whole-genome sequencing (WGS). The 16S rDNA amplicon sequencing results identified a remarkable increase of Vibrio and Providencia in September-2019 and a significant rise of Enterobacter and Shewanella in Septtember-2020. Co-occurrence analysis revealed that Vibrio spp. positively interacted with the above species, leading to the sequencing of their isolates to further understand the sharing of the resistant genomic islands (GIs). Subsequent pan-genomic analysis of V. parahaemolyticus genomes identified 278 horizontally transferred genes in 10 GIs, most of which were associated with antibiotic resistance, virulence, and fitness of metabolism. Most of the GIs have also been identified in Providencia, and Enterobacter, suggesting that exchange of genetic traits might occur in V. parahaemolyticus and other cooperative species in a specific niche. No genetic exchange was found between the species with negative relationships. The knowledge generated from this study would greatly improve our capacity to predict and mitigate the emergence of new resistant population and provide practical guidance on the microbial management during the aquacultural activities.}, }
@article {pmid35074352, year = {2022}, author = {Carcereny, A and Garcia-Pedemonte, D and Martínez-Velázquez, A and Quer, J and Garcia-Cehic, D and Gregori, J and Antón, A and Andrés, C and Pumarola, T and Chacón-Villanueva, C and Borrego, CM and Bosch, A and Guix, S and Pintó, RM}, title = {Dynamics of SARS-CoV-2 Alpha (B.1.1.7) variant spread: The wastewater surveillance approach.}, journal = {Environmental research}, volume = {208}, number = {}, pages = {112720}, pmid = {35074352}, issn = {1096-0953}, mesh = {*COVID-19/epidemiology ; Humans ; *SARS-CoV-2/genetics ; Wastewater ; Wastewater-Based Epidemiological Monitoring ; }, abstract = {Wastewater based epidemiology (WBE) offers an overview of the SARS-CoV-2 variants circulating among the population thereby serving as a proper surveillance method. The variant of concern (VOC) Alpha was first identified in September 2020 in the United Kingdom, and rapidly became dominant across Europe. Our objective was to elucidate the Alpha VOC outcompetition rate and identify mutations in the spike glycoprotein (S) gene, indicative of the circulation of the Alpha VOC and/or other variants in the population through wastewater analysis. In the period covered by this study (November 2020-April 2021), forteen wastewater treatment plants (WWTPs) were weekly sampled. The total number of SARS-CoV-2 genome copies per L (GC/L) was determined with a Real-Time qPCR, targeting the N gene. Surveillance of the Alpha VOC circulation was ascertained using a duplex RT-qPCR, targeting and discriminating the S gene. Our results showed that in a period of 6 weeks the Alpha VOC was present in all the studied WWTPs, and became dominant in 11 weeks on average. The outcompetition rates of the Alpha VOC were estimated, and their relationship with different parameters statistically analyzed. The rapid spread of the Alpha VOC was influenced by its initial input and by the previous circulation of SARS-COV-2 in the population. This latter point could be explained by its higher transmissibility, particularly advantadgeous when a certain degree of herd immunity exists. Moreover, the presence of signature mutations of SARS-COV-2 variants were established by deep-sequencing of the complete S gene. The circulation of the Alpha VOC in the area under study was confirmed, and additionally two combinations of mutations in the S glycoprotein (T73A and D253N, and S477N and A522S) that could affect antibody binding were identified.}, }
@article {pmid35073313, year = {2022}, author = {Bogdanowski, A and Banitz, T and Muhsal, LK and Kost, C and Frank, K}, title = {McComedy: A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems.}, journal = {PLoS computational biology}, volume = {18}, number = {1}, pages = {e1009777}, pmid = {35073313}, issn = {1553-7358}, mesh = {Computational Biology/*methods ; *Microbiota ; Software ; *User-Computer Interface ; }, abstract = {Individual-based modeling is widely applied to investigate the ecological mechanisms driving microbial community dynamics. In such models, the population or community dynamics emerge from the behavior and interplay of individual entities, which are simulated according to a predefined set of rules. If the rules that govern the behavior of individuals are based on generic and mechanistically sound principles, the models are referred to as next-generation individual-based models. These models perform particularly well in recapitulating actual ecological dynamics. However, implementation of such models is time-consuming and requires proficiency in programming or in using specific software, which likely hinders a broader application of this powerful method. Here we present McComedy, a modeling tool designed to facilitate the development of next-generation individual-based models of microbial consumer-resource systems. This tool allows flexibly combining pre-implemented building blocks that represent physical and biological processes. The ability of McComedy to capture the essential dynamics of microbial consumer-resource systems is demonstrated by reproducing and furthermore adding to the results of two distinct studies from the literature. With this article, we provide a versatile tool for developing next-generation individual-based models that can foster understanding of microbial ecology in both research and education.}, }
@article {pmid35071939, year = {2021}, author = {Harder, CB and Persson, S and Christensen, J and Ljubic, A and Nielsen, EM and Hoorfar, J}, title = {Molecular diagnostics of Salmonella and Campylobacter in human/animal fecal samples remain feasible after long-term sample storage without specific requirements.}, journal = {AIMS microbiology}, volume = {7}, number = {4}, pages = {399-414}, pmid = {35071939}, issn = {2471-1888}, abstract = {Rapid advances in the development of sequencing technologies, numbers of commercial providers and diminishing costs have made DNA-based identification and diagnostics increasingly accessible to doctors and laboratories, eliminating the need for local investments in expensive technology and training or hiring of skilled technicians. However, reliable and comparable molecular analyses of bacteria in stool samples are dependent on storage and workflow conditions that do not introduce post-sampling bias, the most important factor being the need to keep the DNA at a stable detectable level. For that reason, there may remain other prohibitively costly requirements for cooling or freezing equipment or special chemical additives. This study investigates the diagnostic detectability of Salmonella and Campylobacter DNA in human, pig and chicken stool samples, stored at different temperatures and with different preservation methods. Stool samples were spiked with 10[6] CFU/mL of both Salmonella and Campylobacter strains stored at -20 °C, 5 °C and 20 °C (Room temperature, RT) and treated with either RNAlater, EDTA or Silica/ethanol. DNA was extracted at 9 different time points within 30 days and quantified by Qubit (total DNA) and qPCR (Salmonella and Campylobacter DNA). We found no statistically significant differences among the different preservation methods, and DNA from both species was easily detected at all time points and at all temperatures, both with and without preservation. This suggests that infections by these bacteria can be diagnosed and possibly also analysed in further detail simply by taking a stool sample in any suitable sealed container that can be transported to laboratory analysis without special storage or preservation requirements. We briefly discuss how this finding can benefit infection control in both developed and developing countries.}, }
@article {pmid35071053, year = {2021}, author = {Rozas, M and Brillet, F and Callewaert, C and Paetzold, B}, title = {MinION™ Nanopore Sequencing of Skin Microbiome 16S and 16S-23S rRNA Gene Amplicons.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {806476}, pmid = {35071053}, issn = {2235-2988}, mesh = {Genes, rRNA ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota/genetics ; *Nanopore Sequencing ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Sequence Analysis, DNA ; Skin/*microbiology ; }, abstract = {Human skin microbiome dysbiosis can have clinical consequences. Characterizing taxonomic composition of bacterial communities associated with skin disorders is important for dermatological advancement in both diagnosis and novel treatments. This study aims to analyze and improve the accuracy of taxonomic classification of skin bacteria with MinION™ nanopore sequencing using a defined skin mock community and a skin microbiome sample. We compared the Oxford Nanopore Technologies recommended procedures and concluded that their protocols highly bias the relative abundance of certain skin microbiome genera, most notably a large overrepresentation of Staphylococcus and underrepresentation of Cutibacterium and Corynebacterium. We demonstrated that changes in the amplification protocols improved the accuracy of the taxonomic classification for these three main skin bacterial genera. This study shows that MinION™ nanopore could be an efficient technology for full-length 16S rRNA sequencing; however, the analytical advantage is strongly influenced by the methodologies. The suggested alternatives in the sample processing improved characterization of a complex skin microbiome community using MinION™ nanopore sequencing.}, }
@article {pmid35069532, year = {2021}, author = {Petit, J and de Bruijn, I and Goldman, MRG and van den Brink, E and Pellikaan, WF and Forlenza, M and Wiegertjes, GF}, title = {β-Glucan-Induced Immuno-Modulation: A Role for the Intestinal Microbiota and Short-Chain Fatty Acids in Common Carp.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {761820}, pmid = {35069532}, issn = {1664-3224}, mesh = {*Animal Feed ; Animals ; *Carps/immunology/microbiology ; Fatty Acids, Volatile/*immunology ; *Gastrointestinal Microbiome/drug effects/immunology ; Immunomodulation/*drug effects ; beta-Glucans/*pharmacology ; }, abstract = {Dietary supplementation of fish with β-glucans has been commonly associated with immunomodulation and generally accepted as beneficial for fish health. However, to date the exact mechanisms of immunomodulation by β-glucan supplementation in fish have remained elusive. In mammals, a clear relation between high-fibre diets, such as those including β-glucans, and diet-induced immunomodulation via intestinal microbiota and associated metabolites has been observed. In this study, first we describe by 16S rRNA sequencing the active naive microbiota of common carp intestine. Based on the abundance of the genus Bacteroides, well known for their capacity to degrade and ferment carbohydrates, we hypothesize that common carp intestinal microbiota could ferment dietary β-glucans. Indeed, two different β-glucan preparations (curdlan and MacroGard[®]) were both fermented in vitro, albeit with distinct fermentation dynamics and distinct production of short-chain fatty acids (SCFA). Second, we describe the potential immunomodulatory effects of the three dominant SCFAs (acetate, butyrate, and propionate) on head kidney leukocytes, showing effects on both nitric oxide production and expression of several cytokines (il-1b, il-6, tnfα, and il-10) in vitro. Interestingly, we also observed a regulation of expression of several gpr40L genes, which were recently described as putative SCFA receptors. Third, we describe how a single in vivo oral gavage of carp with MacroGard[®] modulated simultaneously, the expression of several pro-inflammatory genes (il-1b, il-6, tnfα), type I IFN-associated genes (tlr3.1, mx3), and three specific gpr40L genes. The in vivo observations provide indirect support to our in vitro data and the possible role of SCFAs in β-glucan-induced immunomodulation. We discuss how β-glucan-induced immunomodulatory effects can be explained, at least in part, by fermentation of MacroGard[®] by specific bacteria, part of the naive microbiota of common carp intestine, and how a subsequent production of SFCAs could possibly explain immunomodulation by β-glucan via SCFA receptors present on leukocytes.}, }
@article {pmid35069467, year = {2021}, author = {Rodríguez-Gijón, A and Nuy, JK and Mehrshad, M and Buck, M and Schulz, F and Woyke, T and Garcia, SL}, title = {A Genomic Perspective Across Earth's Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {761869}, pmid = {35069467}, issn = {1664-302X}, abstract = {Our view of genome size in Archaea and Bacteria has remained skewed as the data has been dominated by genomes of microorganisms that have been cultivated under laboratory settings. However, the continuous effort to catalog Earth's microbiomes, specifically propelled by recent extensive work on uncultivated microorganisms, provides an opportunity to revise our perspective on genome size distribution. We present a meta-analysis that includes 26,101 representative genomes from 3 published genomic databases; metagenomic assembled genomes (MAGs) from GEMs and stratfreshDB, and isolates from GTDB. Aquatic and host-associated microbial genomes present on average the smallest estimated genome sizes (3.1 and 3.0 Mbp, respectively). These are followed by terrestrial microbial genomes (average 3.7 Mbp), and genomes from isolated microorganisms (average 4.3 Mbp). On the one hand, aquatic and host-associated ecosystems present smaller genomes sizes in genera of phyla with genome sizes above 3 Mbp. On the other hand, estimated genome size in phyla with genomes under 3 Mbp showed no difference between ecosystems. Moreover, we observed that when using 95% average nucleotide identity (ANI) as an estimator for genetic units, only 3% of MAGs cluster together with genomes from isolated microorganisms. Although there are potential methodological limitations when assembling and binning MAGs, we found that in genome clusters containing both environmental MAGs and isolate genomes, MAGs were estimated only an average 3.7% smaller than isolate genomes. Even when assembly and binning methods introduce biases, estimated genome size of MAGs and isolates are very similar. Finally, to better understand the ecological drivers of genome size, we discuss on the known and the overlooked factors that influence genome size in different ecosystems, phylogenetic groups, and trophic strategies.}, }
@article {pmid35067749, year = {2022}, author = {Zhang, L and Lai, JL and Zhang, Y and Luo, XG and Li, ZG}, title = {Correction to: Degradation of Uranium-Contaminated Decontamination Film by UV Irradiation and Microbial Biodegradation.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {451}, doi = {10.1007/s00248-022-01966-1}, pmid = {35067749}, issn = {1432-184X}, }
@article {pmid35066616, year = {2023}, author = {Sartori, DR and Miñán, AG and Gonzalez, MC and Fernández Lorenzo de Mele, MA}, title = {Different Impact of Suspended Al2O3 Nanoparticles on Microbial Communities: Formation of 2D-Networks (Without Humic Acids) or 3D-Colonies (With Humic Acids).}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {137-145}, pmid = {35066616}, issn = {1432-184X}, support = {2016-1424//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; 2019-0631//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; 2015-1266//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; 11/X900//Universidad Nacional de La Plata/ ; 11/I221//Universidad Nacional de La Plata/ ; PUE 22920170100100CO//Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas/ ; 0601//Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas/ ; }, mesh = {Humic Substances/analysis ; *Zinc Oxide/chemistry ; *Nanoparticles ; Ions ; *Microbiota ; }, abstract = {The use of metal-based and, particularly, Al2O3 nanoparticles (Al2O3-NP) for diverse purposes is exponentially growing. However, the growth of such promissory market is not accompanied by a parallel extensive investigation related to the impact of this pollution on groundwater and biological systems. Pseudomonas species, ubiquitous, environmentally critical microbes, frequently respond to stress conditions with diverse strategies that generally include extracellular polymeric substances (EPS) formation. The aim of this study is to report that changes in the aqueous environment, particularly, the addition of Al2O3-NP without and with humic acids, induce different adaptive strategies of Pseudomonas aeruginosa early biofilms. To this purpose, early biofilms were incubated in diluted culture media without (control) and with Al2O3-NP, and with humic acids (HA-control, HA-Al2O3-NP) for 24 h. 3D colonies with EPS strings and isolated bacteria in their surroundings were detected in the control biofilms. Unlikely, an unusual adaptive behaviour was developed in the presence of Al2O3-NP. Bacteria opt to disassemble the 3D arrangements and to implement a 2D network promoting morphological and size changes of bacterial cells (small coccoid shapes). Remarkably, this strategy allows their temporarily non-EPS-depending survival without decreasing the number of cells. This behaviour was not observed with ZnO-NP, HA-Al2O3-NP, or HA-ZnO-NP. Physicochemical analysis revealed that HA were adsorbed on Al2O3-NP and promoted the Al(III) ions complexation. This supports the hypothesis that the reduction of toxicity of Al ions and the 3D colony formation in the presence of HA-Al2O3-NP is promoted by the complexation of the metal ions with HA components.}, }
@article {pmid35066615, year = {2023}, author = {Offret, C and Gauthier, O and Despréaux, G and Bidault, A and Corporeau, C and Miner, P and Petton, B and Pernet, F and Fabioux, C and Paillard, C and Le Blay, G}, title = {Microbiota of the Digestive Glands and Extrapallial Fluids of Clams Evolve Differently Over Time Depending on the Intertidal Position.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {288-297}, pmid = {35066615}, issn = {1432-184X}, support = {ANR-17-EURE-0015//Agence Nationale de la Recherche/ ; 678589//Horizon 2020/ ; 2017-Strat&#xe9;gie d'Attractivit&#xe9; Durable//R&#xe9;gion Bretagne/ ; }, mesh = {Animals ; *Bivalvia/microbiology ; *Microbiota ; }, abstract = {The Manila clam (Ruditapes philippinarum) is the second most exploited bivalve in the world but remains threatened by diseases and global changes. Their associated microbiota play a key role in their fitness and acclimation capacities. This study aimed at better understanding the behavior of clam digestive glands and extrapallial fluids microbiota at small, but contrasting spatial and temporal scales. Results showed that environmental variations impacted clam microbiota differently according to the considered tissue. Each clam tissue presented its own microbiota and showed different dynamics according to the intertidal position and sampling period. Extrapallial fluids microbiota was modified more rapidly than digestive glands microbiota, for clams placed on the upper and lower intertidal position, respectively. Clam tissues could be considered as different microhabitats for bacteria as they presented different responses to small-scale temporal and spatial variabilities in natural conditions. These differences underlined a more stringent environmental filter capacity of the digestive glands.}, }
@article {pmid35066415, year = {2022}, author = {Kazmi, SSUH and Uroosa,  and Xu, H and Xuexi, T}, title = {An approach to determining the nitrofurazone-induced toxic dynamics for ecotoxicity assessment using protozoan periphytons in marine ecosystems.}, journal = {Marine pollution bulletin}, volume = {175}, number = {}, pages = {113329}, doi = {10.1016/j.marpolbul.2022.113329}, pmid = {35066415}, issn = {1879-3363}, mesh = {Ecosystem ; Multivariate Analysis ; *Nitrofurazone/toxicity ; *Periphyton ; }, abstract = {With several observable responses and sensitivity of protozoans to nitrofurazone (NFZ), the toxic effects of NFZ on protozoans can be an early warning signal of NFZ contamination in the aquatic environment. To evaluate the toxic dynamics induced by NFZ, protozoan samples were collected using microscopy glass slides and exposed to the five concentrations of NFZ: 0, 1, 2, 4, and 8 mg ml[-1]. Substantial differences in the species composition and toxic-dynamics patterns were observed among all concentrations. Briefly, periphytic euplotids and pleurostomatids were the most prevalent at each concentration level, while dysteriids were less dominant among all treatments. Multivariate analysis revealed significant (P < 0.05) differences in the taxonomic patterns of the test organisms among the five treatments. Furthermore, significant deviation of protozoan communities from the expected taxonomic breadth was observed to occur in a dose-dependent manner. Based on these findings, it is suggested that protozoan periphytons could be used as bioindicators to assess the ecotoxicity of NFZ in the marine environment.}, }
@article {pmid35065823, year = {2022}, author = {Scherer-Lorenzen, M and Gessner, MO and Beisner, BE and Messier, C and Paquette, A and Petermann, JS and Soininen, J and Nock, CA}, title = {Pathways for cross-boundary effects of biodiversity on ecosystem functioning.}, journal = {Trends in ecology &amp; evolution}, volume = {37}, number = {5}, pages = {454-467}, doi = {10.1016/j.tree.2021.12.009}, pmid = {35065823}, issn = {1872-8383}, mesh = {*Biodiversity ; *Ecosystem ; }, abstract = {The biodiversity-ecosystem functioning concept asserts that processes in ecosystems are markedly influenced by species richness and other facets of biodiversity. However, biodiversity-ecosystem functioning studies have been largely restricted to single ecosystems, ignoring the importance of functional links - such as the exchange of matter, energy, and organisms - between coupled ecosystems. Here we present a basic concept and outline three pathways of cross-boundary biodiversity effects on ecosystem processes and propose an agenda to assess such effects, focusing on terrestrial-aquatic linkages to illustrate the case. This cross-boundary perspective of biodiversity-ecosystem functioning relationships presents a promising frontier for biodiversity and ecosystem science with repercussions for the conservation, restoration, and management of biodiversity and ecosystems from local to landscape scales.}, }
@article {pmid35065228, year = {2022}, author = {Paquete, CM and Rosenbaum, MA and Bañeras, L and Rotaru, AE and Puig, S}, title = {Let's chat: Communication between electroactive microorganisms.}, journal = {Bioresource technology}, volume = {347}, number = {}, pages = {126705}, doi = {10.1016/j.biortech.2022.126705}, pmid = {35065228}, issn = {1873-2976}, support = {864669/ERC_/European Research Council/International ; }, mesh = {*Bioelectric Energy Sources ; Biofilms ; Communication ; Electrodes ; Electrons ; }, abstract = {Electroactive microorganisms can exchange electrons with other cells or conductive interfaces in their extracellular environment. This property opens the way to a broad range of practical biotechnological applications, from manufacturing sustainable chemicals via electrosynthesis, to bioenergy, bioelectronics or improved, low-energy demanding wastewater treatments. Besides, electroactive microorganisms play key roles in environmental bioremediation, significantly impacting process efficiencies. This review highlights our present knowledge on microbial interactions promoting the communication between electroactive microorganisms in a biofilm on an electrode in bioelectrochemical systems (BES). Furthermore, the immediate knowledge gaps that must be closed to develop novel technologies will also be acknowledged.}, }
@article {pmid35064809, year = {2023}, author = {Tan, Y and Wang, J and He, Y and Yu, X and Chen, S and Penttinen, P and Liu, S and Yang, Y and Zhao, K and Zou, L}, title = {Organic Fertilizers Shape Soil Microbial Communities and Increase Soil Amino Acid Metabolites Content in a Blueberry Orchard.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {232-246}, pmid = {35064809}, issn = {1432-184X}, support = {KLSFGAGP2020.003//Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, the China Conservation and Research Center for the Giant Panda/ ; 2020YJ0338//Department of Science and Technology of Sichuan Province/ ; 2020ZHCG0044//Department of Science and Technology of Sichuan Province/ ; 21GJHZ0113//Department of Science and Technology of Sichuan Province/ ; }, mesh = {Animals ; Cattle ; Soil/chemistry ; Fertilizers/analysis ; *Blueberry Plants/metabolism ; Nitrogen/metabolism ; *Microbiota ; Bacteria ; *Ascomycota/metabolism ; Soil Microbiology ; }, abstract = {The decline in soil nutrients is becoming a major concern of soil degradation. The possibility of using organic waste as a soil additive to increase nutrients and essential components is significant in soil quality protection and waste management. The aim of this study was to investigate the effects of composted spent mushroom substrate (MS), giant panda feces (PF), and cattle manure (CM) as organic fertilizers in soil microbial communities and metabolites in blueberry orchard in China, which were measured by using high-throughput sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomics. Altogether, 45.66% of the bacterial operational taxonomic units (OTUs) and 9.08% of the fungal OTUs were detected in all treatments. Principal coordinates analysis demonstrated that the bacterial and fungal communities in MS and PF treatments were similar, whereas the communities in the not-organic fertilized control (CK) were significantly different from those in the organic fertilizer treatments. Proteobacteria, Acidobacteria, and Bacteroidetes were the dominant bacterial phyla, and Basidiomycota, Ascomycota, and Mortierellomycota the dominant fungal phyla. Redundancy analysis indicated that pH and available potassium were the main factors determining the composition of microbial communities. The fungal genera Postia, Cephalotrichum, and Thermomyces increased in organic fertilizer treatments, and likely promoted the degradation of organic fertilizers into low molecular-weight metabolites (e.g., amino acids). PCA and PLS-DA models showed that the metabolites in CK were different from those in the other three treatments, and those in CM were clearly different from those in MS and PF. Co-occurrence network analysis showed that several taxa correlated positively with amino acid contents. The results of this study provide new insights into organic waste reutilization and new directions for further studies.}, }
@article {pmid35064808, year = {2023}, author = {Cicala, F and Cisterna-Céliz, JA and Paolinelli, M and Moore, JD and Sevigny, J and Rocha-Olivares, A}, title = {The Role of Diversity in Mediating Microbiota Structural and Functional Differences in Two Sympatric Species of Abalone Under Stressed Withering Syndrome Conditions.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {277-287}, pmid = {35064808}, issn = {1432-184X}, support = {2011-CO1-163322//sagarpa-conacyt/ ; CN-14-14//uc mexus-conacyt/ ; Fund for Scientific Research//cicese/ ; Technological Development FID-2012-01//cicese/ ; }, mesh = {Animals ; Sympatry ; *Gastropoda/microbiology ; *Microbiota ; Proteobacteria/genetics ; *Gastrointestinal Microbiome ; }, abstract = {Withering syndrome (WS) is a gastro-intestinal (GI) infectious disease likely affecting all abalone species worldwide. Structural and functional changes in abalone GI microbiotas under WS-stressed conditions remain poorly investigated. It is unclear if interspecific microbiota differences, such as the presence of certain microbes, their abundance, and functional capabilities, may be involved in the occurrence of this disease. Bacterial microbiotas of healthy Haliotis fulgens and Haliotis corrugata are mainly composed by Tenericutes, Proteobacteria, Fusobacteria, and Spirochaetes. We previously reported species-specific structural and functional profiles of those communities and suggested that they are of consequence to the different susceptibility of each species to WS. Here, we address this question by comparing the structure and function of healthy and dysbiotic microbiota through 454 pyrosequencing and PICRUSt 2, respectively. Our findings suggest that the extent to which WS-stressed conditions may explain structural and functional differences in GI microbiota is contingent on the microbiota diversity itself. Indeed, microbiota differences between stressed and healthy abalone were marginal in the more complex bacterial communities of H. corrugata, in which no significant structural or functional changes were detected. Conversely, significant structural changes were observed in the less complex bacterial microbiota of H. fulgens. Moreover, structural alterations led to a significant downregulation of some metabolic activities conducted by GI bacteria. Accordingly, results suggest that gastro-intestinal bacterial diversity appears to be related with both the health of abalone and the etiology of WS.}, }
@article {pmid35064419, year = {2022}, author = {Berrios, L}, title = {The genus Caulobacter and its role in plant microbiomes.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {38}, number = {3}, pages = {43}, pmid = {35064419}, issn = {1573-0972}, support = {2109481//National Science Foundation/ ; }, mesh = {Arabidopsis/microbiology ; Biomass ; Caulobacter/*classification/*physiology ; Citrullus/microbiology ; *Host Microbial Interactions ; *Microbiota ; *Plant Growth Regulators ; Plants/*microbiology ; Zea mays/microbiology ; }, abstract = {Recent omics approaches have revealed the prevalent microbial taxa that constitute the microbiome of various plant species. Across global scales and environmental conditions, strains belonging to the bacterial genus Caulobacter have consistently been found in association with various plant species. Aligned with agroecological relevance and biotechnological advances, many scientific communications have demonstrated that several Caulobacter strains (spanning several Caulobacter species) harbor the potential to enhance plant biomass for various plant species ranging from Arabidopsis to Citrullus and Zea mays. In the past several years, co-occurrence data have driven mechanistically resolved communications about select Caulobacter-plant interactions. Given the long-standing history of Caulobacter as a model organism for cell cycle regulation, genetic studies, and the prevalence of Caulobacter species in various plant microbiomes, the genus Caulobacter offers researchers a unique opportunity to leverage for investigating plant-microbe interactions and realizing targeted biotechnological applications. In this review, recent developments regarding Caulobacter-plant interactions are presented in terms of model utility for future biotechnological investigations.}, }
@article {pmid35061792, year = {2022}, author = {Guo, Z and Lv, L and Liu, D and He, X and Wang, W and Feng, Y and Islam, MS and Wang, Q and Chen, W and Liu, Z and Wu, S and Abied, A}, title = {A global meta-analysis of animal manure application and soil microbial ecology based on random control treatments.}, journal = {PloS one}, volume = {17}, number = {1}, pages = {e0262139}, pmid = {35061792}, issn = {1932-6203}, mesh = {Animals ; Bacteria/genetics/isolation &amp; purification ; Betaproteobacteria/genetics/isolation &amp; purification ; Biomass ; Databases, Factual ; Fungi/genetics/isolation &amp; purification ; Manure/*analysis/microbiology ; RNA, Ribosomal, 16S/genetics/metabolism ; RNA, Ribosomal, 18S/genetics/metabolism ; *Soil Microbiology ; }, abstract = {The processes involved in soil domestication have altered the soil microbial ecology. We examined the question of whether animal manure application affects the soil microbial ecology of farmlands. The effects of global animal manure application on soil microorganisms were subjected to a meta-analysis based on randomized controlled treatments. A total of 2303 studies conducted in the last 30 years were incorporated into the analysis, and an additional 45 soil samples were collected and sequenced to obtain 16S rRNA and 18S rRNA data. The results revealed that manure application increased soil microbial biomass. Manure application alone increased bacterial diversity (M-Z: 7.546 and M-I: 8.68) and inhibited and reduced fungal diversity (M-Z: -1.15 and M-I: -1.03). Inorganic fertilizer replaced cattle and swine manure and provided nutrients to soil microorganisms. The soil samples of the experimental base were analyzed, and the relative abundances of bacteria and fungi were altered compared with no manure application. Manure increased bacterial diversity and reduced fungal diversity. Mrakia frigida and Betaproteobacteriales, which inhibit other microorganisms, increased significantly in the domesticated soil. Moreover, farm sewage treatments resulted in a bottleneck in the manure recovery rate that should be the focus of future research. Our results suggest that the potential risks of restructuring the microbial ecology of cultivated land must be considered.}, }
@article {pmid35061090, year = {2023}, author = {Yang, Y and Hu, L and Li, X and Wang, J and Jin, G}, title = {Nitrogen Fixation and Diazotrophic Community in Plastic-Eating Mealworms Tenebrio molitor L.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {264-276}, pmid = {35061090}, issn = {1432-184X}, mesh = {Animals ; *Tenebrio/metabolism/microbiology ; Plastics ; Polystyrenes/metabolism ; Nitrogen Fixation ; Biodegradation, Environmental ; Larva/microbiology ; Carbon/metabolism ; Nitrogen/metabolism ; }, abstract = {Mealworms, the larvae of a coleopteran insect Tenebrio molitor L., are capable of eating, living on, and degrading non-hydrolyzable vinyl plastics as sole diet. However, vinyl plastics are carbon-rich but nitrogen-deficient. It remains puzzling how plastic-eating mealworms overcome the nutritional obstacle of nitrogen limitation. Here, we provide the evidence for nitrogen fixation activity within plastic-eating mealworms. Acetylene reduction assays illustrate that the nitrogen-fixing activity ranges from 12.3 ± 0.7 to 32.9 ± 9.3 nmol ethylene·h[-1]·gut[-1] and the corresponding fixed nitrogen equivalents of protein are estimated as 8.6 to 23.0 µg per day per mealworm. Nature nitrogen isotopic analyses of plastic-eating mealworms provide further evidence for the assimilation of fixed nitrogen as a new nitrogen source. Eliminating the gut microbial microbiota with antibiotics impairs the mealworm's ability to fix nitrogen from the atmosphere, indicating the contribution of gut microbiota to nitrogen fixation. By using the traditional culture-dependent technique, PCR and RT-PCR of nifH gene, nitrogen-fixing bacteria diversity within the gut was detected, and the genus Klebsiella was demonstrated to be an important nitrogen-fixing symbiont. These findings first build the relationship between plastic degradation (carbon metabolism) and nitrogen fixation (nitrogen metabolism) within mealworms. Combined with previously reported plastic-degrading capability and nitrogen-fixing activity, mealworms may be potential candidates for up-recycling of plastic waste to produce protein sources.}, }
@article {pmid35059821, year = {2023}, author = {Mancini, E and Sabatelli, S and Hu, Y and Frasca, S and Di Giulio, A and Audisio, P and Brown, CD and Russell, JA and Trizzino, M}, title = {Uncovering Active Bacterial Symbionts in Three Species of Pollen-feeding Beetles (Nitidulidae: Meligethinae).}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {335-339}, pmid = {35059821}, issn = {1432-184X}, support = {1442144//national science foundation/ ; RP120172B8C07DF1//sapienza universit&#xe0; di roma/ ; CAL/2016//universit&#xe0; degli studi roma tre/ ; }, mesh = {Animals ; *Coleoptera ; RNA, Ribosomal, 16S/genetics ; Insecta ; Pollen ; Plants ; }, abstract = {Microbial symbionts enable many phytophagous insects to specialize on plant-based diets through a range of metabolic services. Pollen comprises one-plant tissue consumed by such herbivores. While rich in lipids and proteins, its nutrient content is often imbalanced and difficult-to-access due to a digestibly recalcitrant cell wall. Pollen quality can be further degraded by harmful allelochemicals. To identify microbes that may aid in palynivory, we performed cDNA-based 16S rRNA metabarcoding on three related pollen beetles (Nitidulidae: Meligethinae) exhibiting different dietary breadths: Brassicogethes aeneus, B. matronalis, and Meligethes atratus. Nine bacterial symbionts (i.e., 97% OTUs) exhibited high metabolic activity during active feeding. Subsequent PCR surveys revealed varying prevalence of those from three Rickettsialles genera-Lariskella, Rickettsia, and Wolbachia-within beetle populations. Our findings lay the groundwork for future studies on the influence of phylogeny and diet on palynivorous insect microbiomes, and roles of symbionts in the use of challenging diets.}, }
@article {pmid35059602, year = {2022}, author = {Weber, PM and Paredes, GF and Viehboeck, T and Pende, N and Volland, JM and Gros, O and VanNieuwenhze, M and Ott, J and Bulgheresi, S}, title = {FtsZ-mediated fission of a cuboid bacterial symbiont.}, journal = {iScience}, volume = {25}, number = {1}, pages = {103552}, pmid = {35059602}, issn = {2589-0042}, support = {P 28593/FWF_/Austrian Science Fund FWF/Austria ; P 28743/FWF_/Austrian Science Fund FWF/Austria ; P 31594/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Less than a handful of cuboid and squared cells have been described in nature, which makes them a rarity. Here, we show how Candidatus Thiosymbion cuboideus, a cube-like gammaproteobacterium, reproduces on the surface of marine free-living nematodes. Immunostaining of symbiont cells with an anti-fimbriae antibody revealed that they are host-polarized, as these appendages exclusively localized at the host-proximal (animal-attached) pole. Moreover, by applying a fluorescently labeled metabolic probe to track new cell wall insertion in vivo, we observed that the host-attached pole started septation before the distal one. Similarly, Ca. T. cuboideus cells immunostained with an anti-FtsZ antibody revealed a proximal-to-distal localization pattern of this tubulin homolog. Although FtsZ has been shown to arrange into squares in synthetically remodeled cuboid cells, here we show that FtsZ may also mediate the division of naturally occurring ones. This implies that, even in natural settings, membrane roundness is not required for FtsZ function.}, }
@article {pmid35059423, year = {2021}, author = {van der Goot, E and Vink, SN and van Vliet, D and van Spronsen, FJ and Falcao Salles, J and van der Zee, EA}, title = {Gut-Microbiome Composition in Response to Phenylketonuria Depends on Dietary Phenylalanine in BTBR Pah[enu2] Mice.}, journal = {Frontiers in nutrition}, volume = {8}, number = {}, pages = {735366}, pmid = {35059423}, issn = {2296-861X}, abstract = {Phenylketonuria (PKU) is a metabolic disorder caused by a hepatic enzyme deficiency causing high blood and brain levels of the amino acid Phenylalanine (Phe), leading to severe cognitive and psychological deficits that can be prevented, but not completely, by dietary treatment. The behavioral outcome of PKU could be affected by the gut-microbiome-brain axis, as diet is one of the major drivers of the gut microbiome composition. Gut-microbiome alterations have been reported in treated patients with PKU, although the question remains whether this is due to PKU, the dietary treatment, or their interaction. We, therefore, examined the effects of dietary Phe restriction on gut-microbiome composition and relationships with behavioral outcome in mice. Male and female BTBR Pah[enu2] mice received either a control diet (normal protein, "high" Phe), liberalized Phe-restricted (33% natural protein restriction), or severe Phe-restricted (75% natural protein restriction) diet with protein substitutes for 10 weeks (n = 14 per group). Their behavioral performance was examined in an open field test, novel and spatial object location tests, and a balance beam. Fecal samples were collected and sequenced for the bacterial 16S ribosomal RNA (rRNA) region. Results indicated that PKU on a high Phe diet reduced Shannon diversity significantly and altered the microbiome composition compared with wild-type animals. Phe-restriction prevented this loss in Shannon diversity but changed community composition even more than the high-Phe diet, depending on the severity of the restriction. Moreover, on a taxonomic level, we observed the highest number of differentially abundant genera in animals that received 75% Phe-restriction. Based on correlation analyses with differentially abundant taxa, the families Entereococacceae, Erysipelotrichaceae, Porphyromonadaceae, and the genus Alloprevotella showed interesting relationships with either plasma Phe levels and/or object memory. According to our results, these bacterial taxa could be good candidates to start examining the microbial metabolic potential and probiotic properties in the context of PKU. We conclude that PKU leads to an altered gut microbiome composition in mice, which is least severe on a liberalized Phe-restricted diet. This may suggest that the current Phe-restricted diet for PKU patients could be optimized by taking dietary effects on the microbiome into account.}, }
@article {pmid35059329, year = {2021}, author = {Zuppi, M and Hendrickson, HL and O'Sullivan, JM and Vatanen, T}, title = {Phages in the Gut Ecosystem.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {822562}, pmid = {35059329}, issn = {2235-2988}, mesh = {Bacteria ; *Bacteriophages ; Ecosystem ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; *Viruses ; }, abstract = {Phages, short for bacteriophages, are viruses that specifically infect bacteria and are the most abundant biological entities on earth found in every explored environment, from the deep sea to the Sahara Desert. Phages are abundant within the human biome and are gaining increasing recognition as potential modulators of the gut ecosystem. For example, they have been connected to gastrointestinal diseases and the treatment efficacy of Fecal Microbiota Transplant. The ability of phages to modulate the human gut microbiome has been attributed to the predation of bacteria or the promotion of bacterial survival by the transfer of genes that enhance bacterial fitness upon infection. In addition, phages have been shown to interact with the human immune system with variable outcomes. Despite the increasing evidence supporting the importance of phages in the gut ecosystem, the extent of their influence on the shape of the gut ecosystem is yet to be fully understood. Here, we discuss evidence for phage modulation of the gut microbiome, postulating that phages are pivotal contributors to the gut ecosystem dynamics. We therefore propose novel research questions to further elucidate the role(s) that they have within the human ecosystem and its impact on our health and well-being.}, }
@article {pmid35058901, year = {2021}, author = {Gruet, C and Muller, D and Moënne-Loccoz, Y}, title = {Significance of the Diversification of Wheat Species for the Assembly and Functioning of the Root-Associated Microbiome.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {782135}, pmid = {35058901}, issn = {1664-302X}, abstract = {Wheat, one of the major crops in the world, has had a complex history that includes genomic hybridizations between Triticum and Aegilops species and several domestication events, which resulted in various wild and domesticated species (especially Triticum aestivum and Triticum durum), many of them still existing today. The large body of information available on wheat-microbe interactions, however, was mostly obtained without considering the importance of wheat evolutionary history and its consequences for wheat microbial ecology. This review addresses our current understanding of the microbiome of wheat root and rhizosphere in light of the information available on pre- and post-domestication wheat history, including differences between wild and domesticated wheats, ancient and modern types of cultivars as well as individual cultivars within a given wheat species. This analysis highlighted two major trends. First, most data deal with the taxonomic diversity rather than the microbial functioning of root-associated wheat microbiota, with so far a bias toward bacteria and mycorrhizal fungi that will progressively attenuate thanks to the inclusion of markers encompassing other micro-eukaryotes and archaea. Second, the comparison of wheat genotypes has mostly focused on the comparison of T. aestivum cultivars, sometimes with little consideration for their particular genetic and physiological traits. It is expected that the development of current sequencing technologies will enable to revisit the diversity of the wheat microbiome. This will provide a renewed opportunity to better understand the significance of wheat evolutionary history, and also to obtain the baseline information needed to develop microbiome-based breeding strategies for sustainable wheat farming.}, }
@article {pmid35058082, year = {2022}, author = {Cunillera-Montcusí, D and Beklioğlu, M and Cañedo-Argüelles, M and Jeppesen, E and Ptacnik, R and Amorim, CA and Arnott, SE and Berger, SA and Brucet, S and Dugan, HA and Gerhard, M and Horváth, Z and Langenheder, S and Nejstgaard, JC and Reinikainen, M and Striebel, M and Urrutia-Cordero, P and Vad, CF and Zadereev, E and Matias, M}, title = {Freshwater salinisation: a research agenda for a saltier world.}, journal = {Trends in ecology &amp; evolution}, volume = {37}, number = {5}, pages = {440-453}, doi = {10.1016/j.tree.2021.12.005}, pmid = {35058082}, issn = {1872-8383}, mesh = {Biodiversity ; Biological Evolution ; Climate Change ; *Ecosystem ; *Fresh Water ; Humans ; }, abstract = {The widespread salinisation of freshwater ecosystems poses a major threat to the biodiversity, functioning, and services that they provide. Human activities promote freshwater salinisation through multiple drivers (e.g., agriculture, resource extraction, urbanisation) that are amplified by climate change. Due to its complexity, we are still far from fully understanding the ecological and evolutionary consequences of freshwater salinisation. Here, we assess current research gaps and present a research agenda to guide future studies. We identified different gaps in taxonomic groups, levels of biological organisation, and geographic regions. We suggest focusing on global- and landscape-scale processes, functional approaches, genetic and molecular levels, and eco-evolutionary dynamics as key future avenues to predict the consequences of freshwater salinisation for ecosystems and human societies.}, }
@article {pmid35056609, year = {2022}, author = {Tsigkrimani, M and Bakogianni, M and Paramithiotis, S and Bosnea, L and Pappa, E and Drosinos, EH and Skandamis, PN and Mataragas, M}, title = {Microbial Ecology of Artisanal Feta and Kefalograviera Cheeses, Part I: Bacterial Community and Its Functional Characteristics with Focus on Lactic Acid Bacteria as Determined by Culture-Dependent Methods and Phenotype Microarrays.}, journal = {Microorganisms}, volume = {10}, number = {1}, pages = {}, pmid = {35056609}, issn = {2076-2607}, support = {T1EDK-02087//European Union and Greek national funds/ ; }, abstract = {Artisanal cheesemaking is still performed using practices and conditions derived from tradition. Feta and Kefalograviera cheeses are very popular in Greece and have met worldwide commercial success. However, there is a lack of knowledge regarding their lactic acid microecosystem composition and species dynamics during ripening. Thus, the aim of the present study was to assess the microecosystem as well as the autochthonous lactic acid microbiota during the ripening of artisanal Feta and Kefalograviera cheeses. For that purpose, raw sheep's milk intended for cheesemaking, as well as Feta and Kefalograviera cheeses during early and late ripening were analyzed, and the lactic acid microbiota was identified using the classical phenotypic approach, clustering with PCR-RAPD and identification with sequencing of the 16S-rRNA gene, as well as with the Biolog GEN III microplates. In addition, the functional properties of the bacterial community were evaluated using the Biolog EcoPlates, which consists of 31 different carbon sources. In general, concordance between the techniques used was achieved. The most frequently isolated species from raw sheep's milk were Enteroroccus faecium, Lactiplantibacillus plantarum and Pediococcus pentosaceus. The microecosystem of Feta cheese in the early ripening stage was dominated by Lp. plantarum and E. faecium, whereas, in late ripening, the microecosystem was dominated by Weissella paramesenteroides. The microecosystem of Kefalograviera cheese in the early ripening stage was dominated by Levilactobacillus brevis and E. faecium, and in late ripening by W. paramesenteroides and E. faecium. Finally, Carbohydrates was the main carbon source category that metabolized by all microbial communities, but the extent of their utilization was varied. Kefalograviera samples, especially at early ripening, demonstrated higher metabolic activity compared to Feta cheese. However, dominating species within microbial communities of the cheese samples were not significantly different.}, }
@article {pmid35052986, year = {2022}, author = {Lammers, A and Lalk, M and Garbeva, P}, title = {Air Ambulance: Antimicrobial Power of Bacterial Volatiles.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {1}, pages = {}, pmid = {35052986}, issn = {2079-6382}, support = {398967434 - SFB/TRR261//Deutsche Forschungsgemeinschaft/ ; W10/2018//Wissenschaftsgemeinschaft Gottfried Wilhelm Leibniz e. V. via Leibniz WissenschaftsCampus - ComBioCat/ ; NNF16OC0021110//Novo Nordisk Foundation/ ; }, abstract = {We are currently facing an antimicrobial resistance crisis, which means that a lot of bacterial pathogens have developed resistance to common antibiotics. Hence, novel and innovative solutions are urgently needed to combat resistant human pathogens. A new source of antimicrobial compounds could be bacterial volatiles. Volatiles are ubiquitous produced, chemically divers and playing essential roles in intra- and interspecies interactions like communication and antimicrobial defense. In the last years, an increasing number of studies showed bioactivities of bacterial volatiles, including antibacterial, antifungal and anti-oomycete activities, indicating bacterial volatiles as an exciting source for novel antimicrobial compounds. In this review we introduce the chemical diversity of bacterial volatiles, their antimicrobial activities and methods for testing this activity. Concluding, we discuss the possibility of using antimicrobial volatiles to antagonize the antimicrobial resistance crisis.}, }
@article {pmid35051349, year = {2022}, author = {Aranda-Díaz, A and Ng, KM and Thomsen, T and Real-Ramírez, I and Dahan, D and Dittmar, S and Gonzalez, CG and Chavez, T and Vasquez, KS and Nguyen, TH and Yu, FB and Higginbottom, SK and Neff, NF and Elias, JE and Sonnenburg, JL and Huang, KC}, title = {Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota.}, journal = {Cell host &amp; microbe}, volume = {30}, number = {2}, pages = {260-272.e5}, pmid = {35051349}, issn = {1934-6069}, support = {R01 DK085025/DK/NIDDK NIH HHS/United States ; RM1 GM135102/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria ; Bacteroides ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Microbiota ; }, abstract = {Efforts to probe the role of the gut microbiota in disease would benefit from a system in which patient-derived bacterial communities can be studied at scale. We addressed this by validating a strategy to propagate phylogenetically complex, diverse, stable, and highly reproducible stool-derived communities in vitro. We generated hundreds of in vitro communities cultured from diverse stool samples in various media; certain media generally preserved inoculum composition, and inocula from different subjects yielded source-specific community compositions. Upon colonization of germ-free mice, community composition was maintained, and the host proteome resembled the host from which the community was derived. Treatment with ciprofloxacin in vivo increased susceptibility to Salmonella invasion in vitro, and the in vitro response to ciprofloxacin was predictive of compositional changes observed in vivo, including the resilience and sensitivity of each Bacteroides species. These findings demonstrate that stool-derived in vitro communities can serve as a powerful system for microbiota research.}, }
@article {pmid35049116, year = {2022}, author = {Quiroga, MV and Valverde, A and Mataloni, G and Casa, V and Stegen, JC and Cowan, D}, title = {The ecological assembly of bacterial communities in Antarctic wetlands varies across levels of phylogenetic resolution.}, journal = {Environmental microbiology}, volume = {24}, number = {8}, pages = {3486-3499}, pmid = {35049116}, issn = {1462-2920}, mesh = {Antarctic Regions ; Bacteria/genetics ; *Ecosystem ; Phylogeny ; *Wetlands ; }, abstract = {As functional traits are conserved at different phylogenetic depths, the ability to detect community assembly processes can be conditional on the phylogenetic resolution; yet most previous work quantifying their influence has focused on a single level of phylogenetic resolution. Here, we have studied the ecological assembly of bacterial communities from an Antarctic wetland complex, applying null models across different levels of phylogenetic resolution (i.e. clustering ASVs into OTUs with decreasing sequence identity thresholds). We found that the relative influence of the community assembly processes varies with phylogenetic resolution. More specifically, selection processes seem to impose stronger influence at finer (100% sequence similarity ASV) than at coarser (99%-97% sequence similarity OTUs) resolution. We identified environmental features related with the ecological processes and propose a conceptual model for the bacterial community assembly in this Antarctic ecosystem. Briefly, eco-evolutionary processes appear to be leading to different but very closely related ASVs in lotic, lentic and terrestrial environments. In all, this study shows that assessing community assembly processes at different phylogenetic resolutions is key to improve our understanding of microbial ecology. More importantly, a failure to detect selection processes at coarser phylogenetic resolution does not imply the absence of such processes at finer resolutions.}, }
@article {pmid35048168, year = {2023}, author = {Boscaro, V and Manassero, V and Keeling, PJ and Vannini, C}, title = {Single-cell Microbiomics Unveils Distribution and Patterns of Microbial Symbioses in the Natural Environment.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {307-316}, pmid = {35048168}, issn = {1432-184X}, mesh = {Humans ; Phylogeny ; *Ciliophora/microbiology ; Bacteria/genetics ; Environment ; Symbiosis ; Rickettsiales ; *Euplotes/microbiology ; *Burkholderiaceae ; }, abstract = {Protist-bacteria associations are extremely common. Among them, those involving ciliates of the genus Euplotes are emerging as models for symbioses between prokaryotes and eukaryotes, and a great deal of information is available from cultured representatives of this system. Even so, as for most known microbial symbioses, data on natural populations is lacking, and their ecology remains largely unexplored; how well lab cultures represent actual diversity is untested. Here, we describe a survey on natural populations of Euplotes based on a single-cell microbiomic approach, focusing on taxa that include known endosymbionts of this ciliate. The results reveal an unexpected variability in symbiotic communities, with individual hosts of the same population harboring different sets of bacterial endosymbionts. Co-occurring Euplotes individuals of the same population can even have different essential symbionts, Polynucleobacter and "Candidatus Protistobacter," which might suggest that replacement events could be more frequent in nature than previously hypothesized. Accessory symbionts are even more variable: some showed a strong affinity for one host species, some for a sampling site, and two ("Candidatus Cyrtobacter" and "Candidatus Anadelfobacter") displayed an unusual pattern of competitive exclusion. These data represent the first insight into the prevalence and patterns of bacterial symbionts in natural populations of free-living protists.}, }
@article {pmid35044804, year = {2022}, author = {Chen, MY and Alexiev, A and McKenzie, VJ}, title = {Bacterial Biofilm Thickness and Fungal Inhibitory Bacterial Richness Both Prevent Establishment of the Amphibian Fungal Pathogen Batrachochytrium dendrobatidis.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {5}, pages = {e0160421}, pmid = {35044804}, issn = {1098-5336}, mesh = {Amphibians/genetics/microbiology ; Animals ; Bacteria ; Batrachochytrium ; Biofilms ; *Chytridiomycota/genetics ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Skin/microbiology ; }, abstract = {Host-associated microbial biofilms can provide protection against pathogen establishment. In many host-microbe symbioses (including, but not limited to humans, plants, insects, and amphibians), there is a correlation between host-associated microbial diversity and pathogen infection risk. Diversity may prevent infection by pathogens through sampling effects and niche complementarity, but an alternative hypothesis may be that microbial biomass is confounded with diversity and that host-associated biofilms are deterring pathogen establishment through space preemption. In this study, we use the amphibian system as a model for host-microbe-pathogen interactions to ask two questions: (i) is bacterial richness confounded with biofilm thickness or cell density, and (ii) to what extent do biofilm thickness, cell density, and bacterial richness each deter the establishment of the amphibian fungal pathogen Batrachochytrium dendrobatidis? To answer these questions, we built a custom biofilm microcosm that mimics the host-environment interface by allowing nutrients to diffuse out of a fine-pore biofilm scaffolding. This created a competitive environment in which bacteria and the fungal pathogen compete for colonization space. We then challenged bacterial biofilms ranging in community richness, biofilm thickness, bacterial cell density, and B. dendrobatidis (also known as Bd)-inhibitory metabolite production with live B. dendrobatidis zoospores to determine how B. dendrobatidis establishment success on membranes varies. We found that biofilm thickness and B. dendrobatidis-inhibitory isolate richness work in complement to reduce B. dendrobatidis establishment success. This work underscores that physical aspects of biofilm communities can play a large role in pathogen inhibition, and in many studies, these traits are not studied. IMPORTANCE Our finding highlights the fact that diversity, as measured through 16S rRNA gene sequencing, may obscure the true mechanisms behind microbe-mediated pathogen defense and that physical space occupation by biofilm-forming symbionts may significantly contribute to pathogen protection. These findings have implications across a wide range of host-microbe systems since 16S rRNA gene sequencing is a standard tool used across many microbial systems. Further, our results are potentially relevant to many host-pathogen systems since host-associated bacterial biofilms are ubiquitous.}, }
@article {pmid35043221, year = {2023}, author = {Kanisan, DP and Quek, ZBR and Oh, RM and Afiq-Rosli, L and Lee, JN and Huang, D and Wainwright, BJ}, title = {Diversity and Distribution of Microbial Communities Associated with Reef Corals of the Malay Peninsula.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {37-48}, pmid = {35043221}, issn = {1432-184X}, mesh = {Animals ; *Anthozoa/microbiology ; Malaysia ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria/genetics ; Coral Reefs ; }, abstract = {Coral-associated bacteria play critical roles in the regulation of coral health and function. Environmental perturbations that alter the bacterial community structure can render the coral holobiont more susceptible and less resilient to disease. Understanding the natural variation of the coral microbiome across space and host species provides a baseline that can be used to distinguish shifts in community structure. Using a 16S rRNA gene metabarcoding approach, this study examines bacterial community structure across three scleractinian coral hosts. Our results show that corals of three regions-eastern and western Peninsular Malaysia and Singapore-host distinct bacterial communities; despite these differences, we were able to identify a core microbiome shared across all three species. This core microbiome was also present in samples previously collected in Thailand, suggesting that these core microbes play an important role in promoting and maintaining host health. For example, several have been identified as dimethylsulfoniopropionate (DMSP) metabolizers that have roles in sulfur cycling and the suppression of bacterial pathogens. Pachyseris speciosa has the most variable microbiome, followed by Porites lutea, with the composition of the Diploastrea heliopora microbiome the least variable throughout all locations. Microbial taxa associated with each region or site are likely shaped by local environmental conditions. Taken together, host identity is a major driver of differences in microbial community structure, while environmental heterogeneity shapes communities at finer scales.}, }
@article {pmid35043220, year = {2023}, author = {Song, B and Li, Y and Yang, L and Shi, H and Li, L and Bai, W and Zhao, Y}, title = {Soil Acidification Under Long-Term N Addition Decreases the Diversity of Soil Bacteria and Fungi and Changes Their Community Composition in a Semiarid Grassland.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {221-231}, pmid = {35043220}, issn = {1432-184X}, support = {31800403//National Natural Science Foundation of China/ ; 41977009//National Natural Science Foundation of China/ ; 41977039//National Natural Science Foundation of China/ ; ZR2020QD115//Natural Science Foundation of Shandong Province/ ; }, mesh = {*Soil/chemistry ; Grassland ; Soil Microbiology ; Bacteria/genetics ; *Microbiota ; Fungi/genetics ; Hydrogen-Ion Concentration ; }, abstract = {Soil microorganisms play key roles in terrestrial biogeochemical cycles and ecosystem functions. However, few studies address how long-term nitrogen (N) addition gradients impact soil bacterial and fungal diversity and community composition simultaneously. Here, we investigated soil bacterial and fungal diversity and community composition based on a long-term (17 years) N addition gradient experiment (six levels: 0, 2, 4, 8, 16, 32 gN m[-2] year[-1]) in temperate grassland, using the high-throughput Illumina MiSeq sequencing. Results showed that both soil bacterial and fungal alpha diversity responded nonlinearly to the N input gradient and reduced drastically when the N addition rate reached 32 g N m[-2] year[-1]. The relative abundance of soil bacterial phyla Proteobacteria increased and Acidobacteria decreased significantly with increasing N level. In addition, the relative abundance of bacterial functional groups associated with aerobic ammonia oxidation, aerobic nitrite oxidation, nitrification, respiration of sulfate and sulfur compounds, and chitinolysis significantly decreased under the highest N addition treatment. For soil fungi, the relative abundance of Ascomycota increased linearly along the N enrichment gradient. These results suggest that changes in soil microbial community composition under elevated N do not always support the copiotrophic-oligotrophic hypothesis, and some certain functional bacteria would not simply be controlled by soil nutrients. Further analysis illustrated that reduced soil pH under N addition was the main factor driving variations in soil microbial diversity and community structure in this grassland. Our findings highlight the consistently nonlinear responses of soil bacterial and fungal diversity to increasing N input and the significant effects of soil acidification on soil microbial communities, which can be helpful for the prediction of underground ecosystem processes in light of future rising N deposition.}, }
@article {pmid35042853, year = {2022}, author = {Kauffman, KM and Chang, WK and Brown, JM and Hussain, FA and Yang, J and Polz, MF and Kelly, L}, title = {Resolving the structure of phage-bacteria interactions in the context of natural diversity.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {372}, pmid = {35042853}, issn = {2041-1723}, mesh = {Bacteria/*genetics/*virology ; Bacteriophages/*genetics ; *Genetic Variation ; Genome, Viral ; Host Specificity ; Models, Biological ; Nucleotides/metabolism ; Phylogeny ; Recombinases/metabolism ; Recombination, Genetic/genetics ; Sequence Analysis, DNA ; Vibrio/virology ; }, abstract = {Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in the wild remain poorly resolved. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain estimates of strain-level phage predator loads, and use all-by-all host range assays to discover how phage and host genomic diversity shape interactions. We show that lytic interactions in environmental interaction networks (as observed in agar overlay) are sparse-with phage predator loads being low for most bacterial strains, and phages being host-strain-specific. Paradoxically, we also find that although overlap in killing is generally rare between tailed phages, recombination is common. Together, these results suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it is important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on lytic host range.}, }
@article {pmid35042205, year = {2022}, author = {Taylor, D and Verdon, N and Lomax, P and Allen, RJ and Titmuss, S}, title = {Tracking the stochastic growth of bacterial populations in microfluidic droplets.}, journal = {Physical biology}, volume = {19}, number = {2}, pages = {026003}, pmid = {35042205}, issn = {1478-3975}, support = {682237/ERC_/European Research Council/International ; }, mesh = {*Bacteria ; *Microfluidics/methods ; }, abstract = {Bacterial growth in microfluidic droplets is relevant in biotechnology, in microbial ecology, and in understanding stochastic population dynamics in small populations. However, it has proved challenging to automate measurement of absolute bacterial numbers within droplets, forcing the use of proxy measures for population size. Here we present a microfluidic device and imaging protocol that allows high-resolution imaging of thousands of droplets, such that individual bacteria stay in the focal plane and can be counted automatically. Using this approach, we track the stochastic growth of hundreds of replicateEscherichia colipopulations within droplets. We find that, for early times, the statistics of the growth trajectories obey the predictions of the Bellman-Harris model, in which there is no inheritance of division time. Our approach should allow further testing of models for stochastic growth dynamics, as well as contributing to broader applications of droplet-based bacterial culture.}, }
@article {pmid35041070, year = {2023}, author = {Runge, P and Ventura, F and Kemen, E and Stam, R}, title = {Distinct Phyllosphere Microbiome of Wild Tomato Species in Central Peru upon Dysbiosis.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {168-183}, pmid = {35041070}, issn = {1432-184X}, support = {STA1547/2//german science foundation/ ; ERC-2018-COG 820124/ERC_/European Research Council/International ; ERC-2018-COG 820124/ERC_/European Research Council/International ; }, mesh = {*Solanum lycopersicum ; Dysbiosis ; Peru ; *Microbiota ; Plant Leaves/microbiology ; Plants/microbiology ; *Solanum ; }, abstract = {Plants are colonized by myriads of microbes across kingdoms, which affect host development, fitness, and reproduction. Hence, plant microbiomes have been explored across a broad range of host species, including model organisms, crops, and trees under controlled and natural conditions. Tomato is one of the world's most important vegetable crops; however, little is known about the microbiota of wild tomato species. To obtain insights into the tomato microbiota occurring in natural environments, we sampled epiphytic microbes from leaves of four tomato species, Solanum habrochaites, S. corneliomulleri, S. peruvianum, and S. pimpinellifolium, from two geographical locations within the Lima region of Peru over 2 consecutive years. Here, a high-throughput sequencing approach was applied to investigate microbial compositions including bacteria, fungi, and eukaryotes across tomato species and geographical locations. The phyllosphere microbiome composition varies between hosts and location. Yet, we identified persistent microbes across tomato species that form the tomato microbial core community. In addition, we phenotypically defined healthy and dysbiotic samples and performed a downstream analysis to reveal the impact on microbial community structures. To do so, we compared microbial diversities, unique OTUs, relative abundances of core taxa, and microbial hub taxa, as well as co-occurrence network characteristics in healthy and dysbiotic tomato leaves and found that dysbiosis affects the phyllosphere microbial composition in a host species-dependent manner. Yet, overall, the present data suggests an enrichment of plant-promoting microbial taxa in healthy leaves, whereas numerous microbial taxa containing plant pathogens occurred in dysbiotic leaves.Concluding, we identify the core phyllosphere microbiome of wild tomato species, and show that the overall phyllosphere microbiome can be impacted by sampling time point, geographical location, host genotype, and plant health. Future studies in these components will help understand the microbial contribution to plant health in natural systems and can be of use in cultivated tomatoes.}, }
@article {pmid35040702, year = {2022}, author = {Dragone, NB and Henley, JB and Holland-Moritz, H and Diaz, M and Hogg, ID and Lyons, WB and Wall, DH and Adams, BJ and Fierer, N}, title = {Elevational Constraints on the Composition and Genomic Attributes of Microbial Communities in Antarctic Soils.}, journal = {mSystems}, volume = {7}, number = {1}, pages = {e0133021}, pmid = {35040702}, issn = {2379-5077}, mesh = {*Soil/chemistry ; Antarctic Regions ; Soil Microbiology ; Bacteria ; Archaea ; *Microbiota ; Metagenomics/methods ; }, abstract = {The inland soils found on the Antarctic continent represent one of the more challenging environments for microbial life on Earth. Nevertheless, Antarctic soils harbor unique bacterial and archaeal (prokaryotic) communities able to cope with extremely cold and dry conditions. These communities are not homogeneous, and the taxonomic composition and functional capabilities (genomic attributes) of these communities across environmental gradients remain largely undetermined. We analyzed the prokaryotic communities in soil samples collected from across the Shackleton Glacier region of Antarctica by coupling quantitative PCR, marker gene amplicon sequencing, and shotgun metagenomic sequencing. We found that elevation was the dominant factor explaining differences in the structures of the soil prokaryotic communities, with the drier and saltier soils found at higher elevations harboring less diverse communities and unique assemblages of cooccurring taxa. The higher-elevation soil communities also had lower maximum potential growth rates (as inferred from metagenome-based estimates of codon usage bias) and an overrepresentation of genes associated with trace gas metabolism. Together, these results highlight the utility of assessing community shifts across pronounced environmental gradients to improve our understanding of the microbial diversity found in Antarctic soils and the strategies used by soil microbes to persist at the limits of habitability. IMPORTANCE Antarctic soils represent an ideal system to study how environmental properties shape the taxonomic and functional diversity of microbial communities given the relatively low diversity of Antarctic soil microbial communities and the pronounced environmental gradients that occur across soils located in reasonable proximity to one another. Moreover, the challenging environmental conditions typical of most Antarctic soils present an opportunity to investigate the traits that allow soil microbes to persist in some of the most inhospitable habitats on Earth. We used cultivation-independent methods to study the bacterial and archaeal communities found in soil samples collected from across the Shackleton Glacier region of the Transantarctic Mountains. We show that those environmental characteristics associated with elevation have the greatest impact on the structure of these microbial communities, with the colder, drier, and saltier soils found at higher elevations sustaining less diverse communities that were distinct from those in more hospitable soils with respect to their composition, genomic attributes, and overall life-history strategies. Notably, the harsher conditions found in higher-elevation soils likely select for taxa with lower maximum potential growth rates and an increased reliance on trace gas metabolism to support growth.}, }
@article {pmid35040699, year = {2022}, author = {David, MM and Tataru, C and Pope, Q and Baker, LJ and English, MK and Epstein, HE and Hammer, A and Kent, M and Sieler, MJ and Mueller, RS and Sharpton, TJ and Tomas, F and Vega Thurber, R and Fern, XZ}, title = {Revealing General Patterns of Microbiomes That Transcend Systems: Potential and Challenges of Deep Transfer Learning.}, journal = {mSystems}, volume = {7}, number = {1}, pages = {e0105821}, pmid = {35040699}, issn = {2379-5077}, mesh = {*Microbiota/physiology ; Machine Learning ; }, abstract = {A growing body of research has established that the microbiome can mediate the dynamics and functional capacities of diverse biological systems. Yet, we understand little about what governs the response of these microbial communities to host or environmental changes. Most efforts to model microbiomes focus on defining the relationships between the microbiome, host, and environmental features within a specified study system and therefore fail to capture those that may be evident across multiple systems. In parallel with these developments in microbiome research, computer scientists have developed a variety of machine learning tools that can identify subtle, but informative, patterns from complex data. Here, we recommend using deep transfer learning to resolve microbiome patterns that transcend study systems. By leveraging diverse public data sets in an unsupervised way, such models can learn contextual relationships between features and build on those patterns to perform subsequent tasks (e.g., classification) within specific biological contexts.}, }
@article {pmid35039906, year = {2023}, author = {Liu, H and Lin, G and Gao, D and Chen, H and He, M and Lu, J}, title = {Geographic Scale Influences the Interactivities Between Determinism and Stochasticity in the Assembly of Sedimentary Microbial Communities on the South China Sea Shelf.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {121-136}, pmid = {35039906}, issn = {1432-184X}, support = {91858208//National Natural Science Foundation of China/ ; 311020005//Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 2019M663209//China Postdoctoral Science Foundation/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Carbon ; China ; }, abstract = {Determinism and stochasticity in microbial community composition decisions have attracted wide attention. However, there is no consensus on their interrelationships and relative importance, and the mechanism controlling the interaction between the two ecological processes remains to be revealed. The interaction of the two ecological processes on the continental shelf of the South China Sea was studied by performing 16S rRNA gene amplicon sequencing on 90 sediments at multiple depths in five sites. Three nearshore sites have higher microbial diversity than those two close to the shelf margin. Different microbial composition was observed between sites and microbial composition of nearshore sites was positively correlated with total nitrogen, total sulfur, total organic carbon, and dissolved oxygen, while that of offshore was positively correlated with total carbon, salinity, and photosynthetically active radiation. The null model test showed that the community composition among layers of the same site and between nearby sites was mainly dominated by the homogeneous selection, while that between distant sites was mainly affected by dispersal limitation, which indicates that geographic scale influences the interactivities of determinism and stochasticity. Our research indicates that the balance of these two ecological processes along the geographic scale is mainly determined by the dispersal ability of microbes and environmental heterogeneity between areas. The study provides new insights into how deterministic and stochastic processes shape microbial community composition on the continental shelf.}, }
@article {pmid35039905, year = {2023}, author = {Silva-Sanzana, C and Gangas, MV and Zavala, D and Blanco-Herrera, F}, title = {A Recipe for Success: Three Key Strategies Used by Aphids and Pseudomonas syringae to Colonize the Phyllosphere.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {1-8}, pmid = {35039905}, issn = {1432-184X}, support = {1210320//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; 3200902//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; PIA/BASAL FB0002//ANID/ ; Programa Iniciativa Cient&#xed;fica Milenio - ICN17_022//ANID/ ; 2021/21211568//ANID/Doctorado Nacional/ ; }, mesh = {Animals ; *Pseudomonas syringae/genetics ; *Aphids ; Phylogeny ; Plants/metabolism ; Plant Diseases ; Bacterial Proteins/genetics ; }, abstract = {Aphids and Pseudomonas syringae are a permanent challenge for agriculture, causing severe losses to the crop industry worldwide. Despite the obvious phylogenetic distance between them, both have become predominant colonizers of the plant kingdom. In this study, we reviewed three key steps of spread and colonization that aphids and P. syringae have mastered to successfully colonize the phyllosphere. These steps involve (i) plant-to-plant movement for locating new nutritional sources, (ii) disruption and modification of the apoplast to facilitate nutrient acquisition, and (iii) suppression of host defenses through effector proteins. In addition, we will provide insights about the direct interaction between aphids and P. syringae and how this yet underrated phenomenon could bring new ecological implications for both organisms beyond their pathogenicity.}, }
@article {pmid35037090, year = {2023}, author = {Tang, G and Xu, L and Wang, X and Zhang, J}, title = {Effects of Leaf Morphological and Chemical Properties on the Population Sizes of Epiphytes.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {157-167}, pmid = {35037090}, issn = {1432-184X}, mesh = {Population Density ; *Plant Leaves/microbiology ; *Carbohydrates/analysis ; Medicago sativa ; Zea mays ; Sugars/analysis ; }, abstract = {To explore the main factors affecting the distribution of microbes on leaf surfaces, the relationship between population sizes of epiphytes and the morphological structure and main physical and chemical properties of leaves from stylo (Stylosanthes guianensis), alfalfa (Medicago sativa), maize (Zea mays), and cocksfoot (Dactylis glomerata) were investigated. The research results showed that the contents of soluble sugar and total phenolics on the leaf surfaces were positively correlated with those in the leaf tissues (P < 0.001). The leaves with high wax content had better moisture retention capacity. The content of soluble sugar on the leaf surfaces was positively correlated with population sizes of lactic acid bacteria (LAB), aerobic bacteria, yeasts, and molds (P < 0.001). Likewise, a positive correlation was found between the content of inorganic phosphorus on the leaf surfaces and population sizes of LAB and aerobic bacteria. The total amount of wax on leaf surfaces was negatively related to population sizes of microbes, especially aerobic bacteria (P < 0.01) and molds (P < 0.001). On the contrary, the presence of trichomes provides a shelter for epiphytes and was positively correlated with population sizes of epiphytes at different degrees of significance. In conclusion, population sizes of epiphytes on the leaf surfaces were not only affected by chemical properties, but also by morphological traits of leaves.}, }
@article {pmid35034142, year = {2023}, author = {Tran, HT and Nguyen, HM and Nguyen, TM and Chang, C and Huang, WL and Huang, CL and Chiang, TY}, title = {Microbial Communities Along 2,3,7,8-tetrachlorodibenzodioxin Concentration Gradient in Soils Polluted with Agent Orange Based on Metagenomic Analyses.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {197-208}, pmid = {35034142}, issn = {1432-184X}, support = {105-2622-B-006 -008 -CC2//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Agent Orange ; Soil ; *Polychlorinated Dibenzodioxins/analysis ; *Dioxins ; Bacteria/genetics ; *Microbiota ; Acidobacteria/genetics ; Firmicutes ; Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The 2,3,7,8-tetrachlorodibenzodioxin (TCDD), a contaminant in Agent Orange released during the US-Vietnam War, led to a severe environmental crisis. Approximately, 50 years have passed since the end of this war, and vegetation has gradually recovered from the pollution. Soil bacterial communities were investigated by 16S metagenomics in habitats with different vegetation physiognomies in Central Vietnam, namely, forests (S0), barren land (S1), grassland (S2), and developing woods (S3). Vegetation complexity was negatively associated with TCDD concentrations, revealing the reasoning behind the utilization of vegetation physiognomy as an indicator for ecological succession along the gradient of pollutants. Stark changes in bacterial composition were detected between S0 and S1, with an increase in Firmicutes and a decrease in Acidobacteria and Bacteroidetes. Notably, dioxin digesters Arthrobacter, Rhodococcus, Comamonadaceae, and Bacialles were detected in highly contaminated soil (S1). Along the TCDD gradients, following the dioxin decay from S1 to S2, the abundance of Firmicutes and Actinobacteria decreased, while that of Acidobacteria increased; slight changes occurred at the phylum level from S2 to S3. Although metagenomics analyses disclosed a trend toward bacterial communities before contamination with vegetation recovery, non-metric multidimensional scaling analysis unveiled a new trajectory deviating from the native state. Recovery of the bacterial community may have been hindered, as indicated by lower bacterial diversity in S3 compared to S0 due to a significant loss of bacterial taxa and recruitment of fewer colonizers. The results indicate that dioxins significantly altered the soil microbiomes into a state of disorder with a deviating trajectory in restoration.}, }
@article {pmid35034141, year = {2023}, author = {Lin, Y and Ye, G and Hu, HW and Yang, P and Wan, S and Feng, M and He, ZY and He, JZ}, title = {Plant Species-Driven Distribution of Individual Clades of Comammox Nitrospira in a Subtropical Estuarine Wetland.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {209-220}, pmid = {35034141}, issn = {1432-184X}, support = {41930756//National Natural Science Foundation of China/ ; 42077041//National Natural Science Foundation of China/ ; 2021J011038//Natural Science Foundation of Fujian Province/ ; }, mesh = {*Wetlands ; *Nitrification ; Oxidation-Reduction ; Bacteria ; Ammonia ; Soil/chemistry ; Poaceae ; }, abstract = {Plant species play a crucial role in mediating the activity and community structure of soil microbiomes through differential inputs of litter and rhizosphere exudates, but we have a poor understanding of how plant species influence comammox Nitrospira, a newly discovered ammonia oxidizer with pivotal functionality. Here, we investigate the abundance, diversity, and community structure of comammox Nitrospira underneath five plant species and a bare tidal flat at three soil depths in a subtropical estuarine wetland. Plant species played a critical role in driving the distribution of individual clades of comammox Nitrospira, explaining 59.3% of the variation of community structure. Clade A.1 was widely detected in all samples, while clades A.2.1, A.2.2, A.3 and B showed plant species-dependent distribution patterns. Compared with the native species Cyperus malaccensis, the invasion of Spartina alterniflora increased the network complexity and changed the community structure of comammox Nitrospira, while the invasive effects from Kandelia obovata and Phragmites australis were relatively weak. Soil depths significantly influenced the community structure of comammox Nitrospira, but the effect was much weaker than that from plant species. Altogether, our results highlight the previously unrecognized critical role of plant species in driving the distribution of comammox Nitrospira in a subtropical estuarine wetland.}, }
@article {pmid35033929, year = {2022}, author = {Sakarika, M and Ganigué, R and Rabaey, K}, title = {Methylotrophs: from C1 compounds to food.}, journal = {Current opinion in biotechnology}, volume = {75}, number = {}, pages = {102685}, doi = {10.1016/j.copbio.2022.102685}, pmid = {35033929}, issn = {1879-0429}, mesh = {Amino Acids/metabolism ; Bacteria/metabolism ; Carbon/metabolism ; Humans ; *Metabolic Engineering ; Methane/metabolism ; *Methanol/metabolism ; }, abstract = {Microbial protein (MP) is back on the table after decades of slumbering interest. One-carbon (C1) substrates are attractive for MP production due to their efficient production from CO2 and renewable electricity, linking carbon capture to food while circumventing agriculture. Here we compared all reported combinations of C1 (formate/methanol/methane) and microorganisms (bacteria/yeasts) in terms of engineering and biomass quality parameters, focusing on the amino acid match with human requirements. This meta-analysis based on >100 studies suggests that methanol is the most promising C1, and methanol-grown microorganisms seem most nutritional with bacteria and yeasts having different merits. More sustainable MP could be produced if metabolic engineering tools yielding microorganisms with more efficient C1 assimilation pathways and steered amino acid profiles are deployed.}, }
@article {pmid35033479, year = {2022}, author = {Acquier, M and De Précigout, V and Delmas, Y and Dubois, V and M'Zali, F and Zabala, A and De-La-Faille, R and Rubin, S and Cazanave, C and Puges, M and Combe, C and Kaminski, H}, title = {[Diagnosis and treatment of catheter-related bloodstream infection in hemodialysis: 10 years later].}, journal = {Nephrologie &amp; therapeutique}, volume = {18}, number = {2}, pages = {80-88}, doi = {10.1016/j.nephro.2021.08.010}, pmid = {35033479}, issn = {1872-9177}, mesh = {Anti-Bacterial Agents/therapeutic use ; *Bacteremia/diagnosis/drug therapy/epidemiology ; *Catheter-Related Infections/diagnosis/drug therapy/epidemiology ; *Catheterization, Central Venous/adverse effects ; *Central Venous Catheters/adverse effects ; Humans ; *Methicillin-Resistant Staphylococcus aureus ; Renal Dialysis/adverse effects ; }, abstract = {Patients in hemodialysis on central venous catheter as vascular access are at risk of infections. Catheter-related bloodstream infection is one of the most serious catheter-complications in hemodialysis patients. Its clinical and microbiological diagnosis is challenging. The implementation of empiric antibiotic therapy is based on old recommendations proposing the combination of a molecule targeting methicillin-resistant Staphylococcus aureus and a betalactamin active on P. aeruginosa, and also adapting this probabilistic treatment by carrying out a microbiological register on a local scale, which is rarely done. In our hemodialysis center at Bordeaux University Hospital, an analysis of the microorganisms causing all catheter-related bloodstream infection over the period 2018-2020 enabled us to propose, in agreement with the infectious disease specialists, an adapted probabilistic antibiotic therapy protocol. This approach allowed us to observe a low incidence of meticillinoresistance of Staphylococcus. For catheters inserted more than 6 months ago, we observed no Staphylococcus, no multi-resistant Pseudomonas, and only 2% of Enterobacteria resistant to cephalosporins. A frequent updating of the microbiological epidemiology of catheter-related bloodstream infection, in partnership with the infectious diseases team in each hemodialysis center, allowing an adaptation of the probabilistic antibiotic therapy, and seems to have a good feasibility. This strategy might favor the preservation of microbial ecology on an individual and collective scale in maintenance hemodialysis patients.}, }
@article {pmid35031403, year = {2022}, author = {Wang, W and Wang, H and Cheng, X and Wu, M and Song, Y and Liu, X and Loni, PC and Tuovinen, OH}, title = {Different responses of bacteria and fungi to environmental variables and corresponding community assembly in Sb-contaminated soil.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {298}, number = {}, pages = {118812}, doi = {10.1016/j.envpol.2022.118812}, pmid = {35031403}, issn = {1873-6424}, mesh = {Bacteria/genetics ; Biodegradation, Environmental ; Fungi ; RNA, Ribosomal, 16S ; Soil ; *Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {Bacterial communities in antimony (Sb) polluted soils have been well addressed, whereas the important players fungal communities are far less studied to date. Here, we report different responses of bacterial and fungal communities to Sb contamination and the ecological processes controlling their community assembly. Soil samples in the Xikuangshan mining area were collected and subjected to high through-put sequencing of 16S rRNA and ITS1 to investigate bacterial and fungal communities, respectively, along an Sb gradient. Sb speciation in the soil samples and other physicochemical parameters were analyzed as well. Bacterial communities were dominated by Deltaproteobacteria in the soil with highest Sb concentration, whereas Chloroflexi were dominant in the soil with lowest Sb concentration. Fungal communities in high-Sb soils were predominated by unclassified Fungi, whilst Leotiomycetes were dominant in low-Sb soil samples. Multivariate analysis indicated that Sb, pH and soil texture were the main drivers to strongly impact microbial communities. We further identified Sb-resistant microbial groups via correlation analysis. In total, 18 bacterial amplicon sequence variants (ASVs) were found to potentially involve in biogeochemical cycles such as Sb oxidation, sulfur oxidation or nitrate reduction, whereas 12 fungal ASVs were singled out for potential heavy metal resistance and plant growth promotion. Community assembly analysis revealed that variable selection contributed 100% to bacterial community assembly under acidic or high Sb concentration conditions, whereas homogeneous selection dominated fungal community assembly with a contribution over 78.9%. The community assembly of Sb-resistant microorganisms was mainly controlled by stochastic process. The results offer new insights into microbial ecology in Sb-contaminated soils, especially on the different responses of microbial communities under identical environmental stress and the different ecological processes underlining bacterial and fungal community assembly.}, }
@article {pmid35030221, year = {2022}, author = {Lim, K and Rolston, M and Barnum, S and Wademan, C and Leverenz, H}, title = {A biogeographic 16S rRNA survey of bacterial communities of ureolytic biomineralization from California public restrooms.}, journal = {PloS one}, volume = {17}, number = {1}, pages = {e0262425}, pmid = {35030221}, issn = {1932-6203}, mesh = {Bacteria/genetics ; Bathroom Equipment/*microbiology ; Biomineralization/genetics ; California/epidemiology ; DNA, Bacterial/genetics ; Drainage, Sanitary/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Toilet Facilities ; }, abstract = {In this study, we examined the total bacterial community associated with ureolytic biomineralization from urine drainage systems. Biomineral samples were obtained from 11 California Department of Transportation public restrooms fitted with waterless, low-flow, or conventional urinals in 2019. Following high throughput 16S rRNA Illumina sequences processed using the DADA2 pipeline, the microbial diversity assessment of 169 biomineral and urine samples resulted in 3,869 reference sequences aggregated as 598 operational taxonomic units (OTUs). Using PERMANOVA testing, we found strong, significant differences between biomineral samples grouped by intrasystem sampling location and urinal type. Biomineral microbial community profiles and alpha diversities differed significantly when controlling for sampling season. Observational statistics revealed that biomineral samples obtained from waterless urinals contained the largest ureC/16S gene copy ratios and were the least diverse urinal type in terms of Shannon indices. Waterless urinal biomineral samples were largely dominated by the Bacilli class (86.1%) compared to low-flow (41.3%) and conventional samples (20.5%), and had the fewest genera that account for less than 2.5% relative abundance per OTU. Our findings are useful for future microbial ecology studies of urine source-separation technologies, as we have established a comparative basis using a large sample size and study area.}, }
@article {pmid35028982, year = {2022}, author = {Bizic, M and Ionescu, D and Karnatak, R and Musseau, CL and Onandia, G and Berger, SA and Nejstgaard, JC and Lischeid, G and Gessner, MO and Wollrab, S and Grossart, HP}, title = {Land-use type temporarily affects active pond community structure but not gene expression patterns.}, journal = {Molecular ecology}, volume = {31}, number = {6}, pages = {1716-1734}, doi = {10.1111/mec.16348}, pmid = {35028982}, issn = {1365-294X}, mesh = {Agriculture/methods ; Archaea/genetics ; Biodiversity ; *Ecosystem ; *Ponds ; }, abstract = {Changes in land use and agricultural intensification threaten biodiversity and ecosystem functioning of small water bodies. We studied 67 kettle holes (KH) in an agricultural landscape in northeastern Germany using landscape-scale metatranscriptomics to understand the responses of active bacterial, archaeal and eukaryotic communities to land-use type. These KH are proxies of the millions of small standing water bodies of glacial origin spread across the northern hemisphere. Like other landscapes in Europe, the study area has been used for intensive agriculture since the 1950s. In contrast to a parallel environmental DNA study that suggests the homogenization of biodiversity across KH, conceivably resulting from long-lasting intensive agriculture, land-use type affected the structure of the active KH communities during spring crop fertilization, but not a month later. This effect was more pronounced for eukaryotes than for bacteria. In contrast, gene expression patterns did not differ between months or across land-use types, suggesting a high degree of functional redundancy across the KH communities. Variability in gene expression was best explained by active bacterial and eukaryotic community structures, suggesting that these changes in functioning are primarily driven by interactions between organisms. Our results indicate that influences of the surrounding landscape result in temporary changes in the activity of different community members. Thus, even in KH where biodiversity has been homogenized, communities continue to respond to land management. This potential needs to be considered when developing sustainable management options for restoration purposes and for successful mitigation of further biodiversity loss in agricultural landscapes.}, }
@article {pmid35028709, year = {2023}, author = {Guzzon, R and Bertoldi, D and Roman, T and Zanzotti, R and Franciosi, E}, title = {Spatial and Seasonal Structure of Bacterial Communities Within Alpine Vineyards: Trentino as a Case Study.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {108-120}, pmid = {35028709}, issn = {1432-184X}, mesh = {Humans ; Farms ; Seasons ; *Vitis/microbiology ; Bacteria ; *Microbiota ; }, abstract = {Bacteria have a fundamental role in determining the fitness of grapevine, the composition of grapes and the features of wines but at present, little information is available. In this work, the bacteria colonizing the different portions of grapevine (bark, leaves and grapes) were explored in the vineyards of the Alpine region of Trentino, considering the impact of different environmental and agronomical variables. The vineyards included in the work were selected based on their different geographical positions (altitude) and grapevine training systems in order to explore the whole variability of the grapevine ecosystem. Moreover, the surface amount of copper was measured on grapes and leaves during the vegetative growth. Bacterial analysis, performed using plate counts and Illumina MiSeq, revealed an increase in the concentration of grape bacteria proportional to the progress of the ripening stage. Conversely, the peak of bacterial concentration onto leaf and bark samples occurred in August, probably due to the more favourable environmental conditions. In bark samples, the bacterial microbiota reached the 7 log CFU/cm[2], while 6 log UFC/g were measured in grape samples. A remarkable biodiversity was observed, with 13 phyla, 35 classes, 55 orders, 78 families and 95 genera of bacteria present. The presence of some taxa (Alphaproteobacteria, Desulfovibrionaceae, Clostriadiales, Oscillospira, Lachnospiraceae and Bacteroidales) was ubiquitous in all vineyards, but differences in terms of relative abundance were observed according to the vegetative stage, altitude of the vineyard and training system. Bacteria having oenological implication (Lactobacillus, Pediococcus and Oenococcus) were detected in grape samples collected in August, in low abundance. The data revealed a complex bacterial ecosystem inside the vineyard that, while maintaining common traits, evolves according to environmental and agronomical inputs. This study contributes to define the role of bacteria in the complex balance established in each vineyard between human actions and agricultural environment, known as terroir.}, }
@article {pmid35026246, year = {2022}, author = {Gregson, BH and Bani, A and Steinfield, L and Holt, D and Whitby, C}, title = {Anaerobes and methanogens dominate the microbial communities in water harvesting ponds used by Kenyan rural smallholder farmers.}, journal = {The Science of the total environment}, volume = {819}, number = {}, pages = {153040}, doi = {10.1016/j.scitotenv.2022.153040}, pmid = {35026246}, issn = {1879-1026}, mesh = {Farmers ; Humans ; Kenya ; *Microbiota ; *Ponds/microbiology ; Water Microbiology ; Water Quality ; }, abstract = {Many rural smallholder farmers in Kenya use water-harvesting ponds, to collect rainwater, as sustainable sources of water for domestic and agricultural purposes. There is currently limited information regarding the microbial ecology in these ponds. Here, we used High Throughput Sequencing (HTS) to characterize the microorganisms present (including potential pathogens and indicator species) alongside ion chromatography to measure water chemistry (anion and cation concentration). Fluoride and magnesium concentration were the strongest predictor variables of the microbial community. Obligately or facultatively anaerobic bacterial genera (e.g. Spirochaeta and Opitutus) were abundant within the bacterial community, whilst Woesearchaeota and methanogens dominated the archaeal community. This suggests the water in the ponds is hypoxic or anoxic, and if used for irrigation, may potentially impact crop yield and viability. In addition, the opportunistic pathogen non-tuberculous mycobacteria (NTM), Mycobacterium fortuitum was found, comprising >1% of the bacterial community, suggesting a potential human health risk. Here we suggest low-cost changes to pond management, to improve or ameliorate pond anoxia and remove pathogens to benefit the livelihoods and welfare of these farms. This study also shows the applicability of HTS to broadly screen the microbial communities, assess water quality, and identify potentially pathogenic groups.}, }
@article {pmid35025628, year = {2022}, author = {Cowan, DA and Ferrari, BC and McKay, CP}, title = {Out of Thin Air? Astrobiology and Atmospheric Chemotrophy.}, journal = {Astrobiology}, volume = {22}, number = {2}, pages = {225-232}, pmid = {35025628}, issn = {1557-8070}, mesh = {Carbon Monoxide ; Earth, Planet ; *Exobiology ; Extraterrestrial Environment ; Hydrogen ; *Mars ; Planets ; }, abstract = {The emerging understanding of microbial trace gas chemotrophy as a metabolic strategy to support energy and carbon acquisition for microbial survival and growth has significant implications in the search for past, and even extant, life beyond Earth. The use of trace gases, including hydrogen and carbon monoxide as substrates for microbial oxidation, potentially offers a viable strategy with which to support life on planetary bodies that possess a suitable atmospheric composition, such as Mars and Titan. Here, we discuss the current state of knowledge of this process and explore its potential in the field of astrobiological exploration.}, }
@article {pmid35025047, year = {2022}, author = {Pan, C and Feng, Q and Li, Y and Li, Y and Liu, L and Yu, X and Ren, S}, title = {Rare soil bacteria are more responsive in desertification restoration than abundant bacteria.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {22}, pages = {33323-33334}, pmid = {35025047}, issn = {1614-7499}, support = {41773086//National Natural Science Foundation of China/ ; 42042024//National Natural Science Foundation of China/ ; 31400392//National Natural Science Foundation of China/ ; 31670477//National Natural Science Foundation of China/ ; 18JR2RA026//Gansu Science and Technology Department/ ; }, mesh = {Bacteria ; China ; Conservation of Natural Resources ; *Ecosystem ; *Soil ; Soil Microbiology ; }, abstract = {Soil microbes play key roles in ecosystem functions, especially in the recovery of ecosystems from disturbance, and exploring community assembly under changing environments has long been a central theme in microbial ecology. The response of abundant and rare bacteria in desertified land to restoration is still unclear. Here, we investigated the effects of vegetation restoration on the assemblage patterns of abundant and rare bacteria in soil across the four sandy lands (Hulunbeir, Horqin, Otindag, and Mu Us) in northern China. Our results revealed that abundant bacteria maintained a relatively stable state under restoration, whereas rare taxa were more responsive, indicating the higher resilience of the rare community to change. Our network analysis also showed that restoration promoted destabilizing properties in rare, but not in abundant, bacterial co-occurrence networks in soil. Environmental selection played a key role in abundant and rare community assembly under restoration. Of the two, the rare subcommunity was mainly affected by environmental filtering. The variations in the abundant and rare communities at the sampling sites under restoration were controlled mainly by plant species richness, and stronger effects were observed in the rare taxa. Overall, these results provide new insight into the mechanisms controlling bacterial community assembly in response to vegetation restoration.}, }
@article {pmid35024965, year = {2022}, author = {Gao, C and Yang, X and Zhao, C and Li, C and Wang, S and Zhang, X and Xue, B and Cao, Z and Zhou, H and Yang, Y and Shen, Z and Yu, P and Wang, J and Li, L and Niu, Z and Qiu, Z}, title = {Characterization of a novel Vibrio parahaemolyticus host-phage pair and antibacterial effect against the host.}, journal = {Archives of virology}, volume = {167}, number = {2}, pages = {531-544}, pmid = {35024965}, issn = {1432-8798}, support = {2018YFD0800104//National Key R&amp;D Program of China/ ; AWS18J004//Special Fund of China/ ; 2019-JCJQ-JJ-163//Special Fund of China/ ; 17JCZDJC39100//Natural Science Foundation of Tianjin City/ ; 19JCYBJC23800//Natural Science Foundation of Tianjin City/ ; 51808468//National Natural Science Foundation of China/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; *Bacteriophages/genetics ; Genome, Viral ; Humans ; Myoviridae/genetics ; *Vibrio parahaemolyticus/genetics ; }, abstract = {Vibrio parahaemolyticus is a widely recognized pathogen that has caused numerous outbreaks and is prevalent in the marine environment. In this study, we investigated the characteristics of the novel V. parahaemolyticus strain BTXS2 and its associated phage, VB_VpP_BT-1011, isolated from the Bohai Coast (Tianjin, China). Strain BTXS2 is a short coryneform bacterium with a terminal flagellum and is able to utilize and metabolize a wide variety of organic matter because of its unique carbon source utilization and enzyme activity. It grows well in medium between pH 5.0 and 9.0 and salinities of simulated freshwater, estuary water, and seawater (NaCl 0.5%-3%). Multiple antibiotic resistance genes and virulence genes that endanger human health were found in the BTXS2 genome. Phage VB_VpP_BT-1011, which infects BTXS2, is a 40,065-bp double-stranded DNA virus of the family Myoviridae with a latent time of 30 min and burst size of 24 PFU/cell. Like its host, the phage tolerates a broad range of environmental conditions (salinity, 0-3% NaCl; pH 5.0-9.0; temperature, 4-37°C). A host range test showed that the phage only infected and inhibited isolate BTXS2. In summary, we investigated a novel V. parahaemolyticus host-phage pair and the antibacterial effect of the phage on V. parahaemolyticus, providing insights into marine microbial ecology and risks.}, }
@article {pmid35022702, year = {2022}, author = {Djemiel, C and Maron, PA and Terrat, S and Dequiedt, S and Cottin, A and Ranjard, L}, title = {Inferring microbiota functions from taxonomic genes: a review.}, journal = {GigaScience}, volume = {11}, number = {1}, pages = {}, pmid = {35022702}, issn = {2047-217X}, mesh = {*Ecosystem ; Fungi/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota/genetics ; Soil ; Soil Microbiology ; }, abstract = {Deciphering microbiota functions is crucial to predict ecosystem sustainability in response to global change. High-throughput sequencing at the individual or community level has revolutionized our understanding of microbial ecology, leading to the big data era and improving our ability to link microbial diversity with microbial functions. Recent advances in bioinformatics have been key for developing functional prediction tools based on DNA metabarcoding data and using taxonomic gene information. This cheaper approach in every aspect serves as an alternative to shotgun sequencing. Although these tools are increasingly used by ecologists, an objective evaluation of their modularity, portability, and robustness is lacking. Here, we reviewed 100 scientific papers on functional inference and ecological trait assignment to rank the advantages, specificities, and drawbacks of these tools, using a scientific benchmarking. To date, inference tools have been mainly devoted to bacterial functions, and ecological trait assignment tools, to fungal functions. A major limitation is the lack of reference genomes-compared with the human microbiota-especially for complex ecosystems such as soils. Finally, we explore applied research prospects. These tools are promising and already provide relevant information on ecosystem functioning, but standardized indicators and corresponding repositories are still lacking that would enable them to be used for operational diagnosis.}, }
@article {pmid35020220, year = {2022}, author = {Sahu, PK and Tilgam, J and Mishra, S and Hamid, S and Gupta, A and K, J and Verma, SK and Kharwar, RN}, title = {Surface sterilization for isolation of endophytes: Ensuring what (not) to grow.}, journal = {Journal of basic microbiology}, volume = {62}, number = {6}, pages = {647-668}, doi = {10.1002/jobm.202100462}, pmid = {35020220}, issn = {1521-4028}, mesh = {Endophytes ; *Plants, Medicinal ; Prospective Studies ; Sterilization ; *Taxus ; }, abstract = {Endophytic microbiota opens a magnificent arena of metabolites that served as a potential source of medicines for treating a variety of ailments and having prospective uses in agriculture, food, cosmetics, and many more. There are umpteen reports of endophytes improving the growth and tolerance of plants. In addition, endophytes from lifesaving drug-producing plants such as Taxus, Nothapodytes, Catharanthus, and so forth have the ability to produce host mimicking compounds. To harness these benefits, it is imperative to isolate the true endophytes, not the surface microflora. The foremost step in endophyte isolation is the removal of epiphytic microbes from plant tissues, called as surface sterilization. The success of surface sterilization decides "what to grow" (the endophytes) and "what not to grow" (the epiphytes). It is very crucial to use an appropriate sterilant solution, concentration, and exposure time to ensure thorough surface disinfection with minimal damage to the endophytic diversity. Commonly used surface sterilants include sodium hypochlorite (2%-10%), ethanol (70%-90%), mercuric chloride (0.1%), formaldehyde (40%), and so forth. In addition, the efficiency could further be improved by pretreatment with surfactants such as Triton X-100, Tween 80, and Tween 20. This review comprehensively deals with the various sterilants and sterilization methods for the isolation of endophytic microbes. In addition, the mechanisms and rationale behind using specific surface sterilants have also been elaborated at length.}, }
@article {pmid35019779, year = {2022}, author = {Yin, Y and Yuan, Y and Zhang, X and Huhe,  and Cheng, Y and Borjigin, S}, title = {Comparison of the Responses of Soil Fungal Community to Straw, Inorganic Fertilizer, and Compost in a Farmland in the Loess Plateau.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0223021}, pmid = {35019779}, issn = {2165-0497}, mesh = {China ; Composting ; Ecosystem ; Fertilizers/*analysis ; Fungi/classification/genetics/*isolation &amp; purification/metabolism ; *Mycobiome ; Plant Stems/metabolism/microbiology ; Soil/chemistry ; Soil Microbiology ; }, abstract = {The Loess Plateau is located in the arid and semi-arid regions in northern China. The ecosystem is particularly sensitive to natural and anthropogenic disturbances. Fungi can produce extracellular enzymes, decompose a variety of organic matter, and regulate carbon and nutrient balance. We studied the changes of soil fungal community compositions in response to straw, inorganic fertilizer, and compost in a typical farmland in the Loess Plateau. Our results demonstrated that the addition of straw significantly reduces the Shannon index of the fungal community, in addition, the participation of straw significantly affects the composition of the fungal community. Functional prediction based on FUNGuild showed that straw significantly reduced the relative abundance of saprotrophs, pathotrophs, symbiotrophs, lichenized, ectomycorrhizal, and plant pathogens. Although fertilization practices destroyed the co-occurrence pattern among the fungal species, the addition of straw alleviated this affect. No significant effect of straw, compost, and inorganic fertilizers on the co-occurrence pattern among species in the soil fungal community was observed. Compared with compost and inorganic fertilizer, the addition of straw shaped the community composition by changing the relative abundance of fungal functional taxa. Thus, in the fragile Loess Plateau environment, over-fertilizing or non-order-fertilizing may destroy the co-occurrence pattern of the fungal communities and Loess Plateau ecosystem. IMPORTANCE Determining the response of soil fungi in sensitive ecosystems to external environmental disturbances is an important, yet little-known, topic in microbial ecology. In this study, we evaluated the impact of traditional fertilization management practices on the composition, co-occurrence pattern, and functional groups of fungal communities in loessial soil. Our results show that in the fragile Loess Plateau environment, fertilizer management changed the composition of the fungal community and disrupted the co-occurrence pattern between fungi. The application of straw alleviates the destroying of the co-occurrence pattern. The current research emphasizes the necessity of rational fertilization of farmland in loessial soil.}, }
@article {pmid35019678, year = {2022}, author = {Kong, J and Wang, L and Lin, C and Kuang, F and Zhou, X and Laws, EA and Sun, P and Huang, H and Huang, B}, title = {Contrasting Community Assembly Mechanisms Underlie Similar Biogeographic Patterns of Surface Microbiota in the Tropical North Pacific Ocean.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0079821}, pmid = {35019678}, issn = {2165-0497}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Ecosystem ; Eukaryota/classification/genetics/isolation &amp; purification ; *Microbiota ; Pacific Ocean ; Phylogeny ; Seawater/*microbiology/parasitology ; }, abstract = {Marine microbiota are critical components of global biogeochemical cycles. However, the biogeographic patterns and ecological processes that structure them remain poorly understood, especially in the oligotrophic ocean. In this study, we used high-throughput sequencing of 16S and 18S rRNA genes to investigate the distribution patterns of bacterial and microeukaryotic communities and their assembly mechanisms in the surface waters of the tropical North Pacific Ocean. The fact that both the bacterial and the microeukaryotic communities showed similar distribution patterns (i.e., similar distance-decay patterns) and were clustered according to their geographic origin (i.e., the western tropical North Pacific and central tropical North Pacific) suggested that there was a significant biogeographic pattern of microbiota in the North Pacific Ocean. Indices of alpha diversity such as species richness, phylogenetic diversity, and the Shannon diversity index also differed significantly between regions. The correlations were generally similar between spatial and environmental variables and the alpha and beta diversities of bacteria and microeukaryotes across the entire region. The relative importance of ecological processes differed between bacteria and microeukaryotes: ecological drift was the principal mechanism that accounted for the structure of bacterial communities; heterogeneous selection, dispersal limitation, and ecological drift collectively explained much of the turnover of the microeukaryote communities. IMPORTANCE Bacteria and microeukaryotes are extremely diverse groups in the ocean, where they regulate elemental cycling and energy flow. Studies of marine microbial ecology have benefited greatly from the rapid progress that has been made in genomic sequencing and theoretical microbial ecology. However, the spatial distribution of marine bacteria and microeukaryotes and the nature of the assembly mechanisms that determine their distribution patterns in oligotrophic marine waters are poorly understood. In this study, we used high-throughput sequencing methods to identify the distribution patterns and ecological processes of bacteria and microeukaryotes in an oligotrophic, tropical ocean. Our study showed that contrasting community assembly mechanisms underlaid similar biogeographic patterns of surface bacterial and microeukaryotic communities in the tropical North Pacific Ocean.}, }
@article {pmid35018483, year = {2023}, author = {Zhang, W and Qi, T and Yao, L and Wang, W and Yu, F and Yan, Y and Salama, ES and Su, S and Bai, M}, title = {Influence of Environmental Factors on Salivary Microbiota and Their Metabolic Pathway: Next-Generation Sequencing Approach.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {317-329}, pmid = {35018483}, issn = {1432-184X}, support = {31500412//National Natural Science Foundation of China/ ; 20JR5RA327//National Natural Science Foundation of Gansu Province, China/ ; 21JR1RA152//National Natural Science Foundation of Gansu Province, China/ ; 2018-4-66//Lanzhou science and technology plan project/ ; }, mesh = {Humans ; Bacteria/genetics ; *Periodontitis/microbiology ; *Microbiota ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The current study aimed to investigate the effect of periodontitis and long-term heavy metal (HM) exposure on the salivary microbiome. The patients were divided into four groups as Wu Wei control (WWC) group involved healthy individuals, Wu Wei periodontitis (WWP) patients having periodontitis, Jing Chang with metal pollution periodontally healthy individuals (JCP), and Kuang periodontitis (KP). The most abundant bacteria identified at the phylum level in the WWC group were Bacteroides, Firmicutes, and Fusobacteria. Firmicutes were observed in a significantly higher proportion in the KP group than in the WWC, WWP, and JCP. At the genus level, the WWC has major dominating bacterial genera (such as Leptotrichia, Neisseria, and Fusobacterium) which were similar to WWP and KP group. The significant difference (p < 0.05) was found in alpha diversity while in beta diversity, the significant (p = 0.005) results were found among the four groups. The correlation of oral microbiota revealed that HMs present in the soil (Cr, Ni, and Cu) are associated with the growth of Capnocytophaga, Selenomonas, Aggregatibacter, and Campylobacter. The bacterial functions in the KP group were higher in translation and nucleotide metabolism than in the WWP group. This demonstrated that long-term exposure to HMs can influence the salivary microbiota which can alter the functioning, and diversity of bacteria.}, }
@article {pmid35016024, year = {2022}, author = {Cáliz, J and Subirats, J and Triadó-Margarit, X and Borrego, CM and Casamayor, EO}, title = {Global dispersal and potential sources of antibiotic resistance genes in atmospheric remote depositions.}, journal = {Environment international}, volume = {160}, number = {}, pages = {107077}, doi = {10.1016/j.envint.2022.107077}, pmid = {35016024}, issn = {1873-6750}, mesh = {*Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Antibiotic resistance has become a major Global Health concern and a better understanding on the global spread mechanisms of antibiotic resistant bacteria (ARB) and intercontinental ARB exchange is needed. We measured atmospheric depositions of antibiotic resistance genes (ARGs) by quantitative (q)PCR in rain/snow collected fortnightly along 4 y. at a remote high mountain LTER (Long-Term Ecological Research) site located above the atmospheric boundary layer (free troposphere). Bacterial composition was characterized by 16S rRNA gene sequencing, and air mass provenances were determined by modelled back trajectories and rain/snow chemical composition. We hypothesize that the free troposphere may act as permanent reservoir and vector for ARB and ARGs global dispersal. We aimed to i) determine whether ARGs are long-range intercontinental and persistently dispersed through aerosols, ii) assess ARGs long-term atmospheric deposition dynamics in a remote high mountain area, and iii) unveil potential diffuse ARGs pollution sources. We showed that the ARGs sul1 (resistance to sulfonamides), tetO (resistance to tetracyclines), and intI1 (a proxy for horizontal gene transfer and anthropogenic pollution) were long-range and persistently dispersed in free troposphere aerosols. Major depositions of tetracyclines resistance matched with intensification of African dust outbreaks. Potential ARB mostly traced their origin back into agricultural soils. Our study unveils that air masses pathways are shaping ARGs intercontinental dispersal and global spread of antibiotic resistances, with potential predictability for interannual variability and remote deposition rates. Because climate regulates aerosolization and long-range air masses movement patterns, we call for a more careful evaluation of the connections between land use, climate change and ARB long-range intercontinental dispersal.}, }
@article {pmid35014098, year = {2022}, author = {Olesen, AK and Pinilla-Redondo, R and Hansen, MF and Russel, J and Dechesne, A and Smets, BF and Madsen, JS and Nesme, J and Sørensen, SJ}, title = {IncHI1A plasmids potentially facilitate horizontal flow of antibiotic resistance genes to pathogens in microbial communities of urban residential sewage.}, journal = {Molecular ecology}, volume = {31}, number = {5}, pages = {1595-1608}, doi = {10.1111/mec.16346}, pmid = {35014098}, issn = {1365-294X}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal/genetics ; *Microbiota ; Plasmids/genetics ; *Sewage/microbiology ; }, abstract = {Horizontal gene transfer via plasmids is important for the dissemination of antibiotic resistance genes among medically relevant pathogens. Specifically, the transfer of IncHI1A plasmids is believed to facilitate the spread of antibiotic resistance genes, such as carbapenemases, within the clinically important family Enterobacteriaceae. The microbial community of urban wastewater treatment plants has been shown to be highly permissive towards conjugal transfer of IncP1 plasmids. Here, we tracked the transfer of the P1 plasmid pB10 and the clinically relevant HI1A plasmid R27 in the microbial communities present in urban residential sewage entering full-scale wastewater treatment plants. We found that both plasmids readily transferred to these communities and that strains in the sewage were able to further disseminate them. Furthermore, R27 has a broad potential host range, but a low host divergence. Interestingly, although the majority of R27 transfer events were to members of Enterobacteriaceae, we found a subset of transfer events to other families, even other phyla. This indicates that HI1A plasmids facilitate horizontal gene transfer both within Enterobacteriaceae, but also across families of, in particular, Gammaproteobacteria, such as Moraxellaceae, Pseudomonadaceae and Shewanellaceae. pB10 displayed a similar potential host range to R27. In contrast to R27, pB10 had a high host divergence. By culture enrichment of the transconjugant communities, we show that sewage strains of Enterobacteriaceae and Aeromonadaceae can stably maintain R27 and pB10, respectively. Our results suggest that dissemination in the urban residual water system of HI1A plasmids may result in an accelerated acquisition of antibiotic resistance genes among pathogens.}, }
@article {pmid35013291, year = {2022}, author = {Martínez-Pérez, C and Greening, C and Bay, SK and Lappan, RJ and Zhao, Z and De Corte, D and Hulbe, C and Ohneiser, C and Stevens, C and Thomson, B and Stepanauskas, R and González, JM and Logares, R and Herndl, GJ and Morales, SE and Baltar, F}, title = {Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {117}, pmid = {35013291}, issn = {2041-1723}, support = {P 28781/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Antarctic Regions ; Archaea/classification/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Carbon Cycle/genetics ; Geologic Sediments/microbiology ; Ice Cover/*microbiology ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; }, abstract = {Throughout coastal Antarctica, ice shelves separate oceanic waters from sunlight by hundreds of meters of ice. Historical studies have detected activity of nitrifying microorganisms in oceanic cavities below permanent ice shelves. However, little is known about the microbial composition and pathways that mediate these activities. In this study, we profiled the microbial communities beneath the Ross Ice Shelf using a multi-omics approach. Overall, beneath-shelf microorganisms are of comparable abundance and diversity, though distinct composition, relative to those in the open meso- and bathypelagic ocean. Production of new organic carbon is likely driven by aerobic lithoautotrophic archaea and bacteria that can use ammonium, nitrite, and sulfur compounds as electron donors. Also enriched were aerobic organoheterotrophic bacteria capable of degrading complex organic carbon substrates, likely derived from in situ fixed carbon and potentially refractory organic matter laterally advected by the below-shelf waters. Altogether, these findings uncover a taxonomically distinct microbial community potentially adapted to a highly oligotrophic marine environment and suggest that ocean cavity waters are primarily chemosynthetically-driven systems.}, }
@article {pmid35011305, year = {2021}, author = {Li, Q and Van Herreweghen, F and De Mey, M and Goeminne, G and Van de Wiele, T}, title = {The Donor-Dependent and Colon-Region-Dependent Metabolism of (+)-Catechin by Colonic Microbiota in the Simulator of the Human Intestinal Microbial Ecosystem.}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {1}, pages = {}, pmid = {35011305}, issn = {1420-3049}, support = {201806820010//China Scholarship Council/ ; BOF18/CHN/064//Ghent University Preference Program/ ; BOF17/GOA/032//Ghent University Special Research Fund/ ; }, mesh = {Adult ; Biological Variation, Population ; Catechin/*metabolism ; Chromatography, High Pressure Liquid ; *Colon ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/*metabolism/*microbiology ; Male ; Metabolic Networks and Pathways ; Metabolome ; Metabolomics/methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {The intestinal absorption of dietary catechins is quite low, resulting in most of them being metabolized by gut microbiota in the colon. It has been hypothesized that microbiota-derived metabolites may be partly responsible for the association between catechin consumption and beneficial cardiometabolic effects. Given the profound differences in gut microbiota composition and microbial load between individuals and across different colon regions, this study examined how microbial (+)-catechin metabolite profiles differ between colon regions and individuals. Batch exploration of the interindividual variability in (+)-catechin microbial metabolism resulted in a stratification based on metabolic efficiency: from the 12 tested donor microbiota, we identified a fast- and a slow-converting microbiota that was subsequently inoculated to SHIME, a dynamic model of the human gut. Monitoring of microbial (+)-catechin metabolites from proximal and distal colon compartments with UHPLC-MS and UPLC-IMS-Q-TOF-MS revealed profound donor-dependent and colon-region-dependent metabolite profiles with 5-(3',4'-dihydroxyphenyl)-γ-valerolactone being the largest contributor to differences between the fast- and slow-converting microbiota and the distal colon being a more important region for (+)-catechin metabolism than the proximal colon. Our findings may contribute to further understanding the role of the gut microbiota as a determinant of interindividual variation in pharmacokinetics upon (+)-catechin ingestion.}, }
@article {pmid35011218, year = {2022}, author = {Naghizadeh, M and Klaver, L and Schönherz, AA and Rani, S and Dalgaard, TS and Engberg, RM}, title = {Impact of Dietary Sodium Butyrate and Salinomycin on Performance and Intestinal Microbiota in a Broiler Gut Leakage Model.}, journal = {Animals : an open access journal from MDPI}, volume = {12}, number = {1}, pages = {}, pmid = {35011218}, issn = {2076-2615}, support = {000//Poultry Production Levy Fund/ ; }, abstract = {Unfavorable alterations of the commensal gut microbiota and dysbacteriosis is a major health problem in the poultry industry. Understanding how dietary intervention alters the microbial ecology of broiler chickens is important for prevention strategies. A trial was conducted with 672 Ross 308 day-old male broilers fed a basic diet (no additives, control) or the basic diet supplemented with 500 mg/kg encapsulated butyrate or 68 mg/kg salinomycin. Enteric challenge was induced by inclusion of 50 g/kg rye in a grower diet and oral gavage of a 10 times overdose of a vaccine against coccidiosis. Compared to control and butyrate-supplemented birds, salinomycin supplementation alleviated growth depression. Compared to butyrate and non-supplemented control, salinomycin increased potentially beneficial Ruminococcaceae and reduced potentially pathogenic Enterobacteriaceae and counts of Lactobacillus salivarius and Clostridium perfringens. Further, salinomycin supplementation was accompanied by a pH decrease and succinic acid increase in ceca, while coated butyrate (0.5 g/kg) showed no or limited effects. Salinomycin alleviated growth depression and maintained intestinal homeostasis in the challenged broilers, while butyrate in the tested concentration showed limited effects. Thus, further investigations are required to identify optimal dietary inclusion rates for butyrate used as alternative to ionophore coccidiostats in broiler production.}, }
@article {pmid35010187, year = {2021}, author = {Jiang, L and Xian, S and Liu, X and Shen, G and Zhang, Z and Hou, X and Chen, A}, title = {Metagenomic Study on Chinese Homemade Paocai: The Effects of Raw Materials and Fermentation Periods on the Microbial Ecology and Volatile Components.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {1}, pages = {}, pmid = {35010187}, issn = {2304-8158}, support = {No. 2017YFC0505106-3//Research and Development of Utilization Technology of characteristic Biological Resources in Ar-id Valley of Southwest China/ ; }, abstract = {"Chinese paocai" is typically made by fermenting red radish or cabbage with aged brine (6-8 w/w). This study aimed to reveal the effects of paocai raw materials on fermentation microorganisms by metagenomics sequencing technology, and on volatile organic compounds (VOCs) by gas chromatography-mass spectroscopy, using red radish or cabbage fermented for six rounds with aged brine. The results showed that in the same fermentation period, the microbial diversity in cabbage was higher than that in red radish. Secundilactobacillus paracollinoides and Furfurilactobacillus siliginis were the characteristic bacteria in red radish paocai, whereas 15 species of characteristic microbes were found in cabbage. Thirteen kinds of VOCs were different between the two raw materials and the correlation between the microorganisms and VOCs showed that cabbage paocai had stronger correlations than radish paocai for the most significant relationship between 4-isopropylbenzyl alcohol, α-cadinol, terpinolene and isobutyl phenylacetate. The results of this study provide a theoretical basis for understanding the microbiota and their relation to the characteristic flavors of the fermented paocai.}, }
@article {pmid35003029, year = {2021}, author = {Wang, Z and Solanki, MK and Yu, ZX and Anas, M and Dong, DF and Xing, YX and Malviya, MK and Pang, F and Li, YR}, title = {Genome Characteristics Reveal the Biocontrol Potential of Actinobacteria Isolated From Sugarcane Rhizosphere.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {797889}, pmid = {35003029}, issn = {1664-302X}, abstract = {To understand the beneficial interaction of sugarcane rhizosphere actinobacteria in promoting plant growth and managing plant diseases, this study investigated the potential role of sugarcane rhizospheric actinobacteria in promoting plant growth and antagonizing plant pathogens. We isolated 58 actinobacteria from the sugarcane rhizosphere, conducted plant growth-promoting (PGP) characteristics research, and tested the pathogenic fungi in vitro. Results showed that BTU6 (Streptomyces griseorubiginosus), the most representative strain, regulates plant defense enzyme activity and significantly enhances sugarcane smut resistance by regulating stress resistance-related enzyme (substances (POD, PAL, PPO, TP) in sugarcane) activity in sugarcane. The genomic evaluation indicated that BTU6 has the ability to biosynthesize chitinase, β-1,3-glucanase, and various secondary metabolites and plays an essential role in the growth of sugarcane plants under biotic stress. Potential mechanisms of the strain in improving the disease resistance of sugarcane plants and its potential in biodegrading exogenous chemicals were also revealed. This study showed the importance of sugarcane rhizosphere actinobacteria in microbial ecology and plant growth promotion.}, }
@article {pmid34997964, year = {2022}, author = {Li, L and Chen, X and Fang, D and Dong, S and Guo, X and Li, N and Campos-Dominguez, L and Wang, W and Liu, Y and Lang, X and Peng, Y and Tian, D and Thomas, DC and Mu, W and Liu, M and Wu, C and Yang, T and Zhang, S and Yang, L and Yang, J and Liu, ZJ and Zhang, L and Zhang, X and Chen, F and Jiao, Y and Guo, Y and Hughes, M and Wang, W and Liu, X and Zhong, C and Li, A and Sahu, SK and Yang, H and Wu, E and Sharbrough, J and Lisby, M and Liu, X and Xu, X and Soltis, DE and Van de Peer, Y and Kidner, C and Zhang, S and Liu, H}, title = {Genomes shed light on the evolution of Begonia, a mega-diverse genus.}, journal = {The New phytologist}, volume = {234}, number = {1}, pages = {295-310}, pmid = {34997964}, issn = {1469-8137}, support = {833522/ERC_/European Research Council/International ; }, mesh = {*Begoniaceae/genetics ; Evolution, Molecular ; Genome ; Phylogeny ; Synteny/genetics ; }, abstract = {Clarifying the evolutionary processes underlying species diversification and adaptation is a key focus of evolutionary biology. Begonia (Begoniaceae) is one of the most species-rich angiosperm genera with c. 2000 species, most of which are shade-adapted. Here, we present chromosome-scale genome assemblies for four species of Begonia (B. loranthoides, B. masoniana, B. darthvaderiana and B. peltatifolia), and whole genome shotgun data for an additional 74 Begonia representatives to investigate lineage evolution and shade adaptation of the genus. The four genome assemblies range in size from 331.75 Mb (B. peltatifolia) to 799.83 Mb (B. masoniana), and harbor 22 059-23 444 protein-coding genes. Synteny analysis revealed a lineage-specific whole-genome duplication (WGD) that occurred just before the diversification of Begonia. Functional enrichment of gene families retained after WGD highlights the significance of modified carbohydrate metabolism and photosynthesis possibly linked to shade adaptation in the genus, which is further supported by expansions of gene families involved in light perception and harvesting. Phylogenomic reconstructions and genomics studies indicate that genomic introgression has also played a role in the evolution of Begonia. Overall, this study provides valuable genomic resources for Begonia and suggests potential drivers underlying the diversity and adaptive evolution of this mega-diverse clade.}, }
@article {pmid34997311, year = {2023}, author = {Balacco, JR and Vaidya, BP and Hagmann, DF and Goodey, NM and Krumins, JA}, title = {Mycorrhizal Infection Can Ameliorate Abiotic Factors in Urban Soils.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {100-107}, pmid = {34997311}, issn = {1432-184X}, support = {CBET#1603741//national science foundation/ ; }, mesh = {*Mycorrhizae/chemistry ; Soil ; *Metals, Heavy/analysis ; Plants/microbiology ; Biomass ; Plant Roots/microbiology ; *Soil Pollutants/analysis ; }, abstract = {Once abandoned, urban and post-industrial lands can undergo a re-greening, the natural regeneration and succession that leads to surprisingly healthy plant communities, but this process is dependent upon microbial activity and the health of the parent soil. This study aimed to evaluate the effects of arbuscular mycorrhizal fungi (AMF) in facilitating plant production in post-industrial soils. In so doing, we helped to resolve the mechanism through which AMF ameliorate environmental stress in terrestrial plants. An experiment was established in which rye grass (Lolium perenne) was grown in two heavy metal-contaminated soils from an urban brownfield in New Jersey, USA, and one non-contaminated control soil. One set of the treatments received an AMF inoculum (four species in a commercial mix: Glomus intraradices, G. mosseae, G. etunicatum and G. aggregatum) and the other did not. Upon harvest, dried plant biomass, root/shoot ratio, AMF colonization, and extracellular soil phosphatase activity, a proxy for soil microbial functioning, were all measured. Plant biomass increased across all treatments inoculated with AMF, with a significantly higher average shoot and root mass compared to non-inoculated treatments. AMF colonization of the roots in contaminated soil was significantly higher than colonization in control soil, and the root/shoot ratio of plants in contaminated soils was also higher when colonized by AMF. Mycorrhizal infection may help plants to overcome the production limits of post-industrial soils as is seen here with increased infection and growth. The application of this mechanistic understanding to remediation and restoration strategies will improve soil health and plant production in urban environments.}, }
@article {pmid34997310, year = {2023}, author = {Decker, LE and San Juan, PA and Warren, ML and Duckworth, CE and Gao, C and Fukami, T}, title = {Higher Variability in Fungi Compared to Bacteria in the Foraging Honey Bee Gut.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {330-334}, pmid = {34997310}, issn = {1432-184X}, support = {1737758//Division of Environmental Biology/ ; }, mesh = {Bees ; Animals ; *Gastrointestinal Tract/microbiology ; Bacteria ; *Microbiota ; Stomach ; Fungi ; }, abstract = {Along with bacteria, fungi can represent a significant component of animal- and plant-associated microbial communities. However, we have only begun to describe these fungi, much less examine their effects on most animals and plants. Bacteria associated with the honey bee, Apis mellifera, have been well characterized across different regions of the gut. The mid- and hindgut of foraging bees house a deterministic set of core species that affect host health, whereas the crop, or the honey stomach, harbors a more diverse set of bacteria that is highly variable in composition among individual bees. Whether this contrast between the two regions of the gut also applies to fungi remains unclear despite their potential influence on host health. In honey bees caught foraging at four sites across the San Francisco Peninsula of California, we found that fungi were less distinct in species composition between the crop and the mid- and hindgut than bacteria. Unlike bacteria, fungi varied substantially in species composition throughout the honey bee gut, and much of this variation could be predicted by the location where we collected the bees. These observations suggest that fungi may be transient passengers and unimportant as gut symbionts. However, our findings also indicate that honey bees could be vectors of infectious plant diseases as many of the fungi we found in the honey bee gut are recognized as plant pathogens.}, }
@article {pmid34997309, year = {2023}, author = {Li, T and Cai, Y and Ma, Q}, title = {Microbial Diversity on the Surface of Historical Monuments in Lingyan Temple, Jinan, China.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {76-86}, pmid = {34997309}, issn = {1432-184X}, support = {2019M662390//Postdoctoral Research Foundation of China/ ; ZR2020QC045//Natural Science Foundation of Shandong Province/ ; 18ZDA221//Major Program of National Fund of Philosophy and Social Science of China (CN)/ ; }, mesh = {*Cyanobacteria/genetics ; Biofilms ; *Microbiota ; China ; }, abstract = {Lingyan Temple is an important part of the World Heritage Mixed Property on Mount Taishan, in which numerous cultural heritage monuments, including exquisite painted arhat statues and inscriptions, display the ancient Chinese Buddhist culture. However, these monuments are suffering aesthetic and structural damage due to rich biofilms. In this study, the microbial communities colonized on historical monuments in different microenvironments were characterized through a combination of culture-dependent techniques and high-throughput sequencing. Microbial diversity was significantly different among the historical sites with different microenvironments. For example, Actinobacteria and Ascomycota were the core phyla in the indoor samples, while they were less abundant in the outdoor samples, and phototrophic microorganisms including Cyanobacteria and green algae were only dominant in the samples near springs. The results suggested that environmental factors such as water and airborne microorganisms may be the main causes influencing microbial distribution. Most of the identified dominant species were common on the historical monuments and could contribute to biodeterioration. This analysis of microbiota will provide further information on the biodeterioration processes and preservation strategies of cultural heritage monuments in Lingyan Temple.}, }
@article {pmid34997308, year = {2023}, author = {Shi, L and Xia, P and Lin, T and Li, G and Wang, T and Du, X}, title = {Temporal Succession of Bacterial Community Structure, Co-occurrence Patterns, and Community Assembly Process in Epiphytic Biofilms of Submerged Plants in a Plateau Lake.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {87-99}, pmid = {34997308}, issn = {1432-184X}, support = {41867056//National Nature Science Foundation of China/ ; 2021470//Guizhou Science and Technology Department/ ; U1812401//Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou Province/ ; }, mesh = {*Lakes/microbiology ; Biofilms ; *Microbiota ; Seasons ; }, abstract = {In shallow macrophytic lakes, epiphytic biofilms are formed on the surface of submerged plant stems and leaves because of algae and bacterial accumulation. Epiphytic biofilms significantly impact the health of the host vegetation and the biogeochemical cycling of lake elements. However, community diversity, species interactions, and community assembly mechanisms in epiphytic bacterial communities (EBCs) of plants during different growth periods are not well understood. We investigated the successional dynamics, co-occurrence patterns, and community assembly processes of epiphytic biofilm bacterial communities of submerged plants, Najas marina and Potamogeton lucens, from July to November 2020. The results showed a significant seasonal variation in EBC diversity and richness. Community diversity and richness increased from July to November, and the temperature was the most important driving factor for predicting seasonal changes in EBC community structure. Co-occurrence network analysis revealed that the average degree and graph density of the network increased from July to November, indicating that the complexity of the EBC network increased. The bacterial community co-occurrence network was limited by temperature, pH, and transparency. The phylogeny-based null model analysis showed that deterministic processes dominated the microbial community assembly in different periods, increasing their contribution. In addition, we found that as the dominance of deterministic processes increased, the microbial co-occurrence links increased, and the potential interrelationships between species became stronger. Thus, the findings provide insights into the seasonal variability of EBC assemblage and co-occurrence patterns in lacustrine ecosystems.}, }
@article {pmid34994948, year = {2022}, author = {Bist, P and Choudhary, S}, title = {Impact of Heavy Metal Toxicity on the Gut Microbiota and Its Relationship with Metabolites and Future Probiotics Strategy: a Review.}, journal = {Biological trace element research}, volume = {200}, number = {12}, pages = {5328-5350}, pmid = {34994948}, issn = {1559-0720}, mesh = {Dysbiosis/chemically induced ; *Environmental Pollutants ; *Gastrointestinal Microbiome ; Heavy Metal Poisoning ; Humans ; *Metals, Heavy/toxicity ; *Probiotics/therapeutic use ; }, abstract = {The gut microbiota has a vital role in the maintenance of intestinal homeostasis. Several studies have revealed that environmental exposure to pollutants such as heavy metals may contribute to the progression of extensive list of diseases which may further lead to perturbations in the gut leading to dysbiosis. This manuscript critically reviews the alterations in the gut microbiota composition and function upon exposure to various toxic heavy metals prevalent in the environment. The disturbance in gut microbial ecology also affects the microbial metabolic profile which may alter the speciation state and bioavailability heavy metals thus affecting metal uptake-absorption/detoxification mechanisms associated to heavy metal metabolism. The toxic effects of various heavy metals either in single or in multimetallic combination and the gut microbiota associated host health and disease condition need a comprehensive assessment with important consideration for therapeutic and protective strategies against the damage to gut microbiota.}, }
@article {pmid34990848, year = {2022}, author = {Kim, M and Sung, J and Chia, N}, title = {Resource-allocation constraint governs structure and function of microbial communities in metabolic modeling.}, journal = {Metabolic engineering}, volume = {70}, number = {}, pages = {12-22}, doi = {10.1016/j.ymben.2021.12.011}, pmid = {34990848}, issn = {1096-7184}, mesh = {*Microbiota ; }, abstract = {Predictive modeling tools for assessing microbial communities are important for realizing transformative capabilities of microbiomes in agriculture, ecology, and medicine. Constraint-based community-scale metabolic modeling is unique in its potential for making mechanistic predictions regarding both the structure and function of microbial communities. However, accessing this potential requires an understanding of key physicochemical constraints, which are typically considered on a per-species basis. What is needed is a means of incorporating global constraints relevant to microbial ecology into community models. Resource-allocation constraint, which describes how limited resources should be distributed to different cellular processes, sets limits on the efficiency of metabolic and ecological processes. In this study, we investigate the implications of resource-allocation constraints in community-scale metabolic modeling through a simple mechanism-agnostic implementation of resource-allocation constraints directly at the flux level. By systematically performing single-, two-, and multi-species growth simulations, we show that resource-allocation constraints are indispensable for predicting the structure and function of microbial communities. Our findings call for a scalable workflow for implementing a mechanistic version of resource-allocation constraints to ultimately harness the full potential of community-scale metabolic modeling tools.}, }
@article {pmid34990484, year = {2022}, author = {Gestuveo, RJ and Parry, R and Dickson, LB and Lequime, S and Sreenu, VB and Arnold, MJ and Khromykh, AA and Schnettler, E and Lambrechts, L and Varjak, M and Kohl, A}, title = {Mutational analysis of Aedes aegypti Dicer 2 provides insights into the biogenesis of antiviral exogenous small interfering RNAs.}, journal = {PLoS pathogens}, volume = {18}, number = {1}, pages = {e1010202}, pmid = {34990484}, issn = {1553-7374}, support = {/WT_/Wellcome Trust/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Aedes/genetics/*immunology/*virology ; Alphavirus Infections/*immunology ; Animals ; DNA Mutational Analysis ; Mosquito Vectors/virology ; RNA, Small Interfering/immunology ; RNA, Viral/immunology ; Ribonuclease III/genetics/*immunology ; Semliki forest virus ; }, abstract = {The exogenous small interfering RNA (exo-siRNA) pathway is a key antiviral mechanism in the Aedes aegypti mosquito, a widely distributed vector of human-pathogenic arboviruses. This pathway is induced by virus-derived double-stranded RNAs (dsRNA) that are cleaved by the ribonuclease Dicer 2 (Dcr2) into predominantly 21 nucleotide (nt) virus-derived small interfering RNAs (vsiRNAs). These vsiRNAs are used by the effector protein Argonaute 2 within the RNA-induced silencing complex to cleave target viral RNA. Dcr2 contains several domains crucial for its activities, including helicase and RNase III domains. In Drosophila melanogaster Dcr2, the helicase domain has been associated with binding to dsRNA with blunt-ended termini and a processive siRNA production mechanism, while the platform-PAZ domains bind dsRNA with 3' overhangs and subsequent distributive siRNA production. Here we analyzed the contributions of the helicase and RNase III domains in Ae. aegypti Dcr2 to antiviral activity and to the exo-siRNA pathway. Conserved amino acids in the helicase and RNase III domains were identified to investigate Dcr2 antiviral activity in an Ae. aegypti-derived Dcr2 knockout cell line by reporter assays and infection with mosquito-borne Semliki Forest virus (Togaviridae, Alphavirus). Functionally relevant amino acids were found to be conserved in haplotype Dcr2 sequences from field-derived Ae. aegypti across different continents. The helicase and RNase III domains were critical for silencing activity and 21 nt vsiRNA production, with RNase III domain activity alone determined to be insufficient for antiviral activity. Analysis of 21 nt vsiRNA sequences (produced by functional Dcr2) to assess the distribution and phasing along the viral genome revealed diverse yet highly consistent vsiRNA pools, with predominantly short or long sequence overlaps including 19 nt overlaps (the latter representing most likely true Dcr2 cleavage products). Combined with the importance of the Dcr2 helicase domain, this suggests that the majority of 21 nt vsiRNAs originate by processive cleavage. This study sheds new light on Ae. aegypti Dcr2 functions and properties in this important arbovirus vector species.}, }
@article {pmid34989745, year = {2022}, author = {Hua, Q and Han, Y and Zhao, H and Zhang, H and Yan, B and Pei, S and He, X and Li, Y and Meng, X and Chen, L and Zhong, F and Li, D}, title = {Punicalagin alleviates renal injury via the gut-kidney axis in high-fat diet-induced diabetic mice.}, journal = {Food &amp; function}, volume = {13}, number = {2}, pages = {867-879}, doi = {10.1039/d1fo03343c}, pmid = {34989745}, issn = {2042-650X}, mesh = {Animals ; Diabetes Mellitus, Experimental/*complications ; Diabetic Nephropathies/*drug therapy ; *Diet, High-Fat ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Regulation/drug effects ; Hydrolyzable Tannins/*pharmacology ; Inflammation/metabolism ; Kidney/*metabolism ; Mice ; Mice, Inbred C57BL ; Pomegranate/chemistry ; }, abstract = {Diabetic renal injury was associated with dysbiosis of the gut microbiota and intestinal barrier. Punicalagin (PU) from pomegranates potentially impacts the microbial ecosystem, intestinal barrier, and renal function. Therefore, we hypothesized that PU may improve diabetic renal injury by modulating the gut-kidney axis. The present study evaluated the effect of PU on the gut-kidney axis and kidney function in a diabetic renal injury mouse model induced by a high-fat diet (HFD). Mice were fed a HFD without PU or with at doses of 50 and 100 mg kg[-1] d[-1] for 8 weeks. Targeted metabolomics by GC-MS and 16S rRNA sequencing were implemented to determine short-chain fatty acids (SCFAs) and microbes. Further RNA sequencing analyses were performed to determine which differentially expressed genes were changed by PU. Compared with the DM model group, PU supplementation improved diabetic renal injury, ameliorated kidney architecture and function, and reshaped gut microbial ecology. Additionally, PU reversed HFD-induced gut barrier dysfunction, promoted cecal SCFA concentrations and inhibited serum lipopolysaccharide (LPS) and diamine oxidase (DAO) levels. Moreover, correlation analysis found that cecal SCFAs were significantly negatively correlated with inflammation-related genes in the kidney. The present results indicated that PU, a promising bioactive polyphenol, successfully improved diabetic renal injury, most likely through the gut-kidney axis.}, }
@article {pmid34988711, year = {2022}, author = {Liu, Q and Lai, Z and Wang, C and Ni, J and Gao, Y}, title = {Seasonal variation significantly affected bacterioplankton and eukaryoplankton community composition in Xijiang River, China.}, journal = {Environmental monitoring and assessment}, volume = {194}, number = {2}, pages = {55}, pmid = {34988711}, issn = {1573-2959}, support = {NA//Fund of Survey and Evaluation of the Fishery Environmental Capacity in the Important River Waters of Guangxi/ ; 2018YFD0900802//Key Technologies Research and Development Program/ ; 2021SJ-TD1//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; 2019A1515011589//Guangdong Basic and Applied Basic Research Foundation/ ; }, mesh = {Aquatic Organisms ; China ; *Ecosystem ; Environmental Monitoring ; Plankton ; RNA, Ribosomal, 16S ; *Rivers ; Seasons ; }, abstract = {Both bacterioplankton and eukaryoplankton communities play important roles in the geochemical cycles and energy flows of river ecosystems. However, whether a seasonal change in bacterioplankton and eukaryoplankton communities is synchronous remains unclear. To test the synchronicity and analyze how physical and chemical environmental factors affect these communities, we compared bacterioplankton and eukaryoplankton communities in surface water samples between March (dry season) and June (rainfall season) considering water environmental factors. Our results showed that there was no significant difference in operational taxonomic unit number, Shannon index, and Chao1 index in bacterioplankton and eukaryoplankton communities between March and June. However, principal component analysis showed that the communities were significantly different between the sampling times and sampling sites. Water temperature (WT), oxidation-reduction potential (ORP), water transparency (SD), NO3-N, and NH3 significantly influenced bacterioplankton communities, and WT, SD, ORP, and NH4-N significantly influenced eukaryoplankton communities in the river. These results implied that compared with the sampling sites, sampling times more significantly affected the bacterioplankton and eukaryoplankton river communities by influencing WT, ORP, SD, and nitrogen forms.}, }
@article {pmid34988622, year = {2022}, author = {Liberti, A and Natarajan, O and Atkinson, CGF and Dishaw, LJ}, title = {Secreted immunoglobulin domain effector molecules of invertebrates and management of gut microbial ecology.}, journal = {Immunogenetics}, volume = {74}, number = {1}, pages = {99-109}, pmid = {34988622}, issn = {1432-1211}, mesh = {Animals ; Drosophila melanogaster ; *Gastrointestinal Microbiome ; Immunoglobulin Domains ; Invertebrates ; Vertebrates ; }, abstract = {The origins of a "pass-through" gut in early bilaterians facilitated the exploration of new habitats, motivated the innovation of feeding styles and behaviors, and helped drive the evolution of more complex organisms. The gastrointestinal tract has evolved to consist of a series of interwoven exchanges between nutrients, host immunity, and an often microbe-rich environmental interface. Not surprisingly, animals have expanded their immune repertoires to include soluble effectors that can be secreted into luminal spaces, e.g., in the gut, facilitating interactions with microbes in ways that influence their settlement dynamics, virulence, and their interaction with other microbes. The immunoglobulin (Ig) domain, which is also found in some non-immune molecules, is recognized as one of the most versatile recognition domains lying at the interface of innate and adaptive immunity; among vertebrates, secreted Igs are known to play crucial roles in the management of gut microbial communities. In this mini-review, we will focus on secreted immune effectors possessing Ig-like domains in invertebrates, such as the fibrinogen-related effector proteins first described in the gastropod Biomphalaria glabrata, the Down syndrome cellular adhesion molecule first described in the arthropod, Drosophila melanogaster, and the variable region-containing chitin-binding proteins of the protochordates. We will highlight our current understanding of their function and their potential role, if not yet recognized, in the establishment and maintenance of host-microbial interfaces and argue that these Igs are likely also essential to microbiome management.}, }
@article {pmid34983601, year = {2022}, author = {Maitre, A and Wu-Chuang, A and Aželytė, J and Palinauskas, V and Mateos-Hernández, L and Obregon, D and Hodžić, A and Valiente Moro, C and Estrada-Peña, A and Paoli, JC and Falchi, A and Cabezas-Cruz, A}, title = {Vector microbiota manipulation by host antibodies: the forgotten strategy to develop transmission-blocking vaccines.}, journal = {Parasites &amp; vectors}, volume = {15}, number = {1}, pages = {4}, pmid = {34983601}, issn = {1756-3305}, mesh = {Animals ; Antibodies/blood/*immunology ; Arthropod Vectors/*immunology ; Disease Transmission, Infectious/*prevention &amp; control ; Hemolymph/immunology ; Host-Pathogen Interactions ; Humans ; Salivary Glands/immunology ; Vaccine Development/*methods ; }, abstract = {Human and animal pathogens that are transmitted by arthropods are a global concern, particularly those vectored by ticks (e.g. Borrelia burgdorferi and tick-borne encephalitis virus) and mosquitoes (e.g. malaria and dengue virus). Breaking the circulation of pathogens in permanent foci by controlling vectors using acaricide-based approaches is threatened by the selection of acaricide resistance in vector populations, poor management practices and relaxing of control measures. Alternative strategies that can reduce vector populations and/or vector-mediated transmission are encouraged worldwide. In recent years, it has become clear that arthropod-associated microbiota are involved in many aspects of host physiology and vector competence, prompting research into vector microbiota manipulation. Here, we review how increased knowledge of microbial ecology and vector-host interactions is driving the emergence of new concepts and tools for vector and pathogen control. We focus on the immune functions of host antibodies taken in the blood meal as they can target pathogens and microbiota bacteria within hematophagous arthropods. Anti-microbiota vaccines are presented as a tool to manipulate the vector microbiota and interfere with the development of pathogens within their vectors. Since the importance of some bacterial taxa for colonization of vector-borne pathogens is well known, the disruption of the vector microbiota by host antibodies opens the possibility to develop novel transmission-blocking vaccines.}, }
@article {pmid34982540, year = {2022}, author = {Vandermaesen, J and Du, S and Daly, AJ and Baetens, JM and Horemans, B and De Baets, B and Boon, N and Springael, D}, title = {Interspecies Interactions of the 2,6-Dichlorobenzamide Degrading Aminobacter sp. MSH1 with Resident Sand Filter Bacteria: Indications for Mutual Cooperative Interactions That Improve BAM Mineralization Activity.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {2}, pages = {1352-1364}, doi = {10.1021/acs.est.1c06653}, pmid = {34982540}, issn = {1520-5851}, mesh = {Bacteria ; Benzamides ; Biodegradation, Environmental ; *Groundwater ; *Phyllobacteriaceae ; *Water Purification/methods ; }, abstract = {Bioaugmentation often involves an invasion process requiring the establishment and activity of a foreign microbe in the resident community of the target environment. Interactions with resident micro-organisms, either antagonistic or cooperative, are believed to impact invasion. However, few studies have examined the variability of interactions between an invader and resident species of its target environment, and none of them considered a bioremediation context. Aminobacter sp. MSH1 mineralizing the groundwater micropollutant 2,6-dichlorobenzamide (BAM), is proposed for bioaugmentation of sand filters used in drinking water production to avert BAM contamination. We examined the nature of the interactions between MSH1 and 13 sand filter resident bacteria in dual and triple species assemblies in sand microcosms. The residents affected MSH1-mediated BAM mineralization without always impacting MSH1 cell densities, indicating effects on cell physiology rather than on cell number. Exploitative competition explained most of the effects (70%), but indications of interference competition were also found. Two residents improved BAM mineralization in dual species assemblies, apparently in a mutual cooperation, and overruled negative effects by others in triple species systems. The results suggest that sand filter communities contain species that increase MSH1 fitness. This opens doors for assisting bioaugmentation through co-inoculation with "helper" bacteria originating from and adapted to the target environment.}, }
@article {pmid34982193, year = {2023}, author = {Sangodkar, N and Gonsalves, MJ and Nazareth, DR}, title = {Macrofaunal Distribution, Diversity, and Its Ecological Interaction at the Cold Seep Site of Krishna-Godavari Basin, East Coast of India.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {61-75}, pmid = {34982193}, issn = {1432-184X}, mesh = {Animals ; *Ecosystem ; Geologic Sediments/chemistry ; Biodiversity ; Methane/chemistry ; Water ; *Bivalvia ; }, abstract = {Cold seeps are characterized by typical endemic communities with associated microorganisms that depend on sulfide, methane, reduced nitrogenous compounds, and metals as electron donors for their survival through chemosynthesis. The discovery of an active cold seep site in January 2018 in the Krishna-Godavari (K-G) basin of Bay of Bengal was followed by a transit cruise in March 2018 to investigate the distribution and diversity of macrofauna. Further, the ambient sediment and pore water biochemistry were estimated to understand its relationship with macrofauna and the microbial associates of the sediment. Samples were collected at a water depth of around 1750 m at 3 stations: SP1, SP2, and SP3, using the box corer. The benthic fauna at the sites consisted mainly of Bivalvia, shrimps of Caridea family, Gastropoda species, Malacostraca species, Polychaeta, and few species of Echinoidea, Ophiuroidea, and Echiura. A total of 2313 macrofaunal individuals belonging to 8 classes, 18 families, and 20 species were identified from all the three stations. The communities were diverse at these sites with an average Shannon diversity index of 1.64 and are closely related to the lineages previously studied in ecologically similar environments. Most of the macrofauna were found to be filter feeders preferring a low organic carbon environment. Relict vesicomyid clams at the present study site suggest the succession from vesicomyids to the present composition of bivalve mussels and siboglinid worms. The microbial associates in the sediment significantly correlated with methane and hydrogen sulfide concentrations. The study suggests that the K-G basin cold seep serves as a conducive environment for the flourishing of benthic communities and therefore can support a rich biodiversity.}, }
@article {pmid34981145, year = {2023}, author = {Nabeshima, K and Sato, S and Brinkerhoff, RJ and Amano, M and Kabeya, H and Itou, T and Maruyama, S}, title = {Prevalence and Genetic Diversity of Bartonella Spp. in Northern Bats (Eptesicus nilssonii) and Their Blood-Sucking Ectoparasites in Hokkaido, Japan.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {298-306}, pmid = {34981145}, issn = {1432-184X}, support = {18K06003//japan society for the promotion of science/ ; }, mesh = {Animals ; *Bartonella ; *Chiroptera/microbiology ; Phylogeny ; Prevalence ; Japan/epidemiology ; *Bartonella Infections/epidemiology/veterinary/microbiology ; Genetic Variation ; }, abstract = {We investigated the prevalence of Bartonella in 123 northern bats (Eptesicus nilssonii) and their ectoparasites from Hokkaido, Japan. A total of 174 bat fleas (Ischnopsyllus needhami) and two bat bugs (Cimex japonicus) were collected from the bats. Bartonella bacteria were isolated from 32 (26.0%) of 123 bats. Though Bartonella DNA was detected in 79 (45.4%) of the bat fleas, the bacterium was isolated from only one bat flea (0.6%). The gltA sequences of the isolates were categorized into genotypes I, II, and III, which were found in both bats and their fleas. The gltA sequences of genotypes I and II showed 97.6% similarity with Bartonella strains from a Finnish E. nilssonii and a bat flea from a E. serotinus in the Netherlands. The rpoB sequences of the genotypes showed 98.9% similarity with Bartonella strain 44722 from E. serotinus in Republic of Georgia. The gltA and rpoB sequences of genotype III showed 95.9% and 96.7% similarity with Bartonella strains detected in shrews in Kenya and France, respectively. Phylogenetic analysis revealed that Bartonella isolates of genotypes I and II clustered with Bartonella strains from Eptesicus bats in Republic of Georgia and Finland, Myotis bats in Romania and the UK, and a bat flea from an Eptesicus bat in Finland. In contrast, genotype III formed a clade with B. florencae, B. acomydis, and B. birtlesii. These data suggest that northern bats in Japan harbor two Bartonella species and the bat flea serves as a potential vector of Bartonella transmission among the bats.}, }
@article {pmid34980289, year = {2022}, author = {Yang, Y and Sun, J and Chen, C and Zhou, Y and Van Dover, CL and Wang, C and Qiu, JW and Qian, PY}, title = {Metagenomic and metatranscriptomic analyses reveal minor-yet-crucial roles of gut microbiome in deep-sea hydrothermal vent snail.}, journal = {Animal microbiome}, volume = {4}, number = {1}, pages = {3}, pmid = {34980289}, issn = {2524-4671}, support = {DY135-E2-1-03//China Ocean Mineral Resources Research and Development Association/ ; GML2019ZD0409//the Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 2019B030302004-04//the Major Basic and Applied Basic Research Projects of Guangdong Province/ ; SMSEGL20SC01//the Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 91951201//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Marine animals often exhibit complex symbiotic relationship with gut microbes to attain better use of the available resources. Many animals endemic to deep-sea chemosynthetic ecosystems host chemoautotrophic bacteria endocellularly, and they are thought to rely entirely on these symbionts for energy and nutrition. Numerous investigations have been conducted on the interdependence between these animal hosts and their chemoautotrophic symbionts. The provannid snail Alviniconcha marisindica from the Indian Ocean hydrothermal vent fields hosts a Campylobacterial endosymbiont in its gill. Unlike many other chemosymbiotic animals, the gut of A. marisindica is reduced but remains functional; yet the contribution of gut microbiomes and their interactions with the host remain poorly characterised.<br><br>RESULTS: Metagenomic and metatranscriptomic analyses showed that the gut microbiome of A. marisindica plays key nutritional and metabolic roles. The composition and relative abundance of gut microbiota of A. marisindica were different from those of snails that do not depend on endosymbiosis. The relative abundance of microbial taxa was similar amongst three individuals of A. marisindica with significant inter-taxa correlations. These correlations suggest the potential for interactions between taxa that may influence community assembly and stability. Functional profiles of the gut microbiome revealed thousands of additional genes that assist in the use of vent-supplied inorganic compounds (autotrophic energy source), digest host-ingested organics (carbon source), and recycle the metabolic waste of the host. In addition, members of five taxonomic classes have the potential to form slime capsules&#xa0;to protect themselves from the host immune system, thereby contributing to homeostasis. Gut microbial ecology and its interplay with the host thus contribute to the nutritional and metabolic demands of A. marisindica.<br><br>CONCLUSIONS: The findings advance the understanding of how deep-sea chemosymbiotic animals use available resources through contributions from gut microbiota. Gut microbiota may be critical in the survival of invertebrate hosts with autotrophic endosymbionts in extreme environments.}, }
@article {pmid34979467, year = {2022}, author = {Lindner, BG and Suttner, B and Zhu, KJ and Conrad, RE and Rodriguez-R, LM and Hatt, JK and Brown, J and Konstantinidis, KT}, title = {Toward shotgun metagenomic approaches for microbial source tracking sewage spills based on laboratory mesocosms.}, journal = {Water research}, volume = {210}, number = {}, pages = {117993}, doi = {10.1016/j.watres.2021.117993}, pmid = {34979467}, issn = {1879-2448}, mesh = {Laboratories ; *Metagenome ; *Metagenomics ; Sewage ; Water Pollution/analysis ; }, abstract = {Little is known about the genomic diversity of the microbial communities associated with raw municipal wastewater (sewage), including whether microbial populations specific to sewage exist and how such populations could be used to improve source attribution and apportioning in contaminated waters. Herein, we used the influent of three wastewater treatment plants in Atlanta, Georgia (USA) to perturb laboratory freshwater mesocosms, simulating sewage contamination events, and followed these mesocosms with shotgun metagenomics over a 7-day observational period. We describe 15 abundant non-redundant bacterial metagenome-assembled genomes (MAGs) ubiquitous within all sewage inocula yet absent from the unperturbed freshwater control at our analytical limit of detection. Tracking the dynamics of the populations represented by these MAGs revealed varied decay kinetics, depending on (inferred) phenotypes, e.g., anaerobes decayed faster than aerobes under the well-aerated incubation conditions. Notably, a portion of these populations showed decay patterns similar to those of common markers, Enterococcus and HF183. Despite the apparent decay of these populations, the abundance of β-lactamase encoding genes remained high throughout incubation relative to the control. Lastly, we constructed genomic libraries representing several different fecal sources and outline a bioinformatic approach which leverages these libraries for identifying and apportioning contamination signal among multiple probable sources using shotgun metagenomic data.}, }
@article {pmid34977966, year = {2023}, author = {Vidhate, RP and Dawkar, VV and Punekar, SA and Giri, AP}, title = {Genomic Determinants of Entomopathogenic Fungi and Their Involvement in Pathogenesis.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {49-60}, pmid = {34977966}, issn = {1432-184X}, mesh = {Animals ; *Fungi/genetics ; *Insecta/microbiology ; Plants/microbiology ; Genomics ; Endophytes ; }, abstract = {Entomopathogenic fungi offer an effective and eco-friendly alternative to curb insect populations in biocontrol strategy. The evolutionary history of selected entomopathogenic fungi indicates their ancestral relationship with plant endophytes. During this host shifting, entomopathogenic fungi must have acquired multiple mechanisms, including a combination of various biomolecules that make them distinguishable from other fungi. In this review, we focus on understanding various biochemical and molecular mechanisms involved in entomopathogenesis. In particular, we attempt to explain the indispensable role of enlarged gene families of various virulent factors, viz. chitinases, proteases, lipases, specialized metabolites, and cytochrome P450, in entomopathogenesis. Our analysis suggests that entomopathogenic fungi recruit a different set of gene products during the progression of pathogenesis. Knowledge of these bio-molecular interactions between fungi and insect hosts will allow researchers to execute pointed efforts towards the development of improved entomopathogenic fungal strains.}, }
@article {pmid34976074, year = {2021}, author = {Cannesson, A and Elenga, N}, title = {Community-Acquired Pneumonia Requiring Hospitalization among French Guianese Children.}, journal = {International journal of pediatrics}, volume = {2021}, number = {}, pages = {4358818}, pmid = {34976074}, issn = {1687-9740}, abstract = {Community-acquired pneumonia remains a leading cause of hospitalizations among children worldwide. The diagnosis is based on the history, the physical examination results in children with fever plus respiratory signs and symptoms, and chest radiography. The microbiological etiology is confirmed by viral testing and hemocultures. The most likely etiology depends on the age of the child. The features of childhood pneumonia vary between countries and territories. The purpose of this study was to describe the epidemiological characteristics and current microbial ecology of community-acquired pneumonia in children in French Guiana. We performed a retrospective, descriptive, and monocentric study between January 1, 2015, and December 31, 2017, in the pediatric ward of the Cayenne Hospital in French Guiana. The studied population was aged from 0 to 15 years and 3 months and hospitalized for acute community-acquired pneumonia. A total of 415 patients (mean age 3.62 years) were included. A pathogen was identifiable in 22.4% of cases, including bacteria in 61.3%, viruses in 43%, and coinfections in 14%. The main pathogens were respiratory syncytial virus (31.2%), Streptococcus pneumoniae (20.4%), Haemophilus influenzae (11.8%), and Mycoplasma pneumoniae (10.8%). The burden of hospitalization for children with community-acquired pneumonia was highest among less than 2 years, in whom respiratory viruses were the most commonly detected causes of pneumonia. The share of vaccine-preventable diseases (S. pneumoniae, H. influenzae, and influenza) remains high. With the vaccination requirement imposed since 1 January 2018 against pneumococcus, Haemophilus influenzae, and whooping cough and the possibility of practicing multiplex PCR in our hospital, it will be interesting to study the impact of this law enforcement on new child generations and compare these new data to our study.}, }
@article {pmid34971998, year = {2022}, author = {Chen, P and Liu, H and Xing, Z and Wang, Y and Zhang, X and Zhao, T and Zhang, Y}, title = {Cometabolic degradation mechanism and microbial network response of methanotrophic consortia to chlorinated hydrocarbon solvents.}, journal = {Ecotoxicology and environmental safety}, volume = {230}, number = {}, pages = {113110}, doi = {10.1016/j.ecoenv.2021.113110}, pmid = {34971998}, issn = {1090-2414}, abstract = {The cometabolism mechanism of chlorinated hydrocarbon solvents (CHSs) in mixed consortia remains largely unknown. CHS biodegradation characteristics and microbial networks in methanotrophic consortia were studied for the first time. The results showed that all CHSs can efficiently be degraded via cometabolism with a maximum degradation rate of 4.8 mg/(h·gcell). Chloroalkane and chloroethylene were more easily degraded than chlorobenzenes by methanotrophic consortia, especially nonfully chlorinated aliphatic hydrocarbons, which were converted to Cl[-] with a production rate of 0.29-0.36 mg/(h·gcell). In addition, the microecological response results indicated that Methylocystaceae (49.0%), Methylomonas (65.3%) and Methylosarcina (41.9%) may be the major functional degraders in methanotrophic consortia. Furthermore, the results of the microbial correlation network suggested that interactive relationships constructed by type I methanotrophs and heterotrophs determined biodegradability. Additionally, PICRUSt analysis showed that CHSs could increase the relative abundance of CHS degradation genes and reduce the relative abundance of methane oxidation genes, which was in good agreement with the experimental results.}, }
@article {pmid34970700, year = {2023}, author = {Montiel-Molina, JAM and Sexton, JP and Frank, AC and Beman, JM}, title = {Archaeal and Bacterial Diversity and Distribution Patterns in Mediterranean-Climate Vernal Pools of Mexico and the Western USA.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {24-36}, pmid = {34970700}, issn = {1432-184X}, mesh = {*Archaea/genetics ; Mexico ; Ecosystem ; Soil Microbiology ; Bacteria/genetics ; Soil ; *Microbiota ; Water ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; }, abstract = {Biogeographic patterns in microorganisms are poorly understood, despite the importance of microbial communities for a range of ecosystem processes. Our knowledge of microbial ecology and biogeography is particularly deficient in rare and threatened ecosystems. We tested for three ecological patterns in microbial community composition within ephemeral wetlands-vernal pools-located across Baja California (Mexico) and California (USA): (1) habitat filtering; (2) a latitudinal diversity gradient; and (3) distance decay in community composition. Paired water and soil samples were collected along a latitudinal transect of vernal pools, and bacterial and archaeal communities were characterized using 16S rDNA sequencing. We identified two main microbial communities, with one community present in the soil matrix that included archaeal and bacterial soil taxa, and another community present in the overlying water that was dominated by common freshwater bacterial taxa. Aquatic microbial communities were more diverse in the north, and displayed a significant but inverted latitudinal diversity pattern. Aquatic communities also exhibited a significant distance-decay pattern, with geographic proximity, and precipitation explaining part of the community variation. Collectively these results indicate greater sensitivity to spatial and environmental variation in vernal pool aquatic microbial communities than in soil microbial communities. We conclude that vernal pool aquatic microbial communities can display distribution patterns similar to those exhibited by larger organisms, but differ in some key aspects, such as the latitudinal gradient in diversity.}, }
@article {pmid34968587, year = {2022}, author = {Wang, D and Huang, K and He, X and Zhang, XX and Meng, Y}, title = {Varied interspecies interactions between anammox and denitrifying bacteria enhanced nitrogen removal in a single-stage simultaneous anammox and denitrification system.}, journal = {The Science of the total environment}, volume = {813}, number = {}, pages = {152519}, doi = {10.1016/j.scitotenv.2021.152519}, pmid = {34968587}, issn = {1879-1026}, mesh = {Anaerobic Ammonia Oxidation ; Bacteria/genetics ; Bioreactors ; *Denitrification ; *Nitrogen ; Oxidation-Reduction ; Sewage ; Wastewater ; }, abstract = {The simultaneous anammox and denitrification (SAD) system has received growing interest for the enhanced nitrogen removal, while the ecological traits of microbial community including spatial distribution characteristics, assembly processes and interspecies interactions have not been fully unraveled. The present study applied metagenomics and ecological analysis methods to gain the ecological traits of microbial communities in the SAD system across different organic substrate loadings. Results showed that organic matter significantly affected the bioreactor performance, and the optimal total nitrogen removal efficiency reached 93.4 ± 0.7% under the COD concentrations of 180 ± 18.2 mg/L. Functional organisms including Candidatus Brocadia (3.9%), Denitratisoma (1.6%), Dokdonella (4.4%) and Thauera (4.6%) obviously enriched under the optimal organic loading conditions. Moreover, microbial communities were significantly governed by deterministic process under high organic concentrations, and the denitrifying organisms displayed important ecological roles in the communities. Although anammox bacteria obviously enriched at the middle of bioreactor, it possessed the highest expression activities at both bottom and middle sites. Denitrifying bacteria that enriched at the bottom sites strongly achieved nitrate reduction and provided nitrite for anammox bacteria, while these organisms trended to compete nitrite with anammox bacteria at the middle site. These findings highlight the importance of microbial ecology in the SAD systems, which may expand our understanding of the synergistic patterns between anammox and denitrifying bacteria.}, }
@article {pmid34966927, year = {2021}, author = {Scholz, AH and Lange, M and Habekost, P and Oldham, P and Cancio, I and Cochrane, G and Freitag, J}, title = {Myth-busting the provider-user relationship for digital sequence information.}, journal = {GigaScience}, volume = {10}, number = {12}, pages = {}, pmid = {34966927}, issn = {2047-217X}, mesh = {*Biodiversity ; *International Cooperation ; }, abstract = {BACKGROUND: The United Nations Convention on Biological Diversity (CBD) formally recognized the sovereign rights of nations over their biological diversity. Implicit within the treaty is the idea that mega-biodiverse countries will provide genetic resources and grant access to them and scientists in high-income countries will use these resources and share back benefits. However, little research has been conducted on how this framework is reflected in real-life scientific practice.<br><br>RESULT: Currently, parties to the CBD are debating whether digital sequence information (DSI) should be regulated under a new benefit-sharing framework. At this critical time point in the upcoming international negotiations, we test the fundamental hypothesis of provision and use of DSI by looking at the global patterns of access and use in scientific publications.<br><br>CONCLUSION: Our data reject the provider-user relationship and suggest a far more complex information flow for DSI. Therefore, any new policy decisions on DSI should be aware of the high level of use of DSI across low- and middle-income countries and seek to preserve open access to this crucial common good.}, }
@article {pmid34966925, year = {2021}, author = {Lange, M and Alako, BTF and Cochrane, G and Ghaffar, M and Mascher, M and Habekost, PK and Hillebrand, U and Scholz, U and Schorch, F and Freitag, J and Scholz, AH}, title = {Quantitative monitoring of nucleotide sequence data from genetic resources in context of their citation in the scientific literature.}, journal = {GigaScience}, volume = {10}, number = {12}, pages = {}, pmid = {34966925}, issn = {2047-217X}, mesh = {Base Sequence ; *Data Mining ; Databases, Nucleic Acid ; Europe ; *Nucleotides ; }, abstract = {BACKGROUND: Linking nucleotide sequence data (NSD) to scientific publication citations can enhance understanding of NSD provenance, scientific use, and reuse in the community. By connecting publications with NSD records, NSD geographical provenance information, and author geographical information, it becomes possible to assess the contribution of NSD to infer trends in scientific knowledge gain at the global level.<br><br>FINDINGS: We extracted and linked records from the European Nucleotide Archive to citations in open-access publications aggregated at Europe PubMed Central. A total of 8,464,292 ENA accessions with geographical provenance information were associated with publications. We conducted a data quality review to uncover potential issues in publication citation information extraction and author affiliation tagging and developed and implemented best-practice recommendations for citation extraction. We constructed flat data tables and a data warehouse with an interactive web application to enable ad hoc exploration of NSD use and summary statistics.<br><br>CONCLUSIONS: The extraction and linking of NSD with associated publication citations enables transparency. The quality review contributes to enhanced text mining methods for identifier extraction and use. Furthermore, the global provision and use of NSD enable scientists worldwide to join literature and sequence databases in a multidimensional fashion. As a concrete use case, we visualized statistics of country clusters concerning NSD access in the context of discussions around digital sequence information under the United Nations Convention on Biological Diversity.}, }
@article {pmid34964290, year = {2021}, author = {Baliarda, A and Winkler, M and Tournier, L and Tinsley, CR and Aymerich, S}, title = {Dynamic interspecies interactions and robustness in a four-species model biofilm.}, journal = {MicrobiologyOpen}, volume = {10}, number = {6}, pages = {e1254}, pmid = {34964290}, issn = {2045-8827}, mesh = {Bacillus cereus/physiology ; Biofilms/*growth &amp; development ; Ecosystem ; *Microbial Interactions ; *Microbiota ; Micrococcaceae/physiology ; Peptides/metabolism ; Plankton/physiology ; Pseudomonas fluorescens/physiology ; Rhodocyclaceae/physiology ; }, abstract = {Interspecific interactions within biofilms determine relative species abundance, growth dynamics, community resilience, and success or failure of invasion by an extraneous organism. However, deciphering interspecific interactions and assessing their contribution to biofilm properties and function remain a challenge. Here, we describe the constitution of a model biofilm composed of four bacterial species belonging to four different genera (Rhodocyclus sp., Pseudomonas fluorescens, Kocuria varians, and Bacillus cereus), derived from a biofilm isolated from an industrial milk pasteurization unit. We demonstrate that the growth dynamics and equilibrium composition of this biofilm are highly reproducible. Based on its equilibrium composition, we show that the establishment of this four-species biofilm is highly robust against initial, transient perturbations but less so towards continuous perturbations. By comparing biofilms formed from different numbers and combinations of the constituent species and by fitting a growth model to the experimental data, we reveal a network of dynamic, positive, and negative interactions that determine the final composition of the biofilm. Furthermore, we reveal that the molecular determinant of one negative interaction is the thiocillin I synthesized by the B. cereus strain, and demonstrate its importance for species distribution and its impact on robustness by mutational analysis of the biofilm ecosystem.}, }
@article {pmid34963611, year = {2022}, author = {Bouchali, R and Mandon, C and Marti, R and Michalon, J and Aigle, A and Marjolet, L and Vareilles, S and Kouyi, GL and Polomé, P and Toussaint, JY and Cournoyer, B}, title = {Bacterial assemblages of urban microbiomes mobilized by runoff waters match land use typologies and harbor core species involved in pollutant degradation and opportunistic human infections.}, journal = {The Science of the total environment}, volume = {815}, number = {}, pages = {152662}, doi = {10.1016/j.scitotenv.2021.152662}, pmid = {34963611}, issn = {1879-1026}, mesh = {Bacteria/genetics ; *Environmental Pollutants ; Humans ; *Microbiota ; RNA, Ribosomal, 16S ; *Water Pollutants, Chemical/analysis ; }, abstract = {Cities are patchworks of urban catchments divided into functional units according to their commercial, residential and industrial activities, and socio-urbanistic patterns. The hypothesis of city surface microbiomes being structured by socio-urbanistic variables leading to an emergence of synurbic taxa was tested. According to the r/K microbial ecology theory, a gradient of well-adapted synurbic K-strategists and of opportunistic -r-strategists should occur over city surfaces. K-strategists would be core components while r-ones would be transiently detected. To resolve these patterns, sub-catchments (n = 21) of an area of high commercial and industrial activities were investigated over three time periods covering one year. The sub-catchments' land use patterns and associated human behaviors were converted into socio-urbanistic variables and groupings. Bacterial cells mobilized by runoffs per sub-catchment were recovered, and analyzed by classical approaches, microbial source tracking DNA assays and DNA meta-barcoding approaches. Relationships between these datasets, the runoff physico-chemical properties, and descriptors of the socio-urbanistic groupings were investigated. 16S rRNA meta-barcoding analyses showed evidence of the occurrence of K- and r-like strategists. Twenty-eight core genera were identified, and correlation networks revealed large bacterial modules organized around actinobacterial taxa involved in hydrocarbon degradation processes. Other bacterial networks were related to the occurrences of hygienic wastes, and involved bacteria originating from fecal contaminations. Several r-strategists like Sulfurospirillum were recorded and found associated to point source pollutions. The tpm-metabarcoding approach deciphered these r / K strategists at the species level among more than ten genera. Nine core K-like Pseudomomas species were identified. The P. aeruginosa human opportunistic pathogen and P. syringae phytopathogens were part of these K-strategists. Other tpm-harboring bacterial pathogens showed r-like opportunistic distribution patterns. Correlation network analyses indicated a strong incidence of hygienic wastes and hydrocarbon-pollutions on tpm-harboring bacteria. These analyses demonstrated the occurrence of core synurbic bacterial K-strategists over city surfaces.}, }
@article {pmid34959793, year = {2021}, author = {Binder, C and Schned, H and Longford, N and Schwindt, E and Thanhaeuser, M and Thajer, A and Goeral, K and Tardelli, M and Berry, D and Wisgrill, L and Seki, D and Berger, A and Klebermass-Schrehof, K and Repa, A and Giordano, V}, title = {A Mixed-Lipid Emulsion Containing Fish Oil for the Parenteral Nutrition of Preterm Infants: No Impact on Visual Neuronal Conduction.}, journal = {Nutrients}, volume = {13}, number = {12}, pages = {}, pmid = {34959793}, issn = {2072-6643}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Evoked Potentials, Visual/*drug effects ; Fat Emulsions, Intravenous/*administration &amp; dosage/*chemistry ; Female ; Fish Oils/*administration &amp; dosage ; Humans ; Infant, Newborn ; Infant, Premature/physiology ; Male ; Neural Conduction/*drug effects ; Olive Oil/administration &amp; dosage ; Parenteral Nutrition ; Retrospective Studies ; Soybean Oil/administration &amp; dosage ; Triglycerides/administration &amp; dosage ; }, abstract = {Fish oil is rich in omega-3 fatty acids and essential for neuronal myelination and maturation. The aim of this study was to investigate whether the use of a mixed-lipid emulsion composed of soybean oil, medium-chain triglycerides, olive oil, and fish oil (SMOF-LE) compared to a pure soybean oil-based lipid emulsion (S-LE) for parenteral nutrition had an impact on neuronal conduction in preterm infants. This study is a retrospective matched cohort study comparing preterm infants <1000 g who received SMOF-LE in comparison to S-LE for parenteral nutrition. Visual evoked potentials (VEPs) were assessed longitudinally from birth until discharge. The latencies of the evoked peaks N2 and P2 were analyzed. The analysis included 76 infants (SMOF-LE: n = 41 and S-LE: n = 35) with 344 VEP measurements (SMOF-LE: n= 191 and S-LE n = 153). Values of N2 and P2 were not significantly different between the SMOF-LE and S-LE groups. A possible better treatment effect in the SMOF-LE group was seen as a trend toward a shorter latency, indicating faster neural conduction at around term-equivalent age. Prospective trials and follow-up studies are necessary in order to evaluate the potential positive effect of SMOF-LE on neuronal conduction and visual pathway maturation.}, }
@article {pmid34958387, year = {2022}, author = {Kable, ME and Chin, EL and Storms, D and Lemay, DG and Stephensen, CB}, title = {Tree-Based Analysis of Dietary Diversity Captures Associations Between Fiber Intake and Gut Microbiota Composition in a Healthy US Adult Cohort.}, journal = {The Journal of nutrition}, volume = {152}, number = {3}, pages = {779-788}, doi = {10.1093/jn/nxab430}, pmid = {34958387}, issn = {1541-6100}, mesh = {Adolescent ; Adult ; Aged ; Cross-Sectional Studies ; Diet ; Dietary Fiber/analysis ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Middle Aged ; RNA, Ribosomal, 16S/analysis/genetics ; Young Adult ; }, abstract = {BACKGROUND: Diet patterns are a significant and modifiable contributing factor to the composition of the human gut microbiota.<br><br>OBJECTIVES: We set out to identify reproducible relationships between diet and gut microbial community composition in a diverse, healthy US adult cohort.<br><br>METHODS: We collected 2 to 3 automated self-administered 24-hour dietary recalls over 10-14 days, together with a single stool sample, from 343 healthy adults in a cross-sectional phenotyping study. This study examined a multi-ethnic cohort balanced for age (18-65 years), sex, and BMI (18.5-45 kg/m2). Dietary data were edited to a tree format according to published methods. The tree structure was annotated with the average total grams of dry weight, fat, protein, carbohydrate, or fiber from each food item reported. The alpha and beta diversity measurements, calculated using the tree structure, were analyzed relative to the microbial community diversity, determined by a Quantitative Insights Into Microbial Ecology (QIIME) 2 analysis of the bacterial 16S ribosomal RNA V4 region, sequenced from stool samples. K-means clustering was used to form groups of individuals consuming similar diets, and gut microbial communities were compared among groups using differential expression analysis for sequence count data.<br><br>RESULTS: The alpha diversity of diet dry weight was significantly correlated with the gut microbial community alpha diversity (r&#xa0;=&#xa0;0.171). The correlation improved when diet was characterized using grams of carbohydrates (r&#xa0;=&#xa0;0.186) or fiber (r&#xa0;=&#xa0;0.213). Bifidobacterium was enriched with diets containing higher levels of total carbohydrate from cooked grains. Lachnospira, was enriched with diet patterns containing high consumption of fiber from fruits excluding berries.<br><br>CONCLUSIONS: The tree structure, annotated with grams of carbohydrate, is a robust analysis method for comparing self-reported diet to the gut microbial community composition. This method identified consumption of fiber from fruit robustly associated with an abundance of pectinolytic bacterial genus, Lachnospira, in the guts of healthy adults. This trial was registered at clinicaltrials.gov as NCT02367287.}, }
@article {pmid34956127, year = {2021}, author = {Blumberg, KL and Ponsero, AJ and Bomhoff, M and Wood-Charlson, EM and DeLong, EF and Hurwitz, BL}, title = {Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {765268}, pmid = {34956127}, issn = {1664-302X}, abstract = {Marine microbial ecology requires the systematic comparison of biogeochemical and sequence data to analyze environmental influences on the distribution and variability of microbial communities. With ever-increasing quantities of metagenomic data, there is a growing need to make datasets Findable, Accessible, Interoperable, and Reusable (FAIR) across diverse ecosystems. FAIR data is essential to developing analytical frameworks that integrate microbiological, genomic, ecological, oceanographic, and computational methods. Although community standards defining the minimal metadata required to accompany sequence data exist, they haven't been consistently used across projects, precluding interoperability. Moreover, these data are not machine-actionable or discoverable by cyberinfrastructure systems. By making 'omic and physicochemical datasets FAIR to machine systems, we can enable sequence data discovery and reuse based on machine-readable descriptions of environments or physicochemical gradients. In this work, we developed a novel technical specification for dataset encapsulation for the FAIR reuse of marine metagenomic and physicochemical datasets within cyberinfrastructure systems. This includes using Frictionless Data Packages enriched with terminology from environmental and life-science ontologies to annotate measured variables, their units, and the measurement devices used. This approach was implemented in Planet Microbe, a cyberinfrastructure platform and marine metagenomic web-portal. Here, we discuss the data properties built into the specification to make global ocean datasets FAIR within the Planet Microbe portal. We additionally discuss the selection of, and contributions to marine-science ontologies used within the specification. Finally, we use the system to discover data by which to answer various biological questions about environments, physicochemical gradients, and microbial communities in meta-analyses. This work represents a future direction in marine metagenomic research by proposing a specification for FAIR dataset encapsulation that, if adopted within cyberinfrastructure systems, would automate the discovery, exchange, and re-use of data needed to answer broader reaching questions than originally intended.}, }
@article {pmid34956126, year = {2021}, author = {Krukenberg, V and Reichart, NJ and Spietz, RL and Hatzenpichler, R}, title = {Microbial Community Response to Polysaccharide Amendment in Anoxic Hydrothermal Sediments of the Guaymas Basin.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {763971}, pmid = {34956126}, issn = {1664-302X}, abstract = {Organic-rich, hydrothermal sediments of the Guaymas Basin are inhabited by diverse microbial communities including many uncultured lineages with unknown metabolic potential. Here we investigated the short-term effect of polysaccharide amendment on a sediment microbial community to identify taxa involved in the initial stage of macromolecule degradation. We incubated anoxic sediment with cellulose, chitin, laminarin, and starch and analyzed the total and active microbial communities using bioorthogonal non-canonical amino acid tagging (BONCAT) combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Our results show a response of an initially minor but diverse population of Clostridia particularly after amendment with the lower molecular weight polymers starch and laminarin. Thus, Clostridia may readily become key contributors to the heterotrophic community in Guaymas Basin sediments when substrate availability and temperature range permit their metabolic activity and growth, which expands our appreciation of the potential diversity and niche differentiation of heterotrophs in hydrothermally influenced sediments. BONCAT-FACS, although challenging in its application to complex samples, detected metabolic responses prior to growth and thus can provide complementary insight into a microbial community's metabolic potential and succession pattern. As a primary application of BONCAT-FACS on a diverse deep-sea sediment community, our study highlights important considerations and demonstrates inherent limitations associated with this experimental approach.}, }
@article {pmid34956106, year = {2021}, author = {Onyango, SO and Juma, J and De Paepe, K and Van de Wiele, T}, title = {Oral and Gut Microbial Carbohydrate-Active Enzymes Landscape in Health and Disease.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {653448}, pmid = {34956106}, issn = {1664-302X}, abstract = {Inter-individual variability in the microbial gene complement encoding for carbohydrate-active enzymes (CAZymes) can profoundly regulate how the host interacts with diverse carbohydrate sources thereby influencing host health. CAZy-typing, characterizing the microbiota-associated CAZyme-coding genes within a host individual, can be a useful tool to predict carbohydrate pools that the host can metabolize, or identify which CAZyme families are underrepresented requiring supplementation via microbiota transplantation or probiotics. CAZy-typing, moreover, provides a novel framework to search for disease biomarkers. As a proof of concept, we used publicly available metagenomes (935) representing 310 type strain bacterial genomes to establish the link between disease status and CAZymes in the oral and gut microbial ecosystem. The abundance and distribution of 220 recovered CAZyme families in saliva and stool samples from patients with colorectal cancer, rheumatoid arthritis, and type 1 diabetes were compared with healthy subjects. Based on the multivariate discriminant analysis, the disease phenotype did not alter the CAZyme profile suggesting a functional conservation in carbohydrate metabolism in a disease state. When disease and healthy CAZyme profiles were contrasted in differential analysis, CAZyme markers that were underrepresented in type 1 diabetes (15), colorectal cancer (12), and rheumatoid arthritis (5) were identified. Of interest, are the glycosyltransferase which can catalyze the synthesis of glycoconjugates including lipopolysaccharides with the potential to trigger inflammation, a common feature in many diseases. Our analysis has also confirmed the expansive carbohydrate metabolism in the gut as evidenced by the overrepresentation of CAZyme families in the gut compared to the oral site. Nevertheless, each site exhibited specific CAZyme markers. Taken together, our analysis provides an insight into the CAZyme landscape in health and disease and has demonstrated the diversity in carbohydrate metabolism in host-microbiota which can be a sound basis for optimizing the selection of pre, pro, and syn-biotic candidate products.}, }
@article {pmid34954887, year = {2022}, author = {Antonelli, P and Salerno, B and Bordin, P and Peruzzo, A and Orsini, M and Arcangeli, G and Barco, L and Losasso, C}, title = {Tetrodotoxin in live bivalve mollusks from Europe: Is it to be considered an emerging concern for food safety?.}, journal = {Comprehensive reviews in food science and food safety}, volume = {21}, number = {1}, pages = {719-737}, doi = {10.1111/1541-4337.12881}, pmid = {34954887}, issn = {1541-4337}, support = {RC IZSVe 01/2019//Ministero della Salute/ ; }, mesh = {Animals ; *Bivalvia ; Europe ; Food Safety ; Shellfish/analysis ; Tetrodotoxin/analysis/toxicity ; }, abstract = {Tetrodotoxins (TTXs) are a group of potent neurotoxins named after the Tetraodontidae fish family (pufferfish). TTXs have been reported in several animal taxa, both terrestrial and marine. The ingestion of TTX-contaminated flesh can cause serious neurotoxic symptomatology and can eventually lead to death. Traditionally, TTXs have been associated with Asian countries, in particular with pufferfish consumption. However, they have also been reported in bivalve mollusks farmed in the Pacific area and, recently, in European seas. In Europe, different countries have reported TTXs, especially those bordering the Mediterranean Sea. As a consequence, in 2017 the European Food Safety Authority (EFSA) released an opinion with reference to TTX present in marine gastropods and bivalves, proposing a safety limit of 44 µg/kg TTXs in shellfish meat, below which no adverse effects should be observed in humans. Nevertheless, this limit has been exceeded on many occasions in European shellfish and, while for bivalves there have been no registered human intoxications, that is not the case for marine gastropods. However, TTXs have not yet been included in the list of marine biotoxins officially monitored in live bivalve mollusks within the European Union (EU). Thus, the aims of this manuscript are to discuss the increasing occurrence of TTXs in live bivalve mollusks from European sea waters, to acknowledge the still ongoing knowledge gaps that should be covered and to stimulate constructive debate on the eventuality of adopting a shared regulatory context, at least in the EU, for monitoring and managing this potential threat to food safety.}, }
@article {pmid34954170, year = {2022}, author = {Soder-Walz, JM and Torrentó, C and Algora, C and Wasmund, K and Cortés, P and Soler, A and Vicent, T and Rosell, M and Marco-Urrea, E}, title = {Trichloromethane dechlorination by a novel Dehalobacter sp. strain 8M reveals a third contrasting C and Cl isotope fractionation pattern within this genus.}, journal = {The Science of the total environment}, volume = {813}, number = {}, pages = {152659}, doi = {10.1016/j.scitotenv.2021.152659}, pmid = {34954170}, issn = {1879-1026}, mesh = {Biodegradation, Environmental ; Carbon Isotopes/analysis ; Chemical Fractionation ; *Chloroform ; *Groundwater ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Trichloromethane (TCM) is a pollutant frequently detected in contaminated aquifers, and only four bacterial strains are known to respire it. Here, we obtained a novel Dehalobacter strain capable of transforming TCM to dichloromethane, which was denominated Dehalobacter sp. strain 8M. Besides TCM, strain 8M also completely transformed 1,1,2-trichloroethane to vinyl chloride and 1,2-dichloroethane. Quantitative PCR analysis for the 16S rRNA genes confirmed growth of Dehalobacter with TCM and 1,1,2-trichloroethane as electron acceptors. Carbon and chlorine isotope fractionation during TCM transformation was studied in cultured cells and in enzymatic assays with cell suspensions and crude protein extracts. TCM transformation in the three studied systems resulted in small but significant carbon (εC = -2.7 ± 0.1‰ for respiring cells, -3.1 ± 0.1‰ for cell suspensions, and - 4.1 ± 0.5‰ for crude protein extracts) and chlorine (εCl = -0.9 ± 0.1‰, -1.1 ± 0.1‰, and - 1.2 ± 0.2‰, respectively) isotope fractionation. A characteristic and consistent dual CCl isotope fractionation pattern was observed for the three systems (combined Λ[C/Cl] = 2.8 ± 0.3). This Λ[C/Cl] differed significantly from previously reported values for anaerobic dechlorination of TCM by the corrinoid cofactor vitamin B12 and other Dehalobacter strains. These findings widen our knowledge on the existence of different enzyme binding mechanisms underlying TCM-dechlorination within the genus Dehalobacter and demonstrates that dual isotope analysis could be a feasible tool to differentiate TCM degraders at field studies.}, }
@article {pmid34951701, year = {2022}, author = {Etto, RM and Jesus, EC and Cruz, LM and Schneider, BSF and Tomachewski, D and Urrea-Valencia, S and Gonçalves, DRP and Galvão, F and Ayub, RA and Curcio, GR and Steffens, MBR and Galvão, CW}, title = {Influence of environmental factors on the tropical peatlands diazotrophic communities from the Southern Brazilian Atlantic Rain Forest.}, journal = {Letters in applied microbiology}, volume = {74}, number = {4}, pages = {543-554}, doi = {10.1111/lam.13638}, pmid = {34951701}, issn = {1472-765X}, mesh = {Brazil ; Ecosystem ; *Rainforest ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The tropical peatlands of southern Brazil are essential for the maintenance of the Atlantic Rain Forest, one of the 25 hotspots of biodiversity in the world. Although diazotrophic micro-organisms are essential for the maintenance of this nitrogen limited ecosystem, so far studies have focused only on micro-organisms involved in the carbon cycle. In this work, peat samples were collected from three tropical peatland regions during dry and rainy seasons and their chemical and microbial characteristics were evaluated. Our results showed that the structure of the diazotrophic communities in the Brazilian tropical peatlands differs in the evaluated seasons. The abundance of the genus Bradyrhizobium showed to be affected by rainfall and peat pH. Despite the shifts of the nitrogen-fixing population in the tropical peatland caused by seasonality it showed to be constantly dominated by α-Proteobacteria followed by Cyanobacteria. In addition, more than 50% of nifH gene sequences have not been classified, indicating the necessity for more studies in tropical peatland, since the reduction of N supply in the peatlands stimulates the recalcitrant organic matter decomposition performed by peatland micro-organisms, influencing the C stock.}, }
@article {pmid34951695, year = {2021}, author = {Sarker, RK and Chakraborty, P and Sarkar, S and Ghosh, MM and Tribedi, P}, title = {Bioaugmentation of Enterobacter cloacae AKS7 causes an enhanced degradation of low-density polyethylene (LDPE) in soil: a promising approach for the sustainable management of LDPE waste.}, journal = {Archives of microbiology}, volume = {204}, number = {1}, pages = {74}, pmid = {34951695}, issn = {1432-072X}, mesh = {Biodegradation, Environmental ; Ecosystem ; Enterobacter cloacae ; *Polyethylene ; Soil ; Soil Microbiology ; *Soil Pollutants ; }, abstract = {Enterobacter cloacae AKS7 was previously reported to degrade UV-treated low-density polyethylene (LDPE) more efficiently than UV-untreated LDPE. However, the degradation of LDPE by Enterobacter cloacae AKS7 at the LDPE-contaminated soil remained unaddressed. To address this issue, soil microcosms were prepared in which an equal amount of either UV-treated or UV-untreated LDPE was added. Then, the microcosms were either augmented with AKS7 or left non-augmented. We observed that the bioaugmented microcosms exhibited approximately twofold greater polymer degradation than non-bioaugmented microcosms. To investigate the underlying cause, we found that the abundance of LDPE-degrading organisms got increased by approximately fivefold in bioaugmented microcosms than non-bioaugmented microcosms. The microbial biomass carbon and nitrogen content got enhanced by approximately twofold in bioaugmented microcosms as contrasted to non-bioaugmented microcosms. Furthermore, the bioaugmented microcosms showed almost twofold increase in the level of dehydrogenase and fluorescein diacetate (FDA) hydrolyzing activity than the non-bioaugmented microcosms. To add on, Shannon-diversity index and Gini coefficient were determined in each microcosm to measure the microbial richness and evenness, respectively, using the results of carbon source utilization pattern of BiOLOG ECO plate. The bioaugmented microcosms exhibited ~ 30% higher functional richness and ~ 30% enhanced functional evenness than the non-bioaugmented microcosms indicating the formation of an enriched ecosystem that could offer various functions including polymer degradation. Taken together, the results suggested that Enterobacter cloacae AKS7 could be used as a promising bioaugmenting agent for the sustainable degradation of LDPE waste at a contaminated site.}, }
@article {pmid34946990, year = {2021}, author = {Christopher, Y and Aguilar, C and Gálvez, D and Wcislo, WT and Gerardo, NM and Fernández-Marín, H}, title = {Interactions among Escovopsis, Antagonistic Microfungi Associated with the Fungus-Growing Ant Symbiosis.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {7}, number = {12}, pages = {}, pmid = {34946990}, issn = {2309-608X}, support = {FID 18 - 079//Secretar&#xed;a Nacional de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; }, abstract = {Fungi in the genus Escovopsis (Ascomycota: Hypocreales) are prevalent associates of the complex symbiosis between fungus-growing ants (Tribe Attini), the ants' cultivated basidiomycete fungi and a consortium of both beneficial and harmful microbes found within the ants' garden communities. Some Escovopsis spp. have been shown to attack the ants' cultivated fungi, and co-infections by multiple Escovopsis spp. are common in gardens in nature. Yet, little is known about how Escovopsis strains impact each other. Since microbe-microbe interactions play a central role in microbial ecology and evolution, we conducted experiments to assay the types of interactions that govern Escovopsis-Escovopsis relationships. We isolated Escovopsis strains from the gardens of 10 attine ant genera representing basal (lower) and derived groups in the attine ant phylogeny. We conducted in vitro experiments to determine the outcome of both intraclonal and interclonal Escovopsis confrontations. When paired with self (intraclonal interactions), Escovopsis isolated from lower attine colonies exhibited antagonistic (inhibitory) responses, while strains isolated from derived attine colonies exhibited neutral or mutualistic interactions, leading to a clear phylogenetic pattern of interaction outcome. Interclonal interactions were more varied, exhibiting less phylogenetic signal. These results can serve as the basis for future studies on the costs and benefits of Escovopsis coinfection, and on the genetic and chemical mechanisms that regulate the compatibility and incompatibility observed here.}, }
@article {pmid34946177, year = {2021}, author = {Purushotham, N and Jones, E and Monk, J and Ridgway, H}, title = {Fungal Communities in the Native New Zealand Medicinal Plant Pseudowintera colorata (Horopito) Are Determined by Plant Organ Type and Host Maturity with Key Members Promoting Plant Growth.}, journal = {Microorganisms}, volume = {9}, number = {12}, pages = {}, pmid = {34946177}, issn = {2076-2607}, abstract = {The plant Pseudowintera colorata is well known for its antimicrobial and medicinal properties and is endemic to New Zealand. Using PCR-Denaturing gradient gel electrophoresis (DGGE), we investigated the factors influencing the composition of endophytic fungal communities in P. colorata from ten distinct sites across New Zealand. Our results showed that plant organs of P. colorata influenced the diversity and richness of endophytic fungi (PERMANOVA, p < 0.05). In addition, plant maturity and its interactions revealed that endophytic fungal communities formed discrete clusters in leaves, stems, and roots of mature and immature P. colorata plants (PERMANOVA; p = 0.002, p = 0.001 and p = 0.039, respectively). For identifying isolates with biocontrol potential, dual culture tests were set up against four different phytopathogenic fungi. Isolates with high activity (zone of inhibition > 10 mm) were sequenced and identified as Trichoderma harzianum, Pezicula neosporulosa, Fusariumtricinctum, Metarhizium sp., and Chaetomium sp. Applying selected endophytic fungi (n = 7) as soil drenchers significantly increased the growth of P. colorata seedlings and produced more internodes. Seedling shoots treated with Trichoderma sp. PRY2BA21 were 2.2 × longer (8.36 cm) than the untreated controls (3.72 cm). Our results elucidate the main plant factors influencing fungal community composition and demonstrate a role for endophytic fungi in P. colorata growth and further demonstrate that medicinal plants are a rich source of endophytes with potential as biocontrol agents.}, }
@article {pmid34940904, year = {2021}, author = {Das, S and Paul, P and Chatterjee, S and Chakraborty, P and Sarker, RK and Das, A and Maiti, D and Tribedi, P}, title = {Piperine exhibits promising antibiofilm activity against Staphylococcus aureus by accumulating reactive oxygen species (ROS).}, journal = {Archives of microbiology}, volume = {204}, number = {1}, pages = {59}, pmid = {34940904}, issn = {1432-072X}, support = {R&amp;D/2020/F2//The Neotia University/ ; }, mesh = {*Alkaloids/pharmacology ; Anti-Bacterial Agents/pharmacology ; Benzodioxoles ; Biofilms ; Humans ; Microbial Sensitivity Tests ; Piperidines ; Polyunsaturated Alkamides ; Reactive Oxygen Species ; *Staphylococcus aureus ; }, abstract = {Staphylococcus aureus causes numerous community-acquired and nosocomial infections in humans by exploiting biofilm. In this context, this study aims to impede the formation of Staphylococcus aureus biofilm by exposing the cells to a plant-based alkaloid, piperine. Our study revealed that piperine exhibited considerable antimicrobial activity against the test organism. However, we had tested the lower concentrations (up to 32 µg/mL) of piperine to observe whether they could show any antibiofilm activity against the same organism. Several experiments, like crystal violet (CV) assay, estimation of total biofilm protein, and fluorescence microscopic observations, established that lower concentrations (up to 16 µg/mL) of piperine showed efficient antibiofilm activity against Staphylococcus aureus. In this connection, we also noticed that the lower concentrations (8 and 16 µg/mL) of piperine showed a considerable reduction in microbial metabolic activity. Besides, it was also observed that the mentioned concentrations of piperine did not compromise the microbial growth of the target organism while exhibiting antibiofilm activity. To understand the underlying mechanism of microbial biofilm inhibition under the influence of piperine, we observed that the compound was found to accumulate reactive oxygen species in the bacterial cells that could play an important role in the inhibition of biofilm formation. Furthermore, the tested concentrations (8 and 16 µg/mL) of piperine were able to inhibit the motility of the test organism that might compromise the development of biofilm. Thus, piperine could be considered as a potential agent for the effective management of biofilm threat caused by Staphylococcus aureus.}, }
@article {pmid34939130, year = {2023}, author = {Trzebny, A and Slodkowicz-Kowalska, A and Björkroth, J and Dabert, M}, title = {Microsporidian Infection in Mosquitoes (Culicidae) Is Associated with Gut Microbiome Composition and Predicted Gut Microbiome Functional Content.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {247-263}, pmid = {34939130}, issn = {1432-184X}, support = {2020/37/N/NZ8/01735//Narodowe Centrum Nauki/ ; 05/IDUB/2019/94//Initiative of Excellence - Research University at Adam Mickiewicz University, Poznan, Poland/ ; }, mesh = {Animals ; Female ; *Culicidae/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria/genetics ; *Microsporidia/genetics ; }, abstract = {The animal gut microbiota consist of many different microorganisms, mainly bacteria, but archaea, fungi, protozoans, and viruses may also be present. This complex and dynamic community of microorganisms may change during parasitic infection. In the present study, we investigated the effect of the presence of microsporidians on the composition of the mosquito gut microbiota and linked some microbiome taxa and functionalities to infections caused by these parasites. We characterised bacterial communities of 188 mosquito females, of which 108 were positive for microsporidian DNA. To assess how bacterial communities change during microsporidian infection, microbiome structures were identified using 16S rRNA microbial profiling. In total, we identified 46 families and four higher taxa, of which Comamonadaceae, Enterobacteriaceae, Flavobacteriaceae and Pseudomonadaceae were the most abundant mosquito-associated bacterial families. Our data suggest that the mosquito gut microbial composition varies among host species. In addition, we found a correlation between the microbiome composition and the presence of microsporidians. The prediction of metagenome functional content from the 16S rRNA gene sequencing suggests that microsporidian infection is characterised by some bacterial species capable of specific metabolic functions, especially the biosynthesis of ansamycins and vancomycin antibiotics and the pentose phosphate pathway. Moreover, we detected a positive correlation between the presence of microsporidian DNA and bacteria belonging to Spiroplasmataceae and Leuconostocaceae, each represented by a single species, Spiroplasma sp. PL03 and Weissella cf. viridescens, respectively. Additionally, W. cf. viridescens was observed only in microsporidian-infected mosquitoes. More extensive research, including intensive and varied host sampling, as well as determination of metabolic activities based on quantitative methods, should be carried out to confirm our results.}, }
@article {pmid34938278, year = {2021}, author = {Shi, Y and Yang, H and Chu, M and Niu, X and Wang, N and Lin, Q and Lou, K and Zuo, C and Wang, J and Zou, Q and Zhang, Y}, title = {Differentiation and Variability in the Rhizosphere and Endosphere Microbiomes of Healthy and Diseased Cotton (Gossypium sp.).}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {765269}, pmid = {34938278}, issn = {1664-302X}, abstract = {The plant microbiome is a key determinant of health and productivity. However, it is still difficult to understand the structural composition of the bacterial and fungal microbiomes of diseased and healthy plants, especially the spatial dynamics and phylogenies of endophytic and rhizosphere microbial communities. We studied the differentiation and variability in the rhizosphere and endosphere microbiomes of healthy and diseased cotton from north and south of the Tianshan Mountains using the methods of PCR-based high-throughput sequencing and real-time quantitative PCR. The endophytic and rhizosphere bacterial abundances in the diseased plants were greater than those of healthy plants. The numbers of endophytic and rhizosphere fungi associated with diseased plants were greater than those associated healthy plants (p < 0.05). Endophytic and rhizosphere bacteria did not share common OTUs. The dominant rhizosphere bacteria were Proteobacteria (29.70%), Acidobacteria (23.14%), Gemmatimonadetes (15.17%), Actinobacteria (8.31%), Chloroflexi (7.99%), and Bacteroidetes (5.15%). The dominant rhizosphere fungi were Ascomycota (83.52%), Mortierellomycota (7.67%), Basidiomycota (2.13%), Chytridiomycota (0.39%), and Olpidiomycota (0.08%). The distribution of dominant bacteria in different cotton rhizosphere soils and roots differed, with the dominant bacteria Pseudomonas (15.54%) and Pantoea (9.19%), and the dominant fungi Alternaria (16.15%) and Cephalotrichum (9.10%) being present in the greatest numbers. At sampling points in different ecological regions, the total numbers of cotton endophytic and rhizosphere microbiome OTUs from southern to northern Xinjiang showed an increasing trend. There were significant differences in the composition and diversity of rhizosphere microbes and endophytes during the entire cotton growth period and in representative ecological regions (p < 0.01), whereas rhizosphere microbes and endophytes showed no significant differences among the four growth periods and in representative ecological regions. RB41, H16, Nitrospira, and Sphingomonas play important roles in the microbial ecology of cotton rhizosphere soil. Pseudomonas accounted for a large proportion of the microbes in the cotton rhizosphere soil. This study provides an in-depth understanding of the complex microbial composition and diversity associated with cotton north and south of the Tianshan Mountains.}, }
@article {pmid34933408, year = {2022}, author = {Šimek, K and Mukherjee, I and Nedoma, J and de Paula, CCP and Jezberová, J and Sirová, D and Vrba, J}, title = {CARD-FISH and prey tracer techniques reveal the role of overlooked flagellate groups as major bacterivores in freshwater hypertrophic shallow lakes.}, journal = {Environmental microbiology}, volume = {24}, number = {9}, pages = {4256-4273}, pmid = {34933408}, issn = {1462-2920}, mesh = {Bacteria/genetics ; *Ciliophora ; Cryptophyta ; Ecosystem ; In Situ Hybridization, Fluorescence ; *Lakes/microbiology ; Phylogeny ; }, abstract = {Heterotrophic nanoflagellates (HNF) and ciliates are major protistan planktonic bacterivores. The term HNF, however, describes a functional guild only and, in contrast to the morphologically distinguishable ciliates, does not reflect the phylogenetic diversity of flagellates in aquatic ecosystems. Associating a function with taxonomic affiliation of key flagellate taxa is currently a major task in microbial ecology. We investigated seasonal changes in the HNF and ciliate community composition as well as taxa-specific bacterivory in four hypertrophic freshwater lakes. Taxa-specific catalyzed reporter deposition-fluorescence in situ hybridization probes assigned taxonomic affiliations to 51%-96% (average ±SD, 75 ± 14%) of total HNF. Ingestion rates of fluorescently labelled bacteria unveiled that HNF contributed to total protist-induced bacterial mortality rates more (56%) than ciliates (44%). Surprisingly, major HNF bacterivores were aplastidic cryptophytes and their Cry1 lineage, comprising on average 53% and 24% of total HNF abundance and 67% and 21% of total HNF bacterivory respectively. Kinetoplastea were important consumers of bacteria during summer phytoplankton blooms, reaching 38% of total HNF. Katablepharidacea (7.5% of total HNF) comprised mainly omnivores, with changing contributions of bacterivorous and algivorous phylotypes. Our results show that aplastidic cryptophytes, accompanied by small omnivorous ciliate genera Halteria/Pelagohalteria, are the major protistan bacterivores in hypertrophic freshwaters.}, }
@article {pmid34933025, year = {2022}, author = {Qi, P and Li, T and Hu, C and Li, Z and Bi, Z and Chen, Y and Zhou, H and Su, Z and Li, X and Xing, X and Chen, C}, title = {Effects of cast iron pipe corrosion on nitrogenous disinfection by-products formation in drinking water distribution systems via interaction among iron particles, biofilms, and chlorine.}, journal = {Chemosphere}, volume = {292}, number = {}, pages = {133364}, doi = {10.1016/j.chemosphere.2021.133364}, pmid = {34933025}, issn = {1879-1298}, mesh = {Biofilms ; Chlorine ; Corrosion ; Disinfection ; *Drinking Water ; Iron ; Nitrogen ; *Water Purification ; Water Supply ; }, abstract = {The effects of cast iron pipe corrosion on nitrogenous disinfection by-products formation (N-DBPs) in drinking water distribution systems (DWDSs) were investigated. The results verified that in the effluent of corroded DWDSs simulated by annular reactors with corroded cast iron coupons, typical N-DBPs, including haloacetamides, halonitromethanes, and haloacetonitriles, increased significantly compared with the influent of DWDSs. In addition, more dissolved organic carbon, adenosine triphosphate, and iron particles were simultaneously detected in the bulk water of corroded DWDSs, thereby indicating that abundant iron particles acted as a "protective umbrella" for microorganisms. Under the condition of corroded DWDSs, the extracellular polymeric substances gradually exhibited distinct characteristics, including a higher content and lower flocculation efficiency, thereby resulting in a large supply of N-DBPs precursors. Corroded cast iron pipes, equivalent to a unique microbial interface, induced completely distinct microbial community structures and metabolic functions in DWDSs, thereby enhancing the formation of N-DBPs. This is the first study to successfully reveal the interactions among iron particles, biofilms, and chlorine in DWDSs, which may help to fully understand the biofilm transformation and microbial community succession in DWDSs.}, }
@article {pmid34927376, year = {2022}, author = {Ostermeyer, P and Bonin, L and Leon-Fernandez, LF and Dominguez-Benetton, X and Hennebel, T and Rabaey, K}, title = {Electrified bioreactors: the next power-up for biometallurgical wastewater treatment.}, journal = {Microbial biotechnology}, volume = {15}, number = {3}, pages = {755-772}, pmid = {34927376}, issn = {1751-7915}, mesh = {Biomass ; Bioreactors ; *Wastewater ; *Water Purification ; }, abstract = {Over the past decades, biological treatment of metallurgical wastewaters has become commonplace. Passive systems require intensive land use due to their slow treatment rates, do not recover embedded resources and are poorly controllable. Active systems however require the addition of chemicals, increasing operational costs and possibly negatively affecting safety and the environment. Electrification of biological systems can reduce the use of chemicals, operational costs, surface footprint and environmental impact when compared to passive and active technologies whilst increasing the recovery of resources and the extraction of products. Electrification of low rate applications has resulted in the development of bioelectrochemical systems (BES), but electrification of high rate systems has been lagging behind due to the limited mass transfer, electron transfer and biomass density in BES. We postulate that for high rate applications, the electrification of bioreactors, for example, through the use of electrolyzers, may herald a new generation of electrified biological systems (EBS). In this review, we evaluate the latest trends in the field of biometallurgical and microbial-electrochemical wastewater treatment and discuss the advantages and challenges of these existing treatment technologies. We advocate for future research to focus on the development of electrified bioreactors, exploring the boundaries and limitations of these systems, and their validity upon treating industrial wastewaters.}, }
@article {pmid34927211, year = {2021}, author = {Islam, MM and Bhattacharya, R and Sarkar, B and Maiti, PK and Mahanty, S and Chaudhuri, P and Biswas, SR and Mandal, S}, title = {Different soil salinity imparts clear alteration in rhizospheric bacterial community dynamics in rice and peanut.}, journal = {Archives of microbiology}, volume = {204}, number = {1}, pages = {36}, pmid = {34927211}, issn = {1432-072X}, mesh = {Arachis ; Metagenomics ; *Oryza ; Salinity ; Soil ; }, abstract = {The rhizospheric microbiome is capable of changing the physio-chemical properties of its own micro-environment and found to be indispensable in the overall health of the hostplant. The interplay between the rhizospheric environment and the microbiota residing therein tune the physiology of the associated plant. In this study, we have determined how the soil properties and the host-plant remains as an important parameter for microbial community dynamics in the rhizosphere of rice and peanut. In addition to check the physio-chemical parameters of the rhizospheric soil, we have also prepared the metagenomic DNA from each rhizospheric soil followed by high-throughput sequencing and sequence analysis to predict the OTUs that represents the community structure. The alpha-diversity of the bacterial community in the RRN sample was highest, while the lowest was in PRS sample. Actinobacteria is the most predominant phylum in PRN, PRS and RRN, whereas Acidobacteria in RRS. We found a clear shift in bacterial community over the rice and peanut rhizosphere and also over these host-rhizospheres from normal and high saline region. The rhizospheric bacterial community composition found to be affected by the close-by environmental factors. Thus, the rhizospheric bacterial community structure is related to both the adjoining soil characters and the type of the hosts.}, }
@article {pmid34927107, year = {2021}, author = {Cáceres, PFF and Vélez, LP and Junca, H and Moreno-Herrera, CX}, title = {Theobroma cacao L. agricultural soils with natural low and high cadmium (Cd) in Santander (Colombia), contain a persistent shared bacterial composition shaped by multiple soil variables and bacterial isolates highly resistant to Cd concentrations.}, journal = {Current research in microbial sciences}, volume = {2}, number = {}, pages = {100086}, pmid = {34927107}, issn = {2666-5174}, abstract = {Heavy metals can be found in soil as natural components or as product of contaminations events; plants growing in soils are prone to bioaccumulate heavy metals on their biomass. Theobroma cacao L. can bioaccumulate cadmium (Cd) in the seed and could be in derived food products, it considered a human health risk; therefore, removal of Cd is desirable but not vet technically and economically feasible; only to avoid Cd in cocoa is by selecting lands plots exhibiting lower Cd concentrations in soils, imposing a serious limitation to farmers and regulators. The study of bacterial communities and isolation bacteria with tolerance and mechanisms to counteract the translocation of Cd to the parts of cocoa plant exhibits high relevance in Colombia economy and especially to companies producing chocolate and derivatives. Here, we explore bacterial communities associated with soils having relatively high natural Cd concentrations in a large agricultural cocoa plot located in the Santander region. We characterized the bacterial communities' compositions by amplicon 16S rRNA sequencing from metagenomics soil DNA and by culturing-based enumeration and isolation approaches. Culture-dependent techniques allowed the isolation of bacteria tolerant to Cd concentration, complement the information for Colombia, and expand the number of strains characterized with adaptive capacity against Cd with tolerance in a concentration of 120 mg/L, which represents the first capacity for Exiguobacterium sp., Ralstonia sp., Serratia sp., Dermacoccus sp., Klebsiella sp., Lactococcus sp. and Staphylococcus sp. In addition to confirming that there is a greater diversity of Cd-tolerant bacteria present in soils of farms cultivated with cocoa in Colombia. As for the results of new generation sequencing, they revealed that, the alpha-diversity in bacterial composition, according to the ANOVA, there are statistically significant differences of the bacterial communities present in the samples. Regarding Pearson correlation analysis, it was found the Shannon Simpson indices, have a positive correlation against OM, C, pH, Mn, C.E.C.I., Ca, P and negatively correlated with S; respect to bacterial community structure, a principal component analysis, which revealed that independent of the concentration of Cd present in soil samples, separates them according to pH value. Phyla to high abundance relative in all samples were Proteobacteria, Acidobacteriota, Actinobacteriota, Verrucomicrobiota, Myxococcota, Chloroflexi, Plactomycetota, Bacteroidota, Gemmatimonadota, Nitrospirota, Firmicutes and NB1_J; the bacteria genera with higher relative abundance (>0.5%) Nitrospira, candidatus Udaeobacter, Haliangium, Cupriavidus, MND1, Bacillus, Kitasatospora, Niveibacterium, Acidothermus, Burkholderia, Acidibacter, Terrimonas, Gaiella, candidatus Solibacter, Kitasatospora, Sphingomonas, Streptomyces, this genus with a relationship with the Cd tolerance process. After it, redundancy analysis was performed between the variation of the bacterial communities identified by dependent and independent techniques and edaphic soil variables, where their positive correlation was found against K, OM, C, Ca, pH (p<0.01) and P, C.E.C.I (p<0.05). For soil samples, the bacterial genera that make up the core community were identified, which are present in all samples as Nitrospira sp., Cupriavidus sp., Burkholderia sp., Haliangium sp., candidatus Udaeobacter, MND1, Kitasatospora, Acidothermus, Acidibacter, Streptomyces, Gaiella, candidatus Solibacter and Terramonas; the genera identified has a different and fundamental role in ecosystem functioning. The combination of different approaches offers new clues regarding the assessment of bacterial communities in soils cultivated with cocoa in soils with elevated Cd content in Colombia, and the ecological role and interplay of soil components and bacterial communities that contribute to modulate the effect of bioaccumulation in products.}, }
@article {pmid34925416, year = {2021}, author = {Yu, J and Gonzalez, JM and Dong, Z and Shan, Q and Tan, B and Koh, J and Zhang, T and Zhu, N and Dufresne, C and Martin, GB and Chen, S}, title = {Integrative Proteomic and Phosphoproteomic Analyses of Pattern- and Effector-Triggered Immunity in Tomato.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {768693}, pmid = {34925416}, issn = {1664-462X}, abstract = {Plants have evolved a two-layered immune system consisting of pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). PTI and ETI are functionally linked, but also have distinct characteristics. Unraveling how these immune systems coordinate plant responses against pathogens is crucial for understanding the regulatory mechanisms underlying plant defense. Here we report integrative proteomic and phosphoproteomic analyses of the tomato-Pseudomonas syringae (Pst) pathosystem with different Pst mutants that allow the dissection of PTI and ETI. A total of 225 proteins and 79 phosphopeptides differentially accumulated in tomato leaves during Pst infection. The abundances of many proteins and phosphoproteins changed during PTI or ETI, and some responses were triggered by both PTI and ETI. For most proteins, the ETI response was more robust than the PTI response. The patterns of protein abundance and phosphorylation changes revealed key regulators involved in Ca[2+] signaling, mitogen-activated protein kinase cascades, reversible protein phosphorylation, reactive oxygen species (ROS) and redox homeostasis, transcription and protein turnover, transport and trafficking, cell wall remodeling, hormone biosynthesis and signaling, suggesting their common or specific roles in PTI and/or ETI. A NAC (NAM, ATAF, and CUC family) domain protein and lipid particle serine esterase, two PTI-specific genes identified from previous transcriptomic work, were not detected as differentially regulated at the protein level and were not induced by PTI. Based on integrative transcriptomics and proteomics data, as well as qRT-PCR analysis, several potential PTI and ETI-specific markers are proposed. These results provide insights into the regulatory mechanisms underlying PTI and ETI in the tomato-Pst pathosystem, and will promote future validation and application of the disease biomarkers in plant defense.}, }
@article {pmid34920315, year = {2022}, author = {Fu, S and Yang, Q and Sheng, Y and Wang, Q and Wu, J and Qiu, Z and Lan, R and Wang, Y and Liu, Y}, title = {Metagenomics combined with comprehensive validation as a public health risk assessment tool for urban and agricultural run-off.}, journal = {Water research}, volume = {209}, number = {}, pages = {117941}, doi = {10.1016/j.watres.2021.117941}, pmid = {34920315}, issn = {1879-2448}, abstract = {Early detection of emerging and life-threatening pathogens circulating in complex environments is urgently required to combat infectious diseases. This study proposed a public health risk assessment workflow with three stages, pathogen screening, pathogen genotyping, and risk assessment. In stage one, pathogens were screened with metagenomic sequencing, microfluidic chip, and qPCR. In stage two, pathogens were isolated and genotyped with multi-locus sequence typing (MLST) or conventional PCR. Finally, virulence genes from metagenomic data were assessed for pathogenicity. Two regions (Donggang and Zhanjiang) with potential public health concerns were selected for evaluation, each of which comprised of one urban and one farming wastewater sampling location. Overall, metagenomic sequencing reflected the variation in the relative abundance of medically important bacteria. Over 90 bacterial pathogens were monitored in the metagenomic dataset, of which 56 species harbored virulence genes. In Donggang, a pathogenic Acinetobacter sp. reached high abundances in 2018 and 2020, whereas all pathogenic Vibrio spp. peaked in October 2019. In Zhanjiang, A. baumanni, and other Enterobacteriaceae species were abundantly present in 2019 and 2020, whereas Aeromonas and Vibrio spp. peaked in November-2017. Forty species were subsequently isolated and subtyped by MLST, half of which were prevalent genotypes in clinical data. Additionally, we identified the African Swine Fever Virus (ASFV) in water samples collected in 2017, ahead of the first reported ASFV outbreak in 2018 in China. RNA viruses like Hepatitis A virus (HAV) and Enterovirus 71 (EV71) were also detected, with concentrations peaking in April 2020 and April 2018, respectively. The dynamics of HAV and EV71 were consistent with local epidemic trends. Finally, based on the virulence gene profiles, our study identified the risk level in wastewater of two cities. This workflow illustrates the potential for an early warning of local epidemics, which helps to prioritize the preparedness for specific pathogens locally.}, }
@article {pmid34910570, year = {2022}, author = {Abramov, SM and Straub, D and Tejada, J and Grimm, L and Schädler, F and Bulaev, A and Thorwarth, H and Amils, R and Kappler, A and Kleindienst, S}, title = {Biogeochemical Niches of Fe-Cycling Communities Influencing Heavy Metal Transport along the Rio Tinto, Spain.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {4}, pages = {e0229021}, pmid = {34910570}, issn = {1098-5336}, mesh = {*Ferric Compounds ; *Fresh Water/microbiology ; Iron ; RNA, Ribosomal, 16S/genetics ; Spain ; }, abstract = {In the mining-impacted Rio Tinto, Spain, Fe-cycling microorganisms influence the transport of heavy metals (HMs) into the Atlantic Ocean. However, it remains largely unknown how spatial and temporal hydrogeochemical gradients along the Rio Tinto shape the composition of Fe-cycling microbial communities and how this in turn affects HM mobility. Using a combination of DNA- and RNA-based 16S rRNA (gene) amplicon sequencing and hydrogeochemical analyses, we explored the impact of pH, Fe(III), Fe(II), and Cl[-] on Fe-cycling microorganisms. We showed that the water column at the acidic (pH 2.2) middle course of the river was colonized by Fe(II) oxidizers affiliated with Acidithiobacillus and Leptospirillum. At the upper estuary, daily fluctuations of pH (2.7 to 3.7) and Cl[-] (6.9 to 16.6 g/L) contributed to the establishment of a unique microbial community, including Fe(II) oxidizers belonging to Acidihalobacter, Marinobacter, and Mariprofundus, identified at this site. Furthermore, DNA- and RNA-based profiles of the benthic community suggested that acidophilic and neutrophilic Fe(II) oxidizers (e.g., Acidihalobacter, Marinobacter, and Mariprofundus), Fe(III) reducers (e.g., Thermoanaerobaculum), and sulfate-reducing bacteria drive the Fe cycle in the estuarine sediments. RNA-based relative abundances of Leptospirillum at the middle course as well as abundances of Acidihalobacter and Mariprofundus at the upper estuary were higher than DNA-based results, suggesting a potentially higher level of activity of these taxa. Based on our findings, we propose a model of how tidal water affects the composition and activity of the Fe-cycling taxa, playing an important role in the transport of HMs (e.g., As, Cd, Cr, and Pb) along the Rio Tinto. IMPORTANCE The estuary of the Rio Tinto is a unique environment in which extremely acidic, heavy metal-rich, and especially iron-rich river water is mixed with seawater. Due to the mixing events, the estuarine water is characterized by a low pH, almost seawater salinity, and high concentrations of bioavailable iron. The unusual hydrogeochemistry maintains unique microbial communities in the estuarine water and in the sediment. These communities include halotolerant iron-oxidizing microorganisms which typically inhabit acidic saline environments and marine iron-oxidizing microorganisms which, in contrast, are not typically found in acidic environments. Furthermore, highly saline estuarine water favored the prosperity of acidophilic heterotrophs, typically inhabiting brackish and saline environments. The Rio Tinto estuarine sediment harbors a diverse microbial community with both acidophilic and neutrophilic members that can mediate the iron cycle and, in turn, can directly impact the mobility and transport of heavy metals in the Rio Tinto estuary.}, }
@article {pmid34908437, year = {2021}, author = {Kim, J and Hur, JI and Ryu, S and Jeon, B}, title = {Bacteriophage-Mediated Modulation of Bacterial Competition during Selective Enrichment of Campylobacter.}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0170321}, pmid = {34908437}, issn = {2165-0497}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Bacteriophages ; Campylobacter/*growth &amp; development/*isolation &amp; purification ; Chickens/microbiology ; Culture Media/chemistry ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/genetics/*growth &amp; development/metabolism/*virology ; Food Contamination/analysis ; Food Microbiology/methods ; Meat/*microbiology ; Microbial Sensitivity Tests ; beta-Lactamases/metabolism ; }, abstract = {Selective media using antimicrobial supplements generate unique microbial ecology to facilitate bacterial isolation. However, antibiotic-resistant bacteria indigenous to samples can interfere with the isolation process using selective media. Recent studies showed that extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli is highly prevalent on retail raw chicken and compromises the efficacy of Campylobacter isolation because ESBL-producing E. coli are resistant to antimicrobial supplements in Campylobacter-selective media and outgrows Campylobacter. The objective of this study was to improve Campylobacter isolation by inhibiting the growth of ESBL-producing E. coli using bacteriophages (phages). The supplementation of Campylobacter-selective media with E. coli phages reduced the level of ESBL-producing E. coli during the enrichment step. When E. coli phages were combined with the antimicrobial supplements of Campylobacter-selective media, antimicrobial synergy was observed, particularly with rifampicin, an antibiotic used in Preston medium. Although the same materials (i.e., phages and selective media) were used, the sequence of combining the materials markedly influenced the inhibition of ESBL-producing E. coli and the isolation of Campylobacter. These findings indicated that the modulation of microbial competition at the enrichment step was critical to the successful isolation of fastidious bacteria and that phages can be utilized to facilitate the selective enrichment of target bacteria by inhibiting their competitive bacteria. IMPORTANCE Phages are promising antimicrobial alternatives. In this study, we first demonstrated that phages can be used to facilitate selective isolation of fastidious bacteria that are prone to be outgrown by bacterial competitors during isolation. The effectiveness of a phage-based isolation method was primarily dependent on the antimicrobial synergy between phages and antibiotics used in selective media. The same approach could be applied to the development of isolation methods for other fastidious bacteria.}, }
@article {pmid34907449, year = {2023}, author = {Ghignone, S and Zampieri, E and Tinti, F and Torti, V and Giacoma, C and Mello, A}, title = {Fungal Patterns from Soils in Madagascar: an Insight from Maromizaha Forest (Evergreen Humid Forest) to Outside (Deciduous Forest).}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {184-196}, pmid = {34907449}, issn = {1432-184X}, mesh = {*Ecosystem ; *Soil/chemistry ; Madagascar ; Soil Microbiology ; Forests ; Fungi/genetics ; }, abstract = {Soil fungal diversity was studied by next-generation sequencing and compared in two different Malagasy ecosystems, the first a New Protected Area (Maromizaha NAP) that is a rich humid evergreen forest and the second a degraded and declined deciduous forest (Andaravina) whose area has been also eroded. Both areas, however, have comparable annual rainfalls and soil pH values. So it was of interest to examine the soil fungal diversity in each system and compare them. We detected 1,817,658 reads representing Ascomycota, which were dominant in both habitats (55.9%), followed by unidentified fungi (21.5%), Basidiomycota (12.7%) and Mortierellomycota (6.7%), with Mucoromycota, Chytridiomycota, Glomeromycota and other phyla accounting for less than 5% in total. In detail, 1,142 OTUs out of 1,368 constitute the common core shared by both sampling areas, which are characterized by tropical climate, whereas 185 are Maromizaha specific and 41 Andaravina specific. The most represented guilds involve fungi related to saprotrophic behaviour, with a greater tendency towards pathotrophic mode. A significant variability in terms of richness and abundance is present within Maromizaha, which is a heterogeneous environment for fungi but also for plant composition, as it emerged from the vegetational survey of the investigated sites. A few fungal sequences match taxa from Madagascar, highlighting the scarce representativeness of fungi from this island in the fungal databases and their still low knowledge. Enlarging studies in Madagascar will help not only to unravel its largely unknown fungal biodiversity but also to give a contribution for studies on the reconstruction of the diversity of soil fungi worldwide.}, }
@article {pmid34906246, year = {2021}, author = {Chaudhari, NM and Overholt, WA and Figueroa-Gonzalez, PA and Taubert, M and Bornemann, TLV and Probst, AJ and Hölzer, M and Marz, M and Küsel, K}, title = {The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers.}, journal = {Environmental microbiome}, volume = {16}, number = {1}, pages = {24}, pmid = {34906246}, issn = {2524-6372}, support = {SFB 1076 -Project Number 218627073//deutsche forschungsgemeinschaft/ ; FZT 118 - 202548816//deutsche forschungsgemeinschaft/ ; Germany's Excellence Strategy - EXC 2051 - Project-ID 390713860//deutsche forschungsgemeinschaft/ ; Nachwuchsgruppe Dr. Alexander Probst//ministerium f&#xfc;r kultur und wissenschaft des landes nordrhein-westfalen/ ; }, abstract = {BACKGROUND: The highly diverse Cand. Patescibacteria are predicted to have minimal biosynthetic and metabolic pathways, which hinders understanding of how their populations differentiate in response to environmental drivers or host organisms. Their mechanisms employed to cope with oxidative stress are largely unknown. Here, we utilized genome-resolved metagenomics to investigate the adaptive genome repertoire of Patescibacteria in oxic and anoxic groundwaters, and to infer putative host ranges.<br><br>RESULTS: Within six groundwater wells, Cand. Patescibacteria was the most dominant (up to 79%) super-phylum across 32 metagenomes sequenced from DNA retained on 0.2 and 0.1&#xa0;&#xb5;m filters after sequential filtration. Of the reconstructed 1275 metagenome-assembled genomes (MAGs), 291 high-quality MAGs were classified as Cand. Patescibacteria. Cand. Paceibacteria and Cand. Microgenomates were enriched exclusively in the 0.1&#xa0;&#xb5;m fractions, whereas candidate division ABY1 and Cand. Gracilibacteria were enriched in the 0.2&#xa0;&#xb5;m fractions. On average, Patescibacteria enriched in the smaller 0.1&#xa0;&#xb5;m filter fractions had 22% smaller genomes, 13.4% lower replication measures, higher proportion of rod-shape determining proteins, and of genomic features suggesting type IV pili mediated cell-cell attachments. Near-surface wells harbored Patescibacteria with higher replication rates than anoxic downstream wells characterized by longer water residence time. Except prevalence of superoxide dismutase genes in Patescibacteria MAGs enriched in oxic groundwaters (83%), no major metabolic or phylogenetic differences were observed. The most abundant Patescibacteria MAG in oxic groundwater encoded a nitrate transporter, nitrite reductase, and F-type ATPase, suggesting an alternative energy conservation mechanism. Patescibacteria consistently co-occurred with one another or with members of phyla Nanoarchaeota, Bacteroidota, Nitrospirota, and Omnitrophota. Among the MAGs enriched in 0.2&#xa0;&#xb5;m fractions,, only 8% Patescibacteria showed highly significant one-to-one correlation, mostly with Omnitrophota. Motility and transport related genes in certain Patescibacteria were highly similar to genes from other phyla (Omnitrophota, Proteobacteria and Nanoarchaeota).<br><br>CONCLUSION: Other than genes to cope with oxidative stress, we found little genomic evidence for niche adaptation of Patescibacteria to oxic or anoxic groundwaters. Given that we could detect specific host preference only for a few MAGs, we speculate that the majority of Patescibacteria is able to&#xa0;attach multiple hosts just long enough to loot or exchange supplies.}, }
@article {pmid34905647, year = {2022}, author = {Wang, G and Gao, Q and Yang, Y and Hobbie, SE and Reich, PB and Zhou, J}, title = {Soil enzymes as indicators of soil function: A step toward greater realism in microbial ecological modeling.}, journal = {Global change biology}, volume = {28}, number = {5}, pages = {1935-1950}, doi = {10.1111/gcb.16036}, pmid = {34905647}, issn = {1365-2486}, mesh = {Carbon ; *Ecosystem ; Nitrogen/analysis ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {Soil carbon (C) and nitrogen (N) cycles and their complex responses to environmental changes have received increasing attention. However, large uncertainties in model predictions remain, partially due to the lack of explicit representation and parameterization of microbial processes. One great challenge is to effectively integrate rich microbial functional traits into ecosystem modeling for better predictions. Here, using soil enzymes as indicators of soil function, we developed a competitive dynamic enzyme allocation scheme and detailed enzyme-mediated soil inorganic N processes in the Microbial-ENzyme Decomposition (MEND) model. We conducted a rigorous calibration and validation of MEND with diverse soil C-N fluxes, microbial C:N ratios, and functional gene abundances from a 12-year CO2 × N grassland experiment (BioCON) in Minnesota, USA. In addition to accurately simulating soil CO2 fluxes and multiple N variables, the model correctly predicted microbial C:N ratios and their negative response to enriched N supply. Model validation further showed that, compared to the changes in simulated enzyme concentrations and decomposition rates, the changes in simulated activities of eight C-N-associated enzymes were better explained by the measured gene abundances in responses to elevated atmospheric CO2 concentration. Our results demonstrated that using enzymes as indicators of soil function and validating model predictions with functional gene abundances in ecosystem modeling can provide a basis for testing hypotheses about microbially mediated biogeochemical processes in response to environmental changes. Further development and applications of the modeling framework presented here will enable microbial ecologists to address ecosystem-level questions beyond empirical observations, toward more predictive understanding, an ultimate goal of microbial ecology.}, }
@article {pmid34904179, year = {2023}, author = {Razak, NA and Gange, AC}, title = {Multitrophic Interactions Between Arbuscular Mycorrhizal Fungi, Foliar Endophytic Fungi and Aphids.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {146-156}, pmid = {34904179}, issn = {1432-184X}, support = {NE/N00244X/1//Natural Environment Research Council/ ; }, mesh = {Animals ; *Mycorrhizae/physiology ; *Aphids ; Plant Roots/microbiology ; Plants ; Endophytes/physiology ; Fungi/physiology ; }, abstract = {Almost all living plants can be simultaneously colonised by arbuscular mycorrhizal fungi in the roots and endophytes in the shoots, while also being attacked by insect herbivores. However, to date, no study has ever examined the multitrophic interactions between these two different fungal groups and insects on any species of forb. Here, we examined the effects of two commercial species mixtures of arbuscular mycorrhizal fungi (AMF) and two foliar endophytes (Colletotrichum acutatum and Cladosporium oxysporum) on the growth of an invasive weed, Impatiens glandulifera, and the aphids that attack it. AMF reduced plant biomass, which was most evident when C. oxysporum was inoculated. Mycorrhizal fungi had few effects on aphids, and these depended on the identity of the endophytes present. Meanwhile, endophytes tended to increase aphid numbers, but this depended on the identity of the AMF inoculum. Throughout, there were differences in the responses of the plant to the two mycorrhizal mixtures, demonstrating clear AMF specificity in this plant. These specific effects were also strongly affected by the endophytes, with a greater number of interactions found between the AMF and endophytes than between the endophytes themselves. In particular, AMF reduced infection levels by the endophytes, while some endophyte inoculations reduced mycorrhizal colonisation. We suggest that both AMF and endophytes could play an important part in future biological control programmes of weeds, but further multitrophic experiments are required to unravel the complexity of interactions between spatially separated parts of the plant microbiome.}, }
@article {pmid34895142, year = {2021}, author = {Wichmann, S and Scherer, S and Ardern, Z}, title = {Biological factors in the synthetic construction of overlapping genes.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {888}, pmid = {34895142}, issn = {1471-2164}, mesh = {Amino Acid Sequence ; Animals ; *Biological Factors ; *Genes, Overlapping ; Genome ; Open Reading Frames ; }, abstract = {BACKGROUND: Overlapping genes (OLGs) with long protein-coding overlapping sequences are disallowed by standard genome annotation programs, outside of viruses. Recently however they have been discovered in Archaea, diverse Bacteria, and Mammals. The biological factors underlying life's ability to create overlapping genes require more study, and may have important applications in understanding evolution and in biotechnology. A previous study claimed that protein domains from viruses were much better suited to forming overlaps than those from other cellular organisms - in this study we assessed this claim, in order to discover what might underlie taxonomic differences in the creation of gene overlaps.<br><br>RESULTS: After overlapping arbitrary Pfam domain pairs and evaluating them with Hidden Markov Models we find OLG construction to be much less constrained than expected. For instance, close to 10% of the constructed sequences cannot be distinguished from typical sequences in their protein family. Most are also indistinguishable from natural protein sequences regarding identity and secondary structure. Surprisingly, contrary to a previous study, virus domains were much less suitable for designing OLGs than bacterial or eukaryotic domains were. In general, the amount of amino acid change required to force a domain to overlap is approximately equal to the variation observed within a typical domain family. The resulting high similarity between natural sequences and those altered so as to overlap is mostly due to the combination of high redundancy in the genetic code and the evolutionary exchangeability of many amino acids.<br><br>CONCLUSIONS: Synthetic overlapping genes which closely resemble natural gene sequences, as measured by HMM profiles, are remarkably easy to construct, and most arbitrary domain pairs can be altered so as to overlap while retaining high similarity to the original sequences. Future work however will need to assess important factors not considered such as intragenic interactions which affect protein folding. While the analysis here is not sufficient to guarantee functional folding proteins, further analysis of constructed OLGs will improve our understanding of the origin of these remarkable genetic elements across life and opens up exciting possibilities for synthetic biology.}, }
@article {pmid34888738, year = {2022}, author = {Ryther, CM and Ortmann, AC and Wohlgeschaffen, G and Robinson, BJ}, title = {Temperate Coastal Microbial Communities Rapidly Respond to Low Concentrations of Partially Weathered Diesel.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1122-1132}, pmid = {34888738}, issn = {1432-184X}, mesh = {Biodegradation, Environmental ; Seawater/microbiology ; Bacteria/genetics ; *Microbiota ; Nova Scotia ; *Petroleum ; Hydrocarbons ; }, abstract = {Diesel is frequently encountered in coastal ecosystems due to land run-off from road surfaces. The current study investigates how partially weathered diesel at environmentally relevant concentrations, as may be seen during a run-off event, affect coastal microbial communities. A mesocosm experiment using seawater from the Bedford Basin, Nova Scotia, was followed for 72 h after the addition of partially weathered diesel. Sequencing data suggests partially weathered diesel acts quickly to alter the prokaryotic community, as both opportunistic (Vibrio and Lentibacter) and oil-degrading (Colwellia, Sulfitobacter, and Pseudoalteromonas) bacteria proliferated after 24 h in comparison to the control. In addition, total prokaryotes seemed to recover in abundance after 24 h, where eukaryotes only ceased to decrease slightly at 72 h, likely because of an inability to adapt to the oil-laden conditions, unlike the prokaryotes. Considering there were no highly volatile components (benzene, toluene, ethylbenzene, and xylene) present in the diesel when the communities were exposed, the results indicate that even a relatively small concentration of diesel run-off can cause a drastic change to the microbial community under low energy conditions. Higher energy conditions due to wave action may mitigate the response of the microbial communities by dilution and additional weathering of the diesel.}, }
@article {pmid34887434, year = {2021}, author = {Goswami, K and Shope, AJ and Tokarev, V and Wright, JR and Unverdorben, LV and Ly, T and Chen See, J and McLimans, CJ and Wong, HT and Lock, L and Clarkson, S and Parvizi, J and Lamendella, R}, title = {Comparative meta-omics for identifying pathogens associated with prosthetic joint infection.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {23749}, pmid = {34887434}, issn = {2045-2322}, mesh = {Aged ; Aged, 80 and over ; Arthritis, Infectious/diagnosis/*etiology ; Biodiversity ; Computational Biology/methods ; Female ; Gene Expression Profiling ; Humans ; Male ; Metagenome ; Metagenomics/*methods ; Middle Aged ; Prosthesis-Related Infections/diagnosis/*etiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Prosthetic joint infections (PJI) are economically and personally costly, and their incidence has been increasing in the United States. Herein, we compared 16S rRNA amplicon sequencing (16S), shotgun metagenomics (MG) and metatranscriptomics (MT) in identifying pathogens causing PJI. Samples were collected from 30 patients, including 10 patients undergoing revision arthroplasty for infection, 10 patients receiving revision for aseptic failure, and 10 patients undergoing primary total joint arthroplasty. Synovial fluid and peripheral blood samples from the patients were obtained at time of surgery. Analysis revealed distinct microbial communities between primary, aseptic, and infected samples using MG, MT, (PERMANOVA p = 0.001), and 16S sequencing (PERMANOVA p < 0.01). MG and MT had higher concordance with culture (83%) compared to 0% concordance of 16S results. Supervised learning methods revealed MT datasets most clearly differentiated infected, primary, and aseptic sample groups. MT data also revealed more antibiotic resistance genes, with improved concordance results compared to MG. These data suggest that a differential and underlying microbial ecology exists within uninfected and infected joints. This study represents the first application of RNA-based sequencing (MT). Further work on larger cohorts will provide opportunities to employ deep learning approaches to improve accuracy, predictive power, and clinical utility.}, }
@article {pmid34878672, year = {2022}, author = {Wu, L and Yang, F and Feng, J and Tao, X and Qi, Q and Wang, C and Schuur, EAG and Bracho, R and Huang, Y and Cole, JR and Tiedje, JM and Zhou, J}, title = {Permafrost thaw with warming reduces microbial metabolic capacities in subsurface soils.}, journal = {Molecular ecology}, volume = {31}, number = {5}, pages = {1403-1415}, doi = {10.1111/mec.16319}, pmid = {34878672}, issn = {1365-294X}, mesh = {Carbon/metabolism ; Carbon Cycle ; *Permafrost/microbiology ; Soil/chemistry ; Soil Microbiology ; Tundra ; }, abstract = {Microorganisms are major constituents of the total biomass in permafrost regions, whose underlain soils are frozen for at least two consecutive years. To understand potential microbial responses to climate change, here we examined microbial community compositions and functional capacities across four soil depths in an Alaska tundra site. We showed that a 5-year warming treatment increased soil thaw depth by 25.7% (p = .011) within the deep organic layer (15-25 cm). Concurrently, warming reduced 37% of bacterial abundance and 64% of fungal abundances in the deep organic layer, while it did not affect microbial abundance in other soil layers (i.e., 0-5, 5-15, and 45-55 cm). Warming treatment altered fungal community composition and microbial functional structure (p < .050), but not bacterial community composition. Using a functional gene array, we found that the relative abundances of a variety of carbon (C)-decomposing, iron-reducing, and sulphate-reducing genes in the deep organic layer were decreased, which was not observed by the shotgun sequencing-based metagenomics analysis of those samples. To explain the reduced metabolic capacities, we found that warming treatment elicited higher deterministic environmental filtering, which could be linked to water-saturated time, soil moisture, and soil thaw duration. In contrast, plant factors showed little influence on microbial communities in subsurface soils below 15 cm, despite a 25.2% higher (p < .05) aboveground plant biomass by warming treatment. Collectively, we demonstrate that microbial metabolic capacities in subsurface soils are reduced, probably arising from enhanced thaw by warming.}, }
@article {pmid34878610, year = {2021}, author = {Kumar, V and Kumar, S and Singh, D}, title = {Metagenomic insights into Himalayan glacial and kettle lake sediments revealed microbial community structure, function, and stress adaptation strategies.}, journal = {Extremophiles : life under extreme conditions}, volume = {26}, number = {1}, pages = {3}, pmid = {34878610}, issn = {1433-4909}, support = {MLP0143//CSIR-Institute of Himalayan Bioresource Technology/ ; }, mesh = {Geologic Sediments ; *Lakes ; Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Glacial and kettle lakes in the high-altitude Himalayas are unique habitats with significant scope for microbial ecology. The present study provides insights into bacterial community structure and function of the sediments of two high-altitude lakes using 16S amplicon and whole-genome shotgun (WGS) metagenomics. Microbial communities in the sediments of Parvati kund (glacial lake) and Bhoot ground (kettle lake) majorly consist of bacteria and a small fraction of archaea and eukaryota. The bacterial population has an abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Firmicutes, and Verrucomicrobia. Despite the common phyla, the sediments from each lake have a distinct distribution of bacterial and archaeal taxa. The analysis of the WGS metagenomes at the functional level provides a broad picture of microbial community metabolism of key elements and suggested chemotrophs as the major primary producers. In addition, the findings also revealed that polyhydroxyalkanoates (PHA) are a crucial stress adaptation molecule. The abundance of PHA metabolism in Alpha- and Betaproteobacteria and less representation in other bacterial and archaeal classes in both metagenomes was disclosed. The metagenomic insights provided an incisive view of the microbiome from Himalayan lake's sediments. It has also opened the scope for further bioprospection from virgin Himalayan niches.}, }
@article {pmid34878336, year = {2021}, author = {Andrić, S and Meyer, T and Rigolet, A and Prigent-Combaret, C and Höfte, M and Balleux, G and Steels, S and Hoff, G and De Mot, R and McCann, A and De Pauw, E and Argüelles Arias, A and Ongena, M}, title = {Lipopeptide Interplay Mediates Molecular Interactions between Soil Bacilli and Pseudomonads.}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0203821}, pmid = {34878336}, issn = {2165-0497}, mesh = {Bacillus/growth &amp; development/*metabolism ; Lipopeptides/*metabolism ; Microbial Interactions ; Pseudomonas/*metabolism ; Secondary Metabolism ; *Soil Microbiology ; }, abstract = {Some Bacillus species, such as B. velezensis, are important members of the plant-associated microbiome, conferring protection against phytopathogens. However, our knowledge about multitrophic interactions determining the ecological fitness of these biocontrol bacteria in the competitive rhizosphere niche is still limited. Here, we investigated molecular mechanisms underlying interactions between B. velezensis and Pseudomonas as a soil-dwelling competitor. Upon their contact-independent in vitro confrontation, a multifaceted macroscopic outcome was observed and characterized by Bacillus growth inhibition, white line formation in the interaction zone, and enhanced motility. We correlated these phenotypes with the production of bioactive secondary metabolites and identified specific lipopeptides as key compounds involved in the interference interaction and motile response. Bacillus mobilizes its lipopeptide surfactin not only to enhance motility but also to act as a chemical trap to reduce the toxicity of lipopeptides formed by Pseudomonas. We demonstrated the relevance of these unsuspected roles of lipopeptides in the context of competitive tomato root colonization by the two bacterial genera. IMPORTANCE Plant-associated Bacillus velezensis and Pseudomonas spp. represent excellent model species as strong producers of bioactive metabolites involved in phytopathogen inhibition and the elicitation of plant immunity. However, the ecological role of these metabolites during microbial interspecies interactions and the way their expression may be modulated under naturally competitive soil conditions has been poorly investigated. Through this work, we report various phenotypic outcomes from the interactions between B. velezensis and 10 Pseudomonas strains used as competitors and correlate them with the production of specific metabolites called lipopeptides from both species. More precisely, Bacillus overproduces surfactin to enhance motility, which also, by acting as a chemical trap, reduces the toxicity of other lipopeptides formed by Pseudomonas. Based on data from interspecies competition on plant roots, we assume this would allow Bacillus to gain fitness and persistence in its natural rhizosphere niche. The discovery of new ecological functions for Bacillus and Pseudomonas secondary metabolites is crucial to rationally design compatible consortia, more efficient than single-species inoculants, to promote plant health and growth by fighting economically important pathogens in sustainable agriculture.}, }
@article {pmid34877561, year = {2021}, author = {Wang, F and Harindintwali, JD and Yuan, Z and Wang, M and Wang, F and Li, S and Yin, Z and Huang, L and Fu, Y and Li, L and Chang, SX and Zhang, L and Rinklebe, J and Yuan, Z and Zhu, Q and Xiang, L and Tsang, DCW and Xu, L and Jiang, X and Liu, J and Wei, N and Kästner, M and Zou, Y and Ok, YS and Shen, J and Peng, D and Zhang, W and Barceló, D and Zhou, Y and Bai, Z and Li, B and Zhang, B and Wei, K and Cao, H and Tan, Z and Zhao, LB and He, X and Zheng, J and Bolan, N and Liu, X and Huang, C and Dietmann, S and Luo, M and Sun, N and Gong, J and Gong, Y and Brahushi, F and Zhang, T and Xiao, C and Li, X and Chen, W and Jiao, N and Lehmann, J and Zhu, YG and Jin, H and Schäffer, A and Tiedje, JM and Chen, JM}, title = {Technologies and perspectives for achieving carbon neutrality.}, journal = {Innovation (Cambridge (Mass.))}, volume = {2}, number = {4}, pages = {100180}, pmid = {34877561}, issn = {2666-6758}, abstract = {Global development has been heavily reliant on the overexploitation of natural resources since the Industrial Revolution. With the extensive use of fossil fuels, deforestation, and other forms of land-use change, anthropogenic activities have contributed to the ever-increasing concentrations of greenhouse gases (GHGs) in the atmosphere, causing global climate change. In response to the worsening global climate change, achieving carbon neutrality by 2050 is the most pressing task on the planet. To this end, it is of utmost importance and a significant challenge to reform the current production systems to reduce GHG emissions and promote the capture of CO2 from the atmosphere. Herein, we review innovative technologies that offer solutions achieving carbon (C) neutrality and sustainable development, including those for renewable energy production, food system transformation, waste valorization, C sink conservation, and C-negative manufacturing. The wealth of knowledge disseminated in this review could inspire the global community and drive the further development of innovative technologies to mitigate climate change and sustainably support human activities.}, }
@article {pmid34877560, year = {2021}, author = {Xu, Y and Liu, X and Cao, X and Huang, C and Liu, E and Qian, S and Liu, X and Wu, Y and Dong, F and Qiu, CW and Qiu, J and Hua, K and Su, W and Wu, J and Xu, H and Han, Y and Fu, C and Yin, Z and Liu, M and Roepman, R and Dietmann, S and Virta, M and Kengara, F and Zhang, Z and Zhang, L and Zhao, T and Dai, J and Yang, J and Lan, L and Luo, M and Liu, Z and An, T and Zhang, B and He, X and Cong, S and Liu, X and Zhang, W and Lewis, JP and Tiedje, JM and Wang, Q and An, Z and Wang, F and Zhang, L and Huang, T and Lu, C and Cai, Z and Wang, F and Zhang, J}, title = {Artificial intelligence: A powerful paradigm for scientific research.}, journal = {Innovation (Cambridge (Mass.))}, volume = {2}, number = {4}, pages = {100179}, pmid = {34877560}, issn = {2666-6758}, abstract = {Artificial intelligence (AI) coupled with promising machine learning (ML) techniques well known from computer science is broadly affecting many aspects of various fields including science and technology, industry, and even our day-to-day life. The ML techniques have been developed to analyze high-throughput data with a view to obtaining useful insights, categorizing, predicting, and making evidence-based decisions in novel ways, which will promote the growth of novel applications and fuel the sustainable booming of AI. This paper undertakes a comprehensive survey on the development and application of AI in different aspects of fundamental sciences, including information science, mathematics, medical science, materials science, geoscience, life science, physics, and chemistry. The challenges that each discipline of science meets, and the potentials of AI techniques to handle these challenges, are discussed in detail. Moreover, we shed light on new research trends entailing the integration of AI into each scientific discipline. The aim of this paper is to provide a broad research guideline on fundamental sciences with potential infusion of AI, to help motivate researchers to deeply understand the state-of-the-art applications of AI-based fundamental sciences, and thereby to help promote the continuous development of these fundamental sciences.}, }
@article {pmid34875513, year = {2022}, author = {Iasakov, TR and Kanapatskiy, TA and Toshchakov, SV and Korzhenkov, AA and Ulyanova, MO and Pimenov, NV}, title = {The Baltic Sea methane pockmark microbiome: The new insights into the patterns of relative abundance and ANME niche separation.}, journal = {Marine environmental research}, volume = {173}, number = {}, pages = {105533}, doi = {10.1016/j.marenvres.2021.105533}, pmid = {34875513}, issn = {1879-0291}, mesh = {Anaerobiosis ; Archaea/genetics ; Geologic Sediments ; *Methane ; *Microbiota ; Oxidation-Reduction ; Phylogeny ; Planctomycetes ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Pockmarks are important "pumps", which are believed to play a significant role in the global methane cycling and harboring a unique assemblage of very diverse prokaryotes. This study reports the results of massive sequencing of the 16S rRNA gene V4 hypervariable regions for the samples from thirteen pockmark horizons (the Baltic Sea) collected at depths from 0 to 280 cm below seafloor (cmbsf) and the rates of microbially mediated anaerobic oxidation of methane (AOM) and sulfate reduction (SR). Altogether, 76 bacterial and 12 archaeal phyla were identified, 23 of which were candidate divisions. Of the total obtained in the pockmark sequences, 84.3% of them were classified as Bacteria and 12.4% as Archaea; 3.3% of the sequences were assigned to unknown operational taxonomic units (OTUs). Members of the phyla Planctomycetota, Chloroflexota, Desulfobacterota, Caldatribacteriota, Acidobacteriota and Proteobacteria predominated across all horizons, comprising 58.5% of the total prokaryotic community. These phyla showed different types of patterns of relative abundance. Analysis of AOM-SR-mediated prokaryotes abundance and biogeochemical measurements revealed that ANME-2a-2b subcluster was predominant in sulfate-rich upper horizons (including sulfate-methane transition zone (SMTZ)) and together with sulfate-reducing bacterial group SEEP-SRB1 had a primary role in AOM coupled to SR. At deeper sulfate-depleted horizons ANME-2a-2b shifted to ANME-1a and ANME-1b which alone mediated AOM or switch to methanogenic metabolism. Shifting of the ANME subclusters depending on depth reflect a tendency for niche separation in these groups. It was shown that the abundance of Caldatribacteriota and organohalide-respiring Dehalococcoidia (Chloroflexota) exhibited a strong correlation with AOM rates. This is the first detailed study of depth profiles of prokaryotic diversity, patterns of relative abundance, and ANME niche separation in the Baltic Sea pockmark microbiomes sheds light on assembly of prokaryotes in a pockmark.}, }
@article {pmid34875143, year = {2022}, author = {Verstraete, W and Yanuka-Golub, K and Driesen, N and De Vrieze, J}, title = {Engineering microbial technologies for environmental sustainability: choices to make.}, journal = {Microbial biotechnology}, volume = {15}, number = {1}, pages = {215-227}, pmid = {34875143}, issn = {1751-7915}, mesh = {Animals ; Climate Change ; Humans ; *Microbiota ; *Soil ; }, abstract = {Microbial technologies have provided solutions to key challenges in our daily lives for over a century. In the debate about the ongoing climate change and the need for planetary sustainability, microbial ecology and microbial technologies are rarely considered. Nonetheless, they can bring forward vital solutions to decrease and even prevent long-term effects of climate change. The key to the success of microbial technologies is an effective, target-oriented microbiome management. Here, we highlight how microbial technologies can play a key role in both natural, i.e. soils and aquatic ecosystems, and semi-natural or even entirely human-made, engineered ecosystems, e.g. (waste) water treatment and bodily systems. First, we set forward fundamental guidelines for effective soil microbial resource management, especially with respect to nutrient loss and greenhouse gas abatement. Next, we focus on closing the water circle, integrating resource recovery. We also address the essential interaction of the human and animal host with their respective microbiomes. Finally, we set forward some key future potentials, such as microbial protein and the need to overcome microphobia for microbial products and services. Overall, we conclude that by relying on the wisdom of the past, we can tackle the challenges of our current era through microbial technologies.}, }
@article {pmid34874772, year = {2021}, author = {Hilts, AS and Hunjan, MS and Hug, LA}, title = {Adapting Macroecology to Microbiology: Using Occupancy Modeling To Assess Functional Profiles across Metagenomes.}, journal = {mSystems}, volume = {6}, number = {6}, pages = {e0079021}, pmid = {34874772}, issn = {2379-5077}, support = {//Canada Research Chairs (Chaires de recherche du Canada)/ ; 2016-03686//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; }, abstract = {Metagenomic sequencing provides information on the metabolic capacities and taxonomic affiliations for members of a microbial community. When assessing metabolic functions in a community, missing genes in pathways can occur in two ways; the genes may legitimately be missing from the community whose DNA was sequenced, or the genes were missed during shotgun sequencing or failed to assemble, and thus the metabolic capacity of interest is wrongly absent from the sequence data. Here, we borrow and adapt occupancy modeling from macroecology to provide mathematical context to metabolic predictions from metagenomes. We review the five assumptions underlying occupancy modeling through the lens of microbial community sequence data. Using the methane cycle, we apply occupancy modeling to examine the presence and absence of methanogenesis and methanotrophy genes from nearly 10,000 metagenomes spanning global environments. We determine that methanogenesis and methanotrophy are positively correlated across environments, providing a predictive framework for assessing gene absences for these functions. We present this adaptation of macroecology's occupancy modeling to metagenomics as a tool to quantify the uncertainty in predictions of the presence/absence of traits in environmental microbiological surveys. We further initiate a call for stronger metadata standards to accompany metagenome deposition, to enable robust statistical approaches in the future. IMPORTANCE Metagenomics is maturing rapidly as a field but is hampered by a lack of available statistical tools. A primary area of uncertainty is around missing genes or functions from a metagenomic data set. Here, we borrow an established modeling approach from macroecology and adapt it to metagenomic data sets. Rather than multiple sampling trips to a specific area to detect a species of interest (e.g., identifying a cardinal in a forest), we leverage the enormous amount of information within a metagenome and use multiple gene markers for a function of interest (e.g., subunits of an enzyme complex). We applied our adapted occupancy modeling to a case study examining methane cycling capacity. Our models show methanogens and methanotrophs are both more likely to cooccur than be present in the absence of the other guild. The lack of consistent and complete metadata is a significant hurdle for increasing the statistical rigor of metagenomic analyses.}, }
@article {pmid34874481, year = {2021}, author = {Devi, SP and Jani, K and Sharma, A and Jha, DK}, title = {Bacterial communities and their bioremediation capabilities in oil-contaminated agricultural soils.}, journal = {Environmental monitoring and assessment}, volume = {194}, number = {1}, pages = {9}, doi = {10.1007/s10661-021-09669-9}, pmid = {34874481}, issn = {1573-2959}, mesh = {Bacteria/genetics ; Biodegradation, Environmental ; Ecosystem ; Environmental Monitoring ; Humans ; Hydrocarbons/analysis ; *Petroleum/analysis ; RNA, Ribosomal, 16S ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {Rapid industrialization and development in petrochemical industries have resulted in increased hydrocarbon pollution causing substantial damage to the natural ecosystems including agricultural soils. In the recent, past efforts have been made to treat the contaminated soils using microorganisms by natural processes. Soil bacteria, known for their potential to degrade the soil contaminants, play a vital role in maintaining soil health. In the current study, we observed the influence of hydrocarbon contamination on the physicochemical characteristics and enzymatic activities of the soil. Proteobacteria (30.48%), Actinobacteria (13.91%), and Acidobacteria (12.57%) flourished in the non-contaminated soil whereas contaminated sites were dominated by Proteobacteria (44.02 ± 15.65%). In contrast, the sites experiencing the different degrees of exposure to the hydrocarbon pollution allowed specific augmentation of bacterial taxa (in decreasing order of exposure time), viz. Proteobacteria (60.47%), Firmicutes (32.48%), and Bacteroidetes(13.59%), based on culture-independent approach that suggested their potential role in hydrocarbon degradation as compared to the non-contaminated site. The imputation of metabolic function also supported the positive correlation to the exposure to hydrocarbon pollution, with site 2 being highly abundant for gene families involved in xenobiotics biodegradation. The study provides insights into bacterial community structure with special emphasis on their efficiency to degrade hydrocarbons. The results from the study can help in designing appropriate biodegradation strategies to mitigate the serious problems of oil contamination in agricultural soil.}, }
@article {pmid34871418, year = {2022}, author = {Andreopoulos, WB and Geller, AM and Lucke, M and Balewski, J and Clum, A and Ivanova, NN and Levy, A}, title = {Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes.}, journal = {Nucleic acids research}, volume = {50}, number = {3}, pages = {e17}, pmid = {34871418}, issn = {1362-4962}, mesh = {Animals ; Chromosomes, Bacterial/genetics ; *Deep Learning ; *Genome, Bacterial ; *Plasmids/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {Plasmids are mobile genetic elements that play a key role in microbial ecology and evolution by mediating horizontal transfer of important genes, such as antimicrobial resistance genes. Many microbial genomes have been sequenced by short read sequencers and have resulted in a mix of contigs that derive from plasmids or chromosomes. New tools that accurately identify plasmids are needed to elucidate new plasmid-borne genes of high biological importance. We have developed Deeplasmid, a deep learning tool for distinguishing plasmids from bacterial chromosomes based on the DNA sequence and its encoded biological data. It requires as input only assembled sequences generated by any sequencing platform and assembly algorithm and its runtime scales linearly with the number of assembled sequences. Deeplasmid achieves an AUC-ROC of over 89%, and it was more accurate than five other plasmid classification methods. Finally, as a proof of concept, we used Deeplasmid to predict new plasmids in the fish pathogen Yersinia ruckeri ATCC 29473 that has no annotated plasmids. Deeplasmid predicted with high reliability that a long assembled contig is part of a plasmid. Using long read sequencing we indeed validated the existence of a 102 kb long plasmid, demonstrating Deeplasmid's ability to detect novel plasmids.}, }
@article {pmid34867858, year = {2021}, author = {Ahmed, B and Smart, LB and Hijri, M}, title = {Microbiome of Field Grown Hemp Reveals Potential Microbial Interactions With Root and Rhizosphere Soil.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {741597}, pmid = {34867858}, issn = {1664-302X}, abstract = {Hemp (Cannabis sativa L.) is a crop bred and grown for the production of fiber, grain, and floral extracts that contribute to health and wellness. Hemp plants interact with a myriad of microbiota inhabiting the phyllosphere, endosphere, rhizoplane, and rhizosphere. These microbes offer many ecological services, particularly those of below ground biotopes which are involved in nutrient cycling, uptake, and alleviating biotic and abiotic stress. The microbiota communities of the hemp rhizosphere in the field are not well documented. To discover core microbiota associated with field grown hemp, we cultivated single C. sativa cultivar, "TJ's CBD," in six different fields in New York and sampled hemp roots and their rhizospheric soil. We used Illumina MiSeq amplicon sequencing targeting 16S ribosomal DNA of bacteria and ITS of fungi to study microbial community structure of hemp roots and rhizospheres. We found that Planctobacteria and Ascomycota dominated the taxonomic composition of hemp associated microbial community. We identified potential core microbiota in each community (bacteria: eight bacterial amplicon sequence variant - ASV, identified as Gimesia maris, Pirellula sp. Lacipirellula limnantheis, Gemmata sp. and unclassified Planctobacteria; fungi: three ASVs identified as Fusarium oxysporum, Gibellulopsis piscis, and Mortierella minutissima). We found 14 ASVs as hub taxa [eight bacterial ASVs (BASV) in the root, and four bacterial and two fungal ASVs in the rhizosphere soil], and 10 BASV connected the root and rhizosphere soil microbiota to form an extended microbial communication in hemp. The only hub taxa detected in both the root and rhizosphere soil microbiota was ASV37 (Caulifigura coniformis), a bacterial taxon. The core microbiota and Network hub taxa can be studied further for biocontrol activities and functional investigations in the formulation of hemp bioinoculants. This study documented the microbial diversity and community structure of hemp grown in six fields, which could contribute toward the development of bioinoculants for hemp that could be used in organic farming.}, }
@article {pmid34867834, year = {2021}, author = {Thomas, P and Sahu, PK}, title = {Vertical Transmission of Diverse Cultivation-Recalcitrant Endophytic Bacteria Elucidated Using Watermelon Seed Embryos.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {635810}, pmid = {34867834}, issn = {1664-302X}, abstract = {Seed transmission of endophytic microorganisms is a growing research area in plant biology and microbiology. We employed cultivation versus cultivation-independent approaches on excised embryos from watermelon seeds (6-12 months in storage) and on embryo-derived in vitro seedlings (EIVS) to assess the vertical transmission of endophytic bacteria. Surface-disinfected watermelon seeds bore abundant residual bacteria in the testa and perisperm tissues, predominantly Bacillus spp. propounding the essentiality of excluding all non-embryonic tissues for vertical transmission studies. Tissue homogenates from re-disinfected seed embryos displayed no cultivable bacteria during the 1-week monitoring. Bright-field live microscopy revealed abundant bacteria in tissue homogenates and in embryo sections as intracellular motile particles. Confocal imaging on embryo sections after SYTO-9 staining and eubacterial fluorescent in situ hybridization (FISH) endorsed enormous bacterial colonization. Quantitative Insights Into Microbial Ecology (QIIME)-based 16S rRNA V3-V4 taxonomic profiling excluding the preponderant chloroplast and mitochondrial sequences revealed a high bacterial diversity in watermelon seed embryos mainly Firmicutes barring spore formers followed by Proteobacteria, Bacteroidetes, and Actinobacteria, and other minor phyla. Embryo-base (comprising the radicle plus plumule parts) and embryo-cotyledon parts differed in bacterial profiles with the abundance of Firmicutes in the former and Proteobacteria dominance in the latter. EIVS displayed a higher bacterial diversity over seed embryos indicating the activation from the dormant stage of more organisms in seedlings or their better amenability to DNA techniques. It also indicated embryo-to-seedling bacterial transmission, varying taxonomic abundances for seed embryos and seedlings, and differing phylogenic profiles for root, hypocotyl, and cotyledon/shoot-tip tissues. Investigations on different watermelon cultivars confirmed the embryo transmission of diverse cultivation recalcitrant endophytic bacteria. Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes formed the core phyla across different cultivars with 80-90% similarity at genus to phylum levels. Conversely, freshly harvested seeds displayed a dominance of Proteobacteria. The findings revealed that dicot seeds such as in different watermelon cultivars come packaged with abundant and diverse vertical and seedling-transmissible cultivation recalcitrant endophytic bacteria with significant implications for plant biology.}, }
@article {pmid34867016, year = {2021}, author = {Chergui, D and Akretche-Kelfat, S and Lamoudi, L and Al-Rshaidat, M and Boudjelal, F and Ait-Amar, H}, title = {Optimization of citric acid production by Aspergillus niger using two downgraded Algerian date varieties.}, journal = {Saudi journal of biological sciences}, volume = {28}, number = {12}, pages = {7134-7141}, pmid = {34867016}, issn = {1319-562X}, abstract = {In the present work, the GHARS and the MECH DEGLA downgraded date varieties were used in a fermentation medium in order to produce citric acid by the Aspergillus niger. The biochemical characteristics of the dates were investigated, along with the chemical and physical characteristics of the solutions of both samples. The analyzed parameters included the moisture and sugar content, the ash residual, the pH values, and the electrical conductivity. The effect of the following fermentation parameters was studied: initial pH, temperature, incubation period, and methanol. For the GHARS and MECH DEGLA date varieties respectively, the ash residual measured at 1.90% and 2.47%. For each date variety, the moisture and total sugars were measured at 11.59% and 85%, for the GHARS, and 12.82% and 80.47% for the MECH DEGLA. Citric acid production using either of the two varieties of dates showed a high yield in a short time. The obtained results showed that the highest production of citric acid by both medium of dates was achieved at the initial pH value of 3.0, temperature 30 °C, and an incubation period of 8 days. Also, the maximum amount of citric acid was produced when both mediums contained 4% of methanol. Both varieties of dates showed a good yield for the citric acid and can be used as a culture medium since they are economic and ensure good growth for the Aspergillus niger.}, }
@article {pmid34865013, year = {2022}, author = {Kindler, GS and Wong, HL and Larkum, AWD and Johnson, M and MacLeod, FI and Burns, BP}, title = {Genome-resolved metagenomics provides insights into the functional complexity of microbial mats in Blue Holes, Shark Bay.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {1}, pages = {}, doi = {10.1093/femsec/fiab158}, pmid = {34865013}, issn = {1574-6941}, mesh = {Animals ; Archaea/genetics ; Bays ; *Metagenomics ; Phylogeny ; Planctomycetes ; *Sharks ; }, abstract = {The present study describes for the first time the community composition and functional potential of the microbial mats found in the supratidal, gypsum-rich and hypersaline region of Blue Holes, Shark Bay. This was achieved via high-throughput metagenomic sequencing of total mat community DNA and complementary analyses using hyperspectral confocal microscopy. Mat communities were dominated by Proteobacteria (29%), followed by Bacteroidetes/Chlorobi group (11%) and Planctomycetes (10%). These mats were found to also harbour a diverse community of potentially novel microorganisms, including members from the DPANN, Asgard archaea and candidate phyla radiation, with highest diversity found in the lower regions (∼14-20 mm depth) of the mat. In addition to pathways for major metabolic cycles, a range of putative rhodopsins with previously uncharacterized motifs and functions were identified along with heliorhodopsins and putative schizorhodopsins. Critical microbial interactions were also inferred, and from 117 medium- to high-quality metagenome-assembled genomes, viral defence mechanisms (CRISPR, BREX and DISARM), elemental transport, osmoprotection, heavy metal resistance and UV resistance were also detected. These analyses have provided a greater understanding of these distinct mat systems in Shark Bay, including key insights into adaptive responses and proposing that photoheterotrophy may be an important lifestyle in Blue Holes.}, }
@article {pmid34864985, year = {2021}, author = {Voskuhl, L and Akbari, A and Müller, H and Pannekens, M and Brusilova, D and Dyksma, S and Haque, S and Graupner, N and Dunthorn, M and Meckenstock, RU and Brauer, VS}, title = {Indigenous microbial communities in heavy oil show a threshold response to salinity.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {12}, pages = {}, pmid = {34864985}, issn = {1574-6941}, mesh = {Bacteria/genetics ; Lakes ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Salinity ; }, abstract = {Microbial degradation influences the quality of oil resources. The environmental factors that shape the composition of oil microbial communities are largely unknown because most samples from oil fields are impacted by anthropogenic oil production, perturbing the native ecosystem with exogenous fluids and microorganisms. We investigated the relationship between formation water geochemistry and microbial community composition in undisturbed oil samples. We isolated 43 microliter-sized water droplets naturally enclosed in the heavy oil of the Pitch Lake, Trinidad and Tobago. The water chemistry and microbial community composition within the same water droplet were determined by ion chromatography and 16S rRNA gene amplicon sequencing, respectively. The results revealed a high variability in ion concentrations and community composition between water droplets. Microbial community composition was mostly affected by the chloride concentration, which ranged from freshwater to brackish-sea water. Remarkably, microbial communities did not respond gradually to increasing chloride concentration but showed a sudden change to less diverse and uneven communities when exceeding a chloride concentration of 57.3 mM. The results reveal a threshold-regulated response of microbial communities to salinity, offering new insights into the microbial ecology of oil reservoirs.}, }
@article {pmid34864466, year = {2022}, author = {Kazmi, SSUH and Uroosa,  and Warren, A and Zhong, X and Xu, H}, title = {Insights into the ecotoxicity of nitrofurazone in marine ecosystems based on body-size spectra of periphytic ciliates.}, journal = {Marine pollution bulletin}, volume = {174}, number = {}, pages = {113217}, doi = {10.1016/j.marpolbul.2021.113217}, pmid = {34864466}, issn = {1879-3363}, mesh = {Body Size ; *Ciliophora ; Ecosystem ; Ecotoxicology ; *Nitrofurazone/toxicity ; }, abstract = {In ecotoxicological studies, some biological responses known as biomarkers can be used as powerful tools to evaluate the ecotoxicity. In this study, we investigated the disparity of responses shown by body-size spectra of periphytic ciliate communities when used as biomarkers to detect the toxicity of the broad-spectrum veternary antibiotic nitrofurazone. Briefly, in chronic exposure experiments ciliate communities were exposed to different concentrations (0, 1, 2, 4 and 8 mg ml[-1]) of nitrofurazone. Relative Abundance of ciliates in all body-size categories decreased significantly, whereas their frequency of occurrence and probability densities showed hormetic-like responses in a dose dependent manner. Additionally, body-size distinctness indices were influenced by toxic stress and significantly departed from an expectation at higher nitrofurazone concentrations. Taken together, our results demonstrated that body-size spectra and body-size distinctness offered clear evidence of nitrofurazone toxicity in periphytic ciliates. Body-size spectra can therefore be used as a pivotal biomarker to determine the ecotoxicity of nitrofurazone in aquatic environments.}, }
@article {pmid34864020, year = {2022}, author = {Costa, DPD and Araujo, ASF and Pereira, APA and Mendes, LW and França, RFD and Silva, TDGED and Oliveira, JB and Araujo, JS and Duda, GP and Menezes, RSC and Medeiros, EV}, title = {Forest-to-pasture conversion modifies the soil bacterial community in Brazilian dry forest Caatinga.}, journal = {The Science of the total environment}, volume = {810}, number = {}, pages = {151943}, doi = {10.1016/j.scitotenv.2021.151943}, pmid = {34864020}, issn = {1879-1026}, mesh = {Biodiversity ; Forests ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Soil ; Soil Microbiology ; }, abstract = {Soils comprise a huge fraction of the world's biodiversity, contributing to several crucial ecosystem functions. However, how the forest-to-pasture conversion impact soil bacterial diversity remains poorly understood, mainly in the Caatinga biome, the largest tropical dry forest of the world. Here, we hypothesized that forest-to-pasture conversion would shape the microbial community. Thus, the soil bacterial community was assessed using the 16S rRNA gene sequencing into the Illumina MiSeq platform. Then, we analyzed ecological patterns and correlated the bacterial community with environmental parameters in forest, and two distinct pastures areas, one less productive and another more productive. The variation in soil properties in pastures and forest influenced the structure and diversity of the bacterial community. Thus, the more productive pasture positively influenced the proportion of specialists and the co-occurrence network compared to the less productive pasture. Also, Proteobacteria, Acidobacteria, and Verrucomicrobia were abundant under forest, while Actinobacteria, Firmicutes, and Chloroflexi were abundant under pastures. Also, the more productive pasture presented a higher bacterial diversity, which is important since that a more stable and connected bacterial community could benefit the agricultural environment and enhance plant performance, as can be observed by the highest network complexity in this pasture. Together, our findings elucidate a significant shift in soil bacterial communities as a consequence of forest-to-pasture conversion and bring important information for the development of preservation strategies.}, }
@article {pmid34863611, year = {2022}, author = {Nobs, SJ and MacLeod, FI and Wong, HL and Burns, BP}, title = {Eukarya the chimera: eukaryotes, a secondary innovation of the two domains of life?.}, journal = {Trends in microbiology}, volume = {30}, number = {5}, pages = {421-431}, doi = {10.1016/j.tim.2021.11.003}, pmid = {34863611}, issn = {1878-4380}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Biological Evolution ; *Eukaryota/genetics ; Eukaryotic Cells ; Phylogeny ; }, abstract = {One of the most significant events in the evolution of life is the origin of the eukaryotic cell, an increase in cellular complexity that occurred approximately 2 billion years ago. Ground-breaking research has centered around unraveling the characteristics of the Last Eukaryotic Common Ancestor (LECA) and the nuanced archaeal and bacterial contributions in eukaryogenesis, resulting in fundamental changes in our understanding of the Tree of Life. The archaeal and bacterial roles are covered by theories of endosymbiogenesis wherein an ancestral host archaeon and a bacterial endosymbiont merged to create a new complex cell type - Eukarya - and its mitochondrion. Eukarya is often regarded as a unique and distinct domain due to complex innovations not found in archaea or bacteria, despite housing a chimeric genome containing genes of both archaeal and bacterial origin. However, the discovery of complex cell machineries in recently described Asgard archaeal lineages, and the growing support for diverse bacterial gene transfers prior to and during the time of LECA, is redefining our understanding of eukaryogenesis. Indeed, the uniqueness of Eukarya, as a domain, is challenged. It is likely that many microbial syntrophies, encompassing a 'microbial village', were required to 'raise' a eukaryote during the process of eukaryogenesis.}, }
@article {pmid34862696, year = {2022}, author = {Jiao, S and Chen, W and Wei, G}, title = {Core microbiota drive functional stability of soil microbiome in reforestation ecosystems.}, journal = {Global change biology}, volume = {28}, number = {3}, pages = {1038-1047}, doi = {10.1111/gcb.16024}, pmid = {34862696}, issn = {1365-2486}, mesh = {Metagenomics ; *Microbiota ; *Soil ; Soil Microbiology ; }, abstract = {Revealing the ecological roles of core microbiota in the maintenance of the functional stability of soil microbiomes is crucial for sustainable ecosystem functioning; however, there is a dearth of whole-soil profile studies on the fundamental topic in microbial ecology, especially in the context of ecological restoration. Here, we explored whether core microbiota influence the temporal changes in the functional stability of soil microbiomes throughout the soil profile (i.e., soil depths of 0-300 cm) during natural succession in restored ex-arable ecosystems, via high-throughput amplicon and metagenomic sequencing. We revealed that core microbiota were essential for the maintenance of the functional stability of soil microbiomes in reforestation ecosystems. Specifically, the core taxa within one cluster of soil network, which had similar ecological preferences, had major contributions to functional stability. Reforestation significantly decreased the functional stability of soil microbiomes, which exhibited significant variations along the vertical soil profile in the reforested soils. Overall, the findings enhance our understanding of the factors driving functional stability in soil microbiomes, and suggests that core microbiota should be considered a key factor and integrated in policy and management activities targeting the enhancement and maintenance of functional stability and ecosystem sustainability in ecological restoration programs.}, }
@article {pmid34862327, year = {2021}, author = {Neu, AT and Allen, EE and Roy, K}, title = {Defining and quantifying the core microbiome: Challenges and prospects.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {51}, pages = {}, pmid = {34862327}, issn = {1091-6490}, mesh = {Animals ; Environmental Microbiology ; Humans ; *Microbiota ; Phylogeny ; }, abstract = {The term "core microbiome" has become widely used in microbial ecology over the last decade. Broadly, the core microbiome refers to any set of microbial taxa, or the genomic and functional attributes associated with those taxa, that are characteristic of a host or environment of interest. Most commonly, core microbiomes are measured as the microbial taxa shared among two or more samples from a particular host or environment. Despite the popularity of this term and its growing use, there is little consensus about how a core microbiome should be quantified in practice. Here, we present a brief history of the core microbiome concept and use a representative sample of the literature to review the different metrics commonly used for quantifying the core. Empirical analyses have used a wide range of metrics for quantifying the core microbiome, including arbitrary occurrence and abundance cutoff values, with the focal taxonomic level of the core ranging from phyla to amplicon sequence variants. However, many of these metrics are susceptible to sampling and other biases. Developing a standardized set of metrics for quantifying the core that accounts for such biases is necessary for testing specific hypotheses about the functional and ecological roles of core microbiomes.}, }
@article {pmid34861433, year = {2022}, author = {Zhu, X and Lee, LW and Song, G and Zhang, X and Gao, Y and Yang, G and Luo, S and Huang, X}, title = {Deciphering mono/multivalent draw solute-induced microbial ecology and membrane fouling in anaerobic osmotic membrane bioreactor.}, journal = {Water research}, volume = {209}, number = {}, pages = {117869}, doi = {10.1016/j.watres.2021.117869}, pmid = {34861433}, issn = {1879-2448}, abstract = {Anaerobic osmotic membrane bioreactor (AnOMBR) attracted attention due to high quality effluent production with low energy demand, and draw solute has significant effect on the system performance. However, the mutual relationship between draw solute-induced salinity accumulation and microbial community had many unknown questions to be solved. This study purpose was to construct two AnOMBR to compare the impact of draw solutes of NaCl and MgCl2 on the dynamic change of microbial ecology and membrane fouling. The result indicated that the draw solute of MgCl2 caused less salinity and more membrane biofouling than that of the draw solute NaCl. Multiple microbiological analysis methods were applied to discover keystone species related to the conductivity change and membrane fouling, especially for the MgCl2-AnOMBR system. It was found that draw solute NaCl could benefit the growth of Proteobacteria to become the most abundant phylum to affect the membrane fouling, while Mg[2+] introduction could stimulate the growth of NS9, Hydrogenphilaceae and Pedosphaeraceae to potentially cause the biofouling. Furthermore, phylogenetic molecular ecological networks (pMENs) deeply analyzed the microbial structure difference under Na[+] and Mg[2+] introduction, and indicated that the family Lentimicrobiaceae and Candidatus_Kaiserbacteria were the keystone species in NaCl-AnOMBR, while two genus Anaerolinea and SWB02, and two families Saprospiraceae and NS9 were discovered to have key effect in MgCl2-AnOMBR due to their strong extracellular polymeric substances (EPS) production ability for survival of other microorganisms. This study was significant to give microbial targets under the impact of various draw solutes, as the reference for the engineers to further investigate how to improve the microbial structure to enhance AnOMBR performance and inhibit the membrane biofouling.}, }
@article {pmid34858369, year = {2021}, author = {Brüls, T and Baumdicker, F and Smidt, H}, title = {Editorial: Synthetic Microbial Ecology.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {757848}, doi = {10.3389/fmicb.2021.757848}, pmid = {34858369}, issn = {1664-302X}, }
@article {pmid34855091, year = {2021}, author = {Semenov, AV}, title = {Peptidoglycan of Bacterial Cell Wall Affects Competitive Properties of Microorganisms.}, journal = {Bulletin of experimental biology and medicine}, volume = {172}, number = {2}, pages = {164-168}, pmid = {34855091}, issn = {1573-8221}, mesh = {Antibiosis/*physiology ; Bacillus subtilis/physiology ; Bacterial Proteins/metabolism/physiology ; Bifidobacterium/physiology ; Candida/physiology ; Cell Wall/chemistry/metabolism/*physiology ; Enterobacter/physiology ; Enterococcus faecalis/physiology ; Escherichia coli/physiology ; Female ; Humans ; Lacticaseibacillus casei/physiology ; Microbiological Techniques ; Peptidoglycan/analysis/*metabolism ; Staphylococcus aureus/physiology ; }, abstract = {We studied the effect of bacterial wall peptidoglycan of 7 bacterial species on the competitive properties of human-associated microorganisms. Addition of peptidoglycan to the culture medium did not change the growth characteristics of the test cultures; however, an increase in the antagonism and hydrophobicity of Bifidobacterium sp. and Enterococcus sp. was observed, while the effect on enterobacteria was predominantly indifferent or inhibitory. The effect did not depend much on the source of peptidoglycan and was equally manifested on both indigenous and probiotic strains. The observed new property of peptidoglycan indicates its participation in the formation and functioning of microbiota. The obtained data on the regulation of the properties of microorganisms provide new possibilities for the correction and maintenance of host homeostasis through host-associated microbiota.}, }
@article {pmid34854932, year = {2023}, author = {Klawonn, I and Dunker, S and Kagami, M and Grossart, HP and Van den Wyngaert, S}, title = {Intercomparison of Two Fluorescent Dyes to Visualize Parasitic Fungi (Chytridiomycota) on Phytoplankton.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {9-23}, pmid = {34854932}, issn = {1432-184X}, support = {KL3332/1-1//german research foundation/ ; WY175/1-1//german research foundation/ ; GR1540/28-1//german research foundation/ ; RA-373/20//german research foundation/ ; }, mesh = {*Phytoplankton ; *Chytridiomycota ; Fluorescent Dyes ; Lakes/microbiology ; Fungi ; }, abstract = {Fungal microparasites (here chytrids) are widely distributed and yet, they are often overlooked in aquatic environments. To facilitate the detection of microparasites, we revisited the applicability of two fungal cell wall markers, Calcofluor White (CFW) and wheat germ agglutinin (WGA), for the direct visualization of chytrid infections on phytoplankton in laboratory-maintained isolates and field-sampled communities. Using a comprehensive set of chytrid-phytoplankton model pathosystems, we verified the staining pattern on diverse morphological structures of chytrids via fluorescence microscopy. Empty sporangia were stained most effectively, followed by encysted zoospores and im-/mature sporangia, while the staining success was more variable for rhizoids, stalks, and resting spores. In a few instances, the staining was unsuccessful (mostly with WGA), presumably due to insufficient cell fixation, gelatinous cell coatings, and multilayered cell walls. CFW and WGA staining could be done in Utermöhl chambers or on polycarbonate filters, but CFW staining on filters seemed less advisable due to high background fluorescence. To visualize chytrids, 1 µg dye mL[-1] was sufficient (but 5 µg mL[-1] are recommended). Using a dual CFW-WGA staining protocol, we detected multiple, mostly undescribed chytrids in two natural systems (freshwater and coastal), while falsely positive or negative stained cells were well detectable. As a proof-of-concept, we moreover conducted imaging flow cytometry, as a potential high-throughput technology for quantifying chytrid infections. Our guidelines and recommendations are expected to facilitate the detection of chytrid epidemics and to unveil their ecological and economical imprint in natural and engineered aquatic systems.}, }
@article {pmid34854719, year = {2021}, author = {Silveira, SMD and Silva, SD and Macrae, A and Ramos, RTJ and Araújo, FA and Schultz, J and Góes-Neto, A and Costa, MMD and Soares, SC and Azevedo, VAC and Aburjaile, FF and Brenig, B and Rosado, AS and Oliveira, SS}, title = {Genome Sequence of Pseudomonas sp. Strain LAP_36, A Rhizosphere Bacterium Isolated from King George Island, Antarctica.}, journal = {Microbiology resource announcements}, volume = {10}, number = {48}, pages = {e0073121}, pmid = {34854719}, issn = {2576-098X}, abstract = {Pseudomonas sp. strain LAP_36 was isolated from rhizosphere soil from Deschampsia antarctica on King George Island, South Shetland Islands, Antarctica. Here, we report on its draft genome sequence, which consists of 8,794,771 bp with 60.0% GC content and 8,011 protein-coding genes.}, }
@article {pmid34854667, year = {2021}, author = {Carboni, A and Slomberg, DL and Nassar, M and Santaella, C and Masion, A and Rose, J and Auffan, M}, title = {Aquatic Mesocosm Strategies for the Environmental Fate and Risk Assessment of Engineered Nanomaterials.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {24}, pages = {16270-16282}, doi = {10.1021/acs.est.1c02221}, pmid = {34854667}, issn = {1520-5851}, mesh = {*Ecosystem ; *Nanostructures/toxicity ; Risk Assessment ; }, abstract = {In the past decade, mesocosms have emerged as a useful tool for the environmental study of engineered nanomaterials (ENMs) as they can mimic the relevant exposure scenario of contamination. Herein, we analyzed the scientific outcomes of aquatic mesocosm experiments, with regard to their designs, the ENMs tested, and the end points investigated. Several mesocosm designs were consistently applied in the past decade to virtually mimic various contamination scenarios with regard to ecosystem setting as well as ENMs class, dose, and dosing. Statistical analyses were carried out with the literature data to identify the main parameters driving ENM distribution in the mesocosms and the potential risk posed to benthic and planktonic communities as well as global ecosystem responses. These analyses showed that at the end of the exposure, mesocosm size (water volume), experiment duration, and location indoor/outdoor had major roles in defining the ENMs/metal partitioning. Moreover, a higher exposure of the benthic communities is often observed but did not necessarily translate to a higher risk due to the lower hazard posed by transformed ENMs in the sediments (e.g., aggregated, sulfidized). However, planktonic organisms were generally exposed to lower concentrations of potentially more reactive and toxic ENM species. Hence, mesocosms can be complementary tools to existing standard operational procedures for regulatory purposes and environmental fate and risk assessment of ENMs. To date, the research was markedly unbalanced toward the investigation of metal-based ENMs compared to metalloid- and carbon-based ENMs but also nanoenabled products. Future studies are expected to fill this gap, with special regard to high production volume and potentially hazardous ENMs. Finally, to take full advantage of mesocosms, future studies must be carefully planned to incorporate interdisciplinary approaches and ensure that the large data sets produced are fully exploited.}, }
@article {pmid34852879, year = {2021}, author = {Cowan, DA and Burton, SG and Rybicki, EP and Wiliamson, AL and Dorrington, RA and Pepper, MS}, title = {Viruses, variants and vaccines.}, journal = {South African medical journal = Suid-Afrikaanse tydskrif vir geneeskunde}, volume = {111}, number = {5}, pages = {409-411}, doi = {10.7196/SAMJ.2021.v111i5.15578}, pmid = {34852879}, issn = {2078-5135}, mesh = {*COVID-19/epidemiology/genetics/prevention &amp; control ; *COVID-19 Vaccines ; Humans ; Mutation ; Pandemics/prevention &amp; control ; SARS-CoV-2/*genetics/isolation &amp; purification ; South Africa ; Vaccine Efficacy ; *Vaccines ; *Viruses/pathogenicity ; }, abstract = {The current SARS-CoV-2 pandemic has brought a number of major global clinical, sociological and economic issues into sharp focus. We address some of these issues, focusing on short-term factors such as virus mutations and vaccine efficacy, and also considering the longer-term implications of the current pandemic. We discuss societal responses to the presence of a pathogen that will probably remain in circulation for decades or longer, and to future new emergent viruses.}, }
@article {pmid34851441, year = {2022}, author = {Oh, HN and Myeong, NR and Kim, T and Min, GS and Kim, S and Sul, WJ}, title = {Changes in Fecal Pellet Microbiome of the Cold-Adapted Antarctic Copepod Tigriopus kingsejongensis at Different Temperatures and Developmental Stages.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1029-1041}, pmid = {34851441}, issn = {1432-184X}, support = {Graduate Research Scholarship in 2016//Chung-Ang University/ ; NRF-2019R1A2C1090861//National Research Foundation of Korea/ ; PE21140//Korea Polar Research Institute/ ; }, mesh = {Animals ; *Copepoda ; Temperature ; Antarctic Regions ; Cold Temperature ; *Microbiota ; }, abstract = {Tigriopus kingsejongensis, a copepod species reported from the King Sejong Station, Antarctica, serves as a valuable food resource in ecosystems. We cultured T. kingsejongensis at three different temperatures (2 °C, 8 °C, and 15 °C) in a laboratory to observe the changes in its fecal pellet microbiome depending on the cultivation temperatures and developmental stages. We observed that the fecal pellet microbiome of the copepod changed with temperature: a lower microbial diversity, higher abundance of the aquatic bacterium Vibrio, and lower abundance of the psychrophilic bacterium Colwellia were noted at higher temperatures. In addition, the fecal pellet microbiome of the copepod changed according to the developmental stage: a lower microbial diversity was noted in egg-attached copepods than in nauplii at 8 °C. We further analyzed three shotgun metagenomes from the fecal pellet samples of T. kingsejongensis at different temperatures and obtained 44 metagenome-assembled genomes (MAGs). We noted that MAGs of V. splendidus D contained glycosyl hydrolases (GHs) encoding chitinases and virulence factors at a higher relative abundance at 15 °C than at lower temperatures. These results indicate that increasing temperature affects the fecal pellet microbiome and the development of copepods. The findings are helpful to understand the changes in cold-adapted copepods and the effect of temperature on their growth.}, }
@article {pmid34849765, year = {2021}, author = {Tiwari, DP and Shah, P and Van den Abbeele, P and Marzorati, M and Calatayud, M and Ghyselinck, J and Dubey, AK and Narayanan, S and Jain, M}, title = {Microbial fermentation of Fossence™, a short-chain fructo-oligosaccharide, under simulated human proximal colonic condition and assessment of its prebiotic effects-a pilot study.}, journal = {FEMS microbiology letters}, volume = {368}, number = {21-24}, pages = {}, doi = {10.1093/femsle/fnab147}, pmid = {34849765}, issn = {1574-6968}, mesh = {Bacteria/genetics/metabolism ; Colon/metabolism ; Fatty Acids, Volatile/metabolism ; Feces/chemistry ; *Fermentation ; Humans ; Hydrogen-Ion Concentration ; Lactates/metabolism ; *Microbiota ; *Oligosaccharides/metabolism ; Pilot Projects ; *Prebiotics/analysis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A short-chain fructo-oligosaccharide (sc-FOS) was tested in a simulator of the human gut microbial ecosystem (SHIME) in vitro model to quantify its prebiotic effects according to Prebiotic Index (PI) and Measure of prebiotic effect (MPE) equations. FossenceTM, (sc-FOS, 0.5%) was fermented in a simulated human proximal colonic condition, using a fecal inoculum from a healthy individual. We analysed the pH reduction, substrate utilization, lactate and short-chain fatty acid (SCFA) production and microbial community modulation. Microbial fermentation of sc-FOS strongly reduced the media pH indicating the production of lactate and SCFA with accumulation of lactate and enhanced levels of acetate (34.38 ± 0.38 mM), propionate (20.93 ± 0.56 mM) and butyrate (4.93 ± 0.03 mM) compared to 18.46 ± 0.20 mM, 6.24 ± 0.10 mM and 3.3 ± 0.06 mM in the blank, respectively. Total SCFA production in test media was 61.91 ± 0.87 mM compared to 33.65 ± 0.36 mM in blank and the contribution of free-sugars present in sc-FOS to SCFAs was negligible. Modulation of the microbial community was analysed through 16S rRNA sequencing and we found that sc-FOS greatly stimulated the beneficial bacteria such as Bifidobacteria and Lactobacillus. We report the PI and MPE values for FossenceTM, as 14.9 and 0.01 respectively at the end of 24 h, which is an indicator of a strong prebiotic effect.}, }
@article {pmid34849757, year = {2021}, author = {Vargas, P and Bosmans, L and Van Calenberge, B and Van Kerckhove, S and Lievens, B and Rediers, H}, title = {Bacterial community dynamics of tomato hydroponic greenhouses infested with hairy root disease.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {12}, pages = {}, doi = {10.1093/femsec/fiab153}, pmid = {34849757}, issn = {1574-6941}, mesh = {Ecosystem ; Hydroponics ; *Solanum lycopersicum ; Plant Roots ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil Microbiology ; }, abstract = {The rhizosphere is a complex ecosystem consisting of microbes in the interface between growth medium and plant roots, which affects plant productivity and health. This is one of the few studies analysing bacterial communities present in the rhizosphere of hydroponically grown plants. Tomato grown under hydroponic conditions is prone to hairy root disease (HRD) that is caused by rhizogenic Agrobacterium biovar 1 strains. In this study, using high-throughput amplicon sequencing of partial ribosomal RNA (rRNA) genes, we aimed to characterize bacterial communities in rockwool samples obtained from healthy or HRD-infested tomato during an entire growing season. Alpha diversity of rockwool increased in direct relation with time and samples obtained from healthy greenhouses presented a significantly lower alpha diversity than those from HRD-infested greenhouses. Beta diversity showed that bacterial community composition changed throughout the growing season. Amplicon Sequence Variants (ASVs) identified as rhizogenic Agrobacterium bv. 1 were more prevalent in HRD-infected greenhouses. Conversely, ASVs identified as Paenibacillus, previously identified as biocontrol organisms of rhizogenic agrobacteria, were more prevalent in healthy greenhouses. Altogether, our study greatly contributes to the knowledge of bacterial communities in rockwool hydroponics.}, }
@article {pmid35935893, year = {2021}, author = {Crous, PW and Cowan, DA and Maggs-Kölling, G and Yilmaz, N and Thangavel, R and Wingfield, MJ and Noordeloos, ME and Dima, B and Brandrud, TE and Jansen, GM and Morozova, OV and Vila, J and Shivas, RG and Tan, YP and Bishop-Hurley, S and Lacey, E and Marney, TS and Larsson, E and Le Floch, G and Lombard, L and Nodet, P and Hubka, V and Alvarado, P and Berraf-Tebbal, A and Reyes, JD and Delgado, G and Eichmeier, A and Jordal, JB and Kachalkin, AV and Kubátová, A and Maciá-Vicente, JG and Malysheva, EF and Papp, V and Rajeshkumar, KC and Sharma, A and Spetik, M and Szabóová, D and Tomashevskaya, MA and Abad, JA and Abad, ZG and Alexandrova, AV and Anand, G and Arenas, F and Ashtekar, N and Balashov, S and Bañares, &#xc1; and Baroncelli, R and Bera, I and Biketova, AY and Blomquist, CL and Boekhout, T and Boertmann, D and Bulyonkova, TM and Burgess, TI and Carnegie, AJ and Cobo-Diaz, JF and Corriol, G and Cunnington, JH and da Cruz, MO and Damm, U and Davoodian, N and de A Santiago, ALCM and Dearnaley, J and de Freitas, LWS and Dhileepan, K and Dimitrov, R and Di Piazza, S and Fatima, S and Fuljer, F and Galera, H and Ghosh, A and Giraldo, A and Glushakova, AM and Gorczak, M and Gouliamova, DE and Gramaje, D and Groenewald, M and Gunsch, CK and Gutiérrez, A and Holdom, D and Houbraken, J and Ismailov, AB and Istel, &#x141; and Iturriaga, T and Jeppson, M and Jurjević, &#x17d; and Kalinina, LB and Kapitonov, VI and Kautmanová, I and Khalid, AN and Kiran, M and Kiss, L and Kovács, &#xc1; and Kurose, D and Kušan, I and Lad, S and Læssøe, T and Lee, HB and Luangsa-Ard, JJ and Lynch, M and Mahamedi, AE and Malysheva, VF and Mateos, A and Matočec, N and Mešić, A and Miller, AN and Mongkolsamrit, S and Moreno, G and Morte, A and Mostowfizadeh-Ghalamfarsa, R and Naseer, A and Navarro-Ródenas, A and Nguyen, TTT and Noisripoom, W and Ntandu, JE and Nuytinck, J and Ostrý, V and Pankratov, TA and Pawłowska, J and Pecenka, J and Pham, THG and Polhorský, A and Pošta, A and Raudabaugh, DB and Reschke, K and Rodríguez, A and Romero, M and Rooney-Latham, S and Roux, J and Sandoval-Denis, M and Smith, MT and Steinrucken, TV and Svetasheva, TY and Tkalčec, Z and van der Linde, EJ and V D Vegte, M and Vauras, J and Verbeken, A and Visagie, CM and Vitelli, JS and Volobuev, SV and Weill, A and Wrzosek, M and Zmitrovich, IV and Zvyagina, EA and Groenewald, JZ}, title = {Fungal Planet description sheets: 1182-1283.}, journal = {Persoonia}, volume = {46}, number = {}, pages = {313-528}, pmid = {35935893}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Algeria, Phaeoacremonium adelophialidum from Vitis vinifera. Antarctica, Comoclathris antarctica from soil. Australia, Coniochaeta salicifolia as endophyte from healthy leaves of Geijera salicifolia, Eremothecium peggii in fruit of Citrus australis, Microdochium ratticaudae from stem of Sporobolus natalensis, Neocelosporium corymbiae on stems of Corymbia variegata, Phytophthora kelmanii from rhizosphere soil of Ptilotus pyramidatus, Pseudosydowia backhousiae on living leaves of Backhousia citriodora, Pseudosydowia indooroopillyensis, Pseudosydowia louisecottisiae and Pseudosydowia queenslandica on living leaves of Eucalyptus sp. Brazil, Absidia montepascoalis from soil. Chile, Ilyonectria zarorii from soil under Maytenus boaria. Costa Rica, Colletotrichum filicis from an unidentified fern. Croatia, Mollisia endogranulata on deteriorated hardwood. Czech Republic, Arcopilus navicularis from tea bag with fruit tea, Neosetophoma buxi as endophyte from Buxus sempervirens, Xerochrysium bohemicum on surface of biscuits with chocolate glaze and filled with jam. France, Entoloma cyaneobasale on basic to calcareous soil, Fusarium aconidiale from Triticum aestivum, Fusarium juglandicola from buds of Juglans regia. Germany, Tetraploa endophytica as endophyte from Microthlaspi perfoliatum roots. India, Castanediella ambae on leaves of Mangifera indica, Lactifluus kanadii on soil under Castanopsis sp., Penicillium uttarakhandense from soil. Italy, Penicillium ferraniaense from compost. Namibia, Bezerromyces gobabebensis on leaves of unidentified succulent, Cladosporium stipagrostidicola on leaves of Stipagrostis sp., Cymostachys euphorbiae on leaves of Euphorbia sp., Deniquelata hypolithi from hypolith under a rock, Hysterobrevium walvisbayicola on leaves of unidentified tree, Knufia hypolithi and Knufia walvisbayicola from hypolith under a rock, Lapidomyces stipagrostidicola on leaves of Stipagrostis sp., Nothophaeotheca mirabibensis (incl. Nothophaeotheca gen. nov.) on persistent inflorescence remains of Blepharis obmitrata, Paramyrothecium salvadorae on twigs of Salvadora persica, Preussia procaviicola on dung of Procavia sp., Sordaria equicola on zebra dung, Volutella salvadorae on stems of Salvadora persica. Netherlands, Entoloma ammophilum on sandy soil, Entoloma pseudocruentatum on nutrient poor (acid) soil, Entoloma pudens on plant debris, amongst grasses. New Zealand, Amorocoelophoma neoregeliae from leaf spots of Neoregelia sp., Aquilomyces metrosideri and Septoriella callistemonis from stem discolouration and leaf spots of Metrosideros sp., Cadophora neoregeliae from leaf spots of Neoregelia sp., Flexuomyces asteliae (incl. Flexuomyces gen. nov.) and Mollisia asteliae from leaf spots of Astelia chathamica, Ophioceras freycinetiae from leaf spots of Freycinetia banksii, Phaeosphaeria caricis-sectae from leaf spots of Carex secta. Norway, Cuphophyllus flavipesoides on soil in semi-natural grassland, Entoloma coracis on soil in calcareous Pinus and Tilia forests, Entoloma cyaneolilacinum on soil semi-natural grasslands, Inocybe norvegica on gravelly soil. Pakistan, Butyriboletus parachinarensis on soil in association with Quercus baloot. Poland, Hyalodendriella bialowiezensis on debris beneath fallen bark of Norway spruce Picea abies. Russia, Bolbitius sibiricus on à moss covered rotting trunk of Populus tremula, Crepidotus wasseri on debris of Populus tremula, Entoloma isborscanum on soil on calcareous grasslands, Entoloma subcoracis on soil in subalpine grasslands, Hydropus lecythiocystis on rotted wood of Betula pendula, Meruliopsis faginea on fallen dead branches of Fagus orientalis, Metschnikowia taurica from fruits of Ziziphus jujube, Suillus praetermissus on soil, Teunia lichenophila as endophyte from Cladonia rangiferina. Slovakia, Hygrocybe fulgens on mowed grassland, Pleuroflammula pannonica from corticated branches of Quercus sp. South Africa, Acrodontium burrowsianum on leaves of unidentified Poaceae, Castanediella senegaliae on dead pods of Senegalia ataxacantha, Cladophialophora behniae on leaves of Behnia sp., Colletotrichum cliviigenum on leaves of Clivia sp., Diatrype dalbergiae on bark of Dalbergia armata, Falcocladium heteropyxidicola on leaves of Heteropyxis canescens, Lapidomyces aloidendricola as epiphyte on brown stem of Aloidendron dichotomum, Lasionectria sansevieriae and Phaeosphaeriopsis sansevieriae on leaves of Sansevieria hyacinthoides, Lylea dalbergiae on Diatrype dalbergiae on bark of Dalbergia armata, Neochaetothyrina syzygii (incl. Neochaetothyrina gen. nov.) on leaves of Syzygium chordatum, Nothophaeomoniella ekebergiae (incl. Nothophaeomoniella gen. nov.) on leaves of Ekebergia pterophylla, Paracymostachys euphorbiae (incl. Paracymostachys gen. nov.) on leaf litter of Euphorbia ingens, Paramycosphaerella pterocarpi on leaves of Pterocarpus angolensis, Paramycosphaerella syzygii on leaf litter of Syzygium chordatum, Parateichospora phoenicicola (incl. Parateichospora gen. nov.) on leaves of Phoenix reclinata, Seiridium syzygii on twigs of Syzygium chordatum, Setophoma syzygii on leaves of Syzygium sp., Starmerella xylocopis from larval feed of an Afrotropical bee Xylocopa caffra, Teratosphaeria combreti on leaf litter of Combretum kraussii, Teratosphaericola leucadendri on leaves of Leucadendron sp., Toxicocladosporium pterocarpi on pods of Pterocarpus angolensis. Spain, Cortinarius bonachei with Quercus ilex in calcareus soils, Cortinarius brunneovolvatus under Quercus ilex subsp. ballota in calcareous soil, Extremopsis radicicola (incl. Extremopsis gen. nov.) from root-associated soil in a wet heathland, Russula quintanensis on acidic soils, Tubaria vulcanica on volcanic lapilii material, Tuber zambonelliae in calcareus soil. Sweden, Elaphomyces borealis on soil under Pinus sylvestris and Betula pubescens. Tanzania, Curvularia tanzanica on inflorescence of Cyperus aromaticus. Thailand, Simplicillium niveum on Ophiocordyceps camponoti-leonardi on underside of unidentified dicotyledonous leaf. USA, Calonectria californiensis on leaves of Umbellularia californica, Exophiala spartinae from surface sterilised roots of Spartina alterniflora, Neophaeococcomyces oklahomaensis from outside wall of alcohol distillery. Vietnam, Fistulinella aurantioflava on soil. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Cowan DA, Maggs-Kölling, et al. 2021. Fungal Planet description sheets: 1182-1283. Persoonia 46: 313-528. https://doi.org/10.3767/persoonia.2021.46.11.}, }
@article {pmid35707452, year = {2021}, author = {Werbin, ZR and Hackos, B and Lopez-Nava, J and Dietze, MC and Bhatnagar, JM}, title = {The National Ecological Observatory Network's soil metagenomes: assembly and basic analysis.}, journal = {F1000Research}, volume = {10}, number = {}, pages = {299}, pmid = {35707452}, issn = {2046-1402}, mesh = {Computational Biology/methods ; *Metagenome ; Metagenomics/methods ; Neon ; *Soil ; }, abstract = {The largest dataset of soil metagenomes has recently been released by the National Ecological Observatory Network (NEON), which performs annual shotgun sequencing of soils at 47 sites across the United States. NEON serves as a valuable educational resource, thanks to its open data and programming tutorials, but there is currently no introductory tutorial for accessing and analyzing the soil shotgun metagenomic dataset. Here, we describe methods for processing raw soil metagenome sequencing reads using a bioinformatics pipeline tailored to the high complexity and diversity of the soil microbiome. We describe the rationale, necessary resources, and implementation of steps such as cleaning raw reads, taxonomic classification, assembly into contigs or genomes, annotation of predicted genes using custom protein databases, and exporting data for downstream analysis. The workflow presented here aims to increase the accessibility of NEON's shotgun metagenome data, which can provide important clues about soil microbial communities and their ecological roles.}, }
@article {pmid36131874, year = {2021}, author = {Legin, AA and Schintlmeister, A and Sommerfeld, NS and Eckhard, M and Theiner, S and Reipert, S and Strohhofer, D and Jakupec, MA and Galanski, MS and Wagner, M and Keppler, BK}, title = {Nano-scale imaging of dual stable isotope labeled oxaliplatin in human colon cancer cells reveals the nucleolus as a putative node for therapeutic effect.}, journal = {Nanoscale advances}, volume = {3}, number = {1}, pages = {249-262}, pmid = {36131874}, issn = {2516-0230}, support = {P 27749/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Oxaliplatin shows a superior clinical activity in colorectal cancer compared to cisplatin. Nevertheless, the knowledge about its cellular distribution and the mechanisms responsible for the different range of oxaliplatin-responsive tumors is far from complete. In this study, we combined highly sensitive element specific and isotope selective imaging by nanometer-scale secondary ion mass spectrometry (NanoSIMS) with transmission electron microscopy to investigate the subcellular accumulation of oxaliplatin in three human colon cancer cell lines (SW480, HCT116 wt, HCT116 OxR). Oxaliplatin bearing dual stable isotope labeled moieties, i.e. [2]H-labeled diaminocyclohexane (DACH) and [13]C-labeled oxalate, were applied for comparative analysis of the subcellular distribution patterns of the central metal and the ligands. In all the investigated cell lines, oxaliplatin was found to have a pronounced tendency for cytoplasmic aggregation in single membrane bound organelles, presumably related to various stages of the endocytic pathway. Moreover, nuclear structures, heterochromatin and in particular nucleoli, were affected by platinum-drug exposure. In order to explore the consequences of oxaliplatin resistance, subcellular drug distribution patterns were investigated in a pair of isogenic malignant cell lines with distinct levels of drug sensitivity (HCT116 wt and HCT116 OxR, the latter with acquired resistance to oxaliplatin). The subcellular platinum distribution was found to be similar in both cell lines, with only slightly higher accumulation in the sensitive HCT116 wt cells which is inconsistent with the resistance factor of more than 20-fold. Instead, the isotopic analysis revealed a disproportionally high accumulation of the oxalate ligand in the resistant cell line.}, }
@article {pmid35846090, year = {2021}, author = {Ludwig, H and Hausmann, B and Schreder, M and Pönisch, W and Zojer, N and Knop, S and Gunsilius, E and Egle, A and Petzer, A and Einsele, H and Hajek, R and Weisel, K and Krenosz, KJ and Lang, A and Lechner, D and Greil, R and Berry, D}, title = {Reduced alpha diversity of the oral microbiome correlates with short progression-free survival in patients with relapsed/refractory multiple myeloma treated with ixazomib-based therapy (AGMT MM 1, phase II trial).}, journal = {EJHaem}, volume = {2}, number = {1}, pages = {99-103}, pmid = {35846090}, issn = {2688-6146}, abstract = {Alterations in the human microbiome have been linked to several malignant diseases. Here, we investigated the oral microbiome of 79 patients with relapsed/refractory multiple myeloma (MM) treated with ixazomib-thalidomide-dexamethasone. Increased alpha diversity (Shannon index) at the phylum level was associated with longer progression-free survival (PFS) (10.2 vs 8.5 months, P = .04), particularly in patients with very long (>75% quartile) PFS . Additionally, alpha diversity was lower in patients with progressive disease (P < .05). These findings suggest an interrelationship between the oral microbiome and outcome in patients with MM and encourage a novel direction for diagnostic and/or therapeutic strategies.}, }
@article {pmid36157708, year = {2020}, author = {Wang, M and Cernava, T}, title = {Overhauling the assessment of agrochemical-driven interferences with microbial communities for improved global ecosystem integrity.}, journal = {Environmental science and ecotechnology}, volume = {4}, number = {}, pages = {100061}, pmid = {36157708}, issn = {2666-4984}, abstract = {Recent studies have shown that various agrochemicals can substantially affect microbial communities; especially those that are associated with cultivated plants. Under certain circumstances, up to 50% of the naturally occurring microorganisms can be negatively affected by common agricultural practices such as seed coating with fungicide-based matrices. Nevertheless, the off-target effects of commonly applied agrochemicals are still understudied in terms of their interferences with microbial communities. At the same time, agrochemical inputs are steadily increasing due to the intensification of agriculture and the increasing pathogen pressure that is currently observed worldwide. In this article, we briefly reflect on the current knowledge related to pesticide interference with microbial communities and discuss negative implications for the plant holobiont as well as such that are spanning beyond local system borders. Cumulative effects of pesticide inputs that cause alterations in microbial functioning likely have unforeseen implications on geochemical cycles that should be addressed with a high priority in ongoing research. A holistic assessment of such implications will allow us to objectively select the most suitable means for food production under the scenario of a growing global population and aggravating climatic conditions. We present three hypothetical solutions that might facilitate a more sustainable and less damaging application of pesticides in the future.}, }
@article {pmid35021714, year = {2020}, author = {Ghosh, P and Bera, A and Ghosh, A and Bhadury, P and De, P}, title = {Side-Chain Proline-Based Polymers as Effective Inhibitors for In Vitro Aggregation of Insulin.}, journal = {ACS applied bio materials}, volume = {3}, number = {8}, pages = {5407-5419}, doi = {10.1021/acsabm.0c00709}, pmid = {35021714}, issn = {2576-6422}, abstract = {Insulin fibril formation is considered as the hallmark of several debilitating pathological conditions. To develop effective therapeutics that are able to control the amyloidogenesis process and inhibit fibril formation, herein we have designed a side-chain proline (Pro)-based homopolymer and block copolymers through the reversible addition-fragmentation chain transfer (RAFT) polymerization technique and further explored their obligatory role in the in vitro insulin fibrillation process. Using a variety of biophysical tools, including turbidity measurements, thioflavin T (ThT) fluorescence kinetics, tyrosine (Tyr) fluorescence study, Nile red (NR) fluorescence assay, dynamic light scattering (DLS) study, circular dichroism (CD) measurements, and isothermal titration calorimetry (ITC) techniques, we demonstrated that Pro-based polymers can significantly inhibit the insulin fibrillation process. Among them, the Pro-based homopolymer acts as the most potent inhibitor of insulin fibrillation as confirmed by ThT assay, CD study, and transmission electron microscopic (TEM) analysis. Tyrosine fluorescence measurements and NR fluorescence assay revealed that hydrophobic interactions are the crucial factor that mainly controls the inhibition process. Apart from hydrophobic interactions, polar interactions may also be responsible for the inhibition process as evaluated by ITC study.}, }
@article {pmid36159604, year = {2020}, author = {Uria, N and Fiset, E and Pellitero, MA and Muñoz, FX and Rabaey, K and Campo, FJD}, title = {Immobilisation of electrochemically active bacteria on screen-printed electrodes for rapid in situ toxicity biosensing.}, journal = {Environmental science and ecotechnology}, volume = {3}, number = {}, pages = {100053}, pmid = {36159604}, issn = {2666-4984}, abstract = {Microbial biosensors can be an excellent alternative to classical methods for toxicity monitoring, which are time-consuming and not sensitive enough. However, bacteria typically connect to electrodes through biofilm formation, leading to problems due to lack of uniformity or long device production times. A suitable immobilisation technique can overcome these challenges. Still, they may respond more slowly than biofilm-based electrodes because bacteria gradually adapt to electron transfer during biofilm formation. In this study, we propose a controlled and reproducible way to fabricate bacteria-modified electrodes. The method consists of an immobilisation step using a cellulose matrix, followed by an electrode polarization in the presence of ferricyanide and glucose. Our process is short, reproducible and led us to obtain ready-to-use electrodes featuring a high-current response. An excellent shelf-life of the immobilised electrochemically active bacteria was demonstrated for up to one year. After an initial 50% activity loss in the first month, no further declines have been observed over the following 11 months. We implemented our bacteria-modified electrodes to fabricate a lateral flow platform for toxicity monitoring using formaldehyde (3%). Its addition led to a 59% current decrease approximately 20 min after the toxic input. The methods presented here offer the ability to develop a high sensitivity, easy to produce, and long shelf life bacteria-based toxicity detectors.}, }
@article {pmid35122045, year = {2020}, author = {Slowicka, K and Petta, I and Blancke, G and Hoste, E and Dumas, E and Sze, M and Vikkula, H and Radaelli, E and Haigh, JJ and Jonckheere, S and Taminau, J and Vandamme, N and Wullaert, A and Tulchinsky, E and Nittner, D and Van Vlierberghe, P and De Hertogh, G and Baldin, P and Etlioglu, E and Wirapati, P and Boon, L and Lambrecht, BN and Callewaert, C and Tejpar, S and Goossens, S and Berx, G and Vereecke, L and van Loo, G}, title = {Publisher Correction: Zeb2 drives invasive and microbiota-dependent colon carcinoma.}, journal = {Nature cancer}, volume = {1}, number = {7}, pages = {750}, doi = {10.1038/s43018-020-0097-4}, pmid = {35122045}, issn = {2662-1347}, }
@article {pmid35047975, year = {2020}, author = {Belibasakis, GN}, title = {Grand Challenges in Oral Infections and Microbes.}, journal = {Frontiers in oral health}, volume = {1}, number = {}, pages = {2}, pmid = {35047975}, issn = {2673-4842}, }
@article {pmid35121975, year = {2020}, author = {Slowicka, K and Petta, I and Blancke, G and Hoste, E and Dumas, E and Sze, M and Vikkula, H and Radaelli, E and Haigh, JJ and Jonckheere, S and Taminau, J and Vandamme, N and Wullaert, A and Tulchinsky, E and Nittner, D and Van Vlierberghe, P and De Hertogh, G and Baldin, P and Etlioglu, E and Wirapati, P and Boon, L and Lambrecht, BN and Callewaert, C and Tejpar, S and Goossens, S and Berx, G and Vereecke, L and van Loo, G}, title = {Zeb2 drives invasive and microbiota-dependent colon carcinoma.}, journal = {Nature cancer}, volume = {1}, number = {6}, pages = {620-634}, pmid = {35121975}, issn = {2662-1347}, mesh = {Animals ; *Carcinoma/metabolism ; Colon/metabolism ; Mice ; *Microbiota ; }, abstract = {Colorectal cancer (CRC) is highly prevalent in Western society, and increasing evidence indicates strong contributions of environmental factors and the intestinal microbiota to CRC initiation, progression and even metastasis. We have identified a synergistic inflammatory tumor-promoting mechanism through which the resident intestinal microbiota boosts invasive CRC development in an epithelial-to-mesenchymal transition-prone tissue environment. Intestinal epithelial cell (IEC)-specific transgenic expression of the epithelial-to-mesenchymal transition regulator Zeb2 in mice (Zeb2[IEC-Tg/+]) leads to increased intestinal permeability, myeloid cell-driven inflammation and spontaneous invasive CRC development. Zeb2[IEC-Tg/+] mice develop a dysplastic colonic epithelium, which progresses to severely inflamed neoplastic lesions while the small intestinal epithelium remains normal. Zeb2[IEC-Tg/+] mice are characterized by intestinal dysbiosis, and microbiota depletion with broad-spectrum antibiotics or germ-free rederivation completely prevents cancer development. Zeb2[IEC-Tg/+] mice represent the first mouse model of spontaneous microbiota-dependent invasive CRC and will help us to better understand host-microbiome interactions driving CRC development in humans.}, }
@article {pmid36204422, year = {2020}, author = {Li, G and Cortez, MH and Dushoff, J and Weitz, JS}, title = {When to be temperate: on the fitness benefits of lysis vs. lysogeny.}, journal = {Virus evolution}, volume = {6}, number = {2}, pages = {veaa042}, pmid = {36204422}, issn = {2057-1577}, abstract = {Bacterial viruses, that is 'bacteriophage' or 'phage', can infect and lyse their bacterial hosts, releasing new viral progeny. In addition to the lytic pathway, certain bacteriophage (i.e. 'temperate' bacteriophage) can also initiate lysogeny, a latent mode of infection in which the viral genome is integrated into and replicated with the bacterial chromosome. Subsequently, the integrated viral genome, that is the 'prophage', can induce and restart the lytic pathway. Here, we explore the relationship among infection mode, ecological context, and viral fitness, in essence asking: when should viruses be temperate? To do so, we use network loop analysis to quantify fitness in terms of network paths through the life history of an infectious pathogen that start and end with infected cells. This analysis reveals that temperate strategies, particularly those with direct benefits to cellular fitness, should be favored at low host abundances. This finding applies to a spectrum of mechanistic models of phage-bacteria dynamics spanning both explicit and implicit representations of intra-cellular infection dynamics. However, the same analysis reveals that temperate strategies, in and of themselves, do not provide an advantage when infection imposes a cost to cellular fitness. Hence, we use evolutionary invasion analysis to explore when temperate phage can invade microbial communities with circulating lytic phage. We find that lytic phage can drive down niche competition amongst microbial cells, facilitating the subsequent invasion of latent strategies that increase cellular resistance and/or immunity to infection by lytic viruses-notably this finding holds even when the prophage comes at a direct fitness cost to cellular reproduction. Altogether, our analysis identifies broad ecological conditions that favor latency and provide a principled framework for exploring the impacts of ecological context on both the short- and long-term benefits of being temperate.}, }
@article {pmid36159602, year = {2020}, author = {De Vrieze, J}, title = {The next frontier of the anaerobic digestion microbiome: From ecology to process control.}, journal = {Environmental science and ecotechnology}, volume = {3}, number = {}, pages = {100032}, pmid = {36159602}, issn = {2666-4984}, abstract = {The anaerobic digestion process has been one of the key processes for renewable energy recovery from organic waste streams for over a century. The anaerobic digestion microbiome is, through the continuous development of novel techniques, evolving from a black box to a well-defined consortium, but we are not there yet. In this perspective, I provide my view on the current status and challenges of the anaerobic digestion microbiome, as well as the opportunities and solutions to exploit it. I consider identification and fingerprinting of the anaerobic digestion microbiome as complementary tools to monitor the anaerobic digestion microbiome. However, data availability, method-inherent biases and correct taxa identification hamper the accuracy and reproducibility of anaerobic digestion microbiome characterization. Standardisation of microbiome research in anaerobic digestion and other engineered systems will be essential in the coming decades, for which I proposed some targeted solutions. These will bring anaerobic digestion from a single-purpose energy-recovery technology to a versatile process for integrated resource recovery. It is my opinion that the exploitation of the microbiome will be a driver of innovation, and that it has a key role to play in the bio-based economy of the decades to come.}, }
@article {pmid36160374, year = {2020}, author = {Wang, X and Aulenta, F and Puig, S and Esteve-Núñez, A and He, Y and Mu, Y and Rabaey, K}, title = {Microbial electrochemistry for bioremediation.}, journal = {Environmental science and ecotechnology}, volume = {1}, number = {}, pages = {100013}, pmid = {36160374}, issn = {2666-4984}, abstract = {Lack of suitable electron donors or acceptors is in many cases the key reason for pollutants to persist in the environment. Externally supplementation of electron donors or acceptors is often difficult to control and/or involves chemical additions with limited lifespan, residue formation or other adverse side effects. Microbial electrochemistry has evolved very fast in the past years - this field relates to the study of electrochemical interactions between microorganisms and solid-state electron donors or acceptors. Current can be supplied in such so-called bioelectrochemical systems (BESs) at low voltage to provide or extract electrons in a very precise manner. A plethora of metabolisms can be linked to electrical current now, from metals reductions to denitrification and dechlorination. In this perspective, we provide an overview of the emerging applications of BES and derived technologies towards the bioremediation field and outline how this approach can be game changing.}, }
@article {pmid35531503, year = {2019}, author = {Yan, Y and Du, Z and Zhang, L and Feng, L and Sun, D and Dang, Y and Holmes, DE and Smith, JA}, title = {Identification of parameters needed for optimal anaerobic co-digestion of chicken manure and corn stover.}, journal = {RSC advances}, volume = {9}, number = {51}, pages = {29609-29618}, pmid = {35531503}, issn = {2046-2069}, abstract = {While studies have shown that anaerobic co-digestion of chicken manure (CM) and corn stover (CS) is an efficient method to treat these agricultural wastes, the microbial ecology of these systems and optimal parameters for the digestion process are yet to be determined. In this study, the effects of different initial substrate concentrations and CS : CM mixture ratios on co-digestion and microbial community structure were evaluated. Results demonstrated that both the highest cumulative methane yields and methane production rates were obtained from reactors with a CS : CM ratio of 1 : 1 during hemi-solid-state anaerobic digestion (HSS-AD). Cumulative methane yields and methane production rates were 24.8% and 42% lower in solid-state anaerobic digestion (SS-AD) reactors using the same CS : CM ratios. Analysis of microbial community structures revealed that cellulolytic bacteria and a diversity of syntrophic microorganisms capable of direct interspecies electron transfer (DIET) and hydrogen interspecies transfer (HIT) were enriched in the best-performing reactors. Methanosarcina species also dominated during HSS-AD, and their presence was positively correlated with methane production in the reactors.}, }
@article {pmid35557833, year = {2018}, author = {Zhang, R and Wang, L and Chen, P and Pu, Y}, title = {Shifts in microbial community structure and diversity in a novel waterfall biofilm reactor combined with MBBR under light and dark conditions.}, journal = {RSC advances}, volume = {8}, number = {65}, pages = {37462-37471}, pmid = {35557833}, issn = {2046-2069}, abstract = {In this study, a novel, low-cost, easy-maintenance and effective waterfall aeration biofilm reactor (WFBR) was designed to treat wastewater with MBBR. The chemical oxygen demand (COD), nitrogen removal efficiency, and the microbial community structure in this novel system were evaluated for 70 days under light and dark conditions. The COD and ammonium nitrogen (NH3-N) removal efficiency remained at approximately 90% and 100% respectively after 25 days, even if the influent substrate concentration and illumination condition changes. High-throughput sequencing was used to investigate the composition and function of the microbial community in different fillers in the treatment system. Dark padding, illuminate carrier and fabric play the good performance in nitrogen nitrification, denitrification and fixation respectively. The major classes present were Betaproteobacteria (30.2% on average), Cytophagia (19.8%), Gammaproteobacteria (11.7%), Alphaproteobacteria (11.2%), Sphingobacteriia (5.1%), Flavobacteriia (2.6%), Deltaproteobacteria (2.4%), Verrucomicrobiae (0.7%), Chloroplast (0.6%) and Clostridia (0.5%). These results could provide important guidance for the improvement of MBBR or other tradition wastewater treatment process, and could also enrich our theoretical understanding of microbial ecology.}, }
@article {pmid35539271, year = {2018}, author = {Zhang, H and Zhao, Z and Chen, S and Wang, Y and Feng, J and Jia, J and Kang, P and Li, S}, title = {Geographical patterns of denitrifying bacterial communities associated with different urban lakes.}, journal = {RSC advances}, volume = {8}, number = {31}, pages = {17079-17090}, pmid = {35539271}, issn = {2046-2069}, abstract = {The geographical variation of denitrifying bacterial communities and water quality parameters in urban lakes distributed across nine provinces in China were determined. The Illumina sequencing data of the denitrifying encoding gene nirS was examined in the samples collected from nine localities (pairwise geographical distance: 200-2600 km). The results showed that fundamental differences in water quality were observed among different urban lakes. The highest nitrate (2.02 mg L[-1]) and total nitrogen (3.82 mg L[-1]) concentrations were observed in Pingzhuang (P < 0.01). The algal cell concentration ranged from 1.29 × 10[8] to 3.0 × 10[9] cell per L. The sequencing data generated a total of 421058 high quality nirS gene reads that resulted in 6369 OTUs (97% cutoff), with Proteobacteria and Firmicutes being the dominant taxa. A co-occurrence network analysis indicated that the top five genera identified as keystone taxa were Dechlorospirillum sp., Alicycliphilus sp., Dechloromonas sp., Pseudogulbenkiania sp., and Paracoccus sp. A redundancy analysis (RDA) further revealed that distinct denitrifying bacterial communities inhabited the different urban lakes, and influenced by urban lake water ammonia nitrogen, manganese and algal cell concentrations. A variance partitioning analysis (VPA) also showed that geographic location was more important than water quality factors in structuring the denitrifying bacterial communities. Together, these results provide new insight into understanding of denitrifying bacterial communities associated with geographically distributed urban lakes on a larger scale, and these results also expand our exploration of aquatic microbial ecology in freshwater bodies.}, }
@article {pmid35919909, year = {2014}, author = {Legin, AA and Schintlmeister, A and Jakupec, MA and Galanski, MS and Lichtscheidl, I and Wagner, M and Keppler, BK}, title = {NanoSIMS combined with fluorescence microscopy as a tool for subcellular imaging of isotopically labeled platinum-based anticancer drugs.}, journal = {Chemical science}, volume = {5}, number = {8}, pages = {3135-3143}, pmid = {35919909}, issn = {2041-6520}, abstract = {Multi-elemental, isotope selective nano-scale secondary ion mass spectrometry (NanoSIMS) combined with confocal laser-scanning microscopy was used to characterize the subcellular distribution of [15]N-labeled cisplatin in human colon cancer cells. These analyses indicated predominant cisplatin colocalisation with sulfur-rich structures in both the nucleus and cytoplasm. Furthermore, colocalisation of platinum with phosphorus-rich chromatin regions was observed, which is consistent with its binding affinity to DNA as the generally accepted crucial target of the drug. Application of [15]N-labeled cisplatin and subsequent measurement of the nitrogen isotopic composition and determination of the relative intensities of platinum and nitrogen associated secondary ion signals in different cellular compartments with NanoSIMS suggested partial dissociation of Pt-N bonds during the accumulation process, in particular within nucleoli at elevated cisplatin concentrations. This finding raises the question as to whether the observed intracellular dissociation of the drug has implications for the mechanism of action of cisplatin. Within the cytoplasm, platinum mainly accumulated in acidic organelles, as demonstrated by a direct combination of specific fluorescent staining, confocal laser scanning microscopy and NanoSIMS. Different processing of platinum drugs in acidic organelles might be relevant for their detoxification, as well as for their mode of action.}, }
@article {pmid34845558, year = {2022}, author = {Gao, P and Li, Y and Tian, H and Li, G and Zhao, F and Xia, W and Pan, X and Gu, JD and Le, J and Jia, C and Ma, T}, title = {Bacterial and Archaeal Community Distribution in Oilfield Water Re-injection Facilities and the Influences from Microorganisms in Injected Water.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1011-1028}, pmid = {34845558}, issn = {1432-184X}, mesh = {*Archaea/genetics ; Oil and Gas Fields ; Water ; RNA, Ribosomal, 16S ; *Petroleum/microbiology ; Phylogeny ; Bacteria/genetics ; }, abstract = {Water flooding is widely employed for oil production worldwide. However, there has never been a systematic investigation of the microbial communities occurring in oilfield water re-injection facilities. Here, we investigated the distribution of bacterial and archaeal communities in water re-injection facilities of an oilfield, and illustrated the combined influences of environmental variation and the microorganisms in injected water on the microbial communities. Bacterial communities from the surface injection facilities were dominated by aerobic or facultative anaerobic Betaproteobacteria, Alphaproteobacteria, and Flavobacteria, whereas Clostridia, Deltaproteobacteria, Anaerolineae, and Synergistia predominated in downhole of the injection wells, and Gammaproteobacteria, Betaproteobacteria, and Epsilonproteobacteria predominated in the production wells. Methanosaeta, Methanobacterium, and Methanolinea were dominant archaea in the injection facilities, while Methanosaeta, Methanomethylovorans, and Methanoculleus predominated in the production wells. This study also demonstrated that the microorganisms in injected water could be easily transferred from injection station to wellheads and downhole of injection wells, and environmental variation and diffusion-limited microbial transfer resulted from formation filtration were the main factors determining microbial community assembly in oil-bearing strata. The results provide novel information on the bacterial and archaeal communities and the underlying mechanisms occurring in oilfield water re-injection facilities, and benefit the development of effective microbiologically enhanced oil recovery and microbiologically prevented reservoir souring programs.}, }
@article {pmid34841863, year = {2021}, author = {Leistenschneider, C and Burkhardt-Holm, P and Mani, T and Primpke, S and Taubner, H and Gerdts, G}, title = {Microplastics in the Weddell Sea (Antarctica): A Forensic Approach for Discrimination between Environmental and Vessel-Induced Microplastics.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {23}, pages = {15900-15911}, doi = {10.1021/acs.est.1c05207}, pmid = {34841863}, issn = {1520-5851}, mesh = {Antarctic Regions ; Environmental Monitoring ; *Microplastics ; Plastics ; *Water Pollutants, Chemical/analysis ; }, abstract = {Microplastic (MP) pollution has been found in the Southern Ocean surrounding Antarctica, but many local regions within this vast area remain uninvestigated. The remote Weddell Sea contributes to the global thermohaline circulation, and one of the two Antarctic gyres is located in that region. In the present study, we evaluate MP (>300 μm) concentration and composition in surface (n = 34) and subsurface water samples (n = 79, ∼11.2 m depth) of the Weddell Sea. All putative MP were analyzed by attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. MP was found in 65% of surface and 11.4% of subsurface samples, with mean (±standard deviation (SD)) concentrations of 0.01 (±0.01 SD) MP m[-3] and 0.04 (±0.1 SD) MP m[-3], respectively, being within the range of previously reported values for regions south of the Polar Front. Additionally, we aimed to determine whether identified paint fragments (n = 394) derive from the research vessel. Environmentally sampled fragments (n = 101) with similar ATR-FTIR spectra to reference paints from the research vessel and fresh paint references generated in the laboratory were further subjected to micro-X-ray fluorescence spectroscopy (μXRF) to compare their elemental composition. This revealed that 45.5% of all recovered MP derived from vessel-induced contamination. However, 11% of the measured fragments could be distinguished from the reference paints via their elemental composition. This study demonstrates that differentiation based purely on visual characteristics and FTIR spectroscopy might not be sufficient for accurately determining sample contamination sources.}, }
@article {pmid34841346, year = {2021}, author = {Sergio, LS and James Michael, K and Fannie Isela, PC and Valeria, VR and Corina, HK and Luis Fernando, GO and James Michael, T and Sheng Yang, H and Juan Jose, PC}, title = {Draft genome sequence of Paraburkholderia sp. strain XV isolated from the rhizosphere of mango (Mangifera indica L.).}, journal = {Current research in microbial sciences}, volume = {2}, number = {}, pages = {100055}, pmid = {34841346}, issn = {2666-5174}, abstract = {Here, we report the draft genome of Paraburkholderia sp. XV. This strain was isolated from the rhizosphere of mango (Mangifera indica L.). Its genome consists of 9,189 coding DNA sequences, 60 tRNAs, a single copy of the 16S rRNA, 5S rRNA, and 23S rRNA gene, and 1 tmRNA. The GC content is 62.6%.}, }
@article {pmid34839952, year = {2022}, author = {Kazmi, SSUH and Uroosa,  and Xu, H and Warren, A}, title = {A community-based approach to analyzing the ecotoxicity of nitrofurazone using periphytic protozoa.}, journal = {Marine pollution bulletin}, volume = {175}, number = {}, pages = {113165}, doi = {10.1016/j.marpolbul.2021.113165}, pmid = {34839952}, issn = {1879-3363}, mesh = {Biodiversity ; *Ciliophora/physiology ; Ecosystem ; Environmental Monitoring ; *Nitrofurazone/toxicity ; }, abstract = {The ecotoxicity of nitrofurazone was analyzed based on a community-based approach using periphytic protozoa. Median lethal concentrations (LC50) within an exposure time of 30 min were determined by an acute toxicity test at 0, 1.5, 3, 6 and 12 mg ml[-1] nitrofurazone. Toxicity curve tests demonstrated a decreasing trend with increasing exposure time and was well fitted to the toxicity equation LC50 = 32.85e[-0.8143t] (t = exposure time; R[2] = 0.91; P < 0.05). Median inhibition concentrations (IC50) for periphytic protozoan growth rates were obtained by chronic tests at 0, 1, 2, 4 and 8 mg ml[-1] nitrofurazone within 10 days exposure and were well fitted to the equation r% = 0.3686e[-0.35Cnit] (Cnit is the concentration of nitrofurazone; R[2] = 0.92 and P < 0.05). These findings suggest that the LC50 and IC50 values of nitrofurazone can be predicted for any exposure time using periphytic protozoan communities as a bioassay model.}, }
@article {pmid34839384, year = {2022}, author = {Liu, J and Li, C and Ma, W and Liu, W and Wu, W}, title = {Molecular Characterization of Distinct Fungal Communities in the Soil of a Rare Earth Mining Area.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1212-1223}, pmid = {34839384}, issn = {1432-184X}, support = {31760157//national natural science foundation of china/ ; D2019201332//natural science foundation of hebei province/ ; }, mesh = {Soil/chemistry ; *Mycobiome ; Soil Microbiology ; Ecosystem ; Mining ; *Metals, Rare Earth/analysis ; }, abstract = {The exploitation of ion-absorbed rare earth elements (REEs) has caused serious ecological destruction and environmental pollution. Effects on soil fungal structure and diversity exerted by mining activities are usually ignored, although fungus is one of the most important components in soil ecosystems. In the present research, quantitative polymerase chain reaction (qPCR) and high-throughput Illumina MiSeq sequencing were conducted to characterize fungal community composition and structure in soil of a rare earth mining area after in situ leaching. Statistical analyses, network, and FUNGuild were used to conduct in-depth analyses. Ascomycota, Basidiomycota, and Glomeromycota were the most abundant phyla in the mining soils. Fungal community structures were stable after leaching practice, but nutrition contents (organic matter, TC, and TN) significantly and positively contributed to fungal abundances and diversities. Saprotrophs in phyla Ascomycota and Basidiomycota were the dominant fungal trophic mode, and they played critical roles in nutrient cycling, transformation processes, and reducing REE toxicity. Symbiotrophs of phyla Glomeromycota contributed to soil aggregation and slowing down nutrient losses after in situ leaching practice. In addition, fungi could regulate the interactions between species to resist the harsh environment of REE toxicity or ammonium caused by in situ leaching practice.}, }
@article {pmid34836550, year = {2021}, author = {Ter Horst, AM and Santos-Medellín, C and Sorensen, JW and Zinke, LA and Wilson, RM and Johnston, ER and Trubl, G and Pett-Ridge, J and Blazewicz, SJ and Hanson, PJ and Chanton, JP and Schadt, CW and Kostka, JE and Emerson, JB}, title = {Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {233}, pmid = {34836550}, issn = {2049-2618}, mesh = {*Ecosystem ; Minnesota ; *Soil/chemistry ; Soil Microbiology ; Virome ; }, abstract = {BACKGROUND: Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems.<br><br>RESULTS: Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH4 and CO2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes.<br><br>CONCLUSIONS: Results suggest strong viral "species" boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics. Video abstract The importance of Minnesota peat viromes in revealing terrestrial and aquatic niche partitioning for viral populations.}, }
@article {pmid34836151, year = {2021}, author = {Calatayud, M and Börner, RA and Ghyselinck, J and Verstrepen, L and Medts, J and Abbeele, PVD and Boulangé, CL and Priour, S and Marzorati, M and Damak, S}, title = {Water Kefir and Derived Pasteurized Beverages Modulate Gut Microbiota, Intestinal Permeability and Cytokine Production In Vitro.}, journal = {Nutrients}, volume = {13}, number = {11}, pages = {}, pmid = {34836151}, issn = {2072-6643}, mesh = {Beverages/*analysis ; Colon/metabolism/microbiology ; Cytokines/*biosynthesis ; Fatty Acids, Volatile/biosynthesis ; Fermentation ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/metabolism/microbiology ; *Kefir ; Pasteurization ; Permeability ; Water/*pharmacology ; }, abstract = {Fermentation is an ancient food preservation process, and fermented products have been traditionally consumed in different cultures worldwide over the years. The interplay between human gut microbiota, diet and host health is widely recognized. Diet is one of the main factors modulating gut microbiota potentially with beneficial effects on human health. Fermented dairy products have received much attention, but other sources of probiotic delivery through food received far less attention. In this research, a combination of in vitro tools mimicking colonic fermentation and the intestinal epithelium have been applied to study the effect of different pasteurized and non-pasteurized water kefir products on gut microbiota, epithelial barrier function and immunomodulation. Water kefir increased beneficial short-chain fatty acid production at the microbial level, reduced detrimental proteolytic fermentation compounds and increased Bifidobacterium genus abundance. The observed benefits are enhanced by pasteurization. Pasteurized products also had a significant effect at the host level, improving inflammation-induced intestinal epithelial barrier disruption and increasing IL-10 and IL-1β compared to the control condition. Our data support the potential health benefits of water kefir and demonstrate that pasteurization, performed to prolong shelf life and stability of the product, also enhanced these benefits.}, }
@article {pmid34835373, year = {2021}, author = {Nagoya, M and Kouzuma, A and Watanabe, K}, title = {Codh/Acs-Deficient Methanogens Are Prevalent in Anaerobic Digesters.}, journal = {Microorganisms}, volume = {9}, number = {11}, pages = {}, pmid = {34835373}, issn = {2076-2607}, support = {15H01753//Japan Society for the Promotion of Science/ ; }, abstract = {Methanogens are archaea that grow by producing methane as a catabolic end product and thrive in diverse anaerobic habitats, including soil, sediments, oil reservoirs, digestive tracts, and anaerobic digesters. Methanogens have typically been classified into three types-namely, hydrogenotrophic, acetoclastic, and methylotrophic methanogens. In addition, studies have found methanogens that require both hydrogen/CO2 and organics, such as acetate, for growth. Genomic analyses have shown that these methanogens lack genes for carbon monoxide dehydrogenase/acetyl-CoA synthase (Codh/Acs), one of the oldest enzymes that catalyzes the central step in the Wood-Ljungdahl pathway. Since these methanogens have been found dominant in such habitats as digestive tracts and anaerobic digesters, it is suggested that the loss of Codh/Acs confers ecological advantages on methanogens in these habitats. Comparisons in genomes of methanogens suggest the possibility that these methanogens have emerged recently in anaerobic digesters and are currently under the process of prevalence. We propose that an understanding of the genetic and ecological processes associated with the emergence and prevalence of these methanogens in anaerobic digesters would offer novel evolutionary insights into microbial ecology.}, }
@article {pmid34833075, year = {2021}, author = {Glasl, B and Haskell, JB and Aires, T and Serrão, EA and Bourne, DG and Webster, NS and Frade, PR}, title = {Microbial Surface Biofilm Responds to the Growth-Reproduction-Senescence Cycle of the Dominant Coral Reef Macroalgae Sargassum spp.}, journal = {Life (Basel, Switzerland)}, volume = {11}, number = {11}, pages = {}, pmid = {34833075}, issn = {2075-1729}, support = {SFRH/BDP/110285/2015//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; SFRH/BSAB/150485/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; SFRH/BPD/116774/2016//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; UID/Multi/04326/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; Australian Microbiome Initiative//Bioplatforms Australia &amp; Australian Government National Collaborative Research Infrastructure Strategy/ ; PhD Scholarship BG//Advance Queensland/ ; T 1218//FWF Austrian Science Fund/ ; }, abstract = {Macroalgae play an intricate role in microbial-mediated coral reef degradation processes due to the release of dissolved nutrients. However, temporal variabilities of macroalgal surface biofilms and their implication on the wider reef system remain poorly characterized. Here, we study the microbial biofilm of the dominant reef macroalgae Sargassum over a period of one year at an inshore Great Barrier Reef site (Magnetic Island, Australia). Monthly sampling of the Sargassum biofilm links the temporal taxonomic and putative functional metabolic microbiome changes, examined using 16S rRNA gene amplicon and metagenomic sequencing, to the pronounced growth-reproduction-senescence cycle of the host. Overall, the macroalgal biofilm was dominated by the heterotrophic phyla Firmicutes (35% ± 5.9% SD) and Bacteroidetes (12% ± 0.6% SD); their relative abundance ratio shifted significantly along the annual growth-reproduction-senescence cycle of Sargassum. For example, Firmicutes were 1.7 to 3.9 times more abundant during host growth and reproduction cycles than Bacteroidetes. Both phyla varied in their carbohydrate degradation capabilities; hence, temporal fluctuations in the carbohydrate availability are potentially linked to the observed shift. Dominant heterotrophic macroalgal biofilm members, such as Firmicutes and Bacteroidetes, are implicated in exacerbating or ameliorating the release of dissolved nutrients into the ambient environment, though their contribution to microbial-mediated reef degradation processes remains to be determined.}, }
@article {pmid34828889, year = {2021}, author = {Bolaños-Núñez, S and Santiago-Urbina, JA and Guyot, JP and Díaz-Ruiz, G and Wacher, C}, title = {Microbial Interactions between Amylolytic and Non-Amylolytic Lactic Acid Bacteria Strains Isolated during the Fermentation of Pozol.}, journal = {Foods (Basel, Switzerland)}, volume = {10}, number = {11}, pages = {}, pmid = {34828889}, issn = {2304-8158}, support = {CB-2009-131615//CONACYT, M&#xe9;xico/ ; }, abstract = {Pozol is a Mexican beverage prepared from fermented nixtamalized maize dough. To contribute to understanding its complex microbial ecology, the effect of inoculating on MRS-starch pure and mixed cultures of amylolytic Sii-25124 and non-amylolytic W. confusa 17, isolated from pozol, were studied on their interactions and fermentation parameters. These were compared with L. plantarum A6, an amylolytic strain isolated from cassava. Microbial growth, kinetic parameters, amylolytic activity, lactic acid production, and hydrolysis products from starch fermentation were measured. The population dynamics were followed by qPCR. L. plantarum A6 showed higher enzymatic activity, lactic acid, biomass production, and kinetic parameters than pozol LAB in pure cultures. Mixed culture of each pozol LAB with L. plantarum A6 showed a significant decrease in amylolytic activity, lactic acid yield, specific growth rate, and specific rate of amylase production. The interaction between Sii-25124 and W. confusa 17 increased the global maximum specific growth rate (µ), the lactic acid yield from starch (Ylac/s), lactic acid yield from biomass (Ylac/x), and specific rate of lactic acid production (qlac) by 15, 30, 30, and 40%, respectively, compared with the pure culture of Sii-25124. Interactions between the two strains are essential for this fermentation.}, }
@article {pmid34827700, year = {2021}, author = {Jeon, JS and Etalo, DW and Carreno-Quintero, N and de Vos, RCH and Raaijmakers, JM}, title = {Effects of Sulfur Assimilation in Pseudomonas fluorescens SS101 on Growth, Defense, and Metabolome of Different Brassicaceae.}, journal = {Biomolecules}, volume = {11}, number = {11}, pages = {}, pmid = {34827700}, issn = {2218-273X}, mesh = {*Sulfur/metabolism ; *Pseudomonas fluorescens/metabolism/genetics ; *Metabolome ; *Arabidopsis/metabolism/microbiology/genetics/growth &amp; development ; Brassica/microbiology/metabolism/growth &amp; development/genetics ; Glucosinolates/metabolism ; Brassicaceae/metabolism/microbiology/growth &amp; development/genetics ; Plant Shoots/metabolism/growth &amp; development ; Xanthomonas campestris/metabolism ; }, abstract = {Genome-wide analysis of plant-growth-promoting Pseudomonas fluorescens strain SS101 (PfSS101) followed by site-directed mutagenesis previously suggested that sulfur assimilation may play an important role in growth promotion and induced systemic resistance in Arabidopsis. Here, we investigated the effects of sulfur metabolism in PfSS101 on growth, defense, and shoot metabolomes of Arabidopsis and the Brassica crop, Broccoli. Root tips of seedlings of Arabidopsis and two Broccoli cultivars were treated with PfSS101 or with a mutant disrupted in the adenylsulfate reductase cysH, a key gene in cysteine and methionine biosynthesis. Phenotyping of plants treated with wild-type PfSS101 or its cysH mutant revealed that sulfur assimilation in PfSS101 was associated with enhanced growth of Arabidopsis but with a reduction in shoot biomass of two Broccoli cultivars. Untargeted metabolomics revealed that cysH-mediated sulfur assimilation in PfSS101 had significant effects on shoot chemistry of Arabidopsis, in particular on chain elongation of aliphatic glucosinolates (GLSs) and on indole metabolites, including camalexin and the growth hormone indole-3-acetic acid. In Broccoli, PfSS101 sulfur assimilation significantly upregulated the relative abundance of several shoot metabolites, in particular, indolic GLSs and phenylpropanoids. These metabolome changes in Broccoli plants coincided with PfSS101-mediated suppression of leaf infections by Xanthomonas campestris. Our study showed the metabolic interconnectedness of plants and their root-associated microbiota.}, }
@article {pmid34826030, year = {2022}, author = {Barbagallo, G and Santagati, M and Guni, A and Torrisi, P and Spitale, A and Stefani, S and Ferlito, S and Nibali, L}, title = {Microbiome differences in periodontal, peri-implant, and healthy sites: a cross-sectional pilot study.}, journal = {Clinical oral investigations}, volume = {26}, number = {3}, pages = {2771-2781}, pmid = {34826030}, issn = {1436-3771}, mesh = {Cross-Sectional Studies ; *Dental Implants/microbiology ; Humans ; *Microbiota/genetics ; *Peri-Implantitis/microbiology ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVES: To explore microbial communities associated with health and disease status around teeth and dental implants.<br><br>MATERIALS AND METHODS: A total of 10 healthy, 24 periodontitis, and 24 peri-implant sites from 24 patients were sequenced by next-generation sequencing. Microbial DNA was extracted and 16S rRNA gene was amplified. Bioinformatic analyses were performed using quantitative insights into microbial ecology (QIIME), linear discriminant analysis effect size (LEfSE), and STAMP.<br><br>RESULTS: Differences in microbial diversity across three types of sites were not statistically significant. Several genera and species were more prevalent in healthy compared with diseased sites, including Lautropia, Rothia and Capnocytophaga and Kingella. Among diseased sites, Peptostreptococcaceae, Dialister, Mongibacterium, Atopobium, and Filifactor were over-represented in peri-implantitis sites, while Bacteroidales was more abundant in periodontitis sites.<br><br>CONCLUSIONS: Diseased periodontal and peri-implant sites and corresponding healthy sites have distinct microbiological profiles. These findings suggest that microbial analyses could identify biomarkers for periodontal health and disease and lead to the development of new strategies to improve periodontal health and treat peri-implant and periodontal diseases.<br><br>CLINICAL RELEVANCE: The study contributes to improving our understanding of healthy, periodontally affected, and peri-implantitis sites which can improve our ability to diagnose, monitor, and manage these oral conditions.}, }
@article {pmid34820729, year = {2022}, author = {Liu, Q and Pang, Z and Yang, Z and Nyumah, F and Hu, C and Lin, W and Yuan, Z}, title = {Bio-fertilizer Affects Structural Dynamics, Function, and Network Patterns of the Sugarcane Rhizospheric Microbiota.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1195-1211}, pmid = {34820729}, issn = {1432-184X}, support = {CARS- 170208//the Modern Agricultural Industry Technology System of China/ ; 2017J01456//Natural Science Foundation of Fujian Province/ ; KFA17172A//the Special Foundation for Scientific and Technological Innovation of Fujian Agriculture and Forestry University/ ; KFA17528A//the Special Foundation for Scientific and Technological Innovation of Fujian Agriculture and Forestry University/ ; 31771723//the Nature Science Foundation of China/ ; }, mesh = {Fertilizers/analysis ; *Saccharum ; Soil Microbiology ; Soil/chemistry ; *Microbiota ; Fungi/genetics ; Nitrogen/analysis ; Bacteria/genetics ; Phosphorus ; Urea ; Sugars ; }, abstract = {Fertilizers and microbial communities that determine fertilizer efficiency are key to sustainable agricultural development. Sugarcane is an important sugar cash crop in China, and using bio-fertilizers is important for the sustainable development of China's sugar industry. However, information on the effects of bio-fertilizers on sugarcane soil microbiota has rarely been studied. In this study, the effects of bio-fertilizer application on rhizosphere soil physicochemical indicators, microbial community composition, function, and network patterns of sugarcane were discussed using a high-throughput sequencing approach. The experimental design is as follows: CK: urea application (57 kg/ha), CF: compound fertilizer (450 kg/ha), BF1: bio-fertilizer (1500 kg/ha of bio-fertilizer + 57 kg/ha of urea), and BF2: bio-fertilizer (2250 kg/ha of bio-fertilizer + 57 kg/ha of urea). The results showed that the bio-fertilizer was effective in increasing sugarcane yield by 3-12% compared to the CF treatment group, while reducing soil acidification, changing the diversity of fungi and bacteria, and greatly altering the composition and structure of the inter-root microbial community. Variance partitioning canonical correspondence (VPA) analysis showed that soil physicochemical variables explained 80.09% and 73.31% of the variation in bacteria and fungi, respectively. Redundancy analysis and correlation heatmap showed that soil pH, total nitrogen, and available potassium were the main factors influencing bacterial community composition, while total soil phosphorus, available phosphorus, pH, and available nitrogen were the main drivers of fungal communities. Volcano plots showed that using bio-fertilizers contributed to the accumulation of more beneficial bacteria in the sugarcane rhizosphere level and the decline of pathogenic bacteria (e.g., Leifsonia), which may slow down or suppress the occurrence of diseases. Linear discriminant analysis (LDA) and effect size analysis (LEfSe) searched for biomarkers under different fertilizer treatments. Meanwhile, support vector machine (SVM) assessed the importance of the microbial genera contributing to the variability between fertilizers, of interest were the bacteria Anaerolineace, Vulgatibacter, and Paenibacillus and the fungi Cochliobolus, Sordariales, and Dothideomycetes between CF and BF2, compared to the other genera contributing to the variability. Network analysis (co-occurrence network) showed that the network structure of bio-fertilizers was closer to the network characteristics of healthy soils, indicating that bio-fertilizers can improve soil health to some extent, and therefore if bio-fertilizers can be used as an alternative to chemical fertilizers in the future alternative, it is important to achieve green soil development and improve the climate.}, }
@article {pmid34818768, year = {2022}, author = {He, J and Zhang, N and Muhammad, A and Shen, X and Sun, C and Li, Q and Hu, Y and Shao, Y}, title = {From surviving to thriving, the assembly processes of microbial communities in stone biodeterioration: A case study of the West Lake UNESCO World Heritage area in China.}, journal = {The Science of the total environment}, volume = {805}, number = {}, pages = {150395}, doi = {10.1016/j.scitotenv.2021.150395}, pmid = {34818768}, issn = {1879-1026}, mesh = {Archaea ; Biodiversity ; China ; *Lakes ; *Microbiota ; UNESCO ; }, abstract = {Serious concerns regarding stone biodeterioration have been raised due to the loss of aesthetic value and hidden dangers in stone cultural heritages and buildings. Stone biodeterioration involves a complex ecological interplay among organisms, however, the ecological mechanisms (deterministic or stochastic processes) that determine the microbial community on stone remain poorly understood. Here, using both amplicon and shotgun metagenomic sequencing approaches, we comprehensively investigated the biodiversity, assembly, and function of communities (including prokaryotes, fungi, microfauna, and plants) on various types of deteriorating limestone across different habitats in Feilaifeng. By generalizing classic ecological models to stone habitats, we further uncovered and quantified the mechanisms underlying microbial community assembly processes and microbial interactions within the biodeteriorated limestone. Community profiling revealed stable ecosystem functional potential despite high taxonomic variation across different biodeterioration types, suggesting non-random community assembly. Increased niche differentiation occurred in prokaryotes and fungi but not in microfauna and plant during biodeterioration. Certain microbial groups such as nitrifying archaea and bacteria showed wider niche breadth and likely contributing to the initiation, succession and expansion of stone biodeterioration. Consistently, prokaryotes were more strongly structured by selection-based deterministic processes, while micro-eukaryotes were more influenced by dispersal and drift-based stochastic processes. Importantly, microbial coexistence maintains network robustness within stone microbiotas, highlighting mutual cooperation among functional microorganisms. These results provide new insights into microbial community assembly mechanisms in stone ecosystems and may aid in the sustainable conservation of stone materials of interest.}, }
@article {pmid34818104, year = {2022}, author = {Albakistani, EA and Nwosu, FC and Furgason, C and Haupt, ES and Smirnova, AV and Verbeke, TJ and Lee, ES and Kim, JJ and Chan, A and Ruhl, IA and Sheremet, A and Rudderham, SB and Lindsay, MBJ and Dunfield, PF}, title = {Seasonal Dynamics of Methanotrophic Bacteria in a Boreal Oil Sands End Pit Lake.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {3}, pages = {e0145521}, pmid = {34818104}, issn = {1098-5336}, mesh = {Bacteria ; *Lakes/microbiology ; Methane ; *Oil and Gas Fields ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; }, abstract = {Base Mine Lake (BML) is the first full-scale demonstration end pit lake for the oil sands mining industry in Canada. We examined aerobic methanotrophic bacteria over all seasons for 5 years in this dimictic lake. Methanotrophs comprised up to 58% of all bacterial reads in 16S rRNA gene amplicon sequencing analyses (median 2.8%), and up to 2.7 × 10[4] cells mL[-1] of water (median 0.5 × 10[3]) based on qPCR of pmoA genes. Methanotrophic activity and populations in the lake water were highest during fall turnover and remained high through the winter ice-covered period into spring turnover. They declined during summer stratification, especially in the epilimnion. Three methanotroph genera (Methylobacter, Methylovulum, and Methyloparacoccus) cycled seasonally, based on both relative and absolute abundance measurements. Methylobacter and Methylovulum populations peaked in winter/spring, when methane oxidation activity was psychrophilic. Methyloparacoccus populations increased in the water column through summer and fall, when methane oxidation was mesophilic, and also predominated in the underlying tailings sediment. Other, less abundant genera grew primarily during summer, possibly due to distinct CH4/O2 microniches created during thermal stratification. These data are consistent with temporal and spatial niche differentiation based on temperature, CH4 and O2. This pit lake displays methane cycling and methanotroph population dynamics similar to natural boreal lakes. IMPORTANCE The study examined methanotrophic bacteria in an industrial end pit lake, combining molecular DNA methods (both quantitative and descriptive) with biogeochemical measurements. The lake was sampled over 5 years, in all four seasons, as often as weekly, and included sub-ice samples. The resulting multiseason and multiyear data set is unique in its size and intensity, and allowed us to document clear and consistent seasonal patterns of growth and decline of three methanotroph genera (Methylobacter, Methylovulum, and Methyloparacoccus). Laboratory experiments suggested that one major control of this succession was niche partitioning based on temperature. The study helps to understand microbial dynamics in engineered end pit lakes, but we propose that the dynamics are typical of boreal stratified lakes and widely applicable in microbial ecology and limnology. Methane-oxidizing bacteria are important model organisms in microbial ecology and have implications for global climate change.}, }
@article {pmid34817641, year = {2022}, author = {Čanković, M and Dutour-Sikirić, M and Radić, ID and Ciglenečki, I}, title = {Bacterioneuston and Bacterioplankton Structure and Abundance in Two Trophically Distinct Marine Environments - a Marine Lake and the Adjacent Coastal Site on the Adriatic Sea.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {996-1010}, pmid = {34817641}, issn = {1432-184X}, support = {IP-2018-01-1717//hrvatska zaklada za znanost/ ; }, mesh = {*Lakes/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics ; Aquatic Organisms ; Carbon ; Oxygen ; Seawater/microbiology ; }, abstract = {Marine surface microlayer (SML) is a large and extreme marine environment with an important role in biogeochemical cycling and climate regulation. We explored the seasonal structure and abundance of bacterial assemblages in SML (bacterioneuston) and underlying water layer (ULW) (bacterioplankton) in eutrophic marine Rogoznica Lake and more oligotrophic coastal area of the adjacent Adriatic Sea. SML and ULW in each site were similar in pH, salinity, dissolved oxygen, oxygen saturation, and temperature. Rogoznica Lake was colder in winter and warmer in summer compared to the Adriatic Sea. Regarding nutrients, SML and ULW were notably different environments. SML was consistently enriched in nitrate, nitrite, orthophosphate, and total organic carbon than ULW in both investigated environments. Except in spring in Rogoznica Lake, bacterial abundance in SML was also significantly higher (p < 0.05) than in ULW. Both layers and sites show prominent seasonal variability. High-throughput 16S rRNA gene sequencing of DNA and cDNA revealed a considerable difference in bacterial assemblage structure, although study sites were < 200 m apart. Heterotrophs were predominant in both layers with pronounced spatial and temporal structural differences, except in autumn in Rogoznica Lake when, autotrophs became the dominant fraction under oxygen-deprived conditions. All these variations were driven by in situ conditions, the most important ones being total organic carbon and temperature (and additionally dissolved oxygen in Rogoznica Lake). This is especially important in terms of ongoing eutrophication, warming and deoxygenation, noticed not only in the Adriatic Sea and Rogoznica Lake but globally as well. Therefore, further structural and physiological changes in bacterioneuston and bacterioplankton assemblages can be expected.}, }
@article {pmid34817640, year = {2022}, author = {Wu-Chuang, A and Obregon, D and Estrada-Peña, A and Cabezas-Cruz, A}, title = {Thermostable Keystone Bacteria Maintain the Functional Diversity of the Ixodes scapularis Microbiome Under Heat Stress.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1224-1235}, pmid = {34817640}, issn = {1432-184X}, mesh = {Male ; Animals ; *Ixodes/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Heat-Shock Response ; }, abstract = {Variations in the composition and diversity of tick microbiome due to high temperatures may influence the hierarchy of community members as a response to environmental change. Modifications in the community structure are hypothesized to drive alterations in the presence and/or abundance of functional pathways in the bacterial metagenome. In this study, this hypothesis was tested by using published 16S rRNA datasets of Ixodes scapularis males incubated at different temperatures (i.e., 4, 20, 30, and 37 °C) in a laboratory setting. Changes in community structure and functional profiles in response to temperature shifts were measured using co-occurrence networks and metagenome inference. Results from laboratory-reared ticks were then compared with those of field-collected ticks. The results from laboratory-reared ticks showed that high temperature altered the structure of the microbial community and decreased the number of keystone taxa. Notably, four taxa were identified as keystone in all the temperatures, and the functional diversity of the tick microbiome was contained in the four thermostable keystone their associated bacterial taxa. Three of the thermostable keystone taxa were also found in free-living ticks collected in Massachusetts. Moreover, the comparison of functional profiles of laboratory-reared and field-collected ticks revealed the existence of an important set of metabolic pathways that were common among the different datasets. Similar to the laboratory-reared ticks, the keystone taxa identified in field-collected ticks alongside their consortia (co-occurring taxa) were sufficient to retain the majority of the metabolic pathways in the functional profile. These results suggest that keystone taxa are essential in the stability and the functional resiliency of the tick microbiome under heat stress.}, }
@article {pmid34817235, year = {2021}, author = {Bulzu, PA and Kavagutti, VS and Chiriac, MC and Vavourakis, CD and Inoue, K and Kandori, H and Andrei, AS and Ghai, R}, title = {Heliorhodopsin Evolution Is Driven by Photosensory Promiscuity in Monoderms.}, journal = {mSphere}, volume = {6}, number = {6}, pages = {e0066121}, pmid = {34817235}, issn = {2379-5042}, mesh = {*Metagenomics ; Models, Molecular ; Oxidative Stress ; Protein Conformation ; Rhodopsins, Microbial/chemistry/*genetics ; }, abstract = {Rhodopsins are light-activated proteins displaying an enormous versatility of function as cation/anion pumps or sensing environmental stimuli and are widely distributed across all domains of life. Even with wide sequence divergence and uncertain evolutionary linkages between microbial (type 1) and animal (type 2) rhodopsins, the membrane orientation of the core structural scaffold of both was presumed universal. This was recently amended through the discovery of heliorhodopsins (HeRs; type 3), that, in contrast to known rhodopsins, display an inverted membrane topology and yet retain similarities in sequence, structure, and the light-activated response. While no ion-pumping activity has been demonstrated for HeRs and multiple crystal structures are available, fundamental questions regarding their cellular and ecological function or even their taxonomic distribution remain unresolved. Here, we investigated HeR function and distribution using genomic/metagenomic data with protein domain fusions, contextual genomic information, and gene coexpression analysis with strand-specific metatranscriptomics. We bring to resolution the debated monoderm/diderm occurrence patterns and show that HeRs are restricted to monoderms. Moreover, we provide compelling evidence that HeRs are a novel type of sensory rhodopsins linked to histidine kinases and other two-component system genes across phyla. In addition, we also describe two novel putative signal-transducing domains fused to some HeRs. We posit that HeRs likely function as generalized light-dependent switches involved in the mitigation of light-induced oxidative stress and metabolic circuitry regulation. Their role as sensory rhodopsins is corroborated by their photocycle dynamics and their presence/function in monoderms is likely connected to the higher sensitivity of these organisms to light-induced damage. IMPORTANCE Heliorhodopsins are enigmatic, novel rhodopsins with a membrane orientation that is opposite to all known rhodopsins. However, their cellular and ecological functions are unknown, and even their taxonomic distribution remains a subject of debate. We provide evidence that HeRs are a novel type of sensory rhodopsins linked to histidine kinases and other two-component system genes across phyla boundaries. In support of this, we also identify two novel putative signal transducing domains in HeRs that are fused with them. We also observe linkages of HeRs to genes involved in mitigation of light-induced oxidative stress and increased carbon and nitrogen metabolism. Finally, we synthesize these findings into a framework that connects HeRs with the cellular response to light in monoderms, activating light-induced oxidative stress defenses along with carbon/nitrogen metabolic circuitries. These findings are consistent with the evolutionary, taxonomic, structural, and genomic data available so far.}, }
@article {pmid34817222, year = {2021}, author = {Yourstone, SM and Weinstein, I and Ademski, E and Shank, EA and Stasulli, NM}, title = {Selective Bacterial Community Enrichment between the Pitcher Plants Sarracenia minor and Sarracenia flava.}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0069621}, pmid = {34817222}, issn = {2165-0497}, support = {K12 GM000678/GM/NIGMS NIH HHS/United States ; R01 GM112981/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; *Microbiota ; Phylogeny ; Plant Leaves/microbiology ; Sarraceniaceae/classification/*microbiology ; }, abstract = {The interconnected and overlapping habitats present in natural ecosystems remain a challenge in determining the forces driving microbial community composition. The cuplike leaf structures of some carnivorous plants, including those of the family Sarraceniaceae, are self-contained ecological habitats that represent systems for exploring such microbial ecology questions. We investigated whether Sarracenia minor and Sarracenia flava cultivate distinct bacterial communities when sampled at the same geographic location and time. This sampling strategy eliminates many abiotic environmental variables present in other studies that compare samples harvested over time, and it could reveal biotic factors driving the selection of microbes. DNA extracted from the decomposing detritus trapped in each Sarracenia leaf pitcher was profiled using 16S rRNA amplicon sequencing. We identified a surprising amount of bacterial diversity within each pitcher, but we also discovered bacteria whose abundance was specifically enriched in one of the two Sarracenia species. These differences in bacterial community representation suggest some biotic influence of the Sarracenia plant on the bacterial composition of their pitchers. Overall, our results suggest that bacterial selection due to factors other than geographic location, weather, or prey availability is occurring within the pitchers of these two closely related plant species. This indicates that specific characteristics of S. minor and S. flava may play a role in fostering distinct bacterial communities. These confined, naturally occurring microbial ecosystems within Sarracenia pitchers may provide model systems to answer important questions about the drivers of microbial community composition, succession, and response to environmental perturbations. IMPORTANCE This study uses amplicon sequencing to compare the bacterial communities of environmental samples from the detritus of the leaf cavities of Sarracenia minor and Sarracenia flava pitcher plants. We sampled the detritus at the same time and in the same geographic location, eliminating many environmental variables present in other comparative studies. This study revealed that different species of Sarracenia contain distinct bacterial members within their pitchers, suggesting that these communities are not randomly established based on environmental factors and the prey pool but are potentially enriched for by the plants' chemical or physical environment. This study of these naturally occurring, confined microbial ecosystems will help further establish carnivorous pitcher plants as a model system for answering important questions about the development and succession of microbial communities.}, }
@article {pmid34813707, year = {2022}, author = {Hernández-Reyes, C and Lichtenberg, E and Keller, J and Delaux, PM and Ott, T and Schenk, ST}, title = {NIN-Like Proteins: Interesting Players in Rhizobia-Induced Nitrate Signaling Response During Interaction with Non-Legume Host Arabidopsis thaliana.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {35}, number = {3}, pages = {230-243}, doi = {10.1094/MPMI-10-21-0261-R}, pmid = {34813707}, issn = {0894-0282}, mesh = {*Arabidopsis/genetics/metabolism ; *Fabaceae ; Nitrates/metabolism ; Nitrogen Fixation ; *Rhizobium/physiology ; Root Nodules, Plant/metabolism ; Signal Transduction ; Symbiosis/physiology ; }, abstract = {Nitrogen is an essential macronutrient and a key cellular messenger. Plants have evolved refined molecular systems to sense the cellular nitrogen status. This is exemplified by the root nodule symbiosis between legumes and symbiotic rhizobia, where nitrate availability inhibits this mutualistic interaction. Additionally, nitrate also functions as a metabolic messenger, resulting in nitrate signaling cascades which intensively crosstalk with other physiological pathways. Nodule inception-like proteins (NLPs) are key players in nitrate signaling and regulate nitrate-dependent transcription during legume-rhizobia interactions. Nevertheless, the coordinated interplay between nitrate signaling pathways and rhizobacteria-induced responses remains to be elucidated. In our study, we investigated rhizobia-induced changes in the root system architecture of the non-legume host arabidopsis under different nitrate conditions. We demonstrate that rhizobium-induced lateral root growth and increased root hair length and density are regulated by a nitrate-related signaling pathway. Key players in this process are AtNLP4 and AtNLP5, because the corresponding mutants failed to respond to rhizobia. At the cellular level, AtNLP4 and AtNLP5 control a rhizobia-induced decrease in cell elongation rates, while additional cell divisions occurred independently of AtNLP4. In summary, our data suggest that root morphological responses to rhizobia are coordinated by a newly considered nitrate-related NLP pathway that is evolutionarily linked to regulatory circuits described in legumes.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.}, }
@article {pmid34809998, year = {2022}, author = {Sutherland, WJ and Atkinson, PW and Butchart, SHM and Capaja, M and Dicks, LV and Fleishman, E and Gaston, KJ and Hails, RS and Hughes, AC and Le Anstey, B and Le Roux, X and Lickorish, FA and Maggs, L and Noor, N and Oldfield, TEE and Palardy, JE and Peck, LS and Pettorelli, N and Pretty, J and Spalding, MD and Tonneijck, FH and Truelove, G and Watson, JEM and Wentworth, J and Wilson, JD and Thornton, A}, title = {A horizon scan of global biological conservation issues for 2022.}, journal = {Trends in ecology &amp; evolution}, volume = {37}, number = {1}, pages = {95-104}, doi = {10.1016/j.tree.2021.10.014}, pmid = {34809998}, issn = {1872-8383}, mesh = {Animals ; *Biodiversity ; *Conservation of Natural Resources ; Global Health/*trends ; Policy ; }, abstract = {We present the results of our 13th annual horizon scan of issues likely to impact on biodiversity conservation. Issues are either novel within the biological conservation sector or could cause a substantial step-change in impact, either globally or regionally. Our global panel of 26 scientists and practitioners identified 15 issues that we believe to represent the highest priorities for tracking and action. Many of the issues we identified, including the impact of satellite megaconstellations and the use of long-distance wireless energy transfer, have both elements of threats and emerging opportunities. A recent state-sponsored application to commence deep-sea mining represents a significant step-change in impact. We hope that this horizon scan will increase research and policy attention on the highlighted issues.}, }
@article {pmid34809466, year = {2021}, author = {Chase, AB and Sweeney, D and Muskat, MN and Guillén-Matus, DG and Jensen, PR}, title = {Vertical Inheritance Facilitates Interspecies Diversification in Biosynthetic Gene Clusters and Specialized Metabolites.}, journal = {mBio}, volume = {12}, number = {6}, pages = {e0270021}, pmid = {34809466}, issn = {2150-7511}, support = {R01 GM085770/GM/NIGMS NIH HHS/United States ; T32 GM067550/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Biosynthetic Pathways ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Micromonosporaceae/classification/*genetics/*metabolism ; *Multigene Family ; Phylogeny ; Recombination, Genetic ; Secondary Metabolism ; }, abstract = {While specialized metabolites are thought to mediate ecological interactions, the evolutionary processes driving chemical diversification, particularly among closely related lineages, remain poorly understood. Here, we examine the evolutionary dynamics governing the distribution of natural product biosynthetic gene clusters (BGCs) among 118 strains representing all nine currently named species of the marine actinobacterial genus Salinispora. While much attention has been given to the role of horizontal gene transfer (HGT) in structuring BGC distributions, we find that vertical descent facilitates interspecies BGC diversification over evolutionary timescales. Moreover, we identified a distinct phylogenetic signal among Salinispora species at both the BGC and metabolite level, indicating that specialized metabolism represents a conserved phylogenetic trait. Using a combination of genomic analyses and liquid chromatography-high-resolution tandem mass spectrometry (LC-MS/MS) targeting nine experimentally characterized BGCs and their small molecule products, we identified gene gain/loss events, constrained interspecies recombination, and other evolutionary processes associated with vertical inheritance as major contributors to BGC diversification. These evolutionary dynamics had direct consequences for the compounds produced, as exemplified by species-level differences in salinosporamide production. Together, our results support the concept that specialized metabolites, and their cognate BGCs, can represent phylogenetically conserved functional traits with chemical diversification proceeding in species-specific patterns over evolutionary time frames. IMPORTANCE Microbial natural products are traditionally exploited for their pharmaceutical potential, yet our understanding of the evolutionary processes driving BGC evolution and compound diversification remain poorly developed. While HGT is recognized as an integral driver of BGC distributions, we find that the effects of vertical inheritance on BGC diversification had direct implications for species-level specialized metabolite production. As such, understanding the degree of genetic variation that corresponds to species delineations can enhance natural product discovery efforts. Resolving the evolutionary relationships between closely related strains and specialized metabolism can also facilitate our understanding of the ecological roles of small molecules in structuring the environmental distribution of microbes.}, }
@article {pmid34807459, year = {2022}, author = {Hicks, LC and Frey, B and Kjøller, R and Lukac, M and Moora, M and Weedon, JT and Rousk, J}, title = {Toward a function-first framework to make soil microbial ecology predictive.}, journal = {Ecology}, volume = {103}, number = {2}, pages = {e03594}, doi = {10.1002/ecy.3594}, pmid = {34807459}, issn = {1939-9170}, mesh = {Bacteria ; Ecosystem ; *Microbiota ; Salinity ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {Soil microbial communities perform vital ecosystem functions, such as the decomposition of organic matter to provide plant nutrition. However, despite the functional importance of soil microorganisms, attribution of ecosystem function to particular constituents of the microbial community has been impeded by a lack of information linking microbial function to community composition and structure. Here, we propose a function-first framework to predict how microbial communities influence ecosystem functions. We first view the microbial community associated with a specific function as a whole and describe the dependence of microbial functions on environmental factors (e.g., the intrinsic temperature dependence of bacterial growth rates). This step defines the aggregate functional response curve of the community. Second, the contribution of the whole community to ecosystem function can be predicted, by combining the functional response curve with current environmental conditions. Functional response curves can then be linked with taxonomic data in order to identify sets of "biomarker" taxa that signal how microbial communities regulate ecosystem functions. Ultimately, such indicator taxa may be used as a diagnostic tool, enabling predictions of ecosystem function from community composition. In this paper, we provide three examples to illustrate the proposed framework, whereby the dependence of bacterial growth on environmental factors, including temperature, pH, and salinity, is defined as the functional response curve used to interlink soil bacterial community structure and function. Applying this framework will make it possible to predict ecosystem functions directly from microbial community composition.}, }
@article {pmid34806699, year = {2021}, author = {Pioli, R and Stocker, R and Isa, L and Secchi, E}, title = {Patterning of Microorganisms and Microparticles through Sequential Capillarity-assisted Assembly.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {177}, pages = {}, doi = {10.3791/63131}, pmid = {34806699}, issn = {1940-087X}, mesh = {Capillary Action ; *Microfluidic Analytical Techniques/methods ; Microfluidics/methods ; }, abstract = {Controlled patterning of microorganisms into defined spatial arrangements offers unique possibilities for a broad range of biological applications, including studies of microbial physiology and interactions. At the simplest level, accurate spatial patterning of microorganisms would enable reliable, long-term imaging of large numbers of individual cells and transform the ability to quantitatively study distance-dependent microbe-microbe interactions. More uniquely, coupling accurate spatial patterning and full control over environmental conditions, as offered by microfluidic technology, would provide a powerful and versatile platform for single-cell studies in microbial ecology. This paper presents a microfluidic platform to produce versatile and user-defined patterns of microorganisms within a microfluidic channel, allowing complete optical access for long-term, high-throughput monitoring. This new microfluidic technology is based on capillarity-assisted particle assembly and exploits the capillary forces arising from the controlled motion of an evaporating suspension inside a microfluidic channel to deposit individual microsized objects in an array of traps microfabricated onto a polydimethylsiloxane (PDMS) substrate. Sequential depositions generate the desired spatial layout of single or multiple types of micro-sized objects, dictated solely by the geometry of the traps and the filling sequence. The platform has been calibrated using colloidal particles of different dimensions and materials: it has proven to be a powerful tool to generate diverse colloidal patterns and perform surface functionalization of trapped particles. Furthermore, the platform was tested on microbial cells, using Escherichia coli cells as a model bacterium. Thousands of individual cells were patterned on the surface, and their growth was monitored over time. In this platform, the coupling of single-cell deposition and microfluidic technology allows both geometric patterning of microorganisms and precise control of environmental conditions. It thus opens a window into the physiology of single microbes and the ecology of microbe-microbe interactions, as shown by preliminary experiments.}, }
@article {pmid34803951, year = {2021}, author = {Coton, M and Deniel, F and Mounier, J and Joubrel, R and Robieu, E and Pawtowski, A and Jeuge, S and Taminiau, B and Daube, G and Coton, E and Frémaux, B}, title = {Microbial Ecology of French Dry Fermented Sausages and Mycotoxin Risk Evaluation During Storage.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {737140}, pmid = {34803951}, issn = {1664-302X}, abstract = {Dry fermented sausages are produced worldwide by well-controlled fermentation processes involving complex microbiota including many bacterial and fungal species with key technological roles. However, to date, fungal diversity on sausage casings during storage has not been fully described. In this context, we studied the microbial communities from dry fermented sausages naturally colonized or voluntarily surface inoculated with molds during storage using both culture-dependent and metabarcoding methods. Staphylococci and lactic acid bacteria largely dominated in samples, although some halotolerant genera (e.g., Halomonas, Tetragenococcus, and Celerinatantimonas spp.) were also frequently observed. Fungal populations varied from 7.2 to 9.8 log TFU/cm[2] sausage casing during storage, suggesting relatively low count variability among products. Fungal diversity identified on voluntarily inoculated casings was lower (dominated by Penicillium nalgiovense and Debaryomyces hansenii) than naturally environment-inoculated fermented sausages (colonized by P. nalgiovense, Penicillium nordicum, and other Penicillium spp. and sporadically by Scopulariopsis sp., D. hansenii, and Candida zeylanoïdes). P. nalgiovense and D. hansenii were systematically identified, highlighting their key technological role. The mycotoxin risk was then evaluated, and in situ mycotoxin production of selected mold isolates was determined during pilot-scale sausage productions. Among the identified fungal species, P. nalgiovense was confirmed not to produce mycotoxins. However, some P. nordicum, Penicillium chrysogenum, Penicillium bialowienzense, Penicillium brevicompactum, and Penicillium citreonigrum isolates produced one or more mycotoxins in vitro. P. nordicum also produced ochratoxin A during pilot-scale sausage productions using "worst-case" conditions in the absence of biotic competition. These data provide new knowledge on fermented sausage microbiota and the potential mycotoxin risk during storage.}, }
@article {pmid34803947, year = {2021}, author = {Runa, V and Wenk, J and Bengtsson, S and Jones, BV and Lanham, AB}, title = {Bacteriophages in Biological Wastewater Treatment Systems: Occurrence, Characterization, and Function.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {730071}, pmid = {34803947}, issn = {1664-302X}, abstract = {Phage bacteria interactions can affect structure, dynamics, and function of microbial communities. In the context of biological wastewater treatment (BWT), the presence of phages can alter the efficiency of the treatment process and influence the quality of the treated effluent. The active role of phages in BWT has been demonstrated, but many questions remain unanswered regarding the diversity of phages in these engineered environments, the dynamics of infection, the determination of bacterial hosts, and the impact of their activity in full-scale processes. A deeper understanding of the phage ecology in BWT can lead the improvement of process monitoring and control, promote higher influent quality, and potentiate the use of phages as biocontrol agents. In this review, we highlight suitable methods for studying phages in wastewater adapted from other research fields, provide a critical overview on the current state of knowledge on the effect of phages on structure and function of BWT bacterial communities, and highlight gaps, opportunities, and priority questions to be addressed in future research.}, }
@article {pmid34803935, year = {2021}, author = {Hernández-Beltrán, JCR and San Millán, A and Fuentes-Hernández, A and Peña-Miller, R}, title = {Mathematical Models of Plasmid Population Dynamics.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {606396}, pmid = {34803935}, issn = {1664-302X}, abstract = {With plasmid-mediated antibiotic resistance thriving and threatening to become a serious public health problem, it is paramount to increase our understanding of the forces that enable the spread and maintenance of drug resistance genes encoded in mobile genetic elements. The relevance of plasmids as vehicles for the dissemination of antibiotic resistance genes, in addition to the extensive use of plasmid-derived vectors for biotechnological and industrial purposes, has promoted the in-depth study of the molecular mechanisms controlling multiple aspects of a plasmids' life cycle. This body of experimental work has been paralleled by the development of a wealth of mathematical models aimed at understanding the interplay between transmission, replication, and segregation, as well as their consequences in the ecological and evolutionary dynamics of plasmid-bearing bacterial populations. In this review, we discuss theoretical models of plasmid dynamics that span from the molecular mechanisms of plasmid partition and copy-number control occurring at a cellular level, to their consequences in the population dynamics of complex microbial communities. We conclude by discussing future directions for this exciting research topic.}, }
@article {pmid34800493, year = {2022}, author = {Zhang, X and Yoshihara, K and Miyata, N and Hata, T and Altaisaikhan, A and Takakura, S and Asano, Y and Izuno, S and Sudo, N}, title = {Dietary tryptophan, tyrosine, and phenylalanine depletion induce reduced food intake and behavioral alterations in mice.}, journal = {Physiology &amp; behavior}, volume = {244}, number = {}, pages = {113653}, doi = {10.1016/j.physbeh.2021.113653}, pmid = {34800493}, issn = {1873-507X}, mesh = {Animals ; Diet ; Eating ; Mice ; *Phenylalanine ; *Tryptophan/metabolism ; Tyrosine ; }, abstract = {Important precursors of monoaminergic neurotransmitters, dietary tryptophan (TRP), tyrosine, and phenylalanine (all referred to as TTP), play crucial roles in a wide range of behavioral and emotional functions. In the current study, we investigated whether diets devoid of TTP or diets deficient in TRP alone can affect body weight, behavioral characteristics, and gut microbiota, by comparing mice fed on these amino acids-depleted diets to mice fed on diets containing regular levels of amino acids. Both dietary TTP- and TRP-deprived animals showed a reduction in food intake and body weight. In behavioral analyses, the mice fed TTP-deprived diets were more active than mice fed diets containing regular levels of amino acids. The TRP-deprived group exhibited a reduction in serum TRP levels, concomitant with a decrease in serotonin and 5-hydroxyindoleacetic acid levels in some regions of the brain. The TTP-deprived group showed a reduction in TTP levels in the serum, concomitant with decreases in both phenylalanine and tyrosine levels in the hippocampus, as well as serotonin, norepinephrine, and dopamine concentrations in some regions of the brain. Regarding the effects of TRP or TTP deprivation on gut microbial ecology, the relative abundance of genus Roseburia was significantly reduced in the TTP-deprived group than in the dietary restriction control group. Interestingly, TTP was found even in the feces of mice fed TTP- and TRP-deficient diets, suggesting that TTP is produced by microbial or enzymatic digestion of the host-derived proteins. However, microbe generated TTP did not compensate for the systemic TTP deficiency induced by the lack of dietary TTP intake. Collectively, these results indicate that chronic dietary TTP deprivation induces decreased monoamines and their metabolites in a brain region-specific manner. The altered activities of the monoaminergic systems may contribute to increased locomotor activity.}, }
@article {pmid34799747, year = {2022}, author = {Zada, S and Sajjad, W and Rafq, M and Ali, S and Hu, Z and Wang, H and Cai, R}, title = {Correction to: Cave Microbes as a Potential Source of Drugs Development in the Modern Era.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {688}, doi = {10.1007/s00248-021-01916-3}, pmid = {34799747}, issn = {1432-184X}, }
@article {pmid34795658, year = {2021}, author = {Huang, Z and Hou, D and Zhou, R and Zeng, S and Xing, C and Wei, D and Deng, X and Yu, L and Wang, H and Deng, Z and Weng, S and Ning, D and Xiao, C and Yan, Q and Zhou, J and He, Z and He, J}, title = {Environmental Water and Sediment Microbial Communities Shape Intestine Microbiota for Host Health: The Central Dogma in an Anthropogenic Aquaculture Ecosystem.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {772149}, pmid = {34795658}, issn = {1664-302X}, abstract = {From increasing evidence has emerged a tight link among the environment, intestine microbiota, and host health status; moreover, the microbial interaction in different habitats is crucial for ecosystems. However, how the environmental microbial community assembly governs the intestinal microbiota and microbial communities of multiple habitats contribute to the metacommunity remain elusive. Here, we designed two delicate experiments from temporal and spatial scales in a shrimp culture pond ecosystem (SCPE). Of the SCPE metacommunity, the microbial diversity was mainly contributed to by the diversity of[-]β IntraHabitats and β InterHabitats , and water and sediment communities had a large contribution to the shrimp intestine community as shown by SourceTracker and Sloan neutral community model analyses. Also, phylogenetic bin-based null model results show that microbial assembly of three habitats in the SCPE appeared to be largely driven by stochastic processes. These results enrich our understanding of the environment-intestinal microbiota-host health closely linked relationship, making it possible to be the central dogma for an anthropogenic aquaculture ecosystem. Our findings enhance the mechanistic understanding of microbial assembly in the SCPE for further analyzing metacommunities, which has important implications for microbial ecology and animal health.}, }
@article {pmid34795375, year = {2021}, author = {Van Goethem, MW and Osborn, AR and Bowen, BP and Andeer, PF and Swenson, TL and Clum, A and Riley, R and He, G and Koriabine, M and Sandor, L and Yan, M and Daum, CG and Yoshinaga, Y and Makhalanyane, TP and Garcia-Pichel, F and Visel, A and Pennacchio, LA and O'Malley, RC and Northen, TR}, title = {Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {1302}, pmid = {34795375}, issn = {2399-3642}, support = {DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; }, mesh = {Bacteria/genetics/*metabolism ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Multigene Family ; *Secondary Metabolism ; *Soil Microbiology ; Utah ; }, abstract = {Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 712 full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night primarily in cyanobacteria, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts.}, }
@article {pmid34794517, year = {2021}, author = {Van Wylick, A and Monclaro, AV and Elsacker, E and Vandelook, S and Rahier, H and De Laet, L and Cannella, D and Peeters, E}, title = {A review on the potential of filamentous fungi for microbial self-healing of concrete.}, journal = {Fungal biology and biotechnology}, volume = {8}, number = {1}, pages = {16}, pmid = {34794517}, issn = {2054-3085}, support = {1SA9721N//FWO-Vlaanderen/ ; 1SC9220N//FWO-Vlaanderen/ ; FNRS-MIS LUX-project F.4502.19//Fonds De La Recherche Scientifique - FNRS/ ; }, abstract = {Concrete is the most used construction material worldwide due to its abundant availability and inherent ease of manufacturing and application. However, the material bears several drawbacks such as the high susceptibility for crack formation, leading to reinforcement corrosion and structural degradation. Extensive research has therefore been performed on the use of microorganisms for biologically mediated self-healing of concrete by means of CaCO3 precipitation. Recently, filamentous fungi have been recognized as high-potential microorganisms for this application as their hyphae grow in an interwoven three-dimensional network which serves as nucleation site for CaCO3 precipitation to heal the crack. This potential is corroborated by the current state of the art on fungi-mediated self-healing concrete, which is not yet extensive but valuable to direct further research. In this review, we aim to broaden the perspectives on the use of fungi for concrete self-healing applications by first summarizing the major progress made in the field of microbial self-healing of concrete and then discussing pioneering work that has been done with fungi. Starting from insights and hypotheses on the types and principles of biomineralization that occur during microbial self-healing, novel potentially promising candidate species are proposed based on their abilities to promote CaCO3 formation or to survive in extreme conditions that are relevant for concrete. Additionally, an overview will be provided on the challenges, knowledge gaps and future perspectives in the field of fungi-mediated self-healing concrete.}, }
@article {pmid34793902, year = {2022}, author = {Yuan, W and Zeng, X and Cao, Y and Yang, Q and Riaz, L and Wang, Q}, title = {Distribution of antibiotic resistance genes from human and animal origins to their receiving environments: A regional scale survey of urban settings.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {293}, number = {}, pages = {118512}, doi = {10.1016/j.envpol.2021.118512}, pmid = {34793902}, issn = {1873-6424}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; Manure ; *Microbiota ; }, abstract = {Antibiotic resistance is a growing problem for ecosystem health and public healthcare. Hence, the transmission of antibiotic resistance from human and animal origins to natural environments requires careful investigation. In this study, nine antibiotic resistance genes (ARGs), three mobile genetic elements (MGEs), and their relations with antibiotics, heavy metals, and microbiota were investigated in 16 sample sites (Xinxiang, China). Fluoroquinolones (0.13-14.22 μg/L) were most abundant in hospital effluent and oxytetracycline (251.86-5817.47 μg/kg) in animal manure. Animal manure showed the highest levels of zinc (80.79-2597.14 mg/kg) and copper (32.47-85.22 mg/kg), possibly affecting the prevalence of intI1 and aac(6')-Ib genes. Aminoglycoside and sulfonamide resistance genes (aac(6')-Ib, aadA, and sul1) were the main ARGs in this area. In addition, the detected ARGs and MGEs were higher in animal manure than in hospital effluent, except for the sul1 gene. On the other hand, the incomplete removal of antibiotics (29.76-100%), heavy metals (31.25-100%), and ARGs (1-3 orders of magnitude) in MWWTPs resulted in the accumulation of these contaminants in the receiving river. Network analysis suggested that the potential hosts (Jeotgalibaca, Atopostipes, Corynebacterium_1, etc.) of ARGs were more predominant in animal manure rather than hospital effluent, indicating a higher ARG transfer potential in animal manure compared with hospital sources. These results provide useful insights into the different migration and dissemination routes of antibiotics, heavy metals, ARGs, and microbiota from anthropogenic and animal origins to their receiving environments via MWWTP discharge and manure fertilization.}, }
@article {pmid34793801, year = {2022}, author = {Bontemps, Z and Alonso, L and Pommier, T and Hugoni, M and Moënne-Loccoz, Y}, title = {Microbial ecology of tourist Paleolithic caves.}, journal = {The Science of the total environment}, volume = {816}, number = {}, pages = {151492}, doi = {10.1016/j.scitotenv.2021.151492}, pmid = {34793801}, issn = {1879-1026}, mesh = {Animals ; Archaea ; Bacteria ; *Caves ; Fungi ; *Microbiota ; }, abstract = {Microorganisms colonize caves extensively, and in caves open for tourism they may cause alterations on wall surfaces. This is a major concern in caves displaying Paleolithic art, which is usually fragile and may be irremediably damaged by microbial alterations. Therefore, many caves were closed for preservation purposes, e.g. Lascaux (France), Altamira (Spain), while others were never opened to the public to avoid microbial contamination, e.g. Chauvet Cave (France), etc. The recent development of high-throughput sequencing technologies allowed several descriptions of cave microbial diversity and prompted the writing of this review, which focuses on the cave microbiome for the three domains of life (Bacteria, Archaea, microeukaryotes), the impact of tourism-related anthropization on microorganisms in Paleolithic caves, and the development of microbial alterations on the walls of these caves. This review shows that the microbial phyla prevalent in pristine caves are similar to those evidenced in water, soil, plant and metazoan microbiomes, but specificities at lower taxonomic levels remain to be clarified. Most of the data relates to Bacteria and Fungi, while other microeukaryotes and Archaea are poorly documented. Tourism may cause shifts in the microbiota of Paleolithic caves, but larger-scale investigation are required as these shifts may differ from one cave to the next. Finally, different types of alterations can occur in caves, especially in Paleolithic caves. Many microorganisms potentially involved have been identified, but diversity analyses of these alterations have not always included a comparison with neighboring unaltered zones as controls, making such associations uncertain. It is expected that omics technologies will also allow a better understanding of the functional diversities of the cave microbiome. This will be needed to decipher microbiome dynamics in response to touristic frequentation, to guide cave management, and to identify the most appropriate reclamation approaches to mitigate microbial alterations in tourist Paleolithic caves.}, }
@article {pmid34793127, year = {2022}, author = {Schwarz, C and Mathieu, J and Laverde Gomez, JA and Yu, P and Alvarez, PJJ}, title = {Renaissance for Phage-Based Bacterial Control.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {8}, pages = {4691-4701}, doi = {10.1021/acs.est.1c06232}, pmid = {34793127}, issn = {1520-5851}, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; Computational Biology ; *Microbiota ; Sequence Analysis, DNA ; }, abstract = {Bacteriophages (phages) are an underutilized biological resource with vast potential for pathogen control and microbiome editing. Phage research and commercialization have increased rapidly in biomedical and agricultural industries, but adoption has been limited elsewhere. Nevertheless, converging advances in DNA sequencing, bioinformatics, microbial ecology, and synthetic biology are now poised to broaden phage applications beyond pathogen control toward the manipulation of microbial communities for defined functional improvements. Enhancements in sequencing combined with network analysis make it now feasible to identify and disrupt microbial associations to elicit desirable shifts in community structure or function, indirectly modulate species abundance, and target hub or keystone species to achieve broad functional shifts. Sequencing and bioinformatic advancements are also facilitating the use of temperate phages for safe gene delivery applications. Finally, integration of synthetic biology stands to create novel phage chassis and modular genetic components. While some fundamental, regulatory, and commercialization barriers to widespread phage use remain, many major challenges that have impeded the field now have workable solutions. Thus, a new dawn for phage-based (chemical-free) precise biocontrol and microbiome editing is on the horizon to enhance, suppress, or modulate microbial activities important for public health, food security, and more sustainable energy production and water reuse.}, }
@article {pmid34791400, year = {2021}, author = {Semon, AK and Keenan, O and Zackular, JP}, title = {Clostridioides difficile and the Microbiota Early in Life.}, journal = {Journal of the Pediatric Infectious Diseases Society}, volume = {10}, number = {Supplement_3}, pages = {S3-S7}, pmid = {34791400}, issn = {2048-7207}, support = {K22 AI137220/AI/NIAID NIH HHS/United States ; //Children's Hospital of Philadelphia/ ; //National Institute of Allergy and Infectious Diseases/ ; R35GM138369/NH/NIH HHS/United States ; L40 AI147162/AI/NIAID NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Clostridioides ; *Clostridioides difficile ; *Clostridium Infections/epidemiology ; *Enterocolitis, Pseudomembranous ; Humans ; Infant ; *Microbiota ; }, abstract = {Clostridioides difficile is a spore-forming, obligate anaerobe, and ubiquitous nosocomial pathogen. While C. difficile infection in adults causes a spectrum of disease, including pseudomembranous colitis and toxic megacolon, healthy infants are asymptomatically colonized at high rates. The mechanisms leading to high colonization rates and infant protection from C. difficile are currently unknown; however, the ecology and metabolic state of the intestinal microbiome are factors known to influence C. difficile pathogenesis. In this review, we will examine the aspects of the early-life microbiome that may contribute to the incidence of C. difficile and protection from disease manifestation in infants. We will also discuss whether features of the adult microbiota that enable and restrict C. difficile are prevalent during early-life colonization.}, }
@article {pmid34791198, year = {2021}, author = {Vannette, RL and McMunn, MS and Hall, GW and Mueller, TG and Munkres, I and Perry, D}, title = {Culturable bacteria are more common than fungi in floral nectar and are more easily dispersed by thrips, a ubiquitous flower visitor.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {12}, pages = {}, doi = {10.1093/femsec/fiab150}, pmid = {34791198}, issn = {1574-6941}, mesh = {Animals ; Bacteria/genetics ; Flowers ; Fungi ; *Microbiota ; Plant Nectar ; Pollination ; *Thysanoptera ; }, abstract = {Variation in dispersal ability among taxa affects community assembly and biodiversity maintenance within metacommunities. Although fungi and bacteria frequently coexist, their relative dispersal abilities are poorly understood. Nectar-inhabiting microbial communities affect plant reproduction and pollinator behavior, and are excellent models for studying dispersal of bacteria and fungi in a metacommunity framework. Here, we assay dispersal ability of common nectar bacteria and fungi in an insect-based dispersal experiment. We then compare these results with the incidence and abundance of culturable flower-inhabiting bacteria and fungi within naturally occurring flowers across two coflowering communities in California across two flowering seasons. Our microbial dispersal experiment demonstrates that bacteria disperse via thrips among artificial habitat patches more readily than fungi. In the field, incidence and abundance of culturable bacteria and fungi were positively correlated, but bacteria were much more widespread. These patterns suggest shared dispersal routes or habitat requirements among culturable bacteria and fungi, but differences in dispersal or colonization frequency by thrips, common flower visitors. The finding that culturable bacteria are more common among nectar sampled here, in part due to superior thrips-mediated dispersal, may have relevance for microbial life history, community assembly of microbes, and plant-pollinator interactions.}, }
@article {pmid34788940, year = {2022}, author = {Tian, L and Chang, J and Shi, S and Ji, L and Zhang, J and Sun, Y and Li, X and Li, X and Xie, H and Cai, Y and Chen, D and Wang, J and van Veen, JA and Kuramae, EE and Tran, LP and Tian, C}, title = {Comparison of methane metabolism in the rhizomicrobiomes of wild and related cultivated rice accessions reveals a strong impact of crop domestication.}, journal = {The Science of the total environment}, volume = {803}, number = {}, pages = {150131}, doi = {10.1016/j.scitotenv.2021.150131}, pmid = {34788940}, issn = {1879-1026}, mesh = {Domestication ; Methane ; *Oryza/genetics ; Plant Breeding ; Rhizosphere ; }, abstract = {Microbial communities from rhizosphere (rhizomicrobiomes) have been significantly impacted by domestication as evidenced by a comparison of the rhizomicrobiomes of wild and related cultivated rice accessions. While there have been many published studies focusing on the structure of the rhizomicrobiome, studies comparing the functional traits of the microbial communities in the rhizospheres of wild rice and cultivated rice accessions are not yet available. In this study, we used metagenomic data from experimental rice plots to analyze the potential functional traits of the microbial communities in the rhizospheres of wild rice accessions originated from Africa and Asia in comparison with their related cultivated rice accessions. The functional potential of rhizosphere microbial communities involved in alanine, aspartate and glutamate metabolism, methane metabolism, carbon fixation pathways, citrate cycle (TCA cycle), pyruvate metabolism and lipopolysaccharide biosynthesis pathways were found to be enriched in the rhizomicrobiomes of wild rice accessions. Notably, methane metabolism in the rhizomicrobiomes of wild and cultivated rice accessions clearly differed. Key enzymes involved in methane production and utilization were overrepresented in the rhizomicrobiome samples obtained from wild rice accessions, suggesting that the rhizomicrobiomes of wild rice maintain a different ecological balance for methane production and utilization compared with those of the related cultivated rice accessions. A novel assessment of the impact of rice domestication on the primary metabolic pathways associated with microbial taxa in the rhizomicrobiomes was performed. Results indicated a strong impact of rice domestication on methane metabolism; a process that represents a critical function of the rhizosphere microbial community of rice. The findings of this study provide important information for future breeding of rice varieties with reduced methane emission during cultivation for sustainable agriculture.}, }
@article {pmid34787907, year = {2022}, author = {Ampt, EA and van Ruijven, J and Zwart, MP and Raaijmakers, JM and Termorshuizen, AJ and Mommer, L}, title = {Plant neighbours can make or break the disease transmission chain of a fungal root pathogen.}, journal = {The New phytologist}, volume = {233}, number = {3}, pages = {1303-1316}, pmid = {34787907}, issn = {1469-8137}, mesh = {*Biodiversity ; Nutrients ; Plant Development ; *Plants/microbiology ; }, abstract = {Biodiversity can reduce or increase disease transmission. These divergent effects suggest that community composition rather than diversity per se determines disease transmission. In natural plant communities, little is known about the functional roles of neighbouring plant species in belowground disease transmission. Here, we experimentally investigated disease transmission of a fungal root pathogen (Rhizoctonia solani) in two focal plant species in combinations with four neighbour species of two ages. We developed stochastic models to test the relative importance of two transmission-modifying mechanisms: (1) infected hosts serve as nutrient supply to increase hyphal growth, so that successful disease transmission is self-reinforcing; and (2) plant resistance increases during plant development. Neighbouring plants either reduced or increased disease transmission in the focal plants. These effects depended on neighbour age, but could not be explained by a simple dichotomy between hosts and nonhost neighbours. Model selection revealed that both transmission-modifying mechanisms are relevant and that focal host-neighbour interactions changed which mechanisms steered disease transmission rate. Our work shows that neighbour-induced shifts in the importance of these mechanisms across root networks either make or break disease transmission chains. Understanding how diversity affects disease transmission thus requires integrating interactions between focal and neighbour species and their pathogens.}, }
@article {pmid34784962, year = {2021}, author = {Tan, FPY and Beltranena, E and Zijlstra, RT}, title = {Resistant starch: Implications of dietary inclusion on gut health and growth in pigs: a review.}, journal = {Journal of animal science and biotechnology}, volume = {12}, number = {1}, pages = {124}, pmid = {34784962}, issn = {1674-9782}, support = {Discovery Grant//natural sciences and engineering research council of canada/ ; }, abstract = {Starch from cereal grains, pulse grains, and tubers is a major energy substrate in swine rations constituting up to 55% of the diet. In pigs, starch digestion is initiated by salivary and then pancreatic α-amylase, and has as final step the digestion of disaccharides by the brush-border enzymes in the small intestine that produce monosaccharides (glucose) for absorption. Resistant starch (RS) is the proportion of starch that escapes the enzymatic digestion and absorption in the small intestine. The undigested starch reaches the distal small intestine and hindgut for microbial fermentation, which produces short-chain fatty acids (SCFA) for absorption. SCFA in turn, influence microbial ecology and gut health of pigs. These fermentative metabolites exert their benefits on gut health through promoting growth and proliferation of enterocytes, maintenance of intestinal integrity and thus immunity, and modulation of the microbial community in part by suppressing the growth of pathogenic bacteria while selectively enhancing beneficial microbes. Thus, RS has the potential to confer prebiotic effects and may contribute to the improvement of intestinal health in pigs during the post-weaning period. Despite these benefits to the well-being of pigs, RS has a contradictory effect due to lower energetic efficiency of fermented vs. digested starch absorption products. The varying amount and type of RS interact differently with the digestion process along the gastrointestinal tract affecting its energy efficiency and host physiological responses including feed intake, energy metabolism, and feed efficiency. Results of research indicate that the use of RS as prebiotic may improve gut health and thereby, reduce the incidence of post-weaning diarrhea (PWD) and associated mortality. This review summarizes our current knowledge on the effects of RS on microbial ecology, gut health and growth performance in pigs.}, }
@article {pmid34783872, year = {2022}, author = {Berlow, M and Wada, H and Derryberry, EP}, title = {Experimental Exposure to Noise Alters Gut Microbiota in a Captive Songbird.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1264-1277}, pmid = {34783872}, issn = {1432-184X}, support = {IOS-1553657//National Science Foundation/ ; IOS-1827290//National Science Foundation/ ; A18-1243-001//Animal Behavior Society/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Corticosterone ; Noise/adverse effects ; *Sparrows/microbiology ; *Microbiota ; Bacteria ; }, abstract = {Noise pollution is an unprecedented evolutionary pressure on wild animals that can lead to alteration of stress hormone levels and changes in foraging behavior. Both corticosterone and feeding behavior can have direct effects on gut bacteria, as well as indirect effects through changes in gut physiology. Therefore, we hypothesized that exposure to noise will alter gut microbial communities via indirect effects on glucocorticoids and foraging behaviors. We exposed captive white-crowned sparrows to city-like noise and measured each individuals' corticosterone level, food intake, and gut microbial diversity at the end of four treatments (acclimation, noise, recovery, and control) using a balanced repeated measures design. We found evidence that noise acts to increase corticosterone and decrease food intake, adding to a growing body of research indicating noise exposure affects stress hormone levels and foraging behaviors. We also found evidence to support our prediction for a causal, positive relationship between noise exposure and gut microbial diversity, such that birds had higher measures of alpha diversity during noise exposure. These results help to explain previous findings that urban, free-living white-crowned sparrows have higher bacterial richness than rural sparrows. However, noise appeared to act directly on the gut microbiome or, more likely, through an unmeasured variable, rather than through indirect effects via corticosterone and food intake. Altogether, our study indicates that noise affects plasma corticosterone, feeding behavior, and the gut microbiome in a songbird and raises new questions as to the mechanism linking noise exposure to gut microbial diversity.}, }
@article {pmid34782938, year = {2022}, author = {Liebrenz, K and Gómez, C and Brambilla, S and Frare, R and Stritzler, M and Maguire, V and Ruiz, O and Soldini, D and Pascuan, C and Soto, G and Ayub, N}, title = {Whole-Genome Resequencing of Spontaneous Oxidative Stress-Resistant Mutants Reveals an Antioxidant System of Bradyrhizobium japonicum Involved in Soybean Colonization.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1133-1140}, pmid = {34782938}, issn = {1432-184X}, mesh = {*Glycine max/microbiology ; Antioxidants/metabolism ; Phylogeny ; *Bradyrhizobium/genetics/metabolism ; Symbiosis ; Oxidative Stress ; }, abstract = {Soybean is the most inoculant-consuming crop in the world, carrying strains belonging to the extremely related species Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens. Currently, it is well known that B. japonicum has higher efficiency of soybean colonization than B. diazoefficiens, but the molecular mechanism underlying this differential symbiotic performance remains unclear. In the present study, genome resequencing of four spontaneous oxidative stress-resistant mutants derived from the commercial strain B. japonicum E109 combined with molecular and physiological studies allowed identifying an antioxidant cluster (BjAC) containing a transcriptional regulator (glxA) that controls the expression of a catalase (catA) and a phosphohydrolase (yfbR) related to the hydrolysis of hydrogen peroxide and oxidized nucleotides, respectively. Integrated synteny and phylogenetic analyses supported the fact that BjAC emergence in the B. japonicum lineage occurred after its divergence from the B. diazoefficiens lineage. The transformation of the model bacterium B. diazoefficiens USDA110 with BjAC from E109 significantly increased its ability to colonize soybean roots, experimentally recapitulating the beneficial effects of the occurrence of BjAC in B. japonicum. In addition, the glxA mutation significantly increased the nodulation competitiveness and plant growth-promoting efficiency of E109. Finally, the potential applications of these types of non-genetically modified mutant microbes in soybean production worldwide are discussed.}, }
@article {pmid34782937, year = {2022}, author = {Banerji, R and Saroj, SD}, title = {Exposure to Acyl Homoserine Lactone Enhances Survival of Streptococcus pyogenes in Murine Macrophages.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1256-1263}, pmid = {34782937}, issn = {1432-184X}, support = {BT/RLF/Re-entry/41/2015//Department of Biotechnology , Ministry of Science and Technology/ ; }, mesh = {Mice ; Humans ; Animals ; *Acyl-Butyrolactones ; *Homoserine ; Streptococcus pyogenes ; 4-Butyrolactone/pharmacology ; Macrophages ; }, abstract = {Streptococcus pyogenes is an opportunistic pathogen causing infections of the skin and upper respiratory tract of the human host. Due to the polymicrobial community present in the human host, S. pyogenes comes across several interspecies signalling molecules. Among these molecules, N-(3-oxododecanoyl)-L-homoserine lactone (Oxo-C12) modulates the morphology, thereby enhancing virulence characteristics of S. pyogenes. After the initial attachment of the bacteria to the host cell, the pathogen needs to invade the host immune system for a successful infection to occur. The host immune system is activated upon infection, where macrophages engulf the pathogen, thereby killing the bacteria. However, S. pyogenes have evolved various strategies to evade the host immune response. In this study, we investigate the role of Oxo-C12 in enhancing the survival of S. pyogenes M3 in murine macrophages. The observed Oxo-C12-mediated increased survival in murine macrophages was through increased lysozyme and acid stress resistance. Moreover, Oxo-C12 increased the survival of S. pyogenes in normal human serum. Thus, understanding the role of interspecies signalling in enhancing the survival strategies of S. pyogenes in the host will further help fill the gap for therapeutics development.}, }
@article {pmid34780015, year = {2022}, author = {Kazmi, SSUH and Uroosa,  and Warren, A and Xu, G and Xu, H}, title = {Use of functional units of periphytic protozoa for monitoring water quality in marine ecosystems: bioindicator redundancy.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {15}, pages = {22139-22150}, pmid = {34780015}, issn = {1614-7499}, support = {31672308//National Natural Science Foundation of China/ ; }, mesh = {Biodiversity ; China ; *Ciliophora ; *Ecosystem ; Environmental Biomarkers ; Environmental Monitoring/methods ; Water Quality ; }, abstract = {Although periphytic protozoan communities have long been used for the bioassessment of water quality, their utility is hampered by functional redundancy, leading to high "signal-to-noise" ratios. In this study, a 1-year baseline survey of periphytic protozoan communities was carried out in coastal waters of the Yellow Sea, northern China, in order to determine redundancy levels in conditions of differing water quality. Samples were collected at four sampling sites along a pollution gradient. Environmental variables such as salinity, chemical oxygen demand (COD), and concentrations of dissolved oxygen (DO), soluble reactive phosphates (SRP), ammonium nitrogen (NH4-N), and nitrate nitrogen (NO3-N) were measured to compare with biotic factors. A total of 53 functional units (FUs) were identified from 144 observed protozoan species based on four biological traits, i.e., feeding type, body size, movement type, and source of food supply. For reducing the "signal-to-noise" ratios of species-abundance/biomass data, the peeling procedure was used to identify the bioindicator redundancy levels based on these FUs. Three consecutive subsets of response units (RU1-RU3) with correlation coefficients > 0.75 of the full FU dataset were identified, comprising 12 FUs, 21 FUs, and 9 FUs, respectively. Algivores and bacterivores were dominant in RU1 and RU2 among the polluted sites, whereas raptors were dominant in RU3 at the unpolluted site. In terms of relative abundance, RU1 was the primary contributor to the protozoan communities during the 1-year cycle and its relative abundance increased with the increasing pollution, whereas RU2 and RU3, with complementary temporal distributions, generally decreased with increasing pollution. Ordinations based on bootstrapped average analyses revealed a significant variation in the functional pattern of all three RUs among the four sampling sites. Biological-environmental match analysis demonstrated that the variability was driven by the increasing concentrations of nutrients (e.g., NH4-N, NO3-N, and PO4-P) and decreasing concentrations of DO (P < 0.05). There were high levels of functional redundancy among periphytic protozoan communities which could be used as bioindicators of marine water quality.}, }
@article {pmid34779881, year = {2022}, author = {Lee, HB and Jeong, DH and Cho, BC and Park, JS}, title = {The Diversity Patterns of Rare to Abundant Microbial Eukaryotes Across a Broad Range of Salinities in a Solar Saltern.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1103-1121}, pmid = {34779881}, issn = {1432-184X}, support = {NRF-2019R1A2C2002379//National Research Foundation of Korea/ ; NIBR202130203//National Institute of Biological Resources of Korea/ ; }, mesh = {Eukaryota/genetics ; Salinity ; Biodiversity ; DNA, Ribosomal ; *Rhizaria ; *Alveolata ; }, abstract = {Solar salterns are excellent artificial systems for examining species diversity and succession along salinity gradients. Here, the eukaryotic community in surface water of a Korean solar saltern (30 to 380 practical salinity units) was investigated from April 2019 to October 2020 using Illumina sequencing targeting the V4 and V9 regions of 18S rDNA. A total of 926 operational taxonomic units (OTUs) and 1,999 OTUs were obtained with the V4 and V9 regions, respectively. Notably, most of the OTUs were microbial eukaryotes, and the high-abundance groups (> 5% relative abundance (RA), Alveolata, Stramenopila, Archaeplastida, and Opisthokonta) usually accounted for > 90% of the total cumulative read counts and > 80% of all OTUs. Moreover, the high-abundance Alveolata (larger forms) and Stramenopila (smaller forms) groups displayed a significant inverse relationship, probably due to predator-prey interactions. Most of the low-abundance (0.1-5% RA) and rare (< 0.1% RA) groups remained small portion during the field surveys. Taxonomic novelty (at < 90% sequence identity) was high in the Amoebozoa, Cryptista, Haptista, Rhizaria, and Stramenopila groups (69.8% of all novel OTUs), suggesting the presence of a large number of hidden species in hypersaline environments. Remarkably, the high-abundance groups had little overlap with the other groups, implying the weakness of rare-to-prevalent community dynamics. The low-abundance Discoba group alone temporarily became the high-abundance group, suggesting that it is an opportunistic group. Overall, the composition and diversity of the eukaryotic community in hypersaline environments may be persistently stabilized, despite diverse disturbance events.}, }
@article {pmid34777296, year = {2021}, author = {Long, AM and Jurgensen, SK and Petchel, AR and Savoie, ER and Brum, JR}, title = {Microbial Ecology of Oxygen Minimum Zones Amidst Ocean Deoxygenation.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {748961}, pmid = {34777296}, issn = {1664-302X}, abstract = {Oxygen minimum zones (OMZs) have substantial effects on the global ecology and biogeochemical processes of marine microbes. However, the diversity and activity of OMZ microbes and their trophic interactions are only starting to be documented, especially in regard to the potential roles of viruses and protists. OMZs have expanded over the past 60 years and are predicted to expand due to anthropogenic climate change, furthering the need to understand these regions. This review summarizes the current knowledge of OMZ formation, the biotic and abiotic factors involved in OMZ expansion, and the microbial ecology of OMZs, emphasizing the importance of bacteria, archaea, viruses, and protists. We describe the recognized roles of OMZ microbes in carbon, nitrogen, and sulfur cycling, the potential of viruses in altering host metabolisms involved in these cycles, and the control of microbial populations by grazers and viruses. Further, we highlight the microbial community composition and roles of these organisms in oxic and anoxic depths within the water column and how these differences potentially inform how microbial communities will respond to deoxygenation. Additionally, the current literature on the alteration of microbial communities by other key climate change parameters such as temperature and pH are considered regarding how OMZ microbes might respond to these pressures. Finally, we discuss what knowledge gaps are present in understanding OMZ microbial communities and propose directions that will begin to close these gaps.}, }
@article {pmid34775524, year = {2022}, author = {Liu, R and Wang, Q and Zhang, K and Wu, H and Wang, G and Cai, W and Yu, K and Sun, Q and Fan, S and Wang, Z}, title = {Analysis of Postmortem Intestinal Microbiota Successional Patterns with Application in Postmortem Interval Estimation.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1087-1102}, pmid = {34775524}, issn = {1432-184X}, support = {81730056//National Natural Science Foundation of China/ ; 2020SF-133//key research and development program of shaanxi/ ; }, mesh = {Mice ; Animals ; *Gastrointestinal Microbiome ; Postmortem Changes ; Bacteria/genetics ; Intestines ; Lactobacillus ; }, abstract = {Microorganisms play a vital role in the decomposition of vertebrate remains in natural nutrient cycling, and the postmortem microbial succession patterns during decomposition remain unclear. The present study used hierarchical clustering based on Manhattan distances to analyze the similarities and differences among postmortem intestinal microbial succession patterns based on microbial 16S rDNA sequences in a mouse decomposition model. Based on the similarity, seven different classes of succession patterns were obtained. Generally, the normal intestinal flora in the cecum was gradually decreased with changes in the living conditions after death, while some facultative anaerobes and obligate anaerobes grew and multiplied upon oxygen consumption. Furthermore, a random forest regression model was developed to predict the postmortem interval based on the microbial succession trend dataset. The model demonstrated a mean absolute error of 20.01 h and a squared correlation coefficient of 0.95 during 15-day decomposition. Lactobacillus, Dubosiella, Enterococcus, and the Lachnospiraceae NK4A136 group were considered significant biomarkers for this model according to the ranked list. The present study explored microbial succession patterns in terms of relative abundances and variety, aiding in the prediction of postmortem intervals and offering some information on microbial behaviors in decomposition ecology.}, }
@article {pmid34767630, year = {2022}, author = {Wu, G and Miyauchi, S and Morin, E and Kuo, A and Drula, E and Varga, T and Kohler, A and Feng, B and Cao, Y and Lipzen, A and Daum, C and Hundley, H and Pangilinan, J and Johnson, J and Barry, K and LaButti, K and Ng, V and Ahrendt, S and Min, B and Choi, IG and Park, H and Plett, JM and Magnuson, J and Spatafora, JW and Nagy, LG and Henrissat, B and Grigoriev, IV and Yang, ZL and Xu, J and Martin, FM}, title = {Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales.}, journal = {The New phytologist}, volume = {233}, number = {3}, pages = {1383-1400}, doi = {10.1111/nph.17858}, pmid = {34767630}, issn = {1469-8137}, mesh = {*Basidiomycota/genetics ; Biological Evolution ; *Mycorrhizae/genetics ; Phylogeny ; Symbiosis/genetics ; }, abstract = {We aimed to identify genomic traits of transitions to ectomycorrhizal ecology within the Boletales by comparing the genomes of 21 symbiotrophic species with their saprotrophic brown-rot relatives. Gene duplication rate is constant along the backbone of Boletales phylogeny with large loss events in several lineages, while gene family expansion sharply increased in the late Miocene, mostly in the Boletaceae. Ectomycorrhizal Boletales have a reduced set of plant cell-wall-degrading enzymes (PCWDEs) compared with their brown-rot relatives. However, the various lineages retain distinct sets of PCWDEs, suggesting that, over their evolutionary history, symbiotic Boletales have become functionally diverse. A smaller PCWDE repertoire was found in Sclerodermatineae. The gene repertoire of several lignocellulose oxidoreductases (e.g. laccases) is similar in brown-rot and ectomycorrhizal species, suggesting that symbiotic Boletales are capable of mild lignocellulose decomposition. Transposable element (TE) proliferation contributed to the higher evolutionary rate of genes encoding effector-like small secreted proteins, proteases, and lipases. On the other hand, we showed that the loss of secreted CAZymes was not related to TE activity but to DNA decay. This study provides novel insights on our understanding of the mechanisms influencing the evolutionary diversification of symbiotic boletes.}, }
@article {pmid34767049, year = {2022}, author = {Elias, L and Hearn, AM and Blazier, JC and Rogovska, YV and Wang, J and Li, S and Liu, S and Nebogatkin, IV and Rogovskyy, AS}, title = {The Microbiota of Ixodes ricinus and Dermacentor reticulatus Ticks Collected from a Highly Populated City of Eastern Europe.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1072-1086}, pmid = {34767049}, issn = {1432-184X}, mesh = {Male ; Animals ; Female ; *Ixodes/microbiology ; *Dermacentor/microbiology ; RNA, Ribosomal, 16S/genetics ; Europe, Eastern ; *Microbiota ; }, abstract = {Recent investigations have examined, through sequencing the V6 region of 16S rRNA gene, the microbiota of questing Ixodes ricinus and Dermacentor reticulatus ticks collected from rural areas of Central (Dnipropetrovs'k (region D) and Poltava (region P)) and Northeastern (Kharkiv (region K)) Ukraine. In addition to defining the bacterial microbiota of both tick species, the previous investigations also revealed a high degree of inter-sex and inter-regional variations in the tick microbiota. As a continuation of the two studies, the present investigation has analyzed individual microbiota of questing I. ricinus (n = 50) and D. reticulatus (n = 50) ticks originating from Kyiv, the largest city of Ukraine. The Kyiv tick microbiota were compared between males and females for each tick species. Additionally, a cross-regional analysis was performed to compare the microbiota of Kyiv ticks to those from regions D, K, and P. Numerous statistically significant inter-sex and inter-regional variations were detected when alpha diversity, beta diversity, the bacterial relative and differential abundances were assessed. The overall results demonstrated that the microbiota of Kyiv ticks were statistically different compared to the ticks of the other three regions. Besides existing climatic and geographical differences between the four regions, the authors hypothesize that various anthropogenic factors of the megapolis (e.g., animal species translocation, land management, ecology) could have contributed to the distinct microbiota of Kyiv ticks observed in this study.}, }
@article {pmid34767048, year = {2022}, author = {Zhang, W and Yuan, W and Chen, L and Ye, C and Jiang, Y and Yang, Y}, title = {Uniqueness and Dependence of Bacterial Communities on Microplastics: Comparison with Water, Sediment, and Soil.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {985-995}, pmid = {34767048}, issn = {1432-184X}, support = {32071614//National Natural Science Foundation of China/ ; }, mesh = {*Microplastics ; Plastics ; Soil ; RNA, Ribosomal, 16S/genetics ; Water ; Bacteria/genetics ; *Microbiota ; }, abstract = {Revealing the dependence and uniqueness of microbial communities on microplastics could help us better understand the assembly of the microplastic microbial community in river ecosystems. In this study, we investigated the composition and ecological functions of the bacterial community on microplastics from the Three Gorges Reservoir area compared with those in water, sediment, and soil at species-level via full-length 16S rRNA gene sequencing. The results showed that the full-length 16S rRNA sequencing provided more detail and accurate taxa resolution of the bacterial community in microplastics (100%), water (99.90%), sediment (99.95%), and soil (100%). Betaproteobacteriales were the most abundant bacteria in microplastics (14.1%), water (32.3%), sediments (27.2%), and soil (21.0%). Unexpectedly, oligotrophic SAR11 clade was the third abundant bacteria (8.51%) and dominated the ecological functions of the bacterial community in water, but it was less observed on microplastics, with a relative abundance of 2.73×10[-5]. However, four opportunistic pathogens identified at the species level were selectively enriched on microplastics. Stenotrophomonas maltophilia was the main opportunistic pathogen on microplastics (0.29%). Sediment rather than soil and water may be contributed mostly to pathogens on microplastics. Moreover, some bacteria species with the biodegradation function of microplastics were enriched on microplastics, such as bacteria Rhodobacter sp., and endemic bacteria Luteimonas sp. The distinct bacteria composition on microplastics enhanced several ecological functions, such as xenobiotics biodegradation, which allows screening the bacteria with the biodegradation function of microplastics through long-term exposure.}, }
@article {pmid34766210, year = {2022}, author = {Sanseverino, I and Pretto, P and António, DC and Lahm, A and Facca, C and Loos, R and Skejo, H and Beghi, A and Pandolfi, F and Genoni, P and Lettieri, T}, title = {Metagenomics Analysis to Investigate the Microbial Communities and Their Functional Profile During Cyanobacterial Blooms in Lake Varese.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {850-868}, pmid = {34766210}, issn = {1432-184X}, mesh = {*Cyanobacteria/genetics ; Eutrophication ; Humans ; Lakes/microbiology ; Metagenomics ; *Microbiota/genetics ; Water/analysis ; }, abstract = {Toxic cyanobacterial blooms represent a natural phenomenon caused by a mass proliferation of photosynthetic prokaryotic microorganisms in water environments. Bloom events have been increasingly reported worldwide and their occurrence can pose serious threats to aquatic organisms and human health. In this study, we assessed the microbial composition, with a focus on Cyanobacteria, in Lake Varese, a eutrophic lake located in northern Italy. Water samples were collected and used for obtaining a 16S-based taxonomic profile and performing a shotgun sequencing analysis. The phyla found to exhibit the greatest relative abundance in the lake included Proteobacteria, Cyanobacteria, Actinobacteriota and Bacteroidota. In the epilimnion and at 2.5 × Secchi depth, Cyanobacteria were found to be more abundant compared to the low levels detected at greater depths. The blooms appear to be dominated mainly by the species Lyngbya robusta, and a specific functional profile was identified, suggesting that distinct metabolic processes characterized the bacterial population along the water column. Finally, analysis of the shotgun data also indicated the presence of a large and diverse phage population.}, }
@article {pmid34764222, year = {2021}, author = {Thamdrup, B and Schauberger, C and Larsen, M and Trouche, B and Maignien, L and Arnaud-Haond, S and Wenzhöfer, F and Glud, RN}, title = {Anammox bacteria drive fixed nitrogen loss in hadal trench sediments.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {46}, pages = {}, pmid = {34764222}, issn = {1091-6490}, mesh = {Anaerobic Ammonia Oxidation/physiology ; Denitrification/physiology ; Geologic Sediments/*microbiology ; Microbiota/physiology ; Nitrates/metabolism ; Nitrification/physiology ; Nitrogen/*metabolism ; Nitrogen Cycle/physiology ; Nitrogen Fixation/*physiology ; Nitrogen-Fixing Bacteria/*metabolism ; Oceans and Seas ; }, abstract = {Benthic N2 production by microbial denitrification and anammox is the largest sink for fixed nitrogen in the oceans. Most N2 production occurs on the continental shelves, where a high flux of reactive organic matter fuels the depletion of nitrate close to the sediment surface. By contrast, N2 production rates in abyssal sediments are low due to low inputs of reactive organics, and nitrogen transformations are dominated by aerobic nitrification and the release of nitrate to the bottom water. Here, we demonstrate that this trend is reversed in the deepest parts of the oceans, the hadal trenches, where focusing of reactive organic matter enhances benthic microbial activity. Thus, at ∼8-km depth in the Atacama Trench, underlying productive surface waters, nitrate is depleted within a few centimeters of the sediment surface, N2 production rates reach those reported from some continental margin sites, and fixed nitrogen loss is mainly conveyed by anammox bacteria. These bacteria are closely related to those known from shallow oxygen minimum zone waters, and comparison of activities measured in the laboratory and in situ suggest they are piezotolerant. Even the Kermadec Trench, underlying oligotrophic surface waters, exhibits substantial fixed N removal. Our results underline the role of hadal sediments as hot spots of deep-sea biological activity, revealing a fully functional benthic nitrogen cycle at high hydrostatic pressure and pointing to hadal sediments as a previously unexplored niche for anaerobic microbial ecology and diagenesis.}, }
@article {pmid34762992, year = {2022}, author = {Maganha de Almeida Kumlien, AC and Pérez-Vega, C and González-Villalobos, E and Borrego, CM and Balcázar, JL}, title = {Genome analysis of a new Escherichia phage vB_EcoM_C2-3 with lytic activity against multidrug-resistant Escherichia coli.}, journal = {Virus research}, volume = {307}, number = {}, pages = {198623}, doi = {10.1016/j.virusres.2021.198623}, pmid = {34762992}, issn = {1872-7492}, mesh = {*Bacteriophages/genetics ; Escherichia coli/genetics ; Genome, Viral ; Myoviridae/genetics ; *Siphoviridae/genetics ; }, abstract = {In this study, we present the complete, annotated genome of a new member of the Tequatrovirus (T4-like) genus, Escherichia phage vB_EcoM_C2-3. This phage has an isometric head (92 nm in diameter) and a contractile tail (114 nm in length). Its genome consists of a linear, double-stranded DNA of 167,069bp with an average G+C content of 35.3%. There are 267 predicted genes, of which 125 encode functional proteins, including those for DNA replication, transcription and packaging, phage morphogenesis and cell lysis. Neither genes involved in the regulation of lysogeny nor antibiotic resistance genes were identified. Based on our results, its genomic features provide valuable insights into the use of a potential biocontrol agent, as Escherichia phage vB_EcoM_C2-3 exhibited lytic activity against E. coli, including multidrug-resistant strains.}, }
@article {pmid34762695, year = {2021}, author = {Obusan, MCM and Caras, JAA and Lumang, LSL and Calderon, EJS and Villanueva, RMD and Salibay, CC and Siringan, MAT and Rivera, WL and Masangkay, JS and Aragones, LV}, title = {Bacteriological and histopathological findings in cetaceans that stranded in the Philippines from 2017 to 2018.}, journal = {PloS one}, volume = {16}, number = {11}, pages = {e0243691}, pmid = {34762695}, issn = {1932-6203}, mesh = {Animals ; Cetacea/*microbiology ; Liver/pathology ; Lung/pathology ; Muscle, Skeletal/pathology ; Myocardium/pathology ; Philippines ; }, abstract = {The relatively high frequency of marine mammal stranding events in the Philippines provide many research opportunities. A select set of stranders (n = 21) from 2017 to 2018 were sampled for bacteriology and histopathology. Pertinent tissues and bacteria were collected from individuals representing eight cetacean species (i.e. Feresa attenuata, Kogia breviceps, Globicephala macrorhynchus, Grampus griseus, Lagenodelphis hosei, Peponocephala electra, Stenella attenuata and Stenella longirostris) and were subjected to histopathological examination and antibiotic resistance screening, respectively. The antibiotic resistance profiles of 24 bacteria (belonging to genera Escherichia, Enterobacter, Klebsiella, Proteus, and Shigella) that were isolated from four cetaceans were determined using 18 antibiotics. All 24 isolates were resistant to at least one antibiotic class, and 79.17% were classified as multiple antibiotic resistant (MAR). The MAR index values of isolates ranged from 0.06 to 0.39 with all the isolates resistant to erythromycin (100%; n = 24) and susceptible to imipenem, doripenem, ciprofloxacin, chloramphenicol, and gentamicin (100%; n = 24). The resistance profiles of these bacteria show the extent of antimicrobial resistance in the marine environment, and may inform medical management decisions during rehabilitation of stranded cetaceans. Due to inadequate gross descriptions and limited data gathered by the responders during the stranding events, the significance of histopathological lesions in association with disease diagnosis in each cetacean stranding or mortality remained inconclusive; however, these histopathological findings may be indicative or contributory to the resulting debility and stress during their strandings. The findings of the study demonstrate the challenges faced by cetacean species in the wild, such as but not limited to, biological pollution through land-sea movement of effluents, fisheries interactions, and anthropogenic activities.}, }
@article {pmid34760361, year = {2021}, author = {Costantini, MS and Medeiros, MCI and Crampton, LH and Reed, FA}, title = {Wild gut microbiomes reveal individuals, species, and location as drivers of variation in two critically endangered Hawaiian honeycreepers.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e12291}, pmid = {34760361}, issn = {2167-8359}, support = {P20 GM125508/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: The gut microbiome of animals is an important component that has strong influence on the health, fitness, and behavior of its host. Most research in the microbiome field has focused on human populations and commercially important species. However, researchers are now considering the link between endangered species conservation and the microbiome. In Hawai'i, several threats (e.g., avian malaria and habitat loss) have caused widespread population declines of Hawaiian honeycreepers (subfamily: Carduelinae). These threats can have a significant effect on the avian gut microbiome and may even lead to disruption of microbial function. However, the gut microbiome of honeycreeper in the wild has yet to be explored.<br><br>METHODS: We collected 13 and 42 fecal samples, respectively, from two critically endangered honeycreeper species, the 'akikiki (Oreomystis bairdi) and the 'akeke'e (Loxops caeruleirostris). The 16S rRNA gene was sequenced and processed though a MOTHUR-based bioinformatics pipeline. Bacterial ASVs were identified using the DADA2 program and bacterial community analyses, including alpha and beta diversity measures, were conducted using R packages Phyloseq and vegan.<br><br>RESULTS: A total of 8,958 bacterial ASVs were identified from the fecal samples. Intraspecific differences in the gut microbiome among individual birds explained most of the variation present in the dataset, however differences between species did exist. Both species had distinct microbiomes with minimal overlap in beta diversity. 'Akikiki had a more diverse microbiome compared to 'akeke'e. Additionally, small but stastically significant differences in beta diversity also exist between sampling location and sexes in 'akikiki.<br><br>CONCLUSION: 'Akikiki and 'akeke'e are currently the focus of captive breeding efforts and plans to translocate the two species to other islands are underway. This baseline knowledge will help inform management decisions for these honeycreeper species in their native habitats, on other islands, and in captivity.}, }
@article {pmid34760357, year = {2021}, author = {Tucker, SJ and Freel, KC and Monaghan, EA and Sullivan, CES and Ramfelt, O and Rii, YM and Rappé, MS}, title = {Spatial and temporal dynamics of SAR11 marine bacteria across a nearshore to offshore transect in the tropical Pacific Ocean.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e12274}, pmid = {34760357}, issn = {2167-8359}, abstract = {Surveys of microbial communities across transitions coupled with contextual measures of the environment provide a useful approach to dissect the factors determining distributions of microorganisms across ecological niches. Here, monthly time-series samples of surface seawater along a transect spanning the nearshore coastal environment within Kāne'ohe Bay on the island of O'ahu, Hawai'i, and the adjacent offshore environment were collected to investigate the diversity and abundance of SAR11 marine bacteria (order Pelagibacterales) over a 2-year time period. Using 16S ribosomal RNA gene amplicon sequencing, the spatiotemporal distributions of major SAR11 subclades and exact amplicon sequence variants (ASVs) were evaluated. Seven of eight SAR11 subclades detected in this study showed distinct subclade distributions across the coastal to offshore environments. The SAR11 community was dominated by seven (of 106 total) SAR11 ASVs that made up an average of 77% of total SAR11. These seven ASVs spanned five different SAR11 subclades (Ia, Ib, IIa, IV, and Va), and were recovered from all samples collected from either the coastal environment, the offshore, or both. SAR11 ASVs were more often restricted spatially to coastal or offshore environments (64 of 106 ASVs) than they were shared among coastal, transition, and offshore environments (39 of 106 ASVs). Overall, offshore SAR11 communities contained a higher diversity of SAR11 ASVs than their nearshore counterparts, with the highest diversity within the little-studied subclade IIa. This study reveals ecological differentiation of SAR11 marine bacteria across a short physiochemical gradient, further increasing our understanding of how SAR11 genetic diversity partitions into distinct ecological units.}, }
@article {pmid34760346, year = {2021}, author = {Voigt, E and Rall, BC and Chatzinotas, A and Brose, U and Rosenbaum, B}, title = {Phage strategies facilitate bacterial coexistence under environmental variability.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e12194}, pmid = {34760346}, issn = {2167-8359}, abstract = {Bacterial communities are often exposed to temporal variations in resource availability, which exceed bacterial generation times and thereby affect bacterial coexistence. Bacterial population dynamics are also shaped by bacteriophages, which are a main cause of bacterial mortality. Several strategies are proposed in the literature to describe infections by phages, such as "Killing the Winner", "Piggyback the loser" (PtL) or "Piggyback the Winner" (PtW). The two temperate phage strategies PtL and PtW are defined by a change from lytic to lysogenic infection when the host density changes, from high to low or from low to high, respectively. To date, the occurrence of different phage strategies and their response to environmental variability is poorly understood. In our study, we developed a microbial trophic network model using ordinary differential equations (ODEs) and performed 'in silico' experiments. To model the switch from the lysogenic to the lytic cycle, we modified the lysis rate of infected bacteria and their growth was turned on or off using a density-dependent switching point. We addressed whether and how the different phage strategies facilitate bacteria coexistence competing for limiting resources. We also studied the impact of a fluctuating resource inflow to evaluate the response of the different phage strategies to environmental variability. Our results show that the viral shunt (i.e. nutrient release after bacterial lysis) leads to an enrichment of the system. This enrichment enables bacterial coexistence at lower resource concentrations. We were able to show that an established, purely lytic model leads to stable bacterial coexistence despite fluctuating resources. Both temperate phage models differ in their coexistence patterns. The model of PtW yields stable bacterial coexistence at a limited range of resource supply and is most sensitive to resource fluctuations. Interestingly, the purely lytic phage strategy and PtW both result in stable bacteria coexistence at oligotrophic conditions. The PtL model facilitates stable bacterial coexistence over a large range of stable and fluctuating resource inflow. An increase in bacterial growth rate results in a higher resilience to resource variability for the PtL and the lytic infection model. We propose that both temperate phage strategies represent different mechanisms of phages coping with environmental variability. Our study demonstrates how phage strategies can maintain bacterial coexistence in constant and fluctuating environments.}, }
@article {pmid34758284, year = {2022}, author = {Meaden, S and Biswas, A and Arkhipova, K and Morales, SE and Dutilh, BE and Westra, ER and Fineran, PC}, title = {High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems.}, journal = {Current biology : CB}, volume = {32}, number = {1}, pages = {220-227.e5}, pmid = {34758284}, issn = {1879-0445}, mesh = {*Bacteriophages/genetics ; *CRISPR-Cas Systems ; Ecosystem ; Metagenomics ; Prevalence ; }, abstract = {CRISPR-Cas are adaptive immune systems that protect their hosts against viruses and other parasitic mobile genetic elements.[1] Although widely distributed among prokaryotic taxa, CRISPR-Cas systems are not ubiquitous.[2-4] Like most defense-system genes, CRISPR-Cas are frequently lost and gained, suggesting advantages are specific to particular environmental conditions.[5] Selection from viruses is assumed to drive the acquisition and maintenance of these immune systems in nature, and both theory[6-8] and experiments have identified phage density and diversity as key fitness determinants.[9][,][10] However, these approaches lack the biological complexity inherent in nature. Here, we exploit metagenomic data from 324 samples across diverse ecosystems to analyze CRISPR abundance in natural environments. For each metagenome, we quantified viral abundance and diversity to test whether these contribute to CRISPR-Cas abundance across ecosystems. We find a strong positive association between CRISPR-Cas abundance and viral abundance. In addition, when controlling for differences in viral abundance, CRISPR-Cas systems are more abundant when viral diversity is low, suggesting that such adaptive immune systems may offer limited protection when required to target a diverse viral community. CRISPR-Cas abundance also differed among environments, with environmental classification explaining roughly a quarter of the variation in CRISPR-Cas relative abundance. The relationships between CRISPR-Cas abundance, viral abundance, and viral diversity are broadly consistent across environments, providing robust evidence from natural ecosystems that supports predictions of when CRISPR is beneficial. These results indicate that viral abundance and diversity are major ecological factors that drive the selection and maintenance of CRISPR-Cas in microbial ecosystems.}, }
@article {pmid34757460, year = {2022}, author = {Zhang, W and Wang, X and Li, Y and Wei, P and Sun, N and Wen, X and Liu, Z and Li, D and Feng, Y and Zhang, X}, title = {Differences Between Microbial Communities of Pinus Species Having Differing Level of Resistance to the Pine Wood Nematode.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1245-1255}, pmid = {34757460}, issn = {1432-184X}, support = {ZD202001//major emergency science and technology project of national forestry and grassland administration/ ; 2018YFC1200400//key technology research and development program of shandong/ ; 31901315//national natural science foundation of china/ ; }, mesh = {Animals ; *Pinus/microbiology ; Bacteria/genetics ; *Microbiota ; Introduced Species ; *Nematoda ; Plant Diseases ; }, abstract = {The pine wood nematode (PWN), Bursaphelenchus xylophilus, is a destructive invasive species that exerts devastating effects on most native pines in invaded regions, while many of the non-native pines have resistance to PWN. Recently, increasingly more research is focused on how microbial communities can improve host resistance against pathogens. However, the relationship between the microbial community structures and varying levels of pathogen resistance observed in different pine tree species remains unclear. Here, the bacterial and fungal communities of introduced resistant pines Pinus elliottii, P. caribaea, and P. taeda and native susceptible pines healthy and wilted P. massoniana infected by PWN were analyzed. The results showed that 6057 bacterial and 3931 fungal OTUs were annotated. The pine samples shared 944 bacterial OTUs primarily in the phyla Proteobacteria, Acidobacteria, Firmicutes, Bacteroidetes, and Chloroflexi and 111 fungal OTUs primarily in phyla Ascomycota and Basidiomycota, though different pines had unique OTUs. There were significant differences in microbial community diversity between different pines, especially between the bacterial communities of resistant and susceptible pines, and fungal communities between healthy pines (resistant pines included) and the wilted P. massoniana. Resistant pines had a greater abundance of bacteria in the genera Acidothermus (class unidentified_Actinobacteria) and Prevotellaceae (class Alphaproteobacteria), but a lower abundance of Erwinia (class Gammaproteobacteria). Healthy pines had a higher fungal abundance of Cladosporium (class Dothideomycetes) and class Eurotiomycetes, but a lower abundance of Graphilbum, Sporothrix, Geosmithia (class Sordariomycetes), and Cryptoporus (classes Agaricomycetes and Saccharomycetes). These differences in microbial abundance between resistant and healthy pines might be associated with pathogen resistance of the pines, and the results of this study contribute to the studies exploring microbial-based control of PWN.}, }
@article {pmid34756083, year = {2021}, author = {Mills, S and Trego, AC and Lens, PNL and Ijaz, UZ and Collins, G}, title = {A Distinct, Flocculent, Acidogenic Microbial Community Accompanies Methanogenic Granules in Anaerobic Digesters.}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0078421}, pmid = {34756083}, issn = {2165-0497}, mesh = {Bacteria, Anaerobic/*metabolism ; Bacterial Adhesion/physiology ; Biofilms/growth &amp; development ; Bioreactors/*microbiology ; Flocculation ; Methane/*biosynthesis ; Microbiota/*physiology ; Sewage/*microbiology ; Streptococcaceae/metabolism ; Water Purification ; }, abstract = {The formation of dense, well-settling methanogenic granules is essential for the operation of high-rate, up-flow anaerobic bioreactors used for wastewater treatment. Granule formation (granulation) mechanisms have been previously proposed, but an ecological understanding of granule formation is still lacking. Additionally, much of the current research on granulation only examines the start-up phase of bioreactor operation, rather than monitoring the fate of established granules and how new granules emerge over time. This paper, therefore, attempts to provide an insight into the microbial ecology of granule formation outside the start-up phase of bioreactor operation and develop an ecological granulation model. The microbial communities of granules actively undergoing growth, breakage, and reformation were examined, and an ecological granulation model was proposed. A distinct pregranular microbial community, with a high proportion of acidogenic organisms, such as the Streptococcaceae, was identified and suggested to have a role in initiating granulation by providing simpler substrates for the methanogenic and syntrophic communities which developed during granule growth. After initial granule formation, deterministic influences on microbial community assembly increased with granule size and indicated that microbial community succession was influenced by granule growth, leading to the formation of a stepwise ecological model for granulation. IMPORTANCE Complex microbial communities in engineered environments can aggregate to form surface-attached biofilms. Others form suspended biofilms, such as methanogenic granules. The formation of dense, methanogenic granules underpins the performance of high-rate, anaerobic bioreactors in industrial wastewater treatment. Granule formation (granulation) has been well studied from a physico-chemical perspective, but the ecological basis is poorly understood. We identified a distinct, flocculent, microbial community, which was present alongside granules, comprising primary consumers likely key in providing simpler substrates to granules. This flocculent community is understudied in anaerobic digestion and may initiate, or perpetuate, granule formation. We propose that it may be possible to influence bioreactor performance (e.g., to regulate volatile fatty acid concentrations) by manipulating this community. The patterns of microbial community diversity and assembly revealed by the study indicate that cycles of granule growth and breakage lead to overall diversification of the bioreactor meta-community, with implications for bioreactor process stability.}, }
@article {pmid34756066, year = {2021}, author = {Thieringer, PH and Honeyman, AS and Spear, JR}, title = {Spatial and Temporal Constraints on the Composition of Microbial Communities in Subsurface Boreholes of the Edgar Experimental Mine.}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0063121}, pmid = {34756066}, issn = {2165-0497}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; Geologic Sediments/chemistry/*microbiology ; Groundwater/*microbiology ; *Microbiota ; Mining ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The deep biosphere hosts uniquely adapted microorganisms overcoming geochemical extremes at significant depths within the crust of the Earth. Attention is required to understand the near subsurface and its continuity with surface systems, where numerous novel microbial members with unique physiological modifications remain to be identified. This surface-subsurface relationship raises key questions about networking of surface hydrology, geochemistry affecting near-subsurface microbial composition, and resiliency of subsurface ecosystems. Here, we apply molecular and geochemical approaches to determine temporal microbial composition and environmental conditions of filtered borehole fluid from the Edgar Experimental Mine (∼150 m below the surface) in Idaho Springs, CO. Samples were collected over a 4-year collection period from expandable packers deployed to accumulate fluid in previously drilled boreholes located centimeters to meters apart, revealing temporal evolution of borehole microbiology. Meteoric groundwater feeding boreholes demonstrated variable recharge rates likely due to a complex and undefined fracture system within the host rock. 16S rRNA gene analysis determined that unique microbial communities occupy the four boreholes examined. Two boreholes yielded sequences revealing the presence of Desulfosporosinus, Candidatus Nitrotoga, and Chelatococcus associated with endemic subsurface communities. Two other boreholes presented sequences related to nonsubsurface-originating microbiota. High concentration of sulfate along with detected sulfur reducing and oxidizing microorganisms suggests that sulfur related metabolic strategies are prominent within these near-subsurface boreholes. Overall, results indicate that microbial community composition in the near-subsurface is highly dynamic at very fine spatial scales (<20 cm) within fluid-rock equilibrated boreholes, which additionally supports the role of a relationship for surface geochemical processes infiltrating and influencing subsurface environments. IMPORTANCE The Edgar Experimental Mine, Idaho Springs, CO, provides inexpensive and open access to borehole investigations for subsurface microbiology studies. Understanding how microbial processes in the near subsurface are connected to surface hydrological influences is lacking. Investigating microbial communities of subsurface mine boreholes provides evidence of how geochemical processes are linked to biogeochemical processes within each borehole and the geochemical connectedness and mobility of surface influences. This study details microbial community composition and fluid geochemistry over spatial and temporal scales from boreholes within the Edgar Mine. These findings are relevant to biogeochemistry of near-surface mines, caves, and other voids across planetary terrestrial systems. In addition, this work can lead to understanding how microbial communities relate to both fluid-rock equilibration, and geochemical influences may enhance our understanding of subsurface molecular biological tools that aid mining economic practices to reflect biological signals for lucrative veins in the near subsurface.}, }
@article {pmid34755197, year = {2022}, author = {Faghihinia, M and Zou, Y and Bai, Y and Dudáš, M and Marrs, R and Staddon, PL}, title = {Grazing Intensity Rather than Host Plant's Palatability Shapes the Community of Arbuscular Mycorrhizal Fungi in a Steppe Grassland.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1062-1071}, doi = {10.1007/s00248-021-01920-7}, pmid = {34755197}, issn = {1432-184X}, support = {RDF-15-02-13//Xi'an Jiaotong-Liverpool University/ ; }, mesh = {Sheep ; Animals ; *Mycorrhizae/physiology ; Grassland ; Ecosystem ; Soil Microbiology ; Fungi ; Soil ; Poaceae/microbiology ; Plants/microbiology ; Plant Roots/microbiology ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) are the predominant type of mycorrhizal fungi in roots and rhizosphere soil of grass species worldwide. Grasslands are currently experiencing increasing grazing pressure, but it is not yet clear how grazing intensity and host plant grazing preference by large herbivores interact with soil- and root-associated AMF communities. Here, we tested whether the diversity and community composition of AMF in the roots and rhizosphere soil of two dominant perennial grasses, grazed differently by livestock, change in response to grazing intensity. We conducted a study in a long-term field experiment in which seven levels of field-manipulated grazing intensities were maintained for 13 years in a typical steppe grassland in northern China. We extracted DNA from the roots and rhizosphere soil of two dominant grasses, Leymus chinense (Trin.) Tzvel. and Stipa grandis P. Smirn, with contrasting grazing preference by sheep. AMF DNA from root and soil samples was then subjected to molecular analysis. Our results showed that AMF α-diversity (richness) at the virtual taxa (VT) level varied as a function of grazing intensity. Different VT showed completely different responses along the gradient, one increasing, one decreasing, and others showing no response. Glomeraceae was the most abundant AMF family along the grazing gradient, which fits well with the theory of disturbance tolerance of this group. In addition, sheep-grazing preference for host plants did not explain much of the variation in AMF α-diversity. However, the two grass species exhibited different AMF community composition in their roots and rhizosphere soils. Roots exhibited a lower α-diversity and higher β-diversity within the AMF community than soils. Overall, our results suggest that long-term grazing intensity might have changed the abundance of functionally diverse AMF taxa in favor of those with disturbance-tolerant traits. We suggest our results would be useful in informing the choice of mycorrhizal fungi indicator variables when assessing the impacts of grassland management choices on grassland ecosystem functioning.}, }
@article {pmid34753520, year = {2021}, author = {Estensmo, ELF and Morgado, L and Maurice, S and Martin-Sanchez, PM and Engh, IB and Mattsson, J and Kauserud, H and Skrede, I}, title = {Spatiotemporal variation of the indoor mycobiome in daycare centers.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {220}, pmid = {34753520}, issn = {2049-2618}, mesh = {Air Microbiology ; *Air Pollution, Indoor/analysis ; Child ; Dust/analysis ; Environmental Monitoring ; Fungi/genetics ; Humans ; *Mycobiome ; Seasons ; }, abstract = {BACKGROUND: Children spend considerable time in daycare centers in parts of the world and are exposed to the indoor micro- and mycobiomes of these facilities. The level of exposure to microorganisms varies within and between buildings, depending on occupancy, climate, and season. In order to evaluate indoor air quality, and the effect of usage and seasonality, we investigated the spatiotemporal variation in the indoor mycobiomes of two daycare centers. We collected dust samples from different rooms throughout a year and analyzed their mycobiomes using DNA metabarcoding.<br><br>RESULTS: The fungal community composition in rooms with limited occupancy (auxiliary rooms) was similar to the outdoor samples, and clearly different from the rooms with higher occupancy (main rooms). The main rooms had higher abundance of Ascomycota, while the auxiliary rooms contained comparably more Basidiomycota. We observed a strong seasonal pattern in the mycobiome composition, mainly structured by the outdoor climate. Most markedly, basidiomycetes of the orders Agaricales and Polyporales, mainly reflecting typical outdoor fungi, were more abundant during summer and fall. In contrast, ascomycetes of the orders Saccharomycetales and Capnodiales were dominant during winter and spring.<br><br>CONCLUSIONS: Our findings provide clear evidences that the indoor mycobiomes in daycare centers are structured by occupancy as well as outdoor seasonality. We conclude that the temporal variability should be accounted for in indoor mycobiome studies and in the evaluation of indoor air quality of buildings. Video abstract.}, }
@article {pmid34753204, year = {2022}, author = {Figueiredo, ART and Özkaya, &#xd6; and Kümmerli, R and Kramer, J}, title = {Siderophores drive invasion dynamics in bacterial communities through their dual role as public good versus public bad.}, journal = {Ecology letters}, volume = {25}, number = {1}, pages = {138-150}, pmid = {34753204}, issn = {1461-0248}, support = {681295//H2020 European Research Council/ ; 31003A_182499//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; KR 5017/2-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Ecosystem ; Humans ; Iron ; Oligopeptides ; Pseudomonas aeruginosa ; *Siderophores ; }, abstract = {Microbial invasions can compromise ecosystem services and spur dysbiosis and disease in hosts. Nevertheless, the mechanisms determining invasion outcomes often remain unclear. Here, we examine the role of iron-scavenging siderophores in driving invasions of Pseudomonas aeruginosa into resident communities of environmental pseudomonads. Siderophores can be 'public goods' by delivering iron to individuals possessing matching receptors; but they can also be 'public bads' by withholding iron from competitors lacking these receptors. Accordingly, siderophores should either promote or impede invasion, depending on their effects on invader and resident growth. Using supernatant feeding and invasion assays, we show that invasion success indeed increased when the invader could use its siderophores to inhibit (public bad) rather than stimulate (public good) resident growth. Conversely, invasion success decreased the more the invader was inhibited by the residents' siderophores. Our findings identify siderophores as a major driver of invasion dynamics in bacterial communities under iron-limited conditions.}, }
@article {pmid34751801, year = {2022}, author = {LaForgia, ML and Kang, H and Ettinger, CL}, title = {Correction to: Invasive Grass Dominance over Native Forbs Is Linked to Shifts in the Bacterial Rhizosphere Microbiome.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {509}, doi = {10.1007/s00248-021-01895-5}, pmid = {34751801}, issn = {1432-184X}, }
@article {pmid34750668, year = {2022}, author = {Deng, W and Yuan, CL and Li, N and Liu, SR and Yang, XY and Xiao, W}, title = {Island Formation History Determines Microbial Species-Area Relationships.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1055-1061}, pmid = {34750668}, issn = {1432-184X}, support = {31360013//National Natural Science Foundation of China/ ; 31760126//National Natural Science Foundation of China/ ; 2019QZKK2002//Second Tibetan Plateau Scientific Expedition and Research Program (STEP)/ ; }, mesh = {Animals ; *Biodiversity ; Trees ; Plants ; Plant Leaves ; *Microbiota ; }, abstract = {The species-area relationship (SAR) and its mechanisms regarding microbes are not as clear as those of plants and animals; this may result from the impact of sampling effects and the confusion between SAR and distance attenuation. We hypothesize that we can find more accurate microbial SAR curve, after removing these two factors. In this study, 27 leaves of three horticultural plants were selected as island models, and microbial biodiversity assessment was done with HTS (high-throughput sequencing). The separate and small systems using leaves as islands allow us to conduct a comprehensive survey of the microbial biodiversity of the leaves, without disturbance from sampling effects and distance attenuation effects. Interestingly, we did not find microbial SAR in those 27 leaves (also not found in evergreen trees Magnolia grandiflora and Eriobotrya japonica), but we did find significant microbial SAR in deciduous tree Ficus altissima. No significant differences were found between the different trees at the alpha diversity level of microbial biodiversity, but quite different on beta diversity. The results of beta diversity partition showed that F. altissima had the highest similarity of the microbial community among the leaves compared to those of M. grandiflora and E. japonica. Since leaf genesis in deciduous plants is more simultaneous than in evergreen plants; the result suggested that inconsistent historical background of leaf islands may mask microbial SAR. Thus, intensive sampling and consistent historical background are important for understanding microbial SAR.}, }
@article {pmid34748071, year = {2022}, author = {Majaneva, M and Rintala, JM and Blomster, J}, title = {Taxonomically and Functionally Distinct Ciliophora Assemblages Inhabiting Baltic Sea Ice.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {974-984}, pmid = {34748071}, issn = {1432-184X}, mesh = {*Ice Cover/parasitology ; Phylogeny ; *Ciliophora/genetics ; Ecosystem ; Seasons ; }, abstract = {Ciliophora is a phylum of unicellular eukaryotes that are common and have pivotal roles in aquatic environments. Sea ice is a marine habitat, which is composed of a matrix of solid ice and pockets of saline water in which Ciliophora thrive. Here, we used phylogenetic placement to identify Ciliophora 18S ribosomal RNA reads obtained from wintertime water and sea ice, and assigned functions to the reads based on this taxonomic information. Based on our results, sea-ice Ciliophora assemblages are poorer in taxonomic and functional richness than under-ice water and water-column assemblages. Ciliophora diversity stayed stable throughout the ice-covered season both in sea ice and in water, although the assemblages changed during the course of our sampling. Under-ice water and the water column were distinctly predominated by planktonic orders Choreotrichida and Oligotrichida, which led to significantly lower taxonomic and functional evenness in water than in sea ice. In addition to planktonic Ciliophora, assemblages in sea ice included a set of moderately abundant surface-oriented species. Omnivory (feeding on bacteria and unicellular eukaryotes) was the most common feeding type but was not as predominant in sea ice as in water. Sea ice included cytotrophic (feeding on unicellular eukaryotes), bacterivorous and parasitic Ciliophora in addition to the predominant omnivorous Ciliophora. Potentially mixotrophic Ciliophora predominated the water column and heterotrophic Ciliophora sea ice. Our results highlight sea ice as an environment that creates a set of variable habitats, which may be threatened by the diminishing extent of sea ice due to changing climate.}, }
@article {pmid34746021, year = {2021}, author = {Kang, X and Deng, DM and Crielaard, W and Brandt, BW}, title = {Reprocessing 16S rRNA Gene Amplicon Sequencing Studies: (Meta)Data Issues, Robustness, and Reproducibility.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {720637}, pmid = {34746021}, issn = {2235-2988}, mesh = {*Computational Biology ; Genes, rRNA ; *High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {High-throughput sequencing technology provides an efficient method for evaluating microbial ecology. Different bioinformatics pipelines can be used to convert 16S ribosomal RNA gene amplicon sequencing data into an operational taxonomic unit (OTU) table that is used to analyze microbial communities. It is important to assess the robustness of these pipelines, each with specific algorithms and/or parameters, and their influence on the outcome of statistical tests. Articles with publicly available datasets on the oral microbiome were searched for, and five datasets were retrieved. These were from studies on changes in microbiota related to smoking, oral cancer, caries, diabetes, or periodontitis. Next, the data was processed with four pipelines based on VSEARCH, USEARCH, mothur, and UNOISE3. OTU tables were rarefied, and differences in α-diversity and β-diversity were tested for different groups in a dataset. Finally, these results were checked for consistency among these example pipelines. Of articles that deposited data, only 57% made all sequencing and metadata available. When processing the datasets, issues were encountered, caused by read characteristics and differences between tools and their defaults in combination with a lack of detail in the methodology of the articles. In general, the four mainstream pipelines provided similar results, but importantly, P-values sometimes differed between pipelines beyond the significance threshold. Our results indicated that for published articles, the description of bioinformatics methods and data deposition should be improved, and regarding reproducibility, that analysis of multiple subsamples is required when using rarefying as library-size normalization method.}, }
@article {pmid34745150, year = {2021}, author = {Zhu, L and Wu, Y and Lin, C and Tang, L and Yu, B and Wan, W and Xuan, J and Du, Y and Chen, Z and Liang, W}, title = {Dynamic Microbial Shifts and Signatures of Long-Term Remission in Allergic Rhinitis After an Herbal Formula Treatment.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {774966}, pmid = {34745150}, issn = {1664-3224}, mesh = {Adolescent ; Adult ; Biomarkers ; Disease Management ; Disease Susceptibility ; Drugs, Chinese Herbal/*adverse effects/therapeutic use ; Dysbiosis/*diagnosis/*etiology ; Female ; Follow-Up Studies ; Gastrointestinal Microbiome/drug effects ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; RNA, Ribosomal, 16S ; Rhinitis, Allergic/*complications/drug therapy ; Young Adult ; }, abstract = {A mixed Chinese herbal formula, Xiao-Qing-Long-Decoction (XQLD), may contribute to sustained remission in allergic rhinitis (AR), but it is unknown which factors determine such long-term effect. Here, we aimed to identify bacterial signatures associated with sustained remission. To this end, samples from AR patients at four different times were analyzed to compare the dynamic bacterial community and structure shifts. Diversity indices Chao1 showed significant difference across different time (p<0.05), and the Kruskal-Wallis test identified that Dialister (OTU_31), Roseburia (OTU_36), Bacteroides (OTU_22), Bacteroides (OTU_2040), and Prevotella_9 (OTU_5) were the significant differential bacterial taxa (p<0.05). These distinctive genera were significantly associated with the change of AR clinical indices and the predicted functional pathways such as PPAR signaling pathway, peroxisome, and citrate cycle (TCA cycle) (p<0.05), indicating that they may be important bacterial signatures involving in the sustained remission in AR (p<0.05). Besides, lower Firmicutes/Bacteroidetes (F/B) ratio at 6 months follow-up may also contribute to the long-term remission of AR. No seriously adverse events and safety concerns were observed in this study. In conclusion, XQLD is a meaningful, long-term efficient and safe medication for AR treatment. The underlying mechanisms of sustained remission in AR after XQLD treatment may be associated with the dynamic alteration of featured gut bacteria taxa.}, }
@article {pmid34745040, year = {2021}, author = {Johnston-Monje, D and Gutiérrez, JP and Lopez-Lavalle, LAB}, title = {Seed-Transmitted Bacteria and Fungi Dominate Juvenile Plant Microbiomes.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {737616}, pmid = {34745040}, issn = {1664-302X}, abstract = {Plant microbiomes play an important role in agricultural productivity, but there is still much to learn about their provenance, diversity, and organization. In order to study the role of vertical transmission in establishing the bacterial and fungal populations of juvenile plants, we used high-throughput sequencing to survey the microbiomes of seeds, spermospheres, rhizospheres, roots, and shoots of the monocot crops maize (B73), rice (Nipponbare), switchgrass (Alamo), Brachiaria decumbens, wheat, sugarcane, barley, and sorghum; the dicot crops tomato (Heinz 1706), coffee (Geisha), common bean (G19833), cassava, soybean, pea, and sunflower; and the model plants Arabidopsis thaliana (Columbia-0) and Brachypodium distachyon (Bd21). Unsterilized seeds were planted in either sterile sand or farm soil inside hermetically sealed jars, and after as much as 60 days of growth, DNA was extracted to allow for amplicon sequence-based profiling of the bacterial and fungal populations that developed. Seeds of most plants were dominated by Proteobacteria and Ascomycetes, with all containing operational taxonomic units (OTUs) belonging to Pantoea and Enterobacter. All spermospheres also contained DNA belonging to Pseudomonas, Bacillus, and Fusarium. Despite having only seeds as a source of inoculum, all plants grown on sterile sand in sealed jars nevertheless developed rhizospheres, endospheres, and phyllospheres dominated by shared Proteobacteria and diverse fungi. Compared to sterile sand-grown seedlings, growth on soil added new microbial diversity to the plant, especially to rhizospheres; however, all 63 seed-transmitted bacterial OTUs were still present, and the most abundant bacteria (Pantoea, Enterobacter, Pseudomonas, Klebsiella, and Massilia) were the same dominant seed-transmitted microbes observed in sterile sand-grown plants. While most plant mycobiome diversity was observed to come from soil, judging by read abundance, the dominant fungi (Fusarium and Alternaria) were also vertically transmitted. Seed-transmitted fungi and bacteria appear to make up the majority of juvenile crop plant microbial populations by abundance, and based on occupancy, there seems to be a pan-angiosperm seed-transmitted core bacterial microbiome. Further study of these seed-transmitted microbes will be important to understand their role in plant growth and health, as well as their fate during the plant life cycle and may lead to innovations for agricultural inoculant development.}, }
@article {pmid34743196, year = {2021}, author = {Loh, JT and Lee, KG and Lee, AP and Teo, JKH and Lim, HL and Kim, SS and Tan, AH and Lam, KP}, title = {DOK3 maintains intestinal homeostasis by suppressing JAK2/STAT3 signaling and S100a8/9 production in neutrophils.}, journal = {Cell death &amp; disease}, volume = {12}, number = {11}, pages = {1054}, pmid = {34743196}, issn = {2041-4889}, support = {OFYIRG17nov055//MOH | National Medical Research Council (NMRC)/ ; NMRC/OFIRG19may-0083//MOH | National Medical Research Council (NMRC)/ ; NMRC/OFYIRG/083/2018//MOH | National Medical Research Council (NMRC)/ ; NMRC/OFIRG19may-0083//MOH | National Medical Research Council (NMRC)/ ; }, mesh = {Adaptor Proteins, Signal Transducing/deficiency/*metabolism ; Animals ; Calgranulin A/*metabolism ; Calgranulin B/*metabolism ; Colitis/genetics/pathology ; Disease Models, Animal ; Disease Susceptibility ; Dysbiosis/complications/microbiology ; Gene Expression Regulation ; *Homeostasis ; Intestinal Mucosa/pathology ; Intestines/*metabolism/microbiology/pathology ; Janus Kinase 2/*metabolism ; Mice ; Microbiota ; Neutrophils/*metabolism ; STAT3 Transcription Factor/*metabolism ; Signal Transduction ; }, abstract = {How pathogenesis of inflammatory bowel disease (IBD) depends on the complex interplay of host genetics, microbiome and the immune system is not fully understood. Here, we showed that Downstream of Kinase 3 (DOK3), an adapter protein involved in immune signaling, confers protection of mice from dextran sodium sulfate (DSS)-induced colitis. DOK3-deficiency promotes gut microbial dysbiosis and enhanced colitis susceptibility, which can be reversed by the transfer of normal microbiota from wild-type mice. Mechanistically, DOK3 exerts its protective effect by suppressing JAK2/STAT3 signaling in colonic neutrophils to limit their S100a8/9 production, thereby maintaining gut microbial ecology and colon homeostasis. Hence, our findings reveal that the immune system and microbiome function in a feed-forward manner, whereby DOK3 maintains colonic neutrophils in a quiescent state to establish a gut microbiome essential for intestinal homeostasis and protection from IBD.}, }
@article {pmid34743174, year = {2022}, author = {Sakoula, D and Smith, GJ and Frank, J and Mesman, RJ and Kop, LFM and Blom, P and Jetten, MSM and van Kessel, MAHJ and Lücker, S}, title = {Universal activity-based labeling method for ammonia- and alkane-oxidizing bacteria.}, journal = {The ISME journal}, volume = {16}, number = {4}, pages = {958-971}, pmid = {34743174}, issn = {1751-7370}, support = {339880//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 016.Vidi.189.050//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; SIAM 024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 016.Veni.192.062//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 339880//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Euratom (H2020 Euratom Research and Training Programme 2014-2018)/ ; }, mesh = {*Alkanes/metabolism ; *Ammonia/metabolism ; Archaea/genetics ; Bacteria ; In Situ Hybridization, Fluorescence ; Mixed Function Oxygenases/metabolism ; Oxidation-Reduction ; Phylogeny ; }, abstract = {The advance of metagenomics in combination with intricate cultivation approaches has facilitated the discovery of novel ammonia-, methane-, and other short-chain alkane-oxidizing microorganisms, indicating that our understanding of the microbial biodiversity within the biogeochemical nitrogen and carbon cycles still is incomplete. The in situ detection and phylogenetic identification of novel ammonia- and alkane-oxidizing bacteria remain challenging due to their naturally low abundances and difficulties in obtaining new isolates from complex samples. Here, we describe an activity-based protein profiling protocol allowing cultivation-independent unveiling of ammonia- and alkane-oxidizing bacteria. In this protocol, 1,7-octadiyne is used as a bifunctional enzyme probe that, in combination with a highly specific alkyne-azide cycloaddition reaction, enables the fluorescent or biotin labeling of cells harboring active ammonia and alkane monooxygenases. Biotinylation of these enzymes in combination with immunogold labeling revealed the subcellular localization of the tagged proteins, which corroborated expected enzyme targets in model strains. In addition, fluorescent labeling of cells harboring active ammonia or alkane monooxygenases provided a direct link of these functional lifestyles to phylogenetic identification when combined with fluorescence in situ hybridization. Furthermore, we show that this activity-based labeling protocol can be successfully coupled with fluorescence-activated cell sorting for the enrichment of nitrifiers and alkane-oxidizing bacteria from complex environmental samples, enabling the recovery of high-quality metagenome-assembled genomes. In conclusion, this study demonstrates a novel, functional tagging technique for the reliable detection, identification, and enrichment of ammonia- and alkane-oxidizing bacteria present in complex microbial communities.}, }
@article {pmid34742956, year = {2022}, author = {Fu, Y and Wang, F and Wang, Z and Mei, Z and Jiang, X and Schäffer, A and Virta, M and Tiedje, JM}, title = {Application of magnetic biochar/quaternary phosphonium salt to combat the antibiotic resistome in livestock wastewater.}, journal = {The Science of the total environment}, volume = {811}, number = {}, pages = {151386}, doi = {10.1016/j.scitotenv.2021.151386}, pmid = {34742956}, issn = {1879-1026}, mesh = {Animals ; Anti-Bacterial Agents ; Charcoal ; Genes, Bacterial ; Humans ; *Livestock ; Magnetic Phenomena ; *Wastewater ; }, abstract = {The overuse and misuse of antibiotics in animal breeding for disease treatment and growth enhancement have been major drivers of the occurrence, diffusion, and accumulation of antibiotic resistance genes (ARGs) in wastewater. Strategies to combat ARG dissemination are pressingly needed for human and ecological safety. To achieve this goal, a biochar-based polymer, magnetic biochar/quaternary phosphonium salt (MBQ), was applied in livestock wastewater and displayed a high performance in bacterial deactivation and ARG decrease. Efficient antibacterial effects were achieved by both MBQ and quaternary phosphonium salt; however, the abundance and fold change of ARGs in the MBQ treatment indicated a more powerful ARG dissemination control than quaternary phosphonium salt. The application of MBQ evidently reduced the microbial diversity and may primarily be responsible for altering the ARG profiles in wastewater. Network, redundancy, and variation partitioning analyses were further employed to reveal that the microbial community and the presence of mobile genetic elements were two critical factors shaping the pattern of the antibiotic resistome in livestock wastewater. Considered together, these findings extend the application field of biochar and have important implications for reducing ARG dissemination risks in livestock wastewater.}, }
@article {pmid34741647, year = {2022}, author = {Rosca, AS and Castro, J and França, &#xc2; and Vaneechoutte, M and Cerca, N}, title = {Gardnerella Vaginalis Dominates Multi-Species Biofilms in both Pre-Conditioned and Competitive In Vitro Biofilm Formation Models.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1278-1287}, pmid = {34741647}, issn = {1432-184X}, mesh = {Humans ; Female ; *Gardnerella vaginalis/genetics ; In Situ Hybridization, Fluorescence ; *Vaginosis, Bacterial/microbiology ; Biofilms ; Vagina/microbiology ; Bacteria ; }, abstract = {Bacterial vaginosis (BV) is one of the most common bacterial vaginal infections worldwide. Despite its high prevalence, BV etiology is still unknown. Nevertheless, a hallmark of BV is the presence of a highly structured polymicrobial biofilm on the vaginal epithelium, formed primarily by Gardnerella spp. and other anaerobic species, of which co-colonization with Fannyhessea vaginae is considered an important diagnostic marker. We previously developed an in vitro biofilm model wherein Gardnerella was first allowed to establish an early biofilm that served as a scaffold for other species to adhere to. To better understand ecological interactions between BV-associated bacteria, we compared triple-species biofilms formed using two distinct models: a pre-conditioned (wherein Gardnerella vaginalis formed the early biofilm) model and a competitive (wherein all three bacteria were co-incubated together) model. Interestingly, synergistic growth interactions were more significant in the competitive model. Furthermore, the biofilm structure and species-specific distribution, as assessed by confocal laser scanning microscopy and using peptide nucleic acid fluorescence in situ hybridization method, revealed two very different triple-species morphotypes, suggesting that different interactions occur in the different models. Interestingly, independent of the model or triple-species consortium tested, we observed that G. vaginalis represented most of the biofilm bacterial composition, further highlighting the relevance of this taxon in BV.}, }
@article {pmid34741646, year = {2022}, author = {Zakharova, Y and Bashenkhaeva, M and Galachyants, Y and Petrova, D and Tomberg, I and Marchenkov, A and Kopyrina, L and Likhoshway, Y}, title = {Variability of Microbial Communities in Two Long-Term Ice-Covered Freshwater Lakes in the Subarctic Region of Yakutia, Russia.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {958-973}, pmid = {34741646}, issn = {1432-184X}, support = {0297-2021-0023//State Assignments of the Institute for Biological Problems of Cryolithozone/ ; 21-121012190038-0//State Assignments of the Institute for Biological Problems of Cryolithozone/ ; 0279-2021-0008//State Assignments of the Limnological Institute/ ; 121032300186-9//State Assignments of the Limnological Institute/ ; }, mesh = {Humans ; Lakes/microbiology ; RNA, Ribosomal, 16S/genetics ; Ice Cover/microbiology ; *Microbiota ; *Cyanobacteria/genetics ; Proteobacteria/genetics ; Verrucomicrobia/genetics ; }, abstract = {Although under-ice microbial communities are subject to a cold environment, low concentrations of nutrients, and a lack of light, they nevertheless take an active part in biogeochemical cycles. However, we still lack an understanding of how high their diversity is and how these communities are distributed during the long-term ice-cover period. Here, we assessed for the first time the composition and distribution of microbial communities during the ice-cover period in two subarctic lakes (Labynkyr and Vorota) located in the area of the lowest temperature in the Northern Hemisphere. The diversity distribution and abundance of main bacterial taxa as well as the composition of microalgae varied by time and habitat. The 16S rRNA gene sequencing method revealed, in general, a high diversity of bacterial communities where Proteobacteria (~ 45%) and Actinobacteria (~ 21%) prevailed. There were significant differences between the communities of the lakes: Chthoniobacteraceae, Moraxellaceae, and Pirellulaceae were abundant in Lake Labynkyr, while Cyanobiaceae, Oligoflexales, Ilumatobacteraceae, and Methylacidiphilaceae were more abundant in Lake Vorota. The most abundant families were evenly distributed in April, May, and June their contribution was different in different habitats. In April, Moraxellaceae and Ilumatobacteraceae were the most abundant in the water column, while Sphingomonadaceae was abundant both in water column and on the ice bottom. In May, the abundance of Comamonadaceae increased and reached the maximum in June, while Cyanobiaceae, Oxalobacteraceae, and Pirellulaceae followed. We found a correlation of the structure of bacterial communities with snow thickness, pH, Nmin concentration, and conductivity. We isolated psychrophilic heterotrophic bacteria both from dominating and minor taxa of the communities studied. This allowed for specifying their ecological function in the under-ice communities. These findings will advance our knowledge of the under-ice microbial life.}, }
@article {pmid34741645, year = {2022}, author = {Skrodenytė-Arbačiauskienė, V and Virbickas, T and Lukša, J and Servienė, E and Blažytė-Čereškienė, L and Kesminas, V}, title = {Gut Microbiome of Wild Baltic Salmon (Salmo salar L.) Parr.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1294-1298}, pmid = {34741645}, issn = {1432-184X}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Salmo salar ; Bacteria/genetics ; Firmicutes/genetics ; *Actinobacteria/genetics ; }, abstract = {Gut microbiota of wild Baltic salmon (a sub-population of Atlantic salmon Salmo salar L.) parr was first analyzed using microbial profiling of the 16S rRNA gene (V3-V4 region) and high taxonomic richness was revealed. At the phylum level, the gut microbiota was dominated by Firmicutes, Actinobacteria, and Proteobacteria, the most numerous of which were Firmicutes. The phylum Tenericutes (mainly assigned to Mycoplasmataceae), which is common both in wild North- and East- Atlantic salmon parr, was not detected in Baltic salmon parr. Across all samples, unique amplicon sequence variants (ASVs) belonging to the unclassified Bacilli, Actinomycetales, and Rhizobiales were identified as the major taxa. Fifteen ASVs at the family level were found in all gut samples of Baltic salmon parr, the majority of which were Mycobacteriaceae, Cryptosporangiaceae, Microbacteriaceae, and Planctomycetaceae. At the genus level, Mycobacterium, Clostridium sensu stricto, and Hyphomicrobium were dominant but at low levels in all gut samples. Our study has revealed that the gut microbial community of wild Baltic salmon parr differs from those of wild North- and East-Atlantic salmon parr. This can be due to biogeographical differences or host-selective pressures, as the Baltic salmon population is believed to have split from the Atlantic salmon population in the Ancylian period.}, }
@article {pmid34741194, year = {2022}, author = {Yang, YZ and Luo, MX and Yan, HX and Gao, RH and Chang, JT and Chao, CT and Liao, PC}, title = {Physicochemical and Biotic Changes and the Phylogenetic Evenness of Microbial Community in Soil Subjected to Phytoreclamation.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1182-1194}, pmid = {34741194}, issn = {1432-184X}, support = {NSFC31760120//national natural science foundation of china/ ; MOST 109-2621-B-003-003-MY3//ministry of science and technology, taiwan/ ; MOST 109-2628-B-003-001//ministry of science and technology, taiwan/ ; }, mesh = {Phylogeny ; *Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Rhizosphere ; *Microbiota/genetics ; Plants ; Plant Roots ; }, abstract = {Phytoreclamation is the intervention of plants to improve degraded soil quality, changing soil biotic and abiotic properties. Many studies have focused on microbial composition and bioactivity, but few explored the changes in phylogenetic assemblages of soil microbiota after phytoreclamation. This study compared microbiomes of bare land to those of planted soils and investigated how the rhizosphere environment affects microbial assemblages from monocot Poa pratensis and eudicot Dianthus plumarius plantings using 16S rRNA metabarcoding. The results showed that the biotic susceptibility of soil to the rhizosphere environment was higher than that of the abiotic. A noticeable change was in some soil physicochemical properties like Na, P, Zn, Cu, C, and sand-to-silt proportion before and after phytoreclamation, but not between the rhizosphere and bulk soil of plantings. Contrastingly, microbial composition and diversity were significantly affected by both turfing and rhizosphere effects and were more susceptible to differences in turfing or not than in planting species. In the turfgrass, the microbiome differences between plants were greater in the rhizosphere than in the surrounding bulk soil, indicating the proximal influence of root exudates. We also found that the main abiotic factors that influenced microbial composition were Na, Zn, NOx, N, and S; as for the phylogenetic assemblages, were by K levels and the increase of silt. Turfgrass decomposes soil aggregates and changes the physicochemical properties, thereby evens the phylogenetic clustering of the soil microbial community. We demonstrated that the deterministic process affects the microbial assemblage and acts as a selective agent of the soil microbiota in fundamental and realized niches. Phytoreclamation may lead to abiotic soil changes that reallocate resources to microbes. This could affect the phylogeny of the microbial assemblages and increase microbial richness.}, }
@article {pmid34740326, year = {2021}, author = {Ayala-Usma, DA and Cárdenas, M and Guyot, R and Mares, MC and Bernal, A and Muñoz, AR and Restrepo, S}, title = {A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {795}, pmid = {34740326}, issn = {1471-2164}, support = {BB/P027849/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; INV-2018-34-1310//Facultad de Ciencias, Universidad de los Andes/ ; 120471250765//Departamento Administrativo de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n (COLCIENCIAS)/ ; }, mesh = {DNA Transposable Elements ; Evolution, Molecular ; Gene Duplication ; Phylogeny ; *Phytophthora infestans/genetics ; Plant Diseases ; *Solanum tuberosum/genetics ; }, abstract = {BACKGROUND: Pathogens of the genus Phytophthora are the etiological agents of many devastating diseases in several high-value crops and forestry species such as potato, tomato, cocoa, and oak, among many others. Phytophthora betacei is a recently described species that causes late blight almost exclusively in tree tomatoes, and it is closely related to Phytophthora infestans that causes the disease in potato crops and other Solanaceae. This study reports the assembly and annotation of the genomes of P. betacei P8084, the first of its species, and P. infestans RC1-10, a Colombian strain from the EC-1 lineage, using long-read SMRT sequencing technology.<br><br>RESULTS: Our results show that P. betacei has the largest sequenced genome size of the Phytophthora genus so far with 270&#xa0;Mb. A moderate transposable element invasion and a whole genome duplication likely explain its genome size expansion when compared to P. infestans, whereas P. infestans RC1-10 has expanded its genome under the activity of transposable elements. The high diversity and abundance (in terms of copy number) of classified and unclassified transposable elements in P. infestans RC1-10 relative to P. betacei bears testimony of the power of long-read technologies to discover novel repetitive elements in the genomes of organisms. Our data also provides support for the phylogenetic placement of P. betacei as a standalone species and as a sister group of P. infestans. Finally, we found no evidence to support the idea that the genome of P. betacei P8084 follows the same gene-dense/gense-sparse architecture proposed for P. infestans and other filamentous plant pathogens.<br><br>CONCLUSIONS: This study provides the first genome-wide picture of P. betacei and expands the genomic resources available for P. infestans. This is a contribution towards the understanding of the genome biology and evolutionary history of Phytophthora species belonging to the subclade 1c.}, }
@article {pmid34739925, year = {2022}, author = {Leonard, AF and Morris, D and Schmitt, H and Gaze, WH}, title = {Natural recreational waters and the risk that exposure to antibiotic resistant bacteria poses to human health.}, journal = {Current opinion in microbiology}, volume = {65}, number = {}, pages = {40-46}, doi = {10.1016/j.mib.2021.10.004}, pmid = {34739925}, issn = {1879-0364}, support = {MR/S037713/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Animals ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Bacterial ; Drug Resistance, Microbial/genetics ; Humans ; }, abstract = {Antimicrobial resistance (AMR) is widely recognised as a considerable threat to human health, wellbeing and prosperity. Many clinically important antibiotic resistance genes are understood to have originated in the natural environment. However, the complex interactions between humans, animals and the environment makes the health implications of environmental AMR difficult to quantify. This narrative review focuses on the current state of knowledge regarding antibiotic resistant bacteria (ARB) in natural bathing waters and implications for human health. It considers the latest research focusing on the transmission of ARB from bathing waters to humans. The limitations of existing evidence are discussed, as well as research priorities. The authors are of the opinion that future studies should include faecally contaminated bathing waters and people exposed to these environments to accurately parameterise environment-to-human transmission.}, }
@article {pmid34738157, year = {2022}, author = {Khan, AA and Farooq, F and Jain, SK and Golinska, P and Rai, M}, title = {Comparative Host-Pathogen Interaction Analyses of SARS-CoV2 and Aspergillus fumigatus, and Pathogenesis of COVID-19-Associated Aspergillosis.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1236-1244}, pmid = {34738157}, issn = {1432-184X}, mesh = {Humans ; Aspergillus fumigatus ; RNA, Viral ; *COVID-19 ; SARS-CoV-2 ; *Aspergillosis ; Host-Pathogen Interactions ; }, abstract = {COVID-19 caused a global catastrophe with a large number of cases making it one of the major pandemics of the human history. The clinical presentations of the disease are continuously challenging healthcare workers with the variation of pandemic waves and viral variants. Recently, SARS-CoV2 patients have shown increased occurrence of invasive pulmonary aspergillosis infection even in the absence of traditional risk factors. The mechanism of COVID-19-associated aspergillosis is not completely understood and therefore, we performed this system biological study in order to identify mechanistic implications of aspergillosis susceptibility in COVID-19 patients and the important targets associated with this disease. We performed host-pathogen interaction (HPI) analysis of SARS-CoV2, and most common COVID-19-associated aspergillosis pathogen, Aspergillus fumigatus, using in silico approaches. The known host-pathogen interactions data of SARS-CoV2 was obtained from BIOGRID database. In addition, A. fumigatus host-pathogen interactions were predicted through homology modeling. The human targets interacting with both pathogens were separately analyzed for their involvement in aspergillosis. The aspergillosis human targets were screened from DisGeNet and GeneCards. The aspergillosis targets involved in both HPI were further analyzed for functional overrepresentation analysis using PANTHER. The results indicate that both pathogens interact with a number of aspergillosis targets and altogether they recruit more aspergillosis targets in host-pathogen interaction than alone. Common aspergillosis targets involved in HPI with both SARS-CoV2 and A. fumigatus can indicate strategies for the management of both conditions by modulating these common disease targets.}, }
@article {pmid34737136, year = {2022}, author = {Lin, Q and De Vrieze, J and Fang, X and Li, L and Li, X}, title = {Labile carbon feedstocks trigger a priming effect in anaerobic digestion: An insight into microbial mechanisms.}, journal = {Bioresource technology}, volume = {344}, number = {Pt B}, pages = {126243}, doi = {10.1016/j.biortech.2021.126243}, pmid = {34737136}, issn = {1873-2976}, mesh = {Anaerobiosis ; Animals ; *Biofuels ; Carbon ; Manure ; *Methane ; Swine ; }, abstract = {The mechanisms underlying the advanced performance in anaerobic co-digestion (AcoD) are crucial but remain elusive. This study conducted AcoD of swine manure, rice straw and apple waste (AW, mainly consisting of labile carbon) or fructose (a pure labile carbon), and monitored microbial community abundances, activities and transcriptional profiles in the digestate and on straw. The transformation efficiencies of manure (not straw) to CH4 were promoted in AcoD co-fed manure and AW (by 39 ± 13%) or fructose (by 65 ± 14%), compared to the control mono-fed manure, implying labile carbon could trigger a priming effect underlying AcoD advantage. Although digestate-associated and straw-associated communities existed in a same bioreactor, the priming effect mainly linked to the former and was attributed to enhancements in deterministic turnover of active communities, in activities of Firmicutes taxa involved in substrate hydrolysis, and in acetoclastic methanogenesis. These findings provide novel insights to elaborate AcoD processes.}, }
@article {pmid34736408, year = {2021}, author = {Wang, M and Yang, C and Wei, K and Zhao, M and Shen, L and Ji, J and Wang, L and Zhang, D and Guo, J and Zheng, Y and Yu, J and Zhu, M and Liu, H and Li, YF}, title = {Temporal expression study of miRNAs in the crown tissues of winter wheat grown under natural growth conditions.}, journal = {BMC genomics}, volume = {22}, number = {Suppl 3}, pages = {793}, pmid = {34736408}, issn = {1471-2164}, support = {NO.31771703 &amp; 31601241//National Natural Science Foundation of China (CN)/ ; }, mesh = {Gene Expression Profiling ; Gene Expression Regulation, Plant ; Humans ; Meristem ; *MicroRNAs/genetics ; *Triticum/genetics ; }, abstract = {BACKGROUND: Winter wheat requires prolonged exposure to low temperature to initiate flowering (vernalization). Shoot apical meristem of the crown is the site of cold perception, which produces leaf primordia during vegetative growth before developing into floral primordia at the initiation of the reproductive phase. Although many essential genes for winter wheat cold acclimation and floral initiation have been revealed, the importance of microRNA (miRNA) meditated post-transcriptional regulation in crowns is not well understood. To understand the potential roles of miRNAs in crown tissues, we performed a temporal expression study of miRNAs in crown tissues at the three-leaf stage, winter dormancy stage, spring green-up stage, and jointing stage of winter wheat grown under natural growth conditions.<br><br>RESULTS: In total, 348 miRNAs belonging to 298 miRNA families, were identified in wheat crown tissues. Among them, 92 differentially expressed miRNAs (DEMs) were found to be significantly regulated from the three-leaf stage to the jointing stage. Most of these DEMs were highly expressed at the three-leaf stage and winter dormancy stage, and then declined in later stages. Six DEMs, including miR156a-5p were markedly induced during the winter dormancy stage. Eleven DEMs, including miR159a.1, miR390a-5p, miR393-5p, miR160a-5p, and miR1436, were highly expressed at the green-up stage. Twelve DEMs, such as miR172a-5p, miR394a, miR319b-3p, and miR9676-5p were highly induced at the jointing stage. Moreover, 14 novel target genes of nine wheat or Pooideae-specific miRNAs were verified using RLM-5' RACE assay. Notably, six mTERFs and two Rf1 genes, which are associated with mitochondrial gene expression, were confirmed as targets of three wheat-specific miRNAs.<br><br>CONCLUSIONS: The present study not only confirmed the known miRNAs associated with phase transition and floral development, but also identified a number of wheat or Pooideae-specific miRNAs critical for winter wheat cold acclimation and floral development. Most importantly, this study provided experimental evidence that miRNA could regulate mitochondrial gene expression by targeting mTERF and Rf1 genes. Our study provides valuable information for further exploration of the mechanism of miRNA mediated post-transcriptional regulation during winter wheat vernalization and inflorescent initiation.}, }
@article {pmid34735986, year = {2022}, author = {Schnorr, SL and Berry, D}, title = {Lipid synthesis at the trophic base as the source for energy management to build complex structures.}, journal = {Current opinion in biotechnology}, volume = {73}, number = {}, pages = {364-373}, doi = {10.1016/j.copbio.2021.09.014}, pmid = {34735986}, issn = {1879-0429}, mesh = {Aged ; *Biological Evolution ; *Ecosystem ; Humans ; Lipids ; }, abstract = {The review explores the ecological basis for bacterial lipid metabolism in marine and terrestrial ecosystems. We discuss ecosystem stressors that provoked early organisms to modify their lipid membrane structures, and where these stressors are found across a variety of environments. A major role of lipid membranes is to manage cellular energy utility, including how energy is used for signal propagation. As different environments are imbued with properties that necessitate variation in energy regulation, bacterial lipid synthesis has undergone incalculable permutations of functional trial and error. This may hold clues for how biotechnology can improvise a short-hand version of the evolutionary gauntlet to stimulate latent functional competences for the synthesis of rare lipids. Reducing human reliance on marine resources and deriving solutions for production of essential nutrients is a pressing problem in sustainable agriculture and aquaculture, as well as timely considering the increasing fragility of human health in an aging population.}, }
@article {pmid34735604, year = {2022}, author = {Wagener, C and du Plessis, M and Measey, J}, title = {Invasive Amphibian Gut Microbiota and Functions Shift Differentially in an Expanding Population but Remain Conserved Across Established Populations.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1042-1054}, pmid = {34735604}, issn = {1432-184X}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; South Africa ; *Microbiota/genetics ; Bufonidae ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Studies of laboratory animals demonstrate extensive variation of host gut microbiomes and their functional capabilities across populations, but how does anthropogenic change impact the microbiomes of non-model species? The anthropogenic movement of species to novel environments can drastically alter animals' microbiomes; however, factors that shape invasive species gut microbiota during introduction remain relatively unexplored. Through 16S amplicon sequencing on guttural toad (Sclerophrys gutturalis) faecal samples, we determine that residence time does not impact microbiome variation between source and introduced populations. The youngest population (~ 20 years in Cape Town) has the most distinct microbiome and associated functional capabilities, whereas longer residence times (~ 100 years in Réunion and Mauritius) produce less divergent microbial compositional, phylogenetic, and predicted functional diversity and differential abundance from source populations (Durban). Additionally, we show extensive variation of microbial and functional diversity, as well as differential abundance patterns in an expanding introduced population (Cape Town) between core and periphery sites. Contrasting previous studies, we suggest that introduction pathways might be an important factor impacting host microbial divergence. These findings also imply that the microbiome can diverge in accordance with host population dynamics.}, }
@article {pmid34734290, year = {2021}, author = {Higuita Palacio, MF and Montoya, OI and Saldamando, CI and García-Bonilla, E and Junca, H and Cadavid-Restrepo, GE and Moreno-Herrera, CX}, title = {Dry and Rainy Seasons Significantly Alter the Gut Microbiome Composition and Reveal a Key Enterococcus sp. (Lactobacillales: Enterococcaceae) Core Component in Spodoptera frugiperda (Lepidoptera: Noctuidae) Corn Strain From Northwestern Colombia.}, journal = {Journal of insect science (Online)}, volume = {21}, number = {6}, pages = {}, pmid = {34734290}, issn = {1536-2442}, mesh = {Animals ; Colombia ; *Enterococcus ; *Gastrointestinal Microbiome ; Larva ; *Seasons ; Spodoptera/*microbiology ; Zea mays ; }, abstract = {Spodoptera frugiperda is a polyphagous pest of several crops of economic importance. Nowadays, the insect is broadly distributed in America and, recently, in Africa, Asia, and Australia. The species has diverged into corn and rice strains. The role of the gut microbiota in insect physiology is relevant due to its participation in crucial functions. However, knowledge of seasonal variations that alter the gut microbiome in pests is limited. Gut microbiome composition between the dry and rainy seasons was analyzed with cultured and uncultured approaches in S. frugiperda corn strain larvae collected at Northwest Colombia, as seasonal microbiome changes might fluctuate due to environmental changes. On the basis of culture-dependent methods, results show well-defined microbiota with bacterial isolates belonging to Enterococcus, Klebsiella (Enterobacteriales: Enterobacteriaceae), Enterobacter (Enterobacterales: Enterobacteriaceae), and Bacillus (Bacillales: Bacillaceae) genera. The community composition displayed a low bacterial diversity across all samples. The core community detected with uncultured methods was composed of Enterococcus, Erysipelatoclostridium (Erysipelotrichales: Erysipelotrichaceae), Rasltonia (Burkholderiales: Burkholderiaceae), and Rhizobium (Hyphomicrobiales: Rhizobiaceae) genera, and Enterobacteriaceae family members. Significant differences in microbiome diversity were observed between the two seasons. The relative abundance of Erysipelatoclostridium was high in the dry season, while in the phylotype ZOR0006 (Erysipelotrichales: Erysipelotrichaceae) and Tyzzerella (Lachnospirales: Lachnospiraceae) genus, the relative abundance was high in the rainy season. The overall low gut bacterial diversity observed in the S. frugiperda corn strain suggests a strong presence of antagonist activity as a selection factor possibly arising from the host, the dominant bacterial types, or the material ingested. Targeting the stability and predominance of this core microbiome could be an additional alternative to pest control strategies, particularly in this moth.}, }
@article {pmid34732568, year = {2021}, author = {Ortiz, M and Leung, PM and Shelley, G and Jirapanjawat, T and Nauer, PA and Van Goethem, MW and Bay, SK and Islam, ZF and Jordaan, K and Vikram, S and Chown, SL and Hogg, ID and Makhalanyane, TP and Grinter, R and Cowan, DA and Greening, C}, title = {Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {45}, pages = {}, pmid = {34732568}, issn = {1091-6490}, mesh = {Antarctic Regions ; Autotrophic Processes ; Biodiversity ; *Desert Climate ; Gases/*metabolism ; Hydrogenase/metabolism ; Ice Cover/*microbiology ; Metagenome ; *Microbiota ; Oxidation-Reduction ; Phototrophic Processes ; *Soil Microbiology ; }, abstract = {Numerous diverse microorganisms reside in the cold desert soils of continental Antarctica, though we lack a holistic understanding of the metabolic processes that sustain them. Here, we profile the composition, capabilities, and activities of the microbial communities in 16 physicochemically diverse mountainous and glacial soils. We assembled 451 metagenome-assembled genomes from 18 microbial phyla and inferred through Bayesian divergence analysis that the dominant lineages present are likely native to Antarctica. In support of earlier findings, metagenomic analysis revealed that the most abundant and prevalent microorganisms are metabolically versatile aerobes that use atmospheric hydrogen to support aerobic respiration and sometimes carbon fixation. Surprisingly, however, hydrogen oxidation in this region was catalyzed primarily by a phylogenetically and structurally distinct enzyme, the group 1l [NiFe]-hydrogenase, encoded by nine bacterial phyla. Through gas chromatography, we provide evidence that both Antarctic soil communities and an axenic Bacteroidota isolate (Hymenobacter roseosalivarius) oxidize atmospheric hydrogen using this enzyme. Based on ex situ rates at environmentally representative temperatures, hydrogen oxidation is theoretically sufficient for soil communities to meet energy requirements and, through metabolic water production, sustain hydration. Diverse carbon monoxide oxidizers and abundant methanotrophs were also active in the soils. We also recovered genomes of microorganisms capable of oxidizing edaphic inorganic nitrogen, sulfur, and iron compounds and harvesting solar energy via microbial rhodopsins and conventional photosystems. Obligately symbiotic bacteria, including Patescibacteria, Chlamydiae, and predatory Bdellovibrionota, were also present. We conclude that microbial diversity in Antarctic soils reflects the coexistence of metabolically flexible mixotrophs with metabolically constrained specialists.}, }
@article {pmid34731961, year = {2022}, author = {Esquivel-Hernández, DA and García-Pérez, JS and López-Pacheco, IY and Iqbal, HMN and Parra-Saldívar, R}, title = {Resource recovery of lignocellulosic biomass waste into lactic acid - Trends to sustain cleaner production.}, journal = {Journal of environmental management}, volume = {301}, number = {}, pages = {113925}, doi = {10.1016/j.jenvman.2021.113925}, pmid = {34731961}, issn = {1095-8630}, mesh = {Biomass ; Fermentation ; Hydrolysis ; *Lactic Acid ; *Lignin/metabolism ; }, abstract = {Biomass waste generation concerns regulatory authorities to develop novel methods to sustain biotransformation processes. Particularly, lactic acid (LA) is a bulk commodity chemical used in diverse industries and holds a growing global market demand. Recently, lignocellulosic waste biomass is preferred for LA bio-production because of its non-edible and inexpensive nature. However, the information about new pretreatment methods for lignocellulosic feedstock, and novel strains capable to produce LA through fermentation is limited. Therefore, this review highlights the advancement of pretreatments methods of lignocellulosic biomass and biotransformation. Herein, we first briefly explored the main sources of lignocellulosic waste biomass, then we explored their latest advances in pretreatment processes particularly supercritical fluid extraction, and microwave-assisted extraction. Approaches for bioconversion were also analyzed, such as consolidated bioprocessing (CBP), simultaneous saccharification and fermentation (SSF), separate hydrolysis fermentation (SHF), among other alternatives. Also, new trends and approaches were documented, such as metagenomics to find novel strains of microorganisms and the use of recombinant strategies for the creation of new strains. Finally, we developed a holistic and sustainable perspective based on novel microbial ecology tools such as next-gen sequencing, bioinformatics, and metagenomics. All these shed light on the needs to culture powerful microbial isolates, co-cultures, and mixed consortia to improve fermentation processes with the aim of optimizing cultures and feedstock pretreatments.}, }
@article {pmid34731271, year = {2022}, author = {Li, J and Weinberger, F and Saha, M and Majzoub, ME and Egan, S}, title = {Cross-Host Protection of Marine Bacteria Against Macroalgal Disease.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1288-1293}, pmid = {34731271}, issn = {1432-184X}, support = {57381332//Deutscher Akademischer Austauschdienst/ ; }, mesh = {Animals ; *Rhodophyta ; *Seaweed ; *Rhodobacteraceae ; *Microbiota ; *Probiotics ; }, abstract = {Despite an increasing awareness of disease impacts on both cultivated and native seaweed populations, the development of marine probiotics has been limited and predominately focused on farmed animals. Bleaching (loss of thallus pigmentation) is one of the most prevalent diseases observed in marine macroalgae. Endemic probiotic bacteria have been characterized to prevent bleaching disease in red macroalgae Agarophyton vermiculophyllum and Delisea pulchra; however, the extent to which probiotic strains provide cross-protection to non-endemic hosts and the influence of native microbiota remain unknown. Using A. vermiculophyllum as a model, we demonstrate that co-inoculation with the pathogen Pseudoalteromonas arctica G-MAN6 and D. pulchra probiotic strain Phaeobacter sp. BS52 or Pseudoalteromonas sp. PB2-1 reduced the disease risks compared to the pathogen only treatment. Moreover, non-endemic probiotics outperformed the endemic probiotic strain Ralstonia sp. G-NY6 in the presence of the host natural microbiota. This study highlights how the native microbiota can impact the effectiveness of marine probiotics and illustrates the potential of harnessing probiotics that can function across different hosts to mitigate the impact of emerging marine diseases.}, }
@article {pmid34727719, year = {2021}, author = {Duxbury, SJN and Alderliesten, JB and Zwart, MP and Stegeman, A and Fischer, EAJ and de Visser, JAGM}, title = {Chicken gut microbiome members limit the spread of an antimicrobial resistance plasmid in Escherichia coli.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1962}, pages = {20212027}, pmid = {34727719}, issn = {1471-2954}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Chickens ; Drug Resistance, Bacterial/genetics ; *Escherichia coli/genetics ; *Gastrointestinal Microbiome ; Plasmids/genetics ; }, abstract = {Plasmid-mediated antimicrobial resistance is a major contributor to the spread of resistance genes within bacterial communities. Successful plasmid spread depends upon a balance between plasmid fitness effects on the host and rates of horizontal transmission. While these key parameters are readily quantified in vitro, the influence of interactions with other microbiome members is largely unknown. Here, we investigated the influence of three genera of lactic acid bacteria (LAB) derived from the chicken gastrointestinal microbiome on the spread of an epidemic narrow-range ESBL resistance plasmid, IncI1 carrying blaCTX-M-1, in mixed cultures of isogenic Escherichia coli strains. Secreted products of LAB decreased E. coli growth rates in a genus-specific manner but did not affect plasmid transfer rates. Importantly, we quantified plasmid transfer rates by controlling for density-dependent mating opportunities. Parametrization of a mathematical model with our in vitro estimates illustrated that small fitness costs of plasmid carriage may tip the balance towards plasmid loss under growth conditions in the gastrointestinal tract. This work shows that microbial interactions can influence plasmid success and provides an experimental-theoretical framework for further study of plasmid transfer in a microbiome context.}, }
@article {pmid34727498, year = {2021}, author = {Wang, X and Prévoteau, A and Rabaey, K}, title = {Impact of Periodic Polarization on Groundwater Denitrification in Bioelectrochemical Systems.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {22}, pages = {15371-15379}, doi = {10.1021/acs.est.1c03586}, pmid = {34727498}, issn = {1520-5851}, mesh = {Autotrophic Processes ; *Bioelectric Energy Sources ; Denitrification ; *Groundwater ; Nitrates ; }, abstract = {Nitrate contamination is a common problem in groundwater around the world. Nitrate can be cathodically reduced in bioelectrochemical systems using autotrophic denitrifiers with low energy investment and without chemical addition. Successful denitrification was demonstrated in previous studies in both microbial fuel cells and microbial electrolysis cells (MECs) with continuous current flow, whereas the impact of intermittent current supply (e.g., in a fluidized-bed system) on denitrification and particularly the electron-storing capacity of the denitrifying electroactive biofilms (EABs) on the cathodes have not been studied in depth. In this study, two continuously fed MECs were operated in parallel under continuous and periodic polarization modes over 280 days, respectively. Under continuous polarization, the maximum denitrification rate reached 233 g NO3[-]-N/m[3]/d with 98% nitrate removal (0.6 mg NO3[-]-N/L in the effluent) with negligible intermediate production, while under a 30 s open-circuit/30 s polarization mode, 86% of nitrate was removed at a maximum rate of 205 g NO3[-]-N/m[3]/d (4.5 mg NO3[-]-N/L in the effluent) with higher N2O production (6.6-9.3 mg N/L in the effluent). Conversely, periodic polarization could be an interesting approach in other bioelectrochemical processes if the generation of chemical intermediates (partially reduced or oxidized) should be favored. Similar microbial communities dominated byGallionellaceaewere found in both MECs; however, swapping the polarization modes and the electrochemical analyses suggested that the periodically polarized EABs probably developed a higher ability for electron storage and transfer, which supported the direct electron transfer pathway in discontinuous operation or fluidized biocathodes.}, }
@article {pmid34727198, year = {2022}, author = {Floc'h, JB and Hamel, C and Laterrière, M and Tidemann, B and St-Arnaud, M and Hijri, M}, title = {Inter-Kingdom Networks of Canola Microbiome Reveal Bradyrhizobium as Keystone Species and Underline the Importance of Bulk Soil in Microbial Studies to Enhance Canola Production.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1166-1181}, pmid = {34727198}, issn = {1432-184X}, support = {RDC Fund//natural sciences and engineering research council of canada/ ; }, mesh = {Soil ; *Bradyrhizobium ; Soil Microbiology ; Fungi ; Plant Roots/microbiology ; Canada ; *Microbiota ; Rhizosphere ; Bacteria ; Plants ; *Brassica napus ; }, abstract = {The subterranean microbiota of plants is of great importance for plant growth and health, as root-associated microbes can perform crucial ecological functions. As the microbial environment of roots is extremely diverse, identifying keystone microorganisms in plant roots, rhizosphere, and bulk soil is a necessary step towards understanding the network of influence within the microbial community associated with roots and enhancing its beneficial elements. To target these hot spots of microbial interaction, we used inter-kingdom network analysis on the canola growth phase of a long-term cropping system diversification experiment conducted at four locations in the Canadian Prairies. Our aims were to verify whether bacterial and fungal communities of canola roots, rhizosphere, and bulk soil are related and influenced by diversification of the crop rotation system; to determine whether there are common or specific core fungi and bacteria in the roots, rhizosphere, and bulk soil under canola grown in different environments and with different levels of cropping system diversification; and to identify hub taxa at the inter-kingdom level that could play an important ecological role in the microbiota of canola. Our results showed that fungi were influenced by crop diversification, which was not the case on bacteria. We found no core microbiota in canola roots but identified three core fungi in the rhizosphere, one core mycobiota in the bulk soil, and one core bacterium shared by the rhizosphere and bulk soil. We identified two bacterial and one fungal hub taxa in the inter-kingdom networks of the canola rhizosphere, and one bacterial and two fungal hub taxa in the bulk soil. Among these inter-kingdom hub taxa, Bradyrhizobium sp. and Mortierella sp. are particularly influential on the microbial community and the plant. To our knowledge, this is the first inter-kingdom network analysis utilized to identify hot spots of interaction in canola microbial communities.}, }
@article {pmid34726495, year = {2021}, author = {Georgoulis, SJ and Shalvarjian, KE and Helmann, TC and Hamilton, CD and Carlson, HK and Deutschbauer, AM and Lowe-Power, TM}, title = {Genome-Wide Identification of Tomato Xylem Sap Fitness Factors for Three Plant-Pathogenic Ralstonia Species.}, journal = {mSystems}, volume = {6}, number = {6}, pages = {e0122921}, pmid = {34726495}, issn = {2379-5077}, support = {S10 OD018174/OD/NIH HHS/United States ; 2018-67012-31497//U.S. Department of Agriculture (USDA)/ ; }, abstract = {Plant-pathogenic Ralstonia spp. colonize plant xylem and cause wilt diseases on a broad range of host plants. To identify genes that promote growth of diverse Ralstonia strains in xylem sap from tomato plants, we performed genome-scale genetic screens (random barcoded transposon mutant sequencing screens [RB-TnSeq]) in three strains spanning the genetic, geographical, and physiological range of plant-pathogenic Ralstonia: Ralstonia solanacearum IBSBF1503, Ralstonia pseudosolanacearum GMI1000, and Ralstonia syzygii PSI07. Contrasting mutant fitness phenotypes in culture media versus in xylem sap suggest that Ralstonia strains are adapted to ex vivo xylem sap and that culture media impose foreign selective pressures. Although wild-type Ralstonia grew in sap and in rich medium with similar doubling times and to a similar carrying capacity, more genes were essential for growth in sap than in rich medium. Each strain required many genes associated with envelope remodeling and repair processes for full fitness in xylem sap. These genes were associated with peptidoglycan peptide formation (murI), secretion of periplasmic proteins (tatC), periplasmic protein folding (dsbA), synthesis of osmoregulated periplasmic glucans (mdoGH), and lipopolysaccharide (LPS) biosynthesis. Mutant strains with mutations in four genes had strong, sap-specific fitness defects in all strain backgrounds: murI, thiC, purU, and a lipoprotein (RSc2007). Many amino acid biosynthesis genes were required for fitness in both minimal medium and xylem sap. Multiple mutants with insertions in virulence regulators had gains of fitness in culture media and neutral fitness in sap. Our genome-scale genetic screen identified Ralstonia fitness factors that promote growth in xylem sap, an ecologically relevant condition. IMPORTANCE Traditional transposon mutagenesis genetic screens pioneered molecular plant pathology and identified core virulence traits like the type III secretion system. TnSeq approaches that leverage next-generation sequencing to rapidly quantify transposon mutant phenotypes are ushering in a new wave of biological discovery. Here, we have adapted a genome-scale approach, random barcoded transposon mutant sequencing (RB-TnSeq), to discover fitness factors that promote growth of three related bacterial strains in a common niche, tomato xylem sap. Fitness of the wild type and mutants show that Ralstonia spp. are adapted to grow well in xylem sap from their natural host plant, tomato. Our screen identified multiple sap-specific fitness factors with roles in maintaining the bacterial envelope. These factors include putative adaptations to resist plant defenses that may include antimicrobial proteins and specialized metabolites that damage bacterial membranes.}, }
@article {pmid34725713, year = {2022}, author = {Kang, H and Lee, J and Zhou, X and Kim, J and Yang, Y}, title = {The Effects of N Enrichment on Microbial Cycling of Non-CO2 Greenhouse Gases in Soils-a Review and a Meta-analysis.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {945-957}, pmid = {34725713}, issn = {1432-184X}, mesh = {Humans ; *Soil ; *Greenhouse Gases ; Ecosystem ; Nitrous Oxide ; Fertilizers ; Methane/analysis ; Carbon Dioxide/analysis ; }, abstract = {Terrestrial ecosystems are typically nitrogen (N) limited, but recent years have witnessed N enrichment in various soil ecosystems caused by human activities such as fossil fuel combustion and fertilizer application. This enrichment may alter microbial processes in soils in a way that would increase the emissions of methane (CH4) and nitrous oxide (N2O), thereby aggravating global climate change. This review focuses on the effects of N enrichment on methanogens and methanotrophs, which play a central role in the dynamics of CH4 at the global scale. We also address the effects of N enrichment on N2O, which is produced in soils mainly by nitrification and denitrification. Overall, N enrichment inhibits methanogenesis in pure culture experiments, while its effects on CH4 oxidation are more complicated. The majority of previous studies reported that N enrichment, especially NH4[+] enrichment, inhibits CH4 oxidation, resulting in higher CH4 emissions from soils. However, both activation and neutral responses have also been reported, particularly in rice paddies and landfill sites, which is well reflected in our meta-analysis. In contrast, N enrichment substantially increases N2O emission by both nitrification and denitrification, which increases proportionally to the amount of N amended. Future studies should address the effects of N enrichment on the active microbes of those functional groups at multiple scales along with parameterization of microbial communities for the application to climate models at the global scale.}, }
@article {pmid34724047, year = {2021}, author = {Jakus, N and Blackwell, N and Straub, D and Kappler, A and Kleindienst, S}, title = {Presence of Fe(II) and nitrate shapes aquifer-originating communities leading to an autotrophic enrichment dominated by an Fe(II)-oxidizing Gallionellaceae sp.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {11}, pages = {}, doi = {10.1093/femsec/fiab145}, pmid = {34724047}, issn = {1574-6941}, mesh = {Autotrophic Processes ; Denitrification ; Ecosystem ; Ferrous Compounds ; *Gallionellaceae/genetics ; *Groundwater ; Nitrates ; Oxidation-Reduction ; }, abstract = {Autotrophic nitrate reduction coupled to Fe(II) oxidation is an important nitrate removal process in anoxic aquifers. However, it remains unknown how changes of O2 and carbon availability influence the community structure of nitrate-reducing Fe(II)-oxidizing (NRFeOx) microbial assemblages and what the genomic traits of these NRFeOx key players are. We compared three metabolically distinct denitrifying assemblages, supplemented with acetate, acetate/Fe(II) or Fe(II), enriched from an organic-poor, pyrite-rich aquifer. The presence of Fe(II) promoted the growth of denitrifying Burkholderiaceae spp. and an unclassified Gallionellaceae sp. This Gallionellaceae sp. was related to microaerophilic Fe(II) oxidizers; however, it did not grow under microoxic conditions. Furthermore, we explored a metagenome and 15 metagenome-assembled genomes from an aquifer-originating, autotrophic NRFeOx culture. The dominant Gallionellaceae sp. revealed the potential to oxidize Fe(II) (e.g. cyc2), fix CO2 (e.g. rbcL) and perform near-complete denitrification leading to N2O formation (e.g. narGHJI,nirK/S and norBC). In addition, Curvibacter spp.,Methyloversatilis sp. and Thermomonas spp. were identified as novel putative NRFeOx taxa. Our findings provide first insights into the genetic traits of the so far only known autotrophic NRFeOx culture originating from an organic-poor aquifer, providing the genomic basis to study mechanisms of nitrate removal in organic-poor subsurface ecosystems.}, }
@article {pmid34721343, year = {2021}, author = {Van Eesbeeck, V and Props, R and Mysara, M and Petit, PCM and Rivasseau, C and Armengaud, J and Monsieurs, P and Mahillon, J and Leys, N}, title = {Cyclical Patterns Affect Microbial Dynamics in the Water Basin of a Nuclear Research Reactor.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {744115}, pmid = {34721343}, issn = {1664-302X}, abstract = {The BR2 nuclear research reactor in Mol, Belgium, runs in successive phases of operation (cycles) and shutdown, whereby a water basin surrounding the reactor vessel undergoes periodic changes in physico-chemical parameters such as flow rate, temperature, and radiation. The aim of this study was to explore the microbial community in this unique environment and to investigate its long-term dynamics using a 16S rRNA amplicon sequencing approach. Results from two sampling campaigns spanning several months showed a clear shift in community profiles: cycles were mostly dominated by two Operational Taxonomic Units (OTUs) assigned to unclassified Gammaproteobacterium and Pelomonas, whereas shutdowns were dominated by an OTU assigned to Methylobacterium. Although 1 year apart, both campaigns showed similar results, indicating that the system remained stable over this 2-year period. The community shifts were linked with changes in physico-chemical parameters by Non-metric Multidimensional Scaling (NMDS) and correlation analyses. In addition, radiation was hypothesized to cause a decrease in cell number, whereas temperature had the opposite effect. Chemoautotrophic use of H2 and dead cell recycling are proposed to be used as a strategies for nutrient retrieval in this extremely oligotrophic environment.}, }
@article {pmid34721316, year = {2021}, author = {Verbeelen, T and Leys, N and Ganigué, R and Mastroleo, F}, title = {Development of Nitrogen Recycling Strategies for Bioregenerative Life Support Systems in Space.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {700810}, pmid = {34721316}, issn = {1664-302X}, abstract = {To enable long-distance space travel, the development of a highly efficient and robust system to recover nutrients from waste streams is imperative. The inability of the current physicochemical-based environmental control and life support system (ECLSS) on the ISS to produce food in situ and to recover water and oxygen at high enough efficiencies results in the need for frequent resupply missions from Earth. Therefore, alternative strategies like biologically-based technologies called bioregenerative life support systems (BLSSs) are in development. These systems aim to combine biological and physicochemical processes, which enable in situ water, oxygen, and food production (through the highly efficient recovery of minerals from waste streams). Hence, minimalizing the need for external consumables. One of the BLSS initiatives is the European Space Agency's (ESA) Micro-Ecological Life Support System Alternative (MELiSSA). It has been designed as a five-compartment bioengineered system able to produce fresh food and oxygen and to recycle water. As such, it could sustain the needs of a human crew for long-term space exploration missions. A prerequisite for the self-sufficient nature of MELiSSA is the highly efficient recovery of valuable minerals from waste streams. The produced nutrients can be used as a fertilizer for food production. In this review, we discuss the need to shift from the ECLSS to a BLSS, provide a summary of past and current BLSS programs and their unique approaches to nitrogen recovery and processing of urine waste streams. In addition, compartment III of the MELiSSA loop, which is responsible for nitrogen recovery, is reviewed in-depth. Finally, past, current, and future related ground and space demonstration and the space-related challenges for this technology are considered.}, }
@article {pmid34719821, year = {2021}, author = {Beterams, A and De Paepe, K and Maes, L and Wise, IJ and De Keersmaecker, H and Rajkovic, A and Laukens, D and Van de Wiele, T and Calatayud Arroyo, M}, title = {Versatile human in vitro triple coculture model coincubated with adhered gut microbes reproducibly mimics pro-inflammatory host-microbe interactions in the colon.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {35}, number = {12}, pages = {e21992}, doi = {10.1096/fj.202101135R}, pmid = {34719821}, issn = {1530-6860}, mesh = {Coculture Techniques/*methods ; Colon/cytology/*immunology/metabolism/microbiology ; Epithelial Cells/cytology/*immunology/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Host Microbial Interactions ; Humans ; Intestinal Mucosa/cytology/*immunology/metabolism/microbiology ; Lacticaseibacillus rhamnosus/physiology ; Macrophages/cytology/*immunology/metabolism/microbiology ; Transcriptome ; }, abstract = {The colonic epithelial barrier is vital to preserve gut and host health by maintaining the immune homeostasis between host and microbes. The mechanisms underlying beneficial or harmful host-microbe interactions are poorly understood and impossible to study in vivo given the limited accessibility and ethical constraints. Moreover, existing in vitro models lack the required cellular complexity for the routine, yet profound, analysis of the intricate interplay between different types of host and microbial cells. We developed and characterized a broadly applicable, easy-to-handle in vitro triple coculture model that combines chemically-induced macrophage-like, goblet and epithelial cells covered by a mucus layer, which can be coincubated with complex human-derived gut microbiota samples for 16 h. Comparison with a standard epithelial monolayer model revealed that triple cocultures produce thicker mucus layers, morphologically organize in a network and upon exposure to human-derived gut microbiota samples, respond via pro-inflammatory cytokine production. Both model systems, however, were not suffering from cytotoxic stress or different microbial loads, indicating that the obtained endpoints were caused by the imposed conditions. Addition of the probiotic Lactobacillus rhamnosus GG to assess its immunomodulating capacity in the triple coculture slightly suppressed pro-inflammatory cytokine responses, based on transcriptomic microarray analyses. TNF conditioning of the models prior to microbial exposure did not cause shifts in cytokines, suggesting a strong epithelial barrier in which TNF did not reach the basolateral side. To conclude, the triple coculture model is tolerable towards manipulations and allows to address mechanistic host-microbe research questions in a stable in vitro environment.}, }
@article {pmid34716776, year = {2022}, author = {Ho, A and Zuan, ATK and Mendes, LW and Lee, HJ and Zulkeflee, Z and van Dijk, H and Kim, PJ and Horn, MA}, title = {Aerobic Methanotrophy and Co-occurrence Networks of a Tropical Rainforest and Oil Palm Plantations in Malaysia.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1154-1165}, pmid = {34716776}, issn = {1432-184X}, support = {HO6234/1-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Rainforest ; *Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Malaysia ; Soil ; Methane ; Bacteria/genetics ; }, abstract = {Oil palm (OP) plantations are gradually replacing tropical rainforest in Malaysia, one of the largest palm oil producers globally. Conversion of lands to OP plantations has been associated with compositional shifts of the microbial community, with consequences on the greenhouse gas (GHG) emissions. While the impact of the change in land use has recently been investigated for microorganisms involved in N2O emission, the response of the aerobic methanotrophs to OP agriculture remains to be determined. Here, we monitored the bacterial community composition, focusing on the aerobic methanotrophs, in OP agricultural soils since 2012, 2006, and 1993, as well as in a tropical rainforest, in 2019 and 2020. High-affinity methane uptake was confirmed, showing significantly lower rates in the OP plantations than in the tropical rainforest, but values increased with continuous OP agriculture. The bacterial, including the methanotrophic community composition, was modified with ongoing OP agriculture. The methanotrophic community composition was predominantly composed of unclassified methanotrophs, with the canonical (Methylocystis) and putative methanotrophs thought to catalyze high-affinity methane oxidation present at higher relative abundance in the oldest OP plantation. Results suggest that the methanotrophic community was relatively more stable within each site, exhibiting less temporal variations than the total bacterial community. Uncharacteristically, a 16S rRNA gene-based co-occurrence network analysis revealed a more complex and connected community in the OP agricultural soil, which may influence the resilience of the bacterial community to disturbances. Overall, we provide a first insight into the ecology and role of the aerobic methanotrophs as a methane sink in OP agricultural soils.}, }
@article {pmid34714368, year = {2022}, author = {Akbar, S and Li, X and Ding, Z and Liu, Q and Huang, J and Zhou, Q and Gu, L and Yang, Z}, title = {Disentangling Diet- and Medium-Associated Microbes in Shaping Daphnia Gut Microbiome.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {911-921}, pmid = {34714368}, issn = {1432-184X}, support = {31730105//national natural science foundation of china/ ; 31800385//national natural science foundation of china/ ; 2020M681658//postdoctoral research foundation of china/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Daphnia/microbiology ; *Microbiota ; Bacteria/genetics ; Diet ; }, abstract = {Host genotype and environment are considered crucial factors in shaping Daphnia gut microbiome composition. Among the environmental factors, diet is an important factor that regulates Daphnia microbiome. Most of the studies only focused on the use of axenic diet and non-sterile medium to investigate their effects on Daphnia microbiome. However, in natural environment, Daphnia diets such as phytoplankton are associated with microbes and could affect Daphnia microbiome composition and fitness, but remain relatively poorly understood compared to that of axenic diet. To test this, we cultured two Daphnia magna genotypes (genotype-1 and genotype-2) in sterile medium and fed with axenic diet. To check the effects of algal diet-associated microbes versus free water-related microbes, Daphnia were respectively inoculated with three different inoculums: medium microbial inoculum, diet-associated microbial inoculum, and medium and diet-mixed microbial inoculum. Daphnia were cultured for 3 weeks and their gut microbiome and life history traits were recorded. Results showed that Daphnia inoculated with medium microbial inoculum were dominated by Comamonadaceae in both genotypes. In Daphnia inoculated with mixed inoculum, genotype-1 microbiome was highly changed, whereas genotype-2 microbiome was slightly altered. Daphnia inoculated with diet microbial inoculum has almost the same microbiome in both genotypes. The total number of neonates and body size were significantly reduced in Daphnia inoculated with diet microbial inoculum regardless of genotype compared to all other treatments. Overall, this study shows that the microbiome of Daphnia is flexible and varies with genotype and diet- and medium-associated microbes, but not every bacteria is beneficial to Daphnia, and only symbionts can increase Daphnia performance.}, }
@article {pmid34712902, year = {2021}, author = {Baig, U and Dahanukar, N and Shintre, N and Holkar, K and Pund, A and Lele, U and Gujarathi, T and Patel, K and Jakati, A and Singh, R and Vidwans, H and Tamhane, V and Deshpande, N and Watve, M}, title = {Phylogenetic diversity and activity screening of cultivable Actinobacteria isolated from marine sponges and associated environments from the western coast of India.}, journal = {Access microbiology}, volume = {3}, number = {9}, pages = {000242}, pmid = {34712902}, issn = {2516-8290}, abstract = {The phylogenetic diversity of cultivable actinobacteria isolated from sponges (Haliclona spp.) and associated intertidal zone environments along the northern parts of the western coast of India were studied using 16S rRNA gene sequences. A subset of randomly selected actinobacterial cultures were screened for three activities, namely predatory behaviour, antibacterial activity and enzyme inhibition. We recovered 237 isolates from the phylum Actinobacteria belonging to 19 families and 28 genera, which could be attributed to 95 putative species using maximum-likelihood partition and 100 putative species using Bayesian partition in Poisson tree processes. Although the trends in the discovery of actinobacterial genera isolated from sponges were consistent with previous studies from different study areas, we provide the first report of nine actinobacterial species from sponges. We observed widespread non-obligate epibiotic predatory behaviour in eight actinobacterial genera and we provide the first report of predatory activity in Brevibacterium , Glutamicibacter , Micromonospora , Nocardiopsis , Rhodococcus and Rothia . Sponge-associated actinobacteria showed significantly more predatory behaviour than environmental isolates. While antibacterial activity by actinobacterial isolates mainly affected Gram-positive target bacteria with little or no effect on Gram-negative bacteria, predation targeted both Gram-positive and Gram-negative prey with equal propensity. Actinobacterial isolates from both sponges and associated environments produced inhibitors of serine proteases and angiotensin-converting enzyme. Predatory behaviour was strongly associated with inhibition of trypsin and chymotrypsin. Our study suggests that the sponges and associated environments of the western coast of India are rich in actinobacterial diversity, with widespread predatory activity, antibacterial activity and production of enzyme inhibitors. Understanding the diversity and associations among various actinobacterial activities - with each other and the source of isolation - can provide new insights into marine microbial ecology and provide opportunities to isolate novel therapeutic agents.}, }
@article {pmid34710591, year = {2022}, author = {Monclaro, AV and Gorgulho Silva, CO and Gomes, HAR and Moreira, LRS and Filho, EXF}, title = {The enzyme interactome concept in filamentous fungi linked to biomass valorization.}, journal = {Bioresource technology}, volume = {344}, number = {Pt A}, pages = {126200}, doi = {10.1016/j.biortech.2021.126200}, pmid = {34710591}, issn = {1873-2976}, mesh = {Biomass ; Cell Wall ; *Fungi ; Hydrolysis ; *Lignin ; }, abstract = {Biomass represents an abundant and inexpensive source of sugars and aromatic compounds that can be used as raw materials for conversion into value-added bioproducts. Filamentous fungi are sources of plant cell wall degrading enzymes in nature. Understanding the interactions between enzymes is crucial for optimizing biomass degradation processes. Herein, the concept of the interactome is presented as a holistic approach that depicts the interactions among enzymes, substrates, metabolites, and inhibitors. The interactome encompasses several stages of biomass degradation, starting with the sensing of the substrate and the subsequent synthesis of hydrolytic and oxidative enzymes (fungus-substrate interaction). Enzyme-enzyme interactions are exemplified in the complex processes of lignocellulosic biomass degradation. The enzyme-substrate-metabolite-inhibitor interaction also provides a better understanding of biomass conversion, allowing bioproduct production from recalcitrant agro-industrial residues, thus bringing greater value to residual biomass. Finally, technological applications are presented for optimizing the interactome at various levels.}, }
@article {pmid34710415, year = {2022}, author = {Prendergast, DM and O'Doherty, &#xc1; and Burgess, CM and Howe, N and McMahon, F and Murphy, D and Leonard, F and Morris, D and Harrington, C and Carty, A and Moriarty, J and Gutierrez, M}, title = {Critically important antimicrobial resistant Enterobacteriaceae in Irish farm effluent and their removal in integrated constructed wetlands.}, journal = {The Science of the total environment}, volume = {806}, number = {Pt 3}, pages = {151269}, doi = {10.1016/j.scitotenv.2021.151269}, pmid = {34710415}, issn = {1879-1026}, mesh = {Animals ; Anti-Bacterial Agents ; Bacterial Proteins ; *Enterobacteriaceae ; *Escherichia coli ; Farms ; Swine ; Wetlands ; beta-Lactamases ; }, abstract = {This study investigated the ability of Integrated Constructed Wetlands (ICWs) to remove critically important antimicrobial resistant organisms (AROs) from farm wastewater. Influent samples from the untreated farm waste and effluent samples taken at the end of the ICW system were collected monthly from four ICWs, serving four different farm types (suckler, dairy, dairy &amp; poultry and pig). Using selective media to screen for the presence of carbapenemase resistant organisms, plasmid mediated and AmpC β-Lactamase producing organisms (ESBL/pAmpC) and fluoroquinolone resistant organisms, a total of 82 AROs were obtained with the majority being E. coli (n = 79). Statistically significant were the differences on the number of AROs isolated from influent (higher) compared to effluent, as well as a seasonal effect, with less AROs recovered during winter in comparison to other seasons (P < 0.05). On the other hand, there was no significant differences in the recovery of AROs on different farms. The majority of isolates from each of the farms (99%) were multi drug resistant, with 65% resistant to seven or more antimicrobials. A high incidence of tetracycline, trimethoprim/sulfamethoxazole, and ampicillin resistance was common to the isolates from all four farms but there were differences in ESBL levels with 63% of the isolates recovered from Farm 4 (piggery) being ESBLs compared to 18%, 36% and 4.5% recovered from Farms 1 (suckler), 2 (dairy) and 3 (dairy &amp; poultry), respectively. No carbapenemase producing organisms were isolated. Our results showed that ICWs are effective in removing critically important AROs from farm wastewater on all four farm types.}, }
@article {pmid34708599, year = {2021}, author = {Liu, SJ and Corvini, PF and Rabaey, K}, title = {[ELECTRA: electricity-driven low energy and chemical input technology for accelerated bioremediation].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {37}, number = {10}, pages = {3405-3410}, doi = {10.13345/j.cjb.210431}, pmid = {34708599}, issn = {1872-2075}, mesh = {Biodegradation, Environmental ; Biotechnology ; *COVID-19 ; Electricity ; Humans ; *Pandemics ; SARS-CoV-2 ; }, abstract = {The international cooperation project "electricity-driven low energy and chemical input technology for accelerated bioremediation" (abridged as "ELECTRA") is jointly supported by National Nature Science Foundation of China (NSFC) and European Commission (EC). The ELECTRA consortium consists of 5 research institutions and universities from China and 17 European research institutions and universities, as well as high-tech companies of EC countries. ELECTRA focuses on researches of biodegradation of emerging organic compounds (EOCs) and novel environmental biotechnologies of low-energy and low-chemical inputs. The project has been successfully operated for 2 years, and has made important progresses in obtaining EOCs-degrading microbes, developing weak-electricity-accelerated bioremediation, and 3D-printing techniques for microbial consortium. The ELECTRA has promoted collaborations among the Chinese and European scientists. In the future, ELECTRA will overcome the negative impact of the COVID-19 pandemic and fulfill the scientific objectives through strengthening the international collaboration.}, }
@article {pmid34708598, year = {2021}, author = {Liu, SJ and Ji, R and Corvini, PF and Rabaey, K}, title = {[Environmental scientists &amp; microbiologists from China &amp; EU: take the responsibility to cherish the Earth homeland].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {37}, number = {10}, pages = {3401-3404}, doi = {10.13345/j.cjb.210754}, pmid = {34708598}, issn = {1872-2075}, mesh = {Biodegradation, Environmental ; China ; *Ecosystem ; *Plastics ; }, abstract = {Humanity shares the common interest to protect the environment and to maintain a healthy global ecosystem. International collaboration is key in this context, to advance the necessary science and technology. The National Science Foundation of China (NSFC) and European Commission (EC) have agreed to collaborate in innovative knowledge and technology in the field of bioremediation of polluted environments and biodegradation of plastics. In this context, projects on bioremediation of soils, wastewater and sediment matrices and on microbial degradation of plastics were supported. This special issue aimed to introduce these projects and their progresses in the related fields. In total, 23 papers have been collected in this issue, covering both fundamental and applied researches.}, }
@article {pmid34707927, year = {2021}, author = {Schagen, M and Bosch, J and Johnson, J and Duker, R and Lebre, P and Potts, AJ and Cowan, DA}, title = {The soil microbiomics of intact, degraded and partially-restored semi-arid succulent thicket (Albany Subtropical Thicket).}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e12176}, pmid = {34707927}, issn = {2167-8359}, abstract = {This study examines the soil bacterial diversity in the Portulacaria afra-dominated succulent thicket vegetation of the Albany Subtropical Thicket biome; this biome is endemic to South Africa. The aim of the study was to compare the soil microbiomes between intact and degraded zones in the succulent thicket and identify environmental factors which could explain the community compositions. Bacterial diversity, using 16S amplicon sequencing, and soil physicochemistry were compared across three zones: intact (undisturbed and vegetated), degraded (near complete removal of vegetation due to browsing) and restored (a previously degraded area which was replanted approximately 11 years before sampling). Amplicon Sequence Variant (ASV) richness was similar across the three zones, however, the bacterial community composition and soil physicochemistry differed across the intact and degraded zones. We identified, via correlation, the potential drivers of microbial community composition as soil density, pH and the ratio of Ca to Mg. The restored zone was intermediate between the intact and degraded zones. The differences in the microbial communities appeared to be driven by the presence of plants, with plant-associated taxa more common in the intact zone. The dominant taxa in the degraded zone were cosmopolitan organisms, that have been reported globally in a wide variety of habitats. This study provides baseline information on the changes of the soil bacterial community of a spatially restricted and threatened biome. It also provides a starting point for further studies on community composition and function concerning the restoration of degraded succulent thicket ecosystems.}, }
@article {pmid34707578, year = {2021}, author = {Lluansí, A and Llirós, M and Oliver, L and Bahí, A and Elias-Masiques, N and Gonzalez, M and Benejam, P and Cueva, E and Termes, M and Ramió-Pujol, S and Malagón, M and Amoedo, J and Serrano, M and Busquets, D and Torreabla, L and Sabat, M and Buxó, M and Cambra, M and Serra-Pagès, M and Delgado-Aros, S and García-Gil, LJ and Elias, I and Aldeguer, X}, title = {In vitro Prebiotic Effect of Bread-Making Process in Inflammatory Bowel Disease Microbiome.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {716307}, pmid = {34707578}, issn = {1664-302X}, abstract = {Inflammatory bowel disease (IBD), including its two main categories (Crohn's disease and ulcerative colitis), has been linked both to gut microbiota and to diet. Bread is a daily food that has a potential capacity as a prebiotic. Our aim was to evaluate different bread-making processes and their effect on fecal colonic microbiota in IBD patients. The microbial composition of several sourdoughs and dough samples was analyzed by high-throughput sequencing of 16S and 18S rRNA genes. Three types of bread, which followed different bread-making processes, were in vitro digested and incubated with feces from IBD patients. Changes in gut microbiota were assessed by a quantitative polymerase chain reaction using specific bacterial sequence targets. Short-chain fatty acid production was also analyzed by gas chromatography. Lactobacillus sanfranciscensis was the dominant lactic acid bacteria species found in sourdough and bread doughs prepared using sourdough, whereas Saccharomyces cerevisiae was the most dominant yeast in all groups, especially in bread doughs before baking. Differences in microbial composition in raw bread doughs were more related to the type of dough and elaboration than to fermentation time lengths. The analysis of in vitro fecal incubations with bread conditions revealed an increase in most bacterial groups analyzed and short-chain fatty acid production, both in Crohn's disease and ulcerative colitis samples. Most remarkable increases in short-chain fatty acid production mirrored higher abundances of Roseburia species. The potential prebiotic properties observed were mainly obtained when using a high quantity of bread, regardless of bread type. Overall, this study highlights the bacterial dynamics within the bread-making process and the potential prebiotic effect in IBD patients.}, }
@article {pmid34706476, year = {2021}, author = {Herren, LW and Brewton, RA and Wilking, LE and Tarnowski, ME and Vogel, MA and Lapointe, BE}, title = {Septic systems drive nutrient enrichment of groundwaters and eutrophication in the urbanized Indian River Lagoon, Florida.}, journal = {Marine pollution bulletin}, volume = {172}, number = {}, pages = {112928}, doi = {10.1016/j.marpolbul.2021.112928}, pmid = {34706476}, issn = {1879-3363}, mesh = {Environmental Monitoring ; Eutrophication ; Florida ; *Groundwater ; Harmful Algal Bloom ; Nitrogen/analysis ; Nutrients ; Phosphorus/analysis ; Rivers ; *Water Pollutants, Chemical/analysis ; }, abstract = {Effluent from septic systems can pollute groundwater and surface waters in coastal watersheds. These effects are unknown for the highly urbanized central Indian River Lagoon (CIRL), Florida, where septic systems represent > 50% of wastewater disposal. To better understand these impacts, water quality was assessed along both canals and a tributary that drain into the CIRL. Dissolved nutrient concentrations were higher near septic systems than in natural areas. δ[15]N values of groundwater (+7.2‰), surface water (+5.5‰), and macrophytes (+9.7‰) were within the range for wastewater (>+3‰), as were surface water concentrations of the artificial sweetener sucralose (100 to 1700 ng/L) and fecal indicator bacteria density. These results indicate that septic systems are promoting eutrophication in the CIRL by contributing nutrient pollution to surface water via groundwater. This study demonstrates the need to reduce reliance on septic systems in urbanized coastal communities to improve water quality and subsequently mitigate harmful algal blooms.}, }
@article {pmid34705059, year = {2023}, author = {Banister, RB and Schwarz, MT and Fine, M and Ritchie, KB and Muller, EM}, title = {Correction to: In stability and Stasis Among the Microbiome of Seagrass Leaves, Roots and Rhizomes, and Nearby Sediments Within a Natural pH Gradient.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1634}, doi = {10.1007/s00248-021-01903-8}, pmid = {34705059}, issn = {1432-184X}, }
@article {pmid34704828, year = {2021}, author = {Jensen, M and Wippler, J and Kleiner, M}, title = {Evaluation of RNAlater as a Field-Compatible Preservation Method for Metaproteomic Analyses of Bacterium-Animal Symbioses.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0142921}, pmid = {34704828}, issn = {2165-0497}, mesh = {Animals ; Annelida/*microbiology/physiology ; Bacteria/classification/genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/metabolism ; Phylogeny ; Preservation, Biological/*methods ; Proteomics ; *Symbiosis ; }, abstract = {Field studies are central to environmental microbiology and microbial ecology, because they enable studies of natural microbial communities. Metaproteomics, the study of protein abundances in microbial communities, allows investigators to study these communities "in situ," which requires protein preservation directly in the field because protein abundance patterns can change rapidly after sampling. Ideally, a protein preservative for field deployment works rapidly and preserves the whole proteome, is stable in long-term storage, is nonhazardous and easy to transport, and is available at low cost. Although these requirements might be met by several protein preservatives, an assessment of their suitability under field conditions when targeted for metaproteomic analyses is currently lacking. Here, we compared the protein preservation performance of flash freezing and the preservation solution RNAlater using the marine gutless oligochaete Olavius algarvensis and its symbiotic microbes as a test case. In addition, we evaluated long-term RNAlater storage after 1 day, 1 week, and 4 weeks at room temperature (22°C to 23°C). We evaluated protein preservation using one-dimensional liquid chromatography-tandem mass spectrometry. We found that RNAlater and flash freezing preserved proteins equally well in terms of total numbers of identified proteins and relative abundances of individual proteins, and none of the test time points was altered, compared to time zero. Moreover, we did not find biases against specific taxonomic groups or proteins with particular biochemical properties. Based on our metaproteomic data and the logistical requirements for field deployment, we recommend RNAlater for protein preservation of field-collected samples targeted for metaproteomic analyses. IMPORTANCE Metaproteomics, the large-scale identification and quantification of proteins from microbial communities, provide direct insights into the phenotypes of microorganisms on the molecular level. To ensure the integrity of the metaproteomic data, samples need to be preserved immediately after sampling to avoid changes in protein abundance patterns. In laboratory setups, samples for proteomic analyses are most commonly preserved by flash freezing; however, liquid nitrogen or dry ice is often unavailable at remote field locations, due to their hazardous nature and transport restrictions. Our study shows that RNAlater can serve as a low-hazard, easy-to-transport alternative to flash freezing for field preservation of samples for metaproteomic analyses. We show that RNAlater preserves the metaproteome equally well, compared to flash freezing, and protein abundance patterns remain stable during long-term storage for at least 4 weeks at room temperature.}, }
@article {pmid34703919, year = {2021}, author = {Grigoryan, AA and Jalique, DR and Stroes-Gascoyne, S and Wolfaardt, GM and Keech, PG and Korber, DR}, title = {Prediction of bacterial functional diversity in clay microcosms.}, journal = {Heliyon}, volume = {7}, number = {10}, pages = {e08131}, pmid = {34703919}, issn = {2405-8440}, abstract = {Microorganisms in clay barriers could affect the long-term performance of waste containers in future deep geological repositories (DGR) for used nuclear fuel through production of corrosive metabolites (e.g., sulfide), which is why clay materials are highly compacted: to reduce both physical space and access to water for microorganisms to grow. However, the highly compacted nature of clays and the resulting low activity or dormancy of microorganisms complicate the extraction of biomarkers (i.e., PLFA, DNA etc.) from such barriers for predictive analysis of microbial risks. In order to overcome these challenges, we have combined culture- and 16S rRNA gene amplicon sequencing-based approaches to describe the functional diversity of microorganisms in several commercial clay products, including two different samples of Wyoming type MX-80 bentonite (Batch 1 and Batch 2), the reference clay for a future Canadian DGR, and Avonlea type Canaprill, a clay sample for comparison. Microorganisms from as-received bentonites were enriched in anoxic 10% w/v clay microcosms for three months at ambient temperature with addition of 10% hydrogen along with presumable indigenous organics and sulfate in the clay. High-throughput sequencing of 16S rRNA gene fragments indicated a high abundance of Gram-positive bacteria of the phylum Firmicutes (82%) in MX-80 Batch 1 incubations. Bacterial libraries from microcosms with MX-80 Batch 2 were enriched with Firmicutes (53%) and Chloroflexi (43%). Firmicutes also significantly contributed (<15%) to the bacterial community in Canaprill clay microcosm, which was dominated by Gram-negative Proteobacteria (>70%). Sequence analysis revealed presence of the bacterial families Peptostreptococcaceae, Clostridiaceae, Peptococcaceae, Bacillaceae, Enterobacteriaceae, Veillonellaceae, Tissierellaceae and Planococcaceae in MX-80 Batch 1 incubations; Bacillaceae, along with unidentified bacteria of the phylum Chloroflexi, in MX-80 Batch 2 clay microcosms, and Pseudomonadaceae, Hydrogenophilaceae, Bacillaceae, Desulfobacteraceae, Desulfobulbaceae, Peptococcaceae, Pelobacteraceae, Alcaligenaceae, Rhodospirillaceae in Canaprill microcosms. Exploration of potential metabolic pathways in the bacterial communities from the clay microcosms suggested variable patterns of sulfur cycling in the different clays with the possible prevalence of bacterial sulfate-reduction in MX-80 bentonite, and probably successive sulfate-reduction/sulfur-oxidation reactions in Canaprill microcosms. Furthermore, analysis of potential metabolic pathways in the bentonite enrichments suggested that bacteria with acid-producing capabilities (i.e., fermenters and acetogens) together with sulfide-producing prokaryotes might perhaps contribute to corrosion risks in clay systems. However, the low activity or dormancy of microorganisms in highly compacted bentonites as a result of severe environmental constraints (e.g., low water activity and high swelling pressure in the confined bentonite) in situ would be expected to largely inhibit bacterial activity in highly compacted clay-based barriers in a future DGR.}, }
@article {pmid34703658, year = {2021}, author = {Miaow, K and Lacap-Bugler, D and Buckley, HL}, title = {Identifying optimal bioinformatics protocols for aerosol microbial community data.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e12065}, pmid = {34703658}, issn = {2167-8359}, abstract = {Microbes are fundamental to Earth's ecosystems, thus understanding ecosystem connectivity through microbial dispersal is key to predicting future ecosystem changes in a warming world. However, aerial microbial dispersal remains poorly understood. Few studies have been performed on bioaerosols (microorganisms and biological fragments suspended in the atmosphere), despite them harboring pathogens and allergens. Most environmental microbes grow poorly in culture, therefore molecular approaches are required to characterize aerial diversity. Bioinformatic tools are needed for processing the next generation sequencing (NGS) data generated from these molecular approaches; however, there are numerous options and choices in the process. These choices can markedly affect key aspects of the data output including relative abundances, diversity, and taxonomy. Bioaerosol samples have relatively little DNA, and often contain novel and proportionally high levels of contaminant organisms, that are difficult to identify. Therefore, bioinformatics choices are of crucial importance. A bioaerosol dataset for bacteria and fungi based on the 16S rRNA gene (16S) and internal transcribed spacer (ITS) DNA sequencing from parks in the metropolitan area of Auckland, Aotearoa New Zealand was used to develop a process for determining the bioinformatics pipeline that would maximize the data amount and quality generated. Two popular tools (Dada2 and USEARCH) were compared for amplicon sequence variant (ASV) inference and generation of an ASV table. A scorecard was created and used to assess multiple outputs and make systematic choices about the most suitable option. The read number and ASVs were assessed, alpha diversity was calculated (Hill numbers), beta diversity (Bray-Curtis distances), differential abundance by site and consistency of ASVs were considered. USEARCH was selected, due to higher consistency in ASVs identified and greater read counts. Taxonomic assignment is highly dependent on the taxonomic database used. Two popular taxonomy databases were compared in terms of number and confidence of assignments, and a combined approach developed that uses information in both databases to maximize the number and confidence of taxonomic assignments. This approach increased the assignment rate by 12-15%, depending on amplicon and the overall assignment was 77% for bacteria and 47% for fungi. Assessment of decontamination using "decontam" and "microDecon" was performed, based on review of ASVs identified as contaminants by each and consideration of the probability of them being legitimate members of the bioaerosol community. For this example, "microDecon's" subtraction approach for removing background contamination was selected. This study demonstrates a systematic approach to determining the optimal bioinformatics pipeline using a multi-criteria scorecard for microbial bioaerosol data. Example code in the R environment for this data processing pipeline is provided.}, }
@article {pmid34703544, year = {2021}, author = {Schueffl, H and Theiner, S and Hermann, G and Mayr, J and Fronik, P and Groza, D and van Schonhooven, S and Galvez, L and Sommerfeld, NS and Schintlmeister, A and Reipert, S and Wagner, M and Mader, RM and Koellensperger, G and Keppler, BK and Berger, W and Kowol, CR and Legin, A and Heffeter, P}, title = {Albumin-targeting of an oxaliplatin-releasing platinum(iv) prodrug results in pronounced anticancer activity due to endocytotic drug uptake in vivo.}, journal = {Chemical science}, volume = {12}, number = {38}, pages = {12587-12599}, pmid = {34703544}, issn = {2041-6520}, support = {FG 3/FWF_/Austrian Science Fund FWF/Austria ; P 27749/FWF_/Austrian Science Fund FWF/Austria ; P 32886/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Oxaliplatin is a very potent platinum(ii) drug which is frequently used in poly-chemotherapy schemes against advanced colorectal cancer. However, its benefit is limited by severe adverse effects as well as resistance development. Based on their higher tolerability, platinum(iv) prodrugs came into focus of interest. However, comparable to their platinum(ii) counterparts they lack tumor specificity and are frequently prematurely activated in the blood circulation. With the aim to exploit the enhanced albumin consumption and accumulation in the malignant tissue, we have recently developed a new albumin-targeted prodrug, which supposed to release oxaliplatin in a highly tumor-specific manner. In more detail, we designed a platinum(iv) complex containing two maleimide moieties in the axial position (KP2156), which allows selective binding to the cysteine 34. In the present study, diverse cell biological and analytical tools such as laser ablation inductively-coupled plasma mass spectrometry (LA-ICP-MS), isotope labeling, and nano-scale secondary ion mass spectrometry (NanoSIMS) were employed to better understand the in vivo distribution and activation process of KP2156 (in comparison to free oxaliplatin and a non-albumin-binding succinimide analogue). KP2156 forms very stable albumin adducts in the bloodstream resulting in a superior pharmacological profile, such as distinctly prolonged terminal excretion half-life and enhanced effective platinum dose (measured by ICP-MS). The albumin-bound drug is accumulating in the malignant tissue, where it enters the cancer cells via clathrin- and caveolin-dependent endocytosis, and is activated by reduction to release oxaliplatin. This results in profound, long-lasting anticancer activity of KP2156 against CT26 colon cancer tumors in vivo based on cell cycle arrest and apoptotic cell death. Summarizing, albumin-binding of platinum(iv) complexes potently enhances the efficacy of oxaliplatin therapy and should be further developed towards clinical phase I trials.}, }
@article {pmid34700384, year = {2021}, author = {Zrimec, J and Kokina, M and Jonasson, S and Zorrilla, F and Zelezniak, A}, title = {Plastic-Degrading Potential across the Global Microbiome Correlates with Recent Pollution Trends.}, journal = {mBio}, volume = {12}, number = {5}, pages = {e0215521}, pmid = {34700384}, issn = {2150-7511}, mesh = {Bacteria/classification/enzymology/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Environmental Pollutants/metabolism ; *Microbiota ; Plastics/*metabolism ; Seawater/microbiology ; Soil Microbiology ; }, abstract = {Biodegradation is a plausible route toward sustainable management of the millions of tons of plastic waste that have accumulated in terrestrial and marine environments. However, the global diversity of plastic-degrading enzymes remains poorly understood. Taking advantage of global environmental DNA sampling projects, here we constructed hidden Markov models from experimentally verified enzymes and mined ocean and soil metagenomes to assess the global potential of microorganisms to degrade plastics. By controlling for false positives using gut microbiome data, we compiled a catalogue of over 30,000 nonredundant enzyme homologues with the potential to degrade 10 different plastic types. While differences between the ocean and soil microbiomes likely reflect the base compositions of these environments, we find that ocean enzyme abundance increases with depth as a response to plastic pollution and not merely taxonomic composition. By obtaining further pollution measurements, we observed that the abundance of the uncovered enzymes in both ocean and soil habitats significantly correlates with marine and country-specific plastic pollution trends. Our study thus uncovers the earth microbiome's potential to degrade plastics, providing evidence of a measurable effect of plastic pollution on the global microbial ecology as well as a useful resource for further applied research. IMPORTANCE Utilization of synthetic biology approaches to enhance current plastic degradation processes is of crucial importance, as natural plastic degradation processes are very slow. For instance, the predicted lifetime of a polyethylene terephthalate (PET) bottle under ambient conditions ranges from 16 to 48 years. Moreover, although there is still unexplored diversity in microbial communities, synergistic degradation of plastics by microorganisms holds great potential to revolutionize the management of global plastic waste. To this end, the methods and data on novel plastic-degrading enzymes presented here can help researchers by (i) providing further information about the taxonomic diversity of such enzymes as well as understanding of the mechanisms and steps involved in the biological breakdown of plastics, (ii) pointing toward the areas with increased availability of novel enzymes, and (iii) giving a basis for further application in industrial plastic waste biodegradation. Importantly, our findings provide evidence of a measurable effect of plastic pollution on the global microbial ecology.}, }
@article {pmid34700143, year = {2021}, author = {Yang, Y and Azari, M and Herbold, CW and Li, M and Chen, H and Ding, X and Denecke, M and Gu, JD}, title = {Activities and metabolic versatility of distinct anammox bacteria in a full-scale wastewater treatment system.}, journal = {Water research}, volume = {206}, number = {}, pages = {117763}, doi = {10.1016/j.watres.2021.117763}, pmid = {34700143}, issn = {1879-2448}, mesh = {*Ammonium Compounds ; Anaerobiosis ; Bacteria/genetics ; Bioreactors ; Ecosystem ; Nitrogen ; Oxidation-Reduction ; *Water Purification ; }, abstract = {Anaerobic ammonium oxidation (anammox) is a key N2-producing process in the global nitrogen cycle. Major progress in understanding the core mechanism of anammox bacteria has been made, but our knowledge of the survival strategies of anammox bacteria in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Here, by combining metagenomics with in situ metatranscriptomics, complex anammox-driven nitrogen cycles in an anoxic tank and a granular activated carbon (GAC) biofilm module of a full-scale WWTP treating landfill leachate were constructed. Four distinct anammox metagenome-assembled genomes (MAGs), representing a new genus named Ca. Loosdrechtii, a new species in Ca. Kuenenia, a new species in Ca. Brocadia, and a new strain in "Ca. Kuenenia stuttgartiensis", were simultaneously retrieved from the GAC biofilm. Metabolic reconstruction revealed that all anammox organisms highly expressed the core metabolic enzymes and showed a high metabolic versatility. Pathways for dissimilatory nitrate reduction to ammonium (DNRA) coupled to volatile fatty acids (VFAs) oxidation likely assist anammox bacteria to survive unfavorable conditions and facilitate switches between lifestyles in oxygen fluctuating environments. The new Ca. Kuenenia species dominated the anammox community of the GAC biofilm, specifically may be enhanced by the uniquely encoded flexible ammonium and iron acquisition strategies. The new Ca. Brocadia species likely has an extensive niche distribution that is simultaneously established in the anoxic tank and the GAC biofilm, the two distinct niches. The highly diverse and impressive metabolic versatility of anammox bacteria revealed in this study advance our understanding of the survival and application of anammox bacteria in the full-scale wastewater treatment system.}, }
@article {pmid34697646, year = {2022}, author = {Tighilt, L and Boulila, F and De Sousa, BFS and Giraud, E and Ruiz-Argüeso, T and Palacios, JM and Imperial, J and Rey, L}, title = {The Bradyrhizobium Sp. LmicA16 Type VI Secretion System Is Required for Efficient Nodulation of Lupinus Spp.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {844-855}, pmid = {34697646}, issn = {1432-184X}, support = {RTI2018-094985-B-100//ministerio de ciencia tecnolog&#xed;a y telecomunicaciones/ ; CNPq-GDE-204842/2018-2//cnpq brazil/ ; Erasmus+ Programme project 2019-1-ES01-KA107-063778//erasmus +/ ; National Exceptional Program (PNE)//ministry of higher education and scientific research of algeria/ ; ANR- 16-CE20-0013//anr grants (fr)/ ; ANR-20-CE20-0012//anr (fr)/ ; }, mesh = {*Bradyrhizobium/genetics ; *Lupinus/microbiology ; *Type VI Secretion Systems/genetics ; Root Nodules, Plant/microbiology ; Phylogeny ; Symbiosis/genetics ; }, abstract = {Many bacteria of the genus Bradyrhizobium are capable of inducing nodules in legumes. In this work, the importance of a type VI secretion system (T6SS) in a symbiotic strain of the genus Bradyrhizobium is described. T6SS of Bradyrhizobium sp. LmicA16 (A16) is necessary for efficient nodulation with Lupinus micranthus and Lupinus angustifolius. A mutant in the gene vgrG, coding for a component of the T6SS nanostructure, induced less nodules and smaller plants than the wild-type (wt) strain and was less competitive when co-inoculated with the wt strain. A16 T6SS genes are organized in a 26-kb DNA region in two divergent gene clusters of nine genes each. One of these genes codes for a protein (Tsb1) of unknown function but containing a methyltransferase domain. A tsb1 mutant showed an intermediate symbiotic phenotype regarding vgrG mutant and higher mucoidity than the wt strain in free-living conditions. T6SS promoter fusions to the lacZ reporter indicate expression in nodules but not in free-living cells grown in different media and conditions. The analysis of nodule structure revealed that the level of nodule colonization was significantly reduced in the mutants with respect to the wt strain.}, }
@article {pmid34696369, year = {2021}, author = {Hasiów-Jaroszewska, B and Boezen, D and Zwart, MP}, title = {Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities.}, journal = {Viruses}, volume = {13}, number = {10}, pages = {}, pmid = {34696369}, issn = {1999-4915}, mesh = {Biodiversity ; Computational Biology/methods ; DNA Viruses/genetics ; Genome, Viral/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenome/genetics ; Metagenomics/*methods ; Plant Weeds/*genetics/*virology ; Plants/genetics/virology ; Viruses/classification/genetics ; Viruses, Unclassified/genetics ; }, abstract = {High throughput sequencing (HTS) has revolutionised virus detection and discovery, allowing for the untargeted characterisation of whole viromes. Viral metagenomics studies have demonstrated the ubiquity of virus infection - often in the absence of disease symptoms - and tend to discover many novel viruses, highlighting the small fraction of virus biodiversity described to date. The majority of the studies using high-throughput sequencing to characterise plant viromes have focused on economically important crops, and only a small number of studies have considered weeds and wild plants. Characterising the viromes of wild plants is highly relevant, as these plants can affect disease dynamics in crops, often by acting as viral reservoirs. Moreover, the viruses in unmanaged systems may also have important effects on wild plant populations and communities. Here, we review metagenomic studies on weeds and wild plants to show the benefits and limitations of this approach and identify knowledge gaps. We consider key genomics developments that are likely to benefit the field in the near future. Although only a small number of HTS studies have been performed on weeds and wild plants, these studies have already discovered many novel viruses, demonstrated unexpected trends in virus distributions, and highlighted the potential of metagenomics as an approach.}, }
@article {pmid34695355, year = {2021}, author = {Fu, Y and Jia, M and Wang, F and Wang, Z and Mei, Z and Bian, Y and Jiang, X and Virta, M and Tiedje, JM}, title = {Strategy for Mitigating Antibiotic Resistance by Biochar and Hyperaccumulators in Cadmium and Oxytetracycline Co-contaminated Soil.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {24}, pages = {16369-16378}, doi = {10.1021/acs.est.1c03434}, pmid = {34695355}, issn = {1520-5851}, mesh = {Anti-Bacterial Agents/pharmacology ; Biodegradation, Environmental ; Cadmium ; Charcoal ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; Manure ; *Oxytetracycline ; Soil ; Soil Microbiology ; }, abstract = {The global prevalence of antibiotic resistance genes (ARGs) is of increasing concern as a serious threat to ecological security and human health. Irrigation with sewage and farmland application of manure or biosolids in agricultural practices introduce substantial selective agents such as antibiotics and toxic metals, aggravating the transfer of ARGs from the soil environment to humans via the food chain. To address this issue, a hyperaccumulator (Sedum plumbizincicola) combined with biochar amendment was first used to investigate the mitigation of the prevalence of ARGs in cadmium and oxytetracycline co-contaminated soil by conducting a pot experiment. The addition of biochar affected the distribution of ARGs in soil and plants differently by enhancing their prevalence in the soil but restraining transmission from the soil to S. plumbizincicola. The planting of S. plumbizincicola resulted in an increase in ARGs in the soil environment. A structural equation model illustrated that mobile genetic elements played a dominant role in shaping the profile of ARGs. Taken together, these findings provide a practical understanding for mitigating the prevalence of ARGs in this soil system with complex contamination and can have profound significance for agricultural management in regard to ARG dissemination control.}, }
@article {pmid34694450, year = {2022}, author = {Yang, X and Li, Y and Niu, B and Chen, Q and Hu, Y and Yang, Y and Song, L and Wang, J and Zhang, G}, title = {Temperature and Precipitation Drive Elevational Patterns of Microbial Beta Diversity in Alpine Grasslands.}, journal = {Microbial ecology}, volume = {84}, number = {4}, pages = {1141-1153}, doi = {10.1007/s00248-021-01901-w}, pmid = {34694450}, issn = {1432-184X}, support = {41871066//national natural science foundation of china/ ; 41471055//national natural science foundation of china/ ; XDA20050101//strategic priority research program (a) of the chinese academy of sciences/ ; 2019QZKK0503//second tibetan plateau scientific expedition and research program (step)/ ; }, mesh = {*Grassland ; *Ecosystem ; Temperature ; Biodiversity ; Soil/chemistry ; Archaea ; Bacteria/genetics ; }, abstract = {Understanding the mechanisms underlying biodiversity patterns is a central issue in ecology, while how temperature and precipitation jointly control the elevational patterns of microbes is understudied. Here, we studied the effects of temperature, precipitation and their interactions on the alpha and beta diversity of soil archaea and bacteria in alpine grasslands along an elevational gradient of 4300-5200 m on the Tibetan Plateau. Alpha diversity was examined on the basis of species richness and evenness, and beta diversity was quantified with the recently developed metric of local contributions to beta diversity (LCBD). Typical alpine steppe and meadow ecosystems were distributed below and above 4850 m, respectively, which was consistent with the two main constraints of mean annual temperature (MAT) and mean annual precipitation (MAP). Species richness and evenness showed decreasing elevational patterns in archaea and nonsignificant or U-shaped patterns in bacteria. The LCBD of both groups exhibited significant U-shaped elevational patterns, with the lowest values occurring at 4800 m. For the three diversity metrics, soil pH was the primary explanatory variable in archaea, explaining over 20.1% of the observed variation, whereas vegetation richness, total nitrogen and the K/Al ratio presented the strongest effects on bacteria, with relative importance values of 16.1%, 12.5% and 11.6%, respectively. For the microbial community composition of both archaea and bacteria, the moisture index showed the dominant effect, explaining 17.6% of the observed variation, followed by MAT and MAP. Taken together, temperature and precipitation exerted considerable indirect effects on microbial richness and evenness through local environmental and energy supply-related variables, such as vegetation richness, whereas temperature exerted a larger direct influence on LCBD and the community composition. Our findings highlighted the profound influence of temperature and precipitation interactions on microbial beta diversity in alpine grasslands on the Tibetan Plateau.}, }
@article {pmid34693460, year = {2022}, author = {Zada, S and Sajjad, W and Rafiq, M and Ali, S and Hu, Z and Wang, H and Cai, R}, title = {Cave Microbes as a Potential Source of Drugs Development in the Modern Era.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {676-687}, pmid = {34693460}, issn = {1432-184X}, support = {32070113//national natural science foundation of china/ ; 2019ST023//guangdong science and technology department/ ; 2020PC0052//pifi fellowship from the chinese academy of sciences/ ; }, mesh = {Humans ; *Caves ; *Microbiota ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The world is constantly facing threats, including the emergence of new pathogens and antibiotic resistance among extant pathogens, which is a matter of concern. Therefore, the need for natural and effective sources of drugs is inevitable. The ancient and pristine ecosystems of caves contain a unique microbial world and could provide a possible source of antimicrobial metabolites. The association between humans and caves is as old as human history itself. Historically, cave environments have been used to treat patients with respiratory tract infections, which is referred to as speleotherapy. Today, the pristine environment of caves that comprise a poorly explored microbial world is a potential source of antimicrobial and anticancer drugs. Oligotrophic conditions in caves enhance the competition among microbial communities, and unique antimicrobial agents may be used in this competition. This review suggests that the world needs a novel and effective source of drug discovery. Therefore, being the emerging spot of modern human civilization, caves could play a crucial role in the current medical crisis, and cave microorganisms may have the potential to produce novel antimicrobial and anticancer drugs.}, }
@article {pmid34693062, year = {2021}, author = {Lahlali, R and Ibrahim, DSS and Belabess, Z and Kadir Roni, MZ and Radouane, N and Vicente, CSL and Menéndez, E and Mokrini, F and Barka, EA and Galvão de Melo E Mota, M and Peng, G}, title = {High-throughput molecular technologies for unraveling the mystery of soil microbial community: challenges and future prospects.}, journal = {Heliyon}, volume = {7}, number = {10}, pages = {e08142}, pmid = {34693062}, issn = {2405-8440}, abstract = {Soil microbial communities play a crucial role in soil fertility, sustainability, and plant health. However, intensive agriculture with increasing chemical inputs and changing environments have influenced native soil microbial communities. Approaches have been developed to study the structure, diversity, and activity of soil microbes to better understand the biology and plant-microbe interactions in soils. Unfortunately, a good understanding of soil microbial community remains a challenge due to the complexity of community composition, interactions of the soil environment, and limitations of technologies, especially related to the functionality of some taxa rarely detected using conventional techniques. Culture-based methods have been shown unable and sometimes are biased for assessing soil microbial communities. To gain further knowledge, culture-independent methods relying on direct analysis of nucleic acids, proteins, and lipids are worth exploring. In recent years, metagenomics, metaproteomics, metatranscriptomics, and proteogenomics have been increasingly used in studying microbial ecology. In this review, we examined the importance of microbial community to soil quality, the mystery of rhizosphere and plant-microbe interactions, and the biodiversity and multi-trophic interactions that influence the soil structure and functionality. The impact of the cropping system and climate change on the soil microbial community was also explored. Importantly, progresses in molecular biology, especially in the development of high-throughput biotechnological tools, were extensively assessed for potential uses to decipher the diversity and dynamics of soil microbial communities, with the highlighted advantages/limitations.}, }
@article {pmid34690949, year = {2021}, author = {Sichert, A and Cordero, OX}, title = {Polysaccharide-Bacteria Interactions From the Lens of Evolutionary Ecology.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {705082}, pmid = {34690949}, issn = {1664-302X}, abstract = {Microbes have the unique ability to break down the complex polysaccharides that make up the bulk of organic matter, initiating a cascade of events that leads to their recycling. Traditionally, the rate of organic matter degradation is perceived to be limited by the chemical and physical structure of polymers. Recent advances in microbial ecology, however, suggest that polysaccharide persistence can result from non-linear growth dynamics created by the coexistence of alternate degradation strategies, metabolic roles as well as by ecological interactions between microbes. This complex "landscape" of degradation strategies and interspecific interactions present in natural microbial communities appears to be far from evolutionarily stable, as frequent gene gain and loss reshape enzymatic repertoires and metabolic roles. In this perspective, we discuss six challenges at the heart of this problem, ranging from the evolution of genetic repertoires, phenotypic heterogeneity in clonal populations, the development of a trait-based ecology, and the impact of metabolic interactions and microbial cooperation on degradation rates. We aim to reframe some of the key questions in the study of polysaccharide-bacteria interactions in the context of eco-evolutionary dynamics, highlighting possible research directions that, if pursued, would advance our understanding of polysaccharide degraders at the interface between biochemistry, ecology and evolution.}, }
@article {pmid34688835, year = {2022}, author = {Arca-Suárez, J and Rodiño-Janeiro, BK and Pérez, A and Guijarro-Sánchez, P and Vázquez-Ucha, JC and Cruz, F and Gómez-Garrido, J and Alioto, TS and Álvarez-Tejado, M and Gut, M and Gut, I and Oviaño, M and Beceiro, A and Bou, G and , }, title = {Emergence of 16S rRNA methyltransferases among carbapenemase-producing Enterobacterales in Spain studied by whole-genome sequencing.}, journal = {International journal of antimicrobial agents}, volume = {59}, number = {1}, pages = {106456}, doi = {10.1016/j.ijantimicag.2021.106456}, pmid = {34688835}, issn = {1872-7913}, mesh = {Drug Resistance, Bacterial/*genetics ; Enterobacteriaceae/*genetics/*metabolism ; Genetic Variation ; Genome-Wide Association Study ; Genotype ; Humans ; Methyltransferases/*genetics/*metabolism ; RNA, Ribosomal, 16S/*genetics ; Spain ; beta-Lactamases/*genetics/*metabolism ; }, abstract = {The emergence of 16S rRNA methyltransferases (RMTs) in Gram-negative pathogens bearing other clinically relevant resistance mechanisms, such as carbapenemase-producing Enterobacterales (CPE), is becoming an alarming concern. We investigated the prevalence, antimicrobial susceptibility, resistance mechanisms, molecular epidemiology and genetic support of RMTs in CPE isolates from Spain. This study included a collection of 468 CPE isolates recovered during 2018 from 32 participating Spanish hospitals. MICs were determined using the broth microdilution method, the agar dilution method (fosfomycin) or MIC gradient strips (plazomicin). All isolates were subjected to hybrid whole-genome sequencing (WGS). Sequence types (STs), core genome phylogenetic relatedness, horizontally acquired resistance mechanisms, plasmid analysis and the genetic environment of RMTs were determined in silico from WGS data in all RMT-positive isolates. Among the 468 CPE isolates evaluated, 24 isolates (5.1%) recovered from nine different hospitals spanning five Spanish regions showed resistance to all aminoglycosides and were positive for an RMT (21 RmtF, 2 ArmA and 1 RmtC). All RMT-producers showed high-level resistance to all aminoglycosides, including plazomicin, and in most cases exhibited an extensively drug-resistant susceptibility profile. The RMT-positive isolates showed low genetic diversity and were global clones of Klebsiella pneumoniae (ST147, ST101, ST395) and Enterobacter cloacae (ST93) bearing blaOXA-48, blaNDM-1 or blaVIM-1 carbapenemase genes. RMTs were harboured in five different multidrug resistance plasmids and linked to efficient mobile genetic elements. Our findings highlight that RMTs are emerging among clinical CPE isolates from Spain and their spread should be monitored to preserve the future clinical utility of aminoglycosides and plazomicin.}, }
@article {pmid34688084, year = {2021}, author = {Uroosa,  and Kazmi, SSUH and Zhong, X and Xu, H}, title = {An approach to evaluating the acute toxicity of nitrofurazone on community functioning using protozoan periphytons.}, journal = {Marine pollution bulletin}, volume = {173}, number = {Pt B}, pages = {113066}, doi = {10.1016/j.marpolbul.2021.113066}, pmid = {34688084}, issn = {1879-3363}, mesh = {Ecosystem ; *Nitrofurazone/toxicity ; *Periphyton ; Phenotype ; }, abstract = {The acute toxicity of nitrofurazone on community functioning was studied using an acute toxicity test. Consequently, 14-day protozoan periphyton assemblages were used as test organism communities, under a range of nitrofurazone concentrations including 0 (control), 0.5, 3, 6, and 12 mg ml[-1] within 0, 2, 4, 6, 8, 10, and 12 h time duration. Fuzzy coding system of functional traits classified the test protozoan periphyton community into six major traits and 15 categories. Briefly, community-weighted means (CWM) were used to identify the community functioning of test protozoan assemblage. Inferences demonstrate a drastic/significant variation in the functional patterns of the test organisms at a high concentration (12 mg ml[-1]) after an exposure time of 12 h, but the functional diversity indices leveled off at the exposure time of 10 h and then dropped sharply. These results suggested that nitrofurazone may significantly influence the community functioning in marine ecosystems.}, }
@article {pmid34687997, year = {2022}, author = {Macías-Pérez, LA and Levard, C and Barakat, M and Angeletti, B and Borschneck, D and Poizat, L and Achouak, W and Auffan, M}, title = {Contrasted microbial community colonization of a bauxite residue deposit marked by a complex geochemical context.}, journal = {Journal of hazardous materials}, volume = {424}, number = {Pt B}, pages = {127470}, doi = {10.1016/j.jhazmat.2021.127470}, pmid = {34687997}, issn = {1873-3336}, mesh = {*Aluminum Oxide ; Biodegradation, Environmental ; *Microbiota ; Soil ; Soil Microbiology ; }, abstract = {Bauxite residue is the alkaline byproduct generated during alumina extraction and is commonly landfilled in open-air deposits. The growth in global alumina production have raised environmental concerns about these deposits since no large-scale reuses exist to date. Microbial-driven techniques including bioremediation and critical metal bio-recovery are now considered sustainable and cost-effective methods to revalorize bauxite residues. However, the establishment of microbial communities and their active role in these strategies are still poorly understood. We thus determined the geochemical composition of different bauxite residues produced in southern France and explored the development of bacterial and fungal communities using Illumina high-throughput sequencing. Physicochemical parameters were influenced differently by the deposit age and the bauxite origin. Taxonomical analysis revealed an early-stage microbial community dominated by haloalkaliphilic microorganisms and strongly influenced by chemical gradients. Microbial richness, diversity and network complexity increased significantly with the deposit age, reaching an equilibrium community composition similar to typical soils after decades of natural weathering. Our results suggested that salinity, pH, and toxic metals affected the bacterial community structure, while fungal community composition showed no clear correlations with chemical variations.}, }
@article {pmid34686899, year = {2022}, author = {McLeish, AG and Gong, S and Greenfield, P and Midgley, DJ and Paulsen, IT}, title = {Microbial Community Shifts on Organic Rocks of Different Maturities Reveal potential Catabolisers of Organic Matter in Coal.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {780-793}, pmid = {34686899}, issn = {1432-184X}, support = {2017708//Macquarie University/ ; }, mesh = {*Coal ; RNA, Ribosomal, 16S/genetics ; Methane/metabolism ; *Microbiota ; Microbial Consortia/genetics ; }, abstract = {The global trend of transiting to more renewable energy sources requires transition fuels, such as coal seam gas, to supplement and secure energy needs. In order to optimise strategies and technologies for enhancing gas production, an understanding of the fundamental microbial processes and interactions would be advantageous. Models have recently begun mapping the microbial roles and interactions in coal seam environments, from direct coal degradation to methanogenesis. This study seeks to expand those models by observing community compositional shifts in the presence of differing organic matter by conducting 16S rRNA microbial surveys using formation water from the Surat and Sydney Basins grown on varying types of organic matter (black and brown coal, oil shale, humic acid, and lignin). A total of 135 microbes were observed to become enriched in the presence of added organic matter in comparison to carbon-free treatments. These surveys allowed detailed analysis of microbial compositions in order to extrapolate which taxa favour growth in the presence of differing organic matter. This study has experimentally demonstrated shifts in the microbial community composition due to differing carbon sources and, for the first time, generated a conceptual model to map putative degradation pathways regarding subsurface microbial consortia.}, }
@article {pmid34686898, year = {2022}, author = {Qi, R and Xue, N and Zhou, X and Zhao, L and Song, W and Yang, Y}, title = {Distinct Composition and Assembly Processes of Bacterial Communities in a River from the Arid Area: Ecotypes or Habitat Types?.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {769-779}, pmid = {34686898}, issn = {1432-184X}, mesh = {Humans ; *Rivers/microbiology ; Water Microbiology ; Ecotype ; Bacteria/genetics/metabolism ; *Microbiota ; Water/metabolism ; }, abstract = {The composition, function, and assembly mechanism of the bacterial community are the focus of microbial ecology. Unsupervised machine learning may be a better way to understand the characteristics of bacterial metacommunities compared to the empirical habitat types. In this study, the composition, potential function, and assembly mechanism of the bacterial community in the arid river were analysed. The Dirichlet multinomial mixture method recognised four ecotypes across the three habitats (biofilm, water, and sediment). The bacterial communities in water are more sensitive to human activities. Bacterial diversity and richness in water decreased as the intensity of human activities increased from the region of water II to water I. Significant differences in the composition and potential function profile of bacterial communities between water ecotypes were also observed, such as higher relative abundance in the taxonomic composition of Firmicutes and potential function of plastic degradation in water I than those in water II. Habitat filtering may play a more critical role in the assembly of bacterial communities in the river biofilm, while stochastic processes dominate the assembly process of bacterial communities in water and sediment. In water I, salinity and mean annual precipitation were the main drivers shaping the biogeography of taxonomic structure, while mean annual temperature, total organic carbon, and ammonium nitrogen were the main environmental factors influencing the taxonomic structure in water II. These results would provide conceptual frameworks about choosing habitat types or ecotypes for the research of microbial communities among different niches in the aquatic environment.}, }
@article {pmid34683463, year = {2021}, author = {Van den Abbeele, P and Duysburgh, C and Cleenwerck, I and Albers, R and Marzorati, M and Mercenier, A}, title = {Consistent Prebiotic Effects of Carrot RG-I on the Gut Microbiota of Four Human Adult Donors in the SHIME[®] Model despite Baseline Individual Variability.}, journal = {Microorganisms}, volume = {9}, number = {10}, pages = {}, pmid = {34683463}, issn = {2076-2607}, abstract = {The human gut microbiome is currently recognized to play a vital role in human biology and development, with diet as a major modulator. Therefore, novel indigestible polysaccharides that confer a health benefit upon their fermentation by the microbiome are under investigation. Based on the recently demonstrated prebiotic potential of a carrot-derived pectin extract enriched for rhamnogalacturonan I (cRG-I), the current study aimed to assess the impact of cRG-I upon repeated administration using the M-SHIME technology (3 weeks at 3g cRG-I/d). Consistent effects across four simulated adult donors included enhanced levels of acetate (+21.1 mM), propionate (+17.6 mM), and to a lesser extent butyrate (+4.1 mM), coinciding with a marked increase of OTUs related to Bacteroides dorei and Prevotella species with versatile enzymatic potential likely allowing them to serve as primary degraders of cRG-I. These Bacteroidetes members are able to produce succinate, explaining the consistent increase of an OTU related to the succinate-converting Phascolarctobacterium faecium (+0.47 log10(cells/mL)). While the Bifidobacteriaceae family remained unaffected, a specific OTU related to Bifidobacterium longum increased significantly upon cRG-I treatment (+1.32 log10(cells/mL)). Additional monoculture experiments suggested that Bifidobacterium species are unable to ferment cRG-I structures as such and that B. longum probably feeds on arabinan and galactan side chains of cRG-I, released by aforementioned Bacteroidetes members. Overall, this study confirms the prebiotic potential of cRG-I and additionally highlights the marked consistency of the microbial changes observed across simulated subjects, suggesting the involvement of a specialized consortium in cRG-I fermentation by the human gut microbiome.}, }
@article {pmid34683446, year = {2021}, author = {Bi, S and Lai, H and Guo, D and Liu, X and Wang, G and Chen, X and Liu, S and Yi, H and Su, Y and Li, G}, title = {The Characteristics of Intestinal Bacterial Community in Three Omnivorous Fishes and Their Interaction with Microbiota from Habitats.}, journal = {Microorganisms}, volume = {9}, number = {10}, pages = {}, pmid = {34683446}, issn = {2076-2607}, support = {31772853//National Natural Science Foundation of China/ ; }, abstract = {Artificial fishery habitats have been extensively used for fishery resource protection and water habitat restoration, and they could attract a large number of omnivorous fishes to gather together. This study intended to reveal the relationship between bacterial communities in the habitats (water and sediment) and intestines of omnivorous fishes (Oreochromis mossambicus, Toxabramis houdemeri and Hemiculter leucisculus). Therefore, we investigated the bacterial communities of samples collected from intestines, water, and sediments in artificial fishery habitats via 16S rRNA metabarcoding high-throughput sequencing technology. The results showed that there were significant differences in the composition, core indicators, diversity and prediction functions in water, sediments, and intestinal microbial communities of the three omnivorous fish. The microbial diversities were significantly higher in habitats than in intestines. The analysis of similarity (ANOSIM) and nonmetric multidimensional scaling (NMDS) results indicated that the intestine microbial communities (T. houdemeri and H. leucisculus) were more similar to the water microbiota, but the intestine microbial communities (O. mossambicus) were more similar to the sediments. Source tracking analysis also confirmed that the contribution of habitat characteristics to omnivorous fish intestinal microorganisms was different; the sediment had a greater contribution than water to the intestinal microbiota of O. mossambicus, which was consistent with their benthic habit. Moreover, the functional prediction results showed that there were unique core indicators and functions between the bacterial community of habitats and intestines. Altogether, these results can enhance our understanding of the bacterial composition and functions about omnivorous fish intestines and their living with habitats, which have provided new information for the ecological benefits of artificial fishery habitats from the perspective of bacterial ecology and contributed to apply artificial fishery habitats in more rivers.}, }
@article {pmid34683378, year = {2021}, author = {Wang, Y and Brons, JK and van Elsas, JD}, title = {Considerations on the Identity and Diversity of Organisms Affiliated with Sphingobacterium multivorum-Proposal for a New Species, Sphingobacterium paramultivorum.}, journal = {Microorganisms}, volume = {9}, number = {10}, pages = {}, pmid = {34683378}, issn = {2076-2607}, support = {201706240132//China Scholarship Council/ ; }, abstract = {Plant biomass offers great potential as a sustainable resource, and microbial consortia are primordial in its bioconversion. The wheat-straw-biodegradative bacterial strain w15 has drawn much attention as a result of its biodegradative potential and superior degradation performance in bacterial-fungal consortia. Strain w15 was originally assigned to the species Sphingobacterium multivorum based on its 16S ribosomal RNA (rRNA) gene sequence. A closer examination of this taxonomic placement revealed that the sequence used has 98.9% identity with the 'divergent' 16S rRNA gene sequence of S. multivorum NCTC 11343[T], yet lower relatedness with the canonical 16S rRNA sequence. A specific region of the gene, located between positions 186 and 210, was found to be highly variable and determinative for the divergence. To solve the identity of strain w15, genome metrics and analyses of ecophysiological niches were undertaken on a selection of strains assigned to S. multivorum and related species. These analyses separated all strains into three clusters, with strain w15, together with strain BIGb0170, constituting a separate radiation, next to S. multivorum and S. siyangense. Moreover, the strains denoted FDAARGOS 1141 and 1142 were placed inside S. siyangense. We propose the renaming of strains w15 and BIGb0170 as members of the novel species, coined Sphingobacterium paramultivorum.}, }
@article {pmid34683332, year = {2021}, author = {Amat, S and Holman, DB and Schmidt, K and Menezes, ACB and Baumgaertner, F and Winders, T and Kirsch, JD and Liu, T and Schwinghamer, TD and Sedivec, KK and Dahlen, CR}, title = {The Nasopharyngeal, Ruminal, and Vaginal Microbiota and the Core Taxa Shared across These Microbiomes in Virgin Yearling Heifers Exposed to Divergent In Utero Nutrition during Their First Trimester of Gestation and in Pregnant Beef Heifers in Response to Mineral Supplementation.}, journal = {Microorganisms}, volume = {9}, number = {10}, pages = {}, pmid = {34683332}, issn = {2076-2607}, abstract = {In the present study, we evaluated whether the nasopharyngeal, ruminal, and vaginal microbiota would diverge (1) in virgin yearling beef heifers (9 months old) due to the maternal restricted gain during the first trimester of gestation; and (2) in pregnant beef heifers in response to the vitamin and mineral (VTM) supplementation during the first 6 months of pregnancy. As a secondary objective, using the microbiota data obtained from these two cohorts of beef heifers managed at the same location and sampled at the same time, we performed a holistic assessment of the microbial ecology residing within the respiratory, gastrointestinal, and reproductive tract of cattle. Our 16S rRNA gene sequencing results revealed that both α and β-diversity of the nasopharyngeal, ruminal and vaginal microbiota did not differ between virgin heifers raised from dams exposed to either a low gain (targeted average daily gain of 0.28 kg/d, n = 22) or a moderate gain treatment (0.79 kg/d, n = 23) during the first 84 days of gestation. Only in the vaginal microbiota were there relatively abundant genera that were affected by maternal rate of gain during early gestation. Whilst there was no significant difference in community structure and diversity in any of the three microbiota between pregnant heifers received no VTM (n = 15) and VTM supplemented (n = 17) diets, the VTM supplementation resulted in subtle compositional alterations in the nasopharyngeal and ruminal microbiota. Although the nasopharyngeal, ruminal, and vaginal microbiota were clearly distinct, a total of 41 OTUs, including methanogenic archaea, were identified as core taxa shared across the respiratory, gastrointestinal, and reproductive tracts of both virgin and pregnant heifers.}, }
@article {pmid34678684, year = {2021}, author = {de Freitas Nunes Oliveira, A and Saboya de Sousa, LI and Silva da Costa, VA and de Andrade, JVT and Lucena Lima, LA and de Sales, PAF and da Silva, DF and de Araujo Pereira, AP and Maciel Melo, VM}, title = {Long-term effects of grazing on the biological, chemical, and physical soil properties of the Caatinga biome.}, journal = {Microbiological research}, volume = {253}, number = {}, pages = {126893}, doi = {10.1016/j.micres.2021.126893}, pmid = {34678684}, issn = {1618-0623}, mesh = {Animals ; Brazil ; *Ecosystem ; *Herbivory ; Microbiota/physiology ; Nitrophenols/analysis ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {Soil degradation is a global issue that affects both plant productivity and human life. Intensive grazing practices can accelerate this process, mainly due to rapid removal of biomass from the soil surface. However, the long-term effects of grazing on biological, chemical, and physical properties remain poorly understood, particularly in tropical drylands, such as the Caatinga biome. Our aim was to evaluate the soil properties and combine both culture-dependent and -independent analyses to assess metabolic activity and bacterial community structure. We collected samples (0-20 cm) of three different types of soil in the Caatinga biome: secondary Caatinga forest (NC), grazing exclusion (GE), and degraded areas by overgrazing (OG). We sought to investigate how grazing affects soil properties to determine the effectiveness of grazing exclusion in the restoration of soil fertility/functions. Redundancy analysis demonstrated NC were positively correlated with organic carbon (λ = 0.18, p = 0.0012) and total nitrogen (λ = 0.16, p = 0.0011), while OG was correlated with harmful soil parameters such as Na[+] (λ = 0.08, p = 0.0400), electric conductivity (λ = 0.13, p = 0.0060) and exchangeable acidity (λ = 0.11, p = 0.0030). In addition, GE showed lower aluminum content and saturation, reducing these harmful parameters by 48 % and 34 %, respectively. Also, GE showed the highest values for the β-glucosidase (63.62 mg ρ-nitrophenol kg[-1] h[-1]) and arylsulfatase (5.8 mg ρ-nitrophenol kg[-1] h[-1]) activities. Changes in bacterial community structure were significant (p = 0.0096), with a higher difference comparing GE and OG (p = 0.0135). The GE area showed 20 % more phosphate solubilizers than OG, but there were no differences for siderophores production. All isolates were halotolerant and had at least 60 % nitrogen fixers. Our findings indicate that while soil recovery is slow, with grazing-exclusion areas presenting 18 years of implantation, it seems to improve in subsequent years. Finally, our results provide evidence that microbe-based technologies can mitigate soil degradation in the Caatinga biome.}, }
@article {pmid34678229, year = {2022}, author = {Alderliesten, JB and Zwart, MP and de Visser, JAGM and Stegeman, A and Fischer, EAJ}, title = {Second compartment widens plasmid invasion conditions: Two-compartment pair-formation model of conjugation in the gut.}, journal = {Journal of theoretical biology}, volume = {533}, number = {}, pages = {110937}, doi = {10.1016/j.jtbi.2021.110937}, pmid = {34678229}, issn = {1095-8541}, mesh = {Animals ; Bacteria ; *Conjugation, Genetic ; Drug Resistance, Microbial ; *Gene Transfer, Horizontal ; Humans ; Plasmids/genetics ; }, abstract = {Understanding under which conditions conjugative plasmids encoding antibiotic resistance can invade bacterial communities in the gut is of particular interest to combat the spread of antibiotic resistance within and between animals and humans. We extended a one-compartment model of conjugation to a two-compartment model, to analyse how differences in plasmid dynamics in the gut lumen and at the gut wall affect the invasion of plasmids. We compared scenarios with one and two compartments, different migration rates between the lumen and wall compartments, and different population dynamics. We focused on the effect of attachment and detachment rates on plasmid dynamics, explicitly describing pair formation followed by plasmid transfer in the pairs. The parameter space allowing plasmid invasion in the one-compartment model is affected by plasmid costs and intrinsic conjugation rates of the transconjugant, but not by these characteristics of the donor. The parameter space allowing plasmid invasion in the two-compartment model is affected by attachment and detachment rates in the lumen and wall compartment, and by the bacterial density at the wall. The one- and two-compartment models predict the same parameter space for plasmid invasion if the conditions in both compartments are equal to the conditions in the one-compartment model. In contrast, the addition of the wall compartment widens the parameter space allowing invasion compared with the one-compartment model, if the density at the wall is higher than in the lumen, or if the attachment rate at the wall is high and the detachment rate at the wall is low. We also compared the pair-formation models with bulk-conjugation models that describe conjugation by instantaneous transfer of the plasmid at contact between cells, without explicitly describing pair formation. Our results show that pair-formation and bulk-conjugation models predict the same parameter space for plasmid invasion. From our simulations, we conclude that conditions at the gut wall should be taken into account to describe plasmid dynamics in the gut and that transconjugant characteristics rather than donor characteristics should be used to parameterize the models.}, }
@article {pmid34676439, year = {2022}, author = {Sadiq, FA and Wenwei, L and Wei, C and Jianxin, Z and Zhang, H}, title = {Transcriptional Changes in Bifidobacterium bifidum Involved in Synergistic Multispecies Biofilms.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {922-934}, pmid = {34676439}, issn = {1432-184X}, support = {31871774//National Natural Science Foundation of China/ ; JUSRP51903B//the Fundamental Research Funds for the Central Universities/ ; JUFSTR20180102//the National First-class Discipline Program of Food Science and Technology/ ; }, mesh = {Infant ; Humans ; *Bifidobacterium bifidum/metabolism ; Bifidobacterium/genetics/metabolism ; *Gastrointestinal Microbiome ; Biofilms ; *Microbiota ; }, abstract = {Bifidobacterium bifidum is part of the core microbiota of healthy infant guts where it may form biofilms on epithelial cells, mucosa, and food particles in the gut lumen. Little is known about transcriptional changes in B. bifidum engaged in synergistic multispecies biofilms with ecologically relevant species of the human gut. Recently, we reported prevalence of synergism in mixed-species biofilms formed by the human gut microbiota. This study represents a comparative gene expression analysis of B. bifidum when grown in a single-species biofilm and in two multispecies biofilm consortia with Bifidobacterium longum subsp. infantis, Bacteroides ovatus, and Parabacteroides distasonis in order to identify genes involved in this adaptive process in mixed biofilms and the influence on its metabolic and functional traits. Changes up to 58% and 43% in its genome were found when it grew in three- and four-species biofilm consortia, respectively. Upregulation of genes of B. bifidum involved in carbohydrate metabolism (particularly the galE gene), quorum sensing (luxS and pfs), and amino acid metabolism (especially branched chain amino acids) in both multispecies biofilms, compared to single-species biofilms, suggest that they may be contributing factors for the observed synergistic biofilm production when B. bifidum coexists with other species in a biofilm.}, }
@article {pmid34676060, year = {2021}, author = {Li, H and Sun, J and Wang, X and Shi, J}, title = {Oral microbial diversity analysis among atrophic glossitis patients and healthy individuals.}, journal = {Journal of oral microbiology}, volume = {13}, number = {1}, pages = {1984063}, pmid = {34676060}, issn = {2000-2297}, abstract = {Atrophic glossitis is a common disease in oral mucosal diseases. The Current studies have found the human oral cavity contains numerous and diverse microorganisms, their composition and diversity can be changed by various oral diseases. To understand the composition and diversity of oral microbiome in atrophic glossitis is better to explore the cause and mechanism of atrophic glossitis. The salivary microbiome is comprised of indigenous oral microorganisms that are specific to each person, exhibits long-term stability. We used llumina MiSeq high-throughput sequencing based on the V3-V4 region of the bacterial 16S rRNA gene and the internal transcribed spacer (ITS) region of fungal rRNA genes from saliva in atrophic glossitis patients and healthy individuals to explore the composition and diversity of oral microbiome. In our reports, it showed a lower diversity of bacteria and fungi in atrophic glossitis patients than in healthy individuals. The data further suggests that Lactobacillus and Saccharomycetales were potential indicators for the initiation and development of atrophic glossitis. Moreover, we also discuss the relationship between the oral microbial ecology and atrophic glossitis.}, }
@article {pmid34674014, year = {2022}, author = {Agbulu, V and Zaman, R and Ishangulyyeva, G and Cahill, JF and Erbilgin, N}, title = {Host Defense Metabolites Alter the Interactions between a Bark Beetle and its Symbiotic Fungi.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {834-843}, pmid = {34674014}, issn = {1432-184X}, mesh = {Animals ; *Coleoptera/microbiology ; Plant Bark ; *Pinus/microbiology ; Symbiosis ; *Weevils/microbiology ; Monoterpenes/metabolism ; }, abstract = {Successful host plant colonization by tree-killing bark beetle-symbiotic fungal complexes depends on host suitability, which is largely determined by host defense metabolites such as monoterpenes. Studies have shown the ability of specific blends of host monoterpenes to influence bark beetles or their fungal symbionts, but how biologically relevant blends of host monoterpenes influence bark beetle-symbiotic fungal interaction is unknown. We tested how interactions between two host species (lodgepole pine or jack pine) and two fungal symbionts of mountain pine beetle (Grosmannia clavigera or Ophiostoma montium) affect the performance of adult female beetles in vitro. Beetles treated with the propagules of G. clavigera or O. montium or not treated (natural fungal load) were introduced into media amended with a blend of the entire monoterpene profile of either host species and beetle performance was compared. Overall, host blends altered beetle performance depending on the fungal species used in the beetle amendment. When beetles were amended with G. clavigera, their performance was superior over beetles amended with O. montium in either host blend. Furthermore, G. clavigera-amended beetles performed better in media amended with host blends than without a host blend; in contrast, O. montium-amended beetles performed better in media without a host blend than with a host blend. Overall, this study showed that host defense metabolites affect host suitability to bark beetles through influencing their fungal symbionts and that different species of fungal symbionts respond differentlly to host defense metabolites.}, }
@article {pmid34673954, year = {2021}, author = {Wang, D and Du, Y and Huang, S and You, Z and Zheng, D and Liu, Y}, title = {Combined supplementation of sodium humate and glutamine reduced diarrhea incidence of weaned calves by intestinal microbiota and metabolites changes.}, journal = {Journal of animal science}, volume = {99}, number = {11}, pages = {}, pmid = {34673954}, issn = {1525-3163}, mesh = {Animal Feed/analysis ; Animals ; Cattle ; Diarrhea/prevention &amp; control/veterinary ; Diet/veterinary ; Dietary Supplements ; *Gastrointestinal Microbiome ; *Glutamine ; Incidence ; Sodium ; Weaning ; }, abstract = {This study was conducted to investigate the effects of combined supplementation of sodium humate (HNa) and glutamine (Gln) on growth performance, diarrhea incidence, serum parameters, intestinal microbiome, and metabolites of weaned calves. In Exp. 1, 40 calves were randomly assigned to four treatments: 1) NC (negative control, basal diet), 2) 1% H+1% G (basal diet extra orally gavaged with 1 g of HNa and 1 g of Gln daily), 3) 3% H+1% G (basal diet extra orally gavaged with 3 g of HNa and 1 g of Gln daily), and 4) 5% H+1% G (basal diet extra orally gavaged with 5 g of HNa and 1 g of Gln daily). The HNa and Gln were together mixed with 100 mL of milk replacer (51 to 58 d of age) or water (59 to 72 d of age) and orally administrated to each calf from a bottle before morning feeding. In a 21-d trial, calves on the 5% HNa+1% Gln group had higher (P < 0.05) average daily gain (ADG) and lower (P < 0.05) diarrhea incidence than those in the control group. In Exp. 2, 20 calves were randomly assigned to two treatments fed with a basal diet and a basal diet supplemented with 100 mL of 5% HNa+1% Gln. In a 21-d trial, calves supplemented with HNa and Gln had higher (P < 0.05) ADG, IgG concentration and glutathione peroxidase (GSH-Px), and total antioxidant capacity (T-AOC) activities in the serum, but lower (P < 0.05) diarrhea incidence, as well as serum diamine oxidase (DAO), D-isomer of lactic acid (D-lac), tumor necrosis factor-α (TNF-α), and malondialdehyde (MDA) concentrations compared with control group. Results of intestinal microbiota indicated that supplementation with HNa and Gln significantly increased (P < 0.05) the abundance of intestinal beneficial microbiota. Moreover, supplementation with HNa and Gln altered 18 metabolites and enriched 6 Kyoto Encyclopedia of Genes and Genomes pathways in weaned calves. In conclusion, combined supplementation with HNa and Gln could decrease diarrhea incidence of weaned calves via altering intestinal microbial ecology and metabolism profile.}, }
@article {pmid34672730, year = {2021}, author = {Hussain, FA and Dubert, J and Elsherbini, J and Murphy, M and VanInsberghe, D and Arevalo, P and Kauffman, K and Rodino-Janeiro, BK and Gavin, H and Gomez, A and Lopatina, A and Le Roux, F and Polz, MF}, title = {Rapid evolutionary turnover of mobile genetic elements drives bacterial resistance to phages.}, journal = {Science (New York, N.Y.)}, volume = {374}, number = {6566}, pages = {488-492}, doi = {10.1126/science.abb1083}, pmid = {34672730}, issn = {1095-9203}, mesh = {Bacteriophages/*pathogenicity ; Evolution, Molecular ; Genetic Variation ; *Interspersed Repetitive Sequences ; Vibrio/*genetics/*virology ; }, abstract = {Although it is generally accepted that phages drive bacterial evolution, how these dynamics play out in the wild remains poorly understood. We found that susceptibility to viral killing in marine Vibrio is mediated by large and highly diverse mobile genetic elements. These phage defense elements display exceedingly fast evolutionary turnover, resulting in differential phage susceptibility among clonal bacterial strains while phage receptors remain invariant. Protection is cumulative, and a single bacterial genome can harbor 6 to 12 defense elements, accounting for more than 90% of the flexible genome among close relatives. The rapid turnover of these elements decouples phage resistance from other genomic features. Thus, resistance to phages in the wild follows evolutionary trajectories alternative to those predicted from laboratory-based evolutionary experiments.}, }
@article {pmid34671827, year = {2022}, author = {Carbajal-Valenzuela, IA and Muñoz-Sanchez, AH and Hernández-Hernández, J and Barona-Gómez, F and Truong, C and Cibrián-Jaramillo, A}, title = {Microbial Diversity in Cultivated and Feral Vanilla Vanilla planifolia Orchids Affected by Stem and Rot Disease.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {821-833}, pmid = {34671827}, issn = {1432-184X}, support = {285746//consejo nacional de ciencia y tecnolog&#xed;a/ ; 180631//newton fund/ ; }, mesh = {Humans ; *Vanilla/microbiology ; *Microbiota ; DNA, Ribosomal ; Bacteria/genetics ; Mexico ; }, abstract = {The worldwide production of vanilla, a native orchid from Mexico, is greatly affected by stem and root rot disease (SRD), typically associated with Fusarium oxysporum fungi. We hypothesized that the presence of Fusarium species in vanilla is not sufficient for the plant to express symptoms of the disease. We described the taxonomic composition of endophytic microbiomes in symptomatic and asymptomatic vanilla plants using 16S and ITS rDNA metabarcoding, and ITS Sanger sequences generated from fungal isolates. We compared the bacterial and fungal diversity in vanilla plants from a long-term plantation, and from feral plants found near abandoned plantations that did not present SRD symptoms. No significant differences were found in the species richness of the bacterial and fungal microbiome among feral, or asymptomatic and symptomatic cultivated vanilla. However, significant differences were detected in both fungal and bacterial diversity from different organs in the same plant, with roots being more diverse than stems. We found that Proteobacteria and Actinobacteria, as well as the fungal families Nectriaceae and Xylariaceae, constitute the core of the vanilla microbiome that inhabits the root and stem of both cultivated and feral plants. Our work provides information on the microbial diversity associated to root and stem rot in vanilla and lays the groundwork for a better understanding of the role of the microbiome in vanilla fungal diseases.}, }
@article {pmid34671826, year = {2022}, author = {Neely, WJ and Greenspan, SE and Stahl, LM and Heraghty, SD and Marshall, VM and Atkinson, CL and Becker, CG}, title = {Habitat Disturbance Linked with Host Microbiome Dispersion and Bd Dynamics in Temperate Amphibians.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {901-910}, pmid = {34671826}, issn = {1432-184X}, support = {Start-up fund//the university of alabama/ ; Walter F. Coxe Research Fund//alabama audubon/ ; }, mesh = {Animals ; *Chytridiomycota ; Batrachochytrium ; *Mycoses/microbiology ; *Microbiota ; Ranidae/microbiology ; Bacteria ; Anura ; }, abstract = {Anthropogenic habitat disturbances can dramatically alter ecological community interactions, including host-pathogen dynamics. Recent work has highlighted the potential for habitat disturbances to alter host-associated microbial communities, but the associations between anthropogenic disturbance, host microbiomes, and pathogens are unresolved. Amphibian skin microbial communities are particularly responsive to factors like temperature, physiochemistry, pathogen infection, and environmental microbial reservoirs. Through a field survey on wild populations of Acris crepitans (Hylidae) and Lithobates catesbeianus (Ranidae), we assessed the effects of habitat disturbance and connectivity on environmental bacterial reservoirs, Batrachochytrium dendrobatidis (Bd) infection, and skin microbiome composition. We found higher measures of microbiome dispersion (a measure of community variability) in A. crepitans from more disturbed ponds, supporting the hypothesis that disturbance increases stochasticity in biological communities. We also found that habitat disturbance limited microbiome similarity between locations for both species, suggesting greater isolation of bacterial assemblages in more disturbed areas. Higher disturbance was associated with lower Bd prevalence for A. crepitans, which could signify suboptimal microclimates for Bd in disturbed habitats. Combined, our findings show that reduced microbiome stability stemming from habitat disturbance could compromise population health, even in the absence of pathogenic infection.}, }
@article {pmid34671825, year = {2022}, author = {Liu, L and Wang, S and Yang, J and Chen, J}, title = {Nutrient Removal in Eutrophic Water Promotes Stability of Planktonic Bacterial and Protist Communities.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {759-768}, pmid = {34671825}, issn = {1432-184X}, support = {31971469//National Natural Science Foundation of China/ ; XDA23040302//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; GXRC-20061//Qishan Scholar Program of Fuzhou University/ ; 2019-JJFDKY-71//Research Project of Development Center of Science and Education Park, Fuzhou University (JinJiang)/ ; }, mesh = {*Plankton/genetics ; *Water ; Ecosystem ; Eutrophication ; Phosphorus ; Eukaryota/genetics ; Nitrogen ; Bacteria/genetics ; Nutrients ; }, abstract = {Nutrient (nitrogen and phosphorus) removal by using bioremediation technologies in eutrophic water alters bacterial and protist community structure and function, but how it changes the stability of community remains unclear. To fill this gap, in this study, bacterial and protist communities were investigated using 16S and 18S rRNA gene high-throughput sequencing during the nutrient removal by using ecological floating beds of Canna indica L. Our results showed that both bacterial and protist community compositions in the treatment group were similar to those in the control group at the beginning of the experiment (day 1 to day 11), but then bacterial and protist community compositions became more stable with the removal of nutrients in the treatment group than those in the control group (day 12 to day 18). We further explored the mechanisms for this increased stability and found that the contribution of the stochastic process to bacterial and protist community variations was higher in the control group than that in the treatment group. This suggests that the high nutrient concentration in the control group might increase the random colonization or extinction, and therefore resulted in the high temporal variability (i.e., unstable) of bacterial and protist communities. Our findings suggest that bioremediation for eutrophication can promote the stability of aquatic communities, and therefore potentially maintain aquatic ecosystem functions and services to humanity.}, }
@article {pmid34671091, year = {2021}, author = {Song, C and Fu, F and Yang, L and Niu, Y and Tian, Z and He, X and Yang, X and Chen, J and Sun, W and Wan, T and Zhang, H and Yang, Y and Xiao, T and Dossa, K and Meng, X and Cao, F and Van de Peer, Y and Wang, G and Chen, S}, title = {Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {1203}, pmid = {34671091}, issn = {2399-3642}, mesh = {Cycadopsida/*classification ; *Evolution, Molecular ; *Genome, Plant ; Paclitaxel/*biosynthesis ; *Phylogeny ; Taxus/*genetics ; }, abstract = {Taxol, a natural product derived from Taxus, is one of the most effective natural anticancer drugs and the biosynthetic pathway of Taxol is the basis of heterologous bio-production. Here, we report a high-quality genome assembly and annotation of Taxus yunnanensis based on 10.7 Gb sequences assembled into 12 chromosomes with contig N50 and scaffold N50 of 2.89 Mb and 966.80 Mb, respectively. Phylogenomic analyses show that T. yunnanensis is most closely related to Sequoiadendron giganteum among the sampled taxa, with an estimated divergence time of 133.4-213.0 MYA. As with most gymnosperms, and unlike most angiosperms, there is no evidence of a recent whole-genome duplication in T. yunnanensis. Repetitive sequences, especially long terminal repeat retrotransposons, are prevalent in the T. yunnanensis genome, contributing to its large genome size. We further integrated genomic and transcriptomic data to unveil clusters of genes involved in Taxol synthesis, located on the chromosome 12, while gene families encoding hydroxylase in the Taxol pathway exhibited significant expansion. Our study contributes to the further elucidation of gymnosperm relationships and the Taxol biosynthetic pathway.}, }
@article {pmid34669476, year = {2021}, author = {Zaoli, S and Grilli, J}, title = {A macroecological description of alternative stable states reproduces intra- and inter-host variability of gut microbiome.}, journal = {Science advances}, volume = {7}, number = {43}, pages = {eabj2882}, pmid = {34669476}, issn = {2375-2548}, abstract = {The most fundamental questions in microbial ecology concern the diversity and variability of communities. Their composition varies widely across space and time, as a result of a nontrivial combination of stochastic and deterministic processes. The interplay between nonlinear community dynamics and environmental fluctuations determines the rich statistical structure of community variability. We analyze long time series of individual human gut microbiomes and compare intra- and intercommunity dissimilarity under a macroecological framework. We show that most taxa have large but stationary fluctuations over time, while a minority of taxa display rapid changes in average abundance that cluster in time, suggesting the presence of alternative stable states. We disentangle interindividual variability in a stochastic component and a deterministic one, the latter recapitulated by differences in carrying capacities. Last, by combining environmental fluctuations and alternative stable states, we introduce a model that quantitatively predicts the statistical properties of both intra- and interindividual community variability, therefore summarizing variation in a unique macroecological framework.}, }
@article {pmid34669447, year = {2022}, author = {Mendiola, SY and Stoy, KS and DiSalvo, S and Wynn, CL and Civitello, DJ and Gerardo, NM}, title = {Competitive Exclusion of Phytopathogenic Serratia marcescens from Squash Bug Vectors by the Gut Endosymbiont Caballeronia.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {1}, pages = {e0155021}, pmid = {34669447}, issn = {1098-5336}, support = {1R01 AI150774-01//HHS | National Institutes of Health (NIH)/ ; R01 AI150774/AI/NIAID NIH HHS/United States ; NIFA 2019-67013-29371//U.S. Department of Agriculture (USDA)/ ; RC Lewontin Graduate Research Excellence//Society for the Study of Evolution (SSE)/ ; NSF IOS-1755002//National Science Foundation (NSF)/ ; DGE-1444932//National Science Foundation (NSF)/ ; }, mesh = {Animals ; *Burkholderiaceae ; *Heteroptera ; Insecta ; Serratia marcescens ; Symbiosis ; }, abstract = {Many insects harbor microbial symbiotic partners that offer protection against pathogens, parasitoids, and other natural enemies. Mounting evidence suggests that these symbiotic microbes can play key roles in determining infection outcomes in insect vectors, making them important players in the quest to develop novel vector control strategies. Using the squash bug Anasa tristis, we investigated how the presence of Caballeronia symbionts affected the persistence and intensity of phytopathogenic Serratia marcescens within the insect vector. We reared insects aposymbiotically and with different Caballeronia isolates, infected them with S. marcescens, and then sampled the insects periodically to assess the intensity and persistence of pathogen infection. Squash bugs harboring Caballeronia consistently had much lower-intensity infections and cleared S. marcescens significantly faster than their aposymbiotic counterparts. These patterns held even when we reversed the timing of exposure to symbiont and pathogen. Taken together, these results indicate that Caballeronia symbionts play an essential role in S. marcescens infection outcomes in squash bugs and could be used to alter vector competence to enhance agricultural productivity in the future. IMPORTANCE Insect-microbe symbioses have repeatedly been shown to profoundly impact an insect's ability to vector pathogens to other hosts. The use of symbiotic microbes to control insect vector populations is of growing interest in agricultural settings. Our study examines how symbiotic microbes affect the dynamics of a plant pathogen infection within the squash bug vector Anasa tristis, a well-documented pest of squash and other cucurbit plants and a vector of Serratia marcescens, the causative agent of cucurbit yellow vine disease. We provide evidence that the symbiont Caballeronia prevents successful, long-term establishment of S. marcescens in the squash bug. These findings give us insight into symbiont-pathogen dynamics within the squash bug that could ultimately determine its ability to transmit pathogens and be leveraged to interrupt disease transmission in this system.}, }
@article {pmid34669436, year = {2022}, author = {Luna, E and Parkar, SG and Kirmiz, N and Hartel, S and Hearn, E and Hossine, M and Kurdian, A and Mendoza, C and Orr, K and Padilla, L and Ramirez, K and Salcedo, P and Serrano, E and Choudhury, B and Paulchakrabarti, M and Parker, CT and Huynh, S and Cooper, K and Flores, GE}, title = {Utilization Efficiency of Human Milk Oligosaccharides by Human-Associated Akkermansia Is Strain Dependent.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {1}, pages = {e0148721}, pmid = {34669436}, issn = {1098-5336}, support = {SC2 GM122620/GM/NIGMS NIH HHS/United States ; T15 LM009451/LM/NLM NIH HHS/United States ; UL1 GM118976/GM/NIGMS NIH HHS/United States ; RL5 GM118975/GM/NIGMS NIH HHS/United States ; TL4 GM118977/GM/NIGMS NIH HHS/United States ; SC1 GM136546/GM/NIGMS NIH HHS/United States ; }, mesh = {Akkermansia ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; *Milk, Human ; Oligosaccharides ; Verrucomicrobia ; }, abstract = {Akkermansia muciniphila is a mucin-degrading bacterium found in the human gut and is often associated with positive human health. However, despite being detected by as early as 1 month of age, little is known about the role of Akkermansia in the infant gut. Human milk oligosaccharides (HMOs) are abundant components of human milk and are structurally similar to the oligosaccharides that comprise mucin, the preferred growth substrate of human-associated Akkermansia. A limited subset of intestinal bacteria has been shown to grow well on HMOs and mucin. We therefore examined the ability of genomically diverse strains of Akkermansia to grow on HMOs. First, we screened 85 genomes representing the four known Akkermansia phylogroups to examine their metabolic potential to degrade HMOs. Furthermore, we examined the ability of representative isolates to grow on individual HMOs in a mucin background and analyzed the resulting metabolites. All Akkermansia genomes were equipped with an array of glycoside hydrolases associated with HMO deconstruction. Representative strains were all able to grow on HMOs with various efficiencies and growth yields. Strain CSUN-19, belonging to the AmIV phylogroup, grew to the highest level in the presence of fucosylated and sialylated HMOs. This activity may be partially related to the increased copy numbers and/or the enzyme activities of the α-fucosidases, α-sialidases, and β-galactosidases. This study examines the utilization of individual purified HMOs by Akkermansia strains representing all known phylogroups. Further studies are required to examine how HMO ingestion influences gut microbial ecology in infants harboring different Akkermansia phylogroups. IMPORTANCE Human milk oligosaccharides (HMOs) are the third most abundant component of breast milk and provide several benefits to developing infants, including the recruitment of beneficial bacteria to the human gut. Akkermansia strains are largely considered beneficial bacteria and have been detected in colostrum, breast milk, and young infants. A. muciniphila Muc[T], belonging to the AmI phylogroup, contributes to the HMO deconstruction capacity of the infant. Here, using phylogenomics, we examined the genomic capacities of four Akkermansia phylogroups to deconstruct HMOs. Indeed, each phylogroup contained differences in their genomic capacities to deconstruct HMOs, and representative strains of each phylogroup were able to grow using HMOs. These Akkermansia-HMO interactions potentially influence gut microbial ecology in early life, a critical time for the development of the gut microbiome and infant health.}, }
@article {pmid34668755, year = {2021}, author = {Kim, T and Behrens, S and LaPara, TM}, title = {Microbial Community Composition in Municipal Wastewater Treatment Bioreactors Follows a Distance Decay Pattern Primarily Controlled by Environmental Heterogeneity.}, journal = {mSphere}, volume = {6}, number = {5}, pages = {e0064821}, pmid = {34668755}, issn = {2379-5042}, mesh = {Bioreactors/*microbiology ; *Microbiota ; RNA, Ribosomal, 16S/analysis ; Seasons ; Sequence Analysis, DNA ; Sewage/*microbiology ; Wastewater/*microbiology ; Water Purification ; }, abstract = {Understanding spatiotemporal patterns in microbial community composition is a central goal of microbial ecology. The objective of this study was to better understand the biogeography of activated sludge microbial communities, which are important for the protection of surface water quality. Monthly samples were collected from 20 facilities (25 bioreactors) within 442 km of each other for 1 year. Microbial community composition was characterized by sequencing of PCR-amplified 16S rRNA gene fragments. Statistically significant distance decay of community similarity was observed in these bioreactors independent of clustering method (operational taxonomic units [OTUs] at 97% similarity, genus-level phylotypes) and community dissimilarity metric (Sørensen, Bray-Curtis, and weighted Unifrac). Universal colonizers (i.e., detected in all samples) and ubiquitous genus-level phylotypes (i.e., detected in every facility at least once) also exhibited a significant distance decay relationship. Variation partitioning analysis of community composition showed that environmental characteristics (temperature, influent characteristics, etc.) explained more of the variance in community composition than geographic distance did, suggesting that environmental heterogeneity is more important than dispersal limitation as a mechanism for determining microbial community composition. Distance decay relationships also became stronger with increasing distance between facilities. Seasonal variation in community composition was also observed from selected bioreactors, but there was no clear seasonal pattern in the distance decay relationships. IMPORTANCE Understanding the spatiotemporal patterns of biodiversity is a central goal of ecology. The distance decay of community similarity is one of the spatial scaling patterns observed in many forms of life, including plants, animals, and microbial communities. Municipal wastewater treatment relies on microorganisms to prevent the release of excessive quantities of nutrients and other pollutants, but relatively few studies have explored distance decay relationships in wastewater treatment bioreactors. Our results demonstrate a strong distance decay pattern in wastewater treatment bioreactors, regardless of the sequence clustering method or the community dissimilarity metric. Our results suggest that microbial communities in wastewater treatment bioreactors are not randomly assembled but rather exhibit a statistically significant spatial pattern.}, }
@article {pmid34668729, year = {2021}, author = {Coleman, A and Zaugg, J and Wood, A and Cottrell, K and Håkansson, EG and Adams, J and Brown, M and Cervin, A and Bialasiewicz, S}, title = {Upper Respiratory Tract Microbiome of Australian Aboriginal and Torres Strait Islander Children in Ear and Nose Health and Disease.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0036721}, pmid = {34668729}, issn = {2165-0497}, mesh = {Australia/epidemiology ; Bacteria/*classification/genetics/isolation &amp; purification ; Child ; Child, Preschool ; Ear/*microbiology ; Female ; Health Status ; Humans ; Male ; Microbiota/*genetics/physiology ; Nasal Cavity/*microbiology ; Nasal Mucosa/microbiology ; Nasopharynx/microbiology ; Otitis Media/*epidemiology/microbiology ; Persistent Infection/microbiology ; RNA, Ribosomal, 16S/genetics ; Respiratory System/microbiology ; }, abstract = {The objective of this study was to examine the nasal microbiota in relation to otitis media (OM) status and nose health in Indigenous Australian children. Children 2 to 7 years of age were recruited from two northern Australian (Queensland) communities. Clinical histories were obtained through parent interviews and reviews of the medical records. Nasal cavity swab samples were obtained, and the children's ears, nose, and throat were examined. DNA was extracted and analyzed by 16S rRNA amplicon next-generation sequencing of the V3/V4 region, in combination with previously generated culture data. A total of 103 children were recruited (mean age, 4.7 years); 17 (16.8%) were healthy, i.e., normal examination results and no history of OM. The nasal microbiota differed significantly in relation to OM status and nose health. Children with historical OM had greater relative abundance of Moraxella, compared to healthy children, despite both having healthy ears at the time of swabbing. Children with healthy noses had greater relative abundance of Staphylococcus aureus, compared to those with rhinorrhea. Dolosigranulum was correlated with Corynebacterium in healthy children. Haemophilus and Streptococcus were correlated across phenotypes. Ornithobacterium was absent or was present with low relative abundance in healthy children and clustered around otopathogens. It correlated with Helcococcus and Dichelobacter. Dolosigranulum and Corynebacterium form a synergism that promotes upper respiratory tract (URT)/ear health in Indigenous Australian children. Ornithobacterium likely represents "Candidatus Ornithobacterium hominis" and in this population is correlated with a novel bacterium that appears to be related to poor URT/ear health. IMPORTANCE Recurring and chronic infections of the ear (OM) are disproportionately prevalent in disadvantaged communities across the globe and, in particular, within Indigenous communities. Despite numerous intervention strategies, OM persists as a major health issue and is the leading cause of preventable hearing loss. In disadvantaged communities, this hearing loss is associated with negative educational and social development outcomes, and consequently, poorer employment prospects and increased contact with the justice system in adulthood. Thus, a better understanding of the microbial ecology is needed in order to identify new targets to treat, as well as to prevent the infections. This study used a powerful combination of 16S rRNA gene sequencing and extended culturomics to show that Dolosigranulum pigrum, a bacterium previously identified as a candidate protective species, may require cocolonization with Corynebacterium pseudodiphtheriticum in order to prevent OM. Additionally, emerging and potentially novel pathogens and bacteria were identified.}, }
@article {pmid34665776, year = {2021}, author = {Abello, JJM and Malajacan, GT and Labrador, KL and Nacario, MAG and Galarion, LH and Obusan, MCM and Rivera, WL}, title = {Library-independent source tracking of fecal contamination in selected stations and tributaries of Laguna Lake, Philippines.}, journal = {Journal of water and health}, volume = {19}, number = {5}, pages = {846-854}, doi = {10.2166/wh.2021.058}, pmid = {34665776}, issn = {1477-8920}, mesh = {Animals ; Cattle ; *Environmental Monitoring ; Feces ; *Lakes ; Philippines ; Rivers ; Swine ; Water Microbiology ; Water Pollution/analysis ; }, abstract = {Laguna Lake is the largest inland freshwater body in the Philippines. Although it is classified to be usable for agricultural and recreational purposes by the country's Department of Environment and Natural Resources (DENR), studies looking at lake ecology revealed severe fecal contamination which contributes to the deterioration of water quality. Determining the sources of fecal contamination is necessary for lake protection and management. This study utilized a library-independent method of microbial source tracking (LIM-MST) to identify sources of fecal contamination in selected Laguna Lake stations and tributaries. Genetic markers of the host-associated Escherichia coli, heat-labile toxin (LTIIA) and heat-stable II (STII), were used to identify cattle and swine fecal contaminations, respectively. Meanwhile, human mitochondrial DNA (mtDNA) was used to identify human fecal contamination. Results identified the presence of agricultural and human fecal contamination in Laguna Lake Stations 1 and 5, Mangangate River, and Alabang River. The selected sites are known to be surrounded by residential and industrial complexes, and most of their discharges find their way into the lake. The identification of the specific sources of fecal contamination will guide management practices that aim to regulate the discharges in order to improve the water quality of Laguna Lake.}, }
@article {pmid34665286, year = {2022}, author = {Xie, W and Yan, Y and Hu, J and Dong, P and Hou, D and Zhang, H and Yao, Z and Zhu, X and Zhang, D}, title = {Ecological Dynamics and Co-occurrences Among Prokaryotes and Microeukaryotes in a Diatom Bloom Process in Xiangshan Bay, China.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {746-758}, pmid = {34665286}, issn = {1432-184X}, support = {42076158//the National Natural Science Foundation of China/ ; 41706132//the National Natural Science Foundation of China/ ; SJLY2020005//the Fundamental Research Funds for the Provincial Universities of Zhejiang/ ; }, mesh = {*Diatoms ; Bays/microbiology ; *Dinoflagellida ; *Alphaproteobacteria ; *Gammaproteobacteria ; }, abstract = {Diatom blooms can significantly affect the succession of microbial communities, yet little is known about the assembly processes and interactions of microbial communities during autumn bloom events. In this study, we investigated the ecological effects of an autumn diatom bloom on prokaryotic communities (PCCs) and microeukaryotic communities (MECs), focusing on their assembly processes and interactions. The PCCs were largely dominated by Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, and Flavobacteria, while the MECs primarily included Diatomea, Dinoflagellata, and Chlorophyta. The succession of both PCCs and MECs was mainly driven by this diatom bloom and environmental factors, such as nitrate and silicate. Null modeling revealed that homogeneous selection had a more pronounced impact on the structure of PCCs compared with that of MECs. In particular, drift and dispersal limitation cannot be neglected in the assembly processes of MECs. Co-occurrence network analyses showed that Litorimicrobium, Cercozoa, Marine Group I (MGI), Cryptomonadales, Myrionecta, and Micromonas may affect the bloom process. In summary, these results elucidated the complex, robust interactions and obviously distinct assembly mechanisms of PCCs and MECs during a diatom bloom and extend our current comprehension of the ecological mechanisms and microbial interactions involved in an autumn diatom bloom process.}, }
@article {pmid34662276, year = {2021}, author = {Jones, ML and Rivett, DW and Pascual-García, A and Bell, T}, title = {Relationships between community composition, productivity and invasion resistance in semi-natural bacterial microcosms.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34662276}, issn = {2050-084X}, mesh = {*Microbiota ; Pseudomonas fluorescens/genetics/*physiology ; Pseudomonas putida/genetics/*physiology ; }, abstract = {Common garden experiments that inoculate a standardised growth medium with synthetic microbial communities (i.e. constructed from individual isolates or using dilution cultures) suggest that the ability of the community to resist invasions by additional microbial taxa can be predicted by the overall community productivity (broadly defined as cumulative cell density and/or growth rate). However, to the best of our knowledge, no common garden study has yet investigated the relationship between microbial community composition and invasion resistance in microcosms whose compositional differences reflect natural, rather than laboratory-designed, variation. We conducted experimental invasions of two bacterial strains (Pseudomonas fluorescens and Pseudomonas putida) into laboratory microcosms inoculated with 680 different mixtures of bacteria derived from naturally occurring microbial communities collected in the field. Using 16S rRNA gene amplicon sequencing to characterise microcosm starting composition, and high-throughput assays of community phenotypes including productivity and invader survival, we determined that productivity is a key predictor of invasion resistance in natural microbial communities, substantially mediating the effect of composition on invasion resistance. The results suggest that similar general principles govern invasion in artificial and natural communities, and that factors affecting resident community productivity should be a focal point for future microbial invasion experiments.}, }
@article {pmid34661728, year = {2022}, author = {Znój, A and Gawor, J and Gromadka, R and Chwedorzewska, KJ and Grzesiak, J}, title = {Root-Associated Bacteria Community Characteristics of Antarctic Plants: Deschampsia antarctica and Colobanthus quitensis-a Comparison.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {808-820}, pmid = {34661728}, issn = {1432-184X}, support = {2016/21/N/NZ9/01536//narodowe centrum nauki/ ; }, mesh = {Antarctic Regions ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Caryophyllaceae/genetics/microbiology ; Plants ; Bacteria/genetics ; }, abstract = {Colobanthus quitensis (Kunth) Bartl. and Deschampsia antarctica Desv. are the only Magnoliophyta to naturally colonize the Antarctic region. The reason for their sole presence in Antarctica is still debated as there is no definitive consensus on how only two unrelated flowering plants managed to establish breeding populations in this part of the world. In this study, we have explored and compared the rhizosphere and root-endosphere dwelling microbial community of C. quitensis and D. antarctica specimens sampled in maritime Antarctica from sites displaying contrasting edaphic characteristics. Bacterial phylogenetic diversity (high-throughput 16S rRNA gene fragment targeted sequencing) and microbial metabolic activity (Biolog EcoPlates) with a geochemical soil background were assessed. Gathered data showed that the microbiome of C. quitensis root system was mostly site-dependent, displaying different characteristics in each of the examined locations. This plant tolerated an active bacterial community only in severe conditions (salt stress and nutrient deprivation), while in other more favorable circumstances, it restricted microbial activity, with a possibility of microbivory-based nutrient acquisition. The microbial communities of D. antarctica showed a high degree of similarity between samples within a particular rhizocompartment. The grass' endosphere was significantly enriched in plant beneficial taxa of the family Rhizobiaceae, which displayed obligatory endophyte characteristics, suggesting that at least part of this community is transmitted vertically. Ultimately, the ecological success of C. quitensis and D. antarctica in Antarctica might be largely attributed to their associations and management of root-associated microbiota.}, }
@article {pmid34654483, year = {2021}, author = {Gloder, G and Bourne, ME and Verreth, C and Wilberts, L and Bossaert, S and Crauwels, S and Dicke, M and Poelman, EH and Jacquemyn, H and Lievens, B}, title = {Parasitism by endoparasitoid wasps alters the internal but not the external microbiome in host caterpillars.}, journal = {Animal microbiome}, volume = {3}, number = {1}, pages = {73}, pmid = {34654483}, issn = {2524-4671}, support = {FWO//Fonds Wetenschappelijk Onderzoek/ ; G.0961.19N//Fonds Wetenschappelijk Onderzoek/ ; ALWOP.343//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; ALWOP.368//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, abstract = {BACKGROUND: The microbiome of many insects consists of a diverse community of microorganisms that can play critical roles in the functioning and overall health of their hosts. Although the microbial communities of insects have been studied thoroughly over the past decade, little is still known about how biotic interactions affect the microbial community structure in and on the bodies of insects. In insects that are attacked by parasites or parasitoids, it can be expected that the microbiome of the host insect is affected by the presence of these parasitic organisms that develop in close association with their host. In this study, we used high-throughput amplicon sequencing targeting both bacteria and fungi to test the hypothesis that parasitism by the endoparasitoid Cotesia glomerata affected the microbiome of its host Pieris brassicae. Healthy and parasitized caterpillars were collected from both natural populations and a laboratory culture.<br><br>RESULTS: Significant differences in bacterial community structure were found between field-collected caterpillars and laboratory-reared caterpillars, and between the external and the internal microbiome of the caterpillars. Parasitism significantly altered the internal microbiome of caterpillars, but not the external microbiome. The internal microbiome of all parasitized caterpillars and of the parasitoid larvae in the caterpillar hosts was dominated by a Wolbachia strain, which was completely absent in healthy caterpillars, suggesting that the strain was transferred to the caterpillars during oviposition by the parasitoids.<br><br>CONCLUSION: We conclude that biotic interactions such as parasitism have pronounced effects on the microbiome of an insect host and possibly affect interactions with higher-order insects.}, }
@article {pmid34653799, year = {2021}, author = {Srinivasan, VN and Li, G and Wang, D and Tooker, NB and Dai, Z and Onnis-Hayden, A and Bott, C and Dombrowski, P and Schauer, P and Pinto, A and Gu, AZ}, title = {Oligotyping and metagenomics reveal distinct Candidatus Accumulibacter communities in side-stream versus conventional full-scale enhanced biological phosphorus removal (EBPR) systems.}, journal = {Water research}, volume = {206}, number = {}, pages = {117725}, doi = {10.1016/j.watres.2021.117725}, pmid = {34653799}, issn = {1879-2448}, mesh = {Bioreactors ; *Metagenomics ; *Phosphorus ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers ; Sewage ; }, abstract = {Candidatus Accumulibacter phosphatis (CAP) and its clade-level micro-diversity has been associated with and implicated in functional differences in phosphorus removal performance in enhanced biological phosphorus removal (EBPR) systems. Side-stream EBPR (S2EBPR) is an emerging process that has been shown to present a suite of advantages over the conventional EBPR design, however, large knowledge gaps remain in terms of its underlying ecological mechanisms. Here, we compared and revealed the higher-resolution differences in microbial ecology of CAP between a full-scale side-stream EBPR configuration and a conventional A2O EBPR process that were operated in parallel and with the same influent feed. Even though the relative abundance of CAP, revealed by 16S rRNA gene amplicon sequencing, was similar in both treatment trains, a clade-level analysis, using combined 16S rRNA-gene based amplicon sequencing and oligotyping analysis and metagenomics analysis, revealed the distinct CAP microdiversity between the S2EBPR and A2O configurations that likely attributed to the improved performance in S2EBPR in comparison to conventional EBPR. Furthermore, genome-resolved metagenomics enabled extraction of three metagenome-assembled genomes (MAGs) belonging to CAP clades IIB (RCAB4-2), IIC (RC14) and II (RC18), from full-scale EBPR sludge for the first time, including a distinct Ca. Accumulibacter clade that is dominant and associated only with the S2EBPR configuration. The results also revealed the temporally increasing predominance of RC14, which belonged to Clade IIC, during the implementation of the S2EBPR configuration. Finally, we also show the existence of previously uncharacterized diversity of clades of CAP, namely the clades IIB and as yet unidentified clade of type II, in full-scale EBPR communities, highlighting the unknown diversity of CAP communities in full-scale EBPR systems.}, }
@article {pmid34653798, year = {2021}, author = {She, Z and Pan, X and Wang, J and Shao, R and Wang, G and Wang, S and Yue, Z}, title = {Vertical environmental gradient drives prokaryotic microbial community assembly and species coexistence in a stratified acid mine drainage lake.}, journal = {Water research}, volume = {206}, number = {}, pages = {117739}, doi = {10.1016/j.watres.2021.117739}, pmid = {34653798}, issn = {1879-2448}, mesh = {Bacteria/genetics ; *Lakes ; *Microbiota ; Mining ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Acid mine drainage (AMD) lakes are typical hydrologic features caused by open pit mining and represent extreme ecosystems and environmental challenges. Little is known about microbial distribution and community assembly in AMD lakes, especially in deep layers. Here, we investigated prokaryotic microbial diversity and community assembly along a depth profile in a stratified AMD lake using 16S rRNA gene sequencing combined with multivariate ecological and statistical methods. The water column in the AMD lake exhibited tight geochemical gradients, with more acidic surface water. Coupled with vertical hydrochemical variations, prokaryotic microbial community structure changed significantly, and was accompanied by increased diversity with depth. In the surface water, heterogeneous selection was the most important assembly process, whereas stochastic processes gained importance with depth. Meanwhile, microbial co-occurrences, especially positive interactions, were more frequent in the stressful surface water with reduced network modularity and keystone taxa. The pH was identified as the key driver of microbial diversity and community assembly along the vertical profile based on random forest analysis. Taken together, environmental effects dominated by acid stress drove the community assembly and species coexistence that underpinned the spatial scaling patterns of AMD microbiota in the lake. These findings demonstrate the distinct heterogeneity of local prokaryotic microbial community in AMD lake, and provide new insights into the mechanism to maintain microbial diversity in extreme acidic environments.}, }
@article {pmid34647148, year = {2022}, author = {Suyal, DC and Joshi, D and Kumar, S and Bhatt, P and Narayan, A and Giri, K and Singh, M and Soni, R and Kumar, R and Yadav, A and Devi, R and Kaur, T and Kour, D and Yadav, AN}, title = {Himalayan Microbiomes for Agro-environmental Sustainability: Current Perspectives and Future Challenges.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {643-675}, pmid = {34647148}, issn = {1432-184X}, mesh = {Animals ; *Microbiota ; Biodiversity ; Agriculture ; Plant Development ; Crops, Agricultural ; }, abstract = {The Himalayas are one of the most mystical, yet least studied terrains of the world. One of Earth's greatest multifaceted and diverse montane ecosystems is also one of the thirty-four global biodiversity hotspots of the world. These are supposed to have been uplifted about 60-70 million years ago and support, distinct environments, physiography, a variety of orogeny, and great biological diversity (plants, animals, and microbes). Microbes are the pioneer colonizer of the Himalayas that are involved in various bio-geological cycles and play various significant roles. The applications of Himalayan microbiomes inhabiting in lesser to greater Himalayas have been recognized. The researchers explored the applications of indigenous microbiomes in both agricultural and environmental sectors. In agriculture, microbiomes from Himalayan regions have been suggested as better biofertilizers and biopesticides for the crops growing at low temperature and mountainous areas as they help in the alleviation of cold stress and other biotic stresses. Along with alleviation of low temperature, Himalayan microbes also have the capability to enhance plant growth by availing the soluble form of nutrients like nitrogen, phosphorus, potassium, zinc, and iron. These microbes have been recognized for producing plant growth regulators (abscisic acid, auxin, cytokinin, ethylene, and gibberellins). These microbes have been reported for bioremediating the diverse pollutants (pesticides, heavy metals, and xenobiotics) for environmental sustainability. In the current perspectives, present review provides a detailed discussion on the ecology, biodiversity, and adaptive features of the native Himalayan microbiomes in view to achieve agro-environmental sustainability.}, }
@article {pmid34646255, year = {2021}, author = {Glowacki, RWP and Engelhart, MJ and Ahern, PP}, title = {Controlled Complexity: Optimized Systems to Study the Role of the Gut Microbiome in Host Physiology.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {735562}, pmid = {34646255}, issn = {1664-302X}, abstract = {The profound impact of the gut microbiome on host health has led to a revolution in biomedical research, motivating researchers from disparate fields to define the specific molecular mechanisms that mediate host-beneficial effects. The advent of genomic technologies allied to the use of model microbiomes in gnotobiotic mouse models has transformed our understanding of intestinal microbial ecology and the impact of the microbiome on the host. However, despite incredible advances, our understanding of the host-microbiome dialogue that shapes host physiology is still in its infancy. Progress has been limited by challenges associated with developing model systems that are both tractable enough to provide key mechanistic insights while also reflecting the enormous complexity of the gut ecosystem. Simplified model microbiomes have facilitated detailed interrogation of transcriptional and metabolic functions of the microbiome but do not recapitulate the interactions seen in complex communities. Conversely, intact complex communities from mice or humans provide a more physiologically relevant community type, but can limit our ability to uncover high-resolution insights into microbiome function. Moreover, complex microbiomes from lab-derived mice or humans often do not readily imprint human-like phenotypes. Therefore, improved model microbiomes that are highly defined and tractable, but that more accurately recapitulate human microbiome-induced phenotypic variation are required to improve understanding of fundamental processes governing host-microbiome mutualism. This improved understanding will enhance the translational relevance of studies that address how the microbiome promotes host health and influences disease states. Microbial exposures in wild mice, both symbiotic and infectious in nature, have recently been established to more readily recapitulate human-like phenotypes. The development of synthetic model communities from such "wild mice" therefore represents an attractive strategy to overcome the limitations of current approaches. Advances in microbial culturing approaches that allow for the generation of large and diverse libraries of isolates, coupled to ever more affordable large-scale genomic sequencing, mean that we are now ideally positioned to develop such systems. Furthermore, the development of sophisticated in vitro systems is allowing for detailed insights into host-microbiome interactions to be obtained. Here we discuss the need to leverage such approaches and highlight key challenges that remain to be addressed.}, }
@article {pmid34645520, year = {2021}, author = {Cobo-Díaz, JF and Alvarez-Molina, A and Alexa, EA and Walsh, CJ and Mencía-Ares, O and Puente-Gómez, P and Likotrafiti, E and Fernández-Gómez, P and Prieto, B and Crispie, F and Ruiz, L and González-Raurich, M and López, M and Prieto, M and Cotter, P and Alvarez-Ordóñez, A}, title = {Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {204}, pmid = {34645520}, issn = {2049-2618}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Food Handling ; Genes, Bacterial ; *Pork Meat ; *Red Meat ; Swine ; }, abstract = {BACKGROUND: The microorganisms that inhabit food processing environments (FPE) can strongly influence the associated food quality and safety. In particular, the possibility that FPE may act as a reservoir of antibiotic-resistant microorganisms, and a hotspot for the transmission of antibiotic resistance genes (ARGs) is a concern in meat processing plants. Here, we monitor microbial succession and resistome dynamics relating to FPE through a detailed analysis of a newly opened pork cutting plant over 1.5 years of activity.<br><br>RESULTS: We identified a relatively restricted principal microbiota dominated by Pseudomonas during the first 2 months, while a higher taxonomic diversity, an increased representation of other taxa (e.g., Acinetobacter, Psychrobacter), and a certain degree of microbiome specialization on different surfaces was recorded later on. An increase in total abundance, alpha diversity, and &#x3b2;-dispersion of ARGs, which were predominantly assigned to Acinetobacter and associated with resistance to certain antimicrobials frequently used on pig farms of the region, was detected over time. Moreover, a sharp increase in the occurrence of extended-spectrum &#x3b2;-lactamase-producing Enterobacteriaceae and vancomycin-resistant Enterococcaceae was observed when cutting activities started. ARGs associated with resistance to &#x3b2;-lactams, tetracyclines, aminoglycosides, and sulphonamides frequently co-occurred, and mobile genetic elements (i.e., plasmids, integrons) and lateral gene transfer events were mainly detected at the later sampling times in drains.<br><br>CONCLUSIONS: The observations made suggest that pig carcasses were a source of resistant bacteria that then colonized FPE and that drains, together with some food-contact surfaces, such as equipment and table surfaces, represented a reservoir for the spread of ARGs in the meat processing facility. Video Abstract.}, }
@article {pmid34643439, year = {2021}, author = {Tan, H and Liu, T and Yu, Y and Tang, J and Jiang, L and Martin, FM and Peng, W}, title = {Morel Production Related to Soil Microbial Diversity and Evenness.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0022921}, pmid = {34643439}, issn = {2165-0497}, mesh = {Agriculture ; Ascomycota/*metabolism ; Basidiomycota/metabolism ; Crops, Agricultural ; Mycobiome/*physiology ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Black morel is a widely prized ascomycetous mushroom with culinary value. It was once uncultivable but can now be cultivated routinely in ordinary farmland soils. Large-scale morel farming sometimes encounters nonfructification for unknown reasons. In spring 2020, many morel farms in the area of Chengdu-Plain, China, exhibited no fructification at all, causing disastrous economic loss to the farmers. To determine potential ecological factors associated with the different performance of morel production in these farms, 21 affected sites versus 11 sites with normal fructification performance were analyzed to compare soil microbiota and physiochemical characteristics during fructification. The results indicated that soil physiochemical characteristics were unlikely to be a major reason for the difference between successful fructification and nonfructification. The soils with successful fructification had significantly higher diversity in both the fungal and bacterial communities than those with nonfructification. Morel yield was positively correlated with the α-diversity of fungal communities. The higher diversity of the successfully fructified soils was contributed by community evenness rather than taxonomic richness. In contrast, most nonfructification soils were dominated by a high proportion of a certain fungal genus, typically Acremonium or Mortierella, in the fungal communities. Our findings demonstrate the importance of microbial ecology to the large-scale agroindustry of soil-cultivated mushrooms. IMPORTANCE Saprotrophic mushrooms cultivated in soils are subject to complex influences from soil microbial communities. Research on growing edible mushrooms has revealed connections between fungi and a few species of growth-promoting bacteria colonizing the mycosphere. The composition and diversity of the whole microbial community may also have an influence on the growth and production of soil-saprotrophic mushrooms. Morel mushrooms (Morchella spp.) are economically and culturally important and are widely prized throughout the world. This study used the large-scale farming of morels as an example of an agroecosystem for soil-saprotrophic mushroom cultivation. It demonstrated a typical pattern of how the microbial ecology in soil agroecosystems, especially the α-diversity level and community evenness among soil fungal taxa, could affect the production of high-value cash crops and the income of farmers.}, }
@article {pmid34637971, year = {2021}, author = {Farrell, ML and Joyce, A and Duane, S and Fitzhenry, K and Hooban, B and Burke, LP and Morris, D}, title = {Evaluating the potential for exposure to organisms of public health concern in naturally occurring bathing waters in Europe: A scoping review.}, journal = {Water research}, volume = {206}, number = {}, pages = {117711}, doi = {10.1016/j.watres.2021.117711}, pmid = {34637971}, issn = {1879-2448}, mesh = {*Cryptosporidiosis ; *Cryptosporidium ; Humans ; Public Health ; Water Microbiology ; Water Quality ; }, abstract = {Globally, water-based bathing pastimes are important for both mental and physical health. However, exposure to waterborne organisms could present a substantial public health issue. Bathing waters are shown to contribute to the transmission of illness and disease and represent a reservoir and pathway for the dissemination of antimicrobial resistant (AMR) organisms. Current bathing water quality regulations focus on enumeration of faecal indicator organisms and are not designed for detection of specific waterborne organisms of public health concern (WOPHC), such as antimicrobial resistant (AMR)/pathogenic bacteria, or viruses. This investigation presents the first scoping review of the occurrence of waterborne organisms of public health concern (WOPHC) in identified natural bathing waters across the European Union (EU), which aimed to critically evaluate the potential risk of human exposure and to assess the appropriateness of the current EU bathing water regulations for the protection of public health. Accordingly, this review sought to identify and synthesise all literature pertaining to a selection of bacterial (Campylobacter spp., Escherichia coli, Salmonella spp., Shigella spp., Vibrio spp., Pseudomonas spp., AMR bacteria), viral (Hepatitis spp., enteroviruses, rotavirus, adenovirus, norovirus), and protozoan (Giardia spp., and Cryptosporidium spp.) contaminants in EU bathing waters. Sixty investigations were identified as eligible for inclusion and data was extracted. Peer-reviewed investigations included were from 18 countries across the EU, totalling 87 investigations across a period of 35 years, with 30% published between 2011 and 2015. A variety of water bodies were identified, with 27 investigations exclusively assessing coastal waters. Waterborne organisms were classified into three categories; bacteria, viruses, and protozoa; amounting to 58%, 36% and 17% of the total investigations, respectively. The total number of samples across all investigations was 8,118, with detection of one or more organisms in 2,449 (30%) of these. Viruses were detected in 1281 (52%) of all samples where WOPHC were found, followed by bacteria (865(35%)) and protozoa (303(12%)). Where assessed (442 samples), AMR bacteria had a 47% detection rate, emphasising their widespread occurrence in bathing waters. Results of this scoping review highlight the potential public health risk of exposure to WOPHC in bathing waters that normally remain undetected within the current monitoring parameters.}, }
@article {pmid34636925, year = {2022}, author = {Manus, MB}, title = {Ecological Processes and Human Behavior Provide a Framework for Studying the Skin Microbial Metacommunity.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {689-702}, pmid = {34636925}, issn = {1432-184X}, mesh = {Animals ; Humans ; *Microbiota ; *Gastrointestinal Microbiome ; Amphibians ; Skin ; }, abstract = {Metacommunity theory dictates that a microbial community is supported both by local ecological processes and the dispersal of microbes between neighboring communities. Studies that apply this perspective to human-associated microbial communities are thus far limited to the gut microbiome. Yet, the skin serves as the primary barrier between the body and the external environment, suggesting frequent opportunities for microbial dispersal to the variable microbial communities that are housed across skin sites. This paper applies metacommunity theory to understand the dispersal of microbes to the skin from the physical and social environment, as well as between different skin sites on an individual's body. This includes highlighting the role of human behavior in driving microbial dispersal, as well as shaping physiological properties of skin that underscore local microbial community dynamics. By leveraging data from research on the skin microbiomes of amphibians and other animals, this paper provides recommendations for future research on the skin microbial metacommunity, including generating testable predictions about the ecological underpinnings of the skin microbiome.}, }
@article {pmid34636672, year = {2021}, author = {Tran, PQ and Anantharaman, K}, title = {Biogeochemistry Goes Viral: towards a Multifaceted Approach To Study Viruses and Biogeochemical Cycling.}, journal = {mSystems}, volume = {6}, number = {5}, pages = {e0113821}, pmid = {34636672}, issn = {2379-5077}, support = {DBI2047598//National Science Foundation (NSF)/ ; }, abstract = {Viruses are ubiquitous on Earth and are keystone components of environments, ecosystems, and human health. Yet, viruses remain poorly studied because most cannot be isolated in a laboratory. In the field of biogeochemistry, which aims to understand the interactions between biology, geology, and chemistry, there is progress to be made in understanding the different roles played by viruses in nutrient cycling, food webs, and elemental transformations. In this commentary, we outline current microbial ecology frameworks for understanding biogeochemical cycling in aquatic ecosystems. Next, we review some existing experimental and computational techniques that are enabling us to study the role of viruses in biogeochemical cycling, using examples from aquatic environments. Finally, we provide a conceptual model that balances limitations of computational tools when combined with biogeochemistry and ecological data. We envision meeting the grand challenge of understanding how viruses impact biogeochemical cycling by using a multifaceted approach to viral ecology.}, }
@article {pmid34634631, year = {2021}, author = {Piperagkas, O and Papageorgiou, N}, title = {Changes in (micro and macro) plastic pollution in the sediment of three sandy beaches in the Eastern Mediterranean Sea, in relation to seasonality, beach use and granulometry.}, journal = {Marine pollution bulletin}, volume = {173}, number = {Pt A}, pages = {113014}, doi = {10.1016/j.marpolbul.2021.113014}, pmid = {34634631}, issn = {1879-3363}, mesh = {Environmental Monitoring ; Mediterranean Sea ; Microplastics ; *Plastics ; *Water Pollutants, Chemical/analysis ; }, abstract = {Smaller sized plastics (microplastics or MPs <5 mm) are ubiquitous in nature and have been found to interact in diverse ways with most biotic and abiotic systems globally. Most MPs in the seas have a land-based source, however, little is known about how the transfer occurs. In our study, we used three sandy beaches to describe the process of how MPs travel from accumulation points at the backshore of the beach to the sea, and vice versa. MPs differed significantly in all three beaches (both in quantitative and qualitative terms) between the summer and the winter samplings. During the summer, heavy MPs are the majority, while during the winter, lightweight microplastics are predominant, and the ratio of heavy per lightweight MPs is affected by the sediment median diameter after the summer sampling. Macroplastics follow a similar pattern to MPs and appear to provide a source of MPs for the sea.}, }
@article {pmid34633491, year = {2022}, author = {Nasreen, T and Islam, MT and Liang, KYH and Johura, FT and Kirchberger, PC and Hill, E and Sultana, M and Case, RJ and Alam, M and Boucher, YF}, title = {Dynamic Subspecies Population Structure of Vibrio cholerae in Dhaka, Bangladesh.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {730-745}, pmid = {34633491}, issn = {1432-184X}, mesh = {Humans ; *Vibrio cholerae/genetics ; *Cholera/epidemiology ; Bangladesh/epidemiology ; Water ; }, abstract = {Cholera has been endemic to the Ganges Delta for centuries. Although the causative agent, Vibrio cholerae, is autochthonous to coastal and brackish water, cholera occurs continually in Dhaka, the inland capital city of Bangladesh which is surrounded by fresh water. Despite the persistence of this problem, little is known about the environmental abundance and distribution of lineages of V. cholerae, the most important being the pandemic generating (PG) lineage consisting mostly of serogroup O1 strains. To understand spatial and temporal dynamics of PG lineage and other lineages belonging to the V. cholerae species in surface water in and around Dhaka City, we used qPCR and high-throughput amplicon sequencing. Seven different freshwater sites across Dhaka were investigated for six consecutive months, and physiochemical parameters were measured in situ. Total abundance of V. cholerae was found to be relatively stable throughout the 6-month sampling period, with 2 × 10[5] to 4 × 10[5] genome copies/L at six sites and around 5 × 10[5] genome copies/L at the site located in the most densely populated part of Dhaka City. PG O1 V. cholerae was present in high abundance during the entire sampling period and composed between 24 and 92% of the total V. cholerae population, only showing occasional but sudden reductions in abundance. In instances where PG O1 lost its dominance, other lineages underwent a rapid expansion while the size of the total V. cholerae population remained almost unchanged. Intraspecies richness of V. cholerae was positively correlated with salinity, conductivity, and total dissolved solids (TDS), while it was negatively correlated with dissolved oxygen (DO) concentration in water. Interestingly, negative correlation was observed specifically between PG O1 and salinity, even though the changes in this variable were minor (0-0.8 ppt). Observations in this study suggest that at the subspecies level, population composition of naturally occurring V. cholerae can be influenced by fluctuations in environmental factors, which can lead to altered competition dynamics among the lineages.}, }
@article {pmid34632704, year = {2022}, author = {Manning-Berg, A and Selly, T and Bartley, JK}, title = {Actualistic approaches to interpreting the role of biological decomposition in microbial preservation.}, journal = {Geobiology}, volume = {20}, number = {2}, pages = {216-232}, doi = {10.1111/gbi.12475}, pmid = {34632704}, issn = {1472-4669}, mesh = {*Ecosystem ; *Fossils ; Humans ; Siberia ; }, abstract = {Taphonomic processes, especially post-mortem biological decomposition, act as crucial controls on the microbial fossil record. Information loss during the fossilization process obscures interpretation of ancient microbial ecology and limits our view of preserved ecosystems. Conversely, taphonomic information can itself provide insight into fossilization pathways and processes. This information-gain approach requires specific attention to taphonomic patterns in ancient assemblages and robust modern analogue data to serve as points of reference. In this study, we combine experimental taphonomy with decomposition models in order to constrain taphonomic hypotheses regarding Proterozoic microfossil assemblages. Several filamentous and coccoidal prokaryotic and eukaryotic phototrophs were evaluated for taphonomic pattern over the course of a short (~100 days) decomposition experiment. In parallel, simple numerical models were constructed to explain potential taphonomic pathways. These analogue data were then compared to two Mesoproterozoic fossil assemblages, the ~1.5 Ga Kotuikan Formation, Siberia, and the ~1 Ga Angmaat Formation, Canada. Concordant with previous experiments and observations, our results suggest that sheath morphology is more persistent than cell/trichome morphology during early stages of decomposition. These experiments also suggest that taphonomic change in cell morphology may follow one of several trajectories, resulting in distinct taphonomic endpoints. Model output suggests two categories of underlying mechanism and resultant taphonomic trajectory: (1) uniform decomposition, resulting in a low overall taphonomic grade and poor preservation, and (2) faster decomposition of structurally compromised individuals, producing a final population with better overall preservation of very few individuals. In this experiment, cells of coccoidal organisms exhibit the first pattern and trichomes of filamentous organisms and some sheaths exhibit the second. Comparison with preserved microfossil assemblages suggests that differences in taphonomic pattern between parts of an assemblage could be useful in assessing taphonomic processes or degree of taphonomic loss in an entire assemblage.}, }
@article {pmid34628478, year = {2022}, author = {Bottery, MJ and Matthews, JL and Wood, AJ and Johansen, HK and Pitchford, JW and Friman, VP}, title = {Inter-species interactions alter antibiotic efficacy in bacterial communities.}, journal = {The ISME journal}, volume = {16}, number = {3}, pages = {812-821}, pmid = {34628478}, issn = {1751-7370}, support = {204829/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; *Cystic Fibrosis/microbiology ; Humans ; Microbial Sensitivity Tests ; Pseudomonas aeruginosa/genetics ; beta-Lactamases/genetics ; }, abstract = {The efficacy of antibiotic treatments targeting polymicrobial communities is not well predicted by conventional in vitro susceptibility testing based on determining minimum inhibitory concentration (MIC) in monocultures. One reason for this is that inter-species interactions can alter the community members' susceptibility to antibiotics. Here we quantify, and identify mechanisms for, community-modulated changes of efficacy for clinically relevant antibiotics against the pathogen Pseudomonas aeruginosa in model cystic fibrosis (CF) lung communities derived from clinical samples. We demonstrate that multi-drug resistant Stenotrophomonas maltophilia can provide high levels of antibiotic protection to otherwise sensitive P. aeruginosa. Exposure protection to imipenem was provided by chromosomally encoded metallo-β-lactamase that detoxified the environment; protection was dependent upon S. maltophilia cell density and was provided by S. maltophilia strains isolated from CF sputum, increasing the MIC of P. aeruginosa by up to 16-fold. In contrast, the presence of S. maltophilia provided no protection against meropenem, another routinely used carbapenem. Mathematical ordinary differential equation modelling shows that the level of exposure protection provided against different carbapenems can be explained by differences in antibiotic efficacy and inactivation rate. Together, these findings reveal that exploitation of pre-occurring antimicrobial resistance, and inter-specific competition, can have large impacts on pathogen antibiotic susceptibility, highlighting the importance of microbial ecology for designing successful antibiotic treatments for multispecies communities.}, }
@article {pmid34626522, year = {2022}, author = {Xu, Q and Luo, G and Guo, J and Xiao, Y and Zhang, F and Guo, S and Ling, N and Shen, Q}, title = {Microbial generalist or specialist: Intraspecific variation and dormancy potential matter.}, journal = {Molecular ecology}, volume = {31}, number = {1}, pages = {161-173}, doi = {10.1111/mec.16217}, pmid = {34626522}, issn = {1365-294X}, support = {KYZ201718//Fundamental Research Funds for the Central Universities/ ; 2017YFD0200805//National Key Research and Development Program of China/ ; 41977080//National Natural Science Foundation of China/ ; }, mesh = {Adaptation, Physiological ; Bacteria/genetics ; *Biological Evolution ; Humans ; *Microbiota ; Soil ; }, abstract = {Microbial generalists and specialists coexist in the soil environment while having distinctive impacts on microbial community dynamics. In microbial ecology, the underlying mechanisms as to why a species is a generalist or a specialist remain ambiguous. Herein, we collected soils across a national scale and identified bacterial generalists and specialists according to niche breadth at the species level (OTU level), and the single-nucleotide differences in each species were measured to investigate intraspecific variation (at zero-radius OTU level). Compared with that of the specialists, the intraspecific variation of the generalists was much higher, which ensured their wider niche breadth and lower variability. The higher asynchrony and different niche preferences of conspecific individuals and the higher dormancy potential within the generalists further contributed to their stability in varying environments. Besides, generalists were less controlled by environmental filtering, which was indicated by the stronger signature of stochastic processes in their assembly, and had higher diversification and transition rates that allowed them to adapt to environmental changes to a greater extent than specialists. Overall, this study provides a new comprehensive understanding of the rules of assembly and the evolutionary roles of bacterial generalists and specialists. It also highlights the importance of intraspecific variation and the dormancy potential in the stability of species.}, }
@article {pmid34625829, year = {2022}, author = {Bouhnik, O and Alami, S and Lamin, H and Lamrabet, M and Bennis, M and Ouajdi, M and Bellaka, M and Antri, SE and Abbas, Y and Abdelmoumen, H and Bedmar, EJ and Idrissi, MME}, title = {The Fodder Legume Chamaecytisus albidus Establishes Functional Symbiosis with Different Bradyrhizobial Symbiovars in Morocco.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {794-807}, pmid = {34625829}, issn = {1432-184X}, mesh = {Symbiosis/genetics ; *Fabaceae ; Root Nodules, Plant ; Phylogeny ; Ecosystem ; Morocco ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics/chemistry ; *Bradyrhizobium/genetics ; *Lupinus/genetics ; Animal Feed ; Soil ; Sequence Analysis, DNA ; }, abstract = {In this work, we analyzed the symbiotic performance and diversity of rhizobial strains isolated from the endemic shrubby legume Chamaecytisus albidus grown in soils of three different agroforestry ecosystems representing arid and semi-arid forest areas in Morocco. The analysis of the rrs gene sequences from twenty-four representative strains selected after REP-PCR fingerprinting showed that all the strains belong to the genus Bradyrhizobium. Following multi-locus sequence analysis (MLSA) using the rrs, gyrB, recA, glnII, and rpoB housekeeping genes, five representative strains, CA20, CA61, CJ2, CB10, and CB61 were selected for further molecular studies. Phylogenetic analysis of the concatenated glnII, gyrB, recA, and rpoB genes showed that the strain CJ2 isolated from Sahel Doukkala soil is close to Bradyrhizobium canariense BTA-1[ T] (96.95%); that strains CA20 and CA61 isolated from the Amhach site are more related to Bradyrhizobium valentinum LmjM3[T], with 96.40 and 94.57% similarity values; and that the strains CB10 and CB60 isolated from soil in the Bounaga site are more related to Bradyrhizobium murdochi CNPSo 4020[ T] and Bradyrhizobium. retamae Ro19[T], with which they showed 95.45 and 97.34% similarity values, respectively. The phylogenetic analysis of the symbiotic genes showed that the strains belong to symbiovars lupini, genistearum, and retamae. All the five strains are able to nodulate Lupinus luteus, Retama monosperma, and Cytisus monspessilanus, but they do not nodulate Glycine max and Phaseolus vulgaris. The inoculation tests showed that the strains isolated from the 3 regions improve significantly the plant yield as compared to uninoculated plants. However, the strains of Bradyrhizobium sp. sv. retamae isolated from the site of Amhach were the most performing. The phenotypic analysis showed that the strains are able to use a wide range of carbohydrates and amino acids as sole carbon and nitrogen source. The strains isolated from the arid areas of Bounaga and Amhach were more tolerant to salinity and drought stress than strains isolated in the semi-arid area of Sahel Doukkala.}, }
@article {pmid34623811, year = {2021}, author = {Wang, S and De Paepe, K and Van de Wiele, T and Fu, X and Yuan, Y and Zhang, B and Huang, Q}, title = {Starch Microspheres Entrapped with Chitosan Delay In Vitro Fecal Fermentation and Regulate Human Gut Microbiota Composition.}, journal = {Journal of agricultural and food chemistry}, volume = {69}, number = {41}, pages = {12323-12332}, doi = {10.1021/acs.jafc.1c04039}, pmid = {34623811}, issn = {1520-5118}, mesh = {*Chitosan ; Fatty Acids, Volatile ; Feces ; Fermentation ; *Gastrointestinal Microbiome ; Humans ; Microspheres ; Starch/metabolism ; }, abstract = {A slow dietary fiber fermentation rate is desirable to obtain a steady metabolite release and even distribution throughout the entire colon, ensuring to meet the energy needs in the distal colon. In this study, we prepared starch-entrapped microspheres with a variable chitosan-to-starch ratio by means of electrospraying and investigated the fermentability by human fecal microbiota in an in vitro batch system. Starch encapsulation reduced microbial gas production and the concentration of short-chain fatty acids. Butyrate production, in particular, gradually decreased with increasing chitosan proportions. Moreover, the starch and chitosan composites induced a synergistic effect on the gut microbiota composition. Roseburia, Lachnospiraceae, and Clostridiales were promoted by all of the microspheres, and the abundance of the aforementioned health-promoting taxa reached a maximum in chitosan/starch microspheres with a 1:6 (w/w) ratio. Our findings highlight the possible benefits of rationally designing functional foods targeting functional and taxonomic gut microbiota modulation.}, }
@article {pmid34623462, year = {2022}, author = {Ezzedine, JA and Janicot, A and Rasconi, S and Domaizon, I and Jacquet, S}, title = {Short-Term Dynamics of Bdellovibrio and Like Organisms in Lake Geneva in Response to a Simulated Climatic Extreme Event.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {717-729}, pmid = {34623462}, issn = {1432-184X}, mesh = {*Bdellovibrio/genetics ; Lakes ; Phylogeny ; *Deltaproteobacteria/genetics ; }, abstract = {The short time-scale dynamics of three families of Bdellovibrio and like organisms (i.e. Bdellovibrionaceae, Peredibacteraceae, and Bacteriovoracaceae) were studied on the surface waters of Lake Geneva in summer. Using mesocosms deployed nearshore in July 2019, we simulated an extreme climatic event (an input of carbon from the watershed in response to runoff from the catchment, light reduction, and mixing in response to stormy conditions) and aimed to study the impact of both abiotic and biotic factors on their dynamics. The three families of Bdellovibrio and like organisms (BALOs) showed different dynamics during the experiment. Peredibacteraceae was the most abundant group, whereas Bacteriovoracaceae was the least abundant. Compared with the other two families, the abundance of Bdellovibrionaceae did not fluctuate, remaining relatively stable over time. Environmental variables only partially explained the dynamics of these families; in particular, temperature, pH, and chloride concentrations were positively correlated with Bacteriovoracaceae, Bdellovibrionaceae, and Peredibacteraceae abundance, respectively. Prokaryote-like particles (PLPs), such as those with high DNA content (HDNA), were strongly and positively correlated with Peredibacteraceae and Bacteriovoracaceae. In contrast, no relationships were found between Bdellovibrionaceae and PLP abundance, nor between the virus-like particles (VLPs) and the different BALOs. Overall, the experiment revealed that predation was stable in the face of the simulated climatic events. In addition, we observed that Peredibacteraceae and Bacteriovoracaceae share common traits, while Bdellovibrionaceae seems to constitute a distinct category.}, }
@article {pmid34622953, year = {2022}, author = {Brigham, LM and Bueno de Mesquita, CP and Smith, JG and Sartwell, SA and Schmidt, SK and Suding, KN}, title = {Do plant-soil interactions influence how the microbial community responds to environmental change?.}, journal = {Ecology}, volume = {103}, number = {1}, pages = {e03554}, doi = {10.1002/ecy.3554}, pmid = {34622953}, issn = {1939-9170}, mesh = {Bacteria ; Ecosystem ; Fungi ; *Microbiota ; Nitrogen ; *Soil ; Soil Microbiology ; }, abstract = {Global change alters ecosystems and their functioning, and biotic interactions can either buffer or amplify such changes. We utilized a long-term nitrogen (N) addition and species removal experiment in the Front Range of Colorado, USA to determine whether a codominant forb and a codominant grass, with different effects on nutrient cycling and plant community structure, would buffer or amplify the effects of simulated N deposition on soil bacterial and fungal communities. While the plant community was strongly shaped by both the presence of dominant species and N addition, we did not find a mediating effect of the plant community on soil microbial response to N. In contrast to our hypothesis, we found a decoupling of the plant and microbial communities such that the soil microbial community shifted under N independently of directional shifts in the plant community. These findings suggest there are not strong cascading effects of N deposition across the plant-soil interface in our system.}, }
@article {pmid34622529, year = {2021}, author = {Li, WL and Dong, X and Lu, R and Zhou, YL and Zheng, PF and Feng, D and Wang, Y}, title = {Microbial ecology of sulfur cycling near the sulfate-methane transition of deep-sea cold seep sediments.}, journal = {Environmental microbiology}, volume = {23}, number = {11}, pages = {6844-6858}, doi = {10.1111/1462-2920.15796}, pmid = {34622529}, issn = {1462-2920}, mesh = {Geologic Sediments/microbiology ; *Methane/metabolism ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; *Sulfates/metabolism ; Sulfur/metabolism ; }, abstract = {Microbial sulfate reduction is largely associated with anaerobic methane oxidation and alkane degradation in sulfate-methane transition zone (SMTZ) of deep-sea cold seeps. How the sulfur cycling is mediated by microbes near SMTZ has not been fully understood. In this study, we detected a shallow SMTZ in three of eight sediment cores sampled from two cold seep areas in the South China Sea. One hundred ten genomes representing sulfur-oxidizing bacteria (SOB) and sulfur-reducing bacteria (SRB) strains were identified from three SMTZ-bearing cores. In the layers above SMTZ, SOB were mostly constituted by Campylobacterota, Gammaproteobacteria and Alphaproteobacteria that probably depended on nitrogen oxides and/or oxygen for oxidation of sulfide and thiosulfate in near-surface sediment layers. In the layers below the SMTZ, the deltaproteobacterial SRB genomes and metatranscriptomes revealed CO2 fixation by Wood-Ljungdahl pathway, sulfate reduction and nitrogen fixation for syntrophic or fermentative lifestyle. A total of 68% of the metagenome assembled genomes were not adjacent to known species in a phylogenomic tree, indicating a high diversity of bacteria involved in sulfur cycling. With the large number of genomes for SOB and SRB, our study uncovers the microbial populations that potentially mediate sulfur metabolism and associated carbon and nitrogen cycles, which sheds light on complex biogeochemical processes in deep-sea environments.}, }
@article {pmid34618070, year = {2021}, author = {Thiriet-Rupert, S and Gain, G and Jadoul, A and Vigneron, A and Bosman, B and Carnol, M and Motte, P and Cardol, P and Nouet, C and Hanikenne, M}, title = {Long-term acclimation to cadmium exposure reveals extensive phenotypic plasticity in Chlamydomonas.}, journal = {Plant physiology}, volume = {187}, number = {3}, pages = {1653-1678}, pmid = {34618070}, issn = {1532-2548}, mesh = {*Acclimatization ; *Adaptation, Physiological ; Biomass ; Cadmium/*metabolism ; Chlamydomonas/*drug effects/physiology ; Time Factors ; }, abstract = {Increasing industrial and anthropogenic activities are producing and releasing more and more pollutants in the environment. Among them, toxic metals are one of the major threats for human health and natural ecosystems. Because photosynthetic organisms play a critical role in primary productivity and pollution management, investigating their response to metal toxicity is of major interest. Here, the green microalga Chlamydomonas (Chlamydomonas reinhardtii) was subjected to short (3 d) or chronic (6 months) exposure to 50 µM cadmium (Cd), and the recovery from chronic exposure was also examined. An extensive phenotypic characterization and transcriptomic analysis showed that the impact of Cd on biomass production of short-term (ST) exposed cells was almost entirely abolished by long-term (LT) acclimation. The underlying mechanisms were initiated at ST and further amplified after LT exposure resulting in a reversible equilibrium allowing biomass production similar to control condition. This included modification of cell wall-related gene expression and biofilm-like structure formation, dynamics of metal ion uptake and homeostasis, photosynthesis efficiency recovery and Cd acclimation through metal homeostasis adjustment. The contribution of the identified coordination of phosphorus and iron homeostasis (partly) mediated by the main phosphorus homeostasis regulator, Phosphate Starvation Response 1, and a basic Helix-Loop-Helix transcription factor (Cre05.g241636) was further investigated. The study reveals the highly dynamic physiological plasticity enabling algal cell growth in an extreme environment.}, }
@article {pmid34617123, year = {2022}, author = {Medeiros, MCI and Seabourn, PS and Rollins, RL and Yoneishi, NM}, title = {Mosquito Microbiome Diversity Varies Along a Landscape-Scale Moisture Gradient.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {893-900}, pmid = {34617123}, issn = {1432-184X}, support = {P20 GM125508/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Aedes/microbiology ; Mosquito Vectors/physiology ; *Microbiota ; Disease Vectors ; Urbanization ; }, abstract = {Microorganisms live in close association with metazoan hosts and form symbiotic microbiotas that modulate host biology. Although the function of host-associated microbiomes may change with composition, hosts within a population can exhibit high turnover in microbiome composition among individuals. However, environmental drivers of this variation are inadequately described. Here, we test the hypothesis that this diversity among the microbiomes of Aedes albopictus (a mosquito disease vector) is associated with the local climate and land-use patterns on the high Pacific island of O 'ahu, Hawai 'i. Our principal finding demonstrates that the relative abundance of several bacterial symbionts in the Ae. albopictus microbiome varies in response to a landscape-scale moisture gradient, resulting in the turnover of the mosquito microbiome composition across the landscape. However, we find no evidence that mosquito microbiome diversity is tied to an index of urbanization. This result has implications toward understanding the assembly of host-associated microbiomes, especially during an era of rampant global climate change.}, }
@article {pmid34617072, year = {2021}, author = {Pace, RM and Chu, DM and Prince, AL and Ma, J and Seferovic, MD and Aagaard, KM}, title = {Complex species and strain ecology of the vaginal microbiome from pregnancy to postpartum and association with preterm birth.}, journal = {Med (New York, N.Y.)}, volume = {2}, number = {9}, pages = {1027-1049}, pmid = {34617072}, issn = {2666-6340}, support = {U54 HG004973/HG/NHGRI NIH HHS/United States ; K12 GM084897/GM/NIGMS NIH HHS/United States ; R01 HD091731/HD/NICHD NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; R21 ES029462/ES/NIEHS NIH HHS/United States ; R01 DK089201/DK/NIDDK NIH HHS/United States ; T32 GM007330/GM/NIGMS NIH HHS/United States ; R01 NR014792/NR/NINR NIH HHS/United States ; T32 GM088129/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria ; Child ; Female ; Humans ; Infant, Newborn ; Lactobacillus/genetics ; *Microbiota/genetics ; Postpartum Period ; Pregnancy ; *Premature Birth/microbiology ; RNA, Ribosomal, 16S/genetics ; Vagina/chemistry ; }, abstract = {BACKGROUND: Lactobacillus was described as a keystone bacterial taxon in the human vagina over 100 years ago. Using metagenomics, we and others have characterized lactobacilli and other vaginal taxa across health and disease states, including pregnancy. While shifts in community membership have been resolved at the genus/species level, strain dynamics remain poorly characterized.<br><br>METHODS: We performed a metagenomic analysis of the complex ecology of the vaginal econiche during and after pregnancy in a large U.S. based longitudinal cohort of women who were initially sampled in the third trimester of pregnancy, then validated key findings in a second cohort of women initially sampled in the second trimester of pregnancy.<br><br>FINDINGS: First, we resolved microbial species and strains, interrogated their co-occurrence patterns, and probed the relationship between keystone species and preterm birth outcomes. Second, to determine the role of human heredity in shaping vaginal microbial ecology in relation to preterm birth, we performed a mtDNA-bacterial species association analysis. Finally, we explored the clinical utility of metagenomics in detection and co-occurrence patterns for the pathobiont Group B Streptococcus (causative bacterium of invasive neonatal sepsis).<br><br>CONCLUSIONS: Our highly refined resolutions of the vaginal ecology during and post-pregnancy provide insights into not only structural and functional community dynamics, but highlight the capacity of metagenomics to reveal finer aspects of the vaginal microbial ecologic framework.<br><br>FUNDING: NIH-NINR R01NR014792, NIH-NICHD R01HD091731, NIH National Children's Study Formative Research, Burroughs Wellcome Fund Preterm Birth Initiative, March of Dimes Preterm Birth Research Initiative, NIH-NIGMS (K12GM084897, T32GM007330, T32GM088129).}, }
@article {pmid34616379, year = {2021}, author = {Huang, K and Tang, J and Zou, Y and Sun, X and Lan, J and Wang, W and Xu, P and Wu, X and Ma, R and Wang, Q and Wang, Z and Liu, J}, title = {Whole Genome Sequence of Alternaria alternata, the Causal Agent of Black Spot of Kiwifruit.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {713462}, pmid = {34616379}, issn = {1664-302X}, abstract = {Alternaria alternata is a pathogen in a wide range of agriculture crops and causes significant economic losses. A strain of A. alternata (Y784-BC03) was isolated and identified from "Hongyang" kiwifruit and demonstrated to cause black spot infections on fruits. The genome sequence of Y784-BC03 was obtained using Nanopore MinION technology. The assembled genome is composed of 33,869,130bp (32.30Mb) comprising 10 chromosomes and 11,954 genes. A total of 2,180 virulence factors were predicted to be present in the obtained genome sequence. The virulence factors comprised genes encoding secondary metabolites, including non-host-specific toxins, cell wall-degrading enzymes, and major transcriptional regulators. The predicted gene clusters encoding genes for the biosynthesis and export of secondary metabolites in the genome of Y784-BC03 were associated with non-host-specific toxins, including cercosporin, dothistromin, and versicolorin B. Major transcriptional regulators of different mycotoxin biosynthesis pathways were identified, including the transcriptional regulators, polyketide synthase, P450 monooxygenase, and major facilitator superfamily transporters.}, }
@article {pmid34615557, year = {2021}, author = {Wang, Y and Ye, J and Ju, F and Liu, L and Boyd, JA and Deng, Y and Parks, DH and Jiang, X and Yin, X and Woodcroft, BJ and Tyson, GW and Hugenholtz, P and Polz, MF and Zhang, T}, title = {Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {199}, pmid = {34615557}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Bioreactors ; Metagenome ; *Microbiota/genetics ; *Sewage ; }, abstract = {BACKGROUND: Microbial communities in both natural and applied settings reliably carry out myriads of functions, yet how stable these taxonomically diverse assemblages can be and what causes them to transition between states remains poorly understood. We studied monthly activated sludge (AS) samples collected over 9 years from a full-scale wastewater treatment plant to answer how complex AS communities evolve in the long term and how the community functions change when there is a disturbance in operational parameters.<br><br>RESULTS: Here, we show that a microbial community in activated sludge (AS) system fluctuated around a stable average for 3&#xa0;years but was then abruptly pushed into an alternative stable state by a simple transient disturbance (bleaching). While the taxonomic composition rapidly turned into a new state following the disturbance, the metabolic profile of the community and system performance remained remarkably stable. A total of 920 metagenome-assembled genomes (MAGs), representing approximately 70% of the community in the studied AS ecosystem, were recovered from the 97 monthly AS metagenomes. Comparative genomic analysis revealed an increased ability to aggregate in the cohorts of MAGs with correlated dynamics that are dominant after the bleaching event. Fine-scale analysis of dynamics also revealed cohorts that dominated during different periods and showed successional dynamics on seasonal and longer time scales due to temperature fluctuation and gradual changes in mean residence time in the reactor, respectively.<br><br>CONCLUSIONS: Our work highlights that communities can assume different stable states under highly similar environmental conditions and that a specific disturbance threshold may lead to a rapid shift in community composition. Video Abstract.}, }
@article {pmid34612321, year = {2022}, author = {Avalos, M and Garbeva, P and Vader, L and van Wezel, GP and Dickschat, JS and Ulanova, D}, title = {Biosynthesis, evolution and ecology of microbial terpenoids.}, journal = {Natural product reports}, volume = {39}, number = {2}, pages = {249-272}, doi = {10.1039/d1np00047k}, pmid = {34612321}, issn = {1460-4752}, mesh = {*Biological Products/chemistry ; Ecology ; Humans ; Plants/metabolism ; *Terpenes/chemistry ; }, abstract = {Covering: through June 2021Terpenoids are the largest class of natural products recognised to date. While mostly known to humans as bioactive plant metabolites and part of essential oils, structurally diverse terpenoids are increasingly reported to be produced by microorganisms. For many of the compounds biological functions are yet unknown, but during the past years significant insights have been obtained for the role of terpenoids in microbial chemical ecology. Their functions include stress alleviation, maintenance of cell membrane integrity, photoprotection, attraction or repulsion of organisms, host growth promotion and defense. In this review we discuss the current knowledge of the biosynthesis and evolution of microbial terpenoids, and their ecological and biological roles in aquatic and terrestrial environments. Perspectives on their biotechnological applications, knowledge gaps and questions for future studies are discussed.}, }
@article {pmid34610115, year = {2021}, author = {Masetti, R and Muratore, E and Leardini, D and Zama, D and Turroni, S and Brigidi, P and Esposito, S and Pession, A}, title = {Gut microbiome in pediatric acute leukemia: from predisposition to cure.}, journal = {Blood advances}, volume = {5}, number = {22}, pages = {4619-4629}, pmid = {34610115}, issn = {2473-9537}, mesh = {*Gastrointestinal Microbiome ; *Hematopoietic Stem Cell Transplantation ; Humans ; *Leukemia, Myeloid, Acute ; *Microbiota ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/therapy ; }, abstract = {The gut microbiome (GM) has emerged as a key factor in the genesis and progression of many diseases. The intestinal bacterial composition also influences treatment-related side effects and even the efficacy of oncological therapies. Acute leukemia (AL) is the most common cancer among children and the most frequent cause of cancer-related death during childhood. Outcomes have improved considerably over the past 4 decades, with the current long-term survival for acute lymphoblastic leukemia being ∼90%. However, several acute toxicities and long-term sequelae are associated with the multimodal therapy protocols applied in these patients. Specific GM configurations could contribute to the multistep developmental hypothesis for leukemogenesis. Moreover, GM alterations occur during the AL therapeutic course and are associated with treatment-related complications, especially during hematopoietic stem cell transplantation. The GM perturbation could last even after the removal of microbiome-modifying factors, like antibiotics, chemotherapeutic drugs, or alloimmune reactions, contributing to several health-related issues in AL survivors. The purpose of this article is to provide a comprehensive review of the chronological changes of GM in children with AL, from predisposition to cure. The underpinning biological processes and the potential interventions to modulate the GM toward a potentially health-promoting configuration are also highlighted.}, }
@article {pmid34609533, year = {2022}, author = {Bartolomé, C and Buendía-Abad, M and Ornosa, C and De la Rúa, P and Martín-Hernández, R and Higes, M and Maside, X}, title = {Bee Trypanosomatids: First Steps in the Analysis of the Genetic Variation and Population Structure of Lotmaria passim, Crithidia bombi and Crithidia mellificae.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {856-867}, pmid = {34609533}, issn = {1432-184X}, mesh = {Bees ; Animals ; *Crithidia/genetics/parasitology ; *Trypanosomatina/genetics/parasitology ; Genotype ; Genetic Variation ; }, abstract = {Trypanosomatids are among the most prevalent parasites in bees but, despite the fact that their impact on the colonies can be quite important and that their infectivity may potentially depend on their genotypes, little is known about the population diversity of these pathogens. Here we cloned and sequenced three non-repetitive single copy loci (DNA topoisomerase II, glyceraldehyde-3-phosphate dehydrogenase and RNA polymerase II large subunit, RPB1) to produce new genetic data from Crithidia bombi, C. mellificae and Lotmaria passim isolated from honeybees and bumblebees. These were analysed by applying population genetic tools in order to quantify and compare their variability within and between species, and to obtain information on their demography and population structure. The general pattern for the three species was that (1) they were subject to the action of purifying selection on nonsynonymous variants, (2) the levels of within species diversity were similar irrespective of the host, (3) there was evidence of recombination among haplotypes and (4) they showed no haplotype structuring according to the host. C. bombi exhibited the lowest levels of synonymous variation (πS= 0.06 ± 0.04 %) - and a mutation frequency distribution compatible with a population expansion after a bottleneck - that contrasted with the extensive polymorphism displayed by C. mellificae (πS= 2.24 ± 1.00 %), which likely has a more ancient origin. L. passim showed intermediate values (πS= 0.40 ± 0.28 %) and an excess of variants a low frequencies probably linked to the spread of this species to new geographical areas.}, }
@article {pmid34609532, year = {2022}, author = {Deng, Y and Borewicz, K and van Loo, J and Olabarrieta, MZ and Kokou, F and Sipkema, D and Verdegem, MCJ}, title = {In-Situ Biofloc Affects the Core Prokaryotes Community Composition in Gut and Enhances Growth of Nile Tilapia (Oreochromis niloticus).}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {879-892}, pmid = {34609532}, issn = {1432-184X}, support = {847.13.007//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 201606320215//China Scholarship Council/ ; }, mesh = {Animals ; *Cichlids ; Aquaculture ; *Gastrointestinal Microbiome ; Bacteria ; *Microbiota ; Animal Feed/analysis ; Dietary Supplements/analysis ; }, abstract = {Biofloc technology is commonly applied in intensive tilapia (Oreochromis niloticus) culture to maintain water quality, supply the fish with extra protein, and improve fish growth. However, the effect of dietary supplementation of processed biofloc on the gut prokaryotic (bacteria and archaea) community composition of tilapia is not well understood. In this study one recirculating aquaculture system was used to test how biofloc, including in-situ biofloc, dietary supplementation of ex-situ live or dead biofloc, influence fish gut prokaryotic community composition and growth performance in comparison to a biofloc-free control treatment. A core gut prokaryotic community was identified among all treatments by analyzing the temporal variations in gut prokaryotes. In-situ produced biofloc significantly increased the prokaryotic diversity in the gut by reducing the relative abundance of dominant Cetobacterium and increasing the relative abundance of potentially beneficial bacteria. The in-situ biofloc delivered a unique prokaryotic community in fish gut, while dietary supplementation of tilapias with 5% and 10% processed biofloc (live or dead) only changed the relative abundance of minor prokaryotic taxa outside the gut core microbiota. The modulatory effect of in-situ biofloc on tilapia gut microbiota was associated with the distinct microbial community in the biofloc water and undisturbed biofloc. The growth-promoting effect on tilapia was only detected in the in-situ biofloc treatment, while dietary supplementation of processed biofloc had no effect on fish growth performance as compared to the control treatment.}, }
@article {pmid34609161, year = {2021}, author = {Wiles, TJ}, title = {Cultivating Healthy Connections: Exploring and Engineering the Microbial Flow That Shapes Microbiomes.}, journal = {mSystems}, volume = {6}, number = {5}, pages = {e0086321}, pmid = {34609161}, issn = {2379-5077}, support = {DP2 AI154420/AI/NIAID NIH HHS/United States ; DP2AI154420//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, abstract = {Our view of the microbial world has undergone a radical transformation over the past decade. For most of the 20th century, medical microbiological research was focused on understanding the virulent nature of disease-causing pathogens. More recently, advances in DNA sequencing methodologies have exposed a wider diversity of microscopic wildlife that associate with our bodies and the environments around us, and the unexpected roles they play in supporting our health. Our expanding view of the microbial world is now motivating therapeutic interventions that are based not just on the elimination of nefarious pathogens but the nurturing of beneficial microbiomes. In this Commentary, I consider how our historically pathogen-based view of host-microbe interactions may be limiting the scope of new and alternative strategies for engineering microbiomes. I suggest that recognizing the therapeutic potential of the ongoing microbial transmission that connects microbiomes could illuminate unexplored opportunities for cultivating healthy host-microbe relationships.}, }
@article {pmid34608694, year = {2022}, author = {Bouma-Gregson, K and Crits-Christoph, A and Olm, MR and Power, ME and Banfield, JF}, title = {Microcoleus (Cyanobacteria) form watershed-wide populations without strong gradients in population structure.}, journal = {Molecular ecology}, volume = {31}, number = {1}, pages = {86-103}, pmid = {34608694}, issn = {1365-294X}, support = {S10 OD018174/OD/NIH HHS/United States ; CZO EAR-1331940//National Science Foundation/ ; DEB-1656009//National Science Foundation/ ; 91767101-0//US Environmental Protection Agency/ ; }, mesh = {*Cyanobacteria/genetics ; Ecosystem ; Metagenomics ; Rivers ; Russia ; }, abstract = {The relative importance of separation by distance and by environment to population genetic diversity can be conveniently tested in river networks, where these two drivers are often independently distributed over space. To evaluate the importance of dispersal and environmental conditions in shaping microbial population structures, we performed genome-resolved metagenomic analyses of benthic Microcoleus-dominated cyanobacterial mats collected in the Eel and Russian River networks (California, USA). The 64 Microcoleus genomes were clustered into three species that shared >96.5% average nucleotide identity (ANI). Most mats were dominated by one strain, but minor alleles within mats were often shared, even over large spatial distances (>300 km). Within the most common Microcoleus species, the ANI between the dominant strains within mats decreased with increasing spatial separation. However, over shorter spatial distances (tens of kilometres), mats from different subwatersheds had lower ANI than mats from the same subwatershed, suggesting that at shorter spatial distances environmental differences between subwatersheds in factors like canopy cover, conductivity, and mean annual temperature decreases ANI. Since mats in smaller creeks had similar levels of nucleotide diversity (π) as mats in larger downstream subwatersheds, within-mat genetic diversity does not appear to depend on the downstream accumulation of upstream-derived strains. The four-gamete test and sequence length bias suggest recombination occurs between almost all strains within each species, even between populations separated by large distances or living in different habitats. Overall, our results show that, despite some isolation by distance and environmental conditions, sufficient gene-flow occurs among cyanobacterial strains to prevent either driver from producing distinctive population structures across the watershed.}, }
@article {pmid34608508, year = {2022}, author = {Alguacil, MDM and Schlaeppi, K and López-García, &#xc1; and van der Heijden, MGA and Querejeta, JI}, title = {Contrasting Responses of Arbuscular Mycorrhizal Fungal Families to Simulated Climate Warming and Drying in a Semiarid Shrubland.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {941-944}, pmid = {34608508}, issn = {1432-184X}, mesh = {Humans ; *Mycorrhizae/genetics ; Ecosystem ; Soil Microbiology ; Biodiversity ; Soil/chemistry ; *Glomeromycota ; Plant Roots/microbiology ; }, abstract = {We carried out a 4-year manipulative field experiment in a semiarid shrubland in southeastern Spain to assess the impacts of experimental warming (W), rainfall reduction (RR), and their combination (W + RR) on the composition and diversity of arbuscular mycorrhizal fungal (AMF) communities in rhizosphere soil of H. syriacum and G. struthium shrubs using single-molecule real-time (SMRT) DNA sequencing. Across climate treatments, we encountered 109 AMF operational taxonomic units (OTUs) that were assigned to four families: Glomeraceae (93.94%), Gigasporaceae (2.19%), Claroideoglomeraceae (1.95%), and Diversisporaceae (1.92%). AMF community composition and diversity at OTU level were unaffected by the climate manipulation treatments, except for a significant decrease in AMF OTU richness in the W treatment relative to the control. However, we found a significant decrease of AMF family richness in all climate manipulation treatments relative to the control treatment. Members of the Gigasporaceae and Diversisporaceae families appeared to be highly vulnerable to intensification of heat and drought stress, as their abundances decreased by 67% and 77%, respectively, in the W + RR treatment relative to current ambient conditions. In contrast, the relative abundance and dominance of the Glomeraceae family within the AMF community increased significantly under the W + RR treatment, with Glomeraceae being the indicator family for the W + RR treatment. The interaction between warming and rainfall reduction had a significant effect on AMF community structure at family level. These findings provide new insights to help in the conservation of the soil biodiversity facing climate change in dryland ecosystems.}, }
@article {pmid34606240, year = {2021}, author = {Webster, TM and McFarland, A and Gebert, MJ and Oliverio, AM and Nichols, LM and Dunn, RR and Hartmann, EM and Fierer, N}, title = {Structure and Functional Attributes of Bacterial Communities in Premise Plumbing Across the United States.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {20}, pages = {14105-14114}, doi = {10.1021/acs.est.1c03309}, pmid = {34606240}, issn = {1520-5851}, mesh = {*Drinking Water ; Humans ; *Mycobacterium ; RNA, Ribosomal, 16S/genetics ; Sanitary Engineering ; United States ; Water Microbiology ; }, abstract = {Microbes that thrive in premise plumbing can have potentially important effects on human health. Yet, how and why plumbing-associated microbial communities vary across broad spatial scales remain undetermined. We characterized the bacterial communities in 496 showerheads collected from across the continental United States. The overall community structure, determined by 16S rRNA gene amplicon sequencing, revealed high levels of bacterial diversity. Although a large fraction of the observed variation in community composition could not be explained, differences in bacterial community composition were associated with water supply (private well water vs public municipal water), water source (groundwater vs surface water), and associated differences in water chemistry (pH and chlorine). Most notably, showerheads in homes supplied with public water had higher abundances of Blastomonas, Mycobacterium, and Porphyrobacter, while Pseudorhodoplanes, Novosphingobium, and Nitrospira were more abundant in those receiving private well water. We conducted shotgun metagenomic analyses on 92 of these samples to assess differences in genomic attributes. Public water-sourced showerheads had communities enriched in genes related to lipid and xenobiotic metabolisms, virulence factors, and antibiotic resistance. In contrast, genes associated with oxidative stress and membrane transporters were over-represented in communities from private well water-sourced showerheads compared to those supplied by public water systems. These results highlight the broad diversity of bacteria found in premise plumbing across the United States and the role of the water source and treatment in shaping the microbial community structure and functional potential.}, }
@article {pmid34604105, year = {2021}, author = {Zöhrer, PA and Hana, CA and Seyed Khoei, N and Mölzer, C and Hörmann-Wallner, M and Tosevska, A and Doberer, D and Marculescu, R and Bulmer, AC and Herbold, CW and Berry, D and Wagner, KH}, title = {Gilbert's Syndrome and the Gut Microbiota - Insights From the Case-Control BILIHEALTH Study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {701109}, pmid = {34604105}, issn = {2235-2988}, mesh = {Case-Control Studies ; Clostridiales ; Female ; *Gastrointestinal Microbiome ; *Gilbert Disease/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The heme catabolite bilirubin has anti-inflammatory, anti-oxidative and anti-mutagenic effects and its relation to colorectal cancer (CRC) risk is currently under evaluation. Although the main metabolic steps of bilirubin metabolism, including the formation of stercobilin and urobilin, take place in the human gastrointestinal tract, potential interactions with the human gut microbiota are unexplored. This study investigated, whether gut microbiota composition is altered in Gilbert's Syndrome (GS), a mild form of chronically elevated serum unconjugated bilirubin (UCB) compared to matched controls. Potential differences in the incidence of CRC-associated bacterial species in GS were also assessed. To this end, a secondary investigation of the BILIHEALTH study was performed, assessing 45 adults with elevated UCB levels (GS) against 45 age- and sex-matched controls (C). Fecal microbiota analysis was performed using 16S rRNA gene sequencing. No association between mildly increased UCB and the composition of the gut microbiota in this healthy cohort was found. The alpha and beta diversity did not differ between C and GS and both groups showed a typical representation of the known dominant phyla. Furthermore, no difference in abundance of Firmicutes and Proteobacteria, which have been associated with the mucosa of CRC patients were observed between the groups. A sequence related to the Christensenella minuta strain YIT 12065 was identified with a weak association value of 0.521 as an indicator species in the GS group. This strain has been previously associated with a lower body mass index, which is typical for the GS phenotype. Overall, sex was the only driver for an identifiable difference in the study groups, as demonstrated by a greater bacterial diversity in women. After adjusting for confounding factors and multiple testing, we can conclude that the GS phenotype does not affect the composition of the human gut microbiota in this generally healthy study group.}, }
@article {pmid34603252, year = {2021}, author = {Cai, S and Fan, Y and Zhang, B and Lin, J and Yang, X and Liu, Y and Liu, J and Ren, J and Xu, H}, title = {Appendectomy Is Associated With Alteration of Human Gut Bacterial and Fungal Communities.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {724980}, pmid = {34603252}, issn = {1664-302X}, abstract = {Recent research has revealed the importance of the appendix in regulating the intestinal microbiota and mucosal immunity. However, the changes that occur in human gut microbial communities after appendectomy have never been analyzed. We assessed the alterations in gut bacterial and fungal populations associated with a history of appendectomy. In this cross-sectional study, we investigated the association between appendectomy and the gut microbiome using 16S and ITS2 sequencing on fecal samples from 30 healthy individuals with prior appendectomy (HwA) and 30 healthy individuals without appendectomy (HwoA). Analysis showed that the gut bacterial composition of samples from HwA was less diverse than that of samples from HwoA and had a lower abundance of Roseburia, Barnesiella, Butyricicoccus, Odoribacter, and Butyricimonas species, most of which were short-chain fatty acids-producing microbes. The HwA subgroup analysis indicated a trend toward restoration of the HwoA bacterial microbiome over time after appendectomy. HwA had higher gut fungi composition and diversity than HwoA, even 5 years after appendectomy. Compared with those in samples from HwoA, the abundance correlation networks in samples from HwA displayed more complex fungal-fungal and fungal-bacterial community interactions. This study revealed a marked impact of appendectomy on gut bacteria and fungi, which was particularly durable for fungi.}, }
@article {pmid34603220, year = {2021}, author = {Delago, A and Gregor, R and Dubinsky, L and Dandela, R and Hendler, A and Krief, P and Rayo, J and Aharoni, A and Meijler, MM}, title = {A Bacterial Quorum Sensing Molecule Elicits a General Stress Response in Saccharomyces cerevisiae.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {632658}, pmid = {34603220}, issn = {1664-302X}, abstract = {Bacteria assess their population density through a chemical communication mechanism termed quorum sensing, in order to coordinate group behavior. Most research on quorum sensing has focused primarily on its role as an intraspecies chemical signaling mechanism that enables the regulation of certain phenotypes through targeted gene expression. However, in recent years several seminal studies have revealed important phenomena in which quorum sensing molecules appear to serve additional roles as interspecies signals that may regulate microbial ecology. In this study, we asked whether the budding yeast Saccharomyces cerevisiae can sense chemical signals from prokaryotes. When exposed to a variety of quorum sensing molecules from different bacterial species and from Candida albicans we found that N-(3-oxododecanoyl)-L-homoserine lactone (C12) from the opportunistic human pathogen Pseudomonas aeruginosa induces a remarkable stress response in yeast. Microarray experiments confirmed and aided in interpreting these findings, showing a unique and specific expression pattern that differed significantly from the response to previously described stress factors. We further characterized this response and report preliminary findings on the molecular basis for the recognition of C12 by the yeast.}, }
@article {pmid34602304, year = {2022}, author = {Mauger, S and Monard, C and Thion, C and Vandenkoornhuyse, P}, title = {Contribution of single-cell omics to microbial ecology.}, journal = {Trends in ecology &amp; evolution}, volume = {37}, number = {1}, pages = {67-78}, doi = {10.1016/j.tree.2021.09.002}, pmid = {34602304}, issn = {1872-8383}, mesh = {Ecology ; Genome ; Genomics ; *Microbiota ; }, abstract = {Micro-organisms play key roles in various ecosystems, but many of their functions and interactions remain undefined. To investigate the ecological relevance of microbial communities, new molecular tools are being developed. Among them, single-cell omics assessing genetic diversity at the population and community levels and linking each individual cell to its functions is gaining interest in microbial ecology. By giving access to a wider range of ecological scales (from individual to community) than culture-based approaches and meta-omics, single-cell omics can contribute not only to micro-organisms' genomic and functional identification but also to the testing of concepts in ecology. Here, we discuss the contribution of single-cell omics to possible breakthroughs in concepts and knowledge on microbial ecosystems and ecoevolutionary processes.}, }
@article {pmid34601412, year = {2022}, author = {Shi, B and Cheng, C and Zhang, Y and Du, Z and Zhu, L and Wang, J and Wang, J and Li, B}, title = {Effects of 3,6-dichlorocarbazole on microbial ecology and its degradation in soil.}, journal = {Journal of hazardous materials}, volume = {424}, number = {Pt A}, pages = {127315}, doi = {10.1016/j.jhazmat.2021.127315}, pmid = {34601412}, issn = {1873-3336}, mesh = {Carbazoles ; *Dioxins ; *Polychlorinated Dibenzodioxins ; Soil ; Soil Microbiology ; *Soil Pollutants ; }, abstract = {The emerging contaminants polyhalogenated carbazoles (PHCZs) have been verified to be present in soils and sediments globally, and they show dioxin-like toxicity. However, there is a lack of soil ecological risk assessments on PHCZs despite their high detection rate and concentration in soils. The present study investigated the degradation and soil microbial influence of 3,6-dichlorocarbazole (3,6-DCCZ, a frequently detected PHCZ) in soil. The results showed that the half-lives of 3,6-DCCZ at concentrations of 0.100 mg/kg and 1.00 mg/kg were 7.75 d and 16.73 d, respectively. We found that 3,6-DCCZ was transformed into 3-chlorocarbazole (3-CCZ) by dehalogenation in soil. Additionally, intermediate products with higher molecular weights were detected, presumably because the -H on the carbazole ring was replaced by -CH3, -CH2-O-CH3, or -CH2-O-CH2CH3. 3,6-DCCZ exposure slightly increased the soil bacterial abundance and diversity and clearly changed the soil bacterial community structure. Through a comprehensive analysis of FAPROTAX, functional gene qPCR and soil enzyme tests, we concluded that 3,6-DCCZ exposure inhibited nitrification and nitrogen fixation but promoted denitrification, carbon dioxide fixation and hydrocarbon degradation processes in soil. This study provides valuable data for clarifying the PHCZ ecological risk in soil.}, }
@article {pmid34600678, year = {2021}, author = {Marzorati, M and Van den Abbeele, P and Bubeck, S and Bayne, T and Krishnan, K and Young, A}, title = {Treatment with a spore-based probiotic containing five strains of Bacillus induced changes in the metabolic activity and community composition of the gut microbiota in a SHIME® model of the human gastrointestinal system.}, journal = {Food research international (Ottawa, Ont.)}, volume = {149}, number = {}, pages = {110676}, doi = {10.1016/j.foodres.2021.110676}, pmid = {34600678}, issn = {1873-7145}, mesh = {*Bacillus ; Colon ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; *Probiotics ; Spores, Bacterial ; Verrucomicrobia ; }, abstract = {MegaSporeBiotic™ is an oral, spore-based probiotic comprised of five Bacillus spp. (Bacillus indicus HU36, Bacillus subtilis HU58, Bacillus coagulans SC208, Bacillus licheniformis SL307, and Bacillus clausii SC109). The effects of MegaSporeBiotic™ on gut microbiota activity and community composition were evaluated for the first time using an in vitro model of the human gastrointestinal tract, the simulator of the human intestinal microbial ecosystem (SHIME®), under healthy conditions. Following a stabilization period and a control period (2 weeks each), the reactor feed was supplemented with daily MegaSporeBiotic™ for 3 weeks (treatment period). Changes in microbial community activity and composition between the control and treatment periods were evaluated for each colon compartment (ascending [AC], transverse [TC], and descending colon [DC]). Propionate levels increased significantly in the TC (week 2, P = 0.02; week 3, P = 0.0019) and DC (week 2, P = 0.03) with treatment while lactate levels significantly decreased in the TC (week 3, P = 0.03). Ammonium levels were significantly decreased during the final week of treatment (TC, P = 0.02; DC, P = 0.03). Overall, Akkermansia muciniphila, Bifidobacteria spp., and Firmicutes increased with treatment while Lactobacillus spp. and Bacteroidetes decreased. The Firmicutes:Bacteroidetes ratio increased with treatment in the AC compartment. MegaSporeProbiotic™ treatment resulted in changes in metabolism and increased bacterial diversity.}, }
@article {pmid34600491, year = {2021}, author = {Deng, X and Si, J and Qu, Y and Jie, L and He, Y and Wang, C and Zhang, Y}, title = {Vegetarian diet duration's influence on women's gut environment.}, journal = {Genes &amp; nutrition}, volume = {16}, number = {1}, pages = {16}, pmid = {34600491}, issn = {1555-8932}, support = {2018-JYBZZ-JS014//young teacher project of beijing university of chinese medicine/ ; 2017-JYB-JS-022//young teacher project of beijing university of chinese medicine/ ; }, abstract = {BACKGROUND: Nutrient composition of vegetarian diets is greatly different from that of omnivore diets, which may fundamentally influence the gut microbiota and fecal metabolites. The interactions between diet pattern and gut environment need further illustration. This study aims to compare the difference in the gut microbiota and fecal metabolites between vegetarian and omnivore female adults and explore associations between dietary choices/duration and gut environment changes.<br><br>METHODS: In this study, investigations on the fecal metabolome together with the gut microbiome were performed to describe potential interactions with quantitative functional annotation. In order to eliminate the differences brought by factors of gender and living environment, 80 female adults aged 20 to 48 were recruited in the universities in Beijing, China. Quantitative Insights Into Microbial Ecology (QIIME) analysis and Ingenuity Pathway Analysis (IPA) were applied to screen differential data between groups from gut microbiota and fecal metabolites. Furthermore, weighted gene correlation network analysis (WGCNA) was employed as the bioinformatics analysis tool for describing the correlations between gut microbiota and fecal metabolites. Moreover, participants were further subdivided by the vegetarian diet duration for analysis.<br><br>RESULTS: GPCR-mediated integration of enteroendocrine signaling was predicted to be one of the regulatory mechanisms of the vegetarian diet. Intriguingly, changes in the gut environment which occurred along with the vegetarian diet showed attenuated trend as the duration increased. A similar trend of returning to "baseline" after a 10-year vegetarian diet was detected in both gut microbiota and fecal metabolome.<br><br>CONCLUSIONS: The vegetarian diet is beneficial more than harmful to women. Gut microbiota play roles in the ability of the human body to adapt to external changes.}, }
@article {pmid34600011, year = {2022}, author = {Fehlauer, T and Collin, B and Angeletti, B and Santaella, C and Dentant, C and Chaurand, P and Levard, C and Gonneau, C and Borschneck, D and Rose, J}, title = {Uptake patterns of critical metals in alpine plant species growing in an unimpaired natural site.}, journal = {Chemosphere}, volume = {287}, number = {Pt 4}, pages = {132315}, doi = {10.1016/j.chemosphere.2021.132315}, pmid = {34600011}, issn = {1879-1298}, mesh = {Biodegradation, Environmental ; *Brassicaceae ; Environmental Monitoring ; Metals/analysis ; *Metals, Heavy/analysis ; Soil ; *Soil Pollutants/analysis ; }, abstract = {The range of metals used for industrial purposes - electrical engineering, solar panels, batteries - has increased substantially over the last twenty years. Some of these emerging metals are the subject of geopolitical conflict and are considered critical as their unique properties make them irreplaceable. Many of these elements are poorly studied and their biogeochemical cycles still raise many questions. Aim of this study is to analyse the soil-to-plant transfer of some of these chemical elements and to shed light on their uptake pathways. For this purpose, the geological site of Jas Roux (France) was chosen as this alpine site is naturally rich in critical and potentially toxic elements such as As, Sb, Ba and Tl, but nevertheless is host to a high diversity of plants. Elemental concentrations were analysed in the topsoil and in 12 selected alpine plant species sampled in situ. Statistical tools were used to detect species dependent characteristics in elemental uptake. Our analyses revealed accumulation of rare earth elements by Saxifraga paniculata, selective oxyanion absorption by Hippocrepis comosa, accumulation of Tl by Biscutella laevigata and Galium corrudifolium and an exclusion strategy in Juniperus communis. These findings advance our understanding of the environmental behaviour of critical metals and metalloids such as V, As, Y, Sb, Ce, Ba and Tl and might bare valuable information for phytoremediation applications.}, }
@article {pmid34599659, year = {2022}, author = {Aivelo, T and Lemoine, M and Tschirren, B}, title = {Elevational Changes in Bacterial Microbiota Structure and Diversity in an Arthropod-Disease Vector.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {868-878}, pmid = {34599659}, issn = {1432-184X}, support = {17_027//Stiftung f&#xfc;r wissenschaftliche Forschung an der Universit&#xe4;t Z&#xfc;rich/ ; PP00P3_128386//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; PP00P3_157455//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {Animals ; Female ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Arthropods ; *Microbiota/genetics ; *Ixodes/microbiology ; Bacteria/genetics ; Disease Vectors ; }, abstract = {Environmental conditions change rapidly along elevational gradients and have been found to affect community composition in macroscopic taxa, with lower diversity typically observed at higher elevations. In contrast, microbial community responses to elevation are still poorly understood. Specifically, the effects of elevation on vector-associated microbiota have not been studied to date, even though the within-vector microbial community is known to influence vector competence for a range of zoonotic pathogens. Here we characterize the structure and diversity of the bacterial microbiota in an important zoonotic disease vector, the sheep tick Ixodes ricinus, along replicated elevational gradient (630-1673 m) in the Swiss Alps. 16S rRNA sequencing of the whole within-tick bacterial microbiota of questing nymphs and adults revealed a decrease in Faith's phylogenetic microbial alpha diversity with increasing elevation, while beta diversity analyses revealed a lower variation in microbial community composition at higher elevations. We also found a higher microbial diversity later in the season and significant differences in microbial diversity among tick life stages and sexes, with lowest microbial alpha diversity observed in adult females. No associations between tick genetic diversity and bacterial diversity were observed. Our study demonstrates systematic changes in tick bacterial microbiota diversity along elevational gradients. The observed patterns mirror diversity changes along elevational gradients typically observed in macroscopic taxa, and they highlight the key role of environmental factors in shaping within-host microbial communities in ectotherms.}, }
@article {pmid34599356, year = {2022}, author = {Almendras, K and Iannuzzi, S and Carú, M and Orlando, J}, title = {Diversity of Microbial Functional Genes Should Be Considered During the Interpretation of the qPCR Melting Curves.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {935-940}, pmid = {34599356}, issn = {1432-184X}, support = {1181510//fondo nacional de desarrollo cient&#xed;fico y tecnol&#xf3;gico/ ; }, mesh = {*Soil Microbiology ; *Nitrogen/analysis ; Phosphorus ; Bacteria/genetics ; Soil/chemistry ; Real-Time Polymerase Chain Reaction ; }, abstract = {Soil microorganisms play an essential role in biogeochemical cycles. One approach to study these microbial communities is quantifying functional genes by quantitative PCR (qPCR), in which a melting curve analysis is usually assessed to confirm that a single PCR product is being quantified. However, the high diversity of functional genes in environmental samples could generate more than one peak in those curves, so the presence of two or multiple peaks does not always indicate nonspecific amplification. Here, we analyzed the taxonomic diversity of soil microorganisms harboring functional genes involved in nitrogen (N) and phosphorus (P) cycles, based on a database of genomes and metagenomes, and predicted the melting curve profiles of these genes. These functional genes were spread across many bacterial phyla, but mainly Proteobacteria and Actinobacteria. In general, the melting curves exhibited more than one peak or peaks with shoulders, mainly related to the variation of the nucleotide composition of the genes and the expected size of the amplicons. These results indicate that the melting curves of functional genes from environmental samples should be carefully evaluated, being in silico analyses a cost-effective way to identify inherent sequence diversity and avoid interpreting multiple peaks always as unspecific amplifications.}, }
@article {pmid34596724, year = {2021}, author = {Wang, Y and Elzenga, T and van Elsas, JD}, title = {Effect of culture conditions on the performance of lignocellulose-degrading synthetic microbial consortia.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {20}, pages = {7981-7995}, pmid = {34596724}, issn = {1432-0614}, mesh = {*Ascomycota ; Lignin ; *Microbial Consortia ; Sphingobacterium ; }, abstract = {In this study, we examined a synthetic microbial consortium, composed of two selected bacteria, i.e., Citrobacter freundii so4 and Sphingobacterium multivorum w15, next to the fungus Coniochaeta sp. 2T2.1, with respect to their fate and roles in the degradation of wheat straw (WS). A special focus was placed on the effects of pH (7.2, 6.2, or 5.2), temperature (25 versus 28 °C), and shaking speed (60 versus 180 rpm). Coniochaeta sp. 2T2.1 consistently had a key role in the degradation process, with the two bacteria having additional roles. Whereas temperature exerted only minor effects on the degradation, pH and shaking speed were key determinants of both organismal growth and WS degradation levels. In detail, the three-partner degrader consortium showed significantly higher WS degradation values at pH 6.2 and 5.2 than at pH 7.2. Moreover, the two bacteria revealed up to tenfold enhanced final cell densities (ranging from log8.0 to log9.0 colony forming unit (CFU)/mL) in the presence of Coniochaeta sp. 2T2.1 than when growing alone or in a bacterial bi-culture, regardless of pH range or shaking speed. Conversely, at 180 rpm, fungal growth was clearly suppressed by the presence of the bacteria at pH 5.2 and pH 6.2, but not at pH 7.2. In contrast, at 60 rpm, the presence of the bacteria fostered fungal growth. In these latter cultures, oxygen levels were significantly lowered as compared to the maximal levels found at 180 rpm (about 5.67 mg/L, ~ 62% of saturation). Conspicuous effects on biomass appearance pointed to a fungal biofilm-modulating role of the bacteria.Key points• Coniochaeta sp. 2T2.1 has a key role in wheat straw (WS) degradation.• Bacterial impact shifts when conditions change.• pH and shaking speed are key drivers of the growth dynamics and WS degradation.}, }
@article {pmid34596711, year = {2022}, author = {Russell, KA and McFrederick, QS}, title = {Elevated Temperature May Affect Nectar Microbes, Nectar Sugars, and Bumble Bee Foraging Preference.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {473-482}, pmid = {34596711}, issn = {1432-184X}, support = {CA- R-ENT-5109-H//National Institute of Food and Agriculture/ ; 2019-67011-29604//National Institute of Food and Agriculture/ ; }, mesh = {Animals ; Bacteria ; Bees ; Flowers/microbiology ; *Plant Nectar ; *Pollination/physiology ; Sugars ; Temperature ; }, abstract = {Floral nectar, an important resource for pollinators, is inhabited by microbes such as yeasts and bacteria, which have been shown to influence pollinator preference. Dynamic and complex plant-pollinator-microbe interactions are likely to be affected by a rapidly changing climate, as each player has their own optimal growth temperatures and phenological responses to environmental triggers, such as temperature. To understand how warming due to climate change is influencing nectar microbial communities, we incubated a natural nectar microbial community at different temperatures and assessed the subsequent nectar chemistry and preference of the common eastern bumble bee, Bombus impatiens. The microbial community in floral nectar is often species-poor, and the cultured Brassica rapa nectar community was dominated by the bacterium Fructobacillus. Temperature increased the abundance of bacteria in the warmer treatment. Bumble bees preferred nectar inoculated with microbes, but only at the lower, ambient temperature. Warming therefore induced an increase in bacterial abundance which altered nectar sugars and led to significant differences in pollinator preference.}, }
@article {pmid34596710, year = {2022}, author = {Zhang, M and Gao, ZC and Chi, Z and Wang, Z and Liu, GL and Li, XF and Hu, Z and Chi, ZM}, title = {Massoia Lactone Displays Strong Antifungal Property Against Many Crop Pathogens and Its Potential Application.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {376-390}, pmid = {34596710}, issn = {1432-184X}, support = {31970058//innovative research group project of the national natural science foundation of china/ ; }, mesh = {Antifungal Agents/pharmacology ; *Fungicides, Industrial ; *Fusarium/physiology ; Lactones/pharmacology ; Plant Diseases/microbiology/prevention &amp; control ; Triticum/microbiology ; }, abstract = {Massoia lactone could be released from liamocins produced by Aureobasidium melanogenum M39. The obtained Massoia lactone was very stable and highly active against many fungal crop pathogens which cause many plant diseases and food unsafety. Massoia lactone treatment not only could effectively inhibit their hyphal growth and spore germination, but also caused pore formation in cell membrane, reduction of ergosterol content, rise in intracellular ROS levels, and leakage of intracellular components, consequently leading to cellular necrosis and cell death. The direct contact of Massoia lactone with Fusarium graminearum spores could stop the development of Fusarium head blight symptom in the diseased wheats. Therefore, Massoia lactone could be a promising candidate for development as an effective and green bio-fungicide because of its high anti-fungal activity and the multiplicity of mode of its action.}, }
@article {pmid34596709, year = {2022}, author = {Banister, RB and Schwarz, MT and Fine, M and Ritchie, KB and Muller, EM}, title = {Instability and Stasis Among the Microbiome of Seagrass Leaves, Roots and Rhizomes, and Nearby Sediments Within a Natural pH Gradient.}, journal = {Microbial ecology}, volume = {84}, number = {3}, pages = {703-716}, pmid = {34596709}, issn = {1432-184X}, mesh = {*Rhizome/chemistry ; Seawater/microbiology ; RNA, Ribosomal, 16S/genetics/analysis ; Hydrogen-Ion Concentration ; Proton-Motive Force ; *Microbiota ; Bacteria/genetics ; }, abstract = {Seagrass meadows are hotspots of biodiversity with considerable economic and ecological value. The health of seagrass ecosystems is influenced in part by the makeup and stability of their microbiome, but microbiome composition can be sensitive to environmental change such as nutrient availability, elevated temperatures, and reduced pH. The objective of the present study was to characterize the bacterial community of the leaves, bulk samples of roots and rhizomes, and proximal sediment of the seagrass species Cymodocea nodosa along the natural pH gradient of Levante Bay, Vulcano Island, Italy. The bacterial community was determined by characterizing the 16S rRNA amplicon sequencing and analyzing the operational taxonomic unit classification of bacterial DNA within samples. Statistical analyses were used to explore how life-long exposure to different pH/pCO2 conditions may be associated with significant differences in microbial communities, dominant bacterial classes, and microbial diversity within each plant section and sediment. The microbiome of C. nodosa significantly differed among all sample types and site-specific differences were detected within sediment and root/rhizome microbial communities, but not the leaves. These results show that C. nodosa leaves have a consistent microbial community even across a pH range of 8.15 to 6.05. The ability for C. nodosa to regulate and maintain microbial structure may indicate a semblance of resilience within these vital ecosystems under projected changes in environmental conditions such as ocean acidification.}, }
@article {pmid34591681, year = {2021}, author = {Castillo, DJ and Van Goethem, MW and Makhalanyane, TP}, title = {Three Draft Single-Cell Genome Sequences of Novel SAR324 Strains Isolated from the Abyssopelagic Southern Ocean.}, journal = {Microbiology resource announcements}, volume = {10}, number = {39}, pages = {e0075921}, pmid = {34591681}, issn = {2576-098X}, support = {110717//National Research Foundation (NRF)/ ; }, abstract = {SAR324 is a ubiquitous and phylogenetically distinct clade of Deltaproteobacteria in marine environments. Here, we present three single-cell amplified genome sequences from the SAR324 lineage, obtained from the abyssopelagic zone of the Indian sector of the Southern Ocean.}, }
@article {pmid34591135, year = {2022}, author = {Villegas-Plazas, M and Sanabria, J and Arbeli, Z and Vasquez, Y and Roldan, F and Junca, H}, title = {Metagenomic Analysis of Biochemical Passive Reactors During Acid Mine Drainage Bioremediation Reveals Key Co-selected Metabolic Functions.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {465-472}, pmid = {34591135}, issn = {1432-184X}, support = {Beca de Estudios Doctorales Nacionales 727//Minciencias/ ; 120377657722//Minciencias/ ; }, mesh = {Acids ; Biodegradation, Environmental ; *Metagenomics ; *Mining ; Sulfates/metabolism ; }, abstract = {Acid mine drainage (AMD) is the major pollutant generated by the mining industry, and it is characterized by low pH and high concentration of metals and sulfate. The use of biochemical passive reactors (BPRs) is a promising strategy for its bioremediation. To date, there are various studies describing the taxonomical composition of BPR microbial communities, generally consisting of an assemblage of sulfate-reducing organisms inside Deltaproteobacteria, and a diverse set of anaerobic (ligno)cellulolytic bacteria; however, insights about its functional metagenomic content are still scarce. In previous studies, a laboratory-scale AMD bioremediation using biochemical passive reactors was designed and performed, tracking operation parameters, chemical composition, and changes, together with taxonomic composition of the microbiomes harbored in these systems. In order to reveal the main functional content of these communities, we used shotgun metagenomics analyses to explore genes of higher relative frequencies and their inferred functions during the AMD bioremediation from three BPRs representing the main microbiome compositions detected in the system. Remarkably, genes encoding for two-component regulatory systems and ABC transporters related to metal and inorganic ions, cellulose degradation enzymes, dicarboxylic acid production, and sulfite reduction complex were all detected at increased frequency. Our results evidenced that higher taxonomic diversity of the microbiome was arising together with a functional redundancy of the specific metabolic roles, indicating its co-selection and suggesting that its enrichment on BPRs may be implicated in the cumulative efficiency of these systems.}, }
@article {pmid34589797, year = {2021}, author = {Hovens, IB and van Leeuwen, BL and Falcao-Salles, J and de Haan, JJ and Schoemaker, RG}, title = {Enteral enriched nutrition to prevent cognitive dysfunction after surgery; a study in rats.}, journal = {Brain, behavior, &amp; immunity - health}, volume = {16}, number = {}, pages = {100305}, pmid = {34589797}, issn = {2666-3546}, abstract = {BACKGROUND: Inflammation plays an important role in postoperative cognitive dysfunction (POCD), particularly in elderly patients. Enteral enriched nutrition was shown to inhibit the response on inflammatory stimuli. Aim of the present study was to explore the therapeutic potential of enteral enriched nutrition in our rat model for POCD. The anticipated mechanism of action was examined in young rats, while responses in the target group of elderly patients were evaluated in old rats.<br><br>METHODS: Male 3 and 23 months old Wistar rats received a bolus of enteral fat/protein-enriched nutrition 2&#xa0;&#x200b;h and 30&#xa0;&#x200b;min before surgery. The inflammatory response was evaluated by systemic inflammation markers and brain microglia activity. Additionally, in old rats, the role of the gut-brain axis was studied by microbiome analyses of faecal samples. Days 9-14 after surgery, rats were subjected to cognitive testing. Day 16, rats were sacrificed and brains were collected for immunohistochemistry.<br><br>RESULTS: In young rats, enriched nutrition improved long-term spatial learning and memory in the Morris Water Maze, reduced plasma IL1-&#x3b2; and VEGF levels, but left microglia activity and neurogenesis unaffected. In contrast, in old rats, enriched nutrition improved short-term memory in the novel object- and novel location recognition tests, but impaired development of long-term memory in the Morris Water Maze. Systemic inflammation was not affected, but microglia activity seemed even increased. Gut integrity and microbiome were not affected.<br><br>CONCLUSION: Enteral enriched nutrition before surgery in young rats indeed reduced systemic inflammation and improved cognitive performance after surgery, whereas old rats showed a mixed favorable/unfavorable cognitive response, without effect on systemic inflammation. Anti-inflammatory effects of enriched nutrition were not reflected in decreased microglia activity. Neither was an important role for the gut-brain axis observed. Since the relatively straight forward effects of enriched nutrition in young rats could not be shown in old rats, as indicated by a mixed beneficial/detrimental cognitive outcome in the latter, caution is advised by translating effects seen in younger patients to older ones.}, }
@article {pmid34589774, year = {2021}, author = {Agarwala, S and Naik, B and Ramachandra, NB}, title = {Mucosa-associated specific bacterial species disrupt the intestinal epithelial barrier in the autism phenome.}, journal = {Brain, behavior, &amp; immunity - health}, volume = {15}, number = {}, pages = {100269}, pmid = {34589774}, issn = {2666-3546}, abstract = {Gut-Brain Axis provides a bidirectional communicational route, an imbalance of which can have pathophysiological consequences. Differential gut microbiome studies have become a frontier in autism research, affecting 85% of autistic children. The present study aims to understand how gut microbiota of autism subjects differ from their neurotypical counterparts. This study would help to identify the abundance of bacterial signature species in autism and their associated metabolites. 16S rRNA metagenomic sequence datasets of 30 out of 206 autism subjects were selected from the American Gut Project Archive. First, the taxonomic assignment was inferred by similarity-based methods using the Quantitative Insights into Microbial Ecology (QIIME) toolkit. Next, species abundance was characterized, and a co-occurrence network was built to infer species interaction using measures of diversity. Thirdly, statistical parameters were incorporated to validate the findings. Finally, the identification of metabolites associated with these bacterial signature species connects with biological processes in the host through pathway analysis. Gut microbiome data revealed Akkermansia sp. and Faecalibacterium prausnitzii to be statistically lower in abundance in autistic children than their neurotypical peers with a five and two-fold decrease, respectively. While Prevotella sp. and Sutterella sp. showed a five and a two-fold increase in cases, respectively. The constructed pathway revealed succinate and butyrate as the significant metabolites for the bacterial signature species identified. The present study throws light on the role of mucosa-associated bacterial species: Veillonella sp., Prevotella sp., Akkermansia sp., Sutterella sp., Faecalibacterium prausnitzii, Lactobacillus sp., which can act as diagnostic criteria for detection of gut dysbiosis in autism.}, }
@article {pmid34585291, year = {2022}, author = {Martínez-López, V and Ruiz, C and Muñoz, I and Ornosa, C and Higes, M and Martín-Hernández, R and De la Rúa, P}, title = {Detection of Microsporidia in Pollinator Communities of a Mediterranean Biodiversity Hotspot for Wild Bees.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {638-642}, pmid = {34585291}, issn = {1432-184X}, support = {21260/PD/19//Fundaci&#xf3;n S&#xe9;neca/ ; 19908/GERM/2015//Fundaci&#xf3;n S&#xe9;neca/ ; JCI2018-036614-I//Ministerio de Econom&#xed;a y Competitividad/ ; FPU13/05115//Ministerio de Educaci&#xf3;n, Cultura y Deporte/ ; }, mesh = {Animals ; Bees ; Biodiversity ; Ecosystem ; *Moths ; *Nosema/genetics ; Phylogeny ; Pollination ; }, abstract = {Insect pollination is crucial for the maintenance of natural and managed ecosystems but the functioning of this ecosystem service is threatened by a worldwide decline of pollinators. Key factors in this situation include the spread and interspecific transmission of pathogens worldwide through the movement of managed pollinators. Research on this field has been mainly conducted in some particular species, while studies assessing the interspecific transmission of pathogens at a community level are scarce. However, this information is pivotal to design strategies to protect pollinators. Herein, we analysed the prevalence of two common microsporidia pathogens of managed honey bees (Nosema ceranae and N. apis) in bee communities of semiarid Mediterranean areas from the Southeast of the Iberian Peninsula. Our results confirm the ability of N. ceranae to disperse across wild bee communities in semiarid Mediterranean ecosystems since it was detected in 36 Apoidea species (39% of the sampling; for the first time in nine genera). The prevalence of the pathogen did not show any phylogenetic signal which suggests a superfamily host range of the pathogen or that wild bees may be acting only as vectors of N. ceranae. In addition, N. apis was detected in an Eucera species, which is the second time it has been detected by molecular techniques in a host other than the honey bee. Our study represents the primary assessment of the prevalence of microsporidia at community level in Mediterranean areas and provides outstanding results on the ability of Nosema pathogens to spread across the landscape.}, }
@article {pmid34585290, year = {2022}, author = {Kaushal, M and Kolombia, Y and Alakonya, AE and Kuate, AF and Ortega-Beltran, A and Amah, D and Masso, C}, title = {Subterranean Microbiome Affiliations of Plantain (Musa spp.) Under Diverse Agroecologies of Western and Central Africa.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {580-593}, pmid = {34585290}, issn = {1432-184X}, support = {HRST/ST/AURG-II/CALL2/2018//African Union/ ; }, mesh = {Africa, Central ; *Ascomycota/genetics ; Bacteria/genetics ; *Microbiota/physiology ; *Musa/microbiology ; Plant Roots/microbiology ; *Plantago ; Rhizosphere ; Soil Microbiology ; }, abstract = {Plantain (Musa spp.) is a staple food crop and an important source of income for millions of smallholder farmers in sub-Saharan Africa (SSA). However, there is a paucity of knowledge on soil microbial diversity in agroecologies where plantains are grown. Microbial diversity that increases plant performance with multi-trophic interactions involving resiliency to environmental constraints is greatly needed. For this purpose, the bacterial and fungal communities of plantain fields in high rainfall forests (HR) and derived savannas (SV) were studied using Illumina MiSeq for 16S rDNA and ITS amplicon deep sequencing. Microbial richness (α- and β-diversity), operational taxonomic units, and Simpson and Shannon-Wiener indexes (observed species (Sobs), Chao, ACE; P < 0.05) suggested that there were significant differences between HR and SV agroecologies among the most abundant bacterial communities, and some specific dynamic response observed from fungal communities. Proteobacteria formed the predominant bacterial phylum (43.7%) succeeded by Firmicutes (24.7%), and Bacteroidetes (17.6%). Ascomycota, Basidiomycota, and Zygomycota were the three most dominant fungal phyla in both agroecologies. The results also revealed an immense array of beneficial microbes in the roots and rhizosphere of plantain, including Acinetobacter, Bacillus, and Pseudomonas spp. COG and KEGG Orthology database depicted significant variations in the functional attributes of microbes found in the rhizosphere to roots. This result indicates that the different agroecologies and host habitats differentially support the dynamic microbial profile and that helps in altering the structure in the rhizosphere zone for the sake of promoting synergistic host-microbe interactions particularly under resource-poor conditions of SSA.}, }
@article {pmid34585289, year = {2022}, author = {Cao, X and Zhao, D and Li, C and Röttjers, L and Faust, K and Zhang, H}, title = {Regime transition Shapes the Composition, Assembly Processes, and Co-occurrence Pattern of Bacterioplankton Community in a Large Eutrophic Freshwater Lake.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {336-350}, pmid = {34585289}, issn = {1432-184X}, support = {41871096//National Natural Science Foundation of China/ ; 32171563//National Natural Science Foundation of China/ ; BK20181311//Natural Science Foundation of Jiangsu Province/ ; 2018B43414//Fundamental Research Funds for the Central Universities/ ; B200203051//Fundamental Research Funds for the Central Universities/ ; 201906710009//China Scholarship Council/ ; }, mesh = {Aquatic Organisms ; *Biodiversity ; China ; Ecosystem ; *Lakes/chemistry ; Phylogeny ; Phytoplankton/genetics ; Plankton/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {At certain nutrient concentrations, shallow freshwater lakes are generally characterized by two contrasting ecological regimes with disparate patterns of biodiversity and biogeochemical cycles: a macrophyte-dominated regime (MDR) and a phytoplankton-dominated regime (PDR). To reveal ecological mechanisms that affect bacterioplankton along the regime shift, Illumina MiSeq sequencing of the 16S rRNA gene combined with a novel network clustering tool (Manta) were used to identify patterns of bacterioplankton community composition across the regime shift in Taihu Lake, China. Marked divergence in the composition and ecological assembly processes of bacterioplankton community was observed under the regime shift. The alpha diversity of the bacterioplankton community consistently and continuously decreased with the regime shift from MDR to PDR, while the beta diversity presents differently. Moreover, as the regime shifted from MDR to PDR, the contribution of deterministic processes (such as environmental selection) to the assembly of bacterioplankton community initially decreased and then increased again as regime shift from MDR to PDR, most likely as a consequence of differences in nutrient concentration. The topological properties, including modularity, transitivity and network diameter, of the bacterioplankton co-occurrence networks changed along the regime shift, and the co-occurrences among species changed in structure and were significantly shaped by the environmental variables along the regime transition from MDR to PDR. The divergent environmental state of the regimes with diverse nutritional status may be the most important factor that contributes to the dissimilarity of bacterioplankton community composition along the regime shift.}, }
@article {pmid34584531, year = {2021}, author = {Ge, W and Zhang, ZY and Dong, CB and Han, YF and Deshmukh, SK and Liang, ZQ}, title = {Bacterial Community Analysis and Potential Functions of Core Taxa in Different Parts of the Fungus Cantharellus cibarius.}, journal = {Polish journal of microbiology}, volume = {70}, number = {3}, pages = {373-385}, pmid = {34584531}, issn = {2544-4646}, mesh = {Bacteria/genetics ; *Bacterial Physiological Phenomena ; *Basidiomycota ; *Biodiversity ; *Microbial Interactions/physiology ; RNA, Ribosomal, 16S ; }, abstract = {Cantharellus cibarius is a widely distributed, popular, edible fungus with high nutritional and economic value. However, significant challenges persist in the microbial ecology and artificial cultivation of C. cibarius. Based on the 16S rRNA sequencing data, this study analyzed bacterial community structures and diversity of fruit bodies and rhizomorph parts of C. cibarius and mycosphere samples (collected in the Wudang District, Guiyang, Guizhou Province, China). It explored the composition and function of the core bacterial taxa. The analyzed results showed that the rhizomorph bacterial community structure was similar to mycosphere, but differed from the fruit bodies. Members of the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium complex had the highest abundance in the fruit bodies. However, they were either absent or low in abundance in the rhizomorphs and mycosphere. At the same time, members of the Burkholderia-Caballeronia-Paraburkholderia complex were abundant in the fruit bodies and rhizomorphs parts of C. cibarius, as well as mycosphere. Through functional annotation of core bacterial taxa, we found that there was an apparent trend of potential functional differentiation of related bacterial communities in the fruit body and rhizomorph: potential functional groups of core bacterial taxa in the fruit bodies centered on nitrogen fixation, nitrogen metabolism, and degradation of aromatic compounds, while those in rhizomorphs focused on aerobic chemoheterotrophy, chemoheterotrophy, defense against soil pathogens, decomposition of complex organic compounds, and uptake of insoluble inorganic compounds. The analysis of functional groups of bacteria with different structures is of great significance to understand that bacteria promote the growth and development of C. cibarius.}, }
@article {pmid34581470, year = {2021}, author = {Wu, MR and Hou, TT and Liu, Y and Miao, LL and Ai, GM and Ma, L and Zhu, HZ and Zhu, YX and Gao, XY and Herbold, CW and Wagner, M and Li, DF and Liu, ZP and Liu, SJ}, title = {Novel Alcaligenes ammonioxydans sp. nov. from wastewater treatment sludge oxidizes ammonia to N2 with a previously unknown pathway.}, journal = {Environmental microbiology}, volume = {23}, number = {11}, pages = {6965-6980}, doi = {10.1111/1462-2920.15751}, pmid = {34581470}, issn = {1462-2920}, mesh = {Aerobiosis ; Alcaligenes/genetics/metabolism ; *Ammonia/metabolism ; Denitrification ; Escherichia coli/metabolism ; Nitrification ; Nitrites/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Sewage ; *Water Purification/methods ; }, abstract = {Heterotrophic nitrifiers are able to oxidize and remove ammonia from nitrogen-rich wastewaters but the genetic elements of heterotrophic ammonia oxidation are poorly understood. Here, we isolated and identified a novel heterotrophic nitrifier, Alcaligenes ammonioxydans sp. nov. strain HO-1, oxidizing ammonia to hydroxylamine and ending in the production of N2 gas. Genome analysis revealed that strain HO-1 encoded a complete denitrification pathway but lacks any genes coding for homologous to known ammonia monooxygenases or hydroxylamine oxidoreductases. Our results demonstrated strain HO-1 denitrified nitrite (not nitrate) to N2 and N2 O at anaerobic and aerobic conditions respectively. Further experiments demonstrated that inhibition of aerobic denitrification did not stop ammonia oxidation and N2 production. A gene cluster (dnfT1RT2ABCD) was cloned from strain HO-1 and enabled E. coli accumulated hydroxylamine. Sub-cloning showed that genetic cluster dnfAB or dnfABC already enabled E. coli cells to produce hydroxylamine and further to [15] N2 from ([15] NH4)2 SO4 . Transcriptome analysis revealed these three genes dnfA, dnfB and dnfC were significantly upregulated in response to ammonia stimulation. Taken together, we concluded that strain HO-1 has a novel dnf genetic cluster for ammonia oxidation and this dnf genetic cluster encoded a previously unknown pathway of direct ammonia oxidation (Dirammox) to N2 .}, }
@article {pmid34581434, year = {2022}, author = {Zayed, N and Boon, N and Bernaerts, K and Chatzigiannidou, I and Van Holm, W and Verspecht, T and Teughels, W}, title = {Differences in chlorhexidine mouthrinses formulations influence the quantitative and qualitative changes in in-vitro oral biofilms.}, journal = {Journal of periodontal research}, volume = {57}, number = {1}, pages = {52-62}, doi = {10.1111/jre.12937}, pmid = {34581434}, issn = {1600-0765}, support = {//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {*Anti-Infective Agents ; *Anti-Infective Agents, Local/pharmacology ; Biofilms ; Cetylpyridinium/pharmacology ; Chlorhexidine/pharmacology ; Mouthwashes/pharmacology ; }, abstract = {OBJECTIVE: Chlorhexidine mouthrinses are marketed in different formulations. This study aimed at investigating qualitative and quantitative changes in in-vitro multispecies oral biofilms, induced by different chlorhexidine-containing mouthrinses.<br><br>BACKGROUND DATA: Earlier studies comparing chlorhexidine mouthrinses are either clinical studies or in-vitro studies assessing the antimicrobial efficacy of the mouthrinses. However, no clear investigations are available regarding ecological impact of different chlorhexidine formulations on in-vitro multispecies oral biofilms after rinsing with different chlorhexidine formulations.<br><br>METHODS: Nine commercially available chlorhexidine mouthrinses were selected. Multispecies oral communities (14&#xa0;species) were grown for 48&#xa0;h in a Biostat-B Twin bioreactor. After that, they were used to develop biofilms on the surface of hydroxyapatite disks in 24-well pates for 48&#xa0;h. Biofilms were then rinsed once or multiple times with the corresponding mouthrinse. Biofilms were collected before starting the rinsing experiment and every 24&#xa0;h for 3&#xa0;days and vitality quantitative PCR was performed. The experiment was repeated 3 independent times on 3 different days and the results were analyzed using a linear mixed model.<br><br>RESULTS: The mouthrinses provoked different effects in terms of change in total viable bacterial load (VBL), ecology, and community structure of the multispecies biofilms. There was no relation between chlorhexidine concentrations, presence, or absence of cetylpyridinium chloride and/or alcohol, and the observed effects. Some tested chlorhexidine mouthrinses (MC, HG, HH, and HI) strongly lowered the total VBL (&#x2248;10[07] Geq/ml), but disrupted biofilm symbiosis (&#x2265;40% of the biofilms communities are pathobionts). On the other hand, other tested chlorhexidine mouthrinses (MD, ME, and HF) had limited impact on total VBL (&#x2265;10[10] Geq/ml), but improved the biofilm ecology and community structure (&#x2264;10% of the biofilms communities are pathobionts).<br><br>CONCLUSION: Not all chlorhexidine mouthrinses have the same effect on oral biofilms. Their effect seems to be strongly product dependent and vary according to their compositions and formulations.}, }
@article {pmid34581127, year = {2021}, author = {Yang, SH and Qin, ZS and Liang, MC}, title = {[Meta-analysis of Microbial Communities in the Activated Sludge of Wastewater Treatment Plants Under Different Climate Types].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {42}, number = {10}, pages = {4844-4852}, doi = {10.13227/j.hjkx.202101193}, pmid = {34581127}, issn = {0250-3301}, mesh = {China ; *Microbiota ; RNA, Ribosomal, 16S ; Sewage ; Wastewater ; *Water Purification ; }, abstract = {Microbial communities in wastewater treatment plants(WWTPs) are very important for water purification in the context of public drinking water safety and environmental health. Therefore, it is necessary to explore the trends in microbial community structure and diversity in sewage treatment plants and their main environmental impact factors under different climates in China. Based on high-throughput sequencing techniques, a meta-analysis was conducted to screen the 16S rRNA genes in an open database. We analyzed the trends in microbial community structure and diversity in WWTPs under three climate types(Dwa, Cfa, and Cwa) in China. We then constructed cohesion models to examine the core microbial taxa and their interactions within the communities. We also used a piecewise structural equation model(PSEM) to examine the effects of different climate types on microbial community structure. The three climate types significantly affected the structure and diversity of the microbial communities, with patterns correlated with influent pH, mixed liquid temperature, conductivity, and nitrogen concentrations(P<0.05). Based on the PSEM analysis, the β-diversity of the microbial communities was directly correlated with latitude, while α-diversity was indirectly correlated with latitude through conductivity and water temperature. Based on the cohesion modeling, microbial community stability was the highest under Dwa climate followed by the Cfa climate. This could be explained by a small subset of highly connected taxa capable of withstanding disturbance, indicating an important stability role. In contrast, the stability of the microbial communities under the Cwa climate was low, and no species with strong negative cohesion were observed. Overall, the structure, diversity, and stability of microbial community in WWTPs were found to be sensitive to climate, and the responsive mechanisms of α-diversity and β-diversity with respect to latitude were distinct.}, }
@article {pmid34580739, year = {2022}, author = {Garcia-Vozmediano, A and Tomassone, L and Fonville, M and Bertolotti, L and Heylen, D and Fabri, ND and Medlock, JM and Nijhof, AM and Hansford, KM and Sprong, H and Krawczyk, AI}, title = {The Genetic Diversity of Rickettsiella Symbionts in Ixodes ricinus Throughout Europe.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {613-626}, pmid = {34580739}, issn = {1432-184X}, support = {01KI1720//Federal Ministry of Education and Research (BMBF)/ ; 799609//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; }, mesh = {Animals ; *Coxiellaceae ; Europe ; Genetic Variation ; *Ixodes/microbiology ; Phylogeny ; }, abstract = {Rickettsiella species are bacterial symbionts that are present in a great variety of arthropod species, including ixodid ticks. However, little is known about their genetic diversity and distribution in Ixodes ricinus, as well as their relationship with other tick-associated bacteria. In this study, we investigated the occurrence and the genetic diversity of Rickettsiella spp. in I. ricinus throughout Europe and evaluated any preferential and antagonistic associations with Candidatus Midichloria mitochondrii and the pathogens Borrelia burgdorferi sensu lato and Borrelia miyamotoi. Rickettsiella spp. were detected in most I. ricinus populations investigated, encompassing a wide array of climate types and environments. The infection prevalence significantly differed between geographic locations and was significantly higher in adults than in immature life stages. Phylogenetic investigations and protein characterization disclosed four Rickettsiella clades (I-IV). Close phylogenetic relations were observed between Rickettsiella strains of I. ricinus and other arthropod species. Isolation patterns were detected for Clades II and IV, which were restricted to specific geographic areas. Lastly, although coinfections occurred, we did not detect significant associations between Rickettsiella spp. and the other tick-associated bacteria investigated. Our results suggest that Rickettsiella spp. are a genetically and biologically diverse facultative symbiont of I. ricinus and that their distribution among tick populations could be influenced by environmental components.}, }
@article {pmid34579579, year = {2021}, author = {Frederickson, ME and Reese, AT}, title = {Microbial Ecology and Evolution Are Essential for Understanding Pandemics.}, journal = {mBio}, volume = {12}, number = {5}, pages = {e0214421}, pmid = {34579579}, issn = {2150-7511}, support = {RGPIN-2021-03711//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; //Harvard University | Radcliffe Institute for Advanced Study, Harvard University (Radcliffe Institute for Advanced Study)/ ; GBMF9356//Gordon and Betty Moore Foundation | Symbiosis in Aquatic Systems Initiative/ ; }, mesh = {*Biological Evolution ; COVID-19/*epidemiology ; *Ecology ; Humans ; Microbiota/*physiology ; Pandemics ; }, abstract = {Ecology and evolution, especially of microbes, have never been more relevant than in our global fight against SARS-CoV-2, the virus that causes COVID-19. Understanding how populations of SARS-CoV-2 grow, disperse, and evolve is of critical importance to managing the COVID-19 pandemic, and these questions are fundamentally ecological and evolutionary in nature. We compiled data from bioRxiv and medRxiv preprint abstracts and US National Institutes of Health Research Project grant abstracts to visualize the impact that the pivot to COVID-19 research has had on the study of microbes across biological disciplines. Finding that the pivot appears weaker in ecology and evolutionary biology than in other areas of biology, we discuss why the ecology and evolution of microbes, both pathogenic and otherwise, need renewed attention and investment going forward.}, }
@article {pmid34579574, year = {2021}, author = {Bosch, TCG and Zasloff, M}, title = {Antimicrobial Peptides-or How Our Ancestors Learned to Control the Microbiome.}, journal = {mBio}, volume = {12}, number = {5}, pages = {e0184721}, pmid = {34579574}, issn = {2150-7511}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Anti-Infective Agents/pharmacology ; Antimicrobial Cationic Peptides/immunology ; Antimicrobial Peptides/*pharmacology ; Bacteria/drug effects ; Drosophila ; Fungi ; Gastrointestinal Microbiome/*drug effects ; Humans ; Hydra ; Immunity, Innate ; Muramidase ; Plant Immunity ; Symbiosis ; Viruses ; }, abstract = {Antimicrobial peptides (AMPs) are short and generally positively charged peptides found in a wide variety of life forms from microorganisms to humans. Their wide range of activity against pathogens, including Gram-positive and -negative bacteria, yeasts, fungi, and enveloped viruses makes them a fundamental component of innate immunity. Marra et al. (A. Marra, M. A. Hanson, S. Kondo, B. Erkosar, B. Lemaitre, mBio 12:e0082421, 2021, https://doi.org/10.1128/mBio.00824-21) use the analytical potential of Drosophila to show that AMPs and lysozymes play a direct role in controlling the composition and abundance of the beneficial gut microbiome. By comparing mutant and wild-type flies, they demonstrated that the specific loss of AMPs and lysozyme production results in changes in microbiome abundance and composition. Furthermore, they established that AMPs and lysozyme are particularly essential in aging flies. Studies of early emerging metazoans, other invertebrates, and humans support the view of an ancestral function of AMPs in controlling microbial colonization.}, }
@article {pmid34579474, year = {2021}, author = {Smulders, L and Benítez, E and Moreno, B and López-García, &#xc1; and Pozo, MJ and Ferrero, V and de la Peña, E and Alcalá Herrera, R}, title = {Tomato Domestication Affects Potential Functional Molecular Pathways of Root-Associated Soil Bacteria.}, journal = {Plants (Basel, Switzerland)}, volume = {10}, number = {9}, pages = {}, pmid = {34579474}, issn = {2223-7747}, support = {765290//Horizon 2020 Framework Programme/ ; }, abstract = {While it has been well evidenced that plant domestication affects the structure of the root-associated microbiome, there is a poor understanding of how domestication-mediated differences between rhizosphere microorganisms functionally affect microbial ecosystem services. In this study, we explore how domestication influenced functional assembly patterns of bacterial communities in the root-associated soil of 27 tomato accessions through a transect of evolution, from plant ancestors to landraces to modern cultivars. Based on molecular analysis, functional profiles were predicted and co-occurrence networks were constructed based on the identification of co-presences of functional units in the tomato root-associated microbiome. The results revealed differences in eight metabolic pathway categories and highlighted the influence of the host genotype on the potential functions of soil bacterial communities. In general, wild tomatoes differed from modern cultivars and tomato landraces which showed similar values, although all ancestral functional characteristics have been conserved across time. We also found that certain functional groups tended to be more evolutionarily conserved in bacterial communities associated with tomato landraces than those of modern varieties. We hypothesize that the capacity of soil bacteria to provide ecosystem services is affected by agronomic practices linked to the domestication process, particularly those related to the preservation of soil organic matter.}, }
@article {pmid34579172, year = {2021}, author = {Ruebel, ML and Gilley, SP and Sims, CR and Zhong, Y and Turner, D and Chintapalli, SV and Piccolo, BD and Andres, A and Shankar, K}, title = {Associations between Maternal Diet, Body Composition and Gut Microbial Ecology in Pregnancy.}, journal = {Nutrients}, volume = {13}, number = {9}, pages = {}, pmid = {34579172}, issn = {2072-6643}, support = {T32 DK007658/DK/NIDDK NIH HHS/United States ; P30 DK048520/DK/NIDDK NIH HHS/United States ; CRIS 6251-51000-005-00D//U.S. Department of Agriculture/ ; DK007658-30/DK/NIDDK NIH HHS/United States ; R01 DK107516/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; *Body Composition/physiology ; Body Weight ; *Diet ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics/physiology ; Gestational Weight Gain/physiology ; Humans ; *Maternal Nutritional Physiological Phenomena ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Maternal body composition, gestational weight gain (GWG) and diet quality influence offspring obesity risk. While the gut microbiome is thought to play a crucial role, it is understudied in pregnancy. Using a longitudinal pregnancy cohort, maternal anthropometrics, body composition, fecal microbiome and dietary intake were assessed at 12, 24 and 36 weeks of gestation. Fecal samples (n = 101, 98 and 107, at each trimester, respectively) were utilized for microbiome analysis via 16S rRNA amplicon sequencing. Data analysis included alpha- and beta-diversity measures and assessment of compositional changes using MaAsLin2. Correlation analyses of serum metabolic and anthropometric markers were performed against bacterial abundance and predicted functional pathways. α-diversity was unaltered by pregnancy stage or maternal obesity status. Actinobacteria, Lachnospiraceae, Akkermansia, Bifidobacterium, Streptococcus and Anaerotuncus abundances were associated with gestation stage. Maternal obesity status was associated with increased abundance of Lachnospiraceae, Bilophila, Dialister and Roseburia. Maternal BMI, fat mass, triglyceride and insulin levels were positively associated with Bilophila. Correlations of bacterial abundance with diet intake showed that Ruminococcus and Paraprevotella were associated with total fat and unsaturated fatty acid intake, while Collinsella and Anaerostipes were associated with protein intake. While causal relationships remain unclear, collectively, these findings indicate pregnancy- and maternal obesity-dependent interactions between dietary factors and the maternal gut microbiome.}, }
@article {pmid34579126, year = {2021}, author = {Calatayud, M and Verstrepen, L and Ghyselinck, J and Van den Abbeele, P and Marzorati, M and Modica, S and Ranjanoro, T and Maquet, V}, title = {Chitin Glucan Shifts Luminal and Mucosal Microbial Communities, Improve Epithelial Barrier and Modulates Cytokine Production In Vitro.}, journal = {Nutrients}, volume = {13}, number = {9}, pages = {}, pmid = {34579126}, issn = {2072-6643}, support = {ADIPOSTOP project, convention 7366//Gouvernement Wallon/ ; }, mesh = {Bifidobacterium breve/physiology ; Caco-2 Cells ; Chitin/*pharmacology ; Coculture Techniques ; Cytokines/*biosynthesis ; Enterocytes ; Fatty Acids, Volatile/biosynthesis ; Feces/microbiology ; Fermentation ; Gastrointestinal Microbiome/*drug effects/physiology ; Glucans/*pharmacology ; Humans ; Intestinal Mucosa/*drug effects/physiology ; Prebiotics/*administration &amp; dosage ; Probiotics/administration &amp; dosage ; THP-1 Cells ; }, abstract = {The human gut microbiota has been linked to the health status of the host. Modulation of human gut microbiota through pro- and prebiotic interventions has yielded promising results; however, the effect of novel prebiotics, such as chitin-glucan, on gut microbiota-host interplay is still not fully characterized. We assessed the effect of chitin-glucan (CG) and chitin-glucan plus Bifidobacterium breve (CGB) on human gut microbiota from the luminal and mucosal environments in vitro. Further, we tested the effect of filter-sterilized fecal supernatants from CG and CGB fermentation for protective effects on inflammation-induced barrier disruption and cytokine production using a co-culture of enterocytes and macrophage-like cells. Overall, CG and CGB promote health-beneficial short-chain fatty acid production and shift human gut microbiota composition, with a consistent effect increasing Roseburia spp. and butyrate producing-bacteria. In two of three donors, CG and CGB also stimulated Faecalibacterium prausniitzi. Specific colonization of B. breve was observed in the lumen and mucosal compartment; however, no synergy was detected for different endpoints when comparing CGB and CG. Both treatments included a significant improvement of inflammation-disrupted epithelial barrier and shifts on cytokine production, especially by consistent increase in the immunomodulatory cytokines IL10 and IL6.}, }
@article {pmid34579065, year = {2021}, author = {Sauvaitre, T and Durif, C and Sivignon, A and Chalancon, S and Van de Wiele, T and Etienne-Mesmin, L and Blanquet-Diot, S}, title = {In Vitro Evaluation of Dietary Fiber Anti-Infectious Properties against Food-Borne Enterotoxigenic Escherichia coli.}, journal = {Nutrients}, volume = {13}, number = {9}, pages = {}, pmid = {34579065}, issn = {2072-6643}, support = {I-SITE Cap2025 WOW//Universit&#xe9; Clermont-Auvergne/ ; European Funding for Regional Developments (FEDER) from the French Region Auvergne Rh&#xf4;ne-Alpes (Pack Ambition Recherche Dysfibre)//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; }, mesh = {Cell Adhesion ; Diarrhea/*microbiology/prevention &amp; control ; Dietary Fiber/*pharmacology/therapeutic use ; Enterotoxigenic Escherichia coli/*drug effects/growth &amp; development/metabolism/pathogenicity ; Enterotoxins/metabolism ; Escherichia coli Infections/*microbiology/prevention &amp; control ; Escherichia coli Proteins/metabolism ; Foodborne Diseases/*microbiology/prevention &amp; control ; Humans ; Intestines/cytology/microbiology ; Lens Plant/chemistry ; Microbial Sensitivity Tests ; Mucins ; Mucus ; Seeds/chemistry ; Travel ; *Virulence Factors ; Yeasts/chemistry ; }, abstract = {Dietary fibers have well-known beneficial effects on human health, but their anti-infectious properties against human enteric pathogens have been poorly investigated. Enterotoxigenic Escherichia coli (ETEC) is the main agent of travelers' diarrhea, against which targeted preventive strategies are currently lacking. ETEC pathogenesis relies on multiple virulence factors allowing interactions with the intestinal mucosal layer and toxins triggering the onset of diarrheal symptoms. Here, we used complementary in vitro assays to study the antagonistic properties of eight fiber-containing products from cereals, legumes or microbes against the prototypical human ETEC strain H10407. Inhibitory effects of these products on the pathogen were tested through growth, toxin production and mucus/cell adhesion inhibition assays. None of the tested compounds inhibited ETEC strain H10407 growth, while lentil extract was able to decrease heat labile toxin (LT) concentration in culture media. Lentil extract and specific yeast cell walls also interfered with ETEC strain H10407 adhesion to mucin beads and human intestinal cells. These results constitute a first step in the use of dietary fibers as a nutritional strategy to prevent ETEC infection. Further work will be dedicated to the study of fiber/ETEC interactions within a complex gut microbial background.}, }
@article {pmid34578249, year = {2021}, author = {Zhang, D and Verstrepen, L and De Medts, J and Duysburgh, C and Van den Abbeele, P and Marzorati, M and Khoo, C}, title = {A Cranberry Concentrate Decreases Adhesion and Invasion of Escherichia coli (AIEC) LF82 In Vitro.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {9}, pages = {}, pmid = {34578249}, issn = {2076-0817}, abstract = {While many beneficial host-microbiota interactions have been described, imbalanced microbiota in the gut is speculated to contribute to the progression and recurrence of chronic inflammatory diseases such as Crohn's disease (CD). This in vitro study evaluated the impact of a cranberry concentrate Type M (CTM) on adherent-invasive Escherichia coli (AIEC) LF82, a pathobiont associated with CD. Different stages of pathogenic infection were investigated: (i) colonization of the mucus layer, and (ii) adhesion to and (iii) invasion of the epithelial cells. Following 48 h of fecal batch incubation, 0.5 and 1 mM of CTM significantly altered AIEC LF82 levels in a simulated mucus layer, resulting in a decrease of 50.5% in the untreated blank, down to 43.0% and 11.4%, respectively. At 1 mM of CTM, the significant decrease in the levels of AIEC LF82 coincided with a stimulation of the metabolic activity of the background microbiota. The increased levels of health-associated acetate (+7.9 mM) and propionate levels (+3.5 mM) suggested selective utilization of CTM by host microorganisms. Furthermore, 1 mM of both fermented and unfermented CTM decreased the adhesion and invasion of human-derived epithelial Caco-2 cells by AIEC LF82. Altogether, this exploratory in vitro study demonstrates the prebiotic potential of CTM and supports its antipathogenic effects through direct and/or indirect modulation of the gut microbiome.}, }
@article {pmid34576876, year = {2021}, author = {Foltz, M and Zahradnik, AC and Van den Abbeele, P and Ghyselinck, J and Marzorati, M}, title = {A Pectin-Rich, Baobab Fruit Pulp Powder Exerts Prebiotic Potential on the Human Gut Microbiome In Vitro.}, journal = {Microorganisms}, volume = {9}, number = {9}, pages = {}, pmid = {34576876}, issn = {2076-2607}, abstract = {Increasing insight into the impact of the gut microbiota on human health has sustained the development of novel prebiotic ingredients. This exploratory study evaluated the prebiotic potential of baobab fruit pulp powder, which consists of pectic polysaccharides with unique composition as compared to other dietary sources, given that it is rich in low methoxylated homogalacturonan (HG). After applying dialysis procedures to remove simple sugars from the product (simulating their absorption along the upper gastrointestinal tract), 48 h fecal batch incubations were performed. Baobab fruit pulp powder boosted colonic acidification across three simulated human adult donors due to the significant stimulation of health-related metabolites acetate (+18.4 mM at 48 h), propionate (+5.5 mM at 48 h), and to a lesser extent butyrate (0.9 mM at 48 h). Further, there was a trend of increased lactate levels (+2.7 mM at 6h) and reduced branched chain fatty acid (bCFA) levels (-0.4 mM at 48 h). While Bacteroidetes levels increased for all donors, donor-dependent increases in Bifidobacteria, Lactobacilli, and Firmicutes were observed, stressing the potential interindividual differences in microbial composition modulation upon Baobab fruit pulp powder treatment. Overall, Baobab fruit pulp powder fermentation displayed features of selective utilization by host microorganisms and, thus, has promising prebiotic potential (also in comparison with the 'gold standard' prebiotic inulin). Further research will be required to better characterize this prebiotic potential, accounting for the interindividual differences, while aiming to unravel the potential resulting health benefits.}, }
@article {pmid34576827, year = {2021}, author = {Lavoie, C and Wellband, K and Perreault, A and Bernatchez, L and Derome, N}, title = {Artificial Rearing of Atlantic Salmon Juveniles for Supportive Breeding Programs Induces Long-Term Effects on Gut Microbiota after Stocking.}, journal = {Microorganisms}, volume = {9}, number = {9}, pages = {}, pmid = {34576827}, issn = {2076-2607}, support = {RDCPJ 500982-16//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {In supportive breeding programs for wild salmon populations, stocked parr experience higher mortality rates than wild ones. Among other aspects of phenotype, the gut microbiota of artificially raised parr differs from that of wild parr before stocking. Early steps of microbiota ontogeny are tightly dependent upon environmental conditions, both of which exert long-term effects on host physiology. Therefore, our objective was to assess to what extent the resilience capacity of the microbiota of stocked salmon may prevent taxonomic convergence with that of their wild congeners after two months in the same natural environment. Using the 16S SSU rRNA marker gene, we tested the general hypothesis that environmental conditions during the very first steps of microbiota ontogeny imprint a permanent effect on later stages of microbiota recruitment. Our results first showed that gut microbiota composition of stocked and wild parr from the same genetic population, and sharing the same environment, was dependent on the early rearing environment. In contrast, skin microbiota in stocked individuals converged to that of wild individuals. Taxonomic composition and co-occurrence network analyses suggest an impairment of wild bacteria recruitment and a higher instability for the gut microbiota of stocked parr. This study is the first to demonstrate the long-term effect of early microbiota ontogeny in artificial rearing for natural population conservation programs, raising the need to implement microbial ecology.}, }
@article {pmid34576737, year = {2021}, author = {Gnangui, SLE and Fossou, RK and Ebou, A and Amon, CER and Koua, DK and Kouadjo, CGZ and Cowan, DA and Zézé, A}, title = {The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d'Ivoire.}, journal = {Microorganisms}, volume = {9}, number = {9}, pages = {}, pmid = {34576737}, issn = {2076-2607}, support = {674-AA-2010-A1//United States Agency for International Development/ ; }, abstract = {Over the past decade, many projects have been initiated worldwide to decipher the composition and function of the soil microbiome, including the African Soil Microbiome (AfSM) project that aims at providing new insights into the presence and distribution of key groups of soil bacteria from across the African continent. In this national study, carried out under the auspices of the AfSM project, we assessed the taxonomy, diversity and distribution of rhizobial genera in soils from the tropical savannah zones in Northern Côte d'Ivoire. Genomic DNA extracted from seven sampled soils was analyzed by sequencing the V4-V5 variable region of the 16S rDNA using Illumina's MiSeq platform. Subsequent bioinformatic and phylogenetic analyses showed that these soils harbored 12 out of 18 genera of Proteobacteria harboring rhizobia species validly published to date and revealed for the first time that the Bradyrhizobium genus dominates in tropical savannah soils, together with Microvirga and Paraburkholderia. In silico comparisons of different 16S rRNA gene variable regions suggested that the V5-V7 region could be suitable for differentiating rhizobia at the genus level, possibly replacing the use of the V4-V5 region. These data could serve as indicators for future rhizobial microbiome explorations and for land-use decision-making.}, }
@article {pmid34572682, year = {2021}, author = {Gresse, R and Garrido, JJ and Jiménez-Marín, A and Denis, S and Van de Wiele, T and Forano, E and Blanquet-Diot, S and Chaucheyras-Durand, F}, title = {Saccharomyces Cerevisiae Var Boulardii CNCM I-1079 Reduces Expression of Genes Involved in Inflammatory Response in Porcine Cells Challenged by Enterotoxigenic E. Coli and Influences Bacterial Communities in an In Vitro Model of the Weaning Piglet Colon.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {9}, pages = {}, pmid = {34572682}, issn = {2079-6382}, abstract = {Enterotoxigenic Escherichia coli (ETEC) is the main infectious agent responsible for piglet post-weaning diarrhea with high mortality rates. Antimicrobials represent the current principal strategy for treating ETEC infections in pig farms, but the occurrence of multi-resistant bacterial strains has considerably increased in the last decades. Thus, finding non-antibiotic alternatives becomes a real emergency. In this context, we investigated the effect of a live yeast strain, Saccharomyces cerevisiae var boulardii CNCM I-1079 (SB) in an in vitro model of the weaning piglet colon implemented with a mucus phase (MPigut-IVM) inoculated with ETEC and coupled with an intestinal porcine cell line IPI-2I. We showed that SB was able to modulate the in vitro microbiota through an increase in Bacteroidiaceae and a decrease in Prevotellaceae families. Effluents collected from the SB treated bioreactors were able to mitigate the expression level of genes encoding non-gel forming mucins, tight junction proteins, innate immune pathway, and pro-inflammatory response in IPI-2I cells. Furthermore, SB exerted a significant protective effect against ETEC adhesion on porcine IPEC-J2 intestinal cells in a dose-dependent manner and showed a positive effect on ETEC-challenged IPEC-J2 by lowering expression of genes involved in pro-inflammatory immune responses. Our results showed that the strain SB CNCM I-1079 could prevent microbiota dysbiosis associated with weaning and protect porcine enterocytes from ETEC infections by reducing bacterial adhesion and modulating the inflammatory response.}, }
@article {pmid34570249, year = {2021}, author = {Pérez, J and Ferreira, V and Graça, MAS and Boyero, L}, title = {Litter Quality Is a Stronger Driver than Temperature of Early Microbial Decomposition in Oligotrophic Streams: a Microcosm Study.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {897-908}, pmid = {34570249}, issn = {1432-184X}, support = {UIDP/04292/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; IF/00129/2014, CEECIND/02484/2018//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {*Ecosystem ; Fungi ; Plant Leaves ; *Rivers ; Temperature ; }, abstract = {Litter decomposition is an ecological process of key importance for forest headwater stream functioning, with repercussions for the global carbon cycle. The process is directly and indirectly mediated by microbial decomposers, mostly aquatic hyphomycetes, and influenced by environmental and biological factors such as water temperature and litter quality. These two factors are forecasted to change globally within the next few decades, in ways that may have contrasting effects on microbial-induced litter decomposition: while warming is expected to enhance microbial performance, the reduction in litter quality due to increased atmospheric carbon dioxide and community composition alteration may have the opposite outcome. We explored this issue through a microcosm experiment focused on early microbial-mediated litter decomposition under stream oligotrophic conditions, by simultaneously manipulating water temperature (10 °C and 15 °C) and litter quality (12 broadleaf plant species classified into 4 categories based on initial concentrations of nitrogen and tannins). We assessed potential changes in microbial-mediated litter decomposition and the performance of fungal decomposers (i.e., microbial respiration, biomass accrual, and sporulation rate) and species richness. We found stronger effects of litter quality, which enhanced the performance of microbial decomposers and decomposition rates, than temperature, which barely influenced any of the studied variables. Our results suggest that poorer litter quality associated with global change will have a major repercussion on stream ecosystem functioning.}, }
@article {pmid34567033, year = {2021}, author = {Hale, I and Ma, X and Melo, ATO and Padi, FK and Hendre, PS and Kingan, SB and Sullivan, ST and Chen, S and Boffa, JM and Muchugi, A and Danquah, A and Barnor, MT and Jamnadass, R and Van de Peer, Y and Van Deynze, A}, title = {Genomic Resources to Guide Improvement of the Shea Tree.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {720670}, pmid = {34567033}, issn = {1664-462X}, abstract = {A defining component of agroforestry parklands across Sahelo-Sudanian Africa (SSA), the shea tree (Vitellaria paradoxa) is central to sustaining local livelihoods and the farming environments of rural communities. Despite its economic and cultural value, however, not to mention the ecological roles it plays as a dominant parkland species, shea remains semi-domesticated with virtually no history of systematic genetic improvement. In truth, shea's extended juvenile period makes traditional breeding approaches untenable; but the opportunity for genome-assisted breeding is immense, provided the foundational resources are available. Here we report the development and public release of such resources. Using the FALCON-Phase workflow, 162.6 Gb of long-read PacBio sequence data were assembled into a 658.7 Mbp, chromosome-scale reference genome annotated with 38,505 coding genes. Whole genome duplication (WGD) analysis based on this gene space revealed clear signatures of two ancient WGD events in shea's evolutionary past, one prior to the Astrid-Rosid divergence (116-126 Mya) and the other at the root of the order Ericales (65-90 Mya). In a first genome-wide look at the suite of fatty acid (FA) biosynthesis genes that likely govern stearin content, the primary determinant of shea butter quality, relatively high copy numbers of six key enzymes were found (KASI, KASIII, FATB, FAD2, FAD3, and FAX2), some likely originating in shea's more recent WGD event. To help translate these findings into practical tools for characterization, selection, and genome-wide association studies (GWAS), resequencing data from a shea diversity panel was used to develop a database of more than 3.5 million functionally annotated, physically anchored SNPs. Two smaller, more curated sets of suggested SNPs, one for GWAS (104,211 SNPs) and the other targeting FA biosynthesis genes (90 SNPs), are also presented. With these resources, the hope is to support national programs across the shea belt in the strategic, genome-enabled conservation and long-term improvement of the shea tree for SSA.}, }
@article {pmid34564670, year = {2021}, author = {Fournier, C and Riehle, E and Dietrich, DR and Schleheck, D}, title = {Is Toxin-Producing Planktothrix sp. an Emerging Species in Lake Constance?.}, journal = {Toxins}, volume = {13}, number = {9}, pages = {}, pmid = {34564670}, issn = {2072-6651}, mesh = {Environmental Monitoring/*methods ; Germany ; *Harmful Algal Bloom ; Lakes/*microbiology ; Microcystins/*biosynthesis/*toxicity ; Planktothrix/*growth &amp; development/*metabolism ; }, abstract = {Recurring blooms of filamentous, red-pigmented and toxin-producing cyanobacteria Planktothrix rubescens have been reported in numerous deep and stratified prealpine lakes, with the exception of Lake Constance. In a 2019 and 2020 Lake Constance field campaign, we collected samples from a distinct red-pigmented biomass maximum below the chlorophyll-a maximum, which was determined using fluorescence probe measurements at depths between 18 and 20 m. Here, we report the characterization of these deep water red pigment maxima (DRM) as cyanobacterial blooms. Using 16S rRNA gene-amplicon sequencing, we found evidence that the blooms were, indeed, contributed by Planktothrix spp., although phycoerythrin-rich Synechococcus taxa constituted most of the biomass (>96% relative read abundance) of the cyanobacterial DRM community. Through UPLC-MS/MS, we also detected toxic microcystins (MCs) in the DRM in the individual sampling days at concentrations of ≤1.5 ng/L. Subsequently, we reevaluated the fluorescence probe measurements collected over the past decade and found that, in the summer, DRM have been present in Lake Constance, at least since 2009. Our study highlights the need for a continuous monitoring program also targeting the cyanobacterial DRM in Lake Constance, and for future studies on the competition of the different cyanobacterial taxa. Future studies will address the potential community composition changes in response to the climate change driven physiochemical and biological parameters of the lake.}, }
@article {pmid34563431, year = {2021}, author = {Shalev, O and Ratzke, C}, title = {A holistic view of host-associated microbial evolution.}, journal = {Trends in microbiology}, volume = {29}, number = {11}, pages = {961-962}, doi = {10.1016/j.tim.2021.09.003}, pmid = {34563431}, issn = {1878-4380}, mesh = {*Microbiota ; }, abstract = {Microbes often live associated with other organisms. Whereas the impact of microbes on their hosts is well studied, what such a lifestyle means for the microbes is poorly understood. To address this gap, Bansept et al. explore how microbes could evolve to cope with altering between host-associated and host-free lifestyles.}, }
@article {pmid34562129, year = {2022}, author = {Zhou, J and Wang, M and Yi, X}, title = {Alteration of Gut Microbiota of a Food-Storing Hibernator, Siberian Chipmunk Tamias sibiricus.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {603-612}, pmid = {34562129}, issn = {1432-184X}, support = {32070447//National Natural Science Foundation of China/ ; 41807053//National Natural Science Foundation of China/ ; 31760156//National Natural Science Foundation of China/ ; 20190601//Youth Talent Introduction and Education Program of Shandong Province/ ; }, mesh = {Animals ; Bacteroidetes ; *Gastrointestinal Microbiome/physiology ; *Hibernation/physiology ; Mammals ; *Microbiota ; Sciuridae ; }, abstract = {Hibernation represents a state of fasting because hibernators cease eating in the torpid periods. Therefore, food deprivation during hibernation is expected to modify the gut microbiota of host. However, there are few reports of gut microbiota in food-storing hibernators that feed during the interbout arousals. Here we collected fecal samples of Siberian chipmunk T. sibiricus to character and examine changes in the gut microbiota at various stages relative to hibernation: pre-hibernation, early-hibernation, mid-hibernation, late-hibernation, and post-hibernation. Compared to the pre-hibernation state, alpha-diversity of gut microbiota was significantly increased during the interbout arousal periods. In addition, beta-diversity of the fecal communities from pre-hibernation and interbout arousal periods grouped together, and post-hibernation gut microbiota resembled the counterpart at late-hibernation. Hibernation significantly decreased the relative abundance of Firmicutes but increased Bacteroidetes, reflecting a shift of microbiota toward taxa in favor of host-derived substrates. The increased abundance of Ruminococcaceae_UCG-014, Lactobacillus, and Christensenellaceae_R-7_group in gut microbiota may help the chipmunks reduce intestinal inflammation and then maintain healthy bowel during hibernation. KEGG pathway indicated that hibernation altered the metabolic function of gut microflora of T. sibiricus. Our study provides evidence that the gut microbiota of food-storing hibernators, despite feeding during the interbout arousals, shows similar response to hibernation that has well documented in fat-storing counterparts, suggesting the potential for a core gut microbiota during hibernation of mammals. Importantly, these results will broaden our understanding of the effects of hibernation on gut microbiota of mammal hibernators.}, }
@article {pmid34561754, year = {2022}, author = {Varasteh, T and Salazar, V and Tschoeke, D and Francini-Filho, RB and Swings, J and Garcia, G and Thompson, CC and Thompson, FL}, title = {Breviolum and Cladocopium Are Dominant Among Symbiodiniaceae of the Coral Holobiont Madracis decactis.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {325-335}, pmid = {34561754}, issn = {1432-184X}, mesh = {Animals ; *Anthozoa/physiology ; Atlantic Ocean ; Coral Reefs ; DNA, Ribosomal/genetics ; *Dinoflagellida/physiology ; Phylogeny ; Symbiosis ; }, abstract = {The scleractinian reef building coral Madracis decactis is a cosmopolitan species. Understanding host-symbiont associations is critical for assessing coral's habitat requirements and its response to environmental changes. In this study, we performed a fine grained phylogenetic analyses of Symbiodiniaceae associated with Madracis in two locations in the Southwest Atlantic Ocean (Abrolhos Bank and St. Peter and St. Paul Archipelago). Previous studies have argued that Madracis is a specialist coral, with colonies harboring a single symbiont from the genus Breviolum (formerly clade B). However, these previous studies have not precisely addressed if Madracis is colonized by several types of Symbiodiniaceae simultaneously or whether this coral is a specialist. The hypothesis that Madracis is a generalist coral host was evaluated in the present study. A total of 1.9 million reads of ITS2 nuclear ribosomal DNA were obtained by Illumina MiSeq sequencing. While Symbiodiniaceae ITS2 sequences between two sampling depths were almost entirely (62%) from the genus Breviolum (formerly clade B), shallow (10-15 m) populations in Abrolhos had a greater diversity of ITS2 sequences in comparison to deeper (25-35 m) populations of St. Peter and St. Paul Archipelago. Cladocopium (formerly clade C) and Symbiodinium (formerly clade A) were also found in Abrolhos. A single Madracis colony can host different symbiont types with > 30 Symbiodiniaceae ITS2-type profiles. Abrolhos corals presented a higher photosynthetic potential as a possible result of co-occurrence of multiple Symbiodiniaceae in a single coral colony. Multiple genera/clades of Symbiodiniaceae possibly confer coral hosts with broader environmental tolerance and ability to occupy diverse or changing habitats.}, }
@article {pmid34560321, year = {2021}, author = {Zuo, T and Wu, X and Wen, W and Lan, P}, title = {Gut Microbiome Alterations in COVID-19.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {19}, number = {5}, pages = {679-688}, pmid = {34560321}, issn = {2210-3244}, mesh = {Bacteria ; *COVID-19/complications ; Fungi ; *Gastrointestinal Microbiome ; Humans ; SARS-CoV-2 ; Post-Acute COVID-19 Syndrome ; }, abstract = {Since the outset of the coronavirus disease 2019 (COVID-19) pandemic, the gut microbiome in COVID-19 has garnered substantial interest, given its significant roles in human health and pathophysiology. Accumulating evidence is unveiling that the gut microbiome is broadly altered in COVID-19, including the bacterial microbiome, mycobiome, and virome. Overall, the gut microbial ecological network is significantly weakened and becomes sparse in patients with COVID-19, together with a decrease in gut microbiome diversity. Beyond the existence of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), the gut microbiome of patients with COVID-19 is also characterized by enrichment of opportunistic bacteria, fungi, and eukaryotic viruses, which are also associated with disease severity and presentation. Meanwhile, a multitude of symbiotic bacteria and bacteriophages are decreased in abundance in patients with COVID-19. Such gut microbiome features persist in a significant subset of patients with COVID-19 even after disease resolution, coinciding with 'long COVID' (also known as post-acute sequelae of COVID-19). The broadly-altered gut microbiome is largely a consequence of SARS-CoV-2infection and its downstream detrimental effects on the systemic host immunity and the gut milieu. The impaired host immunity and distorted gut microbial ecology, particularly loss of low-abundance beneficial bacteria and blooms of opportunistic fungi including Candida, may hinder the reassembly of the gut microbiome post COVID-19. Future investigation is necessary to fully understand the role of the gut microbiome in host immunity against SARS-CoV-2 infection, as well as the long-term effect of COVID-19 on the gut microbiome in relation to the host health after the pandemic.}, }
@article {pmid34560288, year = {2022}, author = {Wang, Z and Liu, M and Ma, H and Lu, B and Shen, Z and Mu, C and Alfarraj, SA and El-Serehy, HA and Warren, A}, title = {Redescription and molecular characterization of two Trichodina species (Ciliophora, Peritrichia, Mobilida) from freshwater fish in China.}, journal = {Parasitology international}, volume = {86}, number = {}, pages = {102470}, doi = {10.1016/j.parint.2021.102470}, pmid = {34560288}, issn = {1873-0329}, mesh = {Animals ; *Carps ; China/epidemiology ; Ciliophora Infections/epidemiology/parasitology/*veterinary ; Fish Diseases/*epidemiology/parasitology ; Oligohymenophorea/*classification/cytology/genetics/isolation &amp; purification ; Phylogeny ; Prevalence ; }, abstract = {During an investigation of parasitic ciliates in northern China, two Trichodina species, T. acuta Lom, 1970 and T. nigra Lom, 1960, were isolated from the freshwater fish Cyprinus carpio Linnaeus, 1758. The morphology of each species was investigated based on dry silver nitrate-stained specimens. In addition, the molecular phylogeny of each was analyzed based on small subunit ribosomal DNA (SSU rDNA) sequence data. Trichodina acuta can be distinguished from its congeners by the undefined periphery of the central circle, the distinct gap between the rays and the central circle, and the distinctly sickle-shaped blades. Trichodina nigra is a cosmopolitan ciliate and is characterized by its densely linked denticles, broad, rounded spatula-shaped blades, robust central parts, and well developed rays. Phylogenetic analyses revealed that T. acuta and T. nigra nest within different clades, supporting the assertion that the GC content of SSU rDNA sequences could reflect evolutionary relationships among Trichodina species.}, }
@article {pmid34559138, year = {2021}, author = {Tanaka, T and Matsuno, Y and Torisu, T and Shibata, H and Hirano, A and Umeno, J and Kawasaki, K and Fujioka, S and Fuyuno, Y and Moriyama, T and Esaki, M and Kitazono, T}, title = {Gastric microbiota in patients with Helicobacter pylori-negative gastric MALT lymphoma.}, journal = {Medicine}, volume = {100}, number = {38}, pages = {e27287}, pmid = {34559138}, issn = {1536-5964}, mesh = {Aged ; Case-Control Studies ; Cross-Sectional Studies ; Female ; Gastric Mucosa/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Lymphoma, B-Cell, Marginal Zone/*microbiology ; Male ; Metagenomics ; Middle Aged ; Stomach Neoplasms/*microbiology ; }, abstract = {To investigate the mucosal microbiota in the stomach of patients with Helicobacter pylori-negative mucosa-associated lymphoid tissue (MALT) lymphoma by means of metagenomic analysis.Although some gastric MALT lymphomas are associated with the presence of H. pylori, other gastric MALT lymphomas occur independently of H. pylori infection. The pathogenesis of H. pylori-negative MALT lymphoma remains unclear.Mucosal biopsy specimens were collected from the gastric body from 33 MALT lymphoma patients with gastric lesions, including both H. pylori-infection naïve patients and posteradication patients, as well as 27 control participants without H. pylori infection or cancer. Subsequently, the samples were subjected to 16S rRNA gene sequencing. Quantitative insights into microbial ecology, linear discriminant analysis effect size, and phylogenetic investigation of communities by reconstruction of unobserved states softwares were used to analyze the participants' microbiota.H. pylori-negative MALT lymphoma patients had significantly lower alpha diversity (P = .04), compared with control participants. Significant differences were evident in the microbial composition (P = .04), as determined by comparison of beta diversity between the 2 groups. Taxonomic composition analysis indicated that the genera Burkholderia and Sphingomonas were significantly more abundant in MALT lymphoma patients, while the genera Prevotella and Veillonella were less abundant. Functional microbiota prediction showed that the predicted gene pathways "replication and repair," "translation," and "nucleotide metabolism" were downregulated in MALT lymphoma patients.H. pylori-negative MALT lymphoma patients exhibited altered gastric mucosal microbial compositions, suggesting that altered microbiota might be involved in the pathogenesis of H. pylori-negative MALT lymphoma.}, }
@article {pmid34558584, year = {2021}, author = {Iglesias-Aguirre, CE and Cortés-Martín, A and Ávila-Gálvez, M&#xc1; and Giménez-Bastida, JA and Selma, MV and González-Sarrías, A and Espín, JC}, title = {Main drivers of (poly)phenol effects on human health: metabolite production and/or gut microbiota-associated metabotypes?.}, journal = {Food &amp; function}, volume = {12}, number = {21}, pages = {10324-10355}, doi = {10.1039/d1fo02033a}, pmid = {34558584}, issn = {2042-650X}, mesh = {Diet/*methods ; Gastrointestinal Microbiome/drug effects/*physiology ; Humans ; Phenols/*metabolism/*pharmacology ; Polyphenols/metabolism/pharmacology ; }, abstract = {Despite the high human interindividual variability in response to (poly)phenol consumption, the cause-and-effect relationship between some dietary (poly)phenols (flavanols and olive oil phenolics) and health effects (endothelial function and prevention of LDL oxidation, respectively) has been well established. Most of the variables affecting this interindividual variability have been identified (food matrix, gut microbiota, single-nucleotide-polymorphisms, etc.). However, the final drivers for the health effects of (poly)phenol consumption have not been fully identified. At least partially, these drivers could be (i) the (poly)phenols ingested that exert their effect in the gastrointestinal tract, (ii) the bioavailable metabolites that exert their effects systemically and/or (iii) the gut microbial ecology associated with (poly)phenol metabolism (i.e., gut microbiota-associated metabotypes). However, statistical associations between health effects and the occurrence of circulating and/or excreted metabolites, as well as cross-sectional studies that correlate gut microbial ecologies and health, do not prove a causal role unequivocally. We provide a critical overview and perspective on the possible main drivers of the effects of (poly)phenols on human health and suggest possible actions to identify the putative actors responsible for the effects.}, }
@article {pmid34557947, year = {2022}, author = {de Almeida, JCF and da Silva Xavier, A and Cascardo, RS and de Rezende, RR and de Souza, FO and Lopes, CA and Alfenas-Zerbini, P}, title = {Genomic and Biological Characterization of Ralstonia solanacearum Inovirus Brazil 1, an Inovirus that Alters the Pathogenicity of the Phytopathogen Ralstonia pseudosolanacearum.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {527-538}, pmid = {34557947}, issn = {1432-184X}, support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 2456937/2018//Funda&#xe7;&#xe3;o de Apoio &#xe0; Pesquisa do Estado de Minas Gerais/ ; }, mesh = {*Bacteriophages ; Brazil ; Genomics ; *Inovirus/genetics ; Phylogeny ; Plant Diseases/microbiology ; Ralstonia/genetics ; *Ralstonia solanacearum/genetics ; Virulence/genetics ; }, abstract = {Filamentous bacteriophages contain a single-stranded DNA genome and have a peculiar lifestyle, since they do not cause host cell lysis, but establish a persistent association with the host, often causing behavioral changes, with effects on bacterial ecology. Over the years, a gradual reduction in the incidence of bacterial wilt has been observed in some fields from Brazil. This event, which has been associated with the loss of pathogenicity of Rasltonia spp. isolates due to infection by filamentous viruses of the inovirus group, is widely reported for Ralstonia spp. Asian isolates infected by inoviruses. In an attempt to elucidate which factors are associated with the phenomenon reported in Brazil, we investigated one isolate of R. solanacearum (UB-2014), with unusual characteristics for R. solanacearum, obtained from eggplant with mild wilt symptoms. To verify if the presence of filamentous bacteriophage was related to this phenotype, we performed viral purification and nucleic acid extraction. The phage genome was sequenced, and phylogenetic analyses demonstrated that the virus belongs to the family Inoviridae and was named as Ralstonia solanacerarum inovirus Brazil 1 (RSIBR1). RSIBR1 was transmitted to R. pseudosolanacearum GMI1000, and the virus-infected GMI1000 (GMI1000 VI) isolate showed alterations in phenotypic characteristics, as well as loss of pathogenicity, similarly to that observed in R. solanacearum isolate UB-2014. The presence of virus-infected UB-2014 and GMI1000 VI plants without symptoms, after 3 months, confirms that the infected isolates can colonize the plant without causing disease, which demonstrates that the phage infection changed the behavior of these pathogens.}, }
@article {pmid34555741, year = {2021}, author = {McDaniel, EA and Wahl, SA and Ishii, S and Pinto, A and Ziels, R and Nielsen, PH and McMahon, KD and Williams, RBH}, title = {Prospects for multi-omics in the microbial ecology of water engineering.}, journal = {Water research}, volume = {205}, number = {}, pages = {117608}, doi = {10.1016/j.watres.2021.117608}, pmid = {34555741}, issn = {1879-2448}, mesh = {Bioreactors ; Metagenomics ; *Microbiota ; Sewage ; *Water ; }, abstract = {Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions - including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful functional predictions to specific taxonomical groups with increasing fidelity. Additionally, related developments in both whole community gene expression surveys and metabolite profiling have permitted for direct surveys of community-scale functions in specific environmental settings. These advances have allowed for a shift in microbiome science away from descriptive studies and towards mechanistic and predictive frameworks for designing and harnessing microbial communities for desired beneficial outcomes. Water engineers, microbiologists, and microbial ecologists studying activated sludge, anaerobic digestion, and drinking water distribution systems have applied various (meta)omics techniques for connecting microbial community dynamics and physiologies to overall process parameters and system performance. However, the rapid pace at which new omics-based approaches are developed can appear daunting to those looking to apply these state-of-the-art practices for the first time. Here, we review how modern genome-resolved metagenomic approaches have been applied to a variety of water engineering applications from lab-scale bioreactors to full-scale systems. We describe integrated omics analysis across engineered water systems and the foundations for pairing these insights with modeling approaches. Lastly, we summarize emerging omics-based technologies that we believe will be powerful tools for water engineering applications. Overall, we provide a framework for microbial ecologists specializing in water engineering to apply cutting-edge omics approaches to their research questions to achieve novel functional insights. Successful adoption of predictive frameworks in engineered water systems could enable more economically and environmentally sustainable bioprocesses as demand for water and energy resources increases.}, }
@article {pmid34554284, year = {2022}, author = {Zhang, L and Lai, JL and Zhang, Y and Luo, XG and Li, ZG}, title = {Degradation of Uranium-Contaminated Decontamination Film by UV Irradiation and Microbial Biodegradation.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {439-450}, pmid = {34554284}, issn = {1432-184X}, support = {No. SKLNBC2019-21//state key laboratory of nbc protection for civilian/ ; }, mesh = {Bacteria ; Biodegradation, Environmental ; Decontamination ; RNA, Ribosomal, 16S/genetics/metabolism ; Ultraviolet Rays ; *Uranium/metabolism ; }, abstract = {This research provides a complete degradation scheme for acrylic copolymer/cellulose acetate butyrate peelable decontamination films. This study analyzed the removal efficiency of uranium by peelable decontamination film. More importantly, the degradability of the films was evaluated by a combined treatment with UV radiation and microbial biodegradation. The results showed that UV radiation would rupture the surface of the decontamination films, which leaded the weight-average molecular weight decreased by 55.3% and number-average molecular weight decreased by 75.83%. Additionally, the microbial flora induced light-degradable decontamination film weight-average molecular weight and number-average molecular weight decreased by 9.3% and 30.73%, respectively. 16S rRNA microbial diversity analysis indicated that Pantoea, Xylella, Cronobacter, and Olivibacter were the major degrading bacteria genera. Among them, 4 key strains that can be stripped of decontamination films have been isolated and identified from the dominant degrading bacteria group. The results show that UV radiation combined with microbial flora can achieve rapid degradation of the decontamination films.}, }
@article {pmid34554283, year = {2022}, author = {Wu, H and Zhang, Z and Wang, J and Qin, X and Chen, J and Wu, L and Lin, S and Rensing, C and Lin, W}, title = {Bio-fertilizer Amendment Alleviates the Replanting Disease under Consecutive Monoculture Regimes by Reshaping Leaf and Root Microbiome.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {452-464}, pmid = {34554283}, issn = {1432-184X}, support = {U1205021, 81573530//National Science Foundation of China/ ; 82003884//National Science Foundation of China/ ; 2019M650150//Project Funded by China Postdoctoral Science Foundation/ ; }, mesh = {Fertilizers ; *Microbiota ; *Paenibacillus/genetics ; Plant Leaves ; Plant Roots ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Replanting disease is a growing problem in intensive agricultural systems. Application of bio-fertilizer containing beneficial microbes contributes to disease suppression and is a promising strategy to control replanting disease. However, the effect of both replanting disease and bio-fertilizer amendment on the assembly of crop microbiota in leaves and roots and their relationships to crop yield and quality remains elusive. In these experiments, roots and leaves of Radix pseudostellariae were collected from different consecutive monoculture and bio-fertilizer amended fields, and the associated microbiota were characterized by bacterial 16S rRNA gene sequencing and quantitative PCR. Consecutive monoculture altered the bacterial community structure and composition and significantly increased the abundance of potential pathogenic Ralstonia and Fusarium oxysporum in leaves and roots. Furthermore, bio-fertilizer application alleviated replanting disease by decreasing the pathogen load, increasing the potential beneficial genera Pseudomonas, Streptomyces, Paenibacillus, and Bradyrhizobium. The proportion of positive correlations in the co-occurrence network of bio-fertilizer application was the highest, implying that bio-fertilizer potentially enhanced ecological commensalism or mutualism of the bacterial community across the two compartments. Structural equation models indicated that bio-fertilizer had a positive and indirect effect on both yield and quality by shaping the leaf microbiota and the root microbiota. Our findings highlight the role of leaf and root microbiota on replanting disease, showing that bio-fertilizer contributes to alleviating replanting disease by improving microbe-microbe interactions.}, }
@article {pmid34553243, year = {2022}, author = {Villalobos-Flores, LE and Espinosa-Torres, SD and Hernández-Quiroz, F and Piña-Escobedo, A and Cruz-Narváez, Y and Velázquez-Escobar, F and Süssmuth, R and García-Mena, J}, title = {The Bacterial and Fungal Microbiota of the Mexican Rubiaceae Family Medicinal Plant Bouvardia ternifolia.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {510-526}, pmid = {34553243}, issn = {1432-184X}, mesh = {Bacteria/genetics ; Endophytes ; Fungi/genetics ; *Mycobiome ; Plant Roots/microbiology ; *Plants, Medicinal/microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; *Rubiaceae/genetics ; Soil Microbiology ; }, abstract = {Bouvardia ternifolia is a medicinal plant considered a source of therapeutic compounds, like the antitumoral cyclohexapeptide bouvardin. It is known that large number of secondary metabolites produced by plants results from the interaction of the host and adjacent or embedded microorganisms. Using high-throughput DNA sequencing of V3-16S and V5-18S ribosomal gene libraries, we characterized the endophytic, endophytic + epiphyte bacterial, and fungal communities associated to flowers, leaves, stems, and roots, as well as the rhizosphere. The Proteobacteria (average 80.7%) and Actinobacteria (average 14.7%) were the most abundant bacterial phyla, while Leotiomycetes (average 54.8%) and Dothideomycetes (average 27.4%) were the most abundant fungal classes. Differential abundance for the bacterial endophyte group showed a predominance of Erwinia, Propionibacterium, and Microbacterium genera, while Sclerotinia, Coccomyces, and Calycina genera predominated for fungi. The predictive metagenome analysis for bacteria showed significative abundance of pathways for secondary metabolite production, while a FUNguild analysis revealed the presence of pathotroph, symbiotroph, and saprotrophs in the fungal community. Intra and inter copresence and mutual exclusion interactions were identified for bacterial and fungal kingdoms in the endophyte communities. This work provides a description of the diversity and composition of bacterial and fungal microorganisms living in flowers, leaves, stems, roots, and the rhizosphere of this medicinal plant; thus, it paves the way towards an integral understanding in the production of therapeutic metabolites.}, }
@article {pmid34550758, year = {2021}, author = {Moore, MEG and Paulin-Curlee, G and Johnston, BD and Clabots, C and DebRoy, C and Johnson, TJ and Weber, B and Porter, S and Armién, AG and Johnson, JR}, title = {Molecular Characteristics, Ecology, and Zoonotic Potential of Escherichia coli Strains That Cause Hemorrhagic Pneumonia in Animals.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {23}, pages = {e0147121}, pmid = {34550758}, issn = {1098-5336}, support = {//Biomedical Laboratory Research and Development, VA Office of Research and Development (BLR&amp;D, ORD)/ ; }, mesh = {Animals ; *Cat Diseases/microbiology ; Cats ; *Dog Diseases/microbiology ; Dogs ; Escherichia coli/genetics/*pathogenicity ; Phylogeny ; *Pneumonia, Bacterial/veterinary ; }, abstract = {Hemorrhagic pneumonia (HP) is a rare but highly lethal disease, mainly of dogs and cats, caused by hemolytic Escherichia coli strains that contain cnf1 (encoding cytotoxic necrotizing factor 1). After encountering fatal HP in two dogs, we used contemporary molecular methods, including multilocus sequence typing and whole-genome sequencing, to compare the corresponding case isolates with published HP clinical isolates and newly obtained fecal E. coli isolates from 20 humans and animals in the index HP case household. We also compared the aggregated HP clinical isolates, which represented 13 discrete strains, by pulsotype with a large, private pulsotype library of diverse-source E. coli. The HP clinical isolates represented a narrow range of phylogenetic group B2 lineages (mainly sequence types 12 and 127), O types (mainly O4 and O6), and H types (mainly H5 and H31), but diverse fimH alleles (type-1 fimbriae adhesin). Their extensive, highly conserved virulence genotypes, which qualified as extraintestinal pathogenic E. coli (ExPEC), encoded diverse adhesins, toxins, iron uptake systems, and protectins. Household surveillance identified multiple HP-like fecal strains, plus abundant between-host strain sharing, including of the household's index HP strain. The pulsotype library search identified, for five HP clinical strains, same-pulsotype human and animal fecal and clinical (predominantly urine) isolates, from diverse locales and time periods. Thus, E. coli strains that cause HP derive from a narrow range of ExPEC lineages within phylogroup B2, contain multiple virulence genes other than cnf1, are shared extensively between hosts, and likely function in nature mainly as intestinal colonizers and uropathogens. IMPORTANCE This study clarifies the clonal background and extensive virulence genotypes of the E. coli strains that cause hemorrhagic pneumonia in domestic animals (mainly dogs and cats), shows that such strains circulate among animals and humans, identifies a substantial intestinal colonization component to their lifestyle, and extends their known clinical manifestations to include bacteremia and urinary tract infection. The findings place these strains better into context vis-à-vis current understandings of E. coli phylogeny, ecology, and pathogenesis; identify questions for future research; and may prove relevant for surveillance and prevention efforts.}, }
@article {pmid34550753, year = {2021}, author = {Rothman, JA and Loveless, TB and Kapcia, J and Adams, ED and Steele, JA and Zimmer-Faust, AG and Langlois, K and Wanless, D and Griffith, M and Mao, L and Chokry, J and Griffith, JF and Whiteson, KL}, title = {RNA Viromics of Southern California Wastewater and Detection of SARS-CoV-2 Single-Nucleotide Variants.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {23}, pages = {e0144821}, pmid = {34550753}, issn = {1098-5336}, support = {S10 OD021718/OD/NIH HHS/United States ; R00RG2814//University of California Office of the President Research Grants Program Office/ ; R01RG3732//University of California Office of the President Research Grants Program Office/ ; S10 RR025496/RR/NCRR NIH HHS/United States ; S10 OD010794/OD/NIH HHS/United States ; P30 CA062203/CA/NCI NIH HHS/United States ; //Hewitt Foundation for Biomedical Research/ ; }, mesh = {COVID-19/epidemiology ; California ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Humans ; Polymerase Chain Reaction ; RNA Viruses/classification/genetics/*isolation &amp; purification ; SARS-CoV-2/classification/genetics/*isolation &amp; purification ; Sequence Analysis, RNA ; *Virome ; Wastewater/*virology ; *Wastewater-Based Epidemiological Monitoring ; }, abstract = {Municipal wastewater provides an integrated sample of a diversity of human-associated microbes across a sewershed, including viruses. Wastewater-based epidemiology (WBE) is a promising strategy to detect pathogens and may serve as an early warning system for disease outbreaks. Notably, WBE has garnered substantial interest during the coronavirus disease 2019 (COVID-19) pandemic to track disease burden through analyses of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. Throughout the COVID-19 outbreak, tracking SARS-CoV-2 in wastewater has been an important tool for understanding the spread of the virus. Unlike traditional sequencing of SARS-CoV-2 isolated from clinical samples, which adds testing burden to the health care system, in this study, metatranscriptomics was used to sequence virus directly from wastewater. Here, we present a study in which we explored RNA viral diversity through sequencing 94 wastewater influent samples across seven wastewater treatment plants (WTPs), collected from August 2020 to January 2021, representing approximately 16 million people in Southern California. Enriched viral libraries identified a wide diversity of RNA viruses that differed between WTPs and over time, with detected viruses including coronaviruses, influenza A, and noroviruses. Furthermore, single-nucleotide variants (SNVs) of SARS-CoV-2 were identified in wastewater, and we measured proportions of overall virus and SNVs across several months. We detected several SNVs that are markers for clinically important SARS-CoV-2 variants along with SNVs of unknown function, prevalence, or epidemiological consequence. Our study shows the potential of WBE to detect viruses in wastewater and to track the diversity and spread of viral variants in urban and suburban locations, which may aid public health efforts to monitor disease outbreaks. IMPORTANCE Wastewater-based epidemiology (WBE) can detect pathogens across sewersheds, which represents the collective waste of human populations. As there is a wide diversity of RNA viruses in wastewater, monitoring the presence of these viruses is useful for public health, industry, and ecological studies. Specific to public health, WBE has proven valuable during the coronavirus disease 2019 (COVID-19) pandemic to track the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) without adding burden to health care systems. In this study, we used metatranscriptomics and reverse transcription-droplet digital PCR (RT-ddPCR) to assay RNA viruses across Southern California wastewater from August 2020 to January 2021, representing approximately 16 million people from Los Angeles, Orange, and San Diego counties. We found that SARS-CoV-2 quantification in wastewater correlates well with county-wide COVID-19 case data, and that we can detect SARS-CoV-2 single-nucleotide variants through sequencing. Likewise, wastewater treatment plants (WTPs) harbored different viromes, and we detected other human pathogens, such as noroviruses and adenoviruses, furthering our understanding of wastewater viral ecology.}, }
@article {pmid34550379, year = {2021}, author = {Garoña, A and Hülter, NF and Romero Picazo, D and Dagan, T}, title = {Segregational Drift Constrains the Evolutionary Rate of Prokaryotic Plasmids.}, journal = {Molecular biology and evolution}, volume = {38}, number = {12}, pages = {5610-5624}, pmid = {34550379}, issn = {1537-1719}, mesh = {Chromosomes ; *Genetic Drift ; Phylogeny ; Plasmids/genetics ; *Prokaryotic Cells ; }, abstract = {Plasmids are extrachromosomal genetic elements in prokaryotes that have been recognized as important drivers of microbial ecology and evolution. Plasmids are found in multiple copies inside their host cell where independent emergence of mutations may lead to intracellular genetic heterogeneity. The intracellular plasmid diversity is thus subject to changes upon cell division. However, the effect of plasmid segregation on plasmid evolution remains understudied. Here, we show that genetic drift during cell division-segregational drift-leads to the rapid extinction of novel plasmid alleles. We established a novel experimental approach to control plasmid allele frequency at the levels of a single cell and the whole population. Following the dynamics of plasmid alleles in an evolution experiment, we find that the mode of plasmid inheritance-random or clustered-is an important determinant of plasmid allele dynamics. Phylogenetic reconstruction of our model plasmid in clinical isolates furthermore reveals a slow evolutionary rate of plasmid-encoded genes in comparison to chromosomal genes. Our study provides empirical evidence that genetic drift in plasmid evolution occurs at multiple levels: the host cell and the population of hosts. Segregational drift has implications for the evolutionary rate heterogeneity of extrachromosomal genetic elements.}, }
@article {pmid34546074, year = {2021}, author = {Heyse, J and Schattenberg, F and Rubbens, P and Müller, S and Waegeman, W and Boon, N and Props, R}, title = {Predicting the Presence and Abundance of Bacterial Taxa in Environmental Communities through Flow Cytometric Fingerprinting.}, journal = {mSystems}, volume = {6}, number = {5}, pages = {e0055121}, pmid = {34546074}, issn = {2379-5077}, support = {//Onderzoeksprogramma Artifici&#xeb;le Intelligentie (AI) Vlaanderen/ ; 1S80618N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 1221020N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; BOF15/GOA/006//UGent | Bijzonder Onderzoeksfonds UGent (BOF)/ ; }, abstract = {Microbiome management research and applications rely on temporally resolved measurements of community composition. Current technologies to assess community composition make use of either cultivation or sequencing of genomic material, which can become time-consuming and/or laborious in case high-throughput measurements are required. Here, using data from a shrimp hatchery as an economically relevant case study, we combined 16S rRNA gene amplicon sequencing and flow cytometry data to develop a computational workflow that allows the prediction of taxon abundances based on flow cytometry measurements. The first stage of our pipeline consists of a classifier to predict the presence or absence of the taxon of interest, with yielded an average accuracy of 88.13% ± 4.78% across the top 50 operational taxonomic units (OTUs) of our data set. In the second stage, this classifier was combined with a regression model to predict the relative abundances of the taxon of interest, which yielded an average R[2] of 0.35 ± 0.24 across the top 50 OTUs of our data set. Application of the models to flow cytometry time series data showed that the generated models can predict the temporal dynamics of a large fraction of the investigated taxa. Using cell sorting, we validated that the model correctly associates taxa to regions in the cytometric fingerprint, where they are detected using 16S rRNA gene amplicon sequencing. Finally, we applied the approach of our pipeline to two other data sets of microbial ecosystems. This pipeline represents an addition to the expanding toolbox for flow cytometry-based monitoring of bacterial communities and complements the current plating- and marker gene-based methods. IMPORTANCE Monitoring of microbial community composition is crucial for both microbiome management research and applications. Existing technologies, such as plating and amplicon sequencing, can become laborious and expensive when high-throughput measurements are required. In recent years, flow cytometry-based measurements of community diversity have been shown to correlate well with those derived from 16S rRNA gene amplicon sequencing in several aquatic ecosystems, suggesting that there is a link between the taxonomic community composition and phenotypic properties as derived through flow cytometry. Here, we further integrated 16S rRNA gene amplicon sequencing and flow cytometry survey data in order to construct models that enable the prediction of both the presence and the abundances of individual bacterial taxa in mixed communities using flow cytometric fingerprinting. The developed pipeline holds great potential to be integrated into routine monitoring schemes and early warning systems for biotechnological applications.}, }
@article {pmid34546069, year = {2021}, author = {Liu, J and Villanueva, P and Choi, J and Gunturu, S and Ouyang, Y and Tiemann, LK and Cole, JR and Glanville, KR and Hall, SJ and McDaniel, MD and Lee, J and Howe, A}, title = {MetaFunPrimer: an Environment-Specific, High-Throughput Primer Design Tool for Improved Quantification of Target Genes.}, journal = {mSystems}, volume = {6}, number = {5}, pages = {e0020121}, pmid = {34546069}, issn = {2379-5077}, support = {DE-SC0018420//U.S. Department of Energy (DOE)/ ; DE-SC0014108//U.S. Department of Energy (DOE)/ ; }, abstract = {Genes belonging to the same functional group may include numerous and variable gene sequences, making characterizing and quantifying difficult. Therefore, high-throughput design tools are needed to simultaneously create primers for improved quantification of target genes. We developed MetaFunPrimer, a bioinformatic pipeline, to design primers for numerous genes of interest. This tool also enables gene target prioritization based on ranking the presence of genes in user-defined references, such as environment-specific metagenomes. Given inputs of protein and nucleotide sequences for gene targets of interest and an accompanying set of reference metagenomes or genomes, MetaFunPrimer generates primers for ranked genes of interest. To demonstrate the usage and benefits of MetaFunPrimer, a total of 78 primer pairs were designed to target observed ammonia monooxygenase subunit A (amoA) genes of ammonia-oxidizing bacteria (AOB) in 1,550 publicly available soil metagenomes. We demonstrate computationally that these amoA-AOB primers can cover 94% of the amoA-AOB genes observed in the 1,550 soil metagenomes compared with a 49% estimated coverage by previously published primers. Finally, we verified the utility of these primer sets in incubation experiments that used long-term nitrogen fertilized or unfertilized soils. High-throughput quantitative PCR (qPCR) results and statistical analyses showed significant differences in relative quantification patterns between the two soils, and subsequent absolute quantifications also confirmed that target genes enumerated by six selected primer pairs were significantly more abundant in the nitrogen-fertilized soils. This new tool gives microbial ecologists a new approach to assess functional gene abundance and related microbial community dynamics quickly and affordably. IMPORTANCE Amplification-based gene characterization allows for sensitive and specific quantification of functional genes. There is often a large diversity of genes represented for functional gene groups, and multiple primers may be necessary to target associated genes. Current primer design tools are limited to designing primers for only a few genes of interest. MetaFunPrimer allows for high-throughput primer design for various genes of interest and also allows for ranking gene targets by their presence and abundance in environmental data sets. Primers designed by this tool improve the characterization and quantification of functional genes in broad gene amplification platforms and can be powerful with high-throughput qPCR approaches.}, }
@article {pmid34545413, year = {2022}, author = {Wang, L and Wen, Y and Tong, R and Zhang, H and Chen, H and Hu, T and Liu, G and Wang, J and Zhu, L and Wu, T}, title = {Understanding Responses of Soil Microbiome to the Nitrogen and Phosphorus Addition in Metasequoia glyptostroboides Plantations of Different Ages.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {565-579}, pmid = {34545413}, issn = {1432-184X}, mesh = {China ; *Microbiota ; Nitrogen/analysis ; *Phosphorus/analysis ; Soil ; Soil Microbiology ; }, abstract = {Nitrogen (N) and phosphorus (P) have significant effects on soil microbial community diversity, composition, and function. Also, trees of different life stages have different fertilization requirements. In this study, we designed three N additions and three P levels (5 years of experimental treatment) at two Metasequoia glyptostroboides plantations of different ages (young, 6 years old; middle mature, 24 years old) to understand how different addition levels of N and P affect the soil microbiome. Here, the N fertilization of M. glyptostroboides plantation land (5 years of experimental treatment) significantly enriched microbes (e.g., Lysobacter, Luteimonas, and Rhodanobacter) involved in nitrification, denitrification, and P-starvation response regulation, which might further lead to the decreasing in alpha diversity (especially in 6YMP soil). The P addition could impact the genes involved in inorganic P-solubilization and organic P-mineralization by increasing soil AP and TP. Moreover, the functional differences in the soil microbiomes were identified between the 6YMP and 24YMP soil. This study provides valuable information that improves our understanding on the effects of N and P input on the belowground soil microbial community and functional characteristics in plantations of different stand ages.}, }
@article {pmid34545412, year = {2022}, author = {Chan, J and Geng, D and Pan, B and Zhang, Q and Xu, Q}, title = {Gut Microbial Divergence Between Three Hadal Amphipod Species from the Isolated Hadal Trenches.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {627-637}, pmid = {34545412}, issn = {1432-184X}, support = {2018YFC0310600//the National Key Research and Development Program of China/ ; 2018YFD0900601//the National Key R&amp;D Program of China/ ; 31772826//the National Natural Science Foundation of China/ ; 2017-01-07-00-10-E00060//the major scientific innovation project from Shanghai Committee of Education/ ; }, mesh = {*Amphipoda/genetics ; Animals ; *Gastrointestinal Microbiome ; *Microbiota ; Pacific Ocean ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Amphipods are the dominant scavenging metazoan species in the hadal trenches at water depths below 6,000 m. The gut microbiota have been considered to be contribution to the adaptation of deep-sea organisms; however, few comparative analyses of animal gut microbiota between different isolated hadal environments have been done so far. Here, we employed high-throughput 16S rRNA sequencing to compare the gut microbial taxonomic composition and functional potential diversity of three hadal amphipod species, Hirondellea gigas, Bathycallisoma schellenbergi, and Alicella gigantea, collected from the Mariana Trench, Marceau Trench, and New Britain Trench in the Pacific Ocean, respectively. Results showed that different community compositions were detected across all the amphipod specimens based on the analyses of alpha-diversity, hierarchical cluster tree, and PCoA (principal coordinate analysis). Moreover, almost no correlation was observed between genera overrepresented in different amphipods by microbe-microbe correlations analysis, which suggested that the colonization of symbionts were host-specific. At genus level, Psychromonas was dominant in H. gigas, and Candidatus Hepatoplasma was overall dominant in A. gigantea and B. schellenbergi. Comparison of the functional potential showed that, though three hadal amphipod species shared the same predominant functional pathways, the abundances of those most shared pathways showed distinct differences across all the specimens. These findings pointed to the enrichment of particular functional pathways in the gut microbiota of the different isolated trench amphipods. Moreover, in terms of species relative abundance, alpha-diversity and beta-diversity, there was high similarity of gut microbiota between the two A. gigantea populations, which dwelled in two different localities of the same hadal trench. Altogether, this study provides an initial investigation into the gut-microbial interactions and evolution at the hadal depths within amphipod. Each of these three amphipod species would be a model taxa for future studies investigating the influence habitat difference and geography on gut-microbial communities.}, }
@article {pmid34544390, year = {2021}, author = {Bento, FMM and Darolt, JC and Merlin, BL and Penã, L and Wulff, NA and Cônsoli, FL}, title = {The molecular interplay of the establishment of an infection - gene expression of Diaphorina citri gut and Candidatus Liberibacter asiaticus.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {677}, pmid = {34544390}, issn = {1471-2164}, mesh = {Animals ; *Citrus ; Gene Expression ; *Hemiptera/genetics ; Insect Vectors/genetics ; Liberibacter ; Plant Diseases ; *Rhizobiaceae/genetics ; }, abstract = {BACKGROUND: Candidatus Liberibacter asiaticus (CLas) is one the causative agents of greening disease in citrus, an unccurable, devastating disease of citrus worldwide. CLas is vectored by Diaphorina citri, and the understanding of the molecular interplay between vector and pathogen will provide additional basis for the development and implementation of successful management strategies. We focused in the molecular interplay occurring in the gut of the vector, a major barrier for CLas invasion and colonization.<br><br>RESULTS: We investigated the differential expression of vector and CLas genes by analyzing a de novo reference metatranscriptome of the gut of adult psyllids fed of CLas-infected and healthy citrus plants for 1-2, 3-4 and 5-6 days. CLas regulates the immune response of the vector affecting the production of reactive species of oxygen and nitrogen, and the production of antimicrobial peptides. Moreover, CLas overexpressed peroxiredoxin, probably in a protective manner. The major transcript involved in immune expression was related to melanization, a CLIP-domain serine protease we believe participates in the wounding of epithelial cells damaged during infection, which is supported by the down-regulation of pangolin. We also detected that CLas modulates the gut peristalsis of psyllids through the down-regulation of titin, reducing the elimination of CLas with faeces. The up-regulation of the neuromodulator arylalkylamine N-acetyltransferase implies CLas also interferes with the double brain-gut communication circuitry of the vector. CLas colonizes the gut by expressing two Type IVb pilin flp genes and several chaperones that can also function as adhesins. We hypothesized biofilm formation occurs by the expression of the cold shock protein of CLas.<br><br>CONCLUSIONS: The thorough detailed analysis of the transcritome of Ca. L. asiaticus and of D. citri at different time points of their interaction in the gut tissues of the host led to the identification of several host genes targeted for regulation by L. asiaticus, but also bacterial genes coding for potential effector proteins. The identified targets and effector proteins are potential targets for the development of new management strategies directed to interfere with the successful utilization of the psyllid vector by this pathogen.}, }
@article {pmid34540837, year = {2021}, author = {Tudela, H and Claus, SP and Saleh, M}, title = {Next Generation Microbiome Research: Identification of Keystone Species in the Metabolic Regulation of Host-Gut Microbiota Interplay.}, journal = {Frontiers in cell and developmental biology}, volume = {9}, number = {}, pages = {719072}, pmid = {34540837}, issn = {2296-634X}, abstract = {The community of the diverse microorganisms residing in the gastrointestinal tract, known as the gut microbiota, is exceedingly being studied for its impact on health and disease. This community plays a major role in nutrient metabolism, maintenance of the intestinal epithelial barrier but also in local and systemic immunomodulation. A dysbiosis of the gut microbiota, characterized by an unbalanced microbial ecology, often leads to a loss of essential functions that may be associated with proinflammatory conditions. Specifically, some key microbes that are depleted in dysbiotic ecosystems, called keystone species, carry unique functions that are essential for the balance of the microbiota. In this review, we discuss current understanding of reported keystone species and their proposed functions in health. We also elaborate on current and future bioinformatics tools needed to identify missing functions in the gut carried by keystone species. We propose that the identification of such keystone species functions is a major step for the understanding of microbiome dynamics in disease and toward the development of microbiome-based therapeutics.}, }
@article {pmid34540373, year = {2021}, author = {Rodríguez-Barreras, R and Tosado-Rodríguez, EL and Godoy-Vitorino, F}, title = {Trophic niches reflect compositional differences in microbiota among Caribbean sea urchins.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e12084}, pmid = {34540373}, issn = {2167-8359}, support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; }, abstract = {Sea urchins play a critical role in marine ecosystems, as they actively participate in maintaining the balance between coral and algae. We performed the first in-depth survey of the microbiota associated with four free-living populations of Caribbean sea urchins: Lytechinus variegatus, Echinometra lucunter, Tripneustes ventricosus, and Diadema antillarum. We compared the influence of the collection site, echinoid species and trophic niche to the composition of the microbiota. This dataset provides a comprehensive overview to date, of the bacterial communities and their ecological relevance associated with sea urchins in their natural environments. A total of sixty-samples, including surrounding reef water and seagrass leaves underwent 16S rRNA gene sequencing (V4 region) and high-quality reads were analyzed with standard bioinformatic approaches. While water and seagrass were dominated by Cyanobacteria such as Prochlorococcus and Rivularia respectively, echinoid gut samples had dominant Bacteroidetes, Proteobacteria and Fusobacteria. Propionigenium was dominant across all species' guts, revealing a host-associated composition likely responsive to the digestive process of the animals. Beta-diversity analyses showed significant differences in community composition among the three collection sites, animal species, and trophic niches. Alpha diversity was significantly higher among L. variegatus samples compared to the other species. L. variegatus also displayed an increased abundance of Planctomycetes and Cyanobacterial OTUs. The bacterial community of this herbivorous echinoid reflected similarities to the microfilm community found on Thalassia testudinum leaves; a very abundant seagrass and its main food resource. The results of this study elaborate on the microbial ecology of four important Caribbean echinoids, confirming that selection on the microbial community is trophic-niche dependent.}, }
@article {pmid34540243, year = {2021}, author = {Briggs, AA and Brown, AL and Osenberg, CW}, title = {Local versus site-level effects of algae on coral microbial communities.}, journal = {Royal Society open science}, volume = {8}, number = {9}, pages = {210035}, pmid = {34540243}, issn = {2054-5703}, abstract = {Microbes influence ecological processes, including the dynamics and health of macro-organisms and their interactions with other species. In coral reefs, microbes mediate negative effects of algae on corals when corals are in contact with algae. However, it is unknown whether these effects extend to larger spatial scales, such as at sites with high algal densities. We investigated how local algal contact and site-level macroalgal cover influenced coral microbial communities in a field study at two islands in French Polynesia, Mo'orea and Mangareva. At 5 sites at each island, we sampled prokaryotic microbial communities (microbiomes) associated with corals, macroalgae, turf algae and water, with coral samples taken from individuals that were isolated from or in contact with turf or macroalgae. Algal contact and macroalgal cover had antagonistic effects on coral microbiome alpha and beta diversity. Additionally, coral microbiomes shifted and became more similar to macroalgal microbiomes at sites with high macroalgal cover and with algal contact, although the microbial taxa that changed varied by island. Our results indicate that coral microbiomes can be affected by algae outside of the coral's immediate vicinity, and local- and site-level effects of algae can obscure each other's effects when both scales are not considered.}, }
@article {pmid34537690, year = {2022}, author = {Bai, L and Ju, Q and Wang, C and Tian, L and Wang, C and Zhang, H and Jiang, H}, title = {Responses of steroid estrogen biodegradation to cyanobacterial organic matter biodegradability in the water column of a eutrophic lake.}, journal = {The Science of the total environment}, volume = {805}, number = {}, pages = {150058}, doi = {10.1016/j.scitotenv.2021.150058}, pmid = {34537690}, issn = {1879-1026}, mesh = {*Cyanobacteria ; Estrogens ; Estrone ; *Lakes ; Water ; }, abstract = {The co-occurrence of cyanobacterial harmful algal blooms and contaminants is an increasing environmental concern in freshwater worldwide. Our field investigations coupled with laboratory incubations demonstrated that the microbial degradation potential of 17β-estradiol (E2) with estrone as the intermediate was primarily driven by increased dissolved organic matter (DOM) in the water column of a cyanobacterial bloom. To explain the intrinsic contribution of cyanobacterial-derived DOM (C-DOM) to estrogen biodegradation, a combination of methods including bioassay, ultrahigh-resolution mass spectrometry, and microbial ecology were applied. The results showed that preferential assimilation of highly biodegradable structures, including protein-, carbohydrate-, and unsaturated hydrocarbon-like molecules sustained bacterial growth, selected for more diverse microbes, and resulted in greater estrogen biodegradation compared to less biodegradable molecules (lignin- and tannin-like molecules). The biodegradability of C-DOM decreased from 78% to 1%, whereas the E2 biodegradation rate decreased dramatically at first, then increased with the accumulation of recalcitrant, bio-produced lipid-like molecules in C-DOM. This change was linked to alternative substrate-induced selection of the bacterial community under highly refractory conditions, as suggested by the greater biomass-normalized E2 biodegradation rate after a 24-h lag phase. In addition to the increased frequency of potential degraders, such as Sphingobacterium, the network analysis revealed that C-DOM molecules distributed in high H/C (protein- and lipid-like molecules) were the main drivers structuring the bacterial community, inducing strong deterministic selection of the community assemblage and upregulating the metabolic capacity for contaminants. These findings provide strong evidence that estrogen biodegradation in eutrophic water may be facilitated by cyanobacterial blooms and provide a theoretical basis for ecological remediation of estrogen pollution.}, }
@article {pmid34537275, year = {2021}, author = {Majlander, J and Anttila, VJ and Nurmi, W and Seppälä, A and Tiedje, J and Muziasari, W}, title = {Routine wastewater-based monitoring of antibiotic resistance in two Finnish hospitals: focus on carbapenem resistance genes and genes associated with bacteria causing hospital-acquired infections.}, journal = {The Journal of hospital infection}, volume = {117}, number = {}, pages = {157-164}, doi = {10.1016/j.jhin.2021.09.008}, pmid = {34537275}, issn = {1532-2939}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria ; Carbapenems/pharmacology ; Drug Resistance, Microbial ; Finland/epidemiology ; *Genes, Bacterial ; Hospitals ; Humans ; RNA, Ribosomal, 16S ; *Wastewater ; }, abstract = {BACKGROUND: Wastewater-based monitoring represents a useful tool for antibiotic resistance surveillance.<br><br>AIM: To investigate the prevalence and abundance of antibiotic resistance genes (ARGs) in hospital wastewater over time.<br><br>METHODS: Wastewater from two hospitals in Finland (HUS1 and HUS2) was monitored weekly for nine weeks (weeks 25-33) in summer 2020. A high-throughput real-time polymerization chain reaction (HT-qPCR) system was used to detect and quantify 216 ARGs and genes associated with mobile genetic elements (MGEs), integrons, and bacteria causing hospital-acquired infections (HAIs), as well as the 16S rRNA gene. Data from HT-qPCR were analysed and visualized using a novel digital platform, ResistApp. Eight carbapenem resistance genes (blaGES, blaKPC, blaVIM, blaNDM, blaCMY, blaMOX, blaOXA48, and blaOXA51) and three genes associated with bacteria causing HAIs (Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa) were studied.<br><br>FINDINGS: There was a significantly higher number of ARGs at both hospitals in weeks 27-30 (174-191 genes) compared to other sampling weeks (151-171 genes). Our analyses also indicated that the two hospitals, which used different amounts of antibiotics, had significantly different resistance gene profiles. Carbapenem resistance genes were more prevalent and abundant in HUS1 than HUS2. Across both hospitals, blaGES and blaVIM were the most prevalent and abundant. There was also a strong positive association between blaKPC and K.&#xa0;pneumoniae in HUS1 wastewater.<br><br>CONCLUSION: Routine wastewater-based monitoring using ResistApp can provide valuable information on the prevalence and abundance of ARGs in hospitals. This helps hospitals understand the spread of antibiotic resistance in hospitals and identify potential areas for intervention.}, }
@article {pmid34536095, year = {2022}, author = {Gnat, S and Łagowski, D and Dyląg, M and Nowakiewicz, A}, title = {European Hedgehogs (Erinaceus europaeus L.) as a Reservoir of Dermatophytes in Poland.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {363-375}, pmid = {34536095}, issn = {1432-184X}, mesh = {Animals ; Animals, Wild ; Antifungal Agents/pharmacology ; *Arthrodermataceae/genetics ; Hedgehogs/microbiology ; Humans ; Microbial Sensitivity Tests ; Poland/epidemiology ; *Tinea/epidemiology/microbiology/veterinary ; Trichophyton/genetics ; }, abstract = {The European hedgehog (Erinaceus europaeus Linnaeus) frequently colonises areas located close to human life in cities, as these are more suitable nest sites offering an abundance of food and allowing avoidance of predators. However, urbanisation has a significant impact on the epidemiology of infectious diseases, including dermatophytoses, the primary source of which are wild animals. In this study, we determined the spectrum of dermatophytes isolated from the European hedgehog and assessed their susceptibility profile to antifungal drugs. Symptomatic and asymptomatic dermatophyte infections were observed in 7.7% and 8% of the 182 examined free-living hedgehogs, respectively. In the pool of the isolated dermatophyte strains, Trichophyton erinacei was dominant (29.9%), followed by Trichophyton mentagrophytes (17.9%), Trichophyton benhamiae (13.4%), Nannizzia gypsea (11.9%), Microsporum canis (10.4%), Nannizzia nana (7.5%), Paraphyton cookei (6.0%), and Nannizzia fulva (3.0%). Susceptibility tests revealed the highest activity of luliconazole and the lowest of activity fluconazole among the azole drugs applied. Although terbinafine generally exhibited high efficacy, two Trichophyton mentagrophytes isolates showed resistance to this drug (MIC = 2 µg/ml) resulting from missense mutations in the SQLE gene corresponding to the amino acid substitution Leu393Phe. Summarising, our study has also revealed that such wildlife animals as hedgehogs can be a reservoir of pathogenic human dermatophytes, including harmful strains resistant to commonly used antifungal drugs.}, }
@article {pmid34535834, year = {2022}, author = {Li, H and Luo, N and Ji, C and Li, J and Zhang, L and Xiao, L and She, X and Liu, Z and Li, Y and Liu, C and Guo, Q and Lai, H}, title = {Liquid Organic Fertilizer Amendment Alters Rhizosphere Microbial Community Structure and Co-occurrence Patterns and Improves Sunflower Yield Under Salinity-Alkalinity Stress.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {423-438}, pmid = {34535834}, issn = {1432-184X}, support = {31600407//National Natural Science Fund Youth Project/ ; K3380220129//Fundamental Research Fund for Shaanxi agriculture department/ ; K3310220056//Shaanxi Provincial Key Technology R&amp;D Program/ ; }, mesh = {Bacteria ; Fertilizers ; *Helianthus ; *Microbiota ; Rhizosphere ; Salinity ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Response of rhizosphere microbial community structure and co-occurrence patterns to liquid organic fertilizer in sunflower cropland was investigated. Moderate and severe saline-alkaline soils were treated with liquid organic fertilizer containing mainly small molecular organic compounds (450 g L[-1]) at a rate of 4500 L ha[-1] year[-1] over 2 years. Compared with the untreated soils, organic fertilizer treatment increased soil nutrient concentrations by 13.8-137.1% while reducing soil pH and salinity by 5.6% and 54.7%, respectively. Organic fertilizer treatment also improved sunflower yield, plant number, and plant height by 28.6-67.3%. Following organic fertilizer treatment, fungal α-diversity was increased, and the effects of salinity-alkalinity stress on rhizosphere microbial communities were alleviated. The relative abundances of some halotolerant microbes and phytopathogenic fungi were reduced in organic fertilizer-treated soils, in contrast to increases in the relative abundances of plant growth-promoting microbes and organic matter decomposers, such as Nocardioides, Rhizophagus, and Stachybotrys. Network analysis revealed that severe salinity-alkalinity stress stimulated cooperation among bacteria, while organic fertilizer treatment tended to stimulate the ecosystem functions of fungi with higher proportions of fungi-bacteria and fungi-fungi links. More keystone taxa (e.g., Amycolatopsis, Variovorax, and Gemmatimonas) were positively correlated with soil nutrient concentrations and crop yield-related traits in organic fertilizer-treated soils. Overall, liquid organic fertilizer amendment could attenuate the adverse effects of salinity-alkalinity stress on sunflower yield by improving soil quality and optimizing rhizosphere microbial community structure and co-occurrence patterns.}, }
@article {pmid34530674, year = {2021}, author = {Neumann, M and Steimle, A and Grant, ET and Wolter, M and Parrish, A and Willieme, S and Brenner, D and Martens, EC and Desai, MS}, title = {Deprivation of dietary fiber in specific-pathogen-free mice promotes susceptibility to the intestinal mucosal pathogen Citrobacter rodentium.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1966263}, pmid = {34530674}, issn = {1949-0984}, support = {R01 DK118024/DK/NIDDK NIH HHS/United States ; R01 DK125445/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/growth &amp; development/isolation &amp; purification ; Citrobacter rodentium/*growth &amp; development ; Colitis/*microbiology ; Diet, Western/*adverse effects ; Dietary Fiber/*analysis ; Dysbiosis/microbiology ; Enterobacteriaceae Infections/microbiology/pathology ; Fatty Acids, Volatile/metabolism ; Feeding Behavior/physiology ; Female ; Intestinal Mucosa/*microbiology/pathology ; Mice ; Mice, Inbred C57BL ; Specific Pathogen-Free Organisms ; Tight Junctions/*physiology ; }, abstract = {The change of dietary habits in Western societies, including reduced consumption of fiber, is linked to alterations in gut microbial ecology. Nevertheless, mechanistic connections between diet-induced microbiota changes that affect colonization resistance and enteric pathogen susceptibility are still emerging. We sought to investigate how a diet devoid of soluble plant fibers impacts the structure and function of a conventional gut microbiota in specific-pathogen-free (SPF) mice and how such changes alter susceptibility to a rodent enteric pathogen. We show that absence of dietary fiber intake leads to shifts in the abundances of specific taxa, microbiome-mediated erosion of the colonic mucus barrier, a reduction of intestinal barrier-promoting short-chain fatty acids, and increases in markers of mucosal barrier integrity disruption. Importantly, our results highlight that these low-fiber diet-induced changes in the gut microbial ecology collectively contribute to a lethal colitis by the mucosal pathogen Citrobacter rodentium, which is used as a mouse model for enteropathogenic and enterohemorrhagic Escherichia coli (EPEC and EHEC, respectively). Our study indicates that modern, low-fiber Western-style diets might make individuals more prone to infection by enteric pathogens via the disruption of mucosal barrier integrity by diet-driven changes in the gut microbiota, illustrating possible implications for EPEC and EHEC infections.}, }
@article {pmid34530278, year = {2022}, author = {Li, W and Chen, X and Li, M and Cai, Z and Gong, H and Yan, M}, title = {Microplastics as an aquatic pollutant affect gut microbiota within aquatic animals.}, journal = {Journal of hazardous materials}, volume = {423}, number = {Pt B}, pages = {127094}, doi = {10.1016/j.jhazmat.2021.127094}, pmid = {34530278}, issn = {1873-3336}, mesh = {Animals ; *Environmental Pollutants ; *Gastrointestinal Microbiome ; Microplastics ; Plastics/toxicity ; *Water Pollutants, Chemical/analysis/toxicity ; }, abstract = {The adverse impact of microplastics (MPs) on gut microbiota within aquatic animals depends on the overall effect of chemicals and biofilm of MPs. Thus, it is ideal to fully understand the influences that arise from each or even all of these characteristics, which should give us a whole picture of consequences that are brought by MPs. Harmful effects of MPs on gut microbiota within aquatic organisms start from the ingestion of MPs by aquatic organisms. According to this, the present review will discuss the ingestion of MPs and its following results on gut microbial communities within aquatic animals, in which chemical components, such as plastic polymers, heavy metals and POPs, and the biofilm of MPs would be involved. This review firstly analyzed the impacts of MPs on aquatic organisms in detail about its chemical components and biofilm based on previous relevant studies. At last, the significance of field studies, functional studies and complex dynamics of gut microbial ecology in the future research of MPs affecting gut microbiota is discussed.}, }
@article {pmid34528105, year = {2022}, author = {Zhang, J and Peng, S and Li, S and Song, J and Brunel, B and Wang, E and James, EK and Chen, W and Andrews, M}, title = {Arachis hypogaea L. from Acid Soils of Nanyang (China) Is Frequently Associated with Bradyrhizobium guangdongense and Occasionally with Bradyrhizobium ottawaense or Three Bradyrhizobium Genospecies.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {556-564}, pmid = {34528105}, issn = {1432-184X}, mesh = {Arachis ; *Bradyrhizobium/genetics ; DNA, Bacterial/genetics ; *Fabaceae ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Rhizobium/genetics ; Root Nodules, Plant ; Sequence Analysis, DNA ; Soil ; Symbiosis ; }, abstract = {Henan Province is a major area of peanut production in China but the rhizobia nodulating the crop in this region have not been described. A collection of 217 strains of peanut rhizobia was obtained from six field sites across four soil types in Henan Province, North China, by using peanut as a trap host under glasshouse conditions. The 217 strains separated into 8 distinct types on PCR-RFLP analysis of their IGS sequences. Phylogenetic analysis of the 16S rRNA, recA, atpD, and glnII genes of 11 representative strains of the 8 IGS types identified Bradyrhizobium guangdongense, B. ottawaense and three novel Bradyrhizobium genospecies. Bradyrhizobium guangdongense was dominant, accounting for 75.0% of the total isolates across the field sites while B. ottawaense covered 5.1% and the three novel Bradyrhizobium genospecies 4.1 to 8.8% of the total. The symbiosis-related nodA and nifH gene sequences were not congruent with the core genes on phylogenetic analysis and separated into three groups, two of which were similar to sequences of Bradyrhizobium spp. isolated from peanut in south-east China and the third identical to that of B. yuanmingense isolated from Lespedeza cuneata in northern China. A canonical correlation analysis between the distribution of IGS genotypes and soil physicochemical characteristics and climatic factors indicated that the occurrence of IGS types/species was mainly associated with soil pH and available phosphorus.}, }
@article {pmid34527661, year = {2021}, author = {Kerckhof, FM and Sakarika, M and Van Giel, M and Muys, M and Vermeir, P and De Vrieze, J and Vlaeminck, SE and Rabaey, K and Boon, N}, title = {From Biogas and Hydrogen to Microbial Protein Through Co-Cultivation of Methane and Hydrogen Oxidizing Bacteria.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {9}, number = {}, pages = {733753}, pmid = {34527661}, issn = {2296-4185}, abstract = {Increasing efforts are directed towards the development of sustainable alternative protein sources among which microbial protein (MP) is one of the most promising. Especially when waste streams are used as substrates, the case for MP could become environmentally favorable. The risks of using organic waste streams for MP production-the presence of pathogens or toxicants-can be mitigated by their anaerobic digestion and subsequent aerobic assimilation of the (filter-sterilized) biogas. Even though methane and hydrogen oxidizing bacteria (MOB and HOB) have been intensively studied for MP production, the potential benefits of their co-cultivation remain elusive. Here, we isolated a diverse group of novel HOB (that were capable of autotrophic metabolism), and co-cultured them with a defined set of MOB, which could be grown on a mixture of biogas and H2/O2. The combination of MOB and HOB, apart from the CH4 and CO2 contained in biogas, can also enable the valorization of the CO2 that results from the oxidation of methane by the MOB. Different MOB and HOB combinations were grown in serum vials to identify the best-performing ones. We observed synergistic effects on growth for several combinations, and in all combinations a co-culture consisting out of both HOB and MOB could be maintained during five days of cultivation. Relative to the axenic growth, five out of the ten co-cultures exhibited 1.1-3.8 times higher protein concentration and two combinations presented 2.4-6.1 times higher essential amino acid content. The MP produced in this study generally contained lower amounts of the essential amino acids histidine, lysine and threonine, compared to tofu and fishmeal. The most promising combination in terms of protein concentration and essential amino acid profile was Methyloparacoccus murrelli LMG 27482 with Cupriavidus necator LMG 1201. Microbial protein from M. murrelli and C. necator requires 27-67% less quantity than chicken, whole egg and tofu, while it only requires 15% more quantity than the amino acid-dense soybean to cover the needs of an average adult. In conclusion, while limitations still exist, the co-cultivation of MOB and HOB creates an alternative route for MP production leveraging safe and sustainably-produced gaseous substrates.}, }
@article {pmid34526978, year = {2021}, author = {Marvasi, M and Pangallo, D and Cavalieri, D and Poyatos-Jiménez, F}, title = {Editorial: Multi-Omics Revolution in Microbial Cultural Heritage Conservation.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {720509}, pmid = {34526978}, issn = {1664-302X}, }
@article {pmid34526270, year = {2021}, author = {Barros, J and Seena, S}, title = {Plastisphere in freshwaters: An emerging concern.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {290}, number = {}, pages = {118123}, doi = {10.1016/j.envpol.2021.118123}, pmid = {34526270}, issn = {1873-6424}, mesh = {Bacteria ; *Ecosystem ; Fresh Water ; Microplastics ; *Plastics ; }, abstract = {Plastisphere, an ecosystem of microbes thriving on floating plastic debris, has been extensively studied in marine waters since 2013. Currently, very little is known about the freshwater plastisphere. This review seeks to provide a broad insight into the freshwater science of plastisphere in the light of marine plastisphere, including research gaps, suggestions, and rising concerns, which would be of interest to the public, policymakers, and stakeholders. Given that freshwaters are endangered ecosystems, it is imperative to understand the role and impact of plastisphere on freshwaters. Plastic debris, especially microplastics (size <5 mm) in freshwater ecosystems, provide a stable, persistent, and buoyant substrate for microbes. Although current evidence suggests that freshwater environmental conditions and microplastics' physical and chemical properties significantly influence microbial colonisation, its role and integration in the aquatic ecosystems are unknown. Considering that the plastisphere biodiversity is unique, we seek to establish why and how many species co-exist in the plastisphere. Evaluating such fundamental questions should advance our basic understanding of the resilience of plastisphere to the changing environment. Plastisphere microbes, including the pathogenic bacteria, were found in both systems demonstrating their ability to survive on the plastic fragments from one ecosystem to another. A significant concern regarding plastisphere is the potential freshwater dispersal of anthropogenic pollutants and invasive or pathogenic species. Notably, microplastics aggregates may serve as a food source for grazers, which opens the question of the extent to which it can impact freshwater food webs. To gain a thorough understanding of the interplay between microplastics and the biogeochemical cycle, further insight into plastisphere microbes' functional role is needed. This would shed light on the unconsidered freshwater elemental cycling pathways. Given the complexity and universal nature of the plastisphere, strong interdisciplinary global research initiatives or networks are required to address the emerging concerns of plastisphere in freshwaters.}, }
@article {pmid34523560, year = {2021}, author = {Trego, AC and Conall Holohan, B and Keating, C and Graham, A and O'Connor, S and Gerardo, M and Hughes, D and Ijaz, UZ and O'Flaherty, V}, title = {First proof of concept for full-scale, direct, low-temperature anaerobic treatment of municipal wastewater.}, journal = {Bioresource technology}, volume = {341}, number = {}, pages = {125786}, doi = {10.1016/j.biortech.2021.125786}, pmid = {34523560}, issn = {1873-2976}, mesh = {Anaerobiosis ; Bioreactors ; RNA, Ribosomal, 16S/genetics ; Sewage ; Temperature ; *Waste Disposal, Fluid ; *Wastewater ; }, abstract = {Municipal wastewater constitutes the largest fraction of wastewater, and yet treatment processes are largely removal-based. High-rate anaerobic digestion (AD) has revolutionised the sustainability of industrial wastewater treatment and could additionally provide an alternative for municipal wastewater. While AD of dilute municipal wastewater is common in tropical regions, the low temperatures of temperate climates has resulted in slow uptake. Here, we demonstrate for the first time, direct, high-rate, low-temperature AD of low-strength municipal wastewater at full-scale. An 88 m[3] hybrid reactor was installed at the municipal wastewater treatment plant in Builth Wells, UK and operated for 290 days. Ambient temperatures ranged from 2 to 18 °C, but remained below 15 °C for > 100 days. Influent BOD fluctuated between 2 and 200 mg L[-1]. However, BOD removal often reached > 85%. 16S rRNA amplicon sequencing of DNA from the biomass revealed a highly adaptable core microbiome. These findings could provide the basis for the next-generation of municipal wastewater treatment.}, }
@article {pmid34523363, year = {2023}, author = {De Vuyst, L and Comasio, A and Kerrebroeck, SV}, title = {Sourdough production: fermentation strategies, microbial ecology, and use of non-flour ingredients.}, journal = {Critical reviews in food science and nutrition}, volume = {63}, number = {15}, pages = {2447-2479}, doi = {10.1080/10408398.2021.1976100}, pmid = {34523363}, issn = {1549-7852}, mesh = {*Ecosystem ; Fermentation ; Bread/microbiology ; *Lactobacillales ; Yeasts ; Food Microbiology ; }, abstract = {Sourdough production is an ancient method to ferment flour from cereals for the manufacturing of baked goods. This review deals with the state-of-the-art of current fermentation strategies for sourdough production and the microbial ecology of mature sourdoughs, with a particular focus on the use of non-flour ingredients. Flour fermentation processes for sourdough production are typically carried out by heterogeneous communities of lactic acid bacteria and yeasts. Acetic acid bacteria may also occur, although their presence and role in sourdough production can be criticized. Based on the inoculum used, sourdough productions can be distinguished in fermentation processes using backslopping procedures, originating from a spontaneously fermented flour-water mixture (Type 1), starter culture-initiated fermentation processes (Type 2), and starter culture-initiated fermentation processes that are followed by backslopping (Type 3). In traditional recipes for the initiation and/or propagation of Type 1 sourdough productions, non-flour ingredients are often added to the flour-water mixture. These ingredients may be the source of an additional microbial inoculum and/or serve as (co-)substrates for fermentation. An example of the former is the addition of yoghurt; an example of the latter is the use of fruit juices. The survival of microorganisms transferred from the ingredients to the fermenting flour-water mixture depends on the competitiveness toward particular strains of the microbial species present under the harsh conditions of the sourdough ecosystem. Their survival and growth is also determined by the presence of the appropriate substrates, whether or not carried over by the ingredients added.}, }
@article {pmid34522990, year = {2022}, author = {Matsumoto, S and Watanabe, K and Imamura, A and Tachibana, M and Shimizu, T and Watarai, M}, title = {Comparative Analysis Between Paramecium Strains with Different Syngens Using the RAPD Method.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {594-602}, pmid = {34522990}, issn = {1432-184X}, support = {19K06383//Japan Society for the Promotion of Science/ ; 17H03914//Japan Society for the Promotion of Science/ ; }, mesh = {*Chlorella ; *Paramecium/genetics ; Random Amplified Polymorphic DNA Technique ; Symbiosis ; }, abstract = {Paramecium spp. are a genus of free-living protists that live mainly in freshwater environments. They are ciliates with high motility and phagocytosis and have been used to analyze cell motility and as a host model for pathogens. Besides such biological characteristics, apart from the usual morphological and genetic classification of species, the existence of taxonomies (such as syngens) and mating types related to Paramecium's unique reproduction is known. In this study, we attempted to develop a simple method to identify Paramecium strains, which are difficult to distinguish morphologically, using random amplified polymorphic DNA (RAPD) analysis. Consequently, we can observe strain-specific band patterns. We also confirm that the presence of endosymbiotic Chlorella cells affects the band pattern of P. bursaria. Furthermore, the results of the RAPD analysis using several P. caudatum strains with different syngens show that it is possible to detect a band specific to a certain syngen. By improving the reaction conditions and random primers, based on the results of this study, RAPD analysis can be applied to the identification of Paramecium strains and their syngen confirmation tests.}, }
@article {pmid34519519, year = {2021}, author = {Putman, LI and Sabuda, MC and Brazelton, WJ and Kubo, MD and Hoehler, TM and McCollom, TM and Cardace, D and Schrenk, MO}, title = {Microbial Communities in a Serpentinizing Aquifer Are Assembled through Strong Concurrent Dispersal Limitation and Selection.}, journal = {mSystems}, volume = {6}, number = {5}, pages = {e0030021}, pmid = {34519519}, issn = {2379-5077}, support = {NNA15BB02A//NASA | NASA Astrobiology Institute (NAI)/ ; }, abstract = {In recent years, our appreciation of the extent of habitable environments in Earth's subsurface has greatly expanded, as has our understanding of the biodiversity contained within. Most studies have relied on single sampling points, rather than considering the long-term dynamics of subsurface environments and their microbial populations. One such habitat are aquifers associated with the aqueous alteration of ultramafic rocks through a process known as serpentinization. Ecological modeling performed on a multiyear time series of microbiology, hydrology, and geochemistry in an ultrabasic aquifer within the Coast Range Ophiolite reveals that community assembly is governed by undominated assembly (i.e., neither stochastic [random] nor deterministic [selective] processes alone govern assembly). Controls on community assembly were further assessed by characterizing aquifer hydrogeology and microbial community adaptations to the environment. These analyses show that low permeability rocks in the aquifer restrict the transmission of microbial populations between closely situated wells. Alpha and beta diversity measures and metagenomic and metatranscriptomic data from microbial communities indicate that high pH and low dissolved inorganic carbon levels impose strong environmental selection on microbial communities within individual wells. Here, we find that the interaction between strong selection imposed by extreme pH and enhanced ecological drift due to dispersal limitation imposed by slow fluid flow results in the undominated assembly signal observed throughout the site. Strong environmental selection paired with extremely low dispersal in the subsurface results in low diversity microbial communities that are well adapted to extreme pH conditions and subject to enhanced stochasticity introduced by ecological drift over time. IMPORTANCE Microbial communities existing under extreme or stressful conditions have long been thought to be structured primarily by deterministic processes. The application of macroecology theory and modeling to microbial communities in recent years has spurred assessment of assembly processes in microbial communities, revealing that both stochastic and deterministic processes are at play to different extents within natural environments. We show that low diversity microbial communities in a hard-rock serpentinizing aquifer are assembled under the influence of strong selective processes imposed by high pH and enhanced ecological drift that occurs as the result of dispersal limitation due to the slow movement of water in the low permeability aquifer. This study demonstrates the important roles that both selection and dispersal limitation play in terrestrial serpentinites, where extreme pH assembles a microbial metacommunity well adapted to alkaline conditions and dispersal limitation drives compositional differences in microbial community composition between local communities in the subsurface.}, }
@article {pmid34518545, year = {2021}, author = {Chen, Y and Wang, Y and Paez-Espino, D and Polz, MF and Zhang, T}, title = {Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {5398}, pmid = {34518545}, issn = {2041-1723}, mesh = {Archaea/classification/genetics/virology ; Bacteria/classification/genetics/virology ; *Carbon Cycle ; Energy Metabolism/genetics ; Genes, Viral/genetics ; Genetic Variation ; Host-Pathogen Interactions ; Open Reading Frames/genetics ; Prokaryotic Cells/metabolism/*virology ; Sequence Analysis, DNA/methods ; Sewage/microbiology/*virology ; Virome/*genetics ; Viruses/classification/*genetics/metabolism ; Water Purification/*methods ; }, abstract = {As one of the largest biotechnological applications, activated sludge (AS) systems in wastewater treatment plants (WWTPs) harbor enormous viruses, with 10-1,000-fold higher concentrations than in natural environments. However, the compositional variation and host-connections of AS viruses remain poorly explored. Here, we report a catalogue of ~50,000 prokaryotic viruses from six WWTPs, increasing the number of described viral species of AS by 23-fold, and showing the very high viral diversity which is largely unknown (98.4-99.6% of total viral contigs). Most viral genera are represented in more than one AS system with 53 identified across all. Viral infection widely spans 8 archaeal and 58 bacterial phyla, linking viruses with aerobic/anaerobic heterotrophs, and other functional microorganisms controlling nitrogen/phosphorous removal. Notably, Mycobacterium, notorious for causing AS foaming, is associated with 402 viral genera. Our findings expand the current AS virus catalogue and provide reference for the phage treatment to control undesired microorganisms in WWTPs.}, }
@article {pmid34515628, year = {2021}, author = {Undabarrena, A and Pereira, CF and Kruasuwan, W and Parra, J and Sélem-Mojica, N and Vind, K and Schniete, JK}, title = {Integrating perspectives in actinomycete research: an ActinoBase review of 2020-21.}, journal = {Microbiology (Reading, England)}, volume = {167}, number = {9}, pages = {}, pmid = {34515628}, issn = {1465-2080}, support = {BB/S016651/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Actinobacteria/genetics ; Actinomyces ; Anti-Bacterial Agents ; Multigene Family ; Synthetic Biology ; }, abstract = {Last year ActinoBase, a Wiki-style initiative supported by the UK Microbiology Society, published a review highlighting the research of particular interest to the actinomycete community. Here, we present the second ActinoBase review showcasing selected reports published in 2020 and early 2021, integrating perspectives in the actinomycete field. Actinomycetes are well-known for their unsurpassed ability to produce specialised metabolites, of which many are used as therapeutic agents with antibacterial, antifungal, or immunosuppressive activities. Much research is carried out to understand the purpose of these metabolites in the environment, either within communities or in host interactions. Moreover, many efforts have been placed in developing computational tools to handle big data, simplify experimental design, and find new biosynthetic gene cluster prioritisation strategies. Alongside, synthetic biology has provided advances in tools to elucidate the biosynthesis of these metabolites. Additionally, there are still mysteries to be uncovered in understanding the fundamentals of filamentous actinomycetes' developmental cycle and regulation of their metabolism. This review focuses on research using integrative methodologies and approaches to understand the bigger picture of actinomycete biology, covering four research areas: i) technology and methodology; ii) specialised metabolites; iii) development and regulation; and iv) ecology and host interactions.}, }
@article {pmid34515591, year = {2023}, author = {Li, Q and Van de Wiele, T}, title = {Gut microbiota as a driver of the interindividual variability of cardiometabolic effects from tea polyphenols.}, journal = {Critical reviews in food science and nutrition}, volume = {63}, number = {11}, pages = {1500-1526}, doi = {10.1080/10408398.2021.1965536}, pmid = {34515591}, issn = {1549-7852}, mesh = {Humans ; Polyphenols/pharmacology/metabolism ; *Gastrointestinal Microbiome ; Tea/metabolism ; *Microbiota ; *Cardiovascular Diseases/prevention &amp; control ; }, abstract = {Tea polyphenols have been extensively studied for their preventive properties against cardiometabolic diseases. Nevertheless, the evidence of these effects from human intervention studies is not always consistent, mainly because of a large interindividual variability. The bioavailability of tea polyphenols is low, and metabolism of tea polyphenols highly depends on individual gut microbiota. The accompanying reciprocal relationship between tea polyphenols and gut microbiota may result in alterations in the cardiometabolic effects, however, the underlying mechanism of which is little explored. This review summarizes tea polyphenols-microbiota interaction and its contribution to interindividual variability in cardiometabolic effects. Currently, only a few bacteria that can biodegrade tea polyphenols have been identified and generated metabolites and their bioactivities in metabolic pathways are not fully elucidated. A deeper understanding of the role of complex interaction necessitates fully individualized data, the ntegration of multiple-omics platforms and development of polyphenol-centered databases. Knowledge of this microbial contribution will enable the functional stratification of individuals in the gut microbiota profile (metabotypes) to clarify interindividual variability in the health effects of tea polyphenols. This could be used to predict individual responses to tea polyphenols consumption, hence bringing us closer to personalized nutrition with optimal dose and additional supplementation of specific microorganisms.}, }
@article {pmid34512595, year = {2021}, author = {Tavares, TCL and Bezerra, WM and Normando, LRO and Rosado, AS and Melo, VMM}, title = {Brazilian Semi-Arid Mangroves-Associated Microbiome as Pools of Richness and Complexity in a Changing World.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {715991}, pmid = {34512595}, issn = {1664-302X}, abstract = {Mangrove microbiomes play an essential role in the fate of mangroves in our changing planet, but the factors regulating the biogeographical distribution of mangrove microbial communities remain essentially vague. This paper contributes to our understanding of mangrove microbiomes distributed along three biogeographical provinces and ecoregions, covering the exuberant mangroves of Amazonia ecoregion (North Brazil Shelf) as well as mangroves located in the southern limit of distribution (Southeastern ecoregion, Warm Temperate Southwestern Atlantic) and mangroves localized on the drier semi-arid coast (Northeastern ecoregion, Tropical Southwestern Atlantic), two important ecotones where poleward and landward shifts, respectively, are expected to occur related to climate change. This study compared the microbiomes associated with the conspicuous red mangrove (Rhizophora mangle) root soils encompassing soil properties, latitudinal factors, and amplicon sequence variants of 105 samples. We demonstrated that, although the northern and southern sites are over 4,000 km apart, and despite R. mangle genetic divergences between north and south populations, their microbiomes resemble each other more than the northern and northeastern neighbors. In addition, the northeastern semi-arid microbiomes were more diverse and displayed a higher level of complexity than the northern and southern ones. This finding may reflect the endurance of the northeast microbial communities tailored to deal with the stressful conditions of semi-aridity and may play a role in the resistance and growing landward expansion observed in such mangroves. Minimum temperature, precipitation, organic carbon, and potential evapotranspiration were the main microbiota variation drivers and should be considered in mangrove conservation and recovery strategies in the Anthropocene. In the face of changes in climate, land cover, biodiversity, and chemical composition, the richness and complexity harbored by semi-arid mangrove microbiomes may hold the key to mangrove adaptability in our changing planet.}, }
@article {pmid34512593, year = {2021}, author = {Zhao, J and Ma, J and Yang, Y and Yu, H and Zhang, S and Chen, F}, title = {Response of Soil Microbial Community to Vegetation Reconstruction Modes in Mining Areas of the Loess Plateau, China.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {714967}, pmid = {34512593}, issn = {1664-302X}, abstract = {Vegetation reconstruction and restoration is vital to the health of the mine land ecosystem. Different vegetations might change microbial community structure and function of soil, mediating the biogeochemical cycle and nutrition supply to the soil. To clarify the response of soil microbes to different vegetation reconstruction modes in the mining areas of the Loess Plateau, China, soil microbial community structures and functions were determined by the MiSeq high-throughput sequencing along with PICRUSt2 and FUNGuild tools. The fungal community richness was observed to be the highest in grassland soil and positively correlated with soil organic matter, total nitrogen, and nitrate-nitrogen. The bacterial and fungal community structures were similar in grassland and brushland areas, but were significantly differentiated in the coniferous and broadleaf forest, and the leading factors were soil pH and nitrate-nitrogen. Actinobacteriota, Proteobacteria, and Acidobacteriota were the dominant bacterial phyla under different vegetation reconstruction modes. The dominant phyla of fungi were Ascomycota, Basidiomycota, and Mortierellomycota. Different vegetation reconstruction modes did not affect the bacterial functional communities but shaped different functional groups of fungi. The grassland soil was dominated by saprotrophic fungi, while symbiotrophic fungi dominated the coniferous and broadleaf forests. The results suggested that shifts in vegetation reconstruction modes may alter the mining soil bacterial and fungal community structures and function. These findings improve the understanding of microbial ecology in the reclaimed mine soil and provide a reference for the ecological restoration of fragile mining ecosystems.}, }
@article {pmid34510242, year = {2022}, author = {Mikhailov, IS and Galachyants, YP and Bukin, YS and Petrova, DP and Bashenkhaeva, MV and Sakirko, MV and Blinov, VV and Titova, LA and Zakharova, YR and Likhoshway, YV}, title = {Seasonal Succession and Coherence Among Bacteria and Microeukaryotes in Lake Baikal.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {404-422}, pmid = {34510242}, issn = {1432-184X}, support = {0279-2021-0008//Ministry of Science and Higher Education of Russian Federation/ ; 0279-2021-0009//Ministry of Science and Higher Education of Russian Federation/ ; 0279-2021-0004//Ministry of Science and Higher Education of Russian Federation/ ; &#x410;&#x410;&#x410;&#x410;-&#x410;17-117041250054-8//Integration project of the Irkutsk Scientific Center state/ ; }, mesh = {Bacteria/genetics ; *Lakes/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Seasons ; }, abstract = {Microorganisms exhibit seasonal succession governed by physicochemical factors and interspecies interactions, yet drivers of this process in different environments remain to be determined. We used high-throughput sequencing of 16S rRNA and 18S rRNA genes to study seasonal dynamics of bacterial and microeukaryotic communities at pelagic site of Lake Baikal from spring (under-ice, mixing) to autumn (direct stratification). The microbial community was subdivided into distinctive coherent clusters of operational taxonomic units (OTUs). Individual OTUs were consistently replaced during different seasonal events. The coherent clusters change their contribution to the microbial community depending on season. Changes of temperature, concentrations of silicon, and nitrates are the key factors affected the structure of microbial communities. Functional prediction revealed that some bacterial or eukaryotic taxa that switched with seasons had similar functional properties, which demonstrate their functional redundancy. We have also detected specific functional properties in different coherent clusters of bacteria or microeukaryotes, which can indicate their ability to adapt to seasonal changes of environment. Our results revealed a relationship between seasonal succession, coherency, and functional features of freshwater bacteria and microeukaryotes.}, }
@article {pmid34505915, year = {2022}, author = {LaForgia, ML and Kang, H and Ettinger, CL}, title = {Invasive Grass Dominance over Native Forbs Is Linked to Shifts in the Bacterial Rhizosphere Microbiome.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {496-508}, pmid = {34505915}, issn = {1432-184X}, mesh = {Bacteria/genetics ; Humans ; *Microbiota/genetics ; Plant Roots/microbiology ; Plants ; Poaceae/genetics ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil Microbiology ; }, abstract = {Rhizosphere microbiomes have received growing attention in recent years for their role in plant health, stress tolerance, soil nutrition, and invasion. Still, relatively little is known about how these microbial communities are altered under plant competition, and even less about whether these shifts are tied to competitive outcomes between native and invasive plants. We investigated the structure and diversity of rhizosphere bacterial and fungal microbiomes of native annual forbs and invasive annual grasses grown in a shade-house both individually and in competition using high-throughput amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS region. We assessed how differentially abundant microbial families correlate to plant biomass under competition. We find that bacterial diversity and structure differ between native forbs and invasive grasses, but fungal diversity and structure do not. Furthermore, bacterial community structures under competition are distinct from individual bacterial community structures. We also identified five bacterial families that varied in normalized abundance between treatments and that were correlated with plant biomass under competition. We speculate that invasive grass dominance over these natives may be partially due to effects on the rhizosphere community, with changes in specific bacterial families potentially benefiting invaders at the expense of natives.}, }
@article {pmid34504476, year = {2021}, author = {Lammers, A and Zweers, H and Sandfeld, T and Bilde, T and Garbeva, P and Schramm, A and Lalk, M}, title = {Antimicrobial Compounds in the Volatilome of Social Spider Communities.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {700693}, pmid = {34504476}, issn = {1664-302X}, abstract = {Social arthropods such as termites, ants, and bees are among others the most successful animal groups on earth. However, social arthropods face an elevated risk of infections due to the dense colony structure, which facilitates pathogen transmission. An interesting hypothesis is that social arthropods are protected by chemical compounds produced by the arthropods themselves, microbial symbionts, or plants they associate with. Stegodyphus dumicola is an African social spider species, inhabiting communal silk nests. Because of the complex three-dimensional structure of the spider nest antimicrobial volatile organic compounds (VOCs) are a promising protection against pathogens, because of their ability to diffuse through air-filled pores. We analyzed the volatilomes of S. dumicola, their nests, and capture webs in three locations in Namibia and assessed their antimicrobial potential. Volatilomes were collected using polydimethylsiloxane (PDMS) tubes and analyzed using GC/Q-TOF. We showed the presence of 199 VOCs and tentatively identified 53 VOCs. More than 40% of the tentatively identified VOCs are known for their antimicrobial activity. Here, six VOCs were confirmed by analyzing pure compounds namely acetophenone, 1,3-benzothiazole, 1-decanal, 2-decanone, 1-tetradecene, and docosane and for five of these compounds the antimicrobial activity were proven. The nest and web volatilomes had many VOCs in common, whereas the spider volatilomes were more differentiated. Clear differences were identified between the volatilomes from the different sampling sites which is likely justified by differences in the microbiomes of the spiders and nests, the plants, and the different climatic conditions. The results indicate the potential relevance of the volatilomes for the ecological success of S. dumicola.}, }
@article {pmid34499191, year = {2022}, author = {Yaghoubi Khanghahi, M and Crecchio, C and Verbruggen, E}, title = {Shifts in the Rhizosphere and Endosphere Colonizing Bacterial Communities Under Drought and Salinity Stress as Affected by a Biofertilizer Consortium.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {483-495}, pmid = {34499191}, issn = {1432-184X}, mesh = {Bacteria ; *Droughts ; Endophytes/physiology ; Fertilizers ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Salt Stress ; Soil Microbiology ; }, abstract = {The present research asks how plant growth-promoting bacterial (PGPB) inoculants and chemical fertilizers change rhizosphere and root endophytic bacterial communities in durum wheat, and its dependence on environmental stress. A greenhouse experiment was carried out under drought (at 40% field capacity), or salinity (150 mM NaCl) conditions to investigate the effects of a chemical fertilizer (containing nitrogen, phosphorus, potassium and zinc) or a biofertilizer (a bacterial consortium of four PGPBs). High-throughput amplicon sequencing of the 16S rRNA of the rhizosphere, non-sterilized, or surface-sterilized roots, showed shifts in bacterial communities in response to stress treatments, which were greater for salinity than for drought and tended to show increased oligotrophs relative abundances compared to non-stress controls. The results also showed that Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes, Thaumarchaeota, Firmicutes, and Verrucomicrobia had a higher relative abundance in the rhizosphere, while Actinobacteria were more abundant on roots, while Candidatus_Saccharibacteria and Planctomycetes inside roots. The results indicated that the root endophytic bacterial communities were more affected by (bio-) fertilization treatments than those in the rhizosphere, particularly as affected by PGPB inoculation. This greater susceptibility of endophytes to (bio-) fertilizers was associated with increased abundance of the 16S rRNA and acdS genes in plant roots, especially under stress conditions. These changes in root endophytes, which coincided with an improvement in grain yield and photosynthetic capacity of plants, may be considered as one of the mechanisms by which PGPB affect plants.}, }
@article {pmid34498120, year = {2022}, author = {Silva, AMM and Estrada-Bonilla, GA and Lopes, CM and Matteoli, FP and Cotta, SR and Feiler, HP and Rodrigues, YF and Cardoso, EJBN}, title = {Does Organomineral Fertilizer Combined with Phosphate-Solubilizing Bacteria in Sugarcane Modulate Soil Microbial Community and Functions?.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {539-555}, pmid = {34498120}, issn = {1432-184X}, support = {01.13.0209.00//Financiadora de Estudos e Projetos/ ; 2016/18944-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {Bacteria ; Fertilizers/analysis ; *Microbiota ; Phosphates ; *Saccharum ; Soil ; Soil Microbiology ; }, abstract = {Soil bacterial and fungal communities are suitable soil ecosystem health indicators due to their sensitivity to management practices and their role in soil ecosystem processes. Here, information on composition and functions of bacterial and fungal communities were evaluated at two phenological stages of sugarcane (six and twelve months, equivalent to the most intensive vegetative stage and to final maturation, respectively) when organomineral fertilizer, combined with phosphate-solubilizing bacteria (PSB), was added into the soil. Organic compost enriched with apatite (C + A) or phosphorite (C + P) and compost without phosphate enrichment (C) were used in the presence or absence of PSB. In addition, we used a control fertilized with soluble triple superphosphate. The differences were more related to the sampling period than to the type of organomineral fertilizer, being observed higher available phosphorus at six months than at twelve months. Only in the C treatment we observed the presence of Bacillaceae and Planococcaceae, while Pseudomonadaceae were only prevalent in inoculated C + A. As for fungi, the genera Chaetomium and Achroiostachys were only present in inoculated C + P, while the genus Naganishia was most evident in inoculated C + A and in uninoculated C + P. Soliccocozyma represented 75% of the total fungal abundance in uninoculated C while in inoculated C, it represented 45%. The bacterial community was more related to the degradation of easily decomposable organic compounds, while the fungal community was more related to degradation of complex organic compounds. Although the microbial community showed a resilient trait, subtle changes were detected in microbial community composition and function, and this may be related to the increase in yield observed.}, }
@article {pmid34498119, year = {2022}, author = {Yun, J and Jung, JY and Kwon, MJ and Seo, J and Nam, S and Lee, YK and Kang, H}, title = {Temporal Variations Rather than Long-Term Warming Control Extracellular Enzyme Activities and Microbial Community Structures in the High Arctic Soil.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {168-181}, pmid = {34498119}, issn = {1432-184X}, support = {NRF-2019H1A2A1076239//Ministry of Education/ ; NRF-2016M1A5A1901770, PN20081//Ministry of Science and ICT of Korea/ ; NRF-2016M1A5A1901795//Ministry of Science and ICT of Korea/ ; NRF-2020M1A5A1110494//Ministry of Science and ICT of Korea/ ; }, mesh = {Arctic Regions ; *Greenhouse Gases ; Hydrolases ; *Microbiota ; Soil/chemistry ; Soil Microbiology ; }, abstract = {In Arctic soils, warming accelerates decomposition of organic matter and increases emission of greenhouse gases (GHGs), contributing to a positive feedback to climate change. Although microorganisms play a key role in the processes between decomposition of organic matter and GHGs emission, the effects of warming on temporal responses of microbial activity are still elusive. In this study, treatments of warming and precipitation were conducted from 2012 to 2018 in Cambridge Bay, Canada. Soils of organic and mineral layers were collected monthly from June to September in 2018 and analyzed for extracellular enzyme activities and bacterial community structures. The activity of hydrolases was the highest in June and decreased thereafter over summer in both organic and mineral layers. Bacterial community structures changed gradually over summer, and the responses were distinct depending on soil layers and environmental factors; water content and soil temperature affected the shift of bacterial community structures in both layers, whereas bacterial abundance, dissolved organic carbon, and inorganic nitrogen did so in the organic layer only. The activity of hydrolases and bacterial community structures did not differ significantly among treatments but among months. Our results demonstrate that temporal variations may control extracellular enzyme activities and microbial community structure rather than the small effect of warming over a long period in high Arctic soil. Although the effects of the treatments on microbial activity were minor, our study provides insight that microbial activity may increase due to an increase in carbon availability, if the growing season is prolonged in the Arctic.}, }
@article {pmid34498118, year = {2022}, author = {Minahan, NT and Chen, CH and Shen, WC and Lu, TP and Kallawicha, K and Tsai, KH and Guo, YL}, title = {Fungal Spore Richness in School Classrooms is Related to Surrounding Forest in a Season-Dependent Manner.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {351-362}, pmid = {34498118}, issn = {1432-184X}, support = {MOST 108-2621-M-002-018//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Air Microbiology ; *Allergens/genetics ; Child ; *Forests ; Fungi/genetics ; Humans ; Schools ; Seasons ; Spores, Fungal ; }, abstract = {Airborne fungal spores are important aeroallergens that are remarkably diverse in terms of taxonomic richness. Indoor fungal richness is dominated by outdoor fungi and is geographically patterned, but the influence of natural landscape is unclear. We aimed to elucidate the relationship between indoor fungal spore richness and natural landscape by examining the amount of surrounding forest cover. Passive sampling of airborne fungal spores was conducted in 24 schools in Taiwan during hot and cool seasons, and amplicon sequencing was used to study fungal spore (genus) richness targeting the internal transcribed spacer 2 (ITS2) region. In total, 693 fungal genera were identified, 12 of which were ubiquitous. Despite overall similarity of fungal spore richness between seasons, Basidiomycota and Ascomycota richness increased during the hot and cool seasons, respectively. Fungal spore richness in schools had a strong positive correlation with the amount of surrounding forest cover during the cool season, but not during the hot season. Fungal assemblages in schools were more similar during the hot season due to the increased ubiquity of Agaricomycetes genera. These observations indicate dispersal limitation at the kilometer scale during the cool season and increased long-distance dispersal during the hot season. Several allergenic fungi were commonly identified in schools, including some previously overlooked by conventional methods, which may be targeted as sensitizing agents in future investigations into atopic conditions. More generally, the relative importance of fungal spore richness in the development, chronicity, and severity of atopic conditions in children requires investigation.}, }
@article {pmid34495440, year = {2021}, author = {Xie, J and Wang, X and Xu, J and Xie, H and Cai, Y and Liu, Y and Ding, X}, title = {Strategies and Structure Feature of the Aboveground and Belowground Microbial Community Respond to Drought in Wild Rice (Oryza longistaminata).}, journal = {Rice (New York, N.Y.)}, volume = {14}, number = {1}, pages = {79}, pmid = {34495440}, issn = {1939-8425}, support = {81960364//national natural science foundation of china/ ; 31560041//national natural science foundation of china/ ; 81501162//national natural science foundation of china/ ; 20171BCB23020//jiangxi province outstanding young talents funding scheme/ ; 9166-27060003-YB11//interdisciplinary innovation fund of nanchang university/ ; }, abstract = {BACKGROUND: Drought is global environmental stress that limits crop yields. Plant-associated microbiomes play a crucial role in determining plant fitness in response to drought, yet the fundamental mechanisms for maintaining microbial community stability under drought disturbances in wild rice are poorly understood. We make explicit comparisons of leaf, stem, root and rhizosphere microbiomes from the drought-tolerant wild rice (Oryza longistaminata) in response to drought stress.<br><br>RESULTS: We find that the response of the wild rice microbiome to drought was divided into aboveground-underground patterns. Drought reduced the leaf and stem microbial community diversity and networks stability, but not that of the roots and rhizospheres. Contrary to the aboveground microbial networks, the drought-negative response taxa exhibited much closer interconnections than the drought-positive response taxa and were the dominant network hubs of belowground co-occurrence networks, which may contribute to the stability of the belowground network. Notably, drought induces enrichment of Actinobacteria in belowground compartments, but not the aboveground compartment. Additionally, the rhizosphere microbiome exhibited a higher proportion of generalists and broader habitat niche breadth than the microbiome at other compartments, and drought enhanced the proportion of specialists in all compartments. Null model analysis revealed that both the aboveground and belowground-community were governed primarily by the stochastic assembly process, moreover, drought decreased 'dispersal limitation', and enhanced 'drift'.<br><br>CONCLUSIONS: Our results provide new insight into the different strategies and assembly mechanisms of the above and belowground microbial community in response to drought, including enrichment of taxonomic groups, and highlight the important role of the stochastic assembly process in shaping microbial community under drought stress.}, }
@article {pmid34495359, year = {2022}, author = {Agarwal, R and Gupta, M and Antony, A and Sen, R and Raychoudhury, R}, title = {In Vitro Studies Reveal that Pseudomonas, from Odontotermes obesus Colonies, can Function as a Defensive Mutualist as it Prevents the Weedy Fungus While Keeping the Crop Fungus Unaffected.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {391-403}, pmid = {34495359}, issn = {1432-184X}, mesh = {Animals ; Fungi ; *Isoptera/microbiology ; Plant Weeds/genetics ; Pseudomonas/genetics ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Insects that farm monocultures of fungi are canonical examples of nutritional symbiosis as well as independent evolution of agriculture in non-human animals. But just like in human agriculture, these fungal crops face constant threat of invasion by weeds which, if unchecked, take over the crop fungus. In fungus-growing termites, the crop fungus (Termitomyces) faces such challenges from the weedy fungus Pseudoxylaria. The mechanism by which Pseudoxylaria is suppressed is not known. However, evidence suggests that some bacterial secondary symbionts can serve as defensive mutualists by preventing the growth of Pseudoxylaria. However, such secondary symbionts must possess the dual, yet contrasting, capabilities of suppressing the weedy fungus while keeping the growth of the crop fungus unaffected. This study describes the isolation, identification, and culture-dependent estimation of the roles of several such putative defensive mutualists from the colonies of the wide-spread fungus-growing termite from India, Odontotermes obesus. From the 38 bacterial cultures tested, a strain of Pseudomonas showed significantly greater suppression of the weedy fungus than the crop fungus. Moreover, a 16S rRNA pan-microbiome survey, using the Nanopore platform, revealed Pseudomonas to be a part of the core microbiota of O. obesus. A meta-analysis of microbiota composition across different species of Odontotermes also confirms the widespread prevalence of Pseudomonas within this termite. These lines of evidence indicate that Pseudomonas could be playing the role of defensive mutualist within Odontotermes.}, }
@article {pmid34494852, year = {2021}, author = {Ma, L and Huang, X and Wang, H and Yun, Y and Cheng, X and Liu, D and Lu, X and Qiu, X}, title = {Microbial Interactions Drive Distinct Taxonomic and Potential Metabolic Responses to Habitats in Karst Cave Ecosystem.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0115221}, pmid = {34494852}, issn = {2165-0497}, mesh = {Actinobacteria/classification/isolation &amp; purification/*metabolism ; Bacterial Physiological Phenomena ; Carbon Cycle/physiology ; Caves/*microbiology ; Ecosystem ; Geologic Sediments/*microbiology ; Microbial Interactions/*physiology ; Nitrogen Fixation/physiology ; Proteobacteria/classification/isolation &amp; purification/*metabolism ; Soil Microbiology ; }, abstract = {The geological role of microorganisms has been widely studied in the karst cave ecosystem. However, microbial interactions and ecological functions in such a dark, humid, and oligotrophic habitat have received far less attention, which is crucial to understanding cave biogeochemistry. Herein, microorganisms from weathered rock and sediment along the Heshang Cave depth were analyzed by random matrix theory-based network and Tax4Fun functional prediction. The results showed that although the cave microbial communities have spatial heterogeneity, differential habitats drove the community structure and diversity. Actinobacteria were predominant in weathered rock, whereas Proteobacteria dominated the sediment. The sediment communities presented significantly higher alpha diversities due to the relatively abundant nutrition from the outside by the intermittent stream. Consistently, microbial interactions in sediment were more complex, as visualized by more nodes and links. The abundant taxa presented more positive correlations with other community members in both of the two networks, indicating that they relied on promotion effects to adapt to the extreme environment. The keystones in weathered rock were mainly involved in the biodegradation of organic compounds, whereas the keystone Nitrospira in sediment contributed to carbon/nitrogen fixation. Collectively, these findings suggest that microbial interactions may lead to distinct taxonomic and functional communities in weathered rock and sediment in the subsurface Heshang Cave. IMPORTANCE In general, the constant physicochemical conditions and limited nutrient sources over long periods in the subsurface support a stable ecosystem in karst cave. Previous studies on cave microbial ecology were mostly focused on community composition, diversity, and the relationship with local environmental factors. There are still many unknowns about the microbial interactions and functions in such a dark environment with little human interference. Two representative habitats, including weathered rock and sediment in Heshang Cave, were selected to give an integrated insight into microbial interactions and potential functions. The cooccurrence network, especially the subnetwork, was used to characterize the cave microbial interactions in detail. We demonstrated that abundant taxa primarily relied on promotion effects rather than inhibition effects to survive in Heshang Cave. Keystone species may play important metabolic roles in sustaining ecological functions. Our study provides improved understanding of microbial interaction patterns and community ecological functions in the karst cave ecosystem.}, }
@article {pmid34493269, year = {2021}, author = {Hadjirin, NF and Miller, EL and Murray, GGR and Yen, PLK and Phuc, HD and Wileman, TM and Hernandez-Garcia, J and Williamson, SM and Parkhill, J and Maskell, DJ and Zhou, R and Fittipaldi, N and Gottschalk, M and Tucker, AWD and Hoa, NT and Welch, JJ and Weinert, LA}, title = {Large-scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis.}, journal = {BMC biology}, volume = {19}, number = {1}, pages = {191}, pmid = {34493269}, issn = {1741-7007}, support = {MR/N002660/1/MRC_/Medical Research Council/United Kingdom ; MR/R002762/1/MRC_/Medical Research Council/United Kingdom ; BB/L003902/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/G019274/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Anti-Infective Agents ; Drug Resistance, Bacterial/genetics ; Genomics ; Microbial Sensitivity Tests ; Pharmaceutical Preparations ; *Streptococcus suis/drug effects/genetics ; Swine ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is among the gravest threats to human health and food security worldwide. The use of antimicrobials in livestock production can lead to emergence of AMR, which can have direct effects on humans through spread of zoonotic disease. Pigs pose a particular risk as they are a source of zoonotic diseases and receive more antimicrobials than most other livestock. Here we use a large-scale genomic approach to characterise AMR in Streptococcus suis, a commensal found in most pigs, but which can also cause serious disease in both pigs and humans.<br><br>RESULTS: We obtained replicated measures of Minimum Inhibitory Concentration (MIC) for 16 antibiotics, across a panel of 678 isolates, from the major pig-producing regions of the world. For several drugs, there was no natural separation into 'resistant' and 'susceptible', highlighting the need to treat MIC as a quantitative trait. We found differences in MICs between countries, consistent with their patterns of antimicrobial usage. AMR levels were high even for drugs not used to treat S. suis, with many multidrug-resistant isolates. Similar levels of resistance were found in pigs and humans from regions associated with zoonotic transmission. We next used whole genome sequences for each isolate to identify 43 candidate resistance determinants, 22 of which were novel in S. suis. The presence of these determinants explained most of the variation in MIC. But there were also interesting complications, including epistatic interactions, where known resistance alleles had no effect in some genetic backgrounds. Beta-lactam resistance involved many core genome variants of small effect, appearing in a characteristic order.<br><br>CONCLUSIONS: We present a large dataset allowing the analysis of the multiple contributing factors to AMR in S. suis. The high levels of AMR in S. suis that we observe are reflected by antibiotic usage patterns but our results confirm the potential for genomic data to aid in the fight against AMR.}, }
@article {pmid34491099, year = {2022}, author = {Su, L and Qiu, P and Fang, Z and Sun, J and Mo, X and Liu, Y and Kuramae, EE and Zhang, R and Shen, B and Shen, Q}, title = {Potassium Phosphite Enhances the Antagonistic Capability of Bacillus amyloliquefaciens to Manage Tomato Bacterial Wilt.}, journal = {Plant disease}, volume = {106}, number = {2}, pages = {654-660}, doi = {10.1094/PDIS-08-21-1601-RE}, pmid = {34491099}, issn = {0191-2917}, mesh = {*Bacillus amyloliquefaciens/physiology ; *Biological Control Agents ; *Solanum lycopersicum/microbiology ; Phosphites ; *Plant Diseases/microbiology/prevention &amp; control ; *Potassium Compounds ; *Ralstonia solanacearum/pathogenicity ; }, abstract = {Bacterial wilt caused by Ralstonia solanacearum is a distributed and worldwide soilborne disease. The application of biocontrol microbes or agricultural chemicals has been widely used to manage tomato bacterial wilt. However, whether and how agricultural chemicals affect the antagonistic ability of biocontrol microbes is still unknown. Here, we combined potassium phosphite (K-Phite), an environmentally friendly agricultural chemical, and the biocontrol agent Bacillus amyloliquefaciens QPF8 (strain F8) to manage tomato bacterial wilt disease. First, K-Phite at a concentration of 0.05% (wt/vol) could significantly inhibit the growth of R. solanacearum. Second, 0.05% K-Phite enhanced the antagonistic capability of B. amyloliquefaciens F8. Third, the greenhouse soil experiments showed that the control efficiency for tomato bacterial wilt in the combined treatment was significantly higher than that of the application of B. amyloliquefaciens F8 or K-Phite alone. Overall, our results highlighted a novel strategy for the control of tomato bacterial wilt disease via application and revealed a new integrated pattern depending on the enhancement of the antagonistic capability of biocontrol microbes by K-Phite.}, }
@article {pmid34490209, year = {2021}, author = {Medvecky, M and Mandalakis, M}, title = {PepMANDIS: A Peptide Selection Tool for Designing Function-Based Targeted Proteomic Assays in Complex Microbial Systems.}, journal = {Frontiers in chemistry}, volume = {9}, number = {}, pages = {722087}, pmid = {34490209}, issn = {2296-2646}, abstract = {The majority of studies focusing on microbial functioning in various environments are based on DNA or RNA sequencing techniques that have inherent limitations and usually provide a distorted picture about the functional status of the studied system. Untargeted proteomics is better suited for that purpose, but it suffers from low efficiency when applied in complex consortia. In practice, the scanning capabilities of the currently employed LC-MS/MS systems provide limited coverage of key-acting proteins, hardly allowing a semiquantitative assessment of the most abundant ones from most prevalent species. When particular biological processes of high importance are under investigation, the analysis of specific proteins using targeted proteomics is a more appropriate strategy as it offers superior sensitivity and comes with the added benefits of increased throughput, dynamic range and selectivity. However, the development of targeted assays requires a priori knowledge regarding the optimal peptides to be screened for each protein of interest. In complex, multi-species systems, a specific biochemical process may be driven by a large number of homologous proteins having considerable differences in their amino acid sequence, complicating LC-MS/MS detection. To overcome the complexity of such systems, we have developed an automated pipeline that interrogates UniProt database or user-created protein datasets (e.g. from metagenomic studies) to gather homolog proteins with a defined functional role and extract respective peptide sequences, while it computes several protein/peptide properties and relevant statistics to deduce a small list of the most representative, process-specific and LC-MS/MS-amenable peptides for the microbial enzymatic activity of interest.}, }
@article {pmid34487274, year = {2021}, author = {Benedek, T and Szentgyörgyi, F and Gergócs, V and Menashe, O and Gonzalez, PAF and Probst, AJ and Kriszt, B and Táncsics, A}, title = {Potential of Variovorax paradoxus isolate BFB1_13 for bioremediation of BTEX contaminated sites.}, journal = {AMB Express}, volume = {11}, number = {1}, pages = {126}, pmid = {34487274}, issn = {2191-0855}, support = {TKP2020-IKA-12//ministry of innovation and technology/ ; 2018-2.1.16-T&#xc9;T-IL-2018-00002//nemzeti kutat&#xe1;si fejleszt&#xe9;si &#xe9;s innov&#xe1;ci&#xf3;s hivatal/ ; FK 134439//otka young researcher excellence programme/ ; }, abstract = {Here, we report and discuss the applicability of Variovorax paradoxus strain BFB1_13 in the bioremediation of BTEX contaminated sites. Strain BFB1_13 was capable of degrading all the six BTEX-compounds under both aerobic (O2 conc. 8 mg l[-1]) and micro-aerobic/oxygen-limited (O2 conc. 0.5 mg l[-1]) conditions using either individual (8 mg‧l[-1]) or a mixture of compounds (~ 1.3 mg‧l[-1] of each BTEX compound). The BTEX biodegradation capability of SBP-encapsulated cultures (SBP-Small Bioreactor Platform) was also assessed. The fastest degradation rate was observed in the case of aerobic benzene biodegradation (8 mg l[-1] per 90 h). Complete biodegradation of other BTEX occurred after at least 168 h of incubation, irrespective of the oxygenation and encapsulation. No statistically significant difference was observed between aerobic and microaerobic BTEX biodegradation. Genes involved in BTEX biodegradation were annotated and degradation pathways were predicted based on whole-genome shotgun sequencing and metabolic analysis. We conclude that V. paradoxus strain BFB1_13 could be used for the development of reactive biobarriers for the containment and in situ decontamination of BTEX contaminated groundwater plumes. Our results suggest that V. paradoxus strain BFB1_13-alone or in co-culture with other BTEX degrading bacterial isolates-can be a new and efficient commercial bioremediation agent for BTEX contaminated sites.}, }
@article {pmid34487212, year = {2022}, author = {Wahdan, SFM and Hossen, S and Tanunchai, B and Sansupa, C and Schädler, M and Noll, M and Dawoud, TM and Wu, YT and Buscot, F and Purahong, W}, title = {Life in the Wheat Litter: Effects of Future Climate on Microbiome and Function During the Early Phase of Decomposition.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {90-105}, pmid = {34487212}, issn = {1432-184X}, mesh = {Bacteria/genetics ; Ecosystem ; Fungi/genetics ; *Microbiota ; Plant Leaves/microbiology ; *Triticum ; }, abstract = {Even though it is widely acknowledged that litter decomposition can be impacted by climate change, the functional roles of microbes involved in the decomposition and their answer to climate change are less understood. This study used a field experimental facility settled in Central Germany to analyze the effects of ambient vs. future climate that is expected in 50-80 years on mass loss and physicochemical parameters of wheat litter in agricultural cropland at the early phase of litter decomposition process. Additionally, the effects of climate change were assessed on microbial richness, community compositions, interactions, and their functions (production of extracellular enzymes), as well as litter physicochemical factors shaping their colonization. The initial physicochemical properties of wheat litter did not change between both climate conditions; however, future climate significantly accelerated litter mass loss as compared with ambient one. Using MiSeq Illumina sequencing, we found that future climate significantly increased fungal richness and altered fungal communities over time, while bacterial communities were more resistant in wheat residues. Changes on fungal richness and/or community composition corresponded to different physicochemical factors of litter under ambient (Ca[2+], and pH) and future (C/N, N, P, K[+], Ca[2+], pH, and moisture) climate conditions. Moreover, highly correlative interactions between richness of bacteria and fungi were detected under future climate. Furthermore, the co-occurrence networks patterns among dominant microorganisms inhabiting wheat residues were strongly distinct between future and ambient climates. Activities of microbial β-glucosidase and N-acetylglucosaminidase in wheat litter were increased over time. Such increased enzymatic activities were coupled with a significant positive correlation between microbial (both bacteria and fungi) richness and community compositions with these two enzymatic activities only under future climate. Overall, we provide evidence that future climate significantly impacted the early phase of wheat litter decomposition through direct effects on fungal communities and through indirect effects on microbial interactions as well as corresponding enzyme production.}, }
@article {pmid34487211, year = {2022}, author = {Deng, J and Yu, D and Zhou, W and Zhou, L and Zhu, W}, title = {Variations of Phyllosphere and Rhizosphere Microbial Communities of Pinus koraiensis Infected by Bursaphelenchus xylophilus.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {285-301}, pmid = {34487211}, issn = {1432-184X}, support = {E0381601//the Mission of Chinese Academy of Sciences/ ; }, mesh = {Animals ; Bacteria ; *Microbiota ; *Nematoda ; *Pinus/microbiology ; Plant Diseases/microbiology ; Rhizosphere ; Xylophilus ; }, abstract = {Pine wood nematode, Bursaphelenchus xylophilus, as one of the greatest threats to pine trees, is spreading all over the world. Plant microorganisms play an important role in the pathogenesis of nematodes. The phyllosphere and rhizosphere bacterial and fungal communities associated with healthy Pinus koraiensis (PKa) and P. koraiensis infected by B. xylophilus at the early (PKb) and last (PKc) stages were analyzed. Our results demonstrated that pine wood nematode (PWD) could increase the phyllosphere bacterial Pielou_e, Shannon, and Simpson index; phyllosphere fungal Chao 1 index, as well as rhizosphere bacterial Pielou_e, Shannon, and Simpson index; and rhizosphere fungal Pielou_e, Shannon, and Simpson index. What's more, slight shifts of the microbial diversity were observed at the early stage of infection, and the microbial diversity increased significantly as the symptoms of infection worsened. With the infection of B. xylophilus in P. koraiensis, Bradyrhizobium (rhizosphere bacteria), Massilia (phyllosphere bacteria), and Phaeosphaeriaceae (phyllosphere fungi) were the major contributors to the differences in community compositions among different treatments. With the infection of PWD, most of the bacterial groups tended to be co-excluding rather than co-occurring. These changes would correlate with microbial ability to suppress plant pathogen, enhancing the understanding of disease development and providing guidelines to pave the way for its possible management.}, }
@article {pmid34486723, year = {2021}, author = {Stephen, AS and Dhadwal, N and Nagala, V and Gonzales-Marin, C and Gillam, DG and Bradshaw, DJ and Burnett, GR and Allaker, RP}, title = {Interdental and subgingival microbiota may affect the tongue microbial ecology and oral malodour in health, gingivitis and periodontitis.}, journal = {Journal of periodontal research}, volume = {56}, number = {6}, pages = {1174-1184}, doi = {10.1111/jre.12931}, pmid = {34486723}, issn = {1600-0765}, support = {//GlaxoSmithKline/ ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Chronic Periodontitis ; *Dental Plaque ; *Gingivitis ; *Halitosis ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Tongue ; }, abstract = {BACKGROUND AND OBJECTIVE: Oral malodour is often observed in gingivitis and chronic periodontitis patients, and the tongue microbiota is thought to play a major role in malodorous gas production, including volatile sulphur compounds (VSCs) such as hydrogen sulphide (H2 S) and methanethiol (CH3 SH). This study aimed to examine the link between the presence of VSCs in mouth air (as a marker of oral malodour) and the oral bacterial ecology in the tongue and periodontal niches of healthy, gingivitis and periodontitis patients.<br><br>METHODS: Participants were clinically assessed using plaque index, bleeding on probing (BOP) and periodontal probing depths, and VSC concentrations in their oral cavity measured using a portable gas chromatograph. Tongue scrapings, subgingival and interdental plaque were collected from healthy individuals (n&#xa0;=&#xa0;22), and those with gingivitis (n&#xa0;=&#xa0;14) or chronic periodontitis (n&#xa0;=&#xa0;15). The bacterial 16S rRNA gene region V3-V4 in these samples was sequenced, and the sequences were analysed using the minimum entropy decomposition pipeline.<br><br>RESULTS: Elevated VSC concentrations and CH3 SH:H2 S were observed in periodontitis compared with health. Significant ecological differences were observed in the tongue microbiota of healthy subjects with high plaque scores compared to low plaque scores, suggesting a possible connection between the microbiota of the tongue and the periodontium and that key dysbiotic changes may be initiated in the clinically healthy individuals who have higher dental plaque accumulation. Greater subgingival bacterial diversity was positively associated with H2 S in mouth air. Periodontopathic bacteria known to be prolific VSC producers increased in abundance on the tongue associated with increased bleeding on probing (BOP) and total percentage of periodontal pockets >6&#xa0;mm, supporting the suggestion that the tongue may become a reservoir for periodontopathogens.<br><br>CONCLUSION: This study highlights the importance of the periodontal microbiota in malodour and has detected dysbiotic changes in the tongue microbiota in periodontitis.}, }
@article {pmid34480872, year = {2021}, author = {Seki, D and Mayer, M and Hausmann, B and Pjevac, P and Giordano, V and Goeral, K and Unterasinger, L and Klebermaß-Schrehof, K and De Paepe, K and Van de Wiele, T and Spittler, A and Kasprian, G and Warth, B and Berger, A and Berry, D and Wisgrill, L}, title = {Aberrant gut-microbiota-immune-brain axis development in premature neonates with brain damage.}, journal = {Cell host &amp; microbe}, volume = {29}, number = {10}, pages = {1558-1572.e6}, pmid = {34480872}, issn = {1934-6069}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; P 27831/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/classification/genetics/growth &amp; development/isolation &amp; purification ; Brain/growth &amp; development ; Brain Injuries/*immunology/*microbiology/physiopathology ; Female ; *Gastrointestinal Microbiome ; Humans ; Immune System/growth &amp; development ; Infant, Newborn ; Infant, Premature/*growth &amp; development/immunology ; Male ; T-Lymphocytes/immunology ; Vascular Endothelial Growth Factor A/genetics/immunology ; }, abstract = {Premature infants are at substantial risk for suffering from perinatal white matter injury. Though the gut microbiota has been implicated in early-life development, a detailed understanding of the gut-microbiota-immune-brain axis in premature neonates is lacking. Here, we profiled the gut microbiota, immunological, and neurophysiological development of 60 extremely premature infants, which received standard hospital care including antibiotics and probiotics. We found that maturation of electrocortical activity is suppressed in infants with severe brain damage. This is accompanied by elevated γδ T cell levels and increased T cell secretion of vascular endothelial growth factor and reduced secretion of neuroprotectants. Notably, Klebsiella overgrowth in the gut is highly predictive for brain damage and is associated with a pro-inflammatory immunological tone. These results suggest that aberrant development of the gut-microbiota-immune-brain axis may drive or exacerbate brain injury in extremely premature neonates and represents a promising target for novel intervention strategies.}, }
@article {pmid34477968, year = {2021}, author = {Deepika, S and Kothamasi, D}, title = {Plant hosts may influence arbuscular mycorrhizal fungal community composition in mangrove estuaries.}, journal = {Mycorrhiza}, volume = {31}, number = {6}, pages = {699-711}, pmid = {34477968}, issn = {1432-1890}, support = {894188//h2020 marie sk&#x142;odowska-curie actions/ ; }, mesh = {Ecosystem ; Estuaries ; *Mycobiome ; *Mycorrhizae/genetics ; Plant Roots ; Soil ; Soil Microbiology ; }, abstract = {We investigated the role of plant host and soil variables in determining arbuscular mycorrhizal fungi (AMF) community composition in plant roots of two spatially separated mangrove estuaries on the rivers Aghanashini (14° 30' 30″ N-74° 22' 44″ E) and Gangavali (14° 35' 26″ N-74° 17' 51″ E) on the west coast of India. Both mangrove estuaries had similar plant species composition but differed in soil chemistries.We amplified a 550-bp portion of 18S small subunit (SSU) rDNA from mangrove plant roots and analysed it by restriction fragment length polymorphism (RFLP). Clones representing unique RFLP patterns were sequenced. A total of 736 clones were obtained from roots of seven and five plant species sampled at Aghanashini and Gangavali, respectively. AMF phylotype numbers in plant roots at Aghanashini (12) were higher than at Gangavali (9) indicating quantitative differences in the AMF community composition in plant roots at the two mangrove estuaries. Because both estuaries had similar plant species composition, the quantitative difference in AMF communities between the estuaries could be an attribute of the differences in rhizospheric chemistry between the two sites.Non-metric multidimensional scaling (NMDS) revealed overlap in the AMF communities of the two sites. Three and two AMF phylotypes had significant indicator value indices with specific hosts at Aghanashini and Gangavali, respectively. Environmental vector fitting to NMDS ordination did not reveal a significant effect of any soil variable on AMF composition at the two sites. However, significant effects of both plant hosts and sites were observed on rhizospheric P. Our results indicate that root AMF community composition may be an outcome of plant response to rhizospheric variables. This suggests that plant identity may have a primary role in shaping AMF communities in mangroves.}, }
@article {pmid34477107, year = {2021}, author = {Mancuso, CP and Lee, H and Abreu, CI and Gore, J and Khalil, AS}, title = {Environmental fluctuations reshape an unexpected diversity-disturbance relationship in a microbial community.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34477107}, issn = {2050-084X}, support = {DP2 AI131083/AI/NIAID NIH HHS/United States ; R01 EB027793/EB/NIBIB NIH HHS/United States ; R01 GM102311/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics/*growth &amp; development/isolation &amp; purification ; Bacteriological Techniques ; *Biodiversity ; Environmental Monitoring ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Models, Theoretical ; Population Density ; *Soil Microbiology ; Time Factors ; }, abstract = {Environmental disturbances have long been theorized to play a significant role in shaping the diversity and composition of ecosystems. However, an inability to specify the characteristics of a disturbance experimentally has produced an inconsistent picture of diversity-disturbance relationships (DDRs). Here, using a high-throughput programmable culture system, we subjected a soil-derived bacterial community to dilution disturbance profiles with different intensities (mean dilution rates), applied either constantly or with fluctuations of different frequencies. We observed an unexpected U-shaped relationship between community diversity and disturbance intensity in the absence of fluctuations. Adding fluctuations increased community diversity and erased the U-shape. All our results are well-captured by a Monod consumer resource model, which also explains how U-shaped DDRs emerge via a novel 'niche flip' mechanism. Broadly, our combined experimental and modeling framework demonstrates how distinct features of an environmental disturbance can interact in complex ways to govern ecosystem assembly and offers strategies for reshaping the composition of microbiomes.}, }
@article {pmid34474030, year = {2022}, author = {Brennerova, MV and Zavala-Meneses, SG and Josefiova, J and Branny, P and Buriankova, K and Vetrovsky, T and Junca, H}, title = {A global survey reveals a divergent extradiol dioxygenase clade as a widespread complementary contributor to the biodegradation of mono- and polycyclic aromatic hydrocarbons.}, journal = {Environmental research}, volume = {204}, number = {Pt A}, pages = {111954}, doi = {10.1016/j.envres.2021.111954}, pmid = {34474030}, issn = {1096-0953}, mesh = {Biodegradation, Environmental ; Oxygenases/genetics ; Phylogeny ; *Polycyclic Aromatic Hydrocarbons ; }, abstract = {Extradiol dioxygenation is a key reaction in the microbial aerobic degradation of mono- and polycyclic aromatic hydrocarbon catecholic derivatives. It has been reported that many bacterial enzymes exhibiting such converging functions act on a wide range of catecholic substrates. The present study reports a new subfamily of extradiol dioxygenases (EXDOs) with broad substrate specificity, the HrbC EXDOs. The new clade belongs to the XII cluster within family 2 of the vicinal oxygen chelate superfamily (EXDO-VC2), which is typically characterized by a preference for bicyclic substrates. Coding hrbC orthologs were isolated by activity-based screening of fosmid metagenomic libraries from large DNA fragments derived from heavily PAH-contaminated soils. They occurred as solitary genes within conserved sequences encoding enzymes for amino acid metabolism and were stably maintained in the chromosomes of the Betaproteobacteria lineages harboring them. Analysis of contaminated aquifers revealed coexpression of hrbC as a polycistronic mRNA component. The predicted open reading frames were verified by cloning and heterologous expression, confirming the expected molecular mass and meta-cleavage activity of the recombinant enzymes. Evolutionary analysis of the HrbC protein sequences grouped them into a discrete cluster of 1,2-dihydroxynaphthalene dioxygenases represented by a cultured PAH degrader, Rugosibacter aromaticivorans strain Ca6. The ecological importance and relevance of the new EXDO genes were confirmed by PCR-based mapping in different biogeographical localities contaminated with a variety of mono- and polycyclic aromatic compounds. The cosmopolitan distribution of hrbC in PAH-contaminated aquifers supports our hypothesis about its auxiliary role in the degradation of toxic catecholic intermediates, contributing to the composite EXDO catabolic capacity of the world's microbiomes.}, }
@article {pmid34469194, year = {2021}, author = {Wee, SY and Edgcomb, VP and Beaudoin, D and Yvon-Lewis, S and Sylvan, JB}, title = {Microbial Abundance and Diversity in Subsurface Lower Oceanic Crust at Atlantis Bank, Southwest Indian Ridge.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {22}, pages = {e0151921}, pmid = {34469194}, issn = {1098-5336}, support = {OCE1658118//National Science Foundation (NSF)/ ; OCE1658031//National Science Foundation (NSF)/ ; }, mesh = {Ammonium Compounds ; Atlantic Ocean ; *Expeditions ; Indian Ocean ; *Microbiota ; Phosphates ; Seawater/*microbiology ; }, abstract = {International Ocean Discovery Program Expedition 360 drilled Hole U1473A at Atlantis Bank, an oceanic core complex on the Southwest Indian Ridge, with the aim of recovering representative samples of the lower oceanic crust. Recovered cores were primarily gabbro and olivine gabbro. These mineralogies may host serpentinization reactions that have the potential to support microbial life within the recovered rocks or at greater depths beneath Atlantis Bank. We quantified prokaryotic cells and analyzed microbial community composition for rock samples obtained from Hole U1473A and conducted nutrient addition experiments to assess if nutrient supply influences the composition of microbial communities. Microbial abundance was low (≤10[4] cells cm[-3]) but positively correlated with the presence of veins in rocks within some depth ranges. Due to the heterogeneous nature of the rocks downhole (alternating stretches of relatively unaltered gabbros and more significantly altered and fractured rocks), the strength of the positive correlations between rock characteristics and microbial abundances was weaker when all depths were considered. Microbial community diversity varied at each depth analyzed. Surprisingly, addition of simple organic acids, ammonium, phosphate, or ammonium plus phosphate in nutrient addition experiments did not affect microbial diversity or methane production in nutrient addition incubation cultures over 60 weeks. The work presented here from Site U1473A, which is representative of basement rock samples at ultraslow spreading ridges and the usually inaccessible lower oceanic crust, increases our understanding of microbial life present in this rarely studied environment and provides an analog for basement below ocean world systems such as Enceladus. IMPORTANCE The lower oceanic crust below the seafloor is one of the most poorly explored habitats on Earth. The rocks from the Southwest Indian Ridge (SWIR) are similar to rock environments on other ocean-bearing planets and moons. Studying this environment helps us increase our understanding of life in other subsurface rocky environments in our solar system that we do not yet have the capability to access. During an expedition to the SWIR, we drilled 780 m into lower oceanic crust and collected over 50 rock samples to count the number of resident microbes and determine who they are. We also selected some of these rocks for an experiment where we provided them with different nutrients to explore energy and carbon sources preferred for growth. We found that the number of resident microbes and community structure varied with depth. Additionally, added nutrients did not shape the microbial diversity in a predictable manner.}, }
@article {pmid34468785, year = {2022}, author = {Bazzicalupo, AL and Erlandson, S and Branine, M and Ratz, M and Ruffing, L and Nguyen, NH and Branco, S}, title = {Fungal Community Shift Along Steep Environmental Gradients from Geothermal Soils in Yellowstone National Park.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {33-43}, pmid = {34468785}, issn = {1432-184X}, mesh = {Fungi/genetics ; *Mycobiome ; *Mycorrhizae ; Parks, Recreational ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Geothermal soils offer unique insight into the way extreme environmental factors shape communities of organisms. However, little is known about the fungi growing in these environments and in particular how localized steep abiotic gradients affect fungal diversity. We used metabarcoding to characterize soil fungi surrounding a hot spring-fed thermal creek with water up to 84 °C and pH 10 in Yellowstone National Park. We found a significant association between fungal communities and soil variable principal components, and we identify the key trends in co-varying soil variables that explain the variation in fungal community. Saprotrophic and ectomycorrhizal fungi community profiles followed, and were significantly associated with, different soil variable principal components, highlighting potential differences in the factors that structure these different fungal trophic guilds. In addition, in vitro growth experiments in four target fungal species revealed a wide range of tolerances to pH levels but not to heat. Overall, our results documenting turnover in fungal species within a few hundred meters suggest many co-varying environmental factors structure the diverse fungal communities found in the soils of Yellowstone National Park.}, }
@article {pmid34468725, year = {2021}, author = {Varliero, G and Rafiq, M and Singh, S and Summerfield, A and Sgouridis, F and Cowan, DA and Barker, G}, title = {Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {10}, pages = {}, pmid = {34468725}, issn = {1574-6941}, mesh = {Greenland ; Metagenome ; Metagenomics ; *Permafrost ; Soil Microbiology ; }, abstract = {Permafrost represents a reservoir for the biodiscovery of cold-adapted proteins which are advantageous in industrial and medical settings. Comparisons between different thermo-adapted proteins can give important information for cold-adaptation bioengineering. We collected permafrost active layer samples from 34 points along a proglacial transect in southwest Greenland. We obtained a deep read coverage assembly (>164x) from nanopore and Illumina sequences for the purposes of i) analysing metagenomic and metatranscriptomic trends of the microbial community of this area, and ii) creating the Cold-Adapted Predicted Protein (CAPP) database. The community showed a similar taxonomic composition in all samples along the transect, with a solid permafrost-shaped community, rather than microbial trends typical of proglacial systems. We retrieved 69 high- and medium-quality metagenome-assembled clusters, 213 complete biosynthetic gene clusters and more than three million predicted proteins. The latter constitute the CAPP database that can provide cold-adapted protein sequence information for protein- and taxon-focused amino acid sequence modifications for the future bioengineering of cold-adapted enzymes. As an example, we focused on the enzyme polyphenol oxidase, and demonstrated how sequence variation information could inform its protein engineering.}, }
@article {pmid34468165, year = {2021}, author = {Iburg, S and Izabel-Shen, D and Austin, &#xc5;N and Hansen, JP and Eklöf, JS and Nascimento, FJA}, title = {Effects of Recreational Boating on Microbial and Meiofauna Diversity in Coastal Shallow Ecosystems of the Baltic Sea.}, journal = {mSphere}, volume = {6}, number = {5}, pages = {e0012721}, pmid = {34468165}, issn = {2379-5042}, mesh = {Animals ; *Biodiversity ; Ecosystem ; Geologic Sediments ; Invertebrates/classification ; Oceans and Seas ; Salinity ; *Water Sports ; }, abstract = {Recreational boating can impact benthic ecosystems in coastal waters. Reduced height and cover of aquatic vegetation in shallow Baltic Sea inlets with high boat traffic have raised concerns about cascading effects on benthic communities in these ecosystems. Here, we characterized the diversity and composition of sediment-associated microbial and meiofaunal communities across five bays subjected to low and high degrees of boating activity and examined the community-environment relationships and association with bay morphometry. We found that recreational boating activity altered meiofauna alpha diversity and the composition of both micro- and meiobenthic communities, and there were strong correlations between community structure and morphometric variables like topographic openness, wave exposure, water surface area, and total phosphorous concentrations. Inlets with high boat traffic showed an increase of bacterial taxa like Hydrogenophilaceae and Burkholderiaceae. Several meiofauna taxa previously reported to respond positively to high levels of suspended organic matter were found in higher relative abundances in the bays with high boat traffic. Overall, our results show that morphometric characteristics of inlets are the strongest drivers of benthic diversity in shallow coastal environments. However, while the effects were small, we found significant effects of recreational boating on benthic community structure that should be considered when evaluating the new mooring projects. IMPORTANCE With the increase of recreational boating activity and development of boating infrastructure in shallow, wave-protected areas, there is growing concern for their impact on coastal ecosystems. In order to properly assess the effects and consider the potential for recovery, it is important to investigate microbial and meiofaunal communities that underpin the functioning of these ecosystems. Here, we present the first study that uses DNA metabarcoding to assess how benthic biodiversity in shallow coastal areas is impacted by recreational boating. Our study shows a relatively small, but significant, effect of recreational boating both on meiofauna alpha diversity and meiofauna and bacterial community composition. However, both meiofauna and bacterial community composition in shallow benthic habitats is mediated to a higher degree by abiotic variables, such as topographic openness, area or size of the inlets, and wave exposure. Despite the fact that the effects were small, such impacts on benthic biodiversity should be considered in the management of coastal shallow habitats.}, }
@article {pmid34467445, year = {2022}, author = {Gabashvili, E and Kobakhidze, S and Chkhikvishvili, T and Tabatadze, L and Tsiklauri, R and Dadiani, K and Kotetishvili, M}, title = {Bacteriophage-Mediated Risk Pathways Underlying the Emergence of Antimicrobial Resistance via Intrageneric and Intergeneric Recombination of Antibiotic Efflux Genes Across Natural populations of Human Pathogenic Bacteria.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {213-226}, pmid = {34467445}, issn = {1432-184X}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Bacillus cereus ; *Bacteriophages ; Drug Resistance, Bacterial/genetics ; Humans ; Pilot Projects ; Recombination, Genetic ; }, abstract = {Antimicrobial resistance continues to be a significant and growing threat to global public health, being driven by the emerging drug-resistant and multidrug-resistant strains of human and animal bacterial pathogens. While bacteriophages are generally known to be one of the vehicles of antibiotic resistance genes (ARGs), it remains largely unclear how these organisms contribute to the dissemination of the genetic loci encoding for antibiotic efflux pumps, especially those that confer multidrug resistance, in bacteria. In this study, the in-silico recombination analyses provided strong statistical evidence for bacteriophage-mediated intra-species recombination of ARGs, encoding mainly for the antibiotic efflux proteins from the MF superfamily, as well as from the ABC and RND families, in Salmonella enterica, Staphylococcus aureus, Staphylococcus suis, Pseudomonas aeruginosa, and Burkholderia pseudomallei. Events of bacteriophage-driven intrageneric recombination of some of these genes could be also elucidated among Bacillus thuringiensis, Bacillus cereus and Bacillus tropicus natural populations. Moreover, we could also reveal the patterns of intergeneric recombination, involving the MF superfamily transporter-encoding genetic loci, induced by a Mycobacterium smegmatis phage, in natural populations of Streptomyces harbinensis and Streptomyces chartreusis. The SplitsTree- (fit: 100; bootstrap values: 92.7-100; Phi p ≤ 0.2414), RDP4- (p ≤ 0.0361), and GARD-generated data strongly supported the above genetic recombination inferences in these in-silico analyses. Thus, based on this pilot study, it can be suggested that the above mode of bacteriophage-mediated recombination plays at least some role in the emergence and transmission of multidrug resistance across a fairly broad spectrum of bacterial species and genera including human pathogens.}, }
@article {pmid34466168, year = {2021}, author = {Crous, PW and Lombard, L and Sandoval-Denis, M and Seifert, KA and Schroers, HJ and Chaverri, P and Gené, J and Guarro, J and Hirooka, Y and Bensch, K and Kema, GHJ and Lamprecht, SC and Cai, L and Rossman, AY and Stadler, M and Summerbell, RC and Taylor, JW and Ploch, S and Visagie, CM and Yilmaz, N and Frisvad, JC and Abdel-Azeem, AM and Abdollahzadeh, J and Abdolrasouli, A and Akulov, A and Alberts, JF and Araújo, JPM and Ariyawansa, HA and Bakhshi, M and Bendiksby, M and Ben Hadj Amor, A and Bezerra, JDP and Boekhout, T and Câmara, MPS and Carbia, M and Cardinali, G and Castañeda-Ruiz, RF and Celis, A and Chaturvedi, V and Collemare, J and Croll, D and Damm, U and Decock, CA and de Vries, RP and Ezekiel, CN and Fan, XL and Fernández, NB and Gaya, E and González, CD and Gramaje, D and Groenewald, JZ and Grube, M and Guevara-Suarez, M and Gupta, VK and Guarnaccia, V and Haddaji, A and Hagen, F and Haelewaters, D and Hansen, K and Hashimoto, A and Hernández-Restrepo, M and Houbraken, J and Hubka, V and Hyde, KD and Iturriaga, T and Jeewon, R and Johnston, PR and Jurjević, &#x17d; and Karalti, I and Korsten, L and Kuramae, EE and Kušan, I and Labuda, R and Lawrence, DP and Lee, HB and Lechat, C and Li, HY and Litovka, YA and Maharachchikumbura, SSN and Marin-Felix, Y and Matio Kemkuignou, B and Matočec, N and McTaggart, AR and Mlčoch, P and Mugnai, L and Nakashima, C and Nilsson, RH and Noumeur, SR and Pavlov, IN and Peralta, MP and Phillips, AJL and Pitt, JI and Polizzi, G and Quaedvlieg, W and Rajeshkumar, KC and Restrepo, S and Rhaiem, A and Robert, J and Robert, V and Rodrigues, AM and Salgado-Salazar, C and Samson, RA and Santos, ACS and Shivas, RG and Souza-Motta, CM and Sun, GY and Swart, WJ and Szoke, S and Tan, YP and Taylor, JE and Taylor, PWJ and Tiago, PV and Váczy, KZ and van de Wiele, N and van der Merwe, NA and Verkley, GJM and Vieira, WAS and Vizzini, A and Weir, BS and Wijayawardene, NN and Xia, JW and Yáñez-Morales, MJ and Yurkov, A and Zamora, JC and Zare, R and Zhang, CL and Thines, M}, title = {Fusarium: more than a node or a foot-shaped basal cell.}, journal = {Studies in mycology}, volume = {98}, number = {}, pages = {100116}, pmid = {34466168}, issn = {0166-0616}, abstract = {Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).}, }
@article {pmid34465761, year = {2021}, author = {Jia, KH and Liu, H and Zhang, RG and Xu, J and Zhou, SS and Jiao, SQ and Yan, XM and Tian, XC and Shi, TL and Luo, H and Li, ZC and Bao, YT and Nie, S and Guo, JF and Porth, I and El-Kassaby, YA and Wang, XR and Chen, C and Van de Peer, Y and Zhao, W and Mao, JF}, title = {Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome.}, journal = {Horticulture research}, volume = {8}, number = {1}, pages = {177}, pmid = {34465761}, issn = {2662-6810}, support = {31600527//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.}, }
@article {pmid34465293, year = {2021}, author = {De Vos, S and Rombauts, S and Coussement, L and Dermauw, W and Vuylsteke, M and Sorgeloos, P and Clegg, JS and Nambu, Z and Van Nieuwerburgh, F and Norouzitallab, P and Van Leeuwen, T and De Meyer, T and Van Stappen, G and Van de Peer, Y and Bossier, P}, title = {The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {635}, pmid = {34465293}, issn = {1471-2164}, mesh = {Animals ; *Artemia/genetics ; Extreme Environments ; *Extremophiles ; Heat-Shock Proteins ; Salinity ; }, abstract = {BACKGROUND: Brine shrimp Artemia have an unequalled ability to endure extreme salinity and complete anoxia. This study aims to elucidate its strategies to cope with these stressors.<br><br>RESULTS AND DISCUSSION: Here, we present the genome of an inbred A. franciscana Kellogg, 1906. We identified 21,828 genes of which, under high salinity, 674 genes and under anoxia, 900 genes were differentially expressed (42%, respectively 30% were annotated). Under high salinity, relevant stress genes and pathways included several Heat Shock Protein and Leaf Embryogenesis Abundant genes, as well as the trehalose metabolism. In addition, based on differential gene expression analysis, it can be hypothesized that a high oxidative stress response and endocytosis/exocytosis are potential salt management strategies, in addition to the expression of major facilitator superfamily genes responsible for transmembrane ion transport. Under anoxia, genes involved in mitochondrial function, mTOR signalling and autophagy were differentially expressed. Both high salt and anoxia enhanced degradation of erroneous proteins and protein chaperoning. Compared with other branchiopod genomes, Artemia had 0.03% contracted and 6% expanded orthogroups, in which 14% of the genes were differentially expressed under high salinity or anoxia. One phospholipase D gene family, shown to be important in plant stress response, was uniquely present in both extremophiles Artemia and the tardigrade Hypsibius dujardini, yet not differentially expressed under the described experimental conditions.<br><br>CONCLUSIONS: A relatively complete genome of Artemia was assembled, annotated and analysed, facilitating research on its extremophile features, and providing a reference sequence for crustacean research.}, }
@article {pmid34463583, year = {2021}, author = {Dekas, AE}, title = {Quantifying Microbial Activity In Situ: the Link between Cells and Cycles.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0075821}, doi = {10.1128/mSystems.00758-21}, pmid = {34463583}, issn = {2379-5077}, abstract = {Metagenomic sequencing of environmental samples has dramatically expanded our knowledge of microbial taxonomic and metabolic diversity and suggests metabolic interdependence is widespread. However, translating these insights into knowledge of ecosystem function and, therefore, implications for local and global chemistry, remains a challenge. In this commentary, I argue that making direct measurements of microbial activity in situ is an essential step to confirm gene-based hypotheses of microbial physiology and bridge advances in microbial ecology with a predicative understanding of global chemistry and climate. Making these measurements across a range of spatial scales and experimentally manipulated conditions contributes to a process-based understanding and, therefore, more robust predictions of how activity will respond to changing environmental conditions. I discuss recent advancements in quantifying microbial activity in situ and highlight several lines of research in marine microbiology that leverage complementary genomic and isotopic methods to connect microbes and global chemistry.}, }
@article {pmid34463567, year = {2021}, author = {Harrington, V and Lau, L and Seddu, K and Suez, J}, title = {Ecology and Medicine Converge at the Microbiome-Host Interface.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0075621}, doi = {10.1128/mSystems.00756-21}, pmid = {34463567}, issn = {2379-5077}, abstract = {The human body is home to a dense and diverse population of bacteria, viruses, and eukaryotes, collectively termed the microbiome. Research on host-microbiome interactions continuously demonstrates the importance of this microbial community to human physiology and its involvement in a myriad of diseases. This, in turn, sparks great interest in developing means for beneficially modulating the microbiome, such as fecal microbiome transplantation and probiotics. However, these interventions show mixed efficacy in clinical trials and raise safety concerns. How these exogenous microorganisms interact with the microbiome might underlie the efficacy and safety of these therapeutics, yet the signaling mechanisms mediating microbe-microbe interactions between human-dwelling commensals are poorly understood. In this commentary, we discuss known and putative mechanisms of interactions between commensals in the gut and how they can be harnessed for improving microbiome-targeting therapeutics and facilitating translation of microbiome research to the clinic.}, }
@article {pmid34460265, year = {2021}, author = {Wang, S and Xia, J and De Paepe, K and Zhang, B and Fu, X and Huang, Q and Van de Wiele, T}, title = {Ultra-high Pressure Treatment Controls In Vitro Fecal Fermentation Rate of Insoluble Dietary Fiber from Rosa Roxburghii Tratt Pomace and Induces Butyrogenic Shifts in Microbiota Composition.}, journal = {Journal of agricultural and food chemistry}, volume = {69}, number = {36}, pages = {10638-10647}, doi = {10.1021/acs.jafc.1c03453}, pmid = {34460265}, issn = {1520-5118}, mesh = {Dietary Fiber ; Fermentation ; Fruit ; Humans ; *Microbiota ; *Rosa ; }, abstract = {Dietary fiber has been considered a key element in shaping the beneficial host-microbe symbiosis. In the present study, we identified Rosa roxburghii Tratt fruits as a promising dietary fiber source. The physicochemical properties and in vitro fermentability by human fecal microbes of R. roxburghii pomace water insoluble dietary fiber (RIDF) obtained from ultrasonic extraction and ultrahigh pressure (90 MPa)-treated RIDF (RIDF-90) were compared to those of R. roxburghii Tratt pomace (R). Ultrahigh pressure modification significantly increased the water holding, oil holding, and swelling capacity of RIDF-90 in comparison to R and RIDF. RIDF-90 displayed the slowest fermentation rate yet yielded the highest butyrate production. The superior butyrogenic properties of both RIDF-90 and, in part, RIDF were reflected by increased Coprococcus and Ruminococcus levels, demonstrating that ultrasonic extraction and/or further ultrahigh pressure treatment of insoluble fibers promotes the prebiotic value of R. roxburghii Tratt.}, }
@article {pmid34459553, year = {2021}, author = {Lindström, S and Timonen, S and Sundström, L}, title = {The bacterial and fungal community composition in time and space in the nest mounds of the ant Formica exsecta (Hymenoptera: Formicidae).}, journal = {MicrobiologyOpen}, volume = {10}, number = {4}, pages = {e1201}, pmid = {34459553}, issn = {2045-8827}, mesh = {Animals ; Ants/*microbiology ; Arctic Regions ; Bacteria/*classification/genetics/metabolism ; Cold Climate ; Cold Temperature ; Fungi/*classification/genetics/metabolism ; Mycobiome/*genetics ; }, abstract = {In a subarctic climate, the seasonal shifts in temperature, precipitation, and plant cover drive the temporal changes in the microbial communities in the topsoil, forcing soil microbes to adapt or decline. Many organisms, such as mound-building ants, survive the cold winter owing to the favorable microclimate in their nest mounds. We have previously shown that the microbial communities in the nest of the ant Formica exsecta are significantly different from those in the surrounding bulk soil. In the current study, we identified taxa, which were consistently present in the nests over a study period of three years. Some taxa were also significantly enriched in the nest samples compared with spatially corresponding reference soils. We show that the bacterial communities in ant nests are temporally stable across years, whereas the fungal communities show greater variation. It seems that the activities of the ants contribute to unique biochemical processes in the secluded nest environment, and create opportunities for symbiotic interactions between the ants and the microbes. Over time, the microbial communities may come to diverge, due to drift and selection, especially given the long lifespan (up to 30 years) of the ant colonies.}, }
@article {pmid34459548, year = {2021}, author = {Block, KR and O'Brien, JM and Edwards, WJ and Marnocha, CL}, title = {Vertical structure of the bacterial diversity in meromictic Fayetteville Green Lake.}, journal = {MicrobiologyOpen}, volume = {10}, number = {4}, pages = {e1228}, pmid = {34459548}, issn = {2045-8827}, mesh = {Chlorobi/classification/genetics/*isolation &amp; purification ; Chromatiaceae/classification/genetics/*isolation &amp; purification ; Cyanobacteria/classification/genetics/*isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Lakes/*microbiology ; Microbiota/genetics ; New York ; RNA, Ribosomal, 16S/genetics ; Sulfur/*metabolism ; Water Microbiology ; }, abstract = {The permanently stratified water columns in euxinic meromictic lakes produce niche environments for phototrophic sulfur oxidizers and diverse sulfur metabolisms. While Green Lake (Fayetteville, New York, NY) is known to host a diverse community of ecologically important sulfur bacteria, analyses of its microbial communities, to date, have been largely based on pigment analysis and smaller datasets from Sanger sequencing techniques. Here, we present the results of next-generation sequencing of the eubacterial community in the context of the water column geochemistry. We observed abundant purple and green sulfur bacteria, as well as anoxygenic photosynthesis-capable cyanobacteria within the upper monimolimnion. Amidst the phototrophs, we found other sulfur-cycling bacteria including sulfur disproportionators and chemotrophic sulfur oxidizers, further detailing our understanding of the sulfur cycle and microbial ecology of euxinic, meromictic lakes.}, }
@article {pmid34459543, year = {2021}, author = {Toubes-Rodrigo, M and Potgieter-Vermaak, S and Sen, R and Oddsdóttir, ES and Elliott, D and Cook, S}, title = {Active microbial ecosystem in glacier basal ice fuelled by iron and silicate comminution-derived hydrogen.}, journal = {MicrobiologyOpen}, volume = {10}, number = {4}, pages = {e1200}, pmid = {34459543}, issn = {2045-8827}, mesh = {Bacteria/classification/genetics/*metabolism ; Carbon Cycle/physiology ; Chemoautotrophic Growth/physiology ; Ecosystem ; Extremophiles/classification/genetics/*metabolism ; Geologic Sediments/chemistry/microbiology ; Hydrogen/*metabolism ; Ice Cover/*microbiology ; Iron/*metabolism ; Methane/biosynthesis/metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Silicates/*metabolism ; }, abstract = {The basal zone of glaciers is characterized by physicochemical properties that are distinct from firnified ice due to strong interactions with underlying substrate and bedrock. Basal ice (BI) ecology and the roles that the microbiota play in biogeochemical cycling, weathering, and proglacial soil formation remain poorly described. We report on basal ice geochemistry, bacterial diversity (16S rRNA gene phylogeny), and inferred ecological roles at three temperate Icelandic glaciers. We sampled three physically distinct basal ice facies (stratified, dispersed, and debris bands) and found facies dependent on biological similarities and differences; basal ice character is therefore an important sampling consideration in future studies. Based on a high abundance of silicates and Fe-containing minerals and, compared to earlier BI literature, total C was detected that could sustain the basal ice ecosystem. It was hypothesized that C-fixing chemolithotrophic bacteria, especially Fe-oxidisers and hydrogenotrophs, mutualistically support associated heterotrophic communities. Basal ice-derived rRNA gene sequences corresponding to genera known to harbor hydrogenotrophic methanogens suggest that silicate comminution-derived hydrogen can also be utilized for methanogenesis. PICRUSt-predicted metabolism suggests that methane metabolism and C-fixation pathways could be highly relevant in BI, indicating the importance of these metabolic routes. The nutrients and microbial communities release from melting basal ice may play an important role in promoting pioneering communities establishment and soil development in deglaciating forelands.}, }
@article {pmid34456379, year = {2020}, author = {Crous, PW and Cowan, DA and Maggs-Kölling, G and Yilmaz, N and Larsson, E and Angelini, C and Brandrud, TE and Dearnaley, JDW and Dima, B and Dovana, F and Fechner, N and García, D and Gené, J and Halling, RE and Houbraken, J and Leonard, P and Luangsa-Ard, JJ and Noisripoom, W and Rea-Ireland, AE and Ševčíková, H and Smyth, CW and Vizzini, A and Adam, JD and Adams, GC and Alexandrova, AV and Alizadeh, A and Duarte, E&#xc1; and Andjic, V and Antonín, V and Arenas, F and Assabgui, R and Ballarà, J and Banwell, A and Berraf-Tebbal, A and Bhatt, VK and Bonito, G and Botha, W and Burgess, TI and Caboň, M and Calvert, J and Carvalhais, LC and Courtecuisse, R and Cullington, P and Davoodian, N and Decock, CA and Dimitrov, R and Di Piazza, S and Drenth, A and Dumez, S and Eichmeier, A and Etayo, J and Fernández, I and Fiard, JP and Fournier, J and Fuentes-Aponte, S and Ghanbary, MAT and Ghorbani, G and Giraldo, A and Glushakova, AM and Gouliamova, DE and Guarro, J and Halleen, F and Hampe, F and Hernández-Restrepo, M and Iturrieta-González, I and Jeppson, M and Kachalkin, AV and Karimi, O and Khalid, AN and Khonsanit, A and Kim, JI and Kim, K and Kiran, M and Krisai-Greilhuber, I and Kučera, V and Kušan, I and Langenhoven, SD and Lebel, T and Lebeuf, R and Liimatainen, K and Linde, C and Lindner, DL and Lombard, L and Mahamedi, AE and Matočec, N and Maxwell, A and May, TW and McTaggart, AR and Meijer, M and Mešić, A and Mileto, AJ and Miller, AN and Molia, A and Mongkolsamrit, S and Cortés, CM and Muñoz-Mohedano, J and Morte, A and Morozova, OV and Mostert, L and Mostowfizadeh-Ghalamfarsa, R and Nagy, LG and Navarro-Ródenas, A and Örstadius, L and Overton, BE and Papp, V and Para, R and Peintner, U and Pham, THG and Pordel, A and Pošta, A and Rodríguez, A and Romberg, M and Sandoval-Denis, M and Seifert, KA and Semwal, KC and Sewall, BJ and Shivas, RG and Slovák, M and Smith, K and Spetik, M and Spies, CFJ and Syme, K and Tasanathai, K and Thorn, RG and Tkalčec, Z and Tomashevskaya, MA and Torres-Garcia, D and Ullah, Z and Visagie, CM and Voitk, A and Winton, LM and Groenewald, JZ}, title = {Fungal Planet description sheets: 1112-1181.}, journal = {Persoonia}, volume = {45}, number = {}, pages = {251-409}, pmid = {34456379}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Austroboletus asper on soil, Cylindromonium alloxyli on leaves of Alloxylon pinnatum, Davidhawksworthia quintiniae on leaves of Quintinia sieberi, Exophiala prostantherae on leaves of Prostanthera sp., Lactifluus lactiglaucus on soil, Linteromyces quintiniae (incl. Linteromyces gen. nov.) on leaves of Quintinia sieberi, Lophotrichus medusoides from stem tissue of Citrus garrawayi, Mycena pulchra on soil, Neocalonectria tristaniopsidis (incl. Neocalonectria gen. nov.) and Xyladictyochaeta tristaniopsidis on leaves of Tristaniopsis collina, Parasarocladium tasmanniae on leaves of Tasmannia insipida, Phytophthora aquae-cooljarloo from pond water, Serendipita whamiae as endophyte from roots of Eriochilus cucullatus, Veloboletus limbatus (incl. Veloboletus gen. nov.) on soil. Austria, Cortinarius glaucoelotus on soil. Bulgaria, Suhomyces rilaensis from the gut of Bolitophagus interruptus found on a Polyporus sp. Canada, Cantharellus betularum among leaf litter of Betula, Penicillium saanichii from house dust. Chile, Circinella lampensis on soil, Exophiala embothrii from rhizosphere of Embothrium coccineum. China, Colletotrichum cycadis on leaves of Cycas revoluta. Croatia, Phialocephala melitaea on fallen branch of Pinus halepensis. Czech Republic, Geoglossum jirinae on soil, Pyrenochaetopsis rajhradensis from dead wood of Buxus sempervirens. Dominican Republic, Amanita domingensis on litter of deciduous wood, Melanoleuca dominicana on forest litter. France, Crinipellis nigrolamellata (Martinique) on leaves of Pisonia fragrans, Talaromyces pulveris from bore dust of Xestobium rufovillosum infesting floorboards. French Guiana, Hypoxylon hepaticolor on dead corticated branch. Great Britain, Inocybe ionolepis on soil. India, Cortinarius indopurpurascens among leaf litter of Quercus leucotrichophora. Iran, Pseudopyricularia javanii on infected leaves of Cyperus sp., Xenomonodictys iranica (incl. Xenomonodictys gen. nov.) on wood of Fagus orientalis. Italy, Penicillium vallebormidaense from compost. Namibia, Alternaria mirabibensis on plant litter, Curvularia moringae and Moringomyces phantasmae (incl. Moringomyces gen. nov.) on leaves and flowers of Moringa ovalifolia, Gobabebomyces vachelliae (incl. Gobabebomyces gen. nov.) on leaves of Vachellia erioloba, Preussia procaviae on dung of Procavia capensis. Pakistan, Russula shawarensis from soil on forest floor. Russia, Cyberlindnera dauci from Daucus carota. South Africa, Acremonium behniae on leaves of Behnia reticulata, Dothiora aloidendri and Hantamomyces aloidendri (incl. Hantamomyces gen. nov.) on leaves of Aloidendron dichotomum, Endoconidioma euphorbiae on leaves of Euphorbia mauritanica, Eucasphaeria proteae on leaves of Protea neriifolia, Exophiala mali from inner fruit tissue of Malus sp., Graminopassalora geissorhizae on leaves of Geissorhiza splendidissima, Neocamarosporium leipoldtiae on leaves of Leipoldtia schultzii, Neocladosporium osteospermi on leaf spots of Osteospermum moniliferum, Neometulocladosporiella seifertii on leaves of Combretum caffrum, Paramyrothecium pituitipietianum on stems of Grielum humifusum, Phytopythium paucipapillatum from roots of Vitis sp., Stemphylium carpobroti and Verrucocladosporium carpobroti on leaves of Carpobrotus quadrifolius, Suttonomyces cephalophylli on leaves of Cephalophyllum pilansii. Sweden, Coprinopsis rubra on cow dung, Elaphomyces nemoreus from deciduous woodlands. Spain, Polyscytalum pini-canariensis on needles of Pinus canariensis, Pseudosubramaniomyces septatus from stream sediment, Tuber lusitanicum on soil under Quercus suber. Thailand, Tolypocladium flavonigrum on Elaphomyces sp. USA, Chaetothyrina spondiadis on fruits of Spondias mombin, Gymnascella minnisii from bat guano, Juncomyces patwiniorum on culms of Juncus effusus, Moelleriella puertoricoensis on scale insect, Neodothiora populina (incl. Neodothiora gen. nov.) on stem cankers of Populus tremuloides, Pseudogymnoascus palmeri from cave sediment. Vietnam, Cyphellophora vietnamensis on leaf litter, Tylopilus subotsuensis on soil in montane evergreen broadleaf forest. Morphological and culture characteristics are supported by DNA barcodes.}, }
@article {pmid34455914, year = {2021}, author = {Molina Ortiz, JP and McClure, DD and Shanahan, ER and Dehghani, F and Holmes, AJ and Read, MN}, title = {Enabling rational gut microbiome manipulations by understanding gut ecology through experimentally-evidenced in silico models.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1965698}, pmid = {34455914}, issn = {1949-0984}, mesh = {Bacteria/growth &amp; development/metabolism ; *Computer Simulation ; Diet, High-Fat ; Dietary Fiber ; Ecosystem ; Gastrointestinal Microbiome/*physiology ; *Health Status ; Host Microbial Interactions/*physiology ; Humans ; }, abstract = {The gut microbiome has emerged as a contributing factor in non-communicable disease, rendering it a target of health-promoting interventions. Yet current understanding of the host-microbiome dynamic is insufficient to predict the variation in intervention outcomes across individuals. We explore the mechanisms that underpin the gut bacterial ecosystem and highlight how a more complete understanding of this ecology will enable improved intervention outcomes. This ecology varies within the gut over space and time. Interventions disrupt these processes, with cascading consequences throughout the ecosystem. In vivo studies cannot isolate and probe these processes at the required spatiotemporal resolutions, and in vitro studies lack the representative complexity required. However, we highlight that, together, both approaches can inform in silico models that integrate cellular-level dynamics, can extrapolate to explain bacterial community outcomes, permit experimentation and observation over ecological processes at high spatiotemporal resolution, and can serve as predictive platforms on which to prototype interventions. Thus, it is a concerted integration of these techniques that will enable rational targeted manipulations of the gut ecosystem.}, }
@article {pmid34453008, year = {2021}, author = {Che, Y and Yang, Y and Xu, X and Břinda, K and Polz, MF and Hanage, WP and Zhang, T}, title = {Reply to Partridge et al.: Complementary bioinformatics and experimental approaches to investigate the transfer of AMR genes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {35}, pages = {}, pmid = {34453008}, issn = {1091-6490}, mesh = {*Computational Biology ; }, }
@article {pmid34451540, year = {2021}, author = {Dos Santos, IMO and Abe, VY and de Carvalho, K and Barazetti, AR and Simionato, AS and de Almeida Pega, GE and Matis, SH and Cano, BG and Cely, MVT and Marcelino-Guimarães, FC and Chryssafidis, AL and Andrade, G}, title = {Secondary Metabolites of Pseudomonas aeruginosa LV Strain Decrease Asian Soybean Rust Severity in Experimentally Infected Plants.}, journal = {Plants (Basel, Switzerland)}, volume = {10}, number = {8}, pages = {}, pmid = {34451540}, issn = {2223-7747}, abstract = {Asian Soybean Rust (ASR), a disease caused by Phakopsora pachyrhizi, causing yield losses up to 90%. The control is based on the fungicides which may generate resistant fungi. The activation of the plant defense system, should help on ASR control. In this study, secondary metabolites of Pseudomonas aeruginosa LV strain were applied on spore germination and the expression of defense genes in infected soybean plants. The F4A fraction and the pure metabolites were used. In vitro, 10 µg mL[-1] of F4A reduced spore germination by 54%, while 100 µg mL[-1] completely inhibited. Overexpression of phenylalanine ammonia lyase (PAL), O-methyltransferase (OMT) and pathogenesis related protein-2 (PR-2; glucanases) defense-related genes were detected 24 and 72 h after soybean sprouts were sprayed with an organocopper antimicrobial compound (OAC). Under greenhouse conditions, the best control was observed in plants treated with 60 µg mL[-1] of PCA, which reduced ASR severity and lesion frequency by 75% and 43%, respectively. Plants sprayed with 2 and 20 µg mL[-1] of F4A also decreased severity (41%) and lesion frequency (32%). The significant reduction in spore germination ASR in plant suggested that the strain of these metabolites are effective against P. pachyrhizi, and they can be used for ASR control.}, }
@article {pmid34451391, year = {2021}, author = {Vigsnaes, LK and Ghyselinck, J and Van den Abbeele, P and McConnell, B and Moens, F and Marzorati, M and Bajic, D}, title = {2'FL and LNnT Exert Antipathogenic Effects against C. difficile ATCC 9689 In Vitro, Coinciding with Increased Levels of Bifidobacteriaceae and/or Secondary Bile Acids.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {8}, pages = {}, pmid = {34451391}, issn = {2076-0817}, support = {Cut-Off 10: reference number 8404//Eurostars/ ; }, abstract = {Clostridioides difficile (formerly Clostridium difficile) infection (CDI) is one of the most common hospital-acquired infections, which is often triggered by a dysbiosed indigenous gut microbiota (e.g., upon antibiotic therapy). Symptoms can be as severe as life-threatening colitis. The current study assessed the antipathogenic potential of human milk oligosaccharides (HMOs), i.e., 2'-O-fucosyllactose (2'FL), lacto-N-neotetraose (LNnT), and a combination thereof (MIX), against C. difficile ATCC 9689 using in vitro gut models that allowed the evaluation of both direct and, upon microbiota modulation, indirect effects. During a first 48 h fecal batch study, dysbiosis and CDI were induced by dilution of the fecal inoculum. For each of the three donors tested, C. difficile levels strongly decreased (with >4 log CFU/mL) upon treatment with 2'FL, LNnT and MIX versus untreated blanks, coinciding with increased acetate/Bifidobacteriaceae levels. Interindividual differences among donors at an intermediate time point suggested that the antimicrobial effect was microbiota-mediated rather than being a direct effect of the HMOs. During a subsequent 11 week study with the Pathogut[TM] model (specific application of the Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®])), dysbiosis and CDI were induced by clindamycin (CLI) treatment. Vancomycin (VNC) treatment cured CDI, but the further dysbiosis of the indigenous microbiota likely contributed to CDI recurrence. Upon co-supplementation with VNC, both 2'FL and MIX boosted microbial activity (acetate and to lesser extent propionate/butyrate). Moreover, 2'FL avoided CDI recurrence, potentially because of increased secondary bile acid production. Overall, while not elucidating the exact antipathogenic mechanisms-of-action, the current study highlights the potential of HMOs to combat CDI recurrence, help the gut microbial community recover after antibiotic treatment, and hence counteract the adverse effects of antibiotic therapies.}, }
@article {pmid34447362, year = {2021}, author = {Isaac, A and Francis, B and Amann, RI and Amin, SA}, title = {Tight Adherence (Tad) Pilus Genes Indicate Putative Niche Differentiation in Phytoplankton Bloom Associated Rhodobacterales.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {718297}, pmid = {34447362}, issn = {1664-302X}, abstract = {The multiple interactions of phytoplankton and bacterioplankton are central for our understanding of aquatic environments. A prominent example of those is the consistent association of diatoms with Alphaproteobacteria of the order Rhodobacterales. These photoheterotrophic bacteria have traditionally been described as generalists that scavenge dissolved organic matter. Many observations suggest that members of this clade are specialized in colonizing the microenvironment of diatom cells, known as the phycosphere. However, the molecular mechanisms that differentiate Rhodobacterales generalists and phycosphere colonizers are poorly understood. We investigated Rhodobacterales in the North Sea during the 2010-2012 spring blooms using a time series of 38 deeply sequenced metagenomes and 10 metaproteomes collected throughout these events. Rhodobacterales metagenome assembled genomes (MAGs) were recurrently abundant. They exhibited the highest gene enrichment and protein expression of small-molecule transporters, such as monosaccharides, thiamine and polyamine transporters, and anaplerotic pathways, such as ethylmalonyl and propanoyl-CoA metabolic pathways, all suggestive of a generalist lifestyle. Metaproteomes indicated that the species represented by these MAGs were the dominant suppliers of vitamin B12 during the blooms, concomitant with a significant enrichment of genes related to vitamin B12 biosynthesis suggestive of association with diatom phycospheres. A closer examination of putative generalists and colonizers showed that putative generalists had persistently higher relative abundance throughout the blooms and thus produced more than 80% of Rhodobacterales transport proteins, suggesting rapid growth. In contrast, putative phycosphere colonizers exhibited large fluctuation in relative abundance across the different blooms and correlated strongly with particular diatom species that were dominant during the blooms each year. The defining feature of putative phycosphere colonizers is the presence of the tight adherence (tad) gene cluster, which is responsible for the assembly of adhesive pili that presumably enable attachment to diatom hosts. In addition, putative phycosphere colonizers possessed higher prevalence of secondary metabolite biosynthetic gene clusters, particularly homoserine lactones, which can regulate bacterial attachment through quorum sensing. Altogether, these findings suggest that while many members of Rhodobacterales are competitive during diatom blooms, only a subset form close associations with diatoms by colonizing their phycospheres.}, }
@article {pmid34444798, year = {2021}, author = {Homann, CM and Rossel, CAJ and Dizzell, S and Bervoets, L and Simioni, J and Li, J and Gunn, E and Surette, MG and de Souza, RJ and Mommers, M and Hutton, EK and Morrison, KM and Penders, J and van Best, N and Stearns, JC}, title = {Infants' First Solid Foods: Impact on Gut Microbiota Development in Two Intercontinental Cohorts.}, journal = {Nutrients}, volume = {13}, number = {8}, pages = {}, pmid = {34444798}, issn = {2072-6643}, support = {MOP-136811/CAPMC/CIHR/Canada ; IMG-143923/CAPMC/CIHR/Canada ; 529051010//Joint Programming Initiative A healthy diet for a healthy life/ ; }, mesh = {Bacteria/classification ; Biodiversity ; Cohort Studies ; Diet ; Eating ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; *Infant Food ; Infant Nutritional Physiological Phenomena ; Male ; Netherlands ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {The introduction of solid foods is an important dietary event during infancy that causes profound shifts in the gut microbial composition towards a more adult-like state. Infant gut bacterial dynamics, especially in relation to nutritional intake remain understudied. Over 2 weeks surrounding the time of solid food introduction, the day-to-day dynamics in the gut microbiomes of 24 healthy, full-term infants from the Baby, Food &amp; Mi and LucKi-Gut cohort studies were investigated in relation to their dietary intake. Microbial richness (observed species) and diversity (Shannon index) increased over time and were positively associated with dietary diversity. Microbial community structure (Bray-Curtis dissimilarity) was determined predominantly by individual and age (days). The extent of change in community structure in the introductory period was negatively associated with daily dietary diversity. High daily dietary diversity stabilized the gut microbiome. Bifidobacterial taxa were positively associated, while taxa of the genus Veillonella, that may be the same species, were negatively associated with dietary diversity in both cohorts. This study furthers our understanding of the impact of solid food introduction on gut microbiome development in early life. Dietary diversity seems to have the greatest impact on the gut microbiome as solids are introduced.}, }
@article {pmid34438891, year = {2021}, author = {You, I and Kim, MJ}, title = {Comparison of Gut Microbiota of 96 Healthy Dogs by Individual Traits: Breed, Age, and Body Condition Score.}, journal = {Animals : an open access journal from MDPI}, volume = {11}, number = {8}, pages = {}, pmid = {34438891}, issn = {2076-2615}, support = {#PJ015274022021//Rural Development Administration, South Korea/ ; }, abstract = {Since dogs are part of many peoples' lives, research and industry related to their health and longevity are becoming a rising topic. Although gut microbiota (GM) is a key contributor to host health, limited information is available for canines. Therefore, this study characterized GM according to individual signatures (e.g., breed, age, and body condition score-BCS) of dogs living in the same environment. Fresh fecal samples from 96 healthy dogs were analyzed by sequencing the V3-V4 region of the 16S rRNA gene. The major microbial phyla were Firmicutes, Bacteroidetes, Fusobacteria, Proteobacteria, and Actinobacteria. In the comparison by breeds, relative abundance of Fusobacterium was significantly differed. Interestingly, Fusobacterium perfoetens abundance was positively correlated with age (p = 0.018), being significantly more enriched in the 6-10-year-old group (14.3%) than in the 0.5-1-year-old group (7.2%). Moreover, despite the healthy appearance of dogs in all age (0.5-10 years) and BCS (3-6) groups, the gut microbial environment may be disadvantageous in older dogs or in dogs with an abnormal BCS. These findings broaden our understanding of gut microbial ecology according to individual characteristics of dogs and may be used as a reference for providing customized-care to companion animals.}, }
@article {pmid34436641, year = {2022}, author = {Jan, B and Reshi, ZA and Mohiddin, FA}, title = {Correction to: Site and Organ‑Specific Culture‑Dependent Endophytic Diversity of Crocus sativus L. (Saffron) in Kashmir Himalaya, India.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {1007}, doi = {10.1007/s00248-021-01847-z}, pmid = {34436641}, issn = {1432-184X}, }
@article {pmid34436640, year = {2022}, author = {Möhlmann, TWR and Ter Braak, CJF and Te Beest, DE and Hendriks, M and Nijhuis, EH and Warris, S and Drolet, BS and van Overbeek, L and Koenraadt, CJM}, title = {Species Identity, Life History, and Geographic Distance Influence Gut Bacterial Communities in Lab-Reared and European Field-Collected Culicoides Biting midges.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {267-284}, pmid = {34436640}, issn = {1432-184X}, support = {BBS/E/I/00007039/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 1300018161//ANIHWA-EraNet/ ; Global One Health strategic program//Wageningen University/ ; }, mesh = {Animals ; *Ceratopogonidae ; *Gastrointestinal Microbiome ; Insect Vectors/microbiology ; RNA, Ribosomal, 16S/genetics ; *Wolbachia/genetics ; }, abstract = {Bacteria are part of the insect gut system and influence many physiological traits of their host. Gut bacteria may even reduce or block the transmission of arboviruses in several species of arthropod vectors. Culicoides biting midges are important arboviral vectors of several livestock and wildlife diseases, yet limited information is available on their gut bacterial communities. Addressing this gap will help inform how these communities can be manipulated and ultimately used as novel tools to control pathogens. To assess how bacterial communities change during the life stages of lab-reared C. nubeculosus and C. sonorensis, endosymbiotic bacteria were identified using Illumina sequencing of 16S rRNA and taxonomically characterised. Analyses were conducted to determine how gut bacterial communities in adults are influenced by species identity and geographic distance among biting midge populations. Communities of the two lab-reared Culicoides species significantly changed after pupation and with maturation into 6-day-old adults. Pseudomonas, Burkholderiaceae and Leucobacter bacteria were part of a core community that was trans-stadially transmitted and found throughout their life cycle. Among field-collected biting midges, the bacterial communities were unique for almost each species. Cardinium, Rickettsia and Wolbachia were some of the most abundant bacteria in midges collected from wetlands. Only Pseudomonas was present in high relative abundance in all field-collected species. In this study, species identity, as well as geographic distance, influenced the gut bacterial communities and may partly explain known inter- and intra-species variability in vector competence. Additionally, stably associated bacterial species could be candidates for paratransgenic strategies to control vector-borne pathogens.}, }
@article {pmid34434657, year = {2021}, author = {Leonard, LT and Brodie, EL and Williams, KH and Sharp, JO}, title = {Effect of elevation, season and accelerated snowmelt on biogeochemical processes during isolated conifer needle litter decomposition.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e11926}, pmid = {34434657}, issn = {2167-8359}, abstract = {Increased drought and temperatures associated with climate change have implications for ecosystem stress with risk for enhanced carbon release in sensitive biomes. Litter decomposition is a key component of biogeochemical cycling in terrestrial ecosystems, but questions remain regarding the local response of decomposition processes to climate change. This is particularly complex in mountain ecosystems where the variable nature of the slope, aspect, soil type, and snowmelt dynamics play a role. Hence, the goal of this study was to determine the role of elevation, soil type, seasonal shifts in soil moisture, and snowmelt timing on litter decomposition processes. Experimental plots containing replicate deployments of harvested lodgepole and spruce needle litter alongside needle-free controls were established in open meadows at three elevations ranging from 2,800-3,500 m in Crested Butte, Colorado. Soil biogeochemistry variables including gas flux, porewater chemistry, and microbial ecology were monitored over three climatically variable years that shifted from high monsoon rains to drought. Results indicated that elevation and soil type influenced baseline soil biogeochemical indicators; however, needle mass loss and chemical composition were consistent across the 700 m elevation gradient. Rates of gas flux were analogously consistent across a 300 m elevation gradient. The additional variable of early snowmelt by 2-3 weeks had little impact on needle chemistry, microbial composition and gas flux; however, it did result in increased dissolved organic carbon in lodgepole porewater collections suggesting a potential for aqueous export. In contrast to elevation, needle presence and seasonal variability of soil moisture and temperature both played significant roles in soil carbon fluxes. During a pronounced period of lower moisture and higher temperatures, bacterial community diversity increased across elevation with new members supplanting more dominant taxa. Microbial ecological resilience was demonstrated with a return to pre-drought structure and abundance after snowmelt rewetting the following year. These results show similar decomposition processes across a 700 m elevation gradient and reveal the sensitivity but resilience of soil microbial ecology to low moisture conditions.}, }
@article {pmid34432600, year = {2021}, author = {Roussel, C and De Paepe, K and Galia, W and de Bodt, J and Chalancon, S and Denis, S and Leriche, F and Vandekerkove, P and Ballet, N and Blanquet-Diot, S and Van de Wiele, T}, title = {Multi-targeted properties of the probiotic saccharomyces cerevisiae CNCM I-3856 against enterotoxigenic escherichia coli (ETEC) H10407 pathogenesis across human gut models.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1953246}, pmid = {34432600}, issn = {1949-0984}, mesh = {Enterotoxigenic Escherichia coli/*drug effects ; Escherichia coli Infections/*drug therapy/physiopathology ; Foodborne Diseases/*drug therapy ; Gastrointestinal Microbiome/*drug effects ; Humans ; Probiotics/*pharmacology/*therapeutic use ; Saccharomyces cerevisiae/chemistry ; Virulence/*drug effects ; }, abstract = {Enterotoxigenic Escherichia coli (ETEC) is one of the most common causes of acute traveler's diarrhea. Adhesins and enterotoxins constitute the major ETEC virulence traits. With the dramatic increase in antibiotic resistance, probiotics are considered a wholesome alternative to prevent or treat ETEC infections. Here, we examined the antimicrobial properties of the probiotic Saccharomyces cerevisiae CNCM I-3856 against ETEC H10407 pathogenesis upon co-administration in the TNO gastrointestinal Model (TIM-1), simulating the physicochemical and enzymatic conditions of the human upper digestive tract and preventive treatment in the Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME), integrating microbial populations of the ileum and ascending colon. Interindividual variability was assessed by separate M-SHIME experiments with microbiota from six human individuals. The probiotic did not affect ETEC survival along the digestive tract. However, ETEC pathogenicity was significantly reduced: enterotoxin encoding virulence genes were repressed, especially in the TIM-1 system, and a lower enterotoxin production was noted. M-SHIME experiments revealed that 18-days probiotic treatment stimulate the growth of Bifidobacterium and Lactobacillus in different gut regions (mucosal and luminal, ileum and ascending colon) while a stronger metabolic activity was noted in terms of short-chain fatty acids (acetate, propionate, and butyrate) and ethanol production. Moreover, the probiotic pre-treated microbiota displayed a higher robustness in composition following ETEC challenge compared to the control condition. We thus demonstrated the multi-inhibitory properties of the probiotic S. cerevisiae CNCM I-3856 against ETEC in the overall simulated human digestive tract, regardless of the inherent variability across individuals in the M-SHIME.}, }
@article {pmid34432103, year = {2022}, author = {Allsup, CM and Lankau, RA and Paige, KN}, title = {Herbivory and Soil Water Availability Induce Changes in Arbuscular Mycorrhizal Fungal Abundance and Composition.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {141-152}, pmid = {34432103}, issn = {1432-184X}, mesh = {Herbivory ; *Mycorrhizae ; Plant Roots/microbiology ; Soil ; Soil Microbiology ; Water ; }, abstract = {We tested the prediction that abundance and composition of arbuscular mycorrhizal fungi (AMF) in Ipomopsis aggregata roots and soils are influenced by ungulate herbivory and drought conditions by examining the effects in a field setting over two years. We used a multi-metric approach to quantify AMF root colonization, AMF reproduction, and AMF community composition in roots and soils. We incorporated complimentary community characterization assays by morphologically identifying spores from trap cultures and the use of terminal restriction fragment length polymorphism (T-RFLP) fingerprinting. Herbivory caused a twofold increase in spore production, an increase in AMF taxa diversity in roots, and a shift in AMF species composition in rhizosphere soils. The impact of herbivory was dependent on water availability, which differed in the two contrasting years. This study demonstrates that both soil water availability and herbivory shape arbuscular mycorrhizal fungi communities. The changes to mycorrhizal communities may help in understanding mycorrhizal function in changing climates.}, }
@article {pmid34432102, year = {2022}, author = {Babur, E and Dindaroğlu, T and Riaz, M and Uslu, OS}, title = {Seasonal Variations in Litter Layers' Characteristics Control Microbial Respiration and Microbial Carbon Utilization Under Mature Pine, Cedar, and Beech Forest Stands in the Eastern Mediterranean Karstic Ecosystems.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {153-167}, pmid = {34432102}, issn = {1432-184X}, support = {KSU-2017/5-12D//Scientific Research Projects Commission/ ; }, mesh = {Biomass ; Carbon/metabolism ; *Fagus ; Forests ; *Microbiota ; Nitrogen/metabolism ; *Pinus/metabolism ; Seasons ; Soil/chemistry ; Soil Microbiology ; }, abstract = {The forest floor is hotspot of several functions integral to the stability of forest ecosystems. However, seasonal variations in litter decomposition rate contribute to biochemical and structural heterogeneity in the forest floor carbon (C) and nutrient cycling. We investigated the influence of seasonal variations in litter layers' micro-climate (temperature and moisture content) and chemical characteristics such as pH, electrical conductivity (EC), total organic C (TOC), total nitrogen (TN), and C/N ratio on microbial respiration, biomass, and C use efficiency under mature (> 80 years stage age) pine, beech, and cedar forests in eastern Mediterranean Karstic ecosystems. In contrast to significantly higher microbial respiration in fall, winter, and spring under pine, beech, and cedar forests, the significantly lowest microbial biomass C (MBC) and microbial biomass N (MBN) were observed in winter under each forest. Microbial C use efficiency, measured as the metabolic quotient (qCO2 = CO2/MBC), varied strongly between forest stands and seasons but was generally higher in winter. The significant positive correlations between litter layer and microbial biomass C/N ratios, under beech and cedar forests, suggested strong CN stoichiometric coupling and microbial adaptation to substrate resource stoichiometry. qCO2 correlated significantly negatively with litter layers' temperature, positively with moisture content and EC. However, qCO2 had significant negative relationships with pH in pine and beech forests but significant positive under cedar forest. qCO2 showed significant positive relationships with C/N ratios under all forests but much stronger in beech and cedar forests suggesting higher C respired per unit MBC with an increase in C/N ratio. Despite variations between forest species, the highest MBC/TOC and MBN/TN ratios in fall indicated greater C and N incorporation into microbial biomass. Changes in MBC/MBN ratios under pine (9.62-10.6), beech (8.63-15.6), and cedar (7.32-16.2) forests indicated the shift in microbial communities as fungi have a higher C/N ratio than bacteria. Stepwise regression analysis further revealed that microbial respiration and biomass were controlled differently by litter layer characteristics in each forest. This study suggested that qCO2 independently or with other microbial indices can show litter layers' controls on organic matter turnover in Karst ecosystems and, taking into account the strong seasonal variations, can enhance the predictive potential of decomposition models.}, }
@article {pmid34431694, year = {2021}, author = {Moreno Morales, N and Patel, MT and Stewart, CJ and Sweeney, K and McClean, MN}, title = {Optogenetic Tools for Control of Public Goods in Saccharomyces cerevisiae.}, journal = {mSphere}, volume = {6}, number = {4}, pages = {e0058121}, pmid = {34431694}, issn = {2379-5042}, support = {P30 CA014520/CA/NCI NIH HHS/United States ; R35 GM128873/GM/NIGMS NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; }, mesh = {Gene Expression Regulation, Fungal/*radiation effects ; *Light ; Optogenetics/*methods ; Plasmids/*genetics ; Proof of Concept Study ; Saccharomyces cerevisiae/enzymology/*genetics/metabolism/radiation effects ; Sucrose/metabolism ; beta-Fructofuranosidase/genetics/metabolism ; }, abstract = {Microorganisms live in dense and diverse communities, with interactions between cells guiding community development and phenotype. The ability to perturb specific intercellular interactions in space and time provides a powerful route to determining the critical interactions and design rules for microbial communities. Approaches using optogenetic tools to modulate these interactions offer promise, as light can be exquisitely controlled in space and time. We report new plasmids for rapid integration of an optogenetic system into Saccharomyces cerevisiae to engineer light control of expression of a gene of interest. In a proof-of-principle study, we demonstrate the ability to control a model cooperative interaction, namely, the expression of the enzyme invertase (SUC2) which allows S. cerevisiae to hydrolyze sucrose and utilize it as a carbon source. We demonstrate that the strength of this cooperative interaction can be tuned in space and time by modulating light intensity and through spatial control of illumination. Spatial control of light allows cooperators and cheaters to be spatially segregated, and we show that the interplay between cooperative and inhibitory interactions in space can lead to pattern formation. Our strategy can be applied to achieve spatiotemporal control of expression of a gene of interest in S. cerevisiae to perturb both intercellular and interspecies interactions. IMPORTANCE Recent advances in microbial ecology have highlighted the importance of intercellular interactions in controlling the development, composition, and resilience of microbial communities. In order to better understand the role of these interactions in governing community development, it is critical to be able to alter them in a controlled manner. Optogenetically controlled interactions offer advantages over static perturbations or chemically controlled interactions, as light can be manipulated in space and time and does not require the addition of nutrients or antibiotics. Here, we report a system for rapidly achieving light control of a gene of interest in the important model organism Saccharomyces cerevisiae and demonstrate that by controlling expression of the enzyme invertase, we can control cooperative interactions. This approach will be useful for understanding intercellular and interspecies interactions in natural and synthetic microbial consortia containing S. cerevisiae and serves as a proof of principle for implementing this approach in other consortia.}, }
@article {pmid34431166, year = {2021}, author = {Wang, Y and Chen, L and Xiang, W and Ouyang, S and Zhang, T and Zhang, X and Zeng, Y and Hu, Y and Luo, G and Kuzyakov, Y}, title = {Forest conversion to plantations: A meta-analysis of consequences for soil and microbial properties and functions.}, journal = {Global change biology}, volume = {27}, number = {21}, pages = {5643-5656}, doi = {10.1111/gcb.15835}, pmid = {34431166}, issn = {1365-2486}, mesh = {Carbon ; *Ecosystem ; Forests ; Nitrogen/analysis ; *Soil ; }, abstract = {Primary or secondary forests around the world are increasingly being converted into plantations. Soil microorganisms are critical for all biogeochemical processes in ecosystems, but the effects of forest conversion on microbial communities and their functioning remain unclear. Here, we conducted a meta-analysis to quantify the impacts that converting forests to plantations has on soil microbial communities and functioning as well as on the associated plant and soil properties. We collected 524 paired observations from 138 studies globally. We found that conversion leads to broad range of adverse impacts on soils and microorganisms, including on soil organic carbon (-24%), total nitrogen (-29%), bacterial and fungal biomass (-36% and -42%, respectively), microbial biomass carbon (MBC, -31%) and nitrogen (-33%), and fungi to bacteria ratio (F:B, -16%). In addition, we found impacts on the ratio of MBC to soil organic C (qMBC, -20%), microbial respiration (-18%), N mineralization (-18%), and enzyme activities including β-1,4-glucosidase (-54%), β-1,4-N-acetylglucosaminidase (-39%), and acid phosphatase (ACP; -34%). In contrast, conversion to plantations increases bacterial richness (+21%) and microbial metabolic quotient (qCO2 , +21%). The effects of forest conversion were consistent across stand ages, stand types, and climate zone. Soil C and N contents as well as the C:N ratio were the main factors responsible for the changes of microbial C, F:B, and bacterial richness. The responses of qCO2 , N mineralization, and ACP activity were mainly driven by the reductions in F:B, MBC, and soil C:N. Applying macro-ecology theory on ecosystem disturbance in soil microbial ecology, we show that microbial groups shifted from K to r strategists after conversion to plantations. Our meta-analysis underlines the adverse effects of natural forests conversion to plantations on soil microbial communities and functioning, and suggests that the preservation of soil functions should be a consideration in forest management practices.}, }
@article {pmid34428623, year = {2021}, author = {Vaezzadeh, V and Yi, X and Rais, FR and Bong, CW and Thomes, MW and Lee, CW and Zakaria, MP and Wang, AJ and Zhong, G and Zhang, G}, title = {Distribution of black carbon and PAHs in sediments of Peninsular Malaysia.}, journal = {Marine pollution bulletin}, volume = {172}, number = {}, pages = {112871}, doi = {10.1016/j.marpolbul.2021.112871}, pmid = {34428623}, issn = {1879-3363}, mesh = {Carbon/analysis ; Environmental Monitoring ; Geologic Sediments ; Malaysia ; *Polycyclic Aromatic Hydrocarbons/analysis ; *Water Pollutants, Chemical/analysis ; }, abstract = {Concentrations, sources and interactions between black carbon (BC) and polycyclic aromatic hydrocarbons (PAHs) were investigated in 42 sediment samples collected from riverine, coastal and shelf areas in Peninsular Malaysia. The concentrations of BC measured by benzene polycarboxylic acid (BPCA) method and PAHs showed broad spatial variations between the relatively pristine environment of the East coast and developed environment of the West and South coast ranging from 0.02 to 0.36% dw and 57.7 ng g[-1] dw to 19,300 ng g[-1] dw, respectively. Among diagnostic ratios of PAHs, the ratios of Ant/(Ant+Phe) and LMW/HMW drew the clearest distinctions between the East coast versus the West and South coast sediments indicating the predominance of petrogenic sources in the former versus pyrogenic sources in the latter. PAHs significantly correlated with BC and total organic carbon (TOC) in the sediments (p < 0.05) having similar correlation coefficients. BC accounted for 6.06 to 30.6% of TOC in sediments.}, }
@article {pmid34427721, year = {2022}, author = {Basanta, MD and Rebollar, EA and García-Castillo, MG and Parra Olea, G}, title = {Comparative Analysis of Skin Bacterial Diversity and Its Potential Antifungal Function Between Desert and Pine Forest Populations of Boreal Toads Anaxyrus boreas.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {257-266}, pmid = {34427721}, issn = {1432-184X}, support = {CN 18-127//University of California Institute for Mexico and the United States/ ; IN205521//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, mesh = {Animals ; Antifungal Agents ; Bacteria ; Bufonidae/microbiology ; *Chytridiomycota ; Forests ; Humans ; Mexico ; *Pinus ; Skin/microbiology ; }, abstract = {The skin microbiome in amphibians has gained a lot of attention as some of its members play a protective role against pathogens such as the fungus Batrachochytrium dendrobatidis (Bd). The composition of skin bacterial communities has been suggested as one of the factors explaining differences in susceptibility to Bd among amphibian species and populations. The boreal toad Anaxyrus boreas is known to be susceptible to Bd, and severe population declines in its southeastern range have been documented. However, throughout A. boreas distribution, populations present differences in susceptibility to Bd infections which may be associated with differences in skin microbial diversity. This study compared the skin bacterial diversity and Bd infection levels of A. boreas in one desert population and one pine forest population from Baja California, Mexico. We found that desert and pine forest toad populations exhibit differences in skin bacterial community structure but show similar Bd infection levels. Using a predictive method, we found that the abundance of bacteria with potential Bd-inhibitory properties differed between uninfected and infected individuals but not between populations. Our data suggest that several bacteria in the skin community may be offering protection from Bd infections in these A. boreas populations. This study provides foundational evidence for future studies seeking to understand the skin-microbial variation among boreal toads' populations and its relation with Bd susceptibility.}, }
@article {pmid34427533, year = {2021}, author = {Saw, JHW}, title = {Characterizing the Uncultivated Microbial Minority: towards Understanding the Roles of the Rare Biosphere in Microbial Communities.}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0077321}, pmid = {34427533}, issn = {2379-5077}, abstract = {Microbial communities are frequently numerically dominated by just a few species. Often, the long "tail" of the rank-abundance plots of microbial communities constitutes the so-called "rare biosphere," microorganisms that are highly diverse but are typically found in low abundance in these communities. Their presence in microbial communities has only recently become apparent with advances in high-throughput sequencing technologies. Despite their low numbers, they are thought to play important roles in their communities and may function as potential members to keep the communities intact and resilient. Their phylogenetic diversity also means that they are important subjects for better understanding the interplay between microbial diversity and evolution. I propose that more efforts should be put into characterizing these poorly understood and mostly unknown microbial lineages that hold vast potentials for our understanding of microbial diversity, ecology, and evolution of life on this planet.}, }
@article {pmid34427532, year = {2021}, author = {Scanlan, PD}, title = {Evolution in a Community Context: towards Understanding the Causes and Consequences of Adaptive Evolution in the Human Gut Microbiota over Short Time Scales.}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0083221}, pmid = {34427532}, issn = {2379-5077}, support = {//Enterprise Ireland/ ; //Royal Society/ ; //Science Foundation Ireland (SFI)/ ; }, abstract = {How important is adaptive evolution to the unique diversity that we can observe for each individual human gut microbiome? How do gut microbes evolve in response to changes in their environment, and how does evolution in real time impact microbial functionality in the context of host health? My interdisciplinary research uses in vitro microcosm models to test how different abiotic and biotic factors impact microbial evolution in a community context. We complement this approach by tracking focal species as they evolve in real time and in their natural environment of the human gut. Our aim is to provide a better understanding of how the dynamics and outcomes of microbial evolution differ between individual gut environments, and in response to different selection pressures, so that we can move closer to rational gut microbiome treatments that promote host health and prevent and treat human disease.}, }
@article {pmid34427521, year = {2021}, author = {Rodríguez-Verdugo, A}, title = {Evolving Interactions and Emergent Functions in Microbial Consortia.}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0077421}, pmid = {34427521}, issn = {2379-5077}, abstract = {Microbial communities are constantly challenged with environmental stressors, such as antimicrobials, pollutants, and global warming. How do they respond to these changes? Answering this question is crucial given that microbial communities perform essential functions for life on Earth. Our research aims to understand and predict communities' responses to change by addressing the following questions. (i) How do eco-evolutionary feedbacks influence microbial community dynamics? (ii) How do multiple interacting species in a microbial community alter evolutionary processes? (iii) To what extent do microbial communities respond to change by ecological versus evolutionary processes? To answer these questions, we use microbial communities of reduced complexity coupled with experimental evolution, genome sequencing, and mathematical modeling. The overall expectation from this integrative research approach is to generate general concepts that extend beyond specific bacterial species and provide fundamental insights into the consequences of evolution on the functioning of whole microbial communities.}, }
@article {pmid34426366, year = {2021}, author = {Leite, MFA and Dimitrov, MR and Freitas-Iório, RP and de Hollander, M and Cipriano, MAP and Andrade, SAL and da Silveira, APD and Kuramae, EE}, title = {Rearranging the sugarcane holobiont via plant growth-promoting bacteria and nitrogen input.}, journal = {The Science of the total environment}, volume = {800}, number = {}, pages = {149493}, doi = {10.1016/j.scitotenv.2021.149493}, pmid = {34426366}, issn = {1879-1026}, mesh = {Bacteria ; Burkholderiaceae ; Enterobacteriaceae ; Herbaspirillum ; Nitrogen ; Plant Roots ; Rhizosphere ; *Saccharum ; Soil Microbiology ; }, abstract = {The development and productivity of plants are governed by their genetic background, nutrient input, and the microbial communities they host, i.e. the holobiont. Accordingly, engineering beneficial root microbiomes has emerged as a novel and sustainable approach to crop production with reduced nutrient input. Here, we tested the effects of six bacterial strains isolated from sugarcane stalks on sugarcane growth and physiology as well as the dynamics of prokaryote community assembly in the rhizosphere and root endosphere under two N fertilization regimes. All six strains, Paraburkholderia caribensis IAC/BECa 88, Kosakonia oryzae IAC/BECa 90, Kosakonia radicincitans IAC/BECa 95, Paraburkholderia tropica IAC/BECa 135, Pseudomonas fluorescens IAC/BECa 141 and Herbaspirillum frisingense IAC/BECa 152, increased in shoot and root dry mass, and influenced the concentration and accumulation of important macro- and micronutrients. However, N input reduced the impact of inoculation by shifting the sugarcane microbiome (rhizosphere and root endosphere) and weakening the co-dependence between soil microbes and sugarcane biomass and nutrients. The results show that these beneficial microbes improved plant nutrient uptake conditioned to a reduced N nutrient input. Therefore, reduced fertilization is not only desirable consequence of bacterial inoculation but essential for higher impact of these beneficial bacteria on the sugarcane microbiome.}, }
@article {pmid34426295, year = {2022}, author = {Nicomel, NR and Otero-Gonzalez, L and Williamson, A and Ok, YS and Van Der Voort, P and Hennebel, T and Du Laing, G}, title = {Selective copper recovery from ammoniacal waste streams using a systematic biosorption process.}, journal = {Chemosphere}, volume = {286}, number = {Pt 3}, pages = {131935}, doi = {10.1016/j.chemosphere.2021.131935}, pmid = {34426295}, issn = {1879-1298}, mesh = {Adsorption ; Biomass ; *Copper ; Electroplating ; Hydrogen-Ion Concentration ; Kinetics ; *Water Pollutants, Chemical/analysis ; }, abstract = {Cu-NH3 bearing effluents arise from electroplating and metal extraction industries, requiring innovative and sustainable Cu recovery technologies to reduce their adverse environmental impact. CO3[2-] and Zn are often co-occurring, and thus, selective Cu recovery from these complex liquid streams is required for economic viability. This study assessed 23 sustainable biosorbents classified as tannin-rich, lignin-rich, chitosan/chitin, dead biomass, macroalgae or biochar for their Cu adsorption capacity and selectivity in a complex NH3-bearing bioleachate. Under a preliminary screen with 12 mM Cu in 1 M ammoniacal solution, most biosorbents showed optimal Cu adsorption at pH 11, with pinecone remarkably showing high removal efficiencies (up to 68%) at all tested pH values. Further refinements on select biosorbents with pH, contact time, and presence of NH3, Zn and CO3[2-] showed again that pinecone has a high maximum adsorption capacity (1.07 mmol g[-1]), worked over pH 5-12 and was Cu-selective with 3.97 selectivity quotient (KCu/Zn). Importantly, pinecone performance was maintained in a real Cu/NH3/Zn/CO3[2-] bioleachate, with 69.4% Cu removal efficiency. Unlike synthetic adsorbents, pinecones require no pre-treatment, which together with its abundance, selectivity, and efficiency without the need for prior NH3 removal, makes it a competitive and sustainable Cu biosorbent for complex Cu-NH3 bearing streams. Overall, this study demonstrated the potential of integrating bioleaching and biosorption as a clean Cu recovery technology utilizing only sustainable resources (i.e., bio-lixiviant and biosorbents). This presents a closed-loop approach to Cu extraction and recovery from wastes, thus effectively addressing elemental sustainability.}, }
@article {pmid34424345, year = {2022}, author = {Bacha, L and Ventura, R and Barrios, M and Seabra, J and Tschoeke, D and Garcia, G and Masi, B and Macedo, L and Godoy, JMO and Cosenza, C and de Rezende, CE and Lima, V and Ottoni, AB and Thompson, C and Thompson, F}, title = {Risk of Collapse in Water Quality in the Guandu River (Rio de Janeiro, Brazil).}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {314-324}, pmid = {34424345}, issn = {1432-184X}, mesh = {Brazil ; Environmental Monitoring ; Fresh Water ; Humans ; Phosphorus ; *Rivers ; *Water Pollutants, Chemical/analysis ; Water Quality ; }, abstract = {The Guandu River, one of the main rivers in the state of Rio de Janeiro, provides water for more than nine million people in the metropolitan region. However, the Guandu has suffered from massive domestic and industrial pollution for more than two decades, leading to high levels of dissolved total phosphorus, cyanobacteria, and enteric bacteria observed during the summers of 2020 and 2021. The use of Phoslock, a palliative compound, was not effective in mitigating the levels of phosphorus in the Guandu River. Furthermore, potable water driven from the river had levels of 2-MIB/geosmin and a mud smell/taste. With all these problems, several solutions are proposed for improving the Guandu River water quality, including establishment of (i) sewage treatment plants (STPs), (ii) strict water quality monitoring, (iii) environmental recovery (e.g., reforestation), and (iv) permanent protected areas. The objective of this paper is to verify the poor water quality in the Guandu and the ineffectiveness and undesired effects of Phoslock.}, }
@article {pmid34422537, year = {2021}, author = {de Siqueira, KA and Liotti, RG and de Sousa, JR and Vendruscullo, SJ and de Souza, GB and de Vasconcelos, LG and Januário, AH and de Oliveira Mendes, TA and Soares, MA}, title = {Streptomyces griseocarneus R132 expresses antimicrobial genes and produces metabolites that modulate Galleria mellonella immune system.}, journal = {3 Biotech}, volume = {11}, number = {9}, pages = {396}, pmid = {34422537}, issn = {2190-572X}, abstract = {UNLABELLED: Actinobacteria is a phylum composed of aerobic, Gram-positive, and filamentous bacteria with a broad spectrum of biological activity, including antioxidant, antitumor, and antibiotic. The crude extract of Streptomyces griseocarneus R132 was fractionated on a C18 silica column and the isolated compound was identified by [1]H and [13]C nuclear magnetic resonance as 3-(phenylprop-2-enoic acid), also known as trans-cinnamic acid. Antimicrobial activity against human pathogens was assayed in vitro (disk-diffusion qualitative test) and in vivo using Galleria mellonella larvae (RT-qPCR). The methanol fractions 132-F30%, 132-F50%, 132-F70%, and 132-F100% inhibited the Escherichia coli (ATCC 25922) and Staphylococcus aureus (MRSA) growth in vitro the most effectively. Compared with the untreated control (60-80% of larvae death), the fractions and isolated trans-cinnamic acid increased the survival rate and modulated the immune system of G. mellonella larvae infected with pathogenic microorganisms. The anti-infection effect of the S. griseocarneus R132 fermentation product led us to sequence its genome, which was assembled and annotated using the Rast and antiSMASH platforms. The assembled genome consisted of 227 scaffolds represented on a linear chromosome of 8.85 Mb and 71.3% of GC. We detected conserved domains typical of enzymes that produce molecules with biological activity, such as polyketides and non-ribosomal and ribosomal peptides, indicating a great potential for obtaining new antibiotics and molecules with biotechnological application.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02942-1.}, }
@article {pmid34421884, year = {2021}, author = {Carlson, HK and Vuono, DC and Glass, JB and Adams, MWW}, title = {Editorial: Selective Controls on Microbial Energy Metabolisms: From the Microscale to the Macroscale.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {728705}, doi = {10.3389/fmicb.2021.728705}, pmid = {34421884}, issn = {1664-302X}, }
@article {pmid34418848, year = {2021}, author = {Mei, Z and Xiang, L and Wang, F and Xu, M and Fu, Y and Wang, Z and Hashsham, SA and Jiang, X and Tiedje, JM}, title = {Bioaccumulation of Manure-borne antibiotic resistance genes in carrot and its exposure assessment.}, journal = {Environment international}, volume = {157}, number = {}, pages = {106830}, doi = {10.1016/j.envint.2021.106830}, pmid = {34418848}, issn = {1873-6750}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bioaccumulation ; *Daucus carota ; Drug Resistance, Microbial ; Genes, Bacterial ; *Manure ; Soil ; Soil Microbiology ; Swine ; }, abstract = {The effect of manure application on the distribution and accumulation of antibiotic resistance genes (ARGs) in tissue of root vegetables remains unclear, which poses a bottleneck in assessing the health risks from root vegetables due to application of manure. Towards this goal, experiments were conducted in pots to investigate the distribution and bioaccumulation of ARGs in carrot tissues due to application of pig manure. The 144 ARGs targeting nine types of antibiotics were quantified by high throughput qPCR in the soil and plant samples. The rhizosphere was a hot spot for ARGs enrichment in the manured soil. The abundance, diversity, and bioaccumulation factors of ARGs in the phyllosphere were significantly higher than those of carrot root skin and tuber. Manure application increased bioaccumulation of 12 ARGs and 2 MGEs in carrot tuber with 124 the highest factor. The application of manure increased transfer of 10 ARGs and 3 MGEs from carrot skin to inner tuber by factors of 0.1-11.8. The average gene copy number of ARGs of per gram carrot root was about 4.8 × 10[4] and 1.1 × 10[6] in the control and the manured treatment, respectively. Children and adults may co-ingest 2.7 × 10[7] and 3.2 × 10[7] of ARGs copies/d from carrots grown with pig manure, using estimated human intake values. However, peeling may reduce the intake of ARGs by 28-91% and of MGEs by 46-59%. In conclusion, the application of pig manure increased the accumulation of ARGs in the skin of carrots, whereas peeling was an effective strategy to reduce the risk.}, }
@article {pmid34418788, year = {2021}, author = {Verstrepen, L and Van den Abbeele, P and Pignataro, G and Ribecco, C and Gramenzi, A and Hesta, M and Marzorati, M}, title = {Inclusion of small intestinal absorption and simulated mucosal surfaces further improve the Mucosal Simulator of the Canine Intestinal Microbial Ecosystem (M-SCIME™).}, journal = {Research in veterinary science}, volume = {140}, number = {}, pages = {100-108}, doi = {10.1016/j.rvsc.2021.08.011}, pmid = {34418788}, issn = {1532-2661}, mesh = {Animals ; Dogs ; *Gastrointestinal Microbiome ; Intestinal Absorption ; Intestine, Small ; *Microbiota ; *Probiotics ; }, abstract = {While a large set of in vitro models are available to study the effects of specific food ingredients (e.g. pre- and probiotics) on the human gut microbiome, the availability of such models for companion animals is limited. Since improving gut health of such animals is an emerging research field, the Simulator of the Canine Intestinal Microbial Ecosystem (SCIME™) was recently developed and validated with in vivo data. The current study presents a further improvement of this model by using an alternative method for feed preparation, i.e. by administering digestive enzymes to mimic upper gastro-intestinal digestion followed by a dialysis approach to mimic small intestinal absorption. As opposed to the previously implemented method, this resulted in a more optimal simulation of protein digestion and absorption. Further, upon entrance in the colon, increased production of the health-promoting butyrate and lower levels of Lactobacillus spp. and Bifidobacterium spp. were observed, which corresponded better with obtained in vivo data. A second model improvement consisted of the implementation of a mucosal environment to not only simulate luminal but also mucosal microbiota. In consistency with the human model for which this technology was previously validated, it was found that for all canine microbiota mucin beads were enriched with members of the Lachnospiraceae (~ Clostridium cluster XIVa), a family containing multiple well-known butyrate producers. The SCIME™ was thus upgraded to a so-called Mucosal SCIME™ (M-SCIME™). In conclusion, the current study presents improvements of the SCIME™, further increasing the relevance of obtained data with this in vitro model for dogs.}, }
@article {pmid34417850, year = {2021}, author = {Tang, Y and Ma, KY and Cheung, MK and Yang, CH and Wang, Y and Hu, X and Kwan, HS and Chu, KH}, title = {Correction to: Gut Microbiota in Decapod Shrimps: Evidence of Phylosymbiosis.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {1008}, doi = {10.1007/s00248-021-01825-5}, pmid = {34417850}, issn = {1432-184X}, }
@article {pmid34417849, year = {2022}, author = {Sangwan, S and Prasanna, R}, title = {Mycorrhizae Helper Bacteria: Unlocking Their Potential as Bioenhancers of Plant-Arbuscular Mycorrhizal Fungal Associations.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {1-10}, pmid = {34417849}, issn = {1432-184X}, mesh = {Bacteria/genetics/metabolism ; *Mycorrhizae ; Plant Roots/microbiology ; Plants/microbiology ; Soil ; Soil Microbiology ; Symbiosis ; }, abstract = {The dynamic interactions of plants and arbuscular mycorrhizal fungi (AMF) that facilitate the efficient uptake of minerals from soil and provide protection from various environmental stresses (biotic and abiotic) are now also attributed to a third component of the symbiosis. These are the less investigated mycorrhizae helper bacteria (MHB), which constitute a dense, active bacterial community, tightly associated with AMF, and involved in the development and functioning of AMF. Although AMF spores are known to host several bacteria in their spore walls and cytoplasm, their role in promoting the ecological fitness and establishment of AMF symbiosis by influencing spore germination, mycelial growth, root colonization, metabolic diversity, and biocontrol of soil borne diseases is now being deciphered. MHB also promote the functioning of arbuscular mycorrhizal symbiosis by triggering various plant growth factors, leading to better availability of nutrients in the soil and uptake by plants. In order to develop strategies to promote mycorrhization by AMF, and particularly to stimulate the ability to utilize phosphorus from the soil, there is a need to decipher crucial metabolic signalling pathways of MHB and elucidate their functional significance as mycorrhiza helper bacteria. MHB, also referred to as AMF bioenhancers, also improve agronomic efficiency and formulations using AMF along with enriched population of MHB are a promising option. This review covers the aspects related to the specificity and mechanisms of action of MHB, which positively impact the formation and functioning of AMF in mycorrhizal symbiosis, and the need to advocate MHB as AMF bioenhancers towards their inclusion in integrated nutrient management practices in sustainable agriculture.}, }
@article {pmid34411359, year = {2021}, author = {Lajoie, G and Kembel, SW}, title = {Plant-bacteria associations are phylogenetically structured in the phyllosphere.}, journal = {Molecular ecology}, volume = {30}, number = {21}, pages = {5572-5587}, doi = {10.1111/mec.16131}, pmid = {34411359}, issn = {1365-294X}, support = {//Canada Research Chairs/ ; //Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Bacteria/genetics ; Metagenomics ; Phylogeny ; Plant Leaves ; *Plants ; }, abstract = {Determining whether and how global change will lead to novel interactions between hosts and microbes is an important issue in ecology and evolution. Understanding the contribution of host and microbial ecologies and evolutionary histories in driving their contemporary associations is an important step towards addressing this challenge and predicting the fitness consequences of novel associations. Using shotgun metagenomic and amplicon sequencing of bacterial communities from the leaf surfaces (phyllosphere) of trees, we investigated how phylogenetic relatedness among hosts and among their associated bacteria influences the distribution of bacteria among hosts. We also evaluated whether the functional traits of trees and bacteria explained these associations across multiple host species. We show that phylogenetically similar hosts tended to associate with the same bacteria and that phylogenetically similar bacteria tended to associate with the same host species. Phylogenetic interactions between tree and bacterial taxa also explained variation in their associations. The effect of host and symbiont evolutionary histories on bacterial distribution across hosts were observed across phylogenetic scales, but prominently explained variation among higher taxonomic categories of hosts and symbionts. These results suggest that ecological variation arising early in the plant and bacterial phylogenies have been particularly important for driving their contemporary associations. Variation in bacterial functional genes associated with the biosynthesis of aromatic amino acids and compounds and with cell motility were notably important in explaining bacterial community turnover among gymnosperm and angiosperm hosts. Overall, our results suggest an influence of host and bacterial traits and evolutionary histories in driving their contemporary associations.}, }
@article {pmid34410645, year = {2021}, author = {Baker, JL and Edlund, A}, title = {Identification of Oral Bacterial Biosynthetic Gene Clusters Associated with Caries.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2327}, number = {}, pages = {161-189}, pmid = {34410645}, issn = {1940-6029}, support = {F32 DE026947/DE/NIDCR NIH HHS/United States ; K99 DE029228/DE/NIDCR NIH HHS/United States ; R21 DE028609/DE/NIDCR NIH HHS/United States ; }, mesh = {Biological Products ; *Dental Caries ; Dental Caries Susceptibility ; Humans ; *Microbiota ; Multigene Family ; Streptococcus mutans ; }, abstract = {Small molecules are a primary communication media of the microbial world, and play crucial, yet largely unidentified, roles in microbial ecology and disease pathogenesis. Many small molecules are produced by biosynthetic gene clusters, which can be predicted and analyzed computationally given a genome. A recent study examined the biosynthetic repertoire of the oral microbiome and cross-referenced this information against the disease status of the human host, providing leads for biosynthetic gene clusters, and their natural products, which may be key in the oral microbial ecology affecting dental caries and periodontitis. This chapter provides a step-by-step tutorial to bioinformatically to locate biosynthetic gene clusters within genomes, predict the type of natural products that are produced, and cross-reference the identified biosynthetic gene clusters to microbiomes associated with disease or health.}, }
@article {pmid34410455, year = {2022}, author = {Atnafu, B and Desta, A and Assefa, F}, title = {Microbial Community Structure and Diversity in Drinking Water Supply, Distribution Systems as well as Household Point of Use Sites in Addis Ababa City, Ethiopia.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {73-89}, pmid = {34410455}, issn = {1432-184X}, mesh = {*Actinobacteria/genetics ; Bacteria/genetics ; *Cryptosporidiosis ; *Cryptosporidium/genetics ; *Drinking Water ; Ethiopia ; Humans ; *Microbiota ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; *Water Purification ; Water Supply ; }, abstract = {Understanding ecology of microbiomes in drinking water distribution systems is the most important notion in delivering safe drinking water. Drinking water distribution systems harbor various microbiota despite efforts made in improving water infrastructures in the water industry, especially, in developing countries. Intermittent water supply, long time of water storage, low water pressure, and contaminated source water are among many of the factors responsible for poor drinking water quality affecting health of people. The aim of this study was to explore microbial diversity and structure in water samples collected from source water, treated water, reservoirs, and household points of use locations (taps). High-throughput Illumina sequencing technology was employed by targeting the V4 region of the 16S rRNA gene and the V1-V3 region of the 18S rRNA gene to analyze the microbial community structure. Proteobacteria followed by Firmicutes, Bacteroidetes, and Actinobacteria were the core dominating taxa. Gammaproteobacteria was also dominant among other proteobacterial classes across all sampling points. Opportunistic bacterial genera such as Pseudomonas, Legionella, Klebsiella, Escherichia, and Actinobacteria, as well as eukaryotic microbes like Cryptosporidium, Hartmannella, Acanthamoeba, Aspergillus, and Candida were also abundant taxa found along the distribution systems. The shift in microbial community structure from source to point of use locations was influenced by basic factors such as residual chlorine, intermittent water supply, and long-time storage at the household. The complex microbiota detected in different sampling sites in this study brings drinking water quality problem which further causes significant health problems to both human and animal health. Treatment ineffectiveness, disinfection inefficiency, poor maintenance actions, leakage of sewage, and other domestic wastes are few among many other factors responsible for degraded drinking water quality in this study putting health at high risk. Findings of this research provide important and baseline information to understand the microbial profiles of drinking water along source water and distribution systems. Moreover, knowing the microbial profile will help to design proper water quality assurance approaches.}, }
@article {pmid34408269, year = {2022}, author = {Yuan, Z and Druzhinina, IS and Gibbons, JG and Zhong, Z and Van de Peer, Y and Rodriguez, RJ and Liu, Z and Wang, X and Wei, H and Wu, Q and Wang, J and Shi, G and Cai, F and Peng, L and Martin, FM}, title = {Correction: Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus.}, journal = {The ISME journal}, volume = {16}, number = {1}, pages = {321}, doi = {10.1038/s41396-021-01083-w}, pmid = {34408269}, issn = {1751-7370}, }
@article {pmid34406837, year = {2021}, author = {Cheng, XY and Liu, XY and Wang, HM and Su, CT and Zhao, R and Bodelier, PLE and Wang, WQ and Ma, LY and Lu, XL}, title = {USCγ Dominated Community Composition and Cooccurrence Network of Methanotrophs and Bacteria in Subterranean Karst Caves.}, journal = {Microbiology spectrum}, volume = {9}, number = {1}, pages = {e0082021}, pmid = {34406837}, issn = {2165-0497}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Caves/*microbiology ; DNA, Bacterial/genetics ; Methane/analysis/metabolism ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Karst caves have recently been demonstrated to act as a sink for atmospheric methane, due in part to consumption by microbes residing in caves that can oxidize methane at atmospheric levels. However, our knowledge about the responsible atmospheric methane-oxidizing bacteria (atmMOB) in this vast habitat remains limited to date. To address this issue, weathered rock samples from three karst caves were collected in Guilin City and subjected to high-throughput sequencing of pmoA and 16S rRNA genes. The results showed that members of the high-affinity upland soil cluster (USC), especially upland soil cluster gamma (USCγ), with absolute abundances of 10[4] to 10[9] copies · g[-1] dry sample, dominated the atmMOB communities, while Proteobacteria and Actinobacteria dominated the overall bacterial communities. Moreover, USCγ was a keystone taxon in cooccurrence networks of both the atmMOB and the total bacterial community, whereas keystone taxa in the bacterial network also included Gaiella and Aciditerrimonas. Positive links overwhelmingly dominated the cooccurrence networks of both atmMOB and the total bacterial community, indicating a consistent response to environmental disturbances. Our study shed new insights on the diversity and abundances underlining atmMOB and total bacterial communities and on microbial interactions in subterranean karst caves, which increased our understanding about USC and supported karst caves as a methane sink. IMPORTANCE Karst caves have recently been demonstrated to be a potential atmospheric methane sink, presumably due to consumption by methane-oxidizing bacteria. However, the sparse knowledge about the diversity, distribution, and community interactions of methanotrophs requires us to seek further understanding of the ecological significance of methane oxidation in these ecosystems. Our pmoA high-throughput results from weathered rock samples from three karst caves in Guilin City confirm the wide occurrence of atmospheric methane-oxidizing bacteria in this habitat, especially those affiliated with the upland soil cluster, with a gene copy number of 10[4] to 10[9] copies per gram dry sample. Methanotrophs and the total bacterial communities had more positive than negative interactions with each other as indicated by the cooccurrence network, suggesting their consistent response to environmental disturbance. Our results solidly support caves as an atmospheric methane sink, and they contribute to a comprehensive understanding of the diversity, distribution, and interactions of microbial communities in subsurface karst caves.}, }
@article {pmid34406835, year = {2021}, author = {Li, X and Wang, A and Wan, W and Luo, X and Zheng, L and He, G and Huang, D and Chen, W and Huang, Q}, title = {High Salinity Inhibits Soil Bacterial Community Mediating Nitrogen Cycling.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {21}, pages = {e0136621}, pmid = {34406835}, issn = {1098-5336}, mesh = {Acidobacteria ; Actinobacteria ; Chloroflexi ; Ecosystem ; Nitrogen/metabolism ; *Nitrogen Cycle ; Phylogeny ; Planctomycetes ; RNA, Ribosomal, 16S/genetics ; *Salinity ; *Soil/chemistry ; *Soil Microbiology ; }, abstract = {Salinization is considered a major threat to soil fertility and agricultural productivity throughout the world. Soil microbes play a crucial role in maintaining ecosystem stability and function (e.g., nitrogen cycling). However, the response of bacterial community composition and community-level function to soil salinity remains uncertain. Here, we used multiple statistical analyses to assess the effect of high salinity on bacterial community composition and potential metabolism function in the agricultural ecosystem. Results showed that high salinity significantly altered both bacterial alpha (Shannon-Wiener index and phylogenetic diversity) and beta diversity. Salinity, total nitrogen (TN), and soil organic matter (SOM) were the vital environmental factors shaping bacterial community composition. The relative abundance of Actinobacteria, Chloroflexi, Acidobacteria, and Planctomycetes decreased with salinity, whereas Proteobacteria and Bacteroidetes increased with salinity. The modularity and the ratio of negative to positive links remarkedly decreased, indicating that high salinity destabilized bacterial networks. Variable selection, which belongs to deterministic processes, mediated bacterial community assembly within the saline soils. Function prediction results showed that the key nitrogen metabolism (e.g., ammonification, nitrogen fixation, nitrification, and denitrification processes) was inhibited in high salinity habitats. MiSeq sequencing of 16S rRNA genes revealed that the abundance and composition of the nitrifying community were influenced by high salinity. The consistency of function prediction and experimental verification demonstrated that high salinity inhibited soil bacterial community mediating nitrogen cycling. Our study provides strong evidence for a salinity effect on the bacterial community composition and key metabolism function, which could help us understand how soil microbes respond to ongoing environment perturbation. IMPORTANCE Revealing the response of the soil bacterial community to external environmental disturbances is an important but poorly understood topic in microbial ecology. In this study, we evaluated the effect of high salinity on the bacterial community composition and key biogeochemical processes in salinized agricultural soils (0.22 to 19.98 dS m[-1]). Our results showed that high salinity significantly decreased bacterial diversity, altered bacterial community composition, and destabilized the bacterial network. Moreover, variable selection (61% to 66%) mediated bacterial community assembly within the saline soils. Functional prediction combined with microbiological verification proved that high salinity inhibited soil bacterial community mediating nitrogen turnover. Understanding the impact of salinity on soil bacterial community is of great significance for managing saline soils and maintaining a healthy ecosystem.}, }
@article {pmid34406446, year = {2022}, author = {Yu, HW and He, WM}, title = {Arbuscular Mycorrhizal Fungi Compete Asymmetrically for Amino Acids with Native and Invasive Solidago.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {131-140}, pmid = {34406446}, issn = {1432-184X}, support = {31971552//National Natural Science Foundation of China/ ; }, mesh = {Amino Acids/metabolism ; *Mycorrhizae/metabolism ; Nitrogen/metabolism ; Plant Roots/metabolism ; Plants/metabolism ; Soil/chemistry ; *Solidago ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) and soil amino acids both affect plant performance. However, little is known about how AMF compete for amino acids with native and invasive congeners. We conducted a factorial experiment (inoculation, native and invasive species, and amino acids) to examine the competition for amino acids between soil microbes and both native and invasive congeners. The competition for amino acids between AMF and invasive Solidago canadensis was weaker than that observed between AMF and native S. decurrens. This asymmetric competition increased the growth advantage of S. canadensis over S. decurrens. The efficacy (biomass production per unit of nitrogen supply) of amino acids compared to ammonium was smaller in S. canadensis than in S. decurrens when both species were grown without inoculation, but the opposite was the case when both species were grown with AMF. AMF and all microbes differentially altered four phenotypic traits (plant height, leaf chlorophyll content, leaf number, and root biomass allocation) and the pathways determining the effects of amino acids on growth advantages. These findings suggest that AMF could enhance plant invasiveness through asymmetric competition for amino acids and that amino acid-driven invasiveness might be differentially regulated by different microbial guilds.}, }
@article {pmid34406445, year = {2022}, author = {Harris, RL and Vetter, MCYL and van Heerden, E and Cason, E and Vermeulen, JG and Taneja, A and Kieft, TL and DeCoste, CJ and Laevsky, GS and Onstott, TC}, title = {FISH-TAMB, a Fixation-Free mRNA Fluorescent Labeling Technique to Target Transcriptionally Active Members in Microbial Communities.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {182-197}, pmid = {34406445}, issn = {1432-184X}, support = {DGE-1148900//U.S. National Science Foundation/ ; DEB-1441717//U.S. National Science Foundation/ ; EAR-1528492//U.S. National Science Foundation/ ; DEB-1442059//U.S. National Science Foundation/ ; DEB-1441646//U.S. National Science Foundation/ ; P30CA072720-5921//NCI-CCSG/ ; }, mesh = {Archaea ; DNA, Archaeal/genetics ; Escherichia coli/genetics ; In Situ Hybridization, Fluorescence/methods ; *Methane/metabolism ; *Microbiota ; Oxidoreductases/genetics ; Phylogeny ; RNA, Messenger/genetics/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {Keystone species or ecological engineers are vital to the health of an ecosystem; however, often, their low abundance or biomass present challenges for their discovery, identification, visualization and selection. We report the development of fluorescent in situ hybridization of transcript-annealing molecular beacons (FISH-TAMB), a fixation-free protocol that is applicable to archaea and bacteria. The FISH-TAMB method differs from existing FISH methods by the absence of fixatives or surfactants in buffers, the fast hybridization time of as short as 15 min at target cells' growth temperature, and the omission of washing steps. Polyarginine cell-penetrating peptides are employed to deliver molecular beacons (MBs) across prokaryotic cell walls and membranes, fluorescently labeling cells when MBs hybridize to target mRNA sequences. Here, the detailed protocol of the preparation and application of FISH-TAMB is presented. To demonstrate FISH-TAMB's ability to label intracellular mRNA targets, differentiate transcriptional states, detect active and rare taxa, and keep cell viability, labeling experiments were performed that targeted the messenger RNA (mRNA) of methyl-coenzyme M reductase A (mcrA) expressed in (1) Escherichia coli containing a plasmid with a partial mcrA gene of the methanogen Methanosarcina barkeri (E. coli mcrA[+]); (2) M. barkeri; and (3) an anaerobic methanotrophic (ANME) enrichment from a deep continental borehole. Although FISH-TAMB was initially envisioned for mRNA of any functional gene of interest without a requirement of prior knowledge of 16S ribosomal RNA (rRNA)-based taxonomy, FISH-TAMB has the potential for multiplexing and going beyond mRNA and thus is a versatile addition to the molecular ecologist's toolkit, with potentially widespread application in the field of environmental microbiology.}, }
@article {pmid34405252, year = {2022}, author = {Whitaker, BK and Giauque, H and Timmerman, C and Birk, N and Hawkes, CV}, title = {Local Plants, Not Soils, Are the Primary Source of Foliar Fungal Community Assembly in a C4 Grass.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {122-130}, pmid = {34405252}, issn = {1432-184X}, support = {HATCH accesssion no 1018688//U.S. Department of Agriculture/ ; SCW1039//U.S. Department of Energy/ ; }, mesh = {Biodiversity ; Fungi/physiology ; *Mycobiome ; *Panicum ; Plants/microbiology ; Soil ; }, abstract = {Microbial communities, like their macro-organismal counterparts, assemble from multiple source populations and by processes acting at multiple spatial scales. However, the relative importance of different sources to the plant microbiome and the spatial scale at which assembly occurs remains debated. In this study, we analyzed how source contributions to the foliar fungal microbiome of a C4 grass differed between locally abundant plants and soils across an abiotic gradient at different spatial scales. Specifically, we used source-sink analysis to assess the likelihood that fungi in leaves from Panicum hallii came from three putative sources: two plant functional groups (C4 grasses and dicots) and soil. We expected that physiologically similar C4 grasses would be more important sources to P. hallii than dicots. We tested this at ten sites in central Texas spanning a steep precipitation gradient. We also examined source contributions at three spatial scales: individual sites (local), local plus adjacent sites (regional), or all sites (gradient-wide). We found that plants were substantially more important sources than soils, but contributions from the two plant functional groups were similar. Plant contributions overall declined and unexplained variation increased as mean annual precipitation increased. This source-sink analysis, combined with partitioning of beta-diversity into nestedness and turnover components, indicated high dispersal limitation and/or strong environmental filtering. Overall, our results suggest that the source-sink dynamics of foliar fungi are primarily local, that foliar fungi spread from plant-to-plant, and that the abiotic environment may affect fungal community sourcing both directly and via changes to host plant communities.}, }
@article {pmid34405251, year = {2022}, author = {Sharma, R and Gal, L and Garmyn, D and Bru, D and Sharma, S and Piveteau, P}, title = {Plant Growth Promoting Bacterial Consortium Induces Shifts in Indigenous Soil Bacterial Communities and Controls Listeria monocytogenes in Rhizospheres of Cajanus cajan and Festuca arundinacea.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {106-121}, pmid = {34405251}, issn = {1432-184X}, mesh = {*Cajanus/microbiology ; *Festuca ; Humans ; *Listeria monocytogenes ; Plant Roots/microbiology ; Plants ; Rhizosphere ; Soil ; Soil Microbiology ; }, abstract = {The rhizosphere is a dynamic and complex interface between plant roots and microorganisms. Owing to exudates, a web of interactions establishes among the microbial members of this micro-environment. The present study explored the impact of a bacterial consortium (Azotobacter chroococcum, Bacillus megaterium and Pseudomonas fluorescens, ABP), on the fate of a human pathogen, Listeria monocytogenes EGD-e, in soil and in the rhizospheres of Cajanus cajan and Festuca arundinacea, in addition to its plant growth promoting effect. The study further assessed the impact these bioinoculants exert on the autochthonous soil bacterial communities. Experiments in sterilised soil inoculated with bioinoculants and L. monocytogenes revealed the inhibition of L. monocytogenes by approximately 80-fold compared to that without the consortium. Subsequently, experiments were conducted in non-sterile soil microcosms planted with C. cajan and F. arundinacea, and in bulk soil. The consortium led to a significant increase in plant growth in both plants and prevented growth of L. monocytogenes. However, the presence of resident soil bacterial communities overshadowed this inhibitory effect, and a sharp decline in L. monocytogenes populations (5-6 log reduction) was recorded under non-sterile soil conditions. A shift in the soil resident bacterial communities was observed upon amendment with the bioinoculants. A significant increase of potential Plant Growth Promoting Rhizobacteria (PGPR) and biocontrol agents was observed, while the abundance of potential phytopathogens dropped. The present study opens up new avenues for the application of such a consortium given their dual benefits of plant growth promotion and restricting phytopathogens as well as human pathogen.}, }
@article {pmid34405250, year = {2022}, author = {Wang, Z and Xiao, R and Huang, J and Qin, X and Hu, D and Guo, E and Liu, C and Lu, F and You, L and Sun, C and Chen, G}, title = {The Diversity of Vaginal Microbiota Predicts Neoadjuvant Chemotherapy Responsiveness in Locally Advanced Cervical Cancer.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {302-313}, pmid = {34405250}, issn = {1432-184X}, support = {81402163//the Nature and Science Foundation of China/ ; 81402164//the Nature and Science Foundation of China/ ; 81572569//the Nature and Science Foundation of China/ ; 81874106//the Nature and Science Foundation of China/ ; 2020JYCXJJ013//the Technology Innovation Foundation of Innovation Institute of Huazhong University of Science and Technology/ ; }, mesh = {Female ; Humans ; *Microbiota/genetics ; Neoadjuvant Therapy ; RNA, Ribosomal, 16S/genetics ; *Uterine Cervical Neoplasms/drug therapy/microbiology ; Vagina/microbiology ; }, abstract = {The vaginal microbiota is closely related to HPV infection and cervical cancer (CC), but its relationship with platinum-based chemotherapy responsiveness is unknown. The study aimed to investigate the vaginal microbiota diversity of women with locally advanced cervical cancer (LACC) and compare the differences between responders and nonresponders. We characterized the 16S rRNA gene sequencing of vaginal microbiome of 66 vaginal samples, including 26 LACC patients before neoadjuvant chemotherapy and 40 healthy controls. Compared with the healthy controls, alpha diversity was significantly increased in CC patients (p <0.05) with more unconventionality bacterial colonization. Beta diversity also significantly differed between cervical cancer patients and controls (p <0.01). Within the CC patients, alpha diversity in vaginal samples was significantly higher in the nonresponders versus the responders (p <0.01), and the Ace index and Chao index were negatively correlated with mass reduction (p <0.001). Moreover, the Bacteroides genus enriched in the nonresponders had a ROC-plot AUC value reaching 0.84. The study suggests the vaginal microbiota in LACC patients is associated with platinum-based chemotherapy responsiveness. Alpha diversity and Bacteroides abundance have the potential of identifying platinum-resistant patients at an early time. These findings provide a basis for further research on the relationship between vaginal microbiome and chemotherapy effect in LACC.}, }
@article {pmid34405249, year = {2022}, author = {Pascoal, F and Costa, R and Assmy, P and Duarte, P and Magalhães, C}, title = {Exploration of the Types of Rarity in the Arctic Ocean from the Perspective of Multiple Methodologies.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {59-72}, pmid = {34405249}, issn = {1432-184X}, support = {2020.04453.BD//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/CTA-AMB/30997/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/CTA-AMB/4946/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04423/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDP/04423/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04565/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; Project N. 007317//Programa Operacional Regional de Lisboa/ ; Arktis 2030//Norwegian Ministries of Foreign Affairs and Climate and Environment/ ; }, mesh = {*Ecosystem ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; }, abstract = {The Arctic Ocean is facing rapid environmental changes with cascading effects on the entire Arctic marine ecosystem. However, we have a limited understanding of the consequences such changes have on bacteria and archaea (prokaryotes) at the base of the marine food web. In this study, we show how the prokaryotic rare biosphere behaves over a range of highly heterogeneous environmental conditions using 16S rRNA gene reads from amplicon and metagenome sequencing data from seawater samples collected during the Norwegian young sea ICE expedition between late winter and early summer. The prokaryotic rare biosphere was analyzed using different approaches: amplicon sequence variants and operational taxonomic units from the 16S rRNA gene amplicons and operational taxonomic units from the 16S rRNA genes of the metagenomes. We found that prokaryotic rare biosphere communities are specific to certain water masses, and that the majority of the rare taxa identified were always rare and disappeared in at least one sample under changing conditions, suggesting their high sensitivity to environmental heterogeneity. In addition, our methodological comparison revealed a good performance of 16S rRNA gene amplicon sequencing in describing rare biosphere patterns, while the metagenome-derived data were better to capture a significant diversity of so-far uncultivated rare taxa. Our analysis on the dynamics of the rare prokaryotic biosphere, by combining different methodological approaches, improves the description of the types of rarity predicted from Community Assembly theory in the Arctic Ocean.}, }
@article {pmid34403645, year = {2021}, author = {van de Peppel, LJJ and Nieuwenhuis, M and Auxier, B and Grum-Grzhimaylo, AA and Cárdenas, ME and de Beer, ZW and Lodge, DJ and Smith, ME and Kuyper, TW and Franco-Molano, AE and Baroni, TJ and Aanen, DK}, title = {Ancestral predisposition toward a domesticated lifestyle in the termite-cultivated fungus Termitomyces.}, journal = {Current biology : CB}, volume = {31}, number = {19}, pages = {4413-4421.e5}, doi = {10.1016/j.cub.2021.07.070}, pmid = {34403645}, issn = {1879-0445}, mesh = {*Agaricales ; Animals ; Humans ; *Isoptera/microbiology ; Life Style ; Phylogeny ; Symbiosis ; *Termitomyces/genetics ; }, abstract = {The ancestor of termites relied on gut symbionts for degradation of plant material, an association that persists in all termite families.[1][,][2] However, the single-lineage Macrotermitinae has additionally acquired a fungal symbiont that complements digestion of food outside the termite gut.[3] Phylogenetic analysis has shown that fungi grown by these termites form a clade-the genus Termitomyces-but the events leading toward domestication remain unclear.[4] To address this, we reconstructed the lifestyle of the common ancestor of Termitomyces using a combination of ecological data with a phylogenomic analysis of 21 related non-domesticated species and 25 species of Termitomyces. We show that the closely related genera Blastosporella and Arthromyces also contain insect-associated species. Furthermore, the genus Arthromyces produces asexual spores on the mycelium, which may facilitate insect dispersal when growing on aggregated subterranean fecal pellets of a plant-feeding insect. The sister-group relationship between Arthromyces and Termitomyces implies that insect association and asexual sporulation, present in both genera, preceded the domestication of Termitomyces and did not follow domestication as has been proposed previously. Specialization of the common ancestor of these two genera on an insect-fecal substrate is further supported by similar carbohydrate-degrading profiles between Arthromyces and Termitomyces. We describe a set of traits that may have predisposed the ancestor of Termitomyces toward domestication, with each trait found scattered in related taxa outside of the termite-domesticated clade. This pattern indicates that the origin of the termite-fungus symbiosis may not have required large-scale changes of the fungal partner.}, }
@article {pmid34399522, year = {2021}, author = {Bolívar, A and Tarlak, F and Costa, JCCP and Cejudo-Gómez, M and Bover-Cid, S and Zurera, G and Pérez-Rodríguez, F}, title = {A new expanded modelling approach for investigating the bioprotective capacity of Latilactobacillus sakei CTC494 against Listeria monocytogenes in ready-to-eat fish products.}, journal = {Food research international (Ottawa, Ont.)}, volume = {147}, number = {}, pages = {110545}, doi = {10.1016/j.foodres.2021.110545}, pmid = {34399522}, issn = {1873-7145}, mesh = {Animals ; Coculture Techniques ; Fish Products ; *Lactobacillales ; *Listeria monocytogenes ; Microbial Interactions ; }, abstract = {Understanding the role of food-related factors on the efficacy of protective cultures is essential to attain optimal results for developing biopreservation-based strategies. The aim of this work was to assess and model growth of Latilactobacillus sakei CTC494 and Listeria monocytogenes CTC1034, and their interaction, in two different ready-to-eat fish products (i.e., surimi-based product and tuna pâté) at 2 and 12 °C. The existing expanded Jameson-effect and a new expanded Jameson-effect model proposed in this study were evaluated to quantitatively describe the effect of microbial interaction. The inhibiting effect of the selected lactic acid bacteria strain on the pathogen growth was product dependent. In surimi product, a reduction of lag time of both strains was observed when growing in coculture at 2 °C, followed by the inhibition of the pathogen when the bioprotective L. sakei CTC494 reached the maximum population density, suggesting a mutualism-antagonism continuum phenomenon between populations. In tuna pâté, L. sakei CTC494 exerted a strong inhibition of L. monocytogenes at 2 °C (<0.5 log increase) and limited the growth at 12 °C (<2 log increase). The goodness-of-fit indexes indicated that the new expanded Jameson-effect model performed better and appropriately described the different competition patterns observed in the tested fish products. The proposed expanded competition model allowed for description of not only antagonistic but also mutualism-based interactions based on their influence on lag time.}, }
@article {pmid34399325, year = {2021}, author = {Barbosa, RG and Oliveira, FC and Andrés-Torres, M and Sleutels, T and Verstraete, W and Boon, N}, title = {Effective orthophosphate removal from surface water using hydrogen-oxidizing bacteria: Moving towards applicability.}, journal = {The Science of the total environment}, volume = {800}, number = {}, pages = {149648}, doi = {10.1016/j.scitotenv.2021.149648}, pmid = {34399325}, issn = {1879-1026}, mesh = {Bacteria ; *Hydrogen ; Nitrogen ; Oxidation-Reduction ; *Phosphates/analysis ; Phosphorus ; Wastewater ; Water ; }, abstract = {Effective orthophosphate removal strategies are needed to counteract eutrophication and guarantee water quality. Previously, we established that hydrogen-oxidizing bacteria (HOB) have the ability to remove orthophosphate from artificial surface water. In the present study, we expand the application of the HOB orthophosphate removal strategy (1) to treat artificial surface water with low initial orthophosphate concentrations, (2) to treat real surface water and real wastewater effluent, and (3) to remove orthophosphate continuously. For synthetic surface water, irrespective of the initial concentration of 0.7, 0.5, 0.3, and 0.1 mg PO4[3-]-P/L, ultra-low concentrations (0.0058 ± 0.0028 mg PO4[3-]-P/L) were obtained. When artificial surface water was replaced by real surface water, without added nutrients or other chemicals, it was shown that over 90% orthophosphate could be removed within 30 min of operation in a batch configuration (0.031 ± 0.023 mg PO4[3-]-P/L). In continuous operation, orthophosphate removal from surface water left an average concentration of 0.040 ± 0.036 for 60 days, and the lowest orthophosphate concentration measured was 0.013 mg PO4[3-]/L. Simultaneously, nitrate was continuously removed for 60 days below 0.1 mg/L. The ability to remove orthophosphate even under nitrogen limiting conditions might be related to the ability of HOB to fix nitrogen. This study brings valuable insights into the potential use of HOB biofilms for nutrient remediation and recovery.}, }
@article {pmid34399219, year = {2022}, author = {Du, P and He, H and Zhou, L and Dong, F and Liu, X and Zheng, Y}, title = {Different biodegradation potential and the impacted soil functions of epoxiconazole in two soils.}, journal = {Journal of hazardous materials}, volume = {422}, number = {}, pages = {126787}, doi = {10.1016/j.jhazmat.2021.126787}, pmid = {34399219}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; Epoxy Compounds/toxicity ; *Soil ; *Triazoles/analysis/toxicity ; }, abstract = {Epoxiconazole is an effective pesticide to control Fusarium head blight (FHB), and the application will increase. To investigate the ecotoxicity of epoxiconazole to soil microbiome, we carried out an indoor experiment in which soils from two main regions of wheat production in China (Nanjing and Anyang) were treated with epoxiconazole (0, 0.0625, 0.625, or 6.25 mg kg[-1]) and incubated for 90 days. Under epoxiconazole stress, for bacteria and fungi, the abundance was increased and the diversity and community were impacted. In Anyang soil, the half-life of epoxiconazole was short with more increased species (linear discriminant analysis effect size biomarkers) and more increased xenobiotics biodegradation pathways in epoxiconazole treatments. The increased species mostly due to high abundance in initial state and more positive connections of the species. Co-occurrences revealed that epoxiconazole tightened bacterial connection, and increased positive correlations in Anyang soil. The N transformation was influenced with increased nifH and amoA; and the contents of NH4[+]-N and NO3[-]-N were also increased. The functions of C, S, and manganese metabolisms were also impacted by epoxiconazole. This work expands our understanding about epoxiconazole degradation and help us to properly assess the risk of epoxiconazole in soil.}, }
@article {pmid34398256, year = {2022}, author = {Li, Y and Lin, H and Gao, P and Yang, N and Xu, R and Sun, X and Li, B and Xu, F and Wang, X and Song, B and Sun, W}, title = {Synergistic Impacts of Arsenic and Antimony Co-contamination on Diazotrophic Communities.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {44-58}, pmid = {34398256}, issn = {1432-184X}, support = {U20A20109//National Natural Science Foundation of China/ ; 2020GDASYL-20200102015//GDAS' Project of Science and Technology Development/ ; 2021GDASYL-20210103048//GDAS' Project of Science and Technology Development/ ; 2020GDASYL-20200102014//GDAS' Project of Science and Technology Development/ ; 2021GDASYL-20210103041//GDAS' Project of Science and Technology Development/ ; 2019GDASYL-0103052//GDAS' Project of Science and Technology Development/ ; 2020GDASYL-20200103082//GDAS' Project of Science and Technology Development/ ; 2019GDASYL-0301002//GDAS' Project of Science and Technology Development/ ; 2020GDASYL-20200402003//GDAS' Project of Science and Technology Development/ ; 202002020072//the Science and Technology Planning Project of Guangzhou/ ; 2017GC010570//the High-Level Talents Project of the Pearl River Talents Recruitment Program/ ; 2017BT01Z176//the Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program/ ; }, mesh = {Antimony/analysis ; *Arsenic/analysis ; Environmental Monitoring ; *Microbiota ; *Soil Pollutants/analysis ; }, abstract = {Nitrogen (N) shortage poses a great challenge to the implementation of in situ bioremediation practices in mining-contaminated sites. Diazotrophs can fix atmospheric N2 into a bioavailable form to plants and microorganisms inhabiting adverse habitats. Increasing numbers of studies mainly focused on the diazotrophic communities in the agroecosystems, while those communities in mining areas are still not well understood. This study compared the variations of diazotrophic communities in composition and interactions in the mining areas with different extents of arsenic (As) and antimony (Sb) contamination. As and Sb co-contamination increased alpha diversities and the abundance of nifH encoding the dinitrogenase reductase, while inhibited the diazotrophic interactions and substantially changed the composition of communities. Based on the multiple lines of evidence (e.g., the enrichment analysis of diazotrophs, microbe-microbe network, and random forest regression), six diazotrophs (e.g., Sinorhizobium, Dechloromonas, Trichormus, Herbaspirillum, Desmonostoc, and Klebsiella) were identified as keystone taxa. Environment-microbe network and random forest prediction demonstrated that these keystone taxa were highly correlated with the As and Sb contamination fractions. All these results imply that the above-mentioned diazotrophs may be resistant to metal(loid)s.}, }
@article {pmid34396460, year = {2022}, author = {Bamary, Z and Einali, A}, title = {Changes in Carbon Partitioning and Pattern of Antioxidant Enzyme Activity Induced by Arginine Treatment in the Green Microalga Dunaliella salina Under Long-Term Salinity.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {198-212}, pmid = {34396460}, issn = {1432-184X}, support = {27259//University of Sistan and Baluchestan/ ; }, mesh = {*Antioxidants/metabolism/pharmacology ; Arginine/metabolism/pharmacology ; Carbon/metabolism ; Glycerol/metabolism ; Hydrogen Peroxide/metabolism ; *Microalgae/metabolism ; Salinity ; Starch/metabolism ; Sugars/metabolism/pharmacology ; beta Carotene/metabolism/pharmacology ; }, abstract = {In this work, the effects of arginine (Arg) on biochemical responses and antioxidant enzyme activity in the green microalga Dunaliella salina grown at different salt concentrations were investigated. Suspensions adapted with the concentrations of 1, 2, and 3 M NaCl were treated at the exponential growth phase with a concentration of 5 mM Arg. Salt stress was associated with a large decrease in the number of cells and non-reducing sugar levels but accumulated higher amounts of chlorophyll, β-carotene, reducing sugar, starch, total protein, free amino acid, and glycerol. Increased levels of protein carbonylation, lipid peroxidation, proteolysis, hydrogen peroxide, and antioxidant enzyme activity also occurred during salinity. Arg treatment changed the pattern of biochemical responses in the cells grown at high salinity by directing carbon flow to the biosynthesis of non-reducing sugars instead of starch, lowering levels of hydrogen peroxide, and downregulating antioxidant enzyme activity, but the levels of lipid peroxidation, glycerol, and β-carotene remained nearly unchanged. These results suggest that Arg treatment alleviates salinity-induced oxidative stress in D. salina cells by modifying carbon partitioning and inducing signaling molecules rather than antioxidant enzymes.}, }
@article {pmid34394041, year = {2021}, author = {Chu, XL and Zhang, QG and Buckling, A and Castledine, M}, title = {Interspecific Niche Competition Increases Morphological Diversity in Multi-Species Microbial Communities.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {699190}, pmid = {34394041}, issn = {1664-302X}, abstract = {Intraspecific competition for limited niches has been recognized as a driving force for adaptive radiation, but results for the role of interspecific competition have been mixed. Here, we report the adaptive diversification of the model bacteria Pseudomonas fluorescens in the presence of different numbers and combinations of four competing bacterial species. Increasing the diversity of competitive community increased the morphological diversity of focal species, which is caused by impeding the domination of a single morphotype. Specifically, this pattern was driven by more diverse communities being more likely to contain key species that occupy the same niche as otherwise competitively superior morphotype, and thus preventing competitive exclusion within the focal species. Our results suggest that sympatric adaptive radiation is driven by the presence or absence of niche-specific competitors.}, }
@article {pmid34394013, year = {2021}, author = {Danko, D and Malli Mohan, GB and Sierra, MA and Rucker, M and Singh, NK and Regberg, AB and Bell, MS and O'Hara, NB and Ounit, R and Mason, CE and Venkateswaran, K}, title = {Characterization of Spacesuit Associated Microbial Communities and Their Implications for NASA Missions.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {608478}, pmid = {34394013}, issn = {1664-302X}, support = {T32 GM083937/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: Crewed National Aeronautics and Space Administration (NASA) missions to other solar system bodies are currently being planned. One high-profile scientific focus during such expeditions would be life detection, specifically the discovery of past or present microbial life, if they exist. However, both humans and associated objects typically carry a high microbial burden. Thus, it is essential to distinguish between microbes brought with the expedition and those present on the exploring planets. Modern spacesuits are unique, customized spacecraft which provide protection, mobility and life support to crew during spacewalks, yet they vent, and the mobility of microbes through spacesuits has not been studied.<br><br>RESULTS: To evaluate the microbial colonization of spacesuits, NASA used an Extravehicular Activity swab kit to examine viable microbial populations of 48 samples from spacesuits using both traditional microbiological methods and molecular sequencing methods. The cultivable microbial population ranged from below the detection limit to 9 &#xd7; 10[2] colony forming units per 25 cm[2] of sample and also significantly varied by the location. The cultivable microbial diversity was dominated by members of Bacillus, Arthrobacter, and Ascomycota. However, 16S rRNA-based viable bacterial burden ranged from 10[5] to 10[6] copies per 25 cm[2] of sample. Shotgun metagenome sequencing revealed the presence of a diverse microbial population on the spacesuit surfaces, including Curtobacterium and Methylobacterium from across all sets of spacesuits in high abundance. Among bacterial species identified, higher abundance of Cutibacterium acnes, Methylobacterium oryzae, and M. phyllosphaerae reads were documented.<br><br>CONCLUSION: The results of this study provide evidence that identical microbial strains may live on the wrist joint, inner gauntlet, and outer gauntlet of spacesuits. This raises the possibility, but does not confirm that microbial contaminants on the outside of the suits could contaminate planetary science operations unless additional measures are taken. Overall, these data provide the first estimate of microbial distribution associated with spacesuit surfaces, which will help future mission planners develop effective planetary protection strategies.}, }
@article {pmid34390303, year = {2021}, author = {Huang, Z and Liu, B and Yin, Y and Liang, F and Xie, D and Han, T and Liu, Y and Yan, B and Li, Q and Huang, Y and Liu, Q}, title = {Impact of biocontrol microbes on soil microbial diversity in ginger (Zingiber officinale Roscoe).}, journal = {Pest management science}, volume = {77}, number = {12}, pages = {5537-5546}, doi = {10.1002/ps.6595}, pmid = {34390303}, issn = {1526-4998}, support = {//National Key R&amp;D Program of China/ ; //Department of Science and Technology of Sichuan Province/ ; }, mesh = {*Zingiber officinale ; Hypocreales ; Plant Roots ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; *Soil ; Soil Microbiology ; }, abstract = {BACKGROUND: Bacteria are the most diverse and abundant group of soil organisms that influence plant growth and health. Bacillus and Trichoderma are commonly used as biological control agents (BCA) that directly or indirectly act on soil bacteria. Therefore, it is essential to understand how the applied microbes impact the indigenous microbial community before exploring their activity in the control of soilborne diseases.<br><br>RESULTS: MiSeq sequencing of the 16S rRNA gene was used to decipher the shift of rhizosphere bacterial community in ginger (Zingiber officinale Roscoe) treated with Bacillus subtilus and Trichoderma harzianum at different concentrations. The dominant phyla in treated and nontreated samples were Proteobacteria, Actinobacteria, Acidobacteria and comprised up to 54.7% of the total sequences. There were significant differences between BCA treated and nontreated samples in the bacteria community. BCA treated plants presented higher bacterial diversity than nontreated and higher dosage of BCA had a larger impact on rhizosphere microbiota, but the 'dose-response relationship' varied in different bacterial groups. Potential biomarkers at genus level were found, such as RB41, Pseudomonas, Nitrospira, Candidatus_Udaeobacter.<br><br>CONCLUSION: The combined use of Bacillus subtilus and Trichoderma harzianum could alter bacterial community structure and diversity in rhizosphere soil. BCA-microbes interactions as well as soil microbial ecology should be noticed in plant disease management. &#xa9; 2021 Society of Chemical Industry.}, }
@article {pmid34389059, year = {2021}, author = {Boeuf, D and Eppley, JM and Mende, DR and Malmstrom, RR and Woyke, T and DeLong, EF}, title = {Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {172}, pmid = {34389059}, issn = {2049-2618}, mesh = {Bacteria/genetics ; *Microbiota ; Oceans and Seas ; Phylogeny ; *Seawater ; }, abstract = {BACKGROUND: Oceanic microbiomes play a pivotal role in the global carbon cycle and are central to the transformation and recycling of carbon and energy in the ocean's interior. SAR324 is a ubiquitous but poorly understood uncultivated clade of Deltaproteobacteria that inhabits the entire water column, from ocean surface waters to its deep interior. Although some progress has been made in elucidating potential metabolic traits of SAR324 in the dark ocean, very little is known about the ecology and the metabolic capabilities of this group in the euphotic and twilight zones. To investigate the comparative genomics, ecology, and physiological potential of the SAR324 clade, we examined the distribution and variability of key genomic features and metabolic pathways in this group from surface waters to the abyss in the North Pacific Subtropical Gyre, one of the largest biomes on Earth.<br><br>RESULTS: We leveraged a pangenomic ecological approach, combining spatio-temporally resolved single-amplified genome, metagenomic, and metatranscriptomic datasets. The data revealed substantial genomic diversity throughout the SAR324 clade, with distinct depth and temporal distributions that clearly differentiated ecotypes. Phylogenomic subclade delineation, environmental distributions, genomic feature similarities, and metabolic capacities revealed strong congruence. The four SAR324 ecotypes delineated in this study revealed striking divergence from one another with respect to their habitat-specific metabolic potentials. The ecotypes living in the dark or twilight oceans shared genomic features and metabolic capabilities consistent with a sulfur-based chemolithoautotrophic lifestyle. In contrast, those inhabiting the sunlit ocean displayed higher plasticity energy-related metabolic pathways, supporting a presumptive photoheterotrophic lifestyle. In epipelagic SAR324 ecotypes, we observed the presence of two types of proton-pumping rhodopsins, as well as genomic, transcriptomic, and ecological evidence for active photoheterotrophy, based on xanthorhodopsin-like light-harvesting proteins.<br><br>CONCLUSIONS: Combining pangenomic and both metagenomic and metatranscriptomic profiling revealed a striking divergence in the vertical distribution, genomic composition, metabolic potential, and predicted lifestyle strategies of geographically co-located members of the SAR324 bacterial clade. The results highlight the utility of metapangenomic approaches employed across environmental gradients, to decipher the properties and variation in function and ecological traits of specific phylogenetic clades within complex microbiomes. Video abstract.}, }
@article {pmid34388922, year = {2022}, author = {Rogiers, T and Merroun, ML and Williamson, A and Leys, N and Houdt, RV and Boon, N and Mijnendonckx, K}, title = {Cupriavidus metallidurans NA4 actively forms polyhydroxybutyrate-associated uranium-phosphate precipitates.}, journal = {Journal of hazardous materials}, volume = {421}, number = {}, pages = {126737}, doi = {10.1016/j.jhazmat.2021.126737}, pmid = {34388922}, issn = {1873-3336}, mesh = {*Cupriavidus/genetics ; Phosphates ; *Uranium ; }, abstract = {Cupriavidus metallidurans is a model bacterium to study molecular metal resistance mechanisms and its use for the bioremediation of several metals has been shown. However, its mechanisms for radionuclide resistance are unexplored. We investigated the interaction with uranium and associated cellular response to uranium for Cupriavidus metallidurans NA4. Strain NA4 actively captured 98 ± 1% of the uranium in its biomass after growing 24 h in the presence of 100 µM uranyl nitrate. TEM HAADF-EDX microscopy confirmed intracellular uranium-phosphate precipitates that were mainly associated with polyhydroxybutyrate. Furthermore, whole transcriptome sequencing indicated a complex transcriptional response with upregulation of genes encoding general stress-related proteins and several genes involved in metal resistance. More in particular, gene clusters known to be involved in copper and silver resistance were differentially expressed. This study provides further insights into bacterial interactions with and their response to uranium. Our results could be promising for uranium bioremediation purposes with the multi-metal resistant bacterium C. metallidurans NA4.}, }
@article {pmid34387704, year = {2021}, author = {de Siqueira, KA and Senabio, JA and Pietro-Souza, W and de Oliveira Mendes, TA and Soares, MA}, title = {Aspergillus sp. A31 and Curvularia geniculata P1 mitigate mercury toxicity to Oryza sativa L.}, journal = {Archives of microbiology}, volume = {203}, number = {9}, pages = {5345-5361}, pmid = {34387704}, issn = {1432-072X}, support = {568258/2014//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa&#xa0;do Estado de&#xa0;Mato Grosso/ ; 409062/2018-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Aspergillus/genetics ; Curvularia ; Endophytes ; *Mercury/toxicity ; *Oryza ; Phylogeny ; Plant Roots ; }, abstract = {Aspergillus sp. A31 and Curvularia geniculata P1 are endophytes that colonize the roots of Aeschynomene fluminensis Vell. and Polygonum acuminatum Kunth. in humid environments contaminated with mercury. The two strains mitigated mercury toxicity and promoted Oryza sativa L growth. C. geniculata P1 stood out for increasing the host biomass by fourfold and reducing the negative effects of the metal on photosynthesis. Assembling and annotation of Aspergillus sp. A31 and C. geniculata P1 genomes resulted in 28.60 Mb (CG% 53.1; 10,312 coding DNA sequences) and 32.92 Mb (CG% 50.72; 8,692 coding DNA sequences), respectively. Twelve and 27 genomes of Curvularia/Bipolaris and Aspergillus were selected for phylogenomic analyzes, respectively. Phylogenetic analysis inferred the separation of species from the genus Curvularia and Bipolaris into different clades, and the separation of species from the genus Aspergillus into three clades; the species were distinguished by occupied niche. The genomes had essential gene clusters for the adaptation of microorganisms to high metal concentrations, such as proteins of the phytoquelatin-metal complex (GO: 0090423), metal ion binders (GO: 0046872), ABC transporters (GO: 0042626), ATPase transporters (GO: 0016887), and genes related to response to reactive oxygen species (GO: 0000302) and oxidative stress (GO: 0006979). The results reported here help to understand the unique regulatory mechanisms of mercury tolerance and plant development.}, }
@article {pmid34387702, year = {2022}, author = {Qin, M and Jiang, L and Kholmatov, BR and Qiao, G and Chen, J}, title = {Phylosymbiotic Structures of the Microbiota in Mollitrichosiphum tenuicorpus (Hemiptera: Aphididae: Greenideinae).}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {227-239}, pmid = {34387702}, issn = {1432-184X}, support = {No. 31772492//National Natural Science Foundation of China/ ; No. XDA19050303//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; Grant No. ANSO-CR-KP-2020-04//Key Collaborative Research Program of the Alliance of International Science Organizations/ ; No. 2020087//Youth Innovation Promotion Association of Chinese Academy of Sciences/ ; }, mesh = {Animals ; *Aphids ; *Buchnera/genetics ; High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; Plants ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Aphids harbor an array of symbionts that provide hosts with ecological benefits. Microbial community assembly generally varies with respect to aphid species, geography, and host plants. However, the influence of host genetics and ecological factors on shaping intraspecific microbial community structures has not been fully understood. In the present study, using Illumina sequencing of the V3 - V4 hypervariable region of the 16S rRNA gene, we characterized the microbial compositions associated with Mollitrichosiphum tenuicorpus from different regions and plants in China. The primary symbiont Buchnera aphidicola and the secondary symbiont Arsenophonus dominated the microbial flora in M. tenuicorpus. Ordination analyses and statistical tests suggested that geography and aphid genetics primarily contributed to the variation in the microbiota of M. tenuicorpus. We further confirmed the combined effect of aphid genetics and geography on shaping the structures of symbiont and secondary symbiont communities. Moreover, the significant correlation between aphid genetic divergence and symbiont community dissimilarity provides evidence for intraspecific phylosymbiosis in natural systems. Our study helped to elucidate the eco-evolutionary relationship between symbiont communities and aphids within one given species.}, }
@article {pmid34387003, year = {2021}, author = {Yang, S and Liebner, S and Svenning, MM and Tveit, AT}, title = {Decoupling of microbial community dynamics and functions in Arctic peat soil exposed to short term warming.}, journal = {Molecular ecology}, volume = {30}, number = {20}, pages = {5094-5104}, doi = {10.1111/mec.16118}, pmid = {34387003}, issn = {1365-294X}, mesh = {Arctic Regions ; Carbon Dioxide/analysis ; Methane ; *Microbiota/genetics ; *Soil ; Soil Microbiology ; Temperature ; }, abstract = {Temperature is an important factor governing microbe-mediated carbon feedback from permafrost soils. The link between taxonomic and functional microbial responses to temperature change remains elusive due to the lack of studies assessing both aspects of microbial ecology. Our previous study reported microbial metabolic and trophic shifts in response to short-term temperature increases in Arctic peat soil, and linked these shifts to higher CH4 and CO2 production rates (Proceedings of the National Academy of Sciences of the United States of America, 112, E2507-E2516). Here, we studied the taxonomic composition and functional potential of samples from the same experiment. We see that along a high-resolution temperature gradient (1-30°C), microbial communities change discretely, but not continuously or stochastically, in response to rising temperatures. The taxonomic variability may thus in part reflect the varied temperature responses of individual taxa and the competition between these taxa for resources. These taxonomic responses contrast the stable functional potential (metagenomic-based) across all temperatures or the previously observed metabolic or trophic shifts at key temperatures. Furthermore, with rising temperatures we observed a progressive decrease in species diversity (Shannon Index) and increased dispersion of greenhouse gas (GHG) production rates. We conclude that the taxonomic variation is decoupled from both the functional potential of the community and the previously observed temperature-dependent changes in microbial function. However, the reduced diversity at higher temperatures might help explain the higher variability in GHG production at higher temperatures.}, }
@article {pmid34385301, year = {2021}, author = {Shoemaker, WR and Jones, SE and Muscarella, ME and Behringer, MG and Lehmkuhl, BK and Lennon, JT}, title = {Microbial population dynamics and evolutionary outcomes under extreme energy limitation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {33}, pages = {}, pmid = {34385301}, issn = {1091-6490}, mesh = {Bacteria/*classification/*genetics ; *Bacterial Physiological Phenomena ; *Biological Evolution ; Energy Metabolism/*genetics/*physiology ; Mutation ; Species Specificity ; }, abstract = {Microorganisms commonly inhabit energy-limited ecosystems where cellular maintenance and reproduction is highly constrained. To gain insight into how individuals persist under such conditions, we derived demographic parameters from a collection of 21 heterotrophic bacterial taxa by censusing 100 populations in an effectively closed system for 1,000 d. All but one taxon survived prolonged resource scarcity, yielding estimated times to extinction ranging over four orders of magnitude from 10[0] to 10[5] y. Our findings corroborate reports of long-lived bacteria recovered from ancient environmental samples, while providing insight into mechanisms of persistence. As death rates declined over time, lifespan was extended through the scavenging of dead cells. Although reproduction was suppressed in the absence of exogenous resources, populations continued to evolve. Hundreds of mutations were acquired, contributing to genome-wide signatures of purifying selection as well as molecular signals of adaptation. Consistent ecological and evolutionary dynamics indicate that distantly related bacteria respond to energy limitation in a similar and predictable manner, which likely contributes to the stability and robustness of microbial life.}, }
@article {pmid34384885, year = {2021}, author = {Marzorati, M and Calatayud, M and Rotsaert, C and Van Mele, M and Duysburgh, C and Durkee, S and White, T and Fowler, K and Jannin, V and Bellamine, A}, title = {Comparison of protection and release behavior of different capsule polymer combinations based on L. acidophilus survivability and function and caffeine release.}, journal = {International journal of pharmaceutics}, volume = {607}, number = {}, pages = {120977}, doi = {10.1016/j.ijpharm.2021.120977}, pmid = {34384885}, issn = {1873-3476}, mesh = {*Caffeine ; Capsules ; Chemistry, Pharmaceutical ; Ecosystem ; Humans ; *Polymers ; }, abstract = {Oral administration of active pharmaceutical ingredients, nutraceuticals, enzymes or probiotics requires an appropriate delivery system for optimal bioactivity and absorption. The harsh conditions during the gastrointestinal transit can degrade the administered products, hampering their efficacy. Enteric or delayed-release pharmaceutical formulations may help overcome these issues. In a Simulator of Human Intestinal Microbial Ecosystem model (SHIME) and using caffeine as a marker for release kinetics and L. acidophilus survivability as an indicator for protection, we compared the performance of ten capsule configurations, single or DUOCAP® combinations. The function of L. acidophilus and its impact on the gut microbiota was further tested in three selected capsule types, combinations of DRcaps® capsule in DRcaps® capsule (DR-in-DR) and DRcaps® capsule in Vcaps® capsule (DR-in-VC) and single Vcaps® Plus capsule under colonic conditions. We found that under stomach and small intestine conditions, DR-in-DR and DR-in-VC led to the best performance both under fed and fasted conditions based on the slow caffeine release and the highest L. acidophilus survivability. The Vcaps® Plus capsule however, led to the quickest caffeine and probiotic release. When DR-in-DR, DR-in-VC and single Vcaps® Plus capsules were tested through the whole gastrointestinal tract, including under colonic conditions, caffeine release was found to be slower in capsules containing DRcaps® capsules compared to the single Vcaps® capsules. In addition, colonic survival of L. acidophilus was significantly increased under fasted conditions in DR-in-DR or DR-in-VC formulation compared to Vcaps® Plus capsule. To assess the impact of these formulations on the microbial function, acetate, butyrate and propionate as well as ammonia were measured. L. acidophilus released from DR-in-DR or DR-in-VC induced a significant increase in butyrate and a decrease in ammonia, suggesting a proliferation of butyrate-producing bacteria and reduction in ammonia-producing bacteria. These data suggest that L. acidophilus included in DR-in-DR or DR-in-VC reaching the colon is viable and functional, potentially contributing to changes in colonic microbiota composition and diversity.}, }
@article {pmid34384375, year = {2021}, author = {Xi, J and Ding, D and Zhu, H and Wang, R and Su, F and Wu, W and Xiao, Z and Liang, X and Zhao, Q and Hong, Z and Fu, H and Xiao, Q}, title = {Disturbed microbial ecology in Alzheimer's disease: evidence from the gut microbiota and fecal metabolome.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {226}, pmid = {34384375}, issn = {1471-2180}, mesh = {Aged ; Aged, 80 and over ; Alzheimer Disease/*microbiology/physiopathology ; Bacteria/*genetics/pathogenicity ; Chromatography, Liquid ; Dysbiosis/complications/*microbiology ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metabolic Networks and Pathways ; *Metabolome ; Metabolomics/methods ; RNA, Ribosomal, 16S/genetics ; Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: Gut microbiota (GMB) alteration has been reported to influence the Alzheimer's disease (AD) pathogenesis through immune, endocrine, and metabolic pathways. This study aims to investigate metabolic output of the dysbiosis of GMB in AD pathogenesis. In this study, the fecal microbiota and metabolome from 21 AD participants and 44 cognitively normal control participants were measured. Untargeted GMB taxa was analyzed through 16S ribosomal RNA gene profiling based on next-generation sequencing and fecal metabolites were quantified by using ultrahigh performance liquid chromatography-mass spectrometry (UPLC-MS).<br><br>RESULTS: Our analysis revealed that AD was characterized by 15 altered gut bacterial genera, of which 46.7% (7/15 general) was significantly associated with a series of metabolite markers. The predicted metabolic profile of altered gut microbial composition included steroid hormone biosynthesis, N-Acyl amino acid metabolism and piperidine metabolism. Moreover, a combination of 2 gut bacterial genera (Faecalibacterium and Pseudomonas) and 4 metabolites (N-Docosahexaenoyl GABA, 19-Oxoandrost-4-ene-3,17-dione, Trigofoenoside F and 22-Angeloylbarringtogenol C) was able to discriminate AD from NC with AUC of 0.955 in these 65 subjects.<br><br>CONCLUSIONS: These findings demonstrate that gut microbial alterations and related metabolic output changes may be associated with pathogenesis of AD, and suggest that fecal markers might be used as a non-invasive examination to assist screening and diagnosis of AD.}, }
@article {pmid34383807, year = {2021}, author = {Deng, S and Wang, B and Zhang, W and Su, S and Dong, H and Banat, IM and Sun, S and Guo, J and Liu, W and Wang, L and She, Y and Zhang, F}, title = {Elucidate microbial characteristics in a full-scale treatment plant for offshore oil produced wastewater.}, journal = {PloS one}, volume = {16}, number = {8}, pages = {e0255836}, pmid = {34383807}, issn = {1932-6203}, mesh = {Anaerobiosis ; Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Bioreactors ; Oil and Gas Fields/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/metabolism ; Waste Disposal, Fluid/instrumentation/*methods ; Wastewater/*microbiology ; Water Pollutants/isolation &amp; purification/metabolism ; }, abstract = {Oil-produced wastewater treatment plants, especially those involving biological treatment processes, harbor rich and diverse microbes. However, knowledge of microbial ecology and microbial interactions determining the efficiency of plants for oil-produced wastewater is limited. Here, we performed 16S rDNA amplicon sequencing to elucidate the microbial composition and potential microbial functions in a full-scale well-worked offshore oil-produced wastewater treatment plant. Results showed that microbes that inhabited the plant were diverse and originated from oil and marine associated environments. The upstream physical and chemical treatments resulted in low microbial diversity. Organic pollutants were digested in the anaerobic baffled reactor (ABR) dominantly through fermentation combined with sulfur compounds respiration. Three aerobic parallel reactors (APRs) harbored different microbial groups that performed similar potential functions, such as hydrocarbon degradation, acidogenesis, photosynthetic assimilation, and nitrogen removal. Microbial characteristics were important to the performance of oil-produced wastewater treatment plants with biological processes.}, }
@article {pmid34383127, year = {2022}, author = {Vieira, FR and Pecchia, JA}, title = {Bacterial Community Patterns in the Agaricus bisporus Cultivation System, from Compost Raw Materials to Mushroom Caps.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {20-32}, pmid = {34383127}, issn = {1432-184X}, support = {PEN04741//United States Department of Agriculture (USDA/NIFA - National Institute of Food and Agriculture) and Hatch Appropriations/ ; }, mesh = {*Agaricus/genetics ; Bacteria/genetics ; *Composting ; *Microbiota ; }, abstract = {Different from other fungal species that can be largely cultivated in 'axenic conditions' using plant material (e.g., species of Lentinula and Pleurotus in 'sterile' straw-based substrate), the commercial Agaricus bisporus cultivation system relies heavily on ecological relationships with a broad range of microorganisms present in the system (compost and casing). Since the A. bisporus cultivation system consists of a microbial manipulation process, it is important to know the microbial community dynamics during the entire cultivation cycle to design further studies and/or crop management strategies to optimize this system. To capture the bacterial community 'flow' from compost raw materials to the casing to the formation and maturation of mushroom caps, community snapshots were generated by direct DNA recovery (amplicon sequencing). The 'bacterial community flow' revealed that compost, casing and mushrooms represent different niches for bacteria present in the cultivation system, but at the same time, a bacterial exchange between microenvironments can occur for a portion of the community. Within each microenvironment, compost showed intense bacterial populational dynamics, probably due to the environmental changes imposed by composting conditions. In casing, the colonization of A. bisporus appeared, to reshape the native bacterial community which later, with some other members present in compost, becomes the core community in mushroom caps. The current bacterial survey along with previous results provides more cues of specific bacteria groups that can be in association with A. bisporus development and health.}, }
@article {pmid34378984, year = {2021}, author = {Liu, D and Pérez-Moreno, J and He, X and Garibay-Orijel, R and Yu, F}, title = {Truffle Microbiome Is Driven by Fruit Body Compartmentalization Rather than Soils Conditioned by Different Host Trees.}, journal = {mSphere}, volume = {6}, number = {4}, pages = {e0003921}, pmid = {34378984}, issn = {2379-5042}, mesh = {Ascomycota/physiology ; Bacteria/classification/*genetics ; Basidiomycota/*physiology ; Fungi/classification/*genetics ; Microbiota/*genetics/physiology ; Phylogeny ; Rhizosphere ; *Soil Microbiology ; *Symbiosis ; *Trees ; }, abstract = {Truffles are among the most expensive edible mushrooms; their value is worth billions of U.S. dollars annually in international markets. They establish ectomycorrhizal symbiotic relationships with diverse host tree roots and produce hypogeous ascomata. Their whole life cycle is closely related to their associated microbiome. However, whether truffle-associated compartments or host tree rhizospheres are the vital driver for truffle ascomata microbiome is unclear. To identify and compare fungal and bacterial communities in four truffle-associated compartments (Tuber indicum: bulk soil, adhering soil to peridium, peridium, and gleba) from three host trees, we sequenced their ITS (fungal) and 16S (bacterial) ribosomal DNA using the Illumina MiSeq high-throughput platform. We further applied the amplicon data to analyze the core microbiome and microbial ecological networks. Tuber indicum microbiome composition was strongly driven by its associated compartments rather than by their symbiotic host trees. Truffle microbiome was bacteria dominated, and its bacterial community formed a substantially more complex interacting network compared to that of the fungal community. The core fungal community changed from Basidiomycota dominated (bulk soil) to Rozellomycota dominated (interphase soil); the core bacterial community shifted from Bacteroidetes to Proteobacteria dominance from truffle peridium to gleba tissue. Especially, at the truffle and soil interphase, the niche-based selection of truffle microbiome was verified by (i) a clear exclusion of four bacterial phyla (Rokubacteria, Nitrospirae, Chloroflexi, and Planctomycetes) in gleba; (ii) a significant decrease in alpha-diversity (as revealed by Chao 1, Shannon, and Simpson indices); and (iii) the complexity of the network substantially decreased from bulk soil to soil-truffle interphase and further to the peridium and gleba. The network analysis of microbiome showed that the microbial positive interactions were higher in truffle tissues than in both bulk soil and peridium-adhering soil and that Cupriavidus, Bradyrhizobium, Aminobacter, and Mesorhizobium spp. were the keystone network hubs in the truffle gleba. This study provides insights into the factors that drive the truffle microbiome dynamics and the recruitment and function of the microbiome components. IMPORTANCE Currently, the factors that drive the microbiome associated with truffles, the most highly prized fungi in the world, are largely unknown. We demonstrate for the first time here that truffle microbiome composition is strongly driven by associated compartments rather than by symbiotic host trees. The truffle microbiome was bacteria dominated, and its bacterial community formed a substantially more complex (with the higher numbers of nodes, links, and modules) interacting network compared to that of the fungal community. Network analysis showed a higher number of positive microbial interactions with each other in truffle tissues than in both bulk soil and peridium-adhering soil. For the first time, the fungal community structure associated with truffles using high-throughput sequencing, microbial networks, and keystone species analyses is presented. This study provides novel insights into the factors that drive the truffle microbiome dynamics and the recruitment and function of the microbiome components, showing that they are more complex than previously thought.}, }
@article {pmid34378947, year = {2021}, author = {Zhang, SY and Xiao, X and Chen, SC and Zhu, YG and Sun, GX and Konstantinidis, KT}, title = {High Arsenic Levels Increase Activity Rather than Diversity or Abundance of Arsenic Metabolism Genes in Paddy Soils.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {20}, pages = {e0138321}, pmid = {34378947}, issn = {1098-5336}, mesh = {Archaea/genetics/metabolism ; Arsenic/analysis/*metabolism ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; *Genes, Archaeal ; *Genes, Bacterial ; Metals, Heavy/analysis ; Oryza ; RNA, Ribosomal, 16S ; *Soil Microbiology ; Soil Pollutants/analysis/*metabolism ; }, abstract = {Arsenic (As) metabolism genes are generally present in soils, but their diversity, relative abundance, and transcriptional activity in response to different As concentrations remain unclear, limiting our understanding of the microbial activities that control the fate of an important environmental pollutant. To address this issue, we applied metagenomics and metatranscriptomics to paddy soils showing a gradient of As concentrations to investigate As resistance genes (ars) including arsR, acr3, arsB, arsC, arsM, arsI, arsP, and arsH as well as energy-generating As respiratory oxidation (aioA) and reduction (arrA) genes. Somewhat unexpectedly, the relative DNA abundances and diversities of ars, aioA, and arrA genes were not significantly different between low and high (∼10 versus ∼100 mg kg[-1]) As soils. Compared to available metagenomes from other soils, geographic distance rather than As levels drove the different compositions of microbial communities. Arsenic significantly increased ars gene abundance only when its concentration was higher than 410 mg kg[-1]. In contrast, metatranscriptomics revealed that relative to low-As soils, high-As soils showed a significant increase in transcription of ars and aioA genes, which are induced by arsenite, the dominant As species in paddy soils, but not arrA genes, which are induced by arsenate. These patterns appeared to be community wide as opposed to taxon specific. Collectively, our findings advance understanding of how microbes respond to high As levels and the diversity of As metabolism genes in paddy soils and indicated that future studies of As metabolism in soil or other environments should include the function (transcriptome) level. IMPORTANCE Arsenic (As) is a toxic metalloid pervasively present in the environment. Microorganisms have evolved the capacity to metabolize As, and As metabolism genes are ubiquitously present in the environment even in the absence of high concentrations of As. However, these previous studies were carried out at the DNA level; thus, the activity of the As metabolism genes detected remains essentially speculative. Here, we show that the high As levels in paddy soils increased the transcriptional activity rather than the relative DNA abundance and diversity of As metabolism genes. These findings advance our understanding of how microbes respond to and cope with high As levels and have implications for better monitoring and managing an important toxic metalloid in agricultural soils and possibly other ecosystems.}, }
@article {pmid34378531, year = {2021}, author = {Marié, IJ and Brambilla, L and Azzouz, D and Chen, Z and Baracho, GV and Arnett, A and Li, HS and Liu, W and Cimmino, L and Chattopadhyay, P and Silverman, G and Watowich, SS and Khor, B and Levy, DE}, title = {Tonic interferon restricts pathogenic IL-17-driven inflammatory disease via balancing the microbiome.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34378531}, issn = {2050-084X}, support = {P30 CA016087/CA/NCI NIH HHS/United States ; R01 AI133822/AI/NIAID NIH HHS/United States ; R01 AI028900/AI/NIAID NIH HHS/United States ; P50 AR070591/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; Dysbiosis/*immunology ; Female ; *Gastrointestinal Microbiome ; Inflammation/*genetics ; Interferons/*administration &amp; dosage ; Interleukin-17/*genetics/metabolism ; Mice ; Mice, Knockout ; STAT1 Transcription Factor/*genetics/metabolism ; }, abstract = {Maintenance of immune homeostasis involves a synergistic relationship between the host and the microbiome. Canonical interferon (IFN) signaling controls responses to acute microbial infection, through engagement of the STAT1 transcription factor. However, the contribution of tonic levels of IFN to immune homeostasis in the absence of acute infection remains largely unexplored. We report that STAT1 KO mice spontaneously developed an inflammatory disease marked by myeloid hyperplasia and splenic accumulation of hematopoietic stem cells. Moreover, these animals developed inflammatory bowel disease. Profiling gut bacteria revealed a profound dysbiosis in the absence of tonic IFN signaling, which triggered expansion of TH17 cells and loss of splenic Treg cells. Reduction of bacterial load by antibiotic treatment averted the TH17 bias and blocking IL17 signaling prevented myeloid expansion and splenic stem cell accumulation. Thus, tonic IFNs regulate gut microbial ecology, which is crucial for maintaining physiologic immune homeostasis and preventing inflammation.}, }
@article {pmid34370735, year = {2021}, author = {Ghasemian, E and Inic-Kanada, A and Collingro, A and Mejdoubi, L and Alchalabi, H and Keše, D and Elshafie, BE and Hammou, J and Barisani-Asenbauer, T}, title = {Comparison of genovars and Chlamydia trachomatis infection loads in ocular samples from children in two distinct cohorts in Sudan and Morocco.}, journal = {PLoS neglected tropical diseases}, volume = {15}, number = {8}, pages = {e0009655}, pmid = {34370735}, issn = {1935-2735}, mesh = {Adolescent ; Bacterial Outer Membrane Proteins/*genetics ; Case-Control Studies ; Child ; Child, Preschool ; Chlamydia trachomatis/*genetics ; Conjunctivitis, Inclusion/drug therapy/*microbiology/transmission ; Female ; Genotype ; Humans ; Infant ; Male ; Morocco ; Polymerase Chain Reaction ; Sudan ; Trachoma/*genetics ; }, abstract = {Trachoma is a blinding disease caused by repeated conjunctival infection with different Chlamydia trachomatis (Ct) genovars. Ct B genovars have been associated with more severe trachoma symptoms. Here, we investigated associations between Ct genovars and bacterial loads in ocular samples from two distinct geographical locations in Africa, which are currently unclear. We tested ocular swabs from 77 Moroccan children (28 with trachomatous inflammation-follicular (TF) and 49 healthy controls), and 96 Sudanese children (54 with TF and 42 healthy controls) with a Ct-specific real-time polymerase chain reaction (PCR) assay. To estimate bacterial loads, Ct-positive samples were further processed by multiplex real-time qPCR to amplify the chromosomal outer membrane complex B and plasmid open reading frame 2 of Ct. Genotyping was performed by PCR-based amplification of the outer membrane protein A gene (~1120 base pairs) of Ct and Sanger sequencing. Ct-positivities among the Moroccan and Sudanese patient groups were 60·7% and 31·5%, respectively. Significantly more Sudanese patients than Moroccan patients were genovar A-positive. In contrast, B genovars were significantly more prevalent in Moroccan patients than in Sudanese patients. Significantly higher Ct loads were found in samples positive for B genovars (598596) than A genovar (51005). Geographical differences contributed to the distributions of different ocular Ct genovars. B genovars may induce a higher bacterial load than A genovars in trachoma patients. Our findings emphasize the importance of conducting broader studies to elucidate if the noted difference in multiplication abilities are genovar and/or endemicity level dependent.}, }
@article {pmid34370055, year = {2022}, author = {Travanty, NV and Vargo, EL and Apperson, CS and Ponnusamy, L}, title = {Colonization by the Red Imported Fire Ant, Solenopsis invicta, Modifies Soil Bacterial Communities.}, journal = {Microbial ecology}, volume = {84}, number = {1}, pages = {240-256}, pmid = {34370055}, issn = {1432-184X}, mesh = {Animals ; *Ants/microbiology ; Bacteria/genetics ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Soil ; }, abstract = {The long-standing association between insects and microorganisms has been especially crucial to the evolutionary and ecological success of social insect groups. Notably, research on the interaction of the two social forms (monogyne and polygyne) of the red imported fire ant (RIFA), Solenopsis invicta Buren, with microbes in its soil habitat is presently limited. In this study, we characterized bacterial microbiomes associated with RIFA nest soils and native (RIFA-negative) soils to better understand the effects of colonization of RIFA on soil microbial communities. Bacterial community fingerprints of 16S rRNA amplicons using denaturing gradient gel electrophoresis revealed significant differences in the structure of the bacterial communities between RIFA-positive and RIFA-negative soils at 0 and 10 cm depths. Illumina sequencing of 16S rRNA amplicons provided fine-scale analysis to test for effects of RIFA colonization, RIFA social form, and soil depth on the composition of the bacterial microbiomes of the soil and RIFA workers. Our results showed the bacterial community structure of RIFA-colonized soils to be significantly different from native soil communities and to evidence elevated abundances of several taxa, including Actinobacteria. Colony social form was not found to be a significant factor in nest or RIFA worker microbiome compositions. RIFA workers and nest soils were determined to have markedly different bacterial communities, with RIFA worker microbiomes being characterized by high abundances of a Bartonella-like endosymbiont and Entomoplasmataceae. Cloning and sequencing of the 16S rRNA gene revealed the Bartonella sp. to be a novel bacterium.}, }
@article {pmid34368008, year = {2021}, author = {Josephs-Spaulding, J and Krogh, TJ and Rettig, HC and Lyng, M and Chkonia, M and Waschina, S and Graspeuntner, S and Rupp, J and Møller-Jensen, J and Kaleta, C}, title = {Recurrent Urinary Tract Infections: Unraveling the Complicated Environment of Uncomplicated rUTIs.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {562525}, pmid = {34368008}, issn = {2235-2988}, mesh = {Anti-Bacterial Agents/therapeutic use ; Humans ; Inflammation/drug therapy ; Urinary Bladder ; *Urinary Tract Infections ; }, abstract = {Urinary tract infections (UTIs) are frequent in humans, affecting the upper and lower urinary tract. Present diagnosis relies on the positive culture of uropathogenic bacteria from urine and clinical markers of inflammation of the urinary tract. The bladder is constantly challenged by adverse environmental stimuli which influence urinary tract physiology, contributing to a dysbiotic environment. Simultaneously, pathogens are primed by environmental stressors such as antibiotics, favoring recurrent UTIs (rUTIs), resulting in chronic illness. Due to different confounders for UTI onset, a greater understanding of the fundamental environmental mechanisms and microbial ecology of the human urinary tract is required. Such advancements could promote the tandem translation of bench and computational studies for precision treatments and clinical management of UTIs. Therefore, there is an urgent need to understand the ecological interactions of the human urogenital microbial communities which precede rUTIs. This review aims to outline the mechanistic aspects of rUTI ecology underlying dysbiosis between both the human microbiome and host physiology which predisposes humans to rUTIs. By assessing the applications of next generation and systems level methods, we also recommend novel approaches to elucidate the systemic consequences of rUTIs which requires an integrated approach for successful treatment. To this end, we will provide an outlook towards the so-called 'uncomplicated environment of UTIs', a holistic and systems view that applies ecological principles to define patient-specific UTIs. This perspective illustrates the need to withdraw from traditional reductionist perspectives in infection biology and instead, a move towards a systems-view revolving around patient-specific pathophysiology during UTIs.}, }
@article {pmid34367868, year = {2021}, author = {Paul, P and Chakraborty, P and Sarker, RK and Chatterjee, A and Maiti, D and Das, A and Mandal, S and Bhattacharjee, S and Dastidar, DG and Tribedi, P}, title = {Tryptophan interferes with the quorum sensing and cell surface hydrophobicity of Staphylococcus aureus: a promising approach to inhibit the biofilm development.}, journal = {3 Biotech}, volume = {11}, number = {8}, pages = {376}, pmid = {34367868}, issn = {2190-572X}, abstract = {UNLABELLED: Staphylococcus aureus, a Gram-positive bacterium has been implicated in a plethora of human infections by virtue of its biofilm-forming ability. Inhibition in microbial biofilm formation has been found to be a promising approach towards compromising microbial pathogenesis. In this regard, various natural and synthetic molecules have been explored to attenuate microbial biofilm. In this study, the role of an amino acid, L-tryptophan was examined against the biofilm-forming ability of S. aureus. The compound did not execute any antimicrobial characteristics, instead, showed strong antibiofilm activity with the highest biofilm inhibition at a concentration of 50 µg/mL. Towards understanding the underlying mechanism of the same, efforts were given to examine whether tryptophan could inhibit biofilm formation by interfering with the quorum-sensing property of S. aureus. A molecular docking analysis revealed an efficient binding between the quorum-sensing protein, AgrA, and tryptophan. Moreover, the expression of the quorum-sensing gene (agrA) got significantly reduced under the influence of the test compound. These results indicated that tryptophan could interfere with the quorum-sensing property of the organism thereby inhibiting its biofilm formation. Further study revealed that tryptophan could also reduce the cell surface hydrophobicity of S. aureus by downregulating the expression of dltA. Moreover, the tested concentrations of tryptophan did not show any significant cytotoxicity. Hence, tryptophan could be recommended as a potential antibiofilm agent to manage the biofilm-associated infections caused by S. aureus.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02924-3.}, }
@article {pmid34367102, year = {2021}, author = {Rapp, JZ and Sullivan, MB and Deming, JW}, title = {Divergent Genomic Adaptations in the Microbiomes of Arctic Subzero Sea-Ice and Cryopeg Brines.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {701186}, pmid = {34367102}, issn = {1664-302X}, abstract = {Subzero hypersaline brines are liquid microbial habitats within otherwise frozen environments, where concentrated dissolved salts prevent freezing. Such extreme conditions presumably require unique microbial adaptations, and possibly altered ecologies, but specific strategies remain largely unknown. Here we examined prokaryotic taxonomic and functional diversity in two seawater-derived subzero hypersaline brines: first-year sea ice, subject to seasonally fluctuating conditions; and ancient cryopeg, under relatively stable conditions geophysically isolated in permafrost. Overall, both taxonomic composition and functional potential were starkly different. Taxonomically, sea-ice brine communities (∼10[5] cells mL[-1]) had greater richness, more diversity and were dominated by bacterial genera, including Polaribacter, Paraglaciecola, Colwellia, and Glaciecola, whereas the more densely inhabited cryopeg brines (∼10[8] cells mL[-1]) lacked these genera and instead were dominated by Marinobacter. Functionally, however, sea ice encoded fewer accessory traits and lower average genomic copy numbers for shared traits, though DNA replication and repair were elevated; in contrast, microbes in cryopeg brines had greater genetic versatility with elevated abundances of accessory traits involved in sensing, responding to environmental cues, transport, mobile elements (transposases and plasmids), toxin-antitoxin systems, and type VI secretion systems. Together these genomic features suggest adaptations and capabilities of sea-ice communities manifesting at the community level through seasonal ecological succession, whereas the denser cryopeg communities appear adapted to intense bacterial competition, leaving fewer genera to dominate with brine-specific adaptations and social interactions that sacrifice some members for the benefit of others. Such cryopeg genomic traits provide insight into how long-term environmental stability may enable life to survive extreme conditions.}, }
@article {pmid34365235, year = {2022}, author = {Bourhane, Z and Lanzén, A and Cagnon, C and Ben Said, O and Mahmoudi, E and Coulon, F and Atai, E and Borja, A and Cravo-Laureau, C and Duran, R}, title = {Microbial diversity alteration reveals biomarkers of contamination in soil-river-lake continuum.}, journal = {Journal of hazardous materials}, volume = {421}, number = {}, pages = {126789}, doi = {10.1016/j.jhazmat.2021.126789}, pmid = {34365235}, issn = {1873-3336}, mesh = {Biomarkers ; Ecosystem ; Environmental Monitoring ; Geologic Sediments ; Humans ; Lakes ; *Polycyclic Aromatic Hydrocarbons/analysis ; RNA, Ribosomal, 16S/genetics ; Rivers ; Soil ; *Water Pollutants, Chemical/analysis ; }, abstract = {Microbial communities inhabiting soil-water-sediment continuum in coastal areas provide important ecosystem services. Their adaptation in response to environmental stressors, particularly mitigating the impact of pollutants discharged from human activities, has been considered for the development of microbial biomonitoring tools, but their use is still in the infancy. Here, chemical and molecular (16S rRNA gene metabarcoding) approaches were combined in order to determine the impact of pollutants on microbial assemblages inhabiting the aquatic network of a soil-water-sediment continuum around the Ichkeul Lake (Tunisia), an area highly impacted by human activities. Samples were collected within the soil-river-lake continuum at three stations in dry (summer) and wet (winter) seasons. The contaminant pressure index (PI), which integrates Polycyclic aromatic hydrocarbons (PAHs), alkanes, Organochlorine pesticides (OCPs) and metal contents, and the microbial pressure index microgAMBI, based on bacterial community structure, showed significant correlation with contamination level and differences between seasons. The comparison of prokaryotic communities further revealed specific assemblages for soil, river and lake sediments. Correlation analyses identified potential "specialist" genera for the different compartments, whose abundances were correlated with the pollutant type found. Additionally, PICRUSt analysis revealed the metabolic potential for pollutant transformation or degradation of the identified "specialist" species, providing information to estimate the recovery capacity of the ecosystem. Such findings offer the possibility to define a relevant set of microbial indicators for assessing the effects of human activities on aquatic ecosystems. Microbial indicators, including the detection of "specialist" and sensitive taxa, and their functional capacity, might be useful, in combination with integrative microbial indices, to constitute accurate biomonitoring tools for the management and restoration of complex coastal aquatic systems.}, }
@article {pmid34364026, year = {2021}, author = {Rogińska, J and Perdicakis, M and Midoux, C and Bouchez, T and Despas, C and Liu, L and Tian, JH and Chaumont, C and P A Jorand, F and Tournebize, J and Etienne, M}, title = {Electrochemical analysis of a microbial electrochemical snorkel in laboratory and constructed wetlands.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {142}, number = {}, pages = {107895}, doi = {10.1016/j.bioelechem.2021.107895}, pmid = {34364026}, issn = {1878-562X}, mesh = {Bioelectric Energy Sources/*microbiology ; Electrochemical Techniques/*methods ; Nitrates/*chemistry ; Water Purification/*methods ; *Wetlands ; }, abstract = {Microbial electrochemical snorkel (MES) is a short-circuited microbial fuel cell applicable to water treatment that does not produce energy but requires lower cost for its implementation. Few reports have already described its water treatment capabilities but no deeper electrochemical analysis were yet performed. We tested various materials (iron, stainless steel and porous graphite) and configurations of snorkel in order to better understand the rules that will control in a wetland the mixed potential of this self-powered system. We designed a model snorkel that was studied in laboratory and on the field. We confirmed the development of MES by identifying anodic and cathodic parts, by measuring the current between them and by analyzing microbial ecology in laboratory and field experiments. An important application is denitrification of surface water. Here we discuss the influence of nitrate on its electrochemical response and denitrification performances. Introducing nitrate caused the increase of the mixed potential of MES and of current at a potential value relatively more positive than for nitrate-reducing biocathodes described in the literature. The major criteria for promoting application of MES in artificial wetland dedicated to mitigation of non-point source nitrate pollution from agricultural water are considered.}, }
@article {pmid34363579, year = {2022}, author = {Ghosh, A and Bhadury, P}, title = {Exploring changes in bacterioplankton community structure in response to tannic acid, a major component of mangrove litterfall of Sundarbans mangrove ecosystem: a laboratory mesocosm approach.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {2}, pages = {2107-2121}, pmid = {34363579}, issn = {1614-7499}, mesh = {Aquatic Organisms ; *Ecosystem ; Estuaries ; Humans ; *Laboratories ; RNA, Ribosomal, 16S/genetics ; Tannins ; }, abstract = {Tannic acid is a secondary compound produced by vascular plants and is a major component of mangrove litterfall. Tannic acid is water soluble, leaches out from mangrove litterfall and contributes to DOC and DON pools in adjacent estuaries. About 50% of the litterfall may be degraded and channelized into the marine microbial loop. The influence of tannic acid on bacterioplankton community structure was tested by setting up laboratory-based barrel experiments. Estuarine water from Stn3 of Sundarbans Biological Observatory Time Series (SBOTS) was enriched with tannic acid, and the change in concentration of dissolved nutrients was determined on a daily basis over a span of 15 days. Concentrations of tannic acid, gallic acid and other dissolved nutrients such as nitrate and ortho-phosphate were determined using a UV-Vis spectrophotometer. Tannic acid significantly affected the concentrations of gallic acid and dissolved nitrate in the barrels. Degradation of tannic acid was tracked by a decrease in concentration of tannic acid and generation of gallic acid. The influence of tannic acid on bacterioplankton community structure was analysed on the start (day 0), intermediate (day 3, day 5, day 7 and day 9) and end (day 15) of the experiment. Bacterioplankton community structure was elucidated by sequencing the V3-V4 region of 16S ribosomal RNA on an Illumina MiSeq platform. Proteobacteria was found to be the most dominant bacterial phylum in control and tannic acid-enriched barrels (barrels 1 and 2) on day 0. With the progression of experiment, the abundance of Proteobacteria altered significantly in the control barrel indicating the possible role of this phylum in the breakdown of tannic acid within estuarine mangroves. The abundance of Proteobacteria in the tannic acid-enriched barrels remained high, indicating that members of Proteobacteria may be capable of using tannic acid as a source of carbon and nitrogen. Tannic acid appeared to inhibit most of the other bacterioplankton phyla including Actinobacteria, Acidobacteria and Verrucomicrobia that existed in large abundance in the control barrel on day 15 but were almost absent in the tannic acid-enriched barrels. At class level, Bacteroides was found to be present in highest abundance in the tannic acid-enriched barrels. Tannic acid appeared to strongly influence the abundant bacterioplankton phyla and families as indicated by Pearson's correlation coefficient and non-metric multidimensional scaling ordination plots. Gallic acid is one of the final products of tannic acid degradation. Breakdown of tannic acid could influence the marine nitrogen and carbon cycling by releasing DON and DOC, respectively, into the adjacent estuaries. Information of breakdown and remineralization of components of litterfall such as tannic acid would also be important for calculation of carbon and nitrogen budgets of coastal ecosystems including in mangroves.}, }
@article {pmid34363516, year = {2022}, author = {Su, Y and Du, Y and Xing, P}, title = {The Light-to-Nutrient Ratio in Alpine Lakes: Different Scenarios of Bacterial Nutrient Limitation and Community Structure in Lakes Above and Below the Treeline.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {837-849}, pmid = {34363516}, issn = {1432-184X}, support = {31971475//National Natural Science Foundation of China/ ; 31722008//National Natural Science Foundation of China/ ; 31670461//National Natural Science Foundation of China/ ; }, mesh = {Bacteria ; Chlorophyll A ; *Ecosystem ; *Lakes/chemistry ; Nitrogen ; Nutrients ; Phosphorus ; }, abstract = {The light-to-nutrient hypothesis proposes that under high light-to-nutrient conditions, bacteria tend to be limited by phosphorus (P), while under relatively low light-to-nutrient conditions, bacteria are likely driven towards carbon (C) limitation. Exploring whether this light-to-nutrient hypothesis is fitting for alpine lakes has profound implications for predicting the impacts of climatic and environmental changes on the structures and processes of aquatic ecosystems in climate-sensitive regions. We investigated the environmental conditions and bacterioplankton community compositions of 15 high-elevation lakes (7 above and 8 below treeline). High light-to-nutrient conditions (denoted by the reciprocal value of the attenuation coefficient (1/K) to total phosphorus (TP)), high chlorophyll a (Chl a) concentrations, low TP concentrations and low ratios of the dissolved organic carbon concentration to the dissolved total nitrogen concentration (DOC:DTN) were detected in above-treeline lakes. Significant positive correlations between the bacterioplankton community compositions with 1/K:TP ratios and Chl a concentrations indicated that not only high light energy but also nutrient competition between phytoplankton and bacteria could induce P limitation for bacteria. In contrast, low light-to-nutrient conditions and high allochthonous DOC input in below-treeline lakes lessen P limitation and C limitation. The most abundant genus, Polynucleobacter, was significantly enriched, and more diverse oligotypes of Polynucleobacter operational taxonomic units were identified in the below-treeline lakes, indicating the divergence of niche adaptations among Polynucleobacter oligotypes. The discrepancies in the light-to-P ratio and the components of organic matter between the above-treeline and below-treeline lakes have important implications for the nutrient limitation of bacterioplankton and their community compositions.}, }
@article {pmid34363515, year = {2022}, author = {Perera, IA and Abinandan, S and Subashchandrabose, SR and Venkateswarlu, K and Naidu, R and Megharaj, M}, title = {Impact of Nitrate and Ammonium Concentrations on Co-Culturing of Tetradesmus obliquus IS2 with Variovorax paradoxus IS1 as Revealed by Phenotypic Responses.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {951-959}, pmid = {34363515}, issn = {1432-184X}, mesh = {*Ammonium Compounds/metabolism ; Coculture Techniques ; Comamonadaceae ; Nitrates/metabolism ; Nitrogen/metabolism ; }, abstract = {Mutual interactions in co-cultures of microalgae and bacteria are well known for establishing consortia and nutrient uptake in aquatic habitats, but the phenotypic changes in terms of morphological, physiological, and biochemical attributes that drive these interactions have not been clearly understood. In this novel study, we demonstrated the phenotypic response in a co-culture involving a microalga, Tetradesmus obliquus IS2, and a bacterium, Variovorax paradoxus IS1, grown with varying concentrations of two inorganic nitrogen sources. Modified Bold's basal medium was supplemented with five ratios (%) of NO3-N:NH4-N (100:0, 75:25, 50:50, 25:75, and 0:100), and by maintaining N:P Redfield ratio of 16:1. The observed morphological changes in microalga included an increase in granularity and a broad range of cell sizes under the influence of increased ammonium levels. Co-culturing in presence of NO3-N alone or combination with NH4-N up to equimolar concentrations resulted in complete nitrogen uptake, increased growth in both the microbial strains, and enhanced accumulation of carbohydrates, proteins, and lipids. Total chlorophyll content in microalga was also significantly higher when it was grown as a co-culture with NO3-N and NH4-N up to a ratio of 50:50. Significant upregulation in the synthesis of amino acids and sugars and downregulation of organic acids were evident with higher ammonium uptake in the co-culture, indicating the regulation of carbon and nitrogen assimilation pathways and energy synthesis. Our data suggest that the co-culture of strains IS1 and IS2 could be exploited for effluent treatment by considering the concentrations of inorganic sources, particularly ammonium, in the wastewaters.}, }
@article {pmid34361657, year = {2021}, author = {Al-Shaibani, MM and Radin Mohamed, RMS and Sidik, NM and Enshasy, HAE and Al-Gheethi, A and Noman, E and Al-Mekhlafi, NA and Zin, NM}, title = {Biodiversity of Secondary Metabolites Compounds Isolated from Phylum Actinobacteria and Its Therapeutic Applications.}, journal = {Molecules (Basel, Switzerland)}, volume = {26}, number = {15}, pages = {}, pmid = {34361657}, issn = {1420-3049}, mesh = {Actinobacteria/*metabolism ; Anti-Bacterial Agents/isolation &amp; purification/metabolism ; Biological Products ; Enzymes/isolation &amp; purification/metabolism ; Secondary Metabolism ; }, abstract = {The current review aims to summarise the biodiversity and biosynthesis of novel secondary metabolites compounds, of the phylum Actinobacteria and the diverse range of secondary metabolites produced that vary depending on its ecological environments they inhabit. Actinobacteria creates a wide range of bioactive substances that can be of great value to public health and the pharmaceutical industry. The literature analysis process for this review was conducted using the VOSviewer software tool to visualise the bibliometric networks of the most relevant databases from the Scopus database in the period between 2010 and 22 March 2021. Screening and exploring the available literature relating to the extreme environments and ecosystems that Actinobacteria inhabit aims to identify new strains of this major microorganism class, producing unique novel bioactive compounds. The knowledge gained from these studies is intended to encourage scientists in the natural product discovery field to identify and characterise novel strains containing various bioactive gene clusters with potential clinical applications. It is evident that Actinobacteria adapted to survive in extreme environments represent an important source of a wide range of bioactive compounds. Actinobacteria have a large number of secondary metabolite biosynthetic gene clusters. They can synthesise thousands of subordinate metabolites with different biological actions such as anti-bacterial, anti-parasitic, anti-fungal, anti-virus, anti-cancer and growth-promoting compounds. These are highly significant economically due to their potential applications in the food, nutrition and health industries and thus support our communities' well-being.}, }
@article {pmid34360485, year = {2021}, author = {Ramli, NA and Md Yusof, NFF and Zarkasi, KZ and Suroto, A}, title = {Chemical, Biological and Morphological Properties of Fine Particles during Local Rice Straw Burning Activities.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {15}, pages = {}, pmid = {34360485}, issn = {1660-4601}, mesh = {*Air Pollutants/analysis ; Bacillus ; Deltaproteobacteria ; Environmental Monitoring ; Humans ; *Oryza ; Particle Size ; Particulate Matter/analysis ; }, abstract = {Rice straw is commonly burned openly after harvesting in Malaysia and many other Asian countries where rice is the main crop. This operation emits a significant amount of air pollution, which can have severe consequences for indoor air quality, public health, and climate change. Therefore, this study focuses on determining the compositions of trace elements and the morphological properties of fine particles. Furthermore, the species of bacteria found in bioaerosol from rice burning activities were discovered in this study. For morphological observation of fine particles, FESEM-EDX was used in this study. Two main categories of particles were found, which were natural particles and anthropogenic particles. The zinc element was found during the morphological observation and was assumed to come from the fertilizer used by the farmers. ICP-OES identifies the concentration of trace elements in the fine particle samples. A cultured method was used in this study by using nutrient agar. From this study, several bacteria were identified: Exiguobavterium indicum, Bacillus amyloliquefaciens, Desulfonema limicola str. Jadabusan, Exiguobacterium acetylicum, Lysinibacillus macrolides, and Bacillus proteolyticus. This study is important, especially for human health, and further research on the biological composition of aerosols should be conducted to understand the effect of microorganisms on human health.}, }
@article {pmid34358486, year = {2021}, author = {Wauters, L and Slaets, H and De Paepe, K and Ceulemans, M and Wetzels, S and Geboers, K and Toth, J and Thys, W and Dybajlo, R and Walgraeve, D and Biessen, E and Verbeke, K and Tack, J and Van de Wiele, T and Hellings, N and Vanuytsel, T}, title = {Efficacy and safety of spore-forming probiotics in the treatment of functional dyspepsia: a pilot randomised, double-blind, placebo-controlled trial.}, journal = {The lancet. Gastroenterology &amp; hepatology}, volume = {6}, number = {10}, pages = {784-792}, doi = {10.1016/S2468-1253(21)00226-0}, pmid = {34358486}, issn = {2468-1253}, mesh = {Adult ; Bacillus coagulans ; Bacillus subtilis ; Belgium/epidemiology ; Case-Control Studies ; Dietary Supplements/*adverse effects ; Double-Blind Method ; Dyspepsia/*diet therapy/epidemiology/*physiopathology ; Female ; Humans ; Male ; Middle Aged ; Pilot Projects ; Placebos/administration &amp; dosage ; Prevalence ; Probiotics/administration &amp; dosage/adverse effects/*therapeutic use ; Proton Pump Inhibitors/therapeutic use ; Safety ; Spores/chemistry ; Treatment Outcome ; }, abstract = {BACKGROUND: Current treatments for functional dyspepsia have limited efficacy or present safety issues. We aimed to assess spore-forming probiotics in functional dyspepsia as monotherapy or add-on therapy to long-term treatment with proton-pump inhibitors.<br><br>METHODS: In this single-centre, randomised, double-blind, placebo-controlled pilot trial that took place at University Hospitals Leuven (Leuven, Belgium), adult patients (&#x2265;18 years) with functional dyspepsia (as defined by Rome IV criteria, on proton-pump inhibitors or off proton-pump inhibitors) were randomly assigned (1:1) via computer-generated blocked lists, stratified by proton-pump inhibitor status, to receive 8 weeks of treatment with probiotics (Bacillus coagulans MY01 and Bacillus subtilis MY02, 2&#xb7;5&#x2009;&#xd7;&#x2009;10[9] colony-forming units per capsule) or placebo consumed twice per day, followed by an open-label extension phase of 8 weeks. Individuals with a history of abdominal surgery, diabetes, coeliac or inflammatory bowel disease, active psychiatric conditions, and use of immunosuppressant drugs, antibiotics, or probiotics in the past 3 months were excluded. All patients and on-site study personnel were masked to treatment allocation in the first 8 weeks. Symptoms, immune activation, and faecal microbiota were assessed and recorded. The primary endpoint was a decrease of at least 0&#xb7;7 in the postprandial distress syndrome (PDS) score of the Leuven Postprandial Distress Scale in patients with a baseline PDS score of 1 or greater (at least mild symptoms), assessed in the intention-to-treat population. This study is registered with ClinicalTrials.gov, NCT04030780.<br><br>FINDINGS: Between June 3, 2019, and March 11, 2020, of 93 individuals assessed for eligibility, we included 68 patients with functional dyspepsia (51 [75%] women, mean age 40&#xb7;1 years [SD 14&#xb7;4], 34 [50%] on proton-pump inhibitors). We randomly assigned 32 participants to probiotics and 36 to placebo. The proportion of clinical responders was higher with probiotics (12 [48%] of 25) than placebo (six [20%] of 30; relative risk 1&#xb7;95 [95% CI 1&#xb7;07-4&#xb7;11]; p=0&#xb7;028). The number of patients with adverse events was similar with probiotics (five [16%] of 32) and placebo (12 [33%] of 36). Two serious adverse events occurring during the open-label phase (appendicitis and syncope in two separate patients) were assessed as unlikely to be related to the study product.<br><br>INTERPRETATION: In this exploratory study, B coagulans MY01 and B subtilis MY02 were efficacious and safe in the treatment of functional dyspepsia. Participants had potentially beneficial immune and microbial changes, which could provide insights into possible underlying mechanisms as future predictors or treatment targets.<br><br>FUNDING: MY HEALTH.}, }
@article {pmid34356506, year = {2021}, author = {Bapteste, E and Gérard, P and Larose, C and Blouin, M and Not, F and Campos, L and Aïdan, G and Selosse, MA and Adénis, MS and Bouchard, F and Dutreuil, S and Corel, E and Vigliotti, C and Huneman, P and Lapointe, FJ and Lopez, P}, title = {The Epistemic Revolution Induced by Microbiome Studies: An Interdisciplinary View.}, journal = {Biology}, volume = {10}, number = {7}, pages = {}, pmid = {34356506}, issn = {2079-7737}, support = {REVMICNAT//Centre National de la Recherche Scientifique/ ; }, abstract = {Many separate fields and practices nowadays consider microbes as part of their legitimate focus. Therefore, microbiome studies may act as unexpected unifying forces across very different disciplines. Here, we summarize how microbiomes appear as novel major biological players, offer new artistic frontiers, new uses from medicine to laws, and inspire novel ontologies. We identify several convergent emerging themes across ecosystem studies, microbial and evolutionary ecology, arts, medicine, forensic analyses, law and philosophy of science, as well as some outstanding issues raised by microbiome studies across these disciplines and practices. An 'epistemic revolution induced by microbiome studies' seems to be ongoing, characterized by four features: (i) an ecologization of pre-existing concepts within disciplines, (ii) a growing interest in systemic analyses of the investigated or represented phenomena and a greater focus on interactions as their root causes, (iii) the intent to use openly multi-scalar interaction networks as an explanatory framework to investigate phenomena to acknowledge the causal effects of microbiomes, (iv) a reconceptualization of the usual definitions of which individuals are worth considering as an explanans or as an explanandum by a given field, which result in a fifth strong trend, namely (v) a de-anthropocentrification of our perception of the world.}, }
@article {pmid34354050, year = {2021}, author = {Cheng, SP and Jia, KH and Liu, H and Zhang, RG and Li, ZC and Zhou, SS and Shi, TL and Ma, AC and Yu, CW and Gao, C and Cao, GL and Zhao, W and Nie, S and Guo, JF and Jiao, SQ and Tian, XC and Yan, XM and Bao, YT and Yun, QZ and Wang, XZ and Porth, I and El-Kassaby, YA and Wang, XR and Li, Z and Van de Peer, Y and Mao, JF}, title = {Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger.}, journal = {Horticulture research}, volume = {8}, number = {1}, pages = {188}, pmid = {34354050}, issn = {2662-6810}, support = {31600527//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.}, }
@article {pmid34353114, year = {2021}, author = {Czajkowski, R and Rabalski, L and Kosinski, M and de Neergaard, E and Harding, S}, title = {High-Quality Complete Genome Resource of Pathogenic Bacterium Pectobacterium atrosepticum Strain Green1 Isolated from Potato (Solanum tuberosum L.) in Greenland.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {34}, number = {11}, pages = {1328-1333}, doi = {10.1094/MPMI-06-21-0130-A}, pmid = {34353114}, issn = {0894-0282}, mesh = {Greenland ; *Pectobacterium/genetics ; Plant Diseases ; *Solanum tuberosum ; }, abstract = {Pectobacterium atrosepticum is a narrow-host-range, pectinolytic, plant-pathogenic bacterium causing blackleg of potato (Solanum tuberosum L.) worldwide. Till present, several P. atrosepticum genomes have been sequenced and characterized in detail; however, all of these genomes have come from P. atrosepticum isolates from plants grown in temperate zones, not from hosts cultivated under different climatic conditions. Herewith, we present the first complete, high-quality genome of the P. atrosepticum strain Green1 isolated from potato plants grown under a subarctic climate in Greenland. The genome of P. atrosepticum strain Green1 consists of one chromosome of 4,959,719 bp, with a GC content of 51% and no plasmids. The genome contains 4,531 annotated features, including 4,179 protein-coding genes, 22 ribosomal RNA genes, 70 transfer RNA genes, 8 noncoding RNA genes, 2 CRISPRs, and 126 pseudogenes. We believe that the information in this first high-quality, complete, closed genome of P. atrosepticum strains isolated from host plants grown in a subarctic agricultural region will provide resources for comparative genomic studies and for analyses targeting climatic adaptation and ecological fitness mechanisms present in P. atrosepticum.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.}, }
@article {pmid34351469, year = {2022}, author = {Vora, SM and Ankati, S and Patole, C and Podile, AR and Archana, G}, title = {Alterations of Primary Metabolites in Root Exudates of Intercropped Cajanus cajan-Zea mays Modulate the Adaptation and Proteome of Ensifer (Sinorhizobium) fredii NGR234.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {1008-1025}, pmid = {34351469}, issn = {1432-184X}, mesh = {*Cajanus ; Exudates and Transudates ; *Fabaceae/microbiology ; Proteome/metabolism ; *Rhizobium ; *Sinorhizobium fredii/metabolism ; Zea mays/microbiology ; }, abstract = {Legume-cereal intercropping systems, in the context of diversity, ecological function, and better yield have been widely studied. Such systems enhance nutrient phytoavailability by balancing root-rhizosphere interactions. Root exudates (RE) play an important role in the rhizospheric interactions of plant-plant and/or plant-microbiome interaction. However, the influence of the primary metabolites of RE on plant-rhizobia interactions in a legume-cereal intercrop system is not known. To understand the plant communication with rhizobia, Cajanus cajan-Zea mays intercropped plants and the broad host range legume nodulating Ensifer fredii NGR234 as the model plants and rhizobium used respectively. A metabolomics-based approach revealed a clear separation between intercropped and monocropped RE of the two plants. Intercropped C. cajan showed an increase in the myo-inositol, and proline, while intercropped Z. mays showed enhanced galactose, D-glucopyranoside, and arginine in the RE. Physiological assays of NGR234 with the RE of intercropped C. cajan exhibited a significant enhancement in biofilm formation, while intercropped Z. mays RE accelerated the bacterial growth in the late log phase. Further, using label-free proteomics, we identified a total of 2570 proteins of NGR234 covering 50% annotated protein sequences upon exposure to Z. mays RE. Furthermore, intercropped Z. mays RE upregulated bacterioferritin comigratory protein (BCP), putative nitroreductase, IlvD, LeuC, D (branched-chain amino acid proteins), and chaperonin proteins GroEL2. Identification offered new insights into the metabolome of the legume-cereal intercrop and proteome of NGR234-Z. mays interactions that underline the new molecular candidates likely to be involved in the fitness of rhizobium in the intercropping system.}, }
@article {pmid34349744, year = {2021}, author = {Gresse, R and Chaucheyras-Durand, F and Garrido, JJ and Denis, S and Jiménez-Marín, A and Beaumont, M and Van de Wiele, T and Forano, E and Blanquet-Diot, S}, title = {Pathogen Challenge and Dietary Shift Alter Microbiota Composition and Activity in a Mucin-Associated in vitro Model of the Piglet Colon (MPigut-IVM) Simulating Weaning Transition.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {703421}, pmid = {34349744}, issn = {1664-302X}, abstract = {Enterotoxigenic Escherichia coli (ETEC) is the principal pathogen responsible for post-weaning diarrhea in newly weaned piglets. Expansion of ETEC at weaning is thought to be the consequence of various stress factors such as transient anorexia, dietary change or increase in intestinal inflammation and permeability, but the exact mechanisms remain to be elucidated. As the use of animal experiments raise more and more ethical concerns, we used a recently developed in vitro model of piglet colonic microbiome and mucobiome, the MPigut-IVM, to evaluate the effects of a simulated weaning transition and pathogen challenge at weaning. Our data suggested that the tested factors impacted the composition and functionality of the MPigut-IVM microbiota. The simulation of weaning transition led to an increase in relative abundance of the Prevotellaceae family which was further promoted by the presence of the ETEC strain. In contrast, several beneficial families such as Bacteroidiaceae or Ruminococcaceae and gut health related short chain fatty acids like butyrate or acetate were reduced upon simulated weaning. Moreover, the incubation of MPigut-IVM filtrated effluents with porcine intestinal cell cultures showed that ETEC challenge in the in vitro model led to an increased expression of pro-inflammatory genes by the porcine cells. This study provides insights about the etiology of a dysbiotic microbiota in post-weaning piglets.}, }
@article {pmid34347817, year = {2021}, author = {Menden-Deuer, S and Rowlett, J and Nursultanov, M and Collins, S and Rynearson, T}, title = {Biodiversity of marine microbes is safeguarded by phenotypic heterogeneity in ecological traits.}, journal = {PloS one}, volume = {16}, number = {8}, pages = {e0254799}, pmid = {34347817}, issn = {1932-6203}, mesh = {Aquatic Organisms/*physiology ; Bacteria/*metabolism ; *Biodiversity ; Computer Simulation ; Phenotype ; }, abstract = {Why, contrary to theoretical predictions, do marine microbe communities harbor tremendous phenotypic heterogeneity? How can so many marine microbe species competing in the same niche coexist? We discovered a unifying explanation for both phenomena by investigating a non-cooperative game that interpolates between individual-level competitions and species-level outcomes. We identified all equilibrium strategies of the game. These strategies represent the probability distribution of competitive abilities (e.g. traits) and are characterized by maximal phenotypic heterogeneity. They are also neutral towards each other in the sense that an unlimited number of species can co-exist while competing according to the equilibrium strategies. Whereas prior theory predicts that natural selection would minimize trait variation around an optimum value, here we obtained a mathematical proof that species with maximally variable traits are those that endure. This discrepancy may reflect a disparity between predictions from models developed for larger organisms in contrast to our microbe-centric model. Rigorous mathematics proves that phenotypic heterogeneity is itself a mechanistic underpinning of microbial diversity. This discovery has fundamental ramifications for microbial ecology and may represent an adaptive reservoir sheltering biodiversity in changing environmental conditions.}, }
@article {pmid34347524, year = {2021}, author = {Kim, T and Behrens, S and LaPara, TM}, title = {Direct Evidence for Deterministic Assembly of Bacterial Communities in Full-Scale Municipal Wastewater Treatment Facilities.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {20}, pages = {e0108621}, pmid = {34347524}, issn = {1098-5336}, mesh = {Bacteria ; Bioreactors/*microbiology ; Microbiota ; Wastewater/*microbiology ; Water Purification ; }, abstract = {In this study, we investigated whether bacterial community composition in full-scale wastewater treatment bioreactors can be better explained by niche- or neutral-based theory (deterministic or stochastic) and whether bioreactor design (continuous flow versus fill and draw) affected community assembly. Four wastewater treatment facilities (one with quadruplicated continuous-flow bioreactors, two with one continuous-flow bioreactor each, and one with triplicate fill-and-draw bioreactors) were investigated. Bioreactor community composition was characterized by sequencing of PCR-amplified 16S rRNA gene fragments. Replicate bioreactors at the same wastewater treatment facility had largely reproducible (i.e., deterministic) bacterial community composition, although bacterial community composition in continuous-flow bioreactors was significantly more reproducible (P < 0.001) than in fill-and-draw bioreactors (Bray-Curtis dissimilarity, μ = 0.48 ± 0.06 versus 0.58 ± 0.08). Next, we compared our results to previously used indirect methods for distinguishing between deterministic and stochastic community assembly mechanisms. Synchronicity was observed in the bacterial community composition among bioreactors within the same metropolitan region, consistent with deterministic community assembly. Similarly, a null model-based analysis also indicated that all wastewater bioreactor communities were controlled by deterministic factors and that continuous-flow bioreactors were significantly more deterministic (P < 0.001) than fill-and-draw bioreactors (nearest-taxon index, μ = 3.8 ± 0.6 versus 2.7 ± 0.8). Our results indicate that bacterial community composition in wastewater treatment bioreactors is better explained by deterministic community assembly theory; simultaneously, our results validate previously used but indirect methods to quantify whether microbial communities were assembled via deterministic or stochastic mechanisms. IMPORTANCE Understanding the mechanisms of bacterial community assembly is one of the grand challenges of microbial ecology. In environmental systems, this challenge is exacerbated because replicate experiments are typically impossible; that is, microbial ecologists cannot fabricate multiple field-scale experiments of identical, natural ecosystems. Our results directly demonstrate that deterministic mechanisms are more prominent than stochastic mechanisms in the assembly of wastewater treatment bioreactor communities. Our results also suggest that wastewater treatment bioreactor design is pertinent, such that the imposition of feast-famine conditions (i.e., fill-and-draw bioreactors) nudge bacterial community assembly more toward stochastic mechanisms than the imposition of stringent nutrient limitation (i.e., continuous-flow bioreactors). Our research also validates the previously used indirect methods (synchronous community dynamics and an application of a null model) for characterizing the relative importance of deterministic versus stochastic mechanisms of community assembly.}, }
@article {pmid34347349, year = {2021}, author = {Bosch, J and Varliero, G and Hallsworth, JE and Dallas, TD and Hopkins, D and Frey, B and Kong, W and Lebre, P and Makhalanyane, TP and Cowan, DA}, title = {Microbial anhydrobiosis.}, journal = {Environmental microbiology}, volume = {23}, number = {11}, pages = {6377-6390}, doi = {10.1111/1462-2920.15699}, pmid = {34347349}, issn = {1462-2920}, mesh = {Adaptation, Physiological ; *Desiccation ; *Eukaryota/metabolism ; Water/metabolism ; }, abstract = {The loss of cellular water (desiccation) and the resulting low cytosolic water activity are major stress factors for life. Numerous prokaryotic and eukaryotic taxa have evolved molecular and physiological adaptions to periods of low water availability or water-limited environments that occur across the terrestrial Earth. The changes within cells during the processes of desiccation and rehydration, from the activation (and inactivation) of biosynthetic pathways to the accumulation of compatible solutes, have been studied in considerable detail. However, relatively little is known on the metabolic status of organisms in the desiccated state; that is, in the sometimes extended periods between the drying and rewetting phases. During these periods, which can extend beyond decades and which we term 'anhydrobiosis', organismal survival could be dependent on a continued supply of energy to maintain the basal metabolic processes necessary for critical functions such as macromolecular repair. Here, we review the state of knowledge relating to the function of microorganisms during the anhydrobiotic state, highlighting substantial gaps in our understanding of qualitative and quantitative aspects of molecular and biochemical processes in desiccated cells.}, }
@article {pmid34346368, year = {2021}, author = {Tulumello, J and Chabert, N and Rodriguez, J and Long, J and Nalin, R and Achouak, W and Heulin, T}, title = {Rhizobium alamii improves water stress tolerance in a non-legume.}, journal = {The Science of the total environment}, volume = {797}, number = {}, pages = {148895}, doi = {10.1016/j.scitotenv.2021.148895}, pmid = {34346368}, issn = {1879-1026}, mesh = {Dehydration ; Humans ; Plant Roots ; *Rhizobium ; Soil Microbiology ; *Water ; }, abstract = {With the increasing demand for alternative solutions to replace or optimize the use of synthetic fertilizers and pesticides, the inoculation of bacteria that can contribute to the growth and health of plants (PGPR) is essential. The properties classically sought in PGPR are the production of phytohormones and other growth-promoting molecules, and more rarely the production of exopolysaccharides. We compared the effect of two strains of exopolysaccharide-producing Rhizobium alamii on rapeseed grown in a calcareous silty-clay soil under water stress conditions or not. The effect of factors 'water stress' and 'inoculation' were evaluated on plant growth parameters and the diversity of microbiota associated to root and root-adhering soil compartments. Water stress resulted in a significant decrease in leaf area, shoot biomass and RAS/RT ratio (root-adhering soil/root tissues), as well as overall beta-diversity. Inoculation with R. alamii YAS34 and GBV030 under water-stress conditions produced the same shoot dry biomass compared to uninoculated treatment in absence of water stress, and both strains increased shoot biomass under water-stressed conditions (+7% and +15%, respectively). Only R. alamii GBV030 significantly increased shoot biomass under unstressed or water-stressed conditions compared to the non-inoculated control (+39% and +15%, respectively). Alpha-diversity of the root-associated microbiota after inoculation with R. alamii YAS34 was significantly reduced. Beta-diversity was significantly modified after inoculation with R. alamii GBV030 under unstressed conditions. LEfSe analysis identified characteristic bacterial families, Flavobacteriaceae and Comamonadaceae, in the RT and RAS compartments for the treatment inoculated by R. alamii GBV030 under unstressed conditions, as well as Halomonadaceae (RT) and several species belonging to Actinomycetales (RAS). We showed that R. alamii GBV030 had a PGPR effect on rapeseed growth, increasing its tolerance to water stress, probably involving its capacity to produce exopolysaccharides, and other plant growth-promoting (PGP) traits.}, }
@article {pmid34345962, year = {2022}, author = {Chaitra, HS and Singh, A and Pandiyan, K and Kalia, VK}, title = {Sex Biased Variance in the Structural and Functional Diversity of the Midgut Bacterial Community of Last Instar Larvae of Pectinophora gossypiella (Lepidoptera: Gelechiidae).}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {1112-1122}, pmid = {34345962}, issn = {1432-184X}, mesh = {Animals ; Bacteria/genetics ; Bacterial Proteins ; *Endotoxins ; Female ; Gossypium ; Hemolysin Proteins ; Larva/physiology ; Male ; *Moths/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Elucidating the midgut bacterial diversity in an important cotton bollworm Pectinophora gossypiella can be a stepping stone in understanding the possible role of midgut bacteria in field evolved resistance against Bt cotton as well as to commonly used insecticides. Present study targeted metagenomics of 16S rRNA V3-V4 region to understand the influence of sex, if exists, in community diversity of gut microbes vis a vis their function in pink bollworm larvae. The results of the present study revealed that Proteobacteria, Firmicutes, and Actinobacteria were the predominant phyla in the midgut of pink bollworm. Distinctive differences were found in the Shannon and Simpson diversity indices, ChaoI and ACE richness estimates in male and female larvae. The alpha diversity analysis showed that the gut bacteria of male were diverse and rich as compared to that of female. Further, beta diversity analysis indicated that the gut bacterial communities of both larval groups were unique from each other. These findings are the maiden report on sex-based variation in gut bacteria in P. gossypiella larvae. Role of candidate phyla OD1 (Parcubacteria) and TM7 (Saccharibacteria) in the living organisms needs to be studied, and their fairly significant composition in male and negligible composition in female larva raises question on their obvious role. Taxonomic to phenotypic mapping revealed that these gut bacteria play vital role in many metabolic and physiological activities of pink bollworm. Difference in potential functions of gut bacteria also varied with the sex.}, }
@article {pmid34342700, year = {2022}, author = {Chen, H and Verplaetse, E and Jauslin, T and Cosson, P and Slamti, L and Lereclus, D}, title = {The Fate of Bacteria of the Bacillus cereus Group in the Amoeba Environment.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {1088-1104}, pmid = {34342700}, issn = {1432-184X}, mesh = {*Amoeba ; *Bacillus ; *Bacillus anthracis/genetics ; Bacillus cereus/genetics ; *Bacillus thuringiensis ; Soil ; }, abstract = {The Bacillus cereus sensu lato group consists of several closely related species, including B. anthracis, B. cereus sensu stricto, and B. thuringiensis. Spores of these pathogenic bacteria are commonly found in the soil but evidence suggests that they are unable to grow in such a natural environment in the absence of nutrient input. Amoebas have been reported to be an amplifier for several species of pathogenic bacteria and their potential involvement to explain the large amount of B. thuringiensis and B. cereus spores in soil has been frequently proposed. Here, we studied the fate of Bacillus and amoebas when cultured together. We show that the virulence factors produced by B. thuringiensis and B. cereus do not affect the amoeba Acanthamoeba castellanii, which, on the contrary, can phagocytose and effectively digest vegetative Bacillus cells to grow and prevent the formation of cysts. Bacterial spores can germinate in the amoeba environment and the vegetative cells can then form chains or aggregates that appear to be less efficiently phagocyted by the amoeba. The use of transcriptional fusions between fluorescent reporter genes and stationary phase- and sporulation-specific promoters showed that the sporulation process occurs more efficiently in the presence of amoebas than in their absence. Moreover, our results showed the amoeba environment to promote spore germination and allow the bacteria to complete their developmental cycle. Overall, this study suggests that the amoeba-Bacillus interaction creates a virtuous circle in which each protagonist helps the other to develop.}, }
@article {pmid34342699, year = {2022}, author = {Ke, L and Yan, WY and Zhang, LZ and Zeng, ZJ and Evans, JD and Huang, Q}, title = {Honey Bee Habitat Sharing Enhances Gene Flow of the Parasite Nosema ceranae.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {1105-1111}, pmid = {34342699}, issn = {1432-184X}, mesh = {Animals ; Bees ; Ecosystem ; Gene Flow ; *Nosema/genetics ; *Parasites ; }, abstract = {Host-parasite co-evolution is a process of reciprocal, adaptive genetic change. In natural conditions, parasites can shift to other host species, given both host and parasite genotypes allow this. Even though host-parasite co-evolution has been extensively studied both theoretically and empirically, few studies have focused on parasite gene flow between native and novel hosts. Nosema ceranae is a native parasite of the Asian honey bee Apis cerana, which infects epithelial cells of mid-guts. This parasite successfully switched to the European honey bee Apis mellifera, where high virulence has been reported. In this study, we used the parasite N. ceranae and both honey bee species as model organisms to study the impacts of two-host habitat sharing on parasite diversity and virulence. SNVs (Single Nucleotide Variants) were identified from parasites isolated from native and novel hosts from sympatric populations, as well as novel hosts from a parapatric population. Parasites isolated from native hosts showed the highest levels of polymorphism. By comparing the parasites isolated from novel hosts between sympatric and parapatric populations, habitat sharing with the native host significantly enhanced parasite diversity, suggesting there is continuing gene flow of parasites between the two host species in sympatric populations.}, }
@article {pmid34342698, year = {2022}, author = {Jan, B and Reshi, ZA and Mohiddin, FA}, title = {Site and Organ-Specific Culture-Dependent Endophytic Diversity of Crocus sativus L. (Saffron) in Kashmir Himalaya, India.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {989-1006}, pmid = {34342698}, issn = {1432-184X}, mesh = {Bacteria ; *Crocus/genetics/microbiology ; DNA, Ribosomal/genetics ; Endophytes ; Phylogeny ; }, abstract = {The endophytic diversity of a host plant has been shown to vary across various spatio-temporal scales and between different organs of a plant, but no such study has been carried out on the economically important plant Crocus sativus (saffron). To fill this knowledge gap, the present study was undertaken to document the diversity of culturable bacterial, actinomycete and fungal endophytes at multiple sites from vegetative and reproductive organs of C. sativus. A total of 1170 culturable endophytic isolates were recovered from 6480 tissue segments of C. sativus collected from six different study sites in Pampore region of Kashmir valley in India. These isolates were identified using 16S and ITS (internal transcribed spacer) rDNA barcode sequence analysis and were classified into 84 operational taxonomic units (OTUs), including 52 bacterial OTUs, 7 actinomycete OTUs and 25 fungal OTUs. The phylogenetic analysis of sequences separated them into four phyla, namely, Firmicutes (46%), Ascomycota (30%), Proteobacteria (16%) and Actinobacteria (8%). Significant differences were observed in the diversity of endophytic assemblages across various study sites and different plant organs (P ≤ 0.001). Species richness was highest at the Baroosa site and lowest at the Chandhar site while the Shannon index was highest at the Baroosa site and lowest at the Letpur site. Among organs, species richness was highest in stigma and lowest in leaf. Similarly, Shannon index was highest for root and lowest for leaf. Further, 15 culturable endophytic OTUs showed organ specificity. The present study is the first comprehensive report that not only brings out differences in the diversity of endophytes associated with different organs and at different sites but also highlights the complexity of host-endophyte interaction at multiple scales.}, }
@article {pmid34340552, year = {2021}, author = {Munoz-Munoz, J and Ndeh, D and Fernandez-Julia, P and Walton, G and Henrissat, B and Gilbert, HJ}, title = {Sulfation of Arabinogalactan Proteins Confers Privileged Nutrient Status to Bacteroides plebeius.}, journal = {mBio}, volume = {12}, number = {4}, pages = {e0136821}, pmid = {34340552}, issn = {2150-7511}, support = {/WT_/Wellcome Trust/United Kingdom ; WT097907MA/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteroides/enzymology/genetics/growth &amp; development/*metabolism ; Dietary Carbohydrates/metabolism ; Gastrointestinal Microbiome/physiology ; Mucoproteins/*metabolism ; Nutrients/*metabolism ; Plant Proteins/metabolism ; Polysaccharide-Lyases/genetics/metabolism ; Polysaccharides/metabolism ; Sulfatases/*metabolism ; }, abstract = {The human gut microbiota (HGM) contributes to the physiology and health of its host. The health benefits provided by dietary manipulation of the HGM require knowledge of how glycans, the major nutrients available to this ecosystem, are metabolized. Arabinogalactan proteins (AGPs) are a ubiquitous feature of plant polysaccharides available to the HGM. Although the galactan backbone and galactooligosaccharide side chains of AGPs are conserved, the decorations of these structures are highly variable. Here, we tested the hypothesis that these variations in arabinogalactan decoration provide a selection mechanism for specific Bacteroides species within the HGM. The data showed that only a single bacterium, B. plebeius, grew on red wine AGP (Wi-AGP) and seaweed AGP (SW-AGP) in mono- or mixed culture. Wi-AGP thus acts as a privileged nutrient for a Bacteroides species within the HGM that utilizes marine and terrestrial plant glycans. The B. plebeius polysaccharide utilization loci (PULs) upregulated by AGPs encoded a polysaccharide lyase, located in the enzyme family GH145, which hydrolyzed Rha-Glc linkages in Wi-AGP. Further analysis of GH145 identified an enzyme with two active sites that displayed glycoside hydrolase and lyase activities, respectively, which conferred substrate flexibility for different AGPs. The AGP-degrading apparatus of B. plebeius also contained a sulfatase, BpS1_8, active on SW-AGP and Wi-AGP, which played a pivotal role in the utilization of these glycans by the bacterium. BpS1_8 enabled other Bacteroides species to access the sulfated AGPs, providing a route to introducing privileged nutrient utilization into probiotic and commensal organisms that could improve human health. IMPORTANCE Dietary manipulation of the HGM requires knowledge of how glycans available to this ecosystem are metabolized. The variable structures that decorate the core component of plant AGPs may influence their utilization by specific organisms within the HGM. Here, we evaluated the ability of Bacteroides species to utilize a marine and terrestrial AGP. The data showed that a single bacterium, B. plebeius, grew on Wi-AGP and SW-AGP in mono- or mixed culture. Wi-AGP is thus a privileged nutrient for a Bacteroides species that utilizes marine and terrestrial plant glycans. A key component of the AGP-degrading apparatus of B. plebeius is a sulfatase that conferred the ability of the bacterium to utilize these glycans. The enzyme enabled other Bacteroides species to access the sulfated AGPs, providing a route to introducing privileged nutrient utilization into probiotic and commensal organisms that could improve human health.}, }
@article {pmid34340550, year = {2021}, author = {Goordial, J and D'Angelo, T and Labonté, JM and Poulton, NJ and Brown, JM and Stepanauskas, R and Früh-Green, GL and Orcutt, BN}, title = {Microbial Diversity and Function in Shallow Subsurface Sediment and Oceanic Lithosphere of the Atlantis Massif.}, journal = {mBio}, volume = {12}, number = {4}, pages = {e0049021}, pmid = {34340550}, issn = {2150-7511}, mesh = {Genomics ; Geologic Sediments/*microbiology ; Microbiota/*genetics ; *Oceans and Seas ; }, abstract = {The marine lithospheric subsurface is one of the largest biospheres on Earth; however, little is known about the identity and ecological function of microorganisms found in low abundance in this habitat, though these organisms impact global-scale biogeochemical cycling. Here, we describe the diversity and metabolic potential of sediment and endolithic (within rock) microbial communities found in ultrasmall amounts (10[1] to 10[4] cells cm[-3]) in the subsurface of the Atlantis Massif, an oceanic core complex on the Mid-Atlantic Ridge that was sampled on International Ocean Discovery Program (IODP) Expedition 357. This study used fluorescence-activated cell sorting (FACS) to enable the first amplicon, metagenomic, and single-cell genomic study of the shallow (<20 m below seafloor) subsurface of an actively serpentinizing marine system. The shallow subsurface biosphere of the Atlantis Massif was found to be distinct from communities observed in the nearby Lost City alkaline hydrothermal fluids and chimneys, yet similar to other low-temperature, aerobic subsurface settings. Genes associated with autotrophy were rare, although heterotrophy and aerobic carbon monoxide and formate cycling metabolisms were identified. Overall, this study reveals that the shallow subsurface of an oceanic core complex hosts a biosphere that is not fueled by active serpentinization reactions and by-products. IMPORTANCE The subsurface rock beneath the ocean is one of the largest biospheres on Earth, and microorganisms within influence global-scale nutrient cycles. This biosphere is difficult to study, in part due to the low concentrations of microorganisms that inhabit the vast volume of the marine lithosphere. In spite of the global significance of this biosphere, little is currently known about the microbial ecology of such rock-associated microorganisms. This study describes the identity and genomic potential of microorganisms in the subsurface rock and sediment at the Atlantis Massif, an underwater mountain near the Mid-Atlantic Ridge. To enable our analyses, fluorescence-activated cell sorting (FACS) was used as a means to concentrate cells from low biomass environmental samples for genomic analyses. We found distinct rock-associated microorganisms and found that the capacity for microorganisms to utilize organic carbon was the most prevalent form of carbon cycling. We additionally identified a potential role for carbon monoxide metabolism in the subsurface.}, }
@article {pmid34339990, year = {2022}, author = {Zhang, S and Lu, J and Wang, Y and Verstraete, W and Yuan, Z and Guo, J}, title = {Insights of metallic nanoparticles and ions in accelerating the bacterial uptake of antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {421}, number = {}, pages = {126728}, doi = {10.1016/j.jhazmat.2021.126728}, pmid = {34339990}, issn = {1873-3336}, mesh = {Acinetobacter/genetics ; Anti-Bacterial Agents ; *Drug Resistance, Microbial/genetics ; Humans ; *Ions/toxicity ; *Metal Nanoparticles/toxicity ; }, abstract = {The increasing release of nanomaterials has attracted significant concerns for human and environmental health. Similarly, the dissemination of antimicrobial resistance (AMR) is a global health crisis affecting approximately 700,000 people a year. However, a knowledge gap persists between the spread of AMR and nanomaterials. This study aims to fill this gap by investigating whether and how nanomaterials could directly facilitate the dissemination of AMR through horizontal gene transfer. Our results show that commonly-used nanoparticles (NPs) (Ag, CuO and ZnO NPs) and their ion forms (Ag[+], Cu[2+] and Zn[2+]) at realistic concentrations within aquatic environments can significantly promote the transformation of extracellular antibiotic resistance genes in Acinetobacter baylyi ADP1 by a factor of 11.0-folds, which is comparable to the effects of antibiotics. The enhanced transformation by Ag NPs/Ag[+] and CuO NPs/Cu[2+] was primarily associated with the overproduction of reactive oxygen species and cell membrane damage. ZnO NPs/Zn[2+] might increase the natural transformation rate by stimulating the stress response and ATP synthesis. All tested NPs/ions resulted in upregulating the competence and SOS response-associated genes. These findings highlight a new concern that nanomaterials can speed up the spread of AMR, which should not be ignored when assessing the holistic risk of nanomaterials.}, }
@article {pmid34339704, year = {2022}, author = {Torun, F and Hostins, B and De Schryver, P and Boon, N and De Vrieze, J}, title = {Molybdate effectively controls sulphide production in a shrimp pond model.}, journal = {Environmental research}, volume = {203}, number = {}, pages = {111797}, doi = {10.1016/j.envres.2021.111797}, pmid = {34339704}, issn = {1096-0953}, mesh = {Animals ; *Geologic Sediments ; Molybdenum ; *Ponds ; Seawater ; Sulfides ; }, abstract = {The production of shrimp is often performed in earthen outdoor ponds in which the high input of feed and faeces on the bottom can result in deterioration of the water quality, which negatively impacts the animals and the environment. Here, we investigate the potential of sodium molybdate (Na2MoO4·2H2O), sodium nitrate (NaNO3) and sodium percarbonate (Na2CO3·1.5H2O2) to control sulphide production in a simulated shrimp pond bottom system that included the sediment, overlaying artificial seawater and organic matter input in the form of shrimp feed and shrimp faeces. Sediment depth gradient measurements of oxygen, H2S and pH were obtained during 7 days of incubation using microelectrodes. The most significant impact in terms of H2S, was observed for 50 mg/L sodium molybdate. At the water-sediment interface, there was up to 73% less H2S detected for this treatment in comparison to a control treatment, while in the deeper layers of the sediment it was up to 47% less H2S. The residual sulphate concentrations in the molybdate treated samples were 16 ± 4% higher than the control, indicating an inhibition in sulphate reduction. Nitrate and sodium percarbonate treatments also showed a limited capacity to decrease H2S entering in the water column, yet no clear difference in H2S concentrations in the sediment compared to the control were observed. Molybdate treatment appears to work through the inhibition of sulphate reducing bacteria in situ for the control of H2S production better than the chemical oxygen boosters or nitrate treatment.}, }
@article {pmid34339295, year = {2021}, author = {Göing, S and Gasperotti, AF and Yang, Q and Defoirdt, T and Jung, K}, title = {Insights into a Pyruvate Sensing and Uptake System in Vibrio campbellii and Its Importance for Virulence.}, journal = {Journal of bacteriology}, volume = {203}, number = {20}, pages = {e0029621}, pmid = {34339295}, issn = {1098-5530}, mesh = {Animals ; Artemia/microbiology ; Bacterial Proteins/genetics/metabolism ; Biological Transport ; Carrier Proteins/genetics/*metabolism ; Culture Media/chemistry ; Gene Expression Regulation, Bacterial ; Genotype ; Larva/microbiology ; Pyruvic Acid/chemistry/*metabolism ; Vibrio/genetics/*metabolism/*pathogenicity ; Virulence ; }, abstract = {Pyruvate is a key metabolite in living cells and has been shown to play a crucial role in the virulence of several bacterial pathogens. The bioluminescent Vibrio campbellii, a severe infectious burden for marine aquaculture, excretes extraordinarily large amounts of pyruvate during growth and rapidly retrieves it by an as-yet-unknown mechanism. We have now identified the responsible pyruvate transporter, here named BtsU, and our results show that it is the only pyruvate transporter in V. campbellii. Expression of btsU is tightly regulated by the membrane-integrated LytS-type histidine kinase BtsS, a sensor for extracellular pyruvate, and the LytTR-type response regulator BtsR. Cells lacking either the pyruvate transporter or sensing system show no chemotactic response toward pyruvate, indicating that intracellular pyruvate is required to activate the chemotaxis system. Moreover, pyruvate sensing and uptake were found to be important for the resuscitation of V. campbellii from the viable but nonculturable state and the bacterium's virulence against brine shrimp larvae. IMPORTANCE Bacterial infections are a serious threat to marine aquaculture, one of the fastest growing food sectors on earth. Therefore, it is extremely important to learn more about the pathogens responsible, one of which is Vibrio campbellii. This study sheds light on the importance of pyruvate sensing and uptake for V. campbellii, and reveals that the bacterium possesses only one pyruvate transporter, which is activated by a pyruvate-responsive histidine kinase/response regulator system. Without the ability to sense or take up pyruvate, the virulence of V. campbellii toward gnotobiotic brine shrimp larvae is strongly reduced.}, }
@article {pmid34338516, year = {2021}, author = {Tang, JS and Cait, A and Li, Y and Abolins-Thompson, H and Gell, K and Herst, PM and O'Sullivan, D and Gasser, O}, title = {Practical Approach To Explore the Effects of Polyphenols on Aryl Hydrocarbon Receptor Regulated Immune Function.}, journal = {Journal of agricultural and food chemistry}, volume = {69}, number = {31}, pages = {8625-8633}, doi = {10.1021/acs.jafc.1c02095}, pmid = {34338516}, issn = {1520-5118}, mesh = {Humans ; *Immunity ; Ligands ; *Polyphenols/pharmacology ; *Receptors, Aryl Hydrocarbon/genetics ; Tryptophan ; }, abstract = {The ligand-activated aryl hydrocarbon receptor (AhR) is an important molecular regulator of immune function, whose activity can be modulated by dietary glucosinolate- and tryptophan-derived metabolites. In contrast, the potential use of polyphenols as dietary regulators of AhR-dependent immunity remains unclear. In this perspective, we discuss how cellular metabolism may alter the net effect of polyphenols on AhR, thus potentially reconciling some of the conflicting observations reported in the literature. We further provide a methodological roadmap, across the fields of immunology, metabolomics, and gut microbial ecology, to explore the potential effects of polyphenol-rich diets on AhR-regulated immune function in humans.}, }
@article {pmid34335540, year = {2021}, author = {Zhang, J and Zeng, R and Labes, A}, title = {Editorial: Marine Microbial-Derived Molecules and Their Potential Medical and Cosmetic Applications.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {706152}, doi = {10.3389/fmicb.2021.706152}, pmid = {34335540}, issn = {1664-302X}, }
@article {pmid34333553, year = {2022}, author = {Howard, MM and Bass, E and Chautá, A and Mutyambai, D and Kessler, A}, title = {Integrating plant-to-plant communication and rhizosphere microbial dynamics: ecological and evolutionary implications and a call for experimental rigor.}, journal = {The ISME journal}, volume = {16}, number = {1}, pages = {5-9}, pmid = {34333553}, issn = {1751-7370}, mesh = {Plant Roots ; Plants ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {The perception of airborne chemical signals by plants can trigger reconfigurations of their metabolism that alter their biotic interactions. While plant-to-plant chemical communication has primarily been studied in the context of eliciting defenses to herbivores and pathogens, recent work suggests that it can also affect plants’ interactions with their rhizosphere microbiomes. In this perspective, we discuss the potential for integrating the fields of plant-to-plant communication and microbial ecology to understand the chemical ecology of plant−microbiome interactions. As an introduction for microbial ecologists, we highlight mechanistic knowledge gaps in plant volatile organic compound (VOC) perception and provide recommendations for avoiding common experimental errors that have plagued the plant communication field. Lastly, we discuss potential implications of plant VOCs structuring rhizosphere microbiomes, particularly effects on plant community and evolutionary dynamics. As we continue to discover links between plant metabolism and their microbiomes—from molecular to community scales—we hope that this perspective will provide both motivation and words of caution for researchers working at the intersection of these two fields.}, }
@article {pmid34333428, year = {2021}, author = {Boada, E and Santos-Clotas, E and Cabrera-Codony, A and Martín, MJ and Bañeras, L and Gich, F}, title = {The core microbiome is responsible for volatile silicon and organic compounds degradation during anoxic lab scale biotrickling filter performance.}, journal = {The Science of the total environment}, volume = {798}, number = {}, pages = {149162}, doi = {10.1016/j.scitotenv.2021.149162}, pmid = {34333428}, issn = {1879-1026}, mesh = {Biodegradation, Environmental ; Bioreactors ; Filtration ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Silicon ; *Volatile Organic Compounds ; }, abstract = {Volatile silicon compounds present in the biogas of anaerobic digesters can cause severe problems in the energy recovery systems, inducing costly damages. Herein, the microbial community of a lab-scale biotrickling filter (BTF) was studied while testing its biodegradation capacity on octamethylcyclotetrasiloxane (D4) and decamethylcyclopentasiloxane (D5), in the presence of toluene, limonene and hexane. The reactor performance was tested at different empty bed residence times (EBRT) and packing materials. Community structure was analysed by bar-coded amplicon sequencing of the 16S rRNA gene. Microbial diversity and richness were higher in the inoculum and progressively decreased during BTF operation (Simpson's diversity index changing from 0.98-0.90 and Richness from 900 to 200 OTUs). Minimum diversity was found when reactor was operated at relatively low EBRT (7.3 min) using a multicomponent feed. The core community was composed of 36 OTUs (accounting for 55% of total sequences). Packing material played a key role in the community structure. Betaproteobacteriales were dominant in the presence of lava rock and were partially substituted by Corynebacteriales and Rhizobiales when activated carbon was added to the BTF. Despite these changes, a stable and resilient core microbiome was selected defining a set of potentially degrading bacteria for siloxane bioremoval as a complementary alternative to non-regenerative adsorption onto activated carbon.}, }
@article {pmid34333046, year = {2021}, author = {Hunt, KA and Forbes, J and Taub, F and Elliott, N and Hardwicke, J and Petersen, R and Stopnisek, N and Beck, DAC and Stahl, DA}, title = {An automated multiplexed turbidometric and data collection system for measuring growth kinetics of anaerobes dependent on gaseous substrates.}, journal = {Journal of microbiological methods}, volume = {188}, number = {}, pages = {106294}, doi = {10.1016/j.mimet.2021.106294}, pmid = {34333046}, issn = {1872-8359}, mesh = {Bacteria, Anaerobic/*growth &amp; development ; Bacteriological Techniques/instrumentation/*methods ; Data Collection/instrumentation/*methods ; Environmental Monitoring/instrumentation/methods ; *Gases ; High-Throughput Screening Assays ; Kinetics ; Methanococcus/growth &amp; development ; Optical Devices ; Symbiosis ; }, abstract = {Standard methods of monitoring the growth kinetics of anaerobic microorganisms are generally impractical when there is a protracted or indeterminate period of active growth, and when high numbers of samples or replications are required. As part of our studies of the adaptive evolution of a simple anaerobic syntrophic mutualism, requiring the characterization of many isolates and alternative syntrophic pairings, we developed a multiplexed growth monitoring system using a combination of commercially available electronics and custom designed circuitry and materials. This system automatically monitors up to 64 sealed, and as needed pressurized, culture tubes and reports the growth data in real-time through integration with a customized relational database. The utility of this system was demonstrated by resolving minor differences in growth kinetics associated with the adaptive evolution of a simple microbial community comprised of a sulfate reducing bacterium, Desulfovibrio vulgaris, grown in syntrophic association with Methanococcus maripaludis, a hydrogenotrophic methanogen.}, }
@article {pmid34331150, year = {2021}, author = {de Freitas, F and Vendruscolo, SJ and Soares, MA and Battirola, LD and de Andrade, RLT}, title = {Biomass of the macrophyte remedies and detoxifies Cd(II) and Pb(II) in aqueous solution.}, journal = {Environmental monitoring and assessment}, volume = {193}, number = {8}, pages = {537}, pmid = {34331150}, issn = {1573-2959}, mesh = {Adsorption ; Biomass ; *Cadmium/analysis ; Environmental Monitoring ; Hydrogen-Ion Concentration ; Kinetics ; Lead ; Water ; *Water Pollutants, Chemical/analysis/toxicity ; }, abstract = {Aquatic plants are considered to be important remedial agents in aquatic environments contaminated by metals. The Salvinia biloba macrophyte was evaluated in relation to its removal kinetics, adsorption capacity, and toxicology, aiming at its application in the removal of Cd[+2] and Pb[+2] ions from aqueous solutions. A batch-type system was used, in which the plants were cultivated in microcosms containing nutritive solution and metallic ions, stored in a controlled environment (pH, temperature, and luminosity). The removal kinetics consisted in the analysis of efficiency, varying the concentrations of the metals, and time of cultivation of plants in solution. To describe the process, adsorption isotherms were constructed with the equilibrium data, which were later adjusted to Langmuir and Freundlich models. The toxicological trial was performed by sub-acute exposure test of Caenorhabditis elegans nematode to phytoremediated solutions. The results highlight the remedial effect of the plant in solutions contaminated with both metals. The kinetic study demonstrated that the plant responds differently to metals, and physical-chemical and biological processes can be attributed to the removal of metals from the solution by the plant. The equilibrium time obtained was 48 h for both metals, and the adsorption capacity was higher for Cd[2+]. The toxicological evaluation indicates that there was a reduction in toxicity after the remediation of the solutions by S. biloba, for all times and concentrations evaluated. Salvinia biloba was efficient for the removal of Cd[2+] and Pb[2+] metals from aqueous solution. The plant is a low-cost metal biosorbent and can be considered promising for phytoremediation strategies in liquid effluents and water bodies.}, }
@article {pmid34331071, year = {2022}, author = {Haydon, TD and Suggett, DJ and Siboni, N and Kahlke, T and Camp, EF and Seymour, JR}, title = {Temporal Variation in the Microbiome of Tropical and Temperate Octocorals.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {1073-1087}, pmid = {34331071}, issn = {1432-184X}, mesh = {Animals ; *Anthozoa/microbiology ; Bacteria/genetics ; Biodiversity ; Coral Reefs ; *Gammaproteobacteria/genetics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bacterial members of the coral holobiont play an important role in determining coral fitness. However, most knowledge of the coral microbiome has come from reef-building scleractinian corals, with far less known about the nature and importance of the microbiome of octocorals (subclass Octocorallia), which contribute significantly to reef biodiversity and functional complexity. We examined the diversity and structure of the bacterial component of octocoral microbiomes over summer and winter, with a focus on two temperate (Erythropodium hicksoni, Capnella gaboensis; Sydney Harbour) and two tropical (Sinularia sp., Sarcophyton sp.; Heron Island) species common to reefs in eastern Australia. Bacterial communities associated with these octocorals were also compared to common temperate (Plesiastrea versipora) and tropical (Acropora aspera) hard corals from the same reefs. Using 16S rRNA amplicon sequencing, bacterial diversity was found to be heterogeneous among octocorals, but we observed changes in composition between summer and winter for some species (C. gaboensis and Sinularia sp.), but not for others (E. hicksoni and Sarcophyton sp.). Bacterial community structure differed significantly between all octocoral species within both the temperate and tropical environments. However, on a seasonal basis, those differences were less pronounced. The microbiomes of C. gaboensis and Sinularia sp. were dominated by bacteria belonging to the genus Endozoicomonas, which were a key conserved feature of their core microbiomes. In contrast to previous studies, our analysis revealed that Endozoicomonas phylotypes are shared across different octocoral species, inhabiting different environments. Together, our data demonstrates that octocorals harbour a broad diversity of bacterial partners, some of which comprise 'core microbiomes' that potentially impart important functional roles to their hosts.}, }
@article {pmid34330907, year = {2021}, author = {Rahlff, J and Turzynski, V and Esser, SP and Monsees, I and Bornemann, TLV and Figueroa-Gonzalez, PA and Schulz, F and Woyke, T and Klingl, A and Moraru, C and Probst, AJ}, title = {Lytic archaeal viruses infect abundant primary producers in Earth's crust.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {4642}, pmid = {34330907}, issn = {2041-1723}, mesh = {Archaea/classification/*genetics/virology ; Archaeal Viruses/*genetics/metabolism/physiology ; Biofilms/growth &amp; development ; Ecosystem ; Genome, Viral/*genetics ; Genomics/methods ; Host-Pathogen Interactions/genetics ; Lysogeny/genetics ; Metagenome/*genetics ; Metagenomics/*methods ; Microscopy, Fluorescence ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Virus Activation/genetics ; }, abstract = {The continental subsurface houses a major portion of life's abundance and diversity, yet little is known about viruses infecting microbes that reside there. Here, we use a combination of metagenomics and virus-targeted direct-geneFISH (virusFISH) to show that highly abundant carbon-fixing organisms of the uncultivated genus Candidatus Altiarchaeum are frequent targets of previously unrecognized viruses in the deep subsurface. Analysis of CRISPR spacer matches display resistances of Ca. Altiarchaea against eight predicted viral clades, which show genomic relatedness across continents but little similarity to previously identified viruses. Based on metagenomic information, we tag and image a putatively viral genome rich in protospacers using fluorescence microscopy. VirusFISH reveals a lytic lifestyle of the respective virus and challenges previous predictions that lysogeny prevails as the dominant viral lifestyle in the subsurface. CRISPR development over time and imaging of 18 samples from one subsurface ecosystem suggest a sophisticated interplay of viral diversification and adapting CRISPR-mediated resistances of Ca. Altiarchaeum. We conclude that infections of primary producers with lytic viruses followed by cell lysis potentially jump-start heterotrophic carbon cycling in these subsurface ecosystems.}, }
@article {pmid34326823, year = {2021}, author = {Gu, Q and Chen, M and Zhang, J and Guo, W and Wu, H and Sun, M and Wei, L and Wang, J and Wei, X and Zhang, Y and Ye, Q and Xue, L and Pang, R and Ding, Y and Wu, Q}, title = {Genomic Analysis and Stability Evaluation of the Phenol-Degrading Bacterium Acinetobacter sp. DW-1 During Water Treatment.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {687511}, pmid = {34326823}, issn = {1664-302X}, abstract = {Phenol is a toxic organic molecule that is widely detected in the natural environment, even in drinking water sources. Biological methods were considered to be a good tool for phenol removal, especially microbial immobilized technology. However, research on the "seed" bacteria along with microbial community analysis in oligotrophic environment such as drinking water system has not been addressed. In this study, Acinetobacter sp. DW-1 with high phenol degradation ability had been isolated from a drinking water biofilter was used as seeded bacteria to treat phenol micro-polluted drinking water source. Meanwhile, the whole genome of strain DW-1 was sequenced using nanopore technology. The genomic analysis suggests that Acinetobacter sp. DW-1 could utilize phenol via the β-ketoadipate pathway, including the catechol and protocatechuate branches. Subsequently, a bio-enhanced polyhedral hollow polypropylene sphere (BEPHPS) filter was constructed to investigate the stability of the seeded bacteria during the water treatment process. The denatured gradient gel electrophoresis (DGGE) profile and the quantification of phenol hydroxylase gene results indicate that when the BEPHPS filter was operated for 56 days, Acinetobacter sp. was still a persistent and competitive bacterium in the treatment group. In addition, 16S rRNA gene amplicon sequencing results indicate that Acinetobacter sp., as well as Pseudomonas sp., Nitrospira sp., Rubrivivax sp. were the predominant bacteria in the treatment group, which were different from that in the CK group. This study provides a better understanding of the mechanisms of phenol degradation by Acinetobacter sp. DW-1 at the gene level, and provides new insights into the stability of seeded bacteria and its effects on microbial ecology during drinking water treatment.}, }
@article {pmid34324834, year = {2021}, author = {Christensen, SM and Munkres, I and Vannette, RL}, title = {Nectar bacteria stimulate pollen germination and bursting to enhance microbial fitness.}, journal = {Current biology : CB}, volume = {31}, number = {19}, pages = {4373-4380.e6}, doi = {10.1016/j.cub.2021.07.016}, pmid = {34324834}, issn = {1879-0445}, mesh = {Animals ; Bacteria ; Bees ; Flowers ; *Plant Nectar ; Pollen ; *Pollination/physiology ; }, abstract = {Many organisms consume pollen, yet mechanisms of its digestion remain a fundamental enigma in pollination biology,[1-3] as pollen is protected by a recalcitrant outer shell.[4-8] Pollen is commonly found in floral nectar,[9][,][10] as are nectar microbes, which are nearly ubiquitous among flowers.[11-13] Nectar specialist bacteria, like Acinetobacter, can reach high densities (up to 10[9] cells/mL), despite the fact that floral nectar is nitrogen poor.[14-17] Here, we show evidence that the genus Acinetobacter, prevalent nectar- and bee-associated bacteria,[12][,][18-20] can induce pollen germination and bursting, gain access to protoplasm nutrients, and thereby grow to higher densities. Although induced germination had been suggested as a potential method in macroscopic pollen consumers,[2][,][21-23] and fungal inhibition of pollen germination has been shown,[24-27] direct biological induction of germination has not been empirically documented outside of plants.[28-32]Acinetobacter pollinis SCC477[19] induced over 5× greater pollen germination and 20× greater pollen bursting than that of uninoculated pollen by 45 min. When provided with germinable pollen, A. pollinis stimulates protein release and grows to nearly twice the density compared to growth with ungerminable pollen, indicating that stimulation of germination benefits bacterial fitness. In contrast, a common nectar-inhabiting yeast (Metschnikowia)[33] neither induced nor benefited from pollen germination. We conclude that Acinetobacter both specifically causes and benefits from inducing pollen germination and bursting. Further study of microbe-pollen interactions may inform many aspects of pollination ecology, including floral microbial ecology,[34][,][35] pollinator nutrient acquisition from pollen,[2][,][3][,][21][,][36] and cues of pollen germination for plant reproduction.[37-39].}, }
@article {pmid34320736, year = {2021}, author = {Rimboud, M and Etcheverry, L and Barakat, M and Achouak, W and Bergel, A and Délia, ML}, title = {Hypersaline microbial fuel cell equipped with an oxygen-reducing microbial cathode.}, journal = {Bioresource technology}, volume = {337}, number = {}, pages = {125448}, doi = {10.1016/j.biortech.2021.125448}, pmid = {34320736}, issn = {1873-2976}, mesh = {*Bioelectric Energy Sources ; Electricity ; Electrodes ; Oxidation-Reduction ; Oxygen ; }, abstract = {Microbial anodes and oxygen reducing microbial cathodes were designed separately under constant polarization at + 0.1 V/SCE in a hypersaline medium (NaCl 45 g/L). They were then associated to design two-compartment microbial fuel cells (MFCs). These MFCs produced up to 209 ± 24 mW m[-2] during a week. This was the first demonstration that hypersaline MFCs equipped with microbial cathodes can produce power density at this level. Desulfuromonas sp. were confirmed to be key species of the anodes. The efficiency of the cathodes was linked to the development of a redox system centred at + 0.2 V/SCE and to the presence of Gammaproteobacteria (Alteromonadales and Oceanospirillales), especially an unclassified order phylogenetically linked to the genus Thioalobacter. Comparing the different performance of the four MFCs with the population analyses suggested that polarization at + 0.1 V/SCE should be maintained longer to promote the growth of Thioalobacter on the cathode and thus increase the MFC performance.}, }
@article {pmid34320208, year = {2021}, author = {Minnebo, Y and De Paepe, K and Raes, J and de Wiele, TV}, title = {Nutrient load acts as a driver of gut microbiota load, community composition and metabolic functionality in the simulator of the human intestinal microbial ecosystem.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {9}, pages = {}, doi = {10.1093/femsec/fiab111}, pmid = {34320208}, issn = {1574-6941}, mesh = {Fatty Acids, Volatile ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Nutrients ; Verrucomicrobia ; }, abstract = {A recently introduced quantitative framework for gut microbiota analysis indicated that microbial load alterations can be linked to various diseases, making it essential to pinpoint its determinants. We identified nutrient load as a main driver of the quantitative microbial community composition and functionality in vitro by stepwise decreasing standardized feed concentrations from 100% to 33%, 20% and 10% in 5-day intervals. While the proportional composition and metabolic profile were mainly determined by the inter-individual variability (35% and 41%), nutrient load accounted for 58%, 23% and 65% of the observed variation in the microbial load, quantitative composition and net daily metabolite production, respectively. After the 10-fold nutrient reduction, the microbial load decreased by 79.72 ± 9% and 82.96 ± 1.66% in the proximal and distal colon, respectively, while the net total short-chain fatty acid production dropped by 79.42 ± 4.42% and 84.58 ± 2.42%, respectively. The majority of microbial taxa quantitatively decreased, whereas a select group of nutritional specialists, such as Akkermansia muciniphila and Bilophila wadsworthia, and a number of opportunistic pathogens remained unaffected. This shows that nutrient load is an important driver of the human gut microbiome and should be considered in future in vitro and in vivo dietary research.}, }
@article {pmid34313080, year = {2021}, author = {Zou, WX and Shen, JP and Zhang, LM and Hu, A and Wang, JJ and He, JZ}, title = {Quantitative stable isotope probing technique and its applications in microbial ecology.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {32}, number = {7}, pages = {2615-2622}, doi = {10.13287/j.1001-9332.202107.032}, pmid = {34313080}, issn = {1001-9332}, mesh = {Carbon Isotopes ; DNA ; High-Throughput Nucleotide Sequencing ; Isotope Labeling ; *Microbiota ; }, abstract = {Quantitative stable isotope probing (qSIP) is a powerful tool, which links microbial taxon with functional metabolism in ecosystems and quantitatively determines the metabolic activity or growth rate of individual microbial taxa exposed to isotope tracers in the environment. qSIP technique employs quantitative PCR, high-throughput sequencing and stable isotope probing (SIP) techniques. The procedure involves adding labeled substrates to environmental samples for cultivation, separating labeled heavy fraction from unlabeled light fraction via isopycnic ultracentrifugation, making absolute quantification and sequencing analysis for microbial populations in all fractions, and then quantifying the isotope abundance of DNA involved in uptake and transformation based on the DNA density curve of unlabeled treatment and GC content. Here, we reviewed the rationale, data analysis and application of qSIP in microbial ecology, and discussed the existing problems and prospects of qSIP.}, }
@article {pmid34312710, year = {2022}, author = {Islam, MS and Sobur, MA and Rahman, S and Ballah, FM and Ievy, S and Siddique, MP and Rahman, M and Kafi, MA and Rahman, MT}, title = {Detection of blaTEM, blaCTX-M, blaCMY, and blaSHV Genes Among Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolated from Migratory Birds Travelling to Bangladesh.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {942-950}, pmid = {34312710}, issn = {1432-184X}, support = {2019/8/BAU//Bangladesh Agricultural University Research System/ ; 2020/28/UGC//University Grants Commission/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bangladesh ; Chickens ; *Escherichia coli/genetics ; *Escherichia coli Infections/veterinary ; Humans ; beta-Lactamases/genetics ; }, abstract = {Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli cause severe health hazards. Migratory birds are reservoirs and transmitters of many pathogens including ESBL-producing E. coli. To examine migratory birds as potential carriers of ESBL-producing E. coli and E. coli-carrying antibiotic resistance genes, 55 PCR-positive E. coli isolates were screened using the disk diffusion method, double-disk synergy test, and further polymerase chain reaction (PCR) tests. Genes encoding resistance to tetracycline [tetA, 100% (35/35); tetB, 31.43% (11/35)], fluoroquinolone [qnrA, 35.71% (10/28); qnrB, 25% (7/28)], and streptomycin [aadA1, 90.24% (37/41)] were detected in the isolated E. coli. Of the 55 E. coli isolates, 21 (38.18%) were ESBL producers, and all of them were multidrug resistant. All the ESBL-producing E. coli isolates harbored at least two or more beta-lactamase genes, of which blaTEM, blaCMY, blaCTX-M, and blaSHV were detected in 95.24%, 90.48%, 85.71%, and 42.86% of isolates, respectively. All the beta-lactamase genes were present in four of the ESBL-producing E. coli isolates. Furthermore, 95.24% of ESBL-producing E. coli isolates were positive for one or more antibiotic resistance genes. To the best of our knowledge, this is the first study to detect E. coli-carrying antibiotic resistance genes including beta-lactamase blaCMY and blaSHV originating from migratory birds in Bangladesh. These results suggest that migratory birds are potential carriers of ESBL-producing E. coli along with other clinically important antibiotic resistance genes which may have detrimental impacts on human health.}, }
@article {pmid34312709, year = {2022}, author = {de Los Ríos, A and Garrido-Benavent, I and Limón, A and Cason, ED and Maggs-Kölling, G and Cowan, D and Valverde, A}, title = {Novel lichen-dominated hypolithic communities in the Namib Desert.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {1036-1048}, pmid = {34312709}, issn = {1432-184X}, support = {CTM2015-64728-C2-2-R//(MINECO/FEDER, EU)/ ; PID2019-105469RB-C22//MICINN-AEI/ ; }, mesh = {*Cyanobacteria/genetics ; Desert Climate ; Ecosystem ; *Lichens ; Soil Microbiology ; }, abstract = {The ventral surfaces of translucent rocks from hot desert pavements often harbor hypolithic microbial communities, which are mostly dominated by cyanobacteria. The Namib Desert fog belt supports extensive hypolithic colonization of quartz rocks, which are also colonized by lichens on their dorsal surfaces. Here, we aim to evaluate whether lichens colonize the ventral surface of the rocks (i.e., show hypolithic lifestyle) and compare the bacterial composition of these coastal hypolithic communities with those found inland. Fungal DNA barcoding and fungal and bacterial Illumina metabarcoding were combined with electron microscopy to characterize the composition and spatial structure of hypolithic communities from two (coastal and inland) areas in the Namib Desert. We report, for the first time, the structure and composition of lichen-dominated hypolithic communities found in the coastal zone of the Namib Desert with extensive epilithic lichen cover. Lichen modified areoles with inverted morphology of the genus Stellarangia (three lineages) and Buellia (two lineages) were the main components of these hypolithic communities. Some of these lineages were also found in epilithic habitats. These lichen-dominated hypolithic communities differed in structural organization and bacterial community composition from those found in inland areas. The hypolithic lichen colonization characterized here seems not to be an extension of epilithic or biological soil crust lichen growths but the result of specific sublithic microenvironmental conditions. Moisture derived from fog and dew could be the main driver of this unique colonization.}, }
@article {pmid34312335, year = {2021}, author = {Wanner, J}, title = {The development in biological wastewater treatment over the last 50 years.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {84}, number = {2}, pages = {274-283}, doi = {10.2166/wst.2021.095}, pmid = {34312335}, issn = {0273-1223}, mesh = {Bioreactors ; Nitrogen ; Phosphorus ; Sewage ; *Waste Disposal, Fluid ; Wastewater ; *Water Purification ; }, abstract = {The paper summarizes the development in the understanding and practical application of the activated sludge process over the last 50 years. Since its invention, the activated sludge process has been a big challenge to design engineers. Traditionally, the technology was covered by sanitary engineers. However, with the development in the understanding of activated sludge process principles, further progress was not possible without knowledge of reaction kinetics and reactor theory. The shift from BOD removal only to combined removal of organic pollution, nitrogen and phosphorus required a chemical engineering approach with outputs of activated sludge microbiology and microbial ecology. Molecular biology enabled more accurate identification of important activated sludge microorganisms. The development in activated sludge process also required more efficient activated sludge separation and thickening. The paper describes the development from secondary clarifiers to membrane separation. Increasing water stress around the globe has also changed the main wastewater paradigm from wastewater treatment and safe discharge to safe reuse.}, }
@article {pmid34311495, year = {2021}, author = {Pascual, J and Tanner, K and Vilanova, C and Porcar, M and Delgado, A}, title = {The microbial terroir: open questions on the Nagoya protocol applied to microbial resources.}, journal = {Microbial biotechnology}, volume = {14}, number = {5}, pages = {1878-1880}, pmid = {34311495}, issn = {1751-7915}, mesh = {Animals ; Biodiversity ; Conservation of Natural Resources ; *Environmental Microbiology ; }, abstract = {The Nagoya Protocol on Access and Benefit-sharing (https://www.cbd.int/abs/), primarily designed for vascular plant and animal resources, is also extended to the use of microbial resources, but its application to the microbiological realm has raised many doubts and provoked criticisms. This is because of the particularities of microbial ecology and the technical and legal difficulties encompassed in its application.}, }
@article {pmid34311349, year = {2021}, author = {Williams, MR and Stedtfeld, RD and Stedtfeld, TM and Crawford, RB and Kuwahara, T and Kaminski, NE and Tiedje, JM and Hashsham, SA}, title = {MicroRNA-based host response to toxicant exposure is influenced by the presence of gut microbial populations.}, journal = {The Science of the total environment}, volume = {797}, number = {}, pages = {149130}, pmid = {34311349}, issn = {1879-1026}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Immunity ; Mice ; Mice, Inbred C57BL ; *MicroRNAs/genetics ; *Polychlorinated Dibenzodioxins/toxicity ; Receptors, Aryl Hydrocarbon/genetics ; }, abstract = {Segmented filamentous bacteria (SFB) and Bacteroides fragilis are known to interact with the host immune response through the aryl hydrocarbon receptor (Ahr). 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), an environmental toxicant and a high-affinity Ahr ligand has the potential to modify the effect of SFB and B. fragilis. MicroRNAs (miRNA) with their role in regulating gene expression post-transcriptionally, may potentially be used to observe such interactions between SFB, B. fragilis, and TCDD. However, little is known regarding the impact of gut microbial members on miRNA expression or its modulation in the presence of an environmental toxicant. This information is important in understanding toxicant-mediated dysbiosis in gut microbiome and the resulting human health impacts. In this study, C57BL/6 germ-free (GF) mice were colonized with SFB and B. fragilis and administered 30 μg/kg TCDD every 4 d for 28 d and miRNA were measured. Compared to GF mice, colonization with SFB resulted in an increase in up- and down-regulated Ileal miRNAs. TCDD treatment of this group decreased the number of upregulated miRNA and increased the number of down-regulated miRNAs. Association with SFB and B. fragilis together had a similar but less pronounced effect in response to TCDD treatment. TCDD treatment of GF mice had no miRNA expression response. Immune and inflammatory responses and T-cell differentiation were the key functions impacted by these miRNAs. Overall, these results reveal that the host response to toxicants may also depend on the presence of specific gut microbial populations.}, }
@article {pmid34309697, year = {2022}, author = {Begum, N and Wang, L and Ahmad, H and Akhtar, K and Roy, R and Khan, MI and Zhao, T}, title = {Co-inoculation of Arbuscular Mycorrhizal Fungi and the Plant Growth-Promoting Rhizobacteria Improve Growth and Photosynthesis in Tobacco Under Drought Stress by Up-Regulating Antioxidant and Mineral Nutrition Metabolism.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {971-988}, pmid = {34309697}, issn = {1432-184X}, mesh = {Antioxidants/metabolism ; Chlorophyll A/metabolism ; Droughts ; Electrolytes/metabolism ; Minerals/metabolism ; *Mycorrhizae/physiology ; Nutritional Status ; Photosynthesis ; Plant Roots/microbiology ; Nicotiana ; }, abstract = {Drought stress is a major environmental concern that limits crop growth on a large scale around the world. Significant efforts are required to overcome this issue in order to improve crop production. Therefore, the exciting role of beneficial microorganisms under stress conditions needs to be deeply explored. In this study, the role of two biotic entities, i.e., Arbuscular mycorrhizal fungi (AMF, Glomus versiforme) and plant growth-promoting rhizobacteria (PGPR, Bacillus methylotrophicus) inoculation in drought tolerance of tobacco (Nicotiana tabacum L.), was investigated. The present results showed that drought stress considerably reduced tobacco plant's growth and their physiological attributes. However, the plants co-inoculated with AMF and PGPR showed higher drought tolerance by bringing up significant improvement in the growth and biomass of tobacco plants. Moreover, the co-inoculation of AMF and PGPR considerably increased chlorophyll a, b, total chlorophylls, carotenoids, photosynthesis, and PSII efficiency by 96.99%, 76.90%, and 67.96% and 56.88%, 53.22%, and 33.43% under drought stress conditions, respectively. Furthermore, it was observed that drought stress enhanced lipid peroxidation and electrolyte leakage. However, the co-inoculation of AMF and PGPR reduced the electrolyte leakage and lipid peroxidation and significantly enhanced the accumulation of phenols and flavonoids by 57.85% and 71.74%. Similarly, the antioxidant enzymatic activity and the plant nutrition status were also considerably improved in co-inoculated plants under drought stress. Additionally, the AMF and PGPR inoculation also enhanced abscisic acid (ABA) and indole-3-acetic acid (IAA) concentrations by 67.71% and 54.41% in the shoots of tobacco plants. The current findings depicted that inoculation of AMF and PGPR (alone or in combination) enhanced the growth and mitigated the photosynthetic alteration with the consequent up-regulation of secondary metabolism, osmolyte accumulation, and antioxidant system.}, }
@article {pmid34305833, year = {2021}, author = {Hernández, R and Jimenez, H and Vargas-Garcia, C and Caro-Quintero, A and Reyes, A}, title = {Disentangling the Complexity of the Rumen Microbial Diversity Through Fractionation Using a Sucrose Density Gradient.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {664754}, pmid = {34305833}, issn = {1664-302X}, abstract = {The ruminal microbial community is an important element in health, nutrition, livestock productivity, and climate impact. Despite the historic and current efforts to characterize this microbial diversity, many of its members remain unidentified, making it challenging to associate microbial groups with functions. Here we present a low-cost methodology for rumen sample treatment that separates the microbial community based on cell size, allowing for the identification of subtle compositional changes. In brief, the sample is centrifuged through a series of sucrose density gradients, and cells migrate to their corresponding density fraction. From each fraction, DNA is extracted and 16S rRNA gene amplicons are sequenced. We tested our methodology on four animals under two different conditions, fasting, and post-feeding. Each fraction was examined by confocal microscopy showing that the same sucrose fraction consistently separated similar cell-sized microorganisms independent of the animal or treatment. Microbial composition analysis using metabarcoding showed that our methodology detected low abundance bacterial families and population changes between fasting and post-feeding treatments that could not be observed by bulk DNA analysis. In conclusion, the sucrose-based method is a powerful low-cost approximation to untwine, enrich, and potentially isolate uncharacterized members of the ruminal microbiome.}, }
@article {pmid34305582, year = {2021}, author = {Chen, Z and Lv, Y and Xu, H and Deng, L}, title = {Herbal Medicine, Gut Microbiota, and COVID-19.}, journal = {Frontiers in pharmacology}, volume = {12}, number = {}, pages = {646560}, pmid = {34305582}, issn = {1663-9812}, abstract = {Coronavirus Disease 19 (COVID-19) is a respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has grown to a worldwide pandemic with substantial mortality. The symptoms of COVID-19 range from mild flu-like symptoms, including cough and fever, to life threatening complications. There are still quite a number of patients with COVID-19 showed enteric symptoms including nausea, vomiting, and diarrhea. The gastrointestinal tract may be one of the target organs of SARS-CoV-2. Angiotensin converting enzyme 2 (ACE2) is the main receptor of SARS-CoV-2 virus, which is significantly expressed in intestinal cells. ACE2 links amino acid malnutrition to microbial ecology and intestinal inflammation. Intestinal flora imbalance and endotoxemia may accelerate the progression of COVID-19. Many herbs have demonstrated properties relevant to the treatment of COVID-19, by supporting organs and systems of the body affected by the virus. Herbs can restore the structure of the intestinal flora, which may further modulate the immune function after SARS-CoV-2 infection. Regulation of intestinal flora by herbal medicine may be helpful for the treatment and recovery of the disease. Understanding the role of herbs that regulate intestinal flora in fighting respiratory virus infections and maintaining intestinal flora balance can provide new ideas for preventing and treating COVID-19.}, }
@article {pmid34304501, year = {2021}, author = {Liu, X and Liu, H and Li, C}, title = {[Advances in the study of chronic sinusitis microbiology using 16SrRNA gene sequencing technology].}, journal = {Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology head and neck surgery}, volume = {35}, number = {7}, pages = {658-661}, pmid = {34304501}, issn = {2096-7993}, mesh = {Bacteria/genetics ; Chronic Disease ; Humans ; *Rhinitis ; *Sinusitis ; Technology ; }, abstract = {Traditional conventional bacterial culture techniques can cultivate fewer types of bacteria, aiming to isolate and identify specific pathogens, guide antibiotic treatment and eradicate pathogens.Macrogenomics techniques can simultaneously identify both cultured and uncultured bacteria in the flora, providing the possibility for the study of symbiotic flora. With the vigorous development of SrRNA and application of 16 gene sequencing technology, the microbial ecology research of chronic sinusitis （chronic rhinosinusitis,CRS） has once again become a hot topic.And the CRS view of microbial community composition and microbial diversity were presented. This review describes the use of 16 SrRNA gene sequencing in recent years advances in technical studies CRS microbial ecology.}, }
@article {pmid34304356, year = {2021}, author = {Araujo, ASF and de Pereira, APA and Antunes, JEL and Oliveira, LMS and de Melo, WJ and Rocha, SMB and do Amorim, MR and Araujo, FF and Melo, VMM and Mendes, LW}, title = {Dynamics of bacterial and archaeal communities along the composting of tannery sludge.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {45}, pages = {64295-64306}, pmid = {34304356}, issn = {1614-7499}, support = {305069/2018-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {*Archaea/genetics ; *Bacteria/genetics ; *Composting ; *Industrial Waste ; RNA, Ribosomal, 16S/genetics ; Sewage ; Soil ; Tanning ; }, abstract = {The process of composting has been proposed as a biological alternative to improve the quality of tannery sludge (TS) by the action of microbial communities. However, there is limited knowledge about the dynamic of these microbial communities during the composting process. This study assessed the responses of bacterial and archaeal communities during TS composting using the 16S rRNA sequencing. The composting process occurred within 90 days, and samples of compost were collected on day 7 (d7; mesophilic stage), 30 (d30; thermophilic stage), 60 (d60; cooling stage), and 90 (d90; maturation stage). The results showed a succession of microbial phyla during the composting with enrichment of Synergistetes, WS1, and Euryarchaeota at the mesophilic stage, while at the thermophilic stage, there was an enrichment of Hydrogenedentes, WPS-2, Chloroflexi, and Deinococcus-Thermus. At the cooling stage, there was an enrichment of Kiritimatiellaeota, and at the maturation stage, there was an enrichment of Entotheonellaeota, Dadabacteria, Nitrospirae, Dependiatiae, and Fibrobacteres. When analyzing the drivers influencing microbial communities, Cr and pH presented more negative correlations with general phyla. In contrast, S, C, K, temperature, and N presented more positive correlations, while Ni, Cd, and P showed fewer correlations. According to niche occupancy, we observed a decreased proportion of generalists with a consequently increased proportion of specialists following the composting process. This study showed that different stages of the composting present a specific microbial community structure and dynamics, which are related to some specific composting characteristics.}, }
@article {pmid34304060, year = {2021}, author = {Sepúlveda-Correa, A and Daza-Giraldo, LV and Polanía, J and Arenas, NE and Muñoz-García, A and Sandoval-Figueredo, AV and Vanegas, J}, title = {Genes associated with antibiotic tolerance and synthesis of antimicrobial compounds in a mangrove with contrasting salinities.}, journal = {Marine pollution bulletin}, volume = {171}, number = {}, pages = {112740}, doi = {10.1016/j.marpolbul.2021.112740}, pmid = {34304060}, issn = {1879-3363}, mesh = {Anti-Bacterial Agents ; Ecosystem ; Metagenomics ; *Salinity ; *Wetlands ; }, abstract = {Salinity and wastewater pollution in mangrove ecosystems can affect microorganisms and the abundance of genes involved in response to these stressors. This research aimed to identify genes associated with resistance and biosynthesis of antimicrobial compounds in mangrove soils subjected to contrasting salinities and wastewater pollution. Samples of rhizospheric soil were taken from a mangrove at the mouth of the Ranchería River in La Guajira, Colombia. A functional analysis was performed using Illumina HiSeq 2500 sequencing data obtained from total DNA extracted. Increased salt concentration influenced metabolic pathways and differential abundance of genes associated with the synthesis of antimicrobial compounds (e.g., rfbB/rffG, INO1/ISYNA1, rfbA/rffH, sat/met3, asd). Also, among 33 genes involved in intrinsic antibiotic resistance, 16 were significantly influenced by salinity (e.g., cusR/copR/silR, vgb, tolC). We concluded that salt stress tolerance and adaptive mechanisms could favor the biosynthesis of antimicrobial compounds in mangroves contaminated by sewage.}, }
@article {pmid34303166, year = {2021}, author = {Li, C and Wang, L and Ji, S and Chang, M and Wang, L and Gan, Y and Liu, J}, title = {The ecology of the plastisphere: Microbial composition, function, assembly, and network in the freshwater and seawater ecosystems.}, journal = {Water research}, volume = {202}, number = {}, pages = {117428}, doi = {10.1016/j.watres.2021.117428}, pmid = {34303166}, issn = {1879-2448}, mesh = {*Ecosystem ; Fresh Water ; *Microbiota ; Plastics ; Rivers ; Seawater ; }, abstract = {Microplastics provide a unique habitat for microorganisms, forming the plastisphere. Yet the ecology of the plastisphere, including the microbial composition, functions, assembly processes, and interaction networks, needs to be understood. Here, we collected microplastics and their surrounding water samples in freshwater and seawater ecosystems. The bacterial and fungal communities of the plastisphere and the aquatic environment were studied based on 16S and internal transcribed spacer (ITS) high-throughput sequencing. We found that the plastisphere had a distinct microbial community and recruited a noteworthy proportion of unique species compared to the aquatic environment community, potentially altering ecosystem microbial community and causing microbial invasion. Using a random-forest machine-learning model, we identified a group of biomarkers that could best distinguish the plastisphere from the aquatic environment. Significant differences exist in microbial functions between the plastisphere and the aquatic environment, including functions of pathogenicity, compound degradation, as well as functions related to the cycling of carbon, nitrogen, and sulfur. And these functional differences were expressed differently in freshwater and seawater ecosystems. The oxidation-reduction potential, salinity, the concentrations of nitrogen-related ions (NO3[-], NO2[-], and NH4[+]), and the concentration of dissolved organic carbon in the surrounding environment drive the variation of the plastisphere. But environmental physicochemical properties explain less of the microbial community variation in the plastisphere than that in the aquatic environment. Niche-based processes govern the assembly of the plastisphere community, while neutral-based processes dominate the community assembly of the aquatic environment. Furthermore, compared to the aquatic environment, the plastisphere has a network of less complexity, more modules, higher modularity, and more competitive links in freshwater ecosystems, but the pattern is reversed in seawater ecosystems. Altogether, the microbial ecology of the new anthropogenic ecosystem-plastisphere-is unique and exerts different effects in freshwater and seawater ecosystems.}, }
@article {pmid34302509, year = {2022}, author = {Ren, Z and Zhang, Y and Cai, T and Mao, K and Xu, Y and Li, C and He, S and Li, J and Wan, H}, title = {Dynamics of Microbial Communities across the Life Stages of Nilaparvata lugens (Stål).}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {1049-1058}, pmid = {34302509}, issn = {1432-184X}, support = {32072462//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bacteria/genetics ; *Hemiptera/microbiology ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Nymph/microbiology ; }, abstract = {Understanding the composition of microorganismal communities hosted by insect pests is an important prerequisite for revealing their functions and developing new pest control strategies. Although studies of the structure of the microbiome of Nilaparvata lugens have been published, little is known about the dynamic changes in this microbiome across different developmental stages, and an understanding of the core microbiota is still lacking. In this study, we investigated the dynamic changes in bacteria and fungi in different developmental stages of N. lugens using high-throughput sequencing technology. We observed that the microbial diversity in eggs and mated adults was higher than that in nymphs and unmated adults. We also observed a notable strong correlation between fungal and bacterial α-diversity, which suggests that fungi and bacteria are closely linked and may perform functions collaboratively during the whole developmental period. Arsenophonus and Hirsutella were the predominant bacterial and fungal taxa, respectively. Bacteria were more conserved than fungi during the transmission of the microbiota between developmental stages. Compared with that in the nymph and unmated adult stages of N. lugens, the correlation between bacterial and fungal communities in the mated adult and egg stages was stronger. Moreover, the core microbiota across all developmental stages in N. lugens was identified, and there were more bacterial genera than fungal genera; notably, the core microbiota of eggs, nymphs, and mated and unmated adults showed distinctive functional enrichment. These findings highlight the potential value of further exploring microbial functions during different developmental stages and developing new pest management strategies.}, }
@article {pmid34302348, year = {2021}, author = {Dong, X and Zhang, C and Li, W and Weng, S and Song, W and Li, J and Wang, Y}, title = {Functional diversity of microbial communities in inactive seafloor sulfide deposits.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {8}, pages = {}, doi = {10.1093/femsec/fiab108}, pmid = {34302348}, issn = {1574-6941}, mesh = {Bacteria/genetics ; *Hydrothermal Vents ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfides ; }, abstract = {The seafloor sulfide structures of inactive vents are known to host abundant and diverse microorganisms potentially supported by mineralogy of sulfides. However, little is known about the diversity and distribution of microbial functions. Here, we used genome-resolved metagenomics to predict microbial metabolic functions and the contribution of horizontal gene transfer to the functionality of microorganisms inhabiting several hydrothermally inactive seafloor deposits among globally distributed deep-sea vent fields. Despite of geographically distant vent fields, similar microbial community patterns were observed with the dominance of Gammaproteobacteria, Bacteroidota and previously overlooked Candidatus Patescibacteria. Metabolically flexible Gammaproteobacteria are major potential primary producers utilizing mainly sulfur, iron and hydrogen as electron donors coupled with oxygen and nitrate respiration for chemolithoautotrophic growth. In addition to heterotrophic microorganisms like free-living Bacteroidota, Ca. Patescibacteria potentially perform fermentative recycling of organic carbon. Finally, we provided evidence that many functional genes that are central to energy metabolism have been laterally transferred among members within the community and largely within the same class. Taken together, these findings shed light on microbial ecology and evolution in inactive seafloor sulfide deposits after the cessation of hydrothermal activities.}, }
@article {pmid34302194, year = {2022}, author = {Zhang, SK and Wang, Y and Li, ZK and Xue, HJ and Zhou, XD and Huang, JH}, title = {Two Apriona Species Sharing a Host Niche Have Different Gut Microbiome Diversity.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {1059-1072}, doi = {10.1007/s00248-021-01799-4}, pmid = {34302194}, issn = {1432-184X}, support = {2020SY08//Cooperation Project of Zhejiang Province and Chinese Academy of Forestry/ ; }, mesh = {Animals ; Bacteria/genetics ; *Coleoptera ; *Gastrointestinal Microbiome/genetics ; Insecta ; Plants ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The adaptability of herbivorous insects to toxic plant defense compounds is partly related to the structure of the gut microbiome. To overcome plant resistance, the insect gut microbiome should respond to a wide range of allelochemicals derived from dietary niches. Nevertheless, for sibling herbivorous insect species, whether the gut microbiome contributes to success in food niche competition is unclear. Based on 16S rDNA high-throughput sequencing, the gut microbiomes of two Apriona species that share the same food niche were investigated in this study to determine whether the gut microbiome contributes to insect success in food-niche competition. Our observations indicated that the gut microbiome tended to play a part in host niche competition between the two Apriona species. The gut microbiome of Apriona swainsoni had many enriched pathways that can help degrade plant toxic secondary compounds, including xenobiotic biodegradation and metabolism, terpenoid and polyketide metabolism, and secondary metabolite biosynthesis. Meanwhile, A. swainsoni hosted a much greater variety of microorganisms and had more viable bacteria than A. germari. We conclude that gut microbes may influence the coevolution of herbivores and host plants. Gut bacteria may not only serve to boost nutritional relationships, but may also play an important role in insect food niche competition.}, }
@article {pmid34301298, year = {2021}, author = {Wang, Q and Zhang, Y and Yang, Q and Fu, S and Qu, B and Defoirdt, T}, title = {One health pathogen surveillance demonstrated the dissemination of gut pathogens within the two coastal regions associated with intensive farming.}, journal = {Gut pathogens}, volume = {13}, number = {}, pages = {47}, pmid = {34301298}, issn = {1757-4749}, support = {81903372//Young Scientists Fund/ ; }, abstract = {BACKGROUND: Intensive aquaculture farming has caused significant degradation of coastal wetlands and has been proposed as a reservoir for pathogenic Vibrio spp.<br><br>RESULTS: Gut pathogens including Vibrio spp., Salmonella spp., and Klebsiella spp. were isolated from bird feces, shrimp and wetland water in two typical coastal regions of China in 2015 and 2017 and were subsequently subjected to whole-genome sequencing. Meanwhile, local patient isolates were also selected to confirm the epidemiological links. Bacterial community composition analyses of the sediments that were sampled in 2015 and 2017 were conducted by the hypervariable region 4 of the 16S rRNA gene. Together with the local clinical isolates, we observed highly related Vibrio isolates from waterbirds, wetlands and shrimp. Phylogenetic genome comparisons also demonstrated that sequence types ST3 and ST2414 Vibrio parahaemolyticus isolates obtained from aquatic animals were clonally related to patient isolates. Likewise, three Salmonella typhimurium isolates were also genomically related to one clinical strain. The results showed that farming activities significantly altered the community composition and resulted in the emergence of several pathogens, including Acinetobacter, Mycobacterium and Legionella.<br><br>CONCLUSIONS: In conclusion, our results demonstrated that intensive shrimp farming in wetlands has two devastating impacts: pathogen dissemination from aquatic animals into migratory birds and transmission of foodborne pathogens into local communities.}, }
@article {pmid34298185, year = {2021}, author = {Zhao, L and Xu, M and Pan, X and Zhang, B and Dou, Q}, title = {Binding and detoxification ability of lactobacillus acidophilus towards di-n-butyl phthalate: Change of MAPK pathway in Caco-2 cell model.}, journal = {Journal of proteomics}, volume = {247}, number = {}, pages = {104333}, doi = {10.1016/j.jprot.2021.104333}, pmid = {34298185}, issn = {1876-7737}, mesh = {Caco-2 Cells ; Dibutyl Phthalate ; Humans ; Lactobacillus ; *Lactobacillus acidophilus ; *Probiotics ; }, abstract = {Di-n-butyl phthalate (DBP), a common compound of phthalates, can pose a risk to humans as a contaminant in the food industry. At present, the molecular mechanism of gene and protein toxicity caused by DBP in human cells is unclear. This in vitro study investigated the potential of inactivated Lactobacillus acidophilus NCFM in alleviating the damage caused by DBP in Caco-2 cells. According to the results from transcriptome and proteome analyses, the Caco-2 cells treated by DBP was resulted finally endoplasmic reticulum stress and mitochondrial oxidative damage. The most important differentially expressed genes and proteins involved in Caco-2 cells treated with NCFM to relieve DBP's cytotoxicity were TNF, NF-κB, CREB, P21, GADD45, FOS and CASP3. The molecular mechanism of DBP toxicity alleviated by strain NCFM was involved the MAPK pathway, via DBP bind to strain NCFM and avoid the activation of TNF receptor by DBP, so down-regulated the NF-κB, CREB, P21, GADD45, and CASP3, relieving the apoptosis of Caco-2 cells. Overall, our data provide new insights into detoxification of phthalate by using Lactobacillus. SIGNIFICANCE: Here we sequenced and assembled the transcriptome from Caco-2 cells which were treated with 4 groups: Control, DBP, strain NCFM, and strain NCFM+DBP groups, and combined it with proteome to characterize DBP detoxification genes/proteins through multiomics analysis. The cell viability in DBP treated groups were significantly increased by NCFM strain, indicating NCFM strain has the ability to alleviate the cytotoxicity of DBP via their binding ability with toxins. Furthermore, the results of transcriptome and proteome analysis showed that the signaling pathway of strain NCFM can alleviate DBP toxicity through MAPK pathway, and the potential biomarkers were identified too. This research may provided new information for developing new detoxification strategies for DBP.}, }
@article {pmid34297464, year = {2022}, author = {Zhang, S and Yang, Q and Defoirdt, T}, title = {Indole decreases the virulence of pathogenic vibrios belonging to the Harveyi clade.}, journal = {Journal of applied microbiology}, volume = {132}, number = {1}, pages = {167-176}, doi = {10.1111/jam.15227}, pmid = {34297464}, issn = {1365-2672}, mesh = {Animals ; Artemia ; Indoles/pharmacology ; *Penaeidae ; *Vibrio/genetics ; *Vibrio parahaemolyticus ; Virulence/genetics ; Virulence Factors ; }, abstract = {AIM: Indole is a signaling molecule secreted by over 85 species of bacteria, including several Vibrio species, and it has been reported to affect different bacterial phenotypes such as biofilm formation, motility, and virulence. In this study, we aimed at investigating the inter-strain variability of the effect of indole in 12 different strains belonging to the Harveyi clade of vibrios.<br><br>METHODS AND RESULTS: Indole reduced the virulence of all strains towards gnotobiotic brine shrimp larvae. The survival rate of brine shrimp larvae challenged with vibrios pretreated with indole was increased by 1.3-fold to 1.8-fold. Additionally, indole significantly decreased the biofilm formation in all of the strains, decreased the swimming motility in eight of the strains, and decreased swarming motility in five of the strains. When cultured in the presence of exogenous indole, the mRNA level of the pirA and pirB toxin genes were down-regulated to 65% and 46%, and to 62% and 55% in the AHPND-causing strains Vibrio parahaemolyticus M0904 and Vibrio campbellii S01, respectively.<br><br>CONCLUSIONS: These data indicate that indole has a significant impact on the virulence of different strains belonging to the Harveyi clade of vibrios.<br><br>Our results suggest that indole signaling is a valid target for the development of novel therapeutics in order to control infections caused by Harveyi clade vibrios in aquaculture.}, }
@article {pmid34294810, year = {2021}, author = {Verspecht, T and Van Holm, W and Boon, N and Bernaerts, K and Daep, CA and Zayed, N and Quirynen, M and Teughels, W}, title = {Comparison of the modulatory effects of three structurally similar potential prebiotic substrates on an in vitro multi-species oral biofilm.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {15033}, pmid = {34294810}, issn = {2045-2322}, mesh = {Biodiversity ; *Biofilms/drug effects/growth &amp; development ; Host Microbial Interactions ; Metagenome ; Metagenomics/methods ; Microbiota ; Mouth/*microbiology ; Prebiotics/*administration &amp; dosage ; Virulence/genetics ; }, abstract = {Previous research identified potential prebiotic substrates for oral health like the structural analogues N-acetyl-D-mannosamine (NADM) and N-acetyl-D-glucosamine (NADG). The main hypothesis of the current study was twofold. Firstly, it was hypothesized that the modulatory effects of NADM are not limited to changes in multi-species oral biofilm composition, but also include effects on metabolism, virulence, and inflammatory potential. Secondly, the presence and orientation of their N-acetyl group could play a role. Therefore, a comparison was made between the effects of NADM, NADG and D-(+)-mannose on multi-species oral biofilms. Besides a beneficial compositional shift, NADM-treated biofilms also showed an altered metabolism, a reduced virulence and a decreased inflammatory potential. At a substrate concentration of 1 M, these effects were pronounced for all biofilm aspects, whereas at ~ 0.05 M (1%(w/v)) only the effects on virulence were pronounced. When comparing between substrates, both the presence and orientation of the N-acetyl group played a role. However, this was generally only at 1 M and dependent on the biofilm aspect. Overall, NADM was found to have different effects at two concentrations that beneficially modulate in vitro multi-species oral biofilm composition, metabolism, virulence and inflammatory potential. The presence and orientation of the N-acetyl group influenced these effects.}, }
@article {pmid34290548, year = {2021}, author = {Do, H and Kim, SH and Cho, G and Kim, DR and Kwak, YS}, title = {Investigation of Fungal Strains Composition in Fruit Pollens for Artificial Pollination.}, journal = {Mycobiology}, volume = {49}, number = {3}, pages = {249-257}, pmid = {34290548}, issn = {1229-8093}, abstract = {Plants pollination are conducted through various pollinators such as wind, animals, and insects. Recently, the necessity for artificial pollination is drawing attention as the proportion of natural pollinators involved is decreasing over the years. Likewise, the trade in pollen for artificial pollination is also increasing worldwide. Through these imported pollens, many unknown microorganisms can flow from foreign countries. Among them, spores of various fungi present in the particles of pollen can be dispersed throughout the orchard. Therefore, in this study, the composition of fungal communities in imported pollen was revealed, and potential ecological characteristics of the fungi were investigated in four types of imported pollen. Top 10 operational taxonomic unit (OTU) of fungi were ranked among the following groups: Alternaria sp., Cladosporium sp., and Didymella glomerata which belong to many pathogenic species. Through FUNGuild analysis, the proportion of OTUs, which is assumed to be potentially plant pathogens, was higher than 50%, except for apple pollen in 2018. Based on this study of fungal structure, this information can suggest the direction of the pollen quarantine process and contribute to fungal biology in pollen.}, }
@article {pmid34288928, year = {2021}, author = {Harlow, BE and Flythe, MD and Klotz, JL and Harmon, DL and Aiken, GE}, title = {Effect of biochanin A on the rumen microbial community of Holstein steers consuming a high fiber diet and subjected to a subacute acidosis challenge.}, journal = {PloS one}, volume = {16}, number = {7}, pages = {e0253754}, pmid = {34288928}, issn = {1932-6203}, mesh = {Acidosis/*drug therapy/microbiology ; *Animal Feed ; Animals ; Bacteria/drug effects/isolation &amp; purification ; Bacterial Load ; Cattle/*microbiology ; Cattle Diseases/*drug therapy/microbiology ; Cellulose/metabolism ; Deoxyglucose/pharmacology ; Dietary Carbohydrates/metabolism ; *Dietary Fiber/metabolism ; Dietary Proteins/metabolism ; Fermentation ; Gastrointestinal Contents/*microbiology ; Gastrointestinal Microbiome/*drug effects ; Genistein/pharmacology/*therapeutic use ; Hydrogen-Ion Concentration ; Ionophores/pharmacology ; Male ; Random Allocation ; Rumen/*microbiology ; Silage ; Starch/metabolism ; }, abstract = {Subacute rumen acidosis (SARA) occurs when highly fermentable carbohydrates are introduced into the diet, decreasing pH and disturbing the microbial ecology of the rumen. Rumen amylolytic bacteria rapidly catabolize starch, fermentation acids accumulate in the rumen and reduce environmental pH. Historically, antibiotics (e.g., monensin, MON) have been used in the prevention and treatment of SARA. Biochanin A (BCA), an isoflavone produced by red clover (Trifolium pratense), mitigates changes associated with starch fermentation ex vivo. The objective of the study was to determine the effect of BCA on amylolytic bacteria and rumen pH during a SARA challenge. Twelve rumen fistulated steers were assigned to 1 of 4 treatments: HF CON (high fiber control), SARA CON, MON (200 mg d-1), or BCA (6 g d-1). The basal diet consisted of corn silage and dried distiller's grains ad libitum. The study consisted of a 2-wk adaptation, a 1-wk HF period, and an 8-d SARA challenge (d 1-4: 40% corn; d 5-8: 70% cracked corn). Samples for pH and enumeration were taken on the last day of each period (4 h). Amylolytic, cellulolytic, and amino acid/peptide-fermenting bacteria (APB) were enumerated. Enumeration data were normalized by log transformation and data were analyzed by repeated measures ANOVA using the MIXED procedure of SAS. The SARA challenge increased total amylolytics and APB, but decreased pH, cellulolytics, and in situ DMD of hay (P < 0.05). BCA treatment counteracted the pH, microbiological, and fermentative changes associated with SARA challenge (P < 0.05). Similar results were also observed with MON (P < 0.05). These results indicate that BCA may be an effective alternative to antibiotics for mitigating SARA in cattle production systems.}, }
@article {pmid34287300, year = {2021}, author = {Santschi, PH and Chin, WC and Quigg, A and Xu, C and Kamalanathan, M and Lin, P and Shiu, RF}, title = {Marine Gel Interactions with Hydrophilic and Hydrophobic Pollutants.}, journal = {Gels (Basel, Switzerland)}, volume = {7}, number = {3}, pages = {}, pmid = {34287300}, issn = {2310-2861}, abstract = {Microgels play critical roles in a variety of processes in the ocean, including element cycling, particle interactions, microbial ecology, food web dynamics, air-sea exchange, and pollutant distribution and transport. Exopolymeric substances (EPS) from various marine microbes are one of the major sources for marine microgels. Due to their amphiphilic nature, many types of pollutants, especially hydrophobic ones, have been found to preferentially associate with marine microgels. The interactions between pollutants and microgels can significantly impact the transport, sedimentation, distribution, and the ultimate fate of these pollutants in the ocean. This review on marine gels focuses on the discussion of the interactions between gel-forming EPS and pollutants, such as oil and other hydrophobic pollutants, nanoparticles, and metal ions.}, }
@article {pmid34287003, year = {2021}, author = {Schloss, PD}, title = {Amplicon Sequence Variants Artificially Split Bacterial Genomes into Separate Clusters.}, journal = {mSphere}, volume = {6}, number = {4}, pages = {e0019121}, pmid = {34287003}, issn = {2379-5042}, support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; R01 CA215574/CA/NCI NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*classification/*genetics ; DNA, Bacterial/genetics ; *Genetic Variation ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Amplicon sequencing variants (ASVs) have been proposed as an alternative to operational taxonomic units (OTUs) for analyzing microbial communities. ASVs have grown in popularity, in part because of a desire to reflect a more refined level of taxonomy since they do not cluster sequences based on a distance-based threshold. However, ASVs and the use of overly narrow thresholds to identify OTUs increase the risk of splitting a single genome into separate clusters. To assess this risk, I analyzed the intragenomic variation of 16S rRNA genes from the bacterial genomes represented in an rrn copy number database, which contained 20,427 genomes from 5,972 species. As the number of copies of the 16S rRNA gene increased in a genome, the number of ASVs also increased. There was an average of 0.58 ASVs per copy of the 16S rRNA gene for full-length 16S rRNA genes. It was necessary to use a distance threshold of 5.25% to cluster full-length ASVs from the same genome into a single OTU with 95% confidence for genomes with 7 copies of the 16S rRNA, such as Escherichia coli. This research highlights the risk of splitting a single bacterial genome into separate clusters when ASVs are used to analyze 16S rRNA gene sequence data. Although there is also a risk of clustering ASVs from different species into the same OTU when using broad distance thresholds, these risks are of less concern than artificially splitting a genome into separate ASVs and OTUs. IMPORTANCE 16S rRNA gene sequencing has engendered significant interest in studying microbial communities. There has been tension between trying to classify 16S rRNA gene sequences to increasingly lower taxonomic levels and the reality that those levels were defined using more sequence and physiological information than is available from a fragment of the 16S rRNA gene. Furthermore, the naming of bacterial taxa reflects the biases of those who name them. One motivation for the recent push to adopt ASVs in place of OTUs in microbial community analyses is to allow researchers to perform their analyses at the finest possible level that reflects species-level taxonomy. The current research is significant because it quantifies the risk of artificially splitting bacterial genomes into separate clusters. Far from providing a better representation of bacterial taxonomy and biology, the ASV approach can lead to conflicting inferences about the ecology of different ASVs from the same genome.}, }
@article {pmid34285323, year = {2021}, author = {Mafla-Endara, PM and Arellano-Caicedo, C and Aleklett, K and Pucetaite, M and Ohlsson, P and Hammer, EC}, title = {Microfluidic chips provide visual access to in situ soil ecology.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {889}, pmid = {34285323}, issn = {2399-3642}, mesh = {*Bacterial Physiological Phenomena ; Ecology/*instrumentation ; Fungi/*physiology ; Hyphae/physiology ; Lab-On-A-Chip Devices ; Microbiota/*physiology ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Microbes govern most soil functions, but investigation of these processes at the scale of their cells has been difficult to accomplish. Here we incubate microfabricated, transparent 'soil chips' with soil, or bury them directly in the field. Both soil microbes and minerals enter the chips, which enables us to investigate diverse community interdependences, such as inter-kingdom and food-web interactions, and feedbacks between microbes and the pore space microstructures. The presence of hyphae ('fungal highways') strongly and frequently increases the dispersal range and abundance of water-dwelling organisms such as bacteria and protists across air pockets. Physical forces such as water movements, but also organisms and especially fungi form new microhabitats by altering the pore space architecture and distribution of soil minerals in the chip. We show that soil chips hold a large potential for studying in-situ microbial interactions and soil functions, and to interconnect field microbial ecology with laboratory experiments.}, }
@article {pmid34283261, year = {2022}, author = {Xu, R and Tao, W and Lin, H and Huang, D and Su, P and Gao, P and Sun, X and Yang, Z and Sun, W}, title = {Effects of Perfluorooctanoic Acid (PFOA) and Perfluorooctane Sulfonic Acid (PFOS) on Soil Microbial Community.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {929-941}, doi = {10.1007/s00248-021-01808-6}, pmid = {34283261}, issn = {1432-184X}, support = {Grant No. 42007357 and 41771301//National Natural Science Foundation of China (CN)/ ; Grant Nos. 2020T130127 and 2019M662825//postdoctoral research foundation of china/ ; Grant Nos. 202002030271//the Science and Technology Planning Project of Guangzhou/ ; Grant No. 2019A1515110351//Guangdong Basic and Applied Basic Research Foundation/ ; Grant Nos. 2020GDASYL-20200103086, 2020GDASYL-20200102015, 2020GDASYL-20200102014 and 2019GDASYL-0301002//GDAS' Project of Science and Technology Development/ ; Grant No. 2017GC010570//Guangdong Introducing Innovative and Entrepreneurial Talents/ ; Grant No. 2019B121205006//Guangdong Foundation for Program of Science and Technology Research/ ; }, mesh = {Alkanesulfonic Acids ; Caprylates ; *Fluorocarbons/analysis/chemistry ; *Microbiota ; Soil/chemistry ; }, abstract = {The extensive application of perfluoroalkyl and polyfluoroalkyl substances (PFASs) causes their frequent detection in various environments. In this work, two typical PFASs, perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), are selected to investigate their effects on soil microorganisms. Microbial community structure and microbe-microbe relationships were investigated by high-throughput sequencing and co-occurrence network analysis. Under 90 days of exposure, the alpha-diversity of soil microbial communities was increased with the PFOS treatment, followed by the PFOA treatment. The exposure of PFASs substantially changed the compositions of soil microbial communities, leading to the enrichment of more PFASs-tolerant bacteria, such as Proteobacteria, Burkholderiales, and Rhodocyclales. Comparative co-occurrence networks were constructed to investigate the microbe-microbe interactions under different PFASs treatments. The majority of nodes in the PFOA and PFOS networks were associated with the genus Azospirillum and Hydrogenophaga, respectively. The LEfSe analysis further identified a set of biomarkers in the soil microbial communities, such as Azospirillum, Methyloversatilis, Hydrogenophaga, Pseudoxanthomonas, and Fusibacter. The relative abundances of these biomarkers were also changed by different PFASs treatments. Functional gene prediction suggested that the microbial metabolism processes, such as nucleotide transport and metabolism, cell motility, carbohydrate transport and metabolism, energy production and conversion, and secondary metabolites biosynthesis transport and catabolism, might be inhibited under PFAS exposure, which may further affect soil ecological services.}, }
@article {pmid34282938, year = {2021}, author = {Cruz-Loya, M and Tekin, E and Kang, TM and Cardona, N and Lozano-Huntelman, N and Rodriguez-Verdugo, A and Savage, VM and Yeh, PJ}, title = {Antibiotics Shift the Temperature Response Curve of Escherichia coli Growth.}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0022821}, pmid = {34282938}, issn = {2379-5077}, support = {UL1TR001881//HHS | NIH | National Center for Advancing Translational Sciences (NCATS)/ ; //Consejo Nacional de Ciencia y Tecnolog&#xed;a (CONACYT)/ ; //James S. McDonnell Foundation (JSMF)/ ; //Hellman Foundation/ ; //University of California Institute for Mexico and the United States (UC MEXUS)/ ; UL1 TR001881/TR/NCATS NIH HHS/United States ; }, abstract = {Temperature variation-through time and across climatic gradients-affects individuals, populations, and communities. Yet how the thermal response of biological systems is altered by environmental stressors is poorly understood. Here, we quantify two key features-optimal temperature and temperature breadth-to investigate how temperature responses vary in the presence of antibiotics. We use high-throughput screening to measure growth of Escherichia coli under single and pairwise combinations of 12 antibiotics across seven temperatures that range from 22°C to 46°C. We find that antibiotic stress often results in considerable changes in the optimal temperature for growth and a narrower temperature breadth. The direction of the optimal temperature shifts can be explained by the similarities between antibiotic-induced and temperature-induced damage to the physiology of the bacterium. We also find that the effects of pairs of stressors in the temperature response can often be explained by just one antibiotic out of the pair. Our study has implications for a general understanding of how ecological systems adapt and evolve to environmental changes. IMPORTANCE The growth of living organisms varies with temperature. This dependence is described by a temperature response curve that is described by an optimal temperature where growth is maximized and a temperature range (termed breadth) across which the organism can grow. Because an organism's temperature response evolves or acclimates to its environment, it is often assumed to change over only evolutionary or developmental timescales. Counter to this, we show here that antibiotics can quickly (over hours) change the optimal growth temperature and temperature breadth for the bacterium Escherichia coli. Moreover, our results suggest a shared-damage hypothesis: when an antibiotic damages similar cellular components as hot (or cold) temperatures do, this shared damage will combine and compound to more greatly reduce growth when that antibiotic is administered at hot (or cold) temperatures. This hypothesis could potentially also explain how temperature responses are modified by stressors other than antibiotics.}, }
@article {pmid34282310, year = {2021}, author = {Wasmund, K and Pelikan, C and Schintlmeister, A and Wagner, M and Watzka, M and Richter, A and Bhatnagar, S and Noel, A and Hubert, CRJ and Rattei, T and Hofmann, T and Hausmann, B and Herbold, CW and Loy, A}, title = {Publisher Correction: Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments.}, journal = {Nature microbiology}, volume = {6}, number = {8}, pages = {1102}, doi = {10.1038/s41564-021-00936-6}, pmid = {34282310}, issn = {2058-5276}, support = {P29426//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; P25111//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; }, }
@article {pmid34280807, year = {2021}, author = {De Vrieze, J and Heyer, R and Props, R and Van Meulebroek, L and Gille, K and Vanhaecke, L and Benndorf, D and Boon, N}, title = {Triangulation of microbial fingerprinting in anaerobic digestion reveals consistent fingerprinting profiles.}, journal = {Water research}, volume = {202}, number = {}, pages = {117422}, doi = {10.1016/j.watres.2021.117422}, pmid = {34280807}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Bioreactors ; Methane ; *Microbiota ; RNA, Ribosomal, 16S ; Sewage ; }, abstract = {The anaerobic digestion microbiome has been puzzling us since the dawn of molecular methods for mixed microbial community analysis. Monitoring of the anaerobic digestion microbiome can either take place via a non-targeted holistic evaluation of the microbial community through fingerprinting or by targeted monitoring of selected taxa. Here, we compared four different microbial community fingerprinting methods, i.e., amplicon sequencing, metaproteomics, metabolomics and cytomics, in their ability to characterise the full-scale anaerobic digestion microbiome. Cytometric fingerprinting through cytomics reflects a, for anaerobic digestion, novel, single cell-based approach of direct microbial community fingerprinting by flow cytometry. Three different digester types, i.e., sludge digesters, digesters treating agro-industrial waste and dry anaerobic digesters, each reflected different operational parameters. The α-diversity analysis yielded inconsistent results, especially for richness, across the different methods. In contrast, β-diversity analysis resulted in comparable profiles, even when translated into phyla or functions, with clear separation of the three digester types. In-depth analysis of each method's features i.e., operational taxonomic units, metaproteins, metabolites, and cytometric traits, yielded certain similar features, yet, also some clear differences between the different methods, which was related to the complexity of the anaerobic digestion process. In conclusion, cytometric fingerprinting through flow cytometry is a reliable, fast method for holistic monitoring of the anaerobic digestion microbiome, and the complementary identification of key features through other methods could give rise to a direct interpretation of anaerobic digestion process performance.}, }
@article {pmid34279697, year = {2022}, author = {Zhou, D and Wang, R and Li, X and Peng, B and Yang, G and Zhang, KQ and Zhang, Y and Xu, J}, title = {Genetic Diversity and Azole Resistance Among Natural Aspergillus fumigatus Populations in Yunnan, China.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {869-885}, pmid = {34279697}, issn = {1432-184X}, support = {31760010//National Natural Science Foundation of China/ ; 2020R3//McMaster University/ ; KY2018412//Department of Education of Guizhou Province/ ; }, mesh = {Antifungal Agents/pharmacology ; *Aspergillus fumigatus/genetics ; *Azoles/pharmacology ; China ; Genetic Variation ; Humans ; }, abstract = {The emergence and spread of azole resistance alleles in clinical and environmental isolates of Aspergillus fumigatus is a global human health concern and endangers the "One Health" approach in our fight against antifungal resistance (AFR) in this pathogen. A major challenge to combat AFR in A. fumigatus is the massive aerial dispersal ability of its asexual spores. Our recent fine-scale survey of greenhouse populations of A. fumigatus near Kunming, Yunnan, China, suggested that the use of azole fungicides for plant protection was likely a major driver of the high-frequency azole-resistant A. fumigatus (ARAF) in greenhouses. Here, we investigated the potential spread of those ARAF and the structure of geographic populations of A. fumigatus by analyzing 452 isolates from 19 geographic locations across Yunnan. We found lower frequencies of ARAF in these outdoor populations than those in greenhouses near Kunming, but there were abundant new alleles and new genotypes, including those associated with azole resistance, consistent with multiple independent origins of ARAF across Yunnan. Interestingly, among the four ecological niches, the sediments of a large lake near Kunming were found to have the highest frequency of ARAF (~ 43%). While most genetic variations were observed within the 19 local populations, statistically significant genetic differentiations were found between many subpopulations within Yunnan. Furthermore, similar to greenhouse populations, these outdoor populations of A. fumigatus in Yunnan were significantly different from those in other parts of the world. Our results call for increased attention to local and regional studies of this fungal pathogen to help develop targeted control strategies against ARAF.}, }
@article {pmid34279696, year = {2022}, author = {Adomako, MO and Xue, W and Du, DL and Yu, FH}, title = {Soil Microbe-Mediated N:P Stoichiometric Effects on Solidago canadensis Performance Depend on Nutrient Levels.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {960-970}, doi = {10.1007/s00248-021-01814-8}, pmid = {34279696}, issn = {1432-184X}, mesh = {Biomass ; Ecosystem ; Humans ; Nitrogen/analysis ; Nutrients ; Soil ; *Solidago ; }, abstract = {Both soil microbes and soil N:P ratios can affect plant growth, but it is unclear whether they can interact to alter plant growth and whether such an interactive effect depends on nutrient levels. Here, we tested the hypothesis that soil microbes can ameliorate the negative effects of nutrient imbalance caused by low or high N:P ratios on plant growth and that such an ameliorative effect of soil microbes depends on nutrient supply levels. We grew individuals of six populations of the clonal plant Solidago canadensis at three N:P ratios (low (1.7), intermediate (15), and high (135)), under two nutrient levels (low versus high) and in the presence versus absence of soil microbes. The presence of soil microbes significantly increased biomass of S. canadensis at all three N:P ratios and under both nutrient levels. Under the low-nutrient level, biomass, height, and leaf number of S. canadensis did not differ significantly among the three N:P ratio treatments in the absence of soil microbes, but they were higher at the high than at the low and the intermediate N:P ratio in the presence of soil microbes. Under the high-nutrient level, by contrast, biomass, height, and leaf number of S. canadensis were significantly higher at the low than at the high and the intermediate N:P ratio in the absence of soil microbes, but increased with increasing the N:P ratio in the presence of soil microbes. In the presence of soil microbes, number of ramets (asexual individuals) and the accumulation of N and P in plants were significantly higher at the high than at the low and the intermediate N:P ratio under both nutrient levels, whereas in the absence of soil microbes, they did not differ significantly among the three N:P ratio regardless of the nutrient levels. Our results provide empirical evidence that soil microbes can alter effects of N:P ratios on plant performance and that such an effect depends on nutrient availability. Soil microbes may, therefore, play a role in modulating ecosystem functions such as productivity and carbon and nutrient cycling via modulating nutrient imbalance caused by low and high N:P ratios.}, }
@article {pmid34277691, year = {2021}, author = {Calatayud, M and Van den Abbeele, P and Ghyselinck, J and Marzorati, M and Rohs, E and Birkett, A}, title = {Comparative Effect of 22 Dietary Sources of Fiber on Gut Microbiota of Healthy Humans in vitro.}, journal = {Frontiers in nutrition}, volume = {8}, number = {}, pages = {700571}, pmid = {34277691}, issn = {2296-861X}, abstract = {Human gut microbiota has a fundamental role in human health, and diet is one of the most relevant factors modulating the gut microbial ecosystem. Fiber, fat, proteins, and micronutrients can shape microbial activity and structure. Much information is available on the role of defined prebiotic fibers on gut microbiota, but less known are the effects of intact dietary fiber sources on healthy gut ecosystems. This research investigated in vitro the short-term effect of 22 commercially available food sources of dietary fiber on gut microbiota activity [pH, gas, short-chain fatty acids (SCFA), branched fatty acids (BCFA), lactate] and specific composition of Firmicutes, Bacteroidetes, bifidobacteria, and lactobacilli populations. More than 80% (19 of 22) of the products were highly fermentable and induced SCFAs production, with specific product differences. In general, all the whole grain cereals had a similar effect on gut microbiota modulation, inducing acetate and butyrate production and increasing bifidobacteria levels. Incorporating and comparing a large variety of products, including "non-conventional" fiber sources, like konjac, bamboo fiber, or seeds fiber, about which there is little information, contributes to our knowledge on the modulatory activity of diverse food fiber sources on human gut microbiota, and therefore potential health promotion through dietary fiber diversification.}, }
@article {pmid34277527, year = {2021}, author = {Larroya, A and Pantoja, J and Codoñer-Franch, P and Cenit, MC}, title = {Towards Tailored Gut Microbiome-Based and Dietary Interventions for Promoting the Development and Maintenance of a Healthy Brain.}, journal = {Frontiers in pediatrics}, volume = {9}, number = {}, pages = {705859}, pmid = {34277527}, issn = {2296-2360}, abstract = {Mental health is determined by a complex interplay between the Neurological Exposome and the Human Genome. Multiple genetic and non-genetic (exposome) factors interact early in life, modulating the risk of developing the most common complex neurodevelopmental disorders (NDDs), with potential long-term consequences on health. To date, the understating of the precise etiology underpinning these neurological alterations, and their clinical management pose a challenge. The crucial role played by diet and gut microbiota in brain development and functioning would indicate that modulating the gut-brain axis may help protect against the onset and progression of mental-health disorders. Some nutritional deficiencies and gut microbiota alterations have been linked to NDDs, suggesting their potential pathogenic implications. In addition, certain dietary interventions have emerged as promising alternatives or adjuvant strategies for improving the management of particular NDDs, at least in particular subsets of subjects. The gut microbiota can be a key to mediating the effects of other exposome factors such as diet on mental health, and ongoing research in Psychiatry and Neuropediatrics is developing Precision Nutrition Models to classify subjects according to a diet response prediction based on specific individual features, including microbiome signatures. Here, we review current scientific evidence for the impact of early life environmental factors, including diet, on gut microbiota and neuro-development, emphasizing the potential long-term consequences on health; and also summarize the state of the art regarding the mechanisms underlying diet and gut microbiota influence on the brain-gut axis. Furthermore, we describe the evidence supporting the key role played by gut microbiota, diet and nutrition in neurodevelopment, as well as the effectiveness of certain dietary and microbiome-based interventions aimed at preventing or treating NDDs. Finally, we emphasize the need for further research to gain greater insight into the complex interplay between diet, gut microbiome and brain development. Such knowledge would help towards achieving tailored integrative treatments, including personalized nutrition.}, }
@article {pmid34276734, year = {2021}, author = {Yoshiura, CA and Venturini, AM and Braga, LPP and da França, AG and de Lyra, MDCCP and Tsai, SM and Rodrigues, JLM}, title = {Responses of Low-Cost Input Combinations on the Microbial Structure of the Maize Rhizosphere for Greenhouse Gas Mitigation and Plant Biomass Production.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {683658}, pmid = {34276734}, issn = {1664-462X}, abstract = {The microbial composition of the rhizosphere and greenhouse gas (GHG) emissions under the most common input combinations in maize (Zea mays L.) cultivated in Brazil have not been characterized yet. In this study, we evaluated the influence of maize stover coverage (S), urea-topdressing fertilization (F), and the microbial inoculant Azospirillum brasilense (I) on soil GHG emissions and rhizosphere microbial communities during maize development. We conducted a greenhouse experiment and measured methane (CH4), carbon dioxide (CO2), and nitrous oxide (N2O) fluxes from soil cultivated with maize plants under factorial combinations of the inputs and a control treatment (F, I, S, FI, FS, IS, FIS, and control). Plant biomass was evaluated, and rhizosphere soil samples were collected at V5 and V15 stages and DNA was extracted. The abundance of functional genes (mcrA, pmoA, nifH, and nosZ) was determined by quantitative PCR (qPCR) and the structure of the microbial community was assessed through 16S rRNA amplicon sequencing. Our results corroborate with previous studies which used fewer input combinations and revealed different responses for the following three inputs: F increased N2O emissions around 1 week after application; I tended to reduce CH4 and CO2 emissions, acting as a plant growth stimulator through phytohormones; S showed an increment for CO2 emissions by increasing carbon-use efficiency. IS and FIS treatments presented significant gains in biomass that could be related to Actinobacteria (19.0%) and Bacilli (10.0%) in IS, and Bacilli (9.7%) in FIS, which are the microbial taxa commonly associated with lignocellulose degradation. Comparing all factors, the IS (inoculant + maize stover) treatment was considered the best option for plant biomass production and GHG mitigation since FIS provides small gains toward the management effort of F application.}, }
@article {pmid34276600, year = {2021}, author = {Liu, J and Su, J and Zhang, M and Luo, Z and Li, X and Chai, B}, title = {Bacterial Community Spacing Is Mainly Shaped by Unique Species in the Subalpine Natural Lakes of China.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {669131}, pmid = {34276600}, issn = {1664-302X}, abstract = {Bacterial communities have been described as early indicators of both regional and global climatic change and play a critical role in the global biogeochemical cycle. Exploring the mechanisms that determine the diversity patterns of bacterial communities and how they share different habitats along environmental gradients are, therefore, a central theme in microbial ecology research. We characterized the diversity patterns of bacterial communities in Pipahai Lake (PPH), Mayinghai Lake (MYH), and Gonghai Lake (GH), three subalpine natural lakes in Ningwu County, Shanxi, China, and analyzed the distribution of their shared and unique taxa (indicator species). Results showed that the species composition and structure of bacterial communities were significantly different among the three lakes. Both the structure of the entire bacterial community and the unique taxa were significantly influenced by the carbon content (TOC and IC) and space distance; however, the structure of the shared taxa was affected by conductivity (EC), pH, and salinity. The structure of the entire bacterial community and unique taxa were mainly affected by the same factors, suggesting that unique taxa may be important in maintaining the spatial distribution diversity of bacterial communities in subalpine natural freshwater lakes. Our results provide new insights into the diversity maintenance patterns of the bacterial communities in subalpine lakes, and suggest dispersal limitation on bacterial communities between adjacent lakes, even in a small local area. We revealed the importance of unique taxa in maintaining bacterial community structure, and our results are important in understanding how bacterial communities in subalpine lakes respond to environmental change in local habitats.}, }
@article {pmid34273695, year = {2021}, author = {Ntagia, E and Chatzigiannidou, I and Carvajal-Arroyo, JM and Arends, JBA and Rabaey, K}, title = {Continuous H2/CO2 fermentation for acetic acid production under transient and continuous sulfide inhibition.}, journal = {Chemosphere}, volume = {285}, number = {}, pages = {131536}, doi = {10.1016/j.chemosphere.2021.131536}, pmid = {34273695}, issn = {1879-1298}, mesh = {*Acetic Acid ; Bioreactors ; *Carbon Dioxide ; Fermentation ; Hydrogen ; Sulfides ; }, abstract = {Waste gas fermentation powered by renewable H2 is reaching kiloton scale. The presence of sulfide, inherent to many waste gases, can cause inhibition, requiring additional gas treatment. In this work, acetogenesis and methanogenesis inhibition by sulfide were studied in a 10-L mixed-culture fermenter, supplied with CO2 and connected with a water electrolysis unit for electricity-powered H2 supply. Three cycles of inhibition (1.3 mM total dissolved sulfide (TDS)) and recovery were applied, then the fermenter was operated at 0.5 mM TDS for 35 days. During operation at 0.5 mM TDS the acetate production rate reached 7.1 ± 1.5 mmol C L[-1] d[-1]. Furthermore, 43.7 ± 15.6% of the electrons, provided as H2, were distributed to acetate and 7.7 ± 4.1% to butyrate, the second most abundant fermentation product. Selectivity of sulfide as inhibitor was demonstrated by a 7 days lag-phase of methanogenesis recovery, compared to 48 h for acetogenesis and by the less than 1% electrons distribution to CH4, under 0.5 mM TDS. The microbial community was dominated by Eubacterium, Proteiniphilum and an unclassified member of the Eggerthellaceae family. The taxonomic diversity of the community decreased and conversely the phenotypic diversity increased, during operation. This work illustrated the scale-up potential of waste gas fermentations, by elucidating the effect of sulfide as a common gas impurity, and by demonstrating continuous, potentially renewable supply of electrons.}, }
@article {pmid34272992, year = {2022}, author = {Lu, Y and Zhang, Y and Wang, J and Zhang, M and Wu, Y and Xiao, X and Xu, J}, title = {Dynamics in Bacterial Community Affected by Mesoscale Eddies in the Northern Slope of the South China Sea.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {823-836}, pmid = {34272992}, issn = {1432-184X}, support = {2014CB441503//National Basic Research Program of China (973 Program)/ ; }, mesh = {Bacteria/genetics ; *Cyclonic Storms ; Ecosystem ; *Seawater/microbiology ; Water ; }, abstract = {Mesoscale eddies are common oceanographic processes that can enhance primary productivity by transporting nutrients to the euphotic zone. In the northern South China Sea (SCS), eddies were frequently found to promote the exchange between the nutrient-rich shelf water and the oligotrophic water at the slope area. However, the response of bacterial community to eddy perturbations remains unclear. In the present study, we examined the variation of bacterial community under the impact of eddies in early spring and summer. The results showed that both the summer cyclonic eddy and spring anticyclonic eddy enhanced the bacterial abundance in surface water. The bacterial community composition and their functional potentials of surface samples were also influenced by the summer cyclonic eddy, while no significant change was observed in the case of spring anticyclonic eddy. Salinity and nutrients, which varied between the inside and outside of the eddies, were the significant factors explaining the differentiation of the community composition and related functions. Taken together, the results of our present study reveal the effects of mesoscale eddies on the bacterial community and associated metagenomes, providing a better understanding of the dynamics of bacteria in the slope ecosystem of the SCS.}, }
@article {pmid34272991, year = {2021}, author = {Paul, P and Das, S and Chatterjee, S and Shukla, A and Chakraborty, P and Sarkar, S and Maiti, D and Das, A and Tribedi, P}, title = {1,4-Naphthoquinone disintegrates the pre-existing biofilm of Staphylococcus aureus by accumulating reactive oxygen species.}, journal = {Archives of microbiology}, volume = {203}, number = {8}, pages = {4981-4992}, pmid = {34272991}, issn = {1432-072X}, mesh = {Biofilms ; Humans ; Naphthoquinones ; Reactive Oxygen Species ; *Staphylococcal Infections ; *Staphylococcus aureus/genetics ; }, abstract = {Staphylococcus aureus causes several nosocomial and community-acquired infections in human host involving biofilm. Thus, strategies need to be explored to curb biofilm threats by either inhibiting the formation of biofilm or disintegrating the pre-existing biofilm. Towards this direction, we had already revealed the biofilm inhibiting properties of 1,4-naphthoquinone against S. aureus. In this study, we have investigated whether this compound can act on pre-existing biofilm. Hence, biofilm of S. aureus was developed first and challenged further with 1,4-naphthoquinone. Experiments such as crystal violet assay, fluorescence microscopy, and estimation of total biofilm protein were performed to confirm the biofilm disintegration properties of 1,4-naphthoquinone. The disintegration of pre-existing biofilm could be attributed to the generation of reactive oxygen species (ROS). To investigate further, we observed that extracellular DNA (eDNA) was found to play an important role in holding the biofilm network as DNaseI treatment could cause an efficient disintegration of the same. To examine the effect of ROS on the eDNA, we exposed pre-existing biofilm to either 1,4-naphthoquinone or a combination of both 1,4-naphthoquinone and ascorbic acid for different length of time. Post-incubation, ROS generation and the amount of eDNA associated with the biofilm were determined wherein an inversely proportional relationship was observed between them. The result indicated that with the increase of ROS generation, the amount of eDNA associated with biofilm got decreased substantially. Thus, the results indicated that the generation of ROS could degrade the eDNA thereby compromising the integrity of biofilm which lead to the disintegration of pre-existing biofilm.}, }
@article {pmid34272569, year = {2022}, author = {Martínez-Reyes, CM and Rodríguez-Zaragoza, S and Cabirol, N and Alarcón, A and Mendoza-López, MR}, title = {Effect of Predation by Colpoda sp. in Nitrogen Fixation Rate of Two Free-Living Bacteria.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {1026-1035}, pmid = {34272569}, issn = {1432-184X}, support = {IN222618//PAPIIT/ ; }, mesh = {Animals ; Bacteria ; *Ciliophora ; Nitrogen ; *Nitrogen Fixation ; Predatory Behavior ; }, abstract = {Biological nitrogen fixation is limited to several groups of prokaryotes, some of them reduce nitrogen as free-living nitrogen-fixing bacteria. Protozoa predation on these latter releases sequestered nitrogen that may enhance the formation of new bacterial biomass and possibly increase nitrogen fixation within soil microbial communities. We aim to evaluate the predation effect of Colpoda sp. on two nitrogen fixers: Azospirillum lipoferum and Stenotrophomonas sp. during their lag, early exponential, and exponential phases. The kinetics of bacterial population growth was determined in the predators' presence or absence and the effect of predation on the rate of N fixation was evaluated through the reduction of acetylene to ethylene technique. Colpoda sp. showed a non-significant difference in preferences between the two species offered as prey. Consequently, the abundance of A. lipoferum and Stenotrophomonas sp. decreased significantly due to predator's pressure and both species responded by increasing their specific growth rate. Likewise, predation promoted greater nitrogen fixation rate by CFU during the lag phase in A. lipoferum (0.20 nM/CFU with predation vs 0.09 nM/CFU without predation) and Stenotrophomonas sp. (0.22 nM/CFU vs 0.09 nM/CFU respectively). During early exponential phase (29 h), the rate diminished to 0.13 and 0.05 nM/CFU in A. lipoferum and to 0.09 nM/CFU and 0.05 nM/CFU in Stenotrophomonas sp. Finally, during the exponential phase (52 h), only A. lipoferum without predation produced 0.003 nM/CFU of ethylene. Thus, the nitrogenase activity was higher in the lag and the early exponential phases when predator activity was involved.}, }
@article {pmid34269959, year = {2021}, author = {Đurović, G and Van Neerbos, FAC and Bossaert, S and Herrera-Malaver, B and Steensels, J and Arnó, J and Wäckers, F and Sobhy, IS and Verstrepen, KJ and Jacquemyn, H and Lievens, B}, title = {The Pupal Parasitoid Trichopria drosophilae Is Attracted to the Same Yeast Volatiles as Its Adult Host.}, journal = {Journal of chemical ecology}, volume = {47}, number = {8-9}, pages = {788-798}, pmid = {34269959}, issn = {1573-1561}, support = {722642 (INTERFUTURE)//Horizon 2020 Framework Programme/ ; PID2019-107030RB-C21//CERCA Programme/ ; }, mesh = {Animals ; Behavior, Animal/drug effects ; Esters/chemistry/metabolism/pharmacology ; Host-Parasite Interactions/drug effects ; Hymenoptera/growth &amp; development/*physiology ; Principal Component Analysis ; Proteins/genetics/metabolism ; Pupa/drug effects/physiology ; Saccharomyces cerevisiae/*chemistry/metabolism ; Volatile Organic Compounds/*chemistry/pharmacology ; }, abstract = {There is increasing evidence that microorganisms, particularly fungi and bacteria, emit volatile compounds that mediate the foraging behaviour of insects and therefore have the potential to affect key ecological relationships. However, to what extent microbial volatiles affect the olfactory response of insects across different trophic levels remains unclear. Adult parasitoids use a variety of chemical stimuli to locate potential hosts, including those emitted by the host's habitat, the host itself, and microorganisms associated with the host. Given the great capacity of parasitoids to utilize and learn odours to increase foraging success, parasitoids of eggs, larvae, or pupae may respond to the same volatiles the adult stage of their hosts use when locating their resources, but compelling evidence is still scarce. In this study, using Saccharomyces cerevisiae we show that Trichopria drosophilae, a pupal parasitoid of Drosophila species, is attracted to the same yeast volatiles as their hosts in the adult stage, i.e. acetate esters. Parasitoids significantly preferred the odour of S. cerevisiae over the blank medium in a Y-tube olfactometer. Deletion of the yeast ATF1 gene, encoding a key acetate ester synthase, decreased attraction of T. drosophilae, while the addition of synthetic acetate esters to the fermentation medium restored parasitoid attraction. Bioassays with individual compounds revealed that the esters alone were not as attractive as the volatile blend of S. cerevisiae, suggesting that other volatile compounds also contribute to the attraction of T. drosophilae. Altogether, our results indicate that pupal parasitoids respond to the same volatiles as the adult stage of their hosts, which may aid them in locating oviposition sites.}, }
@article {pmid34269858, year = {2022}, author = {Lin, YC and Chin, CP and Yang, JW and Chiang, KP and Hsieh, CH and Gong, GC and Shih, CY and Chen, SY}, title = {How Communities of Marine Stramenopiles Varied with Environmental and Biological Variables in the Subtropical Northwestern Pacific Ocean.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {916-928}, pmid = {34269858}, issn = {1432-184X}, support = {104-2811-M-019- 003//Ministry of Science and Technology, Taiwan/ ; 109-2611-M-019 -018//Ministry of Science and Technology, Taiwan/ ; 107-2611-M-019 -002 -MY3//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Biodiversity ; Nitrites ; Pacific Ocean ; Phylogeny ; Seawater ; *Stramenopiles ; *Synechococcus ; Water ; }, abstract = {MArine STramenopiles (MASTs) have been recognized as parts of heterotrophic protists and contribute substantially to protist abundances in the ocean. However, little is known about their spatiotemporal variations with respect to environmental and biological factors. The objectives of this study are to use canonical correspondence analysis to investigate how MASTs communities are shaped by environmental variables, and co-occurrence networks to examine their potential interactions with prokaryotic communities. Our dataset came from the southern East China Sea (sECS) in the subtropical northwestern Pacific, and involved 14 cruises along a coastal-oceanic transect, each of which sampled surface water from 4 to 7 stations. MASTs communities were revealed by metabarcoding of 18S rDNA V4 region. Most notably, MAST-9 had a high representation in warm waters in terms of read number and diversity. Subclades of MAST-9C and -9D showed slightly different niches, with MAST-9D dominating in more coastal waters where concentrations of nitrite and Synechococcus were higher. MAST-1C was a common component of colder water during spring. Overall, canonical correspondence analysis showed that MASTs communities were significantly influenced by temperature, nitrite and Synechococcus concentrations. The co-occurrence networks showed that certain other minor prokaryotic taxa can influence MAST communities. This study provides insight into how MASTs communities varied with environmental and biological variables.}, }
@article {pmid34267209, year = {2021}, author = {Chen, F and Chen, Z and Chen, M and Chen, G and Huang, Q and Yang, X and Yin, H and Chen, L and Zhang, W and Lin, H and Ou, M and Wang, L and Chen, Y and Lin, C and Xu, W and Yin, G}, title = {Reduced stress-associated FKBP5 DNA methylation together with gut microbiota dysbiosis is linked with the progression of obese PCOS patients.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {60}, pmid = {34267209}, issn = {2055-5008}, mesh = {Adult ; Biodiversity ; Biomarkers ; Case-Control Studies ; Computational Biology ; *DNA Methylation ; Disease Susceptibility ; *Dysbiosis ; Female ; *Gastrointestinal Microbiome ; Humans ; Metabolome ; Metabolomics/methods ; Middle Aged ; Obesity ; Polycystic Ovary Syndrome/diagnosis/*etiology/*metabolism ; *Stress, Physiological ; Tacrolimus Binding Proteins/*genetics ; Young Adult ; }, abstract = {Polycystic ovary syndrome (PCOS) is a common endocrine disease in females that is characterized by hyperandrogenemia, chronic anovulation, and polycystic ovaries. However, the exact etiology and pathogenesis of PCOS are still unknown. The aim of this study was to clarify the bacterial, stress status, and metabolic differences in the gut microbiomes of healthy individuals and patients with high body mass index (BMI) PCOS (PCOS-HB) and normal BMI PCOS (PCOS-LB), respectively. Here, we compared the gut microbiota characteristics of PCOS-HB, PCOS-LB, and healthy controls by 16S rRNA gene sequencing, FK506-binding protein 5 (FKBP5) DNA methylation and plasma metabolite determination. Clinical parameter comparisons indicated that PCOS patients had higher concentrations of total testosterone, androstenedione, dehydroepiandrosterone sulfate, luteinizing hormone, and HOMA-IR while lower FKBP5 DNA methylation. Significant differences in bacterial diversity and community were observed between the PCOS and healthy groups but not between the PCOS-HB and PCOS-LB groups. Bacterial species number was negatively correlated with insulin concentrations (both under fasting status and 120 min after glucose load) and HOMA-IR but positively related to FKBP5 DNA methylation. Compared to the healthy group, both PCOS groups had significant changes in bacterial genera, including Prevotella_9, Dorea, Maihella, and Slackia, and plasma metabolites, including estrone sulfate, lysophosphatidyl choline 18:2, and phosphatidylcholine (22:6e/19:1). The correlation network revealed the complicated interaction of the clinical index, bacterial genus, stress indices, and metabolites. Our work links the stress responses and gut microbiota characteristics of PCOS disease, which might afford perspectives to understand the progression of PCOS.}, }
@article {pmid34263935, year = {2021}, author = {Amini, S and Arsova, B and Gobert, S and Carnol, M and Bosman, B and Motte, P and Watt, M and Hanikenne, M}, title = {Transcriptional regulation of ZIP genes is independent of local zinc status in Brachypodium shoots upon zinc deficiency and resupply.}, journal = {Plant, cell &amp; environment}, volume = {44}, number = {10}, pages = {3376-3397}, doi = {10.1111/pce.14151}, pmid = {34263935}, issn = {1365-3040}, mesh = {Brachypodium/*genetics/*metabolism ; Plant Proteins/*genetics/metabolism ; Plant Shoots/metabolism ; Transcription, Genetic ; Zinc/*deficiency/metabolism ; }, abstract = {The biological processes underlying zinc homeostasis are targets for genetic improvement of crops to counter human malnutrition. Detailed phenotyping, ionomic, RNA-Seq analyses and flux measurements with [67] Zn isotope revealed whole-plant molecular events underlying zinc homeostasis upon varying zinc supply and during zinc resupply to starved Brachypodium distachyon (Brachypodium) plants. Although both zinc deficiency and excess hindered Brachypodium growth, accumulation of biomass and micronutrients into roots and shoots differed depending on zinc supply. The zinc resupply dynamics involved 1,893 zinc-responsive genes. Multiple zinc-regulated transporter and iron-regulated transporter (IRT)-like protein (ZIP) transporter genes and dozens of other genes were rapidly and transiently down-regulated in early stages of zinc resupply, suggesting a transient zinc shock, sensed locally in roots. Notably, genes with identical regulation were observed in shoots without zinc accumulation, pointing to root-to-shoot signals mediating whole-plant responses to zinc resupply. Molecular events uncovered in the grass model Brachypodium are useful for the improvement of staple monocots.}, }
@article {pmid34263341, year = {2022}, author = {González-Dominici, LI and Saati-Santamaría, Z and García-Fraile, P}, title = {Correction to: Genome Analysis and Genomic Comparison of the Novel Species Arthrobacter ipis Reveal Its Potential Protective Role in Its Bark Beetle Host.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {1123}, doi = {10.1007/s00248-021-01811-x}, pmid = {34263341}, issn = {1432-184X}, abstract = {A Correction to this paper has been published: https://doi.org/10.1007/s00248-021-01811-x.}, }
@article {pmid34262548, year = {2021}, author = {Leinberger, J and Holste, J and Bunk, B and Freese, HM and Spröer, C and Dlugosch, L and Kück, AC and Schulz, S and Brinkhoff, T}, title = {High Potential for Secondary Metabolite Production of Paracoccus marcusii CP157, Isolated From the Crustacean Cancer pagurus.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {688754}, pmid = {34262548}, issn = {1664-302X}, abstract = {Secondary metabolites are key components in microbial ecology by mediating interactions between bacteria and their environment, neighboring species or host organisms. Bioactivities can be beneficial for both interaction partners or provide a competitive advantage only for the producer. Colonizers of confined habitats such as biofilms are known as prolific producers of a great number of bioactive secondary metabolites and are a potential source for novel compounds. We investigated the strain Paracoccus marcusii CP157, which originates from the biofilm on the carapace of a shell disease-affected Cancer pagurus specimen, for its potential to produce bioactive secondary metabolites. Its closed genome contains 22 extrachromosomal elements and several gene clusters potentially involved in biosynthesis of bioactive polyketides, bacteriocins, and non-ribosomal peptides. Culture extracts of CP157 showed antagonistic activities against bacteria from different phyla, but also against microalgae and crustacean larvae. Different HPLC-fractions of CP157 culture extracts had antibacterial properties, indicating that several bioactive compounds are produced by CP157. The bioactive extract contains several small, antibacterial compounds that partially withstand elevated temperatures, extreme pH values and exposure to proteolytic enzymes, providing high stability toward environmental conditions in the natural habitat of CP157. Further, screening of 17 Paracoccus spp. revealed that antimicrobial activity, hemolysis and production of N-acyl homoserine lactones are common features within the genus. Taking into account the large habitat diversity and phylogenetic distance of the tested strains, we hypothesize that bioactive secondary metabolites play a central role in the ecology of Paracoccus spp. in their natural environments.}, }
@article {pmid34260793, year = {2022}, author = {Yang, Q and Wang, Q and Wu, J and Zhang, Y and Wei, D and Qu, B and Liu, Y and Fu, S}, title = {Distinct dynamics of Vibrio parahaemolyticus populations in two farming models.}, journal = {Journal of applied microbiology}, volume = {133}, number = {3}, pages = {1146-1155}, doi = {10.1111/jam.15217}, pmid = {34260793}, issn = {1365-2672}, support = {81903372//National Natural Science Foundation of China/ ; QL202005//Youth Fund of Liaoning Provincial Department of Education/ ; 2019B020215001//Key R&amp;D Program of Guangdong Province/ ; GML2019ZD0402//Key R&amp;D Program of Guangdong Province/ ; //Special Research Fund of Ghent University/ ; }, mesh = {Aquaculture ; Humans ; Multilocus Sequence Typing ; *Vibrio Infections/microbiology ; *Vibrio parahaemolyticus/genetics ; Water ; }, abstract = {AIMS: Despite the recent prosperity of shrimp cultivation in China, very little is known about how different shrimp farming models influence the dynamics of Vibrio parahaemolyticus populations and the antibiotic resistance of this bacterium.<br><br>METHODS AND RESULTS: To this end, we conducted continuous surveillance of V. parahaemolyticus on four farms over 3&#xa0;years: two traditional shrimp farms with daily water exchange and two farms operated in the recirculating aquaculture systems (RAS). No antibiotics were used in these farms to exclude the potential impacts of antibiotics on the emergence of antibacterial resistance. Multilocus sequence typing was utilized to characterize the dynamics of V. parahaemolyticus populations. Whole-genome sequencing (WGS) was conducted to determine the representative sequence types (STs) at each farm. Results revealed that the population structure of V. parahaemolyticus remained stable over time in both RAS farms, with only nine and four STs observed at each. In contrast, annual replacement of V. parahaemolyticus populations was observed in traditional farms with 26 and 28 STs identified in rearing water. WGS of 50 isolates divided them into five clusters, of which ST917a isolates harboured a genomic island that disrupted the gene recA. Pair-wised genomic comparison of isolates from the same STs showed that they were genetically related but belonged to different clones associated with geographical distribution.<br><br>CONCLUSIONS: These results suggested that RAS presented a specific ecological niche by minimizing the water exchanges with the external environment. In contrast, traditional farming might pose a food safety issue by introducing new V. parahaemolyticus populations with antibiotic resistance genes.<br><br>Our results expose the potential food safety issue associated with conventional agriculture and should encourage the development of preventive strategies to reduce the emergence of resistant V. parahaemolyticus populations.}, }
@article {pmid34258685, year = {2021}, author = {Carpio, LE and Sanz, Y and Gozalbes, R and Barigye, SJ}, title = {Computational strategies for the discovery of biological functions of health foods, nutraceuticals and cosmeceuticals: a review.}, journal = {Molecular diversity}, volume = {25}, number = {3}, pages = {1425-1438}, pmid = {34258685}, issn = {1573-501X}, support = {INNTAL32/19/002//Agencia Valenciana de la Investigaci&#xf3;n/ ; 893810//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; }, mesh = {Algorithms ; Cheminformatics/*methods ; Cosmeceuticals/*chemistry/pharmacology ; Databases, Chemical ; Dietary Supplements/*analysis ; Functional Food/*analysis ; Humans ; Machine Learning ; *Models, Molecular ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; *Quantitative Structure-Activity Relationship ; }, abstract = {Scientific and consumer interest in healthy foods (also known as functional foods), nutraceuticals and cosmeceuticals has increased in the recent years, leading to an increased presence of these products in the market. However, the regulations across different countries that define the type of claims that may be made, and the degree of evidence required to support these claims, are rather inconsistent. Moreover, there is also controversy on the effectiveness and biological mode of action of many of these products, which should undergo an exhaustive approval process to guarantee the consumer rights. Computational approaches constitute invaluable tools to facilitate the discovery of bioactive molecules and provide biological plausibility on the mode of action of these products. Indeed, methodologies like QSAR, docking or molecular dynamics have been used in drug discovery protocols for decades and can now aid in the discovery of bioactive food components. Thanks to these approaches, it is possible to search for new functions in food constituents, which may be part of our daily diet, and help to prevent disorders like diabetes, hypercholesterolemia or obesity. In the present manuscript, computational studies applied to this field are reviewed to illustrate the potential of these approaches to guide the first screening steps and the mechanistic studies of nutraceutical, cosmeceutical and functional foods.}, }
@article {pmid34255112, year = {2022}, author = {Pavlova, ON and Izosimova, ON and Chernitsyna, SM and Ivanov, VG and Pogodaeva, TV and Khabuev, AV and Gorshkov, AG and Zemskaya, TI}, title = {Anaerobic oxidation of petroleum hydrocarbons in enrichment cultures from sediments of the Gorevoy Utes natural oil seep under methanogenic and sulfate-reducing conditions.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {899-915}, pmid = {34255112}, issn = {1432-184X}, support = {0279-2021-0006 (121032300223-1)//Ministry of Education and Science of the Russian Federation/ ; }, mesh = {Anaerobiosis ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; *Euryarchaeota/genetics ; Geologic Sediments/microbiology ; Hydrocarbons/metabolism ; *Microbiota ; *Petroleum ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Sulfates/metabolism ; }, abstract = {This article presents the first experimental data on the ability of microbial communities from sediments of the Gorevoy Utes natural oil seep to degrade petroleum hydrocarbons under anaerobic conditions. Like in marine ecosystems associated with oil discharge, available electron acceptors, in particular sulfate ions, affect the composition of the microbial community and the degree of hydrocarbon conversion. The cultivation of the surface sediments under sulfate-reducing conditions led to the formation of a more diverse bacterial community and greater loss of n-alkanes (28%) in comparison to methanogenic conditions (6%). Microbial communities of both surface and deep sediments are more oriented to degrade polycyclic aromatic hydrocarbons (PAHs), to which the degree of the PAH conversion testifies (up to 46%) irrespective of the present electron acceptors. Microorganisms with the uncultured closest homologues from thermal habitats, sediments of mud volcanoes, and environments contaminated with hydrocarbons mainly represented microbial communities of enrichment cultures. The members of the phyla Firmicutes, Chloroflexi, and Caldiserica (OP5), as well as the class Deltaproteobacteria and Methanomicrobia, were mostly found in enrichment cultures. The influence of gas-saturated fluids may be responsible for the presence in the bacterial 16S rRNA gene libraries of the sequences of "rare taxa": Planctomycetes, Ca. Atribacteria (OP9), Ca. Armatimonadetes (OP10), Ca. Latescibacteria (WS3), Ca. division (AC1), Ca. division (OP11), and Ca. Parcubacteria (OD1), which can be involved in hydrocarbon oxidation.}, }
@article {pmid34254828, year = {2021}, author = {Harrison, JG and Randolph, GD and Buerkle, CA}, title = {Characterizing Microbiomes via Sequencing of Marker Loci: Techniques To Improve Throughput, Account for Cross-Contamination, and Reduce Cost.}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0029421}, pmid = {34254828}, issn = {2379-5077}, support = {EPS-1655726//National Science Foundation (NSF)/ ; }, abstract = {New approaches to characterizing microbiomes via high-throughput sequencing provide impressive gains in efficiency and cost reduction compared to approaches that were standard just a few years ago. However, the speed of method development has been such that staying abreast of the latest technological advances is challenging. Moreover, shifting laboratory protocols to include new methods can be expensive and time consuming. To facilitate adoption of new techniques, we provide a guide and review of recent advances that are relevant for single-locus sequence-based study of microbiomes-from extraction to library preparation-including a primer regarding the use of liquid-handling automation in small-scale academic settings. Additionally, we describe several amendments to published techniques to improve throughput, track contamination, and reduce cost. Notably, we suggest adding synthetic DNA molecules to each sample during nucleic acid extraction, thus providing a method of documenting incidences of cross-contamination. We also describe a dual-indexing scheme for Illumina sequencers that allows multiplexing of many thousands of samples with minimal PhiX input. Collectively, the techniques that we describe demonstrate that laboratory technology need not impose strict limitations on the scale of molecular microbial ecology studies. IMPORTANCE New methods to characterize microbiomes reduce technology-imposed limitations to study design, but many new approaches have not been widely adopted. Here, we present techniques to increase throughput and reduce contamination alongside a thorough review of current best practices.}, }
@article {pmid34254826, year = {2021}, author = {Ha, AD and Moniruzzaman, M and Aylward, FO}, title = {High Transcriptional Activity and Diverse Functional Repertoires of Hundreds of Giant Viruses in a Coastal Marine System.}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0029321}, pmid = {34254826}, issn = {2379-5077}, support = {Early Career Award in Marine Microbial Ecology and Evolution//Simons Foundation (SF)/ ; 1918271//National Science Foundation (NSF)/ ; }, abstract = {Viruses belonging to the Nucleocytoviricota phylum are globally distributed and include members with notably large genomes and complex functional repertoires. Recent studies have shown that these viruses are particularly diverse and abundant in marine systems, but the magnitude of actively replicating Nucleocytoviricota present in ocean habitats remains unclear. In this study, we compiled a curated database of 2,431 Nucleocytoviricota genomes and used it to examine the gene expression of these viruses in a 2.5-day metatranscriptomic time-series from surface waters of the California Current. We identified 145 viral genomes with high levels of gene expression, including 90 Imitervirales and 49 Algavirales viruses. In addition to recovering high expression of core genes involved in information processing that are commonly expressed during viral infection, we also identified transcripts of diverse viral metabolic genes from pathways such as glycolysis, the TCA cycle, and the pentose phosphate pathway, suggesting that virus-mediated reprogramming of central carbon metabolism is common in oceanic surface waters. Surprisingly, we also identified viral transcripts with homology to actin, myosin, and kinesin domains, suggesting that viruses may use these gene products to manipulate host cytoskeletal dynamics during infection. We performed phylogenetic analysis on the virus-encoded myosin and kinesin proteins, which demonstrated that most belong to deep-branching viral clades, but that others appear to have been acquired from eukaryotes more recently. Our results highlight a remarkable diversity of active Nucleocytoviricota in a coastal marine system and underscore the complex functional repertoires expressed by these viruses during infection. IMPORTANCE The discovery of giant viruses has transformed our understanding of viral complexity. Although viruses have traditionally been viewed as filterable infectious agents that lack metabolism, giant viruses can reach sizes rivalling cellular lineages and possess genomes encoding central metabolic processes. Recent studies have shown that giant viruses are widespread in aquatic systems, but the activity of these viruses and the extent to which they reprogram host physiology in situ remains unclear. Here, we show that numerous giant viruses consistently express central metabolic enzymes in a coastal marine system, including components of glycolysis, the TCA cycle, and other pathways involved in nutrient homeostasis. Moreover, we found expression of several viral-encoded actin, myosin, and kinesin genes, indicating viral manipulation of the host cytoskeleton during infection. Our study reveals a high activity of giant viruses in a coastal marine system and indicates they are a diverse and underappreciated component of microbial diversity in the ocean.}, }
@article {pmid34253727, year = {2021}, author = {Wan, T and Liu, Z and Leitch, IJ and Xin, H and Maggs-Kölling, G and Gong, Y and Li, Z and Marais, E and Liao, Y and Dai, C and Liu, F and Wu, Q and Song, C and Zhou, Y and Huang, W and Jiang, K and Wang, Q and Yang, Y and Zhong, Z and Yang, M and Yan, X and Hu, G and Hou, C and Su, Y and Feng, S and Yang, J and Yan, J and Chu, J and Chen, F and Ran, J and Wang, X and Van de Peer, Y and Leitch, AR and Wang, Q}, title = {The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {4247}, pmid = {34253727}, issn = {2041-1723}, mesh = {Africa ; Cycadopsida/*genetics ; DNA Methylation/genetics ; *Desert Climate ; Evolution, Molecular ; *Genome, Plant ; Geography ; Meristem/genetics ; Molecular Sequence Annotation ; Plant Leaves/genetics ; Rain ; Sequence Analysis, DNA ; Species Specificity ; Transcriptome/genetics ; }, abstract = {The gymnosperm Welwitschia mirabilis belongs to the ancient, enigmatic gnetophyte lineage. It is a unique desert plant with extreme longevity and two ever-elongating leaves. We present a chromosome-level assembly of its genome (6.8 Gb/1 C) together with methylome and transcriptome data to explore its astonishing biology. We also present a refined, high-quality assembly of Gnetum montanum to enhance our understanding of gnetophyte genome evolution. The Welwitschia genome has been shaped by a lineage-specific ancient, whole genome duplication (~86 million years ago) and more recently (1-2 million years) by bursts of retrotransposon activity. High levels of cytosine methylation (particularly at CHH motifs) are associated with retrotransposons, whilst long-term deamination has resulted in an exceptionally GC-poor genome. Changes in copy number and/or expression of gene families and transcription factors (e.g. R2R3MYB, SAUR) controlling cell growth, differentiation and metabolism underpin the plant's longevity and tolerance to temperature, nutrient and water stress.}, }
@article {pmid34252564, year = {2022}, author = {Fournier, E and Roussel, C and Dominicis, A and Ley, D and Peyron, MA and Collado, V and Mercier-Bonin, M and Lacroix, C and Alric, M and Van de Wiele, T and Chassard, C and Etienne-Mesmin, L and Blanquet-Diot, S}, title = {In vitro models of gut digestion across childhood: current developments, challenges and future trends.}, journal = {Biotechnology advances}, volume = {54}, number = {}, pages = {107796}, doi = {10.1016/j.biotechadv.2021.107796}, pmid = {34252564}, issn = {1873-1899}, mesh = {Animals ; Child ; Digestion ; *Environmental Pollutants ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/physiology ; Humans ; }, abstract = {The human digestion is a multi-step and multi-compartment process essential for human health, at the heart of many issues raised by academics, the medical world and industrials from the food, nutrition and pharma fields. In the first years of life, major dietary changes occur and are concomitant with an evolution of the whole child digestive tract anatomy and physiology, including colonization of gut microbiota. All these phenomena are influenced by child exposure to environmental compounds, such as drugs (especially antibiotics) and food pollutants, but also childhood infections. Due to obvious ethical, regulatory and technical limitations, in vivo approaches in animal and human are more and more restricted to favor complementary in vitro approaches. This review summarizes current knowledge on the evolution of child gut physiology from birth to 3 years old regarding physicochemical, mechanical and microbial parameters. Then, all the available in vitro models of the child digestive tract are described, ranging from the simplest static mono-compartmental systems to the most sophisticated dynamic and multi-compartmental models, and mimicking from the oral phase to the colon compartment. Lastly, we detail the main applications of child gut models in nutritional, pharmaceutical and microbiological studies and discuss the limitations and challenges facing this field of research.}, }
@article {pmid34252020, year = {2021}, author = {Doll, EV and Staib, L and Huptas, C and Scherer, S and Wenning, M}, title = {Facklamia lactis sp. nov., isolated from raw milk.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {71}, number = {7}, pages = {}, doi = {10.1099/ijsem.0.004869}, pmid = {34252020}, issn = {1466-5034}, mesh = {Aerococcaceae/*classification/isolation &amp; purification ; Animals ; Bacterial Typing Techniques ; Base Composition ; Cattle ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Germany ; Glycolipids/chemistry ; Milk/*microbiology ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Two strains of a Gram-staining-positive species were isolated from German bulk tank milk. On the basis of their 16S rRNA sequences they were affiliated to the genus Facklamia but could not be assigned to any species with a validly published name. Facklamia miroungae ATCC BAA-466[T] (97.3 % 16S rRNA sequence similarity), Facklamia languida CCUG 37842[T] (96.9 %), and Facklamia hominis CCUG 36813[T] (96.6 %) are the closest relatives. In the 16S rRNA phylogeny and in the core-genome phylogeny strains WS 5301[T] and WS 5302 form a well-supported, separate lineage. Pairwise average nucleotide identity calculated using MUMmer (ANIm) between WS 5301[T] and type strains of other Facklamia species is well below the species cut-off (95 %) and ranges from 83.4 to 87.7 %. The DNA G+C content of the type strain is 36.4 mol% and the assembly size of the genome is 2.2 Mb. Cells of WS 5301[T] are non-motile, non-endospore-forming, oxidase-negative, catalase-negative and facultatively anaerobic cocci. The fastidious species grows at 10-40 °C and with up to 7.0 % (w/v) NaCl in BHI supplemented with 5 g l[-1] yeast extract. Major polar lipids are phosphatidylglycerol, diphosphatidylglycerol and two glycolipids. Predominant fatty acids are C16 : 1ω9c and C18 : 1ω9c. On the basis of their genomic, physiological and chemotaxonomic characteristics the strains examined in this study represent the same, hitherto unknown species. We propose the name Facklamia lactis sp. nov. for which WS 5301[T] (=DSM 111018[T]=LMG 31861[T]) is the type strain and WS 5302 (=DSM 111019=LMG 31862) is an additional strain of this novel species.}, }
@article {pmid34251452, year = {2021}, author = {Nguyen, MP and Lehosmaa, K and Martz, F and Koskimäki, JJ and Pirttilä, AM and Häggman, H}, title = {Host species shape the community structure of culturable endophytes in fruits of wild berry species (Vaccinium myrtillus L., Empetrum nigrum L. and Vaccinium vitis-idaea L.).}, journal = {FEMS microbiology ecology}, volume = {97}, number = {8}, pages = {}, pmid = {34251452}, issn = {1574-6941}, mesh = {Basidiomycota ; Endophytes/genetics ; Fruit ; Humans ; *Vaccinium myrtillus ; *Vaccinium vitis-idaea ; }, abstract = {Wild berries are interesting research subjects due to their rich sources of health-beneficial phenolic compounds. However, the internal microbial communities, endophytes, associated with the wild berry fruits are currently unknown. Endophytes are bacteria or fungi inhabiting inside plant tissues, and their functions vary depending on the host species and environmental parameters. The present study aimed to examine community composition of fungal and bacterial endophytes in fruits of three wild berry species (bilberry Vaccinium myrtillus L., lingonberry Vaccinium vitis-idaea L. and crowberry Empetrum nigrum L.) and the effects of host plant species and their growth sites on shaping the endophytic communities. We found that the endophytic community structures differed between the berry species, and fungi were predominant over bacteria in the total endophytic taxa. We identified previously unknown endophytic fungal taxa including Angustimassarina, Dothidea, Fellozyma, Pseudohyphozyma, Hannaella coprosmae and Oberwinklerozyma straminea. A role of soluble phenolic compounds, the intracellular components in wild berry fruits, in shaping the endophytic communities is proposed. Overall, our study demonstrates that each berry species harbors a unique endophytic community of microbes.}, }
@article {pmid34251412, year = {2021}, author = {Collins, SM and Gibson, GR and Kennedy, OB and Walton, G and Rowland, I and Commane, DM}, title = {Development of a prebiotic blend to influence in vitro fermentation effects, with a focus on propionate, in the gut.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {8}, pages = {}, doi = {10.1093/femsec/fiab101}, pmid = {34251412}, issn = {1574-6941}, mesh = {Fatty Acids, Volatile ; Feces ; Fermentation ; Humans ; Inulin/metabolism ; *Prebiotics ; *Propionates ; }, abstract = {Short chain fatty acids (SCFAs) derived from the human gut microbiota, and in particular propionate, may beneficially influence metabolic processes such as appetite regulation. Development of prebiotics that induce high propionate levels during fermentation is desirable. A total of 11 candidate prebiotics were screened to investigate their fermentation characteristics, with a focus on propionate production in mixed anaerobic batch culture of faecal bacteria. Further to this, a continuous 3-stage colonic fermentation model (simulating the human colon) was used to evaluate changes in microbial ecology, lactate and SCFA production of three 50:50 blends, comprising both slow and rapidly fermented prebiotics. In mixed batch culture: xylo-oligosaccharide, polydextrose and α-gluco-oligosaccharide were associated with the greatest increase in propionate. Polydextrose, α-gluco-oligosaccharide, β-1,4 glucan and oat fibre induced the greatest reductions in the acetate to propionate ratio. The most bifidogenic prebiotics were the oligosaccharides. Fermentation of a 50:50 blend of inulin and arabinoxylan, through the continuous 3-stage colonic fermentation model, induced a substantial and sustained release of propionate. The sustained release of propionate through the colon, if replicable in vivo, could potentially influence blood glucose, blood lipids and appetite regulation, however, dietary intervention studies are needed. Bifidogenic effects were also observed for the inulin and arabinoxylan blend and an increase synthesis of butyrate and lactate, thus indicating wider prebiotic potential.}, }
@article {pmid34249520, year = {2021}, author = {Priest, T and Orellana, LH and Huettel, B and Fuchs, BM and Amann, R}, title = {Microbial metagenome-assembled genomes of the Fram Strait from short and long read sequencing platforms.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e11721}, pmid = {34249520}, issn = {2167-8359}, abstract = {The impacts of climate change on the Arctic Ocean are manifesting throughout the ecosystem at an unprecedented rate. Of global importance are the impacts on heat and freshwater exchange between the Arctic and North Atlantic Oceans. An expanding Atlantic influence in the Arctic has accelerated sea-ice decline, weakened water column stability and supported the northward shift of temperate species. The only deep-water gateway connecting the Arctic and North Atlantic and thus, fundamental for these exchange processes is the Fram Strait. Previous research in this region is extensive, however, data on the ecology of microbial communities is limited, reflecting the wider bias towards temperate and tropical latitudes. Therefore, we present 14 metagenomes, 11 short-read from Illumina and three long-read from PacBio Sequel II, of the 0.2-3 µm fraction to help alleviate such biases and support future analyses on changing ecological patterns. Additionally, we provide 136 species-representative, manually refined metagenome-assembled genomes which can be used for comparative genomics analyses and addressing questions regarding functionality or distribution of taxa.}, }
@article {pmid34249034, year = {2021}, author = {Kaur, J and Sharma, J}, title = {Orchid Root Associated Bacteria: Linchpins or Accessories?.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {661966}, pmid = {34249034}, issn = {1664-462X}, abstract = {Besides the plant-fungus symbiosis in arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) plants, many endorhizal and rhizosphere bacteria (Root Associated Bacteria, or RAB) also enhance plant fitness, diversity, and coexistence among plants via bi- or tripartite interactions with plant hosts and mycorrhizal fungi. Assuming that bacterial associations are just as important for the obligate mycorrhizal plant family Orchidaceae, surprisingly little is known about the RAB associated with orchids. Herein, we first present the current, underwhelming state of RAB research including their interactions with fungi and the influence of holobionts on plant fitness. We then delineate the need for novel investigations specifically in orchid RAB ecology, and sketch out questions and hypotheses which, when addressed, will advance plant-microbial ecology. We specifically discuss the potential effects of beneficial RAB on orchids as: (1) Plant Growth Promoting Rhizobacteria (PGPR), (2) Mycorrhization Helper Bacteria (MHB), and (3) constituents of an orchid holobiont. We further posit that a hologenomic view should be considered as a framework for addressing co-evolution of the plant host, their obligate Orchid Mycorrhizal Fungi (OMF), and orchid RAB. We conclude by discussing implications of the suggested research for conservation of orchids, their microbial partners, and their collective habitats.}, }
@article {pmid34247483, year = {2021}, author = {Jakus, N and Mellage, A and Höschen, C and Maisch, M and Byrne, JM and Mueller, CW and Grathwohl, P and Kappler, A}, title = {Anaerobic Neutrophilic Pyrite Oxidation by a Chemolithoautotrophic Nitrate-Reducing Iron(II)-Oxidizing Culture Enriched from a Fractured Aquifer.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {14}, pages = {9876-9884}, doi = {10.1021/acs.est.1c02049}, pmid = {34247483}, issn = {1520-5851}, mesh = {Anaerobiosis ; Ferric Compounds ; Ferrous Compounds ; *Groundwater ; Iron ; *Nitrates ; Oxidation-Reduction ; Sulfides ; }, abstract = {Neutrophilic microbial pyrite (FeS2) oxidation coupled to denitrification is thought to be an important natural nitrate attenuation pathway in nitrate-contaminated aquifers. However, the poor solubility of pyrite raises questions about its bioavailability and the mechanisms underlying its oxidation. Here, we investigated direct microbial pyrite oxidation by a neutrophilic chemolithoautotrophic nitrate-reducing Fe(II)-oxidizing culture enriched from a pyrite-rich aquifer. We used pyrite with natural abundance (NA) of Fe isotopes ([NA]Fe-pyrite) and [57]Fe-labeled siderite to evaluate whether the oxidation of the more soluble Fe(II)-carbonate (FeCO3) can indirectly drive abiotic pyrite oxidation. Our results showed that in setups where only pyrite was incubated with bacteria, direct microbial pyrite oxidation contributed ca. 26% to overall nitrate reduction. The rest was attributed to the oxidation of elemental sulfur (S[0]), present as a residue from pyrite synthesis. Pyrite oxidation was evidenced in the [NA]Fe-pyrite/[57]Fe-siderite setups by maps of [56]FeO and [32]S obtained using a combination of SEM with nanoscale secondary ion MS (NanoSIMS), which showed the presence of [56]Fe(III) (oxyhydr)oxides that could solely originate from [56]FeS2. Based on the fit of a reaction model to the geochemical data and the Fe-isotope distributions from NanoSIMS, we conclude that anaerobic oxidation of pyrite by our neutrophilic enrichment culture was mainly driven by direct enzymatic activity of the cells. The contribution of abiotic pyrite oxidation by Fe[3+] appeared to be negligible in our experimental setup.}, }
@article {pmid34245330, year = {2022}, author = {Fall, F and Sanguin, H and Fall, D and Tournier, E and Bakhoum, N and Ndiaye, C and Diouf, D and Bâ, AM}, title = {Changes in Intraspecific Diversity of the Arbuscular Mycorrhizal Community Involved in Plant-Plant Interactions Between Sporobolus robustus Kunth and Prosopis juliflora (Swartz) DC Along an Environmental Gradient.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {886-898}, pmid = {34245330}, issn = {1432-184X}, support = {I-1-D-6153-1//International Foundation for Science/ ; }, mesh = {Cebinae ; *Mycorrhizae ; Plants/microbiology ; Poaceae/microbiology ; *Prosopis ; Soil/chemistry ; Soil Microbiology ; }, abstract = {The intensification of biological processes coping with salt stress became a major issue to mitigate land degradation. The Sine-Saloum Delta in Senegal is characterized by salt-affected soils with vegetation dominated by salt-tolerant grass Sporobolus robustus and shrubs like Prosopis juliflora. Plant experiments in controlled conditions suggested that arbuscular mycorrhizal (AM) fungi might be the key actors of facilitation process observed between S. robustus and P. juliflora, but the AM fungal community determinants are largely unknown. The current field-based study aimed at (1) characterizing the environmental drivers (rhizosphere physico-chemical properties, plant type and season) of the AM fungal community along an environmental gradient and (2) identifying the AM fungal taxa that might explain the S. robustus-mediated benefits to P. juliflora. Glomeraceae predominated in the two plants, but a higher richness was observed for S. robustus. The pH and salinity were the main drivers of AM fungal community associated with the two plants, negatively impacting richness and diversity. However, while a negative impact was also observed on mycorrhizal colonization for S. robustus, P. juliflora showed opposite colonization patterns. Furthermore, no change was observed in terms of AM fungal community dissimilarity between the two plants along the environmental gradient as would be expected according to the stress-gradient and complementary hypotheses when a facilitation process occurs. However, changes in intraspecific diversity of shared AM fungal community between the two plants were observed, highlighting 23 AM fungal OTUs associated with both plants and the highest salinity levels. Consequently, the increase of their abundance and frequency along the environmental gradient might suggest their potential role in the facilitation process that can take place between the two plants. Their use in ecological engineering could also represent promising avenues for improving vegetation restoration in saline Senegalese's lands.}, }
@article {pmid34245329, year = {2022}, author = {Rosado, D and Pérez-Losada, M and Severino, R and Xavier, R}, title = {Monitoring Infection and Antibiotic Treatment in the Skin Microbiota of Farmed European Seabass (Dicentrarchus Labrax) Fingerlings.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {789-797}, pmid = {34245329}, issn = {1432-184X}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Aquaculture/methods ; *Bass/genetics/microbiology ; *Fish Diseases/drug therapy/microbiology ; *Microbiota ; Photobacterium/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The microbiota of fish skin, the primary barrier against disease, is highly dynamic and modulated by several factors. In fish aquaculture, disease outbreaks occur mainly during early-life stages, with associated high economic losses. Antibiotic treatments sometimes remain the best option to control bacterial diseases, despite many reported negative impacts of its use on fish and associated microbiota. Notwithstanding, studies monitoring the effects of disease and antibiotic treatment on the microbiota of fingerlings are scarce. We sequenced the bacterial 16S rRNA V4 gene region using a metabarcoding approach to assess the impact of a mixed infection with Photobacterium damselae ssp. piscicida and Vibrio harveyi and subsequent antibiotic treatment with flumequine, on the skin microbiota of farmed seabass (Dicentrarchus labrax) fingerlings. Both infection and antibiotic treatment led to a significant increase in bacterial diversity and core microbial communities and impacted microbiome structure. Dysbiosis was confirmed by changes in the abundance of potential pathogenic and opportunistic bacterial taxa. Skin bacterial metabolic function was also significantly affected by flumequine administration, suggesting a detriment to fish skin health. Our results add to an increasing body of literature, showing how fish microbiome response to infection and antibiotics cannot be easily predicted.}, }
@article {pmid34244148, year = {2021}, author = {Delgado-Baquerizo, M and Eldridge, DJ and Liu, YR and Sokoya, B and Wang, JT and Hu, HW and He, JZ and Bastida, F and Moreno, JL and Bamigboye, AR and Blanco-Pastor, JL and Cano-Díaz, C and Illán, JG and Makhalanyane, TP and Siebe, C and Trivedi, P and Zaady, E and Verma, JP and Wang, L and Wang, J and Grebenc, T and Peñaloza-Bojacá, GF and Nahberger, TU and Teixido, AL and Zhou, XQ and Berdugo, M and Duran, J and Rodríguez, A and Zhou, X and Alfaro, F and Abades, S and Plaza, C and Rey, A and Singh, BK and Tedersoo, L and Fierer, N}, title = {Global homogenization of the structure and function in the soil microbiome of urban greenspaces.}, journal = {Science advances}, volume = {7}, number = {28}, pages = {}, pmid = {34244148}, issn = {2375-2548}, abstract = {The structure and function of the soil microbiome of urban greenspaces remain largely undetermined. We conducted a global field survey in urban greenspaces and neighboring natural ecosystems across 56 cities from six continents, and found that urban soils are important hotspots for soil bacterial, protist and functional gene diversity, but support highly homogenized microbial communities worldwide. Urban greenspaces had a greater proportion of fast-growing bacteria, algae, amoebae, and fungal pathogens, but a lower proportion of ectomycorrhizal fungi than natural ecosystems. These urban ecosystems also showed higher proportions of genes associated with human pathogens, greenhouse gas emissions, faster nutrient cycling, and more intense abiotic stress than natural environments. City affluence, management practices, and climate were fundamental drivers of urban soil communities. Our work paves the way toward a more comprehensive global-scale perspective on urban greenspaces, which is integral to managing the health of these ecosystems and the well-being of human populations.}, }
@article {pmid34243050, year = {2021}, author = {Favere, J and Waegenaar, F and Boon, N and De Gusseme, B}, title = {Online microbial monitoring of drinking water: How do different techniques respond to contaminations in practice?.}, journal = {Water research}, volume = {202}, number = {}, pages = {117387}, doi = {10.1016/j.watres.2021.117387}, pmid = {34243050}, issn = {1879-2448}, mesh = {Bacteria ; *Drinking Water ; *Groundwater ; Water Microbiology ; Water Quality ; }, abstract = {Safeguarding the microbial water quality remains a challenge for drinking water utilities, and because of population growth and climate change, new issues arise regularly. To overcome these problems, biostable drinking water production and water reuse will become increasingly important. In this respect, high-resolution online microbial monitoring during treatment and distribution could prove essential. Here, we present the first scientific and practical comparison of multiple online microbial monitoring techniques in which six commercially available devices were set up in a full-scale drinking water production plant. Both the devices' response towards operational changes and contaminations, as well as their detection limit for different contaminations were evaluated and compared. During normal operation, all devices were able to detect abrupt operational changes such as backwashing of activated carbon filters and interruption of the production process in a fast and sensitive way. To benchmark their response to contaminations, the calculation of a dynamic baseline for sensitive separation between noise and events is proposed. In order of sensitivity, enzymatic analysis, ATP measurement, and flow cytometric fingerprinting were the most performant for detection of rain- and groundwater contaminations (0.01 - 0.1 v%). On the other hand, optical classification and flow cytometric cell counts showed to be more robust techniques, requiring less maintenance and providing direct information about the cell concentration, even though they were still more sensitive than plate counting. The choice for a certain technology will thus depend on the type of application and is a balance between sensitivity, price and maintenance. All things considered, a combination of several devices and use of advanced data analysis such as fingerprinting may be of added value. In general, the strategic implementation of online microbial monitoring as early-warning system will allow for intensive quality control by high-frequency sampling as well as a short event response timeframe.}, }
@article {pmid34242738, year = {2021}, author = {Thompson, RS and Gaffney, M and Hopkins, S and Kelley, T and Gonzalez, A and Bowers, SJ and Vitaterna, MH and Turek, FW and Foxx, CL and Lowry, CA and Vargas, F and Dorrestein, PC and Wright, KP and Knight, R and Fleshner, M}, title = {Ruminiclostridium 5, Parabacteroides distasonis, and bile acid profile are modulated by prebiotic diet and associate with facilitated sleep/clock realignment after chronic disruption of rhythms.}, journal = {Brain, behavior, and immunity}, volume = {97}, number = {}, pages = {150-166}, doi = {10.1016/j.bbi.2021.07.006}, pmid = {34242738}, issn = {1090-2139}, mesh = {Animals ; Bacteroidetes ; *Bile Acids and Salts ; Chromatography, Liquid ; Circadian Rhythm ; Diet ; Male ; *Prebiotics ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; Sleep ; Tandem Mass Spectrometry ; }, abstract = {Chronic disruption of rhythms (CDR) impacts sleep and can result in circadian misalignment of physiological systems which, in turn, is associated with increased disease risk. Exposure to repeated or severe stressors also disturbs sleep and diurnal rhythms. Prebiotic nutrients produce favorable changes in gut microbial ecology, the gut metabolome, and reduce several negative impacts of acute severe stressor exposure, including disturbed sleep, core body temperature rhythmicity, and gut microbial dysbiosis. In light of previous compelling evidence that prebiotic diet broadly reduces negative impacts of acute, severe stressors, we hypothesize that prebiotic diet will also effectively mitigate the negative impacts of chronic disruption of circadian rhythms on physiology and sleep/wake behavior. Male, Sprague Dawley rats were fed diets enriched in prebiotic substrates or calorically matched control chow. After 5 weeks on diet, rats were exposed to CDR (12 h light/dark reversal, weekly for 8 weeks) or remained on undisturbed normal light/dark cycles (NLD). Sleep EEG, core body temperature, and locomotor activity were recorded via biotelemetry in freely moving rats. Fecal samples were collected on experimental days -33, 0 (day of onset of CDR), and 42. Taxonomic identification and relative abundances of gut microbes were measured in fecal samples using 16S rRNA gene sequencing and shotgun metagenomics. Fecal primary, bacterially modified secondary, and conjugated bile acids were measured using liquid chromatography with tandem mass spectrometry (LC-MS/MS). Prebiotic diet produced rapid and stable increases in the relative abundances of Parabacteroides distasonis and Ruminiclostridium 5. Shotgun metagenomics analyses confirmed reliable increases in relative abundances of Parabacteroides distasonis and Clostridium leptum, a member of the Ruminiclostridium genus. Prebiotic diet also modified fecal bile acid profiles; and based on correlational and step-wise regression analyses, Parabacteroides distasonis and Ruminiclostridium 5 were positively associated with each other and negatively associated with secondary and conjugated bile acids. Prebiotic diet, but not CDR, impacted beta diversity. Measures of alpha diversity evenness were decreased by CDR and prebiotic diet prevented that effect. Rats exposed to CDR while eating prebiotic, compared to control diet, more quickly realigned NREM sleep and core body temperature (ClockLab) diurnal rhythms to the altered light/dark cycle. Finally, both cholic acid and Ruminiclostridium 5 prior to CDR were associated with time to realign CBT rhythms to the new light/dark cycle after CDR; whereas both Ruminiclostridium 5 and taurocholic acid prior to CDR were associated with NREM sleep recovery after CDR. These results support our hypothesis and suggest that ingestion of prebiotic substrates is an effective strategy to increase the relative abundance of health promoting microbes, alter the fecal bile acid profile, and facilitate the recovery and realignment of sleep and diurnal rhythms after circadian disruption.}, }
@article {pmid34242413, year = {2021}, author = {Tuganbaev, T and Honda, K}, title = {Non-zero-sum microbiome immune system interactions.}, journal = {European journal of immunology}, volume = {51}, number = {9}, pages = {2120-2136}, pmid = {34242413}, issn = {1521-4141}, mesh = {Adaptive Immunity/immunology ; Enteric Nervous System/*physiology ; Gastrointestinal Microbiome/*immunology ; Gastrointestinal Tract/*immunology/innervation/*microbiology/physiology ; Humans ; Immunity, Innate/immunology ; Symbiosis/immunology ; }, abstract = {Fundamental asymmetries between the host and its microbiome in enzymatic activities and nutrient storage capabilities have promoted mutualistic adaptations on both sides. As a result, the enteric immune system has evolved so as not to cause a zero-sum sterilization of non-self, but rather achieve a non-zero-sum self-reinforcing cooperation with its evolutionary partner the microbiome. In this review, we attempt to integrate the accumulated knowledge of immune-microbiome interactions into an evolutionary framework and trace the pattern of positive immune-microbiome feedback loops across epithelial, enteric nervous system, innate, and adaptive immune circuits. Indeed, the immune system requires commensal signals for its development and function, and reciprocally protects the microbiome from nutrient shortage and pathogen outgrowth. In turn, a healthy microbiome is the result of immune system curatorship as well as microbial ecology. The paradigms of host-microbiome asymmetry and the cooperative nature of their interactions identified in the gut are applicable across all tissues influenced by microbial activities. Incorporation of immune system influences into models of microbiome ecology will be a step forward toward defining what constitutes a healthy human microbiome and guide discoveries of novel host-microbiome mutualistic adaptations that may be harnessed for the promotion of human health.}, }
@article {pmid34241654, year = {2022}, author = {Ahmad, T and Farooq, S and Mirza, DN and Kumar, A and Mir, RA and Riyaz-Ul-Hassan, S}, title = {Insights into the Endophytic Bacterial Microbiome of Crocus sativus: Functional Characterization Leads to Potential Agents that Enhance the Plant Growth, Productivity, and Key Metabolite Content.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {669-688}, pmid = {34241654}, issn = {1432-184X}, mesh = {*Crocus/microbiology ; Endophytes ; Fungi ; *Microbiota ; Plant Development ; }, abstract = {The study was undertaken to unravel the culturable endophytic bacterial microbiome of Crocus sativus L. (saffron crocus) and consequently obtain potential leads to develop plant growth-promoting and biocontrol agents for increased productivity and sustainable cultivation. The endophytes formed 47 different operational taxonomic units (OTUs), spanning over 28 genera. The host was preferentially colonized by the genus Bacillus, followed by Burkholderia and Pantoea, respectively. Several endophytes possessed potential plant growth-promoting properties and inhibitory activities against the specific fungal pathogens of saffron. The endophytes, except for Microbacterium oxydans, did not cause any disease symptoms in the pot experiments. The selected cultures, Burkholderia gladioli, Streptomyces achromogenes, and three species of Bacillus, enhanced the host plant growth significantly. Based on the pot experiment results, two isolates, Bacillus mojavensis CS4EB32 and Burkholderia gladioli E39CS3, were selected for the field experiments. We obtained an increase of 67.5%, 69.8%, and 68.3% in the production of flowers with the individual and collective treatments, respectively. The treatments also enhanced the biomass of the plant and the length and weight of stigmas significantly. The endophyte treatments induced the expression of the pathway genes, resulting in a marked increase in the concentration of apocarotenoids. The study indicates that the dominant endophytes support plant growth and development in nature and present an opportunity for developing microbial formulations for the sustainability of saffron cultivation.}, }
@article {pmid34240513, year = {2021}, author = {Shi, Y and Wang, J and Ao, Y and Han, J and Guo, Z and Liu, X and Zhang, J and Mu, C and Le Roux, X}, title = {Responses of soil N2 O emissions and their abiotic and biotic drivers to altered rainfall regimes and co-occurring wet N deposition in a semi-arid grassland.}, journal = {Global change biology}, volume = {27}, number = {19}, pages = {4894-4908}, doi = {10.1111/gcb.15792}, pmid = {34240513}, issn = {1365-2486}, mesh = {Ecosystem ; *Grassland ; Nitrogen/analysis ; Nitrous Oxide/analysis ; *Soil ; }, abstract = {Global change factors such as changed rainfall regimes and nitrogen (N) deposition contribute to increases in the emission of the greenhouse gas nitrous oxide (N2 O) from the soil. In previous research, N deposition has often been simulated by using a single or a series of N addition events over the course of a year, but wet N deposition actually co-occurs with rainfall. How soil N2 O emissions respond to altered rainfall amount and frequency, wet N deposition, and their interactions is still not fully understood. We designed a three-factor, fully factorial experiment with factors of rainfall amounts (ambient, -30%) rainfall frequency (ambient, ±50%) and wet N deposition (with/without) co-occurring with rainfall in semi-arid grassland mesocosms, and measured N2 O emissions and their possible biotic and abiotic drivers. Across all treatments, reduced rainfall amount and N deposition increased soil N2 O emissions by 35% and 28%, respectively. A significant interactive effect was observed between rainfall amount and N deposition, and to a lesser extent between rainfall frequency and N deposition. Without N deposition, reduced rainfall amount and altered rainfall frequency indirectly affected soil N2 O emissions by changing the abundance of nirK and soil net N mineralization, and the changes in nirK abundance were indirectly driven by soil N availability rather than directly by soil moisture. With N deposition, both the abundance of nirK and the level of soil water-filled pore space contributed to changes in N2 O emissions in response to altered rainfall regimes, and the changes in the abundance of nirK were indirectly driven by plant N uptake and nitrifier (ammonia-oxidizing bacteria) abundance. Our results imply that unlike wetter grassland ecosystems, reduced precipitation may increase N2 O emissions, and N deposition may only slightly increase N2 O emissions in arid and semi-arid N-limited ecosystems that are dominated by grasses with high soil N uptake capacity.}, }
@article {pmid34238491, year = {2021}, author = {Schweyer, L and Pougnet, L}, title = {[Microbial ecology, the understanding of the invisible living].}, journal = {Revue de l'infirmiere}, volume = {70}, number = {272}, pages = {25-26}, doi = {10.1016/j.revinf.2021.04.007}, pmid = {34238491}, issn = {1293-8505}, mesh = {*Ecology ; *Ecosystem ; Humans ; Hygiene ; }, abstract = {Microorganisms are invisible to the naked eye. Hospital hygiene practices are therefore based on the representation that caregivers have of them. This difficulty can generate irrational behavior and fear of blame. Conversely, a better knowledge of the specificities of this invisible living world favors a rationalization of care practices. To do this, caregivers will be able to appropriate the major concepts of microbiology, particularly microbial ecology.}, }
@article {pmid34238316, year = {2021}, author = {Oberman, K and Hovens, I and de Haan, J and Falcao-Salles, J and van Leeuwen, B and Schoemaker, R}, title = {Acute pre-operative ibuprofen improves cognition in a rat model for postoperative cognitive dysfunction.}, journal = {Journal of neuroinflammation}, volume = {18}, number = {1}, pages = {156}, pmid = {34238316}, issn = {1742-2094}, mesh = {Animals ; Anti-Inflammatory Agents, Non-Steroidal/*administration &amp; dosage ; Cognition/*drug effects/physiology ; Hippocampus/drug effects/metabolism ; Ibuprofen/*administration &amp; dosage ; Male ; Maze Learning/drug effects/physiology ; Postoperative Cognitive Complications/*drug therapy/metabolism/psychology ; Preoperative Care/*methods ; Rats ; Rats, Wistar ; }, abstract = {BACKGROUND: Inflammation is considered a key factor in the development of postoperative cognitive dysfunction (POCD). Therefore, we hypothesized that pre-operative anti-inflammatory treatment with ibuprofen would inhibit POCD in our rat-model.<br><br>METHODS: Male Wistar rats of 3 or 23 months old received a single injection of ibuprofen (15 mg/kg i.p.) or were control handled before abdominal surgery. Timed blood and fecal samples were collected for analyses of inflammation markers and gut microbiome changes. Behavioral testing was performed from 9 to 14 days after surgery, in the open field, novel object- and novel location-recognition tests and Morris water maze. Neuroinflammation and neurogenesis were assessed by immune histochemistry after sacrifice on postoperative day 14.<br><br>RESULTS: Ibuprofen improved short-term spatial memory in the novel location recognition test, and increased hippocampal neurogenesis. However, these effects were associated with increased hippocampal microglia activity. Whereas plasma cytokine levels (IL1-&#x3b2;, IL6, IL10, and TNF&#x3b1;) were not significantly affected, VEGF levels increased and IFABP levels decreased after ibuprofen. Long-term memory in the Morris water maze was not significantly improved by ibuprofen. The gut microbiome was neither significantly affected by surgery nor by ibuprofen treatment. In general, effects in aged rats appeared similar to those in young rats, though less pronounced.<br><br>CONCLUSION: A single injection of ibuprofen before surgery improved hippocampus-associated short-term memory after surgery and increased neurogenesis. However, this favorable outcome seemed not attributable to inhibition of (neuro)inflammation. Potential contributions of intestinal and blood-brain barrier integrity need further investigation. Although less pronounced compared to young rats, effects in aged rats indicate that even elderly individuals could benefit from ibuprofen treatment.}, }
@article {pmid34235554, year = {2022}, author = {Buysse, M and Binetruy, F and Leibson, R and Gottlieb, Y and Duron, O}, title = {Ecological Contacts and Host Specificity Promote Replacement of Nutritional Endosymbionts in Ticks.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {776-788}, pmid = {34235554}, issn = {1432-184X}, support = {EVOSYM//Ministry of Science and Technology, Israel/ ; EVOSYM//centre national de la recherche scientifique (CNRS)/ ; ANR-10-LAX-25-01//Agence Nationale de la Recherche (FR)/ ; ISF No. 1074/18//Israel science foundation/ ; }, mesh = {Animals ; *Francisella ; Host Specificity ; Phylogeny ; Symbiosis ; *Ticks ; }, abstract = {Symbiosis with vitamin-provisioning microbes is essential for the nutrition of animals with some specialized feeding habits. While coevolution favors the interdependence between symbiotic partners, their associations are not necessarily stable: Recently acquired symbionts can replace ancestral symbionts. In this study, we demonstrate successful replacement by Francisella-like endosymbionts (-LE), a group of B-vitamin-provisioning endosymbionts, across tick communities driven by horizontal transfers. Using a broad collection of Francisella-LE-infected tick species, we determined the diversity of Francisella-LE haplotypes through a multi-locus strain typing approach and further characterized their phylogenetic relationships and their association with biological traits of their tick hosts. The patterns observed showed that Francisella-LE commonly transfer through similar ecological networks and geographic distributions shared among different tick species and, in certain cases, through preferential shuffling across congeneric tick species. Altogether, these findings reveal the importance of geographic, ecological, and phylogenetic proximity in shaping the replacement pattern in which new nutritional symbioses are initiated.}, }
@article {pmid34232732, year = {2021}, author = {Malki, K and Sawaya, NA and Tisza, MJ and Coutinho, FH and Rosario, K and Székely, AJ and Breitbart, M}, title = {Spatial and Temporal Dynamics of Prokaryotic and Viral Community Assemblages in a Lotic System (Manatee Springs, Florida).}, journal = {Applied and environmental microbiology}, volume = {87}, number = {18}, pages = {e0064621}, pmid = {34232732}, issn = {1098-5336}, mesh = {Florida ; Fresh Water/microbiology ; Genome, Viral ; Natural Springs/*microbiology ; *Prokaryotic Cells ; RNA, Ribosomal, 16S ; *Viruses/genetics ; Water Microbiology ; }, abstract = {Flow from high-magnitude springs fed by the Floridan aquifer system contributes hundreds of liters of water per second to rivers, creating unique lotic systems. Despite their importance as freshwater sources and their contributions to the state's major rivers, little is known about the composition and spatiotemporal variability of prokaryotic and viral communities of these spring systems or their influence on downstream river sites. At four time points throughout a year, we determined the abundance and diversity of prokaryotic and viral communities at three sites within the first-magnitude Manatee Springs system (the spring head where water emerges from the aquifer, a mixed region where the spring run ends, and a downstream site in the Suwannee River). The abundance of prokaryotes and virus-like particles increased 100-fold from the spring head to the river and few members from the head communities persisted in the river at low abundance, suggesting the springs play a minor role in seeding downstream communities. Prokaryotic and viral communities within Manatee Springs clustered by site, with seasonal variability likely driven by flow. As water flowed through the system, microbial community composition was affected by changes in physiochemical parameters and community coalescence. Evidence of species sorting and mass effects could be seen in the assemblages. Greater temporal fluctuations were observed in prokaryotic and viral community composition with increasing distance from the spring outflow, reflecting the relative stability of the groundwater environment, and comparisons to springs from prior work reaffirmed that distinct first-magnitude springs support unique communities. IMPORTANCE Prokaryotic and viral communities are central to food webs and biogeochemical processes in aquatic environments, where they help maintain ecosystem health. The Floridan aquifer system (FAS), which is the primary drinking water source for millions of people in the southeastern United States, contributes large amounts of freshwater to major river systems in Florida through its springs. However, there is a paucity of information regarding the spatiotemporal dynamics of microbial communities in these essential flowing freshwater systems. This work explored the prokaryotic and viral communities in a first-magnitude spring system fed by the FAS that discharges millions of liters of water per day into the Suwannee River. This study examined microbial community composition through space and time as well as the environmental parameters and metacommunity assembly mechanisms that shape these communities, providing a foundational understanding for monitoring future changes.}, }
@article {pmid34231344, year = {2021}, author = {Ossowicki, A and Raaijmakers, JM and Garbeva, P}, title = {Disentangling soil microbiome functions by perturbation.}, journal = {Environmental microbiology reports}, volume = {13}, number = {5}, pages = {582-590}, pmid = {34231344}, issn = {1758-2229}, mesh = {Bacteria ; Microbial Consortia ; *Microbiota/genetics ; *Soil ; Soil Microbiology ; }, abstract = {Soil biota contribute to diverse soil ecosystem services such as greenhouse gas mitigation, carbon sequestration, pollutant degradation, plant disease suppression and nutrient acquisition for plant growth. Here, we provide detailed insight into different perturbation approaches to disentangle soil microbiome functions and to reveal the underlying mechanisms. By applying perturbation, one can generate compositional and functional shifts of complex microbial communities in a controlled way. Perturbations can reduce microbial diversity, diminish the abundance of specific microbial taxa and thereby disturb the interactions within the microbial consortia and with their eukaryotic hosts. Four different microbiome perturbation approaches, namely selective heat, specific biocides, dilution-to-extinction and genome editing are the focus of this mini-review. We also discuss the potential of perturbation approaches to reveal the tipping point at which specific soil functions are lost and to link this change to key microbial taxa involved in specific microbiome-associated phenotypes.}, }
@article {pmid34231036, year = {2022}, author = {Viana, TA and Barbosa, WF and Jojoa, LLB and Bernardes, RC and da Silva, JS and Jacobs-Lorena, M and Martins, GF}, title = {A Genetically Modified Anti-Plasmodium Bacterium Is Harmless to the Foragers of the Stingless Bee Partamona helleri.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {766-775}, pmid = {34231036}, issn = {1432-184X}, support = {CBB-APQ-00247-14//Funda&#xe7;&#xe3;o de Apoio ao Ensino, Pesquisa e Assist&#xea;ncia do Hospital das Cl&#xed;nicas da Faculdade de Medicina de Ribeir&#xe3;o Preto da Universidade de S&#xe3;o Paulo (BR)/ ; R01 AI031478/AI/NIAID NIH HHS/United States ; R01AI031478/NH/NIH HHS/United States ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 301725/2019-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; R01 AI051366/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bees ; Brazil ; *Mosquito Vectors ; *Serratia/genetics ; }, abstract = {Paratransgenesis consists of genetically engineering an insect symbiont to control vector-borne diseases. Biosafety assessments are a prerequisite for the use of genetically modified organisms (GMOs). Assessments rely on the measurement of the possible impacts of GMOs on different organisms, including beneficial organisms, such as pollinators. The bacterium Serratia AS1 has been genetically modified to express anti-Plasmodium effector proteins and does not impose a fitness cost on mosquitoes that carry it. In the present study, we assessed the impact of this bacterium on the native bee Partamona helleri (Meliponini), an ecologically important species in Brazil. Serratia eGFP AS1 (recombinant strain) or a wild strain of Serratia marcescens were suspended in a sucrose solution and fed to foragers, followed by measurements of survival, feeding rate, and behavior (walking and flying). These bacteria did not change any of the variables measured at 24, 72, and 144 h after the onset of the experiment. Recombinant and wild bacteria were detected in the homogenates of digestive tract during the 144 h period analyzed, but their numbers decreased with time. The recombinant strain was detected in the midgut at 24 h and in the hindgut at 72 h and 144 h after the onset of the experiment under the fluorescent microscope. As reported for mosquitoes, Serratia eGFP AS1 did not compromise the foragers of P. helleri, an ecologically relevant bee.}, }
@article {pmid34229570, year = {2022}, author = {Rizwan, T and Kothidar, A and Meghwani, H and Sharma, V and Shobhawat, R and Saini, R and Vaishnav, HK and Singh, V and Pratap, M and Sihag, H and Kumar, S and Dey, JK and Dey, SK}, title = {Comparative analysis of SARS-CoV-2 envelope viroporin mutations from COVID-19 deceased and surviving patients revealed implications on its ion-channel activities and correlation with patient mortality.}, journal = {Journal of biomolecular structure &amp; dynamics}, volume = {40}, number = {20}, pages = {10454-10469}, doi = {10.1080/07391102.2021.1944319}, pmid = {34229570}, issn = {1538-0254}, mesh = {Humans ; *COVID-19/mortality/virology ; Mutation ; *SARS-CoV-2/genetics ; *Viroporin Proteins/genetics ; }, abstract = {One major obstacle in designing a successful therapeutic regimen to combat COVID-19 pandemic is the frequent occurrence of mutations in the SARS-CoV-2 resulting in patient to patient variations. Out of the four structural proteins of SARS-CoV-2 namely, spike, envelope, nucleocapsid and membrane, envelope protein governs the virus pathogenicity and induction of acute-respiratory-distress-syndrome which is the major cause of death in COVID-19 patients. These effects are facilitated by the viroporin (ion-channel) like activities of the envelope protein. Our current work reports metagenomic analysis of envelope protein at the amino acid sequence level through mining all the available SARS-CoV-2 genomes from the GISAID and coronapp servers. We found majority of mutations in envelope protein were localized at or near PDZ binding motif. Our analysis also demonstrates that the acquired mutations might have important implications on its structure and ion-channel activity. A statistical correlation between specific mutations (e.g. F4F, R69I, P71L, L73F) with patient mortalities were also observed, based on the patient data available for 18,691 SARS-CoV-2-genomes in the GISAID database till 30 April 2021. Albeit, whether these mutations exist as the cause or the effect of co-infections and/or co-morbid disorders within COVID-19 patients is still unclear. Moreover, most of the current vaccine and therapeutic interventions are revolving around spike protein. However, emphasizing on envelope protein's (1) conserved epitopes, (2) pathogenicity attenuating mutations, and (3) mutations present in the deceased patients, as reported in our present study, new directions to the ongoing efforts of therapeutic developments against COVID-19 can be achieved by targeting envelope viroporin.}, }
@article {pmid34228269, year = {2021}, author = {Agustí, A and Campillo, I and Balzano, T and Benítez-Páez, A and López-Almela, I and Romaní-Pérez, M and Forteza, J and Felipo, V and Avena, NM and Sanz, Y}, title = {Bacteroides uniformis CECT 7771 Modulates the Brain Reward Response to Reduce Binge Eating and Anxiety-Like Behavior in Rat.}, journal = {Molecular neurobiology}, volume = {58}, number = {10}, pages = {4959-4979}, pmid = {34228269}, issn = {1559-1182}, support = {AGL2014-52101-P//Ministry of Science, Innovationa and Universities (MCIU, Spain)/ ; AGL2017-88801-P//Ministry of Science, Innovation and Universities (MCIU,Spain)/ ; PROMETEO/2019/015//Conselleria de Educaci&#xf3;n, Investigaci&#xf3;n, Cultura y Deporte de la Comunidad valenciana/ ; AGL2017-88801-P//Ministry of Science, Innovation and Universities (MCIU, Spain)/ ; PTA//Ministry of Science, Innovation and Univesities (MCIU, Spain)/ ; }, mesh = {Animals ; Anxiety/*metabolism/therapy ; Bacteroides/isolation &amp; purification/*metabolism ; Binge-Eating Disorder/*metabolism/therapy ; Brain/*metabolism ; Gastrointestinal Microbiome/*physiology ; Humans ; Infant, Newborn ; Male ; Microdialysis/methods ; Rats ; Rats, Inbred WKY ; *Reward ; }, abstract = {Food addiction (FA) is characterized by behavioral and neurochemical changes linked to loss of food intake control. Gut microbiota may influence appetite and food intake via endocrine and neural routes. The gut microbiota is known to impact homeostatic energy mechanisms, but its role in regulating the reward system is less certain. We show that the administration of Bacteroides uniformis CECT 7771 (B. uniformis) in a rat FA model impacts on the brain reward response, ameliorating binge eating and decreasing anxiety-like behavior. These effects are mediated, at least in part, by changes in the levels of dopamine, serotonin, and noradrenaline in the nucleus accumbens and in the expression of dopamine D1 and D2 receptors in the prefrontal cortex and intestine. B. uniformis reverses the fasting-induced microbiota changes and increases the abundance of species linked to healthy metabolotypes. Our data indicate that microbiota-based interventions might help to control compulsive overeating by modulating the reward response.}, }
@article {pmid34228196, year = {2022}, author = {de Menezes, GCA and Câmara, PEAS and Pinto, OHB and Convey, P and Carvalho-Silva, M and Simões, JC and Rosa, CA and Rosa, LH}, title = {Fungi in the Antarctic Cryosphere: Using DNA Metabarcoding to Reveal Fungal Diversity in Glacial Ice from the Antarctic Peninsula Region.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {647-657}, pmid = {34228196}, issn = {1432-184X}, mesh = {Animals ; Antarctic Regions ; *Basidiomycota/genetics ; *DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; Fungi/genetics ; Ice ; }, abstract = {We assessed fungal diversity present in glacial from the Antarctic Peninsula using DNA metabarcoding through high-throughput sequencing (HTS). We detected a total of 353,879 fungal DNA reads, representing 94 genera and 184 taxa, in glacial ice fragments obtained from seven sites in the north-west Antarctic Peninsula and South Shetland Islands. The phylum Ascomycota dominated the sequence diversity, followed by Basidiomycota and Mortierellomycota. Penicillium sp., Cladosporium sp., Penicillium atrovenetum, Epicoccum nigrum, Pseudogymnoascus sp. 1, Pseudogymnoascus sp. 2, Phaeosphaeriaceae sp. and Xylaria grammica were the most dominant taxa, respectively. However, the majority of the fungal diversity comprised taxa of rare and intermediate relative abundance, predominately known mesophilic fungi. High indices of diversity and richness were calculated, along with moderate index of dominance, which varied among the different sampling sites. Only 26 (14%) of the total fungal taxa detected were present at all sampling sites. The identified diversity was dominated by saprophytic taxa, followed by known plant and animal pathogens and a low number of symbiotic fungi. Our data suggest that Antarctic glacial ice may represent a hotspot of previously unreported fungal diversity; however, further studies are required to integrate HTS and culture approaches to confirm viability of the taxa detected.}, }
@article {pmid34227830, year = {2021}, author = {McDaniel, EA and Moya-Flores, F and Keene Beach, N and Camejo, PY and Oyserman, BO and Kizaric, M and Khor, EH and Noguera, DR and McMahon, KD}, title = {Metabolic Differentiation of Co-occurring Accumulibacter Clades Revealed through Genome-Resolved Metatranscriptomics.}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0047421}, pmid = {34227830}, issn = {2379-5077}, support = {//MINEDUC | Comisi&#xf3;n Nacional de Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica (CONICYT)/ ; MCB-1518130//National Science Foundation (NSF)/ ; Department of Bacteriology//University of Wisconsin-Madison (UW)/ ; }, abstract = {Natural microbial communities consist of closely related taxa that may exhibit phenotypic differences and inhabit distinct niches. However, connecting genetic diversity to ecological properties remains a challenge in microbial ecology due to the lack of pure cultures across the microbial tree of life. "Candidatus Accumulibacter phosphatis" (Accumulibacter) is a polyphosphate-accumulating organism that contributes to the enhanced biological phosphorus removal (EBPR) biotechnological process for removing excess phosphorus from wastewater and preventing eutrophication from downstream receiving waters. Distinct Accumulibacter clades often coexist in full-scale wastewater treatment plants and laboratory-scale enrichment bioreactors and have been hypothesized to inhabit distinct ecological niches. However, since individual strains of the Accumulibacter lineage have not been isolated in pure culture to date, these predictions have been made solely on genome-based comparisons and enrichments with varying strain compositions. Here, we used genome-resolved metagenomics and metatranscriptomics to explore the activity of coexisting Accumulibacter strains in an engineered bioreactor environment. We obtained four high-quality genomes of Accumulibacter strains that were present in the bioreactor ecosystem, one of which is a completely contiguous draft genome scaffolded with long Nanopore reads. We identified core and accessory genes to investigate how gene expression patterns differed among the dominating strains. Using this approach, we were able to identify putative pathways and functions that may confer distinct functions to Accumulibacter strains and provide key functional insights into this biotechnologically significant microbial lineage. IMPORTANCE "Candidatus Accumulibacter phosphatis" is a model polyphosphate-accumulating organism that has been studied using genome-resolved metagenomics, metatranscriptomics, and metaproteomics to understand the EBPR process. Within the Accumulibacter lineage, several similar but diverging clades are defined by the shared sequence identity of the polyphosphate kinase (ppk1) locus. These clades are predicted to have key functional differences in acetate uptake rates, phage defense mechanisms, and nitrogen-cycling capabilities. However, such hypotheses have largely been made based on gene content comparisons of sequenced Accumulibacter genomes, some of which were obtained from different systems. Here, we performed time series genome-resolved metatranscriptomics to explore gene expression patterns of coexisting Accumulibacter clades in the same bioreactor ecosystem. Our work provides an approach for elucidating ecologically relevant functions based on gene expression patterns between closely related microbial populations.}, }
@article {pmid34227829, year = {2021}, author = {Trojan, D and Garcia-Robledo, E and Meier, DV and Hausmann, B and Revsbech, NP and Eichorst, SA and Woebken, D}, title = {Microaerobic Lifestyle at Nanomolar O2 Concentrations Mediated by Low-Affinity Terminal Oxidases in Abundant Soil Bacteria.}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0025021}, pmid = {34227829}, issn = {2379-5077}, support = {P 26392/FWF_/Austrian Science Fund FWF/Austria ; FEDER-UCA18-107225//EC | European Regional Development Fund (ERDF)/ ; P26392-B20//Austrian Science Fund (FWF)/ ; }, abstract = {High-affinity terminal oxidases (TOs) are believed to permit microbial respiration at low oxygen (O2) levels. Genes encoding such oxidases are widespread, and their existence in microbial genomes is taken as an indicator for microaerobic respiration. We combined respiratory kinetics determined via highly sensitive optical trace O2 sensors, genomics, and transcriptomics to test the hypothesis that high-affinity TOs are a prerequisite to respire micro- and nanooxic concentrations of O2 in environmentally relevant model soil organisms: acidobacteria. Members of the Acidobacteria harbor branched respiratory chains terminating in low-affinity (caa3-type cytochrome c oxidases) as well as high-affinity (cbb3-type cytochrome c oxidases and/or bd-type quinol oxidases) TOs, potentially enabling them to cope with varying O2 concentrations. The measured apparent Km (Km(app)) values for O2 of selected strains ranged from 37 to 288 nmol O2 liter[-1], comparable to values previously assigned to low-affinity TOs. Surprisingly, we could not detect the expression of the conventional high-affinity TO (cbb3 type) at micro- and nanomolar O2 concentrations but detected the expression of low-affinity TOs. To the best of our knowledge, this is the first observation of microaerobic respiration imparted by low-affinity TOs at O2 concentrations as low as 1 nM. This challenges the standing hypothesis that a microaerobic lifestyle is exclusively imparted by the presence of high-affinity TOs. As low-affinity TOs are more efficient at generating ATP than high-affinity TOs, their utilization could provide a great benefit, even at low-nanomolar O2 levels. Our findings highlight energy conservation strategies that could promote the success of Acidobacteria in soil but might also be important for as-yet-unrevealed microorganisms. IMPORTANCE Low-oxygen habitats are widely distributed on Earth, ranging from the human intestine to soils. Microorganisms are assumed to have the capacity to respire low O2 concentrations via high-affinity terminal oxidases. By utilizing strains of a ubiquitous and abundant group of soil bacteria, the Acidobacteria, and combining respiration kinetics, genomics, and transcriptomics, we provide evidence that these microorganisms use the energetically more efficient low-affinity terminal oxidases to respire low-nanomolar O2 concentrations. This questions the standing hypothesis that the ability to respire traces of O2 stems solely from the activity of high-affinity terminal oxidases. We propose that this energetically efficient strategy extends into other, so-far-unrevealed microbial clades. Our findings also demonstrate that physiological predictions regarding the utilization of different O2 concentrations based solely on the presence or absence of terminal oxidases in bacterial genomes can be misleading.}, }
@article {pmid34226946, year = {2022}, author = {Tan, MH and Loke, S and Croft, LJ and Gleason, FH and Lange, L and Pilgaard, B and Trevathan-Tackett, SM}, title = {Correction to: First Genome of Labyrinthula sp., an Opportunistic Seagrass Pathogen, Reveals Novel Insight into Marine Protist Phylogeny, Ecology and CAZyme Cell-Wall Degradation.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {822}, doi = {10.1007/s00248-021-01807-7}, pmid = {34226946}, issn = {1432-184X}, }
@article {pmid34225812, year = {2021}, author = {Stothart, MR and Newman, AEM}, title = {Shades of grey: host phenotype dependent effect of urbanization on the bacterial microbiome of a wild mammal.}, journal = {Animal microbiome}, volume = {3}, number = {1}, pages = {46}, pmid = {34225812}, issn = {2524-4671}, abstract = {BACKGROUND: Host-associated microbiota are integral to the ecology of their host and may help wildlife species cope with rapid environmental change. Urbanization is a globally replicated form of severe environmental change which we can leverage to better understand wildlife microbiomes. Does the colonization of separate cities result in parallel changes in the intestinal microbiome of wildlife, and if so, does within-city habitat heterogeneity matter? Using 16S rRNA gene amplicon sequencing, we quantified the effect of urbanization (across three cities) on the microbiome of eastern grey squirrels (Sciurus carolinensis). Grey squirrels are ubiquitous in rural and urban environments throughout their native range, across which they display an apparent coat colour polymorphism (agouti, black, intermediate).<br><br>RESULTS: Grey squirrel microbiomes differed between rural and city environments; however, comparable variation was explained by habitat heterogeneity within cities. Our analyses suggest that operational taxonomic unit (OTU) community structure was more strongly influenced by local environmental conditions (rural and city forests versus human built habitats) than urbanization of the broader landscape (city versus rural). The bacterial genera characterizing the microbiomes of built-environment squirrels are thought to specialize on host-derived products and have been linked in previous research to low fibre diets. However, despite an effect of urbanization at fine spatial scales, phylogenetic patterns in the microbiome were coat colour phenotype dependent. City and built-environment agouti squirrels displayed greater phylogenetic beta-dispersion than those in rural or forest environments, and null modelling results indicated that the phylogenetic structure of urban agouti squirrels did not differ greatly from stochastic expectations.<br><br>CONCLUSIONS: Squirrel microbiomes differed between city and rural environments, but differences of comparable magnitude were observed between land classes at a within-city scale. We did not observe strong evidence that inter-environmental differences were the result of disparate selective pressures. Rather, our results suggest that microbiota dispersal and ecological drift are integral to shaping the inter-environmental differences we observed. However, these processes were partly mediated by squirrel coat colour phenotype. Given a well-known urban cline in squirrel coat colour melanism, grey squirrels provide a useful free-living system with which to study how host genetics mediate environment x microbiome interactions.}, }
@article {pmid34223947, year = {2022}, author = {Jiao, L and Kourkoumpetis, T and Hutchinson, D and Ajami, NJ and Hoffman, K and White, DL and Graham, DY and Hair, C and Shah, R and Kanwal, F and Jarbrink-Sehgal, M and Husain, N and Hernaez, R and Hou, J and Cole, R and Velez, M and Ketwaroo, G and Kramer, J and El-Serag, HB and Petrosino, JF}, title = {Spatial Characteristics of Colonic Mucosa-Associated Gut Microbiota in Humans.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {811-821}, pmid = {34223947}, issn = {1432-184X}, support = {I01 CX001430/CX/CSRD VA/United States ; R01 CA172880/CA/NCI NIH HHS/United States ; P30 DK56338/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Colon/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Intestinal Mucosa/microbiology ; RNA, Ribosomal, 16S/genetics ; Verrucomicrobia/genetics ; }, abstract = {Limited data exist on the spatial distribution of the colonic bacteria in humans. We collected the colonic biopsies from five segments of 27 polyp-free adults and collected feces from 13 of them. We sequenced the V4 region of the bacterial 16S rRNA gene using the MiSeq platform. The sequencing data were assigned to the amplicon sequence variant (ASV) using SILVA. Biodiversity and the relative abundance of the ASV were compared across the colonic segments and between the rectal and fecal samples. Bacterial functional capacity was assessed using Tax4fun. Each individual had a unique bacterial community composition (Weighted Bray-Curtis P value = 0.001). There were no significant differences in richness, evenness, community composition, and the taxonomic structure across the colon segments in all the samples. Firmicutes (47%), Bacteroidetes (39%), and Proteobacteria (6%) were the major phyla in all segments, followed by Verrucomicrobia, Fusobacteria, Desulfobacterota, and Actinobacteria. There were 15 genera with relative abundance > 1%, including Bacteroides, Faecalibacterium, Escherichia/Shigella, Sutterella, Akkermansia, Parabacteroides, Prevotella, Lachnoclostridium, Alistipes, Fusobacterium, Erysipelatoclostridium, and four Lachnospiraceae family members. Intra-individually, the community compositional dissimilarity was the greatest between the cecum and the rectum. There were significant differences in biodiversity and the taxonomic structure between the rectal and fecal bacteria. The bacterial community composition and structure were homogeneous across the large intestine in adults. The inter-individual variability of the bacteria was greater than inter-segment variability. The rectal and fecal bacteria differed in the community composition and structure.}, }
@article {pmid34223869, year = {2021}, author = {Smercina, DN and Bailey, VL and Hofmockel, KS}, title = {Micro on a macroscale: relating microbial-scale soil processes to global ecosystem function.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {7}, pages = {}, doi = {10.1093/femsec/fiab091}, pmid = {34223869}, issn = {1574-6941}, mesh = {Climate Change ; Ecology ; *Ecosystem ; *Soil ; Soil Microbiology ; }, abstract = {Soil microorganisms play a key role in driving major biogeochemical cycles and in global responses to climate change. However, understanding and predicting the behavior and function of these microorganisms remains a grand challenge for soil ecology due in part to the microscale complexity of soils. It is becoming increasingly clear that understanding the microbial perspective is vital to accurately predicting global processes. Here, we discuss the microbial perspective including the microbial habitat as it relates to measurement and modeling of ecosystem processes. We argue that clearly defining and quantifying the size, distribution and sphere of influence of microhabitats is crucial to managing microbial activity at the ecosystem scale. This can be achieved using controlled and hierarchical sampling designs. Model microbial systems can provide key data needed to integrate microhabitats into ecosystem models, while adapting soil sampling schemes and statistical methods can allow us to collect microbially-focused data. Quantifying soil processes, like biogeochemical cycles, from a microbial perspective will allow us to more accurately predict soil functions and address long-standing unknowns in soil ecology.}, }
@article {pmid34220760, year = {2021}, author = {Ceron-Chafla, P and Chang, YT and Rabaey, K and van Lier, JB and Lindeboom, REF}, title = {Directional Selection of Microbial Community Reduces Propionate Accumulation in Glycerol and Glucose Anaerobic Bioconversion Under Elevated pCO2.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {675763}, pmid = {34220760}, issn = {1664-302X}, abstract = {Volatile fatty acid accumulation is a sign of digester perturbation. Previous work showed the thermodynamic limitations of hydrogen and CO2 in syntrophic propionate oxidation under elevated partial pressure of CO2 (pCO2). Here we study the effect of directional selection under increasing substrate load as a strategy to restructure the microbial community and induce cross-protection mechanisms to improve glucose and glycerol conversion performance under elevated pCO2. After an adaptive laboratory evolution (ALE) process, viable cell density increased and predominant microbial groups were modified: an increase in Methanosaeta and syntrophic propionate oxidizing bacteria (SPOB) associated with the Smithella genus was found with glycerol as the substrate. A modest increase in SPOB along with a shift in the predominance of Methanobacterium toward Methanosaeta was observed with glucose as the substrate. The evolved inoculum showed affected diversity within archaeal spp. under 5 bar initial pCO2; however, higher CH4 yield resulted from enhanced propionate conversion linked to the community shifts and biomass adaptation during the ALE process. Moreover, the evolved inoculum attained increased cell viability with glucose and a marginal decrease with glycerol as the substrate. Results showed differences in terms of carbon flux distribution using the evolved inoculum under elevated pCO2: glucose conversion resulted in a higher cell density and viability, whereas glycerol conversion led to higher propionate production whose enabled conversion reflected in increased CH4 yield. Our results highlight that limited propionate conversion at elevated pCO2 resulted from decreased cell viability and low abundance of syntrophic partners. This limitation can be mitigated by promoting alternative and more resilient SPOB and building up biomass adaptation to environmental conditions via directional selection of microbial community.}, }
@article {pmid34219185, year = {2021}, author = {Jani, K and Bandal, J and Shouche, Y and Shafi, S and Azhar, EI and Zumla, A and Sharma, A}, title = {Extended Ecological Restoration of Bacterial Communities in the Godavari River During the COVID-19 Lockdown Period: a Spatiotemporal Meta-analysis.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {365-376}, pmid = {34219185}, issn = {1432-184X}, support = {IA/E/17/1/503700/WTDBT_/DBT-Wellcome Trust India Alliance/India ; BT/Coord.II/01/03/2016//Department of Biotechnology , Ministry of Science and Technology/ ; }, mesh = {Bacteria/classification/*isolation &amp; purification ; COVID-19/epidemiology/prevention &amp; control ; Communicable Disease Control/*legislation &amp; jurisprudence ; Drug Resistance, Bacterial ; *Ecosystem ; Environmental Monitoring ; Hinduism ; Human Activities ; India/epidemiology ; Principal Component Analysis ; Rivers/*microbiology ; }, abstract = {The unprecedented COVID-19 pandemic has had major impact on human health worldwide. Whilst national and international COVID-19 lockdown and travel restriction measures have had widespread negative impact on economies and mental health, they may have beneficial effect on the environment, reducing air and water pollution. Mass bathing events (MBE) also known as Kumbh Mela are known to cause perturbations of the ecosystem affecting resilient bacterial populations within water of rivers in India. Lockdowns and travel restrictions provide a unique opportunity to evaluate the impact of minimum anthropogenic activity on the river water ecosystem and changes in bacterial populations including antibiotic-resistant strains. We performed a spatiotemporal meta-analysis of bacterial communities of the Godavari River, India. Targeted metagenomics revealed a 0.87-fold increase in the bacterial diversity during the restricted activity of lockdown. A significant increase in the resilient phyla, viz. Proteobacteria (70.6%), Bacteroidetes (22.5%), Verrucomicrobia (1.8%), Actinobacteria (1.2%) and Cyanobacteria (1.1%), was observed. There was minimal incorporation of allochthonous bacterial communities of human origin. Functional profiling using imputed metagenomics showed reduction in infection and drug resistance genes by - 0.71-fold and - 0.64-fold, respectively. These observations may collectively indicate the positive implications of COVID-19 lockdown measures which restrict MBE, allowing restoration of the river ecosystem and minimise the associated public health risk.}, }
@article {pmid34218293, year = {2022}, author = {Németh, JB and Knapp, DG and Kósa, A and Hegedűs, P&#xc1; and Herczeg, G and Vági, P and Kovács, GM}, title = {Micro-scale Experimental System Coupled with Fluorescence-based Estimation of Fungal Biomass to Study Utilisation of Plant Substrates.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {714-723}, pmid = {34218293}, issn = {1432-184X}, support = {J&#xe1;nos Bolyai Research Scholarship//Magyar Tudom&#xe1;nyos Akad&#xe9;mia/ ; K109102//Hungarian Scientific Research Fund/ ; K105517//Hungarian Scientific Research Fund/ ; ELTE Thematic Excellence Program 2020 (TKP2020-IKA-05)//Nemzeti Kutat&#xe1;si Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal/ ; }, mesh = {Biomass ; *Ecosystem ; *Endophytes ; Fluorescence ; Fungi/metabolism ; Plant Roots/microbiology ; }, abstract = {The degradation capacity and utilisation of complex plant substrates are crucial for the functioning of saprobic fungi and different plant symbionts with fundamental functions in ecosystems. Measuring the growth capacity and biomass of fungi on such systems is a challenging task. We established a new micro-scale experimental setup using substrates made of different plant species and organs as media for fungal growth. We adopted and tested a reliable and simple titration-based method for the estimation of total fungal biomass within the substrates using fluorescence-labelled lectin. We found that the relationship between fluorescence intensity and fungal dry weight was strong and linear but differed among fungi. The effect of the plant organ (i.e. root vs. shoot) used as substrate on fungal growth differed among plant species and between root endophytic fungal species. The novel microscale experimental system is useful for screening the utilisation of different substrates, which can provide insight into the ecological roles and functions of fungi. Furthermore, our fungal biomass estimation method has applications in various fields. As the estimation is based on the fungal cell wall, it measures the total cumulative biomass produced in a certain environment.}, }
@article {pmid34218232, year = {2021}, author = {Huang, YM and Straub, D and Kappler, A and Smith, N and Blackwell, N and Kleindienst, S}, title = {A Novel Enrichment Culture Highlights Core Features of Microbial Networks Contributing to Autotrophic Fe(II) Oxidation Coupled to Nitrate Reduction.}, journal = {Microbial physiology}, volume = {31}, number = {3}, pages = {280-295}, doi = {10.1159/000517083}, pmid = {34218232}, issn = {2673-1673}, mesh = {Carbon Cycle ; *Ferrous Compounds ; *Nitrates ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Fe(II) oxidation coupled to nitrate reduction (NRFO) has been described for many environments. Yet very few autotrophic microorganisms catalysing NRFO have been cultivated and their diversity, as well as their mechanisms for NRFO in situ remain unclear. A novel autotrophic NRFO enrichment culture, named culture BP, was obtained from freshwater sediment. After more than 20 transfers, culture BP oxidized 8.22 mM of Fe(II) and reduced 2.42 mM of nitrate within 6.5 days under autotrophic conditions. We applied metagenomic, metatranscriptomic, and metaproteomic analyses to culture BP to identify the microorganisms involved in autotrophic NRFO and to unravel their metabolism. Overall, twelve metagenome-assembled genomes (MAGs) were constructed, including a dominant Gallionellaceae sp. MAG (≥71% relative abundance). Genes and transcripts associated with potential Fe(II) oxidizers in culture BP, identified as a Gallionellaceae sp., Noviherbaspirillum sp., and Thiobacillus sp., were likely involved in metal oxidation (e.g., cyc2, mtoA), denitrification (e.g., nirK/S, norBC), carbon fixation (e.g., rbcL), and oxidative phosphorylation. The putative Fe(II)-oxidizing protein Cyc2 was detected for the Gallionellaceae sp. Overall, a complex network of microbial interactions among several Fe(II) oxidizers and denitrifiers was deciphered in culture BP that might resemble NRFO mechanisms in situ. Furthermore, 16S rRNA gene amplicon sequencing from environmental samples revealed 36 distinct Gallionellaceae taxa, including the key player of NRFO from culture BP (approx. 0.13% relative abundance in situ). Since several of these in situ-detected Gallionellaceae taxa were closely related to the key player in culture BP, this suggests that the diversity of organisms contributing to NRFO might be higher than currently known.}, }
@article {pmid34214906, year = {2021}, author = {Desiderio, TM and Stacy, NI and Ossiboff, RJ and Iredale, M and Archer, LL and Alexander, AB and Heard, DJ and Crevasse, SE and Craft, WF and Fredholm, DVE and Donnelly, KA and Rosenberg, JF and Childress, AL and Russell, K and Wellehan, JFX}, title = {Identification of a novel mortality-associated Helicobacter species in gopher tortoises (Gopherus polyphemus), qPCR test development and validation, and correlation with mortality in a wildlife rehabilitation population.}, journal = {Veterinary microbiology}, volume = {259}, number = {}, pages = {109136}, doi = {10.1016/j.vetmic.2021.109136}, pmid = {34214906}, issn = {1873-2542}, mesh = {Animals ; Animals, Wild/*microbiology ; DNA Primers/genetics ; Female ; Helicobacter/*genetics/*pathogenicity ; Nasal Mucosa ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction/*methods/*veterinary ; Respiratory Tract Infections/microbiology/*mortality/*veterinary ; Turtles/*microbiology ; }, abstract = {The genus Helicobacter includes spiral-shaped bacteria in the phylum Proteobacteria, class Epsilonproteobacteria, order Campylobacteriales, that have been associated with disease in animals, including reptiles. Three wild gopher tortoise (Gopherus polyphemus) index cases presented between 2012 and 2019 with nasal discharge, lethargy, and weight loss. Cytological examination of nasal discharge from all 3 tortoises identified marked heterophilic and mild histiocytic rhinitis with abundant extracellular and phagocytized spiral shaped bacteria that stained positive with Warthin-Starry stain. Polymerase chain reaction (PCR) and sequencing of the 16S rRNA gene revealed this to be a novel Helicobacter species. Two tortoises died despite treatment attempts, and the third was moribund and was euthanized. Histological examination of the nasal mucosa (n = 3) showed granulocytic to lymphocytic rhinitis with variable mucosal hyperplasia, erosion, and ulceration; Warthin-Starry staining highlighted the presence of spiral bacteria in the untreated tortoise. Genus-specific primers were designed, and the gyrA and groEL genes were amplified by PCR and sequenced. Phylogenetic analysis shows that this organism and other previously characterized Helicobacter from tortoises form a clade. Development and cross-validation of two qPCR diagnostic assays for the gyrA and groEL genes showed significant correlation of the results of two assays (P < 0.0001). These assays were used to survey nasal wash samples from 31 rehabilitating gopher tortoises. Mortality of tortoises significantly correlated with higher Helicobacter loads detected by qPCR (P = 0.028). Appropriate quarantine protocols for tortoises during rehabilitation should consider this organism. Upper respiratory disease in tortoises may involve complex microbial ecology; factors beyond Mycoplasmopsis (Mycoplasma) agassizii should be taken into account.}, }
@article {pmid34214230, year = {2021}, author = {Gyeong, H and Hyun, CU and Kim, SC and Tripathi, BM and Yun, J and Kim, J and Kang, H and Kim, JH and Kim, S and Kim, M}, title = {Contrasting early successional dynamics of bacterial and fungal communities in recently deglaciated soils of the maritime Antarctic.}, journal = {Molecular ecology}, volume = {30}, number = {17}, pages = {4231-4244}, doi = {10.1111/mec.16054}, pmid = {34214230}, issn = {1365-294X}, mesh = {Antarctic Regions ; Bacteria/genetics ; *Mycobiome/genetics ; *Soil ; Soil Microbiology ; }, abstract = {Although microorganisms are the very first colonizers of recently deglaciated soils even prior to plant colonization, the drivers and patterns of microbial community succession at early-successional stages remain poorly understood. The successional dynamics and assembly processes of bacterial and fungal communities were compared on a glacier foreland in the maritime Antarctic across the ~10-year soil-age gradient from bare soil to sparsely vegetated area. Bacterial communities shifted more rapidly than fungal communities in response to glacial retreat; species turnover (primarily the transition from glacier- to soil-favouring taxa) contributed greatly to bacterial beta diversity, but this pattern was less clear in fungi. Bacterial communities underwent more predictable (more deterministic) changes along the soil-age gradient, with compositional changes paralleling the direction of changes in soil physicochemical properties following deglaciation. In contrast, the compositional shift in fungal communities was less associated with changes in deglaciation-induced changes in soil geochemistry and most fungal taxa displayed mosaic abundance distribution across the landscape, suggesting that the successional dynamics of fungal communities are largely governed by stochastic processes. A co-occurrence network analysis revealed that biotic interactions between bacteria and fungi are very weak in early succession. Taken together, these results collectively suggest that bacterial and fungal communities in recently deglaciated soils are largely decoupled from each other during succession and exert very divergent trajectories of succession and assembly under different selective forces.}, }
@article {pmid34213774, year = {2021}, author = {Kiesewetter, KN and Afkhami, ME}, title = {Microbiome-mediated effects of habitat fragmentation on native plant performance.}, journal = {The New phytologist}, volume = {232}, number = {4}, pages = {1823-1838}, doi = {10.1111/nph.17595}, pmid = {34213774}, issn = {1469-8137}, mesh = {Bacteria ; Biodiversity ; *Ecosystem ; *Microbiota ; *Pinus ; Soil Microbiology ; }, abstract = {Habitat fragmentation is a leading cause of biodiversity and ecosystem function loss in the Anthropocene. Despite the importance of plant-microbiome interactions to ecosystem productivity, we have limited knowledge of how fragmentation affects microbiomes and even less knowledge of its consequences for microbial interactions with plants. Combining field surveys, microbiome sequencing, manipulative experiments, and random forest models, we investigated fragmentation legacy effects on soil microbiomes in imperiled pine rocklands, tested how compositional shifts across 14 fragmentation-altered soil microbiomes affected performance and resource allocation of three native plant species, and identified fragmentation-responding microbial families underpinning plant performance. Legacies of habitat fragmentation were associated with significant changes in microbial diversity and composition (across three of four community axes). Experiments showed plants often strongly benefited from the microbiome's presence, but fragmentation-associated changes in microbiome composition also significantly affected plant performance and resource allocation across all seven metrics examined. Finally, random forest models identified ten fungal and six bacterial families important for plant performance that changed significantly with fragmentation. Our findings not only support the existence of significant fragmentation effects on natural microbiomes, but also demonstrate for the first time that fragmentation-associated changes in microbiomes can have meaningful consequences for native plant performance and investment.}, }
@article {pmid34209897, year = {2021}, author = {Hugoni, M and Galland, W and Lecomte, S and Bruto, M and Barakat, M and Piola, F and Achouak, W and Haichar, FEZ}, title = {Effects of the Denitrification Inhibitor "Procyanidins" on the Diversity, Interactions, and Potential Functions of Rhizosphere-Associated Microbiome.}, journal = {Microorganisms}, volume = {9}, number = {7}, pages = {}, pmid = {34209897}, issn = {2076-2607}, support = {ANR-18-CE32-0005, DIORE//The French National Research Agency/ ; }, abstract = {Some plant secondary metabolites, such as procyanidins, have been demonstrated to cause biological denitrification inhibition (BDI) of denitrifiers in soils concomitantly with a gain in plant biomass. The present work evaluated whether procyanidins had an impact on the diversity of nontarget microbial communities that are probably involved in soil fertility and ecosystem services. Lettuce plants were grown in two contrasting soils, namely Manziat (a loamy sand soil) and Serail (a sandy clay loam soil) with and without procyanidin amendment. Microbial diversity was assessed using Illumina sequencing of prokaryotic 16S rRNA gene and fungal ITS regions. We used a functional inference to evaluate the putative microbial functions present in both soils and reconstructed the microbial interaction network. The results showed a segregation of soil microbiomes present in Serail and Manziat that were dependent on specific soil edaphic variables. For example, Deltaproteobacteria was related to total nitrogen content in Manziat, while Leotiomycetes and Firmicutes were linked to Ca[2+] in Serail. Procyanidin amendment did not affect the diversity and putative activity of microbial communities. In contrast, microbial interactions differed according to procyanidin amendment, with the results showing an enrichment of Entotheonellaeota and Mucoromycota in Serail soil and of Dependentiae and Rozellomycetes in Manziat soil.}, }
@article {pmid34209778, year = {2021}, author = {Vanwijnsberghe, S and Peeters, C and De Ridder, E and Dumolin, C and Wieme, AD and Boon, N and Vandamme, P}, title = {Genomic Aromatic Compound Degradation Potential of Novel Paraburkholderia Species: Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov.}, journal = {International journal of molecular sciences}, volume = {22}, number = {13}, pages = {}, pmid = {34209778}, issn = {1422-0067}, support = {/WT_/Wellcome Trust/United Kingdom ; BOF15/GOA/006//Geconcerteerde Onderzoeksacties (GOA) of Ghent University/ ; }, mesh = {Bacterial Typing Techniques ; Burkholderiaceae/*classification/*genetics/isolation &amp; purification/metabolism ; Coumaric Acids/metabolism/pharmacokinetics ; DNA, Bacterial/analysis/genetics ; Environmental Restoration and Remediation/methods ; Forests ; Genome, Bacterial ; Hydrocarbons, Aromatic/*metabolism/pharmacokinetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rec A Recombinases/analysis/genetics ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {We performed a taxonomic and comparative genomics analysis of 67 novel Paraburkholderia isolates from forest soil. Phylogenetic analysis of the recA gene revealed that these isolates formed a coherent lineage within the genus Paraburkholderia that also included Paraburkholderiaaspalathi, Paraburkholderiamadseniana, Paraburkholderiasediminicola, Paraburkholderiacaffeinilytica, Paraburkholderiasolitsugae and Paraburkholderiaelongata and four unidentified soil isolates from earlier studies. A phylogenomic analysis, along with orthoANIu and digital DNA-DNA hybridization calculations revealed that they represented four different species including three novel species and P. aspalathi. Functional genome annotation of the strains revealed several pathways for aromatic compound degradation and the presence of mono- and dioxygenases involved in the degradation of the lignin-derived compounds ferulic acid and p-coumaric acid. This co-occurrence of multiple Paraburkholderia strains and species with the capacity to degrade aromatic compounds in pristine forest soil is likely caused by the abundant presence of aromatic compounds in decomposing plant litter and may highlight a diversity in micro-habitats or be indicative of synergistic relationships. We propose to classify the isolates representing novel species as Paraburkholderia&amp;nbsp;domus with LMG 31832[T] (=CECT 30334) as the type strain, Paraburkholderia&amp;nbsp;nemoris with LMG 31836[T] (=CECT 30335) as the type strain and Paraburkholderia&amp;nbsp;haematera with LMG 31837[T] (=CECT 30336) as the type strain and provide an emended description of Paraburkholderia sediminicola Lim et al. 2008.}, }
@article {pmid34209491, year = {2021}, author = {Inui, T and Hanley, B and Tee, ES and Nishihira, J and Tontisirin, K and Van Dael, P and Eggersdorfer, M}, title = {The Role of Micronutrients in Ageing Asia: What Can Be Implemented with the Existing Insights.}, journal = {Nutrients}, volume = {13}, number = {7}, pages = {}, pmid = {34209491}, issn = {2072-6643}, mesh = {Aged ; Aged, 80 and over ; *Aging ; Asia, Southeastern/epidemiology ; Dietary Supplements ; Elder Nutritional Physiological Phenomena ; Fatty Acids, Omega-3 ; Female ; Humans ; Life Expectancy/trends ; Male ; *Micronutrients ; Minerals ; Noncommunicable Diseases/*epidemiology ; *Nutrition Policy ; Nutritional Status ; *Population Health ; Quality of Life ; Trace Elements ; Vitamins ; }, abstract = {Life expectancy as a measure of population health does not reflect years of healthy life. The average life expectancy in the Asia-Pacific region has more than doubled since 1900 and is now above 70 years. In the Asia-Pacific region, the proportion of aged people in the population is expected to double between 2017 and 2050. Increased life expectancy leads to an increase in non-communicable diseases, which consequently affects quality of life. Suboptimal nutritional status is a contributing factor to the prevalence and severity of non-communicable diseases, including cardiovascular, cognitive, musculoskeletal, immune, metabolic and ophthalmological functions. We have reviewed the published literature on nutrition and healthy ageing as it applies to the Asia-Pacific region, focusing on vitamins, minerals/trace elements and omega-3 fatty acids. Optimal nutritional status needs to start before a senior age is reached and before the consequences of the disease process are irreversible. Based on the nutritional status and health issues in the senior age in the region, micronutrients of particular importance are vitamins A, D, E, C, B-12, zinc and omega-3 fatty acids. The present paper substantiates the creation of micronutrient guidelines and proposes actions to support the achievement of optimal nutritional status as contribution to healthy ageing for Asia-Pacific populations.}, }
@article {pmid34207561, year = {2021}, author = {Abellan-Schneyder, I and Siebert, A and Hofmann, K and Wenning, M and Neuhaus, K}, title = {Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34207561}, issn = {2076-2607}, support = {n/a (grant for a scientist//Research Foundation of Dairy Science at the Technical University of Munich (VFMF)/ ; n/a (grant for a doctorate position)//ZIEL-Institute for Food &amp; Health at the Technical University of Munich/ ; 281A105616//Federal Ministry of Food and Agriculture (BMEL)/ ; AiF 20027N//IGF Project of the FEI via AiF/ ; }, abstract = {Full-length SSU rRNA gene sequencing allows species-level identification of the microorganisms present in milk samples. Here, we used bulk-tank raw milk samples of two German dairies and detected, using this method, a great diversity of bacteria, archaea, and yeasts within the samples. Moreover, the species-level classification was improved in comparison to short amplicon sequencing. Therefore, we anticipate that this approach might be useful for the detection of possible mastitis-causing species, as well as for the control of spoilage-associated microorganisms. In a proof of concept, we showed that we were able to identify several putative mastitis-causing or mastitis-associated species such as Streptococcusuberis, Streptococcusagalactiae, Streptococcusdysgalactiae, Escherichiacoli and Staphylococcusaureus, as well as several Candida species. Overall, the presented full-length approach for the sequencing of SSU rRNA is easy to conduct, able to be standardized, and allows the screening of microorganisms in labs with Illumina sequencing machines.}, }
@article {pmid34207412, year = {2021}, author = {Lopes, LD and Chai, YN and Marsh, EL and Rajewski, JF and Dweikat, I and Schachtman, DP}, title = {Sweet Sorghum Genotypes Tolerant and Sensitive to Nitrogen Stress Select Distinct Root Endosphere and Rhizosphere Bacterial Communities.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34207412}, issn = {2076-2607}, support = {DE-SC0014395//U.S. Department of Energy/ ; }, abstract = {The belowground microbiomes have many beneficial functions that assist plant growth, including nutrient cycling, acquisition and transport, as well as alleviation of stresses caused by nutrient limitations such as nitrogen (N). Here we analyzed the root endosphere, rhizosphere and soil bacterial communities of seven sweet sorghum genotypes differing in sensitivity to N-stress. Sorghum genotypes were grown in fields with no (low-N) or sufficient (high-N) N. The dry shoot weight ratio (low-N/high-N) was used to determine N-stress sensitivity. Our hypothesis was that genotypes tolerant and sensitive to N-stress select distinct bacterial communities. The endosphere and rhizosphere bacterial community structure were significantly different between the N-stress sensitive and tolerant genotypes in the high-N field, but not in the low-N field. However, significant changes in the relative abundance of specific bacterial taxa were observed in both fields. Streptomyces, a bacterial genus known to alleviate plant abiotic stresses, was enriched in the endosphere and rhizosphere of the tolerant genotypes in the low-N field. Our study indicates that sweet sorghum genotypes tolerant to N-stress select taxa that can potentially mitigate the N-stress, suggesting that the interactions between N-stress tolerant lines and the root-associated microbiome might be vital for coping with N-stress.}, }
@article {pmid34207399, year = {2021}, author = {Van Gerrewey, T and El-Nakhel, C and De Pascale, S and De Paepe, J and Clauwaert, P and Kerckhof, FM and Boon, N and Geelen, D}, title = {Root-Associated Bacterial Community Shifts in Hydroponic Lettuce Cultured with Urine-Derived Fertilizer.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34207399}, issn = {2076-2607}, support = {Not applicable//MELiSSA/ ; }, abstract = {Recovery of nutrients from source-separated urine can truncate our dependency on synthetic fertilizers, contributing to more sustainable food production. Urine-derived fertilizers have been successfully applied in soilless cultures. However, little is known about the adaptation of the plant to the nutrient environment. This study investigated the impact of urine-derived fertilizers on plant performance and the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Shoot biomass, chlorophyll, phenolic, antioxidant, and mineral content were associated with shifts in the root-associated bacterial community structures. K-struvite, a high-performing urine-derived fertilizer, supported root-associated bacterial communities that overlapped most strongly with control NPK fertilizer. Contrarily, lettuce performed poorly with electrodialysis (ED) concentrate and hydrolyzed urine and hosted distinct root-associated bacterial communities. Comparing the identified operational taxonomic units (OTU) across the fertilizer conditions revealed strong correlations between specific bacterial genera and the plant physiological characteristics, salinity, and NO3[-]/NH4[+] ratio. The root-associated bacterial community networks of K-struvite and NPK control fertilized plants displayed fewer nodes and node edges, suggesting that good plant growth performance does not require highly complex ecological interactions in hydroponic growth conditions.}, }
@article {pmid34206618, year = {2021}, author = {Rilling, JI and Maruyama, F and Sadowsky, MJ and Acuña, JJ and Jorquera, MA}, title = {CRISPR loci-PCR as Tool for Tracking Azospirillum sp. Strain B510.}, journal = {Microorganisms}, volume = {9}, number = {7}, pages = {}, pmid = {34206618}, issn = {2076-2607}, support = {1201386//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; 1181050//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; }, abstract = {Azospirillum-based plant and soil inoculants are widely used in agriculture. The inoculated Azospirillum strains are commonly tracked by both culture-dependent and culture-independent methods, which are time-consuming or expensive. In this context, clustered regularly interspaced short palindromic repeats (CRISPR) loci structure is unique in the bacterial genome, including some Azospirillum species. Here, we investigated the use of CRISPR loci to track specific Azospirillum strains in soils systems by PCR. Primer sets for Azospirillum sp. strain B510 were designed and evaluated by colony and endpoint PCR. The CRISPRloci-PCR approach was standardized for Azospirillum sp. strain B510, and its specificity was observed by testing against 9 different Azospirillum strains, and 38 strains of diverse bacterial genera isolated from wheat plants. The CRISPRloci-PCR approach was validated in assays with substrate and wheat seedlings. Azospirillum sp. strain B510 was detected after of two weeks of inoculation in both sterile and nonsterile substrates as well as rhizosphere grown in sterile substrate. The CRISPRloci-PCR approach was found to be a useful molecular tool for specific tracking of Azospirillum at the strain level. This technique can be easily adapted to other microbial inoculants carrying CRISPR loci and can be used to complement other microbiological techniques.}, }
@article {pmid34206081, year = {2021}, author = {Lai, CC and Ko, CY and Austria, E and Shiah, FK}, title = {Extreme Weather Events Enhance DOC Consumption in a Subtropical Freshwater Ecosystem: A Multiple-Typhoon Analysis.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34206081}, issn = {2076-2607}, abstract = {Empirical evidence suggests that the frequency/intensity of extreme weather events might increase in a warming climate. It remains unclear how these events quantitatively impact dissolved organic carbon (DOC), a pool approximately equal to CO2 in the atmosphere. This study conducted a weekly-to-biweekly sampling in a deep subtropical reservoir in the typhoon-prevailing season (June to September) from 2004 to 2009, at which 33 typhoons with distinctive precipitation (<1~362 mm d[-1]) had passed the study site. Our analyses indicated that the phosphate (i.e., DIP; <10~181 nMP) varied positively with the intensity of the accumulated rainfall 2-weeks prior; bacteria growth rate (0.05~3.68 d[-1]) behaved as a positive function of DIP, and DOC concentrations (54~119 µMC) changed negatively with bacterial production (1.2~26.1 mgC m[-3] d[-1]). These implied that the elevated DIP-loading in the hyperpycnal flow induced by typhoons could fuel bacteria growth and cause a significant decline of DOC concentrations. As the typhoon's intensity increases, many mineral-limited lentic freshwater ecosystems might become more like a CO2 source injecting more CO2 back to the atmosphere, creating a positive feedback loop that might generate severer extreme weather events.}, }
@article {pmid34204924, year = {2021}, author = {Blanchette, ML and Lund, MA}, title = {Aquatic Ecosystems of the Anthropocene: Limnology and Microbial Ecology of Mine Pit Lakes.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34204924}, issn = {2076-2607}, support = {C27043//Australian Coal Association Research Program/ ; }, abstract = {Mine pit lakes ('pit lakes') are new aquatic ecosystems of the Anthropocene. Potentially hundreds of meters deep, these lakes are prominent in the landscape and in the public consciousness. However, the ecology of pit lakes is underrepresented in the literature. The broad goal of this research was to determine the environmental drivers of pelagic microbe assemblages in Australian coal pit lakes. The overall experimental design was four lakes sampled three times, top and bottom, in 2019. Instrument chains were installed in lakes and measurements of in situ water quality and water samples for metals, metalloids, nutrients and microbe assemblage were collected. Lakes were monomictic and the timing of mixing was influenced by high rainfall events. Water quality and microbial assemblages varied significantly across space and time, and most taxa were rare. Lakes were moderately saline and circumneutral; Archeans were not prevalent. Richness also varied by catchment. Microbial assemblages correlated to environmental variables, and no one variable was consistently significant, spatially or temporally. Study lakes were dominated by 'core' taxa exhibiting temporal turnover likely driven by geography, water quality and interspecific competition, and the presence of water chemistry associated with an artificial aquifer likely influenced microbial community composition. Pit lakes are deceptively complex aquatic ecosystems that host equally complex pelagic microbial communities. This research established links between microbial assemblages and environmental variables in pit lakes and determined core communities; the first steps towards developing a monitoring program using microbes.}, }
@article {pmid34204724, year = {2021}, author = {Clocchiatti, A and Hannula, SE and Rizaludin, MS and Hundscheid, MPJ and Klein Gunnewiek, PJA and Schilder, MT and Postma, J and de Boer, W}, title = {Impact of Cellulose-Rich Organic Soil Amendments on Growth Dynamics and Pathogenicity of Rhizoctonia solani.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34204724}, issn = {2076-2607}, support = {14012//Stichting voor de Technische Wetenschappen/ ; }, abstract = {Cellulose-rich amendments stimulate saprotrophic fungi in arable soils. This may increase competitive and antagonistic interactions with root-infecting pathogenic fungi, resulting in lower disease incidence. However, cellulose-rich amendments may also stimulate pathogenic fungi with saprotrophic abilities, thereby increasing plant disease severity. The current study explores these scenarios, with a focus on the pathogenic fungus Rhizoctonia solani. Saprotrophic growth of R. solani on cellulose-rich materials was tested in vitro. This confirmed paper pulp as a highly suitable substrate for R. solani, whereas its performance on wood sawdusts varied with tree species. In two pot experiments, the effects of amendment of R. solani-infected soil with cellulose-rich materials on performance of beetroot seedlings were tested. All deciduous sawdusts and paper pulp stimulated soil fungal biomass, but only oak, elder and beech sawdusts reduced damping-off of beetroot. Oak sawdust amendment gave a consistent stimulation of saprotrophic Sordariomycetes fungi and of seedling performance, independently of the time between amendment and sowing. In contrast, paper pulp caused a short-term increase in R. solani abundance, coinciding with increased disease severity for beet seedlings sown immediately after amendment. However, damping-off of beetroot was reduced if plants were sown two or four weeks after paper pulp amendment. Cellulolytic bacteria, including Cytophagaceae, responded to paper pulp during the first two weeks and may have counteracted further spread of R. solani. The results showed that fungus-stimulating, cellulose-rich amendments have potential to be used for suppression of R. solani. However, such amendments require a careful consideration of material choice and application strategy.}, }
@article {pmid34201311, year = {2021}, author = {Šulčius, S and Alzbutas, G and Juknevičiūtė, V and Šimoliūnas, E and Venckus, P and Šimoliūnienė, M and Paškauskas, R}, title = {Exploring Viral Diversity in a Gypsum Karst Lake Ecosystem Using Targeted Single-Cell Genomics.}, journal = {Genes}, volume = {12}, number = {6}, pages = {}, pmid = {34201311}, issn = {2073-4425}, mesh = {Bacterial Proteins/genetics/metabolism ; Bacteriophages/*genetics/isolation &amp; purification/pathogenicity ; Calcium Sulfate/analysis/metabolism ; Chlorobium/genetics/metabolism/*virology ; Genomics/methods ; Host-Pathogen Interactions ; Lakes/chemistry/*microbiology/virology ; Metagenome ; Single-Cell Analysis/methods ; Sulfur/metabolism ; *Virome ; }, abstract = {Little is known about the diversity and distribution of viruses infecting green sulfur bacteria (GSB) thriving in euxinic (sulfuric and anoxic) habitats, including gypsum karst lake ecosystems. In this study, we used targeted cell sorting combined with single-cell sequencing to gain insights into the gene content and genomic potential of viruses infecting sulfur-oxidizing bacteria Chlorobium clathratiforme, obtained from water samples collected during summer stratification in gypsum karst Lake Kirkilai (Lithuania). In total, 82 viral contigs were bioinformatically identified in 62 single amplified genomes (SAGs) of C. clathratiforme. The majority of viral gene and protein sequences showed little to no similarity with phage sequences in public databases, uncovering the vast diversity of previously undescribed GSB viruses. We observed a high level of lysogenization in the C. clathratiforme population, as 87% SAGs contained intact prophages. Among the thirty identified auxiliary metabolic genes (AMGs), two, thiosulfate sulfurtransferase (TST) and thioredoxin-dependent phosphoadenosine phosphosulfate (PAPS) reductase (cysH), were found to be involved in the oxidation of inorganic sulfur compounds, suggesting that viruses can influence the metabolism and cycling of this essential element. Finally, the analysis of CRISPR spacers retrieved from the consensus C. clathratiforme genome imply persistent and active virus-host interactions for several putative phages prevalent among C. clathratiforme SAGs. Overall, this study provides a glimpse into the diversity of phages associated with naturally occurring and highly abundant sulfur-oxidizing bacteria.}, }
@article {pmid34199628, year = {2021}, author = {Rizaludin, MS and Stopnisek, N and Raaijmakers, JM and Garbeva, P}, title = {The Chemistry of Stress: Understanding the 'Cry for Help' of Plant Roots.}, journal = {Metabolites}, volume = {11}, number = {6}, pages = {}, pmid = {34199628}, issn = {2218-1989}, abstract = {Plants are faced with various biotic and abiotic stresses during their life cycle. To withstand these stresses, plants have evolved adaptive strategies including the production of a wide array of primary and secondary metabolites. Some of these metabolites can have direct defensive effects, while others act as chemical cues attracting beneficial (micro)organisms for protection. Similar to aboveground plant tissues, plant roots also appear to have evolved "a cry for help" response upon exposure to stress, leading to the recruitment of beneficial microorganisms to help minimize the damage caused by the stress. Furthermore, emerging evidence indicates that microbial recruitment to the plant roots is, at least in part, mediated by quantitative and/or qualitative changes in root exudate composition. Both volatile and water-soluble compounds have been implicated as important signals for the recruitment and activation of beneficial root-associated microbes. Here we provide an overview of our current understanding of belowground chemical communication, particularly how stressed plants shape its protective root microbiome.}, }
@article {pmid34198081, year = {2021}, author = {Yuan, H and Yuan, J and You, Y and Zhang, B and Wu, Y and Huang, S and Zhang, Y}, title = {Simultaneous ammonium and sulfate biotransformation driven by aeration: Nitrogen/sulfur metabolism and metagenome-based microbial ecology.}, journal = {The Science of the total environment}, volume = {794}, number = {}, pages = {148650}, doi = {10.1016/j.scitotenv.2021.148650}, pmid = {34198081}, issn = {1879-1026}, mesh = {*Ammonium Compounds ; Bioreactors ; Biotransformation ; Denitrification ; Metagenome ; Nitrification ; *Nitrogen ; Sewage ; Sulfates ; Sulfur ; }, abstract = {The present study aimed to clarify the effect of oxygen respiration on biotransformation of alternative electron acceptors (e.g., nitrate and sulfate) underlying the simultaneous removal of ammonium and sulfate in a single aerated sequencing batch reactor. Complete nitrification was achieved in feast condition, while denitrification was carried out in both feast and famine conditions when aeration intensity (AI) was higher than 0.22 L/(L·min). Reactors R1 [0.56 L/(L·min)], R2 [0.22 L/(L·min)], and R3 [0.08 L/(L·min)] achieved 72.39% sulfate removal efficiency in feast condition, but H2S release occurred in R3. Following exogenous substrate depletion, sulfate concentration increased again and exceeded the influent value in R1, indicating that sulfate transformation was affected by oxygen intrusion. Metagenomic analysis showed that a higher AI promoted sulfate reduction by switching from dissimilatory to assimilatory pathway. Lower AI-acclimated microorganisms (R3) produced H2S and ammonium, while higher AI-acclimated microorganisms (R1) accumulated nitrite, which confirmed that biotransformation of N and S was strongly regulated by redox imbalance driven by aeration. This implied that respiration control, a microbial self-regulation mechanism, was linked to the dynamic imbalance between electron donors and electron acceptors. Aerobic nitrate (sulfate) reduction, as one of the effects of respiration control, could be used as an alternative strategy to compensate for dynamic imbalance, when supported by efficient endogenous metabolism. Moderate aeration induced microorganisms to change their energy conservation and survival strategy through respiration control and inter-genus protection of respiratory activity among keystone taxa (including Azoarcus in R1, Thauera in R2, and Thiobacillus, Ottowia, and Geoalkalibacter in R3) to form an optimal niche in response to oxygen intrusion and achieve benign biotransformation of C, N, and S without toxic intermediate accumulation. This study clarified the biotransformation mechanism of ammonium and sulfate driven by aeration and provided theoretical guidance for optimizing existing aeration-based techniques.}, }
@article {pmid34195856, year = {2022}, author = {McGirr, S and Clarke, D and Kilcoyne, J and Silke, J and Touzet, N}, title = {Co-localisation of Azaspiracid Analogs with the Dinoflagellate Species Azadinium spinosum and Amphidoma languida in the Southwest of Ireland.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {635-646}, pmid = {34195856}, issn = {1432-184X}, support = {CF/15/01//Marine Research Sub-programme by the Irish Government/ ; }, mesh = {*Dinoflagellida/genetics ; Humans ; Ireland ; Marine Toxins ; *Spiro Compounds/analysis ; }, abstract = {Phytoplankton and biotoxin monitoring programmes have been implemented in many countries to protect human health and to mitigate the impacts of harmful algal blooms (HABs) on the aquaculture industry. Several amphidomatacean species have been confirmed in Irish coastal waters, including the azaspiracid-producing species Azadinium spinosum and Amphidoma languida. Biogeographic distribution studies have been hampered by the fact that these small, armoured dinoflagellates share remarkably similar morphologies when observed by light microscopy. The recent releases of species-specific molecular detection assays have, in this context, been welcome developments. A survey of the south west and west coasts of Ireland was carried out in August 2017 to investigate the late summer distribution of toxic amphidomataceans and azaspiracid toxins. Azadinium spinosum and Am. languida were detected in 83% of samples in the southwest along the Crease Line and Bantry Bay transects between 20 and 70 m depth, with maximal cell concentrations of 7000 and 470,000 cells/L, respectively. Azaspiracid concentrations were well aligned with the distributions of Az. spinosum and Am. languida, up to 1.1 ng/L and 4.9 ng/L for combined AZA-1, -2, -33, and combined AZA-38, -39, respectively. Although a snapshot in time, this survey provides new insights in the late summer prominence of AZAs and AZA-producing species in the southwest of Ireland, where major shellfish aquaculture operations are located. Results showed a substantial overlap in the distribution of amphidomatacean species in the area and provide valuable baseline information in the context of ongoing monitoring efforts of toxigenic amphidomataceans in the region.}, }
@article {pmid34192775, year = {2022}, author = {Vadaq, N and Schirmer, M and Tunjungputri, RN and Vlamakis, H and Chiriac, C and Ardiansyah, E and Gasem, MH and Joosten, LAB and de Groot, PG and Xavier, RJ and Netea, MG and van der Ven, AJ and de Mast, Q}, title = {Untargeted Plasma Metabolomics and Gut Microbiome Profiling Provide Novel Insights into the Regulation of Platelet Reactivity in Healthy Individuals.}, journal = {Thrombosis and haemostasis}, volume = {122}, number = {4}, pages = {529-539}, doi = {10.1055/a-1541-3706}, pmid = {34192775}, issn = {2567-689X}, mesh = {Adult ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Metabolome ; Metabolomics/methods ; Plasma ; }, abstract = {BACKGROUND: Considerable variation exists in platelet reactivity to stimulation among healthy individuals. Various metabolites and metabolic pathways influence platelet reactivity, but a comprehensive overview of these associations is missing. The gut microbiome has a strong influence on the plasma metabolome. Here, we investigated the association of platelet reactivity with results of untargeted plasma metabolomics and gut microbiome profiling.<br><br>METHODS: We used data from a cohort of 534 healthy adult Dutch volunteers (the 500 Functional Genomics study). Platelet activation and reactivity were measured by the expression of the alpha-granule protein P-selectin and the binding of fibrinogen to the activated integrin &#x3b1;IIb&#x3b2;3, both in unstimulated blood and after ex vivo stimulation with platelet agonists. Plasma metabolome was measured using an untargeted metabolic profiling approach by quadrupole time-of-flight mass spectrometry. Gut microbiome data were measured by shotgun metagenomic sequencing from stool samples.<br><br>RESULTS: Untargeted metabolomics yielded 1,979 metabolites, of which 422 were identified to play a role in a human metabolic pathway. Overall, 92/422 (21.8%) metabolites were significantly associated with at least one readout of platelet reactivity. The majority of associations involved lipids, especially members of eicosanoids, including prostaglandins and leukotrienes. Dietary-derived polyphenols were also found to inhibit platelet reactivity. Validation of metabolic pathways with functional microbial profiles revealed two overlapping metabolic pathways ("alanine, aspartate, and glutamate metabolism" and "arginine biosynthesis") that were associated with platelet reactivity.<br><br>CONCLUSION: This comprehensive overview is an resource for understanding the regulation of platelet reactivity by the plasma metabolome and the possible contribution of the gut microbiota.}, }
@article {pmid34192637, year = {2021}, author = {Li, P and Li, K and Xu, P and Liu, X and Pu, Y}, title = {Treatment of wastewater with high carbon-to-nitrogen ratio using a waterfall aeration biofilm reactor combined with sequencing batch reactor: Microbial community structure and metabolism analysis.}, journal = {Bioresource technology}, volume = {337}, number = {}, pages = {125450}, doi = {10.1016/j.biortech.2021.125450}, pmid = {34192637}, issn = {1873-2976}, mesh = {Biofilms ; Bioreactors ; Carbon ; Denitrification ; *Microbiota ; Nitrification ; Nitrogen ; RNA, Ribosomal, 16S/genetics ; *Wastewater ; }, abstract = {A low-cost and high-efficiency waterfall aeration biofilm reactor (WABR) combined with a sequencing batch reactor (SBR) was established to treat wastewater with a C/N ratio of 50. Three WABR-SBR systems with different fillers were used. In the stable operation phase, the removal efficiency of chemical oxygen demand was R1 (approximately 99%), R2 (97-99%), and R3 (96-99%); the effluent concentration of NH4[+]-N was 0.5 mg/L without nitrite or nitrate accumulation. High-throughput 16S rRNA sequencing revealed that the dominant phyla in the microbial community structure were Proteobacteria, Bacteroidetes, and Planctomycetes. Quantitative PCR was used to quantify the nitrification and denitrification gene expressions (Nitrobacter, nirS, and nirK) to evaluate the simultaneous nitrification and denitrification processes. Both anammox and denitrifying bacteria were abundant. Metagenomic annotation of genes that revealed the metabolic pathways of carbohydrates, amino acids, and the two dominant enzymes (GH and GT) provide valuable information for microbial ecology analysis.}, }
@article {pmid34191105, year = {2022}, author = {Paolinelli, M and Escoriaza, G and Cesari, C and Garcia-Lampasona, S and Hernandez-Martinez, R}, title = {Characterization of Grapevine Wood Microbiome Through a Metatranscriptomic Approach.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {658-668}, pmid = {34191105}, issn = {1432-184X}, support = {PRET-1251101//Instituto Nacional de Tecnolog&#xed;a Agropecuaria/ ; }, mesh = {*Ascomycota ; *Microbiota/genetics ; Plant Diseases/microbiology ; *Vitis/microbiology ; Wood/microbiology ; }, abstract = {Grapevine trunk diseases threaten wine and table grape production worldwide, primarily by reducing yields and, in its advanced stages, causing plant death. Among those diseases, the complex etiology disease known as hoja de malvón (HDM) significantly concerns Argentinian and Uruguayan viticulture. At least four different fungi are associated with this disease, but their role and interactions with other wood microorganisms are understudied. In this sense, analyzing grapevine wood microbiome composition could help understand microbial interactions occurring in HDM onset. Hence, a metatranscriptomic study was performed for the microbiome characterization of mature field-grown Vitis vinifera cv. Malbec, leaf-symptomatic or leaf-asymptomatic. The microbiome was mainly represented by Dothideomycetes and Actinobacteria. In the plant with more marked symptoms, higher levels of the Basidiomycota Arambarria destruens and Phellinus laevigatus were detected. Despite this particular difference, discriminating symptomatic from asymptomatic plants based on the presence or abundance of HDM pathogens was not possible. Alpha diversity and rank-abundance curve analyses indicated that plants with foliar symptoms have lower microbial evenness than asymptomatic plants. The co-occurrence network modeled microbial interkingdom interactions. Molecular data generated in this study will help develop future targeted molecular quantification for specific taxa.}, }
@article {pmid34190973, year = {2021}, author = {Sadiq, FA and Wenwei, L and Heyndrickx, M and Flint, S and Wei, C and Jianxin, Z and Zhang, H}, title = {Synergistic interactions prevail in multispecies biofilms formed by the human gut microbiota on mucin.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {8}, pages = {}, doi = {10.1093/femsec/fiab096}, pmid = {34190973}, issn = {1574-6941}, mesh = {Bacteroides ; Bacteroidetes ; Bifidobacterium bifidum ; Bifidobacterium longum subspecies infantis ; *Biofilms ; *Gastrointestinal Microbiome ; Humans ; *Mucins ; }, abstract = {Bacterial species in the human gut predominantly exist in the form of mixed-species biofilms on mucosal surfaces. In this study, the biofilm-forming ability of many human gut bacterial strains (133 strains recovered from human faeces) on mucin-coated and non-coated polystyrene surfaces was determined. A significant variation (P < 0.05) in the biofilm-forming ability of many bacterial species on both surfaces was noticed. Based on some preliminary trials, four bacterial species were selected (Bifidobacterium bifidum, Bifidobacterium longum subsp. infantis, Parabacteroides distasonis and Bacteroides ovatus), which could not form any abundant biofilm individually under the in vitro conditions investigated, but produced abundant biofilms when co-cultured in different combinations of two, three and four species, giving an evidence of synergistic interactions in multispecies biofilm formation. There was a 4.74-fold increase in the biofilm mass when all strains developed a biofilm together. Strain-specific qPCR analysis showed that B. bifidum was the most dominant species (56%) in the four-species biofilm after 24 h, followed by B. longum subsp. infantis (36.2%). Study involving cell free supernatant of the cooperating strains showed that cell viability as well as physical presence of cooperating cells were prerequisites for the observed synergy in biofilms. The molecular mechanism behind these interactions and subsequent effects on the functionality of the strains involved were not determined in our study but merit further work.}, }
@article {pmid34190389, year = {2021}, author = {Barnes, EM and Kutos, S and Naghshineh, N and Mesko, M and You, Q and Lewis, JD}, title = {Assembly of the amphibian microbiome is influenced by the effects of land-use change on environmental reservoirs.}, journal = {Environmental microbiology}, volume = {23}, number = {8}, pages = {4595-4611}, doi = {10.1111/1462-2920.15653}, pmid = {34190389}, issn = {1462-2920}, mesh = {Amphibians ; Animals ; Bacteria/genetics ; Fungi/genetics ; Humans ; *Microbiota ; Soil Microbiology ; }, abstract = {A growing focus in microbial ecology is understanding how beneficial microbiome function is created and maintained through various assembly mechanisms. This study explores the role of both the environment and disease in regulating the composition of microbial species in the soil and on amphibian hosts. We compared the microbial communities of Plethodon cinereus salamanders along a land-use gradient in the New York metropolitan area and paired these with associated soil cores. Additionally, we characterized the diversity of bacterial and fungal symbionts that putatively inhibit the pathogenic fungus Batrachochytrium dendrobatidis. We predicted that variation in skin microbial community composition would correlate with changes seen in the soil which functions as the regional species pool. We found that salamanders and soil share many microbial taxa but that these two communities exhibit differences in the relative abundances of the bacterial phyla Acidobacteria, Actinobacteria, and Proteobacteria and the fungal phyla Ascomycota and genus Basidiobolus. Microbial community composition varies with changes in land-use associated factors creating site-specific compositions. By employing a quantitative, null-based assembly model, we identified that dispersal limitation, variable selection, and drift guide assembly of microbes onto their skin, creating high dissimilarity between individuals with likely consequences in disease preventative function.}, }
@article {pmid34190033, year = {2021}, author = {Duysburgh, C and Van den Abbeele, P and Morera, M and Marzorati, M}, title = {Lacticaseibacillus rhamnosus GG and Saccharomyces cerevisiae boulardii supplementation exert protective effects on human gut microbiome following antibiotic administration in vitro.}, journal = {Beneficial microbes}, volume = {12}, number = {4}, pages = {59-73}, doi = {10.3920/BM2020.0180}, pmid = {34190033}, issn = {1876-2891}, mesh = {Amoxicillin/adverse effects ; Anti-Bacterial Agents/adverse effects ; Clavulanic Acid/adverse effects ; Dysbiosis/chemically induced ; Fatty Acids, Volatile/analysis ; *Gastrointestinal Microbiome ; Humans ; In Vitro Techniques ; *Lacticaseibacillus rhamnosus ; *Probiotics ; *Saccharomyces boulardii ; }, abstract = {Antibiotic-induced dysbiosis of the microbial community has been associated with several gastrointestinal symptoms. The impact of repeated administration of Lacticaseibacillus rhamnosus GG (CNCM-I-4798) (formerly known as Lactobacillus rhamnosus GG), Saccharomyces cerevisiae boulardii (CNCM-I-1079) and their combination (associated in Smebiocta/Smectaflora Protect®) in supporting recovery of gut microbiota functionality and composition during and following amoxicillin:clavulanic acid administration was evaluated in vitro. Antibiotic dosage negatively affected SCFA production, coinciding with detrimental effects on Bacteroidetes, Firmicutes and Bifidobacterium spp. in the simulated proximal colon, while Akkermansia muciniphila was significantly reduced in the distal colon. L. rhamnosus GG and S. boulardii were able to thrive in both colon regions upon dosing, with S. boulardii even showing protective effects on the survival of L. rhamnosus GG during antibiotic administration. The impact of the probiotic strains on microbiome recovery revealed that supplementation with L. rhamnosus GG and/or S. boulardii resulted in a stimulating effect on the most abundant bacterial groups within the bacterial community of each donor. For one of the donors tested, co-dosing of L. rhamnosus GG and S. boulardii resulted in superior short-chain fatty acid recovery accompanied by a stronger increase in abundance of Bifidobacteriaceae. Overall, the current study provides first evidence that combined supplementation of L. rhamnosus GG and S. boulardii might be an interesting candidate in limiting detrimental effects of amoxicillin:clavulanic acid on the human gut microbiome, though further studies are warranted to confirm these findings.}, }
@article {pmid34189610, year = {2022}, author = {Wang, X and Shang, Y and Wei, Q and Wu, X and Dou, H and Zhang, H and Zhou, S and Sha, W and Sun, G and Ma, S and Zhang, H}, title = {Comparative Analyses of the Gut Microbiome of Two Fox Species, the Red Fox (Vulpes Vulpes) and Corsac Fox (Vulpes Corsac), that Occupy Different Ecological Niches.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {753-765}, pmid = {34189610}, issn = {1432-184X}, support = {31872242//the national natural science foundation of china/ ; 31672313//the national natural science foundation of china/ ; 32070405//the national natural science foundation of china/ ; 32001228//the national natural science foundation of china/ ; 32000291//the national natural science foundation of china/ ; 61902368//the national natural science foundation of china/ ; 201404420//the Special Fund for Forest Scientific Research in the Public Welfare/ ; }, mesh = {Animals ; Ecosystem ; *Foxes ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {The gut microbiome is integral for the host's living and environmental adaptation and crucially important for understanding host adaptive mechanisms. The red fox (Vulpes vulpes) dominates a wider ecological niche and more complicated habitat than that of the corsac fox (V. corsac). However, the adaptive mechanisms (in particular, the gut microbiome responsible for this kind of difference) are still unclear. Therefore, we investigated the gut microbiome of these two species in the Hulunbuir grassland, China, and evaluated their microbiome composition, function, and adaptive mechanisms. We profiled the gut microbiome and metabolism function of red and corsac foxes via 16S rRNA gene and metagenome sequencing. The foxes harbored species-specific microbiomes and functions that were related to ecological niche and habitat. The red fox had abundant Bacteroides, which leads to significant enrichment of metabolic pathways (K12373 and K21572) and enzymes related to chitin and carbohydrate degradation that may help the red fox adapt to a wider niche. The corsac fox harbored large proportions of Blautia, Terrisporobacter, and ATP-binding cassette (ABC) transporters (K01990, K02003, and K06147) that can help maintain corsac fox health, allowing it to live in harsh habitats. These results indicate that the gut microbiome of the red and corsac foxes may have different abilities which may provide these species with differing capabilities to adapt to different ecological niches and habitats, thus providing important microbiome data for understanding the mechanisms of host adaptation to different niches and habitats.}, }
@article {pmid34185360, year = {2021}, author = {Jiao, S and Zhang, B and Zhang, G and Chen, W and Wei, G}, title = {Stochastic community assembly decreases soil fungal richness in arid ecosystems.}, journal = {Molecular ecology}, volume = {30}, number = {17}, pages = {4338-4348}, doi = {10.1111/mec.16047}, pmid = {34185360}, issn = {1365-294X}, mesh = {Desert Climate ; *Ecosystem ; Fungi/genetics ; *Soil ; Soil Microbiology ; }, abstract = {Uncovering the linkages between community assembly and species diversity is a fundamental issue in microbial ecology. In this study, a large-scale (transect intervals of 1257.6 km) cross-biome soil survey was conducted, which ranged over agricultural fields, forests, wetlands, grasslands and desert, in the arid regions of northwest China. The aim was to investigate the biogeographic distribution, community assembly and species co-occurrence of soil fungi. The fungal communities in agricultural soils exhibited a steeper distance-decay slope and wider niche breadths, and were more strongly affected by stochastic assembly processes, than fungi in other natural habitats. A strong relationship was revealed between soil fungal richness and community assembly in arid ecosystems, with the influence of stochastic assembly processes decreasing with increasing fungal richness. Moreover, aridity was the most important environmental factor influencing fungal richness, β-diversity and species co-occurrence patterns. Specifically, the predicted increase in arid conditions will probably reduce fungal richness and network complexity. These findings represent a considerable advance in linking fungal richness to mechanisms underlying the biogeographic patterns and assembly processes of fungal communities in arid ecosystems. These results can thus be used to forecast species co-occurrence and diversities pattern of soil fungi under climate aridity and land-use change scenarios.}, }
@article {pmid34184914, year = {2021}, author = {Savoie, ER and Lanclos, VC and Henson, MW and Cheng, C and Getz, EW and Barnes, SJ and LaRowe, DE and Rappé, MS and Thrash, JC}, title = {Ecophysiology of the Cosmopolitan OM252 Bacterioplankton (Gammaproteobacteria).}, journal = {mSystems}, volume = {6}, number = {3}, pages = {e0027621}, pmid = {34184914}, issn = {2379-5077}, abstract = {Among the thousands of species that comprise marine bacterioplankton communities, most remain functionally obscure. One key cosmopolitan group in this understudied majority is the OM252 clade of Gammaproteobacteria. Although frequently found in sequence data and even previously cultured, the diversity, metabolic potential, physiology, and distribution of this clade has not been thoroughly investigated. Here, we examined these features of OM252 bacterioplankton using a newly isolated strain and genomes from publicly available databases. We demonstrated that this group constitutes a globally distributed novel genus ("Candidatus Halomarinus"), sister to Litoricola, comprising two subclades and multiple distinct species. OM252 organisms have small genomes (median, 2.21 Mbp) and are predicted obligate aerobes capable of alternating between chemoorganoheterotrophic and chemolithotrophic growth using reduced sulfur compounds as electron donors. Subclade I genomes encode genes for the Calvin-Benson-Bassham cycle for carbon fixation. One representative strain of subclade I, LSUCC0096, had extensive halotolerance and a mesophilic temperature range for growth, with a maximum rate of 0.36 doublings/h at 35°C. Cells were curved rod/spirillum-shaped, ∼1.5 by 0.2 μm. Growth yield on thiosulfate as the sole electron donor under autotrophic conditions was roughly one-third that of heterotrophic growth, even though calculations indicated similar Gibbs energies for both catabolisms. These phenotypic data show that some "Ca. Halomarinus" organisms can switch between serving as carbon sources or sinks and indicate the likely anabolic cost of lithoautotrophic growth. Our results thus provide new hypotheses about the roles of these organisms in global biogeochemical cycling of carbon and sulfur. IMPORTANCE Marine microbial communities are teeming with understudied taxa due to the sheer numbers of species in any given sample of seawater. One group, the OM252 clade of Gammaproteobacteria, has been identified in gene surveys from myriad locations, and one isolated organism has even been genome sequenced (HIMB30). However, further study of these organisms has not occurred. Using another isolated representative (strain LSUCC0096) and publicly available genome sequences from metagenomic and single-cell genomic data sets, we examined the diversity within the OM252 clade and the distribution of these taxa in the world's oceans, reconstructed the predicted metabolism of the group, and quantified growth dynamics in LSUCC0096. Our results generate new knowledge about the previously enigmatic OM252 clade and point toward the importance of facultative chemolithoautotrophy for supporting some clades of ostensibly "heterotrophic" taxa.}, }
@article {pmid34182782, year = {2021}, author = {Murareanu, BM and Sukhdeo, R and Qu, R and Jiang, J and Reinke, AW}, title = {Generation of a Microsporidia Species Attribute Database and Analysis of the Extensive Ecological and Phenotypic Diversity of Microsporidia.}, journal = {mBio}, volume = {12}, number = {3}, pages = {e0149021}, pmid = {34182782}, issn = {2150-7511}, mesh = {Animals ; *Databases, Factual ; *Ecology ; *Genetic Variation ; Host Specificity ; Humans ; Microsporidia/classification/*genetics ; *Phenotype ; }, abstract = {Microsporidia are a large group of fungus-related obligate intracellular parasites. Though many microsporidia species have been identified over the past 160 years, depiction of the full diversity of this phylum is lacking. To systematically describe the characteristics of these parasites, we created a database of 1,440 species and their attributes, including the hosts they infect and spore characteristics. We find that microsporidia have been reported to infect 16 metazoan and 4 protozoan phyla, with smaller phyla being underrepresented. Most species are reported to infect only a single host, but those that are generalists are also more likely to infect a broader set of host tissues. Strikingly, polar tubes are threefold longer in species that infect tissues besides the intestine, suggesting that polar tube length is a determinant of tissue specificity. Phylogenetic analysis revealed four clades which each contain microsporidia that infect hosts from all major habitats. Although related species are more likely to infect similar hosts, we observe examples of changes in host specificity and convergent evolution. Taken together, our results show that microsporidia display vast diversity in their morphology and the hosts they infect, illustrating the flexibility of these parasites to evolve new traits. IMPORTANCE Microsporidia are a large group of parasites that cause death and disease in humans and many agriculturally important animal species. To fully understand the diverse properties of these parasites, we curated species reports from the last 160 years. Using these data, we describe when and where microsporidia were identified and what types of animals and host tissues these parasites infect. Microsporidia infect hosts using a conserved apparatus known as the polar tube. We observe that the length of this tube is correlated with the tissues that are being infected, suggesting that the polar tube controls where within the animals that the parasite infects. Finally, we show that microsporidia species often exist in multiple environments and are flexible in their ability to evolve new traits. Our study provides insight into the ecology and evolution of microsporidia and provides a useful resource to further understand these fascinating parasites.}, }
@article {pmid34180595, year = {2021}, author = {Suleiman, M and Choffat, Y and Daugaard, U and Petchey, OL}, title = {Large and interacting effects of temperature and nutrient addition on stratified microbial ecosystems in a small, replicated, and liquid-dominated Winogradsky column approach.}, journal = {MicrobiologyOpen}, volume = {10}, number = {3}, pages = {e1189}, pmid = {34180595}, issn = {2045-8827}, mesh = {Cyanobacteria/growth &amp; development/*metabolism ; *Ecological Systems, Closed ; Nutrients/*metabolism ; Sulfur/metabolism ; Temperature ; }, abstract = {Aquatic ecosystems are often stratified, with cyanobacteria in oxic layers and phototrophic sulfur bacteria in anoxic zones. Changes in stratification caused by the global environmental change are an ongoing concern. Increasing understanding of how such aerobic and anaerobic microbial communities, and associated abiotic conditions, respond to multifarious environmental changes is an important endeavor in microbial ecology. Insights can come from observational and experimental studies of naturally occurring stratified aquatic ecosystems, theoretical models of ecological processes, and experimental studies of replicated microbial communities in the laboratory. Here, we demonstrate a laboratory-based approach with small, replicated, and liquid-dominated Winogradsky columns, with distinct oxic/anoxic strata in a highly replicable manner. Our objective was to apply simultaneous global change scenarios (temperature, nutrient addition) on this micro-ecosystem to report how the microbial communities (full-length 16S rRNA gene seq.) and the abiotic conditions (O2 , H2 S, TOC) of the oxic/anoxic layer responded to these environmental changes. The composition of the strongly stratified microbial communities was greatly affected by temperature and by the interaction of temperature and nutrient addition, demonstrating the need of investigating global change treatments simultaneously. Especially phototrophic sulfur bacteria dominated the water column at higher temperatures and may indicate the presence of alternative stable states. We show that the establishment of such a micro-ecosystem has the potential to test global change scenarios in stratified eutrophic limnic systems.}, }
@article {pmid34179320, year = {2021}, author = {Hoogenkamp, MA and Brandt, BW and Laheij, AMGA and de Soet, JJ and Crielaard, W}, title = {16S rDNA sequencing and metadata of Dutch dental unit water.}, journal = {Data in brief}, volume = {37}, number = {}, pages = {107221}, pmid = {34179320}, issn = {2352-3409}, abstract = {Dental practices were approached to fill out a questionnaire on the infection control protocols in use to control biofilm growth in the dental unit and to send two types of water sample. Sampling of the dental units had to be performed prior to any infection control measures and on the second day of operation, to avoid residual effects of biofilm disinfection protocols performed in the weekend. Instructions were given on how to sample the units. Only samples, accompanied with a completed questionnaire and returned within two days by regular mail, were analysed. Samples were processed for heterotrophic plate counts, 16S (V4) rDNA microbiome sequencing and q-PCR for the concentration of bacterial 16S rDNA, fungal 18S rDNA, Legionella spp. and the presence of amoeba. The files contain the metadata needed to interpret and analyse the microbiome data. This dataset can be used by other scientists, members of infection control units, (trainee) bioinformaticians and policy makers. This dataset can provide leads to further unexplored parameters which could influence the microbial ecology of the dental unit.}, }
@article {pmid34177846, year = {2021}, author = {Tláskal, V and Pylro, VS and Žifčáková, L and Baldrian, P}, title = {Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {668644}, pmid = {34177846}, issn = {1664-302X}, abstract = {The bacterial genus Sodalis is represented by insect endosymbionts as well as free-living species. While the former have been studied frequently, the distribution of the latter is not yet clear. Here, we present a description of a free-living strain, Sodalis ligni sp. nov., originating from decomposing deadwood. The favored occurrence of S. ligni in deadwood is confirmed by both 16S rRNA gene distribution and metagenome data. Pangenome analysis of available Sodalis genomes shows at least three groups within the Sodalis genus: deadwood-associated strains, tsetse fly endosymbionts and endosymbionts of other insects. This differentiation is consistent in terms of the gene frequency level, genome similarity and carbohydrate-active enzyme composition of the genomes. Deadwood-associated strains contain genes for active decomposition of biopolymers of plant and fungal origin and can utilize more diverse carbon sources than their symbiotic relatives. Deadwood-associated strains, but not other Sodalis strains, have the genetic potential to fix N2, and the corresponding genes are expressed in deadwood. Nitrogenase genes are located within the genomes of Sodalis, including S. ligni, at multiple loci represented by more gene variants. We show decomposing wood to be a previously undescribed habitat of the genus Sodalis that appears to show striking ecological divergence.}, }
@article {pmid34177841, year = {2021}, author = {Selari, PJRG and Olchanheski, LR and Ferreira, AJ and Paim, TDP and Calgaro Junior, G and Claudio, FL and Alves, EM and Santos, DC and Araújo, WL and Silva, FG}, title = {Short-Term Effect in Soil Microbial Community of Two Strategies of Recovering Degraded Area in Brazilian Savanna: A Pilot Case Study.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {661410}, pmid = {34177841}, issn = {1664-302X}, abstract = {The Brazilian Cerrado is a highland tropical savanna considered a biodiversity hotspot with many endemic species of plants and animals. Over the years, most of the native areas of this biome became arable areas, and with inadequate management, some are nowadays at varying levels of degradation stage. Crop-livestock integrated systems (CLIS) are one option for the recovery of areas in degradation, improving the physicochemical and biological characteristics of the soil while increasing income and mitigating risks due to product diversification. Little is known about the effect of CLIS on the soil microbial community. Therefore, we perform this pilot case study to support further research on recovering degraded areas. The bacterial and fungal soil communities in the area with CLIS were compared to an area under moderate recovery (low-input recovering - LI) and native savanna (NS) area. Bacterial and fungal communities were investigated by 16S and ITS rRNA gene sequencing (deep rRNA sequencing). Ktedonobacteraceae and AD3 families were found predominantly in LI, confirming the relationship of the members of the Chloroflexi phylum in challenging environmental conditions, which can be evidenced in LI. The CLIS soil presented 63 exclusive bacterial families that were not found in LI or NS and presented a higher bacterial richness, which can be related to good land management. The NS area shared 21 and 6 families with CLIS and LI, respectively, suggesting that the intervention method used in the analyzed period brings microbial diversity closer to the conditions of the native area, demonstrating a trend of approximation between NS and CLIS even in the short term. The most abundant fungal phylum in NS treatment was Basidiomycota and Mucoromycota, whereas Ascomycota predominated in CLIS and LI. The fungal community needs more time to recover and to approximate from the native area than the bacterial community. However, according to the analysis of bacteria, the CLIS area behaved differently from the LI area, showing that this treatment induces a faster response to the increase in species richness, tending to more accelerated recovery. Results obtained herein encourage CLIS as a sustainable alternative for recovery and production in degraded areas.}, }
@article {pmid34173031, year = {2022}, author = {Zhang, W and Zhang, YC and Wang, ZG and Gu, QY and Niu, JZ and Wang, JJ}, title = {The Diversity of Viral Community in Invasive Fruit Flies (Bactrocera and Zeugodacus) Revealed by Meta-transcriptomics.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {739-752}, pmid = {34173031}, issn = {1432-184X}, support = {2019YFD1002100//National Key R&amp;D Program of China/ ; 31701846//National Natural Science Foundation of China/ ; CARS-26//earmarked fund for Modern Agro-industry (Citrus) Technology Research System of China/ ; B18044//111 Project/ ; }, mesh = {Animals ; Ecosystem ; Kenya ; *RNA Viruses/genetics ; *Tephritidae ; Transcriptome ; }, abstract = {RNA viruses are extremely diverse and rapidly evolving in various organisms. Our knowledge on viral evolution with interacted hosts in the manner of ecology is still limited. In the agricultural ecosystem, invasive insect species are posing a great threat to sustainable crop production. Among them, fruit flies (Diptera: Tephritidae Bactrocera and Zeugodacus) are destructive to fruits and vegetables, which are also closely related and often share similar ecological niches. Thus, they are ideal models for investigating RNA virome dynamics in host species. Using meta-transcriptomics, we found 39 viral sequences in samples from 12 fly species. These viral species represented the diversity of the viromes including Dicistroviridae, negev-like virus clades, Thika virus clades, Solemoviridae, Narnaviridae, Nodaviridae, Iflaviridae, Orthomyxoviridae, Bunyavirales, Partitiviridae, and Reoviridae. In particular, dicistrovirus, negev-like virus, orthomyxovirus, and orbivirus were common in over four of the fly species, which suggests a positive interaction between fly viromes that exist under the same ecological conditions. For most of the viruses, the virus-derived small RNAs displayed significantly high peaks in 21 nt and were symmetrically distributed throughout the viral genome. These results suggest that infection by these viruses can activate the host's RNAi immunity. Our study provides RNA virome diversity and evidence on their infection activity in ecologically associated invasive fruit fly species, which could help our understanding of interactions between complex species and viruses.}, }
@article {pmid34170682, year = {2021}, author = {Mamet, SD and Jimmo, A and Conway, A and Teymurazyan, A and Talebitaher, A and Papandreou, Z and Chang, YF and Shannon, W and Peak, D and Siciliano, SD}, title = {Soil Buffering Capacity Can Be Used To Optimize Biostimulation of Psychrotrophic Hydrocarbon Remediation.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {14}, pages = {9864-9875}, doi = {10.1021/acs.est.1c01113}, pmid = {34170682}, issn = {1520-5851}, mesh = {Biodegradation, Environmental ; Hydrocarbons ; *Petroleum ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {Effective bioremediation of hydrocarbons requires innovative approaches to minimize phosphate precipitation in soils of different buffering capacities. Understanding the mechanisms underlying sustained stimulation of bacterial activity remains a key challenge for optimizing bioremediation-particularly in northern regions. Positron emission tomography (PET) can trace microbial activity within the naturally occurring soil structure of intact soils. Here, we use PET to test two hypotheses: (1) optimizing phosphate bioavailability in soil will outperform a generic biostimulatory solution in promoting hydrocarbon remediation and (2) oligotrophic biostimulation will be more effective than eutrophic approaches. In so doing, we highlight the key bacterial taxa that underlie aerobic and anaerobic hydrocarbon degradation in subarctic soils. In particular, we showed that (i) optimized phosphate bioavailability outperformed generic biostimulatory solutions in promoting hydrocarbon degradation, (ii) oligotrophic biostimulation is more effective than eutrophic approaches, and (iii) optimized biostimulatory solutions stimulated specific soil regions and bacterial consortia. The knowledge gleaned from this study will be crucial in developing field-scale biodegradation treatments for sustained stimulation of bacterial activity in northern regions.}, }
@article {pmid34169333, year = {2022}, author = {Cobo-Díaz, JF and Legrand, F and Le Floch, G and Picot, A}, title = {Influence of Maize Residues in Shaping Soil Microbiota and Fusarium spp. Communities.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {702-713}, pmid = {34169333}, issn = {1432-184X}, support = {Grant#9097 MycoRes//R&#xe9;gion Bretagne/ ; }, mesh = {*Ascomycota ; *Fusarium/genetics ; *Microbiota ; Plant Diseases/microbiology ; Soil/chemistry ; Zea mays/microbiology ; }, abstract = {Fusarium head blight (FHB) is a devastating fungal disease of small grain cereals including wheat. Causal fungal agents colonize various components of the field during their life cycle including previous crop residues, soil, and grains. Although soil and residues constitute the main inoculum source, these components have received much less attention than grains. This study aimed at disentangling the role of previous crop residues in shaping soil microbiota, including Fusarium spp. communities, in fields under wheat-maize rotation. Such knowledge may contribute to better understand the complex interactions between Fusarium spp. and soil microbiota. Dynamics of bacterial and fungal communities, with a special focus on Fusarium spp., were monitored in soils at 3 time points: during wheat cultivation (April 2015 and 2017) and after maize harvest (November 2016) and in maize residues taken from fields after harvest. Shifts in microbiota were also evaluated under mesocosm experiments using soils amended with maize residues. Fusarium graminearum and F. avenaceum were predominant on maize residues but did not remain in soils during wheat cultivation. Differences in soil bacterial diversity and compositions among years were much lower than variation between fields, suggesting that bacterial communities are field-specific and more conserved over time. In contrast, soil fungal diversity and compositions were more influenced by sampling time. Maize residues, left after harvest, led to a soil enrichment with several fungal genera, including Epicoccum, Fusarium, Vishniacozyma, Papiliotrema, Sarocladium, Xenobotryosphaeria, Ramularia, Cladosporium, Cryptococcus, and Bullera, but not with bacterial genera. Likewise, under mesocosm conditions, the addition of maize residues had a stronger influence on fungal communities than on bacterial communities. In particular, addition of maize significantly increased soil fungal richness, while bacteria were much less prone to changes. Based on co-occurrence networks, OTUs negatively correlated to Fusarium spp. were identified, such as those assigned to Epicoccum and Vishniacozyma. Altogether, our results allowed to gain a deeper insight into the complex microbiota interactions in soils, with bacteria and fungi responding differently to environmental disturbances.}, }
@article {pmid34169332, year = {2022}, author = {Djemai, K and Drancourt, M and Tidjani Alou, M}, title = {Bacteria and Methanogens in the Human Microbiome: a Review of Syntrophic Interactions.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {536-554}, pmid = {34169332}, issn = {1432-184X}, support = {M&#xe9;diterran&#xe9;e Infection 10-IAHU-03//National Research Agency/ ; }, mesh = {Archaea/metabolism ; Bacteria/genetics/metabolism ; *Euryarchaeota/metabolism ; Humans ; Methane/metabolism ; *Microbiota ; }, abstract = {Methanogens are microorganisms belonging to the Archaea domain and represent the primary source of biotic methane. Methanogens encode a series of enzymes which can convert secondary substrates into methane following three major methanogenesis pathways. Initially recognized as environmental microorganisms, methanogens have more recently been acknowledged as host-associated microorganisms after their detection and initial isolation in ruminants in the 1950s. Methanogens have also been co-detected with bacteria in various pathological situations, bringing their role as pathogens into question. Here, we review reported associations between methanogens and bacteria in physiological and pathological situations in order to understand the metabolic interactions explaining these associations. To do so, we describe the origin of the metabolites used for methanogenesis and highlight the central role of methanogens in the syntrophic process during carbon cycling. We then focus on the metabolic abilities of co-detected bacterial species described in the literature and infer from their genomes the probable mechanisms of their association with methanogens. The syntrophic interactions between bacteria and methanogens are paramount to gut homeostasis. Therefore, any dysbiosis affecting methanogens might impact human health. Thus, the monitoring of methanogens may be used as a bio-indicator of dysbiosis. Moreover, new therapeutic approaches can be developed based on their administration as probiotics. We thus insist on the importance of investigating methanogens in clinical microbiology.}, }
@article {pmid34168166, year = {2021}, author = {Gan, L and Xu, WH and Xiong, Y and Lv, Z and Zheng, J and Zhang, Y and Lin, J and Liu, J and Chen, S and Chen, M and Guo, Q and Wu, J and Chen, J and Su, Z and Sun, J and He, Y and Liu, C and Wang, W and Verstraete, W and Sorgeloos, P and Defoirdt, T and Qin, Q and Liu, Y}, title = {Probiotics: their action against pathogens can be turned around.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {13247}, pmid = {34168166}, issn = {2045-2322}, mesh = {Animals ; Disease Susceptibility/diet therapy ; Fish Diseases/diet therapy/microbiology ; Metabolome ; Microbiota/drug effects ; Probiotics/*therapeutic use ; Vibrio/*drug effects ; Vibrio Infections/diet therapy/microbiology/*veterinary ; Zebrafish/microbiology ; }, abstract = {Probiotics when applied in complex evolving (micro-)ecosystems, might be selectively beneficial or detrimental to pathogens when their prophylactic efficacies are prone to ambient interactions. Here, we document a counter-intuitive phenomenon that probiotic-treated zebrafish (Danio rerio) were respectively healthy at higher but succumbed at lower level of challenge with a pathogenic Vibrio isolate. This was confirmed by prominent dissimilarities in fish survival and histology. Based upon the profiling of the zebrafish microbiome, and the probiotic and the pathogen shared gene orthogroups (genetic niche overlaps in genomes), this consequently might have modified the probiotic metabolome as well as the virulence of the pathogen. Although it did not reshuffle the architecture of the commensal microbiome of the vertebrate host, it might have altered the probiotic-pathogen inter-genus and intra-species communications. Such in-depth analyses are needed to avoid counteractive phenomena of probiotics and to optimise their efficacies to magnify human and animal well-being. Moreover, such studies will be valuable to improve the relevant guidelines published by organisations such as FAO, OIE and WHO.}, }
@article {pmid34161269, year = {2021}, author = {Qian, X and Gunturu, S and Sun, W and Cole, JR and Norby, B and Gu, J and Tiedje, JM}, title = {Long-read sequencing revealed cooccurrence, host range, and potential mobility of antibiotic resistome in cow feces.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {25}, pages = {}, pmid = {34161269}, issn = {1091-6490}, mesh = {Animals ; Anti-Bacterial Agents ; Base Sequence ; Cattle ; Drug Resistance, Microbial/*genetics ; Environmental Microbiology ; Feces/*microbiology ; Gene Regulatory Networks ; Genes, Bacterial ; Genetic Linkage ; Genetic Variation ; Host Specificity/*genetics ; Microbiota/genetics ; Phylogeny ; Plasmids/genetics ; *Sequence Analysis, DNA ; }, abstract = {While it is well recognized that the environmental resistome is global, diverse, and augmented by human activities, it has been difficult to assess risk because of the inability to culture many environmental organisms, and it is difficult to evaluate risk from current sequence-based environmental methods. The four most important criteria to determine risk are whether the antibiotic-resistance genes (ARGs) are a complete, potentially functional complement; if they are linked with other resistances; whether they are mobile; and the identity of their host. Long-read sequencing fills this important gap between culture and short sequence-based methods. To address these criteria, we collected feces from a ceftiofur-treated cow, enriched the samples in the presence of antibiotics to favor ARG functionality, and sequenced long reads using Nanopore and PacBio technologies. Multidrug-resistance genes comprised 58% of resistome abundance, but only 0.8% of them were plasmid associated; fluroquinolone-, aminoglycoside-, macrolide-lincosamide-streptogramin (MLS)-, and β-lactam-resistance genes accounted for 2.7 to 12.3% of resistome abundance but with 19 to 78% located on plasmids. A variety of plasmid types were assembled, some of which share low similarity to plasmids in current databases. Enterobacteriaceae were dominant hosts of antibiotic-resistant plasmids; physical linkage of extended-spectrum β-lactamase genes (CTX-M, TEM, CMY, and CARB) was largely found with aminoglycoside-, MLS-, tetracycline-, trimethoprim-, phenicol-, sulfonamide-, and mercury-resistance genes. A draft circular chromosome of Vagococcus lutrae was assembled; it carries MLS-, tetracycline- (including tetM and tetL on an integrative conjugative element), and trimethoprim-resistance genes flanked by many transposase genes and insertion sequences, implying that they remain transferrable.}, }
@article {pmid34160245, year = {2021}, author = {Shi, X and Oliveira, DAF and Holsten, L and Steinhauer, K and de Rezende, JR}, title = {Long-Term Biocide Efficacy and Its Effect on a Souring Microbial Community.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {17}, pages = {e0084221}, pmid = {34160245}, issn = {1098-5336}, mesh = {Acids/analysis/metabolism ; Bacteria/classification/*drug effects/isolation &amp; purification/metabolism ; Disinfectants/*pharmacology ; Microbiota/*drug effects ; Oil and Gas Fields/chemistry/microbiology ; Oxidation-Reduction ; Sulfates/analysis/metabolism ; Time Factors ; }, abstract = {Reservoir souring, which is the production of H2S mainly by sulfate-reducing microorganisms (SRM) in oil reservoirs, has been a long-standing issue for the oil industry. While biocides have been frequently applied to control biogenic souring, the effects of biocide treatment are usually temporary, and biocides eventually fail. The reasons for biocide failure and the long-term response of the microbial community remain poorly understood. In this study, one-time biocide treatments with glutaraldehyde (GA) and an aldehyde-releasing biocide (ARB) at low (100 ppm) and high (750 ppm) doses were individually applied to a complex SRM community, followed by 1 year of monitoring of the chemical responses and the microbial community succession. The chemical results showed that souring control failed after 7 days at a dose of 100 ppm regardless of the biocide type and lasting souring control for the entire 1-year period was achieved only with ARB at 750 ppm. Microbial community analyses suggested that the high-dose biocide treatments resulted in 1 order of magnitude lower average total microbial abundance and average SRM abundance, compared to the low-dose treatments. The recurrence of souring was associated with reduction of alpha diversity and with long-term microbial community structure changes; therefore, monitoring changes in microbial community metrics may provide early warnings of the failure of a biocide-based souring control program in the field. Furthermore, spore-forming sulfate reducers (Desulfotomaculum and Desulfurispora) were enriched and became dominant in both GA-treated groups, which could cause challenges for the design of long-lasting remedial souring control strategies. IMPORTANCE Reservoir souring is a problem for the oil and gas industry, because H2S corrodes the steel infrastructure, downgrades oil quality, and poses substantial risks to field personnel and the environment. Biocides have been widely applied to remedy souring, but the long-term performance of biocide treatments is hard to predict or to optimize due to limited understanding of the microbial ecology affected by biocide treatment. This study investigates the long-term biocide performance and associated changes in the abundance, diversity, and structure of the souring microbial community, thus advancing the knowledge toward a deeper understanding of the microbial ecology of biocide-treated systems and contributing to the improvement of current biocide-based souring control practices. The study showcases the potential application of incorporating microbial community analyses to forecast souring, and it highlights the long-term consequences of biocide treatment in the microbial communities, with relevance to both operators and regulators.}, }
@article {pmid34157595, year = {2021}, author = {Volpiano, CG and Sant'Anna, FH and da Mota, FF and Sangal, V and Sutcliffe, I and Munusamy, M and Saravanan, VS and See-Too, WS and Passaglia, LMP and Rosado, AS}, title = {Proposal of Carbonactinosporaceae fam. nov. within the class Actinomycetia. Reclassification of Streptomyces thermoautotrophicus as Carbonactinospora thermoautotrophica gen. nov., comb. nov.}, journal = {Systematic and applied microbiology}, volume = {44}, number = {4}, pages = {126223}, doi = {10.1016/j.syapm.2021.126223}, pmid = {34157595}, issn = {1618-0984}, mesh = {Actinobacteria ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; *Phylogeny ; Proteomics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Streptomyces/classification ; }, abstract = {Streptomyces thermoautotrophicus UBT1[T] has been suggested to merit generic status due to its phylogenetic placement and distinctive phenotypes among Actinomycetia. To evaluate whether 'S. thermoautotrophicus' represents a higher taxonomic rank, 'S. thermoautotrophicus' strains UBT1[T] and H1 were compared to Actinomycetia using 16S rRNA gene sequences and comparative genome analyses. The UBT1[T] and H1 genomes each contain at least two different 16S rRNA sequences, which are closely related to those of Acidothermus cellulolyticus (order Acidothermales). In multigene-based phylogenomic trees, UBT1[T] and H1 typically formed a sister group to the Streptosporangiales-Acidothermales clade. The Average Amino Acid Identity, Percentage of Conserved Proteins, and whole-genome Average Nucleotide Identity (Alignment Fraction) values were ≤58.5%, ≤48%, ≤75.5% (0.3) between 'S. thermoautotrophicus' and Streptosporangiales members, all below the respective thresholds for delineating genera. The values for genomics comparisons between strains UBT1[T] and H1 with Acidothermales, as well as members of the genus Streptomyces, were even lower. A review of the 'S. thermoautotrophicus' proteomic profiles and KEGG orthology demonstrated that UBT1[T] and H1 present pronounced differences, both tested and predicted, in phenotypic and chemotaxonomic characteristics compared to its sister clades and Streptomyces. The distinct phylogenetic position and the combination of genotypic and phenotypic characteristics justify the proposal of Carbonactinospora gen. nov., with the type species Carbonactinospora thermoautotrophica comb. nov. (type strain UBT1[T], = DSM 100163[T] = KCTC 49540[T]) belonging to Carbonactinosporaceae fam. nov. within Actinomycetia.}, }
@article {pmid34154406, year = {2021}, author = {Guo, H and Rischer, M and Westermann, M and Beemelmanns, C}, title = {Two Distinct Bacterial Biofilm Components Trigger Metamorphosis in the Colonial Hydrozoan Hydractinia echinata.}, journal = {mBio}, volume = {12}, number = {3}, pages = {e0040121}, pmid = {34154406}, issn = {2150-7511}, mesh = {Animals ; *Biofilms ; Coral Reefs ; Ecosystem ; Hydrozoa/*microbiology/*physiology ; Larva/*microbiology ; *Metamorphosis, Biological ; }, abstract = {In marine environments, the bacterially induced metamorphosis of larvae is a widespread cross-kingdom communication phenomenon that is critical for the persistence of many marine invertebrates. However, the majority of inducing bacterial signals and underlying cellular mechanisms remain enigmatic. The marine hydroid Hydractinia echinata is a well-known model system for investigating bacterially stimulated larval metamorphosis, as larvae transform into the colonial adult stage within 24 h of signal detection. Although H. echinata has served as a cell biological model system for decades, the identity and influence of bacterial signals on the morphogenic transition remained largely unexplored. Using a bioassay-guided analysis, we first determined that specific bacterial (lyso)phospholipids, naturally present in bacterial membranes and vesicles, elicit metamorphosis in Hydractinia larvae in a dose-response manner. Lysophospholipids, as single compounds or in combination (50 μM), induced metamorphosis in up to 50% of all larvae within 48 h. Using fluorescence-labeled bacterial phospholipids, we demonstrated that phospholipids are incorporated into the larval membranes, where interactions with internal signaling cascades are proposed to occur. Second, we identified two structurally distinct exopolysaccharides of bacterial biofilms, the new Rha-Man polysaccharide from Pseudoalteromonas sp. strain P1-9 and curdlan from Alcaligenes faecalis, to induce metamorphosis in up to 75% of tested larvae. We also found that combinations of (lyso)phospholipids and curdlan induced transformation within 24 h, thereby exceeding the morphogenic activity observed for single compounds and bacterial biofilms. Our results demonstrate that two structurally distinct, bacterium-derived metabolites converge to induce high transformation rates of Hydractinia larvae and thus may help ensure optimal habitat selection. IMPORTANCE Bacterial biofilms profoundly influence the recruitment and settlement of marine invertebrates, critical steps for diverse marine processes such as the formation of coral reefs, the maintenance of marine fisheries, and the fouling of submerged surfaces. However, the complex composition of biofilms often makes the characterization of individual signals and regulatory mechanisms challenging. Developing tractable model systems to characterize these coevolved interactions is the key to understanding fundamental processes in evolutionary biology. Here, we characterized two types of bacterial signaling molecules, phospholipids and polysaccharides, that induce the morphogenic transition. We then analyzed their abundance and combinatorial activity. This study highlights the general importance of multiple bacterial signal converging activity in development-related cross-kingdom signaling and poses the question of whether complex lipids and polysaccharides are general metamorphic cues for cnidarian larvae.}, }
@article {pmid34148108, year = {2022}, author = {Rosado-Porto, D and Ratering, S and Cardinale, M and Maisinger, C and Moser, G and Deppe, M and Müller, C and Schnell, S}, title = {Elevated Atmospheric CO2 Modifies Mostly the Metabolic Active Rhizosphere Soil Microbiome in the Giessen FACE Experiment.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {619-634}, pmid = {34148108}, issn = {1432-184X}, mesh = {Carbon Dioxide/metabolism ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Elevated levels of atmospheric CO2 lead to the increase of plant photosynthetic rates, carbon inputs into soil and root exudation. In this work, the effects of rising atmospheric CO2 levels on the metabolic active soil microbiome have been investigated at the Giessen free-air CO2 enrichment (Gi-FACE) experiment on a permanent grassland site near Giessen, Germany. The aim was to assess the effects of increased C supply into the soil, due to elevated CO2, on the active soil microbiome composition. RNA extraction and 16S rRNA (cDNA) metabarcoding sequencing were performed from bulk and rhizosphere soils, and the obtained data were processed for a compositional data analysis calculating diversity indices and differential abundance analyses. The structure of the metabolic active microbiome in the rhizospheric soil showed a clear separation between elevated and ambient CO2 (p = 0.002); increased atmospheric CO2 concentration exerted a significant influence on the microbiomes differentiation (p = 0.01). In contrast, elevated CO2 had no major influence on the structure of the bulk soil microbiome (p = 0.097). Differential abundance results demonstrated that 42 bacterial genera were stimulated under elevated CO2. The RNA-based metabarcoding approach used in this research showed that the ongoing atmospheric CO2 increase of climate change will significantly shift the microbiome structure in the rhizosphere.}, }
@article {pmid34148107, year = {2022}, author = {Deignan, LK and McDougald, D}, title = {Differential Response of the Microbiome of Pocillopora acuta to Reciprocal Transplantation Within Singapore.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {608-618}, pmid = {34148107}, issn = {1432-184X}, support = {MSRDP-03//National Research Foundation Singapore/ ; }, mesh = {Animals ; *Anthozoa/physiology ; Coral Reefs ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Singapore ; }, abstract = {As corals continue to decline globally, particularly due to climate change, it is vital to understand the extent to which their microbiome may confer an adaptive resilience against environmental stress. Corals that survive on the urban reefs of Singapore are ideal candidates to study the association of scleractinians with their microbiome, which in turn can inform reef conservation and management. In this study, we monitored differences in the microbiome of Pocillopora acuta colonies reciprocally transplanted between two reefs, Raffles and Kusu, within the Port of Singapore, where corals face intense anthropogenic impacts. Pocillopora acuta had previously been shown to host distinct microbial communities between these two reefs. Amplicon sequencing (16S rRNA) was used to assess the coral microbiomes at 1, 2, 4, and 10 days post-transplantation. Coral microbiomes responded rapidly to transplantation, becoming similar to those of the local corals at the destination reef within one day at Raffles and within two days at Kusu. Elevated nitrate concentrations were detected at Raffles for the duration of the study, potentially influencing the microbiome's response to transplantation. The persistence of corals within the port of Singapore highlights the ability of corals to adapt to stressful environments. Further, coral resilience appears to coincide with a dynamic microbiome which can undergo shifts in composition without succumbing to dysbiosis.}, }
@article {pmid34146566, year = {2021}, author = {Baumgartner, M and Lang, M and Holley, H and Crepaz, D and Hausmann, B and Pjevac, P and Moser, D and Haller, F and Hof, F and Beer, A and Orgler, E and Frick, A and Khare, V and Evstatiev, R and Strohmaier, S and Primas, C and Dolak, W and Köcher, T and Klavins, K and Rath, T and Neurath, MF and Berry, D and Makristathis, A and Muttenthaler, M and Gasche, C}, title = {Mucosal Biofilms Are an Endoscopic Feature of Irritable Bowel Syndrome and Ulcerative Colitis.}, journal = {Gastroenterology}, volume = {161}, number = {4}, pages = {1245-1256.e20}, pmid = {34146566}, issn = {1528-0012}, support = {714366/ERC_/European Research Council/International ; }, mesh = {Austria ; Bacteria/*growth &amp; development/metabolism/ultrastructure ; Biofilms/*growth &amp; development ; Case-Control Studies ; Colitis, Ulcerative/metabolism/*microbiology/pathology ; Colon/metabolism/*microbiology/pathology ; *Colonoscopy ; Deep Learning ; *Gastrointestinal Microbiome ; Germany ; Humans ; Image Interpretation, Computer-Assisted ; Intestinal Mucosa/metabolism/*microbiology/pathology ; Irritable Bowel Syndrome/metabolism/*microbiology/pathology ; Metabolomics ; Microscopy, Confocal ; Microscopy, Electron, Scanning ; Predictive Value of Tests ; Ribotyping ; }, abstract = {BACKGROUND &amp; AIMS: Irritable bowel syndrome (IBS) and inflammatory bowel diseases result in a substantial reduction in quality of life and a considerable socioeconomic impact. In IBS, diagnosis and treatment options are limited, but evidence for involvement of the gut microbiome in disease pathophysiology is emerging. Here we analyzed the prevalence of endoscopically visible mucosal biofilms in gastrointestinal disease and associated changes in microbiome composition and metabolism.<br><br>METHODS: The presence of mucosal biofilms was assessed in 1426 patients at 2 European university-based endoscopy centers. One-hundred and seventeen patients were selected for in-depth molecular and microscopic analysis using 16S ribosomal RNA gene amplicon-sequencing of colonic biopsies and fecal samples, confocal microscopy with deep learning-based image analysis, scanning electron microscopy, metabolomics, and in&#xa0;vitro biofilm formation assays.<br><br>RESULTS: Biofilms were present in 57% of patients with IBS and 34% of patients with ulcerative colitis compared with 6% of controls (P < .001). These yellow-green adherent layers of the ileum and right-sided colon were microscopically confirmed to be dense bacterial biofilms. 16S-sequencing links the presence of biofilms to a dysbiotic gut microbiome, including overgrowth of Escherichia coli and Ruminococcus gnavus. R. gnavus isolates cultivated from patient biofilms also formed biofilms in&#xa0;vitro. Metabolomic analysis found an accumulation of bile acids within biofilms that correlated with fecal bile acid excretion, linking this phenotype with a mechanism of diarrhea.<br><br>CONCLUSIONS: The presence of mucosal biofilms is an endoscopic feature in a subgroup of IBS and ulcerative colitis with disrupted bile acid metabolism and bacterial dysbiosis. They provide novel insight into the pathophysiology of IBS and ulcerative colitis, illustrating that biofilm can be seen as a tipping point in the development of dysbiosis and disease.}, }
@article {pmid34145482, year = {2022}, author = {González-Olalla, JM and Medina-Sánchez, JM and Carrillo, P}, title = {Fluctuation at High Temperature Combined with Nutrients Alters the Thermal Dependence of Phytoplankton.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {555-567}, pmid = {34145482}, issn = {1432-184X}, mesh = {*Ecosystem ; Heterotrophic Processes ; Nutrients/metabolism ; *Phytoplankton/metabolism ; Temperature ; }, abstract = {The Metabolic Theory of Ecology (MTE) predicts that the temperature increases exert a common effect on organisms stimulating metabolic rates, this being stronger for a heterotrophic than for an autotrophic metabolism. However, no available studies within the MTE framework have focused on organisms' response under fluctuation at high temperature interacting with factors such as nutrient availability, or how this interaction could affect the coexistence between mixotrophic and strict autotrophic phytoplankton. Hence, we assess how the phytoplankton metabolism and species composition are affected under scenarios of high temperature and fluctuation at high temperature, and how nutrients alter the direction and magnitude of such impact. For that, we use a mixed culture composed of two phytoplankton species: a strict autotrophic species and a mixotrophic species. Our results indicate that, in agreement with the MTE, only fluctuation at high temperature treatment registered a greater activation energy (Ea) value for respiration than for primary production and stimulated mixotrophic over strict autotrophic species abundance compared to control treatment. Remarkably, fluctuation at high temperature had a strong negative impact on the total abundance of the mixed-culture. The interaction between nutrient enrichment and fluctuation at high temperature increased abundance of the strict autotrophic species and overall species abundance, and led to Ea values that were higher in primary production than in respiration. Changes in community composition, enhanced by nutrient enrichment, could be behind this response, which can have implications in ecosystem functioning in a changing world.}, }
@article {pmid34143976, year = {2021}, author = {Yang, JY and Fang, W and Miranda-Sanchez, F and Brown, JM and Kauffman, KM and Acevero, CM and Bartel, DP and Polz, MF and Kelly, L}, title = {Degradation of host translational machinery drives tRNA acquisition in viruses.}, journal = {Cell systems}, volume = {12}, number = {8}, pages = {771-779.e5}, pmid = {34143976}, issn = {2405-4720}, support = {K99 GM123230/GM/NIGMS NIH HHS/United States ; R35 GM118135/GM/NIGMS NIH HHS/United States ; T32 GM087237/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteriophages/genetics ; Codon/genetics ; Codon Usage ; RNA, Transfer/genetics/metabolism ; *Viruses/genetics ; }, abstract = {Viruses are traditionally thought to be under selective pressure to maintain compact genomes and thus depend on host cell translational machinery for reproduction. However, some viruses encode abundant tRNA and other translation-related genes, potentially optimizing for codon usage differences between phage and host. Here, we systematically interrogate selective advantages that carrying 18 tRNAs may convey to a T4-like Vibriophage. Host DNA and RNA degrade upon infection, including host tRNAs, which are replaced by those of the phage. These tRNAs are expressed at levels slightly better adapted to phage codon usage, especially that of late genes. The phage is unlikely to randomly acquire as diverse an array of tRNAs as observed (p = 0.0017). Together, our results support that the main driver behind phage tRNA acquisition is pressure to sustain translation as host machinery degrades, a process resulting in a dynamically adapted codon usage strategy during the course of infection.}, }
@article {pmid34143648, year = {2021}, author = {Hawkes, CV and Kjøller, R and Raaijmakers, JM and Riber, L and Christensen, S and Rasmussen, S and Christensen, JH and Dahl, AB and Westergaard, JC and Nielsen, M and Brown-Guedira, G and Hestbjerg Hansen, L}, title = {Extension of Plant Phenotypes by the Foliar Microbiome.}, journal = {Annual review of plant biology}, volume = {72}, number = {}, pages = {823-846}, doi = {10.1146/annurev-arplant-080620-114342}, pmid = {34143648}, issn = {1545-2123}, mesh = {Ecology ; *Microbiota ; Phenotype ; Plant Development ; Plants ; }, abstract = {The foliar microbiome can extend the host plant phenotype by expanding its genomic and metabolic capabilities. Despite increasing recognition of the importance of the foliar microbiome for plant fitness, stress physiology, and yield, the diversity, function, and contribution of foliar microbiomes to plant phenotypic traits remain largely elusive. The recent adoption of high-throughput technologies is helping to unravel the diversityand spatiotemporal dynamics of foliar microbiomes, but we have yet to resolve their functional importance for plant growth, development, and ecology. Here, we focus on the processes that govern the assembly of the foliar microbiome and the potential mechanisms involved in extended plant phenotypes. We highlight knowledge gaps and provide suggestions for new research directions that can propel the field forward. These efforts will be instrumental in maximizing the functional potential of the foliar microbiome for sustainable crop production.}, }
@article {pmid34143451, year = {2021}, author = {Romaní-Pérez, M and López-Almela, I and Bullich-Vilarrubias, C and Rueda-Ruzafa, L and Gómez Del Pulgar, EM and Benítez-Páez, A and Liebisch, G and Lamas, JA and Sanz, Y}, title = {Holdemanella biformis improves glucose tolerance and regulates GLP-1 signaling in obese mice.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {35}, number = {7}, pages = {e21734}, doi = {10.1096/fj.202100126R}, pmid = {34143451}, issn = {1530-6860}, mesh = {Animals ; Blood Glucose/metabolism ; Diabetes Mellitus, Type 2/*metabolism/*microbiology ; Disease Models, Animal ; Firmicutes/*physiology ; Glucagon-Like Peptide 1/*metabolism ; Gluconeogenesis/physiology ; Glucose/metabolism ; Glucose Tolerance Test/methods ; Hyperglycemia/metabolism ; Insulin/metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Obese/*metabolism/*microbiology ; Obesity/metabolism/microbiology ; }, abstract = {Impaired glucose homeostasis in obesity is mitigated by enhancing the glucoregulatory actions of glucagon-like peptide 1 (GLP-1), and thus, strategies that improve GLP-1 sensitivity and secretion have therapeutic potential for the treatment of type 2 diabetes. This study shows that Holdemanella biformis, isolated from the feces of a metabolically healthy volunteer, ameliorates hyperglycemia, improves oral glucose tolerance and restores gluconeogenesis and insulin signaling in the liver of obese mice. These effects were associated with the ability of H. biformis to restore GLP-1 levels, enhancing GLP-1 neural signaling in the proximal and distal small intestine and GLP-1 sensitivity of vagal sensory neurons, and to modify the cecal abundance of unsaturated fatty acids and the bacterial species associated with metabolic health. Our findings overall suggest the potential use of H biformis in the management of type 2 diabetes in obesity to optimize the sensitivity and function of the GLP-1 system, through direct and indirect mechanisms.}, }
@article {pmid34142402, year = {2021}, author = {Simonin, M and Rocca, JD and Gerson, JR and Moore, E and Brooks, AC and Czaplicki, L and Ross, MRV and Fierer, N and Craine, JM and Bernhardt, ES}, title = {Consistent declines in aquatic biodiversity across diverse domains of life in rivers impacted by surface coal mining.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {31}, number = {6}, pages = {e02389}, doi = {10.1002/eap.2389}, pmid = {34142402}, issn = {1051-0761}, mesh = {Animals ; Biodiversity ; *Coal Mining ; Ecosystem ; Environmental Monitoring ; Invertebrates ; Mining ; Rivers ; *Water Pollutants, Chemical/analysis ; }, abstract = {The rivers of Appalachia (United States) are among the most biologically diverse freshwater ecosystems in the temperate zone and are home to numerous endemic aquatic organisms. Throughout the Central Appalachian ecoregion, extensive surface coal mines generate alkaline mine drainage that raises the pH, salinity, and trace element concentrations in downstream waters. Previous regional assessments have found significant declines in stream macroinvertebrate and fish communities after draining these mined areas. Here, we expand these assessments with a more comprehensive evaluation across a broad range of organisms (bacteria, algae, macroinvertebrates, all eukaryotes, and fish) using high-throughput amplicon sequencing of environmental DNA (eDNA). We collected water samples from 93 streams in Central Appalachia (West Virginia, United States) spanning a gradient of mountaintop coal mining intensity and legacy to assess how this land use alters downstream water chemistry and affects aquatic biodiversity. For each group of organisms, we identified the sensitive and tolerant taxa along the gradient and calculated stream specific conductivity thresholds in which large synchronous declines in diversity were observed. Streams below mining operations had steep declines in diversity (-18 to -41%) and substantial shifts in community composition that were consistent across multiple taxonomic groups. Overall, large synchronous declines in bacterial, algal, and macroinvertebrate communities occurred even at low levels of mining impact at stream specific conductivity thresholds of 150-200 µS/cm that are substantially below the current U.S. Environmental Protection Agency aquatic life benchmark of 300 µS/cm for Central Appalachian streams. We show that extensive coal surface mining activities led to the extirpation of 40% of biodiversity from impacted rivers throughout the region and that current water quality criteria are likely not protective for many groups of aquatic organisms.}, }
@article {pmid34141244, year = {2021}, author = {Boynton, PJ and Wloch-Salamon, D and Landermann, D and Stukenbrock, EH}, title = {Forest Saccharomyces paradoxus are robust to seasonal biotic and abiotic changes.}, journal = {Ecology and evolution}, volume = {11}, number = {11}, pages = {6604-6619}, pmid = {34141244}, issn = {2045-7758}, abstract = {Microorganisms are famous for adapting quickly to new environments. However, most evidence for rapid microbial adaptation comes from laboratory experiments or domesticated environments, and it is unclear how rates of adaptation scale from human-influenced environments to the great diversity of wild microorganisms. We examined potential monthly-scale selective pressures in the model forest yeast Saccharomyces paradoxus. Contrary to expectations of seasonal adaptation, the S. paradoxus population was stable over four seasons in the face of abiotic and biotic environmental changes. While the S. paradoxus population was diverse, including 41 unique genotypes among 192 sampled isolates, there was no correlation between S. paradoxus genotypes and seasonal environments. Consistent with observations from other S. paradoxus populations, the forest population was highly clonal and inbred. This lack of recombination, paired with population stability, implies that selection is not acting on the forest S. paradoxus population on a seasonal timescale. Saccharomyces paradoxus may instead have evolved generalism or phenotypic plasticity with regard to seasonal environmental changes long ago. Similarly, while the forest population included diversity among phenotypes related to intraspecific interference competition, there was no evidence for active coevolution among these phenotypes. At least ten percent of the forest S. paradoxus individuals produced "killer toxins," which kill sensitive Saccharomyces cells, but the presence of a toxin-producing isolate did not predict resistance to the toxin among nearby isolates. How forest yeasts acclimate to changing environments remains an open question, and future studies should investigate the physiological responses that allow microbial cells to cope with environmental fluctuations in their native habitats.}, }
@article {pmid34141209, year = {2021}, author = {Li, Y and Chesters, D and Wang, MQ and Wubet, T and Schuldt, A and Anttonen, P and Guo, PF and Chen, JT and Zhou, QS and Zhang, NL and Ma, KP and Bruelheide, H and Wu, CS and Zhu, CD}, title = {Tree diversity and functional leaf traits drive herbivore-associated microbiomes in subtropical China.}, journal = {Ecology and evolution}, volume = {11}, number = {11}, pages = {6153-6166}, pmid = {34141209}, issn = {2045-7758}, abstract = {Herbivorous insects acquire microorganisms from host plants or soil, but it remains unclear how the diversity and functional composition of host plants contribute to structuring herbivore microbiomes. Within a controlled tree diversity setting, we used DNA metabarcoding of 16S rRNA to assess the contribution of Lepidoptera species and their local environment (particularly, tree diversity, host tree species, and leaf traits) to the composition of associated bacterial communities. In total, we obtained 7,909 bacterial OTUs from 634 caterpillar individuals comprising 146 species. Tree diversity was found to drive the diversity of caterpillar-associated bacteria both directly and indirectly via effects on caterpillar communities, and tree diversity was a stronger predictor of bacterial diversity than diversity of caterpillars. Leaf toughness and dry matter content were important traits of the host plant determining bacterial species composition, while leaf calcium and potassium concentration influenced bacterial richness. Our study reveals previously unknown linkages between trees and their characteristics, herbivore insects, and their associated microbes, which contributes to developing a more nuanced understanding of functional dependencies between herbivores and their environment, and has implications for the consequences of plant diversity loss for trophic interactions.}, }
@article {pmid34137824, year = {2021}, author = {Abiriga, D and Jenkins, A and Alfsnes, K and Vestgarden, LS and Klempe, H}, title = {Spatiotemporal and seasonal dynamics in the microbial communities of a landfill-leachate contaminated aquifer.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {7}, pages = {}, pmid = {34137824}, issn = {1574-6941}, mesh = {*Groundwater ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Seasons ; Waste Disposal Facilities ; *Water Pollutants, Chemical/analysis ; }, abstract = {The microbiome of an aquifer contaminated by landfill leachate and undergoing intrinsic remediation was characterised using 16S rRNA metabarcoding. The archaeal/bacterial V3-V4 hypervariable region of the 16S rRNA gene was sequenced using Illumina MiSeq, and multivariate statistics were applied to make inferences. Results indicate that the aquifer recharge and aquifer sediment samples harbour different microbial communities compared to the groundwater samples. While Proteobacteria dominated both the recharge and groundwater samples, Acidobacteria dominated the aquifer sediment. The most abundant genera detected from the contaminated aquifer were Polynucleobacter, Rhodoferax, Pedobacter, Brevundimonas, Pseudomonas, Undibacterium, Sulfurifustis, Janthinobacterium, Rhodanobacter, Methylobacter and Aquabacterium. The result also shows that the microbial communities of the groundwater varied spatially, seasonally and interannually, although the interannual variation was significant for only one of the wells. Variation partitioning analysis indicates that water chemistry and well distance are intercorrelated and they jointly accounted for most of the variation in microbial composition. This implies that the species composition and water chemistry characteristics have a similar spatial structuring, presumably caused by the landfill leachate plume. The study improves our understanding of the dynamics in subsurface microbial communities in space and time.}, }
@article {pmid34136953, year = {2022}, author = {Nair, A and Ghugare, GS and Khairnar, K}, title = {An Appraisal of Bacteriophage Isolation Techniques from Environment.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {519-535}, pmid = {34136953}, issn = {1432-184X}, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; *Phage Therapy/methods ; }, abstract = {Researchers have recently renewed interest in bacteriophages. Being valuable models for the study of eukaryotic viruses, and more importantly, natural killers of bacteria, bacteriophages are being tapped for their potential role in multiple applications. Bacteriophages are also being increasingly sought for bacteriophage therapy due to rising antimicrobial resistance among pathogens. Reports show that there is an increasing trend in therapeutic application of natural bacteriophages, genetically engineered bacteriophages, and bacteriophage-encoded products as antimicrobial agents. In view of these applications, the isolation and characterization of bacteriophages from the environment has caught attention. In this review, various methods for isolation of bacteriophages from environmental sources like water, soil, and air are comprehensively described. The review also draws attention towards a handful on-field bacteriophage isolation techniques and the need for their further rapid development.}, }
@article {pmid34136952, year = {2022}, author = {Jorge, F and Dheilly, NM and Froissard, C and Wainwright, E and Poulin, R}, title = {Consistency of Bacterial Communities in a Parasitic Worm: Variation Throughout the Life Cycle and Across Geographic Space.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {724-738}, pmid = {34136952}, issn = {1432-184X}, mesh = {Animals ; Bacteria/genetics ; Birds ; Life Cycle Stages ; Snails ; *Trematoda/genetics ; }, abstract = {Microbial communities within metazoans are increasingly linked with development, health and behaviour, possibly functioning as integrated evolutionary units with the animal in which they live. This would require microbial communities to show some consistency both ontogenetically (across life stages) and geographically (among populations). We characterise the bacteriome of the parasitic trematode Philophthalmus attenuatus, which undergoes major life cycle transitions, and test whether its bacteriome remains consistent on developmental and spatial scales. Based on sequencing the prokaryotic 16S SSU rRNA gene, we compared the parasite bacteriome (i) across three life stages (rediae in snails, cercariae exiting snails, adults in birds) in one locality and (ii) among three geographic localities for rediae only. We found that each life stage harbours a bacteriome different from that of its host (except the adult stage) and the external environment. Very few bacterial taxa were shared among life stages, suggesting substantial ontogenetic turnover in bacteriome composition. Rediae from the three different localities also had different bacteriomes, with dissimilarities increasing with geographical distance. However, rediae from different localities nevertheless shared more bacterial taxa than did different life stages from the same locality. Changes in the bacteriome along the parasite's developmental history but some degree of geographical stability within a given life stage point toward non-random, stage-specific acquisition, selection and/or propagation of bacteria.}, }
@article {pmid34135464, year = {2021}, author = {Ware, IM and Van Nuland, ME and Yang, ZK and Schadt, CW and Schweitzer, JA and Bailey, JK}, title = {Climate-driven divergence in plant-microbiome interactions generates range-wide variation in bud break phenology.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {748}, pmid = {34135464}, issn = {2399-3642}, mesh = {*Climate Change ; *Ecosystem ; Genetic Variation ; Microbiota ; Populus/*microbiology ; Rhizosphere ; Soil/*chemistry ; *Soil Microbiology ; Trees/microbiology ; United States ; }, abstract = {Soil microbiomes are rapidly becoming known as an important driver of plant phenotypic variation and may mediate plant responses to environmental factors. However, integrating spatial scales relevant to climate change with plant intraspecific genetic variation and soil microbial ecology is difficult, making studies of broad inference rare. Here we hypothesize and show: 1) the degree to which tree genotypes condition their soil microbiomes varies by population across the geographic distribution of a widespread riparian tree, Populus angustifolia; 2) geographic dissimilarity in soil microbiomes among populations is influenced by both abiotic and biotic environmental variation; and 3) soil microbiomes that vary in response to abiotic and biotic factors can change plant foliar phenology. We show soil microbiomes respond to intraspecific variation at the tree genotype and population level, and geographic variation in soil characteristics and climate. Using a fully reciprocal plant population by soil location feedback experiment, we identified a climate-based soil microbiome effect that advanced and delayed bud break phenology by approximately 10 days. These results demonstrate a landscape-level feedback between tree populations and associated soil microbial communities and suggest soil microbes may play important roles in mediating and buffering bud break phenology with climate warming, with whole ecosystem implications.}, }
@article {pmid34134353, year = {2021}, author = {Guo, X and Akram, S and Stedtfeld, R and Johnson, M and Chabrelie, A and Yin, D and Mitchell, J}, title = {Distribution of antimicrobial resistance across the overall environment of dairy farms - A case study.}, journal = {The Science of the total environment}, volume = {788}, number = {}, pages = {147489}, doi = {10.1016/j.scitotenv.2021.147489}, pmid = {34134353}, issn = {1879-1026}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents ; Drug Resistance, Bacterial/genetics ; Farms ; Genes, Bacterial ; Manure ; Michigan ; Soil ; Soil Microbiology ; }, abstract = {The environmental implications of antimicrobial resistance arising from food animal farm practice are still a knowledge gap. This study investigates the fate and transport of antimicrobial resistance genes related to the use of antibiotics on a dairy farm in Michigan. Manure, soil, animal feed, animal drinking water, surface and groundwater samples were taken and the abundance of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) were subsequently measured using high parallel quantitative PCR targeting 136 genes. The total abundance and detected numbers of ARGs were found to be highest in the stagnant lagoon. Up to 44 ARG subtypes with high abundance were found in drinking water in pen which was very close to those in manure compost. The ARGs pattern clustered by soil depth although they were treated by different manure. ARGs and MGEs were detected in surface and groundwater surrounded by dairy farmlands, with the occurrence of carbapenemase-encoding KPC gene in two waters, which may be due to transport of ARGs through runoff or other sources. Overall, the results of the study suggest high prevalence of ARGs both inside and outside the animal raising area and their potential contribution to environmental ARGs.}, }
@article {pmid34133848, year = {2021}, author = {Stella, R and Bovo, D and Mastrorilli, E and Pezzolato, M and Bozzetta, E and Biancotto, G}, title = {Anabolic treatments in bovines: quantification of plasma protein markers of dexamethasone administration.}, journal = {Proteomics}, volume = {21}, number = {16}, pages = {e2000238}, doi = {10.1002/pmic.202000238}, pmid = {34133848}, issn = {1615-9861}, mesh = {Animals ; Biomarkers ; Blood Proteins ; Cattle ; *Dexamethasone ; Male ; Proteome ; *Proteomics ; }, abstract = {The aim of this study was to profile plasma proteome responses in bulls experimentally treated with dexamethasone at anabolic dosage. Illicit use of active substances in animal husbandry remains a matter of concern in Europe. Corticosteroids are probably one of the most widespread growth promoter family illegally used in beef cattle and veal calves. Testing for corticosteroids relies on detection of drug residues or their metabolites in biological fluids or tissues. Their indirect detection by mapping altered physiological parameters may overcome limits linked to route of administration, dosage, biotransformation and elimination kinetics that can lower residual drug concentration, hampering official controls. A set of 11 proteins proposed in literature as potential markers of anabolic treatments with dexamethasone, was quantified in bovine plasma by targeted proteomics based on liquid chromatography-high resolution tandem mass spectrometry. Among investigated proteins, sex hormone-binding globulin (SHBG), histidine-rich glycoprotein (HRG) and paraoxonase-1 (PON1) were found to be biomarkers of treatment. To investigate further such biomarkers, an additional group of veal calves was experimentally treated with dexamethasone at anabolic. These animals also demonstrated a significant alteration in SHBG, HRG and PON1 concentration, suggesting that quantification of plasma markers have the potential to detect animals illegally exposed to dexamethasone.}, }
@article {pmid34133817, year = {2022}, author = {Mitiku, AA and Vandeweyer, D and Lievens, B and Bossaert, S and Crauwels, S and Aernouts, B and Kechero, Y and Van Campenhout, L}, title = {Microbial profile during fermentation and aerobic stability of ensiled mixtures of maize stover and banana pseudostem in South Ethiopia.}, journal = {Journal of applied microbiology}, volume = {132}, number = {1}, pages = {126-139}, doi = {10.1111/jam.15183}, pmid = {34133817}, issn = {1365-2672}, support = {AMU 2017IUC035A10//Flemish Interuniversity Council for University Development Cooperation (VLIR-UOS)/ ; }, mesh = {Aerobiosis ; Ethiopia ; Fermentation ; *Musa ; Silage/analysis ; *Zea mays ; }, abstract = {AIMS: This study evaluated pH reduction and microbial growth during fermentation of maize stover (MS) mixed with banana pseudostem (BPS) under South Ethiopian conditions.<br><br>MATERIALS AND RESULTS: The MS and BPS were chopped and mixed into six treatments (T): 80% BPS plus 20% DMS (T1), 70% BPS plus 30% DMS (T2), 40% BPS plus 60% FMS (fresh MS) (T3), 20% BPS plus 80% FMS (T4), 100% FMS (T5), and 95% BPS plus 5% molasses (T6). At 0, 7, 14, 30, 60, and 90&#xa0;days, pH and dry matter were determined. Microbiological quality was assessed using plate counts and Illumina MiSeq sequencing. On day 60 and 90, aerobic stability was investigated. The results showed a significant reduction in pH in all mixtures, except in T1 and T2. Lactic acid bacteria counts reached a maximum in all treatments within 14&#xa0;days. Sequencing showed marked changes in dominant bacteria, such as Buttiauxella and Acinetobacter to Lactobacillus and Bifidobacterium.<br><br>CONCLUSIONS: The fresh MS and BPS mixtures and fresh maize showed significant pH reduction and dominance of desirable microbial groups.<br><br>The study enables year-round livestock feed supplementation to boost milk and meat production in South Ethiopia.}, }
@article {pmid34132846, year = {2022}, author = {Perera, IA and Abinandan, S and Subashchandrabose, SR and Venkateswarlu, K and Cole, N and Naidu, R and Megharaj, M}, title = {Extracellular Polymeric Substances Drive Symbiotic Interactions in Bacterial‒Microalgal Consortia.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {596-607}, pmid = {34132846}, issn = {1432-184X}, support = {RTP//Australian Government/ ; }, mesh = {Extracellular Polymeric Substance Matrix/metabolism ; *Microalgae ; Symbiosis ; Wastewater/microbiology ; }, abstract = {The importance of several factors that drive the symbiotic interactions between bacteria and microalgae in consortia has been well realised. However, the implication of extracellular polymeric substances (EPS) released by the partners remains unclear. Therefore, the present study focused on the influence of EPS in developing consortia of a bacterium, Variovorax paradoxus IS1, with a microalga, Tetradesmus obliquus IS2 or Coelastrella sp. IS3, all isolated from poultry slaughterhouse wastewater. The bacterium increased the specific growth rates of microalgal species significantly in the consortia by enhancing the uptake of nitrate (88‒99%) and phosphate (92‒95%) besides accumulating higher amounts of carbohydrates and proteins. The EPS obtained from exudates, collected from the bacterial or microalgal cultures, contained numerous phytohormones, vitamins, polysaccharides and amino acids that are likely involved in interspecies interactions. The addition of EPS obtained from V. paradoxus IS1 to the culture medium doubled the growth of both the microalgal strains. The EPS collected from T. obliquus IS2 significantly increased the growth of V. paradoxus IS1, but there was no apparent change in bacterial growth when it was cultured in the presence of EPS from Coelastrella sp. IS3. These observations indicate that the interaction between V. paradoxus IS1 and T. obliquus IS2 was mutualism, while commensalism was the interaction between the bacterial strain and Coelastrella sp. IS3. Our present findings thus, for the first time, unveil the EPS-induced symbiotic interactions among the partners involved in bacterial‒microalgal consortia.}, }
@article {pmid34132589, year = {2021}, author = {Tedersoo, L and Albertsen, M and Anslan, S and Callahan, B}, title = {Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {17}, pages = {e0062621}, pmid = {34132589}, issn = {1098-5336}, support = {R35 GM133745/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Microbiota ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Short-read, high-throughput sequencing (HTS) methods have yielded numerous important insights into microbial ecology and function. Yet, in many instances short-read HTS techniques are suboptimal, for example, by providing insufficient phylogenetic resolution or low integrity of assembled genomes. Single-molecule and synthetic long-read (SLR) HTS methods have successfully ameliorated these limitations. In addition, nanopore sequencing has generated a number of unique analysis opportunities, such as rapid molecular diagnostics and direct RNA sequencing, and both Pacific Biosciences (PacBio) and nanopore sequencing support detection of epigenetic modifications. Although initially suffering from relatively low sequence quality, recent advances have greatly improved the accuracy of long-read sequencing technologies. In spite of great technological progress in recent years, the long-read HTS methods (PacBio and nanopore sequencing) are still relatively costly, require large amounts of high-quality starting material, and commonly need specific solutions in various analysis steps. Despite these challenges, long-read sequencing technologies offer high-quality, cutting-edge alternatives for testing hypotheses about microbiome structure and functioning as well as assembly of eukaryote genomes from complex environmental DNA samples.}, }
@article {pmid34130083, year = {2021}, author = {Yan, L and Hermans, SM and Totsche, KU and Lehmann, R and Herrmann, M and Küsel, K}, title = {Groundwater bacterial communities evolve over time in response to recharge.}, journal = {Water research}, volume = {201}, number = {}, pages = {117290}, doi = {10.1016/j.watres.2021.117290}, pmid = {34130083}, issn = {1879-2448}, mesh = {Bacteria/genetics ; *Groundwater ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Water Wells ; }, abstract = {Time series analyses are a crucial tool for uncovering the patterns and processes shaping microbial communities and their functions, especially in aquatic ecosystems. Subsurface aquatic environments are perceived to be more stable than surface oceans and lakes, due to the lack of sunlight, the absence of photosysnthetically-driven primary production, low temperature variations, and oligotrophic conditions. However, periodic groundwater recharge should affect the structure and succession of groundwater microbiomes. To disentangle the long-term temporal changes in bacterial communities of shallow fractured bedrock groundwater, and identify the drivers of the observed patterns, we analysed bacterial 16S rRNA gene sequencing data for samples collected monthly from three groundwater wells over a six-year period (n = 230) along a hillslope recharge area. We showed that the bacterial communities in the groundwater of limestone-mudstone alternations were not stable over time and exhibited non-linear dissimilarity patterns which corresponded to periods of groundwater recharge. Further, we observed an increase in dissimilarity over time (generalized additive model P < 0.001) indicating that the successive recharge events result in communities that are increasingly more dissimilar to the initial reference time point. The sampling period was able to explain up to 29.5% of the variability in bacterial community composition and the impact of recharge events on the groundwater microbiome was linked to the strength of the recharge and local environmental selection. Many groundwater bacteria originated from the recharge-related sources (mean = 66.5%, SD = 15.1%) and specific bacterial taxa were identified as being either enriched or repressed during recharge events. Overall, similar to surface aquatic environments, the microbiomes in shallow fractured-rock groundwater vary through time, though we revealed groundwater recharges as unique driving factors for these patterns. The high temporal resolution employed here highlights the dynamics of bacterial communities in groundwater, which is an essential resource for the provision of clean drinking water; understanding the biological complexities of these systems is therefore crucial.}, }
@article {pmid34128692, year = {2021}, author = {Zhang, ZF and Pan, J and Pan, YP and Li, M}, title = {Biogeography, Assembly Patterns, Driving Factors, and Interactions of Archaeal Community in Mangrove Sediments.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {e0138120}, pmid = {34128692}, issn = {2379-5077}, support = {31970105//National Natural Science Foundation of China (NSFC)/ ; 91851105//National Natural Science Foundation of China (NSFC)/ ; JCYJ20200109105010363//Shenzhen Science and Technology Program/ ; 2019FY100700//National Science and Technology Fundamental Resources Investigation Program of China/ ; 2020KCXTD023//Innovation Team Project of Universities in Guangdong Province/ ; 2020M672779//China Postdoctoral Science Foundation/ ; }, abstract = {Archaea are a major part of Earth's life. They are believed to play important roles in nutrient biogeochemical cycling in the mangrove. However, only a few studies on the archaeal community in mangroves have been reported. In particular, the assembly processes and interaction patterns that impact the archaeal communities in mangroves have not been investigated to date. Here, the biogeography, assembly patterns, and driving factors of archaeal communities in seven representative mangroves across southeastern China were systematically analyzed. The analysis revealed that the archaeal community is more diverse in surface sediments than in subsurface sediments, and more diverse in mangroves at low latitudes than at high latitudes, with Woesearchaeota and Bathyarchaeota as the most diverse and most abundant phyla, respectively. Beta nearest-taxon index analysis suggested a determinant role of homogeneous selection on the overall archaeon community in all mangroves and in each individual mangrove. In addition, the conditionally rare taxon community was strongly shaped by homogeneous selection, while stochastic processes shaped the dominant taxon and always-rare taxon communities. Further, a moderate effect of environmental selection on the archaeal community was noted, with the smallest effect on the always-rare taxon community. Mangrove location, mean annual temperature, and salinity were the major factors that greatly affected the community composition. Finally, network analysis revealed comprehensive cooccurrence relationships in the archaeal community, with a crucial role of Bathyarchaeota. This study expands the understanding of the biogeography, assembly patterns, driving factors, and cooccurrence relationships of the mangrove archaeal community and inspires functional exploration of archaeal resources in mangrove sediments. IMPORTANCE As a key microbial community component with important ecological roles, archaea merit the attention of biologists and ecologists. The mechanisms controlling microbial community diversity, composition, and biogeography are central to microbial ecology but poorly understood. Mangroves are located at the land-ocean interface and are an ideal environment for examining the above questions. We here provided the first-ever overview of archaeal community structure and biogeography in mangroves located along an over-9,000-km coastline of southeastern China. We observed that archaeal diversity in low-latitude mangroves was higher than that in high-latitude mangroves. Furthermore, our data indicated that homogeneous selection strongly controlled the assembly of the overall and conditionally rare taxon communities in mangrove sediments, while the dominant taxon and always-rare taxon communities were mainly controlled by dispersal limitation.}, }
@article {pmid34127845, year = {2021}, author = {Wasmund, K and Pelikan, C and Schintlmeister, A and Wagner, M and Watzka, M and Richter, A and Bhatnagar, S and Noel, A and Hubert, CRJ and Rattei, T and Hofmann, T and Hausmann, B and Herbold, CW and Loy, A}, title = {Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments.}, journal = {Nature microbiology}, volume = {6}, number = {7}, pages = {885-898}, pmid = {34127845}, issn = {2058-5276}, support = {P 25111/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Anaerobiosis ; Bacteria/classification/genetics/*metabolism ; Bacterial Proteins/genetics ; Biodegradation, Environmental ; Biosynthetic Pathways ; Carbon Isotopes/metabolism ; Cold Temperature ; DNA/*metabolism ; Genome, Bacterial/genetics ; Geologic Sediments/*microbiology ; Metagenomics ; Nucleosides/metabolism ; Phylogeny ; Seawater/*microbiology ; }, abstract = {Extracellular DNA is a major macromolecule in global element cycles, and is a particularly crucial phosphorus, nitrogen and carbon source for microorganisms in the seafloor. Nevertheless, the identities, ecophysiology and genetic features of DNA-foraging microorganisms in marine sediments are largely unknown. Here, we combined microcosm experiments, DNA stable isotope probing (SIP), single-cell SIP using nano-scale secondary isotope mass spectrometry (NanoSIMS) and genome-centric metagenomics to study microbial catabolism of DNA and its subcomponents in marine sediments. [13]C-DNA added to sediment microcosms was largely degraded within 10 d and mineralized to [13]CO2. SIP probing of DNA revealed diverse 'Candidatus Izemoplasma', Lutibacter, Shewanella and Fusibacteraceae incorporated DNA-derived [13]C-carbon. NanoSIMS confirmed incorporation of [13]C into individual bacterial cells of Fusibacteraceae sorted from microcosms. Genomes of the [13]C-labelled taxa all encoded enzymatic repertoires for catabolism of DNA or subcomponents of DNA. Comparative genomics indicated that diverse 'Candidatus Izemoplasmatales' (former Tenericutes) are exceptional because they encode multiple (up to five) predicted extracellular nucleases and are probably specialized DNA-degraders. Analyses of additional sediment metagenomes revealed extracellular nuclease genes are prevalent among Bacteroidota at diverse sites. Together, our results reveal the identities and functional properties of microorganisms that may contribute to the key ecosystem function of degrading and recycling DNA in the seabed.}, }
@article {pmid34126927, year = {2021}, author = {Shao, K and Yao, X and Wu, Z and Jiang, X and Hu, Y and Tang, X and Xu, Q and Gao, G}, title = {The bacterial community composition and its environmental drivers in the rivers around eutrophic Chaohu Lake, China.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {179}, pmid = {34126927}, issn = {1471-2180}, support = {41930760//the National Natural Science Foundation of China/ ; 41977322//the National Natural Science Foundation of China/ ; 2017ZX07603-001//the Major Science and Technology Program for Water Pollution Control and Treatment, China/ ; QYZDJSSWDQC008//the Key Research Program of Frontier Sciences, Chinese Academy of Sciences/ ; ZDRW-ZS-2017-3-4//the Key Program of the Chinese Academy of Sciences/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; China ; Ecosystem ; Environmental Monitoring ; Eutrophication ; Lakes/*microbiology ; *Microbiota ; Rivers/*microbiology ; Sewage/microbiology ; }, abstract = {BACKGROUND: Bacterial community play a key role in environmental and ecological processes in river ecosystems. Rivers are used as receiving body for treated and untreated urban wastewaters that brings high loads of sewage and excrement bacteria. However, little is known about the bacterial community structure and functional files in the rivers around the eutrophic Chaohu Lake, the fifth largest freshwater lake in China, has been subjected to severe eutrophication and cyanobacterial blooms over the past few decades. Therefore, understanding the taxonomic and functional compositions of bacterial communities in the river will contribute to understanding aquatic microbial ecology. The main aims were to (1) examine the structure of bacterial communities and functional profiles in this system; (2) find the environmental factors of bacterial community variations.<br><br>RESULTS: We studied 88 sites at rivers in the Chaohu Lake basin, and determined bacterial communities using Illumina Miseq sequencing of the 16&#xa0;S rRNA gene, and predicted functional profiles using PICRUSt2. A total of 3,390,497 bacterial 16&#xa0;S rRNA gene sequences were obtained, representing 17 phyla, and 424 genera; The dominant phyla present in all samples were Bacteroidetes (1.4-82.50&#x2009;%), followed by Proteobacteria (12.6-97.30&#x2009;%), Actinobacteria (0.1-17.20&#x2009;%). Flavobacterium was the most numerous genera, and accounted for 0.12-80.34&#x2009;% of assigned 16&#xa0;S reads, followed by Acinetobacter (0.33-49.28&#x2009;%). Other dominant bacterial genera including Massilia (0.06-25.40&#x2009;%), Psychrobacter (0-36.23&#x2009;%), Chryseobacterium (0.01-22.86&#x2009;%), Brevundimonas (0.01-12.82&#x2009;%), Pseudomonas (0-59.73&#x2009;%), Duganella (0.08-23.37&#x2009;%), Unidentified Micrococcaceae (0-8.49&#x2009;%). The functional profiles of the bacterial populations indicated an relation with many human diseases, including infectious diseases. Overall results, using the &#x3b2; diversity measures, coupled with heatmap and RDA showed that there were spatial variations in the bacterial community composition at river sites, and Chemical oxygen demand (CODMn) and (NH4[+])were the dominant environmental drivers affecting the bacterial community variance.<br><br>CONCLUSIONS: The high proportion of the opportunistic pathogens (Acinetobacter, Massilia, Brevundimonas) indicated that the discharge of sewage without adequate treatment into the rivers around Chaohu Lake. We propose that these bacteria could be more effective bioindicators for long-term sewage monitoring in eutrophic lakes.}, }
@article {pmid34126067, year = {2022}, author = {Li, J and Morrow, C and Barnes, S and Wilson, L and Womack, ED and McLain, A and Yarar-Fisher, C}, title = {Gut Microbiome Composition and Serum Metabolome Profile Among Individuals With Spinal Cord Injury and Normal Glucose Tolerance or Prediabetes/Type 2 Diabetes.}, journal = {Archives of physical medicine and rehabilitation}, volume = {103}, number = {4}, pages = {702-710}, doi = {10.1016/j.apmr.2021.03.043}, pmid = {34126067}, issn = {1532-821X}, support = {R01 NR016443/NR/NINR NIH HHS/United States ; K01 HD087463/HD/NICHD NIH HHS/United States ; }, mesh = {Adult ; Cross-Sectional Studies ; *Diabetes Mellitus, Type 2 ; *Gastrointestinal Microbiome/genetics ; Glucose ; Humans ; Metabolome ; *Prediabetic State ; RNA, Ribosomal, 16S/genetics ; *Spinal Cord Injuries ; }, abstract = {OBJECTIVE: To compare the gut microbiome composition and serum metabolome profile among individuals with spinal cord injury (SCI) and normal glucose tolerance (NGT) or prediabetes/type 2 diabetes (preDM/T2D).<br><br>DESIGN: Cross-sectional design.<br><br>SETTING: Research university.<br><br>PARTICIPANTS: A total of 25 adults (N=25) with SCI were included in the analysis and categorized as NGT (n=16) or preDM/T2D (n=9) based on their glucose concentration at minute 120 during a 75-g oral glucose tolerance test. The American Diabetes Association diagnosis guideline was used for grouping participants.<br><br>INTERVENTIONS: Not applicable.<br><br>MAIN OUTCOME MEASURES: A stool sample was collected and used to assess the gut microbiome composition (alpha and beta diversity, microbial abundance) via the 16s ribosomal RNA sequencing technique. A fasting serum sample was used for liquid chromatography-mass spectrometry-based untargeted metabolomics analysis, the results from which reflect the relative quantity of metabolites detected and identified. Gut microbiome and metabolomics data were analyzed by the Quantitative Insights into Microbial Ecology 2 and Metaboanalyst platforms, respectively.<br><br>RESULTS: Gut microbiome alpha diversity (Pielou's evenness index, Shannon's index) and beta diversity (weighted UniFrac distances) differed between groups. Compared with participants with NGT, participants with preDM/T2D had less evenness in microbial communities. In particular, those with preDM/T2D had a lower abundance of the Clostridiales order and higher abundance of the Akkermansia genus, as well as higher serum levels of gut-derived metabolites, including indoxyl sulfate and phenylacetylglutamine (P < .05 for all).<br><br>CONCLUSIONS: Our results provide evidence for altered gut microbiome composition and dysregulation of gut-derived metabolites in participants with SCI and preDM/T2D. Both indoxyl sulfate and phenylacetylglutamine have been implicated in the development of cardiovascular diseases in the able-bodied population. These findings may inform future investigations in the field of SCI and cardiometabolic health.}, }
@article {pmid34124627, year = {2021}, author = {Crous, PW and Hernández-Restrepo, M and Schumacher, RK and Cowan, DA and Maggs-Kölling, G and Marais, E and Wingfield, MJ and Yilmaz, N and Adan, OCG and Akulov, A and Duarte, E&#xc1; and Berraf-Tebbal, A and Bulgakov, TS and Carnegie, AJ and de Beer, ZW and Decock, C and Dijksterhuis, J and Duong, TA and Eichmeier, A and Hien, LT and Houbraken, JAMP and Khanh, TN and Liem, NV and Lombard, L and Lutzoni, FM and Miadlikowska, JM and Nel, WJ and Pascoe, IG and Roets, F and Roux, J and Samson, RA and Shen, M and Spetik, M and Thangavel, R and Thanh, HM and Thao, LD and van Nieuwenhuijzen, EJ and Zhang, JQ and Zhang, Y and Zhao, LL and Groenewald, JZ}, title = {New and Interesting Fungi. 4.}, journal = {Fungal systematics and evolution}, volume = {7}, number = {}, pages = {255-343}, pmid = {34124627}, issn = {2589-3831}, abstract = {An order, family and genus are validated, seven new genera, 35 new species, two new combinations, two epitypes, two lectotypes, and 17 interesting new host and / or geographical records are introduced in this study. Validated order, family and genus: Superstratomycetales and Superstratomycetaceae (based on Superstratomyces). New genera: Haudseptoria (based on Haudseptoria typhae); Hogelandia (based on Hogelandia lambearum); Neoscirrhia (based on Neoscirrhia osmundae); Nothoanungitopsis (based on Nothoanungitopsis urophyllae); Nothomicrosphaeropsis (based on Nothomicrosphaeropsis welwitschiae); Populomyces (based on Populomyces zwinianus); Pseudoacrospermum (based on Pseudoacrospermum goniomae). New species: Apiospora sasae on dead culms of Sasa veitchii (Netherlands); Apiospora stipae on dead culms of Stipa gigantea (Spain); Bagadiella eucalyptorum on leaves of Eucalyptus sp. (Australia); Calonectria singaporensis from submerged leaf litter (Singapore); Castanediella neomalaysiana on leaves of Eucalyptus sp. (Malaysia); Colletotrichum pleopeltidis on leaves of Pleopeltis sp. (South Africa); Coniochaeta deborreae from soil (Netherlands); Diaporthe durionigena on branches of Durio zibethinus (Vietnam); Floricola juncicola on dead culm of Juncus sp. (France); Haudseptoria typhae on leaf sheath of Typha sp. (Germany); Hogelandia lambearum from soil (Netherlands); Lomentospora valparaisensis from soil (Chile); Neofusicoccum mystacidii on dead stems of Mystacidium capense (South Africa); Neomycosphaerella guibourtiae on leaves of Guibourtia sp. (Angola); Niesslia neoexosporioides on dead leaves of Carex paniculata (Germany); Nothoanungitopsis urophyllae on seed capsules of Eucalyptus urophylla (South Africa); Nothomicrosphaeropsis welwitschiae on dead leaves of Welwitschia mirabilis (Namibia); Paracremonium bendijkiorum from soil (Netherlands); Paraphoma ledniceana on dead wood of Buxus sempervirens (Czech Republic); Paraphoma salicis on leaves of Salix cf. alba (Ukraine); Parasarocladium wereldwijsianum from soil (Netherlands); Peziza ligni on masonry and plastering (France); Phyllosticta phoenicis on leaves of Phoenix reclinata (South Africa); Plectosphaerella slobbergiarum from soil (Netherlands); Populomyces zwinianus from soil (Netherlands); Pseudoacrospermum goniomae on leaves of Gonioma kamassi (South Africa); Pseudopyricularia festucae on leaves of Festuca californica (USA); Sarocladium sasijaorum from soil (Netherlands); Sporothrix hypoxyli in sporocarp of Hypoxylon petriniae on Fraxinus wood (Netherlands); Superstratomyces albomucosus on Pycnanthus angolensis (Netherlands); Superstratomyces atroviridis on Pinus sylvestris (Netherlands); Superstratomyces flavomucosus on leaf of Hakea multilinearis (Australia); Superstratomyces tardicrescens from human eye specimen (USA); Taeniolella platani on twig of Platanus hispanica (Germany), and Tympanis pini on twigs of Pinus sylvestris (Spain). Citation: Crous PW, Hernández-Restrepo M, Schumacher RK, Cowan DA, Maggs-Kölling G, Marais E, Wingfield MJ, Yilmaz N, Adan OCG, Akulov A, Álvarez Duarte E, Berraf-Tebbal A, Bulgakov TS, Carnegie AJ, de Beer ZW, Decock C, Dijksterhuis J, Duong TA, Eichmeier A, Hien LT, Houbraken JAMP, Khanh TN, Liem NV, Lombard L, Lutzoni FM, Miadlikowska JM, Nel WJ, Pascoe IG, Roets F, Roux J, Samson RA, Shen M, Spetik M, Thangavel R, Thanh HM, Thao LD, van Nieuwenhuijzen EJ, Zhang JQ, Zhang Y, Zhao LL, Groenewald JZ (2021). New and Interesting Fungi. 4. Fungal Systematics and Evolution 7: 255-343. doi: 10.3114/fuse.2021.07.13.}, }
@article {pmid34123319, year = {2021}, author = {Prothiwa, M and Filz, V and Oehler, S and Böttcher, T}, title = {Inhibiting quinolone biosynthesis of Burkholderia.}, journal = {Chemical science}, volume = {12}, number = {20}, pages = {6908-6912}, pmid = {34123319}, issn = {2041-6520}, abstract = {2-Alkylquinolones are important signalling molecules of Burkholderia species. We developed a substrate-based chemical probe against the central quinolone biosynthesis enzyme HmqD and applied it in competitive profiling experiments to discover the first known HmqD inhibitors. The most potent inhibitors quantitatively blocked quinolone production in Burkholderia cultures with single-digit micromolar efficacy.}, }
@article {pmid34122370, year = {2021}, author = {Cyriaque, V and Madsen, JS and Fievez, L and Leroy, B and Hansen, LH and Bureau, F and Sørensen, SJ and Wattiez, R}, title = {Lead Drives Complex Dynamics of a Conjugative Plasmid in a Bacterial Community.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {655903}, pmid = {34122370}, issn = {1664-302X}, abstract = {Plasmids carrying metal resistance genes (MRGs) have been suggested to be key ecological players in the adaptation of metal-impacted microbial communities, making them promising drivers of bio-remediation processes. However, the impact of metals on plasmid-mediated spread of MRGs through selection, plasmid loss, and transfer is far from being fully understood. In the present study, we used two-member bacterial communities to test the impact of lead on the dispersal of the IncP plasmid pKJK5 from a Pseudomonas putida KT2440 plasmid donor and two distinct recipients, Variovorax paradoxus B4 or Delftia acidovorans SPH-1 after 4 and 10 days of mating. Two versions of the plasmid were used, carrying or not carrying the lead resistance pbrTRABCD operon, to assess the importance of fitness benefit and conjugative potential for the dispersal of the plasmid. The spread dynamics of metal resistance conveyed by the conjugative plasmid were dependent on the recipient and the lead concentration: For V. paradoxus, the pbr operon did not facilitate neither lead resistance nor variation in plasmid spread. The growth gain brought by the pbr operon to D. acidovorans SPH-1 and P. putida KT2440 at 1 mM Pb enhanced the spread of the plasmid. At 1.5 mM Pb after 4 days, the proteomics results revealed an oxidative stress response and an increased abundance of pKJK5-encoded conjugation and partitioning proteins, which most likely increased the transfer of the control plasmid to D. acidovorans SPH-1 and ensured plasmid maintenance. As a consequence, we observed an increased spread of pKJK5-gfp. Conversely, the pbr operon reduced the oxidative stress response and impeded the rise of conjugation- and partitioning-associated proteins, which slowed down the spread of the pbr carrying plasmid. Ultimately, when a fitness gain was recorded in the recipient strain, the spread of MRG-carrying plasmids was facilitated through positive selection at an intermediate metal concentration, while a high lead concentration induced oxidative stress with positive impacts on proteins encoding plasmid conjugation and partitioning.}, }
@article {pmid34119873, year = {2021}, author = {Batool, M and Blazier, JC and Rogovska, YV and Wang, J and Liu, S and Nebogatkin, IV and Rogovskyy, AS}, title = {Metagenomic analysis of individually analyzed ticks from Eastern Europe demonstrates regional and sex-dependent differences in the microbiota of Ixodes ricinus.}, journal = {Ticks and tick-borne diseases}, volume = {12}, number = {5}, pages = {101768}, doi = {10.1016/j.ttbdis.2021.101768}, pmid = {34119873}, issn = {1877-9603}, mesh = {Animals ; Bacteria/genetics/*isolation &amp; purification ; Female ; Geography ; Ixodes/*microbiology ; Male ; *Metagenome ; Metagenomics ; *Microbiota ; Sex Factors ; Ukraine ; }, abstract = {Understanding the microbial ecology of disease vectors may be useful for development of novel strategies aimed at preventing transmission of vector-borne pathogens. Although Ixodes ricinus is one of the most important tick vectors, the microbiota of this tick has been examined for only limited parts of the globe. To date, the microbiota of I. ricinus ticks collected from Eastern Europe has not been defined. The objective of this study was to compare microbiota of I. ricinus ticks within (males vs. females) and between collection sites that represented three administrative regions of Ukraine, Dnipropetrovs'k (D), Kharkiv (K), and Poltava (P). A total of 89 questing I. ricinus adults were collected from region D (number of ticks, n = 29; 14 males and 15 females), region K (n = 30; 15 males and 15 females) and region P (n = 30; 15 males and 15 females). Each tick was subjected to metagenomic analysis by targeting the V6 region of 16S rRNA gene through the Illumina 4000 Hiseq sequencing. The alpha diversity analysis demonstrated that, regardless of tick sex, patterns of bacterial diversity in ticks from regions K and P were similar, whereas the microbiota of region D ticks was quite distinct. A number of inter-regional differences were detected by most beta diversity metrics for both males and females. The inter-regional variations were also supported by the principal coordinate analysis based on the unweighted UniFrac metrics with three region-specific clusters of female ticks and one distinct cluster of region D males. Lastly, numerous region- and sex-specific differences were also identified in the relative abundance of various bacterial taxa. Collectively, the present findings demonstrate that the microbiota of the I. ricinus tick can exhibit a high degree of variation between tick sexes and geographical regions.}, }
@article {pmid34118665, year = {2021}, author = {Zhang, L and Gong, X and Wang, L and Guo, K and Cao, S and Zhou, Y}, title = {Metagenomic insights into the effect of thermal hydrolysis pre-treatment on microbial community of an anaerobic digestion system.}, journal = {The Science of the total environment}, volume = {791}, number = {}, pages = {148096}, doi = {10.1016/j.scitotenv.2021.148096}, pmid = {34118665}, issn = {1879-1026}, mesh = {Anaerobiosis ; Bioreactors ; Hydrolysis ; *Metagenomics ; Methane ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sewage ; }, abstract = {Thermal hydrolysis process (THP) is an effective pre-treatment method to reduce solids volume and improve biogas production during anaerobic digestion (AD) via increasing the biodegradability of waste activated sludge (WAS). However, the effects of THP pre-treated sludge on microbial diversity, interspecies interactions, and metabolism in AD systems remain largely unknown. We therefore setup and operated an anaerobic digester during a long-term period to shed light on the effect of THP pre-treatment on AD microbial ecology in comparison to conventional AD via Illumina based 16S rRNA gene amplicon sequencing and genome-centric metagenomics analysis. Results showed THP sludge significantly reduced the microbial diversity, shaped the microbial community structure, and resulted in more intense microbial interactions. Compared to WAS as the feed sludge, THP sludge shaped the core functional groups, but functional redundancy ensured the system's stability. The metabolic interactions between methanogens and syntrophic bacteria as well as the specific metabolic pathways were further elucidated. Hydrogenotrophic methanogens, Methanospirillum sp. and Methanolinea sp., were the primary contributors for methane production when treating THP and WAS, respectively, which also have potential for acetate oxidation to methane. Collectively, this study provides in-depth information on the interspecies interactions to better understand how THP pre-treatment influences AD microbial community.}, }
@article {pmid34117524, year = {2022}, author = {Morales Medina, WR and Eramo, A and Fahrenfeld, NL}, title = {Metabolically Active Prokaryotes and Actively Transcribed Antibiotic Resistance Genes in Sewer Systems: Implications for Public Health and Microbially Induced Corrosion.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {583-595}, pmid = {34117524}, issn = {1432-184X}, support = {1510461//National Science Foundation (US)/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; Corrosion ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Public Health ; RNA, Ribosomal, 16S/genetics ; Wastewater/microbiology ; }, abstract = {Sewer systems are reservoirs of pathogens and bacteria carrying antibiotic resistance genes (ARGs). However, most recent high-throughput studies rely on DNA-based techniques that cannot provide information on the physiological state of the cells nor expression of ARGs. In this study, wastewater and sewer sediment samples were collected from combined and separate sanitary sewer systems. The metabolically active prokaryote community was evaluated using 16S rRNA amplicon sequencing and actively transcribed ARG abundance was measured using mRNA RT-qPCR. Three (sul1, blaTEM, tet(G)) of the eight tested ARGs were quantifiable in select samples. Sewer sediment samples had greater abundance of actively transcribed ARGs compared to wastewater. Microbiome analysis showed the presence of metabolically active family taxa that contain clinically relevant pathogens (Pseudomonadaceae, Enterobacteraceae, Streptococcaceae, Arcobacteraceae, and Clostridiaceae) and corrosion-causing prokaryotes (Desulfobulbaceae and Desulfovibrionaceae) in both matrices. Spirochaetaceae and methanogens were more common in the sediment matrix while Mycobacteraceae were more common in wastewater. The microbiome obtained from 16S rRNA sequencing had a significantly different structure from the 16S rRNA gene microbiome. Overall, this study demonstrates active transcription of ARGs in sewer systems and provides insight into the abundance and physiological state of taxa of interest in the different sewer matrices and sewer types relevant for wastewater-based epidemiology, corrosion, and understanding the hazard posed by different matrices during sewer overflows.}, }
@article {pmid34112519, year = {2021}, author = {Vaezzadeh, V and Thomes, MW and Kunisue, T and Tue, NM and Zhang, G and Zakaria, MP and Affendi, YA and Yap, FC and Chew, LL and Teoh, HW and Lee, CW and Bong, CW}, title = {Corrigendum to "Examination of barnacles' potential to be used as bioindicators of persistent organic pollutants in coastal ecosystem: A Malaysia case study" [Chemosphere 263 (2021) 128272].}, journal = {Chemosphere}, volume = {281}, number = {}, pages = {131081}, doi = {10.1016/j.chemosphere.2021.131081}, pmid = {34112519}, issn = {1879-1298}, }
@article {pmid34112387, year = {2021}, author = {Vissenaekens, H and Smagghe, G and Criel, H and Grootaert, C and Raes, K and Rajkovic, A and Goeminne, G and Boon, N and De Schutter, K and Van Camp, J}, title = {Intracellular quercetin accumulation and its impact on mitochondrial dysfunction in intestinal Caco-2 cells.}, journal = {Food research international (Ottawa, Ont.)}, volume = {145}, number = {}, pages = {110430}, doi = {10.1016/j.foodres.2021.110430}, pmid = {34112387}, issn = {1873-7145}, mesh = {Caco-2 Cells ; Humans ; Membrane Potential, Mitochondrial ; *Mitochondria/metabolism ; *Quercetin/metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {PURPOSE: Flavonoid bioavailability and bioactivity is associated with interindividual variability, which is partially due to differences in health status. Previously, it was demonstrated that cellular stress, especially mitochondrial stress, increases intracellular quercetin uptake and this is associated with beneficial health effects. Here, the impact of quercetin on mitochondrial dysfunction, induced by stressors targeting different sites of the electron transport chain, is investigated. The influence of the mitochondrial stress on quercetin uptake and subcellular location is studied and the accumulated quercetin metabolites in intestinal Caco-2 cells and mitochondria are characterized.<br><br>PRINCIPAL RESULTS: It was observed that quercetin counteracted (i) the carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP)-induced decrease in maximum oxygen consumption, (ii) the valinomycin-, oligomycin- and FCCP-induced reactive oxygen species production and (iii) the valinomycin-induced disruption of mitochondrial membrane potential. Using confocal microscopy, it was found that upon mitochondrial stress, the intracellular quercetin accumulation increased and was partially located in the mitochondria. Finally, it was demonstrated that quercetin was present as O-methyl, O-methylglucuronide and O-methylsulfate conjugates in the cell lysate and mitochondria-enriched fraction.<br><br>MAJOR CONCLUSIONS: This study shows that quercetin can partially restore, especially FCCP-induced, mitochondrial dysfunction and this protective effect was linked with an intracellular quercetin accumulation in the mitochondria of intestinal cells.}, }
@article {pmid34110473, year = {2021}, author = {Rivera, AJ and Tyx, RE}, title = {Microbiology of the American Smokeless Tobacco.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {12}, pages = {4843-4853}, pmid = {34110473}, issn = {1432-0614}, mesh = {Carcinogens ; Humans ; Metagenomics ; *Microbiota ; *Tobacco, Smokeless ; United States ; }, abstract = {Smokeless tobacco products (STP) contain diverse microbial communities that contribute to the formation of harmful chemical byproducts. This is concerning since 300 million individuals around the globe are users of smokeless tobacco. Significant evidence has shown that microbial metabolic activities mediate the formation of carcinogens during manufacturing. In recent years, studies have revealed a series of additional health impacts that include lesions and inflammation of the oral mucosa and the gastrointestinal tract, as well as alterations of the endogenous microbiota. These findings are due to recent developments in molecular technologies that allowed researchers to better examine the microbial component of these products. This new information illustrates the scale of the STP microbiota and its diversity in the finished product that is sold for consumption. Additionally, the application of metagenomics and metatranscriptomics has provided the tools to look at phylogenies across bacterial, viral, and eukaryotic groups, their functional capacities, and viability. Here we present key examples of tobacco microbiology research that utilizes newer approaches and strategies to define the microbial component of smokeless tobacco products. We also highlight challenges in these approaches, the knowledge gaps being filled, and those gaps that warrant further study. A better understanding of the microbiology of STP brings vast public health benefits. It will provide important information for the product consumer, impact manufacturing practices, and provide support for the development of attainable and more meaningful regulatory goals. KEY POINTS: Newer technologies allowed quicker and more comprehensive identification of microbes in tobacco samples, encapsulating microorganisms difficult or impossible to culture. Current research in smokeless tobacco microbiology is filling knowledge gaps previously unfilled due to the lack of suitable approaches. The microbial ecology of smokeless tobacco presents a clearer picture of diversity and variability not considered before.}, }
@article {pmid34110072, year = {2022}, author = {Nir, I and Barak, H and Kramarsky-Winter, E and Kushmaro, A and de Los Ríos, A}, title = {Microscopic and biomolecular complementary approaches to characterize bioweathering processes at petroglyph sites from the Negev Desert, Israel.}, journal = {Environmental microbiology}, volume = {24}, number = {2}, pages = {967-980}, doi = {10.1111/1462-2920.15635}, pmid = {34110072}, issn = {1462-2920}, mesh = {*Bacteria ; Israel ; *Metagenomics ; Microscopy, Electron, Scanning ; }, abstract = {Throughout the Negev Desert highlands, thousands of ancient petroglyphs sites are susceptible to deterioration processes that may result in the loss of this unique rock art. Therefore, the overarching goal of the current study was to characterize the composition, diversity and effects of microbial colonization of the rocks to find ways of protecting these unique treasures. The spatial organization of the microbial colonizers and their relationships with the lithic substrate were analysed using scanning electron microscopy. This approach revealed extensive epilithic and endolithic colonization and close microbial-mineral interactions. Shotgun sequencing analysis revealed various taxa from the archaea, bacteria and some eukaryotes. Metagenomic coding sequences (CDS) of these microbial lithobionts exhibited specific metabolic pathways involved in the rock elements' cycles and uptake processes. Thus, our results provide evidence for the potential participation of the microorganisms colonizing these rocks during different solubilization and mineralization processes. These damaging actions may contribute to the deterioration of this extraordinary rock art and thus threaten this valuable heritage. Shotgun metagenomic sequencing, in conjunction with the in situ scanning electron microscopy study, can thus be considered an effective strategy to understand the complexity of the weathering processes occurring at petroglyph sites and other cultural heritage assets.}, }
@article {pmid34108667, year = {2021}, author = {Yuan, Z and Druzhinina, IS and Gibbons, JG and Zhong, Z and Van de Peer, Y and Rodriguez, RJ and Liu, Z and Wang, X and Wei, H and Wu, Q and Wang, J and Shi, G and Cai, F and Peng, L and Martin, FM}, title = {Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus.}, journal = {The ISME journal}, volume = {15}, number = {12}, pages = {3468-3479}, pmid = {34108667}, issn = {1751-7370}, mesh = {*Ascomycota/genetics ; *Chenopodiaceae/microbiology ; Endophytes/genetics ; *Genomic Islands ; Melanins ; Pigmentation ; Salt-Tolerant Plants/*microbiology ; }, abstract = {Understanding how organisms adapt to extreme living conditions is central to evolutionary biology. Dark septate endophytes (DSEs) constitute an important component of the root mycobiome and they are often able to alleviate host abiotic stresses. Here, we investigated the molecular mechanisms underlying the beneficial association between the DSE Laburnicola rhizohalophila and its host, the native halophyte Suaeda salsa, using population genomics. Based on genome-wide Fst (pairwise fixation index) and Vst analyses, which compared the variance in allele frequencies of single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs), respectively, we found a high level of genetic differentiation between two populations. CNV patterns revealed population-specific expansions and contractions. Interestingly, we identified a ~20 kbp genomic island of high divergence with a strong sign of positive selection. This region contains a melanin-biosynthetic polyketide synthase gene cluster linked to six additional genes likely involved in biosynthesis, membrane trafficking, regulation, and localization of melanin. Differences in growth yield and melanin biosynthesis between the two populations grown under 2% NaCl stress suggested that this genomic island contributes to the observed differences in melanin accumulation. Our findings provide a better understanding of the genetic and evolutionary mechanisms underlying the adaptation to saline conditions of the L. rhizohalophila-S. salsa symbiosis.}, }
@article {pmid34108452, year = {2021}, author = {Zhao, T and Zwaenepoel, A and Xue, JY and Kao, SM and Li, Z and Schranz, ME and Van de Peer, Y}, title = {Whole-genome microsynteny-based phylogeny of angiosperms.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3498}, pmid = {34108452}, issn = {2041-1723}, mesh = {Evolution, Molecular ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Magnoliopsida/classification/*genetics ; Models, Genetic ; Multigene Family/genetics ; *Phylogeny ; *Synteny ; }, abstract = {Plant genomes vary greatly in size, organization, and architecture. Such structural differences may be highly relevant for inference of genome evolution dynamics and phylogeny. Indeed, microsynteny-the conservation of local gene content and order-is recognized as a valuable source of phylogenetic information, but its use for the inference of large phylogenies has been limited. Here, by combining synteny network analysis, matrix representation, and maximum likelihood phylogenetic inference, we provide a way to reconstruct phylogenies based on microsynteny information. Both simulations and use of empirical data sets show our method to be accurate, consistent, and widely applicable. As an example, we focus on the analysis of a large-scale whole-genome data set for angiosperms, including more than 120 available high-quality genomes, representing more than 50 different plant families and 30 orders. Our 'microsynteny-based' tree is largely congruent with phylogenies proposed based on more traditional sequence alignment-based methods and current phylogenetic classifications but differs for some long-contested and controversial relationships. For instance, our synteny-based tree finds Vitales as early diverging eudicots, Saxifragales within superasterids, and magnoliids as sister to monocots. We discuss how synteny-based phylogenetic inference can complement traditional methods and could provide additional insights into some long-standing controversial phylogenetic relationships.}, }
@article {pmid34107988, year = {2021}, author = {Flachs, A and Orkin, JD}, title = {On pickles: biological and sociocultural links between fermented foods and the human gut microbiome.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {17}, number = {1}, pages = {39}, pmid = {34107988}, issn = {1746-4269}, support = {Global Synergy Grant//College of Liberal Arts, Purdue University/ ; }, mesh = {Fermentation ; *Fermented Foods/microbiology ; *Food Microbiology ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; }, abstract = {BACKGROUND: The composition of the human microbiome varies considerably in diversity and density across communities as a function of the foods we eat and the places we live. While all foods contain microbes, humans directly shape this microbial ecology through fermentation. Fermented foods are produced from microbial reactions that depend on local environmental conditions, fermentation practices, and the manner in which foods are prepared and consumed. These interactions are of special interest to ethnobiologists because they link investigations of how people shape and know the world around them to local knowledge, food traditions, local flora, and microbial taxa.<br><br>METHODS: In this manuscript, we report on data collected at a fermentation revivalist workshop in Tennessee. To ask how fermentation traditions are learned and influence macro and micro ecologies, we conducted interviews with eleven people and participated in a four-day craft fermentation workshop. We also collected 46 fermented food products and 46 stool samples from workshop participants eating those fermented foods.<br><br>RESULTS: We identified ten major themes comprised of 29 sub-themes drawn from 326 marked codes in the transcripts. In combination, this analysis allowed us to summarize key experiences with fermentation, particularly those related to a sense of authenticity, place, health, and the discovery of tactile work. From the 605 amplicon sequence variants (ASVs) shared between food and fecal samples, we identified 25 candidate ASVs that are suspected to have been transmitted from fermented food samples to the gut microbiomes of the workshop participants. Our results indicate that many of the foods prepared and consumed during the workshop were rich sources of probiotic microbes.<br><br>CONCLUSIONS: By combining these qualitative social and quantitative microbiological data, we suggest that variation in culturally informed fermentation practices introduces variation in bacterial flora even among very similar foods, and that these food products can influence gut microbial ecology.}, }
@article {pmid34106771, year = {2021}, author = {Scales, BS and Cable, RN and Duhaime, MB and Gerdts, G and Fischer, F and Fischer, D and Mothes, S and Hintzki, L and Moldaenke, L and Ruwe, M and Kalinowski, J and Kreikemeyer, B and Pedrotti, ML and Gorsky, G and Elineau, A and Labrenz, M and Oberbeckmann, S}, title = {Cross-Hemisphere Study Reveals Geographically Ubiquitous, Plastic-Specific Bacteria Emerging from the Rare and Unexplored Biosphere.}, journal = {mSphere}, volume = {6}, number = {3}, pages = {e0085120}, pmid = {34106771}, issn = {2379-5042}, mesh = {Bacteria/*genetics/*isolation &amp; purification/metabolism ; Biofilms/growth &amp; development ; Geography ; *Microbiota ; *Plastics ; RNA, Ribosomal, 16S ; Seawater/*microbiology ; Water Pollutants, Chemical/analysis ; }, abstract = {While it is now appreciated that the millions of tons of plastic pollution travelling through marine systems carry complex communities of microorganisms, it is still unknown to what extent these biofilm communities are specific to the plastic or selected by the surrounding ecosystem. To address this, we characterized and compared the microbial communities of microplastic particles, nonplastic (natural and wax) particles, and the surrounding waters from three marine ecosystems (the Baltic, Sargasso and Mediterranean seas) using high-throughput 16S rRNA gene sequencing. We found that biofilm communities on microplastic and nonplastic particles were highly similar to one another across this broad geographical range. The similar temperature and salinity profiles of the Sargasso and Mediterranean seas, compared to the Baltic Sea, were reflected in the biofilm communities. We identified plastic-specific operational taxonomic units (OTUs) that were not detected on nonplastic particles or in the surrounding waters. Twenty-six of the plastic-specific OTUs were geographically ubiquitous across all sampled locations. These geographically ubiquitous plastic-specific OTUs were mostly low-abundance members of their biofilm communities and often represented uncultured members of marine ecosystems. These results demonstrate the potential for plastics to be a reservoir of rare and understudied microbes, thus warranting further investigations into the dynamics and role of these microbes in marine ecosystems. IMPORTANCE This study represents one of the largest comparisons of biofilms from environmentally sampled plastic and nonplastic particles from aquatic environments. By including particles sampled through three separate campaigns in the Baltic, Sargasso, and Mediterranean seas, we were able to make cross-geographical comparisons and discovered common taxonomical signatures that define the plastic biofilm. For the first time, we identified plastic-specific bacteria that reoccur across marine regions. Our data reveal that plastics have selective properties that repeatedly enrich for similar bacteria regardless of location, potentially shifting aquatic microbial communities in areas with high levels of plastic pollution. Furthermore, we show that bacterial communities on plastic do not appear to be strongly influenced by polymer type, suggesting that other properties, such as the absorption and/or leaching of chemicals from the surface, are likely to be more important in the selection and enrichment of specific microorganisms.}, }
@article {pmid34106767, year = {2021}, author = {Dove, NC and Veach, AM and Muchero, W and Wahl, T and Stegen, JC and Schadt, CW and Cregger, MA}, title = {Assembly of the Populus Microbiome Is Temporally Dynamic and Determined by Selective and Stochastic Factors.}, journal = {mSphere}, volume = {6}, number = {3}, pages = {e0131620}, pmid = {34106767}, issn = {2379-5042}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Fungi/classification/*genetics ; *Genotype ; Microbiota/*genetics/physiology ; Plant Leaves/microbiology ; Populus/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Seasons ; Soil Microbiology ; }, abstract = {Recent work shows that the plant microbiome, particularly the initial assembly of this microbiome, influences plant health, survival, and fitness. Here, we characterize the initial assembly of the Populus microbiome across ten genotypes belonging to two poplar species in a common garden using 16S rRNA gene and ITS2 region amplicon sequencing of the leaf endosphere, leaf surface, root endosphere, and rhizosphere. We sampled these microbiomes three times throughout the first growing season and found that the composition of the microbiome changed dramatically over time across all plant-associated habitats and host genotypes. For archaea and bacteria, these changes were dominated by strong homogenizing selection (accounting for 29 to 62% of pairwise comparisons). However, fungal assembly was generally characterized by multiple ecological assembly processes (i.e., a mix of weak selective and dispersal processes). Interestingly, genotype, while a significant moderator of microbiome composition, generally explained less variation than sample date across plant-associated habitats. We defined a set of core genera that accounted for, on average, 36% of the microbiome. The relative abundance of this core community was consistent over time. Additionally, using source tracking modeling, we determined that new microbial taxa colonize from both aboveground and belowground sources, and combined with our ecological assembly null models, we found that both selective and dispersal processes explained the differences between exo- (i.e., leaf surface and rhizosphere) and endospheric microbiomes. Taken together, our results suggest that the initial assembly of the Populus microbiome is time-, genotype-, and habitat-dependent and is moderated by both selective and stochastic factors. IMPORTANCE The initial assembly of the plant microbiome may establish the trajectory of forthcoming microbiome states, which could determine the overall future health of the plant. However, while much is known about the initial microbiome assembly of grasses and agricultural crops, less is known about the initial microbiome of long-lived trees, such as poplar (Populus spp.). Thus, a greater understanding of initial plant microbiome assembly in an ecologically and economically important plant such as Populus is highly desirable. Here, we show that the initial microbiome community composition and assembly in the first growing season of Populus is temporally dynamic and is determined by a combination of both selective and stochastic factors. Our findings could be used to prescribe ecologically informed microbial inoculations and better predict the composition of the Populus microbiome into the future and to better understand its influence on plant health.}, }
@article {pmid34105010, year = {2022}, author = {Naidoo, Y and Valverde, A and Pierneef, RE and Cowan, DA}, title = {Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {689-701}, pmid = {34105010}, issn = {1432-184X}, support = {Free standing//National Research Foundation/ ; }, mesh = {Desert Climate ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {Precipitation is one of the major constraints influencing the diversity, structure, and activity of soil microbial communities in desert ecosystems. However, the effect of changes in precipitation on soil microbial communities in arid soil microbiomes remains unresolved. In this study, using 16S rRNA gene high-throughput sequencing and shotgun metagenome sequencing, we explored changes in taxonomic composition and functional potential across two zones in the Namib Desert with contrasting precipitation regime. We found that precipitation regime had no effect on taxonomic and functional alpha-diversity, but that microbial community composition and functional potential (beta-diversity) changed with increased precipitation. For instance, Acidobacteriota and 'resistance to antibiotics and toxic compounds' related genes were relatively more abundant in the high-rainfall zone. These changes were largely due to a small set of microbial taxa, some of which were present in low abundance (i.e. members of the rare biosphere). Overall, these results indicate that key climatic factors (i.e. precipitation) shape the taxonomic and functional attributes of the arid soil microbiome. This research provides insight into how changes in precipitation patterns associated with global climate change may impact microbial community structure and function in desert soils.}, }
@article {pmid34105009, year = {2022}, author = {Febinia, CA and Malik, SG and Djuwita, R and Weta, IW and Wihandani, DM and Maulida, R and Sudoyo, H and Holmes, AJ}, title = {Distinctive Microbiome Type Distribution in a Young Adult Balinese Cohort May Reflect Environmental Changes Associated with Modernization.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {798-810}, pmid = {34105009}, issn = {1432-184X}, mesh = {Cohort Studies ; Diet ; Feces ; Female ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Young Adult ; }, abstract = {An important public health question is understanding how changes in human environments can drive changes in the gut microbiota that influence risks associated with human health and wellbeing. It is well-documented that the modernization of societies is strongly correlated with intergenerational change in the frequency of nutrition-related chronic diseases in which microbial dysbiosis is implicated. The population of Bali, Indonesia, is well-positioned to study the interconnection between a changing food environment and microbiome patterns in its early stages, because of a recent history of modernization. Here, we characterize the fecal microbiota and diet history of the young adult women in Bali, Indonesia (n = 41) in order to compare microbial patterns in this generation with those of other populations with different histories of a modern food environment (industrialized supply chain). We found strong support for two distinct fecal microbiota community types in our study cohort at similar frequency: a Prevotella-rich (Type-P) and a Bacteroides-rich (Type-B) community (p < 0.001, analysis of similarity, Wilcoxon test). Although Type-P individuals had lower alpha diversity (p < 0.001, Shannon) and higher incidence of obesity, multivariate analyses with diet data showed that community types significantly influenced associations with BMI. In a multi-country dataset (n = 257), we confirmed that microbial beta diversity across subsistent and industrial populations was significantly associated with Prevotella and Bacteroides abundance (p < 0.001, generalized additive model) and that the prevalence of community types differs between societies. The young adult Balinese microbiota was distinctive in having an equal prevalence of two community types. Collectively, our study showed that the incorporation of community types as an explanatory factor into study design or modeling improved the ability to identify microbiome associations with diet and health metrics.}, }
@article {pmid34105008, year = {2022}, author = {Sun, Y and Huang, Y and Xu, S and Li, J and Yin, M and Tian, H}, title = {Seasonal Variations in the Characteristics of Microbial Community Structure and Diversity in Atmospheric Particulate Matter from Clean Days and Smoggy Days in Beijing.}, journal = {Microbial ecology}, volume = {83}, number = {3}, pages = {568-582}, pmid = {34105008}, issn = {1432-184X}, mesh = {*Air Pollutants ; Beijing ; China ; Environmental Monitoring/methods ; Humans ; *Microbiota ; Particulate Matter ; Seasons ; }, abstract = {Microorganisms are an important part of atmospheric particulate matter and are closely related to human health. In this paper, the variations in the characteristics of the chemical components and bacterial communities in PM10 and PM2.5 grouped according to season, pollution degree, particle size, and winter heating stage were studied. The influence of environmental factors on community structure was also analyzed. The results showed that seasonal variations were significant. NO3[-] contributed the most to the formation of particulate matter in spring and winter, while SO4[2-] contributed the most in summer and autumn. The community structures in summer and autumn were similar, while the community structure in spring was significantly different. The dominant phyla were similar among seasons, but their proportions were different. The dominant genera were no-rank_c_Cyanobacteria, Acidovorax, Escherichia-Shigella and Sphingomonas in spring; Massilia, Bacillus, Acinetobacter, Rhodococcus, and Brevibacillus in summer and autumn; and Rhodococcus in winter. The atmospheric microorganisms in Beijing mainly came from soil, water, and plants. The few pathogens detected were mainly affected by the microbial source on the sampling day, regardless of pollution level. RDA (redundancy analysis) showed that the bacterial community was positively correlated with the concentration of particulate matter and that the wind speed in spring was positively correlated with NO3[-] levels, NH4[+] levels, temperature, and relative humidity in summer and autumn, but there was no clear consistency among winter samples. This study comprehensively analyzed the variations in the characteristics of the airborne bacterial community in Beijing over one year and provided a reference for understanding the source, mechanism, and assessment of the health effects of different air qualities.}, }
@article {pmid34100639, year = {2021}, author = {Rochefort, A and Simonin, M and Marais, C and Guillerm-Erckelboudt, AY and Barret, M and Sarniguet, A}, title = {Transmission of Seed and Soil Microbiota to Seedling.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {e0044621}, pmid = {34100639}, issn = {2379-5077}, support = {//INRAE Metaomics and Ecosystems Metaprogram/ ; //INRAE Plant Health and Environment division/ ; //Conseil R&#xe9;gional de Bretagne (Brittany Council)/ ; }, abstract = {The seed microbial community constitutes an initial inoculum for plant microbiota assembly. Still, the persistence of seed microbiota when seeds encounter soil during plant emergence and early growth is barely documented. We characterized the encounter event of seed and soil microbiota and how it structured seedling bacterial and fungal communities by using amplicon sequencing. We performed eight contrasting encounter events to identify drivers influencing seedling microbiota assembly. To do so, four contrasting seed lots of two Brassica napus genotypes were sown in two soils whose microbial diversity levels were manipulated by serial dilution and recolonization. Seedling root and stem microbiota were influenced by soil but not by initial seed microbiota composition or by plant genotype. A strong selection on the seed and soil communities occurred during microbiota assembly, with only 8% to 32% of soil taxa and 0.8% to 1.4% of seed-borne taxa colonizing seedlings. The recruitment of seedling microbiota came mainly from soil (35% to 72% of diversity) and not from seeds (0.3% to 15%). Soil microbiota transmission success was higher for the bacterial community than for the fungal community. Interestingly, seedling microbiota was primarily composed of initially rare taxa (from seed, soil, or unknown origin) and intermediate-abundance soil taxa. IMPORTANCE Seed microbiota can have a crucial role for crop installation by modulating dormancy, germination, seedling development, and recruitment of plant symbionts. Little knowledge is available on the fraction of the plant microbiota that is acquired through seeds. We characterize the encounter between seed and soil communities and how they colonize the seedling together. Transmission success and seedling community assemblage can be influenced by the variation of initial microbial pools, i.e., plant genotype and cropping year for seeds and diversity level for soils. Despite a supposed resident advantage of the seed microbiota, we show that transmission success is in favor of the soil microbiota. Our results also suggest that successful plant-microbiome engineering based on native seed or soil microbiota must include rare taxa.}, }
@article {pmid34100635, year = {2021}, author = {Tracanna, V and Ossowicki, A and Petrus, MLC and Overduin, S and Terlouw, BR and Lund, G and Robinson, SL and Warris, S and Schijlen, EGWM and van Wezel, GP and Raaijmakers, JM and Garbeva, P and Medema, MH}, title = {Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {e0111620}, pmid = {34100635}, issn = {2379-5077}, support = {ALWGR. 2015.1//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; }, abstract = {Disease-suppressive soils protect plants against soilborne fungal pathogens that would otherwise cause root infections. Soil suppressiveness is, in most cases, mediated by the antagonistic activity of the microbial community associated with the plant roots. Considering the enormous taxonomic and functional diversity of the root-associated microbiome, identification of the microbial genera and mechanisms underlying this phenotype is challenging. One approach to unravel the underlying mechanisms is to identify metabolic pathways enriched in the disease-suppressive microbial community, in particular, pathways that harbor natural products with antifungal properties. An important class of these natural products includes peptides produced by nonribosomal peptide synthetases (NRPSs). Here, we applied functional amplicon sequencing of NRPS-associated adenylation domains (A domains) to a collection of eight soils that are suppressive or nonsuppressive (i.e., conducive) to Fusarium culmorum, a fungal root pathogen of wheat. To identify functional elements in the root-associated bacterial community, we developed an open-source pipeline, referred to as dom2BGC, for amplicon annotation and putative gene cluster reconstruction through analyzing A domain co-occurrence across samples. We applied this pipeline to rhizosphere communities from four disease-suppressive and four conducive soils and found significant similarities in NRPS repertoires between suppressive soils. Specifically, several siderophore biosynthetic gene clusters were consistently associated with suppressive soils, hinting at competition for iron as a potential mechanism of suppression. Finally, to validate dom2BGC and to allow more unbiased functional metagenomics, we performed 10× metagenomic sequencing of one suppressive soil, leading to the identification of multiple gene clusters potentially associated with the disease-suppressive phenotype. IMPORTANCE Soil-borne plant-pathogenic fungi continue to be a major threat to agriculture and horticulture. The genus Fusarium in particular is one of the most devastating groups of soilborne fungal pathogens for a wide range of crops. Our approach to develop novel sustainable strategies to control this fungal root pathogen is to explore and exploit an effective, yet poorly understood naturally occurring protection, i.e., disease-suppressive soils. After screening 28 agricultural soils, we recently identified four soils that were suppressive to root disease of wheat caused by Fusarium culmorum. We also confirmed, via sterilization and transplantation, that the microbiomes of these soils play a significant role in the suppressive phenotype. By adopting nonribosomal peptide synthetase (NRPS) functional amplicon screening of suppressive and conducive soils, we here show how computationally driven comparative analysis of combined functional amplicon and metagenomic data can unravel putative mechanisms underlying microbiome-associated plant phenotypes.}, }
@article {pmid34099808, year = {2021}, author = {Timmers, LFSM and Peixoto, JV and Ducati, RG and Bachega, JFR and de Mattos Pereira, L and Caceres, RA and Majolo, F and da Silva, GL and Anton, DB and Dellagostin, OA and Henriques, JAP and Xavier, LL and Goettert, MI and Laufer, S}, title = {SARS-CoV-2 mutations in Brazil: from genomics to putative clinical conditions.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {11998}, pmid = {34099808}, issn = {2045-2322}, mesh = {Brazil ; COVID-19/*genetics ; Genome, Viral ; Genomics ; Humans ; Mutation/*genetics ; SARS-CoV-2/*genetics/pathogenicity ; Severity of Illness Index ; Viral Proteins/*genetics ; }, abstract = {Due to the high rate of transmissibility, Brazil became the new COVID-19 outbreak epicenter and, since then, is being monitored to understand how SARS-CoV-2 mutates and spreads. We combined genomic and structural analysis to evaluate genomes isolated from different regions of Brazil and show that the most prevalent mutations were located in the S, N, ORF3a and ORF6 genes, which are involved in different stages of viral life cycle and its interaction with the host cells. Structural analysis brought to light the positions of these mutations on protein structures, contributing towards studies of selective structure-based drug discovery and vaccine development.}, }
@article {pmid34097120, year = {2021}, author = {Hou, D and Zhou, R and Zeng, S and Wei, D and Deng, X and Xing, C and Weng, S and He, J and Huang, Z}, title = {Stochastic processes shape the bacterial community assembly in shrimp cultural pond sediments.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {12}, pages = {5013-5022}, pmid = {34097120}, issn = {1432-0614}, support = {31902392//National Natural Science Foundation of China/ ; CARS-48//China Agriculture Research System/ ; 2019A1515011557//Natural Science Foundation of Guangdong Province/ ; 19lgpy103//Fundamental Research Funds for the Central Universities/ ; 2020B0202010009//Key Research and Development Projects in Guangdong Province/ ; }, mesh = {Animals ; Bacteria/genetics ; *Geologic Sediments ; *Ponds ; RNA, Ribosomal, 16S ; Stochastic Processes ; }, abstract = {Sediment environments harbor a repertoire of microorganisms that contribute to animal health and the microecosystem in aquaculture ecosystems, but their community diversity and the potential factors that control it remain unclear. Here, we applied 16S rRNA gene amplicon sequencing to investigate bacterial diversity and assembly mechanisms in the sediments of shrimp cultural ponds at the mesoscale. Our results showed that sediment bacterial communities contained 10,333 operational taxonomic units (OTUs) but had only 34 core OTUs and that the relative abundances of these core OTUs were significantly correlated with the physicochemical properties of the sediments. Proteobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Acidobacteria, Firmicutes, Actinobacteria, Ignavibacteriae, Spirochaetae and Planctomycetes were the ten most abundant bacterial phyla. Notably, some opportunistic pathogens (e.g. Vibrio and Photobacterium) and potential functional microbes (e.g. Nitrospira, Nitrosomonas, Desulfobulbus and Desulfuromusa) were widely distributed in shrimp cultural pond sediments. More importantly, we found that there was a significant negative but weak distance-decay relationship among bacterial communities in shrimp culture pond sediments at the mesoscale, and that the spatial turnover of these bacterial communities appeared to be largely driven by stochastic processes. Additionally, environmental factors, such as pH and total nitrogen, also played important roles in influencing the sediment bacterial structure. Our findings enhance our understanding of microbial ecology in aquatic ecosystems and facilitate sediment microbiota management in aquaculture. KEY POINTS: • Core bacterial taxa in cultural pond sediments contributed to the shrimp health and element cycling. • There was a significant negative distance-decay relationship among bacterial communities in shrimp culture pond sediments at the mesoscale, and its spatial turnover appeared to be largely driven by stochastic processes. • Environmental factors (e.g. pH and total nitrogen) played important roles in influencing bacterial structure in shrimp cultural pond sediments.}, }
@article {pmid34094994, year = {2021}, author = {Kumar, S and Kumari, N and Talukdar, D and Kothidar, A and Sarkar, M and Mehta, O and Kshetrapal, P and Wadhwa, N and Thiruvengadam, R and Desiraju, BK and Nair, GB and Bhatnagar, S and Mukherjee, S and Das, B and , }, title = {The Vaginal Microbial Signatures of Preterm Birth Delivery in Indian Women.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {622474}, pmid = {34094994}, issn = {2235-2988}, mesh = {Female ; Fusobacteria ; Humans ; India ; Infant, Newborn ; Lactobacillus ; Pregnancy ; *Premature Birth/epidemiology ; RNA, Ribosomal, 16S/genetics ; Vagina ; }, abstract = {BACKGROUND: The incidence of preterm birth (PTB) in India is around 13%. Specific bacterial communities or individual taxon living in the vaginal milieu of pregnant women is a potential risk factor for PTB and may play an important role in its pathophysiology. Besides, bacterial taxa associated with PTB vary across populations.<br><br>OBJECTIVE: Conduct a comparative analysis of vaginal microbiome composition and microbial genomic repertoires of women who enrolled in the Interdisciplinary Group for Advanced Research on Birth Outcomes - A DBT India Initiative (GARBH-Ini) pregnancy cohort to identify bacterial taxa associated with term birth (TB) and PTB in Indian women.<br><br>METHODS: Vaginal swabs were collected during all three trimesters from 38 pregnant Indian women who delivered spontaneous term (n=20) and preterm (n=18) neonates. Paired-end sequencing of V3-V4 region of 16S rRNA gene was performed using the metagenomic DNA isolated from vaginal swabs (n=115). Whole genome sequencing of bacterial species associated with birth outcomes was carried out by shotgun method. Lactobacillus species were grown anaerobically in the De Man, Rogosa and Sharpe (MRS) agar culture medium for isolation of genomic DNA and whole genome sequencing.<br><br>RESULTS: Vaginal microbiome of both term and preterm samples reveals similar alpha diversity indices. However, significantly higher abundance of Lactobacillus iners (p-value All_Trimesters<0.02), Megasphaera sp (p-value1st_Trimester <0.05), Gardnerella vaginalis (p-value2nd_Trimester= 0.01) and Sneathia sanguinegens (p-value2nd_Trimester <0.0001) were identified in preterm samples whereas higher abundance of L. gasseri (p-value3rd_Trimester =0.010) was observed in term samples by Wilcoxon rank-sum test. The relative abundance of L. iners, and Megasphaera sp. were found to be significantly different over time between term and preterm mothers. Analyses of the representative genomes of L. crispatus and L. gasseri indicate presence of secretory transcriptional regulator and several ribosomally synthesized antimicrobial peptides correlated with anti-inflammatory condition in the vagina. These findings indicate protective role of L. crispatus and L. gasseri in reducing the risk of PTB.<br><br>CONCLUSION: Our findings indicate that the dominance of specific Lactobacillus species and few other facultative anaerobes are associated with birth outcomes.}, }
@article {pmid34093488, year = {2021}, author = {Pjevac, P and Hausmann, B and Schwarz, J and Kohl, G and Herbold, CW and Loy, A and Berry, D}, title = {An Economical and Flexible Dual Barcoding, Two-Step PCR Approach for Highly Multiplexed Amplicon Sequencing.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {669776}, pmid = {34093488}, issn = {1664-302X}, abstract = {In microbiome research, phylogenetic and functional marker gene amplicon sequencing is the most commonly-used community profiling approach. Consequently, a plethora of protocols for the preparation and multiplexing of samples for amplicon sequencing have been developed. Here, we present two economical high-throughput gene amplification and sequencing workflows that are implemented as standard operating procedures at the Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna. These workflows are based on a previously-published two-step PCR approach, but have been updated to either increase the accuracy of results, or alternatively to achieve orders of magnitude higher numbers of samples to be multiplexed in a single sequencing run. The high-accuracy workflow relies on unique dual sample barcoding. It allows the same level of sample multiplexing as the previously-published two-step PCR approach, but effectively eliminates residual read missasignments between samples (crosstalk) which are inherent to single barcoding approaches. The high-multiplexing workflow is based on combinatorial dual sample barcoding, which theoretically allows for multiplexing up to 299,756 amplicon libraries of the same target gene in a single massively-parallelized amplicon sequencing run. Both workflows presented here are highly economical, easy to implement, and can, without significant modifications or cost, be applied to any target gene of interest.}, }
@article {pmid34091718, year = {2022}, author = {Girolamini, L and Salaris, S and Pascale, MR and Mazzotta, M and Cristino, S}, title = {Dynamics of Legionella Community Interactions in Response to Temperature and Disinfection Treatment: 7 Years of Investigation.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {353-362}, pmid = {34091718}, issn = {1432-184X}, mesh = {Disinfection/methods ; Humans ; Hydrogen Peroxide ; *Legionella ; *Legionella pneumophila/genetics ; Temperature ; Water Microbiology ; }, abstract = {In man-made water distribution systems, Legionella community interactions remain unknown, due to their ability to change from sessile to planktonic states or live in viable but non-culturable forms, in response to anthropic and environmental stress. During 7 years of hospital Legionella surveillance, in 191 hot water positive samples, the interactions among the Legionella species, temperature, and disinfection treatment were evaluated. Legionella was isolated following ISO 11731:2017, and identification was performed by mip gene sequencing and sequence-based typing (SBT) for L. anisa or L. rubrilucens and L. pneumophila, respectively. The species with the higher frequency of isolation was L. pneumophila serogroup 1 (78.53%; 4865.36 ± 25,479.11 cfu/L), followed by L. anisa (54.45%; 558.79 ± 2637.41 cfu/L) and L. rubrilucens (21.99%; 307.73 ± 1574.95 cfu/L), which were sometimes present together. Spearman's rho correlation test was conducted among the species with respect to temperature and disinfectant (H2O2/Ag[+]). The results showed a generally positive interaction among these species sharing the same environment, except for competition between L. anisa and L. rubrilucens. High temperature (48.83 ± 2.59 °C) and disinfection treatment (11.58 ± 4.99 mg/L) affected the presence of these species. An exception was observed with L. anisa, which showed disinfection treatment resistance. For the purposes of environmental surveillance, it is fundamental to better understand the interactions and dynamic of the Legionella community in man-made water systems in order to choose the proper physical or chemical treatments. The simultaneous presence of different Legionella species could result in an increased resistance to high temperature and disinfectant treatment, leading to changes in contamination level and species diversity.}, }
@article {pmid34091717, year = {2022}, author = {Jaskulska, A and Šulčius, S and Kokociński, M and Koreivienė, J and Nájera, AF and Mankiewicz-Boczek, J}, title = {Cyanophage Distribution Across European Lakes of the Temperate-Humid Continental Climate Zone Assessed Using PCR-Based Genetic Markers.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {284-295}, pmid = {34091717}, issn = {1432-184X}, mesh = {*Bacteriophages/genetics ; Genetic Markers ; *Lakes ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {Studies of the diversity and distribution of freshwater cyanophages are generally limited to the small geographical areas, in many cases including only one or few lakes. Data from dozens of various lakes distributed at a larger distance are necessary to understand their spatial distribution and sensitivity to biotic and abiotic factors. Thus, the objective of this study was to analyze the diversity and distribution of cyanophages within the infected cells using marker genes (psbA, nblA, and g91) in 21 Polish and Lithuanian lakes. Physicochemical factors that might be related to them were also analyzed. The results demonstrated that genetic markers representing cyanophages were observed in most lakes studied. The frequently detected gene was psbA with 88% of cyanophage-positive samples, while nblA and g91 were found in approximately 50% of lakes. The DNA sequence analyses for each gene demonstrated low variability between them, although the psbA sequences branched within the larger cluster of marine Synechoccocuss counterparts. The principal component analysis allowed to identify significant variation between the lakes that presented high and low cyanobacterial biomass. The lakes with high cyanobacterial biomass were further separated by country and the different diversity of cyanobacteria species, particularly Planktothrix agardhii, was dominant in the Polish lakes and Planktolyngbya limnetica in the Lithuanian lakes. The total phosphorous and the presence of cyanophage genes psbA and nblA were the most important factors that allowed differentiation for the Polish lakes, while the pH and the genes g91 and nblA for the Lithuanian lakes.}, }
@article {pmid34091223, year = {2021}, author = {Sun, C and Zhang, B and Ning, D and Zhang, Y and Dai, T and Wu, L and Li, T and Liu, W and Zhou, J and Wen, X}, title = {Seasonal dynamics of the microbial community in two full-scale wastewater treatment plants: Diversity, composition, phylogenetic group based assembly and co-occurrence pattern.}, journal = {Water research}, volume = {200}, number = {}, pages = {117295}, doi = {10.1016/j.watres.2021.117295}, pmid = {34091223}, issn = {1879-2448}, mesh = {*Microbiota ; Phylogeny ; Seasons ; Sewage ; *Water Purification ; }, abstract = {The optimal operation and functional stability of a wastewater treatment plant (WWTP) strongly depend on the properties of its microbial community. However, a knowledge gap remains regarding the seasonal dynamics of microbial community properties, especially phylogenetic group based assembly and co-occurrence patterns. Accordingly, in this study, influent and activated sludge (AS) samples were weekly collected from 2 full-scale WWTPs for one year (89 influent and 103 AS samples in total) and examined by high-throughput Illumina-MiSeq sequencing. The results suggested that the microbial community diversity and composition in the influent fluctuated substantially with season, while those in the AS had a relatively more stable pattern throughout the year. The phylogenetic group based assembly mechanisms of AS community were identified by using "Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model (iCAMP)". The results showed that drift accounted for the largest proportion (52.8%), while homogeneous selection (18.2%) was the most important deterministic process. Deterministic processes dominated in 47 microbial groups (bins), which were also found (~40%) in the AS core taxa dataset. Moreover, the results suggested that Nitrospira were more susceptible to stochastic processes in winter, which may provide a possible explanation for nitrification failure in winter. Network analysis results suggested that the network structure of the AS community could be more stable in summer and autumn. In addition, there were no identical keystone taxa found in different networks (constructed from different plants, sources, and seasons), which supported the context dependency theory. The results of this study deepened our understanding of the microbial ecology in AS systems and provided a foundation for further studies on the community regulation strategy of WWTPs.}, }
@article {pmid34089088, year = {2022}, author = {Zhao, Z and Cheng, M and Li, Y and Song, X and Wang, Y and Zhang, Y}, title = {A Novel Constructed Wetland Combined with Microbial Desalination Cells and its Application.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {340-352}, pmid = {34089088}, issn = {1432-184X}, support = {51909157//National Natural Science Foundation of China/ ; 2019YFC0408604//National Key Research and Development Project/ ; 19QC1401100//Shanghai Rising-Star Program/ ; hklk201912//Open Foundation of Hebei Key Laboratory of Wetland Ecology and Conservation/ ; SZGXZS2020068//Research project of ecological environment protection and restoration of Yangtze River in Zhoushan/ ; }, mesh = {*Bioelectric Energy Sources/microbiology ; Electrodes ; Wastewater ; *Water Purification/methods ; Wetlands ; }, abstract = {Wastewater recycling can alleviate the shortage of water resources. Saline water is seldom treated with biological processes, and its recycling rate is low. Constructed wetland (CW) is a safe, economical, and ecological water treatment method. However, the saline water treatment performance of CW is not good. Microbial desalination cells (MDC) utilizing a bioelectrochemical approach achieve functions of desalination and power generation. In this study, MDC was used to strengthen CW to form a composite system, MDC-CW. Through optimization of design parameters, MDC-CW was applied in the treatment of salt-containing water. The average total nitrogen removal rate in MDC-CW-P1 reached 87.33% and the average COD removal rate was 92.79%. The average desalination rate of MDC-CW-P1 was 55.78% and the average voltage of MDC-CW-P1 reached 0.40 mV. Planting Canna indica in the MDC-CW was conducive to the functions of desalination and power generation. The above results were also verified by the microbial analysis results of gravels in the substrate, plant rhizosphere, and electrodes. In addition, the decontamination of the device mainly depended on the function of the bacteria commonly used in water treatment, such as Proteobacteria and Bacteroidetes, whereas the generation of power depended on the function of Geobacter. Salt ions moved spontaneously to the cathode and anode under the influence of current generation so that the desalination function was realized under the selective isolation function of exchange membranes. The device design and laboratory applications of MDC-CW experimentally achieved the electrochemical function and broadened the treatment scale of CW.}, }
@article {pmid34086451, year = {2021}, author = {De Paepe, J and Clauwaert, P and Gritti, MC and Ganigué, R and Sas, B and Vlaeminck, SE and Rabaey, K}, title = {Electrochemical In Situ pH Control Enables Chemical-Free Full Urine Nitrification with Concomitant Nitrate Extraction.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {12}, pages = {8287-8298}, doi = {10.1021/acs.est.1c00041}, pmid = {34086451}, issn = {1520-5851}, mesh = {Ammonia ; Bioreactors ; Hydrogen-Ion Concentration ; *Nitrates ; *Nitrification ; Nitrogen ; }, abstract = {Urine is a valuable resource for nutrient recovery. Stabilization is, however, recommended to prevent urea hydrolysis and the associated risk for ammonia volatilization, uncontrolled precipitation, and malodor. This can be achieved by alkalinization and subsequent biological conversion of urea and ammonia into nitrate (nitrification) and organics into CO2. Yet, without pH control, the extent of nitrification is limited as a result of insufficient alkalinity. This study explored the feasibility of an integrated electrochemical cell to obtain on-demand hydroxide production through water reduction at the cathode, compensating for the acidification caused by nitritation, thereby enabling full nitrification. To deal with the inherent variability of the urine influent composition and bioprocess, the electrochemical cell was steered via a controller, modulating the current based on the pH in the bioreactor. This provided a reliable and innovative alternative to base addition, enabling full nitrification while avoiding the use of chemicals, the logistics associated with base storage and dosing, and the associated increase in salinity. Moreover, the electrochemical cell could be used as an in situ extraction and concentration technology, yielding an acidic concentrated nitrate-rich stream. The make-up of the end product could be tailored by tweaking the process configuration, offering versatility for applications on Earth and in space.}, }
@article {pmid34085863, year = {2021}, author = {Jakus, N and Blackwell, N and Osenbrück, K and Straub, D and Byrne, JM and Wang, Z and Glöckler, D and Elsner, M and Lueders, T and Grathwohl, P and Kleindienst, S and Kappler, A}, title = {Nitrate Removal by a Novel Lithoautotrophic Nitrate-Reducing, Iron(II)-Oxidizing Culture Enriched from a Pyrite-Rich Limestone Aquifer.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {16}, pages = {e0046021}, pmid = {34085863}, issn = {1098-5336}, mesh = {Autotrophic Processes ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Calcium Carbonate/analysis/metabolism ; Ferrous Compounds/*metabolism ; Geologic Sediments/analysis/microbiology ; Groundwater/chemistry/*microbiology ; Iron/analysis/metabolism ; Nitrates/*metabolism ; Oxidation-Reduction ; Sulfides/analysis/metabolism ; }, abstract = {Nitrate removal in oligotrophic environments is often limited by the availability of suitable organic electron donors. Chemolithoautotrophic bacteria may play a key role in denitrification in aquifers depleted in organic carbon. Under anoxic and circumneutral pH conditions, iron(II) was hypothesized to serve as an electron donor for microbially mediated nitrate reduction by Fe(II)-oxidizing (NRFeOx) microorganisms. However, lithoautotrophic NRFeOx cultures have never been enriched from any aquifer, and as such, there are no model cultures available to study the physiology and geochemistry of this potentially environmentally relevant process. Using iron(II) as an electron donor, we enriched a lithoautotrophic NRFeOx culture from nitrate-containing groundwater of a pyrite-rich limestone aquifer. In the enriched NRFeOx culture that does not require additional organic cosubstrates for growth, within 7 to 11 days, 0.3 to 0.5 mM nitrate was reduced and 1.3 to 2 mM iron(II) was oxidized, leading to a stoichiometric NO3[-]/Fe(II) ratio of 0.2, with N2 and N2O identified as the main nitrate reduction products. Short-range ordered Fe(III) (oxyhydr)oxides were the product of iron(II) oxidation. Microorganisms were observed to be closely associated with formed minerals, but only few cells were encrusted, suggesting that most of the bacteria were able to avoid mineral precipitation at their surface. Analysis of the microbial community by long-read 16S rRNA gene sequencing revealed that the culture is dominated by members of the Gallionellaceae family that are known as autotrophic, neutrophilic, and microaerophilic iron(II) oxidizers. In summary, our study suggests that NRFeOx mediated by lithoautotrophic bacteria can lead to nitrate removal in anthropogenically affected aquifers. IMPORTANCE Removal of nitrate by microbial denitrification in groundwater is often limited by low concentrations of organic carbon. In these carbon-poor ecosystems, nitrate-reducing bacteria that can use inorganic compounds such as Fe(II) (NRFeOx) as electron donors could play a major role in nitrate removal. However, no lithoautotrophic NRFeOx culture has been successfully isolated or enriched from this type of environment, and as such, there are no model cultures available to study the rate-limiting factors of this potentially important process. Here, we present the physiology and microbial community composition of a novel lithoautotrophic NRFeOx culture enriched from a fractured aquifer in southern Germany. The culture is dominated by a putative Fe(II) oxidizer affiliated with the Gallionellaceae family and performs nitrate reduction coupled to Fe(II) oxidation leading to N2O and N2 formation without the addition of organic substrates. Our analyses demonstrate that lithoautotrophic NRFeOx can potentially lead to nitrate removal in nitrate-contaminated aquifers.}, }
@article {pmid34083720, year = {2021}, author = {Cao, YL and Li, YL and Fan, YF and Li, Z and Yoshida, K and Wang, JY and Ma, XK and Wang, N and Mitsuda, N and Kotake, T and Ishimizu, T and Tsai, KC and Niu, SC and Zhang, D and Sun, WH and Luo, Q and Zhao, JH and Yin, Y and Zhang, B and Wang, JY and Qin, K and An, W and He, J and Dai, GL and Wang, YJ and Shi, ZG and Jiao, EN and Wu, PJ and Liu, X and Liu, B and Liao, XY and Jiang, YT and Yu, X and Hao, Y and Xu, XY and Zou, SQ and Li, MH and Hsiao, YY and Lin, YF and Liang, CK and Chen, YY and Wu, WL and Lu, HC and Lan, SR and Wang, ZW and Zhao, X and Zhong, WY and Yeh, CM and Tsai, WC and Van de Peer, Y and Liu, ZJ}, title = {Wolfberry genomes and the evolution of Lycium (Solanaceae).}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {671}, pmid = {34083720}, issn = {2399-3642}, mesh = {Africa ; Asia ; Chromosomes, Plant/*genetics ; Evolution, Molecular ; Fruit/genetics/metabolism ; Gene Expression Regulation, Plant ; Genome, Plant/*genetics ; Geography ; Lycium/classification/*genetics/metabolism ; North America ; Phylogeny ; Polyploidy ; Polysaccharides/metabolism ; Solanaceae/classification/*genetics/metabolism ; Species Specificity ; Whole Genome Sequencing/*methods ; }, abstract = {Wolfberry Lycium, an economically important genus of the Solanaceae family, contains approximately 80 species and shows a fragmented distribution pattern among the Northern and Southern Hemispheres. Although several herbaceous species of Solanaceae have been subjected to genome sequencing, thus far, no genome sequences of woody representatives have been available. Here, we sequenced the genomes of 13 perennial woody species of Lycium, with a focus on Lycium barbarum. Integration with other genomes provides clear evidence supporting a whole-genome triplication (WGT) event shared by all hitherto sequenced solanaceous plants, which occurred shortly after the divergence of Solanaceae and Convolvulaceae. We identified new gene families and gene family expansions and contractions that first appeared in Solanaceae. Based on the identification of self-incompatibility related-gene families, we inferred that hybridization hotspots are enriched for genes that might be functioning in gametophytic self-incompatibility pathways in wolfberry. Extremely low expression of LOCULE NUBER (LC) and COLORLESS NON-RIPENING (CNR) orthologous genes during Lycium fruit development and ripening processes suggests functional diversification of these two genes between Lycium and tomato. The existence of additional flowering locus C-like MADS-box genes might correlate with the perennial flowering cycle of Lycium. Differential gene expression involved in the lignin biosynthetic pathway between Lycium and tomato likely illustrates woody and herbaceous differentiation. We also provide evidence that Lycium migrated from Africa into Asia, and subsequently from Asia into North America. Our results provide functional insights into Solanaceae origins, evolution and diversification.}, }
@article {pmid34083551, year = {2021}, author = {Fabersani, E and Portune, K and Campillo, I and López-Almela, I and la Paz, SM and Romaní-Pérez, M and Benítez-Páez, A and Sanz, Y}, title = {Bacteroides uniformis CECT 7771 alleviates inflammation within the gut-adipose tissue axis involving TLR5 signaling in obese mice.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {11788}, pmid = {34083551}, issn = {2045-2322}, mesh = {Adaptive Immunity ; Adipose Tissue/metabolism ; Animals ; Bacteroides/*physiology ; Bacteroides Infections/*metabolism/*microbiology/pathology ; Cytokines/metabolism ; Disease Models, Animal ; Energy Metabolism ; Gastroenteritis/*metabolism/*microbiology/pathology ; Gastrointestinal Microbiome ; Immunity, Innate ; Inflammation Mediators/metabolism ; Mice ; Mice, Obese ; Phenotype ; *Signal Transduction ; Toll-Like Receptor 5/*metabolism ; }, abstract = {This study investigated the immune mechanisms whereby administration of Bacteroides uniformis CECT 7771 reduces metabolic dysfunction in obesity. C57BL/6 adult male mice were fed a standard diet or a Western diet high in fat and fructose, supplemented or not with B. uniformis CECT 7771 for 14 weeks. B. uniformis CECT 7771 reduced body weight gain, plasma cholesterol, triglyceride, glucose, and leptin levels; and improved oral glucose tolerance in obese mice. Moreover, B. uniformis CECT 7771 modulated the gut microbiota and immune alterations associated with obesity, increasing Tregs and reducing B cells, total macrophages and the M1/M2 ratio in both the gut and epididymal adipose tissue (EAT) of obese mice. B. uniformis CECT 7771 also increased the concentration of the anti-inflammatory cytokine IL-10 in the gut, EAT and peripheral blood, and protective cytokines TSLP and IL-33, involved in Treg induction and type 2 innate lymphoid cells activation, in the EAT. It also restored the obesity-reduced TLR5 expression in the ileum and EAT. The findings indicate that the administration of a human intestinal bacterium with immunoregulatory properties on the intestinal mucosa helps reverse the immuno-metabolic dysfunction caused by a Western diet acting over the gut-adipose tissue axis.}, }
@article {pmid34081148, year = {2022}, author = {Mezzasoma, A and Coleine, C and Sannino, C and Selbmann, L}, title = {Endolithic Bacterial Diversity in Lichen-Dominated Communities Is Shaped by Sun Exposure in McMurdo Dry Valleys, Antarctica.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {328-339}, pmid = {34081148}, issn = {1432-184X}, mesh = {Antarctic Regions ; Biodiversity ; *Cyanobacteria/genetics ; Humans ; *Lichens ; Sunlight ; }, abstract = {The diversity and composition of endolithic bacterial diversity of several locations in McMurdo Dry Valleys (Continental Antarctica) were explored using amplicon sequencing, targeting the V3 and V4 of the 16S region. Despite the increasing interest in edaphic factors that drive bacterial community composition in Antarctic rocky communities, few researchers focused attention on the direct effects of sun exposure on bacterial diversity; we herein reported significant differences in the northern and southern communities. The analysis of β-diversity showed significant differences among sampled localities. For instance, the most abundant genera found in the north-exposed rocks were Rhodococcus and Blastococcus in Knobhead Mt.; Ktedonobacter and Cyanobacteria Family I Group I in Finger Mt.; Rhodococcus and Endobacter in University Valley; and Segetibacter and Tetrasphaera in Siegfried Peak samples. In south-exposed rocks, instead, the most abundant genera were Escherichia/Shigella and Streptococcus in Knobhead Mt.; Ktedonobacter and Rhodococcus in Finger Mt.; Ktedonobacter and Roseomonas in University Valley; and Blastocatella, Cyanobacteria Family I Group I and Segetibacter in Siegfried Peak. Significant biomarkers, detected by the Linear discriminant analysis Effect Size, were also found among north- and south-exposed communities. Besides, the large number of positive significant co-occurrences may suggest a crucial role of positive associations over competitions under the harsher conditions where these rock-inhabiting microorganisms spread. Although the effect of geographic distances in these extreme environments play a significant role in shaping biodiversity, the study of an edaphic factor, such as solar exposure, adds an important contribution to the mosaic of microbial biodiversity of Antarctic bacterial cryptoendolithic communities.}, }
@article {pmid34081147, year = {2021}, author = {Zhang, T and Wang, NF and Yu, LY}, title = {Geographic Distance and Habitat Type Influence Fungal Communities in the Arctic and Antarctic Sites.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {224-232}, pmid = {34081147}, issn = {1432-184X}, support = {31670025//National Natural Science Foundation of China/ ; }, mesh = {Antarctic Regions ; Arctic Regions ; Ecosystem ; *Mycobiome ; Soil Microbiology ; }, abstract = {The Antarctic and Arctic regions are collectively referred to as the "Two Poles" of the earth and have extremely harsh climate conditions and fragile ecosystems. Until now, the biogeography of the fungal communities in the bipolar regions is not well known. In this study, we focused on the fungal communities in 110 samples collected from four habitat types (i.e., soil, vascular plant, freshwater, moss) in the Antarctic and Arctic sites using high-throughput sequencing. The data showed that the diversity and composition of fungal communities were both geographically patterned and habitat-patterned. ANOSIM tests revealed statistically significant differences among fungal communities in the eight sample types (R = 0.5035, p < 0.001) and those in the bipolar regions (R = 0.32859, p < 0.001). Only 396 OTUs (14.8%) were shared between the bipolar sites. Fungal communities in the four habitat types clustered together in the Arctic site but were separate from those of the Antarctic site, indicating that geographic distance was a more important determinant of fungal communities in the bipolar sites. These findings offer insights into the present-day biogeography of fungal communities in the bipolar sites.}, }
@article {pmid34080061, year = {2021}, author = {Carbonero, F and Strobel, G}, title = {Fungal Ecology Special Issue: Editorial.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {1-4}, pmid = {34080061}, issn = {1432-184X}, mesh = {*Ecology ; *Fungi/genetics ; }, }
@article {pmid34078434, year = {2021}, author = {Gresse, R and Chaucheyras-Durand, F and Denis, S and Beaumont, M and Van de Wiele, T and Forano, E and Blanquet-Diot, S}, title = {Weaning-associated feed deprivation stress causes microbiota disruptions in a novel mucin-containing in vitro model of the piglet colon (MPigut-IVM).}, journal = {Journal of animal science and biotechnology}, volume = {12}, number = {1}, pages = {75}, pmid = {34078434}, issn = {1674-9782}, abstract = {BACKGROUND: Risk factors for the etiology of post-weaning diarrhea, a major problem in swine industry associated with enormous economic losses, remain to be fully elucidated. In concordance with the ethical concerns raised by animal experiments, we developed a new in vitro model of the weaning piglet colon (MPigut-IVM) including a mucin bead compartment to reproduce the mucus surface from the gut to which gut microbes can adhere.<br><br>RESULTS: Our results indicated that the MPigut-IVM is able to establish a representative piglet archaeal and bacterial colon microbiota in terms of taxonomic composition and function. The MPigut-IVM was consequently used to investigate the potential effects of feed deprivation, a common consequence of weaning in piglets, on the microbiota. The lack of nutrients in the MPigut-IVM led to an increased abundance of Prevotellaceae and Escherichia-Shigella and a decrease in Bacteroidiaceae and confirms previous in vivo findings. On top of a strong increase in redox potential, the feed deprivation stress induced modifications of microbial metabolite production such as a decrease in acetate and an increase in proportional valerate, isovalerate and isobutyrate production.<br><br>CONCLUSIONS: The MPigut-IVM is able to simulate luminal and mucosal piglet microbiota and represent an innovative tool for comparative studies to investigate the impact of weaning stressors on piglet microbiota. Besides, weaning-associated feed deprivation in piglets provokes disruptions of MPigut-IVM microbiota composition and functionality and could be implicated in the onset of post-weaning dysbiosis in piglets.}, }
@article {pmid34077260, year = {2021}, author = {Cornell, CR and Zhang, Y and Van Nostrand, JD and Wagle, P and Xiao, X and Zhou, J}, title = {Temporal Changes of Virus-Like Particle Abundance and Metagenomic Comparison of Viral Communities in Cropland and Prairie Soils.}, journal = {mSphere}, volume = {6}, number = {3}, pages = {e0116020}, pmid = {34077260}, issn = {2379-5042}, mesh = {Crops, Agricultural/*virology ; *Grassland ; *Metagenome ; Metagenomics ; *Soil Microbiology ; Spatio-Temporal Analysis ; Virome/*genetics ; Viruses/*genetics ; }, abstract = {During the last several decades, viruses have been increasingly recognized for their abundance, ubiquity, and important roles in different ecosystems. Despite known contributions to aquatic systems, few studies examine viral abundance and community structure over time in terrestrial ecosystems. The effects of land conversion and land management on soil microbes have been previously investigated, but their effects on virus population are not well studied. This study examined annual dynamics of viral abundance in soils from a native tallgrass prairie and two croplands, conventional till winter wheat and no-till canola, in Oklahoma. Virus-like particle (VLP) abundance varied across sites, and showed clear seasonal shifts. VLP abundance significantly correlated with environmental variables that were generally reflective of land use, including air temperature, soil nitrogen, and plant canopy coverage. Structural equation modeling supported the effects of land use on soil communities by emphasizing interactions between management, environmental factors, and viral and bacterial abundance. Between the viral metagenomes from the prairie and tilled wheat field, 1,231 unique viral operational taxonomic units (vOTUs) were identified, and only five were shared that were rare in the contrasting field. Only 13% of the vOTUs had similarity to previously identified viruses in the RefSeq database, with only 7% having known taxonomic classification. Together, our findings indicated land use and tillage practices influence virus abundance and community structure. Analyses of viromes over time and space are vital to viral ecology in providing insight on viral communities and key information on interactions between viruses, their microbial hosts, and the environment. IMPORTANCE Conversion of land alters the physiochemical and biological environments by not only changing the aboveground community, but also modifying the soil environment for viruses and microbes. Soil microbial communities are critical to nutrient cycling, carbon mineralization, and soil quality; and viruses are known for influencing microbial abundance, community structure, and evolution. Therefore, viruses are considered an important part of soil functions in terrestrial ecosystems. In aquatic environments, virus abundance generally exceeds bacterial counts by an order of magnitude, and they are thought to be one of the greatest genetic reservoirs on the planet. However, data are extremely limited on viruses in soils, and even less is known about their responses to the disturbances associated with land use and management. The study provides important insights into the temporal dynamics of viral abundance and the structure of viral communities in response to the common practice of turning native habitats into arable soils.}, }
@article {pmid34073029, year = {2021}, author = {Broadhead, R and Craeye, L and Callewaert, C}, title = {The Future of Functional Clothing for an Improved Skin and Textile Microbiome Relationship.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34073029}, issn = {2076-2607}, support = {F2019/IOF-STARTT/261//Ghent University/ ; }, abstract = {The skin microbiome has become a hot field of research in the last few years. The emergence of next-generation sequencing has given unprecedented insights into the impact and involvement of microbiota in skin conditions. More and more cosmetics contain probiotics or bacteria as an active ingredient, with or without scientific data. This research is also acknowledged by the textile industry. There has been a more holistic approach on how the skin and textile microbiome interacts and how they influence the pH, moisture content and odour generation. To date, most of the ingredients have a broad-spectrum antibacterial action. This manuscript covers the current research and industry developments in the field of skin and textiles. It explores the nature of antimicrobial finishing in textiles which can disrupt the skin microbiome, and the benefits of more natural and microbiome friendly therapies to combat skin conditions, malodour and skin infection.}, }
@article {pmid34072450, year = {2021}, author = {Romaní-Pérez, M and Bullich-Vilarrubias, C and López-Almela, I and Liébana-García, R and Olivares, M and Sanz, Y}, title = {The Microbiota and the Gut-Brain Axis in Controlling Food Intake and Energy Homeostasis.}, journal = {International journal of molecular sciences}, volume = {22}, number = {11}, pages = {}, pmid = {34072450}, issn = {1422-0067}, support = {797297//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; AGL2017-88801-P//Spanish Ministry of Science and Innovation/ ; }, mesh = {Brain/*physiology ; Circadian Rhythm ; Diet ; Disease Susceptibility ; Eating ; *Energy Metabolism ; Feeding Behavior ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*physiology ; *Homeostasis ; Humans ; Microbiota/*physiology ; Micronutrients ; Nutrients ; Obesity/etiology/metabolism ; }, abstract = {Obesity currently represents a major societal and health challenge worldwide. Its prevalence has reached epidemic proportions and trends continue to rise, reflecting the need for more effective preventive measures. Hypothalamic circuits that control energy homeostasis in response to food intake are interesting targets for body-weight management, for example, through interventions that reinforce the gut-to-brain nutrient signalling, whose malfunction contributes to obesity. Gut microbiota-diet interactions might interfere in nutrient sensing and signalling from the gut to the brain, where the information is processed to control energy homeostasis. This gut microbiota-brain crosstalk is mediated by metabolites, mainly short chain fatty acids, secondary bile acids or amino acids-derived metabolites and subcellular bacterial components. These activate gut-endocrine and/or neural-mediated pathways or pass to systemic circulation and then reach the brain. Feeding time and dietary composition are the main drivers of the gut microbiota structure and function. Therefore, aberrant feeding patterns or unhealthy diets might alter gut microbiota-diet interactions and modify nutrient availability and/or microbial ligands transmitting information from the gut to the brain in response to food intake, thus impairing energy homeostasis. Herein, we update the scientific evidence supporting that gut microbiota is a source of novel dietary and non-dietary biological products that may beneficially regulate gut-to-brain communication and, thus, improve metabolic health. Additionally, we evaluate how the feeding time and dietary composition modulate the gut microbiota and, thereby, the intraluminal availability of these biological products with potential effects on energy homeostasis. The review also identifies knowledge gaps and the advances required to clinically apply microbiome-based strategies to improve the gut-brain axis function and, thus, combat obesity.}, }
@article {pmid34068093, year = {2021}, author = {Zhu, J and Sun, X and Zhang, ZD and Tang, QY and Gu, MY and Zhang, LJ and Hou, M and Sharon, A and Yuan, HL}, title = {Effect of Ionizing Radiation on the Bacterial and Fungal Endophytes of the Halophytic Plant Kalidium schrenkianum.}, journal = {Microorganisms}, volume = {9}, number = {5}, pages = {}, pmid = {34068093}, issn = {2076-2607}, support = {31760009//National Natural Science Foundation of China/ ; 2021SKLAB6-9//Project for Extramural Scientists of State Key Laboratory of Agrobiotechnology/ ; nkypt005//Improvement Project of Agricultural Science and Capacity of Technology Innovation Platform in Xinjiang Academy of Agricultural Sciences/ ; KY2019021//Special Project for Basic Scientific Activities of Non-profit Institutes Supported the Government of Xinjiang Uyghur Autonomous Region/ ; }, abstract = {Endophytic bacteria and fungi colonize plants that grow in various types of terrestrial and aquatic ecosystems. Our study investigates the communities of endophytic bacteria and fungi of halophyte Kalidium schrenkianum growing in stressed habitats with ionizing radiation. The geochemical factors and radiation (at low, medium, high level and control) both affected the structure of endophytic communities. The bacterial class Actinobacteria and the fungal class Dothideomycetes predominated the endophytic communities of K. schrenkianum. Aerial tissues of K. schrenkianum had higher fungal diversity, while roots had higher bacterial diversity. Radiation had no significant effect on the abundance of bacterial classes. Soil pH, total nitrogen, and organic matter showed significant effects on the diversity of root endophytes. Radiation affected bacterial and fungal community structure in roots but not in aerial tissues, and had a strong effect on fungal co-occurrence networks. Overall, the genetic diversity of both endophytic bacteria and fungi was higher in radioactive environments, however negative correlations were found between endophytic bacteria and fungi in the plant. The genetic diversity of both endophytic bacteria and fungi was higher in radioactive environments. Our findings suggest that radiation affects root endophytes, and that the endophytes associated with aerial tissues and roots of K. schrenkianum follow different mechanisms for community assembly and different paradigms in stress response.}, }
@article {pmid34064714, year = {2021}, author = {Park, T and Yoon, J and Kim, A and Unno, T and Yun, Y}, title = {Comparison of the Gut Microbiota of Jeju and Thoroughbred Horses in Korea.}, journal = {Veterinary sciences}, volume = {8}, number = {5}, pages = {}, pmid = {34064714}, issn = {2306-7381}, support = {2016R1A6A1A03012862//National Research Foundation of Korea/ ; }, abstract = {(1) Background: The large intestine of horses is an anaerobic fermentative chamber filled with fibrolytic bacteria that play essential roles in digesting and absorbing nutrients for energy production. Although Jeju horses are a prominent local breed in Korea, few studies have investigated the gut microbiota of Jeju horses; (2) Methods: This study performed sequencing of V3 and V4 hypervariable regions of the partial 16S rRNA genes obtained from horse fecal samples and compared the gut microbiota between Jeju and Thoroughbred horses. Thirty and 24 fecal samples were obtained from Jeju and Thoroughbred horses, respectively; (3) Results: The gut microbiota belonged to 23 phyla and 159 families. Firmicutes and Bacteroidetes were the most abundant and predominant phyla, followed by Verrucomicrobia, Euryachaeota, and Spirochaete. The ratio of Firmicutes to Bacteroidetes (F/B), which is known as a relevant marker of gut dysbiosis, was 1.84 for Jeju horses, whereas it was 1.76 for Thoroughbred horses. Moreover, at the genus level, 21 genera were significantly different between the Jeju and Thoroughbred horses (p < 0.05); (4) Conclusions: The Thoroughbred horse's gut microbiotas had significantly higher diversity than the Jeju horses (p < 0.05). In addition, beneficial commensal bacteria that produce short-chain fatty acids thus providing a significant source of energy are also more abundant in Thoroughbred horses. These results provide novel information on the horse gut microbiota and insights for further studies related to the horse gut microbiota.}, }
@article {pmid34064045, year = {2021}, author = {Uriot, O and Kebouchi, M and Lorson, E and Galia, W and Denis, S and Chalancon, S and Hafeez, Z and Roux, E and Genay, M and Blanquet-Diot, S and Dary-Mourot, A}, title = {Identification of Streptococcus thermophilus Genes Specifically Expressed under Simulated Human Digestive Conditions Using R-IVET Technology.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34064045}, issn = {2076-2607}, abstract = {Despite promising health effects, the probiotic status of Streptococcus thermophilus, a lactic acid bacterium widely used in dairy industry, requires further documentation of its physiological status during human gastrointestinal passage. This study aimed to apply recombinant-based in vivo technology (R-IVET) to identify genes triggered in a S. thermophilus LMD-9 reference strain under simulated digestive conditions. First, the R-IVET chromosomal cassette and plasmid genomic library were designed to positively select activated genes. Second, recombinant clones were introduced into complementary models mimicking the human gut, the Netherlands Organization for Applied Scientific Research (TNO) gastrointestinal model imitating the human stomach and small intestine, the Caco-2 TC7 cell line as a model of intestinal epithelium, and anaerobic batch cultures of human feces as a colon model. All inserts of activated clones displayed a promoter activity that differed from one digestive condition to another. Our results also showed that S. thermophilus adapted its metabolism to stressful conditions found in the gastric and colonic competitive environment and modified its surface proteins during adhesion to Caco-2 TC7 cells. Activated genes were investigated in a collection of S. thermophilus strains showing various resistance levels to gastrointestinal stresses, a first stage in the identification of gut resistance markers and a key step in probiotic selection.}, }
@article {pmid34063014, year = {2021}, author = {Weiss, B and Souza, ACO and Constancio, MTL and Alvarenga, DO and Pylro, VS and Alves, LMC and Varani, AM}, title = {Unraveling a Lignocellulose-Decomposing Bacterial Consortium from Soil Associated with Dry Sugarcane Straw by Genomic-Centered Metagenomics.}, journal = {Microorganisms}, volume = {9}, number = {5}, pages = {}, pmid = {34063014}, issn = {2076-2607}, support = {Finance Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior - Brasil (CAPES)/ ; [16/16624-1] and [10/17520-9]//S&#xe3;o Paulo Research Foundation (FAPESP)/ ; [303061/2019-7] and [302085/2017-3]//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, abstract = {Second-generation biofuel production is in high demand, but lignocellulosic biomass' complexity impairs its use due to the vast diversity of enzymes necessary to execute the complete saccharification. In nature, lignocellulose can be rapidly deconstructed due to the division of biochemical labor effectuated in bacterial communities. Here, we analyzed the lignocellulolytic potential of a bacterial consortium obtained from soil and dry straw leftover from a sugarcane milling plant. This consortium was cultivated for 20 weeks in aerobic conditions using sugarcane bagasse as a sole carbon source. Scanning electron microscopy and chemical analyses registered modification of the sugarcane fiber's appearance and biochemical composition, indicating that this consortium can deconstruct cellulose and hemicellulose but no lignin. A total of 52 metagenome-assembled genomes from eight bacterial classes (Actinobacteria, Alphaproteobacteria, Bacilli, Bacteroidia, Cytophagia, Gammaproteobacteria, Oligoflexia, and Thermoleophilia) were recovered from the consortium, in which ~46% of species showed no relevant modification in their abundance during the 20 weeks of cultivation, suggesting a mostly stable consortium. Their CAZymes repertoire indicated that many of the most abundant species are known to deconstruct lignin (e.g., Chryseobacterium) and carry sequences related to hemicellulose and cellulose deconstruction (e.g., Chitinophaga, Niastella, Niabella, and Siphonobacter). Taken together, our results unraveled the bacterial diversity, enzymatic potential, and effectiveness of this lignocellulose-decomposing bacterial consortium.}, }
@article {pmid34059942, year = {2021}, author = {Siebert, A and Hofmann, K and Staib, L and Doll, EV and Scherer, S and Wenning, M}, title = {Amplicon-sequencing of raw milk microbiota: impact of DNA extraction and library-PCR.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {11}, pages = {4761-4773}, pmid = {34059942}, issn = {1432-0614}, support = {Projekt DEAL (German DEAL agreement)//Technische Universit&#xe4;t M&#xfc;nchen/ ; }, mesh = {Animals ; Cattle ; DNA, Bacterial/genetics ; Female ; *Microbiota ; *Milk ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The highly complex raw milk matrix challenges the sample preparation for amplicon-sequencing due to low bacterial counts and high amounts of eukaryotic DNA originating from the cow. In this study, we optimized the extraction of bacterial DNA from raw milk for microbiome analysis and evaluated the impact of cycle numbers in the library-PCR. The selective lysis of eukaryotic cells by proteinase K and digestion of released DNA before bacterial lysis resulted in a high reduction of mostly eukaryotic DNA and increased the proportion of bacterial DNA. Comparative microbiome analysis showed that a combined enzymatic and mechanical lysis procedure using the DNeasy[®] PowerFood[®] Microbial Kit with a modified protocol was best suitable to achieve high DNA quantities after library-PCR and broad coverage of detected bacterial biodiversity. Increasing cycle numbers during library-PCR systematically altered results for species and beta-diversity with a tendency to overrepresentation or underrepresentation of particular taxa. To limit PCR bias, high cycle numbers should thus be avoided. An optimized DNA extraction yielding sufficient bacterial DNA and enabling higher PCR efficiency is fundamental for successful library preparation. We suggest that a protocol using ethylenediaminetetraacetic acid (EDTA) to resolve casein micelles, selective lysis of somatic cells, extraction of bacterial DNA with a combination of mechanical and enzymatic lysis, and restriction of PCR cycles for analysis of raw milk microbiomes is optimal even for samples with low bacterial numbers. KEY POINTS: • Sample preparation for high-throughput 16S rRNA gene sequencing of raw milk microbiota. • Reduction of eukaryotic DNA by enzymatic digestion. • Shift of detected microbiome caused by high cycle numbers in library-PCR.}, }
@article {pmid34059936, year = {2022}, author = {Zhao, XF and Shu, WS and Hao, YQ}, title = {Seasonal Climate Variations Promote Bacterial α-Diversity in Soil.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {513-517}, pmid = {34059936}, issn = {1432-184X}, support = {31901113//National Natural Science Foundation of China/ ; 31901112//National Natural Science Foundation of China/ ; 2019M662951//China Postdoctoral Science Foundation/ ; 2019A1515011879//Natural Science Foundation of Guangdong Province/ ; }, mesh = {Bacteria/genetics ; Seasons ; *Soil ; *Soil Microbiology ; Triticum ; }, abstract = {Ecological theory suggests that temporal environmental fluctuations can contribute greatly to diversity maintenance. Given bacteria's short generation time and rapid responses to environmental change, seasonal climate fluctuations are very likely to play an important role in maintaining the extremely high α-diversity of soil bacterial community, which has been unfortunately neglected in previous studies. Here, with in-depth analyses of two previously published soil bacterial datasets at global scale, we found that soil bacterial α-diversity was positively correlated with both seasonal variations of temperature and precipitation. Furthermore, piecewise structural equation models showed that seasonal variations of temperature or precipitation had weak but significant positive effect on soil bacterial α-diversity in each dataset. However, it is noteworthy that the importance of seasonal climate variations might be underestimated in the above analyses, due to the potential confounding factors (such as vegetation type) and the lack of sampling across seasons. As a supplement, we analyzed a previously published wheat cropland dataset with samples collected in both winter and the following summer across North China Plain. As expected, bacterial α-diversity was positively correlated with seasonal climate variations in the cropland dataset, and climate seasonality explained a larger proportion of variations in bacterial α-diversity. Collectively, these findings implied that fluctuation-dependent mechanisms of diversity maintenance presumably operate in soil bacterial communities. Based on existing evidence, we speculated that the storage effect may be the main mechanism responsible for diversity maintenance in soil bacterial community, but rigorous experimental tests are needed in the future.}, }
@article {pmid34058098, year = {2021}, author = {Paredes, GF and Viehboeck, T and Lee, R and Palatinszky, M and Mausz, MA and Reipert, S and Schintlmeister, A and Maier, A and Volland, JM and Hirschfeld, C and Wagner, M and Berry, D and Markert, S and Bulgheresi, S and König, L}, title = {Anaerobic Sulfur Oxidation Underlies Adaptation of a Chemosynthetic Symbiont to Oxic-Anoxic Interfaces.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {e0118620}, pmid = {34058098}, issn = {2379-5077}, support = {P 28743/FWF_/Austrian Science Fund FWF/Austria ; P28953//Austrian Science Fund (FWF)/ ; P28743//Austrian Science Fund (FWF)/ ; DK plus grant W1257: Microbial Nitrogen Cycling//Austrian Science Fund (FWF)/ ; }, abstract = {Chemosynthetic symbioses occur worldwide in marine habitats, but comprehensive physiological studies of chemoautotrophic bacteria thriving on animals are scarce. Stilbonematinae are coated by thiotrophic Gammaproteobacteria. As these nematodes migrate through the redox zone, their ectosymbionts experience varying oxygen concentrations. However, nothing is known about how these variations affect their physiology. Here, by applying omics, Raman microspectroscopy, and stable isotope labeling, we investigated the effect of oxygen on "Candidatus Thiosymbion oneisti." Unexpectedly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions, but carbon fixation genes and incorporation of [13]C-labeled bicarbonate were not. Instead, several genes involved in carbon fixation were upregulated under oxic conditions, together with genes involved in organic carbon assimilation, polyhydroxyalkanoate (PHA) biosynthesis, nitrogen fixation, and urea utilization. Furthermore, in the presence of oxygen, stress-related genes were upregulated together with vitamin biosynthesis genes likely necessary to withstand oxidative stress, and the symbiont appeared to proliferate less. Based on its physiological response to oxygen, we propose that "Ca. T. oneisti" may exploit anaerobic sulfur oxidation coupled to denitrification to proliferate in anoxic sand. However, the ectosymbiont would still profit from the oxygen available in superficial sand, as the energy-efficient aerobic respiration would facilitate carbon and nitrogen assimilation. IMPORTANCE Chemoautotrophic endosymbionts are famous for exploiting sulfur oxidization to feed marine organisms with fixed carbon. However, the physiology of thiotrophic bacteria thriving on the surface of animals (ectosymbionts) is less understood. One longstanding hypothesis posits that attachment to animals that migrate between reduced and oxic environments would boost sulfur oxidation, as the ectosymbionts would alternatively access sulfide and oxygen, the most favorable electron acceptor. Here, we investigated the effect of oxygen on the physiology of "Candidatus Thiosymbion oneisti," a gammaproteobacterium which lives attached to marine nematodes inhabiting shallow-water sand. Surprisingly, sulfur oxidation genes were upregulated under anoxic relative to oxic conditions. Furthermore, under anoxia, the ectosymbiont appeared to be less stressed and to proliferate more. We propose that animal-mediated access to oxygen, rather than enhancing sulfur oxidation, would facilitate assimilation of carbon and nitrogen by the ectosymbiont.}, }
@article {pmid34054786, year = {2021}, author = {Guerrero-Cruz, S and Vaksmaa, A and Horn, MA and Niemann, H and Pijuan, M and Ho, A}, title = {Methanotrophs: Discoveries, Environmental Relevance, and a Perspective on Current and Future Applications.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {678057}, pmid = {34054786}, issn = {1664-302X}, abstract = {Methane is the final product of the anaerobic decomposition of organic matter. The conversion of organic matter to methane (methanogenesis) as a mechanism for energy conservation is exclusively attributed to the archaeal domain. Methane is oxidized by methanotrophic microorganisms using oxygen or alternative terminal electron acceptors. Aerobic methanotrophic bacteria belong to the phyla Proteobacteria and Verrucomicrobia, while anaerobic methane oxidation is also mediated by more recently discovered anaerobic methanotrophs with representatives in both the bacteria and the archaea domains. The anaerobic oxidation of methane is coupled to the reduction of nitrate, nitrite, iron, manganese, sulfate, and organic electron acceptors (e.g., humic substances) as terminal electron acceptors. This review highlights the relevance of methanotrophy in natural and anthropogenically influenced ecosystems, emphasizing the environmental conditions, distribution, function, co-existence, interactions, and the availability of electron acceptors that likely play a key role in regulating their function. A systematic overview of key aspects of ecology, physiology, metabolism, and genomics is crucial to understand the contribution of methanotrophs in the mitigation of methane efflux to the atmosphere. We give significance to the processes under microaerophilic and anaerobic conditions for both aerobic and anaerobic methane oxidizers. In the context of anthropogenically influenced ecosystems, we emphasize the current and potential future applications of methanotrophs from two different angles, namely methane mitigation in wastewater treatment through the application of anaerobic methanotrophs, and the biotechnological applications of aerobic methanotrophs in resource recovery from methane waste streams. Finally, we identify knowledge gaps that may lead to opportunities to harness further the biotechnological benefits of methanotrophs in methane mitigation and for the production of valuable bioproducts enabling a bio-based and circular economy.}, }
@article {pmid34054772, year = {2021}, author = {Trego, AC and McAteer, PG and Nzeteu, C and Mahony, T and Abram, F and Ijaz, UZ and O'Flaherty, V}, title = {Combined Stochastic and Deterministic Processes Drive Community Assembly of Anaerobic Microbiomes During Granule Flotation.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {666584}, pmid = {34054772}, issn = {1664-302X}, abstract = {Advances in null-model approaches have resulted in a deeper understanding of community assembly mechanisms for a variety of complex microbiomes. One under-explored application is assembly of communities from the built-environment, especially during process disturbances. Anaerobic digestion for biological wastewater treatment is often underpinned by retaining millions of active granular biofilm aggregates. Flotation of granules is a major problem, resulting in process failure. Anaerobic aggregates were sampled from three identical bioreactors treating dairy wastewater. Microbiome structure was analysed using qPCR and 16S rRNA gene amplicon sequencing from DNA and cDNA. A comprehensive null-model approach quantified assembly mechanisms of floating and settled communities. Significant differences in diversity were observed between floating and settled granules, in particular, we highlight the changing abundances of Methanosaeta and Lactococcus. Both stochastic and deterministic processes were important for community assembly. Homogeneous selection was the primary mechanism for all categories, but dispersal processes also contributed. The lottery model was used to identify clade-level competition driving community assembly. Lottery "winners" were identified with different winners between floating and settled groups. Some groups changed their winner status when flotation occurred. Spirochaetaceae, for example, was only a winner in settled biomass (cDNA-level) and lost its winner status during flotation. Alternatively, Arcobacter butzerli gained winner status during flotation. This analysis provides a deeper understanding of changes that occur during process instabilities and identified groups which may be washed out-an important consideration for process control.}, }
@article {pmid34054757, year = {2021}, author = {Rocha, FYO and Negrisoli Júnior, AS and de Matos, GF and Gitahy, PM and Rossi, CN and Vidal, MS and Baldani, JI}, title = {Endophytic Bacillus Bacteria Living in Sugarcane Plant Tissues and Telchin licus licus Larvae (Drury) (Lepidoptera: Castniidae): The Symbiosis That May Open New Paths in the Biological Control.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {659965}, pmid = {34054757}, issn = {1664-302X}, abstract = {Bacteria of the genus Bacillus can colonize endophytically and benefit several crops including the control of some pest orders. In view of the benefits provided by these microorganisms and in order to find out an efficient biotechnological control for the giant borer, our interest in studying the microorganisms in symbiosis with sugarcane and the giant borer has arisen, since there is no efficient chemical or biological control method for this pest. Therefore, endophytic Bacillus strains were isolated from three sugarcane niches (apoplast fluid, central internode cylinder and roots) and also from the giant borer larvae living inside sugarcane varieties grown in the Northeast region of Brazil. The taxonomical characterization (16S rRNA) of 157 Gram-positive isolates showed that 138 strains belonged to the Bacillus genus. The most representative species were phylogenetically closely related to B. megaterium (11.5%) followed by B. safensis (10.8%), B. cereus (8.9%), B. oleronius (8.9%), B. amyloliquefaciens (7.0%), and B. pacificus (6.4%). BOX-PCR analyses showed very distinct band pattern profiles suggesting a great diversity of Bacillus species within the sugarcane niches and the digestive tract, while the B. cereus group remained very closely clustered in the dendrogram. According to XRE biomarker analysis, eleven strains (FORCN005, 007, 008, 011, 012, 014, 067, 076, 092, 093, and 135) correspond to B. thuringiensis species. Additional studies using conserved genes (glp, gmk, pta, and tpi) indicated that most of these strains were phylogenetically closely related to B. thuringiensis and may be considered different subspecies. In conclusion, this study suggests that the culturable Bacillus species are greatly diversified within the plant niches and showed Bacillus species in the digestive tract of the giant borer for the first time. These results open new perspectives to understand the role and functions played by these microorganisms in symbiosis with this pest and also the possibility of developing an efficient biological control method for the giant borer using strains identified as the B. thuringiensis species.}, }
@article {pmid34053521, year = {2021}, author = {Jang, MJ and Kim, SY and Ricke, SC and Rhee, MS and Kim, SA}, title = {Microbial ecology of alfalfa, radish, and rapeseed sprouts based on culture methods and 16S rRNA microbiome sequencing.}, journal = {Food research international (Ottawa, Ont.)}, volume = {144}, number = {}, pages = {110316}, doi = {10.1016/j.foodres.2021.110316}, pmid = {34053521}, issn = {1873-7145}, mesh = {*Brassica napus ; Colony Count, Microbial ; Food Microbiology ; Medicago sativa ; *Microbiota ; RNA, Ribosomal, 16S ; *Raphanus ; }, abstract = {Sprouts harbor high populations of bacteria and cause numerous foodborne disease outbreaks, yet little is known about their microbial composition. The present study aimed to define the microbiological ecology of sprouts using 16S rRNA microbiome sequencing and culture-dependent methods. Different types (radish, alfalfa, and rapeseed), brands (A, B, and C), and distribution routes (online and offline) of sprouts (n = 70) were considered for microbiome analysis, as well as quantitative (aerobic plate count and coliforms) and qualitative analyses (Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella Typhimurium). The aerobic plate count ranged from 7 to 8 CFU/g, and the coliforms ranged from 6 to 7 log CFU/g. Microbiome analysis revealed that Proteobacteria was the dominant phylum, accounting for 79.0% in alfalfa sprouts, 68.5% in rapeseed sprouts, and 61.9% in radish sprouts. Enterobacteriaceae was the dominant family in alfalfa sprouts (33.9%) and rapeseed sprouts (14.6%), while Moraxellaceae (11.9%) were prevalent on radish sprouts. The majority of the dominant genera were common in the environment, such as soil or water. Alfalfa sprouts yielded the lowest aerobic plate count but the highest relative abundance of Enterobacteriaceae compared to the other sprouts. These results could explain why alfalfa sprouts are a leading cause of sprout-related foodborne disease outbreaks. Alpha-diversity results (Chao1 and Shannon indices) suggested that species richness was greater on radish sprouts than the other sprout types. Beta-diversity results showed samples were clustered by types, indicating dissimilarity in microbial communities. However, the distribution route had a limited influence on microbial composition. The present study provides a comparative examination of the microbial profiles of sprouts. Microbiome analyses contribute to an in-depth understanding of the microbial ecology of sprouts, leading to potential control measures for ensuring food safety.}, }
@article {pmid34052880, year = {2022}, author = {Fernández, LD and Seppey, CVW and Singer, D and Fournier, B and Tatti, D and Mitchell, EAD and Lara, E}, title = {Niche Conservatism Drives the Elevational Diversity Gradient in Major Groups of Free-Living Soil Unicellular Eukaryotes.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {459-469}, pmid = {34052880}, issn = {1432-184X}, mesh = {Biodiversity ; *Ciliophora/genetics ; Ecosystem ; Phylogeny ; *Soil ; }, abstract = {Ancestral adaptations to tropical-like climates drive most multicellular biogeography and macroecology. Observational studies suggest that this niche conservatism could also be shaping unicellular biogeography and macroecology, although evidence is limited to Acidobacteria and testate amoebae. We tracked the phylogenetic signal of this niche conservatism in far related and functionally contrasted groups of common soil protists (Bacillariophyta, Cercomonadida, Ciliophora, Euglyphida and Kinetoplastida) along a humid but increasingly cold elevational gradient in Switzerland. Protist diversity decreased, and the size of the geographic ranges of taxa increased with elevation and associated decreasing temperature (climate), which is consistent with a macroecological pattern known as the Rapoport effect. Bacillariophyta exhibited phylogenetically overdispersed communities assembled by competitive exclusion of closely related taxa with shared (conserved) niches. By contrast, Cercomonadida, Ciliophora, Euglyphida and Kinetoplastida exhibited phylogenetically clustered communities assembled by habitat filtering, revealing the coexistence of closely related taxa with shared (conserved) adaptations to cope with the humid but temperate to cold climate of the study site. Phylobetadiversity revealed that soil protists exhibit a strong phylogenetic turnover among elevational sites, suggesting that most taxa have evolutionary constraints that prevent them from colonizing the colder and higher sites of the elevation gradient. Our results suggest that evolutionary constraints determine how soil protists colonize climates departing from warm and humid conditions. We posit that these evolutionary constraints are linked to an ancestral adaptation to tropical-like climates, which limits their survival in exceedingly cold sites. This niche conservatism possibly drives their biogeography and macroecology along latitudinal and altitudinal climatic gradients.}, }
@article {pmid34052601, year = {2021}, author = {Chandler, L and Harford, AJ and Hose, GC and Humphrey, CL and Chariton, A and Greenfield, P and Davis, J}, title = {Saline mine-water alters the structure and function of prokaryote communities in shallow groundwater below a tropical stream.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {284}, number = {}, pages = {117318}, doi = {10.1016/j.envpol.2021.117318}, pmid = {34052601}, issn = {1873-6424}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Ecosystem ; *Groundwater ; Water ; }, abstract = {Bacteria and archaea (prokaryotes) are vital components for maintaining healthy function of groundwater ecosystems. The prokaryotic community composition and associated putative functional processes were examined in a shallow sandy aquifer in a wet-dry tropical environment. The aquifer had a contaminated gradient of saline mine-water, which primarily consisted of elevated magnesium (Mg[2+]) and sulfate (SO4[2-]), although other major ions and trace metals were also present. Groundwaters were sampled from piezometers, approximately 2 m in depth, located in the creek channel upstream and downstream of the mine-water influence. Sampling occurred during the dry-season when only subsurface water flow was present. Next generation sequencing was used to analyse the prokaryote assemblages using 16S rDNA and metabolic functions were predicted with FAPROTAX. Significant changes in community composition and functional processes were observed with exposure to mine-waters. Communities in the exposed sites had significantly lower relative abundance of methanotrophs such as Methylococcaceae and methanogens (Methanobacteriaceae), but higher abundance in Nitrososphaeraceae, associated with nitrification, indicating potentially important changes in the biogeochemistry of the exposed sites. The changes were most strongly correlated with concentrations of SO4[2-], Mg[2+] and Na[+]. This knowledge allows an assessment of the risk of mine-water contamination to groundwater ecosystem function and aids mine-water management.}, }
@article {pmid34049069, year = {2021}, author = {Lim, JH and Lee, CW and Bong, CW and Kudo, I}, title = {The impact of eutrophication towards selected bacterial process rates in tropical coastal waters.}, journal = {Marine pollution bulletin}, volume = {169}, number = {}, pages = {112524}, doi = {10.1016/j.marpolbul.2021.112524}, pmid = {34049069}, issn = {1879-3363}, mesh = {Bacteria ; *Bacterial Physiological Phenomena ; Carbon/analysis ; *Eutrophication ; Malaysia ; Nitrogen/analysis ; }, abstract = {The dissolved organic nutrient conditions and bacterial process rates at two tropical coastal sites in Peninsular Malaysia (Port Klang and Port Dickson) were initially studied in 2004-2005 period and later revisited in 2010-2011. We observed that dissolved organic nitrogen (DON) increased about two- and ten-fold at Port Klang and Port Dickson, respectively and resulted in a significant change in DOC:DON ratio (t ≥ 2.077, p < 0.05). Among the bacterial processes measured, bacterial respiration (BR) was lower in the 2010-2011 period at both stations (t ≥ 3.390, p < 0.01). BR also correlated to the DOC:DON ratio (R[2] ≥ 0.259, p < 0.01). The increase in substrate quality enabled the bacteria to respire less in the dissolved organic matter degradation. As a result, the average bacterial growth efficiency increased slightly in the 2010-2011 period.}, }
@article {pmid34039416, year = {2021}, author = {Leung, MHY and Tong, X and Bøifot, KO and Bezdan, D and Butler, DJ and Danko, DC and Gohli, J and Green, DC and Hernandez, MT and Kelly, FJ and Levy, S and Mason-Buck, G and Nieto-Caballero, M and Syndercombe-Court, D and Udekwu, K and Young, BG and Mason, CE and Dybwad, M and Lee, PKH}, title = {Characterization of the public transit air microbiome and resistome reveals geographical specificity.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {112}, pmid = {34039416}, issn = {2049-2618}, support = {U01 DA053941/DA/NIDA NIH HHS/United States ; /DH_/Department of Health/United Kingdom ; R21 AI129851/AI/NIAID NIH HHS/United States ; R01 NS076465/NS/NINDS NIH HHS/United States ; R01 MH117406/MH/NIMH NIH HHS/United States ; MR/S019669/1/MRC_/Medical Research Council/United Kingdom ; R25 EB020393/EB/NIBIB NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Geography ; Hong Kong ; Humans ; Metagenome/genetics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: The public transit is a built environment with high occupant density across the globe, and identifying factors shaping public transit air microbiomes will help design strategies to minimize the transmission of pathogens. However, the majority of microbiome works dedicated to the public transit air are limited to amplicon sequencing, and our knowledge regarding the functional potentials and the repertoire of resistance genes (i.e. resistome) is limited. Furthermore, current air microbiome investigations on public transit systems are focused on single cities, and a multi-city assessment of the public transit air microbiome will allow a greater understanding of whether and how broad environmental, building, and anthropogenic factors shape the public transit air microbiome in an international scale. Therefore, in this study, the public transit air microbiomes and resistomes of six cities across three continents (Denver, Hong Kong, London, New York City, Oslo, Stockholm) were characterized.<br><br>RESULTS: City was the sole factor associated with public transit air microbiome differences, with diverse taxa identified as drivers for geography-associated functional potentials, concomitant with geographical differences in species- and strain-level inferred growth profiles. Related bacterial strains differed among cities in genes encoding resistance, transposase, and other functions. Sourcetracking estimated that human skin, soil, and wastewater were major presumptive resistome sources of public transit air, and adjacent public transit surfaces may also be considered presumptive sources. Large proportions of detected resistance genes were co-located with mobile genetic elements including plasmids. Biosynthetic gene clusters and city-unique coding sequences were found in the metagenome-assembled genomes.<br><br>CONCLUSIONS: Overall, geographical specificity transcends multiple aspects of the public transit air microbiome, and future efforts on a global scale are warranted to increase our understanding of factors shaping the microbiome of this unique built environment.}, }
@article {pmid34037999, year = {2021}, author = {Petje, LM and Jensen, SA and Szikora, S and Sulzbacher, M and Bartosik, T and Pjevac, P and Hausmann, B and Hufnagl, K and Untersmayr, E and Fischer, L and Vyskocil, E and Eckl-Dorna, J and Jensen-Jarolim, E and Hofstetter, G and Afify, SM and Krenn, CG and Roth, GA and Rivelles, E and Hann, S and Roth-Walter, F}, title = {Functional iron-deficiency in women with allergic rhinitis is associated with symptoms after nasal provocation and lack of iron-sequestering microbes.}, journal = {Allergy}, volume = {76}, number = {9}, pages = {2882-2886}, pmid = {34037999}, issn = {1398-9995}, mesh = {Allergens ; *Anemia, Iron-Deficiency ; Female ; Humans ; Iron ; Nasal Mucosa ; Nasal Provocation Tests ; Nose ; *Rhinitis, Allergic/diagnosis ; }, }
@article {pmid34031701, year = {2022}, author = {Ao, L and Zhao, M and Li, X and Sun, G}, title = {Different Urban Forest Tree Species Affect the Assembly of the Soil Bacterial and Fungal Community.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {447-458}, pmid = {34031701}, issn = {1432-184X}, support = {41701289//National Natural Science Foundation of China/ ; 31870373//National Natural Science Foundation of China/ ; 2018M640287//Postdoctoral Research Foundation of China/ ; }, mesh = {China ; Forests ; *Microbiota ; *Mycobiome ; Soil/chemistry ; Soil Microbiology ; Trees ; }, abstract = {The selection of tree species used for the afforestation of urban forests is very important for maintaining the urban ecosystem, while soil microbe is one of the driving factors of material cycling in the urban forest ecosystem and for health of forests. In this study, the characteristics of surface soil bacterial and fungal community structure in four urban forests (primarily composed of Fraxinus mandshurica (Fm), Quercus mongolica (Qm), Pinus sylvestris var. mongolica (Ps), and Pinus tabulaeformis var. Mukdensis (Pt) as the main dominant tree species, respectively) were investigated by high-throughput sequencing. Our results showed that the alpha diversity of the soil microbial community in the Fm urban forest was the highest, while the lowest was in the Ps urban forest. In the bacterial community, Proteobacteria was the most predominant phylum in soils from Fm, Ps, and Pt urban forests. The most relatively abundant phylum of the Qm urban forest soil was Acidobacteria. The relative abundances of the bacterial communities at the genus level in the soil of four urban forests were significantly different. The soil bacterial communities in Ps and Pt urban forests were more similar, and Qm and Fm were also more similar. In the fungal community, Basidiomycota was the most predominant phylum in soils from Qm, Ps, and Pt urban forests. The phylum with the greatest relative abundance in the Fm urban forest soil was Ascomycota. There were differences in the fungal community between Qm, Fm, Ps, and Pt urban forests. Soil microbial community composition was affected by environmental factors: soil bacterial and fungal community compositions were significantly related to soil electrical conductivity (EC), alkali hydrolysable nitrogen (AHN), total nitrogen (TN), and total phosphorus (TP). In conclusion, the soil microbial community structure was related to both forest's tree species and soil properties.}, }
@article {pmid34030967, year = {2021}, author = {Yang, Y}, title = {Emerging Patterns of Microbial Functional Traits.}, journal = {Trends in microbiology}, volume = {29}, number = {10}, pages = {874-882}, doi = {10.1016/j.tim.2021.04.004}, pmid = {34030967}, issn = {1878-4380}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; *Biodiversity ; Ecosystem ; Environment ; Phenotype ; }, abstract = {Functional traits are measurable characteristics that affect an organism's fitness under certain environmental conditions. The use of functional traits in microbial ecology holds great promise for improving our ability to develop biogeochemical models and predict ecosystem responses to global changes. Notably, functional traits could be decoupled from taxonomic relatedness, owing to horizontal gene transfer among microorganisms and adaptive evolution. In recent years, our knowledge about microbial functional traits has been substantially enhanced, thereby revealing the multitude of ecological processes in driving community assembly and dynamics. Here, I summarize the emerging patterns of how microbial functional traits respond to changing environments, which considerably differ from better-studied microbial taxonomy. I use niche and neutral theories to explain microbial functional traits. Finally, I highlight future challenges to analyze, elucidate, and utilize functional traits in microbial ecology.}, }
@article {pmid34030400, year = {2021}, author = {Hildebrandt, L and Zimmermann, T and Primpke, S and Fischer, D and Gerdts, G and Pröfrock, D}, title = {Comparison and uncertainty evaluation of two centrifugal separators for microplastic sampling.}, journal = {Journal of hazardous materials}, volume = {414}, number = {}, pages = {125482}, doi = {10.1016/j.jhazmat.2021.125482}, pmid = {34030400}, issn = {1873-3336}, abstract = {For commonly applied microplastic sampling approaches based on filtration, high throughput and no size-discrimination are conflicting goals. Therefore, we propose two efficient centrifugal separators for small microplastic sampling, namely the utilization of a hydrocyclone as well as a continuous flow centrifuge. Thorough method optimization was followed by application in an extensive sampling study to investigate the separators' retention behavior for particulate plastics from estuarine waters. Microplastic concentrations ranged from 193 to 2072 particles m[-3]. The most dominant identified polymer types were polypropylene, acrylates, polyvinyl chloride and polyethylene. More than 95% of particles were < 100 µm. For the first time in microplastic research, an expanded uncertainty was calculated according to the "Guide to the expression of Uncertainty in Measurement" (JCGM 100:2008). Bottom-up uncertainty evaluation revealed the different sampling methods (~ 44%), sample replicates (~ 26%) and the different detection techniques (~ 16%) as the major sources of uncertainty. Depending on the number of particles detected in the samples, the relative expanded uncertainty (Urel (k = 2)) ranged from 24% up to > 200% underpinning tremendous importance of sound uncertainty evaluation. Our results indicate that scientist should rethink many "observed patterns" in the literature due to being insignificant and herewith not real.}, }
@article {pmid34030262, year = {2021}, author = {Glodowska, M and Schneider, M and Eiche, E and Kontny, A and Neumann, T and Straub, D and Berg, M and Prommer, H and Bostick, BC and Nghiem, AA and Kleindienst, S and Kappler, A}, title = {Fermentation, methanotrophy and methanogenesis influence sedimentary Fe and As dynamics in As-affected aquifers in Vietnam.}, journal = {The Science of the total environment}, volume = {779}, number = {}, pages = {146501}, doi = {10.1016/j.scitotenv.2021.146501}, pmid = {34030262}, issn = {1879-1026}, mesh = {*Arsenic/analysis ; Fermentation ; Ferric Compounds ; *Groundwater ; Humans ; Oxidation-Reduction ; Vietnam ; *Water Pollutants, Chemical/analysis ; }, abstract = {High arsenic (As) concentrations in groundwater are a worldwide problem threatening the health of millions of people. Microbial processes are central in the (trans)formation of the As-bearing ferric and ferrous minerals, and thus regulate dissolved As levels in many aquifers. Mineralogy, microbiology and dissolved As levels can vary sharply within aquifers, making high-resolution measurements particularly valuable in understanding the linkages between them. We conducted a high spatial resolution geomicrobiological study in combination with analysis of sediment chemistry and mineralogy in an alluvial aquifer system affected by geogenic As in the Red River delta in Vietnam. Microbial community analysis revealed a dominance of fermenters, methanogens and methanotrophs whereas sediment mineralogy along a 46 m deep core showed a diversity of Fe minerals including poorly crystalline Fe (II/III) and Fe(III) (oxyhydr)oxides such as goethite, hematite, and magnetite, but also the presence of Fe(II)-bearing carbonates and sulfides which likely formed as a result of microbially driven organic carbon (OC) degradation. A potential important role of methane (CH4) as electron donor for reductive Fe mineral (trans)formation was supported by the high abundance of Candidatus Methanoperedens, a known Fe(III)-reducing methanotroph. Overall, these results imply that OC turnover including fermentation, methanogenesis and CH4 oxidation are important mechanisms leading to Fe mineral (trans)formation, dissolution and precipitation, and thus indirectly affecting As mobility by changing the Fe-mineral inventory.}, }
@article {pmid34029817, year = {2021}, author = {Zhang, Y and Chen, M and Zhao, YY and Zhang, AY and Peng, DH and Lu, F and Dai, CC}, title = {Destruction of the soil microbial ecological environment caused by the over-utilization of the rice-crayfish co-cropping pattern.}, journal = {The Science of the total environment}, volume = {788}, number = {}, pages = {147794}, doi = {10.1016/j.scitotenv.2021.147794}, pmid = {34029817}, issn = {1879-1026}, mesh = {Animals ; Astacoidea ; China ; *Oryza ; *Soil ; Soil Microbiology ; }, abstract = {The rice-crayfish co-cropping pattern is a traditional method for the intensive utilization of rice fields. In recent years, this pattern has been over-developed in many countries and regions, especially in China, because of its simple agronomic technology and high economic benefits. However, little is known about the potential ecological problems regarding soil microorganisms caused by the over-utilization of this pattern. The results show that rice-crayfish co-cropping, when over-utilized for a long time, reduced soil microbial richness and diversity compared with rice monocropping. A decrease in bacterial abundance in the nitrogen cycle and an increase in bacterial abundance in the carbon cycle led to a decrease in the nitrogen cycle function and an increase in the carbon cycle function. In an analysis of bacteria that are sensitive to cropping patterns, it was found that in the rice-crayfish co-cropping, the relative abundances of sensitive OTUs from Firmicutes (Bacillus and Clostridium) and Chloroflexi (Anaerolineaceae) were significantly higher during the entire growth period than those observed in the rice monocropping pattern, while the relative abundances of sensitive OTUs from Nitrospirae (Nitrospira), Gemmatimonadetes (Gemmatimonas), and Actinobacteria (Nocardioides) were significantly lower than those observed in the rice monocropping pattern. A network analysis shows that growth-period-sensitive OTUs drive the co-occurrence network modules, although the OTUs also have positive and negative correlations among modules but a positive synergistic effect on the regulation of soil nutrients. In addition, OTUs that were sensitive at the booting stage and filling stage were the key microbial groups in the rice-crayfish co-cropping and rice monocropping networks, respectively. Understanding the classifications and functions of sensitive microbes present during the rice growth period is the basis for formulating a microbial flora management strategy for the rice-crayfish co-cropping pattern, which is of great significance for adjusting agricultural management measures and controlling current soil microbial ecological problems.}, }
@article {pmid34025695, year = {2021}, author = {Li, T and Wu, S and Yang, W and Selosse, MA and Gao, J}, title = {How Mycorrhizal Associations Influence Orchid Distribution and Population Dynamics.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {647114}, pmid = {34025695}, issn = {1664-462X}, abstract = {Orchid distribution and population dynamics are influenced by a variety of ecological factors and the formation of holobionts, which play key roles in colonization and ecological community construction. Seed germination, seedling establishment, reproduction, and survival of orchid species are strongly dependent on orchid mycorrhizal fungi (OMF), with mycorrhizal cheating increasingly observed in photosynthetic orchids. Therefore, changes in the composition and abundance of OMF can have profound effects on orchid distribution and fitness. Network analysis is an important tool for the study of interactions between plants, microbes, and the environment, because of the insights that it can provide into the interactions and coexistence patterns among species. Here, we provide a comprehensive overview, systematically describing the current research status of the effects of OMF on orchid distribution and dynamics, phylogenetic signals in orchid-OMF interactions, and OMF networks. We argue that orchid-OMF associations exhibit complementary and specific effects that are highly adapted to their environment. Such specificity of associations may affect the niche breadth of orchid species and act as a stabilizing force in plant-microbe coevolution. We postulate that network analysis is required to elucidate the functions of fungal partners beyond their effects on germination and growth. Such studies may lend insight into the microbial ecology of orchids and provide a scientific basis for the protection of orchids under natural conditions in an efficient and cost-effective manner.}, }
@article {pmid34025597, year = {2021}, author = {Suominen, S and van Vliet, DM and Sánchez-Andrea, I and van der Meer, MTJ and Sinninghe Damsté, JS and Villanueva, L}, title = {Organic Matter Type Defines the Composition of Active Microbial Communities Originating From Anoxic Baltic Sea Sediments.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {628301}, pmid = {34025597}, issn = {1664-302X}, abstract = {Carbon cycling in anoxic marine sediments is dependent on uncultured microbial communities. Niches of heterotrophic microorganisms are defined by organic matter (OM) type and the different phases in OM degradation. We investigated how OM type defines microbial communities originating from organic-rich, anoxic sediments from the Baltic Sea. We compared changes in the sediment microbial community, after incubation with different stable isotope labeled OM types [i.e., particulate algal organic matter (PAOM), protein, and acetate], by using DNA stable isotope probing (DNA-SIP). Incorporation of [13]C and/or [15]N label was predominantly detected in members of the phyla Planctomycetes and Chloroflexi, which also formed the majority (>50%) of the original sediment community. While these phylum-level lineages incorporated label from all OM types, phylogenetic analyses revealed a niche separation at the order level. Members of the MSBL9 (Planctomycetes), the Anaerolineales (Chloroflexi), and the class Bathyarchaeota, were identified as initial degraders of carbohydrate-rich OM, while other uncultured orders, like the CCM11a and Phycisphaerales (Planctomycetes), Dehalococcoidia, and JG30-KF-CM66 (Chloroflexi), incorporated label also from protein and acetate. Our study highlights the importance of initial fermentation of complex carbon pools in shaping anoxic sediment microbial communities and reveals niche specialization at the order level for the most important initial degraders in anoxic sediments.}, }
@article {pmid34025590, year = {2021}, author = {You, Y and Aho, K and Lohse, KA and Schwabedissen, SG and Ledbetter, RN and Magnuson, TS}, title = {Biological Soil Crust Bacterial Communities Vary Along Climatic and Shrub Cover Gradients Within a Sagebrush Steppe Ecosystem.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {569791}, pmid = {34025590}, issn = {1664-302X}, support = {P20 GM103408/GM/NIGMS NIH HHS/United States ; }, abstract = {Numerous studies have examined bacterial communities in biological soil crusts (BSCs) associated with warm arid to semiarid ecosystems. Few, however, have examined bacterial communities in BSCs associated with cold steppe ecosystems, which often span a wide range of climate conditions and are sensitive to trends predicted by relevant climate models. Here, we utilized Illumina sequencing to examine BSC bacterial communities with respect to climatic gradients (elevation), land management practices (grazing vs. non-grazing), and shrub/intershrub patches in a cold sagebrush steppe ecosystem in southwestern Idaho, United States. Particular attention was paid to shifts in bacterial community structure and composition. BSC bacterial communities, including keystone N-fixing taxa, shifted dramatically with both elevation and shrub-canopy microclimates within elevational zones. BSC cover and BSC cyanobacteria abundance were much higher at lower elevation (warmer and drier) sites and in intershrub areas. Shrub-understory BSCs were significantly associated with several non-cyanobacteria diazotrophic genera, including Mesorhizobium and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium. High elevation (wetter and colder) sites had distinct, highly diverse, but low-cover BSC communities that were significantly indicated by non-cyanobacterial diazotrophic taxa including families in the order Rhizobiales and the family Frankiaceae. Abiotic soil characteristics, especially pH and ammonium, varied with both elevation and shrub/intershrub level, and were strongly associated with BSC community composition. Functional inference using the PICRUSt pipeline identified shifts in putative N-fixing taxa with respect to both the elevational gradient and the presence/absence of shrub canopy cover. These results add to current understanding of biocrust microbial ecology in cold steppe, serving as a baseline for future mechanistic research.}, }
@article {pmid34023922, year = {2022}, author = {Kaur, M and Kumari, A and Singh, R}, title = {The Indigenous Volatile Inhibitor 2-Methyl-2-butene Impacts Biofilm Formation and Interspecies Interaction of the Pathogenic Mucorale Rhizopus arrhizus.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {506-512}, pmid = {34023922}, issn = {1432-184X}, support = {ECR/2016/000102//Early Career Research Award, Science and Engineering Research Board (SERB), Department of Science and Technology (DST), Govt. of India/ ; DST/INSPIRE Faculty Award/2013/DST/INSPIRE/04/2013/000925//DST-INSPIRE Faculty Scheme, Govt. of India/ ; }, mesh = {Alkenes ; Biofilms ; *Rhizopus ; *Rhizopus oryzae ; Staphylococcus aureus ; }, abstract = {2-Methyl-2-butene has recently been reported to be a quorum-based volatile self-inhibitor of spore germination and growth in pathogenic Mucorale Rhizopus arrhizus. The present study aimed to elucidate if this compound can influence R. arrhizus biofilm formation and interspecies interaction. The compound was found to significantly decrease R. arrhizus biofilm formation (p < 0.001), with nearly 25% and 50% lesser biomass in the biofilms cultured with exposure to 4 and 32 µg/ml of 2-methyl-2-butene, respectively. The growth of pre-formed biofilms was also impacted, albeit to a lesser extent. Additionally, 2-methyl-2-butene was found to self-limit R. arrhizus growth during interspecies interaction with Staphylococcus aureus and was detected at a substantially greater concentration in the headspace of co-cultures (2338.75 µg/ml) compared with monocultures (69.52 µg/ml). Some of the C5 derivatives of this compound (3-methyl-1-butanol, 2-methyl-2-butanol, and 3-methyl-1-butyne) were also observed to partially mimic its action, such as inhibition of spore germination, but did not impact R. arrhizus biofilm formation. Finally, the treated R. arrhizus displayed changes in fungal morphology suggestive of cytoskeletal alterations, such as filopodia formation, blebs, increased longitudinal folds and/or corrugations, and finger-like and sheet-like surface protrusions, depending upon the concentration of the compound(s) and the planktonic or biofilm growth mode.}, }
@article {pmid34021563, year = {2021}, author = {Wright, ES and Gupta, R and Vetsigian, KH}, title = {Multi-stable bacterial communities exhibit extreme sensitivity to initial conditions.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {6}, pages = {}, doi = {10.1093/femsec/fiab073}, pmid = {34021563}, issn = {1574-6941}, mesh = {Bacteria/genetics ; *Microbiota ; *Models, Biological ; Population Dynamics ; }, abstract = {Microbial communities can have dramatically different compositions even among similar environments. This might be due to the existence of multiple alternative stable states, yet there exists little experimental evidence supporting this possibility. Here, we gathered a large collection of absolute population abundances capturing population dynamics in one- to four-strain communities of soil bacteria with a complex life cycle in a feast-or-famine environment. This dataset led to several observations: (i) some pairwise competitions resulted in bistability with a separatrix near a 1:1 initial ratio across a range of population densities; (ii) bistability propagated to multi-stability in multispecies communities; and (iii) replicate microbial communities reached different stable states when starting close to initial conditions separating basins of attraction, indicating finite-sized regions where the dynamics are unpredictable. The generalized Lotka-Volterra equations qualitatively captured most competition outcomes but were unable to quantitatively recapitulate the observed dynamics. This was partly due to complex and diverse growth dynamics in monocultures that ranged from Allee effects to nonmonotonic behaviors. Overall, our results highlight that multi-stability might be generic in multispecies communities and, combined with ecological noise, can lead to unpredictable community assembly, even in simple environments.}, }
@article {pmid34020935, year = {2021}, author = {Huang, YM and Straub, D and Blackwell, N and Kappler, A and Kleindienst, S}, title = {Meta-omics Reveal Gallionellaceae and Rhodanobacter Species as Interdependent Key Players for Fe(II) Oxidation and Nitrate Reduction in the Autotrophic Enrichment Culture KS.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {15}, pages = {e0049621}, pmid = {34020935}, issn = {1098-5336}, mesh = {Autotrophic Processes ; Gallionellaceae/genetics/*metabolism ; Gammaproteobacteria/genetics/*metabolism ; Gene Expression Profiling ; Heterotrophic Processes ; Iron/*metabolism ; Metagenome ; Metagenomics ; Nitrates/*metabolism ; Oxidation-Reduction ; Proteomics ; }, abstract = {Nitrate reduction coupled to Fe(II) oxidation (NRFO) has been recognized as an environmentally important microbial process in many freshwater ecosystems. However, well-characterized examples of autotrophic nitrate-reducing Fe(II)-oxidizing bacteria are rare, and their pathway of electron transfer as well as their interaction with flanking community members remain largely unknown. Here, we applied meta-omics (i.e., metagenomics, metatranscriptomics, and metaproteomics) to the nitrate-reducing Fe(II)-oxidizing enrichment culture KS growing under autotrophic or heterotrophic conditions and originating from freshwater sediment. We constructed four metagenome-assembled genomes with an estimated completeness of ≥95%, including the key players of NRFO in culture KS, identified as Gallionellaceae sp. and Rhodanobacter sp. The Gallionellaceae sp. and Rhodanobacter sp. transcripts and proteins likely involved in Fe(II) oxidation (e.g., mtoAB, cyc2, and mofA), denitrification (e.g., napGHI), and oxidative phosphorylation (e.g., respiratory chain complexes I to V) along with Gallionellaceae sp. transcripts and proteins for carbon fixation (e.g., rbcL) were detected. Overall, our results indicate that in culture KS, the Gallionellaceae sp. and Rhodanobacter sp. are interdependent: while Gallionellaceae sp. fixes CO2 and provides organic compounds for Rhodanobacter sp., Rhodanobacter sp. likely detoxifies NO through NO reduction and completes denitrification, which cannot be performed by Gallionellaceae sp. alone. Additionally, the transcripts and partial proteins of cbb3- and aa3-type cytochrome c suggest the possibility for a microaerophilic lifestyle of the Gallionellaceae sp., yet culture KS grows under anoxic conditions. Our findings demonstrate that autotrophic NRFO is performed through cooperation among denitrifying and Fe(II)-oxidizing bacteria, which might resemble microbial interactions in freshwater environments. IMPORTANCE Nitrate-reducing Fe(II)-oxidizing bacteria are widespread in the environment, contribute to nitrate removal, and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing Fe(II)-oxidizing bacteria is rarely investigated and not fully understood. The most prominent model system for this type of study is the enrichment culture KS. To gain insights into the metabolism of nitrate reduction coupled to Fe(II) oxidation in the absence of organic carbon and oxygen, we performed metagenomic, metatranscriptomic, and metaproteomic analyses of culture KS and identified Gallionellaceae sp. and Rhodanobacter sp. as interdependent key Fe(II) oxidizers in culture KS. Our work demonstrates that autotrophic nitrate reduction coupled to Fe(II) oxidation is not performed by an individual strain but is a cooperation of at least two members of the bacterial community in culture KS. These findings serve as a foundation for our understanding of nitrate-reducing Fe(II)-oxidizing bacteria in the environment.}, }
@article {pmid34020712, year = {2021}, author = {Silva, DP and Villela, HDM and Santos, HF and Duarte, GAS and Ribeiro, JR and Ghizelini, AM and Vilela, CLS and Rosado, PM and Fazolato, CS and Santoro, EP and Carmo, FL and Ximenes, DS and Soriano, AU and Rachid, CTCC and Vega Thurber, RL and Peixoto, RS}, title = {Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {118}, pmid = {34020712}, issn = {2049-2618}, mesh = {Animals ; *Anthozoa ; Coral Reefs ; *Petroleum ; *Petroleum Pollution ; *Probiotics ; }, abstract = {BACKGROUND: Beginning in the last century, coral reefs have suffered the consequences of anthropogenic activities, including oil contamination. Chemical remediation methods, such as dispersants, can cause substantial harm to corals and reduce their resilience to stressors. To evaluate the impacts of oil contamination and find potential alternative solutions to chemical dispersants, we conducted a mesocosm experiment with the fire coral Millepora alcicornis, which is sensitive to environmental changes. We exposed M. alcicornis to a realistic oil-spill scenario in which we applied an innovative multi-domain bioremediator consortium (bacteria, filamentous fungi, and yeast) and a chemical dispersant (Corexit® 9500, one of the most widely used dispersants), to assess the effects on host health and host-associated microbial communities.<br><br>RESULTS: The selected multi-domain microbial&#xa0;consortium helped to mitigate the impacts of the oil, substantially degrading the polycyclic aromatic and n-alkane fractions and maintaining the physiological integrity of the corals. Exposure to Corexit 9500 negatively impacted the host physiology and altered the coral-associated microbial community. After exposure, the abundances of certain bacterial genera such as Rugeria and Roseovarius increased, as previously reported in stressed or diseased corals. We also identified several bioindicators of Corexit 9500 in the microbiome. The impact of Corexit 9500 on the coral health and microbial community was far greater than oil alone, killing corals after only 4 days of exposure in the flow-through system. In the treatments with Corexit 9500, the action of the bioremediator consortium could not be observed directly because of the extreme toxicity of the dispersant to M. alcicornis and its associated microbiome.<br><br>CONCLUSIONS: Our&#xa0;results emphasize the importance of investigating the host-associated microbiome in order to detect and mitigate the effects of oil contamination on corals and the potential role of microbial mitigation and bioindicators as conservation tools. Chemical dispersants were far more damaging to corals and&#xa0;their associated microbiome&#xa0;than oil, and should not be used close to coral reefs. This study can aid in decision-making to minimize the negative effects of oil and dispersants on coral reefs. Video abstract.}, }
@article {pmid34017060, year = {2021}, author = {Kim, JH and Kim, K and Kim, W}, title = {Gut microbiota restoration through fecal microbiota transplantation: a new atopic dermatitis therapy.}, journal = {Experimental &amp; molecular medicine}, volume = {53}, number = {5}, pages = {907-916}, pmid = {34017060}, issn = {2092-6413}, mesh = {Animals ; Antibodies/pharmacology ; Biomarkers ; Dermatitis, Atopic/etiology/*therapy ; Disease Management ; Disease Models, Animal ; Disease Susceptibility ; Fatty Acids, Volatile/metabolism ; *Fecal Microbiota Transplantation/methods ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/drug effects/immunology ; Immunoglobulin E/blood/immunology ; Immunomodulation ; Lymphocyte Count ; Metagenome ; Metagenomics ; Mice ; T-Lymphocyte Subsets/immunology/metabolism ; Treatment Outcome ; }, abstract = {The pathogenesis of atopic dermatitis (AD) involves complex factors, including gut microbiota and immune modulation, which remain poorly understood. The aim of this study was to restore gut microbiota via fecal microbiota transplantation (FMT) to ameliorate AD in mice. FMT was performed using stool from donor mice. The gut microbiota was characterized via 16S rRNA sequencing and analyzed using Quantitative Insights into Microbial Ecology 2 with the DADA2 plugin. Gut metabolite levels were determined by measuring fecal short-chain fatty acid (SCFA) contents. AD-induced allergic responses were evaluated by analyzing blood parameters (IgE levels and eosinophil percentage, eosinophil count, basophil percentage, and monocyte percentage), the levels of Th1 and Th2 cytokines, dermatitis score, and the number of mast cells in the ileum and skin tissues. Calprotectin level was measured to assess gut inflammation after FMT. FMT resulted in the restoration of gut microbiota to the donor state and increases in the levels of SCFAs as gut metabolites. In addition, FMT restored the Th1/Th2 balance, modulated Tregs through gut microbiota, and reduced IgE levels and the numbers of mast cells, eosinophils, and basophils. FMT is associated with restoration of gut microbiota and immunologic balance (Th1/Th2) along with suppression of AD-induced allergic responses and is thus a potential new therapy for AD.}, }
@article {pmid34016155, year = {2021}, author = {LaMartina, EL and Mohaimani, AA and Newton, RJ}, title = {Urban wastewater bacterial communities assemble into seasonal steady states.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {116}, pmid = {34016155}, issn = {2049-2618}, support = {R01 AI091829/AI/NIAID NIH HHS/United States ; R01AI091829/NH/NIH HHS/United States ; }, mesh = {Ecosystem ; Humans ; RNA, Ribosomal, 16S/genetics ; Seasons ; *Sewage ; *Wastewater ; }, abstract = {BACKGROUND: Microorganisms in urban sanitary sewers exhibit community properties that suggest sewers are a novel ecosystem. Sewer microorganisms present both an opportunity as a control point for wastewater treatment and a risk to human health. If treatment processes are to be improved and health risks quantified, then it is necessary to understand microbial distributions and dynamics within this community. Here, we use 16S rRNA gene sequencing to characterize raw influent wastewater bacterial communities in a 5-year time series from two wastewater treatment plants in Milwaukee, WI; influent wastewater from 77 treatment plants across the USA; and wastewater in 12 Milwaukee residential sewers.<br><br>RESULTS: In Milwaukee, we find that in transit from residences to treatment plants, the human bacterial component of wastewater decreases in proportion and exhibits stochastic temporal variation. In contrast, the resident sewer community increases in abundance during transit and cycles seasonally according to changes in wastewater temperature. The result is a bacterial community that assembles into two distinct community states each year according to the extremes in wastewater temperature. Wastewater bacterial communities from other northern US cities follow temporal trends that mirror those in Milwaukee, but southern US cities have distinct community compositions and differ in their seasonal patterns.<br><br>CONCLUSIONS: Our findings provide evidence that environmental conditions associated with seasonal change and climatic differences related to geography predictably structure the bacterial communities residing in below-ground sewer pipes. Video abstract.}, }
@article {pmid34016152, year = {2021}, author = {Dwużnik-Szarek, D and Mierzejewska, EJ and Rodo, A and Goździk, K and Behnke-Borowczyk, J and Kiewra, D and Kartawik, N and Bajer, A}, title = {Monitoring the expansion of Dermacentor reticulatus and occurrence of canine babesiosis in Poland in 2016-2018.}, journal = {Parasites &amp; vectors}, volume = {14}, number = {1}, pages = {267}, pmid = {34016152}, issn = {1756-3305}, mesh = {Animal Distribution ; Animals ; Babesia/genetics/isolation &amp; purification/physiology ; Babesiosis/epidemiology/parasitology/*transmission ; Dermacentor/*parasitology/physiology ; Dog Diseases/epidemiology/parasitology/*transmission ; Dogs ; Female ; Male ; Poland/epidemiology ; Seasons ; Tick Infestations/epidemiology/parasitology/*veterinary ; Tick-Borne Diseases/epidemiology/parasitology/transmission/*veterinary ; }, abstract = {BACKGROUND: The significance of tick-borne diseases has increased considerably in recent years. Because of the unique distribution of the tick species Dermacentor reticulatus in Poland, comprising two expanding populations, Eastern and Western that are separated by a Dermacentor-free zone, it is important to conduct studies on the process of tick expansion and emergence of canine babesiosis. The main aim of the current study was to monitor the expansion of D. reticulatus populations from spring 2016 to autumn 2018 to determine (1) the actual geographical range of this tick species, and (2) and the seasonal/annual shift in range limits and changes in distance between Western and Eastern populations of ticks (the size of the non-endemic area).<br><br>METHODS: Ticks were collected in spring/autumn during a 3-year study. From each season and year at least three pairs of sites from the Western and Eastern populations were selected. Then the mean distance between paired sites was calculated for each season and year. We collected and analyzed data from veterinary clinics on the number of canine babesiosis cases treated in the clinic during a whole year (2018).<br><br>RESULTS: Accordingly, further expansion of the two D. reticulatus populations was recorded, mainly along river basins. Marked colonization of the gap zone was observed, with a mean annual shift in the range of 2.5-10 km and a steadily decreasing distance between the two tick populations. The occurrence of babesiosis in different regions revealed low numbers of cases in Western Poland (19 cases/year) and the gap area (only 7 cases/year) and high incidence (up to 250 cases/1000 dogs) and fatality (total 3.65%) in Central and Eastern Poland. Strong associations were found geographically between tick and babesiosis occurrence and temporally in the seasonal patterns of occurrence of ticks and outbreaks of babesiosis.<br><br>CONCLUSIONS: We documented the shift in range limits and continued process of colonization of the gap zone accompanied by the emergence of canine babesiosis in the Eastern expansion zone. Updated maps of the distribution of ticks and occurrence of babesiosis in different regions of Poland have allowed us to predict of the emergence of pathogens vectored by D. reticulatus. Incidence (per 1000 dogs) of canine babesiosis in veterinary clinics by current range of D. reticulatus.}, }
@article {pmid34014937, year = {2021}, author = {Tibatá, VM and Sanchez, A and Palmer-Young, E and Junca, H and Solarte, VM and Madella, S and Ariza, F and Figueroa, J and Corona, M}, title = {Africanized honey bees in Colombia exhibit high prevalence but low level of infestation of Varroa mites and low prevalence of pathogenic viruses.}, journal = {PloS one}, volume = {16}, number = {5}, pages = {e0244906}, pmid = {34014937}, issn = {1932-6203}, mesh = {Animals ; Bees/*microbiology/virology ; Colombia ; Insect Viruses/*pathogenicity ; Varroidae/*pathogenicity ; }, abstract = {The global spread of the ectoparasitic mite Varroa destructor has promoted the spread and virulence of highly infectious honey bee viruses. This phenomenon is considered the leading cause for the increased number of colony losses experienced by the mite-susceptible European honey bee populations in the Northern hemisphere. Most of the honey bee populations in Central and South America are Africanized honey bees (AHBs), which are considered more resistant to Varroa compared to European honey bees. However, the relationship between Varroa levels and the spread of honey bee viruses in AHBs remains unknown. In this study, we determined Varroa prevalence and infestation levels as well as the prevalence of seven major honey bee viruses in AHBs from three regions of Colombia. We found that although Varroa exhibited high prevalence (92%), its infestation levels were low (4.5%) considering that these populations never received acaricide treatments. We also detected four viruses in the three regions analyzed, but all colonies were asymptomatic, and virus prevalence was considerably lower than those found in other countries with higher rates of mite-associated colony loss (DWV 19.88%, BQCV 17.39%, SBV 23.4%, ABPV 10.56%). Our findings indicate that AHBs possess a natural resistance to Varroa that does not prevent the spread of this parasite among their population, but restrains mite population growth and suppresses the prevalence and pathogenicity of mite-associated viruses.}, }
@article {pmid34013437, year = {2021}, author = {Romero-Olivares, AL and Morrison, EW and Pringle, A and Frey, SD}, title = {Correction to: Linking Genes to Traits in Fungi.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {156}, doi = {10.1007/s00248-021-01776-x}, pmid = {34013437}, issn = {1432-184X}, }
@article {pmid34009446, year = {2021}, author = {Antunes, VDC and Freitag, D and Serrato, RV}, title = {Differential exopolysaccharide production and composition by Herbaspirillum strains from diverse ecological environments.}, journal = {Archives of microbiology}, volume = {203}, number = {7}, pages = {3883-3892}, pmid = {34009446}, issn = {1432-072X}, mesh = {*Bacteria/metabolism ; *Environment ; *Herbaspirillum/chemistry/genetics/metabolism ; *Polysaccharides, Bacterial/biosynthesis/chemistry ; }, abstract = {Bacteria belonging to the genus Herbaspirillum are found in many different ecological niches. Some species are typically endophytic, while others were reported as free-living organisms that occupy various environments. Also, opportunistic herbaspirilli have been found infecting humans affected by several diseases. We have analyzed the production of exopolysaccharides (EPS) by Herbaspirillum strains isolated from different sources and with distinct ecological characteristics. The monosaccharide composition was determined for the EPS obtained for selected strains including free-living, plant-associated and clinical isolates, and the relationship with the ecological niches occupied by Herbaspirillum spp. is proposed.}, }
@article {pmid34008895, year = {2021}, author = {Ketchum, RN and Smith, EG and Vaughan, GO and McParland, D and Al-Mansoori, N and Burt, JA and Reitzel, AM}, title = {Unraveling the predictive role of temperature in the gut microbiota of the sea urchin Echinometra sp. EZ across spatial and temporal gradients.}, journal = {Molecular ecology}, volume = {30}, number = {15}, pages = {3869-3881}, doi = {10.1111/mec.15990}, pmid = {34008895}, issn = {1365-294X}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Microbiota/genetics ; Sea Urchins ; Seasons ; Temperature ; }, abstract = {Shifts in microbial communities represent a rapid response mechanism for host organisms to respond to changes in environmental conditions. Therefore, they are likely to be important in assisting the acclimatization of hosts to seasonal temperature changes as well as to variation in temperatures across a species' range. The Persian/Arabian Gulf is the world's warmest sea, with large seasonal fluctuations in temperature (20℃ - 37℃) and is connected to the Gulf of Oman which experiences more typical oceanic conditions (<32℃ in the summer). This system is an informative model for understanding how symbiotic microbial assemblages respond to thermal variation across temporal and spatial scales. Here, we elucidate the role of temperature on the microbial gut community of the sea urchin Echinometra sp. EZ and identify microbial taxa that are tightly correlated with the thermal environment. We generated two independent datasets with a high degree of geographic and temporal resolution. The results show that microbial communities vary across thermally variable habitats, display temporal shifts that correlate with temperature, and can become more disperse as temperatures rise. The relative abundances of several ASVs significantly correlate with temperature in both independent datasets despite the >300 km distance between the furthest sites and the extreme seasonal variations. Notably, over 50% of the temperature predictive ASVs identified from the two datasets belonged to the family Vibrionaceae. Together, our results identify temperature as a robust predictor of community-level variation and highlight specific microbial taxa putatively involved in the response to thermal environment.}, }
@article {pmid34006626, year = {2021}, author = {Hwang, Y and Rahlff, J and Schulze-Makuch, D and Schloter, M and Probst, AJ}, title = {Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {}, pmid = {34006626}, issn = {2379-5077}, abstract = {Viruses play an essential role in shaping microbial community structures and serve as reservoirs for genetic diversity in many ecosystems. In hyperarid desert environments, where life itself becomes scarce and loses diversity, the interactions between viruses and host populations have remained elusive. Here, we resolved host-virus interactions in the soil metagenomes of the Atacama Desert hyperarid core, one of the harshest terrestrial environments on Earth. We show evidence of diverse viruses infecting a wide range of hosts found in sites up to 205 km apart. Viral genomes carried putative extremotolerance features (i.e., spore formation proteins) and auxiliary metabolic genes, indicating that viruses could mediate the spread of microbial resilience against environmental stress across the desert. We propose a mutualistic model of host-virus interactions in the hyperarid core where viruses seek protection in microbial cells as lysogens or pseudolysogens, while viral extremotolerance genes aid survival of their hosts. Our results suggest that the host-virus interactions in the Atacama Desert soils are dynamic and complex, shaping uniquely adapted microbiomes in this highly selective and hostile environment.IMPORTANCE Deserts are one of the largest and rapidly expanding terrestrial ecosystems characterized by low biodiversity and biomass. The hyperarid core of the Atacama Desert, previously thought to be devoid of life, is one of the harshest environments, supporting only scant biomass of highly adapted microbes. While there is growing evidence that viruses play essential roles in shaping the diversity and structure of nearly every ecosystem, very little is known about the role of viruses in desert soils, especially where viral contact with viable hosts is significantly reduced. Our results demonstrate that diverse viruses are widely dispersed across the desert, potentially spreading key stress resilience and metabolic genes to ensure host survival. The desertification accelerated by climate change expands both the ecosystem cover and the ecological significance of the desert virome. This study sheds light on the complex virus-host interplay that shapes the unique microbiome in desert soils.}, }
@article {pmid34003315, year = {2022}, author = {Kim, J and Heo, YM and Yun, J and Lee, H and Kim, JJ and Kang, H}, title = {Changes in Archaeal Community and Activity by the Invasion of Spartina anglica Along Soil Depth Profiles of a Coastal Wetland.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {436-446}, pmid = {34003315}, issn = {1432-184X}, support = {2019R1A6A3A01091184//Ministry of Education (KR)/ ; 2020R1I1A2072824//Ministry of Education (KR)/ ; 2018K2A9A1A01090455, 2019K1A3A1A74107424, 2019K1A3A1A80113041//Ministry of Science and ICT (KR)/ ; 20170318//Ministry of Oceans and Fisheries (KR)/ ; 2019H1A2A1076239//Ministry of Education/ ; }, mesh = {Archaea ; Ecosystem ; Introduced Species ; Poaceae/physiology ; *Soil ; *Wetlands ; }, abstract = {Invasion of Spartina spp. in tidal salt marshes may affect the function and characteristics of the ecosystem. Previous studies reported that the invasion alters biogeochemical and microbial processes in marsh ecosystems, yet our knowledge of changing archaeal community due to the invasion is still limited, whereas archaeal communities play a pivotal role in biogeochemical cycles within highly reduced marsh soils. In this study, we aimed to illustrate the influences of the Spartina anglica invasion on soil archaeal community and the depth profile of the influences. The relative abundance of archaeal phyla demonstrated that the invasion substantially shifted the characteristics of tidal salt marsh from marine to terrestrial soil only in surface layer, while the influences indirectly propagated to the deeper soil layer. In particular, two archaeal phyla, Asgardaeota and Diapherotrites, were strongly influenced by the invasion, indicating a shift from marine to terrestrial archaeal communities. The shifts in soil characteristics spread to the deeper soil layer that results in indirect propagation of the influences of the invasion down to the deeper soil, which was underestimated in previous studies. The changes in the concentration of dissolved organic carbon and salinity were the substantial regulating factors for that. Therefore, changes in biogeochemical and microbial characteristics in the deep soil layer, which is below the root zone of the invasive plant, should be accounted for a more accurate illustration of the consequences of the invasion.}, }
@article {pmid33993638, year = {2021}, author = {Ng, CK and Putra, SL and Kennerley, J and Habgood, R and Roy, RA and Raymond, JL and Thompson, IP and Huang, WE}, title = {Genetic engineering biofilms in situ using ultrasound-mediated DNA delivery.}, journal = {Microbial biotechnology}, volume = {14}, number = {4}, pages = {1580-1593}, pmid = {33993638}, issn = {1751-7915}, support = {SGRF-2017-471//Commonwealth Scholarship Commission/ ; EP/M002403/1//Engineering and Physical Sciences Research Council/ ; EP/N009746/1//Engineering and Physical Sciences Research Council/ ; }, mesh = {*Bioelectric Energy Sources ; Biofilms ; DNA ; Genetic Engineering ; *Shewanella/genetics ; }, abstract = {The ability to directly modify native and established biofilms has enormous potential in understanding microbial ecology and application of biofilm in 'real-world' systems. However, efficient genetic transformation of established biofilms at any scale remains challenging. In this study, we applied an ultrasound-mediated DNA delivery (UDD) technique to introduce plasmid to established non-competent biofilms in situ. Two different plasmids containing genes coding for superfolder green fluorescent protein (sfGFP) and the flavin synthesis pathway were introduced into established bacterial biofilms in microfluidic flow (transformation efficiency of 3.9 ± 0.3 × 10[-7] cells in biofilm) and microbial fuel cells (MFCs), respectively, both employing UDD. Gene expression and functional effects of genetically modified bacterial biofilms were observed, where some cells in UDD-treated Pseudomonas putida UWC1 biofilms expressed sfGFP in flow cells and UDD-treated Shewanella oneidensis MR-1 biofilms generated significantly (P < 0.05) greater (61%) bioelectricity production (21.9 ± 1.2 µA cm[-2]) in MFC than a wild-type control group (~ 13.6 ± 1.6 µA cm[-2]). The effects of UDD were amplified in subsequent growth under selection pressure due to antibiotic resistance and metabolism enhancement. UDD-induced gene transfer on biofilms grown in both microbial flow cells and MFC systems was successfully demonstrated, with working volumes of 0.16 cm[3] and 300 cm[3] , respectively, demonstrating a significant scale-up in operating volume. This is the first study to report on a potentially scalable direct genetic engineering method for established non-competent biofilms, which can be exploited in enhancing their capability towards environmental, industrial and medical applications.}, }
@article {pmid33992330, year = {2021}, author = {Battistelli, N and Perpetuini, G and Piva, A and Pepe, A and Sidari, R and Wache, Y and Tofalo, R}, title = {Cultivable microbial ecology and aromatic profile of "mothers" for Vino cotto wine production.}, journal = {Food research international (Ottawa, Ont.)}, volume = {143}, number = {}, pages = {110311}, doi = {10.1016/j.foodres.2021.110311}, pmid = {33992330}, issn = {1873-7145}, mesh = {Fermentation ; Hanseniaspora ; Metschnikowia ; Saccharomycetales ; *Wine/analysis ; }, abstract = {The aim of the present study was to assess the cultivable microbiota of "mothers" of Vino cotto collected from production of different years 1890, 1895, 1920, 1975, 2008. A total of 73 yeasts and 81 bacteria were isolated. Starmerella lactis-condensi, Starmerella bacillaris, Hanseniaspora uvarum, Saccharomyces cerevisiae, Hanseniaspora guillermondi and Metschnikowia pulcherrima were identified. Bacteria isolates belonged to lactic acid bacteria (Lactiplantibacillus plantarum and Pediococcus pentosaceus) and acetic acid bacteria (Gluconobacter oxydans). Remarkable biodiversity was observed for Starm. bacillaris, as well as L. plantarum and G. oxydans. Organic acids and volatile compounds were also determined. Malic and succinic acids were the main ones with values ranging from 8.49 g/L to 11.76 g/L and from 4.15 g/L to 7.73 g/L respectively, while citric acid was present at low concentrations (<0.2 g/L) in all samples. Esters and higher alcohols were the main volatile compounds detected followed by alkanes. This study permits to better understand the microbial communities associated to this product and could be considered a starting point for the definition of tailored starter cultures to improve the quality of Vino cotto preserving its typical traits.}, }
@article {pmid33990304, year = {2021}, author = {Hartwick, MA and Berenson, A and Whistler, CA and Naumova, EN and Jones, SH}, title = {The Seasonal Microbial Ecology of Plankton and Plankton-Associated Vibrio parahaemolyticus in the Northeast United States.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {15}, pages = {e0297320}, pmid = {33990304}, issn = {1098-5336}, mesh = {Animals ; Bays/*microbiology ; *Microbial Interactions ; New England ; *Phytoplankton ; Seasons ; Seawater/microbiology ; *Vibrio parahaemolyticus ; Water Microbiology ; *Zooplankton ; }, abstract = {Microbial ecology studies have proven to be important resources for improving infectious disease response and outbreak prevention. Vibrio parahaemolyticus is an ongoing source of shellfish-borne food illness in the Northeast United States, and there is keen interest in understanding the environmental conditions that coincide with V. parahaemolyticus disease risk, in order to aid harvest management and prevent further illness. Zooplankton and chitinous phytoplankton are associated with V. parahaemolyticus dynamics elsewhere; however, this relationship is undetermined for the Great Bay estuary (GBE), an important emerging shellfish growing region in the Northeast United States. A comprehensive evaluation of the microbial ecology of V. parahaemolyticus associated with plankton was conducted in the GBE using 3 years of data regarding plankton community, nutrient concentration, water quality, and V. parahaemolyticus concentration in plankton. The concentrations of V. parahaemolyticus associated with plankton were highly seasonal, and the highest concentrations of V. parahaemolyticus cultured from zooplankton occurred approximately 1 month before the highest concentrations of V. parahaemolyticus from phytoplankton. The two V. parahaemolyticus peaks corresponded with different water quality variables and a few highly seasonal plankton taxa. Importantly, V. parahaemolyticus concentrations and plankton community dynamics were poorly associated with nutrient concentrations and chlorophyll a, commonly applied proxy variables for assessing ecological health risks and human health risks from harmful plankton and V. parahaemolyticus elsewhere. Together, these statistical associations (or lack thereof) provide valuable insights to characterize the plankton-V. parahaemolyticus dynamic and inform approaches for understanding the potential contribution of plankton to human health risks from V. parahaemolyticus for the Northeast United States. IMPORTANCE The Vibrio-plankton interaction is a focal relationship in Vibrio disease research; however, little is known about this dynamic in the Northeast United States, where V. parahaemolyticus is an established public health issue. We integrated phototactic plankton separation with seasonality analysis to determine the dynamics of the plankton community, water quality, and V. parahaemolyticus concentrations. Distinct bimodal peaks in the seasonal timing of V. parahaemolyticus abundance from phyto- versus zooplankton and differing associations with water quality variables and plankton taxa indicate that monitoring and forecasting approaches should consider the source of exposure when designing predictive methods for V. parahaemolyticus. Helicotheca tamensis has not been previously reported in the GBE. Its detection during this study provides evidence of the changes occurring in the ecology of regional estuaries and potential mechanisms for changes in V. parahaemolyticus populations. The Vibrio monitoring approaches can be translated to aid other areas facing similar public health challenges.}, }
@article {pmid33990222, year = {2021}, author = {Qian, X and Gunturu, S and Guo, J and Chai, B and Cole, JR and Gu, J and Tiedje, JM}, title = {Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {108}, pmid = {33990222}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents ; Ecosystem ; Genes, Bacterial ; Grassland ; Humans ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Soil ; *Soil Microbiology ; Tropical Climate ; Tundra ; }, abstract = {BACKGROUND: Soil is an important reservoir of antibiotic resistance genes (ARGs), but their potential risk in different ecosystems as well as response to anthropogenic land use change is unknown. We used a metagenomic approach and datasets with well-characterized metadata to investigate ARG types and amounts in soil DNA of three native ecosystems: Alaskan tundra, US Midwestern prairie, and Amazon rainforest, as well as the effect of conversion of the latter two to agriculture and pasture, respectively.<br><br>RESULTS: High diversity (242 ARG subtypes) and abundance (0.184-0.242 ARG copies per 16S rRNA gene copy) were observed irrespective of ecosystem, with multidrug resistance and efflux pump the dominant class and mechanism. Ten regulatory genes were identified and they accounted for 13-35% of resistome abundances in soils, among them arlR, cpxR, ompR, vanR, and vanS were dominant and observed in all studied soils. We identified 55 non-regulatory ARGs shared by all 26 soil metagenomes of the three ecosystems, which accounted for more than 81% of non-regulatory resistome abundance. Proteobacteria, Firmicutes, and Actinobacteria were primary ARG hosts, 7 of 10 most abundant ARGs were found in all of them. No significant differences in both ARG diversity and abundance were observed between native prairie soil and adjacent long-term cultivated agriculture soil. We chose 12 clinically important ARGs to evaluate at the sequence level and found them to be distinct from those in human pathogens, and when assembled they were even more dissimilar. Significant correlation was found between bacterial community structure and resistome profile, suggesting that variance in resistome profile was mainly driven by the bacterial community composition.<br><br>CONCLUSIONS: Our results identify candidate background ARGs (shared in all 26 soils), classify ARG hosts, quantify resistance classes, and provide quantitative and sequence information suggestive of very low risk but also revealing resistance gene variants that might emerge in the future. Video abstract.}, }
@article {pmid33989956, year = {2021}, author = {Zhong, X and Yu, S and Xu, H}, title = {Influence of tidal events on the body-size spectrum of periphytic ciliates for marine bioassessment using artificial substrata.}, journal = {Marine pollution bulletin}, volume = {168}, number = {}, pages = {112435}, doi = {10.1016/j.marpolbul.2021.112435}, pmid = {33989956}, issn = {1879-3363}, mesh = {Body Size ; *Ciliophora ; *Ecosystem ; Environmental Monitoring ; Water Quality ; }, abstract = {As an internal functional trait of a community, the body-size spectrum is a highly informative indicator for bioassessment of water/environmental quality in aquatic ecosystems. To determine the influence of tidal events on body-size spectra of protozoan periphytons, a 3-month baseline survey was conducted in Korean coastal waters using the polyurethane foam enveloped slide system (PFES) and conventional slide system (CS). The body-size spectrum of the protozoans showed a clear temporal pattern during the study period using both sampling systems. However, the temporal dynamics showed significantly different trajectories in the body-size spectrum between the two sampling methods during the study period. The bootstrapped average analysis revealed that the patterns of the body-size spectrum were significantly different between the PFES and CS systems, especially in terms of frequency of occurrence. These findings suggest that the tidal events may significantly influence body-size spectrum of periphytic ciliates for bioassessment in marine ecosystems.}, }
@article {pmid33989624, year = {2021}, author = {Singh, NS and Sharma, R and Singh, SK and Singh, DK}, title = {A comprehensive review of environmental fate and degradation of fipronil and its toxic metabolites.}, journal = {Environmental research}, volume = {199}, number = {}, pages = {111316}, doi = {10.1016/j.envres.2021.111316}, pmid = {33989624}, issn = {1096-0953}, mesh = {Agriculture ; *Insecticides/toxicity ; *Pesticides ; Pyrazoles ; }, abstract = {The use of pesticides to increase crop production has become one of the inevitable components of modern agriculture. Fipronil, a phenylpyrazoles insecticide, is one of the most widely used, systemic, broad-spectrum insecticides. Owing to its unique mode of action and selective toxicity, it was once regarded as safer alternatives to more toxic and persistent organochlorine insecticides. However, with the increased use, many studies have reported the toxicity of fipronil and its metabolites in various non-target organisms during the last two decades. Currently, it is regarded as one of the most persistent and lipophilic insecticides in the market. In the environment, fipronil can undergo oxidation, reduction, hydrolysis, or photolysis to form fipronil sulfone, fipronil sulfide, fipronil amide, or fipronil desulfinyl respectively. These metabolites except fipronil amide are more or less toxic and persistent than fipronil and have been reported from diverse environmental samples. Recently many studies have focused on the degradation and removal of fipronil residues from the environment. However, a comprehensive review summarizing and combining these recent findings is lacking. In the present review, we evaluate, summarize, and combine important findings from recent degradation studies of fipronil and its metabolites. An attempt has been made to elucidate the possible mechanism and pathways of degradation of fipronil and its toxic metabolites.}, }
@article {pmid33987687, year = {2022}, author = {Figueiredo, G and Gomes, M and Covas, C and Mendo, S and Caetano, T}, title = {The Unexplored Wealth of Microbial Secondary Metabolites: the Sphingobacteriaceae Case Study.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {470-481}, pmid = {33987687}, issn = {1432-184X}, support = {SFRH/BD/98446/2013//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; CEECIND/01463/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDP/50017/2020+UIDB/50017/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {*Actinobacteria/genetics ; *Bacteroidetes/genetics ; Computational Biology ; Genomics/methods ; Humans ; Multigene Family ; }, abstract = {Research on secondary metabolites (SMs) has been mostly focused on Gram-positive bacteria, especially Actinobacteria. The association of genomics with robust bioinformatics tools revealed the neglected potential of Gram-negative bacteria as promising sources of new SMs. The family Sphingobacteriaceae belongs to the phylum Bacteroidetes having representatives in practically all environments including humans, rhizosphere, soils, wastewaters, among others. Some genera of this family have demonstrated great potential as plant growth promoters, bioremediators and producers of some value-added compounds such as carotenoids and antimicrobials. However, to date, Sphingobacteriaceae's SMs are still poorly characterized, and likewise, little is known about their chemistry. This study revealed that Sphingobacteriaceae pangenome encodes a total of 446 biosynthetic gene clusters (BGCs), which are distributed across 85 strains, highlighting the great potential of this bacterial family to produce SMs. Pedobacter, Mucilaginibacter and Sphingobacterium were the genera with the highest number of BGCs, especially those encoding the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), terpenes, polyketides and nonribosomal peptides (NRPs). In Mucilaginibacter and Sphingobacterium genera, M. lappiensis ATCC BAA-1855, Mucilaginibacter sp. OK098 (both with 11 BGCs) and Sphingobacterium sp. 21 (6 BGCs) are the strains with the highest number of BGCs. Most of the BGCs found in these two genera did not have significant hits with the MIBiG database. These results strongly suggest that the bioactivities and environmental functions of these compounds, especially RiPPs, PKs and NRPs, are still unknown. Among RiPPs, two genera encoded the production of class I and class III lanthipeptides. The last are associated with LanKC proteins bearing uncommon lyase domains, whose dehydration mechanism deserves further investigation. This study translated genomics into functional information that unveils the enormous potential of environmental Gram-negative bacteria to produce metabolites with unknown chemistries, bioactivities and, more importantly, unknown ecological roles.}, }
@article {pmid33986093, year = {2021}, author = {Girolamini, L and Salaris, S and Orsini, M and Pascale, MR and Mazzotta, M and Grottola, A and Cristino, S}, title = {Draft Genome Sequences of Legionella Presumptive Novel Species Isolated during Environmental Surveillance in Artificial Water Systems.}, journal = {Microbiology resource announcements}, volume = {10}, number = {19}, pages = {}, pmid = {33986093}, issn = {2576-098X}, abstract = {We present the draft genome sequences of three Legionella strains that were isolated from a hotel water distribution system. Legionella species identification was performed by macrophage infectivity potentiator (mip) and RNA polymerase β subunit (rpoB) gene sequencing. Whole-genome sequencing and average nucleotide identity results supported the hypothesis of new Legionella species isolation.}, }
@article {pmid33984318, year = {2021}, author = {Stevens, BR and Pepine, CJ and Richards, EM and Kim, S and Raizada, MK}, title = {Depressive hypertension: A proposed human endotype of brain/gut microbiome dysbiosis.}, journal = {American heart journal}, volume = {239}, number = {}, pages = {27-37}, doi = {10.1016/j.ahj.2021.05.002}, pmid = {33984318}, issn = {1097-6744}, mesh = {Adult ; Affect/*physiology ; Biobehavioral Sciences ; Biota/*genetics ; *Depression/diagnosis/metabolism/physiopathology ; *Dysbiosis/diagnosis/physiopathology/psychology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics/physiology ; Gastrointestinal Tract/microbiology/physiopathology ; Humans ; *Hypertension/diagnosis/metabolism/psychology ; Machine Learning ; Male ; Metabolic Networks and Pathways ; Metagenome ; }, abstract = {BACKGROUND: Hypertension (HTN) is frequently linked with depression (DEP) in adults with cardiovascular disease (CVD), yet the underlying mechanism and successful management remain elusive. We approached this knowledge gap through the lens that humans are eukaryote-prokaryote "meta-organisms," such that cardiovascular disease dysregulation is a mosaic disorder involving dysbiosis of the gut. We hypothesized that patients diagnosed with hypertension plus depression harbor a unique gut microbial ecology with attending functional genomics engaged with their hosts' gut/brain axis physiology.<br><br>METHODS: Stool microbiome DNA was analyzed by whole metagenome shotgun sequencing in 54 subjects parsed into cohorts diagnosed with HTN only (N&#x202f;=&#x202f;18), DEP only (N&#x202f;=&#x202f;7), DEP plus HTN (DEP-HTN) (N&#x202f;=&#x202f;8), or reference subjects with neither HTN nor DEP (N&#x202f;=&#x202f;21). A novel battery of machine-learning multivariate analyses of de-noised data yielded effect sizes and permutational covariance-based dissimilarities that significantly differentiated the cohorts (false discovery rate (FDR)-adjusted P &#x2264; .05); data clustering within 95% confidence interval).<br><br>RESULTS: Metagenomic significant differences extricated the four cohorts. Data of the cohort exhibiting DEP-HTN were germane to the interplay of central control of blood pressure concomitant with the neuropathology of depressive disorders. DEP-HTN gut bacterial community ecology was defined by co-occurrence of Eubacterium siraeum, Alistipes obesi, Holdemania filiformis, and Lachnospiraceae bacterium 1.1.57FAA with Streptococcus salivariu. The corresponding microbial functional genomics of DEP-HTN engaged pathways degrading GABA and beneficial short chain fatty acids (SCFA), and are associated with enhanced sodium absorption and inflammasome induction.<br><br>CONCLUSIONS: These data suggest a new putative endotype of hypertension, which we denote "depressive-hypertension" (DEP-HTN), for which we posit a model that is distinctive from either HTN alone or DEP alone. An "endotype" is a subtype of a heterogeneous pathophysiological mechanism. The DEP-HTN model incorporates a unique signature of microbial taxa and functional genomics with crosstalk that putatively intertwines host pathophysiology involving the gastrointestinal tract with disruptions in central control of blood pressure and mood. The DEP-HTN endotype model engages cardiology with gastroenterology and psychiatry, providing a proof-of-concept foundation to explore future treatments, diagnosis, and prevention of HTN-coupled mood disorders.}, }
@article {pmid33981000, year = {2021}, author = {Flieder, M and Buongiorno, J and Herbold, CW and Hausmann, B and Rattei, T and Lloyd, KG and Loy, A and Wasmund, K}, title = {Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling.}, journal = {The ISME journal}, volume = {15}, number = {11}, pages = {3159-3180}, pmid = {33981000}, issn = {1751-7370}, support = {P 25111/FWF_/Austrian Science Fund FWF/Austria ; P 29426/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Geologic Sediments ; *Hydrogensulfite Reductase/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfur ; }, abstract = {Acidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. Meta-analysis of dsrAB datasets also showed Acidobacteriota dsrAB sequences are prominent in marine sediments worldwide, averaging 15% of all sequences analysed, and represent most of the previously unclassified dsrAB in marine sediments. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, "subdivision 23") and Ca. Polarisedimenticola ("subdivision 22"), with distinct genetic properties that may explain their distributions in biogeochemically distinct sediments. Ca. Sulfomarinibacter encode flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen, and acetate. A Ca. Polarisedimenticola MAG encodes various enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling of Svalbard sediments showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.}, }
@article {pmid33980683, year = {2021}, author = {De Leόn, KB}, title = {mSphere of Influence: Surface Sensing in Biofilm Formation.}, journal = {mSphere}, volume = {6}, number = {3}, pages = {}, pmid = {33980683}, issn = {2379-5042}, mesh = {Bacteria/*metabolism ; Bacterial Adhesion ; Bacterial Physiological Phenomena ; Biofilms/*growth &amp; development ; Pseudomonas aeruginosa/growth &amp; development/physiology ; Surface Properties ; }, abstract = {Kara B. De Leόn works in the field of microbial ecology, environmental biofilms, and microbial genetics. In this mSphere of Influence article, she reflects on how the paper "Multigenerational memory and adaptive adhesion in early bacterial biofilm communities" by C. K. Lee et al. (C. K. Lee, J. de Anda, A. E. Baker, R. R. Bennett, et al., Proc Natl Acad Sci U S A 115:4471-4476, 2018, https://dx.doi.org/10.1073/pnas.1720071115) made an impact on her by changing the way she thinks about initial cell attachment to a surface in an environment.}, }
@article {pmid33980476, year = {2021}, author = {Liébana-García, R and Olivares, M and Bullich-Vilarrubias, C and López-Almela, I and Romaní-Pérez, M and Sanz, Y}, title = {The gut microbiota as a versatile immunomodulator in obesity and associated metabolic disorders.}, journal = {Best practice &amp; research. Clinical endocrinology &amp; metabolism}, volume = {35}, number = {3}, pages = {101542}, doi = {10.1016/j.beem.2021.101542}, pmid = {33980476}, issn = {1878-1594}, mesh = {Diet ; *Gastrointestinal Microbiome ; Humans ; Immunologic Factors ; *Metabolic Diseases/etiology ; Obesity ; }, abstract = {Obesity has reached epidemic proportions and is associated with chronic-low-grade inflammation and metabolic morbidities. Energy-dense diets and a sedentary lifestyle are determinants of obesity. The gut microbiome is a novel biological factor involved in obesity via interactions with the host and the diet. The gut microbiome act as a synergistic force protecting or aggravating the effects of the diet on the metabolic phenotype. The role of the microbiome in the regulation of intestinal and systemic immunity is one of the mechanisms by which it contributes to the host's response to the diet and to the pathophysiology of diet-induced obesity. Here, we review the mechanisms whereby "obesogenic" diets and the microbiome impact immunity, locally and systemically, focusing on the consequences in the gut-adipose tissue axis. We also review the structural and microbial metabolites that influence immunity and how advances in this field could help design microbiome-informed strategies to tackle obesity-related disorders more effectively.}, }
@article {pmid33978602, year = {2022}, author = {Jung, CE and Estaki, M and Chopyk, J and Taylor, BC and Gonzalez, A and McDonald, D and Shin, J and Ferrante, K and Wasenda, E and Lippmann, Q and Knight, R and Pride, D and Lukacz, ES}, title = {Impact of Vaginal Estrogen on the Urobiome in Postmenopausal Women With Recurrent Urinary Tract Infection.}, journal = {Female pelvic medicine &amp; reconstructive surgery}, volume = {28}, number = {1}, pages = {20-26}, pmid = {33978602}, issn = {2154-4212}, mesh = {Estrogens ; Female ; Humans ; *Microbiota ; Postmenopause ; RNA, Ribosomal, 16S/genetics ; *Urinary Tract Infections/drug therapy ; Vagina ; }, abstract = {OBJECTIVE: The aim of this study was to describe effects of vaginal estrogen (VE) on the urogenital microbiome in postmenopausal women with recurrent urinary tract infections (rUTIs).<br><br>METHODS: This is a secondary analysis of 17 participants enrolled in a randomized controlled trial of VE versus placebo on urinary tract infection recurrence in postmenopausal women with rUTIs. Paired clean-catch urine samples were collected at baseline and after 6 months of VE and sequenced using 16S rRNA gene sequencing. Sequence reads were analyzed using Quantitative Insights Into Microbial Ecology 2. Changes in &#x3b1; diversity, &#x3b2; diversity, and differentially abundant genera were measured between paired baseline and 6-month samples and between those with a urinary tract infection at 6 months (failures) and those without (successes).<br><br>RESULTS: Of the 17 women, 11 were successes and 6 were failures after 6 months of VE treatment. There was a significant change in &#x3b1; diversity from baseline to month 6 in samples overall (Kruskal-Wallis &#x3c7;2 = 3.47, P = 0.037) and in the treatment success group (Yuen T = -2.53, P = 0.035). The increase in relative abundance of Lactobacillus crispatus, Lactobacillus gasseri, and Lactobacillus iners AB-1 was correlated with month 6. A relative bloom of L. crispatus compared with L. gasseri was associated with treatment success (Kruskal-Wallis &#x3c7;2 = 4.9, P = 0.0014).<br><br>CONCLUSIONS: Lactobacillus increases in the urogenital microbiome of postmenopausal women with rUTI after 6 months of VE. However, only the relative increase in L. crispatus specifically may be associated with treatment success.}, }
@article {pmid33976843, year = {2021}, author = {Eliades, SJ and Brown, JC and Colston, TJ and Fisher, RN and Niukula, JB and Gray, K and Vadada, J and Rasalato, S and Siler, CD}, title = {Gut microbial ecology of the Critically Endangered Fijian crested iguana (Brachylophus vitiensis): Effects of captivity status and host reintroduction on endogenous microbiomes.}, journal = {Ecology and evolution}, volume = {11}, number = {9}, pages = {4731-4743}, pmid = {33976843}, issn = {2045-7758}, abstract = {Animals often exhibit distinct microbial communities when maintained in captivity as compared to when in the wild. Such differentiation may be significant in headstart and reintroduction programs where individuals spend some time in captivity before release into native habitats. Using 16S rRNA gene sequencing, we (i) assessed differences in gut microbial communities between captive and wild Fijian crested iguanas (Brachylophus vitiensis) and (ii) resampled gut microbiota in captive iguanas released onto a native island to monitor microbiome restructuring in the wild. We used both cloacal swabs and fecal samples to further increase our understanding of gut microbial ecology in this IUCN Critically Endangered species. We found significant differentiation in gut microbial community composition and structure between captive and wild iguanas in both sampling schemes. Approximately two months postrelease, microbial communities in cloacal samples from formerly captive iguanas closely resembled wild counterparts. Interestingly, microbial communities in fecal samples from these individuals remained significantly distinct from wild conspecifics. Our results indicate that captive upbringings can lead to differences in microbial assemblages in headstart iguanas as compared to wild individuals even after host reintroduction into native conditions. This investigation highlights the necessity of continuous monitoring of reintroduced animals in the wild to ensure successful acclimatization and release.}, }
@article {pmid33975968, year = {2021}, author = {Sieradzki, ET and Morando, M and Fuhrman, JA}, title = {Metagenomics and Quantitative Stable Isotope Probing Offer Insights into Metabolism of Polycyclic Aromatic Hydrocarbon Degraders in Chronically Polluted Seawater.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {}, pmid = {33975968}, issn = {2379-5077}, abstract = {Bacterial biodegradation is a significant contributor to remineralization of polycyclic aromatic hydrocarbons (PAHs)-toxic and recalcitrant components of crude oil as well as by-products of partial combustion chronically introduced into seawater via atmospheric deposition. The Deepwater Horizon oil spill demonstrated the speed at which a seed PAH-degrading community maintained by chronic inputs responds to acute pollution. We investigated the diversity and functional potential of a similar seed community in the chronically polluted Port of Los Angeles (POLA), using stable isotope probing with naphthalene, deep-sequenced metagenomes, and carbon incorporation rate measurements at the port and in two sites in the San Pedro Channel. We demonstrate the ability of the community of degraders at the POLA to incorporate carbon from naphthalene, leading to a quick shift in microbial community composition to be dominated by the normally rare Colwellia and Cycloclasticus We show that metagenome-assembled genomes (MAGs) belonged to these naphthalene degraders by matching their 16S-rRNA gene with experimental stable isotope probing data. Surprisingly, we did not find a full PAH degradation pathway in those genomes, even when combining genes from the entire microbial community, leading us to hypothesize that promiscuous dehydrogenases replace canonical naphthalene degradation enzymes in this site. We compared metabolic pathways identified in 29 genomes whose abundance increased in the presence of naphthalene to generate genomic-based recommendations for future optimization of PAH bioremediation at the POLA, e.g., ammonium as opposed to urea, heme or hemoproteins as an iron source, and polar amino acids.IMPORTANCE Oil spills in the marine environment have a devastating effect on marine life and biogeochemical cycles through bioaccumulation of toxic hydrocarbons and oxygen depletion by hydrocarbon-degrading bacteria. Oil-degrading bacteria occur naturally in the ocean, especially where they are supported by chronic inputs of oil or other organic carbon sources, and have a significant role in degradation of oil spills. Polycyclic aromatic hydrocarbons are the most persistent and toxic component of crude oil. Therefore, the bacteria that can break those molecules down are of particular importance. We identified such bacteria at the Port of Los Angeles (POLA), one of the busiest ports worldwide, and characterized their metabolic capabilities. We propose chemical targets based on those analyses to stimulate the activity of these bacteria in case of an oil spill in the Port POLA.}, }
@article {pmid33975966, year = {2021}, author = {Chuckran, PF and Fofanov, V and Hungate, BA and Morrissey, EM and Schwartz, E and Walkup, J and Dijkstra, P}, title = {Rapid Response of Nitrogen Cycling Gene Transcription to Labile Carbon Amendments in a Soil Microbial Community.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {}, pmid = {33975966}, issn = {2379-5077}, abstract = {Episodic inputs of labile carbon (C) to soil can rapidly stimulate nitrogen (N) immobilization by soil microorganisms. However, the transcriptional patterns that underlie this process remain unclear. In order to better understand the regulation of N cycling in soil microbial communities, we conducted a 48-h laboratory incubation with agricultural soil where we stimulated the uptake of inorganic N by amending the soil with glucose. We analyzed the metagenome and metatranscriptome of the microbial communities at four time points that corresponded with changes in N availability. The relative abundances of genes remained largely unchanged throughout the incubation. In contrast, glucose addition rapidly increased the transcription of genes encoding ammonium and nitrate transporters, enzymes responsible for N assimilation into biomass, and genes associated with the N regulatory network. This upregulation coincided with an increase in transcripts associated with glucose breakdown and oxoglutarate production, demonstrating a connection between C and N metabolism. When concentrations of ammonium were low, we observed a transient upregulation of genes associated with the nitrogen-fixing enzyme nitrogenase. Transcripts for nitrification and denitrification were downregulated throughout the incubation, suggesting that dissimilatory transformations of N may be suppressed in response to labile C inputs in these soils. These results demonstrate that soil microbial communities can respond rapidly to changes in C availability by drastically altering the transcription of N cycling genes.IMPORTANCE A large portion of activity in soil microbial communities occurs in short time frames in response to an increase in C availability, affecting the biogeochemical cycling of nitrogen. These changes are of particular importance as nitrogen represents both a limiting nutrient for terrestrial plants as well as a potential pollutant. However, we lack a full understanding of the short-term effects of labile carbon inputs on the metabolism of microbes living in soil. Here, we found that soil microbial communities responded to labile carbon addition by rapidly transcribing genes encoding proteins and enzymes responsible for inorganic nitrogen acquisition, including nitrogen fixation. This work demonstrates that soil microbial communities respond within hours to carbon inputs through altered gene expression. These insights are essential for an improved understanding of the microbial processes governing soil organic matter production, decomposition, and nutrient cycling in natural and agricultural ecosystems.}, }
@article {pmid33975908, year = {2021}, author = {Che, Y and Yang, Y and Xu, X and Břinda, K and Polz, MF and Hanage, WP and Zhang, T}, title = {Reply to Shaw: Challenges for enrichment analysis of AMR gene-bearing plasmids.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {21}, pages = {}, pmid = {33975908}, issn = {1091-6490}, mesh = {*Drug Resistance, Bacterial ; Plasmids/genetics ; }, }
@article {pmid33974954, year = {2021}, author = {Lima, J and Manning, T and Rutherford, KM and Baima, ET and Dewhurst, RJ and Walsh, P and Roehe, R}, title = {Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions.}, journal = {Journal of microbiological methods}, volume = {186}, number = {}, pages = {106235}, doi = {10.1016/j.mimet.2021.106235}, pmid = {33974954}, issn = {1872-8359}, support = {BB/N01720X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S006567/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacteria/*classification/genetics/*isolation &amp; purification ; Computational Biology/*methods ; DNA, Bacterial/genetics ; *Gastrointestinal Microbiome ; Intestines/*microbiology ; Molecular Sequence Annotation/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Swine/microbiology ; }, abstract = {Environmental microbiome studies rely on fast and accurate bioinformatics tools to characterize the taxonomic composition of samples based on the 16S rRNA gene. MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights Into Microbial Ecology 2 (QIIME2) are two of the most popular tools available to perform this task. Their underlying algorithms differ in many aspects, and therefore the comparison of the pipelines provides insights into their best use and interpretation of the outcomes. Both of these bioinformatics tools are based on several specialized algorithms pipelined together, but whereas MG-RAST is a user-friendly webserver that clusters rRNA sequences based on their similarity to create Operational Taxonomic Units (OTU), QIIME2 employs DADA2 in the construction of Amplicon Sequence Variants (ASV) by applying an error model that considers the abundance of each sequence and its similarity to other sequences. Taxonomic compositions obtained from the analyses of amplicon sequences of DNA from swine intestinal gut and faecal microbiota samples using MG-RAST and QIIME2 were compared at domain-, phylum-, family- and genus-levels in terms of richness, relative abundance and diversity. We found significant differences between the microbiota profiles obtained from each pipeline. At domain level, bacteria were relatively more abundant using QIIME2 than MG-RAST; at phylum level, seven taxa were identified exclusively by QIIME2; at family level, samples processed in QIIME2 showed higher evenness and richness (assessed by Shannon and Simpson indices). The genus-level compositions obtained from each pipeline were used in partial least squares-discriminant analyses (PLS-DA) to discriminate between sample collection sites (caecum, colon and faeces). The results showed that different genera were found to be significant for the models, based on the Variable Importance in Projection, e.g. when using sequencing data processed by MG-RAST, the three most important genera were Acetitomaculum, Ruminococcus and Methanosphaera, whereas when data was processed using QIIME2, these were Candidatus Methanomethylophilus, Sphaerochaeta and Anaerorhabdus. Furthermore, the application of differential filtering procedures before the PLS-DA revealed higher accuracy when using non-restricted datasets obtained from MG-RAST, whereas datasets obtained from QIIME2 resulted in more accurate discrimination of sample collection sites after removing genera with low relative abundances (<1%) from the datasets. Our results highlight the differences in taxonomic compositions of samples obtained from the two separate pipelines, while underlining the impact on downstream analyses, such as biomarkers identification.}, }
@article {pmid33973345, year = {2021}, author = {Clocchiatti, A and Hannula, SE and Hundscheid, MPJ and Klein Gunnewiek, PJA and de Boer, W}, title = {Stimulated saprotrophic fungi in arable soil extend their activity to the rhizosphere and root microbiomes of crop seedlings.}, journal = {Environmental microbiology}, volume = {23}, number = {10}, pages = {6056-6073}, pmid = {33973345}, issn = {1462-2920}, mesh = {Fungi/genetics ; *Microbiota ; *Mycorrhizae ; Plant Roots/microbiology ; Rhizosphere ; Seedlings ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Saprotrophic fungi play an important role in ecosystem functioning and plant performance, but their abundance in intensively managed arable soils is low. Saprotrophic fungal biomass in arable soils can be enhanced with amendments of cellulose-rich materials. Here, we examined if sawdust-stimulated saprotrophic fungi extend their activity to the rhizosphere of crop seedlings and influence the composition and activity of other rhizosphere and root inhabitants. After growing carrot seedlings in sawdust-amended arable soil, we determined fungal and bacterial biomass and community structure in roots, rhizosphere and soil. Utilization of root exudates was assessed by stable isotope probing (SIP) following [13] CO2 -pulse-labelling of seedlings. This was combined with analysis of lipid fatty acids (PLFA/NLFA-SIP) and nucleic acids (DNA-SIP). Sawdust-stimulated Sordariomycetes colonized the seedling's rhizosphere and roots and actively consumed root exudates. This did not reduce the abundance and activity of bacteria, yet higher proportions of α-Proteobacteria and Bacteroidia were seen. Biomass and activity of mycorrhizal fungi increased with sawdust amendments, whereas exudate consumption and root colonization by functional groups containing plant pathogens did not change. Sawdust amendment of arable soil enhanced abundance and exudate-consuming activity of saprotrophic fungi in the rhizosphere of crop seedlings and promoted potential beneficial microbial groups in root-associated microbiomes.}, }
@article {pmid33973200, year = {2021}, author = {Moossavi, S and Fehr, K and Maleki, H and Seyedpour, S and Keshavarz-Fathi, M and Tabasi, F and Heravi, M and Sharifian, R and Shafiei, G and Badihian, N and Kelishadi, R and Nematollahi, S and Almasi, M and Popescu, S and Keshavarz-Fathi, M and Rezaei, N}, title = {Prevention of COVID-19: Preventive Strategies for General Population, Healthcare Setting, and Various Professions.}, journal = {Advances in experimental medicine and biology}, volume = {1318}, number = {}, pages = {575-604}, pmid = {33973200}, issn = {0065-2598}, mesh = {*COVID-19 ; *Cancer Vaccines ; Delivery of Health Care ; Humans ; Immunotherapy ; SARS-CoV-2 ; }, abstract = {The disease 2019 (COVID-19) made a public health emergency in early 2020. Despite attempts for the development of therapeutic modalities, there is no effective treatment yet. Therefore, preventive measures in various settings could help reduce the burden of disease. In this chapter, the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19, non-pharmaceutical approaches at individual and population level, chemoprevention, immunoprevention, preventive measures in different healthcare settings and other professions, special considerations in high-risk groups, and the role of organizations to hamper the psychosocial effects will be discussed.}, }
@article {pmid33973059, year = {2022}, author = {Castelli, L and Branchiccela, B and Romero, H and Zunino, P and Antúnez, K}, title = {Seasonal Dynamics of the Honey Bee Gut Microbiota in Colonies Under Subtropical Climate : Seasonal Dynamics of Honey Bee Gut Microbiota.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {492-500}, pmid = {33973059}, issn = {1432-184X}, mesh = {Animals ; Bacteria/genetics ; Bees ; Biodiversity ; *Gastrointestinal Microbiome/genetics ; Pollination ; Seasons ; }, abstract = {Honey bees (Apis mellifera) provide invaluable benefits for food production and maintenance of biodiversity of natural environments through pollination. They are widely spread across the world, being adapted to different climatic conditions. To survive the winter in cold temperate regions, honey bees developed different strategies including storage of honey and pollen, confinement of individuals during the winter, and an annual cycle of colony growth and reproduction. Under these conditions, winter honey bees experience physiological changes, including changes in immunity and the composition of honey bee gut microbiota. However, under tropical or subtropical climates, the life cycle can experience alterations, i.e., queens lay eggs during almost all the year and new honey bees emerge constantly. In the present study, we characterized nurses' honey bee gut microbiota in colonies under subtropical region through a year, combining qPCR, PCR-DGGE, and 16S rDNA high-throughput sequencing. We also identified environmental variables involved in those changes. Our results showed that under the mentioned conditions, the number of bacteria is stable throughout the year. Diversity of gut microbiota is higher in spring and lower in summer and winter. Gradual changes in compositions occur between seasons: Lactobacillus spp. predominate in spring while Gilliamella apicola and Snodgrasella alvi predominate in summer and winter. Environmental variables (mainly precipitations) affected the composition of the honey bee gut microbiota. Our findings provide new insights into the dynamics of honey bee gut microbiota and may be useful to understand the adaptation of bees to different environmental conditions.}, }
@article {pmid33970854, year = {2021}, author = {Alvarez-Perez, S and Baker, LJ and Morris, MM and Tsuji, K and Sanchez, VA and Fukami, T and Vannette, RL and Lievens, B and Hendry, TA}, title = {Acinetobacter pollinis sp. nov., Acinetobacter baretiae sp. nov. and Acinetobacter rathckeae sp. nov., isolated from floral nectar and honey bees.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {71}, number = {5}, pages = {}, doi = {10.1099/ijsem.0.004783}, pmid = {33970854}, issn = {1466-5034}, mesh = {Acinetobacter/*classification/isolation &amp; purification ; Animals ; Bacterial Typing Techniques ; Base Composition ; Bees/*microbiology ; California ; DNA, Bacterial/genetics ; Flowers ; Nucleic Acid Hybridization ; *Phylogeny ; *Plant Nectar ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {A detailed evaluation of eight bacterial isolates from floral nectar and animal visitors to flowers shows evidence that they represent three novel species in the genus Acinetobacter. Phylogenomic analysis shows the closest relatives of these new isolates are Acinetobacter apis, Acinetobacter boissieri and Acinetobacter nectaris, previously described species associated with floral nectar and bees, but high genome-wide sequence divergence defines these isolates as novel species. Pairwise comparisons of the average nucleotide identity of the new isolates compared to known species is extremely low (<83 %), thus confirming that these samples are representative of three novel Acinetobacter species, for which the names Acinetobacter pollinis sp. nov., Acinetobacter baretiae sp. nov. and Acinetobacter rathckeae sp. nov. are proposed. The respective type strains are SCC477[T] (=TSD-214[T]=LMG 31655[T]), B10A[T] (=TSD-213[T]=LMG 31702[T]) and EC24[T] (=TSD-215[T]=LMG 31703[T]=DSM 111781[T]).}, }
@article {pmid33970312, year = {2022}, author = {Zhao, J and Wang, B and Zhou, X and Alam, MS and Fan, J and Guo, Z and Zhang, H and Gubry-Rangin, C and Zhongjun, J}, title = {Long-Term Adaptation of Acidophilic Archaeal Ammonia Oxidisers Following Different Soil Fertilisation Histories.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {424-435}, pmid = {33970312}, issn = {1432-184X}, support = {41530857//National Natural Science Foundation of China/ ; 91751204//National Natural Science Foundation of China/ ; 41977056//National Natural Science Foundation of China/ ; URF150571//The Royal Society/ ; NE/ K016342/1//Natural Environment Research Council/ ; }, mesh = {*Ammonia ; *Archaea/genetics ; Bacteria/genetics ; Ecosystem ; Fertilization ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Ammonia oxidising archaea (AOA) are ecologically important nitrifiers in acidic agricultural soils. Two AOA phylogenetic clades, belonging to order-level lineages of Nitrososphaerales (clade C11; also classified as NS-Gamma-2.3.2) and family-level lineage of Candidatus Nitrosotaleaceae (clade C14; NT-Alpha-1.1.1), usually dominate AOA population in low pH soils. This study aimed to investigate the effect of different fertilisation histories on community composition and activity of acidophilic AOA in soils. High-throughput sequencing of ammonia monooxygenase gene (amoA) was performed on six low pH agricultural plots originating from the same soil but amended with different types of fertilisers for over 20 years and nitrification rates in those soils were measured. In these fertilised acidic soils, nitrification was likely dominated by Nitrososphaerales AOA and ammonia-oxidising bacteria, while Ca. Nitrosotaleaceae AOA activity was non-significant. Within Nitrososphaerales AOA, community composition differed based on the fertilisation history, with Nitrososphaerales C11 only representing a low proportion of the community. This study revealed that long-term soil fertilisation selects for different acidophilic nitrifier communities, potentially through soil pH change or through direct effect of nitrogen, potassium and phosphorus. Comparative community composition among the differently fertilised soils also highlighted the existence of AOA phylotypes with different levels of stability to environmental changes, contributing to the understanding of high AOA diversity maintenance in terrestrial ecosystems.}, }
@article {pmid33969432, year = {2022}, author = {Nasehi, SF and Fathipour, Y and Asgari, S and Mehrabadi, M}, title = {Environmental Temperature, but Not Male Age, Affects Wolbachia and Prophage WO Thereby Modulating Cytoplasmic Incompatibility in the Parasitoid Wasp, Habrobracon Hebetor.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {482-491}, pmid = {33969432}, issn = {1432-184X}, support = {98008582//Iran National Science Foundation/ ; }, mesh = {Animals ; Cytoplasm/metabolism ; Female ; Male ; Prophages/genetics ; Temperature ; *Wasps/microbiology ; *Wolbachia/genetics/metabolism ; }, abstract = {Wolbachia is an endosymbiotic bacterium found in many species of arthropods and manipulates its host reproduction. Cytoplasmic incompatibility (CI) is one of the most common manipulations that is induced when an uninfected female mates with a Wolbachia-infected male. The CI factors (cifA and cifB genes) are encoded by phage WO that naturally infects Wolbachia. Here, we questioned whether an environmental factor (temperature) or host factor (male age) affected the strength of the CI phenotype in the ectoparasitoid wasp, Habrobracon hebetor. We found that temperature, but not male age, results in reduced CI penetrance. Consistent with these results, we also found that the expression of the cif CI factors decreased in temperature-exposed males but was consistent across aging male wasps. Similar to studies of other insect systems, cifA showed a higher expression level than cifB, and male hosts showed increased cif expression relative to females. Our results suggest that prophage WO is present in the Wolbachia-infected wasps and expression of cif genes contributes to the induction of CI in this insect. It seems that male aging has no effect on the intensity of CI; however, temperature affects Wolbachia and prophage WO titers as well as expression levels of cif genes, which modulate the CI level.}, }
@article {pmid33968313, year = {2021}, author = {Verspecht, T and Van Holm, W and Boon, N and Bernaerts, K and Daep, CA and Masters, JG and Zayed, N and Quirynen, M and Teughels, W}, title = {Potential prebiotic substrates modulate composition, metabolism, virulence and inflammatory potential of an in vitro multi-species oral biofilm.}, journal = {Journal of oral microbiology}, volume = {13}, number = {1}, pages = {1910462}, pmid = {33968313}, issn = {2000-2297}, abstract = {Background: Modulation of the commensal oral microbiota constitutes a promising preventive/therapeutic approach in oral healthcare. The use of prebiotics for maintaining/restoring the health-associated homeostasis of the oral microbiota has become an important research topic. Aims: This study hypothesised that in vitro 14-species oral biofilms can be modulated by (in)direct stimulation of beneficial/commensal bacteria with new potential prebiotic substrates tested at 1 M and 1%(w/v), resulting in more host-compatible biofilms with fewer pathogens, decreased virulence and less inflammatory potential. Methods: Established biofilms were repeatedly rinsed with N-acetyl-D-glucosamine, α-D-lactose, D-(+)-trehalose or D-(+)-raffinose at 1 M or 1%(w/v). Biofilm composition, metabolic profile, virulence and inflammatory potential were eventually determined. Results: Repeated rinsing caused a shift towards a more health-associated microbiological composition, an altered metabolic profile, often downregulated virulence gene expression and decreased the inflammatory potential on oral keratinocytes. At 1 M, the substrates had pronounced effects on all biofilm aspects, whereas at 1%(w/v) they had a pronounced effect on virulence gene expression and a limited effect on inflammatory potential. Conclusion: Overall, this study identified four new potential prebiotic substrates that exhibit different modulatory effects at two different concentrations that cause in vitro multi-species oral biofilms to become more host-compatible.}, }
@article {pmid33966095, year = {2022}, author = {Frare, R and Pascuan, C and Galindo-Sotomonte, L and McCormick, W and Soto, G and Ayub, N}, title = {Exploring the Role of the NO-Detoxifying Enzyme HmpA in the Evolution of Domesticated Alfalfa Rhizobia.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {501-505}, pmid = {33966095}, issn = {1432-184X}, mesh = {Genomics ; Hempa ; Medicago sativa ; *Rhizobium/genetics ; Symbiosis ; }, abstract = {We have previously shown the extensive loss of genes during the domestication of alfalfa rhizobia and the high nitrous oxide emission associated with the extreme genomic instability of commercial inoculants. In the present note, we describe the molecular mechanism involved in the evolution of alfalfa rhizobia. Genomic analysis showed that most of the gene losses in inoculants are due to large genomic deletions rather than to small deletions or point mutations, a fact consistent with recurrent DNA double-strand breaks (DSBs) at numerous locations throughout the microbial genome. Genetic analysis showed that the loss of the NO-detoxifying enzyme HmpA in inoculants results in growth inhibition and high DSB levels under nitrosative stress, and large genomic deletions in planta but not in the soil. Therefore, besides its known function in the effective establishment of the symbiosis, HmpA can play a critical role in the preservation of the genomic integrity of alfalfa rhizobia under host-derived nitrosative stress.}, }
@article {pmid33959106, year = {2021}, author = {Parks, DH and Rigato, F and Vera-Wolf, P and Krause, L and Hugenholtz, P and Tyson, GW and Wood, DLA}, title = {Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {643682}, pmid = {33959106}, issn = {1664-302X}, abstract = {A fundamental goal of microbial ecology is to accurately determine the species composition in a given microbial ecosystem. In the context of the human microbiome, this is important for establishing links between microbial species and disease states. Here we benchmark the Microba Community Profiler (MCP) against other metagenomic classifiers using 140 moderate to complex in silico microbial communities and a standardized reference genome database. MCP generated accurate relative abundance estimates and made substantially fewer false positive predictions than other classifiers while retaining a high recall rate. We further demonstrated that the accuracy of species classification was substantially increased using the Microba Genome Database, which is more comprehensive than reference datasets used by other classifiers and illustrates the importance of including genomes of uncultured taxa in reference databases. Consequently, MCP classifies appreciably more reads than other classifiers when using their recommended reference databases. These results establish MCP as best-in-class with the ability to produce comprehensive and accurate species profiles of human gastrointestinal samples.}, }
@article {pmid33958420, year = {2021}, author = {McDaniel, EA and Wever, R and Oyserman, BO and Noguera, DR and McMahon, KD}, title = {Genome-Resolved Metagenomics of a Photosynthetic Bioreactor Performing Biological Nutrient Removal.}, journal = {Microbiology resource announcements}, volume = {10}, number = {18}, pages = {}, pmid = {33958420}, issn = {2576-098X}, abstract = {Enhanced biological phosphorus removal (EBPR) is an economically and environmentally significant wastewater treatment process for removing excess phosphorus by harnessing the metabolic physiologies of enriched microbial communities. We present a genome-resolved metagenomic data set consisting of 86 metagenome-assembled genome sequences from a photosynthetically operated lab-scale bioreactor simulating EBPR.}, }
@article {pmid33957514, year = {2021}, author = {Zhao, Z and Li, H and Sun, Y and Yang, Q and Fan, J}, title = {Contrasting the assembly of phytoplankton and zooplankton communities in a polluted semi-closed sea: Effects of marine compartments and environmental selection.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {285}, number = {}, pages = {117256}, doi = {10.1016/j.envpol.2021.117256}, pmid = {33957514}, issn = {1873-6424}, mesh = {Animals ; Ecosystem ; Food Chain ; *Phytoplankton ; Plankton ; *Zooplankton ; }, abstract = {Understanding the underlying mechanisms of community assembly is a major challenge in microbial ecology, particularly in communities composed of diverse organisms with different ecological characteristics. However, very little is known about the effects of marine compartments in shaping marine planktonic communities; primarily, how they are related to organism types and environmental variables. In this study, we used multiple statistical methods to explore the mechanisms driving phytoplankton and zooplankton metacommunity dynamics at the regional scale in the Bohai Sea, China. Clear geographic patterns were observed in both phytoplankton and zooplankton communities. Zooplankton showed a stronger distance-decay of similarity than phytoplankton, which had greater community differences between locations with further distances. Our analyses indicated that the zooplankton communities were primarily governed by species sorting versus dispersal limitation than the phytoplankton communities. Furthermore, we detected that zooplankton exhibited wider habitat niche breadths and dispersal abilities than phytoplankton. Our findings also showed that environmental pollution affected high trophic organisms via food webs; the presence of heavy metals in the Bohai Sea altered the abundance of some phytoplankton, and thus modified the zooplankton that feed on them.}, }
@article {pmid33956174, year = {2022}, author = {Zhou, Q and He, R and Zhao, D and Zeng, J and Yu, Z and Wu, QL}, title = {Contrasting Patterns of the Resident and Active Rhizosphere Bacterial Communities of Phragmites Australis.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {314-327}, pmid = {33956174}, issn = {1432-184X}, support = {32022050 and 31971478//National Natural Science Foundation of China/ ; U2040201//National Natural Science Foundation of China/ ; 41871096//National Natural Science Foundation of China/ ; 2021NIGLAS-CJH01//the Project of Young Scientist Group of NIGLAS/ ; 2017FY100300//Science &amp; Technology Basic Resources Investigation Program of China/ ; BK20181311//Natural Science Foundation of Jiangsu Province/ ; }, mesh = {Bacteria/genetics ; Poaceae/microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Rhizosphere microbes play a key role in maintaining plant health and regulating biogeochemical cycles. The active bacterial community (ABC) in rhizosphere, as a small fraction of the rhizosphere resident bacterial community (RBC), has the potential to actively participate in nutrient cycling processes at the root-sediment interface. Here, we investigated the ABC and RBC within the rhizosphere of Phragmites australis (P. australis) subjected to different environmental conditions (i.e., seasons and flooding conditions) in Lake Taihu, China. Our results indicated that RBC exhibited significantly higher alpha diversity as well as lower beta diversity than ABC. The active ratios of 16S rRNA to 16S rDNA (also RNA/DNA) of the bacterial communities in summer and winter suggested a lower proportion of potential active taxa in the rhizosphere bacterial community during summer. Network analysis showed that negative correlations in each network were observed to dominate the species correlations between the rhizosphere and bulk sediment bacterial communities. Our results revealed that niche differentiation and seasonal variation played crucial roles in driving the assembly of ABC and RBC associated with the rhizospheres of P. australis. These findings broaden our knowledge about how rhizosphere bacterial communities respond to environmental variations through changing their diversity and composition.}, }
@article {pmid33954842, year = {2022}, author = {Fernández-Juárez, V and Jaén-Luchoro, D and Brito-Echeverría, J and Agawin, NSR and Bennasar-Figueras, A and Echeveste, P}, title = {Everything Is Everywhere: Physiological Responses of the Mediterranean Sea and Eastern Pacific Ocean Epiphyte Cobetia Sp. to Varying Nutrient Concentration.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {296-313}, pmid = {33954842}, issn = {1432-184X}, support = {11170837//Fondecyt Iniciaci&#xf3;n/ ; EQM120137//FONDEQUIP/ ; 170403//REDI/ ; CTM2016-75457-P//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; }, mesh = {*Alismatales/physiology ; Ecosystem ; Mediterranean Sea ; Nutrients ; Pacific Ocean ; }, abstract = {Bacteria are essential in the maintenance and sustainment of marine environments (e.g., benthic systems), playing a key role in marine food webs and nutrient cycling. These microorganisms can live associated as epiphytic or endophytic populations with superior organisms with valuable ecological functions, e.g., seagrasses. Here, we isolated, identified, sequenced, and exposed two strains of the same species (i.e., identified as Cobetia sp.) from two different marine environments to different nutrient regimes using batch cultures: (1) Cobetia sp. UIB 001 from the endemic Mediterranean seagrass Posidonia oceanica and (2) Cobetia sp. 4B UA from the endemic Humboldt Current System (HCS) seagrass Heterozostera chilensis. From our physiological studies, both strains behaved as bacteria capable to cope with different nutrient and pH regimes, i.e., N, P, and Fe combined with different pH levels, both in long-term (12 days (d)) and short-term studies (4 d/96 h (h)). We showed that the isolated strains were sensitive to the N source (inorganic and organic) at low and high concentrations and low pH levels. Low availability of phosphorus (P) and Fe had a negative independent effect on growth, especially in the long-term studies. The strain UIB 001 showed a better adaptation to low nutrient concentrations, being a potential N2-fixer, reaching higher growth rates (μ) than the HCS strain. P-acquisition mechanisms were deeply investigated at the enzymatic (i.e., alkaline phosphatase activity, APA) and structural level (e.g., alkaline phosphatase D, PhoD). Finally, these results were complemented with the study of biochemical markers, i.e., reactive oxygen species (ROS). In short, we present how ecological niches (i.e., MS and HCS) might determine, select, and modify the genomic and phenotypic features of the same bacterial species (i.e., Cobetia spp.) found in different marine environments, pointing to a direct correlation between adaptability and oligotrophy of seawater.}, }
@article {pmid33953314, year = {2021}, author = {Melkonian, C and Fillinger, L and Atashgahi, S and da Rocha, UN and Kuiper, E and Olivier, B and Braster, M and Gottstein, W and Helmus, R and Parsons, JR and Smidt, H and van der Waals, M and Gerritse, J and Brandt, BW and Röling, WFM and Molenaar, D and van Spanning, RJM}, title = {High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {530}, pmid = {33953314}, issn = {2399-3642}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; Benzene/*metabolism ; *Biodegradation, Environmental ; *Biodiversity ; *Metagenome ; Nitrates/*metabolism ; }, abstract = {A key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and energy source and nitrate as the electron acceptor. Using genome-centric metagenomics plus metatranscriptomics, we demonstrate that most of the community members likely feed on metabolic left-overs or on necromass while only a few of them, from families Rhodocyclaceae and Peptococcaceae, are candidates to degrade benzene. We verify with an additional succession experiment using metabolomics and metabarcoding that these few community members are the actual drivers of benzene degradation. As such, we hypothesize that high species richness is maintained and the complexity of a natural community is stabilized in a controlled environment by the interdependencies between the few benzene degraders and the rest of the community members, ultimately resulting in a food web with different trophic levels.}, }
@article {pmid33952668, year = {2021}, author = {Lesniak, NA and Schubert, AM and Sinani, H and Schloss, PD}, title = {Clearance of Clostridioides difficile Colonization Is Associated with Antibiotic-Specific Bacterial Changes.}, journal = {mSphere}, volume = {6}, number = {3}, pages = {}, pmid = {33952668}, issn = {2379-5042}, support = {T32 AI007528/AI/NIAID NIH HHS/United States ; U19 AI090871/AI/NIAID NIH HHS/United States ; R01 GM099514/GM/NIGMS NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/administration &amp; dosage/classification/*therapeutic use ; Bacteria/drug effects/*metabolism ; Cefoperazone/therapeutic use ; Clindamycin/therapeutic use ; Clostridioides difficile/*drug effects/*physiology ; Clostridium Infections/*drug therapy/microbiology/prevention &amp; control ; Disease Susceptibility ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects/physiology ; Mice ; Streptomycin/therapeutic use ; }, abstract = {The gut bacterial community prevents many pathogens from colonizing the intestine. Previous studies have associated specific bacteria with clearing Clostridioides difficile colonization across different community perturbations. However, those bacteria alone have been unable to clear C. difficile colonization. To elucidate the changes necessary to clear colonization, we compared differences in bacterial abundance between communities able and unable to clear C. difficile colonization. We treated mice with titrated doses of antibiotics prior to C. difficile challenge, resulting in no colonization, colonization and clearance, or persistent colonization. Previously, we observed that clindamycin-treated mice were susceptible to colonization but spontaneously cleared C. difficile Therefore, we investigated whether other antibiotics would show the same result. We found that reduced doses of cefoperazone and streptomycin permitted colonization and clearance of C. difficile Mice that cleared colonization had antibiotic-specific community changes and predicted interactions with C. difficile Clindamycin treatment led to a bloom in populations related to Enterobacteriaceae Clearance of C. difficile was concurrent with the reduction of those blooming populations and the restoration of community members related to the Porphyromonadaceae and Bacteroides Cefoperazone created a susceptible community characterized by drastic reductions in the community diversity and interactions and a sustained increase in the abundance of many facultative anaerobes. Lastly, clearance in streptomycin-treated mice was associated with the recovery of multiple members of the Porphyromonadaceae, with little overlap in the specific Porphyromonadaceae observed in the clindamycin treatment. Further elucidation of how C. difficile colonization is cleared from different gut bacterial communities will improve C. difficile infection treatments.IMPORTANCE The community of microorganisms, or microbiota, in our intestines prevents pathogens like C. difficile from colonizing and causing infection. However, antibiotics can disturb the gut microbiota, which allows C. difficile to colonize. C. difficile infections (CDI) are primarily treated with antibiotics, which frequently leads to recurrent infections because the microbiota has not yet returned to a resistant state. The recurrent infection cycle often ends when the fecal microbiota from a presumed resistant person is transplanted into the susceptible person. Although this treatment is highly effective, we do not understand the mechanism. We hope to improve the treatment of CDI through elucidating how the bacterial community eliminates CDI. We found that C. difficile colonized susceptible mice but was spontaneously eliminated in an antibiotic treatment-specific manner. These data indicate that each community had different requirements for clearing colonization. Understanding how different communities clear colonization will reveal targets to improve CDI treatments.}, }
@article {pmid33952552, year = {2021}, author = {Tang, H and Bohannon, L and Lew, M and Jensen, D and Jung, SH and Zhao, A and Sung, AD and Wischmeyer, PE}, title = {Randomised, double-blind, placebo-controlled trial of Probiotics To Eliminate COVID-19 Transmission in Exposed Household Contacts (PROTECT-EHC): a clinical trial protocol.}, journal = {BMJ open}, volume = {11}, number = {5}, pages = {e047069}, pmid = {33952552}, issn = {2044-6055}, support = {R03 AG064260/AG/NIA NIH HHS/United States ; }, mesh = {*COVID-19 ; Double-Blind Method ; Humans ; Pandemics ; *Probiotics ; RNA, Ribosomal, 16S/genetics ; Randomized Controlled Trials as Topic ; SARS-CoV-2 ; Treatment Outcome ; }, abstract = {INTRODUCTION: The COVID-19 pandemic has proven to be an unprecedented challenge to worldwide health, and strategies to mitigate the spread and severity of COVID-19 infection are urgently needed. Emerging evidence suggests that the composition of the gut microbiome and modification of microbial ecology via probiotics can affect susceptibility to a wide range of infections, including respiratory tract infections. In this study, we aim to evaluate the effects of the probiotic Lactobacillus rhamnosus GG (LGG) versus placebo on COVID-19 infection status and the gut microbiome in subjects with a household contact who has tested positive for COVID-19.<br><br>METHODS AND ANALYSIS: In this double-blinded, randomised, placebo-controlled trial, we will randomise 1132 subjects having a household contact who has recently (&#x2264;7&#x2009;days) tested positive for COVID-19 to daily oral LGG or placebo for 28 days. We hypothesise that taking LGG as a probiotic will protect against COVID-19 infection and reduce the severity of disease in those who become infected (primary endpoint: decreased symptoms), and will be associated with beneficial changes in the composition of the gut microbiome. Stool samples and nasal swabs will be collected to evaluate the microbiome by 16S rRNA sequencing and the presence of SARS-CoV-2 by PCR, respectively. We will also conduct multivariate analysis of demographic, behavioural, temporal, and other variables that may predict development of symptoms and other outcomes.<br><br>ETHICS AND DISSEMINATION: This trial is conducted under a Food and Drug Administration Investigational New Drug for LGG, has received ethics approval by the institutional review board of Duke University and enrolment has begun. We plan to disseminate the results in peer-reviewed journals and at national and international conferences.<br><br>TRIAL REGISTRATION NUMBER: NCT04399252.}, }
@article {pmid33952355, year = {2021}, author = {Baker, JM and Hinkle, KJ and McDonald, RA and Brown, CA and Falkowski, NR and Huffnagle, GB and Dickson, RP}, title = {Whole lung tissue is the preferred sampling method for amplicon-based characterization of murine lung microbiota.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {99}, pmid = {33952355}, issn = {2049-2618}, support = {R01 AI138348/AI/NIAID NIH HHS/United States ; R01 HL121774/HL/NHLBI NIH HHS/United States ; R01 HL144599/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; DNA, Bacterial/genetics ; Female ; Lung ; Mice ; *Microbiota/genetics ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Low-biomass microbiome studies (such as those of the lungs, placenta, and skin) are vulnerable to contamination and sequencing stochasticity, which obscure legitimate microbial signal. While human lung microbiome studies have rigorously identified sampling strategies that reliably capture microbial signal from these low-biomass microbial communities, the optimal sampling strategy for characterizing murine lung microbiota has not been empirically determined. Performing accurate, reliable characterization of murine lung microbiota and distinguishing true microbial signal from noise in these samples will be critical for further mechanistic microbiome studies in mice.<br><br>RESULTS: Using an analytic approach grounded in microbial ecology, we compared bacterial DNA from the lungs of healthy adult mice collected via two common sampling approaches: homogenized whole lung tissue and bronchoalveolar lavage (BAL) fluid. We quantified bacterial DNA using droplet digital PCR, characterized bacterial communities using 16S rRNA gene sequencing, and systematically assessed the quantity and identity of bacterial DNA in both specimen types. We compared bacteria detected in lung specimens to each other and to potential source communities: negative (background) control specimens and paired oral samples. By all measures, whole lung tissue in mice contained greater bacterial signal and less evidence of contamination than did BAL fluid. Relative to BAL fluid, whole lung tissue exhibited a greater quantity of bacterial DNA, distinct community composition, decreased sample-to-sample variation, and greater biological plausibility when compared to potential source communities. In contrast, bacteria detected in BAL fluid were minimally different from those of procedural, reagent, and sequencing controls.<br><br>CONCLUSIONS: An ecology-based analytical approach discriminates signal from noise in this low-biomass microbiome study and identifies whole lung tissue as the preferred specimen type for murine lung microbiome studies. Sequencing, analysis, and reporting of potential source communities, including negative control specimens and contiguous biological sites, are crucial for biological interpretation of low-biomass microbiome studies, independent of specimen type. Video abstract.}, }
@article {pmid33948706, year = {2022}, author = {Stabili, L and Di Salvo, M and Alifano, P and Talà, A}, title = {An Integrative, Multiparametric Approach for the Comprehensive Assessment of Microbial Quality and Pollution in Aquaculture Systems.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {271-283}, pmid = {33948706}, issn = {1432-184X}, support = {LIFE16 ENV/IT/000343//LIFE Environment and Resource Efficiency 2016/ ; }, mesh = {Animals ; *Aquaculture/methods ; Humans ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; *Vibrio/genetics ; Water Quality ; }, abstract = {As the aquaculture sector significantly expanded worldwide in the past decades, the concept of sustainable aquaculture has developed with the challenge of not only maximizing benefits but also minimizing the negative impacts on the environment assuring, at the same time, food security. In this framework, monitoring and improving the microbiological water quality and animal health are a central topic. In the present study, we evaluated the seawater microbiological quality in a mariculture system located in a Mediterranean coastal area (Northern Ionian Sea, Italy). We furnished, for the first time, a microbial inventory based on conventional culture-based methods, integrated with the 16S rRNA gene metabarcoding approach for vibrios identification and diversity analyses, and further implemented with microbial metabolic profiling data obtained from the Biolog EcoPlate system. Microbiological pollution indicators, vibrios diversity, and microbial metabolism were determined in two different times of the year (July and December). All microbial parameters measured in July were markedly increased compared to those measured in December. The presence of potentially pathogenic vibrios is discussed concerning the risk of fish disease and human infections. Thus, the microbial inventory here proposed might represent a new multiparametric approach for the suitable surveillance of the microbial quality in a mariculture system. Consequently, it could be useful for ensuring the safety of both the reared species and the consumers in the light of sustainable, eco-friendly aquaculture management.}, }
@article {pmid33947808, year = {2021}, author = {Boysen, AK and Carlson, LT and Durham, BP and Groussman, RD and Aylward, FO and Ribalet, F and Heal, KR and White, AE and DeLong, EF and Armbrust, EV and Ingalls, AE}, title = {Particulate Metabolites and Transcripts Reflect Diel Oscillations of Microbial Activity in the Surface Ocean.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {}, pmid = {33947808}, issn = {2379-5077}, abstract = {Light fuels photosynthesis and organic matter production by primary producers in the sunlit ocean. The quantity and quality of the organic matter produced influence community function, yet in situ measurements of metabolites, the products of cellular metabolism, over the diel cycle are lacking. We evaluated community-level biochemical consequences of oscillations of light in the North Pacific Subtropical Gyre by quantifying 79 metabolites in particulate organic matter from 15 m every 4 h over 8 days. Total particulate metabolite concentration peaked at dusk and represented up to 2% of total particulate organic carbon (POC). The concentrations of 55/79 (70%) individual metabolites exhibited significant 24-h periodicity, with daily fold changes from 1.6 to 12.8, often greater than those of POC and flow cytometry-resolvable biomass, which ranged from 1.2 to 2.8. Paired metatranscriptome analysis revealed the taxa involved in production and consumption of a subset of metabolites. Primary metabolites involved in anabolism and redox maintenance had significant 24-h periodicity and diverse organisms exhibited diel periodicity in transcript abundance associated with these metabolites. Compounds with osmotic properties displayed the largest oscillations in concentration, implying rapid turnover and supporting prior evidence of functions beyond cell turgor maintenance. The large daily oscillation of trehalose paired with metatranscriptome and culture data showed that trehalose is produced by the nitrogen-fixing cyanobacterium Crocosphaera, likely to store energy for nighttime metabolism. Together, paired measurements of particulate metabolites and transcripts resolve strategies that microbes use to manage daily energy and redox oscillations and highlight dynamic metabolites with cryptic roles in marine microbial ecosystems.IMPORTANCE Fueled by light, phytoplankton produce the organic matter that supports ocean ecosystems and carbon sequestration. Ocean change impacts microbial metabolism with repercussions for biogeochemical cycling. As the small molecule products of cellular metabolism, metabolites often change rapidly in response to environmental conditions and form the basis of energy and nutrient management and storage within cells. By pairing measurements of metabolites and gene expression in the stratified surface ocean, we reveal strategies of microbial energy management over the day-night cycle and hypothesize that oscillating metabolites are important substrates for dark respiration by phytoplankton. These high-resolution diel measurements of in situ metabolite concentrations form the basis for future work into the specific roles these compounds play in marine microbial communities.}, }
@article {pmid33947800, year = {2021}, author = {Heal, KR and Durham, BP and Boysen, AK and Carlson, LT and Qin, W and Ribalet, F and White, AE and Bundy, RM and Armbrust, EV and Ingalls, AE}, title = {Marine Community Metabolomes Carry Fingerprints of Phytoplankton Community Composition.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {}, pmid = {33947800}, issn = {2379-5077}, abstract = {Phytoplankton transform inorganic carbon into thousands of biomolecules that represent an important pool of fixed carbon, nitrogen, and sulfur in the surface ocean. Metabolite production differs between phytoplankton, and the flux of these molecules through the microbial food web depends on compound-specific bioavailability to members of a wider microbial community. Yet relatively little is known about the diversity or concentration of metabolites within marine plankton. Here, we compare 313 polar metabolites in 21 cultured phytoplankton species and in natural planktonic communities across environmental gradients to show that bulk community metabolomes reflect the chemical composition of the phytoplankton community. We also show that groups of compounds have similar patterns across space and taxonomy, suggesting that the concentrations of these compounds in the environment are controlled by similar sources and sinks. We quantify several compounds in the surface ocean that represent substantial understudied pools of labile carbon. For example, the N-containing metabolite homarine was up to 3% of particulate carbon and is produced in high concentrations by cultured Synechococcus, and S-containing gonyol accumulated up to 2.5 nM in surface particles and likely originates from dinoflagellates or haptophytes. Our results show that phytoplankton composition directly shapes the carbon composition of the surface ocean. Our findings suggest that in order to access these pools of bioavailable carbon, the wider microbial community must be adapted to phytoplankton community composition.IMPORTANCE Microscopic phytoplankton transform 100 million tons of inorganic carbon into thousands of different organic compounds each day. The structure of each chemical is critical to its biological and ecosystem function, yet the diversity of biomolecules produced by marine microbial communities remained mainly unexplored, especially small polar molecules which are often considered the currency of the microbial loop. Here, we explore the abundance and diversity of small biomolecules in planktonic communities across ecological gradients in the North Pacific and within 21 cultured phytoplankton species. Our work demonstrates that phytoplankton diversity is an important determinant of the chemical composition of the highly bioavailable pool of organic carbon in the ocean, and we highlight understudied yet abundant compounds in both the environment and cultured organisms. These findings add to understanding of how the chemical makeup of phytoplankton shapes marine microbial communities where the ability to sense and use biomolecules depends on the chemical structure.}, }
@article {pmid33940748, year = {2021}, author = {Guarin, TC and Pagilla, KR}, title = {Microbial community in biofilters for water reuse applications: A critical review.}, journal = {The Science of the total environment}, volume = {773}, number = {}, pages = {145655}, doi = {10.1016/j.scitotenv.2021.145655}, pmid = {33940748}, issn = {1879-1026}, mesh = {*Drinking Water ; Filtration ; *Microbiota ; Reproducibility of Results ; *Water Purification ; }, abstract = {The combination of ozonation (O3) and biofiltration processes has become practical and desirable in advanced water reclamation for water reuse applications. However, the role of microbial community and its characteristics (source, abundance, composition, viability, structure) on treatment performance has not received the same attention in water reclamation biofilters as in other applications, such as in drinking water biofilters. Microbial community characterization of biofilters used in water reuse applications will add evidence to better understand the potential microorganisms, consequent risks, and mechanisms that will populate drinking water sources and ultimately influence public health and the environment. This critical review provides insights into O3-biofiltration as a treatment barrier with a focus on development, structure, and composition of the microbial community characteristics involved in the process. The effect of microorganism seeding by the influent before and after the biofilter and ozone oxidation effects are explored to capture the microbial ecology interactions and environmental factors affecting the media ecosystem. The findings of reviewed studies concurred in identifying Proteobacteria as the most dominant phylum. However, Proteobacteria and other phyla relative abundance differ substantially depending upon environmental factors (e.g., pH, temperature, nutrients availability, among others) gradients. In general, we found significant gaps to relate and explain the biodegradation performance and metabolic processes within the biofilter, and hence deserve future attention. We highlighted and identified key challenges and future research ideas to assure O3-biofiltration reliability as a promising barrier in advanced water treatment applications.}, }
@article {pmid33935412, year = {2021}, author = {Sergaliev, NK and Kakishev, MG and Ginayatov, NS and Nurzhanova, FK and Andronov, EE}, title = {Microbiome structure in a recirculating aquaculture system and its connection to infections in sturgeon fish.}, journal = {Veterinary world}, volume = {14}, number = {3}, pages = {661-668}, pmid = {33935412}, issn = {0972-8988}, abstract = {AIM: This study aimed to determine the bacterial composition at various stages of the temperature regime in a recirculating aquaculture system (RAS) to assess the pathological risk of a group of opportunistic pathogenic microflora.<br><br>MATERIALS AND METHODS: Water temperature, incidences of illnesses, and fish mortality were monitored, during the research period to identify the causes of pathogens in sturgeons. Analysis of the nucleotide sequences was performed using the quantitative insights into microbial ecology module. Sequence alignment in the analysis of the distribution of gene libraries was performed using the Unclust method. The RDP database was used for the taxonomic identification of operational taxonomic units.<br><br>RESULTS: The pattern of the contraction of infection among sturgeons bred in the RAS was established. A detailed analysis of the microbiome structure's taxonomic features showed dominant taxa during the "artificial wintering" period and at a temperature optimum in industrial aquaculture. It was found that the main outbreaks of pseudomonosis occurred during this period in the RAS. With a decrease in temperature of the aquatic environment, the incidence of illness increased by 75% compared with the optimum temperature period. Pseudomonas, Cetobacterium, and Lactococcus were specific taxa characteristic for the "artificial wintering" period. Xanthomonadaceae and Flavobacterium were specific taxa characteristic for the optimum temperature.<br><br>CONCLUSION: Consequently, the microbial structure was determined at different temperature regimes in a RAS, and the dominant communities were identified. The pattern of the contraction of infection caused by an opportunistic microflora (pseudomonosis) among sturgeons was established, allowing for the development and correction of treatment and preventive measures.}, }
@article {pmid33933764, year = {2021}, author = {Vermeire, ML and Thoresen, J and Lennard, K and Vikram, S and Kirkman, K and Swemmer, AM and Te Beest, M and Siebert, F and Gordijn, P and Venter, Z and Brunel, C and Wolfaard, G and Krumins, JA and Cramer, MD and Hawkins, HJ}, title = {Fire and herbivory drive fungal and bacterial communities through distinct above- and belowground mechanisms.}, journal = {The Science of the total environment}, volume = {785}, number = {}, pages = {147189}, doi = {10.1016/j.scitotenv.2021.147189}, pmid = {33933764}, issn = {1879-1026}, mesh = {Bacteria ; Biomass ; Ecosystem ; *Fires ; Fungi ; Grassland ; *Herbivory ; Soil ; Soil Microbiology ; }, abstract = {Fire and herbivory are important natural disturbances in grassy biomes. Both drivers are likely to influence belowground microbial communities but no studies have unravelled the long-term impact of both fire and herbivory on bacterial and fungal communities. We hypothesized that soil bacterial communities change through disturbance-induced shifts in soil properties (e.g. pH, nutrients) while soil fungal communities change through vegetation modification (biomass and species composition). To test these ideas, we characterised soil physico-chemical properties (pH, acidity, C, N, P and exchangeable cations content, texture, bulk density, moisture), plant species richness and biomass, microbial biomass and bacterial and fungal community composition and diversity (using 16S and ITS rRNA amplicon sequencing, respectively) in six long-term (18 to 70 years) ecological research sites in South African savanna and grassland ecosystems. We found that fire and herbivory regimes profoundly modified soil physico-chemical properties, plant species richness and standing biomass. In all sites, an increase in woody biomass (ranging from 12 to 50%) was observed when natural disturbances were excluded. The intensity and direction of changes in soil properties were highly dependent on the topo-pedo-climatic context. Overall, fire and herbivory shaped bacterial and fungal communities through distinct driving forces: edaphic properties (including Mg, pH, Ca) for bacteria, and vegetation (herbaceous biomass and woody cover) for fungi. Fire and herbivory explained on average 7.5 and 9.8% of the fungal community variability, respectively, compared to 6.0 and 5.6% for bacteria. The relatively small changes in microbial communities due to natural disturbance is in stark contrast to dramatic vegetation and edaphic changes and suggests that soil microbial communities, having evolved with disturbance, are resistant to change. This represents both a buffer to short-term anthropogenic-induced changes and a restoration challenge in the face of long-term changes.}, }
@article {pmid33931358, year = {2021}, author = {Lucas, SK and Feddema, E and Boyer, HC and Hunter, RC}, title = {Diversity of cystic fibrosis chronic rhinosinusitis microbiota correlates with different pathogen dominance.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {20}, number = {4}, pages = {678-681}, pmid = {33931358}, issn = {1873-5010}, support = {R01 HL136919/HL/NHLBI NIH HHS/United States ; T90 DE022732/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/classification/isolation &amp; purification ; Chronic Disease ; Correlation of Data ; Cystic Fibrosis/complications/*microbiology ; Humans ; Microbiota ; Rhinitis/complications/*microbiology ; Sinusitis/complications/*microbiology ; }, abstract = {Chronic rhinosinusitis (CRS) affects nearly all individuals with cystic fibrosis (CF) and is thought to serve as a reservoir for microbiota that subsequently colonize the lung. To better understand the microbial ecology of CRS, we generated a 16S rRNA gene sequencing profile of sinus mucus from CF-CRS patients. We show that CF-CRS sinuses harbor bacterial diversity not entirely captured by clinical culture. Culture data consistently identified the dominant organism in most patients, though lower abundance bacteria were not always identified. We also demonstrate that bacterial communities dominated by Staphylococcus spp. were significantly more diverse compared to those dominated by Pseudomonas spp. Diversity was not significantly associated with clinical factors or patient age, however, younger subjects yielded a much wider range of bacterial diversity. These data mirror bacterial community dynamics in the lung and provide additional insight into the role of sinus microbiota in chronic airway disease progression.}, }
@article {pmid33930130, year = {2021}, author = {Co, R and Hug, LA}, title = {Prediction, enrichment and isolation identify a responsive, competitive community of cellulolytic microorganisms from a municipal landfill.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {5}, pages = {}, doi = {10.1093/femsec/fiab065}, pmid = {33930130}, issn = {1574-6941}, mesh = {Bacteria/genetics ; Metagenome ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Waste Disposal Facilities ; }, abstract = {Landfills are engineered, heterogeneously contaminated sites containing large reservoirs of paper waste. Cellulose degradation is an important process within landfill microbial ecology, and these anoxic, saturated environments are prime locations for discovery of cellulases that may offer improvements on industrial cellulose degradation efforts. We sampled leachate from three locations within a municipal landfill, a leachate collection cistern, and groundwater from an adjacent aquifer to identify cellulolytic populations and their associated cellulases. Metagenomic sequencing identified wide-spread and taxonomically diverse cellulolytic potential, with a notable scarcity of predicted exocellulases. 16S rRNA amplicon sequencing detected nine landfill microorganisms enriched in a customized leachate medium amended with microcrystalline cellulose or common paper stocks. Paper-enrichment cultures showed competition dynamics in response to the specific composition (lignin: hemi-cellulose: cellulose) of the different paper stocks. From leachate biomass, four novel cellulolytic bacteria were isolated, including two with the capacity for cellulolysis at industrially relevant temperatures. None of the isolates demonstrated exocellulase activity, consistent with the metagenome-based predictions. However, there was very little overlap between metagenome-derived predicted cellulolytic organisms, organisms enriched on paper sources, or the isolates, suggesting the landfill cellulolytic community is at low abundance but able to rapidly respond to introduced substrates.}, }
@article {pmid33928415, year = {2022}, author = {Solans, M and Pelliza, YI and Tadey, M}, title = {Inoculation with Native Actinobacteria May Improve Desert Plant Growth and Survival with Potential Use for Restoration Practices.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {380-392}, pmid = {33928415}, issn = {1432-184X}, support = {PIP 0235.//Conicet/ ; PICT 3478//FONCYT/ ; }, mesh = {*Actinobacteria ; *Ecosystem ; Plant Development ; Seedlings/microbiology ; Soil ; }, abstract = {Soil microorganisms, together with water, play a key role in arid ecosystems, being responsible for the nutrient cycle, facilitating nutrient incorporation into plants, influencing plant drought tolerance, and enhancing their establishment. Therefore, their use for restoration practices is promising. We tested the potential of native strains of Actinobacteria from Monte Desert as growth promoters of native vegetation, isolating them from two substrates from their habitat (bare soil and leaf-cutting ant refuse dumps). Strains were inoculated into the soil where seedlings of three native plant species (Atriplex lampa, Grindelia chiloensis, Gutierrezia solbrigii) were growing. Seedlings were grown following a full factorial design experiment under greenhouse and field conditions comparing native Actinobacteria effects with a known growth-promoting strain, Streptomyces sp. (BCRU-MM40 GenBank accession number: FJ771041), and control treatments. Seedlings survived greenhouse condition but species survival and growth were different among treatments at field conditions, varying over time. The highest survival was observed in a native soil strain (S20) while the lowest in MM40. The low survival in MM40 and in the other treatments may be explained by the higher herbivory observed in those seedlings compared to control ones, suggesting a higher nutritional status in inoculated plants. Strains from refuse dumps were the best at enhancing seedling growth, while strains from soil were the best at maintaining their survival. Native Actinobacteria studied may increase plant species survival and growth by improving their nutritional status, suggesting their potential to facilitate vegetation establishment and, therefore, being good candidates for restoration practices. Furthermore, plant species respond differently to different strains, highlighting the importance of microorganism diversity for ecosystem functioning.}, }
@article {pmid33927711, year = {2021}, author = {Griggs, RG and Steenwerth, KL and Mills, DA and Cantu, D and Bokulich, NA}, title = {Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {673810}, pmid = {33927711}, issn = {1664-302X}, abstract = {Microbiomes are integral to viticulture and winemaking - collectively termed winegrowing - where diverse fungi and bacteria can exert positive and negative effects on grape health and wine quality. Wine is a fermented natural product, and the vineyard serves as a key point of entry for quality-modulating microbiota, particularly in wine fermentations that are conducted without the addition of exogenous yeasts. Thus, the sources and persistence of wine-relevant microbiota in vineyards critically impact its quality. Site-specific variations in microbiota within and between vineyards may contribute to regional wine characteristics. This includes distinctions in microbiomes and microbiota at the strain level, which can contribute to wine flavor and aroma, supporting the role of microbes in the accepted notion of terroir as a biological phenomenon. Little is known about the factors driving microbial biodiversity within and between vineyards, or those that influence annual assembly of the fruit microbiome. Fruit is a seasonally ephemeral, yet annually recurrent product of vineyards, and as such, understanding the sources of microbiota in vineyards is critical to the assessment of whether or not microbial terroir persists with inter-annual stability, and is a key factor in regional wine character, as stable as the geographic distances between vineyards. This review examines the potential sources and vectors of microbiota within vineyards, general rules governing plant microbiome assembly, and how these factors combine to influence plant-microbe interactions relevant to winemaking.}, }
@article {pmid33927707, year = {2021}, author = {Orevi, T and Kashtan, N}, title = {Life in a Droplet: Microbial Ecology in Microscopic Surface Wetness.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {655459}, pmid = {33927707}, issn = {1664-302X}, abstract = {While many natural and artificial surfaces may appear dry, they are in fact covered by thin liquid films and microdroplets invisible to the naked eye known as microscopic surface wetness (MSW). Central to the formation and the retention of MSW are the deliquescent properties of hygroscopic salts that prevent complete drying of wet surfaces or that drive the absorption of water until dissolution when the relative humidity is above a salt-specific level. As salts are ubiquitous, MSW occurs in many microbial habitats, such as soil, rocks, plant leaf, and root surfaces, the built environment, and human and animal skin. While key properties of MSW, including very high salinity and segregation into droplets, greatly affect microbial life therein, it has been scarcely studied, and systematic studies are only in their beginnings. Based on recent findings, we propose that the harsh micro-environment that MSW imposes, which is very different from bulk liquid, affects key aspects of bacterial ecology including survival traits, antibiotic response, competition, motility, communication, and exchange of genetic material. Further research is required to uncover the fundamental principles that govern microbial life and ecology in MSW. Such research will require multidisciplinary science cutting across biology, physics, and chemistry, while incorporating approaches from microbiology, genomics, microscopy, and computational modeling. The results of such research will be critical to understand microbial ecology in vast terrestrial habitats, affecting global biogeochemical cycles, as well as plant, animal, and human health.}, }
@article {pmid33925970, year = {2021}, author = {Saw, NMMT and Suwanchaikasem, P and Zuniga-Montanez, R and Qiu, G and Marzinelli, EM and Wuertz, S and Williams, RBH}, title = {Influence of Extraction Solvent on Nontargeted Metabolomics Analysis of Enrichment Reactor Cultures Performing Enhanced Biological Phosphorus Removal (EBPR).}, journal = {Metabolites}, volume = {11}, number = {5}, pages = {}, pmid = {33925970}, issn = {2218-1989}, support = {1102-IRIS-10-02//National Research Foundation, Republic of Singapore/ ; }, abstract = {Metabolome profiling is becoming more commonly used in the study of complex microbial communities and microbiomes; however, to date, little information is available concerning appropriate extraction procedures. We studied the influence of different extraction solvent mixtures on untargeted metabolomics analysis of two continuous culture enrichment communities performing enhanced biological phosphate removal (EBPR), with each enrichment targeting distinct populations of polyphosphate-accumulating organisms (PAOs). We employed one non-polar solvent and up to four polar solvents for extracting metabolites from biomass. In one of the reactor microbial communities, we surveyed both intracellular and extracellular metabolites using the same set of solvents. All samples were analysed using ultra-performance liquid chromatography mass spectrometry (UPLC-MS). UPLC-MS data obtained from polar and non-polar solvents were analysed separately and evaluated using extent of repeatability, overall extraction capacity and the extent of differential abundance between physiological states. Despite both reactors demonstrating the same bioprocess phenotype, the most appropriate extraction method was biomass specific, with methanol: water (50:50 v/v) and methanol: chloroform: water (40:40:20 v/v) being chosen as the most appropriate for each of the two different bioreactors, respectively. Our approach provides new data on the influence of solvent choice on the untargeted surveys of the metabolome of PAO enriched EBPR communities and suggests that metabolome extraction methods need to be carefully tailored to the specific complex microbial community under study.}, }
@article {pmid33923841, year = {2021}, author = {van der Linde, C and Barone, M and Turroni, S and Brigidi, P and Keleszade, E and Swann, JR and Costabile, A}, title = {An In Vitro Pilot Fermentation Study on the Impact of Chlorella pyrenoidosa on Gut Microbiome Composition and Metabolites in Healthy and Coeliac Subjects.}, journal = {Molecules (Basel, Switzerland)}, volume = {26}, number = {8}, pages = {}, pmid = {33923841}, issn = {1420-3049}, mesh = {*Chlorella ; Enterobacteriaceae/classification/genetics ; Fermentation/physiology ; Gastrointestinal Microbiome/*physiology ; RNA, Ribosomal, 16S ; }, abstract = {The response of a coeliac and a healthy gut microbiota to the green algae Chlorella pyrenoidosa was evaluated using an in vitro continuous, pH controlled, gut model system, which simulated the human colon. The effect of C. pyrenoidosa on the microbial structure was determined by 16S rRNA gene sequencing and inferred metagenomics, whereas the metabolic activitywas determined by[1]H-nuclear magnetic resonancespectroscopic analysis. The addition of C. pyrenoidosa significantly increased the abundance of the genera Prevotella, Ruminococcus and Faecalibacterium in the healthy donor, while an increase in Faecalibacterium, Bifidobacterium and Megasphaera and a decrease in Enterobacteriaceae were observed in the coeliac donor. C. pyrenoidosa also altered several microbial pathways including those involved in short-chain fatty acid (SCFA) production. At the metabolic level, a significant increase from baseline was seen in butyrate and propionate (p < 0.0001) in the healthy donor, especially in vessels 2 and 3. While acetate was significantly higher in the healthy donor at baseline in vessel 3 (p < 0.001) compared to the coeliac donor, this was markedly decreased after in vitro fermentation with C. pyrenoidosa. This is the first in vitro fermentation study of C. pyrenoidosa and human gut microbiota, however, further in vivo studies are needed to prove its efficacy.}, }
@article {pmid33922357, year = {2021}, author = {Oh, RM and Bollati, E and Maithani, P and Huang, D and Wainwright, BJ}, title = {The Microbiome of the Reef Macroalga Sargassum ilicifolium in Singapore.}, journal = {Microorganisms}, volume = {9}, number = {5}, pages = {}, pmid = {33922357}, issn = {2076-2607}, abstract = {The large canopy-forming macroalga, Sargassum ilicifolium, provides shelter and food for numerous coral reef species, but it can also be detrimental at high abundances where it outcompetes other benthic organisms for light and space. Here, we investigate the microbial communities associated with S. ilicifolium in Singapore, where it is an abundant and important member of coral reef communities. We collected eight complete S. ilicifolium thalli from eight island locations along an approximate 14 km east-to-west transect. Each thallus was dissected into three separate parts: holdfast, vesicles, and leaves. We then characterized the bacterial communities associated with each part via polymerase chain reaction (PCR) amplification of the 16S rRNA gene V4 region. We then inferred predicted metagenome functions using METAGENassist. Despite the comparatively short distances between sample sites, we show significant differences in microbial community composition, with communities further differentiated by part sampled. Holdfast, vesicles and leaves all harbor distinct microbial communities. Functional predictions reveal some separation between holdfast and leaf communities, with higher representation of sulphur cycling taxa in the holdfast and higher representation of nitrogen cycling taxa in the leaves. This study provides valuable baseline data that can be used to monitor microbial change, and helps lay the foundation upon which we can begin to understand the complexities of reef-associated microbial communities and the roles they play in the functioning and diversity of marine ecosystems.}, }
@article {pmid33920240, year = {2021}, author = {Skliros, D and Kalatzis, PG and Kalloniati, C and Komaitis, F and Papathanasiou, S and Kouri, ED and Udvardi, MK and Kokkari, C and Katharios, P and Flemetakis, E}, title = {The Development of Bacteriophage Resistance in Vibrio alginolyticus Depends on a Complex Metabolic Adaptation Strategy.}, journal = {Viruses}, volume = {13}, number = {4}, pages = {}, pmid = {33920240}, issn = {1999-4915}, mesh = {*Adaptation, Physiological ; Bacteriophages/*genetics/pathogenicity ; Drug Resistance, Bacterial ; Gene Expression Profiling ; Genome, Viral ; Genomics ; Host Microbial Interactions/*genetics ; Metabolic Networks and Pathways/genetics ; Metabolomics ; Phage Therapy ; Phylogeny ; Vibrio alginolyticus/*genetics/*metabolism/virology ; }, abstract = {Lytic bacteriophages have been well documented to play a pivotal role in microbial ecology due to their complex interactions with bacterial species, especially in aquatic habitats. Although the use of phages as antimicrobial agents, known as phage therapy, in the aquatic environment has been increasing, recent research has revealed drawbacks due to the development of phage-resistant strains among Gram-negative species. Acquired phage resistance in marine Vibrios has been proven to be a very complicated process utilizing biochemical, metabolic, and molecular adaptation strategies. The results of our multi-omics approach, incorporating transcriptome and metabolome analyses of Vibrio alginolyticus phage-resistant strains, corroborate this prospect. Our results provide insights into phage-tolerant strains diminishing the expression of phage receptors ompF, lamB, and btuB. The same pattern was observed for genes encoding natural nutrient channels, such as rbsA, ptsG, tryP, livH, lysE, and hisp, meaning that the cell needs to readjust its biochemistry to achieve phage resistance. The results showed reprogramming of bacterial metabolism by transcript regulations in key-metabolic pathways, such as the tricarboxylic acid cycle (TCA) and lysine biosynthesis, as well as the content of intracellular metabolites belonging to processes that could also significantly affect the cell physiology. Finally, SNP analysis in resistant strains revealed no evidence of amino acid alterations in the studied putative bacterial phage receptors, but several SNPs were detected in genes involved in transcriptional regulation. This phenomenon appears to be a phage-specific, fine-tuned metabolic engineering, imposed by the different phage genera the bacteria have interacted with, updating the role of lytic phages in microbial marine ecology.}, }
@article {pmid33919845, year = {2021}, author = {Thompson, HJ and Levitt, JO and McGinley, JN and Chandler, P and Guenther, PM and Huybrechts, I and Playdon, MC}, title = {Measuring Dietary Botanical Diversity as a Proxy for Phytochemical Exposure.}, journal = {Nutrients}, volume = {13}, number = {4}, pages = {}, pmid = {33919845}, issn = {2072-6643}, support = {001/WHO_/World Health Organization/International ; 5R00CA218694-03/CA/NCI NIH HHS/United States ; }, mesh = {Aged ; Algorithms ; Chronic Disease/prevention &amp; control ; Diet Surveys/*methods/statistics &amp; numerical data ; Feeding Behavior/*physiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Middle Aged ; *Phytochemicals ; Plants, Edible/*chemistry ; }, abstract = {The study of natural plant molecules and their medicinal properties, pharmacognosy, provides a taxonomy for botanical families that represent diverse chemical groupings with potentially distinct functions in relation to human health. Yet, this reservoir of knowledge has not been systematically applied to elucidating the role of patterns of plant food consumption on gut microbial ecology and function. All chemical classes of dietary phytochemicals can affect the composition of the microbes that colonize the gut and their function. In turn, the gut microbiome affects the host via multiple mechanisms including gut barrier function, immune function, satiety and taste regulation and the activity of biological signaling pathways that influence health and disease. Herein, we report the development of a botanical diversity index (BDI) to evaluate plant food consumption as a novel metric for identifying and quantifying phytochemicals to which an individual is exposed. A rationale is advanced for using the BDI to investigate how plant food diversity impacts gut microbial ecology and functionality.}, }
@article {pmid33918726, year = {2021}, author = {Khomutovska, N and de Los Ríos, A and Syczewski, MD and Jasser, I}, title = {Connectivity of Edaphic and Endolithic Microbial Niches in Cold Mountain Desert of Eastern Pamir (Tajikistan).}, journal = {Biology}, volume = {10}, number = {4}, pages = {}, pmid = {33918726}, issn = {2079-7737}, support = {DSM501-D114-86-0117600-16//Ministry of Science and Higher Education through the Faculty of Biology, University of Warsaw/ ; PID2019-105469RB-C22//Ministerio de Ciencia e Innovaci&#xf3;n/ ; 2015/19/B/NZ9/00473//Narodowe Centrum Nauki/ ; }, abstract = {Microbial communities found in arid environments are commonly represented by biological soil crusts (BSCs) and endolithic assemblages. There is still limited knowledge concerning endoliths and BSCs occurring in the cold mountain desert of Pamir. The aim of the study was to investigate the composition and structure of endolithic bacterial communities in comparison to surrounding BSCs in three subregions of the Eastern Pamir (Tajikistan). The endolithic and BSC communities were studied using culture-independent and culture-dependent techniques. The structure of the endolithic bacterial communities can be characterized as Actinobacteria-Proteobacteria-Bacteroidetes-Chloroflexi-Cyanobacteria, while the BSCs' can be described as Proteobacteria-Actinobacteria-Bacteroidetes-Cyanobacteria assemblages with low representation of other bacteria. The endolithic cyanobacterial communities were characterized by the high percentage of Chroococcidiopsaceae, Nodosilineaceae, Nostocaceae and Thermosynechococcaceae, while in the BSCs were dominated by Nodosilineaceae, Phormidiaceae and Nostocaceae. The analysis of 16S rRNA genes of the cyanobacterial cultures revealed the presence of possibly novel species of Chroococcidiopsis, Gloeocapsopsis and Wilmottia. Despite the niches' specificity, which is related to the influence of microenvironment factors on the composition and structure of endolithic communities, our results illustrate the interrelation between the endoliths and the surrounding BSCs in some regions. The structure of cyanobacterial communities from BSC was the only one to demonstrate some subregional differences.}, }
@article {pmid33911260, year = {2021}, author = {Kremer, JM and Sohrabi, R and Paasch, BC and Rhodes, D and Thireault, C and Schulze-Lefert, P and Tiedje, JM and He, SY}, title = {Peat-based gnotobiotic plant growth systems for Arabidopsis microbiome research.}, journal = {Nature protocols}, volume = {16}, number = {5}, pages = {2450-2470}, pmid = {33911260}, issn = {1750-2799}, support = {R01 GM109928/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Arabidopsis/*growth &amp; development/*microbiology ; Culture Techniques/*methods ; Germ-Free Life ; Industry ; *Microbiota ; Soil/*chemistry ; }, abstract = {The complex structure and function of a plant microbiome are driven by many variables, including the environment, microbe-microbe interactions and host factors. Likewise, resident microbiota can influence many host phenotypes. Gnotobiotic growth systems and controlled environments empower researchers to isolate these variables, and standardized methods equip a global research community to harmonize protocols, replicate experiments and collaborate broadly. We developed two easily constructed peat-based gnotobiotic growth platforms: the FlowPot system and the GnotoPot system. Sterile peat is amenable to colonization by microbiota and supports growth of the model plant Arabidopsis thaliana in the presence or absence of microorganisms. The FlowPot system uniquely allows one to flush the substrate with water, nutrients and/or suspensions of microbiota via an irrigation port, and a mesh retainer allows for the inversion of plants for dip or vacuum infiltration protocols. The irrigation port also facilitates passive drainage, preventing root anoxia. In contrast, the GnotoPot system utilizes a compressed peat pellet, widely used in the horticultural industry. GnotoPot construction has fewer steps and requires less user handling, thereby reducing the risk of contamination. Both protocols take up to 4 d to complete with 4-5 h of hands-on time, including substrate and seed sterilization. In this protocol, we provide detailed assembly and inoculation procedures for the two systems. Both systems are modular, do not require a sterile growth chamber, and cost less than US$2 per vessel.}, }
@article {pmid33906488, year = {2022}, author = {García-González, I and Corona-Cervantes, K and Hernández-Quiroz, F and Villalobos-Flores, LE and Galván-Rodríguez, F and Romano, MC and Miranda-Brito, C and Piña-Escobedo, A and Borquez-Arreortúa, FG and Rangel-Calvillo, MN and García-Mena, J}, title = {The Influence of Holder Pasteurization on the Diversity of the Human Milk Bacterial Microbiota Using High-Throughput DNA Sequencing.}, journal = {Journal of human lactation : official journal of International Lactation Consultant Association}, volume = {38}, number = {1}, pages = {118-130}, doi = {10.1177/08903344211011946}, pmid = {33906488}, issn = {1552-5732}, mesh = {Bacteria/genetics ; Breast Feeding ; Cross-Sectional Studies ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; *Microbiota/genetics ; *Milk Banks ; Milk, Human/microbiology ; Pasteurization ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Human milk is the best food for infants; however, when breastfeeding is not possible, pasteurized milk from human milk banks is the best alternative. Little has been reported about variations in the bacterial microbiota composition of human milk after pasteurization.<br><br>RESEARCH AIM: To characterize and compare the bacterial microbiota composition and diversity within human milk among Mexican mothers before and after the Holder pasteurization process.<br><br>METHODS: A cross-sectional, observational, and comparative design was used. The effect of the pasteurization process on the bacterial composition and diversity of human milk samples of donors (N = 42) from a public milk bank was assessed before and after pasteurization by high throughput deoxyribonucleic acid sequencing of V3-16S rRNA gene libraries. Sequencing data were examined using the Quantitative Insights into Microbial Ecology software and Phyloseq in R environment.<br><br>RESULTS: A varied community of bacteria was found in both raw and pasteurized human milk. The bacterial diversity of the milk samples was increased by the pasteurization, where some thermoduric bacteria of the phyla Proteobacteria, Firmicutes, and Actinobacteria were more abundant. The source tracker analysis indicated that at most 1.0% of bacteria may have come from another source, showing the safety of the process used to treat milk samples.<br><br>CONCLUSION: The pasteurization process increased the bacterial diversity. We selected taxa capable of surviving the process, which could proliferate after the treatment without being a risk for infants.}, }
@article {pmid33903927, year = {2022}, author = {Kajan, K and Cukrov, N and Cukrov, N and Bishop-Pierce, R and Orlić, S}, title = {Microeukaryotic and Prokaryotic Diversity of Anchialine Caves from Eastern Adriatic Sea Islands.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {257-270}, pmid = {33903927}, issn = {1432-184X}, support = {KK.01.1.1.01//European Regional Development Fund/ ; }, mesh = {*Biodiversity ; *Ecosystem ; Geography ; Islands ; Salinity ; }, abstract = {Anchialine ecosystems in the eastern Adriatic Sea are diverse both morphologically and biologically. In this study, for the first time, we explored the microeukaryotic and prokaryotic community of anchialine caves in the Mediterranean region using high-throughput sequencing. Four anchialine caves located on nearby islands with a well-pronounced salinity gradient were sampled at the surface freshwater area, halocline area, and seawater area. Sequencing revealed a surprisingly wide diversity of the microeukaryotic and prokaryotic community with the relative abundance of major phyla differing within the salinity gradient and between the caves. Interestingly, microeukaryotic and prokaryotic communities clustered into four groups based on location, pointing out that sampled anchialine caves have different microbial community patterns and high microbial endemism. Our results indicate that even with the halocline acting as a selecting barrier, the salinity is not the only community structuring factor. Despite the short geographical distance, the isolation of anchialine caves facilitated high microbial community adaptation and endemism. Our study suggests that anchialine caves represent reservoirs of new biodiversity, maintaining unique and complex microbial diversity influenced by biotic interactions and abiotic environmental conditions.}, }
@article {pmid33902741, year = {2021}, author = {Zhou, X and Leite, MFA and Zhang, Z and Tian, L and Chang, J and Ma, L and Li, X and van Veen, JA and Tian, C and Kuramae, EE}, title = {Facilitation in the soil microbiome does not necessarily lead to niche expansion.}, journal = {Environmental microbiome}, volume = {16}, number = {1}, pages = {4}, pmid = {33902741}, issn = {2524-6372}, support = {XDA23070501, XDB15030103//Science Foundation of the Chinese Academy of Sciences/ ; 2016YFC0501202//National Key Research and Development Program of China/ ; KFZD-SW-112//Key Research Project of the Chinese Academy of Sciences/ ; 41571255//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The soil microbiome drives soil ecosystem function, and soil microbial functionality is directly linked to interactions between microbes and the soil environment. However, the context-dependent interactions in the soil microbiome remain largely unknown.<br><br>RESULTS: Using latent variable models (LVMs), we disentangle the biotic and abiotic interactions of soil bacteria, fungi and environmental factors using the Qinghai-Tibetan Plateau soil ecosystem as a model. Our results show that soil bacteria and fungi not only interact with each other but also shift from competition to facilitation or vice versa depending on environmental variation; that is, the nature of their interactions is context-dependent.<br><br>CONCLUSIONS: Overall, elevation is the environmental gradient that most promotes facilitative interactions among microbes but is not a major driver of soil microbial community composition, as evidenced by variance partitioning. The larger the tolerance of a microbe to a specific environmental gradient, the lesser likely it is to interact with other soil microbes, which suggests that facilitation does not necessarily lead to niche expansion.}, }
@article {pmid33902740, year = {2020}, author = {Chopyk, J and Nasko, DJ and Allard, S and Bui, A and Pop, M and Mongodin, EF and Sapkota, AR}, title = {Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond.}, journal = {Environmental microbiome}, volume = {15}, number = {1}, pages = {18}, pmid = {33902740}, issn = {2524-6372}, support = {2016-68007-25064//United States Department of Agriculture-National Institute of Food and Agriculture/ ; 1632976//National Science Foundation/ ; }, abstract = {BACKGROUND: Ponds are important freshwater habitats that support both human and environmental activities. However, relative to their larger counterparts (e.g. rivers, lakes), ponds are understudied, especially with regard to their microbial communities. Our study aimed to fill this knowledge gap by using culture-independent, high-throughput sequencing to assess the dynamics, taxonomy, and functionality of bacterial and viral communities in a freshwater agricultural pond.<br><br>RESULTS: Water samples (n&#x2009;=&#x2009;14) were collected from a Mid-Atlantic agricultural pond between June 2017 and May 2018 and filtered sequentially through 1 and 0.2&#x2009;&#x3bc;m filter membranes. Total DNA was then extracted from each filter, pooled, and subjected to 16S rRNA gene and shotgun sequencing on the Illumina HiSeq 2500 platform. Additionally, on eight occasions water filtrates were processed for viral metagenomes (viromes) using chemical concentration and then shotgun sequenced. A ubiquitous freshwater phylum, Proteobacteria was abundant at all sampling dates throughout the year. However, environmental characteristics appeared to drive the structure of the community. For instance, the abundance of Cyanobacteria (e.g. Nostoc) increased with rising water temperatures, while a storm event appeared to trigger an increase in overall bacterial diversity, as well as the relative abundance of Bacteroidetes. This event was also associated with an increase in the number of antibiotic resistance genes. The viral fractions were dominated by dsDNA of the order Caudovirales, namely Siphoviridae and Myovirdae.<br><br>CONCLUSIONS: Overall, this study provides one of the&#xa0;largest datasets on pond water microbial ecology to date, revealing seasonal trends in the microbial taxonomic composition and functional potential.}, }
@article {pmid33902721, year = {2020}, author = {Tang, X and Xie, G and Shao, K and Hu, Y and Cai, J and Bai, C and Gong, Y and Gao, G}, title = {Contrast diversity patterns and processes of microbial community assembly in a river-lake continuum across a catchment scale in northwestern China.}, journal = {Environmental microbiome}, volume = {15}, number = {1}, pages = {10}, pmid = {33902721}, issn = {2524-6372}, support = {NIGLAS2017GH05//"One-Three-Five" Strategic Planning of NGLAS, CAS/ ; 41971062//National Natural Science Foundation of China/ ; 41790423//National Natural Science Foundation of China/ ; 41621002//National Natural Science Foundation of China/ ; QYZDJ-SSW-DQC008//Key Research Program of Frontier Sciences, CAS/ ; }, abstract = {BACKGROUND: Microorganisms in rivers and lakes are essential for nutrient recycling in aquatic ecosystems. Understanding the ecological processes shaping microbial communities is of crucial importance for aquatic microbial ecology and biogeography. However, the diversity of microorganisms and the forces that control this diversity are poorly understood. This is particularly true within the framework of the river-lake continuum in arid regions.<br><br>RESULTS: Using a whole catchment-sampling effort, we explored biogeographical patterns and mechanisms of microbial community (bacteria and archaea) assembly within the catchment of the largest inland once&#xa0;freshwater&#xa0;lake (Lake Bosten) in China. Water samples from headstream tributaries, the mainstream of the River Kaidu to downstream Lake Bosten were characterized using amplicon sequencing of 16S rRNA genes. Higher &#x3b1;-diversity was found in mainstream of River Kaidu and in the tributaries compared with Lake Bosten. And the microbial community composition was also significantly different between the&#xa0;lake and its connected river habitats. Canonical correspondence analysis demonstrated that salinity and total suspended solids were the most important environmental factors shaping the community variations. Overall, pure environmental and pure spatial factors explained 13.7 and 5.6% of the community variation, respectively, while 32.0% of the variation was explained by combined environmental and spatial variables. These observations suggested that spatially structured environmental variations mainly shaped the microbial biogeography in this region. Both deterministic and stochastic processes influenced the microbial community assembly in river and lake habitats, and the stochastic pattern was particularly pronounced for microbiome in river habitat. Co-occurrence network analysis revealed more abundant and complicated correlations among frequently occurred taxa in lake habitat compared with the river habitat, implying that ecological multispecies interactions (e.g., competition) shaped lake microbial community structures.<br><br>CONCLUSIONS: Our findings demonstrate an ecological succession along the river-lake continuum of microbial communities across the largest inland once&#xa0;freshwater lake basin in China, and highlight the effects of spatially structured environmental factors on regional microbial &#x3b2;-diversity and species interactions on local community assembly.}, }
@article {pmid33902717, year = {2020}, author = {Bagnaro, A and Baltar, F and Brownstein, G and Lee, WG and Morales, SE and Pritchard, DW and Hepburn, CD}, title = {Reducing the arbitrary: fuzzy detection of microbial ecotones and ecosystems - focus on the pelagic environment.}, journal = {Environmental microbiome}, volume = {15}, number = {1}, pages = {16}, pmid = {33902717}, issn = {2524-6372}, abstract = {BACKGROUND: One of the central objectives of microbial ecology is to study the distribution of microbial communities and their association with their environments. Biogeographical studies have partitioned the oceans into provinces and regions, but the identification of their boundaries remains challenging, hindering our ability to study transition zones (i.e. ecotones) and microbial ecosystem heterogeneity. Fuzzy clustering is a promising method to do so, as it creates overlapping sets of clusters. The outputs of these analyses thus appear both structured (into clusters) and gradual (due to the overlaps), which aligns with the inherent continuity of the pelagic environment, and solves the issue of defining ecosystem boundaries.<br><br>RESULTS: We show the suitability of applying fuzzy clustering to address the patchiness of microbial ecosystems, integrating environmental (Sea Surface Temperature, Salinity) and bacterioplankton data (Operational Taxonomic Units (OTUs) based on 16S rRNA gene) collected during six cruises over 1.5&#x2009;years from the subtropical frontal zone off New Zealand. The technique was able to precisely identify ecological heterogeneity, distinguishing both the patches and the transitions between them. In particular we show that the subtropical front is a distinct, albeit transient, microbial ecosystem. Each water mass harboured a specific microbial community, and the characteristics of their ecotones matched the characteristics of the environmental transitions, highlighting that environmental mixing lead to community mixing. Further explorations into the OTU community compositions revealed that, although only a small proportion of the OTUs explained community variance, their associations with given water mass were consistent through time.<br><br>CONCLUSION: We demonstrate recurrent associations between microbial communities and dynamic oceanic features. Fuzzy clusters can be applied to any ecosystem (terrestrial, human, marine, etc) to solve uncertainties regarding the position of microbial ecological boundaries and to refine the relation between the distribution of microorganisms and their environment.}, }
@article {pmid33901904, year = {2021}, author = {Rahman, MS and Kazmi, SSUH and Uroosa,  and Xu, H}, title = {Insights into seasonal shift in the homogeneity of periphytic protozoan fauna in coastal waters of the Yellow Sea, northern China.}, journal = {Marine pollution bulletin}, volume = {168}, number = {}, pages = {112367}, doi = {10.1016/j.marpolbul.2021.112367}, pmid = {33901904}, issn = {1879-3363}, mesh = {Biodiversity ; China ; *Ciliophora ; *Ecosystem ; Environmental Monitoring ; Seasons ; }, abstract = {The seasonal shift in the homogeneity of the periphytic protozoan fauna was studied based on a four-season baseline survey in the coastal waters of the Yellow Sea, northern China. Samples were collected using glass microscope slides as an artificial substratum at a depth of 2 m after the immersion time of 14 days during each of the four seasons (winter, spring, summer, and autumn, 2017). The protozoan fauna showed a clear seasonal shift in species composition and a significant variation in homogeneity in terms of both compositional and community structure during four seasons. The dispersion measures and β-diversity index represented an increase in the trend from spring to winter. These findings suggest that the homogeneity of the periphytic protozoan fauna was subject to a significant variability shaped mainly by species composition during a four-season cycle in marine ecosystems.}, }
@article {pmid33899919, year = {2021}, author = {Lin, Q and Dini-Andreote, F and Li, L and Umari, R and Novotny, V and Kukla, J and Heděnec, P and Frouz, J}, title = {Soil microbial interconnections along ecological restoration gradients of lowland forests after slash-and-burn agriculture.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {5}, pages = {}, doi = {10.1093/femsec/fiab063}, pmid = {33899919}, issn = {1574-6941}, mesh = {Agriculture ; Basidiomycota ; *Burns ; Ecosystem ; Forests ; Fungi/genetics ; Humans ; Papua New Guinea ; *Soil ; Soil Microbiology ; }, abstract = {Microbial interconnections in soil are pivotal to ecosystem services and restoration. However, little is known about how soil microbial interconnections respond to slash-and-burn agriculture and to the subsequent ecosystem restoration after the practice. Here, we used amplicon sequencing and co-occurrence network analyses to explore the interconnections within soil bacterial and fungal communities in response to slash-and-burn practice and a spontaneous restoration (spanning ca. 60 years) of tropical forests after the practice, in Papua New Guinea. We found significantly higher complexity and greater variations in fungal networks than in those of bacteria, despite no significant changes observed in bacterial or fungal networks across successional stages. Within most successional stages, bacterial core co-occurrences (co-occurrences consistently present across all sub-networks in a stage) were more frequent than those of fungi, indicating higher stability of interconnections between bacteria along succession. The stable interconnections occurred frequently between bacterial taxa (i.e. Sporosarcina, Acidimicrobiale and Bacillaceae) and between ectomycorrhizal fungi (Boletaceae and Russula ochroleuca), implying important ecological roles of these taxa in the ecosystem restoration. Collectively, our results provide new insight into microbial interconnections in response to slash-and-burn agriculture and the subsequent ecosystem restoration, thus promoting a better understanding of microbial roles in ecosystem services and restoration.}, }
@article {pmid33897672, year = {2021}, author = {Estrela, S and Sánchez, &#xc1; and Rebolleda-Gómez, M}, title = {Multi-Replicated Enrichment Communities as a Model System in Microbial Ecology.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {657467}, pmid = {33897672}, issn = {1664-302X}, support = {R35 GM133467/GM/NIGMS NIH HHS/United States ; }, abstract = {Recent advances in robotics and affordable genomic sequencing technologies have made it possible to establish and quantitatively track the assembly of enrichment communities in high-throughput. By conducting community assembly experiments in up to thousands of synthetic habitats, where the extrinsic sources of variation among replicates can be controlled, we can now study the reproducibility and predictability of microbial community assembly at different levels of organization, and its relationship with nutrient composition and other ecological drivers. Through a dialog with mathematical models, high-throughput enrichment communities are bringing us closer to the goal of developing a quantitative predictive theory of microbial community assembly. In this short review, we present an overview of recent research on this growing field, highlighting the connection between theory and experiments and suggesting directions for future work.}, }
@article {pmid33893533, year = {2022}, author = {Ding, L and Zhou, J and Li, Q and Tang, J and Chen, X}, title = {Effects of Land-Use Type and Flooding on the Soil Microbial Community and Functional Genes in Reservoir Riparian Zones.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {393-407}, pmid = {33893533}, issn = {1432-184X}, support = {2016YFC0502703//the National Key Research and Development Program of China/ ; 31470483//National Natural Science Foundation of China/ ; 31570411//National Natural Science Foundation of China/ ; }, mesh = {Archaea/genetics ; *Microbiota/genetics ; Nitrogen Cycle ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {Ecological processes (e.g., nutrient cycling) in riparian zones are often affected by land-use type and flooding. The extent to which land-use types and flooding conditions affect soil microorganisms and their ecological functions in riparian zones is not well known. By using high-throughput sequencing and quantitative PCR (q-PCR), we tested the effects of three land-use types (i.e., forest, wetland, and grassland) and two flooding conditions (i.e., landward locations and waterward locations within the land-use types) on soil microbial communities and microbial functional genes in the riparian zones of a reservoir. Land-use type but not flooding significantly affected soil microbial community composition at the phylum level, while both land-use type and flooding significantly affected the orders Nitrosotaleales and Nitrososphaerales. Alpha diversity was higher in the wetland and forest regardless of flooding conditions. Functional gene abundance differed among the three land-use types. Archaeal amoA (AOA) and nirS genes were more abundant in the wetland than in the grassland or forest. Bacterial amoA (AOB), nirK, nirS, and nosZ genes were more abundant in the waterward location than in the landward location but only in the wetland. Soil pH, moisture, and concentrations of soil organic matter and total soil nitrogen were significantly associated with the composition of archaeal and bacterial communities as well as with their gene abundance. This study revealed that soil microorganisms putatively involved in nitrogen cycling in riparian zones were more affected by land-use type than flooding.}, }
@article {pmid33893532, year = {2022}, author = {Maltsev, Y and Maltseva, S and Maltseva, I}, title = {Diversity of Cyanobacteria and Algae During Primary Succession in Iron Ore Tailing Dumps.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {408-423}, pmid = {33893532}, issn = {1432-184X}, mesh = {*Cyanobacteria ; *Ecosystem ; Iron ; Soil/chemistry ; Soil Microbiology ; }, abstract = {The extraction of commercial minerals is often accompanied by the formation of large areas of quarry and dump technogenic ecosystems. This stimulates the search for measures to reduce their negative impact on the environment, as well as a detailed study of all the constituent elements of ecosystems that spontaneously or after reclamation form on them. Primary stages of syngenesis on the tailing dumps of iron ore mines in Kryvorizhzhia took place involving cyanobacteria and eukaryotic algae. The dynamics of the community structures of algae and cyanobacteria depends on the mineralogical composition of tailings, salinity conditions, pH, and content of particles of physical clay and humus. The assessment of the features of the dynamics of algae communities was carried out based on the ordination procedure because of the method of non-metric multidimensional scaling. The considered environmental variables were statistically significant predictors of community structure and could explain 47-90% of the variation in measurements. Diagnostic signs of the species composition of communities of algae and cyanobacteria tailing dumps were established by physical and chemical parameters. An increase in the content of physical clay particles in the substrate and a pH shift towards the alkaline side increased the species richness of cyanobacteria, while an increase in the humus content increased the total species diversity. Based on the specificity of the type of growth and the species composition of algae communities, when describing the primary successions, it is proposed to allocate the following stages of development of algae and cyanobacteria communities: dispersal aerophyton, stratose epilitophyton, algal crust, mixed moss and algal crust, and edaphone.}, }
@article {pmid33892834, year = {2021}, author = {Delikan, E and Caliskan, S and Cankilic, MY and Aksu, S and Kesim, B and Ulger, ST}, title = {Microbiota of Endodontically Infected Primary and Permanent Teeth.}, journal = {Pediatric dentistry}, volume = {43}, number = {2}, pages = {102-110}, pmid = {33892834}, issn = {1942-5473}, mesh = {Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Tooth, Deciduous ; }, abstract = {Purpose: Differences in the endodontic microbiome of permanent and primary teeth during the mixed dentition period are still unknown. The purpose of this study was to examine bacterial diversity in endodontically infected primary and permanent teeth using 16S rRNA gene sequencing and the QIIME 2 (Quantitative Insights Into Microbial Ecology 2) bioinformatics pipeline. Methods: Microbial samples from endodontically infected primary (n equals 15) and permanent (n equals 15) maxillary or mandibular molar teeth were subjected to next-generation sequencing analysis based on examination of the hypervariable V3 to V4 region of the 16S rRNA gene. Statistical analysis was performed using R software. Results: Of 1,664,926 reads and 2,237 operational taxonomic units, 14 phyla, 89 families, and 236 genera were identified. Firmicutes were the most commonly detected phyla in both endodontically infected primary and permanent root canals. Bacteroides and Proteobacteria were more common in primary teeth, whereas Actinobacteria and Verrucomicrobia were more common in permanent teeth. The overall canal microbiota composition was similar in endodontically infected primary and permanent teeth (P=0.338). Conclusions: This study provides a comprehensive assessment of microbiota composition in endodontically infected primary and permanent teeth and gives a deeper insight into the origin of the root canal infections.}, }
@article {pmid33891367, year = {2021}, author = {Wang, T and Persson, P and Tunlid, A}, title = {A widespread mechanism in ectomycorrhizal fungi to access nitrogen from mineral-associated proteins.}, journal = {Environmental microbiology}, volume = {23}, number = {10}, pages = {5837-5849}, doi = {10.1111/1462-2920.15539}, pmid = {33891367}, issn = {1462-2920}, mesh = {Fungi/metabolism ; Minerals/metabolism ; *Mycorrhizae/metabolism ; Nitrogen/metabolism ; Soil/chemistry ; Soil Microbiology ; }, abstract = {A large fraction of nitrogen (N) in forest soils is present in mineral-associated proteinaceous compounds. The strong association between proteins and minerals limits microbial accessibility to this source, which is a relatively stable reservoir of soil N. We have shown that the ectomycorrhizal (ECM) fungus Paxillus involutus can acquire N from iron oxide-associated proteins. Using tightly controlled isotopic, spectroscopic and chromatographic experiments, we demonstrated that the capacity to access N from iron oxide-associated bovine serum albumin (BSA) is shared with the ECM fungi Hebeloma cylindrosporum and Piloderma olivaceum. Despite differences in evolutionary history, growth rates, exploration types and the decomposition mechanisms of organic matter, their N acquisition mechanisms were similar to those described for P. involutus. The fungi released N from mineral-associated BSA by direct action of extracellular aspartic proteases on the mineral-associated BSA, without initial desorption of the protein. Hydrolysis was suppressed by the adsorption of proteases to minerals, but this adverse effect was counteracted by the secretion of compounds that conditioned the mineral surface. These data suggest that the enzymatic exudate-driven mechanism to access N from mineral-associated proteins is found in ECM fungi of multiple lineages and exploration types.}, }
@article {pmid33890146, year = {2022}, author = {Kanjanapruthipong, T and Sukphopetch, P and Reamtong, O and Isarangkul, D and Muangkaew, W and Thiangtrongjit, T and Sansurin, N and Fongsodsri, K and Ampawong, S}, title = {Cytoskeletal Alteration Is an Early Cellular Response in Pulmonary Epithelium Infected with Aspergillus fumigatus Rather than Scedosporium apiospermum.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {216-235}, pmid = {33890146}, issn = {1432-184X}, support = {CU_FRB640001_01_33_1//TSRI Fund/ ; }, mesh = {A549 Cells ; Animals ; *Aspergillus fumigatus ; Cytoskeleton/*microbiology ; Epithelium/*microbiology ; Humans ; Lung ; Mice ; *Mycoses ; *Scedosporium ; }, abstract = {Invasive aspergillosis and scedosporiosis are life-threatening fungal infections with similar clinical manifestations in immunocompromised patients. Contrarily, Scedosporium apiospermum is susceptible to some azole derivative but often resistant to amphotericin B. Histopathological examination alone cannot diagnose these two fungal species. Pathogenesis studies could contribute to explore candidate protein markers for new diagnosis and treatment methods leading to a decrease in mortality. In the present study, proteomics was conducted to identify significantly altered proteins in A549 cells infected with or without Aspergillus fumigatus and S. apiospermum as measured at initial invasion. Protein validation was performed with immunogold labelling alongside immunohistochemical techniques in infected A549 cells and lungs from murine models. Further, cytokine production was measured, using the Bio-Plex-Multiplex immunoassay. The cytoskeletal proteins HSPA9, PA2G4, VAT1, PSMA2, PEX1, PTGES3, KRT1, KRT9, CLIP1 and CLEC20A were mainly changed during A. fumigatus infection, while the immunologically activated proteins WNT7A, GAPDH and ANXA2 were principally altered during S. apiospermum infection. These proteins are involved in fungal internalisation and structural destruction leading to pulmonary disorders. Interleukin (IL)-21, IL-1α, IL-22, IL-2, IL-8, IL-12, IL-17A, interferon-γ and tumour necrosis factor-α were upregulated in both aspergillosis and scedosporiosis, although more predominately in the latter, in accordance with chitin synthase-1 and matrix metalloproteinase levels. Our results demonstrated that during invasion, A. fumigatus primarily altered host cellular integrity, whereas S. apiospermum chiefly induced and extensively modulated host immune responses.}, }
@article {pmid33890145, year = {2022}, author = {Fisol, AFBC and Saidi, NB and Al-Obaidi, JR and Lamasudin, DU and Atan, S and Razali, N and Sajari, R and Rahmad, N and Hussin, SNIS and Mr, NH}, title = {Differential Analysis of Mycelial Proteins and Metabolites From Rigidoporus Microporus During In Vitro Interaction With Hevea Brasiliensis.}, journal = {Microbial ecology}, volume = {83}, number = {2}, pages = {363-379}, pmid = {33890145}, issn = {1432-184X}, support = {S16IPDM0533//Malaysian Rubber Board/ ; }, mesh = {Gene Expression Regulation, Plant ; *Hevea/chemistry/microbiology ; Plant Diseases/microbiology ; *Polyporales ; Tandem Mass Spectrometry ; }, abstract = {Rigidoporus microporus is the fungus accountable for the white root rot disease that is detrimental to the rubber tree, Hevea brasiliensis. The pathogenicity mechanism of R. microporus and the identity of the fungal proteins and metabolites involved during the infection process remain unclear. In this study, the protein and metabolite profiles of two R. microporus isolates, Segamat (SEG) and Ayer Molek (AM), were investigated during an in vitro interaction with H. brasiliensis. The isolates were used to inoculate H. brasiliensis clone RRIM 2025, and mycelia adhering to the roots of the plant were collected for analysis. Transmission electron microscope (TEM) images acquired confirms the hyphae attachment and colonization of the mycelia on the root of the H. brasiliensis clones after 4 days of inoculation. The protein samples were subjected to 2-DE analysis and analyzed using MALDI-ToF MS/MS, while the metabolites were extracted using methanol and analyzed using LC/MS-QTOF. Based on the differential analyses, upregulation of proteins that are essential for fungal evolution such as malate dehydrogenase, fructose 1,6-biphosphate aldolase, and glyceraldehyde-3-phosphate dehydrogenase hints an indirect role in fungal pathogenicity, while metabolomic analysis suggests an increase in acidic compounds which may lead to increased cell wall degrading enzyme activity. Bioinformatics analyses revealed that the carbohydrate and amino acid metabolisms were prominently affected in response to the fungal pathogenicity. In addition to that, other pathways that were significantly affected include "Protein Ubiquitination Pathway," Unfolded Protein Response," "HIFα Signaling," and "Sirtuin Signaling Pathway." The identification of responsive proteins and metabolites from this study promotes a better understanding of mechanisms underlying R. microporus pathogenesis and provides a list of potential biological markers for early recognition of the white root rot disease.}, }
@article {pmid33886659, year = {2021}, author = {Han, XY}, title = {Effects of climate changes and road exposure on the rapidly rising legionellosis incidence rates in the United States.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0250364}, pmid = {33886659}, issn = {1932-6203}, mesh = {Adolescent ; Adult ; Aged ; Centers for Disease Control and Prevention, U.S. ; Child ; Child, Preschool ; Female ; *Global Warming ; *Hot Temperature ; Humans ; Incidence ; Infant ; Infant, Newborn ; Legionella pneumophila/*pathogenicity ; Legionellosis/*epidemiology/microbiology ; Male ; Middle Aged ; Rural Population ; *Sunlight ; *Ultraviolet Rays ; United States/epidemiology ; Urban Population ; Young Adult ; }, abstract = {Legionellosis is an infection acquired through inhalation of aerosols that are contaminated with environmental bacteria Legionella spp. The bacteria require warm temperature for proliferation in bodies of water and moist soil. The legionellosis incidence in the United States has been rising rapidly in the past two decades without a clear explanation. In the meantime, the US has recorded consecutive years of above-norm temperature since 1997 and precipitation surplus since 2008. The present study analyzed the legionellosis incidence in the US during the 20-year period of 1999 to 2018 and correlated with concurrent temperature, precipitation, solar ultraviolet B (UVB) radiation, and vehicle mileage data. The age-adjusted legionellosis incidence rates rose exponentially from 0.40/100,000 in 1999 (with 1108 cases) to 2.69/100,000 in 2018 (with 9933 cases) at a calculated annual increase of 110%. In regression analyses, the rise correlated with an increase in vehicle miles driven and with temperature and precipitation levels that have been above the 1901-2000 mean since 1997 and 2008, respectively, suggesting more road exposure to traffic-generated aerosols and promotive effects of anomalous climate. Remarkably, the regressions with cumulative anomalies of temperature and precipitation were robust (R2 ≥ 0.9145, P ≤ 4.7E-11), implying possible changes to microbial ecology in the terrestrial and aquatic environments. An interactive synergy between annual precipitation and vehicle miles was also found in multiple regressions. Meanwhile, the bactericidal UVB radiation has been decreasing, which also contributed to the rising incidence in an inverse correlation. The 2018 legionellosis incidence peak corresponded to cumulative effects of the climate anomalies, vast vehicle miles (3,240 billion miles, 15904 km per capita), record high precipitation (880.1 mm), near record low UVB radiation (7488 kJ/m2), and continued above-norm temperature (11.96°C). These effects were examined and demonstrated in California, Florida, New Jersey, Ohio, and Wisconsin, states that represent diverse incidence rates and climates. The incidence and above-norm temperature both rose most in cold Wisconsin. These results suggest that warming temperature and precipitation surplus have likely elevated the density of Legionella bacteria in the environment, and together with road exposure explain the rapidly rising incidence of legionellosis in the United States. These trends are expected to continue, warranting further research and efforts to prevent infection.}, }
@article {pmid33886638, year = {2021}, author = {Colda, A and Bossaert, S and Verreth, C and Vanhoutte, B and Honnay, O and Keulemans, W and Lievens, B}, title = {Inoculation of pear flowers with Metschnikowia reukaufii and Acinetobacter nectaris enhances attraction of honeybees and hoverflies, but does not increase fruit and seed set.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0250203}, pmid = {33886638}, issn = {1932-6203}, mesh = {Animals ; Bees ; Flowers/*microbiology ; Fruit ; *Plant Nectar ; *Pollination ; Pyrus/*microbiology ; }, abstract = {Currently, one of the most important challenges is to provide sufficient and affordable food and energy for a fast-growing world population, alongside preserving natural habitats and maintaining biodiversity. About 35% of the global food production depends on animals for pollination. In recent years, an alarming worldwide decline in pollinators has been reported, putting our food production under additional pressure. Therefore, there is an urgent need to find sustainable ways to ensure this crucial ecosystem service. Recent studies have shown that floral nectar is generally colonized by microorganisms, specifically yeasts and bacteria, which may alter nectar chemistry and enhance attraction of pollinators. In this study, we investigated changes in pollinator foraging behavior and pollination success in European pear (Pyrus communis L.) cultivars 'Regal Red' and 'Sweet Sensation' (red sports of 'Doyenné de Comice') after flower inoculation with the typical nectar-inhabiting microorganisms Metschnikowia reukaufii and Acinetobacter nectaris, and a combination of both. Pollination success was monitored by measuring the number of flower visits, fruit set and seed set in two consecutive years, 2019 and 2020. Results revealed that application of a mixture of M. reukaufii and A. nectaris resulted in significantly higher visitation rates of honeybees and hoverflies. By contrast, no effects on flower visits were found when yeasts and bacteria were applied separately. Fruit set and seed set were not significantly affected by any of the inoculation treatments. The only factors affecting fruit set were initial number of flower clusters on the trees and the year. The absence of treatment effects can most likely be attributed to the fact that pollination was not a limiting factor for fruit set in our experiments. Altogether, our results show that inoculation of flowers with nectar microbes can modify pollinator foraging patterns, but did not lead to increased pollination success under the conditions tested.}, }
@article {pmid33886557, year = {2021}, author = {Hewson, I and Sewell, MA}, title = {Surveillance of densoviruses and mesomycetozoans inhabiting grossly normal tissues of three Aotearoa New Zealand asteroid species.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0241026}, pmid = {33886557}, issn = {1932-6203}, mesh = {Animals ; Densovirus/genetics/*isolation &amp; purification ; Mesomycetozoea/genetics/*isolation &amp; purification ; Metagenome ; Metagenomics ; Microbiota ; New Zealand ; Starfish/*parasitology/*virology ; }, abstract = {Asteroid wasting events and mass mortality have occurred for over a century. We currently lack a fundamental understanding of the microbial ecology of asteroid disease, with disease investigations hindered by sparse information about the microorganisms associated with grossly normal specimens. We surveilled viruses and protists associated with grossly normal specimens of three asteroid species (Patiriella regularis, Stichaster australis, Coscinasterias muricata) on the North Island / Te Ika-a-Māui, Aotearoa New Zealand, using metagenomes prepared from virus and ribosome-sized material. We discovered several densovirus-like genome fragments in our RNA and DNA metagenomic libraries. Subsequent survey of their prevalence within populations by quantitative PCR (qPCR) demonstrated their occurrence in only a few (13%) specimens (n = 36). Survey of large and small subunit rRNAs in metagenomes revealed the presence of a mesomycete (most closely matching Ichthyosporea sp.). Survey of large subunit prevalence and load by qPCR revealed that it is widely detectable (80%) and present predominately in body wall tissues across all 3 species of asteroid. Our results raise interesting questions about the roles of these microbiome constituents in host ecology and pathogenesis under changing ocean conditions.}, }
@article {pmid33885917, year = {2022}, author = {Wallenborn, JT and Gunier, RB and Pappas, DJ and Chevrier, J and Eskenazi, B}, title = {Breastmilk, Stool, and Meconium: Bacterial Communities in South Africa.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {246-251}, pmid = {33885917}, issn = {1432-184X}, support = {R01 ES020360/ES/NIEHS NIH HHS/United States ; U24 ES028529/ES/NIEHS NIH HHS/United States ; 1R01ES020360-01//Foundation for the National Institutes of Health/ ; }, mesh = {Feces/microbiology ; Humans ; Infant ; Infant, Newborn ; *Meconium/microbiology ; *Milk, Human/microbiology ; RNA, Ribosomal, 16S/genetics ; South Africa ; }, abstract = {Human milk optimizes gut microbial richness and diversity, and is critical for proper immune development. Research has shown differing microbial composition based on geographic location, providing evidence that diverse biospecimen data is needed when studying human bacterial communities. Yet, limited research describes human milk and infant gut microbial communities in Africa. Our study uses breastmilk, stool, and meconium samples from a South African birth cohort to describe the microbial diversity, identify distinct taxonomic units, and determine correlations between bacterial abundance in breastmilk and stool samples. Mother-infant dyads (N = 20) were identified from a longitudinal birth cohort in the Vhembe district of Limpopo Province, South Africa. Breastmilk, meconium, and stool samples were analyzed using 16S ribosomal RNA sequencing of the V4-V5 gene region using the MiSeq platform for identification and relative quantification of bacterial taxa. A non-metric multidimensional scaling using Bray-Curtis distances of sample Z-scores showed that meconium, stool, and breastmilk microbial communities are distinct with varying genus. Breastmilk was mostly comprised of Streptococcus, Staphylococcus, Veillonella, and Corynebacterium. Stool samples showed the highest levels of Bifidobacterium, Faecalibacterium, Bacteroides, and Streptococcus. Alpha diversity measures found that stool samples have the highest Shannon index score compared to breastmilk and meconium. The abundance of Bifidobacterium (r = 0.57), Blautia (r = 0.59), and Haemophilus (r = 0.69) was correlated (p < 0.1) between breastmilk and stool samples. Despite the importance of breastmilk in seeding the infant gut microbiome, we found evidence of distinct bacterial communities between breastmilk and stool samples from South African mother-infant dyads.}, }
@article {pmid33880762, year = {2021}, author = {Zeng, T and Yu, X and Chen, Z}, title = {Applying artificial intelligence in the microbiome for gastrointestinal diseases: A review.}, journal = {Journal of gastroenterology and hepatology}, volume = {36}, number = {4}, pages = {832-840}, doi = {10.1111/jgh.15503}, pmid = {33880762}, issn = {1440-1746}, support = {2017SHZDZX01//Shanghai Municipal Science and Technology Major Project/ ; 61803360//National Natural Science Foundation of China/ ; 11871456//National Natural Science Foundation of China/ ; XDB38050200//Strategic Priority Research Program of Chinese Academy of Sciences/ ; }, mesh = {Artificial Intelligence/*trends ; *Big Data ; Datasets as Topic ; Gastrointestinal Diseases/*etiology/*microbiology ; *Gastrointestinal Microbiome ; Information Storage and Retrieval/*methods ; }, abstract = {For a long time, gut bacteria have been recognized for their important roles in the occurrence and progression of gastrointestinal diseases like colorectal cancer, and the ever-increasing amounts of microbiome data combined with other high-quality clinical and imaging datasets are leading the study of gastrointestinal diseases into an era of biomedical big data. The "omics" technologies used for microbiome analysis continuously evolve, and the machine learning or artificial intelligence technologies are key to extract the relevant information from microbiome data. This review intends to provide a focused summary of recent research and applications of microbiome big data and to discuss the use of artificial intelligence to combat gastrointestinal diseases.}, }
@article {pmid33880565, year = {2021}, author = {Golob, JL and Rao, K}, title = {Signal Versus Noise: How to Analyze the Microbiome and Make Progress on Antimicrobial Resistance.}, journal = {The Journal of infectious diseases}, volume = {223}, number = {12 Suppl 2}, pages = {S214-S221}, pmid = {33880565}, issn = {1537-6613}, support = {R01 HS027431/HS/AHRQ HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/adverse effects ; Clostridioides difficile/growth &amp; development/pathogenicity ; Clostridium Infections/etiology/microbiology ; Disease Models, Animal ; Drug Resistance, Microbial/drug effects/*genetics ; Gastrointestinal Microbiome/drug effects/*genetics/immunology ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions ; Humans ; }, abstract = {Antimicrobial resistance has become a worldwide medical challenge [1], so impactful that vancomycin-resistant Enterococcus (VRE) and methicillin-resistant Staphylococcus aureus (MRSA) have entered the common vernacular. We have attempted to reduce the selective pressure through antimicrobial stewardship, curtail the spread by identifying and isolating carriers and individuals with symptomatic infection, and treat antibiotic-resistant organisms (AROs) by developing novel antimicrobials. Despite these extraordinary measures, the challenge of AROs continues to grow. The gut microbiome, the ecosystem of microbes (ie, the microbiota) and metabolites present upon and within all humans, is an emerging target for both the risk for colonization and defense against infection with AROs. Here, informed from experiences and successes with understanding the role of the microbiome in mediating risk of Clostridioides difficile infection (CDI), we (1) review our understanding of the risk from ARO acquisition; (2) review our current understanding of the gut microbiome's ability to resist colonization with AROs; (3) describe how experimental model systems can test these initial, global insights to arrive at more granular, mechanistic ones; and (4) suggest a path forward to make further progress in the field.}, }
@article {pmid33879498, year = {2021}, author = {Taylor, M and Vega, NM}, title = {Host Immunity Alters Community Ecology and Stability of the Microbiome in a Caenorhabditis elegans Model.}, journal = {mSystems}, volume = {6}, number = {2}, pages = {}, pmid = {33879498}, issn = {2379-5077}, abstract = {A growing body of data suggests that the microbiome of a species can vary considerably from individual to individual, but the reasons for this variation-and the consequences for the ecology of these communities-remain only partially explained. In mammals, the emerging picture is that the metabolic state and immune system status of the host affect the composition of the microbiome, but quantitative ecological microbiome studies are challenging to perform in higher organisms. Here, we show that these phenomena can be quantitatively analyzed in the tractable nematode host Caenorhabditis elegans Mutants in innate immunity, in particular the DAF-2/insulin growth factor (IGF) pathway, are shown to contain a microbiome that differs from that of wild-type nematodes. We analyzed the underlying basis of these differences from the perspective of community ecology by comparing experimental observations to the predictions of a neutral sampling model and concluded that fundamental differences in microbiome ecology underlie the observed differences in microbiome composition. We tested this hypothesis by introducing a minor perturbation into the colonization conditions, allowing us to assess stability of communities in different host strains. Our results show that altering host immunity changes the importance of interspecies interactions within the microbiome, resulting in differences in community composition and stability that emerge from these differences in host-microbe ecology.IMPORTANCE Here, we used a Caenorhabditis elegans microbiome model to demonstrate how genetic differences in innate immunity alter microbiome composition, diversity, and stability by changing the ecological processes that shape these communities. These results provide insight into the role of host genetics in controlling the ecology of the host-associated microbiota, resulting in differences in community composition, successional trajectories, and response to perturbation.}, }
@article {pmid33876556, year = {2021}, author = {Mihajlovic, J and Leutner, M and Hausmann, B and Kohl, G and Schwarz, J and Röver, H and Stimakovits, N and Wolf, P and Maruszczak, K and Bastian, M and Kautzky-Willer, A and Berry, D}, title = {Combined hormonal contraceptives are associated with minor changes in composition and diversity in gut microbiota of healthy women.}, journal = {Environmental microbiology}, volume = {23}, number = {6}, pages = {3037-3047}, doi = {10.1111/1462-2920.15517}, pmid = {33876556}, issn = {1462-2920}, mesh = {Animals ; Contraceptive Agents ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Menstrual Cycle ; *Microbiota ; }, abstract = {Recent human and animal studies have found associations between gut microbiota composition and serum levels of sex hormones, indicating that they could be an important factor in shaping the microbiota. However, little is known about the effect of regular hormonal fluctuations over the menstrual cycle or CHC-related changes of hormone levels on gut microbiota structure, diversity and dynamics. The aim of this study was to investigate the effect of CHCs on human gut microbiota composition. The effect of CHC pill intake on gut microbiota composition was studied in a group of seven healthy pre-menopausal women using the CHC pill, compared to the control group of nine age-matched healthy women that have not used hormonal contraceptives in the 6 months prior to the start of the study. By analysing the gut microbiota composition in both groups during one menstrual cycle, we found that CHC usage is associated with a minor decrease in gut microbiota diversity and differences in the abundance of several bacterial taxa. These results call for further investigation of the mechanisms underlying hormonal and hormonal contraceptive-related changes of the gut microbiota and the potential implications of these changes for women's health.}, }
@article {pmid33870123, year = {2021}, author = {Ciobanu, D and Clum, A and Ahrendt, S and Andreopoulos, WB and Salamov, A and Chan, S and Quandt, CA and Foster, B and Meier-Kolthoff, JP and Tang, YT and Schwientek, P and Benny, GL and Smith, ME and Bauer, D and Deshpande, S and Barry, K and Copeland, A and Singer, SW and Woyke, T and Grigoriev, IV and James, TY and Cheng, JF}, title = {A single-cell genomics pipeline for environmental microbial eukaryotes.}, journal = {iScience}, volume = {24}, number = {4}, pages = {102290}, pmid = {33870123}, issn = {2589-0042}, abstract = {Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes.}, }
@article {pmid33868801, year = {2021}, author = {Vikram, S and Arneodo, JD and Calcagno, J and Ortiz, M and Mon, ML and Etcheverry, C and Cowan, DA and Talia, P}, title = {Diversity structure of the microbial communities in the guts of four neotropical termite species.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e10959}, pmid = {33868801}, issn = {2167-8359}, abstract = {The termite gut microbiome is dominated by lignocellulose degrading microorganisms. This study describes the intestinal microbiota of four Argentinian higher termite species with different feeding habits: Microcerotermes strunckii (hardwood), Nasutitermes corniger (softwood), Termes riograndensis (soil organic matter/grass) and Cornitermes cumulans (grass) by deep sequencing of amplified 16S rRNA and ITS genes. In addition, we have performed a taxonomic and gut community structure comparison incorporating into the analysis the previously reported microbiomes of additional termite species with varied diets. The bacterial phylum Spirochaetes was dominant in the guts of M. strunckii, N. corniger and C. cumulans, whereas Firmicutes predominated in the T. riograndensis gut microbiome. A single bacterial genus, Treponema (Spirochaetes), was dominant in all termite species, except for T. riograndensis. Both in our own sequenced samples and in the broader comparison, prokaryotic α-diversity was higher in the soil/grass feeders than in the wood feeders. Meanwhile, the β-diversity of prokaryotes and fungi was highly dissimilar among strict wood-feeders, whereas that of soil- and grass-feeders grouped more closely. Ascomycota and Basidiomycota were the only fungal phyla that could be identified in all gut samples, because of the lack of reference sequences in public databases. In summary, higher microbial diversity was recorded in termites with more versatile feeding sources, providing further evidence that diet, along with other factors (e.g., host taxonomy), influences the microbial community assembly in the termite gut.}, }
@article {pmid33866059, year = {2021}, author = {Hu, R and Zhao, H and Xu, X and Wang, Z and Yu, K and Shu, L and Yan, Q and Wu, B and Mo, C and He, Z and Wang, C}, title = {Bacteria-driven phthalic acid ester biodegradation: Current status and emerging opportunities.}, journal = {Environment international}, volume = {154}, number = {}, pages = {106560}, doi = {10.1016/j.envint.2021.106560}, pmid = {33866059}, issn = {1873-6750}, mesh = {Bacteria ; Biodegradation, Environmental ; *Esters ; Humans ; *Phthalic Acids ; Prospective Studies ; }, abstract = {The extensive use of phthalic acid esters (PAEs) has led to their widespread distribution across various environments. As PAEs pose significant threats to human health, it is urgent to develop efficient strategies to eliminate them from environments. Bacteria-driven PAE biodegradation has been considered as an inexpensive yet effective strategy to restore the contaminated environments. Despite great advances in bacterial culturing and sequencing, the inherent complexity of indigenous microbial community hinders us to mechanistically understand in situ PAE biodegradation and efficiently harness the degrading power of bacteria. The synthetic microbial ecology provides us a simple and controllable model system to address this problem. In this review, we focus on the current progress of PAE biodegradation mediated by bacterial isolates and indigenous bacterial communities, and discuss the prospective of synthetic PAE-degrading bacterial communities in PAE biodegradation research. It is anticipated that the theories and approaches of synthetic microbial ecology will revolutionize the study of bacteria-driven PAE biodegradation and provide novel insights for developing effective bioremediation solutions.}, }
@article {pmid33864491, year = {2022}, author = {Rojas-Gätjens, D and Fuentes-Schweizer, P and Rojas-Jiménez, K and Pérez-Pantoja, D and Avendaño, R and Alpízar, R and Coronado-Ruíz, C and Chavarría, M}, title = {Methylotrophs and Hydrocarbon-Degrading Bacteria Are Key Players in the Microbial Community of an Abandoned Century-Old Oil Exploration Well.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {83-99}, pmid = {33864491}, issn = {1432-184X}, support = {809-B8-518//Vicerrector&#xed;a de Investigaci&#xf3;n, Universidad de Costa Rica/ ; ANID PIA/Anillo ACT172128, ANID PIA/BASAL FB0002 and FONDECYT 1201741.//Chilean government/ ; }, mesh = {Bacteria ; Biodegradation, Environmental ; Hydrocarbons/metabolism ; *Microbiota ; Oil and Gas Fields ; *Petroleum ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {In this work, we studied the microbial community and the physicochemical conditions prevailing in an exploratory oil well, abandoned a century ago, located in the Cahuita National Park (Costa Rica). According to our analysis, Cahuita well is characterized by a continuous efflux of methane and the presence of a mixture of hydrocarbons including phenanthrene/anthracene, fluoranthene, pyrene, dibenzothiophene, tricyclic terpanes, pyrene, sesquiterpenes, sterane, and n-alkanes. Based on the analysis of 16S rRNA gene amplicons, we detected a significant abundance of methylotrophic bacteria such as Methylobacillus (6.3-26.0% of total reads) and Methylococcus (4.1-30.6%) and the presence of common genera associated with hydrocarbon degradation, such as Comamonas (0.8-4.6%), Hydrogenophaga (1.5-3.3%) Rhodobacter (1.0-4.9%), and Flavobacterium (1.1-6.5%). The importance of C1 metabolism in this niche was confirmed by amplifying the methane monooxygenase (MMO)-encoding gene (pmo) from environmental DNA and the isolation of two strains closely related to Methylorubrum rhodesianum and Paracoccus communis with the ability to growth using methanol and formate as sole carbon source respectively. In addition, we were able to isolated 20 bacterial strains from the genera Pseudomonas, Acinetobacter, and Microbacterium which showed the capability to grow using the hydrocarbons detected in the oil well as sole carbon source. This work describes the physicochemical properties and microbiota of an environment exposed to hydrocarbons for 100 years, and it not only represents a contribution to the understanding of microbial communities in environments with permanently high concentrations of these compounds but also has biotechnological implications for bioremediation of petroleum-polluted sites.}, }
@article {pmid33864130, year = {2022}, author = {Álvarez-Pérez, S and Tsuji, K and Donald, M and Van Assche, A and Vannette, RL and Herrera, CM and Jacquemyn, H and Fukami, T and Lievens, B}, title = {Correction to: Nitrogen Assimilation Varies Among Clades of Nectar- and Insect-Associated Acinetobacters.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {256}, doi = {10.1007/s00248-021-01755-2}, pmid = {33864130}, issn = {1432-184X}, }
@article {pmid33864129, year = {2021}, author = {Pereira, A and Figueiredo, A and Ferreira, V}, title = {Invasive Acacia Tree Species Affect Instream Litter Decomposition Through Changes in Water Nitrogen Concentration and Litter Characteristics.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {257-273}, pmid = {33864129}, issn = {1432-184X}, support = {SFRH/BD/118069/2016//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; IF/00129/2014//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDP/04292/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {*Acacia ; Ecosystem ; Introduced Species ; Nitrogen ; Plant Leaves ; Rivers ; *Trees ; Water ; }, abstract = {Non-native nitrogen-fixing Acacia species have been invading riparian ecosystems worldwide, potentially threatening stream communities that strongly depend on allochthonous litter. We examined the effects of the invasion of native deciduous temperate forests by Acacia species on litter decomposition and associated fungal decomposers in streams. Litter of native (Alnus glutinosa and Quercus robur) and invasive (Acacia melanoxylon) species were enclosed in fine-mesh bags and immersed in three native and three invaded streams, for 14-98 days. Litter decomposition rates, fungal biomass, and aquatic hyphomycete sporulation rates were higher in invaded than in native streams, likely due to the higher water nitrogen concentration found in invaded streams. Alnus glutinosa litter had higher aquatic hyphomycete sporulation rates and species richness, and higher decomposition rates, probably because they were soft and nitrogen rich. Quercus robur litter also had high aquatic hyphomycete sporulation rates but lower decomposition rates than Al. glutinosa, probably due to high polyphenol concentration and carbon:nitrogen ratio. Acacia melanoxylon litter had lower aquatic hyphomycete sporulation rates and species richness, and lower decomposition rates, most likely because it was very tough. Thus, litter decomposition rates varied in the order: Al. glutinosa > Q. robur > Ac. melanoxylon. The aquatic hyphomycete community structure strongly differed between native and invaded streams, and among litter species, suggesting that microbes were sensitive to water nitrogen concentration and litter characteristics. Overall, increases in water nitrogen concentration and alterations in litter characteristics promoted by the invasion of native riparian forests by Acacia species may affect the activity and community structure of microbial decomposers, and instream litter decomposition, thus altering the functioning of stream ecosystems.}, }
@article {pmid33863892, year = {2021}, author = {Luhung, I and Uchida, A and Lim, SBY and Gaultier, NE and Kee, C and Lau, KJX and Gusareva, ES and Heinle, CE and Wong, A and Premkrishnan, BNV and Purbojati, RW and Acerbi, E and Kim, HL and Junqueira, ACM and Longford, S and Lohar, SR and Yap, ZH and Panicker, D and Koh, Y and Kushwaha, KK and Ang, PN and Putra, A and Drautz-Moses, DI and Schuster, SC}, title = {Experimental parameters defining ultra-low biomass bioaerosol analysis.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {37}, pmid = {33863892}, issn = {2055-5008}, mesh = {Air Microbiology ; *Biomass ; *Ecosystem ; *Environmental Microbiology ; Environmental Monitoring ; Metagenome ; Metagenomics/methods ; *Microbiota ; Soil Microbiology ; Water Microbiology ; }, abstract = {Investigation of the microbial ecology of terrestrial, aquatic and atmospheric ecosystems requires specific sampling and analytical technologies, owing to vastly different biomass densities typically encountered. In particular, the ultra-low biomass nature of air presents an inherent analytical challenge that is confounded by temporal fluctuations in community structure. Our ultra-low biomass pipeline advances the field of bioaerosol research by significantly reducing sampling times from days/weeks/months to minutes/hours, while maintaining the ability to perform species-level identification through direct metagenomic sequencing. The study further addresses all experimental factors contributing to analysis outcome, such as amassment, storage and extraction, as well as factors that impact on nucleic acid analysis. Quantity and quality of nucleic acid extracts from each optimisation step are evaluated using fluorometry, qPCR and sequencing. Both metagenomics and marker gene amplification-based (16S and ITS) sequencing are assessed with regard to their taxonomic resolution and inter-comparability. The pipeline is robust across a wide range of climatic settings, ranging from arctic to desert to tropical environments. Ultimately, the pipeline can be adapted to environmental settings, such as dust and surfaces, which also require ultra-low biomass analytics.}, }
@article {pmid33860847, year = {2022}, author = {Caragata, EP and Otero, LM and Tikhe, CV and Barrera, R and Dimopoulos, G}, title = {Microbial Diversity of Adult Aedes aegypti and Water Collected from Different Mosquito Aquatic Habitats in Puerto Rico.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {182-201}, pmid = {33860847}, issn = {1432-184X}, support = {CC999999/ImCDC/Intramural CDC HHS/United States ; R21AI136456/NH/NIH HHS/United States ; BAA 2017-N-18041/CC/CDC HHS/United States ; }, mesh = {*Aedes ; Animals ; Humans ; Larva ; *Microbiota ; Mosquito Vectors ; Puerto Rico ; Water ; }, abstract = {Mosquitoes, the major vectors of viruses like dengue, are naturally host to diverse microorganisms, which play an important role in their development, fecundity, immunity, and vector competence. The composition of their microbiota is strongly influenced by the environment, particularly their aquatic larval habitat. In this study, we used 2×300 bp 16s Illumina sequencing to compare the microbial profiles of emerging adult Aedes aegypti mosquitoes and the water collected from common types of aquatic habitat containers in Puerto Rico, which has endemic dengue transmission. We sequenced 141 mosquito and 46 water samples collected from plastic containers, septic tanks, discarded tires, underground trash cans, tree holes, or water meters. We identified 9 bacterial genera that were highly prevalent in the mosquito microbiome, and 77 for the microbiome of the aquatic habitat. The most abundant mosquito-associated bacterial OTUs were from the families Burkholderiaceae, Pseudomonadaceae, Comamonadaceae, and Xanthomonadaceae. Microbial profiles varied greatly between mosquitoes, and there were few major differences explained by container type; however, the microbiome of mosquitoes from plastic containers was more diverse and contained more unique taxa than the other groups. Container water was significantly more diverse than mosquitoes, and our data suggest that mosquitoes filter out many bacteria, with Alphaproteobacteria in particular being far more abundant in water. These findings provide novel insight into the microbiome of mosquitoes in the region and provide a platform to improve our understanding of the fundamental mosquito-microbe interactions.}, }
@article {pmid33859339, year = {2021}, author = {Parras-Moltó, M and Aguirre de Cárcer, D}, title = {Assessment of phylo-functional coherence along the bacterial phylogeny and taxonomy.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {8299}, pmid = {33859339}, issn = {2045-2322}, mesh = {Bacteria/*classification/*genetics ; Genes, Bacterial/*genetics ; *Microbiota ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In this report we use available curated phylogenies, taxonomy, and genome annotations to assess the phylogenetic and gene content similarity associated with each different taxon and taxonomic rank. Subsequently, we employ the same data to assess the frontiers of functional coherence along the bacterial phylogeny. Our results show that within-group phylogenetic and gene content similarity of taxa in the same rank are not homogenous, and that these values show extensive overlap between ranks. Functional coherence along the 16S rRNA gene-based phylogeny was limited to 44 particular nodes presenting large variations in phylogenetic depth. For instance, the deep subtree affiliated to class Actinobacteria presented functional coherence, while the shallower family Enterobacteriaceae-affiliated subtree did not. On the other hand, functional coherence along the genome-based phylogeny delimited deep subtrees affiliated to phyla Actinobacteriota, Deinococcota, Chloroflexota, Firmicutes, and a subtree containing the rest of the bacterial phyla. The results presented here can be used to guide the exploration of results in many microbial ecology and evolution research scenarios. Moreover, we provide dedicated scripts and files that can be used to continue the exploration of functional coherence along the bacterial phylogeny employing different parameters or input data (https://git.io/Jec5U).}, }
@article {pmid33858359, year = {2021}, author = {Xue, H and Kurokawa, M and Ying, BW}, title = {Correlation between the spatial distribution and colony size was common for monogenetic bacteria in laboratory conditions.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {114}, pmid = {33858359}, issn = {1471-2180}, mesh = {Demography ; Escherichia coli/*growth &amp; development ; Laboratories ; }, abstract = {BACKGROUND: Geographically separated population growth of microbes is a common phenomenon in microbial ecology. Colonies are representative of the morphological characteristics of this structured population growth. Pattern formation by single colonies has been intensively studied, whereas the spatial distribution of colonies is poorly investigated.<br><br>RESULTS: The present study describes a first trial to address the questions of whether and how the spatial distribution of colonies determines the final colony size using the model microorganism Escherichia coli, colonies of which can be grown under well-controlled laboratory conditions. A computational tool for image processing was developed to evaluate colony density, colony size and size variation, and the Voronoi diagram was applied for spatial analysis of colonies with identical space resources. A positive correlation between the final colony size and the Voronoi area was commonly identified, independent of genomic and nutritional differences, which disturbed the colony size and size variation.<br><br>CONCLUSIONS: This novel finding of a universal correlation between the spatial distribution and colony size not only indicated the fair distribution of spatial resources for monogenetic colonies growing with identical space resources but also indicated that the initial localization of the microbial colonies decided by chance determined the fate of the subsequent population growth. This study provides a valuable example for quantitative analysis of the complex microbial ecosystems by means of experimental ecology.}, }
@article {pmid33857526, year = {2021}, author = {Diego, D and Hannisdal, B and Dahle, H}, title = {On how the power supply shapes microbial survival.}, journal = {Mathematical biosciences}, volume = {338}, number = {}, pages = {108615}, doi = {10.1016/j.mbs.2021.108615}, pmid = {33857526}, issn = {1879-3134}, mesh = {Electric Power Supplies ; *Microbial Viability ; *Microbiota/physiology ; *Models, Biological ; Population Dynamics ; }, abstract = {Understanding how environmental factors affect microbial survival is an important open problem in microbial ecology. Patterns of microbial community structure have been characterized across a wide range of different environmental settings, but the mechanisms generating these patterns remain poorly understood. Here, we use mathematical modelling to investigate fundamental connections between chemical power supply to a system and patterns of microbial survival. We reveal a complex set of interdependences between power supply and distributions of survival probability across microbial habitats, in a case without interspecific resource competition. We also find that different properties determining power supply, such as substrate fluxes and Gibbs energies of reactions, affect microbial survival in fundamentally different ways. Moreover, we show how simple connections between power supply and growth can give rise to complex patterns of microbial survival across physicochemical gradients, such as pH gradients. Our findings show the importance of taking energy fluxes into account in order to reveal fundamental connections between microbial survival and environmental conditions, and to obtain a better understanding of microbial population dynamics in natural environments.}, }
@article {pmid33854112, year = {2021}, author = {Mahjoubi, M and Aliyu, H and Neifar, M and Cappello, S and Chouchane, H and Souissi, Y and Masmoudi, AS and Cowan, DA and Cherif, A}, title = {Genomic characterization of a polyvalent hydrocarbonoclastic bacterium Pseudomonas sp. strain BUN14.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {8124}, pmid = {33854112}, issn = {2045-2322}, mesh = {Bacterial Proteins/genetics/metabolism ; Chromatography, Gas ; Dioxins/chemistry/metabolism ; *Genome, Bacterial ; Geologic Sediments/microbiology ; Hydrocarbons/chemistry/metabolism ; Naphthalenes/metabolism ; Phylogeny ; Pseudomonas/classification/*genetics/isolation &amp; purification/metabolism ; Surface-Active Agents/metabolism ; Tunisia ; }, abstract = {Bioremediation offers a viable alternative for the reduction of contaminants from the environment, particularly petroleum and its recalcitrant derivatives. In this study, the ability of a strain of Pseudomonas BUN14 to degrade crude oil, pristane and dioxin compounds, and to produce biosurfactants, was investigated. BUN14 is a halotolerant strain isolated from polluted sediment recovered from the refinery harbor on the Bizerte coast, north Tunisia and capable of producing surfactants. The strain BUN14 was assembled into 22 contigs of 4,898,053 bp with a mean GC content of 62.4%. Whole genome phylogeny and comparative genome analyses showed that strain BUN14 could be affiliated with two validly described Pseudomonas Type Strains, P. kunmingensis DSM 25974[T] and P. chloritidismutans AW-1[T]. The current study, however, revealed that the two Type Strains are probably conspecific and, given the priority of the latter, we proposed that P. kunmingensis DSM 25974 is a heteronym of P. chloritidismutans AW-1[T]. Using GC-FID analysis, we determined that BUN14 was able to use a range of hydrocarbons (crude oil, pristane, dibenzofuran, dibenzothiophene, naphthalene) as a sole carbon source. Genome analysis of BUN14 revealed the presence of a large repertoire of proteins (154) related to xenobiotic biodegradation and metabolism. Thus, 44 proteins were linked to the pathways for complete degradation of benzoate and naphthalene. The annotation of conserved functional domains led to the detection of putative genes encoding enzymes of the rhamnolipid biosynthesis pathway. Overall, the polyvalent hydrocarbon degradation capacity of BUN14 makes it a promising candidate for application in the bioremediation of polluted saline environments.}, }
@article {pmid33851256, year = {2021}, author = {Birhane, E and Gebregergs, T and Hailemariam, M and Norgrove, L and Aynekulu, E}, title = {Root Colonization and Spore Abundance of Arbuscular Mycorrhizal Fungi Along Altitudinal Gradients in Fragmented Church Natural Forest Remnants in Northern Ethiopia.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {233-242}, pmid = {33851256}, issn = {1432-184X}, support = {ETH 13/0018//NORAD/NORHED/ ; }, mesh = {Ethiopia ; Forests ; *Mycorrhizae ; Plant Roots ; Soil Microbiology ; Spores, Fungal ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) spore density and root colonization are considered sensitive to host species and abiotic factors such as climate and soil. However, there is a knowledge gap about how fragmented native forest remnants might contribute to AMF conservation, what is the AMF spore density and root colonization, and to what extent climate change, particularly warming, might impact AMF. The aim of the study was to quantify the AMF spore density and root colonization along altitudinal gradients in three agro-ecological zones of nine church forests in northern Ethiopia. Data were collected from 45 plots. All the surveyed church forest species were colonized by AMF. However, we found a significant (p < 0.05) decrease in root colonization and AMF abundance in forests at high elevation. The topsoil had significantly (p < 0.05) higher root colonization and AMF abundance than subsurface soil. We found strong negative correlations between altitude and both spore density and root colonization and soil fertility. While we cannot separate whether spore density was temperature or soil limited, we can demonstrate the importance of conserving certain tree species, particularly Ficus species, which harbor high spore densities, in both lowland and midland church forests. In the highland, no Ficus species were found. However, Hagenia abyssinica, another Rosales, had the highest spore density in the highland ecoregion.}, }
@article {pmid33850046, year = {2021}, author = {Altamia, MA and Lin, Z and Trindade-Silva, AE and Uy, ID and Shipway, JR and Wilke, DV and Concepcion, GP and Distel, DL and Schmidt, EW and Haygood, MG}, title = {Correction for Altamia et al., "Secondary Metabolism in the Gill Microbiota of Shipworms (Teredinidae) as Revealed by Comparison of Metagenomes and Nearly Complete Symbiont Genomes".}, journal = {mSystems}, volume = {6}, number = {2}, pages = {}, doi = {10.1128/mSystems.00288-21}, pmid = {33850046}, issn = {2379-5077}, }
@article {pmid33848236, year = {2021}, author = {Perez-Mon, C and Qi, W and Vikram, S and Frossard, A and Makhalanyane, T and Cowan, D and Frey, B}, title = {Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps).}, journal = {Microbial genomics}, volume = {7}, number = {4}, pages = {}, pmid = {33848236}, issn = {2057-5858}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Carbon/metabolism ; Carbon Cycle ; Metagenome ; Metagenomics ; *Microbiota ; Nitrogen/metabolism ; Permafrost/chemistry/*microbiology ; Phylogeny ; Soil Microbiology ; Switzerland ; }, abstract = {The warming-induced thawing of permafrost promotes microbial activity, often resulting in enhanced greenhouse gas emissions. The ability of permafrost microorganisms to survive the in situ sub-zero temperatures, their energetic strategies and their metabolic versatility in using soil organic materials determine their growth and functionality upon thawing. Hence, functional characterization of the permafrost microbiome, particularly in the underexplored mid-latitudinal alpine regions, is a crucial first step in predicting its responses to the changing climate, and the consequences for soil-climate feedbacks. In this study, for the first time, the functional potential and metabolic capabilities of a temperate mountain permafrost microbiome from central Europe has been analysed using shotgun metagenomics. Permafrost and active layers from the summit of Muot da Barba Peider (MBP) [Swiss Alps, 2979 m above sea level (a.s.l.)] revealed a strikingly high functional diversity in the permafrost (north-facing soils at a depth of 160 cm). Permafrost metagenomes were enriched in stress-response genes (e.g. cold-shock genes, chaperones), as well as in genes involved in cell defence and competition (e.g. antiviral proteins, antibiotics, motility, nutrient-uptake ABC transporters), compared with active-layer metagenomes. Permafrost also showed a higher potential for the synthesis of carbohydrate-active enzymes, and an overrepresentation of genes involved in fermentation, carbon fixation, denitrification and nitrogen reduction reactions. Collectively, these findings demonstrate the potential capabilities of permafrost microorganisms to thrive in cold and oligotrophic conditions, and highlight their metabolic versatility in carbon and nitrogen cycling. Our study provides a first insight into the high functional gene diversity of the central European mountain permafrost microbiome. Our findings extend our understanding of the microbial ecology of permafrost and represent a baseline for future investigations comparing the functional profiles of permafrost microbial communities at different latitudes.}, }
@article {pmid33846820, year = {2022}, author = {Valencia, EY and Barros, JP and Ferenci, T and Spira, B}, title = {A Broad Continuum of E. coli Traits in Nature Associated with the Trade-off Between Self-preservation and Nutritional Competence.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {68-82}, pmid = {33846820}, issn = {1432-184X}, support = {2016/11547-9//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {*Escherichia coli/physiology ; *Escherichia coli Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Phenotype ; Sigma Factor/genetics ; }, abstract = {A trade-off between reproduction and survival is a characteristic of many organisms. In bacteria, growth is constrained when cellular resources are channelled towards environmental stress protection. At the core of this trade-off in Escherichia coli is RpoS, a sigma factor that diverts transcriptional resources towards general stress resistance. The constancy of RpoS levels in natural isolates is unknown. A uniform RpoS content in E. coli would impart a narrow range of resistance properties to the species, whereas a diverse set of RpoS levels in nature should result in a diverse range of stress susceptibilities. We explore the diversity of trade-off settings and phenotypes by measuring the level of RpoS protein in strains of E. coli cohabiting in a natural environment. Strains from a stream polluted with domestic waste were investigated in monthly samples. Analyses included E. coli phylogroup classification, RpoS protein level, RpoS-dependent stress phenotypes and the sequencing of rpoS mutations. The most striking finding was the continuum of RpoS levels, with a 100-fold range of RpoS amounts consistently found in individuals in the stream. Approximately 1.8% of the sampled strains carried null or non-synonymous mutations in rpoS. The natural isolates also exhibited a broad (>100-fold) range of stress resistance responses. Our results are consistent with the view that a multiplicity of survival-multiplication trade-off settings is a feature of the species E. coli. The phenotypic diversity resulting from the trade-off permits bet-hedging and the adaptation of E. coli strains to a very broad range of environments.}, }
@article {pmid33846334, year = {2021}, author = {Deng, X and Zhang, N and Shen, Z and Zhu, C and Liu, H and Xu, Z and Li, R and Shen, Q and Salles, JF}, title = {Soil microbiome manipulation triggers direct and possible indirect suppression against Ralstonia solanacearum and Fusarium oxysporum.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {33}, pmid = {33846334}, issn = {2055-5008}, mesh = {*Antibiosis ; Bacterial Load ; Biodiversity ; Fusarium/*physiology ; Host-Pathogen Interactions ; Solanum lycopersicum/microbiology ; *Microbiota ; Plant Diseases/microbiology/therapy ; Ralstonia solanacearum/*physiology ; *Soil Microbiology ; }, abstract = {Soil microbiome manipulation can potentially reduce the use of pesticides by improving the ability of soils to resist or recover from pathogen infestation, thus generating natural suppressiveness. We simulated disturbance through soil fumigation and investigated how the subsequent application of bio-organic and organic amendments reshapes the taxonomic and functional potential of the soil microbiome to suppress the pathogens Ralstonia solanacearum and Fusarium oxysporum in tomato monocultures. The use of organic amendment alone generated smaller shifts in bacterial and fungal community composition and no suppressiveness. Fumigation directly decreased F. oxysporum and induced drastic changes in the soil microbiome. This was further converted from a disease conducive to a suppressive soil microbiome due to the application of organic amendment, which affected the way the bacterial and fungal communities were reassembled. These direct and possibly indirect effects resulted in a highly efficient disease control rate, providing a promising strategy for the control of the diseases caused by multiple pathogens.}, }
@article {pmid33841364, year = {2021}, author = {Lui, LM and Majumder, EL and Smith, HJ and Carlson, HK and von Netzer, F and Fields, MW and Stahl, DA and Zhou, J and Hazen, TC and Baliga, NS and Adams, PD and Arkin, AP}, title = {Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {642422}, pmid = {33841364}, issn = {1664-302X}, abstract = {Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.}, }
@article {pmid33834428, year = {2021}, author = {Iturbe-Espinoza, P and Brandt, BW and Braster, M and Bonte, M and Brown, DM and van Spanning, RJM}, title = {Effects of DNA preservation solution and DNA extraction methods on microbial community profiling of soil.}, journal = {Folia microbiologica}, volume = {66}, number = {4}, pages = {597-606}, pmid = {33834428}, issn = {1874-9356}, support = {216-2015-FONDECYT//FONDECYT-CONCYTEC/ ; }, mesh = {*DNA, Bacterial/genetics/isolation &amp; purification ; *Environmental Monitoring/methods ; *Genetic Techniques/standards ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Microbial community profiling using high-throughput sequencing relies in part on the preservation of the DNA and the effectiveness of the DNA extraction method. This study aimed at understanding to what extent these parameters affect the profiling. We obtained samples treated with and without a preservation solution. Also, we compared DNA extraction kits from Qiagen and Zymo-Research. The types of samples were defined strains, both as single species and mixtures, as well as undefined indigenous microbial communities from soil. We show that the use of a preservation solution resulted in substantial changes in the 16S rRNA gene profiles either due to an overrepresentation of Gram-positive bacteria or to an underrepresentation of Gram-negative bacteria. In addition, 16S rRNA gene profiles were substantially different depending on the type of kit that was used for extraction. The kit from Zymo extracted DNA from different types of bacteria in roughly equal amounts. In contrast, the kit from Qiagen preferentially extracted DNA from Gram-negative bacteria while DNA from Gram-positive bacteria was extracted less effectively. These differences in kit performance strongly influenced the interpretation of our microbial ecology studies.}, }
@article {pmid33834254, year = {2021}, author = {Conacher, CG and Luyt, NA and Naidoo-Blassoples, RK and Rossouw, D and Setati, ME and Bauer, FF}, title = {The ecology of wine fermentation: a model for the study of complex microbial ecosystems.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {8}, pages = {3027-3043}, pmid = {33834254}, issn = {1432-0614}, support = {83471//South African National Research Foundation/ ; 118505//South African National Research Foundation/ ; FLAIR//The Royal Society/ ; }, mesh = {Ecosystem ; Fermentation ; *Microbiota ; Models, Biological ; *Wine ; }, abstract = {The general interest in microbial ecology has skyrocketed over the past decade, driven by technical advances and by the rapidly increasing appreciation of the fundamental services that these ecosystems provide. In biotechnology, ecosystems have many more functionalities than single species, and, if properly understood and harnessed, will be able to deliver better outcomes for almost all imaginable applications. However, the complexity of microbial ecosystems and of the interactions between species has limited their applicability. In research, next generation sequencing allows accurate mapping of the microbiomes that characterise ecosystems of biotechnological and/or medical relevance. But the gap between mapping and understanding, to be filled by "functional microbiomics", requires the collection and integration of many different layers of complex data sets, from molecular multi-omics to spatial imaging technologies to online ecosystem monitoring tools. Holistically, studying the complexity of most microbial ecosystems, consisting of hundreds of species in specific spatial arrangements, is beyond our current technical capabilities, and simpler model systems with fewer species and reduced spatial complexity are required to establish the fundamental rules of ecosystem functioning. One such ecosystem, the ecosystem responsible for natural alcoholic fermentation, can provide an excellent tool to study evolutionarily relevant interactions between multiple species within a relatively easily controlled environment. This review will critically evaluate the approaches that are currently implemented to dissect the cellular and molecular networks that govern this ecosystem. KEY POINTS: • Evolutionarily isolated fermentation ecosystem can be used as an ecological model. • Experimental toolbox is gearing towards mechanistic understanding of this ecosystem. • Integration of multidisciplinary datasets is key to predictive understanding.}, }
@article {pmid33830034, year = {2021}, author = {Zama, D and Gori, D and Muratore, E and Leardini, D and Rallo, F and Turroni, S and Prete, A and Brigidi, P and Pession, A and Masetti, R}, title = {Enteral versus Parenteral Nutrition as Nutritional Support after Allogeneic Hematopoietic Stem Cell Transplantation: a Systematic Review and Meta-Analysis.}, journal = {Transplantation and cellular therapy}, volume = {27}, number = {2}, pages = {180.e1-180.e8}, doi = {10.1016/j.jtct.2020.11.006}, pmid = {33830034}, issn = {2666-6367}, mesh = {Enteral Nutrition ; *Graft vs Host Disease/prevention &amp; control ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Humans ; Nutritional Support ; Parenteral Nutrition ; }, abstract = {Nutritional support for patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT) has been widely debated. Enteral nutrition (EN) is recommended as first-line nutritional support by the main international guidelines. However, these recommendations are based on weak evidence, and there is wide variability in the types of nutritional support among transplantation centers, with the majority providing parenteral nutrition (PN) instead of EN. Here we provide an up-to-date systematic review and meta-analysis of studies comparing EN and PN for nutritional support during the neutropenic period after allo-HSCT. The literature search strategy identified 13 papers, of which 10 compared clinical transplantation outcomes, 2 compared gut microbiota (GM) compositions, and 1 compared systemic metabolic profiles. For the meta-analysis, among the 10 clinical studies, 8 studies in which 2 groups were compared were selected: in 1 group, EN was provided as primary nutritional support in the neutropenic phase after allo-HSCT with or without the addition of PN (EN group), whereas in the other group, only PN was provided as nutritional support. The incidence rates of acute graft-versus-host disease (aGVHD) (relative risk [RR], 0.69; 95% confidence interval [CI], 0.56 to 0.86; P = .0007), aGVHD grade III-IV (RR, 0.44; 95% CI, 0.30 to 0.64; P < .0001), and gut aGVHD (RR, 0.44; 95% CI, 0.30 to 0.66; P < .0001) were lower in the EN group than in the PN group. No differences were found between the 2 groups with regard to the incidence of severe oral mucositis (RR, 0.95; 95% CI, 0.83 to 1.09; P = .46) or overall survival at day +100 (RR, 1.07; 95% CI, 0.95 to 1.21; P = .29). Other variables were too heterogeneous to perform quantitative analyses. The results of the meta-analysis showed that EN reduced the incidence of aGVHD, specifically grade III-IV and gut aGVHD. This result should prompt improved efforts to implement EN as first-line nutritional support in patients undergoing allo-HSCT. Considering the emerging evidence regarding the association between GM dysbiosis and aGVHD onset, we speculate that this protective effect could be attributed to the improved gut eubiosis observed in enterally fed patients. Further studies are warranted to better address the relationship between the GM composition, aGVHD, and the nutritional administration route during HSCT.}, }
@article {pmid33827912, year = {2021}, author = {Gauthier, J and Derome, N}, title = {Evenness-Richness Scatter Plots: a Visual and Insightful Representation of Shannon Entropy Measurements for Ecological Community Analysis.}, journal = {mSphere}, volume = {6}, number = {2}, pages = {}, pmid = {33827912}, issn = {2379-5042}, mesh = {*Biodiversity ; *Biota ; *Entropy ; Mathematical Concepts ; }, abstract = {Shannon's entropy is a popular alpha diversity metric because it estimates both richness and evenness in a single equation. However, since its value is dependent on both those parameters, there is theoretically an infinite number of richness/evenness value combinations translating into the same index score. By decoupling both components measured by Shannon's entropy, two communities having identical indices can be differentiated by mapping richness and evenness coordinates on a scatter plot. In such graphs, confidence ellipses would allow testing significant differences between groups of samples. Multivariate statistical tests such as permutational multivariate analysis of variance (PERMANOVA) can be performed on distance matrices calculated from richness and evenness coordinates and detect statistically significant differences that would have remained unforeseen otherwise. Therefore, plotting richness and evenness on two-dimensional (2D) graphs gives a more thorough understanding of how alpha diversity differs between groups of samples.}, }
@article {pmid33827413, year = {2021}, author = {Shanmugam, G and Lee, SH and Jeon, J}, title = {EzMAP: Easy Microbiome Analysis Platform.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {179}, pmid = {33827413}, issn = {1471-2105}, support = {918017-04//Ministry of Agriculture, Food, and Rural Affairs/ ; PJ013178//Rural Development Administration , Korea/ ; NRF-2018R1A5A1023599//National Research Foundation of Korea/ ; }, mesh = {*High-Throughput Nucleotide Sequencing ; *Microbiota ; Phylogeny ; Programming Languages ; *Software ; }, abstract = {BACKGROUND: The rapid advances in next-generation sequencing technologies have revolutionized the microbiome research by greatly increasing our ability to understand diversity of microbes in a given sample. Over the past decade, several computational pipelines have been developed to efficiently process and annotate these microbiome data. However, most of these pipelines require an implementation of additional tools for downstream analyses as well as advanced programming skills.<br><br>RESULTS: Here we introduce a user-friendly microbiome analysis platform, EzMAP (Easy Microbiome Analysis Platform), which was developed using Java Swings, Java Script and R programming language. EzMAP is a standalone package providing graphical user interface, enabling easy access to all the functionalities of QIIME2 (Quantitative Insights Into Microbial Ecology) as well as streamlined downstream analyses using QIIME2 output as input. This platform is designed to give users the detailed reports and the intermediate output files that are generated progressively. The users are allowed to download the features/OTU table (.biom;.tsv;.xls), representative sequences (.fasta) and phylogenetic tree (.nwk), taxonomy assignment file (optional). For downstream analyses, users are allowed to perform relative abundances (at all taxonomical levels), community comparison (alpha and beta diversity, core microbiome), differential abundances (DESeq2 and linear discriminant analysis) and functional prediction (PICRust, Tax4Fun and FunGuilds). Our case study using a published rice microbiome dataset demonstrates intuitive user interface and great accessibility of the EzMAP.<br><br>CONCLUSIONS: This EzMAP allows users to consolidate the microbiome analysis processes from raw sequence processing to downstream analyses specific for individual projects. We believe that this will be an invaluable tool for the beginners in their microbiome data analysis. This platform is freely available at https://github.com/gnanibioinfo/EzMAP and will be continually updated for adoption of changes in methods and approaches.}, }
@article {pmid33824198, year = {2021}, author = {Cooper, RO and Vavra, JM and Cressler, CE}, title = {Targeted Manipulation of Abundant and Rare Taxa in the Daphnia magna Microbiota with Antibiotics Impacts Host Fitness Differentially.}, journal = {mSystems}, volume = {6}, number = {2}, pages = {}, pmid = {33824198}, issn = {2379-5077}, abstract = {Host-associated microbes contribute to host fitness, but it is unclear whether these contributions are from rare keystone taxa, numerically abundant taxa, or interactions among community members. Experimental perturbation of the microbiota can highlight functionally important taxa; however, this approach is primarily applied in systems with complex communities where the perturbation affects hundreds of taxa, making it difficult to pinpoint contributions of key community members. Here, we use the ecological model organism Daphnia magna to examine the importance of rare and abundant taxa by perturbing its relatively simple microbiota with targeted antibiotics. We used sublethal antibiotic doses to target either rare or abundant members across two temperatures and then measured key host life history metrics and shifts in microbial community composition. We find that removal of abundant taxa had greater impacts on host fitness than did removal of rare taxa and that the abundances of nontarget taxa were impacted by antibiotic treatment, suggesting that no rare keystone taxa exist in the Daphnia magna microbiota but that microbe-microbe interactions may play a role in host fitness. We also find that microbial community composition was impacted by antibiotics differently across temperatures, indicating that ecological context shapes within-host microbial responses and effects on host fitness.IMPORTANCE Understanding the contributions of rare and abundant taxa to host fitness is an outstanding question in host microbial ecology. In this study, we use the model zooplankton Daphnia magna and its relatively simple cohort of bacterial taxa to disentangle the roles of distinct taxa in host life history metrics, using a suite of antibiotics to selectively reduce the abundance of functionally important taxa. We also examine how environmental context shapes the importance of these bacterial taxa in host fitness.}, }
@article {pmid33824193, year = {2021}, author = {Daisley, BA and Reid, G}, title = {BEExact: a Metataxonomic Database Tool for High-Resolution Inference of Bee-Associated Microbial Communities.}, journal = {mSystems}, volume = {6}, number = {2}, pages = {}, pmid = {33824193}, issn = {2379-5077}, abstract = {High-throughput 16S rRNA gene sequencing technologies have robust potential to improve our understanding of bee (Hymenoptera: Apoidea)-associated microbial communities and their impact on hive health and disease. Despite recent computation algorithms now permitting exact inferencing of high-resolution exact amplicon sequence variants (ASVs), the taxonomic classification of these ASVs remains a challenge due to inadequate reference databases. To address this, we assemble a comprehensive data set of all publicly available bee-associated 16S rRNA gene sequences, systematically annotate poorly resolved identities via inclusion of 618 placeholder labels for uncultivated microbial dark matter, and correct for phylogenetic inconsistencies using a complementary set of distance-based and maximum likelihood correction strategies. To benchmark the resultant database (BEExact), we compare performance against all existing reference databases in silico using a variety of classifier algorithms to produce probabilistic confidence scores. We also validate realistic classification rates on an independent set of ∼234 million short-read sequences derived from 32 studies encompassing 50 different bee types (36 eusocial and 14 solitary). Species-level classification rates on short-read ASVs range from 80 to 90% using BEExact (with ∼20% due to "bxid" placeholder names), whereas only ∼30% at best can be resolved with current universal databases. A series of data-driven recommendations are developed for future studies. We conclude that BEExact (https://github.com/bdaisley/BEExact) enables accurate and standardized microbiota profiling across a broad range of bee species-two factors of key importance to reproducibility and meaningful knowledge exchange within the scientific community that together, can enhance the overall utility and ecological relevance of routine 16S rRNA gene-based sequencing endeavors.IMPORTANCE The failure of current universal taxonomic databases to support the rapidly expanding field of bee microbiota research has led to many investigators relying on "in-house" reference sets or manual classification of sequence reads (usually based on BLAST searches), often with vague identity thresholds and subjective taxonomy choices. This time-consuming, error- and bias-prone process lacks standardization, cripples the potential for comparative cross-study analysis, and in many cases is likely to incorrectly sway study conclusions. BEExact is structured on and leverages several complementary bioinformatic techniques to enable refined inference of bee host-associated microbial communities without any other methodological modifications necessary. It also bridges the gap between current practical outcomes (i.e., phylotype-to-genus level constraints with 97% operational taxonomic units [OTUs]) and the theoretical resolution (i.e., species-to-strain level classification with 100% ASVs) attainable in future microbiota investigations. Other niche habitats could also likely benefit from customized database curation via implementation of the novel approaches introduced in this study.}, }
@article {pmid33820946, year = {2021}, author = {Deng, Y and Huang, Y and Che, Y and Yang, Y and Yin, X and Yan, A and Dai, L and Liu, YY and Polz, M and Zhang, T}, title = {Microbiome assembly for sulfonamide subsistence and the transfer of genetic determinants.}, journal = {The ISME journal}, volume = {15}, number = {10}, pages = {2817-2829}, pmid = {33820946}, issn = {1751-7370}, support = {R01 AI141529/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Drug Resistance, Microbial ; Humans ; Metagenome ; *Microbiota/genetics ; Sulfonamides ; }, abstract = {Antibiotic subsistence in bacteria represents an alternative resistance machinery, while paradoxically, it is also a cure for environmental resistance. Antibiotic-subsisting bacteria can detoxify antibiotic-polluted environments and prevent the development of antibiotic resistance in environments. However, progress toward efficient in situ engineering of antibiotic-subsisting bacteria is hindered by the lack of mechanistic and predictive understanding of the assembly of the functioning microbiome. By top-down manipulation of wastewater microbiomes using sulfadiazine as the single limiting source, we monitored the ecological selection process that forces the wastewater microbiome to perform efficient sulfadiazine subsistence. We found that the community-level assembly selects for the same three families rising to prominence across different initial pools of microbiomes. We further analyzed the assembly patterns using a linear model. Detailed inspections of the sulfonamide metabolic gene clusters in individual genomes of isolates and assembled metagenomes reveal limited transfer potential beyond the boundaries of the Micrococcaceae lineage. Our results open up new possibilities for engineering specialist bacteria for environmental applications.}, }
@article {pmid33817951, year = {2021}, author = {Gwizdala, M and Lebre, PH and Maggs-Kölling, G and Marais, E and Cowan, DA and Krüger, TPJ}, title = {Sub-lithic photosynthesis in hot desert habitats.}, journal = {Environmental microbiology}, volume = {23}, number = {7}, pages = {3867-3880}, doi = {10.1111/1462-2920.15505}, pmid = {33817951}, issn = {1462-2920}, mesh = {*Cyanobacteria/genetics ; *Desert Climate ; Ecosystem ; Photosynthesis ; Soil Microbiology ; }, abstract = {In hyper-arid soil environments, photosynthetic microorganisms are largely restricted to hypolithic (sub-lithic) habitats: i.e., on the ventral surfaces of translucent pebbles in desert pavements. Here, we combined fluorometric, spectroscopic, biochemical and metagenomic approaches to investigate in situ the light transmission properties of quartz stones in the Namib Desert, and assess the photosynthetic activity of the underlying hypolithic cyanobacterial biofilms. Quartz pebbles greatly reduced the total photon flux to the ventral surface biofilms and filtered out primarily the short wavelength portion of the solar spectrum. Chlorophylls d and f were not detected in biofilm pigment extracts; however, hypolithic cyanobacterial communities showed some evidence of adaptation to sub-lithic conditions, including the prevalence of genes encoding Helical Carotenoid Proteins, which are associated with desiccation stress. Under water-saturated conditions, hypolithic communities showed no evidence of light stress, even when the quartz stones were exposed to full midday sunlight. This initial study creates a foundation for future in-situ and laboratory exploration of various adaptation mechanisms employed by photosynthetic organisms forming hypolithic microbial communities.}, }
@article {pmid33813729, year = {2021}, author = {Camacho-Montealegre, CM and Rodrigues, EM and Morais, DK and Tótola, MR}, title = {Prokaryotic community diversity during bioremediation of crude oil contaminated oilfield soil: effects of hydrocarbon concentration and salinity.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {52}, number = {2}, pages = {787-800}, pmid = {33813729}, issn = {1678-4405}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Carbon Dioxide/metabolism ; Hydrocarbons/metabolism ; *Microbiota/genetics ; Oil and Gas Fields/*microbiology ; Petroleum/*metabolism/microbiology ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sodium Chloride/metabolism ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Crude oil extracted from oilfield reservoirs brings together hypersaline produced water. Failure in pipelines transporting this mixture causes contamination of the soil with oil and hypersaline water. Soil salinization is harmful to biological populations, impairing the biodegradation of contaminants. We simulated the contamination of a soil from an oilfield with produced water containing different concentrations of NaCl and crude oil, in order to evaluate the effect of salinity and hydrocarbon concentration on prokaryote community structure and biodegradation activity. Microcosms were incubated in CO2-measuring respirometer. After the incubation, residual aliphatic hydrocarbons were quantified and were performed 16S rRNA gene sequencing. An increase in CO2 emission and hydrocarbon biodegradation was observed with increasing oil concentration up to 100 g kg[-1]. Alpha diversity decreased in oil-contaminated soils with an increase in the relative abundance of Actinobacteria and reduction of Bacteroidetes with increasing oil concentration. In the NaCl-contaminated soils, alpha diversity, CO2 emission, and hydrocarbon biodegradation decreased with increasing NaCl concentration. There was an increase in the relative abundance of Firmicutes and Proteobacteria and a reduction of Actinobacteria with increasing salt concentration. Our results highlight the need to adopt specific bioremediation strategies in soils impacted by mixtures of crude oil and hypersaline produced water.}, }
@article {pmid33813189, year = {2021}, author = {Glodowska, M and Schneider, M and Eiche, E and Kontny, A and Neumann, T and Straub, D and ,  and Kleindienst, S and Kappler, A}, title = {Microbial transformation of biogenic and abiogenic Fe minerals followed by in-situ incubations in an As-contaminated vs. non-contaminated aquifer.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {281}, number = {}, pages = {117012}, doi = {10.1016/j.envpol.2021.117012}, pmid = {33813189}, issn = {1873-6424}, mesh = {*Arsenic ; Ferric Compounds ; *Groundwater ; Iron ; Minerals ; Oxidation-Reduction ; }, abstract = {Fe(III) minerals play a crucial role for arsenic (As) mobility in aquifers as they usually represent the main As-bearing phases. Microbial reductive dissolution of As-bearing Fe(III) minerals is responsible for the release of As and the resulting groundwater contamination in many sites worldwide. So far, in most studies mainly abiogenic iron minerals have been considered. Yet, biogenic minerals that possess different properties to their abiogenic counterparts are also present in the environment. In some environments they dominate the iron mineral inventory but so far, it is unclear what this means for the As mobility. We, therefore, performed an in-situ aquifer Fe(III) minerals exposure experiment i) to evaluate how different biogenic and abiogenic Fe(III) minerals are transformed in a strongly reducing, As-contaminated aquifer (25 m) compared to As-free moderately reducing aquifer (32 m) and ii) to assess which microbial taxa are involved in these Fe(III) minerals transformations. We found that higher numbers of bacteria and archaea were associated with the minerals incubated in the As-contaminated compared to the non-contaminated aquifer and that all Fe(III) minerals were mainly colonized by Fe(III)-reducing bacteria, with Geobacter being the most abundant taxon. Additionally, fermenting microorganisms were abundant on minerals incubated in the As-contaminated aquifer, while methanotrophs were identified on the minerals incubated in the As-free moderately reducing aquifer, implying involvement of these microorganisms in Fe(III) reduction. We observed that biogenic Fe(III) minerals generally tend to become more reduced and when incubated in the As-contaminated aquifer sorbed more As than the abiogenic ones. Most of abiogenic and biogenic Fe(III) minerals were transformed into magnetite while biogenic more crystalline mixed phases were not subjected to visible transformation. This in-situ Fe(III) minerals incubation approach shows that biogenic minerals are more prone to be colonized by (Fe(III)-reducing) microorganisms and bind more As, although ultimately produce similar minerals during Fe(III) reduction.}, }
@article {pmid33811505, year = {2022}, author = {Han, Y and Guo, C and Guan, X and McMinn, A and Liu, L and Zheng, G and Jiang, Y and Liang, Y and Shao, H and Tian, J and Wang, M}, title = {Comparison of Deep-Sea Picoeukaryotic Composition Estimated from the V4 and V9 Regions of 18S rRNA Gene with a Focus on the Hadal Zone of the Mariana Trench.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {34-47}, pmid = {33811505}, issn = {1432-184X}, support = {2018YFC1406704//National Key Research and Development Program of China/ ; No. 2018SDKJ0406-6//Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao), China/ ; 41906126//Natural Science Foundation of China/ ; 41976117//Natural Science Foundation of China/ ; 201912003//Research Funds for the Central Universities/ ; 201812002//Research Funds for the Central Universities/ ; LMB20091001//Open Research Fund of LMB, SCSIO/ ; }, mesh = {*Alveolata/classification ; Pacific Ocean ; RNA, Ribosomal, 18S/genetics ; *Rhizaria/classification ; Seawater/*microbiology ; *Stramenopiles/classification ; }, abstract = {Diversity of microbial eukaryotes is estimated largely based on sequencing analysis of the hypervariable regions of 18S rRNA genes. But the use of different regions of 18S rRNA genes as molecular markers may generate bias in diversity estimation. Here, we compared the differences between the two most widely used markers, V4 and V9 regions of the 18S rRNA gene, in describing the diversity of epipelagic, bathypelagic, and hadal picoeukaryotes in the Challenger Deep of the Mariana Trench, which is a unique and little explored environment. Generally, the V9 region identified more OTUs in deeper waters than V4, while the V4 region provided greater Shannon diversity than V9. In the epipelagic zone, where Alveolata was the dominant group, picoeukaryotic community compositions identified by V4 and V9 markers are similar at different taxonomic levels. However, in the deep waters, the results of the two datasets show clear differences. These differences were mainly contributed by Retaria, Fungi, and Bicosoecida. The primer targeting the V9 region has an advantage in amplifying Bicosoecids in the bathypelagic and hadal zone of the Mariana Trench, and its high abundance in V9 dataset pointed out the possibility of Bicosoecids as a dominant group in this environment. Chrysophyceae, Fungi, MALV-I, and Retaria were identified as the dominant picoeukaryotes in the bathypelagic and hadal zone and potentially play important roles in deep-sea microbial food webs and biogeochemical cycling by their phagotrophic, saprotrophic, and parasitic life styles. Overall, the use of different markers of 18S rRNA gene allows a better assessment and understanding of the picoeukaryotic diversity in deep-sea environments.}, }
@article {pmid33811029, year = {2021}, author = {Rupp, DL and Lamit, LJ and Techtmann, SM and Kane, ES and Lilleskov, EA and Turetsky, MR}, title = {The Rhizosphere Responds: Rich Fen Peat and Root Microbial Ecology after Long-Term Water Table Manipulation.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {12}, pages = {e0024121}, pmid = {33811029}, issn = {1098-5336}, mesh = {Alaska ; Archaea/genetics/isolation &amp; purification/metabolism ; Bacteria/genetics/isolation &amp; purification/metabolism ; Carbon Cycle ; *Groundwater ; Iron/metabolism ; Magnoliopsida/*microbiology ; Methane/metabolism ; Microbiota ; Plant Roots/*microbiology ; *Rhizosphere ; Soil ; *Soil Microbiology ; }, abstract = {Hydrologic shifts due to climate change will affect the cycling of carbon (C) stored in boreal peatlands. Carbon cycling in these systems is carried out by microorganisms and plants in close association. This study investigated the effects of experimentally manipulated water tables (lowered and raised) and plant functional groups on the peat and root microbiomes in a boreal rich fen. All samples were sequenced and processed for bacterial, archaeal (16S DNA genes; V4), and fungal (internal transcribed spacer 2 [ITS2]) DNA. Depth had a strong effect on microbial and fungal communities across all water table treatments. Bacterial and archaeal communities were most sensitive to the water table treatments, particularly at the 10- to 20-cm depth; this area coincides with the rhizosphere or rooting zone. Iron cyclers, particularly members of the family Geobacteraceae, were enriched around the roots of sedges, horsetails, and grasses. The fungal community was affected largely by plant functional group, especially cinquefoils. Fungal endophytes (particularly Acephala spp.) were enriched in sedge and grass roots, which may have underappreciated implications for organic matter breakdown and cycling. Fungal lignocellulose degraders were enriched in the lowered water table treatment. Our results were indicative of two main methanogen communities, a rooting zone community dominated by the archaeal family Methanobacteriaceae and a deep peat community dominated by the family Methanomicrobiaceae. IMPORTANCE This study demonstrated that roots and the rooting zone in boreal fens support organisms likely capable of methanogenesis, iron cycling, and fungal endophytic association and are directly or indirectly affecting carbon cycling in these ecosystems. These taxa, which react to changes in the water table and associate with roots and, particularly, graminoids, may gain greater biogeochemical influence, as projected higher precipitation rates could lead to an increased abundance of sedges and grasses in boreal fens.}, }
@article {pmid33809442, year = {2021}, author = {Jesus, HE and Carreira, RS and Paiva, SSM and Massone, C and Enrich-Prast, A and Peixoto, RS and Rodrigues, JLM and Lee, CK and Cary, C and Rosado, AS}, title = {Microbial Succession under Freeze-Thaw Events and Its Potential for Hydrocarbon Degradation in Nutrient-Amended Antarctic Soil.}, journal = {Microorganisms}, volume = {9}, number = {3}, pages = {}, pmid = {33809442}, issn = {2076-2607}, support = {001//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; BAS/1/1096-01-01//King Abdullah University of Science and Technology/ ; CNE2017//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; }, abstract = {The polar regions have relatively low richness and diversity of plants and animals, and the basis of the entire ecological chain is supported by microbial diversity. In these regions, understanding the microbial response against environmental factors and anthropogenic disturbances is essential to understand patterns better, prevent isolated events, and apply biotechnology strategies. The Antarctic continent has been increasingly affected by anthropogenic contamination, and its constant temperature fluctuations limit the application of clean recovery strategies, such as bioremediation. We evaluated the bacterial response in oil-contaminated soil through a nutrient-amended microcosm experiment using two temperature regimes: (i) 4 °C and (ii) a freeze-thaw cycle (FTC) alternating between -20 and 4 °C. Bacterial taxa, such as Myxococcales, Chitinophagaceae, and Acidimicrobiales, were strongly related to the FTC. Rhodococcus was positively related to contaminated soils and further stimulated under FTC conditions. Additionally, the nutrient-amended treatment under the FTC regime enhanced bacterial groups with known biodegradation potential and was efficient in removing hydrocarbons of diesel oil. The experimental design, rates of bacterial succession, and level of hydrocarbon transformation can be considered as a baseline for further studies aimed at improving bioremediation strategies in environments affected by FTC regimes.}, }
@article {pmid33807581, year = {2021}, author = {Maes, PW and Floyd, AS and Mott, BM and Anderson, KE}, title = {Overwintering Honey Bee Colonies: Effect of Worker Age and Climate on the Hindgut Microbiota.}, journal = {Insects}, volume = {12}, number = {3}, pages = {}, pmid = {33807581}, issn = {2075-4450}, support = {2022-21000-021-00D//Agricultural Research Service/ ; }, abstract = {Honey bee overwintering health is essential to meet the demands of spring pollination. Managed honey bee colonies are overwintered in a variety of climates, and increasing rates of winter colony loss have prompted investigations into overwintering management, including indoor climate controlled overwintering. Central to colony health, the worker hindgut gut microbiota has been largely ignored in this context. We sequenced the hindgut microbiota of overwintering workers from both a warm southern climate and controlled indoor cold climate. Congruently, we sampled a cohort of known chronological age to estimate worker longevity in southern climates, and assess age-associated changes in the core hindgut microbiota. We found that worker longevity over winter in southern climates was much lower than that recorded for northern climates. Workers showed decreased bacterial and fungal load with age, but the relative structure of the core hindgut microbiome remained stable. Compared to cold indoor wintering, collective microbiota changes in the southern outdoor climate suggest compromised host physiology. Fungal abundance increased by two orders of magnitude in southern climate hindguts and was positively correlated with non-core, likely opportunistic bacteria. Our results contribute to understanding overwintering honey bee biology and microbial ecology and provide insight into overwintering strategies.}, }
@article {pmid33807233, year = {2021}, author = {Mulholland, KA and Robinson, MG and Keeler, SJ and Johnson, TJ and Weber, BW and Keeler, CL}, title = {Metagenomic Analysis of the Respiratory Microbiome of a Broiler Flock from Hatching to Processing.}, journal = {Microorganisms}, volume = {9}, number = {4}, pages = {}, pmid = {33807233}, issn = {2076-2607}, support = {2015-68004-23131//U.S. Department of Agriculture/ ; }, abstract = {Elucidating the complex microbial interactions in biological environments requires the identification and characterization of not only the bacterial component but also the eukaryotic viruses, bacteriophage, and fungi. In a proof of concept experiment, next generation sequencing approaches, accompanied by the development of novel computational and bioinformatics tools, were utilized to examine the evolution of the microbial ecology of the avian trachea during the growth of a healthy commercial broiler flock. The flock was sampled weekly, beginning at placement and concluding at 49 days, the day before processing. Metagenomic sequencing of DNA and RNA was utilized to examine the bacteria, virus, bacteriophage, and fungal components during flock growth. The utility of using a metagenomic approach to study the avian respiratory virome was confirmed by detecting the dysbiosis in the avian respiratory virome of broiler chickens diagnosed with infection with infectious laryngotracheitis virus. This study provides the first comprehensive analysis of the ecology of the avian respiratory microbiome and demonstrates the feasibility for the use of this approach in future investigations of avian respiratory diseases.}, }
@article {pmid33805552, year = {2021}, author = {Pham, VT and Calatayud, M and Rotsaert, C and Seifert, N and Richard, N and Van den Abbeele, P and Marzorati, M and Steinert, RE}, title = {Antioxidant Vitamins and Prebiotic FOS and XOS Differentially Shift Microbiota Composition and Function and Improve Intestinal Epithelial Barrier In Vitro.}, journal = {Nutrients}, volume = {13}, number = {4}, pages = {}, pmid = {33805552}, issn = {2072-6643}, mesh = {Adult ; Antioxidants/*pharmacology ; Bacteria/classification/drug effects ; Caco-2 Cells ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Glucuronates/*pharmacology ; HT29 Cells ; Humans ; Intestinal Mucosa/drug effects/microbiology ; Male ; Oligosaccharides/*pharmacology ; Oxidation-Reduction ; *Prebiotics ; Vitamins/*pharmacology ; }, abstract = {Human gut microbiota (HGM) play a significant role in health and disease. Dietary components, including fiber, fat, proteins and micronutrients, can modulate HGM. Much research has been performed on conventional prebiotics such as fructooligosaccharides (FOS) and galactooligosaccharides (GOS), however, novel prebiotics or micronutrients still require further validation. We assessed the effect of FOS, xylooligosaccharides (XOS) and a mixture of an antioxidant vitamin blend (AOB) on gut microbiota composition and activity, and intestinal barrier in vitro. We used batch fermentations and tested the short-term effect of different products on microbial activity in six donors. Next, fecal inocula from two donors were used to inoculate the simulator of the human microbial ecosystem (SHIME) and after long-term exposure of FOS, XOS and AOB, microbial activity (short- and branched-chain fatty acids and lactate) and HGM composition were evaluated. Finally, in vitro assessment of intestinal barrier was performed in a Transwell setup of differentiated Caco-2 and HT29-MTX-E12 cells exposed to fermentation supernatants. Despite some donor-dependent differences, all three tested products showed beneficial modulatory effects on microbial activity represented by an increase in lactate and SCFA levels (acetate, butyrate and to a lesser extent also propionate), while decreasing proteolytic markers. Bifidogenic effect of XOS was consistent, while AOB supplementation appears to exert a specific impact on reducing F. nucleatum and increasing butyrate-producing B. wexlerae. Functional and compositional microbial changes were translated to an in vitro host response by increases of the intestinal barrier integrity by all the products and a decrease of the redox potential by AOB supplementation.}, }
@article {pmid33800578, year = {2021}, author = {Panteli, N and Mastoraki, M and Lazarina, M and Chatzifotis, S and Mente, E and Kormas, KA and Antonopoulou, E}, title = {Configuration of Gut Microbiota Structure and Potential Functionality in Two Teleosts under the Influence of Dietary Insect Meals.}, journal = {Microorganisms}, volume = {9}, number = {4}, pages = {}, pmid = {33800578}, issn = {2076-2607}, support = {MIS 5045857//the European Union and Greek national funds through the National Strategic Reference Framework 2014-2020 (GR &amp; EU), Special Actions Aquaculture-Industrial Materials-Open innovation in culture/ ; }, abstract = {Insect meals are considered promising, eco-friendly, alternative ingredients for aquafeed. Considering the dietary influence on establishment of functioning gut microbiota, the effect of the insect meal diets on the microbial ecology should be addressed. The present study assessed diet- and species-specific shifts in gut resident bacterial communities of juvenile reared Dicentrarchus labrax and Sparus aurata in response to three experimental diets with insect meals from three insects (Hermetia illucens, Tenebrio molitor, Musca domestica), using high-throughput Illumina sequencing of the V3-V4 region of the 16S rRNA gene. The dominant phyla were Firmicutes, Proteobacteria and Actinobacteria in all dietary treatments. Anaerococcus sp., Cutibacterium sp. and Pseudomonas sp. in D. labrax, and Staphylococcus sp., Hafnia sp. and Aeromonas sp. in S. aurata were the most enriched shared species, following insect-meal inclusion. Network analysis of the dietary treatments highlighted diet-induced changes in the microbial community assemblies and revealed unique and shared microbe-to-microbe interactions. PICRUSt-predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were significantly differentiated, including genes associated with metabolic pathways. The present findings strengthen the importance of diet in microbiota configuration and underline that different insects as fish feed ingredients elicit species-specific differential responses of structural and functional dynamics in gut microbial communities.}, }
@article {pmid33799457, year = {2021}, author = {Rao, Z and Li, J and Shi, B and Zeng, Y and Liu, Y and Sun, Z and Wu, L and Sun, W and Tang, Z}, title = {Dietary Tryptophan Levels Impact Growth Performance and Intestinal Microbial Ecology in Weaned Piglets via Tryptophan Metabolites and Intestinal Antimicrobial Peptides.}, journal = {Animals : an open access journal from MDPI}, volume = {11}, number = {3}, pages = {}, pmid = {33799457}, issn = {2076-2615}, support = {31772610, 31872370//National Natural Science Foundation of China/ ; cx2017024//Chongqing key innovation project for overseas students/ ; 2018YFD0501000//National Key R&amp;D Program of China/ ; }, abstract = {Tryptophan (Trp) plays an important role in piglet growth. However, the effect of dietary Trp on microbial flora is still poorly understood. A total of 40 28-d weaned piglets were allocated to four groups with 10 barrows per group and one pig per replicate. Piglets were fed a corn and soybean meal-based diet with 0.14%, 0.21%, 0.28%, or 0.35% Trp for four weeks. Five piglets from each diet group were euthanized, and blood and tissue samples were collected. The average daily body weight gain, average daily feed intake, feed conversion ratio, spleen index, pancreas index, longissimus dorsi muscle index, plasma insulin, 5-hydroxytryptamine, kynurenine, and Trp concentrations of weaned piglets increased in a dose-dependent manner (p < 0.05). Compared with the 0.14% Trp diet, the adequate-Trp diets (0.21%, 0.28%, or 0.35%) down-regulated the relative abundances of 12 genera including Turicibacter, Prevotella, Mitsuokella, Anaerovibrio, Megasphaera, Succinivibrio, Sutterella, Desulfovibrio, and Methanobrevibacter (p < 0.05); up-regulated the abundances of Ruminococcaceae, Lactobacillus, and Muribaculaceae in the colon (p < 0.05); and augmented the mRNA level and concentration of porcine β-defensin 2 in the small intestinal mucosa (p < 0.05). Moreover, Trp-adequate diets increased the abundances of Trp hydroxylase, indoleamine 2,3-dioxygenase, porcine β-defensin 2, phosphorylated mammalian target of rapamycin, and phosphorylated protein kinase B in the small intestinal mucosa (p < 0.05). We noted that a corn and soybean meal-based diet with 0.35% Trp may be a nutritional strategy to improve growth performance, intestinal mucosal barrier integrity, and intestinal microbial ecology in weaned piglets.}, }
@article {pmid33797563, year = {2022}, author = {Frankel-Bricker, J and Frankel, LK}, title = {Re-Analysis of 16S rRNA Gene Sequence Data Sets Uncovers Disparate Laboratory-Specific Microbiomes Associated with the Yellow Fever Mosquito (Aedes aegypti).}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {167-181}, pmid = {33797563}, issn = {1432-184X}, mesh = {*Aedes/microbiology ; Animals ; Female ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Host-microbiome dynamics occurring in the yellow fever mosquito (Aedes aegypti) contribute to host life history traits, and particular bacterial taxa are proposed to comprise a "core" microbiota that influences host physiology. Laboratory-based studies are frequently performed to investigate these processes; however, experimental results are often presumed to be generalizable across laboratories, and few efforts have been made to independently reproduce and replicate significant findings. A recent study by Muturi et al. (FEMS Microbiol Ecol 95 (1):213, 2019) demonstrated the food source imbibed by laboratory-reared adult female mosquitoes significantly impacted the host-associated microbiota-a foundational finding in the field of mosquito biology worthy of independent evaluation. Here, we coalesce these data with two additional mosquito-derived 16S rRNA gene sequence data sets using a unifying bioinformatics pipeline to reproduce the characterization of these microbiota, test for a significant food source effect when independent samples were added to the analyses, assess whether similarly fed mosquito microbiomes were comparable across laboratories, and identify conserved bacterial taxa. Our pipeline characterized similar microbiome composition and structure from the data published previously, and a significant food source effect was detected with the addition of independent samples, increasing the robustness of this previously discovered component of mosquito biology. However, distinct microbial communities were identified from similarly fed but independently reared mosquitoes, and surveys across all samples did not identify conserved bacterial taxa. These findings demonstrated that while the main effect of the food source was supported, laboratory-specific conditions may produce inherently differential microbiomes across independent laboratory environments.}, }
@article {pmid33792742, year = {2022}, author = {Xu, Q and Ling, N and Quaiser, A and Guo, J and Ruan, J and Guo, S and Shen, Q and Vandenkoornhuyse, P}, title = {Rare Bacteria Assembly in Soils Is Mainly Driven by Deterministic Processes.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {137-150}, pmid = {33792742}, issn = {1432-184X}, support = {2016YFD0200900//National Key Research and Development Program of China/ ; }, mesh = {Bacteria/genetics ; China ; *Soil ; *Soil Microbiology ; }, abstract = {Rare species are crucial components of the highly diverse soil microbial pool and over-proportionally contribute to the soil functions. However, much remains unknown about their assembling rules. The biogeographic patterns and species aggregations of the rare bacterial biosphere were assessed using 140 soil samples from a gradient of 2000 km across the main tea-producing areas in China. About 96% OTUs with ~40% sequences were classified as rare taxa. The rare bacterial communities were significantly affected by geographical regions and showed distance-decay effects, indicating that the rare bacteria are not cosmopolitan, they displayed a pattern of limited dispersal and were restricted to certain sites. Variation partitioning analysis (VPA) revealed that environmental variation and spatial factors explained 12.5% and 6.4%, respectively, of the variance in rare bacterial community. The Mantel and partial Mantel tests also showed that the environmental factors had stronger (~3 times) impacts than spatial factors. The null model showed that deterministic processes contributed more than stochastic processes in rare bacterial assembly (75% vs. 25%). There is likely an enrichment in ecological functions within the rare biosphere, considering this high contribution of deterministic processes in the assembly. In addition, the assembly of rare taxa was found to be mainly driven by soil pH. Overall, this study revealed that rare bacteria were not cosmopolitan, and their assembly was more driven by deterministic processes. These findings provided a new comprehensive understanding of rare bacterial biogeographic patterns and assembly rules.}, }
@article {pmid33790426, year = {2021}, author = {Hanson, BT and Dimitri Kits, K and Löffler, J and Burrichter, AG and Fiedler, A and Denger, K and Frommeyer, B and Herbold, CW and Rattei, T and Karcher, N and Segata, N and Schleheck, D and Loy, A}, title = {Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut.}, journal = {The ISME journal}, volume = {15}, number = {9}, pages = {2779-2791}, pmid = {33790426}, issn = {1751-7370}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; I 2320/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/genetics ; Feces ; Humans ; *Hydrogen Sulfide ; Methylglucosides ; Nutrients ; }, abstract = {Responses of the microbiota to diet are highly personalized but mechanistically not well understood because many metabolic capabilities and interactions of human gut microorganisms are unknown. Here we show that sulfoquinovose (SQ), a sulfonated monosaccharide omnipresent in green vegetables, is a selective yet relevant substrate for few but ubiquitous bacteria in the human gut. In human feces and in defined co-culture, Eubacterium rectale and Bilophila wadsworthia used recently identified pathways to cooperatively catabolize SQ with 2,3-dihydroxypropane-1-sulfonate as a transient intermediate to hydrogen sulfide (H2S), a key intestinal metabolite with disparate effects on host health. SQ-degradation capability is encoded in almost half of E. rectale genomes but otherwise sparsely distributed among microbial species in the human intestine. However, re-analysis of fecal metatranscriptome datasets of four human cohorts showed that SQ degradation (mostly from E. rectale and Faecalibacterium prausnitzii) and H2S production (mostly from B. wadsworthia) pathways were expressed abundantly across various health states, demonstrating that these microbial functions are core attributes of the human gut. The discovery of green-diet-derived SQ as an exclusive microbial nutrient and an additional source of H2S in the human gut highlights the role of individual dietary compounds and organosulfur metabolism on microbial activity and has implications for precision editing of the gut microbiota by dietary and prebiotic interventions.}, }
@article {pmid33783701, year = {2021}, author = {Muñoz-Palazon, B and Rodriguez-Sanchez, A and Hurtado-Martinez, M and Gonzalez-Lopez, J and Vahala, R and Gonzalez-Martinez, A}, title = {Evaluating the nitrogen-contaminated groundwater treatment by a denitrifying granular sludge bioreactor: effect of organic matter loading.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {30}, pages = {41351-41364}, pmid = {33783701}, issn = {1614-7499}, mesh = {Bioreactors ; Denitrification ; *Groundwater ; Nitrogen/analysis ; *Sewage ; }, abstract = {A sequential bed granular bioreactor was adapted to treat nitrate-polluted synthetic groundwater under anaerobic conditions and agitation with denitrification gas, achieving very efficient performance in total nitrogen removal at influent organic carbon concentrations of 1 g L[-1] (80-90%) and 0.5 g L[-1] (70-80%) sodium acetate, but concentrations below 0.5 g L[-1] caused accumulation of nitrite and nitrate and led to system failure (30-40% removal). Biomass size and settling velocity were higher above 0.5 g L[-1] sodium acetate. Trichosporonaceae dominated the fungal populations at all times, while a dominance of terrestrial group Thaumarchaeota and Acidovorax at 1 and 0.5 g L[-1] passed to a domination of Methanobrevibacter and an unclassified Comamonadaceae clone for NaAc lower than 0.5 g L[-1]. The results obtained pointed out that the denitrifying granular sludge technology is a feasible solution for the treatment of nitrogen-contaminated groundwater, and that influent organic matter plays an important role on the conformation of microbial communities within it and, therefore, on the overall efficiency of the system.}, }
@article {pmid33782710, year = {2022}, author = {Khan, S and Hill, JE}, title = {Population Density Affects the Outcome of Competition in Co-cultures of Gardnerella Species Isolated from the Human Vaginal Microbiome.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {236-245}, pmid = {33782710}, issn = {1432-184X}, mesh = {Coculture Techniques ; Female ; Gardnerella/genetics ; Humans ; *Microbiota ; Population Density ; RNA, Ribosomal, 16S/genetics ; Vagina ; }, abstract = {Negative frequency-dependent selection is one possible mechanism for maintenance of rare species in communities, but the selective advantage of rare species may be checked at lower overall population densities where resources are abundant. Gardnerella spp. belonging to cpn60 subgroup D, are detected at low levels in vaginal microbiomes and are nutritional generalists relative to other more abundant Gardnerella spp., making them good candidates for negative frequency-dependent selection. The vaginal microbiome is a dynamic environment, and the resulting changes in density of the microbiota may explain why subgroup D never gains dominance. To test this, we co-cultured subgroup D isolates with isolates from the more common and abundant subgroup C. Deep amplicon sequencing of rpoB was used to determine proportional abundance of each isolate at 0 h and 72 h in 152 co-cultures and to calculate change in proportion. D isolates had a positive change in proportional abundance in most co-cultures regardless of initial proportion. Initial density affected the change in proportion of subgroup D isolates either positively or negatively depending on the particular isolates combined, suggesting that growth rate, population density and other intrinsic features of the isolates influenced the outcome. Our results demonstrate that population density is an important factor influencing the outcome of competition between Gardnerella spp. isolated from the human vaginal microbiome.}, }
@article {pmid33782568, year = {2021}, author = {Scoma, A}, title = {Functional groups in microbial ecology: updated definitions of piezophiles as suggested by hydrostatic pressure dependence on temperature.}, journal = {The ISME journal}, volume = {15}, number = {7}, pages = {1871-1878}, pmid = {33782568}, issn = {1751-7370}, mesh = {*Hydrostatic Pressure ; Temperature ; }, }
@article {pmid33777336, year = {2021}, author = {Gutiérrez-Chávez, C and Benaud, N and Ferrari, BC}, title = {The ecological roles of microbial lipopeptides: Where are we going?.}, journal = {Computational and structural biotechnology journal}, volume = {19}, number = {}, pages = {1400-1413}, pmid = {33777336}, issn = {2001-0370}, abstract = {Lipopeptides (LPs) are secondary metabolites produced by a diversity of bacteria and fungi. Their unique chemical structure comprises both a peptide and a lipid moiety. LPs are of major biotechnological interest owing to their emulsification, antitumor, immunomodulatory, and antimicrobial activities. To date, these versatile compounds have been applied across multiple industries, from pharmaceuticals through to food processing, cosmetics, agriculture, heavy metal, and hydrocarbon bioremediation. The variety of LP structures and the diversity of the environments from which LP-producing microorganisms have been isolated suggest important functions in their natural environment. However, our understanding of the ecological role of LPs is limited. In this review, the mode of action and the role of LPs in motility, antimicrobial activity, heavy metals removal and biofilm formation are addressed. We include discussion on the need to characterise LPs from a diversity of microorganisms, with a focus on taxa inhabiting 'extreme' environments. We introduce the use of computational target fishing and molecular dynamics simulations as powerful tools to investigate the process of interaction between LPs and cell membranes. Together, these advances will provide new understanding of the mechanism of action of novel LPs, providing greater insights into the roles of LPs in the natural environment.}, }
@article {pmid33777079, year = {2021}, author = {Stice, SP and Shin, GY and De Armas, S and Koirala, S and Galván, GA and Siri, MI and Severns, PM and Coutinho, T and Dutta, B and Kvitko, BH}, title = {The Distribution of Onion Virulence Gene Clusters Among Pantoea spp.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {643787}, pmid = {33777079}, issn = {1664-462X}, abstract = {Pantoea ananatis is a gram-negative bacterium and the primary causal agent of center rot of onions in Georgia. Previous genomic studies identified two virulence gene clusters, HiVir and alt, associated with center rot. The HiVir gene cluster is required to induce necrosis on onion tissues via synthesis of pantaphos, (2-hydroxy[phosphono-methyl)maleate), a phosphonate phytotoxin. The alt gene cluster aids in tolerance to thiosulfinates generated during onion tissue damage. Whole genome sequencing of other Pantoea species suggests that these gene clusters are present outside of P. ananatis. To assess the distribution of these gene clusters, two PCR primer sets were designed to detect the presence of HiVir and alt. Two hundred fifty-two strains of Pantoea spp. were phenotyped using the red onion scale necrosis (RSN) assay and were genotyped using PCR for the presence of these virulence genes. A diverse panel of strains from three distinct culture collections comprised of 24 Pantoea species, 41 isolation sources, and 23 countries, collected from 1946-2019, was tested. There is a significant association between the alt PCR assay and Pantoea strains recovered from symptomatic onion (P < 0.001). There is also a significant association of a positive HiVir PCR and RSN assay among P. ananatis strains but not among Pantoea spp., congeners. This may indicate a divergent HiVir cluster or different pathogenicity and virulence mechanisms. Last, we describe natural alt positive [RSN[+]/HiVir[+]/alt [+]] P. ananatis strains, which cause extensive bulb necrosis in a neck-to-bulb infection assay compared to alt negative [RSN[+]/HiVir[+]/alt [-]] P. ananatis strains. A combination of assays that include PCR of virulence genes [HiVir and alt] and an RSN assay can potentially aid in identification of onion-bulb-rotting pathogenic P. ananatis strains.}, }
@article {pmid33776147, year = {2021}, author = {Nakato, GV and Studholme, DJ and Blomme, G and Grant, M and Coutinho, TA and Were, EM and Wicker, E and Mahuku, G}, title = {SNP-based genotyping and whole-genome sequencing reveal previously unknown genetic diversity in Xanthomonas vasicola pv. musacearum, causal agent of banana xanthomonas wilt, in its presumed Ethiopian origin.}, journal = {Plant pathology}, volume = {70}, number = {3}, pages = {534-543}, pmid = {33776147}, issn = {0032-0862}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {For decades, Xanthomonas vasicola pv. musacearum (Xvm) has been an economically important bacterial pathogen on enset in Ethiopia. Since 2001, Xvm has also been responsible for significant losses to banana crops in several East and Central African countries, with devastating consequences for smallholder farmers. Understanding the genetic diversity within Xvm populations is essential for the smart design of transnationally reasoned, durable, and effective management practices. Previous studies have revealed limited genetic diversity in Xvm, with East African isolates from banana each falling into one of two closely related clades previously designated as sublineages SL 1 and SL 2, the former of which had also been detected on banana and enset in Ethiopia. Given the presumed origin of Xvm in Ethiopia, we hypothesized that both clades might be found in that country, along with additional genotypes not seen in Central and East African bananas. Genotyping of 97 isolates and whole-genome sequencing of 15 isolates revealed not only the presence of SL 2 in Ethiopia, but additional diversity beyond SL 1 and SL 2 in four new clades. Moreover, SL 2 was detected in the Democratic Republic of Congo, where previously SL 1 was the only clade reported. These results demonstrate a greater range of genetic diversity among Xvm isolates than previously reported, especially in Ethiopia, and further support the hypothesis that the East/Central Africa xanthomonas wilt epidemic has been caused by a restricted set of genotypes drawn from a highly diverse pathogen pool in Ethiopia.}, }
@article {pmid33774510, year = {2021}, author = {Jungreis, I and Nelson, CW and Ardern, Z and Finkel, Y and Krogan, NJ and Sato, K and Ziebuhr, J and Stern-Ginossar, N and Pavesi, A and Firth, AE and Gorbalenya, AE and Kellis, M}, title = {Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution.}, journal = {Virology}, volume = {558}, number = {}, pages = {145-151}, pmid = {33774510}, issn = {1096-0341}, support = {R01 HG004037/HG/NHGRI NIH HHS/United States ; U41 HG007234/HG/NHGRI NIH HHS/United States ; }, mesh = {*Open Reading Frames ; SARS-CoV-2/*genetics/immunology ; *Spike Glycoprotein, Coronavirus/classification/genetics ; *Terminology as Topic ; }, abstract = {At least six small alternative-frame open reading frames (ORFs) overlapping well-characterized SARS-CoV-2 genes have been hypothesized to encode accessory proteins. Researchers have used different names for the same ORF or the same name for different ORFs, resulting in erroneous homological and functional inferences. We propose standard names for these ORFs and their shorter isoforms, developed in consultation with the Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. We recommend calling the 39 codon Spike-overlapping ORF ORF2b; the 41, 57, and 22 codon ORF3a-overlapping ORFs ORF3c, ORF3d, and ORF3b; the 33 codon ORF3d isoform ORF3d-2; and the 97 and 73 codon Nucleocapsid-overlapping ORFs ORF9b and ORF9c. Finally, we document conflicting usage of the name ORF3b in 32 studies, and consequent erroneous inferences, stressing the importance of reserving identical names for homologs. We recommend that authors referring to these ORFs provide lengths and coordinates to minimize ambiguity caused by prior usage of alternative names.}, }
@article {pmid33773678, year = {2021}, author = {Van Hecke, T and Vossen, E and Goethals, S and Boon, N and De Vrieze, J and De Smet, S}, title = {In vitro and in vivo digestion of red cured cooked meat: oxidation, intestinal microbiota and fecal metabolites.}, journal = {Food research international (Ottawa, Ont.)}, volume = {142}, number = {}, pages = {110203}, doi = {10.1016/j.foodres.2021.110203}, pmid = {33773678}, issn = {1873-7145}, mesh = {Animals ; Cattle ; Cooking ; Digestion ; *Gastrointestinal Microbiome ; Meat/analysis ; Rats ; *Red Meat/analysis ; }, abstract = {Mechanisms explaining epidemiological associations between red (processed) meat consumption and chronic disease risk are not yet elucidated, but may involve oxidative reactions, microbial composition alterations, inflammation and/or the formation of toxic bacterial metabolites. First, in vitro gastrointestinal digestion of 23 cooked beef-lard minces, to which varying doses of nitrite salt (range 0-40 g/kg) and sodium ascorbate (range 0-2 g/kg) were added, showed that nitrite salt decreased protein carbonylation up to 3-fold, and inhibited lipid oxidation, demonstrated by up to 4-fold lower levels of 'thiobarbituric acid reactive substances', 32-fold lower 4-hydroxynonenal, and 21-fold lower hexanal values. The use of ascorbate increased the antioxidant effect of low nitrite salt levels, whereas it slightly increased protein carbonylation at higher doses of nitrite salt. The addition of a low dose of ascorbate without nitrite salt slightly promoted oxidation during digestion, whereas higher doses had varying antioxidant effects. Second, 40 rats were fed a diet of cooked chicken- or beef-lard minces, either or not cured, for three weeks. Beef, compared to chicken, consumption increased lipid oxidation (2- to 4-fold) during digestion, and gut protein fermentation (cecal iso-butyrate, (iso-)valerate, and fecal indole, cresol), but oxidative stress and inflammation were generally not affected. Cured, compared to fresh, meat consumption significantly increased stomach protein carbonylation (+16%), colonic Ruminococcaceae (2.1-fold) and cecal propionate (+18%), whereas it decreased cecal butyrate (-25%), fecal phenol (-69%) and dimethyl disulfide (-61%) levels. Fecal acetaldehyde and diacetyl levels were increased in beef-fed rats by 2.8-fold and 5.9-fold respectively, and fecal carbon disulfide was 4-fold higher in rats consuming cured beef vs. fresh chicken. Given their known toxicity, the role of acetaldehyde and carbon disulfide in the relation between meat consumption and health should be investigated in future studies.}, }
@article {pmid33772660, year = {2021}, author = {El Alaoui, A and Raklami, A and Bechtaoui, N and El Gharmali, A and Ouhammou, A and Imziln, B and Achouak, W and Pajuelo, E and Oufdou, K}, title = {Use of native plants and their associated bacteria rhizobiomes to remediate-restore Draa Sfar and Kettara mining sites, Morocco.}, journal = {Environmental monitoring and assessment}, volume = {193}, number = {4}, pages = {232}, doi = {10.1007/s10661-021-08977-4}, pmid = {33772660}, issn = {1573-2959}, mesh = {Bacteria ; Biodegradation, Environmental ; Environmental Monitoring ; *Metals, Heavy/analysis ; Morocco ; Plant Roots/chemistry ; Soil ; *Soil Pollutants/analysis ; }, abstract = {Soil and mine tailings are unreceptive to plant growth representing an imminent threat to the environment and resource sustainability. Using indigenous plants and their associated rhizobacteria to restore mining sites would be an eco-friendly solution to mitigate soil-metal toxicity. Soil prospection from Draa Sfar and Kettara mining sites in Morocco was carried out during different seasons for native plant sampling and rhizobacteria screening. The sites have been colonized by fifteen tolerant plant species having different capacities to accumulate Cu, Zn, and P in their shoots/root systems. In Draa Sfar mine, Suaeda vera J.F. Gmel., Sarcocornia fruticosa (L.) A.J. Scott., and Frankenia corymbosa Desf. accumulated mainly Cu (more than 90 mg kg[-1]), Atriplex halimus L. accumulated Zn (mg kg[-1]), and Frankenia corymbosa Desf. accumulated Pb (14 mg kg[-1]). As for Kettara mine, Aizoon canariense L. mainly accumulated Zn (270 mg kg[-1]), whereas Forsskalea tenacissima L. was the best shoot Cu accumulator with up to 50 mg kg[-1], whereas Cu accumulation in roots was 21 mg kg[-1]. The bacterial screening revealed the strains' abilities to tolerate heavy metals up to 50 mg kg[-1] Cu, 250 mg kg[-1] Pb, and 150 mg kg[-1] Zn. Isolated strains belonged mainly to Bacillaceae (73.33%) and Pseudomonadaceae (10%) and expressed different plant growth-promoting traits, alongside their antifungal activity. Results from this study will provide an insight into the ability of native plants and their associated rhizobacteria to serve as a basis for remediation-restoration strategies.}, }
@article {pmid33771785, year = {2021}, author = {Andreo-Jimenez, B and Schilder, MT and Nijhuis, EH and Te Beest, DE and Bloem, J and Visser, JHM and van Os, G and Brolsma, K and de Boer, W and Postma, J}, title = {Chitin- and Keratin-Rich Soil Amendments Suppress Rhizoctonia solani Disease via Changes to the Soil Microbial Community.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {11}, pages = {}, pmid = {33771785}, issn = {1098-5336}, mesh = {Bacterial Physiological Phenomena ; Chitin/*analysis ; Fertilizers/*analysis ; Fungi/physiology ; Keratins/*analysis ; Microbiota/physiology ; Plant Diseases/*prevention &amp; control ; Rhizoctonia/drug effects/*physiology ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Enhancing soil suppressiveness against plant pathogens or pests is a promising alternative strategy to chemical pesticides. Organic amendments have been shown to reduce crop diseases and pests, with chitin products the most efficient against fungal pathogens. To study which characteristics of organic products are correlated with disease suppression, an experiment was designed in which 10 types of organic amendments with different physicochemical properties were tested against the soilborne pathogen Rhizoctonia solani in sugar beet seedlings. Organic amendments rich in keratin or chitin reduced Rhizoctonia solani disease symptoms in sugar beet plants. The bacterial and fungal microbial communities in amended soils were distinct from the microbial communities in nonamended soil, as well as those in soils that received other nonsuppressive treatments. The Rhizoctonia-suppressive amended soils were rich in saprophytic bacteria and fungi that are known for their keratinolytic and chitinolytic properties (i.e., Oxalobacteraceae and Mortierellaceae). The microbial community in keratin- and chitin-amended soils was associated with higher zinc, copper, and selenium, respectively.IMPORTANCE Our results highlight the importance of soil microorganisms in plant disease suppression and the possibility to steer soil microbial community composition by applying organic amendments to the soil.}, }
@article {pmid33771784, year = {2021}, author = {Yang, X and Wang, H and Hrycauk, S and Klassen, MD}, title = {Effects of Peroxyacetic Acid Spray and Storage Temperature on the Microbiota and Sensory Properties of Vacuum-Packed Subprimal Cuts of Meat.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {11}, pages = {}, pmid = {33771784}, issn = {1098-5336}, mesh = {Disinfectants/*pharmacology ; *Food Microbiology ; *Food Packaging/methods ; *Food Storage/methods ; Meat/analysis/*microbiology ; Microbiota/physiology ; Peracetic Acid/*pharmacology ; *Temperature ; Vacuum ; }, abstract = {We investigated the impact of peroxyacetic acid (PAA; 200 ppm) spray on the microbiota and shelf life of commercial, vacuum-packed beef stored at chiller temperatures. Ribeye cuts (n = 147) were collected from a local beef plant on the day of production for two consecutive days, with one set collected at the start of work with the PAA spray nozzles turned off (control) and during routine production with the PAA spray nozzles turned on (PAA) each day. Packs were stored at 4, 2, and -1°C for up to 34, 104, and 180 days and sampled at appropriate intervals for sensory assessment, microbial enumeration, and microbial profiling by 16S rRNA gene amplicon analysis. Treatment with PAA did not affect the initial meat pH, the initial numbers of total aerobes, lactic acid bacteria, or Enterobacteriaceae (P > 0.05) before storage; however, it delayed the onset of spoilage by 7, 21, and 54 days at 4, 2, and -1°C, respectively. Square-root models of the variation of growth rate with temperature indicated lactic acid bacteria grew faster and Enterobacteriaceae grew slower on PAA-treated than on untreated meat. Negative associations between pH and deterioration of meat during storage were observed for PAA-treated meat. During storage, the microbiota were primarily dominated by Carnobacterium and Lactobacillus/Lactococcus on control meat but by Leuconostoc on PAA-treated meat. Serratia, Yersinia, and Clostridium were identified by linear discriminant effect size analysis as biomarkers for control meat; Clostridium was found in high abundance in samples that had the highest spoilage scores.IMPORTANCE The findings of this study show that PAA solutions applied at low concentrations under commercial settings positively modulated the meat microbiota. It did not have bactericidal effects for beef subprimals with very low microbial loads. However, it differentially impacted the members of the microbiota, which resulted in delayed onset of spoilage of vacuum-packed beef subprimal stored at all three temperatures (4, 2, and -1°C). This differential impact could be through one or a combination of the following factors: favoring the growth of lactic acid bacteria, which may in turn exert a competitive exclusion that might be due to production of antimicrobial compounds such as organic acids and bacteriocins; exerting synergistic antimicrobial effects with low temperatures against members of Enterobacteriaceae; and direct or indirect inhibitory effects against members of the clostridia. These findings not only advance our understanding of the microbial ecology of vacuum-packed meat stored at chiller temperatures but also suggest that bacteriostatic concentrations of antimicrobial interventions can be explored for shelf-life extension.}, }
@article {pmid33768626, year = {2021}, author = {Wang, Y and Xue, K}, title = {Linkage between microbial shift and ecosystem functionality.}, journal = {Global change biology}, volume = {27}, number = {14}, pages = {3197-3199}, pmid = {33768626}, issn = {1365-2486}, mesh = {Carbon ; *Ecosystem ; *Permafrost ; }, abstract = {Exploring the linkage between microbial shifts and ecological processes or ecosystem functionality is a central focus in microbial ecology, but faces considerable obstacles, including the gap between DNA-based information and biochemical processes, as well as the asynchronization in microbial taxonomic shifts and their functionality change. Despite these issues, the well-established linkage between functional genes (reflecting genetic potential) and carbon release via laboratory incubation (reflecting field potential) is a good preliminary step that provides clues about the magnitude of in situ permafrost carbon release under permafrost thaw on the basis of microbial functional gene changes.}, }
@article {pmid33766138, year = {2021}, author = {Pascual-García, A}, title = {Phylogenetic Core Groups: a promising concept in search of a consistent methodological framework : Comment to ``A conceptual framework for the phylogenetically-constrained assembly of microbial communities''.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {73}, pmid = {33766138}, issn = {2049-2618}, mesh = {*Microbiota/genetics ; Phylogeny ; }, abstract = {In this comment, we analyse the conceptual framework proposed by Aguirre de Cárcer (Microbiome 7:142, 2019), introducing the novel concept of Phylogenetic Core Groups (PCGs). This notion aims to complement the traditional classification in operational taxonomic units (OTUs), widely used in microbial ecology, to provide a more intrinsic taxonomical classification which avoids the use of pre-determined thresholds. However, to introduce this concept, the author frames his proposal in a wider theoretical framework based on a conceptualization of selection that we argue is a tautology. This blurs the subsequent formulation of an assembly principle for microbial communities, favouring that some contradictory examples introduced to support the framework appear aligned in their conclusions. And more importantly, under this framework and its derived methodology, it is not possible to infer PCGs from data in a consistent way. We reanalyse the proposal to identify its logical and methodological flaws and, through the analysis of synthetic scenarios, we propose a number of methodological refinements to contribute towards the determination of PCGs in a consistent way. We hope our analysis will promote the exploration of PCGs as a potentially valuable tool, helping to bridge the gap between environmental conditions and community composition in microbial ecology. Video Abstract.}, }
@article {pmid33758981, year = {2022}, author = {Campos, AB and Cavalcante, LC and de Azevedo, AR and Loiola, M and Silva, AET and Ara, A and Meirelles, PM}, title = {CPR and DPANN Have an Overlooked Role in Corals' Microbial Community Structure.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {252-255}, pmid = {33758981}, issn = {1432-184X}, support = {11268//Minist&#xe9;rio da Ci&#xea;ncia, Tecnologia, Inova&#xe7;&#xf5;es e Comunica&#xe7;&#xf5;es/ ; Serra-1709-17818//Instituto Serrapilheira/ ; 132261/2018-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 88887.301758/2018-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {Animals ; *Anthozoa/microbiology ; Archaea/genetics ; Bacteria/genetics ; *Microbiota ; }, abstract = {Understanding how microbial communities are structured in coral holobionts is important to estimate local and global impacts and provide efficient environment management strategies. Several studies investigated the relationship between corals and their microbial communities, including the environmental drivers of shifts in this relationship, associated with diseases and coral cover loss. However, these studies are often geographically or taxonomically restricted and usually focused on the most abundant microbial groups, neglecting the rare biosphere, including archaea in the group DPANN and the recently discovered bacterial members of the candidate phyla radiation (CPR). Although it is known that rare microbes can play essential roles in several environments, we still lack understanding about which taxa comprise the rare biosphere of corals' microbiome. Here, we investigated the host-related and technical factors influencing coral microbial community structure and the importance of CPR and DPANN in this context by analyzing more than a hundred coral metagenomes from independent studies worldwide. We show that coral genera are the main biotic factor shaping coral microbial communities. We also detected several CPR and DPANN phyla comprising corals' rare biosphere for the first time and showed that they significantly contribute to shaping coral microbial communities.}, }
@article {pmid33758980, year = {2022}, author = {Liu, Y and Xu, L and Zhang, Z and Huang, Z and Fang, D and Zheng, X and Yang, Z and Lu, M}, title = {Isolation, Identification, and Analysis of Potential Functions of Culturable Bacteria Associated with an Invasive Gall Wasp, Leptocybe invasa.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {151-166}, pmid = {33758980}, issn = {1432-184X}, support = {2017YFD0600101//the National Key Research and Development Program/ ; 31870634//National Natural Science Foundation of China/ ; 2018GXNSFDA281004//Key projects of Guangxi Natural Science Foundation/ ; }, mesh = {Animals ; Bacteria/genetics ; *Eucalyptus ; Humans ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Wasps/microbiology ; }, abstract = {Symbioses between invasive insects and bacteria are one of the key drivers of insect invasion success. Gall-inducing insects stimulate host plants to produce galls, which affects the normal growth of plants. Leptocybe invasa Fisher et La Salle, an invasive gall-inducing wasp, mainly damages Eucalyptus plantations in Southern China, but little is known about its associated bacteria. The aim of this study was to assess the diversity of bacterial communities at different developmental stages of L. invasa and to identify possible ecological functions of the associated bacteria. Bacteria associated with L. invasa were isolated using culture-dependent methods and their taxonomic statuses were determined by sequencing the 16S rRNA gene. A total of 88 species belonging to four phyla, 27 families, and 44 genera were identified by phylogenetic analysis. The four phyla were Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes, mainly from the genera Pantoea, Enterobacter, Pseudomonas, Bacillus, Acinetobacter, Curtobacterium, Sphingobium, Klebsiella, and Rhizobium. Among them, 72 species were isolated in the insect gall stage and 46 species were isolated from the adult stage. The most abundant bacterial species were γ-Proteobacteria. We found significant differences in total bacterial counts and community compositions at different developmental stages, and identified possible ecological roles of L. invasa-associated bacteria. This study is the first to systematically investigate the associated bacteria of L. invasa using culture-dependent methods, and provides a reference for other gall-inducing insects and associated bacteria.}, }
@article {pmid33758979, year = {2022}, author = {Norte, AC and Araújo, PM and Augusto, L and Guímaro, H and Santos, S and Lopes, RJ and Núncio, MS and Ramos, JA and Lopes de Carvalho, I}, title = {Effects of stress exposure in captivity on physiology and infection in avian hosts: no evidence of increased Borrelia burgdorferi s.l. infectivity to vector ticks.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {202-215}, pmid = {33758979}, issn = {1432-184X}, support = {MARE - UID/MAR/04292/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BPD/108197/2015//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; DL57/2016/CP1370/CT89//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-EVL/31569/2017 - NORTE -01-0145- FEDER-30288//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; DL57/2016/CP1440/CT0006//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; na//Portuguese National Institute of Health Doutor Ricardo Jorge (PT)/ ; }, mesh = {Animals ; *Borrelia ; *Borrelia burgdorferi ; *Borrelia burgdorferi Group/physiology ; *Ixodes/microbiology ; *Lyme Disease/microbiology/veterinary ; *Songbirds/microbiology ; }, abstract = {Exposure to environmental stressors, an increasingly recurring event in natural communities due to anthropogenic-induced environmental change, profoundly impacts disease emergence and spread. One mechanism through which this occurs is through stress-induced immunosuppression increasing disease susceptibility, prevalence, intensity and reactivation in hosts. We experimentally evaluated how exposure to stressors affected both the physiology of avian hosts and the prevalence of the zoonotic bacteria Borrelia burgdorferi sensu lato (s.l.), in two model species-the blackbird Turdus merula and the robin Erithacus rubecula captured in the wild, using xenodiagnoses and analysis of skin biopsies and blood. Although exposure to stressors in captivity induced physiological stress in birds (increased the number of circulating heterophils), there was no evidence of increased infectivity to xenodiagnostic ticks. However, Borrelia detection in the blood for both experimental groups of blackbirds was higher by the end of the captivity period. The infectivity and efficiency of transmission were higher for blackbirds than robins. When comparing different methodologies to determine infection status, xenodiagnosis was a more sensitive method than skin biopsies and blood samples, which could be attributed to mild levels of infection in these avian hosts and/or dynamics and timing of Borrelia infection relapses and redistribution in tissues.}, }
@article {pmid33758030, year = {2021}, author = {Jiao, S and Peng, Z and Qi, J and Gao, J and Wei, G}, title = {Linking Bacterial-Fungal Relationships to Microbial Diversity and Soil Nutrient Cycling.}, journal = {mSystems}, volume = {6}, number = {2}, pages = {}, pmid = {33758030}, issn = {2379-5077}, abstract = {Biodiversity is important for supporting ecosystem functioning. To evaluate the factors contributing to the strength of microbial diversity-function relationships in complex terrestrial ecosystems, we conducted a soil survey over different habitats, including an agricultural field, forest, wetland, grassland, and desert. Soil microbial multidiversity was estimated by the combination of bacterial and fungal diversity. Soil ecosystem functions were evaluated using a multinutrient cycling index (MNC) in relation to carbon, nitrate, phosphorus, and potassium cycling. Significant positive relationships between soil multidiversity and multinutrient cycling were observed in all habitats, except the grassland and desert. Specifically, community compositions showed stronger correlations with multinutrient cycling than α-diversity, indicating the crucial role of microbial community composition differences on soil nutrient cycling. Importantly, we revealed that changes in both the neutral processes (Sloan neutral modeling) and the proportion of negative bacterial-fungal associations were linked to the magnitude and direction of the diversity-MNC relationships. The habitats less governed by neutral processes and dominated by negative bacterial-fungal associations exhibited stronger negative microbial α-diversity-MNC relationships. Our findings suggested that the balance between positive and negative bacterial-fungal associations was connected to the link between soil biodiversity and ecosystem function in complex terrestrial ecosystems. This study elucidates the potential factors influencing diversity-function relationships, thereby enabling future studies to forecast the effects of belowground biodiversity on ecosystem function.IMPORTANCE The relationships between soil biodiversity and ecosystem functions are an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the factors driving the relationships between microbial diversity and potential soil nutrient cycling in complex terrestrial ecosystems. Our structural equation modeling and random forest analysis revealed that the balance between positive and negative bacterial-fungal associations was clearly linked to the strength of the relationships between soil microbial diversity and multiple nutrients cycling across different habitats. This study revealed the potential factors underpinning diversity-function relationships in terrestrial ecosystems and thus helps us to manage soil microbial communities for better provisioning of key ecosystem services.}, }
@article {pmid33755773, year = {2021}, author = {Gorfer, M and Mayer, M and Berger, H and Rewald, B and Tallian, C and Matthews, B and Sandén, H and Katzensteiner, K and Godbold, DL}, title = {High Fungal Diversity but Low Seasonal Dynamics and Ectomycorrhizal Abundance in a Mountain Beech Forest.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {243-256}, pmid = {33755773}, issn = {1432-184X}, support = {C-Alp I//&#xd6;sterreichischen Akademie der Wissenschaften/ ; C-Alp II//&#xd6;sterreichischen Akademie der Wissenschaften/ ; }, mesh = {*Fagus ; Forests ; Fungi/genetics ; *Mycorrhizae/genetics ; Seasons ; Soil ; Soil Microbiology ; }, abstract = {Forests on steep slopes constitute a significant proportion of European mountain areas and are important as production and protection forests. This study describes the soil fungal community structure in a European beech-dominated mountain forest stands in the Northern Calcareous Alps and investigates how it is determined by season and soil properties. Samples were collected at high spatial resolution in an area of ca. 100 m × 700 m in May (spring) and August (summer). Illumina MiSeq high-throughput sequencing of the ITS2-region revealed distinct patterns for the soil fungal communities. In contrast to other studies from temperate European beech forest stands, Ascomycota dominated the highly diverse fungal community, while ectomycorrhizal fungi were of lower abundance. Russulaceae, which are often among the dominant ectomycorrhizal fungi associated with European beech, were absent from all samples. Potentially plant pathogenic fungi were more prevalent than previously reported. Only subtle seasonal differences were found between fungal communities in spring and summer. Especially, dominant saprotrophic taxa were largely unaffected by season, while slightly stronger effects were observed for ectomycorrhizal fungi. Soil characteristics like pH and organic carbon content, on the other hand, strongly shaped abundant taxa among the saprotrophic fungal community.}, }
@article {pmid33752014, year = {2021}, author = {Aponte, H and Mondaca, P and Santander, C and Meier, S and Paolini, J and Butler, B and Rojas, C and Diez, MC and Cornejo, P}, title = {Enzyme activities and microbial functional diversity in metal(loid) contaminated soils near to a copper smelter.}, journal = {The Science of the total environment}, volume = {779}, number = {}, pages = {146423}, doi = {10.1016/j.scitotenv.2021.146423}, pmid = {33752014}, issn = {1879-1026}, mesh = {Copper/analysis ; Environmental Monitoring ; Environmental Pollution ; Metals/analysis ; *Metals, Heavy/analysis ; Soil ; *Soil Pollutants/analysis ; }, abstract = {The monitoring of soil metal(loid) contamination is of global significance due to deleterious effects that metal(loid)s have on living organisms. Soil biological properties such as enzyme activities (EAs) are good indicators of metal(loid) contamination due to their high sensitivity, fast response, and low-cost. Here, the effect of metal(loid) contamination on physicochemical properties and microbial functionality in soils sampled from within 10 km of a Cu smelter is investigated. Soil composite samples were randomly taken within 2, 4, 6, 8 and10 km zones from a mining industry Cu smelter. The EAs of dehydrogenase (DHA), arylsulfatase (ARY), β-glucosidase, urease, and arginine ammonification (AA) were studied as indicators of metal(loid) contamination, which included the ecological dose (ED50) with respect to Cu and As contents. The community level physiological profile (CLPP), functional diversity, and catabolic evenness were evaluated based on the C-substrate utilisation. All EAs decreased in zones with high degrees of metal(loid) contamination, which also had low TOC and clay contents, reflecting long term processes of soil degradation. Positive and strong relationships between EAs and TOC were found. DHA and ARY activities decreased by approximately 85-90% in highly metal(loid) contaminated soils. DHA and AA showed significant ED50 values associated with available Cu (112.8 and 121.6 mg CuDTPA kg[-1], respectively) and total As contents (30.8 and 31.8 mg As kg[-1], respectively). The CLPP showed different metabolic profiles along the metal(loid) contamination gradients. Long-term stress conditions in soils close to industrial areas resulted in the decreasing of general biological activity, catabolic capacity, and functional diversity.}, }
@article {pmid33751575, year = {2021}, author = {Matysik, S and Krautbauer, S and Liebisch, G and Schött, HF and Kjølbaek, L and Astrup, A and Blachier, F and Beaumont, M and Nieuwdorp, M and Hartstra, A and Rampelli, S and Pagotto, U and Iozzo, P}, title = {Short-chain fatty acids and bile acids in human faeces are associated with the intestinal cholesterol conversion status.}, journal = {British journal of pharmacology}, volume = {178}, number = {16}, pages = {3342-3353}, doi = {10.1111/bph.15440}, pmid = {33751575}, issn = {1476-5381}, mesh = {*Bile Acids and Salts ; Cholesterol ; Chromatography, Liquid ; Fatty Acids, Volatile ; Feces ; Humans ; *Tandem Mass Spectrometry ; }, abstract = {BACKGROUND AND PURPOSE: The analysis of human faecal metabolites can provide an insight into metabolic interactions between gut microbiota and the host organism. The creation of metabolic profiles in faeces has received little attention until now, and reference values, especially in the context of dietary and therapeutic interventions, are missing. Exposure to xenobiotics significantly affects the physiology of the microbiome, and microbiota manipulation and short-chain fatty acid administration have been proposed as treatment targets for several diseases. The aim of the present study is to give concomitant concentration ranges of faecal sterol species, bile acids and short-chain fatty acids, based on a large cohort.<br><br>EXPERIMENTAL APPROACH: Sterol species, bile acids and short-chain fatty acids in human faeces from 165 study participants were quantified by LC-MS/MS. For standardization, we refer all values to dry weight of faeces. Based on the individual intestinal sterol conversion, we classified participants into low and high converters according to their coprostanol/cholesterol ratio.<br><br>KEY RESULTS: Low converters excrete more straight-chain fatty acids and bile acids than high converters; 5th and 95th percentile and median of bile acids and short-chain fatty acids were calculated for both groups.<br><br>CONCLUSION AND IMPLICATIONS: We give concentration ranges for 16 faecal metabolites that can serve as reference values. Patient stratification into high or low sterol converter groups is associated with significant differences in faecal metabolites with biological activities. Such stratification should then allow better assessment of faecal metabolites before therapeutic interventions.<br><br>LINKED ARTICLES: This article is part of a themed issue on Oxysterols, Lifelong Health and Therapeutics. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v178.16/issuetoc.}, }
@article {pmid33751165, year = {2022}, author = {Foley, KM and Beard, KH and Atwood, TB and Waring, BG}, title = {Herbivory changes soil microbial communities and greenhouse gas fluxes in a high-latitude wetland.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {127-136}, pmid = {33751165}, issn = {1432-184X}, support = {ARC-1304523//National Science Foundation/ ; ARCCS-1932889//NSF/ ; }, mesh = {Carbon Dioxide/analysis ; *Greenhouse Gases ; Herbivory ; Methane/analysis ; *Microbiota ; Nitrous Oxide ; Soil/chemistry ; Wetlands ; }, abstract = {Herbivory can have strong impacts on greenhouse gas fluxes in high-latitude ecosystems. For example, in the Yukon-Kuskokwim (Y-K) Delta in western Alaska, migratory goose grazing affects the magnitude of soil carbon dioxide (CO2) and methane (CH4) fluxes. However, the underlying drivers of this relationship are unclear, as few studies systematically tease apart the processes by which herbivores influences soil biogeochemistry. To examine these mechanisms in detail, we conducted a laboratory incubation experiment to quantify changes in greenhouse gas fluxes in response to three parameters altered by herbivores in situ: temperature, soil moisture content, and nutrient inputs. These treatments were applied to soils collected in grazing lawns and nearby ungrazed habitat, allowing us to assess how variation in microbial community structure influenced observed responses. We found pronounced differences in both fungal and prokaryotic community composition between grazed and ungrazed areas. In the laboratory incubation experiment, CO2 and CH4 fluxes increased with temperature, soil moisture, and goose fecal addition, suggesting that grazing-related changes in the soil abiotic environment may enhance soil C losses. Yet, these abiotic drivers were insufficient to explain variation in fluxes between soils with and without prior grazing. Differences in trace gas fluxes between grazed and ungrazed areas may result both from herbivore-induced shifts in abiotic parameters and grazing-related alterations in microbial community structure. Our findings suggest that relationships among herbivores and soil microbial communities could mediate carbon-climate feedbacks in rapidly changing high-latitude ecosystems.}, }
@article {pmid33750865, year = {2021}, author = {Wang, S and Tang, W and Delage, E and Gifford, S and Whitby, H and González, AG and Eveillard, D and Planquette, H and Cassar, N}, title = {Investigating the microbial ecology of coastal hotspots of marine nitrogen fixation in the western North Atlantic.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {5508}, pmid = {33750865}, issn = {2045-2322}, abstract = {Variation in the microbial cycling of nutrients and carbon in the ocean is an emergent property of complex planktonic communities. While recent findings have considerably expanded our understanding of the diversity and distribution of nitrogen (N2) fixing marine diazotrophs, knowledge gaps remain regarding ecological interactions between diazotrophs and other community members. Using quantitative 16S and 18S V4 rDNA amplicon sequencing, we surveyed eukaryotic and prokaryotic microbial communities from samples collected in August 2016 and 2017 across the Western North Atlantic. Leveraging and significantly expanding an earlier published 2015 molecular dataset, we examined microbial community structure and ecological co-occurrence relationships associated with intense hotspots of N2 fixation previously reported at sites off the Southern New England Shelf and Mid-Atlantic Bight. Overall, we observed a negative relationship between eukaryotic diversity and both N2 fixation and net community production (NCP). Maximum N2 fixation rates occurred at sites with high abundances of mixotrophic stramenopiles, notably Chrysophyceae. Network analysis revealed such stramenopiles to be keystone taxa alongside the haptophyte diazotroph host Braarudosphaera bigelowii and chlorophytes. Our findings highlight an intriguing relationship between marine stramenopiles and high N2 fixation coastal sites.}, }
@article {pmid33745062, year = {2022}, author = {Glaeser, SP and Silva, LMR and Prieto, R and Silva, MA and Franco, A and Kämpfer, P and Hermosilla, C and Taubert, A and Eisenberg, T}, title = {A Preliminary Comparison on Faecal Microbiomes of Free-Ranging Large Baleen (Balaenoptera musculus, B. physalus, B. borealis) and Toothed (Physeter macrocephalus) Whales.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {18-33}, pmid = {33745062}, issn = {1432-184X}, mesh = {Animals ; *Balaenoptera ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sperm Whale/microbiology ; }, abstract = {Large baleen and toothed whales play crucial ecological roles in oceans; nonetheless, very little is known about their intestinal microbiomes. Based on striking differences in natural history and thus in feeding behaviours, it can be expected that intestinal microbiomes of large baleen whales and toothed whales are different. To test this hypothesis, the phylogenetic composition of faecal microbiomes was investigated by a 16S rRNA gene amplicon sequence-based approach for Bacteria and Archaea. Faecal samples from free-ranging large whales collected off the Azores Archipelago (Portugal) were used, comprising 13 individual baleen whales (one sei, two blue and ten fin whales) and four sperm whales. The phylogenetic composition of the Bacteria faecal microbiomes of baleen and toothed whales showed no significant differences at the phylum level. However, significant differences were detected at the family and genus levels. Most abundant phyla were Firmicutes, Bacteroidetes, Proteobacteria, Tenericutes and Spirochaeta. Few highly abundant bacterial genera were identified as key taxa with a high contribution to differences among baleen and toothed whales microbiomes. Only few archaeal sequences were detected, primarily Methanomassiliicoccales representing potential methanogenic Archaea. This is the first study that directly compares the faecal bacterial and archaeal microbiomes of free-ranging baleen and toothed whales which represent the two parvorders of Cetacea which members are fully aquatic large mammals which were evolutionary split millions of years ago.}, }
@article {pmid33743015, year = {2022}, author = {Xu, MP and Wang, JY and Zhu, YF and Han, XH and Ren, CJ and Yang, GH}, title = {Plant Biomass and Soil Nutrients Mainly Explain the Variation of Soil Microbial Communities During Secondary Succession on the Loess Plateau.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {114-126}, pmid = {33743015}, issn = {1432-184X}, support = {2020132111//Forest and Grass Technology Innovation Development and Research Project of the State Forestry and Grassland Administration/ ; 2018JZ4002//Key project of Shaanxi Provincial Natural Science Foundation/ ; 2019HBGC-13//Shaanxi Engineering Research Center of Circular Agriculture/ ; }, mesh = {Biomass ; China ; *Microbiota ; Nutrients ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {Soil microorganisms play an important role in the circulation of materials and nutrients between plants and soil ecosystems, but the drivers of microbial community composition and diversity remain uncertain in different vegetation restoration patterns. We studied soil physicochemical properties (i.e., soil moisture, bulk density, pH, soil nutrients, available nutrients), plant characteristics (i.e., Shannon index [HPlant] and Richness index [SPlant], litter biomass [LB], and fine root biomass [FRB]), and microbial variables (biomass, enzyme activity, diversity, and composition of bacterial and fungal communities) in different plant succession patterns (Robinia pseudoacacia [MF], Caragana korshinskii [SF], and grassland [GL]) on the Loess Plateau. The herb communities, soil microbial biomass, and enzyme activities were strongly affected by vegetation restoration, and soil bacterial and fungal communities were significantly different from each other at the sites. Correlation analysis showed that LB and FRB were significantly positively correlated with the Chao index of soil bacteria, soil microbial biomass, enzyme activities, Proteobacteria, Zygomycota, and Cercozoa, while negatively correlated with Actinobacteria and Basidiomycota. In addition, soil water content (SW), pH, and nutrients have important effects on the bacterial and fungal diversities, as well as Acidobacteria, Proteobacteria, Actinobacteria, Nitrospirae, Zygomycota, and microbial biomass. Furthermore, plant characteristics and soil properties modulated the composition and diversity of soil microorganisms, respectively. Overall, the relative contribution of vegetation and soil to the diversity and composition of soil bacterial and fungal communities illustrated that plant characteristics and soil properties may synergistically modulate soil microbial communities, and the composition and diversity of soil bacterial and fungal communities mainly depend on plant biomass and soil nutrients.}, }
@article {pmid33742230, year = {2022}, author = {Tipton, L and Zahn, GL and Darcy, JL and Amend, AS and Hynson, NA}, title = {Hawaiian Fungal Amplicon Sequence Variants Reveal Otherwise Hidden Biogeography.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {48-57}, pmid = {33742230}, issn = {1432-184X}, mesh = {*Ecosystem ; *Fungi/genetics ; Hawaii ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {To study biogeography and other ecological patterns of microorganisms, including fungi, scientists have been using operational taxonomic units (OTUs) as representations of species or species hypotheses. However, when defined by 97% sequence similarity cutoff at an accepted barcode locus such as 16S in bacteria or ITS in fungi, these OTUs can obscure biogeographic patterns, mask taxonomic diversity, and hinder meta-analyses. Amplicon sequence variants (ASVs) have been proposed to alleviate all of these issues and have been shown to do so in bacteria. Analyzing ASVs is just emerging as a common practice among fungal studies, and it is unclear whether the benefits found in bacterial studies of using such an approach carryover to fungi. Here, we conducted a meta-analysis of Hawaiian fungi by analyzing ITS1 amplicon sequencing data as ASVs and exploring ecological patterns. These surveys spanned three island groups and five ecosystems combined into the first comprehensive Hawaiian Mycobiome ASV Database. Our results show that ASVs can be used to combine fungal ITS surveys, increase reproducibility, and maintain the broad ecological patterns observed with OTUs, including diversity orderings. Additionally, the ASVs that comprise some of the most common OTUs in our database reveals some island specialists, indicating that traditional OTU clustering can obscure important biogeographic patterns. We recommend that future fungal studies, especially those aimed at assessing biogeography, analyze ASVs rather than OTUs. We conclude that similar to bacterial studies, ASVs improve reproducibility and data sharing for fungal studies.}, }
@article {pmid33741616, year = {2021}, author = {Zhu, X and Feng, X and Liang, C and Li, J and Jia, J and Feng, L and Tao, Y and Chen, Y}, title = {Microbial Ecological Mechanism for Long-Term Production of High Concentrations of n-Caproate via Lactate-Driven Chain Elongation.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {11}, pages = {}, pmid = {33741616}, issn = {1098-5336}, mesh = {*Bacterial Physiological Phenomena ; Biodegradation, Environmental ; Bioreactors/*microbiology ; Caproates/*metabolism ; Clostridiales/*physiology ; Fermentation ; Lactic Acid/*chemistry ; *Microbiota ; }, abstract = {Lactate-driven chain elongation (LCE) has emerged as a new biotechnology to upgrade organic waste streams into a valuable biochemical and fuel precursor, medium-chain carboxylate, n-caproate. Considering that a low cost of downstream extraction is critical for biorefinery technology, a high concentration of n-caproate production is very important to improve the scale-up of the LCE process. We report here that in a nonsterile open environment, the n-caproate concentration was increased from the previous record of 25.7 g·liter[-1] to a new high level of 33.7 g·liter[-1] (76.8 g chemical oxygen demand [COD]·liter [-][1]), with the highest production rate being 11.5 g·liter[-1]·day[-1] (26.2 g COD·liter [-][1]·day[-1]). In addition, the LCE process remained stable, with an average concentration of n-caproate production of 20.2 ± 5.62 g·liter[-1] (46.1 ± 12.8 g COD·liter [-][1]) for 780 days. Dynamic changes in taxonomic composition integrated with metagenomic data reveal the microbial ecology for long-term production of high concentrations of n-caproate: (i) the core microbiome is related to efficient functional groups, such as Ruminococcaceae (with functional strain CPB6); (ii) the core bacteria can maintain stability for long-term operation; (iii) the microbial network has relatively low microbe-microbe interaction strength; and (iv) low relative abundance and variety of competitors. The network structure could be shaped by hydraulic retention time (HRT) over time, and long-term operation at an HRT of 8 days displayed higher efficacy.IMPORTANCE Our research revealed the microbial network of the LCE reactor microbiome for n-caproate production at high concentrations, which will provide a foundation for designing or engineering the LCE reactor microbiome to recover n-caproate from organic waste streams in the future. In addition, the hypothetical model of the reactor microbiome that we proposed may offer guidance for researchers to find the underlying microbial mechanism when they encounter low-efficiency n-caproate production from the LCE process. We anticipate that our research will rapidly advance LCE biotechnology with the goal of promoting the sustainable development of human society.}, }
@article {pmid33734553, year = {2021}, author = {Ruuskanen, MO and Sommeria-Klein, G and Havulinna, AS and Niiranen, TJ and Lahti, L}, title = {Modelling spatial patterns in host-associated microbial communities.}, journal = {Environmental microbiology}, volume = {23}, number = {5}, pages = {2374-2388}, doi = {10.1111/1462-2920.15462}, pmid = {33734553}, issn = {1462-2920}, mesh = {Ecology ; Humans ; *Microbiota ; }, abstract = {Microbial communities exhibit spatial structure at different scales, due to constant interactions with their environment and dispersal limitation. While this spatial structure is often considered in studies focusing on free-living environmental communities, it has received less attention in the context of host-associated microbial communities or microbiota. The wider adoption of methods accounting for spatial variation in these communities will help to address open questions in basic microbial ecology as well as realize the full potential of microbiome-aided medicine. Here, we first overview known factors affecting the composition of microbiota across diverse host types and at different scales, with a focus on the human gut as one of the most actively studied microbiota. We outline a number of topical open questions in the field related to spatial variation and patterns. We then review the existing methodology for the spatial modelling of microbiota. We suggest that methodology from related fields, such as systems biology and macro-organismal ecology, could be adapted to obtain more accurate models of spatial structure. We further posit that methodological developments in the spatial modelling and analysis of microbiota could in turn broadly benefit theoretical and applied ecology and contribute to the development of novel industrial and clinical applications.}, }
@article {pmid33733305, year = {2022}, author = {da Silva, TH and Câmara, PEAS and Pinto, OHB and Carvalho-Silva, M and Oliveira, FS and Convey, P and Rosa, CA and Rosa, LH}, title = {Diversity of Fungi Present in Permafrost in the South Shetland Islands, Maritime Antarctic.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {58-67}, pmid = {33733305}, issn = {1432-184X}, mesh = {Animals ; Antarctic Regions ; DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; Fungi/genetics ; Humans ; Islands ; *Permafrost ; }, abstract = {We assess the fungal diversity present in permafrost from different islands in the South Shetland Islands archipelago, maritime Antarctic, using next-generation sequencing (NGS). We detected 1,003,637 fungal DNA reads representing, in rank abundance order, the phyla Ascomycota, Mortierellomycota, Basidiomycota, Chytridiomycota, Rozellomycota, Mucoromycota, Calcarisporiellomycota and Zoopagomycota. Ten taxa were dominant these being, in order of abundance, Pseudogymnoascus appendiculatus, Penicillium sp., Pseudogymnoascus roseus, Penicillium herquei, Curvularia lunata, Leotiomycetes sp., Mortierella sp. 1, Mortierella fimbricystis, Fungal sp. 1 and Fungal sp. 2. A further 38 taxa had intermediate abundance and 345 were classified as rare. The total fungal community detected in the permafrost showed high indices of diversity, richness and dominance, although these varied between the sampling locations. The use of a metabarcoding approach revealed the presence of DNA of a complex fungal assemblage in the permafrost of the South Shetland Islands including taxa with a range of ecological functions among which were multiple animal, human and plant pathogenic fungi. Further studies are required to determine whether the taxa identified are present in the form of viable cells or propagules and which might be released from melting permafrost to other Antarctic habitats and potentially dispersed more widely.}, }
@article {pmid33733304, year = {2022}, author = {Yang, H and Hu, C}, title = {Soil Chemistry and Nutrients Influence the Distribution of Aerobic Anoxygenic Phototrophic Bacteria and Eukaryotic Phototrophic Microorganisms of Physical Soil Crusts at Different Elevations on the Tibetan Plateau.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {100-113}, pmid = {33733304}, issn = {1432-184X}, support = {Grant No. XDA17010502//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; No. 31900237//National Natural Science Foundation of China/ ; }, mesh = {Bacteria, Aerobic/genetics ; *Eukaryota ; Nutrients ; *Soil/chemistry ; Soil Microbiology ; Tibet ; }, abstract = {Photosynthetic microorganisms are widely distributed in the soil and play an important role in plant-free soil crusts. However, the distribution and environmental drivers of phototrophic microbial communities in physical soil crusts, where the abundance of cyanobacteria is low, are scarcely understood. Here, we performed high-throughput sequencing of pufM and 18S rRNA genes in soil crusts at different elevations on the Tibetan Plateau and used the data combined with environmental variables to analyze the diversity and structure of phototrophic microbial communities. We found that the dominant taxa of aerobic anoxygenic phototrophic bacteria (AAPB) and eukaryotic phototrophic microorganisms (EPM) were shown to shift with elevation. The phototrophic microbial diversity showed a single-peak pattern, with the lowest diversity of AAPB and highest diversity of EPM at middle elevations. Moreover, the elevation and soil property determined the phototrophic microbial community. Soil salts, especially Cl[-], were the most important for AAPB. Likewise, soil nutrients, especially carbon, were the most important for EPM. The relationship between high-abundance taxa and environmental variables showed that Rhizobiales was significantly negatively correlated with salt ions and positively correlated with chlorophyll. Rhodobacterales showed the strongest and significant positive associations with Cl[-]. Chlorophyceae and Bacillariophyceae were positively correlated with CO3[2-]. These results indicated that salinity and soil nutrients affected the diversity and structure of microbial communities. This study contributes to our understanding of the diversity, composition, and structure of photosynthetic microorganisms in physical soil crusts and helps in developing new approaches for controlling desertification and salinization and improving the desert ecological environment.}, }
@article {pmid33730193, year = {2022}, author = {Vignale, FA and Lencina, AI and Stepanenko, TM and Soria, MN and Saona, LA and Kurth, D and Guzmán, D and Foster, JS and Poiré, DG and Villafañe, PG and Albarracín, VH and Contreras, M and Farías, ME}, title = {Lithifying and Non-Lithifying Microbial Ecosystems in the Wetlands and Salt Flats of the Central Andes.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {1-17}, pmid = {33730193}, issn = {1432-184X}, support = {PICT 2013/0730 and PICT V 2015/3825//CONICET-FONCyT/ ; }, mesh = {Geologic Sediments/chemistry ; Lakes/chemistry ; *Microbiota ; Salinity ; *Wetlands ; }, abstract = {The wetlands and salt flats of the Central Andes region are unique extreme environments as they are located in high-altitude saline deserts, largely influenced by volcanic activity. Environmental factors, such as ultraviolet (UV) radiation, arsenic content, high salinity, low dissolved oxygen content, extreme daily temperature fluctuation, and oligotrophic conditions, resemble the early Earth and potentially extraterrestrial conditions. The discovery of modern microbialites and microbial mats in the Central Andes during the past decade has increased the interest in this area as an early Earth analog. In this work, we review the current state of knowledge of Central Andes region environments found within lakes, small ponds or puquios, and salt flats of Argentina, Chile, and Bolivia, many of them harboring a diverse range of microbial communities that we have termed Andean Microbial Ecosystems (AMEs). We have integrated the data recovered from all the known AMEs and compared their biogeochemistry and microbial diversity to achieve a better understanding of them and, consequently, facilitate their protection.}, }
@article {pmid33727400, year = {2021}, author = {Mujakić, I and Andrei, A&#x15e; and Shabarova, T and Fecskeová, LK and Salcher, MM and Piwosz, K and Ghai, R and Koblížek, M}, title = {Common Presence of Phototrophic Gemmatimonadota in Temperate Freshwater Lakes.}, journal = {mSystems}, volume = {6}, number = {2}, pages = {}, pmid = {33727400}, issn = {2379-5077}, abstract = {Members of the bacterial phylum Gemmatimonadota are ubiquitous in most natural environments and represent one of the top 10 most abundant bacterial phyla in soil. Sequences affiliated with Gemmatimonadota were also reported from diverse aquatic habitats; however, it remains unknown whether they are native organisms or represent bacteria passively transported from sediment or soil. To address this question, we analyzed metagenomes constructed from five freshwater lakes in central Europe. Based on the 16S rRNA gene frequency, Gemmatimonadota represented from 0.02 to 0.6% of all bacteria in the epilimnion and between 0.1 and 1% in the hypolimnion. These proportions were independently confirmed using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Some cells in the epilimnion were attached to diatoms (Fragilaria sp.) or cyanobacteria (Microcystis sp.), which suggests a close association with phytoplankton. In addition, we reconstructed 45 metagenome-assembled genomes (MAGs) related to Gemmatimonadota They represent several novel lineages, which persist in the studied lakes during the seasons. Three lineages contained photosynthesis gene clusters. One of these lineages was related to Gemmatimonas phototrophica and represented the majority of Gemmatimonadota retrieved from the lakes' epilimnion. The other two lineages came from hypolimnion and probably represented novel photoheterotrophic genera. None of these phototrophic MAGs contained genes for carbon fixation. Since most of the identified MAGs were present during the whole year and cells associated with phytoplankton were observed, we conclude that they represent truly limnic Gemmatimonadota distinct from the previously described species isolated from soils or sediments.IMPORTANCE Photoheterotrophic bacterial phyla such as Gemmatimonadota are key components of many natural environments. Its first photoheterotrophic cultured member, Gemmatimonas phototrophica, was isolated in 2014 from a shallow lake in the Gobi Desert. It contains a unique type of photosynthetic complex encoded by a set of genes which were likely received via horizontal transfer from Proteobacteria We were intrigued to discover how widespread this group is in the natural environment. In the presented study, we analyzed 45 metagenome-assembled genomes (MAGs) that were obtained from five freshwater lakes in Switzerland and Czechia. Interestingly, it was found that phototrophic Gemmatimonadota are relatively common in euphotic zones of the studied lakes, whereas heterotrophic Gemmatimonadota prevail in deeper waters. Moreover, our analysis of the MAGs documented that these freshwater species contain almost the same set of photosynthesis genes identified before in Gemmatimonas phototrophica originating from the Gobi Desert.}, }
@article {pmid33727399, year = {2021}, author = {Cantrell, K and Fedarko, MW and Rahman, G and McDonald, D and Yang, Y and Zaw, T and Gonzalez, A and Janssen, S and Estaki, M and Haiminen, N and Beck, KL and Zhu, Q and Sayyari, E and Morton, JT and Armstrong, G and Tripathi, A and Gauglitz, JM and Marotz, C and Matteson, NL and Martino, C and Sanders, JG and Carrieri, AP and Song, SJ and Swafford, AD and Dorrestein, PC and Andersen, KG and Parida, L and Kim, HC and Vázquez-Baeza, Y and Knight, R}, title = {EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets.}, journal = {mSystems}, volume = {6}, number = {2}, pages = {}, pmid = {33727399}, issn = {2379-5077}, support = {U19 AG063744/AG/NIA NIH HHS/United States ; U19 AI135995/AI/NIAID NIH HHS/United States ; }, abstract = {Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive web tool for visualizing trees in the context of microbiome, metabolome, and other community data scalable to trees with well over 500,000 nodes. EMPress provides novel functionality-including ordination integration and animations-alongside many standard tree visualization features and thus simplifies exploratory analyses of many forms of 'omic data.IMPORTANCE Phylogenetic trees are integral data structures for the analysis of microbial communities. Recent work has also shown the utility of trees constructed from certain metabolomic data sets, further highlighting their importance in microbiome research. The ever-growing scale of modern microbiome surveys has led to numerous challenges in visualizing these data. In this paper we used five diverse data sets to showcase the versatility and scalability of EMPress, an interactive web visualization tool. EMPress addresses the growing need for exploratory analysis tools that can accommodate large, complex multi-omic data sets.}, }
@article {pmid33727395, year = {2021}, author = {Sun, M and Zhan, Y and Marsan, D and Páez-Espino, D and Cai, L and Chen, F}, title = {Uncultivated Viral Populations Dominate Estuarine Viromes on the Spatiotemporal Scale.}, journal = {mSystems}, volume = {6}, number = {2}, pages = {}, pmid = {33727395}, issn = {2379-5077}, abstract = {Viruses are ubiquitous and abundant in the oceans, and viral metagenomes (viromes) have been investigated extensively via several large-scale ocean sequencing projects. However, there have not been any systematic viromic studies in estuaries. Here, we investigated the viromes of the Delaware Bay and Chesapeake Bay, two Mid-Atlantic estuaries. Deep sequencing generated a total of 48,190 assembled viral sequences (>5 kb) and 26,487 viral populations (9,204 virus clusters and 17,845 singletons), including 319 circular viral contigs between 7.5 kb and 161.8 kb. Unknown viruses represented the vast majority of the dominant populations, while the composition of known viruses, such as pelagiphage and cyanophage, appeared to be relatively consistent across a wide range of salinity gradients and in different seasons. A difference between estuarine and ocean viromes was reflected by the proportions of Myoviridae, Podoviridae, Siphoviridae, Phycodnaviridae, and a few well-studied virus representatives. The difference in viral community between the Delaware Bay and Chesapeake Bay is significantly more pronounced than the difference caused by temperature or salinity, indicating strong local profiles caused by the unique ecology of each estuary. Interestingly, a viral contig similar to phages infecting Acinetobacter baumannii ("Iraqibacter") was found to be highly abundant in the Delaware Bay but not in the Chesapeake Bay, the source of which is yet to be identified. Highly abundant viruses in both estuaries have close hits to viral sequences derived from the marine single-cell genomes or long-read single-molecule sequencing, suggesting that important viruses are still waiting to be discovered in the estuarine environment.IMPORTANCE This is the first systematic study about spatial and temporal variation of virioplankton communities in estuaries using deep metagenomics sequencing. It is among the highest-quality viromic data sets to date, showing remarkably consistent sequencing depth and quality across samples. Our results indicate that there exists a large pool of abundant and diverse viruses in estuaries that have not yet been cultivated, their genomes only available thanks to single-cell genomics or single-molecule sequencing, demonstrating the importance of these methods for viral discovery. The spatiotemporal pattern of these abundant uncultivated viruses is more variable than that of cultured viruses. Despite strong environmental gradients, season and location had surprisingly little impact on the viral community within an estuary, but we saw a significant distinction between the two estuaries and also between estuarine and open ocean viromes.}, }
@article {pmid33725151, year = {2021}, author = {Menéndez-Serra, M and Triadó-Margarit, X and Casamayor, EO}, title = {Ecological and Metabolic Thresholds in the Bacterial, Protist, and Fungal Microbiome of Ephemeral Saline Lakes (Monegros Desert, Spain).}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {885-896}, pmid = {33725151}, issn = {1432-184X}, support = {BRIDGES CGL2015-69043-P and INTERACTOMA RTI2018-101205-B-I00//Agencia Estatal de Investigaci&#xf3;n/ ; FPI PhD scholarships program (BRIDGES-MINECO)//Agencia Estatal de Investigaci&#xf3;n/ ; BRIDGES CGL2015-69043-P and INTERACTOMA RTI2018-101205-B-I00//FEDER/ ; }, mesh = {Eukaryota ; *Lakes ; *Mycobiome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; Spain ; }, abstract = {We studied the 16S and 18S rRNA genes of the bacterial, protist, and fungal microbiomes of 131 samples collected in 14 ephemeral small inland lakes located in the endorheic area of the Monegros Desert (NE Spain). The sampling covered different temporal flooding/desiccation cycles that created natural salinity gradients between 0.1% (w/v) and salt saturation. We aimed to test the hypothesis of a lack of competitive advantage for microorganisms using the "salt-in" strategy in highly fluctuating hypersaline environments where temperature and salinity transitions widely vary within short time periods, as in ephemeral inland lakes. Overall, 5653 bacterial zOTUs and 2658 eukaryal zOTUs were detected heterogeneously distributed with significant variations on taxonomy and general energy-yielding metabolisms and trophic strategies along the gradient. We observed a more diverse bacterial assembly than initially expected at extreme salinities and a lack of dominance of a few "salt-in" organisms. Microbial thresholds were unveiled for these highly fluctuating hypersaline environments with high selective pressures. We conclude that the extremely high dynamism observed in the ephemeral lakes of Monegros may have given a competitive advantage for more versatile ("salt-out") organisms compared to those better adapted to stable high salinities usually more common in solar salterns. Ephemeral inland saline lakes offered a well-suited natural framework for highly detailed evolutionary and ecological studies.}, }
@article {pmid33723621, year = {2021}, author = {Chen, X and Krug, L and Yang, M and Berg, G and Cernava, T}, title = {The Himalayan Onion (Allium wallichii Kunth) Harbors Unique Spatially Organized Bacterial Communities.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {909-918}, pmid = {33723621}, issn = {1432-184X}, support = {31701836//National Natural Science Foundation of China/ ; 31960555//National Natural Science Foundation of China/ ; 32050410297//National Natural Science Foundation of China/ ; 2018-1050//Guizhou Science and Technology Department/ ; SQ2020YFE010090//National Key Research and Development Program of China/ ; D20023//Program for Introducing Talents to Chinese Universities (111 Program)/ ; }, mesh = {*Allium ; *Microbiota ; Onions ; Plant Roots ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil Microbiology ; }, abstract = {Plant-associated microorganisms are known to contribute with various beneficial functions to the health and productivity of their hosts, yet the microbiome of most plants remains unexplored. This especially applies to wild relatives of cultivated plants, which might harbor beneficial microorganisms that were lost during intensive breeding. We studied bacterial communities of the Himalayan onion (Allium wallichii Kunth), a wild relative of onion native to mountains in East Asia. The bacterial community structure was assessed in different plant microhabitats (rhizosphere, endosphere, anthosphere) by sequencing of 16S rRNA gene fragment amplicons. Targeted bioinformatic analyses were implemented in order to identify unique features in each habitat and to map the overall community in the first representative of the Amaryllidaceae plant family. The highest bacterial diversity was found for bulk soil (Shannon index, H' 9.3) at the high-altitude sampling location. It was followed by the plant rhizosphere (H' 8.9) while communities colonizing flowers (H' 6.1) and the endosphere (H' 6.5 and 5.6) where less diverse. Interestingly, we observed a non-significant rhizosphere effect. Another specificity of the microbiome was its high evenness in taxonomic distribution, which was so far not observed in plant microbiomes. Pseudomonas was identified among additional 10 bacterial genera as a plant-specific signature. The first insights into the microbiome of a plant in the widespread Allium genus will facilitate upcoming comparisons with its domesticated relatives while additionally providing a detailed microbiome mapping of the plant's microhabitats to facilitate bioresource mining.}, }
@article {pmid33723620, year = {2021}, author = {Sidrim, JJC and de Maria, GL and Paiva, MAN and Araújo, GDS and da Graça-Filho, RV and de Oliveira, JS and Sales, JA and Pereira-Neto, WA and Guedes, GMM and Castelo-Branco, DSCM and Cordeiro, RA and Brilhante, RSN and Rocha, MFG}, title = {Azole-Resilient Biofilms and Non-wild Type C. albicans Among Candida Species Isolated from Agricultural Soils Cultivated with Azole Fungicides: an Environmental Issue?.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {1080-1083}, pmid = {33723620}, issn = {1432-184X}, support = {Grant 428737/2018-8//CNPQ/ ; }, mesh = {Antifungal Agents/pharmacology ; Azoles/pharmacology ; Biofilms ; *Candida/genetics ; Candida albicans ; *Fungicides, Industrial/pharmacology ; Microbial Sensitivity Tests ; Soil ; }, abstract = {This study aimed to identify Candida spp. from agricultural soils cultivated with azole fungicides and investigate their susceptibility to clinical (fluconazole, itraconazole, voriconazole, and amphotericin B) and agricultural (tetraconazole and tebuconazole) antifungals in planktonic form. Additionally, Candida biofilm-forming ability and biofilm susceptibility to agricultural antifungals and voriconazole were analyzed. Species identification was performed by phenotypic and molecular assays. The susceptibility of planktonic cells was evaluated by the broth microdilution method. The biofilm metabolic activity was evaluated by the XTT reduction assay. The recovered Candida spp. were identified as C. parapsilosis sensu stricto (n = 14), C. albicans (n = 5), C. tropicalis (n = 2), C. fermentati (n = 1), and C. metapsilosis (n = 2). Minimum inhibitory concentration ranges for clinical and agricultural antifungals were ≤ 0.03-4 μg/mL and 1-128 μg/mL, respectively. Two and one C. albicans strains were considered non-wild type for voriconazole and fluconazole, respectively. All strains were biofilm producers. The minimum biofilm inhibitory concentration ranges for tetraconazole and tebuconazole were 128-> 1024 μg/mL, while for voriconazole was 512-> 1024 μg/mL. In summary, this study shows that non-wild type and azole-resilient biofilm-producing Candida species colonize agricultural soils cultivated with azole fungicides.}, }
@article {pmid33723574, year = {2021}, author = {Castilleux, R and Plancot, B and Vicré, M and Nguema-Ona, E and Driouich, A}, title = {Extensin, an underestimated key component of cell wall defence?.}, journal = {Annals of botany}, volume = {127}, number = {6}, pages = {709-713}, pmid = {33723574}, issn = {1095-8290}, mesh = {*Arabidopsis/genetics ; *Cell Wall ; Peroxidases ; Plant Proteins ; }, abstract = {BACKGROUND: Extensins are plant cell wall hydroxyproline-rich glycoproteins known to be involved in cell wall reinforcement in higher plants, and in defence against pathogen attacks. The ability of extensins to form intra- and intermolecular cross-links is directly related to their role in cell wall reinforcement. Formation of such cross-links requires appropriate glycosylation and structural conformation of the glycoprotein.<br><br>SCOPE: Although the role of cell wall components in plant defence has drawn increasing interest over recent years, relatively little focus has been dedicated to extensins. Nevertheless, new insights were recently provided regarding the structure and the role of extensins and their glycosylation in plant-microbe interactions, stimulating an interesting debate from fellow cell wall community experts. We have previously revealed a distinct distribution of extensin epitopes in Arabidopsis thaliana wild-type roots and in mutants impaired in extensin arabinosylation, in response to elicitation with flagellin 22. That study was recently debated in a Commentary by Tan and Mort (Tan L, Mort A. 2020. Extensins at the front line of plant defence. A commentary on: 'Extensin arabinosylation is involved in root response to elicitors and limits oomycete colonization'. Annals of Botany 125: vii-viii) and several points regarding our results were discussed. As a response, we herein clarify the points raised by Tan and Mort, and update the possible epitope structure recognized by the anti-extensin monoclonal antibodies. We also provide additional data showing differential distribution of LM1 extensin epitopes in roots between a mutant defective in PEROXIDASES 33 and 34 and the wild type, similarly to previous observations from the rra2 mutant defective in extensin arabinosylation. We propose these two peroxidases as potential candidates to specifically catalyse the cross-linking of extensins within the cell wall.<br><br>CONCLUSIONS: Extensins play a major role within the cell wall to ensure root protection. The cross-linking of extensins, which requires correct glycosylation and specific peroxidases, is most likely to result in modulation of cell wall architecture that allows enhanced protection of root cells against invading pathogens. Study of the relationship between extensin glycosylation and their cross-linking is a very promising approach to further understand how the cell wall influences root immunity.}, }
@article {pmid33720954, year = {2021}, author = {Paul, B and Sierra, MA and Xu, F and Crystal, YO and Li, X and Saxena, D and Ruff, RR}, title = {Microbial population shift and metabolic characterization of silver diamine fluoride treatment failure on dental caries.}, journal = {PloS one}, volume = {16}, number = {3}, pages = {e0242396}, pmid = {33720954}, issn = {1932-6203}, support = {R56 DE028933/DE/NIDCR NIH HHS/United States ; }, mesh = {Carnobacteriaceae/genetics/isolation &amp; purification ; Child ; Cross-Sectional Studies ; DNA, Bacterial/chemistry/metabolism ; Dental Caries/*drug therapy/pathology ; Dental Plaque/microbiology ; Discriminant Analysis ; Fluorides, Topical/therapeutic use ; Humans ; Leptotrichia/genetics/isolation &amp; purification ; *Microbiota ; Pilot Projects ; Principal Component Analysis ; Quaternary Ammonium Compounds/*therapeutic use ; Saliva/microbiology ; Sequence Analysis, DNA ; Silver Compounds/*therapeutic use ; Treatment Failure ; }, abstract = {The objective of this pilot study was to describe the microbial profiles present in the plaque and saliva of children who continued to develop new carious lesions following treatment with silver diamine fluoride ("nonresponders") compared to caries active, caries-free, and children immediately receiving SDF treatment for untreated caries in order to identify potential microbial differences that may relate to a re-incidence of caries. Saliva and plaque samples from infected and contralateral sites were obtained from twenty children who were either caries free, had active carious lesions, were caries active and received SDF treatment immediately before sampling, or had previously received SDF treatment and developed new caries. In total, 8,057,899 Illumina-generated sequence reads from 60 samples were obtained. Reads were processed using the Quantitative Insights Into Microbial Ecology pipeline. Group differences were assessed using Analysis of Variance Models and Tukey Honest Significant Differences. To identify significant taxa between treatment groups, Linear discriminant analysis Effect Size (LefSe) and Analysis of Differential Abundance Taking Sample Variation Into Account were used. Differential abundant analysis indicated that members of the Lachnospiraceae family were significantly enriched in non-responders and the genus Tannerella and species Granulicatella adiances were also highly abundant in this group. LefSe analysis between non-responders and SDF-treated groups revealed that genera Leptotrichia and Granulicatella were enriched in non-responders. We observed the highest abundance of phosphotransferase system and lowest abundance of lipopolysaccharide synthesis in non-responders. The microbiome in dental biofilms is responsible for initiation and progression of dental caries. SDF has been shown to be effective in arresting the progression carious lesions, in part due to its antimicrobial properties. Findings suggest that the differential abundance of select microbiota and specific pathway functioning in individuals that present with recurrent decay after SDF treatment may contribute to a potential failure of silver diamine fluoride to arrest dental caries. However, the short duration of sample collection following SDF application and the small sample size emphasize the need for further data and additional analysis.}, }
@article {pmid33719323, year = {2021}, author = {Wang, L and Yin, Y and Jing, X and Wang, M and Zhao, M and Yu, J and Qiu, Z and Li, YF}, title = {Profiling of MicroRNAs Involved in Mepiquat Chloride-Mediated Inhibition of Internode Elongation in Cotton (Gossypium hirsutum L.) Seedlings.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {643213}, pmid = {33719323}, issn = {1664-462X}, abstract = {Mepiquat chloride (MC) is the most important plant growth retardant that is widely used in cotton (Gossypium hirsutum L.) production to suppress excessive vegetative growth and improve plant architecture. MicroRNAs (miRNAs) are important gene expression regulators that control plant growth and development. However, miRNA-mediated post-transcriptional regulation in MC-induced growth inhibition remains unclear. In this study, the dynamic expression profiles of miRNAs responsive to MC in cotton internodes were investigated. A total of 508 known miRNAs belonging to 197 families and five novel miRNAs were identified. Among them, 104 miRNAs were differentially expressed at 48, 72, or 96 h post MC treatment compared with the control (0 h); majority of them were highly conserved miRNAs. The number of differentially expressed miRNAs increased with time after treatment. The expression of 14 known miRNAs was continuously suppressed, whereas 12 known miRNAs and one novel miRNA were continuously induced by MC. The expression patterns of the nine differentially expressed miRNAs were verified using qRT-PCR. The targets of the known and novel miRNAs were predicted. Four conserved and six novel targets were validated using the RLM-5' RACE assay. This study revealed that miRNAs play crucial regulatory roles in the MC-induced inhibition of internode elongation. It can improve our understanding of post-transcriptional gene regulation in MC-mediated growth inhibition and could potentially facilitate the breeding of dwarf cotton.}, }
@article {pmid33719058, year = {2021}, author = {Esquivel-Hernández, DA and García-Pérez, JS and Xu, X and Metha, S and Maldonado, J and Xia, S and Zhao, HP and Rittmann, BE and Ontiveros-Valencia, A}, title = {Microbial ecology in selenate-reducing biofilm communities: Rare biosphere and their interactions with abundant phylotypes.}, journal = {Biotechnology and bioengineering}, volume = {118}, number = {7}, pages = {2460-2471}, doi = {10.1002/bit.27754}, pmid = {33719058}, issn = {1097-0290}, mesh = {*Bacteria/classification/growth &amp; development ; *Bacterial Physiological Phenomena ; Biofilms/*growth &amp; development ; *Bioreactors ; Microbial Consortia/*physiology ; *Phylogeny ; Selenic Acid/*metabolism ; }, abstract = {Selenate (SeO4[2-]) reduction in hydrogen (H2)-fed membrane biofilm reactors (H2 -MBfRs) was studied in combinations with other common electron acceptors. We employed H2 -MBfRs with two distinctly different conditions: R1, with ample electron-donor availability and acceptors SeO4[2-] and sulfate (SO4[2-]), and R2, with electron-donor limitation and the presence of electron acceptors SeO4[2-] , nitrate (NO3[-]), and SO4[2-] . Even though H2 was available to reduce all input SeO4[2-] and SO4[2-] in R1, SeO4[2-] reduction was preferred over SO4[2-] reduction. In R2, co-reduction of NO3[-] and SeO4[2-] occurred, and SO4[2-] reduction was mostly suppressed. Biofilms in all MBfRs had high microbial diversity that was influenced by the "rare biosphere" (RB), phylotypes with relative abundance less than 1%. While all MBfR biofilms had abundant members, such as Dechloromonas and Methyloversatilis, the bacterial communities were significantly different between R1 and R2. For R1, abundant genera were Methyloversatilis, Melioribacter, and Propionivibrio; for R2, abundant genera were Dechloromonas, Hydrogenophaga, Cystobacter, Methyloversatilis, and Thauera. Although changes in electron-acceptor or -donor loading altered the phylogenetic structure of the microbial communities, the biofilm communities were resilient in terms of SeO4[2-] and NO3[-] reductions, because interacting members of the RB had the capacity of respiring these electron acceptors.}, }
@article {pmid33717676, year = {2021}, author = {Messer, LF and Brown, MV and Van Ruth, PD and Doubell, M and Seymour, JR}, title = {Temperate southern Australian coastal waters are characterised by surprisingly high rates of nitrogen fixation and diversity of diazotrophs.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e10809}, pmid = {33717676}, issn = {2167-8359}, abstract = {Biological dinitrogen (N2) fixation is one mechanism by which specific microorganisms (diazotrophs) can ameliorate nitrogen (N) limitation. Historically, rates of N2 fixation were believed to be limited outside of the low nutrient tropical and subtropical open ocean; however, emerging evidence suggests that N2 fixation is also a significant process within temperate coastal waters. Using a combination of amplicon sequencing, targeting the nitrogenase reductase gene (nifH), quantitative nifH PCR, and [15]N2 stable isotope tracer experiments, we investigated spatial patterns of diazotroph assemblage structure and N2 fixation rates within the temperate coastal waters of southern Australia during Austral autumn and summer. Relative to previous studies in open ocean environments, including tropical northern Australia, and tropical and temperate estuaries, our results indicate that high rates of N2 fixation (10-64 nmol L[-1] d[-1]) can occur within the large inverse estuary Spencer Gulf, while comparatively low rates of N2 fixation (2 nmol L[-1] d[-1]) were observed in the adjacent continental shelf waters. Across the dataset, low concentrations of NO3/NO2 were significantly correlated with the highest N2 fixation rates, suggesting that N2 fixation could be an important source of new N in the region as dissolved inorganic N concentrations are typically limiting. Overall, the underlying diazotrophic community was dominated by nifH sequences from Cluster 1 unicellular cyanobacteria of the UCYN-A clade, as well as non-cyanobacterial diazotrophs related to Pseudomonas stutzeri, and Cluster 3 sulfate-reducing deltaproteobacteria. Diazotroph community composition was significantly influenced by salinity and SiO4 concentrations, reflecting the transition from UCYN-A-dominated assemblages in the continental shelf waters, to Cluster 3-dominated assemblages in the hypersaline waters of the inverse estuary. Diverse, transitional diazotrophic communities, comprised of a mixture of UCYN-A and putative heterotrophic bacteria, were observed at the mouth and southern edge of Spencer Gulf, where the highest N2 fixation rates were observed. In contrast to observations in other environments, no seasonal patterns in N2 fixation rates and diazotroph community structure were apparent. Collectively, our findings are consistent with the emerging view that N2 fixation within temperate coastal waters is a previously overlooked dynamic and potentially important component of the marine N cycle.}, }
@article {pmid33710327, year = {2021}, author = {Wang, X and Chen, S and Ma, X and Yssel, AEJ and Chaluvadi, SR and Johnson, MS and Gangashetty, P and Hamidou, F and Sanogo, MD and Zwaenepoel, A and Wallace, J and Van de Peer, Y and Bennetzen, JL and Van Deynze, A}, title = {Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis).}, journal = {GigaScience}, volume = {10}, number = {3}, pages = {}, pmid = {33710327}, issn = {2047-217X}, mesh = {*Digitaria/genetics ; Genetic Variation ; Genome, Plant ; Humans ; *Plant Breeding ; Plant Preparations ; }, abstract = {BACKGROUND: Digitaria exilis, white fonio, is a minor but vital crop of West Africa that is valued for its resilience in hot, dry, and low-fertility environments and for the exceptional quality of its grain for human nutrition. Its success is hindered, however, by a low degree of plant breeding and improvement.<br><br>FINDINGS: We sequenced the fonio genome with long-read SMRT-cell technology, yielding a &#x223c;761 Mb assembly in 3,329 contigs (N50, 1.73 Mb; L50, 126). The assembly approaches a high level of completion, with a BUSCO score of >99%. The fonio genome was found to be a tetraploid, with most of the genome retained as homoeologous duplications that differ overall by &#x223c;4.3%, neglecting indels. The 2 genomes within fonio were found to have begun their independent divergence &#x223c;3.1 million years ago. The repeat content (>49%) is fairly standard for a grass genome of this size, but the ratio of Gypsy to Copia long terminal repeat retrotransposons (&#x223c;6.7) was found to be exceptionally high. Several genes related to future improvement of the crop were identified including shattering, plant height, and grain size. Analysis of fonio population genetics, primarily in Mali, indicated that the crop has extensive genetic diversity that is largely partitioned across a north-south gradient coinciding with the Sahel and Sudan grassland domains.<br><br>CONCLUSIONS: We provide a high-quality assembly, annotation, and diversity analysis for a vital African crop. The availability of this information should empower future research into further domestication and improvement of fonio.}, }
@article {pmid33709229, year = {2021}, author = {Yang, ZW and Men, Y and Zhang, J and Liu, ZH and Luo, JY and Wang, YH and Li, WJ and Xie, Q}, title = {Evaluation of Sample Preservation Approaches for Better Insect Microbiome Research According to Next-Generation and Third-Generation Sequencing.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {971-980}, pmid = {33709229}, issn = {1432-184X}, support = {31222051, 31772425//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Biodiversity ; High-Throughput Nucleotide Sequencing ; Insecta ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The microbial communities associated with insects play critical roles in many physiological functions such as digestion, nutrition, and defense. Meanwhile, with the development of sequencing technology, more and more studies begin to focus on broader biodiversity of insects and the corresponding mechanisms of insect microbial symbiosis, which need longer time collecting in the field. However, few studies have evaluated the effect of insect microbiome sample preservation approaches especially in different time durations or have assessed whether these approaches are appropriate for both next-generation sequencing (NGS) and third-generation sequencing (TGS) technologies. Here, we used Tessaratoma papillosa (Hemiptera: Tessaratomidae), an important litchi pest, as the model insect and adopted two sequencing technologies to evaluate the effect of four different preservation approaches (cetyltrimethylammonium bromide (CTAB), ethanol, air dried, and RNAlater). We found the samples treated by air dried method, which entomologists adopted for morphological observation and classical taxonomy, would get worse soon. RNAlater as the most expensive approaches for insect microbiome sample preservation did not suit for field works longer than 1 month. We recommended CTAB and ethanol as better preservatives in longer time field work for their effectiveness and low cost. Comparing with the full-length 16S rRNA gene sequenced by TGS, the V4 region of 16S rRNA gene sequenced by NGS has a lower resolution trait and may misestimate the composition of microbial communities. Our results provided recommendations for suitable preservation approaches applied to insect microbiome studies based on two sequencing technologies, which can help researchers properly preserve samples in field works.}, }
@article {pmid33706038, year = {2021}, author = {Hooban, B and Fitzhenry, K and Cahill, N and Joyce, A and O' Connor, L and Bray, JE and Brisse, S and Passet, V and Abbas Syed, R and Cormican, M and Morris, D}, title = {A Point Prevalence Survey of Antibiotic Resistance in the Irish Environment, 2018-2019.}, journal = {Environment international}, volume = {152}, number = {}, pages = {106466}, doi = {10.1016/j.envint.2021.106466}, pmid = {33706038}, issn = {1873-6750}, mesh = {Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics ; Ireland ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Prevalence ; *beta-Lactamases/genetics ; }, abstract = {Water bodies worldwide have proven to be vast reservoirs of clinically significant antibiotic resistant organisms. Contamination of waters by anthropogenic discharges is a significant contributor to the widespread dissemination of antibiotic resistance. The aim of this research was to investigate multiple different anthropogenic sources on a national scale for the role they play in the environmental propagation of antibiotic resistance. A total of 39 water and 25 sewage samples were collected across four local authority areas in the West, East and South of Ireland. In total, 211 Enterobacterales were isolated (139 water, 72 sewage) and characterised. A subset of isolates (n=60) were chosen for whole genome sequencing. Direct comparisons of the water versus sewage isolate collections revealed a higher percentage of sewage isolates displayed resistance to cefoxitin (46%) and ertapenem (32%), while a higher percentage of water isolates displayed resistance to tetracycline (55%) and ciprofloxacin (71%). Half of all isolates displayed extended spectrum beta-lactamase (ESBL) production phenotypically (n = 105/211; 50%), with blaCTX-M detected in 99/105 isolates by PCR. Carbapenemase genes were identified in 11 isolates (6 sewage, 5 water). The most common variant was blaOXA-48 (n=6), followed by blaNDM-5 (n=2) and blaKPC-2 (n=2). Whole genome sequencing analysis revealed numerous different sequence types in circulation in both waters and sewage including E. coli ST131 (n=15), ST38 (n=8), ST10 (n=4) along with Klebsiella ST405 (n=3) and ST11 (n=2). Core genome MLST (cgMLST) comparisons uncovered three highly similar Klebsiella isolates originating from hospital sewage and two nearby waters. The Klebsiella isolates from an estuary and seawater displayed 99.1% and 98.8% cgMLST identity to the hospital sewage isolate respectively. In addition, three pairs of E. coli isolates from different waters also revealed cgMLST similarities, indicating widespread dissemination and persistence of certain strains in the aquatic environment. These findings highlight the need for routine monitoring of water bodies used for recreational and drinking purposes for the presence of multi-drug resistant organisms.}, }
@article {pmid33705567, year = {2021}, author = {Hicks, LC and Lajtha, K and Rousk, J}, title = {Nutrient limitation may induce microbial mining for resources from persistent soil organic matter.}, journal = {Ecology}, volume = {102}, number = {6}, pages = {e03328}, doi = {10.1002/ecy.3328}, pmid = {33705567}, issn = {1939-9170}, support = {2020-03858//Vetenskapsr&#xe5;det/ ; 2020-04083//Vetenskapsr&#xe5;det/ ; KAW 1017.0171//The Knut and Alice Wallenberg Foundation/ ; 2018-01315//Svenska Forskningsr&#xe5;det Formas/ ; }, mesh = {Ecosystem ; Fungi ; Nutrients ; *Soil ; *Soil Microbiology ; }, abstract = {Fungi and bacteria are the two principal microbial groups in soil, responsible for the breakdown of organic matter (OM). The relative contribution of fungi and bacteria to decomposition is thought to impact biogeochemical cycling at the ecosystem scale, whereby bacterially dominated decomposition supports the fast turnover of easily available substrates, whereas fungal-dominated decomposition leads to the slower turnover of more complex OM. However, empirical support for this is lacking. We used soils from a detritus input and removal treatment experiment in an old-growth coniferous forest, where above- and belowground litter inputs have been manipulated for 20 yr. These manipulations have generated variation in OM quality, as defined by energetic content and proxied as respiration per g soil organic matter (SOM) and the δ[13] C signature in respired CO2 and microbial PLFAs. Respiration per g SOM reflects the availability and lability of C substrate to microorganisms, and the δ[13] C signature indicates whether the C used by microorganisms is plant derived and higher quality (more δ[13] C depleted) or more microbially processed and lower quality (more δ[13] C enriched). Surprisingly, higher quality C did not disproportionately benefit bacterial decomposers. Both fungal and bacterial growth increased with C quality, with no systematic change in the fungal-to-bacterial growth ratio, reflecting the relative contribution of fungi and bacteria to decomposition. There was also no difference in the quality of C targeted by bacterial and fungal decomposers either for catabolism or anabolism. Interestingly, respired CO2 was more δ[13] C enriched than soil C, suggesting preferential use of more microbially processed C, despite its lower quality. Gross N mineralization and consumption were also unaffected by differences in the ratio of fungal-to-bacterial growth. However, the ratio of C to gross N mineralization was lower than the average C/N of SOM, meaning that microorganisms specifically targeted N-rich components of OM, indicative of selective microbial N-mining. Consistent with the δ[13] C data, this reinforces evidence for the use of more microbially processed OM with a lower C/N ratio, rather than plant-derived OM. These results challenge the widely held assumption that microorganisms favor high-quality C sources and suggest that there is a trade-off in OM use that may be related to the growth-limiting factor for microorganisms in the ecosystem.}, }
@article {pmid33704553, year = {2021}, author = {Sochard, C and Dupont, C and Simon, JC and Outreman, Y}, title = {Secondary Symbionts Affect Foraging Capacities of Plant-Specialized Genotypes of the Pea Aphid.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {1009-1019}, pmid = {33704553}, issn = {1432-184X}, support = {ANR Hmicmac 16-CE02-0014//ANR/ ; }, mesh = {Animals ; *Aphids ; Genotype ; Pisum sativum ; Phenotype ; Symbiosis ; }, abstract = {Ecological specialization is widespread in animals, especially in phytophagous insects, which have often a limited range of host plant species. This host plant specialization results from divergent selection on insect populations, which differ consequently in traits like behaviors involved in plant use. Although recent studies highlighted the influence of symbionts on dietary breadth of their insect hosts, whether these microbial partners influence the foraging capacities of plant-specialized insects has received little attention. In this study, we used the pea aphid Acyrthosiphon pisum, which presents distinct plant-specialized lineages and several secondary bacterial symbionts, to examine the possible effects of symbionts on the different foraging steps from plant searching to host plant selection. In particular, we tested the effect of secondary symbionts on the aphid capacity (1) to explore habitat at long distance (estimated through the production of winged offspring), (2) to explore habitat at short distance, and (3) to select its host plant. We found that secondary symbionts had a variable influence on the production of winged offspring in some genotypes, with potential consequences on dispersal and survival. By contrast, symbionts influenced both short-distance exploration and host plant selection only marginally. The implication of symbionts' influence on insect foraging capacities is discussed.}, }
@article {pmid33690989, year = {2021}, author = {Wade, WG}, title = {Resilience of the oral microbiome.}, journal = {Periodontology 2000}, volume = {86}, number = {1}, pages = {113-122}, doi = {10.1111/prd.12365}, pmid = {33690989}, issn = {1600-0757}, support = {R37 DE016937/DE/NIDCR NIH HHS/United States ; }, mesh = {*Dental Caries/prevention &amp; control ; Humans ; *Microbiota ; Mouth ; *Mouth Diseases ; Saliva ; }, abstract = {The human mouth harbors a complex microbiota, the composition of which is potentially influenced by a wide range of factors, including the intake of food and drink, the availability of endogenous nutrients, the host immune system, drug treatments, and systemic diseases. Despite these possible influences, the oral microbiota is remarkably resilient, particularly in comparison with the microbiota of the large intestine. Diet, with the exception of excessive and/or frequent consumption of fermentable carbohydrate or supplementation with nitrate, has minimal impact on the composition of the oral bacterial community. The common oral diseases dental caries and the periodontal diseases is associated with modification of the oral microbiota primarily as a result of the ecological changes induced by excessive acid production and inflammation, respectively. Systemically-administered antimicrobials have only a small effect on the composition of the oral bacterial community, and while locally delivered antimicrobials can have some clinical benefits, the biofilm lifestyle of oral bacteria lends them substantial resistance to the agents used. Saliva plays an important role in oral microbial ecology, by supplying nutrients and providing protection against colonization by nonoral organisms. Dry mouth is one condition that has a major effect on the microbiota, resulting in increased colonization by opportunistic pathogens. Some systemic diseases do affect the oral microbiome, notably diabetes, in which raised levels of glucose in saliva and tissue impact on bacterial nutrition.}, }
@article {pmid33688007, year = {2021}, author = {Huang, S and He, T and Yue, F and Xu, X and Wang, L and Zhu, P and Teng, F and Sun, Z and Liu, X and Jing, G and Su, X and Jin, L and Liu, J and Xu, J}, title = {Longitudinal Multi-omics and Microbiome Meta-analysis Identify an Asymptomatic Gingival State That Links Gingivitis, Periodontitis, and Aging.}, journal = {mBio}, volume = {12}, number = {2}, pages = {}, pmid = {33688007}, issn = {2150-7511}, mesh = {*Aging ; Cohort Studies ; Cytokines/*analysis/immunology ; Dysbiosis ; Genomics ; Gingiva/*microbiology/pathology ; Gingivitis/*microbiology ; Humans ; Longitudinal Studies ; Metabolomics ; *Metagenome ; *Microbiota ; Periodontitis/*microbiology ; Proteomics ; Saliva/immunology ; }, abstract = {Most adults experience episodes of gingivitis, which can progress to the irreversible, chronic state of periodontitis, yet roles of plaque in gingivitis onset and progression to periodontitis remain elusive. Here, we longitudinally profiled the plaque metagenome, the plaque metabolome, and salivary cytokines in 40 adults who transited from naturally occurring gingivitis (NG) to healthy gingivae (baseline) and then to experimental gingivitis (EG). During EG, rapid and consistent alterations in plaque microbiota, metabolites, and salivary cytokines emerged as early as 24 to 72 h after oral-hygiene pause, defining an asymptomatic suboptimal health (SoH) stage of the gingivae. SoH features a swift, full activation of 11 salivary cytokines but a steep synergetic decrease of plaque-derived betaine and Rothia spp., suggesting an anti-gum inflammation mechanism by health-promoting symbionts. Global, cross-cohort meta-analysis revealed, at SoH, a greatly elevated microbiome-based periodontitis index driven by its convergence of both taxonomical and functional profiles toward the periodontitis microbiome. Finally, post-SoH gingivitis development accelerates oral microbiota aging by over 1 year within 28 days, with Rothia spp. depletion and Porphyromonas gingivalis elevation as hallmarks. Thus, the microbiome-defined, transient gum SoH stage is a crucial link among gingivitis, periodontitis, and aging.IMPORTANCE A significant portion of world population still fails to brush teeth daily. As a result, the majority of the global adult population is afflicted with chronic gingivitis, and if it is left untreated, some of them will eventually suffer from periodontitis. Here, we identified periodontitis-like microbiome dysbiosis in an asymptomatic SoH stage as early as 24 to 72 h after oral-hygiene pause. SoH features a swift, full activation of multiple salivary cytokines but a steep synergetic decrease of plaque-derived betaine and Rothia spp. The microbial ecology during early gingivitis is highly similar to that in periodontitis under both taxonomical and functional contexts. Unexpectedly, exposures to gingivitis can accelerate over 10-fold the normal rate of oral microbiota aging. Our findings underscore the importance of intervening at the SoH stage of gingivitis via proper oral-hygiene practices on a daily basis, so as to maintain a periodontitis-preventive plaque and ensure the healthy aging of the oral ecosystem.}, }
@article {pmid33685679, year = {2021}, author = {Lietaer, L and Bogado Pascottini, O and Hernandez-Sanabria, E and Kerckhof, FM and Lacoere, T and Boon, N and Vlaminck, L and Opsomer, G and Van de Wiele, T}, title = {Low microbial biomass within the reproductive tract of mid-lactation dairy cows: A study approach.}, journal = {Journal of dairy science}, volume = {104}, number = {5}, pages = {6159-6174}, doi = {10.3168/jds.2020-19554}, pmid = {33685679}, issn = {1525-3198}, mesh = {Animals ; Cattle ; Female ; Biomass ; *Lactation ; Reproducibility of Results ; RNA, Ribosomal, 16S ; *Uterus ; }, abstract = {The microbiome from the reproductive tract is being investigated for its putative effect on fertility, embryo development, and health status of the human or animal host postpartum. Besides the presence of a vaginal microbiome, recent studies have claimed the existence and putative role of the uterine microbiome. Yet, the extremely low bacterial numbers and high eukaryotic/prokaryotic DNA ratio make this a highly challenging environment to study with next-generation sequencing (NGS) techniques. Here, we describe the methodological challenges that are typically encountered when performing an accurate analysis of low microbial biomass samples, illustrated by data of our own observational study. In terms of the research question, we compared the microbial composition throughout different parts of the reproductive tract of clinically healthy, mid-lactation Holstein-Friesian cows. Samples were collected from 5 dairy cows immediately after killing. Swabs were taken from the vagina, and from 4 pre-established locations of the uterine endometrium. In addition to the conventional DNA extraction blank controls, sterile swabs rubbed over disinfected disposable gloves and the disinfected surface of the uterus (tunica serosa) before incision were taken as sampling controls. The DNA extraction, DNA quantification, quantitative PCR of the 16S rRNA genes, and 16S rRNA gene sequencing were performed. In terms of NGS data analysis, we performed prevalence-based filtering of putative contaminant operational taxonomic units (OTU) using the decontam R package. Although the bacterial composition differed between the vagina and uterus, no differences in bacterial community structure (α and β diversity) were found among the different locations in the uterus. At phylum level, uterine samples had a greater relative abundance of Proteobacteria, and a lesser relative abundance of Firmicutes than vaginal samples. The number of shared OTU between vagina and uterus was limited, suggesting the existence of bacterial transmission routes other than the transcervical one to the uterus. The mid-lactation bovine genital tract is a low microbial biomass environment, which makes it difficult to distinguish between its constitutive versus contaminant microbiome. The integration of key controls is therefore strictly necessary to decrease the effect of accidentally introduced contaminant sequences and improve the reliability of results in samples with low microbial biomass.}, }
@article {pmid33685393, year = {2021}, author = {Zhang, X and Shi, L and Sun, T and Guo, K and Geng, S}, title = {Dysbiosis of gut microbiota and its correlation with dysregulation of cytokines in psoriasis patients.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {78}, pmid = {33685393}, issn = {1471-2180}, support = {51707149//National Natural Science Foundation of China/ ; XJJ2017071//Xi'an Jiaotong University/ ; SKLIPR.1609//State Key Laboratory of Intense Pulsed Radiation Simulation and Effect/ ; }, mesh = {Biodiversity ; Cytokines/*genetics ; Dysbiosis/*complications/immunology ; Feces/microbiology ; Gastrointestinal Microbiome/*immunology ; Humans ; Psoriasis/*complications/immunology/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Psoriasis is an inflammatory skin disease associated with multiple comorbidities and substantially diminishes patients' quality of life. The gut microbiome has become a hot topic in psoriasis as it has been shown to affect both allergy and autoimmunity diseases in recent studies. Our objective was to identify differences in the fecal microbial composition of patients with psoriasis compared with healthy individuals to unravel the microbiota profiling in this autoimmune disease.<br><br>RESULTS: We collected fecal samples from 30 psoriasis patients and 30 healthy controls, sequenced them by 16S rRNA high-throughput sequencing, and identified the gut microbial composition using bioinformatic analyses including Quantitative Insights into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Our results showed that different relative abundance of certain bacterial taxa between psoriasis patients and healthy individuals, including Faecalibacterium and Megamonas, were increased in patients with psoriasis. It's also implicated that many cytokines act as main effect molecules in the pathology of psoriasis. We selected the inflammation-related indicators that were abnormal in psoriasis patients and found the microbiome variations were associated with the level of them, especially interleukin-2 receptor showed a positive relationship with Phascolarctobacterium and a negative relationship with the Dialister. The relative abundance of Phascolarctobacterium and Dialister can be regard as predictors of psoriasis activity. The correlation analysis based on microbiota and Inflammation-related indicators showed that microbiota dysbiosis might induce an abnormal immune response in psoriasis.<br><br>CONCLUSIONS: We concluded that the gut microbiome composition in psoriasis patients has been altered markedly and provides evidence to understand the relationship between gut microbiota and psoriasis. More mechanistic experiments are needed to determine whether the differences observed in gut microbiota are the cause or consequences of psoriasis and whether the relationship between gut microbiota and cytokines was involved.}, }
@article {pmid33684884, year = {2021}, author = {Song, C and Jin, K and Raaijmakers, JM}, title = {Designing a home for beneficial plant microbiomes.}, journal = {Current opinion in plant biology}, volume = {62}, number = {}, pages = {102025}, doi = {10.1016/j.pbi.2021.102025}, pmid = {33684884}, issn = {1879-0356}, mesh = {Agriculture ; *Microbiota/genetics ; *Plant Breeding ; Plant Development ; Plants ; }, abstract = {The plant microbiome comprises a highly diverse community of saprotrophic, mutualistic, and pathogenic microbes that can affect plant growth and plant health. There is substantial interest to exploit beneficial members of plant microbiomes for new sustainable management strategies in crop production. However, poor survival and colonization of plant tissues by introduced microbial isolates as well as lack of expression of the plant growth-promoting or disease-suppressive traits at the right time and place are still major limitations for successful implementation of microbiomes in future agricultural practices and plant breeding programs. Similar to building a home for humans, we discuss different strategies of building a home for beneficial plant microbiomes, here referred to as the 'MicrobiHome'.}, }
@article {pmid33682183, year = {2021}, author = {Sperlea, T and Kreuder, N and Beisser, D and Hattab, G and Boenigk, J and Heider, D}, title = {Quantification of the covariation of lake microbiomes and environmental variables using a machine learning-based framework.}, journal = {Molecular ecology}, volume = {30}, number = {9}, pages = {2131-2144}, doi = {10.1111/mec.15872}, pmid = {33682183}, issn = {1365-294X}, mesh = {Ecology ; *Lakes ; Machine Learning ; *Microbiota/genetics ; }, abstract = {It is known that microorganisms are essential for the functioning of ecosystems, but the extent to which microorganisms respond to different environmental variables in their natural habitats is not clear. In the current study, we present a methodological framework to quantify the covariation of the microbial community of a habitat and environmental variables of this habitat. It is built on theoretical considerations of systems ecology, makes use of state-of-the-art machine learning techniques and can be used to identify bioindicators. We apply the framework to a data set containing operational taxonomic units (OTUs) as well as more than twenty physicochemical and geographic variables measured in a large-scale survey of European lakes. While a large part of variation (up to 61%) in many environmental variables can be explained by microbial community composition, some variables do not show significant covariation with the microbial lake community. Moreover, we have identified OTUs that act as "multitask" bioindicators, i.e., that are indicative for multiple environmental variables, and thus could be candidates for lake water monitoring schemes. Our results represent, for the first time, a quantification of the covariation of the lake microbiome and a wide array of environmental variables for lake ecosystems. Building on the results and methodology presented here, it will be possible to identify microbial taxa and processes that are essential for functioning and stability of lake ecosystems.}, }
@article {pmid33680353, year = {2021}, author = {Ghannam, RB and Techtmann, SM}, title = {Machine learning applications in microbial ecology, human microbiome studies, and environmental monitoring.}, journal = {Computational and structural biotechnology journal}, volume = {19}, number = {}, pages = {1092-1107}, pmid = {33680353}, issn = {2001-0370}, abstract = {Advances in nucleic acid sequencing technology have enabled expansion of our ability to profile microbial diversity. These large datasets of taxonomic and functional diversity are key to better understanding microbial ecology. Machine learning has proven to be a useful approach for analyzing microbial community data and making predictions about outcomes including human and environmental health. Machine learning applied to microbial community profiles has been used to predict disease states in human health, environmental quality and presence of contamination in the environment, and as trace evidence in forensics. Machine learning has appeal as a powerful tool that can provide deep insights into microbial communities and identify patterns in microbial community data. However, often machine learning models can be used as black boxes to predict a specific outcome, with little understanding of how the models arrived at predictions. Complex machine learning algorithms often may value higher accuracy and performance at the sacrifice of interpretability. In order to leverage machine learning into more translational research related to the microbiome and strengthen our ability to extract meaningful biological information, it is important for models to be interpretable. Here we review current trends in machine learning applications in microbial ecology as well as some of the important challenges and opportunities for more broad application of machine learning to understanding microbial communities.}, }
@article {pmid33678886, year = {2021}, author = {Muandze-Nzambe, JU and Onanga, R and Yala, JF and Somda, NS and Cissé, H and Zongo, C and Mavoungou, JF and Savadogo, A}, title = {Technological and microbiological characteristics of indigenous food produced in Gabon.}, journal = {Journal of food science and technology}, volume = {58}, number = {3}, pages = {1027-1041}, pmid = {33678886}, issn = {0022-1155}, abstract = {The purpose of this study was to provide contextual information on indigenous food's technologies and safety from Gabon. The strategic focus being to promote local food with enhanced nutritional value and improved safety. An investigation and monitoring were carried out to elucidate their process flow diagrams and to identify safety failures. Samples were taken for microbiological analysis using conventional culture-based techniques. Detection and identification of Salmonella in samples were confirmed using PCR based method by targeting invasion plasmid antigen B (IpaB) gene. The investigation shows that women play a protagonist role in the technical know-how of Gabonese indigenous foods in a context that is evolving towards the disappearance of this knowledge. The food production process remains archaic, which makes the environment impact on food safety. Indeed, the proximity of food manufacturing environment to animals, waste, or latrines coupled with the lack of hygiene and manufacturing practices affect the quality of these foods. This is reflected in our study's microbiological results, namely, Aerobic Mesophilic Bacteria ranged from 3.53 to 11.96 log CFU/g and indicators of fecal contaminations of up to 8.21 log CFU/g. Salmonella is detected in 18.69% of samples. The presence of these bacteria is a risk for consumer health. Although some of these foods can be considered as a fermented food, the producers should be further educated and encouraged to take preventive measures to ensure the quality of these food products. A much more subtle approach based on microbial ecology of these foods should be explored for better exploitation.}, }
@article {pmid33678560, year = {2021}, author = {Acosta, N and Duh Kang, I and Rabaey, K and De Vrieze, J}, title = {Cow manure stabilizes anaerobic digestion of cocoa waste.}, journal = {Waste management (New York, N.Y.)}, volume = {126}, number = {}, pages = {508-516}, doi = {10.1016/j.wasman.2021.02.010}, pmid = {33678560}, issn = {1879-2456}, mesh = {Anaerobiosis ; Animals ; *Biofuels ; Bioreactors ; Cattle ; Female ; Food ; *Manure ; Methane ; }, abstract = {Anaerobic digestion of a mono-feedstock often causes low methane yields and process instability. An effective strategy to overcome these barriers is co-digestion with animal manure. The obtained process improvement is often attributed to buffer capacity, nutrients, vitamins and trace metals, and microorganisms present in manure, but it remains unknown which factor plays the key role in digester performance. Here, we investigated anaerobic digestion of cocoa waste in four different treatments: mono-digestion, addition of synthetic nutrients, co-digestion with sterile cow manure, and co-digestion with raw cow manure. Co-digestion with raw manure resulted in the highest methane yield of 181 ± 39 L kg[-1] VS (volatile solids), similar to the co-digestion with sterile manure, i.e., 162 ± 52 L kg[-1] VS. The supplementation of synthetic nutrients to the anaerobic digestion of cocoa waste only temporarily increased methane yield, indicating that this will tackle a lack of nutrients in the short term, but has a limited long-term contribution to the stabilization of the process. Hence, because of the inability of synthetic nutrients to stabilize the digestion process and the similarity between the digesters fed sterile and raw manure, both at the physico-chemical and microbial level, the key contribution of manure co-digestion with cocoa seems to be the provision of buffering capacity.}, }
@article {pmid33677560, year = {2021}, author = {Vázquez-Ucha, JC and Seoane-Estévez, A and Rodiño-Janeiro, BK and González-Bardanca, M and Conde-Pérez, K and Martínez-Guitián, M and Alvarez-Fraga, L and Arca-Suárez, J and Lasarte-Monterrubio, C and Gut, M and Gut, I and Álvarez-Tejado, M and Oviaño, M and Beceiro, A and Bou, G and , }, title = {Activity of imipenem/relebactam against a Spanish nationwide collection of carbapenemase-producing Enterobacterales.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {76}, number = {6}, pages = {1498-1510}, doi = {10.1093/jac/dkab043}, pmid = {33677560}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology ; *Azabicyclo Compounds/pharmacology ; Bacterial Proteins ; Ceftazidime ; Drug Combinations ; *Imipenem/pharmacology ; Microbial Sensitivity Tests ; Spain ; beta-Lactamases/genetics ; }, abstract = {BACKGROUND: Imipenem/relebactam is a novel carbapenem/β-lactamase inhibitor combination, developed to act against carbapenemase-producing Enterobacterales (CPE).<br><br>OBJECTIVES: To assess the in vitro activity of imipenem/relebactam against a Spanish nationwide collection of CPE by testing the susceptibility of these isolates to 16 widely used antimicrobials and to determine the underlying &#x3b2;-lactam resistance mechanisms involved and the molecular epidemiology of carbapenemases in Spain.<br><br>MATERIALS AND METHODS: Clinical CPE isolates (n&#x200a;=&#x200a;401) collected for 2&#x2009;months from 24 hospitals in Spain were tested. MIC50, MIC90 and susceptibility/resistance rates were interpreted in accordance with the EUCAST guidelines. &#x3b2;-Lactam resistance mechanisms and molecular epidemiology were characterized by WGS.<br><br>RESULTS: For all isolates, high rates of susceptibility to colistin (86.5%; MIC50/90&#x200a;=&#x200a;0.12/8&#x2009;mg/L), imipenem/relebactam (85.8%; MIC50/90&#x200a;=&#x200a;0.5/4&#x2009;mg/L) and ceftazidime/avibactam (83.8%, MIC50/90&#x200a;=&#x200a;1/&#x2265;256&#x2009;mg/L) were observed. The subgroups of isolates producing OXA-48-like (n&#x200a;=&#x200a;305, 75.1%) and KPC-like enzymes (n&#x200a;=&#x200a;44, 10.8%) were highly susceptible to ceftazidime/avibactam (97.7%, MIC50/90&#x200a;=&#x200a;1/2&#x2009;mg/L) and imipenem/relebactam (100.0%, MIC50/90&#x200a;=&#x200a;&#x2264;0.25/1&#x2009;mg/L), respectively.The most widely disseminated high-risk clones of carbapenemase-producing Klebsiella pneumoniae across Spain were found to be ST11, ST147, ST392 and ST15 (mostly associated with OXA-48) and ST258/512 (in all cases producing KPC).<br><br>CONCLUSIONS: Imipenem/relebactam, colistin and ceftazidime/avibactam were the most active antimicrobials against all CPEs. Imipenem/relebactam is a valuable addition to the antimicrobial arsenal used in the fight against CPE, particularly against KPC-producing isolates, which in all cases were susceptible to this combination.}, }
@article {pmid33676244, year = {2021}, author = {Du, B and Wang, Q and Yang, Q and Wang, R and Yuan, W and Yan, L}, title = {Responses of bacterial and bacteriophage communities to long-term exposure to antimicrobial agents in wastewater treatment systems.}, journal = {Journal of hazardous materials}, volume = {414}, number = {}, pages = {125486}, doi = {10.1016/j.jhazmat.2021.125486}, pmid = {33676244}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents ; *Anti-Infective Agents ; Bacteria/genetics ; *Bacteriophages/genetics ; Humans ; *Microbiota ; *Water Purification ; }, abstract = {The occurrence of antibacterial agents has received increasing concern due to their possible threats to human health. However, the effects of antibacterial residues on the evolution and dynamics between bacteria and bacteriophages in wastewater treatment systems have seldom been researched. Especially for phages, little is known about their response to antimicrobial exposure. In this study, two identical anoxic-aerobic wastewater treatment systems were established to evaluate the responses of bacterial and phage communities to long-term exposure to antimicrobial agents. The results indicated simultaneous exposure to combined antimicrobials significantly inhibited (p < 0.05) the abundance of phages and bacteria. Metagenomic sequencing analysis indicated the community of bacteria and phages changed greatly at the genus level due to combined antibacterial exposure. Additionally, long-term exposure to antimicrobial agents promoted the attachment of receptor-binding protein genes to Klebsiella, Escherichia and Salmonella (which were all members of Enterobacteriaceae). Compared to that in the control system, the numbers of receptor-binding protein genes on their possible phages (such as Lambdalikevirus and P2likevirus) were also obviously higher when the microorganisms were exposed to antimicrobials. The results are helpful to understanding the microbial communities and tracking the relationship of phage-bacterial host systems, especially under the pressure of antimicrobial exposure.}, }
@article {pmid33674901, year = {2021}, author = {Ghosh, A and Bhadury, P}, title = {Correction to: Vibrio chemaguriensis sp. nov., from Sundarbans, Bay of Bengal.}, journal = {Current microbiology}, volume = {78}, number = {3}, pages = {1068}, doi = {10.1007/s00284-021-02363-6}, pmid = {33674901}, issn = {1432-0991}, }
@article {pmid33673660, year = {2021}, author = {Madoroba, E and Magwedere, K and Chaora, NS and Matle, I and Muchadeyi, F and Mathole, MA and Pierneef, R}, title = {Microbial Communities of Meat and Meat Products: An Exploratory Analysis of the Product Quality and Safety at Selected Enterprises in South Africa.}, journal = {Microorganisms}, volume = {9}, number = {3}, pages = {}, pmid = {33673660}, issn = {2076-2607}, support = {21.1.1/VPH-01/OVI and 21.1.1/VPH-02/OVI//the Department of Agriculture, Land Reform and Rural Development (DALRRD) under project number 21.1.1/VPH-01/OVI and 21.1.1/VPH-02/OVI/ ; }, abstract = {Consumption of food that is contaminated by microorganisms, chemicals, and toxins may lead to significant morbidity and mortality, which has negative socioeconomic and public health implications. Monitoring and surveillance of microbial diversity along the food value chain is a key component for hazard identification and evaluation of potential pathogen risks from farm to the consumer. The aim of this study was to determine the microbial diversity in meat and meat products from different enterprises and meat types in South Africa. Samples (n = 2017) were analyzed for Yersinia enterocolitica, Salmonella species, Listeria monocytogenes, Campylobacter jejuni, Campylobacter coli, Staphylococcus aureus, Clostridium perfringens, Bacillus cereus, and Clostridium botulinum using culture-based methods. PCR was used for confirmation of selected pathogens. Of the 2017 samples analyzed, microbial ecology was assessed for selected subsamples where next generation sequencing had been conducted, followed by the application of computational methods to reconstruct individual genomes from the respective sample (metagenomics). With the exception of Clostridium botulinum, selective culture-dependent methods revealed that samples were contaminated with at least one of the tested foodborne pathogens. The data from metagenomics analysis revealed the presence of diverse bacteria, viruses, and fungi. The analyses provide evidence of diverse and highly variable microbial communities in products of animal origin, which is important for food safety, food labeling, biosecurity, and shelf life limiting spoilage by microorganisms.}, }
@article {pmid33671218, year = {2021}, author = {Dumolin, C and Peeters, C and De Canck, E and Boon, N and Vandamme, P}, title = {Network Analysis Based on Unique Spectral Features Enables an Efficient Selection of Genomically Diverse Operational Isolation Units.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, pmid = {33671218}, issn = {2076-2607}, support = {//Wellcome Trust/United Kingdom ; GOH3817N//European Marine Biological Resource Centre Belgium/ ; BOF15/GOA/006//Universiteit Gent/ ; }, abstract = {Culturomics-based bacterial diversity studies benefit from the implementation of MALDI-TOF MS to remove genomically redundant isolates from isolate collections. We previously introduced SPeDE, a novel tool designed to dereplicate spectral datasets at an infraspecific level into operational isolation units (OIUs) based on unique spectral features. However, biological and technical variation may result in methodology-induced differences in MALDI-TOF mass spectra and hence provoke the detection of genomically redundant OIUs. In the present study, we used three datasets to analyze to which extent hierarchical clustering and network analysis allowed to eliminate redundant OIUs obtained through biological and technical sample variation and to describe the diversity within a set of spectra obtained from 134 unknown soil isolates. Overall, network analysis based on unique spectral features in MALDI-TOF mass spectra enabled a superior selection of genomically diverse OIUs compared to hierarchical clustering analysis and provided a better understanding of the inter-OIU relationships.}, }
@article {pmid33670965, year = {2021}, author = {Lambrecht, E and Coillie, EV and Boon, N and Heyndrickx, M and Wiele, TV}, title = {Transfer of Antibiotic Resistance Plasmid from Commensal E. coli Towards Human Intestinal Microbiota in the M-SHIME: Effect of E. coli dosis, Human Individual and Antibiotic Use.}, journal = {Life (Basel, Switzerland)}, volume = {11}, number = {3}, pages = {}, pmid = {33670965}, issn = {2075-1729}, support = {BOF17/GOA/032//Bijzonder Onderzoeksfonds UGent/ ; RF 13/9 TRAMRISK//FOD Volksgezondheid, Veiligheid van de Voedselketen en Leefmilieu/ ; }, abstract = {Along with (in) direct contact with animals and a contaminated environment, humans are exposed to antibiotic-resistant bacteria by consumption of food. The implications of ingesting antibiotic-resistant commensal bacteria are unknown, as dose-response data on resistance transfer and spreading in our gut is lacking. In this study, transfer of a resistance plasmid (IncF), harbouring several antibiotic resistance genes, from a commensal E. coli strain towards human intestinal microbiota was assessed using a Mucosal Simulator of the Human Intestinal Ecosystem (M-SHIME). More specifically, the effect of the initial E. coli plasmid donor concentration (10[5] and 10[7] CFU/meal), antibiotic treatment (cefotaxime) and human individual (n = 6) on plasmid transfer towards lumen coliforms and anaerobes was determined. Transfer of the resistance plasmid to luminal coliforms and anaerobes was observed shortly after the donor strain arrived in the colon and was independent of the ingested dose. Transfer occurred in all six simulated colons and despite their unique microbial community composition, no differences could be detected in antibiotic resistance transfer rates between the simulated human colons. After 72 h, resistant coliform transconjugants levels ranged from 7.6 × 10[4] to 7.9 × 10[6] CFUcefotaxime resistant/Ml colon lumen. Presence of the resistance plasmid was confirmed and quantified by PCR and qPCR. Cefotaxime treatment led to a significant reduction (85%) in resistant coliforms, however no significant effect on the total number of cultivable coliforms and anaerobes was observed.}, }
@article {pmid33670234, year = {2021}, author = {Vigneron, A and Cruaud, P and Ducellier, F and Head, IM and Tsesmetzis, N}, title = {Syntrophic Hydrocarbon Degradation in a Decommissioned Off-Shore Subsea Oil Storage Structure.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, pmid = {33670234}, issn = {2076-2607}, support = {-//Shell Global Solutions International/ ; }, abstract = {Over the last decade, metagenomic studies have revealed the impact of oil production on the microbial ecology of petroleum reservoirs. However, despite their fundamental roles in bioremediation of hydrocarbons, biocorrosion, biofouling and hydrogen sulfide production, oil field and oil production infrastructure microbiomes are poorly explored. Understanding of microbial activities within oil production facilities is therefore crucial for environmental risk mitigation, most notably during decommissioning. The analysis of the planktonic microbial community from the aqueous phase of a subsea oil-storage structure was conducted. This concrete structure was part of the production platform of the Brent oil field (North Sea), which is currently undergoing decommissioning. Quantification and sequencing of microbial 16S rRNA genes, metagenomic analysis and reconstruction of metagenome assembled genomes (MAGs) revealed a unique microbiome, strongly dominated by organisms related to Dethiosulfatibacter and Cloacimonadetes. Consistent with the hydrocarbon content in the aqueous phase of the structure, a strong potential for degradation of low molecular weight aromatic hydrocarbons was apparent in the microbial community. These degradation pathways were associated with taxonomically diverse microorganisms, including the predominant Dethiosulfatibacter and Cloacimonadetes lineages, expanding the list of potential hydrocarbon degraders. Genes associated with direct and indirect interspecies exchanges (multiheme type-C cytochromes, hydrogenases and formate/acetate metabolism) were widespread in the community, suggesting potential syntrophic hydrocarbon degradation processes in the system. Our results illustrate the importance of genomic data for informing decommissioning strategies in marine environments and reveal that hydrocarbon-degrading community composition and metabolisms in man-made marine structures might differ markedly from natural hydrocarbon-rich marine environments.}, }
@article {pmid33670115, year = {2021}, author = {De Pessemier, B and Grine, L and Debaere, M and Maes, A and Paetzold, B and Callewaert, C}, title = {Gut-Skin Axis: Current Knowledge of the Interrelationship between Microbial Dysbiosis and Skin Conditions.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, pmid = {33670115}, issn = {2076-2607}, abstract = {The microbiome plays an important role in a wide variety of skin disorders. Not only is the skin microbiome altered, but also surprisingly many skin diseases are accompanied by an altered gut microbiome. The microbiome is a key regulator for the immune system, as it aims to maintain homeostasis by communicating with tissues and organs in a bidirectional manner. Hence, dysbiosis in the skin and/or gut microbiome is associated with an altered immune response, promoting the development of skin diseases, such as atopic dermatitis, psoriasis, acne vulgaris, dandruff, and even skin cancer. Here, we focus on the associations between the microbiome, diet, metabolites, and immune responses in skin pathologies. This review describes an exhaustive list of common skin conditions with associated dysbiosis in the skin microbiome as well as the current body of evidence on gut microbiome dysbiosis, dietary links, and their interplay with skin conditions. An enhanced understanding of the local skin and gut microbiome including the underlying mechanisms is necessary to shed light on the microbial involvement in human skin diseases and to develop new therapeutic approaches.}, }
@article {pmid33669689, year = {2021}, author = {Duysburgh, C and Van den Abbeele, P and Kamil, A and Fleige, L and De Chavez, PJ and Chu, Y and Barton, W and O'Sullivan, O and Cotter, PD and Quilter, K and Joyce, SA and Murphy, M and DunnGalvin, G and Dinan, TG and Marzorati, M}, title = {In vitro-in vivo Validation of Stimulatory Effect of Oat Ingredients on Lactobacilli.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {2}, pages = {}, pmid = {33669689}, issn = {2076-0817}, abstract = {The prebiotic activity of a commercially available oat product and a novel oat ingredient, at similar β-glucan loads, was tested using a validated in vitro gut model (M-SHIME[®]). The novel oat ingredient was tested further at lower β-glucan loads in vitro, while the commercially available oat product was assessed in a randomised, single-blind, placebo-controlled, and cross-over human study. Both approaches focused on healthy individuals with mild hypercholesterolemia. In vitro analysis revealed that both oat products strongly stimulated Lactobacillaceae and Bifidobacteriaceae in the intestinal lumen and the simulated mucus layer, and corresponded with enhanced levels of acetate and lactate with cross-feeding interactions leading to an associated increase in propionate and butyrate production. The in vitro prebiotic activity of the novel oat ingredient remained at lower β-glucan levels, indicating the prebiotic potential of the novel oat product. Finally, the stimulation of Lactobacillus spp. was confirmed during the in vivo trial, where lactobacilli abundance significantly increased in the overall population at the end of the intervention period with the commercially available oat product relative to the control product, indicating the power of in vitro gut models in predicting in vivo response of the microbial community to dietary modulation.}, }
@article {pmid33669125, year = {2021}, author = {Ugalde-Salas, P and Ramírez C, H and Harmand, J and Desmond-Le Quéméner, E}, title = {Microbial Interactions as Drivers of a Nitrification Process in a Chemostat.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {8}, number = {3}, pages = {}, pmid = {33669125}, issn = {2306-5354}, support = {16-CE04-0003//Agence Nationale de la Recherche/ ; 1200355//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; 170001//Basal Program CMM-AFB/ ; }, abstract = {This article deals with the inclusion of microbial ecology measurements such as abundances of operational taxonomic units in bioprocess modelling. The first part presents the mathematical analysis of a model that may be framed within the class of Lotka-Volterra models fitted to experimental data in a chemostat setting where a nitrification process was operated for over 500 days. The limitations and the insights of such an approach are discussed. In the second part, the use of an optimal tracking technique (developed within the framework of control theory) for the integration of data from genetic sequencing in chemostat models is presented. The optimal tracking revisits the data used in the aforementioned chemostat setting. The resulting model is an explanatory model, not a predictive one, it is able to reconstruct the different forms of nitrogen in the reactor by using the abundances of the operational taxonomic units, providing some insights into the growth rate of microbes in a complex community.}, }
@article {pmid33669086, year = {2021}, author = {Cipriano, MAP and Freitas-Iório, RP and Dimitrov, MR and de Andrade, SAL and Kuramae, EE and Silveira, APDD}, title = {Plant-Growth Endophytic Bacteria Improve Nutrient Use Efficiency and Modulate Foliar N-Metabolites in Sugarcane Seedling.}, journal = {Microorganisms}, volume = {9}, number = {3}, pages = {}, pmid = {33669086}, issn = {2076-2607}, support = {456420-2013-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2008/56147-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; PNPD//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, abstract = {Beneficial plant-microbe interactions lead to physiological and biochemical changes that may result in plant-growth promotion. This study evaluated the effect of the interaction between sugarcane and endophytic bacterial strains on plant physiological and biochemical responses under two levels of nitrogen (N) fertilization. Six strains of endophytic bacteria, previously selected as plant growth-promoting bacteria (PGPB), were used to inoculate sugarcane mini stalks, with and without N fertilization. After 45 days, biomass production; shoot nutrient concentrations; foliar polyamine and free amino acid profiles; activities of nitrate reductase and glutamine synthase; and the relative transcript levels of the GS1, GS2, and SHR5 genes in sugarcane leaves were determined. All six endophytic strains promoted sugarcane growth, increasing shoot and root biomass, plant nutritional status, and the use efficiency of most nutrients. The inoculation-induced changes at the biochemical level altered the foliar free amino acid and polyamine profiles, mainly regarding the relative concentrations of citrulline, putrescine, glycine, alanine, glutamate, glutamine, proline, and aspartate. The transcription of GS1, GS2, and SHR5 was higher in the N fertilized seedlings, and almost not altered by endophytic bacterial strains. The endophytic strains promoted sugarcane seedlings growth mainly by improving nutrient efficiency. This improvement could not be explained by their ability to induce the production of amino acid and polyamine composts, or GS1, GS2, and SHR5, showing that complex interactions may be associated with enhancement of the sugarcane seedlings' performance by endophytic bacteria. The strains demonstrated biotechnological potential for sugarcane seedling production.}, }
@article {pmid33668823, year = {2021}, author = {Van den Abbeele, P and Sprenger, N and Ghyselinck, J and Marsaux, B and Marzorati, M and Rochat, F}, title = {A Comparison of the In Vitro Effects of 2'Fucosyllactose and Lactose on the Composition and Activity of Gut Microbiota from Infants and Toddlers.}, journal = {Nutrients}, volume = {13}, number = {3}, pages = {}, pmid = {33668823}, issn = {2072-6643}, mesh = {Bifidobacterium ; Breast Feeding ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infant ; Infant Nutritional Physiological Phenomena ; Lactose/*pharmacology ; Milk, Human/*chemistry ; Trisaccharides/*pharmacology ; }, abstract = {Because of the recognized health benefits of breast milk, it is recommended as the sole nutrition source during the first 6 months of life. Among the bioactive components are human milk oligosaccharides (HMOs) that exert part of their activity via the gut microbiota. Here, we investigated the gut microbiota fermentation of HMO 2'fucosyllactose (2'-FL), using two in vitro models (48 h fecal incubations and the long-term mucosal simulator of the human intestinal microbial ecosystem [M-SHIME[®]]) with fecal samples from 3-month-old breastfed (BF) infants as well as 2-3 year old toddlers. The short-term model allowed the screening of five donors for each group and provided supportive data for the M-SHIME[®] study. A key finding was the strong and immediate increase in the relative abundance of Bifidobacteriaceae following 2'-FL fermentation by both the BF infant and toddler microbiota in the M-SHIME[®]. At the metabolic level, while decreasing branched-chain fatty acids, 2'-FL strongly increased acetate production together with increases in the health-related propionate and butyrate whilst gas production only mildly increased. Notably, consistently lower gas production was observed with 2'-FL fermentation as compared to lactose, suggesting that reduced discomfort during the dynamic microbiome establishment in early life may be an advantage along with the bifidogenic effect observed.}, }
@article {pmid33668312, year = {2021}, author = {Becker, AAMJ and Hill, KC and Butaye, P}, title = {Unraveling the Gut Microbiome of the Invasive Small Indian Mongoose (Urva auropunctata) in the Caribbean.}, journal = {Microorganisms}, volume = {9}, number = {3}, pages = {}, pmid = {33668312}, issn = {2076-2607}, support = {41001-2016//One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine/ ; }, abstract = {Small Indian mongooses (Urva auropunctata) are among the most pervasive predators to disrupt the native ecology on Caribbean islands and are strongly entrenched in their areas of introduction. Few studies, however, have considered the microbial ecology of such biological invasions. In this study, we investigated the gut microbiota of invasive small Indian mongooses in terms of taxonomic diversity and functional potential. To this end, we collected fecal samples from 60 free-roaming mongooses trapped in different vegetation zones on the island Saint Kitts. The core gut microbiome, assessed by 16S rRNA amplicon gene sequencing on the Ion S5[TM] XL platform, reflects a carnivore-like signature with a dominant abundance of Firmicutes (54.96%), followed by Proteobacteria (13.98%) and Fusobacteria (12.39%), and a relatively minor contribution of Actinobacteria (10.4%) and Bacteroidetes (6.40%). Mongooses trapped at coastal sites exhibited a higher relative abundance of Fusobacterium spp. whereas those trapped in scrubland areas were enriched in Bacteroidetes, but there was no site-specific difference in predicted metabolic properties. Between males and females, beta-diversity was not significantly different and no sex-specific strategies for energy production were observed. However, the relative abundance of Gammaproteobacteria, and more specifically, Enterobacteriaceae, was significantly higher in males. This first description of the microbial profile of small Indian mongooses provides new insights into their bioecology and can serve as a springboard to further elucidating this invasive predator's impact throughout the Caribbean.}, }
@article {pmid33667294, year = {2021}, author = {Ranallo, RT and McDonald, LC and Halpin, AL and Hiltke, T and Young, VB}, title = {The State of Microbiome Science at the Intersection of Infectious Diseases and Antimicrobial Resistance.}, journal = {The Journal of infectious diseases}, volume = {223}, number = {12 Suppl 2}, pages = {S187-S193}, pmid = {33667294}, issn = {1537-6613}, support = {U01 AI124255/AI/NIAID NIH HHS/United States ; U54 CK000481/CK/NCEZID CDC HHS/United States ; U54 CK000607/CK/NCEZID CDC HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Antimicrobial Stewardship ; Communicable Diseases/diagnosis/immunology/*microbiology/therapy ; *Drug Resistance, Microbial ; Fecal Microbiota Transplantation ; Homeostasis ; Host-Pathogen Interactions ; Humans ; Immunity ; *Microbiota/drug effects ; }, abstract = {Along with the rise in modern chronic diseases, ranging from diabetes to asthma, there are challenges posed by increasing antibiotic resistance, which results in difficult-to-treat infections, as well as sepsis. An emerging and unifying theme in the pathogenesis of these diverse public health threats is changes in the microbial communities that inhabit multiple body sites. Although there is great promise in exploring the role of these microbial communities in chronic disease pathogenesis, the shorter timeframe of most infectious disease pathogenesis may allow early translation of our basic scientific understanding of microbial ecology and host-microbiota-pathogen interactions. Likely translation avenues include development of preventive strategies, diagnostics, and therapeutics. For example, as basic research related to microbial pathogenesis continues to progress, Clostridioides difficile infection is already being addressed clinically through at least 2 of these 3 avenues: targeted antibiotic stewardship and treatment of recurrent disease through fecal microbiota transplantation.}, }
@article {pmid33666710, year = {2021}, author = {Fitzgerald, RS and Sanderson, IR and Claesson, MJ}, title = {Paediatric Inflammatory Bowel Disease and its Relationship with the Microbiome.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {833-844}, pmid = {33666710}, issn = {1432-184X}, support = {GOIPG/2017/1573//Irish Research Council/ ; 510264//Crohn's and Colitis Foundation/ ; SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Child ; *Colitis, Ulcerative ; *Crohn Disease ; Humans ; *Inflammatory Bowel Diseases ; *Microbiota ; *Mycobiome ; }, abstract = {Paediatric inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the digestive tract, comprising of Crohn's disease (CD), ulcerative colitis (UC), and, where classification is undetermined, inflammatory bowel disease unclassified (IBDU). Paediatric IBD incidence is increasing globally, with prevalence highest in the developed world. Though no specific causative agent has been identified for paediatric IBD, it is believed that a number of factors may contribute to the development of the disease, including genetics and the environment. Another potential component in the development of IBD is the microbiota in the digestive tract, particularly the gut. While the exact role that the microbiome plays in IBD is unclear, many studies acknowledge the complex relationship between the gut bacteria and pathogenesis of IBD. In this review, we look at the increasing number of studies investigating the role the microbiome and other biomes play in paediatric patients with IBD, particularly changes associated with IBD, varying disease states, and therapeutics. The paediatric IBD microbiome is significantly different to that of healthy children, with decreased diversity and differences in bacterial composition (such as a decrease in Firmicutes). Changes in the microbiome relating to various treatments of IBD and disease severity have also been observed in multiple studies. Changes in diversity and composition may also extend to other biomes in paediatric IBD, such as the virome and the mycobiome. Research into biome differences in IBD paediatric patients may help progress our understanding of the aetiology of the disease.}, }
@article {pmid33665722, year = {2021}, author = {Cureau, N and Threlfall, R and Marasini, D and Lavefve, L and Carbonero, F}, title = {Year, Location, and Variety Impact on Grape-Associated Mycobiota of Arkansas-Grown Wine Grapes for Wine Production.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {845-858}, pmid = {33665722}, issn = {1432-184X}, mesh = {Arkansas ; *Ascomycota ; *Vitis ; *Wine ; Yeasts ; }, abstract = {Wine grape berries (Vitis spp.) harbor a wide variety of yeasts and filamentous fungi that impact grapevine health and the winemaking process. Identification of these fungi could be important for controlling and improving wine production. The use of high-throughput sequencing (HTS) strategies has enabled identification and quantification of bacterial and fungal species in vineyards. The aims of this study were to identify mycobiota from Cabernet Sauvignon and Zinfandel (V. vinifera), Carlos and Noble muscadines (V. rotundifolia), Cynthiana (V. aestivalis), and Vignoles hybrid (cross of different Vitis spp.) grapes, and investigate the effect of grape variety, location, and year on grape fungal communities. Grape berries were collected in 2016 and 2017 from four vineyards located in Arkansas. The HTS of the Internal Transcribed Spacer 1 region was used to identify grape indigenous epiphytic and endophytic fungal communities. The predominant genera identified on the Arkansas wine grapes were Uwebraunia, Zymoseptoria, Papiliotrema, Meyerozyma, Filobasidium, and Curvibasidium. Overall, the data suggested that grape fungal community distribution and relative abundance were influenced by grape variety, year, and location, but each was influenced to a different extent. Not only were grape mycobiota influenced by year, variety, and location but also it appeared that communities from the previous year impacted microbial communities the following year. For example, an increase of the mycoparasite Ampelomyces quisqualis was noticed in 2017 on grapes that carried the causal agent of powdery mildew, Erysiphe necator, in 2016, thus, amplifying the importance of vineyard microbiota knowledge for disease management and winemaking.}, }
@article {pmid33665721, year = {2021}, author = {Zhou, X and Li, B and Wei, J and Ye, Y and Xu, J and Chen, L and Lu, C}, title = {Temperature Influenced the Comammox Community Composition in Drinking Water and Wastewater Treatment Plants.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {870-884}, pmid = {33665721}, issn = {1432-184X}, support = {41807029//National Natural Science Foundation of China/ ; 51679067//National Natural Science Foundation of China/ ; 51879088//National Natural Science Foundation of China/ ; 51709085//National Natural Science Foundation of China/ ; B200201028//Fundamental Research Funds for the Central Universities/ ; B200204002//Fundamental Research Funds for the Central Universities/ ; B200202158//Fundamental Research Funds for the Central Universities/ ; B200204033//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Ammonia ; Archaea ; Bacteria/genetics ; *Drinking Water ; Ecosystem ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Temperature ; *Water Purification ; }, abstract = {Nitrification is a pivotal step applied in water engineered systems for nitrogen removal. Temperature variation due to seasonal changes is a great challenge for maintaining nitrogen removal efficiency in water engineered ecosystems by affecting nitrifier activities. Research on the abundance, activity, and metabolic characteristics of nitrifiers can provide information for selecting suitable design parameters to ensure efficient nitrogen removal in different seasons. To date, the temperature-related niche separation of comammox, a newly discovered nitrifier with potential high-growth yield, has been rarely investigated. This study addressed the distribution of comammox and canonical nitrifying guilds in drinking water treatment plants (DWTPs) and wastewater treatment plants (WWTPs) in different seasons. qPCR-based surveys showed that comammox ubiquitously distributed and greatly outnumbered other ammonia-oxidizing prokaryotes in both DWTPs and WWTPs, except in Aug samples from DWTPs, suggesting the potential competitive advantage of AOA in summer. The nitrificans-like comammox and nitrosa-like comammox comprised the majority of the comammox community in DWTPs and WWTPs, respectively, and COD and NH4[+] concentrations significantly contributed to the distinct comammox phylotype distribution between DWTPs and WWTPs. The temperature-related distribution pattern of the comammox community was observed at each site. Moreover, the network complex of comammox communities was highest in Dec at all the sites, possibly contributing to the survival of comammox community in low temperature conditions.}, }
@article {pmid33664141, year = {2021}, author = {de Assis Costa, OY and Meima-Franke, M and Bodelier, PLE}, title = {Complete and Draft Genome Sequences of Aerobic Methanotrophs Isolated from a Riparian Wetland.}, journal = {Microbiology resource announcements}, volume = {10}, number = {9}, pages = {}, pmid = {33664141}, issn = {2576-098X}, abstract = {Wetlands are important sources of methane emissions, and the impacts of these emissions can be mitigated by methanotrophic bacteria. The genomes of methanotrophs Methylomonas sp. strain LL1 and Methylosinus sp. strain H3A, as well as Methylocystis sp. strains H4A, H15, H62, and L43, were sequenced and are reported here.}, }
@article {pmid33663865, year = {2021}, author = {Petri, RM and Aditya, S and Humer, E and Zebeli, Q}, title = {Effect of an intramammary lipopolysaccharide challenge on the hindgut microbial composition and fermentation of dairy cattle experiencing intermittent subacute ruminal acidosis.}, journal = {Journal of dairy science}, volume = {104}, number = {5}, pages = {5417-5431}, doi = {10.3168/jds.2020-19496}, pmid = {33663865}, issn = {1525-3198}, mesh = {*Acidosis/metabolism/veterinary ; Animals ; Cattle ; *Cattle Diseases/metabolism ; Diet/veterinary ; Female ; Fermentation ; Hydrogen-Ion Concentration ; Lactation ; Lipopolysaccharides/metabolism ; Pregnancy ; Rumen/metabolism ; }, abstract = {Feeding grain-rich diets often results in subacute ruminal acidosis (SARA), a condition associated with ruminal dysbiosis and systemic inflammation. Yet, the effect of SARA on hindgut microbiota, and whether this condition is aggravated by exogenous immune stimuli, is less understood. Therefore, the aims of this study were to determine the effects of an intermittent high-grain SARA model on the hindgut microbial community, and to evaluate whether the effects of SARA on the fecal microbiome and fermentation were further affected by an intramammary lipopolysaccharide (LPS) challenge. A total of 18 early-lactating Simmental cows were divided into 3 groups (n = 6); 2 were fed a SARA-inducing feeding regimen (60% concentrate), 1 was fed a control (CON) diet (40% concentrate). On d 30, 1 SARA group (SARA-LPS) and the CON group (CON-LPS) were intramammarily challenged with a single dose of 50 µg of LPS from Escherichia coli O26:B6, whereas the remaining 6 SARA cows (SARA-PLA) received a placebo. Using a longitudinal randomized controlled design, with grouping according to parity and days in milk), statistical analysis was performed with baseline measurements used as a covariate in a mixed model procedure. The SARA-inducing feeding challenge resulted in decreased fecal pH and increased butyrate as a proportion of total short-chain fatty acids in the feces. On d 30, SARA-challenged cows had decreased fecal diversity as shown by the Shannon and Chao1 indices and a decrease in the relative abundance of Euryarchaeota and cellulolytic genera, and numerical increases in the relative abundance of several Firmicutes associated with starch and secondary fermentation. The LPS challenge did not affect the fecal pH and short-chain fatty acids, but increased the Chao1 richness index in an interaction with the SARA challenge, and affected the relative abundance of Verrucomicrobia (1.13%), Actinobacteria (0.19%), and Spirochaetes (0.002%), suggesting an effect on the microbial ecology of the hindgut during SARA conditions. In conclusion, the SARA-inducing feeding regimen promoted important microbial changes at d 30, including reduced diversity and evenness compared with CON, whereas the external LPS challenge led to changes in the microbial community without affecting fecal fermentation properties.}, }
@article {pmid33661311, year = {2021}, author = {González-Olalla, JM and Medina-Sánchez, JM and Norici, A and Carrillo, P}, title = {Regulation of Phagotrophy by Prey, Low Nutrients, and Low Light in the Mixotrophic Haptophyte Isochrysis galbana.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {981-993}, pmid = {33661311}, issn = {1432-184X}, support = {CGL2015-67682-R//Ministerio de Econom&#xed;a y Competitividad/ ; GA&#x10c;R 16-16343S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; FPU14/00977//Ministerio de Educaci&#xf3;n of Spanish Government/ ; }, mesh = {Autotrophic Processes ; Bacteria ; *Haptophyta ; Light ; Nutrients ; Phosphorus ; }, abstract = {Mixotrophy combines autotrophy and phagotrophy in the same cell. However, it is not known to what extent the phagotrophy influences metabolism, cell composition, and growth. In this work, we assess, on the one hand (first test), the role of phagotrophy on the elemental and biochemical composition, cell metabolism, and enzymes related to C, N, and S metabolism of Isochrysis galbana Parke, 1949. On the other hand, we study how a predicted increase of phagotrophy under environmental conditions of low nutrients (second test) and low light (third test) can affect its metabolism and growth. Our results for the first test revealed that bacterivory increased the phosphorous and iron content per cell, accelerating cell division and improving the cell fitness; in addition, the stimulation of some C and N enzymatic routes help to maintain, to some degree, compositional homeostasis. Under nutrient or light scarcity, I. galbana grew more slowly despite greater bacterial consumption, and the activities of key enzymes involved in C, N, and S metabolism changed according to a predominantly phototrophic strategy of nutrition in this alga. Contrary to recent studies, the stimulation of phagotrophy under low nutrient and low irradiance did not imply greater and more efficient C flux.}, }
@article {pmid33660069, year = {2021}, author = {Wang, H and Li, X and Li, X and Li, F and Su, Z and Zhang, H}, title = {Community Composition and Co-Occurrence Patterns of Diazotrophs along a Soil Profile in Paddy Fields of Three Soil Types in China.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {961-970}, pmid = {33660069}, issn = {1432-184X}, support = {XDB15010101//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; No. 41671258//National Natural Science Foundation of China/ ; }, mesh = {*Bradyrhizobium ; Nitrogen/analysis ; Nitrogen Fixation ; *Soil ; Soil Microbiology ; }, abstract = {Diazotrophs play a key role in biological nitrogen (N2) fixation. However, we know little about the distribution of the diazotrophic community along the soil profile in paddy fields. Here, we used Illumina MiSeq sequencing, targeting the nitrogenase reductase (nifH) gene, to investigate changes with depth (0-100 cm) in the diazotrophic community in paddy soils of three regions (Changshu, Hailun, and Yingtan) in China. The results indicated that most diazotrophs belonged to the phylum Proteobacteria, accounting for 78.05% of the total number of sequences. The diazotrophic diversity was generally highest in the 10-20 cm layer, and then significantly decreased with soil depth. Principal coordinate analysis and PERMANOVA indicated that the diazotrophic community structure was significantly affected by region and soil depth. There were obvious differences in the composition of the diazotrophic community between the topsoil (0-40 cm) and the subsoil (40-100 cm). Anaeromyxobacter, Sideroxydans, Methylomonas, Nostoc, Methanocella, and Methanosaeta were enriched in the topsoil, while Geobacter, Azoarcus, Bradyrhizobium, and Dechloromonas were concentrated in the subsoil. Furthermore, co-occurrence network analysis showed that the diazotrophic network in the topsoil was more complex than that in the subsoil. Distance-based redundancy analysis indicated that soil total C and N content and pH were the main factors influencing the vertical variation in the diazotrophic community. These results highlighted that depth has a great impact on the diazotrophic diversity, community composition, and co-occurrence patterns in paddy soil.}, }
@article {pmid33659955, year = {2020}, author = {Ross, BN and Whiteley, M}, title = {Ignoring social distancing: advances in understanding multi-species bacterial interactions.}, journal = {Faculty reviews}, volume = {9}, number = {}, pages = {23}, pmid = {33659955}, issn = {2732-432X}, abstract = {Almost every ecosystem on this planet is teeming with microbial communities made of diverse bacterial species. At a reductionist view, many of these bacteria form pairwise interactions, but, as the field of view expands, the neighboring organisms and the abiotic environment can play a crucial role in shaping the interactions between species. Over the years, a strong foundation of knowledge has been built on isolated pairwise interactions between bacteria, but now the field is advancing toward understanding how cohabitating bacteria and natural surroundings affect these interactions. Use of bottom-up approaches, piecing communities together, and top-down approaches that deconstruct communities are providing insight on how different species interact. In this review, we highlight how studies are incorporating more complex communities, mimicking the natural environment, and recurring findings such as the importance of cooperation for stability in harsh environments and the impact of bacteria-induced environmental pH shifts. Additionally, we will discuss how omics are being used as a top-down approach to identify previously unknown interspecies bacterial interactions and the challenges of these types of studies for microbial ecology.}, }
@article {pmid33659338, year = {2020}, author = {Marinkovic, ZS and Vulin, C and Acman, M and Song, X and Di Meglio, JM and Lindner, AB and Hersen, P}, title = {Observing Nutrient Gradients, Gene Expression and Growth Variation Using the "Yeast Machine" Microfluidic Device.}, journal = {Bio-protocol}, volume = {10}, number = {13}, pages = {e3668}, pmid = {33659338}, issn = {2331-8325}, abstract = {The natural environment of microbial cells like bacteria and yeast is often a complex community in which growth and internal organization reflect morphogenetic processes and interactions that are dependent on spatial position and time. While most of research is performed in simple homogeneous environments (e.g., bulk liquid cultures), which cannot capture full spatiotemporal community dynamics, studying biofilms or colonies is complex and usually does not give access to the spatiotemporal dynamics at single cell level. Here, we detail a protocol for generation of a microfluidic device, the "yeast machine", with arrays of long monolayers of yeast colonies to advance the global understanding of how intercellular metabolic interactions affect the internal structure of colonies within defined and customizable spatial dimensions. With Saccharomyces cerevisiae as a model yeast system we used the "yeast machine" to demonstrate the emergence of glucose gradients by following expression of fluorescently labelled hexose transporters. We further quantified the expression spatial patterns with intra-colony growth rates and expression of other genes regulated by glucose availability. In addition to this, we showed that gradients of amino acids also form within a colony, potentially opening similar approaches to study spatiotemporal formation of gradients of many other nutrients and metabolic waste products. This approach could be used in the future to decipher the interplay between long-range metabolic interactions, cellular development, and morphogenesis in other same species or more complex multi-species systems at single-cell resolution and timescales relevant to ecology and evolution.}, }
@article {pmid33658719, year = {2021}, author = {Graf, JS and Schorn, S and Kitzinger, K and Ahmerkamp, S and Woehle, C and Huettel, B and Schubert, CJ and Kuypers, MMM and Milucka, J}, title = {Anaerobic endosymbiont generates energy for ciliate host by denitrification.}, journal = {Nature}, volume = {591}, number = {7850}, pages = {445-450}, pmid = {33658719}, issn = {1476-4687}, mesh = {Adenosine Triphosphate/metabolism ; *Anaerobiosis ; Bacteria/genetics/*metabolism ; Biological Evolution ; Cell Respiration ; Ciliophora/chemistry/cytology/*metabolism ; Citric Acid Cycle/genetics ; *Denitrification ; Electron Transport/genetics ; *Energy Metabolism ; Genome, Bacterial/genetics ; *Host Microbial Interactions/genetics ; Mitochondria ; Nitrates/metabolism ; Oxygen/metabolism ; Phylogeny ; *Symbiosis ; }, abstract = {Mitochondria are specialized eukaryotic organelles that have a dedicated function in oxygen respiration and energy production. They evolved about 2 billion years ago from a free-living bacterial ancestor (probably an alphaproteobacterium), in a process known as endosymbiosis[1,2]. Many unicellular eukaryotes have since adapted to life in anoxic habitats and their mitochondria have undergone further reductive evolution[3]. As a result, obligate anaerobic eukaryotes with mitochondrial remnants derive their energy mostly from fermentation[4]. Here we describe 'Candidatus Azoamicus ciliaticola', which is an obligate endosymbiont of an anaerobic ciliate and has a dedicated role in respiration and providing energy for its eukaryotic host. 'Candidatus A. ciliaticola' contains a highly reduced 0.29-Mb genome that encodes core genes for central information processing, the electron transport chain, a truncated tricarboxylic acid cycle, ATP generation and iron-sulfur cluster biosynthesis. The genome encodes a respiratory denitrification pathway instead of aerobic terminal oxidases, which enables its host to breathe nitrate instead of oxygen. 'Candidatus A. ciliaticola' and its ciliate host represent an example of a symbiosis that is based on the transfer of energy in the form of ATP, rather than nutrition. This discovery raises the possibility that eukaryotes with mitochondrial remnants may secondarily acquire energy-providing endosymbionts to complement or replace functions of their mitochondria.}, }
@article {pmid33656687, year = {2021}, author = {Ceola, G and Goss-Souza, D and Alves, J and Alves da Silva, A and Stürmer, SL and Baretta, D and Sousa, JP and Klauberg-Filho, O}, title = {Biogeographic Patterns of Arbuscular Mycorrhizal Fungal Communities Along a Land-Use Intensification Gradient in the Subtropical Atlantic Forest Biome.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {942-960}, pmid = {33656687}, issn = {1432-184X}, support = {CNPq-SisBiota 563251/2010-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Biodiversity ; Ecosystem ; Forests ; Fungi ; *Mycobiome ; *Mycorrhizae/genetics ; Soil ; Soil Microbiology ; }, abstract = {Information concerning arbuscular mycorrhizal (AM) fungal geographical distribution in tropical and subtropical soils from the Atlantic Forest (a global hotspot of biodiversity) are scarce and often restricted to the evaluation of richness and abundance of AM fungal species at specific ecosystems or local landscapes. In this study, we hypothesized that AM fungal diversity and community composition in subtropical soils would display fundamental differences in their geographical patterns, shaped by spatial distance and land-use change, at local and regional scales. AM fungal community composition was examined by spore-based taxonomic analysis, using soil trap cultures. Acaulospora koskei and Glomus were found as generalists, regardless of mesoregions and land uses. Other Acaulospora species were also found generalists within mesoregions. Land-use change and intensification did not influence AM fungal composition, partially rejecting our first hypothesis. We then calculated the distance-decay of similarities among pairs of AM fungal communities and the distance-decay relationship within and over mesoregions. We also performed the Mantel test and redundancy analysis to discriminate the main environmental drivers of AM fungal diversity and composition turnover. Overall, we found significant distance-decays for all land uses. We also observed a distance-decay relationship within the mesoregion scale (< 104 km) and these changes were correlated mainly to soil type (not land use), with the secondary influence of both total organic carbon and clay contents. AM fungal species distribution presented significant distance-decays, regardless of land uses, which was indicative of dispersal limitation, a stochastic neutral process. Although, we found evidence that, coupled with dispersal limitation, niche differentiation also played a role in structuring AM fungal communities, driven by long-term historical contingencies, as represented by soil type, resulting from different soil origin and mineralogy across mesoregions.}, }
@article {pmid33656686, year = {2021}, author = {Salawu-Rotimi, A and Lebre, PH and Vos, HC and Fister, W and Kuhn, N and Eckardt, FD and Cowan, DA}, title = {Gone with the Wind: Microbial Communities Associated with Dust from Emissive Farmlands.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {859-869}, pmid = {33656686}, issn = {1432-184X}, support = {107803//National Research Foundation (ZA)/ ; }, mesh = {Bacteria/genetics ; *Dust/analysis ; Farms ; *Microbiota ; Soil Microbiology ; }, abstract = {Dust is a major vehicle for the dispersal of microorganisms across the globe. While much attention has been focused on microbial dispersal in dust plumes from major natural dust sources, very little is known about the fractionation processes that select for the "dust microbiome." The recent identification of highly emissive, agricultural land dust sources in South Africa has provided the opportunity to study the displacement of microbial communities through dust generation and transport. In this study, we aimed to document the microbial communities that are carried in the dust from one of South Africa's most emissive locations, and to investigate the selective factors that control the partitioning of microbial communities from soil to dust. For this purpose, dust samples were generated at different emission sources using a Portable In-Situ Wind Erosion Lab (PI-SWERL), and the taxonomic composition of the resulting microbiomes was compared with the source soils. Dust emission processes resulted in the clear fractionation of the soil bacterial community, where dust samples were significantly enriched in spore-forming taxa. Conversely, little fractionation was observed in the soil fungal communities, such that the dust fungal fingerprint could be used to identify the source soil. Dust microbiomes were also found to vary according to the emission source, suggesting that land use significantly affected the structure and fractionation of microbial communities transported in dust plumes. In addition, several potential biological allergens of fungal origin were detected in the dust microbiomes, highlighting the potential detrimental effects of dust plumes emitted in South Africa. This study represents the first description of the fractionation of microbial taxa occurring at the source of dust plumes and provides a direct link between land use and its impact on the dust microbiome.}, }
@article {pmid33653941, year = {2021}, author = {Belk, AD and Duarte, T and Quinn, C and Coil, DA and Belk, KE and Eisen, JA and Quinn, JC and Martin, JN and Yang, X and Metcalf, JL}, title = {Air versus Water Chilling of Chicken: a Pilot Study of Quality, Shelf-Life, Microbial Ecology, and Economics.}, journal = {mSystems}, volume = {6}, number = {2}, pages = {}, pmid = {33653941}, issn = {2379-5077}, abstract = {The United States' large-scale poultry meat industry is energy and water intensive, and opportunities may exist to improve sustainability during the broiler chilling process. By USDA regulation, after harvest the internal temperature of the chicken must be reduced to 40°F or less within 16 h to inhibit bacterial growth that would otherwise compromise the safety of the product. This step is accomplished most commonly by water immersion chilling in the United States, while air chilling methods dominate other global markets. A comprehensive understanding of the differences between these chilling methods is lacking. Therefore, we assessed the meat quality, shelf-life, microbial ecology, and techno-economic impacts of chilling methods on chicken broilers in a university meat laboratory setting. We discovered that air chilling methods resulted in superior chicken odor and shelf-life, especially prior to 14 days of dark storage. Moreover, we demonstrated that air chilling resulted in a more diverse microbiome that we hypothesize may delay the dominance of the spoilage organism Pseudomonas Finally, a techno-economic analysis highlighted potential economic advantages to air chilling compared to water chilling in facility locations where water costs are a more significant factor than energy costs.IMPORTANCE As the poultry industry works to become more sustainable and to reduce the volume of food waste, it is critical to consider points in the processing system that can be altered to make the process more efficient. In this study, we demonstrate that the method used during chilling (air versus water chilling) influences the final product microbial community, quality, and physiochemistry. Notably, the use of air chilling appears to delay the bloom of Pseudomonas spp. that are the primary spoilers in packaged meat products. By using air chilling to reduce carcass temperatures instead of water chilling, producers may extend the time until spoilage of the products and, depending on the cost of water in the area, may have economic and sustainability advantages. As a next step, a similar experiment should be done in an industrial setting to confirm these results generated in a small-scale university lab facility.}, }
@article {pmid33653887, year = {2021}, author = {Yanuka-Golub, K and Dubinsky, V and Korenblum, E and Reshef, L and Ofek-Lalzar, M and Rishpon, J and Gophna, U}, title = {Anode Surface Bioaugmentation Enhances Deterministic Biofilm Assembly in Microbial Fuel Cells.}, journal = {mBio}, volume = {12}, number = {2}, pages = {}, pmid = {33653887}, issn = {2150-7511}, mesh = {Bacteria/genetics/growth &amp; development ; *Biodegradation, Environmental ; Bioelectric Energy Sources/microbiology ; Biofilms/*growth &amp; development ; *Electrodes ; *Microbiota ; Wastewater/microbiology ; Water Purification/*methods ; }, abstract = {Microbial fuel cells (MFCs) generate energy while aiding the biodegradation of waste through the activity of an electroactive mixed biofilm. Metabolic cooperation is essential for MFCs' efficiency, especially during early colonization. Thus, examining specific ecological processes that drive the assembly of anode biofilms is highly important for shortening startup times and improving MFC performance, making this technology cost-effective and sustainable. Here, we use metagenomics to show that bioaugmentation of the anode surface with a taxonomically defined electroactive consortium, dominated by Desulfuromonas, resulted in an extremely rapid current density generation. Conversely, the untreated anode surface resulted in a highly stochastic and slower biofilm assembly. Remarkably, an efficient anode colonization process was obtained only if wastewater was added, leading to a nearly complete replacement of the bioaugmented community by Geobacter lovleyi Although different approaches to improve MFC startup have been investigated, we propose that only the combination of anode bioaugmentation with wastewater inoculation can reduce stochasticity. Such an approach provides the conditions that support the growth of specific newly arriving species that positively support the fast establishment of a highly functional anode biofilm.IMPORTANCE Mixed microbial communities play important roles in treating wastewater, in producing renewable energy, and in the bioremediation of pollutants in contaminated environments. While these processes are well known, especially the community structure and biodiversity, how to efficiently and robustly manage microbial community assembly remains unknown. Moreover, it has been shown that a high degree of temporal variation in microbial community composition and structure often occurs even under identical environmental conditions. This heterogeneity is directly related to stochastic processes involved in microbial community organization, similarly during the initial stages of biofilm formation on surfaces. In this study, we show that anode surface pretreatment alone is not sufficient for a substantial improvement in startup times in microbial fuel cells (MFCs), as previously thought. Rather, we have discovered that the combination of applying a well-known consortium directly on the anode surface together with wastewater (including the bacteria that they contain) is the optimized management scheme. This allowed a selected colonization process by the wastewater species, which improved the functionality relative to that of untreated systems.}, }
@article {pmid33652267, year = {2021}, author = {Pavlovic, J and Cavalieri, D and Mastromei, G and Pangallo, D and Perito, B and Marvasi, M}, title = {MinION technology for microbiome sequencing applications for the conservation of cultural heritage.}, journal = {Microbiological research}, volume = {247}, number = {}, pages = {126727}, doi = {10.1016/j.micres.2021.126727}, pmid = {33652267}, issn = {1618-0623}, mesh = {Bacteria/classification/genetics ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/instrumentation/*methods ; Metagenomics/instrumentation/*methods ; Microbiota/*genetics ; Paintings ; Sequence Analysis, DNA ; Textiles ; }, abstract = {The MinION single-molecule sequencing system has been attracting the attention of the community of microbiologists involved in the conservation of cultural heritage. The use of MinION for the conservation of cultural heritage is extremely recent, but surprisingly the only few applications available have been exploring many different substrates: stone, textiles, paintings and wax. The use of MinION sequencing is mainly used to address the metataxonomy (with special emphasis on non-cultivable microorganisms) with the effort to identify species involved in the degradation of the substrates. In this review, we show the current applications available on different artworks, showing how this technology can be a useful tool for microbiologists and conservators also in light of its low cost and the easy chemistry.}, }
@article {pmid33649554, year = {2021}, author = {Li, Z and Pan, D and Wei, G and Pi, W and Zhang, C and Wang, JH and Peng, Y and Zhang, L and Wang, Y and Hubert, CRJ and Dong, X}, title = {Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity.}, journal = {The ISME journal}, volume = {15}, number = {8}, pages = {2366-2378}, pmid = {33649554}, issn = {1751-7370}, support = {TPR 15-229/HX/HSRD VA/United States ; }, mesh = {*Geologic Sediments ; Methane ; *Microbiota ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {In marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse microbial communities, but little is known about viruses infecting these microorganisms. Here, we probed metagenomes from seven geographically diverse cold seeps across global oceans to assess viral diversity, virus-host interaction, and virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons with viruses inhabiting other ecosystems reveal that cold seep sediments harbour considerable unexplored viral diversity. Most cold seep viruses display high degrees of endemism with seep fluid flux being one of the main drivers of viral community composition. In silico predictions linked 14.2% of the viruses to microbial host populations with many belonging to poorly understood candidate bacterial and archaeal phyla. Lysis was predicted to be a predominant viral lifestyle based on lineage-specific virus/host abundance ratios. Metabolic predictions of prokaryotic host genomes and viral AMGs suggest that viruses influence microbial hydrocarbon biodegradation at cold seeps, as well as other carbon, sulfur and nitrogen cycling via virus-induced mortality and/or metabolic augmentation. Overall, these findings reveal the global diversity and biogeography of cold seep viruses and indicate how viruses may manipulate seep microbial ecology and biogeochemistry.}, }
@article {pmid33643242, year = {2021}, author = {Rüger, L and Feng, K and Dumack, K and Freudenthal, J and Chen, Y and Sun, R and Wilson, M and Yu, P and Sun, B and Deng, Y and Hochholdinger, F and Vetterlein, D and Bonkowski, M}, title = {Assembly Patterns of the Rhizosphere Microbiome Along the Longitudinal Root Axis of Maize (Zea mays L.).}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {614501}, pmid = {33643242}, issn = {1664-302X}, abstract = {It is by now well proven that different plant species within their specific root systems select for distinct subsets of microbiota from bulk soil - their individual rhizosphere microbiomes. In maize, root growth advances several centimeters each day, with the locations, quality and quantity of rhizodeposition changing. We investigated the assembly of communities of prokaryotes (archaea and bacteria) and their protistan predators (Cercozoa, Rhizaria) along the longitudinal root axis of maize (Zea mays L.). We grew maize plants in an agricultural loamy soil and sampled rhizosphere soil at distinct locations along maize roots. We applied high-throughput sequencing, followed by diversity and network analyses in order to track changes in relative abundances, diversity and co-occurrence of rhizosphere microbiota along the root axis. Apart from a reduction of operational taxonomic unit (OTU) richness and a strong shift in community composition between bulk soil and root tips, patterns of microbial community assembly along maize-roots were more complex than expected. High variation in beta diversity at root tips and the root hair zone indicated substantial randomness of community assembly. Root hair zone communities were characterized by massive co-occurrence of microbial taxa, likely fueled by abundant resource supply from rhizodeposition. Further up the root where lateral roots emerged processes of community assembly appeared to be more deterministic (e.g., through competition and predation). This shift toward significance of deterministic processes was revealed by low variability of beta diversity, changes in network topology, and the appearance of regular phylogenetic co-occurrence patterns in bipartite networks between prokaryotes and their potential protistan predators. Such patterns were strongest in regions with fully developed laterals, suggesting that a consistent rhizosphere microbiome finally assembled. For the targeted improvement of microbiome function, such knowledge on the processes of microbiome assembly on roots and its temporal and spatial variability is crucially important.}, }
@article {pmid33638074, year = {2021}, author = {Koroleva, E and Mqulwa, AZ and Norris-Jones, S and Reed, S and Tambe, Z and Visagie, A and Jacobs, K}, title = {Impact of cigarette butts on bacterial community structure in soil.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {33638074}, issn = {1614-7499}, abstract = {Cigarette butts contribute significantly to global pollution present on the planet. The filters found in cigarette butts contain a microplastic, cellulose acetate, as well as toxic metals and metalloids which are responsible for pollution in the environment. Although cigarette butt litter is prevalent in many soils, research on the effects of these cigarette butts is limited. In this study, we used Automated Ribosomal Intergenic Spacer Analysis (ARISA) to generate DNA fingerprints of bacterial communities in soil before and after the addition of cigarette butt leachate treatments. An ICP-MS analysis of the biodegradable and non-biodegradable cigarette butts revealed the presence of various elements: Al, As, B, Ba, Cd, Co, Cr, Cu, Fe, Hg, Mn, Mo, Ni, Pb, Sb, Se, Sn, Sr, V, and Zn. The analysis also specified which metals were present at the highest concentrations in the biodegradable and non-biodegradable cigarette butts, and these were, respectively, Al (1,31 g/kg and 2,35 g/kg), Fe (2,03 g/kg and 1,11 g/kg), and Zn (3,18 mg/kg and 15,70 mg/kg). Our results show that biodegradable cigarette butts had a significant effect on bacterial community composition (beta diversity), unlike the non-biodegradable butts. This effect can be attributed to higher concentrations of certain metals and metalloids in the leachate of biodegradable cigarette butts compared to the non-biodegradable ones. Our findings suggest that biodegradable and non-biodegradable cigarette butts can significantly affect bacterial communities in soil as a result of the leaching of significant quantities of certain elements into the surrounding soils.}, }
@article {pmid33637782, year = {2021}, author = {Vashistha, G and Mungi, NA and Lang, JW and Ranjan, V and Dhakate, PM and Khudsar, FA and Kothamasi, D}, title = {Gharial nesting in a reservoir is limited by reduced river flow and by increased bank vegetation.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4805}, pmid = {33637782}, issn = {2045-2322}, abstract = {The gharial (Gavialis gangeticus Gmelin) is a fish-eating specialist crocodylian, endemic to south Asia, and critically endangered in its few remaining wild localities. A secondary gharial population resides in riverine-reservoir habitat adjacent to the Nepal border, within the Katerniaghat Wildlife Sanctuary (KWS), and nests along a 10 km riverbank of the Girwa River. A natural channel shift in the mainstream Karnali River (upstream in Nepal) has reduced seasonal flow in the Girwa stretch where gharials nest, coincident with a gradual loss of nest sites, which in turn was related to an overall shift to woody vegetation at these sites. To understand how these changes in riparian vegetation on riverbanks were related to gharial nesting, we sampled vegetation at these sites from 2017 to 2019, and derived an Enhanced Vegetation Index (EVI) from LANDSAT 8 satellite data to quantify riverside vegetation from 1988 through 2019. We found that sampled sites transitioned to woody cover, the number of nesting sites declined, and the number of nests were reduced by > 40%. At these sites, after the channel shift, woody vegetation replaced open sites that predominated prior to the channel shift. Our findings indicate that the lack of open riverbanks and the increase in woody vegetation at potential nesting sites threatens the reproductive success of the KWS gharial population. This population persists today in a regulated river ecosystem, and nests in an altered riparian habitat which appears to be increasingly unsuitable for the continued successful recruitment of breeding adults. This second-ranking, critically endangered remnant population may have incurred an "extinction debt" by living in a reservoir that will lead to its eventual extirpation.}, }
@article {pmid33637572, year = {2021}, author = {Wang, Z and Chen, Z and Kowalchuk, GA and Xu, Z and Fu, X and Kuramae, EE}, title = {Succession of the Resident Soil Microbial Community in Response to Periodic Inoculations.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {9}, pages = {}, pmid = {33637572}, issn = {1098-5336}, mesh = {*Agricultural Inoculants ; Bacteria/classification/genetics ; Hydrogen-Ion Concentration ; Juglandaceae/*growth &amp; development ; *Microbiota ; RNA, Ribosomal, 16S ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {To maintain the beneficial effects of microbial inoculants on plants and soil, repeated inoculation represents a promising option. Until now, the impacts of one-off inoculation on the native microbiome have been explored, but it remains unclear how long and to what extent the periodic inoculations would affect the succession of the resident microbiome in bulk soil. Here, we examined the dynamic responses of plant growth, soil functions, and the resident bacterial community in the bulk soil to periodic inoculations of phosphate-solubilizing and N2-fixing bacteria alone or in combination. Compared to single-strain inoculation, coinoculation better stimulated plant growth and soil nutrients. However, the benefits from inoculants did not increase with repeated inoculations and were not maintained after transplantation to a different site. In response to microbial inoculants, three patterns of shifts in the bacterial composition were observed: fold increase, fold decrease, and resilience. The periodic inoculations impacted the succession course of resident bacterial communities in bulk soil, mainly driven by changes in soil pH and nitrate, resulting in the development of three main cluster types throughout the investigation. The single and mixed inoculants transiently modulated the variation in the resident community in association with soil pH and the C/N ratio, but finally, the community established and showed resilience to subsequent inoculations. Consequently, the necessity of repeated inoculations should be reconsidered, and while the different microbial inoculants showed distinct impacts on resident microbiome succession, the communities ultimately exhibited resilience.IMPORTANCE Introducing beneficial microbes to the plant-soil system is an environmentally friendly approach to improve the crop yield and soil environment. Numerous studies have attempted to reveal the impacts of inoculation on the rhizosphere microbiome. However, little is known about the effectiveness of periodic inoculations on soil functioning. In addition, the long-term impact of repeated inoculations on the native community remains unclear. Here, we track the succession traits of the resident microbiome in the bulk soil across a growing season and identify the taxon clusters that respond differently to periodic inoculation. Crucially, we compare the development of the resident community composition with and without inoculation, thus providing new insight into the interactions between resident microbes and intruders. Finally, we conclude that initial inoculation plays a more important role in influencing the whole system, and the native microbial community exhibits traits of resilience, but no resistance, to the subsequent inoculations.}, }
@article {pmid33634334, year = {2021}, author = {Srivastava, A and Mishra, S and Verma, D}, title = {Characterization of Oral Bacterial Composition of Adult Smokeless Tobacco Users from Healthy Indians Using 16S rDNA Analysis.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {1061-1073}, pmid = {33634334}, issn = {1432-184X}, support = {SB/YS/LS-102/2014//Science and Engineering Research Board/ ; F 30-442/2018/BSR//University Grants Commission/ ; }, mesh = {Adult ; Bacteria/genetics ; DNA, Ribosomal/genetics ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Tobacco, Smokeless ; }, abstract = {The present investigation is aiming to report the oral bacterial composition of smokeless tobacco (SLT) users and to determine the influence of SLT products on the healthy Indian population. With the aid of the V3 hypervariable region of the 16S rRNA gene, a total of 8,080,889 high-quality reads were clustered into 15 phyla and 180 genera in the oral cavity of the SLT users. Comparative analysis revealed a more diverse microbiome where two phyla and sixteen genera were significantly different among the SLT users as compared to the control group (p-value < 0.05). The prevalence of Fusobacteria-, Porphyromonas-, Desulfobulbus-, Enterococcus-, and Parvimonas-like genera among SLT users indicates altered bacterial communities among SLT users. Besides, the depletion of health-compatible bacteria such as Lactobacillus and Haemophilus also suggests poor oral health. Here, the majority of the altered genera belong to Gram-negative anaerobes that have been reported for assisting biofilm formation that leads in the progression of several oral diseases. The PICRUSt analysis further supports the hypothesis where a significant increase in the count of the genes involved in the metabolism of nitrogen, amino acids, and nicotinate/nicotinamide was observed among tobacco chewers. Moreover, this study has a high significance in Indian prospects where the SLT consumers are prevalent but we are deficient in information on their oral microbiome.}, }
@article {pmid33629948, year = {2019}, author = {Cho, GY and Whang, KS}, title = {Sandarakinorhabdus rubra sp. nov., and Sandarakinorhabdus oryzae sp. nov., isolated from oxidized rice paddy soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {71}, number = {3}, pages = {}, doi = {10.1099/ijsem.0.004722}, pmid = {33629948}, issn = {1466-5034}, abstract = {Three Gram-stain-negative, motile or non-motile, rod-shaped, facultatively aerobic strains, designated MO-4[T], NP-34 and NM-18[T], were isolated from oxidized rice paddy soil in Chungbuk, Republic of Korea. Colonies were circular and convex with entire margins, red in colour on R2A after 3 days at 30 °C. The three strains grew at pH 5.0-10.0 (optimum, pH 8.0), at 15-45 °C (optimum, 30 °C) and at salinities of 0-1.5 % (w/v) NaCl (optimum, 0.4 % NaCl). The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the three isolates represent members of the genus Sandarakinorhabdus and strains MO-4[T] and NP-34 were most closely related to Sandarakinorhabdus cyanobacteriorum TH057[T] (97.7 %) and Sandarakinorhabdus limnophila DSM 17366[T] (97.1 %). NM-18[T] showed highest 16S rRNA gene sequence similarities to Sandarakinorhabdus limnophila DSM 17366[T] (98.7 %) and Sandarakinorhabdus cyanobacteriorum TH057[T] (96.7 %). Genomic similarities between strains MO-4[T] and NM-18[T] and the two type strains of species of the genus Sandarakinorhabdus based on average nucleotide identity and digital DNA-DNA hybridization values were lower than the species delineation thresholds. The major fatty acids were iso-C18 : 1 ω7c and summed feature 3. The DNA G+C contents of strains MO-4[T] and NM-18[T], obtained from genome sequencing data, were 67.6 and 66.6 mol%, respectively. On the basis of these genotypic and phenotypic characteristics, the three strains are assigned to two novel species of the genus Sandarakinorhabdus, for which the names Sandarakinorhabdus rubra sp. nov. (type strain MO-4[T] =KACC 21378=NBRC 114106) and Sandarakinorhabdus oryzae sp. nov. (type strain NM-18[T]=KACC 21379=NBRC 113957) are proposed.}, }
@article {pmid33629529, year = {2021}, author = {Phillips, AA and Speth, DR and Miller, LG and Wang, XT and Wu, F and Medeiros, PM and Monteverde, DR and Osburn, MR and Berelson, WM and Betts, HL and Wijker, RS and Mullin, SW and Johnson, HA and Orphan, VJ and Fischer, WW and ,  and ,  and Sessions, AL}, title = {Microbial succession and dynamics in meromictic Mono Lake, California.}, journal = {Geobiology}, volume = {19}, number = {4}, pages = {376-393}, pmid = {33629529}, issn = {1472-4669}, mesh = {Bacteria ; California ; *Ecosystem ; *Lakes ; Phylogeny ; }, abstract = {Mono Lake is a closed-basin, hypersaline, alkaline lake located in Eastern Sierra Nevada, California, that is dominated by microbial life. This unique ecosystem offers a natural laboratory for probing microbial community responses to environmental change. In 2017, a heavy snowpack and subsequent runoff led Mono Lake to transition from annually mixed (monomictic) to indefinitely stratified (meromictic). We followed microbial succession during this limnological shift, establishing a two-year (2017-2018) water-column time series of geochemical and microbiological data. Following meromictic conditions, anoxia persisted below the chemocline and reduced compounds such as sulfide and ammonium increased in concentration from near 0 to ~400 and ~150 µM, respectively, throughout 2018. We observed significant microbial succession, with trends varying by water depth. In the epilimnion (above the chemocline), aerobic heterotrophs were displaced by phototrophic genera when a large bloom of cyanobacteria appeared in fall 2018. Bacteria in the hypolimnion (below the chemocline) had a delayed, but systematic, response reflecting colonization by sediment "seed bank" communities. Phototrophic sulfide-oxidizing bacteria appeared first in summer 2017, followed by microbes associated with anaerobic fermentation in spring 2018, and eventually sulfate-reducing taxa by fall 2018. This slow shift indicated that multi-year meromixis was required to establish a sulfate-reducing community in Mono Lake, although sulfide oxidizers thrive throughout mixing regimes. The abundant green alga Picocystis remained the dominant primary producer during the meromixis event, abundant throughout the water column including in the hypolimnion despite the absence of light and prevalence of sulfide. Our study adds to the growing literature describing microbial resistance and resilience during lake mixing events related to climatic events and environmental change.}, }
@article {pmid33629506, year = {2021}, author = {Benítez-Páez, A and Hess, AL and Krautbauer, S and Liebisch, G and Christensen, L and Hjorth, MF and Larsen, TM and Sanz, Y and , }, title = {Sex, Food, and the Gut Microbiota: Disparate Response to Caloric Restriction Diet with Fiber Supplementation in Women and Men.}, journal = {Molecular nutrition &amp; food research}, volume = {65}, number = {8}, pages = {e2000996}, doi = {10.1002/mnfr.202000996}, pmid = {33629506}, issn = {1613-4133}, mesh = {Bacteroidetes ; Bile Acids and Salts/metabolism ; Biomarkers ; *Caloric Restriction ; Dietary Fiber/*pharmacology ; Dietary Supplements ; Fatty Acids, Volatile/blood/metabolism ; Feces/chemistry/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Middle Aged ; Multivariate Analysis ; Sex Factors ; Weight Loss ; }, abstract = {SCOPE: Dietary-based strategies are regularly explored in controlled clinical trials to provide cost-effective therapies to tackle obesity and its comorbidities. The article presents a complementary analysis based on a multivariate multi-omics approach of a caloric restriction intervention (CRD) with fiber supplementation to unveil synergic effects on body weight control, lipid metabolism, and gut microbiota.<br><br>METHODS AND RESULTS: The study explores fecal bile acids (BAs) and short-chain fatty acids (SCFAs), plasma BAs, and fecal shotgun metagenomics on 80 overweight participants of a 12-week caloric restriction clinical trial (-500&#xa0;kcal day[-1]) randomly allocated into fiber (10&#xa0;g day[-1] inulin + 10&#xa0;g day[-1] resistant maltodextrin) or placebo (maltodextrin) supplementation groups. The multi-omic data integration analysis uncovered the benefits of the fiber supplementation and/or the CRD (e.g., increase of Parabacteroides distasonis and fecal propionate), showing sex-specific effects on either adiposity and fasting insulin; effects thought to be linked to changes of specific gut microbiota species, functional genes, and bacterially produced metabolites like SCFAs and secondary BAs.<br><br>CONCLUSIONS: This study identifies diet-microbe-host interactions helping to design personalised interventions. It also suggests that sex perspective should be considered routinely in future studies on dietary interventions efficacy. All in all, the study uncovers that the dietary intervention is more beneficial for women than men.}, }
@article {pmid33629169, year = {2021}, author = {Tang, Y and Ma, KY and Cheung, MK and Yang, CH and Wang, Y and Hu, X and Kwan, HS and Chu, KH}, title = {Gut Microbiota in Decapod Shrimps: Evidence of Phylosymbiosis.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {994-1007}, pmid = {33629169}, issn = {1432-184X}, support = {C4042-14G//Research Grants Council, Hong Kong SAR and the Hong Kong Branch of Southern Marine Science and Technology Guangdong Laboratory (Guangzhou), China/ ; }, mesh = {Animals ; *Decapoda ; *Gastrointestinal Microbiome ; Humans ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Gut microbiota have long attracted the interest of scientists due to their profound impact on the well-being of animals. A non-random pattern of microbial assembly that results in a parallelism between host phylogeny and microbial similarity is described as phylosymbiosis. Phylosymbiosis has been consistently observed in different clades of animal hosts, but there have been no studies on crustaceans. In this study, we investigated whether host phylogeny has an impact on the gut microbiota assemblages in decapod shrimps. We examined the gut microbial communities in 20 shrimp species from three families inhabiting distinct environments, using metabarcoding analyses of the V1-V3 hypervariable region of the 16S rRNA gene. Gut microbial communities varied within each shrimp group but were generally dominated by Proteobacteria. A prevalent phylosymbiotic pattern in shrimps was evidenced for the first time by the observations of (1) the distinguishability of microbial communities among species within each group, (2) a significantly lower intraspecific than interspecific gut microbial beta diversity across shrimp groups, (3) topological congruence between host phylogenetic trees and gut microbiota dendrograms, and (4) a correlation between host genetic distances and microbial dissimilarities. Consistent signals of phylosymbiosis were observed across all groups in dendrograms based on the unweighted UniFrac distances at 99% operational taxonomic units (OTUs) level and in Mantel tests based on the weighted UniFrac distances based on 97% OTUs and amplicon sequence variants. Penaeids exhibited phylosymbiosis in most tests, while phylosymbiotic signals in atyids and pandalids were only detected in fewer than half of the tests. A weak phylogenetic signal was detected in the predicted functions of the penaeid gut microbiota. However, the functional diversities of the two caridean groups were not significantly related to host phylogeny. Our observations of a parallelism in the taxonomy of the gut microbiota with host phylogeny for all shrimp groups examined and in the predicted functions for the penaeid shrimps indicate a tight host-microbial relationship during evolution.}, }
@article {pmid33624262, year = {2021}, author = {Cho, JC}, title = {Omics-based microbiome analysis in microbial ecology: from sequences to information.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {59}, number = {3}, pages = {229-232}, pmid = {33624262}, issn = {1976-3794}, mesh = {Bacteria/*genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; Microbial Interactions ; *Microbiota ; }, abstract = {Microbial ecology is the study of microorganisms present in nature. It particularly focuses on microbial interactions with any biota and with surrounding environments. Microbial ecology is entering its golden age with innovative multi-omics methods triggered by next-generation sequencing technologies. However, the extraction of ecologically relevant information from ever-increasing omics data remains one of the most challenging tasks in microbial ecology. This special issue includes 11 review articles that provide an overview of the state of the art of omics-based approaches in the field of microbial ecology, with particular emphasis on the interpretation of omics data, environmental pollution tracking, interactions in microbiomes, and viral ecology.}, }
@article {pmid33624137, year = {2021}, author = {Hyun, HR and Yoon, H and Lyou, ES and Kim, JJ and Kwon, SY and Lee, TK}, title = {Short-Term Legacy Effects of Mercury Contamination on Plant Growth and nifH-Harboring Microbial Community in Rice Paddy Soil.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {932-941}, pmid = {33624137}, issn = {1432-184X}, support = {918014-4//Strategic Initiative for Microbiomes in Agriculture and Food, Ministry of Agriculture, Food and Rural Affairs/ ; 2020002480003//Korea Ministry of Environment as Subsurface Environment Management Projects/ ; }, mesh = {*Mercury ; *Microbiota ; *Oryza ; Soil ; *Soil Pollutants/analysis ; }, abstract = {Methylmercury (MeHg), which is formed in rice paddy soil, exhibits strong neurotoxicity through bioaccumulation in the food chain. A few groups of microorganisms drive both mercury methylation and nitrogen fixation in the rhizosphere. Little is known about how the shifted soil microbial community by Hg contamination affects nitrogen fixation rate and plant growth in paddy soil. Here, we examined how stimulated short-term Hg amendment affects the nitrogen fixing microbial community and influences plant-microbe interactions. Soil was treated with low (0.2 mg/kg) and high (1.1 mg/kg) concentrations of Hg for 4 weeks; then, rice (Oryza sativa) was planted and grown for 12 weeks. The nitrogen-fixation rate and rice growth were measured. The diversity and structure of the microbial community were analyzed by sequencing the nifH gene before and after rice cultivation. Hg treatments significantly decreased the nitrogen fixation rate and dry weight of the rice plants. The structure of the nifH-harboring community was remarkably changed after rice cultivation depending on Hg treatments. Iron- or sulfate-reducing bacteria, including Desulfobacca, Desulfoporosimus, and Geobacter, were observed as legacy response groups; their abundances increased in the soil after Hg treatment. The high abundance of those groups were maintained in control, but the abundance drastically decreased after rice cultivation in the soil treated with Hg, indicating that symbiotic behavior of rice plants changes according to the legacy effects on Hg contamination. These results suggested that Hg contamination can persist in soil microbial communities, affecting their nitrogen-fixation ability and symbiosis with rice plants in paddy soil.}, }
@article {pmid33614160, year = {2021}, author = {Zwart, MP and Blanc, S and Johnson, M and Manrubia, S and Michalakis, Y and Sofonea, MT}, title = {Unresolved advantages of multipartitism in spatially structured environments.}, journal = {Virus evolution}, volume = {7}, number = {1}, pages = {veab004}, pmid = {33614160}, issn = {2057-1577}, abstract = {Multipartite viruses have segmented genomes and package each of their genome segments individually into distinct virus particles. Multipartitism is common among plant viruses, but why this apparently costly genome organization and packaging has evolved remains unclear. Recently Zhang and colleagues developed network epidemiology models to study the epidemic spread of multipartite viruses and their distribution over plant and animal hosts (Phys. Rev. Lett. 2019, 123, 138101). In this short commentary, we call into question the relevance of these results because of key model assumptions. First, the model of plant hosts assumes virus transmission only occurs between adjacent plants. This assumption overlooks the basic but imperative fact that most multipartite viruses are transmitted over variable distances by mobile animal vectors, rendering the model results irrelevant to differences between plant and animal hosts. Second, when not all genome segments of a multipartite virus are transmitted to a host, the model assumes an incessant latent infection occurs. This is a bold assumption for which there is no evidence to date, making the relevance of these results to understanding multipartitism questionable.}, }
@article {pmid33613641, year = {2021}, author = {Gil, J and Andrade-Martínez, JS and Duitama, J}, title = {Accurate, Efficient and User-Friendly Mutation Calling and Sample Identification for TILLING Experiments.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {624513}, pmid = {33613641}, issn = {1664-8021}, abstract = {TILLING (Targeting Induced Local Lesions IN Genomes) is a powerful reverse genetics method in plant functional genomics and breeding to identify mutagenized individuals with improved behavior for a trait of interest. Pooled high throughput sequencing (HTS) of the targeted genes allows efficient identification and sample assignment of variants within genes of interest in hundreds of individuals. Although TILLING has been used successfully in different crops and even applied to natural populations, one of the main issues for a successful TILLING experiment is that most currently available bioinformatics tools for variant detection are not designed to identify mutations with low frequencies in pooled samples or to perform sample identification from variants identified in overlapping pools. Our research group maintains the Next Generation Sequencing Experience Platform (NGSEP), an open source solution for analysis of HTS data. In this manuscript, we present three novel components within NGSEP to facilitate the design and analysis of TILLING experiments: a pooled variants detector, a sample identifier from variants detected in overlapping pools and a simulator of TILLING experiments. A new implementation of the NGSEP calling model for variant detection allows accurate detection of low frequency mutations within pools. The samples identifier implements the process to triangulate the mutations called within overlapping pools in order to assign mutations to single individuals whenever possible. Finally, we developed a complete simulator of TILLING experiments to enable benchmarking of different tools and to facilitate the design of experimental alternatives varying the number of pools and individuals per pool. Simulation experiments based on genes from the common bean genome indicate that NGSEP provides similar accuracy and better efficiency than other tools to perform pooled variants detection. To the best of our knowledge, NGSEP is currently the only tool that generates individual assignments of the mutations discovered from the pooled data. We expect that this development will be of great use for different groups implementing TILLING as an alternative for plant breeding and even to research groups performing pooled sequencing for other applications.}, }
@article {pmid33613482, year = {2021}, author = {Chang, J and Sun, Y and Tian, L and Ji, L and Luo, S and Nasir, F and Kuramae, EE and Tian, C}, title = {The Structure of Rhizosphere Fungal Communities of Wild and Domesticated Rice: Changes in Diversity and Co-occurrence Patterns.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {610823}, pmid = {33613482}, issn = {1664-302X}, abstract = {The rhizosphere fungal community affects the ability of crops to acquire nutrients and their susceptibility to pathogen invasion. However, the effects of rice domestication on the diversity and interactions of rhizosphere fungal community still remain largely unknown. Here, internal transcribed spacer amplicon sequencing was used to systematically analyze the structure of rhizosphere fungal communities of wild and domesticated rice. The results showed that domestication increased the alpha diversity indices of the rice rhizosphere fungal community. The changes of alpha diversity index may be associated with the enrichment of Acremonium, Lecythophora, and other specific rare taxa in the rhizosphere of domesticated rice. The co-occurrence network showed that the complexity of wild rice rhizosphere fungal community was higher than that of the domesticated rice rhizosphere fungal community. Arbuscular mycorrhizal fungi (AMF) and soilborne fungi were positively and negatively correlated with more fungi in the wild rice rhizosphere, respectively. For restructuring the rhizomicrobial community of domesticated crops, we hypothesize that microbes that hold positive connections with AMF and negative connections with soilborne fungi can be used as potential sources for bio-inoculation. Our findings provide a scientific basis for reshaping the structure of rhizomicrobial community and furthermore create potential for novel intelligent and sustainable agricultural solutions.}, }
@article {pmid33612832, year = {2021}, author = {Patin, NV and Dietrich, ZA and Stancil, A and Quinan, M and Beckler, JS and Hall, ER and Culter, J and Smith, CG and Taillefert, M and Stewart, FJ}, title = {Gulf of Mexico blue hole harbors high levels of novel microbial lineages.}, journal = {The ISME journal}, volume = {15}, number = {8}, pages = {2206-2232}, pmid = {33612832}, issn = {1751-7370}, mesh = {*Archaea ; Bacteria/genetics ; Florida ; Gulf of Mexico ; *Metagenomics ; }, abstract = {Exploration of oxygen-depleted marine environments has consistently revealed novel microbial taxa and metabolic capabilities that expand our understanding of microbial evolution and ecology. Marine blue holes are shallow karst formations characterized by low oxygen and high organic matter content. They are logistically challenging to sample, and thus our understanding of their biogeochemistry and microbial ecology is limited. We present a metagenomic and geochemical characterization of Amberjack Hole on the Florida continental shelf (Gulf of Mexico). Dissolved oxygen became depleted at the hole's rim (32 m water depth), remained low but detectable in an intermediate hypoxic zone (40-75 m), and then increased to a secondary peak before falling below detection in the bottom layer (80-110 m), concomitant with increases in nutrients, dissolved iron, and a series of sequentially more reduced sulfur species. Microbial communities in the bottom layer contained heretofore undocumented levels of the recently discovered phylum Woesearchaeota (up to 58% of the community), along with lineages in the bacterial Candidate Phyla Radiation (CPR). Thirty-one high-quality metagenome-assembled genomes (MAGs) showed extensive biochemical capabilities for sulfur and nitrogen cycling, as well as for resisting and respiring arsenic. One uncharacterized gene associated with a CPR lineage differentiated hypoxic from anoxic zone communities. Overall, microbial communities and geochemical profiles were stable across two sampling dates in the spring and fall of 2019. The blue hole habitat is a natural marine laboratory that provides opportunities for sampling taxa with under-characterized but potentially important roles in redox-stratified microbial processes.}, }
@article {pmid33609143, year = {2021}, author = {Green, EA and Smedley, SR and Klassen, JL}, title = {North American Fireflies Host Low Bacterial Diversity.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {793-804}, pmid = {33609143}, issn = {1432-184X}, mesh = {Animals ; Bacteria/genetics ; Female ; *Fireflies ; Male ; *Microbiota ; North America ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Although there are numerous studies of firefly mating flashes, lantern bioluminescence, and anti-predation lucibufagin metabolites, almost nothing is known about their microbiome. We therefore used 16S rRNA community amplicon sequencing to characterize the gut and body microbiomes of four North American firefly taxa: Ellychnia corrusca, the Photuris versicolor species complex, Pyractomena borealis, and Pyropyga decipiens. These firefly microbiomes all have very low species diversity, often dominated by a single species, and each firefly type has a characteristic microbiome. Although the microbiomes of male and female fireflies did not differ from each other, Ph. versicolor gut and body microbiomes did, with their gut microbiomes being enriched in Pseudomonas and Acinetobacter. Ellychnia corrusca egg and adult microbiomes were unique except for a single egg microbiome that shared a community type with E. corrusca adults, which could suggest microbial transmission from mother to offspring. Mollicutes that had been previously isolated from fireflies were common in our firefly microbiomes. These results set the stage for further research concerning the function and transmission of these bacterial symbionts.}, }
@article {pmid33606088, year = {2021}, author = {Tatsumi, C and Azuma, WA and Ogawa, Y and Komada, N}, title = {Nitrogen Availability and Microbial Communities of Canopy Soils in a Large Cercidiphyllum japonicum Tree of a Cool-Temperate Old Growth Forest.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {919-931}, pmid = {33606088}, issn = {1432-184X}, support = {17J07686//Grant-in-Aid for JSPS Research Fellow/ ; }, mesh = {Forests ; *Microbiota ; Nitrogen/analysis ; Soil ; Soil Microbiology ; *Trees ; }, abstract = {Canopy soils on large trees are important for supporting the lives of many canopy plants, and thereby increasing regional biodiversity. However, because of the less accessibility to canopy soils, there is insufficient knowledge on how canopy soils produce available nitrogen (N) for canopy plants through the activity of canopy soil microbes. Canopy soils usually have different soil properties from ground soils, so we hypothesized that canopy soils would have unique microbial communities compared to ground soils, but still provide available N for canopy plants. Here, we compared soil N availability, including net N mineralization and nitrification rate, and microbial communities between canopy soils (organic soils) collected at various heights of a large Cercidiphyllum japonicum tree and ground soils (organic and mineral soils) in a cool-temperate old-growth forest of Japan. The canopy soils had significantly different N availability (mass-based higher but volume-based lower) and microbial communities from the ground mineral soils. Among organic soils, the height of the soil had an impact on the microbial communities but not on the N availability, which agreed with our hypothesis. Despite the decrease in fungal abundance in the higher soils, the increase in certain components of the cellulose-decomposing fungi and oligotrophic bacteria may contribute to the available N production. Also, the abundance of ammonia-oxidizers did not change with the height, which would be important for the nitrification rate. Our study implied canopy soils could provide N to canopy plants partly through the functional redundancy within different microbial communities and constant population of ammonia-oxidizers.}, }
@article {pmid33606087, year = {2021}, author = {Dlamini, ST and Jaiswal, SK and Mohammed, M and Dakora, FD}, title = {Studies of Phylogeny, Symbiotic Functioning and Ecological Traits of Indigenous Microsymbionts Nodulating Bambara Groundnut (Vigna subterranea L. Verdc) in Eswatini.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {688-703}, pmid = {33606087}, issn = {1432-184X}, mesh = {Bradyrhizobium ; Eswatini ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant ; *Vigna ; }, abstract = {Rhizobial microsymbionts of grain legumes are ubiquitous in soils and exhibit a wide range of diversity with respect to colony morphology, genetic variability, biochemical characteristics, and phylogenetic relationships. This study assessed the phylogenetic positions of rhizobial microsymbionts of Bambara groundnut from Eswatini exhibiting variations in morpho-physiology, adaptive characteristics, and N2-fixing efficiency. The isolates' ERIC-PCR profiles revealed the presence of high genetic variation among them. These test isolates also exhibited differences in pH tolerance and IAA production. Multilocus sequence analysis based on the 16S rRNA, atpD, glnII, gyrB, and recA gene sequences of representative test isolates closely aligned them to the type strains of Bradyrhizobium arachidis, B. manausense, B. guangdongense, B. elkanii, and B. pachyrhizi. However, some isolates showed a high divergence from the known reference type strains, indicating that they may represent species yet to be properly characterized and described. Functional characterization in the glasshouse revealed that most of the isolates from the contrasting Agro-ecologies of Eswatini were efficient in N2 fixation, and therefore elicited greater stomatal conductance and photosynthetic rates in the homologous Bambara groundnut. Of the 75 isolates tested, 51% were more effective than the commercial Bradyrhizobium sp. strain CB756, with relative symbiotic effectiveness ranging from 138 to 308%. The findings of this study indicated that the analysis of housekeeping genes and functional traits of Bambara-nodulating microsymbionts can provide a clear view for understanding and predicting rhizobial community structure across environmental gradients.}, }
@article {pmid33604703, year = {2021}, author = {Ritter, CD and Forster, D and Azevedo, JAR and Antonelli, A and Nilsson, RH and Trujillo, ME and Dunthorn, M}, title = {Assessing Biotic and Abiotic Interactions of Microorganisms in Amazonia through Co-Occurrence Networks and DNA Metabarcoding.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {746-760}, pmid = {33604703}, issn = {1432-184X}, mesh = {Biodiversity ; *DNA Barcoding, Taxonomic ; *Ecosystem ; Forests ; Rainforest ; Soil Microbiology ; }, abstract = {Species may co-occur due to responses to similar environmental conditions, biological associations, or simply because of coincident geographical distributions. Disentangling patterns of co-occurrence and potential biotic and abiotic interactions is crucial to understand ecosystem function. Here, we used DNA metabarcoding data from litter and mineral soils collected from a longitudinal transect in Amazonia to explore patterns of co-occurrence. We compared data from different Amazonian habitat types, each with a characteristic biota and environmental conditions. These included non-flooded rainforests (terra-firme), forests seasonally flooded by fertile white waters (várzeas) or by unfertile black waters (igapós), and open areas associated with white sand soil (campinas). We ran co-occurrence network analyses based on null models and Spearman correlation for all samples and for each habitat separately. We found that one third of all operational taxonomic units (OTUs) were bacteria and two thirds were eukaryotes. The resulting networks were nevertheless mostly composed of bacteria, with fewer fungi, protists, and metazoans. Considering the functional traits of the OTUs, there is a combination of metabolism modes including respiration and fermentation for bacteria, and a high frequency of saprotrophic fungi (those that feed on dead organic matter), indicating a high turnover of organic material. The organic carbon and base saturation indices were important in the co-occurrences in Amazonian networks, whereas several other soil properties were important for the co-exclusion. Different habitats had similar network properties with some variation in terms of modularity, probably associated with flooding pulse. We show that Amazonian microorganism communities form highly interconnected co-occurrence and co-exclusion networks, which highlights the importance of complex biotic and abiotic interactions in explaining the outstanding biodiversity of the region.}, }
@article {pmid33600877, year = {2021}, author = {Verspecht, T and Ghesquière, J and Bernaerts, K and Boon, N and Teughels, W}, title = {Evaluating the intrinsic capacity of oral bacteria to produce hydrogen peroxide (H2O2) in liquid cultures: Interference by bacterial growth media.}, journal = {Journal of microbiological methods}, volume = {182}, number = {}, pages = {106170}, doi = {10.1016/j.mimet.2021.106170}, pmid = {33600877}, issn = {1872-8359}, mesh = {*Culture Media ; Hydrogen Peroxide/*metabolism ; *Streptococcus pneumoniae/growth &amp; development/metabolism ; }, abstract = {This work highlights the issue of interference by growth media when measuring bacterial H2O2 production. H2O2 was shown to be stable in phosphate buffered saline (PBS) but not in growth media. The protocol used for evaluating the intrinsic capacity of oral streptococci to produce H2O2 was shown to be reliable.}, }
@article {pmid33598748, year = {2021}, author = {Nava-González, B and Suazo-Ortuño, I and López, PB and Maldonado-López, Y and Lopez-Toledo, L and Raggi, L and Parra-Olea, G and Alvarado-Díaz, J and Gómez-Gil, B}, title = {Inhibition of Batrachochytrium dendrobatidis Infection by Skin Bacterial Communities in Wild Amphibian Populations.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {666-676}, pmid = {33598748}, issn = {1432-184X}, support = {2015-259173//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 444637//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; Programa 2019//Coordinaci&#xf3;n de la Investigaci&#xf3;n Cient&#xed;fica/ ; }, mesh = {Animals ; Bacteria/genetics ; Batrachochytrium ; *Chytridiomycota ; Humans ; *Microbiota ; Ranidae ; Skin ; }, abstract = {Skin-associated bacteria are known to inhibit infection by the fungal pathogen Batrachochytrium dendrobatidis (Bd) in amphibians. It has also been postulated that skin-associated bacterial community is related to Bd infection intensity. However, our understanding of host microbial dynamics and their importance in regulating Bd intensity is limited. We analyzed Bd infection and skin-associated bacteria from two amphibian species, the salamander Ambystoma rivulare and the frog Lithobates spectabilis that co-occurred in a tropical high-altitude site in central Mexico. Sixty-three percent of sampled salamander individuals and 80% of frog individuals tested positive for Bd. Overall, we registered 622 skin-associated bacterial genera, from which 73 are known to have Bd inhibitory effects. These inhibitory taxa represented a relative abundance of 50% in relation to total relative bacterial abundance. Our results indicated that, although sharing some bacterial taxa, bacterial community from the skin of both species was different in taxonomic composition and in relative abundance. Pseudomonas spp. and Stenotrophomonas spp. were among the five most abundant bacterial taxa of both species. Both bacterial taxa inhibit Bd infection. We detected that bacterial richness and relative abundance of inhibitory Bd bacteria were negatively related to intensity of Bd infection independent of species and seasons. Despite the high Bd prevalence in both host species, no dead or sick individuals were registered during field surveys. The relatively low levels of Bd load apparently do not compromise survival of host species. Therefore, our results suggested that individuals analyzed were able to survive and thrive under a dynamic relation with enzootic infections of Bd and their microbiota.}, }
@article {pmid33598747, year = {2021}, author = {Zhang, W and Bahadur, A and Sajjad, W and Wu, X and Zhang, G and Liu, G and Chen, T}, title = {Seasonal Variation in Fungal Community Composition Associated with Tamarix chinensis Roots in the Coastal Saline Soil of Bohai Bay, China.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {652-665}, pmid = {33598747}, issn = {1432-184X}, support = {31870479, 31570498//the National Science Foundation of China/ ; 2021PB0072//CAS-President`s International Fellowship Initiative, Postdoctoral Fellowship/ ; }, mesh = {Bays ; China ; Fungi/genetics ; *Mycobiome ; Seasons ; Soil ; Soil Microbiology ; *Tamaricaceae ; }, abstract = {Coastal salinity typically alters the soil microbial communities, which subsequently affect the biogeochemical cycle of nutrients in the soil. The seasonal variation of the soil fungal communities in the coastal area, closely associated with plant population, is poorly understood. This study provides an insight into the fungal community's variations from autumn to winter and spring to summer at a well-populated area of salt-tolerant Tamarix chinensis and beach. The richness and diversity of fungal community were higher in the spring season and lower in the winter season, as showed by high throughput sequencing of the 18S rRNA gene. Ascomycota was the predominant phylum reported in all samples across the region, and higher difference was reported at order level across the seasonal variations. The redundancy analysis suggested that the abundance and diversity of fungal communities in different seasons are mainly correlated to total organic carbon and total nitrogen. Additionally, the saprotrophic and pathotrophic fungi decreased while symbiotic fungi increased in the autumn season. This study provides a pattern of seasonal variation in fungal community composition that further broadens our limited understanding of how the density of the salt-tolerant T. chinensis population of the coastal saline soil could respond to their seasonal variations.}, }
@article {pmid33598162, year = {2021}, author = {Lyu, W and Jia, H and Deng, C and Yamada, S and Kato, H}, title = {Zeolite-containing mixture alleviates microbial dysbiosis in dextran sodium sulfate-induced colitis in mice.}, journal = {Food science &amp; nutrition}, volume = {9}, number = {2}, pages = {772-780}, pmid = {33598162}, issn = {2048-7177}, abstract = {Inflammatory bowel disease (IBD) is a multifactorial immunomodulatory disorder. In relative nosogenesis, gut microbiota has been the focus of research on IBD. In our previous study, we demonstrated the ameliorating effect of zeolite-containing mixture (Hydryeast[®], HY) on dextran sodium sulfate (DSS)-induced colitis, through transcriptomics and proteomics. In the present study, we performed further investigation from the perspective of metagenomics using the gut microbiota. C57BL6 mice were provided an AIN-93G basal diet or a 0.8% HY-containing diet, and sterilized tap water for 11 days. Thereafter, colitis was induced by providing 1.5% (w/v) DSS-containing water for 9 days. DNA was extracted from the cecal contents and pooled into libraries in a single Illumina MiSeq run. The resulting sequences were analyzed using Quantitative Insights Into Microbial Ecology (QIIME) software. According to the alterations in the relative abundance of certain bacteria, and the related gene and protein expressions, HY supplementation could improve the gut microbiota composition, ameliorate the degree of inflammation, inhibit the colonic mucosal microbial growth, and, to some extent, promote energy metabolism in the colon compared with the DSS treatment. Thus, we believe that HY may be a candidate to prevent and treat IBD.}, }
@article {pmid33598106, year = {2021}, author = {Izabel-Shen, D}, title = {Understanding response of microbial communities to saltwater intrusion through microcosms.}, journal = {Computational and structural biotechnology journal}, volume = {19}, number = {}, pages = {929-933}, pmid = {33598106}, issn = {2001-0370}, abstract = {A central pursuit of microbial ecology is to accurately describe and explain the shifts in microbial community composition and function that occur in response to environmental changes. This goal requires a thorough understanding of the individual responses of different species and of the processes guiding the assembly of microbial populations similar in their response traits and corresponding functional traits. These research topics are addressed and synthesized in this Highlights, in four studies applying a trait-based framework to assess how environmental change affected the composition and functional performance of bacterioplankton of natural origin in microcosm experiments. The salinity of many aquatic environments is currently changing, due to climate change and anthropogenic activities. The mechanisms by which salinity influences community assembly, functional redundancy and functional genes involved in nitrogen cycle, and how dispersal modifies community outcome are explored in the four studies. Together, the findings of these case studies demonstrate the feasibility of using novel experiments in combination with integrative analyses of 16S rRNA and meta-'omic' data to address ecological questions. This combined approach has the potential to elucidate both the processes contributing to bacterial community assembly and the possible links between the compositional and functional changes that occur under shifting environmental conditions.}, }
@article {pmid33597941, year = {2021}, author = {Wahdan, SFM and Heintz-Buschart, A and Sansupa, C and Tanunchai, B and Wu, YT and Schädler, M and Noll, M and Purahong, W and Buscot, F}, title = {Targeting the Active Rhizosphere Microbiome of Trifolium pratense in Grassland Evidences a Stronger-Than-Expected Belowground Biodiversity-Ecosystem Functioning Link.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {629169}, pmid = {33597941}, issn = {1664-302X}, abstract = {The relationship between biodiversity and ecosystem functioning (BEF) is a central issue in soil and microbial ecology. To date, most belowground BEF studies focus on the diversity of microbes analyzed by barcoding on total DNA, which targets both active and inactive microbes. This approach creates a bias as it mixes the part of the microbiome currently steering processes that provide actual ecosystem functions with the part not directly involved. Using experimental extensive grasslands under current and future climate, we used the bromodeoxyuridine (BrdU) immunocapture technique combined with pair-end Illumina sequencing to characterize both total and active microbiomes (including both bacteria and fungi) in the rhizosphere of Trifolium pratense. Rhizosphere function was assessed by measuring the activity of three microbial extracellular enzymes (β-glucosidase, N-acetyl-glucosaminidase, and acid phosphatase), which play central roles in the C, N, and P acquisition. We showed that the richness of overall and specific functional groups of active microbes in rhizosphere soil significantly correlated with the measured enzyme activities, while total microbial richness did not. Active microbes of the rhizosphere represented 42.8 and 32.1% of the total bacterial and fungal taxa, respectively, and were taxonomically and functionally diverse. Nitrogen fixing bacteria were highly active in this system with 71% of the total operational taxonomic units (OTUs) assigned to this group detected as active. We found the total and active microbiomes to display different responses to variations in soil physicochemical factors in the grassland, but with some degree of resistance to a manipulation mimicking future climate. Our findings provide critical insights into the role of active microbes in defining soil ecosystem functions in a grassland ecosystem. We demonstrate that the relationship between biodiversity-ecosystem functioning in soil may be stronger than previously thought.}, }
@article {pmid33597669, year = {2021}, author = {Gupta, S and Shariff, M and Chaturvedi, G and Sharma, A and Goel, N and Yadav, M and Mortensen, MS and Sørensen, SJ and Mukerji, M and Chauhan, NS}, title = {Comparative analysis of the alveolar microbiome in COPD, ECOPD, Sarcoidosis, and ILD patients to identify respiratory illnesses specific microbial signatures.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {3963}, pmid = {33597669}, issn = {2045-2322}, mesh = {Aged ; Bacteria/genetics ; Bronchoalveolar Lavage ; Diagnosis, Differential ; Female ; Humans ; Lung/microbiology ; Lung Diseases, Interstitial/*microbiology ; Male ; Microbiota/genetics ; Middle Aged ; Pulmonary Disease, Chronic Obstructive/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sarcoidosis/*microbiology ; }, abstract = {Studying respiratory illness-specific microbial signatures and their interaction with other micro-residents could provide a better understanding of lung microbial ecology. Each respiratory illness has a specific disease etiology, however, so far no study has revealed disease-specific microbial markers. The present study was designed to determine disease-specific microbial features and their interactions with other residents in chronic obstructive pulmonary diseases (stable and exacerbated), sarcoidosis, and interstitial lung diseases. Broncho-alveolar lavage samples (n = 43) were analyzed by SSU rRNA gene sequencing to study the alveolar microbiome in these diseases. A predominance of Proteobacteria followed by Firmicutes, Bacteroidetes, Actinobacteria, and Fusobacteria was observed in all the disease subsets. Shannon diversity was significantly higher in stable COPD when compared to exacerbated chronic obstructive pulmonary disease (ECOPD) (p = 0.0061), and ILD patient samples (p = 0.037). The lung microbiome of the patients with stable COPD was more diverse in comparison to ECOPD and ILD patients (p < 0.001). Lefse analysis identified 40 disease-differentiating microbial features (LDA score (log10) > 4). Species network analysis indicated a significant correlation (p < 0.05) of diseases specific microbial signature with other lung microbiome members. The current study strengthens the proposed hypothesis that each respiratory illness has unique microbial signatures. These microbial signatures could be used as diagnostic markers to differentiate among various respiratory illnesses.}, }
@article {pmid33597173, year = {2021}, author = {Keller, CM and Kendra, CG and Bruna, RE and Craft, D and Pontes, MH}, title = {Genetic Modification of Sodalis Species by DNA Transduction.}, journal = {mSphere}, volume = {6}, number = {1}, pages = {}, pmid = {33597173}, issn = {2379-5042}, support = {R21 AI148774/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteriophages/genetics/metabolism ; DNA, Bacterial/*genetics ; Enterobacteriaceae/classification/*genetics/*virology ; Escherichia coli/genetics ; *Gene Transfer Techniques ; *Genome, Bacterial ; Host Specificity ; Phylogeny ; Symbiosis ; *Transduction, Genetic ; }, abstract = {Bacteriophages (phages) are ubiquitous in nature. These viruses play a number of central roles in microbial ecology and evolution by, for instance, promoting horizontal gene transfer (HGT) among bacterial species. The ability of phages to mediate HGT through transduction has been widely exploited as an experimental tool for the genetic study of bacteria. As such, bacteriophage P1 represents a prototypical generalized transducing phage with a broad host range that has been extensively employed in the genetic manipulation of Escherichia coli and a number of other model bacterial species. Here we demonstrate that P1 is capable of infecting, lysogenizing, and promoting transduction in members of the bacterial genus Sodalis, including the maternally inherited insect endosymbiont Sodalis glossinidius While establishing new tools for the genetic study of these bacterial species, our results suggest that P1 may be used to deliver DNA to many Gram-negative endosymbionts in their insect host, thereby circumventing a culturing requirement to genetically manipulate these organisms.IMPORTANCE A large number of economically important insects maintain intimate associations with maternally inherited endosymbiotic bacteria. Due to the inherent nature of these associations, insect endosymbionts cannot be usually isolated in pure culture or genetically manipulated. Here we use a broad-host-range bacteriophage to deliver exogenous DNA to an insect endosymbiont and a closely related free-living species. Our results suggest that broad-host-range bacteriophages can be used to genetically alter insect endosymbionts in their insect host and, as a result, bypass a culturing requirement to genetically alter these bacteria.}, }
@article {pmid33596519, year = {2021}, author = {Kleerebezem, R and Stouten, G and Koehorst, J and Langenhoff, A and Schaap, P and Smidt, H}, title = {Experimental infrastructure requirements for quantitative research on microbial communities.}, journal = {Current opinion in biotechnology}, volume = {67}, number = {}, pages = {158-165}, doi = {10.1016/j.copbio.2021.01.017}, pmid = {33596519}, issn = {1879-0429}, mesh = {Bacteria/genetics ; *Ecosystem ; Metagenome ; Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; }, abstract = {Natural microbial communities are composed of a large diversity of interacting microorganisms, each with a specific role in the functional properties of the ecosystem. The objectives in microbial ecology research are related to identifying, understanding and exploring the role of these different microorganisms. Because of the rapidly increasing power of DNA sequencing and the rapid increase of genomic data, main attention of microbial ecology research shifted from cultivation-oriented studies towards metagenomic studies. Despite these efforts, the direct link between the molecular properties and the measurable changes in the functional performance of the ecosystem is often poorly documented. A quantitative understanding of functional properties in relation to the molecular changes requires effective integration, standardization, and parallelization of experiments. High-resolution functional characterization is a prerequisite for interpretation of changes in metagenomic properties, and will improve our understanding of microbial communities and facilitate their exploration for health and circular economy related objectives.}, }
@article {pmid33594548, year = {2021}, author = {Labrador, MDM and Doña, J and Serrano, D and Jovani, R}, title = {Correction to: Quantitative Interspecific Approach to the Stylosphere: Patterns of Bacteria and Fungi Abundance on Passerine Bird Feathers.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {831}, doi = {10.1007/s00248-021-01713-y}, pmid = {33594548}, issn = {1432-184X}, }
@article {pmid33594547, year = {2021}, author = {Katsoula, A and Vasileiadis, S and Karamanoli, K and Vokou, D and Karpouzas, DG}, title = {Factors Structuring the Epiphytic Archaeal and Fungal Communities in a Semi-arid Mediterranean Ecosystem.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {638-651}, pmid = {33594547}, issn = {1432-184X}, support = {-//State Scholarship Foundation of Greece/ ; -//European Social Fund (ESF) and National Resources/ ; -//General Secretariat of Research and Technology, Greece/ ; //State Scholarship Foundation of Greece/ ; //European Social Fund (ESF) and National Resources/ ; //General Secretariat of Research and Technology, Greece/ ; }, mesh = {Archaea/genetics ; Biodiversity ; Ecosystem ; Fungi/genetics ; *Microbiota ; *Mycobiome ; }, abstract = {The phyllosphere microbiome exerts a strong effect on plants' productivity, and its composition is determined by various factors. To date, most phyllosphere studies have focused on bacteria, while fungi and especially archaea have been overlooked. We studied the effects of plant host and season on the abundance and diversity of the epiphytic archaeal and fungal communities in a typical semi-arid Mediterranean ecosystem. We collected leaves in two largely contrasting seasons (summer and winter) from eight perennial species of varying attributes which could be grouped into the following: (i) high-canopy, evergreen sclerophyllοus shrubs with leathery leaves, and low-canopy, either semi-deciduous shrubs or non-woody perennials with non-leathery leaves, and (ii) aromatic and non-aromatic plants. We determined the abundance of epiphytic Crenarchaea, total fungi, Alternaria and Cladosporium (main airborne fungi) via q-PCR and the structure of the epiphytic archaeal and fungal communities via amplicon sequencing. We observed a strong seasonal effect with all microbial groups examined showing higher abundance in summer. Plant host and season were equally important determinants of the composition of the fungal community consisted mostly of Ascomycota, with Hypocreales dominating in winter and Capnodiales and Pleosporales in summer. In contrast, the archaeal community showed plant host driven patterns dominated by the Soil Crenarchaeotic Group (SCG) and Aenigmarchaeota. Plant habit and aromatic nature exhibited filtering effects only on the epiphytic fungal communities. Our study provides a first in-depth analysis of the key determinants shaping the phyllosphere archaeal and fungal communities of a semi-arid Mediterranean ecosystem.}, }
@article {pmid33592536, year = {2021}, author = {Taş, N and de Jong, AE and Li, Y and Trubl, G and Xue, Y and Dove, NC}, title = {Metagenomic tools in microbial ecology research.}, journal = {Current opinion in biotechnology}, volume = {67}, number = {}, pages = {184-191}, doi = {10.1016/j.copbio.2021.01.019}, pmid = {33592536}, issn = {1879-0429}, mesh = {Ecology ; High-Throughput Nucleotide Sequencing ; Metagenome/genetics ; *Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; }, abstract = {Ability to directly sequence DNA from the environment permanently changed microbial ecology. Here, we review the new insights to microbial life gleaned from the applications of metagenomics, as well as the extensive set of analytical tools that facilitate exploration of diversity and function of complex microbial communities. While metagenomics is shaping our understanding of microbial functions in ecosystems via gene-centric and genome-centric methods, annotating functions, metagenome assembly and binning in heterogeneous samples remains challenging. Development of new analysis and sequencing platforms generating high-throughput long-read sequences and functional screening opportunities will aid in harnessing metagenomes to increase our understanding of microbial taxonomy, function, ecology, and evolution in the environment.}, }
@article {pmid33591419, year = {2021}, author = {Luzzi, G and Brinks, E and Fritsche, J and Franz, CMAP}, title = {Effect of reduction of sodium content on the microbial ecology of Edam cheese samples.}, journal = {AMB Express}, volume = {11}, number = {1}, pages = {28}, pmid = {33591419}, issn = {2191-0855}, support = {2819107716//Bundesministerium f&#xfc;r Ern&#xe4;hrung und Landwirtschaft/ ; }, abstract = {Sodium intake is a major risk factor for non-communicable diseases. Consequently, reformulation of cheeses such as Edam to contain less sodium may contribute to lowering disease risk. However, sodium is essential for cheese manufacture, influencing starter culture bacteria activity and abundance during fermentation. This study aimed to assess the microbial diversity of reformulated Edam cheese samples with a reduced sodium content using culture-independent technique. The microbial diversity of samples produced using simple sodium reduction, as well as by substituting salt with a mineral salt compound containing potassium, were analysed in comparison to regular control Edam samples during manufacture and the subsequent 6-week ripening period using 16S rDNA metagenomics. In addition, a challenge test using Listeria (List.) innocua as a surrogate species for List. monocytogenes was performed. Reducing sodium content did not influence the microbiological composition of reformulated samples in comparison to that of regular samples. The starter culture bacteria dominated the microbial diversity and no increase in spoilage or potentially pathogenic bacterial growth was detected, including that of List. innocua. From a microbiological perspective, it can be concluded that lowering sodium content in Edam samples without affecting the microbial composition is achievable through simple sodium reduction and through implementation of a mineral salt replacement approach.}, }
@article {pmid33589842, year = {2021}, author = {Schorn, MA and Verhoeven, S and Ridder, L and Huber, F and Acharya, DD and Aksenov, AA and Aleti, G and Moghaddam, JA and Aron, AT and Aziz, S and Bauermeister, A and Bauman, KD and Baunach, M and Beemelmanns, C and Beman, JM and Berlanga-Clavero, MV and Blacutt, AA and Bode, HB and Boullie, A and Brejnrod, A and Bugni, TS and Calteau, A and Cao, L and Carrión, VJ and Castelo-Branco, R and Chanana, S and Chase, AB and Chevrette, MG and Costa-Lotufo, LV and Crawford, JM and Currie, CR and Cuypers, B and Dang, T and de Rond, T and Demko, AM and Dittmann, E and Du, C and Drozd, C and Dujardin, JC and Dutton, RJ and Edlund, A and Fewer, DP and Garg, N and Gauglitz, JM and Gentry, EC and Gerwick, L and Glukhov, E and Gross, H and Gugger, M and Guillén Matus, DG and Helfrich, EJN and Hempel, BF and Hur, JS and Iorio, M and Jensen, PR and Kang, KB and Kaysser, L and Kelleher, NL and Kim, CS and Kim, KH and Koester, I and König, GM and Leao, T and Lee, SR and Lee, YY and Li, X and Little, JC and Maloney, KN and Männle, D and Martin H, C and McAvoy, AC and Metcalf, WW and Mohimani, H and Molina-Santiago, C and Moore, BS and Mullowney, MW and Muskat, M and Nothias, LF and O'Neill, EC and Parkinson, EI and Petras, D and Piel, J and Pierce, EC and Pires, K and Reher, R and Romero, D and Roper, MC and Rust, M and Saad, H and Saenz, C and Sanchez, LM and Sørensen, SJ and Sosio, M and Süssmuth, RD and Sweeney, D and Tahlan, K and Thomson, RJ and Tobias, NJ and Trindade-Silva, AE and van Wezel, GP and Wang, M and Weldon, KC and Zhang, F and Ziemert, N and Duncan, KR and Crüsemann, M and Rogers, S and Dorrestein, PC and Medema, MH and van der Hooft, JJJ}, title = {A community resource for paired genomic and metabolomic data mining.}, journal = {Nature chemical biology}, volume = {17}, number = {4}, pages = {363-368}, pmid = {33589842}, issn = {1552-4469}, support = {R01 GM118815/GM/NIGMS NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; R35 GM138002/GM/NIGMS NIH HHS/United States ; R01 AT009143/AT/NCCIH NIH HHS/United States ; U19 AI142720/AI/NIAID NIH HHS/United States ; DP2 AT010401/AT/NCCIH NIH HHS/United States ; F32 CA221327/CA/NCI NIH HHS/United States ; U01 GM110706/GM/NIGMS NIH HHS/United States ; }, mesh = {Data Mining/*methods ; Databases, Factual ; Genomics/*methods ; Metabolomics/*methods ; }, abstract = {Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding identification of natural product biosynthetic origins and metabolite structures.}, }
@article {pmid33587250, year = {2021}, author = {Zheng, R and Wu, M and Wang, H and Chai, L and Peng, J}, title = {Copper-induced sublethal effects in Bufo gargarizans tadpoles: growth, intestinal histology and microbial alternations.}, journal = {Ecotoxicology (London, England)}, volume = {30}, number = {3}, pages = {502-513}, doi = {10.1007/s10646-021-02356-y}, pmid = {33587250}, issn = {1573-3017}, support = {No. 42077370//National Natural Science Foundation of China/ ; No. 2020JM232//Natural Science Foundation of Shaanxi Province/ ; }, mesh = {Animals ; Bufonidae ; *Copper/toxicity ; *Gastrointestinal Microbiome ; Intestines ; Larva ; }, abstract = {Copper (Cu) is one of the environmental contaminations which can pose significant risks for organisms. The current study explores the effects of Cu exposure on the growth, intestinal histology and microbial ecology in Bufo gargarizans. The results revealed that 0.5-1 μM Cu exposure induced growth retardation (including reduction of total body length and wet weight) and intestinal histological injury (including disordered enterocyte, changes in the villi and vacuoles) of tadpoles. Also, high-throughput sequencing analysis showed that Cu exposure caused changes in richness, diversity and structure of intestinal microbiota. Moreover, the composition of intestinal microbiota was altered in tadpoles exposed to different concentrations of Cu. At the phylum level, we observed the abundance of proteobacteria was increased, while the abundance of fusobacteria was decreased in the intestinal microbiota of tadpoles exposed to 1 μM Cu. At the genus level, a reduced abundance of kluyvera and aeromonas was observed in the intestinal microbiota of tadpoles under the exposure of 0-0.5 μM Cu. Finally, functional predictions revealed that tadpoles exposed to copper may be at a higher risk of developing metabolic disorders or diseases. Above all, our results will develop a comprehensive view of the Cu exposure in amphibians and will yield a new consideration for sublethal effects of Cu on aquatic organisms.}, }
@article {pmid33584618, year = {2021}, author = {George, SF and Fierer, N and Levy, JS and Adams, B}, title = {Antarctic Water Tracks: Microbial Community Responses to Variation in Soil Moisture, pH, and Salinity.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {616730}, pmid = {33584618}, issn = {1664-302X}, abstract = {Ice-free soils in the McMurdo Dry Valleys select for taxa able to cope with challenging environmental conditions, including extreme chemical water activity gradients, freeze-thaw cycling, desiccation, and solar radiation regimes. The low biotic complexity of Dry Valley soils makes them well suited to investigate environmental and spatial influences on bacterial community structure. Water tracks are annually wetted habitats in the cold-arid soils of Antarctica that form briefly each summer with moisture sourced from snow melt, ground ice thaw, and atmospheric deposition via deliquescence and vapor flow into brines. Compared to neighboring arid soils, water tracks are highly saline and relatively moist habitats. They represent a considerable area (∼5-10 km[2]) of the Dry Valley terrestrial ecosystem, an area that is expected to increase with ongoing climate change. The goal of this study was to determine how variation in the environmental conditions of water tracks influences the composition and diversity of microbial communities. We found significant differences in microbial community composition between on- and off-water track samples, and across two distinct locations. Of the tested environmental variables, soil salinity was the best predictor of community composition, with members of the Bacteroidetes phylum being relatively more abundant at higher salinities and the Actinobacteria phylum showing the opposite pattern. There was also a significant, inverse relationship between salinity and bacterial diversity. Our results suggest water track formation significantly alters dry soil microbial communities, likely influencing subsequent ecosystem functioning. We highlight how Dry Valley water tracks could be a useful model system for understanding the potential habitability of transiently wetted environments found on the surface of Mars.}, }
@article {pmid33584606, year = {2021}, author = {Walker, AM and Leigh, MB and Mincks, SL}, title = {Patterns in Benthic Microbial Community Structure Across Environmental Gradients in the Beaufort Sea Shelf and Slope.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {581124}, pmid = {33584606}, issn = {1664-302X}, support = {P20 GM103395/GM/NIGMS NIH HHS/United States ; }, abstract = {The paradigm of tight pelagic-benthic coupling in the Arctic suggests that current and future fluctuations in sea ice, primary production, and riverine input resulting from global climate change will have major impacts on benthic ecosystems. To understand how these changes will affect benthic ecosystem function, we must characterize diversity, spatial distribution, and community composition for all faunal components. Bacteria and archaea link the biotic and abiotic realms, playing important roles in organic matter (OM) decomposition, biogeochemical cycling, and contaminant degradation, yet sediment microbial communities have rarely been examined in the North American Arctic. Shifts in microbial community structure and composition occur with shifts in OM inputs and contaminant exposure, with implications for shifts in ecological function. Furthermore, the characterization of benthic microbial communities provides a foundation from which to build focused experimental research. We assessed diversity and community structure of benthic prokaryotes in the upper 1 cm of sediments in the southern Beaufort Sea (United States and Canada), and investigated environmental correlates of prokaryotic community structure over a broad spatial scale (spanning 1,229 km) at depths ranging from 17 to 1,200 m. Based on hierarchical clustering, we identified four prokaryotic assemblages from the 85 samples analyzed. Two were largely delineated by the markedly different environmental conditions in shallow shelf vs. upper continental slope sediments. A third assemblage was mainly comprised of operational taxonomic units (OTUs) shared between the shallow shelf and upper slope assemblages. The fourth assemblage corresponded to sediments receiving heavier OM loading, likely resulting in a shallower anoxic layer. These sites may also harbor microbial mats and/or methane seeps. Substructure within these assemblages generally reflected turnover along a longitudinal gradient, which may be related to the quantity and composition of OM deposited to the seafloor; bathymetry and the Mackenzie River were the two major factors influencing prokaryote distribution on this scale. In a broader geographical context, differences in prokaryotic community structure between the Beaufort Sea and Norwegian Arctic suggest that benthic microbes may reflect regional differences in the hydrography, biogeochemistry, and bathymetry of Arctic shelf systems.}, }
@article {pmid33584565, year = {2020}, author = {Rain-Franco, A and de Moraes, GP and Beier, S}, title = {Cryopreservation and Resuscitation of Natural Aquatic Prokaryotic Communities.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {597653}, pmid = {33584565}, issn = {1664-302X}, abstract = {Experimental reproducibility in aquatic microbial ecology is critical to predict the dynamics of microbial communities. However, controlling the initial composition of naturally occurring microbial communities that will be used as the inoculum in experimental setups is challenging, because a proper method for the preservation of those communities is lacking. To provide a feasible method for preservation and resuscitation of natural aquatic prokaryote assemblages, we developed a cryopreservation procedure applied to natural aquatic prokaryotic communities. We studied the impact of inoculum size, processing time, and storage time on the success of resuscitation. We further assessed the effect of different growth media supplemented with dissolved organic matter (DOM) prepared from naturally occurring microorganisms on the recovery of the initially cryopreserved communities obtained from two sites that have contrasting trophic status and environmental heterogeneity. Our results demonstrated that the variability of the resuscitation process among replicates decreased with increasing inoculum size. The degree of similarity between initial and resuscitated communities was influenced by both the growth medium and origin of the community. We further demonstrated that depending on the inoculum source, 45-72% of the abundant species in the initially natural microbial communities could be detected as viable cells after cryopreservation. Processing time and long-term storage up to 12 months did not significantly influence the community composition after resuscitation. However, based on our results, we recommend keeping handling time to a minimum and ensure identical incubation conditions for repeated resuscitations from cryo-preserved aliquots at different time points. Given our results, we recommend cryopreservation as a promising tool to advance experimental research in the field of microbial ecology.}, }
@article {pmid33584558, year = {2020}, author = {Oyserman, BO and Cordovez, V and Flores, SS and Leite, MFA and Nijveen, H and Medema, MH and Raaijmakers, JM}, title = {Extracting the GEMs: Genotype, Environment, and Microbiome Interactions Shaping Host Phenotypes.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {574053}, pmid = {33584558}, issn = {1664-302X}, abstract = {One of the fundamental tenets of biology is that the phenotype of an organism (Y) is determined by its genotype (G), the environment (E), and their interaction (GE). Quantitative phenotypes can then be modeled as Y = G + E + GE + e, where e is the biological variance. This simple and tractable model has long served as the basis for studies investigating the heritability of traits and decomposing the variability in fitness. The importance and contribution of microbe interactions to a given host phenotype is largely unclear, nor how this relates to the traditional GE model. Here we address this fundamental question and propose an expansion of the original model, referred to as GEM, which explicitly incorporates the contribution of the microbiome (M) to the host phenotype, while maintaining the simplicity and tractability of the original GE model. We show that by keeping host, environment, and microbiome as separate but interacting variables, the GEM model can capture the nuanced ecological interactions between these variables. Finally, we demonstrate with an in vitro experiment how the GEM model can be used to statistically disentangle the relative contributions of each component on specific host phenotypes.}, }
@article {pmid33582117, year = {2021}, author = {Petrin, S and Orsini, M and Mastrorilli, E and Longo, A and Cozza, D and Olsen, JE and Ricci, A and Losasso, C and Barco, L}, title = {Identification and characterization of a spreadable IncI1 plasmid harbouring a blaCTX-M-15 gene in an Italian human isolate of Salmonella serovar Napoli.}, journal = {Plasmid}, volume = {114}, number = {}, pages = {102566}, doi = {10.1016/j.plasmid.2021.102566}, pmid = {33582117}, issn = {1095-9890}, mesh = {Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics ; Humans ; Italy ; Plasmids/genetics ; *Salmonella/genetics ; Serogroup ; beta-Lactamases/genetics ; }, abstract = {Salmonella enterica subsp. enterica serovar Napoli (S. Napoli) ranks among the top serovars causing human infections in Italy, although not common in other European countries. Isolates are generally pan-susceptible or resistant to aminoglycosides only, however data on antimicrobial resistance genes in strains of S. Napoli are limited. Recently an isolate encoding resistance to third generation cephalosporins was reported. This study aimed to characterize plasmid-encoded cephalosporin resistance due to the blaCTX-M-15 gene in a human S. Napoli isolate in Italy, and to investigate plasmid stability over time. S. Napoli 16/174478 was confirmed to be ESBL-producing. The blaCTX-M-15 gene was shown to be located on an IncI1α plasmid of 90,272 bp (50.03 GC%) encoding for 107 coding sequences (CDS). The plasmid was successfully transferred by conjugation to an E. coli 1816 recipient strain (conjugation frequency 3.9 × 10[-2] transconjugants per donor). Transconjugants were confirmed to carry the IncI1α plasmid, and to be ESBL-producing strains as well. Moreover, transconjugant colonies maintained the plasmid for up to 10 passages. The identification of S. Napoli isolates able to produce ESBLs is of great concern, as this pathogen is frequently associated with invasive infections and a higher risk of bacteraemia, and its reservoir has not yet been clearly identified.}, }
@article {pmid33581524, year = {2021}, author = {Cordovez, V and Rotoni, C and Dini-Andreote, F and Oyserman, B and Carrión, VJ and Raaijmakers, JM}, title = {Successive plant growth amplifies genotype-specific assembly of the tomato rhizosphere microbiome.}, journal = {The Science of the total environment}, volume = {772}, number = {}, pages = {144825}, doi = {10.1016/j.scitotenv.2020.144825}, pmid = {33581524}, issn = {1879-1026}, mesh = {Genotype ; *Solanum lycopersicum ; *Microbiota ; Plant Roots ; Rhizosphere ; Soil Microbiology ; }, abstract = {Plant microbiome assembly is a spatial and dynamic process driven by root exudates and influenced by soil type, plant developmental stage and genotype. Genotype-dependent microbiome assembly has been reported for different crop plant species. Despite the effect of plant genetics on microbiome assembly, the magnitude of host control over its root microbiome is relatively small or, for many plant species, still largely unknown. Here we cultivated modern and wild tomato genotypes for four successive cycles and showed that divergence in microbiome assembly between the two genotypes was significantly amplified over time. Also, we show that the composition of the rhizosphere microbiome of modern and wild plants became more dissimilar from the initial bulk soil and from each other. Co-occurrence analyses further identified amplicon sequence variants (ASVs) associated with early and late successions of the tomato rhizosphere microbiome. Among the members of the Late Successional Rhizosphere microbiome, we observed an enrichment of ASVs belonging to the genera Acidovorax, Massilia and Rhizobium in the wild tomato rhizosphere, whereas the modern tomato rhizosphere was enriched for an ASV belonging to the genus Pseudomonas. Collectively, our approach allowed us to study the dynamics of rhizosphere microbiome over successional cultivation as well as to categorize rhizobacterial taxa for their ability to form transient or long-term associations with their host plants.}, }
@article {pmid33581124, year = {2021}, author = {Liu, W and Zhang, X and Xu, H and Li, S and Lau, HC and Chen, Q and Zhang, B and Zhao, L and Chen, H and Sung, JJ and Yu, J}, title = {Microbial Community Heterogeneity Within Colorectal Neoplasia and its Correlation With Colorectal Carcinogenesis.}, journal = {Gastroenterology}, volume = {160}, number = {7}, pages = {2395-2408}, doi = {10.1053/j.gastro.2021.02.020}, pmid = {33581124}, issn = {1528-0012}, mesh = {Adenoma/*microbiology ; Aged ; Biopsy ; Carcinogenesis/*genetics ; Colon/microbiology/pathology ; Colorectal Neoplasms/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; *Genetic Heterogeneity ; Humans ; Male ; Microsatellite Instability ; Middle Aged ; Proto-Oncogene Proteins p21(ras)/genetics ; RNA, Ribosomal, 16S/analysis ; }, abstract = {BACKGROUND &amp; AIMS: Gut microbial dysbiosis has pivotal involvement in colorectal cancer (CRC). However, the intratumoral microbiota and its association with CRC progression remain elusive. We aimed to determine the microbial community architecture within a neoplasia (CRC or adenoma) and its contribution to colorectal carcinogenesis.<br><br>METHODS: We collected 436 tissue biopsies from patients with CRC (n&#xa0;= 36) or adenoma (n&#xa0;= 32) (2-6 biopsies from a neoplasia plus 2-5 biopsies from adjacent normal tissues per individual). Microbial profiling was performed using 16S ribosomal RNA gene sequencing with subsequent investigation of microbiota diversities and heterogeneity. The correlation between microbial dysbiosis and host genetic alterations (KRAS mutation and microsatellite instability) in all neoplasia biopsies was also analyzed.<br><br>RESULTS: We discovered that intra-neoplasia microbial communities are heterogeneous. Abundances of some CRC-associated pathobionts (eg, Fusobacterium, Bacteroides, Parvimonas, and Prevotella) were found to be highly varied within a single neoplasia. Correlation of such heterogeneity with CRC development revealed alterations in microbial communities involving microbes with high intra-neoplasia variation in abundance. Moreover, we found that the intra-neoplasia variation in abundance of individual microbes changed along the adenoma-carcinoma sequence. We further determined that there was a significant difference in intra-neoplasia microbiota between biopsies with and without KRAS mutation (P < .001) or microsatellite instability (P < .001), and illustrated the association of intratumoral microbial heterogeneity with genetic alteration.<br><br>CONCLUSIONS: We demonstrated that intra-neoplasia microbiota is heterogeneous and correlated with colorectal carcinogenesis. Our findings provide new insights on the contribution of gut microbiota heterogeneity to CRC progression.}, }
@article {pmid33580950, year = {2021}, author = {Lopes, LD and Hao, J and Schachtman, DP}, title = {Alkaline soil pH affects bulk soil, rhizosphere and root endosphere microbiomes of plants growing in a Sandhills ecosystem.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {4}, pages = {}, doi = {10.1093/femsec/fiab028}, pmid = {33580950}, issn = {1574-6941}, mesh = {Bacteria/genetics ; Hydrogen-Ion Concentration ; *Microbiota ; Plant Roots ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil ; Soil Microbiology ; }, abstract = {Soil pH is a major factor shaping bulk soil microbial communities. However, it is unclear whether the belowground microbial habitats shaped by plants (e.g. rhizosphere and root endosphere) are also affected by soil pH. We investigated this question by comparing the microbial communities associated with plants growing in neutral and strongly alkaline soils in the Sandhills, which is the largest sand dune complex in the northern hemisphere. Bulk soil, rhizosphere and root endosphere DNA were extracted from multiple plant species and analyzed using 16S rRNA amplicon sequencing. Results showed that rhizosphere, root endosphere and bulk soil microbiomes were different in the contrasting soil pH ranges. The strongest impact of plant species on the belowground microbiomes was in alkaline soils, suggesting a greater selective effect under alkali stress. Evaluation of soil chemical components showed that in addition to soil pH, cation exchange capacity also had a strong impact on shaping bulk soil microbial communities. This study extends our knowledge regarding the importance of pH to microbial ecology showing that root endosphere and rhizosphere microbial communities were also influenced by this soil component, and highlights the important role that plants play particularly in shaping the belowground microbiomes in alkaline soils.}, }
@article {pmid33580815, year = {2021}, author = {Kellogg, JA and Reganold, JP and Murphy, KM and Carpenter-Boggs, LA}, title = {A Plant-Fungus Bioassay Supports the Classification of Quinoa (Chenopodium quinoa Willd.) as Inconsistently Mycorrhizal.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {135-144}, pmid = {33580815}, issn = {1432-184X}, support = {2016-51300-25808//USDA National Institute of Food and Agriculture (US)/ ; n/a//Lundberg Family Farms, Richvale, California (US)/ ; 1014754//USDA National Institute of Food and Agriculture Hatch project (US)/ ; }, mesh = {Biological Assay ; *Chenopodium quinoa ; Fungi ; *Mycorrhizae/genetics ; Plant Roots ; }, abstract = {Quinoa (Chenopodium quinoa Willd.) is becoming an increasingly important food crop. Understanding the microbiome of quinoa and its relationships with soil microorganisms may improve crop yield potential or nutrient use efficiency. Whether quinoa is a host or non-host of a key soil symbiont, arbuscular mycorrhizal fungi (AMF), is suddenly up for debate with recent field studies reporting root colonization and presence of arbuscules. This research seeks to add evidence to the mycorrhizal classification of quinoa as we investigated additional conditions not previously explored in quinoa that may affect root colonization. A greenhouse study used six AMF species, two AMF commercial inoculant products, and a diverse set of 10 quinoa genotypes. Results showed 0 to 3% quinoa root colonization by AMF when grown under greenhouse conditions. Across quinoa genotypes, AMF inoculant affected shoot dry weight (p = 0.066) and height (p = 0.031). Mykos Gold produced greater dry biomass than Claroideoglomus eutunicatum (27% increase), Rhizophagus clarus (26% increase), and within genotype CQ119, the control (21% increase). No treatment increased plant height compared to control, but Funneliformis mosseae increased height compared to C. eutunicatum (25% increase) and Rhizophagus intraradices (25% increase). Although quinoa plants were minimally colonized by AMF, plant growth responses fell along the mutualism-parasitism continuum. Individual AMF treatments increased leaf greenness in quinoa genotypes 49ALC and QQ87, while R. clarus decreased greenness in CQ119 compared to the control. Our research findings support the recommendation to classify quinoa as non-mycorrhizal when no companion plant is present and inconsistently mycorrhizal when conditional colonization occurs.}, }
@article {pmid33580272, year = {2021}, author = {He, Y and Huang, D and Li, S and Shi, L and Sun, W and Sanford, RA and Fan, H and Wang, M and Li, B and Li, Y and Tang, X and Dong, Y}, title = {Profiling of Microbial Communities in the Sediments of Jinsha River Watershed Exposed to Different Levels of Impacts by the Vanadium Industry, Panzhihua, China.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {623-637}, pmid = {33580272}, issn = {1432-184X}, support = {92051111//National Natural Science Foundation of China/ ; 91851211//National Natural Science Foundation of China/ ; 41877321//National Natural Science Foundation of China/ ; JG/18011B//China Three Gorges Projects Development Co. Ltd/ ; }, mesh = {China ; Environmental Monitoring ; Geologic Sediments ; *Metals, Heavy/analysis ; *Microbiota ; Mining ; RNA, Ribosomal, 16S/genetics ; Rivers ; Vanadium/analysis ; }, abstract = {The mining, smelting, manufacturing, and disposal of vanadium (V) and associated products have caused serious environmental problems. Although the microbial ecology in V-contaminated soils has been intensively studied, the impacted watershed ecosystems have not been systematically investigated. In this study, geochemistry and microbial structure were analyzed along ~30 km of the Jinsha River and its two tributaries across the industrial areas in Panzhihua, one of the primary V mining and production cities in China. Geochemical analyses showed different levels of contamination by metals and metalloids in the sediments, with high degrees of contamination observed in one of the tributaries close to the industrial park. Analyses of the V4 hypervariable region of 16S rRNA genes of the microbial communities in the sediments showed significant decrease in microbial diversity and microbial structure in response to the environmental gradient (e.g., heavy metals, total sulfur, and total nitrogen). Strong association of the taxa (e.g., Thauera, Algoriphagus, Denitromonas, and Fontibacter species) with the metals suggested selection for these potential metal-resistant and/or metabolizing populations. Further co-occurrence network analysis showed that many identified potential metal-mediating species were among the keystone taxa that were closely associated in the same module, suggesting their strong inter-species interactions but relative independence from other microorganisms in the hydrodynamic ecosystems. This study provided new insight into the microbe-environment interactions in watershed ecosystems differently impacted by the V industries. Some of the phylotypes identified in the highly contaminated samples exhibited potential for bioremediation of toxic metals (e.g., V and Cr).}, }
@article {pmid33579680, year = {2021}, author = {Coban, O and Rasigraf, O and de Jong, AEE and Spott, O and Bebout, BM}, title = {Quantifying potential N turnover rates in hypersaline microbial mats by [15]N tracer techniques.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {8}, pages = {}, pmid = {33579680}, issn = {1098-5336}, abstract = {Microbial mats, due to stratification of the redox zones, have a potential to include a complete N cycle, however an attempt to evaluate a complete N cycle in these ecosystems has not been yet made. In this study, occurrence and rates of major N cycle processes were evaluated in intact microbial mats from Elkhorn Slough, Monterey Bay, CA, USA, and Baja California Sur, Mexico under oxic and anoxic conditions using [15]N-labeling techniques. All of the major N transformation pathways, with the exception of anammox, were detected in both microbial mats. Nitrification rates were found to be low at both sites for both seasons investigated. The highest rates of ammonium assimilation were measured in Elkhorn Slough mats in April and corresponded to high in situ ammonium concentration in the overlying water. Baja mats featured higher ammonification than ammonium assimilation rates and this, along with their higher affinity for nitrate compared to ammonium and low dissimilatory nitrate reduction to ammonium rates, characterized their differences from Elkhorn Slough mats. Nitrogen fixation rates in Elkhorn Slough microbial mats were found to be low implying that other processes such as recycling and assimilation from water are main sources of N for these mats at the times sampled. Denitrification in all of the mats was incomplete with nitrous oxide as end product and not dinitrogen. Our findings highlight N cycling features not previously quantified in microbial mats and indicate a need of further investigations in these microbial ecosystems.Importance: Nitrogen is essential for life. The nitrogen cycle on Earth is mediated by microbial activity and has had a profound impact on both the atmosphere and the biosphere throughout geologic time. Microbial mats, present in many modern environments, have been regarded as living records of the organisms, genes, and phylogenies of microbes, as they are one of the most ancient ecosystems on Earth. While rates of major nitrogen metabolic pathways have been evaluated in a number of ecosystems, it remains elusive in microbial mats. In particular it is unclear what factors affect nitrogen cycling in these ecosystems and how morphological differences between mats impact nitrogen transformations. In this study we investigate nitrogen cycling in two microbial mats having morphological differences. Our findings provide insight for further understanding of biogeochemistry and microbial ecology of microbial mats.}, }
@article {pmid33578056, year = {2021}, author = {Jiang, C and Peces, M and Andersen, MH and Kucheryavskiy, S and Nierychlo, M and Yashiro, E and Andersen, KS and Kirkegaard, RH and Hao, L and Høgh, J and Hansen, AA and Dueholm, MS and Nielsen, PH}, title = {Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbial community structure and key drivers.}, journal = {Water research}, volume = {193}, number = {}, pages = {116871}, doi = {10.1016/j.watres.2021.116871}, pmid = {33578056}, issn = {1879-2448}, mesh = {Anaerobiosis ; Archaea/genetics ; Bioreactors ; Denmark ; Methane ; *Microbiota ; Sewage ; *Water Purification ; }, abstract = {Anaerobic digestion (AD) is a key technology at many wastewater treatment plants (WWTPs) for converting primary and surplus activated sludge to methane-rich biogas. However, the limited number of surveys and the lack of comprehensive datasets have hindered a deeper understanding of the characteristics and associations between key variables and the microbial community composition. Here, we present a six-year survey of 46 anaerobic digesters, located at 22 WWTPs in Denmark, which is the first and largest known study of the microbial ecology of AD at WWTPs at a regional scale. For three types of AD (mesophilic, mesophilic with thermal hydrolysis pretreatment, and thermophilic), we present the typical value range of 12 key parameters including operational variables and performance parameters. High-resolution bacterial and archaeal community analyses were carried out at species level using amplicon sequencing of >1,000 samples and the new ecosystem-specific MiDAS 3 reference database. We detected 42 phyla, 1,600 genera, and 3,584 species in the bacterial community, where 70% of the genera and 93% of the species represented environmental taxa that were only classified based on MiDAS 3 de novo placeholder taxonomy. More than 40% of the bacterial species were found not to grow in the mesophilic and thermophilic digesters and were only present due to immigration with the feed sludge. Ammonium concentration was the main driver shaping the bacterial community while temperature and pH were main drivers for the archaea in the three types of ADs. Sub-setting for the growing microbes improved significantly the correlation analyses and revealed the main drivers for the presence of specific species. Within mesophilic digesters, feed sludge composition and other key parameters (organic loading rate, biogas yield, and ammonium concentration) correlated with specific growing species. This survey provides a comprehensive insight into community structure at species level, providing a foundation for future studies of the ecological significance/characteristics and function of the many novel or poorly described taxa.}, }
@article {pmid33576997, year = {2021}, author = {Pratscher, J}, title = {Extraction of Microbial Cells from Environmental Samples for FISH Approaches.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2246}, number = {}, pages = {291-299}, pmid = {33576997}, issn = {1940-6029}, mesh = {Environmental Microbiology ; In Situ Hybridization, Fluorescence/*methods ; Microbiota/genetics ; }, abstract = {Fluorescent in situ hybridization (FISH) on environmental samples has become a standard technique to identify and enumerate microbial populations. However, visualization and quantification of cells in environmental samples with complex matrices is often challenging to impossible, and downstream protocols might also require the absence of organic and inorganic particles for analysis. Therefore, quite often microbial cells have to be detached and extracted from the sample matrix prior to use in FISH. Here, details are given for a routine protocol to extract intact microbial cells from environmental samples using density gradient centrifugation. This protocol is suitable and adaptable for a wide range of environmental samples.}, }
@article {pmid33576992, year = {2021}, author = {Nielsen, JL}, title = {Assigning Function to Phylogeny: MAR-FISH.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2246}, number = {}, pages = {225-236}, pmid = {33576992}, issn = {1940-6029}, mesh = {Autoradiography/*methods ; Biomass ; Electrons ; In Situ Hybridization, Fluorescence/*methods ; Microbiota/genetics ; Phylogeny ; }, abstract = {Microautoradiography (MAR) is a technique by which assimilated radioactive tracers incorporated into the biomass can be detected by a film emulsion. This allows for the testing of cellular preferences in electron donors and acceptors of individual cells in complex microbial assemblages, as well as the ability to take up substrates under diverse environmental exposures.Combination with staining techniques such as fluorescence in situ hybridization (FISH) can be used to identify the involved cells. Here, the practical aspects of a combined microautoradiography and fluorescence in situ hybridization (MAR-FISH) approach are described.}, }
@article {pmid33576852, year = {2021}, author = {Zhou, G and Tong, H and Cai, L and Huang, H}, title = {Transgenerational Effects on the Coral Pocillopora damicornis Microbiome Under Ocean Acidification.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {572-580}, pmid = {33576852}, issn = {1432-184X}, support = {41876192//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Anthozoa ; Coral Reefs ; Hydrogen-Ion Concentration ; *Microbiota/genetics ; Oceans and Seas ; Seawater ; }, abstract = {Reef-building corals are inhabited by functionally diverse microorganisms which play important roles in coral health and persistence in the Anthropocene. However, our understanding of the complex associations within coral holobionts is largely limited, particularly transgenerational exposure to environmental stress, like ocean acidification. Here we investigated the microbiome development of an ecologically important coral Pocillopora damicornis following transgenerational exposure to moderate and high pCO2 (partial pressure of CO2) levels, using amplicon sequencing and analysis. Our results showed that the Symbiodiniaceae community structures in adult and juvenile had similar patterns, all of which were dominated by Durusdinium spp., previously known as clade D. Conversely, prokaryotic communities varied between adults and juveniles, possibly driven by the effect of host development. Surprisingly, there were no significant changes in both Symbiodiniaceae and prokaryotic communities with different pCO2 treatments, which was independent of the life history stage. This study shows that ocean acidification has no significant effect on P. damicornis microbiome, and warrants further research to test whether transgenerational acclimation exists in coral holobiont to projected future climate change.}, }
@article {pmid33575595, year = {2020}, author = {Yang, P and Tan, C and Han, M and Cheng, L and Cui, X and Ning, K}, title = {Correlation-Centric Network (CCN) representation for microbial co-occurrence patterns: new insights for microbial ecology.}, journal = {NAR genomics and bioinformatics}, volume = {2}, number = {2}, pages = {lqaa042}, pmid = {33575595}, issn = {2631-9268}, abstract = {Mainstream studies of microbial community focused on critical organisms and their physiology. Recent advances in large-scale metagenome analysis projects initiated new researches in the complex correlations between large microbial communities. Specifically, previous studies focused on the nodes (i.e. species) of the Species-Centric Networks (SCNs). However, little was understood about the change of correlation between network members (i.e. edges of the SCNs) when the network was disturbed. Here, we introduced a Correlation-Centric Network (CCN) to the microbial research based on the concept of edge networks. In CCN, each node represented a species-species correlation, and edge represented the species shared by two correlations. In this research, we investigated the CCNs and their corresponding SCNs on two large cohorts of microbiome. The results showed that CCNs not only retained the characteristics of SCNs, but also contained information that cannot be detected by SCNs. In addition, when the members of microbial communities were decreased (i.e. environmental disturbance), the CCNs fluctuated within a small range in terms of network connectivity. Therefore, by highlighting the important species correlations, CCNs could unveil new insights when studying not only the functions of target species, but also the stabilities of their residing microbial communities.}, }
@article {pmid33570667, year = {2021}, author = {Franco-Frías, E and Mercado-Guajardo, V and Merino-Mascorro, A and Pérez-Garza, J and Heredia, N and León, JS and Jaykus, LA and Dávila-Aviña, J and García, S}, title = {Analysis of Bacterial Communities by 16S rRNA Gene Sequencing in a Melon-Producing Agro-environment.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {613-622}, pmid = {33570667}, issn = {1432-184X}, support = {A1-S-250//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 2018-07410, 2019-67017-29642//National Institute of Food and Agriculture/ ; HHSF223201710406P//U.S. Food and Drug Administration/ ; }, mesh = {Bacteria/genetics ; *Cucurbitaceae ; Genes, rRNA ; RNA, Ribosomal, 16S/genetics ; Salmonella ; }, abstract = {Cantaloupe melons, which have been responsible of an increasing number of foodborne disease outbreaks, may become contaminated with microbial pathogens during production. However, little information is available on the microbial populations in the cantaloupe farm environment. The purpose of this work was to characterize the bacterial communities present on cantaloupe farms. Fruit, soil, and harvester hand rinsates were collected from two Mexican cantaloupe farms, each visited three times. Microbiome analysis was performed by sequencing 16sRNA and analyzed using qiime2 software. Correlations were determined between sample type and microbial populations. The α and β diversity analysis identified 2777 sequences across all samples. The soil samples had the highest number and diversity of unique species (from 130 to 1329 OTUs); cantaloupe (from 112 to 205 OTUs), and hands (from 67 to 151 OTUs) had similar diversity. Collectively, Proteobacteria was the most abundant phyla (from 42 to 95%), followed by Firmicutes (1-47%), Actinobacteria (< 1 to 23%), and Bacteroidetes (< 1 to 4.8%). The most abundant genera were Acinetobacter (20-58%), Pseudomonas (14.5%), Erwinia (13%), and Exiguobacterium (6.3%). Genera with potential to be pathogenic included Bacillus (4%), Salmonella (0.85%), Escherichia-Shigella (0.38%), Staphylococcus (0.32%), Listeria (0.29%), Clostridium (0.28%), and Cronobacter (0.27%), which were found at lower frequencies. This study provides information on the cantaloupe production microbiome, which can inform future research into critical food safety issues such as antimicrobial resistance, virulence, and genomic epidemiology.}, }
@article {pmid33568638, year = {2021}, author = {Aubry, F and Jacobs, S and Darmuzey, M and Lequime, S and Delang, L and Fontaine, A and Jupatanakul, N and Miot, EF and Dabo, S and Manet, C and Montagutelli, X and Baidaliuk, A and Gámbaro, F and Simon-Lorière, E and Gilsoul, M and Romero-Vivas, CM and Cao-Lormeau, VM and Jarman, RG and Diagne, CT and Faye, O and Faye, O and Sall, AA and Neyts, J and Nguyen, L and Kaptein, SJF and Lambrechts, L}, title = {Recent African strains of Zika virus display higher transmissibility and fetal pathogenicity than Asian strains.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {916}, pmid = {33568638}, issn = {2041-1723}, mesh = {Aedes/physiology/virology ; Africa ; Animals ; Asia ; Female ; Humans ; Male ; Mice ; Phylogeny ; Virulence ; Zika Virus/classification/genetics/*pathogenicity/*physiology ; Zika Virus Infection/*mortality/transmission/*virology ; }, abstract = {The global emergence of Zika virus (ZIKV) revealed the unprecedented ability for a mosquito-borne virus to cause congenital birth defects. A puzzling aspect of ZIKV emergence is that all human outbreaks and birth defects to date have been exclusively associated with the Asian ZIKV lineage, despite a growing body of laboratory evidence pointing towards higher transmissibility and pathogenicity of the African ZIKV lineage. Whether this apparent paradox reflects the use of relatively old African ZIKV strains in most laboratory studies is unclear. Here, we experimentally compare seven low-passage ZIKV strains representing the recently circulating viral genetic diversity. We find that recent African ZIKV strains display higher transmissibility in mosquitoes and higher lethality in both adult and fetal mice than their Asian counterparts. We emphasize the high epidemic potential of African ZIKV strains and suggest that they could more easily go unnoticed by public health surveillance systems than Asian strains due to their propensity to cause fetal loss rather than birth defects.}, }
@article {pmid33563841, year = {2021}, author = {Westhoff, S and Kloosterman, AM and van Hoesel, SFA and van Wezel, GP and Rozen, DE}, title = {Competition Sensing Changes Antibiotic Production in Streptomyces.}, journal = {mBio}, volume = {12}, number = {1}, pages = {}, pmid = {33563841}, issn = {2150-7511}, mesh = {Anti-Bacterial Agents/*biosynthesis/metabolism ; Antibiosis/*genetics ; *Gene Expression Regulation, Bacterial ; *Microbial Interactions ; Multigene Family ; Secondary Metabolism/genetics/physiology ; Streptomyces/classification/*genetics/growth &amp; development/*physiology ; }, abstract = {One of the most important ways that bacteria compete for resources and space is by producing antibiotics that inhibit competitors. Because antibiotic production is costly, the biosynthetic gene clusters coordinating their synthesis are under strict regulatory control and often require "elicitors" to induce expression, including cues from competing strains. Although these cues are common, they are not produced by all competitors, and so the phenotypes causing induction remain unknown. By studying interactions between 24 antibiotic-producing strains of streptomycetes, we show that strains commonly inhibit each other's growth and that this occurs more frequently if strains are closely related. Next, we show that antibiotic production is more likely to be induced by cues from strains that are closely related or that share secondary metabolite biosynthetic gene clusters (BGCs). Unexpectedly, antibiotic production is less likely to be induced by competitors that inhibit the growth of a focal strain, indicating that cell damage is not a general cue for induction. In addition to induction, antibiotic production often decreases in the presence of a competitor, although this response was not associated with genetic relatedness or overlap in BGCs. Finally, we show that resource limitation increases the chance that antibiotic production declines during competition. Our results reveal the importance of social cues and resource availability in the dynamics of interference competition in streptomycetes.IMPORTANCE Bacteria secrete antibiotics to inhibit their competitors, but the presence of competitors can determine whether these toxins are produced. Here, we study the role of the competitive and resource environment on antibiotic production in Streptomyces, bacteria renowned for their production of antibiotics. We show that Streptomyces cells are more likely to produce antibiotics when grown with competitors that are closely related or that share biosynthetic pathways for secondary metabolites, but not when they are threatened by competitor's toxins, in contrast to predictions of the competition sensing hypothesis. Streptomyces cells also often reduce their output of antibiotics when grown with competitors, especially under nutrient limitation. Our findings highlight that interactions between the social and resource environments strongly regulate antibiotic production in these medicinally important bacteria.}, }
@article {pmid33563788, year = {2021}, author = {Otwell, AE and Carr, AV and Majumder, ELW and Ruiz, MK and Wilpiszeski, RL and Hoang, LT and Webb, B and Turkarslan, S and Gibbons, SM and Elias, DA and Stahl, DA and Siuzdak, G and Baliga, NS}, title = {Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33563788}, issn = {2379-5077}, support = {R35 GM130385/GM/NIGMS NIH HHS/United States ; }, abstract = {Competition between nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) for resources in anoxic environments is generally thought to be governed largely by thermodynamics. It is now recognized that intermediates of nitrogen and sulfur cycling (e.g., hydrogen sulfide, nitrite, etc.) can also directly impact NRB and SRB activities in freshwater, wastewater, and sediment and therefore may play important roles in competitive interactions. Here, through comparative transcriptomic and metabolomic analyses, we have uncovered mechanisms of hydrogen sulfide- and cysteine-mediated inhibition of nitrate respiratory growth for the NRB Intrasporangium calvum C5. Specifically, the systems analysis predicted that cysteine and hydrogen sulfide inhibit growth of I. calvum C5 by disrupting distinct steps across multiple pathways, including branched-chain amino acid (BCAA) biosynthesis, utilization of specific carbon sources, and cofactor metabolism. We have validated these predictions by demonstrating that complementation with BCAAs and specific carbon sources relieves the growth inhibitory effects of cysteine and hydrogen sulfide. We discuss how these mechanistic insights give new context to the interplay and stratification of NRB and SRB in diverse environments.IMPORTANCE Nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) colonize diverse anoxic environments, including soil subsurface, groundwater, and wastewater. NRB and SRB compete for resources, and their interplay has major implications on the global cycling of nitrogen and sulfur species, with undesirable outcomes in some contexts. For instance, the removal of reactive nitrogen species by NRB is desirable for wastewater treatment, but in agricultural soils, NRB can drive the conversion of nitrates from fertilizers into nitrous oxide, a potent greenhouse gas. Similarly, the hydrogen sulfide produced by SRB can help sequester and immobilize toxic heavy metals but is undesirable in oil wells where competition between SRB and NRB has been exploited to suppress hydrogen sulfide production. By characterizing how reduced sulfur compounds inhibit growth and activity of NRB, we have gained systems-level and mechanistic insight into the interplay of these two important groups of organisms and drivers of their stratification in diverse environments.}, }
@article {pmid33563787, year = {2021}, author = {de la Cuesta-Zuluaga, J and Spector, TD and Youngblut, ND and Ley, RE}, title = {Genomic Insights into Adaptations of Trimethylamine-Utilizing Methanogens to Diverse Habitats, Including the Human Gut.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33563787}, issn = {2379-5077}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Archaea of the order Methanomassiliicoccales use methylated amines such as trimethylamine as the substrates for methanogenesis. They form two large phylogenetic clades and reside in diverse environments, from soil to the human gut. Two genera, one from each clade, inhabit the human gut: Methanomassiliicoccus, which has one cultured representative, and "Candidatus Methanomethylophilus," which has none. Questions remain regarding their distribution across biomes and human populations, their association with other taxa in the gut, and whether host genetics correlate with their abundance. To gain insight into the Methanomassiliicoccales clade, particularly its human-associated members, we performed a genomic comparison of 72 Methanomassiliicoccales genomes and assessed their presence in metagenomes derived from the human gut (n = 4,472, representing 22 populations), nonhuman animal gut (n = 145), and nonhost environments (n = 160). Our analyses showed that all taxa are generalists; they were detected in animal gut and environmental samples. We confirmed two large clades, one enriched in the gut and the other enriched in the environment, with notable exceptions. Genomic adaptations to the gut include genome reduction and genes involved in the shikimate pathway and bile resistance. Genomic adaptations differed by clade, not habitat preference, indicating convergent evolution between the clades. In the human gut, the relative abundance of Methanomassiliicoccales spp. correlated with trimethylamine-producing bacteria and was unrelated to host genotype. Our results shed light on the microbial ecology of this group and may help guide Methanomassiliicoccales-based strategies for trimethylamine mitigation in cardiovascular disease.IMPORTANCE Methanomassiliicoccales are less-known members of the human gut archaeome. Members of this order use methylated amines, including trimethylamine, in methane production. This group has only one cultured representative; how its members adapted to inhabit the mammalian gut and how they interact with other microbes is largely unknown. Using bioinformatics methods applied to DNA from a wide range of samples, we profiled the abundances of these Archaea spp. in environmental and host-associated microbial communities. We observed two groups of Methanomassiliicoccales, one largely host associated and one largely found in environmental samples, with some exceptions. When host associated, these Archaea have smaller genomes and possess genes related to bile resistance and aromatic amino acid precursors. We did not detect Methanomassiliicoccales in all human populations tested, but when present, they were correlated with bacteria known to produce trimethylamine. Due to their metabolism of trimethylamine, these intriguing Archaea may form the basis of novel therapies for cardiovascular disease.}, }
@article {pmid33562402, year = {2021}, author = {Maillet, A and Denojean, P and Bouju-Albert, A and Scaon, E and Leuillet, S and Dousset, X and Jaffrès, E and Combrisson, J and Prévost, H}, title = {Characterization of Bacterial Communities of Cold-Smoked Salmon during Storage.}, journal = {Foods (Basel, Switzerland)}, volume = {10}, number = {2}, pages = {}, pmid = {33562402}, issn = {2304-8158}, support = {2016-06930//Conseil R&#xe9;gional des Pays de la Loire/ ; 2016/1546//Association Nationale de la Recherche et de la Technologie/ ; }, abstract = {Cold-smoked salmon is a widely consumed ready-to-eat seafood product that is a fragile commodity with a long shelf-life. The microbial ecology of cold-smoked salmon during its shelf-life is well known. However, to our knowledge, no study on the microbial ecology of cold-smoked salmon using next-generation sequencing has yet been undertaken. In this study, cold-smoked salmon microbiotas were investigated using a polyphasic approach composed of cultivable methods, V3-V4 16S rRNA gene metabarcoding and chemical analyses. Forty-five cold-smoked salmon products processed in three different factories were analyzed. The metabarcoding approach highlighted 12 dominant genera previously reported as fish spoilers: Firmicutes Staphylococcus, Carnobacterium, Lactobacillus, β-Proteobacteria Photobacterium, Vibrio, Aliivibrio, Salinivibrio, Enterobacteriaceae Serratia,Pantoea, γ-Proteobacteria Psychrobacter, Shewanella and Pseudomonas. Specific operational taxonomic units were identified during the 28-day storage study period. Operational taxonomic units specific to the processing environment were also identified. Although the 45 cold-smoked salmon products shared a core microbiota, a processing plant signature was found. This suggest that the bacterial communities of cold-smoked salmon products are impacted by the processing environment, and this environment could have a negative effect on product quality. The use of a polyphasic approach for seafood products and food processing environments could provide better insights into residential bacteria dynamics and their impact on food safety and quality.}, }
@article {pmid33562194, year = {2021}, author = {Szczypta, A and Talaga-Ćwiertnia, K and Kielar, M and Krzyściak, P and Gajewska, A and Szura, M and Bulanda, M and Chmielarczyk, A}, title = {Investigation of Acinetobacter baumannii Activity in Vascular Surgery Units through Epidemiological Management Based on the Analysis of Antimicrobial Resistance, Biofilm Formation and Genotyping.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {4}, pages = {}, pmid = {33562194}, issn = {1660-4601}, mesh = {*Acinetobacter Infections/drug therapy/epidemiology ; *Acinetobacter baumannii/genetics ; Anti-Bacterial Agents/pharmacology ; Biofilms ; *Cross Infection/drug therapy/epidemiology ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial ; Genotype ; Humans ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; beta-Lactamases/genetics ; }, abstract = {BACKGROUND/OBJECTIVES: The genus Acinetobacter demonstrates resistance to antibiotics and has been shown to spread in the hospital environment causing epidemic outbreaks among hospitalized patients. The objectives of the present study was to investigate the antibiotic resistance, biofilm formation, and clonality among Acinetobacter baumannii strains.<br><br>MATERIALS AND METHODS: The study involved 6 (I Outbreak) and 3 (II Outbreak) A. baumannii strains isolated from patients hospitalized in vascular surgery unit.<br><br>RESULTS: All tested A. baumannii strains were extensively drug resistant (XDR) and all the isolates were carbapenem-resistant and among them, all carried the blaOXA-51 gene, the blaOXA-24 gene, as well as the blaOXA-23 gene. All of the investigated strains had the ability to form a biofilm, but all of them produced less biofilm than the reference strain. Multi-locus sequence typing (MLST) showed that all strains belonged to the ST2 clone. Pulsed-field gel electrophoresis (PFGE) divided the tested outbreak strains into two clones (A and B).<br><br>CONCLUSION: This study shows a nosocomial spread of XDR A. baumannii ST2 having the blaOXA-51 gene, the blaOXA-24 gene, as well as the blaOXA-23 gene, low biofilm formers, that was prevalent in the vascular surgery unit. To identify the current situation of vascular surgery departments targeted epidemiological investigation was needed. Effective implementation of infection control prevented the spread of the epidemic outbreaks.}, }
@article {pmid33561237, year = {2021}, author = {Higgins, P and Grace, CA and Lee, SA and Goddard, MR}, title = {Whole-genome sequencing from the New Zealand Saccharomyces cerevisiae population reveals the genomic impacts of novel microbial range expansion.}, journal = {G3 (Bethesda, Md.)}, volume = {11}, number = {1}, pages = {}, pmid = {33561237}, issn = {2160-1836}, mesh = {Fermentation ; Genome, Fungal ; Genomics ; New Zealand ; *Saccharomyces cerevisiae/genetics ; *Wine ; }, abstract = {Saccharomyces cerevisiae is extensively utilized for commercial fermentation, and is also an important biological model; however, its ecology has only recently begun to be understood. Through the use of whole-genome sequencing, the species has been characterized into a number of distinct subpopulations, defined by geographical ranges and industrial uses. Here, the whole-genome sequences of 104 New Zealand (NZ) S. cerevisiae strains, including 52 novel genomes, are analyzed alongside 450 published sequences derived from various global locations. The impact of S. cerevisiae novel range expansion into NZ was investigated and these analyses reveal the positioning of NZ strains as a subgroup to the predominantly European/wine clade. A number of genomic differences with the European group correlate with range expansion into NZ, including 18 highly enriched single-nucleotide polymorphism (SNPs) and novel Ty1/2 insertions. While it is not possible to categorically determine if any genetic differences are due to stochastic process or the operations of natural selection, we suggest that the observation of NZ-specific copy number increases of four sugar transporter genes in the HXT family may reasonably represent an adaptation in the NZ S. cerevisiae subpopulation, and this correlates with the observations of copy number changes during adaptation in small-scale experimental evolution studies.}, }
@article {pmid33559710, year = {2021}, author = {Ayyasamy, A and Kempraj, V and Pagadala Damodaram, KJ}, title = {Endosymbiotic Bacteria Aid to Overcome Temperature Induced Stress in the Oriental Fruit Fly, Bactrocera dorsalis.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {783-792}, pmid = {33559710}, issn = {1432-184X}, support = {NICRA//Indian Council of Agricultural Research/ ; }, mesh = {Animals ; Bacteria/genetics ; DNA, Ribosomal ; Female ; *Gastrointestinal Microbiome ; Male ; Temperature ; *Tephritidae ; }, abstract = {Endosymbiotic microbiota are known to have an enormous impact on their host, influencing its physiology, behavior, fitness, and various other aspects. The present study hypothesizes that certain bacterial symbionts aid the Oriental fruit fly, Bactrocera dorsalis in its adaptation to survive thermal stress encountered in the environment. Investigative studies on the change in gut and reproductive tract microbiota diversity of male and female B. dorsalis revealed that certain genera of Acinetobacter, Brevibacillus, Bacillus, Enterobacter, Enterococcus, Pseudomonas, and Staphylococcus were involved in the adaptation of B. dorsalis to temperature stresses. The intestinal and reproductive tract bacterial community of B. dorsalis varied depending on the temperature the insects were reared at. We hypothesized that the microbiota present in B. dorsalis' gut helped it endure temperature stresses over prolonged periods. Out of 54 bacterial isolates, 25, 15, and 14 isolates were obtained from flies reared at 27 °C, 18 °C, and 35 °C, respectively. A 16S rDNA analysis revealed that the bacterial isolates (reared at different temperatures) belonged to different genera. The flies were supplemented with antibiotics to suppress the existing gut microbiota and subsequently fed with bacterial isolates from flies reared at 18 °C, 27 °C (control) or 35 °C separately. When these flies were placed in incubators pre-set at the above temperatures, the survival rate exhibited by the flies differed significantly. The flies fed with bacterial isolates from 18 °C could survive only in incubators pre-set at 18 °C, while flies fed with bacterial isolates from 35 °C could survive only at 35 °C and not vice versa. The microbiota supplementation assay established that the presence of specific bacterial isolates aided the flies' survival under varied thermal stresses.}, }
@article {pmid33558687, year = {2021}, author = {Joshi, S and Robles, A and Aguiar, S and Delgado, AG}, title = {The occurrence and ecology of microbial chain elongation of carboxylates in soils.}, journal = {The ISME journal}, volume = {15}, number = {7}, pages = {1907-1918}, pmid = {33558687}, issn = {1751-7370}, mesh = {Acetates ; Anaerobiosis ; *Clostridium kluyveri ; Fermentation ; *Soil ; Soil Microbiology ; }, abstract = {Chain elongation is a growth-dependent anaerobic metabolism that combines acetate and ethanol into butyrate, hexanoate, and octanoate. While the model microorganism for chain elongation, Clostridium kluyveri, was isolated from a saturated soil sample in the 1940s, chain elongation has remained unexplored in soil environments. During soil fermentative events, simple carboxylates and alcohols can transiently accumulate up to low mM concentrations, suggesting in situ possibility of microbial chain elongation. Here, we examined the occurrence and microbial ecology of chain elongation in four soil types in microcosms and enrichments amended with chain elongation substrates. All soils showed evidence of chain elongation activity with several days of incubation at high (100 mM) and environmentally relevant (2.5 mM) concentrations of acetate and ethanol. Three soils showed substantial activity in soil microcosms with high substrate concentrations, converting 58% or more of the added carbon as acetate and ethanol to butyrate, butanol, and hexanoate. Semi-batch enrichment yielded hexanoate and octanoate as the most elongated products and microbial communities predominated by C. kluyveri and other Firmicutes genera not known to undergo chain elongation. Collectively, these results strongly suggest a niche for chain elongation in anaerobic soils that should not be overlooked in soil microbial ecology studies.}, }
@article {pmid33555369, year = {2021}, author = {Dou, W and Miao, Y and Xiao, J and Huang, D}, title = {Association of Wolbachia with Gene Expression in Drosophila Testes.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {805-817}, pmid = {33555369}, issn = {1432-184X}, support = {31830084//National Natural Science Foundation of China/ ; 31970440//National Natural Science Foundation of China/ ; 31672336//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Drosophila ; Drosophila melanogaster/genetics ; Male ; Testis ; Transcriptome ; *Wolbachia/genetics ; }, abstract = {Wolbachia is a genus of intracellular symbiotic bacteria that are widely distributed in arthropods and nematodes. These maternally inherited bacteria regulate host reproductive systems in various ways to facilitate their vertical transmission. Since the identification of Wolbachia in many insects, the relationship between Wolbachia and the host has attracted great interest. Numerous studies have indicated that Wolbachia modifies a variety of biological processes in the host. Previous studies in Drosophila melanogaster (D. melanogaster) have demonstrated that Wolbachia can affect spermatid differentiation, chromosome deposition, and sperm activity in the early stages of spermatogenesis, leading to sperm dysfunction. Here, we explored the putative effect of Wolbachia in sperm maturation using transcriptomic approaches to compare gene expression in Wolbachia-infected and Wolbachia-free D. melanogaster adult testes. Our findings show that Wolbachia affects many biological processes in D. melanogaster adult testes, and most of the differentially expressed genes involved in carbohydrate metabolism, lysosomal degradation, proteolysis, lipid metabolism, and immune response were upregulated in the presence of Wolbachia. In contrast, some genes that are putatively associated with cutin and wax biosynthesis and peroxisome pathways were downregulated. We did not find any differentially expressed genes that are predicted to be related to spermatogenesis in the datasets. This work provides additional information for understanding the Wolbachia-host intracellular relationships.}, }
@article {pmid33555368, year = {2021}, author = {Grzesiak, J and Woltyńska, A and Zdanowski, MK and Górniak, D and Świątecki, A and Olech, MA and Aleksandrzak-Piekarczyk, T}, title = {Metabolic fingerprinting of the Antarctic cyanolichen Leptogium puberulum-associated bacterial community (Western Shore of Admiralty Bay, King George Island, Maritime Antarctica).}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {818-829}, pmid = {33555368}, issn = {1432-184X}, support = {2017/25/B/NZ8/01915//Narodowe Centrum Nauki/ ; }, mesh = {Antarctic Regions ; Ascomycota ; Bacteria/genetics ; Bays ; *Lichens ; *Microbiota ; }, abstract = {Lichens are presently regarded as stable biotopes, small ecosystems providing a safe haven for the development of a diverse and numerous microbiome. In this study, we conducted a functional diversity assessment of the microbial community residing on the surface and within the thalli of Leptogium puberulum, a eurytopic cyanolichen endemic to Antarctica, employing the widely used Biolog EcoPlates which test the catabolism of 31 carbon compounds in a colorimetric respiration assay. Lichen thalli occupying moraine ridges of differing age within a proglacial chronosequence, as well as those growing in sites of contrasting nutrient concentrations, were procured from the diverse landscape of the western shore of Admiralty Bay in Maritime Antarctica. The L. puberulum bacterial community catabolized photobiont- (glucose-containing carbohydrates) and mycobiont-specific carbon compounds (D-Mannitol). The bacteria also had the ability to process degradation products of lichen thalli components (D-cellobiose and N-acetyl-D-glucosamine). Lichen thalli growth site characteristics had an impact on metabolic diversity and respiration intensity of the bacterial communities. While high nutrient contents in lichen specimens from "young" proglacial locations and in those from nitrogen enriched sites stimulated bacterial catabolic activity, in old proglacial locations and in nutrient-lacking sites, a metabolic activity restriction was apparent, presumably due to lichen-specific microbial control mechanisms.}, }
@article {pmid33553003, year = {2020}, author = {Yang, Q and Zou, P and Cao, Z and Wang, Q and Fu, S and Xie, G and Huang, J}, title = {QseC Inhibition as a Novel Antivirulence Strategy for the Prevention of Acute Hepatopancreatic Necrosis Disease (AHPND)-Causing Vibrio parahaemolyticus.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {594652}, pmid = {33553003}, issn = {2235-2988}, mesh = {Animals ; Aquaculture ; Necrosis ; *Penaeidae ; *Type VI Secretion Systems/genetics ; *Vibrio parahaemolyticus ; }, abstract = {Acute hepatopancreatic necrosis disease (AHPND) caused by Vibrio parahaemolyticus resulted in great economic losses in global shrimp aquaculture. There is an urgent need for development of novel strategies to combat AHPND-causing V. parahaemolyticus (VpAHPND), given that one of the greatest challenges currently is the widespread use of antibiotics and subsequent emergence of multidrug-resistant bacteria. Here, we proposed a broad-spectrum antivirulence approach targeting a conserved histidine kinase, QseC, which has been demonstrated to activate virulence expression in several Gram-negative pathogens. Our results showed that QseC mediated the catecholamine stimulated effects on growth and flagellar motility of VpAHPND. Transcriptome analysis revealed that QseC was involved in the global regulation of the virulence of VpAHPND as the ΔqseC mutant exhibited a decreased expression of genes related to type IV pilin, flagellar motility, and biofilm formation, while an overexpression of type VI secretion system and cell wall biosynthesis. Subsequently, the bacterial catecholamine receptor antagonist LED209 not only neutralized the stimulatory effects of host catecholamines on the growth and motility of VpAHPNDin vitro, but also attenuated the virulence of VpAHPND towards brine shrimp larvae and white shrimp in vivo. Additionally, LED209 presented no interference with pathogen growth, nor the toxicity to the experimental animals. These results suggest that QseC can be an attractive antivirulence therapy target, and LED209 is a promising candidate for development of broad-spectrum antivirulence agents. This is the first study that demonstrated the role of QseC in the global regulation of VpAHPND infection and demonstrated the antivirulence potential of LED209, which provides insight into the use of an antivirulence approach for targeting not only VpAHPND, but also a much larger collection of pathogenic bacteria.}, }
@article {pmid33552017, year = {2020}, author = {Bovio-Winkler, P and Cabezas, A and Etchebehere, C}, title = {Database Mining to Unravel the Ecology of the Phylum Chloroflexi in Methanogenic Full Scale Bioreactors.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {603234}, pmid = {33552017}, issn = {1664-302X}, abstract = {Although microbial communities of anaerobic bioreactors have been extensively studied using DNA-based tools, there are still several knowledge gaps regarding the microbiology of the process, in particular integration of all generated data is still limited. One understudied core phylum within anaerobic bioreactors is the phylum Chloroflexi, despite being one of the most abundant groups in anaerobic reactors. In order to address the abundance, diversity and phylogeny of this group in full-scale methanogenic reactors globally distributed, a compilation of 16S ribosomal RNA gene sequence data from 62 full-scale methanogenic reactors studied worldwide, fed either with wastewater treatment anaerobic reactors (WTARs) or solid-waste treatment anaerobic reactors (STARs), was performed. One of the barriers to overcome was comparing data generated using different primer sets and different sequencing platforms. The sequence analysis revealed that the average abundance of Chloroflexi in WTARs was higher than in STARs. Four genera belonging to the Anaerolineae class dominated both WTARs and STARs but the core populations were different. According to the phylogenetic analysis, most of the sequences formed clusters with no cultured representatives. The Anaerolineae class was more abundant in reactors with granular biomass than in reactors with disperse biomass supporting the hypothesis that Anaerolineae play an important role in granule formation and structure due to their filamentous morphology. Cross-study comparisons can be fruitfully used to understand the complexity of the anaerobic digestion process. However, more efforts are needed to standardize protocols and report metadata information.}, }
@article {pmid33552002, year = {2020}, author = {García-Ulloa, MI and Escalante, AE and Moreno-Letelier, A and Eguiarte, LE and Souza, V}, title = {Evolutionary Rescue of an Environmental Pseudomonas otitidis in Response to Anthropogenic Perturbation.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {563885}, pmid = {33552002}, issn = {1664-302X}, abstract = {Anthropogenic perturbations introduce novel selective pressures to natural environments, impacting the genomic variability of organisms and thus altering the evolutionary trajectory of populations. Water overexploitation for agricultural purposes and defective policies in Cuatro Cienegas, Coahuila, Mexico, have strongly impacted its water reservoir, pushing entire hydrological systems to the brink of extinction along with their native populations. Here, we studied the effects of continuous water overexploitation on an environmental aquatic lineage of Pseudomonas otitidis over a 13-year period which encompasses three desiccation events. By comparing the genomes of a population sample from 2003 (original state) and 2015 (perturbed state), we analyzed the demographic history and evolutionary response to perturbation of this lineage. Through coalescent simulations, we obtained a demographic model of contraction-expansion-contraction which points to the occurrence of an evolutionary rescue event. Loss of genomic and nucleotide variation alongside an increment in mean and variance of Tajima's D, characteristic of sudden population expansions, support this observation. In addition, a significant increase in recombination rate (R/θ) was observed, pointing to horizontal gene transfer playing a role in population recovery. Furthermore, the gain of phosphorylation, DNA recombination, small-molecule metabolism and transport and loss of biosynthetic and regulatory genes suggest a functional shift in response to the environmental perturbation. Despite subsequent sampling events in the studied site, no pseudomonad was found until the lagoon completely dried in 2017. We speculate about the causes of P. otitidis final decline or possible extinction. Overall our results are evidence of adaptive responses at the genomic level of bacterial populations in a heavily exploited aquifer.}, }
@article {pmid33551270, year = {2021}, author = {Lemos, LN and Mendes, LW and Baldrian, P and Pylro, VS}, title = {Genome-Resolved Metagenomics Is Essential for Unlocking the Microbial Black Box of the Soil.}, journal = {Trends in microbiology}, volume = {29}, number = {4}, pages = {279-282}, doi = {10.1016/j.tim.2021.01.013}, pmid = {33551270}, issn = {1878-4380}, mesh = {Bacteria/*genetics ; *Genetic Variation ; *Genome, Bacterial ; Metagenomics/*methods ; *Soil Microbiology ; }, abstract = {Despite several efforts to unravel the microbial diversity of soil, most microbes are still unknown. A recent large-scale effort based on genome-resolved metagenomics by Nayfach et al. has demonstrated how this approach can expand our understanding of novel bacterial lineages, including those from soils. Genomic catalogs of soil microbiomes are now enabling a deeper investigation of the evolutionary and functional role of high-complex soil microbiomes, promoting new knowledge from the reuse and sharing of multi-omics data.}, }
@article {pmid33547531, year = {2021}, author = {Lesiczka, PM and Hrazdilová, K and Majerová, K and Fonville, M and Sprong, H and Hönig, V and Hofmannová, L and Papežík, P and Růžek, D and Zurek, L and Votýpka, J and Modrý, D}, title = {The Role of Peridomestic Animals in the Eco-Epidemiology of Anaplasma phagocytophilum.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {602-612}, pmid = {33547531}, issn = {1432-184X}, support = {17-16009S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; CZ.02.1.01/16_019/0000759//CePaViP/ ; }, mesh = {*Anaplasma phagocytophilum/genetics ; Animals ; Ecosystem ; Hedgehogs ; Humans ; *Ixodes ; *Tick-Borne Diseases ; }, abstract = {Anaplasma phagocytophilum is an important tick-borne zoonotic agent of human granulocytic anaplasmosis (HGA). In Europe, the Ixodes ticks are the main vector responsible for A. phagocytophilum transmission. A wide range of wild animals is involved in the circulation of this pathogen in the environment. Changes in populations of vertebrates living in different ecosystems impact the ecology of ticks and the epidemiology of tick-borne diseases. In this study, we investigated four species, Western European hedgehog (Erinaceus europaeus), northern white-breasted hedgehog (Erinaceus roumanicus), Eurasian red squirrel (Sciurus vulgaris), and the common blackbird (Turdus merula), to describe their role in the circulation of A. phagocytophilum in urban and periurban ecosystems. Ten different tissues were collected from cadavers of the four species, and blood and ear/skin samples from live blackbirds and hedgehogs. Using qPCR, we detected a high rate of A. phagocytophilum: Western European hedgehogs (96.4%), northern white-breasted hedgehogs (92.9%), Eurasian red squirrels (60%), and common blackbirds (33.8%). In the groEL gene, we found nine genotypes belonging to three ecotypes; seven of the genotypes are associated with HGA symptoms. Our findings underline the role of peridomestic animals in the ecology of A. phagocytophilum and indicate that cadavers are an important source of material for monitoring zoonotic pathogens. Concerning the high prevalence rate, all investigated species play an important role in the circulation of A. phagocytophilum in municipal areas; however, hedgehogs present the greatest anaplasmosis risk for humans. Common blackbirds and squirrels carry different A. phagocytophilum variants some of which are responsible for HGA.}, }
@article {pmid33545473, year = {2021}, author = {Wei, H and Lin, X}, title = {Shifts in the relative abundance and potential rates of sediment ammonia-oxidizing archaea and bacteria along environmental gradients of an urban river-estuary-adjacent sea continuum.}, journal = {The Science of the total environment}, volume = {771}, number = {}, pages = {144824}, doi = {10.1016/j.scitotenv.2020.144824}, pmid = {33545473}, issn = {1879-1026}, mesh = {*Ammonia ; *Archaea/genetics ; Bacteria/genetics ; China ; Estuaries ; Humans ; Oxidation-Reduction ; Phylogeny ; Rivers ; Soil Microbiology ; }, abstract = {Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in N cycling in sediments globally. However, little is known about their ammonia oxidation rates along a river-estuary-sea continuum. In this study, we investigated how the potential ammonia oxidation rates (PARs) of AOA and AOB changed spatially along a continuum comprising three habitats: the Shanghai urban river network, the Yangtze Estuary, and the adjacent East China Sea, in summer and winter. The AOA and AOB PARs (0.53 ± 0.49 and 0.72 ± 0.69 μg N g[-1] d[-1], mean ± SD, respectively) and their amoA gene abundance (0.47 ± 0.85 × 10[6] and 2.4 ± 3.54 × 10[6] copies g[-1], respectively) decreased along the continuum, particularly from the urban river to the estuary, driven by decreasing sediment total organic C and N and other correlated inorganic nutrients (e.g., NH4[+]) along the gradient of anthropogenic influences. These spatial patterns were consistent between the seasons. The urban river network, where the anthropogenic influences were strongest, saw the largest seasonal differences, as both AOA and AOB had higher PARs and abundance in summer than in winter. The ratios between AOA and AOB PARs (~0.87 ± 0.51) and gene abundances (~0.25 ± 0.24), however, were predominantly <1, indicating an AOB-dominated community. Comparing the different NH4[+] consumption pathways, total aerobic oxidation accounted for 12-26% of the total consumption, with the largest proportion in the estuary, where the system was well oxygenated, and the lowest in the adjacent sea, where inorganic N was highly depleted. This study revealed the spatiotemporal patterns of AOA and AOB potential rates and gene abundance along gradients of human influences and identified organic matter and nutrients as key environmental factors that shaped the variation of AOA and AOB along the continuum.}, }
@article {pmid33542279, year = {2021}, author = {Meale, SJ and Popova, M and Saro, C and Martin, C and Bernard, A and Lagree, M and Yáñez-Ruiz, DR and Boudra, H and Duval, S and Morgavi, DP}, title = {Early life dietary intervention in dairy calves results in a long-term reduction in methane emissions.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {3003}, pmid = {33542279}, issn = {2045-2322}, mesh = {Animal Feed ; Animals ; Archaea/isolation &amp; purification ; Body Fluids ; Body Weight ; Cattle ; Diet ; *Ecosystem ; Female ; Fermentation ; Lactation/*metabolism ; Methane/*metabolism ; Propanols/pharmacology ; Rumen/metabolism/*microbiology ; Weaning ; }, abstract = {Recent evidence suggests that changes in microbial colonization of the rumen prior to weaning may imprint the rumen microbiome and impact phenotypes later in life. We investigated how dietary manipulation from birth influences growth, methane production, and gastrointestinal microbial ecology. At birth, 18 female Holstein and Montbéliarde calves were randomly assigned to either treatment or control (CONT). Treatment was 3-nitrooxypropanol (3-NOP), an investigational anti-methanogenic compound that was administered daily from birth until three weeks post-weaning (week 14). Samples of rumen fluid and faecal content were collected at weeks 1, 4, 11, 14, 23, and 60 of life. Calves were tested for methane emissions using the GreenFeed system during the post-weaning period (week 11-23 and week 56-60 of life). Calf physiological parameters (BW, ADG and individual VFA) were similar across groups throughout the trial. Treated calves showed a persistent reduction in methane emissions (g CH4/d) throughout the post-weaning period up to at least 1 year of life, despite treatment ceasing three weeks post-weaning. Similarly, despite variability in the abundance of individual taxa across weeks, the rumen bacterial, archaeal and fungal structure differed between CONT and 3-NOP calves across all weeks, as visualised using sparse-PLS-DA. Similar separation was also observed in the faecal bacterial community. Interestingly, despite modest modifications to the abundance of rumen microbes, the reductive effect of 3-NOP on methane production persisted following cessation of the treatment period, perhaps indicating a differentiation of the ruminal microbial ecosystem or a host response triggered by the treatment in the early development phase.}, }
@article {pmid33542245, year = {2021}, author = {Grum-Grzhimaylo, AA and Bastiaans, E and van den Heuvel, J and Berenguer Millanes, C and Debets, AJM and Aanen, DK}, title = {Somatic deficiency causes reproductive parasitism in a fungus.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {783}, pmid = {33542245}, issn = {2041-1723}, mesh = {Cell Fusion ; DNA Mutational Analysis ; *Evolution, Molecular ; Fungal Proteins/*genetics/metabolism ; Gene Knockout Techniques ; Genes, Fungal/genetics ; Hyphae/*physiology ; Mutation ; Neurospora crassa/*physiology ; }, abstract = {Some multicellular organisms can fuse because mergers potentially provide mutual benefits. However, experimental evolution in the fungus Neurospora crassa has demonstrated that free fusion of mycelia favours cheater lineages, but the mechanism and evolutionary dynamics of this exploitation are unknown. Here we show, paradoxically, that all convergently evolved cheater lineages have similar fusion deficiencies. These mutants are unable to initiate fusion but retain access to wild-type mycelia that fuse with them. This asymmetry reduces cheater-mutant contributions to somatic substrate-bound hyphal networks, but increases representation of their nuclei in the aerial reproductive hyphae. Cheaters only benefit when relatively rare and likely impose genetic load reminiscent of germline senescence. We show that the consequences of somatic fusion can be unequally distributed among fusion partners, with the passive non-fusing partner profiting more. We discuss how our findings may relate to the extensive variation in fusion frequency of fungi found in nature.}, }
@article {pmid33539603, year = {2021}, author = {Fernandes, MF and Lopes, LD and Dick, RP}, title = {Microbial dynamics associated with the decomposition of coconut and maize residues in a microcosm experiment with tropical soils under two nitrogen fertilization levels.}, journal = {Journal of applied microbiology}, volume = {131}, number = {3}, pages = {1261-1273}, doi = {10.1111/jam.15021}, pmid = {33539603}, issn = {1365-2672}, support = {//Empresa Brasileira de Pesquisa Agropecu&#xe1;ria/ ; //Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Carbon ; *Cocos ; Fertilization ; *Nitrogen/analysis ; *Soil ; *Soil Microbiology ; *Zea mays ; }, abstract = {AIMS: The microbial dynamics associated with the decomposition of maize (Zea mays) and coconut (Cocos nucifera) residues were investigated to assess the feasibility of using them as mulch in tropical soils.<br><br>METHODS AND RESULTS: Phospholipid fatty-acid (PLFA) profiling, microbial biomass (MB-C), basal respiration, C-cycle enzyme activities and inorganic N dynamics were monitored in a microcosm experiment incubating soil samples with plant residues for 425&#xa0;days. Maize stover (MS) showed a higher decomposition, respiration rate, MB-C, enzymes activities and shift in microbial community structure than coconut husk (CH), which was barely changed. In MS, the lower N level increased C losses and decreased N mineralization compared to the higher N level.<br><br>CONCLUSIONS: Maize stover is suitable for mulching and has a high potential of increasing soil quality if the proper N fertilization level is used, avoiding excessive C mineralization and N immobilization. Coconut husk decomposition was mostly impaired, indicating that a pre-processing is necessary to improve the benefits of this residue.<br><br>Tropical soils are prone to degradation. Mulching can promote soil conservation, but depends on residue type and soil chemistry. Our study showed that MS managed under the recommended N fertilization level is suitable for mulching while CH is highly inaccessible for microbial degradation.}, }
@article {pmid33538855, year = {2021}, author = {Lyautey, E and Billard, E and Tissot, N and Jacquet, S and Domaizon, I}, title = {Seasonal Dynamics of Abundance, Structure, and Diversity of Methanogens and Methanotrophs in Lake Sediments.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {559-571}, pmid = {33538855}, issn = {1432-184X}, mesh = {Archaea/genetics ; *Euryarchaeota/genetics ; Geologic Sediments ; Lakes ; Methane ; *Methylococcaceae/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; }, abstract = {Understanding temporal and spatial microbial community abundance and diversity variations is necessary to assess the functional roles played by microbial actors in the environment. In this study, we investigated spatial variability and temporal dynamics of two functional microbial sediment communities, methanogenic Archaea and methanotrophic bacteria, in Lake Bourget, France. Microbial communities were studied from 3 sites sampled 4 times over a year, with one core sampled at each site and date, and 5 sediment layers per core were considered. Microbial abundance in the sediment were determined using flow cytometry. Methanogens and methanotrophs community structures, diversity, and abundance were assessed using T-RFLP, sequencing, and real-time PCR targeting mcrA and pmoA genes, respectively. Changes both in structure and abundance were detected mainly at the water-sediment interface in relation to the lake seasonal oxygenation dynamics. Methanogen diversity was dominated by Methanomicrobiales (mainly Methanoregula) members, followed by Methanosarcinales and Methanobacteriales. For methanotrophs, diversity was dominated by Methylobacter in the deeper area and by Methylococcus in the shallow area. Organic matter appeared to be the main environmental parameter controlling methanogens, while oxygen availability influenced both the structure and abundance of the methanotrophic community.}, }
@article {pmid33538813, year = {2021}, author = {Ruiz-González, C and Rodellas, V and Garcia-Orellana, J}, title = {The microbial dimension of submarine groundwater discharge: current challenges and future directions.}, journal = {FEMS microbiology reviews}, volume = {45}, number = {5}, pages = {}, pmid = {33538813}, issn = {1574-6976}, support = {//MICINN/ ; RTI2018-099740-J-I00//GRAMMY Foundation/ ; }, mesh = {Environmental Monitoring ; *Groundwater ; *Microbiota ; Seawater ; }, abstract = {Despite the relevance of submarine groundwater discharge (SGD) for ocean biogeochemistry, the microbial dimension of SGD remains poorly understood. SGD can influence marine microbial communities through supplying chemical compounds and microorganisms, and in turn, microbes at the land-ocean transition zone determine the chemistry of the groundwater reaching the ocean. However, compared with inland groundwater, little is known about microbial communities in coastal aquifers. Here, we review the state of the art of the microbial dimension of SGD, with emphasis on prokaryotes, and identify current challenges and future directions. Main challenges include improving the diversity description of groundwater microbiota, characterized by ultrasmall, inactive and novel taxa, and by high ratios of sediment-attached versus free-living cells. Studies should explore microbial dynamics and their role in chemical cycles in coastal aquifers, the bidirectional dispersal of groundwater and seawater microorganisms, and marine bacterioplankton responses to SGD. This will require not only combining sequencing methods, visualization and linking taxonomy to activity but also considering the entire groundwater-marine continuum. Interactions between traditionally independent disciplines (e.g. hydrogeology, microbial ecology) are needed to frame the study of terrestrial and aquatic microorganisms beyond the limits of their presumed habitats, and to foster our understanding of SGD processes and their influence in coastal biogeochemical cycles.}, }
@article {pmid33538648, year = {2021}, author = {Hennebique, A and Peyroux, J and Brunet, C and Martin, A and Henry, T and Knezevic, M and Santic, M and Boisset, S and Maurin, M}, title = {Amoebae can promote the survival of Francisella species in the aquatic environment.}, journal = {Emerging microbes &amp; infections}, volume = {10}, number = {1}, pages = {277-290}, pmid = {33538648}, issn = {2222-1751}, mesh = {Amoeba/*microbiology ; Francisella tularensis/*growth &amp; development ; Fresh Water/*microbiology ; Microbial Viability ; }, abstract = {Francisella tularensis, a tier 1 select agent, is the causative bacterium of tularemia, a zoonosis with a large animal reservoir. However, F. tularensis, like many other Francisella species, is assumed to have an aquatic reservoir. The mechanisms of Francisella species persistence in surface water remain poorly characterized. In this study, we deeply investigated the long-term interactions of the tularemia agent F. tularensis subsp. holarctica, F. novicida or F. philomiragia with amoebae of the Acanthamoeba species. In amoeba plate screening tests, all the Francisella species tested resisted the attack by amoebae. In in vitro infection models, intra-amoebic growth of Francisella varied according to the involved bacterial species and strains, but also the amoeba culture medium used. In co-culture models, the amoebae favoured Francisella survival over 16 days, which was likely dependent on direct contact between bacteria and amoebae for F. novicida and on amoeba-excreted compounds for F. novicida and for F. tularensis. In a spring water co-culture model, amoebae again enhanced F. novicida survival and preserved bacterial morphology. Overall, our results demonstrate that amoebae likely promote Francisella survival in aquatic environments, including the tularemia agent F. tularensis. However, bacteria-amoebae interactions are complex and depend on the Francisella species considered.}, }
@article {pmid33537111, year = {2021}, author = {Salek, MM and Fernandez, V and D'souza, G and Puigmartí-Luis, J and Stocker, R and Secchi, E}, title = {An interdisciplinary and application-oriented approach to teach microfluidics.}, journal = {Biomicrofluidics}, volume = {15}, number = {1}, pages = {014104}, pmid = {33537111}, issn = {1932-1058}, abstract = {Microfluidics is a relatively novel interdisciplinary research area with broad applications in chemistry, physics, material science, and biology. Despite the rapid growth of the field, students' exposure to microfluidic technologies is still limited and often insufficient to appreciate the advantages over other commonly used technologies. To this end, we designed a five-day course, "Microfluidics for microbial ecology," in which students with very different backgrounds learn the basics of microfluidic technologies and sample a range of applications in microbial ecology. The course was created for Master and Ph.D. students interested in applying microfluidics to their research and, therefore, followed an application-oriented approach. The presentation of critical aspects of fluid flow phenomena at the microscale and an outline of the advantages and constraints of the technology provide students with the background to design and perform microfluidics-based experiments. In order to improve the effectiveness of learning in a class with diverse interests and backgrounds, two active learning exercises were implemented. The first comprised the design of an individualized microfluidics experiment in parallel with the lectures: students were guided to apply each module to their personalized application and discuss it in groups. The second was a group experimental activity, in which students jointly set up, performed, analyzed, and presented a microfluidics-based experiment. Given the multidisciplinary teaching context, the course was able to foster common conceptual ground and promote discussion among students. This application-oriented approach built upon experimental activities and in-class discussion is well suited to promote learning in a technology-related subject such as microfluidics.}, }
@article {pmid33537022, year = {2020}, author = {Haber, M and Burgsdorf, I and Handley, KM and Rubin-Blum, M and Steindler, L}, title = {Genomic Insights Into the Lifestyles of Thaumarchaeota Inside Sponges.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {622824}, pmid = {33537022}, issn = {1664-302X}, abstract = {Sponges are among the oldest metazoans and their success is partly due to their abundant and diverse microbial symbionts. They are one of the few animals that have Thaumarchaeota symbionts. Here we compare genomes of 11 Thaumarchaeota sponge symbionts, including three new genomes, to free-living ones. Like their free-living counterparts, sponge-associated Thaumarchaeota can oxidize ammonia, fix carbon, and produce several vitamins. Adaptions to life inside the sponge host include enrichment in transposases, toxin-antitoxin systems and restriction modifications systems, enrichments previously reported also from bacterial sponge symbionts. Most thaumarchaeal sponge symbionts lost the ability to synthesize rhamnose, which likely alters their cell surface and allows them to evade digestion by the host. All but one archaeal sponge symbiont encoded a high-affinity, branched-chain amino acid transporter system that was absent from the analyzed free-living thaumarchaeota suggesting a mixotrophic lifestyle for the sponge symbionts. Most of the other unique features found in sponge-associated Thaumarchaeota, were limited to only a few specific symbionts. These features included the presence of exopolyphosphatases and a glycine cleavage system found in the novel genomes. Thaumarchaeota have thus likely highly specific interactions with their sponge host, which is supported by the limited number of host sponge species to which each of these symbionts is restricted.}, }
@article {pmid33536337, year = {2021}, author = {Zakem, EJ and Cael, BB and Levine, NM}, title = {A unified theory for organic matter accumulation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {6}, pages = {}, pmid = {33536337}, issn = {1091-6490}, mesh = {Carbon/*metabolism ; Climate ; Microbiota/*genetics ; *Models, Theoretical ; Organic Chemicals/*metabolism ; Temperature ; }, abstract = {Organic matter constitutes a key reservoir in global elemental cycles. However, our understanding of the dynamics of organic matter and its accumulation remains incomplete. Seemingly disparate hypotheses have been proposed to explain organic matter accumulation: the slow degradation of intrinsically recalcitrant substrates, the depletion to concentrations that inhibit microbial consumption, and a dependency on the consumption capabilities of nearby microbial populations. Here, using a mechanistic model, we develop a theoretical framework that explains how organic matter predictably accumulates in natural environments due to biochemical, ecological, and environmental factors. Our framework subsumes the previous hypotheses. Changes in the microbial community or the environment can move a class of organic matter from a state of functional recalcitrance to a state of depletion by microbial consumers. The model explains the vertical profile of dissolved organic carbon in the ocean and connects microbial activity at subannual timescales to organic matter turnover at millennial timescales. The threshold behavior of the model implies that organic matter accumulation may respond nonlinearly to changes in temperature and other factors, providing hypotheses for the observed correlations between organic carbon reservoirs and temperature in past earth climates.}, }
@article {pmid33536320, year = {2021}, author = {Rubbens, P and Props, R and Kerckhof, FM and Boon, N and Waegeman, W}, title = {PhenoGMM: Gaussian Mixture Modeling of Cytometry Data Quantifies Changes in Microbial Community Structure.}, journal = {mSphere}, volume = {6}, number = {1}, pages = {}, pmid = {33536320}, issn = {2379-5042}, mesh = {Biodiversity ; Flow Cytometry/*methods ; *Microbiota ; *Normal Distribution ; }, abstract = {Microbial flow cytometry can rapidly characterize the status of microbial communities. Upon measurement, large amounts of quantitative single-cell data are generated, which need to be analyzed appropriately. Cytometric fingerprinting approaches are often used for this purpose. Traditional approaches either require a manual annotation of regions of interest, do not fully consider the multivariate characteristics of the data, or result in many community-describing variables. To address these shortcomings, we propose an automated model-based fingerprinting approach based on Gaussian mixture models, which we call PhenoGMM. The method successfully quantifies changes in microbial community structure based on flow cytometry data, which can be expressed in terms of cytometric diversity. We evaluate the performance of PhenoGMM using data sets from both synthetic and natural ecosystems and compare the method with a generic binning fingerprinting approach. PhenoGMM supports the rapid and quantitative screening of microbial community structure and dynamics.IMPORTANCE Microorganisms are vital components in various ecosystems on Earth. In order to investigate the microbial diversity, researchers have largely relied on the analysis of 16S rRNA gene sequences from DNA. Flow cytometry has been proposed as an alternative technology to characterize microbial community diversity and dynamics. The technology enables a fast measurement of optical properties of individual cells. So-called fingerprinting techniques are needed in order to describe microbial community diversity and dynamics based on flow cytometry data. In this work, we propose a more advanced fingerprinting strategy based on Gaussian mixture models. We evaluated our workflow on data sets from both synthetic and natural ecosystems, illustrating its general applicability for the analysis of microbial flow cytometry data. PhenoGMM supports a rapid and quantitative analysis of microbial community structure using flow cytometry.}, }
@article {pmid33535686, year = {2021}, author = {M'hir, S and Filannino, P and Mejri, A and Tlais, AZA and Di Cagno, R and Ayed, L}, title = {Functional Exploitation of Carob, Oat Flour, and Whey Permeate as Substrates for a Novel Kefir-Like Fermented Beverage: An Optimized Formulation.}, journal = {Foods (Basel, Switzerland)}, volume = {10}, number = {2}, pages = {}, pmid = {33535686}, issn = {2304-8158}, abstract = {This study investigated the fortification of a carob-based kefir-like beverage (KLB) with whey permeate (WP) and oat flour (OF). The response surface method was used to show the effect of WP and OF concentrations on lactic acid bacteria and yeast cell densities, pH, total titratable acidity (TTA), total phenolics content (TCP), DPPH radical scavenging activity, and overall acceptability (OA) in KLB. The statistical design provided thirteen formulations where OF concentration varied from 3% to 5% and WP from 10% to 15%. The enrichment of carob pods decoction with WP and OF had a positive effect on biomass production. Overall fermentation was shown to increase TPC of KLB. Furthermore, OF supplementation led to the higher levels of TPC and antiradical activity. WP negatively affected OA at linear and quadratic levels, whereas no effect of OF was observed at the linear level. The optimum point was found by using WP at 11.51% and OF at 4.77%. Optimized KLB resulted in an enrichment of bioavailable phenolics derivatives and highly digestible proteins.}, }
@article {pmid33535657, year = {2021}, author = {Bourigault, Y and Chane, A and Barbey, C and Jafra, S and Czajkowski, R and Latour, X}, title = {Biosensors Used for Epifluorescence and Confocal Laser Scanning Microscopies to Study Dickeya and Pectobacterium Virulence and Biocontrol.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, pmid = {33535657}, issn = {2076-2607}, support = {-//Minist&#xe8;re de l'Enseignement Sup&#xe9;rieur, de la Recherche et de l'innovation, the R&#xe9;gion Normandie and the Evreux Portes de Normandie agglom&#xe9;ration, the P&#xf4;le de Comp&#xe9;tivit&#xe9; Valorial, and FEDER (European Union)/ ; DS 531-N105-D786-20//Polish Ministry of Science and Higher Education (Ministerstwo Nauki i Szkolnictwa Wy&#x17c;szego, Polska)/ ; DS 531-N104-D800-20//Polish Ministry of Higher Education (Ministers two Nauki i Szkolnictwa Wy&#x17c;szego, Polska)/ ; }, abstract = {Promoter-probe vectors carrying fluorescent protein-reporter genes are powerful tools used to study microbial ecology, epidemiology, and etiology. In addition, they provide direct visual evidence of molecular interactions related to cell physiology and metabolism. Knowledge and advances carried out thanks to the construction of soft-rot Pectobacteriaceae biosensors, often inoculated in potato Solanum tuberosum, are discussed in this review. Under epifluorescence and confocal laser scanning microscopies, Dickeya and Pectobacterium-tagged strains managed to monitor in situ bacterial viability, microcolony and biofilm formation, and colonization of infected plant organs, as well as disease symptoms, such as cell-wall lysis and their suppression by biocontrol antagonists. The use of dual-colored reporters encoding the first fluorophore expressed from a constitutive promoter as a cell tag, while a second was used as a regulator-based reporter system, was also used to simultaneously visualize bacterial spread and activity. This revealed the chronology of events leading to tuber maceration and quorum-sensing communication, in addition to the disruption of the latter by biocontrol agents. The promising potential of these fluorescent biosensors should make it possible to apprehend other activities, such as subcellular localization of key proteins involved in bacterial virulence in planta, in the near future.}, }
@article {pmid33533410, year = {2021}, author = {Min, D and Doxey, AC and Neufeld, JD}, title = {AXIOME3: Automation, eXtension, and Integration Of Microbial Ecology.}, journal = {GigaScience}, volume = {10}, number = {2}, pages = {}, pmid = {33533410}, issn = {2047-217X}, mesh = {Automation ; Data Visualization ; *High-Throughput Nucleotide Sequencing ; Phylogeny ; *Software ; }, abstract = {BACKGROUND: Advances in high-throughput sequencing accessibility have democratized small subunit ribosomal RNA gene sequence data collection, coincident with an increasing availability of computational tools for sequence data processing, multivariate statistics, and data visualization. However, existing tools often require programming ability and frequent user intervention that may not be suitable for fast-paced and large-scale data analysis by end user microbiologists who are unfamiliar with the Linux command line environment or who prefer interactions with a GUI. Here we present AXIOME3, which is a completely redeveloped AXIOME pipeline that streamlines small subunit ribosomal RNA data analysis by managing QIIME2, R, and Python-associated analyses through an interactive web interface.<br><br>FINDINGS: AXIOME3 comes with web GUI to improve usability by simplifying configuration processes and task status tracking. Internally, it uses an automated pipeline that is wrapped around QIIME2 to generate a range of outputs including amplicon sequence variant tables, taxonomic classifications, phylogenetic trees, biodiversity metrics, and ordinations. The extension module for AXIOME3 provides advanced data visualization tools such as principal coordinate analysis, bubble plots, and triplot ordinations that can be used to visualize interactions between a distance matrix, amplicon sequence variant taxonomy, and sample metadata.<br><br>CONCLUSIONS: Because repeat analysis of small subunit ribosomal RNA amplicon sequence data is challenging for those who have limited experience in command line environments, AXIOME3 now offers rapid and user-friendly options within an automated pipeline, with advanced data visualization tools and the ability for users to incorporate additional analyses easily through extension. AXIOME3 is completely open source (https://github.com/neufeld/AXIOME3, https://github.com/neufeld/AXIOME3-GUI), and researchers are encouraged to modify and redistribute the package.}, }
@article {pmid33532913, year = {2021}, author = {Caillon, F and Besemer, K and Peduzzi, P and Schelker, J}, title = {Soil microbial inoculation during flood events shapes headwater stream microbial communities and diversity.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {591-601}, pmid = {33532913}, issn = {1432-184X}, mesh = {Bacteria/genetics ; Floods ; *Microbiota ; *Soil ; Soil Microbiology ; }, abstract = {Flood events are now recognized as potentially important occasions for the transfer of soil microbes to stream ecosystems. Yet, little is known about these "dynamic pulses of microbial life" for stream bacterial community composition (BCC) and diversity. In this study, we explored the potential alteration of stream BCC by soil inoculation during high flow events in six pre-alpine first order streams and the larger Oberer Seebach. During 1 year, we compared variations of BCC in soil water, stream water and in benthic biofilms at different flow conditions (low to intermediate flows versus high flow). Bacterial diversity was lowest in biofilms, followed by soils and highest in headwater streams and the Oberer Seebach. In headwater streams, bacterial diversity was significantly higher during high flow, as compared to low flow (Shannon diversity: 7.6 versus 7.9 at low versus high flow, respectively, p < 0.001). Approximately 70% of the bacterial operational taxonomic units (OTUs) from streams and stream biofilms were the same as in soil water, while in the latter one third of the OTUs were specific to high flow conditions. These soil high-flow OTUs were also found in streams and biofilms at other times of the year. These results demonstrate the relevance of floods in generating short and reoccurring inoculation events for flowing waters. Moreover, they show that soil microbial inoculation during high flow enhances microbial diversity and shapes fluvial BCC even during low flow. Hence, soil microbial inoculation during floods could act as a previously overlooked driver of microbial diversity in headwater streams.}, }
@article {pmid33531553, year = {2021}, author = {Jeon, JS and Carreno-Quintero, N and van Eekelen, HDLM and De Vos, RCH and Raaijmakers, JM and Etalo, DW}, title = {Impact of root-associated strains of three Paraburkholderia species on primary and secondary metabolism of Brassica oleracea.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2781}, pmid = {33531553}, issn = {2045-2322}, mesh = {*Brassica/metabolism/microbiology ; Burkholderiaceae/*metabolism ; Plant Diseases/*prevention &amp; control ; Plant Leaves/*metabolism ; *Plant Roots/metabolism/microbiology ; Severity of Illness Index ; }, abstract = {Several root-colonizing bacterial species can simultaneously promote plant growth and induce systemic resistance. How these rhizobacteria modulate plant metabolism to accommodate the carbon and energy demand from these two competing processes is largely unknown. Here, we show that strains of three Paraburkholderia species, P. graminis PHS1 (Pbg), P. hospita mHSR1 (Pbh), and P. terricola mHS1 (Pbt), upon colonization of the roots of two Broccoli cultivars led to cultivar-dependent increases in biomass, changes in primary and secondary metabolism and induced resistance against the bacterial leaf pathogen Xanthomonas campestris. Strains that promoted growth led to greater accumulation of soluble sugars in the shoot and particularly fructose levels showed an increase of up to 280-fold relative to the non-treated control plants. Similarly, a number of secondary metabolites constituting chemical and structural defense, including flavonoids, hydroxycinnamates, stilbenoids, coumarins and lignins, showed greater accumulation while other resource-competing metabolite pathways were depleted. High soluble sugar generation, efficient sugar utilization, and suppression or remobilization of resource-competing metabolites potentially contributed to curb the tradeoff between the carbon and energy demanding processes induced by Paraburkholderia-Broccoli interaction. Collectively, our results provide a comprehensive and integrated view of the temporal changes in plant metabolome associated with rhizobacteria-mediated plant growth promotion and induced resistance.}, }
@article {pmid33531404, year = {2021}, author = {Cazares, D and Cazares, A and Figueroa, W and Guarneros, G and Edwards, RA and Vinuesa, P}, title = {A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33531404}, issn = {2379-5077}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Phages are generally described as species specific or even strain specific, implying an inherent limitation for some to be maintained and spread in diverse bacterial communities. Moreover, phage isolation and host range determination rarely consider the phage ecological context, likely biasing our notion on phage specificity. Here we isolated and characterized a novel group of six promiscuous phages, named Atoyac, existing in rivers and sewage by using a diverse collection of over 600 bacteria retrieved from the same environments as potential hosts. These podophages isolated from different regions in Mexico display a remarkably broad host range, infecting bacteria from six genera: Aeromonas, Pseudomonas, Yersinia, Hafnia, Escherichia, and Serratia Atoyac phage genomes are ∼42 kb long and highly similar to each other, but not to those currently available in genome and metagenome public databases. Detailed comparison of the phages' efficiency of plating (EOP) revealed variation among bacterial genera, implying a cost associated with infection of distant hosts, and between phages, despite their sequence similarity. We show, through experimental evolution in single or alternate hosts of different genera, that efficiency of plaque production is highly dynamic and tends toward optimization in hosts rendering low plaque formation. However, adaptation to distinct hosts differed between similar phages; whereas one phage optimized its EOP in all tested hosts, the other reduced plaque production in one host, suggesting that propagation in multiple bacteria may be key to maintain promiscuity in some viruses. Our study expands our knowledge of the virosphere and uncovers bacterium-phage interactions overlooked in natural systems.IMPORTANCE In natural environments, phages coexist and interact with a broad variety of bacteria, posing a conundrum for narrow-host-range phage maintenance in diverse communities. This context is rarely considered in the study of host-phage interactions, typically focused on narrow-host-range viruses and their infectivity in target bacteria isolated from sources distinct to where the phages were retrieved from. By studying phage-host interactions in bacteria and viruses isolated from river microbial communities, we show that novel phages with promiscuous host range encompassing multiple bacterial genera can be found in the environment. Assessment of hundreds of interactions in diverse hosts revealed that similar phages exhibit different infection efficiency and adaptation patterns. Understanding host range is fundamental in our knowledge of bacterium-phage interactions and their impact on microbial communities. The dynamic nature of phage promiscuity revealed in our study has implications in different aspects of phage research such as horizontal gene transfer or phage therapy.}, }
@article {pmid33530561, year = {2021}, author = {Lalaouna, D and Fochesato, S and Harir, M and Ortet, P and Schmitt-Kopplin, P and Heulin, T and Achouak, W}, title = {Amplifying and Fine-Tuning Rsm sRNAs Expression and Stability to Optimize the Survival of Pseudomonas brassicacerum in Nutrient-Poor Environments.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, pmid = {33530561}, issn = {2076-2607}, abstract = {In the beneficial plant root-associated Pseudomonas brassicacearum strain NFM421, the GacS/GacA two-component system positively controls biofilm formation and the production of secondary metabolites through the synthesis of rsmX, rsmY and rsmZ. Here, we evidenced the genetic amplification of Rsm sRNAs by the discovery of a novel 110-nt long sRNA encoding gene, rsmX-2, generated by the duplication of rsmX-1 (formerly rsmX). Like the others rsm genes, its overexpression overrides the gacA mutation. We explored the expression and the stability of rsmX-1, rsmX-2, rsmY and rsmZ encoding genes under rich or nutrient-poor conditions, and showed that their amount is fine-tuned at the transcriptional and more interestingly at the post-transcriptional level. Unlike rsmY and rsmZ, we noticed that the expression of rsmX-1 and rsmX-2 genes was exclusively GacA-dependent. The highest expression level and longest half-life for each sRNA were correlated with the highest ppGpp and cyclic-di-GMP levels and were recorded under nutrient-poor conditions. Together, these data support the view that the Rsm system in P. brassicacearum is likely linked to the stringent response, and seems to be required for bacterial adaptation to nutritional stress.}, }
@article {pmid33530464, year = {2021}, author = {Masetti, R and Zama, D and Leardini, D and Muratore, E and Turroni, S and Brigidi, P and Pession, A}, title = {Microbiome-Derived Metabolites in Allogeneic Hematopoietic Stem Cell Transplantation.}, journal = {International journal of molecular sciences}, volume = {22}, number = {3}, pages = {}, pmid = {33530464}, issn = {1422-0067}, support = {GR-2013-02357136//Ministero della Salute/ ; }, mesh = {Amino Acids/metabolism ; Animals ; Dietary Fiber/metabolism ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome ; *Hematopoietic Stem Cell Transplantation ; Humans ; *Metabolome ; *Microbiota ; Polyamines/metabolism ; Riboflavin/metabolism ; Transplantation, Homologous ; }, abstract = {The gut microbiome has emerged as a major character in the context of hematopoietic stem cell transplantation. The biology underpinning this relationship is still to be defined. Recently, mounting evidence has suggested a role for microbiome-derived metabolites in mediating crosstalk between intestinal microbial communities and the host. Some of these metabolites, such as fiber-derived short-chain fatty acids or amino acid-derived compounds, were found to have a role also in the transplant setting. New interesting data have been published on this topic, posing a new intriguing perspective on comprehension and treatment. This review provides an updated comprehensive overview of the available evidence in the field of gut microbiome-derived metabolites and hematopoietic stem cell transplantation.}, }
@article {pmid33530338, year = {2021}, author = {Fiedler, G and Herbstmann, AD and Doll, E and Wenning, M and Brinks, E and Kabisch, J and Breitenwieser, F and Lappann, M and Böhnlein, C and Franz, CMAP}, title = {Taxonomic Evaluation of the Heyndrickxia (Basonym Bacillus) sporothermodurans Group (H. sporothermodurans, H. vini, H. oleronia) Based on Whole Genome Sequences.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, pmid = {33530338}, issn = {2076-2607}, support = {281A105616//Bundesministerium f&#xfc;r Ern&#xe4;hrung und Landwirtschaft/ ; }, abstract = {The genetic heterogeneity of Heyndrickxia sporothermodurans (formerly Bacillussporothermodurans) was evaluated using whole genome sequencing. The genomes of 29 previously identified Heyndrickxiasporothermodurans and two Heyndrickxia vini strains isolated from ultra-high-temperature (UHT)-treated milk were sequenced by short-read (Illumina) sequencing. After sequence analysis, the two H. vini strains could be reclassified as H. sporothermodurans. In addition, the genomes of the H.sporothermodurans type strain (DSM 10599[T]) and the closest phylogenetic neighbors Heyndrickxiaoleronia (DSM 9356[T]) and Heyndrickxia vini (JCM 19841[T]) were also sequenced using both long (MinION) and short-read (Illumina) sequencing. By hybrid sequence assembly, the genome of the H. sporothermodurans type strain was enlarged by 15% relative to the short-read assembly. This noticeable increase was probably due to numerous mobile elements in the genome that are presumptively related to spore heat tolerance. Phylogenetic studies based on 16S rDNA gene sequence, core genome, single-nucleotide polymorphisms and ANI/dDDH, showed that H. vini is highly related to H. sporothermodurans. When examining the genome sequences of all H.sporothermodurans strains from this study, together with 4 H. sporothermodurans genomes available in the GenBank database, the majority of the 36 strains examined occurred in a clonal lineage with less than 100 SNPs. These data substantiate previous reports on the existence and spread of a genetically highly homogenous and heat resistant spore clone, i.e., the HRS-clone.}, }
@article {pmid33529974, year = {2021}, author = {Candry, P and Ganigué, R}, title = {Chain elongators, friends, and foes.}, journal = {Current opinion in biotechnology}, volume = {67}, number = {}, pages = {99-110}, doi = {10.1016/j.copbio.2021.01.005}, pmid = {33529974}, issn = {1879-0429}, mesh = {Carbohydrates ; Fermentation ; *Friends ; Humans ; Lactic Acid ; *Microbiota/genetics ; }, abstract = {Bioproduction of medium chain carboxylic acids has recently emerged as an alternative strategy to valorize low-value organic waste and side-streams. Key to this route is chain elongation, an anaerobic microbial process driven by ethanol, lactic acid, or carbohydrates. Because these technologies use wastes as feedstocks, mixed microbial communities are often considered as biocatalysts. Understanding and steering these microbiomes is key to optimize bioprocess performance. From a meta-analysis of publicly available sequencing data, we (i) explore how the current collection of isolated chain elongators compares to microbiome members, (ii) discuss the main beneficial and antagonistic interactions with community partners, and (iii) identify the key research gaps and needs to help understand chain elongation microbiomes, and design/steer these novel bioproduction processes.}, }
@article {pmid33529447, year = {2021}, author = {Miantezila Basilua, J and Mesia Kahunu, G and Pochart, P and Tona Lutete, G}, title = {Overview of HIV treatment failure in Africa using the WHO Pharmacovigilance data.}, journal = {Tropical medicine &amp; international health : TM &amp; IH}, volume = {26}, number = {5}, pages = {530-534}, doi = {10.1111/tmi.13556}, pmid = {33529447}, issn = {1365-3156}, mesh = {Adolescent ; Africa ; Anti-Retroviral Agents/*therapeutic use ; Child ; Child, Preschool ; Databases, Factual ; Female ; HIV Infections/*drug therapy ; Humans ; Infant ; Male ; *Pharmacovigilance ; Retrospective Studies ; Treatment Failure ; World Health Organization ; }, abstract = {OBJECTIVE: To characterise the factors associated with HIV treatment failure (HIVTF) from reported pharmacovigilance data in Africa.<br><br>MATERIALS AND METHODS: This is an observational pharmacovigilance analysis of the safety data of HIVTF available in the WHO International Pharmacovigilance database 'VigiBase[&#xae;] '. We used the Standardised MedDRA Queries (SMQ) to identify all the terms corresponding to HIVTF. To identify all relevant molecules and classes of antiretroviral therapy, we used the anatomic, therapeutic, and chemical classification. We presented results as a percentage or an adjusted Reporting Odds Ratio (aROR) with a 95% confidence interval (95% CI).<br><br>RESULTS: HIVTF was more reported in Africa compared with the rest of the world with 19.1% (18.1%-20.1%) corresponding to 1206 of all 6304 HIVTF reports. Among all the 37 WHO country members in Africa, South Africa was the main source of origin for these HIVTF reports with 86.8% (84.9%-88.7%). Compared to adults, children and adolescents were the most population groups affected by HIVTF, aROR&#xa0;=&#xa0;2.7, (95% CI) 1.7-4.2 and aROR&#xa0;=&#xa0;7.9, (95% CI) 4.5-13.9, respectively.<br><br>CONCLUSION: South Africa was the leading country of the reporting of HIVTF in Africa. The proportion of HIVTF was higher in both HIV-infected children and adolescents than in adults. There is a need for the improvement of medical care for children and adolescents with HIV infection in Africa.}, }
@article {pmid33529050, year = {2021}, author = {Poveda, J and Martínez-Gómez, &#xc1; and Fenoll, C and Escobar, C}, title = {The Use of Biochar for Plant Pathogen Control.}, journal = {Phytopathology}, volume = {111}, number = {9}, pages = {1490-1499}, doi = {10.1094/PHYTO-06-20-0248-RVW}, pmid = {33529050}, issn = {0031-949X}, mesh = {*Charcoal ; Nutrients ; *Plant Diseases/prevention &amp; control ; Soil ; }, abstract = {To support the search for alternative, nonchemical plant disease control strategies, we present a review of the pathogen-suppressive effects of biochar, a product derived from agricultural and other organic wastes, used as a soil amendment. A wide range of biochar effects contribute to the control of root or foliar fungal pathogens through modification of root exudates, soil properties, and nutrient availability, which influence the growth of antagonist microorganisms. The induction of systemic plant defenses by biochar in the roots to reduce foliar pathogenic fungi, the activation of stress-hormone responses, as well as changes in active oxygen species are indicative of a coordinated hormonal signaling within the plant. Although scarce data are available for oomycetes and bacterial pathogens, reports indicate that biochar promotes changes in the soil microbiota influencing pathogen motility and colonization, and the induction of plant systemic defenses, both contributing to disease suppression. Biochar also suppresses nematode and insect pests. For plant-parasitic nematodes, the primary modes of action are changes in soil microbial community diversity, the release of nematicidal compounds, and the induction of plant defenses. Use of biochar-based soil amendments is a promising strategy compatible with a circular economy, based on zero waste, as part of integrated pathogen and pest management. Since biochars exert complex and distinct modes of action for the control of plant pathogens, its nature and application regimes should be designed for particular pathogens and its effects studied locally.}, }
@article {pmid33527233, year = {2021}, author = {Din, GMU and Du, Z and Zhang, H and Zhao, S and Liu, T and Chen, W and Gao, L}, title = {Effects of Tilletia foetida on Microbial Communities in the Rhizosphere Soil of Wheat Seeds Coated with Different Concentrations of Jianzhuang.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {736-745}, pmid = {33527233}, issn = {1432-184X}, mesh = {Basidiomycota ; *Microbiota ; Plant Diseases ; Rhizosphere ; Seeds ; Soil ; Soil Microbiology ; *Triticum ; }, abstract = {Tilletia foetida (syn. T. laevis) leads to wheat common bunt, a worldwide disease that can lead to 80% yield loss and even total loss of production, together with degrading the quality of grains and flour by producing a rotten fish smell. To explore the potential microbial community that may contribute to the control of soil- and seed-borne pathogens, in this study, we analyzed the effects of the plant pathogenic fungus T. foetida on rhizosphere soil microorganisms in wheat seeds coated with different concentrations of a fungicide (Jianzhuang) used to control the disease. To analyze the bacterial and fungal abundance in T. foetida-infected and mock-infected plants, the microorganisms were sequenced using high-throughput HiSeq 2500 gene sequencing. The results showed that bacterial communities, including Verrucomicrobia, Patescibacteria, Armatimonadetes, Nitrospirae, Fibrobacteres, Chlamydiae, and Hydrogenedentes, and fungal communities, including Basidiomycota and Ciliophora, were more prevalent in the mock group than in the T. foetida-infected group, which may contribute to the control of wheat common bunt. Moreover, cluster and PCoA analysis revealed that replicates of the same samples were clustered together, and these results were also found in the distance index within-group analysis for bacterial and fungal communities in the T. foetida-infected and mock groups.}, }
@article {pmid33526910, year = {2021}, author = {Weisskopf, L and Schulz, S and Garbeva, P}, title = {Microbial volatile organic compounds in intra-kingdom and inter-kingdom interactions.}, journal = {Nature reviews. Microbiology}, volume = {19}, number = {6}, pages = {391-404}, pmid = {33526910}, issn = {1740-1534}, mesh = {Animals ; Archaea/*metabolism ; Bacteria/*metabolism ; Fungi/*metabolism ; Plants/metabolism ; Volatile Organic Compounds/chemistry/*metabolism ; }, abstract = {Microorganisms produce and excrete a versatile array of metabolites with different physico-chemical properties and biological activities. However, the ability of microorganisms to release volatile compounds has only attracted research attention in the past decade. Recent research has revealed that microbial volatiles are chemically very diverse and have important roles in distant interactions and communication. Microbial volatiles can diffuse fast in both gas and water phases, and thus can mediate swift chemical interactions. As well as constitutively emitted volatiles, microorganisms can emit induced volatiles that are triggered by biological interactions or environmental cues. In this Review, we highlight recent discoveries concerning microbial volatile compounds and their roles in intra-kingdom microbial interactions and inter-kingdom interactions with plants and insects. Furthermore, we indicate the potential biotechnological applications of microbial volatiles and discuss challenges and perspectives in this emerging research field.}, }
@article {pmid33526659, year = {2021}, author = {Che, Y and Yang, Y and Xu, X and Břinda, K and Polz, MF and Hanage, WP and Zhang, T}, title = {Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {6}, pages = {}, pmid = {33526659}, issn = {1091-6490}, mesh = {Chromosomes, Bacterial/genetics ; *Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; *Genes, Bacterial ; Mosaicism ; Mutagenesis, Insertional/*genetics ; Phylogeny ; Plasmids/*genetics ; Synteny/genetics ; }, abstract = {It is well established that plasmids play an important role in the dissemination of antimicrobial resistance (AMR) genes; however, little is known about the role of the underlying interactions between different plasmid categories and other mobile genetic elements (MGEs) in shaping the promiscuous spread of AMR genes. Here, we developed a tool designed for plasmid classification, AMR gene annotation, and plasmid visualization and found that most plasmid-borne AMR genes, including those localized on class 1 integrons, are enriched in conjugative plasmids. Notably, we report the discovery and characterization of a massive insertion sequence (IS)-associated AMR gene transfer network (245 combinations covering 59 AMR gene subtypes and 53 ISs) linking conjugative plasmids and phylogenetically distant pathogens, suggesting a general evolutionary mechanism for the horizontal transfer of AMR genes mediated by the interaction between conjugative plasmids and ISs. Moreover, our experimental results confirmed the importance of the observed interactions in aiding the horizontal transfer and expanding the genetic range of AMR genes within complex microbial communities.}, }
@article {pmid33526186, year = {2021}, author = {Brandenburg, KM and Krock, B and Klip, HCL and Sluijs, A and Garbeva, P and Van de Waal, DB}, title = {Intraspecific variation in multiple trait responses of Alexandrium ostenfeldii towards elevated pCO2.}, journal = {Harmful algae}, volume = {101}, number = {}, pages = {101970}, doi = {10.1016/j.hal.2020.101970}, pmid = {33526186}, issn = {1878-1470}, mesh = {Carbon ; *Dinoflagellida ; Nitrogen ; Oceans and Seas ; Phytoplankton ; }, abstract = {Dissolved oceanic CO2 concentrations are rising as result of increasing atmospheric partial pressure of CO2 (pCO2), which has large consequences for phytoplankton. To test how higher CO2 availability affects different traits of the toxic dinoflagellate Alexandrium ostenfeldii, we exposed three strains of the same population to 400 and 1,000 µatm CO2, and measured traits including growth rate, cell volume, elemental composition, [13]C fractionation, toxin content, and volatile organic compounds (VOCs). Strains largely increased their growth rates and particulate organic carbon and nitrogen production with higher pCO2 and showed significant changes in their VOC profile. One strain showed a significant decrease in both PSP and cyclic imine content and thereby in cellular toxicity. Fractionation against [13]C increased in response to elevated pCO2, which may point towards enhanced CO2 acquisition and/or a downscaling of the carbon concentrating mechanisms. Besides consistent responses in some traits, other traits showed large variation in both direction and strength of responses towards elevated pCO2. The observed intraspecific variation in phenotypic plasticity of important functional traits within the same population may help A. ostenfeldii to negate the effects of immediate environmental fluctuations and allow populations to adapt more quickly to changing environments.}, }
@article {pmid33522965, year = {2021}, author = {Dada, N and Jupatanakul, N and Minard, G and Short, SM and Akorli, J and Villegas, LM}, title = {Considerations for mosquito microbiome research from the Mosquito Microbiome Consortium.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {36}, pmid = {33522965}, issn = {2049-2618}, mesh = {Animals ; Culicidae/*microbiology ; *Metagenomics ; *Microbiota ; Reproducibility of Results ; Research/*organization &amp; administration/*trends ; }, abstract = {In the past decade, there has been increasing interest in mosquito microbiome research, leading to large amounts of data on different mosquito species, with various underlying physiological characteristics, and from diverse geographical locations. However, guidelines and standardized methods for conducting mosquito microbiome research are lacking. To streamline methods in mosquito microbiome research and optimize data quality, reproducibility, and comparability, as well as facilitate data curation in a centralized location, we are establishing the Mosquito Microbiome Consortium, a collaborative initiative for the advancement of mosquito microbiome research. Our overall goal is to collectively work on unraveling the role of the mosquito microbiome in mosquito biology, while critically evaluating its potential for mosquito-borne disease control. This perspective serves to introduce the consortium and invite broader participation. It highlights the issues we view as most pressing to the community and proposes guidelines for conducting mosquito microbiome research. We focus on four broad areas in this piece: (1) sampling/experimental design for field, semi-field, or laboratory studies; (2) metadata collection; (3) sample processing, sequencing, and use of appropriate controls; and (4) data handling and analysis. We finally summarize current challenges and highlight future directions in mosquito microbiome research. We hope that this piece will spark discussions around this area of disease vector biology, as well as encourage careful considerations in the design and implementation of mosquito microbiome research. Video Abstract.}, }
@article {pmid33517091, year = {2021}, author = {Uroosa,  and Kazmi, SSUH and Rahman, MS and Xu, H}, title = {Use of biological trait analysis of periphytic protozoan assemblages for evaluating effects of harmful algal blooms on ecological quality status in marine ecosystem.}, journal = {Marine pollution bulletin}, volume = {164}, number = {}, pages = {112083}, doi = {10.1016/j.marpolbul.2021.112083}, pmid = {33517091}, issn = {1879-3363}, mesh = {*Dinoflagellida ; Ecosystem ; *Harmful Algal Bloom ; }, abstract = {The effects of two harmful algal bloom (HAB) species Alexandrium tamarense and Gymnodinium catenatum on ecological quality status were studied using 14-day protozoan samples as test organisms. A fuzzy coding system with four traits and 11 categories of the test organisms was used for biological trait analysis. Five treatments were designed following the concentrations of 10[0], 10[2], 10[3], 10[4] and 10[5] cell ml[-][1] of each algal species. The community-weighted means were used to summarize the functioning process of the test organism assemblages. The community functioning of the protozoa showed a significant change in the treatments with high algal concentrations (10[4] and 10[5] cell ml[-1]). The functional richness of the test organisms showed continuous increasing trend from 10[2] to 10[4] cell ml[-1], and sharply dropped. These findings suggest that the BTA may be used as a useful tool for assessing the effects of HABs on ecological quality status in marine ecosystems.}, }
@article {pmid33515051, year = {2021}, author = {Keet, JH and Ellis, AG and Hui, C and Novoa, A and Le Roux, JJ}, title = {Impacts of Invasive Australian Acacias on Soil Bacterial Community Composition, Microbial Enzymatic Activities, and Nutrient Availability in Fynbos Soils.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {704-721}, pmid = {33515051}, issn = {1432-184X}, support = {89967//South Africa National Research Foundation/ ; 109244//South African National Research Foundation/ ; 109683//South African National Research Foundation/ ; EXPRO 19-28807X//Czech Science Foundation/ ; RVO 67985939//The Czech Academy of Sciences/ ; }, mesh = {*Acacia ; Australia ; *Microbiota ; Nutrients ; Soil ; Soil Microbiology ; }, abstract = {Invasive plants often impact soil conditions, notably through changes in soil chemistry and microbial community composition, potentially leading to altered soil functionality. We determine the impacts of invasive nitrogen-fixing Australian Acacia trees on soil chemistry and function (carbon, nitrogen, and phosphorus cycling) in South Africa's Core Cape Subregion, and whether any differences in soil function are linked to differences in soil chemical properties and bacterial community composition between neighbouring acacia-invaded and uninvaded sites. We do so by using Illumina MiSeq sequencing data together with soil chemistry and soil enzyme activity profiles. Acacias significantly increased levels of soil nitrogen (NO3[-], NH4[+], and total N), C, and pH. Although we did not find evidence that acacias affected soil bacterial community diversity, we did find them to alter bacterial community composition. Acacias also significantly elevated microbial phosphatase activity, but not β-glucosidase, whilst having contrasting effects on urease. Changes in soil chemical properties under acacia invasion were found to correlate with changes in enzyme activities for urease and phosphatase. Similarly, changes in soil bacterial community composition were correlated to changes in phosphatase enzymatic activity levels under acacia invasion. Whilst we found evidence for acacias altering soil function by changing soil chemical properties and bacterial community composition, these impacts appear to be specific to local site conditions.}, }
@article {pmid33515050, year = {2021}, author = {Cureau, N and Threlfall, R and Savin, M and Marasini, D and Lavefve, L and Carbonero, F}, title = {Year, Location, and Variety Impact on Grape-, Soil-, and Leaf-Associated Fungal Microbiota of Arkansas-Grown Table Grapes.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {73-86}, pmid = {33515050}, issn = {1432-184X}, mesh = {Arkansas ; *Mycobiome ; Plant Leaves ; Soil ; *Vitis ; }, abstract = {With the recent advancement of next-generation sequencing methods, there has been an increase in studies on identification of vineyard microbiota, winery-associated microbiota, and microbiota in wine fermentation. However, there have been few studies investigating the fungal microbiota of table grapes which present distinct spoilage and food safety challenges. The aims of this study were to identify and compare the impact of year, variety, and vineyard location on grape, leaf, and soil fungal communities of two varieties of table grapes, Faith and Gratitude, grown in two open-air vineyards and one high tunnel vineyard. The grape, leaf, and soil mycobiota were analyzed using high throughput amplicon sequencing of the ITS region. The sampling year and location of table grapes had an impact on grape, leaf, and soil mycobiota. Fungal diversity of grape, leaf, and soil was greater in 2017 than in 2016. Grape and leaf samples presented strong similarities in fungal communities with abundance of Sporidiobolaceae and Filobasidium in two vineyards and Cladosporium in another one. The high tunnel structure had distinct grape and leaf fungal communities compared to the two other vineyard locations. Mortierella was the predominant genus (27%) in soil samples for the three locations; however, genera of lower abundance varied between locations. These results provide extensive description of fungal communities in less-studied table grape vineyards and high tunnels, providing useful insight of potential threats and preventive strategies to help improve the production and marketability of table grapes.}, }
@article {pmid33512536, year = {2021}, author = {Adhikari, P and Jain, R and Sharma, A and Pandey, A}, title = {Plant Growth Promotion at Low Temperature by Phosphate-Solubilizing Pseudomonas Spp. Isolated from High-Altitude Himalayan Soil.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {677-687}, pmid = {33512536}, issn = {1432-184X}, support = {NA//Ministry of Environment, Forest and Climate Change, Govt of India/ ; }, mesh = {Altitude ; Ecosystem ; *Phosphates ; Pseudomonas/genetics ; *Soil ; Soil Microbiology ; Temperature ; }, abstract = {Scarcity of arable land, limited soil nutrient availability, and low-temperature conditions in the Himalayan regions need to be smartly managed using sustainable approaches for better crop yields. Microorganisms, able to efficiently solubilize phosphate at low temperatures, provide an opportunity to promote plant growth in an ecofriendly way. In this study, we have investigated the ability of psychrotolerant Pseudomonas spp., isolated from high altitudes of Indian Himalaya to solubilize P at low temperature. Quantitative estimation of phosphate solubilization and production of relevant enzymes at two different temperatures (15 and 25 °C) was performed for 4 out of 11 selected isolates, namely, GBPI_506 (Pseudomonas sp.), GBPI_508 (Pseudomonas palleroniana), GBPI_Hb61 (Pseudomonas proteolytica), and GBPI_CDB143 (Pseudomonas azotoformans). Among all, isolate GBPI_CDB143 showed highest efficiency to solubilize tri-calcium phosphate (110.50 ± 3.44 μg/mL) at 25 °C after 6 days while the culture supernatants of isolate GBPI_506 displayed the highest phytase activity (15.91 ± 0.35 U/mL) at 15 °C and alkaline phosphatase (3.09 ± 0.07 U/mL) at 25 °C in 6 and 9 days, respectively. Out of five different organic acids quantified, oxalic acid and malic acid were produced in maximum quantity by all four isolates. With the exception of GBPI_508, inoculation of bacteria promoted overall growth (rosette diameter, leaf area, and biomass) of Arabidopsis thaliana plants as compared to uninoculated control plants in growth chamber conditions. The plant growth promotion by each bacterial isolate was further validated by monitoring root colonization in the inoculated plants. These bacterial isolates with low-temperature phosphate solubilization potential along with phosphatases and phytase activity at low temperature could be harnessed for sustainable crop production in P-deficient agricultural soils under mountain ecosystems.}, }
@article {pmid33512248, year = {2021}, author = {Shaffer, JP and Marotz, C and Belda-Ferre, P and Martino, C and Wandro, S and Estaki, M and Salido, RA and Carpenter, CS and Zaramela, LS and Minich, JJ and Bryant, M and Sanders, K and Fraraccio, S and Ackermann, G and Humphrey, G and Swafford, AD and Miller-Montgomery, S and Knight, R}, title = {A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities.}, journal = {BioTechniques}, volume = {70}, number = {3}, pages = {149-159}, pmid = {33512248}, issn = {1940-9818}, support = {K12 GM068524/GM/NIGMS NIH HHS/United States ; U01 AI124316/AI/NIAID NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; R01 HL134887/HL/NHLBI NIH HHS/United States ; RF1 AG058942/AG/NIA NIH HHS/United States ; R01 DK102932/DK/NIDDK NIH HHS/United States ; 1RF1-AG058942-01,R01DK102932,R01HL134887,R01HL140976,U01AI124316,U19AG063744/GF/NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Biodiversity ; Cats ; Chemical Fractionation/methods ; DNA, Viral/*isolation &amp; purification ; Feces/microbiology/virology ; Female ; Fermented Foods/microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Limit of Detection ; Male ; Metagenomics/methods ; Mice ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*isolation &amp; purification ; SARS-CoV-2/*genetics ; Saliva/microbiology/virology ; Skin/microbiology/virology ; }, abstract = {One goal of microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused by the RNA virus SARS-CoV-2, has highlighted a gap in traditional DNA-based protocols, including the high-throughput methods the authors previously established as field standards. To enable simultaneous SARS-CoV-2 and microbial community profiling, the authors compared the relative performance of two total nucleic acid extraction protocols with the authors' previously benchmarked protocol. The authors included a diverse panel of environmental and host-associated sample types, including body sites commonly swabbed for COVID-19 testing. Here the authors present results comparing the cost, processing time, DNA and RNA yield, microbial community composition, limit of detection and well-to-well contamination between these protocols.}, }
@article {pmid33511438, year = {2021}, author = {Sabino-Pinto, J and Bletz, MC and Islam, MM and Shimizu, N and Bhuju, S and Geffers, R and Jarek, M and Kurabayashi, A and Vences, M}, title = {Correction to: Composition of the Cutaneous Bacterial Community in Japanese Amphibians: Effects of Captivity, Host Species, and Body Region.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {830}, doi = {10.1007/s00248-021-01693-z}, pmid = {33511438}, issn = {1432-184X}, }
@article {pmid33511437, year = {2021}, author = {Cao, C and Tao, S and Cui, Z and Zhang, Y}, title = {Response of Soil Properties and Microbial Communities to Increasing Salinization in the Meadow Grassland of Northeast China.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {722-735}, pmid = {33511437}, issn = {1432-184X}, support = {41877536//National Natural Science Foundation of China/ ; 41403063//National Natural Science Foundation of China/ ; 41371505//National Natural Science Foundation of China/ ; }, mesh = {China ; Grassland ; *Microbiota ; *Soil ; Soil Microbiology ; }, abstract = {Secondary salinization is a serious environmental issue and a major threat to the sustainable use of grasslands. Information about the response of microbial communities and soil properties in already saline soils to increasing salinity is lacking. We investigated soil properties and the structures of soil bacterial and fungal communities across a gradient of salinization in the Horqin Grassland, China. Three sites with relatively lightly (average soluble salt content = 0.11%), relatively moderately (average soluble salt content = 0.44%), and heavily (average soluble salt content = 1.07%) degraded grassland, were selected as experimental sites. We examined variations in the composition and structure of the soil bacterial and fungal communities by using high-throughput sequencing of the 16S and 18S rRNA genes, respectively. We found degrading effects of salinization on soil properties, i.e., decreased soil moisture, organic matter, total N, NH4-N, and NO3-N and increased soil bulk density, pH, and electrical conductivity. The bacterial and fungal community structures changed with increasing salinity. However, dominant microbial taxa (including phylum, genus, and operational taxonomic unit levels) were similar among experimental sites, indicating that increasing salinization slightly affected the basic compositions of microbial communities in already saline grasslands. Furthermore, the relative abundances of most dominant taxa sensitively responded to the soil salt content. Acidobacteria, Actinobacteria, Chloroflexi, RB4, Rubrobacter, Blastocatella, H16, Glomeromycota, and Aspergillus linearly increased with increasing salinization, suggesting that they could be used as bioindicators for salt-tolerant communities. Overall, the changes in the structures of soil bacterial and fungal communities were determined by the relative quantities of dominant taxa rather than community composition. The structures of soil bacterial and fungal communities were linked to soil properties and vegetation. Increasing soil salt content, and thereby varied pH and organic matter, were likely the direct influencing factors of microbial communities in these saline grasslands.}, }
@article {pmid33511436, year = {2021}, author = {Lu, XM and Liu, XP}, title = {Distribution of Metal Resistance Genes in Estuarine Sediments and Associated Key Impact Factors.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {581-590}, pmid = {33511436}, issn = {1432-184X}, support = {GY-Z19042//Fujian University of Technology/ ; 2020J01880//Fujian Provincial Natural Science Foundation/ ; }, mesh = {Environmental Monitoring ; Estuaries ; Geologic Sediments ; *Metals, Heavy/analysis ; Rivers ; Seawater ; *Water Pollutants, Chemical/analysis ; }, abstract = {Currently, little is known about the distribution of metal resistance genes (MRGs) in estuarine sediments. In this study, we used the high-throughput quantitative real-time polymerase chain reaction (HT-qPCR) to determine the distribution of MRGs in the sediments of an estuary system and the associated key impact factors. The relative abundance of the detected MRGs showed a decreasing trend from the river inlet toward the sea and a decrease from the middle area of the estuary to the near-shore areas on both sides; these decreases were higher in the summer than in the winter. In the estuary system during the summer, the abundance of Zn- and Cu-MRGs from the river inlet to the sea decreased by 99.5% and 93.6%, whereas those of Hg- and Cd-Zn-Co-MRGs increased by 51.5% and 16.7%, respectively. Moreover, the abundance of Zn- and Cu-MRGs in the winter decreased by 88.6% and 97.7%, respectively, whereas that of Cd-Bi-Zn-Pb-MRGs increased by 729.6%. Furthermore, the abundances of MRGs and mobile genetic elements (MGEs) were significantly positively correlated with the levels of antibiotic residues and heavy metals as well as with the particle size and total organic carbon content of the sediment; however, they were significantly negatively correlated with seawater salinity and the oxidation and reduction potential (Eh) and pH of the sediment. The abundance of MGEs was significantly positively correlated with the abundance of MRGs in the sediment. Our findings suggest that antibiotic residues facilitated the proliferation and propagation of MRGs by promoting MGEs in estuarine sediments.}, }
@article {pmid33510866, year = {2021}, author = {Callewaert, C and Knödlseder, N and Karoglan, A and Güell, M and Paetzold, B}, title = {Skin microbiome transplantation and manipulation: Current state of the art.}, journal = {Computational and structural biotechnology journal}, volume = {19}, number = {}, pages = {624-631}, pmid = {33510866}, issn = {2001-0370}, abstract = {Many skin conditions are associated with an imbalance in the skin microbiome. In recent years, the skin microbiome has become a hot topic, for both therapeutic and cosmetic purposes. The possibility of manipulating the human skin microbiome to address skin conditions has opened exciting new paths for therapy. Here we review the skin microbiome manipulation strategies, ranging from skin microbiome transplantation, over skin bacteriotherapy to the use of prebiotics, probiotics and postbiotics. We summarize all efforts undertaken to exchange, manipulate, transplant or selectively apply the skin microbiome to date. Multiple microbial groups have been targeted, since they have been proven to be beneficial for skin health. We focus on the most common skin disorders and their associated skin microbiome dysbiosis and we review the existing scientific data and clinical trials undertaken to combat these skin conditions. The skin microbiome represents a novel platform for therapy. Transplantation of a complete microbiome or application of single strains has demonstrated beneficial therapeutic application.}, }
@article {pmid33510747, year = {2020}, author = {Favero, VO and Carvalho, RH and Motta, VM and Leite, ABC and Coelho, MRR and Xavier, GR and Rumjanek, NG and Urquiaga, S}, title = {Bradyrhizobium as the Only Rhizobial Inhabitant of Mung Bean (Vigna radiata) Nodules in Tropical Soils: A Strategy Based on Microbiome for Improving Biological Nitrogen Fixation Using Bio-Products.}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {602645}, pmid = {33510747}, issn = {1664-462X}, abstract = {The mung bean has a great potential under tropical conditions given its high content of grain protein. Additionally, its ability to benefit from biological nitrogen fixation (BNF) through association with native rhizobia inhabiting nodule microbiome provides most of the nitrogen independence on fertilizers. Soil microbial communities which are influenced by biogeographical factors and soil properties, represent a source of rhizobacteria capable of stimulating plant growth. The objective of this study is to support selection of beneficial bacteria that form positive interactions with mung bean plants cultivated in tropical soils, as part of a seed inoculation program for increasing grain yield based on the BNF and other mechanisms. Two mung bean genotypes (Camaleão and Esmeralda) were cultivated in 10 soil samples. Nodule microbiome was characterized by next-generation sequencing using Illumina MiSeq 16S rRNA. More than 99% of nodule sequences showed similarity with Bradyrhizobium genus, the only rhizobial present in nodules in our study. Higher bacterial diversity of soil samples collected in agribusiness areas (MW_MT-I, II or III) was associated with Esmeralda genotype, while an organic agroecosystem soil sample (SE_RJ-V) showed the highest bacterial diversity independent of genotype. Furthermore, OTUs close to Bradyrhizobium elkanii have dominated in all soil samples, except in the sample from the organic agroecosystem, where just B. japonicum was present. Bacterial community of mung bean nodules is mainly influenced by soil pH, K, Ca, and P. Besides a difference on nodule colonization by OTU sequences close to the Pseudomonas genus regarding the two genotypes was detected too. Although representing a small rate, around 0.1% of the total, Pseudomonas OTUs were only retrieved from nodules of Esmeralda genotype, suggesting a different trait regarding specificity between macro- and micro-symbionts. The microbiome analysis will guide the next steps in the development of an inoculant for mung bean aiming to promote plant growth and grain yield, composed either by an efficient Bradyrhizobium strain on its own or co-inoculated with a Pseudomonas strain. Considering the results achieved, the assessment of microbial ecology parameters is a potent coadjuvant capable to accelerate the inoculant development process and to improve the benefits to the crop by soil microorganisms.}, }
@article {pmid33509983, year = {2021}, author = {Rachek, S and Nikpoor, N and Gómez Del Pulgar, EM and Gonzaga, A and Sanz, Y and Tompkins, TA}, title = {Complete Genome Sequence of Phascolarctobacterium faecium G 104, Isolated from the Stools of a Healthy Lean Donor.}, journal = {Microbiology resource announcements}, volume = {10}, number = {4}, pages = {}, pmid = {33509983}, issn = {2576-098X}, abstract = {Phascolarctobacterium faecium is a strict anaerobe belonging to the Firmicutes phylum that is found abundantly in the human gastrointestinal tract. Here, we report the complete genome sequence of P. faecium G 104, a strain isolated from a fresh stool sample from a healthy lean donor.}, }
@article {pmid33508898, year = {2021}, author = {Babaahmadifooladi, M and Jacxsens, L and Van de Wiele, T and Carlos da Silva Júnior, E and Du Laing, G}, title = {Assessment of bioaccessible and dialyzable fractions of nickel in food products and their impact on the chronic exposure of Belgian population to nickel.}, journal = {Food chemistry}, volume = {342}, number = {}, pages = {128210}, doi = {10.1016/j.foodchem.2020.128210}, pmid = {33508898}, issn = {1873-7072}, mesh = {Belgium ; Dialysis ; Digestion ; Edible Grain/chemistry ; *Food Analysis ; Fruit/chemistry/metabolism ; Humans ; Nickel/*analysis/metabolism ; Tea/chemistry/metabolism ; Triticum/chemistry/metabolism ; }, abstract = {This study aimed to investigate bioaccessible/dialyzable fractions of nickel in selected foods and to clarify the impact of the food digestion/absorption on the final exposure of consumers to nickel. In vitro gastrointestinal incubation experiments were conducted to estimate the bioaccessibility of nickel in different foods. For estimation of a dialyzable fraction, dialysis filtration was conducted. Highest bioaccessibility (99.6%) was observed for wheat-based breakfast cereals. Lowest bioaccessibilities was observed for dried-fruits (on average 20.4%). Highest (61.5%) and lowest (24.5%) dialyzable fractions were observed for wheat-based breakfast cereal and chocolate respectively. Bioaccessible/dialyzable fractions based exposure assessments were highlighted the overestimation of exposures calculated based on total nickel concentrations in foods. This is particularly important when exposure values were compared with toxicological thresholds in a risk characterization study. When threshold values have been obtained through animal studies in which nickel was dosed at 100% accessibility/availability, e.g. nickel salts this is even more important.}, }
@article {pmid33508664, year = {2021}, author = {Durán, J and Rodríguez, A and Fangueiro, D and De Los Ríos, A}, title = {In-situ soil greenhouse gas fluxes under different cryptogamic covers in maritime Antarctica.}, journal = {The Science of the total environment}, volume = {770}, number = {}, pages = {144557}, doi = {10.1016/j.scitotenv.2020.144557}, pmid = {33508664}, issn = {1879-1026}, mesh = {Antarctic Regions ; Carbon Dioxide/analysis ; Ecosystem ; *Greenhouse Gases/analysis ; Methane/analysis ; Nitrous Oxide/analysis ; Soil ; }, abstract = {Soils can influence climate by sequestering or emitting greenhouse gases (GHG) such as carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). We are far from understanding the direct influence of cryptogamic covers on soil GHG fluxes, particularly in areas free of potential anthropogenic confounding factors. We assessed the role of well-developed cryptogamic covers in soil attributes, as well as in the in-situ exchange of GHG between Antarctic soils and the atmosphere during the austral summer. We found lower values of soil organic matter, total organic carbon, and total nitrogen in bare areas than in soils covered by mosses and, particularly, lichens. These differences, together with concomitant decreases and increases in soil temperature and moisture, respectively, resulted in increases in in-situ CO2 emission (i.e. ecosystem respiration) and decreases in CH4 uptake but no significant changes in N2O fluxes. We found consistent linear positive and negative relationships between soil attributes (i.e. soil organic matter, total organic carbon and total nitrogen) and CO2 emissions and CH4 uptake, respectively, and polynomial relationships between these soil attributes and net N2O fluxes. Our results indicate that any increase in the area occupied by cryptogams in terrestrial Antarctic ecosystems (due to increased growing season and increasingly warming conditions) will likely result in parallel increases in soil fertility as well as in an enhanced capacity to emit CO2 and a decreased capacity to uptake CH4. Such changes, unless offset by parallel C uptake processes, would represent a paradigmatic example of a positive climate change feedback. Further, we show that the fate of these terrestrial ecosystems under future climate scenarios, as well as their capacity to exchange GHG with the atmosphere might depend on the relative ability of different aboveground cryptogams to thrive under the new conditions.}, }
@article {pmid33507249, year = {2021}, author = {Del Moral, &#xc1; and Garrido-Benavent, I and Durán, J and Lehmann, JR and Rodríguez, A and Heiðmarsson, S and de Los Ríos, A}, title = {Are recently deglaciated areas at both poles colonised by the same bacteria?.}, journal = {FEMS microbiology letters}, volume = {368}, number = {3}, pages = {}, doi = {10.1093/femsle/fnab011}, pmid = {33507249}, issn = {1574-6968}, mesh = {Antarctic Regions ; Arctic Regions ; Bacteria/classification/*genetics ; *Biodiversity ; Ice Cover/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Polar glacier forefields offer an unprecedented framework for studying community assembly processes in regions that are geographically and climatically isolated. Through amplicon sequence variant (ASV) inference, we compared the composition and structure of soil bacterial communities from glacier forefields in Iceland and Antarctica to assess overlap between communities and the impact of established cryptogamic covers on the uniqueness of their taxa. These pioneer microbial communities were found to share only 8% of ASVs and each taxonomic group's contribution to the shared ASV data subset was heterogeneous and independent of their relative abundance. Although the presence of ASVs specific to one glacier forefield and/or different cryptogam cover values confirms the existence of habitat specialist bacteria, our data show that the influence of cryptogams on the edaphic bacterial community structure also varied also depending on the taxonomic group. Hence, the establishment of distinct cryptogamic covers is probably not the only factor driving the uniqueness of bacterial communities at both poles. The structure of bacterial communities colonising deglaciated areas seems also conditioned by lineage-specific limitations in their dispersal capacity and/or their establishment and persistence in these isolated and hostile regions.}, }
@article {pmid33505795, year = {2021}, author = {Chica Cardenas, LA and Clavijo, V and Vives, M and Reyes, A}, title = {Bacterial meta-analysis of chicken cecal microbiota.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e10571}, pmid = {33505795}, issn = {2167-8359}, abstract = {Poultry production is an industry that generates 90,000 metric tons of chicken meat worldwide. Thus, optimizing chicken growth and sustainable production is of great importance. A central factor determining not only production parameters, but also stability of the immune system and chicken health, is the diversity and variability of the microbiota present throughout the gastrointestinal tract. To date, several studies have investigated the relationship between bacterial communities and the gut microbiome, with limited data to compare. This study aims to create a bacterial meta-analysis based on studies using amplicon sequencing with Illumina sequencing technologies in order to build a baseline for comparison in future analyses of the cecal bacterial composition in chicken. A systematic literature review was performed (SYRF ID: e84f0468-e418-4eec-9da4-b517f1b4809d. Full project URL: https://app.syrf.org.uk/projects/e84f0468-e418-4eec-9da4-b517f1b4809d/detail). From all the available and analyzed manuscripts only nine contained full raw-sequence data available and the corresponding metadata. A total of 324 samples, comprising three different regions within the 16S rRNA gene, were analyzed. Due to the heterogeneity of the data, each region was analyzed independently and an effort for a joint analysis was performed as well. Taxonomic profiling revealed 11 phyla, with Firmicutes as the most prevalent phylum, followed by Bacteroidetes and Proteobacteria. At genus level, 109 genera were found. Shannon metric for alpha diversity showed that factors like type of chickens (Commercial or experimental) and 16S rRNA gene subregion have negligible effect on diversity. Despite the large number of parameters that were taken into account, the identification of common bacteria showed five genera to be common for all sets in at least 50% of the samples. These genera are highly associated to cellulose degradation and short chain fatty acids synthesis. In general, it was possible to identify some commonalities in the bacterial cecal microbial community despite the extensive variability and factors differing from one study to another.}, }
@article {pmid33505541, year = {2021}, author = {Shen, G and Wu, J and Ye, BC and Qi, N}, title = {Gut Microbiota-Derived Metabolites in the Development of Diseases.}, journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2021}, number = {}, pages = {6658674}, pmid = {33505541}, issn = {1712-9532}, abstract = {Gut microbiota is increasingly recognized as a metabolic organ essential for human health. Compelling evidences show a variety set of links between diets and gut microbial homeostasis. Changes in gut microbial flora would probably contribute to the development of certain diseases such as diabetes, heart disease, allergy, and psychiatric diseases. In addition to the composition of gut microbiota, the metabolites derived from gut microbiota have emerged as a pivotal regulator in diseases development. Since high-fat and high-protein diets substantially affect the gut microbial ecology and human health, the current review summarizes the gut microbiota-derived metabolites such as short-chain fatty acids (SCFAs), amino acids, and their derivatives and highlights the mechanisms underlying the host responses to these bioactive substances.}, }
@article {pmid33505386, year = {2020}, author = {Borda-Molina, D and Mátis, G and Mackei, M and Neogrády, Z and Huber, K and Seifert, J and Camarinha-Silva, A}, title = {Caeca Microbial Variation in Broiler Chickens as a Result of Dietary Combinations Using Two Cereal Types, Supplementation of Crude Protein and Sodium Butyrate.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {617800}, pmid = {33505386}, issn = {1664-302X}, abstract = {The intestinal microbiome can influence the efficiency and the health status of its host's digestive system. Indigestible non-starch polysaccharides (NSP) serve as substrates for bacterial fermentation, resulting in short-chain fatty acids like butyrate. In broiler's nutrition, dietary crude protein (CP) and butyrate's presence is of particular interest for its impact on intestinal health and growth performance. In this study, we evaluated the effect on the microbial ecology of the ceca of dietary supplementations, varying the cereal type (maize and wheat), adequate levels of CP and supplementation of sodium butyrate on broiler chickens with 21 days. The overall structure of bacterial communities was statistically affected by cereal type, CP, and sodium butyrate (p = 0.001). Wheat in the diet promoted the presence of Lactobacillaceae, Bifidobacteriaceae and Bacteroides xylanisolvens, which can degrade complex carbohydrates. Maize positively affected the abundance of Bacteroides vulgatus. The addition of CP promoted the family Rikenellaceae, while sodium butyrate as feed supplement was positively related to the family Lachnospiraceae. Functional predictions showed an effect of the cereal type and a statistical significance across all supplementations and their corresponding interactions. The composition of diets affected the overall structure of broilers' intestinal microbiota. The source of NSP as a substrate for bacterial fermentation had a stronger stimulus on bacterial communities than CP content or supplementation of butyrate.}, }
@article {pmid33505154, year = {2021}, author = {Rahayu, ES and Mariyatun, M and Putri Manurung, NE and Hasan, PN and Therdtatha, P and Mishima, R and Komalasari, H and Mahfuzah, NA and Pamungkaningtyas, FH and Yoga, WK and Nurfiana, DA and Liwan, SY and Juffrie, M and Nugroho, AE and Utami, T}, title = {Effect of probiotic Lactobacillus plantarum Dad-13 powder consumption on the gut microbiota and intestinal health of overweight adults.}, journal = {World journal of gastroenterology}, volume = {27}, number = {1}, pages = {107-128}, pmid = {33505154}, issn = {2219-2840}, mesh = {Adult ; Child ; Double-Blind Method ; Escherichia coli ; Feces ; *Gastrointestinal Microbiome ; Humans ; Indonesia/epidemiology ; *Lactobacillus plantarum ; Powders ; *Probiotics/therapeutic use ; }, abstract = {BACKGROUND: Shifting on lifestyle, diet, and physical activity contributed on increasing number of obese people around the world. Multiple factors influence the development of obesity. Some research suggested that gut microbiota (GM) plays an important role in nutrient absorption and energy regulation of individuals, thus affecting their nutritional status. Report of Indonesia Basic Health Research showed that the prevalence of obesity in every province tended to increase. Although the root cause of obesity is excessive calorie intake compared with expenditure, the differences in gut microbial ecology between healthy and obese humans may affect energy homeostasis. GM affect body weight, especially obesity. Probiotics that are consumed while alive and able to colonize in the intestine are expected to increase the population of good bacteria, especially Bifidobacteria and Lactobacilli, and suppress pathogens such as Enterobacteriaceae and Staphylococcus. The strain of L. plantarum Dad-13 has been demonstrated to survive and colonize in the gastrointestinal tract of healthy Indonesian adults who consume fermented milk containing L. plantarum Dad-13. The consumption of probiotic L. plantarum Dad-13 powder decreased E. coli and non-E. coli coliform bacteria in school-aged children in Indonesia. L. plantarum is a dominant bacterium in the average Indonesian's GM. For this reason, this bacterium is probably a more suitable probiotic for Indonesians.<br><br>AIM: To determine the effect of the consumption of indigenous probiotic Lactobacillus plantarum Dad-13 powder in overweight adults in Yogyakarta (Indonesia).<br><br>METHODS: Sixty overweight volunteers with a body mass index (BMI) equal to or greater than 25 consume indigenous probiotic powder L. plantarum Dad-13 (2 &#xd7; 10[9] CFU/gram/sachet) for 90 d. The study was a randomized, double-blind, placebo-controlled study. The volunteers filled in a diary on a daily basis, which consisted of questions on study product intake (only during ingestion period), other food intake, number of bowel movements, fecal quality (consistency and color), any medications received, and any symptom of discomfort, such as diarrhea, constipation, vomiting, gassing, sensation of illness, etc. Fecal samples and the subjects' diaries were collected on the morning of day 10 + 1, which was marked as the end of the baseline period and the start of the ingestion period. During the ingestion period (from day 11 to day 101), several parameters to measure and analyze the results included body weight and height (once a month), the lipid profile, GM analysis using MiSeq, short-chain fatty acid (SCFA) analysis using gas chromatography, and the measurement of fecal pH using a pH meter.<br><br>RESULTS: The consumption of indigenous probiotic powder L. plantarum Dad-13 caused the average body weight and BMI of the probiotic group to decrease from 84.54 &#xb1; 17.64 kg to 83.14 &#xb1; 14.71 kg and 33.10 &#xb1; 6.15 kg/m[2] to 32.57 &#xb1; 5.01 kg/m[2], respectively. No significant reduction of body weight and BMI in the placebo group was observed. An analysis of the microbiota showed that the number of Bacteroidetes, specifically Prevotella, increased significantly, while that of Firmicutes significantly decreased. No significant change in lipid profile in both groups was found. Also, no significant change in SCFAs (e.g., butyrate, propionate, acetic acid) and pH level was found after the consumption of the probiotic.<br><br>CONCLUSION: No significant differences in pH before and after ingestion were observed in both the probiotic and placebo groups as well as in the lipid profile of both cholesterol and triglyceride, high-density lipoprotein (HDL), low-density lipoprotein (LDL), and the LDL/HDL ratio. In addition, no significant changes in the concentration of SCFAs (e.g., acetic acid, propionate, and butyrate) were found after con-sumption. Interestingly, a significant decrease in body weight and BMI (P < 0.05) was determined in the treatment group. An analysis of GM shows that L. plantarum Dad-13 caused the Firmicutes population to decrease and the Bacteroidetes population (especially Prevotella) to increase.}, }
@article {pmid33502573, year = {2021}, author = {Terlova, EF and Holzinger, A and Lewis, LA}, title = {Terrestrial Green Algae Show Higher Tolerance to Dehydration than Do Their Aquatic Sister-Species.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {770-782}, pmid = {33502573}, issn = {1432-184X}, support = {I 1951/FWF_/Austrian Science Fund FWF/Austria ; I 1951-B16//Austrian Science Fund (AT)/ ; }, mesh = {*Chlorophyta ; *Dehydration ; Desiccation ; Ecosystem ; Photosystem II Protein Complex ; }, abstract = {Diverse algae possess the ability to recover from extreme desiccation without forming specialized resting structures. Green algal genera such as Tetradesmus (Sphaeropleales, Chlorophyceae) contain temperate terrestrial, desert, and aquatic species, providing an opportunity to compare physiological traits associated with the transition to land in closely related taxa. We subjected six species from distinct habitats to three dehydration treatments varying in relative humidity (RH 5%, 65%, 80%) followed by short- and long-term rehydration. We tested the capacity of the algae to recover from dehydration using the effective quantum yield of photosystem II as a proxy for physiological activity. The degree of recovery was dependent both on the habitat of origin and the dehydration scenario, with terrestrial, but not aquatic, species recovering from dehydration. Distinct strains of each species responded similarly to dehydration and rehydration, with the exception of one aquatic strain that recovered from the mildest dehydration treatment. Cell ultrastructure was uniformly maintained in both aquatic and desert species during dehydration and rehydration, but staining with an amphiphilic styryl dye indicated damage to the plasma membrane from osmotically induced water loss in the aquatic species. These analyses demonstrate that terrestrial Tetradesmus possess a vegetative desiccation tolerance phenotype, making these species ideal for comparative omics studies.}, }
@article {pmid33500192, year = {2021}, author = {Maganha de Almeida Kumlien, AC and Borrego, CM and Balcázar, JL}, title = {Antimicrobial Resistance and Bacteriophages: An Overlooked Intersection in Water Disinfection.}, journal = {Trends in microbiology}, volume = {29}, number = {6}, pages = {517-527}, doi = {10.1016/j.tim.2020.12.011}, pmid = {33500192}, issn = {1878-4380}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; *Bacteriophages ; Disinfection/*methods ; *Drug Resistance, Bacterial ; Feces ; Genes, Bacterial ; Humans ; Water Purification/*methods ; }, abstract = {This article focuses on how bacteriophages (phages), antibiotic-resistance genes (ARGs), and disinfection practices intersect. Phages are considered to be the most abundant biological entities on Earth and they have the potential to transfer genes (including ARGs) among their bacterial hosts. In the urban water cycle, phages are used as indicators of fecal pollution and surrogates for human viral pathogens but they are also known to withstand common disinfection treatments deployed to produce safe drinking/reclaimed water. Recent studies also suggest that phages have the potential to become an additional footprint to monitor water safety. A precautionary approach should therefore include phages in surveillance programs aimed at monitoring antimicrobial resistance (AMR) in the urban water cycle. This article argues that phages ought to be used to assess the efficiency of disinfection treatments (both classical and novel) on reducing the risk associated with antibiotic resistance. Finally, this article discusses contributions to the advancement of AMR stewardship in aquatic settings and is relevant for researchers and water industry practitioners.}, }
@article {pmid33499970, year = {2020}, author = {van Veelen, HPJ and Falcão Salles, J and Matson, KD and van der Velde, M and Tieleman, BI}, title = {Microbial environment shapes immune function and cloacal microbiota dynamics in zebra finches Taeniopygia guttata.}, journal = {Animal microbiome}, volume = {2}, number = {1}, pages = {21}, pmid = {33499970}, issn = {2524-4671}, support = {Vidi 864.10.012//NWO/ ; }, abstract = {BACKGROUND: The relevance of the host microbiota to host ecology and evolution is well acknowledged. However, the effect of the microbial environment on host immune function and host microbiota dynamics is understudied in terrestrial vertebrates. Using a novel experimental approach centered on the manipulation of the microbial environment of zebra finches Taeniopygia guttata, we carried out a study to investigate effects of the host's microbial environment on: 1) constitutive immune function, 2) the resilience of the host cloacal microbiota; and 3) the degree to which immune function and host microbiota covary in microbial environments that differ in diversity.<br><br>RESULTS: We explored immune indices (hemagglutination, hemolysis, IgY levels and haptoglobin concentration) and host-associated microbiota (diversity and composition) in birds exposed to two experimental microbial environments differing in microbial diversity. According to our expectations, exposure to experimental microbial environments led to differences related to specific antibodies: IgY levels were elevated in the high diversity treatment, whereas we found no effects for the other immune indices. Furthermore, according to predictions, we found significantly increased richness of dominant OTUs for cloacal microbiota of birds of the high diversity compared with the low diversity group. In addition, cloacal microbiota of individual females approached their baseline state sooner in the low diversity environment than females in the high diversity environment. This result supported a direct phenotypically plastic response of host microbiota, and suggests that its resilience depends on environmental microbial diversity. Finally, immune indices and cloacal microbiota composition tend to covary within treatment groups, while at the same time, individuals exhibited consistent differences of immune indices and microbiota characteristics.<br><br>CONCLUSION: We show that microbes in the surroundings of terrestrial vertebrates can influence immune function and host-associated microbiota dynamics over relatively short time scales. We suggest that covariation between immune indices and cloacal microbiota, in addition to large and consistent differences among individuals, provides potential for evolutionary adaptation. Ultimately, our study highlights that linking environmental and host microbiotas may help unravelling immunological variation within and potentially among species, and together these efforts will advance the integration of microbial ecology and ecological immunology.}, }
@article {pmid33499721, year = {2021}, author = {López-Almela, I and Romaní-Pérez, M and Bullich-Vilarrubias, C and Benítez-Páez, A and Gómez Del Pulgar, EM and Francés, R and Liebisch, G and Sanz, Y}, title = {Bacteroides uniformis combined with fiber amplifies metabolic and immune benefits in obese mice.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-20}, pmid = {33499721}, issn = {1949-0984}, mesh = {Adipose Tissue/metabolism ; Animals ; *Bacteroides ; Cecum/metabolism/microbiology ; Diet, High-Fat/adverse effects ; *Dietary Fiber ; Epididymis/metabolism ; Fatty Acids/metabolism ; Gastrointestinal Microbiome ; Inflammation ; Insulin/metabolism ; Interleukins/metabolism ; Intestinal Mucosa/immunology ; Liver/metabolism ; Lymphocytes/metabolism ; Male ; Mice ; Obesity/*diet therapy/etiology/immunology/metabolism ; Signal Transduction ; Thermogenesis ; Weight Gain ; Interleukin-22 ; }, abstract = {Gut microbiota represents a therapeutic target for obesity. We hypothesize that B. uniformis CECT 7771 combined with wheat bran extract (WBE), its preferred carbon source, may exert superior anti-obesity effects. We performed a 17-week intervention in diet-induced obese mice receiving either B. uniformis, WBE, or their combination to identify interactions and independent actions on metabolism and immunity. B. uniformis combined with WBE was the most effective intervention, curbing weight gain and adiposity, while exerting more modest effects separately. The combination restored insulin-dependent metabolic routes in fat and liver, although the bacterium was the primary driver for improving whole-body glucose disposal. Moreover, B. uniformis-combined with WBE caused the highest increases in butyrate and restored the proportion of induced intraepithelial lymphocytes and type-3 innate lymphoid cells in the intestinal epithelium. Thus, strengthening the first line of immune defense against unhealthy diets and associated dysbiosis in the intestine. This intervention also attenuated the altered IL22 signaling and liver inflammation. Our study shows opportunities for employing B. uniformis, combined with WBE, to aid in the treatment of obesity.}, }
@article {pmid33499060, year = {2021}, author = {Patuzzi, I and Orsini, M and Cibin, V and Petrin, S and Mastrorilli, E and Tiengo, A and Gobbo, F and Catania, S and Barco, L and Ricci, A and Losasso, C}, title = {The Interplay between Campylobacter and the Caecal Microbial Community of Commercial Broiler Chickens over Time.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, pmid = {33499060}, issn = {2076-2607}, support = {IZS VE 04/13 RC//Ministero della Salute/ ; }, abstract = {Campylobacter is the most frequent foodborne zoonotic bacteria worldwide, with chicken meat being overwhelmingly the most important reservoir for human infections. Control measures implemented at the farm level (i.e., biosecurity or vaccination), which have been successfully applied to limit other pathogens, such as Salmonella, have not been effective in reducing Campylobacter occurrence. Thus, new approaches are needed to fully understand the ecological interactions of Campylobacter with host animals to effectively comprehend its epidemiology. The objective of this study was to analyse longitudinally the gut microbiota composition of Campylobacter-infected and non-infected farms to identify any difference that could potentially be indicative of gut colonization by Campylobacter spp. Differences in the colonization rate and timing were observed at the farms that became positive for Campylobacter jejuni over the investigated time points, even though in positive tests, the occurrence of Campylobacter jejuni gut colonization was not observed before the second week of the life of the birds. Significant differences were observed in the abundances of specific bacterial taxa between the microbiota of individuals belonging to farms that became Campylobacter positive during the study and those who remained negative with particular reference to Bacteroidales and Clostridiales, respectively. Moreover, Campylobacter colonization dramatically influenced the microbiota richness, although to a different extent depending on the infection timing. Finally, a key role of Faecalibacterium and Lactobacillus genera on the Campylobacter microbial network was observed. Understanding the ecology of the Campylobacter interaction with host microbiota during infection could support novel approaches for broiler microbial barrier restoration. Therefore, evidence obtained through this study can be used to identify options to reduce the incidence of infection at a primary production level based on the targeted influence of the intestinal microbiota, thus helping develop new control strategies in order to mitigate the risk of human exposure to Campylobacter by chicken meat consumption.}, }
@article {pmid33498531, year = {2021}, author = {do Espirito Santo Pereira, A and Caixeta Oliveira, H and Fernandes Fraceto, L and Santaella, C}, title = {Nanotechnology Potential in Seed Priming for Sustainable Agriculture.}, journal = {Nanomaterials (Basel, Switzerland)}, volume = {11}, number = {2}, pages = {}, pmid = {33498531}, issn = {2079-4991}, support = {#88881.191767/2018-01//CAPES-COFECUB/ ; (#88887.363975/2010-00//CAPES-COFECUB/ ; #2017/21004-5//FAPESP/ ; }, abstract = {Our agriculture is threatened by climate change and the depletion of resources and biodiversity. A new agriculture revolution is needed in order to increase the production of crops and ensure the quality and safety of food, in a sustainable way. Nanotechnology can contribute to the sustainability of agriculture. Seed nano-priming is an efficient process that can change seed metabolism and signaling pathways, affecting not only germination and seedling establishment but also the entire plant lifecycle. Studies have shown various benefits of using seed nano-priming, such as improved plant growth and development, increased productivity, and a better nutritional quality of food. Nano-priming modulates biochemical pathways and the balance between reactive oxygen species and plant growth hormones, resulting in the promotion of stress and diseases resistance outcoming in the reduction of pesticides and fertilizers. The present review provides an overview of advances in the field, showing the challenges and possibilities concerning the use of nanotechnology in seed nano-priming, as a contribution to sustainable agricultural practices.}, }
@article {pmid33495891, year = {2021}, author = {Fuentes, E and Prieto, B}, title = {Recovery Capacity of Subaerial Biofilms Grown on Granite Buildings Subjected to Simulated Drought in a Climate Change Context.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {761-769}, pmid = {33495891}, issn = {1432-184X}, support = {BES-2017-079927//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; CGL2016-79778-R//Agencia Estatal de Investigaci&#xf3;n/ ; CGL2016-79778-R//European Regional Development Fund/ ; }, mesh = {Biofilms ; *Climate Change ; *Droughts ; Extracellular Polymeric Substance Matrix ; Silicon Dioxide ; }, abstract = {Variations in environmental conditions in the context of climate change are expected to affect biofilm-associated organisms on granite heritage buildings. The number and duration of drought periods should be considered, as these factors will affect the availability of water for the microorganisms. In this study, mature biofilms were exposed to various drying-rewetting cycles, and the effects of water stress on the SAB and their resilience were evaluated in terms of the variation in microbial composition, extracellular polymeric substance production, and photosynthetic efficiency. The structure of the biofilm changed after exposure to drought, becoming more heterogeneous and with an increase in the carbohydrate to protein ratio, especially after the second day of total drought. YMAX and YEF parameters proved to be the most informative, showing that the photosynthetic efficiency and recovery capacity were inversely related to the duration of the drought period. Furthermore, cyanobacteria resisted drought better than algae, giving rise to a decrease in the algae to cyanobacteria ratio.}, }
@article {pmid33494899, year = {2021}, author = {Hollander, A and Yaron, S}, title = {Pore-forming treatments induce aggregation of Salmonella Senftenberg through protein leakage.}, journal = {Food microbiology}, volume = {96}, number = {}, pages = {103721}, doi = {10.1016/j.fm.2020.103721}, pmid = {33494899}, issn = {1095-9998}, mesh = {Acyclic Monoterpenes/pharmacology ; Bacterial Proteins/*metabolism ; Cell Membrane Permeability/drug effects ; Ocimum ; Ocimum basilicum/chemistry ; Oils, Volatile/*pharmacology ; Plant Oils/*pharmacology ; Salmonella/cytology/*drug effects/metabolism ; }, abstract = {Fresh herbs are not commonly associated with foodborne pathogens, due to the production of essential oils with antimicrobial activity. Recalls of contaminated basil, and basil outbreaks caused by Salmonella motivated studies aimed to comprehend the antimicrobial activity of basil essential oils, and to explore the mechanisms in which Salmonella can overcome them. Linalool, a major constituent of basil oil, increases the permeability of Salmonella Senftenberg cells by damaging their membrane. Linalool also induces bacterial aggregation. We hypothesized that the membrane perforation effect triggers cell aggregation through leakage of intracellular substances from live and dead cells. By exposing S. Senftenberg to additional physical (sonication) or chemical (eugenol, Triton-X-100) treatments, we showed that the aggregation is caused by various membrane-targeted treatments. Enzymatic degradation of leaked proteins restricted the bacterial aggregation, and disassembled existing aggregates. Moreover, supplemented proteins such as bacterial intracellular proteins or BSA also caused aggregation, further supporting the hypothesis that non-specific proteins trigger the bacterial aggregation. This study provides a novel understanding of the role of protein leakage in promoting bacterial aggregation. Since aggregation has significant roles in food safety and microbial ecology, this finding may establish future studies about microbial resistance via formation of clusters similar to biofilm development.}, }
@article {pmid33491139, year = {2021}, author = {Parada-Pinilla, MP and Ferreira, MA and Roncallo, JC and Santos, SN and Melo, IS and Assef, ANB and Wilke, DV and Silva, LF and Garrido, LM and Araújo, WL and Padilla, G}, title = {Biopolymer production by halotolerant bacteria isolated from Caatinga biome.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {52}, number = {2}, pages = {547-559}, pmid = {33491139}, issn = {1678-4405}, support = {2009/52665-4; 2010/51458-9//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Biopolymers/*metabolism ; Brazil ; Phylogeny ; Polyhydroxyalkanoates/metabolism ; Polysaccharides, Bacterial/metabolism ; Sodium Chloride/analysis/*metabolism ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Saline environments are extreme habitats with a high diversity of microorganisms source of a myriad of biomolecules. These microorganisms are assigned as extremophiles recognized to be producers of new natural compounds, which can be synthesized by helping to survive under harshness and extreme conditions. In Brazil, in the saline and semi-arid region of Areia Branca (Caatinga biome), halotolerant bacteria (able to growth at high NaCl concentrations) were isolated from rhizosphere of native plants Blutaparon portulacoides and Spergularia sp. and their biopolymer production was studied. A total of 25 bacterial isolates were identified at genus level based on 16S rRNA gene sequence analysis. Isolates were mainly Gram-positive bacteria from Bacillaceae, Staphylococcaceae, Microbacteriaceae, and Bacillales XII incertae sedis families, affiliates to Bacillus, Staphylococcus, Curtobacterium, and Exiguobacterium genera, respectively. One of the Gram-negative isolates was identified as member of the Pseudomonadaceae family, genus Pseudomonas. All the identified strains were halotolerant bacteria with optimum growth at 0.6-2.0 M salt concentrations. Assays for biopolymer production showed that the halotolerant strains are a rich source of compounds as polyhydroxyalkanoates (PHA), biodegradable biopolymer, such as poly(3-hydroxybutyrate) (PHB) produced from low-cost substrates, and exopolysaccharides (EPS), such as hyaluronic acid (HA), metabolite of great interest to the cosmetic and pharmaceutical industry. Also, eight bacterial EPS extracts showed immunostimulatory activity, promising results that can be used in biomedical applications. Overall, our findings demonstrate that these biomolecules can be produced in culture medium with 0.6-2.0 M NaCl concentrations, relevant feature to avoid costly production processes. This is the first report of biopolymer-producing bacteria from a saline region of Caatinga biome that showed important biological activities.}, }
@article {pmid33490051, year = {2020}, author = {Shahsavari, E and Rouch, D and Khudur, LS and Thomas, D and Aburto-Medina, A and Ball, AS}, title = {Challenges and Current Status of the Biological Treatment of PFAS-Contaminated Soils.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {8}, number = {}, pages = {602040}, pmid = {33490051}, issn = {2296-4185}, abstract = {Per- and polyfluoroalkyl substances (PFAS) are Synthetic Organic Compounds (SOCs) which are of current concern as they are linked to a myriad of adverse health effects in mammals. They can be found in drinking water, rivers, groundwater, wastewater, household dust, and soils. In this review, the current challenge and status of bioremediation of PFAs in soils was examined. While several technologies to remove PFAS from soil have been developed, including adsorption, filtration, thermal treatment, chemical oxidation/reduction and soil washing, these methods are expensive, impractical for in situ treatment, use high pressures and temperatures, with most resulting in toxic waste. Biodegradation has the potential to form the basis of a cost-effective, large scale in situ remediation strategy for PFAS removal from soils. Both fungal and bacterial strains have been isolated that are capable of degrading PFAS; however, to date, information regarding the mechanisms of degradation of PFAS is limited. Through the application of new technologies in microbial ecology, such as stable isotope probing, metagenomics, transcriptomics, and metabolomics there is the potential to examine and identify the biodegradation of PFAS, a process which will underpin the development of any robust PFAS bioremediation technology.}, }
@article {pmid33489789, year = {2021}, author = {Macchi, M and Festa, S and Nieto, E and Irazoqui, JM and Vega-Vela, NE and Junca, H and Valacco, MP and Amadio, AF and Morelli, IS and Coppotelli, BM}, title = {Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics.}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {29}, number = {}, pages = {e00588}, pmid = {33489789}, issn = {2215-017X}, abstract = {Two synthetic bacterial consortia (SC) composed of bacterial strains Sphingobium sp. (AM), Klebsiella aerogenes (B), Pseudomonas sp. (Bc-h and T), Burkholderia sp. (Bk) and Inquilinus limosus (Inq) isolated from a natural phenanthrene (PHN)-degrading consortium (CON) were developed and evaluated as an alternative approach to PHN biodegradation in bioremediation processes. A metabolic network showing the potential role of strains was reconstructed by in silico study of the six genomes and classification of dioxygenase enzymes using RHObase and AromaDeg databases. Network analysis suggested that AM and Bk were responsible for PHN initial attack, while Inq, B, T and Bc-h would degrade PHN metabolites. The predicted roles were further confirmed by physiological, RT-qPCR and metaproteomic assays. SC-1 with AM as the sole PHN degrader was the most efficient. The ecological roles inferred in this study can be applied to optimize the design of bacterial consortia and tackle the biodegradation of complex environmental pollutants.}, }
@article {pmid33484740, year = {2021}, author = {Costa, OYA and Kuramae, EE}, title = {The influence of agar brands and micronutrients in the growth optimization of Granulicella sp. (Acidobacteriota).}, journal = {Journal of microbiological methods}, volume = {181}, number = {}, pages = {106148}, doi = {10.1016/j.mimet.2021.106148}, pmid = {33484740}, issn = {1872-8359}, mesh = {Acidobacteria/*growth &amp; development ; Agar/metabolism ; *Culture Media/chemistry/metabolism ; Micronutrients/*metabolism ; }, abstract = {Acidobacteriota are highly abundant in soils, however, few cultured representatives are available. The purity of the reagents can influence microbial growth in laboratory conditions and successful isolation. Here we investigated the impact of different agar brands in culture medium and advocate that agar origin should be carefully considered for Acidobacteriota strains growth and microbial isolation.}, }
@article {pmid33483845, year = {2021}, author = {Romero-Olivares, AL and Morrison, EW and Pringle, A and Frey, SD}, title = {Linking Genes to Traits in Fungi.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {145-155}, pmid = {33483845}, issn = {1432-184X}, support = {Hatch 1016142//Agricultural Research Service/ ; Diversity &amp; Innovation Scholars program//University of New Hampshire/ ; }, mesh = {*Ecosystem ; Fungi/genetics ; *Mycorrhizae ; Nitrogen ; Soil ; Soil Microbiology ; }, abstract = {Fungi are mediators of the nitrogen and carbon cycles in terrestrial ecosystems. Examining how nitrogen uptake and organic matter decomposition potential differs in fungi can provide insight into the underlying mechanisms driving fungal ecological processes and ecosystem functioning. In this study, we assessed the frequency of genes encoding for specific enzymes that facilitate nitrogen uptake and organic matter decomposition in 879 fungal genomes with fungal taxa grouped into trait-based categories. Our linked gene-trait data approach revealed that gene frequencies vary across and within trait-based groups and that trait-based categories differ in trait space. We present two examples of how this linked gene-trait approach can be used to address ecological questions. First, we show that this type of approach can help us better understand, and potentially predict, how fungi will respond to environmental stress. Specifically, we found that trait-based categories with high nitrogen uptake gene frequency increased in relative abundance when exposed to high soil nitrogen enrichment. Second, by comparing frequencies of nitrogen uptake and organic matter decomposition genes, we found that most ectomycorrhizal fungi in our dataset have similar gene frequencies to brown rot fungi. This demonstrates that gene-trait data approaches can shed light on potential evolutionary trajectories of life history traits in fungi. We present a framework for exploring nitrogen uptake and organic matter decomposition gene frequencies in fungal trait-based groups and provide two concise examples on how to use our framework to address ecological questions from a mechanistic perspective.}, }
@article {pmid33482922, year = {2021}, author = {Okazaki, Y and Fujinaga, S and Salcher, MM and Callieri, C and Tanaka, A and Kohzu, A and Oyagi, H and Tamaki, H and Nakano, SI}, title = {Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {24}, pmid = {33482922}, issn = {2049-2618}, mesh = {Aquatic Organisms/classification/genetics/isolation &amp; purification ; *Biodiversity ; Europe ; *Fresh Water ; Japan ; Phylogeny ; *Phylogeography ; Plankton/classification/*genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe.<br><br>RESULTS: Our single nucleotide-resolved analysis, which was validated using shotgun metagenomic sequencing, uncovered 7-101 amplicon sequence variants for each of the 11 predominant bacterial lineages and demonstrated sympatric, allopatric, and temporal microdiversities that could not be resolved through conventional approaches. Clusters of samples with similar intra-lineage population compositions were identified, which consistently supported genetic isolation between Japan and Europe. At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors or genetic drift were potential determinants of population composition. The extent of microdiversification varied among lineages, suggesting that highly diversified lineages (e.g., Iluma-A2 and acI-A1) achieve their ubiquity by containing a consortium of genotypes specific to each habitat, while less diversified lineages (e.g., CL500-11) may be ubiquitous due to a small number of widespread genotypes. The lowest extent of intra-lineage diversification was observed among the dominant hypolimnion-specific lineage (CL500-11), suggesting that their dispersal among lakes is not limited despite the hypolimnion being a more isolated habitat than the epilimnion.<br><br>CONCLUSIONS: Our novel approach complemented the limited resolution of short-read amplicon sequencing and limited sensitivity of the metagenome assembly-based approach, and highlighted the complex ecological processes underlying the ubiquity of freshwater bacterioplankton lineages. To fully exploit the performance of the method, its relatively low read throughput is the major bottleneck to be overcome in the future. Video abstract.}, }
@article {pmid33482213, year = {2021}, author = {Vinothkanna, A and Sathiyanarayanan, G and Balaji, P and Mathivanan, K and Pugazhendhi, A and Ma, Y and Sekar, S and Thirumurugan, R}, title = {Structural characterization, functional and biological activities of an exopolysaccharide produced by probiotic Bacillus licheniformis AG-06 from Indian polyherbal fermented traditional medicine.}, journal = {International journal of biological macromolecules}, volume = {174}, number = {}, pages = {144-152}, doi = {10.1016/j.ijbiomac.2021.01.117}, pmid = {33482213}, issn = {1879-0003}, mesh = {A549 Cells ; Antineoplastic Agents/pharmacology ; Antioxidants/chemistry/pharmacology ; Bacillus licheniformis/*metabolism ; Chromatography, High Pressure Liquid/methods ; Fermentation/physiology ; Free Radicals ; Humans ; Magnetic Resonance Spectroscopy/methods ; Medicine, Traditional/methods ; Polysaccharides, Bacterial/*chemistry/isolation &amp; purification/*metabolism ; Probiotics/metabolism ; Spectroscopy, Fourier Transform Infrared/methods ; }, abstract = {An exopolysaccharide (EPS) was purified from the probiotic bacterium Bacillus licheniformis AG-06 isolated from the polyherbal fermented traditional medicine (Ashwagandharishta) of Indian Ayurveda. High-performance liquid chromatography (HPLC) based compositional analysis exhibits the heteropolymeric nature of the EPS consisting of galactose, rhamnose, xylose, mannose, and glucose, as the monomeric units. Fourier-transform infrared (FT-IR) and nuclear magnetic resonance (NMR) spectroscopic analyses confirm the presence of typical carbohydrate polymer functional groups and structural units, respectively. The purified EPS demonstrates the web-like fibrous and porous nature in scanning electron microscopic and atomic force microscopic studies. The purified EPS had shown 71.83% and 67.79% of flocculation and emulsification activities, respectively. Antioxidant activity was evaluated against 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), nitric oxide, and superoxide free radicals and the scavenging actions were increased in a dose-dependent manner. Moreover, the purified EPS exhibits a significant cytotoxic activity against the human lung carcinoma cells (A549), which strongly suggests the anticancer potential of the EPS derived from B. licheniformis AG-06.}, }
@article {pmid33480992, year = {2021}, author = {Baunach, M and Chowdhury, S and Stallforth, P and Dittmann, E}, title = {The Landscape of Recombination Events That Create Nonribosomal Peptide Diversity.}, journal = {Molecular biology and evolution}, volume = {38}, number = {5}, pages = {2116-2130}, pmid = {33480992}, issn = {1537-1719}, mesh = {*Evolution, Molecular ; *Models, Genetic ; Multigene Family ; Peptide Biosynthesis, Nucleic Acid-Independent/*genetics ; Peptide Synthases/*genetics ; *Recombination, Genetic ; }, abstract = {Nonribosomal peptides (NRP) are crucial molecular mediators in microbial ecology and provide indispensable drugs. Nevertheless, the evolution of the flexible biosynthetic machineries that correlates with the stunning structural diversity of NRPs is poorly understood. Here, we show that recombination is a key driver in the evolution of bacterial NRP synthetase (NRPS) genes across distant bacterial phyla, which has guided structural diversification in a plethora of NRP families by extensive mixing and matching of biosynthesis genes. The systematic dissection of a large number of individual recombination events did not only unveil a striking plurality in the nature and origin of the exchange units but allowed the deduction of overarching principles that enable the efficient exchange of adenylation (A) domain substrates while keeping the functionality of the dynamic multienzyme complexes. In the majority of cases, recombination events have targeted variable portions of the Acore domains, yet domain interfaces and the flexible Asub domain remained untapped. Our results strongly contradict the widespread assumption that adenylation and condensation (C) domains coevolve and significantly challenge the attributed role of C domains as stringent selectivity filter during NRP synthesis. Moreover, they teach valuable lessons on the choice of natural exchange units in the evolution of NRPS diversity, which may guide future engineering approaches.}, }
@article {pmid33477842, year = {2021}, author = {Ruiz-Roldán, L and de Toro, M and Sáenz, Y}, title = {Whole Genome Analysis of Environmental Pseudomonas mendocina Strains: Virulence Mechanisms and Phylogeny.}, journal = {Genes}, volume = {12}, number = {1}, pages = {}, pmid = {33477842}, issn = {2073-4425}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacterial Proteins/genetics ; Drug Resistance, Microbial/genetics ; Ducks/microbiology ; Endocarditis/drug therapy/*microbiology ; Endodeoxyribonucleases/genetics ; Feces/microbiology ; Food Microbiology ; *Genome, Bacterial ; Humans ; Lactuca/microbiology ; Phylogeny ; Pseudomonas mendocina/genetics/*pathogenicity ; Sepsis/drug therapy/*microbiology ; Virulence Factors/*genetics ; Whole Genome Sequencing ; }, abstract = {Pseudomonas mendocina is an environmental bacterium, rarely isolated in clinical specimens, although it has been described as producing endocarditis and sepsis. Little is known about its genome. Whole genome sequencing can be used to learn about the phylogeny, evolution, or pathogenicity of these isolates. Thus, the aim of this study was to analyze the resistome, virulome, and phylogenetic relationship of two P. mendocina strains, Ps542 and Ps799, isolated from a healthy Anas platyrhynchos fecal sample and a lettuce, respectively. Among all of the small number of P.mendocina genomes available in the National Center for Biotechnology Information (NCBI) repository, both strains were placed within one of two well-defined phylogenetic clusters. Both P. mendocina strains lacked antimicrobial resistance genes, but the Ps799 genome showed a MOBP3 family relaxase. Nevertheless, this study revealed that P. mendocina possesses an important number of virulence factors, including a leukotoxin, flagella, pili, and the Type 2 and Type 6 Secretion Systems, that could be responsible for their pathogenesis. More phenotypical and in vivo studies are needed to deepen the association with human infections and the potential P. mendocina pathogenicity.}, }
@article {pmid33477775, year = {2021}, author = {Zerva, I and Remmas, N and Kagalou, I and Melidis, P and Ariantsi, M and Sylaios, G and Ntougias, S}, title = {Effect of Chlorination on Microbiological Quality of Effluent of a Full-Scale Wastewater Treatment Plant.}, journal = {Life (Basel, Switzerland)}, volume = {11}, number = {1}, pages = {}, pmid = {33477775}, issn = {2075-1729}, abstract = {The evaluation of effluent wastewater quality mainly relies on the assessment of conventional bacterial indicators, such as fecal coliforms and enterococci; however, little is known about opportunistic pathogens, which can resist chlorination and may be transmitted in aquatic environments. In contrast to conventional microbiological methods, high-throughput molecular techniques can provide an accurate evaluation of effluent quality, although a limited number of studies have been performed in this direction. In this work, high-throughput amplicon sequencing was employed to assess the effectiveness of chlorination as a disinfection method for secondary effluents. Common inhabitants of the intestinal tract, such as Bacteroides, Arcobacter and Clostridium, and activated sludge denitrifiers capable of forming biofilms, such as Acidovorax, Pseudomonas and Thauera, were identified in the chlorinated effluent. Chloroflexi with dechlorination capability and the bacteria involved in enhanced biological phosphorus removal, i.e., Candidatus Accumulibacter and Candidatus Competibacter, were also found to resist chlorination. No detection of Escherichia indicates the lack of fecal coliform contamination. Mycobacterium spp. were absent in the chlorinated effluent, whereas toxin-producing cyanobacteria of the genera Anabaena and Microcystis were identified in low abundances. Chlorination significantly affected the filamentous bacteria Nocardioides and Gordonia, whereas Zoogloea proliferated in the disinfected effluent. Moreover, perchlorate/chlorate- and organochlorine-reducing bacteria resisted chlorination.}, }
@article {pmid33476328, year = {2021}, author = {Mariani, N and Borsini, A and Cecil, CAM and Felix, JF and Sebert, S and Cattaneo, A and Walton, E and Milaneschi, Y and Cochrane, G and Amid, C and Rajan, J and Giacobbe, J and Sanz, Y and Agustí, A and Sorg, T and Herault, Y and Miettunen, J and Parmar, P and Cattane, N and Jaddoe, V and Lötjönen, J and Buisan, C and González Ballester, MA and Piella, G and Gelpi, JL and Lamers, F and Penninx, BWJH and Tiemeier, H and von Tottleben, M and Thiel, R and Heil, KF and Järvelin, MR and Pariante, C and Mansuy, IM and Lekadir, K}, title = {Identifying causative mechanisms linking early-life stress to psycho-cardio-metabolic multi-morbidity: The EarlyCause project.}, journal = {PloS one}, volume = {16}, number = {1}, pages = {e0245475}, pmid = {33476328}, issn = {1932-6203}, support = {G108/603/MRC_/Medical Research Council/United Kingdom ; MR/N029488/1/MRC_/Medical Research Council/United Kingdom ; MR/S019669/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Adverse Childhood Experiences/psychology ; Biomarkers/metabolism ; Cardiovascular Diseases/*epidemiology/*etiology/metabolism/psychology ; Child ; Depression/*epidemiology/*etiology/metabolism/psychology ; Diabetes Mellitus/*epidemiology/*etiology/metabolism/psychology ; Environment ; Humans ; Longitudinal Studies ; Morbidity ; Risk Factors ; Stress, Psychological/*complications ; }, abstract = {INTRODUCTION: Depression, cardiovascular diseases and diabetes are among the major non-communicable diseases, leading to significant disability and mortality worldwide. These diseases may share environmental and genetic determinants associated with multimorbid patterns. Stressful early-life events are among the primary factors associated with the development of mental and physical diseases. However, possible causative mechanisms linking early life stress (ELS) with psycho-cardio-metabolic (PCM) multi-morbidity are not well understood. This prevents a full understanding of causal pathways towards the shared risk of these diseases and the development of coordinated preventive and therapeutic interventions.<br><br>METHODS AND ANALYSIS: This paper describes the study protocol for EarlyCause, a large-scale and inter-disciplinary research project funded by the European Union's Horizon 2020 research and innovation programme. The project takes advantage of human longitudinal birth cohort data, animal studies and cellular models to test the hypothesis of shared mechanisms and molecular pathways by which ELS shapes an individual's physical and mental health in adulthood. The study will research in detail how ELS converts into biological signals embedded simultaneously or sequentially in the brain, the cardiovascular and metabolic systems. The research will mainly focus on four biological processes including possible alterations of the epigenome, neuroendocrine system, inflammatome, and the gut microbiome. Life-course models will integrate the role of modifying factors as sex, socioeconomics, and lifestyle with the goal to better identify groups at risk as well as inform promising strategies to reverse the possible mechanisms and/or reduce the impact of ELS on multi-morbidity development in high-risk individuals. These strategies will help better manage the impact of multi-morbidity on human health and the associated risk.}, }
@article {pmid33471175, year = {2021}, author = {Fernandes, NM and Campello-Nunes, PH and Paiva, TS and Soares, CAG and Silva-Neto, ID}, title = {Correction to: Ciliate Diversity From Aquatic Environments in the Brazilian Atlantic Forest as Revealed by High-Throughput DNA Sequencing.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {644}, doi = {10.1007/s00248-021-01691-1}, pmid = {33471175}, issn = {1432-184X}, }
@article {pmid33471174, year = {2021}, author = {Borruso, L and Checcucci, A and Torti, V and Correa, F and Sandri, C and Luise, D and Cavani, L and Modesto, M and Spiezio, C and Mimmo, T and Cesco, S and Di Vito, M and Bugli, F and Randrianarison, RM and Gamba, M and Rarojoson, NJ and Zaborra, CA and Mattarelli, P and Trevisi, P and Giacoma, C}, title = {I Like the Way You Eat It: Lemur (Indri indri) Gut Mycobiome and Geophagy.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {215-223}, pmid = {33471174}, issn = {1432-184X}, mesh = {Animals ; Ecosystem ; *Indriidae ; *Lemur ; *Mycobiome ; Pica ; Soil Microbiology ; }, abstract = {Here, we investigated the possible linkages among geophagy, soil characteristics, and gut mycobiome of indri (Indri indri), an endangered lemur species able to survive only in wild conditions. The soil eaten by indri resulted in enriched secondary oxide-hydroxides and clays, together with a high concentration of specific essential micronutrients. This could partially explain the role of the soil in detoxification and as a nutrient supply. Besides, we found that soil subject to geophagy and indris' faeces shared about 8.9% of the fungal OTUs. Also, several genera (e.g. Fusarium, Aspergillus and Penicillium) commonly associated with soil and plant material were found in both geophagic soil and indri samples. On the contrary, some taxa with pathogenic potentials, such as Cryptococcus, were only found in indri samples. Further, many saprotrophs and plant-associated fungal taxa were detected in the indri faeces. These fungal species may be involved in the digestion processes of leaves and could have a beneficial role in their health. In conclusion, we found an intimate connection between gut mycobiome and soil, highlighting, once again, the potential consequent impacts on the wider habitat.}, }
@article {pmid33469721, year = {2021}, author = {Kim, MS and Kim, KH and Hwang, SJ and Lee, TK}, title = {Role of Algal Community Stability in Harmful Algal Blooms in River-Connected Lakes.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {309-318}, pmid = {33469721}, issn = {1432-184X}, mesh = {Ecosystem ; *Harmful Algal Bloom ; Lakes ; *Microcystis ; Rivers ; }, abstract = {Harmful algal blooms (HABs) in freshwater produce toxins that pose a threat to public health and aquatic ecosystems. Although algal communities have been studied globally to understand the characteristics of HABs, the occurrence of toxic cyanobacteria in freshwater ecosystems is rarely understood. Unlike abiotic factors, the effects of biotic factors (e.g., interaction, dominance, and variability) on the occurrence of toxic cyanobacteria were overlooked due to the intricate interaction of microorganisms under different environmental conditions. To address this problem, a comprehensive ecological concept stability, which encompasses variations in species or communities due to changing biological interactions or environmental fluctuations, was applied in this study. The algal communities in six river-connected lakes in the North Han River, South Korea, were classified into high and low stability groups. The algal species belonging to diatoms and green algae groups played a major role in the interaction within the algal community in highly stable lakes, but the frequency of Microcystis led the interaction within the algal community at the center of the network in low-stability lakes. These results indicate that the interaction within the cluster is easily changed by Microcystis, where the abundance explosively increases in lakes with low algal community stability. Water quality is more strongly associated with the occurrence of toxic cyanobacteria (Microcystis and Dolichospermum). In low-stability lakes, more diverse water quality indicators are correlated with the development of toxic algae than in high-stability lakes. This paper is the first report on the importance of algal community stability in freshwater in the occurrence of toxic cyanobacteria and offers a new perspective on Microcystis monitoring and management.}, }
@article {pmid33468708, year = {2021}, author = {Fu, S and Yang, Q and Wang, Q and Pang, B and Lan, R and Wei, D and Qu, B and Liu, Y}, title = {Continuous Genomic Surveillance Monitored the In Vivo Evolutionary Trajectories of Vibrio parahaemolyticus and Identified a New Virulent Genotype.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33468708}, issn = {2379-5077}, abstract = {Our ability to predict evolutionary trajectories of pathogens is one of the promising leverages to fight against the pandemic disease, yet few studies have addressed this question in situ, due to the difficulty in monitoring the milestone evolutionary events for a given pathogen and in understanding the evolutionary strategies. In this study, we monitored the real-time evolution of Vibrio parahaemolyticus in response to successive antibiotic treatment in three shrimp farms in North China from 2011 to 2018 by whole-genome sequencing. Results showed that the stepwise emergence of resistance was associated with the antibiotic usage. Genomic analysis of resistant isolates showed that the acquisition of the resistant mobile genetic elements flanked by an insertion sequence (ISVal1) closely mirrored the antibiotics used in shrimp farms since 2014. Next, we also identified 50 insertion sites of ISVal1 in the chromosome, which facilitated the formation of pathogenicity islands (PAIs) and fitness islands in the following years. Further, horizontal transfers of a virulent trh-nik-ure genomic island (GI) and two GIs improving the fitness have been observed in two farms since 2016. In this case study, we proposed that the insertion sequence triggered four major evolutionary events during the outbreaks of shrimp disease in three farms, including horizontal transfer of transposon (HTT) (stage 1), the formation of resistance islands (stage 2) and the PAIs (stage 3), and horizontal transfer of the PAIs (stage 4). This study presented the first in vivo evolutionary trajectories for a given bacterial pathogen, which helps us to understand the emergence mechanisms of new genotypes.IMPORTANCE Most human infectious diseases originate from animals. Thus, how to reduce or prevent pandemic zoonoses before they emerge in people is becoming a critical issue. Continuous genomic surveillance of the evolutionary trajectories of potential human pathogens on farms is a promising strategy to realize early warning. Here, we conducted an 8-year surveillance of Vibrio parahaemolyticus in three shrimp farms. The results showed that the use of antibiotics and horizontal transfer of transposons (HTT) drove the evolution of V. parahaemolyticus, which could be divided into four stages: HTT, formation of resistance islands, formation of pathogenicity islands (PAIs), and horizontal transfer of PAIs. This study presented the first in vivo monitoring of evolutionary trajectories for a given bacterial pathogen, providing valuable information for the prevention of pandemic zoonoses.}, }
@article {pmid33468704, year = {2021}, author = {Rubbens, P and Props, R}, title = {Computational Analysis of Microbial Flow Cytometry Data.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33468704}, issn = {2379-5077}, abstract = {Flow cytometry is an important technology for the study of microbial communities. It grants the ability to rapidly generate phenotypic single-cell data that are both quantitative, multivariate and of high temporal resolution. The complexity and amount of data necessitate an objective and streamlined data processing workflow that extends beyond commercial instrument software. No full overview of the necessary steps regarding the computational analysis of microbial flow cytometry data currently exists. In this review, we provide an overview of the full data analysis pipeline, ranging from measurement to data interpretation, tailored toward studies in microbial ecology. At every step, we highlight computational methods that are potentially useful, for which we provide a short nontechnical description. We place this overview in the context of a number of open challenges to the field and offer further motivation for the use of standardized flow cytometry in microbial ecology research.}, }
@article {pmid33468585, year = {2021}, author = {Swaney, MH and Kalan, LR}, title = {Living in Your Skin: Microbes, Molecules, and Mechanisms.}, journal = {Infection and immunity}, volume = {89}, number = {4}, pages = {}, pmid = {33468585}, issn = {1098-5522}, support = {R35 GM137828/GM/NIGMS NIH HHS/United States ; T32 AI055397/AI/NIAID NIH HHS/United States ; }, mesh = {*Biomarkers ; Cell Communication ; Energy Metabolism ; Homeostasis ; Host-Pathogen Interactions ; Humans ; Immune System/immunology/metabolism ; *Microbiota ; Organ Specificity ; Skin/*microbiology ; *Skin Physiological Phenomena ; Wound Healing ; }, abstract = {Human skin functions as a physical, chemical, and immune barrier against the external environment while also providing a protective niche for its resident microbiota, known as the skin microbiome. Cooperation between the microbiota, host skin cells, and the immune system is responsible for maintenance of skin health, and a disruption to this delicate balance, such as by pathogen invasion or a breach in the skin barrier, may lead to impaired skin function. In this minireview, we describe the role of the microbiome in microbe, host, and immune interactions under distinct skin states, including homeostasis, tissue repair, and wound infection. Furthermore, we highlight the growing number of diverse microbial metabolites and products that have been identified to mediate these interactions, particularly those involved in host-microbe communication and defensive symbiosis. We also address the contextual pathogenicity exhibited by many skin commensals and provide insight into future directions in the skin microbiome field.}, }
@article {pmid33467504, year = {2021}, author = {Chang, J and Shi, S and Tian, L and Leite, MFA and Chang, C and Ji, L and Ma, L and Tian, C and Kuramae, EE}, title = {Self-Crossing Leads to Weak Co-Variation of the Bacterial and Fungal Communities in the Rice Rhizosphere.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, pmid = {33467504}, issn = {2076-2607}, support = {41920104008//the National Natural Science Foundation of China/ ; 2016YFC0501202//the National Key Research and Development Program of China/ ; XDA23070501//the Science Foundation of Chinese Academy of Sciences/ ; 2019SYHZ0039//the Cooperative Project between CAS and Jilin Province of China/ ; 20190303070SF//the Science and Technology Development Project of Jilin Province of China/ ; }, abstract = {The rhizomicrobial community is influenced by plant genotype. However, the potential differences in the co-assembly of bacterial and fungal communities between parental lines and different generations of rice progenies have not been examined. Here we compared the bacterial and fungal communities in the rhizomicrobiomes of female parent Oryza rufipogon wild rice; male parent Oryza sativa cultivated rice; their F1 progeny; and the F2, F3 and F4 self-crossing generations. Our results showed that the bacterial and fungal α-diversities of the hybrid F1 and self-crossing generations (F2, F3, F4) were closer to one of the two parental lines, which may indicate a role of the parental line in the diversity of the rhizosphere microbial community assembly. Self-crossing from F1 to F4 led to weak co-variation of the bacterial and fungal communities and distinct rhizosphere microbiomes. In the parental and self-crossing progenies, the reduction of community dissimilarity was higher for the fungal community than for the bacterial community.}, }
@article {pmid33462700, year = {2021}, author = {Moroenyane, I and Mendes, L and Tremblay, J and Tripathi, B and Yergeau, &#xc9;}, title = {Plant Compartments and Developmental Stages Modulate the Balance between Niche-Based and Neutral Processes in Soybean Microbiome.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {416-428}, pmid = {33462700}, issn = {1432-184X}, support = {RGPIN 2014-05274//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Bacteria/genetics ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Glycine max ; }, abstract = {Understanding the dynamics of plant-associated microbial communities within agriculture is well documented. However, the ecological processes that assemble the plant microbiome are not well understood. This study elucidates the relative dominance of assembly processes across plant compartments (root, stem, and leaves) and developmental stages (emergence, growth, flowering, and maturation). Bacterial community composition and assembly processes were assessed using 16S rRNA gene amplicon sequencing. Null models that couple phylogenetic community composition and species distribution models were used to evaluate ecological assembly processes of bacterial communities. All models highlighted that the balance between the assembly process was modulated by compartments and developmental stages. Dispersal limitation dominated amongst the epiphytic communities and at the maturation stage. Homogeneous selection dominated assembly across plant compartments and development stages. Overall, both sets of models were mostly in agreement in predicting the prevailing assembly processes. Our results show, for the first time, that even though niche-based processes dominate in the plant environment, the relative influence of dispersal limitation in community assembly is important.}, }
@article {pmid33461083, year = {2021}, author = {Xiao, R and Ni, BJ and Liu, S and Lu, H}, title = {Impacts of organics on the microbial ecology of wastewater anammox processes: Recent advances and meta-analysis.}, journal = {Water research}, volume = {191}, number = {}, pages = {116817}, doi = {10.1016/j.watres.2021.116817}, pmid = {33461083}, issn = {1879-2448}, mesh = {*Ammonium Compounds ; Anaerobiosis ; Bioreactors ; Denitrification ; Nitrogen ; Oxidation-Reduction ; *Wastewater ; }, abstract = {Anaerobic ammonium oxidation (anammox) represents a promising technology for wastewater nitrogen removal. Organics management is critical to achieving efficient and stable performance of anammox or integrated processes, e.g., denitratation-anammox. The aim of this systematic review is to synthesize the state-of-the-art knowledge on the multifaceted impacts of organics on wastewater anammox community structure and function. Both exogenous and endogenous organics are discussed with respect to their effects on the biofilm/granule structure and function, as well as the interactions between anammox bacteria (AnAOB) and a broad range of coexisting functional groups. A global core community consisting of 19 taxa is identified and a co-occurrence network is constructed by meta-analysis on the 16S rDNA sequences of 149 wastewater anammox samples. Correlations between core taxa, keystone taxa, and environmental factors, including COD, nitrogen loading rate (NLR) and C/N ratio are obtained. This review provides a holistic understanding of the microbial responses to different origins and types of organics in wastewater anammox reactors, which will facilitate the design and operation of more efficient anammox-based wastewater nitrogen removal process.}, }
@article {pmid33459836, year = {2021}, author = {Arias, A and Selander, E and Saiz, E and Calbet, A}, title = {Predator Chemical Cue Effects on the Diel Feeding Behaviour of Marine Protists.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {356-364}, pmid = {33459836}, issn = {1432-184X}, support = {BES-2015-074092//MICINN/ ; }, mesh = {Animals ; *Ciliophora ; Cues ; *Dinoflagellida ; Feeding Behavior ; Predatory Behavior ; }, abstract = {We have assessed the effect of copepod chemical cues on the diel feeding rhythms of heterotrophic and mixotrophic marine protists. All phagotrophic protists studied exhibited relatively high diurnal feeding rates. The magnitude of the diel feeding rhythm, expressed as the quotient of day and night ingestion rates, was inversely related to the time that phagotrophic protists were maintained in the laboratory in an environment without predators. In the case of the recently isolated ciliate Strombidium arenicola, the rhythm was lost after a few months. When challenged with chemical alarm signals (copepodamides) from the copepod Calanus finmarchicus at realistic concentrations (0.6-6 pM), S. arenicola partially re-established diurnal feeding. Conversely, the amplitude of the diel feeding rhythm for the ciliate Mesodinium rubrum was not affected by copepodamides, although the 24-h integrated food intake increased by approximately 23%. For the dinoflagellates Gyrodinium dominans and Karlodinium armiger, copepodamides significantly reduced the amplitude of their diel feeding rhythms; significant positive effects on total daily ingestion were only observed in G. dominans. Finally, the dinoflagellate Oxyrrhis marina, isolated >20 years ago, showed inconsistent responses to copepodamides, except for an average 6% increase in its total ingestion over 24 h. Our results demonstrate that the predation risk by copepods affects the diel feeding rhythm of marine protists and suggests a species-specific response to predation threats.}, }
@article {pmid33997168, year = {2021}, author = {Rai, SN and Qian, C and Pan, J and Rai, JP and Song, M and Bagaitkar, J and Merchant, M and Cave, M and Egilmez, NK and McClain, CJ}, title = {Microbiome data analysis with applications to pre-clinical studies using QIIME2: Statistical considerations.}, journal = {Genes &amp; diseases}, volume = {8}, number = {2}, pages = {215-223}, pmid = {33997168}, issn = {2352-3042}, abstract = {Diversity analysis and taxonomic profiles can be generated from marker-gene sequence data with the help of many available computational tools. The Quantitative Insights into Microbial Ecology Version 2 (QIIME2) has been widely used for 16S rRNA data analysis. While many articles have demonstrated the use of QIIME2 with suitable datasets, the application to pre-clinical data has rarely been talked about. The issues involved in the pre-clinical data include the low-quality score and small sample size that should be addressed properly during analysis. In addition, there are few articles that discuss the detailed statistical methods behind those alpha and beta diversity significance tests that researchers are eager to find. Running the program without knowing the logic behind it is extremely risky. In this article, we first provide a guideline for analyzing 16S rRNA data using QIIME2. Then we will talk about issues in pre-clinical data, and how they could impact the outcome. Finally, we provide brief explanations of statistical methods such as group significance tests and sample size calculation.}, }
@article {pmid33654882, year = {2019}, author = {Chaudhary, DK and Kim, J}, title = {Experimental Setup for a Diffusion Bioreactor to Isolate Unculturable Soil Bacteria.}, journal = {Bio-protocol}, volume = {9}, number = {19}, pages = {e3388}, pmid = {33654882}, issn = {2331-8325}, abstract = {Unculturable bacteria are those bacteria which proliferate in their native habitat but unable to grow or thrive in the normal laboratory media and conditions. The molecular techniques have revealed the significance of these uncultured bacteria in terms of their functional diversity and potential to produce secondary metabolites. To achieve these benefits, scientists have attempted to isolate and cultivate unculturable bacteria in the laboratory using transwell plates, optical tweezers, laser microdissection, microbioreactors, and diffusions bioreactors. However, these techniques are still inadequate to resolve the difficulties of cultivating unculturable bacteria. Therefore, it is essential to develop new cultivation method that enables growth of diverse range of bacteria in the laboratory conditions. Diffusion bioreactor is a membrane bound chamber which allows microbes to proliferate in their native environment by providing the excess to naturally occurring nutrients and signaling compounds. This paper presents efficient and reliable protocol to construct a diffusion bioreactor and its utilization to isolate and cultivate unculturable soil bacteria in laboratory.}, }
@article {pmid33902718, year = {2019}, author = {Voříšková, J and Elberling, B and Priemé, A}, title = {Fast response of fungal and prokaryotic communities to climate change manipulation in two contrasting tundra soils.}, journal = {Environmental microbiome}, volume = {14}, number = {1}, pages = {6}, pmid = {33902718}, issn = {2524-6372}, support = {5298507//Danish Geocenter Grant/ ; CENPERM DNRF100//Danish National Research Foundation/ ; }, abstract = {BACKGROUND: Climate models predict substantial changes in temperature and precipitation patterns across Arctic regions, including increased winter precipitation as snow in the near future. Soil microorganisms are considered key players in organic matter decomposition and regulation of biogeochemical cycles. However, current knowledge regarding their response to future climate changes is limited. Here, we explore the short-term effect of increased snow cover on soil fungal, bacterial and archaeal communities in two tundra sites with contrasting water regimes in Greenland. In order to assess seasonal variation of microbial communities, we collected soil samples four times during the plant-growing season.<br><br>RESULTS: The analysis revealed that soil microbial communities from two tundra sites differed from each other due to contrasting soil chemical properties. Fungal communities showed higher richness at the dry site whereas richness of prokaryotes was higher at the wet tundra site. We demonstrated that fungal and bacterial communities at both sites were significantly affected by short-term increased snow cover manipulation. Our results showed that fungal community composition was more affected by deeper snow cover compared to prokaryotes. The fungal communities showed changes in both taxonomic and ecological groups in response to climate manipulation. However, the changes were not pronounced at all sampling times which points to the need of multiple sampling in ecosystems where environmental factors show seasonal variation. Further, we showed that effects of increased snow cover were manifested after snow had melted.<br><br>CONCLUSIONS: We demonstrated rapid response of soil fungal and bacterial communities to short-term climate manipulation simulating increased winter precipitation at two tundra sites. In particular, we provide evidence that fungal community composition was more affected by increased snow cover compared to prokaryotes indicating fast adaptability to changing environmental conditions. Since fungi are considered the main decomposers of complex organic matter in terrestrial ecosystems, the stronger response of fungal communities may have implications for organic matter turnover in tundra soils under future climate.}, }
@article {pmid33902719, year = {2019}, author = {Breider, S and Sehar, S and Berger, M and Thomas, T and Brinkhoff, T and Egan, S}, title = {Genome sequence of Epibacterium ulvae strain DSM 24752[T], an indigoidine-producing, macroalga-associated member of the marine Roseobacter group.}, journal = {Environmental microbiome}, volume = {14}, number = {1}, pages = {4}, pmid = {33902719}, issn = {2524-6372}, support = {FT130100828//Australian Research Council/ ; Transregio TRR 51//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Strain U95[T] (= DSM 24752[T] = LMG 26464[T]) is the type strain of Epibacterium ulvae, which is the type species of the genus Epibacterium. This genus belongs to the marine Roseobacter group. E. ulvae Strain U95[T] was isolated from the macroalga Ulva australis, is Gram-negative, rod-shaped and motile. Here we describe the permanent draft genome sequence and annotation of E. ulvae U95[T] with a focus on secondary metabolite production and interaction with its host. The genome contains 4,092,893 bp, 3977 protein-coding genes and 60 RNA genes. The genome encodes a gene cluster for synthesis of the blue-pigmented secondary metabolite indigoidine and contains several genes for adhesion mechanisms, putative bacteriocin, siderophores, a type VI secretion system, and enzymes that confer oxidative stress resistance. Combined, these features may aid in the successful colonization and persistence of E. ulvae on host surfaces and in competition with the surrounding microbial consortium.}, }
@article {pmid33654784, year = {2019}, author = {Hennessy, RC and Stougaard, P and Olsson, S}, title = {Imaging Gene Expression Dynamics in Pseudomonas fluorescens In5 duringInteractions with the Fungus Fusarium graminearum PH-1.}, journal = {Bio-protocol}, volume = {9}, number = {12}, pages = {e3264}, pmid = {33654784}, issn = {2331-8325}, abstract = {Genomics, transcriptomics and metabolomics are powerful technologies for studying microbial interactions. The main drawback of these methods is the requirement for destructive sampling. We have established an alternative but complementary technique based on a microplate system combined with promoter fusions for visualizing gene expression in space and time. Here we provide a protocol for measuring spatial and temporal gene expression of a bacterial reporter strain interacting with a fungus on a solid surface.}, }
@article {pmid34179235, year = {2018}, author = {McLeod, KH and Mason, L and Mariño, E}, title = {Transplantation of Fecal Microbiota Shaped by Diet.}, journal = {Bio-protocol}, volume = {8}, number = {1}, pages = {e2683}, pmid = {34179235}, issn = {2331-8325}, abstract = {Alterations in diet and gut microbial ecology underlie the pathogenesis of type 1 diabetes (T1D). In the non-obese diabetic (NOD) mouse, we found high concentrations of bacterial metabolites acetate and butyrate in blood and faeces correlated with protection from disease. We reconstituted germ free (GF) NOD mice with fecal bacteria from protected NOD mice fed with high acetate- and butyrate-yielding diets, to test whether the transferred gut microbiota protect against the development of T1D. GF NOD mice that received a microbiota shaped by high acetate- but not butyrate-yielding diet showed a marked protection against diabetes. This fecal transplantation assay demonstrated the potential for a dietary technology to reshape the gut microbiota that enables specific bacteria to transfer protection against T1D.}, }
@article {pmid33525774, year = {2017}, author = {Rogers, GB}, title = {The lung microbiome.}, journal = {Emerging topics in life sciences}, volume = {1}, number = {4}, pages = {313-324}, doi = {10.1042/ETLS20170043}, pmid = {33525774}, issn = {2397-8554}, abstract = {Historically, our understanding of lung microbiology has relied on insight gained through culture-based diagnostic approaches that employ selective culture conditions to isolate specific pathogens. The relatively recent development of culture-independent microbiota-profiling techniques, particularly 16S rRNA (ribosomal ribonucleic acid) gene amplicon sequencing, has enabled more comprehensive characterisation of the microbial content of respiratory samples. The widespread application of such techniques has led to a fundamental shift in our view of respiratory microbiology. Rather than a sterile lung environment that can become colonised by microbes during infection, it appears that a more nuanced balance exists between what we consider respiratory health and disease, mediated by mechanisms that influence the clearance of microbes from the lungs. Where airway defences are compromised, the ongoing transient exposure of the lower airways to microbes can lead to the establishment of complex microbial communities within the lung. Importantly, the characteristics of these communities, and the manner in which they influence lung pathogenesis, can be very different from those of their constituent members when viewed in isolation. The lung microbiome, a construct that incorporates microbes, their genetic material, and the products of microbial genes, is increasingly central to our understanding of the regulation of respiratory physiology and the processes that underlie lung pathogenesis.}, }
@article {pmid34541249, year = {2017}, author = {Stuart, RK and Mayali, X and Thelen, MP and Pett-Ridge, J and Weber, PK}, title = {Measuring Cyanobacterial Metabolism in Biofilms with NanoSIMS Isotope Imaging and Scanning Electron Microscopy (SEM).}, journal = {Bio-protocol}, volume = {7}, number = {9}, pages = {e2263}, pmid = {34541249}, issn = {2331-8325}, abstract = {To advance the understanding of microbial interactions, it is becoming increasingly important to resolve the individual metabolic contributions of microorganisms in complex communities. Organisms from biofilms can be especially difficult to separate, image and analyze, and methods to address these limitations are needed. High resolution imaging secondary ion mass spectrometry (NanoSIMS) generates single cell isotopic composition measurements, and can be used to quantify incorporation and exchange of an isotopically labeled substrate among individual organisms. Here, incorporation of cyanobacterial extracellular organic matter (EOM) by members of a cyanobacterial mixed species biofilm is used as a model to illustrate this method. Incorporation of stable isotope labeled ([15]N and [13]C) EOM by two groups, cyanobacteria and associated heterotrophic microbes, are quantified. Methods for generating, preparing, and analyzing samples for quantifying uptake of stable isotope-labeled EOM in the biofilm are described.}, }
@article {pmid33873560, year = {2004}, author = {Piotrowski, JS and Denich, T and Klironomos, JN and Graham, JM and Rillig, MC}, title = {The effects of arbuscular mycorrhizas on soil aggregation depend on the interaction between plant and fungal species.}, journal = {The New phytologist}, volume = {164}, number = {2}, pages = {365-373}, doi = {10.1111/j.1469-8137.2004.01181.x}, pmid = {33873560}, issn = {1469-8137}, abstract = {• Arbuscular mycorrhizal fungi (AMF) and roots mediate soil stabilization, although the mechanisms and how their interactions affect soil stabilization are not known. We tested the effects of specific plant-fungus combinations on aggregate stabilization, and whether hyphal length and root biomass determine stabilization, predicting that fungi producing more hyphae, and plants with higher root biomasses, would better stabilize soils. • The percentage of water-stable aggregates (%WSA1-2 mm), hyphal lengths, and root biomass were measured from a five AMF × nine plant factorial experiment. Arbuscular mycorrhizal fungi with greater extradical mycelium production were represented by the Gigasporaceae and plants of high root biomass by grasses. Other taxa represented lower hyphal lengths and root biomass. • An interaction between symbionts with respect to %WSA1-2 mm was observed. Root biomass and total hyphal lengths were not positively correlated with %WSA. Combinations of grasses with Gigasporaceae fungi had the lowest %WSA. • Mechanisms underlying aggregation were not elucidated by measuring root biomass and total hyphal lengths alone, suggesting other physiological or architectural mechanisms may be responsible.}, }
@article {pmid33873615, year = {2004}, author = {Leake, JR and McKendrick, SL and Bidartondo, M and Read, DJ}, title = {Symbiotic germination and development of the myco-heterotroph Monotropa hypopitys in nature and its requirement for locally distributed Tricholoma spp.}, journal = {The New phytologist}, volume = {163}, number = {2}, pages = {405-423}, pmid = {33873615}, issn = {1469-8137}, abstract = {• Germination and symbiotic development of the myco-heterotrophic plant Monotropa hypopitys were studied by sequential recovery of packets of seed buried in dune slacks in relation to distance from mature M. hypopitys and presence and absence of shoots of its autotrophic coassociate Salix repens. • Fungal associates of M. hypopitys growing under S. repens in the dune slacks, and under S. caprea and Pinus sylvestris at two other locations in the UK, were identified by molecular analysis. • While the earliest stage of germination could be found in the absence both of mature M. hypopitys, and S. repens, further development was dependent upon mycorrhizal colonisation, which was most common close to these plants. Molecular analysis showed that when growing with Salix, M. hypopitys associated with the Salix-specific ectomycorrhizal fungus Tricholoma cingulatum, whereas under Pinus it was colonised by the closely related, Pinaceae-specific, T. terreum. • We establish the first definitive chronology of development of M. hypopitys and highlight its critical dependence upon, and specificity for, locally distributed Tricholoma species that link the myco-heterotroph to its autotrophic coassociates.}, }
@article {pmid33873541, year = {2003}, author = {Högberg, MN and Bååth, E and Nordgren, A and Arnebrant, K and Högberg, P}, title = {Contrasting effects of nitrogen availability on plant carbon supply to mycorrhizal fungi and saprotrophs - a hypothesis based on field observations in boreal forest.}, journal = {The New phytologist}, volume = {160}, number = {1}, pages = {225-238}, pmid = {33873541}, issn = {1469-8137}, abstract = {• Soil microorganisms are considered C-limited, while plant productivity is frequently N-limited. Large stores of organic C in boreal forest soils are attributed to negative effects of low temperature, soil acidity and plant residue recalcitrance upon microbial activity. • We examined microbial activity, biomass and community composition along a natural 90-m-long soil N supply gradient, where plant species composition varies profoundly, forest productivity three-fold and soil pH by three units. • There was, however, no significant variation in soil respiration in the field across the gradient. Neither did microbial biomass C determined by fumigation-extraction vary, while other estimates of activity and biomass showed a weak increase with increasing N supply and soil pH. Simultaneously, a phospholipid fatty acid attributed mainly to mycorrhizal fungi declined drastically, while bacterial biomass increased. • We hypothesize that low N supply and plant productivity, and hence low litter C supply to saprotrophs is associated with a high plant C supply to mycorrhizal fungi, while the reverse occurs under high N supply. This should mean that effects of N availability on C supply to these functional groups of microbes acts in opposing directions.}, }
@article {pmid33873670, year = {2003}, author = {Olsson, PA and Larsson, L and Bago, B and Wallander, H and Van Aarle, IM}, title = {Ergosterol and fatty acids for biomass estimation of mycorrhizal fungi.}, journal = {The New phytologist}, volume = {159}, number = {1}, pages = {7-10}, pmid = {33873670}, issn = {1469-8137}, }
@article {pmid33873298, year = {2002}, author = {Van Aarle, IM and Olsson, PA and Söderström, B}, title = {Arbuscular mycorrhizal fungi respond to the substrate pH of their extraradical mycelium by altered growth and root colonization.}, journal = {The New phytologist}, volume = {155}, number = {1}, pages = {173-182}, pmid = {33873298}, issn = {1469-8137}, abstract = {• To test the response of arbuscular mycorrhizal (AM) fungi to a difference in soil pH, the extraradical mycelium of Scutellospora calospora or Glomus intraradices, in association with Plantago lanceolata, was exposed to two different pH treatments, while the root substrate pH was left unchanged. • Seedlings of P. lanceolata, colonized by one or other of the fungal symbionts, and nonmycorrhizal controls, were grown in mesh bags placed in pots containing pH-buffered sand (pH around 5 or 6). The systems were harvested at approximately 2-wk intervals between 20 and 80 d. • Both fungi formed more extraradical mycelium at the higher pH. Glomus intraradices formed almost no detectable extraradical mycelium at lower pH. The extraradical mycelium of S. calospora had higher acid phosphatase activity than that of G. intraradices. Total AM root colonization decreased for both fungi at the higher pH, and high pH also reduced arbuscule and vesicle formation in G. intraradices. • In conclusion, soil pH influences AM root colonization as well as the growth and phosphatase activities of extraradical mycelium, although the two fungi responded differently.}, }
@article {pmid33873464, year = {2002}, author = {Gavito, ME and Bruhn, D and Jakobsen, I}, title = {Phosphorus uptake by arbuscular mycorrhizal hyphae does not increase when the host plant grows under atmospheric CO2 enrichment.}, journal = {The New phytologist}, volume = {154}, number = {3}, pages = {751-760}, pmid = {33873464}, issn = {1469-8137}, abstract = {• We conducted an experiment to test whether phosphorus (P) uptake by mycorrhizal hyphae could be enhanced by growing the host plant under [CO2 ] enrichment and whether any response to [CO2 ] was dependent on C source-sink relationships. • Plant C assimilation, mass allocation, growth and P uptake were measured in pea (Pisum sativum) plants inoculated with 0, 1 or 5% of a mixture of three Glomus spp. Intra- and extra-radical mycorrhizal development was followed and hyphal [33] P uptake from a root-exclusion compartment was measured. • Total P and [33] P content measurements indicated that root, not hyphal, P uptake was increased by elevated [CO2 ] in the mycorrhizal treatments and that hyphal P uptake was actually reduced by elevated [CO2 ] after 57 d. Neither intra- nor extraradical mycorrhizal development was related to this response. • Plant and fungal measurements suggested positive interactions in plant growth and P uptake only when C source-sink relationships were balanced; high C source (enhanced assimilation at elevated [CO2 ]) and high C sink (increasing mycorrhizal development). The results also indicated that enhanced plant C supply does not alter growth or function of arbuscular mycorrhizal fungi.}, }
@article {pmid33873431, year = {2002}, author = {Bordallo, JJ and Lopez-Llorca, LV and Jansson, HB and Salinas, J and Persmark, L and Asensio, L}, title = {Colonization of plant roots by egg-parasitic and nematode-trapping fungi.}, journal = {The New phytologist}, volume = {154}, number = {2}, pages = {491-499}, pmid = {33873431}, issn = {1469-8137}, abstract = {• The ability of the nematode-trapping fungus Arthrobotrys oligospora and the nematode egg parasite Verticillium chlamydosporium to colonize barley (Hordeum vulgare) and tomato (Lycopersicum esculentum) roots was examined, together with capability of the fungi to induce cell wall modifications in root cells. • Chemotropism was studied using an agar plate technique. Root colonization was investigated with light microscopy and scanning electron microscopy, while compounds involved in fungus-plant interactions were studied histochemically. • Only A. oligospora responded chemotropically to roots. Colonization of barley and tomato by both fungi involved appressoria to facilitate epidermis penetration. V. chlamydosporium colonized tomato root epidermis and produced chlamydospores. Papillae, appositions and lignitubers ensheathing hyphae on tomato were also found. Phenolics (including lignin), protein deposits and callose were present in papillae in both hosts. Both fungi were still present in epidermal cells 3 months after inoculation. • Nematophagous fungi colonized endophytically monocotyledon and dicotyledon plant roots. Arthrobotrys oligospora seemed to be more aggressive than V. chlamydosporium on barley roots. Both fungi induced cell wall modifications, but these did not prevent growth. The response of root cells to colonization by nematophagous fungi may have profound implications in the performance of these organisms as biocontrol agents of plant parasitic nematodes.}, }
@article {pmid33853251, year = {2001}, author = {Wallander, H and Nilsson, LO and Hagerberg, D and Bååth, E}, title = {Estimation of the biomass and seasonal growth of external mycelium of ectomycorrhizal fungi in the field.}, journal = {The New phytologist}, volume = {151}, number = {3}, pages = {753-760}, pmid = {33853251}, issn = {1469-8137}, abstract = {• In-growth mesh bags were used to quantify the production of external mycelium of ectomycorrhizal (EM) fungi in the field. • Colonization of the mesh bags was followed by visual estimation of the amount of mycelium, and by measuring fungal biomarkers (the phospholipid fatty acid (PLFA) 18 : 2ω6,9 and ergosterol). Mesh bags were placed inside and outside plots that were root isolated in order to estimate the amount of saprotrophic mycelium in relation to EM mycelium. The majority of mycelium in the mesh bags were EM, and this was confirmed by analysis of the δ[13] C value in mycelia. • Fungal colonization of mesh bags peaked during autumn. The total amount of EM mycelium produced in the mesh bags during a year was calculated to be between 125 and 200 kg ha[-1] . The total amount of EM mycelium (including EM mantles) in the humus was estimated to be 700-900 kg ha[-1] . • The biomass of EM mycelium in the soil was in the same range as the biomass of fine roots and peaks of mycelial growth coincided with periods of maximum growth of fine-roots.}, }
@article {pmid33863172, year = {1997}, author = {Ulrich, K and Lentzsch, P and Seyfarth, W}, title = {Identification of cultivar-specific leghaemoglobin components in Pisum sativum.}, journal = {The New phytologist}, volume = {137}, number = {2}, pages = {285-291}, doi = {10.1046/j.1469-8137.1997.00797.x}, pmid = {33863172}, issn = {1469-8137}, abstract = {The components of leghaemoglobin (Lb) from twelve different Pisum sativum L. cvs and three near-isogenic foliar mutants were investigated by anion-exchange high-performance liquid chromatography (HPLC). Five different Lb component profiles could he found. The number of components varied from four to six dependent on cultivar used. An Lb pattern composed of four Lb components could be detected in thirteen P. sativum cultivars and lines. Ten of them showed an identical profile. In nodules of each cultivar, the two known major components, LbI and LbV, but also LbIV, could be detected. Additionally, cultivar-specific Lb components could be identified, each representing up to 10%, of total Lb. One of these components, LbIII, has been described previously, but three new Lb components (LbII, LbVI, and LbVII) were found. The presence of all Lb components detected by HPLC was confirmed by analytical isoelectric focusing. Further, it was shown that age-dependent changes in the relative concentrations of LbI and LbV are common in P. sativum and that these variations are independent of breeding lines and cultivars.}, }
@article {pmid33657731, year = {1997}, author = {Rosén, S and Sjollema, K and Veenhuis, M and Tunlid, A}, title = {A cytoplasmic lectin produced by the fungus Arthrobotrys oligospora functions as a storage protein during saprophytic and parasitic growth.}, journal = {Microbiology (Reading, England)}, volume = {143}, number = {8}, pages = {2593-2604}, doi = {10.1099/00221287-143-8-2593}, pmid = {33657731}, issn = {1465-2080}, abstract = {It was recently shown that the nematode-infecting fungus Arthrobotrys oligospora contains a saline-soluble lectin (designated AOL) that is a member of a novel family of fungal lectins sharing similar primary sequences and binding specificities. During saprophytic growth in liquid cultures, levels of AOL and AOL mRNA were found to vary depending on the growth phase of the mycelium and the carbon/nitrogen (C/N) ratio of the medium. AOL was not detected in young mycelium. In older mycelium (stationary growth phase) grown in media with low C/N ratios (1 or 6), AOL comprised 5-20% of the total amount of saline-soluble proteins present in the mycelium. Neither the lectin nor its transcript was detected in mycelia grown in medium with higher C/N ratios (≥150). Under conditions of nitrogen starvation, AOL was preferentially degraded in relation to the total amount of saline-soluble proteins present in the mycelium. During the infection of nematodes, the level of AOL protein and AOL mRNA increased significantly once the nematodes had been penetrated and digested. Large amounts of AOL accumulated in the trophic hyphae growing inside the nematode as visualized by immunofluorescence microscopy. Later, AOL labelling was detected outside the digested nematodes, preferentially in strands of aggregated hyphae and in newly developed trap cells. Electron microscopy showed that AOL was localized to the cytoplasm and the nucleus of both vegetative mycelium and trap cells, and in the trophic hyphae growing inside the infected nematodes. These results indicate that AOL functions as a storage protein during both saprophytic and parasitic growth.}, }
@article {pmid33657740, year = {1996}, author = {Langdahl, BR and Bisp, P and Ingvorsen, K}, title = {Nitrile hydrolysis by Rhodococcus erythropolis BL1, an acetonitrile-tolerant strain isolated from a marine sediment.}, journal = {Microbiology (Reading, England)}, volume = {142}, number = {1}, pages = {145-154}, doi = {10.1099/13500872-142-1-145}, pmid = {33657740}, issn = {1465-2080}, abstract = {A number of physiologically different nitrile-hydrolysing bacteria were isolated from coastal marine sediments in Denmark by enrichment culture. One strain, BL1, identified as Rhodococcus erythropolis, grew on acetonitrile as sole carbon and nitrogen source in a defined medium. Growth occurred between 0 and 8% NaCl with an optimum around 2%, thus reflecting the marine origin of the isolate. Intact cells of R. erythropolis BL1 could hydrolyse a large variety of saturated and unsaturated aliphatic nitriles to their corresponding acids. Benzonitrile and benzylcyanide were not hydrolysed, whereas some aromatic compounds containing a -CN group attached to a C3 or C4 aliphatic side chain were accepted as substrates. The substrate spectrum of R. erythropolis BL1 was thus markedly different from those of other Grampositive nitrile-hydrolysing bacteria isolated from non-marine environments. Nitrile hydrolysis during growth and in resting cell suspensions usually occurred without intermediate accumulation of amide outside the cells. Detailed studies, however, showed that nitrile hydrolysis by strain BL1 was due to a nitrile hydratase/amidase enzyme system. Nitrile hydratase activity was found to be inducible whereas amidase activity was constitutive. The amidase activity of cells could, however, be enhanced manyfold by growth in media containing acetamide or acetonitrile. In most cases amides were hydrolysed at a much higher rate than the corresponding nitriles, which explained why amides were rarely detected in the surrounding medium during nitrile hydrolysis. R. erythropolis BL1 exhibited the highest tolerance towards acetonitrile ever reported for a nitrile-hydrolysing bacterium, as demonstrated by its ability to grow exponentially in the presence of 900 mM acetonitrile.}, }
@article {pmid33874368, year = {1994}, author = {Wingler, A and Einig, W and Schaeffer, C and Wallenda, T and Hampp, R and Wallander, H and Nylund, JE}, title = {Influence of different nutrient regimes on the regulation of carbon metabolism in Norway spruce [Picea abies (L.) Karst.] seedlings.}, journal = {The New phytologist}, volume = {128}, number = {2}, pages = {323-330}, doi = {10.1111/j.1469-8137.1994.tb04016.x}, pmid = {33874368}, issn = {1469-8137}, abstract = {Phosphoenolpyruvate carboxylase (PEPC) activity, fructose 2, 6-bisphosphate (F26BP), starch and soluble sugar contents were determined m needles and roots of Norway spruce seedlings grown in a semi-hydroponic cultivation system under different nutrient regimes, tn needles, a surplus of nitrogen caused an increase in specific PEPC activity (up to six times control activity) and F26BP content (up to three times control level) while starch content was reduced. Sucrose contents were not affected. Basically, the responses in root samples were similar. Here, PEPC was highest at an imbalance in nutrition (+ N/ -P) F26BP, with root contents being 3- to 11 -times higher than those in needles, significantly exceeded control values at + N/+ P. The results show that alteration of nitrogen supply leads to marked changes in allocation of carbon between pathways, which is also influenced by P-nutrition. Pool sizes of F26BP and activity of PEPC are indicators for these changes in leaf as well as in root tissues of Norway spruce.}, }
@article {pmid33874472, year = {1994}, author = {Erland, S and Henrion, B and Martin, F and Glover, LA and Alexanders, IJ}, title = {Identification of the ectomycorrhizal basidiomycete Tylospora fibrillosa Donk by RFLP analysis of the PCR-amplified ITS and IGS regions of ribosomal DNA.}, journal = {The New phytologist}, volume = {126}, number = {3}, pages = {525-532}, doi = {10.1111/j.1469-8137.1994.tb04251.x}, pmid = {33874472}, issn = {1469-8137}, abstract = {Sitka spruce mycorrhizas, macroscopically identified as being formed by Tylospora fibritiosa Donk, were sampled from a young and on old plantation and the mycobionts were isolated into pure culture. DNA was extracted and fragments of the ribosomal DNA (rDNA) were amplified using the polymerase chain reaction (PCR). The primers were directed to conserved regions of fungal rDXA and hybridize to a wide range of fungi. One amplified region includes the internal spacer (ITS) region which has a low degree of conservation. The JTS amplification products, which were approximately 600 base pairs (bp), were digested with a variety of restriction endonucleases in order to detect restriction fragment length polymorphisms (RFLPs). The RFLPs clearly separated T. fibrillosa from other ectomycorrhizal species but there were only minor differences between the T. fibrillosa isolates. PCR amplification of the ITS region, digestion with the endonudeasc HinfI and examination of the RFLPs produced proved to be a rapid method by which to distinguish T. fibriHosa from a large number of other basidiomyictes. The method was also applied to DNA extracted, from single mycotrhizal root tips. The imergenic spacer region (1GS) of the rDNA is more variable than the ITS region in several fungal species. The 5'end of the 25S and the intergenic region between the 25S and the 5S genes were amplified and analyzed as above. Polymorphisms between T. fibritiosa isolates within this region were limited and RFLPs were not useful m discriminating between isolates, suggesting a low genetic variability in this species.}, }
@article {pmid33874350, year = {1993}, author = {Arnebrant, K and Ek, H and Finlay, RD and Söderström, B}, title = {Nitrogen translocation between Alnus glutinosa (L.) Gaertn. seedlings inoculated with Frankia sp. and Pinus contorta Doug, ex Loud seedlings connected by a common ectomycorrhizal mycelium.}, journal = {The New phytologist}, volume = {124}, number = {2}, pages = {231-242}, doi = {10.1111/j.1469-8137.1993.tb03812.x}, pmid = {33874350}, issn = {1469-8137}, abstract = {Uptake and translocation of nitrogen was studied in laboratory microcosms consisting of Alnus glutinosa (L.) Gaertn., Frankia sp., Paxillus involutus (Fr.) Fr. and Pinus contorta Dougl. ex Loud. P. involutus was shown to form a fully functional ectomycorrhizal association with alder as well as pine, and the seedlings thus became interconnected by a common mycelium. When microcosms were exposed to [15] N2 gas, interplant translocation of [15] N was observed in two out of three experiments. [15] N2 was fixed by Frankia and translocated to all other parts of the system. In the two experiments in which interplant translocation occurred, between 5 and 15% of the [15] N recovered was found in the pine seedlings. Within seven days, fixed N2 was incorporated into amino acids in the Frankia nodules, translocated to both the A. glutinosa and P. contorta seedlings and incorporated into macromolecules. In alder seedlings, citrulline and ornithine were the free amino acids that had both the highest [15] N enrichment levels and concentrations. In pine, glutamine and citrulline had the highest [15] N concentrations, and glutamine had the highest level of [15] N enrichment. [15] N enrichment levels were greatest in the nodules, at between 5.5 and 29% in the different amino acids and 12% in the macromolecular fraction. Enrichment levels decreased with increasing distance from the nodules. The uptake and translocation of [15] N applied as [15] NH4 Cl to the mycelium was also studied. [15] N was incorporated into amino acids in the mycelium and translocated further in this form. Generally, free amino acids had high [15] N enrichment levels in the mycelium, decreasing along the translocation pathway. Citrulline and glutamine were the amino acids with highest [15] N concentrations in all parts of the system. [15] N was also found in the macromolecular fraction.}, }
@article {pmid33874136, year = {1991}, author = {Erland, S and Finlay, R and Söderström, B}, title = {The influence of substrate pH on carbon translocation in ectomycorrhizal and non-mycorrhizal pine seedlings.}, journal = {The New phytologist}, volume = {119}, number = {2}, pages = {235-242}, doi = {10.1111/j.1469-8137.1991.tb01026.x}, pmid = {33874136}, issn = {1469-8137}, abstract = {The effects of changed substrate pH on translocation and partitioning of [14] C-labeled plant assimilates were examined in laboratory microcosms containing mycorrhizal (unidentified fungal isolate 'Pink FMT 87:2') and non-mycorrhizal seedlings of Pinus sylvestris L. and Pinus contorta Dougl. ex Loud. The mycorrhizal plants had intact mycelial systems at different developmental stages, and microcosms contained non-sterile peat (pH 3.8) or peat adjusted to different pH values with CaO. In systems with mycorrhizal mycelium which had just started to colonize the peat no significant differences in [14] C assimilation were found, either with respect to substrate pH or mycorrhizal status of the plant. Loss of activity from the mycorrhizal plants was more rapid, however, probably mainly as a result of increased respiration from the infected root systems. After 8 wk growth in peat at pH 3.8 and 5.2 shoot weights of all seedlings were the same, whereas non-mycorrhizal plants had root systems twice the size of the mycorrhizal ones. In plants with well developed extramatrical mycelia translocation of labeled carbon to the mycelium growing at pH 3.8 was faster than that to mycelium growing at pH 5.2. After 4 d incubation, however, the percentage of the originally supplied carbon present in the mycelium was 5% regardless of substrate pH. Activity found in the peat surrounding non-mycorrhizal plants rarely exceeded 0.3%.}, }
@article {pmid33874309, year = {1991}, author = {Erland, S and Söerström, B}, title = {Effects of liming on ectomycorrhizal fungi infecting Pinus sylvestris L.: III. Saprophytic growth and host plant infection at different pH values in unsterile humus.}, journal = {The New phytologist}, volume = {117}, number = {3}, pages = {405-411}, doi = {10.1111/j.1469-8137.1991.tb00004.x}, pmid = {33874309}, issn = {1469-8137}, abstract = {Five ectomycorrhizal fungi were studied in relation to the effects of applications of lime and wood ash to the growth substrate. Growth and survival of inoculated fungi in unsterile humus and relative root colonization frequency by inoculated and indigenous ectomycorrhizal fungi were measured. Growth of the fungi was tested in Petri dish systems with humus taken from a field site treated with lime and wood ash. The infection potential of the fungi was tested by introducing Pinus sylvestris L. seedlings into the growth systems. Paxillus involutus (Fr.) Fr. was the only fungus affected both by the pH increase, and by the different treatments applied, in all aspects of its ecology tested (growth and survival in humus, infection potential and competitive ability). No other fungus grew saprophytically, but they showed the similar changes in infection potential in response to pH whether lime or ash had been used.}, }
@article {pmid33874008, year = {1989}, author = {}, title = {Reviews.}, journal = {The New phytologist}, volume = {111}, number = {3}, pages = {559-565}, doi = {10.1111/j.1469-8137.1989.tb00718.x}, pmid = {33874008}, issn = {1469-8137}, abstract = {The Flavonoids. Advances in Research since 1980. Ed. by J. B. Harborne. Hungry crops: a guide to nutrient deficiencies in field crops By N. J. Grundon. Microbial ecology: organisms, habitats, activities. By Heinz Stolp. Evolutionary Biology of the Fungi. Ed. by A. D. M. Rayner, C. M. Brasier and D. Moore. Micro-algal Biotechnology. Edited by M.A. Borowitzka and L. J. Borowitzka and L. J. Borowitzka. Experimental Phycology: A laboratory manual Edited by Christopher S. Lobban, David J. Chapman, and Bruno P. Kremer. 100 Families of Flowering Plants. By M. Hickey and C. King. Differentiation Patterns in Higher Plants. Edited by K. M. Urbanska. The Living Tundra. By Yu. I. Chernov, Translated by D. Löve. North American Terrestrial Vegetation. Edited by M. G. Barbour &amp; W. D. Billings. Biogeography and Quaternary History in Tropical Latin America. By T. C. Whitmore and G. T. Prance (Editors). Biogeographical Evolution of the Malay Archipelago. By T. C. Whitmore (Editor). Postglacial Vegetation of Canada. By J. C. Richie.}, }
@article {pmid33459817, year = {2021}, author = {Kumar, M and Sodhi, KK and Singh, DK}, title = {Addressing the potential role of curcumin in the prevention of COVID-19 by targeting the Nsp9 replicase protein through molecular docking.}, journal = {Archives of microbiology}, volume = {203}, number = {4}, pages = {1691-1696}, pmid = {33459817}, issn = {1432-072X}, support = {NASF/CA-6030/2017-2018//NASF, ICAR/ ; }, mesh = {Curcumin/*pharmacology ; *Molecular Docking Simulation ; RNA-Binding Proteins/*antagonists &amp; inhibitors ; SARS-CoV-2/*drug effects/physiology ; Viral Nonstructural Proteins/*antagonists &amp; inhibitors ; Virus Replication/*drug effects ; }, abstract = {The pandemics have always been a destructive carrier to living organisms. Humans are the ultimate victims, as now we are facing the SARS CoV-2 virus caused COVID-19 since its emergence in Dec 2019, at Wuhan (China). Due to the new coronavirus' unexplored nature, we shed light on curcumin for its potential role against the disease. The Nsp9 replicase protein, which plays an essential role in virus replication, was extracted online, followed by 3D PDB model prediction with its validation. The in silico molecular docking of curcumin with the replicase enzyme gave insights into the preventive measures against the virus as curcumin showed multiple interactions with Nsp9 replicase. The current study showed the use of curcumin against the coronavirus and its possible role in developing medicine against it.}, }
@article {pmid33459471, year = {2021}, author = {DeLong, EF}, title = {Genome-enabled exploration of microbial ecology and evolution in the sea: a rising tide lifts all boats.}, journal = {Environmental microbiology}, volume = {23}, number = {3}, pages = {1301-1321}, pmid = {33459471}, issn = {1462-2920}, mesh = {*Archaea/genetics ; Bacteria/genetics ; *Genome ; Humans ; Metagenomics ; Phylogeny ; }, abstract = {As a young bacteriologist just launching my career during the early days of the 'microbial revolution' in the 1980s, I was fortunate to participate in some early discoveries, and collaborate in the development of cross-disciplinary methods now commonly referred to as "metagenomics". My early scientific career focused on applying phylogenetic and genomic approaches to characterize 'wild' bacteria, archaea and viruses in their natural habitats, with an emphasis on marine systems. These central interests have not changed very much for me over the past three decades, but knowledge, methodological advances and new theoretical perspectives about the microbial world certainly have. In this invited 'How we did it' perspective, I trace some of the trajectories of my lab's collective efforts over the years, including phylogenetic surveys of microbial assemblages in marine plankton and sediments, development of microbial community gene- and genome-enabled surveys, and application of genome-guided, cultivation-independent functional characterization of novel enzymes, pathways and their relationships to in situ biogeochemistry. Throughout this short review, I attempt to acknowledge, all the mentors, students, postdocs and collaborators who enabled this research. Inevitably, a brief autobiographical review like this cannot be fully comprehensive, so sincere apologies to any of my great colleagues who are not explicitly mentioned herein. I salute you all as well!}, }
@article {pmid33454808, year = {2021}, author = {Takano, SI and Gotoh, Y and Hayashi, T}, title = {"Candidatus Mesenet longicola": Novel Endosymbionts of Brontispa longissima that Induce Cytoplasmic Incompatibility.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {512-522}, pmid = {33454808}, issn = {1432-184X}, support = {18H02207//Japan Society for the Promotion of Science/ ; 16H06279//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; *Coleoptera ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; *Wolbachia/genetics ; }, abstract = {Intracellular bacteria that are mainly transmitted maternally affect their arthropod hosts' biology in various ways. One such effect is known as cytoplasmic incompatibility (CI), and three bacterial species are known to induce CI: Wolbachia, Cardinium hertigii, and a recently found alphaproteobacterial symbiont. To clarify the taxonomic status and provide the foundation for future studies to reveal CI mechanisms and other phenotypes, we investigated genetic and morphological properties of the third CI inducer that we have previously reported inducing CI in the coconut beetle Brontispa longissima. The draft genome of the bacteria was obtained from the oocytes of two isofemale lines of B. longissima infected with the bacteria: one from Japan (GL2) and the other from Vietnam (L5). Genome features of the symbionts (sGL2 and sL5) were highly similar, showing 1.3 Mb in size, 32.1% GC content, and 99.83% average nucleotide sequence. A phylogenetic study based on 43 universal and single-copy phylogenetic marker genes indicates that they formed a distinct clade in the family Anaplasmataceae. 16S rRNA gene sequences indicate that they are different from the closest known relatives, at least at the genus level. Therefore, we propose a new genus and species, "Candidatus Mesenet longicola", for the symbionts of B. longissima. Morphological analyses showed that Ca. M. longicola is an intracellular bacterium that is ellipsoidal to rod-shaped and 0.94 ± 0.26 μm (mean ± SD) in length, and accumulated in the anterior part of the oocyte. Candidates for the Ca. M. longicola genes responsible for CI induction are also described.}, }
@article {pmid33452897, year = {2021}, author = {Dahl, MB and Peršoh, D and Jentsch, A and Kreyling, J}, title = {Root-Associated Mycobiomes of Common Temperate Plants (Calluna vulgaris and Holcus lanatus) Are Strongly Affected by Winter Climate Conditions.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {403-415}, pmid = {33452897}, issn = {1432-184X}, support = {DFG JE 282/5-1//Deutsche Forschungsgemeinschaft/ ; RTG 2010//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Ascomycota ; *Calluna ; Climate Change ; *Holcus ; *Mycobiome ; Seasons ; Soil ; }, abstract = {Winter temperatures are projected to increase in Central Europe. Subsequently, snow cover will decrease, leading to increased soil temperature variability, with potentially different consequences for soil frost depending on e.g. altitude. Here, we experimentally evaluated the effects of increased winter soil temperature variability on the root associated mycobiome of two plant species (Calluna vulgaris and Holcus lanatus) at two sites in Germany; a colder and wetter upland site with high snow accumulation and a warmer and drier lowland site, with low snow accumulation. Mesocosm monocultures were set-up in spring 2010 at both sites (with soil and plants originating from the lowland site). In the following winter, an experimental warming pulse treatment was initiated by overhead infrared heaters and warming wires at the soil surface for half of the mesocosms at both sites. At the lowland site, the warming treatment resulted in a reduced number of days with soil frost as well as increased the average daily temperature amplitude. Contrary, the treatment caused no changes in these parameters at the upland site, which was in general a much more frost affected site. Soil and plant roots were sampled before and after the following growing season (spring and autumn 2011). High-throughput sequencing was used for profiling of the root-associated fungal (ITS marker) community (mycobiome). Site was found to have a profound effect on the composition of the mycobiome, which at the upland site was dominated by fast growing saprotrophs (Mortierellomycota), and at the lowland site by plant species-specific symbionts (e.g. Rhizoscyphus ericae and Microdochium bolleyi for C. vulgaris and H. lanatus respectively). The transplantation to the colder upland site and the temperature treatment at the warmer lowland site had comparable consequences for the mycobiome, implying that winter climate change resulting in higher temperature variability has large consequences for mycobiome structures regardless of absolute temperature of a given site.}, }
@article {pmid33452896, year = {2021}, author = {Bergo, NM and Bendia, AG and Ferreira, JCN and Murton, BJ and Brandini, FP and Pellizari, VH}, title = {Microbial Diversity of Deep-Sea Ferromanganese Crust Field in the Rio Grande Rise, Southwestern Atlantic Ocean.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {344-355}, pmid = {33452896}, issn = {1432-184X}, support = {14/50820-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {*Archaea/genetics ; Atlantic Ocean ; Geologic Sediments ; Iron ; *Manganese ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Seamounts are often covered with Fe and Mn oxides, known as ferromanganese (Fe-Mn) crusts. Future mining of these crusts is predicted to have significant effects on biodiversity in mined areas. Although microorganisms have been reported on Fe-Mn crusts, little is known about the role of crusts in shaping microbial communities. Here, we investigated microbial communities based on 16S rRNA gene sequences retrieved from Fe-Mn crusts, coral skeleton, calcarenite, and biofilm at crusts of the Rio Grande Rise (RGR). RGR is a prominent topographic feature in the deep southwestern Atlantic Ocean with Fe-Mn crusts. Our results revealed that crust field of the RGR harbors a usual deep-sea microbiome. No differences were observed on microbial community diversity among Fe-Mn substrates. Bacterial and archaeal groups related to oxidation of nitrogen compounds, such as Nitrospirae, Nitrospinae phyla, Candidatus Nitrosopumilus within Thaumarchaeota group, were present on those substrates. Additionally, we detected abundant assemblages belonging to methane oxidation, i.e., Methylomirabilales (NC10) and SAR324 (Deltaproteobacteria). The chemolithoautotrophs associated with ammonia-oxidizing archaea and nitrite-oxidizing bacteria potentially play an important role as primary producers in the Fe-Mn substrates from RGR. These results provide the first insights into the microbial diversity and potential ecological processes in Fe-Mn substrates from the Atlantic Ocean. This may also support draft regulations for deep-sea mining in the region.}, }
@article {pmid33452613, year = {2021}, author = {Vingiani, GM and Gasulla, F and Barón-Sola, &#xc1; and Sobrino-Plata, J and Henández, LE and Casano, LM}, title = {Physiological and Molecular Alterations of Phycobionts of Genus Trebouxia and Coccomyxa Exposed to Cadmium.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {334-343}, pmid = {33452613}, issn = {1432-184X}, support = {CGL2016- 80259-P//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; AGL2014-53771-R//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; AGL2017-87591-R//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; }, mesh = {Cadmium/toxicity ; *Chlorophyta/genetics ; *Lichens ; *Microalgae/genetics ; Oxidative Stress ; }, abstract = {Several studies on aeroterrestrial microalgae are unravelling their resistance mechanisms to different abiotic stressors, including hazardous metals, pointing to their future role as bioremediation microorganisms. In the present study, physiological and molecular alterations of four phycobionts of genus Trebouxia (T. TR1 and T. TR9) and Coccomyxa (C. subellipsoidea and C. simplex) exposed to Cd were studied. Cd accumulation and subcellular distribution, cell wall structure, production of biothiols (GSH and phytochelatins), reactive oxygen species (ROS) formation, expression of key antioxidant genes and ROS-related enzymes were evaluated to determine the physiological differences among the four microalgae, with the aim to identify the most suitable microorganism for further biotechnological applications. After 7 days of Cd exposure, Coccomyxa algae showed higher capacity of Cd intake than Trebouxia species, with C. subellipsoidea being the highest Cd accumulator at both intracellular and, especially, cell wall level. Cd induced ROS formation in the four microalgae, but to a greater extent in both Coccomyxa algae. Trebouxia TR9 showed the lowest Cd-dependent oxidative stress probably due to glutathione reductase induction. All microalgae synthetized phytochelatins in response to Cd but in a species-specific and a dose-dependent manner. Results from this study agree with the notion that each microalga has evolved a distinct strategy to detoxify hazardous metals like Cd and to cope with oxidative stress associated with them. Coccomyxa subellipsoidea and Trebouxia TR9 appear as the most interesting candidates for further applications.}, }
@article {pmid33449130, year = {2021}, author = {Zai, X and Luo, W and Bai, W and Li, Y and Xiao, X and Gao, X and Wang, E and Wei, G and Chen, W}, title = {Effect of Root Diameter on the Selection and Network Interactions of Root-Associated Bacterial Microbiomes in Robinia pseudoacacia L.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {391-402}, pmid = {33449130}, issn = {1432-184X}, support = {31870476//the National Natural Science Foundation of China/ ; 41830755//the National Natural Science Foundation of China/ ; }, mesh = {*Microbiota ; Plant Roots ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; *Robinia ; Soil Microbiology ; }, abstract = {The high plasticity of root morphology, physiology, and function influences root-associated microbiomes. However, the variation in root-associated microbiome diversity and structures in response to root diameter at different root depths remains poorly understood. Here, we selected black locust (Robinia pseudoacacia L.) as a model plant to investigate the selection and network interactions of rhizospheric and root endophytic bacterial microbiomes associated with roots of different diameters (1, 1-2, and > 2 mm) among root depths of 0-100 cm via the Illumina sequencing of the 16S rRNA gene. The results showed that the alpha diversity of the root-associated bacterial communities decreased with increasing root diameters among different root depths; fewer orders with higher relative abundance, especially in the endosphere, were enriched in association with coarse roots (> 2 mm) than fine roots among root depths. Furthermore, the variation in the enriched bacterial orders associated with different root diameters was explained by bulk soil properties. Higher co-occurrence network complexity and stability emerged in the rhizosphere microbiomes of fine roots than those of coarse roots, in contrast to the situation in the endosphere microbiomes. In particular, the endosphere of roots with a diameter of 1-2 mm exhibited the lowest network complexity and stability and a high proportion of keystone taxa (e.g., Cytophagia, Flavobacteriia, Sphingobacteriia, β-Proteobacteria, and γ-Proteobacteria), suggesting a keystone taxon-reliant strategy in this transitional stage. In summary, this study indicated that root diameter at different root depths differentially affects rhizospheric and endophytic bacterial communities, which implies a close relationship between the bacterial microbiome, root function, and soil properties.}, }
@article {pmid33448446, year = {2020}, author = {Moraes, LC and Lang, PM and Arcanjo, RA and Rampelotto, PH and Fatturi-Parolo, CC and Ferreira, MBC and Montagner, F}, title = {Microbial ecology and predicted metabolic pathways in various oral environments from patients with acute endodontic infections.}, journal = {International endodontic journal}, volume = {53}, number = {12}, pages = {1603-1617}, doi = {10.1111/iej.13389}, pmid = {33448446}, issn = {1365-2591}, support = {//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; //Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio Grande do Sul/ ; }, mesh = {Adult ; Cross-Sectional Studies ; DNA, Bacterial ; Humans ; Metabolic Networks and Pathways ; *Microbiota ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {AIM: To assess in a cross-sectional clinical study the effect of antibiotics on the diversity, structure and metabolic pathways of bacterial communities in various oral environments in patients with acute primary infections.<br><br>METHODOLOGY: Samples of saliva (SA), supragingival biofilm (SB) and from the pulp cavity (PC) were collected from teeth with acute primary infections and then grouped according to previous use of antibiotics (NoAtb&#xa0;=&#xa0;no antibiotics [n&#xa0;=&#xa0;6]; Atb&#xa0;=&#xa0;antibiotics [n&#xa0;=&#xa0;6]). DNA sequencing was conducted using MiSeq (Illumina, San Diego, CA, USA). The V1-V3 hyper-variable region of the 16S rRNA gene was amplified. A custom Mothur pipeline was used for 16S rRNA processing. Subsequent analyses of the sequence dataset were performed in R (using vegan, phyloseq and ggplot2 packages) or QIIME.<br><br>RESULTS: Twelve patients aged from 22 to 56&#xa0;years were recruited. Participants in the Atb group had taken the beta-lactamics amoxicillin (5/6) or cephalexin (1/6) for 2-3&#xa0;days. A total of 332 bacterial taxa (OTUs) were identified, belonging to 120 genera, 60 families and nine phyla. Firmicutes (41%) and Bacteroidetes (38%) were the most abundant phyla in all samples. Taxa clustered significantly by oral site (PCoA analysis; P&#xa0;<&#xa0;0.05, ANOSIM). Use of antibiotics had little effect on this clustering. However, SA, SB and PC had different degrees of richness, diversity and evenness. The greatest diversity was observed in SB samples and the least diversity was observed in PC samples. Metabolic prediction identified 163 pathways and previous use of antibiotics had a major effect on the estimated functional clustering in SA and PC samples.<br><br>CONCLUSION: The ecological niche had a strong influence on the bacterial content of samples from various oral sites. Previous exposure to antibiotics may exert an effect on the phylogenetic composition of SA. Metabolic pathways appear to be modulated by antimicrobial agents in SA and PC samples. The dynamics of host/microbial interactions in the apical region and the functional ecology of the infected pulp cavity should be revisited.}, }
@article {pmid33447808, year = {2020}, author = {Lories, B and Belpaire, TER and Yssel, A and Ramon, H and Steenackers, HP}, title = {Agaric acid reduces Salmonella biofilm formation by inhibiting flagellar motility.}, journal = {Biofilm}, volume = {2}, number = {}, pages = {100022}, pmid = {33447808}, issn = {2590-2075}, abstract = {Salmonella biofilms are a common cause of contaminations in the food or feed industry. In a screening for novel compounds to combat biofilm-associated foodborne outbreaks, we identified agaric acid as a Salmonella Typhimurium biofilm inhibitor that does not affect planktonic growth. Importantly, the remaining biofilm cells after preventive treatment with agaric acid were significantly more sensitive to the common disinfectant hydrogen peroxide. Screening of a GFP-promoter fusion library of biofilm related genes revealed that agaric acid downregulates the transcription of genes responsible for flagellar motility. Concurrently, swimming motility was completely abrogated in the presence of agaric acid, indicating that biofilm inhibition occurs via interference with the motility phenotype. Moreover, agaric acid also reduced biofilm formation of Pseudomonas aeruginosa, Staphylococcus aureus and Escherichia coli. Agaric acid thus shows potential as an anti-virulence compound that inhibits both motility and biofilm formation.}, }
@article {pmid33446998, year = {2020}, author = {Li, M and Shao, D and Zhou, J and Gu, J and Qin, J and Chen, W and Wei, W}, title = {Signatures within esophageal microbiota with progression of esophageal squamous cell carcinoma.}, journal = {Chinese journal of cancer research = Chung-kuo yen cheng yen chiu}, volume = {32}, number = {6}, pages = {755-767}, pmid = {33446998}, issn = {1000-9604}, abstract = {OBJECTIVE: Esophageal squamous cell carcinoma (ESCC) is one of the dominant malignances worldwide, but currently there is less focus on the microbiota with ESCC and its precancerous lesions.<br><br>METHODS: Paired esophageal biopsy and swab specimens were obtained from 236 participants in Linzhou, China. Data from 16S ribosomal RNA gene sequencing were processed using quantitative insights into microbial ecology (QIIME2) and R Studio to evaluate differences. The Wilcoxon rank sum test and Kruskal-Wallis rank sum test were used to compare diversity and characteristic genera by specimens and participant groups. Ordinal logistic regression model was used to build microbiol prediction model.<br><br>RESULTS: Microbial diversity was similar between biopsy and swab specimens, including operational taxonomic unit (OTU) numbers and Shannon index. There were variations and similarities of esophageal microbiota among different pathological characteristics of ESCC. Top 10 relative abundance genera in all groups include Streptococcus, Prevotella, Veillonella, Actinobacillus, Haemophilus, Neisseria, Alloprevotella, Rothia, Gemella and Porphyromonas. Genus Streptococcus, Haemophilus, Neisseria and Porphyromonas showed significantly difference in disease groups when compared to normal control, whereas Streptococcus showed an increasing tendency with the progression of ESCC and others showed a decreasing tendency. About models based on all combinations of characteristic genera, only taken Streptococcus and Neisseria into model, the prediction performance was the ideal one, of which the area under the curve (AUC) was 0.738.<br><br>CONCLUSIONS: Esophageal biopsy and swab specimens could yield similar microbial characterization. The combination of Streptococcus and Neisseria has the potential to predict the progression of ESCC, which is needed to confirm by large-scale, prospective cohort studies.}, }
@article {pmid33446818, year = {2021}, author = {McGill, SL and Yung, Y and Hunt, KA and Henson, MA and Hanley, L and Carlson, RP}, title = {Pseudomonas aeruginosa reverse diauxie is a multidimensional, optimized, resource utilization strategy.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1457}, pmid = {33446818}, issn = {2045-2322}, support = {U01 EB019416/EB/NIBIB NIH HHS/United States ; }, mesh = {Bacterial Proteins/*metabolism ; Humans ; *Models, Biological ; Pseudomonas aeruginosa/*metabolism/pathogenicity ; }, abstract = {Pseudomonas aeruginosa is a globally-distributed bacterium often found in medical infections. The opportunistic pathogen uses a different, carbon catabolite repression (CCR) strategy than many, model microorganisms. It does not utilize a classic diauxie phenotype, nor does it follow common systems biology assumptions including preferential consumption of glucose with an 'overflow' metabolism. Despite these contradictions, P. aeruginosa is competitive in many, disparate environments underscoring knowledge gaps in microbial ecology and systems biology. Physiological, omics, and in silico analyses were used to quantify the P. aeruginosa CCR strategy known as 'reverse diauxie'. An ecological basis of reverse diauxie was identified using a genome-scale, metabolic model interrogated with in vitro omics data. Reverse diauxie preference for lower energy, nonfermentable carbon sources, such as acetate or succinate over glucose, was predicted using a multidimensional strategy which minimized resource investment into central metabolism while completely oxidizing substrates. Application of a common, in silico optimization criterion, which maximizes growth rate, did not predict the reverse diauxie phenotypes. This study quantifies P. aeruginosa metabolic strategies foundational to its wide distribution and virulence including its potentially, mutualistic interactions with microorganisms found commonly in the environment and in medical infections.}, }
@article {pmid33446769, year = {2021}, author = {Berger, C and Rückert, C and Blom, J and Rabaey, K and Kalinowski, J and Rosenbaum, MA}, title = {Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1370}, pmid = {33446769}, issn = {2045-2322}, support = {864669/ERC_/European Research Council/International ; }, mesh = {*Genome, Bacterial ; Genomics ; Pseudomonas Infections/*genetics ; Pseudomonas aeruginosa/*genetics/isolation &amp; purification/*pathogenicity ; Sequence Analysis, DNA ; Virulence ; }, abstract = {The isolation and sequencing of new strains of Pseudomonas aeruginosa created an extensive dataset of closed genomes. Many of the publicly available genomes are only used in their original publication while additional in silico information, based on comparison to previously published genomes, is not being explored. In this study, we defined and investigated the genome of the environmental isolate P. aeruginosa KRP1 and compared it to more than 100 publicly available closed P. aeruginosa genomes. By using different genomic island prediction programs, we could identify a total of 17 genomic islands and 8 genomic islets, marking the majority of the accessory genome that covers ~ 12% of the total genome. Based on intra-strain comparisons, we are able to predict the pathogenic potential of this environmental isolate. It shares a substantial amount of genomic information with the highly virulent PSE9 and LESB58 strains. For both of these, the increased virulence has been directly linked to their accessory genome before. Hence, the integrated use of previously published data can help to minimize expensive and time consuming wetlab work to determine the pathogenetic potential.}, }
@article {pmid33445025, year = {2021}, author = {González-Martínez, A and Muñoz-Palazon, B and Kruglova, A and Vilpanen, M and Kuokkanen, A and Mikola, A and Heinonen, M}, title = {Performance and microbial community structure of a full-scale ANITA[TM]Mox bioreactor for treating reject water located in Finland.}, journal = {Chemosphere}, volume = {271}, number = {}, pages = {129526}, doi = {10.1016/j.chemosphere.2020.129526}, pmid = {33445025}, issn = {1879-1298}, mesh = {Anaerobiosis ; Bioreactors ; Finland ; *Microbiota ; Nitrogen ; Oxidation-Reduction ; Wastewater ; *Water ; }, abstract = {The aim of this work was to study the operational performance and the microbial community dynamics during the start-up of ANITA[TM]Mox technology implemented at full-scale wastewater treatment plant in Finland to treat reject water from anaerobic digesters. The average ammonium removal in the studied setup reached around 90%, withstanding ammonium loads up to 0.13 g N m[-2]h[-1]. The nitrite concentration in the effluent did not exceed 10 mg L[-1], and there was a slight accumulation of NO3[-]-N during the operation which was controlled. Thus, the result showed a robust success to high ammonium loading in presence of organic matter. The sequencing showed a heterogeneous microbial population where Methanosaeta, WCHA1-57 genus, Sphingobacteriia, Chlorobia and diverse unknown fungi were found as dominant phylotypes. Moreover, members of the Brocadiaceae family were dominant in the adhered biomass, mostly represented by Candidatus Scalindua, rarely reported in WWTPs. Overall, the results demonstrated a drastic effect of region-specific operational conditions on carrier biofilm microbial communities as it was demonstrated by the microbial studies.}, }
@article {pmid33444853, year = {2021}, author = {Yang, Y and Herbold, CW and Jung, MY and Qin, W and Cai, M and Du, H and Lin, JG and Li, X and Li, M and Gu, JD}, title = {Survival strategies of ammonia-oxidizing archaea (AOA) in a full-scale WWTP treating mixed landfill leachate containing copper ions and operating at low-intensity of aeration.}, journal = {Water research}, volume = {191}, number = {}, pages = {116798}, doi = {10.1016/j.watres.2020.116798}, pmid = {33444853}, issn = {1879-2448}, mesh = {Ammonia ; *Archaea/genetics ; Bacteria ; Copper ; Ions ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; *Water Pollutants, Chemical ; }, abstract = {Recent studies indicate that ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal by wastewater treatment plants (WWTPs). However, our knowledge of the mechanisms employed by AOA for growth and survival in full-scale WWTPs is still limited. Here, metagenomic and metatranscriptomic analyses combined with a laboratory cultivation experiment revealed that three active AOAs (WS9, WS192, and WS208) belonging to family Nitrososphaeraceae were active in the deep oxidation ditch (DOD) of a full-scale WWTP treating landfill leachate, which is configured with three continuous aerobic-anoxic (OA) modules with low-intensity aeration (≤ 1.5 mg/L). AOA coexisted with AOB and complete ammonia oxidizers (Comammox), while the ammonia-oxidizing microbial (AOM) community was unexpectedly dominated by the novel AOA strain WS9. The low aeration, long retention time, and relatively high inputs of ammonium and copper might be responsible for the survival of AOA over AOB and Comammox, while the dominance of WS9, specifically may be enhanced by substrate preference and uniquely encoded retention strategies. The urease-negative WS9 is specifically adapted for ammonia acquisition as evidenced by the high expression of an ammonium transporter, whereas two metabolically versatile urease-positive AOA strains (WS192 and WS208) can likely supplement ammonia needs with urea. This study provides important information for the survival and application of the eutrophic Nitrososphaeraceae AOA and advances our understanding of archaea-dominated ammonia oxidation in a full-scale wastewater treatment system.}, }
@article {pmid33444433, year = {2021}, author = {Kerkhof, LJ}, title = {Is Oxford Nanopore sequencing ready for analyzing complex microbiomes?.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {3}, pages = {}, pmid = {33444433}, issn = {1574-6941}, mesh = {High-Throughput Nucleotide Sequencing ; *Microbiota ; *Nanopore Sequencing ; *Nanopores ; Sequence Analysis, DNA ; }, abstract = {This minireview will discuss the improvements in Oxford Nanopore (Oxford; sequencing technology that make the MinION a viable platform for microbial ecology studies. Specific issues being addressed are the increase in sequence accuracy from 65 to 96.5% during the last 5 years, the ability to obtain a quantifiable/predictive signal from the MinION with respect to target molecule abundance, simple-to-use GUI-based pathways for data analysis and the modest additional equipment needs for sequencing in the field. Coupling these recent improvements with the low capital costs for equipment and the reasonable per sample cost makes MinION sequencing an attractive option for virtually any laboratory.}, }
@article {pmid33443587, year = {2021}, author = {Hugoni, M and Nunan, N and Thioulouse, J and Dubost, A and Abrouk, D and Martins, JMF and Goffner, D and Prigent-Combaret, C and Grundmann, G}, title = {Small-Scale Variability in Bacterial Community Structure in Different Soil Types.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {470-483}, pmid = {33443587}, issn = {1432-184X}, support = {779949//EC2CO MicrobiEn/ ; ANR-11-LABX-0010//LabEx Chimie des Syst&#xe8;mes Complexes (FR)/ ; }, mesh = {Biodiversity ; Ecosystem ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Soil ; Soil Microbiology ; }, abstract = {Microbial spatial distribution has mostly been studied at field to global scales (i.e., ecosystem scales). However, the spatial organization at small scales (i.e., centimeter to millimeter scales), which can help improve our understanding of the impacts of spatial communities structure on microbial functioning, has received comparatively little attention. Previous work has shown that small-scale spatial structure exists in soil microbial communities, but these studies have not compared soils from geographically distant locations, nor have they utilized community ecology approaches, such as the core and satellite hypothesis and/or abundance-occupancy relationships, often used in macro-ecology, to improve the description of the spatial organization of communities. In the present work, we focused on bacterial diversity (i.e., 16S rRNA gene sequencing) occurring in micro-samples from a variety of locations with different pedo-climatic histories (i.e., from semi-arid, alpine, and temperate climates) and physicochemical properties. The forms of ecological spatial relationships in bacterial communities (i.e., occupancy-frequency and abundance-occupancy) and taxa distributions (i.e., habitat generalists and specialists) were investigated. The results showed that bacterial composition differed in the four soils at the small scale. Moreover, one soil presented a satellite mode distribution, whereas the three others presented bimodal distributions. Interestingly, numerous core taxa were present in the four soils among which 8 OTUs were common to the four sites. These results confirm that analyses of the small-scale spatial distribution are necessary to understand consequent functional processes taking place in soils, affecting thus ecosystem functioning.}, }
@article {pmid33442763, year = {2021}, author = {Mutnale, MC and Reddy, GS and Vasudevan, K}, title = {Bacterial Community in the Skin Microbiome of Frogs in a Coldspot of Chytridiomycosis Infection.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {554-558}, pmid = {33442763}, issn = {1432-184X}, support = {BSC0207//Council&#xa0;of&#xa0;Scientific and Industrial Research, India/ ; }, mesh = {Animals ; Anura ; Bacteria/genetics ; *Chytridiomycota/genetics ; *Microbiota ; *Mycoses ; Skin ; }, abstract = {Chytridiomycosis is a fungal disease caused by the pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), which has caused declines in amphibian populations worldwide. Asia is considered as a coldspot of infection, since adult frogs are less susceptible to Bd-induced mortality or morbidity. Using the next-generation sequencing approach, we assessed the cutaneous bacterial community composition and presence of anti-Bd bacteria in six frog species from India using DNA isolated from skin swabs. All the six frog species sampled were tested using nested PCR and found Bd negative. We found a total of 551 OTUs on frog skin, of which the bacterial phyla such as Proteobacteria (56.15% average relative abundance) was dominated followed by Actinobacteria (21.98% average relative abundance) and Firmicutes (13.7% average relative abundance). The contribution of Proteobacteria in the anti-Bd community was highest and represented by 175 OTUs. Overall, the anti-Bd bacterial community dominated (51.7% anti-Bd OTUs) the skin microbiome of the frogs. The study highlights the putative role of frog skin microbiome in affording resistance to Bd infections in coldspots of infection.}, }
@article {pmid33442762, year = {2021}, author = {Qin, Y and Puppe, D and Zhang, L and Sun, R and Li, P and Xie, S}, title = {How Does Sphagnum Growing Affect Testate Amoeba Communities and Corresponding Protozoic Si Pools? Results from Field Analyses in SW China.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {459-469}, pmid = {33442762}, issn = {1432-184X}, mesh = {*Amoeba ; Biodiversity ; Ecosystem ; *Sphagnopsida ; }, abstract = {The policy and practice of ecological restoration and conservation in China obtained some remarkable results. For example, Sphagnum moss growing on abandoned farmland, which was peatland before agricultural use, has rapidly expanded the wetland area in SW China. Microorganisms such as testate amoebae are sensitive to environmental change and thus have been widely used as ecological indicators in various habitats. We analyzed differently aged Sphagnum growing plots on a Sphagnum growing farmland and natural Sphagnum plots in SW China to examine how Sphagnum-dwelling testate amoeba communities and corresponding protozoic silicon (Si) pools respond to ecological restoration practice. We found that abundance, taxon richness, and diversity of testate amoebae were higher in Sphagnum growing farmland plots compared to natural Sphagnum plots. Protozoic Si pools showed an increase with Sphagnum growing time representing increased Si accumulation by idiosomic testate amoeba shells. However, protozoic Si pools were negatively correlated with taxon richness and diversity of testate amoebae. Our results showed that (i) natural Sphagnum plots were not characterized by the expected higher biodiversity of testate amoebae compared to Sphagnum growing plots and (ii) consequently protozoic Si pool quantity in natural Sphagnum plots was less driven by biodiversity of testate amoebae than expected. We concluded our results to underline the value of (i) environmental restoration policy in general and (ii) testate amoeba communities and corresponding protozoic Si pools for Si cycling in restoration areas of peatlands in particular. Based on our results, we recommend a sustainable cultivation of Sphagnum moss and an additional establishment of protected areas, where no Sphagnum harvesting occurs. These protected Sphagnum areas might represent hot spots of undisturbed testate amoeba communities and corresponding protozoic Si pools and thus of microbial Si cycling.}, }
@article {pmid33441489, year = {2021}, author = {Fritts, RK and McCully, AL and McKinlay, JB}, title = {Extracellular Metabolism Sets the Table for Microbial Cross-Feeding.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {85}, number = {1}, pages = {}, pmid = {33441489}, issn = {1098-5557}, mesh = {Bacteria/*metabolism ; Biofilms/*growth &amp; development ; Biological Transport/*physiology ; Extracellular Vesicles/physiology ; Microbiota/physiology ; Quorum Sensing/*physiology ; Signal Transduction ; Symbiosis/*physiology ; }, abstract = {The transfer of nutrients between cells, or cross-feeding, is a ubiquitous feature of microbial communities with emergent properties that influence our health and orchestrate global biogeochemical cycles. Cross-feeding inevitably involves the externalization of molecules. Some of these molecules directly serve as cross-fed nutrients, while others can facilitate cross-feeding. Altogether, externalized molecules that promote cross-feeding are diverse in structure, ranging from small molecules to macromolecules. The functions of these molecules are equally diverse, encompassing waste products, enzymes, toxins, signaling molecules, biofilm components, and nutrients of high value to most microbes, including the producer cell. As diverse as the externalized and transferred molecules are the cross-feeding relationships that can be derived from them. Many cross-feeding relationships can be summarized as cooperative but are also subject to exploitation. Even those relationships that appear to be cooperative exhibit some level of competition between partners. In this review, we summarize the major types of actively secreted, passively excreted, and directly transferred molecules that either form the basis of cross-feeding relationships or facilitate them. Drawing on examples from both natural and synthetic communities, we explore how the interplay between microbial physiology, environmental parameters, and the diverse functional attributes of extracellular molecules can influence cross-feeding dynamics. Though microbial cross-feeding interactions represent a burgeoning field of interest, we may have only begun to scratch the surface.}, }
@article {pmid33441406, year = {2021}, author = {Hu, J and Jin, VL and Konkel, JYM and Schaeffer, SM and Schneider, LG and DeBruyn, JM}, title = {Soil Health Management Enhances Microbial Nitrogen Cycling Capacity and Activity.}, journal = {mSphere}, volume = {6}, number = {1}, pages = {}, pmid = {33441406}, issn = {2379-5042}, mesh = {Agriculture/*methods ; Bacteria/*genetics ; Bacterial Physiological Phenomena/genetics ; Nitrification ; Nitrogen/metabolism ; Nitrogen Cycle/*genetics/physiology ; Soil/chemistry ; *Soil Microbiology ; Vicia/microbiology ; }, abstract = {Soil microbial transformations of nitrogen (N) can be affected by soil health management practices. Here, we report in situ seasonal dynamics of the population size (gene copy abundances) and functional activity (transcript copy abundances) of five bacterial genes involved in soil N cycling (ammonia-oxidizing bacteria [AOB] amoA, nifH, nirK, nirS, and nosZ) in a long-term continuous cotton production system under different management practices (cover crops, tillage, and inorganic N fertilization). Hairy vetch (Vicia villosa Roth), a leguminous cover crop, most effectively promoted the expression of N cycle genes, which persisted after cover crop termination throughout the growing season. Moreover, we observed similarly high or even higher N cycle gene transcript abundances under vetch with no fertilizer as no cover crop with N fertilization throughout the cover crop peak and cotton growing seasons (April, May, and October). Further, both the gene and transcript abundances of amoA and nosZ were positively correlated to soil nitrous oxide (N2O) emissions. We also found that the abundances of amoA genes and transcripts both positively correlated to field and incubated net nitrification rates. Together, our results revealed relationships between microbial functional capacity and activity and in situ soil N transformations under different agricultural seasons and soil management practices.IMPORTANCE Conservation agriculture practices that promote soil health have distinct and lasting effects on microbial populations involved with soil nitrogen (N) cycling. In particular, using a leguminous winter cover crop (hairy vetch) promoted the expression of key functional genes involved in soil N cycling, equaling or exceeding the effects of inorganic N fertilizer. Hairy vetch also left a legacy on soil nutrient capacity by promoting the continued activity of N cycling microbes after cover crop termination and into the main growing season. By examining both genes and transcripts involved in soil N cycling, we showed different responses of functional capacity (i.e., gene abundances) and functional activity (i.e., transcript abundances) to agricultural seasons and management practices, adding to our understanding of the effects of soil health management practices on microbial ecology.}, }
@article {pmid33440279, year = {2021}, author = {Zhong, Q and Cruz-Paredes, C and Zhang, S and Rousk, J}, title = {Can heavy metal pollution induce bacterial resistance to heavy metals and antibiotics in soils from an ancient land-mine?.}, journal = {Journal of hazardous materials}, volume = {411}, number = {}, pages = {124962}, doi = {10.1016/j.jhazmat.2020.124962}, pmid = {33440279}, issn = {1873-3336}, mesh = {Ancient Lands ; Anti-Bacterial Agents/toxicity ; China ; Ecosystem ; Environmental Monitoring ; Humans ; *Metals, Heavy/analysis/toxicity ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis/toxicity ; }, abstract = {Microbial resistance to antibiotics is a growing challenge to human health. Recent evidence has indicated that antibiotic resistance can be co-selected for by exposure to heavy metals in agricultural soils. It remains unknown if this is a concern in other environments contaminated by metals. We here investigated soil microbial activities, composition and tolerance to heavy metals and antibiotics in a mining soil survey. We found that microbial respiration, growth, and biomass were affected by available metal concentrations. Most of the variation in microbial PLFA composition was explained by differences in heavy metal and pH. Additionally, pollution-induced bacterial community tolerance to toxicants including Cu, Pb, Zn, tetracycline and vancomycin was determined. Although only bacterial tolerance to Pb increased with higher levels of metals, the links between bacterial metal tolerance and soil metal concentrations were clear when considered together with previously published reports, suggesting that bacterial metal tolerance were universally elevated in the surveyed soils. The induced levels of heavy metal tolerance coincided with elevated levels of tolerance to vancomycin, but not to tetracycline. Our study showed that heavy metals can co-select for resistance to clinically important antibiotics also in ecosystems without manure input or antibiotic pollution.}, }
@article {pmid33438074, year = {2021}, author = {Shen, J and Wyness, AJ and Claire, MW and Zerkle, AL}, title = {Spatial Variability of Microbial Communities and Salt Distributions Across a Latitudinal Aridity Gradient in the Atacama Desert.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {442-458}, pmid = {33438074}, issn = {1432-184X}, support = {678812//H2020 European Research Council/ ; 60501//John Templeton Foundation/ ; 201708060070//Chinese Scholarship Council/ ; }, mesh = {Bacteria/genetics ; Bacteroidetes ; *Desert Climate ; *Microbiota ; Soil Microbiology ; }, abstract = {Over the past 150 million years, the Chilean Atacama Desert has been transformed into one of the most inhospitable landscapes by geophysical changes, which makes it an ideal Mars analog that has been explored for decades. However, a heavy rainfall that occurred in the Atacama in 2017 provides a unique opportunity to study the response of resident extremophiles to rapid environmental change associated with excessive water and salt shock. Here we combine mineral/salt composition measurements, amendment cell culture experiments, and next-generation sequencing analyses to study the variations in salts and microbial communities along a latitudinal aridity gradient of the Atacama Desert. In addition, we examine the reshuffling of Atacama microbiomes after the rainfall event. Analysis of microbial community composition revealed that soils within the southern arid desert were consistently dominated by Actinobacteria, Chloroflexi, Proteobacteria, Firmicutes, Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Acidobacteria, and Verrucomicrobia. Intriguingly, the hyperarid microbial consortia exhibited a similar pattern to the more southern desert. Salts at the shallow subsurface were dissolved and leached down to a deeper layer, challenging indigenous microorganisms with the increasing osmotic stress. Microbial viability was found to change with aridity and rainfall events. This study sheds light on the structure of xerotolerant, halotolerant, and radioresistant microbiomes from the hyperarid northern desert to the less arid southern transition region, as well as their response to changes in water availability.}, }
@article {pmid33437426, year = {2021}, author = {Petrén, H and Gloder, G and Posledovich, D and Wiklund, C and Friberg, M}, title = {Innate preference hierarchies coupled with adult experience, rather than larval imprinting or transgenerational acclimation, determine host plant use in Pieris rapae.}, journal = {Ecology and evolution}, volume = {11}, number = {1}, pages = {242-251}, pmid = {33437426}, issn = {2045-7758}, abstract = {The evolution of host range drives diversification in phytophagous insects, and understanding the female oviposition choices is pivotal for understanding host specialization. One controversial mechanism for female host choice is Hopkins' host selection principle, where females are predicted to increase their preference for the host species they were feeding upon as larvae. A recent hypothesis posits that such larval imprinting is especially adaptive in combination with anticipatory transgenerational acclimation, so that females both allocate and adapt their offspring to their future host. We study the butterfly Pieris rapae, for which previous evidence suggests that females prefer to oviposit on host individuals of similar nitrogen content as the plant they were feeding upon as larvae, and where the offspring show higher performance on the mother's host type. We test the hypothesis that larval experience and anticipatory transgenerational effects influence female host plant acceptance (no-choice) and preference (choice) of two host plant species (Barbarea vulgaris and Berteroa incana) of varying nitrogen content. We then test the offspring performance on these hosts. We found no evidence of larval imprinting affecting female decision-making during oviposition, but that an adult female experience of egg laying in no-choice trials on the less-preferred host Be. incana slightly increased the P. rapae propensity to oviposit on Be. incana in subsequent choice trials. We found no transgenerational effects on female host acceptance or preference, but negative transgenerational effects on larval performance, because the offspring of P. rapae females that had developed on Be. incana as larvae grew slower on both hosts, and especially on Be. incana. Our results suggest that among host species, preferences are guided by hard-wired preference hierarchies linked to species-specific host traits and less affected by larval experience or transgenerational effects, which may be more important for females evaluating different host individuals of the same species.}, }
@article {pmid33436516, year = {2021}, author = {Fu, S and Wang, Q and Zhang, Y and Yang, Q and Hao, J and Liu, Y and Pang, B}, title = {Dynamics and Microevolution of Vibrio parahaemolyticus Populations in Shellfish Farms.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33436516}, issn = {2379-5077}, abstract = {Vibrio parahaemolyticus is becoming the leading cause of acute bacterial gastroenteritis, but its population dynamics in aquafarms have received limited attention. To address this research gap, we selected three shellfish farms to examine the impacts of ocean currents and the transport of live aquatic animals on the transmission and microevolution of V. parahaemolyticus by using multilocus sequence typing (MLST) and whole-genome sequencing. MLST and genomic analysis revealed that the community structure of V. parahaemolyticus in Dalian and Donggang was relatively stable in the presence of ocean currents; however, horizontal gene transfer of mobile genetic elements (MGEs) between Dalian and Donggang was very common. Further analysis indicated that the transport of live aquatic animals from Dalian to Xiamen not only introduced new V. parahaemolyticus populations but also allowed the exchange of genetic material between the two sites. More interestingly, Dalian-originated strain ST722 was introduced to Xiamen farms, resulting in one MLST allele change and the acquisition of two genomic islands from indigenous isolates in Xiamen within 8 months; such alterations are thought to promote the adaptation of V. parahaemolyticus These results provide direct observations of how ocean currents and the transport of live aquatic animals contribute to the dissemination and genetic mixture of V. parahaemolyticus, which provides insights into the dynamics and microevolution of V. parahaemolyticus in aquacultural environments.IMPORTANCE Globally, V. parahaemolyticus-related gastroenteritis outbreaks caused by seafood consumption represent an increasing threat to human health. Despite advances in our understanding of the global epidemiology of pandemic V. parahaemolyticus, fundamental questions about the key driving forces for the spread of V. parahaemolyticus at regional and national scales remain unanswered. This study revealed that the transregional transport of aquatic animals and the movement of ocean currents both contributed to the mixing of V. parahaemolyticus populations. More importantly, this study demonstrated how genetic mixture occurred between introduced and endemic V. parahaemolyticus populations via the transport of aquatic animals, which accelerated bacterial adaptation by transferring ecologically important functions. These results suggest that human activities entail a risk of the emergence of new virulent populations for both aquatic animals and humans by horizontal gene transfer and provide important insights into the microevolution and population mixing of V. parahaemolyticus.}, }
@article {pmid33436509, year = {2021}, author = {Meier, DV and Imminger, S and Gillor, O and Woebken, D}, title = {Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33436509}, issn = {2379-5077}, abstract = {Desert surface soils devoid of plant cover are populated by a variety of microorganisms, many with yet unresolved physiologies and lifestyles. Nevertheless, a common feature vital for these microorganisms inhabiting arid soils is their ability to survive long drought periods and reactivate rapidly in rare incidents of rain. Chemolithotrophic processes such as oxidation of atmospheric hydrogen and carbon monoxide are suggested to be a widespread energy source to support dormancy and resuscitation in desert soil microorganisms. Here, we assessed the distribution of chemolithotrophic, phototrophic, and desiccation-related metabolic potential among microbial populations in arid biological soil crusts (BSCs) from the Negev Desert, Israel, via population-resolved metagenomic analysis. While the potential to utilize light and atmospheric hydrogen as additional energy sources was widespread, carbon monoxide oxidation was less common than expected. The ability to utilize continuously available energy sources might decrease the dependency of mixotrophic populations on organic storage compounds and carbon provided by the BSC-founding cyanobacteria. Several populations from five different phyla besides the cyanobacteria encoded CO2 fixation potential, indicating further potential independence from photoautotrophs. However, we also found population genomes with a strictly heterotrophic genetic repertoire. The highly abundant Rubrobacteraceae (Actinobacteriota) genomes showed particular specialization for this extreme habitat, different from their closest cultured relatives. Besides the ability to use light and hydrogen as energy sources, they encoded extensive O2 stress protection and unique DNA repair potential. The uncovered differences in metabolic potential between individual, co-occurring microbial populations enable predictions of their ecological niches and generation of hypotheses on the dynamics and interactions among them.IMPORTANCE This study represents a comprehensive community-wide genome-centered metagenome analysis of biological soil crust (BSC) communities in arid environments, providing insights into the distribution of genes encoding different energy generation mechanisms, as well as survival strategies, among populations in an arid soil ecosystem. It reveals the metabolic potential of several uncultured and previously unsequenced microbial genera, families, and orders, as well as differences in the metabolic potential between the most abundant BSC populations and their cultured relatives, highlighting once more the danger of inferring function on the basis of taxonomy. Assigning functional potential to individual populations allows for the generation of hypotheses on trophic interactions and activity patterns in arid soil microbial communities and represents the basis for future resuscitation and activity studies of the system, e.g., involving metatranscriptomics.}, }
@article {pmid33436507, year = {2021}, author = {Wang, H and Beier, N and Boedeker, C and Sztajer, H and Henke, P and Neumann-Schaal, M and Mansky, J and Rohde, M and Overmann, J and Petersen, J and Klawonn, F and Kucklick, M and Engelmann, S and Tomasch, J and Wagner-Döbler, I}, title = {Dinoroseobacter shibae Outer Membrane Vesicles Are Enriched for the Chromosome Dimer Resolution Site dif.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33436507}, issn = {2379-5077}, abstract = {Outer membrane vesicles (OMVs) are universally produced by prokaryotes and play important roles in symbiotic and pathogenic interactions. They often contain DNA, but a mechanism for its incorporation is lacking. Here, we show that Dinoroseobacter shibae, a dinoflagellate symbiont, constitutively secretes OMVs containing DNA. Time-lapse microscopy captured instances of multiple OMV production at the septum during cell division. DNA from the vesicle lumen was up to 22-fold enriched for the region around the terminus of replication (ter). The peak of coverage was located at dif, a conserved 28-bp palindromic sequence required for binding of the site-specific tyrosine recombinases XerC/XerD. These enzymes are activated at the last stage of cell division immediately prior to septum formation when they are bound by the divisome protein FtsK. We suggest that overreplicated regions around the terminus have been repaired by the FtsK-dif-XerC/XerD molecular machinery. The vesicle proteome was clearly dominated by outer membrane and periplasmic proteins. Some of the most abundant vesicle membrane proteins were predicted to be required for direct interaction with peptidoglycan during cell division (LysM, Tol-Pal, Spol, lytic murein transglycosylase). OMVs were 15-fold enriched for the saturated fatty acid 16:00. We hypothesize that constitutive OMV secretion in D. shibae is coupled to cell division. The footprint of the FtsK-dif-XerC/XerD molecular machinery suggests a novel potentially highly conserved route for incorporation of DNA into OMVs. Clearing the division site from small DNA fragments might be an important function of vesicles produced during exponential growth under optimal conditions.IMPORTANCE Gram-negative bacteria continually form vesicles from their outer membrane (outer membrane vesicles [OMVs]) during normal growth. OMVs frequently contain DNA, and it is unclear how DNA can be shuffled from the cytoplasm to the OMVs. We studied OMV cargo in Dinoroseobacter shibae, a symbiont of dinoflagellates, using microscopy and a multi-omics approach. We found that vesicles formed during undisturbed exponential growth contain DNA which is enriched for genes around the replication terminus, specifically, the binding site for an enzyme complex that is activated at the last stage of cell division. We suggest that the enriched genes are the result of overreplication which is repaired by their excision and excretion via membrane vesicles to clear the divisome from waste DNA.}, }
@article {pmid33435231, year = {2021}, author = {Cohen Kadosh, K and Muhardi, L and Parikh, P and Basso, M and Jan Mohamed, HJ and Prawitasari, T and Samuel, F and Ma, G and Geurts, JM}, title = {Nutritional Support of Neurodevelopment and Cognitive Function in Infants and Young Children-An Update and Novel Insights.}, journal = {Nutrients}, volume = {13}, number = {1}, pages = {}, pmid = {33435231}, issn = {2072-6643}, mesh = {Brain/*growth &amp; development ; Child, Preschool ; *Cognition ; Cognitive Aging ; Emotions ; Fatty Acids ; Food ; Gastrointestinal Microbiome ; Humans ; Infant ; Kynurenine ; Minerals ; Nutrients ; *Nutritional Support ; Prebiotics ; Probiotics ; Quality of Life ; }, abstract = {Proper nutrition is crucial for normal brain and neurocognitive development. Failure to optimize neurodevelopment early in life can have profound long-term implications for both mental health and quality of life. Although the first 1000 days of life represent the most critical period of neurodevelopment, the central and peripheral nervous systems continue to develop and change throughout life. All this time, development and functioning depend on many factors, including adequate nutrition. In this review, we outline the role of nutrients in cognitive, emotional, and neural development in infants and young children with special attention to the emerging roles of polar lipids and high quality (available) protein. Furthermore, we discuss the dynamic nature of the gut-brain axis and the importance of microbial diversity in relation to a variety of outcomes, including brain maturation/function and behavior are discussed. Finally, the promising therapeutic potential of psychobiotics to modify gut microbial ecology in order to improve mental well-being is presented. Here, we show that the individual contribution of nutrients, their interaction with other micro- and macronutrients and the way in which they are organized in the food matrix are of crucial importance for normal neurocognitive development.}, }
@article {pmid33432372, year = {2021}, author = {Nguyen, TTT and Foysal, MJ and Fotedar, R and Gupta, SK and Siddik, MAB and Tay, CY}, title = {The Effect of Two Dietary Protein Sources on Water Quality and the Aquatic Microbial Communities in Marron (Cherax cainii) Culture.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {299-308}, pmid = {33432372}, issn = {1432-184X}, support = {CIPRS) (No. 18508848 - Curtin)//Curtin University of Technology/ ; }, mesh = {Animal Feed/analysis ; Animals ; *Astacoidea ; Dietary Proteins ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Water Quality ; }, abstract = {Feeding freshwater crayfish species with different diets not only affects the water quality but also induces the abundance of various microbial communities in their digestive tracts. In this context, very limited research has been undertaken to understand the impacts of various protein incorporated aqua-diets on the characteristics of water and its microbial communities. In this study, we have critically analysed the water quality parameters including pH, dissolved oxygen, nitrate, nitrite, ammonia and phosphorus, as well as bacterial communities under marron (Cherax cainii) aquaculture, fed fishmeal (FM) and poultry by-product meal (PBM)-based diets for 60 days. The results unveiled that over the time, feeding has significant impacts on organic waste accumulation, especially ammonia, nitrate, nitrite and phosphate, while no effects were observed on pH and dissolved oxygen. Analysis of 16S rRNA sequence data of water sample indicated significant (P < 0.05) shift of microbial abundance in post-fed FM and PBM water with the evidence of microbial transmission from the gut of marron. Post-fed marron resulted in a significant correlation of Hafnia, Enterobacter, Candidatus Bacilloplasma and Aquitella with the quality and microbial population of water. The results of this study generated valuable knowledge database of microbes-water relationship for better health management practices and production of marron aquaculture fed with FM and PBM diets in under restricted feeding regime with the feeding ratios provided.}, }
@article {pmid33429312, year = {2021}, author = {Fu, Y and Wang, F and Sheng, H and Hu, F and Wang, Z and Xu, M and Bian, Y and Jiang, X and Tiedje, JM}, title = {Removal of extracellular antibiotic resistance genes using magnetic biochar/quaternary phosphonium salt in aquatic environments: A mechanistic study.}, journal = {Journal of hazardous materials}, volume = {411}, number = {}, pages = {125048}, doi = {10.1016/j.jhazmat.2021.125048}, pmid = {33429312}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology ; Charcoal ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Humans ; Magnetic Phenomena ; Wastewater ; }, abstract = {The proliferation and spread of antibiotic resistance genes (ARGs) is becoming a worldwide crisis. Extracellular DNA encoding ARGs (eARGs) in aquatic environment plays a critical role in the dispersion of antimicrobial resistance genes. Strategies to control the dissemination of eARGs are urgently required for ecological safety and human health. Towards this goal, magnetic biochar/quaternary phosphonium salt (MBQ), was used to investigate the efficiency and removal mechanism for eARGs. Magnetic biochar modified by quaternary phosphonium salt enhanced the adsorption capacity of extracellular DNA to approximately 9 folds, compared to that of the unmodified. DNA adsorption by MBQ was mainly dominated by chemisorption in heterogeneous systems and was promoted in acidic and low-salt environment. The generation of •OH and MBQ colloid jointly cleaved DNA into fragments, facilitating the adsorption of the phosphate backbone of DNA onto MBQ through electrostatic force as well as the conformational transition of DNA. Furthermore, quantification of extracellular DNA after MBQ was applied in water demonstrated that over 92.7% of resistance genes were removed, indicating a significantly reduced risk of propagation of antimicrobial resistance in aquatic environments. These findings have a practical significance in the application of MBQ in mitigating the spread of ARGs in aquatic environment.}, }
@article {pmid33429117, year = {2021}, author = {Forés, E and Bofill-Mas, S and Itarte, M and Martínez-Puchol, S and Hundesa, A and Calvo, M and Borrego, CM and Corominas, LL and Girones, R and Rusiñol, M}, title = {Evaluation of two rapid ultrafiltration-based methods for SARS-CoV-2 concentration from wastewater.}, journal = {The Science of the total environment}, volume = {768}, number = {}, pages = {144786}, pmid = {33429117}, issn = {1879-1026}, mesh = {Animals ; *COVID-19 ; Communicable Disease Control ; Humans ; Mice ; *SARS-CoV-2 ; Ultrafiltration ; Wastewater ; }, abstract = {Quantitative measurements of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in raw wastewater have been implemented worldwide since the beginning of the pandemic. Recent efforts are being made to evaluate different viral concentration methodologies to overcome supplier shortages during lockdowns. A set of 22-wastewater samples seeded with murine hepatitis virus (MHV), a member of the Coronaviridae family, and the bacteriophage MS2, were used to characterize and compare two ultrafiltration-based methods: a centrifugal ultrafiltration device (Centricon® Plus-70) and the automated concentrating pipette CP-Select™. Based on the recovery efficiencies, significant differences were observed for MHV, with Centricon® Plus-70 (24%) being the most efficient method. Nevertheless, concentrations of naturally occurring SARS-CoV-2, Human adenoviruses and JC polyomaviruses in these samples did not result in significant differences between methods suggesting that testing naturally occurring viruses may complement the evaluation of viral concentration methodologies. Based on the virus adsorption to solids and the necessity of a pre-centrifugation step to remove larger particles and avoid clogging when using ultrafiltration methods, we assessed the percentage of viruses not quantified after ultrafiltration. Around 23% of the detected SARS-CoV-2 would be discarded during the debris removal step. The CP-Select™ provided the highest concentration factor (up to 333×) and the lowest LoD (6.19 × 10[3] GC/l) for MHV and proved to be fast, automatic, highly reproducible and suitable to work under BSL-2 measures.}, }
@article {pmid33428723, year = {2021}, author = {Laursen, MF and Bahl, MI and Licht, TR}, title = {Settlers of our inner surface - factors shaping the gut microbiota from birth to toddlerhood.}, journal = {FEMS microbiology reviews}, volume = {45}, number = {4}, pages = {}, pmid = {33428723}, issn = {1574-6976}, support = {NNF19OC0056246//Novo Nordic Foundation/ ; }, mesh = {Adult ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; }, abstract = {During the first 3 years of life, the microbial ecosystem within the human gut undergoes a process that is unlike what happens in this ecosystem at any other time of our life. This period in time is considered a highly important developmental window, where the gut microbiota is much less resilient and much more responsive to external and environmental factors than seen in the adult gut. While advanced bioinformatics and clinical correlation studies have received extensive focus within studies of the human microbiome, basic microbial growth physiology has attracted much less attention, although it plays a pivotal role to understand the developing gut microbiota during early life. In this review, we will thus take a microbial ecology perspective on the analysis of factors that influence the temporal development of the infant gut microbiota. Such factors include sources of microbes that seed the intestinal environment, physico-chemical (abiotic) conditions influencing microbial growth and the availability of nutrients needed by the intestinal microbes.}, }
@article {pmid33424787, year = {2020}, author = {Figueroa-Gonzalez, PA and Bornemann, TLV and Adam, PS and Plewka, J and Révész, F and von Hagen, CA and Táncsics, A and Probst, AJ}, title = {Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {587782}, pmid = {33424787}, issn = {1664-302X}, abstract = {Organisms of the candidate phylum Saccharibacteria have frequently been detected as active members of hydrocarbon degrading communities, yet their actual role in hydrocarbon degradation remained unclear. Here, we analyzed three enrichment cultures of hydrocarbon-amended groundwater samples using genome-resolved metagenomics to unravel the metabolic potential of indigenous Saccharibacteria. Community profiling based on ribosomal proteins revealed high variation in the enrichment cultures suggesting little reproducibility although identical cultivation conditions were applied. Only 17.5 and 12.5% of the community members were shared between the three enrichment cultures based on ribosomal protein clustering and read mapping of reconstructed genomes, respectively. In one enrichment, two Saccharibacteria strains dominated the community with 16.6% in relative abundance and we were able to recover near-complete genomes for each of them. A detailed analysis of their limited metabolism revealed the capacity for peptide degradation, lactate fermentation from various hexoses, and suggests a scavenging lifestyle with external retrieval of molecular building blocks. In contrast to previous studies suggesting that Saccharibacteria are directly involved in hydrocarbon degradation, our analyses provide evidence that these organisms can be highly abundant scavengers acting rather as organic carbon sinks than hydrocarbon degraders in these communities.}, }
@article {pmid33422757, year = {2021}, author = {Vázquez-Blanco, R and Arias-Estévez, M and Bååth, E and Fernández-Calviño, D}, title = {Comparing the effect of Cu-based fungicides and pure Cu salts on microbial biomass, microbial community structure and bacterial community tolerance to Cu.}, journal = {Journal of hazardous materials}, volume = {409}, number = {}, pages = {124960}, doi = {10.1016/j.jhazmat.2020.124960}, pmid = {33422757}, issn = {1873-3336}, mesh = {Biomass ; Fatty Acids ; *Fungicides, Industrial/toxicity ; *Microbiota ; Salts ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis/toxicity ; }, abstract = {The effect of Cu on three different microbial endpoints was studied using different Cu sources, in order to check the usefulness of pure Cu salts to estimate the toxicity of commercial Cu fungicides on soil microbes. Cu additions caused similar dose-response curves of substrate induced respiration (SIR) decreases regardless of Cu source, i.e. the use of pure Cu salts to estimate the effect of Cu fungicides on microbial biomass using SIR may be useful. Phospholipid fatty acid (PLFA) analysis showed that the Cu source was more important for the microbial community structure than Cu concentration. Thus, the use of Cu salts to infer the effects of Cu fungicides on microbial community structure using PLFA analysis is not recommended, since effects of Cu concentration will be confounded with Cu source. Analyzing pollution induced community tolerance (PICT) to Cu showed that the use of pure Cu salts may overestimate Cu effects if Cu salt additions modified the soil pH. The highest doses of Cu salts increased bacterial community tolerance to Cu between 300 and 600 times, while commercial Cu fungicide increases were between 20 and 160 times. Therefore, the use of pure Cu salts to estimate the Cu fungicides effects on soil microbes is not recommended for PLFAs analyses, not suitable for PICT at high Cu concentrations, while useful for SIR.}, }
@article {pmid33420911, year = {2021}, author = {Doliwa, A and Dunthorn, M and Rassoshanska, E and Mahé, F and Bass, D and Duarte Ritter, C}, title = {Identifying Potential Hosts of Short-Branch Microsporidia.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {549-553}, pmid = {33420911}, issn = {1432-184X}, support = {#DU1319/5-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Cercozoa ; *Microsporidia/genetics ; Phylogeny ; Rainforest ; Soil ; }, abstract = {Microsporidia are obligate parasites that are closely related to Fungi. While the widely known "long-branch" Microsporidia infect mostly metazoans, the hosts of "short-branch" Microsporidia are only partially characterized or not known at all. Here, we used network analyses from Neotropical rainforest soil metabarcoding data, to infer co-occurrences between environmental lineages of short-branch microsporidians and their potential hosts. We found significant co-occurrences with several taxa, especially with Apicomplexa, Cercozoa, and Fungi, as well as some Metazoa. Our results are the first step to identify potential hosts of the environmental lineages of short-branch microsporidians, which can be targeted in future molecular and microscopic studies.}, }
@article {pmid33420910, year = {2021}, author = {García Hernández, E and Berg, MP and Van Oosten, AR and Smit, C and Falcão Salles, J}, title = {Linking Bacterial Communities Associated with the Environment and the Ecosystem Engineer Orchestia gammarellus at Contrasting Salt Marsh Elevations.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {537-548}, pmid = {33420910}, issn = {1432-184X}, support = {484425//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; ALWOP.219.00179028//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, mesh = {Animals ; Bacteria/genetics ; Ecosystem ; *Microbiota ; Phylogeny ; Soil ; Soil Microbiology ; *Wetlands ; }, abstract = {The digestive tract of animals harbors microbiota important for the host's fitness and performance. The interaction between digestive tract bacteria and soil animal hosts is still poorly explored despite the importance of soil fauna for ecosystem processes. In this study, we investigated the interactions between the bacterial communities from the digestive tract of the litter-feeding, semi-terrestrial crustacean Orchestia gammarellus and those obtained from the environment; these organisms thrive in, i.e., soil and plant litter from salt marshes. We hypothesized that elevation is an important driver of soil and litter bacterial communities, which indirectly (via ingested soil and litter bacteria) influences the bacterial communities in the digestive tract of O. gammarellus. Indeed, our results revealed that elevation modulated soil and litter bacterial community composition along with soil organic matter content and the C:N ratio. Soil and plant litter differed in alpha diversity indexes (richness and diversity), and in the case of plant litter, both indexes increased with elevation. In contrast, elevation did not affect the composition of bacterial communities associated with O. gammarellus' digestive tract, suggesting selection by the host, despite the fact that a large component of the bacterial community was also detected in external sources. Importantly, Ca. Bacilloplasma and Vibrio were highly prevalent and abundant in the host. The taxonomic comparison of Ca. Bacilloplasma amplicon sequence variants across the host at different elevations suggested a phylogenetic divergence due to host habitat (i.e., marine or semi-terrestrial), thus supporting their potential functional role in the animal physiology. Our study sheds light on the influence of the environment on soil animal-bacteria interactions and provides insights into the resilience of the O. gammarellus-associated bacteria to increased flooding frequency.}, }
@article {pmid33420625, year = {2021}, author = {Win, PM and Matsumura, E and Fukuda, K}, title = {Effects of Pesticides on the Diversity of Endophytic Fungi in Tea Plants.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {62-72}, pmid = {33420625}, issn = {1432-184X}, mesh = {Ascomycota ; Biodiversity ; *Colletotrichum ; Endophytes/genetics ; Fungi/genetics ; *Pesticides ; Plant Leaves ; Tea ; }, abstract = {We examined the effects of agrochemicals on the endophytic fungal community associated with tea plants. Endophytic fungi were isolated from four different tea plant tissues (bark, xylem, old leaves, new leaves) collected from pesticide-treated and untreated plots. In pesticide-treated plot, the acaricides, fungicides, and insecticides are typically applied 3 times each year. The infection rate was slightly lower in the pesticide-treated plot, but the difference between plots was not statistically significant. Colletotrichum camelliae, Phyllosticta capitalensis, and Pleosporales sp. were common endophytes in both plots. Among a total of 41 fungal species, only 21 were considered common endophytes. Colletotrichum pseudomajus was the predominant endophyte in the bark tissue in the untreated plot, whereas C. camelliae was predominant in the pesticide-treated plot. Paraphaeosphaeria neglecta and Phoma bellendis were predominant in the xylem tissues of samples from the untreated and treated plots, respectively. Colletotrichum camelliae was the most commonly found species in leaf tissues in both plots, but the colonization frequency was significantly lower in the pesticide-treated plot. Species richness was not affected by pesticide treatment. The community structure of endophytic fungi in stem tissues (bark and xylem) differed significantly between plots, but leaf tissue endophytic fungal community structure was not significantly influenced by pesticide treatment.}, }
@article {pmid33420624, year = {2021}, author = {Eraqi, WA and ElRakaiby, MT and Megahed, SA and Yousef, NH and Elshahed, MS and Yassin, AS}, title = {Spatiotemporal Analysis of the Water and Sediment Nile Microbial Community Along an Urban Metropolis.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {288-298}, pmid = {33420624}, issn = {1432-184X}, support = {2016423//National Science Foundation/ ; 3046//Academy of Scientific Research and Technology/ ; }, mesh = {Animals ; *Cyanobacteria ; Geologic Sediments ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Rivers ; Spatio-Temporal Analysis ; Water ; }, abstract = {Assessing microbial identity, diversity, and community structure could be a valuable tool for monitoring the impact of xenobiotics and anthropogenic inputs in rivers, especially in urban and industrial settings. Here, we characterize the Nile River microbial community in water and sediments in summer and winter at five locations that span its natural flow through the Cairo metropolis. 16S rRNA gene datasets were analyzed to identify the role played by sample type (sediment versus water), season, and location in shaping the community, as well as to predict functional potential of the Nile River microbiome. Microbial communities were mostly influenced by sampling type (sediments versus water), while seasonal effects were only observed in water samples. Spatial differences did not represent a significant factor in shaping the community in either summer or winter seasons. Proteobacteria was the most abundant phylum in both water and sediment samples, with the order Betaproteobacteriales being the abundant one. Chloroflexi and Bacteroidetes were also prevalent in sediment samples, while Cyanobacteria and Actinobacteria were abundant in water samples. The linear discriminative analysis effect size (LEfSe) identified the cyanobacterial genus Cyanobium PCC-6307 as the main variable between summer and winter water. Sequences representing human and animal potential pathogens, as well as toxin-producing Cyanobacteria, were identified in low abundance within the Nile microbiome. Functionally predicted metabolic pathways predicted the presence of antibiotic biosynthesis, as well as aerobic xenobiotic degradation pathways in the river microbiome.}, }
@article {pmid33417698, year = {2021}, author = {Moossavi, S and Fontes, ME and Rossi, L and Fusch, G and Surette, MG and Azad, MB}, title = {Capturing the diversity of the human milk microbiota through culture-enriched molecular profiling: a feasibility study.}, journal = {FEMS microbiology letters}, volume = {368}, number = {3}, pages = {}, doi = {10.1093/femsle/fnab001}, pmid = {33417698}, issn = {1574-6968}, mesh = {Bacteria/classification/genetics/*growth &amp; development/*isolation &amp; purification ; *Biodiversity ; Culture Techniques ; *Food Microbiology ; Humans ; Milk, Human/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Previous human milk studies have confirmed the existence of a highly diverse bacterial community using culture-independent and targeted culture-dependent techniques. However, culture-enriched molecular profiling of milk microbiota has not been done. Additionally, the impact of storage conditions and milk fractionation on microbiota composition is not understood. In this feasibility study, we optimized and applied culture-enriched molecular profiling to study culturable milk microbiota in eight milk samples collected from mothers of infants admitted to a neonatal intensive care unit. Fresh samples were immediately plated or stored at -80°C for 2 weeks (short-term frozen). Long-term samples were stored at -20°C for >6 months. Samples were cultured using 10 different culture media and incubated both aerobically and anaerobically. We successfully isolated major milk bacteria, including Streptococcus, Staphylococcus and Bifidobacterium, from fresh milk samples, but were unable to culture any bacteria from the long-term frozen samples. Short-term freezing shifted the composition of viable milk bacteria from the original composition in fresh samples. Nevertheless, the inter-individual variability of milk microbiota composition was observed even after short-term storage. There was no major difference in the overall milk microbiota composition between milk fractions in this feasibility study. This is among the first studies on culture-enriched molecular profiling of the milk microbiota demonstrating the effect of storage and fractionation on milk microbiota composition.}, }
@article {pmid33415825, year = {2021}, author = {Rogiers, T and Claesen, J and Van Gompel, A and Vanhoudt, N and Mysara, M and Williamson, A and Leys, N and Van Houdt, R and Boon, N and Mijnendonckx, K}, title = {Soil microbial community structure and functionality changes in response to long-term metal and radionuclide pollution.}, journal = {Environmental microbiology}, volume = {23}, number = {3}, pages = {1670-1683}, pmid = {33415825}, issn = {1462-2920}, mesh = {*Metals, Heavy ; *Microbiota ; Radioisotopes ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {Microbial communities are essential for a healthy soil ecosystem. Metals and radionuclides can exert a persistent pressure on the soil microbial community. However, little is known on the effect of long-term co-contamination of metals and radionuclides on the microbial community structure and functionality. We investigated the impact of historical discharges of the phosphate and nuclear industry on the microbial community in the Grote Nete river basin in Belgium. Eight locations were sampled along a transect to the river edge and one location further in the field. Chemical analysis demonstrated a metal and radionuclide contamination gradient and revealed a distinct clustering of the locations based on all metadata. Moreover, a relation between the chemical parameters and the bacterial community structure was demonstrated. Although no difference in biomass was observed between locations, cultivation-dependent experiments showed that communities from contaminated locations survived better on singular metals than communities from control locations. Furthermore, nitrification, a key soil ecosystem process seemed affected in contaminated locations when combining metadata with microbial profiling. These results indicate that long-term metal and radionuclide pollution impacts the microbial community structure and functionality and provides important fundamental insights into microbial community dynamics in co-metal-radionuclide contaminated sites.}, }
@article {pmid33415385, year = {2021}, author = {Colin, Y and Berthe, T and Molbert, N and Guigon, E and Vivant, AL and Alliot, F and Collin, S and Goutte, A and Petit, F}, title = {Urbanization Constrains Skin Bacterial Phylogenetic Diversity in Wild Fish Populations and Correlates with the Proliferation of Aeromonads.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {523-536}, pmid = {33415385}, issn = {1432-184X}, mesh = {Animals ; *Bacteria/genetics ; Cell Proliferation ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Urbanization ; }, abstract = {Changes in the state of rivers resulting from the activity and expansion of urban areas are likely to affect aquatic populations by increasing stress and disease, with the microbiota playing a potentially important intermediary role. Unraveling the dynamics of microbial flora is therefore essential to better apprehend the impact of anthropogenic disturbances on the health of host populations and the ecological integrity of hydrosystems. In this context, the present study simultaneously examined changes in the microbial communities associated with mucosal skin and gut tissues of eight fish species along an urbanization gradient in the Orge River (France). 16S rRNA gene metabarcoding revealed that the structure and composition of the skin microbiota varied substantially along the disturbance gradient and to a lesser extent according to fish taxonomy. Sequences affiliated with the Gammaproteobacteria, in particular the genus Aeromonas, prevailed on fish caught in the most urbanized areas, whereas they were nearly absent upstream. This rise of opportunistic taxa was concomitant with a decline in phylogenetic diversity, suggesting more constraining environmental pressures. In comparison, fish gut microbiota varied much more moderately with the degree of urbanization, possibly because this niche might be less directly exposed to environmental stressors. Co-occurrence networks further identified pairs of associated bacterial taxa, co-existing more or less often than expected at random. Few correlations could be identified between skin and gut bacterial taxa, supporting the assumption that these two microbial niches are disconnected and do not suffer from the same vulnerability to anthropic pressures.}, }
@article {pmid33415384, year = {2021}, author = {Shi, Y and Yang, H and Chu, M and Niu, X and Huo, X and Gao, Y and Zeng, J and Lin, Q and Lou, K}, title = {Diversity and Spatiotemporal Dynamics of Fungal Communities in the Rhizosphere Soil of Cotton in the Arid Region of Northwest China.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {87-99}, pmid = {33415384}, issn = {1432-184X}, support = {41471220//the National Natural Science Foundation of China/ ; 31860024//National Natural Science Foundation of China/ ; 2017YFD0200608-05//Nation Key Research Program of China/ ; 2018D01A44//National Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2016M602953XB//China Postdoctoral Science Foundation Funded the Sixtieth Batch/ ; qn2005yx023//Xinjiang Uygur Autonomous Region Outstanding Young Talent Training Program/ ; }, mesh = {Biodiversity ; Fungi/genetics ; Gossypium ; *Mycobiome ; *Rhizosphere ; Soil ; Soil Microbiology ; }, abstract = {This study aimed to investigate the fungal diversity and its temporal and spatial dynamics in the rhizosphere soil of healthy cotton by high-throughput sequencing. We studied species richness, composition, and distribution of cotton rhizosphere fungal community with respect to location (Alaer, Kuerle, Tumushuke, Hami, Shihezi, Wusu, and Jinghe) and plant growth period (seedling stage, bud stage, flowering stage, and boll-opening stage) using the methods of PCR-based high-throughput sequencing and real-time quantitative PCR. A total of 1,838,454 fungal nuclear ribosomal internal transcribed spacer region sequences (rRNA ITS) were obtained from all cotton plants sampled at different growth stages in the seven locations in Xinjiang. The most abundant fungal group in the cotton rhizosphere was the Ascomycota (78.72%), followed by the Zygomycota (9.56%) and Basidiomycota (2.77%). These sequences revealed an enormous number of operational taxonomic units (OTUs) in cotton (1802 unique OTUs), with 67-464 OTUs in a single cotton sample, at a 3% threshold and a sequencing depth of 30,000 sequences. We identified 33 classes and 389 genera from the resulting 1,800,714 sequences. Sordariomycetes was the most frequent class in all samples, followed by Leotiomycetes and Eurotiomycetes. There were some differences in OTUs among different growth stages, but the differences were not significant, with 382 OTUs (14.66%) being common to each of the stages. A marked difference in the diversity of fungi in the rhizosphere soil of cotton was evident among the different locations, with the highest number of OTUs being detected in Jinghe (1084 OTUs) and clusters of OTUs representative of northern and eastern Xinjiang being detected. There were significantly more tags of Mortierella in Jinghe and Wusu than in the other sampling sites. The dynamics of the rhizosphere fungal communities were influenced by sampling sites. To the best of our knowledge, the current study is the first application of PCR-based Illumina to characterize and compare the fungal biodiversity in multiple rhizosphere soil samples from cotton.}, }
@article {pmid33414351, year = {2021}, author = {Verdera, AB and Montecillo, AD and Obusan, MCM}, title = {Draft Genome Sequence of Streptomyces sp. Isolate H28 from the Meycauayan River, Philippines.}, journal = {Microbiology resource announcements}, volume = {10}, number = {1}, pages = {}, pmid = {33414351}, issn = {2576-098X}, abstract = {In this paper, we report the draft genome sequence of Streptomyces sp. isolate H28, isolated from sediments of the Meycauayan River in the Philippines. This species exhibits production of melanin as well as the ability to utilize and degrade both high-density polyethylene (HDPE) and low-density polyethylene (LDPE).}, }
@article {pmid33414343, year = {2021}, author = {Mori, JF and Kanaly, RA}, title = {Complete Genome Sequence of Sphingobium barthaii KK22, a High-Molecular-Weight Polycyclic Aromatic Hydrocarbon-Degrading Soil Bacterium.}, journal = {Microbiology resource announcements}, volume = {10}, number = {1}, pages = {}, pmid = {33414343}, issn = {2576-098X}, abstract = {Sphingobium barthaii KK22[T] is a high-molecular-weight polycyclic aromatic hydrocarbon-degrading soil bacterium that has been investigated in biotransformation, microbial ecology, and DNA damage studies. The complete genome sequence of S. barthaii revealed four closed circular sequences, including two chromosomes, a megaplasmid, and a smaller plasmid, by hybrid assembly using short- and long-read sequencing technologies.}, }
@article {pmid33414017, year = {2021}, author = {Riber, L and Hansen, LH}, title = {Epigenetic Memories: The Hidden Drivers of Bacterial Persistence?.}, journal = {Trends in microbiology}, volume = {29}, number = {3}, pages = {190-194}, doi = {10.1016/j.tim.2020.12.005}, pmid = {33414017}, issn = {1878-4380}, mesh = {Bacteria/*genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; DNA Methylation ; *Epigenesis, Genetic ; Gene Expression Regulation, Bacterial ; }, abstract = {Epigenetic modifications, including DNA methylation, stably alter gene expression without modifying genomic sequences. Recent evidence suggests that epigenetic regulation coupled with a long-term 'memory' effect plays a major role within bacterial persistence formation. Today, emerging high-resolution, single-molecule sequencing technologies allow an increased focus on DNA modifications as regulatory epigenetic marks, which presents a unique opportunity to identify possible epigenetic drivers of bacterial persistence.}, }
@article {pmid33412377, year = {2021}, author = {Wang, B and Ma, J and Zhang, L and Su, Y and Xie, Y and Ahmad, Z and Xie, B}, title = {The synergistic strategy and microbial ecology of the anaerobic co-digestion of food waste under the regulation of domestic garbage classification in China.}, journal = {The Science of the total environment}, volume = {765}, number = {}, pages = {144632}, doi = {10.1016/j.scitotenv.2020.144632}, pmid = {33412377}, issn = {1879-1026}, mesh = {Anaerobiosis ; Bioreactors ; China ; Digestion ; Food ; *Garbage ; Methane ; *Refuse Disposal ; Sewage ; }, abstract = {With the implementation of new domestic garbage classification policy in China, attention is growing to improve the treatment efficiency of municipal 'wet' waste. Combing with the new regulation, the synergistic strategy and the microbial ecology of the anaerobic co-digestion (AcoD) of cooked food waste (CFW), uncooked food waste (UCFW) and rice straw (RS) were analyzed in current study. Results showed that the maximum cumulative methane yield (CMY) and synergic index were obtained when CFW and UCFW were mixed at the ratio of 1:1 (based on volatile solid content). The highest CMY 452.94 ± 0.99 mL/g-VS was obtained when the ratio of CFW, UCFW and RS was 0.81:0.09:0.10, which was 16.29%, 36.20% and 121.84% higher than their mono-digestion, respectively. The AcoD promoted the methane potential by prolonging the release time of organic matter and slowing down the hydrolysis rate. Furthermore, the AcoD increased the species diversification and relative abundance of fermentation bacteria in digesters, and Methanosaeta predominated the methanogen communities. This study demonstrated a clean and sustainable AcoD strategy for safe disposal of urban food waste and revealed the variation of microbial community, which can provide a base for efficient bioenergy recovery from urban domestic garbage.}, }
@article {pmid33411249, year = {2021}, author = {Chakraborty, P and Paul, P and Kumari, M and Bhattacharjee, S and Singh, M and Maiti, D and Dastidar, DG and Akhter, Y and Kundu, T and Das, A and Tribedi, P}, title = {Attenuation of Pseudomonas aeruginosa biofilm by thymoquinone: an individual and combinatorial study with tetrazine-capped silver nanoparticles and tryptophan.}, journal = {Folia microbiologica}, volume = {66}, number = {2}, pages = {255-271}, pmid = {33411249}, issn = {1874-9356}, mesh = {Anti-Bacterial Agents/pharmacology ; Benzoquinones ; Biofilms ; *Metal Nanoparticles ; Microbial Sensitivity Tests ; *Pseudomonas aeruginosa ; Silver/pharmacology ; Tryptophan ; }, abstract = {Microbial biofilm indicates a cluster of microorganisms having the capability to display drug resistance property, thereby increasing its proficiency in spreading diseases. In the present study, the antibiofilm potential of thymoquinone, a black seed-producing natural molecule, was contemplated against the biofilm formation by Pseudomonas aeruginosa. Substantial antimicrobial activity was exhibited by thymoquinone against the test organism wherein the minimum inhibitory concentration of the compound was found to be 20 μg/mL. Thereafter, an array of experiments (crystal violet staining, protein count, and microscopic observation, etc.) were carried out by considering the sub-MIC doses of thymoquinone (5 and 10 μg/mL), each of which confirmed the biofilm attenuating capacity of thymoquinone. However, these concentrations did not show any antimicrobial activity. Further explorations on understanding the underlying mechanism of the same revealed that thymoquinone accumulated reactive oxygen species (ROS) and also inhibited the expression of the quorum sensing gene (lasI) in Pseudomonas aeruginosa. Furthermore, by taking up a combinatorial approach with two other reported antibiofilm agents (tetrazine-capped silver nanoparticles and tryptophan), the antibiofilm efficiency of thymoquinone was expanded. In this regard, the highest antibiofilm activity was observed when thymoquinone, tryptophan, and tetrazine-capped silver nanoparticles were applied together against Pseudomonas aeruginosa. These combinatorial applications of antibiofilm molecules were found to accumulate ROS in cells that resulted in the inhibition of biofilm formation. Thus, the combinatorial study of these antibiofilm molecules could be applied to control biofilm threats as the tested antibiofilm molecules alone or in combinations showed negligible or very little cytotoxicity.}, }
@article {pmid33410938, year = {2021}, author = {Oita, S and Carey, J and Kline, I and Ibáñez, A and Yang, N and Hom, EFY and Carbone, I and U'Ren, JM and Arnold, AE}, title = {Methodological Approaches Frame Insights into Endophyte Richness and Community Composition.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {21-34}, pmid = {33410938}, issn = {1432-184X}, mesh = {*Endophytes/genetics ; *Fungi/genetics ; Phylogeny ; Plant Leaves ; Plants ; }, abstract = {Isolating microbes is vital to study microbiomes, but insights into microbial diversity and ecology can be constrained by recalcitrant or unculturable strains. Culture-free methods (e.g., next-generation sequencing, NGS) have become popular in part because they detect greater richness than culturing alone. Both approaches are used widely to characterize microfungi within healthy leaves (foliar endophytes), but methodological differences among studies can constrain large-scale insights into endophyte ecology. We examined endophytes in a temperate plant community to quantify how certain methodological factors, such as the choice of cultivation media for culturing and storage period after leaf collection, affect inferences regarding endophyte communities; how such effects vary among plant taxa; and how complementary culturing and NGS can be when subsets of the same plant tissue are used for each. We found that endophyte richness and composition from culturing were consistent across five media types. Insights from culturing and NGS were largely robust to differences in storage period (1, 5, and 10 days). Although endophyte richness, composition, and taxonomic diversity identified via culturing vs. NGS differed markedly, both methods revealed host-structured communities. Studies differing only in cultivation media or storage period thus can be compared to estimate endophyte richness, composition, and turnover at scales larger than those of individual studies alone. Our data show that it is likely more important to sample more host species, rather than sampling fewer species more intensively, to quantify endophyte diversity in given locations, with the richest insights into endophyte ecology emerging when culturing and NGS are paired.}, }
@article {pmid33410937, year = {2021}, author = {Rodrigues, LA and da Silva, DKA and Yano-Melo, AM}, title = {Arbuscular Mycorrhizal Fungal Assemblages in Conservation Unit of Atlantic Forest Areas Under Native Vegetation and Natural Regeneration.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {122-134}, pmid = {33410937}, issn = {1432-184X}, support = {CNPq 421241 / 2017-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 131015/2018-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; APQ-0003- 2.03/18//Funda&#xe7;&#xe3;o de Amparo &#xe0; Ci&#xea;ncia e Tecnologia do Estado de Pernambuco/ ; }, mesh = {Biodiversity ; Forests ; *Mycorrhizae ; Plant Roots ; Soil Microbiology ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) play an important role in the dynamic of plant community in the south American Atlantic Rainforest biome. Even in protected areas, this biome is under several anthropic impacts, which can cause shifts in the soil microbiota, including AMF. This study aimed to determine the structure and composition of AMF community in areas of native Atlantic Forest and in natural regeneration and to identify which abiotic factors are influencing this community in these areas. Soil samples were collected at Monte Pascoal National and Historical Park, in Southern Bahia, in native and natural regeneration areas of Atlantic Forest in two seasons (rainy and dry). Greater number of glomerospores and richness and diversity of AMF were found in the area under regeneration, with differences between seasons being observed only for the number of glomerospores. Seventy-seven species of AMF were recorded, considering all areas and seasons, with Acaulospora and Glomus being the most representative genera. Greater abundance of species of the genera Acaulospora, Claroideoglomus, and Septoglomus was found in the regeneration area. The AMF community differed between the study areas, but not between seasons, with soil attributes (pH, K, Al, Mg, m, and clay) structuring factors for this difference in the AMF community. Atlantic Forest areas in natural regeneration and the soil edaphic factors provide changes in the structure and composition of the AMF community, increasing the richness and diversity of these fungi in conservation units.}, }
@article {pmid33410936, year = {2021}, author = {St James, AR and Lin, J and Richardson, RE}, title = {Relationship Between Peat Type and Microbial Ecology in Sphagnum-Containing Peatlands of the Adirondack Mountains, NY, USA.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {429-441}, pmid = {33410936}, issn = {1432-184X}, mesh = {Carbon ; *Microbiota ; Soil ; *Sphagnopsida ; Wetlands ; }, abstract = {Peatland microbial community composition varies with respect to a range of biological and physicochemical variables. While the extent of peat degradation (humification) has been linked to microbial community composition along vertical stratification gradients within peatland sites, across-site variations have been relatively unexplored. In this study, we compared microbial communities across ten pristine Sphagnum-containing peatlands in the Adirondack Mountains, NY, which represented three different peat types-humic fen peat, humic bog peat, and fibric bog peat. Using 16S amplicon sequencing and network correlation analysis, we demonstrate that microbial community composition is primarily linked to peat type, and that distinct taxa networks distinguish microbial communities in each type. Shotgun metagenomic sequencing of the active water table region (mesotelm) from two Sphagnum-dominated bogs-one with fibric peat and one with humic peat-revealed differences in primary carbon degradation pathways, with the fibric peat being dominated by carbohydrate metabolism and hydrogenotrophic methanogenesis, and the humic peat being dominated by aliphatic carbon metabolism and aceticlastic methanogenesis. Our results suggest that peat humification is a major factor driving microbial community dynamics across peatland ecosystems.}, }
@article {pmid33410935, year = {2021}, author = {Li, W and Nelson, KE}, title = {Microbial Species that Initially Colonize the Human Gut at Birth or in Early Childhood Can Stay in Human Body for Lifetime.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {1074-1079}, pmid = {33410935}, issn = {1432-184X}, mesh = {Adult ; Child, Preschool ; *Gastrointestinal Microbiome/genetics ; *Human Body ; Humans ; Infant, Newborn ; Metagenome ; Metagenomics ; Twins, Dizygotic/genetics ; }, abstract = {In recent years, many studies have described the composition and function of the human microbiome at different body sites and suggested a role for the microbiome in various diseases and health conditions. Some studies, using longitudinal samples, have also suggested how the microbiome changes over time due to disease, diet, development, travel, and other environmental factors. However, to date, no study has demonstrated whether the microorganisms established at birth or in early childhood, either transmitted from parents or obtained from the environment, can stay in the human body until adult or senior age. To directly answer this question is difficult, because microbiome samples at childhood and at later adulthood for the same individual will need to be compared and the field is not old enough to have allowed for that type of sample collection. Here, using a metagenomic approach, we analyzed 1004 gut microbiome samples from senior adults (65 ± 7.8 years) from the TwinsUK cohort. Our data indicate that many species in the human gut acquired in early childhood can stay for a lifetime until senior ages. We identified the rare genomic variants (single nucleotide variation and indels) for 27 prevalent species with enough sequencing coverage for confident genomic variant identification. We found that for some species, twin pairs, including both monozygotic (MZ) and dizygotic (DZ) twins, share significantly more rare variants than unrelated subject pairs. But no significant difference is found between MZ and DZ twin pairs. These observations strongly suggest that these species acquired in early childhood remained in these persons until senior adulthood.}, }
@article {pmid33410934, year = {2021}, author = {Tan, MH and Loke, S and Croft, LJ and Gleason, FH and Lange, L and Pilgaard, B and Trevathan-Tackett, SM}, title = {First Genome of Labyrinthula sp., an Opportunistic Seagrass Pathogen, Reveals Novel Insight into Marine Protist Phylogeny, Ecology and CAZyme Cell-Wall Degradation.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {498-511}, pmid = {33410934}, issn = {1432-184X}, support = {ADPRF//Deakin University/ ; }, mesh = {Ecology ; Phylogeny ; *Stramenopiles ; Virulence ; }, abstract = {Labyrinthula spp. are saprobic, marine protists that also act as opportunistic pathogens and are the causative agents of seagrass wasting disease (SWD). Despite the threat of local- and large-scale SWD outbreaks, there are currently gaps in our understanding of the drivers of SWD, particularly surrounding Labyrinthula spp. virulence and ecology. Given these uncertainties, we investigated the Labyrinthula genus from a novel genomic perspective by presenting the first draft genome and predicted proteome of a pathogenic isolate Labyrinthula SR_Ha_C, generated from a hybrid assembly of Nanopore and Illumina sequences. Phylogenetic and cross-phyla comparisons revealed insights into the evolutionary history of Stramenopiles. Genome annotation showed evidence of glideosome-type machinery and an apicoplast protein typically found in protist pathogens and parasites. Proteins involved in Labyrinthula SR_Ha_C's actin-myosin mode of transport, as well as carbohydrate degradation were also prevalent. Further, CAZyme functional predictions revealed a repertoire of enzymes involved in breakdown of cell-wall and carbohydrate storage compounds common to seagrasses. The relatively low number of CAZymes annotated from the genome of Labyrinthula SR_Ha_C compared to other Labyrinthulea species may reflect the conservative annotation parameters, a specialized substrate affinity and the scarcity of characterized protist enzymes. Inherently, there is high probability for finding both unique and novel enzymes from Labyrinthula spp. This study provides resources for further exploration of Labyrinthula spp. ecology and evolution, and will hopefully be the catalyst for new hypothesis-driven SWD research revealing more details of molecular interactions between the Labyrinthula genus and its host substrate.}, }
@article {pmid33410933, year = {2021}, author = {Luo, Y and Wang, H and Liang, J and Qian, H and Ye, J and Chen, L and Yang, X and Chen, Z and Wang, F and Octavia, S and Payne, M and Song, X and Jiang, J and Jin, D and Lan, R}, title = {Population Structure and Multidrug Resistance of Non-O1/Non-O139 Vibrio cholerae in Freshwater Rivers in Zhejiang, China.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {319-333}, pmid = {33410933}, issn = {1432-184X}, support = {2019JZZY011018//Key Technology Research and Development Program of Shandong/ ; }, mesh = {Drug Resistance, Multiple ; Humans ; Multilocus Sequence Typing ; *Rivers ; *Vibrio cholerae non-O1/genetics ; Virulence/genetics ; }, abstract = {To understand the environmental reservoirs of Vibrio cholerae and their public health significance, we surveyed freshwater samples from rivers in two cities (Jiaxing [JX] and Jiande [JD]) in Zhejiang, China. A total of 26 sampling locations were selected, and river water was sampled 456 times from 2015 to 2016 yielding 200 V. cholerae isolates, all of which were non-O1/non-O139. The average isolation rate was 47.3% and 39.1% in JX and JD, respectively. Antibiotic resistance profiles of the V. cholerae isolates were examined with nonsusceptibility to cefazolin (68.70%, 79/115) being most common, followed by ampicillin (47.83%, 55/115) and imipenem (27.83%, 32/115). Forty-two isolates (36.52%, 42/115) were defined as multidrug resistant (MDR). The presence of virulence genes was also determined, and the majority of the isolates were positive for toxR (198/200, 99%) and hlyA (196/200, 98%) with few other virulence genes observed. The population structure of the V. cholerae non-O1/non-O139 sampled was examined using multilocus sequence typing (MLST) with 200 isolates assigned to 128 STs and 6 subpopulations. The non-O1/non-O139 V. cholerae population in JX was more varied than in JD. By clonal complexes (CCs), 31 CCs that contained isolates from this study were shared with other parts of China and/or other countries, suggesting widespread presence of some non-O1/non-O139 clones. Drug resistance profiles differed between subpopulations. The findings suggest that non-O1/non-O139 V. cholerae in the freshwater environment is a potential source of human infections. Routine surveillance of non-O1/non-O139 V. cholerae in freshwater rivers will be of importance to public health.}, }
@article {pmid33410932, year = {2021}, author = {Hutchinson, MI and Bell, TAS and Gallegos-Graves, V and Dunbar, J and Albright, M}, title = {Merging Fungal and Bacterial Community Profiles via an Internal Control.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {484-497}, pmid = {33410932}, issn = {1432-184X}, support = {F255LANL2018//Office of Science/ ; }, mesh = {Bacteria/genetics ; DNA, Fungal/genetics ; *Fungi/genetics ; High-Throughput Nucleotide Sequencing ; *Microbiota ; }, abstract = {Integrated measurements of fungi and bacteria are critical to understand how interactions between these taxa drive key processes in ecosystems ranging from soils to animal guts. High-throughput amplicon sequencing is commonly used to census microbiomes, but the genetic markers targeted for fungi and bacteria (typically ribosomal regions) are domain-specific so profiling must be performed separately, obscuring relationships between these groups. To solve this problem, we developed a spike-in method with an internal control (IC) construct containing primer sites commonly used for bacterial and fungal taxonomic profiling. The internal control offers several advantages: estimation of absolute abundances, estimation of fungal to bacterial ratios (F:B), integration of bacterial and fungal profiles for holistic community analysis, and lower costs compared to other quantitation methods. To validate the IC as a scaling method, we compared IC-derived measures of F:B to measures from quantitative PCR (qPCR) using a commercial mock community (the ZymoBiomic Microbial Community DNA Standard II, containing two fungi and eight bacteria) and complex environmental samples. For both the mock community and the environmental samples, the IC produced F:B values that were statistically consistent with qPCR. Merging the environmental fungal and bacterial profiles based on the IC-derived F:B values revealed new relationships among samples in terms of community similarity. This IC method is the first spike-in method to employ a single construct for cross-domain amplicon sequencing, offering more reliable measurements.}, }
@article {pmid33410931, year = {2021}, author = {Gomez, JA and Primm, TP}, title = {A Slimy Business: the Future of Fish Skin Microbiome Studies.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {275-287}, pmid = {33410931}, issn = {1432-184X}, mesh = {Animals ; *Bacteria/genetics ; Fishes ; Metagenomics ; *Microbiota/genetics ; Skin ; }, abstract = {Fish skin contains a mucosal microbiome for the largest and oldest group of vertebrates, a location ideal for microbial community ecology and practical applications in agriculture and veterinary medicine. These selective microbiomes are dominated by Proteobacteria, with compositions different from the surrounding water. Core taxa are a small percentage of those present and are currently functionally uncharacterized. Methods for skin sampling, DNA extraction and amplification, and sequence data processing are highly varied across the field, and reanalysis of recent studies using a consistent pipeline revealed that some conclusions did change in statistical significance. Further, the 16S gene sequencing approaches lack quantitation of microbes and copy number adjustment. Thus, consistency in the field is a serious limitation in comparing across studies. The most significant area for future study, requiring metagenomic and metabolomics data, is the biochemical pathways and functions within the microbiome community, the interactions between members, and the resulting effects on fish host health being linked to specific nutrients and microbial species. Genes linked to skin colonization, such as those for attachment or mucin degradation, need to be uncovered and explored. Skin immunity factors need to be directly linked to microbiome composition and individual taxa. The basic foundation has been laid, and many exciting future discoveries remain.}, }
@article {pmid33408702, year = {2020}, author = {Riva, A and Kolimár, D and Spittler, A and Wisgrill, L and Herbold, CW and Abrankó, L and Berry, D}, title = {Conversion of Rutin, a Prevalent Dietary Flavonol, by the Human Gut Microbiota.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {585428}, pmid = {33408702}, issn = {1664-302X}, abstract = {The gut microbiota plays a pivotal role in the conversion of dietary flavonoids, which can affect their bioavailability and bioactivity and thereby their health-promoting properties. The ability of flavonoids to metabolically-activate the microbiota has, however, not been systematically evaluated. In the present study, we used a fluorescence-based single-cell activity measure [biorthogonal non-canonical ammino acid-tagging (BONCAT)] combined with fluorescence activated cell sorting (FACS) to determine which microorganisms are metabolically-active after amendment of the flavonoid rutin. We performed anaerobic incubations of human fecal microbiota amended with rutin and in the presence of the cellular activity marker L-azidohomoalanine (AHA) to detect metabolically-active cells. We found that 7.3% of cells in the gut microbiota were active after a 6 h incubation and 26.9% after 24 h. We then sorted BONCAT-positive cells and observed an enrichment of Lachnospiraceae (Lachnoclostridium and Eisenbergiella), Enterobacteriaceae, Tannerellaceae, and Erysipelotrichaceae species in the rutin-responsive fraction of the microbiota. There was marked inter-individual variability in the appearance of rutin conversion products after incubation with rutin. Consistent with this, there was substantial variability in the abundance of rutin-responsive microbiota among different individuals. Specifically, we observed that Enterobacteriaceae were associated with conversion of rutin into quercetin-3-glucoside (Q-glc) and Lachnospiraceae were associated with quercetin (Q) production. This suggests that individual microbiotas differ in their ability to metabolize rutin and utilize different conversion pathways.}, }
@article {pmid33408369, year = {2021}, author = {Meisner, A and Snoek, BL and Nesme, J and Dent, E and Jacquiod, S and Classen, AT and Priemé, A}, title = {Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles.}, journal = {The ISME journal}, volume = {15}, number = {4}, pages = {1207-1221}, pmid = {33408369}, issn = {1751-7370}, mesh = {Climate Change ; Desiccation ; Freezing ; *Soil ; *Soil Microbiology ; }, abstract = {Climate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response to the other (e.g., freezing-thawing). As both phenomenons give similar water availability fluctuations, we hypothesized that freezing-thawing and drying-rewetting cycles have similar effects on the soil microbiome. We tested this hypothesis by establishing targeted microcosm experiments. We created a legacy by exposing soil samples to a freezing-thawing or drying-rewetting cycle (phase 1), followed by an additional drying-rewetting or freezing-thawing cycle (phase 2). We measured soil respiration and analyzed soil microbiome structures. Across experiments, larger CO2 pulses and changes in microbiome structures were observed after rewetting than thawing. Drying-rewetting legacy affected the microbiome and CO2 emissions upon the following freezing-thawing cycle. Conversely, freezing-thawing legacy did not affect the microbial response to the drying-rewetting cycle. Our results suggest that drying-rewetting cycles have stronger effects on soil microbial communities and CO2 production than freezing-thawing cycles and that this pattern is mediated by sustained changes in soil microbiome structures.}, }
@article {pmid33406784, year = {2021}, author = {Mayta-Apaza, AC and García-Cano, I and Dabrowski, K and Jiménez-Flores, R}, title = {Bacterial Diversity Analysis and Evaluation Proteins Hydrolysis During the Acid Whey and Fish Waste Fermentation.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, pmid = {33406784}, issn = {2076-2607}, abstract = {The disposal of acid whey (Aw), a by-product from fermented products, is a problem for the dairy industry. The fishery industry faces a similar dilemma, disposing of nearly 50% of fish processed for human consumption. Economically feasible and science-based alternatives are needed to overcome this problem. One possible solution is to add value to the remaining nutrients from these by-products. This study focuses on the breakdown of nutrients in controlled fermentations of Aw, fish waste (F), molasses (M), and a lactic acid bacteria (LAB) strain (Lr). The aim was to assess the dynamic variations in microbial diversity and the biochemical changes that occur during fermentation. Four treatments were compared (AwF, AwFM, AwFLr, and AwFMLr), and the fermentation lasted 14 days at 22.5 °C. Samples were taken every other day. Colorimetric tests for peptide concentrations, pH, and microbial ecology by 16S-v4 rRNA amplicon using Illumina MiSeq were conducted. The results of the microbial ecology showed elevated levels of alpha and beta diversity in the samples at day zero. By day 2 of fermentation, pH dropped, and the availability of a different set of nutrients was reflected in the microbial diversity. The fermentation started to stabilize and was driven by the Firmicutes phylum, which dominated the microbial community by day 14. Moreover, there was a significant increase (3.6 times) in peptides when comparing day 0 with day 14, making this treatment practical and feasible for protein hydrolysis. This study valorizes two nutrient-dense by-products and provides an alternative to the current handling of these materials.}, }
@article {pmid33406135, year = {2021}, author = {Kanzaki, N and Ekino, T and Hamaguchi, K and Takeuchi-Kaneko, Y}, title = {Three Seinura species from Japan with a description of S. shigaensis n. sp. (Tylenchomorpha: Aphelenchoididae).}, journal = {PloS one}, volume = {16}, number = {1}, pages = {e0244653}, pmid = {33406135}, issn = {1932-6203}, mesh = {Animals ; Electron Transport Complex IV/genetics ; *Genes, Mitochondrial ; Japan ; Rhabditida/genetics/*isolation &amp; purification ; Sequence Analysis, DNA ; }, abstract = {A preliminary survey of Seinura spp. was conducted in the Kyoto area, Western Japan. The survey yielded four new strains of Seinura spp., including two strains of S. caverna, a strain of S. italiensis, and a strain of an undescribed species. Molecularly, the two strains of S. caverna were nearly identical to the type strain but showed some minor variations, particularly in the mitochondrial cytochrome oxidase subunit I gene. The small subunit and D2-D3 large subunit sequences of the Japanese strain of S. italiensis were nearly identical and identical to its original description, respectively, and the difference in the small subunit was due to mis-reading of the sequences. The new species, S. shigaensis n. sp., was phylogenetically close to S. caverna and S. persica, although these three species were clearly different phylogenetically. The new species was typologically similar or nearly identical to several other Seinura spp., including S. chertkovi, S. christiei, S. italiensis, S. steineri, and S. tenuicaudata, but it can be distinguished from those species by the morphometric values. Because the new species is phylogenetically very close to S. caverna, it could be a good comparative system for S. caverna as a potential satellite model for the predatory nematode.}, }
@article {pmid33404822, year = {2021}, author = {Álvarez-Pérez, S and Tsuji, K and Donald, M and Van Assche, A and Vannette, RL and Herrera, CM and Jacquemyn, H and Fukami, T and Lievens, B}, title = {Nitrogen Assimilation Varies Among Clades of Nectar- and Insect-Associated Acinetobacters.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {990-1003}, pmid = {33404822}, issn = {1432-184X}, support = {742964//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; DEB 1737758//National Science Foundation/ ; RYC2018-023847-I//Secretar&#xed;a de Estado de Investigaci&#xf3;n, Desarrollo e Innovaci&#xf3;n/ ; }, mesh = {Acinetobacter ; Animals ; Bees ; Insecta ; *Nitrogen ; Phylogeny ; *Plant Nectar ; }, abstract = {Floral nectar is commonly colonized by yeasts and bacteria, whose growth largely depends on their capacity to assimilate nutrient resources, withstand high osmotic pressures, and cope with unbalanced carbon-to-nitrogen ratios. Although the basis of the ecological success of these microbes in the harsh environment of nectar is still poorly understood, it is reasonable to assume that they are efficient nitrogen scavengers that can consume a wide range of nitrogen sources in nectar. Furthermore, it can be hypothesized that phylogenetically closely related strains have more similar phenotypic characteristics than distant relatives. We tested these hypotheses by investigating the growth performance on different nitrogen-rich substrates of a collection of 82 acinetobacters isolated from nectar and honeybees, representing members of five species (Acinetobacter nectaris, A. boissieri, A. apis, and the recently described taxa A. bareti and A. pollinis). We also analyzed possible links between growth performance and phylogenetic affiliation of the isolates, while taking into account their geographical origin. Results demonstrated that the studied isolates could utilize a wide variety of nitrogen sources, including common metabolic by-products of yeasts (e.g., ammonium and urea), and that phylogenetic relatedness was associated with the variation in nitrogen assimilation among the studied acinetobacters. Finally, nutrient source and the origin (sample type and country) of isolates also predicted the ability of the acinetobacters to assimilate nitrogen-rich compounds. Overall, these results demonstrate inter-clade variation in the potential of the acinetobacters as nitrogen scavengers and suggest that nutritional dependences might influence interactions between bacteria and yeasts in floral nectar.}, }
@article {pmid33404821, year = {2021}, author = {Shar, S and Reith, F and Ball, AS and Shahsavari, E}, title = {Long-term Impact of Gold and Platinum on Microbial Diversity in Australian Soils.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {977-989}, pmid = {33404821}, issn = {1432-184X}, support = {ARC-FT100150200//Australian Research Council/ ; }, mesh = {Australia ; Gold ; Platinum ; *Soil ; *Soil Microbiology ; }, abstract = {The effects of platinum (Pt) and gold (Au) and on the soil bacterial community was evaluated in four different Australian soil types (acidic Burn Grounds (BGR), organic matter-rich Fox Lane, high silt/metal Pinpinio (PPN), and alkali Minnipa (MNP) spiked with either Pt or Au at 1, 25, and 100 mg kg[-1] using a next-generation sequencing approach (amplicon-based, MiSeq). Soil type and metal concentrations were observed to be key drivers of Pt and Au effects on soil microbial community structure. Different trends were therefore observed in the response of the bacterial community to Pt and Au amendments; however in each soil type, Pt and Au amendment caused a detectable shift in community structure that in most samples was positively correlated with increasing metal concentrations. New dominant groups were only observed in BGR and PPN soils at 100 mg kg[-1] (Kazan-3B-28 and Verrucomicrobia groups (BGR, Pt) and Firmicutes and Caldithrix groups (PPN, Pt) and WS2 (BGR, Au). The effects of Pt on soil microbial diversity were largely adverse at 100 mg kg[-1] and were pronounced in acidic, basic, and metal/silt-rich soils. However, this effect was concentration-related; Au appeared to be more toxic to soil bacterial communities than Pt at 25 mg kg[-1] but Pt was more toxic at 100 mg kg[-1]. More bacterial groups such as those belonging to Burkholderiales/Burkholderiaceae, Alicyclobacillaceae, Rubrobacteraceae, Cytophagaceae, Oxalobacteraceae were selectively enriched by Pt compared to Au (Sphingomonadaceae and Rhodospirillaceae) amendments irrespective of soil type. The research outcomes have important implications in the management (remediation) of Pt- and Au-contaminated environments.}, }
@article {pmid33404820, year = {2021}, author = {Leiva, D and Fernández-Mendoza, F and Acevedo, J and Carú, M and Grube, M and Orlando, J}, title = {The Bacterial Community of the Foliose Macro-lichen Peltigera frigida Is More than a Mere Extension of the Microbiota of the Subjacent Substrate.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {965-976}, pmid = {33404820}, issn = {1432-184X}, support = {1181510//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; }, mesh = {*Ascomycota ; *Cyanobacteria ; *Lichens ; *Microbiota ; }, abstract = {Lichens host highly diverse microbial communities, with bacteria being one of the most explored groups in terms of their diversity and functioning. These bacteria could partly originate from symbiotic propagules developed by many lichens and, perhaps more commonly and depending on environmental conditions, from different sources of the surroundings. Using the narrowly distributed species Peltigera frigida as an object of study, we propose that bacterial communities in these lichens are different from those in their subjacent substrates, even if some taxa might be shared. Ten terricolous P. frigida lichens and their substrates were sampled from forested sites in the Coyhaique National Reserve, located in an understudied region in Chile. The mycobiont identity was confirmed using partial 28S and ITS sequences. Besides, 16S fragments revealed that mycobionts were associated with the same cyanobacterial haplotype. From both lichens and substrates, Illumina 16S amplicon sequencing was performed using primers that exclude cyanobacteria. In lichens, Proteobacteria was the most abundant phylum (37%), whereas soil substrates were dominated by Acidobacteriota (39%). At lower taxonomic levels, several bacterial groups differed in relative abundance among P. frigida lichens and their substrates, some of them being highly abundant in lichens but almost absent in substrates, like Sphingomonas (8% vs 0.2%), and others enriched in lichens, as an unassigned genus of Chitinophagaceae (10% vs 2%). These results reinforce the idea that lichens would carry some components of their microbiome when propagating, but they also could acquire part of their bacterial community from the substrates.}, }
@article {pmid33404819, year = {2021}, author = {Ogaki, MB and Pinto, OHB and Vieira, R and Neto, AA and Convey, P and Carvalho-Silva, M and Rosa, CA and Câmara, PEAS and Rosa, LH}, title = {Fungi Present in Antarctic Deep-Sea Sediments Assessed Using DNA Metabarcoding.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {157-164}, pmid = {33404819}, issn = {1432-184X}, mesh = {Animals ; Antarctic Regions ; *Ascomycota ; DNA ; DNA Barcoding, Taxonomic ; Fungi/genetics ; Geologic Sediments ; Humans ; *Mycobiome ; }, abstract = {We assessed fungal diversity in deep-sea sediments obtained from different depths in the Southern Ocean using the internal transcribed spacer 2 (ITS2) region of nuclear ribosomal DNA by metabarcoding through high-throughput sequencing (HTS). We detected 655,991 DNA reads representing 263 fungal amplicon sequence variants (ASVs), dominated by Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota, Chytridiomycota and Rozellomycota, confirming that deep-sea sediments can represent a hotspot of fungal diversity in Antarctica. The community diversity detected included 17 dominant fungal ASVs, 62 intermediate and 213 rare. The dominant fungi included taxa of Mortierella, Penicillium, Cladosporium, Pseudogymnoascus, Phaeosphaeria and Torula. Despite the extreme conditions of the Southern Ocean benthos, the total fungal community detected in these marine sediments displayed high indices of diversity and richness, and moderate dominance, which varied between the different depths sampled. The highest diversity indices were obtained in sediments from 550 m and 250 m depths. Only 49 ASVs (18.63%) were detected at all the depths sampled, while 16 ASVs were detected only in the deepest sediment sampled at 1463 m. Based on sequence identities, the fungal community included some globally distributed taxa, primarily recorded otherwise from terrestrial environments, suggesting transport from these to deep marine sediments. The assigned taxa included symbionts, decomposers and plant-, animal- and human-pathogenic fungi, suggesting that deep-sea sediments host a complex fungal diversity, although metabarcoding does not itself confirm that living or viable organisms are present.}, }
@article {pmid33404818, year = {2021}, author = {Liu, Y and Anastacio, GR and Ishangulyyeva, G and Rodriguez-Ramos, JC and Erbilgin, N}, title = {Mutualistic Ophiostomatoid Fungi Equally Benefit from Both a Bark Beetle Pheromone and Host Tree Volatiles as Nutrient Sources.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {1106-1110}, pmid = {33404818}, issn = {1432-184X}, mesh = {Animals ; *Coleoptera ; Nutrients ; Ophiostoma ; *Ophiostomatales ; Pheromones ; *Pinus ; Plant Bark ; Trees ; }, abstract = {Interactions between mutualistic bark beetles and ophiostomatoid fungi have received considerable attention in recent years. Studies have shown how volatile organic compounds emitted from mutualist fungi affect the behaviors of several bark beetle species. However, we currently lack sufficient knowledge regarding whether bark beetle pheromones can influence mutualist fungi. Here, we measured growth and biomass of two mutualistic fungi of the mountain pine beetle in response to headspace of a beetle pheromone (trans-verbenol), a blend of host tree volatiles, the combination of both, or control (no volatile source) in vitro experiments consisting of a nitrogen-based medium. The surface area and ergosterol content of the mycelia were used as surrogates for fungal growth and biomass respectively. We found that both growth and biomass of Grosmannia clavigera and Ophiostoma montium were greater in medium exposed to any type of volatile sources than the control. While growth and ergosterol content of G. clavigera were highest in the combination treatment, there were no differences in growth or biomass among the types of volatiles introduced for O. montium. These results suggest that both mutualistic fungi can utilize both bark beetle pheromone and host tree volatiles as nutrient sources. Overall, these results support the on-going studies on the role of volatile organic compounds mediating mutualistic bark beetle-fungi interactions.}, }
@article {pmid33401417, year = {2021}, author = {Savadova-Ratkus, K and Mazur-Marzec, H and Karosienė, J and Kasperovičienė, J and Paškauskas, R and Vitonytė, I and Koreivienė, J}, title = {Interplay of Nutrients, Temperature, and Competition of Native and Alien Cyanobacteria Species Growth and Cyanotoxin Production in Temperate Lakes.}, journal = {Toxins}, volume = {13}, number = {1}, pages = {}, pmid = {33401417}, issn = {2072-6651}, support = {European Network for Algal Bioproducts (EUALGAE).//European Cooperation in Science and Technology (COST) Action ES1408/International ; }, mesh = {Cyanobacteria/*classification/*physiology ; Harmful Algal Bloom ; Lakes/chemistry/*microbiology ; Saxitoxin/*chemistry/metabolism ; Species Specificity ; Temperature ; Water Pollutants, Chemical/*chemistry ; }, abstract = {Global warming and eutrophication contribute to formation of HABs and distribution of alien cyanobacteria northward. The current study assessed how alien to Europe Sphaerospermopsis aphanizomenoides and Chrysosporum bergii will co-occur with dominant native Planktothrix agardhii and Aphanizomenon gracile species under changing conditions in temperate freshwaters. The experiments were carried out to examine the effect of nutrients and temperature on the growth rate of cyanobacteria, production of cyanotoxins, and interspecies competition. The highest growth rate was determined for A. gracile (0.43 day[-1]) and S. aphanizomenoides (0.40 day[-1]) strains at all the tested nutrient concentrations (IP and IN were significant factors). S. aphanizomenoides adapted to the wide range of nutrient concentrations and temperature due to high species ecological plasticity; however, A. gracile was able to suppress its dominance under changing conditions. Regularity between tested variables and STX concentration in A. gracile was not found, but IP concentration negatively correlated with the amount of dmMC-RR and other non-ribosomal peptides (NRPs) in P. agardhii strains. The relative concentration of NRPs in nontoxic P. agardhii strain was up to 3-fold higher than in MC-producing strain. Our study indicated that nutrients, temperature, and species had significant effects on interspecies competition. A. gracile had a negative effect on biomass of both alien species and P. agardhii.}, }
@article {pmid33399932, year = {2021}, author = {Aguero, CM and Eyer, PA and Crippen, TL and Vargo, EL}, title = {Reduced Environmental Microbial Diversity on the Cuticle and in the Galleries of a Subterranean Termite Compared to Surrounding Soil.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {1054-1063}, pmid = {33399932}, issn = {1432-184X}, mesh = {Animals ; Fungi/genetics ; Humans ; *Isoptera ; *Microbiota ; Soil ; *Streptomyces ; }, abstract = {Termites are intimately tied to the microbial world, as they utilize their gut microbiome for the conversion of plant cellulose into necessary nutrients. Subterranean termites must also protect themselves from the vast diversity of harmful microbes found in soil. However, not all soil microbes are harmful, such as Streptomyces and methanotrophic bacteria that some species of termites harbor in complex nest structures made of fecal material. The eastern subterranean termite, Reticulitermes flavipes, has a simple nest structure consisting of fecal lined galleries. We tested the hypothesis that R. flavipes maintains a select microbial community in its nests to limit the penetration of harmful soilborne pathogens and favor the growth of beneficial microbes. Using Illumina sequencing, we characterized the bacterial and fungal communities in the surrounding soil, in the nest galleries, and on the cuticle of workers. We found that the galleries provide a more beneficial microbial community than the surrounding soil. Bacterial and fungal diversity was highest in the soil, lower in the galleries, and least on the cuticle. Bacterial communities clustered together according to the substrate from which they were sampled, but this clustering was less clear in fungal communities. Most of the identified bacterial and fungal taxa were unique to one substrate, but the soil and gallery communities had very similar phylum-level taxonomic profiles. Notably, the galleries of R. flavipes also harbored both the potentially beneficial Streptomyces and the methanotrophic Methylacidiphilales, indicating that these microbial associations in fecal material pre-date the emergence of complex fecal nest structures. Surprisingly, several pathogenic groups were relatively abundant in the galleries and on the cuticle, suggesting that pathogens may accumulate within termite nests over time while putatively remaining at enzootic level during the lifetime of the colony.}, }
@article {pmid33399931, year = {2021}, author = {Shih, CM and Ophine, L and Chao, LL}, title = {Molecular Detection and Genetic Identification of Wolbachia Endosymbiont in Wild-Caught Culex quinquefasciatus (Diptera: Culicidae) Mosquitoes from Sumatera Utara, Indonesia.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {1064-1074}, pmid = {33399931}, issn = {1432-184X}, support = {MOST 109-2314-B-037-077//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Animals ; *Culex ; *Culicidae ; Female ; Indonesia ; Male ; Phylogeny ; *Wolbachia/genetics ; }, abstract = {The genetic identity of Wolbachia endosymbiont in wild-caught Culex quinquefasciatus was determined for the first time in Indonesia. A total of 314 Cx. quinquefasciatus were examined for Wolbachia by PCR assay targeting the Wolbachia surface protein (wsp) gene. The prevalence of Wolbachia infection was detected in 29.94% of Cx. specimens (45.86% female and 8.27% male). The group-specific infection was detected with an infection rate of 0.32%, 28.98%, and 0.64% in groups A, B, and A&amp;B, respectively. Phylogenetic analysis revealed all Wolbachia strains from Indonesia were genetically affiliated to the supergroup A and B with the high sequence similarity of 97.9-100% and 99.7-100%, respectively. Phylogenetic relationships can be easily distinguished by neighbor-joining analysis and were congruent by maximum likelihood method. The genetic distance (GD) values of intra- and inter-group analysis indicated a lower level (GD < 0.007 for group A and GD < 0.003 for group B) within the Indonesia strains and a higher level (GD > 1.125 for group A and GD > 1.129 for group B) as compared with other Wolbachia strains. Our results provide the first genetic identification of Wolbachia endosymbiont in Cx. quinquefasciatus collected from Indonesia, and the phylogenetic analysis revealed a new discovery of group A Wolbachia in wild-caught Cx. quinquefasciatus mosquitoes.}, }
@article {pmid33399896, year = {2021}, author = {Asha, K and Bhadury, P}, title = {Myceligenerans indicum sp. nov., an actinobacterium isolated from mangrove sediment of Sundarbans, India.}, journal = {Archives of microbiology}, volume = {203}, number = {4}, pages = {1577-1585}, pmid = {33399896}, issn = {1432-072X}, mesh = {*Actinobacteria/chemistry/classification/genetics ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Genome, Bacterial/genetics ; *Geologic Sediments/microbiology ; Glycolipids/analysis ; India ; Peptidoglycan/chemistry ; Phospholipids/analysis ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Species Specificity ; Wetlands ; }, abstract = {A new actinobacterial species of the genus Myceligenerans has been isolated from the intertidal sediment of Indian Sundarbans mangrove ecosystem. The isolate has been characterized based on polyphasic approaches. The isolate exhibit well-developed substrate mycelia along with the presence of cocci- and rod-shaped elements. The organism can grow across a wide range of temperature, salinity, and pH as well as on different carbon sources. Phylogenetic analyses based on 16S rRNA showed that this isolate is closely related to Myceligenerans salitolerans XHU 5031 (99% identity; 100% coverage). Presence of ketosynthase domain representing polyketide synthases in the isolate provides evidence of its potential ability to produce secondary metabolites. Multigene phylogeny based on atpD and rpoB gene sequences confirmed it as a new species within the family Promicromonosporaceae (Phylum Actinobacteria). The DNA G + C content of the isolate has been determined as 72 mol%. The peptidoglycan type was A4α and the whole-cell hydrolysates contained glucose, galactose, and mannose. The polar lipids were represented by diphosphatidylglycerol, one unknown phospholipid and one unknown glycolipid. Major fatty acids present in the isolate are anteiso-C15, iso-C15, iso-C16, and anteiso-C17. Whole-genome sequence indicates the size of genome is ~ 5 Mbp. GGDC (%), orthoANIu (%), and AAI of I2 genome indicated 28.9%, 77.44% and 0.859 identity with the genome of Myceligenerans xiligouense strain DSM 15,700. The isolate I2 has been proposed as a new species, Myceligenerans indicum sp. nov. The genome sequence has been deposited to GenBank/ENA/DDBJ under the accession number JABBYC000000000.}, }
@article {pmid33398112, year = {2021}, author = {Marco, ML and Sanders, ME and Gänzle, M and Arrieta, MC and Cotter, PD and De Vuyst, L and Hill, C and Holzapfel, W and Lebeer, S and Merenstein, D and Reid, G and Wolfe, BE and Hutkins, R}, title = {The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {18}, number = {3}, pages = {196-208}, pmid = {33398112}, issn = {1759-5053}, mesh = {Consensus ; *Fermented Foods ; Humans ; *Nutrition Policy ; *Prebiotics ; *Probiotics ; }, abstract = {An expert panel was convened in September 2019 by The International Scientific Association for Probiotics and Prebiotics (ISAPP) to develop a definition for fermented foods and to describe their role in the human diet. Although these foods have been consumed for thousands of years, they are receiving increased attention among biologists, nutritionists, technologists, clinicians and consumers. Despite this interest, inconsistencies related to the use of the term 'fermented' led the panel to define fermented foods and beverages as "foods made through desired microbial growth and enzymatic conversions of food components". This definition, encompassing the many varieties of fermented foods, is intended to clarify what is (and is not) a fermented food. The distinction between fermented foods and probiotics is further clarified. The panel also addressed the current state of knowledge on the safety, risks and health benefits, including an assessment of the nutritional attributes and a mechanistic rationale for how fermented foods could improve gastrointestinal and general health. The latest advancements in our understanding of the microbial ecology and systems biology of these foods were discussed. Finally, the panel reviewed how fermented foods are regulated and discussed efforts to include them as a separate category in national dietary guidelines.}, }
@article {pmid33396683, year = {2020}, author = {Kuramae, EE and Dimitrov, MR and da Silva, GHR and Lucheta, AR and Mendes, LW and Luz, RL and Vet, LEM and Fernandes, TV}, title = {On-Site Blackwater Treatment Fosters Microbial Groups and Functions to Efficiently and Robustly Recover Carbon and Nutrients.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, pmid = {33396683}, issn = {2076-2607}, support = {729.004.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 2013/50351-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 206884/2014-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 99999.008090/2015-07;0622/2014//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, abstract = {Wastewater is considered a renewable resource water and energy. An advantage of decentralized sanitation systems is the separation of the blackwater (BW) stream, contaminated with human pathogens, from the remaining household water. However, the composition and functions of the microbial community in BW are not known. In this study, we used shotgun metagenomics to assess the dynamics of microbial community structure and function throughout a new BW anaerobic digestion system installed at The Netherlands Institute of Ecology. Samples from the influent (BW), primary effluent (anaerobic digested BW), sludge and final effluent of the pilot upflow anaerobic sludge blanket (UASB) reactor and microalgae pilot tubular photobioreactor (PBR) were analyzed. Our results showed a decrease in microbial richness and diversity followed by a decrease in functional complexity and co-occurrence along the different modules of the bioreactor. The microbial diversity and function decrease were reflected both changes in substrate composition and wash conditions. Our wastewater treatment system also decreased microbial functions related to pathogenesis. In summary, the new sanitation system studied here fosters microbial groups and functions that allow the system to efficiently and robustly recover carbon and nutrients while reducing pathogenic groups, ultimately generating a final effluent safe for discharge and reuse.}, }
@article {pmid33392630, year = {2021}, author = {Oliveira, MM and Proenca, AM and Moreira-Silva, E and de Castro, AM and Dos Santos, FM and Marconatto, L and Medina-Silva, R}, title = {Biofilms of Pseudomonas and Lysinibacillus Marine Strains on High-Density Polyethylene.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {833-846}, pmid = {33392630}, issn = {1432-184X}, support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 0050.0096017.15.9//Petrobras/ ; }, mesh = {Bacteria ; Biodegradation, Environmental ; Biofilms ; *Polyethylene ; *Pseudomonas ; }, abstract = {Environmental pollution by plastic debris is estimated on a scale of 100 million metric tons, a portion of which is fragmented into micro- and nanoplastics. These fragments are often colonized by bacterial species in marine environments, possibly contributing to the biodegradation of such materials. However, further investigations are necessary to determine the impact of abiotic polymer weathering on biofilm adhesion, as well as the specific biofilm formation strategies employed by marine isolates. Here, we evaluate deep-sea sediment bacterial isolates for biofilm adhesion, extracellular matrix production, and polymer degradation ability. Our study focuses on high-density polyethylene (HDPE) fragments for their high durability and environmental persistence, subjecting fragments to abiotic weathering prior to bacterial colonization. Marine isolates identified as Pseudomonas sp. and Lysinibacillus sp. exhibited decreasing biofilm formation on weathered HDPE, especially over the first 24 h of incubation. This effect was countered by increased extracellular matrix production, likely improving cell adhesion to surfaces roughened by abiotic degradation. These adhesion strategies were contrasted with a reference Pseudomonas aeruginosa strain, which displayed high levels of biofilm formation on non-weathered HDPE and lower extracellular matrix production over the first 24 h of incubation. Furthermore, our results suggest that an increase in biofilm biomass correlated with changes to HDPE structure, indicating that these strains have a potential for biodegradation of plastic fragments. Therefore, this work provides a detailed account of biofilm formation strategies and bacteria-plastic interactions that represent crucial steps in the biodegradation of plastic fragments in marine environments.}, }
@article {pmid33392629, year = {2021}, author = {do Carmo Linhares, D and Saia, FT and Duarte, RTD and Nakayama, CR and de Melo, IS and Pellizari, VH}, title = {Methanotrophic Community Detected by DNA-SIP at Bertioga's Mangrove Area, Southeast Brazil.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {954-964}, pmid = {33392629}, issn = {1432-184X}, support = {04/13910-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2009/06601-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {Brazil ; DNA ; Isotopes ; *Methane ; *Microbiota ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; }, abstract = {Methanotrophic bacteria can use methane as sole carbon and energy source. Its importance in the environment is related to the mitigation of methane emissions from soil and water to the atmosphere. Brazilian mangroves are highly productive, have potential to methane production, and it is inferred that methanotrophic community is of great importance for this ecosystem. The scope of this study was to investigate the functional and taxonomic diversity of methanotrophic bacteria present in the anthropogenic impacted sediments from Bertioga´s mangrove (SP, Brazil). Sediment sample was cultivated with methane and the microbiota actively involved in methane oxidation was identified by DNA-based stable isotope probing (DNA-SIP) using methane as a labeled substrate. After 4 days (96 h) of incubation and consumption of 0.7 mmol of methane, the most active microorganisms were related to methanotrophs Methylomonas and Methylobacter as well as to methylotrophic Methylotenera, indicating a possible association of these bacterial groups within a methane-derived food chain in the Bertioga mangrove. The abundance of genera Methylomonas, able to couple methane oxidation to nitrate reduction, may indicate that under low dissolved oxygen tensions, some aerobic methanotrophs could shift to intraerobic methane oxidation to avoid oxygen starvation.}, }
@article {pmid33392628, year = {2021}, author = {Vega, L and Jaimes, J and Morales, D and Martínez, D and Cruz-Saavedra, L and Muñoz, M and Ramírez, JD}, title = {Microbial Communities' Characterization in Urban Recreational Surface Waters Using Next Generation Sequencing.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {847-863}, pmid = {33392628}, issn = {1432-184X}, support = {Direcci&#xf3;n de Investigaci&#xf3;n e Innovaci&#xf3;n//Universidad del Rosario/ ; }, mesh = {*Cyanobacteria/genetics ; Eutrophication ; High-Throughput Nucleotide Sequencing ; Humans ; Lakes ; *Microbiota ; Water Microbiology ; }, abstract = {Microbial communities in surface waters used for recreational purposes are indicators of contamination and risk of contact with human pathogens. Hence, monitoring microbial communities in recreational waters is important for potential public health threats to humans. Such monitoring is rare in Colombia, even in its capital, Bogotá, the most populous city in the country. This city encompasses metropolitan and linear parks with recreational water bodies that are used frequently by the public, and the presence of pathogens can compromise the health of the citizens. Therefore, we examined the bacterial, and eukaryotic communities in urban recreational lakes (URL) in four metropolitan parks in Bogotá, Colombia. Samples from four metropolitan parks (Los Novios, Simon Bolivar, El Tunal, and Timiza) and one stream contaminated with sewage from a linear park (El Virrey) were collected. We used amplicon next-generation sequencing of the 16S-rRNA gene and 18S-rRNA gene to characterize microbial communities followed by bioinformatics analyses. In addition, general water quality parameters-pH, hardness, acidity, alkalinity, dissolved oxygen, and nitrites-were recorded using a commercial kit. Genera of pathogens, including Legionella, Pseudomonas, Mycobacterium, Candida, and Naegleria, were found in lake waters. The stream El Virrey was, however, the only surface water that showed an abundance of fecal bacteria, often associated with low oxygen concentrations. All water bodies showed a predominance of fungal phyla, except for the lake at Timiza. This lake showed the highest pH, and its ecological dynamics are likely different from other water bodies. Likewise, some URLs displayed a greater abundance of cyanobacteria, including toxin-producing species. Algal genera associated with eutrophication were predominant among primary producing microorganisms. This study shows for the first time the description of the bacterial and eukaryotic communities of some URLs and a stream in Bogotá. The URLs and the stream harbored various pathogens that might pose a risk to the citizen's health.}, }
@article {pmid33392158, year = {2020}, author = {Cerruti, M and Stevens, B and Ebrahimi, S and Alloul, A and Vlaeminck, SE and Weissbrodt, DG}, title = {Enrichment and Aggregation of Purple Non-sulfur Bacteria in a Mixed-Culture Sequencing-Batch Photobioreactor for Biological Nutrient Removal From Wastewater.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {8}, number = {}, pages = {557234}, pmid = {33392158}, issn = {2296-4185}, abstract = {Mixed-culture biotechnologies are widely used to capture nutrients from wastewater. Purple non-sulfur bacteria (PNSB), a guild of anoxygenic photomixotrophic organisms, rise interest for their ability to directly assimilate nutrients in the biomass. One challenge targets the aggregation and accumulation of PNSB biomass to separate it from the treated water. Our aim was to enrich and produce a concentrated, fast-settling PNSB biomass with high nutrient removal capacity in a 1.5-L, stirred-tank, anaerobic sequencing-batch photobioreactor (SBR). PNSB were rapidly enriched after inoculation with activated sludge at 0.1 gVSS L[-1] in a first batch of 24 h under continuous irradiance of infrared (IR) light (>700 nm) at 375 W m[-2], with Rhodobacter reaching 54% of amplicon sequencing read counts. SBR operations with decreasing hydraulic retention times (48 to 16 h, i.e., 1-3 cycles d[-1]) and increasing volumetric organic loading rates (0.2-1.3 kg COD d[-1] m[-3]) stimulated biomass aggregation, settling, and accumulation in the system, reaching as high as 3.8 g VSS L[-1]. The sludge retention time (SRT) increased freely from 2.5 to 11 days. Acetate, ammonium, and orthophosphate were removed up to 96% at a rate of 1.1 kg COD d[-1] m[-3], 77% at 113 g N d[-1] m[-3], and 73% at 15 g P d[-1] m[-3], respectively, with COD:N:P assimilation ratio of 100:6.7:0.9 m/m/m. SBR regime shifts sequentially selected for Rhodobacter (90%) under shorter SRT and non-limiting concentration of acetate during reaction phases, for Rhodopseudomonas (70%) under longer SRT and acetate limitation during reaction, and Blastochloris (10%) under higher biomass concentrations, underlying competition for substrate and photons in the PNSB guild. With SBR operations we produced a fast-settling biomass, highly (>90%) enriched in PNSB. A high nutrient removal was achieved by biomass assimilation, reaching the European nutrient discharge limits. We opened further insights on the microbial ecology of PNSB-based processes for water resource recovery.}, }
@article {pmid33391698, year = {2020}, author = {Kroetsch, SA and Kidd, KA and Monk, WA and Culp, JM and Compson, ZG and Pavey, SA}, title = {The effects of taxonomy, diet, and ecology on the microbiota of riverine macroinvertebrates.}, journal = {Ecology and evolution}, volume = {10}, number = {24}, pages = {14000-14019}, pmid = {33391698}, issn = {2045-7758}, abstract = {Freshwater macroinvertebrates play key ecological roles in riverine food webs, such as the transfer of nutrients to consumers and decomposition of organic matter. Although local habitat quality drives macroinvertebrate diversity and abundance, little is known about their microbiota. In most animals, the microbiota provides benefits, such as increasing the rate at which nutrients are metabolized, facilitating immune system development, and defending against pathogenic attack. Our objectives were to identify the bacteria within aquatic invertebrates and determine whether their composition varied with taxonomy, habitat, diet, and time of sample collection. In 2016 and 2017, we collected 264 aquatic invertebrates from the mainstem Saint John (Wolastoq) River in New Brunswick, Canada, representing 15 orders. We then amplified the V3-V4 hypervariable region of the 16S rRNA gene within each individual, which revealed nearly 20,000 bacterial operational taxonomic units (OTUs). The microbiota across all aquatic invertebrates were dominated by Proteobacteria (69.25% of the total sequence reads), but they differed significantly in beta diversity, both among host invertebrate taxa (genus-, family-, and order-levels) and temporally. In contrast to previous work, we observed no microbiota differences among functional feeding groups or traditional feeding habits, and neither water velocity nor microhabitat type structured microbiota variability. Our findings suggest that host invertebrate taxonomy was the most important factor in modulating the composition of the microbiota, likely through a combination of vertical and horizontal bacterial transmission, and evolutionary processes. This is one of the most comprehensive studies of freshwater invertebrate microbiota to date, and it underscores the need for future studies of invertebrate microbiota evolution and linkages to environmental bacteria and physico-chemical conditions.}, }
@article {pmid33388944, year = {2021}, author = {Saona, LA and Soria, M and Durán-Toro, V and Wörmer, L and Milucka, J and Castro-Nallar, E and Meneses, C and Contreras, M and Farías, ME}, title = {Phosphate-Arsenic Interactions in Halophilic Microorganisms of the Microbial Mat from Laguna Tebenquiche: from the Microenvironment to the Genomes.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {941-953}, pmid = {33388944}, issn = {1432-184X}, support = {1200834//ANID-FONDECYT/ ; ACT192057//ANID-PIA-Anillo INACH/ ; PICT 3825//Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas/ ; }, mesh = {*Arsenic ; Geologic Sediments ; Lakes ; *Microbiota ; Phosphates ; }, abstract = {Arsenic (As) is a metalloid present in the earth's crust and widely distributed in the environment. Due to its high concentrations in the Andean valleys and its chemical similarity with phosphorus (P), its biological role in Andean Microbial Ecosystems (AMEs) has begun to be studied. The AMEs are home to extremophilic microbial communities that form microbial mats, evaporites, and microbialites inhabiting Andean lakes, puquios, or salt flats. In this work, we characterize the biological role of As and the effect of phosphate in AMEs from the Laguna Tebenquiche (Atacama Desert, Chile). Using micro X-ray fluorescence, the distribution of As in microbial mat samples was mapped. Taxonomic and inferred functional profiles were obtained from enriched cultures of microbial mats incubated under As stress and different phosphate conditions. Additionally, representative microorganisms highly resistant to As and able to grow under low phosphate concentration were isolated and studied physiologically. Finally, the genomes of the isolated Salicola sp. and Halorubrum sp. were sequenced to analyze genes related to both phosphate metabolism and As resistance. The results revealed As as a key component of the microbial mat ecosystem: (i) As was distributed across all sections of the microbial mat and represented a significant weight percentage of the mat (0.17 %) in comparison with P (0.40%); (ii) Low phosphate concentration drastically changed the microbial community in microbial mat samples incubated under high salinity and high As concentrations; (iii) Archaea and Bacteria isolated from the microbial mat were highly resistant to arsenate (up to 500 mM), even under low phosphate concentration; (iv) The genomes of the two isolates were predicted to contain key genes in As metabolism (aioAB and arsC/acr3) and the genes predicted to encode the phosphate-specific transport operon (pstSCAB-phoU) are next to the arsC gene, suggesting a functional relationship between these two elements.}, }
@article {pmid33387813, year = {2021}, author = {Bossaert, S and Winne, V and Van Opstaele, F and Buyse, J and Verreth, C and Herrera-Malaver, B and Van Geel, M and Verstrepen, KJ and Crauwels, S and De Rouck, G and Lievens, B}, title = {Description of the temporal dynamics in microbial community composition and beer chemistry in sour beer production via barrel ageing of finished beers.}, journal = {International journal of food microbiology}, volume = {339}, number = {}, pages = {109030}, doi = {10.1016/j.ijfoodmicro.2020.109030}, pmid = {33387813}, issn = {1879-3460}, mesh = {Bacteria/*classification/*genetics ; Beer/*microbiology ; Biodiversity ; Fermentation ; Flavoring Agents ; *Food Microbiology ; *Microbiota ; Pediococcus ; Polyphenols/analysis ; RNA, Ribosomal, 16S/genetics ; Taste ; Time Factors ; }, abstract = {Currently, there is a strong interest in barrel ageing of finished, conventionally fermented beers, as a novel way to produce sour beers with a rich and complex flavour profile. The production process, however, remains largely a process of trial and error, often resulting in profit losses and inconsistency in quality. To improve product quality and consistency, a better understanding of the interactions between microorganisms, wood and maturing beer is needed. The aim of this study was to describe the temporal dynamics in microbial community composition, beer chemistry and sensory characteristics during barrel ageing of three conventionally fermented beers that differed in parameters like alcohol content and bitterness. Beers were matured for 38 weeks in new (two types of wood) and used (one type of wood) oak barrels. Beer samples were taken at the start of the maturation and after 2, 12 and 38 weeks. Microbial community composition, determined using amplicon sequencing of the V4 region of the bacterial 16S rRNA gene and the fungal ITS1 region, beer chemistry and sensory characteristics substantially changed throughout the maturation process. Likewise, total bacterial and fungal population densities generally increased during maturation. PerMANOVA revealed significant differences in the bacterial and fungal community composition of the three beers and across time points, but not between the different wood types. By contrast, significant differences in beer chemistry were found across the different beers, wood types and sampling points. Results also indicated that the outcome of the maturation process likely depends on the initial beer properties. Specifically, results suggested that beer bitterness may restrain the bacterial community composition, thereby having an impact on beer souring. While the bacterial community composition of moderately-hopped beers shifted to a dominance of lactic acid bacteria, the bacterial community of the high-bitterness beer remained fairly constant, with low population densities. Bacterial community composition of the moderate-bitterness beers also resembled those of traditional sours like lambic beers, hosting typical lambic brewing species like Pediococcus damnosus, Lactobacillus brevis and Acetobacter sp. Furthermore, results suggested that alcohol level may have affected the fungal community composition and extraction of wood compounds. More specifically, the concentration of wood compounds like cis-3-methyl-4-octanolide, trans-3-methyl-4-octanolide, eugenol and total polyphenols was higher in beers with a high alcohol content. Altogether, our results provide novel insights into the barrel ageing process of beer, and may pave the way for a new generation of sour beers.}, }
@article {pmid33385649, year = {2021}, author = {Park, Y and Yu, J and Nguyen, VK and Park, S and Kim, J and Lee, T}, title = {Understanding complete ammonium removal mechanism in single-chamber microbial fuel cells based on microbial ecology.}, journal = {The Science of the total environment}, volume = {764}, number = {}, pages = {144231}, doi = {10.1016/j.scitotenv.2020.144231}, pmid = {33385649}, issn = {1879-1026}, mesh = {*Ammonium Compounds ; *Bioelectric Energy Sources ; Biofilms ; Bioreactors ; Humans ; Nitrites ; Nitrogen ; Wastewater ; }, abstract = {The removal of organics and ammonium from domestic wastewater was successfully achieved by a flat-panel air-cathode microbial fuel cell (FA-MFC). To elucidate the reason for complete ammonium removal in the single-chamber MFCs, microbial communities were analyzed in biofilms on the surface of each anode, separator, and cathode of separator-electrode assemblies (SEAs). The spatial distribution of bacterial families related to the nitrogen cycle varied based on local conditions. Since oxygen diffusing from the air-cathode created a locally aerobic condition, ammonia-oxidizing bacteria (AOB) Nitrosomonadacea and nitrite-oxidizing bacteria (NOB) Nitrospiraceae were present near the cathode. NOB (~12.1%) was more abundant than AOB (~4.4%), suggesting that the nitrate produced by NOB may be reduced back to nitrite by heterotrophic denitrifiers such as Rhodocyclaceae (~21.7%) and Comamonadaceae (~5%) in the anoxic zone close to the NOB layer. Near that zone, the "nitrite loop" also substantially enriched two nitrite-reducing bacterial families: Ignavibacteriaceae (~18.1%), facultative heterotrophs, and Brocadiaceae (~11.2%), anaerobic ammonium oxidizing autotrophs. A larger inner area of biofilm contained abundant heterotrophic denitrifiers and fermentation bacteria. These results indicate that the large-surface SEA of FA-MFC allows counter-diffusion between substrates and oxygen, resulting in interactions of bacteria involved in the nitrogen cycle for complete ammonium removal.}, }
@article {pmid33384680, year = {2020}, author = {Amacker, N and Gao, Z and Agaras, BC and Latz, E and Kowalchuk, GA and Valverde, CF and Jousset, A and Weidner, S}, title = {Biocontrol Traits Correlate With Resistance to Predation by Protists in Soil Pseudomonads.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {614194}, pmid = {33384680}, issn = {1664-302X}, abstract = {Root-colonizing bacteria can support plant growth and help fend off pathogens. It is clear that such bacteria benefit from plant-derived carbon, but it remains ambiguous why they invest in plant-beneficial traits. We suggest that selection via protist predation contributes to recruitment of plant-beneficial traits in rhizosphere bacteria. To this end, we examined the extent to which bacterial traits associated with pathogen inhibition coincide with resistance to protist predation. We investigated the resistance to predation of a collection of Pseudomonas spp. against a range of representative soil protists covering three eukaryotic supergroups. We then examined whether patterns of resistance to predation could be explained by functional traits related to plant growth promotion, disease suppression and root colonization success. We observed a strong correlation between resistance to predation and phytopathogen inhibition. In addition, our analysis highlighted an important contribution of lytic enzymes and motility traits to resist predation by protists. We conclude that the widespread occurrence of plant-protective traits in the rhizosphere microbiome may be driven by the evolutionary pressure for resistance against predation by protists. Protists may therefore act as microbiome regulators promoting native bacteria involved in plant protection against diseases.}, }
@article {pmid33384676, year = {2020}, author = {Assis, JM and Abreu, F and Villela, HMD and Barno, A and Valle, RF and Vieira, R and Taveira, I and Duarte, G and Bourne, DG and Høj, L and Peixoto, RS}, title = {Delivering Beneficial Microorganisms for Corals: Rotifers as Carriers of Probiotic Bacteria.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {608506}, pmid = {33384676}, issn = {1664-302X}, abstract = {The use of Beneficial Microorganisms for Corals (BMCs) to increase the resistance of corals to environmental stress has proven to be effective in laboratory trials. Because direct inoculation of BMCs in larger tanks or in the field can be challenging, a delivery mechanism is needed for efficient transmission of the BMC consortium. Packaged delivery mechanisms have been successfully used to transmit probiotics to other organisms, including humans, lobsters, and fish. Here, we tested a method for utilizing rotifers of the species Brachionus plicatilis for delivery of BMCs to corals of the species Pocillopora damicornis. Epifluorescence microscopy combined with a live/dead cell staining assay was used to evaluate the viability of the BMCs and monitor their in vivo uptake by the rotifers. The rotifers efficiently ingested BMCs, which accumulated in the digestive system and on the body surface after 10 min of interaction. Scanning electron microscopy confirmed the adherence of BMCs to the rotifer surfaces. BMC-enriched rotifers were actively ingested by P. damicornis corals, indicating that this is a promising technique for administering coral probiotics in situ. Studies to track the delivery of probiotics through carriers such as B. plicatilis, and the provision or establishment of beneficial traits in corals are the next proof-of-concept research priorities.}, }
@article {pmid33382858, year = {2020}, author = {Lequime, S and Dehecq, JS and Matheus, S and de Laval, F and Almeras, L and Briolant, S and Fontaine, A}, title = {Modeling intra-mosquito dynamics of Zika virus and its dose-dependence confirms the low epidemic potential of Aedes albopictus.}, journal = {PLoS pathogens}, volume = {16}, number = {12}, pages = {e1009068}, pmid = {33382858}, issn = {1553-7374}, mesh = {Aedes/metabolism/virology ; Animals ; Disease Outbreaks ; Disease Vectors ; Epidemics ; Humans ; Models, Theoretical ; Mosquito Vectors/*metabolism/*virology ; Saliva/virology ; Viral Load ; Viremia/transmission ; Zika Virus/pathogenicity ; Zika Virus Infection/epidemiology/*transmission/virology ; }, abstract = {Originating from African forests, Zika virus (ZIKV) has now emerged worldwide in urbanized areas, mainly transmitted by Aedes aegypti mosquitoes. Although Aedes albopictus can transmit ZIKV experimentally and was suspected to be a ZIKV vector in Central Africa, the potential of this species to sustain virus transmission was yet to be uncovered until the end of 2019, when several autochthonous transmissions of the virus vectored by Ae. albopictus occurred in France. Aside from these few locally acquired ZIKV infections, most territories colonized by Ae. albopictus have been spared so far. The risk level of ZIKV emergence in these areas remains however an open question. To assess Ae. albopictus' vector potential for ZIKV and identify key virus outbreak predictors, we built a complete framework using the complementary combination of (i) dose-dependent experimental Ae. albopictus exposure to ZIKV followed by time-dependent assessment of infection and systemic infection rates, (ii) modeling of intra-human ZIKV viremia dynamics, and (iii) in silico epidemiological simulations using an Agent-Based Model. The highest risk of transmission occurred during the pre-symptomatic stage of the disease, at the peak of viremia. At this dose, mosquito infection probability was estimated to be 20%, and 21 days were required to reach the median systemic infection rates. Mosquito population origin, either temperate or tropical, had no impact on infection rates or intra-host virus dynamic. Despite these unfavorable characteristics for transmission, Ae. albopictus was still able to trigger and yield large outbreaks in a simulated environment in the presence of sufficiently high mosquito biting rates. Our results reveal a low but existing epidemic potential of Ae. albopictus for ZIKV, that might explain the absence of large scale ZIKV epidemics so far in territories occupied only by Ae. albopictus. They nevertheless support active surveillance and eradication programs in these territories to maintain the risk of emergence to a low level.}, }
@article {pmid33382250, year = {2021}, author = {Kirchner, N and Cano-Prieto, C and Schulz-Fincke, AC and Gütschow, M and Ortlieb, N and Moschny, J and Niedermeyer, THJ and Horak, J and Lämmerhofer, M and van der Voort, M and Raaijmakers, JM and Gross, H}, title = {Discovery of Thanafactin A, a Linear, Proline-Containing Octalipopeptide from Pseudomonas sp. SH-C52, Motivated by Genome Mining.}, journal = {Journal of natural products}, volume = {84}, number = {1}, pages = {101-109}, doi = {10.1021/acs.jnatprod.0c01174}, pmid = {33382250}, issn = {1520-6025}, mesh = {Genome, Bacterial ; Multigene Family ; Peptide Synthases/*chemistry/metabolism ; Proline/*chemistry ; Pseudomonas/*chemistry/drug effects ; Pseudomonas fluorescens/genetics ; }, abstract = {Genome mining of the bacterial strains Pseudomonas sp. SH-C52 and Pseudomonas fluorescens DSM 11579 showed that both strains contained a highly similar gene cluster encoding an octamodular nonribosomal peptide synthetase (NRPS) system which was not associated with a known secondary metabolite. Insertional mutagenesis of an NRPS component followed by comparative profiling led to the discovery of the corresponding novel linear octalipopeptide thanafactin A, which was subsequently isolated and its structure determined by two-dimensional NMR and further spectroscopic and chromatographic methods. In bioassays, thanafactin A exhibited weak protease inhibitory activity and was found to modulate swarming motility in a strain-specific manner.}, }
@article {pmid33381966, year = {2021}, author = {Yu, Z and Schwarz, C and Zhu, L and Chen, L and Shen, Y and Yu, P}, title = {Hitchhiking Behavior in Bacteriophages Facilitates Phage Infection and Enhances Carrier Bacteria Colonization.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {4}, pages = {2462-2472}, doi = {10.1021/acs.est.0c06969}, pmid = {33381966}, issn = {1520-5851}, mesh = {Bacillus cereus ; *Bacteriophages ; Biofilms ; Coliphages ; Escherichia coli ; }, abstract = {Interactions between bacteriophages (phages) and biofilms remain poorly understood despite the broad implications for microbial ecology, water quality, and microbiome engineering. Here, we demonstrate that lytic coliphage PHH01 can hitchhike on carrier bacteria Bacillus cereus to facilitate its infection of host bacteria, Escherichia coli, in biofilms. Specifically, PHH01 could adsorb onto the flagella of B. cereus, and thus phage motility was increased, resulting in 4.36-fold more effective infection of E. coli in biofilm relative to free PHH01 alone. Moreover, phage infection mitigated interspecies competition and enhanced B. cereus colonization; the fraction of B. cereus in the final biofilm increased from 9% without phages to 43% with phages. The mutualistic relationship between the coliphage and carrier bacteria was substantiated by migration tests on an E. coli lawn: the conjugation of PHH01 and B. cereus enhanced B. cereus colonization by 6.54-fold compared to B. cereus alone (6.15 vs 0.94 cm[2] in 24 h) and PHH01 migration by 5.15-fold compared to PHH01 alone (10.3 vs 2.0 mm in 24 h). Metagenomic and electron microscopic analysis revealed that the phages of diverse taxonomies and different morphologies could be adsorbed by the flagella of B. cereus, suggesting hitchhiking on flagellated bacteria might be a widespread strategy in aquatic phage populations. Overall, our study highlights that hitchhiking behavior in phages can facilitate phage infection of biofilm bacteria, promote carrier bacteria colonization, and thus significantly influence biofilm composition, which holds promise for mediating biofilm functions and moderating associated risks.}, }
@article {pmid33378450, year = {2021}, author = {Metze, D and Popp, D and Schwab, L and Keller, NS and da Rocha, UN and Richnow, HH and Vogt, C}, title = {Temperature management potentially affects carbon mineralization capacity and microbial community composition of a shallow aquifer.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {2}, pages = {}, doi = {10.1093/femsec/fiaa261}, pmid = {33378450}, issn = {1574-6941}, mesh = {Carbon ; *Groundwater ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Temperature ; }, abstract = {High-temperature aquifer thermal energy storage (HT-ATES) is a promising technique to reduce the CO2 footprint of heat supply in the frame of transitioning to renewable energies. However, HT-ATES causes temperature fluctuations in groundwater ecosystems potentially affecting important microbial-mediated ecosystem services. Hence, assessing the impact of increasing temperatures on the structure and functioning of aquifer microbiomes is crucial to evaluate potential environmental risks associated with HT-ATES. In this study, we investigated the effects of temperature variations (12-80°C) on microbial communities and their capacity to mineralize acetate in aerobically incubated sediment sampled from a pristine aquifer. Compared to natural conditions (12°C), increased acetate mineralization rates were observed at 25°C, 37°C and 45°C, whereas mineralization was decelerated at 60°C and absent at 80°C. Sequencing of 16S rRNA genes revealed that the bacterial diversity in acetate-amended and non-acetate-amended sediments decreased with rising temperatures. Distinct communities dominated by bacterial groups affiliated with meso- and thermophilic bacteria established at 45°C and 60°C, respectively, while the number of archaeal phylotypes decreased. The changes in microbial diversity observed at 45°C and 60°C indicate a potential loss of ecosystem functioning, functional redundancy and resilience, while heat storage at 80°C bears the risk of ecological collapse.}, }
@article {pmid33378284, year = {2020}, author = {Afolayan, AO and Ayeni, FA}, title = {Metagenomic Analysis of Bacterial Communities in Water and Soil of the Fulani and non-Fulani in Nigeria.}, journal = {Journal of infection in developing countries}, volume = {14}, number = {12}, pages = {}, doi = {10.3855/jidc.12975}, pmid = {33378284}, issn = {1972-2680}, mesh = {DNA, Bacterial ; Humans ; Metagenomics ; *Microbiota ; Nigeria ; Proteobacteria/classification/genetics ; Pseudomonas/classification/genetics ; Public Health ; RNA, Ribosomal, 16S ; Rural Population ; *Soil Microbiology ; *Water Microbiology ; }, abstract = {INTRODUCTION: Interactions between environmental factors (water and soil) and humans are inevitable, particularly in rural and semi-urbanized regions. As such, knowledge on the microbial constituents of these environmental factors is key to understanding potential risk to public health. However, the microbial profile of soil and water present in vulnerable human communities in Nigeria is currently unknown. This study sought to investigate the composition of soil and water microbiota in the environment inhabited by recently studied human communities (the Fulani nomadic group and the urbanized Jarawa ethnic group) and estimate the contribution of these environmental factors to the microbiome of the aforementioned human communities.<br><br>METHODOLOGY: Soil and water samples were collected from the Fulani and non-Fulani community in Jengre (Plateau State, Nigeria) and Jos (Plateau State, Nigeria), respectively. Genomic DNA was extracted from these environmental samples, followed by Illumina sequencing of the V4 region of the 16S rRNA gene and bioinformatics analysis via Quantitative Insights into Microbial Ecology QIIME.<br><br>RESULTS: There is abundance of Proteobacteria (43%) signature members in soil samples obtained from both human communities. Analysis of the water samples revealed the abundance of Proteobacteria, particularly in water sourced from the borehole (Fulani). Pseudomonas (30%) had higher relative abundance in the drinking water of the Fulani.<br><br>CONCLUSIONS: The drinking water of the Fulani could be a potential health risk to the studied Fulani community. Factors that increase the abundance of public health threats and health risk, such as hygiene practices, soil and water quality need to be studied further for the improvement of health in vulnerable populations.}, }
@article {pmid33375064, year = {2020}, author = {Duranti, S and Longhi, G and Ventura, M and van Sinderen, D and Turroni, F}, title = {Exploring the Ecology of Bifidobacteria and Their Genetic Adaptation to the Mammalian Gut.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, pmid = {33375064}, issn = {2076-2607}, support = {SFI/12/RC/2273-P2/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273-P1/SFI_/Science Foundation Ireland/Ireland ; }, abstract = {The mammalian gut is densely inhabited by microorganisms that have coevolved with their host. Amongst these latter microorganisms, bifidobacteria represent a key model to study host-microbe interaction within the mammalian gut. Remarkably, bifidobacteria naturally occur in a range of ecological niches that are either directly or indirectly connected to the animal gastrointestinal tract. They constitute one of the dominant bacterial members of the intestinal microbiota and are among the first colonizers of the mammalian gut. Notably, the presence of bifidobacteria in the gut has been associated with several health-promoting activities. In this review, we aim to provide an overview of current knowledge on the genetic diversity and ecology of bifidobacteria. Furthermore, we will discuss how this important group of gut bacteria is able to colonize and survive in the mammalian gut, so as to facilitate host interactions.}, }
@article {pmid33375046, year = {2020}, author = {Khomutovska, N and de Los Ríos, A and Jasser, I}, title = {Diversity and Colonization Strategies of Endolithic Cyanobacteria in the Cold Mountain Desert of Pamir.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, pmid = {33375046}, issn = {2076-2607}, abstract = {Microorganisms can survive in extreme environments and oligotrophic habitats thanks to their specific adaptive capacity. Due to its severe and contrasting climate conditions, the cold mountain desert in Eastern Pamir provides a unique environment for analyzing microbial adaptation mechanisms occurring within colonization of endolithic habitats. This study aims to investigate the composition and structure of endolithic microbial communities and analyze the interactions between microorganisms and colonized lithic substrates. Endolithic biofilms were examined using scanning electron microscopy in backscattered electron mode (SEM-BSE) and next-generation sequencing (NGS) applying amplicon sequence variants (ASVs) approach. The investigation of the V3-V4 region of 16S rRNA gene revealed that endolithic communities are dominated by Actinobacteria (26%), Proteobacteria (23%), and Cyanobacteria (11.4%). Cyanobacteria were represented by Oxyphotobacteria with a predominance of subclasses of Oscillatoriophycidae, Synechococcophycideae, and Nostocophycidae as well as the rarely occurring Sericytochromatia. The positive correlation between the contribution of the orders Synechococcales and Rhizobiales to community structure suggests that some functionally closed taxa of Cyanobacteria and Proteobacteria can complement each other, for example, in nitrogen fixation in endolithic communities. The endolithic communities occurring in Eastern Pamir were identified as complex systems whose composition and structure seem to be influenced by the architecture of microhabitats and related microenvironmental conditions.}, }
@article {pmid33374976, year = {2020}, author = {Rughöft, S and Jehmlich, N and Gutierrez, T and Kleindienst, S}, title = {Comparative Proteomics of Marinobacter sp. TT1 Reveals Corexit Impacts on Hydrocarbon Metabolism, Chemotactic Motility, and Biofilm Formation.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, pmid = {33374976}, issn = {2076-2607}, support = {Elite Program for Postdocs//Baden-W&#xfc;rttemberg Stiftung/ ; 326028733//Deutsche Forschungsgemeinschaft/ ; }, abstract = {The application of chemical dispersants during marine oil spills can affect the community composition and activity of marine microorganisms. Several studies have indicated that certain marine hydrocarbon-degrading bacteria, such as Marinobacter spp., can be inhibited by chemical dispersants, resulting in lower abundances and/or reduced biodegradation rates. However, a major knowledge gap exists regarding the mechanisms underlying these physiological effects. Here, we performed comparative proteomics of the Deepwater Horizon isolate Marinobacter sp. TT1 grown under different conditions. Strain TT1 received different carbon sources (pyruvate vs. n-hexadecane) with and without added dispersant (Corexit EC9500A). Additional treatments contained crude oil in the form of a water-accommodated fraction (WAF) or chemically-enhanced WAF (CEWAF; with Corexit). For the first time, we identified the proteins associated with alkane metabolism and alginate biosynthesis in strain TT1, report on its potential for aromatic hydrocarbon biodegradation and present a protein-based proposed metabolism of Corexit components as carbon substrates. Our findings revealed that Corexit exposure affects hydrocarbon metabolism, chemotactic motility, biofilm formation, and induces solvent tolerance mechanisms, like efflux pumps, in strain TT1. This study provides novel insights into dispersant impacts on microbial hydrocarbon degraders that should be taken into consideration for future oil spill response actions.}, }
@article {pmid33374225, year = {2020}, author = {Shah, F and Gressler, M and Nehzati, S and Op De Beeck, M and Gentile, L and Hoffmeister, D and Persson, P and Tunlid, A}, title = {Secretion of Iron(III)-Reducing Metabolites during Protein Acquisition by the Ectomycorrhizal Fungus Paxillus involutus.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, pmid = {33374225}, issn = {2076-2607}, support = {P41 GM103393/GM/NIGMS NIH HHS/United States ; 2013.0073//Knut and Alice Wallenberg Foundation/ ; 2016-04561 and 2017-04261//Swedish Research Council/ ; }, abstract = {The ectomycorrhizal fungus Paxillus involutus decomposes proteins using a two-step mechanism, including oxidation and proteolysis. Oxidation involves the action of extracellular hydroxyl radicals (•OH) generated by the Fenton reaction. This reaction requires the presence of iron(II). Here, we monitored the speciation of extracellular iron and the secretion of iron(III)-reducing metabolites during the decomposition of proteins by P. involutus. X-ray absorption spectroscopy showed that extracellular iron was mainly present as solid iron(III) phosphates and oxides. Within 1 to 2 days, these compounds were reductively dissolved, and iron(II) complexes were formed, which remained in the medium throughout the incubation. HPLC and mass spectrometry detected five extracellular iron(III)-reducing metabolites. Four of them were also secreted when the fungus grew on a medium containing ammonium as the sole nitrogen source. NMR identified the unique iron(III)-reductant as the diarylcyclopentenone involutin. Involutin was produced from day 2, just before the elevated •OH production, preceding the oxidation of BSA. The other, not yet fully characterized iron(III)-reductants likely participate in the rapid reduction and dissolution of solid iron(III) complexes observed on day one. The production of these metabolites is induced by other environmental cues than for involutin, suggesting that they play a role beyond the Fenton chemistry associated with protein oxidation.}, }
@article {pmid33374112, year = {2020}, author = {LeBrun, ES and Nighot, M and Dharmaprakash, V and Kumar, A and Lo, CC and Chain, PSG and Ma, TY}, title = {The Gut Microbiome and Alcoholic Liver Disease: Ethanol Consumption Drives Consistent and Reproducible Alteration in Gut Microbiota in Mice.}, journal = {Life (Basel, Switzerland)}, volume = {11}, number = {1}, pages = {}, pmid = {33374112}, issn = {2075-1729}, support = {R01 DK121073/DK/NIDDK NIH HHS/United States ; R01Dk121073/NH/NIH HHS/United States ; R01DK106072/NH/NIH HHS/United States ; J. Lloyd Huck Chair in Medicine//Penn State College of Medicine/ ; }, abstract = {Phenotypic health effects, both positive and negative, have been well studied in association with the consumption of alcohol in humans as well as several other mammals including mice. Many studies have also associated these same health effects and phenotypes to specific members of gut microbiome communities. Here we utilized a chronic plus binge ethanol feed model (Gao-binge model) to explore microbiome community changes across three independent experiments performed in mice. We found significant and reproducible differences in microbiome community assemblies between ethanol-treated mice and control mice on the same diet absent of ethanol. We also identified significant differences in gut microbiota occurring temporally with ethanol treatment. Peak shift in communities was observed 4 days after the start of daily alcohol consumption. We quantitatively identified many of the bacterial genera indicative of these ethanol-induced shifts including 20 significant genera when comparing ethanol treatments with controls and 14 significant genera based on temporal investigation. Including overlap of treatment with temporal shifts, we identified 25 specific genera of interest in ethanol treatment microbiome shifts. Shifts coincide with observed presentation of fatty deposits in the liver tissue, i.e., Alcoholic Liver Disease-associated phenotype. The evidence presented herein, derived from three independent experiments, points to the existence of a common, reproducible, and characterizable "mouse ethanol gut microbiome".}, }
@article {pmid33370423, year = {2020}, author = {Parks, M and Kedy, C and Skalla, C}, title = {Consistent patterns in 16S and 18S microbial diversity from the shells of the common and widespread red-eared slider turtle (Trachemys scripta).}, journal = {PloS one}, volume = {15}, number = {12}, pages = {e0244489}, pmid = {33370423}, issn = {1932-6203}, mesh = {Animal Shells/*microbiology ; Animals ; Conservation of Natural Resources ; DNA Barcoding, Taxonomic ; DNA, Bacterial/isolation &amp; purification ; Fresh Water/microbiology ; Iowa ; Microbiota/*genetics ; Oklahoma ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Turtles/*microbiology ; }, abstract = {Microbial communities associated with freshwater aquatic habitats and resident species are both critical to and indicative of ecosystem status and organismal health. External surfaces of turtle shells readily accumulate microbial growth and could carry representation of habitat-wide microbial diversity, since they are in regular contact with multiple elements of freshwater environments. Yet, microbial diversity residing on freshwater turtle shells is poorly understood. We applied 16S and 18S metabarcoding to characterize microbiota associated with external shell surfaces of 20 red-eared slider (Trachemys scripta) turtles collected from varied habitats in central and western Oklahoma, and ranging to southeast Iowa. Shell-associated microbial communities were highly diverse, with samples dominated by Bacteroidia and alpha-/gamma-proteobacteria, and ciliophoran alveolates. Alpha diversity was lower on turtle shells compared to shallow-water-associated environmental samples, likely resulting from basking-drying behavior and seasonal scute shedding, while alpha diversity was higher on carapace than plastron surfaces. Beta diversity of turtle shells was similarly differentiated from environmental samples, although sampling site was consistently a significant factor. Deinococcus-Thermus bacteria and ciliophoran alveolates were recovered with significantly higher abundance on turtle shells versus environmental samples, while bacterial taxa known to include human-pathogenic species were variably more abundant between shell and environmental samples. Microbial communities from a single, shared-site collection of the ecologically similar river cooter (P. concinna) largely overlapped with those of T. scripta. These data add to a foundation for further characterization of turtle shell microbial communities across species and habitats, with implications for freshwater habitat assessment, microbial ecology and wildlife conservation efforts.}, }
@article {pmid33363527, year = {2020}, author = {Smith, PE and Waters, SM and Gómez Expósito, R and Smidt, H and Carberry, CA and McCabe, MS}, title = {Synthetic Sequencing Standards: A Guide to Database Choice for Rumen Microbiota Amplicon Sequencing Analysis.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {606825}, pmid = {33363527}, issn = {1664-302X}, abstract = {Our understanding of complex microbial communities, such as those residing in the rumen, has drastically advanced through the use of high throughput sequencing (HTS) technologies. Indeed, with the use of barcoded amplicon sequencing, it is now cost effective and computationally feasible to identify individual rumen microbial genera associated with ruminant livestock nutrition, genetics, performance and greenhouse gas production. However, across all disciplines of microbial ecology, there is currently little reporting of the use of internal controls for validating HTS results. Furthermore, there is little consensus of the most appropriate reference database for analyzing rumen microbiota amplicon sequencing data. Therefore, in this study, a synthetic rumen-specific sequencing standard was used to assess the effects of database choice on results obtained from rumen microbial amplicon sequencing. Four DADA2 reference training sets (RDP, SILVA, GTDB, and RefSeq + RDP) were compared to assess their ability to correctly classify sequences included in the rumen-specific sequencing standard. In addition, two thresholds of phylogenetic bootstrapping, 50 and 80, were applied to investigate the effect of increasing stringency. Sequence classification differences were apparent amongst the databases. For example the classification of Clostridium differed between all databases, thus highlighting the need for a consistent approach to nomenclature amongst different reference databases. It is hoped the effect of database on taxonomic classification observed in this study, will encourage research groups across various microbial disciplines to develop and routinely use their own microbiome-specific reference standard to validate analysis pipelines and database choice.}, }
@article {pmid33362871, year = {2020}, author = {Setubal, JC and Stoye, J and Dutilh, BE}, title = {Editorial: Computational Methods for Microbiome Analysis.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {623897}, doi = {10.3389/fgene.2020.623897}, pmid = {33362871}, issn = {1664-8021}, }
@article {pmid33361365, year = {2021}, author = {Van Holm, W and Ghesquière, J and Boon, N and Verspecht, T and Bernaerts, K and Zayed, N and Chatzigiannidou, I and Teughels, W}, title = {A Viability Quantitative PCR Dilemma: Are Longer Amplicons Better?.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {5}, pages = {e0265320}, pmid = {33361365}, issn = {1098-5336}, support = {C24/17/086//KU Leuven (Katholieke Universiteit Leuven)/ ; G0B2719N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; G091219N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; FWO-1SA5719N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; }, mesh = {DNA, Bacterial ; *Microbial Viability ; *Polymerase Chain Reaction ; }, abstract = {The development of viability quantitative PCR (v-qPCR) has allowed for a more accurate assessment of the viability of a microbial sample by limiting the amplification of DNA from dead cells. Although valuable, v-qPCR is not infallible. One of the most limiting factors for accurate live/dead distinction is the length of the qPCR amplicon used. However, no consensus or guidelines exist for selecting and designing amplicon lengths for optimal results. In this study, a wide range of incrementally increasing amplicon lengths (68 to 906 base pairs [bp]) was used on live and killed cells of nine bacterial species treated with a viability dye (propidium monoazide [PMA]). Increasing amplicon lengths up to approximately 200 bp resulted in increasing quantification cycle (Cq) differences between live and killed cells while maintaining a good qPCR efficiency. Longer amplicon lengths, up to approximately 400 bp, further increased the Cq difference but at the cost of qPCR efficiency. Above 400 bp, no valuable increase in Cq differences was observed. IMPORTANCE Viability quantitative PCR (v-qPCR) has evolved into a valuable, mainstream technique for determining the number of viable microorganisms in samples by qPCR. Amplicon length is known to be positively correlated with the ability to distinguish between live and dead bacteria but is negatively correlated with qPCR efficiency. This trade-off is often not taken into account and might have an impact on the accuracy of v-qPCR data. Currently, there is no consensus on the optimal amplicon length. This paper provides methods to determine the optimal amplicon length and suggests an amplicon length range for optimal v-qPCR, taking into consideration the trade-off between qPCR efficiency and live/dead distinction.}, }
@article {pmid33360128, year = {2021}, author = {Yuan, W and Wei, Y and Zhang, Y and Riaz, L and Yang, Q and Wang, Q and Wang, R}, title = {Resistance of multidrug resistant Escherichia coli to environmental nanoscale TiO2 and ZnO.}, journal = {The Science of the total environment}, volume = {761}, number = {}, pages = {144303}, doi = {10.1016/j.scitotenv.2020.144303}, pmid = {33360128}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/toxicity ; Ecosystem ; Escherichia coli ; *Metal Nanoparticles/toxicity ; *Nanoparticles ; Titanium/toxicity ; *Zinc Oxide/toxicity ; }, abstract = {Excessive production and utilization of nanoparticles (NPs) at industrial and household levels releases substantial quantities of NPs into the environment. These can be harmful to different types of organisms and cause adverse effects on ecosystems. Purchased TiO2 and ZnO NPs were characterized via XRD, XPS, FESEM, and Zeta potential. This study elucidates how multidrug resistant Escherichia coli LM13, which was recovered from livestock manure, counteracts the antibacterial activities of TiO2 and ZnO NPs to survive in the environment. E. coli ATCC25922, which is susceptible to antibiotics, was used as control. A dose-response experiment showed that the antibacterial activity of TiO2 was lower than that of ZnO NPs and, LM13 was more resistant to NPs than ATCC25922. An AcrAB-TolC efflux pump along with its regulation genes helped LM13 to minimize NP toxicity. Flow cytometry findings also indicated that the intensity of the side-scatter light parameter increased with TiO2 and ZnO NPs in a dose dependent manner, suggesting NP uptake by the both strains. The generation of reactive oxygen species in LM13 was several-fold lower than in ATCC25922, suggesting that reactive oxygen species mainly contribute to the toxicity mechanism. These results illustrate the necessity to evaluate the impacts of NPs on the survival capacity of bacteria and on the resistance genes in bacteria with higher NP resistance than NP susceptible bacteria.}, }
@article {pmid33360101, year = {2021}, author = {Ngo, KN and Van Winckel, T and Massoudieh, A and Wett, B and Al-Omari, A and Murthy, S and Takács, I and De Clippeleir, H}, title = {Towards more predictive clarification models via experimental determination of flocculent settling coefficient value.}, journal = {Water research}, volume = {190}, number = {}, pages = {116294}, doi = {10.1016/j.watres.2020.116294}, pmid = {33360101}, issn = {1879-2448}, mesh = {Calibration ; Flocculation ; Models, Theoretical ; Sewage ; *Waste Disposal, Fluid ; *Water Purification ; }, abstract = {Improved settleability has become an essential feature of new wastewater treatment innovations. To accelerate adoption of such new technologies, improved clarifier models are needed to help with designing and predicting improvement in settleability. In general, the level of mathematics of settling clarifier models has gone far beyond the level of existing experimental methods available to support these models. To date, even for simple one-dimensional (1D) clarifier models, no experimental method has been described for flocculent settling coefficient (rp). As a consequence, rp cannot be considered as a sludge characteristic and is used as a calibration parameter to achieve observed effluent quality. In this study, we focused on the development of an empirical function based on a simple and practical experimental approach for the calculation of the rp value from sludge characteristics. This approach provided a similar approach as currently taken for hindered settling coefficient calculations (Veslind equation) and allowed for the model to predict effluent quality, thus increasing the power of the 1D model. The threshold of flocculation (TOF), which describes the collision efficiency of particles, directly correlated with the effluent quality of the five tested activated sludge systems and was selected as experimental method. The proposed empirical function between TOF and rp was validated for four years of validating data with five different sludge types operated under different operational conditions and configurations. The good effluent quality prediction with this approach brings us one step closer in making the clarification models more predictive towards effluent quality and clarifier performance.}, }
@article {pmid33360100, year = {2021}, author = {Ceballos-Escalera, A and Pous, N and Chiluiza-Ramos, P and Korth, B and Harnisch, F and Bañeras, L and Balaguer, MD and Puig, S}, title = {Electro-bioremediation of nitrate and arsenite polluted groundwater.}, journal = {Water research}, volume = {190}, number = {}, pages = {116748}, doi = {10.1016/j.watres.2020.116748}, pmid = {33360100}, issn = {1879-2448}, mesh = {*Arsenic ; *Arsenites ; Biodegradation, Environmental ; *Groundwater ; Nitrates/analysis ; Oxidation-Reduction ; *Water Pollutants, Chemical/analysis ; }, abstract = {The coexistence of different pollutants in groundwater is a common threat. Sustainable and resilient technologies are required for their treatment. The present study aims to evaluate microbial electrochemical technologies (METs) for treating groundwater contaminated with nitrate (NO3[-]) while containing arsenic (in form of arsenite (As(III)) as a co-contaminant. The treatment was based on the combination of nitrate reduction to dinitrogen gas and arsenite oxidation to arsenate (exhibiting less toxicity, solubility, and mobility), which can be removed more easily in further post-treatment. We operated a bioelectrochemical reactor at continuous-flow mode with synthetic contaminated groundwater (33 mg N-NO3[-] L[-1] and 5 mg As(III) L[-1]) identifying the key operational conditions. Different hydraulic retention times (HRT) were evaluated, reaching a maximum nitrate reduction rate of 519 g N-NO3[-] m[3]Net Cathodic Compartment d[-1] at HRT of 2.3 h with a cathodic coulombic efficiency of around 100 %. Simultaneously, arsenic oxidation was complete at all HRT tested down to 1.6 h reaching an oxidation rate of up to 90 g As(III) m[-3]Net Reactor Volume d [-1]. Electrochemical and microbiological characterization of single granules suggested that arsenite at 5 mg L[-1] did not have an inhibitory effect on a denitrifying biocathode mainly represented by Sideroxydans sp. Although the coexistence of abiotic and biotic arsenic oxidation pathways was shown to be likely, microbial arsenite oxidation linked to denitrification by Achromobacter sp. was the most probable pathway. This research paves the ground towards a real application for treating groundwater with widespread pollutants.}, }
@article {pmid33355923, year = {2021}, author = {Lofgren, LA and Nguyen, NH and Vilgalys, R and Ruytinx, J and Liao, HL and Branco, S and Kuo, A and LaButti, K and Lipzen, A and Andreopoulos, W and Pangilinan, J and Riley, R and Hundley, H and Na, H and Barry, K and Grigoriev, IV and Stajich, JE and Kennedy, PG}, title = {Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi.}, journal = {The New phytologist}, volume = {230}, number = {2}, pages = {774-792}, pmid = {33355923}, issn = {1469-8137}, support = {S10 OD016290/OD/NIH HHS/United States ; }, mesh = {Evolution, Molecular ; Fungi/genetics ; Genome, Fungal ; Genomics ; *Mycorrhizae/genetics ; *Pinus ; Specialization ; }, abstract = {While there has been significant progress characterizing the 'symbiotic toolkit' of ectomycorrhizal (ECM) fungi, how host specificity may be encoded into ECM fungal genomes remains poorly understood. We conducted a comparative genomic analysis of ECM fungal host specialists and generalists, focusing on the specialist genus Suillus. Global analyses of genome dynamics across 46 species were assessed, along with targeted analyses of three classes of molecules previously identified as important determinants of host specificity: small secreted proteins (SSPs), secondary metabolites (SMs) and G-protein coupled receptors (GPCRs). Relative to other ECM fungi, including other host specialists, Suillus had highly dynamic genomes including numerous rapidly evolving gene families and many domain expansions and contractions. Targeted analyses supported a role for SMs but not SSPs or GPCRs in Suillus host specificity. Phylogenomic-based ancestral state reconstruction identified Larix as the ancestral host of Suillus, with multiple independent switches between white and red pine hosts. These results suggest that like other defining characteristics of the ECM lifestyle, host specificity is a dynamic process at the genome level. In the case of Suillus, both SMs and pathways involved in the deactivation of reactive oxygen species appear to be strongly associated with enhanced host specificity.}, }
@article {pmid33351643, year = {2021}, author = {Oesterle, I and Braun, D and Berry, D and Wisgrill, L and Rompel, A and Warth, B}, title = {Polyphenol Exposure, Metabolism, and Analysis: A Global Exposomics Perspective.}, journal = {Annual review of food science and technology}, volume = {12}, number = {}, pages = {461-484}, doi = {10.1146/annurev-food-062220-090807}, pmid = {33351643}, issn = {1941-1421}, mesh = {Humans ; Mass Spectrometry ; *Metabolomics ; *Polyphenols ; }, abstract = {Polyphenols are generally known for their health benefits and estimating actual exposure levels in health-related studies can be improved by human biomonitoring. Here, the application of newly available exposomic and metabolomic technology, notably high-resolution mass spectrometry, in the context of polyphenols and their biotransformation products, is reviewed. Comprehensive workflows for investigating these important bioactives in biological fluids or microbiome-related experiments are scarce. Consequently, this new era of nontargeted analysis and omic-scale exposure assessment offers a unique chance for better assessing exposure to, as well as metabolism of, polyphenols. In clinical and nutritional trials, polyphenols can be investigated simultaneously with the plethora of other chemicals to which we are exposed, i.e., the exposome, which may interact abundantly and modulate bioactivity. This research direction aims at ultimately eluting into atrue systems biology/toxicology evaluation of health effects associated with polyphenol exposure, especially during early life, to unravel their potential for preventing chronic diseases.}, }
@article {pmid33350826, year = {2021}, author = {Kosgey, K and Chandran, K and Gokal, J and Kiambi, SL and Bux, F and Kumari, S}, title = {Critical Analysis of Biomass Retention Strategies in Mainstream and Sidestream ANAMMOX-Mediated Nitrogen Removal Systems.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {1}, pages = {9-24}, doi = {10.1021/acs.est.0c00276}, pmid = {33350826}, issn = {1520-5851}, mesh = {*Ammonium Compounds ; Anaerobiosis ; Biomass ; Bioreactors ; Denitrification ; *Nitrogen ; Oxidation-Reduction ; Wastewater ; }, abstract = {ANAMMOX (anaerobic ammonium oxidation) represents an energy-efficient process for biological nitrogen removal, particularly from wastewater streams with low chemical oxygen demand (COD) to nitrogen (C/N) ratios. Its widespread application, however, is still hampered by a lack of access to biomass-enriched with ANAMMOX bacteria (AMX), slow growth rates of AMX, and their sensitivity to inhibition. Although the coupling of ANAMMOX processes with partial nitrification is already widespread, especially for sidestream treatment, maintaining a functional population density of AMX remains a challenge in these systems. Therefore, strategies that maximize retention of AMX-rich biomass are essential to promote process stability. This paper reviews existing methods of biomass retention in ANAMMOX-mediated systems, focusing on (i) granulation; (ii) biofilm formation on carrier materials; (iii) gel entrapment; and (iv) membrane technology in mainstream and sidestream systems. In addition, the microbial ecology of different ANAMMOX-mediated systems is reviewed.}, }
@article {pmid33350010, year = {2021}, author = {Peñalver, L and Schmid, P and Szamosvári, D and Schildknecht, S and Globisch, C and Sawade, K and Peter, C and Böttcher, T}, title = {A Ligand Selection Strategy Identifies Chemical Probes Targeting the Proteases of SARS-CoV-2.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {60}, number = {12}, pages = {6799-6806}, pmid = {33350010}, issn = {1521-3773}, support = {Emmy Noether//Deutsche Forschungsgemeinschaft/ ; SFB969//Deutsche Forschungsgemeinschaft/ ; Zukunftskolleg Incomming Felowship (ZIF)//FP7 People: Marie-Curie Actions/ ; }, mesh = {Catalytic Domain ; Coronavirus 3C Proteases/*chemistry/metabolism ; Coronavirus Papain-Like Proteases/*chemistry/metabolism ; Cysteine Proteinase Inhibitors/*chemistry/metabolism ; Hep G2 Cells ; Humans ; Ligands ; Molecular Docking Simulation ; *Molecular Probe Techniques ; Molecular Probes/*chemistry ; Molecular Structure ; Proof of Concept Study ; Protein Binding ; SARS-CoV-2/*enzymology ; Small Molecule Libraries/*chemistry/metabolism ; Structure-Activity Relationship ; }, abstract = {Activity-based probes are valuable tools for chemical biology. However, finding probes that specifically target the active site of an enzyme remains a challenging task. Herein, we present a ligand selection strategy that allows to rapidly tailor electrophilic probes to a target of choice and showcase its application for the two cysteine proteases of SARS-CoV-2 as proof of concept. The resulting probes were specific for the active site labeling of 3CL[pro] and PL[pro] with sufficient selectivity in a live cell model as well as in the background of a native human proteome. Exploiting the probes as tools for competitive profiling of a natural product library identified salvianolic acid derivatives as promising 3CL[pro] inhibitors. We anticipate that our ligand selection strategy will be useful to rapidly develop customized probes and discover inhibitors for a wide range of target proteins also beyond corona virus proteases.}, }
@article {pmid33349634, year = {2020}, author = {Molinaro, A and Bel Lassen, P and Henricsson, M and Wu, H and Adriouch, S and Belda, E and Chakaroun, R and Nielsen, T and Bergh, PO and Rouault, C and André, S and Marquet, F and Andreelli, F and Salem, JE and Assmann, K and Bastard, JP and Forslund, S and Le Chatelier, E and Falony, G and Pons, N and Prifti, E and Quinquis, B and Roume, H and Vieira-Silva, S and Hansen, TH and Pedersen, HK and Lewinter, C and Sønderskov, NB and ,  and Køber, L and Vestergaard, H and Hansen, T and Zucker, JD and Galan, P and Dumas, ME and Raes, J and Oppert, JM and Letunic, I and Nielsen, J and Bork, P and Ehrlich, SD and Stumvoll, M and Pedersen, O and Aron-Wisnewsky, J and Clément, K and Bäckhed, F}, title = {Author Correction: Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {6448}, doi = {10.1038/s41467-020-20412-9}, pmid = {33349634}, issn = {2041-1723}, }
@article {pmid33348645, year = {2020}, author = {Álvarez-Mena, A and Cámara-Almirón, J and de Vicente, A and Romero, D}, title = {Multifunctional Amyloids in the Biology of Gram-Positive Bacteria.}, journal = {Microorganisms}, volume = {8}, number = {12}, pages = {}, pmid = {33348645}, issn = {2076-2607}, support = {BacBio 637971//H2020 European Research Council/ ; AGL2016-78662-R//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; PID2019-107724GB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; }, abstract = {Since they were discovered, amyloids have proven to be versatile proteins able to participate in a variety of cellular functions across all kingdoms of life. This multitask trait seems to reside in their ability to coexist as monomers, aggregates or fibrillar entities, with morphological and biochemical peculiarities. It is precisely this common molecular behaviour that allows amyloids to cross react with one another, triggering heterologous aggregation. In bacteria, many of these functional amyloids are devoted to the assembly of biofilms by organizing the matrix scaffold that keeps cells together. However, consistent with their notion of multifunctional proteins, functional amyloids participate in other biological roles within the same organisms, and emerging unprecedented functions are being discovered. In this review, we focus on functional amyloids reported in gram-positive bacteria, which are diverse in their assembly mechanisms and remarkably specific in their biological functions that they perform. Finally, we consider cross-seeding between functional amyloids as an emerging theme in interspecies interactions that contributes to the diversification of bacterial biology.}, }
@article {pmid33341792, year = {2020}, author = {ElNaker, NA and Sallam, AM and El-Sayed, EM and El Ghandoor, H and Talaat, MS and Yousef, AF and Hasan, SW}, title = {A conceptual framework modeling of functional microbial communities in wastewater treatment electro-bioreactors.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {82}, number = {12}, pages = {3047-3061}, doi = {10.2166/wst.2020.553}, pmid = {33341792}, issn = {0273-1223}, mesh = {Bioreactors ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Waste Disposal, Fluid ; Wastewater ; *Water Purification ; }, abstract = {Understanding the microbial ecology of a system allows linking members of the community and their metabolic functions to the performance of the wastewater bioreactor. This study provided a comprehensive conceptual framework for microbial communities in wastewater treatment electro-bioreactors (EBRs). The model was based on data acquired from monitoring the effect of altering different bioreactor operational parameters, such as current density and hydraulic retention time, on the microbial communities of an EBR and its nutrient removal efficiency. The model was also based on the 16S rRNA gene high-throughput sequencing data analysis and bioreactor efficiency data. The collective data clearly demonstrated that applying various electric currents affected the microbial community composition and stability and the reactor efficiency in terms of chemical oxygen demand, N and P removals. Moreover, a schematic that recommends operating conditions that are tailored to the type of wastewater that needs to be treated based on the functional microbial communities enriched at specific operating conditions was suggested. In this study, a conceptual model as a simplified representation of the behavior of microbial communities in EBRs was developed. The proposed conceptual model can be used to predict how biological treatment of wastewater in EBRs can be improved by varying several operating conditions.}, }
@article {pmid33332530, year = {2021}, author = {Liu, C and Cui, Y and Li, X and Yao, M}, title = {microeco: an R package for data mining in microbial community ecology.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {2}, pages = {}, doi = {10.1093/femsec/fiaa255}, pmid = {33332530}, issn = {1574-6941}, mesh = {Computational Biology ; Data Mining ; Ecology ; *Microbiota ; *Software ; }, abstract = {A large amount of sequencing data is produced in microbial community ecology studies using the high-throughput sequencing technique, especially amplicon-sequencing-based community data. After conducting the initial bioinformatic analysis of amplicon sequencing data, performing the subsequent statistics and data mining based on the operational taxonomic unit and taxonomic assignment tables is still complicated and time-consuming. To address this problem, we present an integrated R package-'microeco' as an analysis pipeline for treating microbial community and environmental data. This package was developed based on the R6 class system and combines a series of commonly used and advanced approaches in microbial community ecology research. The package includes classes for data preprocessing, taxa abundance plotting, venn diagram, alpha diversity analysis, beta diversity analysis, differential abundance test and indicator taxon analysis, environmental data analysis, null model analysis, network analysis and functional analysis. Each class is designed to provide a set of approaches that can be easily accessible to users. Compared with other R packages in the microbial ecology field, the microeco package is fast, flexible and modularized to use and provides powerful and convenient tools for researchers. The microeco package can be installed from CRAN (The Comprehensive R Archive Network) or github (https://github.com/ChiLiubio/microeco).}, }
@article {pmid33329631, year = {2020}, author = {Robles-Aguilar, AA and Grunert, O and Hernandez-Sanabria, E and Mysara, M and Meers, E and Boon, N and Jablonowski, ND}, title = {Effect of Applying Struvite and Organic N as Recovered Fertilizers on the Rhizosphere Dynamics and Cultivation of Lupine (Lupinus angustifolius).}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {572741}, pmid = {33329631}, issn = {1664-462X}, abstract = {Intensive agriculture and horticulture heavily rely on the input of fertilizers to sustain food (and feed) production. However, high carbon footprint and pollution are associated with the mining processes of P and K, and the artificial nitrogen fixation for the production of synthetic fertilizers. Organic fertilizers or recovered nutrients from different waste sources can be used to reduce the environmental impact of fertilizers. We tested two recovered nutrients with slow-release patterns as promising alternatives for synthetic fertilizers: struvite and a commercially available organic fertilizer. Using these fertilizers as a nitrogen source, we conducted a rhizotron experiment to test their effect on plant performance and nutrient recovery in lupine plants. Plant performance was not affected by the fertilizer applied; however, N recovery was higher from the organic fertilizer than from struvite. As root architecture is fundamental for plant productivity, variations in root structure and length as a result of soil nutrient availability driven by plant-bacteria interactions were compared showing also no differences between fertilizers. However, fertilized plants were considerably different in the root length and morphology compared with the no fertilized plants. Since the microbial community influences plant nitrogen availability, we characterized the root-associated microbial community structure and functionality. Analyses revealed that the fertilizer applied had a significant impact on the associations and functionality of the bacteria inhabiting the growing medium used. The type of fertilizer significantly influenced the interindividual dissimilarities in the most abundant genera between treatments. This means that different plant species have a distinct effect on modulating the associated microbial community, but in the case of lupine, the fertilizer had a bigger effect than the plant itself. These novel insights on interactions between recovered fertilizers, plant, and associated microbes can contribute to developing sustainable crop production systems.}, }
@article {pmid33329472, year = {2020}, author = {Kohler, TJ and Peter, H and Fodelianakis, S and Pramateftaki, P and Styllas, M and Tolosano, M and de Staercke, V and Schön, M and Busi, SB and Wilmes, P and Washburne, A and Battin, TJ}, title = {Patterns and Drivers of Extracellular Enzyme Activity in New Zealand Glacier-Fed Streams.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {591465}, pmid = {33329472}, issn = {1664-302X}, abstract = {Glacier-fed streams (GFSs) exhibit near-freezing temperatures, variable flows, and often high turbidities. Currently, the rapid shrinkage of mountain glaciers is altering the delivery of meltwater, solutes, and particulate matter to GFSs, with unknown consequences for their ecology. Benthic biofilms dominate microbial life in GFSs, and play a major role in their biogeochemical cycling. Mineralization is likely an important process for microbes to meet elemental budgets in these systems due to commonly oligotrophic conditions, and extracellular enzymes retained within the biofilm enable the degradation of organic matter and acquisition of carbon (C), nitrogen (N), and phosphorus (P). The measurement and comparison of these extracellular enzyme activities (EEA) can in turn provide insight into microbial elemental acquisition effort relative to environmental availability. To better understand how benthic biofilm communities meet resource demands, and how this might shift as glaciers vanish under climate change, we investigated biofilm EEA in 20 GFSs varying in glacier influence from New Zealand's Southern Alps. Using turbidity and distance to the glacier snout normalized for glacier size as proxies for glacier influence, we found that bacterial abundance (BA), chlorophyll a (Chl a), extracellular polymeric substances (EPS), and total EEA per gram of sediment increased with decreasing glacier influence. Yet, when normalized by BA, EPS decreased with decreasing glacier influence, Chl a still increased, and there was no relationship with total EEA. Based on EEA ratios, we found that the majority of GFS microbial communities were N-limited, with a few streams of different underlying bedrock geology exhibiting P-limitation. Cell-specific C-acquiring EEA was positively related to the ratio of Chl a to BA, presumably reflecting the utilization of algal exudates. Meanwhile, cell-specific N-acquiring EEA were positively correlated with the concentration of dissolved inorganic nitrogen (DIN), and both N- and P-acquiring EEA increased with greater cell-specific EPS. Overall, our results reveal greater glacier influence to be negatively related to GFS biofilm biomass parameters, and generally associated with greater microbial N demand. These results help to illuminate the ecology of GFS biofilms, along with their biogeochemical response to a shifting habitat template with ongoing climate change.}, }
@article {pmid33329469, year = {2020}, author = {Shintani, M and Nour, E and Elsayed, T and Blau, K and Wall, I and Jechalke, S and Spröer, C and Bunk, B and Overmann, J and Smalla, K}, title = {Plant Species-Dependent Increased Abundance and Diversity of IncP-1 Plasmids in the Rhizosphere: New Insights Into Their Role and Ecology.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {590776}, pmid = {33329469}, issn = {1664-302X}, abstract = {IncP-1 plasmids, first isolated from clinical specimens (R751, RP4), are recognized as important vectors spreading antibiotic resistance genes. The abundance of IncP-1 plasmids in the environment, previously reported, suggested a correlation with anthropogenic pollution. Unexpectedly, qPCR-based detection of IncP-1 plasmids revealed also an increased relative abundance of IncP-1 plasmids in total community DNA from the rhizosphere of lettuce and tomato plants grown in non-polluted soil along with plant age. Here we report the successful isolation of IncP-1 plasmids by exploiting their ability to mobilize plasmid pSM1890. IncP-1 plasmids were captured from the rhizosphere but not from bulk soil, and a high diversity was revealed by sequencing 14 different plasmids that were assigned to IncP-1β, δ, and ε subgroups. Although backbone genes were highly conserved and mobile elements or remnants as Tn501, IS1071, Tn402, or class 1 integron were carried by 13 of the sequenced IncP-1 plasmids, no antibiotic resistance genes were found. Instead, seven plasmids had a mer operon with Tn501-like transposon and five plasmids contained putative metabolic gene clusters linked to these mobile elements. In-depth sequence comparisons with previously known plasmids indicate that the IncP-1 plasmids captured from the rhizosphere are archetypes of those found in clinical isolates. Our findings that IncP-1 plasmids do not always carry accessory genes in unpolluted rhizospheres are important to understand the ecology and role of the IncP-1 plasmids in the natural environment.}, }
@article {pmid33329459, year = {2020}, author = {Ruiz-Lopez, S and Foster, L and Boothman, C and Cole, N and Morris, K and Lloyd, JR}, title = {Identification of a Stable Hydrogen-Driven Microbiome in a Highly Radioactive Storage Facility on the Sellafield Site.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {587556}, pmid = {33329459}, issn = {1664-302X}, abstract = {The use of nuclear power has been a significant part of the United Kingdom's energy portfolio with the Sellafield site being used for power production and more recently reprocessing and decommissioning of spent nuclear fuel activities. Before being reprocessed, spent nuclear fuel is stored in water ponds with significant levels of background radioactivity and in high alkalinity (to minimize fuel corrosion). Despite these challenging conditions, the presence of microbial communities has been detected. To gain further insight into the microbial communities present in extreme environments, an indoor, hyper-alkaline, oligotrophic, and radioactive spent fuel storage pond (INP) located on the Sellafield site was analyzed. Water samples were collected from sample points within the INP complex, and also the purge water feeding tank (FT) that supplies water to the pond, and were screened for the presence of the 16S and 18S rRNA genes to inform sequencing requirements over a period of 30 months. Only 16S rRNA genes were successfully amplified for sequencing, suggesting that the microbial communities in the INP were dominated by prokaryotes. Quantitative Polymerase Chain Reaction (qPCR) analysis targeting 16S rRNA genes suggested that bacterial cells in the order of 10[4]-10[6] mL[-1] were present in the samples, with loadings rising with time. Next generation Illumina MiSeq sequencing was performed to identify the dominant microorganisms at eight sampling times. The 16S rRNA gene sequence analysis suggested that 70% and 91% from of the OTUs samples, from the FT and INP respectively, belonged to the phylum Proteobacteria, mainly from the alpha and beta subclasses. The remaining OTUs were assigned primarily to the phyla Acidobacteria, Bacteroidetes, and, Cyanobacteria. Overall the most abundant genera identified were Hydrogenophaga, Curvibacter, Porphyrobacter, Rhodoferax, Polaromonas, Sediminibacterium, Roseococcus, and Sphingomonas. The presence of organisms most closely related to Hydrogenophaga species in the INP areas, suggests the metabolism of hydrogen as an energy source, most likely linked to hydrolysis of water caused by the stored fuel. Isolation of axenic cultures using a range of minimal and rich media was also attempted, but only relatively minor components (from the phylum Bacteroidetes) of the pond water communities were obtained, emphasizing the importance of DNA-based, not culture-dependent techniques, for assessing the microbiome of nuclear facilities.}, }
@article {pmid33329422, year = {2020}, author = {Mony, C and Vandenkoornhuyse, P and Bohannan, BJM and Peay, K and Leibold, MA}, title = {A Landscape of Opportunities for Microbial Ecology Research.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {561427}, pmid = {33329422}, issn = {1664-302X}, abstract = {Microbes encompass tremendous biodiversity, provide support to all living forms, including humans, and play an important role in many ecosystem services. The rules that govern microorganism community assembly are increasingly revealed due to key advances in molecular and analytical methods but their understanding remain a key challenge in microbial ecology. The existence of biogeographic patterns within microbial communities has been established and explained in relation to landscape-scale processes, including selection, drift, dispersal and mutation. The effect of habitat patchiness on microorganisms' assembly rules remains though incompletely understood. Here, we review how landscape ecology principles can be adapted to explore new perspectives on the mechanisms that determine microbial community structure. To provide a general overview, we characterize microbial landscapes, the spatial and temporal scales of the mechanisms that drive microbial assembly and the feedback between microorganisms and landscape structure. We provide evidence for the effects of landscape heterogeneity, landscape fragmentation and landscape dynamics on microbial community structure, and show that predictions made for macro-organisms at least partly also apply to microorganisms. We explain why emerging metacommunity approaches in microbial ecology should include explicit characterization of landscape structure in their development and interpretation. We also explain how biotic interactions, such as competition, prey-predator or mutualist relations may influence the microbial landscape and may be involved in the above-mentioned feedback process. However, we argue that the application of landscape ecology to the microbial world cannot simply involve transposing existing theoretical frameworks. This is due to the particularity of these organisms, in terms of size, generation time, and for some of them, tight interaction with hosts. These characteristics imply dealing with unusual and dependent space and time scales of effect. Evolutionary processes have also a strong importance in microorganisms' response to their landscapes. Lastly, microorganisms' activity and distribution induce feedback effects on the landscape that have to be taken into account. The transposition of the landscape ecology framework to microorganisms provides many challenging research directions for microbial ecology.}, }
@article {pmid33329414, year = {2020}, author = {Mullin, SW and Wanger, G and Kruger, BR and Sackett, JD and Hamilton-Brehm, SD and Bhartia, R and Amend, JP and Moser, DP and Orphan, VJ}, title = {Patterns of in situ Mineral Colonization by Microorganisms in a ~60°C Deep Continental Subsurface Aquifer.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {536535}, pmid = {33329414}, issn = {1664-302X}, abstract = {The microbial ecology of the deep biosphere is difficult to characterize, owing in part to sampling challenges and poorly understood response mechanisms to environmental change. Pre-drilled wells, including oil wells or boreholes, offer convenient access, but sampling is frequently limited to the water alone, which may provide only a partial view of the native diversity. Mineral heterogeneity demonstrably affects colonization by deep biosphere microorganisms, but the connections between the mineral-associated and planktonic communities remain unclear. To understand the substrate effects on microbial colonization and the community response to changes in organic carbon, we conducted an 18-month series of in situ experiments in a warm (57°C), anoxic, fractured carbonate aquifer at 752 m depth using replicate open, screened cartridges containing different solid substrates, with a proteinaceous organic matter perturbation halfway through this series. Samples from these cartridges were analyzed microscopically and by Illumina (iTag) 16S rRNA gene libraries to characterize changes in mineralogy and the diversity of the colonizing microbial community. The substrate-attached and planktonic communities were significantly different in our data, with some taxa (e.g., Candidate Division KB-1) rare or undetectable in the first fraction and abundant in the other. The substrate-attached community composition also varied significantly with mineralogy, such as with two Rhodocyclaceae OTUs, one of which was abundant on carbonate minerals and the other on silicic substrates. Secondary sulfide mineral formation, including iron sulfide framboids, was observed on two sets of incubated carbonates. Notably, microorganisms were attached to the framboids, which were correlated with abundant Sulfurovum and Desulfotomaculum sp. sequences in our analysis. Upon organic matter perturbation, mineral-associated microbial diversity differences were temporarily masked by the dominance of putative heterotrophic taxa in all samples, including OTUs identified as Caulobacter, Methyloversatilis, and Pseudomonas. Subsequent experimental deployments included a methanogen-dominated stage (Methanobacteriales and Methanomicrobiales) 6 months after the perturbation and a return to an assemblage similar to the pre-perturbation community after 9 months. Substrate-associated community differences were again significant within these subsequent phases, however, demonstrating the value of in situ time course experiments to capture a fraction of the microbial assemblage that is frequently difficult to observe in pre-drilled wells.}, }
@article {pmid33323508, year = {2020}, author = {Brooks, CN and Field, EK}, title = {Iron Flocs and the Three Domains: Microbial Interactions in Freshwater Iron Mats.}, journal = {mBio}, volume = {11}, number = {6}, pages = {}, pmid = {33323508}, issn = {2150-7511}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Fresh Water/chemistry/*microbiology ; Iron/chemistry/*metabolism ; Microbial Interactions ; Microbiota ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Freshwater iron mats are dynamic geochemical environments with broad ecological diversity, primarily formed by the iron-oxidizing bacteria. The community features functional groups involved in biogeochemical cycles for iron, sulfur, carbon, and nitrogen. Despite this complexity, iron mat communities provide an excellent model system for exploring microbial ecological interactions and ecological theories in situ Syntrophies and competition between the functional groups in iron mats, how they connect cycles, and the maintenance of these communities by taxons outside bacteria (the eukaryota, archaea, and viruses) have been largely unstudied. Here, we review what is currently known about freshwater iron mat communities, the taxa that reside there, and the interactions between these organisms, and we propose ways in which future studies may uncover exciting new discoveries. For example, the archaea in these mats may play a greater role than previously thought as they are diverse and widespread in iron mats based on 16S rRNA genes and include methanogenic taxa. Studies with a holistic view of the iron mat community members focusing on their diverse interactions will expand our understanding of community functions, such as those involved in pollution removal. To begin addressing questions regarding the fundamental interactions and to identify the conditions in which they occur, more laboratory culturing techniques and coculture studies, more network and keystone species analyses, and the expansion of studies to more freshwater iron mat systems are necessary. Increasingly accessible bioinformatic, geochemical, and culturing tools now open avenues to address the questions that we pose herein.}, }
@article {pmid33321044, year = {2021}, author = {Peixoto, RS and Sweet, M and Villela, HDM and Cardoso, P and Thomas, T and Voolstra, CR and Høj, L and Bourne, DG}, title = {Coral Probiotics: Premise, Promise, Prospects.}, journal = {Annual review of animal biosciences}, volume = {9}, number = {}, pages = {265-288}, doi = {10.1146/annurev-animal-090120-115444}, pmid = {33321044}, issn = {2165-8110}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Dinoflagellida ; Microbiota ; *Probiotics ; Symbiosis ; }, abstract = {The use of Beneficial Microorganisms for Corals (BMCs) has been proposed recently as a tool for the improvement of coral health, with knowledge in this research topic advancing rapidly. BMCs are defined as consortia of microorganisms that contribute to coral health through mechanisms that include (a) promoting coral nutrition and growth, (b) mitigating stress and impacts of toxic compounds, (c) deterring pathogens, and (d) benefiting early life-stage development. Here, we review the current proposed BMC approach and outline the studies that have proven its potential to increase coral resilience to stress. We revisit and expand the list of putative beneficial microorganisms associated with corals and their proposed mechanismsthat facilitate improved host performance. Further, we discuss the caveats and bottlenecks affecting the efficacy of BMCs and close by focusing on the next steps to facilitate application at larger scales that can improve outcomes for corals and reefs globally.}, }
@article {pmid33319645, year = {2020}, author = {Christensen, L and Sørensen, CV and Wøhlk, FU and Kjølbæk, L and Astrup, A and Sanz, Y and Hjorth, MF and Benítez-Páez, A}, title = {Microbial enterotypes beyond genus level: Bacteroides species as a predictive biomarker for weight change upon controlled intervention with arabinoxylan oligosaccharides in overweight subjects.}, journal = {Gut microbes}, volume = {12}, number = {1}, pages = {1847627}, pmid = {33319645}, issn = {1949-0984}, mesh = {Adolescent ; Adult ; Bacteroides/classification/genetics/*growth &amp; development/isolation &amp; purification ; Biomarkers/metabolism ; Body Weight ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; Oligosaccharides/*metabolism ; Overweight/*diet therapy/*microbiology/physiopathology ; Xylans/*metabolism ; Young Adult ; }, abstract = {Recent studies indicate that microbial enterotypes may influence the beneficial effects of wholegrain enriched diets including bodyweight regulation. In a 4-week intervention trial, overweight subjects were randomized to consume either arabinoxylan-oligosaccharides (AXOS) (10.4 g/d) from wheat bran or polyunsaturated fatty acids (PUFA) (3.6 g/d). In the present study, we have stratified the subjects participating in the intervention (n = 29) according to the baseline Prevotella-to-Bacteroides (P/B) ratios through a post-hoc analysis and applied a linear mixed model analysis to identify the influence of this P/B ratio on the differences in weight changes in the intervention arms. Following AXOS consumption (n = 15), the high P/B group showed no bodyweight changes [-0.14 kg (95% CI: -0.67; 0.38, p = .59)], while the low P/B group gained 0.65 kg (95% CI: 0.16; 1.14, p = .009). Consequently, a difference of -0.79 kg was found between P/B groups (95% CI: -1.51; -0.08, p = .030). No differences were found between P/B groups following PUFA consumption (0.61 kg, 95% CI: -0.13; 1.35, p = .10). Among the Bacteroides species, B. cellulosilyticus relative abundance exhibited the highest positive rank correlation (Kendall's tau = 0.51, FDR p = .070) with 4-week weight change on AXOS, and such association was further supported by using supervised classification methods (Random Forest). We outlined several carbohydrate-active enzyme (CAZy) genes involved in xylan-binding and degradation to be enriched in B. cellulosilyticus genomes, as well as multiple accessory genes, suggesting a supreme AXOS-derived glycan scavenging role of such species. This post-hoc analysis, ensuring species and strain demarcation at the human gut microbiota, permitted to uncover the predictive role of Bacteroides species over P/B enterotype in weight gain during a fiber-based intervention. The results of this pilot trial pave the way for future assessments on fiber fermentation outputs from Bacteroides species affecting lipid metabolism in the host and with direct impact on adiposity, thus helping to design personalized interventions.}, }
@article {pmid33315910, year = {2020}, author = {Oyuela Aguilar, M and Gobbi, A and Browne, PD and Ellegaard-Jensen, L and Hansen, LH and Semorile, L and Pistorio, M}, title = {Influence of vintage, geographic location and cultivar on the structure of microbial communities associated with the grapevine rhizosphere in vineyards of San Juan Province, Argentina.}, journal = {PloS one}, volume = {15}, number = {12}, pages = {e0243848}, pmid = {33315910}, issn = {1932-6203}, mesh = {Argentina ; Bacteria/classification ; Biodiversity ; Climate ; Fungi/classification ; *Geography ; *Microbiota ; *Rhizosphere ; Soil/chemistry ; Vitis/*microbiology ; }, abstract = {Soil microbiomes, as a primary reservoir for plant colonizing fungi and bacteria, play a major role in determining plant productivity and preventing invasion by pathogenic microorganisms. The use of 16S rRNA and ITS high-throughput amplicon sequencing for analysis of complex microbial communities have increased dramatically in recent years, establishing links between wine specificity and, environmental and viticultural factors, which are framed into the elusive terroir concept. Given the diverse and complex role these factors play on microbial soil structuring of agricultural crops, the main aim of this study is to evaluate how external factors, such as vintage, vineyard location, cultivar and soil characteristics, may affect the diversity of the microbial communities present. Additionally, we aim to compare the influence these factors have on the structuring of bacterial and fungal populations associated with Malbec grapevine rhizosphere with that of the more widespread Cabernet Sauvignon grapevine cultivar. Samples were taken from Malbec and Cabernet Sauvignon cultivars from two different vineyards in the San Juan Province of Argentina. Total DNA extracts from the rhizosphere soil samples were sequenced using Illumina's Miseq technology, targeting the V3-V4 hypervariable 16S rRNA region in prokaryotes and the ITS1 region in yeasts. The major bacterial taxa identified were Proteobacteria, Bacteroidetes and Firmicutes, while the major fungal taxa were Ascomycetes, Basidiomycetes, Mortierellomycetes and a low percentage of Glomeromycetes. Significant differences in microbial community composition were found between vintages and vineyard locations, whose soils showed variances in pH, organic matter, and content of carbon, nitrogen, and absorbable phosphorus.}, }
@article {pmid33311714, year = {2021}, author = {Lee, KS and Pereira, FC and Palatinszky, M and Behrendt, L and Alcolombri, U and Berry, D and Wagner, M and Stocker, R}, title = {Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions.}, journal = {Nature protocols}, volume = {16}, number = {2}, pages = {634-676}, pmid = {33311714}, issn = {1750-2799}, support = {GBMF3783//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 542395//Simons Foundation/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; P26127-B20//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; P27831-B28//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; 2019-04401//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; }, mesh = {Cell Separation/methods ; Flow Cytometry/*methods ; Genome/genetics ; Genomics/methods ; In Situ Hybridization, Fluorescence/methods ; Isotope Labeling/methods ; Metagenomics/methods ; Microbiota/genetics ; Microfluidics/methods ; Optical Tweezers ; Optogenetics/methods ; Single-Cell Analysis/methods ; Spectrum Analysis, Raman/*methods ; }, abstract = {Stable isotope labeling of microbial taxa of interest and their sorting provide an efficient and direct way to answer the question "who does what?" in complex microbial communities when coupled with fluorescence in situ hybridization or downstream 'omics' analyses. We have developed a platform for automated Raman-based sorting in which optical tweezers and microfluidics are used to sort individual cells of interest from microbial communities on the basis of their Raman spectra. This sorting of cells and their downstream DNA analysis, such as by mini-metagenomics or single-cell genomics, or cultivation permits a direct link to be made between the metabolic roles and the genomes of microbial cells within complex microbial communities, as well as targeted isolation of novel microbes with a specific physiology of interest. We describe a protocol from sample preparation through Raman-activated live cell sorting. Subsequent cultivation of sorted cells is described, whereas downstream DNA analysis involves well-established approaches with abundant methods available in the literature. Compared with manual sorting, this technique provides a substantially higher throughput (up to 500 cells per h). Furthermore, the platform has very high sorting accuracy (98.3 ± 1.7%) and is fully automated, thus avoiding user biases that might accompany manual sorting. We anticipate that this protocol will empower in particular environmental and host-associated microbiome research with a versatile tool to elucidate the metabolic contributions of microbial taxa within their complex communities. After a 1-d preparation of cells, sorting takes on the order of 4 h, depending on the number of cells required.}, }
@article {pmid33310220, year = {2021}, author = {Thwaites, BJ and Stuetz, R and Short, M and Reeve, P and Alvarez-Gaitan, JP and Dinesh, N and Philips, R and van den Akker, B}, title = {Analysis of nitrous oxide emissions from aerobic granular sludge treating high saline municipal wastewater.}, journal = {The Science of the total environment}, volume = {756}, number = {}, pages = {143653}, doi = {10.1016/j.scitotenv.2020.143653}, pmid = {33310220}, issn = {1879-1026}, mesh = {Bioreactors ; Denitrification ; Nitrification ; Nitrogen/analysis ; Nitrous Oxide/analysis ; *Sewage ; Waste Disposal, Fluid ; *Wastewater ; }, abstract = {Conventional activated sludge (CAS)-based wastewater treatment processes have the potential to emit high concentrations of nitrous oxide (N2O) during nitrification and denitrification, which can significantly impact the environmental performance and carbon footprint of wastewater treatment operations. While N2O emissions from CAS have been extensively studied, there is little knowledge of N2O emissions from aerobic granular sludge (AGS) which is now an increasingly popular secondary treatment alternative. The N2O emissions performance of AGS needs to be investigated to ensure that the positive benefits of AGS, such as increased capacity and stable nutrient removal, are not offset by higher emissions. This study quantified N2O emissions from a pilot-scale AGS reactor operated under a range of organic loading rates. A second CAS pilot plant was operated in parallel and under identical loading rates to allow for side-by-side comparison of N2O emissions from floc-based activated sludge. Under low loadings of <0.6 kg COD/m[3]/d the N2O emission factor from AGS and CAS were similar, at around 1.46 ± 0.1% g N2Oemitted/g ammonium loaded. A step increase in the organic loading rate increased N2O emissions from AGS more so than CAS which appeared to be attributed to the reactor feeding strategy that was required for AGS formation. The use of a separate anaerobic feeding phase which was followed by the aeration phase, resulted in extended periods of low dissolved oxygen (DO) concentrations combined with an initial high biomass ammonium loading rate, which favours N2O production and was exacerbated at higher organic loads. Conversely, the combined feeding plus aeration operation (aerobic feed) employed by the CAS system enabled a more even biomass ammonium loading rate and DO supply. This work has shown that while AGS has many operational benefits, the impacts that aeration profile, loading rate and feeding strategy have on N2O emissions must be considered.}, }
@article {pmid33308279, year = {2020}, author = {Yulandi, A and Suwanto, A and Waturangi, DE and Wahyudi, AT}, title = {Shotgun metagenomic analysis reveals new insights into bacterial community profiles in tempeh.}, journal = {BMC research notes}, volume = {13}, number = {1}, pages = {562}, pmid = {33308279}, issn = {1756-0500}, mesh = {Enterococcus ; *Metagenome ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Soy Foods ; }, abstract = {OBJECTIVE: Amplicon sequencing targeting 16S ribosomal RNA (rRNA) has been widely used to profile the microbial community from fermented food samples. However, polymerase chain reaction (PCR) steps on amplicon sequencing analysis and intragenomic heterogeneity within 16S rRNA are believed to contribute to bias in estimating microbial community composition. As potential paraprobiotics sources, a comprehensive profiling study of tempeh microbial ecology could contribute to tempeh product development. This study employed a shotgun metagenomic approach, where metagenome fragments from tempeh samples were sequenced directly for taxonomic and functional profiling analysis.<br><br>RESULTS: Taxonomic profiling showed that Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla from the shotgun metagenomic analysis in all tempeh samples. In terms of composition, this shotgun metagenomic study revealed that Proteobacteria was the most abundant phylum. Functional profiling showed that iron complex outer-membrane recepter protein (KEGG ID: K02014) was the most transcribed gene based on this metagenomic analysis. The metagenome-assembled genomes (MAGs) results from the binning pipeline could reveal almost complete whole genome sequence of Lactobacillus fermentum, Enterococcus cecorum, Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii.}, }
@article {pmid33305821, year = {2021}, author = {Leininger, A and Yates, MD and Ramirez, M and Kjellerup, B}, title = {Biofilm structure, dynamics, and ecology of an upscaled biocathode wastewater microbial fuel cell.}, journal = {Biotechnology and bioengineering}, volume = {118}, number = {3}, pages = {1305-1316}, doi = {10.1002/bit.27653}, pmid = {33305821}, issn = {1097-0290}, mesh = {*Bioelectric Energy Sources ; *Biofilms ; Electrodes ; *Microbiota ; Wastewater/*microbiology ; }, abstract = {A microbial fuel cell (MFC) system containing modular half-submerged biocathode was operated for 6 months in an 800 L flow-through system with domestic wastewater. For the first time, spatial and temporal differences in biofilm communities were examined on large three-dimensional electrodes in a wastewater MFC. Biocathode microbial community analysis showed a specialized biofilm community with electrogenic and electrotrophic taxa forming during operation, suggesting potentially opposing electrode reactions. The anodic community structure shifted during operation, but no spatial differences were observed along the length of the electrode. Power output from the system was most strongly influenced by pH. Higher power densities were associated with the use of solids-dewatering filtrate with increased organic matter, conductivity, and pH. The results show that the biocathode was the rate-limiting step and that future MFC design should consider the effect of size, shape, and orientation of biocathodes on their community assembly and electrotrophic ability.}, }
@article {pmid33305411, year = {2021}, author = {Cheng, J and Yang, Y and Yuan, MM and Gao, Q and Wu, L and Qin, Z and Shi, ZJ and Schuur, EAG and Cole, JR and Tiedje, JM and Zhou, J}, title = {Winter warming rapidly increases carbon degradation capacities of fungal communities in tundra soil: Potential consequences on carbon stability.}, journal = {Molecular ecology}, volume = {30}, number = {4}, pages = {926-937}, doi = {10.1111/mec.15773}, pmid = {33305411}, issn = {1365-294X}, mesh = {Carbon ; Climate Change ; Ecosystem ; *Mycobiome ; *Soil ; Soil Microbiology ; Tundra ; }, abstract = {High-latitude tundra ecosystems are increasingly affected by climate warming. As an important fraction of soil microorganisms, fungi play essential roles in carbon degradation, especially the old, chemically recalcitrant carbon. However, it remains obscure how fungi respond to climate warming and whether fungi, in turn, affect carbon stability of tundra. In a 2-year winter soil warming experiment of 2°C by snow fences, we investigated responses of fungal communities to warming in the active layer of an Alaskan tundra. Although fungal community composition, revealed by the 28S rRNA gene amplicon sequencing, remained unchanged (p > .05), fungal functional gene composition, revealed by a microarray named GeoChip, was altered (p < .05). Changes in functional gene composition were linked to winter soil temperature, thaw depth, soil moisture, and gross primary productivity (canonical correlation analysis, p < .05). Specifically, relative abundances of fungal genes encoding invertase, xylose reductase and vanillin dehydrogenase significantly increased (p < .05), indicating higher carbon degradation capacities of fungal communities under warming. Accordingly, we detected changes in fungal gene networks under warming, including higher average path distance, lower average clustering coefficient and lower percentage of negative links, indicating that warming potentially changed fungal interactions. Together, our study reveals higher carbon degradation capacities of fungal communities under short-term warming and highlights the potential impacts of fungal communities on tundra ecosystem respiration, and consequently future carbon stability of high-latitude tundra.}, }
@article {pmid33304469, year = {2020}, author = {Bassani, I and Larousse, M and Tran, QD and Attard, A and Galiana, E}, title = {Phytophthora zoospores: From perception of environmental signals to inoculum formation on the host-root surface.}, journal = {Computational and structural biotechnology journal}, volume = {18}, number = {}, pages = {3766-3773}, pmid = {33304469}, issn = {2001-0370}, abstract = {To explore moist soils and to target host plants, phytopathogenic Phytophthora species utilize the sensory and propulsion capabilities of the biflagellate unicellular zoospores they produce. Zoospore motion and interactions with the microenvironment are of primary importance for Phytophthora physiology. These are also of critical significance for plant pathology in early infection sequential events and their regulation: the directed zoospore migration toward the host, the local aggregation and adhesion at the host penetration site. In the soil, these early events preceding the root colonization are orchestrated by guidance factors, released from the soil particles in water films, or emitted within microbiota and by host plants. This signaling network is perceived by zoospores and results in coordinated behavior and preferential localization in the rhizosphere. Recent computational and structural studies suggest that rhizospheric ion and plant metabolite sensing is a key determinant in driving zoospore motion, orientation and aggregation. To reach their target, zoospores respond to various molecular, chemical and electrical stimuli. However, it is not yet clear how these signals are generated in local soil niches and which gene functions govern the sensing and subsequent responses of zoospores. Here we review studies on the soil, microbial and host-plant factors that drive zoospore motion, as well as the adaptations governing zoospore behavior. We propose several research directions that could be explored to characterize the role of zoospore microbial ecology in disease.}, }
@article {pmid33303324, year = {2021}, author = {Molderez, TR and Prévoteau, A and Ceyssens, F and Verhelst, M and Rabaey, K}, title = {A chip-based 128-channel potentiostat for high-throughput studies of bioelectrochemical systems: Optimal electrode potentials for anodic biofilms.}, journal = {Biosensors &amp; bioelectronics}, volume = {174}, number = {}, pages = {112813}, doi = {10.1016/j.bios.2020.112813}, pmid = {33303324}, issn = {1873-4235}, mesh = {*Bioelectric Energy Sources ; Biofilms ; *Biosensing Techniques ; Electrodes ; Electron Transport ; *Geobacter ; Reproducibility of Results ; }, abstract = {The presence of microorganisms performing extracellular electron transfer has been established in many environments. Research to determine their role is moving slowly due to the high cost of potentiostats and the variance of data with small number of replicates. Here, we present a 128-channel potentiostat, connected to a 128 gold electrode array. Whereas the system is able to perform simultaneously 128 (bio)electrochemical measurements with an independent electrical signal input, the present manufacturing of the array limited the number of effective channels for this study to 77. We assessed the impact of 11 electrode potentials ranging from -0.45V to +0.2V vs. Ag/AgCl (7 replicates per potential) on the growth and electrochemical characteristics of anodic electroactive biofilms (EABs) formed by acetate-fed microbial communities. After 7 days of growth, maximum current was reached for electrodes poised at -0.3V, closely followed by -0.25V and -0.1V to +0.1V, a range well-fitting the midpoint potential of minerals naturally reduced by electroactive bacteria such as Geobacter Sulfurreducens. There was no significant difference in apparent midpoint potential of the EABs (-0.35V), suggesting that the mechanism of heterogeneous electron transfer was not affected by the electrode potential. The EABs poised below current plateau potential (≤-0.3V) exhibited slower growth but higher charge transfer parameters. The high-throughput and high reproducibility provided by the array may have a major facilitating impact on the field of electromicrobiology. Key aspects to improve are data processing algorithms to deal with the vast amount of generated data, and manufacturing of the electrode array itself.}, }
@article {pmid33297305, year = {2020}, author = {Nikolausz, M and Kretzschmar, J}, title = {Anaerobic Digestion in the 21st Century.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {7}, number = {4}, pages = {}, pmid = {33297305}, issn = {2306-5354}, abstract = {Despite being a mature biotechnological process, anaerobic digestion is still attracting considerable research attention, mainly due to its versatility both in substrate and product spectra, as well as being a perfect test system for the microbial ecology of anaerobes [...].}, }
@article {pmid33297216, year = {2021}, author = {Vaezzadeh, V and Thomes, MW and Kunisue, T and Tue, NM and Zhang, G and Zakaria, MP and Affendi, YA and Yap, FC and Chew, LL and Teoh, HW and Lee, CW and Bong, CW}, title = {Examination of barnacles' potential to be used as bioindicators of persistent organic pollutants in coastal ecosystem: A Malaysia case study.}, journal = {Chemosphere}, volume = {263}, number = {}, pages = {128272}, doi = {10.1016/j.chemosphere.2020.128272}, pmid = {33297216}, issn = {1879-1298}, mesh = {Animals ; Ecosystem ; Environmental Biomarkers ; Environmental Monitoring ; Halogenated Diphenyl Ethers/analysis ; *Hydrocarbons, Chlorinated/analysis ; Malaysia ; Persistent Organic Pollutants ; *Pesticides/analysis ; *Polychlorinated Biphenyls/analysis ; *Thoracica ; }, abstract = {Barnacles are ubiquitous in coastal ecosystems of different geographical regions worldwide. This is the first study attempting to assess the suitability of barnacles as bioindicators of persistent organic pollutants (POPs) in coastal environments. Barnacles were collected from the coasts around Peninsular Malaysia and analyzed for POPs including polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs) and organochlorine pesticides (OCPs). Among POPs, PCBs showed the highest concentrations with elevated contributions of CB28 and CB153. As for PBDEs, BDE47 was the most frequently detected congener, while BDE209 was detected in barnacles from two stations in Port Klang and the levels reached up to >70% of total PBDE concentrations. Concentrations of OCPs detected in barnacles were in the order of CHLs > DDTs > HCHs > HCB and 4,4'-DDE and cis- and trans-chlordane were the predominant OCP compounds. A comparison with previous studies in Malaysia showed consistent levels of POPs. Green mussels collected from selected barnacles' habitats, for the sake of a comparison, showed almost similar profiles but lower concentrations of POPs. The spatial distribution of POPs observed in barnacles and comparison of POP levels and profiles with mussels indicated that barnacles can be useful bioindicators for monitoring POPs contamination in the coastal ecosystems.}, }
@article {pmid33296424, year = {2020}, author = {Fiedler, S and Wünnemann, H and Hofmann, I and Theobalt, N and Feuchtinger, A and Walch, A and Schwaiger, J and Wanke, R and Blutke, A}, title = {A practical guide to unbiased quantitative morphological analyses of the gills of rainbow trout (Oncorhynchus mykiss) in ecotoxicological studies.}, journal = {PloS one}, volume = {15}, number = {12}, pages = {e0243462}, pmid = {33296424}, issn = {1932-6203}, mesh = {Animals ; Female ; Gills/*anatomy &amp; histology/drug effects/physiology/ultrastructure ; Male ; Microscopy, Fluorescence ; Oncorhynchus mykiss/*anatomy &amp; histology/physiology ; Reproducibility of Results ; Water Pollutants, Chemical/chemistry/*toxicity ; }, abstract = {Rainbow trout (Oncorhynchus mykiss) are frequently used as experimental animals in ecotoxicological studies, in which they are experimentally exposed to defined concentrations of test substances, such as heavy metals, pesticides, or pharmaceuticals. Following exposure to a broad variety of aquatic pollutants, early morphologically detectable toxic effects often manifest in alterations of the gills. Suitable methods for an accurate and unbiased quantitative characterization of the type and the extent of morphological gill alterations are therefore essential prerequisites for recognition, objective evaluation and comparison of the severity of gill lesions. The aim of the present guidelines is to provide practicable, standardized and detailed protocols for the application of unbiased quantitative stereological analyses of relevant morphological parameters of the gills of rainbow trout. These gill parameters inter alia include the total volume of the primary and secondary gill lamellae, the surface area of the secondary gill lamellae epithelium (i.e., the respiratory surface) and the thickness of the diffusion barrier. The featured protocols are adapted to fish of frequently used body size classes (300-2000 g). They include well-established, conventional sampling methods, probes and test systems for unbiased quantitative stereological analyses of light- and electron microscopic 2-D gill sections, as well as the application of modern 3-D light sheet fluorescence microscopy (LSFM) of optically cleared gill samples as an innovative, fast and efficient quantitative morphological analysis approach. The methods shown here provide a basis for standardized and representative state-of-the-art quantitative morphological analyses of trout gills, ensuring the unbiasedness and reproducibility, as well as the intra- and inter-study comparability of analyses results. Their broad implementation will therefore significantly contribute to the reliable identification of no observed effect concentration (NOEC) limits in ecotoxicological studies and, moreover, to limit the number of experimental animals by reduction of unnecessary repetition of experiments.}, }
@article {pmid33295059, year = {2021}, author = {Li, J and Bååth, E and Pei, J and Fang, C and Nie, M}, title = {Temperature adaptation of soil microbial respiration in alpine, boreal and tropical soils: An application of the square root (Ratkowsky) model.}, journal = {Global change biology}, volume = {27}, number = {6}, pages = {1281-1292}, doi = {10.1111/gcb.15476}, pmid = {33295059}, issn = {1365-2486}, support = {2020M670975//The Postdoctoral Science Foundation of China/ ; 31830009//The National Science Foundation of China/ ; 32030067//The National Science Foundation of China/ ; 91951112//The National Science Foundation of China/ ; 2020PJD003//The Shanghai Pujiang Program/ ; }, mesh = {Carbon ; China ; Ecosystem ; Respiration ; *Soil ; *Soil Microbiology ; Temperature ; }, abstract = {Warming is expected to stimulate soil microbial respiration triggering a positive soil carbon-climate feedback loop while a consensus remains elusive regarding the magnitude of this feedback. This is partly due to our limited understanding of the temperature-adaptive response of soil microbial respiration, especially over broad climatic scales. We used the square root (Ratkowsky) model to calculate the minimum temperature for soil microbial respiration (Tmin , which describes the temperature adaptation of soil microbial respiration) of 298 soil samples from alpine grasslands on the Tibetan Plateau and forest ecosystems across China with a mean annual temperature (MAT) range from -6°C to +25°C. The instantaneous soil microbial respiration was determined between 4°C and 28°C. The square root model could well fit the temperature effect on soil microbial respiration for each individual soil, with R[2] higher than 0.98 for all soils. Tmin ranged from -8.1°C to -0.1°C and increased linearly with increasing MAT (R[2] = 0.68). MAT dominantly regulated Tmin variation when accounting simultaneously for multiple other drivers (mean annual precipitation, soil pH and carbon quality); an independent experiment showed that carbon availability had no significant effect on Tmin . Using the relationship between Tmin and MAT, soil microbial respiration after an increased MAT could be estimated, resulting in a relative increase in respiration with decreasing MAT. Thus, soil microbial respiration responses are adapted to long-term temperature differences in MAT. We suggest that Tmin = -5 + 0.2 × MAT, that is, every 1°C rise in MAT is estimated to increase Tmin of respiration by approximately 0.2°C, could be used as a first approximation to incorporate temperature adaptation of soil microbial respiration in model predictions. Our results can be used to predict future changes in the response of soil microbial respiration to temperature over different levels of warming and across broad geographic scales with different MAT.}, }
@article {pmid33294135, year = {2020}, author = {Tobias, NJ and Eberhard, FE and Guarneri, AA}, title = {Enzymatic biosynthesis of B-complex vitamins is supplied by diverse microbiota in the Rhodnius prolixus anterior midgut following Trypanosoma cruzi infection.}, journal = {Computational and structural biotechnology journal}, volume = {18}, number = {}, pages = {3395-3401}, pmid = {33294135}, issn = {2001-0370}, abstract = {Trypanosoma cruzi, the causative agent of Chagas disease, colonizes the gut of triatomine insects, including Rhodnius prolixus. It is believed that this colonization upsets the microbiota that are normally present, presumably switching the environment to one more favorable for parasite survival. It was previously thought that one particular bacterium, Rhodococcus rhodnii, was essential for insect survival due to its ability to produce vital B-complex vitamins. However, these bacteria are not always identified in great abundance in studies on R. prolixus microbiota. Here we sequenced the microbiota of the insect anterior midgut using shotgun metagenomic sequencing in order to obtain a high-resolution snapshot of the microbes inside at two different time points and under two conditions; in the presence or absence of parasite and immediately following infection, or three days post-infection. We identify a total of 217 metagenomic bins, and recovered one metagenome-assembled genome, which we placed in the genus Dickeya. We show that, despite Rhodococcus being present, it is not the only microbe capable of synthesizing B-complex vitamins, with the genes required for biosynthesis present in a number of different microbes. This work helps to gain a new insight into the microbial ecology of R. prolixus.}, }
@article {pmid33292591, year = {2020}, author = {Zhang, W and Bao, C and Wang, J and Zang, J and Cao, Y}, title = {Administration of Saccharomyces boulardii mafic-1701 improves feed conversion ratio, promotes antioxidant capacity, alleviates intestinal inflammation and modulates gut microbiota in weaned piglets.}, journal = {Journal of animal science and biotechnology}, volume = {11}, number = {1}, pages = {112}, pmid = {33292591}, issn = {1674-9782}, abstract = {BACKGROUND: Probiotics are used as a means to improve animal health and intestinal development. Saccharomyces boulardii is a well-known probiotic; however, few studies have examined the effects of S. boulardii on weaned piglet performance. Therefore, this 28-day study compared the effects of S. boulardii mafic-1701 and aureomycin in diets for weaned piglets on growth performance, antioxidant parameters, inflammation and intestinal microbiota. One hundred and eight piglets, weaned at 28 d of age (8.5 ± 1.1 kg), were randomly divided into the three dietary treatment groups with six pens and six piglets per pen (half male and half female). The dietary treatment groups were as follows: 1) basal diet (CON); 2) basal diet supplemented with 75 mg/kg aureomycin (ANT); 3) basal diet supplemented with 1 × 10[8] CFU/kg S. boulardii mafic-1701 (SB).<br><br>RESULTS: Compared to CON group, SB group had higher feed efficiency (P&#x2009;<&#x2009;0.05) in the last 14&#x2009;d and lower diarrhea rate (P&#x2009;<&#x2009;&#xa0;0.05) over the entire 28&#x2009;d. Total superoxide dismutase in serum was markedly increased in SB group (P&#x2009;<&#x2009;0.05). Moreover, compared with CON group, SB group decreased the levels of pro-inflammatory cytokines interleukin-6 (P&#x2009;<&#x2009;&#xa0;0.01) and Tumor necrosis factor-&#x3b1; (P&#x2009;<&#x2009;0.05) in jejunum. Supplementation of S. boulardii mafic-1701 increased the abundance of Ruminococcaceae_UCG_009 and Turicibacter (P&#x2009;<&#x2009;0.05), whereas the abundance of unclassified_Clostridiaceae_4 was decreased (P&#x2009;<&#x2009;0.05). Furthermore, S. boulardii mafic-1701 administration increased cecal concentration of microbial metabolites, isobutyrate and valerate (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: The improvement in feed conversion ratio, reduction in diarrhea rate in weaned piglets provided diets supplemented with S. boulardii mafic-1701 may be associated with enhanced antioxidant activity, anti-inflammatory responses and improved intestinal microbial ecology.}, }
@article {pmid33290744, year = {2020}, author = {Songailiene, I and Juozapaitis, J and Tamulaitiene, G and Ruksenaite, A and Šulčius, S and Sasnauskas, G and Venclovas, &#x10c; and Siksnys, V}, title = {HEPN-MNT Toxin-Antitoxin System: The HEPN Ribonuclease Is Neutralized by OligoAMPylation.}, journal = {Molecular cell}, volume = {80}, number = {6}, pages = {955-970.e7}, doi = {10.1016/j.molcel.2020.11.034}, pmid = {33290744}, issn = {1097-4164}, mesh = {Adenosine Monophosphate/genetics ; Antidotes/chemistry ; Antitoxins/*genetics/metabolism ; Aphanizomenon/chemistry/genetics ; Bacterial Toxins/*genetics ; CRISPR-Cas Systems/genetics ; Nucleotidyltransferases/genetics/metabolism ; Ribonucleases/*genetics/metabolism ; Toxin-Antitoxin Systems/*genetics ; Tyrosine/genetics ; }, abstract = {Prokaryotic toxin-antitoxin (TA) systems are composed of a toxin capable of interfering with key cellular processes and its neutralizing antidote, the antitoxin. Here, we focus on the HEPN-MNT TA system encoded in the vicinity of a subtype I-D CRISPR-Cas system in the cyanobacterium Aphanizomenon flos-aquae. We show that HEPN acts as a toxic RNase, which cleaves off 4 nt from the 3' end in a subset of tRNAs, thereby interfering with translation. Surprisingly, we find that the MNT (minimal nucleotidyltransferase) antitoxin inhibits HEPN RNase through covalent di-AMPylation (diadenylylation) of a conserved tyrosine residue, Y109, in the active site loop. Furthermore, we present crystallographic snapshots of the di-AMPylation reaction at different stages that explain the mechanism of HEPN RNase inactivation. Finally, we propose that the HEPN-MNT system functions as a cellular ATP sensor that monitors ATP homeostasis and, at low ATP levels, releases active HEPN toxin.}, }
@article {pmid33289627, year = {2021}, author = {Hofmann, K and Woller, A and Huptas, C and Wenning, M and Scherer, S and Doll, EV}, title = {Pseudomonas cremoris sp. nov., a novel proteolytic species isolated from cream.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {71}, number = {1}, pages = {}, doi = {10.1099/ijsem.0.004597}, pmid = {33289627}, issn = {1466-5034}, mesh = {Animals ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Genes, Bacterial ; Germany ; Milk/*microbiology ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; Proteolysis ; Pseudomonas/*classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Ubiquinone/chemistry ; }, abstract = {During a study investigating the microbiota of raw milk and its semi-finished products, strains WS 5106[T] and WS 5096 were isolated from cream and skimmed milk concentrate. They could be assigned to the genus Pseudomonas by their 16S rRNA sequences, but not to any validly named species. In this work, a polyphasic approach was used to characterize the novel strains and to investigate their taxonomic status. Examinations based on the topology of core genome phylogenomy as well as average nucleotide identity (ANIm) comparisons suggested a novel Pseudomonas species within the Pseudomonas fluorescens subgroup. With pairwise ANIm values of 90.1 and 89.8 %, WS 5106[T] was most closely related to Pseudomonas nabeulensis CECT 9765[T] and Pseudomonas kairouanensis CECT 9766[T]. The G+C content of strain WS 5106[T] was 60.1 mol%. Morphologic analyses revealed Gram-stain-negative, aerobic, catalase and oxidase positive, rod-shaped and motile cells. Proteolysis on skimmed milk agar as well as lipolysis on tributyrin agar occurred at both 28 and 6 °C. Tolerated growth conditions were temperatures between 4 and 34 °C, pH values between 6.0 and 8.0, and salt concentrations of up to 5 %. Fatty acid profiles showed a pattern typical for Pseudomonas, with C16 : 0 as the dominant component. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol and the dominating quinone was Q-9. Based on these results, it is proposed to classify the strains as a novel species, Pseudomonas cremoris sp. nov., with WS 5106[T] (=DSM 111143[T]=LMG 31863[T]) as type strain and WS 5096 (=DSM 111129=LMG 31864) as an additional strain.}, }
@article {pmid33288837, year = {2020}, author = {Busti, S and Rossi, B and Volpe, E and Ciulli, S and Piva, A and D'Amico, F and Soverini, M and Candela, M and Gatta, PP and Bonaldo, A and Grilli, E and Parma, L}, title = {Effects of dietary organic acids and nature identical compounds on growth, immune parameters and gut microbiota of European sea bass.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {21321}, pmid = {33288837}, issn = {2045-2322}, mesh = {Animals ; Bass/*metabolism ; Biodiversity ; Gastrointestinal Microbiome/genetics/*physiology ; High-Throughput Nucleotide Sequencing ; Interleukin-10/metabolism ; Interleukin-8/metabolism ; Transforming Growth Factor beta/metabolism ; }, abstract = {A 71-day study was conducted to explore the effect of increasing dietary levels (0, 250, 500, 1000 mg kg feed[-1]; D0, D250, D500 and D1000, respectively) of a blend of microencapsulated organic acids (OA, specifically citric and sorbic acid) and nature identical compounds (NIC, specifically thymol and vanillin), on growth, intestinal immune parameters and gut microbiota (GM) of European sea bass juveniles reared under normal and subsequently suboptimal environmental conditions (high temperature, 30.0 ± 0.4 °C and low oxygen, 4.6 ± 0.6 mg L[-1]). OA and NIC did not promote growth, feed utilisation and feed intake at the inclusion tested but induced a significantly upregulation of IL-8, IL-10 and TGFβ. GM analyzed by next-generation sequencing showed that OA and NIC were able to exert prebiotic properties stimulating the development of beneficial bacteria taxa such as Lactobacillus, Leuconostoc, and Bacillus sp. Picrust analyses displayed a significant potential functional reconfiguration of GM promoting a decrease in inflammation-promoting and homeostatic functions at increasing OA and NIC administration. For the first time on this species the exposure to suboptimal rearing conditions was able to modify GM structure reducing LAB and increasing Proteobacteria, findings which were consistent with the inflammatory process observed at mRNA level.}, }
@article {pmid33282266, year = {2020}, author = {Zhao, L and Li, X and Yang, Q and Zhuang, D and Pan, X and Li, L}, title = {Adsorption kinetics and mechanism of di-n-butyl phthalate by Leuconostoc mesenteroides.}, journal = {Food science &amp; nutrition}, volume = {8}, number = {11}, pages = {6153-6163}, pmid = {33282266}, issn = {2048-7177}, abstract = {Di-n-butyl phthalate (DBP) poses a risk to humans as a ubiquitous environmental contaminant. A strain of Leuconostoc mesenteroides DM12 was chosen from lactic acid bacteria strains to study the DBP binding mechanisms. Adsorption of DBP by strain DM12 reached the highest binding rate of 87% after 11 hr of incubation, which could be explained by pseudo-second-order kinetics. The adsorption isotherm coincided with the model of Langmuir-Freundlich, indicating physical and chemical adsorption processes involved. Further, NaIO4 and TCA treatments were used to analyze the DBP binding mechanism of strain DM12, which indicated that peptidoglycan on the bacterial cell wall was involved in the process. The O-H, C-O, and N-H bonds were possibly involved in the binding process as the main functional groups.}, }
@article {pmid33281127, year = {2020}, author = {Nakajima, Y and Kojima, K and Kashiyama, Y and Doi, S and Nakai, R and Sudo, Y and Kogure, K and Yoshizawa, S}, title = {Bacterium Lacking a Known Gene for Retinal Biosynthesis Constructs Functional Rhodopsins.}, journal = {Microbes and environments}, volume = {35}, number = {4}, pages = {}, pmid = {33281127}, issn = {1347-4405}, mesh = {Actinobacteria/chemistry/genetics/*metabolism/radiation effects ; Bacterial Proteins/*genetics/metabolism ; Biosynthetic Pathways ; Chromatography, High Pressure Liquid ; Light ; Rhodopsin/*biosynthesis/chemistry ; Tandem Mass Spectrometry ; }, abstract = {Microbial rhodopsins, comprising a protein moiety (rhodopsin apoprotein) bound to the light-absorbing chromophore retinal, function as ion pumps, ion channels, or light sensors. However, recent genomic and metagenomic surveys showed that some rhodopsin-possessing prokaryotes lack the known genes for retinal biosynthesis. Since rhodopsin apoproteins cannot absorb light energy, rhodopsins produced by prokaryotic strains lacking genes for retinal biosynthesis are hypothesized to be non-functional in cells. In the present study, we investigated whether Aurantimicrobium minutum KNC[T], which is widely distributed in terrestrial environments and lacks any previously identified retinal biosynthesis genes, possesses functional rhodopsin. We initially measured ion transport activity in cultured cells. A light-induced pH change in a cell suspension of rhodopsin-possessing bacteria was detected in the absence of exogenous retinal. Furthermore, spectroscopic analyses of the cell lysate and HPLC-MS/MS analyses revealed that this strain contained an endogenous retinal. These results confirmed that A. minutum KNC[T] possesses functional rhodopsin and, hence, produces retinal via an unknown biosynthetic pathway. These results suggest that rhodopsin-possessing prokaryotes lacking known retinal biosynthesis genes also have functional rhodopsins.}, }
@article {pmid33279744, year = {2021}, author = {Agrawal, S and Weissbrodt, DG and Annavajhala, M and Jensen, MM and Arroyo, JMC and Wells, G and Chandran, K and Vlaeminck, SE and Terada, A and Smets, BF and Lackner, S}, title = {Time to act-assessing variations in qPCR analyses in biological nitrogen removal with examples from partial nitritation/anammox systems.}, journal = {Water research}, volume = {190}, number = {}, pages = {116604}, doi = {10.1016/j.watres.2020.116604}, pmid = {33279744}, issn = {1879-2448}, mesh = {*Ammonium Compounds ; Bacteria/genetics ; Bioreactors ; Denitrification ; *Microbiota ; Nitrification ; Nitrogen ; Oxidation-Reduction ; }, abstract = {Quantitative PCR (qPCR) is broadly used as the gold standard to quantify microbial community fractions in environmental microbiology and biotechnology. Benchmarking efforts to ensure the comparability of qPCR data for environmental bioprocesses are still scarce. Also, for partial nitritation/anammox (PN/A) systems systematic investigations are still missing, rendering meta-analysis of reported trends and generic insights potentially precarious. We report a baseline investigation of the variability of qPCR-based analyses for microbial communities applied to PN/A systems. Round-robin testing was performed for three PN/A biomass samples in six laboratories, using the respective in-house DNA extraction and qPCR protocols. The concentration of extracted DNA was significantly different between labs, ranged between 2.7 and 328 ng mg[-1] wet biomass. The variability among the qPCR abundance data of different labs was very high (1-7 log fold) but differed for different target microbial guilds. DNA extraction caused maximum variation (3-7 log fold), followed by the primers (1-3 log fold). These insights will guide environmental scientists and engineers as well as treatment plant operators in the interpretation of qPCR data.}, }
@article {pmid33279588, year = {2021}, author = {Huang, L and Duan, C and Xia, X and Wang, H and Wang, Y and Zhong, Z and Wang, B and Ding, W and Yang, Y}, title = {Commensal microbe-derived propionic acid mediates juvenile social isolation-induced social deficits and anxiety-like behaviors.}, journal = {Brain research bulletin}, volume = {166}, number = {}, pages = {161-171}, doi = {10.1016/j.brainresbull.2020.12.001}, pmid = {33279588}, issn = {1873-2747}, mesh = {Animals ; Anxiety/*metabolism ; Behavior, Animal ; Gastrointestinal Microbiome/*physiology ; Male ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Prefrontal Cortex/*metabolism ; Propionates/*metabolism ; Receptors, Oxytocin/*metabolism ; *Social Isolation ; }, abstract = {Social experiences during early life are thought to be critical for proper social and emotional development. Conversely, social insults during development causes long-lasting behavioral abnormalities later in life. However, how juvenile social deprivation influences social and emotional behaviors remains poorly understood. Here, we show that juvenile social isolation induces a shift in microbial ecology that negatively impacts social and emotional behaviors in adulthood. These behavioral changes, which occur during this critical period are transferable to antibiotic pre-treated mice by fecal microbiota transplant. In addition, juvenile social isolation decreases the expression of oxytocin receptor (OXTR) in the medial prefrontal cortex (mPFC), and increases the amounts of fecal propionic acid (PA), a short-chain fatty acid derived from gut micobiota. Accordingly, infusion with an OXTR antagonist (OXTR-A, l-368,899) specifically in the mPFC or supplementation of PA both can cause social deficits and anxiety-like behaviors in group housed mice. Collectively, our findings reveal that juvenile social experience regulates prefrontal cortical OXTR expression through gut microbiota-produced PA and that is essential for normal social and emotional behaviors, thus providing a cellular and molecular context to understand the consequences of juvenile social deprivation.}, }
@article {pmid33279067, year = {2021}, author = {Kim, E and Cho, EJ and Yang, SM and Kim, MJ and Kim, HY}, title = {Novel approaches for the identification of microbial communities in kimchi: MALDI-TOF MS analysis and high-throughput sequencing.}, journal = {Food microbiology}, volume = {94}, number = {}, pages = {103641}, doi = {10.1016/j.fm.2020.103641}, pmid = {33279067}, issn = {1095-9998}, mesh = {Bacteria/chemistry/classification/genetics/*isolation &amp; purification ; Brassica/*microbiology ; Fermentation ; Fermented Foods/*microbiology ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Vegetables/microbiology ; Yeasts/classification/genetics/*isolation &amp; purification/metabolism ; }, abstract = {Complex interactions occur within microbial communities during the fermentation process of kimchi. Identification of these microorganisms provides the essential information required to improve food quality and to understand their role in this process. This was the first study to compare two methods for accuracy in the identification of microbial community changes during the fermentation of kimchi by comparing a culture-dependent (MALDI-TOF MS analysis) and a culture-independent method (high-throughput sequencing) of 16S rRNA gene fragment). Members of the Lactobacillus-related genera, Leuconostoc, and Weissella were identified as the predominant microorganisms by both methods. The culture-independent method was able to additionally identify non-lactic acid bacteria and yeasts, such as Kazachstania in kimchi. However, high-throughput sequencing failed to accurately recognize Latilactobacillus sakei, Latilactobacillus curvatus, Lactiplantibacillus plantarum, and W. cibaria, which played an important role in kimchi fermentation, as this method only allowed for identification at the genus level. Conversely, MALDI-TOF MS analysis could identify the isolates at the species level. Also, culture-dependent method could identify predominant species in viable cell communities. The culture-dependent method and culture-independent method provided complementary information by producing a more comprehensive view of the microbial ecology in fermented kimchi.}, }
@article {pmid33277271, year = {2021}, author = {Van Herreweghen, F and De Paepe, K and Marzorati, M and Van de Wiele, T}, title = {Mucin as a Functional Niche is a More Important Driver of in Vitro Gut Microbiota Composition and Functionality than Supplementation of Akkermansia m uciniphila.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {4}, pages = {}, pmid = {33277271}, issn = {1098-5336}, abstract = {IMPORTANCE SECTION Research into identification of biomarkers for gut health and ways to modulate the microbiota composition and activity to improve health, has put Akkermansia muciniphila in the spotlight. As a mucin degrader, A. muciniphila colonizes the interesting but not-fully described host-glycan degradation niche., . Plenty of research concerning A. muciniphila has been done, but little is known about its behavior in the complex microbial ecosystem in the colon, about the potential role of mucins to influence A. muciniphila behavior and the impact of its probiotic administration on the microbial ecosystem.This study aimed at investigating the impact of A. muciniphila administration on the endogenous community while also taking into account its nutritional specificity. As such, the effect of A.mucinihpila administration was investigated with and without addition of mucin. This allowed us to elucidate the importance of mucin presence to modulate the efficiency of the probiotic supplementation with A. muciniphila Akkermansia muciniphila is an abundantly present commensal mucin degrading gut bacterium (1 - 4%) , widely distributed among healthy individuals. It has been positioned as a health biomarker and is currently explored as a biotherapeutic agent and next generation probiotic. Preliminary and ongoing research is mostly based on in vivo mouse models and human intervention trials. While these allow the assessment of physiologically relevant endpoints, the analysis of fecal samples presents limitations with respect to the in-depth mechanistic characterization of Akkermansia effects at the level of the microbiome. We aimed to evaluate the effect of A. muciniphila treatment on the endogenous community from four different donors in a validated, controlled in vitro model of the gut microbial ecosystem (SHIME). Taking into account the nutritional specificity of A. muciniphila, and the prebiotic-like action of mucins in the colon environment, the interplay between mucin, A. muciniphila and the endogenous community was investigated. The effects on the microbial community composition and functionality of A. muciniphila supplementation without mucin were limited, whereas mucin addition successfully induced compositional and metabolic changes in the gut microbiota. Indeed, mucin addition resulted in significantly higher acetate, propionate and butyrate production for all four donors, and the increase of several species, including A. muciniphila, Ruminococcus, Clostridium cluster XIVa, and Lachnospiraceae This study revealed that the supplementation of A. muciniphila together with mucin limited the observed prebiotic-like effect of mucin in inducing compositional changes.}, }
@article {pmid33274397, year = {2021}, author = {Bien, T and Hambleton, EA and Dreisewerd, K and Soltwisch, J}, title = {Molecular insights into symbiosis-mapping sterols in a marine flatworm-algae-system using high spatial resolution MALDI-2-MS imaging with ion mobility separation.}, journal = {Analytical and bioanalytical chemistry}, volume = {413}, number = {10}, pages = {2767-2777}, pmid = {33274397}, issn = {1618-2650}, support = {Drei2/018/17//Interdisciplinary Center for Clinical Research, M&#xfc;nster, Germany/ ; SO976/5-1, project number 400912714//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; Dinoflagellida/*chemistry/physiology ; Ion Mobility Spectrometry/methods ; Platyhelminths/*chemistry/physiology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; Sterols/*analysis/metabolism ; Symbiosis ; }, abstract = {Waminoa sp. acoel flatworms hosting Symbiodiniaceae and the related Amphidinium dinoflagellate algae are an interesting model system for symbiosis in marine environments. While the host provides a microhabitat and safety, the algae power the system by photosynthesis and supply the worm with nutrients. Among these nutrients are sterols, including cholesterol and numerous phytosterols. While it is widely accepted that these compounds are produced by the symbiotic dinoflagellates, their transfer to and fate within the sterol-auxotrophic Waminoa worm host as well as their role in its metabolism are unknown. Here we used matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging combined with laser-induced post-ionization and trapped ion mobility spectrometry (MALDI-2-TIMS-MSI) to map the spatial distribution of over 30 different sterol species in sections of the symbiotic system. The use of laser post-ionization crucially increased ion yields and allowed the recording of images with a pixel size of 5 μm. Trapped ion mobility spectrometry (TIMS) helped with the tentative assignment of over 30 sterol species. Correlation with anatomical features of the worm, revealed by host-derived phospholipid signals, and the location of the dinoflagellates, revealed by chlorophyll a signal, disclosed peculiar differences in the distribution of different sterol species (e.g. of cholesterol versus stigmasterol) within the receiving host. These findings point to sterol species-specific roles in the metabolism of Waminoa beyond a mere source of energy. They also underline the value of the MALDI-2-TIMS-MSI method to future research in the spatially resolved analysis of sterols.}, }
@article {pmid33272988, year = {2020}, author = {Singh, RP and Johri, AK and Dua, M}, title = {Metagenomic Analysis of Microbial Diversity in Cotton Rhizosphere Soil in Alwar, India.}, journal = {Microbiology resource announcements}, volume = {9}, number = {49}, pages = {}, pmid = {33272988}, issn = {2576-098X}, abstract = {Cotton is an important cash crop for both the Indian economy and rural livelihoods. In the present study, metagenomic analysis is used to characterize microbial diversity in cotton rhizosphere soil from the Alwar district, located in the semiarid northeast region of the state of Rajasthan in India.}, }
@article {pmid33266447, year = {2020}, author = {Martucci, M and Conte, M and Bucci, L and Giampieri, E and Fabbri, C and Palmas, MG and Izzi, M and Salvioli, S and Zambrini, AV and Orsi, C and Brigidi, P and Santoro, A and Capri, M and Monti, D and Franceschi, C}, title = {Twelve-Week Daily Consumption of ad hoc Fortified Milk with ω-3, D, and Group B Vitamins Has a Positive Impact on Inflammaging Parameters: A Randomized Cross-Over Trial.}, journal = {Nutrients}, volume = {12}, number = {11}, pages = {}, pmid = {33266447}, issn = {2072-6643}, support = {00088MI01//Italian Ministry of Agriculture/ ; }, mesh = {Aged ; Aged, 80 and over ; Animals ; Cross-Over Studies ; Double-Blind Method ; Fatty Acids, Omega-3/*administration &amp; dosage ; Female ; *Food, Fortified ; Health Status ; Humans ; Inflammation/*epidemiology ; Male ; Micronutrients/blood ; Middle Aged ; *Milk ; Placebos ; Vitamin B Complex/*administration &amp; dosage ; Vitamin D/administration &amp; dosage/*analogs &amp; derivatives ; }, abstract = {BACKGROUND AND AIM: A state of chronic, subclinical inflammation known as inflammaging is present in elderly people and represents a risk factor for all age-related diseases. Dietary supplementation with ad hoc fortified foods seems an appealing strategy to counteract inflammaging. The purpose of this study was to test the efficacy of elderly-tailored fortified milk on inflammaging and different health parameters.<br><br>METHODS: A double-blind randomized cross-over study was performed on forty-eight volunteers aged 63-80 years. The fortified milk was enriched with &#x3c9;-3 polyunsaturated fatty acids (eicosapentaenoic acid, EPA; docosahexaenoic acid, DHA), vitamins (25-hydroxyvitamin D, E, C, B6, B9, B12), and trace elements (zinc, selenium). The two intervention periods lasted for 12 weeks, with a 16-week washout intermission.<br><br>RESULTS: Compared to placebo, the consumption of fortified milk increased the circulating levels of different micronutrients, including vitamins and the &#x3c9;-3 index of erythrocyte membranes. Conversely, it reduced the amount of arachidonic acid, homocysteine, and &#x3c9;-6/&#x3c9;-3 ratio.<br><br>CONCLUSION: Twelve-week daily consumption of adhoc fortified milk has an overall positive impact on different health parameters related to inflammaging in the elderly.}, }
@article {pmid33264963, year = {2021}, author = {Rai, PK and Lee, J and Brown, RJC and Kim, KH}, title = {Environmental fate, ecotoxicity biomarkers, and potential health effects of micro- and nano-scale plastic contamination.}, journal = {Journal of hazardous materials}, volume = {403}, number = {}, pages = {123910}, doi = {10.1016/j.jhazmat.2020.123910}, pmid = {33264963}, issn = {1873-3336}, mesh = {Animals ; Biomarkers ; Environmental Pollution ; Humans ; Microplastics ; *Plastics/toxicity ; *Water Pollutants, Chemical/analysis ; }, abstract = {In recent decades, the quantity of plastic waste products has increased tremendously. As plastic wastes are released into the environment, they exert harmful effects on biota and human health. In this work, a comprehensive review is offered to describe the physical and chemical characteristics of microplastics and nanoplastics in relation to their fate, microbial ecology, transport, and ecotoxic behavior. Present discussion is expanded further to cover the biochemical, physiological, and molecular mechanisms controlling the environmental fate, ecotoxicity, and human health hazards of micro- and nanoplastics. The risks of their exposure to microbes, plants, animals, and human health are also reviewed with special emphasis. Finally, a direction for future interdisciplinary research in materials and polymer science is also discussed to help control the pollution caused by micro- and nanoplastics.}, }
@article {pmid33264923, year = {2021}, author = {Williamson, AJ and Verbruggen, F and Chavez Rico, VS and Bergmans, J and Spooren, J and Yurramendi, L and Laing, GD and Boon, N and Hennebel, T}, title = {Selective leaching of copper and zinc from primary ores and secondary mineral residues using biogenic ammonia.}, journal = {Journal of hazardous materials}, volume = {403}, number = {}, pages = {123842}, doi = {10.1016/j.jhazmat.2020.123842}, pmid = {33264923}, issn = {1873-3336}, mesh = {Ammonia ; Bacillaceae ; *Copper ; Minerals ; *Zinc ; }, abstract = {With the number of easily accessible ores depleting, alternate primary and secondary sources are required to meet the increasing demand of economically important metals. Whilst highly abundant, these materials are of lower grade with respect to traditional ores, thus highly selective and sustainable metal extraction technologies are needed to reduce processing costs. Here, we investigated the metal leaching potential of biogenic ammonia produced by a ureolytic strain of Lysinibacillus sphaericus on eight primary and secondary materials, comprised of mining and metallurgical residues, sludges and automotive shredder residues (ASR). For the majority of materials, moderate to high yields (30-70%) and very high selectivity (>97% against iron) of copper and zinc were obtained with 1 mol L[-1] total ammonia. Optimal leaching was achieved and further refined for the ASR in a two-step indirect leaching system with biogenic ammonia. Copper leaching was the result of local corrosion and differences in leaching against the synthetic (NH4)2CO3 control could be accounted for by pH shifts from microbial metabolism, subsequently altering free NH3 required for coordination. These results provide important findings for future sustainable metal recovery technologies from secondary materials.}, }
@article {pmid33264383, year = {2021}, author = {Ghuneim, LJ and Distaso, MA and Chernikova, TN and Bargiela, R and Lunev, EA and Korzhenkov, AA and Toshchakov, SV and Rojo, D and Barbas, C and Ferrer, M and Golyshina, OV and Golyshin, PN and Jones, DL}, title = {Utilization of low-molecular-weight organic compounds by the filterable fraction of a lotic microbiome.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {2}, pages = {}, pmid = {33264383}, issn = {1574-6941}, mesh = {Carbon ; Fresh Water ; *Microbiota ; *Organic Chemicals ; RNA, Ribosomal, 16S/genetics ; Rivers ; }, abstract = {Filterable microorganisms participate in dissolved organic carbon (DOC) cycling in freshwater systems, however their exact functional role remains unknown. We determined the taxonomic identity and community dynamics of prokaryotic microbiomes in the 0.22 µm-filtered fraction and unfiltered freshwater from the Conwy River (North Wales, UK) in microcosms and, using targeted metabolomics and 14C-labelling, examined their role in the utilization of amino acids, organic acids and sugars spiked at environmentally-relevant (nanomolar) concentrations. To identify changes in community structure, we used 16S rRNA amplicon and shotgun sequencing. Unlike the unfiltered water samples where the consumption of DOC was rapid, the filtered fraction showed a 3-day lag phase before the consumption started. Analysis of functional categories of clusters of orthologous groups of proteins (COGs) showed that COGs associated with energy production increased in number in both fractions with substrate addition. The filtered fraction utilized low-molecular-weight (LMW) DOC at much slower rates than the whole community. Addition of nanomolar concentrations of LMW DOC did not measurably influence the composition of the microbial community nor the rate of consumption across all substrate types in either fraction. We conclude that due to their low activity, filterable microorganisms play a minor role in LMW DOC processing within a short residence time of lotic freshwater systems.}, }
@article {pmid33262758, year = {2020}, author = {Batista, MA and Calvo-Fortes, F and Silveira-Nunes, G and Camatta, GC and Speziali, E and Turroni, S and Teixeira-Carvalho, A and Martins-Filho, OA and Neretti, N and Maioli, TU and Santos, RR and Brigidi, P and Franceschi, C and Faria, AMC}, title = {Inflammaging in Endemic Areas for Infectious Diseases.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {579972}, pmid = {33262758}, issn = {1664-3224}, mesh = {Aging/*physiology ; Animals ; Communicable Diseases/epidemiology/*immunology/microbiology ; Diet, Western ; Endemic Diseases ; Frailty ; Healthy Aging ; Humans ; Immunosenescence ; Inflammation/epidemiology/*immunology/microbiology ; Italy/epidemiology ; Microbiota/*immunology ; }, abstract = {Immunosenescence is marked by a systemic process named inflammaging along with a series of defects in the immunological activity that results in poor responses to infectious agents and to vaccination. Inflammaging, a state of low-grade chronic inflammation, usually leads to chronic inflammatory diseases and frailty in the elderly. However, some elderly escape from frailty and reach advanced age free of the consequences of inflammaging. This process has been called immunological remodeling, and it is the hallmark of healthy aging as described in the studies of centenarians in Italy. The biological markers of healthy aging are still a matter of debate, and the studies on the topic have focused on inflammatory versus remodeling processes and molecules. The sub-clinical inflammatory status associated with aging might be a deleterious event for populations living in countries where chronic infectious diseases are not prevalent. Nevertheless, in other parts of the world where they are, two possibilities may occur. Inflammatory responses may have a protective effect against these infectious agents. At the same time, the long-term consequences of protective immune responses during chronic infections may result in accelerated immunosenescence in these individuals. Therefore, the biological markers of healthy aging can vary according to environmental, cultural, and geographical settings that reflect worldwide, and in a non-biased, non-westernized perspective, the changes that we experience regarding our contacts with microorganisms and the outcomes of such contacts.}, }
@article {pmid33262754, year = {2020}, author = {Baksi, KD and Kuntal, BK and Mande, SS}, title = {Corrigendum: 'TIME': A Web Application for Obtaining Insights into Microbial Ecology Using Longitudinal Microbiome Data.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {605295}, doi = {10.3389/fmicb.2020.605295}, pmid = {33262754}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2018.00036.].}, }
@article {pmid33262240, year = {2020}, author = {Khanolkar, RA and Clark, ST and Wang, PW and Hwang, DM and Yau, YCW and Waters, VJ and Guttman, DS}, title = {Ecological Succession of Polymicrobial Communities in the Cystic Fibrosis Airways.}, journal = {mSystems}, volume = {5}, number = {6}, pages = {}, pmid = {33262240}, issn = {2379-5077}, abstract = {Antimicrobial therapies against cystic fibrosis (CF) lung infections are largely aimed at the traditional, well-studied CF pathogens such as Pseudomonas aeruginosa and Burkholderia cepacia complex, despite the fact that the CF lung harbors a complex and dynamic polymicrobial community. A clinical focus on the dominant pathogens ignores potentially important community-level interactions in disease pathology, perhaps explaining why these treatments are often less effective than predicted based on in vitro testing. A better understanding of the ecological dynamics of this ecosystem may enable clinicians to harness these interactions and thereby improve treatment outcomes. Like all ecosystems, the CF lung microbial community develops through a series of stages, each of which may present with distinct microbial communities that generate unique host-microbe and microbe-microbe interactions, metabolic profiles, and clinical phenotypes. While insightful models have been developed to explain some of these stages and interactions, there is no unifying model to describe how these infections develop and persist. Here, we review current perspectives on the ecology of the CF airway and present the CF Ecological Succession (CFES) model that aims to capture the spatial and temporal complexity of CF lung infection, address current challenges in disease management, and inform the development of ecologically driven therapeutic strategies.}, }
@article {pmid33261862, year = {2021}, author = {Liu, D and Legras, JL and Zhang, P and Chen, D and Howell, K}, title = {Diversity and dynamics of fungi during spontaneous fermentations and association with unique aroma profiles in wine.}, journal = {International journal of food microbiology}, volume = {338}, number = {}, pages = {108983}, doi = {10.1016/j.ijfoodmicro.2020.108983}, pmid = {33261862}, issn = {1879-3460}, mesh = {Agriculture ; *Biodiversity ; Farms ; *Fermentation ; Fungi/chemistry/*classification/metabolism ; *Microbiota ; Odorants ; Saccharomyces cerevisiae ; Vitis/microbiology ; Wine/*microbiology ; }, abstract = {Microbial ecology is an integral part of an agricultural ecosystem and influences the quality of agricultural commodities. Microbial activity influences grapevine health and crop production, conversion of sugar to ethanol during fermentation, thus forming wine aroma and flavour. There are regionally differentiated microbial patterns in grapevines and must but how microbial patterns contribute to wine regional distinctiveness (terroir) at small scale (<100 km) is not well defined. Here we characterise fungal communities, yeast populations, and Saccharomyces cerevisiae populations during spontaneous fermentation using metagenomics and population genetics to investigate microbial distribution and fungal contributions to the resultant wine. We found differentiation of fungi, yeasts, and S. cerevisiae between geographic origins (estate/vineyard), with influences from the grape variety. Growth and dominance of S. cerevisiae during fermentation reshaped the fungal community and showed geographic structure at the strain level. Associations between fungal microbiota diversity and wine chemicals suggest that S. cerevisiae plays a primary role in determining wine aroma profiles at a sub-regional scale. The geographic distribution at scales of less than 12 km supports that differential microbial communities, including the dominant fermentative yeast S. cerevisiae can be distinct in a local setting. These findings provide further evidence for microbial contributions to wine terroir, and perspectives for sustainable agricultural practices to maintain microbial diversity and optimise fermentation function to craft beverage quality.}, }
@article {pmid33258525, year = {2021}, author = {Gweon, HS and Bowes, MJ and Moorhouse, HL and Oliver, AE and Bailey, MJ and Acreman, MC and Read, DS}, title = {Contrasting community assembly processes structure lotic bacteria metacommunities along the river continuum.}, journal = {Environmental microbiology}, volume = {23}, number = {1}, pages = {484-498}, pmid = {33258525}, issn = {1462-2920}, support = {NE/N018125/1//Natural Environment Research Council/ ; NE/R016429/1//Natural Environment Research Council/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Ecosystem ; *Microbiota ; Phylogeny ; Rivers/chemistry/*microbiology ; United Kingdom ; }, abstract = {The heterogeneous nature of lotic habitats plays an important role in the complex ecological and evolutionary processes that structure the microbial communities within them. Due to such complexity, our understanding of lotic microbial ecology still lacks conceptual frameworks for the ecological processes that shape these communities. We explored how bacterial community composition and underlying ecological assembly processes differ between lotic habitats by examining community composition and inferring community assembly processes across four major habitat types (free-living, particle-associated, biofilm on benthic stones and rocks, and sediment). This was conducted at 12 river sites from headwater streams to the main river in the River Thames, UK. Our results indicate that there are distinct differences in the bacterial communities between four major habitat types, with contrasting ecological processes shaping their community assembly processes. While the mobile free-living and particle-associated communities were consistently less diverse than the fixed sediment and biofilm communities, the latter two communities displayed higher homogeneity across the sampling sites. This indicates that the relative influence of deterministic environmental filtering is elevated in sediment and biofilm communities compared with free-living and particle-associated communities, where stochastic processes play a larger role.}, }
@article {pmid33257312, year = {2021}, author = {Barbosa, RG and van Veelen, HPJ and Pinheiro, V and Sleutels, T and Verstraete, W and Boon, N}, title = {Enrichment of Hydrogen Oxidizing Bacteria from High Temperature and Salinity Environments.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {4}, pages = {}, pmid = {33257312}, issn = {1098-5336}, abstract = {There is an urgent need for sustainable protein supply routes with low environmental footprint. Recently, the use of hydrogen oxidizing bacteria (HOB) as a platform for high quality microbial protein (MP) production has regained interest. This study aims to investigate the added value of using conditions such as salt and temperature to steer HOB communities to lower diversities, while maintaining a high protein content and a high quality amino acid profile. Pressure drop and hydrogen consumption were measured for 56 days to evaluate autotrophy of a total of six communities in serum flasks. Of the six communities, four were enriched under saline (0.0, 0.25, 0.5 and 1.0 mol NaCl l[-1]) and two under thermophilic conditions (65°C). Five communities enriched for HOB were subsequently cultivated in continuously stirred reactors under the same conditions to evaluate their potential as microbial protein producers. The protein percentages ranged from 41 to 80%. The highest protein content was obtained for the thermophilic enrichments. Amino acid profiles were comparable to protein sources commonly used for feed purposes. Members of the genus Achromobacter were found to dominate the saline enrichments while members of the genus Hydrogenibacillus were found to dominate the thermophilic enrichments. Here we show that enriching for HOB while steering the community toward low diversity and maintaining a high quality protein content can be successfully achieved, both in saline and thermophilic conditions.IMPORTANCE Alternative feed and food supply chains are required to decrease water and land use. HOB offer a promising substitute for traditional agricultural practice to produce microbial protein (MP) from residual materials and renewable energy. To safeguard product stability, the composition of the HOB community should be controlled. Defining strategies to maintain the stability of the communities is therefore key for optimization purposes. In this study, we use salt and temperature as independent conditions to stabilize the composition of the HOB communities. Based on the results presented, we conclude that HOB communities can be steered to have low diversity using the presented conditions while producing a desirable protein content with a valuable amino acid profile.}, }
@article {pmid33257152, year = {2021}, author = {Abel, SM and Primpke, S and Int-Veen, I and Brandt, A and Gerdts, G}, title = {Systematic identification of microplastics in abyssal and hadal sediments of the Kuril Kamchatka trench.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {269}, number = {}, pages = {116095}, doi = {10.1016/j.envpol.2020.116095}, pmid = {33257152}, issn = {1873-6424}, mesh = {Environmental Monitoring ; Geologic Sediments ; *Microplastics ; Oceans and Seas ; Pacific Ocean ; Plastics ; *Water Pollutants, Chemical/analysis ; }, abstract = {The occurrence of microplastics throughout marine environments worldwide, from pelagic to benthic habitats, has become serious cause for concern. Hadal zones were recently described as the "trash bins of the oceans" and ultimate sink for marine plastic debris. The Kuril region covers a substantial area of the North Pacific Ocean and is characterised by high biological productivity, intense marine traffic through the Kuril straits, and anthropogenic activity. Moreover, strong tidal currents and eddy activity, as well as the influence of Pacific currents, have the potential for long distance transport and retention of microplastics in this area. To verify the hypothesis that the underlying Kuril Kamchatka Trench might accumulate microplastics from the surrounding environments and act as the final sink for high quantities of microplastics, we analysed eight sediment samples collected in the Kuril Kamchatka Trench at a depth range of 5143-8250 m during the Kuril Kamchatka Biodiversity Studies II (KuramBio II) expedition in summer 2016. Microplastics were characterised via Micro Fourier Transform Infrared spectroscopy. All samples were analysed in their entirety to avoid inaccuracies due to extrapolations of microplastic concentrations and polymer diversities, which would otherwise be based on commonly applied representative aliquots. The number of microplastic particles detected ranged from 14 to 209 kg[-1] sediment (dry weight) with a total of 15 different plastic polymers detected. Polypropylene accounted for the largest proportion (33.2%), followed by acrylates/polyurethane/varnish (19%) and oxidized polypropylene (17.4%). By comparing extrapolated sample aliquots with in toto results, it was shown that aliquot-based extrapolations lead to severe under- or overestimations of microplastic concentrations, and an underestimation of polymer diversity.}, }
@article {pmid33256756, year = {2020}, author = {Gao, S and Kong, Y and Yu, J and Miao, L and Ji, L and Song, L and Zeng, C}, title = {Isolation of axenic cyanobacterium and the promoting effect of associated bacterium on axenic cyanobacterium.}, journal = {BMC biotechnology}, volume = {20}, number = {1}, pages = {61}, pmid = {33256756}, issn = {1472-6750}, support = {No.2013AA102805-04//National High-tech Research and Development Program/International ; No. 2019EC61-15//Key Project of Jingzhou Science and Technology/International ; No. 2016M591832//Postdoctoral Research Foundation of China/International ; No. BK20150165//Natural Science Foundation of Jiangsu Province/International ; No. KJ15ZB01//General Administration of Quality Supervision, Inspection and Quarantine of the People's Republic of China (CN)/International ; No. 2018ZJSHKF06//Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province/International ; }, mesh = {Chryseobacterium ; Cyanobacteria/classification/genetics/*isolation &amp; purification/*physiology ; Ecology ; Ecosystem ; Heterotrophic Processes ; Microcystis/classification/genetics/isolation &amp; purification/physiology ; Phylogeny ; Symbiosis ; }, abstract = {BACKGROUND: Harmful cyanobacterial blooms have attracted wide attention all over the world as they cause water quality deterioration and ecosystem health issues. Microcystis aeruginosa associated with a large number of bacteria is one of the most common and widespread bloom-forming cyanobacteria that secret toxins. These associated bacteria are considered to benefit from organic substrates released by the cyanobacterium. In order to avoid the influence of associated heterotrophic bacteria on the target cyanobacteria for physiological and molecular studies, it is urgent to obtain an axenic M. aeruginosa culture and further investigate the specific interaction between the heterotroph and the cyanobacterium.<br><br>RESULTS: A traditional and reliable method based on solid-liquid alternate cultivation was carried out to purify the xenic cyanobacterium M. aeruginosa FACHB-905. On the basis of 16S rDNA gene sequences, two associated bacteria named strain B905-1 and strain B905-2, were identified as Pannonibacter sp. and Chryseobacterium sp. with a 99 and 97% similarity value, respectively. The axenic M. aeruginosa FACHB-905A (Microcystis 905A) was not able to form colonies on BG11 agar medium without the addition of strain B905-1, while it grew well in BG11 liquid medium. Although the presence of B905-1 was not indispensable for the growth of Microcystis 905A, B905-1 had a positive effect on promoting the growth of Microcystis 905A.<br><br>CONCLUSIONS: The associated bacteria were eliminated by solid-liquid alternate cultivation method and the axenic Microcystis 905A was successfully purified. The associated bacterium B905-1 has the potentiality to promote the growth of Microcystis 905A. Moreover, the purification technique for cyanobacteria described in this study is potentially applicable to a wider range of unicellular cyanobacteria.}, }
@article {pmid33256601, year = {2020}, author = {Wagner, E and Zaiser, A and Leitner, R and Quijada, NM and Pracser, N and Pietzka, A and Ruppitsch, W and Schmitz-Esser, S and Wagner, M and Rychli, K}, title = {Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {847}, pmid = {33256601}, issn = {1471-2164}, support = {P 27920/FWF_/Austrian Science Fund FWF/Austria ; P27920-B22//Austrian Science Fund/ ; n.a.//Bundesministerium f&#xfc;r Verkehr, Innovation und Technologie/ ; }, mesh = {Bacterial Proteins ; Caco-2 Cells ; Food Microbiology ; Genomics ; Humans ; *Listeria monocytogenes/genetics ; *Listeriosis ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Listeria (L.) monocytogenes strains show a high diversity regarding stress tolerance and virulence potential. Genome studies have mainly focused on specific sequence types (STs) predominantly associated with either food or human listeriosis. This study focused on the prevalent ST155, showing equal distribution among clinical and food isolates. We evaluated the virulence potential of 20 ST155 strains and performed comparative genomic analysis of 130 ST155 strains isolated from food, food processing environments and human listeriosis cases in different countries and years.<br><br>RESULTS: The in vitro virulence assays using human intestinal epithelial Caco2 and hepatocytic HEPG2 cells showed an impaired virulence phenotype for six of the 20 selected ST155 strains. Genome analysis revealed no distinct clustering of strains from the same source category (food, food processing environment, and clinical isolates). All strains harbored an intact inlA and inlB locus, except four strains, which had an internal deletion in the inlA gene. All strains harbored LIPI-1, but prfA was present in a longer variant in six strains, all showing impaired virulence. The longer PrfA variant resulted in lower expression of inlA, inlB, and prfA, and no expression of hly and actA. Regarding stress-related gene content, SSI-1 was present, whereas qacH was absent in all strains. 34.6% of the strains harbored a plasmid. All but one ST155 plasmids showed high conservation and harbored cadA2, bcrABC, and a triphenylmethane reductase.<br><br>CONCLUSIONS: This study contributes to an enhanced understanding of L. monocytogenes ST155 strains, being equally distributed among isolates from humans, food, and food processing environments. The conservation of the present genetic traits and the absence of unique inherent genetic features makes these types of STs especially interesting since they are apparently equally adapted to the conditions in food processing environments,&#xa0;as well as in food as to the human host environment. However, a ST155-specific mutation resulting in a longer PrfA variant impaired the virulence potential of several ST155 strains.}, }
@article {pmid33254950, year = {2021}, author = {Del Olmo, G and Husband, S and Sánchez Briones, C and Soriano, A and Calero Preciado, C and Macian, J and Douterelo, I}, title = {The microbial ecology of a Mediterranean chlorinated drinking water distribution systems in the city of Valencia (Spain).}, journal = {The Science of the total environment}, volume = {754}, number = {}, pages = {142016}, doi = {10.1016/j.scitotenv.2020.142016}, pmid = {33254950}, issn = {1879-1026}, mesh = {Animals ; Biofilms ; *Cyprinodontiformes ; *Drinking Water ; *Mycobiome ; Spain ; Water Microbiology ; Water Quality ; Water Supply ; }, abstract = {Drinking water distribution systems host extensive microbiomes with diverse biofilm communities regardless of treatment, disinfection, or operational practices. In Mediterranean countries higher temperatures can accelerate reactions and microbial growth that may increase aesthetic water quality issues, particularly where material deposits can develop as a result of net zero flows within looped urban networks. This study investigated the use of flow and turbidity monitoring to hydraulically manage mobilisation of pipe wall biofilms and associated material from the Mediterranean city of Valencia (Spain). Pipe sections of different properties were subjected to controlled incremental flushing with monitoring and sample collection for physico-chemical and DNA analysis with Illumina sequencing of bacterial and fungal communities. A core microbial community was detected throughout the network with microorganisms like Pseudomonas, Aspergillus or Alternaria increasing during flushing, indicating greater abundance in underlying and more consolidated material layers. Bacterial and fungal communities were found to be highly correlated, with bacteria more diverse and dynamic during flushing whilst fungi were more dominant and less variable between sampling sites. Results highlight that water quality management can be achieved through hydraulic strategies yet understanding community dynamics, including the fungal component, will be key to maintaining safe and ultimately beneficial microbiomes in drinking water distribution systems.}, }
@article {pmid33254908, year = {2021}, author = {Dong, J and Hunt, J and Delhaize, E and Zheng, SJ and Jin, CW and Tang, C}, title = {Impacts of elevated CO2 on plant resistance to nutrient deficiency and toxic ions via root exudates: A review.}, journal = {The Science of the total environment}, volume = {754}, number = {}, pages = {142434}, doi = {10.1016/j.scitotenv.2020.142434}, pmid = {33254908}, issn = {1879-1026}, mesh = {Biological Transport ; Biomass ; *Carbon Dioxide/toxicity ; Ions ; *Nutrients ; Plant Exudates ; Plant Roots ; }, abstract = {Elevated atmospheric CO2 (eCO2) concentration can increase root exudation into soils, which improves plant tolerance to abiotic stresses. This review used a meta-analysis to assess effect sizes of eCO2 on both efflux rates and total amounts of some specific root exudates, and dissected whether eCO2 enhances plant's resistance to nutrient deficiency and ion toxicity via root exudates. Elevated CO2 did not affect efflux rates of total dissolved organic carbon, a measure of combined root exudates per unit of root biomass or length, but increased the efflux amount of root systems per plant by 31% which is likely attributed to increased root biomass (29%). Elevated CO2 increased efflux rates of soluble-sugars, carboxylates, and citrate by 47%, 111%, and 16%, respectively, but did not affect those of amino acids and malate. The increased carbon allocation to roots, increased plant requirements of mineral nutrients, and heightened detoxification responses to toxic ions under eCO2 collectively contribute to the increased efflux rates despite lacking molecular evidence. The increased efflux rates of root exudates under eCO2 were closely associated with improved nutrient uptake whilst less studies have validated the associations between root exudates and resistance to toxic ions of plants when grown under eCO2. Future studies are required to reveal how climate change (eCO2) affect the efflux of specific root exudates, particularly organic anions, the corresponding nutrient uptake and toxic ion resistance from plant molecular biology and soil microbial ecology perspectives.}, }
@article {pmid33254807, year = {2021}, author = {Yuan, W and Zhang, Y and Riaz, L and Yang, Q and Du, B and Wang, R}, title = {Multiple antibiotic resistance and DNA methylation in Enterobacteriaceae isolates from different environments.}, journal = {Journal of hazardous materials}, volume = {402}, number = {}, pages = {123822}, doi = {10.1016/j.jhazmat.2020.123822}, pmid = {33254807}, issn = {1873-3336}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *DNA Methylation ; Drug Resistance, Microbial ; *Enterobacteriaceae/genetics ; Humans ; Integrons ; Microbial Sensitivity Tests ; beta-Lactamases/genetics ; }, abstract = {Antibiotic resistant bacteria with diverse resistance phenotypes and genotypes are ubiquitous in the environments that have become a global health concern. The role of DNA methylation in the dissemination of antibiotic resistance among different environments is currently unclear. We recovered 646 Enterobacteriaceae (Eb) isolates from hospital, livestock manure, municipal wastewater-treatment plants, river sediment and soil for comprehensive analysis of resistance phenotypes, β-lactamase genes, integrons, integron-associated gene cassettes and the levels of DNA methylation. Antibiotic susceptibility testing revealed that approximately 87.31 % isolates were multidrug resistant Eb. The β-lactamase genes were positively detected in 473 isolates with greater diversity in human or animal sourced Eb, while its prevalence was found to be highest in the Eb isolates from the natural environments. Forty-three gene cassettes (28 different types mediated by intI1) were detected in 53 (19.63 %) isolates, with greater diversity in Eb isolates from hospital and livestock manure. The multiple antibiotic resistance index of single strain was positively correlated with the 5-methylcytosine and showed a negative correlation with 6-methylademine. We conclude that the development of antibiotic resistance could possibly be coupled with DNA methylation, which might enhance the antimicrobial resistance and survival capacity of Eb.}, }
@article {pmid33254460, year = {2021}, author = {Ghysels, S and Buffel, S and Rabaey, K and Ronsse, F and Ganigué, R}, title = {Biochar and activated carbon enhance ethanol conversion and selectivity to caproic acid by Clostridium kluyveri.}, journal = {Bioresource technology}, volume = {319}, number = {}, pages = {124236}, doi = {10.1016/j.biortech.2020.124236}, pmid = {33254460}, issn = {1873-2976}, mesh = {Caproates ; Charcoal ; *Clostridium kluyveri ; Ethanol ; }, abstract = {Syngas from biomass or steel mills can be fermented into a dilute stream of ethanol and acetic acid, which requires energy intensive distillation for product recovery. This can be circumvented by selective secondary fermentation of the syngas fermentation effluent to caproic acid as easier recoverable platform chemical with Clostridium kluyveri. Here, we explore the impact of biochar and activated carbon on this process. Changes during the fermentation with biochar or activated carbon were monitored, different doses were tested and the recyclability of biochar and activated carbon was assessed. Biochar decreased the lag phase and increased the caproic acid production rate (up to 0.50 g·L[-1]·h[-1]). Upon recycling for subsequent fermentation, biochar retained this property largely. Activated carbon addition, especially at high dose, could potentially increase the conversion and selectivity towards caproic acid to 14.15 g·L[-1] (control: 11.01 g·L[-1]) and 92% (control: 84%), respectively.}, }
@article {pmid33253458, year = {2021}, author = {Ndhlovu, A and Durand, PM and Ramsey, G}, title = {Programmed cell death as a black queen in microbial communities.}, journal = {Molecular ecology}, volume = {30}, number = {5}, pages = {1110-1119}, doi = {10.1111/mec.15757}, pmid = {33253458}, issn = {1365-294X}, mesh = {*Apoptosis ; *Microbiota/genetics ; }, abstract = {Programmed cell death (PCD) in unicellular organisms is in some instances an altruistic trait. When the beneficiaries are clones or close kin, kin selection theory may be used to explain the evolution of the trait, and when the trait evolves in groups of distantly related individuals, group or multilevel selection theory is invoked. In mixed microbial communities, the benefits are also available to unrelated taxa. But the evolutionary ecology of PCD in communities is poorly understood. Few hypotheses have been offered concerning the community role of PCD despite its far-reaching effects. The hypothesis we consider here is that PCD is a black queen. The Black Queen Hypothesis (BQH) outlines how public goods arising from a leaky function are exploited by other taxa in the community. Black Queen (BQ) traits are essential for community survival, but only some members bear the cost of possessing them, while others lose the trait In addition, BQ traits have been defined in terms of adaptive gene loss, and it is unknown whether this has occurred for PCD. Our conclusion is that PCD fulfils the two most important criteria of a BQ (leakiness and costliness), but that more empirical data are needed for assessing the remaining two criteria. In addition, we hold that for viewing PCD as a BQ, the original BQH needs to include social traits. Thus, despite some empirical and conceptual shortcomings, the BQH provides a helpful avenue for investigating PCD in microbial communities.}, }
@article {pmid33252774, year = {2021}, author = {Lee, JC and Whang, KS}, title = {Altererythrobacter segetis sp. nov., Isolated from Farmland Soil.}, journal = {Current microbiology}, volume = {78}, number = {1}, pages = {389-396}, pmid = {33252774}, issn = {1432-0991}, mesh = {Alphaproteobacteria ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Farms ; Fatty Acids ; Phospholipids ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; *Soil ; *Soil Microbiology ; }, abstract = {A Gram-stain-negative bacterium, designated YJ20[T], was isolated from rhizosphere soil of a spinach farmland at Shinan in Korea. Strain YJ20[T] was found to be aerobic, non-motile rods which can grow at 10-33 °C (optimum, 28 °C), at pH 6.5-8.5 (optimum, pH 6.5-7.5) and in the absence of NaCl. The 16S rRNA gene sequence analysis showed that strain YJ20[T] belongs to the genus Altererythrobacter with moderate sequence similarities to Altererythrobacter dongtanensis KCTC 22672[T] (96.8%), Altererythrobacter soli MN-1[T] (96.6%) and Altererythrobacter xinjiangensis S3-63[T] (96.5%). The phylogenomic analysis based on the whole-genome sequence demonstrated that strain YJ20[T] formed a distinct phyletic line with Altererythrobacter soli MN-1[T] and Altererythrobacter salegens XY-R17[T] showing average nucleotide identity (ANI) values of 79.4 and 77.5%, respectively. The predominant ubiquinone was identified as Q-10, and the major fatty acids were C17:1 ω6c, C18:1 ω7c and C15:0 2-OH. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidycholin, sphingoglycolipid, an unidentified glycolipid, an unidentified phospholipid and an unidentified lipid. The G+C content of the genome was determined to be 66.3 mol%. On the basis of phenotypic, chemotaxonomic properties and phylogenetic and phylogenomic analyses in this study, strain YJ20[T] is considered to represent a novel species in the genus Altererythrobacter, for which the name Altererythrobacter segetis sp. nov. is proposed. The type strain is YJ20[T] (= KACC 19554[T] = NBRC 113199[T]).}, }
@article {pmid33252655, year = {2020}, author = {Weißbecker, C and Schnabel, B and Heintz-Buschart, A}, title = {Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology.}, journal = {GigaScience}, volume = {9}, number = {12}, pages = {}, pmid = {33252655}, issn = {2047-217X}, mesh = {High-Throughput Nucleotide Sequencing ; *Microbiota ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Software ; }, abstract = {BACKGROUND: Amplicon sequencing of phylogenetic marker genes, e.g., 16S, 18S, or ITS ribosomal RNA sequences, is still the most commonly used method to determine the composition of microbial communities. Microbial ecologists often have expert knowledge on their biological question and data analysis in general, and most research institutes have computational infrastructures to use the bioinformatics command line tools and workflows for amplicon sequencing analysis, but requirements of bioinformatics skills often limit the efficient and up-to-date use of computational resources.<br><br>RESULTS: We present dadasnake, a user-friendly, 1-command Snakemake pipeline that wraps the preprocessing of sequencing reads and the delineation of exact sequence variants by using the favorably benchmarked and widely used DADA2 algorithm with a taxonomic classification and the post-processing of the resultant tables, including hand-off in standard formats. The suitability of the provided default configurations is demonstrated using mock community data from bacteria and archaea, as well as fungi.<br><br>CONCLUSIONS: By use of Snakemake, dadasnake makes efficient use of high-performance computing infrastructures. Easy user configuration guarantees flexibility of all steps, including the processing of data from multiple sequencing platforms. It is easy to install dadasnake via conda environments. dadasnake is available at https://github.com/a-h-b/dadasnake.}, }
@article {pmid33250870, year = {2020}, author = {Miclotte, L and De Paepe, K and Rymenans, L and Callewaert, C and Raes, J and Rajkovic, A and Van Camp, J and Van de Wiele, T}, title = {Dietary Emulsifiers Alter Composition and Activity of the Human Gut Microbiota in vitro, Irrespective of Chemical or Natural Emulsifier Origin.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {577474}, pmid = {33250870}, issn = {1664-302X}, abstract = {The use of additives in food products has become an important public health concern. In recent reports, dietary emulsifiers have been shown to affect the gut microbiota, contributing to a pro-inflammatory phenotype and metabolic syndrome. So far, it is not yet known whether similar microbiome shifts are observable for a more diverse set of emulsifier types and to what extent these effects vary with the unique features of an individual's microbiome. To bridge this gap, we investigated the effect of five dietary emulsifiers on the fecal microbiota from 10 human individuals upon a 48 h exposure. Community structure was assessed with quantitative microbial profiling, functionality was evaluated by measuring fermentation metabolites, and pro-inflammatory properties were assessed with the phylogenetic prediction algorithm PICRUSt, together with a TLR5 reporter cell assay for flagellin. A comparison was made between two mainstream chemical emulsifiers (carboxymethylcellulose and P80), a natural extract (soy lecithin), and biotechnological emulsifiers (sophorolipids and rhamnolipids). While fecal microbiota responded in a donor-dependent manner to the different emulsifiers, profound differences between emulsifiers were observed. Rhamnolipids, sophorolipids, and soy lecithin eliminated 91 ± 0, 89 ± 1, and 87 ± 1% of the viable bacterial population after 48 h, yet they all selectively increased the proportional abundance of putative pathogens. Moreover, profound shifts in butyrate (-96 ± 6, -73 ± 24, and -34 ± 25%) and propionate (+13 ± 24, +88 ± 50, and +29 ± 16%) production were observed for these emulsifiers. Phylogenetic prediction indicated higher motility, which was, however, not confirmed by increased flagellin levels using the TLR5 reporter cell assay. We conclude that dietary emulsifiers can severely impact the gut microbiota, and this seems to be proportional to their emulsifying strength, rather than emulsifier type or origin. As biotechnological emulsifiers were especially more impactful than chemical emulsifiers, caution is warranted when considering them as more natural alternatives for clean label strategies.}, }
@article {pmid33250307, year = {2021}, author = {Ostermeyer, P and Bonin, L and Folens, K and Verbruggen, F and García-Timermans, C and Verbeken, K and Rabaey, K and Hennebel, T}, title = {Effect of speciation and composition on the kinetics and precipitation of arsenic sulfide from industrial metallurgical wastewater.}, journal = {Journal of hazardous materials}, volume = {409}, number = {}, pages = {124418}, doi = {10.1016/j.jhazmat.2020.124418}, pmid = {33250307}, issn = {1873-3336}, abstract = {Precipitation of arsenic as As2S3 produces little waste sludge, has the potential for low chemical consumption and for selective metal(loid) removal. In this study, arsenic removal from acidic (pH 2), metallurgical wastewater was tested in industrially relevant conditions. Sulfides added at a S:As molar ratio of 2.5 and 5 resulted in removal of 99% and 84% of As(III) and As(V). Precipitation of As2S3 from the As(III) and industrial wastewater containing 17% As(V) was nearly instantaneous. For the synthetic As(V) solution, reduction to As(III) was the rate limiting step. At a S:As ratio of 20 and an observed removal rate (k2 = 4.8 (mol L[-1]) h[-1]), two hours were required to remove of 93% of arsenic from a 1 g As L[-1] solution. In the case of As(V) in industrial samples this time lag was not observed, showing that components in the industrial wastewater affected the removal and reduction of arsenate. Speciation also affected flocculation and coagulation characteristics of As2S3 particles: As(V) reduction resulted in poor coagulation and flocculation. Selective precipitation of arsenic was possible, but depended on speciation, S:As ratio and other metals present.}, }
@article {pmid33247364, year = {2021}, author = {Burtseva, O and Baulina, O and Zaytseva, A and Fedorenko, T and Chekanov, K and Lobakova, E}, title = {In vitro Biofilm Formation by Bioluminescent Bacteria Isolated from the Marine Fish Gut.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {932-940}, pmid = {33247364}, issn = {1432-184X}, mesh = {Animals ; Bacteria/genetics ; *Biofilms ; *Enterobacteriaceae ; Fimbriae, Bacterial ; }, abstract = {The internal surface of the animal gastrointestinal tract is covered by microbial biofilms. They play an important role in the development and functioning of the host organism and protect it against pathogens. Microbial communities of gastrointestinal biofilms are less elucidated than luminal microbiota. Therefore, the studies of biofilm formation by gastrointestinal microorganisms are a topical issue. For the first time, we report the formation of a biofilm in vitro by the strains of bioluminescent bacteria isolated from the intestines of marine fish. These bacteria exhibit co-aggregation and tend to attach to solid surfaces. The attachment of cells is accompanied by appearance of the pili. Then, we observed the formation of microcolonies and the production of extracellular polymer substances (EPSs) connecting bacterial cells into an integrated system. The presence of acidic polysaccharides is shown in the EPS when using the ruthenium red staining. Acidic polysaccharides in this matrix is a biochemical evidence of microbial biofilms. On the fibers of the polymer matrix, these bacteria form the "mushroom body"-type structures. Matured biofilms exhibit a specific three-dimensional architecture with pores and channels formed by cells and EPS. We also demonstrated the formation of a biofilm by binary culture of the luminous enterobacterium Kosakonia cowanii and a Gram-positive Macrococcus sp. The data obtained help to understand the role of these bacteria in the intestines of fish. They lead to a new study in the field of investigation of the intestinal microbiome of fish.}, }
@article {pmid33244619, year = {2021}, author = {Mathai, PP and Bertram, JH and Padhi, SK and Singh, V and Tolo, IE and Primus, A and Mor, SK and Phelps, NBD and Sadowsky, MJ}, title = {Influence of Environmental Stressors on the Microbiota of Zebra Mussels (Dreissena polymorpha).}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {1042-1053}, pmid = {33244619}, issn = {1432-184X}, support = {Minnesota Agricultural Experiment Station.//Minnesota Agricultural Experiment Station./ ; }, mesh = {Animals ; *Bivalvia ; *Dreissena ; Lakes ; *Microbiota ; Temperature ; }, abstract = {Host-associated microbiota play a critical role in host fitness by providing nutrition, enhancing digestion capabilities, and by providing protection from pathogens. Here, we investigated the effects of two environmental stressors, temperature, and salinity, on the microbiota associated with zebra mussels (ZMs), a highly invasive bivalve in North America. To examine this in detail, lake-collected ZMs were acclimated to laboratory conditions, and subjected to temperature and salinity stress conditions. The impact of these stressors on the diversity, composition, and dynamics of ZM-associated microbiota were assessed by using amplicon- and shotgun-based sequencing, and qPCR-based approaches. Elevated temperature was found to be the primary driver of ZM mortality, although salinity alone also increased its likelihood. Stressor-induced ZM mortality, which ranged between 53 and 100%, was concomitant with significant increases in the relative abundance of several genera of putative opportunistic pathogens including Aeromonas. These genera were only present in low relative abundance in ZMs obtained from the control tank with 0% mortality. Shotgun sequencing and qPCR analyses indicated that the relative and absolute abundances of pathogenic Aeromonas species (particularly A. veronii) were significantly greater in temperature-induced dead ZMs. Taken together, our results show that environmental stress, especially elevated temperature (> 25 °C), is associated with the rapid mortality of ZMs as well as the proliferation of putative opportunistic bacterial pathogens.}, }
@article {pmid33244064, year = {2020}, author = {Shilts, MH and Rosas-Salazar, C and Lynch, CE and Tovchigrechko, A and Boone, HH and Russell, PB and Connolly, AS and Costello, KM and McCollum, MD and Mai, A and Wiggins, DA and Rajagopala, SV and Yooseph, S and Peebles, RS and Hartert, TV and Das, SR}, title = {Evaluation of the upper airway microbiome and immune response with nasal epithelial lining fluid absorption and nasal washes.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {20618}, pmid = {33244064}, issn = {2045-2322}, support = {K24AI77930//National Institute of Allergy and Infectious Diseases/International ; HHSN272200900007C/AI/NIAID NIH HHS/United States ; K12HD087023//Eunice Kennedy Shriver National Institute of Child Health and Human Development/International ; U19AI095227//NIAID, NIH/International ; U2CDK059637/DK/NIDDK NIH HHS/United States ; P30DK020593/DK/NIDDK NIH HHS/United States ; R21 AI149262/AI/NIAID NIH HHS/United States ; R21 AI154016/AI/NIAID NIH HHS/United States ; U19 AI110819/AI/NIAID NIH HHS/United States ; UL1 TR000445/TR/NCATS NIH HHS/United States ; UL1 RR024975/RR/NCRR NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; P30 EY008126/EY/NEI NIH HHS/United States ; G20 RR030956/RR/NCRR NIH HHS/United States ; }, mesh = {Adult ; Child ; Female ; Humans ; Immunity/genetics/immunology ; Male ; Metagenome/genetics/immunology ; Microbiota/*genetics/*immunology ; Nasal Absorption/immunology ; Nasal Cavity/immunology/microbiology ; Nasal Lavage Fluid/*immunology/*microbiology ; Nose/*immunology/*microbiology ; RNA, Ribosomal, 16S/genetics/immunology ; Specimen Handling/methods ; }, abstract = {Despite being commonly used to collect upper airway epithelial lining fluid, nasal washes are poorly reproducible, not suitable for serial sampling, and limited by a dilution effect. In contrast, nasal filters lack these limitations and are an attractive alternative. To examine whether nasal filters are superior to nasal washes as a sampling method for the characterization of the upper airway microbiome and immune response, we collected paired nasal filters and washes from a group of 40 healthy children and adults. To characterize the upper airway microbiome, we used 16S ribosomal RNA and shotgun metagenomic sequencing. To characterize the immune response, we measured total protein using a BCA assay and 53 immune mediators using multiplex magnetic bead-based assays. We conducted statistical analyses to compare common microbial ecology indices and immune-mediator median fluorescence intensities (MFIs) between sample types. In general, nasal filters were more likely to pass quality control in both children and adults. There were no significant differences in microbiome community richness, α-diversity, or structure between pediatric samples types; however, these were all highly dissimilar between adult sample types. In addition, there were significant differences in the abundance of amplicon sequence variants between sample types in children and adults. In adults, total proteins were significantly higher in nasal filters than nasal washes; consequently, the immune-mediator MFIs were not well detected in nasal washes. Based on better quality control sequencing metrics and higher immunoassay sensitivity, our results suggest that nasal filters are a superior sampling method to characterize the upper airway microbiome and immune response in both children and adults.}, }
@article {pmid33243511, year = {2021}, author = {Xu, M and Wang, F and Sheng, H and Stedtfeld, RD and Li, Z and Hashsham, SA and Jiang, X and Tiedje, JM}, title = {Does anaerobic condition play a more positive role in dissipation of antibiotic resistance genes in soil?.}, journal = {The Science of the total environment}, volume = {757}, number = {}, pages = {143737}, doi = {10.1016/j.scitotenv.2020.143737}, pmid = {33243511}, issn = {1879-1026}, mesh = {Anaerobiosis ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Soil ; Soil Microbiology ; }, abstract = {The persistence of antibiotic resistance genes (ARGs) under the aerobic vs. anaerobic conditions is unknown, especially under different fertilization. Towards this goal, a microcosm experiment was carried out with chemical fertilized and manured soil under aerobic and anaerobic conditions. High throughput qPCR was used to analyze ARGs with 144 primer sets and sequencing for microorganisms. Completely different dynamics of ARGs were observed in soil under aerobic and anaerobic conditions, regardless of the fertilization type. ARGs had different half-lives, even though they confer resistance to the same type of antibiotics. Aminoglycoside, chloramphenicol, macrolide - lincosamide - streptogramin B (MLSB) and tetracycline resistance genes were significantly accumulated in the aerobic soils. Anaerobic soil possessed a higher harboring capacity for exogenous microorganisms and ARGs than aerobic soil. The interaction between ARGs and mobile genetic elements (MGEs) in manured soil under aerobic condition was more pronounced than the anaerobic condition. These findings unveil that anaerobic soil could play a more positive role in reducing potential risk of ARGs in the farmland environment.}, }
@article {pmid33242583, year = {2021}, author = {Garrido-Benavent, I and Pérez-Ortega, S and de Los Ríos, A and Mayrhofer, H and Fernández-Mendoza, F}, title = {Neogene speciation and Pleistocene expansion of the genus Pseudephebe (Parmeliaceae, lichenized fungi) involving multiple colonizations of Antarctica.}, journal = {Molecular phylogenetics and evolution}, volume = {155}, number = {}, pages = {107020}, doi = {10.1016/j.ympev.2020.107020}, pmid = {33242583}, issn = {1095-9513}, mesh = {Antarctic Regions ; Ecosystem ; *Genetic Speciation ; Haplotypes/genetics ; Lichens/*classification ; Parmeliaceae/*classification ; Phylogeny ; Phylogeography ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Species Specificity ; Time Factors ; }, abstract = {Widespread geographic distributions in lichens have been usually explained by the high dispersal capacity of their tiny diaspores. However, recent phylogenetic surveys have challenged this assumption and provided compelling evidence for cryptic speciation and more restricted distribution ranges in diverse lineages of lichen-forming fungi. To evaluate these scenarios, we focus on the fungal genus Pseudephebe (Parmeliaceae) which includes amphitropical species, a distribution pattern whose origin has been a matter of debate since first recognized in the nineteenth century. In our study, a six-locus dataset and a broad specimen sampling covering almost all Earth's continents is used to investigate species delimitation in Pseudephebe. Population structure, gene flow and dating analyses, as well as genealogical reconstruction methods, are employed to disentangle the most plausible transcontinental migration routes, and estimate the timing of the origin of the amphitropical distribution and the Antarctic populations. Our results demonstrate the existence of three partly admixed phylogenetic species that diverged between the Miocene and Pliocene, and whose Quaternary distribution has been strongly driven by glacial cycles. Pseudephebe minuscula is the only species showing an amphitropical distribution, with populations in Antarctica, whereas the restricted distribution of P. pubescens and an undescribed Alaskan species might reflect the survival of these species in European and North American refugia. Our microevolutionary analyses suggest a Northern Hemisphere origin for P. minuscula, which could have dispersed into the Southern Hemisphere directly and/or through "mountain-hopping" during the Pleistocene. The Antarctic populations of this species are sorted into two genetic clusters: populations of the Antarctic Peninsula were grouped together with South American ones, and the Antarctic Continental populations formed a second cluster with Bolivian and Svalbard populations. Therefore, our data strongly suggest that the current distribution of P. minuscula in Antarctica is the outcome of multiple, recent colonizations. In conclusion, our results stress the need for integrating species delimitation and population analyses to properly approach historical biogeography in lichen-forming fungi.}, }
@article {pmid33242086, year = {2021}, author = {Yue, L and Kong, W and Li, C and Zhu, G and Zhu, L and Makhalanyane, TP and Cowan, DA}, title = {Dissolved inorganic carbon determines the abundance of microbial primary producers and primary production in Tibetan Plateau lakes.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {2}, pages = {}, doi = {10.1093/femsec/fiaa242}, pmid = {33242086}, issn = {1574-6941}, mesh = {*Carbon ; Ecosystem ; *Lakes ; Salinity ; Tibet ; }, abstract = {Climate change globally accelerates the shrinkage of inland lakes, resulting in increases in both water salinity and dissolved inorganic carbon (DIC). The increases of salinity and DIC generate contrasting effects on microbial primary producers and primary production, however, their combined effects remain unclear in aquatic ecosystems. We hypothesized that increased DIC mitigates the constraints of enhanced salinity on microbial primary producers and primary production. To test this, we employed isotope labeling and molecular methods to explore primary production and four dominant types of microbial primary producers (form IA, IB, IC and ID) in lakes on the Tibetan Plateau. Results showed that DIC was positively correlated with the abundance of the form IAB and ID microbial primary producers and primary production (all P < 0.001) and offset salinity constraints. Structural equation models elucidated that DIC substantially enhanced primary production by stimulating the abundance of form ID microbial primary producers. The abundance of form ID primary producers explained more variations (14.6%) of primary production than form IAB (6%) and physicochemical factors (6.8%). Diatoms (form ID) played a determinant role in primary production in the lakes by adapting to high DIC and high salinity. Our findings suggest that inland lakes may support higher primary productivity in future climate change scenarios.}, }
@article {pmid33242082, year = {2020}, author = {Stahl, LM and Olson, JB}, title = {Environmental abiotic and biotic factors affecting the distribution and abundance of Naegleria fowleri.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {1}, pages = {}, pmid = {33242082}, issn = {1574-6941}, mesh = {*Amoeba ; *Central Nervous System Protozoal Infections ; Fresh Water ; Humans ; *Naegleria fowleri ; Water ; }, abstract = {Naegleria fowleri is a free-living protozoan that resides in soil and freshwater. Human intranasal amoebae exposure through water or potentially dust particles can culminate in primary amoebic meningoencephalitis, which generally causes death. While many questions remain regarding pathogenesis, the microbial ecology of N. fowleri is even less understood. This review outlines current knowledge of the environmental abiotic and biotic factors that affect the distribution and abundance of N. fowleri. Although the impacts of some abiotic factors remain poorly investigated or inconclusive, N. fowleri appears to have a wide pH range, low salinity tolerance and thermophilic preference. From what is known about biotic factors, the amoebae preferentially feed upon bacteria and are preyed upon by other free-living amoebae. Additional laboratory and environmental studies are needed to fill in knowledge gaps, which are crucial for surveillance and management of N. fowleri in freshwaters. As surface water temperatures increase with climate change, it is likely that this amoeba will pose a greater threat to human health, suggesting that identifying its abiotic and biotic preferences is critical to mitigating this risk.}, }
@article {pmid33240229, year = {2020}, author = {Shaw, C and Brooke, C and Hawley, E and Connolly, MP and Garcia, JA and Harmon-Smith, M and Shapiro, N and Barton, M and Tringe, SG and Glavina Del Rio, T and Culley, DE and Castenholz, R and Hess, M}, title = {Phototrophic Co-cultures From Extreme Environments: Community Structure and Potential Value for Fundamental and Applied Research.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {572131}, pmid = {33240229}, issn = {1664-302X}, abstract = {Cyanobacteria are found in most illuminated environments and are key players in global carbon and nitrogen cycling. Although significant efforts have been made to advance our understanding of this important phylum, still little is known about how members of the cyanobacteria affect and respond to changes in complex biological systems. This lack of knowledge is in part due to our dependence on pure cultures when determining the metabolism and function of a microorganism. We took advantage of the Culture Collection of Microorganisms from Extreme Environments (CCMEE), a collection of more than 1,000 publicly available photosynthetic co-cultures maintained at the Pacific Northwest National Laboratory, and assessed via 16S rRNA amplicon sequencing if samples readily available from public culture collection could be used in the future to generate new insights into the role of microbial communities in global and local carbon and nitrogen cycling. Results from this work support the existing notion that culture depositories in general hold the potential to advance fundamental and applied research. Although it remains to be seen if co-cultures can be used at large scale to infer roles of individual organisms, samples that are publicly available from existing co-cultures depositories, such as the CCMEE, might be an economical starting point for such studies. Access to archived biological samples, without the need for costly field work, might in some circumstances be one of the few remaining ways to advance the field and to generate new insights into the biology of ecosystems that are not easily accessible. The current COVID-19 pandemic, which makes sampling expeditions almost impossible without putting the health of the participating scientists on the line, is a very timely example.}, }
@article {pmid33239370, year = {2020}, author = {Props, R and Monsieurs, P and Vandamme, P and Leys, N and Denef, VJ and Boon, N}, title = {Correction for Props et al., "Gene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic Conditions".}, journal = {mSphere}, volume = {5}, number = {6}, pages = {}, doi = {10.1128/mSphere.01143-20}, pmid = {33239370}, issn = {2379-5042}, }
@article {pmid33238123, year = {2020}, author = {Zhang, H and Madi, A and Yosef, N and Chihara, N and Awasthi, A and Pot, C and Lambden, C and Srivastava, A and Burkett, PR and Nyman, J and Christian, E and Etminan, Y and Lee, A and Stroh, H and Xia, J and Karwacz, K and Thakore, PI and Acharya, N and Schnell, A and Wang, C and Apetoh, L and Rozenblatt-Rosen, O and Anderson, AC and Regev, A and Kuchroo, VK}, title = {An IL-27-Driven Transcriptional Network Identifies Regulators of IL-10 Expression across T Helper Cell Subsets.}, journal = {Cell reports}, volume = {33}, number = {8}, pages = {108433}, pmid = {33238123}, issn = {2211-1247}, support = {677251/ERC_/European Research Council/International ; U19 AI133524/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Gene Regulatory Networks/*genetics ; Humans ; Interleukin-10/*metabolism ; Interleukin-27/*metabolism ; Mice ; Mice, Knockout ; Th1 Cells/*metabolism ; }, abstract = {Interleukin-27 (IL-27) is an immunoregulatory cytokine that suppresses inflammation through multiple mechanisms, including induction of IL-10, but the transcriptional network mediating its diverse functions remains unclear. Combining temporal RNA profiling with computational algorithms, we predict 79 transcription factors induced by IL-27 in T cells. We validate 11 known and discover 5 positive (Cebpb, Fosl2, Tbx21, Hlx, and Atf3) and 2 negative (Irf9 and Irf8) Il10 regulators, generating an experimentally refined regulatory network for Il10. We report two central regulators, Prdm1 and Maf, that cooperatively drive the expression of signature genes induced by IL-27 in type 1 regulatory T cells, mediate IL-10 expression in all T helper cells, and determine the regulatory phenotype of colonic Foxp3[+] regulatory T cells. Prdm1/Maf double-knockout mice develop spontaneous colitis, phenocopying ll10-deficient mice. Our work provides insights into IL-27-driven transcriptional networks and identifies two shared Il10 regulators that orchestrate immunoregulatory programs across T helper cell subsets.}, }
@article {pmid33237956, year = {2020}, author = {Buranarom, N and Komin, O and Matangkasombut, O}, title = {Hyposalivation, oral health, and Candida colonization in independent dentate elders.}, journal = {PloS one}, volume = {15}, number = {11}, pages = {e0242832}, pmid = {33237956}, issn = {1932-6203}, mesh = {Aged ; Candida albicans/pathogenicity ; Candidiasis, Oral/epidemiology/*microbiology/pathology/prevention &amp; control ; Dental Prosthesis/*microbiology ; Female ; Humans ; Male ; Middle Aged ; Mouth/*microbiology ; Mouth, Edentulous/epidemiology/*microbiology/pathology ; Oral Health ; Risk Factors ; Saliva/microbiology ; Secretory Rate ; Xerostomia/epidemiology/microbiology/pathology ; }, abstract = {Hyposalivation is an important problem in elders and could interfere with several oral functions and microbial ecology. While the number of independent elders who retain more natural teeth increases worldwide, few studies examined hyposalivation in this population. Thus, this study aims to examine relationships between hyposalivation, oral health conditions and oral Candida colonization in independent dentate elders and evaluate factors associated with salivary flow and Candida carriage. We conducted a cross-sectional study in fifty-three dentate elders (≥65 years old with at least 4 pairs of posterior occlusal contacts) with no, or well-controlled, systemic conditions. Participants were interviewed for medical history, subjective dry mouth symptoms, oral hygiene practices and denture information. Unstimulated and stimulated salivary flow rates, objective dry mouth signs, gingival, tongue-coating, and root-caries indices were recorded. Stimulated saliva was cultured on Sabouraud-dextrose agar for Candida counts. Candida species were identified using chromogenic Candida agar and polymerase chain reaction. Statistical significance level was set at p<0.05. The results showed that hyposalivation was associated with higher gingival and tongue-coating indices (p = 0.003 and 0.015, respectively), but not root-caries index. Hyposalivation was also associated with higher prevalence of oral Candida colonization (p = 0.010; adjusted OR = 4.36, 95% confidence interval = 1.29-14.72). These two indices and Candida load were negatively correlated with unstimulated and stimulated salivary flow rates. Interestingly, non-albicans Candida species were more prevalent in denture wearers (p = 0.017). Hence, hyposalivation is a risk factor for poorer oral health and oral Candida colonization in independent dentate elders. Because of its potential adverse effects on oral and systemic health, hyposalivation should be carefully monitored in elders.}, }
@article {pmid33236218, year = {2021}, author = {Saxena, S and Strobel, GA}, title = {Marvellous Muscodor spp.: Update on Their Biology and Applications.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {5-20}, pmid = {33236218}, issn = {1432-184X}, mesh = {Ascomycota ; Biology ; Endophytes ; Humans ; *Volatile Organic Compounds ; *Xylariales ; }, abstract = {Nearly 20 years ago, the first report appeared on the discovery of a novel genus-Muscodor. This organism was isolated as an endophyte from a cinnamon tree that had been introduced to Honduras from Sri Lanka in the early part of the last century. Characteristically, the original Muscodor albus, and all of its species isolated since that time are non-spore producers and each one exudes a characteristic spectrum of volatile bioactive compounds. The majority have a whitish mycelium, which is sometimes coiling, intertwined and decorated with variously shaped structures. Presently, there are at least 22 type species known/documented and each has been described as an endophyte from various plant families with widely varying habitats. An enormous variety of volatile organic compounds (VOCs) are produced by Muscodor spp. and some of these include esters, acids, aldehydes, ketones, aromatics, alkanes, alcohols, nitrosamides and terpenoids. The VOCs are both inhibitory and lethal to a wide variety of fungi and bacteria including some major pathogens of plants and humans. Interestingly, in almost all cases studied, no one compound by itself can mimic the bioactivity of the complete gas mixture, suggesting that the volatiles are acting in a synergistic manner and this has been tested with individual as well as the VOCs in various mixtures and concentrations. This review will discuss some of the recent findings in all aspects of this unique fungal genus whilst at the same time pointing out some of the major questions that remain about its biology, ecology and its applications in agriculture, medicine and other sectors. Most importantly, the authors provide arguments supporting the claim that Muscodor is taxonomically distinct from Induratia, a recently proposed change to its nomenclature.}, }
@article {pmid33233106, year = {2020}, author = {Lianou, A and Nychas, GE and Koutsoumanis, KP}, title = {Strain variability in biofilm formation: A food safety and quality perspective.}, journal = {Food research international (Ottawa, Ont.)}, volume = {137}, number = {}, pages = {109424}, doi = {10.1016/j.foodres.2020.109424}, pmid = {33233106}, issn = {1873-7145}, mesh = {*Biofilms ; *Food Microbiology ; Food Safety ; }, abstract = {The inherent differences in microbial behavior among identically treated strains of the same microbial species, referred to as "strain variability", are regarded as an important source of variability in microbiological studies. Biofilms are defined as the structured multicellular communities with complex architecture that enable microorganisms to grow adhered to abiotic or living surfaces and constitute a fundamental aspect of microbial ecology. The research studies assessing the strain variability in biofilm formation are relatively few compared to the ones evaluating other aspects of microbial behavior such as virulence, growth and stress resistance. Among the available research data on intra-species variability in biofilm formation, compiled and discussed in the present review, most of them refer to foodborne pathogens as compared to spoilage microorganisms. Molecular and physiological aspects of biofilm formation potentially related to strain-specific responses, as well as information on the characterization and quantitative description of this type of biological variability are presented and discussed. Despite the considerable amount of available information on the strain variability in biofilm formation, there are certain data gaps and still-existing challenges that future research should cover and address. Current and future advances in systems biology and omics technologies are expected to aid significantly in the explanation of phenotypic strain variability, including biofilm formation variability, allowing for its integration in microbiological risk assessment.}, }
@article {pmid33232448, year = {2021}, author = {d'Enfert, C and Kaune, AK and Alaban, LR and Chakraborty, S and Cole, N and Delavy, M and Kosmala, D and Marsaux, B and Fróis-Martins, R and Morelli, M and Rosati, D and Valentine, M and Xie, Z and Emritloll, Y and Warn, PA and Bequet, F and Bougnoux, ME and Bornes, S and Gresnigt, MS and Hube, B and Jacobsen, ID and Legrand, M and Leibundgut-Landmann, S and Manichanh, C and Munro, CA and Netea, MG and Queiroz, K and Roget, K and Thomas, V and Thoral, C and Van den Abbeele, P and Walker, AW and Brown, AJP}, title = {The impact of the Fungus-Host-Microbiota interplay upon Candida albicans infections: current knowledge and new perspectives.}, journal = {FEMS microbiology reviews}, volume = {45}, number = {3}, pages = {}, pmid = {33232448}, issn = {1574-6976}, support = {MR/M026663/1/MRC_/Medical Research Council/United Kingdom ; MR/N006364/1/MRC_/Medical Research Council/United Kingdom ; MR/M026663/2/MRC_/Medical Research Council/United Kingdom ; MR/N006364/2/MRC_/Medical Research Council/United Kingdom ; MR/V033417/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Candida albicans/immunology/pathogenicity ; Candidiasis/*immunology/*microbiology ; Host Microbial Interactions/*physiology ; Humans ; Microbial Interactions/*physiology ; }, abstract = {Candida albicans is a major fungal pathogen of humans. It exists as a commensal in the oral cavity, gut or genital tract of most individuals, constrained by the local microbiota, epithelial barriers and immune defences. Their perturbation can lead to fungal outgrowth and the development of mucosal infections such as oropharyngeal or vulvovaginal candidiasis, and patients with compromised immunity are susceptible to life-threatening systemic infections. The importance of the interplay between fungus, host and microbiota in driving the transition from C. albicans commensalism to pathogenicity is widely appreciated. However, the complexity of these interactions, and the significant impact of fungal, host and microbiota variability upon disease severity and outcome, are less well understood. Therefore, we summarise the features of the fungus that promote infection, and how genetic variation between clinical isolates influences pathogenicity. We discuss antifungal immunity, how this differs between mucosae, and how individual variation influences a person's susceptibility to infection. Also, we describe factors that influence the composition of gut, oral and vaginal microbiotas, and how these affect fungal colonisation and antifungal immunity. We argue that a detailed understanding of these variables, which underlie fungal-host-microbiota interactions, will present opportunities for directed antifungal therapies that benefit vulnerable patients.}, }
@article {pmid33232202, year = {2021}, author = {Coleine, C and Stajich, JE and de Los Ríos, A and Selbmann, L}, title = {Beyond the extremes: Rocks as ultimate refuge for fungi in drylands.}, journal = {Mycologia}, volume = {113}, number = {1}, pages = {108-133}, doi = {10.1080/00275514.2020.1816761}, pmid = {33232202}, issn = {1557-2536}, mesh = {Adaptation, Physiological ; Antarctic Regions ; Biodiversity ; Climate Change ; *Desert Climate ; Droughts ; *Extreme Environments ; *Fungi/classification/isolation &amp; purification ; Geologic Sediments/microbiology ; Lichens ; }, abstract = {In an era of rapid climate change and expansion of desertification, the extremely harsh conditions of drylands are a true challenge for microbial life. Under drought conditions, where most life forms cannot survive, rocks represent the main refuge for life. Indeed, the endolithic habitat provides thermal buffering, physical stability, and protection against incident ultraviolet (UV) radiation and solar radiation and, to some extent, ensures water retention to microorganisms. The study of these highly specialized extreme-tolerant and extremophiles may provide tools for understanding microbial interactions and processes that allow them to keep their metabolic machinery active under conditions of dryness and oligotrophy that are typically incompatible with active life, up to the dry limits for life. Despite lithobiontic communities being studied all over the world, a comprehensive understanding of their ecology, evolution, and adaptation is still nascent. Herein, we survey the fungal component of these microbial ecosystems. We first provide an overview of the main defined groups (i.e., lichen-forming fungi, black fungi, and yeasts) of the most known and studied Antarctic endolithic communities that are almost the only life forms ensuring ecosystem functionality in the ice-free areas of the continent. For each group, we discuss their main traits and their diversity. Then, we focus on the fungal taxonomy and ecology of other worldwide endolithic communities. Finally, we highlight the utmost importance of a global rock survey in order to have a comprehensive view of the diversity, distribution, and functionality of these fungi in drylands, to obtain tools in desert area management, and as early alarm systems to climate change.}, }
@article {pmid33231332, year = {2021}, author = {Stothart, MR and Greuel, RJ and Gavriliuc, S and Henry, A and Wilson, AJ and McLoughlin, PD and Poissant, J}, title = {Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters.}, journal = {Molecular ecology}, volume = {30}, number = {2}, pages = {555-571}, doi = {10.1111/mec.15747}, pmid = {33231332}, issn = {1365-294X}, mesh = {Animals ; Bacteria/genetics ; Canada ; Female ; Horses ; Islands ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Studies of microbiome variation in wildlife often emphasize host physiology and diet as proximate selective pressures acting on host-associated microbiota. In contrast, microbial dispersal and ecological drift are more rarely considered. Using amplicon sequencing, we characterized the bacterial microbiome of adult female (n = 86) Sable Island horses (Nova Scotia, Canada) as part of a detailed individual-based study of this feral population. Using data on sampling date, horse location, age, parental status, and local habitat variables, we contrasted the ability of spatiotemporal, life history, and environmental factors to explain microbiome diversity among Sable Island horses. We extended inferences made from these analyses with both phylogeny-informed and phylogeny-independent null modelling approaches to identify deviations from stochastic expectations. Phylogeny-informed diversity measures were correlated with spatial and local habitat variables, but null modelling results suggested that heterogeneity in ecological drift, rather than differential selective pressures acting on the microbiome, was responsible for these correlations. Conversely, phylogeny-independent diversity measures were best explained by host spatial and social structure, suggesting that taxonomic composition of the microbiome was shaped most strongly by bacterial dispersal. Parental status was important but correlated with measures of β-dispersion rather than β-diversity (mares without foals had lower alpha diversity and more variable microbiomes than mares with foals). Our results suggest that between host microbiome variation within the Sable Island horse population is driven more strongly by bacterial dispersal and ecological drift than by differential selective pressures. These results emphasize the need to consider alternative ecological processes in the study of microbiomes.}, }
@article {pmid33230594, year = {2021}, author = {Paul, P and Chakraborty, P and Chatterjee, A and Sarker, RK and Dastidar, DG and Kundu, T and Sarkar, N and Das, A and Tribedi, P}, title = {1,4-Naphthoquinone accumulates reactive oxygen species in Staphylococcus aureus: a promising approach towards effective management of biofilm threat.}, journal = {Archives of microbiology}, volume = {203}, number = {3}, pages = {1183-1193}, pmid = {33230594}, issn = {1432-072X}, mesh = {Anti-Bacterial Agents/pharmacology ; Biofilms/*drug effects ; Humans ; Microbial Sensitivity Tests ; Naphthoquinones/*pharmacology ; Reactive Oxygen Species/*metabolism ; Staphylococcal Infections/prevention &amp; control ; Staphylococcus aureus/*drug effects ; }, abstract = {Staphylococcus aureus, a Gram-positive opportunistic microorganism, promotes pathogenicity in the human host through biofilm formation. Microorganisms associated with biofilm often exhibit drug-resistance property that poses a major threat to public healthcare. Thus, the exploration of new therapeutic approaches is the need of the hour to manage biofilm-borne infections. In the present study, efforts are put together to test the antimicrobial as well as antibiofilm activity of 1,4-naphthoquinone against Staphylococcus aureus. The result showed that the minimum bactericidal concentration (MBC) of this compound was found to be 100 µg/mL against Staphylococcus aureus. In this regard, an array of experiments (crystal violet, biofilm protein measurement, and microscopic analysis) related to biofilm assay were conducted with the sub-MBC concentrations (1/20 and 1/10 MBC) of 1,4-naphthoquinone. All the results of biofilm assay demonstrated that these tested concentrations (1/20 and 1/10 MBC) of the compound (1,4-naphthoquinone) showed a significant reduction in biofilm development by Staphylococcus aureus. Moreover, the tested concentrations (1/20 and 1/10 MBC) of the compound (1,4-naphthoquinone) were able to reduce the microbial motility of Staphylococcus aureus that might affect the development of biofilm. Further studies revealed that the treatment of 1,4-naphthoquinone to the organism was found to increase the cellular accumulation of reactive oxygen species (ROS) that resulted in the inhibition of biofilm formation by Staphylococcus aureus. Hence, it can be concluded that 1,4-naphthoquinone might be considered as a promising compound towards biofilm inhibition caused by Staphylococcus aureus.}, }
@article {pmid33228011, year = {2020}, author = {Cano-Ortiz, A and Laborda-Illanes, A and Plaza-Andrades, I and Membrillo Del Pozo, A and Villarrubia Cuadrado, A and Rodríguez Calvo de Mora, M and Leiva-Gea, I and Sanchez-Alcoholado, L and Queipo-Ortuño, MI}, title = {Connection between the Gut Microbiome, Systemic Inflammation, Gut Permeability and FOXP3 Expression in Patients with Primary Sjögren's Syndrome.}, journal = {International journal of molecular sciences}, volume = {21}, number = {22}, pages = {}, pmid = {33228011}, issn = {1422-0067}, support = {CPI13/00003//Miguel Servet Type II" program, ISCIII, Spain/ ; C-0030-2018//"Nicolas Monardes" research program of the Consejer&#xed;a de Salud (C-0030-2018, Junta de Andaluc&#xed;a, Spain/ ; PE-0106-2019//Predoctoral grant from Consejer&#xed;a de Salud y Familia, Andalucia, Spain/ ; FI19-00112//predoctoral grant PFIS-ISCIII, Madrid, Spain/ ; }, mesh = {Actinobacteria/classification/genetics/isolation &amp; purification ; Adolescent ; Adult ; Aged ; Bacteroides/classification/genetics/isolation &amp; purification ; Body Mass Index ; Case-Control Studies ; Dysbiosis/genetics/immunology/*microbiology/pathology ; Feces/microbiology ; Female ; Firmicutes/classification/genetics/isolation &amp; purification ; Forkhead Transcription Factors/genetics/*immunology ; Gastrointestinal Microbiome/*immunology ; Genetic Variation ; Humans ; Inflammation ; Interleukin-10/genetics/immunology ; Intestines/immunology/*microbiology ; Middle Aged ; Permeability ; Proteobacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sjogren's Syndrome/genetics/immunology/*microbiology/pathology ; T-Lymphocytes, Regulatory/microbiology ; }, abstract = {The aims of this study were to explore intestinal microbial composition and functionality in primary Sjögren's syndrome (pSS) and to relate these findings to inflammation, permeability and the transcription factor Forkhead box protein P3 (FOXP3) gene expression in peripheral blood. The study included 19 pSS patients and 19 healthy controls matched for age, sex, and body mass index. Fecal bacterial DNA was extracted and analyzed by 16S rRNA sequencing using an Ion S5 platform followed by a bioinformatics analysis using Quantitative Insights into Microbial Ecology (QIIME II) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Our data suggest that the gut microbiota of pSS patients differs at both the taxonomic and functional levels with respect to healthy controls. The gut microbiota profile of our pSS patients was characterized by a lower diversity and richness and with Bacteroidetes dominating at the phylum level. The pSS patients had less beneficial or commensal butyrate-producing bacteria and a higher proportion of opportunistic pathogens with proinflammatory activity, which may impair intestinal barrier function and therefore contribute to inflammatory processes associated with pSS by increasing the production of proinflammatory cytokines and decreasing the release of the anti-inflammatory cytokine IL-10 and the peripheral FOXP3 mRNA expression, implicated in the development and function of regulatory T cells (Treg) cells. Further studies are needed to better understand the real impact of dysbiosis on the course of pSS and to conceive preventive or therapeutic strategies to counteract microbiome-driven inflammation.}, }
@article {pmid33226191, year = {2020}, author = {Gonçalves E Silva, F and Dos Santos, HF and de Assis Leite, DC and Lutfi, DS and Vianna, M and Rosado, AS}, title = {Skin and stinger bacterial communities in two critically endangered rays from the South Atlantic in natural and aquarium settings.}, journal = {MicrobiologyOpen}, volume = {9}, number = {12}, pages = {e1141}, pmid = {33226191}, issn = {2045-8827}, mesh = {Animals ; Atlantic Ocean ; Bacteria/*classification/*genetics/isolation &amp; purification ; Brazil ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Skates, Fish/classification/*microbiology ; Skin/*microbiology ; }, abstract = {Bacterial communities of two critically endangered rays from the South Atlantic, the butterfly ray (Gymnura altavela) and the groovebelly ray (Dasyatis hypostigma), were described using 16S rRNA gene metabarcoding. The study characterized the bacterial communities associated with (i) G. altavela in natural (in situ) and aquarium (ex situ) settings, (ii) skin and stinger of G. altavela, and D. hypostigma in aquaria, and (iii) newborns and adults of D. hypostigma. The results revealed potentially antibiotic-producing bacterial groups on the skin of rays from the natural environment, and some taxa with the potential to benefit ray health, mainly in rays from the natural environment, as well as possible pathogens to other animals, including fish and humans. Differences were observed between the G. altavela and D. hypostigma bacteria composition, as well as between the skin and stinger bacterial composition. The bacterial community associated with D. hypostigma changed with the age of the ray. The aquarium environment severely impacted the G. altavela bacteria composition, which changed from a complex bacterial community to one dominated almost exclusively by two taxa, Oceanimonas sp. and Sediminibacterium sp. on the skin and stinger, respectively.}, }
@article {pmid33225409, year = {2021}, author = {Labrador, MDM and Doña, J and Serrano, D and Jovani, R}, title = {Quantitative Interspecific Approach to the Stylosphere: Patterns of Bacteria and Fungi Abundance on Passerine Bird Feathers.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {1088-1097}, pmid = {33225409}, issn = {1432-184X}, mesh = {Animals ; Bacteria/genetics ; *Bird Diseases ; Feathers ; Fungi/genetics ; Humans ; *Mites ; *Passeriformes ; }, abstract = {Feathers are the habitat of a myriad of organisms, from fungi and bacteria to lice and mites. Although most studies focus on specific taxa and their interaction with the bird host, anecdotal data glimpse feathers as holders of a system with its own ecology, what we call here the stylosphere. A major gap in our knowledge of the stylosphere is the ecology of the total abundance of microorganisms, being also rare to find studies that analyze abundance of more than one group of microorganisms at the bird interspecific level. Here, we quantified bacterial and fungi abundances through qPCR on the wing feathers of 144 birds from 24 passerine and one non-passerine bird species from three localities in Southern Spain. Bacteria and fungi abundances spanned three orders of magnitude among individual birds, but were consistent when comparing the right and the left wing feathers of individuals. Sampling locality explained ca. 14% of the variation in both bacteria and fungi abundances. Even when statistically controlling for sampling locality, microbial abundances consistently differed between birds from different species, but these differences were not explained by bird phylogeny. Finally, bird individuals and species having more bacteria also tended to held larger abundances of fungi. Our results suggest a quite complex explanation for stylosphere microorganisms' abundance, being shaped by bird individual and species traits, as well as environmental factors, and likely bacteria-fungi interactions.}, }
@article {pmid33220680, year = {2020}, author = {Hall, MA and Brettell, LE and Liu, H and Nacko, S and Spooner-Hart, R and Riegler, M and Cook, JM}, title = {Temporal changes in the microbiome of stingless bee foragers following colony relocation.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {1}, pages = {}, doi = {10.1093/femsec/fiaa236}, pmid = {33220680}, issn = {1574-6941}, mesh = {Animals ; Bacteria/genetics ; Bees ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Maintaining beneficial interactions with microbial symbionts is vital for animal health. Yet, for social insects, the stability of microbial associations within and between cohorts is largely unknown. We investigated temporal changes in the microbiomes of nine stingless bee (Tetragonula carbonaria) colonies at seven timepoints across a 10-month period when moved between two climatically and florally different sites. Bacterial 16S rRNA gene and fungal ITS amplicon sequencing confirmed that microbiomes varied considerably between colonies initially at site one. However, following relocation, considerable changes occurred in bacterial community composition within each colony, and the microbiome composition became more similar across colonies. Notably, Snodgrassella disappeared and Zymobacter appeared as relatively abundant taxa. Remarkably, bacterial communities within colonies continued to shift over time but remained similar across colonies, becoming dominated by Acinetobacter six months after returning to the original site. Our results indicate that the stingless bee microbiome can undergo major changes in response to the environment, and that these changes can be long-lasting. Such legacy effects have not been reported for corbiculate bees. Further understanding the microbial ecology of stingless bees will aid future management of colonies used in agricultural production.}, }
@article {pmid33220679, year = {2020}, author = {Nilsson, JF and Castellani, LG and Draghi, WO and Mogro, EG and Wibberg, D and Winkler, A and Hansen, LH and Schlüter, A and Pühler, A and Kalinowski, J and Torres Tejerizo, GA and Pistorio, M}, title = {Global transcriptome analysis of Rhizobium favelukesii LPU83 in response to acid stress.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {1}, pages = {}, doi = {10.1093/femsec/fiaa235}, pmid = {33220679}, issn = {1574-6941}, mesh = {Acids/toxicity ; Gene Expression Profiling ; *Rhizobium/genetics ; Symbiosis ; }, abstract = {Acidic environments naturally occur worldwide and inappropriate agricultural management may also cause acidification of soils. Low soil pH values are an important barrier in the plant-rhizobia interaction. Acidic conditions disturb the establishment of the efficient rhizobia usually used as biofertilizer. This negative effect on the rhizobia-legume symbiosis is mainly due to the low acid tolerance of the bacteria. Here, we describe the identification of relevant factors in the acid tolerance of Rhizobium favelukesii using transcriptome sequencing. A total of 1924 genes were differentially expressed under acidic conditions, with ∼60% underexpressed. Rhizobium favelukesii acid response mainly includes changes in the energy metabolism and protein turnover, as well as a combination of mechanisms that may contribute to this phenotype, including GABA and histidine metabolism, cell envelope modifications and reverse proton efflux. We confirmed the acid-sensitive phenotype of a mutant in the braD gene, which showed higher expression under acid stress. Remarkably, 60% of the coding sequences encoded in the symbiotic plasmid were underexpressed and we evidenced that a strain cured for this plasmid featured an improved performance under acidic conditions. Hence, this work provides relevant information in the characterization of genes associated with tolerance or adaptation to acidic stress of R. favelukesii.}, }
@article {pmid33219851, year = {2021}, author = {Sun, M and Li, T and Li, D and Zhao, Y and Gao, F and Sun, L and Li, X}, title = {Conversion of Land Use from Upland to Paddy Field Changes Soil Bacterial Community Structure in Mollisols of Northeast China.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {1018-1028}, pmid = {33219851}, issn = {1432-184X}, support = {41701289//National Natural Science Foundation of China/ ; 2018M640287//China Postdoctoral Science Foundation/ ; }, mesh = {Agriculture ; Carbon/analysis ; China ; *Oryza ; RNA, Ribosomal, 16S ; *Soil ; Soil Microbiology ; }, abstract = {Mollisols are extremely important soil resource for crop and forage production. In northeast China, it is a major land use management practice from dry land crops to irrigated rice. However, there is few data regarding soil quality and microbial composition in Mollisols during land use transition. Here, we analyzed the upper 30 cm of soil from land with more than 30 years of paddy use and from adjacent areas with upland crops. Our results showed that land use and soil depth had a significant effect on soil properties and enzyme activities. Soil moisture (SM) and soil organic carbon (SOC) contents were substantially higher in paddy fields than in upland crop lands, while nitrogen-related enzyme activities were lower. Following the land use change, bacterial diversity was increased and bacterial community composition changed. Taxonomic analyses showed that Proteobacteria, Chloroflexi, Firmicutes, and Bacteroidetes were the dominant phyla present. At family level, Gemmatimonadaceae decreased with land use change, while Syntrophorhabdaceae and Syntrophacea that play a part in methane cycling and nitrifying bacteria such as Nitrospiraceae increased, indicating that the structure and composition of the bacterial community might be a promising indicator of Mollisol health. Redundancy analysis indicated that land use type had a stronger effect on the soil bacterial community composition than soil depth. Additionally, bacterial community composition was closely associated with soil parameters such as soil moisture, pH, SOC, NO3[-]-N, and NH4[+]-N. Overall, land use change affects the physical and chemical properties of the soil, resulting in changes in the composition of the soil bacterial community and flora. These changes could provide a view of the bacterial community assembly and functional shifts following land use change.}, }
@article {pmid33219400, year = {2021}, author = {Torralba, MG and Aleti, G and Li, W and Moncera, KJ and Lin, YH and Yu, Y and Masternak, MM and Golusinski, W and Golusinski, P and Lamperska, K and Edlund, A and Freire, M and Nelson, KE}, title = {Correction to: Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {1047}, doi = {10.1007/s00248-020-01641-3}, pmid = {33219400}, issn = {1432-184X}, }
@article {pmid33219399, year = {2021}, author = {Khan, S and Vancuren, SJ and Hill, JE}, title = {A Generalist Lifestyle Allows Rare Gardnerella spp. to Persist at Low Levels in the Vaginal Microbiome.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {1048-1060}, pmid = {33219399}, issn = {1432-184X}, mesh = {Female ; Gardnerella ; Humans ; Life Style ; *Microbiota/genetics ; Vagina ; *Vaginosis, Bacterial ; }, abstract = {Gardnerella spp. are considered a hallmark of bacterial vaginosis, a dysbiosis of the vaginal microbiome. There are four cpn60 sequence-based subgroups within the genus (A, B, C and D), and thirteen genome species have been defined recently. Gardnerella spp. co-occur in the vaginal microbiome with varying abundance, and these patterns are shaped by a resource-dependent, exploitative competition, which affects the growth rate of subgroups A, B and C negatively. The growth rate of rarely abundant subgroup D, however, increases with the increasing number of competitors, negatively affecting the growth rate of others. We hypothesized that a nutritional generalist lifestyle and minimal niche overlap with the other more abundant Gardnerella spp. facilitate the maintenance of subgroup D in the vaginal microbiome through negative frequency-dependent selection. Using 40 whole-genome sequences from isolates representing all four subgroups, we found that they could be distinguished based on the content of their predicted proteomes. Proteins associated with carbohydrate and amino acid uptake and metabolism were significant contributors to the separation of subgroups. Subgroup D isolates had significantly more of their proteins assigned to amino acid metabolism than the other subgroups. Subgroup D isolates were also significantly different from others in terms of number and type of carbon sources utilized in a phenotypic assay, while the other three could not be distinguished. Overall, the results suggest that a generalist lifestyle and lack of niche overlap with other Gardnerella spp. leads to subgroup D being favoured by negative frequency-dependent selection in the vaginal microbiome.}, }
@article {pmid33218996, year = {2021}, author = {Hansen, ML and He, Z and Wibowo, M and Jelsbak, L}, title = {A Whole-Cell Biosensor for Detection of 2,4-Diacetylphloroglucinol (DAPG)-Producing Bacteria from Grassland Soil.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {3}, pages = {}, pmid = {33218996}, issn = {1098-5336}, mesh = {*Biosensing Techniques ; Grassland ; Pest Control, Biological ; Phloroglucinol/*analogs &amp; derivatives/metabolism ; Pseudomonas/*isolation &amp; purification/*metabolism ; Soil ; Soil Microbiology ; }, abstract = {Fluorescent Pseudomonas spp. producing the antibiotic 2,4-diacetylphloroglucinol (DAPG) are ecologically important in the rhizosphere, as they can control phytopathogens and contribute to disease suppression. DAPG can also trigger a systemic resistance response in plants and stimulate root exudation and branching as well as induce plant-beneficial activities in other rhizobacteria. While studies of DAPG-producing Pseudomonas have predominantly focused on rhizosphere niches, the ecological role of DAPG as well as the distribution and dynamics of DAPG-producing bacteria remains less well understood for other environments, such as bulk soil and grassland, where the level of DAPG producers are predicted to be low. In this study, we constructed a whole-cell biosensor for detection of DAPG and DAPG-producing bacteria from environmental samples. The constructed biosensor contains a phlF response module and either lacZ or lux genes as output modules assembled on a pSEVA plasmid backbone for easy transfer to different host species and to enable easy future genetic modifications. We show that the sensor is highly specific toward DAPG, with a sensitivity in the low nanomolar range (>20 nM). This sensitivity is comparable to the DAPG levels identified in rhizosphere samples by chemical analysis. The biosensor enables guided isolation of DAPG-producing Pseudomonas Using the biosensor, we probed the same grassland soil sampling site to isolate genetically related DAPG-producing Pseudomonas kilonensis strains over a period of 12 months. Next, we used the biosensor to determine the frequency of DAPG-producing pseudomonads within three different grassland soil sites and showed that DAPG producers can constitute part of the Pseudomonas population in the range of 0.35 to 17% at these sites. Finally, we showed that the biosensor enables detection of DAPG produced by non-Pseudomonas species. Our study shows that a whole-cell biosensor for DAPG detection can facilitate isolation of bacteria that produce this important secondary metabolite and provide insight into the population dynamics of DAPG producers in natural grassland soil.IMPORTANCE The interest in bacterial biocontrol agents as biosustainable alternatives to pesticides to increase crop yields has grown. To date, we have a broad knowledge of antimicrobial compounds, such as DAPG, produced by bacteria growing in the rhizosphere surrounding plant roots. However, compared to the rhizosphere niches, the ecological role of DAPG as well as the distribution and dynamics of DAPG-producing bacteria remains less well understood for other environments, such as bulk and grassland soil. Currently, we are restricted to chemical methods with detection limits and time-consuming PCR-based and probe hybridization approaches to detect DAPG and its respective producer. In this study, we developed a whole-cell biosensor, which can circumvent the labor-intensive screening process as well as increase the sensitivity at which DAPG can be detected. This enables quantification of relative amounts of DAPG producers, which, in turn, increases our understanding of the dynamics and ecology of these producers in natural soil environments.}, }
@article {pmid33218113, year = {2020}, author = {Sperling, JLH and Fitzgerald, D and Sperling, FAH and Magor, KE}, title = {Microbiome Composition and Borrelia Detection in Ixodes scapularis Ticks at the Northwestern Edge of Their Range.}, journal = {Tropical medicine and infectious disease}, volume = {5}, number = {4}, pages = {}, pmid = {33218113}, issn = {2414-6366}, support = {RGPIN-2015-05045//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2020-04668//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2018-04920//Natural Sciences and Engineering Research Council of Canada/ ; Grant in Biodiversity to J. Sperling//Alberta Conservation Association/ ; scholarship to J. Sperling//Alberta Innovates - Technology Futures/ ; }, abstract = {Lyme disease-causing Borrelia burgdorferi has been reported in 10-19% of Ixodes ticks from Alberta, Canada, where the tick vector Ixodes scapularis is at the northwestern edge of its range. However, the presence of Borrelia has not been verified independently, and the bacterial microbiome of these ticks has not been described. We performed 16S rRNA bacterial surveys on female I. scapularis from Alberta that were previously qPCR-tested in a Lyme disease surveillance program. Both 16S and qPCR methods were concordant for the presence of Borrelia. The 16S studies also provided a profile of associated bacteria that showed the microbiome of I. scapularis in Alberta was similar to other areas of North America. Ticks that were qPCR-positive for Borrelia had significantly greater bacterial diversity than Borrelia-negative ticks, on the basis of generalized linear model testing. This study adds value to ongoing tick surveillance and is a foundation for deeper understanding of tick microbial ecology and disease transmission in a region where I. scapularis range expansion, induced by climate and land use changes, is likely to have increasing public health implications.}, }
@article {pmid33218015, year = {2020}, author = {Koller, G and Foschi, F and Mitchell, P and Witherden, E and Bruce, K and Mannocci, F}, title = {Amoebae in Chronic, Polymicrobial Endodontic Infections Are Associated with Altered Microbial Communities of Increased Virulence.}, journal = {Journal of clinical medicine}, volume = {9}, number = {11}, pages = {}, pmid = {33218015}, issn = {2077-0383}, abstract = {BACKGROUND: Infections of the root canal space involve polymicrobial biofilms and lead to chronic, low grade inflammatory responses arising from the seeding of microbes and by-products. Acute exacerbation and/or disseminating infections occur when established microbial communities undergo sudden changes in phenotypic behaviour.<br><br>METHODS: Within clinical endodontic infections, we assessedcategorical determinants comprising, and changing microbial composition of, chronic polymicrobial infections and their association with amoebae. After standardised assessment, primary or secondary infections underwent sampling and DNA processing, targeting bacteria, fungi and amoebae, including 16S high-throughput sequencing. After taxonomic assignment, community composition was correlated with clinical signs and symptoms. Diversity and abundance analyses were carried out in relation to the presence of non-bacterial amplicons.<br><br>RESULTS: Clinical specimens revealed two distinct community clusters, where specific changes correlated with clinical signs. An association between the compositions of microbiomes was found between these groups and the presence of Entamoeba gingivalis in 44% of cases. When amoebae were present in endodontic infections, we demonstrate changes in microbial community structure that mirror those observed in treatment-resistant or recurrent infections.<br><br>CONCLUSIONS: Amoeba are present in endodontic infections at a high prevalence, and may promote increased virulence by enrichment for phagocytosis-resistant bacteria.}, }
@article {pmid33217780, year = {2021}, author = {Ontiveros, VJ and Capitán, JA and Casamayor, EO and Alonso, D}, title = {The characteristic time of ecological communities.}, journal = {Ecology}, volume = {102}, number = {2}, pages = {e03247}, pmid = {33217780}, issn = {1939-9170}, mesh = {*Biodiversity ; Biota ; *Ecosystem ; Islands ; }, abstract = {A simple description of temporal dynamics of ecological communities may help us understand how community assembly proceeds, predict ecological responses to environmental disturbances, and improve the performance of biological conservation actions. Although community changes take place at multiple temporal scales, the variation of species composition and richness over time across communities and habitats shows general patterns that may potentially reveal the main drivers of community dynamics. We used the simplest stochastic model of island biogeography to propose two quantities to characterize community dynamics: the community characteristic time, as a measure of the typical time scale of species-richness change, and the characteristic Jaccard index, as a measure of temporal β diversity, that is, the variation of community composition over time. In addition, the community characteristic time, which sets the temporal scale at which null, noninteracting species assemblages operate, allowed us to define a relative sampling frequency (to the characteristic time). Here we estimate these quantities across microbial and macroscopic species assemblages to highlight two related results. First, we illustrated both characteristic time and Jaccard index and their relation with classic time-series in ecology, and found that the most thoroughly sampled communities, relative to their characteristic time, presented the largest similarity between consecutive samples. Second, our analysis across a variety of habitats and taxa show that communities span a large range of species turnover, from potentially very fast (short characteristic times) to rather slow (long characteristic times) communities. This was in agreement with previous knowledge, but indicated that some habitats may have been sampled less frequently than required. Our work provides new perspectives to explore the temporal component in ecological studies and highlights the usefulness of simple approximations to the complex dynamics of ecological communities.}, }
@article {pmid33215610, year = {2020}, author = {Madi, N and Vos, M and Murall, CL and Legendre, P and Shapiro, BJ}, title = {Does diversity beget diversity in microbiomes?.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {33215610}, issn = {2050-084X}, mesh = {*Biodiversity ; Biota/genetics ; Ecosystem ; High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; }, abstract = {Microbes are embedded in complex communities where they engage in a wide array of intra- and inter-specific interactions. The extent to which these interactions drive or impede microbiome diversity is not well understood. Historically, two contrasting hypotheses have been suggested to explain how species interactions could influence diversity. 'Ecological Controls' (EC) predicts a negative relationship, where the evolution or migration of novel types is constrained as niches become filled. In contrast, 'Diversity Begets Diversity' (DBD) predicts a positive relationship, with existing diversity promoting the accumulation of further diversity via niche construction and other interactions. Using high-throughput amplicon sequencing data from the Earth Microbiome Project, we provide evidence that DBD is strongest in low-diversity biomes, but weaker in more diverse biomes, consistent with biotic interactions initially favouring the accumulation of diversity (as predicted by DBD). However, as niches become increasingly filled, diversity hits a plateau (as predicted by EC).}, }
@article {pmid33213979, year = {2021}, author = {Glodowska, M and Stopelli, E and Straub, D and Vu Thi, D and Trang, PTK and Viet, PH and AdvectAs Team Members,  and Berg, M and Kappler, A and Kleindienst, S}, title = {Arsenic behavior in groundwater in Hanoi (Vietnam) influenced by a complex biogeochemical network of iron, methane, and sulfur cycling.}, journal = {Journal of hazardous materials}, volume = {407}, number = {}, pages = {124398}, doi = {10.1016/j.jhazmat.2020.124398}, pmid = {33213979}, issn = {1873-3336}, abstract = {The fate of arsenic (As) in groundwater is determined by multiple interrelated microbial and abiotic processes that contribute to As (im)mobilization. Most studies to date have investigated individual processes related to As (im)mobilization rather than the complex networks present in situ. In this study, we used RNA-based microbial community analysis in combination with groundwater hydrogeochemical measurements to elucidate the behavior of As along a 2 km transect near Hanoi, Vietnam. The transect stretches from the riverbank across a strongly reducing and As-contaminated Holocene aquifer, followed by a redox transition zone (RTZ) and a Pleistocene aquifer, at which As concentrations are low. Our analyses revealed fermentation and methanogenesis as important processes providing electron donors, fueling the microbially mediated reductive dissolution of As-bearing Fe(III) minerals and ultimately promoting As mobilization. As a consequence of high CH4 concentrations, methanotrophs thrive across the Holocene aquifer and the redox transition zone. Finally, our results underline the role of SO4[2-]-reducing and putative Fe(II)-/As(III)-oxidizing bacteria as a sink for As, particularly at the RTZ. Overall, our results suggest that a complex network of microbial and biogeochemical processes has to be considered to better understand the biogeochemical behavior of As in groundwater.}, }
@article {pmid33213887, year = {2021}, author = {Sutherland, WJ and Atkinson, PW and Broad, S and Brown, S and Clout, M and Dias, MP and Dicks, LV and Doran, H and Fleishman, E and Garratt, EL and Gaston, KJ and Hughes, AC and Le Roux, X and Lickorish, FA and Maggs, L and Palardy, JE and Peck, LS and Pettorelli, N and Pretty, J and Spalding, MD and Tonneijck, FH and Walpole, M and Watson, JEM and Wentworth, J and Thornton, A}, title = {A 2021 Horizon Scan of Emerging Global Biological Conservation Issues.}, journal = {Trends in ecology &amp; evolution}, volume = {36}, number = {1}, pages = {87-97}, doi = {10.1016/j.tree.2020.10.014}, pmid = {33213887}, issn = {1872-8383}, mesh = {Biodiversity ; Climate Change ; *Conservation of Natural Resources ; Coral Reefs ; *Ecosystem ; Forecasting ; Humans ; }, abstract = {We present the results from our 12th annual horizon scan of issues likely to impact biological conservation in the future. From a list of 97 topics, our global panel of 25 scientists and practitioners identified the top 15 issues that we believe society may urgently need to address. These issues are either novel in the biological conservation sector or represent a substantial positive or negative step-change in impact at global or regional level. Six issues, such as coral reef deoxygenation and changes in polar coastal productivity, affect marine or coastal ecosystems and seven relate to human and ecosystem-level responses to climate change. Identification of potential forthcoming issues for biological conservation may enable increased preparedness by researchers, practitioners, and decision-makers.}, }
@article {pmid33208892, year = {2021}, author = {Pelikan, C and Wasmund, K and Glombitza, C and Hausmann, B and Herbold, CW and Flieder, M and Loy, A}, title = {Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment.}, journal = {The ISME journal}, volume = {15}, number = {3}, pages = {833-847}, pmid = {33208892}, issn = {1751-7370}, support = {P 25111/FWF_/Austrian Science Fund FWF/Austria ; P 29426/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Anaerobiosis ; *Fusobacteria ; *Geologic Sediments ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microorganisms in marine sediments play major roles in marine biogeochemical cycles by mineralizing substantial quantities of organic matter from decaying cells. Proteins and lipids are abundant components of necromass, yet the taxonomic identities of microorganisms that actively degrade them remain poorly resolved. Here, we revealed identities, trophic interactions, and genomic features of bacteria that degraded [13]C-labeled proteins and lipids in cold anoxic microcosms containing sulfidic subarctic marine sediment. Supplemented proteins and lipids were rapidly fermented to various volatile fatty acids within 5 days. DNA-stable isotope probing (SIP) suggested Psychrilyobacter atlanticus was an important primary degrader of proteins, and Psychromonas members were important primary degraders of both proteins and lipids. Closely related Psychromonas populations, as represented by distinct 16S rRNA gene variants, differentially utilized either proteins or lipids. DNA-SIP also showed [13]C-labeling of various Deltaproteobacteria within 10 days, indicating trophic transfer of carbon to putative sulfate-reducers. Metagenome-assembled genomes revealed the primary hydrolyzers encoded secreted peptidases or lipases, and enzymes for catabolism of protein or lipid degradation products. Psychromonas species are prevalent in diverse marine sediments, suggesting they are important players in organic carbon processing in situ. Together, this study provides new insights into the identities, functions, and genomes of bacteria that actively degrade abundant necromass macromolecules in the seafloor.}, }
@article {pmid33208748, year = {2020}, author = {Molinaro, A and Bel Lassen, P and Henricsson, M and Wu, H and Adriouch, S and Belda, E and Chakaroun, R and Nielsen, T and Bergh, PO and Rouault, C and André, S and Marquet, F and Andreelli, F and Salem, JE and Assmann, K and Bastard, JP and Forslund, S and Le Chatelier, E and Falony, G and Pons, N and Prifti, E and Quinquis, B and Roume, H and Vieira-Silva, S and Hansen, TH and Pedersen, HK and Lewinter, C and Sønderskov, NB and ,  and Køber, L and Vestergaard, H and Hansen, T and Zucker, JD and Galan, P and Dumas, ME and Raes, J and Oppert, JM and Letunic, I and Nielsen, J and Bork, P and Ehrlich, SD and Stumvoll, M and Pedersen, O and Aron-Wisnewsky, J and Clément, K and Bäckhed, F}, title = {Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5881}, pmid = {33208748}, issn = {2041-1723}, support = {/DH_/Department of Health/United Kingdom ; }, mesh = {Adult ; Aged ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Cohort Studies ; Diabetes Mellitus, Type 2/blood/metabolism/*microbiology ; Female ; *Gastrointestinal Microbiome ; Histidine/metabolism ; Humans ; Imidazoles/*blood ; Male ; Middle Aged ; }, abstract = {Microbiota-host-diet interactions contribute to the development of metabolic diseases. Imidazole propionate is a novel microbially produced metabolite from histidine, which impairs glucose metabolism. Here, we show that subjects with prediabetes and diabetes in the MetaCardis cohort from three European countries have elevated serum imidazole propionate levels. Furthermore, imidazole propionate levels were increased in subjects with low bacterial gene richness and Bacteroides 2 enterotype, which have previously been associated with obesity. The Bacteroides 2 enterotype was also associated with increased abundance of the genes involved in imidazole propionate biosynthesis from dietary histidine. Since patients and controls did not differ in their histidine dietary intake, the elevated levels of imidazole propionate in type 2 diabetes likely reflects altered microbial metabolism of histidine, rather than histidine intake per se. Thus the microbiota may contribute to type 2 diabetes by generating imidazole propionate that can modulate host inflammation and metabolism.}, }
@article {pmid33207956, year = {2022}, author = {de Melo Pereira, GV and de Carvalho Neto, DP and Maske, BL and De Dea Lindner, J and Vale, AS and Favero, GR and Viesser, J and de Carvalho, JC and Góes-Neto, A and Soccol, CR}, title = {An updated review on bacterial community composition of traditional fermented milk products: what next-generation sequencing has revealed so far?.}, journal = {Critical reviews in food science and nutrition}, volume = {62}, number = {7}, pages = {1870-1889}, doi = {10.1080/10408398.2020.1848787}, pmid = {33207956}, issn = {1549-7852}, mesh = {Bacteria/genetics ; *Cultured Milk Products/microbiology ; Fermentation ; High-Throughput Nucleotide Sequencing ; Lactobacillus ; Phylogeny ; }, abstract = {The emergence of next-generation sequencing (NGS) technologies has revolutionized the way to investigate the microbial diversity in traditional fermentations. In the field of food microbial ecology, different NGS platforms have been used for community analysis, including 454 pyrosequencing from Roche, Illumina's instruments and Thermo Fisher's SOLiD/Ion Torrent sequencers. These recent platforms generate information about millions of rDNA amplicons in a single running, enabling accurate phylogenetic resolution of microbial taxa. This review provides a comprehensive overview of the application of NGS for microbiome analysis of traditional fermented milk products worldwide. Fermented milk products covered in this review include kefir, buttermilk, koumiss, dahi, kurut, airag, tarag, khoormog, lait caillé, and suero costeño. Lactobacillus-mainly represented by Lb. helveticus, Lb. kefiranofaciens, and Lb. delbrueckii-is the most important and frequent genus with 51 reported species. In general, dominant species detected by culturing were also identified by NGS. However, NGS studies have revealed a more complex bacterial diversity, with estimated 400-600 operational taxonomic units, comprising uncultivable microorganisms, sub-dominant populations, and late-growing species. This review explores the importance of these discoveries and address related topics on workflow, NGS platforms, and knowledge bioinformatics devoted to fermented milk products. The knowledge that has been gained is vital in improving the monitoring, manipulation, and safety of these traditional fermented foods.}, }
@article {pmid33205286, year = {2021}, author = {Fernandez-Gonzalez, N and Braz, GHR and Regueiro, L and Lema, JM and Carballa, M}, title = {Microbial invasions in sludge anaerobic digesters.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {1}, pages = {21-33}, pmid = {33205286}, issn = {1432-0614}, support = {2014-CE224//Centre for Industrial Technological Development/ ; ED431C 2017/29//Secretaria Xeral de Investigaci&#xf3;n e Desenvolvemento, Xunta de Galicia/ ; AGRUP2017/01//Secretaria Xeral de Investigaci&#xf3;n e Desenvolvemento, Xunta de Galicia/ ; BEX-2160/2015-03//Minist&#xe9;rio da Educa&#xe7;&#xe3;o/ ; }, mesh = {Anaerobiosis ; Bioreactors ; Methane ; *Microbiota ; *Sewage ; }, abstract = {Among processes that control microbial community assembly, microbial invasion has received little attention until recently, especially in the field of anaerobic digestion. However, knowledge of the principles regulating the taxonomic and functional stability of microbial communities is key to truly develop better predictive models and effective management strategies for the anaerobic digestion process. To date, available studies focus on microbial invasions in digesters feed with activated sludge from municipal wastewater treatment plants. Herein, this review summarizes the importance of invasions for anaerobic digestion management, the ecological theories about microbial invasions, the traits of activated sludge microorganisms entering the digesters, and the resident communities of anaerobic reactors that are relevant for invasions and the current knowledge about the success and impacts of invasions, and discusses the research needs on this topic. The initial data indicate that the impact of invasions is low and only a small percentage of the mostly aerobic microorganisms present in the activated sludge feed are able to become stablished in the anaerobic digesters. However, there are still numerous unknowns about microbial invasions in anaerobic digestion including the influence of anaerobic feedstocks or process perturbances that new approaches on microbial ecology could unveil. KEY POINTS: • Microbial invasions are key processes to develop better strategies for digesters management. • Knowledge on pathogen invasions can improve anaerobic digestion microbial safety. • To date, the number of successful invasions on anaerobic digesters from activated sludge organisms is low. • Feed organisms detected in digesters are mostly inactive residual populations. • Need to expand the range of invaders and operational scenarios studied.}, }
@article {pmid33204208, year = {2020}, author = {Naseer, A and Garrido-Benavent, I and Khan, J and Ballarà, J and Mahiques, R and Khalid, AN and Sher, H}, title = {Cortinarius pakistanicus and C. pseudotorvus: two new species in oak forests in the Pakistan Himalayas.}, journal = {MycoKeys}, volume = {74}, number = {}, pages = {91-108}, pmid = {33204208}, issn = {1314-4049}, abstract = {The genus of basidiomycetous fungi Cortinarius occurs worldwide, from subtropical to boreal latitudes. Although molecular systematics has triggered the study of these fungi in the Americas and Europe in the last two decades, there is still limited research on its diversity in large portions of the planet, such as the high mountain ranges of Asia. Several collections of Cortinarius were made during mycological field trips conducted between 2014 and 2018 in pure oak forests in the Pakistan Himalayas. An integrative framework combining morphological and phylogenetic data was employed for their study. As a result, the two species C. pakistanicus and C. pseudotorvus are here described as new to science. Detailed macro- and micro-morphological descriptions, including SEM images of spores, and a molecular phylogenetic reconstruction based on nrITS sequence data are provided and used to discriminate the new species from morphologically and phylogenetically close taxa. Whereas our phylogenetic tree inference gave unequivocal support for the inclusion of C. pseudotorvus within C. sect. Telamonia, the assignment of C. pakistanicus to any known sections remained elusive. These species likely establish ectomycorrhizal associations with trees in the genus Quercus, making this type of forest in the Pakistan Himalayas a promising focus for future research on the diversity of Cortinarius.}, }
@article {pmid33203691, year = {2020}, author = {Jordaan, K and Lappan, R and Dong, X and Aitkenhead, IJ and Bay, SK and Chiri, E and Wieler, N and Meredith, LK and Cowan, DA and Chown, SL and Greening, C}, title = {Hydrogen-Oxidizing Bacteria Are Abundant in Desert Soils and Strongly Stimulated by Hydration.}, journal = {mSystems}, volume = {5}, number = {6}, pages = {}, pmid = {33203691}, issn = {2379-5077}, abstract = {How the diverse bacterial communities inhabiting desert soils maintain energy and carbon needs is much debated. Traditionally, most bacteria are thought to persist by using organic carbon synthesized by photoautotrophs following transient hydration events. Recent studies focused on Antarctic desert soils have revealed, however, that some bacteria use atmospheric trace gases, such as hydrogen (H2), to conserve energy and fix carbon independently of photosynthesis. In this study, we investigated whether atmospheric H2 oxidation occurs in four nonpolar desert soils and compared this process to photosynthesis. To do so, we first profiled the distribution, expression, and activities of hydrogenases and photosystems in surface soils collected from the South Australian desert over a simulated hydration-desiccation cycle. Hydrogenase-encoding sequences were abundant in the metagenomes and metatranscriptomes and were detected in actinobacterial, acidobacterial, and cyanobacterial metagenome-assembled genomes. Native dry soil samples mediated H2 oxidation, but rates increased 950-fold following wetting. Oxygenic and anoxygenic phototrophs were also detected in the community but at lower abundances. Hydration significantly stimulated rates of photosynthetic carbon fixation and, to a lesser extent, dark carbon assimilation. Hydrogenase genes were also widespread in samples from three other climatically distinct deserts, the Namib, Gobi, and Mojave, and atmospheric H2 oxidation was also greatly stimulated by hydration at these sites. Together, these findings highlight that H2 is an important, hitherto-overlooked energy source supporting bacterial communities in desert soils. Contrary to our previous hypotheses, however, H2 oxidation occurs simultaneously rather than alternately with photosynthesis in such ecosystems and may even be mediated by some photoautotrophs.IMPORTANCE Desert ecosystems, spanning a third of the earth's surface, harbor remarkably diverse microbial life despite having a low potential for photosynthesis. In this work, we reveal that atmospheric hydrogen serves as a major previously overlooked energy source for a large proportion of desert bacteria. We show that both chemoheterotrophic and photoautotrophic bacteria have the potential to oxidize hydrogen across deserts sampled across four continents. Whereas hydrogen oxidation was slow in native dry deserts, it increased by three orders of magnitude together with photosynthesis following hydration. This study revealed that continual harvesting of atmospheric energy sources may be a major way that desert communities adapt to long periods of water and energy deprivation, with significant ecological and biogeochemical ramifications.}, }
@article {pmid33200135, year = {2020}, author = {Shaffer, JP and Marotz, C and Belda-Ferre, P and Martino, C and Wandro, S and Estaki, M and Salido, RA and Carpenter, CS and Zaramela, LS and Minich, JJ and Bryant, M and Sanders, K and Fraraccio, S and Ackermann, G and Humphrey, G and Swafford, AD and Miller-Montgomery, S and Knight, R}, title = {A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2020.11.13.370387}, pmid = {33200135}, issn = {2692-8205}, abstract = {UNLABELLED: One goal among microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused by the RNA virus SARS-CoV-2, has highlighted a gap in traditional DNA-based protocols, including the high-throughput methods we previously established as field standards. To enable simultaneous SARS-CoV-2 and microbial community profiling, we compare the relative performance of two total nucleic acid extraction protocols and our previously benchmarked protocol. We included a diverse panel of environmental and host-associated sample types, including body sites commonly swabbed for COVID-19 testing. Here we present results comparing the cost, processing time, DNA and RNA yield, microbial community composition, limit of detection, and well-to-well contamination, between these protocols.<br><br>ACCESSION NUMBERS: Raw sequence data were deposited at the European Nucleotide Archive (accession#: ERP124610) and raw and processed data are available at Qiita (Study ID: 12201). All processing and analysis code is available on GitHub (github.com/justinshaffer/Extraction_test_MagMAX).<br><br>METHODS SUMMARY: To allow for downstream applications involving RNA-based organisms such as SARS-CoV-2, we compared the two extraction protocols designed to extract DNA and RNA against our previously established protocol for extracting only DNA for microbial community analyses. Across 10 diverse sample types, one of the two protocols was equivalent or better than our established DNA-based protocol. Our conclusion is based on per-sample comparisons of DNA and RNA yield, the number of quality sequences generated, microbial community alpha- and beta-diversity and taxonomic composition, the limit of detection, and extent of well-to-well contamination.}, }
@article {pmid33199799, year = {2020}, author = {Perona-Vico, E and Feliu-Paradeda, L and Puig, S and Bañeras, L}, title = {Bacteria coated cathodes as an in-situ hydrogen evolving platform for microbial electrosynthesis.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {19852}, pmid = {33199799}, issn = {2045-2322}, mesh = {Bacteria/genetics/*growth &amp; development/metabolism ; Bacterial Physiological Phenomena ; Bioelectric Energy Sources/*microbiology ; Biofilms ; Biosensing Techniques/instrumentation ; Electrochemical Techniques ; Hydrogen/*analysis ; RNA, Ribosomal, 16S/genetics ; Stress, Physiological ; }, abstract = {Hydrogen is a key intermediate element in microbial electrosynthesis as a mediator of the reduction of carbon dioxide (CO2) into added value compounds. In the present work we aimed at studying the biological production of hydrogen in biocathodes operated at - 1.0 V vs. Ag/AgCl, using a highly comparable technology and CO2 as carbon feedstock. Ten bacterial strains were chosen from genera Rhodobacter, Rhodopseudomonas, Rhodocyclus, Desulfovibrio and Sporomusa, all described as hydrogen producing candidates. Monospecific biofilms were formed on carbon cloth cathodes and hydrogen evolution was constantly monitored using a microsensor. Eight over ten bacteria strains showed electroactivity and H2 production rates increased significantly (two to eightfold) compared to abiotic conditions for two of them (Desulfovibrio paquesii and Desulfovibrio desulfuricans). D. paquesii DSM 16681 exhibited the highest production rate (45.6 ± 18.8 µM min[-1]) compared to abiotic conditions (5.5 ± 0.6 µM min[-1]), although specific production rates (per 16S rRNA copy) were similar to those obtained for other strains. This study demonstrated that many microorganisms are suspected to participate in net hydrogen production but inherent differences among strains do occur, which are relevant for future developments of resilient biofilm coated cathodes as a stable hydrogen production platform in microbial electrosynthesis.}, }
@article {pmid33196853, year = {2021}, author = {Sánchez-Soto, MF and Cerqueda-García, D and Alcántara-Hernández, RJ and Falcón, LI and Pech, D and Árcega-Cabrera, F and Aguirre-Macedo, ML and García-Maldonado, JQ}, title = {Assessing the Diversity of Benthic Sulfate-Reducing Microorganisms in Northwestern Gulf of Mexico by Illumina Sequencing of dsrB Gene.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {908-921}, pmid = {33196853}, issn = {1432-184X}, support = {201441//Mexican National Council for Science and Technology - Mexican Ministry of Energy Hydrocarbon Fund/ ; 251622 - 2015//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; }, mesh = {*Bacteria/genetics ; Geologic Sediments ; Gulf of Mexico ; High-Throughput Nucleotide Sequencing ; Phylogeny ; *Sulfates ; }, abstract = {This study investigates the community composition, structure, and abundance of sulfate-reducing microorganisms (SRM) in surficial sediments of the Northwestern Gulf of Mexico (NWGoM) along a bathymetric gradient. For these purposes, Illumina sequencing and quantitative PCR (qPCR) of the dissimilatory sulfite reductase gene beta subunit (dsrB gene) were performed. Bioinformatic analyses indicated that SRM community was predominantly composed by members of Proteobacteria and Firmicutes across all the samples. However, Actinobacteria, Thermodesulfobacteria, and Chlorobi were also detected. Phylogenetic analysis indicated that unassigned dsrB sequences were related to Deltaproteobacteria and Nitrospirota superclusters, Euryarchaeota, and to environmental clusters. PCoA ordination revealed that samples clustered in three different groups. PERMANOVA indicated that water depth, temperature, redox, and nickel and cadmium content were the main environmental drivers for the SRM communities in the studied sites. Alpha diversity and abundance of SRM were lower for deeper sites, suggesting decreasing sulfate reduction activity with respect to water depth. This study contributes with the understanding of distribution and composition of dsrAB-containing microorganisms involved in sulfur transformations that may contribute to the resilience and stability of the benthic microbial communities facing metal and hydrocarbon pollution in the NWGoM, a region of recent development for oil and gas drilling.}, }
@article {pmid33194800, year = {2020}, author = {Jaiswal, S and Kumar, M and Mandeep,  and Sunita,  and Singh, Y and Shukla, P}, title = {Systems Biology Approaches for Therapeutics Development Against COVID-19.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {560240}, pmid = {33194800}, issn = {2235-2988}, mesh = {Animals ; Antiviral Agents/pharmacology ; COVID-19/immunology/virology ; COVID-19 Vaccines/administration &amp; dosage/genetics/immunology ; Humans ; SARS-CoV-2/drug effects/genetics/immunology/*physiology ; Systems Biology ; *COVID-19 Drug Treatment ; }, abstract = {Understanding the systems biology approaches for promoting the development of new therapeutic drugs is attaining importance nowadays. The threat of COVID-19 outbreak needs to be vanished for global welfare, and every section of research is focusing on it. There is an opportunity for finding new, quick, and accurate tools for developing treatment options, including the vaccine against COVID-19. The review at this moment covers various aspects of pathogenesis and host factors for exploring the virus target and developing suitable therapeutic solutions through systems biology tools. Furthermore, this review also covers the extensive details of multiomics tools i.e., transcriptomics, proteomics, genomics, lipidomics, immunomics, and in silico computational modeling aiming towards the study of host-virus interactions in search of therapeutic targets against the COVID-19.}, }
@article {pmid33193238, year = {2020}, author = {Abdelhamid, MK and Quijada, NM and Dzieciol, M and Hatfaludi, T and Bilic, I and Selberherr, E and Liebhart, D and Hess, C and Hess, M and Paudel, S}, title = {Co-infection of Chicken Layers With Histomonas meleagridis and Avian Pathogenic Escherichia coli Is Associated With Dysbiosis, Cecal Colonization and Translocation of the Bacteria From the Gut Lumen.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {586437}, pmid = {33193238}, issn = {1664-302X}, abstract = {Histomonosis in chickens often appears together with colibacillosis in the field. Thus, we have experimentally investigated consequences of the co-infection of birds with Histomonas meleagridis and avian pathogenic Escherichia coli (APEC) on the pathology, host microbiota and bacterial translocation from the gut. Commercial chicken layers were infected via oral and cloacal routes with lux-tagged APEC with or without H. meleagridis whereas negative controls were left uninfected. Except one bird, which died due to colibacillosis, no clinical signs were recorded in birds infected with bioluminescence lux gene tagged E. coli. In co-infected birds, depression and ruffled feathers were observed in 4 birds and average body weight gain significantly decreased. Typhlitis caused by H. meleagridis was present only in co-infected birds, which also had pronounced microscopic lesions in systemic organs such as liver, heart and spleen. The 16S rRNA gene amplicon sequencing showed that in co-infected birds, corresponding to the severity of cecal lesions, microbial species richness and diversity in caeca greatly decreased and the abundance of the Escherichia group, Helicobacter and Bacteroides was relatively higher with a reduction of commensals. Most of the shared Amplicon Sequencing Variants between cecum and blood in co-infected birds belonged to Pseudomonas, Staphylococcus, and members of Enterobacteriaceae while those assigned as Lactobacillus and members of Ruminococcaceae and Lachnospiraceae were found mainly in negative controls. In infected birds, E. coli in the cecal lumen penetrated into deeper layers, a phenomenon noticed with higher incidence in the dead and co-infected birds. Furthermore, numbers of lux-tagged E. coli in caeca were significantly higher at every sampling date in co-infected birds. Altogether, infection of layers with H. meleagridis and E. coli resulted in more severe pathological changes, dramatic shift in the cecal mucosa-associated microbiota, higher tissue colonization of pathogenic bacteria such as avian pathogenic E. coli in the gut and increased penetration of E. coli from the cecal lumen toward peritoneum. This study provides novel insights into the parasite-bacteria interaction in vivo highlighting the role of H. meleagridis to support E. coli in the pathogenesis of colibacillosis in chickens.}, }
@article {pmid33193131, year = {2020}, author = {Straub, D and Blackwell, N and Langarica-Fuentes, A and Peltzer, A and Nahnsen, S and Kleindienst, S}, title = {Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {550420}, pmid = {33193131}, issn = {1664-302X}, abstract = {One of the major methods to identify microbial community composition, to unravel microbial population dynamics, and to explore microbial diversity in environmental samples is high-throughput DNA- or RNA-based 16S rRNA (gene) amplicon sequencing in combination with bioinformatics analyses. However, focusing on environmental samples from contrasting habitats, it was not systematically evaluated (i) which analysis methods provide results that reflect reality most accurately, (ii) how the interpretations of microbial community studies are biased by different analysis methods and (iii) if the most optimal analysis workflow can be implemented in an easy-to-use pipeline. Here, we compared the performance of 16S rRNA (gene) amplicon sequencing analysis tools (i.e., Mothur, QIIME1, QIIME2, and MEGAN) using three mock datasets with known microbial community composition that differed in sequencing quality, species number and abundance distribution (i.e., even or uneven), and phylogenetic diversity (i.e., closely related or well-separated amplicon sequences). Our results showed that QIIME2 outcompeted all other investigated tools in sequence recovery (>10 times fewer false positives), taxonomic assignments (>22% better F-score) and diversity estimates (>5% better assessment), suggesting that this approach is able to reflect the in situ microbial community most accurately. Further analysis of 24 environmental datasets obtained from four contrasting terrestrial and freshwater sites revealed dramatic differences in the resulting microbial community composition for all pipelines at genus level. For instance, at the investigated river water sites Sphaerotilus was only reported when using QIIME1 (8% abundance) and Agitococcus with QIIME1 or QIIME2 (2 or 3% abundance, respectively), but both genera remained undetected when analyzed with Mothur or MEGAN. Since these abundant taxa probably have implications for important biogeochemical cycles (e.g., nitrate and sulfate reduction) at these sites, their detection and semi-quantitative enumeration is crucial for valid interpretations. A high-performance computing conformant workflow was constructed to allow FAIR (Findable, Accessible, Interoperable, and Re-usable) 16S rRNA (gene) amplicon sequence analysis starting from raw sequence files, using the most optimal methods identified in our study. Our presented workflow should be considered for future studies, thereby facilitating the analysis of high-throughput 16S rRNA (gene) sequencing data substantially, while maximizing reliability and confidence in microbial community data analysis.}, }
@article {pmid33193120, year = {2020}, author = {Rosen, GL and Hammrich, P}, title = {Teaching Microbiome Analysis: From Design to Computation Through Inquiry.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {528051}, pmid = {33193120}, issn = {1664-302X}, abstract = {In this article, we present our three-class course sequence to educate students about microbiome analysis and metagenomics through experiential learning by taking them from inquiry to analysis of the microbiome: Molecular Ecology Lab, Bioinformatics, and Computational Microbiome Analysis. Students developed hypotheses, designed lab experiments, sequenced the DNA from microbiomes, learned basic python/R scripting, became proficient in at least one microbiome analysis software, and were able to analyze data generated from the microbiome experiments. While over 150 students (graduate and undergraduate) were impacted by the development of the series of courses, our assessment was only on undergraduate learning, where 45 students enrolled in at least one of the three courses and 4 students took all three. Students gained skills in bioinformatics through the courses, and several positive comments were received through surveys and private correspondence. Through a summative assessment, general trends show that students became more proficient in comparative genomic techniques and had positive attitudes toward their abilities to bridge biology and bioinformatics. While most students took individual or 2 of the courses, we show that pre- and post-surveys of these individual classes still showed progress toward learning objectives. It is expected that students trained will enter the workforce with skills needed to innovate in the biotechnology, health, and environmental industries. Students are trained to maximize impact and tackle real world problems in biology and medicine with their learned knowledge of data science and machine learning. The course materials for the new microbiome analysis course are available on Github: https://github.com/EESI/Comp_Metagenomics_resources.}, }
@article {pmid33190166, year = {2021}, author = {Yi, X and Guo, J and Wang, M and Xue, C and Ju, M}, title = {Inter-trophic Interaction of Gut Microbiota in a Tripartite System.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {1075-1087}, pmid = {33190166}, issn = {1432-184X}, support = {3207047 and 31760156//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Quercus ; Sciuridae ; Seeds ; *Weevils ; }, abstract = {Gut microbiota can be transmitted either environmentally or socially and vertically at intraspecific level; however, whether gut microbiota interact along trophic levels has been largely overlooked. Here, we characterized the gut bacterial communities of weevil larvae of Curculio arakawai that infest acorns of Mongolian oak (Quercus mongolica) as well as acorn-eating mammals, Siberian chipmunk (Tamias sibiricus), to test whether consumption of seed-borne larvae remodels the gut bacterial communities of T. sibiricus. Ingestion of weevil larvae of C. arakawai significantly altered the gut bacterial communities of T. sibiricus. Consequently, T. sibiricus fed larvae of C. arakawai showed higher capability to counter the negative effects of tannins, in terms of body weight maintenance, acorn consumption, N content in feces, urine pH, and blood ALT activity. Our results may first show that seed-borne insects as hidden players have a potential to alter the gut microbiota of seed predators in the tripartite system.}, }
@article {pmid33189472, year = {2021}, author = {Miao, Y and Heintz, MB and Bell, CH and Johnson, NW and Polasko, AL and Favero, D and Mahendra, S}, title = {Profiling microbial community structures and functions in bioremediation strategies for treating 1,4-dioxane-contaminated groundwater.}, journal = {Journal of hazardous materials}, volume = {408}, number = {}, pages = {124457}, doi = {10.1016/j.jhazmat.2020.124457}, pmid = {33189472}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; Dioxanes ; *Groundwater ; *Microbiota ; Rhodococcus ; *Water Pollutants, Chemical ; }, abstract = {Microbial community compositions and functional profiles were analyzed in microcosms established using aquifer materials from a former automobile factory site, where 1,4-dioxane was identified as the primary contaminant of concern. Propane or oxygen biostimulation resulted in limited 1,4-dioxane degradation, which was markedly enhanced with the addition of nutrients, resulting in abundant Mycobacterium and Methyloversatilis taxa and high expressions of propane monooxygenase gene, prmA. In bioaugmented treatments, Pseudonocardia dioxanivorans CB1190 or Rhodococcus ruber ENV425 strains dominated immediately after augmentation and degraded 1,4-dioxane rapidly which was consistent with increased representation of xenobiotic and lipid metabolism-related functions. Although the bioaugmented microbes decreased due to insufficient growth substrates and microbial competition, they did continue to degrade 1,4-dioxane, presumably by indigenous propanotrophic and heterotrophic bacteria, inducing similar community structures across bioaugmentation conditions. In various treatments, functional redundancy acted as buffer capacity to ensure a stable microbiome, drove the restoration of the structure and microbial functions to original levels, and induced the decoupling between basic metabolic functions and taxonomy. The results of this study provided valuable information for design and decision-making for ex-situ bioreactors and in-situ bioremediation applications. A metagenomics-based understanding of the treatment process will enable efficient and accurate adjustments when encountering unexpected issues in bioremediation.}, }
@article {pmid33188444, year = {2021}, author = {Xu, Z and Wu, C and Lv, Y and Meng, F and Ban, Y}, title = {Effects of Aeration on the Formation of Arbuscular Mycorrhiza under a Flooded State and Copper Oxide Nanoparticle Removal in Vertical Flow Constructed Wetlands.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {922-931}, pmid = {33188444}, issn = {1432-184X}, mesh = {Copper ; Fungi ; *Mycorrhizae ; *Nanoparticles ; Oxides ; Wetlands ; }, abstract = {In this study, six vertical flow constructed wetlands (VFCWs) planted with Phragmites australis were operated at different aeration times (4 h day[-1] and 8 h day[-1]), aeration modes (continuous and intermittent), and arbuscular mycorrhizal fungi (AMF) inoculation treatments (inoculation with Rhizophagus intraradices and no inoculation) to explore the effects of different aeration strategies on the formation of arbuscular mycorrhiza under a flooded state in VFCWs. In addition, these VFCWs were further used to treat copper oxide nanoparticle (CuO-NP) wastewater to evaluate the correlations among aeration, colonization, growth, and CuO-NP removal. The highest AMF 28S copy number (1.99×10[5]) and colonization in reed roots, with values of 67%, 21%, and 1% for frequency (F%), intensity (M%), and arbuscule abundance (A%), were observed in the treatment with intermittent aeration for 4 h day[-1]. Aeration significantly increased the dissolved oxygen (DO) concentration and AMF colonization in VFCWs, thereby promoting plant growth and the purification of the CuO-NPs. However, excessive and continuous aeration had little positive effect on AMF colonization. This study provides a theoretical basis for the application of AMF for improving pollutant removal performance in constructed wetlands.}, }
@article {pmid33188298, year = {2021}, author = {Sakoula, D and Koch, H and Frank, J and Jetten, MSM and van Kessel, MAHJ and Lücker, S}, title = {Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification.}, journal = {The ISME journal}, volume = {15}, number = {4}, pages = {1010-1024}, pmid = {33188298}, issn = {1751-7370}, mesh = {Ammonia ; *Ammonium Compounds ; Bacteria/genetics ; Ecosystem ; *Nitrification ; Nitrites ; Oxidation-Reduction ; }, abstract = {The recent discovery of bacteria within the genus Nitrospira capable of complete ammonia oxidation (comammox) demonstrated that the sequential oxidation of ammonia to nitrate via nitrite can also be performed within a single bacterial cell. Although comammox Nitrospira exhibit a wide distribution in natural and engineered ecosystems, information on their physiological properties is scarce due to the limited number of cultured representatives. Additionally, most available genomic information is derived from metagenomic sequencing and high-quality genomes of Nitrospira in general are limited. In this study, we obtained a high (90%) enrichment of a novel comammox species, tentatively named "Candidatus Nitrospira kreftii", and performed a detailed genomic and physiological characterization. The complete genome of "Ca. N. kreftii" allowed reconstruction of its basic metabolic traits. Similar to Nitrospira inopinata, the enrichment culture exhibited a very high ammonia affinity (Km(app)_NH3 ≈ 0.040 ± 0.01 µM), but a higher nitrite affinity (Km(app)_NO2- = 12.5 ± 4.0 µM), indicating an adaptation to highly oligotrophic environments. Furthermore, we observed partial inhibition of ammonia oxidation at ammonium concentrations as low as 25 µM. This inhibition of "Ca. N. kreftii" indicates that differences in ammonium tolerance rather than affinity could potentially be a niche determining factor for different comammox Nitrospira.}, }
@article {pmid33188000, year = {2021}, author = {Coe, GL and Pinkham, NV and Celis, AI and Johnson, C and DuBois, JL and Walk, ST}, title = {Dynamic Gut Microbiome Changes in Response to Low-Iron Challenge.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {3}, pages = {}, pmid = {33188000}, issn = {1098-5336}, support = {R01 GM086755/GM/NIGMS NIH HHS/United States ; R21 DK114607/DK/NIDDK NIH HHS/United States ; R35 GM136390/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/drug effects/genetics/isolation &amp; purification ; Feces/chemistry ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Iron/*administration &amp; dosage/blood/pharmacokinetics ; Male ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S ; Mice ; }, abstract = {Iron is an essential micronutrient for life. In mammals, dietary iron is absorbed primarily in the small intestine. Currently, the impacts of dietary iron on the taxonomic structure and function of the gut microbiome and reciprocal effects on the animal host are not well understood. Here, we establish a mouse model of low-iron challenge in which intestinal biomarkers and reduced fecal iron reveal iron stress while serum iron and mouse behavioral markers indicate maintenance of iron homeostasis. We show that the diversity of the gut microbiome in conventional C57BL/6 mice changes dramatically during 2 weeks on a low-iron diet. We also show the effects of a low-iron diet on microbiome diversity are long lasting and not easily recovered when iron is returned to the diet. Finally, after optimizing taxon association methods, we show that some bacteria are unable to fully recover after the low-iron challenge and appear to be extirpated from the gut entirely. In particular, operational taxonomic units (OTUs) from the Prevotellaceae and Porphyromonadaceae families and Bacteroidales order are highly sensitive to low-iron conditions, while other seemingly insensitive OTUs recover. These results provide new insights into the iron requirements of gut microbiome members and add to the growing understanding of mammalian iron cycling.IMPORTANCE All cells need iron. Both too much and too little iron lead to diseases and unwanted outcomes. Although the impact of dietary iron on human cells and tissues has been well studied, there is currently a lack of understanding about how different levels of iron influence the abundant and diverse members of the human microbiome. This study develops a well-characterized mouse model for studying low-iron levels and identifies key groups of bacteria that are most affected. We found that the microbiome undergoes large changes when iron is removed from the diet but that many individual bacteria are able to rebound when iron levels are changed back to normal. That said, a select few members, referred to as iron-sensitive bacteria, seem to be lost. This study begins to identify individual members of the mammalian microbiome most affected by changes in dietary iron levels.}, }
@article {pmid33187698, year = {2021}, author = {Zheng, Z and Li, L and Makhalanyane, TP and Xu, C and Li, K and Xue, K and Xu, C and Qian, R and Zhang, B and Du, J and Yu, H and Cui, X and Wang, Y and Hao, Y}, title = {The composition of antibiotic resistance genes is not affected by grazing but is determined by microorganisms in grassland soils.}, journal = {The Science of the total environment}, volume = {761}, number = {}, pages = {143205}, doi = {10.1016/j.scitotenv.2020.143205}, pmid = {33187698}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Drug Resistance, Microbial/genetics ; Ecosystem ; Genes, Bacterial ; *Grassland ; *Soil ; Soil Microbiology ; }, abstract = {Grazing is expected to exert a substantial influence on antibiotic resistance genes (ARGs) in grassland ecosystems. However, the precise effects of grazing on the composition of ARGs in grassland soils remain unclear. This is especially the case for grassland soils subject to long-term grazing. Here, we investigated ARGs and bacterial community composition in soils subject to long-term historic grazing (13-39 years) and corresponding ungrazed samples. Using a combination of shotgun metagenomics, amplicon analyses and associated soil physicochemical data, we provide novel insights regarding the structure of ARGs in grassland soils. Interestingly, our analysis revealed that long-term historic grazing had no impacts on the composition of ARGs in grassland soils. An average of 378 ARGs, conferring resistance to 14 major categories of antibiotics (80%), were identified in both grazing and ungrazed sites. Actinobacteria, Proteobacteria and Acidobacteria were the most prevalent predicted hosts in these soils and were also shown to harbour genetic capacity for multiple-resistant ARGs. Our results suggested that positive effects of bacterial community composition on ARGs could potentially be controlled by affecting MGEs. Soil properties had direct effects on the composition of ARGs through affecting the frequency of horizontal gene transfer among bacteria. Twelve novel ARGs were found in S. grandis steppe grasslands, indicating that different vegetation types might induce shifts in soil ARGs. Collectively, these findings suggest that soil properties, plants and microorganisms play critical roles in shaping ARG patterns in grasslands. Together, these data establish a solid baseline for understanding environmental antibiotic resistance in grasslands.}, }
@article {pmid33184503, year = {2021}, author = {Murray, AE and Freudenstein, J and Gribaldo, S and Hatzenpichler, R and Hugenholtz, P and Kämpfer, P and Konstantinidis, KT and Lane, CE and Papke, RT and Parks, DH and Rossello-Mora, R and Stott, MB and Sutcliffe, IC and Thrash, JC and Venter, SN and Whitman, WB and Acinas, SG and Amann, RI and Anantharaman, K and Armengaud, J and Baker, BJ and Barco, RA and Bode, HB and Boyd, ES and Brady, CL and Carini, P and Chain, PSG and Colman, DR and DeAngelis, KM and de Los Rios, MA and Estrada-de Los Santos, P and Dunlap, CA and Eisen, JA and Emerson, D and Ettema, TJG and Eveillard, D and Girguis, PR and Hentschel, U and Hollibaugh, JT and Hug, LA and Inskeep, WP and Ivanova, EP and Klenk, HP and Li, WJ and Lloyd, KG and Löffler, FE and Makhalanyane, TP and Moser, DP and Nunoura, T and Palmer, M and Parro, V and Pedrós-Alió, C and Probst, AJ and Smits, THM and Steen, AD and Steenkamp, ET and Spang, A and Stewart, FJ and Tiedje, JM and Vandamme, P and Wagner, M and Wang, FP and Yarza, P and Hedlund, BP and Reysenbach, AL}, title = {Author Correction: Roadmap for naming uncultivated Archaea and Bacteria.}, journal = {Nature microbiology}, volume = {6}, number = {1}, pages = {136}, doi = {10.1038/s41564-020-00827-2}, pmid = {33184503}, issn = {2058-5276}, support = {DEB-1841658//National Science Foundation (NSF)/ ; }, }
@article {pmid33184155, year = {2020}, author = {Yadav, B and Johri, AK and Dua, M}, title = {Metagenomic Analysis of the Microbial Diversity in Solid Waste from Okhla Landfill, New Delhi, India.}, journal = {Microbiology resource announcements}, volume = {9}, number = {46}, pages = {}, pmid = {33184155}, issn = {2576-098X}, abstract = {The Okhla landfill site is consistently in the news for having pollution levels higher than the city average. Here, we report the taxonomic characterization of the microbial diversity of Okhla landfill solid waste. The metagenome analyses revealed the microbial and metabolic diversity of the site.}, }
@article {pmid33183698, year = {2021}, author = {Chow, LKM and Ghaly, TM and Gillings, MR}, title = {A survey of sub-inhibitory concentrations of antibiotics in the environment.}, journal = {Journal of environmental sciences (China)}, volume = {99}, number = {}, pages = {21-27}, doi = {10.1016/j.jes.2020.05.030}, pmid = {33183698}, issn = {1001-0742}, mesh = {*Anti-Bacterial Agents ; Bacteria ; *Environmental Pollutants ; Humans ; Surveys and Questionnaires ; }, abstract = {Antibiotics are poorly metabolized, and can enter the environment via human waste streams, agricultural run-off and pharmaceutical effluent. We consequently expect to see a concentration gradient of antibiotic compounds radiating from areas of human population. Such antibiotics should be thought of as pollutants, as they can accumulate, and have biological effects. These antibiotic pollutants can increase rates of mutation and lateral transfer events, and continue to exert selection pressure even at sub-inhibitory concentrations. Here, we conducted a literature survey on environmental concentrations of antibiotics. We collated 887 data points from 40 peer-reviewed papers. We then determined whether these concentrations were biologically relevant by comparing them to their minimum selective concentrations, usually defined as between 1/4 and 1/230 of the minimum inhibitory concentration. Environmental concentrations of antibiotics surveyed often fall into this range. In general, the antibiotic concentrations recorded in aquatic and sediment samples were similar. These findings indicate that environmental concentrations of antibiotics are likely to be influencing microbial ecology, and to be driving the selection of antibiotic resistant bacteria.}, }
@article {pmid33182220, year = {2021}, author = {Li, M and Mi, T and He, H and Chen, Y and Zhen, Y and Yu, Z}, title = {Active bacterial and archaeal communities in coastal sediments: Biogeography pattern, assembly process and co-occurrence relationship.}, journal = {The Science of the total environment}, volume = {750}, number = {}, pages = {142252}, doi = {10.1016/j.scitotenv.2020.142252}, pmid = {33182220}, issn = {1879-1026}, mesh = {*Archaea/genetics ; *Bacteria/genetics ; China ; Geologic Sediments ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The biogeography of active microbial communities and the underlying mechanisms in marine sediments are important in microbial ecology but remain unclear. Here, using qPCR and high-throughput sequencing, we investigated bacterial and archaeal community abundances and activities by quantifying the abundance and expression of the 16S rRNA gene respectively, RNA-derived bacterial and archaeal community biogeography, assembly mechanisms and co-occurrence relationships in surface sediment samples from the Bohai Sea (BS), South Yellow Sea (SYS) and the north East China Sea (NECS) of the eastern Chinese marginal seas. The results revealed a higher heterogeneity of bacterial and archaeal community activities than of abundances and heterogeneous ecological functions among areas reflected by community compositions. Furthermore, clear geographic groups (i.e., the BS, SYS and NECS groups) were observed for all, abundant and rare active bacterial and archaeal communities, accompanied by significant distance-decay patterns. However, the abundant and rare taxa showed inconsistent geographic patterns. More importantly, deterministic processes played a greater role than stochastic processes in active bacterial and archaeal community assembly. The rare taxa had weaker abilities to disperse and/or adapt and more complex ecological processes than the abundant taxa. In addition, this study also showed that intertaxa competition was the dominant interaction between active bacterial and archaeal members, which could greatly contribute to dispersal limitation. Moreover, active bacterial and archaeal co-occurrence patterns showed significant distance-decay patterns, which were consistent with the community compositions.}, }
@article {pmid33178725, year = {2020}, author = {Vadopalas, L and Ruzauskas, M and Lele, V and Starkute, V and Zavistanaviciute, P and Zokaityte, E and Bartkevics, V and Pugajeva, I and Reinolds, I and Badaras, S and Klupsaite, D and Mozuriene, E and Dauksiene, A and Gruzauskas, R and Bartkiene, E}, title = {Combination of Antimicrobial Starters for Feed Fermentation: Influence on Piglet Feces Microbiota and Health and Growth Performance, Including Mycotoxin Biotransformation in vivo.}, journal = {Frontiers in veterinary science}, volume = {7}, number = {}, pages = {528990}, pmid = {33178725}, issn = {2297-1769}, abstract = {The aim of this study was to apply a combination of the microbial starters Lactobacillus uvarum LUHS245, Lactobacillus casei LUHS210, Pediococcus acidilactici LUHS29, and Pediococcus pentosaceus LUHS183 for feed fermentation and to evaluate the influence of fermentation on feed acidity and microbiological characteristics, as well as on the piglet feces microbiota, health, and growth performance. Additionally, mycotoxin biotransformation was analyzed, including masked mycotoxins, in feed and piglet feces samples. The 36-day experiment was conducted using 25-day-old Large White/Norwegian Landrace (LW/NL) piglets with an initial body weight of 6.9-7.0 kg, which were randomly distributed into two groups (in each 100 piglets): control group, fed with basal diet (based on barley, wheat, potato protein, soybean protein concentrate, and whey powder), and treated group, fed with fermented feed at 500 g kg[-1] of total feed. Compared to a commercially available lactic acid bacteria (LAB) combination, the novel LAB mixture effectively reduced feed pH (on average pH 3.65), produced a 2-fold higher content of L(+) lactic acid, increased viable LAB count [on average 8.8 log10 colony-forming units (CFU) g[-1]], and led to stable feed fermentation during the entire test period (36 days). Fecal microbiota analysis showed an increased number of probiotic bacteria in the treated group, particularly Lactobacillus, when compared with the control group at the end of experiment. This finding indicates that fermented feed can modify microbial profile change in the gut of pigs. In treated piglets' blood (at day 61), the serum high-density lipoprotein (HDL) cholesterol and triglycerides (TG) were significantly higher, but the levels of T4, glucose, K, alkaline phosphatase (AP), and urea were significantly decreased (p ≤ 0.05) compared with the control group. Mycotoxin analysis showed that alternariol monomethyl ether (AME) and altenuene were found in 61-day-old control piglets' feces and in fermented feed samples. However, AME was not found in treated piglets' feces. Feed fermentation with the novel LAB combination is a promising means to modulate piglets' microbiota, which is essential to improve nutrient absorption, growth performance, and health parameters. The new LAB composition suggests a novel dietary strategy to positively manipulate fermented feed chemicals and bio-safety and the piglet gut microbial ecology to reduce antimicrobials use in pig production and increase local feed stock uses and economical effectiveness of the process.}, }
@article {pmid33175111, year = {2021}, author = {Pascoal, F and Costa, R and Magalhães, C}, title = {The microbial rare biosphere: current concepts, methods and ecological principles.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {1}, pages = {}, doi = {10.1093/femsec/fiaa227}, pmid = {33175111}, issn = {1574-6941}, mesh = {*Biodiversity ; *Microbiota ; Phylogeny ; }, abstract = {Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions and metabolic activity which make-up this communal pool, usually referred to as the 'rare biosphere', across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition and function.}, }
@article {pmid33174822, year = {2021}, author = {Fu, B and Olawole, O and Beattie, GA}, title = {Biological Control and Microbial Ecology Draft Genome Sequence Data of Glutamicibacter sp. FBE-19, a Bacterium Antagonistic to the Plant Pathogen Erwinia tracheiphila.}, journal = {Phytopathology}, volume = {111}, number = {4}, pages = {765-768}, doi = {10.1094/PHYTO-09-20-0380-A}, pmid = {33174822}, issn = {0031-949X}, mesh = {*Cucurbita ; *Cucurbitaceae ; *Erwinia/genetics ; Genome, Bacterial/genetics ; Plant Diseases ; }, abstract = {Glutamicibacter sp. FBE-19 was isolated based on its strong antagonism to the cucurbit bacterial blight pathogen Erwinia tracheiphila on plates. Members of the Glutamicibacter genus can promote plant growth under saline conditions and antagonize fungi on plates via chitinolytic activity; however, their production of antibacterial compounds has not been examined. Here, we report the genome sequence of strain FBE-19. The genome is 3.85 Mbp with a G+C content of 60.1% and comprises 3,791 genes. Genes that may contribute to its antagonistic activity include genes for the secondary metabolites stenothricin, salinosporamide A, a second β-lactone compound, and a carotenoid. The Glutamicibacter sp. FBE-19 genome data may be a useful resource if this strain proves to be an effective biocontrol agent against E. tracheiphila.}, }
@article {pmid33173062, year = {2020}, author = {Zakem, EJ and Polz, MF and Follows, MJ}, title = {Redox-informed models of global biogeochemical cycles.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5680}, pmid = {33173062}, issn = {2041-1723}, mesh = {Bacteria/metabolism ; *Computer Simulation ; Ecology ; Ecosystem ; *Global Warming ; *Greenhouse Effect ; Greenhouse Gases/metabolism ; Methane/metabolism ; Models, Theoretical ; Nitrous Oxide/metabolism ; *Oxidation-Reduction ; }, abstract = {Microbial activity mediates the fluxes of greenhouse gases. However, in the global models of the marine and terrestrial biospheres used for climate change projections, typically only photosynthetic microbial activity is resolved mechanistically. To move forward, we argue that global biogeochemical models need a theoretically grounded framework with which to constrain parameterizations of diverse microbial metabolisms. Here, we explain how the key redox chemistry underlying metabolisms provides a path towards this goal. Using this first-principles approach, the presence or absence of metabolic functional types emerges dynamically from ecological interactions, expanding model applicability to unobserved environments."Nothing is less real than realism. It is only by selection, by elimination, by emphasis, that we get at the real meaning of things." -Georgia O'Keefe.}, }
@article {pmid33171770, year = {2020}, author = {Rico-Reséndiz, F and Cervantes-Pérez, SA and Espinal-Centeno, A and Dipp-Álvarez, M and Oropeza-Aburto, A and Hurtado-Bautista, E and Cruz-Hernández, A and Bowman, JL and Ishizaki, K and Arteaga-Vázquez, MA and Herrera-Estrella, L and Cruz-Ramírez, A}, title = {Transcriptional and Morpho-Physiological Responses of Marchantia polymorpha upon Phosphate Starvation.}, journal = {International journal of molecular sciences}, volume = {21}, number = {21}, pages = {}, pmid = {33171770}, issn = {1422-0067}, support = {PhD scholarships (No. 629985), (No. 420770), (No. 487660).//CONACYT/ ; (19H03247)//JSPS KAKENHI grant/ ; 19941-44//UCMEXUS/ ; 158550 &amp; A1-S-38383//CONACYT Ciencia B&#xe1;sica/ ; NA150181//Royal Society Newton Advanced Fellowship/ ; }, mesh = {Ecosystem ; Gene Expression Regulation, Plant/drug effects/genetics ; Gene Regulatory Networks/drug effects/genetics ; Hepatophyta/metabolism ; Marchantia/*genetics/*metabolism ; Phosphates/*metabolism ; Phylogeny ; Transcription Factors/metabolism ; }, abstract = {Phosphate (Pi) is a pivotal nutrient that constraints plant development and productivity in natural ecosystems. Land colonization by plants, more than 470 million years ago, evolved adaptive mechanisms to conquer Pi-scarce environments. However, little is known about the molecular basis underlying such adaptations at early branches of plant phylogeny. To shed light on how early divergent plants respond to Pi limitation, we analyzed the morpho-physiological and transcriptional dynamics of Marchantia polymorpha upon Pi starvation. Our phylogenomic analysis highlights some gene networks present since the Chlorophytes and others established in the Streptophytes (e.g., PHR1-SPX1 and STOP1-ALMT1, respectively). At the morpho-physiological level, the response is characterized by the induction of phosphatase activity, media acidification, accumulation of auronidins, reduction of internal Pi concentration, and developmental modifications of rhizoids. The transcriptional response involves the induction of MpPHR1, Pi transporters, lipid turnover enzymes, and MpMYB14, which is an essential transcription factor for auronidins biosynthesis. MpSTOP2 up-regulation correlates with expression changes in genes related to organic acid biosynthesis and transport, suggesting a preference for citrate exudation. An analysis of MpPHR1 binding sequences (P1BS) shows an enrichment of this cis regulatory element in differentially expressed genes. Our study unravels the strategies, at diverse levels of organization, exerted by M. polymorpha to cope with low Pi availability.}, }
@article {pmid33170351, year = {2021}, author = {Rose, A and Padovan, A and Christian, K and van de Kamp, J and Kaestli, M and Tsoukalis, S and Bodrossy, L and Gibb, K}, title = {The Diversity of Nitrogen-Cycling Microbial Genes in a Waste Stabilization Pond Reveals Changes over Space and Time that Is Uncoupled to Changing Nitrogen Chemistry.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {1029-1041}, pmid = {33170351}, issn = {1432-184X}, support = {Australian Postgraduate Awards Scheme (APA)//Australian Government/ ; D2012/55671//PowerWater Corporation/ ; R-04202//OCE Science Leader Fellowship/ ; Environmental Genomics grant (R-02412)//CSIRO Oceans and Atmosphere/ ; }, mesh = {Archaea/genetics ; Denitrification ; Genes, Microbial ; *Nitrogen/analysis ; Nitrogen Cycle ; Oxidation-Reduction ; *Ponds ; Wastewater ; }, abstract = {Nitrogen removal is an important process for wastewater ponds prior to effluent release. Bacteria and archaea can drive nitrogen removal if they possess the genes required to metabolize nitrogen. In the tropical savanna of northern Australia, we identified the previously unresolved microbial communities responsible for nitrogen cycling in a multi-pond wastewater stabilization system by measuring genomic DNA and cDNA for the following: nifH (nitrogen fixation); nosZ (denitrification); hzsA (anammox); archaeal AamoA and bacterial BamoA (ammonia oxidation); nxrB (nitrite oxidation); and nrfA (dissimilatory NO3 reduction to NH3). By collecting 160 DNA and 40 cDNA wastewater samples and measuring nitrogen (N)-cycling genes using a functional gene array, we found that genes from all steps of the N cycle were present and, except for nxrB, were also expressed. As expected, N-cycling communities showed daily, seasonal, and yearly shifts. However, contrary to our prediction, probes from most functional groups, excluding nosZ and AamoA, were different between ponds. Further, different genes that perform the same N-cycling role sometimes had different trends over space and time, resulting in only weak correlations between the different functional communities. Although N-cycling communities were correlated with wastewater nitrogen levels and physico-chemistry, the relationship was not strong enough to reliably predict the presence or diversity of N-cycling microbes. The complex and dynamic response of these genes to other functional groups and the changing physico-chemical environment provides insight into why altering wastewater pond conditions can result an abundance of some gene variants while others are lost.}, }
@article {pmid33169932, year = {2021}, author = {Heyse, J and Props, R and Kongnuan, P and De Schryver, P and Rombaut, G and Defoirdt, T and Boon, N}, title = {Rearing water microbiomes in white leg shrimp (Litopenaeus vannamei) larviculture assemble stochastically and are influenced by the microbiomes of live feed products.}, journal = {Environmental microbiology}, volume = {23}, number = {1}, pages = {281-298}, doi = {10.1111/1462-2920.15310}, pmid = {33169932}, issn = {1462-2920}, support = {20180033//European Asian aquaculture Technology and innovation Platform (EURASTiP)/ ; 20180045//European Asian aquaculture Technology and innovation Platform (EURASTiP)/ ; 1S80618N//Flemish Fund for Scientific research (FWO-Vlaanderen)/ ; }, mesh = {Animal Feed/*microbiology ; Animals ; Aquaculture ; Artemia/*microbiology ; Bacteria/*growth &amp; development/*metabolism ; Fish Diseases/epidemiology/microbiology/prevention &amp; control ; Microbiota ; Penaeidae/*microbiology ; Water ; Water Microbiology ; }, abstract = {The development of effective management strategies to reduce the occurrence of diseases in aquaculture is hampered by the limited knowledge on the microbial ecology of these systems. In this study, the dynamics and dominant community assembly processes in the rearing water of Litopenaeus vannamei larviculture tanks were determined. Additionally, the contribution of peripheral microbiomes, such as those of live and dry feeds, to the rearing water microbiome were quantified. The community assembly in the hatchery rearing water over time was dominated by stochasticity, which explains the observed heterogeneity between replicate cultivations. The community undergoes two shifts that match with the dynamics of the algal abundances in the rearing water. Source tracking analysis revealed that 37% of all bacteria in the hatchery rearing water were introduced either by the live or dry feeds, or during water exchanges. The contribution of the microbiome from the algae was the largest, followed by that of the Artemia, the exchange water and the dry feeds. Our findings provide fundamental knowledge on the assembly processes and dynamics of rearing water microbiomes and illustrate the crucial role of these peripheral microbiomes in maintaining health-promoting rearing water microbiomes.}, }
@article {pmid33169788, year = {2021}, author = {Ionescu, D and Zoccarato, L and Zaduryan, A and Schorn, S and Bizic, M and Pinnow, S and Cypionka, H and Grossart, HP}, title = {Heterozygous, Polyploid, Giant Bacterium, Achromatium, Possesses an Identical Functional Inventory Worldwide across Drastically Different Ecosystems.}, journal = {Molecular biology and evolution}, volume = {38}, number = {3}, pages = {1040-1059}, pmid = {33169788}, issn = {1537-1719}, mesh = {*Biological Evolution ; Ecosystem ; *Genome, Bacterial ; Geologic Sediments/*microbiology ; Gram-Negative Aerobic Bacteria/*genetics/metabolism ; Heterozygote ; Phylogeny ; Polyploidy ; *Water Microbiology ; }, abstract = {Achromatium is large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain approximately 300 different chromosomes with allelic diversity far exceeding that typically harbored by single bacteria genera. Surveying all publicly available sediment sequence archives, we show that Achromatium is common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Although saline and freshwater Achromatium spp. appear phylogenetically separated, the genus Achromatium contains a globally identical, complete functional inventory regardless of habitat. Achromatium spp. cells from differing ecosystems (e.g., from freshwater to saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest that environmental adaptation occurs by increasing the copy number of relevant genes across the cell's hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium and its genomic features reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.}, }
@article {pmid33169034, year = {2021}, author = {Aksenov, AA and Laponogov, I and Zhang, Z and Doran, SLF and Belluomo, I and Veselkov, D and Bittremieux, W and Nothias, LF and Nothias-Esposito, M and Maloney, KN and Misra, BB and Melnik, AV and Smirnov, A and Du, X and Jones, KL and Dorrestein, K and Panitchpakdi, M and Ernst, M and van der Hooft, JJJ and Gonzalez, M and Carazzone, C and Amézquita, A and Callewaert, C and Morton, JT and Quinn, RA and Bouslimani, A and Orio, AA and Petras, D and Smania, AM and Couvillion, SP and Burnet, MC and Nicora, CD and Zink, E and Metz, TO and Artaev, V and Humston-Fulmer, E and Gregor, R and Meijler, MM and Mizrahi, I and Eyal, S and Anderson, B and Dutton, R and Lugan, R and Boulch, PL and Guitton, Y and Prevost, S and Poirier, A and Dervilly, G and Le Bizec, B and Fait, A and Persi, NS and Song, C and Gashu, K and Coras, R and Guma, M and Manasson, J and Scher, JU and Barupal, DK and Alseekh, S and Fernie, AR and Mirnezami, R and Vasiliou, V and Schmid, R and Borisov, RS and Kulikova, LN and Knight, R and Wang, M and Hanna, GB and Dorrestein, PC and Veselkov, K}, title = {Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data.}, journal = {Nature biotechnology}, volume = {39}, number = {2}, pages = {169-173}, pmid = {33169034}, issn = {1546-1696}, support = {R01 GM107550/GM/NIGMS NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; R01 AR073324/AR/NIAMS NIH HHS/United States ; P41 GM103484/GM/NIGMS NIH HHS/United States ; /DH_/Department of Health/United Kingdom ; U19 AG063744/AG/NIA NIH HHS/United States ; R21 AA028432/AA/NIAAA NIH HHS/United States ; T32 AR069515/AR/NIAMS NIH HHS/United States ; T32 AR064194/AR/NIAMS NIH HHS/United States ; R03 AR072182/AR/NIAMS NIH HHS/United States ; R03 CA211211/CA/NCI NIH HHS/United States ; U01 CA235507/CA/NCI NIH HHS/United States ; R24 AA022057/AA/NIAAA NIH HHS/United States ; }, mesh = {*Algorithms ; Animals ; Anura ; *Gas Chromatography-Mass Spectrometry ; Humans ; *Metabolomics ; }, abstract = {We engineered a machine learning approach, MSHub, to enable auto-deconvolution of gas chromatography-mass spectrometry (GC-MS) data. We then designed workflows to enable the community to store, process, share, annotate, compare and perform molecular networking of GC-MS data within the Global Natural Product Social (GNPS) Molecular Networking analysis platform. MSHub/GNPS performs auto-deconvolution of compound fragmentation patterns via unsupervised non-negative matrix factorization and quantifies the reproducibility of fragmentation patterns across samples.}, }
@article {pmid33167488, year = {2020}, author = {Oba, PM and Holscher, HD and Mathai, RA and Kim, J and Swanson, KS}, title = {Diet Influences the Oral Microbiota of Infants during the First Six Months of Life.}, journal = {Nutrients}, volume = {12}, number = {11}, pages = {}, pmid = {33167488}, issn = {2072-6643}, support = {USDA Hatch #ILLU 538-937//U.S. Department of Agriculture/ ; }, mesh = {Bacteria ; Breast Feeding ; *Diet ; Fungi ; Humans ; Infant ; *Microbiota ; Mouth/*microbiology ; Phylogeny ; Species Specificity ; }, abstract = {Background: Oral microorganisms contribute to oral health and disease, but few have studied how infant feeding methods affect their establishment. Methods: Infant (n = 12) feeding records and tongue and cheek swabs were collected within 48 h of birth, and after 2, 4, and 6 mo. DNA was extracted from samples, bacterial and fungal amplicons were generated and sequenced using Illumina MiSeq, and sequences were analyzed using Quantitative Insights Into Microbial Ecology (QIIME) and Statistical Analysis System (SAS) to evaluate differences over time and among breast-fed, formula-fed, mixed-fed, and solid food-fed infants. Results: Considering all time points, breast milk- and mixed-fed infants had lower oral species richness than solid food-fed infants (p = 0.006). Regardless of feeding mode, species richness was lower at birth than at other time points (p = 0.006). Principal coordinates analysis (PCoA) of unique fraction metric (UniFrac) distances indicated that bacterial communities were impacted by feeding method (p < 0.005). Considering all time points, breast-fed infants had higher Streptococcus, while formula-fed infants had higher Actinomyces and Prevotella. Regardless of feeding mode, Propionibacterium, Porphyromonas, Prevotella, Gemella, Granulicatella, Veillonella, Fusobacterium, Leptotrichia, Neisseria, and Haemophilus increased with age, while Cloacibacterium and Dechloromonas decreased with age. Oral fungi were detected in infants but were not impacted by diet. Conclusions: These findings demonstrate that the establishment of oral bacteria depends on dietary composition and age. More research is necessary to determine whether this affects risk of oral caries and other health outcomes later in life.}, }
@article {pmid33166536, year = {2021}, author = {Goraj, W and Pytlak, A and Kowalska, B and Kowalski, D and Grządziel, J and Szafranek-Nakonieczna, A and Gałązka, A and Stępniewska, Z and Stępniewski, W}, title = {Influence of pipe material on biofilm microbial communities found in drinking water supply system.}, journal = {Environmental research}, volume = {196}, number = {}, pages = {110433}, doi = {10.1016/j.envres.2020.110433}, pmid = {33166536}, issn = {1096-0953}, mesh = {Biofilms ; *Drinking Water ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; Water Supply ; }, abstract = {The biofilms and water samples from a model installation built of PVC-U, PE-HD and cast iron pipes were investigated using standard heterotrophic plate count and 16S rRNA Next Generation Sequencing. The results of the high throughput identification imply that the construction material strongly influences the microbiome composition. PVC-U and PE-HD pipes were dominated with Proteobacteria (54-60%) while the cast pipe was overgrown by Nitrospirae (64%). It was deduced that the plastic pipes create a more convenient environment for the potentially pathogenic taxa than the cast iron. The 7-year old biofilms were described as complex habitats with sharp oxidation-reduction gradients, where co-existence of methanogenic and methanotrophic microbiota takes place. Furthermore, it was found that the drinking water distribution systems (DWDS) are a useful tool for studying the ecology of rare bacterial phyla. New ecophysiological aspects were described for Aquihabitans, Thermogutta and Vampirovibrio. The discrepancy between identity of HPC-derived bacteria and NGS-revealed composition of biofilm and water microbiomes point to the need of introducing new diagnostical protocols to enable proper assessment of the drinking water safety, especially in DWDSs operating without disinfection.}, }
@article {pmid33166079, year = {2021}, author = {Nie, Y and Wu, XL}, title = {Getting back to the nature of the microbial world: from the description and inductive reasoning to deductive study after 'meta-omics'.}, journal = {Microbial biotechnology}, volume = {14}, number = {1}, pages = {22-25}, pmid = {33166079}, issn = {1751-7915}, mesh = {Databases, Factual ; *Microbiota ; }, abstract = {'Omics' studies have by now deposited massive amounts of data into the databases, and it is now time to return to the question as to what can we actually learn from them. Increased application of the deductive approach in synthetic microbial ecology and synthetic microbiome research will undoubtedly provide exciting new opportunities for advancing our understanding of microbial ecology.}, }
@article {pmid33162209, year = {2021}, author = {Hou, D and Hong, M and Wang, K and Yan, H and Wang, Y and Dong, P and Li, D and Liu, K and Zhou, Z and Zhang, D}, title = {Prokaryotic community succession and assembly on different types of microplastics in a mariculture cage.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {268}, number = {Pt A}, pages = {115756}, doi = {10.1016/j.envpol.2020.115756}, pmid = {33162209}, issn = {1873-6424}, mesh = {China ; Microplastics ; *Plastics ; RNA, Ribosomal, 16S ; *Water Pollutants, Chemical/analysis ; }, abstract = {Microplastics have emerged as a new anthropogenic substrate that can readily be colonized by microorganisms. Nevertheless, microbial community succession and assembly among different microplastics in nearshore mariculture cages remains poorly understood. Using an in situ incubation experiment, 16S rRNA gene amplicon sequencing, and the neutral model, we investigated the prokaryotic communities attached to polyethylene terephthalate (PET), polyethylene (PE), and polypropylene (PP) in a mariculture cage in Xiangshan Harbor, China. The α-diversities and compositions of microplastic-attached prokaryotic communities were significantly distinct from free-living and small particle-attached communities in the surrounding water but relatively similar to the large particle-attached communities. Although a distinct prokaryotic community was developed on each type of microplastic, the communities on PE and PP more closely resembled each other. Furthermore, the prokaryotic community dissimilarity among all media (microplastics and water fractions) tended to decrease over time. Hydrocarbon-degrading bacteria Alcanivorax preferentially colonized PE, and the genus Vibrio with opportunistically pathogenic members has the potential to colonize PET. Additionally, neutral processes dominated the prokaryotic community assembly on PE and PP, while selection was more responsible for the prokaryotic assembly on PET. The assembly of Planctomycetaceae and Thaumarchaeota Marine Group I taxa on three microplastics were mainly governed by selection and neutral processes, respectively. Our study provides further understanding of microplastic-associated microbial ecology in mariculture environments.}, }
@article {pmid33161552, year = {2021}, author = {Navarrete, AA and de Cássia Bonassi, R and Américo-Pinheiro, JHP and Vazquez, GH and Mendes, LW and de Souza Loureiro, E and Kuramae, EE and Tsai, SM}, title = {Methods to Identify Soil Microbial Bioindicators of Sustainable Management of Bioenergy Crops.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2232}, number = {}, pages = {251-263}, doi = {10.1007/978-1-0716-1040-4_19}, pmid = {33161552}, issn = {1940-6029}, mesh = {Agriculture/*methods ; Biofuels/microbiology ; Biomass ; Carbon/metabolism ; Crops, Agricultural/*genetics/microbiology ; Environmental Biomarkers/genetics ; Greenhouse Effect ; *Soil Microbiology ; }, abstract = {Here we describe a suite of methods to identify potential taxonomic and functional soil microbial indicators of soil quality and plant health in biofuel crops in various areas and land types. This approach draws on tools to assess microbial diversity, greenhouse gas fluxes, and soil physicochemical properties in bioenergy cropping systems. Integrative statistical models are then used to identify potential microbial indicators for sustainable management of bioenergy crops.}, }
@article {pmid33161546, year = {2021}, author = {Yeoh, YK}, title = {Removing Host-derived DNA Sequences from Microbial Metagenomes via Mapping to Reference Genomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2232}, number = {}, pages = {147-153}, doi = {10.1007/978-1-0716-1040-4_13}, pmid = {33161546}, issn = {1940-6029}, mesh = {Animals ; Arthropods/microbiology ; Base Sequence/*genetics ; Eukaryota/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota ; Plants/microbiology ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {DNA sequencing has become a common tool in environmental microbial ecology, facilitating characterization of microbial populations as well as complex microbial communities by circumventing culture bottlenecks. However, certain samples especially from host-associated environments (rhizosphere, human tissue) or complex communities (soils) can contain a high degree of DNA sequences derived from hosts (plants, human) or other organisms of non-interest (arthropods, unicellular eukaryotes). This chapter presents a simple in silico method to remove contaminating sequences in metagenomes based on aligning sequences to reference genomes of the target organism.}, }
@article {pmid33161522, year = {2021}, author = {Rosa, LH and Pinto, OHB and Convey, P and Carvalho-Silva, M and Rosa, CA and Câmara, PEAS}, title = {DNA Metabarcoding to Assess the Diversity of Airborne Fungi Present over Keller Peninsula, King George Island, Antarctica.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {165-172}, pmid = {33161522}, issn = {1432-184X}, mesh = {Animals ; Antarctic Regions ; *Ascomycota ; Basidiomycota ; DNA Barcoding, Taxonomic ; *Ecosystem ; Fungi/genetics ; Mortierella ; }, abstract = {We assessed fungal diversity present in air samples obtained from King George Island, Antarctica, using DNA metabarcoding through high-throughput sequencing. We detected 186 fungal amplicon sequence variants (ASVs) dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota, and Chytridiomycota. Fungi sp. 1, Agaricomycetes sp. 1, Mortierella parvispora, Mortierella sp. 2, Penicillium sp., Pseudogymnoascus roseus, Microdochium lycopodinum, Mortierella gamsii, Arrhenia sp., Cladosporium sp., Mortierella fimbricystis, Moniliella pollinis, Omphalina sp., Mortierella antarctica, and Pseudogymnoascus appendiculatus were the most dominant ASVs. In addition, several ASVs could only be identified at higher taxonomic levels and may represent previously unknown fungi and/or new records for Antarctica. The fungi detected in the air displayed high indices of diversity, richness, and dominance. The airborne fungal diversity included saprophytic, mutualistic, and plant and animal opportunistic pathogenic taxa. The diversity of taxa detected reinforces the hypothesis that the Antarctic airspora includes fungal propagules of both intra- and inter-continental origin. If regional Antarctic environmental conditions ameliorate further in concert with climate warming, these fungi might be able to reactivate and colonize different Antarctic ecosystems, with as yet unknown consequences for ecosystem function in Antarctica. Further aeromycological studies are necessary to understand how and from where these fungi arrive and move within Antarctica and if environmental changes will encourage the development of non-native fungal species in Antarctica.}, }
@article {pmid33161521, year = {2021}, author = {Tanuwidjaja, I and Vogel, C and Pronk, GJ and Schöler, A and Kublik, S and Vestergaard, G and Kögel-Knabner, I and Mrkonjic Fuka, M and Schloter, M and Schulz, S}, title = {Microbial Key Players Involved in P Turnover Differ in Artificial Soil Mixtures Depending on Clay Mineral Composition.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {897-907}, pmid = {33161521}, issn = {1432-184X}, support = {SCHL 446/4-2//Deutsche Forschungsgemeinschaft (DE)/ ; KO 1035/33-1//Deutsche Forschungsgemeinschaft/ ; KO 1035/33-2//Deutsche Forschungsgemeinschaft/ ; 031B0509 B//Bundesministerium f&#xfc;r Bildung und Forschung/ ; }, mesh = {Bacteria/genetics ; Clay ; Minerals ; *Soil ; *Soil Microbiology ; }, abstract = {Nutrient turnover in soils is strongly driven by soil properties, including clay mineral composition. One main nutrient is phosphorus (P), which is known to be easily immobilized in soil. Therefore, the specific surface characteristics of clay minerals might substantially influence P availability in soil and thus the microbial strategies for accessing P pools. We used a metagenomic approach to analyze the microbial potential to access P after 842 days of incubation in artificial soils with a clay mineral composition of either non-expandable illite (IL) or expandable montmorillonite (MT), which differ in their surface characteristics like soil surface area and surface charge. Our data indicate that microorganisms of the two soils developed different strategies to overcome P depletion, resulting in similar total P concentrations. Genes predicted to encode inorganic pyrophosphatase (ppa), exopolyphosphatase (ppx), and the pstSCAB transport system were higher in MT, suggesting effective P uptake and the use of internal poly-P stores. Genes predicted to encode enzymes involved in organic P turnover like alkaline phosphatases (phoA, phoD) and glycerophosphoryl diester phosphodiesterase were detected in both soils in comparable numbers. In addition, Po concentrations did not differ significantly. Most identified genes were assigned to microbial lineages generally abundant in agricultural fields, but some were assigned to lineages known to include oligotrophic specialists, such as Bacillaceae and Microchaetaceae.}, }
@article {pmid33160238, year = {2021}, author = {Gao, Y and Zhang, W and Li, Y and Wu, H and Yang, N and Hui, C}, title = {Dams shift microbial community assembly and imprint nitrogen transformation along the Yangtze River.}, journal = {Water research}, volume = {189}, number = {}, pages = {116579}, doi = {10.1016/j.watres.2020.116579}, pmid = {33160238}, issn = {1879-2448}, mesh = {China ; *Microbiota ; Nitrogen ; RNA, Ribosomal, 16S/genetics ; *Rivers ; }, abstract = {Dams are important for flood control, water storage, irrigation, electric generation, navigation, and have been regarded as the largest anthropogenic disturbance in aquatic ecosystems. However, how dams impact nitrogen transformation on a large watershed scale remained less studied. To explicitly address the impact of dams on nitrogen transformation, we used 16S rRNA gene sequencing to investigate the microbial dynamics and ecological processes under different dam conditions along the Yangtze River, as microbial communities are playing a key role in aquatic nitrogen transformation. Compared with landforms, dams exerted a more significant impact on the distribution patterns of microbial communities along the Yangtze River. The results showed that, by controlling suspended sand concentration, dams filtered keystone species, reshaped distribution of metacommunities, and mediated ecological assembly processes of microbial communities. Moreover, direct causal relationships between dams and nitrogen transformation were chained via microbial communities. To summarize, by combining knowledge in hydrology, microbial ecology, and biogeochemistry, this research exhibited the impact of different dams on the nitrogen transformation along a large river, and the key roles of suspended sand and microbial communities were emphasized. We anticipate a more precise modelling and prediction of nitrogen transformation in large watersheds, which may provide new perspectives for controlling the nitrogen in aquatic environments.}, }
@article {pmid33158898, year = {2021}, author = {Jiang, Y and Brandt, BW and Buijs, MJ and Cheng, L and Exterkate, RAM and Crielaard, W and Deng, DM}, title = {Manipulation of Saliva-Derived Microcosm Biofilms To Resemble Dysbiotic Subgingival Microbiota.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {3}, pages = {}, pmid = {33158898}, issn = {1098-5336}, mesh = {Biofilms ; Butyric Acid/metabolism ; Dipeptidyl Peptidase 4/metabolism ; Dysbiosis/*microbiology ; Gingiva/*microbiology ; Humans ; Microbiota/genetics/physiology ; Porphyromonas gingivalis/enzymology/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; }, abstract = {Periodontitis is a highly prevalent oral inflammatory disease triggered by dysbiotic subgingival microbiota. For the development of microbiome modulators that can reverse the dysbiotic state and reestablish a health-associated microbiota, a high-throughput in vitro multispecies biofilm model is needed. Our aim is to establish a model that resembles a dysbiotic subgingival microbial biofilm by incorporating the major periodontal pathogen Porphyromonas gingivalis into microcosm biofilms cultured from pooled saliva of healthy volunteers. The biofilms were grown for 3, 7, and 10 days and analyzed for their microbial composition by 16S rRNA gene amplicon sequencing as well as measurement of dipeptidyl peptidase IV (DPP4) activity and butyric acid production. The addition of P. gingivalis increased its abundance in saliva-derived microcosm biofilms from 2.7% on day 3 to >50% on day 10, which significantly reduced the Shannon diversity but did not affect the total number of operational taxonomic units (OTUs). The P. gingivalis-enriched biofilms displayed altered microbial composition as revealed by principal-component analysis and reduced interactions among microbial species. Moreover, these biofilms exhibited enhanced DPP4 activity and butyric acid production. In conclusion, by adding P. gingivalis to saliva-derived microcosm biofilms, we established an in vitro pathogen-enriched dysbiotic microbiota which resembles periodontitis-associated subgingival microbiota in terms of increased P. gingivalis abundance and higher DPP4 activity and butyric acid production. This model may allow for investigating factors that accelerate or hinder a microbial shift from symbiosis to dysbiosis and for developing microbiome modulation strategies.IMPORTANCE In line with the new paradigm of the etiology of periodontitis, an inflammatory disorder initiated by dysbiotic subgingival microbiota, novel therapeutic strategies have been proposed targeting reversing dysbiosis and restoring host-compatible microbiota rather than eliminating the biofilms unselectively. Thus, appropriate laboratory models are required to evaluate the efficacy of potential microbiome modulators. In the present study, we used the easily obtainable saliva as an inoculum, spiked the microcosm biofilms with the periodontal pathogen Porphyromonas gingivalis, and obtained a P. gingivalis-enriched microbiota, which resembles the in vivo pathogen-enriched subgingival microbiota in severe periodontitis. This biofilm model circumvents the difficulties encountered when using subgingival plaque as the inoculum and achieves microbiota in a dysbiotic state in a controlled and reproducible manner, which is required for high-throughput and large-scale evaluation of strategies that can potentially modulate microbial ecology.}, }
@article {pmid33158547, year = {2021}, author = {Rahman, MS and Sikder, MNA and Xu, H}, title = {Insights into β-diversity of periphytic protozoan fauna along the water column of marine ecosystems.}, journal = {Marine pollution bulletin}, volume = {162}, number = {}, pages = {111801}, doi = {10.1016/j.marpolbul.2020.111801}, pmid = {33158547}, issn = {1879-3363}, mesh = {Biodiversity ; China ; *Ciliophora ; *Ecosystem ; Environmental Monitoring ; Water ; }, abstract = {It has been increasingly recognized that there is high relevance in determining the β-diversity of communities along an environmental gradient for bioassessment of environmental quality status. To evaluate the vertical variations in β-diversity of periphytic protozoan fauna, in response to environmental heterogeneity in marine ecosystems, a baseline survey was conducted at the four water depths in the coastal waters of the Yellow Sea, northern China. Results demonstrated that (1) the species distribution presented different patterns at four water depths; (2) both compositional and community structure showed a significant vertical variation in multivariate dispersions from surface layer to the deeper layers; and (3) β-diversity measures generally increased from depths of 1 m to 5 m. These findings suggest that the homogeneity in the periphytic communities are of a high variability along the water column of marine ecosystems.}, }
@article {pmid33158546, year = {2020}, author = {Gui, Y and Uroosa,  and Bai, X and Wang, Z and Xu, G and Xu, H}, title = {An approach to assessing ecological quality status due to microalgae bloom using biofilm-dwelling protozoa based on biological trait analysis.}, journal = {Marine pollution bulletin}, volume = {161}, number = {Pt A}, pages = {111795}, doi = {10.1016/j.marpolbul.2020.111795}, pmid = {33158546}, issn = {1879-3363}, mesh = {Biofilms ; *Biological Products ; Environmental Monitoring ; *Microalgae ; Water Quality ; }, abstract = {Functional diversity/distinctness measure based trait has been proved to be a robust indicator to summarize the description of community structures and to assess water quality in different types of aquatic environment. In this study, for identifying the shielding effect of microalgae against protozoan grazing, a nine-day survey was conducted by exposing protozoan communities to a series of concentration gradients (10[0] (control), 10[4], 10[5], 10[6] and 10[7] cells ml[-1]) of two microalgae, respectively. Our results showed clear resistance of two test microalgae against protozoan grazing in five treatments. The functional distinctness measures commonly represented a decreasing trend along the gradient of concentrations of both microalgae. Ellipse tests based on the paired functional distinctness indices revealed that community functioning represented an uptrend departure from the expected pattern with the concentrations of both microalgae increase. Therefore, we suggest that the functional distinctness measures might be a reliable approach to detect the ecological effect of microalgae against protozoan grazing.}, }
@article {pmid33158141, year = {2020}, author = {Syrokou, MK and Themeli, C and Paramithiotis, S and Mataragas, M and Bosnea, L and Argyri, AA and Chorianopoulos, NG and Skandamis, PN and Drosinos, EH}, title = {Microbial Ecology of Greek Wheat Sourdoughs, Identified by a Culture-Dependent and a Culture-Independent Approach.}, journal = {Foods (Basel, Switzerland)}, volume = {9}, number = {11}, pages = {}, pmid = {33158141}, issn = {2304-8158}, support = {T1EDK-05339//European Union and Greek national funds/ ; }, abstract = {The aim of the present study was to assess the microecosystem of 13 homemade spontaneously fermented wheat sourdoughs from different regions of Greece, through the combined use of culture-dependent (classical approach; clustering by Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) and identification by PCR species-specific for Lactiplantibacillus plantarum, and sequencing of the 16S-rRNA and 26S-rRNA gene, for Lactic Acid Bacteria (LAB) and yeasts, respectively) and independent approaches [DNA- and RNA-based PCR-Denaturing Gradient Gel Electrophoresis (DGGE)]. The pH and Total Titratable Acidity (TTA) values ranged from 3.64-5.05 and from 0.50-1.59% lactic acid, respectively. Yeast and lactic acid bacteria populations ranged within 4.60-6.32 and 6.28-9.20 log CFU/g, respectively. The yeast: LAB ratio varied from 1:23-1:10,000. A total of 207 bacterial and 195 yeast isolates were obtained and a culture-dependent assessment of their taxonomic affiliation revealed dominance of Lb. plantarum in three sourdoughs, Levilactobacillus brevis in four sourdoughs and co-dominance of these species in two sourdoughs. In addition, Companilactobacillusparalimentarius dominated in two sourdoughs and Fructilactobacillussanfranciscensis and Latilactobacillus sakei in one sourdough each. Lactococcus lactis, Lb. curvatus, Leuconostoc citreum, Ln. mesenteroides and Lb. zymae were also recovered from some samples. Regarding the yeast microbiota, it was dominated by Saccharomyces cerevisiae in 11 sourdoughs and Pichia membranifaciens and P. fermentans in one sourdough each. Wickerhamomyces anomalus and Kazachstania humilis were also recovered from one sample. RNA-based PCR-DGGE provided with nearly identical results with DNA-based one; in only one sample the latter provided an additional band. In general, the limitations of this approach, namely co-migration of amplicons from different species to the same electrophoretic position and multiband profile of specific isolates, greatly reduced resolution capacity, which resulted in only partial verification of the microbial ecology detected by culture-dependent approach in the majority of sourdough samples. Our knowledge regarding the microecosystem of spontaneously fermented Greek wheat-based sourdoughs was expanded, through the study of sourdoughs originating from regions of Greece that were not previously assessed.}, }
@article {pmid33157349, year = {2021}, author = {Kiewra, D and Szymanowski, M and Czułowska, A and Kolanek, A}, title = {The local-scale expansion of Dermacentor reticulatus ticks in Lower Silesia, SW Poland.}, journal = {Ticks and tick-borne diseases}, volume = {12}, number = {1}, pages = {101599}, doi = {10.1016/j.ttbdis.2020.101599}, pmid = {33157349}, issn = {1877-9603}, mesh = {*Animal Distribution ; Animals ; Dermacentor/*physiology ; Female ; Male ; Models, Biological ; Poland ; }, abstract = {The range of D. reticulatus is discontinuous in Europe, with a gap between the Western and Eastern European populations. Recent studies have shown, however, a decrease in the gap as a consequence of D. reticulatus spreading to new areas. This study aims to analyze the dynamic of local-scale changes in the D. reticulatus range in Lower Silesia, SW Poland. All sites of D. reticulatus presence recognized in our research were located in the north-western part of the study area (Wroclaw and its surroundings), whereas the south-eastern part was found to be free of these ticks. However, a five-year observation period (2014-2019) indicates the expansion of D. reticulatus on a local scale, with a general tendency to expand to the east, with northerly or southerly deviations from year to year. The settled sites differed in distance to the nearest built-up area, the density of resident population, as well as land development intensity in the immediate vicinity. The 100% probability isolines of D. reticulatus presence in Wroclaw and its surroundings allowed the determination of the rate of range change, which turned out to be uneven in terms of direction and speed. The average rate of change in the range of tick occurrence was estimated at 7 km in 3 years. A more accurate analysis of the estimated range changes-made using modeling and verification of predicted changes in the field-showed that the likely rate of range change can be estimated at around 0.6-2.3 km/year.}, }
@article {pmid33157023, year = {2021}, author = {Köstlbacher, S and Collingro, A and Halter, T and Domman, D and Horn, M}, title = {Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria.}, journal = {Current biology : CB}, volume = {31}, number = {2}, pages = {346-357.e3}, pmid = {33157023}, issn = {1879-0445}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Adaptation, Physiological/*genetics ; Chlamydia/*genetics/pathogenicity ; Chromosomes, Bacterial/genetics ; DNA, Bacterial/genetics ; *Evolution, Molecular ; *Gene Flow ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Host Microbial Interactions/genetics ; Plasmids/*genetics ; }, abstract = {Plasmids are important in microbial evolution and adaptation to new environments. Yet, carrying a plasmid can be costly, and long-term association of plasmids with their hosts is poorly understood. Here, we provide evidence that the Chlamydiae, a phylum of strictly host-associated intracellular bacteria, have coevolved with their plasmids since their last common ancestor. Current chlamydial plasmids are amalgamations of at least one ancestral plasmid and a bacteriophage. We show that the majority of plasmid genes are also found on chromosomes of extant chlamydiae. The most conserved plasmid gene families are predominantly vertically inherited, while accessory plasmid gene families show significantly increased mobility. We reconstructed the evolutionary history of plasmid gene content of an entire bacterial phylum over a period of around one billion years. Frequent horizontal gene transfer and chromosomal integration events illustrate the pronounced impact of coevolution with these extrachromosomal elements on bacterial genome dynamics in host-dependent microbes.}, }
@article {pmid33156501, year = {2021}, author = {Trabelsi, ABH and Zaafouri, K and Friaa, A and Abidi, S and Naoui, S and Jamaaoui, F}, title = {Municipal sewage sludge energetic conversion as a tool for environmental sustainability: production of innovative biofuels and biochar.}, journal = {Environmental science and pollution research international}, volume = {28}, number = {8}, pages = {9777-9791}, pmid = {33156501}, issn = {1614-7499}, support = {Project : "Thermo-chemical conversion of solid wastes into renewable biofuels and bio-products"//Ministry of Higher Education and Scientific Research (MESRST) in Tunisia/ ; }, mesh = {*Biofuels/analysis ; Charcoal ; Hot Temperature ; Pyrolysis ; *Sewage ; }, abstract = {In this study, municipal sewage sludge (MSS) is converted simultaneously into renewable biofuels (bio-oil, syngas) and high value-added products (biochar) using a fixed bed pyrolyzer. This work examines the combined effect of two factors: final pyrolysis temperature (°C) and MSS moisture content (%) on pyrogenic product yields and characteristics. A centered composite experimental design (CCD) is established for pyrolysis process optimization by adopting the response surface methodology (RSM). The statistical results indicate that the optimal conditions considering all studied factors and responses are 550 °C as final pyrolysis temperature and 15% as MSS moisture content. In these optimal conditions, biofuels yield is around 48 wt%, whereas biochar yield is about 52 wt%. The pyrolysis products characterizations reveal that (i) pyrolytic oil has a complex molecular composition rich with n-alkanes, n-alkenes, carboxylic acids, and aromatic compounds; (ii) bio-oil presents a high-energy content (high heating value HHV around 30.6 MJ/kg); (iii) syngas mixture has a good calorific value (HHV up to 8 MJ/kg), which could be used as renewable energy vector or for pyrolysis reactor heating; and (iv) biochar residue has good aliphatic and oxygenated group contents favoring its application as biofertilizer. These findings suggest that MSS conversion into biofuels and biochar is an appropriate approach for MSS treatment. MSS-to-energy could be proposed as an element for circular economy concept due to its effectiveness in producing high value-added and sustainable products and reducing environmental problems linked to MSS disposal.}, }
@article {pmid33156395, year = {2021}, author = {Addesso, R and Gonzalez-Pimentel, JL and D'Angeli, IM and De Waele, J and Saiz-Jimenez, C and Jurado, V and Miller, AZ and Cubero, B and Vigliotta, G and Baldantoni, D}, title = {Microbial Community Characterizing Vermiculations from Karst Caves and Its Role in Their Formation.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {884-896}, pmid = {33156395}, issn = {1432-184X}, support = {MINECO [CGL2016-75590-P]//European Regional Development Fund/ ; }, mesh = {Acidobacteria ; Bacteria/genetics ; *Caves ; *Microbiota ; Proteobacteria ; }, abstract = {The microbiota associated with vermiculations from karst caves is largely unknown. Vermiculations are enigmatic deposits forming worm-like patterns on cave walls all over the world. They represent a precious focus for geomicrobiological studies aimed at exploring both the microbial life of these ecosystems and the vermiculation genesis. This study comprises the first approach on the microbial communities thriving in Pertosa-Auletta Cave (southern Italy) vermiculations by next-generation sequencing. The most abundant phylum in vermiculations was Proteobacteria, followed by Acidobacteria > Actinobacteria > Nitrospirae > Firmicutes > Planctomycetes > Chloroflexi > Gemmatimonadetes > Bacteroidetes > Latescibacteria. Numerous less-represented taxonomic groups (< 1%), as well as unclassified ones, were also detected. From an ecological point of view, all the groups co-participate in the biogeochemical cycles in these underground environments, mediating oxidation-reduction reactions, promoting host rock dissolution and secondary mineral precipitation, and enriching the matrix in organic matter. Confocal laser scanning microscopy and field emission scanning electron microscopy brought evidence of a strong interaction between the biotic community and the abiotic matrix, supporting the role of microbial communities in the formation process of vermiculations.}, }
@article {pmid33155101, year = {2021}, author = {Torralba, MG and Aleti, G and Li, W and Moncera, KJ and Lin, YH and Yu, Y and Masternak, MM and Golusinski, W and Golusinski, P and Lamperska, K and Edlund, A and Freire, M and Nelson, KE}, title = {Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {1030-1046}, pmid = {33155101}, issn = {1432-184X}, support = {R00 DE023584/DE/NIDCR NIH HHS/United States ; }, mesh = {*Carcinoma, Squamous Cell ; *Head and Neck Neoplasms ; Humans ; *Mouth Neoplasms ; RNA, Ribosomal, 16S/genetics ; Squamous Cell Carcinoma of Head and Neck ; Virulence Factors/genetics ; }, abstract = {The human microbiome has been the focus of numerous research efforts to elucidate the pathogenesis of human diseases including cancer. Oral cancer mortality is high when compared with other cancers, as diagnosis often occurs during late stages. Its prevalence has increased in the USA over the past decade and accounts for over 40,000 new cancer patients each year. Additionally, oral cancer pathogenesis is not fully understood and is likely multifactorial. To unravel the relationships that are associated with the oral microbiome and their virulence factors, we used 16S rDNA and metagenomic sequencing to characterize the microbial composition and functional content in oral squamous cell carcinoma (OSCC) tumor tissue, non-tumor tissue, and saliva from 18 OSCC patients. Results indicate a higher number of bacteria belonging to the Fusobacteria, Bacteroidetes, and Firmicutes phyla associated with tumor tissue when compared with all other sample types. Additionally, saliva metaproteomics revealed a significant increase of Prevotella in five OSCC subjects, while Corynebacterium was mostly associated with ten healthy subjects. Lastly, we determined that there are adhesion and virulence factors associated with Streptococcus gordonii as well as from known oral pathogens belonging to the Fusobacterium genera found mostly in OSCC tissues. From these results, we propose that not only will the methods utilized in this study drastically improve OSCC diagnostics, but the organisms and specific virulence factors from the phyla detected in tumor tissue may be excellent biomarkers for characterizing disease progression.}, }
@article {pmid33153747, year = {2021}, author = {Gu, Z and Liu, K and Pedersen, MW and Wang, F and Chen, Y and Zeng, C and Liu, Y}, title = {Community assembly processes underlying the temporal dynamics of glacial stream and lake bacterial communities.}, journal = {The Science of the total environment}, volume = {761}, number = {}, pages = {143178}, doi = {10.1016/j.scitotenv.2020.143178}, pmid = {33153747}, issn = {1879-1026}, mesh = {Bacteria/genetics ; Ice Cover ; *Lakes ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Community assembly processes are important in structuring aquatic microbial communities; however, the influence of these processes on the dynamics of bacterial communities in glacial streams and lakes remains largely unstudied. To investigate the assembly processes underlying the temporal variation of the bacterial community, we collected 50 water samples over five months in an ephemeral glacial stream and its downstream lake at the terminus of the Qiangyong glacier on the Tibetan Plateau. Using the V4 hypervariable region of the bacterial 16S rRNA gene combined with environmental measurements, such as water temperature, pH, total nitrogen (TN), dissolved organic carbon (DOC) and water conductivity, we found that temporal variation in the environmental factors promoted the shift in the proglacial stream and the lake bacterial communities. The quantification of ecological processes showed that the stream microbial communities were influenced by the ecological drift (40%) in June, then changed to homogeneous selection (40%) in July and variable selection (60%) in September, while the dynamic pattern of proglacial lake bacterioplankton was governed by homogeneous selection (≥ 50%) over the time. Overall, the dynamic of bacterial community in the proglacial stream and lake water is influenced by environmental factors, and the community composition assembly of the Qiangyong glacial stream and lake could be dynamic and primarily governed by deterministic processes.}, }
@article {pmid33151560, year = {2021}, author = {Yang, Q and Fu, S and Zou, P and Hao, J and Wei, D and Xie, G and Huang, J}, title = {Coordination of primary metabolism and virulence factors expression mediates the virulence of Vibrio parahaemolyticus towards cultured shrimp (Penaeus vannamei).}, journal = {Journal of applied microbiology}, volume = {131}, number = {1}, pages = {50-67}, doi = {10.1111/jam.14922}, pmid = {33151560}, issn = {1365-2672}, support = {31702385//National Natural Science Foundation of China/ ; 81903372//National Natural Science Foundation of China/ ; QL202005//Youth Program of Education Department of Liaoning Province/ ; QNLM201706//Pilot National Laboratory for Marine Science and Technology (Qingdao)/ ; }, mesh = {Animals ; Bacterial Toxins/genetics/metabolism ; DNA Transposable Elements/genetics ; Penaeidae/*microbiology ; Plasmids/genetics ; Seafood/microbiology ; Vibrio Infections/microbiology/mortality/*veterinary ; Vibrio parahaemolyticus/genetics/metabolism/*pathogenicity ; Virulence/genetics ; Virulence Factors/genetics/*metabolism ; }, abstract = {AIMS: Acute hepatopancreatic necrosis disease (AHPND) caused by Vibrio parahaemolyticus has emerged as a severe bacterial disease of cultured shrimp. To identify the key virulence factors, two AHPND-causing V. parahaemolyticus (VpAHPND) strains (123 and 137) and two non-VpAHPND strains (HZ56 and ATCC 17082) were selected.<br><br>METHODS AND RESULTS: Challenge tests showed that the four strains exhibited different virulence towards shrimp with cumulative mortalities at 48&#xa0;h postinfection (hpi) ranging from 10 to 92%. The expression of pirAB[VP] in strain 123 and 137 was not significantly different. Genomic analysis revealed that the two VpAHPND strains contain a plasmid with the PirAB[VP] toxins (pirAB[VP]) flanked by the insertion sequence (ISVal1) that has been identified in various locations of chromosomes in VpAHPND strains. The two VpAHPND strains possessed almost identical virulence factors, while ISVal1 disrupted three genes related to flagellar motility in strain 137. Phenotype assay showed that strain 123 possessed the highest growth rate and swimming motility, followed by strain 137, suggesting that the disruption of essential genes mediated by ISVal1 significantly affected the virulence level. Transcriptome analysis of two VpAHPND strains (123 and 137) further suggested that virulence genes related to the capsule, flagella and primary metabolism were highly expressed in strain 123.<br><br>CONCLUSIONS: Here for the first time, it is demonstrated that the virulence of VpAHPND is not only determined by the expression of pirAB[VP] , but also is mediated by ISVal1 which affects the genes involved in flagellar motility and primary metabolism.<br><br>The genomic and transcriptomic analysis of VpAHPND strains provides valuable information on the virulence factors affecting the pathogenicity of VpAHPND.}, }
@article {pmid33151140, year = {2020}, author = {Waite, DW and Chuvochina, M and Pelikan, C and Parks, DH and Yilmaz, P and Wagner, M and Loy, A and Naganuma, T and Nakai, R and Whitman, WB and Hahn, MW and Kuever, J and Hugenholtz, P}, title = {Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {70}, number = {11}, pages = {5972-6016}, doi = {10.1099/ijsem.0.004213}, pmid = {33151140}, issn = {1466-5034}, support = {I 2320/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/*classification ; Deltaproteobacteria/*classification ; Phylogeny ; Proteobacteria/*classification ; Terminology as Topic ; }, abstract = {The class Deltaproteobacteria comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum Proteobacteria, it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the class Deltaproteobacteria encompassing Bdellovibrio-like predators was recently reclassified into a separate proteobacterial class, the Oligoflexia. Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classes Deltaproteobacteria and Oligoflexia in the phylum Proteobacteria. Instead, the great majority of currently recognized members of the class Deltaproteobacteria are better classified into four novel phylum-level lineages. We propose the names Desulfobacterota phyl. nov. and Myxococcota phyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the class Oligoflexia represent a separate phylum for which we propose the name Bdellovibrionota phyl. nov. based on priority in the literature and general recognition of the genus Bdellovibrio. Desulfobacterota phyl. nov. includes the taxa previously classified in the phylum Thermodesulfobacteria, and these reclassifications imply that the ability of sulphate reduction was vertically inherited in the Thermodesulfobacteria rather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phyla Myxococcota and Bdellovibrionota, which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.}, }
@article {pmid33150937, year = {2020}, author = {Hopkins, JR and Semenova-Nelsen, T and Sikes, BA}, title = {Fungal community structure and seasonal trajectories respond similarly to fire across pyrophilic ecosystems.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {1}, pages = {}, doi = {10.1093/femsec/fiaa219}, pmid = {33150937}, issn = {1574-6941}, mesh = {Ecosystem ; *Fires ; *Mycobiome ; Seasons ; Soil ; }, abstract = {Fire alters microbial community composition, and is expected to increase in frequency due to climate change. Testing whether microbes in different ecosystems will respond similarly to increased fire disturbance is difficult though, because fires are often unpredictable and hard to manage. Fire recurrent or pyrophilic ecosystems, however, may be useful models for testing the effects of frequent disturbance on microbes. We hypothesized that across pyrophilic ecosystems, fire would drive similar alterations to fungal communities, including altering seasonal community dynamics. We tested fire's effects on fungal communities in two pyrophilic ecosystems, a longleaf pine savanna and tallgrass prairie. Fire caused similar fungal community shifts, including (i) driving immediate changes that favored taxa able to survive fire and take advantage of post-fire environments and (ii) altering seasonal trajectories due to fire-associated changes to soil nutrient availability. This suggests that fire has predictable effects on fungal community structure and intra-annual community dynamics in pyrophilic ecosystems, and that these changes could significantly alter fungal function. Parallel fire responses in these key microbes may also suggest that recurrent fires drive convergent changes across ecosystems, including less fire-frequented systems that may start burning more often due to climate change.}, }
@article {pmid33150935, year = {2020}, author = {Landazuri, CFG and Gomez, JS and Raaijmakers, JM and Oyserman, BO}, title = {Restoring degraded microbiome function with self-assembled communities.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {12}, pages = {}, doi = {10.1093/femsec/fiaa225}, pmid = {33150935}, issn = {1574-6941}, mesh = {Bacteria/genetics ; Microbial Consortia ; *Microbiota ; Soil ; *Soil Microbiology ; }, abstract = {The natural microbial functions of many soils are severely degraded. Current state-of-the-art technology to restore these functions is through the isolation, screening, formulation and application of microbial inoculants and synthetic consortia. These approaches have inconsistent success, in part due to the incompatibility between the biofertilizer, crop, climate, existing soil microbiome and physicochemical characteristics of the soils. Here, we review the current state of the art in biofertilization and identify two key deficiencies in current strategies: the difficulty in designing complex multispecies biofertilizers and the bottleneck in scaling the production of complex multispecies biofertilizers. To address the challenge of producing scalable, multispecies biofertilizers, we propose to merge ecological theory with bioprocess engineering to produce 'self-assembled communities' enriched for particular functional guilds and adapted to a target soil and host plant. Using the nitrogen problem as an anchor, we review relevant ecology (microbial, plant and environmental), as well as reactor design strategies and operational parameters for the production of functionally enriched self-assembled communities. The use of self-assembled communities for biofertilization addresses two major hurdles in microbiome engineering: the importance of enriching microbes indigenous to (and targeted for) a specific environment and the recognized potential benefits of microbial consortia over isolates (e.g. functional redundancy). The proposed community enrichment model could also be instrumental for other microbial functions such as phosphorus solubilization, plant growth promotion or disease suppression.}, }
@article {pmid33150499, year = {2021}, author = {Rasmussen, AN and Damashek, J and Eloe-Fadrosh, EA and Francis, CA}, title = {In-depth Spatiotemporal Characterization of Planktonic Archaeal and Bacterial Communities in North and South San Francisco Bay.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {601-616}, pmid = {33150499}, issn = {1432-184X}, support = {OCE-0847266//Division of Ocean Sciences/ ; }, mesh = {*Archaea/genetics ; Bays ; *Plankton/genetics ; RNA, Ribosomal, 16S/genetics ; San Francisco ; }, abstract = {Despite being the largest estuary on the west coast of North America, no in-depth survey of microbial communities in San Francisco Bay (SFB) waters currently exists. In this study, we analyze bacterioplankton and archaeoplankton communities at several taxonomic levels and spatial extents (i.e., North versus South Bay) to reveal patterns in alpha and beta diversity. We assess communities using high-throughput sequencing of the 16S rRNA gene in 177 water column samples collected along a 150-km transect over a 2-year monthly time-series. In North Bay, the microbial community is strongly structured by spatial salinity changes while in South Bay seasonal variations dominate community dynamics. Along the steep salinity gradient in North Bay, we find that operational taxonomic units (OTUs; 97% identity) have higher site specificity than at coarser taxonomic levels and turnover ("species" replacement) is high, revealing a distinct brackish community (in oligo-, meso-, and polyhaline samples) from fresh and marine end-members. At coarser taxonomic levels (e.g., phylum, class), taxa are broadly distributed across salinity zones (i.e., present/abundant in a large number of samples) and brackish communities appear to be a mix of fresh and marine communities. We also observe variations in brackish communities between samples with similar salinities, likely related to differences in water residence times between North and South Bay. Throughout SFB, suspended particulate matter is positively correlated with richness and influences changes in beta diversity. Within several abundant groups, including the SAR11 clade (comprising up to 30% of reads in a sample), OTUs appear to be specialized to a specific salinity range. Some other organisms also showed pronounced seasonal abundance, including Synechococcus, Ca. Actinomarina, and Nitrosopumilus-like OTUs. Overall, this study represents the first in-depth spatiotemporal survey of SFB microbial communities and provides insight into how planktonic microorganisms have specialized to different niches along the salinity gradient.}, }
@article {pmid33150498, year = {2021}, author = {Pino-Bodas, R and Stenroos, S}, title = {Global Biodiversity Patterns of the Photobionts Associated with the Genus Cladonia (Lecanorales, Ascomycota).}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {173-187}, pmid = {33150498}, issn = {1432-184X}, support = {FLF program//Royal Botanical Gardens, Kew/ ; Juan de la Cierva-Incorporaci&#xf3;n 2015-23526//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; }, mesh = {*Ascomycota/genetics ; Biodiversity ; *Chlorophyta/genetics ; *Lichens ; Phylogeny ; Symbiosis ; }, abstract = {The diversity of lichen photobionts is not fully known. We studied here the diversity of the photobionts associated with Cladonia, a sub-cosmopolitan genus ecologically important, whose photobionts belong to the green algae genus Asterochloris. The genetic diversity of Asterochloris was screened by using the ITS rDNA and actin type I regions in 223 specimens and 135 species of Cladonia collected all over the world. These data, added to those available in GenBank, were compiled in a dataset of altogether 545 Asterochloris sequences occurring in 172 species of Cladonia. A high diversity of Asterochloris associated with Cladonia was found. The commonest photobiont lineages associated with this genus are A. glomerata, A. italiana, and A. mediterranea. Analyses of partitioned variation were carried out in order to elucidate the relative influence on the photobiont genetic variation of the following factors: mycobiont identity, geographic distribution, climate, and mycobiont phylogeny. The mycobiont identity and climate were found to be the main drivers for the genetic variation of Asterochloris. The geographical distribution of the different Asterochloris lineages was described. Some lineages showed a clear dominance in one or several climatic regions. In addition, the specificity and the selectivity were studied for 18 species of Cladonia. Potentially specialist and generalist species of Cladonia were identified. A correlation was found between the sexual reproduction frequency of the host and the frequency of certain Asterochloris OTUs. Some Asterochloris lineages co-occur with higher frequency than randomly expected in the Cladonia species.}, }
@article {pmid33149844, year = {2020}, author = {Skelly, E and Johnson, NW and Kapellas, K and Kroon, J and Lalloo, R and Weyrich, L}, title = {Response of Salivary Microbiota to Caries Preventive Treatment in Aboriginal and Torres Strait Islander Children.}, journal = {Journal of oral microbiology}, volume = {12}, number = {1}, pages = {1830623}, pmid = {33149844}, issn = {2000-2297}, abstract = {A once-annual caries preventive (Intervention) treatment was offered to Aboriginal and Torres Strait Islander schoolchildren-a population with disproportionately poorer oral health than non-Indigenous Australian children-in the Northern Peninsula Area (NPA) of Far North Queensland (FNQ), which significantly improved their oral health. Here, we examine the salivary microbiota of these children (mean age = 10 ± 2.96 years; n = 103), reconstructing the bacterial community composition with high-throughput sequencing of the V4 region of bacterial 16S rRNA gene. Microbial communities of children who received the Intervention had lower taxonomic diversity than those who did not receive treatment (Shannon, p < 0.05). Moreover, the Intervention resulted in further decreased microbial diversity in children with active carious lesions existing at the time of saliva collection. Microbial species associated with caries were detected; Lactobacillus salivarius, Lactobacillus reuteri, Lactobacillus gasseri, Prevotella multisaccharivorax, Parascardovia denticolens, and Mitsuokella HMT 131 were significantly increased (p < 0.05) in children with severe caries, especially in children who did not receive the Intervention. These insights into microbial associations and community differences prompt future considerations to the mechanisms behind caries-preventive therapy induced change; important for understanding the long-term implications of like treatment to improve oral health disparities within Australia. Trial registration: ANZCTR, ACTRN12615000693527. Registered 3 July 2015, https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=368750&amp;isReview=true.}, }
@article {pmid33149734, year = {2020}, author = {Pereira, LM and Messias, EA and Sorroche, BP and Oliveira, ADN and Arantes, LMRB and de Carvalho, AC and Tanaka-Azevedo, AM and Grego, KF and Carvalho, AL and Melendez, ME}, title = {In-depth transcriptome reveals the potential biotechnological application of Bothrops jararaca venom gland.}, journal = {The journal of venomous animals and toxins including tropical diseases}, volume = {26}, number = {}, pages = {e20190058}, pmid = {33149734}, issn = {1678-9199}, abstract = {BACKGROUND: Lack of complete genomic data of Bothrops jararaca impedes molecular biology research focusing on biotechnological applications of venom gland components. Identification of full-length coding regions of genes is crucial for the correct molecular cloning design.<br><br>METHODS: RNA was extracted from the venom gland of one adult female specimen of Bothrops jararaca. Deep sequencing of the mRNA library was performed using Illumina NextSeq 500 platform. De novo assembly of B. jararaca transcriptome was done using Trinity. Annotation was performed using Blast2GO. All predicted proteins after clustering step were blasted against non-redundant protein database of NCBI using BLASTP. Metabolic pathways present in the transcriptome were annotated using the KAAS-KEGG Automatic Annotation Server. Toxins were identified in the B. jararaca predicted proteome using BLASTP against all protein sequences obtained from Animal Toxin Annotation Project from Uniprot KB/Swiss-Pro database. Figures and data visualization were performed using ggplot2 package in R language environment.<br><br>RESULTS: We described the in-depth transcriptome analysis of B. jararaca venom gland, in which 76,765 de novo assembled isoforms, 96,044 transcribed genes and 41,196 unique proteins were identified. The most abundant transcript was the zinc metalloproteinase-disintegrin-like jararhagin. Moreover, we identified 78 distinct functional classes of proteins, including toxins, inhibitors and tumor suppressors. Other venom proteins identified were the hemolytic lethal factors stonustoxin and verrucotoxin.<br><br>CONCLUSION: It is believed that the application of deep sequencing to the analysis of snake venom transcriptomes may represent invaluable insight on their biotechnological potential focusing on candidate molecules.}, }
@article {pmid33149208, year = {2021}, author = {Du, Q and Ren, B and He, J and Peng, X and Guo, Q and Zheng, L and Li, J and Dai, H and Chen, V and Zhang, L and Zhou, X and Xu, X}, title = {Candida albicans promotes tooth decay by inducing oral microbial dysbiosis.}, journal = {The ISME journal}, volume = {15}, number = {3}, pages = {894-908}, pmid = {33149208}, issn = {1751-7370}, mesh = {Acids ; Animals ; Biofilms ; *Candida albicans ; Carbohydrate Metabolism ; *Dental Caries ; Dysbiosis ; Rats ; }, abstract = {Candida albicans has been detected in root carious lesions. The current study aimed to explore the action of this fungal species on the microbial ecology and the pathogenesis of root caries. Here, by analyzing C. albicans in supragingival dental plaque collected from root carious lesions and sound root surfaces of root-caries subjects as well as caries-free individuals, we observed significantly increased colonization of C. albicans in root carious lesions. Further in vitro and animal studies showed that C. albicans colonization increased the cariogenicity of oral biofilm by altering its microbial ecology, leading to a polymicrobial biofilm with enhanced acidogenicity, and consequently exacerbated tooth demineralization and carious lesion severity. More importantly, we demonstrated that the cariogenicity-promoting activity of C. albicans was dependent on PHR2. Deletion of PHR2 restored microbial equilibrium and led to a less cariogenic biofilm as demonstrated by in vitro artificial caries model or in vivo root-caries rat model. Our data indicate the critical role of C. albicans infection in the occurrence of root caries. PHR2 is the major factor that determines the ecological impact and caries-promoting activity of C. albicans in a mixed microbial consortium.}, }
@article {pmid33145650, year = {2021}, author = {Albornoz, FE and Orchard, S and Standish, RJ and Dickie, IA and Bending, GD and Hilton, S and Lardner, T and Foster, KJ and Gleeson, DB and Bougoure, J and Barbetti, MJ and You, MP and Ryan, MH}, title = {Evidence for Niche Differentiation in the Environmental Responses of Co-occurring Mucoromycotinian Fine Root Endophytes and Glomeromycotinian Arbuscular Mycorrhizal Fungi.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {864-873}, pmid = {33145650}, issn = {1432-184X}, support = {DP180103157//Australian Research Council (ARC) Discovery/ ; NE/S010270/1//Natural Environment Research Council/ ; FT140100103//ARC Future Fellowship/ ; ON-279//Australian Wool Innovation Ltd/ ; }, mesh = {Carbon ; Endophytes/genetics ; Fungi ; *Mycorrhizae ; Plant Roots ; Soil ; Soil Microbiology ; }, abstract = {Fine root endophytes (FRE) were traditionally considered a morphotype of arbuscular mycorrhizal fungi (AMF), but recent genetic studies demonstrate that FRE belong within the subphylum Mucoromycotina, rather than in the subphylum Glomeromycotina with the AMF. These findings prompt enquiry into the fundamental ecology of FRE and AMF. We sampled FRE and AMF in roots of Trifolium subterraneum from 58 sites across temperate southern Australia. We investigated the environmental drivers of composition, richness, and root colonization of FRE and AMF by using structural equation modelling and canonical correspondence analyses. Root colonization by FRE increased with increasing temperature and rainfall but decreased with increasing phosphorus (P). Root colonization by AMF increased with increasing soil organic carbon but decreased with increasing P. Richness of FRE decreased with increasing temperature and soil pH. Richness of AMF increased with increasing temperature and rainfall but decreased with increasing soil aluminium (Al) and pH. Aluminium, soil pH, and rainfall were, in decreasing order, the strongest drivers of community composition of FRE; they were also important drivers of community composition of AMF, along with temperature, in decreasing order: rainfall, Al, temperature, and soil pH. Thus, FRE and AMF showed the same responses to some (e.g. soil P, soil pH) and different responses to other (e.g. temperature) key environmental factors. Overall, our data are evidence for niche differentiation among these co-occurring mycorrhizal associates.}, }
@article {pmid33144313, year = {2020}, author = {Manus, MB and Kuthyar, S and Perroni-Marañón, AG and Núñez-de la Mora, A and Amato, KR}, title = {Infant Skin Bacterial Communities Vary by Skin Site and Infant Age across Populations in Mexico and the United States.}, journal = {mSystems}, volume = {5}, number = {6}, pages = {}, pmid = {33144313}, issn = {2379-5077}, abstract = {Daily practices put humans in close contact with the surrounding environment, and differences in these practices have an impact on human physiology, development, and health. There is mounting evidence that the microbiome represents an interface that mediates interactions between the human body and the environment. In particular, the skin microbiome serves as the primary interface with the external environment and aids in host immune function by contributing as the first line of defense against pathogens. Despite these important connections, we have only a basic understanding of how the skin microbiome is first established, or which environmental factors contribute to its development. To this end, this study compared the skin bacterial communities of infants (n = 47) living in four populations in Mexico and the United States that span the socioeconomic gradient, where we predicted that variation in physical and social environments would shape the infant skin microbiome. Results of 16S rRNA bacterial gene sequencing on 119 samples (armpit, hand, and forehead) showed that infant skin bacterial diversity and composition are shaped by population-level factors, including those related to socioeconomic status and household composition, and vary by skin site and infant age. Differences in infant-environment interactions, including with other people, appear to vary across the populations, likely influencing infant microbial exposures and, in turn, the composition of infant skin bacterial communities. These findings suggest that variation in microbial exposures stemming from the local environment in infancy can impact the establishment of the skin microbiome across body sites, with implications for developmental and health outcomes.IMPORTANCE This study contributes to the sparse literature on the infant skin microbiome in general, and the virtually nonexistent literature on the infant skin microbiome in a field setting. While microbiome research often addresses patterns at a national scale, this study addresses the influence of population-level factors, such as maternal socioeconomic status and contact with caregivers, on infant skin bacterial communities. This approach strengthens our understanding of how local variables influence the infant skin microbiome, and paves the way for additional studies to combine biological sample collection with questionnaires to adequately capture how specific behaviors dictate infant microbial exposures. Work in this realm has implications for infant care and health, as well as for investigating how the microbial communities of different body sites develop over time, with applications to specific health outcomes associated with the skin microbiome (e.g., immune system development or atopic dermatitis).}, }
@article {pmid33142974, year = {2020}, author = {Sánchez-Clemente, R and Guijo, MI and Nogales, J and Blasco, R}, title = {Carbon Source Influence on Extracellular pH Changes along Bacterial Cell-Growth.}, journal = {Genes}, volume = {11}, number = {11}, pages = {}, pmid = {33142974}, issn = {2073-4425}, mesh = {Bacteria/genetics/*growth &amp; development/*metabolism ; Bacterial Proteins/genetics ; Carbon/*metabolism ; Culture Media/chemistry/metabolism ; Escherichia coli/genetics/growth &amp; development/metabolism ; Gene Expression Regulation, Bacterial/genetics ; Hydrogen-Ion Concentration ; Pseudomonas pseudoalcaligenes/genetics/growth &amp; development/metabolism ; Pseudomonas putida/genetics/growth &amp; development/metabolism ; }, abstract = {The effect of initial pH on bacterial cell-growth and its change over time was studied under aerobic heterotrophic conditions by using three bacterial strains: Escherichia coli ATCC 25922, Pseudomonas putida KT2440, and Pseudomonas pseudoalcaligenes CECT 5344. In Luria-Bertani (LB) media, pH evolved by converging to a certain value that is specific for each bacterium. By contrast, in the buffered Minimal Medium (MM), pH was generally more stable along the growth curve. In MM with glucose as carbon source, a slight acidification of the medium was observed for all strains. In the case of E. coli, a sudden drop in pH was observed during exponential cell growth that was later recovered at initial pH 7 or 8, but was irreversible below pH 6, thus arresting further cell-growth. When using other carbon sources in MM at a fixed initial pH, pH changes depended mainly on the carbon source itself. While glucose, glycerol, or octanoate slightly decreased extracellular pH, more oxidized carbon sources, such as citrate, 2-furoate, 2-oxoglutarate, and fumarate, ended up with the alkalinization of the medium. These observations are in accordance with pH change predictions using genome-scale metabolic models for the three strains, thus revealing the metabolic reasons behind pH change. Therefore, we conclude that the composition of the medium, specifically the carbon source, determines pH change during bacterial growth to a great extent and unravel the main molecular mechanism behind this phenotype. These findings pave the way for predicting pH changes in a given bacterial culture and may anticipate the interspecies interactions and fitness of bacteria in their environment.}, }
@article {pmid33142874, year = {2020}, author = {Van Herreweghen, F and Amberg, C and Marques, R and Callewaert, C}, title = {Biological and Chemical Processes that Lead to Textile Malodour Development.}, journal = {Microorganisms}, volume = {8}, number = {11}, pages = {}, pmid = {33142874}, issn = {2076-2607}, abstract = {The development of malodour on clothing is a well-known problem with social, economic and ecological consequences. Many people still think malodour is the result of a lack of hygiene, which causes social stigma and embarrassment. Clothing is washed more frequently due to odour formation or even discarded when permastink develops. The malodour formation process is impacted by many variables and processes throughout the textile lifecycle. The contact with the skin with consequent transfer of microorganisms, volatiles and odour precursors leads to the formation of a distinctive textile microbiome and volatilome. The washing and drying processes further shape the textile microbiome and impact malodour formation. These processes are impacted by interindividual differences and fabric type as well. This review describes the current knowledge on the volatilome and microbiome of the skin, textile and washing machine, the multiple factors that determine malodour formation on textiles and points out what information is still missing.}, }
@article {pmid33140722, year = {2020}, author = {Sharma, K and Palatinszky, M and Nikolov, G and Berry, D and Shank, EA}, title = {Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {33140722}, issn = {2050-084X}, support = {DE-SC0013887//Biological and Environmental Research/International ; DE-SC0019012//Biological and Environmental Research/International ; FunKeyGut 741623/ERC_/European Research Council/International ; }, mesh = {Bacillus subtilis ; Bacteria ; Carbon Isotopes ; Deuterium Oxide ; Dimethylpolysiloxanes ; Fluorescent Dyes/chemistry ; Fluorocarbon Polymers/chemistry ; Fungi ; Isotope Labeling/*methods ; Mucor ; Particle Size ; Sodium Fluoride/chemistry ; Soil/*chemistry ; *Soil Microbiology ; Spectrum Analysis, Raman ; }, abstract = {Microscale processes are critically important to soil ecology and biogeochemistry yet are difficult to study due to soil's opacity and complexity. To advance the study of soil processes, we constructed transparent soil microcosms that enable the visualization of microbes via fluorescence microscopy and the non-destructive measurement of microbial activity and carbon uptake in situ via Raman microspectroscopy. We assessed the polymer Nafion and the crystal cryolite as optically transparent soil substrates. We demonstrated that both substrates enable the growth, maintenance, and visualization of microbial cells in three dimensions over time, and are compatible with stable isotope probing using Raman. We applied this system to ascertain that after a dry-down/rewetting cycle, bacteria on and near dead fungal hyphae were more metabolically active than those far from hyphae. These data underscore the impact fungi have facilitating bacterial survival in fluctuating conditions and how these microcosms can yield insights into microscale microbial activities.}, }
@article {pmid33140283, year = {2021}, author = {Zhao, Y and Chen, J and Bai, B and Wang, Y and Zheng, J and Yu, Z and Deng, Q and Li, P}, title = {Pathogen determination from clinical abscess fluids using metagenomic next-generation sequencing.}, journal = {Folia microbiologica}, volume = {66}, number = {2}, pages = {197-202}, pmid = {33140283}, issn = {1874-9356}, support = {2020A1515010979//Natural Science Foundation of Guangdong Province/ ; JCYJ20170412143551332//Science, Technology and Innovation Commission of Shenzhen Municipality of key funds/ ; JCYJ20180302144721183//Science, Technology and Innovation Commission of Shenzhen Municipality of basic research funds/ ; JCYJ20180302144340004//Science, Technology and Innovation Commission of Shenzhen Municipality of basic research funds/ ; JCYJ20180302144345028//Science, Technology and Innovation Commission of Shenzhen Municipality of basic research funds/ ; JCYJ20180302144431923//Science, Technology and Innovation Commission of Shenzhen Municipality of basic research funds/ ; 2019001//Shenzhen Nanshan District Scientific Research Program of the People's Republic of China/ ; 2019004//Shenzhen Nanshan District Scientific Research Program of the People's Republic of China/ ; 2019005//Shenzhen Nanshan District Scientific Research Program of the People's Republic of China/ ; 2019027//Shenzhen Nanshan District Scientific Research Program of the People's Republic of China/ ; A2018163//provincial medical funds of Guangdong/ ; SZXK06162//Shenzhen Key Medical Discipline Construction Fund/ ; }, mesh = {*Abscess/diagnosis ; Firmicutes ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; Sensitivity and Specificity ; }, abstract = {Abscesses are often clinically manifested as local necrotic tissues in various organs or systems of the human body, which is commonly caused by microbial infection. Rapid and accurate identification of pathogens from clinical abscetic samples would greatly guide a clinician to make the precise choices of the antimicrobial treatment. Here, this study aimed to investigate the application of metagenomic next-generation sequencing (mNGS) in the microbial detection of clinical samples of abscess fluids from various organs or systems. Nine patients with abscess from various organs or systems were enrolled in this study. The pathogenic bacteria in abscess fluid were detected and compared by the conventional bacterial culture and mNGS respectively. The dominant pathogens of abscess fluids in 8 cases can be found directly from mNGS, dominating over 80% of the total reads abundance of the microbiome. Although the pathogens from 6 cases detected by mNGS were consistent with that from the conventional bacteria culture method, the fastidious obligate anaerobic bacteria in 2 cases additionally detected by mNGS were not found by the conventional culture method. Moreover, complex polymicrobial infection containing Parvimonas micra in one case negatively with conventional bacterial culture were demonstrated by the mNGS method. And the mNGS method can directly reflect the diversity of microbial ecology in the abscess fluids from the different parts of the human body. Conclusively, mNGS can be used as a supplemental method for the pathogen detection of clinically abscess fluids.}, }
@article {pmid33139872, year = {2021}, author = {Lecoeuvre, A and Ménez, B and Cannat, M and Chavagnac, V and Gérard, E}, title = {Microbial ecology of the newly discovered serpentinite-hosted Old City hydrothermal field (southwest Indian ridge).}, journal = {The ISME journal}, volume = {15}, number = {3}, pages = {818-832}, pmid = {33139872}, issn = {1751-7370}, mesh = {Archaea/genetics ; Carbon ; *Ecosystem ; *Hydrothermal Vents ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Lost City (mid-Atlantic ridge) is a unique oceanic hydrothermal field where carbonate-brucite chimneys are colonized by a single phylotype of archaeal Methanosarcinales, as well as sulfur- and methane-metabolizing bacteria. So far, only one submarine analog of Lost City has been characterized, the Prony Bay hydrothermal field (New Caledonia), which nonetheless shows more microbiological similarities with ecosystems associated with continental ophiolites. This study presents the microbial ecology of the 'Lost City'-type Old City hydrothermal field, recently discovered along the southwest Indian ridge. Five carbonate-brucite chimneys were sampled and subjected to mineralogical and geochemical analyses, microimaging, as well as 16S rRNA-encoding gene and metagenomic sequencing. Dominant taxa and metabolisms vary between chimneys, in conjunction with the predicted redox state, while potential formate- and CO-metabolizing microorganisms as well as sulfur-metabolizing bacteria are always abundant. We hypothesize that the variable environmental conditions resulting from the slow and diffuse hydrothermal fluid discharge that currently characterizes Old City could lead to different microbial populations between chimneys that utilize CO and formate differently as carbon or electron sources. Old City discovery and this first description of its microbial ecology opens up attractive perspectives for understanding environmental factors shaping communities and metabolisms in oceanic serpentinite-hosted ecosystems.}, }
@article {pmid33139480, year = {2021}, author = {Sibinelli-Sousa, S and Hespanhol, JT and Bayer-Santos, E}, title = {Targeting the Achilles' Heel of Bacteria: Different Mechanisms To Break Down the Peptidoglycan Cell Wall during Bacterial Warfare.}, journal = {Journal of bacteriology}, volume = {203}, number = {7}, pages = {}, pmid = {33139480}, issn = {1098-5530}, mesh = {Bacteria/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biological Warfare ; Cell Wall/genetics/*metabolism ; Peptidoglycan/*metabolism ; }, abstract = {Bacteria commonly live in dense polymicrobial communities and compete for scarce resources. Consequently, they employ a diverse array of mechanisms to harm, inhibit, and kill their competitors. The cell wall is essential for bacterial survival by providing mechanical strength to resist osmotic stress. Because peptidoglycan is the major component of the cell wall and its synthesis is a complex multistep pathway that requires the coordinate action of several enzymes, it provides a target for rival bacteria, which have developed a large arsenal of antibacterial molecules to attack the peptidoglycan of competitors. These molecules include antibiotics, bacteriocins, and contact-dependent effectors that are either secreted into the medium or directly translocated into a target cell. In this minireview, we summarize the diversity of these molecules and highlight distinct mechanisms to disrupt the peptidoglycan, giving special attention to molecules that are known or have the potential to be used during interbacterial competitions.}, }
@article {pmid33138291, year = {2020}, author = {Lyu, Y and Debevere, S and Bourgeois, H and Ran, M and Broeckx, BJG and Vanhaecke, L and Wiele, TV and Hesta, M}, title = {Dose-Dependent Effects of Dietary Xylooligosaccharides Supplementation on Microbiota, Fermentation and Metabolism in Healthy Adult Cats.}, journal = {Molecules (Basel, Switzerland)}, volume = {25}, number = {21}, pages = {}, pmid = {33138291}, issn = {1420-3049}, mesh = {*Animal Feed ; Animals ; *Bacteria/classification/growth &amp; development ; Cats ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Glucuronates/*pharmacology ; Oligosaccharides/*pharmacology ; }, abstract = {In order to investigate the effect and appropriate dose of prebiotics, this study evaluated the effect of two levels of xylooligosaccharides (XOS) in cats. Twenty-four healthy adult cats were divided into three groups: no-XOS control diet with 1% cellulose; low XOS supplementation (LXOS) with 0.04% XOS and 0.96% cellulose; and high XOS supplementation (HXOS) with 0.40% XOS and 0.60% cellulose. Both XOS groups increased blood 3-hydroxybutyryl carnitine levels and decreased hexadecanedioyl carnitine levels. Both XOS treatments displayed an increased bacterial abundance of Blautia, Clostridium XI, and Collinsella and a decreased abundance of Megasphaera and Bifidobacterium. LXOS groups increased fecal pH and bacterial abundance of Streptococcus and Lactobacillus, decreased blood glutaryl carnitine concentration, and Catenibacterium abundance. HXOS group showed a more distinct microbiome profile and higher species richness, and an increased bacterial abundance of Subdoligranulum, Ruminococcaceae genus (unassigned genus), Erysipelotrichaceae genus, and Lachnospiraceae. Correlations between bacterial abundances and blood and fecal parameters were also observed. In conclusion, XOS could benefit feline gut health by altering microbiota; its effects dependant on the dose. The higher-dose XOS increased bacterial populations that possibly promoted intestinal fermentation, while the lower dose altered populations of carbohydrate-metabolic microbiota and possibly modulated host metabolism. Low-dose prebiotics may become a trend in future studies.}, }
@article {pmid33134552, year = {2020}, author = {Latorre-Pérez, A and Pascual, J and Porcar, M and Vilanova, C}, title = {A lab in the field: applications of real-time, in situ metagenomic sequencing.}, journal = {Biology methods &amp; protocols}, volume = {5}, number = {1}, pages = {bpaa016}, pmid = {33134552}, issn = {2396-8923}, abstract = {High-throughput metagenomic sequencing is considered one of the main technologies fostering the development of microbial ecology. Widely used second-generation sequencers have enabled the analysis of extremely diverse microbial communities, the discovery of novel gene functions, and the comprehension of the metabolic interconnections established among microbial consortia. However, the high cost of the sequencers and the complexity of library preparation and sequencing protocols still hamper the application of metagenomic sequencing in a vast range of real-life applications. In this context, the emergence of portable, third-generation sequencers is becoming a popular alternative for the rapid analysis of microbial communities in particular scenarios, due to their low cost, simplicity of operation, and rapid yield of results. This review discusses the main applications of real-time, in situ metagenomic sequencing developed to date, highlighting the relevance of this technology in current challenges (such as the management of global pathogen outbreaks) and in the next future of industry and clinical diagnosis.}, }
@article {pmid33133427, year = {2020}, author = {Harvey, HJ and Wildman, RD and Mooney, SJ and Avery, SV}, title = {Challenges and approaches in assessing the interplay between microorganisms and their physical micro-environments.}, journal = {Computational and structural biotechnology journal}, volume = {18}, number = {}, pages = {2860-2866}, pmid = {33133427}, issn = {2001-0370}, abstract = {Spatial structure over scales ranging from nanometres to centimetres (and beyond) varies markedly in diverse habitats and the industry-relevant settings that support microbial activity. Developing an understanding of the interplay between a structured environment and the associated microbial processes and ecology is fundamental, but challenging. Several novel approaches have recently been developed and implemented to help address key questions for the field: from the use of imaging tools such as X-ray Computed Tomography to explore microbial growth in soils, to the fabrication of scratched materials to examine microbial-surface interactions, to the design of microfluidic devices to track microbial biofilm formation and the metabolic processes therein. This review discusses new approaches and challenges for incorporating structured elements into the study of microbial processes across different scales. We highlight how such methods can be pivotal for furthering our understanding of microbial interactions with their environments.}, }
@article {pmid33133035, year = {2020}, author = {Colby, GA and Ruuskanen, MO and St Pierre, KA and St Louis, VL and Poulain, AJ and Aris-Brosou, S}, title = {Warming Climate Is Reducing the Diversity of Dominant Microbes in the Largest High Arctic Lake.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {561194}, pmid = {33133035}, issn = {1664-302X}, abstract = {Temperatures in the Arctic are expected to increase dramatically over the next century, and transform high latitude watersheds. However, little is known about how microbial communities and their underlying metabolic processes will be affected by these environmental changes in freshwater sedimentary systems. To address this knowledge gap, we analyzed sediments from Lake Hazen, NU Canada. Here, we exploit the spatial heterogeneity created by varying runoff regimes across the watershed of this uniquely large high-latitude lake to test how a transition from low to high runoff, used as one proxy for climate change, affects the community structure and functional potential of dominant microbes. Based on metagenomic analyses of lake sediments along these spatial gradients, we show that increasing runoff leads to a decrease in taxonomic and functional diversity of sediment microbes. Our findings are likely to apply to other, smaller, glacierized watersheds typical of polar or high latitude ecosystems; we can predict that such changes will have far reaching consequences on these ecosystems by affecting nutrient biogeochemical cycling, the direction and magnitude of which are yet to be determined.}, }
@article {pmid33131854, year = {2021}, author = {Durán, J and Rodríguez, A and Heiðmarsson, S and Lehmann, JRK and Del Moral, &#xc1; and Garrido-Benavent, I and De Los Ríos, A}, title = {Cryptogamic cover determines soil attributes and functioning in polar terrestrial ecosystems.}, journal = {The Science of the total environment}, volume = {762}, number = {}, pages = {143169}, doi = {10.1016/j.scitotenv.2020.143169}, pmid = {33131854}, issn = {1879-1026}, mesh = {Biodiversity ; Climate Change ; *Ecosystem ; *Soil ; Soil Microbiology ; }, abstract = {We still lack studies that provide evidence for direct links between the development of soil surface cryptogamic communities and soil attributes and functioning. This is particularly true in areas free of potentially confounding factors such as different soil types, land uses, or anthropogenic disturbances. Despite the ecological importance of polar ecosystems and their sensitivity to climate change, we are far from understanding how their soils function and will respond to climate change-driven alterations in above- and belowground features. We used two complementary approaches (i.e. cover gradients in the forefront of retreating glaciers as well as long-time deglaciated areas with well-developed cryptogamic cover types) to evaluate the role of cryptogams driving multiple soil biotic and abiotic attributes and functioning rates in polar terrestrial ecosystems. Increases in cryptogamic cover were consistently related to increases in organic matter accumulation, soil fertility, and bacterial diversity, but also in enhanced soil functioning rates in both sampling areas. However, we also show that the ability to influence soil attributes varies among different polar cryptogamic covers, indicating that their differential ability to thrive under climate-change scenarios will largely determine the fate of polar soils in coming decades.}, }
@article {pmid33130421, year = {2020}, author = {Boulard, L and Parrhysius, P and Jacobs, B and Dierkes, G and Wick, A and Buchmeier, G and Koschorreck, J and Ternes, TA}, title = {Development of an analytical method to quantify pharmaceuticals in fish tissues by liquid chromatography-tandem mass spectrometry detection and application to environmental samples.}, journal = {Journal of chromatography. A}, volume = {1633}, number = {}, pages = {461612}, doi = {10.1016/j.chroma.2020.461612}, pmid = {33130421}, issn = {1873-3778}, mesh = {Animals ; *Chromatography, Liquid ; Drug Residues/*analysis ; Environmental Monitoring/*methods ; *Fishes/metabolism ; Food Analysis/*methods ; Limit of Detection ; Rivers/*chemistry ; Solid Phase Extraction ; *Tandem Mass Spectrometry ; Wastewater/analysis ; Water Pollutants, Chemical/analysis ; }, abstract = {A sensitive multiresidue method was developed to quantify 35 pharmaceuticals and 28 metabolites/transformation products (TPs) in fish liver, fish fillet and fish plasma via LC-MS/MS. The method was designed to cover a broad range of substance polarities. This objective was realized by using non-discriminating sample clean-ups including separation technique based on size exclusion, namely restricted access media (RAM) chromatography. This universal clean-up allows for an easy integration of further organic micropollutants into the analytical method. Limits of quantification (LOQ) ranged from 0.05 to 5.5 ng/mL in fish plasma, from 0.1 to 19 ng/g d.w. (dry weight) in fish fillet and from 0.46 to 48 ng/g d.w. in fish liver. The method was applied for the analysis of fillets and livers of breams from the rivers Rhine and Saar, the Teltow Canal as well as carps kept in fish monitoring ponds fed by effluent from municipal wastewater treatment plants. This allowed for the first detection of 17 analytes including 10 metabolites/TPs such as gabapentin lactam and norlidocaine in fish tissues. These results highlight the importance of including metabolites and transformation products of pharmaceuticals in fish monitoring campaigns and further investigating their potential effects.}, }
@article {pmid33129268, year = {2020}, author = {Djemiel, C and Dequiedt, S and Karimi, B and Cottin, A and Girier, T and El Djoudi, Y and Wincker, P and Lelièvre, M and Mondy, S and Chemidlin Prévost-Bouré, N and Maron, PA and Ranjard, L and Terrat, S}, title = {BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {492}, pmid = {33129268}, issn = {1471-2105}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biodiversity ; Cluster Analysis ; Computational Biology/*methods ; Computer Simulation ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Fungi/*genetics ; *Genes, rRNA ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; *Software ; Soil Microbiology ; }, abstract = {BACKGROUND: The ability to compare samples or studies easily using metabarcoding so as to better interpret microbial ecology results is an upcoming challenge. A growing number of metabarcoding pipelines are available, each with its own benefits and limitations. However, very few have been developed to offer the opportunity to characterize various microbial communities (e.g., archaea, bacteria, fungi, photosynthetic microeukaryotes) with the same tool.<br><br>RESULTS: BIOCOM-PIPE is a flexible and independent suite of tools for processing data from high-throughput sequencing technologies, Roche 454 and Illumina platforms, and focused on the diversity of archaeal, bacterial, fungal, and photosynthetic microeukaryote amplicons. Various original methods were implemented in BIOCOM-PIPE to (1) remove chimeras based on read abundance, (2) align sequences with structure-based alignments of RNA homologs using covariance models, and (3) a post-clustering tool (ReClustOR) to improve OTUs consistency based on a reference OTU database. The comparison with two other pipelines (FROGS and mothur) and Amplicon Sequence Variant definition highlighted that BIOCOM-PIPE was better at discriminating land use groups.<br><br>CONCLUSIONS: The BIOCOM-PIPE pipeline makes it possible to analyze 16S, 18S and 23S rRNA genes in the same packaged tool. The new post-clustering approach defines a biological database from previously analyzed samples and performs post-clustering of reads with this reference database by using open-reference clustering. This makes it easier to compare projects from various sequencing runs, and increased the congruence among results. For all users, the pipeline was developed to allow for adding or modifying the components, the databases and the bioinformatics tools easily, giving high modularity for each analysis.}, }
@article {pmid33125668, year = {2020}, author = {Kim, S and Park, MS and Song, J and Kang, I and Cho, JC}, title = {High-throughput cultivation based on dilution-to-extinction with catalase supplementation and a case study of cultivating acI bacteria from Lake Soyang.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {58}, number = {11}, pages = {893-905}, doi = {10.1007/s12275-020-0452-2}, pmid = {33125668}, issn = {1976-3794}, mesh = {*Bacteria/classification/isolation &amp; purification ; Bacteriological Techniques/*methods ; Culture Media/*chemistry ; Ecosystem ; Lakes/*microbiology ; Metagenomics ; *Water Microbiology ; }, abstract = {Multi-omics approaches, including metagenomics and single-cell amplified genomics, have revolutionized our understanding of the hidden diversity and function of microbes in nature. Even in the omics age, cultivation is an essential discipline in microbial ecology since microbial cultures are necessary to assess the validity of an in silico prediction about the microbial metabolism and to isolate viruses infecting bacteria and archaea. However, the ecophysiological characteristics of predominant freshwater bacterial lineages remain largely unknown due to the scarcity of cultured representatives. In an ongoing effort to cultivate the uncultured majority of freshwater bacteria, the most abundant freshwater Actinobacteria acI clade has recently been cultivated from Lake Soyang through catalase-supplemented high-throughput cultivation based on dilution-to-extinction. This method involves physical isolation of target microbes from mixed populations, culture media simulating natural habitats, and removal of toxic compounds. In this protocol, we describe detailed procedures for isolating freshwater oligotrophic microbes, as well as the essence of the dilution-to-extinction culturing. As a case study employing the catalase-supplemented dilution-to-extinction protocol, we also report a cultivation trial using a water sample collected from Lake Soyang. Of the 480 cultivation wells inoculated with a single lake-water sample, 75 new acI strains belonging to 8 acI tribes (acI-A1, A2, A4, A5, A6, A7, B1, B4, C1, and C2) were cultivated, and each representative strain per subclade could be revived from glycerol stocks. These cultivation results demonstrate that the protocol described in this study is efficient in isolating freshwater bacterioplankton harboring streamlined genomes.}, }
@article {pmid33123759, year = {2021}, author = {Janiszewska, M and Sobkowiak, S and Stefańczyk, E and Śliwka, J}, title = {Population Structure of Phytophthora infestans from a Single Location in Poland Over a Long Period of Time in Context of Weather Conditions.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {746-757}, pmid = {33123759}, issn = {1432-184X}, support = {PW Task 3.1//Polish Ministry of Agriculture and Rural Development/ ; 1-3-00-1-02//Polish Ministry of Science and Higher Education/ ; MN 1-3-00-3-01//Polish Ministry of Science and Higher Education/ ; }, mesh = {*Phytophthora infestans/genetics ; Plant Diseases ; Poland ; *Solanum tuberosum ; Weather ; }, abstract = {Phytophthora infestans (Mont.) de Bary is a destructive potato pathogen. Changing weather conditions are among the factors that influence the pathogen population structure. In this study, 237 P. infestans isolates were collected from a single unprotected experimental field in an area with high late-blight pressure located in Boguchwała in the southeastern part of Poland during 15 growing seasons (2000-2014). The isolates were assessed for mating type, mitochondrial haplotype, resistance to metalaxyl, virulence, and polymorphism of 14 single-sequence repeat markers (SSRs). The results revealed 89 unique genotypes among the 237 P. infestans isolates. Eighty-seven isolates belonged to genotype 34_A1, which was detected in all the years of research except 2012. Isolates of P. infestans from individual years were very similar to each other, as shown by Nei's genetic identity based on 14 SSR markers. The obtained results on isolate characteristics were analyzed in terms of meteorological data (air temperature and precipitation) and indicated that frost, long winters, and hot, dry summers did not directly affect the P. infestans population structure. We described the variability in metalaxyl resistance and virulence among isolates of the P. infestans genotype 34_A1.}, }
@article {pmid33123758, year = {2021}, author = {Tzuri, N and Caspi-Fluger, A and Betelman, K and Rohkin Shalom, S and Chiel, E}, title = {Horizontal Transmission of Microbial Symbionts Within a Guild of Fly Parasitoids.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {818-827}, pmid = {33123758}, issn = {1432-184X}, support = {435/2018//Israel science Foundation/ ; }, mesh = {Animals ; Host-Parasite Interactions ; Larva ; Pupa ; *Wasps ; *Wolbachia/genetics ; }, abstract = {Many insects harbor facultative microbial symbionts which affect the ecology of their hosts in diverse ways. Most symbionts are transmitted vertically with high fidelity, whereas horizontal transmission occurs rarely. Parasitoid larvae feed on a single host and are in close physical contact with it, providing an ecological opportunity for symbionts' horizontal transmission, but there is little empirical evidence documenting this. Here we studied horizontal transmission of three bacterial symbionts-Rickettsia, Sodalis, and Wolbachia-between three fly pupal ectoparasitoid species: Spalangia cameroni, S. endius, and Muscidifurax raptor. Muscidifurax raptor readily parasitized and successfully developed on the Spalangia spp., while the inverse did not happen. The two Spalangia spp. attacked each other and conspecifics in very low rates. Symbiont horizontal transmissions followed by stable vertical transmission in the recipient species were achieved, in low percentages, only between conspecifics: Wolbachia from infected to uninfected M. raptor, Rickettsia in S. endius, and Sodalis in S. cameroni. Low frequency of horizontal transmissions occurred in the interspecific combinations, but none of them persisted in the recipient species beyond F4, at most. Our study is one of few to demonstrate symbionts' horizontal transmission between hosts within the same trophic level and guild and highlights the rarity of such events.}, }
@article {pmid33123113, year = {2020}, author = {Mitchell, K and Ronas, J and Dao, C and Freise, AC and Mangul, S and Shapiro, C and Moberg Parker, J}, title = {PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {584699}, pmid = {33123113}, issn = {1664-302X}, abstract = {Improvements in high-throughput sequencing makes targeted amplicon analysis an ideal method for the study of human and environmental microbiomes by undergraduates. Multiple bioinformatics programs are available to process and interpret raw microbial diversity datasets, and the choice of programs to use in curricula is largely determined by student learning goals. Many of the most commonly used microbiome bioinformatics platforms offer end-to-end data processing and data analysis using a command line interface (CLI), but the downside for novice microbiome researchers is the steep learning curve often required. Alternatively, some sequencing providers include processing of raw data and taxonomy assignments as part of their pipelines. This, when coupled with available web-based or graphical user interface (GUI) analysis and visualization tools, eliminates the need for students or instructors to have extensive CLI experience. However, lack of universal data formats can make integration of these tools challenging. For example, tools for upstream and downstream analyses frequently use multiple different data formats which then require writing custom scripts or hours of manual work to make the files compatible. Here, we describe a microbial ecology bioinformatics curriculum that focuses on data analysis, visualization, and statistical reasoning by taking advantage of existing web-based and GUI tools. We created the Program for Unifying Microbiome Analysis Applications (PUMAA), which solves the problem of inconsistent files by formatting the output files from several raw data processing programs to seamlessly transition to a suite of GUI programs for analysis and visualization of microbiome taxonomic and inferred functional profiles. Additionally, we created a series of tutorials to accompany each of the microbiome analysis curricular modules. From pre- and post-course surveys, students in this curriculum self-reported conceptual and confidence gains in bioinformatics and data analysis skills. Students also demonstrated gains in biologically relevant statistical reasoning based on rubric-guided evaluations of open-ended survey questions and the Statistical Reasoning in Biology Concept Inventory. The PUMAA program and associated analysis tutorials enable students and researchers with no computational experience to effectively analyze real microbiome datasets to investigate real-world research questions.}, }
@article {pmid33123105, year = {2020}, author = {Navarro, MOP and Dilarri, G and Simionato, AS and Grzegorczyk, K and Dealis, ML and Cano, BG and Barazetti, AR and Afonso, L and Chryssafidis, AL and Ferreira, H and Andrade, G}, title = {Corrigendum: Determining the Targets of Fluopsin C Action on Gram-Negative and Gram-Positive Bacteria.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {574002}, doi = {10.3389/fmicb.2020.574002}, pmid = {33123105}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2020.01076.].}, }
@article {pmid33118857, year = {2021}, author = {Patel, D and Shittu, TA and Baroncelli, R and Muthumeenakshi, S and Osborne, TH and Janganan, TK and Sreenivasaprasad, S}, title = {Genome Sequence of the Biocontrol Agent Coniothyrium minitans Conio (IMI 134523).}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {34}, number = {2}, pages = {222-225}, doi = {10.1094/MPMI-05-20-0124-A}, pmid = {33118857}, issn = {0894-0282}, mesh = {*Ascomycota/genetics ; Crops, Agricultural/microbiology ; *Genome, Fungal/genetics ; Microbial Interactions/genetics ; }, abstract = {Coniothyrium minitans (synonym, Paraphaeosphaeria minitans) is a highly specific mycoparasite of the wide host range crop pathogen Sclerotinia sclerotiorum. The capability of C. minitans to destroy the sclerotia of S. sclerotiorum has been well recognized and it is available as a widely used biocontrol product Contans WG. We present the draft genome sequence of C. minitans Conio (IMI 134523), which has previously been used in extensive studies that formed part of a registration package of the commercial product. This work provides a distinctive resource for further research into the molecular basis of mycoparasitism to harness the biocontrol potential of C. minitans.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.}, }
@article {pmid33117398, year = {2020}, author = {Pirr, S and Viemann, D}, title = {Host Factors of Favorable Intestinal Microbial Colonization.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {584288}, pmid = {33117398}, issn = {1664-3224}, mesh = {Animals ; Gastrointestinal Microbiome/*immunology ; Homeostasis/immunology ; Humans ; Immune System/immunology ; Immunity, Mucosal/*immunology ; Symbiosis/immunology ; }, abstract = {Gut microbial colonization starts with birth and initiates a complex process between the host and the microbiota. Successful co-development of both establishes a symbiotic mutual relationship and functional homeostasis, while alterations thereof predispose the individual life-long to inflammatory and metabolic diseases. Multiple data have been provided how colonizing microbes induce a reprogramming and maturation of immunity by providing crucial instructing information to the newborn immune system. Less is known about what host factors have influence on the interplay between intestinal immunity and the composition of the gut microbial ecology. Here we review existing evidence regarding host factors that contribute to a favorable development of the gut microbiome and thereby successful maturation of gut mucosal immunity.}, }
@article {pmid33116344, year = {2020}, author = {Crous, PW and Wingfield, MJ and Chooi, YH and Gilchrist, CLM and Lacey, E and Pitt, JI and Roets, F and Swart, WJ and Cano-Lira, JF and Valenzuela-Lopez, N and Hubka, V and Shivas, RG and Stchigel, AM and Holdom, DG and Jurjević, &#x17d; and Kachalkin, AV and Lebel, T and Lock, C and Martín, MP and Tan, YP and Tomashevskaya, MA and Vitelli, JS and Baseia, IG and Bhatt, VK and Brandrud, TE and De Souza, JT and Dima, B and Lacey, HJ and Lombard, L and Johnston, PR and Morte, A and Papp, V and Rodríguez, A and Rodríguez-Andrade, E and Semwal, KC and Tegart, L and Abad, ZG and Akulov, A and Alvarado, P and Alves, A and Andrade, JP and Arenas, F and Asenjo, C and Ballarà, J and Barrett, MD and Berná, LM and Berraf-Tebbal, A and Bianchinotti, MV and Bransgrove, K and Burgess, TI and Carmo, FS and Chávez, R and Čmoková, A and Dearnaley, JDW and de A Santiago, ALCM and Freitas-Neto, JF and Denman, S and Douglas, B and Dovana, F and Eichmeier, A and Esteve-Raventós, F and Farid, A and Fedosova, AG and Ferisin, G and Ferreira, RJ and Ferrer, A and Figueiredo, CN and Figueiredo, YF and Reinoso-Fuentealba, CG and Garrido-Benavent, I and Cañete-Gibas, CF and Gil-Durán, C and Glushakova, AM and Gonçalves, MFM and González, M and Gorczak, M and Gorton, C and Guard, FE and Guarnizo, AL and Guarro, J and Gutiérrez, M and Hamal, P and Hien, LT and Hocking, AD and Houbraken, J and Hunter, GC and Inácio, CA and Jourdan, M and Kapitonov, VI and Kelly, L and Khanh, TN and Kisło, K and Kiss, L and Kiyashko, A and Kolařík, M and Kruse, J and Kubátová, A and Kučera, V and Kučerová, I and Kušan, I and Lee, HB and Levicán, G and Lewis, A and Liem, NV and Liimatainen, K and Lim, HJ and Lyons, MN and Maciá-Vicente, JG and Magaña-Dueñas, V and Mahiques, R and Malysheva, EF and Marbach, PAS and Marinho, P and Matočec, N and McTaggart, AR and Mešić, A and Morin, L and Muñoz-Mohedano, JM and Navarro-Ródenas, A and Nicolli, CP and Oliveira, RL and Otsing, E and Ovrebo, CL and Pankratov, TA and Paños, A and Paz-Conde, A and Pérez-Sierra, A and Phosri, C and Pintos, &#xc1; and Pošta, A and Prencipe, S and Rubio, E and Saitta, A and Sales, LS and Sanhueza, L and Shuttleworth, LA and Smith, J and Smith, ME and Spadaro, D and Spetik, M and Sochor, M and Sochorová, Z and Sousa, JO and Suwannasai, N and Tedersoo, L and Thanh, HM and Thao, LD and Tkalčec, Z and Vaghefi, N and Venzhik, AS and Verbeken, A and Vizzini, A and Voyron, S and Wainhouse, M and Whalley, AJS and Wrzosek, M and Zapata, M and Zeil-Rolfe, I and Groenewald, JZ}, title = {Fungal Planet description sheets: 1042-1111.}, journal = {Persoonia}, volume = {44}, number = {}, pages = {301-459}, pmid = {33116344}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Antarctica, Cladosporium arenosum from marine sediment sand. Argentina, Kosmimatamyces alatophylus (incl. Kosmimatamyces gen. nov.) from soil. Australia, Aspergillus banksianus, Aspergillus kumbius, Aspergillus luteorubrus, Aspergillus malvicolor and Aspergillus nanangensis from soil, Erysiphe medicaginis from leaves of Medicago polymorpha, Hymenotorrendiella communis on leaf litter of Eucalyptus bicostata, Lactifluus albopicri and Lactifluus austropiperatus on soil, Macalpinomyces collinsiae on Eriachne benthamii, Marasmius vagus on soil, Microdochium dawsoniorum from leaves of Sporobolus natalensis, Neopestalotiopsis nebuloides from leaves of Sporobolus elongatus, Pestalotiopsis etonensis from leaves of Sporobolus jacquemontii, Phytophthora personensis from soil associated with dying Grevillea mccutcheonii. Brazil, Aspergillus oxumiae from soil, Calvatia baixaverdensis on soil, Geastrum calycicoriaceum on leaf litter, Greeneria kielmeyerae on leaf spots of Kielmeyera coriacea. Chile, Phytophthora aysenensis on collar rot and stem of Aristotelia chilensis. Croatia, Mollisia gibbospora on fallen branch of Fagus sylvatica. Czech Republic, Neosetophoma hnaniceana from Buxus sempervirens. Ecuador, Exophiala frigidotolerans from soil. Estonia, Elaphomyces bucholtzii in soil. France, Venturia paralias from leaves of Euphorbia paralias. India, Cortinarius balteatoindicus and Cortinarius ulkhagarhiensis on leaf litter. Indonesia, Hymenotorrendiella indonesiana on Eucalyptus urophylla leaf litter. Italy, Penicillium taurinense from indoor chestnut mill. Malaysia, Hemileucoglossum kelabitense on soil, Satchmopsis pini on dead needles of Pinus tecunumanii. Poland, Lecanicillium praecognitum on insects' frass. Portugal, Neodevriesia aestuarina from saline water. Republic of Korea, Gongronella namwonensis from freshwater. Russia, Candida pellucida from Exomias pellucidus, Heterocephalacria septentrionalis as endophyte from Cladonia rangiferina, Vishniacozyma phoenicis from dates fruit, Volvariella paludosa from swamp. Slovenia, Mallocybe crassivelata on soil. South Africa, Beltraniella podocarpi, Hamatocanthoscypha podocarpi, Coleophoma podocarpi and Nothoseiridium podocarpi (incl. Nothoseiridium gen. nov.) from leaves of Podocarpus latifolius, Gyrothrix encephalarti from leaves of Encephalartos sp., Paraphyton cutaneum from skin of human patient, Phacidiella alsophilae from leaves of Alsophila capensis, and Satchmopsis metrosideri on leaf litter of Metrosideros excelsa. Spain, Cladophialophora cabanerensis from soil, Cortinarius paezii on soil, Cylindrium magnoliae from leaves of Magnolia grandiflora, Trichophoma cylindrospora (incl. Trichophoma gen. nov.) from plant debris, Tuber alcaracense in calcareus soil, Tuber buendiae in calcareus soil. Thailand, Annulohypoxylon spougei on corticated wood, Poaceascoma filiforme from leaves of unknown Poaceae. UK, Dendrostoma luteum on branch lesions of Castanea sativa, Ypsilina buttingtonensis from heartwood of Quercus sp. Ukraine, Myrmecridium phragmiticola from leaves of Phragmites australis. USA, Absidia pararepens from air, Juncomyces californiensis (incl. Juncomyces gen. nov.) from leaves of Juncus effusus, Montagnula cylindrospora from a human skin sample, Muriphila oklahomaensis (incl. Muriphila gen. nov.) on outside wall of alcohol distillery, Neofabraea eucalyptorum from leaves of Eucalyptus macrandra, Diabolocovidia claustri (incl. Diabolocovidia gen. nov.) from leaves of Serenoa repens, Paecilomyces penicilliformis from air, Pseudopezicula betulae from leaves of leaf spots of Populus tremuloides. Vietnam, Diaporthe durionigena on branches of Durio zibethinus and Roridomyces pseudoirritans on rotten wood. Morphological and culture characteristics are supported by DNA barcodes.}, }
@article {pmid33115951, year = {2020}, author = {Khan, S and Waliullah, S and Godfrey, V and Khan, MAW and Ramachandran, RA and Cantarel, BL and Behrendt, C and Peng, L and Hooper, LV and Zaki, H}, title = {Dietary simple sugars alter microbial ecology in the gut and promote colitis in mice.}, journal = {Science translational medicine}, volume = {12}, number = {567}, pages = {}, doi = {10.1126/scitranslmed.aay6218}, pmid = {33115951}, issn = {1946-6242}, support = {P30 CA142543/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Colitis/chemically induced ; Dextran Sulfate ; Diet ; *Dietary Sugars/adverse effects ; Disease Models, Animal ; Mice ; Mice, Inbred C57BL ; Monosaccharides ; }, abstract = {The higher prevalence of inflammatory bowel disease (IBD) in Western countries points to Western diet as a possible IBD risk factor. High sugar, which is linked to many noncommunicable diseases, is a hallmark of the Western diet, but its role in IBD remains unknown. Here, we studied the effects of simple sugars such as glucose and fructose on colitis pathogenesis in wild-type and Il10[-/-] mice. Wild-type mice fed 10% glucose in drinking water or high-glucose diet developed severe colitis induced by dextran sulfate sodium. High-glucose-fed Il10[-/-] mice also developed a worsened colitis compared to glucose-untreated Il10[-/-] mice. Short-term intake of high glucose or fructose did not trigger inflammatory responses in healthy gut but markedly altered gut microbiota composition. In particular, the abundance of the mucus-degrading bacteria Akkermansia muciniphila and Bacteroides fragilis was increased. Consistently, bacteria-derived mucolytic enzymes were enriched leading to erosion of the colonic mucus layer of sugar-fed wild-type and Il10[-/-] mice. Sugar-induced exacerbation of colitis was not observed when mice were treated with antibiotics or maintained in a germ-free environment, suggesting that altered microbiota played a critical role in sugar-induced colitis pathogenesis. Furthermore, germ-free mice colonized with microbiota from sugar-treated mice showed increased colitis susceptibility. Together, these data suggest that intake of simple sugars predisposes to colitis and enhances its pathogenesis via modulation of gut microbiota in mice.}, }
@article {pmid33115836, year = {2020}, author = {García-Timermans, C and Props, R and Zacchetti, B and Sakarika, M and Delvigne, F and Boon, N}, title = {Raman Spectroscopy-Based Measurements of Single-Cell Phenotypic Diversity in Microbial Populations.}, journal = {mSphere}, volume = {5}, number = {5}, pages = {}, pmid = {33115836}, issn = {2379-5042}, mesh = {Biodiversity ; Escherichia coli/drug effects/metabolism ; Ethanol/pharmacology ; *Microbiota ; Phenotype ; Saccharomyces cerevisiae/metabolism ; Single-Cell Analysis/instrumentation/*methods ; Spectrum Analysis, Raman/*methods ; Stress, Physiological/drug effects ; }, abstract = {Microbial cells experience physiological changes due to environmental change, such as pH and temperature, the release of bactericidal agents, or nutrient limitation. This has been shown to affect community assembly and physiological processes (e.g., stress tolerance, virulence, or cellular metabolic activity). Metabolic stress is typically quantified by measuring community phenotypic properties such as biomass growth, reactive oxygen species, or cell permeability. However, bulk community measurements do not take into account single-cell phenotypic diversity, which is important for a better understanding and the subsequent management of microbial populations. Raman spectroscopy is a nondestructive alternative that provides detailed information on the biochemical makeup of each individual cell. Here, we introduce a method for describing single-cell phenotypic diversity using the Hill diversity framework of Raman spectra. Using the biomolecular profile of individual cells, we obtained a metric to compare cellular states and used it to study stress-induced changes. First, in two Escherichia coli populations either treated with ethanol or nontreated and then in two Saccharomyces cerevisiae subpopulations with either high or low expression of a stress reporter. In both cases, we were able to quantify single-cell phenotypic diversity and to discriminate metabolically stressed cells using a clustering algorithm. We also described how the lipid, protein, and nucleic acid compositions changed after the exposure to the stressor using information from the Raman spectra. Our results show that Raman spectroscopy delivers the necessary resolution to quantify phenotypic diversity within individual cells and that this information can be used to study stress-driven metabolic diversity in microbial populations.IMPORTANCE Microbial cells that live in the same community can exist in different physiological and morphological states that change as a function of spatiotemporal variations in environmental conditions. This phenomenon is commonly known as phenotypic heterogeneity and/or diversity. Measuring this plethora of cellular expressions is needed to better understand and manage microbial processes. However, most tools to study phenotypic diversity only average the behavior of the sampled community. In this work, we present a way to quantify the phenotypic diversity of microbial samples by inferring the (bio)molecular profile of its constituent cells using Raman spectroscopy. We demonstrate how this tool can be used to quantify the phenotypic diversity that arises after the exposure of microbes to stress. Raman spectroscopy holds potential for the detection of stressed cells in bioproduction.}, }
@article {pmid33114469, year = {2020}, author = {Cornejo-Pareja, I and Ruiz-Limón, P and Gómez-Pérez, AM and Molina-Vega, M and Moreno-Indias, I and Tinahones, FJ}, title = {Differential Microbial Pattern Description in Subjects with Autoimmune-Based Thyroid Diseases: A Pilot Study.}, journal = {Journal of personalized medicine}, volume = {10}, number = {4}, pages = {}, pmid = {33114469}, issn = {2075-4426}, support = {CP16/00163, PI18/01160//Carlos III Health Institute-co-founded by Fondo Europeo de Desarrollo Regional - FEDER/ ; }, abstract = {The interaction between genetic susceptibility, epigenetic, endogenous, and environmental factors play a key role in the initiation and progression of autoimmune thyroid diseases (AITDs). Studies have shown that gut microbiota alterations take part in the development of autoimmune diseases. We have investigated the possible relationship between gut microbiota composition and the most frequent AITDs. A total of nine Hashimoto's thyroiditis (HT), nine Graves-Basedow's disease (GD), and 11 otherwise healthy donors (HDs) were evaluated. 16S rRNA pyrosequencing and bioinformatics analysis by Quantitative Insights into Microbial Ecology and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) were used to analyze the gut microbiota. Beta diversity analysis showed that gut microbiota from our groups was different. We observed an increase in bacterial richness in HT and a lower evenness in GD in comparison to the HDs. GD showed a significant increase of Fusobacteriaceae, Fusobacterium and Sutterella compared to HDs and the core microbiome features showed that Prevotellaceae and Prevotella characterized this group. Victivallaceae was increased in HT and was part of their core microbiome. Streptococcaceae, Streptococcus and Rikenellaceae were greater in HT compared to GD. Core microbiome features of HT were represented by Streptococcus, Alistipes, Anaerostipes, Dorea and Haemophilus. Faecalibacterium decreased in both AITDs compared to HDs. PICRUSt analysis demonstrated enrichment in the xenobiotics degradation, metabolism, and the metabolism of cofactors and vitamins in GD patients compared to HDs. Moreover, correlation studies showed that some bacteria were widely correlated with autoimmunity parameters. A prediction model evaluated a possible relationship between predominant concrete bacteria such as an unclassified genus of Ruminococcaceae, Sutterella and Faecalibacterium in AITDs. AITD patients present altered gut microbiota compared to HDs. These alterations could be related to the immune system development in AITD patients and the loss of tolerance to self-antigens.}, }
@article {pmid33111499, year = {2020}, author = {Zrimec, J}, title = {Multiple plasmid origin-of-transfer regions might aid the spread of antimicrobial resistance to human pathogens.}, journal = {MicrobiologyOpen}, volume = {9}, number = {12}, pages = {e1129}, pmid = {33111499}, issn = {2045-8827}, mesh = {Algorithms ; Bacteria/drug effects/*genetics ; Conjugation, Genetic/*genetics ; Databases, Genetic ; Drug Resistance, Bacterial/*genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Nucleic Acid Conformation ; Plasmids/*genetics ; Sequence Alignment ; Transformation, Bacterial/*genetics ; }, abstract = {Antimicrobial resistance poses a great danger to humanity, in part due to the widespread horizontal gene transfer of plasmids via conjugation. Modeling of plasmid transfer is essential to uncovering the fundamentals of resistance transfer and for the development of predictive measures to limit the spread of resistance. However, a major limitation in the current understanding of plasmids is the incomplete characterization of the conjugative DNA transfer mechanisms, which conceals the actual potential for plasmid transfer in nature. Here, we consider that the plasmid-borne origin-of-transfer substrates encode specific DNA structural properties that can facilitate finding these regions in large datasets and develop a DNA structure-based alignment procedure for typing the transfer substrates that outperforms sequence-based approaches. Thousands of putative DNA transfer substrates are identified, showing that plasmid mobility can be twofold higher and span almost twofold more host species than is currently known. Over half of all putative mobile plasmids contain the means for mobilization by conjugation systems belonging to different mobility groups, which can hypothetically link previously confined host ranges across ecological habitats into a robust plasmid transfer network. This hypothetical network is found to facilitate the transfer of antimicrobial resistance from environmental genetic reservoirs to human pathogens, which might be an important driver of the observed rapid resistance development in humans and thus an important point of focus for future prevention measures.}, }
@article {pmid33110109, year = {2020}, author = {Bellone, R and Lequime, S and Jupille, H and Göertz, GP and Aubry, F and Mousson, L and Piorkowski, G and Yen, PS and Gabiane, G and Vazeille, M and Sakuntabhai, A and Pijlman, GP and de Lamballerie, X and Lambrechts, L and Failloux, AB}, title = {Experimental adaptation of dengue virus 1 to Aedes albopictus mosquitoes by in vivo selection.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {18404}, pmid = {33110109}, issn = {2045-2322}, mesh = {*Adaptation, Physiological ; Aedes/*virology ; Animals ; Dengue/epidemiology/transmission ; Dengue Virus/*physiology ; Epistasis, Genetic ; Humans ; Mosquito Vectors/*virology ; }, abstract = {In most of the world, Dengue virus (DENV) is mainly transmitted by the mosquito Aedes aegypti while in Europe, Aedes albopictus is responsible for human DENV cases since 2010. Identifying mutations that make DENV more competent for transmission by Ae. albopictus will help to predict emergence of epidemic strains. Ten serial passages in vivo in Ae. albopictus led to select DENV-1 strains with greater infectivity for this vector in vivo and in cultured mosquito cells. These changes were mediated by multiple adaptive mutations in the virus genome, including a mutation at position 10,418 in the DENV 3'UTR within an RNA stem-loop structure involved in subgenomic flavivirus RNA production. Using reverse genetics, we showed that the 10,418 mutation alone does not confer a detectable increase in transmission efficiency in vivo. These results reveal the complex adaptive landscape of DENV transmission by mosquitoes and emphasize the role of epistasis in shaping evolutionary trajectories of DENV variants.}, }
@article {pmid33108474, year = {2021}, author = {Sahu, KP and Kumar, A and Patel, A and Kumar, M and Gopalakrishnan, S and Prakash, G and Rathour, R and Gogoi, R}, title = {Rice Blast Lesions: an Unexplored Phyllosphere Microhabitat for Novel Antagonistic Bacterial Species Against Magnaporthe oryzae.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {731-745}, pmid = {33108474}, issn = {1432-184X}, support = {09/083(0367)/2016-EMR-I//Council&#xa0;of&#xa0;Scientific and Industrial Research, India/ ; }, mesh = {Actinobacteria ; Ascomycota ; *Magnaporthe/genetics ; *Oryza ; Pantoea ; Plant Diseases ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Dark brown necrotic lesions caused by Magnaporthe oryzae on rice foliage is a contrasting microhabitat for leaf-colonizing microbiome as compared with the surrounding healthy chlorophyll-rich tissues. We explored culturable bacterial communities of blast lesions by adopting microbiological tools for isolating effective biocontrol bacterial strains against M. oryzae. 16S rRNA gene sequencing-based molecular identification revealed a total of 17 bacterial species belonging to Achromobacter (2), Comamonas (1), Curtobacterium (1), Enterobacter (1), Leclercia (2), Microbacterium (1), Pantoea (3), Sphingobacterium (1), and Stenotrophomonas (5) found colonizing the lesion. Over 50% of the bacterial isolates were able to suppress the mycelial growth of M. oryzae either by secretory or volatile metabolites. Volatiles released by Achromobacter sp., Curtobacterium luteum, Microbacterium oleivorans, Pantoea ananatis, Stenotrophomonas maltophilia, and Stenotrophomonas sp., and were found to be fungicidal while others showed fungistatic action. In planta pathogen challenged evaluation trial revealed the biocontrol potential of Stenotrophomonas sp. and Microbacterium oleivorans that showed over 60% blast severity suppression on the rice leaf. The lesion-associated bacterial isolates were found to trigger expression of defense genes such as OsCEBiP, OsCERK1, OsEDS1, and OsPAD4 indicating their capability to elicit innate defense in rice against blast disease. The investigation culminated in the identification of potential biocontrol agents for the management of rice blast disease.}, }
@article {pmid33105583, year = {2020}, author = {Rabieh, S and Bayaraa, O and Romeo, E and Amosa, P and Calnek, K and Idaghdour, Y and Ochsenkühn, MA and Amin, SA and Goldstein, G and Bromage, TG}, title = {MH-ICP-MS Analysis of the Freshwater and Saltwater Environmental Resources of Upolu Island, Samoa.}, journal = {Molecules (Basel, Switzerland)}, volume = {25}, number = {21}, pages = {}, pmid = {33105583}, issn = {1420-3049}, support = {S10 OD026989/OD/NIH HHS/United States ; UN-India Development Partnership Fund//United Nations Development Programme, United Nations United Nations Educational, Scientific and Cultural Organisation/ ; }, mesh = {Coral Reefs ; Environmental Monitoring/*methods ; Fresh Water/chemistry ; Geologic Sediments/chemistry ; Herbicides/analysis ; Humans ; Islands ; Mass Spectrometry/*methods ; Pesticides/analysis ; Samoa ; Seawater/chemistry ; Water Pollutants, Chemical/*analysis ; Water Quality ; }, abstract = {The elemental composition of freshwater and saltwater samples around the South Pacific island of Upolu, Samoa has been investigated together with other indicators of water quality. Up to 69 elements from Li (3) to U (92) are measured in each sample, analyzed by Mattauch-Herzog-inductively coupled plasma-mass spectrometry (MH-ICP-MS). One hundred and seventy-six samples were collected from surface freshwater sources (24 rivers, two volcanic lakes, one dam) and from seawater sources from the surface to 30 m depth (45 inner reef, reef, and outer reef locations) around Upolu Island, including river mouths and estuaries. Principal component and hierarchical clustering correlation analyses were performed on quantile normalized log transformed elemental composition data to identify groups of samples with similar characteristics and to improve the visualization of the full spectrum of elements. Human activities, such as the use of herbicides and pesticides, may relate to observed elevated concentrations of some elements contained in chemicals known to have deleterious obesogenic effects on humans that may also cause coral reef decline. Furthermore, the salinity of some saltwater samples tested were very high, possibly due to climate variability, which may additionally harm the health and biodiversity of coral reefs.}, }
@article {pmid33099662, year = {2021}, author = {Sepehri, M and Khatabi, B}, title = {Combination of Siderophore-Producing Bacteria and Piriformospora indica Provides an Efficient Approach to Improve Cadmium Tolerance in Alfalfa.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {717-730}, pmid = {33099662}, issn = {1432-184X}, mesh = {Basidiomycota ; Biodegradation, Environmental ; Cadmium/toxicity ; Humans ; Medicago sativa ; Plant Roots ; *Rhizobium ; Siderophores ; *Soil Pollutants ; }, abstract = {Application of siderophore-producing microorganisms (SPMs), as an environmentally friendly approach, facilitates plant growth and survival under heavy metals toxicity. This study evaluated the effectiveness of SPMs, belonging to the bacterial genera Rhizobium and Pseudomonas and a root endophytic fungus (Piriformospora indica) to improve the fitness of alfalfa under cadmium (Cd) stress. A greenhouse experiment was performed as a randomized design with factorial arrangement of treatments. Treatments included microbial inoculations (Sinorhizobium meliloti, Pseudomonas fluorescence, and P. indica) and different Cd concentrations (0, 2, 5, 10 mg/kg) with three replications in potting media containing sand and sterile perlite (v/v, 2:1). The effect of Cd on plant growth and development, antioxidant enzymes activities, and accumulation of Cd and nutrients in alfalfa plant was investigated. Alfalfa inoculated with SPMs showed significantly higher biomass and nutrients uptake under both normal and Cd stress conditions than the controls. Under the highest Cd concentration (10 mg/kg), alfalfa plants inoculated with P. fluorescens and P. indica, either alone or in combination, showed the highest shoot dry weights. Cd-induced oxidative stress was mitigated by SPMs through enhanced antioxidant enzyme activities of catalase, ascorbate peroxidase, and guaiacol peroxidase. We showed that P. indica either alone or in combination with the siderophore producing bacteria (SPB) minimized the toxicity of Cd by enhanced growth rate and the lower Cd concentration in the shoots. In conclusion, metal-resistant SPMs could assist alfalfa to survive in Cd-contaminated soil by enhancing plant growth and development. Application of plant-associated microbes is an efficient, environmentally friendly approach to surmount the adverse effects of heavy metals toxicity on plants, animals, and humans. Graphical abstract.}, }
@article {pmid33099661, year = {2021}, author = {Kubera, &#x141;}, title = {Spread Patterns of Antibiotic Resistance in Faecal Indicator Bacteria Contaminating an Urbanized Section of the Brda River.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {592-600}, pmid = {33099661}, issn = {1432-184X}, support = {Grant No. 008/RID/2018/19//Ministerstwo Nauki i Szkolnictwa Wy&#x17c;szego/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria ; Drug Resistance, Microbial ; *Enterococcus ; Feces ; Microbial Sensitivity Tests ; *Rivers ; }, abstract = {This paper presents the spatio-temporal distribution of faecal indicator bacteria (FIB) in the river section subject to anthropogenic stress and describes spread patterns of antibiotic resistance in the studied bacterial groups. The analysis involved 58 strains of Escherichia coli and 61 strains of enterococci. Antibiotic resistance profiles were prepared in accordance with the recommendations of the European Committee on Antimicrobial Susceptibility Testing (EUCAST). The results indicated a correlation between the location of a sampling site and the concentration of faecal bacteria. The highest average concentrations were recorded at the site located in the city centre, where the river is used mainly for recreation. Antibiotic resistance profiles showed that Escherichia coli had 100% sensitivity to tigecycline, levofloxacin and imipenem. The highest percentaage of strains (17%) were resistant to piperacillin. Enterococci were 100% sensitive to levofloxacin. No strains were vancomycin-resistant (VRE). The highest percentage of strains was resistant to imipenem (23%), and the lowest, to ampicillin (2%). The spatio-temporal distribution of antibiotic-resistant strains (ARS) indicated a high concentration of drug-resistant Escherichia coli (47%) in the summer season at the sampling site located in the last part of the river. At the same time, drug resistance in enterococci increased along the river course and was considerably higher in spring. There were no significant relationships between physico-chemical parameters of water and the levels of faecal bacteria. On the other hand, strong relationships were observed between the percentage of strains showing resistance to the applied antibiotics and physico-chemical and biological parameters of water. The percentage of antibiotic resistant strains of Escherichia coli was negatively correlated with dissolved oxygen concentration (r = - 0.9; p < 0.001) and BOD5 (r = - 0.85; p < 0.05). The percentage of antibiotic resistant strains of enterococci was most strongly correlated with water pH (r = - 0.92; p < 0.001).}, }
@article {pmid33099264, year = {2021}, author = {Gao, R and Bonin, L and Arroyo, JMC and Logan, BE and Rabaey, K}, title = {Separation and recovery of ammonium from industrial wastewater containing methanol using copper hexacyanoferrate (CuHCF) electrodes.}, journal = {Water research}, volume = {188}, number = {}, pages = {116532}, doi = {10.1016/j.watres.2020.116532}, pmid = {33099264}, issn = {1879-2448}, mesh = {*Ammonium Compounds ; Copper ; Electrodes ; Ferrocyanides ; Methanol ; *Wastewater ; }, abstract = {Ammonium is typically removed from wastewater by converting it to nitrogen gas using microorganisms, precluding its recovery. Copper hexacyanoferrate (CuHCF) is known to reversibly intercalate alkali cations in aqueous electrolytes due to the Prussian Blue crystal structure. We used this property to create a carbon-based intercalation electrode within an electrochemical cell. Depending on the electrode potential, it can recover NH4[+] from wastewater via insertion/regeneration while leaving organics. In the first phase, different binders were evaluated towards creating a stable electrode matrix, with sodium carboxymethyl cellulose giving the best performance. Subsequently, based on voltammetry, we determined an intercalation potential for NH4[+] removal of + 0.3 V vs. Ag/AgCl, while the regeneration potential of the electrode was + 1.1 V (vs. Ag/AgCl). Using the CuHCF electrodes 95% of the NH4[+] in a synthetic wastewater containing 56 mM NH4[+] and 68 mM methanol was removed with an energy input of 0.34 ± 0.01 Wh g[-1] NH4[+]. A similar removal of 93% was obtained using an actual industrial wastewater (56 mM NH4[+], 68 mM methanol, 0.02 mM NO2[-], 0.05 mM NO3[-], 0.04 mM SO4[2-] and 0.34 mM ethanol), with an energy input of 0.40 ± 0.01 Wh g[-1] NH4[+]. In both cases, there was negligible removal of organics. The stability of CuHCF electrodes was evaluated either by open circuit potential monitoring (61 h) or by cyclic voltammetry (50 h, 116 cycles). The stability during cycling of the electrode was determined in both synthetic and real streams for 25 h (125 cycles). The charge density (C cm[-1]) of the CuHCF electrodes declined by 17 % and 19% after 125 cycles in the synthetic stream and the actual wastewater, respectively. This study highlights the possibility of low-cost CuHCF coated electrodes for achieving separation of NH4[+] from streams containing methanol. The stability of electrodes has been improved but needs to be further enhanced for large-scale applications and long-term operation.}, }
@article {pmid33098438, year = {2021}, author = {Gunnabo, AH and van Heerwaarden, J and Geurts, R and Wolde-Meskel, E and Degefu, T and Giller, KE}, title = {Phylogeography and Symbiotic Effectiveness of Rhizobia Nodulating Chickpea (Cicer arietinum L.) in Ethiopia.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {703-716}, pmid = {33098438}, issn = {1432-184X}, mesh = {*Cicer ; DNA, Bacterial ; Ethiopia ; *Mesorhizobium/genetics ; Phylogeny ; Phylogeography ; RNA, Ribosomal, 16S ; *Rhizobium ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Chickpea (Cicer arietinum L.) used to be considered a restrictive host that nodulated and fixed nitrogen only with Mesorhizobium ciceri and M. mediterraneum. Recent analysis revealed that chickpea can also establish effective symbioses with strains of several other Mesorhizobium species such as M. loti, M. haukuii, M. amorphae, M. muleiense, etc. These strains vary in their nitrogen fixation potential inviting further exploration. We characterized newly collected mesorhizobial strains isolated from various locations in Ethiopia to evaluate genetic diversity, biogeographic structure and symbiotic effectiveness. Symbiotic effectiveness was evaluated in Leonard Jars using a locally released chickpea cultivar "Nattoli". Most of the new isolates belonged to a clade related to M. plurifarium, with very few sequence differences, while the total collection of strains contained three additional mesorhizobial genospecies associated with M. ciceri, M. abyssinicae and an unidentified Mesorhizobium species isolated from a wild host in Eritrea. The four genospecies identified represented a subset of the eight major Mesorhizobium clades recently reported for Ethiopia based on metagenomic data. All Ethiopian strains had nearly identical symbiotic genes that grouped them in a single cluster with M. ciceri, M. mediterraneum and M. muleiense, but not with M. plurifarium. Some phylogeographic structure was observed, with elevation and geography explaining some of the genetic differences among strains, but the relation between genetic identity and symbiotic effectiveness was observed to be weak.}, }
@article {pmid33096434, year = {2021}, author = {Prévoteau, A and Kerckhof, FM and Clauwaert, P and Rabaey, K}, title = {Electrochemical and phylogenetic comparisons of oxygen-reducing electroautotrophic communities.}, journal = {Biosensors &amp; bioelectronics}, volume = {171}, number = {}, pages = {112700}, doi = {10.1016/j.bios.2020.112700}, pmid = {33096434}, issn = {1873-4235}, mesh = {Biofilms ; *Biosensing Techniques ; Electrodes ; Oxidation-Reduction ; *Oxygen ; *Phylogeny ; }, abstract = {The mechanisms of extracellular electron transfer and the microbial taxa associated with the observed electroactivity are fundamental to oxygen-reducing microbial cathodes. Here we confirmed the apparent 'electroautotrophic' behavior of electroactive biofilms (EABs) grown on carbon electrodes at + 0.20V vs. Ag/AgCl under air. The EABs catalyzed O2 electroreduction into water ─ as demonstrated by a rotating ring disc experiment ─ and performed quasi-reversible heterogeneous electron transfer (HET). By using electrodes of low surface capacitance, we report for the first time nonturnover redox peaks that are very likely intrinsic to the redox protein(s) performing the HET. Because the formal potential of redox proteins is pH-dependent, we investigated the evolution of characteristic potentials of the EABs with the solution pH: (i) open circuit potential, (ii) half-wave potential, and (iii) averaged peak potential of nonturnover cyclic voltammograms, which is presumably the formal potential of the primary electron acceptor(s) for the community. In addition to describing the redox thermodynamics behind HET, we suggest that the corresponding data provides an electrochemical fingerprint that could help in comparing the electroactivity of diverse microbial communities. The taxon with the highest relative abundance in our EABs was an unclassified member of the Gammaproteobacteria that was phylogenetically closely related to most other abundant unclassified Gammaproteobacteria commonly reported in EABs reducing O2 at high potentials, further suggesting that those taxa are responsible for the bioelectroactivity. Phylogenetic and electrochemical similarities between reported EABs jointly support the hypothesis that similar biomolecular mechanisms may be responsible for this highly probable electroautotrophic metabolism.}, }
@article {pmid33096247, year = {2020}, author = {Pelusio, NF and Rossi, B and Parma, L and Volpe, E and Ciulli, S and Piva, A and D'Amico, F and Scicchitano, D and Candela, M and Gatta, PP and Bonaldo, A and Grilli, E}, title = {Effects of increasing dietary level of organic acids and nature-identical compounds on growth, intestinal cytokine gene expression and gut microbiota of rainbow trout (Oncorhynchus mykiss) reared at normal and high temperature.}, journal = {Fish &amp; shellfish immunology}, volume = {107}, number = {Pt A}, pages = {324-335}, doi = {10.1016/j.fsi.2020.10.021}, pmid = {33096247}, issn = {1095-9947}, mesh = {Animal Feed/analysis ; Animals ; Bacterial Physiological Phenomena/drug effects ; Benzaldehydes/administration &amp; dosage/*metabolism ; Citric Acid/administration &amp; dosage/*metabolism ; Cytokines/drug effects/metabolism ; Diet/veterinary ; Eating/*drug effects ; Gastrointestinal Microbiome/physiology ; Gene Expression/drug effects/immunology ; Hot Temperature ; Intestines/*drug effects/microbiology/physiology ; Oncorhynchus mykiss/genetics/growth &amp; development/*immunology/microbiology ; Sorbic Acid/administration &amp; dosage/*metabolism ; Thymol/administration &amp; dosage/*metabolism ; Time Factors ; }, abstract = {Organic acids (OA) and nature-identical compounds (NIC) such as monoterpenes and aldehydes are well-known growth and health promoters in terrestrial livestock while their application for fish production is recent and their mechanisms of action require further study. Hence, this study tested the increasing dietary level (D0, D250, D500, D1000; 0, 250, 500 and 1000 mg kg feed[-1] respectively) of a microencapsulated blend containing citric and sorbic acid, thymol and vanillin over 82 days on rainbow trout to assess the effects on growth, feed utilization, intestine cytokine gene expression and gut microbiota (GM). Furthermore, the effects on intestinal cytokine gene expression and GM were also explored after one week at high water temperature (23 °C). OA and NIC improved specific growth rate (SGR) and feed conversion rate (FCR) during the second half (day 40-82) of the feeding trial, while at the end of the trial protein (PER) and lipid efficiency (LER) increased with increasing dietary level. GM diversity and composition and cytokine gene expression analysis showed no significant differences in fish fed with increasing doses of OA and NIC (82 days) demonstrating the absence of inflammatory activity in the intestinal mucosa. Although there were no statistical differences, GM structure showed a tendency in clustering D0 group separately from the other dietary groups and a trend towards reduction of Streptococcus spp. was observed in the D250 and D1000 groups. After exposure to high water temperature, lower GM diversity and increased gene expression of inflammatory intestinal cytokines were observed for both inclusions (D0 vs. D1000) compared to groups in standard condition. However, the gene up-regulation involved a limited number of cytokines showing the absence of a substantial inflammation process able to compromise the functional activity of the intestine. Despite further study should be conducted to fully clarify this mechanism, cytokines up-regulation seems to be concomitant to the reduction of the GM diversity and, particularly, to the reduction of specific lactic acid bacteria such as Leuconostoc. The application of the microencapsulate blend tested can be a useful strategy to improve growth and feed utilization in rainbow trout under normal temperature conditions. According to the results organic acids and nature-identical compounds did not revert the effects triggered by the increased temperature of water.}, }
@article {pmid33095158, year = {2020}, author = {Greenhalgh, R and Dermauw, W and Glas, JJ and Rombauts, S and Wybouw, N and Thomas, J and Alba, JM and Pritham, EJ and Legarrea, S and Feyereisen, R and Van de Peer, Y and Van Leeuwen, T and Clark, RM and Kant, MR}, title = {Genome streamlining in a minute herbivore that manipulates its host plant.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {33095158}, issn = {2050-084X}, support = {773902-SuperPests//Horizon 2020 - Research and Innovation Framework Programme/International ; STW-GAP/13550//Netherlands Organisation for Scientific Research/International ; 12T9818N//Research Foundation Flanders/International ; 772026-POLYADAPT//European Union Horizon 2020 research and innovation program/International ; 1457346//USA National Science Foundation/International ; 1274917N//Research Foundation Flanders/International ; 1457346//National Science Foundation/International ; T32 GM007464/GM/NIGMS NIH HHS/United States ; STW-VIDI/13492//Netherlands Organisation for Scientific Research/International ; 773902-SuperPests//European Union Horizon 2020 research and innovation program/International ; }, mesh = {Animals ; Evolution, Molecular ; *Genome ; *Herbivory ; Host-Pathogen Interactions ; Solanum lycopersicum/*parasitology ; Mites/*genetics ; Phylogeny ; }, abstract = {The tomato russet mite, Aculops lycopersici, is among the smallest animals on earth. It is a worldwide pest on tomato and can potently suppress the host's natural resistance. We sequenced its genome, the first of an eriophyoid, and explored whether there are genomic features associated with the mite's minute size and lifestyle. At only 32.5 Mb, the genome is the smallest yet reported for any arthropod and, reminiscent of microbial eukaryotes, exceptionally streamlined. It has few transposable elements, tiny intergenic regions, and is remarkably intron-poor, as more than 80% of coding genes are intronless. Furthermore, in accordance with ecological specialization theory, this defense-suppressing herbivore has extremely reduced environmental response gene families such as those involved in chemoreception and detoxification. Other losses associate with this species' highly derived body plan. Our findings accelerate the understanding of evolutionary forces underpinning metazoan life at the limits of small physical and genome size.}, }
@article {pmid33094372, year = {2021}, author = {Jeong, SY and Kim, TG}, title = {Effects of Plants on Metacommunities and Correlation Networks of Soil Microbial Groups in an Ecologically Restored Wetland.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {657-672}, pmid = {33094372}, issn = {1432-184X}, support = {2018R1D1A1B07048872//Ministry of Education/ ; }, mesh = {Fungi/genetics ; *Microbiota ; Plants ; Soil ; Soil Microbiology ; *Wetlands ; }, abstract = {Plants may influence different aspects of the belowground microorganisms, including abundance, distribution, and interaction, in wetlands. Microbial communities were scrutinized in a 4-year-old restored wetland ecosystem with 5 distinct sites: a bare-soil site (10 local patches) and sites dominated by Miscanthus, Phragmites, Typha, and Zizania (20 patches per site). Ordination analysis revealed that plant-induced attributes (e.g., organic matter and total carbon and nitrogen) could explain the total environmental variance. Community comparisons showed that all groups (Bacteria, Fungi, Protista, and Metazoa) differed in community structure among the 5 sites (P < 0.05). Comparisons between the community and environmental ordination plots revealed that community structural variation among the sites correlated with the environmental change across all groups (R[2] ≥ 0.61). This indicates that all groups were primarily influenced by plant detritus. In addition, correlation networks markedly varied in topology and composition among the sites across all groups. There was a strong coupling between the metacommunity and correlation network for both Bacteria and Fungi (R[2] ≥ 0.58), indicating that the plants determined the spatial covariation patterns of microbial populations. Multi-group networks and group synchrony results revealed that Bacteria, Fungi, and Protista were synchronized with each other (R[2] ≥ 0.52) as the key founders of the microbial systems, while Metazoa participated in the system only under Miscanthus. Our findings concluded that the plants shaped the communities by controlling the abundance and interaction of their populations.}, }
@article {pmid33087520, year = {2020}, author = {Tomkovich, S and Stough, JMA and Bishop, L and Schloss, PD}, title = {The Initial Gut Microbiota and Response to Antibiotic Perturbation Influence Clostridioides difficile Clearance in Mice.}, journal = {mSphere}, volume = {5}, number = {5}, pages = {}, pmid = {33087520}, issn = {2379-5042}, support = {U01 AI124255/AI/NIAID NIH HHS/United States ; UL1 TR002240/TR/NCATS NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*administration &amp; dosage ; Bacteria/classification/*drug effects ; Breeding ; Clostridioides difficile ; Clostridium Infections/*drug therapy/microbiology ; Disease Models, Animal ; Feces ; Female ; Gastrointestinal Microbiome/*drug effects ; Mice ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The gut microbiota has a key role in determining susceptibility to Clostridioides difficile infections (CDIs). However, much of the mechanistic work examining CDIs in mouse models uses animals obtained from a single source. We treated mice from 6 sources (2 University of Michigan colonies and 4 commercial vendors) with clindamycin, followed by a C. difficile challenge, and then measured C. difficile colonization levels throughout the infection. The microbiota were profiled via 16S rRNA gene sequencing to examine the variation across sources and alterations due to clindamycin treatment and C. difficile challenge. While all mice were colonized 1 day postinfection, variation emerged from days 3 to 7 postinfection with animals from some sources colonized with C. difficile for longer and at higher levels. We identified bacteria that varied in relative abundance across sources and throughout the experiment. Some bacteria were consistently impacted by clindamycin treatment in all sources of mice, including Lachnospiraceae, Ruminococcaceae, and Enterobacteriaceae To identify bacteria that were most important to colonization regardless of the source, we created logistic regression models that successfully classified mice based on whether they cleared C. difficile by 7 days postinfection using community composition data at baseline, post-clindamycin treatment, and 1 day postinfection. With these models, we identified 4 bacterial taxa that were predictive of whether C. difficile cleared. They varied across sources (Bacteroides) or were altered by clindamycin (Porphyromonadaceae) or both (Enterobacteriaceae and Enterococcus). Allowing for microbiota variation across sources better emulates human interindividual variation and can help identify bacterial drivers of phenotypic variation in the context of CDIs.IMPORTANCEClostridioides difficile is a leading nosocomial infection. Although perturbation to the gut microbiota is an established risk, there is variation in who becomes asymptomatically colonized, develops an infection, or has adverse infection outcomes. Mouse models of C. difficile infection (CDI) are widely used to answer a variety of C. difficile pathogenesis questions. However, the interindividual variation between mice from the same breeding facility is less than what is observed in humans. Therefore, we challenged mice from 6 different breeding colonies with C. difficile We found that the starting microbial community structures and C. difficile persistence varied by the source of mice. Interestingly, a subset of the bacteria that varied across sources were associated with how long C. difficile was able to colonize. By increasing the interindividual diversity of the starting communities, we were able to better model human diversity. This provided a more nuanced perspective of C. difficile pathogenesis.}, }
@article {pmid33083833, year = {2021}, author = {Arca-Suárez, J and Lasarte-Monterrubio, C and Rodiño-Janeiro, BK and Cabot, G and Vázquez-Ucha, JC and Rodríguez-Iglesias, M and Galán-Sánchez, F and Beceiro, A and González-Bello, C and Oliver, A and Bou, G}, title = {Molecular mechanisms driving the in vivo development of OXA-10-mediated resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of XDR Pseudomonas aeruginosa infections.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {76}, number = {1}, pages = {91-100}, doi = {10.1093/jac/dkaa396}, pmid = {33083833}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Azabicyclo Compounds/pharmacology/therapeutic use ; *Ceftazidime/pharmacology ; Cephalosporins/pharmacology ; Drug Combinations ; Humans ; Microbial Sensitivity Tests ; *Pseudomonas Infections/drug therapy ; Pseudomonas aeruginosa/genetics ; Tazobactam/pharmacology ; beta-Lactamases/genetics ; }, abstract = {BACKGROUND: The development of resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of Pseudomonas aeruginosa infections is concerning.<br><br>OBJECTIVES: Characterization of the mechanisms leading to the development of OXA-10-mediated resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of XDR P. aeruginosa infections.<br><br>METHODS: Four paired ceftolozane/tazobactam- and ceftazidime/avibactam-susceptible/resistant isolates were evaluated. MICs were determined by broth microdilution. STs, resistance mechanisms and genetic context of &#x3b2;-lactamases were determined by genotypic methods, including WGS. The OXA-10 variants were cloned in PAO1 to assess their impact on resistance. Models for the OXA-10 derivatives were constructed to evaluate the structural impact of the amino acid changes.<br><br>RESULTS: The same XDR ST253 P. aeruginosa clone was detected in all four cases evaluated. All initial isolates showed OprD deficiency, produced an OXA-10 enzyme and were susceptible to ceftazidime, ceftolozane/tazobactam, ceftazidime/avibactam and colistin. During treatment, the isolates developed resistance to all cephalosporins. Comparative genomic analysis revealed that the evolved resistant isolates had acquired mutations in the OXA-10 enzyme: OXA-14 (Gly157Asp), OXA-794 (Trp154Cys), OXA-795 (&#x394;Phe153-Trp154) and OXA-824 (Asn143Lys). PAO1 transformants producing the evolved OXA-10 derivatives showed enhanced ceftolozane/tazobactam and ceftazidime/avibactam resistance but decreased meropenem MICs in a PAO1 background. Imipenem/relebactam retained activity against all strains. Homology models revealed important changes in regions adjacent to the active site of the OXA-10 enzyme. The blaOXA-10 gene was plasmid borne and acquired due to transposition of Tn6746 in the pHUPM plasmid scaffold.<br><br>CONCLUSIONS: Modification of OXA-10 is a mechanism involved in the in vivo acquisition of resistance to cephalosporin/&#x3b2;-lactamase inhibitor combinations in P. aeruginosa.}, }
@article {pmid33082281, year = {2020}, author = {Allard, SM and Costa, MT and Bulseco, AN and Helfer, V and Wilkins, LGE and Hassenrück, C and Zengler, K and Zimmer, M and Erazo, N and Mazza Rodrigues, JL and Duke, N and Melo, VMM and Vanwonterghem, I and Junca, H and Makonde, HM and Jiménez, DJ and Tavares, TCL and Fusi, M and Daffonchio, D and Duarte, CM and Peixoto, RS and Rosado, AS and Gilbert, JA and Bowman, J}, title = {Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems.}, journal = {mSystems}, volume = {5}, number = {5}, pages = {}, pmid = {33082281}, issn = {2379-5077}, abstract = {Mangrove ecosystems provide important ecological benefits and ecosystem services, including carbon storage and coastline stabilization, but they also suffer great anthropogenic pressures. Microorganisms associated with mangrove sediments and the rhizosphere play key roles in this ecosystem and make essential contributions to its productivity and carbon budget. Understanding this nexus and moving from descriptive studies of microbial taxonomy to hypothesis-driven field and lab studies will facilitate a mechanistic understanding of mangrove ecosystem interaction webs and open opportunities for microorganism-mediated approaches to mangrove protection and rehabilitation. Such an effort calls for a multidisciplinary and collaborative approach, involving chemists, ecologists, evolutionary biologists, microbiologists, oceanographers, plant scientists, conservation biologists, and stakeholders, and it requires standardized methods to support reproducible experiments. Here, we outline the Mangrove Microbiome Initiative, which is focused around three urgent priorities and three approaches for advancing mangrove microbiome research.}, }
@article {pmid33078238, year = {2021}, author = {Jayakumar, A and Nair, IC and Radhakrishnan, EK}, title = {Environmental Adaptations of an Extremely Plant Beneficial Bacillus subtilis Dcl1 Identified Through the Genomic and Metabolomic Analysis.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {687-702}, pmid = {33078238}, issn = {1432-184X}, mesh = {*Bacillus subtilis/genetics ; Endophytes ; Genomics ; *Plant Diseases ; Plants ; }, abstract = {Bacterial endophytes ubiquitously colonize the internal tissues of plants and promote the plant growth through diverse mechanisms. The current study describes the mechanistic basis of plant-specific adaptations present in an extremely beneficial endophytic bacterium. Here, the endophytic Bacillus subtilis Dcl1 isolated from the dried rhizome of Curcuma longa was found to have the drought tolerance, IAA and ACC deaminase production and phosphate solubilization properties. The whole genome sequencing and annotation further showed the genome of B. subtilis Dcl1 to have the size of 4,321,654 bp. This also showed the presence of genes for IAA, H2S, acetoin, butanediol, flagella and siderophore production along with phosphate solubilization and biofilm formation for the B. subtilis Dcl1. In addition, the genes responsible for the synthesis of surfactin, iturin, fengycin, bacillibactin, bacillaene, bacilysin, chitinase, chitosanase, protease and glycoside hydrolase could also be annotated from the genome of B. subtilis Dcl1. Identification of genes for the glycine betaine, glutamate and trehalose further indicated the drought stress tolerance features of B. subtilis Dcl1. The presence of the genetic basis to produce the catalase, superoxide dismutase, peroxidases, gamma-glutamyltranspeptidase, glutathione and glycolate oxidase also indicated the plant oxidative stress protective effect of B. subtilis Dcl1. Identification of these properties and the demonstration of its plant probiotic effect in Vigna unguiculata confirmed the applicability of B. subtilis Dcl1 as a biofertilizer, biocontrol and bioremediator agent to enhance the agricultural productivity.}, }
@article {pmid33077749, year = {2020}, author = {Yang, FS and Nie, S and Liu, H and Shi, TL and Tian, XC and Zhou, SS and Bao, YT and Jia, KH and Guo, JF and Zhao, W and An, N and Zhang, RG and Yun, QZ and Wang, XZ and Mannapperuma, C and Porth, I and El-Kassaby, YA and Street, NR and Wang, XR and Van de Peer, Y and Mao, JF}, title = {Chromosome-level genome assembly of a parent species of widely cultivated azaleas.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5269}, pmid = {33077749}, issn = {2041-1723}, mesh = {Anthocyanins/biosynthesis ; Biosynthetic Pathways ; Carotenoids/metabolism ; Chromosomes, Plant/*genetics/metabolism ; Flowers/genetics/growth &amp; development/metabolism ; Gene Expression Regulation, Plant ; *Genome, Plant ; Multigene Family ; Plant Proteins/*genetics/metabolism ; Rhododendron/*genetics/growth &amp; development/metabolism ; Transcription Factors/genetics/metabolism ; }, abstract = {Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for Rhododendron simsii, the primary ancestor of azalea cultivars. Genome analyses unveil the remnants of an ancient whole-genome duplication preceding the radiation of most Ericaceae, likely contributing to the genomic architecture of flowering time. Small-scale gene duplications contribute to the expansion of gene families involved in azalea pigment biosynthesis. We reconstruct entire metabolic pathways for anthocyanins and carotenoids and their potential regulatory networks by detailed analysis of time-ordered gene co-expression networks. MYB, bHLH, and WD40 transcription factors may collectively regulate anthocyanin accumulation in R. simsii, particularly at the initial stages of flower coloration, and with WRKY transcription factors controlling progressive flower coloring at later stages. This work provides a cornerstone for understanding the underlying genetics governing flower timing and coloration and could accelerate selective breeding in azalea.}, }
@article {pmid33075580, year = {2021}, author = {Francis, JS and Tatarko, AR and Richman, SK and Vaudo, AD and Leonard, AS}, title = {Microbes and pollinator behavior in the floral marketplace.}, journal = {Current opinion in insect science}, volume = {44}, number = {}, pages = {16-22}, doi = {10.1016/j.cois.2020.10.003}, pmid = {33075580}, issn = {2214-5753}, mesh = {Animals ; *Behavior, Animal ; Flowers/*microbiology ; *Pollination ; }, abstract = {Pollinator foraging decisions shape microbial dispersal, and microbes change floral phenotypes in ways perceivable by pollinators. Yet, the role microbes play in the cognitive ecology of pollination is relatively unexplored. Reviewing recent literature on floral microbial ecology and pollinator behavior, we advocate for further integration between these two fields. Insights into pollinator learning, memory, and decision-making can help explain their responses to microbially-altered floral phenotypes. Specifically, considering how pollinators forage for multiple nutrients, cope with uncertainty, structure foraging bouts, and move through their environment could inform predictions about microbial dispersal within plant communities. We highlight how behavior connects microbial changes in floral phenotype to downstream effects on both microbial dispersal and plant fitness.}, }
@article {pmid33072042, year = {2020}, author = {Sabino, YNV and de Araújo, KC and de Assis, FGDV and Moreira, SM and Lopes, TDS and Mendes, TAO and Huws, SA and Mantovani, HC}, title = {In silico Screening Unveil the Great Potential of Ruminal Bacteria Synthesizing Lasso Peptides.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {576738}, pmid = {33072042}, issn = {1664-302X}, abstract = {Studies of rumen microbial ecology suggest that the capacity to produce antimicrobial peptides could be a useful trait in species competing for ecological niches in the ruminal ecosystem. However, little is known about the synthesis of lasso peptides by ruminal microorganisms. Here we analyzed the distribution and diversity of lasso peptide gene clusters in 425 bacterial genomes from the rumen ecosystem. Genome mining was performed using antiSMASH 5, BAGEL4, and a database of well-known precursor sequences. The genomic context of the biosynthetic clusters was investigated to identify putative lasA genes and protein sequences from enzymes of the biosynthetic machinery were evaluated to identify conserved motifs. Metatranscriptome analysis evaluated the expression of the biosynthetic genes in the rumen microbiome. Several incomplete (n = 23) and complete (n = 11) putative lasso peptide clusters were detected in the genomes of ruminal bacteria. The complete gene clusters were exclusively found within the phylum Firmicutes, mainly (48%) in strains of the genus Butyrivibrio. The analysis of the genetic organization of complete putative lasso peptide clusters revealed the presence of co-occurring genes, including kinases (85%), transcriptional regulators (49%), and glycosyltransferases (36%). Moreover, a conserved pattern of cluster organization was detected between strains of the same genus/species. The maturation enzymes LasB, LasC, and LasD showed regions highly conserved, including the presence of a transglutaminase core in LasB, an asparagine synthetase domain in LasC, and an ABC-type transporter system in LasD. Phylogenetic trees of the essential biosynthetic proteins revealed that sequences split into monophyletic groups according to their shared single common ancestor. Metatranscriptome analyses indicated the expression of the lasso peptides biosynthetic genes within the active rumen microbiota. Overall, our in silico screening allowed the discovery of novel biosynthetic gene clusters in the genomes of ruminal bacteria and revealed several strains with the genetic potential to synthesize lasso peptides, suggesting that the ruminal microbiota represents a potential source of these promising peptides.}, }
@article {pmid33072023, year = {2020}, author = {Dias, T and Pimentel, V and Cogo, AJD and Costa, R and Bertolazi, AA and Miranda, C and de Souza, SB and Melo, J and Carolino, M and Varma, A and Eutrópio, F and Olivares, FL and Ramos, AC and Cruz, C}, title = {The Free-Living Stage Growth Conditions of the Endophytic Fungus Serendipita indica May Regulate Its Potential as Plant Growth Promoting Microbe.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {562238}, pmid = {33072023}, issn = {1664-302X}, abstract = {Serendipita indica (former Piriformospora indica) is a non-obligate endophytic fungus and generally a plant growth and defence promoter with high potential to be used in agriculture. However, S. indica may switch from biotrophy to saprotrophy losing its plant growth promoting traits. Our aim was to understand if the free-living stage growth conditions (namely C availability) regulate S. indica's phenotype, and its potential as plant-growth-promoting-microbe (PGPM). We grew S. indica in its free-living stage under increasing C availabilities (2-20 g L[-1] of glucose or sucrose). We first characterised the effect of C availability during free-living stage growth on fungal phenotype: colonies growth and physiology (plasma membrane proton pumps, stable isotopic signatures, and potential extracellular decomposing enzymes). The effect of the C availability during the free-living stage of the PGPM was evaluated on wheat. We observed that C availability during the free-living stage regulated S. indica's growth, ultrastructure and physiology, resulting in two distinct colony phenotypes: compact and explorer. The compact phenotype developed at low C, used peptone as the major C and N source, and displayed higher decomposing potential for C providing substrates; while the explorer phenotype developed at high C, used glucose and sucrose as major C sources and casein and yeast extract as major N sources, and displayed higher decomposing potential for N and P providing substrates. The C availability, or the C/N ratio, during the free-living stage left a legacy to the symbiosis stage, regulating S. indica's potential to promote plant growth: wheat growth promotion by the explorer phenotype was ± 40% higher than that by the compact phenotype. Our study highlights the importance of considering microbial ecology in designing PGPM/biofertilizers. Further studies are needed to test the phenotypes under more extreme conditions, and to understand if the in vitro acquired characteristics persist under field conditions.}, }
@article {pmid33072015, year = {2020}, author = {Zhu, C and Bass, D and Wang, Y and Shen, Z and Song, W and Yi, Z}, title = {Environmental Parameters and Substrate Type Drive Microeukaryotic Community Structure During Short-Term Experimental Colonization in Subtropical Eutrophic Freshwaters.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {555795}, pmid = {33072015}, issn = {1664-302X}, abstract = {Microeukaryotes are key components of aquatic ecosystems and play crucial roles in aquatic food webs. However, influencing factors and potential assembly mechanisms for microeukaryotic community on biofilms are rarely studied. Here, those of microeukaryotic biofilms in subtropical eutrophic freshwaters were investigated for the first time based on 2,585 operational taxonomic units (OTUs) from 41 samples, across different environmental conditions and substrate types. Following conclusions were drawn: (1) Environmental parameters were more important than substrate types in structuring microeukaryotic community of biofilms in subtropical eutrophic freshwaters. (2) In the fluctuating river, there was a higher diversity of OTUs and less predictability of community composition than in the stable lake. Sessile species were more likely to be enriched on smooth surfaces of glass slides, while both free-swimming and attached organisms occurred within holes inside PFUs (polyurethane foam units). (3) Both species sorting and neutral process were mechanisms for assembly of microeukaryotic biofilms, but their importance varied depending on different habitats and substrates. (4) The effect of species sorting was slightly higher than the neutral process in river biofilms due to stronger environmental filtering. Species sorting was a stronger force structuring communities on glass slides than PFUs with more niche availability. Our study sheds light on assembly mechanisms for microeukaryotic community on different habitat and substrate types, showing that the resulting communities are determined by both sets of variables, in this case primarily habitat type. The balance of neutral process and species sorting differed between habitats, but the high alpha diversity of microeukaryotes in both led to similar sets of lifecycle traits being selected for in each case.}, }
@article {pmid33072010, year = {2020}, author = {Shang, Y and Wu, X and Wei, Q and Dou, H and Wang, X and Chen, J and Zhang, H and Ma, S and Zhang, H}, title = {Total Arsenic, pH, and Sulfate Are the Main Environmental Factors Affecting the Microbial Ecology of the Water and Sediments in Hulun Lake, China.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {548607}, pmid = {33072010}, issn = {1664-302X}, abstract = {Bacteria have the metabolic potential to produce a diverse array of secondary metabolites, which have important roles in biogeochemical cycling processes. However, for Hulun Lake and the rivers that enter into it, the bacterial community structures and their effects have not previously been widely studied, limiting our ecological understanding of this habitat. To address this, we have analyzed the bacterial communities in the water ecosystem of the Hulun Lake Basin. 16S rRNA high-throughput sequencing identified 64 phyla, 165 classes, 218 orders, 386 families, and 740 genera of bacteria across all samples. The dominant phyla in the central area of the lake were Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria, while in all other areas, Proteobacteria, Actinobacteria, and Bacteroidetes were dominant. The microbial community structures were significantly affected by environmental factors [arsenic (As), pH, and sulfate (SO4 [2-])] and their location in the lake. The species richness in the sediments of Hulun Lake was higher than in the water, and this ecosystem harbored the highest proportion of unclassified sequences, representing unclassified bacteria. This study provides basic data for future investigations into the Hulun lake ecosystem and for water microbial monitoring and protection measures.}, }
@article {pmid33072003, year = {2020}, author = {Brown, JM and Labonté, JM and Brown, J and Record, NR and Poulton, NJ and Sieracki, ME and Logares, R and Stepanauskas, R}, title = {Single Cell Genomics Reveals Viruses Consumed by Marine Protists.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {524828}, pmid = {33072003}, issn = {1664-302X}, abstract = {The predominant model of the role of viruses in the marine trophic web is that of the "viral shunt," where viral infection funnels a substantial fraction of the microbial primary and secondary production back to the pool of dissolved organic matter. Here, we analyzed the composition of non-eukaryotic DNA associated with individual cells of small, planktonic protists in the Gulf of Maine (GoM) and the Mediterranean Sea. We found viral DNA associated with a substantial fraction cells from the GoM (51%) and the Mediterranean Sea (35%). While Mediterranean SAGs contained a larger proportion of cells containing bacterial sequences (49%), a smaller fraction of cells contained bacterial sequences in the GoM (19%). In GoM cells, nearly identical bacteriophage and ssDNA virus sequences where found across diverse lineages of protists, suggesting many of these viruses are non-infective. The fraction of cells containing viral DNA varied among protistan lineages and reached 100% in Picozoa and Choanozoa. These two groups also contained significantly higher numbers of viral sequences than other identified taxa. We consider mechanisms that may explain the presence of viral DNA in protistan cells and conclude that protistan predation on free viral particles contributed to the observed patterns. These findings confirm prior experiments with protistan isolates and indicate that the viral shunt is complemented by a viral link in the marine microbial food web. This link may constitute a sink of viral particles in the ocean and has implications for the flow of carbon through the microbial food web.}, }
@article {pmid33070212, year = {2021}, author = {Xu, S and Jiang, L and Qiao, G and Chen, J}, title = {Diversity of bacterial symbionts associated with Myzus persicae (Sulzer) (Hemiptera: Aphididae: Aphidinae) revealed by 16S rRNA Illumina sequencing.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {784-794}, pmid = {33070212}, issn = {1432-184X}, support = {2016YFE0203100//National Key R &amp; D Program of China/ ; 31620103916//National Natural Science Foundation of China (CN)/ ; 31772492//National Natural Science Foundation of China/ ; XDA19050303//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2020087//Youth Innovation Promotion Association of Chinese Academy of Sciences/ ; }, mesh = {Animals ; *Aphids ; Bacteria/genetics ; *Buchnera/genetics ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Aphids are known to be associated with a variety of symbiotic bacteria. To improve our knowledge of the bacterial diversity of polyphagous aphids, in the present study, we investigated the microbiota of the cosmopolitan agricultural pest Myzus persicae (Sulzer). Ninety-two aphid samples collected from different host plants in various regions of China were examined using high-throughput amplicon sequencing. We comprehensively characterized the symbiont diversity of M. persicae and assessed the variations in aphid-associated symbiont communities. We detected a higher diversity of symbionts than has been previously observed. M. persicae hosted the primary endosymbiont Buchnera aphidicola and seven secondary symbionts, among which Wolbachia was the most prevalent and Rickettsia, Arsenophonus, and Spiroplasma were reported for the first time. Ordination analyses and statistical tests revealed that the symbiont flora associated with M. persicae did not change with respect to host plant or geography, which may be due to frequent migrations between different aphid populations. These findings will advance our knowledge of the microbiota of polyphagous insects and will enrich our understanding of assembly of host-microbiome systems.}, }
@article {pmid33069997, year = {2021}, author = {Dai, H and Gao, J and Li, D and Wang, Z and Duan, W}, title = {Metagenomics combined with DNA-based stable isotope probing provide comprehensive insights of active triclosan-degrading bacteria in wastewater treatment.}, journal = {Journal of hazardous materials}, volume = {404}, number = {Pt B}, pages = {124192}, doi = {10.1016/j.jhazmat.2020.124192}, pmid = {33069997}, issn = {1873-3336}, mesh = {Beijing ; DNA ; Isotopes ; Metagenomics ; *Triclosan ; *Water Purification ; }, abstract = {The biotransformation of triclosan (TCS) during wastewater treatment occurred frequently, while little researches are known the identity of microorganisms involved in the biodegradation process. In this work, DNA-based stable isotope probing (DNA-SIP) was occupied to investigate the TCS assimilation microbes originated from a full-scale cyclic activated sludge system in Beijing. Results of TCS removal pathway showed that the TCS removal in nitrification process was mainly contributed by the metabolism of heterotrophic bacteria, accounting for about 18.54%. DNA-SIP assay indicated that Sphingobium dominated the degradation of TCS. Oligotyping analysis further indicated that oligotype GCTAAT and ATGTTA of Sphingobium played important roles in degrading TCS. Furthermore, the Kyoto Encyclopedia of Genes and Genomes functional abundance statistics based on PICRUSt2 showed that glutathione transferase was the most prevalent enzyme involved in TCS metabolism, and TCS might be removed through microbial carbon metabolism. Metagenomics made clear that Sphingobium might play irrelevant role on the propagation of antibiotics resistance genes (ARGs), even though, it could degrade TCS. Thauera and Dechloromonas were identified as the key hosts of most ARGs. This study revealed the potential metabolic pathway and microbial ecology of TCS biodegradation in nitrification process of wastewater treatment system.}, }
@article {pmid33068395, year = {2020}, author = {Lebre, PH and Bottos, E and Makhalanyane, TP and Hogg, I and Cowan, DA}, title = {Islands in the sand: are all hypolithic microbial communities the same?.}, journal = {FEMS microbiology ecology}, volume = {97}, number = {1}, pages = {}, doi = {10.1093/femsec/fiaa216}, pmid = {33068395}, issn = {1574-6941}, mesh = {Antarctic Regions ; Islands ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sand ; *Soil Microbiology ; }, abstract = {Hypolithic microbial communities (hypolithons) are complex assemblages of phototrophic and heterotrophic organisms associated with the ventral surfaces of translucent minerals embedded in soil surfaces. Past studies on the assembly, structure and function of hypolithic communities have tended to use composite samples (i.e. bulked hypolithic biomass) with the underlying assumption that samples collected from within a 'homogeneous' locality are phylogenetically homogeneous. In this study, we question this assumption by analysing the prokaryote phylogenetic diversity of multiple individual hypolithons: i.e. asking the seemingly simple question of 'Are all hypolithons the same'? Using 16S rRNA gene-based phylogenetic analysis of hypolithons recovered for a localized moraine region in the Taylor Valley, McMurdo Dry Valleys, Antarctica, we demonstrate that these communities are heterogeneous at very small spatial scales (<5 m). Using null models of phylogenetic turnover, we showed that this heterogeneity between hypolithons is probably due to stochastic effects such as dispersal limitations, which is entirely consistent with the physically isolated nature of the hypolithic communities ('islands in the sand') and the almost complete absence of a liquid continuum as a mode of microbial transport between communities.}, }
@article {pmid33067657, year = {2021}, author = {Han, D and Richter-Heitmann, T and Kim, IN and Choy, E and Park, KT and Unno, T and Kim, J and Nam, SI}, title = {Survey of Bacterial Phylogenetic Diversity During the Glacier Melting Season in an Arctic Fjord.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {579-591}, pmid = {33067657}, issn = {1432-184X}, support = {NRF-2015M1A5A1037243//National Research Foundation of Korea/ ; NRF-2018R1D1A3B07041743//National Research Foundation of Korea/ ; NRF-2019R1I1A1A01058140//National Research Foundation of Korea/ ; }, mesh = {Arctic Regions ; *Estuaries ; *Ice Cover ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; }, abstract = {To understand bacterial biogeography in response to the hydrographic impact of climate change derived from the Arctic glacier melting, we surveyed bacterial diversity and community composition using bacterial 16S rRNA gene metabarcoding in the seawaters of Kongsfjorden, Svalbard, during summer 2016. In the present study, bacterial biogeography in the Kongsfjorden seawaters showed distinct habitat patterns according to water mass classification and habitat transition between Atlantic and fjord surface waters. Moreover, we estimated phylogenetic diversity of bacterial communities using the net relatedness, nearest taxon, and beta nearest taxon indices. We found the influence of freshwater input from glacier melting in shaping bacterial assemblage composition through the stochastic model. We further evaluated bacterial contributions to phytoplankton-derived dimethylsulfoniopropionate (DMSP) using a quantitative PCR (qPCR) measurement with demethylation (dmdA) and cleavage (dddP) genes of two fundamentally different processes. Our qPCR results imply that bacterial DMSP degradation follows the Atlantic inflow during summer in Kongsfjorden. These findings suggest that the Atlantic inflow and glacial melting influence bacterial community composition and assembly processes and thus affect the degradation of phytoplankton-derived organic matter in an Arctic fjord.}, }
@article {pmid33067588, year = {2021}, author = {Mueller, AJ and Jung, MY and Strachan, CR and Herbold, CW and Kirkegaard, RH and Wagner, M and Daims, H}, title = {Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting.}, journal = {The ISME journal}, volume = {15}, number = {3}, pages = {732-745}, pmid = {33067588}, issn = {1751-7370}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Bacteria/genetics ; Genomics ; Kinetics ; *Nitrites ; Oceans and Seas ; Oxidation-Reduction ; }, abstract = {Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players in global nitrogen and carbon cycling. Members of the phylum Nitrospinae are the most abundant, known NOB in the oceans. To date, only two closely affiliated Nitrospinae species have been isolated, which are only distantly related to the environmentally abundant uncultured Nitrospinae clades. Here, we applied live cell sorting, activity screening, and subcultivation on marine nitrite-oxidizing enrichments to obtain novel marine Nitrospinae. Two binary cultures were obtained, each containing one Nitrospinae strain and one alphaproteobacterial heterotroph. The Nitrospinae strains represent two new genera, and one strain is more closely related to environmentally abundant Nitrospinae than previously cultured NOB. With an apparent half-saturation constant of 8.7 ± 2.5 µM, this strain has the highest affinity for nitrite among characterized marine NOB, while the other strain (16.2 ± 1.6 µM) and Nitrospina gracilis (20.1 ± 2.1 µM) displayed slightly lower nitrite affinities. The new strains and N. gracilis share core metabolic pathways for nitrite oxidation and CO2 fixation but differ remarkably in their genomic repertoires of terminal oxidases, use of organic N sources, alternative energy metabolisms, osmotic stress and phage defense. The new strains, tentatively named "Candidatus Nitrohelix vancouverensis" and "Candidatus Nitronauta litoralis", shed light on the niche differentiation and potential ecological roles of Nitrospinae.}, }
@article {pmid33067398, year = {2020}, author = {Shibl, AA and Isaac, A and Ochsenkühn, MA and Cárdenas, A and Fei, C and Behringer, G and Arnoux, M and Drou, N and Santos, MP and Gunsalus, KC and Voolstra, CR and Amin, SA}, title = {Diatom modulation of select bacteria through use of two unique secondary metabolites.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {44}, pages = {27445-27455}, pmid = {33067398}, issn = {1091-6490}, mesh = {Animals ; Bacteria/genetics/*growth &amp; development ; Cinnamates/metabolism ; Depsides/metabolism ; Diatoms/genetics/*metabolism ; Dicarboxylic Acids/metabolism ; Gene Expression Profiling ; Metabolomics ; Metagenome ; Metagenomics ; Microbiota/*physiology ; Oceans and Seas ; Phytoplankton/genetics/*metabolism ; Secondary Metabolism/physiology ; *Water Microbiology ; Rosmarinic Acid ; }, abstract = {Unicellular eukaryotic phytoplankton, such as diatoms, rely on microbial communities for survival despite lacking specialized compartments to house microbiomes (e.g., animal gut). Microbial communities have been widely shown to benefit from diatom excretions that accumulate within the microenvironment surrounding phytoplankton cells, known as the phycosphere. However, mechanisms that enable diatoms and other unicellular eukaryotes to nurture specific microbiomes by fostering beneficial bacteria and repelling harmful ones are mostly unknown. We hypothesized that diatom exudates may tune microbial communities and employed an integrated multiomics approach using the ubiquitous diatom Asterionellopsis glacialis to reveal how it modulates its naturally associated bacteria. We show that A. glacialis reprograms its transcriptional and metabolic profiles in response to bacteria to secrete a suite of central metabolites and two unusual secondary metabolites, rosmarinic acid and azelaic acid. While central metabolites are utilized by potential bacterial symbionts and opportunists alike, rosmarinic acid promotes attachment of beneficial bacteria to the diatom and simultaneously suppresses the attachment of opportunists. Similarly, azelaic acid enhances growth of beneficial bacteria while simultaneously inhibiting growth of opportunistic ones. We further show that the bacterial response to azelaic acid is numerically rare but globally distributed in the world's oceans and taxonomically restricted to a handful of bacterial genera. Our results demonstrate the innate ability of an important unicellular eukaryotic group to modulate select bacteria in their microbial consortia, similar to higher eukaryotes, using unique secondary metabolites that regulate bacterial growth and behavior inversely across different bacterial populations.}, }
@article {pmid33067195, year = {2020}, author = {Co, R and Hug, LA}, title = {A Need for Improved Cellulase Identification from Metagenomic Sequence Data.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {1}, pages = {}, pmid = {33067195}, issn = {1098-5336}, mesh = {Bacteria/*isolation &amp; purification ; Cellulase/*analysis ; *Environmental Microbiology ; *Metagenome ; Metagenomics/*methods ; }, abstract = {Improved sequencing technologies and the maturation of metagenomic approaches allow the identification of gene variants with potential industrial applications, including cellulases. Cellulase identification from metagenomic environmental surveys is complicated by inconsistent nomenclature and multiple categorization systems. Here, we summarize the current classification and nomenclature systems, with recommendations for improvements to these systems. Addressing the issues described will strengthen the annotation of cellulose-active enzymes from environmental sequence data sets-a rapidly growing resource in environmental and applied microbiology.}, }
@article {pmid33066774, year = {2020}, author = {Yan, H and Yu, B and Degroote, J and Spranghers, T and Van Noten, N and Majdeddin, M and Van Poucke, M and Peelman, L and De Vrieze, J and Boon, N and Gielen, I and Smet, S and Chen, D and Michiels, J}, title = {Antibiotic affects the gut microbiota composition and expression of genes related to lipid metabolism and myofiber types in skeletal muscle of piglets.}, journal = {BMC veterinary research}, volume = {16}, number = {1}, pages = {392}, pmid = {33066774}, issn = {1746-6148}, support = {CARS-36//earmarked fund for the China Agriculture Research System/ ; 31672436//National Natural Science Foundation of China/ ; 31730091//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Regulation/drug effects ; Lipid Metabolism/drug effects/*genetics ; Muscle, Skeletal/*drug effects/metabolism ; Myofibrils/chemistry/*drug effects ; *Swine/genetics/metabolism ; Tylosin/*pharmacology ; }, abstract = {BACKGROUND: Early-life antibiotic administration is known to affect gut microbiota and host adiposity, but the effects of antibiotic exposure on skeletal muscle properties remain unknown. The present study evaluated the changes in skeletal muscle properties including myofiber characteristics and composition, as well as intramuscular fat (IMF) content in skeletal muscle of piglets when exposed to a tylosin-containing diet.<br><br>RESULTS: A total of 18 piglets (28&#x2009;days of age) were randomly allocated into two groups: control basal diet (Control) and Control +&#x2009;100&#x2009;mg tylosin phosphate/kg of feed (Antibiotic). The trial lasted for 39&#x2009;days. High-throughput amplicon sequencing revealed that no significant difference in initial gut microbiota composition was existed between Control and Antibiotic groups. Antibiotic administration increased body weight and growth rate and decreased feed to gain ratio of pigs (P&#x2009;<&#x2009;0.05). The carcass lean and fat volumes of pigs were increased by the tylosin administration (P&#x2009;<&#x2009;0.05). Antibiotic treatment increased myofiber density and the expression of genes related to type I and type IIb myofibers in longissimus muscle (P&#x2009;<&#x2009;0.05). The IMF content in longissimus muscle was increased by antibiotic exposure (P&#x2009;<&#x2009;0.05). Antibiotic administration increased expression of genes related to fatty acid uptake and de novo synthesis, and decreased expression of genes related to triglyceride hydrolysis (P&#x2009;<&#x2009;0.05). Tylosin administration affected taxonomic distribution and beta diversity of the caecal and colonic microbiota of piglets.<br><br>CONCLUSION: These results confirm that the growth performance, myofiber composition and muscle lipid metabolism are affected by antibiotic administration, which may be associated with an altered gut microbiota, suggesting that the gut microbiota could be served as a potential target for modulating skeletal muscle properties of host.}, }
@article {pmid33066697, year = {2020}, author = {Amat, S and Lantz, H and Munyaka, PM and Willing, BP}, title = {Prevotella in Pigs: The Positive and Negative Associations with Production and Health.}, journal = {Microorganisms}, volume = {8}, number = {10}, pages = {}, pmid = {33066697}, issn = {2076-2607}, abstract = {A diverse and dynamic microbial community (known as microbiota) resides within the pig gastrointestinal tract (GIT). The microbiota contributes to host health and performance by mediating nutrient metabolism, stimulating the immune system, and providing colonization resistance against pathogens. Manipulation of gut microbiota to enhance growth performance and disease resilience in pigs has recently become an active area of research in an era defined by increasing scrutiny of antimicrobial use in swine production. In order to develop microbiota-targeted strategies, or to identify potential next-generation probiotic strains originating from the endogenous members of GIT microbiota in pigs, it is necessary to understand the role of key commensal members in host health. Many, though not all, correlative studies have associated members of the genus Prevotella with positive outcomes in pig production, including growth performance and immune response; therefore, a comprehensive review of the genus in the context of pig production is needed. In the present review, we summarize the current state of knowledge about the genus Prevotella in the intestinal microbial community of pigs, including relevant information from other animal species that provide mechanistic insights, and identify gaps in knowledge that must be addressed before development of Prevotella species as next-generation probiotics can be supported.}, }
@article {pmid33065340, year = {2021}, author = {Jacquemyn, H and Pozo, MI and Álvarez-Pérez, S and Lievens, B and Fukami, T}, title = {Yeast-nectar interactions: metacommunities and effects on pollinators.}, journal = {Current opinion in insect science}, volume = {44}, number = {}, pages = {35-40}, doi = {10.1016/j.cois.2020.09.014}, pmid = {33065340}, issn = {2214-5753}, mesh = {Animals ; *Behavior, Animal ; Genetic Fitness ; Mycobiome ; Plant Nectar/*chemistry ; *Pollination ; *Yeasts ; }, abstract = {About 90% of all flowering plant species are pollinated by animals. Animals are attracted to flowers because they often provide food in the form of nectar and pollen. While floral nectar is assumed to be initially sterile, it commonly becomes colonized by yeasts after animals have visited the flowers. Although yeast communities in floral nectar appear simple, community assembly depends on a complex interaction between multiple factors. Yeast colonization has a significant effect on the scent of floral nectar, foraging behavior of insects and nectar consumption. Consumption of nectar colonized by yeasts has been shown to improve bee fitness, but effects largely depended on yeast species. Altogether, these results indicate that dispersal, colonization history and nectar chemistry strongly interact and have pronounced effects on yeast metacommunities and, as a result, on bee foraging behavior and fitness. Future research directions to better understand the dynamics of plant-microbe-pollinator interactions are discussed.}, }
@article {pmid33062716, year = {2020}, author = {Almugadam, BS and Liu, Y and Chen, SM and Wang, CH and Shao, CY and Ren, BW and Tang, L}, title = {Alterations of Gut Microbiota in Type 2 Diabetes Individuals and the Confounding Effect of Antidiabetic Agents.}, journal = {Journal of diabetes research}, volume = {2020}, number = {}, pages = {7253978}, pmid = {33062716}, issn = {2314-6753}, mesh = {Adult ; Bacteria/classification ; Biodiversity ; Blood Glucose ; Case-Control Studies ; DNA/analysis ; Diabetes Mellitus, Type 2/*complications ; Faecalibacterium ; Feces/microbiology ; Female ; Fusobacterium ; Gastrointestinal Microbiome/*drug effects ; Glycated Hemoglobin/biosynthesis ; Humans ; Hypoglycemic Agents/*pharmacology ; Intestines ; Male ; Metformin/therapeutic use ; Microbiology ; Middle Aged ; RNA, Ribosomal, 16S/metabolism ; Risk ; Sudan/epidemiology ; }, abstract = {Type 2 diabetes is a leading cause of morbidity and a common risk of several disorders. Identifying the microbial ecology changes is essential for disease prediction, therapy, and prevention. Thus, our study is aimed at investigating the intestinal microbiota among healthy and type 2 diabetes individuals and exploring the effect of antidiabetic agents on gut bacterial flora. 24 type 2 diabetes (metformin, glimepiride, and nontherapeutic subgroups; N = 8) and 24 healthy control subjects were enrolled in this study, and intestinal bacterial microbiota was investigated by analyzing V3-V4 regions of 16S rRNA gene sequence. Numerous alterations were observed in the gut microbial community of diabetic individuals. These changes were characterized by a significant lowered abundance of Faecalibacterium, Fusobacterium, Dialister, and Elusimicrobium in the nontherapeutic subgroup compared to the healthy control group. Likewise, correlation analysis showed a substantial decline in gut microbiota richness and diversity with the duration of illness. Furthermore, antidiabetic agents restored to some extent the richness and diversity of gut microbiota and improved the abundance of many beneficial bacteria with a significant increase of Methanobrevibacter in the metformin subcategory compared to the nontherapeutic subgroup. In return, they decreased the abundance of some opportunistic pathogens. The findings of this study have added a novel understanding about the pathogenesis of the disease and the mechanisms underlying antidiabetic therapy, which are of potential interest for therapeutic lines and further studies.}, }
@article {pmid33059158, year = {2021}, author = {Chique, C and Hynds, P and Burke, LP and Morris, D and Ryan, MP and O'Dwyer, J}, title = {Contamination of domestic groundwater systems by verotoxigenic escherichia coli (VTEC), 2003-2019: A global scoping review.}, journal = {Water research}, volume = {188}, number = {}, pages = {116496}, doi = {10.1016/j.watres.2020.116496}, pmid = {33059158}, issn = {1879-2448}, mesh = {*Groundwater ; Humans ; Prospective Studies ; *Shiga-Toxigenic Escherichia coli ; Water Supply ; *Waterborne Diseases ; }, abstract = {Verocytotoxin-producing E. coli (VTEC) are important agents of diarrhoeal disease in humans globally. As a noted waterborne disease, emphasis has been given to the study VTEC in surface waters, readily susceptible to microbial contamination. Conversely, the status of VTEC in potable groundwater sources, generally regarded as a "safe" drinking-water supply remains largely understudied. As such, this investigation presents the first scoping review seeking to determine the global prevalence of VTEC in groundwater supply sources intended for human consumption. Twenty-three peer-reviewed studies were identified and included for data extraction. Groundwater sample and supply detection rates (estimated 0.6 and 1.3%, respectively) indicate VTEC is infrequently present in domestic groundwater sources. However, where generic (fecal indicator) E. coli are present, the VTEC to E. coli ratio was found to be 9.9%, representing a latent health concern for groundwater consumers. Geographically, extracted data indicates higher VTEC detection rates in urban (5.4%) and peri‑urban (4.9%) environments than in rural areas (0.9%); however, this finding is confounded by the predominance of research studies in lower income regions. Climate trends indicate local environments classified as 'temperate' (14/554; 2.5%) and 'cold' (8/392; 2%) accounted for a majority of supply sources with VTEC present, with similar detection rates encountered among supplies sampled during periods typically characterized by 'high' precipitation (15/649; 2.3%). Proposed prevalence figures may find application in preventive risk-based catchment and groundwater quality management including development of Quantitative Microbial Risk Assessments (QMRA). Notwithstanding, to an extent, a large geographical disparity in available investigations, lack of standardized reporting, and bias in source selection, restrict the transferability of research findings. Overall, the mechanisms responsible for VTEC transport and ingress into groundwater supplies remain ambiguous, representing a critical knowledge gap, and denoting a distinctive lack of integration between hydrogeological and public health research. Key recommendations and guidelines are provided for prospective studies directed at increasingly integrative and multi-disciplinary research.}, }
@article {pmid33059136, year = {2021}, author = {Ávila, C and García-Galán, MJ and Borrego, CM and Rodríguez-Mozaz, S and García, J and Barceló, D}, title = {New insights on the combined removal of antibiotics and ARGs in urban wastewater through the use of two configurations of vertical subsurface flow constructed wetlands.}, journal = {The Science of the total environment}, volume = {755}, number = {Pt 2}, pages = {142554}, doi = {10.1016/j.scitotenv.2020.142554}, pmid = {33059136}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Drug Resistance, Microbial ; Genes, Bacterial ; Waste Disposal, Fluid ; *Wastewater/analysis ; *Wetlands ; }, abstract = {The occurrence and removal of 49 antibiotics and 11 selected antibiotic resistance genes (ARGs) were investigated in 2 vertical subsurface flow (VF) constructed wetlands (1.5 m[2] each): an unsaturated (UVF) unit and a partially saturated (SVF) unit (0.35 m saturated out of 0.8 m) operating in parallel and treating urban wastewater. Thirteen antibiotics were detected in influent wastewater, 6 of which were present in all samples. The SVF showed statistical significance on the removal of 4 compounds (namely ciprofloxacin, ofloxacin, pipemidic acid and azithromycin), suggesting that the wider range of pH and/or redox conditions of this configuration might promote the microbial degradation of some antibiotics. In contrast, the concentration of the latter (except pipemidic acid) and also clindamycin was higher in the effluent than in the influent of the UVF. Five ARGs were detected in influent wastewater, sul1 and sul2, blaTEM, ermB and qnrS. All of them were detected also in the biofilm of both wetlands, except qnrS. Average removal rates of ARGs showed no statistical differences between both wetland units, and ranged between 46 and 97% for sul1, 33 and 97% for sul2, 9 and 99% for ermB, 18 and 97% for qnrS and 11 and 98% for blaTEM.}, }
@article {pmid33054775, year = {2020}, author = {Roussel, C and De Paepe, K and Galia, W and De Bodt, J and Chalancon, S and Leriche, F and Ballet, N and Denis, S and Alric, M and Van de Wiele, T and Blanquet-Diot, S}, title = {Spatial and temporal modulation of enterotoxigenic E. coli H10407 pathogenesis and interplay with microbiota in human gut models.}, journal = {BMC biology}, volume = {18}, number = {1}, pages = {141}, pmid = {33054775}, issn = {1741-7007}, mesh = {Colon, Ascending/microbiology ; Enterotoxigenic Escherichia coli/*pathogenicity/*physiology ; Escherichia coli Infections/*microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Ileum/microbiology ; Microbial Viability ; }, abstract = {BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) substantially contributes to the burden of diarrheal illnesses in developing countries. With the use of complementary in vitro models of the human digestive environment, TNO gastrointestinal model (TIM-1), and Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME), we provided the first detailed report on the spatial-temporal modulation of ETEC H10407 survival, virulence, and its interplay with gut microbiota. These systems integrate the main physicochemical parameters of the human upper digestion (TIM-1) and simulate the ileum vs ascending colon microbial communities and luminal vs mucosal microenvironments, captured from six fecal donors (M-SHIME).<br><br>RESULTS: A loss of ETEC viability was noticed upon gastric digestion, while a growth renewal was found at the end of jejunal and ileal digestion. The remarkable ETEC mucosal attachment helped to maintain luminal concentrations above 6&#xa0;log10&#xa0;mL[-1] in the ileum and ascending colon up to 5&#x2009;days post-infection. Seven ETEC virulence genes were monitored. Most of them were switched on in the stomach and switched off in the TIM-1 ileal effluents and in a late post-infectious stage in the M-SHIME ascending colon. No heat-labile enterotoxin production was measured in the stomach in contrast to the ileum and ascending colon. Using 16S rRNA gene-based amplicon sequencing, ETEC infection modulated the microbial community structure of the ileum mucus and ascending colon lumen.<br><br>CONCLUSIONS: This study provides a better understanding of the interplay between ETEC and gastrointestinal cues and may serve to complete knowledge on ETEC pathogenesis and inspire novel prophylactic strategies for diarrheal diseases.}, }
@article {pmid33054212, year = {2020}, author = {Li, Y and Wang, T and Camps-Arbestain, M and Suárez-Abelenda, M and Whitby, CP}, title = {Lime and/or Phosphate Application Affects the Stability of Soil Organic Carbon: Evidence from Changes in Quantity and Chemistry of the Soil Water-Extractable Organic Matter.}, journal = {Environmental science &amp; technology}, volume = {54}, number = {21}, pages = {13908-13916}, doi = {10.1021/acs.est.0c01341}, pmid = {33054212}, issn = {1520-5851}, mesh = {Calcium Compounds ; *Carbon ; Oxides ; Phosphates ; *Soil ; Water ; }, abstract = {The mechanisms by which lime and/or phosphate addition impacts the preservation of soil organic matter (OM) are poorly understood. We explored the changes in quantity and chemistry of water-extractable organic matter (WEOM) in the bulk soil and its heavy density fraction (>1.6 g/cm[3]) of an unmanaged C-rich volcanic soil caused by lime and/or phosphate application. The addition of lime or phosphate caused (i) a significant increase in the WEOM, along with a decrease in its C/N ratio and an increase in its aromaticity, and (ii) changes in the WEOM chemical composition, measured with pyrolysis-gas chromatography/mass spectrometry, this being most impacted by lime application. The combined effect of lime and phosphate addition on the quantity and chemistry of WEOM was larger than the effects of separate lime and phosphate additions. By comparing the response of the bulk soil and the heavy fraction, we infer that phosphate has a greater contribution to the destabilization of vulnerable particulate OM, while lime causes a comparable disruption in the particulate OM and that in the heavy fraction. These findings provide a mechanistic insight into the decreased OM stability after liming and/or P fertilizing Andosols. They have implications for designing climate-smart management practices for these soils.}, }
@article {pmid33051738, year = {2021}, author = {Zhang, W and Wang, X and Li, Y and Liu, Z and Li, D and Wen, X and Feng, Y and Zhang, X}, title = {Pinewood Nematode Alters the Endophytic and Rhizospheric Microbial Communities of Pinus massoniana.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {807-817}, pmid = {33051738}, issn = {1432-184X}, support = {2018YFC1200400//National Key R &amp; D Program of China/ ; 31901315//Young Scientists Fund/ ; }, mesh = {Animals ; Bacteria/genetics ; China ; *Microbiota ; *Nematoda ; *Pinus ; }, abstract = {Pinewood nematode, Bursaphelenchus xylophilus, is one of the greatest threats to pine trees and is spreading all over the world. During the nematode's pathogenesis, plant microorganisms play important roles. However, many microbial communities, such as that in Pinus massoniana, a major host of B. xylophilus that is widely distributed in China, are not well studied, especially the fungal communities. Here, the endophytic and rhizospheric bacterial and fungal communities associated with healthy and B. xylophilus-infected P. massoniana were analyzed. The results showed that 7639 bacterial and 3108 fungal OTUs were annotated from samples of P. massoniana, the rhizosphere, and B. xylophilus. There were significant diversity differences of endophytic microbes between healthy and infected P. massoniana. The abundances of endophytic bacteria Paenibacillus, unidentified_Burkholderiaceae, Serratia, Erwinia, and Pseudoxanthomonas and fungi Penicillifer, Zygoascus, Kirschsteiniothelia, Cyberlindnera, and Sporothrix in infected pines were greater than those in healthy pines, suggesting an association of particular microbial abundances with the pathogenesis of B. xylophilus in pines. Meanwhile, the abundances of microbes of unidentified_Burkholderiaceae, Saitozyma, and Pestalotiopsis were greater and Acidothermus and Trichoderma were lower in the rhizosphere under infected pines than those under healthy pines and the differences might be caused by B. xylophilus-induced weakening of the health of pines. Our study explored the endophytic and rhizospheric microbial community changes potentially caused by B. xylophilus infection of pines.}, }
@article {pmid33049639, year = {2021}, author = {Ni, N and Li, X and Yao, S and Shi, R and Kong, D and Bian, Y and Jiang, X and Song, Y}, title = {Biochar applications combined with paddy-upland rotation cropping systems benefit the safe use of PAH-contaminated soils: From risk assessment to microbial ecology.}, journal = {Journal of hazardous materials}, volume = {404}, number = {Pt A}, pages = {124123}, doi = {10.1016/j.jhazmat.2020.124123}, pmid = {33049639}, issn = {1873-3336}, mesh = {Charcoal ; Humans ; *Oryza ; *Polycyclic Aromatic Hydrocarbons/analysis ; Risk Assessment ; Rotation ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {This study aimed to establish a method allowing the safe use of polycyclic aromatic hydrocarbon (PAH)-contaminated soils through the combination of biochar applications and different cropping systems. The impact of biochar applications under different cropping systems on the human health risks of PAHs and soil microbiology was elucidated. The residual PAHs were the lowest in rhizosphere soils amended with 2% corn straw-derived biochar pyrolyzed at 300 °C (CB300) under the paddy-upland rotation cropping (PURC) system. Human health risks resulting from the ingestion of PAH-contaminated carrot roots / rice grains under the PURC system were significantly lower than those under continuous upland cropping systems. The greatest diversity, richness and network complexity of soil microbial communities occurred under the PURC system combined with the 2% CB300 treatment. Soil microbial functions associated with soil health and PAH biodegradation were enhanced under this strategy, while the pathogen group was inhibited. Primarily owing to its high sorption capacity, bamboo-derived biochar pyrolyzed at 700 °C realized in the reduction of PAHs, but weakly influenced shifts in soil microbial communities. Overall, the combination of PURC systems and low-temperature-pyrolyzed nutrient-rich biochar could efficiently reduce the human health risks of PAHs and improve soil microbial ecology in agricultural fields.}, }
@article {pmid33047413, year = {2021}, author = {Dini-Andreote, F and Kowalchuk, GA and Prosser, JI and Raaijmakers, JM}, title = {Towards meaningful scales in ecosystem microbiome research.}, journal = {Environmental microbiology}, volume = {23}, number = {1}, pages = {1-4}, doi = {10.1111/1462-2920.15276}, pmid = {33047413}, issn = {1462-2920}, }
@article {pmid33043868, year = {2020}, author = {Seto, M and Iwasa, Y}, title = {Microbial material cycling, energetic constraints and ecosystem expansion in subsurface ecosystems.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1931}, pages = {20200610}, pmid = {33043868}, issn = {1471-2954}, mesh = {*Ecological and Environmental Phenomena ; *Ecosystem ; *Environmental Microbiology ; }, abstract = {To harvest energy from chemical reactions, microbes engage in diverse catabolic interactions that drive material cycles in the environment. Here, we consider a simple mathematical model for cycling reactions between alternative forms of an element (A and Ae), where reaction 1 converts A to Ae and reaction 2 converts Ae to A. There are two types of microbes: type 1 microbes harness reaction 1, and type 2 microbes harness reaction 2. Each type receives its own catabolic resources from the other type and provides the other type with the by-products as the catabolic resources. Analyses of the model show that each type increases its steady-state abundance in the presence of the other type. The flux of material flow becomes faster in the presence of microbes. By coupling two catabolic reactions, types 1 and 2 can also expand their realized niches through the abundant resource premium, the effect of relative quantities of products and reactants on the available chemical energy, which is especially important for microbes under strong energetic limitations. The plausibility of mutually beneficial interactions is controlled by the available chemical energy (Gibbs energy) of the system. We conclude that mutualistic catabolic interactions can be an important factor that enables microbes in subsurface ecosystems to increase ecosystem productivity and expand the ecosystem.}, }
@article {pmid33042180, year = {2020}, author = {Otlewska, A and Migliore, M and Dybka-Stępień, K and Manfredini, A and Struszczyk-Świta, K and Napoli, R and Białkowska, A and Canfora, L and Pinzari, F}, title = {When Salt Meddles Between Plant, Soil, and Microorganisms.}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {553087}, pmid = {33042180}, issn = {1664-462X}, abstract = {In extreme environments, the relationships between species are often exclusive and based on complex mechanisms. This review aims to give an overview of the microbial ecology of saline soils, but in particular of what is known about the interaction between plants and their soil microbiome, and the mechanisms linked to higher resistance of some plants to harsh saline soil conditions. Agricultural soils affected by salinity is a matter of concern in many countries. Soil salinization is caused by readily soluble salts containing anions like chloride, sulphate and nitrate, as well as sodium and potassium cations. Salinity harms plants because it affects their photosynthesis, respiration, distribution of assimilates and causes wilting, drying, and death of entire organs. Despite these life-unfavorable conditions, saline soils are unique ecological niches inhabited by extremophilic microorganisms that have specific adaptation strategies. Important traits related to the resistance to salinity are also associated with the rhizosphere-microbiota and the endophytic compartments of plants. For some years now, there have been studies dedicated to the isolation and characterization of species of plants' endophytes living in extreme environments. The metabolic and biotechnological potential of some of these microorganisms is promising. However, the selection of microorganisms capable of living in association with host plants and promoting their survival under stressful conditions is only just beginning. Understanding the mechanisms of these processes and the specificity of such interactions will allow us to focus our efforts on species that can potentially be used as beneficial bioinoculants for crops.}, }
@article {pmid33040164, year = {2021}, author = {Wisnoski, NI and Lennon, JT}, title = {Microbial community assembly in a multi-layer dendritic metacommunity.}, journal = {Oecologia}, volume = {195}, number = {1}, pages = {13-24}, pmid = {33040164}, issn = {1432-1939}, support = {DEB-1442246//National Science Foundation (US)/ ; W911NF-14-1-0411//Army Research Office/ ; }, mesh = {*Ecosystem ; *Microbiota ; Phylogeny ; }, abstract = {A major goal of metacommunity ecology is to infer the local- and regional-scale processes that underlie community assembly. In dendritic ecological networks, branching patterns and directional flow can alter the balance between local and regional factors during assembly. Vertical habitat structure may further affect community assembly in dendritic metacommunities. In this study, we analyzed the bacterial metacommunity of a fifth-order mountain stream network to assess differences in community assembly (1) between planktonic and benthic habitats, (2) across spatial scales, and (3) between headwater and downstream regions of the network. Using taxonomic and phylogenetic null modeling, we found habitat-specific spatial patterns of community assembly across the dendritic network. Compositional differences between planktonic and benthic communities were maintained by variable selection, but we also found evidence of local dispersal limitation between the two habitats. Planktonic community assembly was scale dependent, transitioning from homogeneous selection at local scales to variable selection at regional scales, while benthic community assembly was less scale dependent. Variable selection structured headwaters in both habitat types, but downstream communities were primarily structured by homogeneous selection, especially in sediments. Taken together, our results show that vertical habitat structure contributes to the scale-dependent processes of community assembly across the dendritic metacommunity.}, }
@article {pmid33039899, year = {2020}, author = {Douterelo, I and Dutilh, BE and Calero, C and Rosales, E and Martin, K and Husband, S}, title = {Impact of phosphate dosing on the microbial ecology of drinking water distribution systems: Fieldwork studies in chlorinated networks.}, journal = {Water research}, volume = {187}, number = {}, pages = {116416}, doi = {10.1016/j.watres.2020.116416}, pmid = {33039899}, issn = {1879-2448}, mesh = {Biofilms ; *Drinking Water ; Phosphates ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; Water Quality ; Water Supply ; }, abstract = {Phosphate is routinely dosed to ensure regulatory compliance for lead in drinking water distribution systems. Little is known about the impact of the phosphate dose on the microbial ecology in these systems and in particular the endemic biofilms. Disturbance of the biofilms and embedded material in distribution can cause regulatory failures for turbidity and metals. To investigate the impact of phosphate on developing biofilms, pipe wall material from four independent pipe sections was mobilised and collected using two twin-flushing operations a year apart in a chlorinated UK network pre- and post-phosphate dosing. Intensive monitoring was undertaken, including turbidity and water physico-chemistry, traditional microbial culture-based indicators, and microbial community structure via sequencing the 16S rRNA gene for bacteria and the ITS2 gene for fungi. Whole metagenome sequencing was used to study shifts in functional characteristics following the addition of phosphate. As an operational consequence, turbidity responses from the phosphate-enriched water were increased, particularly from cast iron pipes. Differences in the taxonomic composition of both bacteria and fungi were also observed, emphasising a community shift towards microorganisms able to use or metabolise phosphate. Phosphate increased the relative abundance of bacteria such as Pseudomonas, Paenibacillus, Massilia, Acinetobacter and the fungi Cadophora, Rhizophagus and Eupenicillium. Whole metagenome sequencing showed with phosphate a favouring of sequences related to Gram-negative bacterium type cell wall function, virions and thylakoids, but a reduction in the number of sequences associated to vitamin binding, methanogenesis and toxin biosynthesis. With current faecal indicator tests only providing risk detection in bulk water samples, this work improves understanding of how network changes effect microbial ecology and highlights the potential for new approaches to inform future monitoring or control strategies to protect drinking water quality.}, }
@article {pmid33039841, year = {2021}, author = {Alloul, A and Muys, M and Hertoghs, N and Kerckhof, FM and Vlaeminck, SE}, title = {Cocultivating aerobic heterotrophs and purple bacteria for microbial protein in sequential photo- and chemotrophic reactors.}, journal = {Bioresource technology}, volume = {319}, number = {}, pages = {124192}, doi = {10.1016/j.biortech.2020.124192}, pmid = {33039841}, issn = {1873-2976}, mesh = {Kinetics ; *Proteobacteria ; Rhodobacter ; *Rhodopseudomonas ; Wastewater ; }, abstract = {Aerobic heterotrophic bacteria (AHB) and purple non-sulfur bacteria (PNSB) are typically explored as two separate types of microbial protein, yet their properties as respectively a bulk and added-value feed ingredient make them appealing for combined use. The feasibility of cocultivation in a sequential photo- and chemotrophic approach was investigated. First, mapping the chemotrophic growth kinetics for four Rhodobacter, Rhodopseudomonas and Rhodospirillum species on different carbon sources showed a preference for fructose (µmax 2.4-3.9 d[-1] 28 °C; protein 36-59%DW). Secondly, a continuous photobioreactor inoculated with Rhodobacter capsulatus (VFA as C-source) delivered the starter culture for an aerobic batch reactor (fructose as C-source). This two-stage system showed an improved nutritional quality compared to AHB production: higher protein content (45-71%DW), more attractive amino/fatty acid profile and contained up to 10% PNSB. The findings strengthen protein production with cocultures and might enable the implementation of the technology for resource recovery on streams such as wastewater.}, }
@article {pmid33037304, year = {2020}, author = {De Rudder, C and Garcia-Tímermans, C and De Boeck, I and Lebeer, S and Van de Wiele, T and Calatayud Arroyo, M}, title = {Lacticaseibacillus casei AMBR2 modulates the epithelial barrier function and immune response in a donor-derived nasal microbiota manner.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {16939}, pmid = {33037304}, issn = {2045-2322}, mesh = {Cells, Cultured ; Cytokines/immunology ; Epithelial Cells/immunology/microbiology ; Epithelium ; Host Microbial Interactions/immunology ; Humans ; Immunity/immunology ; Inflammation/immunology/microbiology ; Lacticaseibacillus casei/*immunology ; Macrophages/immunology ; Microbiota/*immunology ; Nose/immunology/*microbiology ; Respiratory Mucosa/*immunology/*microbiology ; }, abstract = {Live biotherapeutic products (LBP) are emerging as alternative treatment strategies for chronic rhinosinusitis. The selection of interesting candidate LBPs often involves model systems that do not include the polymicrobial background (i.e. the host microbiota) in which they will be introduced. Here, we performed a screening in a simplified model system of upper respiratory epithelium to assess the effect of nasal microbiota composition on the ability to attach and grow of a potential LBP, Lacticaseibacillus casei AMBR2, in this polymicrobial background. After selecting the most permissive and least permissive donor, L. casei AMBR2 colonisation in their respective polymicrobial backgrounds was assessed in more physiologically relevant model systems. We examined cytotoxicity, epithelial barrier function, and cytokine secretion, as well as bacterial cell density and phenotypic diversity in differentiated airway epithelium based models, with or without macrophage-like cells. L. casei AMBR2 could colonize in the presence of both selected donor microbiota and increased epithelial barrier resistance in presence of donor-derived nasal bacteria, as well as anti-inflammatory cytokine secretion in the presence of macrophage-like cells. This study highlights the potential of L. casei AMBR2 as LBP and the necessity to employ physiologically relevant model systems to investigate host-microbe interaction in LBP research.}, }
@article {pmid33033618, year = {2020}, author = {Medina, WRM and Eramo, A and Tu, M and Fahrenfeld, NL}, title = {Sewer biofilm microbiome and antibiotic resistance genes as function of pipe material, source of microbes, and disinfection: field and laboratory studies.}, journal = {Environmental science : water research &amp; technology}, volume = {6}, number = {8}, pages = {2122-2137}, pmid = {33033618}, issn = {2053-1400}, support = {R25 GM058389/GM/NIGMS NIH HHS/United States ; }, abstract = {Wastewater systems are recognized pathways for the spread of antibiotic resistant bacteria, but relatively little is known about the microbial ecology of the sewer environment. Sewer biofilm colonization by antibiotic resistance gene (ARG) carrying bacteria may impact interpretations of sewage epidemiology data, water quality during sewer overflows, and hazard to utility workers. The objectives of this research were to evaluate the (1) microbiome of real and simulated sewer biofilms and their potential to accumulate ARGs and (2) susceptibility of simulated sewer biofilms to bleach disinfection. First, biofilm samples were collected from sewer municipal systems. Next, an annular biofilm reactor was used to simulate the sewer environment while controlling the pipe material (concrete vs. PVC). The reactor was operated either as fed semi-batch with sewer sediment and synthetic wastewater (Sed-SB) or fed with a continuous flow of raw sewage (WW-CF). The abundance of ARGs, human fecal marker HF183, and 16S rRNA gene copies in these biofilm samples was measured with qPCR. Amplicon sequencing was performed to compare the prokaryotic diversity between samples. Finally, the susceptibility of reactor biofilm to a 4.6% bleach disnfection protocol was evaluated using viability qPCR and amplicon sequencing. Field and WW-CF biofilms contained the most ARG copies and the microbial community compositions varied between the different biofilm samples (field, Sed-SB, and WW-CF). Pipe material did not affect the abundance of ARGs in the reactor samples. However, log removal following bleach treatment suggested that the biofilm grown on PVC surface was primarily dislodged from the surface by the bleach treatment whereas more bacteria were lysed within the biofilm that remained on the concrete surface. Viable bacteria carrying ARGs were observed following 10 minutes of treatment. This study showed that sewer biofilms can accumulate bacteria carrying ARGs and that while bleach can reduce sewer biofilm density, the protocol tested here will not completely remove the biofilms.}, }
@article {pmid33033140, year = {2020}, author = {Peruzzo, A and Salerno, B and Tiengo, A and Petrin, S and Barco, L and Losasso, C and Orsini, M}, title = {Genome Sequence of a Persistent Campylobacter jejuni Strain, 2016-IZSVE-19-111250.}, journal = {Microbiology resource announcements}, volume = {9}, number = {41}, pages = {}, pmid = {33033140}, issn = {2576-098X}, abstract = {In this report, we present the whole-genome sequence of a Campylobacter jejuni strain isolated recursively for the last 3 years from an Italian poultry farm.}, }
@article {pmid33032584, year = {2020}, author = {Zhu, L and Xu, F and Wan, W and Yu, B and Tang, L and Yang, Y and Du, Y and Chen, Z and Xu, H}, title = {Correction to: Gut microbial characteristics of adult patients with allergy rhinitis.}, journal = {Microbial cell factories}, volume = {19}, number = {1}, pages = {192}, pmid = {33032584}, issn = {1475-2859}, abstract = {An amendment to this paper has been published and can be accessed via the original article.}, }
@article {pmid33032128, year = {2021}, author = {Zhang, S and Xia, X and Ke, Y and Song, S and Shen, Z and Cheung, S and Liu, H}, title = {Population dynamics and interactions of Noctiluca scintillans and Mesodinium rubrum during their successive blooms in a subtropical coastal water.}, journal = {The Science of the total environment}, volume = {755}, number = {Pt 1}, pages = {142349}, doi = {10.1016/j.scitotenv.2020.142349}, pmid = {33032128}, issn = {1879-1026}, mesh = {*Dinoflagellida ; Environmental Monitoring ; *Phytoplankton ; Population Dynamics ; Water ; }, abstract = {A time series field survey were conducted in Port Shelter, a subtropical coastal water in NW Pacific, beginning before the onset of a chain of Noctiluca scintillans and/or Mesodinium rubrum blooms, and ending after the blooms had declined. At the first mixed bloom stage, seed of N. scintillans and the consequent outbreak of both N. scintillans and M. rubrum were largely due to the physical forcing. Plenty food supply and their different feeding habits supported N. scintillans and M. rubrum to bloom massively and concomitantly. Following that, there was a small N. scintillans bloom followed by a small crest of M. rubrum. Their initiation and scale were mainly affected by limited food supply and/or the inferior food source. Sudden change of wind from mild northeast wind to strong southeast wind might contribute to the termination of N. scintillans bloom. Finally, physical accumulation was the most important driving factors of the formation and dispersal of the third and largest bloom of N. scintillans. Formation of these bloom events may involve vertical migration and/or the concentrating mechanism of M. rubrum and N. scintillans. Meanwhile, biotic interactions such as mutual supportive relationship between N. scintillans and M. rubrum, and O. hongkongense fed on the progametes of N. scintillans, as well as other abiotic factors like seawater temperature and rainfall, also play important roles in this series of bloom events. Our findings have important implications for coastal zones worldwide, which are affected recurrently by these two ubiquitous red tide-forming species.}, }
@article {pmid33031481, year = {2020}, author = {Klaps, J and de Vega, C and Herrera, CM and Junker, RR and Lievens, B and Álvarez-Pérez, S}, title = {Candida metrosideri pro tempore sp. nov. and Candida ohialehuae pro tempore sp. nov., two antifungal-resistant yeasts associated with Metrosideros polymorpha flowers in Hawaii.}, journal = {PloS one}, volume = {15}, number = {10}, pages = {e0240093}, pmid = {33031481}, issn = {1932-6203}, mesh = {Amphotericin B/pharmacology ; Antifungal Agents/pharmacology ; Candida/*classification/drug effects/genetics/isolation &amp; purification ; Drug Resistance, Fungal ; Flowers/microbiology ; Hawaii ; Microbial Sensitivity Tests ; Myrtaceae/*microbiology ; Phenotype ; Phylogeny ; RNA, Ribosomal/classification/genetics/metabolism ; }, abstract = {Flowers produce an array of nutrient-rich exudates in which microbes can thrive, making them hotspots for microbial abundance and diversity. During a diversity study of yeasts inhabiting the flowers of Metrosideros polymorpha (Myrtaceae) in the Hawai'i Volcanoes National Park (HI, USA), five isolates were found to represent two novel species. Morphological and physiological characterization, and sequence analysis of the small subunit ribosomal RNA (rRNA) genes, the D1/D2 domains of the large subunit rRNA genes, the internal transcribed spacer (ITS) regions, and the genes encoding the largest and second largest subunits of the RNA polymerase II (RPB1 and RPB2, respectively), classified both species in the family Metschnikowiaceae, and we propose the names Candida metrosideri pro tempore sp. nov. (JK22T = CBS 16091 = MUCL 57821) and Candida ohialehuae pro tempore sp. nov. (JK58.2T = CBS 16092 = MUCL 57822) for such new taxa. Both novel Candida species form a well-supported subclade in the Metschnikowiaceae containing species associated with insects, flowers, and a few species of clinical importance. The ascosporic state of the novel species was not observed. The two novel yeast species showed elevated minimum inhibitory concentrations to the antifungal drug amphotericin B (>4 μg/mL). The ecology and phylogenetic relationships of C. metrosideri and C. ohialehuae are also discussed.}, }
@article {pmid33027736, year = {2020}, author = {Dettling, A and Wedel, C and Huptas, C and Hinrichs, J and Scherer, S and Wenning, M}, title = {High counts of thermophilic spore formers in dairy powders originate from persisting strains in processing lines.}, journal = {International journal of food microbiology}, volume = {335}, number = {}, pages = {108888}, doi = {10.1016/j.ijfoodmicro.2020.108888}, pmid = {33027736}, issn = {1879-3460}, mesh = {Animals ; Colony Count, Microbial ; Dairy Products/*microbiology ; Endospore-Forming Bacteria/classification/genetics/*isolation &amp; purification ; *Food Handling ; Food Microbiology ; Genome, Bacterial/genetics ; Germany ; Milk/microbiology ; Spores, Bacterial/classification/genetics/*isolation &amp; purification ; }, abstract = {During the last decades, thermophilic spore counts became a very important quality parameter for manufacturers with regard to powdered dairy products. Low-spore count powders are highly demanded but challenging to produce when high production volume and long process times are intended. In this study a detailed monitoring of microbial levels in three skim milk powder plants was conducted. Anoxybacillus flavithermus was found to be primarily responsible for increased spore levels with increasing spore numbers being detected after 6-8 h already during initial processing steps. Simultaneously, the species composition shifted from a diverse bulk tank milk microbiota where different Bacillus species represented around 90% of the thermophilic bacteria to a dominance of A. flavithermus in the end product. The analysis of A. flavithermus isolates from different powder batches with RAPD PCR revealed recurring patterns in each of the eight German manufacturers sampled over several months. The high relatedness of isolates exhibiting identical RAPD patterns was exemplified by cgMLST based on whole genome sequences. We assume that A. flavithermus strains persisted in production plants and were not eliminated by cleaning. It is concluded that such persisting strains recurrently recontaminated subsequent powder productions. The data highlight that a targeted optimization of cleaning and disinfection procedures is the most promising measure to effectively reduce thermophilic spore counts in German dairy powders.}, }
@article {pmid33026073, year = {2021}, author = {Sauvaitre, T and Etienne-Mesmin, L and Sivignon, A and Mosoni, P and Courtin, CM and Van de Wiele, T and Blanquet-Diot, S}, title = {Tripartite relationship between gut microbiota, intestinal mucus and dietary fibers: towards preventive strategies against enteric infections.}, journal = {FEMS microbiology reviews}, volume = {45}, number = {2}, pages = {}, doi = {10.1093/femsre/fuaa052}, pmid = {33026073}, issn = {1574-6976}, mesh = {Dietary Fiber/*metabolism ; Gastrointestinal Diseases/*prevention &amp; control ; Gastrointestinal Microbiome/*physiology ; Humans ; Intestines/*microbiology ; Mucus/*metabolism ; }, abstract = {The human gut is inhabited by a large variety of microorganims involved in many physiological processes and collectively referred as to gut microbiota. Disrupted microbiome has been associated with negative health outcomes and especially could promote the onset of enteric infections. To sustain their growth and persistence within the human digestive tract, gut microbes and enteric pathogens rely on two main polysaccharide compartments, namely dietary fibers and mucus carbohydrates. Several evidences suggest that the three-way relationship between gut microbiota, dietary fibers and mucus layer could unravel the capacity of enteric pathogens to colonise the human digestive tract and ultimately lead to infection. The review starts by shedding light on similarities and differences between dietary fibers and mucus carbohydrates structures and functions. Next, we provide an overview of the interactions of these two components with the third partner, namely, the gut microbiota, under health and disease situations. The review will then provide insights into the relevance of using dietary fibers interventions to prevent enteric infections with a focus on gut microbial imbalance and impaired-mucus integrity. Facing the numerous challenges in studying microbiota-pathogen-dietary fiber-mucus interactions, we lastly describe the characteristics and potentialities of currently available in vitro models of the human gut.}, }
@article {pmid33025063, year = {2021}, author = {Gomard, Y and Flores, O and Vittecoq, M and Blanchon, T and Toty, C and Duron, O and Mavingui, P and Tortosa, P and McCoy, KD}, title = {Changes in Bacterial Diversity, Composition and Interactions During the Development of the Seabird Tick Ornithodoros maritimus (Argasidae).}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {770-783}, pmid = {33025063}, issn = {1432-184X}, support = {ESPEVEC (ANR blanc ANR-13-BSV7-0018-01)//Agence Nationale de la Recherche/ ; DISTIC//Labex CeMEB (Centre M&#xe9;diterran&#xe9;en de l'Environnement et de la Biodiversit&#xe9;)/ ; }, mesh = {Animals ; *Argasidae ; Birds ; Female ; Male ; *Ornithodoros ; RNA, Ribosomal, 16S/genetics ; *Rickettsia/genetics ; }, abstract = {Characterising within-host microbial interactions is essential to understand the drivers that shape these interactions and their consequences for host ecology and evolution. Here, we examined the bacterial microbiota hosted by the seabird soft tick Ornithodoros maritimus (Argasidae) in order to uncover bacterial interactions within ticks and how these interactions change over tick development. Bacterial communities were characterised through next-generation sequencing of the V3-V4 hypervariable region of the bacterial 16S ribosomal RNA gene. Bacterial co-occurrence and co-exclusion were determined by analysing networks generated from the metagenomic data obtained at each life stage. Overall, the microbiota of O. maritimus was dominated by four bacterial genera, namely Coxiella, Rickettsia, Brevibacterium and Arsenophonus, representing almost 60% of the reads. Bacterial diversity increased over tick development, and adult male ticks showed higher diversity than did adult female ticks. Bacterial networks showed that co-occurrence was more frequent than co-exclusion and highlighted substantial shifts across tick life stages; interaction networks changed from one stage to the next with a steady increase in the number of interactions through development. Although many bacterial interactions appeared unstable across life stages, some were maintained throughout development and were found in both sexes, such as Coxiella and Arsenophonus. Our data support the existence of a few stable interactions in O. maritimus ticks, on top of which bacterial taxa accumulate from hosts and/or the environment during development. We propose that stable associations delineate core microbial interactions, which are likely to be responsible for key biological functions.}, }
@article {pmid33025062, year = {2021}, author = {Baeza, N and Mercade, E}, title = {Relationship Between Membrane Vesicles, Extracellular ATP and Biofilm Formation in Antarctic Gram-Negative Bacteria.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {645-656}, pmid = {33025062}, issn = {1432-184X}, support = {CTQ2014-59632-R//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; BES-2015-074582//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; 2014SGR1017//Departament d'Innovaci&#xf3;, Universitats i Empresa, Generalitat de Catalunya/ ; }, mesh = {Adenosine Triphosphate ; Antarctic Regions ; Biofilms ; *Extracellular Vesicles ; Gram-Negative Bacteria ; *Shewanella ; }, abstract = {Biofilms offer a safe environment that favors bacterial survival; for this reason, most pathogenic and environmental bacteria live integrated in biofilm communities. The development of biofilms is complex and involves many factors, which need to be studied in order to understand bacterial behavior and control biofilm formation when necessary. We used a collection of cold-adapted Antarctic Gram-negative bacteria to study whether their ability to form biofilms is associated with a capacity to produce membrane vesicles and secrete extracellular ATP. In most of the studied strains, no correlation was found between biofilm formation and these two factors. Only Shewanella vesiculosa M7[T] secreted high levels of extracellular ATP, and its membrane vesicles caused a significant increase in the speed and amount of biofilm formation. In this strain, an important portion of the exogenous ATP was contained in membrane vesicles, where it was protected from apyrase treatment. These results confirm that ATP influences biofilm formation. Although the role of extracellular ATP in prokaryotes is still not well understood, the metabolic cost of its production suggests it has an important function, such as a role in biofilm formation. Thus, the liberation of extracellular ATP through membrane vesicles and its function deserve further study.}, }
@article {pmid33025061, year = {2021}, author = {Boraks, A and Plunkett, GM and Doro, TM and Alo, F and Sam, C and Tuiwawa, M and Ticktin, T and Amend, AS}, title = {Scale-Dependent Influences of Distance and Vegetation on the Composition of Aboveground and Belowground Tropical Fungal Communities.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {874-883}, pmid = {33025061}, issn = {1432-184X}, support = {1555793//National Science Foundation (US)/ ; 1555657//National Science Foundation/ ; }, mesh = {Biodiversity ; *Ecosystem ; Fungi/genetics ; *Mycobiome ; Soil Microbiology ; Trees ; }, abstract = {Fungi provide essential ecosystem services and engage in a variety of symbiotic relationships with trees. In this study, we investigate the spatial relationship of trees and fungi at a community level. We characterized the spatial dynamics for above- and belowground fungi using a series of forest monitoring plots, at nested spatial scales, located in the tropical South Pacific, in Vanuatu. Fungal communities from different habitats were sampled using metagenomic analysis of the nuclear ribosomal ITS1 region. Fungal communities exhibited strong distance-decay of similarity across our entire sampling range (3-110,000 m) and also at small spatial scales (< 50 m). Unexpectedly, this pattern was inverted at an intermediate scale (3.7-26 km). At large scales (80-110 km), belowground and aboveground fungal communities responded inversely to increasing geographic distance. Aboveground fungal community turnover (beta diversity) was best explained, at all scales, by geographic distance. In contrast, belowground fungal community turnover was best explained by geographic distance at small scales and tree community composition at large scales. Fungal communities from various habitats respond differently to the influences of habitat and geographic distance. At large geographic distances (80-110 km), community turnover for aboveground fungi is better explained by spatial distance, whereas community turnover for belowground fungi is better explained by plant community turnover. Future syntheses of spatial dynamics among fungal communities must explicitly consider geographic scale to appropriately contextualize community turnover.}, }
@article {pmid33025060, year = {2021}, author = {Fernandes, NM and Campello-Nunes, PH and Paiva, TS and Soares, CAG and Silva-Neto, ID}, title = {Ciliate Diversity From Aquatic Environments in the Brazilian Atlantic Forest as Revealed by High-Throughput DNA Sequencing.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {630-643}, pmid = {33025060}, issn = {1432-184X}, support = {E-26/202.325/2018//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; E-26/202.326/2018//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; 426648/2016-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {*Ciliophora/genetics ; *Ecosystem ; Forests ; High-Throughput Nucleotide Sequencing ; Phylogeny ; }, abstract = {Rainforest aquatic ecosystems include complex habitats with scarce information on their unicellular eukaryote diversity and community structure. We have investigated the diversity of ciliates in freshwater and brackish environments along the Brazilian Atlantic Forest, based on the hypervariable V4 region of the 18S-rDNA obtained by high-throughput DNA sequencing. Our analyses detected 409 ciliate taxonomic units (OTUs), mostly attributed to the classes Oligohymenophorea and Spirotrichea. A total of 11 classes, 12 subclasses, 112 genera, and 144 species were reported. We found the following: (a) the ciliate communities are more diverse in freshwater- than in Atlantic Forest-associated brackish environments; (b) the ciliate communities are composed by a small amount of highly abundant OTUs, but a high number of low-abundant or rare OTUs; (c) nearly one-third of the ciliate OTUs share less than 97% sequence identity to reference sequences and (d) phylogenetic inference supports the hypothesis that the V4 region of the Ciliophora 18S-rDNA is a suitable marker for accurate evolutionary inferences at class level. Our results showed that a considerable fraction of the HTS-detected diversity of ciliates from Brazilian Atlantic Forest is not represented in the currently available molecular databases.}, }
@article {pmid33024291, year = {2021}, author = {Giguere, AT and Eichorst, SA and Meier, DV and Herbold, CW and Richter, A and Greening, C and Woebken, D}, title = {Acidobacteria are active and abundant members of diverse atmospheric H2-oxidizing communities detected in temperate soils.}, journal = {The ISME journal}, volume = {15}, number = {2}, pages = {363-376}, pmid = {33024291}, issn = {1751-7370}, support = {P 26392/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Acidobacteria/metabolism ; Hydrogen ; *Hydrogenase/genetics/metabolism ; Oxidation-Reduction ; Soil ; Soil Microbiology ; }, abstract = {Significant rates of atmospheric dihydrogen (H2) consumption have been observed in temperate soils due to the activity of high-affinity enzymes, such as the group 1h [NiFe]-hydrogenase. We designed broadly inclusive primers targeting the large subunit gene (hhyL) of group 1h [NiFe]-hydrogenases for long-read sequencing to explore its taxonomic distribution across soils. This approach revealed a diverse collection of microorganisms harboring hhyL, including previously unknown groups and taxonomically not assignable sequences. Acidobacterial group 1h [NiFe]-hydrogenase genes were abundant and expressed in temperate soils. To support the participation of acidobacteria in H2 consumption, we studied two representative mesophilic soil acidobacteria, which expressed group 1h [NiFe]-hydrogenases and consumed atmospheric H2 during carbon starvation. This is the first time mesophilic acidobacteria, which are abundant in ubiquitous temperate soils, have been shown to oxidize H2 down to below atmospheric concentrations. As this physiology allows bacteria to survive periods of carbon starvation, it could explain the success of soil acidobacteria. With our long-read sequencing approach of group 1h [NiFe]-hydrogenase genes, we show that the ability to oxidize atmospheric levels of H2 is more widely distributed among soil bacteria than previously recognized and could represent a common mechanism enabling bacteria to persist during periods of carbon deprivation.}, }
@article {pmid33022257, year = {2020}, author = {Koskella, B}, title = {The phyllosphere.}, journal = {Current biology : CB}, volume = {30}, number = {19}, pages = {R1143-R1146}, doi = {10.1016/j.cub.2020.07.037}, pmid = {33022257}, issn = {1879-0445}, mesh = {Bacteria/classification/*growth &amp; development ; *Biodiversity ; *Ecosystem ; *Host Microbial Interactions ; *Microbiota ; Plant Leaves/*microbiology ; Plants/*microbiology ; Soil Microbiology ; }, abstract = {There is longstanding interest in studying microbial communities below ground, while little attention has historically been paid to the above ground portions of plants (the phyllosphere). The phyllosphere has been estimated to make up around 60% of the biomass across all taxa on Earth, making it a key habitat for microbial organisms. The more we study these complex and dynamic communities, the more we come to realize their importance to the health of plant hosts. Overall, the phyllosphere is proving to be both an important microbial habitat and a tractable model system for asking questions in microbial ecology and evolution.}, }
@article {pmid33021904, year = {2021}, author = {Taparia, T and Hendrix, E and Hendriks, M and Krijger, M and de Boer, W and van der Wolf, J}, title = {Comparative Studies on the Disease Prevalence and Population Dynamics of Ginger Blotch and Brown Blotch Pathogens of Button Mushrooms.}, journal = {Plant disease}, volume = {105}, number = {3}, pages = {542-547}, doi = {10.1094/PDIS-06-20-1260-RE}, pmid = {33021904}, issn = {0191-2917}, mesh = {Agaricus ; Europe ; *Zingiber officinale ; Population Dynamics ; Prevalence ; Pseudomonas ; }, abstract = {Bacterial blotch is one of the most economically important diseases of button 'mushroom. Knowledge of mechanisms of disease expression, inoculum thresholds, and disease management is limited to the most well-known pathogen, Pseudomonas tolaasii. Recent outbreaks in Europe have been attributed to 'P. gingeri' and P. salomonii for ginger and brown blotch, respectively. Information about their identity, infection dynamics, and pathogenicity is largely lacking. The disease pressure in an experimental mushroom cultivation facility was evaluated for 'P. gingeri' and P. salomonii over varying inoculation densities, casing soil types, environmental humidity, and cultivation cycles. The pathogen population structures in the casing soils were simultaneously tracked across the cropping cycle using highly specific and sensitive TaqMan-quantitative PCR assays. 'P. gingeri' caused disease outbreaks at lower inoculum thresholds (10[4] CFU/g) in the soil than P. salomonii (10[5] CFU/g). Ginger blotch generically declined in later harvest cycles, although brown blotch did not. Casing soils were differentially suppressive to blotch diseases, based on their composition and supplementation. Endemic pathogen populations increased across the cultivation cycle although the inoculated pathogen populations were consistent between the first and second flush. In conclusion, 'P. gingeri' and P. salomonii have unique infection and population dynamics that vary over soil types. Their endemic populations are also differently abundant in peat-based casing soils. This knowledge is essential for interpreting diagnostic results from screening mushroom farms and designing localized disease control strategies.}, }
@article {pmid33021677, year = {2021}, author = {Kolátková, V and Čepička, I and Hoffman, R and Vohník, M}, title = {Marinomyxa Gen. Nov. Accommodates Gall-Forming Parasites of the Tropical to Subtropical Seagrass Genus Halophila and Constitutes a Novel Deep-Branching Lineage Within Phytomyxea (Rhizaria: Endomyxa).}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {673-686}, pmid = {33021677}, issn = {1432-184X}, support = {1308218//Grantov&#xe1; Agentura, Univerzita Karlova/ ; }, mesh = {Animals ; *Hydrocharitaceae ; *Parasites ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; *Rhizaria ; }, abstract = {Marine representatives of Phytomyxea (SAR: Rhizaria: Endomyxa), a peculiar class of obligate endobiotic parasites, are a greatly understudied ecological group of protists infecting many algal, diatom, and seagrass species. Very little is known about the actual diversity, ecology, and pathogenic potential of these organisms and their taxonomic treatment in many cases follows outdated morphotaxonomic concepts. Here we focused on resolving the phylogenetic relations of the phytomyxean parasites of the widespread seagrass genus Halophila. We report the first finding of Plasmodiophora halophilae, the parasite of ovate-leaf Halophila species, after more than 100 years since its original description in 1913. We provide additional information on its anatomy, morphology, distribution, and host range, together with a phylogenetic evidence that it is congeneric with the recently rediscovered species infecting the invasive seagrass Halophila stipulacea in the Mediterranean Sea. Despite the previously hypothesized affiliation of the latter to Tetramyxa, our phylogenetic analyses of the 18S rRNA gene place Tetramyxa parasitica (a parasite of brackish water phanerogams and the type species of the genus) in the freshwater/terrestrial phytomyxean order Plasmodiophorida and reveal that phytomyxids associated with Halophila spp. form a separate deep-branching clade within the class proposed here as Marinomyxa gen. nov. We further argue that M. marina infecting H. stipulacea is most likely a species-specific parasite and implies their comigration through the Suez Canal.}, }
@article {pmid33013993, year = {2020}, author = {Jueterbock, A and Boström, C and Coyer, JA and Olsen, JL and Kopp, M and Dhanasiri, AKS and Smolina, I and Arnaud-Haond, S and Van de Peer, Y and Hoarau, G}, title = {The Seagrass Methylome Is Associated With Variation in Photosynthetic Performance Among Clonal Shoots.}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {571646}, pmid = {33013993}, issn = {1664-462X}, abstract = {Evolutionary theory predicts that clonal organisms are more susceptible to extinction than sexually reproducing organisms, due to low genetic variation and slow rates of evolution. In agreement, conservation management considers genetic variation as the ultimate measure of a population's ability to survive over time. However, clonal plants are among the oldest living organisms on our planet. Here, we test the hypothesis that clonal seagrass meadows display epigenetic variation that complements genetic variation as a source of phenotypic variation. In a clonal meadow of the seagrass Zostera marina, we characterized DNA methylation among 42 shoots. We also sequenced the whole genome of 10 shoots to correlate methylation patterns with photosynthetic performance under exposure to and recovery from 27°C, while controlling for somatic mutations. Here, we show for the first time that clonal seagrass shoots display DNA methylation variation that is independent from underlying genetic variation, and associated with variation in photosynthetic performance under experimental conditions. It remains unknown to what degree this association could be influenced by epigenetic responses to transplantation-related stress, given that the methylomes showed a strong shift under acclimation to laboratory conditions. The lack of untreated control samples in the heat stress experiment did not allow us to distinguish methylome shifts induced by acclimation from such induced by heat stress. Notwithstanding, the co-variation in DNA methylation and photosynthetic performance may be linked via gene expression because methylation patterns varied in functionally relevant genes involved in photosynthesis, and in the repair and prevention of heat-induced protein damage. While genotypic diversity has been shown to enhance stress resilience in seagrass meadows, we suggest that epigenetic variation plays a similar role in meadows dominated by a single genotype. Consequently, conservation management of clonal plants should consider epigenetic variation as indicator of resilience and stability.}, }
@article {pmid33013873, year = {2020}, author = {Ou, J and Liang, S and Guo, XK and Hu, X}, title = {α-Defensins Promote Bacteroides Colonization on Mucosal Reservoir to Prevent Antibiotic-Induced Dysbiosis.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {2065}, pmid = {33013873}, issn = {1664-3224}, mesh = {Animals ; Anti-Bacterial Agents/*adverse effects/therapeutic use ; Bacteroides/*physiology ; Bacteroides Infections/*immunology ; Drug-Related Side Effects and Adverse Reactions/*immunology ; Dysbiosis/*immunology ; Homeostasis ; Intestinal Mucosa/*immunology ; Matrix Metalloproteinase 7/genetics ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; alpha-Defensins/*metabolism ; }, abstract = {In addition to their established functions in host defense, accumulating evidence has suggested an emerging role for antimicrobial proteins (AMPs) in shaping commensal microbiota. However, the role of α-defensins, the most abundant AMPs of intestine, in regulating microbial ecology remains inconclusive. Here, we report that α-defensins promote commensal Bacteroides colonization by enhancing bacterial adhesion to the mucosal reservoir. Experiments utilizing mice deficient in matrix metalloproteinase 7 (MMP7), the α-defensin-activating enzyme, with rigorous littermate controls showed that α-defensin deficiency did not significantly influence steady-state intestinal microbiota. In contrast, α-defensins are essential for replenishment of commensal Bacteroides from the mucosal reservoir following antibiotics-induced dysbiosis, shown by markedly compromised recovery of Bacteroides in Mmp7[-/-] animals. Mechanistically, α-defensins promote Bacteroides colonization on epithelial surfaces in vivo and adhesion to epithelial cells in vitro. Moreover, α-defensins unexpectedly does not show any microbicidal activities against Bacteroides. Together, we propose that α-defensins promote commensal bacterial colonization and recovery to maintain microbial diversity upon environmental challenges.}, }
@article {pmid33013780, year = {2020}, author = {Yang, Y and Zhang, Y and Cápiro, NL and Yan, J}, title = {Genomic Characteristics Distinguish Geographically Distributed Dehalococcoidia.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {546063}, pmid = {33013780}, issn = {1664-302X}, abstract = {Dehalococcoidia (Dia) class microorganisms are frequently found in various pristine and contaminated environments. Metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) studies have substantially improved the understanding of Dia microbial ecology and evolution; however, an updated thorough investigation on the genomic and evolutionary characteristics of Dia microorganisms distributed in geographically distinct environments has not been implemented. In this study, we analyzed available genomic data to unravel Dia evolutionary and metabolic traits. Based on the phylogeny of 16S rRNA genes retrieved from sixty-seven genomes, Dia microorganisms can be categorized into three groups, the terrestrial cluster that contains all Dehalococcoides and Dehalogenimonas strains, the marine cluster I, and the marine cluster II. These results reveal that a higher ratio of horizontally transferred genetic materials was found in the Dia marine clusters compared to that of the Dia terrestrial cluster. Pangenome analysis further suggests that Dia microorganisms have evolved cluster-specific enzymes (e.g., dehalogenase in terrestrial Dia, sulfite reductase in marine Dia) and biosynthesis capabilities (e.g., siroheme biosynthesis in marine Dia). Marine Dia microorganisms are likely adapted to versatile metabolisms for energy conservation besides organohalide respiration. The genomic differences between marine and terrestrial Dia may suggest distinct functions and roles in element cycling (e.g., carbon, sulfur, chlorine), which require interdisciplinary approaches to unravel the physiology and evolution of Dia in various environments.}, }
@article {pmid33013755, year = {2020}, author = {Whitworth, DE and Jurkevitch, E and Pérez, J and Fuhrmann, G and Koval, SF}, title = {Editorial: Mechanisms of Prokaryotic Predation.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {2071}, doi = {10.3389/fmicb.2020.02071}, pmid = {33013755}, issn = {1664-302X}, }
@article {pmid33013480, year = {2020}, author = {Turroni, S and Magnani, M and Kc, P and Lesnik, P and Vidal, H and Heer, M}, title = {Gut Microbiome and Space Travelers' Health: State of the Art and Possible Pro/Prebiotic Strategies for Long-Term Space Missions.}, journal = {Frontiers in physiology}, volume = {11}, number = {}, pages = {553929}, pmid = {33013480}, issn = {1664-042X}, abstract = {The upcoming exploration missions will imply a much longer duration than any of the missions flown so far. In these missions, physiological adaptation to the new environment leads to changes in different body systems, such as the cardiovascular and musculoskeletal systems, metabolic and neurobehavioral health and immune function. To keep space travelers healthy on their trip to Moon, Mars and beyond and their return to Earth, a variety of countermeasures need to be provided to maintain body functionality. From research on the International Space Station (ISS) we know today, that for instance prescribing an adequate training regime for each individual with the devices available in the respective spacecraft is still a challenge. Nutrient supply is not yet optimal and must be optimized in exploration missions. Food intake is intrinsically linked to changes in the gut microbiome composition. Most of the microbes that inhabit our body supply ecosystem benefit to the host-microbe system, including production of important resources, bioconversion of nutrients, and protection against pathogenic microbes. The gut microbiome has also the ability to signal the host, regulating the processes of energy storage and appetite perception, and influencing immune and neurobehavioral function. The composition and functionality of the microbiome most likely changes during spaceflight. Supporting a healthy microbiome by respective measures in space travelers might maintain their health during the mission but also support rehabilitation when being back on Earth. In this review we are summarizing the changes in the gut microbiome observed in spaceflight and analog models, focusing particularly on the effects on metabolism, the musculoskeletal and immune systems and neurobehavioral disorders. Since space travelers are healthy volunteers, we focus on the potential of countermeasures based on pre- and probiotics supplements.}, }
@article {pmid33008820, year = {2020}, author = {Stracke, C and Meyer, BH and Hagemann, A and Jo, E and Lee, A and Albers, SV and Cha, J and Bräsen, C and Siebers, B}, title = {Salt Stress Response of Sulfolobus acidocaldarius Involves Complex Trehalose Metabolism Utilizing a Novel Trehalose-6-Phosphate Synthase (TPS)/Trehalose-6-Phosphate Phosphatase (TPP) Pathway.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {24}, pages = {}, pmid = {33008820}, issn = {1098-5336}, mesh = {Archaeal Proteins/*genetics/metabolism ; Glucosyltransferases/genetics/metabolism ; Metabolic Networks and Pathways ; Phosphoric Monoester Hydrolases/genetics/metabolism ; Salt Stress/*genetics ; Sulfolobus acidocaldarius/*enzymology ; Trehalose/*metabolism ; }, abstract = {The crenarchaeon Sulfolobus acidocaldarius has been described to synthesize trehalose via the maltooligosyltrehalose synthase (TreY) and maltooligosyltrehalose trehalohydrolase (TreZ) pathway, and the trehalose glycosyltransferring synthase (TreT) pathway has been predicted. Deletion mutant analysis of strains with single and double deletions of ΔtreY and ΔtreT in S. acidocaldarius revealed that in addition to these two pathways, a third, novel trehalose biosynthesis pathway is operative in vivo: the trehalose-6-phosphate (T6P) synthase/T6P phosphatase (TPS/TPP) pathway. In contrast to known TPS proteins, which belong to the GT20 family, the S. acidocaldarius TPS belongs to the GT4 family, establishing a new function within this group of enzymes. This novel GT4-like TPS was found to be present mainly in the Sulfolobales The ΔtreY ΔtreT Δtps triple mutant of S. acidocaldarius, which lacks the ability to synthesize trehalose, showed no altered phenotype under standard conditions or heat stress but was unable to grow under salt stress. Accordingly, in the wild-type strain, a significant increase of intracellular trehalose formation was observed under salt stress. Quantitative real-time PCR showed a salt stress-mediated induction of all three trehalose-synthesizing pathways. This demonstrates that in Archaea, trehalose plays an essential role for growth under high-salt conditions.IMPORTANCE The metabolism and function of trehalose as a compatible solute in Archaea was not well understood. This combined genetic and enzymatic approach at the interface of microbiology, physiology, and microbial ecology gives important insights into survival under stress, adaptation to extreme environments, and the role of compatible solutes in Archaea Here, we unraveled the complexity of trehalose metabolism, and we present a comprehensive study on trehalose function in stress response in S. acidocaldarius This sheds light on the general microbiology and the fascinating metabolic repertoire of Archaea, involving many novel biocatalysts, such as glycosyltransferases, with great potential in biotechnology.}, }
@article {pmid33007535, year = {2021}, author = {Wang, H and Chen, J and Ren, P and Zhang, Y and Omondi Onyango, S}, title = {Ultrasound irradiation alters the spatial structure and improves the antioxidant activity of the yellow tea polysaccharide.}, journal = {Ultrasonics sonochemistry}, volume = {70}, number = {}, pages = {105355}, pmid = {33007535}, issn = {1873-2828}, mesh = {Antioxidants/*pharmacology ; Camellia/*chemistry ; Carbohydrate Conformation ; Molecular Weight ; Polysaccharides/*chemistry/pharmacology ; *Ultrasonic Waves ; }, abstract = {In this study, the impact of ultrasound irradiation on the structural characteristics and antioxidant properties of yellow tea polysaccharides with different molecular weights (Mw) were investigated. Native yellow tea polysaccharide containing YTPS-3N, YTPS-5N and YTPS-7N were prepared through precipitation with ethanol at various concentrations of 30%, 50%, and 70%, respectively, and irradiated with high intensity ultrasound (20 kHz) for 55 min to yield yellow tea polysaccharide including YTPS-3U, YTPS-5U and YTPS-7U. The molecular weight (Mw) of YTPS-3N (from 37.7 to 15.1 kDa) and YTPS-5N (from 14.6 to 5.2 kDa) sharply decreased upon ultrasound irradiation, coincidentally particle size (Zavg) was also significantly reduced for YTPS-3N (40%), YTPS-5N (48%) and YTPS-7N (54%). The high-performance liquid chromatography and Fourier transform-infrared spectroscopy analysis revealed a partial degradation of native yellow tea polysaccharide treated with ultrasound, though the monosaccharide composition was not altered. Furthermore, changes in morphology and the breakdown of native yellow tea polysaccharide upon irradiation was confirmed with the circular dichroism spectrum, atomic force and scanning electron microscopy. As a consequence, irradiation of yellow tea polysaccharide increased free radical scavenging activity with YTPS-7U exhibiting the highest levels of 2, 2-diphenyl-1-picrylhydrazyl free radical, superoxide and hydroxyl radicals scavenging activity. These results suggest that the alteration of the spatial structure of yellow tea polysaccharide can enhance its antioxidant activity which is an important property for functional foods or medicines.}, }
@article {pmid33006023, year = {2021}, author = {Gao, X and Xu, H and Yuan, X}, title = {The Overlooked Genetic Diversity in the Dryland Soil Surface-Dwelling Cyanobacterium Nostoc flagelliforme as Revealed by the Marker Gene wspA.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {828-831}, pmid = {33006023}, issn = {1432-184X}, support = {31670104//the National Natural Science Foundation of China/ ; 2020JZ-51//Natural Science Foundation of Shaanxi Province (CN)/ ; }, mesh = {Ecosystem ; Genetic Variation ; *Nostoc/genetics ; Phylogeny ; *Soil ; }, abstract = {Biodiversity is recognized to be relatively low in the dryland ecosystem. However, we might overlook the accumulating genetic variation in those dryland micro-populations, which should eventually increase the dryland biodiversity. In the xeric steppes of western and northwestern China, there are two soil surface-dwelling and genetically close cyanobacterial species, Nostoc commune and Nostoc flagelliforme. They respectively exhibit lamellate and filamentous colony shapes. Their individual colony is consisted of hundreds of trichomes and the common exopolysaccharide matrix. N. flagelliforme is exclusively distributed in the dryland and supposed to be evolved from N. commune. We previously reported that the morphological diversity of N. flagelliforme colonies was very limited, being either cylindrical or strip-like. In this communication, we performed single-nucleotide polymorphism (SNP) analysis of the marker gene wspA as well as phylogenetic analysis of the WspA protein in N. flagelliforme colonies to gain insights into its genetic diversity. SNP analysis suggested that there existed plentiful nucleotide variations in the individual colonies and meanwhile these variations shared certain evolutionary regularity. Phylogenetic analysis of the deduced proteins from the cloned wspA sequences suggested that the relatively regular variations were possibly dispersed in the N. flagelliforme populations of different regions. Thus, these results presented a scenario of the underestimated genetic diversity hidden behind the limited morphotype of dryland cyanobacteria. Maybe, we can consider the individual cyanobacterial colony as a potential biodiversity pool in the drylands.}, }
@article {pmid33004967, year = {2020}, author = {Walker, SP and Barrett, M and Hogan, G and Flores Bueso, Y and Claesson, MJ and Tangney, M}, title = {Non-specific amplification of human DNA is a major challenge for 16S rRNA gene sequence analysis.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {16356}, pmid = {33004967}, issn = {2045-2322}, support = {12/RC/2273/SFI_/Science Foundation Ireland/Ireland ; 15/CDA/3630/SFI_/Science Foundation Ireland/Ireland ; MRCG2016-25/HRBI_/Health Research Board/Ireland ; }, mesh = {Bacteria/genetics ; Breast Neoplasms/genetics ; DNA, Bacterial/*genetics ; Female ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; RNA, Ribosomal, 16S/*analysis ; Sequence Analysis, DNA/*methods ; }, abstract = {The targeted sequencing of the 16S rRNA gene is one of the most frequently employed techniques in the field of microbial ecology, with the bacterial communities of a wide variety of niches in the human body have been characterised in this way. This is performed by targeting one or more hypervariable (V) regions within the 16S rRNA gene in order to produce an amplicon suitable in size for next generation sequencing. To date, all technical research has focused on the ability of different V regions to accurately resolve the composition of bacterial communities. We present here an underreported artefact associated with 16S rRNA gene sequencing, namely the off-target amplification of human DNA. By analysing 16S rRNA gene sequencing data from a selection of human sites we highlighted samples susceptible to this off-target amplification when using the popular primer pair targeting the V3-V4 region of the gene. The most severely affected sample type identified (breast tumour samples) were then re-analysed using the V1-V2 primer set, showing considerable reduction in off target amplification. Our data indicate that human biopsy samples should preferably be amplified using primers targeting the V1-V2 region. It is shown here that these primers result in on average 80% less human genome aligning reads, allowing for more statistically significant analysis of the bacterial communities residing in these samples.}, }
@article {pmid33002118, year = {2020}, author = {Song, J and Klümper, U and Riber, L and Dechesne, A and Smets, BF and Sørensen, SJ and Brandt, KK}, title = {A converging subset of soil bacterial taxa is permissive to the IncP-1 plasmid pKJK5 across a range of soil copper contamination.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {11}, pages = {}, doi = {10.1093/femsec/fiaa200}, pmid = {33002118}, issn = {1574-6941}, mesh = {*Conjugation, Genetic ; *Copper ; Permissiveness ; Plasmids/genetics ; RNA, Ribosomal, 16S/genetics ; Soil ; Soil Microbiology ; }, abstract = {Stressors like metals or antibiotics can affect bacterial community permissiveness for plasmid uptake, but there is little knowledge about long-term effects of such stressors on the evolution of community permissiveness. We assessed the effect of more than 90 years of soil Cu contamination on bacterial community permissiveness (i.e. uptake ability) toward a gfp-tagged IncP-1 plasmid (pKJK5) introduced via an Escherichia coli donor. Plasmid transfer events from the donor to the recipient soil bacterial community were quantified and transconjugants were subsequently isolated by fluorescence activated cell sorting and identified by 16S rRNA gene amplicon sequencing. Transfer frequency of plasmid pKJK5 was reduced in bacterial communities extracted from highly Cu contaminated (4526 mg kg-1) soil compared to corresponding communities extracted from moderately (458 mg kg-1) Cu contaminated soil and a low Cu reference soil (15 mg kg-1). The taxonomic composition of the transconjugal pools showed remarkable similarities irrespective of the degree of soil Cu contamination and despite contrasting compositions of the extracted recipient communities and the original soil communities. Permissiveness assessed at the level of individual operational taxonomic units (OTUs; 16S rRNA gene 97% sequence similarity threshold) was only slightly affected by soil Cu level and high replicate variability of OTU-level permissiveness indicated a role of stochastic events in IncP-1 plasmid transfer or strain-to-strain permissiveness variability.}, }
@article {pmid33001506, year = {2020}, author = {Beier, S and Andersson, AF and Galand, PE and Hochart, C and Logue, JB and McMahon, K and Bertilsson, S}, title = {The environment drives microbial trait variability in aquatic habitats.}, journal = {Molecular ecology}, volume = {29}, number = {23}, pages = {4605-4617}, doi = {10.1111/mec.15656}, pmid = {33001506}, issn = {1365-294X}, mesh = {*Bacteriophages/genetics ; Lakes ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {A prerequisite to improve the predictability of microbial community dynamics is to understand the mechanisms of microbial assembly. To study factors that contribute to microbial community assembly, we examined the temporal dynamics of genes in five aquatic metagenome time-series, originating from marine offshore or coastal sites and one lake. With this trait-based approach we expected to find gene-specific patterns of temporal allele variability that depended on the seasonal metacommunity size of carrier-taxa and the variability of the milieu and the substrates to which the resulting proteins were exposed. In more detail, we hypothesized that a larger seasonal metacommunity size would result in increased temporal variability of functional units (i.e., gene alleles), as shown previously for taxonomic units. We further hypothesized that multicopy genes would feature higher temporal variability than single-copy genes, as gene multiplication can result from high variability in substrate quality and quantity. Finally, we hypothesized that direct exposure of proteins to the extracellular environment would result in increased temporal variability of the respective gene compared to intracellular proteins that are less exposed to environmental fluctuations. The first two hypotheses were confirmed in all data sets, while significant effects of the subcellular location of gene products was only seen in three of the five time-series. The gene with the highest allele variability throughout all data sets was an iron transporter, also representing a target for phage infection. Previous work has emphasized the role of phage-prokaryote interactions as a major driver of microbial diversity. Our finding therefore points to a potentially important role of iron transporter-mediated phage infections for the assembly and maintenance of diversity in aquatic prokaryotes.}, }
@article {pmid33001224, year = {2021}, author = {Yavitt, JB and Roco, CA and Debenport, SJ and Barnett, SE and Shapleigh, JP}, title = {Community Organization and Metagenomics of Bacterial Assemblages Across Local Scale pH Gradients in Northern Forest Soils.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {758-769}, pmid = {33001224}, issn = {1432-184X}, support = {1007286//Agricultural Research Service/ ; }, mesh = {Bacteria/genetics ; Biodiversity ; Ecosystem ; Forests ; *Metagenomics ; Proton-Motive Force ; *Soil ; Soil Microbiology ; }, abstract = {Soil pH has shown to predict bacterial diversity, but mechanisms are still poorly understood. To investigate how bacteria distribute themselves as a function of soil pH, we assessed community composition, diversity, assembly, and gene abundance across local (ca. 1 km) scale gradients in soil pH from ~ 3.8 to 6.5 created by differences in soil parent material in three northern forests. Plant species were the same on all sites, with no evidence of agriculture in the past. Concentrations of extractable calcium, iron, and phosphorus also varied significantly across the pH gradients. Among taxa, Alphaproteobacteria and Acidobacteria were more common in soils with acidic pH values. Overall richness and diversity of OTUs peaked at intermediate pH values. Variations in OTU richness and diversity also had a quadratic fit with concentrations of extractable calcium and phosphorus. Community assembly was via homogeneous deterministic processes in soils with acidic pH values, whereas stochastic processes dominated in soils with near-neutral pH values. Although we expected selection via genes for acid tolerance response in acidic soils, genes for genetic information processing were more selective. Taxa in higher pH soils had differential abundance of transporter genes, suggesting adaptation to acquire metabolic substrates from soils. Soil bacterial communities in northern forest soils are incredibly diverse, and we still have much to learn about how soil pH and co-varying soil parameters directly drive gene selection in this critical component of ecosystem structure.}, }
@article {pmid33001029, year = {2020}, author = {Nelson, CW and Ardern, Z and Goldberg, TL and Meng, C and Kuo, CH and Ludwig, C and Kolokotronis, SO and Wei, X}, title = {Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {33001029}, issn = {2050-084X}, support = {Postdoctoral Research Fellowship//Academia Sinica/International ; Grant//National Philanthropic Trust/International ; John D. MacArthur Professorship Chair//University of Wisconsin-Madison/International ; IOS grants #1755370 and #1758800//National Science Foundation/International ; John D MacArthur Professorship Chair//University of Wisconsin-Madison/International ; }, mesh = {Amino Acid Sequence ; Animals ; Antibodies, Viral/immunology ; Antibody Specificity ; Antigens, Viral/biosynthesis/genetics/immunology ; Betacoronavirus/*genetics/pathogenicity/physiology ; COVID-19 ; China/epidemiology ; Chiroptera/virology ; Coronavirus/genetics ; Coronavirus Infections/epidemiology/*virology ; Epitopes/genetics/immunology ; Europe/epidemiology ; Eutheria/virology ; *Evolution, Molecular ; Gene Expression Regulation, Viral ; *Genes, Overlapping ; *Genes, Viral ; Genetic Variation ; Haplotypes/genetics ; Host Specificity/*genetics ; Humans ; Models, Molecular ; Mutation ; Open Reading Frames/*genetics ; *Pandemics ; Phylogeny ; Pneumonia, Viral/epidemiology/*virology ; Protein Biosynthesis ; Protein Conformation ; RNA, Viral/genetics ; SARS-CoV-2 ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Viral Proteins/*genetics/immunology ; }, abstract = {Understanding the emergence of novel viruses requires an accurate and comprehensive annotation of their genomes. Overlapping genes (OLGs) are common in viruses and have been associated with pandemics but are still widely overlooked. We identify and characterize ORF3d, a novel OLG in SARS-CoV-2 that is also present in Guangxi pangolin-CoVs but not other closely related pangolin-CoVs or bat-CoVs. We then document evidence of ORF3d translation, characterize its protein sequence, and conduct an evolutionary analysis at three levels: between taxa (21 members of Severe acute respiratory syndrome-related coronavirus), between human hosts (3978 SARS-CoV-2 consensus sequences), and within human hosts (401 deeply sequenced SARS-CoV-2 samples). ORF3d has been independently identified and shown to elicit a strong antibody response in COVID-19 patients. However, it has been misclassified as the unrelated gene ORF3b, leading to confusion. Our results liken ORF3d to other accessory genes in emerging viruses and highlight the importance of OLGs.}, }
@article {pmid33000311, year = {2021}, author = {Silva-Lima, AW and Froes, AM and Garcia, GD and Tonon, LAC and Swings, J and Cosenza, CAN and Medina, M and Penn, K and Thompson, JR and Thompson, CC and Thompson, FL}, title = {Mussismilia braziliensis White Plague Disease Is Characterized by an Affected Coral Immune System and Dysbiosis.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {795-806}, pmid = {33000311}, issn = {1432-184X}, support = {Biocomp, IODP//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; PQ//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (BR)/ ; CNE//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; }, mesh = {Animals ; *Anthozoa ; Coral Reefs ; Dysbiosis ; Immune System ; Symbiosis ; }, abstract = {Infectious diseases are one of the major drivers of coral reef decline worldwide. White plague-like disease (WPL) is a widespread disease with a complex etiology that infects several coral species, including the Brazilian endemic species Mussismilia braziliensis. Gene expression profiles of healthy and WPL-affected M. braziliensis were analyzed in winter and summer seasons. The de novo assembly of the M. braziliensis transcriptome from healthy and white plague samples produced a reference transcriptome containing 119,088 transcripts. WPL-diseased samples were characterized by repression of immune system and cellular defense processes. Autophagy and cellular adhesion transcripts were also repressed in WPL samples, suggesting exhaustion of the coral host defenses. Seasonal variation leads to plasticity in transcription with upregulation of intracellular signal transduction, apoptosis regulation, and oocyte development in the summer. Analysis of the active bacterial rRNA indicated that Pantoea bacteria were more abundant in WPL corals, while Tistlia, Fulvivirga, and Gammaproteobacteria Ga0077536 were more abundant in healthy samples. Cyanobacteria proliferation was also observed in WPL, mostly in the winter. These results indicate a scenario of dysbiosis in WPL-affected M. braziliensis, with the loss of potentially symbiotic bacteria and proliferation of opportunistic microbes after the start of the infection process.}, }
@article {pmid32998695, year = {2020}, author = {Soverini, M and Rampelli, S and Turroni, S and Brigidi, P and Biagi, E and Candela, M}, title = {Do the human gut metagenomic species possess the minimal set of core functionalities necessary for life?.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {678}, pmid = {32998695}, issn = {1471-2164}, mesh = {*Gastrointestinal Microbiome ; *Genes, Bacterial ; Genes, Essential ; Humans ; Intestinal Mucosa/metabolism/microbiology ; *Metagenome ; Metagenomics/methods/standards ; }, abstract = {BACKGROUND: Advances in bioinformatics recently allowed for the recovery of 'metagenomes assembled genomes' from human microbiome studies carried on with shotgun sequencing techniques. Such approach is used as a mean to discover new unclassified metagenomic species, putative biological entities having distinct metabolic traits.<br><br>RESULTS: In the present analysis we compare 400 genomes from isolates available on NCBI database and 10,000 human gut metagenomic species, screening all of them for the presence of a minimal set of core functionalities necessary, but not sufficient, for life. As a result, the metagenome-assembled genomes resulted systematically depleted in genes encoding for essential functions apparently needed to support autonomous bacterial life.<br><br>CONCLUSIONS: The relevant degree of lacking core functionalities that we observed in metagenome-assembled genomes raises some concerns about the effective completeness of metagenome-assembled genomes, suggesting caution in extrapolating biological information about their metabolic propensity and ecology in a complex environment like the human gastrointestinal tract.}, }
@article {pmid32996612, year = {2021}, author = {Moisan, K and Raaijmakers, JM and Dicke, M and Lucas-Barbosa, D and Cordovez, V}, title = {Volatiles from soil-borne fungi affect directional growth of roots.}, journal = {Plant, cell &amp; environment}, volume = {44}, number = {1}, pages = {339-345}, pmid = {32996612}, issn = {1365-3040}, mesh = {Brassica rapa/*growth &amp; development/metabolism ; Gas Chromatography-Mass Spectrometry ; Plant Roots/*growth &amp; development/metabolism ; *Soil Microbiology ; Volatile Organic Compounds/*metabolism ; }, abstract = {Volatiles play major roles in mediating ecological interactions between soil (micro)organisms and plants. It is well-established that microbial volatiles can increase root biomass and lateral root formation. To date, however, it is unknown whether microbial volatiles can affect directional root growth. Here, we present a novel method to study belowground volatile-mediated interactions. As proof-of-concept, we designed a root Y-tube olfactometer, and tested the effects of volatiles from four different soil-borne fungi on directional growth of Brassica rapa roots in soil. Subsequently, we compared the fungal volatile organic compounds (VOCs) previously profiled with Gas Chromatography-Mass Spectrometry (GC-MS). Using our newly designed setup, we show that directional root growth in soil is differentially affected by fungal volatiles. Roots grew more frequently toward volatiles from the root pathogen Rhizoctonia solani, whereas volatiles from the other three saprophytic fungi did not impact directional root growth. GC-MS profiling showed that six VOCs were exclusively emitted by R. solani. These findings verify that this novel method is suitable to unravel the intriguing chemical cross-talk between roots and soil-borne fungi and its impact on root growth.}, }
@article {pmid32996237, year = {2021}, author = {Barbera, P and Czech, L and Lutteropp, S and Stamatakis, A}, title = {SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements.}, journal = {Molecular ecology resources}, volume = {21}, number = {1}, pages = {340-349}, pmid = {32996237}, issn = {1755-0998}, support = {//Klaus Tschira Stiftung/ ; }, mesh = {*Algorithms ; *Microbiota ; *Phylogeny ; Sequence Analysis, DNA ; *Software ; }, abstract = {Microbial ecology research is currently driven by the continuously decreasing cost of DNA sequencing and the improving accuracy of data analysis methods. One such analysis method is phylogenetic placement, which establishes the phylogenetic identity of the anonymous environmental sequences in a sample by means of a given phylogenetic reference tree. However, assessing the diversity of a sample remains challenging, as traditional methods do not scale well with the increasing data volumes and/or do not leverage the phylogenetic placement information. Here, we present scrapp, a highly parallel and scalable tool that uses a molecular species delimitation algorithm to quantify the diversity distribution over the reference phylogeny for a given phylogenetic placement of the sample. scrapp employs a novel approach to cluster phylogenetic placements, called placement space clustering, to efficiently perform dimensionality reduction, so as to scale on large data volumes. Furthermore, it uses the phylogeny-aware molecular species delimitation method mPTP to quantify diversity. We evaluated scrapp using both, simulated and empirical data sets. We use simulated data to verify our approach. Tests on an empirical data set show that scrapp-derived metrics can classify samples by their diversity-correlated features equally well or better than existing, commonly used approaches. scrapp is available at https://github.com/pbdas/scrapp.}, }
@article {pmid32995929, year = {2021}, author = {Wang, H and Zhang, Y and Bartlett, DH and Xiao, X}, title = {Transcriptomic Analysis Reveals Common Adaptation Mechanisms Under Different Stresses for Moderately Piezophilic Bacteria.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {617-629}, pmid = {32995929}, issn = {1432-184X}, support = {2018YFC0309800//National Key Research and Development Program of China/ ; 41776173//National Natural Science Foundation of China/ ; 41530967//National Natural Science Foundation of China/ ; 91951117//National Natural Science Foundation of China/ ; 41921006//National Natural Science Foundation of China/ ; }, mesh = {*Adaptation, Physiological/genetics ; Bacillaceae ; Bacteria/genetics ; Sporosarcina ; *Transcriptome ; }, abstract = {Piezophiles, by the commonly accepted definition, grow faster under high hydrostatic pressure (HHP) than under ambient pressure and are believed to exist only in pressurized environments where life has adapted to HHP during evolution. However, recent findings suggest that piezophiles have developed a common adaptation strategy to cope with multiple types of stresses including HHP. These results raise a question on the ecological niches of piezophiles: are piezophiles restricted to habitats with HHP? In this study, we observed that the bacterial strains Sporosarcina psychrophila DSM 6497 and Lysinibacillus sphaericus LMG 22257, which were isolated from surface environments and then transferred under ambient pressure for half a century, possess moderately piezophilic characteristics with optimal growth pressures of 7 and 20 MPa, respectively. Their tolerance to HHP was further enhanced by MgCl2 supplementation under the highest tested pressure of 50 MPa. Transcriptomic analysis was performed to compare gene expression with and without MgCl2 supplementation under 50 MPa for S. psychrophila DSM 6497. Among 4390 genes or transcripts obtained, 915 differentially expressed genes (DEGs) were identified. These DEGs are primarily associated with the antioxidant defense system, intracellular compatible solute accumulation, and membrane lipid biosynthesis, which have been reported to be essential for cells to cope with HHP. These findings indicate no in situ pressure barrier for piezophile isolation, and cells may adopt a common adaptation strategy to cope with different stresses.}, }
@article {pmid32994415, year = {2020}, author = {Guo, X and Gao, Q and Yuan, M and Wang, G and Zhou, X and Feng, J and Shi, Z and Hale, L and Wu, L and Zhou, A and Tian, R and Liu, F and Wu, B and Chen, L and Jung, CG and Niu, S and Li, D and Xu, X and Jiang, L and Escalas, A and Wu, L and He, Z and Van Nostrand, JD and Ning, D and Liu, X and Yang, Y and Schuur, EAG and Konstantinidis, KT and Cole, JR and Penton, CR and Luo, Y and Tiedje, JM and Zhou, J}, title = {Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4897}, pmid = {32994415}, issn = {2041-1723}, mesh = {Acclimatization/genetics ; Archaea/genetics/isolation &amp; purification/metabolism ; Bacteria/genetics/isolation &amp; purification/metabolism ; Carbon/*analysis/metabolism ; Carbon Cycle ; Cellulose/metabolism ; DNA, Environmental/genetics/isolation &amp; purification ; Fungi/genetics/isolation &amp; purification/metabolism ; Global Warming ; Grassland ; Hot Temperature/adverse effects ; Metagenome/*genetics ; Metagenomics ; Microbiota/*physiology ; Models, Genetic ; Plant Roots/chemistry ; Poaceae/chemistry ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Soil microbial respiration is an important source of uncertainty in projecting future climate and carbon (C) cycle feedbacks. However, its feedbacks to climate warming and underlying microbial mechanisms are still poorly understood. Here we show that the temperature sensitivity of soil microbial respiration (Q10) in a temperate grassland ecosystem persistently decreases by 12.0 ± 3.7% across 7 years of warming. Also, the shifts of microbial communities play critical roles in regulating thermal adaptation of soil respiration. Incorporating microbial functional gene abundance data into a microbially-enabled ecosystem model significantly improves the modeling performance of soil microbial respiration by 5-19%, and reduces model parametric uncertainty by 55-71%. In addition, modeling analyses show that the microbial thermal adaptation can lead to considerably less heterotrophic respiration (11.6 ± 7.5%), and hence less soil C loss. If such microbially mediated dampening effects occur generally across different spatial and temporal scales, the potential positive feedback of soil microbial respiration in response to climate warming may be less than previously predicted.}, }
@article {pmid32994285, year = {2020}, author = {Trego, AC and O'Sullivan, S and Quince, C and Mills, S and Ijaz, UZ and Collins, G}, title = {Size Shapes the Active Microbiome of Methanogenic Granules, Corroborating a Biofilm Life Cycle.}, journal = {mSystems}, volume = {5}, number = {5}, pages = {}, pmid = {32994285}, issn = {2379-5077}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Methanogenic archaea are key players in cycling organic matter in nature but also in engineered waste treatment systems, where they generate methane, which can be used as a renewable energy source. In such systems in the built environment, complex methanogenic consortia are known to aggregate into highly organized, spherical granular biofilms comprising the interdependent microbial trophic groups mediating the successive stages of the anaerobic digestion (AD) process. This study separated methanogenic granules into a range of discrete size fractions, hypothesizing different biofilm growth stages, and separately supplied each with specific substrates to stimulate the activity of key AD trophic groups, including syntrophic acid oxidizers and methanogens. Rates of specific methanogenic activity were measured, and amplicon sequencing of 16S rRNA gene transcripts was used to resolve phylotranscriptomes across the series of size fractions. Increased rates of methane production were observed in each of the size fractions when hydrogen was supplied as the substrate compared with those of volatile fatty acids (acetate, propionate, and butyrate). This was connected to a shift toward hydrogenotrophic methanogenesis dominated by Methanobacterium and Methanolinea Interestingly, the specific active microbiomes measured in this way indicated that size was significantly more important than substrate in driving the structure of the active community in granules. Multivariate integration studywise discriminant analysis identified 56 genera shaping changes in the active community across both substrate and size. Half of those were found to be upregulated in the medium-sized granules, which were also the most active and potentially of the most important size, or life stage, for precision management of AD systems.IMPORTANCE Biological wastewater conversion processes collectively constitute one of the single biggest worldwide applications of microbial communities. There is an obvious requirement, therefore, to study the microbial systems central to the success of such technologies. Methanogenic granules, in particular, are architecturally fascinating biofilms that facilitate highly organized cooperation within the metabolic network of the anaerobic digestion (AD) process and, thus, are especially intriguing model systems for microbial ecology. This study, in a way not previously reported, provoked syntrophic and methanogenic activity and the structure of the microbial community, using specific substrates targeting the key trophic groups in AD. Unexpectedly, granule size more strongly than substrate shaped the active portion of the microbial community. Importantly, the findings suggest the size, or age, of granules inherently shapes the active microbiome linked to a life cycle. This provides exciting insights into the function of, and the potential for additional modeling of biofilm development in, methanogenic granules.}, }
@article {pmid32993824, year = {2021}, author = {Hanley-Cook, GT and Argaw, AA and de Kok, BP and Vanslambrouck, KW and Toe, LC and Kolsteren, PW and Jones, AD and Lachat, CK}, title = {EAT-Lancet diet score requires minimum intake values to predict higher micronutrient adequacy of diets in rural women of reproductive age from five low- and middle-income countries.}, journal = {The British journal of nutrition}, volume = {126}, number = {1}, pages = {92-100}, doi = {10.1017/S0007114520003864}, pmid = {32993824}, issn = {1475-2662}, mesh = {Democratic Republic of the Congo ; *Developing Countries ; *Diet ; Eating ; Ecuador ; Female ; Humans ; Kenya ; Micronutrients/*administration &amp; dosage ; Rural Population ; Sri Lanka ; *Trace Elements/administration &amp; dosage ; Vietnam ; }, abstract = {The EAT-Lancet Commission promulgated a universal reference diet. Subsequently, researchers constructed an EAT-Lancet diet score (0-14 points), with minimum intake values for various dietary components set at 0 g/d, and reported inverse associations with risks of major health outcomes in a high-income population. We assessed associations between EAT-Lancet diet scores, without or with lower bound values, and the mean probability of micronutrient adequacy (MPA) among nutrition-insecure women of reproductive age (WRA) from low- and middle-income countries (LMIC). We analysed single 24-h diet recall data (n 1950) from studies in rural DRC, Ecuador, Kenya, Sri Lanka and Vietnam. Associations between EAT-Lancet diet scores and MPA were assessed by fitting linear mixed-effects models. Mean EAT-Lancet diet scores were 8·8 (SD 1·3) and 1·9 (SD 1·1) without or with minimum intake values, respectively. Pooled MPA was 0·58 (SD 0·22) and energy intake was 10·5 (SD 4·6) MJ/d. A one-point increase in the EAT-Lancet diet score, without minimum intake values, was associated with a 2·6 (SD 0·7) percentage points decrease in MPA (P < 0·001). In contrast, the EAT-Lancet diet score, with minimum intake values, was associated with a 2·4 (SD 1·3) percentage points increase in MPA (P = 0·07). Further analysis indicated positive associations between EAT-Lancet diet scores and MPA adjusted for energy intake (P < 0·05). Our findings indicate that the EAT-Lancet diet score requires minimum intake values for nutrient-dense dietary components to avoid positively scoring non-consumption of food groups and subsequently predicting lower MPA of diets, when applied to rural WRA in LMIC.}, }
@article {pmid32993503, year = {2020}, author = {De Maayer, P and Pillay, T and Coutinho, TA}, title = {Flagella by numbers: comparative genomic analysis of the supernumerary flagellar systems among the Enterobacterales.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {670}, pmid = {32993503}, issn = {1471-2164}, support = {SFH180109299856//National Research Foundation/ ; }, mesh = {Conserved Sequence ; Enterobacteriaceae/classification/*genetics ; Evolution, Molecular ; Flagella/*genetics ; Flagellin/*genetics ; Phylogeny ; Sequence Homology ; }, abstract = {BACKGROUND: Flagellar motility is an efficient means of movement that allows bacteria to successfully colonize and compete with other microorganisms within their respective environments. The production and functioning of flagella is highly energy intensive and therefore flagellar motility is a tightly regulated process. Despite this, some bacteria have been observed to possess multiple flagellar systems which allow distinct forms of motility.<br><br>RESULTS: Comparative genomic analyses showed that, in addition to the previously identified primary peritrichous (flag-1) and secondary, lateral (flag-2) flagellar loci, three novel types of flagellar loci, varying in both gene content and gene order, are encoded on the genomes of members of the order Enterobacterales. The flag-3 and flag-4 loci encode predicted peritrichous flagellar systems while the flag-5 locus encodes a polar flagellum. In total, 798/4028 (~&#x2009;20%) of the studied taxa incorporate dual flagellar systems, while nineteen taxa incorporate three distinct flagellar loci. Phylogenetic analyses indicate the complex evolutionary histories of the flagellar systems among the Enterobacterales.<br><br>CONCLUSIONS: Supernumerary flagellar loci are relatively common features across a broad taxonomic spectrum in the order Enterobacterales. Here, we report the occurrence of five (flag-1 to flag-5) flagellar loci on the genomes of enterobacterial taxa, as well as the occurrence of three flagellar systems in select members of the Enterobacterales. Considering the energetic burden of maintaining and operating multiple flagellar systems, they are likely to play a role in the ecological success of members of this family and we postulate on their potential biological functions.}, }
@article {pmid32992776, year = {2020}, author = {García-Vega, &#xc1;S and Corrales-Agudelo, V and Reyes, A and Escobar, JS}, title = {Diet Quality, Food Groups and Nutrients Associated with the Gut Microbiota in a Nonwestern Population.}, journal = {Nutrients}, volume = {12}, number = {10}, pages = {}, pmid = {32992776}, issn = {2072-6643}, mesh = {Adolescent ; Adult ; Animals ; *Diet ; Dietary Fiber ; Fatty Acids, Volatile ; Female ; *Food Quality ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Middle Aged ; *Nutrients ; Obesity ; Overweight ; RNA, Ribosomal, 16S/analysis ; Vegetables ; Young Adult ; }, abstract = {Diet plays an important role in shaping gut microbiota. However, much remains to be learned regarding this association. We analyzed dietary intake and gut microbiota in a community-dwelling cohort of 441 Colombians. Diet quality, intake of food groups and nutrient consumption were paired with microbial diversity and composition using linear regressions, Procrustes analyses and a random-forest machine-learning algorithm. Analyses were adjusted for potential confounders, including the five cities from where the participants originated, sex (male, female), age group (18-40 and 41-62 years), BMI (lean, overweight, obese) and socioeconomic status. Microbial diversity was higher in individuals with increased intake of nutrients obtained from plant-food sources, whereas the intake of food groups and nutrients correlated with microbiota structure. Random-forest regressions identified microbial communities associated with different diet components. Two remarkable results confirmed previous expectations regarding the link between diet and microbiota: communities composed of short-chain fatty acid (SCFA) producers were more prevalent in the microbiota of individuals consuming diets rich in fiber and plant-food sources, such as fruits, vegetables and beans. In contrast, an inflammatory microbiota composed of bile-tolerant and putrefactive microorganisms along with opportunistic pathogens thrived in individuals consuming diets enriched in animal-food sources and of low quality, i.e., enriched in ultraprocessed foods and depleted in dietary fiber. This study expands our understanding of the relationship between dietary intake and gut microbiota. We provide evidence that diet is strongly associated with the gut microbial community and highlight generalizable connections between them.}, }
@article {pmid32990279, year = {2020}, author = {Zhu, Y and Xiong, Y and Gu, Y and Li, Q and Liu, Y}, title = {Chiropractic Therapy Modulated Gut Microbiota and Attenuated Allergic Airway Inflammation in an Immature Rat Model.}, journal = {Medical science monitor : international medical journal of experimental and clinical research}, volume = {26}, number = {}, pages = {e926039}, pmid = {32990279}, issn = {1643-3750}, mesh = {Animals ; *Asthma/microbiology/physiopathology/therapy ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Male ; *Manipulation, Chiropractic ; Rats ; Rats, Sprague-Dawley ; }, abstract = {BACKGROUND As a type of traditional Chinese massage, chiropractic therapy is applied to prevent and treat children with asthma in China. However, its mechanism of action is unclear. Allergic airway inflammation plays a key role in the occurrence and development of asthma, in which changes in gut microbiota are involved. The present study investigated the influence of chiropractic therapy on allergic airway inflammation (AAI) and gut microbiota in an immature rat model. MATERIAL AND METHODS Three-week-old male Sprague-Dawley rats were divided randomly into control (CN), AAI, and chiropractic (CP) groups. AAI and CP groups were sensitized and challenged with ovalbumin (OVA) to induce AAI. The CP group received chiropractic therapy during AAI modelling. AAI was assessed by cell counts in bronchoalveolar lavage fluid and HE staining of lung tissues. Plasma OVA-sIgE, IFN-γ, IL-4, and IL-10 levels were detected by ELISA. DNA extraction from feces samples was used for 16S rRNA gene sequencing and analyzed for gut microbiota by Quantitative Insights Into Microbial Ecology (QIIME). RESULTS AAI group had significantly lower richness and diversity of gut microbiota along with Th2 response and allergic airway inflammation. Moreover, the AAI group had lower abundance of butyrate-producing bacterial taxa with more Lactobacillus. Chiropractic therapy significantly increased the richness and diversity of gut microbiota and increased butyrate-producing bacterial taxa and decreased Lactobacillus, along with attenuating Th2 response and allergic airway inflammation during AAI modelling. CONCLUSIONS Chiropractic therapy attenuated allergic airway inflammation and optimized gut microbiota in an immature rat model, which might promote the development of adult-like butyrogenic milieu, immunotolerance, and inflammation attenuation.}, }
@article {pmid32989484, year = {2021}, author = {González-Hourcade, M and Del Campo, EM and Casano, LM}, title = {The Under-explored Extracellular Proteome of Aero-Terrestrial Microalgae Provides Clues on Different Mechanisms of Desiccation Tolerance in Non-Model Organisms.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {437-453}, pmid = {32989484}, issn = {1432-184X}, support = {CGL2016-80259-P//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; }, mesh = {*Acclimatization ; Algal Proteins/metabolism ; Cell Wall/metabolism ; Chlorophyta/classification/metabolism/physiology ; Desiccation ; Extracellular Polymeric Substance Matrix/*metabolism ; Lichens/classification/metabolism/physiology ; Microalgae/classification/metabolism/*physiology ; Plant Proteins/metabolism ; Proteome/*metabolism ; Species Specificity ; Water/metabolism ; }, abstract = {Trebouxia sp. (TR9) and Coccomyxa simplex (Csol) are desiccation-tolerant lichen microalgae with different adaptive strategies in accordance with the prevailing conditions of their habitats. The remodelling of cell wall and extracellular polysaccharides depending on water availability are key elements in the tolerance to desiccation of both microalgae. Currently, there is no information about the extracellular proteins of these algae and other aero-terrestrial microalgae in response to limited water availability. To our knowledge, this is the first report on the proteins associated with the extracellular polymeric substances (EPS) of aero-terrestrial microalgae subjected to cyclic desiccation/rehydration. LC-MS/MS and bioinformatic analyses of the EPS-associated proteins in the two lichen microalgae submitted to four desiccation/rehydration cycles allowed the compilation of 111 and 121 identified proteins for TR9 and Csol, respectively. Both sets of EPS-associated proteins shared a variety of predicted biological functions but showed a constitutive expression in Csol and partially inducible in TR9. In both algae, the EPS-associated proteins included a number of proteins of unknown functions, some of which could be considered as small intrinsically disordered proteins related with desiccation-tolerant organisms. Differences in the composition and the expression pattern between the studied EPS-associated proteins would be oriented to preserve the biochemical and biophysical properties of the extracellular structures under the different conditions of water availability in which each alga thrives.}, }
@article {pmid32984478, year = {2020}, author = {Hassen, AI and Pierneef, R and Swanevelder, ZH and Bopape, FL}, title = {Microbial and functional diversity of Cyclopia intermedia rhizosphere microbiome revealed by analysis of shotgun metagenomics sequence data.}, journal = {Data in brief}, volume = {32}, number = {}, pages = {106288}, pmid = {32984478}, issn = {2352-3409}, abstract = {Cyclopia spp., commonly referred to as honeybush due to the honey scented flowers, are indigenous legumes mainly growing in the Cape Floristic Region of the Western Cape, South Africa. Dozens of species, including Cyclopia intermedia, C. subternata, C. plicata, C. genistoides are used to make the well-known, popular and widely enjoyed beverage called 'honeybush tea'. In the past, most rhizosphere microbial studies associated with Cyclopia spp. focused mainly on the taxonomy and diversity of the root nodule associated symbiotic nitrogen fixing rhizobia. The work presented here is the first report on the microbial and functional diversity of rhizosphere microbiome associated with Cyclopia intermedia. Metagenomic shotgun sequencing was performed on the rhizosphere soil sample collected from this Cyclopia sp. using illumina Hiseq 2500 platform which resulted in an α- diversity of 312 species. Analysis of the metagenome sequence using the Metagenomic analysis server (MG-RAST) indicated that bacteria constitute the dominant domain followed by Eukaryota, Archaea and other sequences derived from fungi and viruses. Functional diversity of the metagenome based on analysis using the Cluster Orthologous Group (COG) method showed metabolism as the most important function in the community. The raw sequence data is uploaded in FASTQ format on MG-RAST server with ID mgm4855911.3 which can be accessed at http://www.mg-rast.org/linkin.cgi?project=mgp90368. The data on the microbial and functional diversity of the rhizosphere community of Cyclopia intermedia generates a baseline information about the microbial ecology of this indigenous legume. The microbial profile data can also be used as indicators of soil health characteristic of the rhizosphere of this important legume.}, }
@article {pmid32983401, year = {2020}, author = {Lequime, S and Bastide, P and Dellicour, S and Lemey, P and Baele, G}, title = {nosoi: A stochastic agent-based transmission chain simulation framework in r.}, journal = {Methods in ecology and evolution}, volume = {11}, number = {8}, pages = {1002-1007}, pmid = {32983401}, issn = {2041-210X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {The transmission process of an infectious agent creates a connected chain of hosts linked by transmission events, known as a transmission chain. Reconstructing transmission chains remains a challenging endeavour, except in rare cases characterized by intense surveillance and epidemiological inquiry. Inference frameworks attempt to estimate or approximate these transmission chains but the accuracy and validity of such methods generally lack formal assessment on datasets for which the actual transmission chain was observed.We here introduce nosoi, an open-source r package that offers a complete, tunable and expandable agent-based framework to simulate transmission chains under a wide range of epidemiological scenarios for single-host and dual-host epidemics. nosoi is accessible through GitHub and CRAN, and is accompanied by extensive documentation, providing help and practical examples to assist users in setting up their own simulations.Once infected, each host or agent can undergo a series of events during each time step, such as moving (between locations) or transmitting the infection, all of these being driven by user-specified rules or data, such as travel patterns between locations. nosoi is able to generate a multitude of epidemic scenarios, that can-for example-be used to validate a wide range of reconstruction methods, including epidemic modelling and phylodynamic analyses. nosoi also offers a comprehensive framework to leverage empirically acquired data, allowing the user to explore how variations in parameters can affect epidemic potential. Aside from research questions, nosoi can provide lecturers with a complete teaching tool to offer students a hands-on exploration of the dynamics of epidemiological processes and the factors that impact it. Because the package does not rely on mathematical formalism but uses a more intuitive algorithmic approach, even extensive changes of the entire model can be easily and quickly implemented.}, }
@article {pmid32983187, year = {2020}, author = {de Souza, RSC and Armanhi, JSL and Arruda, P}, title = {From Microbiome to Traits: Designing Synthetic Microbial Communities for Improved Crop Resiliency.}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {1179}, pmid = {32983187}, issn = {1664-462X}, abstract = {Plants teem with microorganisms, whose tremendous diversity and role in plant-microbe interactions are being increasingly explored. Microbial communities create a functional bond with their hosts and express beneficial traits capable of enhancing plant performance. Therefore, a significant task of microbiome research has been identifying novel beneficial microbial traits that can contribute to crop productivity, particularly under adverse environmental conditions. However, although knowledge has exponentially accumulated in recent years, few novel methods regarding the process of designing inoculants for agriculture have been presented. A recently introduced approach is the use of synthetic microbial communities (SynComs), which involves applying concepts from both microbial ecology and genetics to design inoculants. Here, we discuss how to translate this rationale for delivering stable and effective inoculants for agriculture by tailoring SynComs with microorganisms possessing traits for robust colonization, prevalence throughout plant development and specific beneficial functions for plants. Computational methods, including machine learning and artificial intelligence, will leverage the approaches of screening and identifying beneficial microbes while improving the process of determining the best combination of microbes for a desired plant phenotype. We focus on recent advances that deepen our knowledge of plant-microbe interactions and critically discuss the prospect of using microbes to create SynComs capable of enhancing crop resiliency against stressful conditions.}, }
@article {pmid32983012, year = {2020}, author = {Hounmanou, YMG and Dalsgaard, A and Sopacua, TF and Uddin, GMN and Leekitcharoenphon, P and Hendriksen, RS and Olsen, JE and Larsen, MH}, title = {Molecular Characteristics and Zoonotic Potential of Salmonella Weltevreden From Cultured Shrimp and Tilapia in Vietnam and China.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1985}, pmid = {32983012}, issn = {1664-302X}, abstract = {Salmonella Weltevreden is increasingly reported from aquatic environments, seafood, and patients in several Southeast Asian countries. Using genome-wide analysis, we characterized S. Weltevreden isolated from cultured shrimp and tilapia from Vietnam and China to study their genetic characteristics and relatedness to clinical isolates of S. Weltevreden ST-365. The phylogenetic analysis revealed up to 312 single-nucleotide polymorphism (SNP) difference between tilapia isolates, whereas isolates from shrimp were genetically more closely related. Epidemiologically unrelated isolates from Vietnam were closely related to isolates from China, e.g., 20 SNPs differences between strains 28V and 75C. In comparison with strains from other parts of the world, our environmental isolates predominantly clustered within the continental South Asia lineage, constituted mostly of strains from human stool with as low as seven SNPs difference, e.g., 30V versus Cont_ERR495254. All sequenced isolates were MLST type ST-365 and contained the major virulence-related genes encoded by the Salmonella Pathogenicity Islands 1-5. Ten of the isolates harbored the IncFII(S) plasmid similar to the virulence genes-mediated plasmid pSPCV of S. Paratyphi C, and one isolate had the IncQ1 plasmid on the same contig with strA/B, sul2, and tetA resistance genes similar to the IncQ1 type, pNUC of S. Typhimurium. A pangenomic analysis yielded 7891 genes including a core genome of 4892 genes, with a closely related accessory genome content between clinical and environmental isolates (Benjamini p > 0.05). In a search for differences that could explain the higher prevalence of S. Weltevreden in aquatic samples, genomes were compared with those of other Salmonella enterica serovars. S. Weltevreden revealed specific regions harboring glpX (Fructose-1;6-bisphosphatase; class II), rfbC (dTDP-4-dehydrorhamnose 3;5-epimerase), and cmtB (PTS Mannitol-specific cryptic phosphotransferase enzyme IIA component) involved in carbohydrate biosynthesis pathways. Our study builds grounds for future experiments to determine genes or pathways that are essential when S. Weltevreden are in aquatic environments and microbial interactions providing survival advantages to S. Weltevreden in such environments.}, }
@article {pmid32982988, year = {2020}, author = {van der Goot, E and van Spronsen, FJ and Falcão Salles, J and van der Zee, EA}, title = {A Microbial Community Ecology Perspective on the Gut-Microbiome-Brain Axis.}, journal = {Frontiers in endocrinology}, volume = {11}, number = {}, pages = {611}, pmid = {32982988}, issn = {1664-2392}, mesh = {Brain/*microbiology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology ; Humans ; Microbiota/*physiology ; }, }
@article {pmid32979812, year = {2020}, author = {Meyer, KM and Morris, AH and Webster, K and Klein, AM and Kroeger, ME and Meredith, LK and Brændholt, A and Nakamura, F and Venturini, A and Fonseca de Souza, L and Shek, KL and Danielson, R and van Haren, J and Barbosa de Camargo, P and Tsai, SM and Dini-Andreote, F and de Mauro, JMS and Barlow, J and Berenguer, E and Nüsslein, K and Saleska, S and Rodrigues, JLM and Bohannan, BJM}, title = {Belowground changes to community structure alter methane-cycling dynamics in Amazonia.}, journal = {Environment international}, volume = {145}, number = {}, pages = {106131}, doi = {10.1016/j.envint.2020.106131}, pmid = {32979812}, issn = {1873-6750}, mesh = {Animals ; Brazil ; Cattle ; Forests ; *Methane ; *Soil ; Soil Microbiology ; }, abstract = {Amazonian rainforest is undergoing increasing rates of deforestation, driven primarily by cattle pasture expansion. Forest-to-pasture conversion has been associated with increases in soil methane (CH4) emission. To better understand the drivers of this change, we measured soil CH4 flux, environmental conditions, and belowground microbial community structure across primary forests, cattle pastures, and secondary forests in two Amazonian regions. We show that pasture soils emit high levels of CH4 (mean: 3454.6 ± 9482.3 μg CH4 m[-2] d[-1]), consistent with previous reports, while forest soils on average emit CH4 at modest rates (mean: 9.8 ± 120.5 μg CH4 m[-2] d[-1]), but often act as CH4 sinks. We report that secondary forest soils tend to consume CH4 (mean: -10.2 ± 35.7 μg CH4 m[-2] d[-1]), demonstrating that pasture CH4 emissions can be reversed. We apply a novel computational approach to identify microbial community attributes associated with flux independent of soil chemistry. While this revealed taxa known to produce or consume CH4 directly (i.e. methanogens and methanotrophs, respectively), the vast majority of identified taxa are not known to cycle CH4. Each land use type had a unique subset of taxa associated with CH4 flux, suggesting that land use change alters CH4 cycling through shifts in microbial community composition. Taken together, we show that microbial composition is crucial for understanding the observed CH4 dynamics and that microorganisms provide explanatory power that cannot be captured by environmental variables.}, }
@article {pmid32978127, year = {2020}, author = {Xia, WW and Zhao, J and Zheng, Y and Zhang, HM and Zhang, JB and Chen, RR and Lin, XG and Jia, ZJ}, title = {Active Soil Nitrifying Communities Revealed by In Situ Transcriptomics and Microcosm-Based Stable-Isotope Probing.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {23}, pages = {}, pmid = {32978127}, issn = {1098-5336}, mesh = {Archaea/genetics/*isolation &amp; purification ; Bacteria/genetics/*isolation &amp; purification ; Fertilizers/analysis ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Nitrogen/*metabolism ; RNA, Archaeal/analysis ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Real-Time Polymerase Chain Reaction ; *Soil Microbiology ; Transcription, Genetic ; }, abstract = {Long-term nitrogen field fertilization often results in significant changes in nitrifying communities that catalyze a key step in the global N cycle. However, whether microcosm studies are able to inform the dynamic changes in communities of ammonia-oxidizing bacteria (AOB) and archaea (AOA) under field conditions remains poorly understood. This study aimed to evaluate the transcriptional activities of nitrifying communities under in situ conditions, and we found that they were largely similar to those of [13]C-labeled nitrifying communities in the urea-amended microcosms of soils that had received different N fertilization regimens for 22 years. High-throughput sequencing of 16S rRNA genes and transcripts suggested that Nitrosospira cluster 3-like AOB and Nitrososphaera viennensis-like AOA were significantly stimulated in N-fertilized fresh soils. Real-time quantitative PCR demonstrated that the significant increase of AOA and AOB in fresh soils upon nitrogen fertilization could be preserved in the air-dried soils. DNA-based stable-isotope probing (SIP) further revealed the greatest labeling of Nitrosospira cluster 3-like AOB and Nitrosospira viennensis-like AOA, despite the strong advantage of AOB over AOA in the N-fertilized soils. Nitrobacter-like nitrite-oxidizing bacteria (NOB) played more important roles than Nitrospira-like NOB in urea-amended SIP microcosms, while the situation was the opposite under field conditions. Our results suggest that long-term fertilization selected for physiologically versatile AOB and AOA that could have been adapted to a wide range of substrate ammonium concentrations. It also provides compelling evidence that the dominant communities of transcriptionally active nitrifiers under field conditions were largely similar to those revealed in [13]C-labeled microcosms.IMPORTANCE The role of manipulated microcosms in microbial ecology has been much debated, because they cannot entirely represent the in situ situation. We collected soil samples from 20 field plots, including 5 different treatments with and without nitrogen fertilizers for 22 years, in order to assess active nitrifying communities by in situ transcriptomics and microcosm-based stable-isotope probing. The results showed that chronic N enrichment led to competitive advantages of Nitrosospira cluster 3-like AOB over N. viennensis-like AOA in soils under field conditions. Microcosm labeling revealed similar results for active AOA and AOB, although an apparent discrepancy was observed for nitrite-oxidizing bacteria. This study suggests that the soil microbiome represents a relatively stable community resulting from complex evolutionary processes over a large time scale, and microcosms can serve as powerful tools to test the theory of environmental filtering on the key functional microbial guilds.}, }
@article {pmid32975888, year = {2021}, author = {Goelen, T and Vuts, J and Sobhy, IS and Wäckers, F and Caulfield, JC and Birkett, MA and Rediers, H and Jacquemyn, H and Lievens, B}, title = {Identification and application of bacterial volatiles to attract a generalist aphid parasitoid: from laboratory to greenhouse assays.}, journal = {Pest management science}, volume = {77}, number = {2}, pages = {930-938}, doi = {10.1002/ps.6102}, pmid = {32975888}, issn = {1526-4998}, support = {HBC.2018/2022//Agentschap Innoveren en Ondernemen/ ; 1S15116316N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {Animals ; *Aphids ; Bacteria ; Biological Assay ; Laboratories ; *Volatile Organic Compounds/pharmacology ; }, abstract = {BACKGROUND: Recent studies have shown that microorganisms emit volatile compounds that affect insect behaviour. However, it remains largely unclear whether microbes can be exploited as a source of attractants to improve biological control of insect pests. In this study, we used a combination of coupled gas chromatography-electroantennography (GC-EAG) and Y-tube olfactometer bioassays to identify attractive compounds in the volatile extracts of three bacterial strains that are associated with the habitat of the generalist aphid parasitoid Aphidius colemani, and to create mixtures of synthetic compounds to find attractive blends for A. colemani. Subsequently, the most attractive blend was evaluated in two-choice cage experiments under greenhouse conditions.<br><br>RESULTS: GC-EAG analysis revealed 20 compounds that were linked to behaviourally attractive bacterial strains. A mixture of two EAG-active compounds, styrene and benzaldehyde applied at a respective dose of 1 &#x3bc;g and 10 ng, was more attractive than the single compounds or the culture medium of the bacteria in Y-tube olfactometer bioassays. Application of this synthetic mixture under greenhouse conditions resulted in significant attraction of the parasitoids, and outperformed application of the bacterial culture medium.<br><br>CONCLUSION: Compounds isolated from bacterial blends were capable of attracting parasitoids both in laboratory and greenhouse assays, indicating that microbial cultures are an effective source of insect attractants. This opens new opportunities to attract and retain natural enemies of pest species and to enhance biological pest control.}, }
@article {pmid32975751, year = {2020}, author = {Garbisu, C and Alkorta, I and Kidd, P and Epelde, L and Mench, M}, title = {Keep and promote biodiversity at polluted sites under phytomanagement.}, journal = {Environmental science and pollution research international}, volume = {27}, number = {36}, pages = {44820-44834}, pmid = {32975751}, issn = {1614-7499}, support = {SOE1/P5/E0189//Interreg/ ; }, mesh = {Biodegradation, Environmental ; Biodiversity ; Biomass ; Ecosystem ; Soil ; *Soil Pollutants/analysis ; }, abstract = {The phytomanagement concept combines a sustainable reduction of pollutant linkages at risk-assessed contaminated sites with the generation of both valuable biomass for the (bio)economy and ecosystem services. One of the potential benefits of phytomanagement is the possibility to increase biodiversity in polluted sites. However, the unique biodiversity present in some polluted sites can be severely impacted by the implementation of phytomanagement practices, even resulting in the local extinction of endemic ecotypes or species of great conservation value. Here, we highlight the importance of promoting measures to minimise the potential adverse impact of phytomanagement on biodiversity at polluted sites, as well as recommend practices to increase biodiversity at phytomanaged sites without compromising its effectiveness in terms of reduction of pollutant linkages and the generation of valuable biomass and ecosystem services.}, }
@article {pmid32975677, year = {2021}, author = {Ouarabi, L and Drider, D and Taminiau, B and Daube, G and Bendali, F and Lucau-Danila, A}, title = {Vaginal Microbiota: Age Dynamic and Ethnic Particularities of Algerian Women.}, journal = {Microbial ecology}, volume = {82}, number = {4}, pages = {1020-1029}, pmid = {32975677}, issn = {1432-184X}, mesh = {*Ethnicity ; Female ; Humans ; Lactobacillus/genetics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Vagina ; }, abstract = {The composition of the vaginal microbiota is a key element for maintaining gynecological and reproductive health. With the aim of obtaining an accurate overview of the vaginal microbiota of Algerian women, in terms of their age and ethnic group, we conducted a 16S rRNA gene targeted metagenomic analysis of 100 vaginal samples taken from healthy childbearing and menopausal women. These data were used to establish the pattern of the vaginal microbiota during reproductive and postreproductive phases. Hormone levels were correlated to changes in microbial composition for menopausal women. The ethnic comparison revealed a particular microbiota profile for Algerian women, with a dominance of CST III and CST I. A rapid qPCR method developed by the authors was successfully used to identify the vaginal bacterial pattern for a customized gynecological management.}, }
@article {pmid32975666, year = {2020}, author = {Lee, CW and Lim, JH and Heng, PL and Marican, NF and Narayanan, K and Sim, EUH and Bong, CW}, title = {Influence of elevated river flow on hypoxia occurrence, nutrient concentration and microbial dynamics in a tropical estuary.}, journal = {Environmental monitoring and assessment}, volume = {192}, number = {10}, pages = {660}, pmid = {32975666}, issn = {1573-2959}, support = {HiCOE (IOES-2014D)//Ministry of Higher Education/ ; FRGS (FP061-2018A)//Ministry of Higher Education/ ; }, mesh = {Chlorophyll A ; Environmental Monitoring ; *Estuaries ; Humans ; Hypoxia ; Nutrients ; *Rivers ; Seasons ; }, abstract = {We sampled the Klang estuary during the inter-monsoon and northeast monsoon period (July-Nov 2011, Oct-Nov 2012), which coincided with higher rainfall and elevated Klang River flow. The increased freshwater inflow into the estuary resulted in water column stratification that was observed during both sampling periods. Dissolved oxygen (DO) dropped below 63 μM, and hypoxia was observed. Elevated river flow also transported dissolved inorganic nutrients, chlorophyll a and bacteria to the estuary. However, bacterial production did not correlate with DO concentration in this study. As hypoxia was probably not due to in situ heterotrophic processes, deoxygenated waters were probably from upstream. We surmised this as DO correlated with salinity (R[2] = 0.664, df = 86, p < 0.001). DO also decreased with increasing flushing time (R[2] = 0.556, df = 11, p < 0.01), suggesting that when flushing time (> 6.7 h), hypoxia could occur at the Klang estuary. Here, we presented a model that related riverine flow rate to the post-heavy rainfall hypoxia that explicated the episodic hypoxia at Klang estuary. As Klang estuary supports aquaculture and cockle culture, our results could help protect the aquaculture and cockle culture industry here.}, }
@article {pmid32975419, year = {2021}, author = {Trueba-Santiso, A and Wasmund, K and Soder-Walz, JM and Marco-Urrea, E and Adrian, L}, title = {Genome Sequence, Proteome Profile, and Identification of a Multiprotein Reductive Dehalogenase Complex in Dehalogenimonas alkenigignens Strain BRE15M.}, journal = {Journal of proteome research}, volume = {20}, number = {1}, pages = {613-623}, pmid = {32975419}, issn = {1535-3907}, support = {P 29426/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacterial Proteins/genetics/metabolism ; *Chloroflexi ; Halogenation ; *Proteome/genetics ; *Proteomics ; }, abstract = {Bacteria of the genus Dehalogenimonas respire with vicinally halogenated alkanes via dihaloelimination. We aimed to describe involved proteins and their supermolecular organization. Metagenomic sequencing of a Dehalogenimonas-containing culture resulted in a 1.65 Mbp draft genome of Dehalogenimonas alkenigignens strain BRE15M. It contained 31 full-length reductive dehalogenase homologous genes (rdhA), but only eight had cognate rdhB gene coding for membrane-anchoring proteins. Shotgun proteomics of cells grown with 1,2-dichloropropane as an electron acceptor identified 1152 proteins representing more than 60% of the total proteome. Ten RdhA proteins were detected, including a DcpA ortholog, which was the strongest expressed RdhA. Blue native gel electrophoresis (BNE) demonstrating maximum activity was localized in a protein complex of 146-242 kDa. Protein mass spectrometry revealed the presence of DcpA, its membrane-anchoring protein DcpB, two hydrogen uptake hydrogenase subunits (HupL and HupS), an iron-sulfur protein (HupX), and subunits of a redox protein with a molybdopterin-binding motif (OmeA and OmeB) in the complex. BNE after protein solubilization with different detergent concentrations revealed no evidence for an interaction between the putative respiratory electron input module (HupLS) and the OmeA/OmeB/HupX module. All detected RdhAs comigrated with the organohalide respiration complex. Based on genomic and proteomic analysis, we propose quinone-independent respiration in Dehalogenimonas.}, }
@article {pmid32974747, year = {2021}, author = {Souza, UA and Webster, A and Dall'Agnol, B and Morel, AP and Peters, FB and Favarini, MO and Mazim, FD and Soares, JBG and Tirelli, FP and Tortato, MA and de Lemos, ERS and Trigo, TC and Soares, JF and Reck, J}, title = {Molecular and Serological Survey of the Cat-Scratch Disease Agent (Bartonella henselae) in Free-Ranging Leopardus geoffroyi and Leopardus wiedii (Carnivora: Felidae) From Pampa Biome, Brazil.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {483-492}, pmid = {32974747}, issn = {1432-184X}, mesh = {Animals ; Animals, Wild ; Antibodies, Bacterial/blood ; Bacterial Proteins/genetics ; Bartonella/classification/genetics/immunology/isolation &amp; purification ; Bartonella henselae/classification/genetics/immunology/*isolation &amp; purification ; Brazil ; Cat-Scratch Disease/microbiology/*veterinary ; DNA, Bacterial/genetics ; Felidae/*microbiology ; Grassland ; Nucleotidyltransferases/genetics ; Phosphotransferases (Alcohol Group Acceptor)/genetics ; Phylogeny ; }, abstract = {The genus Bartonella comprises emerging bacteria that affect humans and other mammals worldwide. Felids represent an important reservoir for several Bartonella species. Domestic cats are the main reservoir of Bartonella henselae, the agent of cat scratch disease (CSD). It can be transmitted directly by scratches and bites from infected cats and via cat fleas. This study aims to investigate the circulation of Bartonella spp. in free-ranging Neotropical wild felids from Southern Brazil using serological and molecular methods. In this study, 53 live-trapped free-ranging wild felids were sampled, 39 Leopardus geoffroyi and 14 Leopardus wiedii, from five municipalities in the Rio Grande, do Sul state, southern Brazil. All captured animals were clinically healthy. Two blood samples of L. geoffroyi were positive, by PCR, for the presence of B. henselae DNA. Conversely, none of L. wiedii blood samples were positive when tested using PCR. Indirect immunofluorescence assay (IFA) showed that 28% of serum samples of wild felids were reactive (seropositive) for B. henselae by immunofluorescence, with titers ranging from 64 to 256. The results presented here provide the first evidence of a Bartonella-enzootic cycle involving L. geoffroyi and L. wiedii, which may account for the spillover of the emerging zoonotic pathogen B. henselae for the indigenous fauna in Southern Brazil.}, }
@article {pmid32974213, year = {2020}, author = {de Souza-Basqueira, M and Ribeiro, RM and de Oliveira, LC and Moreira, CHV and Martins, RCR and Franco, DC and Amado, PPP and Mayer, MPA and Sabino, EC}, title = {Gut Dysbiosis in Chagas Disease. A Possible Link to the Pathogenesis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {402}, pmid = {32974213}, issn = {2235-2988}, support = {P50 AI098461/AI/NIAID NIH HHS/United States ; U19 AI098461/AI/NIAID NIH HHS/United States ; }, mesh = {*Chagas Disease ; Dysbiosis ; Feces ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S/genetics ; *Trypanosoma cruzi ; }, abstract = {Chagas disease is caused by the flagellate protozoan Trypanosoma cruzi. Cardiomyopathy and damage to gastrointestinal tissue are the main disease manifestations. There are data suggesting that the immune response to T. cruzi depends on the intestinal microbiota. We hypothesized that Chagas disease is associated with an altered gut microbiome and that these changes are related to the disease phenotype. The stool microbiome from 104 individuals, 73 with Chagas disease (30 with the cardiac, 11 with the digestive, and 32 with the indeterminate form), and 31 healthy controls was characterized using 16S rRNA amplification and sequencing. The QIIME (Quantitative Insights Into Microbial Ecology) platform was used to analyze the data. Alpha and beta diversity indexes did not indicate differences between the groups. However, the relative abundance of Verrucomicrobia, represented primarily by the genus Akkermansia, was significantly lower in the Chagas disease groups, especially the cardiac group, compared to the controls. Furthermore, differences in the relative abundances of Alistipes, Bilophila, and Dialister were observed between the groups. We conclude that T. cruzi infection results in changes in the gut microbiome that may play a role in the myocardial and intestinal inflammation seen in Chagas disease.}, }
@article {pmid32974121, year = {2020}, author = {Lee, NLY and Huang, D and Quek, ZBR and Lee, JN and Wainwright, BJ}, title = {Distinct fungal communities associated with different organs of the mangrove Sonneratia alba in the Malay Peninsula.}, journal = {IMA fungus}, volume = {11}, number = {}, pages = {17}, pmid = {32974121}, issn = {2210-6340}, abstract = {Mangrove forests are key tropical marine ecosystems that are rich in fungi, but our understanding of fungal communities associated with mangrove trees and their various organs remains limited because much of the diversity lies within the microbiome. In this study, we investigated the fungal communities associated with the mangrove tree Sonneratia alba throughout Peninsular Malaysia and Singapore. At each sampling location, we collected leaves, fruits, pneumatophores and sediment samples and performed amplicon sequencing of the ribosomal internal transcribed spacer 1 to characterise the associated communities. Results show distinct fungal communities at each sampled location with further differentiation according to the plant part. We find a significant distance decay of similarity, particularly for sediment samples due to the greater variability of sediment environments relative to the more stable fungal habitats provided by living plant organs. We are able to assign taxonomy to the majority of sequences from leaves and fruits, but a much larger portion of the sequences recovered from pneumatophores and sediment samples could not be identified. This pattern underscores the limited mycological research performed in marine environments and demonstrates the need for a concerted research effort on multiple species to fully characterise the coastal microbiome and its role in the functioning of marine ecosystems.}, }
@article {pmid32973727, year = {2020}, author = {Kuznecova, J and Šulčius, S and Vogts, A and Voss, M and Jürgens, K and Šimoliūnas, E}, title = {Nitrogen Flow in Diazotrophic Cyanobacterium Aphanizomenon flos-aquae Is Altered by Cyanophage Infection.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {2010}, pmid = {32973727}, issn = {1664-302X}, abstract = {Viruses can significantly influence cyanobacteria population dynamics and activity, and through this the biogeochemical cycling of major nutrients. However, surprisingly little attention has been given to understand how viral infections alter the ability of diazotrophic cyanobacteria for atmospheric nitrogen fixation and its release to the environment. This study addressed the importance of cyanophages for net [15]N2 assimilation rate, expression of nitrogenase reductase gene (nifH) and changes in nitrogen enrichment ([15]N/[14]N) in the diazotrophic cyanobacterium Aphanizomenon flos-aquae during infection by the cyanophage vB_AphaS-CL131. We found that while the growth of A. flos-aquae was inhibited by cyanophage addition (decreased from 0.02 h[-1] to 0.002 h[-1]), there were no significant differences in nitrogen fixation rates (control: 22.7 × 10[-7] nmol N heterocyte[-1]; infected: 23.9 × 10[-7] nmol N heterocyte[-1]) and nifH expression level (control: 0.6-1.6 transcripts heterocyte[-1]; infected: 0.7-1.1 transcripts heterocyte[-1]) between the infected and control A. flos-aquae cultures. This implies that cyanophage genome replication and progeny production within the vegetative cells does not interfere with the N2 fixation reactions in the heterocytes of these cyanobacteria. However, higher [15]N enrichment at the poles of heterocytes of the infected A. flos-aquae, revealed by NanoSIMS analysis indicates the accumulation of fixed nitrogen in response to cyanophage addition. This suggests reduced nitrogen transport to vegetative cells and the alterations in the flow of fixed nitrogen within the filaments. In addition, we found that cyanophage lysis resulted in a substantial release of ammonium into culture medium. Cyanophage infection seems to substantially redirect N flow from cyanobacterial biomass to the production of N storage compounds and N release.}, }
@article {pmid32973299, year = {2020}, author = {Hernández-Del Amo, E and Dolinová, I and la Ramis-Jorba, G and Gich, F and Bañeras, L}, title = {Limited effect of radial oxygen loss on ammonia oxidizers in Typha angustifolia root hairs.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15694}, pmid = {32973299}, issn = {2045-2322}, mesh = {Ammonia/*metabolism ; Microbiota ; Nitrification/*physiology ; Oxygen/metabolism ; Plant Roots/*metabolism ; RNA, Ribosomal, 16S/genetics ; Typhaceae/*metabolism ; }, abstract = {The benefits of plant-microbe interactions have been exploited extensively for nutrient removal. Radial oxygen loss in aquatic macrophytes potentially promotes nitrification and accelerates nitrogen removal through coupled nitrification-denitrification process. Nitrification is likely the limiting activity for an effective nitrogen removal in wetlands. In this work, we have quantified the effect of radial oxygen losses in Typha angustifolia plants in environments of contrasting salinities, including a temporary lagoon, a constructed wetland, and a river estuary. In all sites, radial oxygen diffusion occurred mainly at a narrow band, from 1 to 5 cm from the root tip, and were almost absent at the tip and basal sections of the root (> 5 cm). Root sections with active oxygen diffusion tended to show higher bacterial and archaeal densities in the rhizoplane according to 16S rRNA gene abundance data, except at higher salinities. Archaeal amoA /bacterial amoA gene ratios were highly variable among sites. Archaeal nitrifiers were only favoured over bacteria on the root surface of Typha collected from the constructed wetland. Collectively, radial oxygen loss had little effect on the nitrifying microbial community at the smaller scale (differences according to root-section), and observed differences were more likely related to prevailing physicochemical conditions of the studied environments or to long-term effects of the root microenvironment (root vs sediment comparisons).}, }
@article {pmid32970805, year = {2020}, author = {Sakarika, M and Sosa, DAT and Depoortere, M and Rottiers, H and Ganigué, R and Dewettinck, K and Rabaey, K}, title = {The type of microorganism and substrate determines the odor fingerprint of dried bacteria targeting microbial protein production.}, journal = {FEMS microbiology letters}, volume = {367}, number = {18}, pages = {}, doi = {10.1093/femsle/fnaa138}, pmid = {32970805}, issn = {1574-6968}, mesh = {Bacteria/classification/growth &amp; development/*metabolism ; Bacterial Proteins/analysis/*metabolism ; Culture Media/chemistry/*metabolism ; Electronic Nose ; Food Microbiology ; Microbiota ; Odorants/*analysis ; Volatile Organic Compounds/analysis/metabolism ; }, abstract = {The rapidly increasing demand for protein has led to the pursuit of new protein sources, among which microbial protein (MP) is one of the most promising. Although the nutritional properties of MP are important and often well-studied, the sensory properties of the microbial cells will in part determine the commercial success of the product and are much less investigated. Here we assessed the odor fingerprint of dried bacteria originating from pure cultures and enriched mixed microbial communities using an electronic nose (e-nose). The e-nose discriminated between the different MP sources, while the choice of culture and substrate substantially affected their volatile organic compound (VOC) profile. The most dominant odor descriptors (>20% of VOC peak area) were sweet, fruity and fishy, while the mixed cultures presented higher peak areas indicating potentially more intense aromas than the pure cultures. The e-nose can detect the suitability of new MP sources and determine their best end-use.}, }
@article {pmid32969526, year = {2021}, author = {Niemeier-Walsh, C and Ryan, PH and Meller, J and Ollberding, NJ and Adhikari, A and Indugula, R and Reponen, T}, title = {The mycobiomes and bacteriomes of sputum, saliva, and home dust.}, journal = {Indoor air}, volume = {31}, number = {2}, pages = {357-368}, doi = {10.1111/ina.12750}, pmid = {32969526}, issn = {1600-0668}, support = {T42OH008432/OH/NIOSH CDC HHS/United States ; R21ES024807/ES/NIEHS NIH HHS/United States ; }, mesh = {Adolescent ; Air Microbiology ; *Air Pollution, Indoor ; Bacteria ; Cohort Studies ; DNA, Bacterial ; DNA, Fungal ; Dust/analysis ; *Environmental Monitoring ; Fungi ; Housing ; Humans ; *Microbiota ; *Mycobiome ; RNA, Ribosomal, 16S ; Respiratory System ; Saliva/microbiology ; }, abstract = {Respiratory microbiome is an understudied area of research compared to other microbiomes of the human body. The respiratory tract is exposed to an array of environmental pollutants, including microbes. Yet, we know very little about the relationship between environmental and respiratory microbiome. The primary aim of our study was to compare the mycobiomes and bacteriomes between three sample types from the same participants, including home dust, saliva, and sputum. Samples were collected from 40 adolescents in a longitudinal cohort. We analyzed the samples using 16s bacterial rDNA and ITS fungal rDNA gene sequencing, as well as quantitative PCR with universal fungal and bacterial primers. Results showed that home dust had the greatest alpha diversity between the three sample types for both bacteria and fungi. Dust had the highest total fungal load and the lowest total bacterial load. Sputum had greater bacterial diversity than saliva, but saliva had greater fungal diversity than sputum. The distribution of major bacterial phyla differed between all sample types. However, the distribution of major fungal classes differed only between sputum and saliva. Future research should examine the biological significance of the taxa found in each sample type based on microbial ecology and associations with health effects.}, }
@article {pmid32968841, year = {2021}, author = {Zhao, D and Zhang, Z and Niu, H and Guo, H}, title = {Win by Quantity: a Striking Rickettsia-Bias Symbiont Community Revealed by Seasonal Tracking in the Whitefly Bemisia tabaci.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {523-534}, pmid = {32968841}, issn = {1432-184X}, support = {31701797//the National Natural Science Foundation of China/ ; BK20170598//the Natural Science Foundation of Jiangsu Province, China/ ; BE2010342//the Key Research and Development Program of Jiangsu Province, China/ ; }, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; China ; Cucumis sativus/parasitology ; Gossypium/parasitology ; Hemiptera/*microbiology ; Microbial Interactions ; *Microbiota ; Rickettsia/classification/genetics/*isolation &amp; purification ; Seasons ; *Symbiosis ; }, abstract = {Maintaining an adaptive seasonality is a basic ecological requisite for cold-blooded organism insects which usually harbor various symbionts. However, how coexisting symbionts coordinate in insects during seasonal progress is still unknown. The whitefly Bemisia tabaci in China harbors the obligate symbiont Portiera that infects each individual, as well as various facultative symbionts. In this study, we investigated whitefly populations in cucumber and cotton fields from May to December 2019, aiming to reveal the fluctuations of symbiont infection frequencies, symbiont coordination in multiple infected individuals, and host plants effects on symbiont infections. The results indicated that the facultative symbionts Hamiltonella (H), Rickettsia (R), and Cardinium (C) exist in field whiteflies, with single (H) and double (HC and HR) infections occurring frequently. Infection frequencies of Hamiltonella (always 100%) and Cardinium (29.50-34.38%) remained steady during seasonal progression. Rickettsia infection frequency in the cucumber whitefly population decreased from 64.47% in summer to 35.29% in winter. Significantly lower Rickettsia infection frequency (15.55%) was identified in cotton whitefly populations and was not subject to seasonal fluctuation. Nevertheless, Rickettsia had a significantly quantitative advantage in the symbiont community of whitefly individuals and populations from both cucumber and cotton field all through the seasons. Moreover, higher Portiera and Hamiltonella densities were found in HC and HR whitefly than in H whitefly, suggesting these symbionts may contribute to producing nutrients for their symbiont partners. These results provide ample cues to further explore the interactions between coexisting symbionts, the coevolutionary relationship between symbionts and host symbiont-induced effects on host plant use.}, }
@article {pmid32967081, year = {2020}, author = {Ortiz, M and Bosch, J and Coclet, C and Johnson, J and Lebre, P and Salawu-Rotimi, A and Vikram, S and Makhalanyane, T and Cowan, D}, title = {Microbial Nitrogen Cycling in Antarctic Soils.}, journal = {Microorganisms}, volume = {8}, number = {9}, pages = {}, pmid = {32967081}, issn = {2076-2607}, abstract = {The Antarctic continent is widely considered to be one of the most hostile biological habitats on Earth. Despite extreme environmental conditions, the ice-free areas of the continent, which constitute some 0.44% of the total continental land area, harbour substantial and diverse communities of macro-organisms and especially microorganisms, particularly in the more "hospitable" maritime regions. In the more extreme non-maritime regions, exemplified by the McMurdo Dry Valleys of South Victoria Land, nutrient cycling and ecosystem servicing processes in soils are largely driven by microbial communities. Nitrogen turnover is a cornerstone of ecosystem servicing. In Antarctic continental soils, specifically those lacking macrophytes, cold-active free-living diazotrophic microorganisms, particularly Cyanobacteria, are keystone taxa. The diazotrophs are complemented by heterotrophic bacterial and archaeal taxa which show the genetic capacity to perform elements of the entire N cycle, including nitrification processes such as the anammox reaction. Here, we review the current literature on nitrogen cycling genes, taxa, processes and rates from studies of Antarctic soils. In particular, we highlight the current gaps in our knowledge of the scale and contribution of these processes in south polar soils as critical data to underpin viable predictions of how such processes may alter under the impacts of future climate change.}, }
@article {pmid32963580, year = {2020}, author = {Floková, K and Shimels, M and Andreo Jimenez, B and Bardaro, N and Strnad, M and Novák, O and Bouwmeester, HJ}, title = {An improved strategy to analyse strigolactones in complex sample matrices using UHPLC-MS/MS.}, journal = {Plant methods}, volume = {16}, number = {}, pages = {125}, pmid = {32963580}, issn = {1746-4811}, abstract = {BACKGROUND: Strigolactones represent the most recently described group of plant hormones involved in many aspects of plant growth regulation. Simultaneously, root exuded strigolactones mediate rhizosphere signaling towards beneficial arbuscular mycorrhizal fungi, but also attract parasitic plants. The seed germination of parasitic plants induced by host strigolactones leads to serious agricultural problems worldwide. More insight in these signaling molecules is hampered by their extremely low concentrations in complex soil and plant tissue matrices, as well as their instability. So far, the combination of tailored isolation-that would replace current unspecific, time-consuming and labour-intensive processing of large samples-and a highly sensitive method for the simultaneous profiling of a broad spectrum of strigolactones has not been reported.<br><br>RESULTS: Depending on the sample matrix, two different strategies for the rapid extraction of the seven structurally similar strigolactones and highly efficient single-step pre-concentration on polymeric RP SPE sorbent were developed and validated. Compared to conventional methods, controlled temperature during the extraction and the addition of an organic modifier (acetonitrile, acetone) to the extraction solvent helped to tailor strigolactone isolation from low initial amounts of root tissue (150&#xa0;mg fresh weight, FW) and root exudate (20&#xa0;ml), which improved both strigolactone stability and sample purity. We have designed an efficient UHPLC separation with sensitive MS/MS detection for simultaneous analysis of seven natural strigolactones including their biosynthetic precursors-carlactone and carlactonoic acid. In combination with the optimized UHPLC-MS/MS method, attomolar detection limits were achieved. The new method allowed successful profiling of seven strigolactones in small exudate and root tissue samples of four different agriculturally important plant species-sorghum, rice, pea and tomato.<br><br>CONCLUSION: The established method provides efficient strigolactone extraction with aqueous mixtures of less nucleophilic organic solvents from small root tissue and root exudate samples, in combination with rapid single-step pre-concentration. This method improves strigolactone stability and eliminates the co-extraction and signal of matrix-associated contaminants during the final UHPLC-MS/MS analysis with an electrospray interface, which dramatically increases the overall sensitivity of the analysis. We show that the method can be applied to a variety of plant species.}, }
@article {pmid32963001, year = {2020}, author = {Dueholm, MS and Andersen, KS and McIlroy, SJ and Kristensen, JM and Yashiro, E and Karst, SM and Albertsen, M and Nielsen, PH}, title = {Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax).}, journal = {mBio}, volume = {11}, number = {5}, pages = {}, pmid = {32963001}, issn = {2150-7511}, mesh = {Automation, Laboratory ; Bacteria/*classification ; DNA Primers ; *Databases, Nucleic Acid ; *Ecosystem ; *High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Reference Values ; Sequence Analysis, DNA ; Wastewater/microbiology ; }, abstract = {High-throughput 16S rRNA gene amplicon sequencing is an essential method for studying the diversity and dynamics of microbial communities. However, this method is presently hampered by the lack of high-identity reference sequences for many environmental microbes in the public 16S rRNA gene reference databases and by the absence of a systematic and comprehensive taxonomy for the uncultured majority. Here, we demonstrate how high-throughput synthetic long-read sequencing can be applied to create ecosystem-specific full-length 16S rRNA gene amplicon sequence variant (FL-ASV) resolved reference databases that include high-identity references (>98.7% identity) for nearly all abundant bacteria (>0.01% relative abundance) using Danish wastewater treatment systems and anaerobic digesters as an example. In addition, we introduce a novel sequence identity-based approach for automated taxonomy assignment (AutoTax) that provides a complete seven-rank taxonomy for all reference sequences, using the SILVA taxonomy as a backbone, with stable placeholder names for unclassified taxa. The FL-ASVs are perfectly suited for the evaluation of taxonomic resolution and bias associated with primers commonly used for amplicon sequencing, allowing researchers to choose those that are ideal for their ecosystem. Reference databases processed with AutoTax greatly improves the classification of short-read 16S rRNA ASVs at the genus- and species-level, compared with the commonly used universal reference databases. Importantly, the placeholder names provide a way to explore the unclassified environmental taxa at different taxonomic ranks, which in combination with in situ analyses can be used to uncover their ecological roles.}, }
@article {pmid32962223, year = {2020}, author = {Rothman, JA and Cox-Foster, DL and Andrikopoulos, C and McFrederick, QS}, title = {Diet Breadth Affects Bacterial Identity but Not Diversity in the Pollen Provisions of Closely Related Polylectic and Oligolectic Bees.}, journal = {Insects}, volume = {11}, number = {9}, pages = {}, pmid = {32962223}, issn = {2075-4450}, support = {NNX15AP99A/NASA/NASA/United States ; 2018-67011- 28123//U.S. Department of Agriculture/ ; CA-R-ENT-5109-H//U.S. Department of Agriculture/ ; 1929572//National Science Foundation/ ; Pollinating Insect Research Unit Base Funds//U.S. Department of Agriculture/ ; }, abstract = {Mounting evidence suggests that microbes found in the pollen provisions of wild and solitary bees are important drivers of larval development. As these microbes are also known to be transmitted via the environment, most likely from flowers, the diet breadth of a bee may affect the diversity and identity of the microbes that occur in its pollen provisions. Here, we tested the hypothesis that, due to the importance of floral transmission of microbes, diet breadth affects pollen provision microbial community composition. We collected pollen provisions at four sites from the polylectic bee Osmia lignaria and the oligolectic bee Osmia ribifloris. We used high-throughput sequencing of the bacterial 16S rRNA gene to characterize the bacteria found in these provisions. We found minimal overlap in the specific bacterial variants in pollen provisions across the host species, even when the bees were constrained to foraging from the same flowers in cages at one site. Similarly, there was minimal overlap in the specific bacterial variants across sites, even within the same host species. Together, these findings highlight the importance of environmental transmission and host specific sorting influenced by diet breadth for microbes found in pollen provisions. Future studies addressing the functional consequences of this filtering, along with tests for differences between more species of oligoletic and polylectic bees will provide rich insights into the microbial ecology of solitary bees.}, }
@article {pmid32962069, year = {2020}, author = {Cold, F and Kousgaard, SJ and Halkjaer, SI and Petersen, AM and Nielsen, HL and Thorlacius-Ussing, O and Hansen, LH}, title = {Fecal Microbiota Transplantation in the Treatment of Chronic Pouchitis: A Systematic Review.}, journal = {Microorganisms}, volume = {8}, number = {9}, pages = {}, pmid = {32962069}, issn = {2076-2607}, support = {7076-00129B//Danish Innovation Fund/ ; }, abstract = {The objective was to evaluate available literature on treatment of chronic pouchitis with fecal microbiota transplantation (FMT) focusing on clinical outcomes, safety, and different approaches to FMT preparation and delivery. A systematic review of electronic databases was conducted using Medline, EMBASE, and the Cochrane Central Register of Controlled Trials Library from inception through April 2020. Human studies of all study types reporting results of FMT to treat chronic pouchitis were included. Nine studies, reporting FMT treatment of 69 patients with chronic pouchitis were found eligible for the review. Most studies were case series and cohort studies rated as having fair to poor quality due to high risk of bias and small sample size. Only one randomized controlled trial was included, finding no beneficial effect of FMT. In total clinical response after FMT was reported in 14 (31.8%) out of 44 evaluated patients at various timepoints after FMT, and clinical remission in ten (22.7%) patients. Only minor self-limiting adverse events were reported. FMT varied greatly regarding preparation, length of treatment, and route of delivery. The effects of FMT on symptoms of chronic pouchitis are not established, though some studies show promising results. Future controlled well-designed studies are warranted.}, }
@article {pmid32962009, year = {2020}, author = {Pantanella, F and Lekunberri, I and Gagliardi, A and Venuto, G and Sànchez-Melsió, A and Fabiani, M and Balcázar, JL and Schippa, S and De Giusti, M and Borrego, C and Solimini, A}, title = {Effect of Urban Wastewater Discharge on the Abundance of Antibiotic Resistance Genes and Antibiotic-Resistant Escherichia coli in Two Italian Rivers.}, journal = {International journal of environmental research and public health}, volume = {17}, number = {18}, pages = {}, pmid = {32962009}, issn = {1660-4601}, mesh = {Anti-Bacterial Agents ; *Drug Resistance, Microbial/genetics ; *Escherichia coli/drug effects/genetics ; *Genes, Bacterial ; Italy ; RNA, Ribosomal, 16S ; *Wastewater/analysis ; }, abstract = {BACKGROUND: Wastewater treatment plants (WWTPs) are microbial factories aimed to reduce the amount of nutrients and pathogenic microorganisms in the treated wastewater before its discharge into the environment. We studied the impact of urban WWTP effluents on the abundance of antibiotic resistance genes (ARGs) and antibiotic-resistant Escherichia coli (AR-E. coli) in the last stretch of two rivers (Arrone and Tiber) in Central Italy that differ in size and flow volume.<br><br>METHODS: Water samples were collected in three seasons upstream and downstream of the WWTP, at the WWTP outlet, and at sea sites near the river mouth, and analyzed for the abundance of ARGs by qPCR and AR-E. coli using cultivation followed by disk diffusion assays.<br><br>RESULTS: For all studied genes (16S rRNA, intI1, sul1, ermB, blaTEM, tetW and qnrS), absolute concentrations were significantly higher in the Tiber than in the Arrone at all sampling sites, despite their collection date, but the prevalence of target ARGs within bacterial communities in both rivers was similar. The absolute concentrations of most ARGs were also generally higher in the WWTP effluent with median levels between log 4 and log 6 copies per ml but did not show differences along the studied stretches of rivers. Statistically significant site effect was found for E. coli phenotypic resistance to tetracycline and ciprofloxacin in the Arrone but not in the Tiber.<br><br>CONCLUSIONS: In both rivers, diffuse or point pollution sources other than the studied WWTP effluents may account for the observed resistance pattern, although the Arrone appears as more sensitive to the wastewater impact considering its lower flow volume.}, }
@article {pmid32961710, year = {2020}, author = {Yacoub, A and Magnin, N and Gerbore, J and Haidar, R and Bruez, E and Compant, S and Guyoneaud, R and Rey, P}, title = {The Biocontrol Root-Oomycete, Pythium Oligandrum, Triggers Grapevine Resistance and Shifts in the Transcriptome of the Trunk Pathogenic Fungus, Phaeomoniella Chlamydospora.}, journal = {International journal of molecular sciences}, volume = {21}, number = {18}, pages = {}, pmid = {32961710}, issn = {1422-0067}, mesh = {Ascomycota/*growth &amp; development ; *Disease Resistance ; *Pest Control, Biological ; Plant Diseases/*microbiology ; Pythium/*growth &amp; development ; Vitis/*microbiology ; }, abstract = {The worldwide increase in grapevine trunk diseases, mainly esca, represents a major threat for vineyard sustainability. Biocontrol of a pioneer fungus of esca, Phaeomoniella chlamydospora, was investigated here by deciphering the tripartite interaction between this trunk-esca pathogen, grapevine and the biocontrol-oomycete, Pythium oligandrum. When P. oligandrum colonizes grapevine roots, it was observed that the wood necroses caused by P. chlamydospora were significantly reduced. Transcriptomic analyses of plant and fungus responses were performed to determine the molecular events occurring, with the aim to relate P.chlamydospora degradation of wood to gene expression modulation. Following P. oligandrum-root colonization, major transcriptomic changes occurred both, in the grapevine-defense system and in the P. chlamydospore-virulence factors. Grapevine-defense was enhanced in response to P. chlamydospora attacks, with P. oligandrum acting as a plant-systemic resistance inducer, promoting jasmonic/ethylene signaling pathways and grapevine priming. P. chlamydospora pathogenicity genes, such as those related to secondary metabolite biosynthesis, carbohydrate-active enzymes and transcription regulators, were also affected in their expression. Shifts in grapevine responses and key-fungal functions were associated with the reduction of P. chlamydospora wood necroses. This study provides evidence of wood fungal pathogen transcriptional changes induced by a root biocontrol agent, P. oligandrum, in which there is no contact between the two microorganisms.}, }
@article {pmid32961324, year = {2020}, author = {de Souza, CM and Garcia, MT and de Barros, PP and Pedroso, LLC and Ward, RADC and Strixino, JF and Melo, VMM and Junqueira, JC}, title = {Chitosan enhances the antimicrobial photodynamic inactivation mediated by Photoditazine® against Streptococcus mutans.}, journal = {Photodiagnosis and photodynamic therapy}, volume = {32}, number = {}, pages = {102001}, doi = {10.1016/j.pdpdt.2020.102001}, pmid = {32961324}, issn = {1873-1597}, mesh = {*Anti-Infective Agents ; Biofilms ; *Chitosan ; *Dental Caries/drug therapy ; Humans ; *Photochemotherapy/methods ; Photosensitizing Agents/pharmacology ; Streptococcus mutans ; }, abstract = {Chitosan (CS), a biopolymer with intrinsic antimicrobial activity, can increase antimicrobial photodynamic inactivation (aPDI). The aim of this study was to evaluate the capacity of CS to potentiate the efficacy of Photoditazine® (PDZ)-mediated aPDI of the cariogenic bacterium Streptococcus mutans. CS effectively augmented the effects of aPDI, with reductions of approximately 4.5 logs in both planktonic and biofilm states. The combined treatment was also capable of reducing the number of S. mutans cells and amount of extracellular matrix in biofilms formed on enamel surfaces, which were characterized using scanning electron microscopy analysis. Furthermore, CS increased the absorption of PDZ by S. mutans cells. The combination of CS with PDZ-mediated aPDI is hence a promising antimicrobial approach against S. mutans and may be useful to control dental caries.}, }
@article {pmid32960315, year = {2021}, author = {Sodhi, KK and Kumar, M and Singh, DK}, title = {Assessing the bacterial diversity and functional profiles of the River Yamuna using Illumina MiSeq sequencing.}, journal = {Archives of microbiology}, volume = {203}, number = {1}, pages = {367-375}, pmid = {32960315}, issn = {1432-072X}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; DNA, Bacterial/genetics ; *High-Throughput Nucleotide Sequencing ; Industrial Waste ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; }, abstract = {A small percentage of the total freshwater on Earth is represented by river water. Microbes have an essential role to play in the biogeochemical cycles, mineralization of organic water, along with xenobiotics degradation. Microbial dynamics are susceptible to environmental stressors which includes pollutants such as antibiotics, metals, and other degradants. River Yamuna is polluted extensively by domestic and industrial wastes. Xenobiotics, when released into the environment, can lead to water pollution. The present study evaluates the microbial diversity in Yamuna River (28°40'5.53'' N, 77°15'0.35'' E) along with the prediction of the metagenome function. In this context, the metagenomic DNA was extracted and sequencing was done on Illumina@MiSeq platform. The total number of OTUs picked was 41,994, out of which 74% were classified within the kingdom Bacteria. 35% of the OTUs were assigned to phylum Proteobacteria, followed by Bacteriodetes (22%), whereas 26% of OTUs were unassigned. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used to predict metagenomic functions using 16S rDNA as a marker. Metagenomic reads were assigned to the Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous (COG), and Gene Ontology (GO). Functional characterization reveals the presence of methyl-accepting chemotaxis protein which is an important adaptation for the microbes in the environment. The enzymes can be mapped for the bioremediation of xenobiotics. Information obtained from the amplicon sequencing of River Yamuna, collaborated with "omic" studies, may help in the design of bioremediation strategies and can be used for environmental clean-up of pollutants.}, }
@article {pmid32958725, year = {2020}, author = {Wünsch, D and Strijkstra, A and Wöhlbrand, L and Freese, HM and Scheve, S and Hinrichs, C and Trautwein, K and Maczka, M and Petersen, J and Schulz, S and Overmann, J and Rabus, R}, title = {Global Response of Phaeobacter inhibens DSM 17395 to Deletion of Its 262-kb Chromid Encoding Antibiotic Synthesis.}, journal = {Microbial physiology}, volume = {30}, number = {1-6}, pages = {9-24}, doi = {10.1159/000508591}, pmid = {32958725}, issn = {2673-1673}, mesh = {Amino Acids ; Anti-Bacterial Agents/*biosynthesis ; Bacterial Proteins/genetics/metabolism ; Biological Transport ; Bioreactors ; Carbon Dioxide ; Chromosomes ; Proteome ; Replicon ; Rhodobacteraceae/*genetics/*metabolism ; Transcriptome ; Tropolone/analogs &amp; derivatives ; }, abstract = {The marine alphaproteobacterium Phaeobacter inhibens DSM 17395, a member of the Roseobacter group, was recently shown to markedly enhance growth upon deletion of its 262-kb chromid encoding biosynthesis of tropodithietic acid (TDA). To scrutinize the metabolic/regulatory adaptations that underlie enhanced growth of the Δ262 mutant, its transcriptome and proteome compared to the wild type were investigated in process-controlled bioreactors with Casamino Acids as growth substrate. Genome resequencing revealed only few additional genetic changes (a heterogenic insertion, prophage activation, and several point mutations) between wild type and Δ262 mutant, albeit with no conceivable effect on the studied growth physiology. The abundances of the vast majority of transcripts and proteins involved in the catabolic network for complete substrate oxidation to CO2 were found to be unchanged, suggesting that the enhanced amino acid utilization of the Δ262 mutant did not require elevated synthesis of most enzymes of the catabolic network. Similarly, constituents of genetic information processing and cellular processes remained mostly unchanged. In contrast, 426 genes displayed differential expression, of which 410 were localized on the 3.2-Mb chromosome, 5 on the 65-kb chromid, and 11 on the 78-kb chromid. Notably, the branched-chain amino transferase IlvE acting on rapidly utilized Val, Ile, and Leu was upregulated. Moreover, the transportome was reconfigured, as evidenced from increased abundances of transcripts and proteins of several uptake systems for amino acids and inorganic nutrients (e.g., phosphate). Some components of the respiratory chain were also upregulated, which correlates with the higher respiration rates of the Δ262 mutant. Furthermore, chromosomally encoded transcripts and proteins that are peripherally related to TDA biosynthesis (e.g., the serine acyl transferase CysE) were strongly downregulated in the Δ262 mutant. Taken together, these observations reflect adaptations to enhanced growth as well as the functional interconnectivity of the replicons of P. inhibens DSM 17395.}, }
@article {pmid32957572, year = {2020}, author = {Wang, Q and Fu, S and Yang, Q and Hao, J and Zhou, C and Liu, Y}, title = {The Impact of Water Intrusion on Pathogenic Vibrio Species to Inland Brackish Waters of China.}, journal = {International journal of environmental research and public health}, volume = {17}, number = {18}, pages = {}, pmid = {32957572}, issn = {1660-4601}, mesh = {China ; Multilocus Sequence Typing ; *Seawater/virology ; *Vibrio cholerae ; *Vibrio parahaemolyticus/genetics ; Water ; Water Microbiology ; Water Movements ; }, abstract = {The estuary is the ecological niche of pathogenic Vibrio spp. as it provides abundant organic and inorganic nutrients from seawater and rivers. However, little is known about the ecology of these Vibrio species in the inland brackish water area. In this study, their co-occurrence and relationships to key environmental constraints (salinity and temperature) in the Hun-Tai River of China were examined using the most probable number polymerase chain reaction (MPN-PCR) approach. We hereby report 2-year continuous surveillance based on six water indices of the Hun-Tai River. The results showed that seawater intrusion maximally reached inland as far as 26.5 km for the Hun-Tai River. Pathogenic Vibrio spp. were detected in 21.9% of the water samples. In particular, V. cholerae, V. parahaemolyticus, and V. vulnificus were isolated in 10 (10.4%), 20 (20.8.5%), and 2 (2.08%) samples, respectively. All V. parahaemolyticus strains were tdh gene negative, 10% were positive for the trh gene. Multi-locus sequence typing (MLST) divided V. parahaemolyticus strains into 12 sequence types (STs) for the Hun-Tai River. Five STs were respectively present in various locations along the Hun-Tai River. The PCR assay for detecting six virulence genes and Vibrio seventh pandemic island I and II revealed three genotypes in 12 V. cholerae isolates. The results of our study showed that seawater intrusion and salinity have profound effects on the distribution of pathogenic Vibrio spp. in the inland river, suggesting a potential health risk associated with the waters of the Hun-Tai River used for irrigation and drinking.}, }
@article {pmid32950135, year = {2020}, author = {Peruzy, MF and Aponte, M and Proroga, YTR and Capuano, F and Cristiano, D and Delibato, E and Houf, K and Murru, N}, title = {Yersinia enterocolitica detection in pork products: Evaluation of isolation protocols.}, journal = {Food microbiology}, volume = {92}, number = {}, pages = {103593}, doi = {10.1016/j.fm.2020.103593}, pmid = {32950135}, issn = {1095-9998}, mesh = {Animals ; Culture Media/chemistry/metabolism ; Food Contamination/analysis ; Meat Products/analysis/*microbiology ; Swine ; Yersinia enterocolitica/classification/genetics/*isolation &amp; purification/metabolism ; }, abstract = {Conventional methods for Yersinia enterocolitica detection in food samples are generally considered inadequate. Problems arise from the presence of the so-called "background flora", coupled to the low contamination level of the pathogen. Since, data on the microbial ecology occurring in competitive microflora are still lacking, MALDI TOF MS was used for strains 'identification after enrichment in PSB or ITC broths, and after plating on selective CIN medium at different incubation times. SYBR Green Real time PCR was used for the Y. enterocolitica strains' detection (4/O:3, 1A/O:5) in experimentally contaminated foods, as well as in naturally contaminated samples. A higher number of different bacterial genera (10 on CIN and 18 on PCA) was recorded after enrichment in PSB, whilst enrichment in ITC led to recovery of 6 and 10 genera on CIN and PCA, respectively. Yersiniaceae was the dominant family on the first day of incubation, but on the second day the percentage of isolation considerably decreased. By testing experimentally contaminated samples, substantial difficulties were encountered. The biotype 1A was always detected, whereas strain 4/O:3 proved to be poorly competitive. Based on the data, the enrichment media PSB and ITC, currently proposed for Y. enterocolitica detection, need to be improved to promote a successful pathogen's recovery.}, }
@article {pmid32949457, year = {2020}, author = {Hermans, SM and Buckley, HL and Curran-Cournane, F and Taylor, M and Lear, G}, title = {Temporal variation in soil bacterial communities can be confounded with spatial variation.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {12}, pages = {}, doi = {10.1093/femsec/fiaa192}, pmid = {32949457}, issn = {1574-6941}, mesh = {Bacteria/genetics ; Biodiversity ; *Ecosystem ; Forests ; Humans ; RNA, Ribosomal, 16S/genetics ; *Soil ; Soil Microbiology ; }, abstract = {Investigating temporal variation in soil bacterial communities advances our fundamental understanding of the causal processes driving biological variation, and how the composition of these important ecosystem members may change into the future. Despite this, temporal variation in soil bacteria remains understudied, and the effects of spatial heterogeneity in bacterial communities on the detection of temporal changes is largely unknown. Using 16S rRNA gene amplicon sequencing, we evaluated temporal patterns in soil bacterial communities from indigenous forest and human-impacted sites sampled repeatedly over a 5-year period. Temporal variation appeared to be greater when fewer spatial samples per site were analysed, as well as in human-impacted compared to indigenous sites (P < 0.01 for both). The biggest portion of variation in bacterial community richness and composition was explained by soil physicochemical variables (13-24%) rather than spatial distance or sampling time (<1%). These results highlight the importance of adequate spatiotemporal replication when sampling soil communities for environmental monitoring, and the importance of conducting temporal research across a wide variety of land uses. This will ensure we have a true understanding of how bacterial communities change over space and time; the work presented here provides important considerations for how such research should be designed.}, }
@article {pmid32948906, year = {2021}, author = {Jeong, SY and Kim, TG}, title = {Spatial Variance of Species Distribution Predicts the Interspecies Interactions within a Microbial Metacommunity.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {549-552}, pmid = {32948906}, issn = {1432-184X}, support = {2018R1D1A1B07048872//Ministry of Education/ ; }, mesh = {Bacteria ; Biofilms ; *Ecosystem ; Lakes/microbiology ; *Microbial Interactions ; *Microbiota ; Reproducibility of Results ; Soil Microbiology ; }, abstract = {Interspecies interactions have a profound influence on spatial distribution of coexisting microbial species. We explored whether spatial variance of species distribution (SVSD) predicts the degree of interspecies interactions within a microbial metacommunity. Simulations were used to determine the relationships from random, lake, soil, and biofilm metacommunity datasets (1,000 times). All of the bacterial datasets showed a negative correlation between the habitat breadth (inverse to SVSD) and the numbers of total, positive, and negative interspecies interactions (P < 0.05); the only exception was the relationship between habitat breadth and negative interactions in the biofilm dataset. The random dataset had no significant relationships (P > 0.05). We repeated the simulations to determine the degree of correlation and reproducibility (100 times). Habitat breadth was negatively correlated with the total and positive interactions in all of the real datasets (P < 0.05), and the negative relationships persisted across repetitions. Despite variability in the slope of total interactions, the slope values of positive interactions were similar for the real datasets (- 19.9, - 19.2, and - 25.8 for lake, soil, and biofilm, respectively). In conclusion, our results demonstrate the patterns of species interaction-distribution and show that interspecies interactions are positively correlated with the SVSD.}, }
@article {pmid32948905, year = {2020}, author = {Mars Brisbin, M and Conover, AE and Mitarai, S}, title = {Influence of Regional Oceanography and Hydrothermal Activity on Protist Diversity and Community Structure in the Okinawa Trough.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {746-761}, doi = {10.1007/s00248-020-01583-w}, pmid = {32948905}, issn = {1432-184X}, mesh = {*Biodiversity ; Eukaryota/*isolation &amp; purification ; *Hydrothermal Vents ; *Oceans and Seas ; Pacific Ocean ; Seawater/*chemistry ; }, abstract = {Microbial eukaryotes (protists) contribute substantially to ecological functioning in marine ecosystems, but the relative importance of factors shaping protist diversity, such as environmental selection and dispersal, remains difficult to parse. Water masses of a back-arc basin with hydrothermal activity provide a unique opportunity for studying the effects of dispersal and environmental selection on protist communities. In this study, we used metabarcoding to characterize protist communities in the Okinawa Trough, a back-arc spreading basin containing at least twenty-five active hydrothermal vent fields. Water was sampled from four depths at fourteen stations spanning the length of the Okinawa Trough, including three sites influenced by nearby hydrothermal vent sites. While significant differences in community structure reflecting water depth were present, protist communities were mostly homogeneous horizontally. Protist communities in the bottom waters affected by hydrothermal activity were significantly different from communities in other bottom waters, suggesting that environmental factors can be especially important in shaping community composition under specific conditions. Amplicon sequence variants that were enriched in hydrothermally influenced bottom waters largely derived from cosmopolitan protists that were present, but rare, in other near-bottom samples, thus highlighting the importance of the rare biosphere.}, }
@article {pmid32948266, year = {2020}, author = {Morimoto, D and Šulčius, S and Tominaga, K and Yoshida, T}, title = {Predetermined clockwork microbial worlds: Current understanding of aquatic microbial diel response from model systems to complex environments.}, journal = {Advances in applied microbiology}, volume = {113}, number = {}, pages = {163-191}, doi = {10.1016/bs.aambs.2020.06.001}, pmid = {32948266}, issn = {0065-2164}, mesh = {Aquatic Organisms/metabolism/*physiology ; Carbon/metabolism ; Energy Metabolism ; Food Chain ; Microbial Interactions ; Microbiota/*physiology ; Models, Biological ; *Periodicity ; Photosynthesis ; Sunlight ; }, abstract = {In the photic zone of aquatic ecosystems, microorganisms with different metabolisms and their viruses form complex interactions and food webs. Within these interactions, phototrophic microorganisms such as eukaryotic microalgae and cyanobacteria interact directly with sunlight, and thereby generate circadian rhythms. Diel cycling originally generated in microbial phototrophs is directly transmitted toward heterotrophic microorganisms utilizing the photosynthetic products as they are excreted or exuded. Such diel cycling seems to be indirectly propagated toward heterotrophs as a result of complex biotic interactions. For example, cell death of phototrophic microorganisms induced by viral lysis and protistan grazing provides additional resources of dissolved organic matter to the microbial community, and so generates diel cycling in other heterotrophs with different nutrient dependencies. Likewise, differences in the diel transmitting pathway via complex interactions among heterotrophs, and between heterotrophs and their viruses, may also generate higher variation and time lag diel rhythms in different heterotrophic taxa. Thus, sunlight and photosynthesis not only contribute energy and carbon supply, but also directly or indirectly control diel cycling of the microbial community through complex interactions in the photic zone of aquatic ecosystems.}, }
@article {pmid32945836, year = {2020}, author = {Pajdak-Stós, A and Fiałkowski, W and Fiałkowska, E}, title = {Rotifers weaken the efficiency of the cyanobacterium defence against ciliate grazers.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {11}, pages = {}, pmid = {32945836}, issn = {1574-6941}, mesh = {Animals ; *Ciliophora ; *Cyanobacteria ; *Rotifera ; }, abstract = {Cyanobacteria can protect themselves through limited dispersion and by increasing the compactness of the mucilage-covered cyanobacterial mat as well as by producing sheaths covering their trichomes. These features have been used in research to measure their degree of inducible defence. The influence of the presence of the rotifers Lecane inermis on the effectiveness of Phormidium sp. (Ph2) cyanobacterium defence was investigated. Experiments were conducted on the ciliates Pseudomicrothorax dubius and Furgasonia blochmanni, specialised in the ingestion of filamentous cyanobacteria. The most compact were cyanobacterial mats that were subjected exclusively to ciliates and the most dispersed were mats in the presence of rotifers alone. The presence of rotifers feeding on cyanobacterial mucilage led to the decreased effectiveness of the defence in two ways, by increasing the dispersion of cyanobacterial trichomes, thus loosening the cyanobacterial mat, and through the ingestion of the exopolysaccharide material covering the trichomes. As a result, in the presence of rotifers and the high density of ciliates, almost all the trichomes were removed. Moreover, in comparison with other treatments, a higher number of ciliates and rotifers remained active until the end of the experiments. This is the first report to show how rotifers can weaken the defence of cyanobacteria.}, }
@article {pmid32941745, year = {2021}, author = {Fu, S and Ni, P and Yang, Q and Hu, H and Wang, Q and Ye, S and Liu, Y}, title = {Delineating the key virulence factors and intraspecies divergence of Vibrio harveyi via whole-genome sequencing.}, journal = {Canadian journal of microbiology}, volume = {67}, number = {3}, pages = {231-248}, doi = {10.1139/cjm-2020-0079}, pmid = {32941745}, issn = {1480-3275}, mesh = {Animals ; Biofilms/growth &amp; development ; Fishes/microbiology ; Genetic Variation ; Genome, Bacterial/*genetics ; Movement ; Multilocus Sequence Typing ; Phylogeny ; Type VI Secretion Systems/genetics ; Vibrio/classification/*genetics/*pathogenicity ; Virulence Factors/*genetics ; Whole Genome Sequencing ; }, abstract = {Vibrio harveyi is one of the major pathogens in aquaculture. To identify the key virulence factors affecting pathogenesis of V. harveyi towards fish, we conducted a field investigation for three representative fish farms infected with V. harveyi. Multilocus sequence typing (MLST) and whole-genome sequencing were conducted to delineate the phylogenetic relationship and genetic divergence of V. harveyi. A total of 25 V. harveyi strains were isolated from the diseased fish and groundwater and were subtyped into 12 sequence types by MLST. Five virulence genes, mshB, pilA, hutR, ureB, and ureG, were variably presented in the sequenced strains. The virulence gene profiles strongly correlated with the distinct pathogenicity of V. harveyi strains, with a strain harboring all five genes exhibiting the highest virulence towards fish. Phenotype assay confirmed that reduced virulence correlated with decreased motility and biofilm formation ability. Additionally, three types of type VI secretion system, namely T6SS1, T6SS2, and T6SS3, were identified in V. harveyi strains, which can be classified into six, four, and 12 subtypes, respectively. In conclusion, the results indicated that the virulence level of V. harveyi is mainly determined by the above virulence genes, which may play vital roles in environmental adaptation for V. harveyi.}, }
@article {pmid32939928, year = {2020}, author = {Masetti, R and Zama, D and Leardini, D and Muratore, E and Turroni, S and Prete, A and Brigidi, P and Pession, A}, title = {The gut microbiome in pediatric patients undergoing allogeneic hematopoietic stem cell transplantation.}, journal = {Pediatric blood &amp; cancer}, volume = {67}, number = {12}, pages = {e28711}, doi = {10.1002/pbc.28711}, pmid = {32939928}, issn = {1545-5017}, mesh = {Gastrointestinal Microbiome/*immunology ; Graft vs Host Disease/*etiology/pathology ; Hematologic Neoplasms/*therapy ; Hematopoietic Stem Cell Transplantation/*adverse effects ; Humans ; Transplantation, Homologous ; }, abstract = {The gut microbiome (GM) has been associated with different clinical outcomes in the context of allogeneic hematopoietic stem cell transplantation (HSCT). Large multicenter cohort studies in adults have found significant correlations with overall survival, relapse, and incidence of complications. Moreover, GM is already a promising target for therapeutic interventions. However, few data are available in children, a population presenting unique features and challenges. During childhood, the GM evolves rapidly with large structural fluctuations, alongside with the maturation of the immune system. Furthermore, the HSCT procedure presents significant differences in children. These considerations underline the importance of a specific focus on the pediatric setting, and the role of GM and its age-dependent trajectory in influencing the immunity reconstitution and clinical outcomes. This review provides a comprehensive overview of the available evidence in the field of GM and pediatric HSCT, highlighting age-specific issues and discussing GM-based therapeutic approaches.}, }
@article {pmid32935184, year = {2021}, author = {He, Y and Zhou, Y and Weng, R and Wang, J and Chen, J and Huang, M}, title = {Responses of Ammonia-Oxidizing Archaea and Bacteria in Malodorous River Sediments to Different Remediation Techniques.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {314-322}, pmid = {32935184}, issn = {1432-184X}, support = {41877477//National Natural Science Foundation of China/ ; 18DZ1203806//Shanghai Science and Technology Development Funds/ ; 2017ZX07207001//National Science and Technology Major Project for Water Pollution Control and Treatment/ ; 2018ZX07208008//National Science and Technology Major Project for Water Pollution Control and Treatment/ ; }, mesh = {Ammonia/analysis/*metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Calcium Compounds/analysis ; Environmental Restoration and Remediation/*methods ; Geologic Sediments/chemistry/*microbiology ; Nitrates/analysis ; Oxidation-Reduction ; Oxygen/analysis ; Rivers/chemistry/*microbiology ; Species Specificity ; Water Pollutants, Chemical/metabolism ; }, abstract = {In this study, the joint use of high throughput sequencing, real-time quantitative PCR, and ammonia-oxidizing bacteria (AOB)-inhibiting allylthiourea was used to differentiate between the contributions of ammonia-oxidizing archaea (AOA) vs AOB to ammonia oxidation and ascertain how AOA and AOB responded to two widely used river remediation techniques (aeration and Ca(NO3)2 injection). Results showed that ammonia oxidation was largely attributed to ATU-sensitive AOB rather than AOA and Nitrosomonas was the predominant AOB-related genus (53.86%) in the malodorous river. The contribution of AOB to ammonia oxidation in the context of aeration and Ca(NO3)2 injection was 75.51 ± 2.77% and 60.19 ± 10.44%, respectively. The peak of AOB/AOA ratio and the marked increase of relative abundances of Nitrosomonas and Nitrosospira in aeration runs further demonstrated aeration favored the ammonia oxidation of AOB. Comparatively, Ca(NO3)2 injection could increase the ammonia oxidation contribution of AOA from 31.32 ± 6.06 to 39.81 ± 10.44% and was significantly correlated with Nitrosococcus of AOB (r = 0.796, p < 0.05), Candidatus_Nitrosopelagicus of AOA (r = 0.986, p < 0.01), and AOA Simpson diversity (r = - 0.791, p < 0.05). Moreover, Candidatus_Nitrosopelagicus was only present in Ca(NO3)2 runs. Taken together, Ca(NO3)2 was recognized as an important factor in mediating the growth and ecological niches of ammonia oxidizers.Graphical abstract.}, }
@article {pmid32935183, year = {2021}, author = {Phoma, BS and Makhalanyane, TP}, title = {Depth-Dependent Variables Shape Community Structure and Functionality in the Prince Edward Islands.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {396-409}, pmid = {32935183}, issn = {1432-184X}, mesh = {Archaea/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Enzymes/analysis/metabolism ; Indian Ocean ; Microbiota/genetics/*physiology ; Nutrients/analysis/metabolism ; Plankton/classification/genetics/isolation &amp; purification ; Prince Edward Island ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; }, abstract = {Physicochemical variables limit and control the distribution of microbial communities in all environments. In the oceans, this may significantly influence functional processes such the consumption of dissolved organic material and nutrient sequestration. Yet, the relative contributions of physical factors, such as water mass variability and depth, on functional processes are underexplored. We assessed microbial community structure and functionality in the Prince Edward Islands (PEIs) using 16S rRNA gene amplicon analysis and extracellular enzymatic activity assays, respectively. We found that depth and nutrients substantially drive the structural patterns of bacteria and archaea in this region. Shifts from epipelagic to bathypelagic zones were linked to decreases in the activities of several extracellular enzymes. These extracellular enzymatic activities were positively correlated with several phyla including several Alphaproteobacteria (including members of the SAR 11 clade and order Rhodospirillales) and Cyanobacteria. We show that depth-dependent variables may be essential drivers of community structure and functionality in the PEIs.}, }
@article {pmid32930890, year = {2020}, author = {Gupta, D and Guzman, MS and Bose, A}, title = {Extracellular electron uptake by autotrophic microbes: physiological, ecological, and evolutionary implications.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {47}, number = {9-10}, pages = {863-876}, pmid = {32930890}, issn = {1476-5535}, support = {MCB2021822//National Science Foundation/ ; 201563111//David and Lucile Packard Foundation/ ; DESC0014613//U.S. Department of Energy/ ; W911NF-18-1-0037//U.S. Department of Defense/ ; }, mesh = {*Autotrophic Processes ; Biological Transport ; Carbon Cycle ; Electrodes ; Electron Transport ; *Electrons ; Oxidation-Reduction ; Photosynthesis/physiology ; }, abstract = {Microbes exchange electrons with their extracellular environment via direct or indirect means. This exchange is bidirectional and supports essential microbial oxidation-reduction processes, such as respiration and photosynthesis. The microbial capacity to use electrons from insoluble electron donors, such as redox-active minerals, poised electrodes, or even other microbial cells is called extracellular electron uptake (EEU). Autotrophs with this capability can thrive in nutrient and soluble electron donor-deficient environments. As primary producers, autotrophic microbes capable of EEU greatly impact microbial ecology and play important roles in matter and energy flow in the biosphere. In this review, we discuss EEU-driven autotrophic metabolisms, their mechanism and physiology, and highlight their ecological, evolutionary, and biotechnological implications.}, }
@article {pmid32929739, year = {2021}, author = {Raymond, NS and Gómez-Muñoz, B and van der Bom, FJT and Nybroe, O and Jensen, LS and Müller-Stöver, DS and Oberson, A and Richardson, AE}, title = {Phosphate-solubilising microorganisms for improved crop productivity: a critical assessment.}, journal = {The New phytologist}, volume = {229}, number = {3}, pages = {1268-1277}, doi = {10.1111/nph.16924}, pmid = {32929739}, issn = {1469-8137}, mesh = {Agriculture ; Crops, Agricultural ; *Phosphates ; Phosphorus ; *Soil ; Soil Microbiology ; }, abstract = {Phosphate-solubilising microorganisms (PSM) are often reported to have positive effects on crop productivity through enhanced phosphorus (P) nutrition. Our aim was to evaluate the validity of this concept. Most studies that report 'positive effects' of PSM on plant growth have been conducted under controlled conditions, whereas field experiments more frequently fail to demonstrate a positive response. Many studies have indicated that the mechanisms seen in vitro do not translate into improved crop P nutrition in complex soil-plant systems. Furthermore, associated mechanisms are often not rigorously assessed. We suggest that PSM do not mobilise sufficient P to change the crops' nutritional environment under field conditions. The current concept, in which PSM solubilise P 'for the plant' should thus be revised. Although PSM have the capacity to solubilise P to meet their own needs, it is the turnover of the microbial biomass that subsequently provides P to plants over a longer time. Therefore, the existing concept of PSM function is unlikely to deliver a reliable strategy for increasing crop P nutrition. A further mechanistic understanding is needed to determine how P mobilisation by PSM as a component of the whole soil community can be manipulated to become more effective for plant P nutrition.}, }
@article {pmid32925728, year = {2020}, author = {Berentsen, B and Nagaraja, BH and Teige, EP and Lied, GA and Lundervold, AJ and Lundervold, K and Steinsvik, EK and Hillestad, ER and Valeur, J and Brønstad, I and Gilja, OH and Osnes, B and Hatlebakk, JG and Haász, J and Labus, J and Gupta, A and Mayer, EA and Benitez-Páez, A and Sanz, Y and Lundervold, A and Hausken, T}, title = {Study protocol of the Bergen brain-gut-microbiota-axis study: A prospective case-report characterization and dietary intervention study to evaluate the effects of microbiota alterations on cognition and anatomical and functional brain connectivity in patients with irritable bowel syndrome.}, journal = {Medicine}, volume = {99}, number = {37}, pages = {e21950}, pmid = {32925728}, issn = {1536-5964}, mesh = {Adolescent ; Adult ; Aged ; Brain/microbiology/physiopathology ; Case-Control Studies ; Cognition/physiology ; Diet, Carbohydrate-Restricted/*methods ; Female ; Fermentation ; Gastrointestinal Microbiome/*physiology ; Humans ; Irritable Bowel Syndrome/*diet therapy/*microbiology/psychology ; Male ; Middle Aged ; Prospective Studies ; Young Adult ; }, abstract = {INTRODUCTION: Irritable bowel syndrome (IBS) is a common clinical label for medically unexplained gastrointestinal (GI) symptoms, recently described as a disturbance of the brain-gut-microbiota (BGM) axis. To gain a better understanding of the mechanisms underlying the poorly understood etiology of IBS, we have designed a multifaceted study that aim to stratify the complex interaction and dysfunction between the brain, the gut, and the microbiota in patients with IBS.<br><br>METHODS: Deep phenotyping data from patients with IBS (n&#x200a;=&#x200a;100) and healthy age- (between 18 and 65) and gender-matched controls (n&#x200a;=&#x200a;40) will be collected between May 2019 and December 2021. Psychometric tests, questionnaires, human biological tissue/samples (blood, faeces, saliva, and GI biopsies from antrum, duodenum, and sigmoid colon), assessment of gastric accommodation and emptying using transabdominal ultrasound, vagal activity, and functional and structural magnetic resonance imaging (MRI) of the brain, are included in the investigation of each participant. A subgroup of 60 patients with IBS-D will be further included in a 12-week low FODMAP dietary intervention-study to determine short and long-term effects of diet on GI symptoms, microbiota composition and functions, molecular GI signatures, cognitive, emotional and social functions, and structural and functional brain signatures. Deep machine learning, prediction tools, and big data analyses will be used for multivariate analyses allowing disease stratification and diagnostic biomarker detection.<br><br>DISCUSSION: To our knowledge, this is the first study to employ unsupervised machine learning techniques and incorporate systems-based interactions between the central and the peripheral components of the brain-gut-microbiota axis at the levels of the multiomics, microbiota profiles, and brain connectome of a cohort of 100 patients with IBS and matched controls; study long-term safety and efficacy of the low-FODMAP diet on changes in nutritional status, gut microbiota composition, and metabolites; and to investigate changes in the brain and gut connectome after 12 weeks strict low-FODMAP-diet in patients with IBS. However, there are also limitations to the study. As a restrictive diet, the low-FODMAP diet carries risks of nutritional inadequacy and may foster disordered eating patterns. Strict FODMAP restriction induces a potentially unfavourable gut microbiota, although the health effects are unknown.<br><br>TRIAL REGISTRATION NUMBER: NCT04296552 (ClinicalTrials.gov).}, }
@article {pmid32923720, year = {2020}, author = {Giongo, A and Dos Anjos Borges, LG and Marconatto, L and de Lara Palhano, P and Serbent, MP and Moreira-Silva, E and de Abreu Siqueira, T and Martinho, CT and Barili, R and Paz, LV and Moser, LI and De Marco Veríssimo, C and Ketzer, JMM and Medina-Silva, R}, title = {Adaption of microbial communities to the hostile environment in the Doce River after the collapse of two iron ore tailing dams.}, journal = {Heliyon}, volume = {6}, number = {8}, pages = {e04778}, pmid = {32923720}, issn = {2405-8440}, abstract = {In November 2015, two iron ore tailing dams collapsed in the city of Mariana, Brazil. The dams' collapse generated a wave of approximately 50 million m[3] of a mixture of mining waste and water. It was a major environmental tragedy in Brazilian history, which damaged rivers, and cities 660 km away in the Doce River basin until it reached the ocean coast. Shortly after the incident, several reports informed that the concentration of metals in the water was above acceptable legal limits under Brazilian laws. Here the microbial communities in samples of water, mud, foam, and rhizosphere of Eichhornia from Doce River were analyzed for 16S and 18S rRNA-based amplicon sequencing, along with microbial isolation, chemical and mineralogical analyses. Samples were collected one month and thirteen months after the collapse. Prokaryotic communities from mud shifted drastically over time (33% Bray-Curtis similarity), while water samples were more similar (63% Bray-Curtis similarity) in the same period. After 12 months, mud samples remained with high levels of heavy metals and a reduction in the diversity of microeukaryotes was detected. Amoebozoans increased in mud samples, reaching 49% of microeukaryote abundance, with Discosea and Lobosa groups being the most abundant. The microbial communities' structure in mud samples changed adapting to the new environment condition. The characterization of microbial communities and metal-tolerant organisms from such impacted environments is essential for understanding the ecological consequences of massive anthropogenic impacts and strategies for the restoration of contaminated sites such as the Doce River.}, }
@article {pmid32923454, year = {2020}, author = {Ardern, Z and Neuhaus, K and Scherer, S}, title = {Are Antisense Proteins in Prokaryotes Functional?.}, journal = {Frontiers in molecular biosciences}, volume = {7}, number = {}, pages = {187}, pmid = {32923454}, issn = {2296-889X}, abstract = {Many prokaryotic RNAs are transcribed from loci outside of annotated protein coding genes. Across bacterial species hundreds of short open reading frames antisense to annotated genes show evidence of both transcription and translation, for instance in ribosome profiling data. Determining the functional fraction of these protein products awaits further research, including insights from studies of molecular interactions and detailed evolutionary analysis. There are multiple lines of evidence, however, that many of these newly discovered proteins are of use to the organism. Condition-specific phenotypes have been characterized for a few. These proteins should be added to genome annotations, and the methods for predicting them standardized. Evolutionary analysis of these typically young sequences also may provide important insights into gene evolution. This research should be prioritized for its exciting potential to uncover large numbers of novel proteins with extremely diverse potential practical uses, including applications in synthetic biology and responding to pathogens.}, }
@article {pmid32920672, year = {2021}, author = {Valverde, A and Cason, ED and Gómez-Arias, A and Bozkale, D and Govender, D and Riddell, E and Cowan, D}, title = {Pollution shapes the microbial communities in river water and sediments from the Olifants River catchment, South Africa.}, journal = {Archives of microbiology}, volume = {203}, number = {1}, pages = {295-303}, pmid = {32920672}, issn = {1432-072X}, mesh = {Archaea/*drug effects/genetics ; Bacteria/*drug effects/genetics ; Geologic Sediments/chemistry/*microbiology ; Microbiota/*drug effects ; Mining ; RNA, Ribosomal, 16S/genetics ; Rivers/chemistry/*microbiology ; South Africa ; Water Pollutants/*toxicity ; }, abstract = {Human activities such as agriculture and mining are leading causes of water pollution worldwide. Individual contaminants are known to negatively affect microbial communities. However, the effect of multifaceted pollution on these communities is less well understood. We investigated, using next-generation sequencing of the 16S rRNA genes, the effects of multisource (i.e., fertilizer industry and mining) chronic pollution on bacterial and archaeal communities in water and sediments from the Olifants River catchment, South Africa. Water samples showed less microbial species diversity than sediments and both habitats displayed different microbial communities. Within each of these habitats, pollution had no effect on alpha diversity but shaped the microbial composition and taxonomy-based predicted functions. Certain prokaryotic taxa and functional groups were indicative of different degrees of pollution. Heterotrophic taxa (e.g., Flavobacterium sp.) and sulphur-oxidizing bacteria (i.e., Thiobacillus sp.) were indicators of pollution in water and sediments, respectively. Ultimately, this information could be used to develop microbial indicators of water quality degradation.}, }
@article {pmid32920671, year = {2021}, author = {Lee, JC and Whang, KS}, title = {Lysobacter telluris sp. nov., isolated from Korean rhizosphere soil.}, journal = {Archives of microbiology}, volume = {203}, number = {1}, pages = {287-293}, pmid = {32920671}, issn = {1432-072X}, mesh = {DNA, Bacterial/genetics ; Lysobacter/*classification/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Rhizosphere ; *Soil Microbiology ; Species Specificity ; }, abstract = {A Gram-stain-negative, aerobic, non-motile, non-spore-forming light-yellow-coloured rod-shaped bacterial strain, designated YJ15[T], was isolated from soil at Bigeum island in Korea. Growth was observed at 10-37 °C (optimum, 28 °C), at pH 6.0-7.5 (optimum, pH 7.0) and in the absence of NaCl. Based on 16S rRNA gene sequence analysis, strain YJ15[T] was closely related to 'Lysobacter tongrenensis' YS037[T] (97.8%), Lysobacter pocheonensis Gsoil193[T] (96.5%) and Lysobacter daecheongensis Dae08[T] (95.8%) and phylogenetically grouped together with 'Lysobacter tongrenensis' YS037[T], Lysobacter dokdonensis DS-58[T] and Lysobacter pocheonensis Gsoil 193[T]. The DNA-DNA relatedness between strain YJ15[T] and 'Lysobacter tongrenensis' KCTC 52206[T] was 12% and the phylogenomic analysis based on the whole genome sequence demonstrated that strain YJ20[T] formed a distinct phyletic line with Lysobacterlter dokdonensis DS-58[T] showing average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of 76.3 and 21.3%, respectively. The predominant ubiquinone was identified as Q-8, and polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unidentified aminolipids. The major fatty acids were iso-C17:1 ω9c, iso-C15:0, iso-C16:0 and iso-C17:0. The genomic DNA G + C content was 68.2 mol %. On the basis of phenotypic, chemotaxonomic properties and phylogenetic analyses in this study, strain YJ15[T] is considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter telluris sp. nov. is proposed. The type strain is YJ15[T] (= KACC 19552[T] = NBRC 113197[T]).}, }
@article {pmid32920663, year = {2021}, author = {Paz, C and Öpik, M and Bulascoschi, L and Bueno, CG and Galetti, M}, title = {Dispersal of Arbuscular Mycorrhizal Fungi: Evidence and Insights for Ecological Studies.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {283-292}, pmid = {32920663}, issn = {1432-184X}, support = {2018/16697-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2018/00212-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {Animals ; Biota ; Environment ; Geography ; Hyphae/cytology/physiology ; Mycorrhizae/cytology/isolation &amp; purification/*physiology ; Plant Roots/microbiology ; Spores, Fungal/cytology/physiology ; }, abstract = {Dispersal is a critical ecological process that modulates gene flow and contributes to the maintenance of genetic and taxonomic diversity within ecosystems. Despite an increasing global understanding of the arbuscular mycorrhizal (AM) fungal diversity, distribution and prevalence in different biomes, we have largely ignored the main dispersal mechanisms of these organisms. To provide a geographical and scientific overview of the available data, we systematically searched for the direct evidence on the AM fungal dispersal agents (abiotic and biotic) and different propagule types (i.e. spores, extraradical hyphae or colonized root fragments). We show that the available data (37 articles) on AM fungal dispersal originates mostly from North America, from temperate ecosystems, from biotic dispersal agents (small mammals) and AM fungal spores as propagule type. Much lesser evidence exists from South American, Asian and African tropical systems and other dispersers such as large-bodied birds and mammals and non-spore propagule types. We did not find strong evidence that spore size varies across dispersal agents, but wind and large animals seem to be more efficient dispersers. However, the data is still too scarce to draw firm conclusions from this finding. We further discuss and propose critical research questions and potential approaches to advance the understanding of the ecology of AM fungi dispersal.}, }
@article {pmid32920539, year = {2021}, author = {Zhang, R and Weinbauer, MG and Peduzzi, P}, title = {Aquatic Viruses and Climate Change.}, journal = {Current issues in molecular biology}, volume = {41}, number = {}, pages = {357-380}, doi = {10.21775/cimb.041.357}, pmid = {32920539}, issn = {1467-3045}, mesh = {Carbon/metabolism ; Climate Change ; Ecosystem ; Host Microbial Interactions/physiology ; Humans ; Viruses/*metabolism ; }, abstract = {The viral component in aquatic systems clearly needs to be incorporated into future ocean and inland water climate models. Viruses have the potential to influence carbon and nutrient cycling in aquatic ecosystems significantly. Changing climate likely has both direct and indirect influence on virus-mediated processes, among them an impact on food webs, biogeochemical cycles and on the overall metabolic performance of whole ecosystems. Here we synthesise current knowledge on potential climate-related consequences for viral assemblages, virus-host interactions and virus functions, and in turn, viral processes contributing to climate change. There is a need to increase the accuracy of predictions of climate change impacts on virus- driven processes, particularly of those linked to biological production and biogeochemical cycles. Comprehension of the relationships between microbial/viral processes and global phenomena is essential to predict the influence on as well as the response of the biosphere to global change.}, }
@article {pmid32920408, year = {2021}, author = {Soh, YNA and Kunacheva, C and Menon, S and Webster, RD and Stuckey, DC}, title = {Comparison of soluble microbial product (SMP) production in full-scale anaerobic/aerobic industrial wastewater treatment and a laboratory based synthetic feed anaerobic membrane system.}, journal = {The Science of the total environment}, volume = {754}, number = {}, pages = {142173}, doi = {10.1016/j.scitotenv.2020.142173}, pmid = {32920408}, issn = {1879-1026}, mesh = {Anaerobiosis ; Bioreactors ; Sewage ; *Waste Disposal, Fluid ; *Wastewater ; }, abstract = {This study focused on the characterisation of soluble microbial products (SMPs) produced from a full-scale multi-stage (anaerobic/aerobic) industrial wastewater treatment plant, and contrasted them to the SMPs detected in the effluent of a lab-scale AnMBR treating synthetic wastewater to determine if there were any common solutes detected irrespective of the feed organics. Recently developed analytical methods using gas chromatography coupled mass spectrometry (GC-MS) and liquid chromatography coupled quadrupole-time-of-flight (LC-Q-ToF) for SMP characterisation in a wide molecular weight (MW) range of 30-2000 Da (Da) were applied. Samples collected from the Industrial Wastewater plant were the upflow anaerobic sludge blanket (UASB) influent and effluent, and aerobic membrane bioreactor (MBR) effluent before discharge. The GC-MS detected a spike in cyclooctasulphur in the UASB effluent, an indicator of shock-loading, which disappeared after the MBR process. Alkanes, acids and nitrogenous compounds were found to be the end-products from the GC-MS results, while LC-Q-ToF analysis revealed that eicosanoids, a group of cell-signalling molecules, were produced in the aerobic MBR, and made up 71% of its effluent. A comparison of the submerged anaerobic membrane bioreactor (SAMBR) and aerobic MBR effluents using GC-MS showed that there was only a small degree of similarity between the SMPs, comprising mainly long chain alkanes and phthalate. On the other hand, LC-Q-ToF showed a large contrast in compound composition, mostly having cell-signalling functions, which deepened our understanding of the different metabolic processes occurring in aerobic and anaerobic systems. These data could be useful for future work in various areas such as controlling quorum-sensing and biofilm formation, process optimisation and control, and microbial ecology.}, }
@article {pmid32920334, year = {2020}, author = {Candry, P and Radić, L and Favere, J and Carvajal-Arroyo, JM and Rabaey, K and Ganigué, R}, title = {Mildly acidic pH selects for chain elongation to caproic acid over alternative pathways during lactic acid fermentation.}, journal = {Water research}, volume = {186}, number = {}, pages = {116396}, doi = {10.1016/j.watres.2020.116396}, pmid = {32920334}, issn = {1879-2448}, mesh = {*Caproates ; Carbohydrates ; Fermentation ; Hydrogen-Ion Concentration ; *Lactic Acid ; }, abstract = {Carbohydrate-rich waste streams can be used for bioproduction of medium-chain carboxylic acids (MCCA) such as caproic acid. The carbohydrates in these streams can be converted to lactic acid as the initial fermentation product, which can then be fermented to MCCA by chain elongation. In this process, chain elongators compete for lactic acid with other bacterial groups that, for instance, ferment lactic acid to propionic and acetic acid. Understanding the drivers that control the competition between these two pathways is essential to maximizing MCCA production. This study aimed to investigate the competition between chain elongating and propionic acid producing organisms as a function of operational pH. Operation of long-term lactic acid fermenting reactors with varying pH values showed that pH values above 6 resulted in a propionic acid producing community dominated by Veillonella and Aminobacterium. At pH values below 6, the community moved towards chain elongation, with communities dominated by Caproiciproducens. Short-term incubations showed that rates of lactic acid consumption were strongly reduced at pH below 6 (7.7 ± 1.2 mM lactic acid·h[-1] at pH 6.5; 0.74 ± 0.33 mM lactic acid·h[-1] at pH 5.5). Similar to observations in long-term reactors, when a chain elongating community adapted to pH 5.5 was used for short-term incubations at pH 6.5, propionic acid was the dominant product. The results of this study show that pH below 6 stimulate lactic acid chain elongators through kinetic effects, and potentially improved energetics, providing a tool for microbial management of MCCA-producing systems.}, }
@article {pmid32919387, year = {2021}, author = {Casterline, BW and Paller, AS}, title = {Early development of the skin microbiome: therapeutic opportunities.}, journal = {Pediatric research}, volume = {90}, number = {4}, pages = {731-737}, pmid = {32919387}, issn = {1530-0447}, support = {F30 AI126791/AI/NIAID NIH HHS/United States ; }, mesh = {Child ; Humans ; *Microbiota ; Skin/*microbiology ; }, abstract = {As human skin hosts a diverse microbiota in health and disease, there is an emerging consensus that dysregulated interactions between host and microbiome may contribute to chronic inflammatory disease of the skin. Neonatal skin is a unique habitat, structurally similar to the adult but with a different profile of metabolic substrates, environmental stressors, and immune activity. The surface is colonized within moments of birth with a bias toward maternal strains. Initial colonists are outcompeted as environmental exposures increase and host skin matures. Nonetheless, early life microbial acquisitions may have long-lasting effects on health through modulation of host immunity and competitive interactions between bacteria. Microbial ecology and its influence on health have been of interest to dermatologists for >50 years, and an explosion of recent interest in the microbiome has prompted ongoing investigations of several microbial therapeutics for dermatological disease. In this review, we consider how recent insight into the host and microbial factors driving development of the skin microbiome in early life offers new opportunities for therapeutic intervention. IMPACT: Advancement in understanding molecular mechanisms of bacterial competition opens new avenues of investigation into dermatological disease. Primary development of the skin microbiome is determined by immunological features of the cutaneous habitat. Understanding coordinated microbial and immunological development in the pediatric patient requires a multidisciplinary synthesis of primary literature.}, }
@article {pmid32919372, year = {2020}, author = {Frommeyer, B and Fiedler, AW and Oehler, SR and Hanson, BT and Loy, A and Franchini, P and Spiteller, D and Schleheck, D}, title = {Environmental and Intestinal Phylum Firmicutes Bacteria Metabolize the Plant Sugar Sulfoquinovose via a 6-Deoxy-6-sulfofructose Transaldolase Pathway.}, journal = {iScience}, volume = {23}, number = {9}, pages = {101510}, pmid = {32919372}, issn = {2589-0042}, support = {I 2320/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Bacterial degradation of the sugar sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) produced by plants, algae, and cyanobacteria, is an important component of the biogeochemical carbon and sulfur cycles. Here, we reveal a third biochemical pathway for primary SQ degradation in an aerobic Bacillus aryabhattai strain. An isomerase converts SQ to 6-deoxy-6-sulfofructose (SF). A novel transaldolase enzyme cleaves the SF to 3-sulfolactaldehyde (SLA), while the non-sulfonated C3-(glycerone)-moiety is transferred to an acceptor molecule, glyceraldehyde phosphate (GAP), yielding fructose-6-phosphate (F6P). Intestinal anaerobic bacteria such as Enterococcus gilvus, Clostridium symbiosum, and Eubacterium rectale strains also express transaldolase pathway gene clusters during fermentative growth with SQ. The now three known biochemical strategies for SQ catabolism reflect adaptations to the aerobic or anaerobic lifestyle of the different bacteria. The occurrence of these pathways in intestinal (family) Enterobacteriaceae and (phylum) Firmicutes strains further highlights a potential importance of metabolism of green-diet SQ by gut microbial communities to, ultimately, hydrogen sulfide.}, }
@article {pmid32918562, year = {2021}, author = {Ennis, NJ and Dharumaduri, D and Bryce, JG and Tisa, LS}, title = {Metagenome Across a Geochemical Gradient of Indian Stone Ruins Found at Historic Sites in Tamil Nadu, India.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {385-395}, pmid = {32918562}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Climate ; India ; *Metagenome ; Microbiota/*genetics ; Minerals/analysis ; Quartz/analysis ; Silicon Dioxide/*chemistry ; }, abstract = {Although stone surfaces seem unlikely to be habitable, they support microbial life. Life on these surfaces are subjected to many varying harsh conditions and require the inhabitants to exhibit resistance to environmental factors including UV irradiation, toxic metal exposure, and fluctuating temperatures and humidity. Here we report the effect of hosting stone geochemistry on the microbiome of stone ruins found in Tamil Nadu, India. The microbial communities found on the two lithologies, granite and granodiorite, hosted distinct populations of bacteria. Geochemical composition analysis of sampled stones revealed quartz mineral content as a major driver of microbial community structure, particularly promoting community richness and proportions of Cyanobacteria and Deinococcus-Thermus. Other geochemical parameters including ilmenite, albite, anorthite, and orthoclase components or elemental concentrations (Ti, Fe, Mn, Na, and K) also influenced community structure to a lesser degree than quartz. Core members of the stone microbiome community found on both lithologies were also identified and included Cyanobacteria (Chroococcidiopsaceae and Dapisostemonum CCIBt 3536), Rubrobacter, and Deinococcus. A cluster of taxa including Sphingomonas, Geodermatophilus, and Truepera were mostly found in the granodiorite samples. Community diversity correlated with quartz mineral content in these samples may indicate that the microbial communities that attach to quartz surfaces may be transient and regularly changing. This work has expanded our understanding of built-stone microbial community structure based on lithology and geochemistry.}, }
@article {pmid32918153, year = {2021}, author = {Sajjad, W and Ali, B and Bahadur, A and Ghimire, PS and Kang, S}, title = {Bacterial Diversity and Communities Structural Dynamics in Soil and Meltwater Runoff at the Frontier of Baishui Glacier No.1, China.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {370-384}, pmid = {32918153}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; China ; Ecosystem ; Ice Cover/chemistry/*microbiology ; *Microbiota ; Soil/chemistry ; *Soil Microbiology ; Water/chemistry ; *Water Microbiology ; }, abstract = {Comprehensive knowledge of bacterial ecology mainly in supraglacial habitats is pivotal particularly at the frontier of accelerated glacier retreat. In this study, bacterial diversity and community composition in glacial soil and meltwater runoff at the frontier of Baishui Glacier No.1 were evaluated using high throughput sequencing. Significant variations in the physiochemical parameters formed an ecological gradient between soil and meltwater runoff. Based on the richness and evenness indexes, the bacterial diversity was relatively higher in soil compared with meltwater runoff. Hierarchical clustering and bi-plot ordination revealed that the taxonomic composition of soil samples was highly similar and significantly influenced by the ecological parameters than the meltwater runoff. The overall relative abundance trend of bacterial phyla and genera were greatly varied in soil and water samples. The relative abundance of Proteobacteria was higher in water runoff samples (40.5-87%) compared with soil samples (32-52.7%). Proteobacteria, Firmicutes, and a little part of Cyanobacteria occupied a major portion of water runoff while the soil was dominated by Acidobacteria (6-16.2%), Actinobacteria (5-16%), Bacteroidetes (0.5-8.8%), and Cyanobacteria (0.1-8.3%) besides Proteobacteria and Firmicutes. Higher numbers of biomarkers were found in soil group compared with the water group. The study area is diverse in terms of richness, while community structures are not evenly distributed. This study provides a preliminary understanding of the bacterial diversity and shifts in community structure in soil and meltwater runoff at the frontier of the glacial. The findings revealed that the environmental factors are a significantly strong determinant of bacterial community structures in such a closely linked ecosystem.}, }
@article {pmid32917751, year = {2020}, author = {Park, SJ and Andrei, A&#x15e; and Bulzu, PA and Kavagutti, VS and Ghai, R and Mosier, AC}, title = {Expanded Diversity and Metabolic Versatility of Marine Nitrite-Oxidizing Bacteria Revealed by Cultivation- and Genomics-Based Approaches.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {22}, pages = {}, pmid = {32917751}, issn = {1098-5336}, mesh = {Bacteria/*classification/isolation &amp; purification/*metabolism ; Geologic Sediments/microbiology ; Metabolic Networks and Pathways ; *Microbiota ; Nitrites/*metabolism ; Oxidation-Reduction ; Republic of Korea ; Seawater/microbiology ; }, abstract = {Nitrite-oxidizing bacteria (NOB) are ubiquitous and abundant microorganisms that play key roles in global nitrogen and carbon biogeochemical cycling. Despite recent advances in understanding NOB physiology and taxonomy, currently very few cultured NOB or representative NOB genome sequences from marine environments exist. In this study, we employed enrichment culturing and genomic approaches to shed light on the phylogeny and metabolic capacity of marine NOB. We successfully enriched two marine NOB (designated MSP and DJ) and obtained a high-quality metagenome-assembled genome (MAG) from each organism. The maximum nitrite oxidation rates of the MSP and DJ enrichment cultures were 13.8 and 30.0 μM nitrite per day, respectively, with these optimum rates occurring at 0.1 mM and 0.3 mM nitrite, respectively. Each enrichment culture exhibited a different tolerance to various nitrite and salt concentrations. Based on phylogenomic position and overall genome relatedness indices, both NOB MAGs were proposed as novel taxa within the Nitrospinota and Nitrospirota phyla. Functional predictions indicated that both NOB MAGs shared many highly conserved metabolic features with other NOB. Both NOB MAGs encoded proteins for hydrogen and organic compound metabolism and defense mechanisms for oxidative stress. Additionally, these organisms may have the genetic potential to produce cobalamin (an essential enzyme cofactor that is limiting in many environments) and, thus, may play an important role in recycling cobalamin in marine sediment. Overall, this study appreciably expands our understanding of the Nitrospinota and Nitrospirota phyla and suggests that these NOB play important biogeochemical roles in marine habitats.IMPORTANCE Nitrification is a key process in the biogeochemical and global nitrogen cycle. Nitrite-oxidizing bacteria (NOB) perform the second step of aerobic nitrification (converting nitrite to nitrate), which is critical for transferring nitrogen to other organisms for assimilation or energy. Despite their ecological importance, there are few cultured or genomic representatives from marine systems. Here, we obtained two NOB (designated MSP and DJ) enriched from marine sediments and estimated the physiological and genomic traits of these marine microbes. Both NOB enrichment cultures exhibit distinct responses to various nitrite and salt concentrations. Genomic analyses suggest that these NOB are metabolically flexible (similar to other previously described NOB) yet also have individual genomic differences that likely support distinct niche distribution. In conclusion, this study provides more insights into the ecological roles of NOB in marine environments.}, }
@article {pmid32917275, year = {2020}, author = {Modin, O and Liébana, R and Saheb-Alam, S and Wilén, BM and Suarez, C and Hermansson, M and Persson, F}, title = {Hill-based dissimilarity indices and null models for analysis of microbial community assembly.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {132}, pmid = {32917275}, issn = {2049-2618}, mesh = {Archaea/*isolation &amp; purification ; Bacteria/*isolation &amp; purification ; *Computer Simulation ; *Microbiota ; *Software ; }, abstract = {BACKGROUND: High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases, and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.<br><br>RESULTS: Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems.<br><br>CONCLUSIONS: Hill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines. Video Abstract.}, }
@article {pmid32916620, year = {2020}, author = {Lukumbuzya, M and Kristensen, JM and Kitzinger, K and Pommerening-Röser, A and Nielsen, PH and Wagner, M and Daims, H and Pjevac, P}, title = {A refined set of rRNA-targeted oligonucleotide probes for in situ detection and quantification of ammonia-oxidizing bacteria.}, journal = {Water research}, volume = {186}, number = {}, pages = {116372}, doi = {10.1016/j.watres.2020.116372}, pmid = {32916620}, issn = {1879-2448}, mesh = {*Ammonia ; *Ecosystem ; In Situ Hybridization, Fluorescence ; Oligonucleotide Probes/genetics ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Ammonia-oxidizing bacteria (AOB) of the betaproteobacterial genera Nitrosomonas and Nitrosospira are key nitrifying microorganisms in many natural and engineered ecosystems. Since many AOB remain uncultured, fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has been one of the most widely used approaches to study the community composition, abundance, and other features of AOB directly in environmental samples. However, the established and widely used AOB-specific 16S rRNA-targeted FISH probes were designed up to two decades ago, based on much smaller rRNA gene sequence datasets than available today. Several of these probes cover their target AOB lineages incompletely and suffer from a weak target specificity, which causes cross-hybridization of probes that should detect different AOB lineages. Here, a set of new highly specific 16S rRNA-targeted oligonucleotide probes was developed and experimentally evaluated that complements the existing probes and enables the specific detection and differentiation of the known, major phylogenetic clusters of betaproteobacterial AOB. The new probes were successfully applied to visualize and quantify AOB in activated sludge and biofilm samples from seven pilot- and full-scale wastewater treatment systems. Based on its improved target group coverage and specificity, the refined probe set will facilitate future in situ analyses of AOB.}, }
@article {pmid32915303, year = {2021}, author = {Chan, YF and Chiang, PW and Tandon, K and Rogozin, D and Degermendzhi, A and Zykov, V and Tang, SL}, title = {Spatiotemporal Changes in the Bacterial Community of the Meromictic Lake Uchum, Siberia.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {357-369}, pmid = {32915303}, issn = {1432-184X}, support = {No. 19-05-00428//&#x420;&#x43e;&#x441;&#x441;&#x438;&#x439;&#x441;&#x43a;&#x438;&#x439; &#x424;&#x43e;&#x43d;&#x434; &#x424;&#x443;&#x43d;&#x434;&#x430;&#x43c;&#x435;&#x43d;&#x442;&#x430;&#x43b;&#x44c;&#x43d;&#x44b;&#x445; &#x418;&#x441;&#x441;&#x43b;&#x435;&#x434;&#x43e;&#x432;&#x430;&#x43d;&#x438;&#x439; (&#x420;&#x424;&#x424;&#x418;) (RU)/ ; No. 18-45-243002//Krasnoyarsk Regional Fund of Science/ ; 105-2923-B-001-001-MY3//Ministry of Science and Technology, Taiwan/ ; 108-2811-M-001-603//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Hydrogen Sulfide/analysis/metabolism ; Lakes/chemistry/*microbiology ; *Microbiota ; Oxidation-Reduction ; Oxygen/analysis ; Seasons ; Siberia ; Sulfates/metabolism ; Sulfur/metabolism ; }, abstract = {Lake Uchum is a newly defined meromictic lake in Siberia with clear seasonal changes in its mixolimnion. This study characterized the temporal dynamics and vertical profile of bacterial communities in oxic and anoxic zones of the lake across all four seasons: October (autumn), March (winter), May (spring), and August (summer). Bacterial richness and diversity in the anoxic zone varied widely between time points. Proteobacteria was the dominant bacterial phylum throughout the oxic and anoxic zones across all four seasons. Alphaproteobacteria (Loktanella) and Gammaproteobacteria (Aliidiomarina) exhibited the highest abundance in the oxic and anoxic zone, respectively. Furthermore, there was a successional shift in sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria in the anoxic zone across the seasons. The most dominant SRB, Desulfonatronovibrio sp., is likely one of the main producers of hydrogen sulfide (H2S) and typically accumulates the most H2S in winter. The representative anoxygenic phototrophic bacterial group in Lake Uchum was purple sulfur bacteria (PSB). PSB were dominant (60.76%) in summer, but only had 0.2-1.5% relative abundance from autumn to spring. Multivariate analysis revealed that the abundance of these SRB and PSB correlated to the concentration of H2S in Lake Uchum. Taken together, this study provides insights into the relationships between changes in bacterial community and environmental features in Lake Uchum.}, }
@article {pmid32914254, year = {2021}, author = {Chen, J and Xie, P and Yu, D and Xie, L and Zeng, C and Chen, J}, title = {Dynamic Change of Sedimental Microbial Community During Black Bloom-an In Situ Enclosure Simulation Study.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {304-313}, pmid = {32914254}, issn = {1432-184X}, support = {2012ZX07101-010//Major Science and Technology Program for Water Pollution Control and Treatment/ ; 2014FBZ02, 2014FB15//State Key Laboratory of Freshwater Ecology and Biotechnology/ ; 31901081//National Natural Science Foundation of China/ ; }, mesh = {Cluster Analysis ; Cyanobacteria/classification/genetics/isolation &amp; purification ; *Eutrophication ; Geologic Sediments/chemistry/*microbiology ; Lakes/chemistry/microbiology ; *Microbiota/genetics ; Odorants/analysis ; Phylogeny ; Water Pollutants, Chemical/analysis ; }, abstract = {Black bloom is a worldwide environmental problem. Sediment microbes play important roles in the process of black bloom. The dynamic change of sedimental microbial community and their potential link between taste and odor compounds during black bloom was investigated in an in situ black bloom enclosure simulation experiment. Through high-throughput sequencing and analysis, pronounced shifts of sedimental microbial community were observed on the 3rd and 7th day in the black bloom group. Microbes in Cyanobacteria, Verrucomicrobia, Planctomycetes, and Actinobacteria were obviously increased, while microbes from the phyla OP8, Chloroflexi, and Acidobacteria were decreased significantly. RDA analysis revealed that the concentrations of chlorophyll a (Chla), total phosphorus (TP), and turbidity (NTU) in the water and the TP, TN concentrations in the sediment were the main environmental factors that affect the microbial community in the sediment. Correlation analysis revealed that microbes Dechloromonas sp. (OTU003567 and OTU000093), Desulfococcus sp. (OTU000911), Chromatiaceae (OTU001222), and Methanosaeta sp. (OTU004809) were positively correlated with the taste and odor substances in the sediment, such as dimethyl sulfide (DMS), β-ionone, β-cyclocitral and geosmin. The sedimental microbial community gradually recovered in the late phase of black bloom, indicating the stability and self-recovery ability of the sedimental microbial community during black bloom. Noteworthily, we observed many possible pathogens increased significantly during the black bloom, which alerts us to keep away from contaminated sediment when black bloom occurred.}, }
@article {pmid32911871, year = {2020}, author = {Mbareche, H and Dumont-Leblond, N and Bilodeau, GJ and Duchaine, C}, title = {An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists.}, journal = {Life (Basel, Switzerland)}, volume = {10}, number = {9}, pages = {}, pmid = {32911871}, issn = {2075-1729}, abstract = {High-throughput DNA sequencing (HTS) has changed our understanding of the microbial composition present in a wide range of environments. Applying HTS methods to air samples from different environments allows the identification and quantification (relative abundance) of the microorganisms present and gives a better understanding of human exposure to indoor and outdoor bioaerosols. To make full use of the avalanche of information made available by these sequences, repeated measurements must be taken, community composition described, error estimates made, correlations of microbiota with covariates (variables) must be examined, and increasingly sophisticated statistical tests must be conducted, all by using bioinformatics tools. Knowing which analysis to conduct and which tools to apply remains confusing for bioaerosol scientists, as a litany of tools and data resources are now available for characterizing microbial communities. The goal of this review paper is to offer a guided tour through the bioinformatics tools that are useful in studying the microbial ecology of bioaerosols. This work explains microbial ecology features like alpha and beta diversity, multivariate analyses, differential abundances, taxonomic analyses, visualization tools and statistical tests using bioinformatics tools for bioaerosol scientists new to the field. It illustrates and promotes the use of selected bioinformatic tools in the study of bioaerosols and serves as a good source for learning the "dos and don'ts" involved in conducting a precise microbial ecology study.}, }
@article {pmid32910439, year = {2020}, author = {Callewaert, C and Ravard Helffer, K and Lebaron, P}, title = {Skin Microbiome and its Interplay with the Environment.}, journal = {American journal of clinical dermatology}, volume = {21}, number = {Suppl 1}, pages = {4-11}, pmid = {32910439}, issn = {1179-1888}, mesh = {Animals ; Humans ; Humpback Whale/*microbiology ; Microbiota/*physiology ; Phylogeny ; Skin/*microbiology ; *Water Microbiology ; }, abstract = {Advances in sequencing, bioinformatics and analytics now allow the structure, function and interrelations of whole microbial communities to be studied in greater detail. Collaborative efforts and multidisciplinary studies, crossing the boundary between environmental and medical microbiology, have allowed specific environmental, animal and human microbiomes to be characterized. One of the main challenges for microbial ecology is to link the phylogenetic diversity of host-associated microbes to their functional roles within the community. Much remains to be learned on the way microbes colonize the skin of different living organisms and the way the skin microbiome reacts to the surrounding environment (air, water, etc.). In this review, we discuss examples of recent studies that have used modern technology to provide insights into microbial communities in water and on skin, such as those in natural resources (thermal spring water), large mammals (humpback whales) and humans (the skin microbiome). The results of these studies demonstrate how a greater understanding of the structure and functioning of microbiota, together with their interactions with the environment, may facilitate the discovery of new probiotics or postbiotics, provide indicators for the quality of the environment, and show how changes in lifestyle and living environment, such as urbanization, can impact on the skin microbiome and skin health and disease in humans.}, }
@article {pmid32909073, year = {2021}, author = {Mootapally, C and Mahajan, MS and Nathani, NM}, title = {Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {540-548}, pmid = {32909073}, issn = {1432-184X}, support = {PDF/2016/001239//Science and Engineering Research Board/ ; PDF/2016/000190//Science and Engineering Research Board/ ; }, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Drug Resistance, Bacterial/genetics ; Ecosystem ; Genes, Bacterial/genetics ; Geologic Sediments/*microbiology ; Metagenome/*genetics ; Oceans and Seas ; Plasmids/*genetics ; Seawater/*microbiology ; Virulence Factors/genetics ; }, abstract = {Plasmidomes have become the research area of interest for ecologists exploring bacteria rich ecosystems. Marine environments are among such niche that host a huge number of microbes and have a complex environment which pose the need to study these bacterial indicators of horizontal gene transfer events for survival and stability. The plasmid content of the metagenomics data from 8 sediment samples of the Gulfs of Kathiawar and an open Arabian Sea sample was screened. The reads corresponding to hits against the plasmid database were assembled and studied for diversity using Kraken and functional content using MG-RAST. The sequences were also checked for resistome and virulence factors. The replicon hosts were overall dominated by Proteobacteria, Firmicutes, and Actinobacteria while red algae specific to the Kutch samples. The genes encoded were dominant in the flagella motility and type VI secretion systems. Overall, results from the study confirmed that the plasmids encoded traits for metal, antibiotic, and phage resistance along with virulence systems, and these would be conferring benefit to the hosts. The study throws insights into the environmental role of the plasmidome in adaptation of the microbes in the studied sites to the environmental stresses.}, }
@article {pmid32906802, year = {2020}, author = {Nakai, R and Naganuma, T and Tazato, N and Morohoshi, S and Koide, T}, title = {Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage.}, journal = {Microorganisms}, volume = {8}, number = {9}, pages = {}, pmid = {32906802}, issn = {2076-2607}, support = {KAKENHI Grant Number JP13J03441//Japan Society for the Promotion of Science/ ; KAKENHI Grant Number JP15H05620//Japan Society for the Promotion of Science/ ; KAKENHI Grant Number JP19H05683//Ministry of Education, Culture, Sports, Science and Technology/ ; KAKENHI Grant Number JP19H05679//Ministry of Education, Culture, Sports, Science and Technology/ ; KAKENHI Grant Number JP23570117//Japan Society for the Promotion of Science/ ; }, abstract = {Rhizobiales bacterium strain IZ6 is a novel filterable bacterium that was isolated from a suspension filtrate (<0.22 µm) of soil collected in Shimane Prefecture, western Japan. Additional closely related isolates were recovered from filterable fractions of terrestrial environmental samples collected from other places in Japan; the Gobi Desert, north-central China; and Svalbard, Arctic Norway. These findings indicate a wide distribution of this lineage. This study reports the cell variation and genomic structure of IZ6. When cultured at lower temperatures (4 °C and 15 °C), this strain contained ultra-small cells and cell-like particles in the filtrate. PacBio sequencing revealed that this chromosome (3,114,641 bp) contained 3150 protein-coding, 51 tRNA, and three rRNA genes. IZ6 showed low 16S rRNA gene sequence identity (<97%) and low average nucleotide identity (<76%) with its closest known relative, Flaviflagellibacter deserti. Unlike the methylotrophic bacteria and nitrogen-fixing bacteria in related genera, there were no genes that encoded enzymes for one-carbon-compound utilization and nitrogen fixation in the IZ6 genome; the genes related to nitrate and nitrite reductase are retained and those related to the cell membrane function tend to be slightly enriched in the genome. This genomic information helps elucidate the eco-physiological function of a phenotypically heterogeneous and diverse Rhizobiales group.}, }
@article {pmid32903459, year = {2020}, author = {Álvarez-Rodríguez, I and Arana, L and Ugarte-Uribe, B and Gómez-Rubio, E and Martín-Santamaría, S and Garbisu, C and Alkorta, I}, title = {Type IV Coupling Proteins as Potential Targets to Control the Dissemination of Antibiotic Resistance.}, journal = {Frontiers in molecular biosciences}, volume = {7}, number = {}, pages = {201}, pmid = {32903459}, issn = {2296-889X}, abstract = {The increase of infections caused by multidrug-resistant bacteria, together with the loss of effectiveness of currently available antibiotics, represents one of the most serious threats to public health worldwide. The loss of human lives and the economic costs associated to the problem of the dissemination of antibiotic resistance require immediate action. Bacteria, known by their great genetic plasticity, are capable not only of mutating their genes to adapt to disturbances and environmental changes but also of acquiring new genes that allow them to survive in hostile environments, such as in the presence of antibiotics. One of the major mechanisms responsible for the horizontal acquisition of new genes (e.g., antibiotic resistance genes) is bacterial conjugation, a process mediated by mobile genetic elements such as conjugative plasmids and integrative conjugative elements. Conjugative plasmids harboring antibiotic resistance genes can be transferred from a donor to a recipient bacterium in a process that requires physical contact. After conjugation, the recipient bacterium not only harbors the antibiotic resistance genes but it can also transfer the acquired plasmid to other bacteria, thus contributing to the spread of antibiotic resistance. Conjugative plasmids have genes that encode all the proteins necessary for the conjugation to take place, such as the type IV coupling proteins (T4CPs) present in all conjugative plasmids. Type VI coupling proteins constitute a heterogeneous family of hexameric ATPases that use energy from the ATP hydrolysis for plasmid transfer. Taking into account their essential role in bacterial conjugation, T4CPs are attractive targets for the inhibition of bacterial conjugation and, concomitantly, the limitation of antibiotic resistance dissemination. This review aims to compile present knowledge on T4CPs as a starting point for delving into their molecular structure and functioning in future studies. Likewise, the scientific literature on bacterial conjugation inhibitors has been reviewed here, in an attempt to elucidate the possibility of designing T4CP-inhibitors as a potential solution to the dissemination of multidrug-resistant bacteria.}, }
@article {pmid32903319, year = {2020}, author = {Møller, TE and van der Bilt, WGM and Roerdink, DL and Jørgensen, SL}, title = {Microbial Community Structure in Arctic Lake Sediments Reflect Variations in Holocene Climate Conditions.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1520}, pmid = {32903319}, issn = {1664-302X}, abstract = {The reconstruction of past climate variability using physical and geochemical parameters from lake sedimentary records is a well-established and widely used approach. These geological records are also known to contain large and active microbial communities, believed to be responsive to their surroundings at the time of deposition, and proceed to interact intimately with their physical and chemical environment for millennia after deposition. However, less is known about the potential legacy of past climate conditions on the contemporary microbial community structure. We analysed two Holocene-length (past 10 ka BP) sediment cores from the glacier-fed Ymer Lake, located in a highly climate-sensitive region on south-eastern Greenland. By combining physical proxies, solid as well as fluid geochemistry, and microbial population profiling in a comprehensive statistical framework, we show that the microbial community structure clusters according to established lithological units, and thus captures past environmental conditions and climatic transitions. Further, comparative analyses of the two sedimentary records indicates that the manifestation of regional climate depends on local settings such as water column depth, which ultimately constrains microbial variability in the deposited sediments. The strong coupling between physical and geochemical shifts in the lake and microbial variation highlights the potential of molecular microbiological data to strengthen and refine existing sedimentological classifications of past environmental conditions and transitions. Furthermore, this coupling implies that microbially controlled transformation and partitioning of geochemical species (e.g., manganese and sulphate) in Ymer lake today is still affected by climatic conditions that prevailed thousands of years back in time.}, }
@article {pmid32901388, year = {2021}, author = {González-Dominici, LI and Saati-Santamaría, Z and García-Fraile, P}, title = {Genome Analysis and Genomic Comparison of the Novel Species Arthrobacter ipsi Reveal Its Potential Protective Role in Its Bark Beetle Host.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {471-482}, pmid = {32901388}, issn = {1432-184X}, support = {19-09072S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; CLU-2018-04//Junta de Castilla y Le&#xf3;n (ES)/ ; }, mesh = {Animals ; Antibiosis ; Arthrobacter/classification/genetics/*physiology ; Coleoptera/*microbiology ; DNA, Bacterial/genetics ; Fungi/growth &amp; development ; Genes, Bacterial/genetics ; Genome, Bacterial/*genetics ; Host Microbial Interactions ; Phenotype ; Phylogeny ; Pinus/parasitology ; Plant Bark/*parasitology ; Plant Diseases/parasitology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The pine engraver beetle, Ips acuminatus Gyll, is a bark beetle that causes important damages in Scots pine (Pinus sylvestris) forests and plantations. As almost all higher organisms, Ips acuminatus harbours a microbiome, although the role of most members of its microbiome is not well understood. As part of a work in which we analysed the bacterial diversity associated to Ips acuminatus, we isolated the strain Arthrobacter sp. IA7. In order to study its potential role within the bark beetle holobiont, we sequenced and explored its genome and performed a pan-genome analysis of the genus Arthrobacter, showing specific genes of strain IA7 that might be related with its particular role in its niche. Based on these investigations, we suggest several potential roles of the bacterium within the beetle. Analysis of genes related to secondary metabolism indicated potential antifungal capability, confirmed by the inhibition of several entomopathogenic fungal strains (Metarhizium anisopliae CCF0966, Lecanicillium muscarium CCF6041, L. muscarium CCF3297, Isaria fumosorosea CCF4401, I. farinosa CCF4808, Beauveria bassiana CCF4422 and B. brongniartii CCF1547). Phylogenetic analyses of the 16S rRNA gene, six concatenated housekeeping genes (tuf-secY-rpoB-recA-fusA-atpD) and genome sequences indicated that strain IA7 is closely related to A. globiformis NBRC 12137[T] but forms a new species within the genus Arthrobacter; this was confirmed by digital DNA-DNA hybridization (37.10%) and average nucleotide identity (ANIb) (88.9%). Based on phenotypic and genotypic features, we propose strain IA7[T] as the novel species Arthrobacter ipsi sp. nov. (type strain IA7[T] = CECT 30100[T] = LMG 31782[T]) and suggest its protective role for its host.}, }
@article {pmid32901387, year = {2021}, author = {Wu, C and Wei, X and Hu, Z and Liu, Y and Hu, Y and Qin, H and Chen, X and Wu, J and Ge, T and Zhran, M and Su, Y}, title = {Diazotrophic Community Variation Underlies Differences in Nitrogen Fixation Potential in Paddy Soils Across a Climatic Gradient in China.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {425-436}, pmid = {32901387}, issn = {1432-184X}, support = {2017YFD0800104//National Key Research and Development program/ ; 41977100//National Natural Science Foundation of China/ ; 41771300//National Natural Science Foundation of China/ ; 2018WK4012//Hunan Province Base for Scientific and Technological Innovation Cooperation/ ; 2017QNCXTD_GTD//Youth Innovation Team Project of Institute of Subtropical Agriculture, Chinese Academy of Sciences/ ; 2019JJ10003//Natural Science Foundation of&#xa0;Hunan Province/ ; }, mesh = {Carbon/analysis ; *Climate ; Hydrogen-Ion Concentration ; Microbiota/genetics/*physiology ; Nitrogen/analysis/metabolism ; Nitrogen Fixation/*physiology ; Nitrogenase/analysis/metabolism ; Oryza ; Oxidoreductases/genetics ; Phosphates/analysis ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Biological nitrogen (N2) fixation as a source of new N input into the soil by free-living diazotrophs is important for achieving sustainable rice agriculture. However, the dominant environmental drivers or factors influencing N2 fixation and the functional significance of the diazotroph community structure in paddy soil across a climatic gradient are not yet well understood. Thus, we characterized the diazotroph community and identified the ecological predictors of N2 fixation potential in four different climate zones (mid-temperate, warm-temperate, subtropical, and tropical paddy soils) in eastern China. Comprehensive nifH gene sequencing, functional activity detection, and correlation analysis with environmental factors were estimated. The potential nitrogenase activity (PNA) was highest in warm-temperate regions, where it was 6.2-, 2.9-, and 2.2-fold greater than in the tropical, subtropical, and mid-temperate regions, respectively; nifH gene abundance was significantly higher in warm-temperate and subtropical zones than in the tropical or mid-temperate zones. Diazotroph diversity was significantly higher in the tropical climate zone and significantly lower in the mid-temperate zone. Non-metric multidimensional scaling and canonical correlation analysis indicated that paddy soil diazotroph populations differed significantly among the four climate zones, mainly owing to differences in climate and soil pH. Structural equation models and automatic linear models revealed that climate and nutrients indirectly affected PNA by affecting soil pH and diazotroph community, respectively, while diazotroph community, C/P, and nifH gene abundance directly affected PNA. And C/P ratio, pH, and the diazotroph community structure were the main predictors of PNA in paddy soils. Collectively, the differences in diazotroph community structure have ecological significance, with important implications for the prediction of soil N2-fixing functions under climate change scenarios.}, }
@article {pmid32901386, year = {2021}, author = {Petrzik, K and Lukavský, J and Koloniuk, I}, title = {Novel Virus on Filamentous Arthronema africanum Cyanobacterium.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {454-459}, pmid = {32901386}, issn = {1432-184X}, support = {RVO60077344//institutional support/ ; RVO67985939//institutional support/ ; Biocirtech T01000048//Technologick&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; }, mesh = {Amino Acid Sequence ; Bacteriophages/classification/genetics/*physiology ; Base Composition ; Cyanobacteria/*virology ; DNA, Viral/genetics ; Fresh Water/microbiology ; Genome Size ; Genome, Viral/genetics ; Host Specificity ; Lysogeny ; Phylogeny ; Podoviridae/classification/genetics/*physiology ; Sequence Analysis, DNA ; Viral Proteins/genetics ; }, abstract = {Widely distributed in water environments and in soil, cyanobacteria are hosts of lysogenic or lytic bacterioviruses. A novel, probably lysogenic virus (phage) for which the name Arthronema africanum virus TR020 (Aa-TR020) is proposed, has been isolated from filamentous freshwater cyanobacterium Arthronema africanum. The virus formed turbid plaques on plate culture of A. africanum strain 1980/01 but not on other Arthronema strain and other bacterial species. The genome of Aa-TR020 is linear molecule of dsDNA, 44,805 bp in length with 216 bp long terminal repeats and with G + C content of 46%. Fifty-five genes organized on plus and minus strands were predicted there. The genome size, gene arrangement, and selected protein sequences showed relatedness to Phormidium virus Pf-WMP3 and other viruses known to infect cyanobacteria and classified in the family Podoviridae.}, }
@article {pmid32897365, year = {2020}, author = {Rodrigues, GR and Pinto, OHB and Schroeder, LF and Fernandes, GDR and Costa, OYA and Quirino, BF and Kuramae, EE and Barreto, CC}, title = {Unraveling the xylanolytic potential of Acidobacteria bacterium AB60 from Cerrado soils.}, journal = {FEMS microbiology letters}, volume = {367}, number = {18}, pages = {}, doi = {10.1093/femsle/fnaa149}, pmid = {32897365}, issn = {1574-6968}, mesh = {Acidobacteria/classification/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Brazil ; Cellulose/metabolism ; Genome, Bacterial/genetics ; Hydrolysis ; Pectins/metabolism ; Phylogeny ; Polysaccharides/metabolism ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Xylans/*metabolism ; }, abstract = {The presence of genes for glycosyl hydrolases in many Acidobacteria genomes indicates an important role in the degradation of plant cell wall material. Acidobacteria bacterium AB60 was obtained from Cerrado oligotrophic soil in Brazil, where this phylum is abundant. The 16S rRNA gene analyses showed that AB60 was closely related to the genera Occallatibacter and Telmatobacter. However, AB60 grew on xylan as carbon source, which was not observed in Occallatibacter species; but growth was not detected on medium containing carboxymethyl cellulose, as observed in Telmatobacter. Nevertheless, the genome analysis of AB60 revealed genes for the enzymes involved in cellulose as well as xylan degradation. In addition to enzymes involved in xylan degradation, α-l-rhamnosidase was detected in the cultures of AB60. Functional screening of a small-insert genomic library did not identify any clones capable of carboxymethyl cellulose degradation, but open reading frames coding α-l-arabinofuranosidase and α-l-rhamnosidase were present in clones showing xylan degradation halos. Both enzymes act on the lateral chains of heteropolymers such as pectin and some hemicelluloses. These results indicate that the hydrolysis of α-linked sugars may offer a metabolic niche for slow-growing Acidobacteria, allowing them to co-exist with other plant-degrading microbes that hydrolyze β-linked sugars from cellulose or hemicellulose backbones.}, }
@article {pmid32897356, year = {2020}, author = {Bandini, F and Misci, C and Taskin, E and Cocconcelli, PS and Puglisi, E}, title = {Biopolymers modulate microbial communities in municipal organic waste digestion.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {10}, pages = {}, doi = {10.1093/femsec/fiaa183}, pmid = {32897356}, issn = {1574-6941}, mesh = {Anaerobiosis ; Biopolymers ; Bioreactors ; Digestion ; *Microbiota ; Phylogeny ; *Refuse Disposal ; }, abstract = {The development of biopolymers has raised issues about their recalcitrance in the environment. Their disposal is mainly carried out with the organic fraction of municipal solid waste (OFMSW) through thermophilic anaerobic digestion and aerobic composting, bioprocesses aimed at turning organic matter into biogas and compost. However, the effects of biopolymers on OFMSW treatment, on the final compost and on the microbial communities involved are partly unexplored. In this study, the OFMSW treatment was reproduced on a laboratory-scale respecting real plant conditions and testing the impacts of mixing polylactic acid (PLA) and starch-based bioplastic (SBB) separately. The dynamics of bacterial, archaeal and fungal communities during the process was screened by high-throughput sequencing (HTS) of phylogenetic amplicons. Starch-based bioplastic showed a minor and heterogeneous microbial diversity between the anaerobic and aerobic phases. Contrariwise, PLA treatment resulted in wider and more diverse bacterial and fungal communities for the compost and the aerobic biofilm. Since the biodiversity in compost may play a crucial role in its stability and safety, the modulation of environmental microbial communities induced by higher concentrations of PLA in OFMSW treatment can pose relevant issues.}, }
@article {pmid32896070, year = {2020}, author = {Fei, C and Ochsenkühn, MA and Shibl, AA and Isaac, A and Wang, C and Amin, SA}, title = {Quorum sensing regulates 'swim-or-stick' lifestyle in the phycosphere.}, journal = {Environmental microbiology}, volume = {22}, number = {11}, pages = {4761-4778}, pmid = {32896070}, issn = {1462-2920}, support = {AD179//New York University Abu Dhabi/ ; NA19NOS4780183//National Oceanic and Atmospheric Administration (NOAA)/ ; }, mesh = {4-Butyrolactone/analogs &amp; derivatives/metabolism ; Bacteria/classification/genetics/metabolism ; *Bacterial Adhesion/genetics ; Diatoms/*microbiology ; Genes, Bacterial ; *Locomotion/genetics ; Microbiota ; Oceans and Seas ; Phytoplankton/*microbiology ; Quorum Sensing/genetics/*physiology ; }, abstract = {Interactions between phytoplankton and bacteria play major roles in global biogeochemical cycles and oceanic nutrient fluxes. These interactions occur in the microenvironment surrounding phytoplankton cells, known as the phycosphere. Bacteria in the phycosphere use either chemotaxis or attachment to benefit from algal excretions. Both processes are regulated by quorum sensing (QS), a cell-cell signalling mechanism that uses small infochemicals to coordinate bacterial gene expression. However, the role of QS in regulating bacterial attachment in the phycosphere is not clear. Here, we isolated a Sulfitobacter pseudonitzschiae F5 and a Phaeobacter sp. F10 belonging to the marine Roseobacter group and an Alteromonas macleodii F12 belonging to Alteromonadaceae, from the microbial community of the ubiquitous diatom Asterionellopsis glacialis. We show that only the Roseobacter group isolates (diatom symbionts) can attach to diatom transparent exopolymeric particles. Despite all three bacteria possessing genes involved in motility, chemotaxis, and attachment, only S. pseudonitzschiae F5 and Phaeobacter sp. F10 possessed complete QS systems and could synthesize QS signals. Using UHPLC-MS/MS, we identified three QS molecules produced by both bacteria of which only 3-oxo-C16:1 -HSL strongly inhibited bacterial motility and stimulated attachment in the phycosphere. These findings suggest that QS signals enable colonization of the phycosphere by algal symbionts.}, }
@article {pmid32894355, year = {2021}, author = {He, W and Zhang, M and Jin, G and Sui, X and Zhang, T and Song, F}, title = {Effects of Nitrogen Deposition on Nitrogen-Mineralizing Enzyme Activity and Soil Microbial Community Structure in a Korean Pine Plantation.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {410-424}, pmid = {32894355}, issn = {1432-184X}, support = {31971527//National Natural Science Foundation of China/ ; TD2019C002//Natural Science Foudation of Heilongjiang Province/ ; }, mesh = {Bacteria/classification/genetics/isolation &amp; purification/metabolism ; China ; Forests ; Fungi/classification/genetics/isolation &amp; purification/metabolism ; *Microbiota ; Nitrates/analysis/metabolism ; Nitrogen/analysis/*metabolism ; Peptide Hydrolases/metabolism ; Pinus/microbiology ; Soil/chemistry ; *Soil Microbiology ; Urease/metabolism ; }, abstract = {To predict the effects of nitrogen deposition on nitrogen-mineralizing enzyme activity and soil microbial community structure in artificial temperate forests in northern China, we studied the soil properties, nitrogen-mineralizing enzyme activity, and microbial community structure in the soil of a Korean pine plantation in which different concentrations (0, 20, 40, 80 kg N ha[-1] year[-1]) of ammonium nitrate were applied for 5 consecutive years. The results showed that nitrogen addition at different concentrations did not significantly affect the soil pH. High nitrogen addition (80 kg N ha[-1] year[-1]) significantly increased the soil organic matter, ammonium nitrogen, and nitrate nitrogen content in the Korean pine plantation, and ammonium nitrogen was the key factor that influenced the soil fungal community structure. The urease activity under the moderate nitrogen addition treatment (40 kg N ha[-1] year[-1]) was significantly lower than that under the control (0 kg N ha[-1] year[-1]), and the protease activity in the three treatments was also significantly lower than that in the control. There was no significant correlation between microbial community structure and the four mineralizing enzymes. After nitrogen addition at different concentrations, the Simpson and Shannon indexes of soil bacteria decreased significantly under low nitrogen addition (20 kg N ha[-1] year[-1]), but the α-diversity index of soil fungi did not show significant differences under nitrogen addition. The microbial community composition was significantly changed by the different treatments. PLS-DA analysis showed that Tardiphaga was an important genus that made the greatest contribution to the differences in bacterial community composition among treatments, as was Taeniolella for fungal community composition. The low level of nitrogen addition inhibited nitrogen mineralization in the Korean pine plantation by reducing the relative abundances of Nitrosomonadaceae and Betaproteobacteriales and by reducing the abundances of symbiotrophic fungi. Berkelbacteria and Polyporales were bacteria and fungi, respectively, that changed significantly under the high nitrogen addition treatment (80 kg N ha[-1] year[-1]). This study provides more data to support predictions of the changes in nitrogen-mineralizing enzyme activity and microbial community structure in artificial temperate forest soils in response to increased nitrogen deposition.}, }
@article {pmid32893477, year = {2020}, author = {Castledine, M and Padfield, D and Buckling, A}, title = {Experimental (co)evolution in a multi-species microbial community results in local maladaptation.}, journal = {Ecology letters}, volume = {23}, number = {11}, pages = {1673-1681}, doi = {10.1111/ele.13599}, pmid = {32893477}, issn = {1461-0248}, support = {BB/T002522/1//NERC National Environmental research council/ ; NE/S000771/1//NERC National Environmental research council/ ; NE/P001130/1//NERC National Environmental research council/ ; }, mesh = {Acclimatization ; Adaptation, Physiological ; Biological Evolution ; *Microbiota ; }, abstract = {Interspecific coevolutionary interactions can result in rapid biotic adaptation, but most studies have focused only on species pairs. Here, we (co)evolved five microbial species in replicate polycultures and monocultures and quantified local adaptation. Specifically, growth rate assays were used to determine adaptations of each species' populations to (1) the presence of the other four species in general and (2) sympatric vs. allopatric communities. We found that species did not show an increase in net biotic adaptation:ancestral, polyculture- and monoculture-evolved populations did not have significantly different growth rates within communities. However, 4/5 species' growth rates were significantly lower within the community they evolved in relative to an allopatric community. 'Local maladaptation' suggests that species evolved increased competitive interactions to sympatric species' populations. This increased competition did not affect community stability or productivity. Our results suggest that (co)evolution within communities can increase competitive interactions that are specific to (co)evolved community members.}, }
@article {pmid32892232, year = {2021}, author = {Dwidar, M and Jang, H and Sangwan, N and Mun, W and Im, H and Yoon, S and Choi, S and Nam, D and Mitchell, RJ}, title = {Diffusible Signaling Factor, a Quorum-Sensing Molecule, Interferes with and Is Toxic Towards Bdellovibrio bacteriovorus 109J.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {347-356}, pmid = {32892232}, issn = {1432-184X}, support = {2020R1A2C2012158//National Research Foundation of Korea/ ; 2017M1A3A3A02016642//National Research Foundation of Korea/ ; }, mesh = {4-Butyrolactone/analogs &amp; derivatives/toxicity ; Antibiosis/drug effects ; Bdellovibrio bacteriovorus/*drug effects/genetics/metabolism/physiology ; Cell Membrane/drug effects/metabolism ; Fatty Acids, Monounsaturated/*toxicity ; Flagella/genetics ; *Quorum Sensing ; Serine Proteases/genetics/metabolism ; Stress, Physiological/drug effects ; Transcriptome/drug effects ; }, abstract = {Bdellovibrio bacteriovorus 109J is a predatory bacterium which lives by predating on other Gram-negative bacteria to obtain the nutrients it needs for replication and survival. Here, we evaluated the effects two classes of bacterial signaling molecules (acyl homoserine lactones (AHLs) and diffusible signaling factor (DSF)) have on B. bacteriovorus 109J behavior and viability. While AHLs had a non-significant impact on predation rates, DSF considerably delayed predation and bdelloplast lysis. Subsequent experiments showed that 50 μM DSF also reduced the motility of attack-phase B. bacteriovorus 109J cells by 50% (38.2 ± 14.9 vs. 17 ± 8.9 μm/s). Transcriptomic analyses found that DSF caused genome-wide changes in B. bacteriovorus 109J gene expression patterns during both the attack and intraperiplasmic phases, including the significant downregulation of the flagellum assembly genes and numerous serine protease genes. While the former accounts for the reduced speeds observed, the latter was confirmed experimentally with 50 μM DSF completely blocking protease secretion from attack-phase cells. Additional experiments found that 30% of the total cellular ATP was released into the supernatant when B. bacteriovorus 109J was exposed to 200 μM DSF, implying that this QS molecule negatively impacts membrane integrity.}, }
@article {pmid32889760, year = {2021}, author = {Harrison, JG and John Calder, W and Shuman, B and Alex Buerkle, C}, title = {The quest for absolute abundance: The use of internal standards for DNA-based community ecology.}, journal = {Molecular ecology resources}, volume = {21}, number = {1}, pages = {30-43}, doi = {10.1111/1755-0998.13247}, pmid = {32889760}, issn = {1755-0998}, support = {EPS-1655726//National Science Foundation/ ; }, mesh = {Bacteria/classification ; DNA ; *High-Throughput Nucleotide Sequencing ; *Microbiota ; *Sequence Analysis, DNA ; }, abstract = {To characterize microbiomes and other ecological assemblages, ecologists routinely sequence and compare loci that differ among focal taxa. Counts of these sequences convey information regarding the occurrence and relative abundances of taxa, but provide no direct measure of their absolute abundances, due to the technical limitations of the sequencing process. The relative abundances in compositional data are inherently constrained and difficult to interpret. The incorporation of internal standards (ISDs; colloquially referred to as 'spike-ins') into DNA pools can ameliorate the problems posed by relative abundance data and allow absolute abundances to be approximated. Unfortunately, many laboratory and sampling biases cause ISDs to underperform or fail. Here, we discuss how careful deployment of ISDs can avoid these complications and be an integral component of well-designed studies seeking to characterize ecological assemblages via sequencing of DNA.}, }
@article {pmid32888042, year = {2020}, author = {Dickey, JR and Fordyce, JA and Lebeis, SL}, title = {Bacterial communities of the Salvia lyrata rhizosphere explained by spatial structure and sampling grain.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {846-858}, doi = {10.1007/s00248-020-01594-7}, pmid = {32888042}, issn = {1432-184X}, support = {DEB1638922//National Science Foundation (USA)/ ; }, mesh = {Bacteria/*isolation &amp; purification ; *Microbiota ; *Rhizosphere ; Salvia/*microbiology ; Sample Size ; Soil Microbiology ; Spatial Analysis ; Tennessee ; }, abstract = {Advancements in molecular technology have reduced the constraints that the grain of observation, or the spatial resolution and volume of the sampling unit, has on the characterization of plant-associated microbiomes. With discrete ecological sampling and massive parallel sequencing, we can more precisely portray microbiome community assembly and microbial recruitment to host tissue over space and time. Here, we differentiate rarefied community richness and relative abundance in bacterial microbiomes of Salvia lyrata dependent on three spatial depths, which are discrete physical distances from the soil surface within the rhizosphere microhabitat as a proxy for the root system zones. To assess the impact of sampling grain on rarefied community richness and relative abundance, we evaluated the variation of these metrics between samples pooled prior to DNA extraction and samples pooled after sequencing. A distance-based redundancy analysis with the quantitative Jaccard distance revealed that rhizosphere microbiomes vary in richness between rhizosphere soil depths. At all orders of diversity, rarefied microbial richness was consistently lowest at the deepest samples taken (approximately 4 cm from soil surface) in comparison with other rhizosphere soil depths. We additionally show that finer grain sampling (i.e., three samples of equal volume pooled after sequencing) recovers greater microbial richness when using 16S rRNA gene sequencing to describe microbial communities found within the rhizosphere system. In summary, to further elucidate the extent host-specific microbiomes assemble within the rhizosphere, the grain at which bacterial communities are sampled should reflect and encompass fine-scale heterogeneity of the system.}, }
@article {pmid32887945, year = {2021}, author = {Gao, CH and Cao, H and Cai, P and Sørensen, SJ}, title = {The initial inoculation ratio regulates bacterial coculture interactions and metabolic capacity.}, journal = {The ISME journal}, volume = {15}, number = {1}, pages = {29-40}, pmid = {32887945}, issn = {1751-7370}, mesh = {*Bacteria/genetics ; *Carbon ; Coculture Techniques ; Reproducibility of Results ; }, abstract = {Coculture is an important model system in microbial ecology studies. As a key experimental parameter, the initial inoculation ratio has a crucial impact on the results of the coculture system. However, such an effect has never been investigated under multiple niche conditions. In this study, we established a simple coculture system with two model bacteria in various carbon sources and investigated the influence of initial inoculum ratios of 1:1000 to 1000:1 on community structure, function, and bacterial interaction. We found that the final ratio of the cocultures with different initial inoculum ratios differed in approximately five-sixths of the carbon sources, suggesting that the final ratio is highly dependent on the initial inoculum ratio, while the carbon source preferences of bacteria could not predict the final ratio of cocultures. Furthermore, we found that the initial ratio could regulate the metabolic capacity of the coculture, as only cocultures with initial ratios of 1:1 and 1000:1 gained high capacity on 14 specific carbon sources. The underlying reason may be that the pattern of species interaction is changed by the initial ratio. In conclusion, we showed that the initial ratio can induce emergent properties in coculture. These findings suggest that the initial ratio not only impacts the reproducibility of coculture experiments but also can influence our understanding of generic microbial ecology.}, }
@article {pmid32887010, year = {2020}, author = {Oliveira, BB and Veigas, B and Carlos, FF and Sánchez-Melsió, A and Balcázar, JL and Borrego, CM and Baptista, PV}, title = {Water safety screening via multiplex LAMP-Au-nanoprobe integrated approach.}, journal = {The Science of the total environment}, volume = {741}, number = {}, pages = {140447}, doi = {10.1016/j.scitotenv.2020.140447}, pmid = {32887010}, issn = {1879-1026}, mesh = {*Escherichia coli ; Feces ; *Nucleic Acid Amplification Techniques ; Real-Time Polymerase Chain Reaction ; Sensitivity and Specificity ; }, abstract = {Contaminated water resources remain a major global concern regarding public health. The majority of water safety protocols include indicators of microbial contamination to evaluate the potential risk to public health and are key elements of quality guidelines. Among these, markers for total coliforms and fecal coliforms are strong indicators of co-contamination with other pathogens. Traditional methods, recurring to slow and cumbersome culture-based approaches, have been gradually replaced by molecular methods, capable of faster and more specific screening. These are usually PCR-based methods that may allow for multiple pathogen detection but require dedicated laboratory equipment, hindering the rapid on-site assessment. Here, we used a multiplex Loop-Mediated Isothermal Amplification (mLAMP) strategy for the amplification of two markers associated with the contamination by total and fecal coliforms (e.g. Escherichia coli) - lacZ and uidA genes, respectively - thus allowing for single tube multiplex detection. The mLAMP products were then subject to an Au-nanoprobe colorimetric detection assay for precise discrimination of targets. This approach was validated in 22 water samples that were also screened for the presence of lacZ and uidA using standard and quantitative PCR, with the capability for discriminating the contamination level, e.g. a semi-quantitative evaluation of water quality.}, }
@article {pmid32885507, year = {2020}, author = {Wall, CB and Egan, CP and Swift, SIO and Hynson, NA}, title = {Three decades post-reforestation has not led to the reassembly of arbuscular mycorrhizal fungal communities associated with remnant primary forests.}, journal = {Molecular ecology}, volume = {29}, number = {21}, pages = {4234-4247}, doi = {10.1111/mec.15624}, pmid = {32885507}, issn = {1365-294X}, mesh = {Ecosystem ; Forests ; Hawaii ; *Mycobiome ; *Mycorrhizae/genetics ; Soil ; Soil Microbiology ; }, abstract = {The negative effects of deforestation can potentially be ameliorated through ecological restoration. However, reforestation alone may not reassemble the same ecological communities or functions as primary forests. In part, this failure may be owed to forest ecosystems inherently involving complex interactions among guilds of organisms. Plants, which structure forest food webs, rely on intimate associations with symbiotic microbes such as root-inhabiting mycorrhizal fungi. Here, we leverage a large-scale reforestation project on Hawai'i Island underway for over three decades to assess whether arbuscular mycorrhizal (AM) fungal communities have concurrently been restored. The reference ecosystem for this restoration project is a remnant montane native Hawaiian forest that provides critical habitat for endangered birds. We sampled soils from 12 plots within remnant and restored forest patches and characterized AM fungal communities using high-throughput amplicon sequencing. While some AM fungal community metrics were comparable between remnant and restored forest (e.g. species richness), other key characteristics were not. Specifically, community membership and the identity of AM fungal keystone species differed between the two habitat types, as well as the primary environmental factors influencing community composition. Remnant forest AM fungal communities were strongly associated with soil chemical properties, especially pH, while restored forest communities were influenced by the spatial proximity to remnant forests. We posit that combined, these differences in soil AM fungal communities could be negatively affecting the recruitment of native plant hosts and that future restoration efforts should consider plant-microbe interactions as an important facet of forest health.}, }
@article {pmid32884655, year = {2020}, author = {Duplouy, A and Minard, G and Saastamoinen, M}, title = {The gut bacterial community affects immunity but not metabolism in a specialist herbivorous butterfly.}, journal = {Ecology and evolution}, volume = {10}, number = {16}, pages = {8755-8769}, pmid = {32884655}, issn = {2045-7758}, abstract = {Plant tissues often lack essential nutritive elements and may contain a range of secondary toxic compounds. As nutritional imbalance in food intake may affect the performances of herbivores, the latter have evolved a variety of physiological mechanisms to cope with the challenges of digesting their plant-based diet. Some of these strategies involve living in association with symbiotic microbes that promote the digestion and detoxification of plant compounds or supply their host with essential nutrients missing from the plant diet. In Lepidoptera, a growing body of evidence has, however, recently challenged the idea that herbivores are nutritionally dependent on their gut microbial community. It is suggested that many of the herbivorous Lepidopteran species may not host a resident microbial community, but rather a transient one, acquired from their environment and diet. Studies directly testing these hypotheses are however scarce and come from an even more limited number of species.By coupling comparative metabarcoding, immune gene expression, and metabolomics analyses with experimental manipulation of the gut microbial community of prediapause larvae of the Glanville fritillary butterfly (Melitaea cinxia, L.), we tested whether the gut microbial community supports early larval growth and survival, or modulates metabolism or immunity during early stages of development.We successfully altered this microbiota through antibiotic treatments and consecutively restored it through fecal transplants from conspecifics. Our study suggests that although the microbiota is involved in the up-regulation of an antimicrobial peptide, it did not affect the life history traits or the metabolism of early instars larvae.This study confirms the poor impact of the microbiota on diverse life history traits of yet another Lepidoptera species. However, it also suggests that potential eco-evolutionary host-symbiont strategies that take place in the gut of herbivorous butterfly hosts might have been disregarded, particularly how the microbiota may affect the host immune system homeostasis.}, }
@article {pmid32882545, year = {2021}, author = {Li, L and Ning, D and Jeon, Y and Ryu, H and Santo Domingo, JW and Kang, DW and Kadudula, A and Seo, Y}, title = {Ecological insights into assembly processes and network structures of bacterial biofilms in full-scale biologically active carbon filters under ozone implementation.}, journal = {The Science of the total environment}, volume = {751}, number = {}, pages = {141409}, pmid = {32882545}, issn = {1879-1026}, support = {EPA999999/ImEPA/Intramural EPA/United States ; }, mesh = {Bacteria ; Biofilms ; Charcoal ; *Ozone ; *Water Purification ; }, abstract = {To address the adverse effects of harmful algal blooms, there are increased demands over the implementation of ozone coupled with biologically active carbon (BAC) filters in the drinking water treatment plants. Although the microbial biofilms are vital elements to support the proper performance of BAC filters, except for taxonomic affiliations, little is known about the assembly mechanisms of microbial communities in the full-scale BAC filters. This study aimed to examine how the assembly processes and their associated factors (e.g., influent characteristics, biological interactions) drive the temporal dynamics of bacterial communities in full-scale BAC filters, which underwent ozone implementation (five consecutive seasons from 2017 to 2018). The results revealed that along with the increase of bacterial taxonomic richness and evenness, stochastic processes became more crucial to determine the bacterial community assembly in the summer and autumn after ozone implementation (relative contribution: 61.23% and 83.75%, respectively). Moreover, their corresponding networks possessed simple network structures with lower modularity than other seasons, which implied lesser biological interactions among bacterial populations. The correlation between taxonomic and predicted functional diversities using functional redundancy index indicated that relatively high levels of bacterial functional redundancy (>0.83) were generally present in BAC filters. However, compared to other seasons, significantly higher degrees of functional redundancy existed in the summer and autumn after ozone implementation (0.85 ± 0.01 and 0.86 ± 0.01, respectively). Overall, this work improves our understanding of the microbial ecology of full-scale BAC filters by providing a conceptual framework that characterizes bacterial biofilm assembly processes relevant to performance optimization of full-scale BAC filters.}, }
@article {pmid32880700, year = {2021}, author = {Sabu, EA and Gonsalves, MJ and Sreepada, RA and Shivaramu, MS and Ramaiah, N}, title = {Evaluation of the Physiological Bacterial Groups in a Tropical Biosecured, Zero-Exchange System Growing Whiteleg Shrimp, Litopenaeus vannamei.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {335-346}, pmid = {32880700}, issn = {1432-184X}, support = {PSC 0206//Council&#xa0;of&#xa0;Scientific and Industrial Research, India/ ; }, mesh = {Aerobiosis ; Anaerobiosis ; Animals ; Aquaculture ; Bacteria/classification/genetics/metabolism ; *Bacterial Physiological Phenomena ; *Ecosystem ; Nitrogen/analysis/chemistry ; Penaeidae/*growth &amp; development ; Phytoplankton/classification/genetics/metabolism ; Ponds/chemistry/microbiology ; Water Quality ; }, abstract = {To elucidate the individual and multiple roles of physiological bacterial groups involved in biogeochemical cycles of carbon, nitrogen, phosphorus and sulfur, the changes in the abundance of aerobic bacteria (heterotrophs, methane oxidizers, ammonia oxidizers, sulfur oxidizers, phosphate solubilizers, phosphate accumulators) and anaerobic bacteria (total anaerobes, nitrate reducers, denitrifiers and sulfate reducers) were investigated in a biosecured, zero-exchange system stocked with whiteleg shrimp, Litopenaeus vannamei for one production cycle. Key water quality parameters during the 96-day production cycle fell within the normal range for L. vannamei culture. Results of Spearman's correlation matrix revealed that different sets of variables correlated at varying levels of significance of the interrelationships between bacterial abundances and water quality parameters. The three nitrogenous species (ammonia, nitrite and nitrate) strongly influenced the physiological bacterial groups' abundance. The strong relationship of bacterial groups with phytoplankton biomass and abundance clearly showed the trophic interconnections in nutrient exchange/recycling. Canonical correspondence analysis performed to assess the total variation revealed that the three dissolved nitrogen species followed by salinity, temperature, phytoplankton biomass and pH collectively accounted for as much as 82% of the total variation. In conclusion, the results of the study revealed that the major drivers that interweaved biogeochemical cycles are the three dissolved nitrogen species, which microbially mediated various aerobic-anaerobic assimilation/dissimilation processes in the pond ecosystem. Considering the pond microbial ecology becoming an important management tool where applied research could improve the economic and environmental sustainability of the aquaculture industry, the findings of the present study are practically relevant.}, }
@article {pmid32880699, year = {2020}, author = {Wei, J and Segraves, KA and Li, WZ and Yang, XK and Xue, HJ}, title = {Gut bacterial communities and their contribution to performance of specialist Altica flea beetles.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {946-959}, doi = {10.1007/s00248-020-01590-x}, pmid = {32880699}, issn = {1432-184X}, support = {31672334//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bacteria/classification/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Coleoptera/*microbiology/physiology ; Female ; *Gastrointestinal Microbiome ; Male ; Metagenome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Host plant shifts are a common mode of speciation in herbivorous insects. Although insects can evolve adaptations to successfully incorporate a new host plant, it is becoming increasingly recognized that the gut bacterial community may play a significant role in allowing insects to detoxify novel plant chemical defenses. Here, we examined differences in gut bacterial communities between Altica flea beetle species that feed on phylogenetically unrelated host plants in sympatry. We surveyed the gut bacterial communities of three closely related flea beetles from multiple locations using 16S rRNA amplicon sequencing. The results showed that the beetle species shared a high proportion (80.7%) of operational taxonomic units. Alpha-diversity indicators suggested that gut bacterial diversity did not differ among host species, whereas geography had a significant effect on bacterial diversity. In contrast, analyses of beta-diversity showed significant differences in gut bacterial composition among beetle species when we used species composition and relative abundance metrics, but there was no difference in composition when species presence/absence and phylogenetic distance indices were used. Within host beetle species, gut bacterial composition varied significantly among sites. A metagenomic functionality analysis predicted that the gut microbes had functions involved in xenobiotic biodegradation and metabolism as well as metabolism of terpenoids and polyketides. These predictions, however, did not differ among beetle host species. Antibiotic curing experiments showed that development time was significantly prolonged, and there was a significant decline in body weight of newly emerged adults in beetles lacking gut bacteria, suggesting the beetles may receive a potential benefit from the gut microbe-insect interaction. On the whole, our results suggest that although the gut bacterial community did not show clear host-specific patterns among Altica species, spatiotemporal variability is an important determinant of gut bacterial communities. Furthermore, the similarity of communities among these beetle species suggests that microbial facilitation may not be a determinant of host plant shifts in Altica.}, }
@article {pmid32879989, year = {2020}, author = {Gonzalo, M and Deveau, A and Aigle, B}, title = {Inhibitions Dominate but Stimulations and Growth Rescues Are Not Rare Among Bacterial Isolates from Grains of Forest Soil.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {872-884}, doi = {10.1007/s00248-020-01579-6}, pmid = {32879989}, issn = {1432-184X}, support = {ANR-11-LABX 0002 01//ANR/ ; }, mesh = {Bacteria/*growth &amp; development/isolation &amp; purification ; Forests ; France ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Rhizosphere ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Soil is a complex environment made of multiple microhabitats in which a wide variety of microorganisms co-exist and interact to form dynamic communities. While the abiotic factors that regulate the structure of these communities are now quite well documented, our knowledge of how bacteria interact with each other within these communities is still insufficient. Literature reveals so far contradictory results and is mainly focused on antagonistic interactions. To start filling this gap, we isolated 35 different bacterial isolates from grains of soil assuming that, at this scale, these bacteria would have been likely interacting in their natural habitat. We tested pairwise interactions between all isolates from each grain and scored positive and negative interactions. We compared the effects of simultaneous versus delayed co-inoculations, allowing or not to a strain to modify first its environment. One hundred fifty-seven interactions, either positive or negative, were recorded among the 525 possible one's. Members of the Bacillus subtilis, Pseudomonas and Streptomyces genera were responsible for most inhibitions, while positive interactions occurred between isolates of the Bacillales order and only in delayed inoculation conditions. Antagonist isolates had broad spectral abilities to acquire nutrients from organic and inorganic matter, while inhibited isolates tended to have little potentials. Despite an overall domination of antagonistic interactions (87%), a third of the isolates were able to stimulate or rescue the growth of other isolates, suggesting that cooperation between bacteria may be underestimated.}, }
@article {pmid32879459, year = {2021}, author = {Rubbens, P and Props, R and Kerckhof, FM and Boon, N and Waegeman, W}, title = {Cytometric fingerprints of gut microbiota predict Crohn's disease state.}, journal = {The ISME journal}, volume = {15}, number = {1}, pages = {354-358}, pmid = {32879459}, issn = {1751-7370}, mesh = {*Crohn Disease/diagnosis ; Feces ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Variations in the gut microbiome have been associated with changes in health state such as Crohn's disease (CD). Most surveys characterize the microbiome through analysis of the 16S rRNA gene. An alternative technology that can be used is flow cytometry. In this report, we reanalyzed a disease cohort that has been characterized by both technologies. Changes in microbial community structure are reflected in both types of data. We demonstrate that cytometric fingerprints can be used as a diagnostic tool in order to classify samples according to CD state. These results highlight the potential of flow cytometry to perform rapid diagnostics of microbiome-associated diseases.}, }
@article {pmid32879458, year = {2021}, author = {Mooshammer, M and Kitzinger, K and Schintlmeister, A and Ahmerkamp, S and Nielsen, JL and Nielsen, PH and Wagner, M}, title = {Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities.}, journal = {The ISME journal}, volume = {15}, number = {1}, pages = {348-353}, pmid = {32879458}, issn = {1751-7370}, mesh = {Carbon Isotopes/analysis ; Food Chain ; Isotope Labeling ; Isotopes ; *Microbiota ; }, abstract = {Stable isotope probing (SIP) is a key tool for identifying the microorganisms catalyzing the turnover of specific substrates in the environment and to quantify their relative contributions to biogeochemical processes. However, SIP-based studies are subject to the uncertainties posed by cross-feeding, where microorganisms release isotopically labeled products, which are then used by other microorganisms, instead of incorporating the added tracer directly. Here, we introduce a SIP approach that has the potential to strongly reduce cross-feeding in complex microbial communities. In this approach, the microbial cells are exposed on a membrane filter to a continuous flow of medium containing isotopically labeled substrate. Thereby, metabolites and degradation products are constantly removed, preventing consumption of these secondary substrates. A nanoSIMS-based proof-of-concept experiment using nitrifiers in activated sludge and [13]C-bicarbonate as an activity tracer showed that Flow-SIP significantly reduces cross-feeding and thus allows distinguishing primary consumers from other members of microbial food webs.}, }
@article {pmid32877326, year = {2020}, author = {Lee, HJ and Kim, SY and Whang, KS}, title = {Cellulomonas citrea sp. nov., isolated from paddy soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {70}, number = {10}, pages = {5304-5311}, doi = {10.1099/ijsem.0.004409}, pmid = {32877326}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; Cellulomonas/*classification/isolation &amp; purification ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Nucleic Acid Hybridization ; *Oryza ; *Phylogeny ; Pigmentation ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {Two Gram-stain-positive, facultatively anaerobic, motile, aerobic, rod-shaped and non-spore-forming actinobacteria, strains AO-9[T] and AO-18, were isolated from paddy soil collected from Daejeon, Republic of Korea. Colonies were smooth, lemon-yellow and circular and 0.5-0.8×2.0-2.4 µm in diameter after 3 days of incubation at 28 °C on tryptic soy agar. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains AO-9[T] and AO-18 belonged to the genus Cellulomonas, showing the highest sequence similarities to Cellulomonas marina FXJ8.089[T] (96.6 %), Cellulomonas endophytica SYSUP0004[T] (96.5 %), Cellulomonas gelida DSM 20111[T] (96.2 %), Cellulomonas uda DSM 20107[T] (96.1 %), Cellulomonas rhizosphaerae NEAU-TCZ24[T] (96.1 %), Cellulomonas composti TR7-06[T] (96.0 %), Cellulomonas persica JCM 18111[T] (96.0 %) and less than 96 % to other closely related species. The DNA-DNA hybridization values between strains AO-9[T] and AO-18 were 87 %. The average nucleotide identity and digital DNA-DNA hybridization values between strain AO-9[T] and type strains of related species of the genus Cellulomonas were 84.0-85.8 % and 20.3-20.9 %, respectively. The major cellular fatty acids are anteiso-C15:0 (49.9 %), C14:0 (12.9 %) and iso-C14:0 (12.1 %). The predominant isoprenoid quinone was MK-9 (H4). The polar lipid profile consists of diphosphatidylglycerol, phosphatidylglycerol and one unidentified lipid. The DNA G+C content was 72.9 mol%. Based on its distinctive phenotypic, phylogenetic and chemotaxonomic characteristics, the two strains are considered to represent novel species of the genus Cellulomonas, for which the name Cellulomonas citrea sp. nov. is proposed. The type strain is AO-9[T] (=KACC 19069[T]=NBRC 112523[T]).}, }
@article {pmid32875141, year = {2020}, author = {Corbin, KD and Krajmalnik-Brown, R and Carnero, EA and Bock, C and Emerson, R and Rittmann, BE and Marcus, AK and Davis, T and Dirks, B and Ilhan, ZE and Champagne, C and Smith, SR}, title = {Integrative and quantitative bioenergetics: Design of a study to assess the impact of the gut microbiome on host energy balance.}, journal = {Contemporary clinical trials communications}, volume = {19}, number = {}, pages = {100646}, pmid = {32875141}, issn = {2451-8654}, support = {R01 DK105829/DK/NIDDK NIH HHS/United States ; }, abstract = {UNLABELLED: The literature is replete with clinical studies that characterize the structure, diversity, and function of the gut microbiome and correlate the results to different disease states, including obesity. Whether the microbiome has a direct impact on obesity has not been established. To address this gap, we asked whether the gut microbiome and its bioenergetics quantitatively change host energy balance. This paper describes the design of a randomized crossover clinical trial that combines outpatient feeding with precisely controlled metabolic phenotyping in an inpatient metabolic ward. The target population was healthy, weight-stable individuals, age 18-45 and with a body mass index ≤30 kg/m[2]. Our primary objective was to determine within-participant differences in energy balance after consuming a control Western Diet versus a Microbiome Enhancer Diet intervention specifically designed to optimize the gut microbiome for positive impacts on host energy balance. We assessed the complete energy-balance equation via whole-room calorimetry, quantified energy intake, fecal energy losses, and methane production. We implemented conditions of tight weight stability and balance between metabolizable energy intake and predicted energy expenditure. We explored key factors that modulate the balance between host and microbial nutrient accessibility by measuring enteroendocrine hormone profiles, appetite/satiety, gut transit and gastric emptying. By integrating these clinical measurements with future bioreactor experiments, gut microbial ecology analysis, and mathematical modeling, our goal is to describe initial cause-and-effect mechanisms of gut microbiome metabolism on host energy balance. Our innovative methods will enable subsequent studies on the interacting roles of diet, the gut microbiome, and human physiology.<br><br>CLINICALTRIALSGOV IDENTIFIER: NCT02939703. The present study reference can be found here: https://clinicaltrials.gov/ct2/show/NCT02939703.}, }
@article {pmid32874778, year = {2020}, author = {Marchioro, GM and Glasl, B and Engelen, AH and Serrão, EA and Bourne, DG and Webster, NS and Frade, PR}, title = {Microbiome dynamics in the tissue and mucus of acroporid corals differ in relation to host and environmental parameters.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e9644}, pmid = {32874778}, issn = {2167-8359}, abstract = {Corals are associated with diverse microbial assemblages; however, the spatial-temporal dynamics of intra-species microbial interactions are poorly understood. The coral-associated microbial community varies substantially between tissue and mucus microhabitats; however, the factors controlling the occurrence, abundance, and distribution of microbial taxa over time have rarely been explored for different coral compartments simultaneously. Here, we test (1) differentiation in microbiome diversity and composition between coral compartments (surface mucus and tissue) of two Acropora hosts (A. tenuis and A. millepora) common along inshore reefs of the Great Barrier Reef, as well as (2) the potential linkage between shifts in individual coral microbiome families and underlying host and environmental parameters. Amplicon based 16S ribosomal RNA gene sequencing of 136 samples collected over 14 months, revealed significant differences in bacterial richness, diversity and community structure among mucus, tissue and the surrounding seawater. Seawater samples were dominated by members of the Synechococcaceae and Pelagibacteraceae bacterial families. The mucus microbiome of Acropora spp. was dominated by members of Flavobacteriaceae, Synechococcaceae and Rhodobacteraceae and the tissue was dominated by Endozoicimonaceae. Mucus microbiome in both Acropora species was primarily correlated with seawater parameters including levels of chlorophyll a, ammonium, particulate organic carbon and the sum of nitrate and nitrite. In contrast, the correlation of the tissue microbiome to the measured environmental (i.e., seawater parameters) and host health physiological factors differed between host species, suggesting host-specific modulation of the tissue-associated microbiome to intrinsic and extrinsic factors. Furthermore, the correlation between individual coral microbiome members and environmental factors provides novel insights into coral microbiome-by-environment dynamics and hence has potential implications for current reef restoration and management efforts (e.g. microbial monitoring and observatory programs).}, }
@article {pmid32873609, year = {2020}, author = {Kloosterman, AM and Shelton, KE and van Wezel, GP and Medema, MH and Mitchell, DA}, title = {RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery.}, journal = {mSystems}, volume = {5}, number = {5}, pages = {}, pmid = {32873609}, issn = {2379-5077}, support = {R01 AI144967/AI/NIAID NIH HHS/United States ; T32 GM070421/GM/NIGMS NIH HHS/United States ; }, abstract = {Many ribosomally synthesized and posttranslationally modified peptide classes (RiPPs) are reliant on a domain called the RiPP recognition element (RRE). The RRE binds specifically to a precursor peptide and directs the posttranslational modification enzymes to their substrates. Given its prevalence across various types of RiPP biosynthetic gene clusters (BGCs), the RRE could theoretically be used as a bioinformatic handle to identify novel classes of RiPPs. In addition, due to the high affinity and specificity of most RRE-precursor peptide complexes, a thorough understanding of the RRE domain could be exploited for biotechnological applications. However, sequence divergence of RREs across RiPP classes has precluded automated identification based solely on sequence similarity. Here, we introduce RRE-Finder, a new tool for identifying RRE domains with high sensitivity. RRE-Finder can be used in precision mode to confidently identify RREs in a class-specific manner or in exploratory mode to assist in the discovery of novel RiPP classes. RRE-Finder operating in precision mode on the UniProtKB protein database retrieved ∼25,000 high-confidence RREs spanning all characterized RRE-dependent RiPP classes, as well as several yet-uncharacterized RiPP classes that require future experimental confirmation. Finally, RRE-Finder was used in precision mode to explore a possible evolutionary origin of the RRE domain. The results suggest RREs originated from a co-opted DNA-binding transcriptional regulator domain. Altogether, RRE-Finder provides a powerful new method to probe RiPP biosynthetic diversity and delivers a rich data set of RRE sequences that will provide a foundation for deeper biochemical studies into this intriguing and versatile protein domain.IMPORTANCE Bioinformatics-powered discovery of novel ribosomal natural products (RiPPs) has historically been hindered by the lack of a common genetic feature across RiPP classes. Herein, we introduce RRE-Finder, a method for identifying RRE domains, which are present in a majority of prokaryotic RiPP biosynthetic gene clusters (BGCs). RRE-Finder identifies RRE domains 3,000 times faster than current methods, which rely on time-consuming secondary structure prediction. Depending on user goals, RRE-Finder can operate in precision mode to accurately identify RREs present in known RiPP classes or in exploratory mode to assist with novel RiPP discovery. Employing RRE-Finder on the UniProtKB database revealed several high-confidence RREs in novel RiPP-like clusters, suggesting that many new RiPP classes remain to be discovered.}, }
@article {pmid32873292, year = {2020}, author = {Zhu, L and Xu, F and Wan, W and Yu, B and Tang, L and Yang, Y and Du, Y and Chen, Z and Xu, H}, title = {Gut microbial characteristics of adult patients with allergy rhinitis.}, journal = {Microbial cell factories}, volume = {19}, number = {1}, pages = {171}, pmid = {32873292}, issn = {1475-2859}, support = {81900541//National Natural Science Foundation of China/ ; 2019J05005//Natural Science Foundation of Fujian Province/ ; }, mesh = {Adult ; *Biodiversity ; China/epidemiology ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; Male ; Metagenome ; Quality of Life ; RNA, Ribosomal, 16S ; Rhinitis, Allergic/*microbiology ; Severity of Illness Index ; Surveys and Questionnaires ; Young Adult ; }, abstract = {BACKGROUND: Although recent studies have indicated that intestinal microbiota dweller are involved in the pathogenesis of allergy rhinitis (AR), the influence of gut microbiota on AR adult has not been fully elucidated yet. Hence, we carried out this study to uncover the distinctive bacterial taxa that differentiate allergy rhinitis patients from healthy individuals. Feces samples from thirty three AR patients and thirty one healthy individuals were analyzed by 16S rRNA gene sequencing.<br><br>RESULTS: Results showed that the bacterial diversity in AR group was significantly higher than that of the non-AR group. Bacterial communities between AR and non-AR group were significantly differentiated as revealed by Principal coordinates analysis (PCoA) and the variation within non-AR were higher than that of the counterpart. Firmicutes, Fusobacteria, Actinobacteria, Cyanobacteria and Chloroflexi were the significantly differed phyla taxa and the top significantly distinguished bacterial genus included Prevotella_9, Phascolarctobacterium, Roseburia, Megamonas, Alistipes, Lachnoclostridium and Fusobacterium. The higher network complexity in AR group were dominated by taxa belonging to Firmicutes. The predicted function, alpha linolenic acid metabolism and bacterial invasion of epithelial cells pathway were higher in non-AR group while gonadotropin-releasing hormone (GnRH) signaling pathway, Fc &#x3b3;-R mediated phagocytosis and endocytosis were higher in AR patients. Although the bacterial diversity between moderate and severe AR patients showed no significant difference, the significant correlation between featured genus and total nasal symptom score or rhinoconjunctivitis quality of life questionnaire, such as Butyricicoccus and Eisenbergiella, revealed the potential to intervene the AR status by means of gut microbiota.<br><br>CONCLUSIONS: In conclusion, patients with allergy rhinitis had distinguished gut microbiota characteritics in comparison with healthy controls. The results suggest that gut microbiota might play crucial roles in influencing the course and different symptoms of AR. Trial registration ChiCTR, ChiCTR1900028613. Registered 29 December 2019, https://www.chictr.org.cn/showproj.aspx?proj=47650 .}, }
@article {pmid32870508, year = {2021}, author = {Kedia, S and Ghosh, TS and Jain, S and Desigamani, A and Kumar, A and Gupta, V and Bopanna, S and Yadav, DP and Goyal, S and Makharia, G and Travis, SPL and Das, B and Ahuja, V}, title = {Gut microbiome diversity in acute severe colitis is distinct from mild to moderate ulcerative colitis.}, journal = {Journal of gastroenterology and hepatology}, volume = {36}, number = {3}, pages = {731-739}, doi = {10.1111/jgh.15232}, pmid = {32870508}, issn = {1440-1746}, support = {//Intramural THSTI research funds/ ; //Scheme for Promotion of Academic and Research Collaboration (SPARC)/ ; }, mesh = {Acute Disease ; Adolescent ; Adult ; Colitis/*microbiology ; Colitis, Ulcerative/*microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Microbiological Techniques ; Middle Aged ; Nucleic Acid Amplification Techniques ; RNA, Ribosomal, 16S ; Severity of Illness Index ; }, abstract = {BACKGROUND AND AIM: Although the gut microbiome of patients with ulcerative colitis (UC) has been characterized, no study has characterized the gut microbiome in acute severe colitis (ASC). We compared the gut microbiome of patients with UC, ASC, and healthy controls (HCs).<br><br>METHODS: Patients with mild to moderate UC (n&#xa0;=&#xa0;24), ASC (n&#xa0;=&#xa0;19 with 21 episodes) and HCs (n&#xa0;=&#xa0;50) were recruited prospectively. A 16SrDNA amplicon approach was used to explore gut microbial diversity and taxonomic repertoires. UC was diagnosed using European Crohn's and Colitis Organization guidelines, and ASC was diagnosed using Truelove and Witts' criteria.<br><br>RESULTS: The normalized alpha diversity was significantly lower in ASC than mild-moderately active UC (P&#xa0;<&#xa0;0.05) or HC (P&#xa0;<&#xa0;0.001). The gut microbiome in ASC was highly unstable, as characterized by high intracohort variation (analyzed using J-divergence measure), which was significantly greater than in UC or HC. On principal coordinate analysis, the microbiome of HC and UC were similar, with the ASC cohort being distinct from both. Comparison of ranked abundances identified four distinct clusters of genera (G1, G2, G3, and G4), with specific trends in their abundance across three groups: G1/G2A clusters had the least, whereas G3 had the highest abundance in the ASC cohort.<br><br>CONCLUSIONS: Gut microbial diversity is lower in ASC than mild-moderate UC or HCs. Gut microbiome composition is increasingly unstable in ASC, with a distinct abundance of specific genera varying between HCs and ASC. Mild-moderate UC lies within the spectrum.}, }
@article {pmid32862246, year = {2021}, author = {Starke, R and Pylro, VS and Morais, DK}, title = {16S rRNA Gene Copy Number Normalization Does Not Provide More Reliable Conclusions in Metataxonomic Surveys.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {535-539}, pmid = {32862246}, issn = {1432-184X}, support = {18-25706S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 20-02022Y//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; }, mesh = {Gene Dosage ; Gene Library ; Metagenome/genetics ; Metagenomics/*standards ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Sequencing 16S rRNA gene amplicons is the gold standard to uncover the composition of prokaryotic communities. The presence of multiple copies of this gene makes the community abundance data distorted and gene copy normalization (GCN) necessary for correction. Even though GCN of 16S data provided a picture closer to the metagenome before, it should also be compared with communities of known composition due to the fact that library preparation is prone to methodological biases. Here, we process 16S rRNA gene amplicon data from eleven simple mock communities with DADA2 and estimate the impact of GCN. In all cases, the mock community composition derived from the 16S sequencing differs from those expected, and GCN fails to improve the classification for most of the analysed communities. Our approach provides empirical evidence that GCN does not improve the 16S target sequencing analyses in real scenarios. We therefore question the use of GCN for metataxonomic surveys until a more comprehensive catalogue of copy numbers becomes available.}, }
@article {pmid32861933, year = {2020}, author = {Uroosa,  and Kazmi, SSUH and Xu, G and Xu, H}, title = {Insights into the effects of harmful algal bloom on ecological quality status using body-size spectrum of biofilm-dwelling ciliates in marine ecosystems.}, journal = {Marine pollution bulletin}, volume = {160}, number = {}, pages = {111596}, doi = {10.1016/j.marpolbul.2020.111596}, pmid = {32861933}, issn = {1879-3363}, mesh = {Biofilms ; *Ciliophora ; *Dinoflagellida ; Ecosystem ; Harmful Algal Bloom ; }, abstract = {The effects of two harmful algae Alexandrium tamarense and Gymnodinium catenatum on ecological quality status were identified using biofilm-dwelling ciliate assemblage as test organism communities. The body-size spectra of the test ciliates were observed at a gradient of cell concentrations of both algal species: 10[0] (control), followed by10[2], 10[3], 10[4] and 10[5] cells ml[-1]. The test ciliates showed clear variations in body-size spectra along the concentration gradients of both algal species. In terms of probability density, the ciliates generally peaked at low levels of algal concentrations (10[0]-10[4] cells ml[-1]) in small size forms, followed by the forms with large sizes at the concentration of 10[5] cells ml[-1] of both algal species. Bootstrapped-average analysis demonstrated a significant change in body-size spectrum when algal concentrations were higher than 10[4] cells ml[-1]. It is suggested that the body-size spectrum of the ciliates may be used to indicate the effects of harmful algal bloom.}, }
@article {pmid32860516, year = {2021}, author = {Virta, L and Soininen, J and Norkko, A}, title = {Biodiversity Loss Threatens the Current Functional Similarity of Beta Diversity in Benthic Diatom Communities.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {293-303}, pmid = {32860516}, issn = {1432-184X}, support = {294853//Academy of Finland/ ; }, mesh = {*Biodiversity ; Diatoms/classification/*isolation &amp; purification ; Environment ; Estuaries ; Water Microbiology ; }, abstract = {The global biodiversity loss has increased the need to understand the effects of decreasing diversity, but our knowledge on how species loss will affect the functioning of communities and ecosystems is still very limited. Here, the levels of taxonomic and functional beta diversity and the effect of species loss on functional beta diversity were investigated in an estuary that provides a naturally steep environmental gradient. The study was conducted using diatoms that are among the most important microorganisms in all aquatic ecosystems and globally account for 40% of marine primary production. Along the estuary, the taxonomic beta diversity of diatom communities was high (Bray-Curtis taxonomic similarity 0.044) and strongly controlled by the environment, particularly wind exposure, salinity, and temperature. In contrast, the functional beta diversity was low (Bray-Curtis functional similarity 0.658) and much less controlled by the environment. Thus, the diatom communities stayed functionally almost similar despite large changes in species composition and environment. This may indicate that, through high taxonomic diversity and redundancy in functions, microorganisms provide an insurance effect against environmental change. However, when studying the effect of decreasing species richness on functional similarity of communities, simulated species loss to 45% of the current species richness decreased functional similarity significantly. This suggests that decreasing species richness may increase variability and reduce the stability and resilience of communities. These results highlight the importance of high taxonomic biodiversity for the stable functioning of benthic communities.}, }
@article {pmid32860076, year = {2021}, author = {Câmara, PEAS and Carvalho-Silva, M and Pinto, OHB and Amorim, ET and Henriques, DK and da Silva, TH and Pellizzari, F and Convey, P and Rosa, LH}, title = {Diversity and Ecology of Chlorophyta (Viridiplantae) Assemblages in Protected and Non-protected Sites in Deception Island (Antarctica, South Shetland Islands) Assessed Using an NGS Approach.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {323-334}, pmid = {32860076}, issn = {1432-184X}, support = {23/2018//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Antarctic Regions ; *Biodiversity ; Chlorophyta/classification/genetics/*growth &amp; development ; Ecosystem ; Geography ; Humans ; Introduced Species ; *Islands ; Soil Microbiology ; }, abstract = {Assessment of the diversity of algal assemblages in Antarctica has until now largely relied on traditional microbiological culture approaches. Here we used DNA metabarcoding through high-throughput sequencing (HTS) to assess the uncultured algal diversity at two sites on Deception Island, Antarctica. The first was a relatively undisturbed site within an Antarctic Specially Protected Area (ASPA 140), and the second was a site heavily impacted by human visitation, the Whalers Bay historic site. We detected 65 distinct algal taxa, 50 from within ASPA 140 and 61 from Whalers Bay. Of these taxa, 46 were common to both sites, and 19 only occurred at one site. Algal richness was about six times greater than reported in previous studies using culture methods. A high proportion of DNA reads obtained was assigned to the highly invasive species Caulerpa webbiana at Whalers Bay, and the potentially pathogenic genus Desmodesmus was found at both sites. Our data demonstrate that important differences exist between these two protected and human-impacted sites on Deception Island in terms of algal diversity, richness, and abundance. The South Shetland Islands have experienced considerable effects of climate change in recent decades, while warming through geothermal activity on Deception Island itself makes this island one of the most vulnerable to colonization by non-native species. The detection of DNA of non-native taxa highlights concerns about how human impacts, which take place primarily through tourism and national research operations, may influence future biological colonization processes in Antarctica.}, }
@article {pmid32859925, year = {2020}, author = {Jurburg, SD and Konzack, M and Eisenhauer, N and Heintz-Buschart, A}, title = {The archives are half-empty: an assessment of the availability of microbial community sequencing data.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {474}, pmid = {32859925}, issn = {2399-3642}, mesh = {Databases, Nucleic Acid ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {As DNA sequencing has become more popular, the public genetic repositories where sequences are archived have experienced explosive growth. These repositories now hold invaluable collections of sequences, e.g., for microbial ecology, but whether these data are reusable has not been evaluated. We assessed the availability and state of 16S rRNA gene amplicon sequences archived in public genetic repositories (SRA, EBI, and DDJ). We screened 26,927 publications in 17 microbiology journals, identifying 2015 16S rRNA gene sequencing studies. Of these, 7.2% had not made their data public at the time of analysis. Among a subset of 635 studies sequencing the same gene region, 40.3% contained data which was not available or not reusable, and an additional 25.5% contained faults in data formatting or data labeling, creating obstacles for data reuse. Our study reveals gaps in data availability, identifies major contributors to data loss, and offers suggestions for improving data archiving practices.}, }
@article {pmid32859275, year = {2020}, author = {Lu, J and Salzberg, SL}, title = {Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {124}, pmid = {32859275}, issn = {2049-2618}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics/*isolation &amp; purification ; Humans ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; *Software ; Time Factors ; }, abstract = {BACKGROUND: For decades, 16S ribosomal RNA sequencing has been the primary means for identifying the bacterial species present in a sample with unknown composition. One of the most widely used tools for this purpose today is the QIIME (Quantitative Insights Into Microbial Ecology) package. Recent results have shown that the newest release, QIIME 2, has higher accuracy than QIIME, MAPseq, and mothur when classifying bacterial genera from simulated human gut, ocean, and soil metagenomes, although QIIME 2 also proved to be the most computationally expensive. Kraken, first released in 2014, has been shown to provide exceptionally fast and accurate classification for shotgun metagenomics sequencing projects. Bracken, released in 2016, then provided users with the ability to accurately estimate species or genus relative abundances using Kraken classification results. Kraken 2, which matches the accuracy and speed of Kraken 1, now supports 16S rRNA databases, allowing for direct comparisons to QIIME and similar systems.<br><br>METHODS: For a comprehensive assessment of each tool, we compare the computational resources and speed of QIIME 2's q2-feature-classifier, Kraken 2, and Bracken in generating the three main 16S rRNA databases: Greengenes, SILVA, and RDP. For an evaluation of accuracy, we evaluated each tool using the same simulated 16S rRNA reads from human gut, ocean, and soil metagenomes that were previously used to compare QIIME, MAPseq, mothur, and QIIME 2. We evaluated accuracy based on the accuracy of the final genera read counts assigned by each tool. Finally, as Kraken 2 is the only tool providing per-read taxonomic assignments, we evaluate the sensitivity and precision of Kraken 2's per-read classifications.<br><br>RESULTS: For both the Greengenes and SILVA database, Kraken 2 and Bracken are up to 100 times faster at database generation. For classification, using the same data as previous studies, Kraken 2 and Bracken are up to 300 times faster, use 100x less RAM, and generate results that more accurate at 16S rRNA profiling than QIIME 2's q2-feature-classifier.<br><br>CONCLUSION: Kraken 2 and Bracken provide a very fast, efficient, and accurate solution for 16S rRNA metataxonomic data analysis. Video Abstract.}, }
@article {pmid32857837, year = {2020}, author = {Ho, A and Mendes, LW and Lee, HJ and Kaupper, T and Mo, Y and Poehlein, A and Bodelier, PLE and Jia, Z and Horn, MA}, title = {Response of a methane-driven interaction network to stressor intensification.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {10}, pages = {}, doi = {10.1093/femsec/fiaa180}, pmid = {32857837}, issn = {1574-6941}, mesh = {*Methane ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil ; *Soil Microbiology ; }, abstract = {Microorganisms may reciprocally select for specific interacting partners, forming a network with interdependent relationships. The methanotrophic interaction network, comprising methanotrophs and non-methanotrophs, is thought to modulate methane oxidation and give rise to emergent properties beneficial for the methanotrophs. Therefore, microbial interaction may become relevant for community functioning under stress. However, empirical validation of the role and stressor-induced response of the interaction network remains scarce. Here, we determined the response of a complex methane-driven interaction network to a stepwise increase in NH4Cl-induced stress (0.5-4.75 g L-1, in 0.25-0.5 g L-1 increments) using enrichment of a naturally occurring complex community derived from a paddy soil in laboratory-scale incubations. Although ammonium and intermediates of ammonium oxidation are known to inhibit methane oxidation, methanotrophic activity was unexpectedly detected even in incubations with high ammonium levels, albeit rates were significantly reduced. Sequencing analysis of the 16S rRNA and pmoA genes consistently revealed divergent communities in the reference and stressed incubations. The 16S rRNA-based co-occurrence network analysis revealed that NH4Cl-induced stress intensification resulted in a less complex and modular network, likely driven by less stable interaction. Interestingly, the non-methanotrophs formed the key nodes, and appear to be relevant members of the community. Overall, stressor intensification unravels the interaction network, with adverse consequences for community functioning.}, }
@article {pmid32855435, year = {2021}, author = {Fodelianakis, S and Valenzuela-Cuevas, A and Barozzi, A and Daffonchio, D}, title = {Direct quantification of ecological drift at the population level in synthetic bacterial communities.}, journal = {The ISME journal}, volume = {15}, number = {1}, pages = {55-66}, pmid = {32855435}, issn = {1751-7370}, mesh = {*Bacteria/genetics ; *Microbiota ; }, abstract = {In community ecology, drift refers to random births and deaths in a population. In microbial ecology, drift is estimated indirectly via community snapshots but in this way, it is almost impossible to distinguish the effect of drift from the effect of other ecological processes. Controlled experiments where drift is quantified in isolation from other processes are still missing. Here we isolate and quantify drift in a series of controlled experiments on simplified and tractable bacterial communities. We detect drift arising randomly in the populations within the communities and resulting in a 1.4-2% increase in their growth rate variability on average. We further use our experimental findings to simulate complex microbial communities under various conditions of selection and dispersal. We find that the importance of drift increases under high selection and low dispersal, where it can lead to ~5% of species loss and to ~15% increase in β-diversity. The species extinct by drift are mainly rare, but they become increasingly less rare when selection increases, and dispersal decreases. Our results provide quantitative insights regarding the properties of drift in bacterial communities and suggest that it accounts for a consistent fraction of the observed stochasticity in natural surveys.}, }
@article {pmid32854141, year = {2020}, author = {Altinli, M and Lequime, S and Atyame, C and Justy, F and Weill, M and Sicard, M}, title = {Wolbachia modulates prevalence and viral load of Culex pipiens densoviruses in natural populations.}, journal = {Molecular ecology}, volume = {29}, number = {20}, pages = {4000-4013}, doi = {10.1111/mec.15609}, pmid = {32854141}, issn = {1365-294X}, mesh = {Animals ; *Culex/genetics ; *Densovirus/genetics ; Phylogeny ; Prevalence ; Viral Load ; *Wolbachia/genetics ; }, abstract = {The inadequacy of standard mosquito control strategies calls for ecologically safe novel approaches, for example the use of biological agents such as the endosymbiotic α-proteobacteria Wolbachia or insect-specific viruses (ISVs). Understanding the ecological interactions between these "biocontrol endosymbionts" is thus a fundamental step. Wolbachia are transmitted vertically from mother to offspring and modify their hosts' phenotypes, including reproduction (e.g., cytoplasmic incompatibility) and survival (e.g., viral interference). In nature, Culex pipiens (sensu lato) mosquitoes are always found infected with genetically diverse Wolbachia called wPip that belong to five phylogenetic groups. In recent years, ISVs have also been discovered in these mosquito species, although their interactions with Wolbachia in nature are unknown. Here, we studied the interactions between a widely prevalent ISV, the Culex pipiens densovirus (CpDV, Densovirinae), and Wolbachia in northern Tunisian C. pipiens populations. We showed an influence of different Wolbachia groups on CpDV prevalence and a general positive correlation between Wolbachia and CpDV loads. By investigating the putative relationship between CpDV diversification and wPip groups in the different sites, we detected a signal linked to wPip groups in CpDV phylogeny in sites where all larvae were infected by the same wPip group. However, no such signal was detected where the wPip groups coexisted, suggesting CpDV horizontal transfer between hosts. Overall, our results provide good evidence for an ecological influence of Wolbachia on an ISV, CpDV, in natural populations and highlight the importance of integrating Wolbachia in our understanding of ISV ecology in nature.}, }
@article {pmid32853201, year = {2020}, author = {Buongiorno, J and Sipes, K and Wasmund, K and Loy, A and Lloyd, KG}, title = {Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0234839}, pmid = {32853201}, issn = {1932-6203}, support = {P 25111/FWF_/Austrian Science Fund FWF/Austria ; P 29426/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Arctic Regions ; Bacterial Proteins/genetics ; Estuaries ; Gammaproteobacteria/classification/*genetics/metabolism ; Genome, Bacterial ; Geologic Sediments/*microbiology ; Heat-Shock Proteins/genetics ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Svalbard ; Transcriptome ; }, abstract = {Distinct lineages of Gammaproteobacteria clade Woeseiales are globally distributed in marine sediments, based on metagenomic and 16S rRNA gene analysis. Yet little is known about why they are dominant or their ecological role in Arctic fjord sediments, where glacial retreat is rapidly imposing change. This study combined 16S rRNA gene analysis, metagenome-assembled genomes (MAGs), and genome-resolved metatranscriptomics uncovered the in situ abundance and transcriptional activity of Woeseiales with burial in four shallow sediment sites of Kongsfjorden and Van Keulenfjorden of Svalbard (79°N). We present five novel Woeseiales MAGs and show transcriptional evidence for metabolic plasticity during burial, including sulfur oxidation with reverse dissimilatory sulfite reductase (dsrAB) down to 4 cm depth and nitrite reduction down to 6 cm depth. A single stress protein, spore protein SP21 (hspA), had a tenfold higher mRNA abundance than any other transcript, and was a hundredfold higher on average than other transcripts. At three out of the four sites, SP21 transcript abundance increased with depth, while total mRNA abundance and richness decreased, indicating a shift in investment from metabolism and other cellular processes to build-up of spore protein SP21. The SP21 gene in MAGs was often flanked by genes involved in membrane-associated stress response. The ability of Woeseiales to shift from sulfur oxidation to nitrite reduction with burial into marine sediments with decreasing access to overlying oxic bottom waters, as well as enter into a dormant state dominated by SP21, may account for its ubiquity and high abundance in marine sediments worldwide, including those of the rapidly shifting Arctic.}, }
@article {pmid32852571, year = {2021}, author = {Hubert, J and Nesvorna, M and Green, SJ and Klimov, PB}, title = {Microbial Communities of Stored Product Mites: Variation by Species and Population.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {506-522}, pmid = {32852571}, issn = {1432-184X}, support = {GA19-09998S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 19-14-00004//Russian Science Foundation/ ; }, mesh = {Acaridae/classification/growth &amp; development/*microbiology ; Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Diet ; Feces/microbiology ; Host Microbial Interactions ; *Microbiota ; Ovum/microbiology ; Phylogeny ; }, abstract = {Arthropod-associated microorganisms are important because they affect host fitness, protect hosts from pathogens, and influence the host's ability to vector pathogens. Stored product mites (Astigmata) often establish large populations in various types of food items, damaging the food by direct feeding and introducing contaminants, including their own bodies, allergen-containing feces, and associated microorganisms. Here we access the microbial structure and abundance in rearing diets, eggs, feces fraction, and mite bodies of 16 mite populations belonging to three species (Carpoglyphus lactis, Acarus siro, and Tyrophagus putrescentiae) using quantitative PCR and 16S ribosomal RNA (rRNA) gene amplicon sequencing. The mite microbiomes had a complex structure dominated by the following bacterial taxa (OTUs): (a) intracellular symbionts of the genera Cardinium and Wolbachia in the mite bodies and eggs; (b) putative gut symbionts of the genera Solitalea, Bartonella, and Sodalis abundant in mite bodies and also present in mite feces; (c) feces-associated or environmental bacteria of the genera Bacillus, Staphylococcus, and Kocuria in the diet, mite bodies, and feces. Interestingly and counterintuitively, the differences between microbial communities in various conspecific mite populations were higher than those between different mite species. To explain some of these differences, we hypothesize that the intracellular bacterial symbionts can affect microbiome composition in mite bodies, causing differences between microbial profiles. Microbial profiles differed between various sample types, such as mite eggs, bodies, and the environment (spent growth medium-SPGM). Low bacterial abundances in eggs may result in stochastic effects in parent-offspring microbial transmission, except for the intracellular symbionts. Bacteria in the rearing diet had little effect on the microbial community structure in SPGM and mite bodies. Mite fitness was positively correlated with bacterial abundance in SPGM and negatively correlated with bacterial abundances in mite bodies. Our study demonstrates critical host-microbe interactions, affecting all stages of mite growth and leading to alteration of the environmental microbiome. Correlational evidence based on absolute quantitation of bacterial 16S rRNA gene copies suggests that mite-associated microorganisms are critical for modulating important pest properties of mites by altering population growth.}, }
@article {pmid32850972, year = {2020}, author = {Álvarez-Rodríguez, I and Ugarte-Uribe, B and de la Arada, I and Arrondo, JLR and Garbisu, C and Alkorta, I}, title = {Conjugative Coupling Proteins and the Role of Their Domains in Conjugation, Secondary Structure and in vivo Subcellular Location.}, journal = {Frontiers in molecular biosciences}, volume = {7}, number = {}, pages = {185}, pmid = {32850972}, issn = {2296-889X}, abstract = {Type IV Coupling Proteins (T4CPs) are essential elements in many type IV secretion systems (T4SSs). The members of this family display sequence, length, and domain architecture heterogeneity, being the conserved Nucleotide-Binding Domain the motif that defines them. In addition, most T4CPs contain a Transmembrane Domain (TMD) in the amino end and an All-Alpha Domain facing the cytoplasm. Additionally, a few T4CPs present a variable domain at the carboxyl end. The structural paradigm of this family is TrwBR388, the T4CP of conjugative plasmid R388. This protein has been widely studied, in particular the role of the TMD on the different characteristics of TrwBR388. To gain knowledge about T4CPs and their TMD, in this work a chimeric protein containing the TMD of TraJpKM101 and the cytosolic domain of TrwBR388 has been constructed. Additionally, one of the few T4CPs of mobilizable plasmids, MobBCloDF13 of mobilizable plasmid CloDF13, together with its TMD-less mutant MobBΔTMD have been studied. Mating studies showed that the chimeric protein is functional in vivo and that it exerted negative dominance against the native proteins TrwBR388 and TraJpKM101. Also, it was observed that the TMD of MobBCloDF13 is essential for the mobilization of CloDF13 plasmid. Analysis of the secondary structure components showed that the presence of a heterologous TMD alters the structure of the cytosolic domain in the chimeric protein. On the contrary, the absence of the TMD in MobBCloDF13 does not affect the secondary structure of its cytosolic domain. Subcellular localization studies showed that T4CPs have a unipolar or bipolar location, which is enhanced by the presence of the remaining proteins of the conjugative system. Unlike what has been described for TrwBR388, the TMD is not an essential element for the polar location of MobBCloDF13. The main conclusion is that the characteristics described for the paradigmatic TrwBR388 T4CP should not be ascribed to the whole T4CP family. Specifically, it has been proven that the mobilizable plasmid-related MobBCloDF13 presents different characteristics regarding the role of its TMD. This work will contribute to better understand the T4CP family, a key element in bacterial conjugation, the main mechanism responsible for antibiotic resistance spread.}, }
@article {pmid32850744, year = {2020}, author = {Song, C and Zhu, F and Carrión, VJ and Cordovez, V}, title = {Beyond Plant Microbiome Composition: Exploiting Microbial Functions and Plant Traits via Integrated Approaches.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {8}, number = {}, pages = {896}, pmid = {32850744}, issn = {2296-4185}, abstract = {Plants recruit specific microorganisms to live inside and outside their roots that provide essential functions for plant growth and health. The study of the microbial communities living in close association with plants helps in understanding the mechanisms involved in these beneficial interactions. Currently, most of the research in this field has been focusing on the description of the taxonomic composition of the microbiome. Therefore, a focus on the plant-associated microbiome functions is pivotal for the development of novel agricultural practices which, in turn, will increase plant fitness. Recent advances in microbiome research using model plant species started to shed light on the functions of specific microorganisms and the underlying mechanisms of plant-microbial interaction. Here, we review (1) microbiome-mediated functions associated with plant growth and protection, (2) insights from native and agricultural habitats that can be used to improve soil health and crop productivity, (3) current -omics and new approaches for studying the plant microbiome, and (4) challenges and future perspectives for exploiting the plant microbiome for beneficial outcomes. We posit that integrated approaches will help in translating fundamental knowledge into agricultural practices.}, }
@article {pmid32849473, year = {2020}, author = {Sedlacek, CJ}, title = {It Takes a Village: Discovering and Isolating the Nitrifiers.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1900}, pmid = {32849473}, issn = {1664-302X}, support = {P 30570/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {It has been almost 150 years since Jean-Jacques Schloesing and Achille Müntz discovered that the process of nitrification, the oxidation of ammonium to nitrate, is a biological process carried out by microorganisms. In the following 15 years, numerous researchers independently contributed paradigm shifting discoveries that formed the foundation of nitrification and nitrification-related research. One of them was Sergei Winogradsky, whose major accomplishments include the discovery of both lithotrophy (in sulfur-oxidizing bacteria) and chemoautotrophy (in nitrifying bacteria). However, Winogradsky often receives most of the credit for many other foundational nitrification discoveries made by his contemporaries. This accumulation of credit over time is at least in part due to the increased attention, Winogradsky receives in the scientific literature and textbooks as a "founder of microbiology" and "the founder of microbial ecology." Here, some light is shed on several other researchers who are often overlooked, but whose work was instrumental to the emerging field of nitrification and to the work of Winogradsky himself. Specifically, the discovery of the biological process of nitrification by Schloesing and Müntz, the isolation of the first nitrifier by Grace and Percy Frankland, and the observation that nitrification is carried out by two distinct groups of microorganisms by Robert Warington are highlighted. Finally, the more recent discoveries of the chemolithoautotrophic ammonia-oxidizing archaea and complete ammonia oxidizers are put into this historical context.}, }
@article {pmid32849470, year = {2020}, author = {Nagler, M and Podmirseg, SM and Mayr, M and Ascher-Jenull, J and Insam, H}, title = {Quantities of Intra- and Extracellular DNA Reveal Information About Activity and Physiological State of Methanogenic Archaea.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1894}, pmid = {32849470}, issn = {1664-302X}, abstract = {Although being a common aim of many microbial ecology studies, measuring individual physiological conditions of a microbial group or species within a complex consortium is still a challenge. Here, we propose a novel approach that is based on the quantification of sequentially extracted extracellular (exDNA) and intracellular DNA (iDNA) and reveals information about cell lysis and activity of methanogenic archaea within a biogas-producing microbial community. We monitored the methane production rates of differently treated batch anaerobic cultures and compared the concentrations of the alpha subunit of the methyl coenzyme M reductase gene of methanogenic archaea in extracellular and intracellular DNA fractions and in the classically extracted total DNA pool. Our results showed that this fine-tuned DNA approach coupled with the interpretation of the ratio between free exDNA and iDNA considerably improved microbial activity tracking compared to the classical extraction/quantification of total DNA. Additionally, it allowed to identify and quantify methanogenic populations that are inactive and those that are strongly influenced by cell lysis. We argue that despite the need of further studies, this method represents a novel approach to gain specific physiological information from a complex environmental sample and holds the potential to be applied to other microbes of interest.}, }
@article {pmid32849423, year = {2020}, author = {Moonga, HB and Schoustra, SE and van den Heuvel, J and Linnemann, AR and Samad, MS and Shindano, J and Smid, EJ}, title = {Composition and Diversity of Natural Bacterial Communities in Mabisi, a Traditionally Fermented Milk.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1816}, pmid = {32849423}, issn = {1664-302X}, abstract = {Many traditionally fermented milk products such as mabisi involve spontaneous fermentation, which can result in bacterial community composition variation due to selection pressure. The aim of this study was to determine the composition of bacterial communities in the different types of mabisi produced across Zambia and identify the factors that influence their composition. Samples of mabisi were collected across the country, and analyzed for pH and bacterial communities using 16S rRNA amplicon sequencing. We found that the bacterial community composition was dominated by members of two phyla, i.e., Firmicutes and Proteobacteria, from which the top 10 most abundant genera were Lactococcus, Lactobacillus, Streptococcus, Enterobacter, Citrobacter, Klebsiella, Kluyvera, Buttiauxella, Aeromonas, and Acinetobacter. The most dominant genus was Lactococcus, which was present in all types of mabisi produced from all regions. The mabisi products from traditional mabisi production regions (TMPRs) were dominated by lactic acid bacteria (LAB) whereas products from non-TMPRs were dominated by non-LAB species. Tonga mabisi, the most popular type of mabisi produced in non-TMPRs, had the most complex and diverse bacterial community composition compared to the other types, which included barotse, backslopping, creamy, and thick-tonga mabisi. Other factors that influenced bacterial community composition were geographical location, fermentation duration and pH while the type of fermentation container and producer did not. This study provides new insights that can be applied in starter culture development as well as microbial functionality studies.}, }
@article {pmid32849396, year = {2020}, author = {Huang, J and Yang, J and Jiang, H and Wu, G and Liu, W and Wang, B and Xiao, H and Han, J}, title = {Microbial Responses to Simulated Salinization and Desalinization in the Sediments of the Qinghai-Tibetan Lakes.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1772}, pmid = {32849396}, issn = {1664-302X}, abstract = {Uncovering microbial response to salinization or desalinization is of great importance to understanding of the influence of global climate change on lacustrine microbial ecology. In this study, to simulate salinization and desalinization, sediments from Erhai Lake (salinity 0.3-0.8 g/L) and Chaka Lake (salinity 299.3-350.7 g/L) on the Qinghai-Tibetan Plateau were transplanted into different lakes with a range of salinity of 0.3-299.3 g/L, followed by in situ incubation for 50 days and subsequent geochemical and microbial analyses. Desalinization was faster than salinization in the transplanted sediments. The salinity of the transplanted sediment increased and decreased in the salinization and desalinization simulation experiments, respectively. The TOC contents of the transplanted sediments were lower than that of their undisturbed counterparts in the salinization experiments, whereas they had a strong negative linear relationship with salinity in the desalinization experiments. Microbial diversity decreased in response to salinization and desalinization, and microbial community dissimilarity significantly (P < 0.01) increased with salinity differences between the transplanted sediments and their undisturbed counterparts. Microbial groups belonging to Gammaproteobacteria and Actinobacteria became abundant in salinization whereas Bacteroidetes and Chloroflexi became dominant in desalinization. Among the predicted microbial functions, hydrogenotrophic methanogenesis, methanogenesis through CO2 reduction with H2, nitrate/nitrogen respiration, and nitrification increased in salinization; in desalinization, enhancement was observed for respiration of sulfur compounds, sulfate respiration, sulfur respiration, thiosulfate respiration, hydrocarbon degradation, chemoheterotrophy, and fermentation, whereas depressing was found for aerobic ammonia oxidation, nitrate/nitrogen respiration, nitrification, nitrite respiration, manganese oxidation, aerobic chemoheterotrophy, and phototrophy. Such microbial variations could be explained by changes of transplantation, salinity, and covarying variables. In summary, salinization and desalinization had profound influence on the geochemistry, microbial community, and function in lakes.}, }
@article {pmid32849356, year = {2020}, author = {Arbour, TJ and Gilbert, B and Banfield, JF}, title = {Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1694}, pmid = {32849356}, issn = {1664-302X}, abstract = {Extracellular electron transfer (EET) between microbes and iron minerals, and syntrophically between species, is a widespread process affecting biogeochemical cycles and microbial ecology. The distribution of this capacity among microbial taxa, and the thermodynamic controls on EET in complex microbial communities, are not fully known. Microbial electrochemical cells (MXCs), in which electrodes serve as the electron acceptor or donor, provide a powerful approach to enrich for organisms capable of EET and to study their metabolism. We used MXCs coupled with genome-resolved metagenomics to investigate the capacity for EET in microorganisms present in a well-studied aquifer near Rifle, CO. Electroactive biofilms were established and maintained for almost 4 years on anodes poised mostly at -0.2 to -0.25 V vs. SHE, a range that mimics the redox potential of iron-oxide minerals, using acetate as the sole carbon source. Here we report the metagenomic characterization of anode-biofilm and planktonic microbial communities from samples collected at timepoints across the study period. From two biofilm and 26 planktonic samples we reconstructed draft-quality and near-complete genomes for 84 bacteria and 2 archaea that represent the majority of organisms present. A novel Geobacter sp. with at least 72 putative multiheme c-type cytochromes (MHCs) was the dominant electrode-attached organism. However, a diverse range of other electrode-associated organisms also harbored putative MHCs with at least 10 heme-binding motifs, as well as porin-cytochrome complexes and e-pili, including Actinobacteria, Ignavibacteria, Chloroflexi, Acidobacteria, Firmicutes, Beta- and Gammaproteobacteria. Our results identify a small subset of the thousands of organisms previously detected in the Rifle aquifer that may have the potential to mediate mineral redox transformations.}, }
@article {pmid32849338, year = {2020}, author = {Presley, GN and Zhang, J and Purvine, SO and Schilling, JS}, title = {Functional Genomics, Transcriptomics, and Proteomics Reveal Distinct Combat Strategies Between Lineages of Wood-Degrading Fungi With Redundant Wood Decay Mechanisms.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1646}, pmid = {32849338}, issn = {1664-302X}, abstract = {Wood-degrading fungi vary in their strategies for deconstructing wood, and their competitive successes shape the rate and fate of carbon released from wood, Earth's largest pool of aboveground terrestrial carbon. In this study, one-on-one interspecific interactions between two model brown rot (carbohydrate-selective) fungi, Gloeophyllum trabeum and Rhodonia (Postia) placenta, were studied on wood wafers where a clearly resolved interaction zone (IZ) could be generated, reproducibly. Comparative RNAseq and proteomics between the IZ and non-interacting hyphae of each species identified combative strategies for each fungus. Glycoside hydrolases were a relatively smaller portion of the interaction secretome compared to non-interacting hyphae. The interaction zone showed higher pectinase specific activity than all other sampling locations, and higher laminarinase specific activity (branched β-glucan proxy) was seen in the IZ secretome relative to equivalent hyphae in single-species cultures. Our efforts also identified two distinct competitive strategies in these two fungi with a shared nutritional mode (brown rot) but polyphyletic ancestral lineages. Gloeophyllum trabeum (Gloeophyllum clade) upregulated more secondary metabolite (SM) synthesis genes in response to a competitor than did R. placenta. R. placenta (Antrodia clade) upregulated a larger variety of uncharacterized oxidoreductases in interacting hyphae, suggesting that these may play a role in mediating competitor response in this fungus. Both species produced several hypothetical proteins exclusively in the interaction zone, leaving questions as to the function of these proteins. This work supports the existence of multiple interaction strategies among brown rot fungi and highlights the functional diversity among wood decay fungi.}, }
@article {pmid32849330, year = {2020}, author = {Floc'h, JB and Hamel, C and Lupwayi, N and Harker, KN and Hijri, M and St-Arnaud, M}, title = {Bacterial Communities of the Canola Rhizosphere: Network Analysis Reveals a Core Bacterium Shaping Microbial Interactions.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1587}, pmid = {32849330}, issn = {1664-302X}, abstract = {The rhizosphere hosts a complex web of prokaryotes interacting with one another that may modulate crucial functions related to plant growth and health. Identifying the key factors structuring the prokaryotic community of the plant rhizosphere is a necessary step toward the enhancement of plant production and crop yield with beneficial associative microorganisms. We used a long-term field experiment conducted at three locations in the Canadian prairies to verify that: (1) the level of cropping system diversity influences the α- and β-diversity of the prokaryotic community of canola (Brassica napus) rhizosphere; (2) the canola rhizosphere community has a stable prokaryotic core; and (3) some highly connected taxa of this community fit the description of hub-taxa. We sampled the rhizosphere of canola grown in monoculture, in a 2-phase rotation (canola-wheat), in a 3-phase rotation (pea-barley-canola), and in a highly diversified 6-phase rotation, five and eight years after cropping system establishment. We detected only one core bacterial Amplicon Sequence Variant (ASV) in the prokaryotic component of the microbiota of canola rhizosphere, a hub taxon identified as cf. Pseudarthrobacter sp. This ASV was also the only hub taxon found in the networks of interactions present in both years and at all three sites. We highlight a cohort of bacteria and archaea that were always connected with the core taxon in the network analyses.}, }
@article {pmid32846525, year = {2020}, author = {Jilani, H and Cilla, A and Barberá, R and Hamdi, M}, title = {Antiproliferative activity of green, black tea and olive leaves polyphenols subjected to biosorption and in vitro gastrointestinal digestion in Caco-2 cells.}, journal = {Food research international (Ottawa, Ont.)}, volume = {136}, number = {}, pages = {109317}, doi = {10.1016/j.foodres.2020.109317}, pmid = {32846525}, issn = {1873-7145}, mesh = {Apoptosis/drug effects ; Biological Availability ; Caco-2 Cells ; Camellia sinensis/*chemistry ; Cell Cycle/drug effects ; Cell Proliferation/*drug effects ; Cell Survival/drug effects ; *Digestion ; Humans ; Olea/*chemistry ; Plant Leaves/*chemistry ; Polyphenols/metabolism/pharmacokinetics/*pharmacology ; Saccharomyces cerevisiae/metabolism ; Tea/chemistry ; }, abstract = {Olive (Olea europaea L.) leaves and tea (Camellia sinensis) are rich sources of bioactive compounds, especially polyphenols. Our previous studies have evidenced the potential use of Saccharomyces cerevisiae as a natural delivery system for these antioxidants and a means to improve their bioaccessibility in the human gut. In the present work, the antiproliferative effect of green tea (GT), black tea (BT) and olive leaves (OL) infusions and suspensions of S. cerevisiae were evaluated, for the first time, in human colon cancer cells (Caco-2) after biosorption and in vitro gastrointestinal digestion. The bioaccessible fractions (BF) were not overtly cytotoxic, not affecting cell viability. ROS and mitochondrial membrane potential changes (Δψm) values were reduced compared with control cells. Moreover, all the BF after biosorption induced a significant (p < 0.05) increase in cell proportions in S-phase. The arrest of the cell cycle was reversible without induction of apoptosis, suggesting that the biosorbed phenolics in both infusions and suspensions act as cytostatic agents.}, }
@article {pmid32845305, year = {2020}, author = {Imchen, M and Kumavath, R}, title = {Shotgun metagenomics reveals a heterogeneous prokaryotic community and a wide array of antibiotic resistance genes in mangrove sediment.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {10}, pages = {}, doi = {10.1093/femsec/fiaa173}, pmid = {32845305}, issn = {1574-6941}, mesh = {*Anti-Bacterial Agents/pharmacology ; Brazil ; China ; Drug Resistance, Microbial/genetics ; Humans ; India ; Malaysia ; *Metagenomics ; Saudi Arabia ; Wetlands ; }, abstract = {Saline tolerant mangrove forests partake in vital biogeochemical cycles. However, they are endangered due to deforestation as a result of urbanization. In this study, we have carried out a metagenomic snapshot of the mangrove ecosystem from five countries to assess its taxonomic, functional and antibiotic resistome structure. Chao1 alpha diversity varied significantly (P < 0.001) between the countries (Brazil, Saudi Arabia, China, India and Malaysia). All datasets were composed of 33 phyla dominated by eight major phyla covering >90% relative abundance. Comparative analysis of mangrove with terrestrial and marine ecosystems revealed the strongest heterogeneity in the mangrove microbial community. We also observed that the mangrove community shared similarities to both the terrestrial and marine microbiome, forming a link between the two contrasting ecosystems. The antibiotic resistant genes (ARG) resistome was comprised of nineteen level 3 classifications dominated by multidrug resistance efflux pumps (46.7 ± 4.3%) and BlaR1 family regulatory sensor-transducer disambiguation (25.2 ± 4.8%). ARG relative abundance was significantly higher in Asian countries and in human intervention datasets at a global scale. Our study shows that the mangrove microbial community and its antibiotic resistance are affected by geography as well as human intervention and are unique to the mangrove ecosystem. Understanding changes in the mangrove microbiome and its ARG is significant for sustainable development and public health.}, }
@article {pmid32845128, year = {2020}, author = {Ceron-Chafla, P and Kleerebezem, R and Rabaey, K and van Lier, JB and Lindeboom, REF}, title = {Direct and Indirect Effects of Increased CO2 Partial Pressure on the Bioenergetics of Syntrophic Propionate and Butyrate Conversion.}, journal = {Environmental science &amp; technology}, volume = {54}, number = {19}, pages = {12583-12592}, pmid = {32845128}, issn = {1520-5851}, mesh = {Anaerobiosis ; Bioreactors ; *Butyrates ; Carbon Dioxide ; Energy Metabolism ; Methane ; Partial Pressure ; *Propionates ; }, abstract = {Simultaneous digestion and in situ biogas upgrading in high-pressure bioreactors will result in elevated CO2 partial pressure (pCO2). With the concomitant increase in dissolved CO2, microbial conversion processes may be affected beyond the impact of increased acidity. Elevated pCO2 was reported to affect the kinetics and thermodynamics of biochemical conversions because CO2 is an intermediate and end-product of the digestion process and modifies the carbonate equilibrium. Our results showed that increasing pCO2 from 0.3 to 8 bar in lab-scale batch reactors decreased the maximum substrate utilization rate (rsmax) for both syntrophic propionate and butyrate oxidation. These kinetic limitations are linked to an increased overall Gibbs free energy change (ΔGOverall) and a potential biochemical energy redistribution among syntrophic partners, which showed interdependence with hydrogen partial pressure (pH2). The bioenergetics analysis identified a moderate, direct impact of elevated pCO2 on propionate oxidation and a pH-mediated effect on butyrate oxidation. These constraints, combined with physiological limitations on growth exerted by increased acidity and inhibition due to higher concentrations of undissociated volatile fatty acids, help to explain the observed phenomena. Overall, this investigation sheds light on the role of elevated pCO2 in delicate biochemical syntrophic conversions by connecting kinetic, bioenergetic, and physiological effects.}, }
@article {pmid32844509, year = {2020}, author = {Zhu, X and Jackson, RD and DeLucia, EH and Tiedje, JM and Liang, C}, title = {The soil microbial carbon pump: From conceptual insights to empirical assessments.}, journal = {Global change biology}, volume = {26}, number = {11}, pages = {6032-6039}, doi = {10.1111/gcb.15319}, pmid = {32844509}, issn = {1365-2486}, support = {31930070//National Natural Science Foundation of China/ ; 41977051//National Natural Science Foundation of China/ ; GJTD-2019-10//K.C. Wong Education Foundation/ ; }, mesh = {Agriculture ; *Carbon ; Crops, Agricultural ; *Soil ; Soil Microbiology ; }, abstract = {The global soil carbon (C) pool is massive, so relatively small changes in soil organic carbon (SOC) stocks can significantly alter atmospheric C and global climate. The recently proposed concept of the soil microbial carbon pump (MCP) emphasizes the active role of soil microbes in SOC storage by integrating the continual microbial transformation of organic C from labile to persistent anabolic forms. However, the concept has not been evaluated with data. Here, we combine datasets, including microbial necromass biomarker amino sugars and SOC, from two long-term agricultural field studies conducted by large United States bioenergy research programs. We interrogate the soil MCP concept by investigating the asynchronous responses of microbial necromass and SOC to land-use change. Microbial necromass appeared to preferentially accumulate in soil and be the dominant contributor to SOC accrual in diversified perennial bioenergy crops. Specifically, ~92% of the additional SOC enhanced by plant diversity was estimated to be microbial necromass C, and >76% of the additional SOC enhanced by land-use transition from annual to perennial crops was estimated to be microbial necromass. This suggests that the soil MCP was stimulated in diversified perennial agroecosystems. We further delineate and suggest two parameters-soil MCP capacity and efficacy-reflecting the conversion of plant C into microbial necromass and the contribution of microbial necromass to SOC, respectively, that should serve as valuable metrics for future studies evaluating SOC storage under alternative management in changing climates.}, }
@article {pmid32843743, year = {2021}, author = {Khoruts, A and Staley, C and Sadowsky, MJ}, title = {Faecal microbiota transplantation for Clostridioides difficile: mechanisms and pharmacology.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {18}, number = {1}, pages = {67-80}, pmid = {32843743}, issn = {1759-5053}, mesh = {Anti-Bacterial Agents/adverse effects/therapeutic use ; *Clostridioides difficile/metabolism/pathogenicity/physiology ; Clostridium Infections/etiology/*physiopathology/*therapy ; *Fecal Microbiota Transplantation ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Recurrence ; Treatment Outcome ; }, abstract = {Faecal microbiota transplantation (FMT) has emerged as a remarkably successful treatment for recurrent Clostridioides difficile infection that cannot be cured with antibiotics alone. Understanding the complex biology and pathogenesis of C. difficile infection, which we discuss in this Perspective, is essential for understanding the potential mechanisms by which FMT cures this disease. Although FMT has already entered clinical practice, different microbiota-based products are currently in clinical trials and are vying for regulatory approval. However, all these therapeutics belong to an entirely new class of agents that require the development of a new branch of pharmacology. Characterization of microbiota therapeutics uses novel and rapidly evolving technologies and requires incorporation of microbial ecology concepts. Here, we consider FMT within a pharmacological framework, including its essential elements: formulation, pharmacokinetics and pharmacodynamics. From this viewpoint, multiple gaps in knowledge become apparent, identifying areas that require systematic research. This knowledge is needed to help clinical providers use microbiota therapeutics appropriately and to facilitate development of next-generation microbiota products with improved safety and efficacy. The discussion here is limited to FMT as a representative of microbiota therapeutics and recurrent C. difficile as the indication; however, consideration of the intrinsic basic principles is relevant to this entire class of microbiota-based therapeutics.}, }
@article {pmid32843539, year = {2020}, author = {Santillan, E and Constancias, F and Wuertz, S}, title = {Press Disturbance Alters Community Structure and Assembly Mechanisms of Bacterial Taxa and Functional Genes in Mesocosm-Scale Bioreactors.}, journal = {mSystems}, volume = {5}, number = {4}, pages = {}, pmid = {32843539}, issn = {2379-5077}, abstract = {Press disturbances are of interest in microbial ecology, as they can drive microbial communities to alternative stable states. However, the effect of press disturbances in community assembly mechanisms, particularly with regard to taxa and functional genes at different levels of abundance (i.e., common and rare), remains largely unknown. Here, we tested the effect of a continuous alteration in substrate feeding scheme on the structure, function, and assembly of bacterial communities. Two sets of replicate 5-liter sequencing batch reactors were operated at two different organic carbon loads for a period of 74 days, following 53 days of acclimation after inoculation with sludge from a full-scale treatment plant. Temporal dynamics of community taxonomic and functional gene structure were derived from metagenomics and 16S rRNA gene metabarcoding data. Disturbed reactors exhibited different community function, structure, and assembly compared to undisturbed reactors. Bacterial taxa and functional genes showed dissimilar α-diversity and community assembly patterns. Deterministic assembly mechanisms were generally stronger in disturbed reactors and in common fractions compared to rare ones. Function quickly recovered after the disturbance was removed, but community structure did not. Our results highlight that functional gene data from metagenomics can indicate patterns of community assembly that differ from those obtained from taxon data. This study reveals how a joint evaluation of assembly mechanisms and community structure of bacterial taxa and functional genes as well as ecosystem function can unravel the response of complex microbial systems to a press disturbance.IMPORTANCE Ecosystem management must be viewed in the context of increasing frequencies and magnitudes of various disturbances that occur at different scales. This work provides a glimpse of the changes in assembly mechanisms found in microbial communities exposed to sustained changes in their environment. These mechanisms, deterministic or stochastic, can cause communities to reach a similar or variable composition and function. For a comprehensive view, we use a joint evaluation of temporal dynamics in assembly mechanisms and community structure for both bacterial taxa and their functional genes at different abundance levels, in both disturbed and undisturbed states. We further reverted the disturbance state to contrast recovery of function with community structure. Our findings are relevant, as very few studies have employed such an approach, while there is a need to assess the relative importance of assembly mechanisms for microbial communities across different spatial and temporal scales, environmental gradients, and types of disturbance.}, }
@article {pmid32842646, year = {2020}, author = {Finore, I and Vigneron, A and Vincent, WF and Leone, L and Di Donato, P and Schiano Moriello, A and Nicolaus, B and Poli, A}, title = {Novel Psychrophiles and Exopolymers from Permafrost Thaw Lake Sediments.}, journal = {Microorganisms}, volume = {8}, number = {9}, pages = {}, pmid = {32842646}, issn = {2076-2607}, support = {UMI-MicroMeNu//Program Sentinel North financed by the Canada First Research Excellence Fund (CFREF); the Natural Sciences and Engineering Research Council of Canada (NSERC); the CNR (Italy)-Universit&#xe9; Laval UMI-MicroMeNu program; the Fonds de Recherche du Qu&#xe9;bec-Nature/ ; }, abstract = {Thermokarst lakes are one of the most abundant types of microbial ecosystems in the circumpolar North. These shallow basins are formed by the thawing and collapse of ice-rich permafrost, with subsequent filling by snow and ice melt. Until now, permafrost thaw lakes have received little attention for isolation of microorganisms by culture-based analysis. The discovery of novel psychrophiles and their biomolecules makes these extreme environments suitable sources for the isolation of new strains, including for potential biotechnological applications. In this study, samples of bottom sediments were collected from three permafrost thaw lakes in subarctic Québec, Canada. Their diverse microbial communities were characterized by 16S rRNA gene amplicon analysis, and subsamples were cultured for the isolation of bacterial strains. Phenotypic and genetic characterization of the isolates revealed affinities to the genera Pseudomonas, Paenibacillus, Acinetobacter,Staphylococcus and Sphingomonas. The isolates were then evaluated for their production of extracellular enzymes and exopolymers. Enzymes of potential biotechnological interest included α and β-glucosidase, α and β-maltosidase, β-xylosidase and cellobiohydrolase. One isolate, Pseudomonas extremaustralis strain 2ASCA, also showed the capability to produce, in the loosely bound cell fraction, a levan-type polysaccharide with a yield of 613 mg/L of culture, suggesting its suitability as a candidate for eco-sustainable alternatives to commercial polymers.}, }
@article {pmid32841483, year = {2020}, author = {Mammola, S and Amorim, IR and Bichuette, ME and Borges, PAV and Cheeptham, N and Cooper, SJB and Culver, DC and Deharveng, L and Eme, D and Ferreira, RL and Fišer, C and Fišer, &#x17d; and Fong, DW and Griebler, C and Jeffery, WR and Jugovic, J and Kowalko, JE and Lilley, TM and Malard, F and Manenti, R and Martínez, A and Meierhofer, MB and Niemiller, ML and Northup, DE and Pellegrini, TG and Pipan, T and Protas, M and Reboleira, ASPS and Venarsky, MP and Wynne, JJ and Zagmajster, M and Cardoso, P}, title = {Fundamental research questions in subterranean biology.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {95}, number = {6}, pages = {1855-1872}, doi = {10.1111/brv.12642}, pmid = {32841483}, issn = {1469-185X}, support = {eLTER//Horizon 2020 Framework Programme/International ; N1-0069//Javna Agencija za Raziskovalno Dejavnost RS/International ; 15471//Villum Fonden/International ; 678193//Horizon 2020 Framework Programme/International ; RDP 00092-18//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/International ; 882221//H2020 Marie Sk&#x142;odowska-Curie Actions/International ; ANR-15-CE32-0005//Agence Nationale de la Recherche/International ; 745530//H2020 Marie Sk&#x142;odowska-Curie Actions/International ; CF19-0609//Carlsbergfondet/International ; }, mesh = {Adaptation, Physiological ; *Caves ; *Ecology ; Genomics ; }, abstract = {Five decades ago, a landmark paper in Science titled The Cave Environment heralded caves as ideal natural experimental laboratories in which to develop and address general questions in geology, ecology, biogeography, and evolutionary biology. Although the 'caves as laboratory' paradigm has since been advocated by subterranean biologists, there are few examples of studies that successfully translated their results into general principles. The contemporary era of big data, modelling tools, and revolutionary advances in genetics and (meta)genomics provides an opportunity to revisit unresolved questions and challenges, as well as examine promising new avenues of research in subterranean biology. Accordingly, we have developed a roadmap to guide future research endeavours in subterranean biology by adapting a well-established methodology of 'horizon scanning' to identify the highest priority research questions across six subject areas. Based on the expert opinion of 30 scientists from around the globe with complementary expertise and of different academic ages, we assembled an initial list of 258 fundamental questions concentrating on macroecology and microbial ecology, adaptation, evolution, and conservation. Subsequently, through online surveys, 130 subterranean biologists with various backgrounds assisted us in reducing our list to 50 top-priority questions. These research questions are broad in scope and ready to be addressed in the next decade. We believe this exercise will stimulate research towards a deeper understanding of subterranean biology and foster hypothesis-driven studies likely to resonate broadly from the traditional boundaries of this field.}, }
@article {pmid32840670, year = {2021}, author = {Nikouli, E and Meziti, A and Smeti, E and Antonopoulou, E and Mente, E and Kormas, KA}, title = {Gut Microbiota of Five Sympatrically Farmed Marine Fish Species in the Aegean Sea.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {460-470}, pmid = {32840670}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Diet/veterinary ; *Fisheries ; Fishes/classification/growth &amp; development/*microbiology ; *Gastrointestinal Microbiome ; Greece ; Mediterranean Sea ; RNA, Ribosomal, 16S ; Species Specificity ; }, abstract = {In this study, we hypothesized that sympatrically grown farmed fish, i.e. fish which experience similar environmental conditions and nutritionally similar diets, would have more convergent gut microbiota. Using a "common garden" approach, we identified the core microbiota and bacterial community structure differences between five fish species farmed in the same aquaculture site on the west coast of the Aegean Sea, Greece. The investigated individuals were at similar developmental stages and reared in adjacent (< 50 m) aquaculture cages; each cage had 15 kg fish m[-3]. The diets were nutritionally similar to support optimal growth for each fish species. DNA from the midgut of 3-6 individuals per fish species was extracted and sequenced for the V3-V4 region of the bacterial 16S rRNA. Only 3.9% of the total 181 operational taxonomic units (OTUs) were shared among all fish. Between 5 and 74 OTUs were unique to each fish species. Each of the investigated fish species had a distinct profile of dominant OTUs, i.e. cumulative relative abundance of ≥ 80%. Co-occurrence network analysis for each fish species showed that all networks were strongly dominated by positive correlations between the abundances of their OTUs. However, each fish species had different network characteristics suggesting the differential significance of the OTUs in each of the five fish species midgut. The results of the present study may provide evidence that adult fish farmed in the Mediterranean Sea have a rather divergent and species-specific gut microbiota profile, which are shaped independently of the similar environmental conditions under which they grow.}, }
@article {pmid32840024, year = {2020}, author = {Sizikov, S and Burgsdorf, I and Handley, KM and Lahyani, M and Haber, M and Steindler, L}, title = {Characterization of sponge-associated Verrucomicrobia: microcompartment-based sugar utilization and enhanced toxin-antitoxin modules as features of host-associated Opitutales.}, journal = {Environmental microbiology}, volume = {22}, number = {11}, pages = {4669-4688}, doi = {10.1111/1462-2920.15210}, pmid = {32840024}, issn = {1462-2920}, support = {1243/16//Israel Science Foundation/ ; }, mesh = {Animals ; Mediterranean Sea ; Microbiota ; Phylogeny ; Porifera/*microbiology ; Seawater/microbiology ; Sugars/*metabolism ; *Symbiosis ; Toxin-Antitoxin Systems/*genetics ; Verrucomicrobia/classification/genetics/metabolism/*physiology ; }, abstract = {Bacteria of the phylum Verrucomicrobia are ubiquitous in marine environments and can be found as free-living organisms or as symbionts of eukaryotic hosts. Little is known about host-associated Verrucomicrobia in the marine environment. Here we reconstructed two genomes of symbiotic Verrucomicrobia from bacterial metagenomes derived from the Atlanto-Mediterranean sponge Petrosia ficiformis and three genomes from strains that we isolated from offshore seawater of the Eastern Mediterranean Sea. Phylogenomic analysis of these five strains indicated that they are all members of Verrucomicrobia subdivision 4, order Opitutales. We compared these novel sponge-associated and seawater-isolated genomes to closely related Verrucomicrobia. Genomic analysis revealed that Planctomycetes-Verrucomicrobia microcompartment gene clusters are enriched in the genomes of symbiotic Opitutales including sponge symbionts but not in free-living ones. We hypothesize that in sponge symbionts these microcompartments are used for degradation of l-fucose and l-rhamnose, which are components of algal and bacterial cell walls and therefore may be found at high concentrations in the sponge tissue. Furthermore, we observed an enrichment of toxin-antitoxin modules in symbiotic Opitutales. We suggest that, in sponges, verrucomicrobial symbionts utilize these modules as a defence mechanism against antimicrobial activity deriving from the abundant microbial community co-inhabiting the host.}, }
@article {pmid32839879, year = {2021}, author = {Noskov, YA and Kabilov, MR and Polenogova, OV and Yurchenko, YA and Belevich, OE and Yaroslavtseva, ON and Alikina, TY and Byvaltsev, AM and Rotskaya, UN and Morozova, VV and Glupov, VV and Kryukov, VY}, title = {A Neurotoxic Insecticide Promotes Fungal Infection in Aedes aegypti Larvae by Altering the Bacterial Community.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {493-505}, pmid = {32839879}, issn = {1432-184X}, support = {18-74-00090//Russian Science Foundation (RU)/ ; }, mesh = {Aedes/*microbiology ; Animals ; Antibiosis/drug effects ; Bacteria/classification/drug effects/genetics/isolation &amp; purification ; Bacterial Load ; Insecticides/*pharmacology ; Ivermectin/analogs &amp; derivatives/pharmacology ; Larva/microbiology ; Metarhizium/*physiology ; Microbiota/*drug effects ; Mosquito Control ; Spores, Fungal/physiology ; }, abstract = {Symbiotic bacteria have a significant impact on the formation of defensive mechanisms against fungal pathogens and insecticides. The microbiome of the mosquito Aedes aegypti has been well studied; however, there are no data on the influence of insecticides and pathogenic fungi on its structure. The fungus Metarhizium robertsii and a neurotoxic insecticide (avermectin complex) interact synergistically, and the colonization of larvae with hyphal bodies is observed after fungal and combined (conidia + avermectins) treatments. The changes in the bacterial communities (16S rRNA) of Ae. aegypti larvae under the influence of fungal infection, avermectin toxicosis, and their combination were studied. In addition, we studied the interactions between the fungus and the predominant cultivable bacteria in vitro and in vivo after the coinfection of the larvae. Avermectins increased the total bacterial load and diversity. The fungus decreased the diversity and insignificantly increased the bacterial load. Importantly, avermectins reduced the relative abundance of Microbacterium (Actinobacteria), which exhibited a strong antagonistic effect towards the fungus in in vitro and in vivo assays. The avermectin treatment led to an increased abundance of Chryseobacterium (Flavobacteria), which exerted a neutral effect on mycosis development. In addition, avermectin treatment led to an elevation of some subdominant bacteria (Pseudomonas) that interacted synergistically with the fungus. We suggest that avermectins change the bacterial community to favor the development of fungal infection.}, }
@article {pmid32836127, year = {2020}, author = {Li, X and Wang, T and Chang, SX and Jiang, X and Song, Y}, title = {Biochar increases soil microbial biomass but has variable effects on microbial diversity: A meta-analysis.}, journal = {The Science of the total environment}, volume = {749}, number = {}, pages = {141593}, doi = {10.1016/j.scitotenv.2020.141593}, pmid = {32836127}, issn = {1879-1026}, mesh = {Biomass ; *Carbon ; Charcoal ; *Soil ; Soil Microbiology ; }, abstract = {Biochar has been extensively studied as a soil amendment for carbon sequestration and for improving soil quality; however, a systematic understanding of the responses of soil microbial biomass and diversity to biochar addition is lacking. Here, a meta-analysis of 999 paired data points from 194 studies shows that biochar increases microbial biomass but has variable effects on microbial diversity. Generally, the effects of biochar on microbial biomass are dependent on biochar properties, while that on microbial diversity is dependent on soil properties. The application of biochar, particularly that produced under low temperature and from nutrient-rich feedstocks, could better increase soil microbial biomass (based on phospholipid fatty acid analysis (MBCPLFA)) and diversity. The increases of total microbial biomass with biochar addition are greater in the field than in laboratory studies, in sandy than in clay soils, and when measured by fumigation-extraction (MBCFE) than by MBCPLFA. The bacterial biomass only significantly increases in laboratory studies and fungal biomass only in soils with pH ≤ 7.5 and soil organic carbon ≤30 g kg[-1]. The increases in total microbial diversity with biochar addition were greater in acidic and sandy soils with low soil organic carbon content and in laboratory incubation studies. In addition, long-term and low-rate addition of biochar always increases microbial diversity. To better guide the use of biochar as a soil amendment, we suggest that establishing long-term and field studies, using a standard method for measuring microbial communities, on different soil types should be our emphasis in future research.}, }
@article {pmid32835181, year = {2020}, author = {Kirubakaran, R and ArulJothi, KN and Revathi, S and Shameem, N and Parray, JA}, title = {Emerging priorities for microbial metagenome research.}, journal = {Bioresource technology reports}, volume = {11}, number = {}, pages = {100485}, pmid = {32835181}, issn = {2589-014X}, abstract = {Overwhelming anthropogenic activities lead to deterioration of natural resources and the environment. The microorganisms are considered desirable, due to their suitability for easy genetic manipulation and handling. With the aid of modern biotechnological techniques, the culturable microorganisms have been widely exploited for the benefit of mankind. Metagenomics, a powerful tool to access the abundant biodiversity of the environmental samples including the unculturable microbes, to determine microbial diversity and population structure, their ecological roles and expose novel genes of interest. This review focuses on the microbial adaptations to the adverse environmental conditions, metagenomic techniques employed towards microbial biotechnology. Metagenomic approach helps to understand microbial ecology and to identify useful microbial derivatives like antibiotics, toxins, and enzymes with diverse and enhanced function. It also summarizes the application of metagenomics in clinical diagnosis, improving microbial ecology, therapeutics, xenobiotic degradation and impact on agricultural crops.}, }
@article {pmid32834061, year = {2020}, author = {D'Abramo, F and Neumeyer, S}, title = {A historical and political epistemology of microbes.}, journal = {Centaurus; international magazine of the history of science and medicine}, volume = {62}, number = {2}, pages = {321-330}, pmid = {32834061}, issn = {0008-8994}, abstract = {This article traces the historical co-evolution of microbiology, bacteriology, and virology, framed within industrial and agricultural contexts, as well as their role in colonial and national history between the end of the 19th century and the first decades of the 20th century. The epistemology of germ theory, coupled with the economic interests of European colonies, has shaped the understanding of human-microbial relationships in a reductionist way. We explore a brief history of the medical and biological sciences, focusing on microbes and the difficulty of implementing germ theory outside of biology laboratories. Furthermore, we highlight the work of Lynn Margulis, who conceptualized microbes within their ecological contexts. Such research shows the active role microbes play in handling life-sustaining biological and biochemical processes. We outline how the industrial and technological advancements of the last two centuries not only impacted almost all human societies, but also changed the world on microbial, biological, and geological levels. The narration of these histories is a complex task, and depends on how national, international, and intergovernmental institutions (such as the World Health Organization) conceive of the selective environmental pressures exerted by industry and biotechnological companies.}, }
@article {pmid32832265, year = {2020}, author = {Li, X and Li, Z and He, Y and Li, P and Zhou, H and Zeng, N}, title = {Regional distribution of Christensenellaceae and its associations with metabolic syndrome based on a population-level analysis.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e9591}, pmid = {32832265}, issn = {2167-8359}, abstract = {The link between the gut microbiota and metabolic syndrome (MetS) has attracted widespread attention. Christensenellaceae was recently described as an important player in human health, while its distribution and relationship with MetS in Chinese population is still unknown. This study sought to observe the association between Christensenellaceae and metabolic indexes in a large sample of residents in South China. A total of 4,781 people from the GGMP project were included, and the fecal microbiota composition of these individuals was characterized by 16S rRNA sequencing and analyzed the relation between Christensenellaceae and metabolism using QIIME (Quantitative Insight Into Microbial Ecology, Version 1.9.1). The results demonstrated that microbial richness and diversity were increased in the group with a high abundance of Christensenellaceae, who showed a greater complexity of the co-occurrence network with other bacteria than residents who lacked Christensenellaceae. The enriched bacterial taxa were predominantly represented by Oscillospira, Ruminococcaceae, RF39, Rikenellaceae and Akkermansia as the Christensenellaceae abundance increased, while the abundances of Veillonella, Fusobacterium and Klebsiella were significantly reduced. Furthermore, Christensenellaceae was negatively correlated with the pathological features of MetS, such as obesity, hypertriglyceridemia and body mass index (BMI). We found reduced levels of lipid biosynthesis and energy metabolism pathways in people with a high abundance of Christensenellaceae, which may explain the negative relationship between body weight and Christensenellaceae. In conclusion, we found a negative correlation between Christensenellaceae and MetS in a large Chinese population and reported the geographical distribution of Christensenellaceae in the GGMP study. The association data from this population-level research support the investigation of strains within Christensenellaceae as potentially beneficial gut microbes.}, }
@article {pmid32830554, year = {2020}, author = {Van Hul, M and Karnik, K and Canene-Adams, K and De Souza, M and Van den Abbeele, P and Marzorati, M and Delzenne, NM and Everard, A and Cani, PD}, title = {Comparison of the effects of soluble corn fiber and fructooligosaccharides on metabolism, inflammation, and gut microbiome of high-fat diet-fed mice.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {319}, number = {4}, pages = {E779-E791}, doi = {10.1152/ajpendo.00108.2020}, pmid = {32830554}, issn = {1522-1555}, mesh = {Animals ; Body Composition ; Body Weight ; Diet, High-Fat/*adverse effects ; Dietary Fiber/*pharmacology ; Energy Metabolism/drug effects ; Gastrointestinal Microbiome/*drug effects ; *Inflammation ; Insulin Resistance ; Male ; Metabolism/*drug effects ; Mice ; Mice, Inbred C57BL ; Oligosaccharides/*pharmacology ; Probiotics ; *Zea mays ; }, abstract = {Dietary fibers are essential components of a balanced diet and have beneficial effects on metabolic functions. To gain insight into their impact on host physiology and gut microbiota, we performed a direct comparison of two specific prebiotic fibers in mice. During an 8-wk follow up, mice fed a high-fat diet (HFD) were compared with mice on a normal diet (basal condition, controls) and to mice fed the HFD but treated with one of the following prebiotics: fructooligosaccharides (FOS) or soluble corn fiber (SCF). Both prebiotic fibers led to a similar reduction of body weight and fat mass, lower inflammation and improved metabolic parameters. However, these health benefits were the result of different actions of the fibers, as SCF impacted energy excretion, whereas FOS did not. Interestingly, both fibers had very distinct gut microbial signatures with different short-chain fatty acid profiles, indicating that they do not favor the growth of the same bacterial communities. Although the prebiotic potential of different fibers may seem physiologically equivalent, our data show that the underlying mechanisms of action are different, and this by targeting different gut microbes. Altogether, our data provide evidence that beneficial health effects of specific dietary fibers must be documented to be considered a prebiotic and that studies devoted to understanding how structures relate to specific microbiota modulation and metabolic effects are warranted.}, }
@article {pmid32830371, year = {2020}, author = {Mukherjee, I and Salcher, MM and Andrei, A&#x15e; and Kavagutti, VS and Shabarova, T and Grujčić, V and Haber, M and Layoun, P and Hodoki, Y and Nakano, SI and Šimek, K and Ghai, R}, title = {A freshwater radiation of diplonemids.}, journal = {Environmental microbiology}, volume = {22}, number = {11}, pages = {4658-4668}, doi = {10.1111/1462-2920.15209}, pmid = {32830371}, issn = {1462-2920}, support = {MSM200961801//Akademie V&#x11b;d &#x10c;esk&#xe9; Republiky/ ; 17-04828S//Grant Agency of the Czech Republic/ ; 19-23469S//Grant Agency of the Czech Republic/ ; 20-12496X//Grant Agency of the Czech Republic/ ; 022/2019/P//Grant Agency of the University of South Bohemia/ ; 116/2019/P//Grant Agency of the University of South Bohemia/ ; JSPS-17-17//JSPS Bilateral Japanese-Czech Joint Research Project/ ; 310030_185108/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Biodiversity ; Ecosystem ; Euglenozoa/*classification/cytology/genetics/*isolation &amp; purification ; In Situ Hybridization, Fluorescence ; Japan ; Lakes/*microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Species Specificity ; }, abstract = {Diplonemids are considered marine protists and have been reported among the most abundant and diverse eukaryotes in the world oceans. Recently we detected the presence of freshwater diplonemids in Japanese deep freshwater lakes. However, their distribution and abundances in freshwater ecosystems remain unknown. We assessed abundance and diversity of diplonemids from several geographically distant deep freshwater lakes of the world by amplicon-sequencing, shotgun metagenomics and catalysed reporter deposition-fluorescent in situ hybridization (CARD-FISH). We found diplonemids in all the studied lakes, albeit with low abundances and diversity. We assembled long 18S rRNA sequences from freshwater diplonemids and showed that they form a new lineage distinct from the diverse marine clades. Freshwater diplonemids are a sister-group to a marine clade, which are mainly isolates from coastal and bay areas, suggesting a recent habitat transition from marine to freshwater habitats. Images of CARD-FISH targeted freshwater diplonemids suggest they feed on bacteria. Our analyses of 18S rRNA sequences retrieved from single-cell genomes of marine diplonemids show they encode multiple rRNA copies that may be very divergent from each other, suggesting that marine diplonemid abundance and diversity both have been overestimated. These results have wider implications on assessing eukaryotic abundances in natural habitats by using amplicon-sequencing alone.}, }
@article {pmid32829442, year = {2021}, author = {Cabrerizo, MJ and Marañón, E}, title = {Grazing Pressure Is Independent of Prey Size in a Generalist Herbivorous Protist: Insights from Experimental Temperature Gradients.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {553-562}, pmid = {32829442}, issn = {1432-184X}, support = {PGC2018-094553B-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; FJCI2017-32318//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; }, mesh = {*Dinoflagellida ; *Food Chain ; Phytoplankton ; Plankton ; Temperature ; }, abstract = {Grazing by herbivorous protists contributes to structuring plankton communities through its effect on the growth, biomass, and competitiveness of prey organisms and also impacts the transfer of primary production towards higher trophic levels. Previous evidence shows that heterotrophic processes (grazing rates, g) are more sensitive to temperature than autotrophic ones (phytoplankton growth rates, μ) and also that small cells tend to be more heavily predated than larger ones; however, it remains unresolved how the interplay between changes in temperature and cell size modulates grazing pressure (i.e., g:μ ratio). We addressed this problem by conducting an experiment with four phytoplankton populations, from pico- to microphytoplankton, over a 12 °C gradient and in the presence/absence of a generalist herbivorous protist, Oxyrrhis marina. We found that highest g rates coincided with highest μ rates, which corresponded to intermediate cell sizes. There were no significant differences in either μ or g between the smallest and largest cell sizes considered. The g:μ ratio was largely independent of cell size and C:N ratios, and its thermal dependence was low although species-specific differences were large. We suggest that the similar g:μ found could be the consequence that the energetic demand imposed by rising temperatures would be a more important issue than the mechanical constriction to ingestion derived from prey cell size. Despite the difficulty of quantifying μ and g in natural planktonic communities, we suggest that the g:μ ratio is a key response variable to evaluate thermal sensitivity of food webs because it gives a more integrative view of trophic functioning than both rates separately.}, }
@article {pmid32829441, year = {2021}, author = {Silveira, R and Silva, MRSS and de Roure Bandeira de Mello, T and Alvim, EACC and Marques, NCS and Kruger, RH and da Cunha Bustamante, MM}, title = {Bacteria and Archaea Communities in Cerrado Natural Pond Sediments.}, journal = {Microbial ecology}, volume = {81}, number = {3}, pages = {563-578}, pmid = {32829441}, issn = {1432-184X}, support = {process number 193.000.567/2009//Funda&#xe7;&#xe3;o de Apoio &#xe0; Pesquisa do Distrito Federal/ ; }, mesh = {*Archaea/genetics ; Bacteria/genetics ; Biodiversity ; Geologic Sediments ; Phylogeny ; *Ponds ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Natural ponds in the Brazilian Cerrado harbor high biodiversity but are still poorly studied, especially their microbial assemblage. The characterization of the microbial community in aquatic environments is fundamental for understanding its functioning, particularly under the increasing pressure posed by land conversion and climate change. Here, we aim to characterize the structure (abundance, richness, and diversity) and composition of the Bacteria and Archaea in the sediment of two natural ponds belonging to different basins that primarily differ in size and depth in the Cerrado. Sediment samples were collected in the dry and rainy seasons and the transition periods between both. The structure and composition of Bacteria and Archaea were assessed by 16S rRNA gene pyrosequencing. We identified 45 bacterial and four archaeal groups. Proteobacteria and Acidobacteria dominated the bacterial community, while Euryarchaeota and Thaumarchaeota dominated the archaeal community. Seasonal fluctuations in the relative abundance of microbial taxa were observed, but pond characteristics were more determinant to community composition differences. Microbial communities are highly diverse, and local variability could partially explain the microbial structure's main differences. Functional predictions based in 16S rRNA gene accessed with Tax4Fun indicated an enriched abundance of predicted methane metabolism in the deeper pond, where higher abundance of methanogenic archaea Methanocella, Methanosaeta, and Methanomicrobiaceae was detected. Our dataset encompasses the more comprehensive survey of prokaryotic microbes in Cerrado's aquatic environments. Here, we present basic and essential information about composition and diversity, for initial insights into the ecology of Bacteria and Archaea in these environments.}, }
@article {pmid32829154, year = {2021}, author = {Jamwal, R and Amit,  and Kumari, S and Balan, B and Kelly, S and Cannavan, A and Singh, DK}, title = {Rapid and non-destructive approach for the detection of fried mustard oil adulteration in pure mustard oil via ATR-FTIR spectroscopy-chemometrics.}, journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy}, volume = {244}, number = {}, pages = {118822}, doi = {10.1016/j.saa.2020.118822}, pmid = {32829154}, issn = {1873-3557}, abstract = {Attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy integrated with chemometrics was effectively applied for the rapid detection and accurate quantification of fried mustard oil (FMO) adulteration in pure mustard oil (PMO). PMO was adulterated with FMO in the range of 0.5-50% v/v. Principal component analysis (PCA) elucidated the studied adulteration using two components with an explained variance of 97%. The linear discriminant analysis (LDA) was adopted to classify the adulterated PMO samples with FMO. LDA model showed 100% accuracy initially, as well as when cross-validated. To enhance the overall quality of models, characteristic spectral regions were optimized, and principal component regression (PCR) and partial least square regression (PLS-R) models were constructed with high accuracy and precision. PLS-R model for the 2nd derivative of the optimized spectral region 1260-1080 cm[-1] showed best results for prediction sample sets in terms of high R[2] and residual predictive deviation (RPD) value of 0.999 and 31.91 with low root mean square error (RMSE) and relative prediction error (RE %) of 0.53% v/v and 3.37% respectively. Thus, the suggested method can detect up to 0.5% v/v of adulterated FMO in PMO in a short time interval.}, }
@article {pmid32829116, year = {2020}, author = {Sakarika, M and Candry, P and Depoortere, M and Ganigué, R and Rabaey, K}, title = {Impact of substrate and growth conditions on microbial protein production and composition.}, journal = {Bioresource technology}, volume = {317}, number = {}, pages = {124021}, doi = {10.1016/j.biortech.2020.124021}, pmid = {32829116}, issn = {1873-2976}, mesh = {Biomass ; *Carbon ; }, abstract = {Production of microbial protein (MP) from recovered resources - e.g. CO2-sourced formate and acetate - could provide protein while enabling CO2 capture. To assess the protein quality obtained from this process, pure cultures and enriched communities were selected and characterized kinetically, stoichiometrically and nutritionally. Growth on acetate resulted in up to 5.3 times higher maximum specific growth rate (μmax) than formate (i.e. 0.15-0.41 h[-1] for acetate compared to 0.061-0.29 h[-1] for formate at pH = 7). The protein content was a function of the growth phase, with the highest values during stationary phase, ranging between 18 and 82%CDW protein depending on the organism and substrate. The negative correlation between biomass productivity and protein content indicated a trade-off between production rate and product quality. The final product (i.e. dried MP) quality was in most cases superior to soybean and all cultures were rich in threonine, phenylalanine and tyrosine, regardless of the carbon source.}, }
@article {pmid32827977, year = {2020}, author = {Dai, H and Gao, J and Wang, S and Li, D and Wang, Z}, title = {The key active degrader, metabolic pathway and microbial ecology of triclosan biodegradation in an anoxic/oxic system.}, journal = {Bioresource technology}, volume = {317}, number = {}, pages = {124014}, doi = {10.1016/j.biortech.2020.124014}, pmid = {32827977}, issn = {1873-2976}, mesh = {Bacteria/genetics ; Biodegradation, Environmental ; Drug Resistance, Microbial ; Metabolic Networks and Pathways ; *Triclosan ; }, abstract = {A lab-scale anoxic/oxic (A/O) system was used to reveal the key active triclosan-degrading bacteria (TCS-DB) in this study. The results showed that TCS was mainly removed by metabolism of heterotrophic bacteria (accounting for about 62%), and the potential metabolic pathway was the break of ether bond in TCS formed 2,4-dichlorophenol, and further dechlorination formed phenol or other metabolic end products. DNA-based stable isotope probing (DNA-SIP) assay further revealed that Methylobacillus accounting for 20.75% in [13]C sample was the key active TCS-DB. Furthermore, methylotrophy and methanol oxidation were found to be the potential metabolic routes of TCS degradation by functional annotation of prokaryotic taxa analysis. Interestingly, TCS accelerated the propagation of antibiotic resistance genes (fabI) and intI1 which positively correlated with several functional microorganisms (p < 0.05). This study contributes to comprehend the potential mechanism, metabolic pathway and microbial ecology of TCS biodegradation in A/O system.}, }
@article {pmid32827089, year = {2021}, author = {Maher, AMD and Asaiyah, M and Quinn, S and Burke, R and Wolff, H and Bode, HB and Griffin, CT}, title = {Competition and Co-existence of Two Photorhabdus Symbionts with a Nematode Host.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {223-239}, pmid = {32827089}, issn = {1432-184X}, support = {16/RI/3399/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Animals ; Anthraquinones/metabolism ; Grassland ; Luminescent Measurements ; Photorhabdus/growth &amp; development/*metabolism ; Secondary Metabolism/physiology ; Strongyloidea/*microbiology ; Symbiosis/*physiology ; }, abstract = {Photorhabdus spp. (Enterobacteriales: Morganellaceae) occur exclusively as symbionts of Heterorhabditis nematodes for which they provide numerous services, including killing insects and providing nutrition and defence within the cadavers. Unusually, two species (Photorhabdus cinerea and Photorhabdus temperata) associate with a single population of Heterorhabditis downesi at a dune grassland site. Building on previous work, we investigated competition between these two Photorhabdus species both at the regional (between insects) and local (within insect) level by trait comparison and co-culture experiments. There was no difference between the species with respect to supporting nematode reproduction and protection of cadavers against invertebrate scavengers, but P. cinerea was superior to P. temperata in several traits: faster growth rate, greater antibacterial and antifungal activity and colonisation of a higher proportion of nematodes in co-culture. Moreover, where both bacterial symbionts colonised single nematode infective juveniles, P. cinerea tended to dominate in numbers. Differences between Photorhabdus species were detected in the suite of secondary metabolites produced: P. temperata produced several compounds not produced by P. cinerea including anthraquinone pigments. Bioluminescence emitted by P. temperata also tended to be brighter than that from P. cinerea. Bioluminescence and pigmentation may protect cadavers against scavengers that rely on sight. We conclude that while P. cinerea may show greater local level (within-cadaver) competitive success, co-existence of the two Photorhabdus species in the spatially heterogeneous environment of the dunes is favoured by differing specialisations in defence of the cadaver against differing locally important threats.}, }
@article {pmid32826215, year = {2020}, author = {Gofstein, TR and Perkins, M and Field, J and Leigh, MB}, title = {The Interactive Effects of Crude Oil and Corexit 9500 on Their Biodegradation in Arctic Seawater.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {21}, pages = {}, pmid = {32826215}, issn = {1098-5336}, support = {RL5 GM118990/GM/NIGMS NIH HHS/United States ; TL4 GM118992/GM/NIGMS NIH HHS/United States ; UL1 GM118991/GM/NIGMS NIH HHS/United States ; }, mesh = {Arctic Regions ; Bacteria/*metabolism ; Biodegradation, Environmental ; *Lipids ; *Microbiota ; Petroleum/*metabolism ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Seawater/microbiology ; }, abstract = {The risk of petroleum spills coupled with the potential application of chemical dispersants as a spill response strategy necessitates further understanding of the fate of oil and dispersants and their interactive effects during biodegradation. Using Arctic seawater mesocosms amended with either crude oil, Corexit 9500, or both together, we quantified the chemical losses of crude oil and Corexit 9500 and identified microbial taxa implicated in their biodegradation based on shifts in the microbial community structure over a 30-day time course. Chemical analyses included total petroleum hydrocarbons (TPH), n-alkanes, branched alkanes, and polycyclic aromatic hydrocarbons (PAHs) for oil loss and the surfactant components dioctyl sodium sulfosuccinate (DOSS), Span 80, Tween 80, Tween 85, and the DOSS metabolite ethylhexyl sulfosuccinate (EHSS) for Corexit loss. Changes to the microbial communities and identification of key taxa were determined by 16S rRNA gene amplicon sequencing. The nonionic surfactants of Corexit 9500 (Span 80 and Tweens 80 and 85) biodegraded rapidly, dropping to below the limits of detection within 5 days and prior to any detectable initiation of oil biodegradation. This resulted in no observable suppression of petroleum biodegradation in the presence of Corexit compared to that of oil alone. In contrast, biodegradation of DOSS was delayed in the presence of oil, based on the prolonged presence of DOSS and accumulation of the degradation intermediate EHSS that did not occur in the absence of oil. Microbial analyses revealed that oil and Corexit enriched different overall microbial communities, with the presence of both resulting in a community composition that shifted from one more similar to that of Corexit only to one reflecting the oil-only community over time, in parallel with the degradation of predominantly Corexit and then oil components. Some microbial taxa (Oleispira, Pseudofulvibacter, and Roseobacter) responded to either oil or Corexit, suggesting that some organisms may be capable of utilizing both substrates. Together, these findings reveal interactive effects of crude oil and Corexit 9500 on chemical losses and microbial communities as they biodegrade, providing further insight into their fate when copresent in the environment.IMPORTANCE Chemical dispersants such as Corexit 9500 are commonly used in oil spill response and are currently under consideration for use in the Arctic, where their fate and effects have not been well studied. This research was performed to determine the interactive effects of the copresence of crude oil and Corexit 9500 on the degradation of components from each mixture and the associated microbial community structure over time in Arctic seawater. These findings will help yield a better understanding of the biodegradability of dispersant components applied to an oil spill, the temporal microbial community response to dispersed oil, and the fundamental microbial ecology of organic contaminant biodegradation processes in the Arctic marine environment.}, }
@article {pmid32825355, year = {2020}, author = {Floyd, AS and Mott, BM and Maes, P and Copeland, DC and McFrederick, QS and Anderson, KE}, title = {Microbial Ecology of European Foul Brood Disease in the Honey Bee (Apis mellifera): Towards a Microbiome Understanding of Disease Susceptibility.}, journal = {Insects}, volume = {11}, number = {9}, pages = {}, pmid = {32825355}, issn = {2075-4450}, abstract = {European honey bees (Apis mellifera Linnaeus) are beneficial insects that provide essential pollination services for agriculture and ecosystems worldwide. Modern commercial beekeeping is plagued by a variety of pathogenic and environmental stressors often confounding attempts to understand colony loss. European foulbrood (EFB) is considered a larval-specific disease whose causative agent, Melissococcus plutonius, has received limited attention due to methodological challenges in the field and laboratory. Here, we improve the experimental and informational context of larval disease with the end goal of developing an EFB management strategy. We sequenced the bacterial microbiota associated with larval disease transmission, isolated a variety of M.plutonius strains, determined their virulence against larvae in vitro, and explored the potential for probiotic treatment of EFB disease. The larval microbiota was a low diversity environment similar to honey, while worker mouthparts and stored pollen contained significantly greater bacterial diversity. Virulence of M. plutonius against larvae varied markedly by strain and inoculant concentration. Our chosen probiotic, Parasaccharibacter apium strain C6, did not improve larval survival when introduced alone, or in combination with a virulent EFB strain. We discuss the importance of positive and negative controls for in vitro studies of the larval microbiome and disease.}, }
@article {pmid32824323, year = {2020}, author = {Rutere, C and Knoop, K and Posselt, M and Ho, A and Horn, MA}, title = {Ibuprofen Degradation and Associated Bacterial Communities in Hyporheic Zone Sediments.}, journal = {Microorganisms}, volume = {8}, number = {8}, pages = {}, pmid = {32824323}, issn = {2076-2607}, support = {641939//European Commission/ ; }, abstract = {Ibuprofen, a non-steroidal anti-inflammatory pain reliever, is among pharmaceutical residues of environmental concern ubiquitously detected in wastewater effluents and receiving rivers. Thus, ibuprofen removal potentials and associated bacteria in the hyporheic zone sediments of an impacted river were investigated. Microbially mediated ibuprofen degradation was determined in oxic sediment microcosms amended with ibuprofen (5, 40, 200, and 400 µM), or ibuprofen and acetate, relative to an un-amended control. Ibuprofen was removed by the original sediment microbial community as well as in ibuprofen-enrichments obtained by re-feeding of ibuprofen. Here, 1-, 2-, 3-hydroxy- and carboxy-ibuprofen were the primary transformation products. Quantitative real-time PCR analysis revealed a significantly higher 16S rRNA abundance in ibuprofen-amended relative to un-amended incubations. Time-resolved microbial community dynamics evaluated by 16S rRNA gene and 16S rRNA analyses revealed many new ibuprofen responsive taxa of the Acidobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Latescibacteria, and Proteobacteria. Two ibuprofen-degrading strains belonging to the genera Novosphingobium and Pseudomonas were isolated from the ibuprofen-enriched sediments, consuming 400 and 300 µM ibuprofen within three and eight days, respectively. The collective results indicated that the hyporheic zone sediments sustain an efficient biotic (micro-)pollutant degradation potential, and hitherto unknown microbial diversity associated with such (micro)pollutant removal.}, }
@article {pmid32823898, year = {2020}, author = {Francis, F and Jacquemyn, H and Delvigne, F and Lievens, B}, title = {From Diverse Origins to Specific Targets: Role of Microorganisms in Indirect Pest Biological Control.}, journal = {Insects}, volume = {11}, number = {8}, pages = {}, pmid = {32823898}, issn = {2075-4450}, abstract = {Integrated pest management (IPM) is today a widely accepted pest management strategy to select and use the most efficient control tactics and at the same time reduce over-dependence on chemical insecticides and their potentially negative environmental effects. One of the main pillars of IPM is biological control. While biological control programs of pest insects commonly rely on natural enemies such as predatory insects, parasitoids and microbial pathogens, there is increasing evidence that plant, soil and insect microbiomes can also be exploited to enhance plant defense against herbivores. In this mini-review, we illustrate how microorganisms from diverse origins can contribute to plant fitness, functional traits and indirect defense responses against pest insects, and therefore be indirectly used to improve biological pest control practices. Microorganisms in the rhizosphere, phyllosphere and endosphere have not only been shown to enhance plant growth and plant strength, but also promote plant defense against herbivores both above- and belowground by providing feeding deterrence or antibiosis. Also, herbivore associated molecular patterns may be induced by microorganisms that come from oral phytophagous insect secretions and elicit plant-specific responses to herbivore attacks. Furthermore, microorganisms that inhabit floral nectar and insect honeydew produce volatile organic compounds that attract beneficial insects like natural enemies, thereby providing indirect pest control. Given the multiple benefits of microorganisms to plants, we argue that future IPMs should consider and exploit the whole range of possibilities that microorganisms offer to enhance plant defense and increase attraction, fecundity and performance of natural enemies.}, }
@article {pmid32823755, year = {2020}, author = {Quijada, NM and Bodas, R and Lorenzo, JM and Schmitz-Esser, S and Rodríguez-Lázaro, D and Hernández, M}, title = {Dietary Supplementation with Sugar Beet Fructooligosaccharides and Garlic Residues Promotes Growth of Beneficial Bacteria and Increases Weight Gain in Neonatal Lambs.}, journal = {Biomolecules}, volume = {10}, number = {8}, pages = {}, pmid = {32823755}, issn = {2218-273X}, support = {IDMICRO//Consejer&#xed;a de Agricultura y Ganader&#xed;a, Castilla y Le&#xf3;n/International ; }, mesh = {Animals ; Animals, Newborn ; Bacteria/*classification/genetics/growth &amp; development/isolation &amp; purification ; Beta vulgaris/*chemistry ; Bifidobacterium/classification/genetics/growth &amp; development/isolation &amp; purification ; Body Weight/*drug effects ; Dietary Supplements ; Garlic/*chemistry ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Lactobacillus/classification/genetics/growth &amp; development/isolation &amp; purification ; Milk/chemistry ; Oligosaccharides/*administration &amp; dosage/pharmacology ; Plant Extracts/*administration &amp; dosage/pharmacology ; Prebiotics/administration &amp; dosage ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sheep ; Veillonella/classification/genetics/growth &amp; development/isolation &amp; purification ; }, abstract = {The proper development of the early gastrointestinal tract (GIT) microbiota is critical for newborn ruminants. This microbiota is susceptible to modification by diverse external factors (such as diet) that can lead to long-lasting results when occurring in young ruminants. Dietary supplementation with prebiotics, ingredients nondigestible and nonabsorbable by the host that stimulate the growth of beneficial GIT bacteria, has been applied worldwide as a potential approach in order to improve ruminant health and production yields. However, how prebiotics affect the GIT microbiota during ruminants' early life is still poorly understood. We investigated the effect of milk supplementation with a combination of two well-known prebiotics, fructooligosaccharides (FOS) from sugar beet and garlic residues (all together named as "additive"), exerted on preweaned lamb growth and the composition of their fecal microbiota, by using 16S rRNA gene amplicon high-throughput sequencing. The results showed a significant increase in the mean daily weight gain of lambs fed with the additive. Lamb fecal microbiota was also influenced by the additive intake, as additive-diet lambs showed lower bacterial diversity and were significantly more abundant in Bifidobacterium, Enterococcus, Lactobacillus and Veillonella. These bacteria have been previously reported to confer beneficial properties to the ruminant, including promotion of growth and health status, and our results showed that they were strongly linked to the additive intake and the increased weight gain of lambs. This study points out the combination of FOS from sugar beet and garlic residues as a potential prebiotic to be used in young ruminants' nutrition in order to improve production yields.}, }
@article {pmid32819450, year = {2020}, author = {Berg, G and Rybakova, D and Fischer, D and Cernava, T and Vergès, MC and Charles, T and Chen, X and Cocolin, L and Eversole, K and Corral, GH and Kazou, M and Kinkel, L and Lange, L and Lima, N and Loy, A and Macklin, JA and Maguin, E and Mauchline, T and McClure, R and Mitter, B and Ryan, M and Sarand, I and Smidt, H and Schelkle, B and Roume, H and Kiran, GS and Selvin, J and de Souza, RSC and van Overbeek, L and Singh, BK and Wagner, M and Walsh, A and Sessitsch, A and Schloter, M}, title = {Correction to: Microbiome definition re-visited: old concepts and new challenges.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {119}, pmid = {32819450}, issn = {2049-2618}, abstract = {An amendment to this paper has been published and can be accessed via the original article.}, }
@article {pmid32818149, year = {2020}, author = {Kaplan, F and Shapiro-Ilan, D and Schiller, KC}, title = {Dynamics of entomopathogenic nematode foraging and infectivity in microgravity.}, journal = {NPJ microgravity}, volume = {6}, number = {}, pages = {20}, pmid = {32818149}, issn = {2373-8065}, abstract = {Microgravity is a unique environment to elucidate host-parasite biology. Entomopathogenic nematodes (EPNs), model parasites, kill host insects with mutualistic bacteria and provide environmentally friendly pest control. It is unknown how microgravity affects a multistep insect invasion by parasites with mutualistic bacteria. EPNs respond directionally to electromagnetic cues and their sinusoidal locomotion is affected by various physical factors. Therefore, we expected microgravity to impact EPN functionality. Microgravity experiments during space flight on the International Space Station (ISS) indicated that EPNs successfully emerged from consumed insect host cadavers, moved through soil, found and infected bait insects in a manner equivalent to Earth controls. However, nematodes that developed entirely in space, from the egg stage, died upon return to Earth, unlike controls in microgravity and on Earth. This agricultural biocontrol experiment in space gives insight to long-term space flight for symbiotic organisms, parasite biology, and the potential for sustainable crop protection in space.}, }
@article {pmid32817104, year = {2020}, author = {Miller, JI and Techtmann, S and Joyner, D and Mahmoudi, N and Fortney, J and Fordyce, JA and GaraJayeva, N and Askerov, FS and Cravid, C and Kuijper, M and Pelz, O and Hazen, TC}, title = {Microbial Communities across Global Marine Basins Show Important Compositional Similarities by Depth.}, journal = {mBio}, volume = {11}, number = {4}, pages = {}, pmid = {32817104}, issn = {2150-7511}, mesh = {Bacteria/*classification ; Biodegradation, Environmental ; *Genetic Variation ; *Microbiota ; Petroleum/metabolism ; Phylogeny ; Seawater/*microbiology ; }, abstract = {The environmental surveys following the 2010 Deepwater Horizon (DWH) spill identified a variety of hydrocarbon-degrading microorganisms, and laboratory studies with field-collected water samples then demonstrated faster-than-expected hydrocarbon biodegradation rates at 5°C. Knowledge about microbial community composition, diversity, and functional metabolic capabilities aids in understanding and predicting petroleum biodegradation by microbial communities in situ and is therefore an important component of the petroleum spill response decision-making process. This study investigates the taxonomic composition of microbial communities in six different global basins where petroleum and gas activities occur. Shallow-water communities were strikingly similar across basins, while deep-water communities tended to show subclusters by basin, with communities from the epipelagic, mesopelagic, and bathypelagic zones sometimes appearing within the same cluster. Microbial taxa that were enriched in the water column in the Gulf of Mexico following the DWH spill were found across marine basins. Several hydrocarbon-degrading genera (e.g., Actinobacteria, Pseudomonas, and Rhodobacteriacea) were common across all basins. Other genera such as Pseudoalteromonas and Oleibacter were highly enriched in specific basins.IMPORTANCE Marine microbial communities are a vital component of global carbon cycling, and numerous studies have shown that populations of petroleum-degrading bacteria are ubiquitous in the oceans. Few studies have attempted to distinguish all of the taxa that might contribute to petroleum biodegradation (including, e.g., heterotrophic and nondesignated microbes that respond positively to petroleum and microbes that grow on petroleum as the sole carbon source). This study quantifies the subpopulations of microorganisms that are expected to be involved in petroleum hydrocarbon biodegradation, which is important information during the decision-making process in the event of a petroleum spill accident.}, }
@article {pmid32816051, year = {2021}, author = {Zhang, Q and Campos, M and Larama, G and Acuña, JJ and Valenzuela, B and Solis, F and Zamorano, P and Araya, R and Sadowsky, MJ and Jorquera, MA}, title = {Composition and predicted functions of the bacterial community in spouting pool sediments from the El Tatio Geyser field in Chile.}, journal = {Archives of microbiology}, volume = {203}, number = {1}, pages = {389-397}, pmid = {32816051}, issn = {1432-072X}, support = {1201386//FONDECYT/ ; NSFC190012//CONICYT/ ; }, mesh = {Bacteria/*classification/genetics/metabolism ; *Biodiversity ; Chile ; Geologic Sediments/*microbiology ; High-Throughput Nucleotide Sequencing ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The El Tatio Geyser Field (ETGF), located in Northern Chile, is the main geyser field in the southern hemisphere. Despite this, details of its microbial ecology are still unknown. Here, we briefly report on the composition and predicted functions of the bacterial community in spouting pool sediments from the ETGF as revealed by high-throughput sequencing of 16S rRNA genes. Results of this analysis showed that while there were differences in richness and diversity between samples, bacterial communities were primarily dominated by the phyla Proteobacteria, followed Firmicutes, Bacteroidetes, Acidobacteria, and Chloroflexi. Analyses of predicted functional activity indicated that the functions were mostly attributed to chemoheterotrophy and aerobic chemoheterotrophy, followed by sulfur (respiration of sulfur compounds and sulfate) and nitrogen (nitrate reduction, respiration of nitrogen and nitrate) cycling. Taken together, our results suggest a high diversity in taxonomy and predictive functions of bacterial communities in sediments from spouting pools. This study provides fundamentally important information on the structure and function predictive functions of microbiota communities in spouting pools. Moreover, since the ETGF is intensively visited and impacted by tens of thousands of tourists every year, our results can be used to help guide the design of sustainable conservation strategies.}, }
@article {pmid32816010, year = {2020}, author = {Vestrum, RI and Attramadal, KJK and Vadstein, O and Gundersen, MS and Bakke, I}, title = {Bacterial community assembly in Atlantic cod larvae (Gadus morhua): contributions of ecological processes and metacommunity structure.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {9}, pages = {}, pmid = {32816010}, issn = {1574-6941}, mesh = {Animals ; Bacteria/genetics ; *Gadus morhua ; *Gastrointestinal Microbiome ; Larva ; *Microbiota ; }, abstract = {Many studies demonstrate the importance of the commensal microbiomes to animal health and development. However, the initial community assembly process is poorly understood. It is unclear to what extent the hosts select for their commensal microbiota, whether stochastic processes contribute, and how environmental conditions affect the community assembly. We investigated community assembly in Atlantic cod larvae exposed to distinct microbial metacommunities. We aimed to quantify ecological processes influencing community assembly in cod larvae and to elucidate the complex relationship between the bacteria of the environment and the fish. Selection within the fish was the major determinant for community assembly, but drift resulted in inter-individual variation. The environmental bacterial communities were highly dissimilar from those associated with the fish. Still, differences in the environmental bacterial communities strongly influenced the fish communities. The most striking difference was an excessive dominance of a single OTU (Arcobacter) for larvae reared in two of the three systems. These larvae were exposed to environments with higher fractions of opportunistic bacteria, and we hypothesise that detrimental host-microbe interactions might have made the fish susceptible to Arcobacter colonisation. Despite strong selection within the host, this points to a possibility to steer the metacommunity towards mutualistic host-microbe interactions and improved fish health and survival.}, }
@article {pmid32815317, year = {2020}, author = {Nascimento Lemos, L and Manoharan, L and William Mendes, L and Monteiro Venturini, A and Satler Pylro, V and Tsai, SM}, title = {Metagenome assembled-genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils.}, journal = {Environmental microbiology reports}, volume = {12}, number = {6}, pages = {651-655}, doi = {10.1111/1758-2229.12880}, pmid = {32815317}, issn = {1758-2229}, support = {//Brazilian Microbiome Project/International ; 140032/2015-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/International ; 161931/2015-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/International ; Finance Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/International ; 2014/50320-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/International ; 2015/13546-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/International ; 2016/18215-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/International ; 2017/09643-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/International ; 2017/24037-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/International ; //Coordination for the Improvement of Higher Education Personnel/International ; //National Council for Scientific and Technological Development/International ; //S&#xe3;o Paulo Research Foundation/International ; }, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Databases, Genetic ; Genome Size ; *Genome, Bacterial ; Metagenome ; Microbiota ; Phylogeny ; *Soil Microbiology ; }, abstract = {Soil microbiome is one of the most heterogeneous biological systems. State-of-the-art molecular approaches such as those based on single-amplified genomes (SAGs) and metagenome assembled-genomes (MAGs) are now improving our capacity for disentailing soil microbial-mediated processes. Here, we analysed publicly available datasets of soil microbial genomes and MAG's reconstructed from the Amazon's tropical soil (primary forest and pasture) and active layer of permafrost, aiming to evaluate their genome size. Our results suggest that the Candidate Phyla Radiation (CPR)/Patescibacteria phyla have genomes with an average size fourfold smaller than the mean identified in the RefSoil database, which lacks any representative of this phylum. Also, by analysing the potential metabolism of 888 soil microbial genomes, we show that CPR/Patescibacteria representatives share similar functional profiles, but different from other microbial phyla and are frequently neglected in the soil microbial surveys. Finally, we argue that the use of MAGs may be a better choice over SAGs to expand the soil microbial databases, like RefSoil.}, }
@article {pmid32814025, year = {2020}, author = {Alexander, M and Turnbaugh, PJ}, title = {Deconstructing Mechanisms of Diet-Microbiome-Immune Interactions.}, journal = {Immunity}, volume = {53}, number = {2}, pages = {264-276}, pmid = {32814025}, issn = {1097-4180}, support = {T32 AI060537/AI/NIAID NIH HHS/United States ; R21 CA227232/CA/NCI NIH HHS/United States ; M01 RR001271/RR/NCRR NIH HHS/United States ; P30 DK098722/DK/NIDDK NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; F32 AI147456/AI/NIAID NIH HHS/United States ; R01 AR074500/AR/NIAMS NIH HHS/United States ; }, mesh = {*Diet ; Gastrointestinal Microbiome/*physiology ; Humans ; Immunity/physiology ; Immunomodulation/*physiology ; Inflammation/pathology ; }, abstract = {Emerging evidence suggests that the effect of dietary intake on human health and disease is linked to both the immune system and the microbiota. Yet, we lack an integrated mechanistic model for how these three complex systems relate, limiting our ability to understand and treat chronic and infectious disease. Here, we review recent findings at the interface of microbiology, immunology, and nutrition, with an emphasis on experimentally tractable models and hypothesis-driven mechanistic work. We outline emerging mechanistic concepts and generalizable approaches to bridge the gap between microbial ecology and molecular mechanism. These set the stage for a new era of precision human nutrition informed by a deep and comprehensive knowledge of the diverse cell types in and on the human body.}, }
@article {pmid32812858, year = {2020}, author = {Lee, JC and Whang, KS}, title = {Agriterribacter humi gen. nov., sp. nov., a novel bacterium of the family Chitinophagaceae isolated from soil of a farming field.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {70}, number = {9}, pages = {5123-5130}, doi = {10.1099/ijsem.0.004397}, pmid = {32812858}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Bacteroidetes/*classification/isolation &amp; purification ; Base Composition ; DNA, Bacterial/genetics ; *Farms ; Fatty Acids/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {A Gram-stain-negative bacterium, designated strain YJ03[T], was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ03[T] was found to be an aerobic, non-motile and non-spore-forming bacterium which can grow at 10-33 °C (optimum, 25-28 °C), at pH 6.6-9.5 (optimum, pH 7.0-7.5) and at salinities of 0-1.0 % (w/v) NaCl (optimum, 0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ03[T] with the closely related relatives were in the range 93.9-92.2 %, and the results of phylogenomic analysis indicated that strain YJ03[T] was clearly separated from species of the genera in the family Chitinophagaceae, showing average nucleotide identity values of 68.8-64.3 %. The predominant isoprenoid quinone was identified as MK-7 and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and an unidentified fatty acid with an equivalent chain-length of 13.565. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, four unidentified aminolipids and six unidentified lipids. The G+C content of the genome was determined to be 41.8 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences in this study, strain YJ03[T] is considered to represent a novel species of a new genus in the family Chitinophagaceae, for which the name Agriterribacter humi gen. nov., sp. nov., is proposed. The type strain of Agriterribacter humi is YJ03[T] (=KACC 19548[T]=NBRC 113195[T]).}, }
@article {pmid32807105, year = {2020}, author = {Kabwe, MH and Vikram, S and Mulaudzi, K and Jansson, JK and Makhalanyane, TP}, title = {The gut mycobiota of rural and urban individuals is shaped by geography.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {257}, pmid = {32807105}, issn = {1471-2180}, mesh = {Adult ; DNA, Fungal/genetics ; DNA, Intergenic/*genetics ; Diet/adverse effects/classification ; Feces/*microbiology ; Female ; Fungi/*classification/genetics/isolation &amp; purification ; Gastrointestinal Microbiome/drug effects ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Phylogeny ; Phylogeography ; Rural Population ; Sequence Analysis, DNA/*methods ; Smoking/adverse effects ; South Africa ; Urban Population ; Young Adult ; }, abstract = {BACKGROUND: Understanding the structure and drivers of gut microbiota remains a major ecological endeavour. Recent studies have shown that several factors including diet, lifestyle and geography may substantially shape the human gut microbiota. However, most of these studies have focused on the more abundant bacterial component and comparatively less is known regarding fungi in the human gut. This knowledge deficit is especially true for rural and urban African populations. Therefore, we assessed the structure and drivers of rural and urban gut mycobiota.<br><br>RESULTS: Our participants (n&#x2009;=&#x2009;100) were balanced by geography and sex. The mycobiota of these geographically separated cohorts was characterized using amplicon analysis of the Internal Transcribed Spacer (ITS) gene. We further assessed biomarker species specific to rural and urban cohorts. In addition to phyla which have been shown to be ubiquitous constituents of gut microbiota, Pichia were key constituents of the mycobiota. We found that geographic location was a major driver of gut mycobiota. Other factors such as smoking where also determined gut mycobiota albeit to a lower extent, as explained by the small proportion of total variation. Linear discriminant and the linear discriminant analysis effect size analysis revealed several distinct urban and rural biomarkers.<br><br>CONCLUSIONS: Together, our analysis reveals distinct community structure in urban and rural South African individuals. Geography was shown to be a key driver of rural and urban gut mycobiota.}, }
@article {pmid32806693, year = {2020}, author = {Martin-Rivilla, H and Gutierrez-Mañero, FJ and Gradillas, A and P Navarro, MO and Andrade, G and Lucas, JA}, title = {Identifying the Compounds of the Metabolic Elicitors of Pseudomonas fluorescens N 21.4 Responsible for Their Ability to Induce Plant Resistance.}, journal = {Plants (Basel, Switzerland)}, volume = {9}, number = {8}, pages = {}, pmid = {32806693}, issn = {2223-7747}, support = {AGL-2013-45189-R//Ministerio de Econom&#xed;a y Competitividad of Spain/ ; }, abstract = {In this work, the metabolic elicitors extracted from the beneficial rhizobacterium Pseudomonas fluorescens N 21.4 were sequentially fragmented by vacuum liquid chromatography to isolate, purify and identify the compounds responsible for the extraordinary capacities of this strain to induce systemic resistance and to elicit secondary defensive metabolism in diverse plant species. To check if the fractions sequentially obtained were able to increase the synthesis of isoflavones and if, therefore, they still maintained the eliciting capacity of the live strain, rapid and controlled experiments were done with soybean seeds. The optimal action concentration of the fractions was established and all of them elicited isoflavone secondary metabolism-the fractions that had been extracted with n-hexane being more effective. The purest fraction was the one with the highest eliciting capacity and was also tested in Arabidopsis thaliana seedlings to induce systemic resistance against the pathogen Pseudomonas syringae pv. tomato DC 3000. This fraction was then analyzed by UHPLC/ESI-QTOF-MS, and an alkaloid, two amino lipids, three arylalkylamines and a terpenoid were tentatively identified. These identified compounds could be part of commercial plant inoculants of biological and sustainable origin to be applied in crops, due to their potential to enhance the plant immune response and since many of them have putative antibiotic and/or antifungal potential.}, }
@article {pmid32804245, year = {2021}, author = {Wei, X and Chi, Z and Liu, GL and Hu, Z and Chi, ZM}, title = {The Genome-Wide Mutation Shows the Importance of Cell Wall Integrity in Growth of the Psychrophilic Yeast Metschnikowia australis W7-5 at Different Temperatures.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {52-66}, pmid = {32804245}, issn = {1432-184X}, support = {31970058//Major Research Plan/ ; }, mesh = {Acclimatization/*genetics ; Cell Wall/*physiology ; Cold Temperature ; Gene Editing/methods ; Gene Expression Regulation, Fungal ; Genome, Fungal/genetics ; Glucosyltransferases/genetics ; Glycerol/metabolism ; Glycerol-3-Phosphate Dehydrogenase (NAD+)/genetics ; Glycogen/metabolism ; Integrases/metabolism ; Metschnikowia/*genetics/*growth &amp; development/physiology ; Mitogen-Activated Protein Kinases/genetics ; Signal Transduction/genetics ; Transcription Factors/*genetics ; Trehalose/metabolism ; }, abstract = {In this study, it was found that a Cre/loxP system could be successfully used as a tool for editing the genome of the psychrophilic yeast Metschnikowia australis W7-5 isolated from Antarctica. The deletion and over-expression of the TPS1 gene for trehalose biosynthesis, the GSY gene for glycogen biosynthesis, and the GPD1 and GPP genes for glycerol biosynthesis had no influence on cell growth of the mutants and transformants compared to cell growth of their wild-type strain M. australis W7-5, indicating that trehalose, glycogen, and glycerol had no function in growth of the psychrophilic yeast at different temperatures. However, removal of the SLT2 gene encoding the mitogen-activated protein kinase in the cell wall integrity (CWI) signaling pathway and the SWI4 and SWI6 genes encoding the transcriptional activators Swi4/6 had the crucial influence on cell growth of the psychrophilic yeast at the low temperature, especially at 25 °C and expression of the genes related to cell wall and lipid biosynthesis. Therefore, the cell wall could play an important role in growth of the psychrophilic yeast at different temperatures and biosynthesis of cell wall was actively regulated by the CWI signaling pathway. This was the first time to show that the genome of the psychrophilic yeast was successfully edited and the molecular evidences were obtained to elucidate mechanisms of low temperature growth of the psychrophilic yeast from Antarctica.}, }
@article {pmid32804239, year = {2020}, author = {Andras, JP and Rodriguez-Reillo, WG and Truchon, A and Blanchard, JL and Pierce, EA and Ballantine, KA}, title = {Rewilding the small stuff: the effect of ecological restoration on prokaryotic communities of peatland soils.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {10}, pages = {}, doi = {10.1093/femsec/fiaa144}, pmid = {32804239}, issn = {1574-6941}, mesh = {Carbon ; Carbon Sequestration ; *Microbiota ; *Soil ; Soil Microbiology ; Wetlands ; }, abstract = {To investigate the effect that restoration has on the microbiome of wetland soils, we used 16S amplicon sequencing to characterize the soil prokaryotic communities of retired cranberry farms that were restored to approximate the peat wetlands they once were. For comparison, we also surveyed the soil communities of active cranberry farms, retired cranberry farms and natural peat wetlands that were never farmed. Our results show that the prokaryotic communities of active cranberry farms are distinct from those of natural peat wetlands. Moreover, 4 years after restoration, the prokaryotic community structure of restored cranberry farms had shifted, resulting in a community more similar to natural peat wetlands than to active farms. Meanwhile, the prokaryotic communities of retired cranberry farms remained similar to those of active farms. The observed differences in community structure across site types corresponded with significant differences in inferred capacity for denitrification, methanotrophy and methanogenesis, and community composition was also correlated with previously published patterns of denitrification and carbon sequestration measured from the same soil samples. Taken together, these results suggest that ecological restoration efforts have the potential to restore ecosystem functions of soils and that they do so by 'rewilding' the communities of resident soil microbes.}, }
@article {pmid32803365, year = {2020}, author = {Li, CX and Fan, YF and Luan, W and Dai, Y and Wang, MX and Wei, CM and Wang, Y and Tao, X and Mao, P and Ma, XR}, title = {Correction to: Titanium Ions Inhibit the Bacteria in Vase Solutions of Freshly Cut Gerbera jamesonii and Extend the Flower Longevity.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {960}, doi = {10.1007/s00248-020-01572-z}, pmid = {32803365}, issn = {1432-184X}, abstract = {We request that the following corrections be made in our article.}, }
@article {pmid32803364, year = {2021}, author = {Berlow, M and Phillips, JN and Derryberry, EP}, title = {Effects of Urbanization and Landscape on Gut Microbiomes in White-Crowned Sparrows.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {253-266}, pmid = {32803364}, issn = {1432-184X}, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Ecosystem ; Gastrointestinal Microbiome/*genetics ; Male ; Noise/adverse effects ; RNA, Ribosomal, 16S/genetics ; Rural Population/statistics &amp; numerical data ; San Francisco ; Sparrows/*microbiology ; Urban Population/statistics &amp; numerical data ; *Urbanization ; Wilderness ; }, abstract = {Habitats are changing rapidly around the globe and urbanization is one of the primary drivers. Urbanization changes food availability, environmental stressors, and the prevalence of disease for many species. These changes can lead to divergence in phenotypic traits, including behavioral, physiological, and morphological features between urban and rural populations. Recent research highlights that urbanization is also changing the gut microbial communities found in a diverse group of host species. These changes have not been uniform, leaving uncertainty as to how urban habitats are shaping gut microbial communities. To better understand these effects, we investigated the gut bacterial communities of White-Crowned Sparrow (Zonotrichia leucophrys) populations along an urbanization gradient in the San Francisco Bay area. We examined how gut bacterial communities vary with the local environment and host morphological characteristics. We found direct effects of environmental factors, including urban noise levels and territory land cover, as well as indirect effects through body size and condition, on alpha and beta diversity of gut microbial communities. We also found that urban and rural birds' microbiomes differed in which variables predicted their diversity, with urban communities driven by host morphology, and rural communities driven by environmental factors. Elucidating these effects provides a better understanding of how urbanization affects wild avian physiology.}, }
@article {pmid32803363, year = {2020}, author = {Cai, Y and Zhou, X and Shi, L and Jia, Z}, title = {Atmospheric Methane Oxidizers Are Dominated by Upland Soil Cluster Alpha in 20 Forest Soils of China.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {859-871}, doi = {10.1007/s00248-020-01570-1}, pmid = {32803363}, issn = {1432-184X}, support = {41401294//National Natural Science Foundation of China/ ; 41877062//National Natural Science Foundation of China/ ; 91751204//National Natural Science Foundation of China/ ; 2019311//Youth Innovation Promotion Association, CAS/ ; }, mesh = {Bacteria/isolation &amp; purification/*metabolism ; China ; Forests ; Genes, Bacterial ; Methane/*metabolism ; Methylocystaceae/isolation &amp; purification/metabolism ; *Microbiota ; Oxidation-Reduction ; Polymerase Chain Reaction ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Soil Microbiology ; }, abstract = {Upland soil clusters alpha and gamma (USCα and USCγ) are considered a major biological sink of atmospheric methane and are often detected in forest and grassland soils. These clusters are phylogenetically classified using the particulate methane monooxygenase gene pmoA because of the difficulty of cultivation. Recent studies have established a direct link of pmoA genes to 16S rRNA genes based on their isolated strain or draft genomes. However, whether the results of pmoA-based assays could be largely represented by 16S rRNA gene sequencing in upland soils remains unclear. In this study, we collected 20 forest soils across China and compared methane-oxidizing bacterial (MOB) communities by high-throughput sequencing of 16S rRNA and pmoA genes using different primer sets. The results showed that 16S rRNA gene sequencing and the semi-nested polymerase chain reaction (PCR) of the pmoA gene (A189/A682r nested with a mixture of mb661 and A650) consistently revealed the dominance of USCα (accounting for more than 50% of the total MOB) in 12 forest soils. A189f/A682r successfully amplified pmoA genes (mainly RA14 of USCα) in only three forest soils. A189f/mb661 could amplify USCα (mainly JR1) in several forest soils but showed a strong preferential amplification of Methylocystis and many other type I MOB groups. A189f/A650 almost exclusively amplified USCα (mainly JR1) and largely discriminated against Methylocystis and most of the other MOB groups. The semi-nested PCR approach weakened the bias of A189f/mb661 and A189f/A650 for JR1 and balanced the coverage of all USCα members. The canonical correspondence analysis indicated that soil NH4[+]-N and pH were the main environmental factors affecting the MOB community of Chinese forest soils. The RA14 of the USCα group prefers to live in soils with low pH, low temperature, low elevation, high precipitation, and rich in nitrogen. JR1's preferences for temperature and elevation were opposite to RA14. Our study suggests that combining the deep sequencing of 16S rRNA and pmoA genes to characterize MOB in forest soils is the best choice.}, }
@article {pmid32803362, year = {2021}, author = {Zilius, M and Samuiloviene, A and Stanislauskienė, R and Broman, E and Bonaglia, S and Meškys, R and Zaiko, A}, title = {Depicting Temporal, Functional, and Phylogenetic Patterns in Estuarine Diazotrophic Communities from Environmental DNA and RNA.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {36-51}, pmid = {32803362}, issn = {1432-184X}, support = {P-MIP-17-126//Lietuvos Mokslo Taryba/ ; }, mesh = {Cyanobacteria/*genetics/*metabolism ; DNA, Environmental/genetics ; Estuaries ; Fresh Water/*microbiology ; Heterotrophic Processes ; Microbiota ; Nitrogen Cycle/*physiology ; Nitrogen Fixation/*physiology ; Oxidoreductases/genetics ; Phylogeny ; RNA/genetics ; Seasons ; Water Microbiology ; }, abstract = {Seasonally nitrogen-limited and phosphorus-replete temperate coastal waters generally host dense and diverse diazotrophic communities. Despite numerous studies in marine systems, little is known about diazotrophs and their functioning in oligohaline estuarine environments. Here we applied a combination of nifH transcript and metagenomic shotgun sequencing approaches to investigate temporal shifts in taxonomic composition and nifH activity of size-fractionated diazotrophic communities in a shallow and mostly freshwater coastal lagoon. Patterns in active nifH phylotypes exhibited a clear seasonal succession, which reflected their different tolerances to temperature change and nitrogen (N) availability. Thus, in spring, heterotrophic diazotrophs (Proteobacteria) dominated the nifH phylotypes, while increasing water temperature and depletion of inorganic N fostered heterocystous Cyanobacteria in summer. Metagenomic data demonstrated four main N-cycling pathways and three of them with a clear seasonal pattern: denitrification (spring) → N2 fixation (summer) → assimilative NO3[-] reduction (fall), with NH4[+] uptake into cells occurring across all seasons. Although a substantial denitrification signal was observed in spring, it could have originated from the re-suspended benthic rather than planktonic community. Our results contribute to a better understanding of the realized genetic potential of pelagic N2 fixation and its seasonal dynamics in oligohaline estuarine ecosystems, which are natural coastal biogeochemical reactors.}, }
@article {pmid32801177, year = {2020}, author = {Pilgrim, J and Siozios, S and Baylis, M and Hurst, GDD}, title = {Tissue Tropisms and Transstadial Transmission of a Rickettsia Endosymbiont in the Highland Midge, Culicoides impunctatus (Diptera: Ceratopogonidae).}, journal = {Applied and environmental microbiology}, volume = {86}, number = {20}, pages = {}, pmid = {32801177}, issn = {1098-5336}, support = {BBS/E/I/00001701/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M011186/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M012441/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Ceratopogonidae/*microbiology ; Female ; In Situ Hybridization, Fluorescence ; Insect Vectors/*microbiology ; Male ; Phylogeny ; Rickettsia/*physiology ; *Symbiosis ; Tropism ; }, abstract = {Rickettsia is a genus of intracellular bacteria which can manipulate host reproduction and alter sensitivity to natural enemy attack in a diverse range of arthropods. The maintenance of Rickettsia endosymbionts in insect populations can be achieved through both vertical and horizontal transmission routes. For example, the presence of the symbiont in the follicle cells and salivary glands of Bemisia whiteflies allows Belli group Rickettsia transmission via the germ line and plants, respectively. However, the transmission routes of other Rickettsia bacteria, such as those in the Torix group of the genus, remain underexplored. Through fluorescence in situ hybridization (FISH) and transmission electron microscopy (TEM) screening, this study describes the pattern of Torix Rickettsia tissue tropisms in the highland midge, Culicoides impunctatus (Diptera: Ceratopogonidae). Of note is the high intensity of infection of the ovarian suspensory ligament, suggestive of a novel germ line targeting strategy. Additionally, localization of the symbiont in tissues of several developmental stages suggests transstadial transmission is a major route for ensuring maintenance of Rickettsia within C. impunctatus populations. Aside from providing insights into transmission strategies, the presence of Rickettsia bacteria in the fat body of larvae indicates potential host fitness and vector capacity impacts to be investigated in the future.IMPORTANCE Microbial symbionts of disease vectors have garnered recent attention due to their ability to alter vectorial capacity. Their consideration as a means of arbovirus control depends on symbiont vertical transmission, which leads to spread of the bacteria through a population. Previous work has identified a Rickettsia symbiont present in several species of biting midges (Culicoides spp.), which transmit bluetongue and Schmallenberg arboviruses. However, symbiont transmission strategies and host effects remain underexplored. In this study, we describe the presence of Rickettsia in the ovarian suspensory ligament of Culicoides impunctatus Infection of this organ suggests the connective tissue surrounding developing eggs is important for ensuring vertical transmission of the symbiont in midges and possibly other insects. Additionally, our results indicate Rickettsia localization in the fat body of Culicoides impunctatus As the arboviruses spread by midges often replicate in the fat body, this location implies possible symbiont-virus interactions to be further investigated.}, }
@article {pmid32801031, year = {2020}, author = {Hodges, JK and Sasaki, GY and Bruno, RS}, title = {Anti-inflammatory activities of green tea catechins along the gut-liver axis in nonalcoholic fatty liver disease: lessons learned from preclinical and human studies.}, journal = {The Journal of nutritional biochemistry}, volume = {85}, number = {}, pages = {108478}, doi = {10.1016/j.jnutbio.2020.108478}, pmid = {32801031}, issn = {1873-4847}, mesh = {Animals ; Anti-Inflammatory Agents/pharmacology/*therapeutic use ; Catechin/pharmacology/*therapeutic use ; Gastrointestinal Microbiome/drug effects ; Humans ; Liver/drug effects/metabolism/pathology ; NF-kappa B/metabolism ; Non-alcoholic Fatty Liver Disease/*drug therapy/metabolism/pathology ; Plant Extracts/pharmacology/therapeutic use ; *Tea/chemistry ; Toll-Like Receptor 4/metabolism ; }, abstract = {Nonalcoholic fatty liver disease (NAFLD), which is the most prevalent hepatic disorder worldwide, affecting 25% of the general population, describes a spectrum of progressive liver conditions ranging from relatively benign liver steatosis and advancing to nonalcoholic steatohepatitis (NASH), fibrosis, and cirrhosis. Hallmark features of NASH are fatty hepatocytes and inflammatory cell infiltrates in association with increased activation of hepatic nuclear factor kappa-B (NFκB) that exacerbates liver injury. Because no pharmacological treatments exist for NAFLD, emphasis has been placed on dietary approaches to manage NASH risk. Anti-inflammatory bioactivities of catechin-rich green tea extract (GTE) have been well-studied, especially in preclinical models that have detailed its effects on inflammatory responses downstream of NFκB activation. This review will therefore discuss the experimental evidence that has advanced an understanding of the mechanisms by which GTE, either directly through its catechins or potentially indirectly through microbiota-derived metabolites, limits NFκB activation and NASH-associated liver injury. Specifically, it will describe the hepatic-level benefits of GTE that attenuate intracellular redox distress and pro-inflammatory signaling from extracellular receptors that otherwise activate NFκB. In addition, it will discuss the anti-inflammatory activities of GTE on gut barrier function as well as prebiotic and antimicrobial effects on gut microbial ecology that help to limit the translocation of gut-derived endotoxins (e.g. lipopolysaccharides) to the liver where they otherwise upregulate NFκB activation by Toll-like receptor-4 signaling. This summary is therefore expected to advance research translation of the hepatic- and intestinal-level benefits of GTE and its catechins to help manage NAFLD-associated morbidity.}, }
@article {pmid32800221, year = {2020}, author = {Yadav, R and Rajput, V and Gohil, K and Khairnar, K and Dharne, M}, title = {Comprehensive metagenomic insights into a unique mass gathering and bathing event reveals transient influence on a riverine ecosystem.}, journal = {Ecotoxicology and environmental safety}, volume = {202}, number = {}, pages = {110938}, doi = {10.1016/j.ecoenv.2020.110938}, pmid = {32800221}, issn = {1090-2414}, mesh = {Drug Resistance, Microbial ; Ecosystem ; *Environmental Monitoring ; Humans ; India ; Metagenome ; Microbiota ; Rivers/*chemistry ; Water Pollution/*statistics &amp; numerical data ; Water Quality ; }, abstract = {The religious mass gathering and bathing can pose a multitude of significant public health challenges and lead to severe alterations in the river microbial ecology. The Pandharpur Wari is an annual pilgrimage of Maharashtra, India, where millions of devotees carry the footprints of the saint-poets and pay their obeisance to Lord Vitthal on the 11th day of moon's waxing phase (Ashadi Ekadashi). As a part of the ritual, the engrossed devotees, walk over 250 km, take a first holy dip in a sacred river Indrayani at Alandi and secondly in Bhima River at Pandharpur. The MinION-based shotgun metagenomic approach was employed to examine the impact of spiritual mass bathing on environmental changes (concerning the river microbial community structure and functions); and public health aspects (in terms of changes in the pathogenic potential and antibiotic resistance). The analysis of bathing and post-bathing samples of both the rivers revealed alterations in the alpha and beta diversity, indicating significant spatiotemporal variations in the overall microbial structure and function. Furthermore, the analysis revealed up to 80% of differences in the abundance of virulence genes between the bathing and post bathing samples. We observed parallel increase of priority skin and enteric pathogens (ranging from 11% to 80%) such as Acinetobacter baumannii, Staphylococcus aureus, Streptococcus pyogenes, Mycobacterium tuberculosis, and Pseudomonas aeruginosa during the bathing event. Moreover, we observed a significant increase in the antibiotic resistance in the bathing samples of Bhima and Indrayani rivers respectively. Altogether, this is the first comprehensive metagenomic study unravelling the influence of religious mass-bathing on the riverine ecosystem.}, }
@article {pmid32798895, year = {2020}, author = {Rabaey, K and Vandekerckhove, T and de Walle, AV and Sedlak, DL}, title = {The third route: Using extreme decentralization to create resilient urban water systems.}, journal = {Water research}, volume = {185}, number = {}, pages = {116276}, doi = {10.1016/j.watres.2020.116276}, pmid = {32798895}, issn = {1879-2448}, mesh = {Humans ; Politics ; Public Health ; *Sanitation ; *Water ; Water Supply ; }, abstract = {For much of the world's urban population, centralized treatment plants and pipe networks built in the nineteenth and twentieth centuries provide homes with water and a means of disposing of the resulting wastewater. Due to the real or perceived inability of existing systems to deliver safe and palatable water, many users apply additional treatment prior to consumption. Where piped water supply is lacking, drinking water is obtained through water vendors at considerable cost. Despite economic inefficiencies and public health risks inherent in these two water supply systems, the high sunk costs of existing water infrastructure along with low returns on investment and the inflexible nature of the institutions involved in water provision have slowed down the diffusion of alternative approaches that may prove to be less expensive, more adaptable and safer than the current system. We advocate a third, complementary route: household-based personalized water systems. Initially, relatively affluent people expecting more functionality and sustainability from water systems will invest in personalized water systems that allow them to tailor their water to their personal preferences. This approach will tap into the tremendous creativity-base of individual users and entrepreneurs, facilitating the type of co-creation that accelerated the rapid development of consumer electronics. Competition among manufacturers and economies of scale that accrue as these systems become more popular will lead to rapid innovation that drives down costs, improves performance and expands access. These solutions complement emerging approaches for sanitation and resource recovery that do not rely upon sewers for the management of human waste.}, }
@article {pmid32795675, year = {2020}, author = {Fernández-Murga, ML and Olivares, M and Sanz, Y}, title = {Bifidobacterium pseudocatenulatum CECT 7765 reverses the adverse effects of diet-induced obesity through the gut-bone axis.}, journal = {Bone}, volume = {141}, number = {}, pages = {115580}, doi = {10.1016/j.bone.2020.115580}, pmid = {32795675}, issn = {1873-2763}, mesh = {Animals ; *Bifidobacterium pseudocatenulatum ; Bone Density ; Diet, High-Fat/adverse effects ; Dietary Supplements ; Male ; Mice ; Mice, Inbred C57BL ; Obesity ; }, abstract = {Obesity and the associated chronic metabolic diseases (e.g., type-2 diabetes) adversely affect bone metabolism and health. Gut microbiota is considered to be involved in the pathophysiology of obesity and also represents a therapeutic target. This study has investigated the contribution of diet-induced obesity to alterations in bone health and metabolism and whether these could be restored by oral administration of Bifidobacterium pseudocatenulatum CECT 7765. To do so, adult male wild-type C57BL-6 mice were fed either a standard or high-fat diet (HFD), supplemented or not with B. pseudocatenulatum CECT 7765 (10[9] CFU/day) for 14 weeks. Effects on bone mass density (BMD), bone mineral content, bone remodeling, bone structure and gene expression were assessed. In HFD-fed mice, bone microstructural properties at the distal femur showed deteriorated trabecular architecture in bone volumetric fraction, trabecular number and trabecular pattern factor. Besides, the HFD reduced the volumetric bone mineral density in the trabecular bone, but not in the cortical bone. All these bone microstructural alterations found in obese mice were reversed by B. pseudocatenulatum CECT 7765. Administration of the bacterium increased (p < .05) the Wnt/β-catenin pathway gene expression, which could mediate effects on BMD. Bifidobacterium pseudocatenulatum CECT 7765 supplementation increased (p < .05) serum osteocalcin (OC, bone formation parameter), and decreased serum C-terminal telopeptide (CTX) (p < .01) and parathormone (PTH) (p < .05) (both bone resorption parameters). It also altered the microstructure of the femur. In summary, HFD interfered with the normal bone homeostasis leading to increased bone loss. In obese mice, B. pseudocatenulatum CECT 7765 lowered bone mass loss and enhanced BMD by decreasing bone resorption and increasing bone formation.}, }
@article {pmid32795263, year = {2020}, author = {Puente-Sánchez, F and García-García, N and Tamames, J}, title = {SQMtools: automated processing and visual analysis of 'omics data with R and anvi'o.}, journal = {BMC bioinformatics}, volume = {21}, number = {1}, pages = {358}, pmid = {32795263}, issn = {1471-2105}, support = {CTM2016-80095-C2-1-R//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; PID2019-110011RB-C31//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; IJC2018-035180-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; SEV-2013-0347-17-2//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; }, mesh = {Computational Biology/*methods ; Contig Mapping ; Databases, Factual ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Software ; }, abstract = {BACKGROUND: The dramatic decrease in sequencing costs over the last decade has boosted the adoption of high-throughput sequencing applications as a standard tool for the analysis of environmental microbial communities. Nowadays even small research groups can easily obtain raw sequencing data. After that, however, non-specialists are faced with the double challenge of choosing among an ever-increasing array of analysis methodologies, and navigating the vast amounts of results returned by these approaches.<br><br>RESULTS: Here we present a workflow that relies on the SqueezeMeta software for the automated processing of raw reads into annotated contigs and reconstructed genomes (bins). A set of custom scripts seamlessly integrates the output into the anvi'o analysis platform, allowing filtering and visual exploration of the results. Furthermore, we provide a software package with utility functions to expose the SqueezeMeta results to the R analysis environment.<br><br>CONCLUSIONS: Altogether, our workflow allows non-expert users to go from raw sequencing reads to custom plots with only a few powerful, flexible and well-documented commands.}, }
@article {pmid32793165, year = {2020}, author = {Guyet, U and Nguyen, NA and Doré, H and Haguait, J and Pittera, J and Conan, M and Ratin, M and Corre, E and Le Corguillé, G and Brillet-Guéguen, L and Hoebeke, M and Six, C and Steglich, C and Siegel, A and Eveillard, D and Partensky, F and Garczarek, L}, title = {Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1707}, pmid = {32793165}, issn = {1664-302X}, abstract = {Understanding how microorganisms adjust their metabolism to maintain their ability to cope with short-term environmental variations constitutes one of the major current challenges in microbial ecology. Here, the best physiologically characterized marine Synechococcus strain, WH7803, was exposed to modulated light/dark cycles or acclimated to continuous high-light (HL) or low-light (LL), then shifted to various stress conditions, including low (LT) or high temperature (HT), HL and ultraviolet (UV) radiations. Physiological responses were analyzed by measuring time courses of photosystem (PS) II quantum yield, PSII repair rate, pigment ratios and global changes in gene expression. Previously published membrane lipid composition were also used for correlation analyses. These data revealed that cells previously acclimated to HL are better prepared than LL-acclimated cells to sustain an additional light or UV stress, but not a LT stress. Indeed, LT seems to induce a synergic effect with the HL treatment, as previously observed with oxidative stress. While all tested shift conditions induced the downregulation of many photosynthetic genes, notably those encoding PSI, cytochrome b6/f and phycobilisomes, UV stress proved to be more deleterious for PSII than the other treatments, and full recovery of damaged PSII from UV stress seemed to involve the neo-synthesis of a fairly large number of PSII subunits and not just the reassembly of pre-existing subunits after D1 replacement. In contrast, genes involved in glycogen degradation and carotenoid biosynthesis pathways were more particularly upregulated in response to LT. Altogether, these experiments allowed us to identify responses common to all stresses and those more specific to a given stress, thus highlighting genes potentially involved in niche acclimation of a key member of marine ecosystems. Our data also revealed important specific features of the stress responses compared to model freshwater cyanobacteria.}, }
@article {pmid32793158, year = {2020}, author = {Procopio, N and Ghignone, S and Voyron, S and Chiapello, M and Williams, A and Chamberlain, A and Mello, A and Buckley, M}, title = {Soil Fungal Communities Investigated by Metabarcoding Within Simulated Forensic Burial Contexts.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1686}, pmid = {32793158}, issn = {1664-302X}, support = {MR/S032878/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Decomposition of animal bodies in the burial environment plays a key role in the biochemistry of the soil, altering the balance of the local microbial populations present before the introduction of the carcass. Despite the growing number of studies on decomposition and soil bacterial populations, less is known on its effects on fungal communities. Shifts in the fungal populations at different post-mortem intervals (PMIs) could provide insights for PMI estimation and clarify the role that specific fungal taxa have at specific decomposition stages. In this study, we buried pig carcasses over a period of 1- to 6-months, and we sampled the soil in contact with each carcass at different PMIs. We performed metabarcoding analysis of the mycobiome targeting both the internal transcribed spacer (ITS) 1 and 2, to elucidate which one was more suitable for this purpose. Our results showed a decrease in the fungal taxonomic richness associated with increasing PMIs, and the alteration of the soil fungal signature even after 6 months post-burial, showing the inability of soil communities to restore their original composition within this timeframe. The results highlighted taxonomic trends associated with specific PMIs, such as the increase of the Mortierellomycota after 4- and 6-months and of Ascomycota particularly after 2 months, and the decrease of Basidiomycota from the first to the last time point. We have found a limited number of taxa specifically associated with the carrion and not present in the control soil, showing that the major contributors to the recorded changes are originated from the soil and were not introduced by the carrion. As this is the first study conducted on burial graves, it sets the baseline for additional studies to investigate the role of fungal communities on prolonged decomposition periods and to identify fungal biomarkers to improve the accuracy of PMI prediction for forensic applications.}, }
@article {pmid32793152, year = {2020}, author = {Lyu, Y and Su, C and Verbrugghe, A and Van de Wiele, T and Martos Martinez-Caja, A and Hesta, M}, title = {Past, Present, and Future of Gastrointestinal Microbiota Research in Cats.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1661}, pmid = {32793152}, issn = {1664-302X}, abstract = {The relationship between microbial community and host has profound effects on the health of animals. A balanced gastrointestinal (GI) microbial population provides nutritional and metabolic benefits to its host, regulates the immune system and various signaling molecules, protects the intestine from pathogen invasion, and promotes a healthy intestinal structure and an optimal intestinal function. With the fast development of next-generation sequencing, molecular techniques have become standard tools for microbiota research, having been used to demonstrate the complex intestinal ecosystem. Similarly to other mammals, the vast majority of GI microbiota in cats (over 99%) is composed of the predominant bacterial phyla Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Many nutritional and clinical studies have shown that cats' microbiota can be affected by several different factors including body condition, age, diet, and inflammatory diseases. All these factors have different size effects, and some of these may be very minor, and it is currently unknown how important these are. Further research is needed to determine the functional variations in the microbiome in disease states and in response to environmental and/or dietary modulations. Additionally, further studies are also needed to explain the intricate relationship between GI microbiota and the genetics and immunity of its host. This review summarizes past and present knowledge of the feline GI microbiota and looks into the future possibilities and challenges of the field.}, }
@article {pmid32790601, year = {2020}, author = {Lee, JC and Whang, KS}, title = {Agromyces humi sp. nov., actinobacterium isolated from farm soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {70}, number = {9}, pages = {5032-5039}, doi = {10.1099/ijsem.0.004376}, pmid = {32790601}, issn = {1466-5034}, mesh = {Actinobacteria/*classification/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; *Farms ; Fatty Acids/chemistry ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; Spinacia oleracea ; Vitamin K 2/chemistry ; }, abstract = {A Gram-stain-positive actinobacterial strain, designated ANK073[T], was isolated from rhizosphere soil sampled at a spinach farming field in Shinan, Republic of Korea. Cells of strain ANK073[T] were found to be aerobic, non-motile, non-spore-forming rods which could grow at 20-40 °C (optimum, 30 °C), at pH 6.0-10.0 (optimum, pH 6.5-7.5) and at salinities of 0-4 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence analysis showed that strain ANK073[T] belongs to the genus Agromyces with high sequence similarities to Agromyces humatus CD5[T] (98.8 %), Agromyces tardus SJ-23[T] (98.5 %) and Agromyces iriomotensis IY07-20[T] (98.4 %). The phylogenetic analysis indicated that strain ANK073[T] formed a distinct phyletic line in the genus Agromyces and the results of DNA-DNA relatedness and phylogenomic analysis based on whole genome sequences demonstrated that strain ANK073[T] could be separated from its closest relatives in the genus Agromyces. The strain contained 2,4-diaminobutylic acid, glycine, d-glutamic acid and d-alanine in the peptidoglycan. The predominant menaquinones were identified as MK-12 and MK-11, and the major fatty acids were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C15:0. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genome was determined to be 70.2 mol%. On the basis of its phenotypic and chemotaxonomic properties and the results of phylogenetic and phylogenomic analyses, strain ANK073[T] is considered to represent a novel species in the genus Agromyces, for which the name Agromyces humi sp. nov. is proposed. The type strain is ANK073[T] (=KACC 18683[T]=NBRC 111825[T]).}, }
@article {pmid32789440, year = {2021}, author = {Kim, JW and Jeong, Y and Park, SJ and Jin, H and Lee, J and Ju, JH and Ji, GE and Park, SH}, title = {Influence of proton pump inhibitor or rebamipide use on gut microbiota of rheumatoid arthritis patients.}, journal = {Rheumatology (Oxford, England)}, volume = {60}, number = {2}, pages = {708-716}, doi = {10.1093/rheumatology/keaa316}, pmid = {32789440}, issn = {1462-0332}, mesh = {Alanine/*analogs &amp; derivatives/pharmacology ; Arthritis, Rheumatoid/complications/*drug therapy ; Bacteria/genetics/*isolation &amp; purification ; DNA, Bacterial/analysis ; Enzyme Inhibitors/pharmacology ; Female ; Gastrointestinal Diseases/etiology/microbiology/*prevention &amp; control ; Gastrointestinal Microbiome/*drug effects ; Humans ; Male ; Middle Aged ; Prognosis ; Proton Pump Inhibitors/*therapeutic use ; Quinolones/*pharmacology ; }, abstract = {OBJECTIVE: Patients with RA commonly use gastrointestinal (GI) protective drugs for treatment and prevention of drug-associated GI injuries. However, how these drugs affect the gut microbiota in RA patients remains unknown. The objective of this study was to examine the gut microbiota of RA patients according to use of GI protective drugs such as proton pump inhibitors (PPIs), histamine 2-receptor antagonists and rebamipide.<br><br>METHODS: Faecal samples were obtained from 15 healthy controls and 32 RA patients who were receiving PPI, histamine 2-receptor antagonist or rebamipide. Bacterial DNA was extracted from the faecal samples and 16S rRNA sequencing was performed. Microbial composition and function were analysed using Quantitative Insights Into Microbial Ecology and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States.<br><br>RESULTS: RA patients exhibited reduced diversity and altered composition of the gut microbiota compared with healthy controls. The gut microbiota of RA patients receiving acid-suppressing drugs, particularly PPIs, was distinct from that of RA patients receiving rebamipide (PPI vs rebamipide, P&#x2009;=&#x2009;0.005). Streptococcus was enriched in RA patients receiving PPI, while Clostridium bolteae was enriched in RA patients receiving rebamipide. The gut microbiota of PPI users was abundant with microbial functional pathway involved in the production of virulence factors. This featured microbial function was positively correlated with relative abundance of Streptococcus, the differentially abundant taxa of PPI users.<br><br>CONCLUSION: The gut microbiota of RA patients receiving PPIs was distinguishable from that of those receiving rebamipide. The enriched virulent function in the gut microbiota of PPI users suggests that inappropriate PPI use may be harmful in RA patients.}, }
@article {pmid32785735, year = {2021}, author = {Balan, B and Dhaulaniya, AS and Varma, DA and Sodhi, KK and Kumar, M and Tiwari, M and Singh, DK}, title = {Microbial biofilm ecology, in silico study of quorum sensing receptor-ligand interactions and biofilm mediated bioremediation.}, journal = {Archives of microbiology}, volume = {203}, number = {1}, pages = {13-30}, pmid = {32785735}, issn = {1432-072X}, mesh = {Bacteria/*metabolism ; Bacterial Proteins/*metabolism ; *Biodegradation, Environmental ; *Biofilms ; Computer Simulation ; *Ligands ; Quorum Sensing/*physiology ; }, abstract = {Biofilms are structured microbial communities of single or multiple populations in which microbial cells adhere to a surface and get embedded in extracellular polymeric substances (EPS). This review attempts to explain biofilm architecture, development phases, and forces that drive bacteria to promote biofilm mode of growth. Bacterial chemical communication, also known as Quorum sensing (QS), which involves the production, detection, and response to small molecules called autoinducers, is highlighted. The review also provides a brief outline of interspecies and intraspecies cell-cell communication. Additionally, we have performed docking studies using Discovery Studio 4.0, which has enabled our understanding of the prominent interactions between autoinducers and their receptors in different bacterial species while also scoring their interaction energies. Receptors, such as LuxN (Phosphoreceiver domain and RecA domain), LuxP, and LuxR, interacted with their ligands (AI-1, AI-2, and AHL) with a CDocker interaction energy of - 31.6083 kcal/mole; - 34.5821 kcal/mole, - 48.2226 kcal/mole and - 41.5885 kcal/mole, respectively. Since biofilms are ideal for the remediation of contaminants due to their high microbial biomass and their potential to immobilize pollutants, this article also provides an overview of biofilm-mediated bioremediation.}, }
@article {pmid32785584, year = {2020}, author = {Nardi, P and Laanbroek, HJ and Nicol, GW and Renella, G and Cardinale, M and Pietramellara, G and Weckwerth, W and Trinchera, A and Ghatak, A and Nannipieri, P}, title = {Biological nitrification inhibition in the rhizosphere: determining interactions and impact on microbially mediated processes and potential applications.}, journal = {FEMS microbiology reviews}, volume = {44}, number = {6}, pages = {874-908}, doi = {10.1093/femsre/fuaa037}, pmid = {32785584}, issn = {1574-6976}, mesh = {Bacteria/*metabolism ; Host Microbial Interactions/*physiology ; Nitrification/*physiology ; *Rhizosphere ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Nitrification is the microbial conversion of reduced forms of nitrogen (N) to nitrate (NO3-), and in fertilized soils it can lead to substantial N losses via NO3- leaching or nitrous oxide (N2O) production. To limit such problems, synthetic nitrification inhibitors have been applied but their performance differs between soils. In recent years, there has been an increasing interest in the occurrence of biological nitrification inhibition (BNI), a natural phenomenon according to which certain plants can inhibit nitrification through the release of active compounds in root exudates. Here, we synthesize the current state of research but also unravel knowledge gaps in the field. The nitrification process is discussed considering recent discoveries in genomics, biochemistry and ecology of nitrifiers. Secondly, we focus on the 'where' and 'how' of BNI. The N transformations and their interconnections as they occur in, and are affected by, the rhizosphere, are also discussed. The NH4+ and NO3- retention pathways alternative to BNI are reviewed as well. We also provide hypotheses on how plant compounds with putative BNI ability can reach their targets inside the cell and inhibit ammonia oxidation. Finally, we discuss a set of techniques that can be successfully applied to solve unresearched questions in BNI studies.}, }
@article {pmid32784779, year = {2020}, author = {Kumar, H and Jang, YN and Kim, K and Park, J and Jung, MW and Park, JE}, title = {Compositional and Functional Characteristics of Swine Slurry Microbes through 16S rRNA Metagenomic Sequencing Approach.}, journal = {Animals : an open access journal from MDPI}, volume = {10}, number = {8}, pages = {}, pmid = {32784779}, issn = {2076-2615}, support = {PJ01252102//Rural Development Administration/ ; }, abstract = {Traditionally slurry is used as source of nitrogen, phosphorous, and potassium in bio fertilizers to improve crop production. However, poorly managed slurry causes a hazardous effect to the environment by producing greenhouse gases, causing the eutrophication of water bodies, and polluting the groundwater. It has been largely reported that the microbial presence in slurry causing a diverse effect on its storage and disposal system. However, the diversity of bacterial populations in pig slurries remains largely unexplored. Here we report the bacterial diversity present in the slurry from slurry pits, and the effect of storage time on bacterial population. We collected 42 samples from three different pig slurry pits, as three replicates from each one until the 14th week. We used the 16S rRNA, Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) protocols for the metagenomic downstream analysis. Taxonomic annotation using the Greengenes metagenomic database indicated that on an average 76.2% Firmicutes, 14.4% Bacteroidetes, 4.9% Proteobacteria, etc. microbial populations were present. Comparative microbial analysis showed that the population of Firmicutes decreased from the first to the 14th week, whereas the population of Bacteroidetes increased from the first to the 14th week. Through principal coordinate analysis (PCoA), (linear discriminant analysis effect size (LEfSe), and Pearson's correlation analysis, we found microbial biomarkers according to the storage time point. All bacterial populations were well clustered according to the early, middle, and last weeks of storage. LEfSe showed that Actinobacteria, Lachnospiraceae, Ruminococcaceae, and Bacteroidia are dominantly present in first, seventh, ninth, and 14th week, respectively. Lachnospiraceae and Ruminococcaceae are ubiquitous gastrointestinal non-pathogenic bacteria. KEGG pathways, such as membrane transport, carbohydrate and amino acid metabolism, genetic replication and repair, were significant among all samples. Such a KEGG pathway may indicate the association between the host organism's metabolic activity and the microbes present in the gastro intestinal tract (GIT).}, }
@article {pmid32783779, year = {2021}, author = {Belibasakis, GN and Manoil, D}, title = {Microbial Community-Driven Etiopathogenesis of Peri-Implantitis.}, journal = {Journal of dental research}, volume = {100}, number = {1}, pages = {21-28}, pmid = {32783779}, issn = {1544-0591}, mesh = {*Dental Implants ; Humans ; *Microbiota ; *Peri-Implantitis/etiology ; *Periodontitis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Osseointegrated dental implants are a revolutionary tool in the armament of reconstructive dentistry, employed to replace missing teeth and restore masticatory, occlusal, and esthetic functions. Like natural teeth, the orally exposed part of dental implants offers a pristine nonshedding surface for salivary pellicle-mediated microbial adhesion and biofilm formation. In early colonization stages, these bacterial communities closely resemble those of healthy periodontal sites, with lower diversity. Because the peri-implant tissues are more susceptible to endogenous oral infections, understanding of the ecological triggers that underpin the microbial pathogenesis of peri-implantitis is central to developing improved prevention, diagnosis, and therapeutic strategies. The advent of next-generation sequencing (NGS) technologies, notably applied to 16S ribosomal RNA gene amplicons, has enabled the comprehensive taxonomic characterization of peri-implant bacterial communities in health and disease, revealing a differentially abundant microbiota between these 2 states, or with periodontitis. With that, the peri-implant niche is highlighted as a distinct ecosystem that shapes its individual resident microbial community. Shifts from health to disease include an increase in diversity and a gradual depletion of commensals, along with an enrichment of classical and emerging periodontal pathogens. Metatranscriptomic profiling revealed similarities in the virulence characteristics of microbial communities from peri-implantitis and periodontitis, nonetheless with some distinctive pathways and interbacterial networks. Deeper functional assessment of the physiology and virulence of the well-characterized microbial communities of the peri-implant niche will elucidate further the etiopathogenic mechanisms and drivers of the disease.}, }
@article {pmid32780919, year = {2020}, author = {Robles-Vera, I and de la Visitación, N and Toral, M and Sánchez, M and Romero, M and Gómez-Guzmán, M and Yang, T and Izquierdo-García, JL and Guerra-Hernández, E and Ruiz-Cabello, J and Raizada, MK and Pérez-Vizcaíno, F and Jiménez, R and Duarte, J}, title = {Probiotic Bifidobacterium breve prevents DOCA-salt hypertension.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {34}, number = {10}, pages = {13626-13640}, doi = {10.1096/fj.202001532R}, pmid = {32780919}, issn = {1530-6860}, support = {HL102033//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; }, mesh = {Animals ; *Bifidobacterium breve ; *Blood Pressure ; Desoxycorticosterone Acetate ; *Gastrointestinal Microbiome ; Hypertension/chemically induced/*therapy ; Male ; Probiotics/*therapeutic use ; Rats ; Rats, Wistar ; *Vasodilation ; }, abstract = {Many probiotics that affect gut microbial ecology have been shown to produce beneficial effects on renin-angiotensin-dependent rodent models and human hypertension. We hypothesized that Bifidobacterium breve CECT7263 (BFM) would attenuate hypertension in deoxycorticosterone acetate (DOCA)-salt rats, a renin-independent model of hypertension. Rats were randomly divided into five groups: control, DOCA-salt, treated DOCA-salt-BFM, treated DOCA-salt-butyrate, and treated DOCA-salt-acetate, for 5 weeks. BFM prevented the increase in systolic blood pressure, cardiac weight, and renal damage induced by DOCA-salt. BFM increased acetate-producing bacterial population and gut acetate levels, improved colonic integrity, normalized endotoxemia, plasma trimethylamine (TMA) levels, and restored the Th17 and Treg content in mesenteric lymph nodes and aorta. Furthermore, BFM improved nitric oxide-dependent vasorelaxation induced by acetylcholine in aortic rings and reduced NADPH oxidase activity in DOCA-salt animals. These protective effects were mimicked by acetate, but not by butyrate supplementation. These data demonstrate that BFM induces changes in gut microbiota linked with attenuation of endothelial dysfunction and increase in blood pressure in this low-renin form of hypertension. These beneficial effects seem to be mediated by increased acetate and reduced TMA production by gut microbiota, thus, improving gut integrity and restoring Th17/Tregs polarization and endotoxemia.}, }
@article {pmid32780840, year = {2020}, author = {Looby, CI and Martin, PH}, title = {Diversity and function of soil microbes on montane gradients: the state of knowledge in a changing world.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {9}, pages = {}, doi = {10.1093/femsec/fiaa122}, pmid = {32780840}, issn = {1574-6941}, mesh = {Archaea/genetics ; Biodiversity ; Fungi/genetics ; *Soil ; *Soil Microbiology ; }, abstract = {Mountains have a long history in the study of diversity. Like macroscopic taxa, soil microbes are hypothesized to be strongly structured by montane gradients, and recently there has been important progress in understanding how microbes are shaped by these conditions. Here, we summarize this literature and synthesize patterns of microbial diversity on mountains. Unlike flora and fauna that often display a mid-elevation peak in diversity, we found a decline (34% of the time) or no trend (33%) in total microbial diversity with increasing elevation. Diversity of functional groups also varied with elevation (e.g. saprotrophic fungi declined 83% of the time). Most studies (82%) found that climate and soils (especially pH) were the primary mechanisms driving shifts in composition, and drivers differed across taxa-fungi were mostly determined by climate, while bacteria (48%) and archaea (71%) were structured primarily by soils. We hypothesize that the central role of soils-which can vary independently of other abiotic and geographic gradients-in structuring microbial communities weakens diversity patterns expected on montane gradients. Moving forward, we need improved cross-study comparability of microbial diversity indices (i.e. standardizing sequencing) and more geographic replication using experiments to broaden our knowledge of microbial biogeography on global gradients.}, }
@article {pmid32778917, year = {2020}, author = {Gamez, RM and Ramirez, S and Montes, M and Cardinale, M}, title = {Complementary Dynamics of Banana Root Colonization by the Plant Growth-Promoting Rhizobacteria Bacillus amyloliquefaciens Bs006 and Pseudomonas palleroniana Ps006 at Spatial and Temporal Scales.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {656-668}, pmid = {32778917}, issn = {1432-184X}, support = {Public resources from Ministerio de Agricultura y Desarrollo Rural [Ministry of Agriculture and Rural Development] (MADR)//Corporaci&#xf3;n Colombiana de Investigaci&#xf3;n Agropecuaria - Agrosavia/ ; }, mesh = {Bacillus amyloliquefaciens/*physiology ; Colombia ; Musa/*microbiology ; Plant Roots/*microbiology ; Pseudomonas/*physiology ; Rhizosphere ; Spatio-Temporal Analysis ; }, abstract = {Banana (Musa acuminata) growth for commercial purposes requires high amounts of chemical fertilizers, generating high costs and deleterious effects on the environment. In a previous study, we demonstrated that two plant growth-promoting rhizobacteria (PGPR), Bacillus amyloliquefaciens Bs006 and Pseudomonas palleroniana Ps006, isolated in Colombia, could partially replace chemical fertilizers for banana seedling growth. In a second work, the effects of the two inoculants on banana transcripts were found to occur at different times, earlier for Bs006 and later for Ps006. This leads to the hypothesis that the two rhizobacteria have different colonization dynamics. Accordingly, the aim of this work was to analyze the dynamics of root colonization of the two PGPR, Bs006 and Ps006, on banana growth over a time frame of 30 days. We used fluorescence in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM), followed by three-dimensional reconstruction and quantitative image analysis. Bacillus amyloliquefaciens Bs006 abundantly colonized banana roots earlier (from 1 to 48 h), ectophytically on the rhizoplane, and then decreased. Pseudomonas palleroniana Ps006 was initially scarce, but after 96 h it increased dramatically and became clearly endophytic. Here we identify and discuss the potential genetic factors responsible for this complementary behavior. This information is crucial for optimizing the formulation of an effective biofertilizer for banana and its inoculation strategy.}, }
@article {pmid32771820, year = {2020}, author = {Elhalis, H and Cox, J and Frank, D and Zhao, J}, title = {The crucial role of yeasts in the wet fermentation of coffee beans and quality.}, journal = {International journal of food microbiology}, volume = {333}, number = {}, pages = {108796}, doi = {10.1016/j.ijfoodmicro.2020.108796}, pmid = {32771820}, issn = {1879-3460}, mesh = {Acetaldehyde/metabolism ; Acetates/metabolism ; Acetic Acid/metabolism ; Anti-Infective Agents/pharmacology ; Bacteria/classification/*metabolism ; Bioreactors/microbiology ; Coffee/*metabolism/microbiology ; Ethanol/metabolism ; Fermentation/*physiology ; Hanseniaspora/*metabolism ; Lactic Acid/metabolism ; Natamycin/pharmacology ; Odorants/analysis ; Pentanols/metabolism ; Pichia/*metabolism ; Taste ; Yeasts/*metabolism ; }, abstract = {The objective of this study was to investigate the role of yeasts in the wet fermentation of coffee beans and their contribution to coffee quality using a novel approach. Natamycin (300 ppm) was added to the fermentation mass to suppress yeast growth and their metabolic activities, and the resultant microbial ecology, bean chemistry and sensory quality were analyzed and compared to non-treated spontaneous fermentation we reported previously. The yeast community was dominated by Hanseniaspora uvarum and Pichia kudriavzevii and grew to a maximum population of about 5.5 log CFU/g in the absence of Natamycin, while when Natamycin was added yeasts were suppressed. The major bacterial species in both the spontaneous and yeast-suppressed fermentations included the lactic acid bacteria Leuconostoc mesenteroides and Lactococcus lactis, the acetic acid bacteria Gluconobacter cerinus and Acetobacter persici and the Enterobacteriaceae Enterobacter, Citrobacter and Erwinia. For both fermentations, the mucilage layers were completely degraded by the end of the process and the absence of yeast activities had no significant impact on mucilage degradation. During fermentation, reducing sugars were consumed while lactic acid was accumulated inside the beans, and its concentration was significantly higher in the spontaneous fermentation (3 times) than that where yeasts were suppressed by Natamycin. Glycerol was detected with a concentration of 0.08% in the absence of Natamycin and was not identified when Natamycin was added. Green beans fermented with yeast growth contained a higher amount of isoamyl alcohol (21 times), ethanol (3.7 times), acetaldehyde (8 times), and ethyl acetate (25 times) compared to beans fermented in the absence of yeast activities, which remained higher in the former after roasting. Beans fermented without yeast activities had a mild fruity aroma, and lower sensory scores of fragrances (7.0), flavor (6.5), acidity (6.3), body (7.0) and overall score (6.5) compared to the former. These findings demonstrated the crucial roles of yeasts in wet fermentation of coffee beans and for producing high quality coffee.}, }
@article {pmid32770272, year = {2021}, author = {Thongprem, P and Davison, HR and Thompson, DJ and Lorenzo-Carballa, MO and Hurst, GDD}, title = {Incidence and Diversity of Torix Rickettsia-Odonata Symbioses.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {203-212}, pmid = {32770272}, issn = {1432-184X}, support = {CGL2008-02799//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {Animals ; DNA Barcoding, Taxonomic ; Female ; Infectious Disease Transmission, Vertical ; Odonata/*microbiology ; Ovary/microbiology ; Rickettsia/classification/genetics/*physiology ; Rickettsia Infections/*transmission ; Symbiosis/*physiology ; }, abstract = {Heritable microbes are an important component of invertebrate biology, acting both as beneficial symbionts and reproductive parasites. Whilst most previous research has focussed on the 'Wolbachia pandemic', recent work has emphasised the importance of other microbial symbionts. In this study, we present a survey of odonates (dragonflies and damselflies) for torix group Rickettsia, following previous research indicating that this clade can be common in other aquatic insect groups. PCR assays were used to screen a broad range of odonates from two continents and revealed 8 of 76 species tested were infected with Rickettsia. We then conducted further deeper screening of UK representatives of the Coenagrionidae damselfly family, revealing 6 of 8 UK coenagrionid species to be positive for torix Rickettsia. Analysis of Rickettsia gene sequences supported multiple establishments of symbiosis in the group. Some strains were shared between UK coenagrionid species that shared mtDNA barcodes, indicating a likely route for mitochondrial introgression between sister species. There was also evidence of coinfecting Rickettsia strains in two species. FISH analysis indicated Rickettsia were observed in the ovarioles, consistent with heritable symbiosis. We conclude that torix Rickettsia represent an important associate of odonates, being found in a broad range of species from both Europe and South America. There is evidence that coinfection can occur, vertical transmission is likely, and that symbiont movement following hybridisation may underpin the lack of 'barcoding gap' between well-established species pairs in the genus. Future work should establish the biological significance of the symbioses observed.}, }
@article {pmid32770154, year = {2020}, author = {Cichocki, N and Hübschmann, T and Schattenberg, F and Kerckhof, FM and Overmann, J and Müller, S}, title = {Bacterial mock communities as standards for reproducible cytometric microbiome analysis.}, journal = {Nature protocols}, volume = {15}, number = {9}, pages = {2788-2812}, pmid = {32770154}, issn = {1750-2799}, mesh = {Bacteria/*cytology ; Computational Biology ; Cytological Techniques/*standards ; *Microbiota ; Reference Standards ; Reproducibility of Results ; }, abstract = {Flow cytometry has recently established itself as a tool to track short-term dynamics in microbial community assembly and link those dynamics with ecological parameters. However, instrumental configurations of commercial cytometers and variability introduced through differential handling of the cells and instruments frequently cause data set variability at the single-cell level. This is especially pronounced with microorganisms, which are in the lower range of optical resolution. Although alignment beads are valuable to generally minimize instrumental noise and align overall machine settings, an artificial microbial cytometric mock community (mCMC) is mandatory for validating lab workflows and enabling comparison of data between experiments, thus representing a necessary reference standard for the reproducible cytometric characterization of microbial communities, especially in long-term studies. In this study, the mock community consisted of two Gram-positive and two Gram-negative bacterial strains, which can be assembled with respective subsets of cells, including spores, in any selected ratio or concentration. The preparation of the four strains takes a maximum of 5 d, and the stains are storable with either PFA/ethanol fixation at -20 °C or drying at 4 °C for at least 6 months. Starting from this stock, an mCMC can be assembled within 1 h. Fluorescence staining methods are presented and representatively applied with two high-resolution cell sorters and three benchtop flow cytometers. Benchmarked data sets allow the use of bioinformatic evaluation procedures to decode community behavior or convey qualified cell sorting decisions for subsequent high-resolution sequencing or proteomic routines.}, }
@article {pmid32770005, year = {2020}, author = {Yang, S and Lv, Y and Liu, X and Wang, Y and Fan, Q and Yang, Z and Boon, N and Wang, F and Xiao, X and Zhang, Y}, title = {Genomic and enzymatic evidence of acetogenesis by anaerobic methanotrophic archaea.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {3941}, pmid = {32770005}, issn = {2041-1723}, mesh = {Acetates/*metabolism ; Anaerobiosis ; Archaea/*enzymology/genetics ; Bacterial Proteins/genetics/*metabolism ; Carbon Cycle/physiology ; Coenzyme A Ligases/genetics/*metabolism ; Genome, Archaeal ; Geologic Sediments/microbiology ; Metabolic Networks and Pathways/genetics ; Methane/*metabolism ; Oxidation-Reduction ; Seawater/microbiology ; }, abstract = {Anaerobic oxidation of methane (AOM) mediated by anaerobic methanotrophic archaea (ANME) is the primary process that provides energy to cold seep ecosystems by converting methane into inorganic carbon. Notably, cold seep ecosystems are dominated by highly divergent heterotrophic microorganisms. The role of the AOM process in supporting heterotrophic population remains unknown. We investigate the acetogenic capacity of ANME-2a in a simulated cold seep ecosystem using high-pressure biotechnology, where both AOM activity and acetate production are detected. The production of acetate from methane is confirmed by isotope-labeling experiments. A complete archaeal acetogenesis pathway is identified in the ANME-2a genome, and apparent acetogenic activity of the key enzymes ADP-forming acetate-CoA ligase and acetyl-CoA synthetase is demonstrated. Here, we propose a modified model of carbon cycling in cold seeps: during AOM process, methane can be converted into organic carbon, such as acetate, which further fuels the heterotrophic community in the ecosystem.}, }
@article {pmid32767092, year = {2020}, author = {Greer, JA and Swei, A and Vredenburg, VT and Zink, AG}, title = {Parental Care Alters the Egg Microbiome of Maritime Earwigs.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {920-934}, doi = {10.1007/s00248-020-01558-x}, pmid = {32767092}, issn = {1432-184X}, support = {IOS-1258133//National Science Foundation/ ; DBI-1427772//National Science Foundation/ ; DEB-1745411//National Science Foundation/ ; DEB-175037//National Science Foundation/ ; R25-GM059298//Foundation for the National Institutes of Health/ ; }, mesh = {Animals ; Female ; Insecta/microbiology/*physiology ; Maternal Behavior ; *Microbiota ; Ovum/*microbiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Recruitment of beneficial microbes to protect offspring, often reducing the energetic costs of care, is now recognized as an important component of parental care in many animals. Studies on earwigs (order Dermaptera) have revealed that removal of females from egg tending increases mortality of eggs due to fungal infections, possibly caused by changes in the bacterial microbiome on the egg surface. We used a controlled female-removal experiment to evaluate whether female nest attendance in the maritime earwig, Anisolabis maritima, influences the bacterial microbiome on the egg surface. Further, we analyzed the microbiomes of mothers and their eggs to determine if there are a core set of bacteria transferred to eggs through female care. Microbiomes were analyzed using 16S rRNA bacterial DNA sequencing, revealing that bacterial operational taxonomic unit (OTU) richness and diversity were both significantly higher for female attended versus unattended eggs. The core microbiome of adult females contained bacteria which have the potential to carry anti-fungal characteristics; these bacteria were found in higher presence and relative abundance on eggs where females were allowed to provide care. These results demonstrate that female egg attendance significantly impacts the bacterial microbiome of A. maritima eggs, and identifies specific bacteria within the egg microbiome that should be investigated further for beneficial anti-fungal properties in this system.}, }
@article {pmid32767091, year = {2021}, author = {Vargas, S and Leiva, L and Wörheide, G}, title = {Short-Term Exposure to High-Temperature Water Causes a Shift in the Microbiome of the Common Aquarium Sponge Lendenfeldia chondrodes.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {213-222}, pmid = {32767091}, issn = {1432-184X}, mesh = {Animals ; Bacteroidetes/*classification/genetics/isolation &amp; purification ; Biodiversity ; Climate ; Climate Change ; Cyanobacteria/*classification/genetics/isolation &amp; purification ; Hot Temperature ; Microbiota/*genetics ; Planctomycetales/*classification/genetics/isolation &amp; purification ; Porifera/*microbiology ; Proteobacteria/*classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Thermotolerance/genetics ; }, abstract = {Marine sponges harbor diverse microbiomes that contribute to their energetic and metabolic needs. Although numerous studies on sponge microbial diversity exist, relatively few focused on sponge microbial community changes under different sources of environmental stress. In this study, we assess the impact of elevated seawater temperature on the microbiome of cultured Lendenfeldia chondrodes, a coral reef sponge commonly found in marine aquaria. Lendenfeldia chondrodes exhibits high thermal tolerance showing no evidence of tissue damage or bleaching at 5 °C above control water temperature (26 °C). High-throughput sequencing of the bacterial 16S rRNA V4 region revealed a response of the microbiome of L. chondrodes to short-term exposure to elevated seawater temperature. Shifts in abundance and richness of the dominant bacterial phyla found in the microbiome of this species, namely Proteobacteria, Cyanobacteria, Planctomycetes, and Bacteroidetes, characterized this response. The observed resilience of L. chondrodes and the responsiveness of its microbiome to short-term increases in seawater temperature suggest that this holobiont may be capable of acclimating to anthropogenic-driven sublethal environmental stress via a re-accommodation of its associated bacterial community. This sheds a new light on the potential for resilience of some sponges to increasing surface seawater temperatures and associated projected regime shifts in coral reefs.}, }
@article {pmid32765428, year = {2020}, author = {Zhang, H and Sekar, R and Visser, PM}, title = {Editorial: Microbial Ecology in Reservoirs and Lakes.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1348}, pmid = {32765428}, issn = {1664-302X}, }
@article {pmid32763579, year = {2021}, author = {Gong, L and Wang, J and Abbas, T and Zhang, Q and Cai, M and Tahir, M and Wu, D and Di, H}, title = {Immobilization of exchangeable Cd in soil using mixed amendment and its effect on soil microbial communities under paddy upland rotation system.}, journal = {Chemosphere}, volume = {262}, number = {}, pages = {127828}, doi = {10.1016/j.chemosphere.2020.127828}, pmid = {32763579}, issn = {1879-1298}, mesh = {Agriculture/methods ; Cadmium/analysis/*chemistry/toxicity ; Calcium Compounds ; Charcoal ; Crops, Agricultural ; Environmental Pollution ; Environmental Restoration and Remediation/methods ; Fertilizers ; Humans ; Microbiota/*drug effects/physiology ; Oryza/drug effects ; Oxides ; Phosphates ; Rotation ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/analysis/*chemistry/toxicity ; Triticum ; }, abstract = {Cadmium (Cd) pollution is a widespread environmental problem that decreases crop production, destroys the microbial ecology of soil, and poses a severe risk to human health. Organo-chemical amendment is a cost-effective, eco-friendly, and community-acceptable widely applied an in situ technique for metal-contaminated farmland. In this study, we mixed lime, zeolite, calcium magnesium phosphate fertilizer, and biochar in a mixture ratio of 71:23:5:1 to form a mixed amendment. Field and laboratory experiments were conducted to study the effects of the mixed amendment on soil exchangeable Cd content, plant Cd accumulation, and soil microbial community. It was found that the application of 0.5% mixed amendment decreased exchangeable soil Cd by more than 85% and 64% in wheat and rice season, respectively, compared with control (CK), without increasing pH. Moreover, the application of 0.5% mixed amendment decreased Cd accumulation in grains by 22.9% and 41.2% in wheat and rice season, respectively, compared to CK. The result of phospholipid fatty acids (PLFAs) shows that the level of soil microbial diversity and species richness under mixed amendment treatments were higher than in lime treatment, indicating more copiotrophic conditions and faster rate of nutrient turnover in mixed amendment than pure lime treatment. Hence, it concluded that the mixed amendment has a strong effect on fixing exchangeable soil Cd and reducing the accumulation of Cd in crops. Finally, it was observed that the mixed amendment improved the soil microbial community structure and accelerate the rate of nutrient turnover by microbes under this favorable condition comparative to individual treatments.}, }
@article {pmid32761502, year = {2021}, author = {Herrmann, M and Geesink, P and Richter, R and Küsel, K}, title = {Canopy Position Has a Stronger Effect than Tree Species Identity on Phyllosphere Bacterial Diversity in a Floodplain Hardwood Forest.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {157-168}, pmid = {32761502}, issn = {1432-184X}, support = {FZT 118//Deutsche Forschungsgemeinschaft/ ; CRC1076 AquaDiva//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Acer/*microbiology ; Actinobacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Forests ; Germany ; High-Throughput Nucleotide Sequencing ; Microbiota/physiology ; Plant Leaves/*microbiology ; Quercus/*microbiology ; RNA, Ribosomal, 16S/genetics ; Tilia/*microbiology ; Trees/microbiology ; }, abstract = {The phyllosphere is a challenging microbial habitat in which microorganisms can flourish on organic carbon released by plant leaves but are also exposed to harsh environmental conditions. Here, we assessed the relative importance of canopy position-top, mid, and bottom at a height between 31 and 20 m-and tree species identity for shaping the phyllosphere microbiome in a floodplain hardwood forest. Leaf material was sampled from three tree species-maple (Acer pseudoplatanus L.), oak (Quercus robur L.), and linden (Tilia cordata MILL.)-at the Leipzig canopy crane facility (Germany). Estimated bacterial species richness (Chao1) and bacterial abundances approximated by quantitative PCR of 16S rRNA genes exhibited clear vertical trends with a strong increase from the top to the mid and bottom position of the canopy. Thirty operational taxonomic units (OTUs) formed the core microbiome, which accounted for 77% of all sequence reads. These core OTUs showed contrasting trends in their vertical distribution within the canopy, pointing to different ecological preferences and tolerance to presumably more extreme conditions at the top position of the canopy. Co-occurrence analysis revealed distinct tree species-specific OTU networks, and 55-57% of the OTUs were unique to each tree species. Overall, the phyllosphere microbiome harbored surprisingly high fractions of Actinobacteria of up to 66%. Our results clearly demonstrate strong effects of the position in the canopy on phyllosphere bacterial communities in a floodplain hardwood forest and-in contrast to other temperate or tropical forests-a strong predominance of Actinobacteria.}, }
@article {pmid32761501, year = {2021}, author = {Dos Passos, JH and Maia, LC and de Assis, DMA and da Silva, JA and Oehl, F and da Silva, IR}, title = {Arbuscular Mycorrhizal Fungal Community Structure in the Rhizosphere of Three Plant Species of Crystalline and Sedimentary Areas in the Brazilian Dry Forest.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {104-121}, pmid = {32761501}, issn = {1432-184X}, support = {420.129/2018-9; 307.129/2015-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 100.900/2018-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; Financie Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; Finance Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; IBPG-0010-2.03/18//Funda&#xe7;&#xe3;o de Amparo &#xe0; Ci&#xea;ncia e Tecnologia do Estado de Pernambuco/ ; APV-0014-2.03/19//Funda&#xe7;&#xe3;o de Amparo &#xe0; Ci&#xea;ncia e Tecnologia do Estado de Pernambuco/ ; }, mesh = {Biodiversity ; Forests ; *Mycobiome ; *Mycorrhizae ; Plant Roots ; Rhizosphere ; Soil Microbiology ; }, abstract = {The Brazilian dry forest (Caatinga) is located in one of the world's largest tropical semiarid regions, and it occurs on two large geological environments named the crystalline and sedimentary basins. In order to determine the structure and the main drivers of the composition of communities of arbuscular mycorrhizal fungi (AMF) in the Caatinga, we collected soil samples from the rhizosphere of Jatropha mollissima, J. mutabilis, and Mimosa tenuiflora, species that occur in crystalline and sedimentary areas. Ninety-six AMF taxa were identified from soils collected directly in the field and trap cultures. Acaulospora, Glomus, and Rhizoglomus represented almost 49% of the taxon richness. The composition of the AMF communities differed between the crystalline and sedimentary areas and between the rhizospheres of the three plant species. Coarse sand, total sand, natural clay, calcium, soil particles density, flocculation, pH, and base saturation were the principal edaphic variables related to the distribution of these organisms. We registered nine and 17 AMF species classified as indicators, for the geological environments and plant species, respectively. Glomerospores of Glomerales predominated in crystalline basins, whereas glomerospores of Gigasporales prevailed in sedimentary areas; among the plant species, lower number of glomerospores of Archaeosporales and Glomerales was recorded in the rhizosphere of J. mollissima. The results show that the AMF community composition is shaped by geological environments and plant hosts. In addition, soil characteristics, mainly physical attributes, significantly influence the structure of Glomeromycota communities occurring in areas of the Brazilian semiarid.}, }
@article {pmid32760678, year = {2020}, author = {Celis Ramírez, AM and Amézquita, A and Cardona Jaramillo, JEC and Matiz-Cerón, LF and Andrade-Martínez, JS and Triana, S and Mantilla, MJ and Restrepo, S and Barrios, AFG and de Cock, H}, title = {Analysis of Malassezia Lipidome Disclosed Differences Among the Species and Reveals Presence of Unusual Yeast Lipids.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {338}, pmid = {32760678}, issn = {2235-2988}, mesh = {Animals ; Humans ; Lipidomics ; Lipids ; *Malassezia/genetics ; Saccharomyces cerevisiae ; }, abstract = {Malassezia yeasts are lipid dependent and part of the human and animal skin microbiome. However, they are also associated with a variety of dermatological conditions and even cause systemic infections. How these yeasts can live as commensals on the skin and switch to a pathogenic stage has long been a matter of debate. Lipids are important cellular molecules, and understanding the lipid metabolism and composition of Malassezia species is crucial to comprehending their biology and host-microbe interaction. Here, we investigated the lipid composition of Malassezia strains grown to the stationary phase in a complex Dixon medium broth. In this study, we perform a lipidomic analysis of a subset of species; in addition, we conducted a gene prediction analysis for the detection of lipid metabolic proteins. We identified 18 lipid classes and 428 lipidic compounds. The most commonly found lipids were triglycerides (TAG), sterol (CH), diglycerides (DG), fatty acids (FAs), phosphatidylcholine (PC), phosphatidylethanolamine (PE), ceramides, cholesteryl ester (CE), sphingomyelin (SM), acylcarnitine, and lysophospholipids. Particularly, we found a low content of CEs in Malassezia furfur, atypical M. furfur, and Malassezia pachydermatis and undetectable traces of these components in Malassezia globosa, Malassezia restricta, and Malassezia sympodialis. Remarkably, uncommon lipids in yeast, like diacylglyceryltrimethylhomoserine and FA esters of hydroxyl FAs, were found in a variable concentration in these Malassezia species. The latter are bioactive lipids recently reported to have antidiabetic and anti-inflammatory properties. The results obtained can be used to discriminate different Malassezia species and offer a new overview of the lipid composition of these yeasts. We could confirm the presence and the absence of certain lipid-biosynthesis genes in specific species. Further analyses are necessary to continue disclosing the complex lipidome of Malassezia species and the impact of the lipid metabolism in connection with the host interaction.}, }
@article {pmid32760379, year = {2020}, author = {Podar, PT and Yang, Z and Björnsdóttir, SH and Podar, M}, title = {Comparative Analysis of Microbial Diversity Across Temperature Gradients in Hot Springs From Yellowstone and Iceland.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1625}, pmid = {32760379}, issn = {1664-302X}, abstract = {Geothermal hot springs are a natural setting to study microbial adaptation to a wide range of temperatures reaching up to boiling. Temperature gradients lead to distinct microbial communities that inhabit their optimum niches. We sampled three alkaline, high temperature (80-100°C) hot springs in Yellowstone and Iceland that had cooling outflows and whose microbial communities had not been studied previously. The microbial composition in sediments and mats was determined by DNA sequencing of rRNA gene amplicons. Over three dozen phyla of Archaea and Bacteria were identified, representing over 1700 distinct organisms. We observed a significant non-linear reduction in the number of microbial taxa as the temperature increased from warm (38°C) to boiling. At high taxonomic levels, the community structure was similar between the Yellowstone and Iceland hot springs. We identified potential endemism at the genus level, especially in thermophilic phototrophs, which may have been potentially driven by distinct environmental conditions and dispersal limitations.}, }
@article {pmid32757814, year = {2020}, author = {Zhu, Y and Guo, J}, title = {Impact of dichlorprop on soil microbial community structure and diversity during its enantioselective biodegradation in agricultural soils.}, journal = {Journal of environmental science and health. Part. B, Pesticides, food contaminants, and agricultural wastes}, volume = {55}, number = {11}, pages = {974-982}, doi = {10.1080/03601234.2020.1802186}, pmid = {32757814}, issn = {1532-4109}, mesh = {2,4-Dichlorophenoxyacetic Acid/*analogs &amp; derivatives/analysis/chemistry/pharmacokinetics/pharmacology ; Agriculture ; Bacteria/drug effects/genetics/metabolism ; Biodegradation, Environmental ; Kinetics ; Michigan ; Microbiota/*drug effects/genetics ; RNA, Ribosomal, 16S ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/analysis/chemistry/pharmacokinetics/*pharmacology ; Stereoisomerism ; }, abstract = {Enantioselective biodegradation of racemic dichlorprop in two soils was investigated in the laboratory. Chiral separation of racemic dichlorprop was achieved by using HPLC with Phenomenex Lux Amylose-2. The first-order kinetic model fitted well the dissipation data of racemic dichlorprop and its pure R- and S-enantiomers. S-dichlorprop was preferentially degraded in both soils and enantioselectivity was affected by soil pH. The half-lives (DT50) of S-dichlorprop were 8.22 days in soil A and 8.06 days in soil D, while R-dichlorprop was more persistent with DT50 of 12.93 days in soil A and 12.38 days in soil D, respectively. Dichlorprop dissipated faster in soil D with lower organic matter content. In sterilized soils, neglected dissipation was observed and enantiomer fraction values remained constant, indicating that the enantioselective degradation was mainly controlled by soil microorganisms. Soil microbial community structure and diversity was assessed by Illumina MiSeq sequencing of 16S rRNA genes from dichlorprop and no dichlorprop contaminated microcosms. Compared with controls, dichlorprop application had no significant effect on microbial community structures at phylum level, but increased bacterial diversity and dichlorprop degradation related taxa in both soils. S-dichlorprop preferential degradation might be attributed to the S-enantiomer preferred degraders in the family of Sphingomonadaceae.}, }
@article {pmid32757488, year = {2021}, author = {Xu, Y and Tandon, R and Ancheta, C and Arroyo, P and Gilbert, JA and Stephens, B and Kelley, ST}, title = {Quantitative profiling of built environment bacterial and fungal communities reveals dynamic material dependent growth patterns and microbial interactions.}, journal = {Indoor air}, volume = {31}, number = {1}, pages = {188-205}, doi = {10.1111/ina.12727}, pmid = {32757488}, issn = {1600-0668}, support = {F32 GM020013/GM/NIGMS NIH HHS/United States ; }, mesh = {Air Pollution, Indoor ; Bacteria ; *Built Environment ; Construction Materials ; *Environmental Microbiology ; Fungi ; Humans ; Humidity ; Microbial Interactions ; Microbiota ; Mycobiome ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Indoor microbial communities vary in composition and diversity depending on material type, moisture levels, and occupancy. In this study, we integrated bacterial cell counting, fungal biomass estimation, and fluorescence-assisted cell sorting (FACS) with amplicon sequencing of bacterial (16S rRNA) and fungal (ITS) communities to investigate the influence of wetting on medium density fiberboard (MDF) and gypsum wallboard. Surface samples were collected longitudinally from wetted materials maintained at high relative humidity (~95%). Bacterial and fungal growth patterns were strongly time-dependent and material-specific. Fungal growth phenotypes differed between materials: spores dominated MDF surfaces while fungi transitioned from spores to hyphae on gypsum. FACS confirmed that most of the bacterial cells were intact (viable) on both materials over the course of the study. Integrated cell count and biomass data (quantitative profiling) revealed that small changes in relative abundance often resulted from large changes in absolute abundance, while negative correlations in relative abundances were explained by rapid growth of only one group of bacteria or fungi. Comparisons of bacterial-bacterial and fungal-bacterial networks suggested a top-down control of fungi on bacterial growth, possibly via antibiotic production. In conclusion, quantitative profiling provides novel insights into microbial growth dynamics on building materials with potential implications for human health.}, }
@article {pmid32756341, year = {2020}, author = {Sierra, MA and Li, Q and Pushalkar, S and Paul, B and Sandoval, TA and Kamer, AR and Corby, P and Guo, Y and Ruff, RR and Alekseyenko, AV and Li, X and Saxena, D}, title = {The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community.}, journal = {Genes}, volume = {11}, number = {8}, pages = {}, pmid = {32756341}, issn = {2073-4425}, support = {R01 LM012517/LM/NLM NIH HHS/United States ; CA206105/NH/NIH HHS/United States ; DE025992/NH/NIH HHS/United States ; DE027074/NH/NIH HHS/United States ; }, mesh = {Computational Biology/methods/*standards ; DNA Barcoding, Taxonomic/methods/standards ; Databases, Genetic/*standards ; Humans ; *Microbiota ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {There is currently no criterion to select appropriate bioinformatics tools and reference databases for analysis of 16S rRNA amplicon data in the human oral microbiome. Our study aims to determine the influence of multiple tools and reference databases on α-diversity measurements and β-diversity comparisons analyzing the human oral microbiome. We compared the results of taxonomical classification by Greengenes, the Human Oral Microbiome Database (HOMD), National Center for Biotechnology Information (NCBI) 16S, SILVA, and the Ribosomal Database Project (RDP) using Quantitative Insights Into Microbial Ecology (QIIME) and the Divisive Amplicon Denoising Algorithm (DADA2). There were 15 phyla present in all of the analyses, four phyla exclusive to certain databases, and different numbers of genera were identified in each database. Common genera found in the oral microbiome, such as Veillonella, Rothia, and Prevotella, are annotated by all databases; however, less common genera, such as Bulleidia and Paludibacter, are only annotated by large databases, such as Greengenes. Our results indicate that using different reference databases in 16S rRNA amplicon data analysis could lead to different taxonomic compositions, especially at genus level. There are a variety of databases available, but there are no defined criteria for data curation and validation of annotations, which can affect the accuracy and reproducibility of results, making it difficult to compare data across studies.}, }
@article {pmid32754956, year = {2020}, author = {Morimoto, D and Šulčius, S and Yoshida, T}, title = {Viruses of freshwater bloom-forming cyanobacteria: genomic features, infection strategies and coexistence with the host.}, journal = {Environmental microbiology reports}, volume = {12}, number = {5}, pages = {486-502}, doi = {10.1111/1758-2229.12872}, pmid = {32754956}, issn = {1758-2229}, support = {//Bilateral Open Partnership Joint Research Project/International ; 16H06437//JSPS Scientific Research on Innovative Areas/International ; 203143100025//The Canon Foundation/International ; //Research Council of Lithuania/International ; S-MIP-17-28//Japan Society for the Promotion of Science/International ; 17H03850//Japan Society for the Promotion of Science/International ; }, mesh = {Bacteriophages/classification/*genetics/isolation &amp; purification/metabolism ; Cyanobacteria/classification/genetics/growth &amp; development/*virology ; Fresh Water/*microbiology/*virology ; Genome, Viral ; Genomics ; Phylogeny ; Viruses/classification/*genetics/isolation &amp; purification/metabolism ; }, abstract = {Freshwater bloom-forming cyanobacteria densely grow in the aquatic environments, leading to an increase in the viral-contact rate. They possess numerous antiviral genes, as well as cell differentiation- and physiological performance-related genes, owing to genome expansion. Their genomic features and unique lifestyles suggest that they coexist with cyanoviruses in ways different from marine cyanobacteria. Furthermore, genome contents of isolated freshwater bloom-forming cyanobacterial viruses have little in common with those of marine cyanoviruses studied to date. They lack the marine cyanoviral hallmark genes that sustain photosynthetic activity and redirect host metabolism to viral reproduction; therefore, they are predicted to share metabolisms and precursor pools with host cyanobacteria to ensure efficient viral reproduction and avoid nutrient deficiencies and antiviral response. Additionally, cyanovirus-cyanobacteria coexistence strategies may change as bloom density increases. Diverse genotypic populations of cyanoviruses and hosts coexist and fluctuate under high viral-contact rate conditions, leading to their rapid coevolution through antiviral responses. The ancestral and newly evolved genotypes coexist, thereby expanding the diversity levels of host and viral populations. Bottleneck events occurring due to season-related decreases in bloom-forming species abundance provide each genotype within cyanobacterial population an equal chance to increase in prevalence during the next bloom and enhance further diversification.}, }
@article {pmid32751149, year = {2020}, author = {Marsaux, B and Van den Abbeele, P and Ghyselinck, J and Prioult, G and Marzorati, M and Bogićević, B}, title = {Synbiotic Effect of Bifidobacterium lactis CNCM I-3446 and Bovine Milk-Derived Oligosaccharides on Infant Gut Microbiota.}, journal = {Nutrients}, volume = {12}, number = {8}, pages = {}, pmid = {32751149}, issn = {2072-6643}, mesh = {Animals ; *Bifidobacterium animalis ; Cattle ; Feces/microbiology ; Female ; Fermentation/drug effects ; Gastrointestinal Microbiome/drug effects ; Humans ; Infant ; Male ; Milk/*chemistry ; Oligosaccharides/*pharmacology ; Probiotics/*pharmacology ; RNA, Ribosomal, 16S/analysis ; *Synbiotics ; }, abstract = {BACKGROUND: This study evaluated the impact of Bifidobacterium animalis ssp. lactis CNCM I-3446, Bovine Milk-derived OligoSaccharides (BMOS) and their combination on infant gut microbiota in vitro. In addition, a novel strategy consisting of preculturing B. lactis with BMOS to further enhance their potential synbiotic effects was assessed.<br><br>METHOD: Short-term fecal batch fermentations (48 h) were used to assess the microbial composition and activity modulated by BMOS alone, B. lactis grown on BMOS or dextrose alone, or their combinations on different three-month-old infant microbiota.<br><br>RESULTS: BMOS alone significantly induced acetate and lactate production (leading to pH decrease) and stimulated bifidobacterial growth in 10 donors. A further in-depth study on two different donors proved B. lactis ability to colonize the infant microbiota, regardless of the competitiveness of the environment. BMOS further enhanced this engraftment, suggesting a strong synbiotic effect. This was also observed at the microbiota activity level, especially in a donor containing low initial levels of bifidobacteria. In this donor, preculturing B. lactis with BMOS strengthened further the early modulation of microbiota activity observed after 6 h.<br><br>CONCLUSION: This study demonstrated the strong synbiotic effect of BMOS and B. lactis on the infant gut microbiota, and suggests a strategy to improve its effectiveness in an otherwise low-Bifidobacterium microbiota.}, }
@article {pmid32748335, year = {2020}, author = {Maal-Bared, R}, title = {Operational impacts of heavy metals on activated sludge systems: the need for improved monitoring.}, journal = {Environmental monitoring and assessment}, volume = {192}, number = {9}, pages = {560}, doi = {10.1007/s10661-020-08529-2}, pmid = {32748335}, issn = {1573-2959}, mesh = {Environmental Monitoring ; Metals, Heavy/*analysis ; *Microbiota ; Sewage ; Wastewater/analysis ; }, abstract = {Biological nutrient removal is highly reliant on maintaining a heterogeneous, balanced, and metabolically active microbial community that can adapt to the fluctuating composition of influent wastewater and encompassing environmental conditions. Maintaining this balance can be challenging in municipal wastewater systems that sporadically receive wastewater from industrial facilities due to the impact of heavy metals and other contaminants on the microbial ecology of the activated sludge. A thorough understanding of the impacts of heavy metals on activated sludge and of practical monitoring options is needed to support decision-making at the wastewater utility level. This paper is divided into two parts. In the first part, the review explains what happens when heavy metals interact with activated sludge systems by highlighting biosorption and bioaccumulation processes, and when an activated sludge system switches from bioaccumulation to toxic shock. Here, it also summarizes the impacts of heavy metal exposure on plant performance. In the second part, the review summarizes practical approaches that can be used at the plant outside the realm of traditional toxicological bioassays testing to determine the possible impacts of influent heavy metal concentrations on the BNR process. These approaches include the following: monitoring operational parameters for major shifts; respirometry; microscopy; ATP; chemical analyses of heavy metals with a focus on synergistic impacts and inhibitory limits; and other novel approaches, such as EPS chemical analyses, molecular techniques, and quorum sensing.}, }
@article {pmid32747713, year = {2020}, author = {Pieper, R and Dadi, TH and Pieper, L and Vahjen, W and Franke, A and Reinert, K and Zentek, J}, title = {Concentration and chemical form of dietary zinc shape the porcine colon microbiome, its functional capacity and antibiotic resistance gene repertoire.}, journal = {The ISME journal}, volume = {14}, number = {11}, pages = {2783-2793}, pmid = {32747713}, issn = {1751-7370}, mesh = {Animal Feed/analysis ; Animals ; *Anti-Bacterial Agents ; Colon ; Diet ; Drug Resistance, Microbial ; Swine ; Weaning ; *Zinc ; }, abstract = {Despite a well-documented effect of high dietary zinc oxide on the pig intestinal microbiota composition less is it yet known about changes in microbial functional properties or the effect of organic zinc sources. Forty weaning piglets in four groups were fed diets supplemented with 40 or 110 ppm zinc as zinc oxide, 110 ppm as Zn-Lysinate, or 2500 ppm as zinc oxide. Host zinc homeostasis, intestinal zinc fractions, and ileal nutrient digestibility were determined as main nutritional and physiological factors putatively driving colon microbial ecology. Metagenomic sequencing of colon microbiota revealed only clear differences at genus level for the group receiving 2500 ppm zinc oxide. However, a clear group differentiation according to dietary zinc concentration and source was observed at species level. Functional analysis revealed significant differences in genes related to stress response, mineral, and carbohydrate metabolism. Taxonomic and functional gene differences were accompanied with clear effects in microbial metabolite concentration. Finally, a selection of certain antibiotic resistance genes by dietary zinc was observed. This study sheds further light onto the consequences of concentration and chemical form of dietary zinc on microbial ecology measures and the resistome in the porcine colon.}, }
@article {pmid32747679, year = {2020}, author = {Hach, PF and Marchant, HK and Krupke, A and Riedel, T and Meier, DV and Lavik, G and Holtappels, M and Dittmar, T and Kuypers, MMM}, title = {Rapid microbial diversification of dissolved organic matter in oceanic surface waters leads to carbon sequestration.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {13025}, pmid = {32747679}, issn = {2045-2322}, abstract = {The pool of dissolved organic matter (DOM) in the deep ocean represents one of the largest carbon sinks on the planet. In recent years, studies have shown that most of this pool is recalcitrant, because individual compounds are present at low concentrations and because certain compounds seem resistant to microbial degradation. The formation of the diverse and recalcitrant deep ocean DOM pool has been attributed to repeated and successive processing of DOM by microorganisms over time scales of weeks to years. Little is known however, about the transformation and cycling that labile DOM undergoes in the first hours upon its release from phytoplankton. Here we provide direct experimental evidence showing that within hours of labile DOM release, its breakdown and recombination with ambient DOM leads to the formation of a diverse array of new molecules in oligotrophic North Atlantic surface waters. Furthermore, our results reveal a preferential breakdown of N and P containing molecules versus those containing only carbon. Hence, we show the preferential breakdown and molecular diversification are the crucial first steps in the eventual formation of carbon rich DOM that is resistant to microbial remineralization.}, }
@article {pmid32747621, year = {2020}, author = {Guerra, CA and Heintz-Buschart, A and Sikorski, J and Chatzinotas, A and Guerrero-Ramírez, N and Cesarz, S and Beaumelle, L and Rillig, MC and Maestre, FT and Delgado-Baquerizo, M and Buscot, F and Overmann, J and Patoine, G and Phillips, HRP and Winter, M and Wubet, T and Küsel, K and Bardgett, RD and Cameron, EK and Cowan, D and Grebenc, T and Marín, C and Orgiazzi, A and Singh, BK and Wall, DH and Eisenhauer, N}, title = {Blind spots in global soil biodiversity and ecosystem function research.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {3870}, pmid = {32747621}, issn = {2041-1723}, mesh = {Animals ; Bacteria/classification/metabolism ; *Biodiversity ; Biomass ; Climate ; *Ecosystem ; Fungi/classification/metabolism ; Geography ; Hydrogen-Ion Concentration ; Nematoda/classification/metabolism ; Oligochaeta/classification/metabolism ; Soil/chemistry/*parasitology ; *Soil Microbiology ; Temperature ; }, abstract = {Soils harbor a substantial fraction of the world's biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to represent the diversity of environmental conditions that can be found worldwide. Here we identify and characterize existing environmental gaps in soil taxa and ecosystem functioning data across soil macroecological studies and 17,186 sampling sites across the globe. These data gaps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.3% of all sampling sites having both information about biodiversity and function, although with different taxonomic groups and functions at each site. Based on this information, we provide clear priorities to support and expand soil macroecological research.}, }
@article {pmid32744986, year = {2020}, author = {Siebert, A and Huptas, C and Wenning, M and Scherer, S and Doll, EV}, title = {Fundicoccus ignavus gen. nov., sp. nov., a novel genus of the family Aerococcaceae isolated from bulk tank milk.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {70}, number = {8}, pages = {4774-4781}, doi = {10.1099/ijsem.0.004344}, pmid = {32744986}, issn = {1466-5034}, mesh = {Aerococcaceae/*classification/isolation &amp; purification ; Animals ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Glycolipids/chemistry ; Milk/*microbiology ; Peptidoglycan/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Three strains of a Gram-stain-positive, catalase-negative, facultative anaerobic, and coccoid species were isolated from German bulk tank milk. Phylogenetic analyses based on the 16S rRNA gene sequences indicated that the three strains (WS4937[T], WS4759 and WS5303) constitute an independent phylogenetic lineage within the family Aerococcaceae with Facklamia hominis CCUG 36813[T] (93.7-94.1 %) and Eremococcus coleocola M1831/95/2[T] (93.5 %) as most closely related type species. The unclassified strains demonstrated variable growth with 6.5 % (w/v) NaCl and tolerated pH 6.5-9.5. Growth was observed from 12 to 39 °C. Their cell-wall peptidoglycan belongs to the A1α type (l-Lys-direct) consisting of alanine, glutamic acid and lysine. The predominant fatty acids were C16 : 1 ω9c, C16 : 0 and C18 : 1 ω9c and in the polar lipids profile three glycolipids, a phospholipid, phosphatidylglycerol, phosphoglycolipid and diphosphatidylglycerol were found. The G+C content of strain WS4937[T] was 37.4 mol% with a genome size of ~3.0 Mb. Based on phylogenetic, phylogenomic and biochemical characterizations, the isolates can be demarcated from all other genera of the family Aerococcaceae and, therefore, the novel genus Fundicoccus gen. nov. is proposed. The type species of the novel genus is Fundicoccus ignavus gen. nov., sp. nov. WS4937[T] (=DSM 109652[T]=LMG 31441[T]).}, }
@article {pmid32742267, year = {2020}, author = {Breitenwieser, F and Doll, EV and Clavel, T and Scherer, S and Wenning, M}, title = {Complementary Use of Cultivation and High-Throughput Amplicon Sequencing Reveals High Biodiversity Within Raw Milk Microbiota.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1557}, pmid = {32742267}, issn = {1664-302X}, abstract = {Raw milk microbiota are complex communities with a significant impact on the hygienic, sensory and technological quality of milk products. However, there is a lack of knowledge on factors determining their composition. In the present study, four bulk tank milk samples of two farms at two different time points were analyzed in detail for their microbiota using cultivation and 16S rRNA amplicon sequencing. Diversity in samples from the first time point was assessed via cultivation of 500 aerobic mesophilic bacterial isolates in each sample. A high biodiversity of 70 and 110 species per sample was determined, of which 25-28% corresponded to yet unknown taxa. The isolates were dominated by Gram-positive members of the genera Staphylococcus, Corynebacterium, Streptococcus, or Janibacter, whilst Chryseobacterium and Acinetobacter were most abundant among the Gram-negative taxa. At the second time point, samples of the same farms were analyzed via both cultivation (1,500 individual colonies each) and high-throughput 16S rRNA gene amplicon sequencing. The latter revealed a threefold higher biodiversity at the genus level, as anaerobic or fastidious species were also detected. However, cultivation identified genera not captured by sequencing, indicating that both approaches are complementary. Using amplicon sequencing, the relative abundance of a few genera was distorted, which seems to be an artifact of sample preparation. Therefore, attention needs to be paid to the library preparation procedure with special emphasis on cell lysis and PCR.}, }
@article {pmid32740757, year = {2021}, author = {Bose, T and Wingfield, MJ and Roux, J and Vivas, M and Burgess, TI}, title = {Phytophthora Species Associated with Roots of Native and Non-native Trees in Natural and Managed Forests.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {122-133}, pmid = {32740757}, issn = {1432-184X}, mesh = {Acacia/parasitology ; Biodiversity ; Eucalyptus/parasitology ; Forests ; Phytophthora/*classification/genetics/*isolation &amp; purification ; Plant Diseases/parasitology ; Plant Roots/*parasitology ; Soil/*parasitology ; South Africa ; Trees/*parasitology ; }, abstract = {Roots act as a biological filter that exclusively allows only a portion of the soil-associated microbial diversity to infect the plant. This microbial diversity includes organisms both beneficial and detrimental to plants. Phytophthora species are among the most important groups of detrimental microbes that cause various soil-borne plant diseases. We used a metabarcoding approach with Phytophthora-specific primers to compare the diversity and richness of Phytophthora species associated with roots of native and non-native trees, using different types of soil inocula collected from native and managed forests. Specifically, we analysed (1) roots of two non-native tree species (Eucalyptus grandis and Acacia mearnsii) and native trees, (2) roots of two non-native tree species from an in vivo plant baiting trial, (3) roots collected from the field versus those from the baiting trial, and (4) roots and soil samples collected from the field. The origin of the soil and the interaction between root and soil significantly influenced Phytophthora species richness. Moreover, species richness and community composition were significantly different between the field root samples and field soil samples with a higher number of Phytophthora species in the soil than in the roots. The results also revealed a substantial and previously undetected diversity of Phytophthora species from South Africa.}, }
@article {pmid32740714, year = {2020}, author = {Xian, L and Wan, T and Cao, Y and Sun, J and Wu, T and Apudo, AA and Li, W and Liu, F}, title = {Structural Variability and Functional Prediction in the Epiphytic Bacteria Assemblies of Myriophyllum spicatum.}, journal = {Current microbiology}, volume = {77}, number = {11}, pages = {3582-3594}, pmid = {32740714}, issn = {1432-0991}, support = {31370262//National Natural Science Foundation of China/ ; 31670368//National Natural Science Foundation of China/ ; 31670369//National Natural Science Foundation of China/ ; 31500296//National Natural Science Foundation of China/ ; 2016YFA0601001//National Key R &amp; D Program of China/ ; }, mesh = {Aquatic Organisms ; *Bacteria/genetics ; *Microbiota ; Nitrogen ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The underlying principles influencing bacteria community assembly have long been of interest in the field of microbial ecology. Environmental heterogeneity is believed to be important in controlling the uniqueness and variability of communities. However, little is known about the influence of the host macrophytes on epiphytic bacteria assembly. In this study, we used two contrasting artificial water environments (eutrophic and oligotrophic) for reciprocal transplant experiment of Myriophyllum spicatum to examine the colonization of epiphytic bacteria accompanied with plants growth. Comparative analysis addressed a higher species diversity in epiphytic bacteria than in bacterioplankton, and the highest microbiome richness in sediment. Our data revealed that the organization of epiphytic bacterial community was affected by both plant status (i.e. branch number, net photosynthesis rate etc.) and water bodies (i.e. total phosphate, total nitrogen, pH etc.). Moreover, plant status effected the assembly in priority to water. 16S rRNA gene sequencing further indicated that the epiphytic assemblies were motivated by functionalization and interplay with hosts as a whole. The results complemented new evidences for the 'lottery process' in the epiphytic bacteria assembly traits and shed insights into the assembly patterns referring to functional adaptation across epiphytic bacteria and macrophytes.}, }
@article {pmid32739699, year = {2020}, author = {De Paepe, J and De Paepe, K and Gòdia, F and Rabaey, K and Vlaeminck, SE and Clauwaert, P}, title = {Bio-electrochemical COD removal for energy-efficient, maximum and robust nitrogen recovery from urine through membrane aerated nitrification.}, journal = {Water research}, volume = {185}, number = {}, pages = {116223}, doi = {10.1016/j.watres.2020.116223}, pmid = {32739699}, issn = {1879-2448}, mesh = {Biofilms ; Bioreactors ; Denitrification ; Humans ; *Nitrification ; *Nitrogen ; Nitrosomonas ; Waste Disposal, Fluid ; }, abstract = {Resource recovery from source-separated urine can shorten nutrient cycles on Earth and is essential in regenerative life support systems for deep-space exploration. In this study, a robust two-stage, energy-efficient, gravity-independent urine treatment system was developed to transform fresh real human urine into a stable nutrient solution. In the first stage, up to 85% of the COD was removed in a microbial electrolysis cell (MEC), converting part of the energy in organic compounds (27-46%) into hydrogen gas and enabling full nitrogen recovery by preventing nitrogen losses through denitrification in the second stage. Besides COD removal, all urea was hydrolysed in the MEC, resulting in a stream rich in ammoniacal nitrogen and alkalinity, and low in COD. This stream was fed into a membrane-aerated biofilm reactor (MABR) in order to convert the volatile and toxic ammoniacal nitrogen to non-volatile nitrate by nitrification. Bio-electrochemical pre-treatment allowed to recover all nitrogen as nitrate in the MABR at a bulk-phase dissolved oxygen level below 0.1 mg O2 L[-1]. In contrast, feeding the MABR directly with raw urine (omitting the first stage), at the same nitrogen loading rate, resulted in nitrogen loss (18%) due to denitrification. The MEC and MABR were characterised by very distinct and diverse microbial communities. While (strictly) anaerobic genera, such as Geobacter (electroactive bacteria), Thiopseudomonas, a Lentimicrobiaceae member, Alcaligenes and Proteiniphilum prevailed in the MEC, the MABR was dominated by aerobic genera, including Nitrosomonas (a known ammonium oxidiser), Moheibacter and Gordonia. The two-stage approach yielded a stable nitrate-rich, COD-low nutrient solution, suitable for plant and microalgae cultivation.}, }
@article {pmid32737846, year = {2021}, author = {Adeleke, BS and Babalola, OO}, title = {The endosphere microbial communities, a great promise in agriculture.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {24}, number = {1}, pages = {1-17}, pmid = {32737846}, issn = {1618-1905}, support = {123634//National Research Foundation/ ; }, mesh = {Agriculture ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Endophytes/classification/genetics/*isolation &amp; purification/metabolism ; Fertilizers/analysis/microbiology ; *Microbiota ; *Soil Microbiology ; }, abstract = {Agricultural food production and sustainability need intensification to address the current global food supply to meet human demand. The continuous human population increase and other anthropogenic activities threaten food security. Agrochemical inputs have long been used in conventional agricultural systems to boost crop productivity, but they are disadvantageous to a safe environment. Towards developing environmentally friendly agriculture, efforts are being directed in exploring biological resources from soil and plant microbes. The survival of the rhizosphere and endosphere microbiota is influenced by biotic and abiotic factors. Plant microbiota live interdependently with the host plants. Endophytes are regarded as colonizer microbes inhabiting and establishing microbial communities within the plant tissue. Their activities are varied and include fixing atmospheric nitrogen, solubilizing phosphate, synthesis of siderophores, secretion of metabolite-like compounds containing active biocontrol agents in the control of phytopathogens, and induced systemic resistance that stimulates plant response to withstand stress. Exploring beneficial endophyte resources in the formulation of bio-inoculants, such as biofertilizers, as an alternative to agrochemicals (fertilizers and pesticides) in developing environmentally friendly agriculture and for incorporation into crop breeding and disease control program is promising. Therefore, in this review, endosphere microbial ecology, associating environmental factors, and their roles that contribute to their effectiveness in promoting plant growth for maximum agricultural crop productivity were highlighted.}, }
@article {pmid32737539, year = {2021}, author = {Takamatsu, T and Arai, H and Abe, N and Nakai, M and Kunimi, Y and Inoue, MN}, title = {Coexistence of Two Male-Killers and Their Impact on the Development of Oriental Tea Tortrix Homona magnanima.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {193-202}, pmid = {32737539}, issn = {1432-184X}, support = {24580076//Japan Society for the Promotion of Science/ ; 19J13123//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; Female ; Male ; Moths/*microbiology ; RNA Virus Infections/*mortality ; RNA Viruses/*pathogenicity ; Reproduction/*physiology ; Spiroplasma/*physiology ; Wolbachia/metabolism ; }, abstract = {Male-killing, the death of male offspring induced by maternally transmitted microbes, is classified as early, or late, male-killing. The primary advantage afforded by early male-killing, which typically occurs during embryogenesis, is the reallocation of resources to females, that would have otherwise been consumed by males. Meanwhile, the key advantage of late male-killing, which typically occurs during late larval development, is the maximized potential for horizontal transmission. To date, no studies have reported on the associated developmental and physiological effects of host coinfection with early and late male-killers, which may have a significant impact on the population dynamics of the male-killers. Here we used a lepidopteran tea pest Homona magnanima as a model, which is a unique system wherein an early male-killer (a Spiroplasma bacterium) and a late male-killer (an RNA virus) can coexist in nature. An artificially established matriline, coinfected with both Spiroplasma and RNA virus, exhibited embryonic death (early male-killing) as seen in the host line singly infected with Spiroplasma. Moreover, the coinfected line also exhibited developmental retardation and low pupal weight similar to the host line singly infected with the RNA virus. A series of field surveys revealed that Spiroplasma-RNA virus coinfection occurs in nature at a low frequency. Hence, although the two male-killers are capable of coexisting within the H. magnanima population independently, high associated fitness cost appears to limit the prevalence of male-killer coinfection in the field host population.}, }
@article {pmid32737538, year = {2021}, author = {Stone, BWG and Jackson, CR}, title = {Seasonal Patterns Contribute More Towards Phyllosphere Bacterial Community Structure than Short-Term Perturbations.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {146-156}, pmid = {32737538}, issn = {1432-184X}, support = {P20 GM103476/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*classification/*genetics/isolation &amp; purification ; Cellular Senescence/physiology ; Climate ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics ; Plant Leaves/*microbiology ; Plants/microbiology ; RNA, Ribosomal, 16S/genetics ; Rain ; Seasons ; Typhaceae/*microbiology ; }, abstract = {Phyllosphere microorganisms are sensitive to fluctuations in wind, temperature, solar radiation, and rain. However, recent explorations of patterns in phyllosphere communities across time often focus on seasonal shifts and leaf senescence without measuring the contribution of environmental drivers and leaf traits. Here, we focus on the effects of rain on the phyllosphere bacterial community of the wetland macrophyte broadleaf cattail (Typha latifolia) across an entire year, specifically targeting days before and 1, 3, and 5 days after rain events. To isolate the contribution of precipitation from other factors, we covered a subset of plants to shield them from rainfall. We used targeted Illumina sequencing of the V4 region of the bacterial 16S rRNA gene to characterize phyllosphere community composition. Rain events did not have a detectable effect on phyllosphere community richness or evenness regardless of whether the leaves were covered from rain or not, suggesting that foliar microbial communities are robust to such disturbances. While climatic and leaf-based variables effectively modeled seasonal trends in phyllosphere diversity and composition, they provided more limited explanatory value at shorter time scales. These findings underscore the dominance of long-term seasonal patterns related to climatic variation as the main factor influencing the phyllosphere community.}, }
@article {pmid32733460, year = {2020}, author = {Saresella, M and Marventano, I and Barone, M and La Rosa, F and Piancone, F and Mendozzi, L and d'Arma, A and Rossi, V and Pugnetti, L and Roda, G and Casagni, E and Cas, MD and Paroni, R and Brigidi, P and Turroni, S and Clerici, M}, title = {Alterations in Circulating Fatty Acid Are Associated With Gut Microbiota Dysbiosis and Inflammation in Multiple Sclerosis.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {1390}, pmid = {32733460}, issn = {1664-3224}, mesh = {Adult ; Biodiversity ; Biomarkers ; Butyric Acid/blood ; Caproates/blood ; Chromatography, Liquid ; Cytokines/metabolism ; Disease Susceptibility ; Dysbiosis/*blood ; Fatty Acids/*blood ; Female ; Flow Cytometry ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/metabolism/microbiology ; Male ; Middle Aged ; Multiple Sclerosis/*blood/*etiology ; Permeability ; T-Lymphocyte Subsets/immunology/metabolism ; Tandem Mass Spectrometry ; Transcription Factors/metabolism ; }, abstract = {Background: Butyric acid (BA) is a short-chain fatty acid (SCFA) with anti-inflammatory properties, which promotes intestinal barrier function. Medium-chain fatty acids (MCFA), including caproic acid (CA), promote TH1 and TH17 differentiation, thus supporting inflammation. Aim: Since most SCFAs are absorbed in the cecum and colon, the measurement of BA in peripheral blood could provide information on the health status of the intestinal ecosystem. Additionally, given the different immunomodulatory properties of BA and CA the evaluation of their serum concentration, as well as their ratio could be as a simple and rapid biomarker of disease activity and/or treatment efficacy in MS. Methods: We evaluated serum BA and CA concentrations, immune parameters, intestinal barrier integrity and the gut microbiota composition in patients with multiple sclerosis (MS) comparing result to those obtained in healthy controls. Results: In MS, the concentration of BA was reduced and that of CA was increased. Concurrently, the microbiota was depleted of BA producers while it was enriched in mucin-degrading, pro-inflammatory components. The reduced serum concentration of BA seen in MS patients correlated with alterations of the barrier permeability, as evidenced by the higher plasma concentrations of lipopolysaccharide and intestinal fatty acid-binding protein, and inflammation. Specifically, CA was positively associated with CD4+/IFNγ+ T lymphocytes, and the BA/CA ratio correlated positively with CD4+/CD25[high]/Foxp3+ and negatively with CD4+/IFNγ+ T lymphocytes. Conclusion: The gut microbiota dysbiosis found in MS is possibly associated with alterations of the SCFA/MCFA ratio and of the intestinal barrier; this could explain the chronic inflammation that characterizes this disease. SCFA and MCFA quantification could be a simple biomarker to evaluate the efficacy of therapeutic and rehabilitation procedures in MS.}, }
@article {pmid32733417, year = {2020}, author = {Dove, NC and Rogers, TJ and Leppanen, C and Simberloff, D and Fordyce, JA and Brown, VA and LeBude, AV and Ranney, TG and Cregger, MA}, title = {Microbiome Variation Across Two Hemlock Species With Hemlock Woolly Adelgid Infestation.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1528}, pmid = {32733417}, issn = {1664-302X}, abstract = {The hemlock woolly adelgid (Adelges tsugae, HWA), an invasive insect, is devastating native hemlock populations in eastern North America, and management outcomes have so far had limited success. While many plant microbiomes influence and even support plant immune responses to insect herbivory, relatively little is known about the hemlock microbiome and its interactions with pathogens or herbivores such as HWA. Using 16S rRNA and ITS gene amplicon sequencing, we characterized the needle, branch, root, and rhizosphere microbiome of two hemlock species, Tsuga canadensis and T. sieboldii, that displayed low and high levels of HWA populations. We found that both archaeal/bacterial and fungal needle communities, as well as the archaeal/bacterial branch and root communities, varied in composition in both hemlock species relative to HWA population levels. While host species and plant-associated habitats explained a greater proportion of the variance in the microbiome than did HWA population level, high HWA populations were associated with enrichment of 100 likely fungal pathogen sequence variants across the four plant-associated habitats (e.g., needle, branch, root, rhizosphere) compared to trees with lower HWA populations. This work contributes to a growing body of literature linking plant pathogens and pests with the changes in the associated plant microbiome and host health. Furthermore, this work demonstrates the need to further investigate plant microbiome effects across multiple plant tissues to understand their influences on host health.}, }
@article {pmid32728091, year = {2020}, author = {Gulati, S and Ballhausen, MB and Kulkarni, P and Grosch, R and Garbeva, P}, title = {A non-invasive soil-based setup to study tomato root volatiles released by healthy and infected roots.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12704}, pmid = {32728091}, issn = {2045-2322}, mesh = {Bacillus/genetics/growth &amp; development/*isolation &amp; purification ; Chromatography, Gas ; DNA, Bacterial/genetics ; Fusarium/*pathogenicity ; Solanum lycopersicum/chemistry/*growth &amp; development/microbiology ; Metabolomics ; Plant Extracts/analysis ; Plant Roots/chemistry/growth &amp; development/microbiology ; Soil Microbiology ; Volatile Organic Compounds/*analysis ; }, abstract = {The role of root exudates in mediating plant-microbe interactions has been well documented. However, the function of volatile organic compounds (VOCs) emitted by plant roots has only recently begun to attract attention. This newly recognized relevance of belowground VOCs has so far mostly been tested using systems limited to a two-compartment Petri-dish design. Furthermore, many of the plant-microbe interaction studies have only investigated the effects of microbial VOCs on plant growth. Here, we go two steps further. First we investigated the volatile profile of healthy and pathogen (Fusarium oxysporum) infected tomato roots grown in soil. We then used a unique soil-based olfactometer-choice assay to compare the migration pattern of four beneficial bacteria (Bacillus spp.) towards the roots of the tomato plants. We demonstrate that the blend of root-emitted VOCs differs between healthy and diseased plants. Our results show that VOCs are involved in attracting bacteria to plant roots.}, }
@article {pmid32727863, year = {2020}, author = {Salcher, MM and Andrei, A&#x15e; and Bulzu, PA and Keresztes, ZG and Banciu, HL and Ghai, R}, title = {Visualization of Lokiarchaeia and Heimdallarchaeia (Asgardarchaeota) by Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition (CARD-FISH).}, journal = {mSphere}, volume = {5}, number = {4}, pages = {}, pmid = {32727863}, issn = {2379-5042}, mesh = {Archaea/classification/*genetics ; Geologic Sediments/microbiology ; In Situ Hybridization, Fluorescence/*methods ; Microscopy, Fluorescence ; Oligonucleotide Probes/*genetics ; Phylogeny ; }, abstract = {Metagenome-assembled genomes (MAGs) of Asgardarchaeota have been recovered from a variety of habitats, broadening their environmental distribution and providing access to the genetic makeup of this archaeal lineage. The recent success in cultivating the first representative of Lokiarchaeia was a breakthrough in science at large and gave rise to new hypotheses about the evolution of eukaryotes. Despite their singular phylogenetic position at the base of the eukaryotic tree of life, the morphology of these bewildering organisms remains a mystery, except for the report of an unusual morphology with long, branching protrusions of the cultivated Lokiarchaeion strain "Candidatus Prometheoarchaeum syntrophicum" MK-D1. In order to visualize this elusive group, we applied a combination of fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) and epifluorescence microscopy on coastal hypersaline sediment samples, using specifically designed CARD-FISH probes for Heimdallarchaeia and Lokiarchaeia lineages, and provide the first visual evidence for Heimdallarchaeia and new images of a lineage of Lokiarchaeia that is different from the cultured representative. Here, we show that while Heimdallarchaeia are characterized by a uniform cellular morphology typified by a centralized DNA localization, Lokiarchaeia display a plethora of shapes and sizes that likely reflect their broad phylogenetic diversity and ecological distribution.IMPORTANCE Asgardarchaeota are considered to be the closest relatives to modern eukaryotes. These enigmatic microbes have been mainly studied using metagenome-assembled genomes (MAGs). Only very recently, a first member of Lokiarchaeia was isolated and characterized in detail; it featured a striking morphology with long, branching protrusions. In order to visualize additional members of the phylum Asgardarchaeota, we applied a fluorescence in situ hybridization technique and epifluorescence microscopy on coastal hypersaline sediment samples, using specifically designed probes for Heimdallarchaeia and Lokiarchaeia lineages. We provide the first visual evidence for Heimdallarchaeia that are characterized by a uniform cellular morphology typified by an apparently centralized DNA localization. Further, we provide new images of a lineage of Lokiarchaeia that is different from the cultured representative and with multiple morphologies, ranging from small ovoid cells to long filaments. This diversity in observed cell shapes is likely owing to the large phylogenetic diversity within Asgardarchaeota, the vast majority of which remain uncultured.}, }
@article {pmid32727027, year = {2020}, author = {Pédron, J and Guyon, L and Lecomte, A and Blottière, L and Chandeysson, C and Rochelle-Newall, E and Raynaud, X and Berge, O and Barny, MA}, title = {Comparison of Environmental and Culture-Derived Bacterial Communities through 16S Metabarcoding: A Powerful Tool to Assess Media Selectivity and Detect Rare Taxa.}, journal = {Microorganisms}, volume = {8}, number = {8}, pages = {}, pmid = {32727027}, issn = {2076-2607}, support = {Ec2co-CARTOBACTER//Centre National de la Recherche Scientifique/ ; CE32-2017-SPREE//Agence Nationale de la Recherche/ ; }, abstract = {To compare environmental and culture-derived microbial communities, we performed 16S metabarcoding of uncultured samples and their culture-derived bacterial lawns. Microbial communities were obtained from freshwater river samples representative of an anthropization gradient along a river stream. Their culture-derived bacterial lawns were obtained by growing aliquots of the samples on a broad range medium and on two different semi-selective media. The V3-V4 16S rRNA region was amplified and sequenced. The bacterial diversity of water samples decreased from the upper to lower stream sampling sites and, as expected, these differences were mostly suppressed by the culture step. Overall, the diversity of cultured-derived bacterial communities reflected selectivity of each tested medium. Comparison of treatments indicated that the culture selected both detected and rare undetected environmental species. Accurate detection of rare environmental bacteria of the Pectobacterium genus by 16S metabarcoding of the culture lawn was demonstrated. Interestingly, for abundant taxa, such as those of the Pseudomonas genus, the culture/environment ratio varied between sampled sites, indicating the difficulty of comparing cultured-derived taxa abundance between environmental sites. Finally, our study also highlighted media specificity and complementarity: bacterial communities grown on the two selective media, while selecting a small set of specific species, were mostly a subset of the bacterial community observed on the broad range medium.}, }
@article {pmid32723798, year = {2020}, author = {Xu, L and Xiang, M and Zhu, W and Zhang, M and Chen, H and Huang, J and Chen, Y and Chang, Q and Jiang, J and Zhu, L}, title = {The Behavior of Amphibians Shapes Their Symbiotic Microbiomes.}, journal = {mSystems}, volume = {5}, number = {4}, pages = {}, pmid = {32723798}, issn = {2379-5077}, abstract = {Seasonal dynamics in symbiotic microbiomes have been investigated in a number of vertebrates and are mainly caused by changes in the diet (in the gut microbiome) or the living environment (in the skin microbiome). Most amphibian microbiome studies focus on the skin, whereas internal microbiome structure and dynamics are often overlooked. The present study investigated the seasonal dynamics in three types of symbiotic microbiomes (the skin, stomach, and gut) across four wild frog species, belonging to different families, in May and October. The frogs harbored more water source microbes in May than in October. On the contrary, the frogs harbored more soil source microbes in October than in May. The frog species investigated tend to live in a water environment in May to maintain body surface humidity at high environmental temperatures and to breed. In October, these four species prefer to live on the land, as the environmental temperature decreases, to prepare for hibernation in caves or under stones. Thus, seasonal changes in the wild amphibian symbiotic microbiome may be caused by the difference in microbe transmission from their living environment due to specific behaviors. This study demonstrated that the behavior and living environment of wild amphibians shape their symbiotic microbiome externally (on the skin) and internally (in the stomach and gut). We revealed the potential association between specific behaviors in poikilothermic animals and host symbiotic microbiomes.IMPORTANCE Understanding the interactions between host behavior and microbiome dynamics remains an outstanding priority in the field of microbial ecology. Here, we provide the reader with a simple example of how the behavior and living environment of wild amphibians shape their symbiotic microbiome externally (on the skin) and internally (in the stomach and gut).}, }
@article {pmid32723791, year = {2020}, author = {Malli Mohan, GB and Parker, CW and Urbaniak, C and Singh, NK and Hood, A and Minich, JJ and Knight, R and Rucker, M and Venkateswaran, K}, title = {Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation.}, journal = {mSystems}, volume = {5}, number = {4}, pages = {}, pmid = {32723791}, issn = {2379-5077}, abstract = {Microbial contamination during long-term confinements of space exploration presents potential risks for both crew members and spacecraft life support systems. A novel swab kit was used to sample various surfaces from a submerged, closed, analog habitat to characterize the microbial populations. Samples were collected from various locations across the habitat which were constructed from various surface materials (linoleum, dry wall, particle board, glass, and metal), and microbial populations were examined by culture, quantitative PCR (qPCR), microbiome 16S rRNA gene sequencing, and shotgun metagenomics. Propidium monoazide (PMA)-treated samples identified the viable/intact microbial population of the habitat. The cultivable microbial population ranged from below the detection limit to 10[6] CFU/sample, and their identity was characterized using Sanger sequencing. Both 16S rRNA amplicon and shotgun sequencing were used to characterize the microbial dynamics, community profiles, and functional attributes (metabolism, virulence, and antimicrobial resistance). The 16S rRNA amplicon sequencing revealed abundance of viable (after PMA treatment) Actinobacteria (Brevibacterium, Nesternkonia, Mycobacterium, Pseudonocardia, and Corynebacterium), Firmicutes (Virgibacillus, Staphylococcus, and Oceanobacillus), and Proteobacteria (especially Acinetobacter) on linoleum, dry wall, and particle board (LDP) surfaces, while members of Firmicutes (Leuconostocaceae) and Proteobacteria (Enterobacteriaceae) were high on the glass/metal surfaces. Nonmetric multidimensional scaling determined from both 16S rRNA and metagenomic analyses revealed differential microbial species on LDP surfaces and glass/metal surfaces. The shotgun metagenomic sequencing of samples after PMA treatment showed bacterial predominance of viable Brevibacterium (53.6%), Brachybacterium (7.8%), Pseudonocardia (9.9%), Mycobacterium (3.7%), and Staphylococcus (2.1%), while fungal analyses revealed Aspergillus and Penicillium dominance.IMPORTANCE This study provides the first assessment of monitoring cultivable and viable microorganisms on surfaces within a submerged, closed, analog habitat. The results of the analyses presented herein suggest that the surface material plays a role in microbial community structure, as the microbial populations differed between LDP and metal/glass surfaces. The metal/glass surfaces had less-complex community, lower bioburden, and more closely resembled the controls. These results indicated that material choice is crucial when building closed habitats, even if they are simply analogs. Finally, while a few species were associated with previously cultivated isolates from the International Space Station and MIR spacecraft, the majority of the microbial ecology of the submerged analog habitat differs greatly from that of previously studied analog habitats.}, }
@article {pmid32721842, year = {2020}, author = {Pascual-Benito, M and Ballesté, E and Monleón-Getino, T and Urmeneta, J and Blanch, AR and García-Aljaro, C and Lucena, F}, title = {Impact of treated sewage effluent on the bacterial community composition in an intermittent mediterranean stream.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {266}, number = {Pt 1}, pages = {115254}, doi = {10.1016/j.envpol.2020.115254}, pmid = {32721842}, issn = {1873-6424}, mesh = {Bacteria/genetics ; Humans ; *Microbiota ; RNA, Ribosomal, 16S ; *Sewage ; Wastewater ; }, abstract = {Water quality monitoring is essential to safeguard human and environmental health. The advent of next-generation sequencing techniques in recent years, which allow a more in-depth study of environmental microbial communities in the environment, could broaden the perspective of water quality monitoring to include impact of faecal pollution bacteria on ecosystem. In this study, 16 S rRNA amplicon sequencing was used to evaluate the impact of wastewater treatment plant (WWTP) effluent on autochthonous microbial communities of a temporary Mediterranean stream characterized by high flow seasonality (from 0.02 m[3]/s in winter to 0.006 m[3]/s in summer). Seven sampling campaigns were performed under different temperatures and streamflow conditions (winter and summer). Water samples were collected upstream (Upper) of the WWTP, the secondary effluent (EF) discharge and 75 m (P75) and 1000 m (P1000) downstream of the WWTP. A total of 5,593,724 sequences were obtained, giving rise to 20,650 amplicon sequence variants (ASV), which were further analysed and classified into phylum, class, family and genus. Each sample presented different distribution and abundance of taxa. Although taxon distribution and abundance differed in each sample, the microbial community structure of P75 resembled that of EF samples, and Upper and P1000 samples mostly clustered together. Alpha diversity showed the highest values for Upper and P1000 samples and presented seasonal differences, being higher in winter conditions of high streamflow and low temperature. Our results suggest the microbial ecology re-establishment, since autochthonous bacterial communities were able to recover from the impact of the WWTP effluent in 1 km. Alpha diversity results indicates a possible influence of environmental factors on the bacterial community structure. This study shows the potential of next-generation sequencing techniques as useful tools in water quality monitoring and management within the climate change scenario.}, }
@article {pmid32720097, year = {2020}, author = {Zou, P and Yang, Q and Wang, H and Xie, G and Cao, Z and Chen, X and Gao, W and Huang, J}, title = {In vitro disinfection efficacy and clinical protective effects of common disinfectants against acute hepatopancreatic necrosis disease (AHPND)-causing Vibrio isolates in Pacific white shrimp Penaeus vannamei.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {58}, number = {8}, pages = {675-686}, doi = {10.1007/s12275-020-9537-1}, pmid = {32720097}, issn = {1976-3794}, mesh = {Animals ; Anti-Infective Agents, Local/*pharmacology ; Aquaculture/methods ; Biguanides/pharmacology ; Disinfection/*methods ; Hepatopancreas/microbiology/pathology ; Hydrogen Peroxide/pharmacology ; Penaeidae/*microbiology ; Seafood/microbiology ; Vibrio/*drug effects/isolation &amp; purification ; Vibrio parahaemolyticus/*drug effects/isolation &amp; purification ; }, abstract = {Acute hepatopancreatic necrosis disease (AHPND) is one of the most significant bacterial diseases in global shrimp culture, causing severe economic losses. In the present study, we carried out in vitro antimicrobial tests to investigate the disinfection efficacy of 14 common disinfectants toward different AHPND-causing Vibrio spp., including eight isolates of V. parahaemolyticus, four isolates of V. campbellii, and one isolate of V. owensii. Polyhexamethylene biguanidine hydrochloride (PHMB) was revealed to possess the strongest inhibitory activity. Through analyzing and evaluating the results of antimicrobial tests and acute toxicity test, we selected PHMB and hydrogen peroxide (H2O2) for further clinical protection test. Clinical manifestations indicated that both PHMB (2 mg/L and 4 mg/L) and H2O2 (12 mg/L) could effectively protect juvenile Penaeus vannamei from the infection of V. parahaemolyticus isolate Vp362 at 10[6] CFU/ml, and the survival rate was over 80%. When the bacterial concentration was reduced to 10[5] CFU/ml, 10[4] CFU/ml, and 10[3] CFU/ml, the survival rate after treated by 1 mg/L PHMB was 64.44%, 93.33%, and 100%, respectively. According to the results, PHMB and H2O2 showed a lower toxicity while a better protection activity, particularly against a lower concentration of the pathogens. Therefore, these two disinfectants are proved to be promising disinfectants that can be applied to prevent and control AHPND in shrimp culture. Moreover, the methods of this study also provided valuable information for the prevention of other important bacterial diseases and suggested a reliable means for screening potential drugs in aquaculture.}, }
@article {pmid32719667, year = {2020}, author = {Geelhoed, JS and van de Velde, SJ and Meysman, FJR}, title = {Quantification of Cable Bacteria in Marine Sediments via qPCR.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1506}, pmid = {32719667}, issn = {1664-302X}, abstract = {Cable bacteria (Deltaproteobacteria, Desulfobulbaceae) are long filamentous sulfur-oxidizing bacteria that generate long-distance electric currents running through the bacterial filaments. This way, they couple the oxidation of sulfide in deeper sediment layers to the reduction of oxygen or nitrate near the sediment-water interface. Cable bacteria are found in a wide range of aquatic sediments, but an accurate procedure to assess their abundance is lacking. We developed a qPCR approach that quantifies cable bacteria in relation to other bacteria within the family Desulfobulbaceae. Primer sets targeting cable bacteria, Desulfobulbaceae and the total bacterial community were applied in qPCR with DNA extracted from marine sediment incubations. Amplicon sequencing of the 16S rRNA gene V4 region confirmed that cable bacteria were accurately enumerated by qPCR, and suggested novel diversity of cable bacteria. The conjoint quantification of current densities and cell densities revealed that individual filaments carry a mean current of ∼110 pA and have a cell specific oxygen consumption rate of 69 fmol O2 cell[-1] day[-1]. Overall, the qPCR method enables a better quantitative assessment of cable bacteria abundance, providing new metabolic insights at filament and cell level, and improving our understanding of the microbial ecology of electrogenic sediments.}, }
@article {pmid32719401, year = {2020}, author = {Huber, P and Metz, S and Unrein, F and Mayora, G and Sarmento, H and Devercelli, M}, title = {Environmental heterogeneity determines the ecological processes that govern bacterial metacommunity assembly in a floodplain river system.}, journal = {The ISME journal}, volume = {14}, number = {12}, pages = {2951-2966}, pmid = {32719401}, issn = {1751-7370}, mesh = {Aquatic Organisms ; Bacteria/genetics ; *Ecosystem ; Phylogeny ; *Rivers ; }, abstract = {How diversity is structured has been a central goal of microbial ecology. In freshwater ecosystems, selection has been found to be the main driver shaping bacterial communities. However, its relative importance compared with other processes (dispersal, drift, diversification) may depend on spatial heterogeneity and the dispersal rates within a metacommunity. Still, a decrease in the role of selection is expected with increasing dispersal homogenization. Here, we investigate the main ecological processes modulating bacterial assembly in contrasting scenarios of environmental heterogeneity. We carried out a spatiotemporal survey in the floodplain system of the Paraná River. The bacterioplankton metacommunity was studied using both statistical inferences based on phylogenetic and taxa turnover as well as co-occurrence networks. We found that selection was the main process determining community assembly even at both extremes of environmental heterogeneity and homogeneity, challenging the general view that the strength of selection is weakened due to dispersal homogenization. The ecological processes acting on the community also determined the connectedness of bacterial networks associations. Heterogeneous selection promoted more interconnected networks increasing β-diversity. Finally, spatiotemporal heterogeneity was an important factor determining the number and identity of the most highly connected taxa in the system. Integrating all these empirical evidences, we propose a new conceptual model that elucidates how the environmental heterogeneity determines the action of the ecological processes shaping the bacterial metacommunity.}, }
@article {pmid32717345, year = {2020}, author = {Ahlawat, S and Asha,  and Sharma, KK}, title = {Immunological co-ordination between gut and lungs in SARS-CoV-2 infection.}, journal = {Virus research}, volume = {286}, number = {}, pages = {198103}, pmid = {32717345}, issn = {1872-7492}, mesh = {Angiotensin-Converting Enzyme 2 ; Antibodies, Monoclonal/therapeutic use ; Antiviral Agents/therapeutic use ; Betacoronavirus/immunology/*pathogenicity ; COVID-19 ; Coronavirus Infections/drug therapy/*immunology/microbiology/virology ; Cytokine Release Syndrome/drug therapy/*immunology/microbiology/virology ; Cytokines/antagonists &amp; inhibitors/genetics/immunology ; Dysbiosis/drug therapy/*immunology/microbiology/virology ; Gastrointestinal Microbiome/immunology ; Gastrointestinal Tract/drug effects/*immunology/microbiology/virology ; Gene Expression ; Host-Pathogen Interactions/immunology ; Humans ; Inflammatory Bowel Diseases/drug therapy/*immunology/microbiology/virology ; Lung/drug effects/*immunology/microbiology/virology ; Pandemics ; Peptidyl-Dipeptidase A/genetics/immunology ; Pneumonia, Viral/drug therapy/*immunology/microbiology/virology ; Receptors, Virus/genetics/immunology ; SARS-CoV-2 ; }, abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into a major pandemic called coronavirus disease 2019 (COVID-19) that has created unprecedented global health emergencies, and emerged as a serious threat due to its strong ability for human-to-human transmission. The reports indicate the ability of SARS-CoV-2 to affect almost any organ due to the presence of a receptor known as angiotensin converting enzyme 2 (ACE2) across the body. ACE2 receptor is majorly expressed in the brush border of gut enterocytes along with the ciliated cells and alveolar epithelial type II cells in the lungs. The amino acid transport function of ACE2 has been linked to gut microbial ecology in gastrointestinal (GI) tract, thereby suggesting that COVID-19 may, to some level, be linked to the enteric microbiota. The significant number of COVID-19 patients shows extra-pulmonary symptoms in the GI tract. Many subsequent studies revealed viral RNA of SARS-CoV-2 in fecal samples of COVID-19 patients. This presents a new challenge in the diagnosis and control of COVID-19 infection with a caution for proper sanitation and hygiene. Here, we aim to discuss the immunological co-ordination between gut and lungs that facilitates SARS-CoV-2 to infect and multiply in the inflammatory bowel disease (IBD) and non-IBD patients.}, }
@article {pmid32710789, year = {2020}, author = {Zhang, QF and Laanbroek, HJ}, title = {Tannins from senescent Rhizophora mangle mangrove leaves have a distinctive effect on prokaryotic and eukaryotic communities in a Distichlis spicata salt marsh soil.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {9}, pages = {}, doi = {10.1093/femsec/fiaa148}, pmid = {32710789}, issn = {1574-6941}, mesh = {Eukaryota ; Plant Leaves ; RNA, Ribosomal, 16S/genetics ; *Rhizophoraceae ; Soil ; Soil Microbiology ; Tannins ; Wetlands ; }, abstract = {Due to climate warming, tannin-rich Rhizophora mangle migrates into tannin-poor salt marshes, where the tannins interfere with the biogeochemistry in the soil. Changes in biogeochemistry are likely associated with changes in microbial communities. This was studied in microcosms filled with salt marsh soil and amended with leaf powder, crude condensed tannins, purified condensed tannins (PCT), all from senescent R. mangle leaves, or with tannic acid. Size and composition of the microbial communities were determined by denaturing gradient gel electrophoresis, high-throughput sequencing and real-time PCR based on the 16S and 18S rRNA genes. Compared with the control, the 16S rRNA gene abundance was lowered by PCT, while the 18S rRNA gene abundance was enhanced by all treatments. The treatments also affected the composition of the 16S rRNA and 18S rRNA gene assemblies, but the effects on the 18S rRNA gene were greater. The composition of the 18S rRNA gene, but not of the 16S rRNA gene, was significantly correlated with the mineralization of carbon, nitrogen and phosphorus. Distinctive microbial groups emerged during the different treatments. This study revealed that migration of mangroves may affect both the prokaryotic and the eukaryotic communities in salt marsh soils, but that the effects on the eukaryotes will likely be greater.}, }
@article {pmid32710756, year = {2020}, author = {Pedrinho, A and Mendes, LW and Merloti, LF and Andreote, FD and Tsai, SM}, title = {The natural recovery of soil microbial community and nitrogen functions after pasture abandonment in the Amazon region.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {9}, pages = {}, doi = {10.1093/femsec/fiaa149}, pmid = {32710756}, issn = {1574-6941}, mesh = {Forests ; *Microbiota ; Nitrogen/analysis ; *Soil ; Soil Microbiology ; }, abstract = {We assessed the impacts of forest-to-pasture conversion on the dynamic of soil microbial communities, especially those involved in the N-cycle, and their potential functions, using DNA-metagenomic sequencing coupled with the quantification of marker genes for N-cycling. We also evaluated whether the community's dynamic was reestablished with secondary forest growth. In general, the microbial community structure was influenced by changes in soil chemical properties. Aluminum and nitrate significantly correlated to community structure and with 12 out of 21 microbial phyla. The N-related microbial groups and their potential functions were also affected by land-use change, with pasture being clearly different from primary and secondary forest systems. The microbial community analysis demonstrated that forest-to-pasture conversion increased the abundance of different microbial groups related to nitrogen fixation, including Bacteroidetes, Chloroflexi and Firmicutes. In contrast, after pasture abandonment and with the secondary forest regeneration, there was an increase in the abundance of Proteobacteria taxa and denitrification genes. Our multi-analytical approach indicated that the secondary forest presented some signs of resilience, suggesting that the N-related microbial groups and their potential functions can be recovered over time with implications for future ecological restoration programs.}, }
@article {pmid32710182, year = {2020}, author = {Luzzi, G and Brinks, E and Fritsche, J and Franz, CMAP}, title = {Microbial composition of sweetness-enhanced yoghurt during fermentation and storage.}, journal = {AMB Express}, volume = {10}, number = {1}, pages = {131}, pmid = {32710182}, issn = {2191-0855}, support = {2819107616//Bundesanstalt f&#xfc;r Landwirtschaft und Ern&#xe4;hrung/ ; }, abstract = {The reformulation of dairy products to contain less added sugar can contribute to reducing sugar consumption, thereby reducing the risk of non-communicable diseases. The objective of this study was to investigate the microbial ecology of reformulated yoghurt, which was produced using bi-enzymatic modification of lactose to increase its sweetness by a factor of 2-3. Ultimately, this reformulation strategy could reduce the amount of added sugar needed for equal sweetness of the end product. The bi-enzymatic modification relied on utilisation of a β-galactosidase enzyme to convert the milk sugar lactose to galactose and glucose, followed by the enzymatic conversion of the glucose moiety to fructose using a glucose isomerase. The microbial ecology of reformulated yoghurt produced with two mixed starter culture preparations containing either Streptococcus (S.) thermophilus and Lactobacillus (Lb.) delbrueckii or S. thermophilus, Lb. acidophilus and Bifidobacterium sp. strains, was analysed during fermentation and cool storage using 16S rRNA based metagenomics. None of the yoghurt samples showed a significant difference in microbial composition between sweetness-enhanced and regular milk at all sampling time points during manufacture and storage of yoghurt. However, a significant difference between the microbiota of inoculated milk before and after fermentation was observed. In both types of yoghurt, the starter culture genera dominated the microbial ecology at the end of fermentation as expected, reducing the possibility of growth of potentially pathogenic or spoilage bacteria possibly resulting from a changed carbohydrate spectrum.}, }
@article {pmid32709974, year = {2020}, author = {Daebeler, A and Kitzinger, K and Koch, H and Herbold, CW and Steinfeder, M and Schwarz, J and Zechmeister, T and Karst, SM and Albertsen, M and Nielsen, PH and Wagner, M and Daims, H}, title = {Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira.}, journal = {The ISME journal}, volume = {14}, number = {12}, pages = {2967-2979}, pmid = {32709974}, issn = {1751-7370}, support = {P 25231/FWF_/Austrian Science Fund FWF/Austria ; P 27319/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Bacteria/genetics ; Hydrogen-Ion Concentration ; Metagenome ; *Nitrites ; Nitrogen Cycle ; Oxidation-Reduction ; }, abstract = {Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high pH. Nitrospira distribution, diversity, and ecophysiology were studied in hypo- and subsaline (1.3-12.8 g salt/l), highly alkaline (pH 8.9-10.3) lakes by amplicon sequencing, metagenomics, and cultivation-based approaches. Surprisingly, not only were Nitrospira populations detected, but they were also considerably diverse with presence of members from Nitrospira lineages I, II and IV. Furthermore, the ability of Nitrospira enrichment cultures to oxidize nitrite at neutral to highly alkaline pH of 10.5 was demonstrated. Metagenomic analysis of a newly enriched Nitrospira lineage IV species, "Candidatus Nitrospira alkalitolerans", revealed numerous adaptive features of this organism to its extreme environment. Among them were a sodium-dependent N-type ATPase and NADH:quinone oxidoreductase next to the proton-driven forms usually found in Nitrospira. Other functions aid in pH and cation homeostasis and osmotic stress defense. "Ca. Nitrospira alkalitolerans" also possesses group 2a and 3b [NiFe] hydrogenases, suggesting it can use hydrogen as alternative energy source. These results reveal how Nitrospira cope with strongly fluctuating pH and salinity conditions and expand our knowledge of nitrogen cycling in extreme habitats.}, }
@article {pmid32709258, year = {2020}, author = {Nobu, MK and Narihiro, T and Mei, R and Kamagata, Y and Lee, PKH and Lee, PH and McInerney, MJ and Liu, WT}, title = {Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {111}, pmid = {32709258}, issn = {2049-2618}, support = {DE-AC02-05CH1123//Department of Energy/International ; DE-FG02-96ER20214//Department of Energy/International ; }, mesh = {Acetates/metabolism ; Anaerobiosis ; Archaea/*metabolism ; *Chemoautotrophic Growth ; *Ecosystem ; Formates/metabolism ; Methane/*metabolism ; Thermodynamics ; }, abstract = {BACKGROUND: Current understanding of the carbon cycle in methanogenic environments involves trophic interactions such as interspecies H2 transfer between organotrophs and methanogens. However, many metabolic processes are thermodynamically sensitive to H2 accumulation and can be inhibited by H2 produced from co-occurring metabolisms. Strategies for driving thermodynamically competing metabolisms in methanogenic environments remain unexplored.<br><br>RESULTS: To uncover how anaerobes combat this H2 conflict in situ, we employ metagenomics and metatranscriptomics to revisit a model ecosystem that has inspired many foundational discoveries in anaerobic ecology-methanogenic bioreactors. Through analysis of 17 anaerobic digesters, we recovered 1343 high-quality metagenome-assembled genomes and corresponding gene expression profiles for uncultured lineages spanning 66 phyla and reconstructed their metabolic capacities. We discovered that diverse uncultured populations can drive H2-sensitive metabolisms through (i) metabolic coupling with concurrent H2-tolerant catabolism, (ii) forgoing H2 generation in favor of interspecies transfer of formate and electrons (cytochrome- and pili-mediated) to avoid thermodynamic conflict, and (iii) integration of low-concentration O2 metabolism as an ancillary thermodynamics-enhancing electron sink. Archaeal populations support these processes through unique methanogenic metabolisms-highly favorable H2 oxidation driven by methyl-reducing methanogenesis and tripartite uptake of formate, electrons, and acetate.<br><br>CONCLUSION: Integration of omics and eco-thermodynamics revealed overlooked behavior and interactions of uncultured organisms, including coupling favorable and unfavorable metabolisms, shifting from H2 to formate transfer, respiring low-concentration O2, performing direct interspecies electron transfer, and interacting with high H2-affinity methanogenesis. These findings shed light on how microorganisms overcome a&#xa0;critical obstacle in methanogenic carbon cycles we had hitherto disregarded&#xa0;and provide foundational&#xa0;insight into anaerobic microbial&#xa0;ecology. Video Abstract.}, }
@article {pmid32708991, year = {2020}, author = {Swarte, JC and Eelderink, C and Douwes, RM and Said, MY and Hu, S and Post, A and Westerhuis, R and Bakker, SJL and Harmsen, HJM}, title = {Effect of High versus Low Dairy Consumption on the Gut Microbiome: Results of a Randomized, Cross-Over Study.}, journal = {Nutrients}, volume = {12}, number = {7}, pages = {}, pmid = {32708991}, issn = {2072-6643}, mesh = {Aged ; Body Composition ; Body Mass Index ; Body Weight ; Cholesterol/blood ; Constipation/microbiology ; Cross-Over Studies ; *Dairy Products ; *Diet ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Male ; Middle Aged ; Overweight/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics/*isolation &amp; purification ; Sequence Analysis, DNA ; Surveys and Questionnaires ; Triglycerides/blood ; }, abstract = {The influence of dairy on the gut microbiome has not been studied extensively. We performed a randomized cross-over study to analyze the effect of high dairy intake on the gut microbiome. Subjects were randomly assigned to a high-dairy diet (HDD) (5-6 dairy portions per day) and a low-dairy diet (LDD) (≤1 dairy portion per day) for 6 weeks with a washout period of 4 weeks in between both diets. The gut microbiome was assessed using 16S rRNA gene sequencing. Compositionality and functionality of the gut microbiome was assessed using Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Stool consistency was evaluated using the Bristol stool chart. In total, 46 healthy overweight subjects (BMI range 25-30 kg/m[2]) completed both intervention periods. During the HDD, there was a significantly higher abundance of the genera Streptococcus, Leuconostoc, and Lactococcus, and the species Streptococcus thermophilus, Erysipelatoclostridium ramosum and Leuconostoc mesenteroides (pFDR < 0.10). Furthermore, during the HDD, there was a significantly lower abundance of the genera Faecalibacterium and Bilophila, and the species Faecalibacterium prausnitzii, Clostridium aldenense, Acetivibrio ethanolgignens, Bilophila wadsworthia and Lactococcus lactis (pFDR < 0.10). There were eight subjects who became constipated during the HDD and these subjects all had a lower abundance of F. prausnitzii. This is the first cross-over study in which the effect of an HDD compared to an LDD on the gut microbiome has been studied. An HDD led to a significantly different composition of the gut microbiome, with a particularly lower abundance of F. prausnitzii and a higher abundance of S. thermophilus. Constipation was observed in several subjects during the HDD. Predicted metabolic pathways were not significantly altered due to an HDD.}, }
@article {pmid32706331, year = {2020}, author = {Pérez-Cobas, AE and Gomez-Valero, L and Buchrieser, C}, title = {Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses.}, journal = {Microbial genomics}, volume = {6}, number = {8}, pages = {}, pmid = {32706331}, issn = {2057-5858}, mesh = {Computational Biology/methods ; Genetic Markers/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Software ; Whole Genome Sequencing/*methods ; }, abstract = {Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture-independent method that allows the identification and characterization of organisms from all kinds of samples. Whole-genome shotgun sequencing analyses the total DNA of a chosen sample to determine the presence of micro-organisms from all domains of life and their genomic content. Importantly, the whole-genome shotgun sequencing approach reveals the genomic diversity present, but can also give insights into the functional potential of the micro-organisms identified. The marker gene approach is based on the sequencing of a specific gene region. It allows one to describe the microbial composition based on the taxonomic groups present in the sample. It is frequently used to analyse the biodiversity of microbial ecosystems. Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge. Here we review the primary workflows and software used for both approaches and discuss the current challenges in the field.}, }
@article {pmid32705812, year = {2020}, author = {Mitiku, AA and Andeta, AF and Borremans, A and Lievens, B and Bossaert, S and Crauwels, S and Aernouts, B and Kechero, Y and Van Campenhout, L}, title = {Silage making of maize stover and banana pseudostem under South Ethiopian conditions: evolution of pH, dry matter and microbiological profile.}, journal = {Microbial biotechnology}, volume = {13}, number = {5}, pages = {1477-1488}, pmid = {32705812}, issn = {1751-7915}, mesh = {Fermentation ; Hydrogen-Ion Concentration ; *Musa ; *Silage ; Zea mays ; }, abstract = {The study was conducted to evaluate the microbial dynamics during silage of maize stover and banana pseudostem in the environmental conditions of southern Ethiopia. To meet this objective, microsilos containing either maize stover or banana pseudostem, both with and without molasses, were prepared. Subsequently, samples were analysed on day 0, 7, 14, 30, 60 and 90 of the fermentation process. As a result, on day 7, all treatments except banana pseudostem without molasses showed a significant reduction in pH. It was also this silage type that supported the growth of Enterobacteriaceae longer than three other silage types, i.e. until 30 days. The yeasts and moulds and the Clostridum endospore counts also showed a reducing trend in early fermentation and afterwards remained constant until day 90. Illumina MiSeq sequencing revealed that Leuconostoc, Buttiauxella species and Enterobacteriaceae were the most abundant bacteria in the initial phases of the fermentation. Later on, Buttiauxella, Lactobacillus, Weissella and Bifidobacterium species were found to be dominant. In conclusion, silage of the two crop by-products is possible under South Ethiopian conditions. For banana pseudostem, the addition of molasses is crucial for a fast fermentation, in contrast to maize. Upscaling needs to be investigated for the two by-products.}, }
@article {pmid32705311, year = {2021}, author = {Mateus-Barros, E and de Melo, ML and Bagatini, IL and Caliman, A and Sarmento, H}, title = {Local and Geographic Factors Shape the Occupancy-Frequency Distribution of Freshwater Bacteria.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {26-35}, pmid = {32705311}, issn = {1432-184X}, support = {2014/14139-3//S&#xe3;o Paulo Research Foundation - FAPESP/ ; 2011/50054-4//S&#xe3;o Paulo Research Foundation - FAPESP/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior - Brasil (CAPES)/ ; 309514/2017-7//National Council for Scientific and Technological Development - CNPq/ ; }, mesh = {Bacteria/classification/genetics/*growth &amp; development ; *Bacterial Load ; Biodiversity ; Brazil ; Demography ; Ecosystem ; Fresh Water/*microbiology ; Geography ; Microbial Consortia/*physiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Species prevalence across the landscape is related to their local abundance, which is a result of deterministic and stochastic processes that select organisms capable of recolonizing sites where they were once extinct, a process known as the rescue effect. The occupancy-frequency distribution (OFD) describes these patterns and has been extensively used to understand organism's distribution but has been poorly tested on microorganisms. In order to test OFD on freshwater bacteria, we collected data from 60 shallow lakes distributed across a wide area in southeastern Brazil, to determine the bacterial operational taxonomic units (OTUs) that were present in all sites (core) and at only one site (satellite). Then, we analyzed the spatial abundance distributions of individual OTUs to understand the influence of local abundances on regional occupancy patterns. Finally, we tested the environmental factors that influenced occupancy and abundance. We found a significant bimodal OFD for freshwater bacteria using both OTUs (97% clustering) and amplicon sequence variants (ASVs, unique sequences), with 13 core OTUs and 1169 satellite OTUs, but only three core ASVs. Core organisms had a bimodal or gamma abundance distribution. The main driver of the core community was pH, while nutrients were key when the core community was excluded and the rest of the community (mild and satellite taxa) was considered. This study demonstrates the close relationship between local environmental conditions and the abundance and dispersion of microorganisms, which shapes their distribution across the landscape.}, }
@article {pmid32704052, year = {2020}, author = {González-Ramos, S and Paz-García, M and Fernández-García, V and Portune, KJ and Acosta-Medina, EF and Sanz, Y and Castrillo, A and Martín-Sanz, P and Obregon, MJ and Boscá, L}, title = {NOD1 deficiency promotes an imbalance of thyroid hormones and microbiota homeostasis in mice fed high fat diet.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12317}, pmid = {32704052}, issn = {2045-2322}, mesh = {Adipocytes/metabolism ; Adipose Tissue, White/pathology ; Animals ; Biodiversity ; Body Weight ; *Diet, High-Fat ; Fatty Liver/pathology ; *Feeding Behavior ; *Gastrointestinal Microbiome ; Glucose Tolerance Test ; *Homeostasis ; Inflammation/pathology ; Intestines/pathology ; Lipids/chemistry ; Liver/pathology ; Metabolomics ; Mice, Inbred C57BL ; Mice, Knockout ; Nod1 Signaling Adaptor Protein/*deficiency/metabolism ; Obesity/blood/microbiology/pathology ; Thyroid Gland/pathology/physiopathology ; Thyroid Hormones/blood/*metabolism ; }, abstract = {The contribution of the nucleotide-binding oligomerization domain protein NOD1 to obesity has been investigated in mice fed a high fat diet (HFD). Absence of NOD1 accelerates obesity as early as 2 weeks after feeding a HFD. The obesity was due to increases in abdominal and inguinal adipose tissues. Analysis of the resting energy expenditure showed an impaired function in NOD1-deficient animals, compatible with an alteration in thyroid hormone homeostasis. Interestingly, free thyroidal T4 increased in NOD1-deficient mice fed a HFD and the expression levels of UCP1 in brown adipose tissue were significantly lower in NOD1-deficient mice than in the wild type animals eating a HFD, thus contributing to the observed adiposity in NOD1-deficient mice. Feeding a HFD resulted in an alteration of the proinflammatory profile of these animals, with an increase in the infiltration of inflammatory cells in the liver and in the white adipose tissue, and an elevation of the circulating levels of TNF-α. In addition, alterations in the gut microbiota in NOD1-deficient mice correlate with increased vulnerability of their ecosystem to the HFD challenge and affect the immune-metabolic phenotype of obese mice. Together, the data are compatible with a protective function of NOD1 against low-grade inflammation and obesity under nutritional conditions enriched in saturated lipids. Moreover, one of the key players of this early obesity onset is a dysregulation in the metabolism and release of thyroid hormones leading to reduced energy expenditure, which represents a new role for these hormones in the metabolic actions controlled by NOD1.}, }
@article {pmid32702578, year = {2020}, author = {Zhang, Q and Chen, X and Zhang, Z and Luo, W and Wu, H and Zhang, L and Zhang, X and Zhao, T}, title = {Performance and microbial ecology of a novel moving bed biofilm reactor process inoculated with heterotrophic nitrification-aerobic denitrification bacteria for high ammonia nitrogen wastewater treatment.}, journal = {Bioresource technology}, volume = {315}, number = {}, pages = {123813}, doi = {10.1016/j.biortech.2020.123813}, pmid = {32702578}, issn = {1873-2976}, mesh = {Ammonia ; Biofilms ; Bioreactors ; Denitrification ; *Nitrification ; Nitrogen/analysis ; *Wastewater ; }, abstract = {To overcome long start-up time, poor ammonia tolerance and removal performance of traditional moving bed biofilm reactor (MBBR) inoculated with activated sludge for high-ammonia wastewater treatment, a novel MBBR based on heterotrophic nitrification-aerobic denitrification (HN-AD) was proposed. Start-up of MBBR was firstly performed via inoculated with HN-AD bacteria. Start-up time was shortened from 39 d to 15 d, NH4[+] tolerance was enhanced from 200 mg/L to 1000 mg/L, and TN removal was increased from 30.4% to 80.7%. The carrier types and NH4[+] concentration had significant effects on nitrogen removal and microbial ecology. When the NH4[+] concentration was increased to 900 mg/L in MBBR using polyvinyl alcohol gel as carrier, the TN removal, the abundance of HN-AD bacteria Acinetobacter, Pseudomonas and Paracoccus, which played a key role in TN removal and ammonia tolerance, and the abundance of genes related to nitrogen removal were much higher than those of MBBR using kaldness.}, }
@article {pmid32699992, year = {2020}, author = {Hopkins, JR and Huffman, JM and Platt, WJ and Sikes, BA}, title = {Frequent fire slows microbial decomposition of newly deposited fine fuels in a pyrophilic ecosystem.}, journal = {Oecologia}, volume = {193}, number = {3}, pages = {631-643}, doi = {10.1007/s00442-020-04699-5}, pmid = {32699992}, issn = {1432-1939}, support = {DEB-1557000//National Science Foundation/ ; DEB-1556837//National Science Foundation/ ; 1451148//National Science Foundation/ ; }, mesh = {Ecosystem ; *Fires ; *Pinus ; Soil ; }, abstract = {Frequent fires maintain nearly 50% of terrestrial ecosystems, and drive ecosystem changes that govern future fires. Since fires are dependent on available plant or fine fuels, ecosystem processes that alter fine fuel loads like microbial decomposition are particularly important and could modify future fires. We hypothesized that variation in short-term fire history would influence fuel dynamics in such ecosystems. We predicted that frequent fires within a short-time period would slow microbial decomposition of new fine fuels. We expected that fire effects would differ based on dominant substrates and that fire history would also alter soil nutrient availability, indirectly slowing decomposition. We measured decomposition of newly deposited fine fuels in a Longleaf pine savanna, comparing plots that burned 0, 1, 2, or 3 times between 2014 and 2016, and which were located in either close proximity to or away from overstory pines (Longleaf pine, Pinus palustris). Microbial decomposition was slower in plots near longleaf pines and, as the numbers of fires increased, decomposition slowed. We then used structural equation modeling to assess pathways for these effects (number of fires, 2016 fuel/fire characteristics, and soil chemistry). Increased fire frequency was directly associated with decreased microbial decomposition. While increased fires decreased nutrient availability, changes in nutrients were not associated with decomposition. Our findings indicate that increasing numbers of fires over short-time intervals can slow microbial decomposition of newly deposited fine fuels. This could favor fine fuel accumulation and drive positive feedbacks on future fires.}, }
@article {pmid32698767, year = {2020}, author = {Taparia, T and Krijger, M and Haynes, E and Elphinstone, JG and Noble, R and van der Wolf, J}, title = {Molecular characterization of Pseudomonas from Agaricus bisporus caps reveal novel blotch pathogens in Western Europe.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {505}, pmid = {32698767}, issn = {1471-2164}, support = {KV1509-050//Dutch Ministry of Economic Affairs (NL)/ ; M063//Agriculture and Horticulture Development Board/ ; }, mesh = {*Agaricus/genetics ; Belgium ; Europe ; Phylogeny ; Pseudomonas/genetics ; United Kingdom ; }, abstract = {BACKGROUND: Bacterial blotch is a group of economically important diseases affecting the cultivation of common button mushroom, Agaricus bisporus. Despite being studied for more than a century, the identity and nomenclature of blotch-causing Pseudomonas species is still unclear. This study aims to molecularly characterize the phylogenetic and phenotypic diversity of blotch pathogens in Western Europe.<br><br>METHODS: In this study, blotched mushrooms were sampled from farms across the Netherlands, United Kingdom and Belgium. Bacteria were isolated from symptomatic cap tissue and tested in pathogenicity assays on fresh caps and in pots. Whole genome sequences of pathogenic and non-pathogenic isolates were used to establish phylogeny via multi-locus sequence alignment (MLSA), average nucleotide identity (ANI) and in-silico DNA:DNA hybridization (DDH) analyses.<br><br>RESULTS: The known pathogens "Pseudomonas gingeri", P. tolaasii, "P. reactans" and P. costantinii were recovered from blotched mushroom caps. Seven novel pathogens were also identified, namely, P. yamanorum, P. edaphica, P. salomonii and strains that clustered with Pseudomonas sp. NC02 in one genomic species, and three non-pseudomonads, i.e. Serratia liquefaciens, S. proteamaculans and a Pantoea sp. Insights on the pathogenicity and symptom severity of these blotch pathogens were also generated.<br><br>CONCLUSION: A detailed overview of genetic and regional diversity and the virulence of blotch pathogens in Western Europe, was obtained via the phylogenetic and phenotypic analyses. This information has implications in the study of symptomatic disease expression, development of diagnostic tools and design of localized strategies for disease management.}, }
@article {pmid32697840, year = {2020}, author = {Cary, C and Cowan, DA and McMinn, A and Häggblom, MM}, title = {Editorial: Thematic issue on polar and alpine microbiology.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {8}, pages = {}, doi = {10.1093/femsec/fiaa136}, pmid = {32697840}, issn = {1574-6941}, }
@article {pmid32696567, year = {2020}, author = {Kuranaga, T and Matsuda, K and Takaoka, M and Tachikawa, C and Sano, A and Itoh, K and Enomoto, A and Fujita, K and Abe, I and Wakimoto, T}, title = {Total Synthesis and Structural Revision of Kasumigamide, and Identification of a New Analogue.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {21}, number = {23}, pages = {3329-3332}, doi = {10.1002/cbic.202000409}, pmid = {32696567}, issn = {1439-7633}, mesh = {Biological Products/*analysis/*chemical synthesis/metabolism ; Molecular Conformation ; Oligopeptides/*analysis/biosynthesis/*chemical synthesis ; }, abstract = {Kasumigamide is an antialgal hybrid peptide-polyketide isolated from the freshwater cyanobacterium Microcystis aeruginosa (NIES-87). The biosynthetic gene cluster was identified from not only the cyanobacterium but also Candidatus "Entotheonella", associated with the Japanese marine sponge Discodermia calyx. Therefore, kasumigamide is considered to play a key role in microbial ecology, regardless of the terrestrial and marine habitats. We now report synthetic studies on this intriguing natural product that have led to a structural revision and the first total synthesis. During this study, a new analogue, deoxykasumigamide, was also isolated and structurally validated. This study confirmed the presence of the unusual pathway in the biosynthesis of a hybrid peptide-polyketide natural product.}, }
@article {pmid32696239, year = {2021}, author = {Cassán, F and López, G and Nievas, S and Coniglio, A and Torres, D and Donadio, F and Molina, R and Mora, V}, title = {What Do We Know About the Publications Related with Azospirillum? A Metadata Analysis.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {278-281}, pmid = {32696239}, issn = {1432-184X}, support = {PICT-2017-0572//FONCyT-MINCYT/ ; }, mesh = {Azospirillum/classification/*metabolism ; Host Microbial Interactions/*physiology ; Plant Development ; *Plant Growth Regulators ; Plant Roots/microbiology ; Plants/*microbiology ; }, abstract = {Azospirillum is one of the most successful plant growth-promoting bacteria (PGPB) genera and it is considered a study model for plant-bacteria interactions. Because of that, a wide broad of topics has been boarded and discussed in a significant number of publications in the last four decades. Using the Scopus® database, we conducted a bibliographic search in order to analyze the number and type of publications, the authors responsible of these contributions, and the origin of the researchers, as well as the keywords and journals selected by the authors, among other related characteristics, with the aim to understand some less addressed details about the work done with Azospirillum worldwide since its discovery in 1925. Despite that the largest numbers of publications about this bacterium were obtained between the 1970 and 1980s, there is still a linear increase tendency in the number of published works. Understanding the mechanisms involved in the ability of these bacteria to promote growth in a wide broad of plant species under both laboratory and field conditions has been a preferential target for these published articles. This tendency could be considered a cause or consequence of the current increase in the number of commercial products formulated with Azospirillum around the world and a catalyzer for the increase of published articles along time.}, }
@article {pmid32694129, year = {2020}, author = {Wang, S and Xiong, W and Wang, Y and Nie, Y and Wu, Q and Xu, Y and Geisen, S}, title = {Temperature-Induced Annual Variation in Microbial Community Changes and Resulting Metabolome Shifts in a Controlled Fermentation System.}, journal = {mSystems}, volume = {5}, number = {4}, pages = {}, pmid = {32694129}, issn = {2379-5077}, abstract = {We are rapidly increasing our understanding on the spatial distribution of microbial communities. However, microbial functioning, as well as temporal differences and mechanisms causing microbial community shifts, remains comparably little explored. Here, using Chinese liquor fermentation as a model system containing a low microbial diversity, we studied temporal changes in microbial community structure and functioning. For that, we used high-throughput sequencing to analyze the composition of bacteria and fungi and analyzed the microbially derived metabolome throughout the fermentation process in all four seasons in both 2018 and 2019. We show that microbial communities and the metabolome changed throughout the fermentation process in each of the four seasons, with metabolome diversity increasing throughout the fermentation process. Across seasons, bacterial and fungal communities as well as the metabolome driven by 10 indicator microorganisms and six metabolites varied even more. Daily average temperature in the external surroundings was the primary determinant of the observed temporal microbial community and metabolome changes. Collectively, our work reveals critical insights into patterns and processes determining temporal changes of microbial community composition and functioning. We highlight the importance of linking taxonomic to functional changes in microbial ecology to enable predictions of human-relevant applications.IMPORTANCE We used Chinese liquor fermentation as a model system to show that microbiome composition changes more dramatically across seasons than throughout the fermentation process within seasons. These changes translate to differences in the metabolome as the ultimate functional outcome of microbial activity, suggesting that temporal changes in microbiome composition are translating into functional changes. This result is striking as it suggests that microbial functioning, despite controlled conditions in the fermentors, fluctuates over season along with external temperature differences, which threatens a reproducible food taste. As such, we believe that our study provides a stepping-stone into novel taxonomy-functional studies that promote future work in other systems and that also is relevant in applied settings to better control surrounding conditions in food production.}, }
@article {pmid32694124, year = {2020}, author = {Sieradzki, ET and Koch, BJ and Greenlon, A and Sachdeva, R and Malmstrom, RR and Mau, RL and Blazewicz, SJ and Firestone, MK and Hofmockel, KS and Schwartz, E and Hungate, BA and Pett-Ridge, J}, title = {Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design.}, journal = {mSystems}, volume = {5}, number = {4}, pages = {}, pmid = {32694124}, issn = {2379-5077}, abstract = {Quantitative stable isotope probing (qSIP) estimates isotope tracer incorporation into DNA of individual microbes and can link microbial biodiversity and biogeochemistry in complex communities. As with any quantitative estimation technique, qSIP involves measurement error, and a fuller understanding of error, precision, and statistical power benefits qSIP experimental design and data interpretation. We used several qSIP data sets-from soil and seawater microbiomes-to evaluate how variance in isotope incorporation estimates depends on organism abundance and resolution of the density fractionation scheme. We assessed statistical power for replicated qSIP studies, plus sensitivity and specificity for unreplicated designs. As a taxon's abundance increases, the variance of its weighted mean density declines. Nine fractions appear to be a reasonable trade-off between cost and precision for most qSIP applications. Increasing the number of density fractions beyond that reduces variance, although the magnitude of this benefit declines with additional fractions. Our analysis suggests that, if a taxon has an isotope enrichment of 10 atom% excess, there is a 60% chance that this will be detected as significantly different from zero (with alpha 0.1). With five replicates, isotope enrichment of 5 atom% could be detected with power (0.6) and alpha (0.1). Finally, we illustrate the importance of internal standards, which can help to calibrate per sample conversions of %GC to mean weighted density. These results should benefit researchers designing future SIP experiments and provide a useful reference for metagenomic SIP applications where both financial and computational limitations constrain experimental scope.IMPORTANCE One of the biggest challenges in microbial ecology is correlating the identity of microorganisms with the roles they fulfill in natural environmental systems. Studies of microbes in pure culture reveal much about their genomic content and potential functions but may not reflect an organism's activity within its natural community. Culture-independent studies supply a community-wide view of composition and function in the context of community interactions but often fail to link the two. Quantitative stable isotope probing (qSIP) is a method that can link the identity and functional activity of specific microbes within a naturally occurring community. Here, we explore how the resolution of density gradient fractionation affects the error and precision of qSIP results, how they may be improved via additional experimental replication, and discuss cost-benefit balanced scenarios for SIP experimental design.}, }
@article {pmid32691599, year = {2020}, author = {Elsayed, SS and Genta-Jouve, G and Carrión, VJ and Nibbering, PH and Siegler, MA and de Boer, W and Hankemeier, T and van Wezel, GP}, title = {Atypical Spirotetronate Polyketides Identified in the Underexplored Genus Streptacidiphilus.}, journal = {The Journal of organic chemistry}, volume = {85}, number = {16}, pages = {10648-10657}, pmid = {32691599}, issn = {1520-6904}, mesh = {Anti-Bacterial Agents ; *Polyketides ; *Streptomyces/genetics ; *Streptomycetaceae ; }, abstract = {More than half of all antibiotics and many other bioactive compounds are produced by the actinobacterial members of the genus Streptomyces. It is therefore surprising that virtually no natural products have been described for its sister genus Streptacidiphilus within Streptomycetaceae. Here, we describe an unusual family of spirotetronate polyketides, called streptaspironates, which are produced by Streptacidiphilus sp. P02-A3a, isolated from decaying pinewood. The characteristic structural and genetic features delineating spirotetronate polyketides could be identified in streptaspironates A (1) and B (2). Conversely, streptaspironate C (3) showed an unprecedented tetronate-less macrocycle-less structure, which was likely produced from an incomplete polyketide chain, together with an intriguing decarboxylation step, indicating a hypervariable biosynthetic machinery. Taken together, our work enriches the chemical space of actinobacterial natural products and shows the potential of Streptacidiphilus as producers of new compounds.}, }
@article {pmid32690378, year = {2020}, author = {Zhang, X and Fan, L and Wu, J and Xu, H and Leung, WY and Fu, K and Wu, J and Liu, K and Man, K and Yang, X and Han, J and Ren, J and Yu, J}, title = {Erratum to: "Macrophage p38 alpha promotes nutritional steatohepatitis through M1 polarization (J Hepatol 2019; 71(1):163-174)".}, journal = {Journal of hepatology}, volume = {73}, number = {3}, pages = {742-743}, doi = {10.1016/j.jhep.2020.06.019}, pmid = {32690378}, issn = {1600-0641}, }
@article {pmid32688217, year = {2020}, author = {Dey, P and Olmstead, BD and Sasaki, GY and Vodovotz, Y and Yu, Z and Bruno, RS}, title = {Epigallocatechin gallate but not catechin prevents nonalcoholic steatohepatitis in mice similar to green tea extract while differentially affecting the gut microbiota.}, journal = {The Journal of nutritional biochemistry}, volume = {84}, number = {}, pages = {108455}, doi = {10.1016/j.jnutbio.2020.108455}, pmid = {32688217}, issn = {1873-4847}, mesh = {Animals ; Catechin/*analogs &amp; derivatives/pharmacology/*therapeutic use ; Gastrointestinal Microbiome/*drug effects ; Male ; Mice ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/microbiology/pathology/*prevention &amp; control ; Protective Agents/pharmacology/*therapeutic use ; *Tea/chemistry ; }, abstract = {Catechin-rich green tea extract (GTE) protects against nonalcoholic steatohepatitis (NASH) by alleviating gut-derived endotoxin translocation and hepatic Toll-like receptor-4 (TLR4)-nuclear factor κB (NFκB) inflammation. We hypothesized that intact GTE would attenuate NASH-associated responses along the gut-liver axis to a greater extent than purified (-)-epigallocatechin gallate (EGCG) or (+)-catechin (CAT). Male C57BL/6J mice were fed a low-fat diet, a high-fat (HF) diet, or the HF diet with 2% GTE, 0.3% EGCG or 0.3% CAT for 8 weeks prior to assessing NASH relative to endotoxemia, hepatic and intestinal inflammation, intestinal tight junction proteins (TJPs) and gut microbial ecology. GTE prevented HF-induced obesity to a greater extent than EGCG and CAT, whereas GTE and EGCG more favorably attenuated insulin resistance. GTE, EGCG and CAT similarly attenuated serum alanine aminotransferase and serum endotoxin, but only GTE and EGCG fully alleviated HF-induced NASH. However, hepatic TLR4/NFκB inflammatory responses that were otherwise increased in HF mice were similarly attenuated by GTE, EGCG and CAT. Each treatment also similarly prevented the HF-induced loss in expression of intestinal TJPs and hypoxia inducible factor-1α and the otherwise increased levels of ileal and colonic TNFα mRNA and fecal calprotectin protein concentrations. Gut microbial diversity that was otherwise lowered in HF mice was maintained by GTE and CAT only. Further, microbial metabolic functions were more similar between GTE and CAT. Collectively, GTE catechins similarly protect against endotoxin-TLR4-NFκB inflammation in NASH, but EGCG and CAT exert differential prebiotic and antimicrobial activities suggesting that catechin-mediated shifts in microbiota composition are not entirely responsible for their benefits along the gut-liver axis.}, }
@article {pmid32688002, year = {2020}, author = {Zhou, WH and Wang, YT and Lian, ZH and Yang, TT and Zeng, QW and Feng, SW and Fang, Z and Shu, WS and Huang, LN and Ye, ZH and Liao, B and Li, JT}, title = {Revegetation approach and plant identity unequally affect structure, ecological network and function of soil microbial community in a highly acidified mine tailings pond.}, journal = {The Science of the total environment}, volume = {744}, number = {}, pages = {140793}, doi = {10.1016/j.scitotenv.2020.140793}, pmid = {32688002}, issn = {1879-1026}, mesh = {Biodegradation, Environmental ; *Microbiota ; Ponds ; Soil ; Soil Microbiology ; Soil Pollutants/*analysis ; }, abstract = {Owing to its sustainability and low cost, direct revegetation (DR) has been considered a promising alternative to capped revegetation (CR) for dealing with the serious environmental problem derived from various types of mine wastelands that are widespread in the world. However, a direct comparison of the performance of these two revegetation approaches for reclamation of extremely acidic mine wastelands and the underlying mechanisms is still lacking. To bridge this critical knowledge gap, we established 5000 m[2] of vegetation on a highly acidified (pH < 3) Pb/Zn mine tailings pond employing both CR and DR schemes (2500 m[2] for each scheme). We then profiled the structure, ecological network and function of soil microbial communities associated with two dominant plant species of the vegetations via high-throughput sequencing. Our results showed that CR and DR achieved a vegetation coverage of 59.7% and 90.5% within two years, respectively. This pattern was accompanied by higher concentrations of plant nutrients and lower acidification potentials in topsoils of the rhizospheres of the vegetation established by DR compared to those of CR. Revegetation approach, rather than plant identity, mostly affected the structure, ecological network and function of soil microbial community in the mine tailings pond. Rhizosphere soils of the vegetation established by DR generally had higher microbial diversity, higher relative abundances of dominant microbial phyla (e.g. Nitrospirae) that can aid plant uptake of nutrients, more complicated microbial interactive networks and more microbial genes responsible for nutrient cycling than those by CR. As the first report on a direct comparison of CR and DR schemes for reclamation of an extremely acidic mine wasteland, our study has important implications for not only the understanding of microbial ecology in revegetated mine wastelands but also the further development of sustainable revegetation schemes.}, }
@article {pmid32686214, year = {2021}, author = {Liu, D and Howell, K}, title = {Community succession of the grapevine fungal microbiome in the annual growth cycle.}, journal = {Environmental microbiology}, volume = {23}, number = {4}, pages = {1842-1857}, doi = {10.1111/1462-2920.15172}, pmid = {32686214}, issn = {1462-2920}, mesh = {Fungi/classification/*physiology ; *Mycobiome ; *Vitis/microbiology ; *Wine ; }, abstract = {Microbial ecology and activity in wine production influences grapevine health and productivity, conversion of sugar to ethanol during fermentation, wine aroma, wine quality and distinctiveness. Fungi in the vineyard ecosystem are not well described. Here, we characterized the spatial and temporal dynamics of fungal communities associated with the grapevine (grapes, flowers, leaves, and roots) and soils over an annual growth cycle in two vineyards to investigate the influences of grape habitat, plant developmental stage (flowering, fruit set, veraison, and harvest), vineyards, and climatic conditions. Fungi were influenced by both the grapevine habitat and plant development stage. The core microbiome was prioritized over space and time, and the identified core members drove seasonal community succession. The developmental stage of veraison, where the grapes undergo a dramatic change in metabolism and start accumulating sugar, coincided with a distinct shift in fungal communities. Co-occurrence networks showed strong correlations between the plant microbiome, the soil microbiome, and weather indices. Our study describes the complex ecological dynamics that occur in microbial assemblages over a growing season and highlight succession of the core community in vineyards.}, }
@article {pmid32685479, year = {2020}, author = {Li, Z and Ni, M and Yu, H and Wang, L and Zhou, X and Chen, T and Liu, G and Gao, Y}, title = {Gut Microbiota and Liver Fibrosis: One Potential Biomarker for Predicting Liver Fibrosis.}, journal = {BioMed research international}, volume = {2020}, number = {}, pages = {3905130}, pmid = {32685479}, issn = {2314-6141}, mesh = {Animals ; Bacteria/classification/*genetics/isolation &amp; purification ; Biomarkers/analysis ; Carbon Tetrachloride/toxicity ; Disease Models, Animal ; Feces/microbiology ; *Gastrointestinal Microbiome ; Liver Cirrhosis/chemically induced/*microbiology/*pathology ; Male ; RNA, Ribosomal, 16S/genetics ; ROC Curve ; Rats ; Rats, Wistar ; }, abstract = {PURPOSE: To investigate the relationship between gut microbiota and liver fibrosis and establish a microbiota biomarker for detecting and staging liver fibrosis.<br><br>METHODS: 131 Wistar rats were used in our study, and liver fibrosis was induced by carbon tetrachloride. Stool samples were collected within 72 hours after the last administration. The V4 regions of 16S rRNA gene were amplified. The sequencing data was processed using the Quantitative Insights Into Microbial Ecology (QIIME version 1.9). The diversity, principal coordinate analysis (PCoA), nonmetric multidimensional scaling (NMDS), and linear discriminant analysis (LDA) effect size (LEfSe) were performed. Random-Forest classification was performed for discriminating the samples from different groups. Microbial function was assessed using the PICRUST.<br><br>RESULTS: The Simpson in the control group was lower than that in the liver fibrosis group (p = 0.048) and differed significantly among different fibrosis stages (p = 0.047). The Chao1 index in the control group was higher than that in the liver fibrosis group (p < 0.001). NMDS analysis showed a marked difference between the control and liver fibrosis groups (p < 0.001). PCoA analysis indicated the different community composition between the control and liver fibrosis groups with variances of PC1 13.76% and PC2 5.89% and between different liver fibrosis stages with variances of PC1 10.51% and PC2 7.78%. LEfSe analysis showed alteration of gut microbiota in the liver fibrosis group. Biomarkers obtained from Random-Forest classification showed excellent diagnostic accuracy in prediction of liver fibrosis with AUROCs of 0.99. The AUROCs were 0.77~0.84 in prediction of stage F4. There were six increased and 17 decreased metabolic functions in the liver fibrosis group and 6 metabolic functions significantly differed among four liver fibrosis stages.<br><br>CONCLUSION: Gut microbiota is a potential biomarker for detecting and staging liver fibrosis with high diagnostic accuracies.}, }
@article {pmid32681284, year = {2021}, author = {Varasteh, T and Hamerski, L and Tschoeke, D and Lima, AS and Garcia, G and Cosenza, CAN and Thompson, C and Thompson, F}, title = {Conserved Pigment Profiles in Phylogenetically Diverse Symbiotic Bacteria Associated with the Corals Montastraea cavernosa and Mussismilia braziliensis.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {267-277}, pmid = {32681284}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology ; Antioxidants/*metabolism ; Bacteroidetes/genetics/isolation &amp; purification/*metabolism ; Brazil ; Carotenoids/metabolism ; Catalase/biosynthesis ; DNA, Bacterial/genetics ; Genome, Bacterial/genetics ; Oxidoreductases/biosynthesis ; Paracoccus/genetics/isolation &amp; purification/*metabolism ; Peroxidase/biosynthesis ; Pigments, Biological/genetics/*metabolism ; Pseudoalteromonas/genetics/isolation &amp; purification/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Pigmented bacterial symbionts play major roles in the health of coral holobionts. However, there is scarce knowledge on the diversity of these microbes for several coral species. To gain further insights into holobiont health, pigmented bacterial isolates of Fabibacter pacificus (Bacteroidetes; n = 4), Paracoccus marcusii (Alphaproteobacteria; n = 1), and Pseudoalteromonas shioyasakiensis (Gammaproteobacteria; n = 1) were obtained from the corals Mussismilia braziliensis and Montastraea cavernosa in Abrolhos Bank, Brazil. Cultures of these bacterial symbionts produced strong antioxidant activity (catalase, peroxidase, and oxidase). To explore these bacterial isolates further, we identified their major pigments by HPLC and mass spectrometry. The six phylogenetically diverse symbionts had similar pigment patterns and produced myxol and keto-carotene. In addition, similar carotenoid gene clusters were confirmed in the whole genome sequences of these symbionts, which reinforce their antioxidant potential. This study highlights the possible roles of bacterial symbionts in Montastraea and Mussismilia holobionts.}, }
@article {pmid32681144, year = {2020}, author = {Hylling, O and Carstens, AB and Kot, W and Hansen, M and Neve, H and Franz, CMAP and Johansen, A and Ellegaard-Jensen, L and Hansen, LH}, title = {Two novel bacteriophage genera from a groundwater reservoir highlight subsurface environments as underexplored biotopes in bacteriophage ecology.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {11879}, pmid = {32681144}, issn = {2045-2322}, mesh = {Bacteriophages/*classification/genetics/isolation &amp; purification/ultrastructure ; Ecology ; Gene Order ; Genome, Viral ; Genomics/methods ; Groundwater/*microbiology ; Phylogeny ; Virion ; *Water Microbiology ; }, abstract = {Although bacteriophages are central entities in bacterial ecology and population dynamics, there is currently no literature on the genomes of bacteriophages isolated from groundwater. Using a collection of bacterial isolates from an aquifer as hosts, this study isolated, sequenced and characterised two bacteriophages native to the groundwater reservoir. Host phylogenetic analyses revealed that the phages targeted B. mycoides and a novel Pseudomonas species. These results suggest that both bacteriophages represent new genera, highlighting that groundwater reservoirs, and probably other subsurface environments as well, are underexplored biotopes in terms of the presence and ecology of bacteriophages.}, }
@article {pmid32680791, year = {2020}, author = {Daisley, BA and Chmiel, JA and Pitek, AP and Thompson, GJ and Reid, G}, title = {Missing Microbes in Bees: How Systematic Depletion of Key Symbionts Erodes Immunity.}, journal = {Trends in microbiology}, volume = {28}, number = {12}, pages = {1010-1021}, doi = {10.1016/j.tim.2020.06.006}, pmid = {32680791}, issn = {1878-4380}, mesh = {Animals ; Bees/*immunology/*microbiology ; Disease Resistance/physiology ; Ecology ; Host Microbial Interactions/*physiology ; *Immunity ; Lactobacillus ; Microbiota ; Nutrients/deficiency ; Pesticides/pharmacology ; Probiotics ; Stress, Physiological ; Symbiosis ; }, abstract = {Pesticide exposure, infectious disease, and nutritional stress contribute to honey bee mortality and a high rate of colony loss. This realization has fueled a decades-long investigation into the single and combined effects of each stressor and their overall bearing on insect physiology. However, one element largely missing from this research effort has been the evaluation of underlying microbial communities in resisting environmental stressors and their influence on host immunity and disease tolerance. In humans, multigenerational bombardment by antibiotics is linked with many contemporary diseases. Here, we draw a parallel conclusion for the case in honey bees and suggest that chronic exposure to antimicrobial xenobiotics can systematically deplete honey bees of their microbes and hamper cross-generational preservation of host-adapted symbionts that are crucial to health.}, }
@article {pmid32679495, year = {2020}, author = {Moopantakath, J and Imchen, M and Siddhardha, B and Kumavath, R}, title = {16s rRNA metagenomic analysis reveals predominance of Crtl and CruF genes in Arabian Sea coast of India.}, journal = {The Science of the total environment}, volume = {743}, number = {}, pages = {140699}, doi = {10.1016/j.scitotenv.2020.140699}, pmid = {32679495}, issn = {1879-1026}, mesh = {Archaea/*genetics ; Bacteria/genetics ; Geologic Sediments ; India ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Microbial communities perform crucial biogeochemical cycles in distinct ecosystems. Halophilic microbial communities are enriched in the saline areas. Hence, haloarchaea have been primarily studied in salterns and marine biosystems with the aim to harness haloarcheal carotenoids biosynthesis. In this study, sediment from several distinct biosystems (mangrove, seashore, estuary, river, lake, salt pan and island) across the Arabian coastal region of India were collected and analyzed though 16s rRNA metagenomic and whole genome approach to elucidated the dominant representative genre, haloarcheal diversity, and the prevalence of Crtl and CruF genes. We found that the microbial diversity in mangrove sediment (794 OTUs) was highest and lowest in lake and river (558-560 OTUs). Moreover, the bacterial domain dominated in all biosystems (96.00-99.45%). Top 10 abundant genera were involved in biochemical cycles such as sulfur, methane, ammonia, hydrocarbon degradation, and antibiotics production. The Archaea was mainly composed of Haloarchaea, Methanobacteria, Methanococci, Methanomicrobia and Crenarchaeota. Carotenoid gene, Crtl, was observed in a major portion (abundance 60%; diversity 45%) of microbial community. Interestingly, we found that all species under haloarcheal class that were represented in fresh as well as marine biosystems encodes CruF gene (bacterioruberin carotenoid). Our study demonstrates the high microbial diversity in various ecosystems, enrichment of Crtl gene, and also shows that Crtl and CruF genes are highly abundant in haloarcheal genera. The finding of ecosystems specific Crtl and CruF encoding genera opens up a promising area in bioprospecting the carotenoid derivatives from the wide range of natural biosystems.}, }
@article {pmid32678322, year = {2020}, author = {Li, L and Wang, S and Wang, H and Sahu, SK and Marin, B and Li, H and Xu, Y and Liang, H and Li, Z and Cheng, S and Reder, T and Çebi, Z and Wittek, S and Petersen, M and Melkonian, B and Du, H and Yang, H and Wang, J and Wong, GK and Xu, X and Liu, X and Van de Peer, Y and Melkonian, M and Liu, H}, title = {Author Correction: The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {9}, pages = {1280}, pmid = {32678322}, issn = {2397-334X}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid32677880, year = {2020}, author = {Zhang, Q and Xu, J and Warren, A and Yang, R and Shen, Z and Yi, Z}, title = {Assessing the utility of Hsp90 gene for inferring evolutionary relationships within the ciliate subclass Hypotricha (Protista, Ciliophora).}, journal = {BMC evolutionary biology}, volume = {20}, number = {1}, pages = {86}, pmid = {32677880}, issn = {1471-2148}, support = {31772440//National Natural Science Foundation of China/International ; 31970486//National Natural Science Foundation of China/International ; 31672279//National Natural Science Foundation of China/International ; 2018SDKJ0406-1//Marine S&amp;T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao)/International ; GDOE(2019)A23//Guangdong MEPP Fund/International ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Ciliophora/classification/*genetics ; DNA, Ribosomal/genetics ; Databases, Genetic ; Databases, Protein ; *Evolution, Molecular ; HSP90 Heat-Shock Proteins/chemistry/*genetics ; Phylogeny ; }, abstract = {BACKGROUND: Although phylogenomic analyses are increasingly used to reveal evolutionary relationships among ciliates, relatively few nuclear protein-coding gene markers have been tested for their suitability as candidates for inferring phylogenies within this group. In this study, we investigate the utility of the heat-shock protein 90 gene (Hsp90) as a marker for inferring phylogenetic relationships among hypotrich ciliates.<br><br>RESULTS: A total of 87 novel Hsp90 gene sequences of 10 hypotrich species were generated. Of these, 85 were distinct sequences. Phylogenetic analyses based on these data showed that: (1) the Hsp90 gene amino acid trees are comparable to the small subunit rDNA tree for recovering phylogenetic relationships at the rank of class, but lack sufficient phylogenetic signal for inferring evolutionary relationships at the genus level; (2) Hsp90 gene paralogs are recent and therefore unlikely to pose a significant problem for recovering hypotrich clades; (3) definitions of some hypotrich orders and families need to be revised as their monophylies are not supported by various gene markers; (4) The order Sporadotrichida is paraphyletic, but the monophyly of the "core" Urostylida is supported; (5) both the subfamily Oxytrichinae and the genus Urosoma seem to be non-monophyletic, but monophyly of Urosoma is not rejected by AU tests.<br><br>CONCLUSIONS: Our results for the first time demonstrate that the Hsp90 gene is comparable to SSU rDNA for recovering phylogenetic relationships at the rank of class, and its paralogs are unlikely to pose a significant problem for recovering hypotrich clades. This study shows the value of careful gene marker selection for phylogenomic analyses of ciliates.}, }
@article {pmid32673982, year = {2020}, author = {Ali, M and Yue, D}, title = {Population dynamics of microbial species under high and low ammonia nitrogen in the alternate layer bioreactor landfill (ALBL) approach.}, journal = {Bioresource technology}, volume = {315}, number = {}, pages = {123787}, doi = {10.1016/j.biortech.2020.123787}, pmid = {32673982}, issn = {1873-2976}, mesh = {*Ammonia ; Bioreactors ; Ecosystem ; Methane ; Nitrogen ; Population Dynamics ; *Refuse Disposal ; Waste Disposal Facilities ; }, abstract = {Anaerobic landfill process is still believed to be a complex ecosystem due to the lack of knowledge on the functional activities of microbial species. This research sought to introduce a novel landfill bioreactor, named here as the alternate layer bioreactor landfill (ALBL) of fresh MSW (FW) and stabilized waste (CT) to avoid inhibitory conditions for the microbial species in anaerobic landfill. The stabilized waste layer in the bottom of landfill cell significantly changed microbial ecology of fresh MSW which in turn reduced the concentrations of NH4-N (29-31%) and VFAs (33-38%) in the ALBL approach, compared to fresh MSW disposal in sanitary landfill. The reduction of NH4-N favored early onset of methanogenesis within 6 weeks and methane (CH4) content of landfill gas increased from 11% to 40-50% (v/v), owing to the coexistence of Methanosarcinales (36-50%) and Methanomicrobiales (26-28%) archaea. The acetoclastic methanogenesis was achieved by reducing NH4-N toxicity in the ALBL.}, }
@article {pmid32670501, year = {2020}, author = {Khot, V and Strous, M and Hawley, AK}, title = {Computational approaches in viral ecology.}, journal = {Computational and structural biotechnology journal}, volume = {18}, number = {}, pages = {1605-1612}, pmid = {32670501}, issn = {2001-0370}, abstract = {Dynamic virus-host interactions play a critical role in regulating microbial community structure and function. Yet for decades prior to the genomics era, viruses were largely overlooked in microbial ecology research, as only low-throughput culture-based methods of discovering viruses were available. With the advent of metagenomics, culture-independent techniques have provided exciting opportunities to discover and study new viruses. Here, we review recently developed computational methods for identifying viral sequences, exploring viral diversity in environmental samples, and predicting hosts from metagenomic sequence data. Methods to analyze viruses in silico utilize unconventional approaches to tackle challenges unique to viruses, such as vast diversity, mosaic viral genomes, and the lack of universal marker genes. As the field of viral ecology expands exponentially, computational advances have become increasingly important to gain insight into the role viruses in diverse habitats.}, }
@article {pmid32666305, year = {2020}, author = {Castelli, L and Branchiccela, B and Garrido, M and Invernizzi, C and Porrini, M and Romero, H and Santos, E and Zunino, P and Antúnez, K}, title = {Impact of Nutritional Stress on Honeybee Gut Microbiota, Immunity, and Nosema ceranae Infection.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {908-919}, doi = {10.1007/s00248-020-01538-1}, pmid = {32666305}, issn = {1432-184X}, support = {CSIC 6406//Comisi&#xf3;n Sectorial de Investigaci&#xf3;n Cient&#xed;fica (UY)/ ; POS_NAC_2013_1_12228//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n/ ; }, mesh = {Animal Nutritional Physiological Phenomena/immunology/physiology ; Animals ; Bees/*immunology/*microbiology ; *Gastrointestinal Microbiome ; *Immunity, Innate ; Nosema/*physiology ; }, abstract = {Honeybees are important pollinators, having an essential role in the ecology of natural and agricultural environments. Honeybee colony losses episodes reported worldwide and have been associated with different pests and pathogens, pesticide exposure, and nutritional stress. This nutritional stress is related to the increase in monoculture areas which leads to a reduction of pollen availability and diversity. In this study, we examined whether nutritional stress affects honeybee gut microbiota, bee immunity, and infection by Nosema ceranae, under laboratory conditions. Consumption of Eucalyptus grandis pollen was used as a nutritionally poor-quality diet to study nutritional stress, in contraposition to the consumption of polyfloral pollen. Honeybees feed with Eucalyptus grandis pollen showed a lower abundance of Lactobacillus mellifer and Lactobacillus apis (Firm-4 and Firm-5, respectively) and Bifidobacterium spp. and a higher abundance of Bartonella apis, than honeybees fed with polyfloral pollen. Besides the impact of nutritional stress on honeybee microbiota, it also decreased the expression levels of vitellogenin and genes associated to immunity (glucose oxidase, hymenoptaecin and lysozyme). Finally, Eucalyptus grandis pollen favored the multiplication of Nosema ceranae. These results show that nutritional stress impacts the honeybee gut microbiota, having consequences on honeybee immunity and pathogen development. Those results may be useful to understand the influence of modern agriculture on honeybee health.}, }
@article {pmid32666084, year = {2020}, author = {Zhang, T and Fukuda, K and Topp, E and Zhu, YG and Smalla, K and Tiedje, JM and Larsson, DGJ}, title = {Editorial: The Environmental Dimension of Antibiotic Resistance.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {8}, pages = {}, doi = {10.1093/femsec/fiaa130}, pmid = {32666084}, issn = {1574-6941}, }
@article {pmid32664604, year = {2020}, author = {Marzorati, M and Abbeele, PVD and Bubeck, SS and Bayne, T and Krishnan, K and Young, A and Mehta, D and DeSouza, A}, title = {Bacillus subtilis HU58 and Bacillus coagulans SC208 Probiotics Reduced the Effects of Antibiotic-Induced Gut Microbiome Dysbiosis in An M-SHIME[®] Model.}, journal = {Microorganisms}, volume = {8}, number = {7}, pages = {}, pmid = {32664604}, issn = {2076-2607}, abstract = {Benefits associated with probiotic use have been reported; however, the mechanisms behind these benefits are poorly understood. The effects of a probiotic formulation (MegaDuo™) containing Bacillus coagulans SC208 and Bacillus subtilis HU58 on intestinal permeability and immune markers was assessed using a combination of the in vitro gut model, the mucosal simulator of the human intestinal microbial ecosystem (M-SHIME[®]), and an in vitro inflammatory bowel disease-like Caco-2/THP1 co-culture model in both healthy and antibiotic-induced dysbiosis conditions. Established M-SHIME[®] proximal colon vessels were treated with/without clindamycin (1 week) and then with/without daily MegaDuo™ treatment (2 weeks). The mucosal and luminal microbial communities were sampled weekly. Suspensions were removed from the proximal colon vessels after 1 and 2 weeks of MegaDuo™ treatment and added to the co-culture system. Transepithelial resistance (membrane barrier function), cytokine/chemokine release, and NFκB activity were then measured. Under conditions of antibiotic-induced dysbiosis, suspensions from MegaDuo™ treated vessels showed reduced gut membrane barrier damage and decreased levels of TNFα and IL-6 compared with suspensions from untreated vessels; no appreciable differences were observed under healthy conditions. MegaDuo™ treatment had no effect on NFκB activity of THP1-Blue™ cells. The potential benefits of MegaDuo™ treatment appeared most evident after 2 weeks of treatment.}, }
@article {pmid32661888, year = {2020}, author = {Szczepańska, A and Kiewra, D and Plewa-Tutaj, K and Dyczko, D and Guz-Regner, K}, title = {Sensitivity of Ixodes ricinus (L., 1758) and Dermacentor reticulatus (Fabr., 1794) ticks to entomopathogenic fungi isolates: preliminary study.}, journal = {Parasitology research}, volume = {119}, number = {11}, pages = {3857-3861}, pmid = {32661888}, issn = {1432-1955}, mesh = {Animals ; Biological Assay ; Dermacentor/*microbiology ; Europe ; Female ; Fungi/*pathogenicity ; Ixodes/*microbiology ; Metarhizium/pathogenicity ; Pest Control, Biological ; Sensitivity and Specificity ; Survival Analysis ; }, abstract = {Entomopathogenic fungi of the genus Beauveria and Metarhizium play an important role in controlling the population of arthropods. However, the data on their effectiveness against ticks focus mainly on species that do not occur in Europe. The aim of the study was to assess the effectiveness of entomopathogenic fungi against two of the most important tick species in Europe: Ixodes ricinus and Dermacentor reticulatus. In our study, the majority of tested entomopathogenic fungi strains showed potential efficacy against both tick species; however, D. reticulatus was less susceptible in comparison to I. ricinus. The observed mortality of ticks was up to 100% by using all commercial strains as well as three out of nine of the environmental strains. Among all tested fungi, the most effective against both tick species was environmental strain Metarhizium anisopliae LO4(1) with LC50 values: 2.6 × 10[3] cfu/ml-5.7 × 10[5] cfu/ml. Botanigard proved to be more effective than MET52 with LC50 values: 6.8 × 10[3] cfu/ml-3.3 × 10[6] cfu/ml. The conducted bioassays indicate the potential possibility of using the environmental isolates of entomopathogenic fungi, as well as commercial strains in control of local populations of I. ricinus and D. reticulatus; however, the possibility of using them in vivo requires more research.}, }
@article {pmid32659564, year = {2020}, author = {Ray, D and Leary, P and Livens, F and Gray, N and Morris, K and Law, KA and Fuller, AJ and Abrahamsen-Mills, L and Howe, J and Tierney, K and Muir, G and Law, GTW}, title = {Controls on anthropogenic radionuclide distribution in the Sellafield-impacted Eastern Irish Sea.}, journal = {The Science of the total environment}, volume = {743}, number = {}, pages = {140765}, doi = {10.1016/j.scitotenv.2020.140765}, pmid = {32659564}, issn = {1879-1026}, abstract = {Understanding anthropogenic radionuclide biogeochemistry and mobility in natural systems is key to improving the management of radioactively contaminated environments and radioactive wastes. Here, we describe the contemporary depth distribution and phase partitioning of [137]Cs, Pu, and [241]Am in two sediment cores taken from the Irish Sea (Site 1: the Irish Sea Mudpatch; Site 2: the Esk Estuary). Both sites are located ~10 km from the Sellafield nuclear site. Low-level aqueous radioactive waste has been discharged from the Sellafield site into the Irish Sea for >50 y. We compare the depth distribution of the radionuclides at each site to trends in sediment and porewater redox chemistry, using trace element abundance, microbial ecology, and sequential extractions, to better understand the relative importance of sediment biogeochemistry vs. physical controls on radionuclide distribution/post-depositional mobility in the sediments. We highlight that the distribution of [137]Cs, Pu, and [241]Am at both sites is largely controlled by physical mixing of the sediments, physical transport processes, and sediment accumulation. Interestingly, at the Esk Estuary, microbially-mediated redox processes (considered for Pu) do not appear to offer significant controls on Pu distribution, even over decadal timescales. We also highlight that the Irish Sea Mudpatch likely still acts as a source of historical pollution to other areas in the Irish Sea, despite ever decreasing levels of waste output from the Sellafield site.}, }
@article {pmid32658690, year = {2020}, author = {Bai, X and Zhong, X and Guo, C and Gui, Y and Xu, H}, title = {Colonization dynamics of protozoan communities in marine bioassessment surveys using two modified sampling systems.}, journal = {Marine pollution bulletin}, volume = {157}, number = {}, pages = {111325}, doi = {10.1016/j.marpolbul.2020.111325}, pmid = {32658690}, issn = {1879-3363}, mesh = {Biodiversity ; China ; *Ciliophora ; Ecosystem ; Environmental Monitoring ; Surveys and Questionnaires ; }, abstract = {Colonization dynamics of protozoan communities were investigated at a depth of 1 m in the coastal waters of the Yellow Sea, northern China from May to June 2019, using modified glass slide (mGS) and modified polyurethane foam unit (mPFU) systems. The colonization process and growth curves of protozoa were well fitted to the MacArthur-Wilson and logistic models in both systems, respectively. However, they showed significant differences in both colonization dynamics and biodiversity/functional parameters between the mGS and mPFU systems. The H' (species diversity), the G (colonization rate), and Amax (maximum abundance) were higher, while the value of T90% (the time for reaching 90% equilibrium species number) was lower in the mGS system than those in the mPFU system. Multivariate analyses demonstrated that protozoa showed different models of colonization dynamics in both systems. The results suggest that the mGS system might be more effective than the mPFU system in marine bioassessment surveys.}, }
@article {pmid32656607, year = {2021}, author = {Xie, XG and Zhao, YY and Yang, Y and Lu, F and Dai, CC}, title = {Endophytic Fungus Alleviates Soil Sickness in Peanut Crops by Improving the Carbon Metabolism and Rhizosphere Bacterial Diversity.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {49-61}, pmid = {32656607}, issn = {1432-184X}, support = {31870478//National Natural Science Foundation of China/ ; 17CXTD00014//Program for Jiangsu Excellent Scientific and Technological Innovation Team/ ; }, mesh = {Arachis ; Carbon ; Fungi ; Plant Roots ; *Rhizosphere ; *Soil ; Soil Microbiology ; }, abstract = {Endophytic fungi can profoundly affect host productivity, but the underlying mechanisms of these effects are only partly understood. As the most important regulators of plant-soil feedback, root exudates can easily cause soil sickness in continuous monoculture systems by reducing certain microbes in the rhizosphere. In this study, exudates from roots colonized by the endophytic fungus Phomopsis liquidambaris significantly increased rhizosphere bacterial abundance, soil respiration, microbial biomass and enzyme activities in a long-term continuously cropped peanut soil. Further analysis revealed that P. liquidambaris-colonized root exudates clearly altered the carbon metabolism and rhizosphere bacterial diversity, which were closely correlated with changes in soil chemical properties caused by the exudates from the colonized roots. Finally, a synthetic root exudate experiment further confirmed that the root exudates derived from P. liquidambaris colonization can indeed play an important role in promoting peanut growth. Therefore, these results show that this endophytic fungus could improve the carbon metabolism and rhizosphere bacterial community in long-term monoculture soils via exudates from colonized roots, which contribute to the alleviation of soil sickness.}, }
@article {pmid32656252, year = {2020}, author = {Adhikari, B and Jun, SR and Kwon, YM and Kiess, AS and Adhikari, P}, title = {Effects of Housing Types on Cecal Microbiota of Two Different Strains of Laying Hens During the Late Production Phase.}, journal = {Frontiers in veterinary science}, volume = {7}, number = {}, pages = {331}, pmid = {32656252}, issn = {2297-1769}, abstract = {Due to animal welfare issues, European Union has banned the use of conventional cages (CC) and non-EU countries including the US are also under constant public pressure to restrict their use in egg production. Very limited information is available on the composition of the microbial community of hens raised in different housing environments. This study was conducted to determine the effects of CC and enriched colony cages (EC) on cecal microbiota of two commercial laying hen strains, Hy-Line W36 (W36) and Hy-Line Brown (HB) during the late production stage (53, 58, 67, and 72 weeks of age). Cecal microbiota was studied by analyzing 16S rRNA gene sequences with Quantitative Insights Into Microbial Ecology (QIIME) 2 ver. 2018.8. Differentially abundant taxa were identified by Linear discriminant analysis Effect Size (LEfSe) analysis (P < 0.05, LDA score > 2.0). At phylum level, Actinobacteria was significantly enriched in W36 at all time points while Synergistetes (53 weeks), Spirochaetes (58 weeks), and Synergistetes and Spirochaetes (67 weeks) were significantly higher in HB. At genus level, Bifidobacterium (at all time points) and butyric acid producing genera such as Butyricicoccus and Subdoligranulum (58 and 72 weeks) were significantly higher in W36 as compared to HB. Moreover, Proteobacteria (72 weeks) and its associated genus Campylobacter (67 and 72 weeks) were significantly enriched in EC as compared to CC. Alpha diversity was significantly higher in HB (at all time points) and in EC (67 weeks) as compared to W36 and CC, respectively. Similarly, there was a significant difference in community structure (beta diversity) between W36 and HB (all time points) as well as between EC and CC (67 weeks). The effect of housing and strains was not only seen at the bacterial composition and structure but also reflected at their functional level. Notably, KEGG metabolic pathways predicted to be involved in carbohydrates degradation and amino acids biosynthesis by PICRUSt analysis were significantly different between W36 and HB housed at CC and EC. In sum, cecal microbiota composition, diversities, and their functional pathways were affected by housing type which further varied between two commercial laying hen strains, HB and W36. This suggests that both housing and genetic strains of laying hens should be considered for selection of the alternative housing systems such as enriched colony cage.}, }
@article {pmid32655529, year = {2020}, author = {Benítez-Páez, A and Olivares, M and Szajewska, H and Pieścik-Lech, M and Polanco, I and Castillejo, G and Nuñez, M and Ribes-Koninckx, C and Korponay-Szabó, IR and Koletzko, S and Meijer, CR and Mearin, ML and Sanz, Y}, title = {Breast-Milk Microbiota Linked to Celiac Disease Development in Children: A Pilot Study From the PreventCD Cohort.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1335}, pmid = {32655529}, issn = {1664-302X}, abstract = {Celiac disease (CeD) is an immune-mediated disorder triggered by exposure to dietary gluten proteins in genetically predisposed individuals. In addition to the host genome, the microbiome has recently been linked to CeD risk and pathogenesis. To progress in our understanding of the role of breast milk microbiota profiles in CeD, we have analyzed samples from a sub-set of mothers (n = 49) included in the PreventCD project, whose children did or did not develop CeD. The results of the microbiota data analysis indicated that neither the BMI, HLA-DQ genotype, the CeD condition nor the gluten-free diet of the mothers could explain the human milk microbiota profiles. Nevertheless, we found that origin country, the offspring's birth date and, consequently, the milk sampling date influenced the abundance and prevalence of microbes in human milk, undergoing a transition from an anaerobic to a more aerobic microbiota, including potential pathogenic species. Furthermore, certain microbial species were more abundant in milk samples from mothers whose children went on to develop CeD compared to those that remained healthy. These included increases in facultative methylotrophs such as Methylobacterium komagatae and Methylocapsa palsarum as well as in species such as Bacteroides vulgatus, that consumes fucosylated-oligosaccharides present in human milk, and other breast-abscess associated species. Theoretically, these microbiota components could be vertically transmitted from mothers-to-infants during breastfeeding, thereby influencing CeD risk.}, }
@article {pmid32655525, year = {2020}, author = {Raes, EJ and Karsh, K and Kessler, AJ and Cook, PLM and Holmes, BH and van de Kamp, J and Bodrossy, L and Bissett, A}, title = {Can We Use Functional Genetics to Predict the Fate of Nitrogen in Estuaries?.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1261}, pmid = {32655525}, issn = {1664-302X}, abstract = {Increasing nitrogen (N) loads present a threat to estuaries, which are among the most heavily populated and perturbed parts of the world. N removal is largely mediated by the sediment microbial process of denitrification, in direct competition to dissimilatory nitrate reduction to ammonium (DNRA), which recycles nitrate to ammonium. Molecular proxies for N pathways are increasingly measured and analyzed, a major question in microbial ecology, however, is whether these proxies can add predictive power around the fate of N. We analyzed the diversity and community composition of sediment nirS and nrfA genes in 11 temperate estuaries, covering four types of land use in Australia, and analyzed how these might be used to predict N removal. Our data suggest that sediment microbiomes play a central role in controlling the magnitude of the individual N removal rates in the 11 estuaries. Inclusion, however, of relative gene abundances of 16S, nirS, nrfA, including their ratios did not improve physicochemical measurement-based regression models to predict rates of denitrification or DNRA. Co-occurrence network analyses of nirS showed a greater modularity and a lower number of keystone OTUs in pristine sites compared to urban estuaries, suggesting a higher degree of niche partitioning in pristine estuaries. The distinctive differences between the urban and pristine network structures suggest that the nirS gene could be a likely gene candidate to understand the mechanisms by which these denitrifying communities form and respond to anthropogenic pressures.}, }
@article {pmid32651453, year = {2020}, author = {Sauder, LA and Albertsen, M and Engel, K and Schwarz, J and Nielsen, PH and Wagner, M and Neufeld, JD}, title = {Correction: Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system.}, journal = {The ISME journal}, volume = {14}, number = {9}, pages = {2366}, doi = {10.1038/s41396-020-0714-3}, pmid = {32651453}, issn = {1751-7370}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid32651355, year = {2020}, author = {Lian, Y and Yan, C and Lian, Y and Yang, R and Chen, Q and Ma, D and Lian, W and Liu, J and Luo, C and Ren, J and Xu, H}, title = {Long intergenic non-protein-coding RNA 01446 facilitates the proliferation and metastasis of gastric cancer cells through interacting with the histone lysine-specific demethylase LSD1.}, journal = {Cell death &amp; disease}, volume = {11}, number = {7}, pages = {522}, pmid = {32651355}, issn = {2041-4889}, mesh = {Cell Proliferation/physiology ; Disease Progression ; Female ; Histone Demethylases/*metabolism ; Humans ; Male ; Middle Aged ; Neoplasm Metastasis ; RNA, Long Noncoding/*genetics ; Stomach Neoplasms/genetics/*metabolism/pathology ; }, abstract = {Growing evidences illustrated that long non-coding RNAs (lncRNAs) exhibited widespread effects on the progression of human cancers via various mechanisms. Long intergenic non-protein-coding RNA 01446 (LINC01446), a 3484-bp ncRNA, is known to locate at chromosome 7p12.1. However, its biological functions and specific action mechanism in gastric cancer (GC) are still unclear. In our study, LINC01446 was proved to be markedly upregulated in GC tissues relative to the normal tissues, and positively correlated with the poor survival of GC patients. The multivariate Cox regression model showed that LINC01446 functioned as an independent prognostic factor for the survival of GC patients. Functionally, LINC01446 facilitated the proliferation and metastasis of GC cells. Moreover, RNA-seq analysis demonstrated that LINC01446 knockdown primarily regulated the genes relating to the growth and migration of GC. Mechanistically, LINC01446 could widely interact with histone lysine-specific demethylase LSD1 and recruit LSD1 to the Ras-related dexamethasone-induced 1 (RASD1) promoter, thereby suppressing RASD1 transcription. Overall, these findings suggest that LINC01446/LSD1/RASD1 regulatory axis may provide bona fide targets for anti-GC therapies.}, }
@article {pmid32647153, year = {2020}, author = {Borrego, C and Sabater, S and Proia, L}, title = {Lifestyle preferences drive the structure and diversity of bacterial and archaeal communities in a small riverine reservoir.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {11288}, pmid = {32647153}, issn = {2045-2322}, mesh = {Archaea/*classification ; Bacteria/*classification ; Biota ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Geologic Sediments/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Rivers/*microbiology ; Spain ; Water Microbiology ; }, abstract = {Spatial heterogeneity along river networks is interrupted by dams, affecting the transport, processing, and storage of organic matter, as well as the distribution of biota. We here investigated the structure of planktonic (free-living, FL), particle-attached (PA) and sediment-associated (SD) bacterial and archaeal communities within a small reservoir. We combined targeted-amplicon sequencing of bacterial and archaeal 16S rRNA genes in the DNA and RNA community fractions from FL, PA and SD, followed by imputed functional metagenomics, in order to unveil differences in their potential metabolic capabilities within the reservoir (tail, mid, and dam sections) and lifestyles (FL, PA, SD). Both bacterial and archaeal communities were structured according to their life-style preferences rather than to their location in the reservoir. Bacterial communities were richer and more diverse when attached to particles or inhabiting the sediment, while Archaea showed an opposing trend. Differences between PA and FL bacterial communities were consistent at functional level, the PA community showing higher potential capacity to degrade complex carbohydrates, aromatic compounds, and proteinaceous materials. Our results stressed that particle-attached prokaryotes were phylogenetically and metabolically distinct from their free-living counterparts, and that performed as hotspots for organic matter processing within the small reservoir.}, }
@article {pmid32638044, year = {2021}, author = {Lukoseviciute, L and Lebedeva, J and Kuisiene, N}, title = {Diversity of Polyketide Synthases and Nonribosomal Peptide Synthetases Revealed Through Metagenomic Analysis of a Deep Oligotrophic Cave.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {110-121}, pmid = {32638044}, issn = {1432-184X}, mesh = {Acidobacteria/genetics ; Actinobacteria/genetics ; Bacteria/classification/*genetics/metabolism ; Caves/*microbiology ; Chloroflexi/genetics ; Firmicutes/genetics ; Geologic Sediments/*microbiology ; Georgia (Republic) ; Metagenome/genetics ; Microbiota/genetics ; Peptide Synthases/*genetics ; Polyketide Synthases/*genetics ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Secondary Metabolism/*genetics ; Soil Microbiology ; }, abstract = {Caves are considered to be extreme and challenging environments. It is believed that the ability of microorganisms to produce secondary metabolites enhances their survivability and adaptiveness in the energy-starved cave environment. Unfortunately, information on the genetic potential for the production of secondary metabolites, such as polyketides and nonribosomal peptides, is limited. In the present study, we aimed to identify and characterize genes responsible for the production of secondary metabolites in the microbial community of one of the deepest caves in the world, Krubera-Voronja Cave (43.4184 N 40.3083 E, Western Caucasus). The analysed sample materials included sediments, drinkable water from underground camps, soil and clay from the cave walls, speleothems and coloured spots from the cave walls. The type II polyketide synthases (PKSs) ketosynthases α and β and the adenylation domains of nonribosomal peptide synthetases (NRPSs) were investigated using a metagenomic approach. Taxonomic diversity analysis showed that most PKS sequences could be attributed to Actinobacteria followed by unclassified bacteria and Acidobacteria, while the NRPS sequences were more taxonomically diverse and could be assigned to Proteobacteria, Actinobacteria, Cyanobacteria, Firmicutes, Chloroflexi, etc. Only three putative metabolites could be predicted: an angucycline group polyketide, a massetolide A-like cyclic lipopeptide and a surfactin-like lipopeptide. The absolute majority of PKS and NRPS sequences showed low similarity with the sequences of the reference biosynthetic pathways, suggesting that these sequences could be involved in the production of novel secondary metabolites.}, }
@article {pmid32638043, year = {2021}, author = {Griffin, TW and Baer, JG and Ward, JE}, title = {Direct Comparison of Fecal and Gut Microbiota in the Blue Mussel (Mytilus edulis) Discourages Fecal Sampling as a Proxy for Resident Gut Community.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {180-192}, pmid = {32638043}, issn = {1432-184X}, support = {1559180//Directorate for Biological Sciences/ ; }, mesh = {Animals ; Feces/*microbiology ; Food Microbiology ; Gastrointestinal Microbiome/*genetics ; Mytilus edulis/*microbiology ; RNA, Ribosomal, 16S/genetics ; Stomach/*microbiology ; }, abstract = {Bivalves have ecological and economic importance but information regarding their associated microbiomes is lacking. As suspension feeders, bivalves capture and ingest a myriad of particles, and their digestive organs have a high throughput of particle-associated microbiota. To better understand the complement of transient and resident microbial communities, standard methods need to be developed. For example, fecal sampling could represent a convenient proxy for the gut microbiome and is simple, nondestructive, and allows for sampling of individuals through time. The goal of this study was to evaluate fecal sampling as a reliable proxy for gut microbiome assessment in the blue mussel (Mytilus edulis). Mussels were collected from the natural environment and placed into individual sterilized microcosms for 6 h to allow for fecal egestion. Feces and gut homogenates from the same individuals were sampled and subjected to 16S rRNA gene amplicon sequencing. Fecal communities of different mussels resembled each other but did not resemble gut communities. Fecal communities were significantly more diverse, in terms of amplicon sequence variant (ASV) richness and evenness, than gut communities. Results suggested a mostly transient nature for fecal microbiota. Nonetheless, mussels retained a distinct resident microbial community in their gut after fecal egestion that was dominated by ASVs belonging to Mycoplasma. The use of fecal sampling as a nondestructive substitute for direct sampling of the gut is strongly discouraged. Experiments that aim to study solely resident bivalve gut microbiota should employ an egestion period prior to gut sampling to allow time for voidance of transient microbes.}, }
@article {pmid32629308, year = {2020}, author = {Qi, Y and Beriot, N and Gort, G and Huerta Lwanga, E and Gooren, H and Yang, X and Geissen, V}, title = {Impact of plastic mulch film debris on soil physicochemical and hydrological properties.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {266}, number = {Pt 3}, pages = {115097}, doi = {10.1016/j.envpol.2020.115097}, pmid = {32629308}, issn = {1873-6424}, mesh = {Agriculture ; Ecosystem ; Hydrology ; Plastics ; *Soil ; *Soil Pollutants ; }, abstract = {The plastic mulch films used in agriculture are considered to be a major source of the plastic residues found in soil. Mulching with low-density polyethylene (LDPE) is widely practiced and the resulting macro- and microscopic plastic residues in agricultural soil have aroused concerns for years. Over the past decades, a variety of biodegradable (Bio) plastics have been developed in the hope of reducing plastic contamination of the terrestrial ecosystem. However, the impact of these Bio plastics in agroecosystems have not been sufficiently studied. Therefore, we investigated the impact of macro (around 5 mm) and micro (<1 mm) sized plastic debris from LDPE and one type of starch-based Bio mulch film on soil physicochemical and hydrological properties. We used environmentally relevant concentrations of plastics, ranging from 0 to 2% (w/w), identified by field studies and literature review. We studied the effects of the plastic residue on a sandy soil for one month in a laboratory experiment. The bulk density, porosity, saturated hydraulic conductivity, field capacity and soil water repellency were altered significantly in the presence of the four kinds of plastic debris, while pH, electrical conductivity and aggregate stability were not substantially affected. Overall, our research provides clear experimental evidence that microplastics affect soil properties. The type, size and content of plastic debris as well as the interactions between these three factors played complex roles in the variations of the measured soil parameters. Living in a plastic era, it is crucial to conduct further interdisciplinary studies in order to have a comprehensive understanding of plastic debris in soil and agroecosystems.}, }
@article {pmid32628807, year = {2020}, author = {Rejeb, IB and Dhen, N and Gargouri, M and Boulila, A}, title = {Chemical Composition, Antioxidant Potential and Enzymes Inhibitory Properties of Globe Artichoke By-Products.}, journal = {Chemistry &amp; biodiversity}, volume = {17}, number = {9}, pages = {e2000073}, doi = {10.1002/cbdv.202000073}, pmid = {32628807}, issn = {1612-1880}, mesh = {Acetylcholinesterase/metabolism ; Antioxidants/chemistry/isolation &amp; purification/*pharmacology ; Benzothiazoles/antagonists &amp; inhibitors ; Biphenyl Compounds/antagonists &amp; inhibitors ; Butyrylcholinesterase/metabolism ; Cynara scolymus/*chemistry ; Enzyme Inhibitors/chemistry/isolation &amp; purification/*pharmacology ; Flavonoids/chemistry/isolation &amp; purification/*pharmacology ; Fluorescence Recovery After Photobleaching ; Phenols/chemistry/isolation &amp; purification/*pharmacology ; Picrates/antagonists &amp; inhibitors ; Plant Components, Aerial/chemistry ; Plant Extracts/chemistry/isolation &amp; purification/*pharmacology ; Sulfonic Acids/antagonists &amp; inhibitors ; alpha-Amylases/antagonists &amp; inhibitors/metabolism ; }, abstract = {In this study, chemical composition and in vitro biological activities of artichoke by-products (leaves, floral stems and bracts) issued from two Tunisian varieties were evaluated. Analysis was performed by means of high-performance liquid chromatography with diode array detection coupled to electrospray ionization mass spectrometric (LC/DAD/ESI-MS). Total phenolic (TPC) and flavonoid (TFC) contents as well as the antioxidant activity conducted by three complementary methods, DPPH, ABTS and FRAP tests, were performed for each sample. Enzyme inhibitory effects against acetylcholinesterase, butyrylcholinesterase and α-amylase were also studied. Results showed that TPC and TFC varied according to variety as well as the plant part. Bracts presented the highest TPC values (10-15 mg GAE/g DW), while leaves were distinguished by the highest TFC values (52-58 mg EQ/g DW). In vitro assays showed that Violet d'Hyères bracts and Blanc d'Oran leaves present the most antioxidant activities (30.040 and 20.428 mgET/gDW, respectively, by the DPPH method). Leaves demonstrated the highest acetylcholinesterase and butyrylcholinesterase inhibitory effects. Moreover, all organs displayed a noticeable inhibition towards α-amylase. LC/DAD/MS analysis revealed that artichoke by-products are a potential source of biopharmaceuticals such as luteolin derivatives from leaves and mono/dicaffeoylquinic acids in the other parts. This research demonstrates that globe artichoke by-products, unexploited in our country, are a promising source of natural health promoting compounds with potential applications in the food and pharmaceutical industries.}, }
@article {pmid32628343, year = {2020}, author = {Aguilar, P and Sommaruga, R}, title = {The balance between deterministic and stochastic processes in structuring lake bacterioplankton community over time.}, journal = {Molecular ecology}, volume = {29}, number = {16}, pages = {3117-3130}, pmid = {32628343}, issn = {1365-294X}, mesh = {Aquatic Organisms ; *Lakes ; *Microbiota/genetics ; RNA, Ribosomal, 16S ; Stochastic Processes ; }, abstract = {One major goal in microbial ecology is to establish the importance of deterministic and stochastic processes for community assembly. This is relevant to explain and predict how diversity changes at different temporal scales. However, understanding of the relative quantitative contribution of these processes and particularly of how they may change over time is limited. Here, we assessed the importance of deterministic and stochastic processes based on the analysis of the bacterial microbiome in one alpine oligotrophic and in one subalpine mesotrophic lake, which were sampled over two consecutive years at different time scales. We found that in both lakes, homogeneous selection (i.e., a deterministic process) was the main assembly process at the annual scale and explained 66.7% of the bacterial community turnover, despite differences in diversity and temporal variability patterns between ecosystems. However, in the alpine lake, homogenizing dispersal (i.e., a stochastic process) was the most important assembly process at the short-term (daily and weekly) sampling scale and explained 55% of the community turnover. Alpha diversity differed between lakes, and seasonal stability of the bacterial community was more evident in the oligotrophic lake than in the mesotrophic one. Our results demonstrate how important forces that govern temporal changes in bacterial communities act at different time scales. Overall, our study validates on a quantitative basis, the importance and dominance of deterministic processes in structuring bacterial communities in freshwater environments over long time scales.}, }
@article {pmid32625179, year = {2020}, author = {Costa, OYA and Oguejiofor, C and Zühlke, D and Barreto, CC and Wünsche, C and Riedel, K and Kuramae, EE}, title = {Impact of Different Trace Elements on the Growth and Proteome of Two Strains of Granulicella, Class "Acidobacteriia".}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1227}, pmid = {32625179}, issn = {1664-302X}, abstract = {Acidobacteria represents one of the most dominant bacterial groups across diverse ecosystems. However, insight into their ecology and physiology has been hampered by difficulties in cultivating members of this phylum. Previous cultivation efforts have suggested an important role of trace elements for the proliferation of Acidobacteria, however, the impact of these metals on their growth and metabolism is not known. In order to gain insight into this relationship, we evaluated the effect of trace element solution SL10 on the growth of two strains (5B5 and WH15) of Acidobacteria belonging to the genus Granulicella and studied the proteomic responses to manganese (Mn). Granulicella species had highest growth with the addition of Mn, as well as higher tolerance to this metal compared to seven other metal salts. Variations in tolerance to metal salt concentrations suggests that Granulicella sp. strains possess different mechanisms to deal with metal ion homeostasis and stress. Furthermore, Granulicella sp. 5B5 might be more adapted to survive in an environment with higher concentration of several metal ions when compared to Granulicella sp. WH15. The proteomic profiles of both strains indicated that Mn was more important in enhancing enzymatic activity than to protein expression regulation. In the genomic analyses, we did not find the most common transcriptional regulation of Mn homeostasis, but we found candidate transporters that could be potentially involved in Mn homeostasis for Granulicella species. The presence of such transporters might be involved in tolerance to higher Mn concentrations, improving the adaptability of bacteria to metal enriched environments, such as the decaying wood-rich Mn environment from which these two Granulicella strains were isolated.}, }
@article {pmid32623832, year = {2020}, author = {Morvan, S and Meglouli, H and Lounès-Hadj Sahraoui, A and Hijri, M}, title = {Into the wild blueberry (Vaccinium angustifolium) rhizosphere microbiota.}, journal = {Environmental microbiology}, volume = {22}, number = {9}, pages = {3803-3822}, doi = {10.1111/1462-2920.15151}, pmid = {32623832}, issn = {1462-2920}, support = {RGPIN-2018-04178//Natural Sciences and Engineering Research Council of Canada/International ; }, mesh = {Ascomycota/classification/genetics/isolation &amp; purification/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Blueberry Plants/chemistry/*microbiology ; *Microbiota ; Mycorrhizae/classification/genetics/isolation &amp; purification/metabolism ; Nitrogen/analysis ; Plant Leaves/chemistry/microbiology ; *Rhizosphere ; Symbiosis ; }, abstract = {The ability of wild blueberries to adapt to their harsh environment is believed to be closely related to their symbiosis with ericoid mycorrhizal fungi, which produce enzymes capable of organic matter mineralization. Although some of these fungi have been identified and characterized, we still know little about the microbial ecology of wild blueberry. Our study aims to characterize the fungal and bacterial rhizosphere communities of Vaccinium angustifolium (the main species encountered in wild blueberry fields). Our results clearly show that the fungal order Helotiales was the most abundant taxon associated with V. angustifolium. Helotiales contains most of the known ericoid mycorrhizal fungi which are expected to dominate in such a biotope. Furthermore, we found the dominant bacterial order was the nitrogen-fixing Rhizobiales. The Bradyrhizobium genus, whose members are known to form nodules with legumes, was among the 10 most abundant genera in the bacterial communities. In addition, Bradyrhizobium and Roseiarcus sequences significantly correlated with higher leaf-nitrogen content. Overall, our data documented fungal and bacterial community structure differences in three wild blueberry production fields.}, }
@article {pmid32623497, year = {2021}, author = {Pereira, A and Ferreira, V}, title = {Invasion of Native Riparian Forests by Acacia Species Affects In-Stream Litter Decomposition and Associated Microbial Decomposers.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {14-25}, pmid = {32623497}, issn = {1432-184X}, support = {SFRH/BD/118069/2016//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; IF/00129/2014//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UID/MAR/04292/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {Acacia/*metabolism ; Alnus/microbiology ; Bacteria/*growth &amp; development ; Biomass ; Ecology ; Forests ; Fungi/*growth &amp; development ; *Introduced Species ; Microbiota ; Nitrogen Fixation/physiology ; Portugal ; Quercus/microbiology ; Rivers/*chemistry/*microbiology ; }, abstract = {The invasion of native riparian forests by exotic tree species can lead to profound changes in the ecological integrity of freshwater ecosystems. We assessed litter decomposition of native (Alnus glutinosa and Quercus robur) and invasive (Acacia melanoxylon and Acacia dealbata) tree species, and associated microbial activity and community structure, after being immersed for conditioning in 3 reference and 3 "invaded" streams in Serra da Lousã (central Portugal) and used in microcosms simulating stream conditions. Litter decomposition differed among species, in the order: Al. glutinosa > Q. robur > (Ac. melanoxylon ~ Ac. dealbata). Alnus glutinosa litter decomposed faster probably because it was soft and had high nitrogen concentration for decomposers. Quercus robur litter decomposed slower most likely because it was tough and had high polyphenol and low nitrogen concentrations. Acacia melanoxylon litter was the toughest and had a thick cuticle that likely acted as a physical barrier for microbial colonization. In Ac. dealbata, the small-sized leaflets and high lignin concentration may have limited microbial litter decomposition. Litter decomposition was faster in "invaded" streams, probably because they were N-limited and increases in nitrogen concentration in water, promoted by Acacia species invasion, stimulated microbial activity on litter. The aquatic hyphomycete community structure differed among litter species and between stream types, further suggesting that microbes were sensitive to litter characteristics and water nutrient concentrations. Overall, the invasion of native riparian forests by Acacia species may affect microbial decomposer activity, thus altering important stream ecosystem processes, such as litter decomposition and nutrient cycles.}, }
@article {pmid32622275, year = {2020}, author = {Seuntjens, D and Carvajal Arroyo, JM and Van Tendeloo, M and Chatzigiannidou, I and Molina, J and Nop, S and Boon, N and Vlaeminck, SE}, title = {Mainstream partial nitritation/anammox with integrated fixed-film activated sludge: Combined aeration and floc retention time control strategies limit nitrate production.}, journal = {Bioresource technology}, volume = {314}, number = {}, pages = {123711}, doi = {10.1016/j.biortech.2020.123711}, pmid = {32622275}, issn = {1873-2976}, mesh = {*Ammonium Compounds ; Bioreactors ; Nitrites ; Nitrogen ; Oxidation-Reduction ; *Sewage ; }, abstract = {Implementation of mainstream partial nitritation/anammox (PN/A) can lead to more sustainable and cost-effective sewage treatment. For mainstream PN/A reactor, an integrated fixed-film activated sludge (IFAS) was operated (26 °C). The effects of floccular aerobic sludge retention time (AerSRTfloc), a novel aeration strategy, and N-loading rate were tested to optimize the operational strategy. The best performance was observed with a low, but sufficient AerSRTfloc (~7d) and continuous aeration with two alternating dissolved oxygen setpoints: 10 min at 0.07-0.13 mg O2 L[-1] and 5 min at 0.27-0.43 mg O2 L[-1]. Nitrogen removal rates were 122 ± 23 mg N L[-1] d[-1], and removal efficiencies 73 ± 13%. These conditions enabled flocs to act as nitrite sources while the carriers were nitrite sinks, with low abundance of nitrite oxidizing bacteria. The operational strategies in the source-sink framework can serve as a guideline for successful operation of mainstream PN/A reactors.}, }
@article {pmid32621211, year = {2021}, author = {Stricker, E and Crain, G and Rudgers, J and Sinsabaugh, R and Fernandes, V and Nelson, C and Giraldo-Silva, A and Garcia-Pichel, F and Belnap, J and Darrouzet-Nardi, A}, title = {What Could Explain δ[13]C Signatures in Biocrust Cyanobacteria of Drylands?.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {134-145}, pmid = {32621211}, issn = {1432-184X}, support = {1557135//Directorate for Biological Sciences/ ; 1557162//Directorate for Biological Sciences/ ; 1832194//Directorate for Biological Sciences/ ; 1655499//National Science Foundation/ ; }, mesh = {Carbon Cycle/*physiology ; Carbon Isotopes/*analysis ; Cyanobacteria/*metabolism ; Desert Climate ; Ecosystem ; Microbiota/physiology ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Plants/*microbiology ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Dryland ecosystems are increasing in geographic extent and contribute greatly to interannual variability in global carbon dynamics. Disentangling interactions among dominant primary producers, including plants and autotrophic microbes, can help partition their contributions to dryland C dynamics. We measured the δ[13]C signatures of biological soil crust cyanobacteria and dominant plant species (C3 and C4) across a regional scale in the southwestern USA to determine if biocrust cyanobacteria were coupled to plant productivity (using plant-derived C mixotrophically), or independent of plant activity (and therefore purely autotrophic). Cyanobacterial assemblages located next to all C3 plants and one C4 species had consistently more negative δ[13]C (by 2‰) than the cyanobacteria collected from plant interspaces or adjacent to two C4 Bouteloua grass species. The differences among cyanobacterial assemblages in δ[13]C could not be explained by cyanobacterial community composition, photosynthetic capacity, or any measured leaf or root characteristics (all slopes not different from zero). Thus, microsite differences in abiotic conditions near plants, rather than biotic interactions, remain a likely mechanism underlying the observed δ[13]C patterns to be tested experimentally.}, }
@article {pmid32621210, year = {2021}, author = {Hery, L and Guidez, A and Durand, AA and Delannay, C and Normandeau-Guimond, J and Reynaud, Y and Issaly, J and Goindin, D and Legrave, G and Gustave, J and Raffestin, S and Breurec, S and Constant, P and Dusfour, I and Guertin, C and Vega-Rúa, A}, title = {Natural Variation in Physicochemical Profiles and Bacterial Communities Associated with Aedes aegypti Breeding Sites and Larvae on Guadeloupe and French Guiana.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {93-109}, pmid = {32621210}, issn = {1432-184X}, support = {Grant ACIP 01-2016//Action Concert&#xe9;es Inter Pasteuriennes/ ; grant 2015-FED-192//Programme Op&#xe9;rationnel FEDER-Guadeloupe-Conseil R&#xe9;gional 2014-2020/ ; Stage-2018//Calmette &amp; Yersin/ ; 2017-2020//La R&#xe9;gion Guadeloupe/ ; }, mesh = {Aedes/*growth &amp; development/*microbiology ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; French Guiana ; Guadeloupe ; Larva/growth &amp; development/microbiology ; Microbiota/*genetics ; Mosquito Vectors/growth &amp; development/microbiology ; RNA, Ribosomal, 16S/genetics ; Water/*chemistry ; }, abstract = {Aedes aegypti develop in aquatic habitats in which mosquito larvae are exposed to physicochemical elements and microorganisms that may influence their life cycle and their ability to transmit arboviruses. Little is known about the natural bacterial communities associated with A. aegypti or their relation to the biotic and abiotic characteristics of their aquatic habitats. We characterized the physicochemical properties and bacterial microbiota of A. aegypti breeding sites and larvae on Guadeloupe and in French Guiana. In addition, we explored whether geographic location, the type of breeding site and physicochemical parameters influenced the microbiota associated with this mosquito species. We used large-scale 16S rRNA gene sequencing of 160 breeding sites and 147 pools of A. aegypti larvae and recorded 12 physicochemical parameters at the sampled breeding sites. Ordination plots and multiple linear regression were used to assess the influence of environmental factors on the bacterial microbiota of water and larvae. We found territory-specific differences in physicochemical properties (dissolved oxygen, conductivity) and the composition of bacterial communities in A. aegypti breeding sites that influenced the relative abundance of several bacteria genera (e.g., Methylobacterium, Roseoccocus) on the corresponding larvae. A significant fraction of the bacterial communities identified on larvae, dominated by Herbiconiux and Microvirga genera, were consistently enriched in mosquitoes regardless the location. In conclusion, territory-specific differences observed in the biotic and abiotic properties of A. aegypti breeding sites raise concern about the impact of these changes on pathogen transmission by different A. aegypti populations.}, }
@article {pmid32621209, year = {2021}, author = {Shahraki, AH and Chaganti, SR and Heath, DD}, title = {Diel Dynamics of Freshwater Bacterial Communities at Beaches in Lake Erie and Lake St. Clair, Windsor, Ontario.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {1-13}, pmid = {32621209}, issn = {1432-184X}, mesh = {Actinobacteria/genetics/*isolation &amp; purification ; Bathing Beaches ; Biodiversity ; *Environmental Monitoring ; Escherichia coli/genetics/*isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Humans ; Lakes/*microbiology ; Microbiota/*genetics ; Ontario ; Population Dynamics ; Proteobacteria/genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Seasons ; Time Factors ; Water Microbiology ; }, abstract = {Bacteria play a key role in freshwater biogeochemical cycling as well as water safety, but short-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We sampled four public beaches in southern Ontario, Canada; in June, July, and August (2016) over a 24-h (diel) cycle at 2-h intervals. Using high-throughput sequencing of 16S rRNA gene, we found substantial bi-hourly and day/night variation in the bacterial communities with considerable fluctuation in the relative abundance of Actinobacteria and Proteobacteria phyla. Moreover, relative abundance of Enterobacteriaceae (associated with potential health risk) was significantly high at night in some dial cycles. Diversity was significantly high at night across most of the diel sampling events. qPCR assays showed a substantial bi-hourly variation of Escherichia coli levels with a significant high level of E. coli at night hours in comparison with day hours and the lowest levels at noon and during the afternoon hours. Taken together, these findings highlighted a considerable short-term temporal variation of bacterial communities which helps better understanding of freshwater bacterial dynamics and their ecology. E. coli monitoring showed that multiple samples in different hours will provide more accurate picture of freshwater safety and human health risk. Graphical abstract.}, }
@article {pmid32620132, year = {2020}, author = {Wang, Y and Wang, K and Huang, L and Dong, P and Wang, S and Chen, H and Lu, Z and Hou, D and Zhang, D}, title = {Fine-scale succession patterns and assembly mechanisms of bacterial community of Litopenaeus vannamei larvae across the developmental cycle.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {106}, pmid = {32620132}, issn = {2049-2618}, support = {LY18C030002//Zhejiang Provincial Natural Science Foundation of China/International ; 31672658//National Natural Science Foundation of China/International ; 2017C110001//Agricultural Major Project of Ningbo, China/International ; LGN20C190008//Basic Public Welfare Research Project of Zhejiang Province/International ; }, mesh = {Animals ; Bacteria/*classification/genetics/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; Larva/*microbiology ; Penaeidae/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Microbiome assembly in early life may have a long-term impact on host health. Larval nursery is a crucial period that determines the success in culture of Litopenaeus vannamei, the most productive shrimp species in world aquaculture industry. However, the succession patterns and assembly mechanisms of larval shrimp bacterial community still lack characterization at a fine temporal scale. Here, using a high-frequency sampling strategy and 16S rRNA gene amplicon sequencing, we investigated dynamics of larval shrimp bacterial community and its relationship with bacterioplankton in the rearing water across the whole developmental cycle in a realistic aquaculture practice.<br><br>RESULTS: Alpha-diversity of larval shrimp bacteria showed a U-shaped pattern across the developmental cycle with the stages zoea and mysis as the valley. Correspondingly, the compositions of dominant bacterial taxa at the stages nauplius and early postlarvae were more complex than other stages. Remarkably, Rhodobacteraceae maintained the overwhelming dominance after the mouth opening of larvae (zoea I~early postlarvae). The taxonomic and phylogenetic compositions of larval bacterial community both showed stage-dependent patterns with higher rate of taxonomic turnover, suggesting that taxonomic turnover was mainly driven by temporal switching among closely related taxa (such as Rhodobacteraceae taxa). The assembly of larval bacteria was overall governed by neutral processes (dispersal among individuals and ecological drift) at all the stages, but bacterioplankton also had certain contribution during three sub-stages of zoea, when larval and water bacterial communities were most associated. Furthermore, the positive host selection for Rhodobacteraceae taxa from the rearing water during the zoea stage and its persistent dominance and large predicted contribution to metabolic potentials of organic matters at post-mouth opening stages suggest a crucial role of this family in larval microbiome and thus a potential source of probiotic candidates for shrimp larval nursery.<br><br>CONCLUSIONS: Our results reveal pronounced succession patterns and dynamic assembly processes of larval shrimp bacterial communities during the developmental cycle, highlighting the importance of the mouth opening stage from the perspective of microbial ecology. We also suggest the possibility and potential timing in microbial management of the rearing water for achieving the beneficial larval microbiota in the nursery practice. Video Abstract.}, }
@article {pmid32617619, year = {2021}, author = {Pinto, OHB and Costa, FS and Rodrigues, GR and da Costa, RA and da Rocha Fernandes, G and Júnior, ORP and Barreto, CC}, title = {Soil Acidobacteria Strain AB23 Resistance to Oxidative Stress Through Production of Carotenoids.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {169-179}, pmid = {32617619}, issn = {1432-184X}, support = {88881.062152/2014-01//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {Acidobacteria/drug effects/*genetics/isolation &amp; purification/*metabolism ; Carotenoids/metabolism ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Genome, Bacterial/genetics ; Hydrogen Peroxide/*toxicity ; Multigene Family/genetics ; Oxidative Stress/*physiology ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Metagenomic studies revealed the prevalence of Acidobacteria in soils, but the physiological and ecological reasons for their success are not well understood. Many Acidobacteria exhibit carotenoid-related pigments, which may be involved in their tolerance of environmental stress. The aim of this work was to investigate the role of the orange pigments produced by Acidobacteria strain AB23 isolated from a savannah-like soil and to identify putative carotenoid genes in Acidobacteria genomes. Phylogenetic analysis revealed that strain AB23 belongs to the Occallatibacter genus from the class Acidobacteriia (subdivision 1). Strain AB23 produced carotenoids in the presence of light and vitamins; however, the growth rate and biomass decreased when cells were exposed to light. The presence of carotenoids resulted in tolerance to hydrogen peroxide. Comparative genomics revealed that all members of Acidobacteriia with available genomes possess the complete gene cluster for phytoene production. Some Acidobacteriia members have an additional gene cluster that may be involved in the production of colored carotenoids. Both colored and colorless carotenoids are involved in tolerance to oxidative stress. These results show that the presence of carotenoid genes is widespread among Acidobacteriia. Light and atmospheric oxygen stimulate carotenoid synthesis, but there are other natural sources of oxidative stress in soils. Tolerance to environmental oxidative stress provided by carotenoids may offer a competitive advantage for Acidobacteria in soils.}, }
@article {pmid32615432, year = {2020}, author = {Yang, L and Hou, K and Zhang, B and Ouyang, C and Lin, A and Xu, S and Ke, D and Fang, L and Chen, Q and Wu, J and Yan, C and Lian, Y and Jiang, T and He, J and Wang, H and Fu, Y and Xiao, C and Chen, Z}, title = {Preservation of the fecal samples at ambient temperature for microbiota analysis with a cost-effective and reliable stabilizer EffcGut.}, journal = {The Science of the total environment}, volume = {741}, number = {}, pages = {140423}, doi = {10.1016/j.scitotenv.2020.140423}, pmid = {32615432}, issn = {1879-1026}, mesh = {Cost-Benefit Analysis ; Feces ; Humans ; *Microbiota ; RNA, Ribosomal, 16S ; *Specimen Handling ; Temperature ; }, abstract = {With the increasing researches on the role of gut microbiota in human health and disease, appropriate storage method of fecal samples at ambient temperature would conveniently guarantee the precise and reliable microbiota results. Nevertheless, less choice of stabilizer that is cost-efficient and feasible to be used in longer preservation period obstructed the large-scale metagenomics studies. Here, we evaluated the efficacy of a guanidine isothiocyanate-based reagent method EffcGut and compared it with the other already used storage method by means of 16S rRNA gene sequencing technology. We found that guanidine isothiocyanate-based reagent method at ambient temperature was not inferior to OMNIgene·GUT OM-200 and it could retain the similar bacterial community as that of -80 °C within 24 weeks. Furthermore, bacterial diversity and community structure difference were compared among different sample fraction (supernatant, suspension and precipitate) preserved in EffcGut and -80 °C. We found that supernatant under the preservation of EffcGut retained the similar community structure and composition as that of the low temperature preservation method.}, }
@article {pmid32615392, year = {2020}, author = {Kassaian, N and Feizi, A and Rostami, S and Aminorroaya, A and Yaran, M and Amini, M}, title = {The effects of 6 mo of supplementation with probiotics and synbiotics on gut microbiota in the adults with prediabetes: A double blind randomized clinical trial.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {79-80}, number = {}, pages = {110854}, doi = {10.1016/j.nut.2020.110854}, pmid = {32615392}, issn = {1873-1244}, mesh = {Adult ; Double-Blind Method ; Feces ; *Gastrointestinal Microbiome ; Humans ; *Prediabetic State/therapy ; *Probiotics ; RNA, Ribosomal, 16S/genetics ; *Synbiotics ; }, abstract = {OBJECTIVES: The evidence of 16S rRNA genes in the gut microbiota distinguished a higher Firmicutes-to-Bacteroidetes ratio in individuals who were obese and had diabetes than in a healthy cohort. So, it seems that the modulation of intestinal microbial ecology by pro-/pre-/synbiotics may contribute to the progression and prevention of metabolic diseases. The aim of this study was to assess the effects of probiotics and synbiotic supplementation on the modification of the intestinal microbiome in adults with prediabetes.<br><br>METHODS: In a randomized, double-blinded, placebo-controlled clinical trial, 120 patients with prediabetes were randomly assigned to consume 6 g/d of either a placebo containing maltodextrin (control) or multispecies probiotic or inulin-based synbiotic for 6 mo. Fecal samples were obtained at baseline and after 6 mo of supplementation. Dietary intake was assessed throughout the study (at baseline and after 3 and 6 mo). Total energy, macronutrients, and dietary fiber were calculated using a dietary program Nutritionist 4. DNA was extracted from fecal samples and the numbers of Clostridium perfringens (the represent of phylum Firmicutes), Bacteroides fragilis (the representative of Bacteroidetes) and Escherichia coli (as universal bacteria) were determined by quantitative real-time polymerase chain reactions (qPCR). The changes in the relative abundance of the two fecal bacteria before and after supplementation were analyzed and compared within and between groups.<br><br>RESULTS: There were no significant changes in dietary intake during the study. Six mo of supplementation with probiotics resulted in a statistically significant increase in the abundance of the B. fragilis-to-E.coli ratio (mean difference [MD] &#xb1; SE 0.47 &#xb1; 0.37, P&#xa0;=&#xa0;0.04) and decrease of the relative proportion of Firmicutes-to-Bacteroidetes representatives (MD &#xb1; SE -118.8 &#xb1; 114.6, P&#xa0;=&#xa0;0.02). Synbiotic had no significant effect on the changes in the bacteria. There were no significant differences between the three groups.<br><br>CONCLUSION: The results of this study suggest that manipulation of the human gut microbiome by using probiotics could provide a potential therapeutic approach in the prevention and management of obesity and metabolic disorders such as diabetes.}, }
@article {pmid32614521, year = {2020}, author = {Cheng, XS and Huo, YN and Fan, YY and Xiao, CX and Ouyang, XM and Liang, LY and Lin, Y and Wu, JF and Ren, JL and Guleng, B}, title = {Mindin serves as a tumour suppressor gene during colon cancer progression through MAPK/ERK signalling pathway in mice.}, journal = {Journal of cellular and molecular medicine}, volume = {24}, number = {15}, pages = {8391-8404}, pmid = {32614521}, issn = {1582-4934}, mesh = {Animals ; Cell Cycle/genetics ; Cell Line ; Cell Line, Tumor ; Cell Proliferation/genetics ; Colitis/genetics/pathology ; Colon/pathology ; Colonic Neoplasms/*genetics/pathology ; Disease Models, Animal ; Disease Progression ; Extracellular Matrix Proteins/*genetics ; Genes, Tumor Suppressor/*physiology ; Humans ; MAP Kinase Signaling System/*genetics ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; RAW 264.7 Cells ; Signal Transduction/*genetics ; }, abstract = {Mindin is important in broad spectrum of immune responses. On the other hand, we previously reported that mindin attenuated human colon cancer development by blocking angiogenesis through Egr-1-mediated regulation. However, the mice original mindin directly suppressed the syngenic colorectal cancer (CRC) growth in our recent study and we aimed to further define the role of mindin during CRC development in mice. We established the mouse syngeneic CRC CMT93 and CT26 WT cell lines with stable mindin knock-down or overexpression. These cells were also subcutaneously injected into C57BL/6 and BALB/c mice as well as established a colitis-associated colorectal cancer (CAC) mouse model treated with lentiviral-based overexpression and knocked-down of mindin. Furthermore, we generated mindin knockout mice using a CRISPR-Cas9 system with CAC model. Our data showed that overexpression of mindin suppressed cell proliferation in both of CMT93 and CT26 WT colon cancer cell lines, while the silencing of mindin promoted in vitro cell proliferation via the ERK and c-Fos pathways and cell cycle control. Moreover, the overexpression of mindin significantly suppressed in vivo tumour growth in both the subcutaneous transplantation and the AOM/DSS-induced CAC models. Consistently, the silencing of mindin reversed these in vivo observations. Expectedly, the tumour growth was promoted in the CAC model on mindin-deficient mice. Thus, mindin plays a direct tumour suppressive function during colon cancer progression and suggesting that mindin might be exploited as a therapeutic target for CRC.}, }
@article {pmid32613267, year = {2021}, author = {Douglas, AJ and Hug, LA and Katzenback, BA}, title = {Composition of the North American Wood Frog (Rana sylvatica) Bacterial Skin Microbiome and Seasonal Variation in Community Structure.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {78-92}, pmid = {32613267}, issn = {1432-184X}, support = {RGPIN-2017-04218//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Actinobacteria/classification/genetics/*isolation &amp; purification ; Animals ; Bacteroidetes/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Microbiota/genetics ; Ponds ; Proteobacteria/classification/genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Ranidae/*microbiology ; Seasons ; Skin/*microbiology ; United States ; }, abstract = {While a number of amphibian skin microbiomes have been characterized, it is unclear how these communities might vary in response to seasonal changes in the environment and the corresponding behaviors that many amphibians exhibit. Given recent studies demonstrating the importance of the skin microbiome in frog innate immune defense against pathogens, investigating how changes in the environment impact the microbial species present will provide a better understanding of conditions that may alter host susceptibility to pathogens in their environment. We sampled the bacterial skin microbiome of North American wood frogs (Rana sylvatica) from two breeding ponds in the spring, along with the bacterial community present in their vernal breeding pools, and frogs from the nearby forest floor in the summer and fall to determine whether community composition differs by sex, vernal pond site, or temporally across season (spring, summer, fall). Taxon relative abundance data reveals a profile of bacterial phyla similar to those previously described on anuran skin, with Proteobacteria, Bacteroidetes, and Actinobacteria dominating the wood frog skin microbiome. Our results indicate that sex had no significant effect on skin microbiota diversity; however, this may be due to our limited female frog sample size. Vernal pool site had a small but significant effect on skin microbiota, but skin-associated communities were more similar to each other than to the communities observed in the frogs' respective pond water. Across seasons, diversity analyses suggest that there are significant differences between the bacterial skin microbiome of frogs from spring and summer/fall groups while the average α-diversity per frog remained consistent. These results illustrate seasonal variation in wood frog skin microbiome structure and highlight the importance of considering temporal trends in an amphibian microbiome, particularly for species whose life history requires recurrent shifts in habitat and behavior.}, }
@article {pmid32610452, year = {2020}, author = {Van den Abbeele, P and Verstrepen, L and Ghyselinck, J and Albers, R and Marzorati, M and Mercenier, A}, title = {A Novel Non-Digestible, Carrot-Derived Polysaccharide (cRG-I) Selectively Modulates the Human Gut Microbiota while Promoting Gut Barrier Integrity: An Integrated in Vitro Approach.}, journal = {Nutrients}, volume = {12}, number = {7}, pages = {}, pmid = {32610452}, issn = {2072-6643}, support = {SMEi 811592//Horizon 2020/ ; Eurostars E! 10574-NIMF//European Commission/ ; }, mesh = {Bifidobacterium/metabolism ; Colon/metabolism ; Daucus carota/*chemistry ; Digestion/*drug effects ; Electric Impedance ; Fermentation ; Gastrointestinal Microbiome/*drug effects ; Host Microbial Interactions/drug effects ; Humans ; Intestinal Mucosa/drug effects ; Pectins/*pharmacology ; Prebiotics/*analysis/microbiology ; }, abstract = {Modulation of the gut microbiome as a means to improve human health has recently gained increasing interest. In this study, it was investigated whether cRG-I, a carrot-derived pectic polysaccharide, enriched in rhamnogalacturonan-I (RG-I) classifies as a potential prebiotic ingredient using novel in vitro models. First, digestion methods involving α-amylase/brush border enzymes demonstrated the non-digestibility of cRG-I by host-derived enzymes versus digestible (starch/maltose) and non-digestible controls (inulin). Then, a recently developed short-term (48 h) colonic incubation strategy was applied and revealed that cRG-I fermentation increased levels of health-promoting short-chain fatty acids (SCFA; mainly acetate and propionate) and lactate comparable but not identical to the reference prebiotic inulin. Upon upgrading this fermentation model by inclusion of a simulated mucosal environment while applying quantitative 16S-targeted Illumina sequencing, cRG-I was additionally shown to specifically stimulate operational taxonomic units (OTUs) related to health-associated species such as Bifidobacterium longum, Bifidobacterium adolescentis, Bacteroides dorei, Bacteroides ovatus, Roseburia hominis, Faecalibacterium prausnitzii, and Eubacterium hallii. Finally, in a novel model to assess host-microbe interactions (Caco-2/peripheral blood mononuclear cells (PBMC) co-culture) fermented cRG-I increased barrier integrity while decreasing markers for inflammation. In conclusion, by using novel in vitro models, cRG-I was identified as a promising prebiotic candidate to proceed to clinical studies.}, }
@article {pmid32607236, year = {2020}, author = {Skarżyńska, E and Wilczyńska, P and Kiersztyn, B and Żytyńska-Daniluk, J and Jakimiuk, A and Lisowska-Myjak, B}, title = {Comparison of protease and aminopeptidase activities in meconium: A pilot study.}, journal = {Biomedical reports}, volume = {13}, number = {2}, pages = {7}, pmid = {32607236}, issn = {2049-9434}, abstract = {The successive accumulation of proteases and aminopeptidases in meconium are important physiological components of the intrauterine environment in which a fetus develops. The aim of the present study was to assess the changes in the activities of these enzymes in meconium of healthy infants, and to investigate whether there were any statistically significant associations between activity of the enzymes of interest and the mode of delivery. The activities of proteases and aminopeptidases were determined in meconium portions (n=110) using the substrates BODIPY FL casein and L-leucine-7-amido-4-methylcoumarin hydrochloride, respectively. Serial meconium samples (2-5 per neonate) were collected from healthy infants born vaginally (n=14), and by a cesarean section (n=16). Protease activity (10[4] RFU/h) was lower in the first meconium sample compared with the final sample from the same infant (3.99±2.03 vs. 5.76±2.24, respectively, mean ± standard deviation; P=0.004). Conversely, there was no significant difference in aminopeptidase activity (10[3] nM/l/h) between consecutive meconium samples (P=0.702). The ratios of the first-meconium sample enzyme activity to the last-meconium sample enzyme activity were lower for proteases compared with aminopeptidases (0.76±0.48 vs. 1.35±1.04, respectively mean ± standard deviation; P=0.014), and sustained in the infants born by a cesarean section (P=0.008). Spearman's correlation coefficient analysis between the first and last meconium samples showed the correlation increased in the infants born vaginally compared with the rest of the infants (proteases, R=0.618 vs. R=0.314; aminopeptidases, R=0.688 vs. R=0.566). Aminopeptidase activity did not exhibit any notable dynamic changes during meconium accumulation in the fetal intestine. In infants born vaginally compared with those born by a cesarean section, the activity of both proteases and aminopeptidases in the first meconium sample showed an improved correlation with the activity of the final meconium sample. This may suggest that in the intrauterine environment, during accumulation of meconium in the digestive tract of the fetus, the activity and/or levels of these enzymes and the substrates they catalyze were more stable in newborns born vaginally compared with infants born by caesarean section.}, }
@article {pmid32606027, year = {2020}, author = {Altamia, MA and Lin, Z and Trindade-Silva, AE and Uy, ID and Shipway, JR and Wilke, DV and Concepcion, GP and Distel, DL and Schmidt, EW and Haygood, MG}, title = {Secondary Metabolism in the Gill Microbiota of Shipworms (Teredinidae) as Revealed by Comparison of Metagenomes and Nearly Complete Symbiont Genomes.}, journal = {mSystems}, volume = {5}, number = {3}, pages = {}, pmid = {32606027}, issn = {2379-5077}, support = {R35 GM122521/GM/NIGMS NIH HHS/United States ; U01 TW008163/TW/FIC NIH HHS/United States ; U19 TW008163/TW/FIC NIH HHS/United States ; }, abstract = {Shipworms play critical roles in recycling wood in the sea. Symbiotic bacteria supply enzymes that the organisms need for nutrition and wood degradation. Some of these bacteria have been grown in pure culture and have the capacity to make many secondary metabolites. However, little is known about whether such secondary metabolite pathways are represented in the symbiont communities within their hosts. In addition, little has been reported about the patterns of host-symbiont co-occurrence. Here, we collected shipworms from the United States, the Philippines, and Brazil and cultivated symbiotic bacteria from their gills. We analyzed sequences from 22 shipworm gill metagenomes from seven shipworm species and from 23 cultivated symbiont isolates. Using (meta)genome sequencing, we demonstrate that the cultivated isolates represent all the major bacterial symbiont species and strains in shipworm gills. We show that the bacterial symbionts are distributed among shipworm hosts in consistent, predictable patterns. The symbiotic bacteria harbor many gene cluster families (GCFs) for biosynthesis of bioactive secondary metabolites, only <5% of which match previously described biosynthetic pathways. Because we were able to cultivate the symbionts and to sequence their genomes, we can definitively enumerate the biosynthetic pathways in these symbiont communities, showing that ∼150 of ∼200 total biosynthetic gene clusters (BGCs) present in the animal gill metagenomes are represented in our culture collection. Shipworm symbionts occur in suites that differ predictably across a wide taxonomic and geographic range of host species and collectively constitute an immense resource for the discovery of new biosynthetic pathways corresponding to bioactive secondary metabolites.IMPORTANCE We define a system in which the major symbionts that are important to host biology and to the production of secondary metabolites can be cultivated. We show that symbiotic bacteria that are critical to host nutrition and lifestyle also have an immense capacity to produce a multitude of diverse and likely novel bioactive secondary metabolites that could lead to the discovery of drugs and that these pathways are found within shipworm gills. We propose that, by shaping associated microbial communities within the host, the compounds support the ability of shipworms to degrade wood in marine environments. Because these symbionts can be cultivated and genetically manipulated, they provide a powerful model for understanding how secondary metabolism impacts microbial symbiosis.}, }
@article {pmid32605663, year = {2020}, author = {Berg, G and Rybakova, D and Fischer, D and Cernava, T and Vergès, MC and Charles, T and Chen, X and Cocolin, L and Eversole, K and Corral, GH and Kazou, M and Kinkel, L and Lange, L and Lima, N and Loy, A and Macklin, JA and Maguin, E and Mauchline, T and McClure, R and Mitter, B and Ryan, M and Sarand, I and Smidt, H and Schelkle, B and Roume, H and Kiran, GS and Selvin, J and Souza, RSC and van Overbeek, L and Singh, BK and Wagner, M and Walsh, A and Sessitsch, A and Schloter, M}, title = {Microbiome definition re-visited: old concepts and new challenges.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {103}, pmid = {32605663}, issn = {2049-2618}, support = {I 2320/FWF_/Austrian Science Fund FWF/Austria ; European Union's Horizon 2020//Horizon 2020/International ; }, mesh = {*Microbiota ; Surveys and Questionnaires ; *Terminology as Topic ; }, abstract = {The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term "microbiome." Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstract.}, }
@article {pmid32599485, year = {2020}, author = {Balan, B and Dhaulaniya, AS and Jamwal, R and Yadav, A and Kelly, S and Cannavan, A and Singh, DK}, title = {Rapid detection and quantification of sucrose adulteration in cow milk using Attenuated total reflectance-Fourier transform infrared spectroscopy coupled with multivariate analysis.}, journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy}, volume = {240}, number = {}, pages = {118628}, doi = {10.1016/j.saa.2020.118628}, pmid = {32599485}, issn = {1873-3557}, mesh = {Animals ; Cattle ; Female ; *Food Contamination/analysis ; Least-Squares Analysis ; *Milk ; Multivariate Analysis ; Spectroscopy, Fourier Transform Infrared ; Sucrose ; }, abstract = {Adulteration of milk to gain economic benefit has become a common practice in recent years. Sucrose is illegally added in milk to reconstitute its compositional requirement by improving the total solid contents. The present study is aimed to use FTIR spectroscopy in combination with multivariate chemometric modelling for the differentiation and quantification of sucrose in cow milk. Pure milk and adulterated milk spectra (0.5-7.5% w/v) were observed in the spectral region 4000-400 cm[-1]. Principal component analysis (PCA) was used for the discrimination of pure milk and adulterated milk. Soft independent modelling of class analogy (SIMCA) was able to classify test samples with a classification efficiency of 100%. Partial least square regression (PLS-R) and principle component regression (PCR) models were established for normal spectra, 1st derivative and 2nd derivative for the quantification of sucrose in milk. PLS-R model (normal spectra) in the combined wavenumber range of 1070-980 cm[-1] showed the best prediction based on parameters like coefficient of determination (R[2]) (Cal: 0.996; Val: 0.993), RMSE (Cal: 0.15% w/v; Val: 0.20% w/v), RE% (Cal: 4.9% w/v; Val: 5.1% w/v) and RPD (13.40). This method has a detection level of 0.5% w/v sucrose adulteration.}, }
@article {pmid32595912, year = {2020}, author = {Hernández, M and Planells, P and Martínez, E and Mira, A and Carda-Diéguez, M}, title = {Microbiology of molar-incisor hypomineralization lesions. A pilot study.}, journal = {Journal of oral microbiology}, volume = {12}, number = {1}, pages = {1766166}, pmid = {32595912}, issn = {2000-2297}, abstract = {Objective: An insufficient mineralization (hypomineralization) in the teeth during the maturation stage of amelogenesis cause defects in 3-44% of children. Here, we describe for the first time the microbiota associated with these defects and compared it to healthy teeth within the same subjects. Methods: Supragingival dental plaque was sampled from healthy and affected teeth from 25 children with molar-incisor hypomineralization (MIH). Total DNA was extracted and the 16S rRNA gene was sequenced by Illumina sequencing in order to describe the bacterial composition. Results: We detected a higher bacterial diversity in MIH samples, suggesting better bacterial adhesion or higher number of niches in those surfaces. We found the genera Catonella, Fusobacterium, Campylobacter, Tannerella, Centipeda, Streptobacillus, Alloprevotella and Selenomonas associated with hypomineralized teeth, whereas Rothia and Lautropia were associated with healthy sites. Conclusion: The higher protein content of MIH-affected teeth could favour colonization by proteolytic microorganisms. The over-representation of bacteria associated with endodontic infections and periodontal pathologies suggests that, in addition to promote caries development, MIH could increase the risk of other oral diseases.}, }
@article {pmid32595184, year = {2020}, author = {Morono, Y and Kubota, K and Tsukagoshi, D and Terada, T}, title = {EDTA-FISH: A Simple and Effective Approach to Reduce Non-specific Adsorption of Probes in Fluorescence in situ Hybridization (FISH) for Environmental Samples.}, journal = {Microbes and environments}, volume = {35}, number = {3}, pages = {}, pmid = {32595184}, issn = {1347-4405}, mesh = {Adsorption ; Edetic Acid/*chemistry ; Fluorescence ; Geologic Sediments/microbiology ; In Situ Hybridization, Fluorescence/*methods ; Indicators and Reagents/chemistry ; Oligonucleotide Probes/*chemistry ; Seawater/microbiology ; }, abstract = {Fluorescence in situ hybridization (FISH) is a widely used molecular technique in microbial ecology. However, the non-specific adsorption of fluorescent probes and resulting high intensity of background signals from mineral particles hampers the specific detection of microbial cells in grain-rich environmental samples, such as subseafloor sediments. We herein demonstrated that a new buffer composition containing EDTA efficiently reduced the adsorption of probes without compromising the properties of the FISH-based probing of microbes. The inclusion of a high concentration of EDTA in the buffer in our protocol provides a simple and effective approach for reducing the background in FISH for environmental samples.}, }
@article {pmid32594248, year = {2021}, author = {Sugden, S and St Clair, CC and Stein, LY}, title = {Individual and Site-Specific Variation in a Biogeographical Profile of the Coyote Gastrointestinal Microbiota.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {240-252}, pmid = {32594248}, issn = {1432-184X}, support = {RGPIN-2017-05915//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2019-04399//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Coyotes/*microbiology ; DNA, Bacterial/genetics ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Most knowledge of the vertebrate gut microbiota comes from fecal samples; due to difficulties involved in sample collection, the upper intestinal microbiota is poorly understood in wild animals despite its potential to inform broad interpretations about host-gut microbe relationships under natural conditions. Here, we used 16S rRNA gene sequencing to characterize the microbiota of wild coyotes (Canis latrans) along the gastrointestinal tract, including samples from the duodenum, jejunum, ileum, caecum, ascending and descending colon, and feces. We used this intestinal profile to (1) quantify how intestinal site and individual identity interact to shape the microbiota in an uncontrolled setting, and (2) evaluate whether the fecal microbiota adequately represent other intestinal sites. Microbial communities in the large intestine were distinct from those in the small intestine, with higher diversity and a greater abundance of anaerobic taxa. Within each of the small and large intestine, individual identity explained significantly more among-sample variation than specific intestinal sites, revealing the importance of individual variation in the microbiota of free-living animals. Fecal samples were not an adequate proxy for studying upper intestinal environments, as they contained only half the amplicon sequence variants (ASVs) present in the small intestine at three- to four-fold higher abundances. Our study is a unique biogeographical investigation of the microbiota using free-living mammals rather than livestock or laboratory organisms and provides a foundational understanding of the gastrointestinal microbiota in a wild canid.}, }
@article {pmid32592942, year = {2020}, author = {Valencia, A and Ordonez, D and Wen, D and McKenna, AM and Chang, NB and Wanielista, MP}, title = {The interaction of dissolved organic nitrogen removal and microbial abundance in iron-filings based green environmental media for stormwater treatment.}, journal = {Environmental research}, volume = {188}, number = {}, pages = {109815}, doi = {10.1016/j.envres.2020.109815}, pmid = {32592942}, issn = {1096-0953}, mesh = {*Denitrification ; Filing ; Iron ; Nitrogen ; Oxidation-Reduction ; Rain ; *Water Purification ; Water Supply ; }, abstract = {Nonpoint sources pollution from agricultural crop fields and urbanized regions oftentimes have elevated concentrations of dissolved organic nitrogen (DON) in stormwater runoff, which are difficult for microbial communities to decompose. The impact of elevated DON can be circumvented through the use of green sorption media, such as Biosorption Activated Media (BAM) and Iron-Filing Green Environmental Media (IFGEM), which, as integral parts of microbial ecology, can contribute to the decomposition of DON. To compare the fate, transport, and transformation of DON in green sorption media relative to natural soil (control), a series of fixed-bed columns, which contain natural soil, BAM, and two types of IFGEM, respectively, were constructed to compare nutrient removal efficiency under three distinct stormwater influent conditions containing nitrogen and phosphorus. The interactions among six microbial species, including ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, complete ammonia oxidation (comammox) bacteria, anaerobic ammonium oxidation (anammox) bacteria, dissimilatory nitrate reduction to ammonium bacteria, and iron-reducing bacteria, were further analyzed from microbial ecology perspectives to determine the DON impact on nutrient removal in BAM and IFGEM. Natural soil was only able to achieve adequate DON transformation at the influent condition of lower nutrient concentration. However, the two types of IFGEM showed satisfactory nutrient removals and achieved greater transformation of DON relative to BAM when treating stormwater in all three influent conditions.}, }
@article {pmid32591381, year = {2020}, author = {Luo, Y and Huang, Y and Xu, RX and Qian, B and Zhou, JW and Xia, XL}, title = {Primary and Secondary Succession Mediate the Accumulation of Biogenic Amines during Industrial Semidry Chinese Rice Wine Fermentation.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {17}, pages = {}, pmid = {32591381}, issn = {1098-5336}, mesh = {Bacteria/isolation &amp; purification ; Biogenic Amines/*metabolism ; China ; *Fermentation ; Microbiota/*physiology ; Wine/*microbiology ; }, abstract = {The use of exogenous functional microorganisms to regulate biogenic amine (BA) content is a common approach in fermentation systems. Here, to better understand the microbial traits of succession trajectories in resource-based and biotic interference systems, the BA-related primary and secondary succession were tracked during industrial semidry Chinese rice wine (CRW) fermentation. Dominant abundance and BA-associated microbial functionality based on phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) indicated that Citrobacter, Acinetobacter, Lactobacillus, Exiguobacterium, Bacillus, Pseudomonas, and Enterobacter spp. prominently contributed to the decarboxylase gene family in CRW. The expression levels of tyrosine decarboxylase (tyrDC), ornithine decarboxylase (odc), and agmatine deiminase (aguA) genes were assessed by quantitative PCR (qPCR). The transcription levels of these genes did not correlate with the BA formation rate during postfermentation, indicating that acidification and carbon source depletion upregulated the expression and microbes launch the dormancy strategy to respond to unfavorable conditions. Furthermore, microbial interference with CRW fermentation by Lactobacillus plantarum (ACBC271) and Staphylococcus xylosus (CGMCC1.8382) coinoculated at a ratio of 1:2 exhibited the best synergetic control of BA content. Spearman correlations revealed that Lactobacillus and Staphylococcus exhibited influence on BA-associated microbiota (|ρ| > 0), Exiguobacterium and Pseudomonas were strongly suppressed by Lactobacillus (ρ = -0.867 and ρ = -0.782, respectively; P < 0.05), and Staphylococcus showed the strongest inhibitory effect toward Lactobacillus (ρ = -0.115) and Citrobacter (ρ = -0.188) in the coinoculated 1:2 group. The high inhibitory effect of exogenous added strains on specific bacteria presented evidence for the obtained BA-associated contributors. Overall, this work provides important insight into the microbial traits that rely on resource usage and functional microbiota within food microbial ecology.IMPORTANCE Understanding the shifting patterns of substance usage and microbial interactions is a fundamental objective within microbiology and ecology. Analyses of primary and secondary microbial succession allow for determinations of taxonomic diversity, community traits, and functional transformations over time or after a disturbance. The kinetics of BA generation and the patterns of resource consumption, functional metagenome prediction, and microbial interactions were profiled to elucidate the equilibrium mechanism of microbial systems. Secondary succession after a disturbance triggers a change in resource usage, which in turn affects primary succession and metabolism. In this study, the functional potential of exogenous microorganisms under disturbance synergized with secondary succession strategies, including rebalancing and dormancy, which ultimately reduced BA accumulation. Thus, this succession system could facilitate the settling of essential issues with respect to microbial traits that rely on resource usage and microbial interactions that occur in natural ecosystems.}, }
@article {pmid32588072, year = {2021}, author = {Zhou, X and Wang, JT and Wang, WH and Tsui, CK and Cai, L}, title = {Changes in Bacterial and Fungal Microbiomes Associated with Tomatoes of Healthy and Infected by Fusarium oxysporum f. sp. lycopersici.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {1004-1017}, pmid = {32588072}, issn = {1432-184X}, support = {NSFC 31725001//National Natural Science Foundation of China/ ; QYZDB-SSW-SMC044//Key Research Program of Frontier Sciences,CAS/ ; }, mesh = {Bacteria/genetics ; *Fusarium/genetics ; *Solanum lycopersicum ; *Mycobiome ; Plant Diseases ; }, abstract = {Fusarium wilt of tomato caused by the pathogen Fusarium oxysporum f. sp. lycopersici (Fol) is one of the most devastating soilborne diseases of tomato. To evaluate whether microbial community composition associated with Fol-infected tomato is different from healthy tomato, we analyzed the tomato-associated microbes in both healthy and Fol-infected tomato plants at both the taxonomic and functional levels; both bacterial and fungal communities have been characterized from bulk soil, rhizosphere, rhizoplane, and endosphere of tomatoes using metabarcoding and metagenomics approaches. The microbial community (bacteria and fungi) composition of healthy tomato was significantly different from that of diseased tomato, despite similar soil physicochemical characteristics. Both fungal and bacterial diversities were significantly higher in the tomato plants that remained healthy than in those that became diseased; microbial diversities were also negatively correlated with the concentration of Fol pathogen. Network analysis revealed the microbial community of healthy tomato formed a larger and more complex network than that of diseased tomato, probably providing a more stable community beneficial to plant health. Our findings also suggested that healthy tomato contained significantly greater microbial consortia, including some well-known biocontrol agents (BCAs), and enriched more functional genes than diseased tomato. The microbial taxa enriched in healthy tomato plants are recognized as potential suppressors of Fol pathogen invasion.}, }
@article {pmid32583006, year = {2020}, author = {Mapelli, F and Riva, V and Vergani, L and Choukrallah, R and Borin, S}, title = {Unveiling the Microbiota Diversity of the Xerophyte Argania spinosa L. Skeels Root System and Residuesphere.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {822-836}, pmid = {32583006}, issn = {1432-184X}, support = {688320//Horizon 2020 Framework Programme (Research and Innovation)/ ; 20172TZHYX//MIUR-PRIN2017/ ; }, mesh = {Bacteria/*isolation &amp; purification ; *Microbiota ; Morocco ; Plant Roots/*microbiology ; *Rhizosphere ; Sapotaceae/*microbiology ; *Soil Microbiology ; Trees/microbiology ; }, abstract = {The microbiota associated to xerophyte is a "black box" that might include microbes involved in plant adaptation to the extreme conditions that characterize their habitat, like water shortage. In this work, we studied the bacterial communities inhabiting the root system of Argania spinosa L. Skeels, a tree of high economic value and ecological relevance in Northern Africa. Illumina 16S rRNA gene sequencing and cultivation techniques were applied to unravel the bacterial microbiota's structure in environmental niches associated to argan plants (i.e., root endosphere, rhizosphere, root-surrounding soil), not associated to the plant (i.e., bulk soil), and indirectly influenced by the plant being partially composed by its leafy residue and the associated microbes (i.e., residuesphere). Illumina dataset indicated that the root system portions of A. spinosa hosted different bacterial communities according to their degree of association with the plant, enriching for taxa typical of the plant microbiome. Similar alpha- and beta-diversity trends were observed for the total microbiota and its cultivable fraction, which included 371 isolates. In particular, the residuesphere was the niche with the highest bacterial diversity. The Plant Growth Promotion (PGP) potential of 219 isolates was investigated in vitro, assessing several traits related to biofertilization and biocontrol, besides the production of exopolysaccharides. Most of the multivalent isolates showing the higher PGP score were identified in the residuesphere, suggesting it as a habitat that favor their proliferation. We hypothesized that these bacteria can contribute, in partnership with the argan root system, to the litter effect played by this tree in its native arid lands.}, }
@article {pmid32582085, year = {2020}, author = {Trego, AC and Galvin, E and Sweeney, C and Dunning, S and Murphy, C and Mills, S and Nzeteu, C and Quince, C and Connelly, S and Ijaz, UZ and Collins, G}, title = {Growth and Break-Up of Methanogenic Granules Suggests Mechanisms for Biofilm and Community Development.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1126}, pmid = {32582085}, issn = {1664-302X}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Methanogenic sludge granules are densely packed, small, spherical biofilms found in anaerobic digesters used to treat industrial wastewaters, where they underpin efficient organic waste conversion and biogas production. Each granule theoretically houses representative microorganisms from all of the trophic groups implicated in the successive and interdependent reactions of the anaerobic digestion (AD) process. Information on exactly how methanogenic granules develop, and their eventual fate will be important for precision management of environmental biotechnologies. Granules from a full-scale bioreactor were size-separated into small (0.6-1 mm), medium (1-1.4 mm), and large (1.4-1.8 mm) size fractions. Twelve laboratory-scale bioreactors were operated using either small, medium, or large granules, or unfractionated sludge. After >50 days of operation, the granule size distribution in each of the small, medium, and large bioreactor sets had diversified beyond-to both bigger and smaller than-the size fraction used for inoculation. Interestingly, extra-small (XS; <0.6 mm) granules were observed, and retained in all of the bioreactors, suggesting the continuous nature of granulation, and/or the breakage of larger granules into XS bits. Moreover, evidence suggested that even granules with small diameters could break. "New" granules from each emerging size were analyzed by studying community structure based on high-throughput 16S rRNA gene sequencing. Methanobacterium, Aminobacterium, Propionibacteriaceae, and Desulfovibrio represented the majority of the community in new granules. H2-using, and not acetoclastic, methanogens appeared more important, and were associated with abundant syntrophic bacteria. Multivariate integration (MINT) analyses identified distinct discriminant taxa responsible for shaping the microbial communities in different-sized granules.}, }
@article {pmid32582065, year = {2020}, author = {Navarro, MOP and Dilarri, G and Simionato, AS and Grzegorczyk, K and Dealis, ML and Cano, BG and Barazetti, AR and Afonso, L and Chryssafidis, AL and Ferreira, H and Andrade, G}, title = {Determining the Targets of Fluopsin C Action on Gram-Negative and Gram-Positive Bacteria.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1076}, pmid = {32582065}, issn = {1664-302X}, abstract = {The antibiotic activity of metalloantibiotic compounds has been evaluated since the 90s, and many different modes of action were characterized. In the last decade, the effects of secondary metabolites produced by Pseudomonas aeruginosa LV strain, including a cupric compound identified as Fluopsin C, were tested against many pathogenic bacteria strains, proving their high antibiotic activity. In the present study, the bactericidal mechanisms of action of Fluopsin C and the semi-purified fraction F4A were elucidated. The results found in electron microscopy [scanning electron microscopy (SEM) and transmission electronic microscopy (TEM)] demonstrated that both Fluopsin C and F4A are affecting the cytoplasmatic membrane of Gram-positive and Gram-negative bacteria. These results were confirmed by fluorescence microscopy, where these bacteria presented permeabilization of their cytoplasmatic membranes after contact with the semi-purified fraction and pure compound. Using electronic and fluorescence microscopy, along with bacterial mutant strains with marked divisional septum, the membrane was defined as the primary target of Fluopsin C in the tested bacteria.}, }
@article {pmid32582043, year = {2020}, author = {Gill, AS and Purnell, K and Palmer, MI and Stein, J and McGuire, KL}, title = {Microbial Composition and Functional Diversity Differ Across Urban Green Infrastructure Types.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {912}, pmid = {32582043}, issn = {1664-302X}, abstract = {Functional and biogeographical properties of soil microbial communities in urban ecosystems are poorly understood despite their role in metabolic processes underlying valuable ecosystem services. The worldwide emergence of engineered habitats in urban landscapes-green roofs, bioswales, and other types of soil-based green infrastructure-highlights the importance of understanding how environmental changes affect the community assembly processes that shape urban microbial diversity and function. In this study we investigated (1) whether engineered green roofs and bioswales in New York City had distinct microbial community composition and trait-associated diversity compared to non-engineered soils in parks and tree pits, and (2) if these patterns were consistent with divergent community assembly processes associated with engineered specifications of green infrastructure habitats not present in conventional, non-engineered green infrastructure; specifically, tree pit and park lawn soils. We found that green roofs and bioswales each had distinct bacterial and fungal communities, but that community composition and diversity were not significantly associated with geographic distance, suggesting that the processes structuring these differences are related to aspects of the habitats themselves. Bioswales, and to a lesser extent green roofs, also contained increased functional potential compared to conventional GI soils, based on the diversity and abundance of taxa associated with nitrogen cycling, biodegradation, decomposition, and traits positively associated with plant growth. We discuss these results in the context of community assembly theory, concluding that urban soil microbial community composition and diversity in engineered habitats are driven largely by environmental filtering, whereas stochastic processes are more important among non-engineered soils.}, }
@article {pmid32580805, year = {2020}, author = {Garber, A and Hastie, PM and Farci, V and McGuinness, D and Bulmer, L and Alzahal, O and Murray, JMD}, title = {The effect of supplementing pony diets with yeast on 2. The faecal microbiome.}, journal = {Animal : an international journal of animal bioscience}, volume = {14}, number = {12}, pages = {2493-2502}, doi = {10.1017/S1751731120001512}, pmid = {32580805}, issn = {1751-732X}, mesh = {Animal Feed/analysis ; Animals ; Diet/veterinary ; Feces ; Horses ; Male ; *Microbiota ; *Saccharomyces cerevisiae ; }, abstract = {There is a need to develop feeding strategies to prevent the adverse effect of concentrate feeding in high-performance horses fed energy-dense diets aiming to maintain their health and welfare. The objective of this study is to determine the effect of a VistaEQ product containing 4% live yeast Saccharomyces cerevisiae (S. cerevisiae), with activity 5 × 108 colony-forming unit/g and fed 2 g/pony per day, on faecal microbial populations when supplemented with high-starch and high-fibre diets using Illumina next generation sequencing of the V3-V4 region of the 16S ribosomal RNA gene. The four treatments were allocated to eight mature Welsh section A pony geldings enrolled in a 4-period × 8 animal crossover design. Each 19-day experimental period consisted of an 18-day adaptation phase and a single collection day, followed by a 7-day wash out period. After DNA extraction from faeces and library preparation, α-diversity and linear discriminant analysis effect size were performed using 16S metagenomics pipeline in Quantitative Insights Into Microbial Ecology (QIIME™) and Galaxy/Hutlab. Differences between the groups were considered significant when linear discriminant analysis score was >2 corresponding to P < 0.05. The present study showed that S. cerevisiae used was able to induce positive changes in the equine microbiota when supplemented to a high-fibre diet: it increased relative abundance (RA) of Lachnospiraceae and Dehalobacteriaceae family members associated with a healthy core microbiome. Yeast supplementation also increased the RA of fibrolytic bacteria (Ruminococcus) when fed with a high-fibre diet and reduced the RA of lactate producing bacteria (Streptococcus) when a high-starch diet was fed. In addition, yeast increased the RA of acetic, succinic acid producing bacterial family (Succinivibrionaceae) and butyrate producing bacterial genus (Roseburia) when fed with high-starch and high-fibre diets, respectively. VistaEQ supplementation to equine diets can be potentially used to prevent acidosis and increase fibre digestibility. It may help to meet the energy requirements of performance horses while maintaining gut health.}, }
@article {pmid32577778, year = {2020}, author = {Huang, R and Zeng, J and Zhao, D and Yong, B and Yu, Z}, title = {Co-association of Two nir Denitrifiers Under the Influence of Emergent Macrophytes.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {809-821}, doi = {10.1007/s00248-020-01545-2}, pmid = {32577778}, issn = {1432-184X}, support = {31730013, 41621002, 41871096, and 31971478//National Natural Science Foundation of China/ ; 2018B43414, 2019B17814//Fundamental Research Funds for the Central Universities/ ; 2018M642147//China Postdoctoral Science Foundation/ ; 2017FY100300//Science &amp; Technology Basic Resources Investigation Program of China/ ; }, mesh = {Bacteria/*enzymology ; *Bacterial Physiological Phenomena ; China ; *Denitrification ; Lakes/*microbiology ; *Microbiota ; Nitrate Reductase/*metabolism ; Poaceae ; }, abstract = {Diverse microorganisms perform similar metabolic process in biogeochemical cycles, whereas they are found of highly genomic differentiation. Biotic interactions should be considered in any community survey of these functional groups, as they contribute to community assembly and ultimately alter ecosystem properties. Current knowledge has mainly been achieved based on functional community characterized by a single gene using co-occurrence network analysis. Biotic interactions between functionally equivalent microorganisms, however, have received much less attention. Herein, we propose the nirK- and nirS-type denitrifier communities represented by these two nitrite reductase (nir)-encoding genes, as model communities to investigate the potential interactions of two nir denitrifiers. We evaluated co-occurrence patterns and co-association network structures of nir denitrifier community from an emergent macrophyte-dominated riparian zone of highly active denitrification in Lake Taihu, China. We found a more segregated pattern in combined nir communities than in individual communities. Network analyses revealed a modularized structure of associating nir denitrifiers. An increased proportion of negative associations among combined communities relative to those of individual communities indicated potential interspecific competition between nirK and nirS denitrifiers. pH and NH4[+]-N were the most important factors driving co-occurrence and mutual exclusion between nirK and nirS denitrifiers. We also showed the topological importance of nirK denitrifiers acting as module hubs for constructing entire association networks. We revealed previously unexplored co-association relationships between nirK and nirS denitrifiers, which were previously neglected in network analyses of individual communities. Using nir denitrifier community as a model, these findings would be helpful for us to understand the biotic interactions and mechanisms underlying how functional groups co-exist in performing biogeochemical cycles.}, }
@article {pmid32576522, year = {2020}, author = {Lopetuso, LR and Quagliariello, A and Schiavoni, M and Petito, V and Russo, A and Reddel, S and Del Chierico, F and Ianiro, G and Scaldaferri, F and Neri, M and Cammarota, G and Putignani, L and Gasbarrini, A}, title = {Towards a disease-associated common trait of gut microbiota dysbiosis: The pivotal role of Akkermansia muciniphila.}, journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver}, volume = {52}, number = {9}, pages = {1002-1010}, doi = {10.1016/j.dld.2020.05.020}, pmid = {32576522}, issn = {1878-3562}, mesh = {Akkermansia/physiology ; Case-Control Studies ; Dysbiosis/metabolism/*physiopathology ; Feces/*microbiology ; Gastrointestinal Diseases/metabolism/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Intestinal Mucosa/*metabolism/microbiology ; Permeability ; Phenotype ; }, abstract = {BACKGROUND: Gut microbiota exerts a crucial role in gastrointestinal (GI) and extra-intestinal (EI) disorders. In this context, Akkermansia muciniphila is pivotal for the maintenance of host health and has been correlated with several disorders.<br><br>AIM: To explore the potential role of A. muciniphila as common dysbiotic marker linked to the disease status.<br><br>METHODS: A cohort of patients affected by GI and EI disorders was enrolled and compared to healthy controls (CTRLs). A targeted-metagenomics approach combined to unsupervised cluster and machine learning (ML) analyses provided microbiota signatures.<br><br>RESULTS: Microbiota composition was associated to disease phenotype, therapies, diet and anthropometric features, identifying phenotype and therapies as the most impacting variables on microbiota ecology. Unsupervised cluster analyses identified one cluster composed by the majority of patients. DESeq2 algorithm identified ten microbial discriminatory features of patients and CTRLs clusters. Among these microbes, Akkermansia muciniphila resulted the discriminating ML node between patients and CTRLs, independently of specific GI/EI disease or confounding effects. A. muciniphila decrease represented a transversal signature of gut microbiota alteration, showing also an inverse correlation with &#x3b1;-diversity.<br><br>CONCLUSION: Overall, A. muciniphila decline may have a crucial role in affecting microbial ecology and in discriminating patients from healthy subjects. Its grading may be considered as a gut dysbiosis feature associated to disease-related microbiota profile.}, }
@article {pmid32574158, year = {2020}, author = {Desai, C and Handley, SA and Rodgers, R and Rodriguez, C and Ordiz, MI and Manary, MJ and Holtz, LR}, title = {Growth velocity in children with Environmental Enteric Dysfunction is associated with specific bacterial and viral taxa of the gastrointestinal tract in Malawian children.}, journal = {PLoS neglected tropical diseases}, volume = {14}, number = {6}, pages = {e0008387}, pmid = {32574158}, issn = {1935-2735}, support = {R21 AI121939/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics/isolation &amp; purification/virology ; Bacteriophages/*classification/genetics/growth &amp; development/isolation &amp; purification ; Child, Preschool ; Female ; Gastrointestinal Diseases/microbiology/virology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology/*virology ; Growth Disorders/*microbiology/*virology ; Humans ; Infant ; Intestine, Small/microbiology/virology ; Malawi ; Male ; Microbial Viability ; Permeability ; RNA, Ribosomal, 16S ; }, abstract = {Environmental enteric dysfunction (EED) is characterized by diffuse villous atrophy of the small bowel. EED is strongly associated with stunting, a major public health problem linked to increased childhood morbidity and mortality. EED and subsequent stunting of linear growth are surmised to have microbial origins. To interrogate this relationship, we defined the comprehensive virome (eukaryotic virus and bacteriophage) and bacterial microbiome of a longitudinal cohort of rural Malawian children with extensive metadata and intestinal permeability testing at each time point. We found thirty bacterial taxa differentially associated with linear growth. We detected many eukaryotic viruses. Neither the total number of eukaryotic families nor a specific viral family was statistically associated with improved linear growth. We identified 3 differentially abundant bacteriophage among growth velocities. Interestingly, there was a positive correlation between bacteria and bacteriophage richness in children with subsequent adequate/moderate growth which children with subsequent poor growth lacked. This suggests that a disruption in the equilibrium between bacteria and bacteriophage communities might be associated with subsequent poor growth. Future studies of EED and stunting should include the evaluation of viral communities in addition to bacterial microbiota to understand the complete microbial ecology of these poorly understood entities.}, }
@article {pmid32572536, year = {2020}, author = {Díaz-García, L and Bugg, TDH and Jiménez, DJ}, title = {Exploring the Lignin Catabolism Potential of Soil-Derived Lignocellulolytic Microbial Consortia by a Gene-Centric Metagenomic Approach.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {885-896}, doi = {10.1007/s00248-020-01546-1}, pmid = {32572536}, issn = {1432-184X}, support = {PR.3.2018.5287//Universidad de Los Andes/ ; BB/P01738X/1//BBSRC/ ; }, mesh = {Bacteria/*enzymology/genetics ; Biomass ; Lignin/*metabolism ; *Metagenome ; Metagenomics ; *Microbial Consortia ; Panicum/microbiology ; *Soil Microbiology ; Triticum/microbiology ; Zea mays/microbiology ; }, abstract = {An exploration of the ligninolytic potential of lignocellulolytic microbial consortia can improve our understanding of the eco-enzymology of lignin conversion in nature. In this study, we aimed to detect enriched lignin-transforming enzymes on metagenomes from three soil-derived microbial consortia that were cultivated on "pre-digested" plant biomass (wheat straw, WS1-M; switchgrass, SG-M; and corn stover, CS-M). Of 60 selected enzyme-encoding genes putatively involved in lignin catabolism, 20 genes were significantly abundant in WS1-M, CS-M, and/or SG-M consortia compared with the initial forest soil inoculum metagenome (FS1). These genes could be involved in lignin oxidation (e.g., superoxide dismutases), oxidative stress responses (e.g., catalase/peroxidases), generation of protocatechuate (e.g., vanAB genes), catabolism of gentisate, catechol and 3-phenylpropionic acid (e.g., gentisate 1,2-dioxygenases, muconate cycloisomerases, and hcaAB genes), the beta-ketoadipate pathway (e.g., pcaIJ genes), and tolerance to lignocellulose-derived inhibitors (e.g., thymidylate synthases). The taxonomic affiliation of 22 selected lignin-transforming enzymes from WS1-M and CS-M consortia metagenomes revealed that Pseudomonadaceae, Alcaligenaceae, Sphingomonadaceae, Caulobacteraceae, Comamonadaceae, and Xanthomonadaceae are the key bacterial families in the catabolism of lignin. A predictive "model" was sketched out, where each microbial population has the potential to metabolize an array of aromatic compounds through different pathways, suggesting that lignin catabolism can follow a "task division" strategy. Here, we have established an association between functions and taxonomy, allowing a better understanding of lignin transformations in soil-derived lignocellulolytic microbial consortia, and pinpointing some bacterial taxa and catabolic genes as ligninolytic trait-markers.}, }
@article {pmid32572535, year = {2020}, author = {Cohen, H and McFrederick, QS and Philpott, SM}, title = {Environment Shapes the Microbiome of the Blue Orchard Bee, Osmia lignaria : RRH: Environmental Drivers of Bee Microbiome.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {897-907}, doi = {10.1007/s00248-020-01549-y}, pmid = {32572535}, issn = {1432-184X}, support = {2016-67019-25185//USDA-NIFA/ ; }, mesh = {Animals ; Bees/*microbiology ; Biodiversity ; California ; *Ecosystem ; Gardening/*methods ; *Gardens/classification ; *Microbiota ; }, abstract = {Wild bees encounter environmental microbes while foraging. While environmental context affects bee diversity, little is known about it how affects the wild bee microbiome. We used field surveys in 17 urban gardens to examine whether and how variation in local and landscape habitat features shapes the microbiome of the solitary Blue Orchard Bee, Osmia lignaria. We installed O. lignaria cocoons at each site, allowed bees to emerge and forage, then collected them. We measured local features of gardens using vegetation transects and landscape features with GIS. We found that in microbiome composition between bee individuals varied by environmental features such as natural habitat, floral resources, and bee species richness. We also found that environmental features were associated with the abundance of bacterial groups important for bee health, such as Lactobacillus. Our study highlights complex interactions between environment context, bee species diversity, and the bee-associated microbes.}, }
@article {pmid32572534, year = {2020}, author = {Arce-Rodríguez, A and Puente-Sánchez, F and Avendaño, R and Libby, E and Mora-Amador, R and Rojas-Jimenez, K and Martínez, M and Pieper, DH and Chavarría, M}, title = {Microbial Community Structure Along a Horizontal Oxygen Gradient in a Costa Rican Volcanic Influenced Acid Rock Drainage System.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {793-808}, doi = {10.1007/s00248-020-01530-9}, pmid = {32572534}, issn = {1432-184X}, support = {VI 809-B6-524//Vicerrector&#xed;a de Investigaci&#xf3;n, Universidad de Costa Rica/ ; No FI-255B-17//The Costa Rican Ministry of Science, Technology and Telecommunication (MICITT) and Federal Ministry of Education and Research (BMBF)/ ; ERC250350-IPBSL//ERC grant IPBSL/ ; CTM2016-80095-C2-1-R//Spanish Economy and Competitiveness Ministry (MINECO)/ ; }, mesh = {Archaea/*isolation &amp; purification ; Bacteria/*isolation &amp; purification ; Costa Rica ; Hydrogen-Ion Concentration ; Microbiota/*physiology ; Oxygen/*analysis ; RNA, Archaeal/analysis ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Rivers ; Volcanic Eruptions ; }, abstract = {We describe the geochemistry and microbial diversity of a pristine environment that resembles an acid rock drainage (ARD) but it is actually the result of hydrothermal and volcanic influences. We designate this environment, and other comparable sites, as volcanic influenced acid rock drainage (VARD) systems. The metal content and sulfuric acid in this ecosystem stem from the volcanic milieu and not from the product of pyrite oxidation. Based on the analysis of 16S rRNA gene amplicons, we report the microbial community structure in the pristine San Cayetano Costa Rican VARD environment (pH = 2.94-3.06, sulfate ~ 0.87-1.19 g L[-1], iron ~ 35-61 mg L[-1] (waters), and ~ 8-293 g kg[-1] (sediments)). San Cayetano was found to be dominated by microorganisms involved in the geochemical cycling of iron, sulfur, and nitrogen; however, the identity and abundance of the species changed with the oxygen content (0.40-6.06 mg L[-1]) along the river course. The hypoxic source of San Cayetano is dominated by a putative anaerobic sulfate-reducing Deltaproteobacterium. Sulfur-oxidizing bacteria such as Acidithiobacillus or Sulfobacillus are found in smaller proportions with respect to typical ARD. In the oxic downstream, we identified aerobic iron-oxidizers (Leptospirillum, Acidithrix, Ferrovum) and heterotrophic bacteria (Burkholderiaceae bacterium, Trichococcus, Acidocella). Thermoplasmatales archaea closely related to environmental phylotypes found in other ARD niches were also observed throughout the entire ecosystem. Overall, our study shows the differences and similarities in the diversity and distribution of the microbial communities between an ARD and a VARD system at the source and along the oxygen gradient that establishes on the course of the river.}, }
@article {pmid32572216, year = {2020}, author = {Li, L and Wang, S and Wang, H and Sahu, SK and Marin, B and Li, H and Xu, Y and Liang, H and Li, Z and Cheng, S and Reder, T and Çebi, Z and Wittek, S and Petersen, M and Melkonian, B and Du, H and Yang, H and Wang, J and Wong, GK and Xu, X and Liu, X and Van de Peer, Y and Melkonian, M and Liu, H}, title = {The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {9}, pages = {1220-1231}, pmid = {32572216}, issn = {2397-334X}, mesh = {*Chlorophyta/genetics ; Genome ; Phylogeny ; }, abstract = {Genome analysis of the pico-eukaryotic marine green alga Prasinoderma coloniale CCMP 1413 unveils the existence of a novel phylum within green plants (Viridiplantae), the Prasinodermophyta, which diverged before the split of Chlorophyta and Streptophyta. Structural features of the genome and gene family comparisons revealed an intermediate position of the P. coloniale genome (25.3 Mb) between the extremely compact, small genomes of picoplanktonic Mamiellophyceae (Chlorophyta) and the larger, more complex genomes of early-diverging streptophyte algae. Reconstruction of the minimal core genome of Viridiplantae allowed identification of an ancestral toolkit of transcription factors and flagellar proteins. Adaptations of P. coloniale to its deep-water, oligotrophic environment involved expansion of light-harvesting proteins, reduction of early light-induced proteins, evolution of a distinct type of C4 photosynthesis and carbon-concentrating mechanism, synthesis of the metal-complexing metabolite picolinic acid, and vitamin B1, B7 and B12 auxotrophy. The P. coloniale genome provides first insights into the dawn of green plant evolution.}, }
@article {pmid32572143, year = {2020}, author = {Ren, FR and Sun, X and Wang, TY and Yao, YL and Huang, YZ and Zhang, X and Luan, JB}, title = {Biotin provisioning by horizontally transferred genes from bacteria confers animal fitness benefits.}, journal = {The ISME journal}, volume = {14}, number = {10}, pages = {2542-2553}, pmid = {32572143}, issn = {1751-7370}, mesh = {Animals ; Bacteria/genetics ; *Biotin ; Escherichia coli ; *Hemiptera ; Symbiosis ; }, abstract = {Insect symbionts are widespread in nature and lateral gene transfer is prevalent in insect symbiosis. However, the function of horizontally transferred genes (HTGs) in insect symbiosis remains speculative, including the mechanism that enables insects to feed on plant phloem deficient in B vitamins. Previously, we found there is redundancy in biotin synthesis pathways from both whitefly Bemisia tabaci and symbiotic Hamiltonella due to the presence of whitefly HTGs. Here, we demonstrate that elimination of Hamiltonella decreased biotin levels but elevated the expression of horizontally transferred biotin genes in whiteflies. HTGs proteins exhibit specific expression patterns in specialized insect cells called bacteriocytes housing symbionts. Complementation with whitefly HTGs rescued E. coli biotin gene knockout mutants. Furthermore, silencing whitefly HTGs in Hamiltonella-infected whiteflies reduced biotin levels and hindered adult survival and fecundity, which was partially rescued by biotin supplementation. Each of horizontally transferred biotin genes are conserved in various laboratory cultures and species of whiteflies with geographically diverse distributions, which shares an evolutionary origin. We provide the first experimental evidence that biotin synthesized through acquired HTGs is important in whiteflies and may be as well in other animals. Our findings suggest that B vitamin provisioning in animal-microbe symbiosis frequently evolved from bacterial symbionts to animal hosts through horizontal gene transfer events. This study will also shed light on how the animal genomes evolve through functional transfer of genes with bacterial origin in the wider contexts of microbial ecology.}, }
@article {pmid32568403, year = {2020}, author = {Toe, LC and Kerckhof, FM and De Bodt, J and Morel, FB and Ouedraogo, JB and Kolsteren, P and Van de Wiele, T}, title = {A prebiotic-enhanced lipid-based nutrient supplement (LNSp) increases Bifidobacterium relative abundance and enhances short-chain fatty acid production in simulated colonic microbiota from undernourished infants.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {7}, pages = {}, doi = {10.1093/femsec/fiaa105}, pmid = {32568403}, issn = {1574-6941}, mesh = {Bifidobacterium ; Child ; Fatty Acids, Volatile ; Humans ; Infant ; Lipids ; *Microbiota ; Nutrients ; *Prebiotics/analysis ; }, abstract = {Undernutrition remains a public health problem in the developing world with an attributable under-five death proportion of 45%. Lower gut microbiota diversity and poor metabolic output are associated with undernutrition and new therapeutic paths may come from steering gut microbiota composition and functionality. Using a dynamic gut model, the Simulator of Human Intestinal Microbial Ecosystem (SHIME®), we investigated the effect of a lipid-based nutrient supplement enriched with prebiotics (LNSp), compared to LNS alone and control treatment, on the composition and metabolic functionality of fecal microbiota from three infants suffering from undernutrition. LNS elicited a significant increase in acetate and branched-chain fatty acid production, and a higher relative abundance of the genera Prevotella, Megasphaera, Acinetobacter, Acidaminococcus and Pseudomonas. In contrast, LNSp treatment resulted in a significant 9-fold increase in Bifidobacterium relative abundance and a decrease in that of potential pathogens and detrimental bacteria such as Enterobacteriaceae spp. and Bilophila sp. Moreover, the LNSp treatment resulted in a significantly higher production of acetate, butyrate and propionate, as compared to control and LNS. Our results suggest that provision of prebiotic-enhanced LNS to undernourished children could be a possible strategy to steer the microbiota toward a more beneficial composition and metabolic activity. Further in vivo investigations are needed to assess these effects and their repercussion on nutritional status.}, }
@article {pmid32562995, year = {2020}, author = {Rowles Iii, LS and Hossain, AI and Ramirez, I and Durst, NJ and Ward, PM and Kirisits, MJ and Araiza, I and Lawler, DF and Saleh, NB}, title = {Seasonal contamination of well-water in flood-prone colonias and other unincorporated U.S. communities.}, journal = {The Science of the total environment}, volume = {740}, number = {}, pages = {140111}, doi = {10.1016/j.scitotenv.2020.140111}, pmid = {32562995}, issn = {1879-1026}, mesh = {*Floods ; Humans ; Seasons ; Southwestern United States ; Texas ; United States ; Water Supply ; *Water Wells ; }, abstract = {Many of the six million residents of unincorporated communities in the United States depend on well-water to meet their needs. One group of unincorporated communities is the colonias, located primarily in several southwestern U.S. states. Texas is home to the largest number of these self-built communities, of mostly low-income families, lacking basic infrastructure. While some states have regulations that mandate minimum infrastructure for these communities, water and sewage systems are still lacking for many of their residents. Unprotected wells and self-built septic/cesspool systems serve as the primary infrastructure for many such colonias. This research was designed to probe how wells and septic/cesspool systems are influenced by heavy rainfall events. Such events are hypothesized to impact water quality with regard to human health. Inorganic and microbiological water quality of the wells in nine colonias located in Nueces County, Texas, were evaluated during dry and wet periods. Nueces County was selected as an example based on its flooding history and the fact that many colonias there depend entirely on well-water and septic/cesspool systems. The results demonstrate that well-water quality in these communities varies seasonally with respect to arsenic (up to 35 μg/L) and bacterial contamination (Escherichia coli), dependent on the amount of rainfall, which leaves this population vulnerable to health risks during both wet and dry periods. Microbial community analyses were also conducted on selected samples. To explore similar seasonal contamination of well-water, an analysis of unincorporated communities, flooding frequency, and arsenic contamination in wells was conducted by county throughout the United States. This nationwide analysis indicates that unincorporated communities elsewhere in the United States are likely experiencing comparable challenges for potable water access because of a confluence of socioeconomic, infrastructural, and policy realities.}, }
@article {pmid32561945, year = {2021}, author = {Rapp, D and Ross, CM and Maclean, P and Cave, VM and Brightwell, G}, title = {Investigation of On-Farm Transmission Routes for Contamination of Dairy Cows with Top 7 Escherichia coli O-Serogroups.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {67-77}, pmid = {32561945}, issn = {1432-184X}, mesh = {Animals ; Animals, Wild/microbiology ; Cattle ; Dairying ; Escherichia coli Infections/*transmission ; Farms ; Feces/microbiology ; Foodborne Diseases/*microbiology ; Molecular Typing/methods ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Shiga-Toxigenic Escherichia coli/genetics/*isolation &amp; purification ; }, abstract = {Shiga toxin-producing Escherichia coli (STEC) are foodborne bacterial pathogens, with cattle a significant reservoir for human infection. This study evaluated environmental reservoirs, intermediate hosts and key pathways that could drive the presence of Top 7 STEC (O157:H7, O26, O45, O103, O111, O121 and O145) on pasture-based dairy herds, using molecular and culture-based methods. A total of 235 composite environmental samples (including soil, bedding, pasture, stock drinking water, bird droppings and flies and faecal samples of dairy animals) were collected from two dairy farms, with four sampling events on each farm. Molecular detection revealed O26, O45, O103 and O121 as the most common O-serogroups, with the greatest occurrence in dairy animal faeces (> 91%), environments freshly contaminated with faeces (> 73%) and birds and flies (> 71%). STEC (79 isolates) were a minor population within the target O-serogroups in all sample types but were widespread in the farm environment in the summer samplings. Phylogenetic analysis of whole genome sequence data targeting single nucleotide polymorphisms revealed the presence of several clonal strains on a farm; a single STEC clonal strain could be found in several sample types concurrently, indicating the existence of more than one possible route for transmission to dairy animals and a high rate of transmission of STEC between dairy animals and wildlife. Overall, the findings improved the understanding of the ecology of the Top 7 STEC in open farm environments, which is required to develop on-farm intervention strategies controlling these zoonoses.}, }
@article {pmid32561944, year = {2020}, author = {Adomako, MO and Xue, W and Tang, M and Du, DL and Yu, FH}, title = {Synergistic Effects of Soil Microbes on Solidago canadensis Depend on Water and Nutrient Availability.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {837-845}, doi = {10.1007/s00248-020-01537-2}, pmid = {32561944}, issn = {1432-184X}, mesh = {*Microbiota ; Nutrients/*metabolism ; Soil/*chemistry ; *Soil Microbiology ; Solidago/*growth &amp; development ; Water/*metabolism ; }, abstract = {Soil microbes may greatly affect plant growth. While plants are commonly associated with diverse communities of soil microbes, complementary roles of different microbial communities that may stimulate synergistic effects on plant growth are not adequately tested. Also, such synergistic effects may vary with environmental conditions such as soil nutrient and water availability. We conducted a greenhouse experiment with a widespread clonal plant Solidago canadensis. The experiment was a factorial design with four levels of soil microbial inoculation (fresh soil inocula from grasslands in northern and southern China that were expected to differ in soil microbial composition, a mixture of the two fresh soil inocula, and a sterilized mixed inoculum control), two levels of nutrient availability (low vs. high), and two levels of water supply (low vs. high, i.e., 1376 vs. 352 mm per year). Irrespective of water supply and nutrient availability, total, aboveground, and belowground mass of S. canadensis were generally higher when the plant grew in soil inoculated with a mixture of soil microbes from the south and north of China (in the mixed inoculum treatment) than when it grew in soil inoculated with soil microbes from only the north or the south or the sterilized control. Such effects of soil microbes on total and aboveground mass were stronger under high than under low nutrient availability and also under high than under low water supply. Our results suggest that interactions of different soil microbial communities can result in a synergistic effect on plant growth and such a synergistic effect depends on environmental conditions. The findings shed light on the importance of plant-microbe interactions during the spreading of some plant species in face of increased atmospheric nutrient deposition coupled with altered rainfall pattern due to global change.}, }
@article {pmid32561583, year = {2020}, author = {Henson, MW and Lanclos, VC and Pitre, DM and Weckhorst, JL and Lucchesi, AM and Cheng, C and Temperton, B and Thrash, JC}, title = {Expanding the Diversity of Bacterioplankton Isolates and Modeling Isolation Efficacy with Large-Scale Dilution-to-Extinction Cultivation.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {17}, pages = {}, pmid = {32561583}, issn = {1098-5336}, mesh = {Bacteria/*isolation &amp; purification ; Bacteriological Techniques/*methods ; *Biodiversity ; Models, Biological ; Phytoplankton/*isolation &amp; purification ; }, abstract = {Cultivated bacterioplankton representatives from diverse lineages and locations are essential for microbiology, but the large majority of taxa either remain uncultivated or lack isolates from diverse geographic locales. We paired large-scale dilution-to-extinction (DTE) cultivation with microbial community analysis and modeling to expand the phylogenetic and geographic diversity of cultivated bacterioplankton and to evaluate DTE cultivation success. Here, we report results from 17 DTE experiments totaling 7,820 individual incubations over 3 years, yielding 328 repeatably transferable isolates. Comparison of isolates to microbial community data for source waters indicated that we successfully isolated 5% of the observed bacterioplankton community throughout the study; 43% and 26% of our isolates matched operational taxonomic units and amplicon single-nucleotide variants, respectively, within the top 50 most abundant taxa. Isolates included those from previously uncultivated clades such as SAR11 LD12 and Actinobacteria acIV, as well as geographically novel members from other ecologically important groups like SAR11 subclade IIIa, SAR116, and others, providing isolates in eight putatively new genera and seven putatively new species. Using a newly developed DTE cultivation model, we evaluated taxon viability by comparing relative abundance with cultivation success. The model (i) revealed the minimum attempts required for successful isolation of taxa amenable to growth on our media and (ii) identified possible subpopulation viability variation in abundant taxa such as SAR11 that likely impacts cultivation success. By incorporating viability in experimental design, we can now statistically constrain the effort necessary for successful cultivation of specific taxa on a defined medium.IMPORTANCE Even before the coining of the term "great plate count anomaly" in the 1980s, scientists had noted the discrepancy between the number of microorganisms observed under the microscope and the number of colonies that grew on traditional agar media. New cultivation approaches have reduced this disparity, resulting in the isolation of some of the "most wanted" bacterial lineages. Nevertheless, the vast majority of microorganisms remain uncultured, hampering progress toward answering fundamental biological questions about many important microorganisms. Furthermore, few studies have evaluated the underlying factors influencing cultivation success, limiting our ability to improve cultivation efficacy. Our work details the use of dilution-to-extinction (DTE) cultivation to expand the phylogenetic and geographic diversity of available axenic cultures. We also provide a new model of the DTE approach that uses cultivation results and natural abundance information to predict taxon-specific viability and iteratively constrain DTE experimental design to improve cultivation success.}, }
@article {pmid32561582, year = {2020}, author = {Blackwell, N and Bryce, C and Straub, D and Kappler, A and Kleindienst, S}, title = {Genomic Insights into Two Novel Fe(II)-Oxidizing Zetaproteobacteria Isolates Reveal Lifestyle Adaption to Coastal Marine Sediments.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {17}, pages = {}, pmid = {32561582}, issn = {1098-5336}, mesh = {*Adaptation, Biological ; Environment ; Ferrous Compounds/*metabolism ; *Genome, Bacterial ; Geologic Sediments/*microbiology ; Oxidation-Reduction ; Phylogeny ; Proteobacteria/*genetics ; Seawater/microbiology ; }, abstract = {The discovery of the novel Zetaproteobacteria class greatly expanded our understanding of neutrophilic, microaerophilic microbial Fe(II) oxidation in marine environments. Despite molecular techniques demonstrating their global distribution, relatively few isolates exist, especially from low-Fe(II) environments. Furthermore, the Fe(II) oxidation pathways used by Zetaproteobacteria remain poorly understood. Here, we present the genomes (>99% genome completeness) of two Zetaproteobacteria, which are the only cultivated isolates originating from typical low-Fe [porewater Fe(II), 70 to 100 μM] coastal marine sediments. The two strains share <90% average nucleotide identity (ANI) with each other and <80% ANI with any other Zetaproteobacteria genome. The closest relatives were Mariprofundus aestuarium strain CP-5 and Mariprofundus ferrinatatus strain CP-8 (96 to 98% 16S rRNA gene sequence similarity). Fe(II) oxidation of strains KV and NF is most likely mediated by the putative Fe(II) oxidase Cyc2. Interestingly, the genome of strain KV also encodes a putative multicopper oxidase, PcoAB, which could play a role in Fe(II) oxidation, a pathway found only in two other Zetaproteobacteria genomes (Ghiorsea bivora TAG-1 and SCGC AB-602-C20). The strains show potential adaptations to fluctuating O2 concentrations, indicated by the presence of both cbb3- and aa3-type cytochrome c oxidases, which are adapted to low and high O2 concentrations, respectively. This is further supported by the presence of several oxidative-stress-related genes. In summary, our results reveal the potential Fe(II) oxidation pathways employed by these two novel chemolithoautotrophic Fe(II)-oxidizing species and the lifestyle adaptations which enable the Zetaproteobacteria to survive in coastal environments with low Fe(II) and regular redox fluctuations.IMPORTANCE Until recently, the importance and relevance of Zetaproteobacteria were mainly thought to be restricted to high-Fe(II) environments, such as deep-sea hydrothermal vents. The two novel Mariprofundus isolates presented here originate from typical low-Fe(II) coastal marine sediments. As well as being low in Fe(II), these environments are often subjected to fluctuating O2 concentrations and regular mixing by wave action and bioturbation. The discovery of two novel isolates highlights the importance of these organisms in such environments, as Fe(II) oxidation has been shown to impact nutrients and trace metals. Genome analysis of these two strains further supported their lifestyle adaptation and therefore their potential preference for coastal marine sediments, as genes necessary for surviving dynamic O2 concentrations and oxidative stress were identified. Furthermore, our analyses also expand our understanding of the poorly understood Fe(II) oxidation pathways used by neutrophilic, microaerophilic Fe(II) oxidizers.}, }
@article {pmid32561577, year = {2020}, author = {Onyango, SO and De Clercq, N and Beerens, K and Van Camp, J and Desmet, T and Van de Wiele, T}, title = {Oral Microbiota Display Profound Differential Metabolic Kinetics and Community Shifts upon Incubation with Sucrose, Trehalose, Kojibiose, and Xylitol.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {16}, pages = {}, pmid = {32561577}, issn = {1098-5336}, mesh = {Bacteria/*metabolism ; Disaccharides/metabolism ; Humans ; Kinetics ; *Microbiota ; Mouth/*microbiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sucrose/metabolism ; Sugars/*metabolism ; Trehalose/metabolism ; Xylitol/*metabolism ; }, abstract = {This study compares the metabolic properties of kojibiose, trehalose, sucrose, and xylitol upon incubation with representative oral bacteria as monocultures or synthetic communities or with human salivary bacteria in a defined medium. Compared to sucrose and trehalose, kojibiose resisted metabolism during a 48-h incubation with monocultures, except for Actinomyces viscosus Incubations with Lactobacillus-based communities, as well as salivary bacteria, displayed kojibiose metabolism, yet to a lesser extent than sucrose and trehalose. Concurring with our in vitro findings, screening for carbohydrate-active enzymes revealed that only Lactobacillus spp. and A. viscosus possess enzymes from glycohydrolase (GH) families GH65 and GH15, respectively, which are associated with kojibiose metabolism. Donor-dependent differences in salivary microbiome composition were noted, and differences in pH drop during incubation indicated different rates of sugar metabolism. However, functional analysis indicated that lactate, acetate, and formate evenly dominated the metabolic profile for all sugars except for xylitol. 16S rRNA gene sequencing analysis and α-diversity markers revealed that a significant shift of the microbiome community by sugars was more pronounced in sucrose and trehalose than in kojibiose and xylitol. In Streptococcus spp., a taxon linked to cariogenesis dominated in sucrose (mean ± standard deviation, 91.8 ± 6.4%) and trehalose (55.9 ± 38.6%), representing a high diversity loss. In contrast, Streptococcus (5.1 ± 3.7%) was less abundant in kojibiose, which instead was dominated by Veillonella (26.8 ± 19.6%), while for xylitol, Neisseria (29.4 ± 19.1%) was most abundant. Overall, kojibiose and xylitol incubations stimulated cariogenic species less yet closely maintained an abundance of key phyla and genera of the salivary microbiome, suggesting that kojibiose has low cariogenic properties.IMPORTANCE This study provides a detailed scientific insight on the metabolism of a rare disaccharide, kojibiose, whose mass production has recently been made possible. While the resistance of kojibiose was established with monocultures, delayed utilization of kojibiose was observed with communities containing lactobacilli and A. viscosus as well as with complex communities of bacteria from human saliva. Kojibiose is, therefore, less metabolizable than sucrose and trehalose. Moreover, although conventional sugars cause distinct shifts in salivary microbial communities, our study has revealed that kojibiose is able to closely maintain the salivary microbiome composition, suggesting its low cariogenic properties. This study furthermore underscores the importance and relevance of microbial culture and ex vivo mixed cultures to study cariogenicity and substrate utilization; this is in sharp contrast with tests that solely rely on monocultures such as Streptococcus mutans, which clearly fail to capture complex interactions between oral microbiota.}, }
@article {pmid32558638, year = {2020}, author = {Prudence, SMM and Addington, E and Castaño-Espriu, L and Mark, DR and Pintor-Escobar, L and Russell, AH and McLean, TC}, title = {Advances in actinomycete research: an ActinoBase review of 2019.}, journal = {Microbiology (Reading, England)}, volume = {166}, number = {8}, pages = {683-694}, pmid = {32558638}, issn = {1465-2080}, support = {BB/M011216/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Actinobacteria/genetics/growth &amp; development/metabolism/*physiology ; Animals ; Bacteriological Techniques ; Biological Products/metabolism ; Biomedical Research/instrumentation/organization &amp; administration ; *Databases, Factual ; Environmental Microbiology ; Gene Expression Regulation, Bacterial ; Streptomyces/genetics/growth &amp; development/metabolism/physiology ; Symbiosis ; }, abstract = {The actinomycetes are Gram-positive bacteria belonging to the order Actinomycetales within the phylum Actinobacteria. They include members with significant economic and medical importance, for example filamentous actinomycetes such as Streptomyces species, which have a propensity to produce a plethora of bioactive secondary metabolites and form symbioses with higher organisms, such as plants and insects. Studying these bacteria is challenging, but also fascinating and very rewarding. As a Microbiology Society initiative, members of the actinomycete research community have been developing a Wikipedia-style resource, called ActinoBase, the purpose of which is to aid in the study of these filamentous bacteria. This review will highlight 10 publications from 2019 that have been of special interest to the ActinoBase community, covering 4 major components of actinomycete research: (i) development and regulation; (ii) specialized metabolites; (iii) ecology and host interactions; and (iv) technology and methodology.}, }
@article {pmid32556417, year = {2020}, author = {Fuster, M and Billard, H and Mandart, M and Steiger, J and Sime-Ngando, T and Colombet, J}, title = {Trophic Conditions Influence Widespread Distribution of Aster-Like Nanoparticles Within Aquatic Environments.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {741-745}, doi = {10.1007/s00248-020-01541-6}, pmid = {32556417}, issn = {1432-184X}, mesh = {*Ecosystem ; France ; Nanoparticles/*analysis ; Prokaryotic Cells/*physiology ; *Rivers ; }, abstract = {Aster-like nanoparticles (ALNs) are newly described femto-entities. Their ecology (e.g., geographic distribution, spatial dynamic, preferences, forcing factors) is still unknown. Here, we report that these entities, which have largely been ignored until now, can develop or maintain themselves in most aquatic environments in the Loire River catchment, France. We observed a significant influence of the trophic state on ALN ecological distributions. A positive relationship between prokaryotic abundance and ALN (r[2] = 0.72, p < 0.01) has been identified, but its exact nature remains to be clarified. Combined with their ubiquitous distribution and high abundances (up to 7.9 × 10[6] ALNs mL[-1]) recorded in our samples, this probably makes ALNs an overlooked functional component in aquatic ecosystems.}, }
@article {pmid32556393, year = {2021}, author = {Carteron, A and Beigas, M and Joly, S and Turner, BL and Laliberté, E}, title = {Temperate Forests Dominated by Arbuscular or Ectomycorrhizal Fungi Are Characterized by Strong Shifts from Saprotrophic to Mycorrhizal Fungi with Increasing Soil Depth.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {377-390}, pmid = {32556393}, issn = {1432-184X}, support = {RGPIN-2014-06106, RGPIN-2019-04537//Natural Sciences and Engineering Research Council of Canada/ ; 2016-NC-188823//Fonds de Recherche du Qu&#xe9;bec - Nature et Technologies/ ; }, mesh = {Forests ; Fungi/genetics ; *Mycorrhizae/genetics ; Soil ; Soil Microbiology ; Trees ; }, abstract = {In temperate and boreal forests, competition for soil resources between free-living saprotrophs and ectomycorrhizal (EcM) fungi has been suggested to restrict saprotrophic fungal dominance to the most superficial organic soil horizons in forests dominated by EcM trees. By contrast, lower niche overlap with arbuscular mycorrhizal (AM) fungi could allow fungal saprotrophs to maintain this dominance into deeper soil horizons in AM-dominated forests. Here we used a natural gradient of adjacent forest patches that were dominated by either AM or EcM trees, or a mixture of both to determine how fungal communities characterized with high-throughput amplicon sequencing change across organic and mineral soil horizons. We found a general shift from saprotrophic to mycorrhizal fungal dominance with increasing soil depth in all forest mycorrhizal types, especially in organic horizons. Vertical changes in soil chemistry, including pH, organic matter, exchangeable cations, and extractable phosphorus, coincided with shifts in fungal community composition. Although fungal communities and soil chemistry differed among adjacent forest mycorrhizal types, variations were stronger within a given soil profile, pointing to the importance of considering horizons when characterizing soil fungal communities. Our results also suggest that in temperate forests, vertical shifts from saprotrophic to mycorrhizal fungi within organic and mineral horizons occur similarly in both ectomycorrhizal and arbuscular mycorrhizal forests.}, }
@article {pmid32551196, year = {2020}, author = {Coil, DA and Neches, RY and Lang, JM and Jospin, G and Brown, WE and Cavalier, D and Hampton-Marcell, J and Gilbert, JA and Eisen, JA}, title = {Bacterial communities associated with cell phones and shoes.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e9235}, pmid = {32551196}, issn = {2167-8359}, abstract = {BACKGROUND: Every human being carries with them a collection of microbes, a collection that is likely both unique to that person, but also dynamic as a result of significant flux with the surrounding environment. The interaction of the human microbiome (i.e., the microbes that are found directly in contact with a person in places such as the gut, mouth, and skin) and the microbiome of accessory objects (e.g., shoes, clothing, phones, jewelry) is of potential interest to both epidemiology and the developing field of microbial forensics. Therefore, the microbiome of personal accessories are of interest because they serve as both a microbial source and sink for an individual, they may provide information about the microbial exposure experienced by an individual, and they can be sampled non-invasively.<br><br>FINDINGS: We report here a large-scale study of the microbiome found on cell phones and shoes. Cell phones serve as a potential source and sink for skin and oral microbiome, while shoes can act as sampling devices for microbial environmental experience. Using 16S rRNA gene sequencing, we characterized the microbiome of thousands of paired sets of cell phones and shoes from individuals at sporting events, museums, and other venues around the United States.<br><br>CONCLUSIONS: We place this data in the context of previous studies and demonstrate that the microbiome of phones and shoes are different. This difference is driven largely by the presence of "environmental" taxa (taxa from groups that tend to be found in places like soil) on shoes and human-associated taxa (taxa from groups that are abundant in the human microbiome) on phones. This large dataset also contains many novel taxa, highlighting the fact that much of microbial diversity remains uncharacterized, even on commonplace objects.}, }
@article {pmid32547588, year = {2020}, author = {Rantsiou, K and Giacosa, S and Pugliese, M and Englezos, V and Ferrocino, I and Río Segade, S and Monchiero, M and Gribaudo, I and Gambino, G and Gullino, ML and Rolle, L}, title = {Impact of Chemical and Alternative Fungicides Applied to Grapevine cv Nebbiolo on Microbial Ecology and Chemical-Physical Grape Characteristics at Harvest.}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {700}, pmid = {32547588}, issn = {1664-462X}, abstract = {Viticulture is a cropping system in which treatment against fungal diseases (in particular powdery and downy mildews) can be extremely frequent. Accordingly, a reduction in antimicrobial treatments and the application of environmentally-friendly compounds are becoming increasingly important for a more sustainable viticulture. In addition to their effect against pathogens, the impact of these products on the quality of the grapes is very important for the oenological industries, but unfortunately at present few data are available. We evaluated the effect of the application of biocontrol products and resistance inducers in the vineyard on the mechanical properties, microbial ecology, technological and phenolic maturity of Vitis vinifera "Nebbiolo" grapes at harvest. The yield and vigor of vines were not influenced by the treatments, nor were the production of primary and secondary metabolites. However, the active ingredients influenced the mechanical properties of the skin (hardness and thickness). A significant hardening of the skin was detected when laminarin and chito-oligosaccharides were used, and sulfur induced a thickening of the skin with potential consequences for wine quality. Furthermore, the yeast community present on grape berries was influenced by the treatments. The abundance of Aureobasidium pullulans, the dominant species on the grape berry, changed in response to the compounds used. In addition, Alternaria sp. was reduced in some treatments with a potentially positive effect on the quality and the safety of the grapes. This study provides an overview of the effect of biocontrol products and resistance inducers on microbial ecology and "Nebbiolo" grape quality, contributing to the establishment of more sustainable and effective defense strategies in viticulture.}, }
@article {pmid32546676, year = {2020}, author = {Gulino, K and Rahman, J and Badri, M and Morton, J and Bonneau, R and Ghedin, E}, title = {Initial Mapping of the New York City Wastewater Virome.}, journal = {mSystems}, volume = {5}, number = {3}, pages = {}, pmid = {32546676}, issn = {2379-5077}, abstract = {Bacteriophages are abundant members of all microbiomes studied to date, influencing microbial communities through interactions with their bacterial hosts. Despite their functional importance and ubiquity, phages have been underexplored in urban environments compared to their bacterial counterparts. We profiled the viral communities in New York City (NYC) wastewater using metagenomic data collected in November 2014 from 14 wastewater treatment plants. We show that phages accounted for the largest viral component of the sewage samples and that specific virus communities were associated with local environmental conditions within boroughs. The vast majority of the virus sequences had no homology matches in public databases, forming an average of 1,700 unique virus clusters (putative genera). These new clusters contribute to elucidating the overwhelming proportion of data that frequently goes unidentified in viral metagenomic studies. We assigned potential hosts to these phages, which appear to infect a wide range of bacterial genera, often outside their presumed host. We determined that infection networks form a modular-nested pattern, indicating that phages include a range of host specificities, from generalists to specialists, with most interactions organized into distinct groups. We identified genes in viral contigs involved in carbon and sulfur cycling, suggesting functional importance of viruses in circulating pathways and gene functions in the wastewater environment. In addition, we identified virophage genes as well as a nearly complete novel virophage genome. These findings provide an understanding of phage abundance and diversity in NYC wastewater, previously uncharacterized, and further examine geographic patterns of phage-host association in urban environments.IMPORTANCE Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment.}, }
@article {pmid32540743, year = {2020}, author = {Cahill, N and Morris, D}, title = {Recreational waters - A potential transmission route for SARS-CoV-2 to humans?.}, journal = {The Science of the total environment}, volume = {740}, number = {}, pages = {140122}, pmid = {32540743}, issn = {1879-1026}, mesh = {*Betacoronavirus ; COVID-19 ; *Coronavirus Infections/transmission ; Humans ; Pandemics ; Pneumonia, Viral ; *Recreation ; SARS-CoV-2 ; *Water Microbiology ; }, abstract = {Coronavirus disease 2019 (COVID-19), the respiratory illness caused by the novel virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has lead to high morbidity and mortality rates worldwide, has been causing major public health concerns since first detected in late 2019. Following identification of novel pathogens, questions in relation to dissemination of the pathogen and transmission routes begin to emerge. This rapidly spreading SARS-CoV-2 virus has been detected in both faecal and wastewater samples across the globe, highlighting the potential for faecal-oral transmission of the virus. As a result, concerns regarding the transmission of the virus in the environment and the risk associated with contracting the virus in recreational waters, particularly where inadequately treated wastewater is discharged, have been emerging in recent weeks. This paper highlights the need for further research to be carried out to investigate the presence, infectivity and viability of this newly identified SARS-CoV-2 virus in wastewater effluent and receiving recreational waters.}, }
@article {pmid32540193, year = {2020}, author = {Candry, P and Ulcar, B and Petrognani, C and Rabaey, K and Ganigué, R}, title = {Ethanol:propionate ratio drives product selectivity in odd-chain elongation with Clostridium kluyveri and mixed communities.}, journal = {Bioresource technology}, volume = {313}, number = {}, pages = {123651}, doi = {10.1016/j.biortech.2020.123651}, pmid = {32540193}, issn = {1873-2976}, mesh = {Caproates ; *Clostridium kluyveri ; Ethanol ; Fermentation ; Propionates ; }, abstract = {Microbial production of valerate, a five-carbon carboxylate, can occur from propionate and ethanol through a process called odd-chain elongation. The generation of even-chain compounds in this process lowers product selectivity, forming a key challenge. This study investigated factors determining product selectivity during odd-chain elongation in an odd-chain elongating mixed community and the pure culture Clostridium kluyveri DSM555. Incubations at different ratios of ethanol:propionate showed that increasing ratios (from 0.5 to 7) lowered product specificity, as evidenced by a decrease in the odd:even product ratio from 5.5 to 1.5 for C. kluyveri and from 15 to 0.8 for the mixed community. The consistency of these observations with literature data suggests that control of ethanol:propionate ratio offers a robust tool for process control in odd-chain elongation, while the flexible metabolism can also have implications for efficient use of ethanol during even-chain elongation processes.}, }
@article {pmid32539984, year = {2020}, author = {Zagdoun, M and Coeuret, G and N'Dione, M and Champomier-Vergès, MC and Chaillou, S}, title = {Large microbiota survey reveals how the microbial ecology of cooked ham is shaped by different processing steps.}, journal = {Food microbiology}, volume = {91}, number = {}, pages = {103547}, doi = {10.1016/j.fm.2020.103547}, pmid = {32539984}, issn = {1095-9998}, mesh = {Acids/analysis/metabolism ; Animals ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Cooking ; Ethanol/analysis/metabolism ; Food Handling/*methods ; Food Microbiology ; Meat Products/analysis/*microbiology ; *Microbiota/genetics ; Pork Meat/*microbiology ; Seasons ; Swine ; }, abstract = {Cooked ham production involves numerous steps shaping the microbial communities of the final product, with consequences on spoilage metabolites production. To identify the main factors driving the ecology of ham and its spoilage, we designed a study encompassing five variables related to ham production: type of storage during meat transportation, churning speed, drain-off time, slicing line and O2 packaging permeability. About 200 samples from the same facility were obtained and characterized with respect to i) their microbiota based on gyrB amplicon sequencing ii) their production of spoilage-related metabolites based on E-Nose analysis and enzymatic assays. The slicing was the most critical step, shaping two general types of microbiota according to the slicing line: one dominated by Carnobacterium divergens and another one dominated by Leuconostoc carnosum and Serratia proteamaculans. Regarding metabolites production, L. carnosum was associated to d-lactic acid, ethanol and acetic acid production, whereas Serratia proteamaculans was associated to acetic acid production. This last species prevailed with highly O2-permeable packaging. Within a given slicing line, campaign-based variations were observed, with Lactobacillus sakei, Leuconostoc mesenteroides and Carnobacterium maltaromaticum prevalent in summer. L. sakei was associated with l-lactic acid production and C. maltaromaticum with formic and acetic acid productions.}, }
@article {pmid32539232, year = {2021}, author = {Hussan, JR and Hunter, PJ}, title = {Our natural "makeup" reveals more than it hides: Modeling the skin and its microbiome.}, journal = {WIREs mechanisms of disease}, volume = {13}, number = {1}, pages = {e1497}, doi = {10.1002/wsbm.1497}, pmid = {32539232}, issn = {2692-9368}, mesh = {*Microbiota ; Skin ; }, abstract = {Skin is our primary interface with the environment. A structurally and functionally complex organ that hosts a dynamic ecosystem of microbes, and synthesizes many compounds that affect our well-being and psychosocial interactions. It is a natural platform of signal exchange between internal organs, skin resident microbes, and the environment. These interactions have gained a great deal of attention due to the increased prevalence of atopic diseases, and the co-occurrence of multiple allergic diseases related to allergic sensitization in early life. Despite significant advances in experimentally characterizing the skin, its microbial ecology, and disease phenotypes, high-levels of variability in these characteristics even for the same clinical phenotype are observed. Addressing this variability and resolving the relevant biological processes requires a systems approach. This review presents some of our current understanding of the skin, skin-immune, skin-neuroendocrine, skin-microbiome interactions, and computer-based modeling approaches to simulate this ecosystem in the context of health and disease. The review highlights the need for a systems-based understanding of this sophisticated ecosystem. This article is categorized under: Infectious Diseases > Computational Models.}, }
@article {pmid32535638, year = {2020}, author = {Cardarelli, EL and Bargar, JR and Francis, CA}, title = {Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {778-792}, doi = {10.1007/s00248-020-01534-5}, pmid = {32535638}, issn = {1432-184X}, support = {DE-AC02-76SF00515//Office of Science/ ; DE-SC0019119//U.S. Department of Energy/ ; }, mesh = {Ammonia/*metabolism ; Archaea/isolation &amp; purification/*physiology ; Colorado ; Ecosystem ; Floods ; Microbiota/*physiology ; New Mexico ; Oxidation-Reduction ; *Soil Microbiology ; Wyoming ; }, abstract = {Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (< 30 cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤ 10 m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.}, }
@article {pmid32529471, year = {2020}, author = {López-López, A and Mira, A}, title = {Shifts in Composition and Activity of Oral Biofilms After Fluoride Exposure.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {729-738}, doi = {10.1007/s00248-020-01531-8}, pmid = {32529471}, issn = {1432-184X}, support = {RTI 2018-102032-B-100//Ministerio de Ciencia y Tecnolog&#xed;a/ ; }, mesh = {Adult ; Bacteria/classification/*drug effects/genetics/metabolism ; Bacterial Physiological Phenomena/*drug effects ; Biofilms/*drug effects ; Cariostatic Agents/*pharmacology ; Dental Caries/*prevention &amp; control ; Humans ; Sodium Fluoride/*pharmacology ; Species Specificity ; }, abstract = {Oral diseases are biofilm-mediated diseases caused by imbalances in the ecology of resident microflora. Among them, dental caries (tooth decay) is considered the most common disease worldwide, and toothbrushing, which physically eliminates the oral biofilm, is the most widespread prevention strategy. Although it is well established that fluoride increases enamel resistance to acidic pH and promotes tooth remineralization, its effect on the biofilm bacterial communities' composition and metabolism is not fully understood. We have grown in vitro oral biofilms and used 16S rRNA Illumina sequencing to study the effect of fluoride on DNA- and RNA-based bacterial populations. In addition, a metatranscriptomic approach has also been performed, in which total RNA has been sequenced to study gene expression profiles in the presence/absence of 500 ppm sodium fluoride. Our data show a lower pH drop and a clear shift in total and metabolically active bacterial composition after fluoride exposure. Streptococcus oralis was the species most affected, with a 10-fold reduction in both DNA and RNA samples, whereas Rothia mucilaginosa underwent an 8-fold increase in the DNA and S. salivarius a 4- and 5-fold increase in the RNA and DNA samples, respectively. The metatranscriptomes indicated that fluoride exposure induced a dramatic shutdown of sugar metabolism, including significant under-expression of different sugar transporters, fucosidases, and a pyruvate oxidase, among others. The reduction in saccharolytic organisms and the inhibition of sugar fermentation pathways by fluoride may therefore be considered instrumental for the beneficial effect of fluoride-containing oral hygiene products.}, }
@article {pmid32525738, year = {2020}, author = {Aszalós, JM and Szabó, A and Megyes, M and Anda, D and Nagy, B and Borsodi, AK}, title = {Bacterial Diversity of a High-Altitude Permafrost Thaw Pond Located on Ojos del Salado (Dry Andes, Altiplano-Atacama Region).}, journal = {Astrobiology}, volume = {20}, number = {6}, pages = {754-765}, doi = {10.1089/ast.2018.2012}, pmid = {32525738}, issn = {1557-8070}, mesh = {*Altitude ; Bacteria/*genetics/growth &amp; development/isolation &amp; purification ; Colony Count, Microbial ; *Genetic Variation ; Geologic Sediments/microbiology ; High-Throughput Nucleotide Sequencing ; Permafrost/*microbiology ; Phylogeny ; Ponds/*microbiology ; Principal Component Analysis ; South America ; Water ; }, abstract = {Microbial ecology of permafrost, due to its ecological and astrobiological importance, has been in the focus of studies in past decades. Although permafrost is an ancient and stable environment, it is also subjected to current climate changes. Permafrost degradation often results in generation of thaw ponds, a phenomenon not only reported mainly from polar regions but also present in high-altitude permafrost environments. Our knowledge about microbial communities of thaw ponds in these unique, remote mountain habitats is sparse. This study presents the first culture collection and results of the next-generation DNA sequencing (NGS) analysis of bacterial communities inhabiting a high-altitude permafrost thaw pond. In February 2016, a permafrost thaw pond on the Ojos del Salado at 5900 m a.s.l. (meters above sea level) was sampled as part of the Hungarian Dry Andes Research Programme. A culture collection of 125 isolates was established, containing altogether 11 genera belonging to phyla Bacteroidetes, Actinobacteria, and Proteobacteria. Simplified bacterial communities with a high proportion of candidate and hitherto uncultured bacteria were revealed by Illumina MiSeq NGS. Water of the thaw pond was dominated by Bacteroidetes and Proteobacteria, while in the sediment of the lake and permafrost, members of Acidobacteria, Actinobacteria, Bacteroidetes, Patescibacteria, Proteobacteria, and Verrucomicrobia were abundant. This permafrost habitat can be interesting as a potential Mars analog.}, }
@article {pmid32525284, year = {2021}, author = {Verbeeck, K and De Vrieze, J and Pikaar, I and Verstraete, W and Rabaey, K}, title = {Assessing the potential for up-cycling recovered resources from anaerobic digestion through microbial protein production.}, journal = {Microbial biotechnology}, volume = {14}, number = {3}, pages = {897-910}, pmid = {32525284}, issn = {1751-7915}, mesh = {Anaerobiosis ; Animals ; *Biofuels ; Bioreactors ; *Manure ; Methane ; Swine ; }, abstract = {Anaerobic digesters produce biogas, a mixture of predominantly CH4 and CO2 , which is typically incinerated to recover electrical and/or thermal energy. In a context of circular economy, the CH4 and CO2 could be used as chemical feedstock in combination with ammonium from the digestate. Their combination into protein-rich bacterial, used as animal feed additive, could contribute to the ever growing global demand for nutritive protein sources and improve the overall nitrogen efficiency of the current agro- feed/food chain. In this concept, renewable CH4 and H2 can serve as carbon-neutral energy sources for the production of protein-rich cellular biomass, while assimilating and upgrading recovered ammonia from the digestate. This study evaluated the potential of producing sustainable high-quality protein additives in a decentralized way through coupling anaerobic digestion and microbial protein production using methanotrophic and hydrogenotrophic bacteria in an on-farm bioreactor. We show that a practical case digester handling liquid piggery manure, of which the energy content is supplemented for 30% with co-substrates, provides sufficient biogas to allow the subsequent microbial protein as feed production for about 37% of the number of pigs from which the manure was derived. Overall, producing microbial protein on the farm from available methane and ammonia liberated by anaerobic digesters treating manure appears economically and technically feasible within the current range of market prices existing for high-quality protein. The case of producing biomethane for grid injection and upgrading the CO2 with electrolytic hydrogen to microbial protein by means of hydrogen-oxidizing bacteria was also examined but found less attractive at the current production prices of renewable hydrogen. Our calculations show that this route is only of commercial interest if the protein value equals the value of high-value protein additives like fishmeal and if the avoided costs for nutrient removal from the digestate are taken into consideration.}, }
@article {pmid32523566, year = {2020}, author = {Taparia, T and Krijger, M and Hodgetts, J and Hendriks, M and Elphinstone, JG and van der Wolf, J}, title = {Six Multiplex TaqMan[TM]-qPCR Assays for Quantitative Diagnostics of Pseudomonas Species Causative of Bacterial Blotch Diseases of Mushrooms.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {989}, pmid = {32523566}, issn = {1664-302X}, abstract = {Bacterial blotch is a group of economically important diseases of the common button mushroom (Agaricus bisporus). Once the pathogens are introduced to a farm, mesophilic growing conditions (that are optimum for mushroom production) result in severe and widespread secondary infections. Efficient, timely and quantitative detection of the pathogens is hence critical for the design of localized control strategies and prediction of disease risk. This study describes the development of real-time TaqMan[TM] assays that allow molecular diagnosis of three currently prevalent bacterial blotch pathogens: "Pseudomonas gingeri," Pseudomonas tolaasii and (as yet uncharacterized) Pseudomonas strains (belonging to Pseudomonas salomonii and Pseudomonas edaphica). For each pathogen, assays targeting specific DNA markers on two different loci, were developed for primary detection and secondary verification. All six developed assays showed high diagnostic specificity and sensitivity when tested against a panel of 63 Pseudomonas strains and 40 other plant pathogenic bacteria. The assays demonstrated good analytical performance indicated by linearity across calibration curve (>0.95), amplification efficiency (>90%) and magnitude of amplification signal (>2.1). The limits of detection were optimized for efficient quantification in bacterial cultures, symptomatic tissue, infected casing soil and water samples from mushroom farms. Each target assay was multiplexed with two additional assays. Xanthomonas campestris was detected as an extraction control, to account for loss of DNA during sample processing. And the total Pseudomonas population was detected, to quantify the proportion of pathogenic to beneficial Pseudomonas in the soil. This ratio is speculated to be an indicator for blotch outbreaks. The multiplexed assays were successfully validated and applied by routine testing of diseased mushrooms, peat sources, casing soils, and water from commercial production units.}, }
@article {pmid32518182, year = {2020}, author = {Topçuoğlu, BD and Lesniak, NA and Ruffin, MT and Wiens, J and Schloss, PD}, title = {A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems.}, journal = {mBio}, volume = {11}, number = {3}, pages = {}, pmid = {32518182}, issn = {2150-7511}, support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; R01 CA215574/CA/NCI NIH HHS/United States ; }, mesh = {Colonic Neoplasms/diagnosis ; Feces/microbiology ; Gastrointestinal Diseases/*diagnosis ; Humans ; Linear Models ; Logistic Models ; Machine Learning/*standards ; Microbiota/*genetics ; Predictive Value of Tests ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Machine learning (ML) modeling of the human microbiome has the potential to identify microbial biomarkers and aid in the diagnosis of many diseases such as inflammatory bowel disease, diabetes, and colorectal cancer. Progress has been made toward developing ML models that predict health outcomes using bacterial abundances, but inconsistent adoption of training and evaluation methods call the validity of these models into question. Furthermore, there appears to be a preference by many researchers to favor increased model complexity over interpretability. To overcome these challenges, we trained seven models that used fecal 16S rRNA sequence data to predict the presence of colonic screen relevant neoplasias (SRNs) (n = 490 patients, 261 controls and 229 cases). We developed a reusable open-source pipeline to train, validate, and interpret ML models. To show the effect of model selection, we assessed the predictive performance, interpretability, and training time of L2-regularized logistic regression, L1- and L2-regularized support vector machines (SVM) with linear and radial basis function kernels, a decision tree, random forest, and gradient boosted trees (XGBoost). The random forest model performed best at detecting SRNs with an area under the receiver operating characteristic curve (AUROC) of 0.695 (interquartile range [IQR], 0.651 to 0.739) but was slow to train (83.2 h) and not inherently interpretable. Despite its simplicity, L2-regularized logistic regression followed random forest in predictive performance with an AUROC of 0.680 (IQR, 0.625 to 0.735), trained faster (12 min), and was inherently interpretable. Our analysis highlights the importance of choosing an ML approach based on the goal of the study, as the choice will inform expectations of performance and interpretability.IMPORTANCE Diagnosing diseases using machine learning (ML) is rapidly being adopted in microbiome studies. However, the estimated performance associated with these models is likely overoptimistic. Moreover, there is a trend toward using black box models without a discussion of the difficulty of interpreting such models when trying to identify microbial biomarkers of disease. This work represents a step toward developing more-reproducible ML practices in applying ML to microbiome research. We implement a rigorous pipeline and emphasize the importance of selecting ML models that reflect the goal of the study. These concepts are not particular to the study of human health but can also be applied to environmental microbiology studies.}, }
@article {pmid32515051, year = {2020}, author = {Koch, C and Kuchenbuch, A and Marosvölgyi, M and Weisshart, K and Harnisch, F}, title = {Label-Free Four-Dimensional Visualization of Anaerobically Growing Electroactive Biofilms.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {97}, number = {7}, pages = {737-741}, doi = {10.1002/cyto.a.24169}, pmid = {32515051}, issn = {1552-4930}, mesh = {*Biofilms ; Microscopy, Fluorescence ; }, abstract = {Light sheet fluorescence microscopy (LSFM) allows nondestructive, label-free and in vivo imaging of large specimen, even at nontransparent surfaces. We show that LSFM can be applied for label-free analyses of prokaryotes on the example of electroactive biofilms. Biofilm growth is linked to the production of current serving as measure of metabolic activity in vivo by monitoring with high spatial and temporal resolution. After 35 h of exponential growth, a homogeneous biofilm with a thickness of 9 μm was formed. This was followed by a stratification of the biofilm including the formation of 3D structures over the next 100 h. Light reflection was sufficient to visualize the biofilm structure and development over time and the terminal morphology was confirmed using fluorescence staining. This proof of concept on using LSFM for investigation of biofilms opens the door for its application in the entire field of microbial ecology. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC. on behalf of International Society for Advancement of Cytometry.}, }
@article {pmid32514926, year = {2020}, author = {McGee, CF}, title = {The effects of silver nanoparticles on the microbial nitrogen cycle: a review of the known risks.}, journal = {Environmental science and pollution research international}, volume = {27}, number = {25}, pages = {31061-31073}, doi = {10.1007/s11356-020-09548-9}, pmid = {32514926}, issn = {1614-7499}, mesh = {*Metal Nanoparticles ; Nitrogen Cycle ; Sewage ; Silver/*analysis ; Soil ; }, abstract = {The nitrogen cycle is an integral biogeochemical function for maintaining healthy environments. Nitrogen is a key nutrient that must be continuously replenished through recycling mechanisms to sustain ecosystems, disruption to which can result in compromised ecosystem functioning. Certain stages in the microbial conversion of nitrogen compounds are performed by a limited range of micro-organisms making these key functional species in ecosystems. The growing industrial use of silver nanoparticles (AgNPs) potentially poses significant risks for microbial nitrogen cycling species. AgNPs possess potent antimicrobial properties and are expected to reach a range of natural environments through several routes of exposure. Certain functional nitrogen cycling microbes have been shown to be highly susceptible to AgNP toxicity. The current literature indicates that AgNPs can negatively affect certain nitrogen fixing, nitrifying and denitrifying microbes in vitro. In vivo studies investigating the effect of AgNPs on nitrogen cycling microbial communities and nitrogen transformation rates in soil, sediment and sludge environments have also indicated disruption of these functional processes. This review provides a comprehensive description of the current state of knowledge regarding the toxicity of AgNPs to nitrogen cycling communities. The aim of the review is to highlight the most susceptible stages in the nitrogen cycle and the implications for the affected ecosystems.}, }
@article {pmid32514604, year = {2020}, author = {Ruan, Y and Wang, T and Guo, S and Ling, N and Shen, Q}, title = {Plant Grafting Shapes Complexity and Co-occurrence of Rhizobacterial Assemblages.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {643-655}, doi = {10.1007/s00248-020-01532-7}, pmid = {32514604}, issn = {1432-184X}, support = {IRT_17R56//Innovative Research Team Development Plan of the Ministry of Education of China/ ; KYT201802//Fundamental Research Funds for the Central Universities/ ; 31772398//National Nature Science Foundation of China/ ; }, mesh = {Bacteria/*isolation &amp; purification ; Citrullus/microbiology ; Cucurbitaceae/*microbiology ; Microbiota/*physiology ; Plant Roots/*microbiology ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Grafting is a basic technique which is widely used to increase yield and enhance biotic and abiotic stress tolerance in plant production. The diversity and interactions of rhizobacterial assemblages shaped by grafting are important for the growth of their hosts but remain poorly understood. To test the hypothesis that plant grafting shapes complexity and co-occurrence of rhizobacterial assemblage, four types of plants, including ungrafted bottle gourd (B), ungrafted watermelon (W), grafted watermelon with bottle gourd rootstock (W/B), and grafted bottle gourd with watermelon rootstock (B/W), were cultivated in two soil types in a greenhouse, and the rhizosphere bacterial communities were analyzed by 16S rRNA gene high-throughput sequencing. Both the soil type and grafting significantly influenced the bacterial community composition. Grafting increased bacterial within-sample diversity in both soils. Core enriched operational taxonomic units (OTUs) in the W/B rhizosphere compared with the other three treatments (B, W, and B/W) were mainly affiliated with Alphaproteobacteria, Deltaproteobacteria, and Bacteroidetes, which are likely related to methanol oxidation, methylotrophy, fermentation, and ureolysis. Co-occurrence network analysis proved that grafting increased network complexity, including the number of nodes, edges, and modules. Moreover, grafting strengthened the structural robustness of the network in the rhizosphere, while ungrafted watermelon had the lowest network robustness. Homogeneous selection played a predominant role in bacterial community assembly, and the contribution of dispersal limitation was increased in grafted watermelon with bottle gourd rootstock. Grafting increased the diversity and transformed the network topology of the bacterial community, which indicated that grafting could improve species coexistence in the watermelon rhizosphere.}, }
@article {pmid32514073, year = {2020}, author = {Murray, AE and Freudenstein, J and Gribaldo, S and Hatzenpichler, R and Hugenholtz, P and Kämpfer, P and Konstantinidis, KT and Lane, CE and Papke, RT and Parks, DH and Rossello-Mora, R and Stott, MB and Sutcliffe, IC and Thrash, JC and Venter, SN and Whitman, WB and Acinas, SG and Amann, RI and Anantharaman, K and Armengaud, J and Baker, BJ and Barco, RA and Bode, HB and Boyd, ES and Brady, CL and Carini, P and Chain, PSG and Colman, DR and DeAngelis, KM and de Los Rios, MA and Estrada-de Los Santos, P and Dunlap, CA and Eisen, JA and Emerson, D and Ettema, TJG and Eveillard, D and Girguis, PR and Hentschel, U and Hollibaugh, JT and Hug, LA and Inskeep, WP and Ivanova, EP and Klenk, HP and Li, WJ and Lloyd, KG and Löffler, FE and Makhalanyane, TP and Moser, DP and Nunoura, T and Palmer, M and Parro, V and Pedrós-Alió, C and Probst, AJ and Smits, THM and Steen, AD and Steenkamp, ET and Spang, A and Stewart, FJ and Tiedje, JM and Vandamme, P and Wagner, M and Wang, FP and Yarza, P and Hedlund, BP and Reysenbach, AL}, title = {Roadmap for naming uncultivated Archaea and Bacteria.}, journal = {Nature microbiology}, volume = {5}, number = {8}, pages = {987-994}, pmid = {32514073}, issn = {2058-5276}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; DNA, Bacterial ; Metagenome ; Phylogeny ; Prokaryotic Cells/classification ; Sequence Analysis, DNA ; Terminology as Topic ; }, abstract = {The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.}, }
@article {pmid32512474, year = {2020}, author = {Di Cesare, A and Pjevac, P and Eckert, E and Curkov, N and Miko Šparica, M and Corno, G and Orlić, S}, title = {The role of metal contamination in shaping microbial communities in heavily polluted marine sediments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {265}, number = {Pt B}, pages = {114823}, doi = {10.1016/j.envpol.2020.114823}, pmid = {32512474}, issn = {1873-6424}, mesh = {Croatia ; Environmental Monitoring ; Environmental Pollution ; Geologic Sediments ; Metals, Heavy/*analysis ; *Microbiota ; Water Pollutants, Chemical/*analysis ; }, abstract = {Microorganisms in coastal sediments are fundamental for ecosystem functioning, and regulate processes relevant in global biogeochemical cycles. Still, our understanding of the effects anthropogenic perturbation and pollution can have on microbial communities in marine sediments is limited. We surveyed the microbial diversity, and the occurrence and abundance of metal and antibiotic resistance genes is sediments collected from the Pula Bay (Croatia), one of the most significantly polluted sites along the Croatian coast. With a collection of 14 samples from the bay area, we were able to generate a detailed status quo picture of a site that only recently started a cleaning and remediation process (closing of sewage pipes and reduction of industrial activity). The concentrations of heavy metals in Pula Bay sediments are significantly higher than in pristine sediments from the Adriatic Sea, and in some cases, manifold exceed international sediment quality guidelines. While the sedimentary concentrations of heavy metals did significantly influence the abundance of the tested metal resistance genes, no strong effect of heavy metal pollution on the overall microbial community composition was observed. Like in many other marine sediments, Gammaproteobacteria, Bacteroidota and Desulfobacterota dominated the microbial community composition in most samples, and community assembly was primarily driven by water column depth and nutrient (carbon and nitrogen) availability, regardless of the degree of heavy metal pollution.}, }
@article {pmid32511085, year = {2020}, author = {Gurney, J and Azimi, S and Brown, SP and Diggle, SP}, title = {Combinatorial quorum sensing in Pseudomonas aeruginosa allows for novel cheating strategies.}, journal = {Microbiology (Reading, England)}, volume = {166}, number = {8}, pages = {777-784}, doi = {10.1099/mic.0.000941}, pmid = {32511085}, issn = {1465-2080}, mesh = {4-Butyrolactone/analogs &amp; derivatives/metabolism ; Bacterial Proteins/genetics/metabolism ; Biological Evolution ; Culture Media/metabolism ; Genetic Fitness ; Microbial Interactions ; Mutation ; Pseudomonas aeruginosa/*physiology ; Quorum Sensing/genetics/*physiology ; Signal Transduction/genetics ; }, abstract = {In the opportunistic pathogen Pseudomonas aeruginosa, quorum sensing (QS) is a social trait that is exploitable by non-cooperating cheats. Previously it has been shown that by linking QS to the production of both public and private goods, cheats can be prevented from invading populations of cooperators and this was described by Dandekar et al. (Science 2012;338:264-266) as 'a metabolic incentive to cooperate'. We hypothesized that P. aeruginosa could evolve novel cheating strategies to circumvent private goods metabolism by rewiring its combinatorial response to two QS signals (3O-C12-HSL and C4-HSL). We performed a selection experiment that cycled P. aeruginosa between public and private goods growth media and evolved an isolate that rewired its control of cooperative protease expression from a synergistic (AND-gate) response to dual-signal input to a 3O-C12-HSL-only response. We show that this isolate circumvents metabolic incentives to cooperate and acts as a combinatorial signalling cheat, with higher fitness in competition with its ancestor. Our results show three important principles: first, combinatorial QS allows for diverse social strategies to emerge; second, restrictions levied by private goods are not sufficient to explain the maintenance of cooperation in natural populations; and third, modifying combinatorial QS responses could result in important physiological outcomes in bacterial populations.}, }
@article {pmid32510910, year = {2020}, author = {Iddins, BO and Waugh, MH and Robbins, T and Cunningham, J and Graham, DE and Finn, MT}, title = {Antimicrobial Silver Touch Surfaces in an Occupational Medicine Clinic.}, journal = {Journal of occupational and environmental medicine}, volume = {62}, number = {6}, pages = {e287-e288}, pmid = {32510910}, issn = {1536-5948}, mesh = {*Anti-Infective Agents/pharmacology ; Health Facilities ; Humans ; *Occupational Medicine ; Silver/*pharmacology ; }, }
@article {pmid32510000, year = {2020}, author = {Chopra, S and Kumar, D}, title = {Ibuprofen as an emerging organic contaminant in environment, distribution and remediation.}, journal = {Heliyon}, volume = {6}, number = {6}, pages = {e04087}, pmid = {32510000}, issn = {2405-8440}, abstract = {Pharmaceutical and personal care products (PPCPs) are the one of sub-class under emerging organic contaminants (EOCs). Ibuprofen is the world's third most consumable drug. This drug enters into our water system through human pharmaceutical use. It attracts the attention of environmentalist on the basis of risk associated, presence and transformation in the environment. The detection and removal are the two key area where we need to focus. The concentration of such compounds in waterbodies detected through conventional and also by the advanced methods. This review we described the available technologies including chemical, physical and biological methods, etc used the for removal of Ibuprofen. The pure culture based method, mixed culture approach and activated sludge culture approach focused and pathway of degradation of ibuprofen was deciphered by using the various methods of structure determination. The various degradation methods used for Ibuprofen are discussed. The advanced methods coupled with physical, chemical, biological, chemical methods like ozonolysis, oxidation and adsorption, nanotechnology based methods, nanocatalysis and use of nonosensors to detect the presence of small amount in waterbodies can enhance the future degradation of this drug. It is necessary to develop the new detection methods to enhance the detection of such pollutants. With the developments in new detection methods based on GC-MS//MS, HPLC, LC/MS and nanotechnology based sensors makes easier detection of these compounds which can detect even very minute amount with great sensitivity and in less time. Also, the isolation and characterization of more potent microbial strains and nano-photocatalysis will significantly increase the future degradation of such harmful compounds from the environment.}, }
@article {pmid32508155, year = {2020}, author = {Mercer, KE and Yeruva, L and Pack, L and Graham, JL and Stanhope, KL and Chintapalli, SV and Wankhade, UD and Shankar, K and Havel, PJ and Adams, SH and Piccolo, BD}, title = {Xenometabolite signatures in the UC Davis type 2 diabetes mellitus rat model revealed using a metabolomics platform enriched with microbe-derived metabolites.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {319}, number = {2}, pages = {G157-G169}, pmid = {32508155}, issn = {1522-1547}, support = {RC1DK087307//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/International ; 6026-51000-010-05S//U.S. Department of Agriculture (USDA)/International ; R01 HL121324/HL/NHLBI NIH HHS/United States ; R01HL107256//HHS | NIH | National Heart, Lung, and Blood Institute (NHBLI)/International ; R01DK095060//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/International ; U24DK092933//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/International ; R01HL091333//HHS | NIH | National Heart, Lung, and Blood Institute (NHBLI)/International ; RO1HL121324//HHS | NIH | National Heart, Lung, and Blood Institute (NHBLI)/International ; }, mesh = {Animals ; Bacteria/classification/isolation &amp; purification ; Cecum/microbiology ; Diabetes Mellitus, Type 2/*metabolism ; Gastrointestinal Microbiome/*physiology ; Male ; Metabolic Networks and Pathways ; *Metabolomics ; Rats ; Rats, Sprague-Dawley ; }, abstract = {The gut microbiome has the potential to create or modify xenometabolites (i.e., nonhost-derived metabolites) through de novo synthesis or modification of exogenous and endogenous compounds. While there are isolated examples of xenometabolites influencing host health and disease, wide-scale characterization of these metabolites remains limited. We developed a metabolomics platform ("XenoScan") using liquid chromatography-mass spectrometry to characterize a range of known and suspected xenometabolites and their derivatives. This assay currently applies authentic standards for 190 molecules, enriched for metabolites of microbial origin. As a proof-of-principle, we characterized the cecal content xenometabolomics profile in adult male lean Sprague-Dawley (LSD) and University of California, Davis type 2 diabetes mellitus (UCD-T2DM) rats at different stages of diabetes. These results were correlated to specific bacterial species generated via shotgun metagenomic sequencing. UCD-T2DM rats had a unique xenometabolite profile compared with LSD rats, regardless of diabetes status, suggesting that at least some of the variation is associated with host genetics. Furthermore, modeling approaches revealed that several xenometabolites discriminated UCD-T2DM rats at early stages of diabetes versus those at 3 mo postdiabetes onset. Several xenometabolite hubs correlated with specific bacterial species in both LSD and UCD-T2DM rats. For example, indole-3-propionic acid negatively correlated with species within the Oscillibacter genus in UCD-T2DM rats considered to be prediabetic or recently diagnosed diabetic, in contrast to gluconic acid and trimethylamine, which were positively correlated with Oscillibacter species. The application of a xenometabolite-enriched metabolomics assay in relevant milieus will enable rapid identification of a wide variety of gut-derived metabolites, their derivatives, and their potential biochemical origins of xenometabolites in relationship to host gastrointestinal microbial ecology.NEW &amp; NOTEWORTHY We debut a liquid chromatography-mass spectrometry (LC/MS) platform called the XenoScan, which is a metabolomics platform for xenometabolites (nonself-originating metabolites). This assay has 190 in-house standards with the majority enriched for microbe-derived metabolites. As a proof-of-principle, we used the XenoScan to discriminate genetic differences from cecal samples associated with different rat lineages, in addition to characterizing diabetes progression in rat model of type 2 diabetes. Complementing microbial sequencing data with xenometabolites uncovered novel microbial metabolism in targeted organisms.}, }
@article {pmid32504423, year = {2020}, author = {Lacalle, RG and Garbisu, C and Becerril, JM}, title = {Effects of the application of an organic amendment and nanoscale zero-valent iron particles on soil Cr(VI) remediation.}, journal = {Environmental science and pollution research international}, volume = {27}, number = {25}, pages = {31726-31736}, pmid = {32504423}, issn = {1614-7499}, support = {AGL2015-64481-C2-1-R//Ministerio de Econom&#xed;a y Competitividad/ ; AGL2016-76592-R//Ministerio de Econom&#xed;a y Competitividad/ ; GV IT1018-16//Eusko Jaurlaritza/ ; PhytoSUDOE-SOE1/P5/E0189//Interreg/ ; }, mesh = {Chromium/analysis ; *Environmental Restoration and Remediation ; Iron ; Soil ; Soil Pollutants/*analysis ; }, abstract = {Chromium is considered an environmental pollutant of much concern whose toxicity depends, to a great extent, on its valence state, with Cr(VI) being more soluble, bioavailable, and toxic, compared to Cr(III). Nanoremediation is a promising strategy for the remediation of metal pollutants by changing their valence state. However, among other aspects, its effectiveness for soil remediation is seriously hampered by the interaction of nanoparticles with soil organic matter. In this study, soil was (i) amended with two doses of a municipal solid organic waste and (ii) artificially polluted with 300 mg Cr(VI) kg[-1] DW soil. After a period of aging, a nanoremediation treatment with nanoscale zero-valent iron particles (1 g nZVI kg[-1] DW soil) was applied. The efficiency of the remediation treatment was assessed in terms of Cr(VI) immobilization and recovery of soil health. The presence of the organic amendment caused (i) a decrease of redox potential, (ii) Cr(VI) immobilization via its reduction to Cr(III), (iii) a stimulation of soil microbial communities, and (iv) an improvement of soil health, compared to unamended soil. By contrast, nZVI did not have any impact on Cr(VI) immobilization nor on soil health. It was concluded that, unlike the presence of the organic amendment, nanoremediation with nZVI was not a valid option for soils polluted with Cr(VI) under our experimental conditions.}, }
@article {pmid32503635, year = {2020}, author = {Tao, X and Feng, J and Yang, Y and Wang, G and Tian, R and Fan, F and Ning, D and Bates, CT and Hale, L and Yuan, MM and Wu, L and Gao, Q and Lei, J and Schuur, EAG and Yu, J and Bracho, R and Luo, Y and Konstantinidis, KT and Johnston, ER and Cole, JR and Penton, CR and Tiedje, JM and Zhou, J}, title = {Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {84}, pmid = {32503635}, issn = {2049-2618}, support = {DE-SC0004601//U.S. Department of Energy/International ; DE-SC0010715//U.S. Department of Energy/International ; 41430856//National Natural Science Foundation of China/International ; 41877048//National Natural Science Foundation of China/International ; 41825016//National Natural Science Foundation of China/International ; }, mesh = {Alaska ; Burkholderia/metabolism ; Climate Change ; Hot Temperature ; *Lignin/metabolism ; Permafrost ; *Proteobacteria/metabolism ; Soil/chemistry ; *Soil Microbiology ; Tundra ; }, abstract = {BACKGROUND: In a warmer world, microbial decomposition of previously frozen organic carbon (C) is one of the most likely positive climate feedbacks of permafrost regions to the atmosphere. However, mechanistic understanding of microbial mediation on chemically recalcitrant C instability is limited; thus, it is crucial to identify and evaluate active decomposers of chemically recalcitrant C, which is essential for predicting C-cycle feedbacks and their relative strength of influence on climate change. Using stable isotope probing of the active layer of Arctic tundra soils after depleting soil labile C through a 975-day laboratory incubation, the identity of microbial decomposers of lignin and, their responses to warming were revealed.<br><br>RESULTS: The &#x3b2;-Proteobacteria genus Burkholderia accounted for 95.1% of total abundance of potential lignin decomposers. Consistently, Burkholderia isolated from our tundra soils could grow with lignin as the sole C source. A 2.2&#x2009;&#xb0;C increase of warming considerably increased total abundance and functional capacities of all potential lignin decomposers. In addition to Burkholderia, &#x3b1;-Proteobacteria capable of lignin decomposition (e.g. Bradyrhizobium and Methylobacterium genera) were stimulated by warming by 82-fold. Those community changes collectively doubled the priming effect, i.e., decomposition of existing C after fresh C input to soil. Consequently, warming aggravates soil C instability, as verified by microbially enabled climate-C modeling.<br><br>CONCLUSIONS: Our findings are alarming, which demonstrate that accelerated C decomposition under warming conditions will make tundra soils a larger biospheric C source than anticipated. Video Abstract.}, }
@article {pmid32502166, year = {2020}, author = {Lu, GS and LaRowe, DE and Fike, DA and Druschel, GK and Gilhooly, WP and Price, RE and Amend, JP}, title = {Bioenergetic characterization of a shallow-sea hydrothermal vent system: Milos Island, Greece.}, journal = {PloS one}, volume = {15}, number = {6}, pages = {e0234175}, pmid = {32502166}, issn = {1932-6203}, mesh = {*Energy Metabolism ; Greece ; *Hydrothermal Vents/microbiology ; Islands ; Thermodynamics ; }, abstract = {Shallow-sea hydrothermal systems, like their deep-sea and terrestrial counterparts, can serve as relatively accessible portals into the microbial ecology of subsurface environments. In this study, we determined the chemical composition of 47 sediment porewater samples along a transect from a diffuse shallow-sea hydrothermal vent to a non-thermal background area in Paleochori Bay, Milos Island, Greece. These geochemical data were combined with thermodynamic calculations to quantify potential sources of energy that may support in situ chemolithotrophy. The Gibbs energies (ΔGr) of 730 redox reactions involving 23 inorganic H-, O-, C-, N-, S-, Fe-, Mn-, and As-bearing compounds were calculated. Of these reactions, 379 were exergonic at one or more sampling locations. The greatest energy yields were from anaerobic CO oxidation with NO2- (-136 to -162 kJ/mol e-), followed by reactions in which the electron acceptor/donor pairs were O2/CO, NO3-/CO, and NO2-/H2S. When expressed as energy densities (where the concentration of the limiting reactant is taken into account), a different set of redox reactions are the most exergonic: in sediments affected by hydrothermal input, sulfide oxidation with a range of electron acceptors or nitrite reduction with different electron donors provide 85~245 J per kg of sediment, whereas in sediments less affected or unaffected by hydrothermal input, various S0 oxidation reactions and aerobic respiration reactions with several different electron donors are most energy-yielding (80~95 J per kg of sediment). A model that considers seawater mixing with hydrothermal fluids revealed that there is up to ~50 times more energy available for microorganisms that can use S0 or H2S as electron donors and NO2- or O2 as electron acceptors compared to other reactions. In addition to revealing likely metabolic pathways in the near-surface and subsurface mixing zones, thermodynamic calculations like these can help guide novel microbial cultivation efforts to isolate new species.}, }
@article {pmid32501785, year = {2020}, author = {Lee, JC and Whang, KS}, title = {Sphingomonas segetis sp. nov., isolated from spinach farming field soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {70}, number = {6}, pages = {3905-3911}, doi = {10.1099/ijsem.0.004257}, pmid = {32501785}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; *Farms ; Fatty Acids/chemistry ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; Pigmentation ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; *Soil Microbiology ; Spermidine/chemistry ; Sphingomonas/*classification ; Spinacia oleracea ; Ubiquinone/analogs &amp; derivatives/chemistry ; }, abstract = {A Gram-stain-negative bacterium, designated strain YJ09[T], was isolated from spinach farming field soil at Shinan in the Republic of Korea. Cells of strain YJ09[T] were found to be strictly aerobic, non-motile, non-spore-forming creamy-yellow rods which can grow at 20-37 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.0) and at salinities of 0-0.5 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence analysis showed that strain YJ09[T] belongs to the genus Sphingomonas with high sequence similarities to Sphingomonas parvus GP20-2 [T] (98.0 %), Sphingomonas agri HKS-06[T] (97.7 %) and Sphingomonas lutea JS5[T] (97.4 %). The results of phylogenetic analysis indicated that strain YJ09[T] formed a distinct phyletic line in the genus Sphingomonas and the results of DNA-DNA relatedness studies demonstrated that strain YJ09[T] could be separated from its closest relatives in the genus Sphingomonas. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified glycolipids, an unidentified phospholipid and sphingoglycolipid. The predominant ubiquinone and polyamine components were Q-10 and spermidine, respectively. The major fatty acids were C18:1 ω7c, C16 : 0 and C16:1 ω7c and/or iso-C15 : 0 2-OH. The DNA G+C content of this novel isolate was 65.9 mol%. On the basis of phenotypic, chemotaxonomic properties and phylogenetic analyses in this study, strain YJ09[T] is considered to represent a novel species in the genus Sphingomonas, for which the name Sphingomonas segetis sp. nov. is proposed. The type strain is YJ09[T] (=KACC 19551[T]=NBRC 113247[T]).}, }
@article {pmid32500958, year = {2020}, author = {Kundu, K and Weber, N and Griebler, C and Elsner, M}, title = {Phenotypic heterogeneity as key factor for growth and survival under oligotrophic conditions.}, journal = {Environmental microbiology}, volume = {22}, number = {8}, pages = {3339-3356}, doi = {10.1111/1462-2920.15106}, pmid = {32500958}, issn = {1462-2920}, mesh = {Adaptation, Physiological/*physiology ; Computer Simulation ; Energy Metabolism/physiology ; *Genetic Speciation ; *Micrococcaceae/cytology/growth &amp; development/metabolism ; Phenotype ; }, abstract = {Productivity-poor oligotrophic environments are plentiful on earth. Yet it is not well understood how organisms maintain population sizes under these extreme conditions. Most scenarios consider the adaptation of a single microorganism (isogenic) at the cellular level, which increases their fitness in such an environment. However, in oligotrophic environments, the adaptation of microorganisms at population level - that is, the ability of living cells to differentiate into subtypes with specialized attributes leading to the coexistence of different phenotypes in isogenic populations - remains a little-explored area of microbiology research. In this study, we performed experiments to demonstrate that an isogenic population differentiated to two subpopulations under low energy-flux in chemostats. Fluorescence cytometry and turnover rates revealed that these subpopulations differ in their nucleic acid content and metabolic activity. A mechanistic modelling framework for the dynamic adaptation of microorganisms with the consideration of their ability to switch between different phenotypes was experimentally calibrated and validated. Simulation of hypothetical scenarios suggests that responsive diversification upon a change in energy availability offers a competitive advantage over homogenous adaptation for maintaining viability and metabolic activity with time.}, }
@article {pmid32500269, year = {2020}, author = {Yang, Y and Liu, W and Zhang, Z and Grossart, HP and Gadd, GM}, title = {Microplastics provide new microbial niches in aquatic environments.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {15}, pages = {6501-6511}, pmid = {32500269}, issn = {1432-0614}, support = {2015282 and 2017388//Chinese Academy of Sciences/ ; }, mesh = {*Biofilms ; Ecosystem ; Lakes/microbiology ; *Microbial Interactions ; Microbiota/*physiology ; *Microplastics ; Rivers/microbiology ; *Water Microbiology ; Water Pollutants, Chemical ; }, abstract = {Microplastics in the biosphere are currently of great environmental concern because of their potential toxicity for aquatic biota and human health and association with pathogenic microbiota. Microplastics can occur in high abundance in all aquatic environments, including oceans, rivers and lakes. Recent findings have highlighted the role of microplastics as important vectors for microorganisms, which can form fully developed biofilms on this artificial substrate. Microplastics therefore provide new microbial niches in the aquatic environment, and the developing biofilms may significantly differ in microbial composition compared to natural free-living or particle-associated microbial populations in the surrounding water. In this article, we discuss the composition and ecological function of the microbial communities found in microplastic biofilms. The potential factors that influence the richness and diversity of such microbial microplastic communities are also evaluated. Microbe-microbe and microbe-substrate interactions in microplastic biofilms have been little studied and are not well understood. Multiomics tools together with morphological, physiological and biochemical analyses should be combined to provide a more comprehensive overview on the ecological role of microplastic biofilms. These new microbial niches have so far unknown consequences for microbial ecology and environmental processes in aquatic ecosystems. More knowledge is required on the microbial community composition of microplastic biofilms and their ecological functions in order to better evaluate consequences for the environment and animal health, including humans, especially since the worldwide abundance of microplastics is predicted to dramatically increase. Key Points • Bacteria are mainly studied in community analyses: fungi are neglected. • Microbial colonization of microplastics depends on substrate, location and time. • Community ecology is a promising approach to investigate microbial colonization. • Biodegradable plastics, and ecological roles of microplastic biofilms, need analysis.}, }
@article {pmid32499774, year = {2020}, author = {Hallin, S and Bodelier, PLE}, title = {Grand Challenges in Terrestrial Microbiology: Moving on From a Decade of Progress in Microbial Biogeochemistry.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {981}, pmid = {32499774}, issn = {1664-302X}, }
@article {pmid32499764, year = {2020}, author = {Liu, W and Graham, EB and Zhong, L and Zhang, J and Li, S and Lin, X and Feng, Y}, title = {Long-Term Stochasticity Combines With Short-Term Variability in Assembly Processes to Underlie Rice Paddy Sustainability.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {873}, pmid = {32499764}, issn = {1664-302X}, abstract = {Revealing temporal patterns of community assembly processes is important for understanding how microorganisms underlie the sustainability of agroecosystem. The ancient terraced rice paddies at Longji provide an ideal platform to study temporal dynamics of agroecosystem sustainability due to their chronosequential records of soil physicochemistry and well-archived microbial information along 630-year rice cultivation. We used statistical null models to evaluate microbial assembly processes along the soil chronosequences of Longji rice paddies through time. Stochastic and deterministic assembly processes jointly governed microbial community composition within successional eras (less than 250 years), and within-era determinism was mainly driven by soil fertility and redox conditions alone or in combination. Conversely, across successional eras (i.e., over 300 years), stochasticity linearly increased with increasing duration between eras and was eventually predominant for the whole 630 years. We suggest that the impact of stochasticity vs. determinism on assembly is timescale-dependent, and we propose that the importance of stochastic assembly of microbial community at longer timescales is due to the gradual changes in soil properties under long-term rice cultivation, which in turn contribute to the sustainability of paddy ecosystem by maintaining a diverse community of microorganisms with multi-functional traits. In total, our results indicate that knowledge on the timescales at which assembly processes govern microbial community composition is key to understanding the ecological mechanisms generating agroecosystem sustainability.}, }
@article {pmid32498175, year = {2020}, author = {Benidire, L and El Khalloufi, F and Oufdou, K and Barakat, M and Tulumello, J and Ortet, P and Heulin, T and Achouak, W}, title = {Phytobeneficial bacteria improve saline stress tolerance in Vicia faba and modulate microbial interaction network.}, journal = {The Science of the total environment}, volume = {729}, number = {}, pages = {139020}, doi = {10.1016/j.scitotenv.2020.139020}, pmid = {32498175}, issn = {1879-1026}, mesh = {Bacteria ; Humans ; Microbial Consortia ; Microbial Interactions ; Plant Roots ; RNA, Ribosomal, 16S ; Soil Microbiology ; *Vicia faba ; }, abstract = {Increased global warming, caused by climate change and human activities, will seriously hinder plant development, such as increasing salt concentrations in soils, which will limit water availability for plants. To ensure optimal plant growth under such changing conditions, microorganisms that improve plant growth and health must be integrated into agricultural practices. In the present work, we examined the fate of Vicia faba microbiota structure and interaction network upon inoculation with plant-nodulating rhizobia (Rhizobium leguminosarum RhOF125) and non-nodulating strains (Paenibacillus mucilaginosus BLA7 and Ensifer meliloti RhOL1) in the presence (or absence) of saline stress. Inoculated strains significantly improved plant tolerance to saline stress, suggesting either a direct or indirect effect on the plant response to such stress. To determine the structure of microbiota associated with V. faba, samples of the root-adhering soil (RAS), and the root tissues (RT) of seedlings inoculated (or not) with equal population size of RhOF125, BLA7 and RhOL1 strains and grown in the presence (or absence) of salt, were used to profile the microbial composition by 16S rRNA gene sequencing. The inoculation did not show a significant impact on the composition of the RT microbiota or RAS microbiota. The saline stress shifted the RAS microbiota composition, which correlated with a decrease in Enterobacteriaceae and an increase in Sphingobacterium, Chryseobacterium, Stenotrophomonas, Agrobacterium and Sinorhizobium. When the microbiota of roots and RAS are considered together, the interaction networks for each treatment are quite different and display different key populations involved in community assembly. These findings indicate that upon seed inoculation, community interaction networks rather than their composition may contribute to helping plants to better tolerate environmental stresses. The way microbial populations interfere with each other can have an impact on their functions and thus on their ability to express the genes required to help plants tolerate stresses.}, }
@article {pmid32497654, year = {2020}, author = {Nardello, LCL and Amado, PPP and Franco, DC and Cazares, RXR and Nogales, CG and Mayer, MPA and Karygianni, L and Thurnheer, T and Pinheiro, ET}, title = {Next-Generation Sequencing to Assess Potentially Active Bacteria in Endodontic Infections.}, journal = {Journal of endodontics}, volume = {46}, number = {8}, pages = {1105-1112}, doi = {10.1016/j.joen.2020.05.004}, pmid = {32497654}, issn = {1878-3554}, mesh = {Actinobacteria ; Bacteria ; *Bacterial Infections ; Clostridiales ; DNA, Bacterial ; *High-Throughput Nucleotide Sequencing ; Humans ; RNA, Ribosomal, 16S ; }, abstract = {INTRODUCTION: Because active bacteria present a higher abundance of ribosomal RNA (rRNA) than DNA (rRNA gene), the rRNA/DNA ratio of next-generation sequencing (NGS) data was measured to search for active bacteria in endodontic infections.<br><br>METHODS: Paired complementary DNA and DNA samples from 5 root canals of teeth with apical periodontitis were subjected to polymerase chain reaction with bar-coded primers amplifying the 16S rRNA gene hypervariable regions V4-V5. High-throughput sequencing was performed using MiSeq (Illumina, San Deigo, CA), and data were analyzed using Quantitative Insights Into Microbial Ecology and Human Oral Microbiome Database. Statistical analysis was performed for relative abundance of bacteria in the DNA- and rRNA-based NGS data using the Mann-Whitney test, whereas differences in the diversity and richness indexes were assessed using a nonparametric 2-sample t test (P < .05). For bacterial taxa detected in both approaches, the rRNA/DNA ratios were calculated by dividing the average abundance of individual species in the respective analysis.<br><br>RESULTS: Although no significant difference was found in the indexes of bacterial richness and diversity, the relative abundance of bacterial members varied in both analyses. Comparing rRNA with DNA data, there was a significant decrease in the relative abundance of Firmicutes (P < .05). The bacterial taxa Bacteroidales [G-2] bacterium HMT 274, Porphyromonas endodontalis, Tannerella forsythia, Alloprevotella tannerae, Prevotella intermedia, Pseudoramibacter alactolyticus, Olsenella sp. HMT 809, Olsenella sp. HMT 939, Olsenella uli, and Fusobacterium nucleatum subsp. animalis were both dominant (DNA &#x2265; 1%) and active (rRNA/DNA &#x2265; 1).<br><br>CONCLUSIONS: The integrated DNA- and rRNA-based NGS strategy was particularly important to disclose the activity of as-yet-uncultivated or difficult-to-culture bacteria in endodontic infections.}, }
@article {pmid32497185, year = {2020}, author = {Van den Abbeele, P and Duysburgh, C and Rakebrandt, M and Marzorati, M}, title = {Dried yeast cell walls high in beta-glucan and mannan-oligosaccharides positively affect microbial composition and activity in the canine gastrointestinal tract in vitro.}, journal = {Journal of animal science}, volume = {98}, number = {6}, pages = {}, pmid = {32497185}, issn = {1525-3163}, mesh = {Animals ; Cell Wall/chemistry ; Diet/veterinary ; Dietary Supplements/*analysis ; Dogs/microbiology/*physiology ; Enterobacteriaceae/drug effects/growth &amp; development ; Fermentation ; Fusobacteria/drug effects/growth &amp; development ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/metabolism/microbiology ; Mannans/*pharmacology ; Oligosaccharides/*pharmacology ; Saccharomyces cerevisiae/*chemistry ; Yeast, Dried/chemistry ; beta-Glucans/*pharmacology ; }, abstract = {The outer cell wall of yeast is characterized by high levels of β-glucans and mannan-oligosaccharides (MOS), which have been linked with beneficial effects on intestinal health and immune status in dogs. In this study, a standardized in vitro simulation of the canine gastrointestinal tract (Simulator of the Canine Intestinal Microbial Ecosystem; SCIME) was used to evaluate the effect of a Saccharomyces cerevisiae-based product, consisting of 27.5% β-glucans and 22.5% MOS, on the activity (as assessed by measurement of fermentative metabolites) and composition (as assessed by 16S-targeted Illumina sequencing) of canine intestinal microbiota. The S. cerevisiae-based product was tested at three different dosages, i.e., 0.5, 1.0, and 2.0 g/d. A dose-dependent fermentation pattern was observed along the entire length of the colon, as shown by the increased production of the health-related acetate, propionate, and butyrate for the three concentrations tested (0.5, 1.0, and 2.0 g/d). A consistent finding for all three tested concentrations was the increased propionate production (P < 0.05) in the simulated proximal and distal colon. These changes in terms of fermentative metabolites could be linked to specific microbial alterations at the family level, such as the specific stimulation of the propionate-producing families Porphyromonadaceae and Prevotellaceae upon in vitro exposure to the S. cerevisiae-based product. Other consistent changes in community composition upon repeated exposure included the decrease in the Enterobacteriaceae and the Fusobacteriaceae families, which both contain several potentially opportunistic pathogens. Altogether, the generated data support a possible health-promoting role of a product high in β-glucans and MOS when supplemented to the dogs' diet.}, }
@article {pmid32494840, year = {2020}, author = {Xiong, J and Li, X and Yan, M and Lu, J and Qiu, Q and Chen, J}, title = {Comparable Ecological Processes Govern the Temporal Succession of Gut Bacteria and Microeukaryotes as Shrimp Aged.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {935-945}, doi = {10.1007/s00248-020-01533-6}, pmid = {32494840}, issn = {1432-184X}, support = {31872693//the National Natural Science Foundation of China/ ; LR19C030001//Natural Science Fund for Distinguished Young Scholars of Zhejiang Province/ ; 2015C110018//Technology Innovation Team of Ningbo/ ; }, mesh = {Animals ; Bacteria/isolation &amp; purification ; Bacterial Physiological Phenomena ; Eukaryota/*physiology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology ; Penaeidae/*microbiology ; Time Factors ; }, abstract = {Understanding the rules that govern the successions of gut microbiota is prerequisite for testing general ecological theories and sustaining a desirable microbiota. However, the ignorance of microeukaryotes raises the question of whether gut microeukaryotes are assembled according to the same rules as bacteria. We tracked the shrimp gut bacterial and microeukaryotic communities by a longitudinal dense sampling. The successions of both domains were significantly correlated with host age, with relatively stable microeukaryotic communities in adult shrimp. Gut microeukaryotes exhibited significantly higher turnover rate, but fewer transient species, lower proportion of temporal generalists, and narrower habitat niche breadth than bacteria. The γ-diversity partitioning analysis revealed that the successions of gut microbiotas were primarily ascribed to the high dissimilarity as shrimp aged ([Formula: see text]IntraTimes), whereas the relative importance of [Formula: see text]IntraTimes was significantly higher for microeukaryotes than that for bacteria. Compared with contrasting ecological processes in governing free-living bacteria and microeukaryotes, the ecological patterns were comparable between host-associated gut counterparts. However, the gut microeukaryotes were governed more strongly by deterministic selection relative to nestedness compared with the gut bacteria, which supports the "size-plasticity" hypothesis. Our results highlight the importance of independently interpreting free-living and host-associated meta-communities for a comprehensive understanding of the processes that govern microbial successions.}, }
@article {pmid32493970, year = {2020}, author = {Monteiro, DA and Fonseca, EDS and Rodrigues, RAR and da Silva, JJN and da Silva, EP and Balieiro, FC and Alves, BJR and Rachid, CTCDC}, title = {Structural and functional shifts of soil prokaryotic community due to Eucalyptus plantation and rotation phase.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {9075}, pmid = {32493970}, issn = {2045-2322}, mesh = {Agriculture/methods ; Carbon/chemistry/metabolism ; Carbon Dioxide/chemistry/metabolism ; Environmental Monitoring/methods ; Eucalyptus/genetics/metabolism/*physiology ; Forestry/methods ; Forests ; Greenhouse Gases/chemistry/metabolism ; Nitrogen/chemistry/metabolism ; Nitrous Oxide/chemistry/metabolism ; Prokaryotic Cells/metabolism/*physiology ; RNA, Ribosomal, 16S/genetics ; Rotation ; Soil/*chemistry ; }, abstract = {Agriculture, forestry and other land uses are currently the second highest source of anthropogenic greenhouse gases (GHGs) emissions. In soil, these gases derive from microbial activity, during carbon (C) and nitrogen (N) cycling. To investigate how Eucalyptus land use and growth period impact the microbial community, GHG fluxes and inorganic N levels, and if there is a link among these variables, we monitored three adjacent areas for 9 months: a recently planted Eucalyptus area, fully developed Eucalyptus forest (final of rotation) and native forest. We assessed the microbial community using 16S rRNA gene sequencing and qPCR of key genes involved in C and N cycles. No considerable differences in GHG flux were evident among the areas, but logging considerably increased inorganic N levels. Eucalyptus areas displayed richer and more diverse communities, with selection for specific groups. Land use influenced communities more extensively than the time of sampling or growth phase, although all were significant modulators. Several microbial groups and genes shifted temporally, and inorganic N levels shaped several of these changes. No correlations among microbial groups or genes and GHG were found, suggesting no link among these variables in this short-rotation Eucalyptus study.}, }
@article {pmid32488484, year = {2020}, author = {Semiatizki, A and Weiss, B and Bagim, S and Rohkin-Shalom, S and Kaltenpoth, M and Chiel, E}, title = {Effects, interactions, and localization of Rickettsia and Wolbachia in the house fly parasitoid, Spalangia endius.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {718-728}, doi = {10.1007/s00248-020-01520-x}, pmid = {32488484}, issn = {1432-184X}, support = {435/18//Planning and Budgeting Committee of the Council for Higher Education of Israel/ ; CoG 819585/ERC_/European Research Council/International ; }, mesh = {Animals ; Female ; *Host-Parasite Interactions ; Houseflies/parasitology ; Male ; Reproduction ; Rickettsia/*physiology ; *Symbiosis ; Wasps/*microbiology/physiology ; Wolbachia/*physiology ; }, abstract = {Many insect species harbor facultative microbial symbionts that affect their biology in diverse ways. Here, we studied the effects, interactions, and localization of two bacterial symbionts-Wolbachia and Rickettsia-in the parasitoid Spalangia endius. We crossed between four S. endius colonies-Wolbachia only (W), Rickettsia only (R), both (WR), and none (aposymbiotic, APS) (16 possible crosses) and found that Wolbachia induces incomplete cytoplasmic incompatibility (CI), both when the males are W or WR. Rickettsia did not cause reproductive manipulations and did not rescue the Wolbachia-induced CI. However, when R females were crossed with W or WR males, significantly less offspring were produced compared with that of control crosses. In non-CI crosses, the presence of Wolbachia in males caused a significant reduction in offspring numbers. Females' developmental time was significantly prolonged in the R colony, with adults starting to emerge one day later than the other colonies. Other fitness parameters did not differ significantly between the colonies. Using fluorescence in situ hybridization microscopy in females, we found that Wolbachia is localized alongside Rickettsia inside oocytes, follicle cells, and nurse cells in the ovaries. However, Rickettsia is distributed also in muscle cells all over the body, in ganglia, and even in the brain.}, }
@article {pmid32488483, year = {2020}, author = {Hejduková, E and Elster, J and Nedbalová, L}, title = {Annual Cycle of Freshwater Diatoms in the High Arctic Revealed by Multiparameter Fluorescent Staining.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {559-572}, doi = {10.1007/s00248-020-01521-w}, pmid = {32488483}, issn = {1432-184X}, support = {20217//Grantov&#xe1; Agentura, Univerzita Karlova/ ; LM2015078//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; }, mesh = {Arctic Regions ; Diatoms/*physiology ; Fresh Water ; *Life History Traits ; Seasons ; Staining and Labeling ; Svalbard ; }, abstract = {Diatoms (Bacillariophyceae) are important primary producers in a wide range of hydro-terrestrial habitats in polar regions that are characterized by many extreme environmental conditions. Nevertheless, how they survive periods of drought and/or freeze remains unknown. A general strategy of microorganisms to overcome adverse conditions is dormancy, but morphologically distinct diatom resting stages are rare. This study aimed to evaluate the annual cycle of freshwater diatoms in the High Arctic (Central Spitsbergen) and provide an insight into their physiological cell status variability. The diversity and viability of diatom cells were studied in samples collected five times at four study sites, tracing the key events for survival (summer vegetative season, autumn dry-freezing, winter freezing, spring melting, summer vegetative season [again]). For viability evaluation, a multiparameter fluorescent staining was used in combination with light microscopy and allowed to reveal the physiological status at a single-cell level. The proportions of the cell categories were seasonally and locality dependent. The results suggested that a significant portion of vegetative cells survive winter and provide an inoculum for the following vegetative season. The ice thickness significantly influenced spring survival. The thicker the ice layer was, the more dead cells and fewer other stages were observed. The influence of the average week max-min temperature differences in autumn and winter was not proven.}, }
@article {pmid32485888, year = {2020}, author = {Aliyu, H and Mohr, T and Cowan, D and de Maayer, P and Neumann, A}, title = {Time-Course Transcriptome of Parageobacillus thermoglucosidasius DSM 6285 Grown in the Presence of Carbon Monoxide and Air.}, journal = {International journal of molecular sciences}, volume = {21}, number = {11}, pages = {}, pmid = {32485888}, issn = {1422-0067}, mesh = {Air ; Bacillaceae/drug effects/*genetics/metabolism ; Carbon Monoxide/*pharmacology ; *Gene Expression Regulation, Bacterial ; Oxygen/metabolism ; *Transcriptome ; }, abstract = {Parageobacillus thermoglucosidasius is a metabolically versatile, facultatively anaerobic thermophile belonging to the family Bacillaceae. Previous studies have shown that this bacterium harbours co-localised genes coding for a carbon monoxide (CO) dehydrogenase (CODH) and Ni-Fe hydrogenase (Phc) complex and oxidises CO and produces hydrogen (H2) gas via the water-gas shift (WGS) reaction. To elucidate the genetic events culminating in the WGS reaction, P. thermoglucosidasius DSM 6285 was cultivated under an initial gas atmosphere of 50% CO and 50% air and total RNA was extracted at ~8 (aerobic phase), 20 (anaerobic phase), 27 and 44 (early and late hydrogenogenic phases) hours post inoculation. The rRNA-depleted fraction was sequenced using Illumina NextSeq, v2.5, 1x75bp chemistry. Differential expression revealed that at 8 vs 20, 20 vs 27 and 27 vs 44 hours post inoculation, 2190, 2118 and 231 transcripts were differentially (FDR < 0.05) expressed. Cluster analysis revealed 26 distinct gene expression trajectories across the four time points. Of these, two similar clusters, showing overexpression at 20 relative to 8 hours and depletion at 27 and 44 hours, harboured the CODH and Phc transcripts, suggesting possible regulation by O2. The transition between aerobic respiration and anaerobic growth was marked by initial metabolic deterioration, as reflected by up-regulation of transcripts linked to sporulation and down-regulation of transcripts linked to flagellar assembly and metabolism. However, the transcriptome and growth profiles revealed the reversal of this trend during the hydrogenogenic phase.}, }
@article {pmid32483324, year = {2020}, author = {van Bergeijk, DA and Terlouw, BR and Medema, MH and van Wezel, GP}, title = {Ecology and genomics of Actinobacteria: new concepts for natural product discovery.}, journal = {Nature reviews. Microbiology}, volume = {18}, number = {10}, pages = {546-558}, pmid = {32483324}, issn = {1740-1534}, mesh = {Actinobacteria/*genetics/metabolism ; Anti-Bacterial Agents/biosynthesis/*isolation &amp; purification/pharmacology ; Biological Products/*isolation &amp; purification/metabolism/pharmacology ; Drug Discovery ; Ecology ; *Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genome, Bacterial ; Genomics/methods ; Humans ; Metabolic Networks and Pathways/genetics ; Multigene Family ; }, abstract = {Actinobacteria constitute a highly diverse bacterial phylum with an unrivalled metabolic versatility. They produce most of the clinically used antibiotics and a plethora of other natural products with medical or agricultural applications. Modern 'omics'-based technologies have revealed that the genomic potential of Actinobacteria greatly outmatches the known chemical space. In this Review, we argue that combining insights into actinobacterial ecology with state-of-the-art computational approaches holds great promise to unlock this unexplored reservoir of actinobacterial metabolism. This enables the identification of small molecules and other stimuli that elicit the induction of poorly expressed biosynthetic gene clusters, which should help reinvigorate screening efforts for their precious bioactive natural products.}, }
@article {pmid32482859, year = {2020}, author = {Roach, TNF and Little, M and Arts, MGI and Huckeba, J and Haas, AF and George, EE and Quinn, RA and Cobián-Güemes, AG and Naliboff, DS and Silveira, CB and Vermeij, MJA and Kelly, LW and Dorrestein, PC and Rohwer, F}, title = {A multiomic analysis of in situ coral-turf algal interactions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {24}, pages = {13588-13595}, pmid = {32482859}, issn = {1091-6490}, mesh = {Animals ; Anthozoa/chemistry/*metabolism/microbiology/parasitology ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Chlorophyta/chemistry/*metabolism ; Coral Reefs ; Ecosystem ; Metagenomics ; Microbiota ; }, abstract = {Viruses, microbes, and host macroorganisms form ecological units called holobionts. Here, a combination of metagenomic sequencing, metabolomic profiling, and epifluorescence microscopy was used to investigate how the different components of the holobiont including bacteria, viruses, and their associated metabolites mediate ecological interactions between corals and turf algae. The data demonstrate that there was a microbial assemblage unique to the coral-turf algae interface displaying higher microbial abundances and larger microbial cells. This was consistent with previous studies showing that turf algae exudates feed interface and coral-associated microbial communities, often at the detriment of the coral. Further supporting this hypothesis, when the metabolites were assigned a nominal oxidation state of carbon (NOSC), we found that the turf algal metabolites were significantly more reduced (i.e., have higher potential energy) compared to the corals and interfaces. The algae feeding hypothesis was further supported when the ecological outcomes of interactions (e.g., whether coral was winning or losing) were considered. For example, coral holobionts losing the competition with turf algae had higher Bacteroidetes-to-Firmicutes ratios and an elevated abundance of genes involved in bacterial growth and division. These changes were similar to trends observed in the obese human gut microbiome, where overfeeding of the microbiome creates a dysbiosis detrimental to the long-term health of the metazoan host. Together these results show that there are specific biogeochemical changes at coral-turf algal interfaces that predict the competitive outcomes between holobionts and are consistent with algal exudates feeding coral-associated microbes.}, }
@article {pmid32482164, year = {2020}, author = {Costa, OYA and de Hollander, M and Pijl, A and Liu, B and Kuramae, EE}, title = {Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {76}, pmid = {32482164}, issn = {2049-2618}, support = {729.004.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/International ; 202496/2015-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/International ; }, mesh = {Bacteria/enzymology/genetics ; Biodegradation, Environmental ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; *Polymers/metabolism ; }, abstract = {BACKGROUND: Cultivation-independent methods, including metagenomics, are tools for the exploration and discovery of biotechnological compounds produced by microbes in natural environments. Glycoside hydrolases (GHs) enzymes are extremely desired and important in the industry of production for goods and biofuel and removal of problematic biofilms and exopolysaccharide (EPS). Biofilms and EPS are complex, requiring a wide range of enzymes for a complete degradation. The aim of this study was to identify potential GH microbial producers and GH genes with biotechnological potential, using EPS-complex structure (WH15EPS) of Acidobacteria Granulicella sp. strain WH15 as an enrichment factor, in cultivation-independent and cultivation-dependent methods. We performed stable isotope probing (SIP) combined with metagenomics on topsoil litter amended with WH15EPS and coupled solid culture-EPS amended medium with metagenomics.<br><br>RESULTS: SIP metagenome analysis of the soil litter demonstrated that phyla Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes were the most abundant in WH15EPS amended and unamended treatments. The enrichment cultures in solid culture medium coupled to metagenomics demonstrated an enrichment in Proteobacteria, and the metagenome assembly of this enrichment cultures resulted in 4 metagenome-assembled genomes (MAGs) of microbes with low identity (42-86%) to known microorganisms. Among all carbohydrate-active enzymes (CAZymes) retrieved genes, glycoside transferase (GT) was the most abundant family, either in culture-independent or culture-based metagenome datasets. Within the glycoside hydrolases (GHs), GH13 was the most abundant family in both metagenome datasets. In the "heavy" fraction of the culture-independent metagenome SIP dataset, GH109 (&#x3b1;-N-acetylgalactosaminidases), GH117 (agarases), GH50 (agarases), GH32 (invertases and inulinases), GH17 (endoglucanases), and GH71 (mutanases) families were more abundant in comparison with the controls. Those GH families are affiliated to microorganism that are probably capable to degrade WH15EPS and potentially applicable for biofilm deconstruction. Subsequent in culture-based metagenome, the assembled 4 MAGs (unclassified Proteobacteria) also contained GH families of interest, involving mannosidases, lysozymes, galactosidases, and chitinases.<br><br>CONCLUSIONS: We demonstrated that functional diversity induced by the presence of WH15EPS in both culture-independent and culture-dependent approaches was enriched in GHs, such as amylases and endoglucanases that could be applied in chemical, pharmaceutical, and food industrial sectors. Furthermore, WH15EPS may be used for the investigation and isolation of yet unknown taxa, such as unclassified Proteobacteria and Planctomycetes, increasing the number of current cultured bacterial representatives with potential biotechnological traits. Video Abstract.}, }
@article {pmid32477286, year = {2020}, author = {Bagnoud, A and Pramateftaki, P and Bogard, MJ and Battin, TJ and Peter, H}, title = {Microbial Ecology of Methanotrophy in Streams Along a Gradient of CH4 Availability.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {771}, pmid = {32477286}, issn = {1664-302X}, abstract = {Despite the recognition of streams and rivers as sources of methane (CH4) to the atmosphere, the role of CH4 oxidation (MOX) in these ecosystems remains poorly understood to date. Here, we measured the kinetics of MOX in stream sediments of 14 sites to resolve the ecophysiology of CH4 oxidizing bacteria (MOB) communities. The streams cover a gradient of land cover and associated physicochemical parameter and differed in stream- and porewater CH4 concentrations. Michealis-Menten kinetic parameter of MOX, maximum reaction velocity (V max), and CH4 concentration at half V max (K S) increased with CH4 supply. K S values in the micromolar range matched the CH4 concentrations measured in shallow stream sediments and indicate that MOX is mostly driven by low-affinity MOB. 16S rRNA gene sequencing identified MOB classified as Methylococcaceae and particularly Crenothrix. Their relative abundance correlated with pmoA gene counts and MOX rates, underscoring their pivotal role as CH4 oxidizers in stream sediments. Building on the concept of enterotypes, we identify two distinct groups of co-occurring MOB. While there was no taxonomic difference among the members of each cluster, one cluster contained abundant and common MOB, whereas the other cluster contained rare operational taxonomic units (OTUs) specific to a subset of streams. These integrated analyses of changes in MOB community structure, gene abundance, and the corresponding ecosystem process contribute to a better understanding of the distal controls on MOX in streams.}, }
@article {pmid32475802, year = {2020}, author = {Zhang, Z and van Kleunen, M and Becks, L and Thakur, MP}, title = {Towards a General Understanding of Bacterial Interactions.}, journal = {Trends in microbiology}, volume = {28}, number = {10}, pages = {783-785}, doi = {10.1016/j.tim.2020.05.010}, pmid = {32475802}, issn = {1878-4380}, mesh = {Bacteria/genetics ; *Bacterial Physiological Phenomena ; Ecology ; *Microbial Interactions ; Microbiota ; }, abstract = {Understanding the general rules of microbial interactions is central for advancing microbial ecology. Recent studies show that interaction range, interaction strength, and community context determine bacterial interactions and the coexistence and evolution of bacteria. We highlight how these factors could contribute to a general understanding of bacterial interactions.}, }
@article {pmid32474660, year = {2020}, author = {Musonerimana, S and Bez, C and Licastro, D and Habarugira, G and Bigirimana, J and Venturi, V}, title = {Pathobiomes Revealed that Pseudomonas fuscovaginae and Sarocladium oryzae Are Independently Associated with Rice Sheath Rot.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {627-642}, doi = {10.1007/s00248-020-01529-2}, pmid = {32474660}, issn = {1432-184X}, mesh = {Hypocreales/genetics/*physiology ; Oryza/*microbiology ; Plant Diseases/*microbiology ; Pseudomonas/genetics/*physiology ; }, abstract = {Rice sheath rot has been mainly associated with the bacterial pathogen Pseudomonas fuscovaginae and in some cases to the fungal pathogen Sarocladium oryzae; it is yet unclear if they are part of a complex disease. The bacterial and fungal community associated with rice sheath rot symptomatic and asymptomatic rice plants was determined/studied with the main aim to shed light on the pathogen(s) causing rice sheath rot. Plant samples were collected from different rice varieties in two locations (highland and lowland) in two rice-growing seasons (wet and dry season) in Burundi. Our results showed that the bacterial Pseudomonas genus was prevalent in highland in both rice-growing seasons and was not affected by rice plant varieties. Pseudomonas sequence reads displayed a significant high similarity to Pseudomonas fuscovaginae indicating that it is the causal agent of rice sheath rot as previously reported. The fungal Sarocladium genus was on the other hand prevalent in lowland only in the wet season; the sequence reads were most significantly similar to Sarocladium oryzae. These studies showed that plant microbiome analysis is very useful in determining the microorganisms involved in a plant disease. P. fuscovaginae and S. oryzae were prevalent in symptomatic samples in highland and lowland respectively being present independently and hence are not part of a complex disease. The significant presence of other bacterial and fungal taxa in symptomatic samples is also discussed possibly making this disease more complex. Finally, we also report the microbial communities that are associated with the plant sheath in symptomatic and asymptomatic plants from the same rice fields.}, }
@article {pmid32474659, year = {2020}, author = {Liu, RR and Tian, Y and Zhou, EM and Xiong, MJ and Xiao, M and Li, WJ}, title = {Distinct Expression of the Two NO-Forming Nitrite Reductases in Thermus antranikianii DSM 12462[T] Improved Environmental Adaptability.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {614-626}, doi = {10.1007/s00248-020-01528-3}, pmid = {32474659}, issn = {1432-184X}, support = {91951205//National Natural Science Foundation of China/ ; 31970122//National Natural Science Foundation of China/ ; 31470139//National Natural Science Foundation of China/ ; 31600298//National Natural Science Foundation of China/ ; 2018B020206001//Guangdong Province Science and Technology Innovation Strategy Special Fund/ ; }, mesh = {Adaptation, Physiological/*genetics ; Bacterial Proteins/*genetics/metabolism ; Nitric Oxide/*metabolism ; Nitrite Reductases/*genetics/metabolism ; Thermus/enzymology/*genetics ; }, abstract = {Hot spring ecosystems are analogous to some thermal environments on the early Earth and represent ideal models to understand life forms and element cycling on the early Earth. Denitrification, an important component of biogeochemical nitrogen cycle, is highly active in hot springs. Nitrite (NO2[-]) reduction to nitric oxide (NO) is the significant and rate-limiting pathway in denitrification and is catalyzed by two types of nitrite reductases, encoded by nirS and nirK genes. NirS and NirK were originally considered incompatible in most denitrifying organisms, although a few strains have been reported to possess both genes. Herein, we report the functional division of nirS and nirK in Thermus, a thermophilic genus widespread in thermal ecosystems. Transcriptional levels of nirS and nirK coexisting in Thermus antranikianii DSM 12462[T] were measured to assess the effects of nitrite, oxygen, and stimulation time. Thirty-nine Thermus strains were used to analyze the phylogeny and distribution of nirS and nirK; six representative strains were used to assess the denitrification phenotype. The results showed that both genes were actively transcribed and expressed independently in T. antranikianii DSM 12462[T]. Strains with both nirS and nirK had a wider range of nitrite adaptation and revealed nir-related physiological adaptations in Thermus: nirK facilitated adaptation to rapid changes and extended the adaptation range of nitrite under oxygen-limited conditions, while nirS expression was higher under oxic and relatively stable conditions.}, }
@article {pmid32471167, year = {2020}, author = {Su, L and Zhang, L and Nie, D and Kuramae, EE and Shen, B and Shen, Q}, title = {Bacterial Tomato Pathogen Ralstonia solanacearum Invasion Modulates Rhizosphere Compounds and Facilitates the Cascade Effect of Fungal Pathogen Fusarium solani.}, journal = {Microorganisms}, volume = {8}, number = {6}, pages = {}, pmid = {32471167}, issn = {2076-2607}, support = {41571242//Chinese Natural Science Fund Program/ ; }, abstract = {Soil-borne pathogen invasions can significantly change the microbial communities of the host rhizosphere. However, whether bacterial Ralstonia solanacearum pathogen invasion influences the abundance of fungal pathogens remains unclear. In this study, we combined high-throughput sequencing, qPCR, liquid chromatography and soil culture experiments to analyze the rhizosphere fungal composition, co-occurrence of fungal communities, copy numbers of functional genes, contents of phenolic acids and their associations in healthy and bacterial wilt-diseased tomato plants. We found that R. solanacearum invasion increased the abundance of the soil-borne pathogen Fusarium solani. The concentrations of three phenolic acids in the rhizosphere soil of bacterial wilt-diseased tomato plants were significantly higher than those in the rhizosphere soil of healthy tomato plants. In addition, the increased concentrations of phenolic acids significantly stimulated F. solani growth in the soil. Furthermore, a simple fungal network with fewer links, nodes and hubs (highly connected nodes) was found in the diseased tomato plant rhizosphere. These results indicate that once the symptom of bacterial wilt disease is observed in tomato, the roots of the wilt-diseased tomato plants need to be removed in a timely manner to prevent the enrichment of other fungal soil-borne pathogens. These findings provide some ecological clues for the mixed co-occurrence of bacterial wilt disease and other fungal soil-borne diseases.}, }
@article {pmid32470594, year = {2020}, author = {Capson-Tojo, G and Batstone, DJ and Grassino, M and Vlaeminck, SE and Puyol, D and Verstraete, W and Kleerebezem, R and Oehmen, A and Ghimire, A and Pikaar, I and Lema, JM and Hülsen, T}, title = {Purple phototrophic bacteria for resource recovery: Challenges and opportunities.}, journal = {Biotechnology advances}, volume = {43}, number = {}, pages = {107567}, doi = {10.1016/j.biotechadv.2020.107567}, pmid = {32470594}, issn = {1873-1899}, mesh = {Biomass ; *Microalgae ; Nitrogen ; Phosphorus ; *Proteobacteria ; Wastewater ; }, abstract = {Sustainable development is driving a rapid focus shift in the wastewater and organic waste treatment sectors, from a "removal and disposal" approach towards the recovery and reuse of water, energy and materials (e.g. carbon or nutrients). Purple phototrophic bacteria (PPB) are receiving increasing attention due to their capability of growing photoheterotrophically under anaerobic conditions. Using light as energy source, PPB can simultaneously assimilate carbon and nutrients at high efficiencies (with biomass yields close to unity (1 g CODbiomass·g CODremoved[-1])), facilitating the maximum recovery of these resources as different value-added products. The effective use of infrared light enables selective PPB enrichment in non-sterile conditions, without competition with other phototrophs such as microalgae if ultraviolet-visible wavelengths are filtered. This review reunites results systematically gathered from over 177 scientific articles, aiming at producing generalized conclusions. The most critical aspects of PPB-based production and valorisation processes are addressed, including: (i) the identification of the main challenges and potentials of different growth strategies, (ii) a critical analysis of the production of value-added compounds, (iii) a comparison of the different value-added products, (iv) insights into the general challenges and opportunities and (v) recommendations for future research and development towards practical implementation. To date, most of the work has not been executed under real-life conditions, relevant for full-scale application. With the savings in wastewater discharge due to removal of organics, nitrogen and phosphorus as an important economic driver, priorities must go to using PPB-enriched cultures and real waste matrices. The costs associated with artificial illumination, followed by centrifugal harvesting/dewatering and drying, are estimated to be 1.9, 0.3-2.2 and 0.1-0.3 $·kgdry biomass[-1]. At present, these costs are likely to exceed revenues. Future research efforts must be carried out outdoors, using sunlight as energy source. The growth of bulk biomass on relatively clean wastewater streams (e.g. from food processing) and its utilization as a protein-rich feed (e.g. to replace fishmeal, 1.5-2.0 $·kg[-1]) appears as a promising valorisation route.}, }
@article {pmid32469071, year = {2021}, author = {Rampal, R and Wari, N and Singh, AK and Das, U and Bopanna, S and Gupta, V and Nayak, B and Velapandian, T and Kedia, S and Kumar, D and Awasthi, A and Ahuja, V}, title = {Retinoic Acid Is Elevated in the Mucosa of Patients With Active Ulcerative Colitis and Displays a Proinflammatory Role by Augmenting IL-17 and IFNγ Production.}, journal = {Inflammatory bowel diseases}, volume = {27}, number = {1}, pages = {74-83}, doi = {10.1093/ibd/izaa121}, pmid = {32469071}, issn = {1536-4844}, mesh = {Adult ; Cell Differentiation/drug effects ; Colitis, Ulcerative/*metabolism ; Cross-Sectional Studies ; Female ; Forkhead Transcription Factors/metabolism ; Humans ; Inflammation ; Inflammation Mediators/*metabolism ; Interferon-gamma/*biosynthesis ; Interleukin-10/metabolism ; Interleukin-17/*biosynthesis ; Intestinal Mucosa/*metabolism ; Male ; Middle Aged ; T-Lymphocytes, Regulatory/metabolism ; Tretinoin/*metabolism ; }, abstract = {BACKGROUND: All-trans retinoic acid (RA) plays a crucial role in promoting Foxp3+ Treg generation while reciprocally inhibiting Th1/Th17 generation. Our previous research highlighted that in the face of inflammatory conditions, RA plays a contrary role where it aggravates intestinal inflammation by promoting interferon (IFN) γ and interleukin (IL)-17 differentiation in vitro.<br><br>METHODS: In this study we translated our in vitro results into a clinical setting where we estimated mucosal and serum RA levels along with the immunophenotypic profile (IL-17, IFN&#x3b3;, Foxp3, IL-10) in adaptive (CD4, CD8) and innate-like T cells (mucosal associated invariant T cells and &#x3b3;&#x3b4; T cells) in patients with ulcerative colitis in remission or with active inflammation.<br><br>RESULTS: This is the first study to estimate RA levels in the human gut and shows that patients with active disease had increased mucosal RA levels as compared with patients in remission (4.0 vs 2.5 ng/mL; P&#x2005;<&#x2005;0.01) and control patients (3.4 vs 0.8 ng/mL; P&#x2005;<&#x2005;0.0001). This effect was accompanied by significantly elevated IL-17 and IFN&#x3b3; in tissue CD4+, CD8+, mucosal associated invariant T+ cells, and &#x3b3;&#x3b4;&#x200a;+ T cells. Moreover, the raised RA levels in patients with active disease showed a positive correlation with proinflammatory cytokines (IL-17, IFN&#x3b3;) and a negative correlation with IL-10. We also found that RA negatively correlated with IL-9, thereby reinstating our previous finding that RA inhibits Th9 differentiation.<br><br>CONCLUSIONS: These data confirm our previous in vitro results that in the presence of inflammation, RA plays a crucial role in maintaining gut inflammation by upregulating proinflammatory markers.}, }
@article {pmid32468160, year = {2020}, author = {Tschoeke, D and Salazar, VW and Vidal, L and Campeão, M and Swings, J and Thompson, F and Thompson, C}, title = {Unlocking the Genomic Taxonomy of the Prochlorococcus Collective.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {546-558}, doi = {10.1007/s00248-020-01526-5}, pmid = {32468160}, issn = {1432-184X}, mesh = {*Genome, Bacterial ; Genomics ; *Life History Traits ; Prochlorococcus/*classification/genetics/physiology ; }, abstract = {Prochlorococcus is the most abundant photosynthetic prokaryote on our planet. The extensive ecological literature on the Prochlorococcus collective (PC) is based on the assumption that it comprises one single genus comprising the species Prochlorococcus marinus, containing itself a collective of ecotypes. Ecologists adopt the distributed genome hypothesis of an open pan-genome to explain the observed genomic diversity and evolution patterns of the ecotypes within PC. Novel genomic data for the PC prompted us to revisit this group, applying the current methods used in genomic taxonomy. As a result, we were able to distinguish the five genera: Prochlorococcus, Eurycolium, Prolificoccus, Thaumococcus, and Riococcus. The novel genera have distinct genomic and ecological attributes.}, }
@article {pmid32466615, year = {2020}, author = {Van den Abbeele, P and Ghyselinck, J and Marzorati, M and Villar, A and Zangara, A and Smidt, CR and Risco, E}, title = {In Vitro Evaluation of Prebiotic Properties of a Commercial Artichoke Inflorescence Extract Revealed Bifidogenic Effects.}, journal = {Nutrients}, volume = {12}, number = {6}, pages = {}, pmid = {32466615}, issn = {2072-6643}, mesh = {Bifidobacterium/drug effects ; Colon/metabolism/microbiology ; Cynara scolymus/*chemistry ; Dietary Supplements ; Ecosystem ; Fatty Acids, Volatile/metabolism ; Fermentation ; Gastrointestinal Microbiome/drug effects ; Humans ; Inflorescence/*chemistry ; Inulin ; Lactobacillus/drug effects ; Oligosaccharides/pharmacology ; Plant Extracts/*pharmacology ; Prebiotics/*analysis ; Propionates/metabolism ; }, abstract = {UNLABELLED: : Background: Prebiotics used as a dietary supplement, stimulate health-related gut microbiota (e.g., bifidobacteria, lactobacilli, etc.). This study evaluated potential prebiotic effects of an artichoke aqueous dry extract (AADE) using in vitro gut model based on the Simulator of Human Intestinal Microbial Ecosystem (SHIME[®]).<br><br>METHODS: Short-term colonic fermentations (48 h) of AADE, fructo-oligosaccharides (FOS), and a blank were performed. Microbial metabolites were assessed at 0, 6, 24, and 48 h of colonic incubation via measuring pH, gas pressure, lactate, ammonium, and short-chain fatty acids (SCFAs) levels. Community composition was assessed via targeted qPCRs.<br><br>RESULTS: After 24 and 48 h of incubation, bifidobacteria levels increased 25-fold with AADE (p < 0.05) and >100-fold with FOS (p < 0.05) compared to blank. Lactobacillus spp. levels only tended to increase with AADE, whereas they increased 10-fold with FOS. At 6 h, pH decreased with AADE and FOS and remained stable until 48 h; however, gas pressure increased significantly till the end of study. Acetate, propionate, and total SCFA production increased significantly with both at all time-points. Lactate levels initially increased but branched SCFA and ammonium levels remained low till 48 h.<br><br>CONCLUSION: AADE displayed prebiotic potential by exerting bifidogenic effects that stimulated production of health-related microbial metabolites, which is potentially due to inulin in AADE.}, }
@article {pmid32466517, year = {2020}, author = {Jia, X and Dini-Andreote, F and Falcão Salles, J}, title = {Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data.}, journal = {Microorganisms}, volume = {8}, number = {6}, pages = {}, pmid = {32466517}, issn = {2076-2607}, abstract = {Quantifying which assembly processes structure microbiomes can assist prediction, manipulation, and engineering of community outcomes. However, the relative importance of these processes might depend on whether DNA or RNA are used, as they differ in stability. We hypothesized that. RNA-inferred community responses to (a)biotic fluctuations are faster than those inferred by DNA; the relative influence of variable selection is stronger in RNA-inferred communities (environmental factors are spatiotemporally heterogeneous), whereas homogeneous selection largely influences DNA-inferred communities (environmental filters are constant). To test these hypotheses, we characterized soil bacterial communities by sequencing both 16S rRNA amplicons from the extracted DNA and RNA transcripts across distinct stages of soil primary succession and quantified the relative influence of each assembly process using ecological null model analysis. Our results revealed that variations in α-diversity and temporal turnover were higher in RNA- than in DNA-inferred communities across successional stages, albeit there was a similar community composition; in line with our hypotheses, the assembly of RNA-inferred community was more closely associated with environmental variability (variable selection) than using the standard DNA-based approach, which was largely influenced by homogeneous selection. This study illustrates the need for benchmarking approaches to properly elucidate how community assembly processes structure microbial communities.}, }
@article {pmid32462391, year = {2020}, author = {Möhlmann, TWR and Vogels, CBF and Göertz, GP and Pijlman, GP and Ter Braak, CJF and Te Beest, DE and Hendriks, M and Nijhuis, EH and Warris, S and Drolet, BS and van Overbeek, L and Koenraadt, CJM}, title = {Impact of Gut Bacteria on the Infection and Transmission of Pathogenic Arboviruses by Biting Midges and Mosquitoes.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {703-717}, pmid = {32462391}, issn = {1432-184X}, support = {BBS/E/I/00007039/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Aedes/*virology ; Animals ; Bacterial Physiological Phenomena ; Ceratopogonidae/*virology ; Chikungunya virus/*physiology ; Female ; Gastrointestinal Microbiome/*physiology ; Insect Vectors/*virology ; Mosquito Vectors/virology ; Orthobunyavirus/*physiology ; Zika Virus/*physiology ; }, abstract = {Tripartite interactions among insect vectors, midgut bacteria, and viruses may determine the ability of insects to transmit pathogenic arboviruses. Here, we investigated the impact of gut bacteria on the susceptibility of Culicoides nubeculosus and Culicoides sonorensis biting midges for Schmallenberg virus, and of Aedes aegypti mosquitoes for Zika and chikungunya viruses. Gut bacteria were manipulated by treating the adult insects with antibiotics. The gut bacterial communities were investigated using Illumina MiSeq sequencing of 16S rRNA, and susceptibility to arbovirus infection was tested by feeding insects with an infectious blood meal. Antibiotic treatment led to changes in gut bacteria for all insects. Interestingly, the gut bacterial composition of untreated Ae. aegypti and C. nubeculosus showed Asaia as the dominant genus, which was drastically reduced after antibiotic treatment. Furthermore, antibiotic treatment resulted in relatively more Delftia bacteria in both biting midge species, but not in mosquitoes. Antibiotic treatment and subsequent changes in gut bacterial communities were associated with a significant, 1.8-fold increased infection rate of C. nubeculosus with Schmallenberg virus, but not for C. sonorensis. We did not find any changes in infection rates for Ae. aegypti mosquitoes with Zika or chikungunya virus. We conclude that resident gut bacteria may dampen arbovirus transmission in biting midges, but not so in mosquitoes. Use of antimicrobial compounds at livestock farms might therefore have an unexpected contradictory effect on the health of animals, by increasing the transmission of viral pathogens by biting midges.}, }
@article {pmid32462390, year = {2020}, author = {Yang, M and Shi, J and Wang, B and Xiao, J and Li, W and Liu, CQ}, title = {Control of Hydraulic Load on Bacterioplankton Diversity in Cascade Hydropower Reservoirs, Southwest China.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {537-545}, doi = {10.1007/s00248-020-01523-8}, pmid = {32462390}, issn = {1432-184X}, support = {2016YFA0601001//the National Key R &amp; D Program of China/ ; U1612441//Innovative Research Group Project of the National Natural Science Foundation of China (CN)/ ; }, mesh = {*Bacterial Physiological Phenomena ; China ; Hydrology ; Lakes/analysis/*microbiology ; Microbiota/*physiology ; Plankton/*physiology ; Water Supply ; }, abstract = {Hydroelectric reservoirs are highly regulated ecosystems, where the understanding on bacterioplankton has been very limited so far. In view of significant changes in river hydrological conditions by dam construction, hydraulic load (i.e., the ratio of mean water depth to water retention time) was assumed to control bacterioplankton diversity in cascading hydropower reservoirs. To evaluate this hypothesis, we investigated bacterioplankton composition and diversity using high-throughput sequencing and related environmental variables in eleven reservoirs on the Wujiang River, Southwest China. Our results showed a decrease of bacterioplankton diversity index with an increase of reservoir hydraulic load. This is because hydraulic load governs dissolved oxygen variation in the water column, which is a key factor shaping bacterioplankton composition in these hydroelectric reservoirs. In contrast, bacterioplankton abundance was mainly affected by nutrient-related environmental factors. Therefore, from a hydrological perspective, hydraulic load is a decisive factor for the bacterioplankton diversity in the hydroelectric reservoirs. This study can improve the understanding of reservoir bacterial ecology, and the empirical relationship between hydraulic load and bacterioplankton diversity index will help to quantitatively evaluate ecological effects of river damming.}, }
@article {pmid32461136, year = {2020}, author = {Flanagan, E and Lamport, D and Brennan, L and Burnet, P and Calabrese, V and Cunnane, SC and de Wilde, MC and Dye, L and Farrimond, JA and Emerson Lombardo, N and Hartmann, T and Hartung, T and Kalliomäki, M and Kuhnle, GG and La Fata, G and Sala-Vila, A and Samieri, C and Smith, AD and Spencer, JPE and Thuret, S and Tuohy, K and Turroni, S and Vanden Berghe, W and Verkuijl, M and Verzijden, K and Yannakoulia, M and Geurts, L and Vauzour, D}, title = {Nutrition and the ageing brain: Moving towards clinical applications.}, journal = {Ageing research reviews}, volume = {62}, number = {}, pages = {101079}, doi = {10.1016/j.arr.2020.101079}, pmid = {32461136}, issn = {1872-9649}, support = {MR/N030087/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Aging ; Brain ; Diet ; *Healthy Aging ; Humans ; *Nutritional Status ; }, abstract = {The global increases in life expectancy and population have resulted in a growing ageing population and with it a growing number of people living with age-related neurodegenerative conditions and dementia, shifting focus towards methods of prevention, with lifestyle approaches such as nutrition representing a promising avenue for further development. This overview summarises the main themes discussed during the 3[rd] Symposium on "Nutrition for the Ageing Brain: Moving Towards Clinical Applications" held in Madrid in August 2018, enlarged with the current state of knowledge on how nutrition influences healthy ageing and gives recommendations regarding how the critical field of nutrition and neurodegeneration research should move forward into the future. Specific nutrients are discussed as well as the impact of multi-nutrient and whole diet approaches, showing particular promise to combatting the growing burden of age-related cognitive decline. The emergence of new avenues for exploring the role of diet in healthy ageing, such as the impact of the gut microbiome and development of new techniques (imaging measures of brain metabolism, metabolomics, biomarkers) are enabling researchers to approach finding answers to these questions. But the translation of these findings into clinical and public health contexts remains an obstacle due to significant shortcomings in nutrition research or pressure on the scientific community to communicate recommendations to the general public in a convincing and accessible way. Some promising programs exist but further investigation to improve our understanding of the mechanisms by which nutrition can improve brain health across the human lifespan is still required.}, }
@article {pmid32460826, year = {2020}, author = {Roelofs, D and Zwaenepoel, A and Sistermans, T and Nap, J and Kampfraath, AA and Van de Peer, Y and Ellers, J and Kraaijeveld, K}, title = {Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution.}, journal = {BMC biology}, volume = {18}, number = {1}, pages = {57}, pmid = {32460826}, issn = {1741-7007}, support = {PhD fellowship//Fonds Wetenschappelijk Onderzoek/International ; 15494//Stichting voor de Technische Wetenschappen/International ; NWA StartImpulse//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/International ; }, mesh = {Animals ; Arthropods/genetics ; *Evolution, Molecular ; *Gene Duplication ; *Genome ; Insecta/*genetics ; Phylogeny ; }, abstract = {BACKGROUND: Gene duplication events play an important role in the evolution and adaptation of organisms. Duplicated genes can arise through different mechanisms, including whole-genome duplications (WGDs). Recently, WGD was suggested to be an important driver of evolution, also in hexapod animals.<br><br>RESULTS: Here, we analyzed 20 high-quality hexapod genomes using whole-paranome distributions of estimated synonymous distances (KS), patterns of within-genome co-linearity, and phylogenomic gene tree-species tree reconciliation methods. We observe an abundance of gene duplicates in the majority of these hexapod genomes, yet we find little evidence for WGD. The majority of gene duplicates seem to have originated through small-scale gene duplication processes. We did detect segmental duplications in six genomes, but these lacked the within-genome co-linearity signature typically associated with WGD, and the age of these duplications did not coincide with particular peaks in KS distributions. Furthermore, statistical gene tree-species tree reconciliation failed to support all but one of the previously hypothesized WGDs.<br><br>CONCLUSIONS: Our analyses therefore provide very limited evidence for WGD having played a significant role in the evolution of hexapods and suggest that alternative mechanisms drive gene duplication events in this group of animals. For instance, we propose that, along with small-scale gene duplication events, episodes of increased transposable element activity could have been an important source for gene duplicates in hexapods.}, }
@article {pmid32460009, year = {2020}, author = {De Boeck, I and van den Broek, MFL and Allonsius, CN and Spacova, I and Wittouck, S and Martens, K and Wuyts, S and Cauwenberghs, E and Jokicevic, K and Vandenheuvel, D and Eilers, T and Lemarcq, M and De Rudder, C and Thys, S and Timmermans, JP and Vroegop, AV and Verplaetse, A and Van de Wiele, T and Kiekens, F and Hellings, PW and Vanderveken, OM and Lebeer, S}, title = {Lactobacilli Have a Niche in the Human Nose.}, journal = {Cell reports}, volume = {31}, number = {8}, pages = {107674}, doi = {10.1016/j.celrep.2020.107674}, pmid = {32460009}, issn = {2211-1247}, mesh = {Female ; Humans ; Lactobacillus/*pathogenicity ; Male ; Nose/*microbiology ; }, abstract = {Although an increasing number of beneficial microbiome members are characterized for the human gut and vagina, beneficial microbes are underexplored for the human upper respiratory tract (URT). In this study, we demonstrate that taxa from the beneficial Lactobacillus genus complex are more prevalent in the healthy URT than in patients with chronic rhinosinusitis (CRS). Several URT-specific isolates are cultured, characterized, and further explored for their genetic and functional properties related to adaptation to the URT. Catalase genes are found in the identified lactobacilli, which is a unique feature within this mostly facultative anaerobic genus. Moreover, one of our isolated strains, Lactobacillus casei AMBR2, contains fimbriae that enable strong adherence to URT epithelium, inhibit the growth and virulence of several URT pathogens, and successfully colonize nasal epithelium of healthy volunteers. This study thus demonstrates that specific lactobacilli are adapted to the URT and could have a beneficial keystone function in this habitat.}, }
@article {pmid32456625, year = {2020}, author = {Alderliesten, JB and Duxbury, SJN and Zwart, MP and de Visser, JAGM and Stegeman, A and Fischer, EAJ}, title = {Effect of donor-recipient relatedness on the plasmid conjugation frequency: a meta-analysis.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {135}, pmid = {32456625}, issn = {1471-2180}, support = {50-54100-98-1 19//ZonMw/International ; }, mesh = {Bacteria/*classification/genetics ; Bacterial Physiological Phenomena ; Conjugation, Genetic ; Drug Resistance, Bacterial ; Escherichia coli/genetics/*growth &amp; development ; Escherichia coli Proteins/genetics ; Phylogeny ; Plasmids/*genetics ; Species Specificity ; }, abstract = {BACKGROUND: Conjugation plays a major role in the transmission of plasmids encoding antibiotic resistance genes in both clinical and general settings. The conjugation efficiency is influenced by many biotic and abiotic factors, one of which is the taxonomic relatedness between donor and recipient bacteria. A comprehensive overview of the influence of donor-recipient relatedness on conjugation is still lacking, but such an overview is important to quantitatively assess the risk of plasmid transfer and the effect of interventions which limit the spread of antibiotic resistance, and to obtain parameter values for conjugation in mathematical models. Therefore, we performed a meta-analysis on reported conjugation frequencies from Escherichia coli donors to various recipient species.<br><br>RESULTS: Thirty-two studies reporting 313 conjugation frequencies for liquid broth matings and 270 conjugation frequencies for filter matings were included in our meta-analysis. The reported conjugation frequencies varied over 11 orders of magnitude. Decreasing taxonomic relatedness between donor and recipient bacteria, when adjusted for confounding factors, was associated with a lower conjugation frequency in liquid matings. The mean conjugation frequency for bacteria of the same order, the same class, and other classes was 10, 20, and 789 times lower than the mean conjugation frequency within the same species, respectively. This association between relatedness and conjugation frequency was not found for filter matings. The conjugation frequency was furthermore found to be influenced by temperature in both types of mating experiments, and in addition by plasmid incompatibility group in liquid matings, and by recipient origin and mating time in filter matings.<br><br>CONCLUSIONS: In our meta-analysis, taxonomic relatedness is limiting conjugation in liquid matings, but not in filter matings, suggesting that taxonomic relatedness is not a limiting factor for conjugation in environments where bacteria are fixed in space.}, }
@article {pmid32455626, year = {2020}, author = {Xu, J and Bu, F and Zhu, W and Luo, G and Xie, L}, title = {Microbial Consortiums of Hydrogenotrophic Methanogenic Mixed Cultures in Lab-Scale Ex-Situ Biogas Upgrading Systems under Different Conditions of Temperature, pH and CO.}, journal = {Microorganisms}, volume = {8}, number = {5}, pages = {}, pmid = {32455626}, issn = {2076-2607}, support = {51678424 and 51378373//National Natural Science Foundation of China/ ; }, abstract = {In this study, hydrogenotrophic methanogenic mixed cultures taken from 13 lab-scale ex-situ biogas upgrading systems under different temperature (20-70 °C), pH (6.0-8.5), and CO (0-10%, v/v) variables were systematically investigated. High-throughput 16S rRNA gene sequencing was used to identify the microbial consortia, and statistical analyses were conducted to reveal the microbial diversity, the core functional microbes, and their correlative relationships with tested variables. Overall, bacterial community was more complex than the archaea community in all mixed cultures. Hydrogenotrophic methanogens Methanothermobacter, Methanobacterium, and Methanomassiliicoccus, and putative syntrophic acetate-oxidizing bacterium Coprothermobacter and Caldanaerobacter were found to predominate, but the core functional microbes varied under different conditions. Multivariable sensitivity analysis indicated that temperature (p < 0.01) was the crucial variable to determine the microbial consortium structures in hydrogenotrophic methanogenic mixed cultures. pH (0.01 < p < 0.05) significantly interfered with the relative abundance of dominant archaea. Although CO did not affect community (p > 0.1), some potential CO-utilizing syntrophic metabolisms might be enhanced. Understanding of microbial consortia in the hydrogenotrophic methanogenic mixed cultures related to environmental variables was a great advance to reveal the microbial ecology in microbial biogas upgrading process.}, }
@article {pmid32454384, year = {2020}, author = {Zhang, H and Zhang, B and Wang, S and Chen, J and Jiang, B and Xing, Y}, title = {Spatiotemporal vanadium distribution in soils with microbial community dynamics at vanadium smelting site.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {265}, number = {Pt A}, pages = {114782}, doi = {10.1016/j.envpol.2020.114782}, pmid = {32454384}, issn = {1873-6424}, mesh = {China ; Environmental Monitoring ; *Microbiota ; Soil ; Soil Pollutants/*analysis ; Vanadium/analysis ; }, abstract = {Whereas the adverse effects of vanadium released from smelting activities on soil microbial ecology have been widely recognized, little is known about spatiotemporal vanadium distribution and microbial community dynamics in typical contaminated sites. This study describes vanadium contents associated with health risk and microbial responses in both topsoil and subsoil during four consecutive seasons around an ongoing-production smelter in Panzhihua, China. Higher levels of vanadium concentration exceeding soil background value in China (82 mg/kg) were found close to the smelter. Vanadium concentrations decreased generally with the increase in distance to the smelter and depth below surface, as soil vanadium pollution is induced mainly by atmospheric deposition of vanadium bearing dust during smelting. Residual fraction was the predominated vanadium form in soils, with pronounced increase in bioavailable vanadium during rainfall period due to frequent drought-rewetting process. Topsoil close to the smelter exhibited significant contamination, inducing high probability of adverse health effects. Spatiotemporal vanadium distribution creates filtering effects on soil microorganisms, promoting metal tolerant genera in topsoil (e.g. Microvirga) and subsoil (e.g. Bacillus, Geobacter), which is the key in maintaining the community structure by promoting cooperative relation with other taxa. Our results reveal spatiotemporal vanadium distribution in soils at site scale with potential health risk and microbial responses, which is helpful in identifying severe contamination and implementing bioremediation.}, }
@article {pmid32454291, year = {2020}, author = {Lourenço, KS and Suleiman, AKA and Pijl, A and Cantarella, H and Kuramae, EE}, title = {Dynamics and resilience of soil mycobiome under multiple organic and inorganic pulse disturbances.}, journal = {The Science of the total environment}, volume = {733}, number = {}, pages = {139173}, doi = {10.1016/j.scitotenv.2020.139173}, pmid = {32454291}, issn = {1879-1026}, mesh = {Fertilizers/analysis ; Fungi ; *Mycobiome ; Soil ; Soil Microbiology ; }, abstract = {Disturbances in soil can cause short-term soil changes, consequently changes in microbial community what may result in long-lasting ecological effects. Here, we evaluate how multiple pulse disturbances effect the dynamics and resilience of fungal community, and the co-occurrence of fungal and bacterial communities in a 389 days field experiment. We used soil under sugarcane cultivation as soil ecosystem model, and organic residue (vinasse - by-product of sugarcane ethanol production) combined or not with inorganic (organic residue applied 30 days before or together with mineral N fertilizer) amendments as disturbances. Application of organic residue alone as a single disturbance or 30 days prior to a second disturbance with mineral N resulted in similar changes in the fungal community. The simultaneous application of organic and mineral N as a single pulse disturbance had the greatest impact on the fungal community. Organic amendment increased the abundance of saprotrophs, fungal species capable of denitrification, and fungi described to have copiotrophic and oligotrophic lifestyles. Furthermore, the changes in the fungal community were not correlated with the changes in the bacterial community. The fungal community was neither resistant nor resilient to organic and inorganic disturbances over the one-year sampling period. Our findings provide insights on the immediate and delayed responses of the fungal community over one year to disturbance by organic and inorganic amendments.}, }
@article {pmid32451559, year = {2020}, author = {Nettles, R and Ricks, KD and Koide, RT}, title = {The Dynamics of Interacting Bacterial and Fungal Communities of the Mouse Colon Following Antibiotics.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {573-592}, doi = {10.1007/s00248-020-01525-6}, pmid = {32451559}, issn = {1432-184X}, support = {2011-67009-20072//National Institute of Food and Agriculture/ ; }, mesh = {Animal Feed/analysis ; Animals ; Anti-Bacterial Agents/*administration &amp; dosage ; *Bacterial Physiological Phenomena ; Colon/*microbiology ; Female ; Fungi/*physiology ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred C57BL ; *Mycobiome ; Random Allocation ; }, abstract = {We tested two hypotheses concerning the dynamics of intestinal microbial communities of young mice following antibiotic-induced disturbance. The first is that disturbance of the bacterial community causes disturbance of the fungal community. Our results were consistent with that hypothesis. Antibiotics significantly altered bacterial community structure. Antibiotics also altered fungal community structure, significantly increasing the relative abundance of Candida lusitaniae, a known pathogen, while simultaneously significantly decreasing the relative abundances of several other common fungal species. The result was a temporary decrease in fungal diversity. Moreover, bacterial load was negatively correlated with the relative abundances of Candida lusitaniae and Candida parapsilosis, while it was positively correlated with the relative abundances of many other fungal species. Our second hypothesis is that control mice serve as a source of probiotics capable of invading intestines of mice with disturbed microbial communities and restoring pre-antibiotic bacterial and fungal communities. However, we found that control mice did not restore disturbed microbial communities. Instead, mice with disturbed microbial communities induced disturbance in control mice, consistent with the hypothesis that antibiotic-induced disturbance represents an alternate stable state that is easier to achieve than to correct. Our results indicate the occurrence of significant interactions among intestinal bacteria and fungi and suggest that the stimulation of certain bacterial groups may potentially be useful in countering the dominance of fungal pathogens such as Candida spp. However, the stability of disturbed microbial communities could complicate recovery.}, }
@article {pmid32451471, year = {2020}, author = {Sichert, A and Corzett, CH and Schechter, MS and Unfried, F and Markert, S and Becher, D and Fernandez-Guerra, A and Liebeke, M and Schweder, T and Polz, MF and Hehemann, JH}, title = {Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan.}, journal = {Nature microbiology}, volume = {5}, number = {8}, pages = {1026-1039}, pmid = {32451471}, issn = {2058-5276}, mesh = {Bacterial Proteins/metabolism ; Cell Wall/metabolism ; Esterases ; Genes, Bacterial/genetics ; Glycoside Hydrolases ; Metabolic Networks and Pathways ; Metagenome ; Phaeophyceae/*metabolism ; Phylogeny ; Polysaccharides/*metabolism ; Proteome ; Substrate Specificity ; Sulfatases ; Sulfates/metabolism ; Transcriptome ; United States ; Verrucomicrobia/*enzymology/genetics/isolation &amp; purification/*metabolism ; }, abstract = {Brown algae are important players in the global carbon cycle by fixing carbon dioxide into 1 Gt of biomass annually, yet the fate of fucoidan-their major cell wall polysaccharide-remains poorly understood. Microbial degradation of fucoidans is slower than that of other polysaccharides, suggesting that fucoidans are more recalcitrant and may sequester carbon in the ocean. This may be due to the complex, branched and highly sulfated structure of fucoidans, which also varies among species of brown algae. Here, we show that 'Lentimonas' sp. CC4, belonging to the Verrucomicrobia, acquired a remarkably complex machinery for the degradation of six different fucoidans. The strain accumulated 284 putative fucoidanases, including glycoside hydrolases, sulfatases and carbohydrate esterases, which are primarily located on a 0.89-megabase pair plasmid. Proteomics reveals that these enzymes assemble into substrate-specific pathways requiring about 100 enzymes per fucoidan from different species of brown algae. These enzymes depolymerize fucoidan into fucose, which is metabolized in a proteome-costly bacterial microcompartment that spatially constrains the metabolism of the toxic intermediate lactaldehyde. Marine metagenomes and microbial genomes show that Verrucomicrobia including 'Lentimonas' are abundant and highly specialized degraders of fucoidans and other complex polysaccharides. Overall, the complexity of the pathways underscores why fucoidans are probably recalcitrant and more slowly degraded, since only highly specialized organisms can effectively degrade them in the ocean.}, }
@article {pmid32446079, year = {2020}, author = {Schröer, L and De Kock, T and Cnudde, V and Boon, N}, title = {Differential colonization of microbial communities inhabiting Lede stone in the urban and rural environment.}, journal = {The Science of the total environment}, volume = {733}, number = {}, pages = {139339}, doi = {10.1016/j.scitotenv.2020.139339}, pmid = {32446079}, issn = {1879-1026}, mesh = {Archaea ; Belgium ; High-Throughput Nucleotide Sequencing ; *Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {Air pollution is one of the main actors of stone deterioration. It influences not only the material itself but also prokaryotes colonizing rocks. Prokaryotes can affect rock substrates and biological colonization will most likely become relatively more important during the course of the 21st century. Therefore, it is necessary to understand the effects of air pollution on biological colonization and on the impact of this colonization on rock weathering. For this reason, we studied the prokaryotic community of Lede stone from two deteriorated monuments in Belgium: one in the urban and one in the rural environment. This research conducts 16S rRNA gene Next Generation Sequencing combined with an isolation campaign. It revealed diverse and complex prokaryotic communities with more specialized bacteria present in the urban environment, while archaea were barely detected. Some genera could cause biodeterioration but the isolates did not produce a significant amount of acid. Soluble salts analysis revealed an important effect of salts on the prokaryotic community. Colour measurements at least indicate that a main effect of prokaryotes might be on the aesthetics: In the countryside prokaryotic communities seemed to discolour Lede stone, while pollution most likely blackened building stones in the urban environment.}, }
@article {pmid32445418, year = {2020}, author = {Spielmann, J and Ahmadi, H and Scheepers, M and Weber, M and Nitsche, S and Carnol, M and Bosman, B and Kroymann, J and Motte, P and Clemens, S and Hanikenne, M}, title = {The two copies of the zinc and cadmium ZIP6 transporter of Arabidopsis halleri have distinct effects on cadmium tolerance.}, journal = {Plant, cell &amp; environment}, volume = {43}, number = {9}, pages = {2143-2157}, doi = {10.1111/pce.13806}, pmid = {32445418}, issn = {1365-3040}, mesh = {Arabidopsis/drug effects/genetics/growth &amp; development/*physiology ; Cadmium/metabolism/*toxicity ; Carrier Proteins/genetics/metabolism ; Ecotype ; Gene Duplication ; Gene Expression Regulation, Plant ; Gene Silencing ; Genome, Plant ; Plant Proteins/*genetics/metabolism ; Plants, Genetically Modified ; Yeasts/genetics/metabolism ; Zinc/metabolism ; }, abstract = {Plants have the ability to colonize highly diverse environments. The zinc and cadmium hyperaccumulator Arabidopsis halleri has adapted to establish populations on soils covering an extreme range of metal availabilities. The A. halleri ZIP6 gene presents several hallmarks of hyperaccumulation candidate genes: it is constitutively highly expressed in roots and shoots and is associated with a zinc accumulation quantitative trait locus. Here, we show that AhZIP6 is duplicated in the A. halleri genome. The two copies are expressed mainly in the vasculature in both A. halleri and Arabidopsis thaliana, indicative of conserved cis regulation, and acquired partial organ specialization. Yeast complementation assays determined that AhZIP6 is a zinc and cadmium transporter. AhZIP6 silencing in A. halleri or expression in A. thaliana alters cadmium tolerance, but has no impact on zinc and cadmium accumulation. AhZIP6-silenced plants display reduced cadmium uptake upon short-term exposure, adding AhZIP6 to the limited number of Cd transporters supported by in planta evidence. Altogether, our data suggest that AhZIP6 is key to fine-tune metal homeostasis in specific cell types. This study additionally highlights the distinct fates of duplicated genes in A. halleri.}, }
@article {pmid32444696, year = {2020}, author = {Zhang, R and Li, Y and Yan, W and Wang, Y and Cai, L and Luo, T and Li, H and Weinbauer, MG and Jiao, N}, title = {Viral control of biomass and diversity of bacterioplankton in the deep sea.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {256}, pmid = {32444696}, issn = {2399-3642}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biomass ; *Ecosystem ; Plankton/classification/genetics/*isolation &amp; purification ; Seawater/*microbiology/*virology ; Viruses/*growth &amp; development ; }, abstract = {Viral abundance in deep-sea environments is high. However, the biological, ecological and biogeochemical roles of viruses in the deep sea are under debate. In the present study, microcosm incubations of deep-sea bacterioplankton (2,000 m deep) with normal and reduced pressure of viral lysis were conducted in the western Pacific Ocean. We observed a negative effect of viruses on prokaryotic abundance, indicating the top-down control of bacterioplankton by virioplankton in the deep-sea. The decreased bacterial diversity and a different bacterial community structure with diluted viruses indicate that viruses are sustaining a diverse microbial community in deep-sea environments. Network analysis showed that relieving viral pressure decreased the complexity and clustering coefficients but increased the proportion of positive correlations for the potentially active bacterial community, which suggests that viruses impact deep-sea bacterioplankton interactions. Our study provides experimental evidences of the crucial role of viruses in microbial ecology and biogeochemistry in deep-sea ecosystems.}, }
@article {pmid32444671, year = {2020}, author = {van Tilburg Bernardes, E and Pettersen, VK and Gutierrez, MW and Laforest-Lapointe, I and Jendzjowsky, NG and Cavin, JB and Vicentini, FA and Keenan, CM and Ramay, HR and Samara, J and MacNaughton, WK and Wilson, RJA and Kelly, MM and McCoy, KD and Sharkey, KA and Arrieta, MC}, title = {Intestinal fungi are causally implicated in microbiome assembly and immune development in mice.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2577}, pmid = {32444671}, issn = {2041-1723}, support = {//CIHR/Canada ; }, mesh = {Animals ; Bacterial Physiological Phenomena ; Colitis/chemically induced/microbiology ; Dextran Sulfate/toxicity ; Feces/microbiology ; Female ; Fungi/isolation &amp; purification/*physiology ; Gastrointestinal Microbiome/immunology/*physiology ; Germ-Free Life ; Humans ; Immune System/*growth &amp; development ; Inflammation/chemically induced/microbiology ; Intestines/*microbiology ; Metabolome ; Mice, Inbred C57BL ; Ovalbumin/toxicity ; }, abstract = {The gut microbiome consists of a multi-kingdom microbial community. Whilst the role of bacteria as causal contributors governing host physiological development is well established, the role of fungi remains to be determined. Here, we use germ-free mice colonized with defined species of bacteria, fungi, or both to differentiate the causal role of fungi on microbiome assembly, immune development, susceptibility to colitis, and airway inflammation. Fungal colonization promotes major shifts in bacterial microbiome ecology, and has an independent effect on innate and adaptive immune development in young mice. While exclusive fungal colonization is insufficient to elicit overt dextran sulfate sodium-induced colitis, bacterial and fungal co-colonization increase colonic inflammation. Ovalbumin-induced airway inflammation reveals that bacterial, but not fungal colonization is necessary to decrease airway inflammation, yet fungi selectively promotes macrophage infiltration in the airway. Together, our findings demonstrate a causal role for fungi in microbial ecology and host immune functionality, and therefore prompt the inclusion of fungi in therapeutic approaches aimed at modulating early life microbiomes.}, }
@article {pmid32441612, year = {2020}, author = {Murrell, JC and McGenity, TJ and Crombie, AT}, title = {Microbial metabolism of isoprene: a much-neglected climate-active gas.}, journal = {Microbiology (Reading, England)}, volume = {166}, number = {7}, pages = {600-613}, pmid = {32441612}, issn = {1465-2080}, mesh = {Bacteria/*genetics/*metabolism ; Biodegradation, Environmental ; Butadienes/*metabolism ; Genes, Bacterial ; Hemiterpenes/*metabolism ; Metabolic Networks and Pathways/*genetics ; Plants/microbiology ; Seawater/microbiology ; Soil Microbiology ; }, abstract = {The climate-active gas isoprene is the major volatile produced by a variety of trees and is released into the atmosphere in enormous quantities, on a par with global emissions of methane. While isoprene production in plants and its effect on atmospheric chemistry have received considerable attention, research into the biological isoprene sink has been neglected until recently. Here, we review current knowledge on the sources and sinks of isoprene and outline its environmental effects. Focusing on degradation by microbes, many of which are able to use isoprene as the sole source of carbon and energy, we review recent studies characterizing novel isoprene degraders isolated from soils, marine sediments and in association with plants. We describe the development and use of molecular methods to identify, quantify and genetically characterize isoprene-degrading strains in environmental samples. Finally, this review identifies research imperatives for the further study of the environmental impact, ecology, regulation and biochemistry of this interesting group of microbes.}, }
@article {pmid32440700, year = {2020}, author = {Des Marteaux, LE and Kullik, SA and Habash, M and Schmidt, JM}, title = {Terrestrial Isopods Porcellio scaber and Oniscus asellus (Crustacea: Isopoda) Increase Bacterial Abundance and Modify Microbial Community Structure in Leaf Litter Microcosms: a Short-Term Decomposition Study.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {690-702}, doi = {10.1007/s00248-020-01527-4}, pmid = {32440700}, issn = {1432-184X}, mesh = {Animals ; *Bacterial Physiological Phenomena ; Food Chain ; Fungi/*physiology ; *Herbivory ; Introduced Species ; Isopoda/*physiology ; *Microbiota ; Ontario ; Plant Leaves/*microbiology ; *Soil Microbiology ; }, abstract = {Invasive terrestrial isopods are likely to have altered leaf litter decomposition processes in North American forests, but the mechanisms underlying these alterations and the degree to which they differ among isopod species are poorly characterized. Using mixed-deciduous leaf litter microcosms, we quantified the effects of two common, invasive isopods (Oniscus asellus and Porcellio scaber) on short-term leaf litter decomposition and microbial community structure and function. Microcosms containing ground litter and a microbial inoculant were exposed to one of the two isopod species or no isopods for 21 days. Mass loss was then quantified as the change in litter dry mass after leaching, and microbial respiration was quantified as the mass of CO2 absorbed by soda lime. Litter leachates were plated on agar to quantify culturable bacterial and fungal abundance, and denaturing gradient gel electrophoresis of amplified leachate microbial DNA was used to characterize shifts in microbial community structure. Isopod presence increased litter mass loss by a modest ~ 6%, but did not affect litter microbial respiration. Bacterial abundance increased significantly in the presence of isopods, while fungal abundance was either unchanged or reduced. Overall litter microbial species richness was reduced by isopods, with O. asellus specifically reducing fungal abundance and diversity. Isopods modified the microbial community structure by suppressing four bacterial and one fungal species, while promoting growth of four other bacterial species (two unique to each isopod species) and two fungal species (one which was unique to O. asellus).}, }
@article {pmid32440699, year = {2020}, author = {Grimes, DJ}, title = {The Vibrios: Scavengers, Symbionts, and Pathogens from the Sea.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {501-506}, doi = {10.1007/s00248-020-01524-7}, pmid = {32440699}, issn = {1432-184X}, mesh = {Carbon/*metabolism ; Carbon Cycle ; Life History Traits ; Symbiosis ; Vibrio/metabolism/*physiology ; }, abstract = {Bacteria belonging to the genus Vibrio are major carbon cycle drivers in marine and estuarine environments. As is the case for most carbon cycle participants, the vibrios metabolize degradable compounds such as sugars and amino acids; they can also degrade some more recalcitrant compounds including hydrocarbons and lignins. Several vibrios are symbionts and even fewer are pathogenic for animals, including humans and marine animals and plants. This paper reviews Vibrio ecology, metabolism, and survival, and it also discusses select vibrios-V. alginolyticus, V. cholerae, V. coralliilyticus, V. cortegadensis, V. fischeri, V. harveyi, V. harveyi var. carahariae, V. ordalii, V. parahaemolyticus, and V. vulnificus.}, }
@article {pmid32440698, year = {2021}, author = {Torralba, MG and Kuelbs, C and Moncera, KJ and Roby, R and Nelson, KE}, title = {Characterizing Microbial Signatures on Sculptures and Paintings of Similar Provenance.}, journal = {Microbial ecology}, volume = {81}, number = {4}, pages = {1098-1105}, pmid = {32440698}, issn = {1432-184X}, mesh = {Bacteria/genetics ; DNA, Ribosomal ; Fungi/genetics ; *Microbiota ; *Paintings ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The preservation of artwork challenges museums, collectors, and art enthusiasts. Currently, reducing moisture, adjusting the type of lighting, and preventing the formation of mold are primary methods to preserving and preventing deterioration. Other methods such as ones based in detailed knowledge of molecular biology such as microbial community characterization using polymerase chain reaction (PCR) and sequencing have yet to be explored. Such molecular biology approaches are essential to explore as some environmental bacteria are capable of oxidizing nonpolar chemical substances rich in hydrocarbons such as oil-based paints. Using 16S rDNA Illumina Sequencing, we demonstrate a novel finding that there are differing bacterial communities for artwork from roughly the same era when comparing paintings on wood, paintings on canvases, and sculptures made of stone and marble. We also demonstrate that there are specific genera such as Aeromonas known for having oxidase positive strains, present on paintings on wood and paintings on canvas that could potentially be responsible for deterioration and fading as such organisms produce water or hydrogen peroxide as a byproduct of cytochrome c oxidase activity. The advantages of these genomics-based approaches to characterizing the microbial population on deteriorating artwork provides immense potential by identifying potentially damaging species that may not be detected using conventional methods in addition to addressing challenges to identification, restoration, and preservation efforts.}, }
@article {pmid32440491, year = {2020}, author = {Zheng, P and Li, Y and Wu, J and Zhang, H and Huang, Y and Tan, X and Pan, J and Duan, J and Liang, W and Yin, B and Deng, F and Perry, SW and Wong, ML and Licinio, J and Wei, H and Yu, G and Xie, P}, title = {Erratum: Perturbed Microbial Ecology in Myasthenia Gravis: Evidence from the Gut Microbiome and Fecal Metabolome.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {7}, number = {10}, pages = {2001296}, doi = {10.1002/advs.202001296}, pmid = {32440491}, issn = {2198-3844}, abstract = {[This corrects the article DOI: 10.1002/advs.201901441.].}, }
@article {pmid32439665, year = {2020}, author = {Kirchner, N and Cano-Prieto, C and van der Voort, M and Raaijmakers, JM and Gross, H}, title = {Draft Genome Sequence of Lipopeptide-Producing Strain Pseudomonas fluorescens DSM 11579 and Comparative Genomics with Pseudomonas sp. Strain SH-C52, a Closely Related Lipopeptide-Producing Strain.}, journal = {Microbiology resource announcements}, volume = {9}, number = {21}, pages = {}, pmid = {32439665}, issn = {2576-098X}, abstract = {Pseudomonas fluorescens DSM 11579 is known to be a producer of the lipopeptides brabantamide and thanamycin. Its draft genome gives insight into the complete secondary metabolite production capacity of the strain and builds the basis for a comparative study with Pseudomonas sp. strain SH-C52, a lipopeptide-producing strain involved in natural disease-suppressive soils.}, }
@article {pmid32438141, year = {2020}, author = {Hooban, B and Joyce, A and Fitzhenry, K and Chique, C and Morris, D}, title = {The role of the natural aquatic environment in the dissemination of extended spectrum beta-lactamase and carbapenemase encoding genes: A scoping review.}, journal = {Water research}, volume = {180}, number = {}, pages = {115880}, doi = {10.1016/j.watres.2020.115880}, pmid = {32438141}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; Bacterial Proteins ; Drug Resistance, Microbial ; *Genes, Bacterial ; *beta-Lactamases ; }, abstract = {The natural aquatic environment is a significant contributor to the development and circulation of clinically significant antibiotic resistance genes (ARGs). The potential for the aquatic environment to act as a reservoir for ARG accumulation in areas receiving anthropogenic contamination has been thoroughly researched. However, the emergence of novel ARGs in the absence of external influences, as well as the capacity of environmental bacteria to disseminate ARGs via mobile genetic elements remain relatively unchallenged. In order to address these knowledge gaps, this scoping literature review was established focusing on the detection of two important and readily mobile ARGs, namely, extended spectrum beta-lactamase (ESBL) and carbapenemase genes. This review included 41 studies from 19 different countries. A range of different water bodies including rivers (n = 26), seawaters (n = 6) and lakes (n = 3), amongst others, were analysed in the included studies. ESBL genes were reported in 29/41 (70.7%) studies, while carbapenemase genes were reported in 13/41 (31.7%), including joint reporting in 9 studies. The occurrence of mobile genetic elements was evaluated, which included the detection of integrons (n = 22), plasmids (n = 18), insertion sequences (n = 4) and transposons (n = 3). The ability of environmental bacteria to successfully transfer resistance genes via conjugation was also examined in 11 of the included studies. The findings of this scoping review expose the presence of clinically significant ARGs in the natural aquatic environment and highlights the potential ability of environmental isolates to disseminate these genes among different bacterial species. As such, the results presented demonstrate how anthropogenic point discharges may not act as the sole contributor to the development and spread of clinically significant antibiotic resistances. A number of critical knowledge gaps in current research were also identified. Key highlights include the limited number of studies focusing on antibiotic resistance in uncontaminated aquatic environments as well as the lack of standardisation among methodologies of reviewed investigations.}, }
@article {pmid32436568, year = {2020}, author = {Van Landuyt, J and Cimmino, L and Dumolin, C and Chatzigiannidou, I and Taveirne, F and Mattelin, V and Zhang, Y and Vandamme, P and Scoma, A and Williamson, A and Boon, N}, title = {Microbial enrichment, functional characterization and isolation from a cold seep yield piezotolerant obligate hydrocarbon degraders.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {9}, pages = {}, doi = {10.1093/femsec/fiaa097}, pmid = {32436568}, issn = {1574-6941}, mesh = {Bacteria/genetics ; Biodegradation, Environmental ; Hydrocarbons ; *Petroleum ; *Seawater ; }, abstract = {Deep-sea environments can become contaminated with petroleum hydrocarbons. The effects of hydrostatic pressure (HP) in the deep sea on microbial oil degradation are poorly understood. Here, we performed long-term enrichments (100 days) from a natural cold seep while providing optimal conditions to sustain high hydrocarbon degradation rates. Through enrichments performed at increased HP and ambient pressure (AP) and by using control enrichments with marine broth, we demonstrated that both pressure and carbon source can have a big impact on the community structure. In contrast to previous studies, hydrocarbonoclastic operational taxonomic units (OTUs) remained dominant at both AP and increased HP, suggesting piezotolerance of these OTUs over the tested pressure range. Twenty-three isolates were obtained after isolation and dereplication. After recultivation at increased HP, an Alcanivorax sp. showed promising piezotolerance in axenic culture. Furthermore, preliminary co-cultivation tests indicated synergistic growth between some isolates, which shows promise for future synthetic community construction. Overall, more insights into the effect of increased HP on oil-degrading communities were obtained as well as several interesting isolates, e.g. a piezotolerant hydrocarbonoclastic bacterium for future deep-sea bioaugmentation investigation.}, }
@article {pmid32436040, year = {2020}, author = {Rocha, KF and Kuramae, EE and Borges, BMF and Leite, MFA and Rosolem, CA}, title = {Microbial N-cycling gene abundance is affected by cover crop specie and development stage in an integrated cropping system.}, journal = {Archives of microbiology}, volume = {202}, number = {7}, pages = {2005-2012}, doi = {10.1007/s00203-020-01910-2}, pmid = {32436040}, issn = {1432-072X}, support = {2015/50305-8//FAPESP/ ; BB/N013201/1//BBRSC/ ; }, mesh = {*Agriculture ; Ammonia/metabolism ; Archaea/genetics ; Bacteria/genetics ; Crops, Agricultural/*microbiology ; Nitrification ; Nitrogen/metabolism ; Nitrogen Cycle/*genetics ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Zea mays ; }, abstract = {Grasses of the Urochloa genus have been widely used in crop-livestock integration systems or as cover crops in no-till systems such as in rotation with maize. Some species of Urochloa have mechanisms to reduce nitrification. However, the responses of microbial functions in crop-rotation systems with grasses and its consequence on soil N dynamics are not well-understood. In this study, the soil nitrification potential and the abundance of ammonifying microorganisms, total bacteria and total archaea (16S rRNA gene), nitrogen-fixing bacteria (NFB, nifH), ammonia-oxidizing bacteria (AOB, amoA) and archaea (AOA, amoA) were assessed in soil cultivated with ruzigrass (Urochloa ruziziensis), palisade grass (Urochloa brizantha) and Guinea grass (Panicum maximum). The abundance of ammonifying microorganisms was not affected by ruzigrass. Ruzigrass increased the soil nitrification potential compared with palisade and Guinea grass. Ruzigrass increased the abundance of N-fixing microorganisms at the middle and late growth stages. The abundances of nitrifying microorganisms and N-fixers in soil were positively correlated with the soil N-NH4[+] content. Thus, biological nitrogen fixation might be an important input of N in systems of rotational production of maize with forage grasses. The abundance of microorganisms related to ammonification, nitrification and nitrogen fixing and ammonia-oxidizing archea was related to the development stage of the forage grass.}, }
@article {pmid32434844, year = {2020}, author = {Minich, JJ and Petrus, S and Michael, JD and Michael, TP and Knight, R and Allen, EE}, title = {Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus.}, journal = {mSphere}, volume = {5}, number = {3}, pages = {}, pmid = {32434844}, issn = {2379-5042}, support = {P01 ES021921/ES/NIEHS NIH HHS/United States ; R01 ES030316/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Cecum/microbiology ; *Environment ; Gastrointestinal Microbiome ; *Genetic Variation ; Gills/microbiology ; *Microbiota ; Mucous Membrane/*microbiology ; Oceans and Seas ; Perciformes/*microbiology ; Skin/microbiology ; Temperature ; }, abstract = {Changing ocean conditions driven by anthropogenic activities may have a negative impact on fisheries by increasing stress and disease. To understand how environment and host biology drives mucosal microbiomes in a marine fish, we surveyed five body sites (gill, skin, digesta, gastrointestinal tract [GI], and pyloric ceca) from 229 Pacific chub mackerel, Scomber japonicus, collected across 38 time points spanning 1 year from the Scripps Institution of Oceanography Pier (La Jolla, CA). Mucosal sites had unique microbial communities significantly different from the surrounding seawater and sediment communities with over 10 times more total diversity than seawater. The external surfaces of skin and gill were more similar to seawater, while digesta was more similar to sediment. Alpha and beta diversity of the skin and gill was explained by environmental and biological factors, specifically, sea surface temperature, chlorophyll a, and fish age, consistent with an exposure gradient relationship. We verified that seasonal microbial changes were not confounded by regional migration of chub mackerel subpopulations by nanopore sequencing a 14,769-bp region of the 16,568-bp mitochondria across all temporal fish specimens. A cosmopolitan pathogen, Photobacterium damselae, was prevalent across multiple body sites all year but highest in the skin, GI, and digesta between June and September, when the ocean is warmest. The longitudinal fish microbiome study evaluates the extent to which the environment and host biology drives mucosal microbial ecology and establishes a baseline for long-term surveys linking environment stressors to mucosal health of wild marine fish.IMPORTANCE Pacific chub mackerel, Scomber japonicus, are one of the largest and most economically important fisheries in the world. The fish is harvested for both human consumption and fish meal. Changing ocean conditions driven by anthropogenic stressors like climate change may negatively impact fisheries. One mechanism for this is through disease. As waters warm and chemistry changes, the microbial communities associated with fish may change. In this study, we performed a holistic analysis of all mucosal sites on the fish over a 1-year time series to explore seasonal variation and to understand the environmental drivers of the microbiome. Understanding seasonality in the fish microbiome is also applicable to aquaculture production for producers to better understand and predict when disease outbreaks may occur based on changing environmental conditions in the ocean.}, }
@article {pmid32432525, year = {2020}, author = {Jakubovics, NS and Shi, W}, title = {A New Era for the Oral Microbiome.}, journal = {Journal of dental research}, volume = {99}, number = {6}, pages = {595-596}, doi = {10.1177/0022034520918536}, pmid = {32432525}, issn = {1544-0591}, mesh = {*Microbiota ; Mouth ; Saliva ; }, }
@article {pmid32430405, year = {2020}, author = {Fu, X and Li, Y and Yuan, Q and Cai, GH and Deng, Y and Zhang, X and Norbäck, D and Sun, Y}, title = {Continental-Scale Microbiome Study Reveals Different Environmental Characteristics Determining Microbial Richness, Composition, and Quantity in Hotel Rooms.}, journal = {mSystems}, volume = {5}, number = {3}, pages = {}, pmid = {32430405}, issn = {2379-5077}, abstract = {Culture-independent microbiome surveys have been conducted in homes, hospitals, schools, kindergartens and vehicles for public transport, revealing diverse microbial distributions in built environments. However, microbiome composition and the associated environmental characteristics have not been characterized in hotel environments. We presented here the first continental-scale microbiome study of hotel rooms (n = 68) spanning Asia and Europe. Bacterial and fungal communities were described by amplicon sequencing of the 16S rRNA gene and internal transcribed spacer (ITS) region and quantitative PCR. Similar numbers of bacterial (4,344) and fungal (4,555) operational taxonomic units were identified in the same sequencing depth, but most fungal taxa showed a restricted distribution compared to bacterial taxa. Aerobic, ubiquitous bacteria dominated the hotel microbiome with compositional similarity to previous samples from building and human nasopharynx environments. The abundance of Aspergillus was negatively correlated with latitude and accounted for ∼80% of the total fungal load in seven low-latitude hotels. We calculated the association between hotel microbiome and 16 indoor and outdoor environmental characteristics. Fungal composition and absolute quantity showed concordant associations with the same environmental characteristics, including latitude, quality of the interior, proximity to the sea, and visible mold, while fungal richness was negatively associated with heavy traffic (95% confidence interval [CI] = -127.05 to -0.25) and wall-to-wall carpet (95% CI = -47.60 to -3.82). Bacterial compositional variation was associated with latitude, quality of the interior, and floor type, while bacterial richness was negatively associated with recent redecoration (95% CI -179.00 to -44.55) and mechanical ventilation (95% CI = -136.71 to -5.12).IMPORTANCE This is the first microbiome study to characterize the microbiome data and associated environmental characteristics in hotel environments. In this study, we found concordant variation between fungal compositional variation and absolute quantity and discordant variation between community variation/quantity and richness. Our study can be used to promote hotel hygiene standards and provide resource information for future microbiome and exposure studies associated with health effects in hotel rooms.}, }
@article {pmid32426533, year = {2020}, author = {Venturini, AM and Nakamura, FM and Gontijo, JB and da França, AG and Yoshiura, CA and Mandro, JA and Tsai, SM}, title = {Robust DNA protocols for tropical soils.}, journal = {Heliyon}, volume = {6}, number = {5}, pages = {e03830}, pmid = {32426533}, issn = {2405-8440}, abstract = {Studies in the Amazon are being intensified to evaluate the alterations in the microbial communities of soils and sediments in the face of increasing deforestation and land-use changes in the region. However, since these environments present highly heterogeneous physicochemical properties, including contaminants that hinder nucleic acids isolation and downstream techniques, the development of best molecular practices is crucial. This work aimed to optimize standard protocols for DNA extraction and gene quantification by quantitative real-time PCR (qPCR) based on natural and anthropogenic soils and sediments (primary forest, pasture, Amazonian Dark Earth, and várzea, a seasonally flooded area) of the Eastern Amazon. Our modified extraction protocol increased the fluorometric DNA concentration by 48%, reaching twice the original amount for most of the pasture and várzea samples, and the 260/280 purity ratio by 15% to values between 1.8 to 2.0, considered ideal for DNA. The addition of bovine serum albumin in the qPCR reaction improved the quantification of the 16S rRNA genes of Archaea and Bacteria and its precision among technical replicates, as well as allowed their detection in previously non-amplifiable samples. It is concluded that the changes made in the protocols improved the parameters of the DNA samples and their amplification, thus increasing the reliability of microbial communities' analysis and its ecological interpretations.}, }
@article {pmid32425165, year = {2020}, author = {Oliveira, BG and Mendes, LW and Smyth, EM and Tsai, SM and Feigl, BJ and Mackie, RI}, title = {Assessment of microbial diversity associated with CH4 emission from sugarcane vinasse storage and transportation systems.}, journal = {Journal of environmental management}, volume = {269}, number = {}, pages = {110748}, doi = {10.1016/j.jenvman.2020.110748}, pmid = {32425165}, issn = {1095-8630}, mesh = {Brazil ; *Greenhouse Gases ; Methane ; RNA, Ribosomal, 16S ; *Saccharum ; }, abstract = {Sugarcane bioethanol has favorable energy and greenhouse gas balance, although the production process generates several residues including vinasse, which deserves attention because of its significant methane (CH4) emission during storage and transportation stages. Considering that CH4 emissions are dependent on the structure and abundance of microbial communities, we hypothesized that different vinasse transportation systems would harbor different microbial community composition, resulting in distinct CH4 patterns. To test this hypothesis, we used high-throughput 16S rRNA sequencing with real-time PCR to evaluate the composition and abundance of microorganisms in the two main systems of vinasse storage and transportation (i.e. open channels and tanks systems) in Brazil. Our results showed higher microbial diversity and CH4 emissions in channel system, especially in the uncoated section. Significant differences in microbial community structure, diversity, and abundance between the uncoated/coated open channel and tanks indicated a clear selection at taxonomic and functional levels, especially in relation to CH4 production. These responses included higher methanogens diversity in the uncoated section of the channel and are in agreement with the methanogen abundance determined by mcrA and mba genes copy number (1.5 × 10[7] and 4.3 × 10[10]) and subsequent positive correlation with CH4 emissions (R[2] = 0.8). The most representative methanogen genus across the samples was Methanobrevibacter. The results observed herein shows that the use of the coating in the bottom of channels and tanks prevent the growth and development of a methanogen-related community. We concluded that the improvements in vinasse storage and transportation systems would significantly change the microbial community and reduce CH4 emissions, thereby making bioethanol a greener biofuel.}, }
@article {pmid32424717, year = {2020}, author = {Grajal-Puche, A and Murray, CM and Kearley, M and Merchant, M and Nix, C and Warner, JK and Walker, DM}, title = {Microbial Assemblage Dynamics Within the American Alligator Nesting Ecosystem: a Comparative Approach Across Ecological Scales.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {603-613}, doi = {10.1007/s00248-020-01522-9}, pmid = {32424717}, issn = {1432-184X}, mesh = {*Alligators and Crocodiles ; Animals ; Bacteria/classification/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; Ecology ; *Ecosystem ; Environmental Microbiology ; *Microbiota ; Nesting Behavior ; Texas ; }, abstract = {Understanding the ecological processes that shape species assemblage patterns is central to community ecology. The effects of ecological processes on assemblage patterns are scale-dependent. We used metabarcoding and shotgun sequencing to determine bacterial taxonomic and functional assemblage patterns among varying defined focal scales (micro-, meso-, and macroscale) within the American alligator (Alligator mississippiensis) nesting microbiome. We correlate bacterial assemblage patterns among eight nesting compartments within and proximal to alligator nests (micro-), across 18 nests (meso-), and between 4 geographic sampling sites (macro-), to determine which ecological processes may drive bacterial assemblage patterns within the nesting environment. Among all focal scales, bacterial taxonomic and functional richness (α-diversity) did not statistically differ. In contrast, bacterial assemblage structure (β-diversity) was unique across all focal scales, whereas functional pathways were redundant within nests and across geographic sites. Considering these observed scale-based patterns, taxonomic bacterial composition may be governed by unique environmental filters and dispersal limitations relative to microbial functional attributes within the alligator nesting environment. These results advance pattern-process dynamics within the field of microbial community ecology and describe processes influencing the American alligator nest microbiome.}, }
@article {pmid32419297, year = {2021}, author = {Xing, J and Jia, X and Wang, H and Ma, B and Falcão Salles, J and Xu, J}, title = {The legacy of bacterial invasions on soil native communities.}, journal = {Environmental microbiology}, volume = {23}, number = {2}, pages = {669-681}, doi = {10.1111/1462-2920.15086}, pmid = {32419297}, issn = {1462-2920}, support = {B17039//Higher Education Discipline Innovation Project/ ; //KNAW-CSC/ ; 2016YFD0800207//National Key Research and Development Program of China/ ; 41721001//National Natural Science Foundation of China/ ; }, mesh = {Ecosystem ; Escherichia coli O157/*growth &amp; development/*metabolism ; *Introduced Species ; Microbial Interactions/*physiology ; Microbiota ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Soil microbial communities are often not resistant to the impact caused by microbial invasions, both in terms of structure and functionality, but it remains unclear whether these changes persist over time. Here, we used three strains of Escherichia coli O157:H7 (E. coli O157:H7), a species used for modelling bacterial invasions, to evaluate the resilience of the bacterial communities from four Chinese soils to invasion. The impact of E. coli O157:H7 strains on soil native communities was tracked for 120 days by analysing bacterial community composition as well as their metabolic potential. We showed that soil native communities were not resistant to invasion, as demonstrated by a decline in bacterial diversity and shifts in bacterial composition in all treatments. The resilience of native bacterial communities (diversity and composition) was inversely correlated with invader's persistence in soils (R[2] = 0.487, p < 0.001). Microbial invasions also impacted the functionality of the soil communities (niche breadth and community niche), the degree of resilience being dependent on soil or native community diversity. Collectively, our results indicate that bacteria invasions can potentially leave a footprint in the structure and functionality of soil communities, indicating the need of assessing the legacy of introducing exotic species in soil environments.}, }
@article {pmid32417556, year = {2020}, author = {Gallego, S and Barkay, T and Fahrenfeld, NL}, title = {Tagging the vanA gene in wastewater microbial communities for cell sorting and taxonomy of vanA carrying cells.}, journal = {The Science of the total environment}, volume = {732}, number = {}, pages = {138865}, doi = {10.1016/j.scitotenv.2020.138865}, pmid = {32417556}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Bacterial Proteins ; Carbon-Oxygen Ligases ; In Situ Hybridization, Fluorescence ; Microbial Sensitivity Tests ; *Microbiota ; Phylogeny ; Wastewater ; }, abstract = {Failure to understand the microbial ecology driving the proliferation of antibiotic resistance in the environment prevents us from developing strategies to limit the spread of antibiotic resistant infectious disease. In this study, we developed for the first time a tyramide signal amplification-fluorescence in situ hybridization-fluorescence-activated cell sorting protocol (TSA-FISH-FACS) for the characterization of all vanA carrying bacteria in wastewater samples. Firstly, we validated the TSA-FISH protocol through microscopy in pure cultures and wastewater influent. Then, samples were sorted and quantified by FACS and qPCR. Significantly higher percentage tagging of cells was detected in vanA carrying pure cultures and wastewater samples spiked with vanA carrying cells as compared to vanA negative Gram positive strains and non-spiked wastewater samples respectively. qPCR analysis targeting vanZ, a regulating gene in the vanA cluster, showed its relative abundance was significantly greater in Enterococcus faecium ATCC 700221-spiked and positively sorted samples compared to the E. faecium spiked and negatively sorted samples. Phylogenetic analysis was then performed. Although further efforts are needed to overcome technical problems, we have, for the first time, demonstrated sorting bacterial-cells carrying antibiotic resistance genes from wastewater samples through a TSA-FISH-FACS protocol and provided insight into the microbial ecology of vancomycin resistant bacteria. Future potential applications using this approach will include the separation of members of an environmental microbial community (cultured and hard-to-culture) to allow for metagenomics on single cells or, in the case of clumping, targeting a smaller portion of the community with a priori knowledge that the target gene is present.}, }
@article {pmid32415330, year = {2020}, author = {Pajares, S and Varona-Cordero, F and Hernández-Becerril, DU}, title = {Spatial Distribution Patterns of Bacterioplankton in the Oxygen Minimum Zone of the Tropical Mexican Pacific.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {519-536}, doi = {10.1007/s00248-020-01508-7}, pmid = {32415330}, issn = {1432-184X}, support = {PAPIIT-IA201617//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, mesh = {*Bacterial Physiological Phenomena ; Mexico ; Microbiota/*physiology ; Oxygen/analysis ; Pacific Ocean ; Plankton/*physiology ; Seawater/*microbiology ; Tropical Climate ; }, abstract = {Microbial communities within oxygen minimum zones (OMZs) are crucial drivers of marine biogeochemical cycles; however, we still lack an understanding of how these communities are distributed across an OMZ. We explored vertical (from 5 to 500 m depth) and horizontal (coast to open ocean) distribution of bacterioplankton and its relationships with the main oceanographic conditions in three transects of the tropical Mexican Pacific OMZ. The distribution of the microbial diversity and the main clades changed along the transition from oxygen-rich surface water to the OMZ core, demonstrating the sensitivity of key bacterial groups to deoxygenation. The euphotic zone was dominated by Synechococcales, followed by Flavobacteriales, Verrucomicrobiales, Rhodobacterales, SAR86, and Cellvibrionales, whereas the OMZ core was dominated by SAR11, followed by SAR406, SAR324, SAR202, UBA10353 marine group, Thiomicrospirales and Nitrospinales. The marked environmental gradients along the water column also supported a high potential for niche partitioning among OMZ microorganisms. Additionally, in the OMZ core, bacterial assemblages from the same water mass were more similar to each other than those from another water mass. There were also important differences between coastal and open-ocean communities: Flavobacteriales, Verrucomicrobiales, Rhodobacterales, SAR86, and Cellvibrionales were more abundant in coastal areas, while Synechococcales, SAR406, SAR324, SAR202, UBA10353 marine group, and Thiomicrospirales were more abundant in the open ocean. Our results suggest a biogeographic structure of the bacterioplankton in this OMZ region, with limited community mixing across water masses, except in upwelling events, and little dispersion of the community by currents in the euphotic zone.}, }
@article {pmid32414800, year = {2020}, author = {Jiang, W and Wang, Y and Luo, J and Chen, X and Zeng, Y and Li, X and Feng, Z and Zhang, L}, title = {Antimicrobial Peptide GH12 Prevents Dental Caries by Regulating Dental Plaque Microbiota.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {14}, pages = {}, pmid = {32414800}, issn = {1098-5336}, mesh = {Adult ; Animals ; Anti-Bacterial Agents/*pharmacology ; Antimicrobial Cationic Peptides/*pharmacology ; Bacterial Physiological Phenomena/*drug effects ; Biofilms/*drug effects/growth &amp; development ; Dental Caries/genetics/*prevention &amp; control ; Dental Plaque/*microbiology ; Female ; Humans ; Male ; Microbiota/*drug effects ; Rats ; Rats, Sprague-Dawley ; Specific Pathogen-Free Organisms ; Young Adult ; }, abstract = {Due to the complex microecology and microenvironment of dental plaque, novel caries prevention strategies require modulating the microbial communities ecologically and reducing the cariogenic properties effectively. Antimicrobial peptide GH12 reduced the lactic acid production and exopolysaccharide (EPS) synthesis of a Streptococcus mutans biofilm and a three-species biofilm in vitro in previous studies. However, the anticaries effects and microecological effects of GH12 remained to be investigated in a complex biofilm model in vitro and an animal caries model in vivo In the present study, GH12 at 64 mg/liter showed the most effective inhibition of lactic acid production, EPS synthesis, pH decline, and biofilm integrity of human dental plaque-derived multispecies biofilms in vitro, and GH12 at 64 mg/liter was therefore chosen for use in subsequent in vitro and in vivo assays. When treated with 64-mg/liter GH12, the dental plaque-derived multispecies biofilms sampled from healthy volunteers maintained its microbial diversity and showed a microbial community structure similar to that of the control group. In the rat caries model with a caries-promoting diet, 64-mg/liter GH12 regulated the microbiota of dental plaque, in which the abundance of caries-associated bacteria was decreased and the abundance of commensal bacteria was increased. In addition, 64-mg/liter GH12 significantly reduced the caries scores of sulcal and smooth surface caries in all locations. In conclusion, GH12 inhibited the cariogenic properties of dental plaque without perturbing the dental plaque microbiota of healthy individuals and GH12 regulated the dysbiotic microbial ecology and arrested caries development under cariogenic conditions.IMPORTANCE The anticaries effects and microecological regulation effects of the antimicrobial peptide GH12 were evaluated systematically in vitro and in vivo GH12 inhibited the cariogenic virulence of dental plaque without overintervening in the microbial ecology of healthy individuals in vitro GH12 regulated the microbial ecology of dental plaque to a certain extent in vivo under cariogenic conditions, increased the proportion of commensal bacteria, and decreased the abundance of caries-associated bacteria. GH12 significantly suppressed the incidence and severity of dental caries in vivo This study thus describes an alternative antimicrobial therapy for dental caries.}, }
@article {pmid32414048, year = {2020}, author = {Kuramae, EE and Derksen, S and Schlemper, TR and Dimitrov, MR and Costa, OYA and Silveira, APDD}, title = {Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics.}, journal = {Microorganisms}, volume = {8}, number = {5}, pages = {}, pmid = {32414048}, issn = {2076-2607}, support = {729.004.013//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 456420/2013-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, abstract = {Bacteria from the genera Paraburkholderia and Herbaspirillum can promote the growth of Sorghum bicolor, but the underlying mechanisms are not yet known. In a pot experiment, sorghum plants grown on sterilized substrate were inoculated with Paraburkholderia tropica strain IAC/BECa 135 and Herbaspirillum frisingense strain IAC/BECa 152 under phosphate-deficient conditions. These strains significantly increased Sorghum bicolor cultivar SRN-39 root and shoot biomass. Shotgun metagenomic analysis of the rhizosphere revealed successful colonization by both strains; however, the incidence of colonization was higher in plants inoculated with P. tropica strain IAC/BECa 135 than in those inoculated with H. frisingense strain IAC/BECa 152. Conversely, plants inoculated with H. frisingense strain IAC/BECa 152 showed the highest increase in biomass. Genomic analysis of the two inoculants implied a high degree of rhizosphere fitness of P. tropica strain IAC/BECa 135 through environmental signal processing, biofilm formation, and nutrient acquisition. Both genomes contained genes related to plant growth-promoting bacterial (PGPB) traits, including genes related to indole-3-acetate (IAA) synthesis, nitrogen fixation, nodulation, siderophore production, and phosphate solubilization, although the P. tropica strain IAC/BECa 135 genome contained a slightly more extensive repertoire. This study provides evidence that complementary mechanisms of growth promotion in Sorghum might occur, i.e., that P. tropica strain IAC/BECa 135 acts in the rhizosphere and increases the availability of nutrients, while H. frisingense strain IAC/BECa 152 influences plant hormone signaling. While the functional and taxonomic profiles of the rhizobiomes were similar in all treatments, significant differences in plant biomass were observed, indicating that the rhizobiome and the endophytic microbial community may play equally important roles in the complicated plant-microbial interplay underlying increased host plant growth.}, }
@article {pmid32413640, year = {2020}, author = {Barbosa, RG and Sleutels, T and Verstraete, W and Boon, N}, title = {Hydrogen oxidizing bacteria are capable of removing orthophosphate to ultra-low concentrations in a fed batch reactor configuration.}, journal = {Bioresource technology}, volume = {311}, number = {}, pages = {123494}, doi = {10.1016/j.biortech.2020.123494}, pmid = {32413640}, issn = {1873-2976}, mesh = {Bacteria ; Bioreactors ; *Hydrogen ; Oxidation-Reduction ; *Phosphates ; Phosphorus ; }, abstract = {This paper proposes the use of hydrogen oxidizing bacteria (HOB) for the removal of orthophosphate from surface water as treatment step to prevent cyanobacterial blooms. To be effective as an orthophosphate removal strategy, an efficient transfer of hydrogen to the HOB is essential. A trickling filter was selected for this purpose. Using this system, a removal rate of 11.32 ± 0.43 mg PO4[-3]-P/L.d was achieved. The HOB biomass, developed on the trickling filter, is composed of 1.25% phosphorus on dry matter, which suggests that the orthophosphate removal principle is based on HOB growth. Cyanobacterial growth assays of the untreated and treated water showed that Synechocystis sp was only able to grow in the untreated water. Orthophosphate was removed to average residual values of 0.008 mg/L. In this proof of principle study, it is shown that HOB are able to remove orthophosphate from water to concentrations that prevent cyanobacterial growth.}, }
@article {pmid32410366, year = {2021}, author = {Durán-Viseras, A and Andrei, A&#x15e; and Vera-Gargallo, B and Ghai, R and Sánchez-Porro, C and Ventosa, A}, title = {Culturomics-based genomics sheds light on the ecology of the new haloarchaeal genus Halosegnis.}, journal = {Environmental microbiology}, volume = {23}, number = {7}, pages = {3418-3434}, doi = {10.1111/1462-2920.15082}, pmid = {32410366}, issn = {1462-2920}, mesh = {DNA, Bacterial ; *Genomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salinity ; }, abstract = {The development of culture-independent techniques has revolutionized our understanding of microbial ecology, especially through the illustration of the vast gap between the environmentally abundant microbial diversity and that accessible through cultivation. However, culture-based approaches are not only crucial for understanding the evolutionary, metabolic and ecological milieu of microbial diversity but also for the development of novel biotechnological applications. In this study, we used a culturomics-based approach in order to isolate novel microbial taxa from hypersaline environments (i.e. Isla Cristina and Isla Bacuta salterns in Huelva, Spain). We managed to obtain axenic cultures of four haloarchaeal strains that belong to a new haloarchaeal genus and to obtain their genomic sequences. The phylogenomic and phylogenetic analyses (together with AAI, ANI and digital DDH indices) showed that the isolates constitute two new species, for which we propose the names Halosegnis longus sp. nov. and Halosegnis rubeus sp. nov. The genomic-based metabolic reconstructions indicated that members of this new haloarchaeal genus have photoheterotrophic aerobic lifestyle with a typical salt-in signature. 16S rRNA gene sequence reads abundance profiles and genomic recruitment analyses revealed that the Halosegnis genus has a worldwide geographical distribution, reaching high abundance (up to 8%) in habitats with intermediate salinities.}, }
@article {pmid32410293, year = {2020}, author = {Qureshi, SS and Kedo, M and Berthrong, ST}, title = {Gender-neutral bathroom surfaces recolonized by microbes more quickly than single-gender bathrooms.}, journal = {Letters in applied microbiology}, volume = {71}, number = {2}, pages = {134-137}, doi = {10.1111/lam.13316}, pmid = {32410293}, issn = {1472-765X}, support = {//Butler University's Center for High Achievement and Scholarly Engagement Honors Program/ ; }, mesh = {Bacteria/classification/*growth &amp; development/isolation &amp; purification ; Bacterial Load/*statistics &amp; numerical data ; Female ; Humans ; Male ; Microbiota/*physiology ; Sex Factors ; Sexual and Gender Minorities/statistics &amp; numerical data ; Toilet Facilities/*statistics &amp; numerical data ; United States ; }, abstract = {As humans become increasingly urban and spend more time inside the built environment, there will be increased interactions between humans and shared public surface microbiomes. Recent cultural changes in the United States have led to increased numbers of gender-neutral bathrooms. Given that bathroom surfaces are frequently sanitized, we used this increased availability of gender-neutral bathrooms to examine how single-gender or gender-neutral surfaces are recolonized with microbes. Given that male and female microbiomes vary, we hypothesized that rates of recolonization would differ between male, female and gender-neutral bathroom surfaces. We collected swabs from common hand-contacted surfaces in bathrooms and cultured microbes on selective and rich media to determine microbial abundance after cleaning. Recolonization was dominated by Gram-positive bacteria and was slowest on male, intermediate on female and fastest on gender-neutral surfaces. These results imply that gender-neutral surfaces approach normal climax microbial communities more quickly than single-gender bathrooms. SIGNIFICANCE OF IMPACT OF THE STUDY: Humans now spend substantial amount of time within the built environment, and as a consequence the human microbiome interacts frequently with indoor surfaces. Social changes are making gender-neutral public bathrooms more common, so it is important to study how humans and microbiomes interact with these bathroom surfaces. We found that the gender-neutral bathroom surfaces recolonize more quickly than single-gender, which suggests that there are more potential human-surface microbiome connections in these public spaces. These results will potentially add a new layer to our understanding of the interactions of humans, our microbiomes and how we design our built environment.}, }
@article {pmid32409544, year = {2020}, author = {Šimoliūnienė, M and Tumėnas, D and Kvederavičiūtė, K and Meškys, R and Šulčius, S and Šimoliūnas, E}, title = {Complete Genome Sequence of Bacillus cereus Bacteriophage vB_BceS_KLEB30-3S.}, journal = {Microbiology resource announcements}, volume = {9}, number = {20}, pages = {}, pmid = {32409544}, issn = {2576-098X}, abstract = {In this study, we present the genomic characterization of the temperate bacteriophage vB_BceS_KLEB30-3S (KLEB30-3S), which was induced from Bacillus cereus strain KR3M-30, isolated from a gypsum karst lake ecosystem in Lithuania. The 37,134-bp genome of KLEB30-3S contains 58 predicted protein-encoding genes and no tRNA genes.}, }
@article {pmid32409535, year = {2020}, author = {Köstlbacher, S and Michels, S and Siegl, A and Schulz, F and Domman, D and Jongwutiwes, S and Putaporntip, C and Horn, M and Collingro, A}, title = {Draft Genome Sequences of Chlamydiales Bacterium STE3 and Neochlamydia sp. Strain AcF84, Endosymbionts of Acanthamoeba spp.}, journal = {Microbiology resource announcements}, volume = {9}, number = {20}, pages = {}, pmid = {32409535}, issn = {2576-098X}, abstract = {Chlamydiales bacterium STE3 and Neochlamydia sp. strain AcF84 are obligate intracellular symbionts of Acanthamoeba spp. isolated from the biofilm of a littoral cave wall and gills from striped tiger leaf fish, respectively. We report the draft genome sequences of these two environmental chlamydiae affiliated with the family Parachlamydiaceae.}, }
@article {pmid32405432, year = {2020}, author = {Zwart, MP and Elena, SF}, title = {Modeling multipartite virus evolution: the genome formula facilitates rapid adaptation to heterogeneous environments[†].}, journal = {Virus evolution}, volume = {6}, number = {1}, pages = {veaa022}, pmid = {32405432}, issn = {2057-1577}, abstract = {Multipartite viruses have two or more genome segments, and package different segments into different particle types. Although multipartition is thought to have a cost for virus transmission, its benefits are not clear. Recent experimental work has shown that the equilibrium frequency of viral genome segments, the setpoint genome formula (SGF), can be unbalanced and host-species dependent. These observations have reinvigorated the hypothesis that changes in genome-segment frequencies can lead to changes in virus-gene expression that might be adaptive. Here we explore this hypothesis by developing models of bipartite virus infection, leading to a threefold contribution. First, we show that the SGF depends on the cellular multiplicity of infection (MOI), when the requirements for infection clash with optimizing the SGF for virus-particle yield per cell. Second, we find that convergence on the SGF is very rapid, often occurring within a few cellular rounds of infection. Low and intermediate MOIs lead to faster convergence on the SGF. For low MOIs, this effect occurs because of the requirements for infection, whereas for intermediate MOIs this effect is also due to the high levels of variation generated in the genome formula (GF). Third, we explored the conditions under which a bipartite virus could outcompete a monopartite one. As the heterogeneity between environments and specificity of gene-expression requirements for each environment increased, the bipartite virus was more likely to outcompete the monopartite virus. Under some conditions, changes in the GF helped to exclude the monopartite competitor, highlighting the versatility of the GF. Our results show the inextricable relationship between MOI and the SGF, and suggest that under some conditions, the cost of multipartition can be outweighed by its benefits for the rapid tuning of viral gene expression.}, }
@article {pmid32404904, year = {2020}, author = {Pascual-García, A and Bell, T}, title = {Community-level signatures of ecological succession in natural bacterial communities.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2386}, pmid = {32404904}, issn = {2041-1723}, mesh = {Bacteria/classification/genetics/*growth &amp; development ; *Biodiversity ; *Biota ; DNA, Bacterial/genetics ; Ecosystem ; Metagenome/genetics ; Microbiota ; Phylogeny ; Population Dynamics ; RNA, Ribosomal, 16S/*genetics ; Stochastic Processes ; }, abstract = {A central goal in microbial ecology is to simplify the extraordinary biodiversity that inhabits natural environments into ecologically coherent units. We profiled (16S rRNA sequencing) > 700 semi-aquatic bacterial communities while measuring their functional capacity when grown in laboratory conditions. This approach allowed us to investigate the relationship between composition and function excluding confounding environmental factors. Simulated data allowed us to reject the hypothesis that stochastic processes were responsible for community assembly, suggesting that niche effects prevailed. Consistent with this idea we identified six distinct community classes that contained samples collected from distant locations. Structural equation models showed there was a functional signature associated with each community class. We obtained a more mechanistic understanding of the classes using metagenomic predictions (PiCRUST). This approach allowed us to show that the classes contained distinct genetic repertoires reflecting community-level ecological strategies. The ecological strategies resemble the classical distinction between r- and K-strategists, suggesting that bacterial community assembly may be explained by simple ecological mechanisms.}, }
@article {pmid32402266, year = {2020}, author = {Mahú, I and Barateiro, A and Rial-Pensado, E and Martinéz-Sánchez, N and Vaz, SH and Cal, PMSD and Jenkins, B and Rodrigues, T and Cordeiro, C and Costa, MF and Mendes, R and Seixas, E and Pereira, MMA and Kubasova, N and Gres, V and Morris, I and Temporão, C and Olivares, M and Sanz, Y and Koulman, A and Corzana, F and Sebastião, AM and López, M and Bernardes, GJL and Domingos, AI}, title = {Brain-Sparing Sympathofacilitators Mitigate Obesity without Adverse Cardiovascular Effects.}, journal = {Cell metabolism}, volume = {31}, number = {6}, pages = {1120-1135.e7}, pmid = {32402266}, issn = {1932-7420}, support = {MC_UU_00014/5/MRC_/Medical Research Council/United Kingdom ; /HHMI/Howard Hughes Medical Institute/United States ; MC_UU_12012/5/MRC_/Medical Research Council/United Kingdom ; 208576/WT_/Wellcome Trust/United Kingdom ; BB/M027252/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 208576/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Amphetamine/*pharmacology ; Animals ; Anti-Obesity Agents/*pharmacology ; Brain/*drug effects/metabolism ; Cells, Cultured ; Female ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Obesity/*drug therapy/metabolism ; }, abstract = {Anti-obesity drugs in the amphetamine (AMPH) class act in the brain to reduce appetite and increase locomotion. They are also characterized by adverse cardiovascular effects with origin that, despite absence of any in vivo evidence, is attributed to a direct sympathomimetic action in the heart. Here, we show that the cardiac side effects of AMPH originate from the brain and can be circumvented by PEGylation (PEGyAMPH) to exclude its central action. PEGyAMPH does not enter the brain and facilitates SNS activity via theβ2-adrenoceptor, protecting mice against obesity by increasing lipolysis and thermogenesis, coupled to higher heat dissipation, which acts as an energy sink to increase energy expenditure without altering food intake or locomotor activity. Thus, we provide proof-of-principle for a novel class of exclusively peripheral anti-obesity sympathofacilitators that are devoid of any cardiovascular and brain-related side effects.}, }
@article {pmid32399630, year = {2020}, author = {Brunel, C and Da Silva, AF and Gros, R}, title = {Environmental Drivers of Microbial Functioning in Mediterranean Forest Soils.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {669-681}, doi = {10.1007/s00248-020-01518-5}, pmid = {32399630}, issn = {1432-184X}, mesh = {Bacteria/*metabolism ; *Bacterial Physiological Phenomena ; Carbon/*metabolism ; *Forests ; France ; *Soil Microbiology ; }, abstract = {Mediterranean forests own distinct characteristics resulting from climate, soil, and vegetation that affect soil microbial communities' assembly and their associated functions. We initiated a multi-scalar analysis of environmental drivers of soil functioning to (1) identify pertinent factorial scales and (2) determine the relative importance of soil, vegetation, and geoclimate influences in shaping soil microbial functions across the French Mediterranean forests. Soil samples (0-15 cm) were collected from 60 forest sites and soil physicochemical and microbiological properties were assessed across different factorial scales i.e., bioclimates, slope exposures, and forest stands. Patterns in microbial catabolic potential (i.e., extracellular enzymes and microbial respiration) and carbon (C) source utilization (i.e., catabolic-level physiological profiling) were partitioned between vegetation cover, soil characteristics, and geoclimate components. Our results reveal that the catabolic potential of soil microbes was strongly influenced by the forest stands and mainly relied on ammonium and nitrate contents. In contrast, variation in C source utilization was mainly explained by vegetation cover. Soil metabolic capacities of microorganisms and resulting C dynamics were largely constrained by climate parameters, which suggests potentially important consequences for soil C storage. Our study revealed diverse structuration patterns between the catabolic potential and the carbon source utilization of soil microbial communities, and gives insights into the underlying mechanisms of soil microbial functioning in Mediterranean forests.}, }
@article {pmid32398103, year = {2020}, author = {Mohr, AE and Jäger, R and Carpenter, KC and Kerksick, CM and Purpura, M and Townsend, JR and West, NP and Black, K and Gleeson, M and Pyne, DB and Wells, SD and Arent, SM and Kreider, RB and Campbell, BI and Bannock, L and Scheiman, J and Wissent, CJ and Pane, M and Kalman, DS and Pugh, JN and Ortega-Santos, CP and Ter Haar, JA and Arciero, PJ and Antonio, J}, title = {The athletic gut microbiota.}, journal = {Journal of the International Society of Sports Nutrition}, volume = {17}, number = {1}, pages = {24}, pmid = {32398103}, issn = {1550-2783}, mesh = {Athletic Performance/*physiology ; *Diet ; Exercise/*physiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Sports Nutritional Physiological Phenomena ; }, abstract = {The microorganisms in the gastrointestinal tract play a significant role in nutrient uptake, vitamin synthesis, energy harvest, inflammatory modulation, and host immune response, collectively contributing to human health. Important factors such as age, birth method, antibiotic use, and diet have been established as formative factors that shape the gut microbiota. Yet, less described is the role that exercise plays, particularly how associated factors and stressors, such as sport/exercise-specific diet, environment, and their interactions, may influence the gut microbiota. In particular, high-level athletes offer remarkable physiology and metabolism (including muscular strength/power, aerobic capacity, energy expenditure, and heat production) compared to sedentary individuals, and provide unique insight in gut microbiota research. In addition, the gut microbiota with its ability to harvest energy, modulate the immune system, and influence gastrointestinal health, likely plays an important role in athlete health, wellbeing, and sports performance. Therefore, understanding the mechanisms in which the gut microbiota could play in the role of influencing athletic performance is of considerable interest to athletes who work to improve their results in competition as well as reduce recovery time during training. Ultimately this research is expected to extend beyond athletics as understanding optimal fitness has applications for overall health and wellness in larger communities. Therefore, the purpose of this narrative review is to summarize current knowledge of the athletic gut microbiota and the factors that shape it. Exercise, associated dietary factors, and the athletic classification promote a more "health-associated" gut microbiota. Such features include a higher abundance of health-promoting bacterial species, increased microbial diversity, functional metabolic capacity, and microbial-associated metabolites, stimulation of bacterial abundance that can modulate mucosal immunity, and improved gastrointestinal barrier function.}, }
@article {pmid32397606, year = {2020}, author = {Colquhoun, C and Duncan, M and Grant, G}, title = {Inflammatory Bowel Diseases: Host-Microbial-Environmental Interactions in Dysbiosis.}, journal = {Diseases (Basel, Switzerland)}, volume = {8}, number = {2}, pages = {}, pmid = {32397606}, issn = {2079-9721}, abstract = {Crohn's Disease (CD) and Ulcerative Colitis (UC) are world-wide health problems in which intestinal dysbiosis or adverse functional changes in the microbiome are causative or exacerbating factors. The reduced abundance and diversity of the microbiome may be a result of a lack of exposure to vital commensal microbes or overexposure to competitive pathobionts during early life. Alternatively, many commensal bacteria may not find a suitable intestinal niche or fail to proliferate or function in a protective/competitive manner if they do colonize. Bacteria express a range of factors, such as fimbriae, flagella, and secretory compounds that enable them to attach to the gut, modulate metabolism, and outcompete other species. However, the host also releases factors, such as secretory IgA, antimicrobial factors, hormones, and mucins, which can prevent or regulate bacterial interactions with the gut or disable the bacterium. The delicate balance between these competing host and bacteria factors dictates whether a bacterium can colonize, proliferate or function in the intestine. Impaired functioning of NOD2 in Paneth cells and disrupted colonic mucus production are exacerbating features of CD and UC, respectively, that contribute to dysbiosis. This review evaluates the roles of these and other the host, bacterial and environmental factors in inflammatory bowel diseases.}, }
@article {pmid32396806, year = {2020}, author = {Herren, CM}, title = {Disruption of cross-feeding interactions by invading taxa can cause invasional meltdown in microbial communities.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1927}, pages = {20192945}, pmid = {32396806}, issn = {1471-2954}, mesh = {Biota ; *Ecosystem ; *Introduced Species ; *Microbiota ; }, abstract = {The strength of biotic interactions within an ecological community affects the susceptibility of the community to invasion by introduced taxa. In microbial communities, cross-feeding is a widespread type of biotic interaction that has the potential to affect community assembly and stability. Yet, there is little understanding of how the presence of cross-feeding within a community affects invasion risk. Here, I develop a metabolite-explicit model where native microbial taxa interact through both cross-feeding and competition for metabolites. I use this model to study how the strength of biotic interactions, especially cross-feeding, influence whether an introduced taxon can join the community. I found that stronger cross-feeding and competition led to much lower invasion risk, as both types of biotic interactions lead to greater metabolite scarcity for the invader. I also evaluated the impact of a successful invader on community composition and structure. The effect of invaders on the native community was greatest at intermediate levels of cross-feeding; at this 'critical' level of cross-feeding, successful invaders generally cause decreased diversity, decreased productivity, greater metabolite availability, and decreased quantities of metabolites exchanged among taxa. Furthermore, these changes resulting from a successful primary invader made communities further susceptible to future invaders. The increase in invasion risk was greatest when the network of metabolite exchange between taxa was minimally redundant. Thus, this model demonstrates a case of invasional meltdown that is mediated by initial invaders disrupting the metabolite exchange networks of the native community.}, }
@article {pmid32394640, year = {2020}, author = {Paula, CCP and Bichuette, ME and Seleghim, MHR}, title = {Nutrient availability in tropical caves influences the dynamics of microbial biomass.}, journal = {MicrobiologyOpen}, volume = {9}, number = {7}, pages = {e1044}, pmid = {32394640}, issn = {2045-8827}, mesh = {Bacteria/*growth &amp; development/*metabolism ; Biomass ; Brazil ; Carbon/analysis ; Caves/*chemistry/*microbiology ; Nitrogen/analysis ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {Few studies have evaluated the trophic level in tropical caves, and none related the microbial biomass dynamics in the immobilization of carbon and nitrogen. Here, four tropical caves of Terra Ronca State Park, Brazil, were studied: Angélica, São Bernardo, Terra Ronca I, and Terra Ronca II caves. Physical, chemical, and microbiological parameters (microbial biomass and respiration) were estimated in the dry and wet seasons. São Bernardo, Terra Ronca I, and Terra Ronca II caves presented higher nitrogen and microbial biomass nitrogen (MBN) values in the wet season than in the dry season. On the other hand, the Angélica cave showed larger amounts of nitrogen and lower MBN values in the dry season. These results indicate that caves can be adjusted in two ecological theories known as "stoichiometric decomposition" and "microbial nitrogen mining"-to the effects of nutrient availability on organic matter decomposition. The caves studied showed different environmental dynamics in relation to organic matter decomposition, which allows them to be considered unique and possess specific characteristics. Microbial biomass dynamics can be an important parameter to evaluate the availability of nutrients and ecological dynamics of the trophic network in subterranean environments.}, }
@article {pmid32393397, year = {2020}, author = {Koh, H and Zhao, N}, title = {A powerful microbial group association test based on the higher criticism analysis for sparse microbial association signals.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {63}, pmid = {32393397}, issn = {2049-2618}, support = {P30 AI094189/AI/NIAID NIH HHS/United States ; U24 OD023382/OD/NIH HHS/United States ; }, mesh = {*Computational Biology ; Humans ; *Microbiota ; *Software ; }, abstract = {BACKGROUND: In human microbiome studies, it is crucial to evaluate the association between microbial group (e.g., community or clade) composition and a host phenotype of interest. In response, a number of microbial group association tests have been proposed, which account for the unique features of the microbiome data (e.g., high-dimensionality, compositionality, phylogenetic relationship). These tests generally fall in the class of aggregation tests which amplify the overall group association by combining all the underlying microbial association signals, and, therefore, they are powerful when many microbial species are associated with a given host phenotype (i.e., low sparsity). However, in practice, the microbial association signals can be highly sparse, and this is especially the situation where we have a difficulty to discover the microbial group association.<br><br>METHODS: Here, we introduce a powerful microbial group association test for sparse microbial association signals, namely, microbiome higher criticism analysis (MiHC). MiHC is a data-driven omnibus test taken in a search space spanned by tailoring the higher criticism test to incorporate phylogenetic information and/or modulate sparsity levels and including the Simes test for excessively high sparsity levels. Therefore, MiHC robustly adapts to diverse phylogenetic relevance and sparsity levels.<br><br>RESULTS: Our simulations show that MiHC maintains a high power at different phylogenetic relevance and sparsity levels with correct type I error controls. We also apply MiHC to four real microbiome datasets to test the association between respiratory tract microbiome and smoking status, the association between the infant's gut microbiome and delivery mode, the association between the gut microbiome and type 1 diabetes status, and the association between the gut microbiome and human immunodeficiency virus status.<br><br>CONCLUSIONS: In practice, the true underlying association pattern on the extent of phylogenetic relevance and sparsity is usually unknown. Therefore, MiHC can be a useful analytic tool because of its high adaptivity to diverse phylogenetic relevance and sparsity levels. MiHC can be implemented in the R computing environment using our software package freely available at https://github.com/hk1785/MiHC.}, }
@article {pmid32392181, year = {2020}, author = {He, J and Xu, S and Zhang, B and Xiao, C and Chen, Z and Si, F and Fu, J and Lin, X and Zheng, G and Yu, G and Chen, J}, title = {Gut microbiota and metabolite alterations associated with reduced bone mineral density or bone metabolic indexes in postmenopausal osteoporosis.}, journal = {Aging}, volume = {12}, number = {9}, pages = {8583-8604}, pmid = {32392181}, issn = {1945-4589}, mesh = {Absorptiometry, Photon ; *Bone Density ; Bone Remodeling ; Bone and Bones/*physiology ; Collagen Type I/metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Mass Spectrometry ; Metabolomics ; Middle Aged ; Osteoporosis, Postmenopausal/diagnosis/*metabolism/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Reduced bone mineral density (BMD) is associated with an altered microbiota in senile osteoporosis. However, the relationship among gut microbiota, BMD and bone metabolic indexes remains unknown in postmenopausal osteoporosis. In this study, fecal microbiota profiles for 106 postmenopausal individuals with osteopenia (n=33) or osteoporosis (n=42) or with normal BMD (n=31) were determined. An integrated 16S rRNA gene sequencing and LC-MS-based metabolomics approach was applied to explore the association of estrogen-reduced osteoporosis with the gut microbiota and fecal metabolic phenotype. Adjustments were made using several statistical models for potential confounding variables identified from the literature. The results demonstrated decreased bacterial richness and diversity in postmenopausal osteoporosis. Additionally, showed significant differences in abundance levels among phyla and genera in the gut microbial community were found. Moreover, postmenopausal osteopenia-enriched N-acetylmannosamine correlated negatively with BMD, and distinguishing metabolites were closely associated with gut bacterial variation. Both serum procollagen type I N propeptide (P1NP) and C-terminal telopeptide of type I collagen (CTX-1) correlated positively with osteopenia-enriched Allisonella, Klebsiella and Megasphaera. However, we did not find a significant correlation between bacterial diversity and estrogen. These observations will lead to a better understanding of the relationship between bone homeostasis and the microbiota in postmenopausal osteoporosis.}, }
@article {pmid32391139, year = {2019}, author = {Obolski, U and Perez, PN and Villabona-Arenas, CJ and Thézé, J and Faria, NR and Lourenço, J}, title = {MVSE: An R-package that estimates a climate-driven mosquito-borne viral suitability index.}, journal = {Methods in ecology and evolution}, volume = {10}, number = {8}, pages = {1357-1370}, pmid = {32391139}, issn = {2041-210X}, abstract = {Viruses, such as dengue, Zika, yellow fever and chikungunya, depend on mosquitoes for transmission. Their epidemics typically present periodic patterns, linked to the underlying mosquito population dynamics, which are known to be driven by natural climate fluctuations. Understanding how climate dictates the timing and potential of viral transmission is essential for preparedness of public health systems and design of control strategies. While various alternative approaches have been proposed to estimate local transmission potential of such viruses, few open-source, ready to use and freely available software tools exist.We developed the Mosquito-borne Viral Suitability Estimator (MVSE) software package for the R programming environment. MVSE estimates the index P, a novel suitability index based on a climate-driven mathematical expression for the basic reproductive number of mosquito-borne viruses. By accounting for local humidity and temperature, as well as viral, vector and human priors, the index P can be estimated for specific host and viral species in different regions of the globe.We describe the background theory, empirical support and biological interpretation of the index P. Using real-world examples spanning multiple epidemiological contexts, we further demonstrate MVSE's basic functionality, research and educational potentials.}, }
@article {pmid32390961, year = {2020}, author = {Samad, MS and Lee, HJ and Cerbin, S and Meima-Franke, M and Bodelier, PLE}, title = {Niche Differentiation of Host-Associated Pelagic Microbes and Their Potential Contribution to Biogeochemical Cycling in Artificially Warmed Lakes.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {582}, pmid = {32390961}, issn = {1664-302X}, abstract = {It has been proposed that zooplankton-associated microbes provide numerous beneficial services to their "host". However, there is still a lack of understanding concerning the effect of temperature on the zooplankton microbiome. Furthermore, it is unclear to what extent the zooplankton microbiome differs from free-living and particle-associated (PA) microbes. Here, we explicitly addressed these issues by investigating (1) the differences in free-living, PA, and zooplankton associated microbes and (2) the impact of temperature on these microbes in the water column of a series of lakes artificially warmed by two power plants. High-throughput amplicon sequencing of the 16S rRNA gene showed that diversity and composition of the bacterial community associated to zooplankton, PA, and bacterioplankton varied significantly from one another, grouping in different clusters indicating niche differentiation of pelagic microbes. From the abiotic parameters measured, temperature significantly affected the diversity and composition of all analyzed microbiomes. Two phyla (e.g., Proteobacteria and Bacteroidetes) dominated in zooplankton microbiomes whereas Actinobacteria was the dominant phylum in the bacterioplankton. The microbial species richness and diversity was lower in zooplankton compared to bacterioplankton and PA. Surprisingly, genera of methane-oxidizing bacteria, methylotrophs and nitrifiers (e.g., Nitrobacter) significantly associated with the microbiome of zooplankton and PA. Our study clearly demonstrates niche differentiation of pelagic microbes and their potential link to biogeochemical cycling in freshwater systems.}, }
@article {pmid32389289, year = {2020}, author = {Araújo, CAS and Ferreira, PC and Pupin, B and Dias, LP and Avalos, J and Edwards, J and Hallsworth, JE and Rangel, DEN}, title = {Osmotolerance as a determinant of microbial ecology: A study of phylogenetically diverse fungi.}, journal = {Fungal biology}, volume = {124}, number = {5}, pages = {273-288}, doi = {10.1016/j.funbio.2019.09.001}, pmid = {32389289}, issn = {1878-6146}, mesh = {*Ecosystem ; *Fungi/classification/physiology ; Phylogeny ; *Salt Tolerance ; }, abstract = {Osmotic stress induced by high solute concentration can prevent fungal metabolism and growth due to alterations in properties of the cytosol, changes in turgor, and the energy required to synthesize and retain compatible solutes. We used germination to quantify tolerance/sensitivity to the osmolyte KCl (0.1-4.5 M, in 0.1 M increments) for 71 strains (40 species) of ecologically diverse fungi. These include 11 saprotrophic species (17 strains, including two xerophilic species), five mycoparasitic species (five strains), six plant-pathogenic species (13 strains), and 19 entomopathogenic species (36 strains). A dendrogram obtained from cluster analyses, based on KCl inhibitory concentrations 50 % and 90 % calculated by Probit Analysis, revealed three groups of fungal isolates accordingly to their osmotolerance. The most-osmotolerant group (Group 3) contained the majority of saprotrophic fungi, and Aspergillus niger (F19) was the most tolerant. The highly xerophilic Aspergillus montevidense and Aspergillus pseudoglaucus were the second- and third-most tolerant species, respectively. All Aspergillus and Cladosporium species belonged to Group 3, followed by the entomopathogens Colletotrichum fioriniae, Simplicillium lanosoniveum, and Trichothecium roseum. Group 2 exhibited a moderate osmotolerance, and included plant-pathogens such as Colletotrichum and Fusarium, mycoparasites such as Clonostachys spp, some saprotrophs such as Mucor and Penicillium spp., and some entomopathogens such as Isaria, Lecanicillium, Mariannaea, Simplicillium, and Torrubiella. Group 1 contained the osmo-sensitive strains: the rest of the entomopathogens and the mycoparasitic Gliocladium and Trichoderma. Although stress tolerance did not correlate with their primary ecological niche, classification of these 71 fungal strains was more closely aligned with their ecology than with their phylogenetic relatedness. We discuss the implications for both microbial ecology and fungal taxonomy.}, }
@article {pmid32388577, year = {2020}, author = {Seward, J and Carson, MA and Lamit, LJ and Basiliko, N and Yavitt, JB and Lilleskov, E and Schadt, CW and Smith, DS and Mclaughlin, J and Mykytczuk, N and Willims-Johnson, S and Roulet, N and Moore, T and Harris, L and Bräuer, S}, title = {Peatland Microbial Community Composition Is Driven by a Natural Climate Gradient.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {593-602}, doi = {10.1007/s00248-020-01510-z}, pmid = {32388577}, issn = {1432-184X}, mesh = {Archaea/*isolation &amp; purification ; Bacteria/*isolation &amp; purification ; *Climate ; *Microbiota ; Ontario ; Soil Microbiology ; United States ; *Wetlands ; }, abstract = {Peatlands are important players in climate change-biosphere feedbacks via long-term net carbon (C) accumulation in soil organic matter and as potential net C sources including the potent greenhouse gas methane (CH4). Interactions of climate, site-hydrology, plant community, and groundwater chemical factors influence peatland development and functioning, including C dioxide (CO2) and CH4 fluxes, but the role of microbial community composition is not well understood. To assess microbial functional and taxonomic dissimilarities, we used high throughput sequencing of the small subunit ribosomal DNA (SSU rDNA) to determine bacterial and archaeal community composition in soils from twenty North American peatlands. Targeted DNA metabarcoding showed that although Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla on average, intermediate and rich fens hosted greater diversity and taxonomic richness, as well as an array of candidate phyla when compared with acidic and nutrient-poor poor fens and bogs. Moreover, pH was revealed to be the strongest predictor of microbial community structure across sites. Predictive metagenome content (PICRUSt) showed increases in specific genes, such as purine/pyrimidine and amino-acid metabolism in mid-latitude peatlands from 38 to 45° N, suggesting a shift toward utilization of microbial biomass over utilization of initial plant biomass in these microbial communities. Overall, there appears to be noticeable differences in community structure between peatland classes, as well as differences in microbial metabolic activity between latitudes. These findings are in line with a predicted increase in the decomposition and accelerated C turnover, and suggest that peatlands north of 37° latitude may be particularly vulnerable to climate change.}, }
@article {pmid32388576, year = {2020}, author = {Gnanasekaran, G}, title = {Correction to: Disappearance of Quorum Sensing in Burkholderia Glumae During Experimental Evolution.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {739}, doi = {10.1007/s00248-020-01516-7}, pmid = {32388576}, issn = {1432-184X}, abstract = {Following the publication of this article [ 1 ], authors Jae Yun Lim and Ingyu Hwang have stated that they were not aware of, nor were they involved in the drafting, submission, or revision of this manuscript.}, }
@article {pmid32385877, year = {2020}, author = {Loos, BG and Van Dyke, TE}, title = {The role of inflammation and genetics in periodontal disease.}, journal = {Periodontology 2000}, volume = {83}, number = {1}, pages = {26-39}, pmid = {32385877}, issn = {1600-0757}, mesh = {Genome-Wide Association Study ; *Gingivitis ; Humans ; Inflammation ; *Periodontal Diseases ; *Periodontitis ; }, abstract = {Periodontitis is a complex disease: (a) various causative factors play a role simultaneously and interact with each other; and (b) the disease is episodic in nature, and bursts of disease activity can be recognized, ie, the disease develops and cycles in a nonlinear fashion. We recognize that various causative factors determine the immune blueprint and, consequently, the immune fitness of a subject. Normally, the host lives in a state of homeostasis or symbiosis with the oral microbiome; however, disturbances in homeostatic balance can occur, because of an aberrant host response (inherited and/or acquired during life). This imbalance results from hyper- or hyporesponsiveness and/or lack of sufficient resolution of inflammation, which in turn is responsible for much of the disease destruction seen in periodontitis. The control of this destruction by anti-inflammatory processes and proresolution processes limits the destruction to the tissues surrounding the teeth. The local inflammatory processes can also become systemic, which in turn affect organs such as the heart. Gingival inflammation also elicits changes in the ecology of the subgingival environment providing optimal conditions for the outgrowth of gram-negative, anaerobic species, which become pathobionts and can propagate periodontal inflammation and can further negatively impact immune fitness. The factors that determine immune fitness are often the same factors that determine the response to the resident biofilm, and are clustered as follows: (a) genetic and epigenetic factors; (b) lifestyle factors, such as smoking, diet, and psychosocial conditions; (c) comorbidities, such as diabetes; and (d) local and dental factors, as well as randomly determined factors (stochasticity). Of critical importance are the pathobionts in a dysbiotic biofilm that drive the viscious cycle. Focusing on genetic factors, currently variants in at least 65 genes have been suggested as being associated with periodontitis based on genome-wide association studies and candidate gene case control studies. These studies have found pleiotropy between periodontitis and cardiovascular diseases. Most of these studies point to potential pathways in the pathogenesis of periodontal disease. Also, most contribute to a small portion of the total risk profile of periodontitis, often limited to specific racial and ethnic groups. To date, 4 genetic loci are shared between atherosclerotic cardiovascular diseases and periodontitis, ie, CDKN2B-AS1(ANRIL), a conserved noncoding element within CAMTA1 upstream of VAMP3, PLG, and a haplotype block at the VAMP8 locus. The shared genes suggest that periodontitis is not causally related to atherosclerotic diseases, but rather both conditions are sequelae of similar (the same?) aberrant inflammatory pathways. In addition to variations in genomic sequences, epigenetic modifications of DNA can affect the genetic blueprint of the host responses. This emerging field will yield new valuable information about susceptibility to periodontitis and subsequent persisting inflammatory reactions in periodontitis. Further studies are required to verify and expand our knowledge base before final cause and effect conclusions about the role of inflammation and genetic factors in periodontitis can be made.}, }
@article {pmid32385616, year = {2020}, author = {Cockburn, CF and Gregory, BRB and Nasser, NA and Patterson, RT}, title = {Intra-Lake Arcellinida (Testate Lobose Amoebae) Response to Winter De-icing Contamination in an Eastern Canada Road-Side "Salt Belt" Lake.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {366-383}, doi = {10.1007/s00248-020-01513-w}, pmid = {32385616}, issn = {1432-184X}, mesh = {*Environmental Monitoring ; Lakes/chemistry/*parasitology ; Lobosea/drug effects/*isolation &amp; purification ; Ontario ; Salinity ; Seasons ; Sodium Chloride/*adverse effects ; Water Pollutants, Chemical/*adverse effects ; }, abstract = {Salt contamination of lakes, due to the application of winter de-icing salts on roads, presents a significant environmental challenge in the "salt belt" region of eastern North America. The research reported here presents the first deployment of a previously published proxy tool based on Arcellinida (testate lobose amoebae) for monitoring road salt contamination. The research was conducted at Silver Lake in Eastern Ontario, a 4-km-long lake with the heavily traveled Trans-Canada Highway (HWY 7) transiting the entire southern shore. The lake showed elevated conductivity (297-310 μS/cm) and sub-brackish conditions (0.14-0.15 ppt). Sodium levels were also elevated near the roadside (median Na = 1020 ppm). Cluster analysis and nonmetric multidimensional scaling results revealed four distinct Arcellinida assemblages: "Stressed Cool Water Assemblage (SCWA)," "Deep Cold Water Assemblage (DCWA)," both from below the 8-m thermocline, and the shallower water "Shallow Water Assemblage 1 (SWA-1)" and "Shallow Water Assemblage 2 (SWA-2)". Redundancy analysis showed a minor response of Arcellinida to road salt contamination in shallower areas of the lake, with confounding variables significantly impacting assemblage distribution, particularly beneath the thermocline (e.g., water temperature, water depth, sediment runoff from catchment [Ti], sediment geochemistry [Ca, S]). The results of this study indicate that the trophic structure of the lake has to date only been modestly impacted by the cumulative nature of road salt contamination. Nonetheless, the Silver Lake results should be considered of concern and warrant continued arcellinidan biomonitoring to gauge the ongoing and long-term effects of road salt on its ecosystem.}, }
@article {pmid32385615, year = {2020}, author = {Vences, A and Abushattal, S and Matanza, XM and Dubert, J and Uzun, E and Ogut, H and Osorio, CR}, title = {Highly Transferable pAQU-Related Plasmids Encoding Multidrug Resistance Are Widespread in the Human and Fish Pathogen Photobacterium damselae subsp. damselae in Aquaculture Areas in the Black Sea.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {507-518}, doi = {10.1007/s00248-020-01519-4}, pmid = {32385615}, issn = {1432-184X}, support = {AGL2016-79738-R//Agencia Estatal de Investigaci&#xf3;n/ ; AGL2016-79738-R//FEDER/ ; ED431C 2018/18//Secretaria Xeral de Investigaci&#xf3;n e Desenvolvemento, Xunta de Galicia/ ; }, mesh = {Aquaculture ; Black Sea ; Drug Resistance, Multiple, Bacterial/*genetics ; Photobacterium/*genetics ; Plasmids/*genetics ; }, abstract = {The marine bacterium Photobacterium damselae subsp. damselae is a pathogen that causes disease in diverse marine animals, and is also a serious opportunistic human pathogen that can cause fatal infections. Strains of this pathogen isolated from diseased European sea bass in aquaculture facilities in the Turkish coast of the Black Sea were found to exhibit reduced sensitivity to multiple antimicrobials. Selected representative strains were subjected to complete genome sequencing and plasmid characterization. It was found that multidrug resistant (MDR) isolates harboured large conjugative plasmids sharing part of their sequence backbone with pAQU-group plasmids, hitherto reported exclusively in China and Japan. Four new pAQU-group versions of plasmids were identified in the present study, containing distinct combinations of the resistance determinants tetB, floR, sul2, qnrVC, dfrA and strAB. Conjugative transfer of pPHDD2-OG2, a representative plasmid of 170,998 bp, occurred at high frequencies (2.2 × 10[-2] transconjugants per donor cell), to E. coli and to pathogenic P. damselae subsp. damselae and subsp. piscicida strains. Upon transfer, pPHDD2-OG2 conferred reduced susceptibility to a number of antimicrobials to the recipient strains. Comparative genomics analysis of host strains suggested that these MDR plasmids of the pAQU-group were acquired by different genetic lineages of Pdd. This study provides evidence that P. damselae subsp. damselae isolated from diseased fish constitute a reservoir for conjugative MDR pAQU-group plasmids in the Mediterranean basin, and have the potential to spread to diverse bacterial species.}, }
@article {pmid32385111, year = {2020}, author = {Glaub, A and Huptas, C and Neuhaus, K and Ardern, Z}, title = {Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data.}, journal = {The Journal of biological chemistry}, volume = {295}, number = {27}, pages = {8999-9011}, pmid = {32385111}, issn = {1083-351X}, mesh = {Bacteria/*genetics ; Computational Biology/methods ; Genetic Profile ; High-Throughput Nucleotide Sequencing/methods ; Molecular Sequence Annotation/methods ; Protein Biosynthesis/genetics ; RNA, Messenger/genetics ; RNA, Ribosomal/metabolism ; Ribosomes/*genetics ; Sequence Analysis, RNA/*methods ; }, abstract = {Ribosome profiling (RIBO-Seq) has improved our understanding of bacterial translation, including finding many unannotated genes. However, protocols for RIBO-Seq and corresponding data analysis are not yet standardized. Here, we analyzed 48 RIBO-Seq samples from nine studies of Escherichia coli K12 grown in lysogeny broth medium and particularly focused on the size-selection step. We show that for conventional expression analysis, a size range between 22 and 30 nucleotides is sufficient to obtain protein-coding fragments, which has the advantage of removing many unwanted rRNA and tRNA reads. More specific analyses may require longer reads and a corresponding improvement in rRNA/tRNA depletion. There is no consensus about the appropriate sequencing depth for RIBO-Seq experiments in prokaryotes, and studies vary significantly in total read number. Our analysis suggests that 20 million reads that are not mapping to rRNA/tRNA are required for global detection of translated annotated genes. We also highlight the influence of drug-induced ribosome stalling, which causes bias at translation start sites. The resulting accumulation of reads at the start site may be especially useful for detecting weakly expressed genes. As different methods suit different questions, it may not be possible to produce a "one-size-fits-all" ribosome profiling data set. Therefore, experiments should be carefully designed in light of the scientific questions of interest. We propose some basic characteristics that should be reported with any new RIBO-Seq data sets. Careful attention to the factors discussed should improve prokaryotic gene detection and the comparability of ribosome profiling data sets.}, }
@article {pmid32384669, year = {2020}, author = {Kazou, M and Tzamourani, A and Panagou, EZ and Tsakalidou, E}, title = {Unraveling the Microbiota of Natural Black cv. Kalamata Fermented Olives through 16S and ITS Metataxonomic Analysis.}, journal = {Microorganisms}, volume = {8}, number = {5}, pages = {}, pmid = {32384669}, issn = {2076-2607}, support = {2018&#x3a3;&#x395;01300000//Greek national funds through the Public Investments Program (PIP) of General Secretariat for Research &amp; Technology (GSRT), under the Emblematic Action "The Olive Road"/ ; }, abstract = {Kalamata natural black olives are one of the most economically important Greek varieties. The microbial ecology of table olives is highly influenced by the co-existence of bacteria and yeasts/fungi, as well as the physicochemical parameters throughout the fermentation. Therefore, the aim of this study was the identification of bacterial and yeast/fungal microbiota of both olives and brines obtained from 29 cv. Kalamata olive samples industrially fermented in the two main producing geographical regions of Greece, namely Aitoloakarnania and Messinia/Lakonia. The potential microbial biogeography association between certain taxa and geographical area was also assessed. The dominant bacterial family identified in olive and brine samples from both regions was Lactobacillaceae, presenting, however, higher average abundances in the samples from Aitoloakarnania compared to Messinia/Lakonia. At the genus level, Lactobacillus, Celerinatantimonas, Propionibacterium and Pseudomonas were the most abundant. In addition, the yeasts/fungal communities were less diverse compared to those of bacteria, with Pichiaceae being the dominant family and Pichia, Ogataea, and Saccharomyces being the most abundant genera. To the best of our knowledge, this is the first report on the microbiota of both olives and brines of cv. Kalamata black olives fermented on an industrial scale between two geographical regions of Greece using metagenomics analysis.}, }
@article {pmid32382073, year = {2020}, author = {Floudas, D and Bentzer, J and Ahrén, D and Johansson, T and Persson, P and Tunlid, A}, title = {Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi.}, journal = {The ISME journal}, volume = {14}, number = {8}, pages = {2046-2059}, pmid = {32382073}, issn = {1751-7370}, mesh = {*Agaricales ; *Basidiomycota ; Fungi/genetics ; Humans ; Lignin ; Phylogeny ; Wood ; }, abstract = {Litter decomposing Agaricales play key role in terrestrial carbon cycling, but little is known about their decomposition mechanisms. We assembled datasets of 42 gene families involved in plant-cell-wall decomposition from seven newly sequenced litter decomposers and 35 other Agaricomycotina members, mostly white-rot and brown-rot species. Using sequence similarity and phylogenetics, we split the families into phylogroups and compared their gene composition across nutritional strategies. Subsequently, we used Raman spectroscopy to examine the ability of litter decomposers, white-rot fungi, and brown-rot fungi to decompose crystalline cellulose. Both litter decomposers and white-rot fungi share the enzymatic cellulose decomposition, whereas brown-rot fungi possess a distinct mechanism that disrupts cellulose crystallinity. However, litter decomposers and white-rot fungi differ with respect to hemicellulose and lignin degradation phylogroups, suggesting adaptation of the former group to the litter environment. Litter decomposers show high phylogroup diversity, which is indicative of high functional versatility within the group, whereas a set of white-rot species shows adaptation to bulk-wood decomposition. In both groups, we detected species that have unique characteristics associated with hitherto unknown adaptations to diverse wood and litter substrates. Our results suggest that the terms white-rot fungi and litter decomposers mask a much larger functional diversity.}, }
@article {pmid32379897, year = {2020}, author = {Hicks, LC and Leizeaga, A and Rousk, K and Michelsen, A and Rousk, J}, title = {Simulated rhizosphere deposits induce microbial N-mining that may accelerate shrubification in the subarctic.}, journal = {Ecology}, volume = {101}, number = {9}, pages = {e03094}, doi = {10.1002/ecy.3094}, pmid = {32379897}, issn = {1939-9170}, support = {20150561//The Crafoord Foundation/ ; 2018-01315//The Swedish Research Council Formas/ ; KAW 2017.0171//The Knut and Alice Wallenberg Foundation/ ; CTS16: 385//Carl Tryggers Foundation/ ; }, mesh = {Carbon ; Climate Change ; Nitrogen ; *Rhizosphere ; Soil ; *Soil Microbiology ; }, abstract = {Climate change is exposing high-latitude systems to warming and a shift towards more shrub-dominated plant communities, resulting in increased leaf-litter inputs at the soil surface, and more labile root-derived organic matter (OM) input in the soil profile. Labile OM can stimulate the mineralization of soil organic matter (SOM); a phenomenon termed "priming." In N-poor subarctic soils, it is hypothesized that microorganisms may "prime" SOM in order to acquire N (microbial N-mining). Increased leaf-litter inputs with a high C/N ratio might further exacerbate microbial N demand, and increase the susceptibility of N-poor soils to N-mining. We investigated the N-control of SOM mineralization by amending soils from climate change-simulation treatments in the subarctic (+1.1°C warming, birch litter addition, willow litter addition, and fungal sporocarp addition) with labile OM either in the form of glucose (labile C; equivalent to 400 µg C/g fresh [fwt] soil) or alanine (labile C + N; equivalent to 400 µg C and 157 µg N/g fwt soil), to simulate rhizosphere inputs. Surprisingly, we found that despite 5 yr of simulated climate change treatments, there were no significant effects of the field-treatments on microbial process rates, community structure or responses to labile OM. Glucose primed the mineralization of both C and N from SOM, but gross mineralization of N was stimulated more than that of C, suggesting that microbial SOM use increased in magnitude and shifted to components richer in N (i.e., selective microbial N-mining). The addition of alanine also resulted in priming of both C and N mineralization, but the N mineralization stimulated by alanine was greater than that stimulated by glucose, indicating strong N-mining even when a source of labile OM including N was supplied. Microbial carbon use efficiency was reduced in response to both labile OM inputs. Overall, these findings suggest that shrub expansion could fundamentally alter biogeochemical cycling in the subarctic, yielding more N available for plant uptake in these N-limited soils, thus driving positive plant-soil feedbacks.}, }
@article {pmid32377220, year = {2020}, author = {Masteling, R and Voorhoeve, L and IJsselmuiden, J and Dini-Andreote, F and de Boer, W and Raaijmakers, JM}, title = {DiSCount: computer vision for automated quantification of Striga seed germination.}, journal = {Plant methods}, volume = {16}, number = {}, pages = {60}, pmid = {32377220}, issn = {1746-4811}, abstract = {BACKGROUND: Plant parasitic weeds belonging to the genus Striga are a major threat for food production in Sub-Saharan Africa and Southeast Asia. The parasite's life cycle starts with the induction of seed germination by host plant-derived signals, followed by parasite attachment, infection, outgrowth, flowering, reproduction, seed set and dispersal. Given the small seed size of the parasite (< 200 μm), quantification of the impact of new control measures that interfere with seed germination relies on manual, labour-intensive counting of seed batches under the microscope. Hence, there is a need for high-throughput assays that allow for large-scale screening of compounds or microorganisms that adversely affect Striga seed germination.<br><br>RESULTS: Here, we introduce DiSCount (Digital Striga Counter): a computer vision tool for automated quantification of total and germinated Striga seed numbers in standard glass fibre filter assays. We developed the software using a machine learning approach trained with a dataset of 98 manually annotated images. Then, we validated and tested the model against a total dataset of 188 manually counted images. The results showed that DiSCount has an average error of 3.38 percentage points per image compared to the manually counted dataset. Most importantly, DiSCount achieves a 100 to 3000-fold speed increase in image analysis when compared to manual analysis, with an inference time of approximately 3&#xa0;s per image on a single CPU and 0.1&#xa0;s on a GPU.<br><br>CONCLUSIONS: DiSCount is accurate and efficient in quantifying total and germinated Striga seeds in a standardized germination assay. This automated computer vision tool enables for high-throughput, large-scale screening of chemical compound libraries and biological control agents of this devastating parasitic weed. The complete software and manual are hosted at https://gitlab.com/lodewijk-track32/discount_paper and the archived version is available at Zenodo with the DOI 10.5281/zenodo.3627138. The dataset used for testing is available at Zenodo with the DOI 10.5281/zenodo.3403956.}, }
@article {pmid32375874, year = {2020}, author = {Rifkin, RF and Vikram, S and Ramond, JB and Rey-Iglesia, A and Brand, TB and Porraz, G and Val, A and Hall, G and Woodborne, S and Le Bailly, M and Potgieter, M and Underdown, SJ and Koopman, JE and Cowan, DA and Van de Peer, Y and Willerslev, E and Hansen, AJ}, title = {Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the 'ancestral' sub-Saharan African intestinal microbiome.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {62}, pmid = {32375874}, issn = {2049-2618}, mesh = {Africa South of the Sahara ; *Archaeology ; Feces/*microbiology ; *Gastrointestinal Microbiome ; History, 15th Century ; Humans ; Metagenomics ; }, abstract = {BACKGROUND: The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen.<br><br>METHODS: Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM.<br><br>RESULTS: Our results indicate that the distal IM of the Neolithic 'Middle Iron Age' (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (&#xd6;tzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to 'Western' diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants.<br><br>CONCLUSIONS: Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000&#x2009;years ago. Video Abtract.}, }
@article {pmid32373631, year = {2020}, author = {Zannoni, A and Pietra, M and Gaspardo, A and Accorsi, PA and Barone, M and Turroni, S and Laghi, L and Zhu, C and Brigidi, P and Forni, M}, title = {Non-invasive Assessment of Fecal Stress Biomarkers in Hunting Dogs During Exercise and at Rest.}, journal = {Frontiers in veterinary science}, volume = {7}, number = {}, pages = {126}, pmid = {32373631}, issn = {2297-1769}, abstract = {Intense exercise causes to organisms to have oxidative stress and inflammation at the gastrointestinal (GI) level. The reduction in intestinal blood flow and the exercise-linked thermal damage to the intestinal mucosa can cause intestinal barrier disruption, followed by an inflammatory response. Furthermore, the adaptation to exercise may affect the gut microbiota and the metabolome of the biofluids. The aim of the present research was to evaluate the presence of a GI derangement in hunting dogs through a non-invasive sampling as a consequence of a period of intense exercise in comparison with samples collected at rest. The study included nine dogs that underwent the same training regime for hunting wild boar. In order to counterbalance physiological variations, multiple-day replicates were collected and pooled at each experimental point for each dog. The samples were collected immediately at rest before the training (T0), after 60 days of training (T1), after 60 days of hunting wild boar (T2), and finally, at 60 days of rest after hunting (T3). A number of potential stress markers were evaluated: fecal cortisol metabolites (FCMs) as a major indicator of altered physiological states, immunoglobulin A (IgA) as an indicator of intestinal immune protection, and total antioxidant activity [total antioxidant capacity (TAC)]. Since stool samples contain exfoliated cells, we investigated also the presence of some transcripts involved in GI permeability [occludin (OCLN), protease-activated receptor-2 (PAR-2)] and in the inflammatory mechanism [interleukin (IL)-8, IL-6, IL-1b, tumor necrosis factor alpha (TNFα), calprotectin (CALP), heme oxygenase-1 (HO-1)]. Finally, the metabolome and the microbiota profiles were analyzed. No variation in FCM and IgA content and no differences in OCLN and CALP gene expression between rest and training were observed. On the contrary, an increase in PAR-2 and HO-1 transcripts, a reduction in total antioxidant activity, and a different profile of microbiota and metabolomics data were observed. Collectively, the data in the present study indicated that physical exercise in our model could be considered a mild stressor stimulus.}, }
@article {pmid32373155, year = {2020}, author = {Coenen, AR and Hu, SK and Luo, E and Muratore, D and Weitz, JS}, title = {A Primer for Microbiome Time-Series Analysis.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {310}, pmid = {32373155}, issn = {1664-8021}, abstract = {Time-series can provide critical insights into the structure and function of microbial communities. The analysis of temporal data warrants statistical considerations, distinct from comparative microbiome studies, to address ecological questions. This primer identifies unique challenges and approaches for analyzing microbiome time-series. In doing so, we focus on (1) identifying compositionally similar samples, (2) inferring putative interactions among populations, and (3) detecting periodic signals. We connect theory, code and data via a series of hands-on modules with a motivating biological question centered on marine microbial ecology. The topics of the modules include characterizing shifts in community structure and activity, identifying expression levels with a diel periodic signal, and identifying putative interactions within a complex community. Modules are presented as self-contained, open-access, interactive tutorials in R and Matlab. Throughout, we highlight statistical considerations for dealing with autocorrelated and compositional data, with an eye to improving the robustness of inferences from microbiome time-series. In doing so, we hope that this primer helps to broaden the use of time-series analytic methods within the microbial ecology research community.}, }
@article {pmid32371471, year = {2020}, author = {Bezuidt, OKI and Lebre, PH and Pierneef, R and León-Sobrino, C and Adriaenssens, EM and Cowan, DA and Van de Peer, Y and Makhalanyane, TP}, title = {Phages Actively Challenge Niche Communities in Antarctic Soils.}, journal = {mSystems}, volume = {5}, number = {3}, pages = {}, pmid = {32371471}, issn = {2379-5077}, support = {BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {By modulating the structure, diversity, and trophic outputs of microbial communities, phages play crucial roles in many biomes. In oligotrophic polar deserts, the effects of katabatic winds, constrained nutrients, and low water availability are known to limit microbial activity. Although phages may substantially govern trophic interactions in cold deserts, relatively little is known regarding the precise ecological mechanisms. Here, we provide the first evidence of widespread antiphage innate immunity in Antarctic environments using metagenomic sequence data from hypolith communities as model systems. In particular, immunity systems such as DISARM and BREX are shown to be dominant systems in these communities. Additionally, we show a direct correlation between the CRISPR-Cas adaptive immunity and the metavirome of hypolith communities, suggesting the existence of dynamic host-phage interactions. In addition to providing the first exploration of immune systems in cold deserts, our results suggest that phages actively challenge niche communities in Antarctic polar deserts. We provide evidence suggesting that the regulatory role played by phages in this system is an important determinant of bacterial host interactions in this environment.IMPORTANCE In Antarctic environments, the combination of both abiotic and biotic stressors results in simple trophic levels dominated by microbiomes. Although the past two decades have revealed substantial insights regarding the diversity and structure of microbiomes, we lack mechanistic insights regarding community interactions and how phages may affect these. By providing the first evidence of widespread antiphage innate immunity, we shed light on phage-host dynamics in Antarctic niche communities. Our analyses reveal several antiphage defense systems, including DISARM and BREX, which appear to dominate in cold desert niche communities. In contrast, our analyses revealed that genes which encode antiphage adaptive immunity were underrepresented in these communities, suggesting lower infection frequencies in cold edaphic environments. We propose that by actively challenging niche communities, phages play crucial roles in the diversification of Antarctic communities.}, }
@article {pmid32367214, year = {2020}, author = {Muñoz-Leal, S and Ramirez, DG and Luz, HR and Faccini, JLH and Labruna, MB}, title = {"Candidatus Borrelia ibitipoquensis," a Borrelia valaisiana-Related Genospecies Characterized from Ixodes paranaensis in Brazil.}, journal = {Microbial ecology}, volume = {80}, number = {3}, pages = {682-689}, doi = {10.1007/s00248-020-01512-x}, pmid = {32367214}, issn = {1432-184X}, support = {150961/2017-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2018/02521-1 and 2019/17960-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {Animals ; Borrelia/classification/genetics/*isolation &amp; purification ; Brazil ; Caves ; Female ; Ixodes/growth &amp; development/*microbiology ; Larva/growth &amp; development/microbiology ; Male ; Nymph/growth &amp; development/microbiology ; Spirochaetales/classification ; }, abstract = {Borrelia burgdorferi sensu lato (Bbsl) spirochetes include the agents of Lyme borreliosis in temperate regions of the Northern Hemisphere, and merge their transmission cycles mainly with ticks of the Ixodes ricinus complex. Twenty genospecies compose Bbsl currently, and with the exception of Borrelia chilensis, and Borrelia garinii, all have been described only for North America, Europe, North Africa, and Asia. Here, we collected specimens of Ixodes paranaensis, a tick associated with swifts in a Brazilian natural park from the state of Minas Gerais, and performed a molecular characterization of 11 borrelial genes. Based on comparisons of inter and intraspecific genetic divergences, and Bayesian phylogenetic trees inferred for 16S rRNA, flaB, p66, and concatenated clpA, clpX, pepX, pyrG, recG, nifS rlpB, and uvrA genes, we demonstrate the occurrence of a new genospecies of Bbsl. "Candidatus Borrelia ibitipoquensis" Ip37 is closely related to Borrelia sp. Am501, and Borrelia valaisiana, a spirochete transmitted by ticks of the I. ricinus complex in Eurasia that uses birds as reservoirs. In a similar ecological scenario involving ticks and avian hosts, the migratory swift Streptoprocne biscutata is the sole-documented bird associated with I. paranaensis, and, although not assessed in this study, could correspond to the vertebrate reservoir of this newly described genospecies in Brazil. Pathogenic roles of "Ca. B. ibitipoquensis" are still unknown. However, its possible vector I. paranaensis is not an anthropophilic tick, so human infections would be unlikely to occur. Our finding enhances the knowledge on Bbsl in South America, highlights the occurrence of ecologically and genetically related genospecies with vastly separated geographical distributions, and calls for the attention to explore a barely known diversity of spirochetes of this group in the region.}, }
@article {pmid32366030, year = {2020}, author = {Perricone, V and Comi, M and Giromini, C and Rebucci, R and Agazzi, A and Savoini, G and Bontempo, V}, title = {Green Tea and Pomegranate Extract Administered During Critical Moments of the Production Cycle Improves Blood Antiradical Activity and Alters Cecal Microbial Ecology of Broiler Chickens.}, journal = {Animals : an open access journal from MDPI}, volume = {10}, number = {5}, pages = {}, pmid = {32366030}, issn = {2076-2615}, abstract = {Phytobiotics are usually tested in feed and throughout the production cycle. However, it could be beneficial to evaluate their effects when administered only during critical moments, such as changes in feeding phases. The aim of the trial was to investigate the effect of a commercial plant extract (PE; IQV-10-P01, InQpharm Animal Health, Kuala Lumpur, Malaysia) on growth performance, blood antiradical activity and cecal microbiome when administered in drinking water to broiler chickens during the post-hatching phase and at each change of diet. In the experiment, 480 1-day-old male broiler chicks were assigned to two groups in a 50-day trial. Broilers received drinking water (C) or drinking water plus PE (T) at a rate of 2 mL/L on days 0 to 4, 10-11 and 20-21. PE did not affect performance and water intake, while total antiradical activity was improved (p < 0.05). A greater abundance of lactic acid bacteria (false discovery rate (FDR) < 0.05) was found in the T group and the result was confirmed at a lower taxonomic level with higher Lactobacillaceae abundance (FDR < 0.05). Our findings suggest that PE administration during critical moments of the production cycle of broiler chickens may exert beneficial effects at a systemic level and on gut microbial ecology.}, }
@article {pmid32364226, year = {2020}, author = {Ramoneda, J and Le Roux, JJ and Frossard, E and Frey, B and Gamper, HA}, title = {Experimental assembly reveals ecological drift as a major driver of root nodule bacterial diversity in a woody legume crop.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {6}, pages = {}, doi = {10.1093/femsec/fiaa083}, pmid = {32364226}, issn = {1574-6941}, mesh = {Bacteria/genetics ; *Fabaceae ; *Mesorhizobium ; *Rhizobium/genetics ; Soil Microbiology ; Symbiosis ; }, abstract = {Understanding how plant-associated microbial communities assemble and the role they play in plant performance are major goals in microbial ecology. For nitrogen-fixing rhizobia, community assembly is generally driven by host plant selection and soil conditions. Here, we aimed to determine the relative importance of neutral and deterministic processes in the assembly of bacterial communities of root nodules of a legume shrub adapted to extreme nutrient limitation, rooibos (Aspalathus linearis Burm. Dahlgren). We grew rooibos seedlings in soil from cultivated land and wild habitats, and mixtures of these soils, sampled from a wide geographic area, and with a fertilization treatment. Bacterial communities were characterized using next generation sequencing of part of the nodA gene (i.e. common to the core rhizobial symbionts of rooibos), and part of the gyrB gene (i.e. common to all bacterial taxa). Ecological drift alone was a major driver of taxonomic turnover in the bacterial communities of root nodules (62.6% of gyrB communities). In contrast, the assembly of core rhizobial communities (genus Mesorhizobium) was driven by dispersal limitation in concert with drift (81.1% of nodA communities). This agrees with a scenario of rooibos-Mesorhizobium specificity in spatially separated subpopulations, and low host filtering of other bacteria colonizing root nodules in a stochastic manner.}, }
@article {pmid32361351, year = {2020}, author = {Liu, W and Wu, Y and Zhang, S and Gao, Y and Jiang, Y and Horn, H and Li, J}, title = {Successful granulation and microbial differentiation of activated sludge in anaerobic/anoxic/aerobic (A[2]O) reactor with two-zone sedimentation tank treating municipal sewage.}, journal = {Water research}, volume = {178}, number = {}, pages = {115825}, doi = {10.1016/j.watres.2020.115825}, pmid = {32361351}, issn = {1879-2448}, mesh = {Aerobiosis ; Anaerobiosis ; *Bioreactors ; Motor Vehicles ; Nitrogen ; Phosphorus ; *Sewage ; Waste Disposal, Fluid ; }, abstract = {A continuous pilot-scale A[2]O reactor with a two-zone sedimentation tank (A[2]O-TST) was constructed for the formation of aerobic granular sludge (AGS) to treat real municipal sewage. The characteristics of sludge, nutrient removal performance and the corresponding microbial ecology dynamics were studied during granulation process. Experimental results indicated that AGS with a mean particle size of 210 μm and sludge volume index after 30 min of 47.5 mL/g was successfully formed with effluent COD, total nitrogen and total phosphorus concentrations in the reactor reaching 22.8, 3.5 and 0.2 mg/L, respectively. Furthermore, high throughput data indicated that granules in settling tank-1 (ST-1) harbored slow-growing autotrophic organisms like Nitrosomonas and Nitrospira, while the flocs in settling tank-2 (ST-2) were dominated by fast-growing heterotrophic organisms including Ca. Accumulibacter, Dechloromonas, Flavobacterium, Arcobacter and Halomonas. Simulation results using computational fluid dynamics and discrete element method (CFD-DEM) modeling verified that the selection pressure created by the TST separator contributed to the retention of heavy granules (>1.011 kg/m[3] density) in ST-1 zone and the withdrawal of light flocs (<1.011 kg/m[3] density) from ST-2 zone. Therefore, the segregation of biomass using the TST system provides an opportunity to select for desired microbial populations and to optimize the nitrogen and phosphorus removal performance of the A[2]O-TST reactor. This study could add a guiding sight into the application of two-sludge system based on AGS technology for upgrading traditional A[2]O process.}, }
@article {pmid32360380, year = {2020}, author = {Wang, J and Zhang, X and Yao, H}, title = {Optimizing ultracentrifugation conditions for DNA-based stable isotope probing (DNA-SIP).}, journal = {Journal of microbiological methods}, volume = {173}, number = {}, pages = {105938}, doi = {10.1016/j.mimet.2020.105938}, pmid = {32360380}, issn = {1872-8359}, mesh = {Archaea/genetics ; Bacteria/genetics ; Centrifugation, Density Gradient/methods ; Cesium ; China ; Chlorides ; DNA/*chemistry/genetics/isolation &amp; purification ; *DNA Probes ; DNA, Archaeal/chemistry/genetics/isolation &amp; purification ; DNA, Bacterial/*chemistry/genetics/isolation &amp; purification ; *Isotopes ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Soil ; Soil Microbiology ; Ultracentrifugation/*methods ; }, abstract = {DNA-SIP (DNA-based stable isotope probing) is increasingly being employed in soil microbial ecology to identify those microbes assimilating the [13]C/[15]N labelled substrate. Isopycnic gradient centrifugation is the primary experimental process for conducting DNA-SIP. However, diverse centrifugal conditions have been used in various recent studies. In order to get the optimum conditions of centrifugation for DNA-SIP, centrifugation time (36, 42, 48, 60 h), speed (45,000, 55,000 rpm) and the initial buoyant density (1.69, 1.71, 1.725 g ml[-1]), as were used extensively in related studies, were tested in this experiment with the Vti 65.2 rotor. DNA with either [13]C-labelling or unlabelled was extracted from a paddy soil pre-incubated with either [13]C-labelled or natural abundance glucose. After ultracentrifugation, the gene abundance of bacterial 16S rRNA, fungal 18S rRNA, bacterial and archaeal amoA within the fractioned DNA was detected. The results showed that centrifugation for 48 h was enough for the DNA to reach stabilization in the CsCl solution. The initial density of the mixed solution was best adjusted to 1.71 g ml[-1] to ensure that most of the genes were concentrated on the middle fractions of the density gradient. Increasing the centrifugation speed would increase the density gradient of fractions; therefore, 45,000 rpm (184,000 g) was recommended so as to obtain the more widespread pattern of DNA in the centrifugal tube. We hope these findings will assist future researchers to conduct optimum ultracentrifugation for DNA-SIP.}, }
@article {pmid32358041, year = {2020}, author = {Li, YJ and Chen, X and Kwan, TK and Loh, YW and Singer, J and Liu, Y and Ma, J and Tan, J and Macia, L and Mackay, CR and Chadban, SJ and Wu, H}, title = {Dietary Fiber Protects against Diabetic Nephropathy through Short-Chain Fatty Acid-Mediated Activation of G Protein-Coupled Receptors GPR43 and GPR109A.}, journal = {Journal of the American Society of Nephrology : JASN}, volume = {31}, number = {6}, pages = {1267-1281}, pmid = {32358041}, issn = {1533-3450}, mesh = {Albuminuria/prevention &amp; control ; Animals ; Diabetes Mellitus, Experimental/complications ; Diabetic Nephropathies/*prevention &amp; control ; Dietary Fiber/*administration &amp; dosage ; Dysbiosis ; Fatty Acids, Volatile/*physiology ; Gastrointestinal Microbiome ; Male ; Mice ; Mice, Inbred C57BL ; Receptors, G-Protein-Coupled/*physiology ; Streptozocin ; }, abstract = {BACKGROUND: Studies have reported "dysbiotic" changes to gut microbiota, such as depletion of gut bacteria that produce short-chain fatty acids (SCFAs) through gut fermentation of fiber, in CKD and diabetes. Dietary fiber is associated with decreased inflammation and mortality in CKD, and SCFAs have been proposed to mediate this effect.<br><br>METHODS: To explore dietary fiber's effect on development of experimental diabetic nephropathy, we used streptozotocin to induce diabetes in wild-type C57BL/6 and knockout mice lacking the genes encoding G protein-coupled receptors GPR43 or GPR109A. Diabetic mice were randomized to high-fiber, normal chow, or zero-fiber diets, or SCFAs in drinking water. We used proton nuclear magnetic resonance spectroscopy for metabolic profiling and 16S ribosomal RNA sequencing to assess the gut microbiome.<br><br>RESULTS: Diabetic mice fed a high-fiber diet were significantly less likely to develop diabetic nephropathy, exhibiting less albuminuria, glomerular hypertrophy, podocyte injury, and interstitial fibrosis compared with diabetic controls fed normal chow or a zero-fiber diet. Fiber beneficially reshaped gut microbial ecology and improved dysbiosis, promoting expansion of SCFA-producing bacteria of the genera Prevotella and Bifidobacterium, which increased fecal and systemic SCFA concentrations. Fiber reduced expression of genes encoding inflammatory cytokines, chemokines, and fibrosis-promoting proteins in diabetic kidneys. SCFA-treated diabetic mice were protected from nephropathy, but not in the absence of GPR43 or GPR109A. In vitro, SCFAs modulated inflammation in renal tubular cells and podocytes under hyperglycemic conditions.<br><br>CONCLUSIONS: Dietary fiber protects against diabetic nephropathy through modulation of the gut microbiota, enrichment of SCFA-producing bacteria, and increased SCFA production. GPR43 and GPR109A are critical to SCFA-mediated protection against this condition. Interventions targeting the gut microbiota warrant further investigation as a novel renoprotective therapy in diabetic nephropathy.}, }
@article {pmid32355200, year = {2020}, author = {Wang, W and Li, Z and Zeng, L and Dong, C and Shao, Z}, title = {The oxidation of hydrocarbons by diverse heterotrophic and mixotrophic bacteria that inhabit deep-sea hydrothermal ecosystems.}, journal = {The ISME journal}, volume = {14}, number = {8}, pages = {1994-2006}, pmid = {32355200}, issn = {1751-7370}, mesh = {Bacteria/genetics ; Hydrocarbons ; *Hydrothermal Vents ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Hydrothermal activity can generate numerous and diverse hydrocarbon compounds. However, little is known about the influence of such hydrocarbons on deep-sea hydrothermal microbial ecology. We hypothesize that certain bacteria live on these hydrocarbons. Therefore, in this study, the distribution of hydrocarbons and their associated hydrocarbon-degrading bacteria were investigated at deep-sea hydrothermal vents at the Southern Mid-Atlantic Ridge, the Southwest Indian Ridge, and the East Pacific Rise. A variety of hydrocarbon-degrading consortia were obtained from hydrothermal samples collected at the aforementioned sites after low-temperature enrichment under high hydrostatic pressures, and the bacteria responsible for the degradation of hydrocarbons were investigated by DNA-based stable-isotope probing with uniformly [13]C-labeled hydrocarbons. Unusually, we identified several previously recognized sulfur-oxidizing chemoautotrophs as hydrocarbon-degrading bacteria, e.g., the SAR324 group, the SUP05 clade, and Sulfurimonas, and for the first time confirmed their ability to degrade hydrocarbons. In addition, Erythrobacter, Pusillimonas, and SAR202 clade were shown to degrade polycyclic aromatic hydrocarbons for the first time. These results together with relatively high abundance in situ of most of the above-described bacteria highlight the potential influence of hydrocarbons in configuring the vent microbial community, and have made the importance of mixotrophs in hydrothermal vent ecosystems evident.}, }
@article {pmid32351795, year = {2020}, author = {Johnston-Monje, D and Lopez Mejia, J}, title = {Botanical microbiomes on the cheap: Inexpensive molecular fingerprinting methods to study plant-associated communities of bacteria and fungi.}, journal = {Applications in plant sciences}, volume = {8}, number = {4}, pages = {e11334}, pmid = {32351795}, issn = {2168-0450}, abstract = {High-throughput sequencing technologies have revolutionized the study of plant-associated microbial populations, but they are relatively expensive. Molecular fingerprinting techniques are more affordable, yet yield considerably less information about the microbial community. Does this mean they are no longer useful for plant microbiome research? In this paper, we review the past 10 years of studies on plant-associated microbiomes using molecular fingerprinting methodologies, including single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), amplicon length heterogeneity PCR (LH-PCR), ribosomal intergenic spacer analysis (RISA) and automated ribosomal intergenic spacer analysis (ARISA), and terminal restriction fragment length polymorphism (TRFLP). We also present data juxtaposing results from TRFLP methods with those generated using Illumina sequencing in the comparison of rhizobacterial populations of Brazilian maize and fungal surveys in Canadian tomato roots. In both cases, the TRFLP approach yielded the desired results at a level of resolution comparable to that of the MiSeq method, but at a fraction of the cost. Community fingerprinting methods (especially TRFLP) remain relevant for the identification of dominant microbes in a population, the observation of shifts in plant microbiome community diversity, and for screening samples before their use in more sensitive and expensive approaches.}, }
@article {pmid32351470, year = {2020}, author = {Kopprio, GA and Neogi, SB and Rashid, H and Alonso, C and Yamasaki, S and Koch, BP and Gärdes, A and Lara, RJ}, title = {Vibrio and Bacterial Communities Across a Pollution Gradient in the Bay of Bengal: Unraveling Their Biogeochemical Drivers.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {594}, pmid = {32351470}, issn = {1664-302X}, abstract = {The highly populated coasts of the Bay of Bengal are particularly vulnerable to water-borne diseases, pollution and climatic extremes. The environmental factors behind bacterial community composition and Vibrio distribution were investigated in an estuarine system of a cholera-endemic region in the coastline of Bangladesh. Higher temperatures and sewage pollution were important drivers of the abundance of toxigenic Vibrio cholerae. A closer relation between non-culturable Vibrio and particulate organic matter (POM) was inferred during the post-monsoon. The distribution of operational taxonomic units (OTUs) of Vibrio genus was likely driven by salinity and temperature. The resuspension of sediments increased Vibrio abundance and organic nutrient concentrations. The δ[13]C dynamic in POM followed an increasing gradient from freshwater to marine stations; nevertheless, it was not a marker of sewage pollution. Bacteroidales and culturable coliforms were reliable indicators of untreated wastewater during pre and post-monsoon seasons. The presumptive incorporation of depleted-ammonium derived from ammonification processes under the hypoxic conditions, by some microorganisms such as Cloacibacterium and particularly by Arcobacter nearby the sewage discharge, contributed to the drastic [15]N depletion in the POM. The likely capacity of extracellular polymeric substances production of these taxa may facilitate the colonization of POM from anthropogenic origin and may signify important properties for wastewater bioremediation. Genera of potential pathogens other than Vibrio associated with sewage pollution were Acinetobacter, Aeromonas, Arcobacter, and Bergeyella. The changing environmental conditions of the estuary favored the abundance of early colonizers and the island biogeography theory explained the distribution of some bacterial groups. This multidisciplinary study evidenced clearly the eutrophic conditions of the Karnaphuli estuary and assessed comprehensively its current bacterial baseline and potential risks. The prevailing conditions together with human overpopulation and frequent natural disasters, transform the region in one of the most vulnerable to climate change. Adaptive management strategies are urgently needed to enhance ecosystem health.}, }
@article {pmid32350866, year = {2020}, author = {Lang, M and Baumgartner, M and Rożalska, A and Frick, A and Riva, A and Jarek, M and Berry, D and Gasche, C}, title = {Crypt residing bacteria and proximal colonic carcinogenesis in a mouse model of Lynch syndrome.}, journal = {International journal of cancer}, volume = {147}, number = {8}, pages = {2316-2326}, pmid = {32350866}, issn = {1097-0215}, support = {741623/ERC_/European Research Council/International ; KLI 557/FWF_/Austrian Science Fund FWF/Austria ; I 1573-B19/FWF_/Austrian Science Fund FWF/Austria ; P27831-B28/FWF_/Austrian Science Fund FWF/Austria ; KLI 557-B22/FWF_/Austrian Science Fund FWF/Austria ; P 32302/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Bacteria/pathogenicity ; Biofilms/growth &amp; development ; Carcinogenesis/genetics/*pathology ; Cell Transformation, Neoplastic/genetics/pathology ; Colorectal Neoplasms/genetics/*microbiology/*pathology ; Colorectal Neoplasms, Hereditary Nonpolyposis/genetics/*microbiology/*parasitology ; DNA Mismatch Repair/genetics ; Disease Models, Animal ; Dysbiosis/genetics/microbiology/pathology ; Gastrointestinal Microbiome/genetics ; Germ-Line Mutation/genetics ; Inflammation/genetics/microbiology/pathology ; Interleukin-10/genetics ; Intestinal Mucosa/microbiology/pathology ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; }, abstract = {Colorectal cancer is a multifactorial disease involving inherited DNA mutations, environmental factors, gut inflammation and intestinal microbiota. Certain germline mutations within the DNA mismatch repair system are associated with Lynch syndrome tumors including right-sided colorectal cancer with mucinous phenotype and presence of an inflammatory infiltrate. Such tumors are more often associated with bacterial biofilms, which may contribute to disease onset and progression. Inflammatory bowel diseases are also associated with colorectal cancer and intestinal dysbiosis. Herein we addressed the question, whether inflammation can aggravate colorectal cancer development under mismatch repair deficiency. MSH2[loxP/loxP Vill-cre] mice were crossed into the IL-10[-/-] background to study the importance of inflammation and mucosal bacteria as a driver of tumorigenesis in a Lynch syndrome mouse model. An increase in large bowel tumorigenesis was found in double knockout mice both under conventional housing and under specific pathogen-free conditions. This increase was mostly due to the development of proximal tumors, a hotspot for tumorigenesis in Lynch syndrome, and was associated with a higher degree of inflammation. Additionally, bacterial invasion into the mucus of tumor crypts was observed in the proximal tumors. Inflammation shifted fecal and mucosal microbiota composition and was associated with enrichment in Escherichia-Shigella as well as Akkermansia, Bacteroides and Parabacteroides genera in fecal samples. Tumor-bearing double knockout mice showed a similar enrichment for Escherichia-Shigella and Parabacteroides. Lactobacilli, Lachnospiraceae and Muribaculaceae family members were depleted upon inflammation. In summary, chronic inflammation aggravates colonic tumorigenesis under mismatch repair deficiency and is associated with a shift in microbiota composition.}, }
@article {pmid32346537, year = {2020}, author = {Duar, RM and Henrick, BM and Casaburi, G and Frese, SA}, title = {Integrating the Ecosystem Services Framework to Define Dysbiosis of the Breastfed Infant Gut: The Role of B. infantis and Human Milk Oligosaccharides.}, journal = {Frontiers in nutrition}, volume = {7}, number = {}, pages = {33}, pmid = {32346537}, issn = {2296-861X}, abstract = {Mounting evidence supports a connection between the composition of the infant gut microbiome and long-term health. In fact, aberrant microbiome compositions during key developmental windows in early life are associated with increased disease risk; therefore, making pertinent modifications to the microbiome during infancy offers significant promise to improve human health. There is growing support for integrating the concept of ecosystem services (the provision of benefits from ecosystems to humans) in linking specific microbiome functions to human well-being. This framework is widely applied in conservation efforts of macro-ecosystems and offers a systematic approach to guide restoration actions aimed to recover critical ecological functions. The aim of this work is to apply the ecosystem services framework to integrate recent studies demonstrating stable alteration of the gut microbiome of breastfed infants when Bifidobacterium longum subsp. infantis EVC001, a gut symbiont capable of efficiently utilizing human milk oligosaccharides into organic acids that are beneficial for the infant and lower intestinal pH, is reintroduced. Additionally, using examples from the literature we illustrate how the absence of B. infantis results in diminished ecosystem services, which may be associated with health consequences related to immune and metabolic disorders. Finally, we propose a model by which infant gut dysbiosis can be defined as a reduction in ecosystem services supplied to the host by the gut microbiome rather than merely changes in diversity or taxonomic composition. Given the increased interest in targeted microbiome modification therapies to decrease acute and chronic disease risk, the model presented here provides a framework to assess the effectiveness of such strategies from a host-centered perspective.}, }
@article {pmid32341569, year = {2020}, author = {López-García, P and Moreira, D}, title = {The Syntrophy hypothesis for the origin of eukaryotes revisited.}, journal = {Nature microbiology}, volume = {5}, number = {5}, pages = {655-667}, pmid = {32341569}, issn = {2058-5276}, mesh = {Archaea/genetics/*metabolism ; Bacteria/genetics ; *Biological Evolution ; Cell Nucleus ; Eukaryota/genetics/*metabolism ; Eukaryotic Cells/*metabolism ; Genome, Archaeal ; Hydrogen/metabolism ; Membranes/metabolism ; Mitochondria/metabolism ; Oxidation-Reduction ; *Phylogeny ; Sulfur/metabolism ; Symbiosis/physiology ; }, abstract = {The discovery of Asgard archaea, phylogenetically closer to eukaryotes than other archaea, together with improved knowledge of microbial ecology, impose new constraints on emerging models for the origin of the eukaryotic cell (eukaryogenesis). Long-held views are metamorphosing in favour of symbiogenetic models based on metabolic interactions between archaea and bacteria. These include the classical Searcy's and Hydrogen hypothesis, and the more recent Reverse Flow and Entangle-Engulf-Endogenize models. Two decades ago, we put forward the Syntrophy hypothesis for the origin of eukaryotes based on a tripartite metabolic symbiosis involving a methanogenic archaeon (future nucleus), a fermentative myxobacterial-like deltaproteobacterium (future eukaryotic cytoplasm) and a metabolically versatile methanotrophic alphaproteobacterium (future mitochondrion). A refined version later proposed the evolution of the endomembrane and nuclear membrane system by invagination of the deltaproteobacterial membrane. Here, we adapt the Syntrophy hypothesis to contemporary knowledge, shifting from the original hydrogen and methane-transfer-based symbiosis (HM Syntrophy) to a tripartite hydrogen and sulfur-transfer-based model (HS Syntrophy). We propose a sensible ecological scenario for eukaryogenesis in which eukaryotes originated in early Proterozoic microbial mats from the endosymbiosis of a hydrogen-producing Asgard archaeon within a complex sulfate-reducing deltaproteobacterium. Mitochondria evolved from versatile, facultatively aerobic, sulfide-oxidizing and, potentially, anoxygenic photosynthesizing alphaproteobacterial endosymbionts that recycled sulfur in the consortium. The HS Syntrophy hypothesis accounts for (endo)membrane, nucleus and metabolic evolution in a realistic ecological context. We compare and contrast the HS Syntrophy hypothesis to other models of eukaryogenesis, notably in terms of the mode and tempo of eukaryotic trait evolution, and discuss several model predictions and how these can be tested.}, }
@article {pmid32339893, year = {2020}, author = {Pishchany, G}, title = {Applying microbial ecology to antimicrobial discovery.}, journal = {Current opinion in microbiology}, volume = {57}, number = {}, pages = {7-12}, doi = {10.1016/j.mib.2020.03.007}, pmid = {32339893}, issn = {1879-0364}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/metabolism ; Bacterial Infections/microbiology ; *Drug Evaluation, Preclinical ; Drug Resistance, Bacterial ; Humans ; }, abstract = {Introduction of antibiotics into clinical use has contributed to some of the greatest improvements to public health in the 20th century. Most antibiotics are based on antimicrobials that were isolated from environmental microorganisms over 50 years ago, but emerging resistance requires discovery of new molecules and development of these molecules into therapeutics. Bioinformatic analyses of microbial genomes indicate that many more microbial bioactive molecules remain undiscovered. Understanding when, where, and why these molecules are produced informs efforts to tap into the hidden unexplored chemical diversity. Expanding the search to undersampled ecological niches and improving culturing techniques will ensure discovery of new antibiotics.}, }
@article {pmid32335713, year = {2020}, author = {Sun, H and Zhang, Y and Tan, S and Zheng, Y and Zhou, S and Ma, QY and Yang, GP and Todd, JD and Zhang, XH}, title = {DMSP-Producing Bacteria Are More Abundant in the Surface Microlayer than Subsurface Seawater of the East China Sea.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {350-365}, doi = {10.1007/s00248-020-01507-8}, pmid = {32335713}, issn = {1432-184X}, support = {2016YFA0601303//National Key Research and Development Program of China/ ; 91751202//National Natural Science Foundation of China/ ; 41730530//National Natural Science Foundation of China/ ; 41476112//National Natural Science Foundation of China/ ; NE/N002385//Natural Environmental Research Council, UK, grants/ ; NE/P012671//Natural Environmental Research Council, UK, grants/ ; NE/S001352//Natural Environmental Research Council, UK, grants/ ; }, mesh = {Bacteria/classification/*isolation &amp; purification ; Bacterial Physiological Phenomena ; China ; Microbiota/*physiology ; Seawater/*microbiology ; Sulfonium Compounds/*metabolism ; }, abstract = {Microbial production and catabolism of dimethylsulfoniopropionate (DMSP), generating the climatically active gases dimethyl sulfide (DMS) and methanethiol (MeSH), have key roles in global carbon and sulfur cycling, chemotaxis, and atmospheric chemistry. Microorganisms in the sea surface microlayer (SML), the interface between seawater and atmosphere, likely play an important role in the generation of DMS and MeSH and their exchange to the atmosphere, but little is known about these SML microorganisms. Here, we investigated the differences between bacterial community structure and the distribution and transcription profiles of the key bacterial DMSP synthesis (dsyB and mmtN) and catabolic (dmdA and dddP) genes in East China Sea SML and subsurface seawater (SSW) samples. Per equivalent volume, bacteria were far more abundant (~ 7.5-fold) in SML than SSW, as were those genera predicted to produce DMSP. Indeed, dsyB (~ 7-fold) and mmtN (~ 4-fold), robust reporters for bacterial DMSP production, were also far more abundant in SML than SSW. In addition, the SML had higher dsyB transcripts (~ 3-fold) than SSW samples, which may contribute to the significantly higher DMSP level observed in SML compared with SSW. Furthermore, the abundance of bacteria with dmdA and their transcription were higher in SML than SSW samples. Bacteria with dddP and transcripts were also prominent, but less than dmdA and presented at similar levels in both layers. These data indicate that the SML might be an important hotspot for bacterial DMSP production as well as generating the climatically active gases DMS and MeSH, a portion of which are likely transferred to the atmosphere.}, }
@article {pmid32334223, year = {2020}, author = {Gorski, G and Dailey, H and Fisher, AT and Schrad, N and Saltikov, C}, title = {Denitrification during infiltration for managed aquifer recharge: Infiltration rate controls and microbial response.}, journal = {The Science of the total environment}, volume = {727}, number = {}, pages = {138642}, doi = {10.1016/j.scitotenv.2020.138642}, pmid = {32334223}, issn = {1879-1026}, mesh = {Carbon ; *Denitrification ; *Groundwater ; Nitrates/analysis ; Soil ; }, abstract = {Managed aquifer recharge (MAR) systems can be designed and operated to improve water supply and quality simultaneously by creating favorable conditions for contaminant removal during infiltration through shallow soils. We present results from laboratory flow-through column experiments, using intact soil cores from two MAR sites, elucidating conditions that are favorable to nitrate (NO3) removal via microbial denitrification during infiltration. Experiments focused on quantitative relations between infiltration rate and the presence or absence of a carbon-rich permeable reactive barrier (PRB) on both amounts and rates of nitrate removal during infiltration and associated shifts in microbial ecology. Experiments were conducted using a range of infiltration rates relevant to MAR (0.3-1.4 m/day), with PRBs made of native soil (NS), woodchips (WC) and a 50:50 mixture of woodchips and native soil (MIX). The latter two (carbon-rich) PRB treatments led to statistically significant increases in the amount of nitrate removed by increasing zero-order denitrification rates, both within the PRB materials and in the underlying soil. The highest fraction of nitrate removal occurred at the lowest infiltration rates for all treatments. However, the highest nitrogen mass removal (∆NL) was observed at 0.4-0.7 m/day for both the WC and MIX treatments. In contrast, the maximum ∆NL for the NS treatment was observed at the lowest infiltration rates measured (~0.3 m/day). Further, both carbon-rich PRBs had a substantial impact on the soil microbial ecology in the underlying soil, with lower overall diversity and a greater relative abundance of groups known to degrade carbon and metabolize nitrogen. These results demonstrate that infiltration rates and carbon availability can combine to create favorable conditions for denitrification during infiltration for MAR and show how these factors shape and sustain the microbial community structures responsible for nutrient cycling in associated soils.}, }
@article {pmid32332139, year = {2020}, author = {LaSarre, B and Deutschbauer, AM and Love, CE and McKinlay, JB}, title = {Covert Cross-Feeding Revealed by Genome-Wide Analysis of Fitness Determinants in a Synthetic Bacterial Mutualism.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {13}, pages = {}, pmid = {32332139}, issn = {1098-5336}, mesh = {Coculture Techniques ; Escherichia coli/*genetics ; *Genetic Fitness ; Genome-Wide Association Study ; Microbial Interactions/*genetics ; Rhodopseudomonas/*genetics ; Symbiosis/*genetics ; }, abstract = {Microbial interactions abound in natural ecosystems and shape community structure and function. Substantial attention has been given to cataloging mechanisms by which microbes interact, but there is a limited understanding of the genetic landscapes that promote or hinder microbial interactions. We previously developed a mutualistic coculture pairing Escherichia coli and Rhodopseudomonas palustris, wherein E. coli provides carbon to R. palustris in the form of glucose fermentation products and R. palustris fixes N2 gas and provides nitrogen to E. coli in the form of NH4[+] The stable coexistence and reproducible trends exhibited by this coculture make it ideal for interrogating the genetic underpinnings of a cross-feeding mutualism. Here, we used random barcode transposon sequencing (RB-TnSeq) to conduct a genome-wide search for E. coli genes that influence fitness during cooperative growth with R. palustris RB-TnSeq revealed hundreds of genes that increased or decreased E. coli fitness in a mutualism-dependent manner. Some identified genes were involved in nitrogen sensing and assimilation, as expected given the coculture design. The other identified genes were involved in diverse cellular processes, including energy production and cell wall and membrane biogenesis. In addition, we discovered unexpected purine cross-feeding from R. palustris to E. coli, with coculture rescuing growth of an E. coli purine auxotroph. Our data provide insight into the genes and gene networks that can influence a cross-feeding mutualism and underscore that microbial interactions are not necessarily predictable a prioriIMPORTANCE Microbial communities impact life on Earth in profound ways, including driving global nutrient cycles and influencing human health and disease. These community functions depend on the interactions that resident microbes have with the environment and each other. Thus, identifying genes that influence these interactions will aid the management of natural communities and the use of microbial consortia as biotechnology. Here, we identified genes that influenced Escherichia coli fitness during cooperative growth with a mutualistic partner, Rhodopseudomonas palustris Although this mutualism centers on the bidirectional exchange of essential carbon and nitrogen, E. coli fitness was positively and negatively affected by genes involved in diverse cellular processes. Furthermore, we discovered an unexpected purine cross-feeding interaction. These results contribute knowledge on the genetic foundation of a microbial cross-feeding interaction and highlight that unanticipated interactions can occur even within engineered microbial communities.}, }
@article {pmid32331569, year = {2020}, author = {Moran, MC and Beck, LA and Richardson, CT}, title = {A Spectrum of Skin Disease: How Staphylococcus aureus Colonization, Barrier Dysfunction, and Cytokines Shape the Skin.}, journal = {The Journal of investigative dermatology}, volume = {140}, number = {5}, pages = {941-944}, pmid = {32331569}, issn = {1523-1747}, support = {T32 AI118689/AI/NIAID NIH HHS/United States ; U01 AI152011/AI/NIAID NIH HHS/United States ; U19 AI117673/AI/NIAID NIH HHS/United States ; }, mesh = {Cytokines ; *Dermatitis, Atopic ; Humans ; Skin ; *Staphylococcal Infections ; Staphylococcus aureus ; }, abstract = {Cytokines are key mediators of skin homeostasis and disease through their effects on keratinocytes, skin barrier integrity, immune activation, and microbial ecology. Sirobhushanam et al. (2020) suggest that the IFN signature in lupus erythematosus (LE) alters expression of epithelial barrier and adhesin genes, which, in turn, promotes Staphylococcus aureus colonization. This work highlights the need to better understand both barrier function and S. aureus colonization in LE, two new potential therapeutic targets for the treatment of LE.}, }
@article {pmid32328670, year = {2020}, author = {Hanya, G and Tackmann, J and Sawada, A and Lee, W and Pokharel, SS and de Castro Maciel, VG and Toge, A and Kuroki, K and Otsuka, R and Mabuchi, R and Liu, J and Hatakeyama, M and Yamasaki, E and von Mering, C and Shimizu-Inatsugi, R and Hayakawa, T and Shimizu, KK and Ushida, K}, title = {Fermentation Ability of Gut Microbiota of Wild Japanese Macaques in the Highland and Lowland Yakushima: In Vitro Fermentation Assay and Genetic Analyses.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {459-474}, doi = {10.1007/s00248-020-01515-8}, pmid = {32328670}, issn = {1432-184X}, support = {15KK0256//MEXT Grant-in-Aid for Promotion of Joint International Research (Fostering Joint International Research)/ ; 19KK0186//MEXT Grant-in-Aid for Promotion of Joint International Research (Fostering Joint International Research)/ ; 25291100//MEXT Grant-in-Aid for Scientific Research B/ ; 18H02508//MEXT Grant-in-Aid for Scientific Research B/ ; }, mesh = {Animals ; Bacteria/genetics/*metabolism ; Diet ; *Digestion ; *Feeding Behavior ; Fermentation ; Gastrointestinal Microbiome/*physiology ; Macaca fuscata/*microbiology/*physiology ; Metagenome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Wild Japanese macaques (Macaca fuscata Blyth) living in the highland and lowland areas of Yakushima are known to have different diets, with highland individuals consuming more leaves. We aim to clarify whether and how these differences in diet are also reflected by gut microbial composition and fermentation ability. Therefore, we conduct an in vitro fermentation assay using fresh feces from macaques as inoculum and dry leaf powder of Eurya japonica Thunb. as a substrate. Fermentation activity was higher for feces collected in the highland, as evidenced by higher gas and butyric acid production and lower pH. Genetic analysis indicated separation of highland and lowland in terms of both community structure and function of the gut microbiota. Comparison of feces and suspension after fermentation indicated that the community structure changed during fermentation, and the change was larger for lowland samples. Analysis of the 16S rRNA V3-V4 barcoding region of the gut microbiota showed that community structure was clearly clustered between the two areas. Furthermore, metagenomic analysis indicated separation by gene and pathway abundance patterns. Two pathways (glycogen biosynthesis I and D-galacturonate degradation I) were enriched in lowland samples, possibly related to the fruit-eating lifestyle in the lowland. Overall, we demonstrated that the more leaf-eating highland Japanese macaques harbor gut microbiota with higher leaf fermentation ability compared with the more fruit-eating lowland ones. Broad, non-specific taxonomic and functional gut microbiome differences suggest that this pattern may be driven by a complex interplay between many taxa and pathways rather than single functional traits.}, }
@article {pmid32326329, year = {2020}, author = {Dagher, DJ and de la Providencia, IE and Pitre, FE and St-Arnaud, M and Hijri, M}, title = {Arbuscular Mycorrhizal Fungal Assemblages Significantly Shifted upon Bacterial Inoculation in Non-Contaminated and Petroleum-Contaminated Environments.}, journal = {Microorganisms}, volume = {8}, number = {4}, pages = {}, pmid = {32326329}, issn = {2076-2607}, support = {RGPIN-2018-04178//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) have been shown to reduce plant stress and improve their health and growth, making them important components of the plant-root associated microbiome, especially in stressful conditions such as petroleum hydrocarbons (PHs) contaminated environments. Purposely manipulating the root-associated AMF assemblages in order to improve plant health and modulate their interaction with the rhizosphere microbes could lead to increased agricultural crop yields and phytoremediation performance by the host plant and its root-associated microbiota. In this study, we tested whether repeated inoculations with a Proteobacteria consortium influenced plant productivity and the AMF assemblages associated with the root and rhizosphere of four plant species growing either in non-contaminated natural soil or in sediments contaminated with petroleum hydrocarbons. A mesocosm experiment was performed in a randomized complete block design in four blocks with two factors: (1) substrate contamination (contaminated or not contaminated), and (2) inoculation (or not) with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over four months, after which the effect of treatments on plant biomass and petroleum hydrocarbon concentrations in the substrate were determined. MiSeq amplicon sequencing, targeting the 18S rRNA gene, was used to assess AMF community structures in the roots and rhizosphere of plants growing in both contaminated and non-contaminated substrates. We also investigated the contribution of plant identity and biotope (plant roots and rhizospheric soil) in shaping the associated AMF assemblages. Our results showed that while inoculation caused a significant shift in AMF communities, the substrate contamination had a much stronger influence on their structure, followed by the biotope and plant identity to a lesser extent. Moreover, inoculation significantly increased plant biomass production and was associated with a decreased petroleum hydrocarbons dissipation in the contaminated soil. The outcome of this study provides knowledge on the factors influencing the diversity and community structure of AMF associated with indigenous plants following repeated inoculation of a bacterial consortium. It highlights the dominance of soil chemical properties, such as petroleum hydrocarbon presence, over biotic factors and inputs, such as plant species and microbial inoculations, in determining the plant-associated arbuscular mycorrhizal fungi communities.}, }
@article {pmid32322922, year = {2021}, author = {Huang, M and Chai, L and Jiang, D and Zhang, M and Jia, W and Huang, Y}, title = {Spatial Patterns of Soil Fungal Communities Are Driven by Dissolved Organic Matter (DOM) Quality in Semi-Arid Regions.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {202-214}, pmid = {32322922}, issn = {1432-184X}, support = {2016YFC0500903//National Key Research and Development Program of China/ ; 18Y01ESTCT//State Key Joint Laboratory of Environmental Simulation and Pollution Control/ ; }, mesh = {Desert Climate ; Ecosystem ; Fungi/genetics ; *Mycobiome ; *Soil ; Soil Microbiology ; }, abstract = {Soil fungi are ecologically important as decomposers, pathogens, and symbionts in nature. Understanding their biogeographic patterns and driving forces is pivotal to predict alterations arising from environmental changes in ecosystem. Dissolved organic matter (DOM) is an essential resource for soil fungi; however, the role of its quality in structuring fungal community patterns remains elusive. Here using Illumina MiSeq sequencing, we characterized total fungi and their functional groups in 45 soil samples collected from a 1500-km sampling transect through semi-arid regions in northern China, which are currently suffering great pressure from climate change. Total fungi and their functional groups were all observed to exhibit significant biogeographic patterns which were primarily driven by environmental variables. DOM quality was the best and consistent predictor of diversity of both total fungi and functional groups. Specifically, plant-derived DOM was associated with greater diversity relative to microbe-dominated origins. In addition, fungal diversity linearly increased with increases in degree of humification in DOM. Similarly, among all measured environmental variables, DOM quality had the strongest effects on the community composition of total fungi and functional groups. Together, our work contributes to the factors underlying fungal biogeographic patterns and adds detail to the importance of DOM quality in structuring fungal communities.}, }
@article {pmid32320735, year = {2020}, author = {Stevens, ML and Gonzalez, T and Schauberger, E and Baatyrbek Kyzy, A and Andersen, H and Spagna, D and Kalra, MK and Martin, LJ and Haslam, D and Herr, AB and Biagini Myers, JM and Khurana Hershey, GK}, title = {Simultaneous skin biome and keratinocyte genomic capture reveals microbiome differences by depth of sampling.}, journal = {The Journal of allergy and clinical immunology}, volume = {146}, number = {6}, pages = {1442-1445}, pmid = {32320735}, issn = {1097-6825}, support = {T32 GM063483/GM/NIGMS NIH HHS/United States ; U19 AI070235/AI/NIAID NIH HHS/United States ; UL1 TR001425/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Child ; *Dermatitis, Atopic/immunology/microbiology/pathology ; Female ; Gene Expression Regulation/*immunology ; Humans ; *Keratinocytes/immunology/microbiology/pathology ; Male ; Microbiota/*immunology ; *Skin/immunology/microbiology/pathology ; }, abstract = {Novel skin tape strip method allows for simultaneous collection of the skin microbiome and underlying host DNA and RNA, and reveals that microbial ecology is dependent on the depth of sampling.}, }
@article {pmid32317112, year = {2020}, author = {Gryp, T and De Paepe, K and Vanholder, R and Kerckhof, FM and Van Biesen, W and Van de Wiele, T and Verbeke, F and Speeckaert, M and Joossens, M and Couttenye, MM and Vaneechoutte, M and Glorieux, G}, title = {Gut microbiota generation of protein-bound uremic toxins and related metabolites is not altered at different stages of chronic kidney disease.}, journal = {Kidney international}, volume = {97}, number = {6}, pages = {1230-1242}, doi = {10.1016/j.kint.2020.01.028}, pmid = {32317112}, issn = {1523-1755}, mesh = {Feces ; *Gastrointestinal Microbiome ; Humans ; Indican ; *Renal Insufficiency, Chronic/diagnosis ; *Toxins, Biological ; *Uremia ; }, abstract = {Chronic kidney disease (CKD) is characterized by accumulation of protein-bound uremic toxins such as p-cresyl sulfate, p-cresyl glucuronide, indoxyl sulfate and indole-3-acetic acid, which originate in the gut. Intestinal bacteria metabolize aromatic amino acids into p-cresol and indole, (further conjugated in the colon mucosa and liver) and indole-3-acetic acid. Here we measured fecal, plasma and urine metabolite concentrations; the contribution of gut bacterial generation to plasma protein-bound uremic toxins accumulation; and influx into the gut of circulating protein-bound uremic toxins at different stages of CKD. Feces, blood and urine were collected from 14 control individuals and 141 patients with CKD. Solutes were quantified by ultra-high performance liquid chromatography. To assess the rate of bacterial generation of p-cresol, indole and indole-3-acetic acid, fecal samples were cultured ex vivo. With CKD progression, an increase in protein-bound uremic toxins levels was observed in plasma, whereas the levels of these toxins and their precursors remained the same in feces and urine. Anaerobic culture of fecal samples showed no difference in ex vivo p-cresol, indole and indole-3-acetic acid generation. Therefore, differences in plasma protein-bound uremic toxins levels between different CKD stages cannot be explained by differences in bacterial generation rates in the gut, suggesting retention due to impaired kidney function as the main contributor to their increased plasma levels. Thus, as fractional clearance decreased with the progression of CKD, tubular clearance appeared to be more affected than the glomerular filtration rate, and there was no net increase in protein-bound uremic toxins influx into the gut lumen with increased plasma levels.}, }
@article {pmid32315566, year = {2020}, author = {Hong, BY and Hoare, A and Cardenas, A and Dupuy, AK and Choquette, L and Salner, AL and Schauer, PK and Hegde, U and Peterson, DE and Dongari-Bagtzoglou, A and Strausbaugh, LD and Diaz, PI}, title = {The Salivary Mycobiome Contains 2 Ecologically Distinct Mycotypes.}, journal = {Journal of dental research}, volume = {99}, number = {6}, pages = {730-738}, pmid = {32315566}, issn = {1544-0591}, support = {M01 RR006192/RR/NCRR NIH HHS/United States ; R01 DE021578/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Aged ; Bacteria ; Cross-Sectional Studies ; Female ; Fungi ; Humans ; Malassezia ; Male ; Middle Aged ; *Mycobiome/genetics ; }, abstract = {A broad range of fungi has been detected in molecular surveys of the oral mycobiome. However, knowledge is still lacking on interindividual variability of these communities and the ecologic and clinical significance of oral fungal commensals. In this cross-sectional study, we use internal transcribed spacer 1 amplicon sequencing to evaluate the salivary mycobiome in 59 subjects, 36 of whom were scheduled to receive cancer chemotherapy. Analysis of the broad population structure of fungal communities in the whole cohort identified 2 well-demarcated genus-level community types (mycotypes), with Candida and Malassezia as the main taxa driving cluster partitioning. The Candida mycotype had lower diversity than the Malassezia mycotype and was positively correlated with cancer and steroid use in these subjects, smoking, caries, utilizing a removable prosthesis, and plaque index. Mycotypes were also associated with metabolically distinct bacteria indicative of divergent oral environments, with aciduric species enriched in the Candida mycotype and inflammophilic bacteria increased in the Malassezia mycotype. Similar to their fungal counterparts, coexisting bacterial communities associated with the Candida mycotype showed lower diversity than those associated with the Malassezia mycotype, suggesting that common environmental pressures affected bacteria and fungi. Mycotypes were also seen in an independent cohort of 24 subjects, in which cultivation revealed Malassezia as viable oral mycobiome members, although the low-abundance Malassezia sympodialis was the only Malassezia species recovered. There was a high degree of concordance between the molecular detection and cultivability of Candida, while cultivation showed low sensitivity for detection of the Malassezia mycotype. Overall, our work provides insights into the oral mycobiome landscape, revealing 2 community classes with apparently distinct ecologic constraints and specific associations with coexisting bacteria and clinical parameters. The utility of mycotypes as biomarkers for oral diseases warrants further study.}, }
@article {pmid32315331, year = {2020}, author = {Nigro, LM and Elling, FJ and Hinrichs, KU and Joye, SB and Teske, A}, title = {Microbial ecology and biogeochemistry of hypersaline sediments in Orca Basin.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0231676}, pmid = {32315331}, issn = {1932-6203}, mesh = {Archaea/classification/genetics ; DNA, Archaeal/classification/genetics ; *Ecosystem ; Geologic Sediments/chemistry/classification/*microbiology ; Gulf of Mexico ; RNA, Ribosomal, 16S/classification/genetics ; Salinity ; Seawater/chemistry/*microbiology ; Sulfates/chemistry ; }, abstract = {In deep ocean hypersaline basins, the combination of high salinity, unusual ionic composition and anoxic conditions represents significant challenges for microbial life. We used geochemical porewater characterization and DNA sequencing based taxonomic surveys to enable environmental and microbial characterization of anoxic hypersaline sediments and brines in the Orca Basin, the largest brine basin in the Gulf of Mexico. Full-length bacterial 16S rRNA gene clone libraries from hypersaline sediments and the overlying brine were dominated by the uncultured halophilic KB1 lineage, Deltaproteobacteria related to cultured sulfate-reducing halophilic genera, and specific lineages of heterotrophic Bacteroidetes. Archaeal clones were dominated by members of the halophilic methanogen genus Methanohalophilus, and the ammonia-oxidizing Marine Group I (MG-I) within the Thaumarchaeota. Illumina sequencing revealed higher phylum- and subphylum-level complexity, especially in lower-salinity sediments from the Orca Basin slope. Illumina and clone library surveys consistently detected MG-I Thaumarchaeota and halotolerant Deltaproteobacteria in the hypersaline anoxic sediments, but relative abundances of the KB1 lineage differed between the two sequencing methods. The stable isotopic composition of dissolved inorganic carbon and methane in porewater, and sulfate concentrations decreasing downcore indicated methanogenesis and sulfate reduction in the anoxic sediments. While anaerobic microbial processes likely occur at low rates near their maximal salinity thresholds in Orca Basin, long-term accumulation of reaction products leads to high methane concentrations and reducing conditions within the Orca Basin brine and sediments.}, }
@article {pmid32314003, year = {2020}, author = {Parker, ES and Newton, ILG and Moczek, AP}, title = {(My Microbiome) Would Walk 10,000 miles: Maintenance and Turnover of Microbial Communities in Introduced Dung Beetles.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {435-446}, doi = {10.1007/s00248-020-01514-9}, pmid = {32314003}, issn = {1432-184X}, support = {1901680//Division of Integrative Organismal Systems/ ; 1256689//Division of Integrative Organismal Systems/ ; 61369//John Templeton Foundation/ ; }, mesh = {Animals ; Australian Capital Territory ; Bacteria/*isolation &amp; purification ; Coleoptera/*microbiology ; Introduced Species ; Italy ; *Microbiota ; *Symbiosis ; West Virginia ; }, abstract = {Host-associated microbes facilitate diverse biotic and abiotic interactions between hosts and their environments. Experimental alterations of host-associated microbial communities frequently decrease host fitness, yet much less is known about if and how host-microbiome interactions are altered by natural perturbations, such as introduction events. Here, we begin to assess this question in Onthophagus dung beetles, a species-rich and geographically widely distributed genus whose members rely on vertically transmitted microbiota to support normal development. Specifically, we investigated to what extent microbiome community membership shifts during host introduction events and the relative significance of ancestral associations and novel environmental conditions in the structuring of microbial communities of introduced host species. Our results demonstrate that both evolutionary history and local environmental forces structure the microbial communities of these animals, but that their relative importance is shaped by the specific circumstances that characterize individual introduction events. Furthermore, we identify microbial taxa such as Dysgonomonas that may constitute members of the core Onthophagus microbiome regardless of host population or species, but also Wolbachia which associates with Onthophagus beetles in a species or even population-specific manner. We discuss the implications of our results for our understanding of the evolutionary ecology of symbiosis in dung beetles and beyond.}, }
@article {pmid32313622, year = {2020}, author = {Böckelmann, J and Tremetsberger, K and Šumberová, K and Kohl, G and Grausgruber, H and Bernhardt, KG}, title = {Genetic variation in an ephemeral mudflat species: The role of the soil seed bank and dispersal in river and secondary anthropogenic habitats.}, journal = {Ecology and evolution}, volume = {10}, number = {8}, pages = {3620-3635}, pmid = {32313622}, issn = {2045-7758}, support = {P 24558/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Many ephemeral mudflat species, which rely on a soil seed bank to build up the next generation, are endangered in their natural habitat due to the widespread regulation of rivers. The aim of the present study was to elucidate the role of the soil seed bank and dispersal for the maintenance of genetic diversity in populations of near-natural river habitats and anthropogenic habitats created by traditional fish farming practices using Cyperus fuscus as a model. Using microsatellite markers, we found no difference in genetic diversity levels between soil seed bank and above-ground population and only moderate differentiation between the two fractions. One possible interpretation is the difference in short-term selection during germination under specific conditions (glasshouse versus field) resulting in an ecological filtering of genotypes out of the reservoir in the soil. River populations harbored significantly more genetic diversity than populations from the anthropogenic pond types. We suggest that altered levels and patterns of dispersal together with stronger selection pressures and historical bottlenecks in anthropogenic habitats are responsible for the observed reduction in genetic diversity. Dispersal is also supposed to largely prohibit genetic structure across Europe, although there is a gradient in private allelic richness from southern Europe (high values) to northern, especially north-western, Europe (low values), which probably relates to postglacial expansion out of southern and/or eastern refugia.}, }
@article {pmid32313597, year = {2020}, author = {Parks, S and Joyner, JL and Nusnbaum, M}, title = {Reaching a Large Urban Undergraduate Population through Microbial Ecology Course-Based Research Experiences.}, journal = {Journal of microbiology &amp; biology education}, volume = {21}, number = {1}, pages = {}, pmid = {32313597}, issn = {1935-7877}, abstract = {Traditional postsecondary education is making progress on embracing the diversity of student backgrounds and experiences while preparing them for the demands of STEM careers. Course-based undergraduate research experiences (CUREs) are effective tools to concurrently achieve many student and faculty goals: facilitating training of students, building career competencies, generating publishable research results and enabling research experiences where students apply their knowledge and interest. Georgia State University is not unique with a high student demand for research experiences and mentors that is greater than traditional research faculty labs can accommodate. Georgia State University is, however, unique in that it is a demographically diverse campus which serves minority and non-traditional students (i.e., second career and veterans) and is also rapidly growing. Therefore, to enhance the microbiology curriculum and facilitate authentic research experiences for the growing number of biology majors, a cluster of course-based research experiences in microbial ecology was developed. A former research lab space was converted to a collaborative teaching lab to serve the growth in course offerings, as well as to accommodate multiple microbial ecology research projects occurring in the same space. The courses offered appeal to students, build on the strengths of faculty experiences, and facilitate collaboration amongst students and with the greater Atlanta community. To ensure that our CUREs are accessible to the diverse students in our department, we addressed a variety of logistical and curricular challenges. Solutions to such challenges align with the goals of the university to offer research and signature experiences to ensure students are included and trained in STEM skills.}, }
@article {pmid32311222, year = {2020}, author = {De Vrieze, J and De Mulder, T and Matassa, S and Zhou, J and Angenent, LT and Boon, N and Verstraete, W}, title = {Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals.}, journal = {Microbial biotechnology}, volume = {13}, number = {4}, pages = {829-843}, pmid = {32311222}, issn = {1751-7915}, mesh = {Goals ; Humans ; *Microbiota ; Stochastic Processes ; *Sustainable Development ; }, abstract = {Pure (single) cultures of microorganisms and mixed microbial communities (microbiomes) have been important for centuries in providing renewable energy, clean water and food products to human society and will continue to play a crucial role to pursue the Sustainable Development Goals. To use microorganisms effectively, microbial engineered processes require adequate control. Microbial communities are shaped by manageable deterministic processes, but also by stochastic processes, which can promote unforeseeable variations and adaptations. Here, we highlight the impact of stochasticity in single culture and microbiome engineering. First, we discuss the concepts and mechanisms of stochasticity in relation to microbial ecology of single cultures and microbiomes. Second, we discuss the consequences of stochasticity in relation to process performance and human health, which are reflected in key disadvantages and important opportunities. Third, we propose a suitable decision tool to deal with stochasticity in which monitoring of stochasticity and setting the boundaries of stochasticity by regulators are central aspects. Stochasticity may give rise to some risks, such as the presence of pathogens in microbiomes. We argue here that by taking the necessary precautions and through clever monitoring and interpretation, these risks can be mitigated.}, }
@article {pmid32310264, year = {2020}, author = {Liu, K and Liu, Y and Hu, A and Wang, F and Chen, Y and Gu, Z and Anslan, S and Hou, J}, title = {Different community assembly mechanisms underlie similar biogeography of bacteria and microeukaryotes in Tibetan lakes.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {6}, pages = {}, doi = {10.1093/femsec/fiaa071}, pmid = {32310264}, issn = {1574-6941}, mesh = {Bacteria/genetics ; Biodiversity ; *Lakes ; *Microbiota ; Salinity ; Tibet ; }, abstract = {Geographic patterns of bacteria and microeukaryotes have attracted increasing attention. However, mechanisms underlying geographic patterns in the community composition of both microbial groups are still poorly resolved. In particular, knowledge of whether bacterial communities and microeukaryotic communities are subject to the same or different assembly mechanisms is still limited. In this study, we investigated the biogeographic patterns of bacterial and microeukaryotic communities of 23 lakes on the Tibetan Plateau and quantified the relative influence of assembly mechanisms in shaping both microbial communities. Results showed that water salinity was the major driving force in controlling the community structures of bacteria and microeukaryotes. Although bacterial and microeukaryotic communities exhibited similar distance-decay patterns, the bacterial communities were mainly governed by environmental filtering (a niche-related process), whereas microeukaryotic communities were strongly driven by dispersal limitation (a neutral-related process). Furthermore, we found that bacteria exhibited wider niche breadths and higher dispersal ability but lower community stabilities than microeukaryotes. The similar distribution patterns but contrasting assembly mechanisms effecting bacteria and microeukaryotes resulted from the differences in dispersal ability and community stability. Our results highlight the importance of considering organism types in studies of the assembly mechanisms that shape microbial communities in microbial ecology.}, }
@article {pmid32307553, year = {2020}, author = {Lu, J and Zhang, X and Qiu, Q and Chen, J and Xiong, J}, title = {Identifying Potential Polymicrobial Pathogens: Moving Beyond Differential Abundance to Driver Taxa.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {447-458}, doi = {10.1007/s00248-020-01511-y}, pmid = {32307553}, issn = {1432-184X}, support = {31872693//National Natural Science Foundation of China/ ; LR19C030001//the Natural Science Fund for Distinguished Young Scholars of Zhejiang Province/ ; 2015C110018//the Technology Innovation Team of Ningbo/ ; }, mesh = {Actinobacteria/isolation &amp; purification/physiology ; Animals ; Aquaculture ; Bacteria/*isolation &amp; purification ; China ; *Gastrointestinal Microbiome ; Penaeidae/*microbiology ; Vibrio/physiology ; }, abstract = {It is now recognized that some diseases of aquatic animals are attributed to polymicrobial pathogens infection. Thus, the traditional view of "one pathogen, one disease" might mislead the identification of multiple pathogens, which in turn impedes the design of probiotics. To address this gap, we explored polymicrobial pathogens based on the origin and timing of increased abundance over shrimp white feces syndrome (WFS) progression. OTU70848 Vibrio fluvialis, OTU35090 V. coralliilyticus, and OTU28721 V. tubiashii were identified as the primary colonizers, whose abundances increased only in individuals that eventually showed disease signs but were stable in healthy subjects over the same timeframe. Notably, the random Forest model revealed that the profiles of the three primary colonizers contributed an overall 91.4% of diagnosing accuracy of shrimp health status. Additionally, NetShift analysis quantified that the three primary colonizers were important "drivers" in the gut microbiotas from healthy to WFS shrimp. For these reasons, the primary colonizers were potential pathogens that contributed to the exacerbation of WFS. By this logic, we further identified a few "drivers" commensals in healthy individuals, such as OUT50531 Demequina sediminicola and OTU_74495 Ruegeria lacuscaerulensis, which directly antagonized the three primary colonizers. The predicted functional pathways involved in energy metabolism, genetic information processing, terpenoids and polyketides metabolism, lipid and amino acid metabolism significantly decreased in diseased shrimp compared with those in healthy cohorts, in concordant with the knowledge that the attenuations of these functional pathways increase shrimp sensitivity to pathogen infection. Collectively, we provide an ecological framework for inferring polymicrobial pathogens and designing antagonized probiotics by quantifying their changed "driver" feature that intimately links shrimp WFS progression. This approach might generalize to the exploring disease etiology for other aquatic animals.}, }
@article {pmid32303845, year = {2020}, author = {Yu, L and Wang, Y and Su, X and Fu, Y and Ma, F and Guo, H}, title = {Biodiversity, isolation and genome analysis of sulfamethazine-degrading bacteria using high-throughput analysis.}, journal = {Bioprocess and biosystems engineering}, volume = {43}, number = {8}, pages = {1521-1531}, doi = {10.1007/s00449-020-02345-1}, pmid = {32303845}, issn = {1615-7605}, mesh = {*Biodiversity ; *Genome, Bacterial ; *Microbial Consortia ; *Micrococcaceae/genetics/isolation &amp; purification/metabolism ; Sulfamethazine/*metabolism ; Wastewater/microbiology ; *Water Microbiology ; }, abstract = {Sulfamethazine (SM2) is one of the sulfonamide antibiotics that is frequently detected in aquatic environment. Given the complex structure of SM2 and its potential threat to the environment, it is necessary to determine the degradation behavior of high-concentration SM2. The mechanisms of community structure and diversity of activated sludge were analyzed. A novel SM2-degrading strain YL1 was isolated which can degrade SM2 with high concentration of 100 mg L[-1]. Strain YL1 was identified as Paenarthrobacter ureafaciens and there was also a significant increase in the genus during acclimation. Additional SM2 metabolic mechanisms and genomic information of YL1 were analyzed for further research. The succession of the community structure also investigated the effect of SM2 on the activated sludge. This result not only advances the current understanding of microbial ecology in activated sludge, but also has practical implications for the design and operation of the environmental bioprocesses for treatment of antimicrobial-bearing waste streams.}, }
@article {pmid32303543, year = {2020}, author = {Minich, JJ and Poore, GD and Jantawongsri, K and Johnston, C and Bowie, K and Bowman, J and Knight, R and Nowak, B and Allen, EE}, title = {Microbial Ecology of Atlantic Salmon (Salmo salar) Hatcheries: Impacts of the Built Environment on Fish Mucosal Microbiota.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {12}, pages = {}, pmid = {32303543}, issn = {1098-5336}, support = {F30 CA243480/CA/NCI NIH HHS/United States ; T32 GM007198/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Aquaculture ; Biofilms ; *Built Environment ; *Fisheries ; Gastrointestinal Contents/microbiology ; Gills/microbiology ; Microbiota/*physiology ; Mucous Membrane/*microbiology ; Salmo salar ; Skin/microbiology ; Water Microbiology ; }, abstract = {Successful rearing of fish in hatcheries is critical for conservation, recreational fishing, commercial fishing through wild stock enhancements, and aquaculture production. Flowthrough (FT) hatcheries require more water than recirculating aquaculture systems (RAS), which enable up to 99% of their water to be recycled, thus significantly reducing environmental impacts. Here, we evaluated the biological and physical microbiome interactions of three Atlantic salmon hatcheries (RAS n = 2, FT n = 1). Gill, skin, and digesta from six juvenile fish along with tank biofilms and water were sampled from tanks in each of the hatcheries (60 fish across 10 tanks) to assess the built environment and mucosal microbiota using 16S rRNA gene sequencing. The water and tank biofilm had more microbial richness than fish mucus, while skin and digesta from RAS fish had 2 times the richness of FT fish. Body sites each had unique microbiomes (P < 0.001) and were influenced by hatchery system type (P < 0.001), with RAS being more similar. A strong association between the tank and fish microbiome was observed. Water and tank biofilm richness was positively correlated with skin and digesta richness. Strikingly, the gill, skin, and digesta communities were more similar to that in the origin tank biofilm than those in all other experimental tanks, suggesting that the tank biofilm has a direct influence on fish-associated microbial communities. Lastly, microbial diversity and mucous cell density were positively associated with fish growth and length. The results from this study provide evidence for a link between the tank microbiome and the fish microbiome, with the skin microbiome as an important intermediate.IMPORTANCE Atlantic salmon, Salmo salar, is the most farmed marine fish worldwide, with an annual production of 2,248 million metric tons in 2016. Salmon hatcheries are increasingly changing from flowthrough toward recirculating aquaculture system (RAS) design to accommodate more control over production along with improved environmental sustainability due to lower impacts on water consumption. To date, microbiome studies of hatcheries have focused either on the fish mucosal microbiota or on the built environment microbiota but have not combined the two to understand their interactions. Our study evaluates how the water and tank biofilm microbiota influences the fish microbiota across three mucosal environments (gill, skin, and digesta). Results from this study highlight how the built environment is a unique source of microbes to colonize fish mucus and, furthermore, how this can influence fish health. Further studies can use this knowledge to engineer built environments to modulate fish microbiota for beneficial phenotypes.}, }
@article {pmid32300926, year = {2020}, author = {Barman, D and Dkhar, MS}, title = {Seasonal Variation Influence Endophytic Actinobacterial Communities of Medicinal Plants from Tropical Deciduous Forest of Meghalaya and Characterization of Their Plant Growth-Promoting Potentials.}, journal = {Current microbiology}, volume = {77}, number = {8}, pages = {1689-1698}, pmid = {32300926}, issn = {1432-0991}, mesh = {Actinobacteria/genetics/*physiology ; Biodiversity ; Endophytes/*physiology ; Forests ; *Host Microbial Interactions ; India ; Phylogeny ; Plant Roots/microbiology ; Plants, Medicinal/classification/*growth &amp; development/*microbiology ; *Seasons ; Species Specificity ; Tropical Climate ; }, abstract = {The endophytic actinobacteria constitute a diverse community which has vast potential importance that may be exploited in pharmaceutical, agricultural, and biotechnological industries. However, the effects of seasonal changes on distribution of endophytic actinobacteria in medicinal plants of Meghalaya are largely uncharacterized. Here, we investigated host and seasonal influence on diversity of endophytic actinobacteria residing in roots of six medicinal plant species of Meghalaya. A total of 493 cultivable endophytic actinobacterial isolates representing 41 species were obtained from root segments of six plant species which had been collected during four different seasons of 2011-2012 and 2012-2013. Among the host plant species, maximum actinobacterial colonization was observed in Costus speciosus and minimum in Potentilla fulgens. In regard to seasons, the highest actinobacterial colonization and relative abundance were observed during summer season and least was recorded during the winter season. It was ascertained that though endophytic actinobacteria have varying capacity to colonize in different plant species during the seasons, colonization is not found to be species-specific. Culture-independent attempt also inferred that actinobacterial community varied amongst the six medicinal plants during the different seasons. Hence, seasons are influential factors in the colonization capacity of endophytic actinobacterial community. Furthermore, plant growth-promoting activities were recorded in 34.15% of the isolates. Hence, these results indicate that endophytic actinobacteria from the selected medicinal plants also represent an important source of plant growth-promoting bioactive metabolites.}, }
@article {pmid32300830, year = {2020}, author = {Zhang, W and Gu, Q and Niu, J and Wang, JJ}, title = {The RNA Virome and Its Dynamics in an Invasive Fruit Fly, Bactrocera dorsalis, Imply Interactions Between Host and Viruses.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {423-434}, doi = {10.1007/s00248-020-01506-9}, pmid = {32300830}, issn = {1432-184X}, support = {31701846//National Natural Science Foundation of China/ ; CARS-26//Earmarked Fund for Modern Agro-industry Technology Research System/ ; }, mesh = {Animals ; Female ; *Host Microbial Interactions ; Male ; RNA Viruses/classification/*isolation &amp; purification/physiology ; RNA, Viral/analysis ; Tephritidae/immunology/*virology ; *Virome ; }, abstract = {The oriental fruit fly, Bactrocera dorsalis (Hendel), is an important invasive agricultural insect pest with a wide host range, and has spread around the world over the last century. This evolutionary trait may have arisen primarily from interactions between B. dorsalis and other invertebrates that share the same ecological niches. The invasive behavior of B. dorsalis also frequently exposes them to diverse species of viruses. Thereby, RNA viromes may be useful microbial markers to understand the ecological evolution of B. dorsalis as well as to investigate virus-host interactions. Here, we reported eight novel RNA viruses in B. dorsalis of a lab colony, including four positive-strand RNA viruses, two negative-strand RNA viruses, and two double-stranded RNA viruses using high-throughput sequencing technology. Analysis of the virus-derived small RNAs suggested that most of these viruses may be active and trigger the host antiviral RNAi responses. The viruses were also detected in various geographical populations of B. dorsalis, implying that there is a strong association between the viromes and host. In addition, these viruses infected specific fly tissues, predominately the central nervous system and gut. Furthermore, we explored the dynamics of the viruses when hosts were exposed to short- or long-term stressors, which showed that titers of some viruses were responsively altered in the stressed B. dorsalis. The discovery of these viruses may enrich our understanding of the species diversity of RNA viruses and also provide information on viruses in association with host adaptation in insects.}, }
@article {pmid32300653, year = {2020}, author = {Inoue, K and Tsunoda, SP and Singh, M and Tomida, S and Hososhima, S and Konno, M and Nakamura, R and Watanabe, H and Bulzu, PA and Banciu, HL and Andrei, A&#x15e; and Uchihashi, T and Ghai, R and Béjà, O and Kandori, H}, title = {Schizorhodopsins: A family of rhodopsins from Asgard archaea that function as light-driven inward H[+] pumps.}, journal = {Science advances}, volume = {6}, number = {15}, pages = {eaaz2441}, pmid = {32300653}, issn = {2375-2548}, mesh = {Archaea/genetics/*metabolism ; Cell Membrane/metabolism ; Fluorescent Antibody Technique ; Ion Channel Gating/*radiation effects ; Light ; Models, Molecular ; Multigene Family ; Mutation ; Protein Conformation ; Proton Pumps/chemistry/genetics/*metabolism ; Rhodopsin/chemistry/genetics/*metabolism ; Spectroscopy, Fourier Transform Infrared ; Structure-Activity Relationship ; }, abstract = {Schizorhodopsins (SzRs), a rhodopsin family first identified in Asgard archaea, the archaeal group closest to eukaryotes, are present at a phylogenetically intermediate position between typical microbial rhodopsins and heliorhodopsins. However, the biological function and molecular properties of SzRs have not been reported. Here, SzRs from Asgardarchaeota and from a yet unknown microorganism are expressed in Escherichia coli and mammalian cells, and ion transport assays and patch clamp analyses are used to demonstrate SzR as a novel type of light-driven inward H[+] pump. The mutation of a cytoplasmic glutamate inhibited inward H[+] transport, suggesting that it functions as a cytoplasmic H[+] acceptor. The function, trimeric structure, and H[+] transport mechanism of SzR are similar to that of xenorhodopsin (XeR), a light-driven inward H[+] pumping microbial rhodopsins, implying that they evolved convergently. The inward H[+] pump function of SzR provides new insight into the photobiological life cycle of the Asgardarchaeota.}, }
@article {pmid32300619, year = {2020}, author = {Poirier, S and Luong, NM and Anthoine, V and Guillou, S and Membré, JM and Moriceau, N and Rezé, S and Zagorec, M and Feurer, C and Frémaux, B and Jeuge, S and Robieu, E and Champomier-Vergès, M and Coeuret, G and Cauchie, E and Daube, G and Korsak, N and Coroller, L and Desriac, N and Desmonts, MH and Gohier, R and Werner, D and Loux, V and Rué, O and Dohollou, MH and Defosse, T and Chaillou, S}, title = {Large-scale multivariate dataset on the characterization of microbiota diversity, microbial growth dynamics, metabolic spoilage volatilome and sensorial profiles of two industrially produced meat products subjected to changes in lactate concentration and packaging atmosphere.}, journal = {Data in brief}, volume = {30}, number = {}, pages = {105453}, pmid = {32300619}, issn = {2352-3409}, abstract = {Data in this article provide detailed information on the diversity of bacterial communities present on 576 samples of raw pork or poultry sausages produced industrially in 2017. Bacterial growth dynamics and diversity were monitored throughout the refrigerated storage period to estimate the impact of packaging atmosphere and the use of potassium lactate as chemical preservative. The data include several types of analysis aiming at providing a comprehensive microbial ecology of spoilage during storage and how the process parameters do influence this phenomenon. The analysis includes: the gas content in packaging, pH, chromametric measurements, plate counts (total mesophilic aerobic flora and lactic acid bacteria), sensorial properties of the products, meta-metabolomic quantification of volatile organic compounds and bacterial community metagenetic analysis. Bacterial diversity was monitored using two types of amplicon sequencing (16S rRNA and GyrB encoding genes) at different time points for the different conditions (576 samples for gyrB and 436 samples for 16S rDNA). Sequencing data were generated by using Illumina MiSeq. The sequencing data have been deposited in the bioproject PRJNA522361. Samples accession numbers vary from SAMN10964863 to SAMN10965438 for gyrB amplicon and from SAMN10970131 to SAMN10970566 for 16S.}, }
@article {pmid32300601, year = {2020}, author = {Gaspardo, A and Zannoni, A and Turroni, S and Barone, M and Sabetti, MC and Zanoni, RG and Forni, M and Brigidi, P and Pietra, M}, title = {Influence of Lactobacillus kefiri on Intestinal Microbiota and Fecal IgA Content of Healthy Dogs.}, journal = {Frontiers in veterinary science}, volume = {7}, number = {}, pages = {146}, pmid = {32300601}, issn = {2297-1769}, abstract = {The increasing incidence of gastrointestinal tract pathologies in dogs and the worrisome topic of antibiotic resistance have raised the need to look for new therapeutic frontiers. Of these, the use of probiotics represents a potential therapeutic alternative. Lactobacillus kefiri (Lk) is a species of Lactobacillus isolated from kefir. Previous studies have demonstrated that its administration in mice downregulates the expression of proinflammatory mediators and increases anti-inflammatory molecules in the gut immune system. It also regulates intestinal homeostasis, incrementing immunoglobulin A (IgA) secretion. Since Lk has never been studied as a single probiotic in dogs, the aim of this study was to evaluate the safety of Lk in dogs, and its effect on IgA secretion and on intestinal microbiota composition. Ten healthy dogs without a history of gastrointestinal diseases were included. The dogs received Lk at a dose of 10[7] live microorganisms orally, once daily for 30 days. The fecal samples were tested before administration, in the middle, at the end, and 30 days after discontinuation. The IgA secretion concentration and the microbiota composition were evaluated on the fecal samples. The results in this study suggested that Lk did not influence the concentration of IgA, nor significant changes of the intestinal microbiota were observed during and after the treatment. Therefore, additional studies are needed to investigate if a higher daily dosage of Lk can influence the intestinal homeostasis of dogs.}, }
@article {pmid32300339, year = {2020}, author = {Scoma, A and Khor, WC and Coma, M and Heyer, R and Props, R and Schoelynck, J and Bouts, T and Benndorf, D and Li, D and Zhang, H and Rabaey, K}, title = {Substrate-Dependent Fermentation of Bamboo in Giant Panda Gut Microbiomes: Leaf Primarily to Ethanol and Pith to Lactate.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {530}, pmid = {32300339}, issn = {1664-302X}, abstract = {The giant panda is known worldwide for having successfully moved to a diet almost exclusively based on bamboo. Provided that no lignocellulose-degrading enzyme was detected in panda's genome, bamboo digestion is believed to depend on its gut microbiome. However, pandas retain the digestive system of a carnivore, with retention times of maximum 12 h. Cultivation of their unique gut microbiome under controlled laboratory conditions may be a valid tool to understand giant pandas' dietary habits, and provide valuable insights about what component of lignocellulose may be metabolized. Here, we collected gut microbiomes from fresh fecal samples of a giant panda (either entirely green or yellow stools) and supplied them with green leaves or yellow pith (i.e., the peeled stem). Microbial community composition was substrate dependent, and resulted in markedly different fermentation profiles, with yellow pith fermented to lactate and green leaves to lactate, acetate and ethanol, the latter to strikingly high concentrations (∼3%, v:v, within 3.5 h). Microbial metaproteins pointed to hemicellulose rather than cellulose degradation. The alpha-amylase from the giant panda (E.C. 3.2.1.1) was the predominant identified metaprotein, particularly in reactors inoculated with pellets derived from fecal samples (up to 60%). Gut microbiomes assemblage was most prominently impacted by the change in substrate (either leaf or pith). Removal of soluble organics from inocula to force lignocellulose degradation significantly enriched Bacteroides (in green leaf) and Escherichia/Shigella (in yellow pith). Overall, different substrates (either leaf or pith) markedly shaped gut microbiome assemblies and fermentation profiles. The biochemical profile of fermentation products may be an underestimated factor contributing to explain the peculiar dietary behavior of giant pandas, and should be implemented in large scale studies together with short-term lab-scale cultivation of gut microbiomes.}, }
@article {pmid32298910, year = {2020}, author = {Dasgupta, S and Podder, A and Goel, R}, title = {Response of an aerobic granular and conventional flocculated reactors against changing feed composition from simple composition to more complex.}, journal = {Chemosphere}, volume = {253}, number = {}, pages = {126694}, doi = {10.1016/j.chemosphere.2020.126694}, pmid = {32298910}, issn = {1879-1298}, mesh = {Aerobiosis ; Bacteria/classification ; Bioreactors ; Flocculation ; Polyphosphates ; Sewage ; Waste Disposal, Fluid/*methods ; Wastewater ; }, abstract = {This research evaluated the effect of changing feed composition on the performances of a conventional activated sludge (CAS) and an aerobic granular sludge (AGS) reactor operated simultaneously. Both reactors were initially fed with 100% synthetic feed. In a stepwise manner, the feed composition was slowly changed to real primary effluent collected from a local wastewater treatment plant. After an initial stabilization period, both reactors could achieve more than 90% NH4[+]-N removal. However, PO4[3-]-P removal eventually reached to a maximum of 92% in the AGS and 88% in the CAS. COD removal in both reactors was least affected, with the lowest percent removal of 81 ± 3% achieved in AGS and 62 ± 4% in CAS respectively when fed with 100% real wastewater. Despite granule breakage the AGS reactor was able to remove the pollutants (COD, N, P). The abundance of Candidatus Accumulibacter, a polyphosphate accumulating organism, in the AGS system increased over the operational phases: II (6.2%), III (10.32%), and IV (11.9%). While in CAS, it increased from phase I to phase II (12.6%), but decreased in phase III to 9.9%. Genus-based classification revealed a successive increase in the relative abundance of Nitrospira to 11.05% during Phase III and 10.3% during Phase IV in the AGS. In contrast with its presence in the CAS, which was, 3.4% during Phase III and 9.5% during Phase IV.}, }
@article {pmid32296869, year = {2020}, author = {Procópio, L and Pádula, M and van Elsas, JD and Seldin, L}, title = {Adaptative transcriptional response of Dietzia cinnamea P4 strain to sunlight simulator.}, journal = {Archives of microbiology}, volume = {202}, number = {7}, pages = {1701-1708}, doi = {10.1007/s00203-020-01879-y}, pmid = {32296869}, issn = {1432-072X}, mesh = {Actinobacteria/*genetics/*radiation effects ; Adaptation, Physiological ; Bacterial Proteins/genetics ; DNA Repair/genetics ; Gene Expression Regulation, Bacterial/*radiation effects ; Hydrolases/genetics ; Oxidoreductases/genetics ; Real-Time Polymerase Chain Reaction ; *Sunlight ; }, abstract = {Responses to sunlight exposure of the oil-degrading Dietzia cinnamea P4 strain were evaluated by transcriptional levels of SOS genes, photoreactivation and genes involved in tolerance to high levels of reactive oxygen species. The P4 strain was exposed for 1 and 2 h and the magnitude of level changes in the mRNA was evaluated by qPCR. The results described the activation of the SOS system, with the decline of the repressor lexA gene levels and the concomitant increase of recA and uvrAD genes levels. The genes that participate in the photoreactivation process were also responsive to sunlight. The phrB gene encoding deoxyribodipyrimidine photo-lyase had its expression increased after 1-h exposure, while the phytAB genes showed a progressive increase over the studied period. The protective genes against reactive oxygen species, catalases, superoxides, peroxidases, and thioredoxins, had their expression rates detected under the conditions validated in this study. These results show a fast and coordinated response of genes from different DNA repair and tolerance mechanisms employed by strain P4, suggesting a complex concerted protective action against environmental stressors.}, }
@article {pmid32296073, year = {2020}, author = {Remizovschi, A and Carpa, R and Forray, FL and Chiriac, C and Roba, CA and Beldean-Galea, S and Andrei, A&#x218; and Szekeres, E and Baricz, A and Lupan, I and Rudi, K and Coman, C}, title = {Author Correction: Mud volcanoes and the presence of PAHs.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {6668}, doi = {10.1038/s41598-020-62513-x}, pmid = {32296073}, issn = {2045-2322}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid32293257, year = {2020}, author = {Meparambu Prabhakaran, D and Ramamurthy, T and Thomas, S}, title = {Genetic and virulence characterisation of Vibrio parahaemolyticus isolated from Indian coast.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {62}, pmid = {32293257}, issn = {1471-2180}, mesh = {Actin Cytoskeleton/genetics ; Bacterial Proteins/genetics ; Bacterial Toxins/genetics ; Caco-2 Cells ; Hemolysin Proteins/genetics ; Humans ; India ; Phylogeny ; Plankton/*microbiology ; Seafood/*microbiology ; Type III Secretion Systems/genetics ; Vibrio Infections/genetics/metabolism/*microbiology ; Vibrio parahaemolyticus/classification/genetics/isolation &amp; purification/*pathogenicity ; Virulence Factors/*genetics ; Water Microbiology ; Zonula Occludens-1 Protein/genetics ; }, abstract = {BACKGROUND: V. parahaemolyticus is autochthonous to the marine environment and causes seafood-borne gastroenteritis in humans. Generally, V. parahaemolyticus recovered from the environment and/or seafood is thought to be non-pathogenic and the relationship between environmental isolates and acute diarrhoeal disease is poorly understood. In this study, we explored the virulence potential of environmental V. parahaemolyticus isolated from water, plankton and assorted seafood samples collected from the Indian coast.<br><br>RESULTS: Twenty-two V. parahaemolyticus isolates from seafood harboured virulence associated genes encoding the thermostable-direct haemolysin (TDH), TDH-related haemolysin (TRH), and Type 3 secretion systems (T3SS) and 95.5% of the toxigenic isolates had pandemic strain attributes (toxRS/new[+]). Nine serovars, with pandemic strain traits were newly identified and an O4:K36 tdh[-]trh[+]V. parahaemolyticus bearing pandemic marker gene was recognised for the first time. Results obtained by reverse transcription PCR showed trh, T3SS1 and T3SS2&#x3b2; to be functional in the seafood isolates. Moreover, the environmental strains were cytotoxic and could invade Caco-2 cells upon infection as well as induce changes to the tight junction protein, ZO-1 and the actin cytoskeleton.<br><br>CONCLUSION: Our study provides evidence that environmental isolates of V. parahaemolyticus are potentially invasive and capable of eliciting pathogenic characteristics typical of clinical strains and present a potential health risk. We also demonstrate that virulence of this pathogen is highly complex and hence draws attention for the need to investigate more reliable virulence markers in order to distinguish the environmental and clinical isolates, which will be crucial for the pathogenomics and control of this pathogen.}, }
@article {pmid32291478, year = {2020}, author = {Gilbert, KJ and Bittleston, LS and Naive, MAK and Kiszewski, AE and Buenavente, PAC and Lohman, DJ and Pierce, NE}, title = {Investigation of an Elevational Gradient Reveals Strong Differences Between Bacterial and Eukaryotic Communities Coinhabiting Nepenthes Phytotelmata.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {334-349}, pmid = {32291478}, issn = {1432-184X}, mesh = {*Altitude ; Animals ; Arthropods ; Bacteria/classification/*isolation &amp; purification ; *Biodiversity ; Caryophyllales/*microbiology/parasitology ; Eukaryota ; Microbiota ; Philippines ; }, abstract = {Elevation is an important determinant of ecological community composition. It integrates several abiotic features and leads to strong, repeatable patterns of community structure, including changes in the abundance and richness of numerous taxa. However, the influence of elevational gradients on microbes is understudied relative to plants and animals. To compare the influence of elevation on multiple taxa simultaneously, we sampled phytotelm communities within a tropical pitcher plant (Nepenthes mindanaoensis) along a gradient from 400 to 1200 m a.s.l. We use a combination of metabarcoding and physical counts to assess diversity and richness of bacteria, micro-eukaryotes, and arthropods, and compare the effect of elevation on community structure to that of regulation by a number of plant factors. Patterns of community structure differed between bacteria and eukaryotes, despite their living together in the same aquatic microhabitats. Elevation influences community composition of eukaryotes to a significantly greater degree than it does bacteria. When examining pitcher characteristics, pitcher dimorphism has an effect on eukaryotes but not bacteria, while variation in pH levels strongly influences both taxa. Consistent with previous ecological studies, arthropod abundance in phytotelmata decreases with elevation, but some patterns of abundance differ between living inquilines and prey.}, }
@article {pmid32291352, year = {2020}, author = {Leung, PM and Bay, SK and Meier, DV and Chiri, E and Cowan, DA and Gillor, O and Woebken, D and Greening, C}, title = {Energetic Basis of Microbial Growth and Persistence in Desert Ecosystems.}, journal = {mSystems}, volume = {5}, number = {2}, pages = {}, pmid = {32291352}, issn = {2379-5077}, abstract = {Microbial life is surprisingly abundant and diverse in global desert ecosystems. In these environments, microorganisms endure a multitude of physicochemical stresses, including low water potential, carbon and nitrogen starvation, and extreme temperatures. In this review, we summarize our current understanding of the energetic mechanisms and trophic dynamics that underpin microbial function in desert ecosystems. Accumulating evidence suggests that dormancy is a common strategy that facilitates microbial survival in response to water and carbon limitation. Whereas photoautotrophs are restricted to specific niches in extreme deserts, metabolically versatile heterotrophs persist even in the hyper-arid topsoils of the Atacama Desert and Antarctica. At least three distinct strategies appear to allow such microorganisms to conserve energy in these oligotrophic environments: degradation of organic energy reserves, rhodopsin- and bacteriochlorophyll-dependent light harvesting, and oxidation of the atmospheric trace gases hydrogen and carbon monoxide. In turn, these principles are relevant for understanding the composition, functionality, and resilience of desert ecosystems, as well as predicting responses to the growing problem of desertification.}, }
@article {pmid32291348, year = {2020}, author = {Mo, Z and Huang, P and Yang, C and Xiao, S and Zhang, G and Ling, F and Li, L}, title = {Meta-analysis of 16S rRNA Microbial Data Identified Distinctive and Predictive Microbiota Dysbiosis in Colorectal Carcinoma Adjacent Tissue.}, journal = {mSystems}, volume = {5}, number = {2}, pages = {}, pmid = {32291348}, issn = {2379-5077}, abstract = {As research focusing on the colorectal cancer fecal microbiome using shotgun sequencing continues, increasing evidence has supported correlations between colorectal carcinomas (CRCs) and fecal microbiome dysbiosis. However, large-scale on-site and off-site (surrounding adjacent) tissue microbiome characterization of CRC was underrepresented. Here, considering each taxon as a feature, we demonstrate a machine learning-based method to investigate tissue microbial differences among CRC, colorectal adenoma (CRA), and healthy control groups using 16S rRNA data sets retrieved from 15 studies. A total of 2,099 samples were included and analyzed in case-control comparisons. Multiple methods, including differential abundance analysis, random forest classification, cooccurrence network analysis, and Dirichlet multinomial mixture analysis, were conducted to investigate the microbial signatures. We showed that the dysbiosis of the off-site tissue of colonic cancer was distinctive and predictive. The AUCs (areas under the curve) were 80.7%, 96.0%, and 95.8% for CRC versus healthy control random forest models using stool, tissue, and adjacent tissue samples and 69.9%, 91.5%, and 89.5% for the corresponding CRA models, respectively. We also found that the microbiota ecologies of the surrounding adjacent tissues of CRC and CRA were similar to their on-site counterparts according to network analysis. Furthermore, based on the enterotyping of tissue samples, the cohort-specific microbial signature might be the crux in addressing classification generalization problems. Despite cohort heterogeneity, the dysbiosis of lesion-adjacent tissues might provide us with further perspectives in demonstrating the role of the microbiota in colorectal cancer tumorigenesis.IMPORTANCE Turbulent fecal and tissue microbiome dysbiosis of colorectal carcinoma and adenoma has been identified, and some taxa have been proven to be carcinogenic. However, the microbiomes of surrounding adjacent tissues of colonic cancerous tissues were seldom investigated uniformly on a large scale. Here, we characterize the microbiome signatures and dysbiosis of various colonic cancer sample groups. We found a high correlation between colorectal carcinoma adjacent tissue microbiomes and their on-site counterparts. We also discovered that the microbiome dysbiosis in adjacent tissues could discriminate colorectal carcinomas from healthy controls effectively. These results extend our knowledge on the microbial profile of colorectal cancer tissues and highlight microbiota dysbiosis in the surrounding tissues. They also suggest that microbial feature variations of cancerous lesion-adjacent tissues might help to reveal the microbial etiology of colonic cancer and could ultimately be applied for diagnostic and screening purposes.}, }
@article {pmid32285532, year = {2020}, author = {Meyer, KM and Hopple, AM and Klein, AM and Morris, AH and Bridgham, SD and Bohannan, BJM}, title = {Community structure - Ecosystem function relationships in the Congo Basin methane cycle depend on the physiological scale of function.}, journal = {Molecular ecology}, volume = {29}, number = {10}, pages = {1806-1819}, doi = {10.1111/mec.15442}, pmid = {32285532}, issn = {1365-294X}, mesh = {Biodiversity ; Congo ; *Ecosystem ; *Methane ; *Microbiota ; *Soil Microbiology ; Wetlands ; }, abstract = {Belowground ecosystem processes can be highly variable and difficult to predict using microbial community data. Here, we argue that this stems from at least three issues: (a) complex covariance structure of samples (with environmental conditions or spatial proximity) can make distinguishing biotic drivers a challenge; (b) communities can control ecosystem processes through multiple mechanisms, making the identification of these controls a challenge; and (c) ecosystem function assessments can be broad in physiological scale, encapsulating multiple processes with unique microbially mediated controls. We test these assertions using methane (CH4)-cycling processes in soil samples collected along a wetland-to-upland habitat gradient in the Congo Basin. We perform our measurements of function under controlled laboratory conditions and statistically control for environmental covariates to aid in identifying biotic drivers. We divide measurements of microbial communities into four attributes (abundance, activity, composition, and diversity) that represent different forms of community control. Lastly, our process measurements differ in physiological scale, including broader processes (gross methanogenesis and methanotrophy) that involve more mediating groups, to finer processes (hydrogenotrophic methanogenesis and high-affinity CH4 oxidation) with fewer mediating groups. We observed that finer scale processes can be more readily predicted from microbial community structure than broader scale processes. In addition, the nature of those relationships differed, with broad processes limited by abundance while fine-scale processes were associated with diversity and composition. These findings demonstrate the importance of carefully defining the physiological scale of ecosystem function and performing community measurements that represent the range of possible controls on ecosystem processes.}, }
@article {pmid32279319, year = {2020}, author = {Wang, T and Tian, Z and Tunlid, A and Persson, P}, title = {Nitrogen acquisition from mineral-associated proteins by an ectomycorrhizal fungus.}, journal = {The New phytologist}, volume = {228}, number = {2}, pages = {697-711}, doi = {10.1111/nph.16596}, pmid = {32279319}, issn = {1469-8137}, mesh = {Basidiomycota ; Minerals ; *Mycorrhizae ; Nitrogen ; Soil ; Soil Microbiology ; }, abstract = {In nitrogen (N)-limited boreal forests, trees depend on the decomposing activity of their ectomycorrhizal (ECM) fungal symbionts to access soil N. A large fraction of this N exists as proteinaceous compounds associated with mineral particles. However, it is not known if ECM fungi can access these mineral-associated proteins; accordingly, possible acquisition mechanisms have not been investigated. With tightly controlled isotopic, spectroscopic, and chromatographic experiments, we quantified and analyzed the mechanisms of N acquisition from iron oxide mineral-associated proteins by Paxillus involutus, a widespread ECM fungus in boreal forests. The fungus acquired N from the mineral-associated proteins. The collective results indicated a proteolytic mechanism involving formation of the crucial enzyme-substrate complexes at the mineral surfaces. Hence, the enzymes hydrolyzed the mineral-associated proteins without initial desorption of the proteins. The proteolytic activity was suppressed by adsorption of proteases to the mineral particles. This process was counteracted by fungal secretion of mineral-surface-reactive compounds that decreased the protease-mineral interactions and thereby promoted the formation of enzyme-substrate complexes. The ability of ECM fungi to simultaneously generate extracellular proteases and surface-reactive metabolites suggests that they can play an important role in unlocking the large N pool of mineral-associated proteins to trees in boreal forests.}, }
@article {pmid32276974, year = {2020}, author = {Du, R and Wu, Q and Xu, Y}, title = {Chinese Liquor Fermentation: Identification of Key Flavor-Producing Lactobacillus spp. by Quantitative Profiling with Indigenous Internal Standards.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {12}, pages = {}, pmid = {32276974}, issn = {1098-5336}, mesh = {Alcoholic Beverages/*microbiology ; China ; *Fermentation ; Flavoring Agents/*analysis ; High-Throughput Nucleotide Sequencing ; Lactobacillus/*metabolism ; Sequence Analysis, DNA ; }, abstract = {Identifying the functional microbes in spontaneous food fermentation is important for improving food quality. To identify the key flavor producers in Chinese liquor fermentation, we propose a novel quantitative microbiome profiling method that uses indigenous internal standards to normalize high-throughput amplicon sequencing results. We screened Lactobacillus acetotolerans and Lactobacillus jinshani as indigenous internal standards based on their high distribution frequencies and relative abundances. After determining the absolute abundance of indigenous internal standards using quantitative PCR with species-specific primers, the liquor-fermented bacterial community and its dynamics were better characterized by internal standards normalization. Based on quantitative microbiome profiling, we identified that Lactobacillus was a key flavor producer correlated with eight flavor compounds. Metatranscriptomic analysis indicated that Lactobacillus was active in transcribing genes involving the biosynthesis of flavor compounds and their precursors. This work has developed a novel and extensible absolute quantification method for microbiota that will alleviate concerns in the statistical analyses based on relative microbiome profiling, and shed insights into the function of Lactobacillus in food fermentation. It can potentially be applied to other microbial ecology studies.IMPORTANCE In this study, we developed a novel strategy using indigenous internal standards to normalize the high-throughput amplicon sequencing results. We chose two Lactobacillus species as indigenous internal standards and characterized the absolute abundance of the bacterial community. Further, we identified Lactobacillus as the key flavor producer using quantitative microbiome profiling combined with multivariate statistics and metatranscriptomic analysis. This work developed a novel strategy for absolute quantitative abundance analysis of microbiota and expanded our understanding of the role of Lactobacillus in food fermentation.}, }
@article {pmid32276972, year = {2020}, author = {Cheng, CC and Duar, RM and Lin, X and Perez-Munoz, ME and Tollenaar, S and Oh, JH and van Pijkeren, JP and Li, F and van Sinderen, D and Gänzle, MG and Walter, J}, title = {Ecological Importance of Cross-Feeding of the Intermediate Metabolite 1,2-Propanediol between Bacterial Gut Symbionts.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {11}, pages = {}, pmid = {32276972}, issn = {1098-5336}, support = {CC2003/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bifidobacterium breve/*metabolism ; Escherichia coli/*metabolism ; Female ; *Gastrointestinal Microbiome ; *Germ-Free Life ; Limosilactobacillus reuteri/*metabolism ; Male ; Mice ; Propylene Glycol/*metabolism ; }, abstract = {Cross-feeding based on the metabolite 1,2-propanediol has been proposed to have an important role in the establishment of trophic interactions among gut symbionts, but its ecological importance has not been empirically established. Here, we show that in vitro growth of Lactobacillus reuteri (syn. Limosilactobacillus reuteri) ATCC PTA 6475 is enhanced through 1,2-propanediol produced by Bifidobacterium breve UCC2003 and Escherichia coli MG1655 from the metabolization of fucose and rhamnose, respectively. Work with isogenic mutants showed that the trophic interaction is dependent on the pduCDE operon in L. reuteri, which encodes the ability to use 1,2-propanediol, and the l-fucose permease (fucP) gene in B. breve, which is required for 1,2-propanediol formation from fucose. Experiments in gnotobiotic mice revealed that, although the pduCDE operon bestows a fitness burden on L. reuteri ATCC PTA 6475 in the mouse digestive tract, the ecological performance of the strain was enhanced in the presence of B. breve UCC2003 and the mucus-degrading species Bifidobacterium bifidum The use of the respective pduCDE and fucP mutants of L. reuteri and B. breve in the mouse experiments indicated that the trophic interaction was specifically based on 1,2-propanediol. Overall, our work established the ecological importance of cross-feeding relationships based on 1,2-propanediol for the fitness of a bacterial symbiont in the vertebrate gut.IMPORTANCE Through experiments in gnotobiotic mice that employed isogenic mutants of bacterial strains that produce (Bifidobacterium breve) and utilize (Lactobacillus reuteri) 1,2-propanediol, this study provides mechanistic insight into the ecological ramifications of a trophic interaction between gut symbionts. The findings improve our understanding on how cross-feeding influences the competitive fitness of L. reuteri in the vertebrate gut and revealed a putative selective force that shaped the evolution of the species. The findings are relevant since they provide a basis to design rational microbial-based strategies to modulate gut ecosystems, which could employ mixtures of bacterial strains that establish trophic interactions or a personalized approach based on the ability of a resident microbiota to provide resources for the incoming microbe.}, }
@article {pmid32275302, year = {2020}, author = {Barnard, S and Van Goethem, MW and de Scally, SZ and Cowan, DA and van Rensburg, PJ and Claassens, S and Makhalanyane, TP}, title = {Increased temperatures alter viable microbial biomass, ammonia oxidizing bacteria and extracellular enzymatic activities in Antarctic soils.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {5}, pages = {}, doi = {10.1093/femsec/fiaa065}, pmid = {32275302}, issn = {1574-6941}, mesh = {Ammonia/metabolism ; Antarctic Regions ; Archaea/genetics ; Bacteria/metabolism ; *Betaproteobacteria/metabolism ; Biomass ; Carbon/metabolism ; Oxidation-Reduction ; *Soil/chemistry ; Soil Microbiology ; Temperature ; }, abstract = {The effects of temperature on microorganisms in high latitude regions, and their possible feedbacks in response to change, are unclear. Here, we assess microbial functionality and composition in response to a substantial temperature change. Total soil biomass, amoA gene sequencing, extracellular activity assays and soil physicochemistry were measured to assess a warming scenario. Soil warming to 15°C for 30 days triggered a significant decrease in microbial biomass compared to baseline soils (0°C; P < 0.05) after incubations had induced an initial increase. These changes coincided with increases in extracellular enzymatic activity for peptide hydrolysis and phenolic oxidation at higher temperatures, but not for the degradation of carbon substrates. Shifts in ammonia-oxidising bacteria (AOB) community composition related most significantly to changes in soil carbon content (P < 0.05), which gradually increased in microcosms exposed to a persistently elevated temperature relative to baseline incubations, while temperature did not influence AOBs. The concentration of soil ammonium (NH4+) decreased significantly at higher temperatures subsequent to an initial increase, possibly due to higher conversion rates of NH4+ to nitrate by nitrifying bacteria. We show that higher soil temperatures may reduce viable microbial biomass in cold environments but stimulate their activity over a short period.}, }
@article {pmid32272752, year = {2020}, author = {Mena-Vázquez, N and Ruiz-Limón, P and Moreno-Indias, I and Manrique-Arija, S and Tinahones, FJ and Fernández-Nebro, A}, title = {Expansion of Rare and Harmful Lineages is Associated with Established Rheumatoid Arthritis.}, journal = {Journal of clinical medicine}, volume = {9}, number = {4}, pages = {}, pmid = {32272752}, issn = {2077-0383}, support = {FIS Grant PI18/00824//Instituto de Salud Carlos III/ ; Grant for medical researchers of the "Fundaci&#xf3;n Espa&#xf1;ola de Reumatolog&#xed;a"//Sociedad Espa&#xf1;ola de Reumatolog&#xed;a/ ; Grant PI17/00016//Fundaci&#xf3;n Andaluza de Reumatologia/ ; The research groups belong to the "Centros de Investigaci&#xf3;n en Red"CIBERobn"//Instituto de Salud Carlos III/ ; }, abstract = {OBJECTIVES: To characterize the gut microbiota profile in rheumatoid arthritis (RA) patients and investigate its association with certain characteristics of RA.<br><br>PATIENTS AND METHODS: A nested case-control cohort of 40 patients with RA and 40 sex-age matched controls was studied. Subjects with diabetes, with any other inflammatory disease, practicing extreme diets, taking antibiotics, probiotics or under any new treatment for at least three months prior to sampling were excluded. The microbiota composition was determined by 16S rRNA pyrosequencing and bioinformatics analysis by Quantitative Insights Into Microbial Ecology (QIIME). Other variables included clinical-laboratory variables and average Disease Activity Score 28 points during the follow-up period. Multiple linear regression models were constructed to investigate the possible risk factors for the microbiota.<br><br>RESULTS: &#x3b2;-diversity data showed that patients tend to differ from healthy subjects according to their microbiota (p = 0.07). The analysis showed an increase in Collinsella aerofaciens, Sedimentibacter and Enterococcus genera in patients compared to controls, as well as a decrease in Dorea formicigenerans. Likewise, an increase in the activity of arginine deiminase was observed, which was found in approximately 90% of the RA genes of the genus Collinsela. The sequence number of Collinsella aerofaciens was independently associated with age (B (95%CI), -0.347 (-21.6, -2.1)), high ACPA (0.323 (27.4-390.0)) and smoking (0.300 (8.8-256.4)) in RA patients. In addition, we observed decreases in Sarcina, 02d06 and Porphyromonas bacterial lineages.<br><br>CONCLUSION: Patients with RA present dysbiosis, resulting from an abundance of certain bacterial lineages and a decrease in others. These alterations could influence the maintenance of autoimmunity to this disease.}, }
@article {pmid32271651, year = {2020}, author = {Ortiz-Castro, M and Hartman, T and Coutinho, T and Lang, JM and Korus, K and Leach, JE and Jackson-Ziems, T and Broders, K}, title = {Current Understanding of the History, Global Spread, Ecology, Evolution, and Management of the Corn Bacterial Leaf Streak Pathogen, Xanthomonas vasicola pv. vasculorum.}, journal = {Phytopathology}, volume = {110}, number = {6}, pages = {1124-1131}, doi = {10.1094/PHYTO-01-20-0018-PER}, pmid = {32271651}, issn = {0031-949X}, mesh = {Plant Diseases ; South Africa ; South America ; *Xanthomonas ; Zea mays ; }, abstract = {Bacterial leaf streak of corn, caused by Xanthomonas vasicola pv. vasculorum, has been present in South Africa for over 70 years, but is an emerging disease of corn in North and South America. The only scientific information pertaining to this disease on corn came from work done in South Africa, which primarily investigated host range on other African crops, such as sugarcane and banana. As a result, when the disease was first reported in the United States in 2016, there was very limited information on where this pathogen came from, how it infects its host, what plant tissue(s) it is capable of infecting, where initial inoculum comes from at the beginning of each crop season, how the bacterium spreads from plant to plant and long distance, what meteorological variables and agronomic practices favor disease development and spread, how many other plant species X. vasicola pv. vasculorum is capable of infecting or using as alternate hosts, and if the bacterium will be able to persist in all corn growing regions of the United States. There were also no rapid diagnostic assays available which initially hindered prompt identification prior to the development of molecular diagnostic tools. The goal of this synthesis is to review the history of X. vasicola pv. vasculorum and bacterial leaf streak in South Africa and its movement to North and South America, and highlight the recent research that has been done in response to the emergence of this bacterial disease.}, }
@article {pmid32268481, year = {2020}, author = {Blasi, MF and Migliore, L and Mattei, D and Rotini, A and Thaller, MC and Alduina, R}, title = {Antibiotic Resistance of Gram-Negative Bacteria from Wild Captured Loggerhead Sea Turtles.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {9}, number = {4}, pages = {}, pmid = {32268481}, issn = {2079-6382}, abstract = {Sea turtles have been proposed as health indicators of marine habitats and carriers of antibiotic-resistant bacterial strains, for their longevity and migratory lifestyle. Up to now, a few studies evaluated the antibacterial resistant flora of Mediterranean loggerhead sea turtles (Caretta caretta) and most of them were carried out on stranded or recovered animals. In this study, the isolation and the antibiotic resistance profile of 90 Gram negative bacteria from cloacal swabs of 33 Mediterranean wild captured loggerhead sea turtles are described. Among sea turtles found in their foraging sites, 23 were in good health and 10 needed recovery for different health problems (hereafter named weak). Isolated cloacal bacteria belonged mainly to Enterobacteriaceae (59%), Shewanellaceae (31%) and Vibrionaceae families (5%). Although slight differences in the bacterial composition, healthy and weak sea turtles shared antibiotic-resistant strains. In total, 74 strains were endowed with one or multi resistance (up to five different drugs) phenotypes, mainly towards ampicillin (~70%) or sulfamethoxazole/trimethoprim (more than 30%). Hence, our results confirmed the presence of antibiotic-resistant strains also in healthy marine animals and the role of the loggerhead sea turtles in spreading antibiotic-resistant bacteria.}, }
@article {pmid32267873, year = {2020}, author = {Compte-Port, S and Fillol, M and Gich, F and Borrego, CM}, title = {Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0231238}, pmid = {32267873}, issn = {1932-6203}, mesh = {Biodiversity ; Biofilms ; Carbon/metabolism ; Carbon Cycle/*physiology ; Crenarchaeota/*genetics/*metabolism ; DNA, Archaeal/genetics ; Ecosystem ; Euryarchaeota/*genetics/*metabolism ; *Geologic Sediments ; Humic Substances ; *Lakes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tryptophan ; }, abstract = {Members of the phylum Bathyarchaeota and the class Thermoplasmata are widespread in marine and freshwater sediments where they have been recognized as key players in the carbon cycle. Here, we tested the responsiveness of archaeal communities on settled plant debris and sediment from a karstic lake to different organic carbon amendments (amino acids, plant-derived carbohydrates, and aromatics) using a lab-scale microcosm. Changes in the composition and abundance of sediment and biofilm archaeal communities in both DNA and RNA fractions were assessed by 16S rRNA gene amplicon sequencing and qPCR, respectively, after 7 and 30 days of incubation. Archaeal communities showed compositional changes in terms of alpha and beta diversity in relation to the type of carbon source (amino acids vs. plant-derived compounds), the nucleic acid fraction (DNA vs. RNA), and the incubation time (7 vs. 30 days). Distinct groups within the Bathyarchaeota (Bathy-15 and Bathy-6) and the Thermoplasmata (MBG-D) differently reacted to carbon supplements as deduced from the analysis of RNA libraries. Whereas Bathyarchaeota in biofilms showed a long-term positive response to humic acids, their counterparts in the sediment were mainly stimulated by the addition of tryptophan, suggesting the presence of different subpopulations in both habitats. Overall, our work presents an in vitro assessment of the versatility of archaea inhabiting freshwater sediments towards organic carbon and introduces settled leaf litter as a new habitat for the Bathyarchaeota and the Thermoplasmata.}, }
@article {pmid32265872, year = {2020}, author = {Altermann, E and Hickey, WJ}, title = {Grand Challenges in Microbiotechnology: Through the Prism of Microbiotechnology.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {430}, pmid = {32265872}, issn = {1664-302X}, }
@article {pmid32265857, year = {2020}, author = {Chen, Z and Xie, Y and Zhou, F and Zhang, B and Wu, J and Yang, L and Xu, S and Stedtfeld, R and Chen, Q and Liu, J and Zhang, X and Xu, H and Ren, J}, title = {Featured Gut Microbiomes Associated With the Progression of Chronic Hepatitis B Disease.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {383}, pmid = {32265857}, issn = {1664-302X}, abstract = {Dysbiosis of gut microbiota during the progression of HBV-related liver disease is not well understood, as there are very few reports that discuss the featured bacterial taxa in different stages. The aim of this study was to reveal the featured bacterial species whose abundances are directly associated with HBV disease progression, that is, progression from healthy subjects to, chronic HBV infection, chronic hepatitis B to liver cirrhosis. Approximately 400 fecal samples were collected, and 97 samples were subjected to 16S rRNA gene sequencing after age and BMI matching. Compared with the healthy individuals, significant gut microbiota alterations were associated with the progression of liver disease. LEfSe results showed that the HBV infected patients had higher Fusobacteria, Veillonella, and Haemophilus abundance while the healthy individuals had higher levels of Prevotella and Phascolarctobacterium. Indicator analysis revealed that 57 OTUs changed as the disease progressed, and their combination produced an AUC value of 90% (95% CI: 86-94%) between the LC and non-LC groups. In addition, the abundances of OTU51 (Dialister succinatiphilus) and OTU50 (Alistipes onderdonkii) decreased as the disease progressed, and these results were further verified by qPCR. The LC patients had the higher bacterial network complexity, which was accompanied with a lower abundance of potential beneficial bacterial taxa, such as Dialister and Alistipes, while they had a higher abundance of pathogenic species within Actinobacteria. The compositional and network changes in the gut microbiota in varied CHB stages, suggest the potential contributions of gut microbiota in CHB disease progression.}, }
@article {pmid32265854, year = {2020}, author = {Zehentner, B and Ardern, Z and Kreitmeier, M and Scherer, S and Neuhaus, K}, title = {A Novel pH-Regulated, Unusual 603 bp Overlapping Protein Coding Gene pop Is Encoded Antisense to ompA in Escherichia coli O157:H7 (EHEC).}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {377}, pmid = {32265854}, issn = {1664-302X}, abstract = {Antisense transcription is well known in bacteria. However, translation of antisense RNAs is typically not considered, as the implied overlapping coding at a DNA locus is assumed to be highly improbable. Therefore, such overlapping genes are systematically excluded in prokaryotic genome annotation. Here we report an exceptional 603 bp long open reading frame completely embedded in antisense to the gene of the outer membrane protein ompA. An active σ[70] promoter, transcription start site (TSS), Shine-Dalgarno motif and rho-independent terminator were experimentally validated, providing evidence that this open reading frame has all the structural features of a functional gene. Furthermore, ribosomal profiling revealed translation of the mRNA, the protein was detected in Western blots and a pH-dependent phenotype conferred by the protein was shown in competitive overexpression growth experiments of a translationally arrested mutant versus wild type. We designate this novel gene pop (pH-regulated overlapping protein-coding gene), thus adding another example to the growing list of overlapping, protein coding genes in bacteria.}, }
@article {pmid32265327, year = {2020}, author = {Malki, K and Rosario, K and Sawaya, NA and Székely, AJ and Tisza, MJ and Breitbart, M}, title = {Prokaryotic and Viral Community Composition of Freshwater Springs in Florida, USA.}, journal = {mBio}, volume = {11}, number = {2}, pages = {}, pmid = {32265327}, issn = {2150-7511}, mesh = {Bacteria/*classification ; Biodiversity ; DNA, Bacterial/genetics ; DNA, Viral/genetics ; Ecosystem ; Florida ; Fresh Water/microbiology/virology ; *Metagenome ; Natural Springs/*microbiology/*virology ; Phylogeny ; Sequence Analysis, DNA ; Viruses/*classification ; }, abstract = {Aquifers, which are essential underground freshwater reservoirs worldwide, are understudied ecosystems that harbor diverse forms of microbial life. This study investigated the abundance and composition of prokaryotic and viral communities in the outflow of five springs across northern Florida, USA, as a proxy of microbial communities found in one of the most productive aquifers in the world, the Floridan aquifer. The average abundances of virus-like particles and prokaryotic cells were slightly lower than those reported from other groundwater systems, ranging from 9.6 × 10[3] ml[-1] to 1.1 × 10[5] ml[-1] and 2.2 × 10[3] ml[-1] to 3.4 × 10[4] ml[-1], respectively. Despite all of the springs being fed by the Floridan aquifer, sequencing of 16S rRNA genes and viral metagenomes (viromes) revealed unique communities in each spring, suggesting that groundwater microbial communities are influenced by land usage in recharge zones. The prokaryotic communities were dominated by Bacteria, and though the most abundant phyla (Proteobacteria, Cyanobacteria, and Bacteroidetes) were found in relatively high abundance across springs, variation was seen at finer taxonomic resolution. The viral sequences were most similar to those described from other aquatic environments. Sequencing resulted in the completion of 58 novel viral genomes representing members of the order Caudovirales as well as prokaryotic and eukaryotic single-stranded DNA (ssDNA) viruses. Sequences similar to those of ssDNA viruses were detected at all spring sites and dominated the identifiable sequences at one spring site, showing that these small viruses merit further investigation in groundwater systems.IMPORTANCE Aquifer systems may hold up to 40% of the total microbial biomass on Earth. However, little is known about the composition of microbial communities within these critical freshwater ecosystems. Here, we took advantage of Florida's first-magnitude springs (the highest spring classification based on water discharge), each discharging at least 246 million liters of water each day from the Floridan aquifer system (FAS), to investigate prokaryotic and viral communities from the aquifer. The FAS serves as a major source of potable water in the Southeastern United States, providing water for large cities and citizens in three states. Unfortunately, the health of the FAS and its associated springs has declined in the past few decades due to nutrient loading, increased urbanization and agricultural activity in aquifer recharge zones, and saltwater intrusion. This is the first study to describe the prokaryotic and viral communities in Florida's first-magnitude springs, providing a baseline against which to compare future ecosystem change.}, }
@article {pmid32258466, year = {2020}, author = {Gizaw, F and Kekeba, T and Teshome, F and Kebede, M and Abreham, T and Hayishe, H and Waktole, H and Tufa, TB and Edao, BM and Ayana, D and Abunna, F and Beyi, AF and Abdi, RD}, title = {Distribution and antimicrobial resistance profile of coagulase-negative staphylococci from cattle, equipment, and personnel on dairy farm and abattoir settings.}, journal = {Heliyon}, volume = {6}, number = {3}, pages = {e03606}, pmid = {32258466}, issn = {2405-8440}, abstract = {BACKGROUND: Safe food is central to social wellbeing. Coagulase-negative staphylococci (CNS) are a threat to food safety because they may harbor multiple enterotoxins and antimicrobial resistance (AMR) genes. CNS bacteria are an emerging nosocomial pathogen in public health. CNS also cause bovine mastitis with a significant economic loss in the dairy industry and may introduce toxins to the food supply chain resulting in foodborne illnesses. However, information on CNS and their AMR status are scarce in food animal production and processing lines in Ethiopia.<br><br>METHODOLOGY: This cross-sectional study evaluated the prevalence and AMR patterns of CNS in dairy farms and abattoirs using samples (n = 1001) from udder milk, beef carcass, personnel, and different abattoir and dairy equipment across five locations of central Oromia. The CNS isolates were identified via standard microbiological protocols and evaluated using disc diffusion test against 14 antimicrobials belonging to nine different broad classes. Uni-and-multivariable logistic regressions were used to analyze the association between potential risk factors (location, sample source, and sample type) and positivity to CNS.<br><br>RESULTS: The overall prevalence of CNS in the five different geographic locations studied was 9.6% (range: 6.7-12.4%) and varied between abattoirs (11.3%) and dairy farms (8.0%). CNS were prevalent on the carcass, milk, equipment, personnel hands, and nasal samples. Of all CNS isolates, 7.1, 10.7, 7.1, 12.5, 17.9, 10.7, 12.5, 7.1, 1.8, 5.4, 1.8, and 5.4% exhibited AMR simultaneously to single, double, 3, 4, 5, 6, 7, 7, 8, 9, 10, 11, and 13 antimicrobials, respectively. Overall, the isolates displayed 51 different AMR phenotypic patterns in which 50% of the isolates exhibited quadruple-resistance simultaneously based on the nine broad antimicrobial classes tested using 14 representative antimicrobials. The prevalence of multidrug-resistant (MDR) CNS (i.e. &#x2265; 3 classes of antimicrobials) was significantly (p = 0.037) different between locations with 100, 57.1, 50, 86.7, and 76.9% in Addis Ababa, Adama, Assela, Bishoftu, and Holeta, respectively. However, the prevalence of MDR CNS was not significantly (p = 0.20) different between dairy farms (87.5%) and abattoirs (71.9%). We evaluated the effect of acquiring cefoxitin-resistance of the isolates on the efficacy (i.e. inhibition zone) of the rest antimicrobials using General Linear Model after adjusting geographical locations as a random effect. Isolates with cefoxitin-resistance significantly displayed resistance to eight antimicrobials of 14 tested including amoxicillin, penicillin, cloxacillin, chloramphenicol, nalidixic acid, nitrofurantoin, and tetracycline (p = 0.000), and erythromycin (p = 0.02). On the other hand, cefoxitin-resistant isolates were susceptible to gentamicin, ciprofloxacin, kanamycin, streptomycin, and sulphamethoxazone trimethoprim (p = 0.000). Thus, antimicrobials such as gentamicin and ciprofloxacin may be an alternative therapy to treat cefoxitin-resistant CNS, as 96.4% of CNS isolates were susceptible to these antimicrobials. Overall, 94.1 and 54.5% of the CNS isolates among cefoxitin-resistant and cefoxitin-susceptible, respectively, harbored resistance to 3 or more classes of antimicrobials i.e. MDR.<br><br>CONCLUSION: The overall prevalence of CNS in milk, meat, equipment, and food handlers in central Oromia was 9.6% but varied by location and sample source. Some specific niches such as equipment, hands, and nasal cavities of personnel are significant sites for the source of CNS. Most, but not all, MDR CNS isolates were cefoxitin-resistant. Overall, 78.6% of the CNS tested were MDR and 50% had resistance to four or more broad classes of antimicrobials. CNS in food animals (raw milk and meat), equipment, and food handlers can be the source of MDR to the public. Personnel safety and hygienic food handling practices are needed. In addition, further investigation into the risk factors for the transmission and mechanisms of resistance of the CNS is required for intervention.}, }
@article {pmid32255838, year = {2020}, author = {Redmile-Gordon, M and Gregory, AS and White, RP and Watts, CW}, title = {Soil organic carbon, extracellular polymeric substances (EPS), and soil structural stability as affected by previous and current land-use.}, journal = {Geoderma}, volume = {363}, number = {}, pages = {114143}, pmid = {32255838}, issn = {0016-7061}, abstract = {While soil microbial ecology, soil organic carbon (SOC) and soil physical quality are widely understood to be interrelated - the underlying drivers of emergent properties, from land management to biochemistry, are hotly debated. Biological binding agents, microbial exudates, or 'extracellular polymeric substances' (EPS) in soil are now receiving increased attention due to several of the existing methodological challenges having been overcome. We applied a recently developed approach to quantify soil EPS, as extracellular protein and extracellular polysaccharide, on the well-characterised soils of the Highfield Experiment, Rothamsted Research, UK. Our aim was to investigate the links between agricultural land use, SOC, transient binding agents known as EPS, and their impacts on soil physical quality (given by mean weight diameter of water stable aggregates; MWD). We compared the legacy effects from long-term previous land-uses (unfertilised grassland, fertilised arable, and fallow) which were established > 50 years prior to investigation, crossed with the same current land-uses established for a duration of only 2.5 years prior to sampling. Continuously fallow and grassland soils represented the poorest and greatest states of structural integrity, respectively. Total SOC and N were found to be affected by both previous and current land-uses, while extractable EPS and MWD were driven primarily by the current land-use. Land-use change between these two extremes (fallow → grass; grass → fallow) resulted in smaller SOC differences (64% increase or 37% loss) compared to MWD (125% increase or 78% loss). SOC concentration correlated well to MWD (adjusted R [2] = 0.72) but the greater SOC content from previous grassland was not found to contribute directly to the current stability (p < 0.05). Our work thus supports the view that certain distinct components of SOC, rather than the total pool, have disproportionately important effects on a soil's structural stability. EPS-protein was more closely related to aggregate stability than EPS-polysaccharide (p values of 0.002 and 0.027, respectively), and ranking soils with the 5 greatest concentrations of EPS-protein to their corresponding orders of stability (MWD) resulted in a perfect match. We confirmed that both EPS-protein and EPS-polysaccharide were transient fractions: supporting the founding models for aggregate formation. We suggest that management of transient binding agents such as EPS -as opposed to simply increasing the total SOC content- may be a more feasible strategy to improve soil structural integrity and help achieve environmental objectives.}, }
@article {pmid32253628, year = {2020}, author = {Nisenbaum, M and Corti-Monzón, G and Villegas-Plazas, M and Junca, H and Mangani, A and Patat, ML and González, JF and Murialdo, SE}, title = {Enrichment and key features of a robust and consistent indigenous marine-cognate microbial consortium growing on oily bilge wastewaters.}, journal = {Biodegradation}, volume = {31}, number = {1-2}, pages = {91-108}, doi = {10.1007/s10532-020-09896-w}, pmid = {32253628}, issn = {1572-9729}, support = {VT38-UNMdP10982//Universidad Nacional de Mar del Plata/International ; PIT-AP-BA-2016//Consejo de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas de la Provincia de Buenos Aires/International ; PICT 2014-1567//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/International ; }, mesh = {Biodegradation, Environmental ; Hydrocarbons ; Microbial Consortia ; *Petroleum ; *Wastewater ; }, abstract = {Oily bilge wastewater (OBW) is a hazardous hydrocarbon-waste generated by ships worldwide. In this research, we enriched, characterized and study the hydrocarbon biodegradation potential of a microbial consortium from the bilges of maritime ships. The consortium cZ presented a biodegradation efficiency of 66.65% for total petroleum hydrocarbons, 72.33% for aromatics and 97.76% removal of n-alkanes. This consortium showed the ability to grow in OBWs of diverse origin and concentration. A 67-fold increase in biomass was achieved using a Sequential Batch Reactor with OBW as the only carbon and energy source. The bacterial community composition of the enriched OBW bacterial consortium at the final stable stage was characterized by 16S amplicon Illumina sequencing showing that 25 out of 915 of the emerged predominant bacterial types detected summed up for 84% of total composition. Out of the 140 taxa detected, 13 alone accumulated 94.9% of the reads and were classified as Marinobacter, Alcanivorax, Parvibaculum, Flavobacteriaceae, Gammaproteobacteria PYR10d3, Novispirillum and Xanthomonadaceae among the most predominant, followed by Thalassospira, Shewanella, Rhodospirillaceae, Gammaprotobacteria, Rhodobacteriaceae and Achromobacter. The microbial community from OBW bioreactor enrichments is intrinsically diverse with clear selection of predominant types and remarkably exhibiting consistent and efficient biodegradation achieved without any nutrient or surfactant addition. Due to there is very little information available in the OBW biodegradation field, this work contributes to the body of knowledge surrounding the treatment improvement of this toxic waste and its potential application in wastewater management.}, }
@article {pmid32248436, year = {2020}, author = {Huang, S and Kleerebezem, R and Rabaey, K and Ganigué, R}, title = {Open microbiome dominated by Clostridium and Eubacterium converts methanol into i-butyrate and n-butyrate.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {11}, pages = {5119-5131}, doi = {10.1007/s00253-020-10551-w}, pmid = {32248436}, issn = {1432-0614}, support = {676070//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; BOF15/PDO/068//Ghent University BOF fellowship/ ; 745828//Horizon 2020/ ; }, mesh = {Bioreactors ; Butyrates/*metabolism ; Clostridium/isolation &amp; purification/*metabolism ; Eubacterium/isolation &amp; purification/*metabolism ; Fermentation ; Isobutyrates/*metabolism ; Methanol/*metabolism ; *Microbiota ; }, abstract = {Isobutyrate (i-butyrate) is a versatile platform chemical, whose acid form is used as a precursor of plastic and emulsifier. It can be produced microbially either using genetically engineered organisms or via microbiomes, in the latter case starting from methanol and short-chain carboxylates. This opens the opportunity to produce i-butyrate from non-sterile feedstocks. Little is known on the ecology and process conditions leading to i-butyrate production. In this study, we steered i-butyrate production in a bioreactor fed with methanol and acetate under various conditions, achieving maximum i-butyrate productivity of 5.0 mM day[-1], with a concurrent production of n-butyrate of 7.9 mM day[-1]. The production of i-butyrate was reversibly inhibited by methanogenic inhibitor 2-bromoethanesulfonate. The microbial community data revealed the co-dominance of two major OTUs during co-production of i-butyrate and n-butyrate in two distinctive phases throughout a period of 54 days and 28 days, respectively. The cross-comparison of product profile with microbial community composition suggests that the relative abundance of Clostridium sp. over Eubacterium sp. is correlated with i-butyrate productivity over n-butyrate productivity.}, }
@article {pmid32248417, year = {2020}, author = {Kalaimurugan, D and Durairaj, K and Kumar, AJ and Senthilkumar, P and Venkatesan, S}, title = {Novel preparation of fungal conidiophores biomass as adsorbent for removal of phosphorus from aqueous solution.}, journal = {Environmental science and pollution research international}, volume = {27}, number = {17}, pages = {20757-20769}, doi = {10.1007/s11356-020-08307-0}, pmid = {32248417}, issn = {1614-7499}, mesh = {Adsorption ; Biomass ; Hydrogen-Ion Concentration ; Kinetics ; *Phosphorus ; Solutions ; Temperature ; Thermodynamics ; *Water Pollutants, Chemical ; }, abstract = {The present study focused on phosphorus adsorption by novel fungal conidiophores biomass in aqueous solution. Fungal Conidiophores biomass was prepared from the fungal strains Aspergillus oryzae (YFK) and Fusarium oxysporum (YVS2). The functional groups and morphology of Conidiophores Biomass (CB) from these strains were characterized by FTIR and SEM. FTIR confirms the presence of alcohol, carboxylic acid, carbon dioxide, cyclic alkene, amine, alkene, fluoro compound, and halo compound groups. Batch mode study was carried out with two CB's such as Aspergillus oryzae CB (ACB) and Fusarium oxysporum CB (FCB) with initial concentration of phosphorus ranging from 20 to 100 mg L[-1]. Based on the batch experiments, the adsorption kinetics (pseudo first order and pseudo second order), isotherms (Freundlich and Langmuir models), and thermodynamic (standard entropy, energy, and enthalpy) parameters were calculated. The adsorption kinetics and isotherm studies showed that the adsorption data well fitted with PSO kinetic model. From the isotherm results, it was found that ACB and FCB exhibited highest adsorption capacity 25.64 mg g[-1] and 26.32 mg g[-1] of phosphorus respectively at the optimal condition of pH (7), time (90 min), dose (250 mg), and room temperature (35 °C). Thermodynamics values were found to be endothermic and spontaneous in nature for phosphorus adsorption. Finally, the results suggested that the ACB and FCB are economically feasible cost-effective adsorbent for removal of phosphorus in wastewater treatment. Graphical abstract.}, }
@article {pmid32247994, year = {2020}, author = {Chique, C and Hynds, PD and Andrade, L and Burke, L and Morris, D and Ryan, MP and O'Dwyer, J}, title = {Cryptosporidium spp. in groundwater supplies intended for human consumption - A descriptive review of global prevalence, risk factors and knowledge gaps.}, journal = {Water research}, volume = {176}, number = {}, pages = {115726}, doi = {10.1016/j.watres.2020.115726}, pmid = {32247994}, issn = {1879-2448}, mesh = {Animals ; *Cryptosporidiosis ; *Cryptosporidium ; *Groundwater ; Humans ; Prevalence ; Prospective Studies ; Risk Factors ; Water Supply ; }, abstract = {Cryptosporidiosis is one of the leading causes of diarrhoeal illness and mortality induced by protozoan pathogens worldwide. As a largely waterborne disease, emphasis has been given to the study of Cryptosporidium spp. in surface waters, readily susceptible to pathogenic contamination. Conversely, the status of Cryptosporidium in potable groundwater sources, generally regarded as a pristine and "safe" drinking-water supply owing to (sub)-soil protection, remains largely unknown. As such, this investigation presents the first literature review aimed to ascertain the global prevalence of Cryptosporidium in groundwater supply sources intended for human consumption. Thirty-seven peer-reviewed studies were identified and included in the review. Groundwater sample and supply detection rates (estimated 10-20%) indicate Cryptosporidium is frequently present in domestic groundwater sources, representing a latent health concern for groundwater consumers. Specifically, sample (10.4%) and source (19.1%) detection rates deriving from comprehensive "temporal" investigations are put forward as representative of a contamination 'baseline' for Cryptosporidium in 'domestic' groundwater supplies. Proposed 'baseline' prevalence figures are largely applicable in preventive risk-based catchment and groundwater quality management including the formulation of Quantitative Microbial Risk Assessment (QMRA). Notwithstanding, a large geographical disparity in available investigations and lack of standardized reporting restrict the transferability of research findings. Overall, the mechanisms responsible for Cryptosporidium transport and ingress into groundwater supplies remain ambiguous, representing a critical knowledge gap, and denoting a distinctive lack of integration between groundwater and public-health sub-disciplines among investigations. Key recommendations and guidelines are provided for prospective studies directed at more integrative and multi-disciplinary research.}, }
@article {pmid32247910, year = {2020}, author = {Jin, D and Zhang, F and Shi, Y and Kong, X and Xie, Y and Du, X and Li, Y and Zhang, R}, title = {Diversity of bacteria and archaea in the groundwater contaminated by chlorinated solvents undergoing natural attenuation.}, journal = {Environmental research}, volume = {185}, number = {}, pages = {109457}, doi = {10.1016/j.envres.2020.109457}, pmid = {32247910}, issn = {1096-0953}, mesh = {*Archaea/genetics ; Bacteria/genetics ; *Groundwater ; RNA, Ribosomal, 16S/genetics ; Solvents ; }, abstract = {Chlorinated solvents (CS)-contaminated groundwater poses serious risks to the environment and public health. Microorganisms play a vital role in efficient remediation of CS. In this study, the microbial community (bacterial and archaeal) composition of three CS-contaminated groundwater wells located at an abandoned chemical factory which covers three orders of magnitude in concentration (0.02-16.15 mg/L) were investigated via 16S rRNA gene high-throughput sequencing. The results indicated that Proteobacteria and Thaumarchaeota were the most abundant bacterial and archaeal groups at the phylum level in groundwater, respectively. The major bacterial genera (Flavobacterium sp., Mycobacterium sp. and unclassified Parcubacteria taxa, etc.) and archaeal genera (Thaumarchaeota Group C3, Miscellaneous Crenarchaeotic Group and Miscellaneous Euryarchaeotic Group, etc.) might be involved in the dechlorination processes. In addition, Pearson's correlation analyses showed that alpha diversity of the bacterial community was not significantly correlated with CS concentration, while alpha diversity of archaeal community greatly decreased with the increased contamination of CS. Moreover, partial Mantel test indicated that oxidation-reduction potential, dissolved oxygen, temperature and methane concentration were major drivers of bacterial and archaeal community composition, whereas CS concentration had no significant impact, indicating that both indigenous bacterial and archaeal community compositions are capable of withstanding elevated CS contamination. This study improves our understanding of how the natural microbial community responds to high CS-contaminated groundwater.}, }
@article {pmid32245969, year = {2020}, author = {Chen, YC and Li, Z and Zhao, YX and Gao, M and Wang, JY and Liu, KW and Wang, X and Wu, LW and Jiao, YL and Xu, ZL and He, WG and Zhang, QY and Liang, CK and Hsiao, YY and Zhang, DY and Lan, SR and Huang, L and Xu, W and Tsai, WC and Liu, ZJ and Van de Peer, Y and Wang, YD}, title = {The Litsea genome and the evolution of the laurel family.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {1675}, pmid = {32245969}, issn = {2041-1723}, mesh = {Biosynthetic Pathways/genetics ; Chromosomes, Plant/*genetics ; DNA, Plant/genetics/isolation &amp; purification ; *Evolution, Molecular ; Gene Duplication ; Gene Expression Profiling ; *Genetic Speciation ; *Genome, Plant ; Genomics ; Inflorescence/genetics ; Litsea/*genetics/metabolism ; Molecular Sequence Annotation ; Odorants ; Phylogeny ; Plant Proteins/genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {The laurel family within the Magnoliids has attracted attentions owing to its scents, variable inflorescences, and controversial phylogenetic position. Here, we present a chromosome-level assembly of the Litsea cubeba genome, together with low-coverage genomic and transcriptomic data for many other Lauraceae. Phylogenomic analyses show phylogenetic discordance at the position of Magnoliids, suggesting incomplete lineage sorting during the divergence of monocots, eudicots, and Magnoliids. An ancient whole-genome duplication (WGD) event occurred just before the divergence of Laurales and Magnoliales; subsequently, independent WGDs occurred almost simultaneously in the three Lauralean lineages. The phylogenetic relationships within Lauraceae correspond to the divergence of inflorescences, as evidenced by the phylogeny of FUWA, a conserved gene involved in determining panicle architecture in Lauraceae. Monoterpene synthases responsible for production of specific volatile compounds in Lauraceae are functionally verified. Our work sheds light on the evolution of the Lauraceae, the genetic basis for floral evolution and specific scents.}, }
@article {pmid32243542, year = {2020}, author = {Nelson, CW and Ardern, Z and Wei, X}, title = {OLGenie: Estimating Natural Selection to Predict Functional Overlapping Genes.}, journal = {Molecular biology and evolution}, volume = {37}, number = {8}, pages = {2440-2449}, pmid = {32243542}, issn = {1537-1719}, mesh = {*Genes, Overlapping ; *Genetic Techniques ; HIV-1/genetics ; *Selection, Genetic ; *Silent Mutation ; *Software ; }, abstract = {Purifying (negative) natural selection is a hallmark of functional biological sequences, and can be detected in protein-coding genes using the ratio of nonsynonymous to synonymous substitutions per site (dN/dS). However, when two genes overlap the same nucleotide sites in different frames, synonymous changes in one gene may be nonsynonymous in the other, perturbing dN/dS. Thus, scalable methods are needed to estimate functional constraint specifically for overlapping genes (OLGs). We propose OLGenie, which implements a modification of the Wei-Zhang method. Assessment with simulations and controls from viral genomes (58 OLGs and 176 non-OLGs) demonstrates low false-positive rates and good discriminatory ability in differentiating true OLGs from non-OLGs. We also apply OLGenie to the unresolved case of HIV-1's putative antisense protein gene, showing significant purifying selection. OLGenie can be used to study known OLGs and to predict new OLGs in genome annotation. Software and example data are freely available at https://github.com/chasewnelson/OLGenie (last accessed April 10, 2020).}, }
@article {pmid32240065, year = {2020}, author = {Sedighian, N and Krijger, M and Taparia, T and Taghavi, SM and Wicker, E and van der Wolf, JM and Osdaghi, E}, title = {Genome Resource of Two Potato Strains of Ralstonia solanacearum Biovar 2 (Phylotype IIB Sequevar 1) and Biovar 2T (Phylotype IIB Sequevar 25) Isolated from Lowlands in Iran.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {33}, number = {7}, pages = {872-875}, doi = {10.1094/MPMI-02-20-0026-A}, pmid = {32240065}, issn = {0894-0282}, mesh = {*Genome, Bacterial ; Iran ; Phylogeny ; Plant Diseases/*microbiology ; *Ralstonia solanacearum/genetics/pathogenicity ; Solanum tuberosum/*microbiology ; }, abstract = {Ralstonia solanacearum, the causal agent of bacterial wilt and brown rot disease, is one of the major pathogens of solanaceous crops, including potato, around the globe. Biovar 2T (phylotype II/sequevar 25) of R. solanacearum is adapted to tropical lowlands and is only reported in South America and Iran. Thus far, no genome resource of the biovar 2T of the pathogen has been available. Here, we present the near-complete genome sequences of the biovar 2T strain CFBP 8697 as well as strain CFBP 8695 belonging to biovar 2 race 3, both isolated from potato in Iran. The genomic data of biovar 2T will extend our understanding of the virulence features of R. solanacearum and pave the way for research on biovar 2T functional and interaction genetics.}, }
@article {pmid32237500, year = {2020}, author = {Zhang, JQ and Zhou, T and Guo, LP and Jiang, WK and Wang, X and Zhang, GW and Pan, C and Liu, P and Cao, YZ and Xiao, CH}, title = {[Ecological benefits of Gastrodia elata-Phallus impudicus sequential planting pattern].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {45}, number = {3}, pages = {457-462}, doi = {10.19540/j.cnki.cjcmm.20191204.105}, pmid = {32237500}, issn = {1001-5302}, mesh = {Agaricales/*growth &amp; development ; Agriculture/*methods ; Gastrodia/*growth &amp; development ; Medicine, Chinese Traditional ; Plants, Medicinal/*growth &amp; development ; }, abstract = {Gastrodia elata is a kind of precious traditional Chinese medicine. In the process of cultivation of G. elata, due to the influence of continuous cropping obstacles and other factors, the fungus materials and land that have been planted with G. elata are often abandoned, resulting in a great waste of resources. Based on the planting characteristics of G. elata and Phallus impudicus and the previous research experience in ecological agriculture, this paper analyzed the ecological adaptability characteristics of G. elata and P. impudicus, and summarized the key techniques of the G. elata-P. impudicus sequential planting pattern. Keeping track of the planting area, fungus-growing materials consumption and market sales of G. elata-P. impudicus sequential planting pattern, the ecological benefits of G. elata-P. impudicus sequential planting pattern from the aspects of utilization rate of fungus-growing materials were analyzed, the value of land resources per unit area, ecological environmental protection, labor cost and economic benefits were consi-dered. The technical principle of G. elata-P. impudicus sequential planting pattern was expounded according to their ecological habit, the season of harvest and planting, the difference of composition of fungus-growing materials, and the microbial ecology. The sequential planting pattern of G. elata-P. impudicus not only realized the double production of medicinal materials and edible fungi, reduced the waste of old fungus-growing materials, but also transformed the energy from nutrition-supplied fungi to edible and medicinal fungi, which guaranteed the ecological recycling and utilization of G. elata in the process of cultivation.}, }
@article {pmid32233983, year = {2020}, author = {Zheng, Y and Hu, X and Jia, Z and Bodelier, PLE and Guo, Z and Zhang, Y and Li, F and He, P}, title = {Co-occurrence patterns among prokaryotes across an age gradient in pit mud of Chinese strong-flavor liquor.}, journal = {Canadian journal of microbiology}, volume = {66}, number = {9}, pages = {495-504}, doi = {10.1139/cjm-2020-0012}, pmid = {32233983}, issn = {1480-3275}, mesh = {Alcoholic Beverages/*microbiology ; Bacteria/*classification/genetics/*isolation &amp; purification ; China ; Fermentation ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Taste ; Time Factors ; }, abstract = {It is widely believed that the quality and characteristics of Chinese strong-flavor liquor (CSFL) are closely related to the age of the pit mud; CSFL produced from older pit mud tastes better. This study aimed to investigate the alteration and interaction of prokaryotic communities across an age gradient in pit mud. Prokaryotic microbes in different-aged pit mud (1, 6, and 10 years old) were analyzed by Illumina MiSeq sequencing of the 16S rRNA gene. Analysis of the 16S rRNA gene indicated that the prokaryotic community was significantly altered with pit mud age. There was a significant increase in the genera Methanosarcina, Methanobacterium, and Aminobacterium with increased age of pit mud, while the genus Lactobacillus showed a significant decreasing trend. Network analysis demonstrated that both synergetic co-occurrence and niche competition were dominated by 68 prokaryotic genera. These genera formed 10 hubs of co-occurrence patterns, mainly under the phyla Firmicutes, Euryarchaeota, and Bacteroidetes, playing important roles on ecosystem stability of the pit mud. Environmental variables (pH, NH4[+], available P, available K, and Ca[2+]) correlated significantly with prokaryotic community assembly. The interaction of prokaryotic communities in the pit mud ecosystem and the relationship among prokaryotic communities and environmental factors contribute to the higher quality of the pit mud in older fermentation pits.}, }
@article {pmid32226422, year = {2020}, author = {Chen, ML and Becraft, ED and Pachiadaki, M and Brown, JM and Jarett, JK and Gasol, JM and Ravin, NV and Moser, DP and Nunoura, T and Herndl, GJ and Woyke, T and Stepanauskas, R}, title = {Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {376}, pmid = {32226422}, issn = {1664-302X}, support = {268595/ERC_/European Research Council/International ; P 28781/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments.}, }
@article {pmid32226382, year = {2020}, author = {Silveira-Nunes, G and Durso, DF and Jr, LRAO and Cunha, EHM and Maioli, TU and Vieira, AT and Speziali, E and Corrêa-Oliveira, R and Martins-Filho, OA and Teixeira-Carvalho, A and Franceschi, C and Rampelli, S and Turroni, S and Brigidi, P and Faria, AMC}, title = {Hypertension Is Associated With Intestinal Microbiota Dysbiosis and Inflammation in a Brazilian Population.}, journal = {Frontiers in pharmacology}, volume = {11}, number = {}, pages = {258}, pmid = {32226382}, issn = {1663-9812}, abstract = {Hypertension is a major global health challenge, as it represents the main risk factor for stroke and cardiovascular disease. It is a multifactorial clinical condition characterized by high and sustained levels of blood pressure, likely resulting from a complex interplay of endogenous and environmental factors. The gut microbiota has been strongly supposed to be involved but its role in hypertension is still poorly understood. In an attempt to fill this gap, here we characterized the microbial composition of fecal samples from 48 hypertensive and 32 normotensive Brazilian individuals by next-generation sequencing of the 16S rRNA gene. In addition, the cytokine production of peripheral blood samples was investigated to build an immunological profile of these individuals. We identified a dysbiosis of the intestinal microbiota in hypertensive subjects, featured by reduced biodiversity and distinct bacterial signatures compared with the normotensive counterpart. Along with a reduction in Bacteroidetes members, hypertensive individuals were indeed mainly characterized by increased proportions of Lactobacillus and Akkermansia while decreased relative abundances of well-known butyrate-producing commensals, including Roseburia and Faecalibacterium within the Lachnospiraceae and Ruminococcaceae families. We also observed an inflamed immune profile in hypertensive individuals with an increase in TNF/IFN-γ ratio, and in TNF and IL-6 production when compared to normotensive ones. Our work provides the first evidence of association of hypertension with altered gut microbiota and inflammation in a Brazilian population. While lending support to the existence of potential microbial signatures of hypertension, likely to be robust to age and geography, our findings point to largely neglected bacteria as potential contributors to intestinal homeostasis loss and emphasize the high vulnerability of hypertensive individuals to inflammation-related disorders.}, }
@article {pmid32222691, year = {2020}, author = {McAteer, PG and Christine Trego, A and Thorn, C and Mahony, T and Abram, F and O'Flaherty, V}, title = {Reactor configuration influences microbial community structure during high-rate, low-temperature anaerobic treatment of dairy wastewater.}, journal = {Bioresource technology}, volume = {307}, number = {}, pages = {123221}, doi = {10.1016/j.biortech.2020.123221}, pmid = {32222691}, issn = {1873-2976}, mesh = {Anaerobiosis ; Bioreactors ; *Microbiota ; RNA, Ribosomal, 16S ; Sewage ; Temperature ; Waste Disposal, Fluid ; *Wastewater ; }, abstract = {Low temperature anaerobic digestion remains in its infancy, despite increasing interest for the treatment of complex wastewaters. In this study, the feasibility of low-temperature anaerobic treatment of dairy wastewater was assessed during a 443-day laboratory-scale bioreactor trial. The bioreactors were operated in triplicate at organic loading rates of 7.5-9 kgCODm[-3]d[-1] throughout five operational phases. The structure of the microbial community was analysed using quantitative real-time PCR and amplicon sequencing of 16S rRNA genes from DNA and rRNA. The results indicated that low-temperature treatment of dairy wastewater is feasible at 15 °C, but that reactor configuration remains extremely important. The upflow anaerobic sludge bed (UASB) configuration out-performed the expanded granular sludge bed (EGSB)-based configurations. Decreased temperatures resulted in significant reductions in microbiome diversity. Methanosaeta was identified as a dominant genus throughout the trial, while Lactococcus was identified as an important bacterial genus at low-temperatures. However, the relative abundance of Lactococcus was significantly influenced by reactor configuration.}, }
@article {pmid32222116, year = {2020}, author = {Morita, D and Takahashi, E and Morita, M and Ohnishi, M and Mizuno, T and Miyoshi, SI and Dutta, D and Ramamurthy, T and Chowdhury, G and Mukhopadhyay, AK and Okamoto, K}, title = {Genomic characterization of antibiotic resistance-encoding genes in clinical isolates of Vibrio cholerae non-O1/non-O139 strains from Kolkata, India: generation of novel types of genomic islands containing plural antibiotic resistance genes.}, journal = {Microbiology and immunology}, volume = {64}, number = {6}, pages = {435-444}, doi = {10.1111/1348-0421.12790}, pmid = {32222116}, issn = {1348-0421}, support = {//Japan Initiative for Global Research Network on Infectious Diseases (J-GRID)/ ; //Ministry of Education, Culture, Sports, Science and Technology in Japan/ ; JP18fm0108002//Japan Agency for Medical Research and Development/ ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Genomic Islands/*genetics ; Humans ; India ; Integrons/*genetics ; Microbial Sensitivity Tests/methods ; Serotyping/methods ; *Vibrio Infections/epidemiology/microbiology ; *Vibrio cholerae non-O1/classification/drug effects/genetics ; Whole Genome Sequencing/methods ; }, abstract = {Non-O1/non-O139 nontoxigenic Vibrio cholerae associated with cholera-like diarrhea has been reported in Kolkata, India. However, the property involved in the pathogenicity of these strains has remained unclear. The character of 25 non-O1/non-O139 nontoxigenic V. cholerae isolated during 8 years from 2007 to 2014 in Kolkata was examined. Determination of the serogroup showed that the serogroups O6, O10, O35, O36, O39, and O70 were represented by two strains in each serogroup, and the remaining isolates belonged to different serogroups. To clarify the character of antibiotic resistance of these isolates, an antibiotic resistance test and the gene analysis were performed. According to antimicrobial drug susceptibility testing, 13 strains were classified as drug resistant. Among them, 10 strains were quinolone resistant and 6 of the 13 strains were resistant to more than three antibiotics. To define the genetic background of the antibiotic character of these strains, whole-genome sequences of these strains were determined. From the analysis of these sequences, it becomes clear that all quinolone resistance isolates have mutations in quinolone resistance-determining regions. Further research on the genome sequence showed that four strains possess Class 1 integrons in their genomes, and that three of the four integrons are found to be located in their genomic islands. These genomic islands are novel types. This indicates that various integrons containing drug resistance genes are spreading among V. cholerae non-O1/non-O139 strains through the action of newly generated genomic islands.}, }
@article {pmid32221644, year = {2020}, author = {Núñez, A and Moreno, DA}, title = {The Differential Vertical Distribution of the Airborne Biological Particles Reveals an Atmospheric Reservoir of Microbial Pathogens and Aeroallergens.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {322-333}, doi = {10.1007/s00248-020-01505-w}, pmid = {32221644}, issn = {1432-184X}, support = {S2013/MAE-2874//Comunidad de Madrid/ ; }, mesh = {*Air Microbiology ; Allergens/*isolation &amp; purification ; Altitude ; Bacteria/*isolation &amp; purification ; Fungi/*isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Particulate Matter/*isolation &amp; purification ; *Plants ; Seasons ; Spain ; }, abstract = {The most abundant biological particles present in the air are bacteria, fungal propagules and pollen grains. Many of them are proved allergens or even responsible for airborne infectious diseases, which supports the increase of studies in recent years on their composition, diversity, and factors involved in their variability. However, most studies in urban areas are conducted close to ground level and a factor such as height is rarely taken into account. Thus, the information about how the composition of biological particles changes with this variable is scarce. Here, we examined the differential distribution of bacteria, fungi, and plants at four altitudes (up to ∼ 250 m) in a metropolitan area using high-throughput DNA sequencing. Most taxa were present at all levels (common taxa). However, a transitional layer between 80 and 150 m seemed to affect the scattering of these bioaerosols. Taxa not present at all altitudes (non-common) showed an upward tendency of diversity for bacteria and plants with height, while the opposite trend was observed for fungi. Certain patterns were observed for fungi and specific plant genera, while bacterial taxa showed a more arbitrary distribution and no patterns were found. We detected a wide variety of aeroallergens and potential pathogens at all heights, which summed a substantial portion of the total abundance for fungi and plants. We also identified potential connections between the biological particles based on their abundances across the vertical section.}, }
@article {pmid32221408, year = {2020}, author = {Wu, R and Chai, B and Cole, JR and Gunturu, SK and Guo, X and Tian, R and Gu, JD and Zhou, J and Tiedje, JM}, title = {Targeted assemblies of cas1 suggest CRISPR-Cas's response to soil warming.}, journal = {The ISME journal}, volume = {14}, number = {7}, pages = {1651-1662}, pmid = {32221408}, issn = {1751-7370}, mesh = {CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Genome ; Oklahoma ; *Soil ; }, abstract = {There is an increasing interest in the clustered regularly interspaced short palindromic repeats CRISPR-associated protein (CRISPR-Cas) system to reveal potential virus-host dynamics. The universal and most conserved Cas protein, cas1 is an ideal marker to elucidate CRISPR-Cas ecology. We constructed eight Hidden Markov Models (HMMs) and assembled cas1 directly from metagenomes by a targeted-gene assembler, Xander, to improve detection capacity and resolve the diverse CRISPR-Cas systems. The eight HMMs were first validated by recovering all 17 cas1 subtypes from the simulated metagenome generated from 91 prokaryotic genomes across 11 phyla. We challenged the targeted method with 48 metagenomes from a tallgrass prairie in Central Oklahoma recovering 3394 cas1. Among those, 88 were near full length, 5 times more than in de-novo assemblies from the Oklahoma metagenomes. To validate the host assignment by cas1, the targeted-assembled cas1 was mapped to the de-novo assembled contigs. All the phylum assignments of those mapped contigs were assigned independent of CRISPR-Cas genes on the same contigs and consistent with the host taxonomies predicted by the mapped cas1. We then investigated whether 8 years of soil warming altered cas1 prevalence within the communities. A shift in microbial abundances was observed during the year with the biggest temperature differential (mean 4.16 °C above ambient). cas1 prevalence increased and even in the phyla with decreased microbial abundances over the next 3 years, suggesting increasing virus-host interactions in response to soil warming. This targeted method provides an alternative means to effectively mine cas1 from metagenomes and uncover the host communities.}, }
@article {pmid32220841, year = {2020}, author = {Sims, IM and Tannock, GW}, title = {Galacto- and Fructo-oligosaccharides Utilized for Growth by Cocultures of Bifidobacterial Species Characteristic of the Infant Gut.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {11}, pages = {}, pmid = {32220841}, issn = {1098-5336}, mesh = {Bifidobacterium/*metabolism ; Bifidobacterium bifidum/*metabolism ; Bifidobacterium breve/*metabolism ; Bifidobacterium longum subspecies infantis/*metabolism ; Coculture Techniques ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Oligosaccharides/*metabolism ; }, abstract = {Bifidobacterial species are common inhabitants of the gut of human infants during the period when milk is a major component of the diet. Bifidobacterium breve, Bifidobacterium bifidum, Bifidobacterium longum subspecies longum, and B. longum subspecies infantis have been detected frequently in infant feces, but B. longum subsp. infantis may be disadvantaged numerically in the gut of infants in westernized countries. This may be due to the different durations of breast milk feeding in different countries. Supplementation of the infant diet or replacement of breast milk using formula feeds is common in Western countries. Formula milks often contain galacto- and/or fructo-oligosaccharides (GOS and FOS, respectively) as additives to augment the concentration of oligosaccharides in ruminant milks, but the ability of B. longum subsp. infantis to utilize these potential growth substrates when they are in competition with other bifidobacterial species is unknown. We compared the growth and oligosaccharide utilization of GOS and FOS by bifidobacterial species in pure culture and coculture. Short-chain GOS and FOS (degrees of polymerization [DP] 2 and 3) were favored growth substrates for strains of B. bifidum and B. longum subsp. longum, whereas both B. breve and B. longum subsp. infantis had the ability to utilize both short- and longer-chain GOS and FOS (DP 2 to 6). B. breve was nevertheless numerically dominant over B. longum subsp. infantis in cocultures. This was probably related to the slower use of GOS of DP 3 by B. longum subsp. infantis, indicating that the kinetics of substrate utilization is an important ecological factor in the assemblage of gut communities.IMPORTANCE The kinds of bacteria that form the collection of microbes (the microbiota) in the gut of human infants may influence health and well-being. Knowledge of how the composition of the infant diet influences the assemblage of the bacterial collection is therefore important because dietary interventions may offer opportunities to alter the microbiota with the aim of improving health. Bifidobacterium longum subspecies infantis is a well-known bacterial species, but under modern child-rearing conditions it may be disadvantaged in the gut. Modern formula milks often contain particular oligosaccharide additives that are generally considered to support bifidobacterial growth. However, studies of the ability of various bifidobacterial species to grow together in the presence of these oligosaccharides have not been conducted. These kinds of studies are essential for developing concepts of microbial ecology related to the influence of human nutrition on the development of the gut microbiota.}, }
@article {pmid32220814, year = {2020}, author = {Belleggia, L and Milanović, V and Ferrocino, I and Cocolin, L and Haouet, MN and Scuota, S and Maoloni, A and Garofalo, C and Cardinali, F and Aquilanti, L and Mozzon, M and Foligni, R and Pasquini, M and Trombetta, MF and Clementi, F and Osimani, A}, title = {Is there any still undisclosed biodiversity in Ciauscolo salami? A new glance into the microbiota of an artisan production as revealed by high-throughput sequencing.}, journal = {Meat science}, volume = {165}, number = {}, pages = {108128}, doi = {10.1016/j.meatsci.2020.108128}, pmid = {32220814}, issn = {1873-4138}, mesh = {Animals ; Bacteria/isolation &amp; purification ; Botulinum Toxins/genetics ; Fermentation ; *Food Microbiology ; Fungi/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Meat Products/analysis/*microbiology ; *Microbiota ; Multiplex Polymerase Chain Reaction/methods ; Sus scrofa ; Volatile Organic Compounds/analysis ; Yeasts/isolation &amp; purification ; }, abstract = {Ciauscolo is a fermented sausage with the Protected Geographical Indication (PGI) status. To disclose the microbial ecology of a model Ciauscolo salami manufacture during its natural fermentation, viable counting, amplicon-based sequencing and real-time PCR were applied. The volatilome during fermentation was also characterized. The results allowed previously undetected species to be discovered. The core microbiota was composed by Lactobacillus algidus, Leuconostoc carnosum, Lactobacillus sakei, Debaryomyces hansenii, Glomus hyderabadensis, Tilletiopsis washingtonensis, and Kurtzmaniella zeylanoides. Salmonella spp. and Listeria monocytogenes were absent in all the samples; moreover, multiplex real-time PCR revealed the absence of the target genes bont/A, bont/B, bont/E, bont/F, and 4gyrB (CP), encoding botulinic toxins. Volatilome, deeply depending on microbiological metabolism, was characterized by spices-derived components. Limonene, sabinene, α- and β-pinene, 3-carene, and α-thujene were the most represented monoterpene hydrocarbons, whereas β- and α-copaene were the most represented sesquiterpene hydrocarbons. Allyl methyl sulphide and diallyl disulphide were the major aliphatic sulphur compounds, together with diallyl sulphide and allyl methyl disulphide.}, }
@article {pmid32219941, year = {2021}, author = {Huang, Z and Shen, Y and Huang, X and Qiao, M and He, RK and Song, L}, title = {Microbial diversity of representative traditional fermented sausages in different regions of China.}, journal = {Journal of applied microbiology}, volume = {130}, number = {1}, pages = {133-141}, doi = {10.1111/jam.14648}, pmid = {32219941}, issn = {1365-2672}, support = {31671916//National Natural Science Foundation of China/ ; }, mesh = {Bacteria/classification/genetics/isolation &amp; purification/metabolism ; China ; Colony Count, Microbial ; Fermentation ; Fermented Foods/*microbiology ; Food Microbiology ; Food Safety ; Meat Products/*microbiology ; *Microbiota ; Taste ; }, abstract = {AIMS: The purpose of this experiment was to study the bacterial diversity of traditional fermented sausages from four typical regions of China (Chengdu, Shenzhen, Changsha and Harbin) and to further evaluate their microbiological safety.<br><br>METHODS AND RESULTS: The diversity of the microbiota of the sausages was studied using the Illumina HiSeq platform. The results showed that compared with the highest diversity of fermented bacteria in Guangdong, the bacterial diversity of fermented sausage was the lowest in Sichuan. The percentage of dominant phylum (Firmicutes, Cyanophyta, Proteobacter) were 78&#xb7;39, 13&#xb7;13 and 7&#xb7;14% in SC, 35&#xb7;47, 30&#xb7;36 and 28&#xb7;04% in GD, 54&#xb7;81, 28&#xb7;91 and 14&#xb7;00% in HN, 20&#xb7;20, 58&#xb7;16 and 17&#xb7;31% in HB respectively. The main genus distribution of fermented sausages in different regions is varied, but lactic acid bacteria and cyanobacteria are generally the main ones. Traditional fermented sausages using natural fermentation methods have poor microbiological safety, and pathogenic and spoilage micro-organisms such as Acinetobacter, Brochothrix and Pseudomonas have been detected in all four regions.<br><br>CONCLUSIONS: The results in this paper provide a microbiota profile of four typical fermented sausages in China. There is a big difference in the microbiota of sausages in different regions, and the good flavour of traditional Chinese fermented sausage is related closely with the abundant microbial resources, however, the natural fermentation method also expose to the product security threats, including spoilage, pathogenic micro-organisms and biogenic amines, etc. SIGNIFICANCE AND IMPACT OF THE STUDY: The results would offer guidance for industrial fermented sausage production with certain flavour and also improve the microbial resource utilization, and contribute to the control of harmful micro-organisms in traditional fermented sausage.}, }
@article {pmid32219483, year = {2020}, author = {Sodhi, KK and Kumar, M and Singh, DK}, title = {Potential application in amoxicillin removal of Alcaligenes sp. MMA and enzymatic studies through molecular docking.}, journal = {Archives of microbiology}, volume = {202}, number = {6}, pages = {1489-1495}, pmid = {32219483}, issn = {1432-072X}, support = {NASF/CA-6030/2017-18//INDIAN AGRICULTURE RESEARCH INSTITUTE/ ; }, mesh = {Alcaligenes/genetics/*metabolism ; Amoxicillin/*metabolism ; Anti-Bacterial Agents/*metabolism ; *Biodegradation, Environmental ; Chromatography, Liquid ; Drug Resistance, Bacterial/physiology ; Microbial Sensitivity Tests ; Molecular Docking Simulation ; Porins/biosynthesis ; Tandem Mass Spectrometry ; }, abstract = {Antibiotic contamination in environmental matrices is a serious global problem which leads to an increase in the proliferation of antibiotic resistance genes. Amoxicillin is ubiquitous in the environment, but there is hardly any information on the dissipation of amoxicillin by the microbial community. In view of this, the present study focusses on the removal of amoxicillin using amoxicillin-resistant bacteria, Alcaligenes sp. MMA. Bacteria were characterized using antibiotic tests, biochemical and molecular analysis. Alcaligenes sp. MMA was able to remove up to 84% of amoxicillin in 14 days in M9 minimal media, and the degradation products were confirmed using LC-MS/MS, including the benzothiazole, 2-Amino-3-methoxyl benzoic acid, 4-Hydroxy-2-methyl benzoic acid, 5-Amino-2-methylphenol and 3,5-Bis(tert-butyl)-2-hydroxybenzaldehyde, at the end of 14th day which further shows the removal of amoxicillin by the bacterial strain. Differential expression of porins was found in the presence of amoxicillin as a sole source of carbon and energy for the bacterial strain. Molecular interaction using in silico studies were performed which showed the formation of a hydrogen bond between amoxicillin and porins.}, }
@article {pmid32217314, year = {2020}, author = {Urra, J and Alkorta, I and Mijangos, I and Garbisu, C}, title = {Commercial and farm fermented liquid organic amendments to improve soil quality and lettuce yield.}, journal = {Journal of environmental management}, volume = {264}, number = {}, pages = {110422}, doi = {10.1016/j.jenvman.2020.110422}, pmid = {32217314}, issn = {1095-8630}, mesh = {Agriculture ; Farms ; Fertilizers ; Lactuca ; *Soil ; *Soil Pollutants ; }, abstract = {The anaerobic decomposition of organic wastes might lead to the formation of organic-byproducts which can then be successfully used as organic fertilizers. This study evaluated the impact of the application of two fermented liquid organic amendments (commercial vs. farm-made) at two doses of application (optimal vs. suboptimal), compared to mineral fertilization, on lettuce growth and soil quality. To this purpose, two experiments were conducted at microcosm- and field-scale, respectively. In the microcosm experiment, organically amended soils resulted in lower lettuce yield than minerally fertilized soil but, in contrast, they enhanced microbial activity and biomass, thus leading to an improvement in soil quality. The fertilization regime (organic vs. inorganic) significantly affected soil microbial composition but did not have any significant effect on structural or functional prokaryotic diversity. In the field experiment, at the optimal dose of application, organically-amended soils resulted in comparable lettuce yield to that displayed by minerally fertilized soils. The application of organic amendments did not result in an enhanced microbial activity and biomass, compared to mineral fertilization, but led to a higher soil prokaryotic diversity. Among the organically-amended plots, the optimal application dose resulted in a higher lettuce yield and soil microbial activity and biomass, but led to a decline in soil prokaryotic diversity, compared to the suboptimal application dose. Our results indicate that commercial and farm-made fermented liquid organic amendments possess the potential to ameliorate soil quality while sustaining crop yield. Given the strong influence of other factors (e.g., type of soil, dose of application) on the effects exerted by such amendments on soil quality and fertility, we recommend that an exhaustive characterization of both the amendments and the recipient soils should be carried out prior to their application, in order to better ensure their potential beneficial effects.}, }
@article {pmid32216022, year = {2020}, author = {Ji, M and Kong, W and Stegen, J and Yue, L and Wang, F and Dong, X and Cowan, DA and Ferrari, BC}, title = {Distinct assembly mechanisms underlie similar biogeographical patterns of rare and abundant bacteria in Tibetan Plateau grassland soils.}, journal = {Environmental microbiology}, volume = {22}, number = {6}, pages = {2261-2272}, doi = {10.1111/1462-2920.14993}, pmid = {32216022}, issn = {1462-2920}, support = {DE-AC06-76RLO 1830//Battelle Memorial Institute/International ; //Pacific Northwest National Laboratory/International ; //Office of Biological and Environmental Research/International ; //US Department of Energy (DOE)/International ; 41771303//National Natural Science Foundation of China/International ; XDA20050101//Chinese Academy of Sciences/International ; QYZDB-SSW-DQC033//Chinese Academy of Sciences/International ; XDA19070304//Chinese Academy of Sciences/International ; }, mesh = {Bacteria/*classification/genetics ; Biodiversity ; *Grassland ; Phylogeny ; Soil ; *Soil Microbiology ; Tibet ; }, abstract = {Rare biosphere represents the majority of Earth's biodiversity and performs vital ecological functions, yet little is known about its biogeographical patterns and community assembly processes in terrestrial ecosystems. Herein, we investigated the community composition and phylogeny of rare (relative abundance <0.1%) and abundant (>1%) bacteria in dryland grassland soils on the Tibetan Plateau. Results revealed similar biogeographical patterns of rare and abundant bacteria at both compositional and phylogenetic levels, but rare subcommunity was more heavily influenced by stochasticity (72%) than the abundant (57%). The compositional variation of rare bacteria was less explained by environmental factors (41%) than that of the abundant (80%), while the phylogeny of rare bacteria (36%) was more explained than that of the abundant (29%). The phylogeny of rare bacteria was equally explained by local factors (soil and vegetation) and geospatial distance (11.5% and 11.9% respectively), while that of the abundant was more explained by geospatial distance (22.1%) than local factors (11.3%). Furthermore, a substantially tighter connection between the community phylogeny and composition was observed in rare (R[2] = 0.65) than in abundant bacteria (R[2] = 0.08). Our study provides novel insights into the assembly processes and biographical patterns of rare and abundant bacteria in dryland soils.}, }
@article {pmid32213901, year = {2020}, author = {Paduano, S and Marchesi, I and Casali, ME and Valeriani, F and Frezza, G and Vecchi, E and Sircana, L and Romano Spica, V and Borella, P and Bargellini, A}, title = {Characterisation of Microbial Community Associated with Different Disinfection Treatments in Hospital hot Water Networks.}, journal = {International journal of environmental research and public health}, volume = {17}, number = {6}, pages = {}, pmid = {32213901}, issn = {1660-4601}, mesh = {*Disinfection ; *Hospitals ; Humans ; Legionella ; *Microbiota ; *Water Microbiology ; *Water Purification ; *Water Supply ; }, abstract = {Many disinfection treatments can be adopted for controlling opportunistic pathogens in hospital water networks in order to reduce infection risk for immunocompromised patients. Each method has limits and strengths and it could determine modifications on bacterial community. The aim of our investigation was to study under real-life conditions the microbial community associated with different chemical (monochloramine, hydrogen peroxide, chlorine dioxide) and non-chemical (hyperthermia) treatments, continuously applied since many years in four hot water networks of the same hospital. Municipal cold water, untreated secondary, and treated hot water were analysed for microbiome characterization by 16S amplicon sequencing. Cold waters had a common microbial profile at genera level. The hot water bacterial profiles differed according to treatment. Our results confirm the effectiveness of disinfection strategies in our hospital for controlling potential pathogens such as Legionella, as the investigated genera containing opportunistic pathogens were absent or had relative abundances ≤1%, except for non-tuberculous mycobacteria, Sphingomonas, Ochrobactrum and Brevundimonas. Monitoring the microbial complexity of healthcare water networks through 16S amplicon sequencing is an innovative and effective approach useful for Public Health purpose in order to verify possible modifications of microbiota associated with disinfection treatments.}, }
@article {pmid32213375, year = {2020}, author = {Vandekerckhove, TGL and Boon, N and Vlaeminck, SE}, title = {Pioneering on single-sludge nitrification/denitrification at 50 °C.}, journal = {Chemosphere}, volume = {252}, number = {}, pages = {126527}, doi = {10.1016/j.chemosphere.2020.126527}, pmid = {32213375}, issn = {1879-1298}, mesh = {Ammonium Compounds ; *Bioreactors ; Carbon ; Denitrification ; Nitrification ; Nitrogen ; Oxidation-Reduction ; Sewage ; Waste Disposal, Fluid ; }, abstract = {Thermophilic nitrification has been proven in lab-scale bioreactors at 50 °C. The challenge is now to develop a solution for thermophilic nitrogen removal, integrating nitrification with denitrification and aerobic carbon removal. This pioneering study aimed at a single-sludge nitrification/denitrification process at 50 °C, through exposing nitrification in a step by step approach to anoxia and/or organics. Firstly, recurrent anoxia was tolerated by a nitrifying community during long-term membrane bioreactor (MBR) operation (85 days), with high ammonium oxidation efficiencies (>98%). Secondly, five organic carbon sources did not affect thermophilic ammonium and nitrite oxidation rates in three-day aerobic batch flask incubations. Moving to long-term tests with sequencing batch reactors (SBR) and MBR (>250 days), good nitrification performance was obtained at increasing COD/Ninfluent ratios (0, 0.5, 1, 2 and 3). Thirdly, combining nitrification, recurrent anoxia and presence of organic carbon resulted in a nitrogen removal efficiency of 92-100%, with a COD/Nremoved of 4.8 ± 0.6 and a nitrogen removal rate of 50 ± 14 mg N g[-1] VSS d[-1]. Overall, this is the first proof of principle thermophilic nitrifiers can cope with redox fluctuations (aerobic/anoxic) and the aerobic or anoxic presence of organic carbon, can functionally co-exist with heterotrophs and that single-sludge nitrification/denitrification can be achieved.}, }
@article {pmid32209719, year = {2020}, author = {Benítez-Páez, A and Gómez Del Pugar, EM and López-Almela, I and Moya-Pérez, &#xc1; and Codoñer-Franch, P and Sanz, Y}, title = {Depletion of Blautia Species in the Microbiota of Obese Children Relates to Intestinal Inflammation and Metabolic Phenotype Worsening.}, journal = {mSystems}, volume = {5}, number = {2}, pages = {}, pmid = {32209719}, issn = {2379-5077}, abstract = {Cross-sectional studies conducted with obese and control subjects have suggested associations between gut microbiota alterations and obesity, but the links with specific disease phenotypes and proofs of causality are still scarce. The present study aimed to profile the gut microbiota of lean and obese children with and without insulin resistance to characterize associations with specific obesity-related complications and understand the role played in metabolic inflammation. Through massive sequencing of 16S rRNA gene amplicons and data analysis using a novel permutation approach, we have detected decreased incidence of Blautia species, especially Blautia luti and B. wexlerae, in the gut microbiota of obese children, which was even more pronounced in cases with both obesity and insulin resistance. There was also a parallel increase in proinflammatory cytokines and chemokines (gamma interferon [IFN-γ], tumor necrosis factor alpha [TNF-α], and monocyte chemoattractant protein 1 [MCP-1]) in feces of obese children compared to those of lean ones. B. luti and B. wexlerae were also shown to exert an anti-inflammatory effect in peripheral blood mononuclear cell cultures in vitro, compared to non-obesity-associated species. We suggest that the depletion of B. luti and B. wexlerae species in the gut ecosystem may occur in cases of obesity and contribute to metabolic inflammation leading to insulin resistance.IMPORTANCE Child obesity constitutes a risk factor for developing insulin resistance which, if sustained, could lead to more severe conditions like type 2 diabetes (T2D) in adulthood. Our study identified previously unknown species whose depletion (Blautia luti and Blautia wexlerae) is associated with insulin resistance in obese individuals. Our results also indicate that these bacterial species might help to reduce inflammation causally linked to obesity-related complications. Childhood is considered a window of opportunity to tackle obesity. These new findings provide, therefore, valuable information for the future design of microbiota-based strategies for the early prevention of obesity-related complications.}, }
@article {pmid32209716, year = {2020}, author = {Rampelli, S and Soverini, M and D'Amico, F and Barone, M and Tavella, T and Monti, D and Capri, M and Astolfi, A and Brigidi, P and Biagi, E and Franceschi, C and Turroni, S and Candela, M}, title = {Shotgun Metagenomics of Gut Microbiota in Humans with up to Extreme Longevity and the Increasing Role of Xenobiotic Degradation.}, journal = {mSystems}, volume = {5}, number = {2}, pages = {}, pmid = {32209716}, issn = {2379-5077}, abstract = {The gut microbiome of long-lived people display an increasing abundance of subdominant species, as well as a rearrangement in health-associated bacteria, but less is known about microbiome functions. In order to disentangle the contribution of the gut microbiome to the complex trait of human longevity, we here describe the metagenomic change of the human gut microbiome along with aging in subjects with up to extreme longevity, including centenarians (aged 99 to 104 years) and semisupercentenarians (aged 105 to 109 years), i.e., demographically very uncommon subjects who reach the extreme limit of the human life span. According to our findings, the gut microbiome of centenarians and semisupercentenarians is more suited for xenobiotic degradation and shows a rearrangement in metabolic pathways related to carbohydrate, amino acid, and lipid metabolism. Collectively, our data go beyond the relationship between intestinal bacteria and physiological changes that occur with aging by detailing the shifts in the potential metagenomic functions of the gut microbiome of centenarians and semisupercentenarians as a response to progressive dietary and lifestyle modifications.IMPORTANCE The study of longevity may help us understand how human beings can delay or survive the most frequent age-related diseases and morbidities. In this scenario, the gut microbiome has been proposed as one of the variables to monitor and possibly support healthy aging. Indeed, the disruption of host-gut microbiome homeostasis has been associated with inflammation and intestinal permeability as well as a general decline in bone and cognitive health. Here, we performed a metagenomic assessment of fecal samples from semisupercentenarians, i.e., 105 to 109 years old, in comparison to young adults, the elderly, and centenarians, shedding light on the longest compositional and functional trajectory of the human gut microbiome with aging. In addition to providing a fine taxonomic resolution down to the species level, our study emphasizes the progressive age-related increase in degradation pathways of pervasive xenobiotics in Western societies, possibly as a result of a supportive process within the molecular continuum characterizing aging.}, }
@article {pmid32209464, year = {2020}, author = {Wilbert, SA and Mark Welch, JL and Borisy, GG}, title = {Spatial Ecology of the Human Tongue Dorsum Microbiome.}, journal = {Cell reports}, volume = {30}, number = {12}, pages = {4003-4015.e3}, pmid = {32209464}, issn = {2211-1247}, support = {R01 DE022586/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Aged ; Biofilms ; Ecosystem ; Female ; Humans ; Male ; Microbial Consortia ; *Microbiota ; Middle Aged ; Phylogeny ; Species Specificity ; Tongue/*microbiology ; Young Adult ; }, abstract = {A fundamental question in microbial ecology is how microbes are spatially organized with respect to each other and their host. A test bed for examining this question is the tongue dorsum, which harbors a complex and important microbial community. Here, we use multiplexed fluorescence spectral imaging to investigate the organization of the tongue microbiome at micron to hundred-micron scales. We design oligonucleotide probes for taxa both abundant and prevalent, as determined by sequence analysis. Imaging reveals a highly structured spatial organization of microbial consortia, ranging in linear dimension from tens to hundreds of microns. The consortia appear to develop from a core of epithelial cells, with taxa clustering in domains suggestive of clonal expansion. Quantitative proximity analysis provides the basis for a model of tongue dorsum microbiome organization and dynamics. Our work illustrates how high-resolution analysis of micron-scale organization provides insights into physiological functions and microbiome-host interactions.}, }
@article {pmid32208652, year = {2020}, author = {Tian, Z and Wang, T and Tunlid, A and Persson, P}, title = {Proteolysis of Iron Oxide-Associated Bovine Serum Albumin.}, journal = {Environmental science &amp; technology}, volume = {54}, number = {8}, pages = {5121-5130}, pmid = {32208652}, issn = {1520-5851}, mesh = {Adsorption ; *Ferric Compounds ; Proteolysis ; *Serum Albumin, Bovine ; Surface Properties ; }, abstract = {Proteins are a substantial nitrogen source in soils provided that they can be hydrolyzed into bioavailable small peptides or amino acids. However, the strong associations between proteins and soil minerals restrict such proteolytic reactions. This study focused on how an extracellular fungal protease (Rhizopus sp.) hydrolyzed iron oxide-associated bovine serum albumin (BSA) and the factors that affected the proteolysis. We combined batch experiments with size-exclusion and reversed phase liquid chromatography and in situ infrared spectroscopic measurements to monitor the generation of proteolytic products in solution as well as the real-time changes of the adsorbed BSA during 24 h. Results showed that protease hydrolyzed the iron oxide-associated BSA directly at the surface without an initial desorption of BSA. Concurrently, the protease was adsorbed to vacant surface sites at the iron oxides, which significantly slowed down the rate of proteolysis. This inhibiting effect was counteracted by the presence of preadsorbed phosphate or by increasing the BSA coverage, which prevented protease adsorption. Fast initial rates of iron oxide-associated BSA proteolysis, comparable to proteolysis of BSA in solution, and very slow rates at prolonged proteolysis suggest a large variability in mineral-associated proteins as a nitrogen source in soils and that only a fraction of the protein is bioavailable.}, }
@article {pmid32208436, year = {2020}, author = {Marsland, R and Cui, W and Goldford, J and Mehta, P}, title = {The Community Simulator: A Python package for microbial ecology.}, journal = {PloS one}, volume = {15}, number = {3}, pages = {e0230430}, pmid = {32208436}, issn = {1932-6203}, support = {R35 GM119461/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Computer Simulation ; Ecology/*methods ; *Microbiota ; Population Dynamics ; *Software ; }, abstract = {Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing an increasingly important role in microbial ecology. In this manuscript, we present a new open-source, freely available Python package called Community Simulator for simulating microbial population dynamics in a reproducible, transparent and scalable way. The Community Simulator includes five major elements: tools for preparing the initial states and environmental conditions for a set of samples, automatic generation of dynamical equations based on a dictionary of modeling assumptions, random parameter sampling with tunable levels of metabolic and taxonomic structure, parallel integration of the dynamical equations, and support for metacommunity dynamics with migration between samples. To significantly speed up simulations using Community Simulator, our Python package implements a new Expectation-Maximization (EM) algorithm for finding equilibrium states of community dynamics that exploits a recently discovered duality between ecological dynamics and convex optimization. We present data showing that this EM algorithm improves performance by between one and two orders compared to direct numerical integration of the corresponding ordinary differential equations. We conclude by listing several recent applications of the Community Simulator to problems in microbial ecology, and discussing possible extensions of the package for directly analyzing microbiome compositional data.}, }
@article {pmid32206831, year = {2020}, author = {Mehta, O and Ghosh, TS and Kothidar, A and Gowtham, MR and Mitra, R and Kshetrapal, P and Wadhwa, N and Thiruvengadam, R and ,  and Nair, GB and Bhatnagar, S and Das, B}, title = {Vaginal Microbiome of Pregnant Indian Women: Insights into the Genome of Dominant Lactobacillus Species.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {487-499}, doi = {10.1007/s00248-020-01501-0}, pmid = {32206831}, issn = {1432-184X}, support = {No.BT/PR9983/MED/97/194/2013//Department of Biotechnology, Government of India/ ; }, mesh = {Adult ; Bacteria/isolation &amp; purification ; Female ; Genome, Bacterial/*physiology ; Humans ; India ; Lactobacillus/genetics/*physiology ; *Microbiota ; Pregnancy ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Vagina/*microbiology ; Young Adult ; }, abstract = {The trillions of microorganisms residing in the human body display varying degrees of compositional and functional diversities within and between individuals and contribute significantly to host physiology and susceptibility to disease. Microbial species present in the vaginal milieu of reproductive age women showed a large personal component and varies widely in different ethnic groups at the taxonomic, genomic, and functional levels. Lactobacillus iners, L. crispatus, L. gasseri, L. jensenii, and L. johnsonii are most frequently detected bacterial species in the vaginal milieu of reproductive age women. However, we currently lack (i) an understanding of the baseline vaginal microbiota of reproductive age Indian women, (ii) the extent of taxonomic and functional variations of vaginal microbiota between individuals and (iii) the genomic repertoires of the dominant vaginal microbiota associated with the Indian subjects. In our study, we analyzed the metagenome of high vaginal swab (HVS) samples collected from 40 pregnant Indian women enrolled in the GARBH-Ini cohort. Composition and abundance of bacterial species was characterized by pyrosequencing 16S rRNA gene. We identified 3067 OTUs with ≥ 10 reads from four different bacterial phyla. Several species of lactobacilli were clustered into three community state types (CSTs). L. iners, L. crispatus, L. gasseri, and L. jensenii are the most frequently detected Lactobacillus species in the vaginal environment of Indian women. Other than Lactobacillus, several species of Halomonas were also identified in the vaginal environment of most of the women sampled. To gain genomic and functional insights, we isolated several Lactobacillus species from the HVS samples and explored their whole genome sequences by shotgun sequencing. We analyzed the genome of dominant Lactobacillus species, L. iners, L. crispatus, L. gasseri, and L. paragesseri to represent the CSTs and identify functions that may influence the composition of complex vaginal microbial ecology. This study reports for the first time the vaginal microbial ecology of Indian women and genomic insights into L. iners, L. crispatus, L. gasseri, and L. paragesseri commonly found in the genital tract of reproductive age women.}, }
@article {pmid32203519, year = {2020}, author = {Botterweg-Paredes, E and Blaakmeer, A and Hong, SY and Sun, B and Mineri, L and Kruusvee, V and Xie, Y and Straub, D and Ménard, D and Pesquet, E and Wenkel, S}, title = {Light affects tissue patterning of the hypocotyl in the shade-avoidance response.}, journal = {PLoS genetics}, volume = {16}, number = {3}, pages = {e1008678}, pmid = {32203519}, issn = {1553-7404}, mesh = {Arabidopsis/genetics/growth &amp; development ; Arabidopsis Proteins/genetics/metabolism ; Body Patterning/*physiology ; Gene Expression Regulation, Plant/genetics ; Homeodomain Proteins/genetics/metabolism ; Hypocotyl/*metabolism/physiology ; *Light ; Plant Leaves/growth &amp; development ; Transcription Factors/genetics/metabolism ; }, abstract = {Plants have evolved strategies to avoid shade and optimize the capture of sunlight. While some species are tolerant to shade, plants such as Arabidopsis thaliana are shade-intolerant and induce elongation of their hypocotyl to outcompete neighboring plants. We report the identification of a developmental module acting downstream of shade perception controlling vascular patterning. We show that Arabidopsis plants react to shade by increasing the number and types of water-conducting tracheary elements in the vascular cylinder to maintain vascular density constant. Mutations in genes affecting vascular patterning impair the production of additional xylem and also show defects in the shade-induced hypocotyl elongation response. Comparative analysis of the shade-induced transcriptomes revealed differences between wild type and vascular patterning mutants and it appears that the latter mutants fail to induce sets of genes encoding biosynthetic and cell wall modifying enzymes. Our results thus set the stage for a deeper understanding of how growth and patterning are coordinated in a dynamic environment.}, }
@article {pmid32201415, year = {2020}, author = {Kamagata, Y}, title = {Recent Biofilm Studies Open a New Door in Microbial Ecology.}, journal = {Microbes and environments}, volume = {35}, number = {1}, pages = {}, pmid = {32201415}, issn = {1347-4405}, mesh = {*Biofilms ; *Ecology ; Environmental Pollutants ; Japan ; Research/*statistics &amp; numerical data ; }, }
@article {pmid32200752, year = {2020}, author = {Castledine, M and Sierocinski, P and Padfield, D and Buckling, A}, title = {Community coalescence: an eco-evolutionary perspective.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1798}, pages = {20190252}, pmid = {32200752}, issn = {1471-2970}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Biological Evolution ; *Life History Traits ; *Microbiota ; }, abstract = {Community coalescence, the mixing of different communities, is widespread throughout microbial ecology. Coalescence can result in approximately equal contributions from the founding communities or dominance of one community over another. These different outcomes have ramifications for community structure and function in natural communities, and the use of microbial communities in biotechnology and medicine. However, we have little understanding of when a particular outcome might be expected. Here, we integrate existing theory and data to speculate on how a crucial characteristic of microbial communities-the type of species interaction that dominates the community-might affect the outcome of microbial community coalescence. Given the often comparable timescales of microbial ecology and microevolution, we explicitly consider ecological and evolutionary dynamics, and their interplay, in determining coalescence outcomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.}, }
@article {pmid32200748, year = {2020}, author = {VanInsberghe, D and Arevalo, P and Chien, D and Polz, MF}, title = {How can microbial population genomics inform community ecology?.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1798}, pages = {20190253}, pmid = {32200748}, issn = {1471-2970}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Gene Flow ; *Metagenomics ; Microbiota/*genetics ; }, abstract = {Populations are fundamental units of ecology and evolution, but can we define them for bacteria and archaea in a biologically meaningful way? Here, we review why population structure is difficult to recognize in microbes and how recent advances in measuring contemporary gene flow allow us to identify clearly delineated populations among collections of closely related genomes. Such structure can arise from preferential gene flow caused by coexistence and genetic similarity, defining populations based on biological mechanisms. We show that such gene flow units are sufficiently genetically isolated for specific adaptations to spread, making them also ecological units that are differentially adapted compared to their closest relatives. We discuss the implications of these observations for measuring bacterial and archaeal diversity in the environment. We show that operational taxonomic units defined by 16S rRNA gene sequencing have woefully poor resolution for ecologically defined populations and propose monophyletic clusters of nearly identical ribosomal protein genes as an alternative measure for population mapping in community ecological studies employing metagenomics. These population-based approaches have the potential to provide much-needed clarity in interpreting the vast microbial diversity in human and environmental microbiomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.}, }
@article {pmid32200745, year = {2020}, author = {Prosser, JI}, title = {Putting science back into microbial ecology: a question of approach.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1798}, pages = {20190240}, pmid = {32200745}, issn = {1471-2970}, mesh = {Ecology ; Microbiology ; *Microbiota ; }, abstract = {Microbial ecology, the scientific study of interactions between natural microbial communities and their environments, has been facilitated by the application of molecular and 'omics'-based techniques that overcome some of the limitations of cultivation-based studies. This has increased emphasis on community ecology and 'microbiome' studies, but the majority address technical, rather than scientific challenges. Most are descriptive, do not address scientific aims or questions and are not designed to increase understanding or test hypotheses. The term 'hypothesis' is increasingly misused and critical testing of ideas or theory is restricted to a small minority of studies. This article discusses current microbial ecology research within the context of four approaches: description, induction, inference to the best explanation and deduction. The first three of these do not follow the established scientific method and are not based on scientific ecological questions. Observations are made and sometimes compared with published data, sometimes with attempts to explain findings in the context of existing ideas or hypotheses, but all lack objectivity and are biased by the observations made. By contrast, deductive studies address ecological questions and attempt to explain currently unexplained phenomena through the construction of hypotheses, from mechanism-based assumptions, that generate predictions that are then tested experimentally. Identification of key scientific questions, research driven by meaningful hypotheses and adoption of scientific method are essential for progress in microbial ecology, rather than the current emphasis on descriptive approaches that address only technical challenges. It is, therefore, imperative that we carefully consider and define the fundamental scientific questions that drive our own research and focus on ideas, concepts and hypotheses that can increase understanding, and only then consider which techniques are required for experimental testing. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.}, }
@article {pmid32200744, year = {2020}, author = {Pascual-García, A and Bonhoeffer, S and Bell, T}, title = {Metabolically cohesive microbial consortia and ecosystem functioning.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1798}, pages = {20190245}, pmid = {32200744}, issn = {1471-2970}, mesh = {Bacteria/*metabolism ; *Ecosystem ; Microbial Consortia/*physiology ; }, abstract = {Recent theory and experiments have reported a reproducible tendency for the coexistence of microbial species under controlled environmental conditions. This observation has been explained in the context of competition for resources and metabolic complementarity given that, in microbial communities (MCs), many excreted by-products of metabolism may also be resources. MCs therefore play a key role in promoting their own stability and in shaping the niches of the constituent taxa. We suggest that an intermediate level of organization between the species and the community level may be pervasive, where tightly knit metabolic interactions create discrete consortia that are stably maintained. We call these units Metabolically Cohesive Consortia (MeCoCos) and we discuss the environmental context in which we expect their formation, and the ecological and evolutionary consequences of their existence. We argue that the ability to identify MeCoCos would open new avenues to link the species-, community- and ecosystem-level properties, with consequences for our understanding of microbial ecology and evolution, and an improved ability to predict ecosystem functioning in the wild. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.}, }
@article {pmid32200742, year = {2020}, author = {Ciccarese, D and Zuidema, A and Merlo, V and Johnson, DR}, title = {Interaction-dependent effects of surface structure on microbial spatial self-organization.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1798}, pages = {20190246}, pmid = {32200742}, issn = {1471-2970}, mesh = {Microbiota/*physiology ; Pseudomonas stutzeri/*physiology ; }, abstract = {Surface-attached microbial communities consist of different cell types that, at least to some degree, organize themselves non-randomly across space (referred to as spatial self-organization). While spatial self-organization can have important effects on the functioning, ecology and evolution of communities, the underlying determinants of spatial self-organization remain unclear. Here, we hypothesize that the presence of physical objects across a surface can have important effects on spatial self-organization. Using pairs of isogenic strains of Pseudomonas stutzeri, we performed range expansion experiments in the absence or presence of physical objects and quantified the effects on spatial self-organization. We demonstrate that physical objects create local deformities along the expansion frontier, and these deformities increase in magnitude during range expansion. The deformities affect the densities of interspecific boundaries and diversity along the expansion frontier, and thus affect spatial self-organization, but the effects are interaction-dependent. For competitive interactions that promote sectorized patterns of spatial self-organization, physical objects increase the density of interspecific boundaries and diversity. By contrast, for cross-feeding interactions that promote dendritic patterns, they decrease the density of interspecific boundaries and diversity. These qualitatively different outcomes are probably caused by fundamental differences in the orientations of the interspecific boundaries. Thus, in order to predict the effects of physical objects on spatial self-organization, information is needed regarding the interactions present within a community and the general geometric shapes of spatial self-organization that emerge from those interactions. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.}, }
@article {pmid32200741, year = {2020}, author = {Locey, KJ and Muscarella, ME and Larsen, ML and Bray, SR and Jones, SE and Lennon, JT}, title = {Dormancy dampens the microbial distance-decay relationship.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1798}, pages = {20190243}, pmid = {32200741}, issn = {1471-2970}, mesh = {Bacteria/classification/*isolation &amp; purification ; Environment ; *Forests ; Geography ; Indiana ; *Microbiota ; Ponds/*microbiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Wetlands ; }, abstract = {Much of Earth's biodiversity has the capacity to engage in dormancy, a reversible state of reduced metabolic activity. By increasing resilience to unfavourable conditions, dormancy leads to the accumulation of 'seed banks'. These reservoirs of genetic and phenotypic diversity should diminish the strength of environmental filtering and increase rates of dispersal. Although prevalent among single-celled organisms, evidence that dormancy influences patterns of microbial biogeography is lacking. We constructed geographical and environmental distance-decay relationships (DDRs) for the total (DNA) and active (RNA) portions of bacterial communities in a regional-scale 16S rRNA survey of forested ponds in Indiana, USA. As predicted, total communities harboured greater diversity and exhibited weaker DDRs than active communities. These observations were robust to random resampling and different community metrics. To evaluate the processes underlying the biogeographic patterns, we developed a platform of mechanistic models that used the geographical coordinates and environmental characteristics of our study system. Based on more than 10[6] simulations, our models approximated the empirical DDRs when there was strong environmental filtering along with the presence of long-lived seed banks. By contrast, the inclusion of dispersal generally decreased model performance. Together, our findings support recent theoretical predictions that seed banks can influence the biogeographic patterns of microbial communities. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.}, }
@article {pmid32200739, year = {2020}, author = {Morris, A and Meyer, K and Bohannan, B}, title = {Linking microbial communities to ecosystem functions: what we can learn from genotype-phenotype mapping in organisms.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1798}, pages = {20190244}, pmid = {32200739}, issn = {1471-2970}, mesh = {Bacteria/*genetics ; Bacterial Physiological Phenomena ; *Ecosystem ; *Genotype ; Microbiota/*physiology ; *Phenotype ; }, abstract = {Microbial physiological processes are intimately involved in nutrient cycling. However, it remains unclear to what extent microbial diversity or community composition is important for determining the rates of ecosystem-scale functions. There are many examples of positive correlations between microbial diversity and ecosystem function, but how microbial communities 'map' onto ecosystem functions remain unresolved. This uncertainty limits our ability to predict and manage crucial microbially mediated processes such as nutrient losses and greenhouse gas emissions. To overcome this challenge, we propose integrating traditional biodiversity-ecosystem function research with ideas from genotype-phenotype mapping in organisms. We identify two insights from genotype-phenotype mapping that could be useful for microbial biodiversity-ecosystem function studies: the concept of searching 'agnostically' for markers of ecosystem function and controlling for population stratification to identify microorganisms uniquely associated with ecosystem function. We illustrate the potential for these approaches to elucidate microbial biodiversity-ecosystem function relationships by analysing a subset of published data measuring methane oxidation rates from tropical soils. We assert that combining the approaches of traditional biodiversity-ecosystem function research with ideas from genotype-phenotype mapping will generate novel hypotheses about how complex microbial communities drive ecosystem function and help scientists predict and manage changes to ecosystem functions resulting from human activities. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.}, }
@article {pmid32200738, year = {2020}, author = {Sorensen, JW and Shade, A}, title = {Dormancy dynamics and dispersal contribute to soil microbiome resilience.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1798}, pages = {20190255}, pmid = {32200738}, issn = {1471-2970}, mesh = {Bacteria/classification ; *Bacterial Physiological Phenomena ; *Microbiota ; Population Dynamics ; *Soil Microbiology ; }, abstract = {In disturbance ecology, stability is composed of resistance to change and resilience towards recovery after the disturbance subsides. Two key microbial mechanisms that can support microbiome stability include dormancy and dispersal. Specifically, microbial populations that are sensitive to disturbance can be re-seeded by local dormant pools of viable and reactivated cells, or by immigrants dispersed from regional metacommunities. However, it is difficult to quantify the contributions of these mechanisms to stability without, first, distinguishing the active from inactive membership, and, second, distinguishing the populations recovered by local resuscitation from those recovered by dispersed immigrants. Here, we investigate the contributions of dormancy dynamics (activation and inactivation), and dispersal to soil microbial community resistance and resilience. We designed a replicated, 45-week time-series experiment to quantify the responses of the active soil microbial community to a thermal press disturbance, including unwarmed control mesocosms, disturbed mesocosms without dispersal, and disturbed mesocosms with dispersal after the release of the stressor. Communities changed in structure within one week of warming. Though the disturbed mesocosms did not fully recover within 29 weeks, resuscitation of thermotolerant taxa was key for community transition during the press, and both resuscitation of opportunistic taxa and immigration contributed to community resilience. Also, mesocosms with dispersal were more resilient than mesocosms without. This work advances the mechanistic understanding of how microbiomes respond to disturbances in their environment. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.}, }
@article {pmid32200737, year = {2020}, author = {Nunan, N and Schmidt, H and Raynaud, X}, title = {The ecology of heterogeneity: soil bacterial communities and C dynamics.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1798}, pages = {20190249}, pmid = {32200737}, issn = {1471-2970}, mesh = {Bacteria/*metabolism ; Bacterial Physiological Phenomena ; Carbon/*metabolism ; *Ecosystem ; *Microbiota ; *Soil Microbiology ; }, abstract = {Heterogeneity is a fundamental property of soil that is often overlooked in microbial ecology. Although it is generally accepted that the heterogeneity of soil underpins the emergence and maintenance of microbial diversity, the profound and far-reaching consequences that heterogeneity can have on many aspects of microbial ecology and activity have yet to be fully apprehended and have not been fully integrated into our understanding of microbial functioning. In this contribution we first discuss how the heterogeneity of the soil microbial environment, and the consequent uncertainty associated with acquiring resources, may have affected how microbial metabolism, motility and interactions evolved and, ultimately, the overall microbial activity that is represented in ecosystem models, such as heterotrophic decomposition or respiration. We then present an analysis of predicted metabolic pathways for soil bacteria, obtained from the MetaCyc pathway/genome database collection (https://metacyc.org/). The analysis suggests that while there is a relationship between phylogenic affiliation and the catabolic range of soil bacterial taxa, there does not appear to be a trade-off between the 16S rRNA gene copy number, taken as a proxy of potential growth rate, of bacterial strains and the range of substrates that can be used. Finally, we present a simple, spatially explicit model that can be used to understand how the interactions between decomposers and environmental heterogeneity affect the bacterial decomposition of organic matter, suggesting that environmental heterogeneity might have important consequences on the variability of this process. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.}, }
@article {pmid32200418, year = {2021}, author = {Ferreira, DA and da Silva, TF and Pylro, VS and Salles, JF and Andreote, FD and Dini-Andreote, F}, title = {Soil Microbial Diversity Affects the Plant-Root Colonization by Arbuscular Mycorrhizal Fungi.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {100-103}, pmid = {32200418}, issn = {1432-184X}, mesh = {Fungi/genetics ; *Mycorrhizae ; Plant Roots ; Soil ; Soil Microbiology ; }, abstract = {Terrestrial plants establish symbiosis with arbuscular mycorrhizal fungi (AMF) to exchange water and nutrients. However, the extent to which soil biodiversity influences such association remains still unclear. Here, we manipulated the soil microbial diversity using a "dilution-to-extinction" approach in a controlled pot microcosm system and quantified the root length colonization of maize plants by the AMF Rhizophagus clarus. The experiment was performed by manipulating the soil microbiome within a native and foreign soil having distinct physicochemical properties. Overall, our data revealed significant positive correlations between the soil microbial diversity and AMF colonization. Most importantly, this finding opposes the diversity-invasibility hypothesis and highlights for a potential overall helper effect of the soil biodiversity on plant-AMF symbiosis.}, }
@article {pmid32200249, year = {2020}, author = {Santos, A and Rachid, C and Pacheco, AB and Magalhães, V}, title = {Biotic and abiotic factors affect microcystin-LR concentrations in water/sediment interface.}, journal = {Microbiological research}, volume = {236}, number = {}, pages = {126452}, doi = {10.1016/j.micres.2020.126452}, pmid = {32200249}, issn = {1618-0623}, mesh = {Biodegradation, Environmental ; Cyanobacteria/*metabolism ; Genes, Bacterial ; Geologic Sediments/analysis/*microbiology ; *Harmful Algal Bloom ; Humans ; Hydrogen-Ion Concentration ; Lakes/microbiology ; Marine Toxins ; Metagenomics ; Microbiota/*genetics ; *Microcystins/analysis ; RNA, Ribosomal, 16S/genetics ; Temperature ; Water/analysis ; Water Pollutants, Chemical/*analysis ; }, abstract = {Harmful cyanobacterial blooms are increasingly common in aquatic environments. This can lead to higher concentrations of cyanotoxins, such as microcystins (MCs), posing a great risk to diverse organisms, including humans. MCs are among the most commonly reported cyanotoxins in freshwater environments worldwide, where they may have different fates. MCs can adsorb to suspended particles into the water column and deposit onto the sediment where they can be affected by physical factors (e.g. winds in shallow lakes causing sediment resuspension) or biological factors (e.g. biodegradation). Here we focused on the conditions of a coastal shallow lagoon contaminated by MCs aiming to estimate the return of pre-existing MCs from the sediment to the water column, to evaluate the adsorption of dissolved MC-LR to the sediment and to verify the occurrence of biodegradation. In experiments with sediment, desorption and adsorption were tested under the influence of temperature, pH and aeration, reproducing conditions observed in the lagoon. MC-desorption was not detected under the tested conditions. Spiking MC-LR into lagoon water samples in the presence of sediment resulted in a 50 % reduction of soluble MC-LR concentration in control conditions (25 °C, pH 8.0, no aeration). Increasing temperature (45 °C) or introducing aeration further stimulated MC-LR removal from the water. Biodegradation was observed in sediment samples and interstitial water (even with tetracycline). The composition of the bacterial community differed in sediment and interstitial water: major phyla were Chloroflexi, Proteobacteria, Firmicutes, and OP3. From the assigned OTUs, we identified genera already described as MC degrading bacteria. Thus, the sediment is a key factor influencing the fate of MC-LR in this shallow coastal lake contributing to stable adsorption and biodegradation.}, }
@article {pmid32198347, year = {2020}, author = {Chatzigiannidou, I and Teughels, W and Van de Wiele, T and Boon, N}, title = {Oral biofilms exposure to chlorhexidine results in altered microbial composition and metabolic profile.}, journal = {NPJ biofilms and microbiomes}, volume = {6}, number = {1}, pages = {13}, pmid = {32198347}, issn = {2055-5008}, mesh = {Acetates/analysis ; Bacteria/drug effects/genetics/*growth &amp; development ; Biofilms/*drug effects/growth &amp; development ; Butyrates/analysis ; Chlorhexidine/*pharmacology ; Formates/analysis ; Humans ; Lactic Acid/analysis ; Metabolomics ; Microbial Sensitivity Tests ; Microbial Viability/drug effects ; Mouth/drug effects/*microbiology ; Mouthwashes/*pharmacology ; Propionates/analysis ; Symbiosis/drug effects ; }, abstract = {Oral diseases (e.g., dental caries, periodontitis) are developed when the healthy oral microbiome is imbalanced allowing the increase of pathobiont strains. Common practice to prevent or treat such diseases is the use of antiseptics, like chlorhexidine. However, the impact of these antiseptics on the composition and metabolic activity of the oral microbiome is poorly addressed. Using two types of oral biofilms-a 14-species community (more controllable) and human tongue microbiota (more representative)-the impact of short-term chlorhexidine exposure was explored in-depth. In both models, oral biofilms treated with chlorhexidine exhibited a pattern of inactivation (>3 log units) and fast regrowth to the initial bacterial concentrations. Moreover, the chlorhexidine treatment induced profound shifts in microbiota composition and metabolic activity. In some cases, disease associated traits were increased (such as higher abundance of pathobiont strains or shift in high lactate production). Our results highlight the need for alternative treatments that selectively target the disease-associated bacteria in the biofilm without targeting the commensal microorganisms.}, }
@article {pmid32196510, year = {2020}, author = {Farhana, L and Sarkar, S and Nangia-Makker, P and Yu, Y and Khosla, P and Levi, E and Azmi, A and Majumdar, APN}, title = {Natural agents inhibit colon cancer cell proliferation and alter microbial diversity in mice.}, journal = {PloS one}, volume = {15}, number = {3}, pages = {e0229823}, pmid = {32196510}, issn = {1932-6203}, support = {I01 BX001927/BX/BLRD VA/United States ; R21 CA175916/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Biological Products/*pharmacology/therapeutic use ; Cell Proliferation/drug effects ; Colonic Neoplasms/*drug therapy/pathology ; Curcuma ; Curcumin/*pharmacology/therapeutic use ; Gastrointestinal Microbiome/*drug effects ; HCT116 Cells ; Humans ; Mice ; Mice, SCID ; Plant Extracts/*pharmacology/therapeutic use ; Tocotrienols/*pharmacology/therapeutic use ; Xenograft Model Antitumor Assays ; }, abstract = {The current study was undertaken to investigate the effect of differentially formulated polyphenolic compound Essential Turmeric Oil-Curcumin (ETO-Cur), and Tocotrienol-rich fraction (TRF) of vitamin E isomers on colorectal cancer (CRC) cells that produce aggressive tumors. Combinations of ETO-Cur and TRF were used to determine the combinatorial effects of ETO-Cur and TRF-mediated inhibition of growth of CRC cells in vitro and HCT-116 cells xenograft in SCID mice. 16S rRNA gene sequence profiling was performed to determine the outcome of gut microbial communities in mice feces between control and ETO-Cur-TRF groups. Bacterial identifications were validated by performing SYBR-based Real Time (RT) PCR. For metagenomics analysis to characterize the microbial communities, multiple software/tools were used, including Quantitative Insights into Microbial Ecology (QIIME) processing tool. We found ETO-Cur and TRF to synergize and that the combination of ETO-Cur-TRF significantly inhibited growth of HCT-116 xenografts in SCID mice. This was associated with a marked alteration in microbial communities and increased microbial OTU (operation taxonomic unit) number. The relative abundance of taxa was increased and the level of microbial diversity after 34 days of combinatorial treatment was found to be 44% higher over the control. Shifting of microbial family composition was observed in ETO-Cur-TRF treated mice as evidenced by marked reductions in Bacteroidaceae, Ruminococcaceae, Clostridiales, Firmicutes and Parabacteroids families, compared to controls. Interestingly, during the inhibition of tumor growth in ETO-Cur treated mice, probiotic Lactobacillaceae and Bifidobacteriaceae were increased by 20-fold and 6-fold, respectively. The relative abundance of anti-inflammatory Clostridium XIVa was also increased in ETO-Cur-TRF treated mice when compared with the control. Our data suggest that ETO-Cur-TRF show synergistic effects in inhibiting colorectal cancer cell proliferation in vitro and in mouse xenografts in vivo, and might induce changes in microbial diversity in mice.}, }
@article {pmid32195301, year = {2020}, author = {Ghosh, A and Debnath, M and Bhadury, P}, title = {Datasets of surface water microbial populations from two anthropogenically impacted sites on the Bhagirathi-Hooghly River.}, journal = {Data in brief}, volume = {29}, number = {}, pages = {105371}, pmid = {32195301}, issn = {2352-3409}, abstract = {The Bhagirathi-Hooghly River, part of the River Ganga, flows along densely urbanized areas in West Bengal, India. The River water is extensively used for household activities, human consumption including bathing, social purposes and multifaceted industrial usage. As a result of discharge of untreated municipal sewage and effluents from industries there is evidence of heavy pollution in this River. Two urbanized sites on the Bhagirathi-Hooghly River, namely Kalyani and Kolkata, were sampled to elucidate the resident microbial communities in lieu of anthropogenic forcing with respect to pollution. The Kalyani station (Kal_Stn1) lies upstream to the Kolkata station (Kol_Stn7) and are approximate 50 km away from each other and located along the bank of Bhagirathi-Hooghly River. Sampling was undertaken in monsoon (September 2018). In situ environmental parameters were measured during sampling and dissolved nutrients were estimated from formalin fixed filtered surface water along with pesticides analysis. One litre surface water sample was collected from each station and environmental DNA was sequenced to identify resident microbial communities (bacterioplankton and oxygenic photoautrophs-phytoplankton). The bacterioplankton community structure was elucidated by sequencing the V4 region of the 16S rDNA on an Illumina MiSeq platform. Proteobacteria was found to be the most abundant bacterioplankton phylum in both sampling stations. Similar to bacterioplankton, variation in oxygenic photoautotrophic community structure including phytoplankton forms was found at phylum, class and family levels. The phytoplankton communities were elucidated by sequencing the V9 region of the 18S rDNA on an Illumina MiSeq platform. Chrysophyta was found to be the most abundant phytoplankton phylum identified from both stations, followed by Chlorophyta and other groups. Variation in phytoplankton community structure between the stations was distinct at phylum, class and family levels.}, }
@article {pmid32194964, year = {2020}, author = {Gueneau, R and Blanchet, D and Rodriguez-Nava, V and Bergeron, E and Soulier, M and Bestandji, N and Demar, M and Couppie, P and Blaizot, R}, title = {Actinomycetoma caused by Gordonia westfalica: first reported case of human infection.}, journal = {New microbes and new infections}, volume = {34}, number = {}, pages = {100658}, pmid = {32194964}, issn = {2052-2975}, abstract = {Bacteria of the genus Gordonia are rarely involved in human infections. We report here the case of a 30-year-old man from Guinea Buissau with mycetoma of the foot. 16S DNA sequencing after surgical biopsy identified Gordonia westfalica. To our knowledge, this is the first report of human infection caused by G. westfalica.}, }
@article {pmid32194531, year = {2020}, author = {Flores, N and Hoyos, S and Venegas, M and Galetović, A and Zúñiga, LM and Fábrega, F and Paredes, B and Salazar-Ardiles, C and Vilo, C and Ascaso, C and Wierzchos, J and Souza-Egipsy, V and Araya, JE and Batista-García, RA and Gómez-Silva, B}, title = {Haloterrigena sp. Strain SGH1, a Bacterioruberin-Rich, Perchlorate-Tolerant Halophilic Archaeon Isolated From Halite Microbial Communities, Atacama Desert, Chile.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {324}, pmid = {32194531}, issn = {1664-302X}, abstract = {An extreme halophilic archaeon, strain SGH1, is a novel microorganism isolated from endolithic microbial communities colonizing halites at Salar Grande, Atacama Desert, in northern Chile. Our study provides structural, biochemical, genomic, and physiological information on this new isolate living at the edge of the physical and chemical extremes at the Atacama Desert. SGH1 is a Gram-negative, red-pigmented, non-motile unicellular coccoid organism. Under the transmission electron microscope, strain SGH1 showed an abundant electro-dense material surrounding electron-lucent globular structures resembling gas vacuoles. Strain SGH1 showed a 16S rRNA gene sequence with a close phylogenetic relationship to the extreme halophilic archaea Haloterrigena turkmenica and Haloterrigena salina and has been denominated Haloterrigena sp. strain SGH1. Strain SGH1 grew at 20-40°C (optimum 37°C), at salinities between 15 and 30% (w/v) NaCl (optimum 25%) and growth was improved by addition of 50 mM KCl and 0.5% w/v casamino acids. Growth was severely restricted at salinities below 15% NaCl and cell lysis is avoided at a minimal 10% NaCl. Maximal concentrations of magnesium chloride and sodium or magnesium perchlorates that supported SGH1 growth were 0.5 and 0.15M, respectively. Haloterrigena sp. strain SGH1 accumulates bacterioruberin (BR), a C50 xanthophyll, as the major carotenoid. Total carotenoids in strain SGH1 amounted to nearly 400 μg BR per gram of dry biomass. Nearly 80% of total carotenoids accumulated as geometric isomers of BR: all-trans-BR (50%), 5-cis-BR (15%), 9-cis-BR (10%), 13-cis-BR (4%); other carotenoids were dehydrated derivatives of BR. Carotenogenesis in SGH1 was a reversible and salt-dependent process; transferring BR-rich cells grown in 25% (w/v) NaCl to 15% (w/v) NaCl medium resulted in depigmentation, and BR content was recovered after transference and growth of unpigmented cells to high salinity medium. Methanol extracts and purified BR isomers showed an 8-9-fold higher antioxidant activity than Trolox or β-carotene. Both, plasma membrane integrity and mitochondrial membrane potential measurements under acute 18-h assays showed that purified BR isomers were non-toxic to cultured human THP-1 cells.}, }
@article {pmid32194522, year = {2020}, author = {Cortes-Tolalpa, L and Wang, Y and Salles, JF and van Elsas, JD}, title = {Comparative Genome Analysis of the Lignocellulose Degrading Bacteria Citrobacter freundii so4 and Sphingobacterium multivorum w15.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {248}, pmid = {32194522}, issn = {1664-302X}, abstract = {Two bacterial strains, denoted so4 and w15, isolated from wheat straw (WS)-degrading microbial consortia, were found to grow synergistically in media containing WS as the single carbon and energy source. They were identified as Citrobacter freundii so4 and Sphingobacterium multivorum w15 based on 16S rRNA gene sequencing and comparison to the respective C. freundii and S. multivorum type strains. In order to identify the mechanisms driving the synergistic interactions, we analyzed the draft genomes of the two strains and further characterized their metabolic potential. The latter analyses revealed that the strains had largely complementary substrate utilization patterns, with only 22 out of 190 compounds shared. The analyses further indicated C. freundii so4 to primarily consume amino acids and simple sugars, with laminarin as a key exception. In contrast, S. multivorum w15 showed ample capacity to transform complex polysaccharides, including intermediates of starch degradation. Sequence analyses revealed C. freundii so4 to have a genome of 4,883,214 bp, with a G + C content of 52.5%, 4,554 protein-encoding genes and 86 RNA genes. S. multivorum w15 has a genome of 6,678,278 bp, with a G + C content of 39.7%, 5,999 protein-encoding genes and 76 RNA genes. Genes for motility apparatuses (flagella, chemotaxis) were present in the genome of C. freundii so4, but absent from that of S. multivorum w15. In the genome of S. multivorum w15, 348 genes had regions matching CAZy family enzymes and/or carbohydrate-binding modules (CBMs), with 193 glycosyl hydrolase (GH) and 50 CBM domains. Remarkably, 22 domains matched enzymes of glycoside hydrolase family GH43, suggesting a strong investment in the degradation of arabinoxylan. In contrast, 130 CAZy family genes were found in C. freundii so4, with 61 GH and 12 CBM domains identified. Collectively, our results, based on both metabolic potential and genome analyses, revealed the two strains to harbor complementary catabolic armories, with S. multivorum w15 primarily attacking the WS hemicellulose and C. freundii so4 the cellobiose derived from cellulose, next to emerging oligo- or monosaccharides. Finally, C. freundii so4 may secrete secondary metabolites that S. multivorum w15 can consume, and detoxify the system by reducing the levels of (toxic) by-products.}, }
@article {pmid32193752, year = {2020}, author = {Corti-Monzón, G and Nisenbaum, M and Villegas-Plazas, M and Junca, H and Murialdo, S}, title = {Enrichment and characterization of a bilge microbial consortium with oil in water-emulsions breaking ability for oily wastewater treatment.}, journal = {Biodegradation}, volume = {31}, number = {1-2}, pages = {57-72}, doi = {10.1007/s10532-020-09894-y}, pmid = {32193752}, issn = {1572-9729}, support = {Resoluci&#xf3;n N&#xba; 428/16 y 429/16//Comisi&#xf3;n de Investigaciones Cient&#xed;ficas/International ; VT38-UNMdP10982//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n Productiva/International ; }, mesh = {Biodegradation, Environmental ; Emulsions ; *Microbial Consortia ; RNA, Ribosomal, 16S ; Shewanella ; *Wastewater ; }, abstract = {Oily bilge wastewater is one of the main sources of hydrocarbons pollution in marine environments due to accidental or clandestine discharges. The main technical challenge for its effective treatment is the presence of stable oil-in-water (O/W) emulsions. In this work we are reporting an enriched microbial consortium from bilge wastewater with remarkable ability to demulsify oil in water emulsions. The consortium showed emulsion-breaking ratios up to 72.6% in the exponential growth phase, while the values range from 11.9 to 8.5% in stationary phase. A positive association was observed between demulsifying ability and microbial adhesion to hydrocarbons, as well as between cell concentration and demulsifying ability. Also, an interesting ability to demulsify under different temperatures, conditions of agitation, and bilge emulsions from different vessels was observed. The Bacterial and Archaeal composition was analyzed by 16S rRNA gene amplicon lllumina sequencing analyses, revealing an assemblage composed of bacterial types highly related to well characterized bacterial isolates and also to non-yet cultured bacterial types previously detected in marine and sediment samples. Hydrocarbonoclastic microbial types such as Marinobacter, Flavobacteriaceae, Alcanivorax and Gammaproteobacteria PYR10d3 were found in high relative abundance (27.0%-11.1%) and types of marine oligotrophs and surfactant degraders such as Thallasospira, Parvibaculum, Novospirillum, Shewanella algae, and Opitutae were in a group of middle predominance (1.7-3.5%). The microbial consortium reported has promising potential for the biological demulsification of bilge wastewater and other oily wastewaters.}, }
@article {pmid32192536, year = {2020}, author = {Kavagutti, VS and Andrei, A&#x15e; and Mehrshad, M and Salcher, MM and Ghai, R}, title = {Correction to: Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {40}, pmid = {32192536}, issn = {2049-2618}, abstract = {Following publication of the original article [1], the authors reported that an affiliation of the first author was missing.}, }
@article {pmid32191867, year = {2020}, author = {Dini-Andreote, F}, title = {Endophytes: The Second Layer of Plant Defense.}, journal = {Trends in plant science}, volume = {25}, number = {4}, pages = {319-322}, doi = {10.1016/j.tplants.2020.01.007}, pmid = {32191867}, issn = {1878-4372}, mesh = {*Endophytes ; Plant Roots ; Plants ; *Rhizosphere ; Soil Microbiology ; }, abstract = {Microorganisms in association with roots can protect plants against soil-borne diseases. A recent study mechanistically revealed how root endophytes act as a second microbiological layer of plant defense. Integrating ecological concepts with principles of plant pathology provides an innovative way to manipulate and engineer beneficial plant microbiomes.}, }
@article {pmid32187685, year = {2020}, author = {Pu, X and Li, Z and Tian, Y and Gao, R and Hao, L and Hu, Y and He, C and Sun, W and Xu, M and Peters, RJ and Van de Peer, Y and Xu, Z and Song, J}, title = {The honeysuckle genome provides insight into the molecular mechanism of carotenoid metabolism underlying dynamic flower coloration.}, journal = {The New phytologist}, volume = {227}, number = {3}, pages = {930-943}, pmid = {32187685}, issn = {1469-8137}, support = {833522/ERC_/European Research Council/International ; }, mesh = {Carotenoids ; Flowers/genetics ; Gene Expression Profiling ; *Lonicera/genetics ; }, abstract = {Lonicera japonica is a widespread member of the Caprifoliaceae (honeysuckle) family utilized in traditional medical practices. This twining vine honeysuckle also is a much-sought ornamental, in part due to its dynamic flower coloration, which changes from white to gold during development. The molecular mechanism underlying dynamic flower coloration in L. japonica was elucidated by integrating whole genome sequencing, transcriptomic analysis and biochemical assays. Here, we report a chromosome-level genome assembly of L. japonica, comprising nine pseudochromosomes with a total size of 843.2 Mb. We also provide evidence for a whole-genome duplication event in the lineage leading to L. japonica, which occurred after its divergence from Dipsacales and Asterales. Moreover, gene expression analysis not only revealed correlated expression of the relevant biosynthetic genes with carotenoid accumulation, but also suggested a role for carotenoid degradation in L. japonica's dynamic flower coloration. The variation of flower color is consistent with not only the observed carotenoid accumulation pattern, but also with the release of volatile apocarotenoids that presumably serve as pollinator attractants. Beyond novel insights into the evolution and dynamics of flower coloration, the high-quality L. japonica genome sequence also provides a foundation for molecular breeding to improve desired characteristics.}, }
@article {pmid32184367, year = {2020}, author = {Danczak, RE and Daly, RA and Borton, MA and Stegen, JC and Roux, S and Wrighton, KC and Wilkins, MJ}, title = {Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems.}, journal = {mSystems}, volume = {5}, number = {2}, pages = {}, pmid = {32184367}, issn = {2379-5077}, abstract = {The ecological drivers that concurrently act upon both a virus and its host and that drive community assembly are poorly understood despite known interactions between viral populations and their microbial hosts. Hydraulically fractured shale environments provide access to a closed ecosystem in the deep subsurface where constrained microbial and viral community assembly processes can be examined. Here, we used metagenomic analyses of time-resolved-produced fluid samples from two wells in the Appalachian Basin to track viral and host dynamics and to investigate community assembly processes. Hypersaline conditions within these ecosystems should drive microbial community structure to a similar configuration through time in response to common osmotic stress. However, viral predation appears to counterbalance this potentially strong homogeneous selection and pushes the microbial community toward undominated assembly. In comparison, while the viral community was also influenced by substantial undominated processes, it assembled, in part, due to homogeneous selection. When the overall assembly processes acting upon both these communities were directly compared with each other, a significant relationship was revealed, suggesting an association between microbial and viral community development despite differing selective pressures. These results reveal a potentially important balance of ecological dynamics that must be in maintained within this deep subsurface ecosystem in order for the microbial community to persist over extended time periods. More broadly, this relationship begins to provide knowledge underlying metacommunity development across trophic levels.IMPORTANCE Interactions between viral communities and their microbial hosts have been the subject of many recent studies in a wide range of ecosystems. The degree of coordination between ecological assembly processes influencing viral and microbial communities, however, has been explored to a much lesser degree. By using a combined null modeling approach, this study investigated the ecological assembly processes influencing both viral and microbial community structure within hydraulically fractured shale environments. Among other results, significant relationships between the structuring processes affecting both the viral and microbial community were observed, indicating that ecological assembly might be coordinated between these communities despite differing selective pressures. Within this deep subsurface ecosystem, these results reveal a potentially important balance of ecological dynamics that must be maintained to enable long-term microbial community persistence. More broadly, this relationship begins to provide insight into the development of communities across trophic levels.}, }
@article {pmid32184363, year = {2020}, author = {Fu, S and Wei, D and Yang, Q and Xie, G and Pang, B and Wang, Y and Lan, R and Wang, Q and Dong, X and Zhang, X and Huang, J and Feng, J and Liu, Y}, title = {Horizontal Plasmid Transfer Promotes the Dissemination of Asian Acute Hepatopancreatic Necrosis Disease and Provides a Novel Mechanism for Genetic Exchange and Environmental Adaptation.}, journal = {mSystems}, volume = {5}, number = {2}, pages = {}, pmid = {32184363}, issn = {2379-5077}, abstract = {Vibrio parahaemolyticus is an important foodborne pathogen and has recently gained particular notoriety because it causes acute hepatopancreatic necrosis disease (AHPND) in shrimp, which has caused significant economic loss in the shrimp industry. Here, we report a whole-genome analysis of 233 V. parahaemolyticus strains isolated from humans, diseased shrimp, and environmental samples collected between 2008 and 2017, providing unprecedented insight into the historical spread of AHPND. The results show that V. parahaemolyticus is genetically diverse and can be divided into 84 sequence types (STs). However, genomic analysis of three STs of V. parahaemolyticus identified seven transmission routes in Asia since 1996, which promoted the transfer of an AHPND-associated plasmid. Notably, the insertion sequence (ISVal1) from the plasmid subsequently mediated the genetic exchange among V. parahaemolyticus STs and resulted in the deletion of an 11-kb region regulating cell mobility and the production of capsular polysaccharides. Phenotype assays confirmed that this deletion enhanced biofilm formation, providing a novel mechanism for environmental adaptation. We conclude that the transmission mode of AHPND consists of two steps, the transmission of V. parahaemolyticus and the subsequent horizontal transfer of the AHPND-associated plasmid. This plasmid allows ISVal1 to mediate genetic exchange and improve pathogen fitness in shrimp ponds. Current shrimp farming practices promoted such genetic exchanges, which highlighted a risk of the emergence of new virulent populations, with potentially devastating consequences for both aquaculture and human health. This study addressed the basic questions regarding the transmission mechanism of AHPND and provided novel insights into shrimp and human disease management.IMPORTANCE Global outbreaks of shrimp acute hepatopancreatic necrosis disease (AHPND) caused by V. parahaemolyticus represent an urgent issue for the shrimp industry. This study revealed that the transmission mode of AHPND consists of two steps, the transregional dissemination of V. parahaemolyticus and the horizontal transfer of an AHPND-associated plasmid. Surprisingly, the introduction of the AHPND-associated plasmid also offers a novel mechanism of genetic exchange mediated by insertion sequences, and it improved the fitness of V. parahaemolyticus in a harsh environment. The results presented herein suggest that current shrimp farming practices promote genetic mixture between endemic and oceanic V. parahaemolyticus populations, which introduced the plasmid and accelerated bacterial adaptation by the acquisition of ecologically important functions. This entails a risk of the emergence of new virulent populations both for shrimp and humans. This study improves our understanding of the global dissemination of the AHPND-associated plasmid and highlights the urgent need to improve biosecurity for shrimp farming.}, }
@article {pmid32184251, year = {2020}, author = {Yang, Y and Daims, H and Liu, Y and Herbold, CW and Pjevac, P and Lin, JG and Li, M and Gu, JD}, title = {Activity and Metabolic Versatility of Complete Ammonia Oxidizers in Full-Scale Wastewater Treatment Systems.}, journal = {mBio}, volume = {11}, number = {2}, pages = {}, pmid = {32184251}, issn = {2150-7511}, support = {P 30570/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Ammonia/*metabolism ; Bacteria/classification/*genetics/*metabolism ; Genome, Bacterial ; Metagenome ; Multigene Family ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Transcriptome ; Wastewater/*microbiology ; *Water Purification ; }, abstract = {The recent discovery of complete ammonia oxidizers (comammox) contradicts the paradigm that chemolithoautotrophic nitrification is always catalyzed by two different microorganisms. However, our knowledge of the survival strategies of comammox in complex ecosystems, such as full-scale wastewater treatment plants (WWTPs), remains limited. Analyses of genomes and in situ transcriptomes of four comammox organisms from two full-scale WWTPs revealed that comammox were active and showed a surprisingly high metabolic versatility. A gene cluster for the utilization of urea and a gene encoding cyanase suggest that comammox may use diverse organic nitrogen compounds in addition to free ammonia as the substrates. The comammox organisms also encoded the genomic potential for multiple alternative energy metabolisms, including respiration with hydrogen, formate, and sulfite as electron donors. Pathways for the biosynthesis and degradation of polyphosphate, glycogen, and polyhydroxyalkanoates as intracellular storage compounds likely help comammox survive unfavorable conditions and facilitate switches between lifestyles in fluctuating environments. One of the comammox strains acquired from the anaerobic tank encoded and transcribed genes involved in homoacetate fermentation or in the utilization of exogenous acetate, both pathways being unexpected in a nitrifying bacterium. Surprisingly, this strain also encoded a respiratory nitrate reductase which has not yet been found in any other Nitrospira genome and might confer a selective advantage to this strain over other Nitrospira strains in anoxic conditions.IMPORTANCE The discovery of comammox in the genus Nitrospira changes our perception of nitrification. However, genomes of comammox organisms have not been acquired from full-scale WWTPs, and very little is known about their survival strategies and potential metabolisms in complex wastewater treatment systems. Here, four comammox metagenome-assembled genomes and metatranscriptomic data sets were retrieved from two full-scale WWTPs. Their impressive and-among nitrifiers-unsurpassed ecophysiological versatility could make comammox Nitrospira an interesting target for optimizing nitrification in current and future bioreactor configurations.}, }
@article {pmid32180337, year = {2020}, author = {Spanoghe, J and Grunert, O and Wambacq, E and Sakarika, M and Papini, G and Alloul, A and Spiller, M and Derycke, V and Stragier, L and Verstraete, H and Fauconnier, K and Verstraete, W and Haesaert, G and Vlaeminck, SE}, title = {Storage, fertilization and cost properties highlight the potential of dried microbial biomass as organic fertilizer.}, journal = {Microbial biotechnology}, volume = {13}, number = {5}, pages = {1377-1389}, pmid = {32180337}, issn = {1751-7915}, mesh = {Agriculture ; Biomass ; Fertilization ; *Fertilizers ; Nitrogen/analysis ; *Soil ; Spirulina ; }, abstract = {The transition to sustainable agriculture and horticulture is a societal challenge of global importance. Fertilization with a minimum impact on the environment can facilitate this. Organic fertilizers can play an important role, given their typical release pattern and production through resource recovery. Microbial fertilizers (MFs) constitute an emerging class of organic fertilizers and consist of dried microbial biomass, for instance produced on effluents from the food and beverage industry. In this study, three groups of organisms were tested as MFs: a high-rate consortium aerobic bacteria (CAB), the microalga Arthrospira platensis ('Spirulina') and a purple non-sulfur bacterium (PNSB) Rhodobacter sp. During storage as dry products, the MFs showed light hygroscopic activity, but the mineral and organic fractions remained stable over a storage period of 91 days. For biological tests, a reference organic fertilizer (ROF) was used as positive control, and a commercial organic growing medium (GM) as substrate. The mineralization patterns without and with plants were similar for all MFs and ROF, with more than 70% of the organic nitrogen mineralized in 77 days. In a first fertilization trial with parsley, all MFs showed equal performance compared to ROF, and the plant fresh weight was even higher with CAB fertilization. CAB was subsequently used in a follow-up trial with petunia and resulted in elevated plant height, comparable chlorophyll content and a higher amount of flowers compared to ROF. Finally, a cost estimation for packed GM with supplemented fertilizer indicated that CAB and a blend of CAB/PNSB (85%/15%) were most cost competitive, with an increase of 6% and 7% in cost compared to ROF. In conclusion, as bio-based fertilizers, MFs have the potential to contribute to sustainable plant nutrition, performing as good as a commercially available organic fertilizer, and to a circular economy.}, }
@article {pmid32179899, year = {2020}, author = {Byers, AK and Condron, L and Donavan, T and O'Callaghan, M and Patuawa, T and Waipara, N and Black, A}, title = {Soil microbial diversity in adjacent forest systems - contrasting native, old growth kauri (Agathis australis) forest with exotic pine (Pinus radiata) plantation forest.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {5}, pages = {}, pmid = {32179899}, issn = {1574-6941}, mesh = {Ecosystem ; Forests ; New Zealand ; *Pinus ; RNA, Ribosomal, 16S/genetics ; Soil ; Soil Microbiology ; }, abstract = {Globally, the conversion of primary forests to plantations and agricultural landscapes is a common land use change. Kauri (Agathis australis) is one of the most heavily impacted indigenous tree species of New Zealand with <1% of primary forest remaining as fragments adjacent to pastoral farming and exotic forest plantations. By contrasting two forest systems, we investigated if the fragmentation of kauri forests and introduction of pine plantations (Pinus radiata) are significantly impacting the diversity and composition of soil microbial communities across Waipoua kauri forest, New Zealand. Using next generation based 16S rRNA and ITS gene region sequencing, we identified that fungal and bacterial community composition significantly differed between kauri and pine forest soils. However, fungal communities displayed the largest differences in diversity and composition. This research revealed significant shifts in the soil microbial communities surrounding remnant kauri fragments, including the loss of microbial taxa with functions in disease suppression and plant health. Kauri dieback disease, caused by Phytophthora agathidicida, currently threatens the kauri forest ecosystem. Results from this research highlight the need for further investigations into how changes to soil microbial diversity surrounding remnant kauri fragments impact tree health and disease expression.}, }
@article {pmid32179343, year = {2020}, author = {Gurmessa, B and Pedretti, EF and Cocco, S and Cardelli, V and Corti, G}, title = {Manure anaerobic digestion effects and the role of pre- and post-treatments on veterinary antibiotics and antibiotic resistance genes removal efficiency.}, journal = {The Science of the total environment}, volume = {721}, number = {}, pages = {137532}, doi = {10.1016/j.scitotenv.2020.137532}, pmid = {32179343}, issn = {1879-1026}, mesh = {Anaerobiosis ; Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Microbial/drug effects ; Genes, Bacterial/drug effects ; *Manure ; }, abstract = {This review was aimed to summarize and critically evaluate studies on removal of veterinary antibiotics (VAs), antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) with anaerobic digestion (AD) of manure and demonstrate areas of focus for improved removal efficiency. The environmental risks associated to the release of the same were also critically evaluated. The potential of AD and advanced AD of manure on removal rate of VAs, ARGs and MGEs was thoroughly assessed. In addition, the role of post and pre-AD treatments and their potential to support VAs and ARGs removal efficiency were evaluated. The overall review results show disparity among the different groups of VAs in terms of removal rate with relatively higher efficiency for β-lactams and tetracyclines compared to the other groups. Some of sulfonamides, fluoroquinolones and macrolides were reported to be highly persistent with removal rates as low as zero. Within group differences were also reported in many literatures. Moreover, removal of ARGs and MGEs by AD was widely reported although complete removal was hardly possible. Even in rare scenarios, some AD conditions were reported to increase copies of specific groups of the genes. Temperature pretreatments and temperature phased advanced AD were also reported to improve removal efficiency of VAs while contributing to increased biogas production. Moreover, a few studies also showed the possibility of further removal by post-AD treatments such as liquid-solid separation, drying and composting. In conclusion, the various studies revealed that AD in its current technological level is not a guarantee for complete removal of VAs, ARGs and MGEs from manure. Consequently, their possible release to the soils with digestate could threaten the healthcare and disturb soil microbial ecology. Thus, intensive management strategies need to be designed to increase removal efficiency at the different manure management points along the anaerobic digestion process.}, }
@article {pmid32175570, year = {2020}, author = {Ruiz, C and Villegas-Plazas, M and Thomas, OP and Junca, H and Pérez, T}, title = {Specialized microbiome of the cave-dwelling sponge Plakina kanaky (Porifera, Homoscleromorpha).}, journal = {FEMS microbiology ecology}, volume = {96}, number = {4}, pages = {}, doi = {10.1093/femsec/fiaa043}, pmid = {32175570}, issn = {1574-6941}, mesh = {Animals ; *Microbiota ; Phylogeny ; *Porifera ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The recent description of the polychromatic sponge Plakina kanaky revealed original microsymbionts, with some morphotypes recorded for the first time in Homoscleromorpha and others never before observed in other sponge groups. Illumina 16S amplicon sequencing was used to characterize this microbial community by comparing contents of seven specimens of this Plakinidae with five other sponge species: one Homoscleromopha of the Oscarellidae family and four Demospongiae. A total of 256 458 sequences of the hypervariable V5-V6 region of the 16S rRNA gene were clustered into 2,829 OTUs at 97% similarity, with Proteobacteria, Poribacteria and Chloroflexi being the most abundant phyla. The Plakina kanaky specific community appeared to be mainly composed by five OTUs representing about 10% of the total microbiome. Among these, the filamentous bacterium Candidatus Entotheonella, which was among the dominant morphotypes previously observed in the mesohyl and the larvae of P. kanaky, was detected in all studied specimens. However, other original and dominant morphotypes could not be assigned to a known prokaryotic taxon. This cave dwelling sponge species harbors a distinctive microbiome composition of potential taxonomic and metabolic novelties that may be linked to its ecological success in such extreme environments.}, }
@article {pmid32172072, year = {2020}, author = {Wen, D and Valencia, A and Ordonez, D and Chang, NB and Wanielista, M}, title = {Comparative nitrogen removal via microbial ecology between soil and green sorption media in a rapid infiltration basin for co-disposal of stormwater and wastewater.}, journal = {Environmental research}, volume = {184}, number = {}, pages = {109338}, doi = {10.1016/j.envres.2020.109338}, pmid = {32172072}, issn = {1096-0953}, mesh = {Ammonia ; Denitrification ; *Nitrogen ; Oxidation-Reduction ; Soil ; *Wastewater ; }, abstract = {In this study, a rapid infiltration basin (RIB) designed as green infrastructure for co-disposal of wastewater effluent and stormwater runoff was retrofitted for sustainable groundwater recharge after nitrogen removal. For comparison of nitrogen removal efficiency via different filtration media, the RIB was divided into two sub-basins for different filtration processes. One sub-basin was filled with a native sandy soil with about 2-4% clay (Control RIB), and the other sub-basin was modified with Biosorption Activated Media (BAM) (BAM RIB), for the enhancement of microbial nitrogen removal. The two sub-basins accept an equal amount of excess reclaimed wastewater in non-storm periods, and stormwater during periodic storm events. The infiltrate in both the BAM RIB and the Control RIB eventually reaches the Upper Floridan Aquifer. The seven microbial species involved in this microbial ecology study are nitrite oxidizing bacteria (NOB), ammonia oxidizing bacteria (AOB), anaerobic oxidation of ammonium (anammox) bacteria, complete ammonia oxidizer (Comammox) bacteria, denitrifiers, dissimilatory nitrate reduction to ammonium (DNRA) and ammonia-oxidizing archaea (AOA). The population dynamics study was conducted with the aid of the quantitative polymerase chain reaction (qPCR) for the quantification of the microbial gene population in support of microbial ecology discovery. The qPCR results demonstrated the competition effect between AOA, AOB, and Comammox, the inhibition effect between NOB and DNRA with the presence of anammox, and the complementary effect due to an abundance of NOB and AOB in the microbial ecology. Although, competition between denitrifiers and DNRA was expected to impact population dynamics, both microbial species were found to be the most predominant in both control and BAM RIBs. Research findings indicate that the use of BAM RIB achieves significantly efficient nitrogen removal driven by complementary effects in the microbial ecology.}, }
@article {pmid32171709, year = {2020}, author = {Garin-Fernandez, A and Glöckner, FO and Wichels, A}, title = {Genomic characterization of filamentous phage vB_VpaI_VP-3218, an inducible prophage of Vibrio parahaemolyticus.}, journal = {Marine genomics}, volume = {53}, number = {}, pages = {100767}, doi = {10.1016/j.margen.2020.100767}, pmid = {32171709}, issn = {1876-7478}, mesh = {*Genome, Viral ; Inoviridae/*genetics ; North Sea ; Prophages/*genetics ; Vibrio parahaemolyticus/*virology ; Virus Activation ; }, abstract = {The seawater temperature rise can promote the growth of potentially pathogenic Vibrio species. In the North Sea, V. parahaemolyticus strains have been isolated and characterized. These strains contain prophages that may contribute to the emergence of pathogenic strains in the marine environment. Here, we present the genome structure and possible biological functions of the inducible phage vB_VpaI_VP-3218, a novel filamentous phage carried by the V. parahaemolyticus strain VN-3218. Prophages of the strain VN-3218 were induced with mitomycin C and the DNA from the phage induction was sequenced. Two incomplete prophages were identified, only one complete phage genome with length of 11,082 bp was characterized. The phage vB_VpaI_VP-3218 belongs to the Inoviridae family and shows close homology to the Saetivirus genus. This phage can integrate into the chromosomal host genome and carries host-related regions absent in similar phage genomes, suggesting that this phage might integrate in other Vibrio host genomes from the environment. Furthermore, this phage might have a role in pathogenicity due to potential zonula occludens toxin genes. Based on its genomic similarity, the genome of vB_VpaI_VP-3218 phage probably integrates into the lysogen's chromosome and replicates as episome. This study complements prophage induction and bioinformatic studies applied to non-model species of potentially pathogenic Vibrio species. The characterization of this phage provides new insights with respect to the presence of filamentous phages in environmental V. parahaemolyticus strains, which might have a role in the emergence of new pathogenic strains in the North Sea.}, }
@article {pmid32169939, year = {2020}, author = {Props, R and Denef, VJ}, title = {Temperature and Nutrient Levels Correspond with Lineage-Specific Microdiversification in the Ubiquitous and Abundant Freshwater Genus Limnohabitans.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {10}, pages = {}, pmid = {32169939}, issn = {1098-5336}, mesh = {Comamonadaceae/classification/*genetics/*physiology ; *Gene Expression ; *Genes, Bacterial ; *Genetic Variation ; Lakes/microbiology ; Michigan ; Microbiota ; Nutrients ; Temperature ; }, abstract = {Most freshwater bacterial communities are characterized by a few dominant taxa that are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic diversity within these taxonomic groups is limited to a subset of taxa. Here, we investigated the genomic diversity that enables Limnohabitans, a freshwater genus key in funneling carbon from primary producers to higher trophic levels, to achieve abundance and ubiquity. We reconstructed eight putative Limnohabitans metagenome-assembled genomes (MAGs) from stations located along broad environmental gradients existing in Lake Michigan, part of Earth's largest surface freshwater system. De novo strain inference analysis resolved a total of 23 strains from these MAGs, which strongly partitioned into two habitat-specific clusters with cooccurring strains from different lineages. The largest number of strains belonged to the abundant LimB lineage, for which robust in situ strain delineation had not previously been achieved. Our data show that temperature and nutrient levels may be important environmental parameters associated with microdiversification within the Limnohabitans genus. In addition, strains predominant in low- and high-phosphorus conditions had larger genomic divergence than strains abundant under different temperatures. Comparative genomics and gene expression analysis yielded evidence for the ability of LimB populations to exhibit cellular motility and chemotaxis, a phenotype not yet associated with available Limnohabitans isolates. Our findings broaden historical marker gene-based surveys of Limnohabitans microdiversification and provide in situ evidence of genome diversity and its functional implications across freshwater gradients.IMPORTANCELimnohabitans is an important bacterial taxonomic group for cycling carbon in freshwater ecosystems worldwide. Here, we examined the genomic diversity of different Limnohabitans lineages. We focused on the LimB lineage of this genus, which is globally distributed and often abundant, and its abundance has shown to be largely invariant to environmental change. Our data show that the LimB lineage is actually comprised of multiple cooccurring populations for which the composition and genomic characteristics are associated with variations in temperature and nutrient levels. The gene expression profiles of this lineage suggest the importance of chemotaxis and motility, traits that had not yet been associated with the Limnohabitans genus, in adapting to environmental conditions.}, }
@article {pmid32167574, year = {2020}, author = {Paramasivan, S and Bassiouni, A and Shiffer, A and Dillon, MR and Cope, EK and Cooksley, C and Ramezanpour, M and Moraitis, S and Ali, MJ and Bleier, B and Callejas, C and Cornet, ME and Douglas, RG and Dutra, D and Georgalas, C and Harvey, RJ and Hwang, PH and Luong, AU and Schlosser, RJ and Tantilipikorn, P and Tewfik, MA and Vreugde, S and Wormald, PJ and Caporaso, JG and Psaltis, AJ}, title = {The international sinonasal microbiome study: A multicentre, multinational characterization of sinonasal bacterial ecology.}, journal = {Allergy}, volume = {75}, number = {8}, pages = {2037-2049}, doi = {10.1111/all.14276}, pmid = {32167574}, issn = {1398-9995}, mesh = {Bacteria/genetics ; Chronic Disease ; Humans ; *Microbiota ; *Paranasal Sinuses ; RNA, Ribosomal, 16S/genetics ; *Sinusitis/epidemiology ; }, abstract = {The sinonasal microbiome remains poorly defined, with our current knowledge based on a few cohort studies whose findings are inconsistent. Furthermore, the variability of the sinus microbiome across geographical divides remains unexplored. We characterize the sinonasal microbiome and its geographical variations in both health and disease using 16S rRNA gene sequencing of 410 individuals from across the world. Although the sinus microbial ecology is highly variable between individuals, we identify a core microbiome comprised of Corynebacterium, Staphylococcus, Streptococcus, Haemophilus and Moraxella species in both healthy and chronic rhinosinusitis (CRS) cohorts. Corynebacterium (mean relative abundance = 44.02%) and Staphylococcus (mean relative abundance = 27.34%) appear particularly dominant in the majority of patients sampled. Amongst patients suffering from CRS with nasal polyps, a statistically significant reduction in relative abundance of Corynebacterium (40.29% vs 50.43%; P = .02) was identified. Despite some measured differences in microbiome composition and diversity between some of the participating centres in our cohort, these differences would not alter the general pattern of core organisms described. Nevertheless, atypical or unusual organisms reported in short-read amplicon sequencing studies and that are not part of the core microbiome should be interpreted with caution. The delineation of the sinonasal microbiome and standardized methodology described within our study will enable further characterization and translational application of the sinus microbiota.}, }
@article {pmid32162597, year = {2020}, author = {van Hougenhouck-Tulleken, WG and Lebre, PH and Said, M and Cowan, DA}, title = {Bacterial pathogens in peritoneal dialysis peritonitis: Insights from next-generation sequencing.}, journal = {Peritoneal dialysis international : journal of the International Society for Peritoneal Dialysis}, volume = {40}, number = {6}, pages = {581-586}, doi = {10.1177/0896860820908473}, pmid = {32162597}, issn = {1718-4304}, mesh = {Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Peritoneal Dialysis/adverse effects ; *Peritonitis/etiology ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Peritoneal dialysis (PD) peritonitis is a feared complication of PD, with significant sequelae for the patient. The cause of PD peritonitis is largely due to a single organism (≥75% of cases) and rarely due to multiple organisms.<br><br>METHODS: In this pilot study, we investigated 25 cases of PD peritonitis with 16S ribosomal RNA (rRNA) next-generation sequencing (NGS) techniques.<br><br>RESULTS: Total concordance between culture and NGS was noted. In addition, the NGS technique was highly sensitive, identifying 33 different bacteria (including a nonculturable bacterium), compared to 13 bacterial species using culture-based techniques. This was counterbalanced by a lack of specificity with NGS, largely due to the small size of the 16S rRNA gene segment sequenced.<br><br>CONCLUSIONS: For the clinician, our results suggest that PD peritonitis may often be a polymicrobial disease and that treating a dominant organism may not totally eradicate all bacterial contamination within the peritoneum. For the clinical scientist, additional use of a larger 16S rRNA segment (V5 or V6) is likely to outperform the use of the V4 segment only.}, }
@article {pmid32162039, year = {2020}, author = {Neissi, A and Rafiee, G and Farahmand, H and Rahimi, S and Mijakovic, I}, title = {Cold-Resistant Heterotrophic Ammonium and Nitrite-Removing Bacteria Improve Aquaculture Conditions of Rainbow Trout (Oncorhynchus mykiss).}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {266-277}, pmid = {32162039}, issn = {1432-184X}, support = {CTS17:312//Carl Tryggers Foundation/ ; 96016671//Iran National Science Foundation/ ; }, mesh = {Ammonium Compounds/*metabolism ; Animals ; *Aquaculture ; Bacteria/*metabolism ; Heterotrophic Processes ; Nitrites/*metabolism ; *Oncorhynchus mykiss/growth &amp; development ; }, abstract = {The aim of this study was isolation and characterization of heterotrophic bacteria capable of ammonium and nitrite removal at 15 °C (optimal temperature for growing rainbow trout Oncorhynchus mykiss). Environmental isolates were grown in liquid media containing ammonium or nitrite, and best strains in terms of growth and ammonium or nitrite removal were identified via 16S rRNA sequencing. Dyadobacter sp. (no. 68) and Janthinobacterium sp. (no. 100) were selected for optimal adaptation to growth at 15 °C and best ammonium and nitrite removal (P < 0.05), respectively. A heterotrophic ammonium and nitrite removal (HAN) microbial complex, containing selected strains, was prepared and applied in a trout culture system. After 10 days, the effect of microbial HAN complex was investigated in terms of ammonium and nitrite removal, as well as stress and immune indices present in the plasma of cultivated trout. Compared to a standard cultivation setup, addition of the HAN complex had a clear beneficial effect on keeping the un-ionized ammonia and nitrite level below prescribed standards (P < 0.05). This resulted in reduction of stress and immune reactions of cultivated fish (P < 0.05), leading to an augmentation of final weight and survival. Application of the selected microbial complex resulted in a significant improvement of the aquaculture ecosystem.}, }
@article {pmid32157881, year = {2020}, author = {Glodowska, M and Stopelli, E and Schneider, M and Lightfoot, A and Rathi, B and Straub, D and Patzner, M and Duyen, VT and ,  and Berg, M and Kleindienst, S and Kappler, A}, title = {Role of in Situ Natural Organic Matter in Mobilizing As during Microbial Reduction of Fe[III]-Mineral-Bearing Aquifer Sediments from Hanoi (Vietnam).}, journal = {Environmental science &amp; technology}, volume = {54}, number = {7}, pages = {4149-4159}, doi = {10.1021/acs.est.9b07183}, pmid = {32157881}, issn = {1520-5851}, mesh = {*Arsenic ; Ferric Compounds ; Geologic Sediments ; *Groundwater ; Minerals ; Oxidation-Reduction ; RNA, Ribosomal, 16S ; Vietnam ; }, abstract = {Natural organic matter (NOM) can contribute to arsenic (As) mobilization as an electron donor for microbially-mediated reductive dissolution of As-bearing Fe(III) (oxyhydr)oxides. However, to investigate this process, instead of using NOM, most laboratory studies used simple fatty acids or sugars, often at relatively high concentrations. To investigate the role of relevant C sources, we therefore extracted in situ NOM from the upper aquitard (clayey silt) and lower sandy aquifer sediments in Van Phuc (Hanoi area, Vietnam), characterized its composition, and used 100-day microcosm experiments to determine the effect of in situ OM on Fe(III) mineral reduction, As mobilization, and microbial community composition. We found that OM extracted from the clayey silt (OMC) aquitard resembles young, not fully degraded plant-related material, while OM from the sandy sediments (OMS) is more bioavailable and related to microbial biomass. Although all microcosms were amended with the same amount of C (12 mg C/L), the extent of Fe(III) reduction after 100 days was the highest with acetate/lactate (43 ± 3.5% of total Fe present in the sediments) followed by OMS (28 ± 0.3%) and OMC (19 ± 0.8%). Initial Fe(III) reduction rates were also higher with acetate/lactate (0.53 mg Fe(II) in 6 days) than with OMS and OMC (0.18 and 0.08 mg Fe(II) in 6 days, respectively). Although initially more dissolved As was detected in the acetate/lactate setups, after 100 days, higher concentrations of As (8.3 ± 0.3 and 8.8 ± 0.8 μg As/L) were reached in OMC and OMS, respectively, compared to acetate/lactate-amended setups (6.3 ± 0.7 μg As/L). 16S rRNA amplicon sequence analyses revealed that acetate/lactate mainly enriched Geobacter, while in situ OM supported growth and activity of a more diverse microbial community. Our results suggest that although the in situ NOM is less efficient in stimulating microbial Fe(III) reduction than highly bioavailable acetate/lactate, it ultimately has the potential to mobilize the same amount or even more As.}, }
@article {pmid32157374, year = {2020}, author = {Stastney, P and Black, S}, title = {Bog Microtopography and the Climatic Sensitivity of Testate Amoeba Communities: Implications for Transfer Function-Based Paleo-Water Table Reconstructions.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {309-321}, doi = {10.1007/s00248-020-01499-5}, pmid = {32157374}, issn = {1432-184X}, mesh = {Amoebozoa/classification/*isolation &amp; purification ; Archaeology/*methods ; *Climate ; Climate Change ; Ecology/*methods ; Groundwater/*parasitology ; Ireland ; *Wetlands ; }, abstract = {Although the use of sub-fossil testate amoebae as a proxy for raised bog hydrology in Holocene paleoecological studies is well-established, some detailed aspects of species-environment relationships remain under-researched. One such issue is the effect of bog surface microtopography on the climatic sensitivity of testate amoeba communities. Although it has been suggested that some microforms-especially hummocks-may be less sensitive to climatic forcing than others, this has rarely been objectively tested. To investigate this, subfossil testate amoebae assemblages have been examined in a series of shallow cores collected along a hummock-lawn-hollow transect from a bog in central Ireland and the resulting reconstructed water table records, dated using [210]Pb, have been compared with instrumental weather data. Testate amoebae communities in the hollow microform were found to be significantly less diverse than those in the hummock and lawn, and both the hummock and lawn showed statistically significant correlations with instrumental temperature and precipitation data. Therefore, whilst the suggestion that paleoecological investigations should target intermediate bog microforms remains sound, the notion that hummock-based testate amoebae hydrological data are climatically-insensitive is challenged.}, }
@article {pmid32156798, year = {2020}, author = {Alteio, LV and Schulz, F and Seshadri, R and Varghese, N and Rodriguez-Reillo, W and Ryan, E and Goudeau, D and Eichorst, SA and Malmstrom, RR and Bowers, RM and Katz, LA and Blanchard, JL and Woyke, T}, title = {Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil.}, journal = {mSystems}, volume = {5}, number = {2}, pages = {}, pmid = {32156798}, issn = {2379-5077}, abstract = {Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this "uncultivated majority" remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Bacteroidetes Analysis of 67 Bacteroidetes sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages.IMPORTANCE Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented Bacteroidetes phylum provided insights into conserved and clade-specific patterns of carbon metabolism.}, }
@article {pmid32155967, year = {2020}, author = {Cabello-Olmo, M and Oneca, M and Torre, P and Díaz, JV and Encio, IJ and Barajas, M and Araña, M}, title = {Influence of Storage Temperature and Packaging on Bacteria and Yeast Viability in a Plant-Based Fermented Food.}, journal = {Foods (Basel, Switzerland)}, volume = {9}, number = {3}, pages = {}, pmid = {32155967}, issn = {2304-8158}, support = {Reference: PT022 SIMDIACOL//Advanced Innovation &amp; Technology Corporation (ADItech Corp, Department of Economic Development, Navarre Government)/ ; Reference: 001114082016000011//Miriam Cabello-Olmo was granted by the Industrial PhD program (Navarre Government)/ ; }, abstract = {Optimization of food storage has become a central issue for food science and biotechnology, especially in the field of functional foods. The aim of this work was to investigate the influence of different storage strategies in a fermented food product (FFP) and further determine whether the regular storage (room temperature (RT) and standard packaging (SP)) could be refined. Eight experimental conditions (four different temperatures × two packaging) were simulated and changes in FFP's microbial ecology (total bacteria, lactic acid bacteria (LAB), and yeasts) and physicochemical characteristics (pH and moisture content (MC)) were determined following 1, 3, 6, and 12 months. All conditions tested showed a decline in microbial content due to the effect of the temperature, 37 °C being the most detrimental condition, while -20 and 4 °C seemed to be better than RT in some parameters. Vacuum packaging (VP) only had a major effect on MC and we found that VP preserved greater MC values than SP at 3, 6, and 12 months. The correlation analysis revealed that total bacteria, LAB, and yeasts were positively associated, and also both pH and MC showed a correlation. According to our results and with the purpose to maintain the load of viable microorganisms, we observed that the best storage conditions should contemplate SP and freezing or cooling temperature during a period no longer than 3 months.}, }
@article {pmid32155432, year = {2020}, author = {Moscoviz, R and Quéméner, ED and Trably, E and Bernet, N and Hamelin, J}, title = {Novel Outlook in Microbial Ecology: Nonmutualistic Interspecies Electron Transfer.}, journal = {Trends in microbiology}, volume = {28}, number = {4}, pages = {245-253}, doi = {10.1016/j.tim.2020.01.008}, pmid = {32155432}, issn = {1878-4380}, mesh = {Bacteria ; Biotechnology ; *Ecology ; Electrodes ; *Electron Transport ; *Electrons ; Energy Metabolism ; Fermentation ; Microbiota/*physiology ; }, abstract = {Recent advances in microbial electrochemical technologies have revealed the existence of numerous and highly diverse microorganisms able to exchange electrons with electrodes. This diversity could reflect the capacity of microorganisms to release and/or retrieve electrons with each other in natural environments. So far, this interspecies electron transfer has been studied with a special focus on syntrophy and was successfully demonstrated for several couples of species. In this article we argue that electron exchange between microbes exists beyond syntrophy or mutualism and could also promote competitive and even parasitic behaviour. Based on three interesting case studies identified from the literature, we also highlight that such nonmutualistic interactions could be widespread and of particular significance for the survival of pathogens or the shaping of complex microbial communities.}, }
@article {pmid32155265, year = {2020}, author = {Mukherjee, S and Naha, S and Bhadury, P and Saha, B and Dutta, M and Dutta, S and Basu, S}, title = {Emergence of OXA-232-producing hypervirulent Klebsiella pneumoniae ST23 causing neonatal sepsis.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {75}, number = {7}, pages = {2004-2006}, doi = {10.1093/jac/dkaa080}, pmid = {32155265}, issn = {1460-2091}, mesh = {Humans ; Infant, Newborn ; *Klebsiella Infections ; Klebsiella pneumoniae/genetics ; *Neonatal Sepsis/epidemiology ; beta-Lactamases/genetics ; }, }
@article {pmid32153553, year = {2020}, author = {Cliffe, L and Nixon, SL and Daly, RA and Eden, B and Taylor, KG and Boothman, C and Wilkins, MJ and Wrighton, KC and Lloyd, JR}, title = {Identification of Persistent Sulfidogenic Bacteria in Shale Gas Produced Waters.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {286}, pmid = {32153553}, issn = {1664-302X}, abstract = {Produced waters from hydraulically fractured shale formations give insight into the microbial ecology and biogeochemical conditions down-well. This study explores the potential for sulfide production by persistent microorganisms recovered from produced water samples collected from the Marcellus shale formation. Hydrogen sulfide is highly toxic and corrosive, and can lead to the formation of "sour gas" which is costly to refine. Furthermore, microbial colonization of hydraulically fractured shale could result in formation plugging and a reduction in well productivity. It is vital to assess the potential for sulfide production in persistent microbial taxa, especially when considering the trend of reusing produced waters as input fluids, potentially enriching for problematic microorganisms. Using most probable number (MPN) counts and 16S rRNA gene sequencing, multiple viable strains of bacteria were identified from stored produced waters, mostly belonging to the Genus Halanaerobium, that were capable of growth via fermentation, and produced sulfide when supplied with thiosulfate. No sulfate-reducing bacteria (SRB) were detected through culturing, despite the detection of relatively low numbers of sulfate-reducing lineages by high-throughput 16S rRNA gene sequencing. These results demonstrate that sulfidogenic produced water populations remain viable for years post production and, if left unchecked, have the potential to lead to natural gas souring during shale gas extraction.}, }
@article {pmid32151461, year = {2019}, author = {Chriswell, ME and Kuhn, KA}, title = {Microbiota-mediated mucosal inflammation in arthritis.}, journal = {Best practice &amp; research. Clinical rheumatology}, volume = {33}, number = {6}, pages = {101492}, pmid = {32151461}, issn = {1532-1770}, support = {K08 DK107905/DK/NIDDK NIH HHS/United States ; R01 AR075033/AR/NIAMS NIH HHS/United States ; T32 AR007534/AR/NIAMS NIH HHS/United States ; }, mesh = {*Arthritis/microbiology ; Humans ; Immune Tolerance ; Immunity, Mucosal ; *Inflammation ; *Microbiota ; }, abstract = {Mucosal surfaces are a unique symbiotic environment between a host and a vast and diverse ecology of microbes. These microbes have great immunomodulatory potential with respect to the host organism. Indeed, the mucosal immune system strikes a delicate balance between tolerance of commensal organisms and overt inflammation to ward off pathogens. Disruptions of the microbial ecology at mucosal surfaces has been described in a vast number of different human disease processes including many forms of arthritis, and the resulting implications are still being understood to their fullest. Herein, we review the current state of knowledge in microbe-host interactions as it relates to the development of arthritis through bacterial translocation, bacterial metabolite production, education of the immune response, and molecular mimicry.}, }
@article {pmid32149022, year = {2020}, author = {Moore, RM and Harrison, AO and McAllister, SM and Polson, SW and Wommack, KE}, title = {Iroki: automatic customization and visualization of phylogenetic trees.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e8584}, pmid = {32149022}, issn = {2167-8359}, support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; }, abstract = {Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki's utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal http://virome.dbi.udel.edu. Iroki's source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.}, }
@article {pmid32144464, year = {2020}, author = {Nuzzo, A and Satpute, A and Albrecht, U and Strauss, SL}, title = {Impact of Soil Microbial Amendments on Tomato Rhizosphere Microbiome and Plant Growth in Field Soil.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {398-409}, doi = {10.1007/s00248-020-01497-7}, pmid = {32144464}, issn = {1432-184X}, support = {1011186//USDA-NIFA Hatch/ ; }, mesh = {Bacteria/classification/growth &amp; development/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Solanum lycopersicum/*growth &amp; development/*microbiology ; *Microbiota ; Mycorrhizae/*physiology ; *Rhizosphere ; Soil Microbiology ; Yeasts/*physiology ; }, abstract = {There is increased interest by the agricultural industry in microbial amendments that leverage natural beneficial interactions between plants and soil microbes to improve crop production. However, translating fundamental knowledge from laboratory experiments into efficient field application often has mixed results, and there is less clarity about the interaction between added microbes and the native microbial community, where microorganisms belonging to the same phylogenic clades often reside. In this study, four commercially available microbial amendments were examined in two greenhouse experiments using field soil to assess their impact on tomato plant growth and the native soil microbial communities. The amendments contained different formulations of plant growth-promoting bacteria (Lactobacilli, Rhizobia, etc.), yeasts, and mycorrhizal fungi. The application of the tested amendments in greenhouse conditions resulted in no significant impact on plant growth. A deeper statistical analysis detected variations in the microbial communities that accounted only for 0.25% of the total species, particularly in native taxa not related to the inoculated species and represented less than 1% of the total variance. This suggests that under commercial field conditions, additional confounding variables may play a role in the efficacy of soil microbial amendments. This study confirms the necessity of more in-depth validation requirements for the formulations of soil microbial amendments before delivery to the agricultural market in order to leverage their benefits for the producers, the consumers, and the environment.}, }
@article {pmid32144110, year = {2020}, author = {Zhang, Y and Hao, X and Garcia-Lemos, AM and Nunes, I and Nicolaisen, MH and Nybroe, O}, title = {Different Effects of Soil Fertilization on Bacterial Community Composition in the Penicillium canescens Hyphosphere and in Bulk Soil.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {10}, pages = {}, pmid = {32144110}, issn = {1098-5336}, mesh = {Bacteria/classification/*metabolism ; Fertilizers ; Hyphae/metabolism ; Microbiota ; *Nitrogen Cycle ; Penicillium/*metabolism ; Phosphorus/*metabolism ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {This study investigated the effects of long-term soil fertilization on the composition and potential for phosphorus (P) and nitrogen (N) cycling of bacterial communities associated with hyphae of the P-solubilizing fungus Penicillium canescens Using a baiting approach, hyphosphere bacterial communities were recovered from three soils that had received long-term amendment in the field with mineral or mineral plus organic fertilizers. P. canescens hyphae recruited bacterial communities with a decreased diversity and an increased abundance of Proteobacteria relative to what was observed in soil communities. As core bacterial taxa, Delftia and Pseudomonas spp. were present in all hyphosphere samples irrespective of soil fertilization. However, the type of fertilization showed significant impacts on the diversity, composition, and distinctive taxa/operational taxonomic units (OTUs) of hyphosphere communities. The soil factors P (Olsen method), exchangeable Mg, exchangeable K, and pH were important for shaping soil and hyphosphere bacterial community compositions. An increased relative abundance of organic P metabolism genes was found in hyphosphere communities from soil that had not received P fertilizers, which could indicate P limitation near the fungal hyphae. Additionally, P. canescens hyphae recruited bacterial communities with a higher abundance of N fixation genes than found in soil communities, which might imply a role of hyphosphere communities for fungal N nutrition. Furthermore, the relative abundances of denitrification genes were greater in several hyphosphere communities, indicating an at least partly anoxic microenvironment with a high carbon-to-N ratio around the hyphae. In conclusion, soil fertilization legacy shapes P. canescens hyphosphere microbiomes and their functional potential related to P and N cycling.IMPORTANCE P-solubilizing Penicillium strains are introduced as biofertilizers to agricultural soils to improve plant P nutrition. Currently, little is known about the ecology of these biofertilizers, including their interactions with other soil microorganisms. This study shows that communities dominated by Betaproteobacteria and Gammaproteobacteria colonize P. canescens hyphae in soil and that the compositions of these communities depend on the soil conditions. The potential of these communities for N and organic P cycling is generally higher than that of soil communities. The high potential for organic P metabolism might complement the ability of the fungus to solubilize inorganic P, and it points to the hyphosphere as a hot spot for P metabolism. Furthermore, the high potential for N fixation could indicate that P. canescens recruits bacteria that are able to improve its N nutrition. Hence, this community study identifies functional groups relevant for the future optimization of next-generation biofertilizer consortia for applications in soil.}, }
@article {pmid32143053, year = {2020}, author = {Song, J and Jongmans-Hochschulz, E and Mauder, N and Imirzalioglu, C and Wichels, A and Gerdts, G}, title = {The Travelling Particles: Investigating microplastics as possible transport vectors for multidrug resistant E. coli in the Weser estuary (Germany).}, journal = {The Science of the total environment}, volume = {720}, number = {}, pages = {137603}, doi = {10.1016/j.scitotenv.2020.137603}, pmid = {32143053}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; *Escherichia coli ; Estuaries ; Germany ; Microbial Sensitivity Tests ; Microplastics ; North Sea ; beta-Lactamases ; }, abstract = {The prevalence of multidrug-resistant Gram-negative bacteria in aquatic environments has been a long withstanding health concern, namely extended-spectrum beta-lactamase (ESBL) producing Escherichia coli. Given increasing reports on microplastic (MP) pollution in these environments, it has become crucial to better understand the role of MP particles as transport vectors for such multidrug-resistant bacteria. In this study, an incubation experiment was designed where particles of both synthetic and natural material (HDPE, tyre wear, and wood) were sequentially incubated at multiple sites along a salinity gradient from the Lower Weser estuary (Germany) to the offshore island Helgoland (German Bight, North Sea). Following each incubation period, particle biofilms and water samples were assessed for ESBL-producing E. coli, first by the enrichment and detection of E. coli using Fluorocult® LMX Broth followed by cultivation on CHROMAgar™ ESBL media to select for ESBL-producers. Results showed that general E. coli populations were present on the surfaces of wood particles across all sites but none were found to produce ESBLs. Additionally, neither HDPE nor tyre wear particles were found to harbour any E. coli. Conversely, ESBL-producing E. coli were present in surrounding waters from all sites, 64% of which conferred resistances against up to 3 other antibiotic groups, additional to the beta-lactam resistances intrinsic to ESBL-producers. This study provides a first look into the potential of MP to harbour and transport multidrug-resistant E. coli across different environments and the approach serves as an important precursor to further studies on other potentially harmful MP-colonizing species.}, }
@article {pmid32140148, year = {2020}, author = {Pascoal, F and Magalhães, C and Costa, R}, title = {The Link Between the Ecology of the Prokaryotic Rare Biosphere and Its Biotechnological Potential.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {231}, pmid = {32140148}, issn = {1664-302X}, abstract = {Current research on the prokaryotic low abundance taxa, the prokaryotic rare biosphere, is growing, leading to a greater understanding of the mechanisms underlying organismal rarity and its relevance in ecology. From this emerging knowledge it is possible to envision innovative approaches in biotechnology applicable to several sectors. Bioremediation and bioprospecting are two of the most promising areas where such approaches could find feasible implementation, involving possible new solutions to the decontamination of polluted sites and to the discovery of novel gene variants and pathways based on the attributes of rare microbial communities. Bioremediation can be improved through the realization that diverse rare species can grow abundant and degrade different pollutants or possibly transfer useful genes. Further, most of the prokaryotic diversity found in virtually all environments belongs in the rare biosphere and remains uncultivatable, suggesting great bioprospecting potential within this vast and understudied genetic pool. This Mini Review argues that knowledge of the ecophysiology of rare prokaryotes can aid the development of future, efficient biotechnology-based processes, products and services. However, this promise may only be fulfilled through improvements in (and optimal blending of) advanced microbial culturing and physiology, metagenomics, genome annotation and editing, and synthetic biology, to name a few areas of relevance. In the future, it will be important to understand how activity profiles relate with abundance, as some rare taxa can remain rare and increase activity, whereas other taxa can grow abundant. The metabolic mechanisms behind those patterns can be useful in designing biotechnological processes.}, }
@article {pmid32138992, year = {2020}, author = {Charmpi, C and Van der Veken, D and Van Reckem, E and De Vuyst, L and Leroy, F}, title = {Raw meat quality and salt levels affect the bacterial species diversity and community dynamics during the fermentation of pork mince.}, journal = {Food microbiology}, volume = {89}, number = {}, pages = {103434}, doi = {10.1016/j.fm.2020.103434}, pmid = {32138992}, issn = {1095-9998}, mesh = {Animals ; Fermentation ; *Food Microbiology ; Lactobacillus/*genetics ; Meat Products/*microbiology ; Pork Meat/*microbiology ; Sodium Chloride, Dietary ; Staphylococcus/*genetics ; Swine ; }, abstract = {Acidification level and temperature modulate the beneficial consortia of lactic acid bacteria (LAB) and coagulase-negative staphylococci (CNS) during meat fermentation. Less is known about the impact of other factors, such as raw meat quality and salting. These could for instance affect the growth of the pathogen Staphylococcus aureus or of Enterobacterales species, potentially indicative of poor fermentation practice. Therefore, pork batters from either normal or borderline quality (dark-firm-dry, DFD) were compared at various salt concentrations (0-4%) in meat fermentation models. Microbial ecology of the samples was investigated with culture-dependent techniques and (GTG)5-PCR fingerprinting of genomic DNA. Whilst Lactobacillus sakei governed the fermentation of normal meat, Lactobacillus curvatus was more prominent in the fermentation of the DFD meat variant. CNS were favoured during fermentation at rising salt concentrations without much effects on species diversity, consisting mostly of Staphylococcus equorum, Staphylococcus saprophyticus, and Staphylococcus xylosus. During fermentation of DFD meat, S. saprophyticus was less manifest than during that of normal meat. Enterobacterales mainly emerged in DFD meat during fermentation at low salt concentrations. The salt hurdle was insufficient to prevent Enterobacterales when acidification and initial pH were favourable for their growth.}, }
@article {pmid32138583, year = {2020}, author = {Tian, Y and Gui, W and Koo, I and Smith, PB and Allman, EL and Nichols, RG and Rimal, B and Cai, J and Liu, Q and Patterson, AD}, title = {The microbiome modulating activity of bile acids.}, journal = {Gut microbes}, volume = {11}, number = {4}, pages = {979-996}, pmid = {32138583}, issn = {1949-0984}, support = {S10 OD021750/OD/NIH HHS/United States ; T32 GM102057/GM/NIGMS NIH HHS/United States ; U01 DK119702/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/drug effects/*growth &amp; development/*metabolism ; Bile Acids and Salts/administration &amp; dosage/*metabolism/*pharmacology ; Cecum/*microbiology ; *Gastrointestinal Microbiome ; Glycolysis ; Male ; Metabolomics ; Mice ; Mice, Inbred C57BL ; Microbial Sensitivity Tests ; Probiotics ; }, abstract = {Bile acids are potent antibacterial compounds and play an important role in shaping the microbial ecology of the gut. Here, we combined flow cytometry, growth rate measurements (OD600), and NMR- and mass spectrometry-based metabolomics to systematically profile the impact of bile acids on the microbiome using in vitro and in vivo models. This study confirmed that (1) unconjugated bile acids possess more potent antibacterial activity than conjugated bile acids; (2) Gram-positive bacteria are more sensitive to bile acids than Gram-negative bacteria; (3) some probiotic bacteria such as Lactobacillus and Bifidobacterium and 7α-dehydroxylating bacteria such as Clostridium scindens show bile acid resistance that is associated with activation of glycolysis. Moreover, we demonstrated that (4) as one of most hydrophobic bile acids, lithocholic acid (LCA) shows reduced toxicity to bacteria in the cecal microbiome in both in vivo and in vitro models; (5) bile acids directly and rapidly affect bacterial global metabolism including membrane damage, disrupted amino acid, nucleotide, and carbohydrate metabolism; and (6) in vivo, short-term exposure to bile acids significantly affected host metabolism via alterations of the bacterial community structure. This study systematically profiled interactions between bile acids and gut bacteria providing validation of previous observation and new insights into the interaction of bile acids with the microbiome and mechanisms related to bile acid tolerance.}, }
@article {pmid32138281, year = {2020}, author = {Gutiérrez-Sarmiento, W and Sáyago-Ayerdi, SG and Goñi, I and Gutiérrez-Miceli, FA and Abud-Archila, M and Rejón-Orantes, JDC and Rincón-Rosales, R and Peña-Ocaña, BA and Ruíz-Valdiviezo, VM}, title = {Changes in Intestinal Microbiota and Predicted Metabolic Pathways During Colonic Fermentation of Mango (Mangifera indica L.)-Based Bar Indigestible Fraction.}, journal = {Nutrients}, volume = {12}, number = {3}, pages = {}, pmid = {32138281}, issn = {2072-6643}, support = {6257.19-P//Tecnol&#xf3;gico Nacional de M&#xe9;xico/ ; Doctoral grant number 636047//Consejo Nacional de Ciencia y Tecnolog&#xed;a (CONACyT)/ ; }, mesh = {Adult ; Bacteria/classification/*growth &amp; development ; *Colon/metabolism/microbiology ; Dietary Fiber/*administration &amp; dosage/metabolism ; *Digestion ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; *Mangifera ; *Metabolic Networks and Pathways ; }, abstract = {Mango (Mangifera indica L.) peel and pulp are a source of dietary fiber (DF) and phenolic compounds (PCs) that constituent part of the indigestible fraction (IF). This fraction reaches the colon and acts as a carbon and energy source for intestinal microbiota. The effect of mango IF on intestinal microbiota during colonic fermentation is unknown. In this study, the isolated IF of a novel 'Ataulfo' mango-based bar (snack) UV-C irradiated and non-irradiated (UVMangoB and MangoB) were fermented. Colonic fermentation occurred in vitro under chemical-enzymatic, semi-anaerobic, batch culture and controlled pH colonic conditions. Changes in the structure of fecal microbiota were analyzed by 16s rRNA gene Illumina MiSeq sequencing. The community´s functional capabilities were determined in silico. The MangoB and UVMangoB increased the presence of Faecalibacterium, Roseburia, Eubacterium, Fusicatenibacter, Holdemanella, Catenibacterium, Phascolarctobacterium, Buttiauxella, Bifidobacterium, Collinsella, Prevotella and Bacteroides genera. The alpha indexes showed a decrease in microbial diversity after 6 h of colonic fermentation. The coordinates analysis indicated any differences between irradiated and non-irradiated bar. The metabolic prediction demonstrated that MangoB and UVMangoB increase the microbiota carbohydrate metabolism pathway. This study suggests that IF of mango-based bar induced beneficial changes on microbial ecology and metabolic pathway that could be promissory to prevention or treatment of metabolic dysbiosis. However, in vivo interventions are necessary to confirm the interactions between microbiota modulating and intestinal beneficial effects.}, }
@article {pmid32134703, year = {2020}, author = {Weis, S and Schnell, S and Egert, M}, title = {Towards safer stable isotope probing - effect of formamide on the separation of isotope-labeled and unlabeled Escherichia coli RNA by isopycnic density ultracentrifugation.}, journal = {Canadian journal of microbiology}, volume = {66}, number = {8}, pages = {491-494}, doi = {10.1139/cjm-2019-0612}, pmid = {32134703}, issn = {1480-3275}, mesh = {Carbon Isotopes/chemistry ; Centrifugation, Density Gradient/methods ; Escherichia coli/chemistry/*genetics ; Formamides/chemistry ; Isotope Labeling/methods ; RNA, Bacterial/chemistry/*genetics/*isolation &amp; purification ; Ultracentrifugation/methods ; }, abstract = {RNA-based stable isotope probing (RNA-SIP) is used in molecular microbial ecology to link the identity of microorganisms in a complex community with the assimilation of a distinct substrate. The technique is highly dependent on a reliable separation of isotopic-labeled RNA from unlabeled RNA by isopycnic density gradient ultracentrifugation. Here we show that [13]C-labeled and unlabeled Escherichia coli RNA can be sufficiently separated by isopycnic ultracentrifugation even in the absence of formamide. However, a slightly lower starting density is needed to obtain a distribution pattern similar to that obtained when formamide was used. Hence, the commonly used addition of formamide to the centrifugation solution might not be needed to separate [13]C-labeled RNA from unlabeled RNA, but this must be verified for more complex environmental mixtures of RNA. Clearly, an omission of formamide would increase the safety of RNA-SIP analyses.}, }
@article {pmid32132275, year = {2020}, author = {Gignoux-Wolfsohn, SA and Precht, WF and Peters, EC and Gintert, BE and Kaufman, LS}, title = {Ecology, histopathology, and microbial ecology of a white-band disease outbreak in the threatened staghorn coral Acropora cervicornis.}, journal = {Diseases of aquatic organisms}, volume = {137}, number = {3}, pages = {217-237}, doi = {10.3354/dao03441}, pmid = {32132275}, issn = {0177-5103}, mesh = {Animals ; *Anthozoa ; Bacteria ; Coral Reefs ; Disease Outbreaks ; Ecosystem ; Florida ; }, abstract = {This study is a multi-pronged description of a temperature-induced outbreak of white-band disease (WBD) that occurred in Acropora cervicornis off northern Miami Beach, Florida (USA), from July to October 2014. We describe the ecology of the disease and examine diseased corals using both histopathology and next-generation bacterial 16S gene sequencing, making it possible to better understand the effect this disease has on the coral holobiont, and to address some of the seeming contradictions among previous studies of WBD that employed either a purely histological or molecular approach. The outbreak began in July 2014, as sea surface temperatures reached 29°C, and peaked in mid-September, a month after the sea surface temperature maximum. The microscopic anatomy of apparently healthy portions of colonies displaying active disease signs appeared normal except for some tissue atrophy and dissociation of mesenterial filaments deep within the branch. Structural changes were more pronounced in visibly diseased fragments, with atrophy, necrosis, and lysing of surface and basal body wall and polyp structures at the tissue-loss margin. The only bacteria evident microscopically in both diseased and apparently healthy tissues with Giemsa staining was a Rickettsiales-like organism (RLO) occupying mucocytes. Sequencing also identified bacteria belonging to the order Rickettsiales in all fragments. When compared to apparently healthy fragments, diseased fragments had more diverse bacterial communities made up of many previously suggested potential primary pathogens and secondary (opportunistic) colonizers. Interactions between elevated seawater temperatures, the coral host, and pathogenic members of the diseased microbiome all contribute to the coral displaying signs of WBD.}, }
@article {pmid32131727, year = {2020}, author = {Mastrorilli, E and Petrin, S and Orsini, M and Longo, A and Cozza, D and Luzzi, I and Ricci, A and Barco, L and Losasso, C}, title = {Comparative genomic analysis reveals high intra-serovar plasticity within Salmonella Napoli isolated in 2005-2017.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {202}, pmid = {32131727}, issn = {1471-2164}, support = {GP/EFSA/AFSCO/2015/01/CT1//European Food Safety Authority/ ; }, mesh = {DNA, Bacterial/*genetics ; Drug Resistance, Multiple, Bacterial ; Genomic Islands ; Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; Italy ; Phylogeny ; Plasmids/genetics ; Salmonella Infections/*microbiology ; Salmonella enterica/*classification/genetics/immunology/isolation &amp; purification ; Serogroup ; Typhoid Fever/microbiology ; Whole Genome Sequencing/*methods ; beta-Lactam Resistance ; }, abstract = {BACKGROUND: Salmonella enterica subsp. enterica serovar Napoli (S. Napoli) is among the top serovars causing human infections in Italy, although it is relatively uncommon in other European countries; it is mainly isolated from humans and the environment, but neither the reservoir nor its route of infection are clearly defined. This serovar is characterized by high genomic diversity, and molecular evidences revealed important similarities with typhoidal serovars.<br><br>RESULTS: 179&#x2009;S. Napoli genomes as well as 239 genomes of typhoidal and non-typhoidal serovars were analyzed in a comparative genomic study. Phylogenetic analysis and draft genome characterization in terms of Multi Locus Sequence Typing (MLST), plasmid replicons, Salmonella Pathogenicity Islands (SPIs), antimicrobial resistance genes (ARGs), phages, biocide and metal-tolerance genes confirm the high genetic variability of S. Napoli, also revealing a within-serovar phylogenetic structure more complex than previously known. Our work also confirms genomic similarity of S. Napoli to typhoidal serovars (S. Typhi and S. Paratyphi A), with S. Napoli samples clustering primarily according to ST, each being characterized by specific genomic traits. Moreover, two major subclades of S. Napoli can be clearly identified, with ST-474 being biphyletic. All STs span among isolation sources and years of isolation, highlighting the challenge this serovar poses to define its epidemiology and evolution. Altogether, S. Napoli strains carry less SPIs and less ARGs than other non-typhoidal serovars and seldom acquire plasmids. However, we here report the second case of an extended-spectrum &#x3b2;-lactamases (ESBLs) producing S. Napoli strain and the first cases of multidrug resistant (MDR) S. Napoli strains, all isolated from humans.<br><br>CONCLUSIONS: Our results provide evidence of genomic plasticity of S. Napoli, highlighting genomic similarity with typhoidal serovars and genomic features typical of non-typhoidal serovars, supporting the possibility of survival in different niches, both enteric and non-enteric. Presence of horizontally acquired ARGs and MDR profiles rises concerns regarding possible selective pressure exerted by human environment on this pathogen.}, }
@article {pmid32128982, year = {2020}, author = {Tu, Q}, title = {Random sampling in metagenomic sequencing leads to overestimated spatial scaling of microbial diversity.}, journal = {Environmental microbiology}, volume = {22}, number = {6}, pages = {2140-2149}, doi = {10.1111/1462-2920.14973}, pmid = {32128982}, issn = {1462-2920}, support = {31700427//National Natural Science Foundation of China/International ; 31971446//National Natural Science Foundation of China/International ; LQ17D060002//Zhejiang Provincial Natural Science Foundation of China/International ; kf2016002//Open Project of Key Laboratory of Environmental Biotechnology, CAS/International ; SKYAM002-2016//Open Funding of State Key Laboratory of Applied Microbiology Southern China/International ; 2017C82218//Bureau of Science and Technology of Zhoushan/International ; //Qilu Young Scholarship of Shandong University/International ; }, mesh = {*Biodiversity ; Forests ; Geography ; Metagenome ; Metagenomics ; Microbiota/*genetics ; Random Allocation ; *Soil Microbiology ; }, abstract = {Revealing the spatial scaling patterns of microbial diversity is of special interest in microbial ecology. One critical question is whether the observed spatial turnover rate truly reflect the actual spatial patterns of extremely diverse microbial communities. Using simulated mock communities, this study suggested that the currently observed microbial spatial turnover rates were overestimated by random sampling processes associated with high-throughput metagenomic sequencing. The observed z values were largely contributed by accumulated microbial taxa due to cumulative number of samples. This is a crucial issue because microbial communities already have very low spatial turnover rate due to the small size and potential cosmopolitism nature of microorganisms. Further investigations suggested a linear relationship between the observed and expected z values, which can be applied to remove random sampling noises from the observed z values. Adjustment of z values for data sets from six American forests showed much lower spatial turnover rate than that before adjustment. However, the patterns of z values among these six forests remained unchanged. This study suggested that our current understanding of microbial taxa-area relationships could be inaccurate. Therefore, cautions and efforts should be made for more accurate estimation and interpretation of microbial spatial patterns.}, }
@article {pmid32127448, year = {2020}, author = {McClelland, HLO and Jones, C and Chubiz, LM and Fike, DA and Bradley, AS}, title = {Direct Observation of the Dynamics of Single-Cell Metabolic Activity during Microbial Diauxic Growth.}, journal = {mBio}, volume = {11}, number = {2}, pages = {}, pmid = {32127448}, issn = {2150-7511}, mesh = {Biomass ; Carbon/metabolism ; Isotope Labeling ; Methylobacterium extorquens/*growth &amp; development/*metabolism ; Nitrogen/metabolism ; Phenotype ; Single-Cell Analysis/*methods ; Spectrometry, Mass, Secondary Ion/methods ; }, abstract = {Population-level analyses are rapidly becoming inadequate to answer many of biomedical science and microbial ecology's most pressing questions. The role of microbial populations within ecosystems and the evolutionary selective pressure on individuals depend fundamentally on the metabolic activity of single cells. Yet, many existing single-cell technologies provide only indirect evidence of metabolic specialization because they rely on correlations between transcription and phenotype established at the level of the population to infer activity. In this study, we take a top-down approach using isotope labels and secondary ion mass spectrometry to track the uptake of carbon and nitrogen atoms from different sources into biomass and directly observe dynamic changes in anabolic specialization at the level of single cells. We investigate the classic microbiological phenomenon of diauxic growth at the single-cell level in the model methylotroph Methylobacterium extorquens In nature, this organism inhabits the phyllosphere, where it experiences diurnal changes in the available carbon substrates, necessitating an overhaul of central carbon metabolism. We show that the population exhibits a unimodal response to the changing availability of viable substrates, a conclusion that supports the canonical model but has thus far been supported by only indirect evidence. We anticipate that the ability to monitor the dynamics of anabolism in individual cells directly will have important applications across the fields of ecology, medicine, and biogeochemistry, especially where regulation downstream of transcription has the potential to manifest as heterogeneity that would be undetectable with other existing single-cell approaches.IMPORTANCE Understanding how genetic information is realized as the behavior of individual cells is a long-term goal of biology but represents a significant technological challenge. In clonal microbial populations, variation in gene regulation is often interpreted as metabolic heterogeneity. This follows the central dogma of biology, in which information flows from DNA to RNA to protein and ultimately manifests as activity. At present, DNA and RNA can be characterized in single cells, but the abundance and activity of proteins cannot. Inferences about metabolic activity usually therefore rely on the assumption that transcription reflects activity. By tracking the atoms from which they build their biomass, we make direct observations of growth rate and substrate specialization in individual cells throughout a period of growth in a changing environment. This approach allows the flow of information from DNA to be constrained from the distal end of the regulatory cascade and will become an essential tool in the rapidly advancing field of single-cell metabolism.}, }
@article {pmid32126162, year = {2020}, author = {Ntagia, E and Chatzigiannidou, I and Williamson, AJ and Arends, JBA and Rabaey, K}, title = {Homoacetogenesis and microbial community composition are shaped by pH and total sulfide concentration.}, journal = {Microbial biotechnology}, volume = {13}, number = {4}, pages = {1026-1038}, pmid = {32126162}, issn = {1751-7915}, mesh = {Acetates ; Fermentation ; Hydrogen-Ion Concentration ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sulfides ; }, abstract = {Biological CO2 sequestration through acetogenesis with H2 as electron donor is a promising technology to reduce greenhouse gas emissions. Today, a major issue is the presence of impurities such as hydrogen sulfide (H2 S) in CO2 containing gases, as they are known to inhibit acetogenesis in CO2 -based fermentations. However, exact values of toxicity and inhibition are not well-defined. To tackle this uncertainty, a series of toxicity experiments were conducted, with a mixed homoacetogenic culture, total dissolved sulfide concentrations ([TDS]) varied between 0 and 5 mM and pH between 5 and 7. The extent of inhibition was evaluated based on acetate production rates and microbial growth. Maximum acetate production rates of 0.12, 0.09 and 0.04 mM h[-1] were achieved in the controls without sulfide at pH 7, pH 6 and pH 5. The half-maximal inhibitory concentration (IC50 [qAc]) was 0.86, 1.16 and 1.36 mM [TDS] for pH 7, pH 6 and pH 5. At [TDS] above 3.33 mM, acetate production and microbial growth were completely inhibited at all pHs. 16S rRNA gene amplicon sequencing revealed major community composition transitions that could be attributed to both pH and [TDS]. Based on the observed toxicity levels, treatment approaches for incoming industrial CO2 streams can be determined.}, }
@article {pmid32125831, year = {2020}, author = {Hu, X and Kerckhof, FM and Ghesquière, J and Bernaerts, K and Boeckx, P and Clauwaert, P and Boon, N}, title = {Microbial Protein out of Thin Air: Fixation of Nitrogen Gas by an Autotrophic Hydrogen-Oxidizing Bacterial Enrichment.}, journal = {Environmental science &amp; technology}, volume = {54}, number = {6}, pages = {3609-3617}, doi = {10.1021/acs.est.9b06755}, pmid = {32125831}, issn = {1520-5851}, mesh = {*Autotrophic Processes ; Bacteria ; *Hydrogen ; Nitrogen ; Nitrogen Fixation ; Oxidation-Reduction ; }, abstract = {For the production of edible microbial protein (MP), ammonia generated by the Haber-Bosch process or reclaimed ammonia from waste streams is typically considered as the nitrogen source. These processes for ammonia production are highly energy intensive. In this study, the potential for using nitrogen gas (N2) as a direct nitrogen source for MP production by hydrogen-oxidizing bacteria (HOB) was evaluated. The use of N2 versus ammonium as nitrogen source during the enrichment process resulted in differentiation of the bacterial community composition of the enrichments. A few previously unknown potential N2-fixing HOB taxa (i.e., representatives of the genus Azonexus and the family Comamonadaceae) dominated the enrichments. The biomass yield of a N2-fixing HOB enrichment was 30-50% lower than that of the ammonium-based HOB enrichment from the same inoculum source. The dried biomass of N2-fixing HOB had a high protein content (62.0 ± 6.3%) and an essential amino acid profile comparable to MP from ammonium-based HOB. MP from N2-fixing HOB could potentially be produced in situ without entailing the emissions caused by ammonia production and transportation by conventional means. It could be a promising substitute for N2-fixing protein-rich soybean because it has 70% higher protein content and double energy conversion efficiency from solar energy to biomass.}, }
@article {pmid32124916, year = {2020}, author = {Rossmann, M and Pérez-Jaramillo, JE and Kavamura, VN and Chiaramonte, JB and Dumack, K and Fiore-Donno, AM and Mendes, LW and Ferreira, MMC and Bonkowski, M and Raaijmakers, JM and Mauchline, TH and Mendes, R}, title = {Multitrophic interactions in the rhizosphere microbiome of wheat: from bacteria and fungi to protists.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {4}, pages = {}, doi = {10.1093/femsec/fiaa032}, pmid = {32124916}, issn = {1574-6941}, support = {BB/N016246/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/C/0 0005196/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/C/000I0310/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/genetics ; Fungi/genetics ; *Microbiota ; Plant Roots ; *Rhizosphere ; Soil Microbiology ; Triticum ; }, abstract = {Plants modulate the soil microbiota by root exudation assembling a complex rhizosphere microbiome with organisms spanning different trophic levels. Here, we assessed the diversity of bacterial, fungal and cercozoan communities in landraces and modern varieties of wheat. The dominant taxa within each group were the bacterial phyla Proteobacteria, Actinobacteria and Acidobacteria; the fungi phyla Ascomycota, Chytridiomycota and Basidiomycota; and the Cercozoa classes Sarcomonadea, Thecofilosea and Imbricatea. We showed that microbial networks of the wheat landraces formed a more intricate network topology than that of modern wheat cultivars, suggesting that breeding selection resulted in a reduced ability to recruit specific microbes in the rhizosphere. The high connectedness of certain cercozoan taxa to bacteria and fungi indicated trophic network hierarchies where certain predators gain predominance over others. Positive correlations between protists and bacteria in landraces were preserved as a subset in cultivars as was the case for the Sarcomonadea class with Actinobacteria. The correlations between the microbiome structure and plant genotype observed in our results suggest the importance of top-down control by organisms of higher trophic levels as a key factor for understanding the drivers of microbiome community assembly in the rhizosphere.}, }
@article {pmid32123959, year = {2020}, author = {O'Brien, AM and Laurich, J and Lash, E and Frederickson, ME}, title = {Mutualistic Outcomes Across Plant Populations, Microbes, and Environments in the Duckweed Lemna minor.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {384-397}, doi = {10.1007/s00248-019-01452-1}, pmid = {32123959}, issn = {1432-184X}, support = {RGPIN-2015-06742//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Araceae/drug effects/genetics/growth &amp; development/*microbiology ; Bacteria/*growth &amp; development ; Genetic Fitness ; Genotype ; Host Microbial Interactions ; Microbiota/*physiology ; *Symbiosis ; Water Pollutants, Chemical/*adverse effects ; Zinc/*adverse effects ; }, abstract = {The picture emerging from the rapidly growing literature on host-associated microbiota is that host traits and fitness often depend on interactive effects of host genotype, microbiota, and abiotic environment. However, testing interactive effects typically requires large, multi-factorial experiments and thus remains challenging in many systems. Furthermore, most studies of plant microbiomes focus on terrestrial hosts and microbes. Aquatic habitats may confer unique properties to microbiomes. We grew different populations of duckweed (Lemna minor), a floating aquatic plant, in three microbial treatments (adding no, "home", or "away" microbes) at two levels of zinc, a common water contaminant in urban areas, and measured both plant and microbial performance. Thus, we simultaneously manipulated plant source population, microbial community, and abiotic environment. We found strong effects of plant source, microbial treatment, and zinc on duckweed and microbial growth, with significant variation among duckweed genotypes and microbial communities. However, we found little evidence of interactive effects: zinc did not alter effects of host genotype or microbial community, and host genotype did not alter effects of microbial communities. Despite strong positive correlations between duckweed and microbe growth, zinc consistently decreased plant growth, but increased microbial growth. Furthermore, as in recent studies of terrestrial plants, microbial interactions altered a duckweed phenotype (frond aggregation). Our results suggest that duckweed source population, associated microbiome, and contaminant environment should all be considered for duckweed applications, such as phytoremediation. Lastly, we propose that duckweed microbes offer a robust experimental system for study of host-microbiota interactions under a range of environmental stresses.}, }
@article {pmid32123275, year = {2020}, author = {Romero Victorica, M and Soria, MA and Batista-García, RA and Ceja-Navarro, JA and Vikram, S and Ortiz, M and Ontañon, O and Ghio, S and Martínez-Ávila, L and Quintero García, OJ and Etcheverry, C and Campos, E and Cowan, D and Arneodo, J and Talia, PM}, title = {Neotropical termite microbiomes as sources of novel plant cell wall degrading enzymes.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {3864}, pmid = {32123275}, issn = {2045-2322}, mesh = {Animals ; Bacteria/*enzymology/genetics ; Bacterial Proteins/genetics/*metabolism ; Cell Wall ; Cellulose/*chemistry ; Gastrointestinal Microbiome/*physiology ; Glycoside Hydrolases/genetics/*metabolism ; Isoptera/metabolism/*microbiology ; Plant Cells ; Species Specificity ; *Wood ; }, abstract = {In this study, we used shotgun metagenomic sequencing to characterise the microbial metabolic potential for lignocellulose transformation in the gut of two colonies of Argentine higher termite species with different feeding habits, Cortaritermes fulviceps and Nasutitermes aquilinus. Our goal was to assess the microbial community compositions and metabolic capacity, and to identify genes involved in lignocellulose degradation. Individuals from both termite species contained the same five dominant bacterial phyla (Spirochaetes, Firmicutes, Proteobacteria, Fibrobacteres and Bacteroidetes) although with different relative abundances. However, detected functional capacity varied, with C. fulviceps (a grass-wood-feeder) gut microbiome samples containing more genes related to amino acid metabolism, whereas N. aquilinus (a wood-feeder) gut microbiome samples were enriched in genes involved in carbohydrate metabolism and cellulose degradation. The C. fulviceps gut microbiome was enriched specifically in genes coding for debranching- and oligosaccharide-degrading enzymes. These findings suggest an association between the primary food source and the predicted categories of the enzymes present in the gut microbiomes of each species. To further investigate the termite microbiomes as sources of biotechnologically relevant glycosyl hydrolases, a putative GH10 endo-β-1,4-xylanase, Xyl10E, was cloned and expressed in Escherichia coli. Functional analysis of the recombinant metagenome-derived enzyme showed high specificity towards beechwood xylan (288.1 IU/mg), with the optimum activity at 50 °C and a pH-activity range from 5 to 10. These characteristics suggest that Xy110E may be a promising candidate for further development in lignocellulose deconstruction applications.}, }
@article {pmid32120208, year = {2020}, author = {Ogbughalu, OT and Vasileiadis, S and Schumann, RC and Gerson, AR and Li, J and Smart, RSC and Short, MD}, title = {Role of microbial diversity for sustainable pyrite oxidation control in acid and metalliferous drainage prevention.}, journal = {Journal of hazardous materials}, volume = {393}, number = {}, pages = {122338}, doi = {10.1016/j.jhazmat.2020.122338}, pmid = {32120208}, issn = {1873-3336}, mesh = {Bacteria/classification/genetics/*metabolism ; Bacterial Typing Techniques ; Ferric Compounds/chemistry ; High-Throughput Nucleotide Sequencing ; Hydrogen-Ion Concentration ; Industrial Waste/*prevention &amp; control ; Iron/*chemistry ; Mining/*methods ; Oxidation-Reduction ; Silicates/chemistry ; Soil Microbiology ; Sulfides/*chemistry ; }, abstract = {Acid and metalliferous drainage (AMD) remains a challenging issue for the mining sector. AMD management strategies have attempted to shift from treatment of acid leachates post-generation to more sustainable at-source prevention. Here, the efficacy of microbial-geochemical at-source control approach was investigated over a period of 84 weeks. Diverse microbial communities were stimulated using organic carbon amendment in a simulated silicate-containing sulfidic mine waste rock environment. Mineral waste in the unamended leach system generated AMD quickly and throughout the study, with known lithotrophic iron- and sulfur-oxidising microbes dominating column communities. The organic-amended mineral waste column showed suppressed metal dissolution and AMD generation. Molecular DNA-based next generation sequencing confirmed a less diverse lithotrophic community in the acid-producing control, with a more diverse microbial community under organic amendment comprising organotrophic iron/sulfur-reducers, autotrophs, hydrogenotrophs and heterotrophs. Time-series multivariate statistical analyses displayed distinct ecological patterns in microbial diversity between AMD- and non-AMD-environments. Focused ion beam-TEM micrographs and elemental mapping showed that silicate-stabilised passivation layers were successfully established across pyrite surfaces in organic-amended treatments, with these layers absent in unamended controls. Organic amendment and resulting increases in microbial abundance and diversity played an important role in sustaining these passivating layers in the long-term.}, }
@article {pmid32117135, year = {2020}, author = {Sarrocco, S and Herrera-Estrella, A and Collinge, DB}, title = {Editorial: Plant Disease Management in the Post-genomic Era: From Functional Genomics to Genome Editing.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {107}, pmid = {32117135}, issn = {1664-302X}, }
@article {pmid32114382, year = {2020}, author = {Cermak, N and Datta, MS and Conwill, A}, title = {Rapid, Inexpensive Measurement of Synthetic Bacterial Community Composition by Sanger Sequencing of Amplicon Mixtures.}, journal = {iScience}, volume = {23}, number = {3}, pages = {100915}, pmid = {32114382}, issn = {2589-0042}, abstract = {Synthetic bacterial communities are powerful tools for studying microbial ecology and evolution, as they enable rapid iteration between controlled laboratory experiments and theoretical modeling. However, their utility is hampered by the lack of fast, inexpensive, and accurate methods for quantifying bacterial community composition. Although next-generation amplicon sequencing can be very accurate, high costs (>$30 per sample) and turnaround times (>1 month) limit the nature and pace of experiments. Here, we quantify amplicon composition in synthetic bacterial communities through Sanger sequencing. We PCR amplify a universal marker gene, then we sequence this amplicon mixture in a single Sanger sequencing reaction. We then fit the "mixed" electropherogram with contributions from each community member as a linear combination of time-warped single-strain electropherograms, allowing us to estimate the fractional amplicon abundance of each strain within the community. This approach can provide results within one day and costs ∼$5 per sample.}, }
@article {pmid32111851, year = {2020}, author = {Candry, P and Huang, S and Carvajal-Arroyo, JM and Rabaey, K and Ganigue, R}, title = {Enrichment and characterisation of ethanol chain elongating communities from natural and engineered environments.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {3682}, pmid = {32111851}, issn = {2045-2322}, abstract = {Chain elongation is a microbial process in which an electron donor, such as ethanol, is used to elongate short chain carboxylic acids, such as acetic acid, to medium chain carboxylic acids. This metabolism has been extensively investigated, but the spread and differentiation of chain elongators in the environment remains unexplored. Here, chain elongating communities were enriched from several inocula (3 anaerobic digesters, 2 animal faeces and 1 caproic acid producing environment) using ethanol and acetic acid as substrates at pH 7 and 5.5. This approach showed that (i) the inoculum's origin determines the pH where native chain elongators can grow; (ii) pH affects caproic acid production, with average caproic acid concentrations of 6.4 ± 1.6 g·L[-1] at pH 7, versus 2.3 ± 1.8 g·L[-1] at pH 5.5; however (iii) pH does not affect growth rates significantly; (iv) all communities contained a close relative of the known chain elongator Clostridium kluyveri; and (v) low pH selects for communities more enriched in this Clostridium kluyveri-relative (57.6 ± 23.2% at pH 7, 96.9 ± 1.2% at pH 5.5). These observations show that ethanol-consuming chain elongators can be found in several natural and engineered environments, but are not the same everywhere, emphasising the need for careful inoculum selection during process development.}, }
@article {pmid32106521, year = {2020}, author = {Wang, Y and Jiang, Y and Liu, Y and Li, Y and Katz, LA and Gao, F and Yan, Y}, title = {Comparative Studies on the Polymorphism and Copy Number Variation of mtSSU rDNA in Ciliates (Protista, Ciliophora): Implications for Phylogenetic, Environmental, and Ecological Research.}, journal = {Microorganisms}, volume = {8}, number = {3}, pages = {}, pmid = {32106521}, issn = {2076-2607}, support = {2018SDKJ0406-1//Marine S&amp;T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology/ ; 31772428, 31801984 and 31672279//National Natural Science Foundation of China/ ; }, abstract = {While nuclear small subunit ribosomal DNA (nSSU rDNA) is the most commonly-used gene marker in studying phylogeny, ecology, abundance, and biodiversity of microbial eukaryotes, mitochondrial small subunit ribosomal DNA (mtSSU rDNA) provides an alternative. Recently, both copy number variation and sequence variation of nSSU rDNA have been demonstrated for diverse organisms, which can contribute to misinterpretation of microbiome data. Given this, we explore patterns for mtSSU rDNA among 13 selected ciliates (representing five classes), a major component of microbial eukaryotes, estimating copy number and sequence variation and comparing to that of nSSU rDNA. Our study reveals: (1) mtSSU rDNA copy number variation is substantially lower than that for nSSU rDNA; (2) mtSSU rDNA copy number ranges from 1.0 × 10[4] to 8.1 × 10[5]; (3) a most common sequence of mtSSU rDNA is also found in each cell; (4) the sequence variation of mtSSU rDNA are mainly indels in poly A/T regions, and only half of species have sequence variation, which is fewer than that for nSSU rDNA; and (5) the polymorphisms between haplotypes of mtSSU rDNA would not influence the phylogenetic topology. Together, these data provide more insights into mtSSU rDNA as a powerful marker especially for microbial ecology studies.}, }
@article {pmid32105920, year = {2020}, author = {Riaz, L and Wang, Q and Yang, Q and Li, X and Yuan, W}, title = {Potential of industrial composting and anaerobic digestion for the removal of antibiotics, antibiotic resistance genes and heavy metals from chicken manure.}, journal = {The Science of the total environment}, volume = {718}, number = {}, pages = {137414}, doi = {10.1016/j.scitotenv.2020.137414}, pmid = {32105920}, issn = {1879-1026}, mesh = {Anaerobiosis ; Animals ; Anti-Bacterial Agents ; Chickens ; *Composting ; Drug Resistance, Microbial ; Genes, Bacterial ; Manure ; Metals, Heavy ; }, abstract = {Composting and anaerobic digestion techniques are widely used for manure recycling, but these methods have shown conflicting results in the removal of antibiotics, antibiotic resistance genes (ARGs), and heavy metals. In the present study, anaerobically digested chicken manure and various types of composted chicken manure were investigated on an industrial scale. Antibiotics, ARGs, and heavy metals had shown inconsistent results for anaerobic digestion and composting. The different composting processes either declined or completely removed the blaCTX-M, intl1 and oqxB genes. In addition, composting processes decreased the absolute abundance of aac6'-Ib and aadA genes, while increased the absolute abundance of qnrD, sul1, and tet(A) genes. On the other hand, anaerobic digestion of chicken manure increased the absolute abundance of ere(A) and tet(A). High throughput sequencing showed that Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria dominated the total bacterial composition of composted and anaerobically digested samples. Network analysis revealed the co-occurrence of ARGs and intl1. The redundancy analysis showed a significant correlation between some heavy metals and ARGs. Similarly, the bacterial composition showed a positive correlation with the prevalence of ARGs in treated manure. These findings suggest that bacterial community, heavy metals, and mobile genetic elements can play a significant role in the abundance and variation of ARGs during composting and anaerobic digestion. In conclusion, anaerobic digestion and composting methods at industrial scale need to be improved for the effective removal of antibiotics, ARGs and heavy metals from chicken manure.}, }
@article {pmid32105814, year = {2020}, author = {Rizowy, GM and Poloni, S and Colonetti, K and Donis, KC and Dobbler, PT and Leistner-Segal, S and Roesch, LFW and Schwartz, IVD}, title = {Is the gut microbiota dysbiotic in patients with classical homocystinuria?.}, journal = {Biochimie}, volume = {173}, number = {}, pages = {3-11}, doi = {10.1016/j.biochi.2020.02.013}, pmid = {32105814}, issn = {1638-6183}, mesh = {Adolescent ; Adult ; Betaine/administration &amp; dosage ; Case-Control Studies ; Dietary Supplements ; Dysbiosis/*microbiology ; Female ; *Gastrointestinal Microbiome ; *Homocystinuria/diet therapy/drug therapy/microbiology ; Humans ; Male ; Vitamin B Complex/administration &amp; dosage ; Young Adult ; }, abstract = {Classical homocystinuria (HCU) is characterized by increased plasma levels of total homocysteine (tHcy) and methionine (Met). Treatment may involve supplementation of B vitamins and essential amino acids, as well as restricted Met intake. Dysbiosis has been described in some inborn errors of metabolism, but has not been investigated in HCU. The aim of this study was to investigate the gut microbiota of HCU patients on treatment. Six unrelated HCU patients (males = 5, median age = 25.5 years) and six age-and-sex-matched healthy controls (males = 5, median age = 24.5 years) had their fecal microbiota characterized through partial 16S rRNA gene sequencing. Fecal pH, a 3-day dietary record, medical history, and current medications were recorded for both groups. All patients were nonresponsive to pyridoxine and were on a Met-restricted diet and presented with high tHcy. Oral supplementation of folate (n = 6) and pyridoxine (n = 5), oral intake of betaine (n = 4), and IM vitamin B12 supplementation (n = 4), were reported only in the HCU group. Patients had decreased daily intake of fat, cholesterol, vitamin D, and selenium compared to controls (p < 0.05). There was no difference in alpha and beta diversity between the groups. HCU patients had overrepresentation of the Eubacterium coprostanoligenes group and underrepresentation of the Alistipes, Family XIII UCG-001, and Parabacteroidetes genera. HCU patients and controls had similar gut microbiota diversity, despite differential abundance of some bacterial genera. Diet, betaine, vitamin B supplementation, and host genetics may contribute to these differences in microbial ecology.}, }
@article {pmid32105635, year = {2020}, author = {Pushalkar, S and Paul, B and Li, Q and Yang, J and Vasconcelos, R and Makwana, S and González, JM and Shah, S and Xie, C and Janal, MN and Queiroz, E and Bederoff, M and Leinwand, J and Solarewicz, J and Xu, F and Aboseria, E and Guo, Y and Aguallo, D and Gomez, C and Kamer, A and Shelley, D and Aphinyanaphongs, Y and Barber, C and Gordon, T and Corby, P and Li, X and Saxena, D}, title = {Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection.}, journal = {iScience}, volume = {23}, number = {3}, pages = {100884}, pmid = {32105635}, issn = {2589-0042}, support = {P30 DA011041/DA/NIDA NIH HHS/United States ; P30 ES000260/ES/NIEHS NIH HHS/United States ; R01 CA206105/CA/NCI NIH HHS/United States ; R01 DE025992/DE/NIDCR NIH HHS/United States ; R01 DE027074/DE/NIDCR NIH HHS/United States ; }, abstract = {The trend of e-cigarette use among teens is ever increasing. Here we show the dysbiotic oral microbial ecology in e-cigarette users influencing the local host immune environment compared with non-smoker controls and cigarette smokers. Using 16S rRNA high-throughput sequencing, we evaluated 119 human participants, 40 in each of the three cohorts, and found significantly altered beta-diversity in e-cigarette users (p = 0.006) when compared with never smokers or tobacco cigarette smokers. The abundance of Porphyromonas and Veillonella (p = 0.008) was higher among vapers. Interleukin (IL)-6 and IL-1β were highly elevated in e-cigarette users when compared with non-users. Epithelial cell-exposed e-cigarette aerosols were more susceptible for infection. In vitro infection model of premalignant Leuk-1 and malignant cell lines exposed to e-cigarette aerosol and challenged by Porphyromonas gingivalis and Fusobacterium nucleatum resulted in elevated inflammatory response. Our findings for the first time demonstrate that e-cigarette users are more prone to infection.}, }
@article {pmid32105331, year = {2020}, author = {Schmidt, ML and Biddanda, BA and Weinke, AD and Chiang, E and Januska, F and Props, R and Denef, VJ}, title = {Microhabitats are associated with diversity-productivity relationships in freshwater bacterial communities.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {4}, pages = {}, pmid = {32105331}, issn = {1574-6941}, support = {T32 GM008349/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics ; *Biodiversity ; *Ecosystem ; Lakes ; Phylogeny ; }, abstract = {Eukaryotic communities commonly display a positive relationship between biodiversity and ecosystem function (BEF) but the results have been mixed when assessed in bacterial communities. Habitat heterogeneity, a factor in eukaryotic BEFs, may explain these variable observations but it has not been thoroughly evaluated in bacterial communities. Here, we examined the impact of habitat on the relationship between diversity assessed based on the (phylogenetic) Hill diversity metrics and heterotrophic productivity. We sampled co-occurring free-living (more homogenous) and particle-associated (more heterogeneous) bacterial habitats in a freshwater, estuarine lake over three seasons: spring, summer and fall. There was a strong, positive, linear relationship between particle-associated bacterial richness and heterotrophic productivity that strengthened when considering dominant taxa. There were no observable BEF trends in free-living bacterial communities for any diversity metric. Biodiversity, richness and Inverse Simpson's index, were the best predictors of particle-associated production whereas pH was the best predictor of free-living production. Our findings show that heterotrophic productivity is positively correlated with the effective number of taxa and that BEF relationships are associated with microhabitats. These results add to the understanding of the highly distinct contributions to diversity and functioning contributed by bacteria in free-living and particle-associated habitats.}, }
@article {pmid32101723, year = {2020}, author = {Xavier, JB and Young, VB and Skufca, J and Ginty, F and Testerman, T and Pearson, AT and Macklin, P and Mitchell, A and Shmulevich, I and Xie, L and Caporaso, JG and Crandall, KA and Simone, NL and Godoy-Vitorino, F and Griffin, TJ and Whiteson, KL and Gustafson, HH and Slade, DJ and Schmidt, TM and Walther-Antonio, MRS and Korem, T and Webb-Robertson, BM and Styczynski, MP and Johnson, WE and Jobin, C and Ridlon, JM and Koh, AY and Yu, M and Kelly, L and Wargo, JA}, title = {The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View.}, journal = {Trends in cancer}, volume = {6}, number = {3}, pages = {192-204}, pmid = {32101723}, issn = {2405-8025}, support = {R01 CA208179/CA/NCI NIH HHS/United States ; KL2 TR002379/TR/NCATS NIH HHS/United States ; R01 CA227479/CA/NCI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; U54 CA209975/CA/NCI NIH HHS/United States ; }, mesh = {Analgesics, Opioid/therapeutic use ; Animals ; Bacteria/metabolism ; Central Nervous System/physiology ; Drug Synergism ; Environmental Microbiology ; Gastritis/microbiology ; Gastrointestinal Microbiome ; Helicobacter Infections/complications ; Host-Pathogen Interactions ; Humans ; Immunotherapy ; Mice ; *Microbiota/drug effects/radiation effects ; Neoplasms/etiology/*microbiology/therapy/virology ; Oncogenic Viruses/pathogenicity ; Probiotics ; Stomach Neoplasms/etiology/microbiology ; Symbiosis ; Tumor Virus Infections ; }, abstract = {The collection of microbes that live in and on the human body - the human microbiome - can impact on cancer initiation, progression, and response to therapy, including cancer immunotherapy. The mechanisms by which microbiomes impact on cancers can yield new diagnostics and treatments, but much remains unknown. The interactions between microbes, diet, host factors, drugs, and cell-cell interactions within the cancer itself likely involve intricate feedbacks, and no single component can explain all the behavior of the system. Understanding the role of host-associated microbial communities in cancer systems will require a multidisciplinary approach combining microbial ecology, immunology, cancer cell biology, and computational biology - a systems biology approach.}, }
@article {pmid32100456, year = {2020}, author = {Wang, B and He, Y and Tang, J and Ou, Q and Lin, J}, title = {Alteration of the gut microbiota in tumor necrosis factor-α antagonist-treated collagen-induced arthritis mice.}, journal = {International journal of rheumatic diseases}, volume = {23}, number = {4}, pages = {472-479}, doi = {10.1111/1756-185X.13802}, pmid = {32100456}, issn = {1756-185X}, support = {81871710//National Natural Science Foundation of China/ ; 2017J01190//Fujian Provincial Department of Science and Technology/ ; 2018QH1056//Fujian Medical University Startup Fund for scientific research/ ; C18117//Fujian Medical University Innovation Training Program/ ; 2018J06022//Fujian Science Fund for Distinguished Young Scholars/ ; }, mesh = {Animals ; Arthritis, Experimental/chemically induced/*drug therapy/immunology/microbiology ; Bacteria/classification/*drug effects/growth &amp; development ; Collagen Type II ; Cytokines/blood ; Etanercept/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Inflammation Mediators/blood ; Male ; Mice, Inbred DBA ; Tumor Necrosis Factor Inhibitors/*pharmacology ; }, abstract = {AIM: Gut microbiota play an important role in rheumatoid arthritis (RA). Biological therapies targeting tumor necrosis factor-α (TNF-α) have been used for treatment in RA patients. However, whether TNF-α antagonist has some influence on gut microbiota is still unknown. This study aims to investigate the distribution of gut microbiota in collagen-induced arthritis (CIA) mice treated with the TNF-α antagonist etanercept.<br><br>METHODS: Collagen-induced arthritis mice were induced by type II collagen. Cytokine expression was detected by real-time polymerase chain reaction. 16S ribosomal RNA sequencing was performed to characterize the gut microbiota in CIA mice treated with vehicle or etanercept. Sequencing reads were processed by Microbial Ecology software program.<br><br>RESULTS: Compared with vehicle-treated mice, we showed that CIA mice treated with etanercept led to attenuation of inflammation and reduced expression of TNF-&#x3b1;, interferon (IFN)-&#x3b3;, interleukin (IL)-6 and IL-21. Meanwhile, results showed operational taxonomic units, richness estimators and the diversity indices of gut microbiota in etanercept-treated mice were lower than that in vehicle-treated mice. Moreover, bacterial abundance analyses showed that genus Escherichia/Shigella was more abundant in etanercept-treated mice, and Lactobacillus, Clostridium XlVa, Tannerella were less abundant. The altered bacterial genus was correlated with TNF-&#x3b1;, IFN-&#x3b3;, IL-6, IL-21 and IL-10.<br><br>CONCLUSION: Our results revealed that TNF-&#x3b1; antagonist treatment can reduce the abundance and diversity of gut microbiota in CIA mice. Targeted gut microbiota may be a new therapeutic strategy for the treatment of RA.}, }
@article {pmid32100127, year = {2020}, author = {Chen, K and Fu, Y and Wang, Y and Liao, L and Xu, H and Zhang, A and Zhang, J and Fan, L and Ren, J and Fang, B}, title = {Therapeutic Effects of the In Vitro Cultured Human Gut Microbiota as Transplants on Altering Gut Microbiota and Improving Symptoms Associated with Autism Spectrum Disorder.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {475-486}, doi = {10.1007/s00248-020-01494-w}, pmid = {32100127}, issn = {1432-184X}, support = {81770558//National Natural Science Foundation of China/ ; 3502Z20149031//Xiamen Joint Projects for Major Diseases/ ; }, mesh = {Animals ; Autism Spectrum Disorder/*therapy ; Bacteria/*metabolism ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; }, abstract = {Autism spectrum disorder (ASD) is a brain-based neurodevelopmental disorder characterized by behavioral abnormalities. Accumulating studies show that the gut microbiota plays a vital role in the pathogenesis of ASD, and gut microbiota transplantation (GMT) is a promising technique for the treatment of ASD. In clinical applications of GMT, it is challenging to obtain effective transplants because of the high costs of donor selection and heterogeneity of donors' gut microbiota, which can cause different clinical responses. In vitro batch culture is a fast, easy-to-operate, and repeatable method to culture gut microbiota. Thus, the present study investigates the feasibility of treating ASD with in vitro cultured gut microbiota as transplants. We cultured gut microbiota via the in vitro batch culture method and performed GMT in the maternal immune activation (MIA)-induced ASD mouse model with original donor microbiota and in vitro cultured microbiota. Open field, three-chamber social, marble burying, and self-grooming tests were used for behavioral improvement assessment. Serum levels of chemokines were detected. Microbial total DNA was extracted from mouse fecal samples, and 16S rDNA was sequenced using Illumina. Our results showed that GMT treatment with original and cultured donor gut microbiota significantly ameliorated anxiety-like and repetitive behaviors and improved serum levels of chemokines including GRO-α (CXCL1), MIP-1α (CCL3), MCP-3 (CCL7), RANTES (CCL5), and Eotaxin (CCL11) in ASD mice. Meanwhile, the gut microbial communities of the two groups that received GMT treatment were changed compared with the ASD mice groups. In the group treated with in vitro cultured donor gut microbiota, there was a significant decrease in the relative abundance of key differential taxa, including S24-7, Clostridiaceae, Prevotella_other, and Candidatus Arthromitus. The relative abundance of these taxa reached close to the level of healthy mice. Prevotella_other also decreased in the group treated with original donor gut microbiota, with a significant increase in Ruminococcaceae and Oscillospira. The present study demonstrated that GMT with in vitro cultured microbiota also improved behavioral abnormalities and chemokine disorders in an ASD mouse model compared with GMT with original donor gut microbiota. In addition, it significantly modified several key differential taxa in gut microbial composition.}, }
@article {pmid32097837, year = {2020}, author = {Abramov, SM and Tejada, J and Grimm, L and Schädler, F and Bulaev, A and Tomaszewski, EJ and Byrne, JM and Straub, D and Thorwarth, H and Amils, R and Kleindienst, S and Kappler, A}, title = {Role of biogenic Fe(III) minerals as a sink and carrier of heavy metals in the Rio Tinto, Spain.}, journal = {The Science of the total environment}, volume = {718}, number = {}, pages = {137294}, doi = {10.1016/j.scitotenv.2020.137294}, pmid = {32097837}, issn = {1879-1026}, abstract = {Oxidation of sulfide ores in the Iberian Pyrite Belt region leads to the presence of extremely high concentration of dissolved heavy metals (HMs) in the acidic water of the Rio Tinto. Fe(II) is microbially oxidized resulting in the formation of suspended particulate matter (SPM) consisting of microbial cells and Fe(III) minerals with co-precipitated HMs. Although substantial amount of HM-bearing SPM is likely deposited to river sediment, a portion can still be transported through estuary to the coastal ocean. Therefore, the mechanisms of SPM formation and transport along the Rio Tinto are important for coastal-estuarine zone. In order to reveal these mechanisms, we performed diurnal sampling of Rio Tinto water, mineralogical and elemental analysis of sediment from the middle course and the estuary of the river. We identified two divergent but interrelated pathways of HM transfer. The first longitudinal pathway is the transport of SPM-associated metals such as As (6.58 μg/L), Pb (3.51 μg/L) and Cr (1.30 μg/L) to the coastal ocean. The second sedimentation pathway contributes to the continuous burial of HMs in the sediment throughout the river. In the middle course, sediment undergoes mineralogical transformations during early diagenesis and traps HMs (e.g. 1.6 mg/g of As, 1.23 mg/g of Pb and 0.1 mg/g of Cr). In the estuary, HMs are accumulated in a distinct anoxic layer of sediment (e.g. 1.5 mg/g of As, 2.09 mg/g of Pb and 0.04 mg/g of Cr). Our results indicate that microbially precipitated Fe(III) minerals (identified as ferrihydrite and schwertmannite) play a key role in maintaining these divergent HM pathways and as a consequence are crucial for HM mobility in the Rio Tinto.}, }
@article {pmid32094388, year = {2020}, author = {Marsland, R and Cui, W and Mehta, P}, title = {A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {3308}, pmid = {32094388}, issn = {2045-2322}, support = {R35 GM119461/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/metabolism ; *Biodiversity ; Humans ; Microbiota ; *Models, Biological ; Principal Component Analysis ; }, abstract = {Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP) have revealed robust ecological patterns across different environments. A major goal in ecology is to leverage these patterns to identify the ecological processes shaping microbial ecosystems. One promising approach is to use minimal models that can relate mechanistic assumptions at the microbe scale to community-level patterns. Here, we demonstrate the utility of this approach by showing that the Microbial Consumer Resource Model (MiCRM) - a minimal model for microbial communities with resource competition, metabolic crossfeeding and stochastic colonization - can qualitatively reproduce patterns found in survey data including compositional gradients, dissimilarity/overlap correlations, richness/harshness correlations, and nestedness of community composition. By using the MiCRM to generate synthetic data with different environmental and taxonomical structure, we show that large scale patterns in the EMP can be reproduced by considering the energetic cost of surviving in harsh environments and HMP patterns may reflect the importance of environmental filtering in shaping competition. We also show that recently discovered dissimilarity-overlap correlations in the HMP likely arise from communities that share similar environments rather than reflecting universal dynamics. We identify ecologically meaningful changes in parameters that alter or destroy each one of these patterns, suggesting new mechanistic hypotheses for further investigation. These findings highlight the promise of minimal models for microbial ecology.}, }
@article {pmid32094260, year = {2020}, author = {Samanta, P and Mandal, RS and Saha, RN and Shaw, S and Ghosh, P and Dutta, S and Ghosh, A and Imamura, D and Morita, M and Ohnishi, M and Ramamurthy, T and Mukhopadhyay, AK}, title = {A Point Mutation in carR Is Involved in the Emergence of Polymyxin B-Sensitive Vibrio cholerae O1 El Tor Biotype by Influencing Gene Transcription.}, journal = {Infection and immunity}, volume = {88}, number = {5}, pages = {}, pmid = {32094260}, issn = {1098-5522}, mesh = {Alleles ; Anti-Bacterial Agents/pharmacology ; Calcium/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Down-Regulation/genetics ; Escherichia coli/genetics ; Point Mutation/*genetics ; Polymorphism, Single Nucleotide/genetics ; Polymyxin B/*pharmacology ; Transcription, Genetic/*genetics ; Vibrio cholerae O1/*drug effects/*genetics/metabolism ; }, abstract = {Antimicrobial peptides play an important role in host defense against Vibrio cholerae Generally, the V. cholerae O1 classical biotype is polymyxin B (PB) sensitive and El Tor is relatively resistant. Detection of classical biotype traits like the production of classical cholera toxin and PB sensitivity in El Tor strains has been reported in recent years, including in the devastating Yemen cholera outbreak during 2016-2018. To investigate the factor(s) responsible for the shift in the trend of sensitivity to PB, we studied the two-component system encoded by carRS, regulating the lipid A modification of El Tor vibrios, and found that only carR contains a single nucleotide polymorphism (SNP) in recently emerged PB-sensitive strains. We designated the two alleles present in PB-resistant and -sensitive strains carR[r] and carR[s] alleles, respectively, and replaced the carR[s] allele of a sensitive strain with the carR[r] allele, using an allelic-exchange approach. The sensitive strain then became resistant. The PB-resistant strain N16961 was made susceptible to PB in a similar fashion. Our in silico CarR protein models suggested that the D89N substitution in the more stable CarR[s] protein brings the two structural domains of CarR closer, constricting the DNA binding cleft. This probably reduces the expression of the carR-regulated almEFG operon, inducing PB susceptibility. Expression of almEFG in PB-sensitive strains was found to be downregulated under natural culturing conditions. In addition, the expression of carR and almEG decreased in all strains with increased concentrations of extracellular Ca[2+] but increased with a rise in pH. The downregulation of almEFG in CarR[s] strains confirmed that the G265A mutation is responsible for the emergence of PB-sensitive El Tor strains.}, }
@article {pmid32093252, year = {2020}, author = {Gómez Del Pulgar, EM and Benítez-Páez, A and Sanz, Y}, title = {Safety Assessment of Bacteroides Uniformis CECT 7771, a Symbiont of the Gut Microbiota in Infants.}, journal = {Nutrients}, volume = {12}, number = {2}, pages = {}, pmid = {32093252}, issn = {2072-6643}, support = {613979//Seventh Framework Programme/ ; }, mesh = {Animals ; *Bacteroides ; Cytokines/blood ; Female ; Gastrointestinal Microbiome/*physiology ; Male ; Microbiota/physiology ; Probiotics/*administration &amp; dosage ; Rats ; Rats, Wistar ; }, abstract = {The formulation of next-generation probiotics requires competent preclinical studies to show their efficacy and safety status. This study aims to confirm the safety of the prolonged oral use of Bacteroides uniformis CECT 7771, a strain that protected against metabolic disorders and obesity in preclinical trials, in a sub-chronic 90 day trial in animals. The safety assessment was conducted in male and female Wistar rats (n = 50) administered increasing doses (10[8] CFU/day, 10[9] CFU/day, or 10[10] CFU/day) of B. uniformis CECT 7771, 10[10] CFU/day of B. longum ATCC 15707[T], which complies with the qualifying presumption of safety (QPS) status of the EU, or vehicle (placebo), as the control. Pancreatic, liver, and kidney functions and cytokine concentrations were analyzed. Bacterial translocation to peripheral tissues was evaluated, and colon integrity was investigated histologically. No adverse metabolic or tissue integrity alterations were associated with treatments; however, alanine aminotransferase levels and the ratio of anti-inflammatory to pro-inflammatory cytokines in serum indicated a potentially beneficial role of B. uniformis CECT 7771 at specific doses. Additionally, the microbial community structure was modified by the interventions, and potentially beneficial gut bacteria were increased. The results indicated that the oral consumption of B. uniformis CECT 7771 during a sub-chronic 90 day study in rats did not raise safety concerns.}, }
@article {pmid32092511, year = {2020}, author = {Wei, H and Gao, D and Liu, Y and Lin, X}, title = {Sediment nitrate reduction processes in response to environmental gradients along an urban river-estuary-sea continuum.}, journal = {The Science of the total environment}, volume = {718}, number = {}, pages = {137185}, doi = {10.1016/j.scitotenv.2020.137185}, pmid = {32092511}, issn = {1879-1026}, abstract = {Sediment denitrification (DEN), anaerobic ammonium oxidation (Anammox), and dissimilatory nitrate reduction to ammonium (DNRA) are three important nitrate (NO3[-]) reduction pathways in aquatic ecosystems. These processes modify nitrogen (N) loadings from land to the ocean, with important implications on the management of coastal eutrophication. While NO3[-] reduction has been studied intensively for various types of habitats, studies on its distributions along river-estuary-sea continua remain scarce. In this study, we examined these three pathways along a N-laden urban river-estuary-sea continuum comprised of three types of habitats (urban river, estuary, and adjacent sea) in the densely populated Shanghai-East China Sea area. The potential DEN, Anammox, and DNRA rates decreased seaward both in summer and winter in response to decreasing sediment organic matter (OM, 20 to 7 to 7 mg C g[-1]), ferrous oxide (9 to 2.7 to 2.8 mg Fe g[-1]), and bottom water dissolved inorganic nitrogen (543 to 112 to 21 μM). Among these pathways, DEN remained a major component (~69.6%) across habitats, while Anammox (47.9%) rivaled DEN (48.3%) in the urban river in winter. N retention index (NIRI), the ratio between retained and removed NO3[-], ranged from 0 to 0.5 and increased downstream. Together, these results suggest that the decreasing gradients of OM and inorganic matter shape the distribution of NO3[-] reduction along the continuum, reflecting the diminishing impact of the river and human inputs from the urban river to the ocean. Our results highlight the importance of taking a continuum perspective in N cycling studies and emphasize the role of urban rivers as N removal hotspots, which should be a focus of research and management.}, }
@article {pmid32091935, year = {2020}, author = {Balachandran, M and Cross, KL and Podar, M}, title = {Single-Cell Genomics and the Oral Microbiome.}, journal = {Journal of dental research}, volume = {99}, number = {6}, pages = {613-620}, pmid = {32091935}, issn = {1544-0591}, support = {R01 DE024463/DE/NIDCR NIH HHS/United States ; R01 HG004857/HG/NHGRI NIH HHS/United States ; }, mesh = {Dental Caries/genetics ; Dysbiosis/genetics ; Genomics ; Humans ; *Microbiota/genetics ; Mouth ; }, abstract = {The human oral cavity is one of the first environments where microbes have been discovered and studied since the dawn of microbiology. Nevertheless, approximately 200 types of bacteria from the oral microbiota have remained uncultured in the laboratory. Some are associated with a healthy oral microbial community, while others are linked to oral diseases, from dental caries to gum disease. Single-cell genomics has enabled inferences on the physiology, virulence, and evolution of such uncultured microorganisms and has further enabled isolation and cultivation of several novel oral bacteria, including the discovery of novel interspecies interactions. This review summarizes some of the more recent advances in this field, which is rapidly moving toward physiologic characterization of single cells and ultimately cultivation of the yet uncultured. A combination of traditional microbiological approaches with genomic-based physiologic predictions and isolation strategies may lead to the oral microbiome being the first complex microbial community to have all its members cultivable in the laboratory. Studying the biology of the individual microbes when in association with other members of the community, in controlled laboratory conditions and in vivo, should lead to a better understanding of oral dysbiosis and its prevention and reversion.}, }
@article {pmid32090516, year = {2020}, author = {Hess, AL and Larsen, LH and Udesen, PB and Sanz, Y and Larsen, TM and Dalgaard, LT}, title = {Levels of Circulating miR-122 are Associated with Weight Loss and Metabolic Syndrome.}, journal = {Obesity (Silver Spring, Md.)}, volume = {28}, number = {3}, pages = {493-501}, doi = {10.1002/oby.22704}, pmid = {32090516}, issn = {1930-739X}, support = {115372//EU/EFPIA Innovative Medicines Initiative Joint Undertaking EMIF/International ; 613979//Seventh Framework Programme/International ; }, mesh = {Adolescent ; Adult ; Double-Blind Method ; Female ; Humans ; Male ; Metabolic Syndrome/*genetics ; MicroRNAs/*metabolism ; Middle Aged ; Obesity/*genetics ; Weight Loss/*genetics ; Young Adult ; }, abstract = {OBJECTIVE: This study investigated whether the levels of specific serum microRNAs (miRNAs) were altered following diet-induced weight loss and whether the serum miRNAs differed in the presence of the metabolic syndrome.<br><br>METHODS: The study was a weight loss intervention trial with a prescribed energy deficit of approximately 500 kcal/d. Levels of 22 miRNAs were determined in serum samples from 85 participants with overweight or obesity. miRNAs were analyzed using TaqMan Array miRNA&#xa0;Cards and normalized to the geometric mean of spiked-in ath-miR-159a and U6 small nuclear RNA using the &#x394;CT method.<br><br>RESULTS: The average weight loss was 5.7 kg (P&#x2009;<&#x2009;0.001). miR-122-5p (-0.18&#x2009;&#xb1;&#x2009;0.06 log fold relative to initial, P&#x2009;<&#x2009;0.01) and miR-193a-5p (-0.12&#x2009;&#xb1;&#x2009;0.04, P&#x2009;<&#x2009;0.01) levels decreased in response to weight loss. miR-126a-3p (0.11&#x2009;&#xb1;&#x2009;0.04, P&#x2009;=&#x2009;0.01) and miR-222-3p (1.51&#x2009;&#xb1;&#x2009;0.12, P&#x2009;<&#x2009;0.001) levels increased. Furthermore, a higher level of miR-122-5p was observed at baseline in participants with the metabolic syndrome compared with participants without (0.28&#x2009;&#xb1;&#x2009;0.08, P&#x2009;<&#x2009;0.01).<br><br>CONCLUSIONS: Changes in circulating miR-122-5p, miR-126a-3p, miR-193a-5p, and miR-222-3p in response to diet-induced weight loss are demonstrated. Furthermore, assessment of miR-122-5p could be an indicator of an adverse metabolic health status independent of obesity.}, }
@article {pmid32088790, year = {2020}, author = {Zhang, S and Shao, Y and Zhao, X and Li, C and Guo, M and Lv, Z and Zhang, W}, title = {Indole contributes to tetracycline resistance via the outer membrane protein OmpN in Vibrio splendidus.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {36}, number = {3}, pages = {36}, pmid = {32088790}, issn = {1573-0972}, support = {2018YFD0900603//the National Key R&amp;D Program of China/ ; 41676141//the National Natural Science Foundation of China/ ; }, mesh = {Bacterial Outer Membrane Proteins/*genetics/metabolism ; Culture Media/chemistry ; Electrophoresis, Polyacrylamide Gel ; Gene Expression Regulation, Bacterial/drug effects ; Indoles/*pharmacology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Tetracycline/pharmacology ; *Tetracycline Resistance ; Up-Regulation ; Vibrio/drug effects/*growth &amp; development/metabolism ; }, abstract = {As an interspecies and interkingdom signaling molecule, indole has recently received attention for its diverse effects on the physiology of both bacteria and hosts. In this study, indole increased the tetracycline resistance of Vibrio splendidus. The minimal inhibitory concentration of tetracycline was 10 μg/mL, and the OD600 of V. splendidus decreased by 94.5% in the presence of 20 μg/mL tetracycline; however, the OD600 of V. splendidus with a mixture of 20 μg/mL tetracycline and 125 μM indole was 10- or 4.5-fold higher than that with only 20 μg/mL tetracycline at different time points. The percentage of cells resistant to 10 μg/mL tetracycline was 600-fold higher in the culture with an OD600 of approximately 2.0 (higher level of indole) than that in the culture with an OD600 of 0.5, which also meant that the level of indole was correlated to the tetracycline resistance of V. splendidus. Furthermore, one differentially expressed protein, which was identified as the outer membrane porin OmpN using SDS-PAGE combined with MALDI-TOF/TOF MS, was upregulated. Consequently, the expression of the ompN gene in the presence of either tetracycline or indole and simultaneously in the presence of indole and tetracycline was upregulated by 1.8-, 2.54-, and 6.01-fold, respectively, compared to the control samples. The combined results demonstrated that indole enhanced the tetracycline resistance of V. splendidus, and this resistance was probably due to upregulation of the outer membrane porin OmpN.}, }
@article {pmid32088758, year = {2020}, author = {Law, CKY and De Henau, R and De Vrieze, J}, title = {Feedstock thermal pretreatment selectively steers process stability during the anaerobic digestion of waste activated sludge.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {8}, pages = {3675-3686}, pmid = {32088758}, issn = {1432-0614}, support = {GA 826244//Horizon 2020/ ; }, mesh = {Anaerobiosis ; Biofuels/microbiology ; *Bioreactors ; Methane/biosynthesis ; *Microbiota ; Sewage/*microbiology ; *Temperature ; }, abstract = {Strategies to enhance process performance of anaerobic digestion remain of key importance to promote wider usage of this technology for integrated resource recovery from organic waste streams. Continuous inoculation of the microbial community in the digester via the feedstock could be such a cost-effective strategy. Here, anaerobic digestion of fresh waste activated sludge (WAS) was compared with sterilized WAS in response to two common process disturbances, i.e. organic overloading and increasing levels of salts, to determine the importance of feedstock inoculation. A pulse in the organic loading rate severely impacted process stability of the digesters fed sterile WAS, with a 92 ± 45% decrease in methane production, compared to a 42 ± 31% increase in the digesters fed fresh WAS, relative to methane production before the pulse. Increasing salt pulses did not show a clear difference in process stability between the digesters fed fresh and sterile WAS, and process recovery was obtained even at the highest salt pulse of 25 g Na[+] L[-1]. Feedstock sterilization through thermal pretreatment strongly impacted the microbial community in the digesters. In conclusion, feedstock thermal pretreatment strongly impacted anaerobic digestion process stability, due to feedstock inoculation and compositional modification.}, }
@article {pmid32086543, year = {2021}, author = {Bao, G and Song, M and Wang, Y and Saikkonen, K and Li, C}, title = {Does Epichloë Endophyte Enhance Host Tolerance to Root Hemiparasite?.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {35-48}, pmid = {32086543}, issn = {1432-184X}, support = {31660690//National Natural Science Foundation of China/ ; 31700098//National Natural Science Foundation of China/ ; 1111126//Cooperation Program of Qinghai Province/ ; 295976//Academy of Finland/ ; 326226//Academy of Finland/ ; 2017-ZJ-Y12//QingHai Department of Science and Technology/ ; }, mesh = {*Elymus ; Endophytes ; *Epichloe ; Plant Weeds ; Poaceae ; Symbiosis ; }, abstract = {Epichloë endophytes have been shown to be mutualistic symbionts of cool-season grasses under most environmental conditions. Although pairwise interactions between hemiparasites and their hosts are heavily affected by host-associated symbiotic microorganisms, little attention has been paid to the effects of microbe-plant interactions, particularly endophytic symbiosis, in studies examining the effects of parasitic plants on host performance. In this study, we performed a greenhouse experiment to examine the effects of hereditary Epichloë endophyte symbiosis on the growth of two host grasses (Stipa purpurea and Elymus tangutorum) in the presence or absence of a facultative root hemiparasite (Pedicularis kansuensis Maxim). We observed parasitism of both hosts by P. kansuensis: when grown with a host plant, the hemiparasite decreased the performance of the host while improving its own biomass and survival rate of the hemiparasite. Parasitized endophyte-infected S. purpurea plants had higher biomass, tillers, root:shoot ratio, and photosynthetic parameters and a lower number of functional haustoria than the endophyte-free S. purpurea conspecifics. By contrast, parasitized endophyte-infected E. tangutorum had a lower biomass, root:shoot ratio, and photosynthetic parameters and a higher number of haustoria and functional haustoria than their endophyte-free counterparts. Our results reveal that the interactions between the endophytes and the host grasses are context dependent and that plant-plant interactions can strongly affect their mutualistic interactions. Endophytes originating from S. purpurea alleviate the host biomass reduction by P. kansuensis and growth depression in the hemiparasite. These findings shed new light on using grass-endophyte symbionts as biocontrol methods for the effective and sustainable management of this weedy hemiparasite.}, }
@article {pmid32086129, year = {2020}, author = {Elhalis, H and Cox, J and Zhao, J}, title = {Ecological diversity, evolution and metabolism of microbial communities in the wet fermentation of Australian coffee beans.}, journal = {International journal of food microbiology}, volume = {321}, number = {}, pages = {108544}, doi = {10.1016/j.ijfoodmicro.2020.108544}, pmid = {32086129}, issn = {1879-3460}, mesh = {Australia ; Bacteria/classification/growth &amp; development/isolation &amp; purification/metabolism ; Coffea/chemistry/*microbiology ; Coffee/chemistry ; Fermentation ; Food Handling/*methods ; Food Microbiology ; *Microbiota/genetics ; Seeds/chemistry/microbiology ; Yeasts/classification/growth &amp; development/isolation &amp; purification/metabolism ; }, abstract = {The microbial ecology in the fermentation of Australian coffee beans was investigated in this study. Pulped coffee beans were kept underwater for 36 h before air dried. Samples were collected periodically, and the microbial communities were analyzed by culture-dependent and independent methods. Changes in sugars, organic acids and microbial metabolites in the mucilage and endosperm of the coffee beans during fermentation were monitored by HPLC. Culture-dependent methods identified 6 yeast and 17 bacterial species, while the culture-independent methods, multiple-step total direct DNA extraction and high throughput sequencing, identified 212 fungal and 40 bacterial species. Most of the microbial species in the community have been reported for wet fermentation of coffee beans in other parts of the world, but the yeast Pichia kudriavzevii was isolated for the first time in wet coffee bean fermentation. The bacterial community was dominated by aerobic mesophilic bacteria (AMB) with Citrobacter being the predominant genus. Hanseniaspora uvarum and Pichia kudriavzevii were the predominant yeasts while Leuconostoc mesenteroides and Lactococcus lactis were the predominant LAB. The yeasts and bacteria grew significantly during fermentation, utilizing sugars in the mucilage and produced mannitol, glycerol, and lactic acid, leading to a significant decrease in pH. The results of this study provided a preliminary understanding of the microbial ecology of wet coffee fermentation under Australian conditions. Further studies are needed to explore the impact of microbial growth and metabolism on coffee quality, especially flavour.}, }
@article {pmid32084407, year = {2020}, author = {Lories, B and Roberfroid, S and Dieltjens, L and De Coster, D and Foster, KR and Steenackers, HP}, title = {Biofilm Bacteria Use Stress Responses to Detect and Respond to Competitors.}, journal = {Current biology : CB}, volume = {30}, number = {7}, pages = {1231-1244.e4}, pmid = {32084407}, issn = {1879-0445}, support = {209397/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Biofilms ; Drug Resistance, Bacterial/*genetics ; Genome, Bacterial/*physiology ; Microbial Interactions/*genetics ; Phenotype ; Salmonella typhimurium/*physiology ; Single-Cell Analysis ; }, abstract = {Bacteria use complex regulatory networks to cope with stress, but the function of these networks in natural habitats is poorly understood. The competition sensing hypothesis states that bacterial stress response systems can serve to detect ecological competition, but studying regulatory responses in diverse communities is challenging. Here, we solve this problem by using differential fluorescence induction to screen the Salmonella Typhimurium genome for loci that respond, at the single-cell level, to life in biofilms with competing strains of S. Typhimurium and Escherichia coli. This screening reveals the presence of competing strains drives up the expression of genes associated with biofilm matrix production (CsgD pathway), epithelial invasion (SPI1 invasion system), and, finally, chemical efflux and antibiotic tolerance (TolC efflux pump and AadA aminoglycoside 3-adenyltransferase). We validate that these regulatory changes result in the predicted phenotypic changes in biofilm, mammalian cell invasion, and antibiotic tolerance. We further show that these responses arise via activation of major stress responses, providing direct support for the competition sensing hypothesis. Moreover, inactivation of the type VI secretion system (T6SS) of a competitor annuls the responses to competition, indicating that T6SS-derived cell damage activates these stress response systems. Our work shows that bacteria use stress responses to detect and respond to competition in a manner important for major phenotypes, including biofilm formation, virulence, and antibiotic tolerance.}, }
@article {pmid32080691, year = {2020}, author = {Xu, J and Ma, Z and Li, X and Liu, L and Hu, X}, title = {A more pronounced effect of type III resistant starch vs. type II resistant starch on ameliorating hyperlipidemia in high fat diet-fed mice is associated with its supramolecular structural characteristics.}, journal = {Food &amp; function}, volume = {11}, number = {3}, pages = {1982-1995}, doi = {10.1039/c9fo02025j}, pmid = {32080691}, issn = {2042-650X}, mesh = {Animals ; Diet, High-Fat/*adverse effects ; Gastrointestinal Microbiome/drug effects ; Hyperlipidemias/*chemically induced/prevention &amp; control ; Male ; Mice ; Mice, Inbred BALB C ; Random Allocation ; Starch/chemistry/*classification/*pharmacology ; Structure-Activity Relationship ; }, abstract = {The anti-obesity effects of two categories of resistant starch (RS) including RS2 (isolated from untreated lentil starch, URS) and RS3 (isolated from autoclaved and retrograded lentil starch, ARS) on mice with high-fat (HF) diet-induced obesity and the supramolecular structure-in vivo physiological functionality relationship of RS were investigated. Following 6 consecutive weeks, the obese mice in the two RS administered groups displayed suppression of body/liver weight gain and an improvement in serum glucose/lipid profile, antioxidant status, and gut microbiota structure. Compared with the URS intervention group, the ARS administration resulted in a more pronounced effect in controlling body weight, together with a more prominent reduction in blood glucose and triglyceride concentration, as well as a significant increase in the HDL-c level in obese mice. The ARS group also showed an absolute advantage over URS in suppressing the oxidative stress and regulating the liver function induced by the HF diet. Simultaneously, the administration of URS and ARS efficiently suppressed the HF-diet induced alterations in gut microbial ecology, with an obviously decreased ratio of Firmicutes to Bacteroidetes, especially for the ARS group, suggesting its beneficial role in gastrointestinal tract health. The structural characterization results revealed that ARS and URS differed significantly in their supramolecular structural characteristics, where ARS exhibited a higher proportion of crystallinity and double helix content with an X-ray diffraction pattern of a CB type crystal polymorph and a low proportion of molecular inhomogeneity. This study suggested that the difference in the anti-obesity effect of resistant starches was a consequence of the diversity in their structural features.}, }
@article {pmid32076744, year = {2020}, author = {Chen, H and Wang, M and Chang, S}, title = {Disentangling Community Structure of Ecological System in Activated Sludge: Core Communities, Functionality, and Functional Redundancy.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {296-308}, doi = {10.1007/s00248-020-01492-y}, pmid = {32076744}, issn = {1432-184X}, mesh = {*Bacterial Physiological Phenomena ; Microbiota/*physiology ; Ontario ; Seasons ; Sewage/*microbiology ; }, abstract = {The microbial ecosystems of the sludge were characterized in terms of the core community structure, functional pathways, and functional redundancy through Illumina MiSeq sequencing and PICRUSt analysis on the activated sludge (AS) samples from an extended activated aeration process. Based on the identified OTU distribution, we identified 125 core community genera, including 3 abundant core genera and 21 intermittent abundant core genera. Putative genera Nitrosomonas, Nitrotoga, Zoogloea, Novosphingobium, Thermomonas, Amaricoccus, Tetrasphaera, Candidatus Microthrix, and Haliscomenobacter, which are associated with functions of nitrifying, denitrifying, phosphorus accumulating, and bulking and foaming, were found to present as the core community organisms in the AS sampled from the conventional extended aeration AS processes. The high-abundant nitrogen metabolic pathways were associated with nitrate reduction to ammonium (DNRA and ANRA), denitrification, and nitrogen fixation, while the ammonia oxidation-related genes (amo) were rarely annotated in the AS samples. Strict functional redundancy was not found with the AS ecosystem as it showed a high correlation between the community composition similarity and function similarity. In addition, the classified dominant core genera community was found to be sufficient to characterize the functionality of AS, which could invigorate applications of 16S rDNA MiSeq sequencing and PICRUSt for the prediction of functions of AS ecosystems.}, }
@article {pmid32076743, year = {2020}, author = {Aubé, J and Senin, P and Bonin, P and Pringault, O and Jeziorski, C and Bouchez, O and Klopp, C and Guyoneaud, R and Goñi-Urriza, M}, title = {Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {286-295}, doi = {10.1007/s00248-020-01493-x}, pmid = {32076743}, issn = {1432-184X}, support = {ANR11 BSV7 014 01//Agence Nationale de la Recherche/ ; }, mesh = {Bacteria/drug effects/genetics/metabolism ; Hydrocarbons/*metabolism ; *Metagenome ; *Transcriptome ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Photosynthetic microbial mats are stable, self-supported communities. Due to their coastal localization, these mats are frequently exposed to hydrocarbon contamination and are able to grow on it. To decipher how this contamination disturbs the functioning of microbial mats, we compared two mats: a contaminated mat exposed to chronic petroleum contamination and a reference mat. The taxonomic and metabolic structures of the mats in spring and fall were determined using metagenomic and metatranscriptomic approaches. Extremely high contamination disturbed the seasonal variations of the mat. ABC transporters, two-component systems, and type IV secretion system-related genes were overabundant in the contaminated mats. Xenobiotic degradation metabolism was minor in the metagenomes of both mats, and only the expression of genes involved in polycyclic aromatic hydrocarbon degradation was higher in the contaminated mat. Interestingly, the expression rates of genes involved in hydrocarbon activation decreased during the 1-year study period, concomitant with the decrease in easily degradable hydrocarbons, suggesting a transient effect of hydrocarbon contamination. Alteromonadales and Oceanospirillales hydrocarbonoclastic bacteria appeared to be key in hydrocarbon remediation in the contaminated mat. Overall, the contaminated microbial mat was able to cope with hydrocarbon contamination and displayed an adaptive functioning that modified seasonal behaviour.}, }
@article {pmid32075981, year = {2020}, author = {Hernandez-Sanabria, E and Heiremans, E and Calatayud Arroyo, M and Props, R and Leclercq, L and Snoeys, J and Van de Wiele, T}, title = {Short-term supplementation of celecoxib-shifted butyrate production on a simulated model of the gut microbial ecosystem and ameliorated in vitro inflammation.}, journal = {NPJ biofilms and microbiomes}, volume = {6}, number = {1}, pages = {9}, pmid = {32075981}, issn = {2055-5008}, mesh = {Adult ; Bacteria/*classification/drug effects/genetics/metabolism ; Batch Cell Culture Techniques ; Butyrates/*metabolism ; Caco-2 Cells ; Celecoxib/*pharmacology ; Cell Line, Tumor ; Chemokine CXCL16/*metabolism ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Feces/microbiology ; Female ; Fermentation ; Gastrointestinal Microbiome/*drug effects ; HT29 Cells ; High-Throughput Nucleotide Sequencing ; Humans ; Interleukin-6/*metabolism ; Male ; Proof of Concept Study ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; THP-1 Cells ; }, abstract = {Celecoxib has been effective in the prevention and treatment of chronic inflammatory disorders through inhibition of altered cyclooxygenase-2 (COX-2) pathways. Despite the benefits, continuous administration may increase risk of cardiovascular events. Understanding microbiome-drug-host interactions is fundamental for improving drug disposition and safety responses of colon-targeted formulations, but little information is available on the bidirectional interaction between individual microbiomes and celecoxib. Here, we conducted in vitro batch incubations of human faecal microbiota to obtain a mechanistic proof-of-concept of the short-term impact of celecoxib on activity and composition of colon bacterial communities. Celecoxib-exposed microbiota shifted metabolic activity and community composition, whereas total transcriptionally active bacterial population was not significantly changed. Butyrate production decreased by 50% in a donor-dependent manner, suggesting that celecoxib impacts in vitro fermentation. Microbiota-derived acetate has been associated with inhibition of cancer markers and our results suggest uptake of acetate for bacterial functions when celecoxib was supplied, which potentially favoured bacterial competition for acetyl-CoA. We further assessed whether colon microbiota modulates anti-inflammatory efficacy of celecoxib using a simplified inflammation model, and a novel in vitro simulation of the enterohepatic metabolism. Celecoxib was responsible for only 5% of the variance in bacterial community composition but celecoxib-exposed microbiota preserved barrier function and decreased concentrations of IL-8 and CXCL16 in a donor-dependent manner in our two models simulating gut inflammatory milieu. Our results suggest that celecoxib-microbiome-host interactions may not only elicit adaptations in community composition but also in microbiota functionality, and these may need to be considered for guaranteeing efficient COX-2 inhibition.}, }
@article {pmid32075196, year = {2020}, author = {Dhakar, K and Pandey, A}, title = {Microbial Ecology from the Himalayan Cryosphere Perspective.}, journal = {Microorganisms}, volume = {8}, number = {2}, pages = {}, pmid = {32075196}, issn = {2076-2607}, abstract = {Cold-adapted microorganisms represent a large fraction of biomass on Earth because of the dominance of low-temperature environments. Extreme cold environments are mainly dependent on microbial activities because this climate restricts higher plants and animals. Himalaya is one of the most important cold environments on Earth as it shares climatic similarities with the polar regions. It includes a wide range of ecosystems, from temperate to extreme cold, distributed along the higher altitudes. These regions are characterized as stressful environments because of the heavy exposure to harmful rays, scarcity of nutrition, and freezing conditions. The microorganisms that colonize these regions are recognized as cold-tolerant (psychrotolerants) or/and cold-loving (psychrophiles) microorganisms. These microorganisms possess several structural and functional adaptations in order to perform normal life processes under the stressful low-temperature environments. Their biological activities maintain the nutrient flux in the environment and contribute to the global biogeochemical cycles. Limited culture-dependent and culture-independent studies have revealed their diversity in community structure and functional potential. Apart from the ecological importance, these microorganisms have been recognized as source of cold-active enzymes and novel bioactive compounds of industrial and biotechnological importance. Being an important part of the cryosphere, Himalaya needs to be explored at different dimensions related to the life of the inhabiting extremophiles. The present review discusses the distinct facts associated with microbial ecology from the Himalayan cryosphere perspective.}, }
@article {pmid32072187, year = {2020}, author = {Junges, DSB and Delabeneta, MF and Rosseto, LRB and Nascimento, BL and Paris, AP and Persel, C and Loth, EA and Simão, RCG and Menolli, RA and Paula, CR and Gandra, RF}, title = {Antibiotic Activity of Wickerhamomyces anomalus Mycocins on Multidrug-Resistant Acinetobacter baumannii.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {278-285}, doi = {10.1007/s00248-020-01495-9}, pmid = {32072187}, issn = {1432-184X}, mesh = {Acinetobacter baumannii/*drug effects ; Animals ; Anti-Infective Agents/adverse effects/chemistry/*pharmacology ; Artemia/*drug effects ; Erythrocytes/*drug effects ; Humans ; Saccharomycetales/*chemistry ; }, abstract = {To evaluate the susceptibility of multidrug-resistant Acinetobacter baumannii to mycocins produced by Wickerhamomyces anomalus and to verify the cytotoxicity of these compounds. Three culture supernatants of W. anomalus (WA40, WA45, and WA92), containing mycocins (WA40M1, WA45M2, and WA92M3), were tested on A. baumannii using broth microdilution methods, solid medium tests, and cytotoxicity tests in human erythrocytes and in Artemia saline Leach. W. anomalus was able to produce high antimicrobial mycocins, as even at high dilutions, they inhibited A. baumannii. In a solid medium, it was possible to observe the inhibition of A. baumannii, caused by the diffusion of mycocins between agar. Finally, the three supernatants were not cytotoxic when tested on human erythrocytes and Artemia salina. According to the evidence in this study, the mycocins of W. anomalus have been effective and could be used in the development of new antimicrobial substances.}, }
@article {pmid32071708, year = {2020}, author = {Klimenko, NS and Tyakht, AV and Toshchakov, SV and Shevchenko, MA and Korzhenkov, AA and Afshinnekoo, E and Mason, CE and Alexeev, DG}, title = {Co-occurrence patterns of bacteria within microbiome of Moscow subway.}, journal = {Computational and structural biotechnology journal}, volume = {18}, number = {}, pages = {314-322}, pmid = {32071708}, issn = {2001-0370}, abstract = {Microbial ecosystems of the built environments have become key mediators of health as people worldwide tend to spend large amount of time indoors. Underexposure to microbes at an early age is linked to increased risks of allergic and autoimmune diseases. Transportation systems are of particular interest, as they are globally the largest space for interactions between city-dwellers. Here we performed the first pilot study of the Moscow subway microbiome by analyzing swabs collected from 5 types of surfaces at 4 stations using high-throughput 16S rRNA gene sequencing. The study was conducted as a part of The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) project. The most abundant microbial taxa comprising the subway microbiome originated from soil and human skin. Microbiome diversity was positively correlated with passenger traffic. No substantial evidence of major human pathogens presence was found. Co-occurrence analysis revealed clusters of microbial genera including combinations of microbes likely originating from different niches. The clusters as well as the most abundant microbes were similar to ones obtained for the published data on New-York City subway microbiome. Our results suggest that people are the main source and driving force of diversity in subway-associated microbiome. The data form a basis for a wider survey of Moscow subway microbiome to explore its longitudinal dynamics by analyzing an extended set of sample types and stations. Complementation of methods with viability testing, "shotgun" metagenomics, sequencing of bacterial isolates and culturomics will provide insights for public health, biosafety, microbial ecology and urban design.}, }
@article {pmid32071705, year = {2020}, author = {Chen, X and Krug, L and Yang, H and Li, H and Yang, M and Berg, G and Cernava, T}, title = {Nicotiana tabacum seed endophytic communities share a common core structure and genotype-specific signatures in diverging cultivars.}, journal = {Computational and structural biotechnology journal}, volume = {18}, number = {}, pages = {287-295}, pmid = {32071705}, issn = {2001-0370}, abstract = {Seed endophytes of crop plants have recently received increased attention due to their implications in plant health and the potential to be included in agro-biotechnological applications. While previous studies indicated that plants from the Solanaceae family harbor a highly diverse seed microbiome, genotype-specific effects on the community composition and structure remained largely unexplored. The present study revealed Enterobacteriaceae-dominated seed-endophytic communities in four Nicotiana tabacum L. cultivars originating from Brazil, China, and the USA. When the dissimilarity of bacterial communities was assessed, none of the cultivars showed significant differences in microbial community composition. Various unusual endophyte signatures were represented by Spirochaetaceae family members and the genera Mycobacterium, Clostridium, and Staphylococcus. The bacterial fraction shared by all cultivars was dominated by members of the phyla Proteobacteria and Firmicutes. In total, 29 OTUs were present in all investigated cultivars and accounted for 65.5% of the combined core microbiome reads. Cultivars from the same breeding line were shown to share a higher number of common OTUs than more distant lines. Moreover, the Chinese cultivar Yunyan 87 contained the highest number (33 taxa) of unique signatures. Our results indicate that a distinct proportion of the seed microbiome of N. tabacum remained unaffected by breeding approaches of the last century, while a substantial proportion co-diverged with the plant genotype. Moreover, they provide the basis to identify plant-specific endophytes that could be addressed for upcoming biotechnological approaches in agriculture.}, }
@article {pmid32071163, year = {2020}, author = {Röttjers, L and Faust, K}, title = {manta: a Clustering Algorithm for Weighted Ecological Networks.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, pmid = {32071163}, issn = {2379-5077}, abstract = {Microbial network inference and analysis have become successful approaches to extract biological hypotheses from microbial sequencing data. Network clustering is a crucial step in this analysis. Here, we present a novel heuristic network clustering algorithm, manta, which clusters nodes in weighted networks. In contrast to existing algorithms, manta exploits negative edges while differentiating between weak and strong cluster assignments. For this reason, manta can tackle gradients and is able to avoid clustering problematic nodes. In addition, manta assesses the robustness of cluster assignment, which makes it more robust to noisy data than most existing tools. On noise-free synthetic data, manta equals or outperforms existing algorithms, while it identifies biologically relevant subcompositions in real-world data sets. On a cheese rind data set, manta identifies groups of taxa that correspond to intermediate moisture content in the rinds, while on an ocean data set, the algorithm identifies a cluster of organisms that were reduced in abundance during a transition period but did not correlate strongly to biochemical parameters that changed during the transition period. These case studies demonstrate the power of manta as a tool that identifies biologically informative groups within microbial networks.IMPORTANCE manta comes with unique strengths, such as the abilities to identify nodes that represent an intermediate between clusters, to exploit negative edges, and to assess the robustness of cluster membership. manta does not require parameter tuning, is straightforward to install and run, and can be easily combined with existing microbial network inference tools.}, }
@article {pmid32071161, year = {2020}, author = {Clark, CM and Murphy, BT and Sanchez, LM}, title = {A Call to Action: the Need for Standardization in Developing Open-Source Mass Spectrometry-Based Methods for Microbial Subspecies Discrimination.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, pmid = {32071161}, issn = {2379-5077}, support = {D43 TW010530/TW/FIC NIH HHS/United States ; F31 AT010419/AT/NCCIH NIH HHS/United States ; R01 GM125943/GM/NIGMS NIH HHS/United States ; }, }
@article {pmid32071158, year = {2020}, author = {McAllister, SM and Polson, SW and Butterfield, DA and Glazer, BT and Sylvan, JB and Chan, CS}, title = {Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, pmid = {32071158}, issn = {2379-5077}, support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; }, abstract = {Zetaproteobacteria create extensive iron (Fe) oxide mats at marine hydrothermal vents, making them an ideal model for microbial Fe oxidation at circumneutral pH. Comparison of neutrophilic Fe oxidizer isolate genomes has revealed a hypothetical Fe oxidation pathway, featuring a homolog of the Fe oxidase Cyc2 from Acidithiobacillus ferrooxidans However, Cyc2 function is not well verified in neutrophilic Fe oxidizers, particularly in Fe-oxidizing environments. Toward this, we analyzed genomes and metatranscriptomes of Zetaproteobacteria, using 53 new high-quality metagenome-assembled genomes reconstructed from Fe mats at Mid-Atlantic Ridge, Mariana Backarc, and Loihi Seamount (Hawaii) hydrothermal vents. Phylogenetic analysis demonstrated conservation of Cyc2 sequences among most neutrophilic Fe oxidizers, suggesting a common function. We confirmed the widespread distribution of cyc2 and other model Fe oxidation pathway genes across all represented Zetaproteobacteria lineages. High expression of these genes was observed in diverse Zetaproteobacteria under multiple environmental conditions and in incubations. The putative Fe oxidase gene cyc2 was highly expressed in situ, often as the top expressed gene. The cyc2 gene showed increased expression in Fe(II)-amended incubations, with corresponding increases in carbon fixation and central metabolism gene expression. These results substantiate the Cyc2-based Fe oxidation pathway in neutrophiles and demonstrate its significance in marine Fe-mineralizing environments.IMPORTANCE Iron oxides are important components of our soil, water supplies, and ecosystems, as they sequester nutrients, carbon, and metals. Microorganisms can form iron oxides, but it is unclear whether this is a significant mechanism in the environment. Unlike other major microbial energy metabolisms, there is no marker gene for iron oxidation, hindering our ability to track these microbes. Here, we investigate a promising possible iron oxidation gene, cyc2, in iron-rich hydrothermal vents, where iron-oxidizing microbes dominate. We pieced together diverse Zetaproteobacteria genomes, compared these genomes, and analyzed expression of cyc2 and other hypothetical iron oxidation genes. We show that cyc2 is widespread among iron oxidizers and is highly expressed and potentially regulated, making it a good marker for the capacity for iron oxidation and potentially a marker for activity. These findings will help us understand and potentially quantify the impacts of neutrophilic iron oxidizers in a wide variety of marine and terrestrial environments.}, }
@article {pmid32070256, year = {2020}, author = {Ossowicki, A and Tracanna, V and Petrus, MLC and van Wezel, G and Raaijmakers, JM and Medema, MH and Garbeva, P}, title = {Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1921}, pages = {20192527}, pmid = {32070256}, issn = {1471-2954}, mesh = {Fusarium/*physiology ; Microbiota ; Plant Roots/microbiology ; Soil/chemistry ; *Soil Microbiology ; Triticum/*microbiology ; }, abstract = {In disease-suppressive soils, microbiota protect plants from root infections. Bacterial members of this microbiota have been shown to produce specific molecules that mediate this phenotype. To date, however, studies have focused on individual suppressive soils and the degree of natural variability of soil suppressiveness remains unclear. Here, we screened a large collection of field soils for suppressiveness to Fusarium culmorum using wheat (Triticum aestivum) as a model host plant. A high variation of disease suppressiveness was observed, with 14% showing a clear suppressive phenotype. The microbiological basis of suppressiveness to F. culmorum was confirmed by gamma sterilization and soil transplantation. Amplicon sequencing revealed diverse bacterial taxonomic compositions and no specific taxa were found exclusively enriched in all suppressive soils. Nonetheless, co-occurrence network analysis revealed that two suppressive soils shared an overrepresented bacterial guild dominated by various Acidobacteria. In addition, our study revealed that volatile emission may contribute to suppression, but not for all suppressive soils. Our study raises new questions regarding the possible mechanistic variability of disease-suppressive phenotypes across physico-chemically different soils. Accordingly, we anticipate that larger-scale soil profiling, along with functional studies, will enable a deeper understanding of disease-suppressive microbiomes.}, }
@article {pmid32068849, year = {2020}, author = {Pratama, AA and Jiménez, DJ and Chen, Q and Bunk, B and Spröer, C and Overmann, J and van Elsas, JD}, title = {Delineation of a Subgroup of the Genus Paraburkholderia, Including P. terrae DSM 17804T, P. hospita DSM 17164T, and Four Soil-Isolated Fungiphiles, Reveals Remarkable Genomic and Ecological Features-Proposal for the Definition of a P. hospita Species Cluster.}, journal = {Genome biology and evolution}, volume = {12}, number = {4}, pages = {325-344}, pmid = {32068849}, issn = {1759-6653}, mesh = {Burkholderiaceae/*genetics/growth &amp; development/metabolism ; Ecology ; Fungi/*genetics/growth &amp; development/metabolism ; *Genome, Bacterial ; *Genome, Fungal ; Genomics/*methods ; Phylogeny ; Soil Microbiology ; Species Specificity ; }, abstract = {The fungal-interactive (fungiphilic) strains BS001, BS007, BS110, and BS437 have previously been preliminarily assigned to the species Paraburkholderia terrae. However, in the (novel) genus Paraburkholderia, an as-yet unresolved subgroup exists, that clusters around Paraburkholderia hospita (containing the species P. terrae, P. hospita, and Paraburkholderia caribensis). To shed light on the precise relationships across the respective type strains and the novel fungiphiles, we here compare their genomic and ecophysiological features. To reach this goal, the genomes of the three type strains, with sizes ranging from 9.0 to 11.5 Mb, were de novo sequenced and the high-quality genomes analyzed. Using whole-genome, ribosomal RNA and marker-gene-concatenate analyses, close relationships between P. hospita DSM 17164T and P. terrae DSM 17804T, versus more remote relationships to P. caribensis DSM 13236T, were found. All four fungiphilic strains clustered closely to the two-species cluster. Analyses of average nucleotide identities (ANIm) and tetranucleotide frequencies (TETRA) confirmed the close relationships between P. hospita DSM 17164T and P. terrae DSM 17804T (ANIm = 95.42; TETRA = 0.99784), as compared with the similarities of each one of these strains to P. caribensis DSM 13236T. A species cluster was thus proposed. Furthermore, high similarities of the fungiphilic strains BS001, BS007, BS110, and BS437 with this cluster were found, indicating that these strains also make part of it, being closely linked to P. hospita DSM 17164T (ANIm = 99%; TETRA = 0.99). We propose to coin this cluster the P. hospita species cluster (containing P. hospita DSM 17164T, P. terrae DSM 17804T, and strains BS001, BS007, BS110, and BS437), being clearly divergent from the closely related species P. caribensis (type strain DSM 13236T). Moreover, given their close relatedness to P. hospita DSM 17164T within the cluster, we propose to rename the four fungiphilic strains as members of P. hospita. Analysis of migratory behavior along with fungal growth through soil revealed both P. terrae DSM 17804T and P. hospita DSM 17164T (next to the four fungiphilic strains) to be migration-proficient, whereas P. caribensis DSM 13236T was a relatively poor migrator. Examination of predicted functions across the genomes of the seven investigated strains, next to several selected additional ones, revealed the common presence of features in the P. hospita cluster strains that are potentially important in interactions with soil fungi. Thus, genes encoding specific metabolic functions, biofilm formation (pelABCDEFG, pgaABCD, alginate-related genes), motility/chemotaxis, type-4 pili, and diverse secretion systems were found.}, }
@article {pmid32066625, year = {2020}, author = {Ghosh, TS and Rampelli, S and Jeffery, IB and Santoro, A and Neto, M and Capri, M and Giampieri, E and Jennings, A and Candela, M and Turroni, S and Zoetendal, EG and Hermes, GDA and Elodie, C and Meunier, N and Brugere, CM and Pujos-Guillot, E and Berendsen, AM and De Groot, LCPGM and Feskins, EJM and Kaluza, J and Pietruszka, B and Bielak, MJ and Comte, B and Maijo-Ferre, M and Nicoletti, C and De Vos, WM and Fairweather-Tait, S and Cassidy, A and Brigidi, P and Franceschi, C and O'Toole, PW}, title = {Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries.}, journal = {Gut}, volume = {69}, number = {7}, pages = {1218-1228}, pmid = {32066625}, issn = {1468-3288}, mesh = {Aged ; *Diet, Mediterranean ; Europe ; Female ; Frailty/diet therapy/*prevention &amp; control ; *Gastrointestinal Microbiome/genetics ; Health Status ; Humans ; Male ; Patient Compliance ; RNA, Ribosomal, 16S/genetics ; Single-Blind Method ; }, abstract = {OBJECTIVE: Ageing is accompanied by deterioration of multiple bodily functions and inflammation, which collectively contribute to frailty. We and others have shown that frailty co-varies with alterations in the gut microbiota in a manner accelerated by consumption of a restricted diversity diet. The Mediterranean diet (MedDiet) is associated with health. In the NU-AGE project, we investigated if a 1-year MedDiet intervention could alter the gut microbiota and reduce frailty.<br><br>DESIGN: We profiled the gut microbiota in 612 non-frail or pre-frail subjects across five European countries (UK, France, Netherlands, Italy and Poland) before and after the administration of a 12-month long MedDiet intervention tailored to elderly subjects (NU-AGE diet).<br><br>RESULTS: Adherence to the diet was associated with specific microbiome alterations. Taxa enriched by adherence to the diet were positively associated with several markers of lower frailty and improved cognitive function, and negatively associated with inflammatory markers including C-reactive protein and interleukin-17. Analysis of the inferred microbial metabolite profiles indicated that the diet-modulated microbiome change was associated with an increase in short/branch chained fatty acid production and lower production of secondary bile acids, p-cresols, ethanol and carbon dioxide. Microbiome ecosystem network analysis showed that the bacterial taxa that responded positively to the MedDiet intervention occupy keystone interaction positions, whereas frailty-associated taxa are peripheral in the networks.<br><br>CONCLUSION: Collectively, our findings support the feasibility of improving the habitual diet to modulate the gut microbiota which in turn has the potential to promote healthier ageing.}, }
@article {pmid32063916, year = {2019}, author = {Orr, JN and Neilson, R and Freitag, TE and Roberts, DM and Davies, KG and Blok, VC and Cock, PJA}, title = {Parallel Microbial Ecology of Pasteuria and Nematode Species in Scottish Soils.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {1763}, pmid = {32063916}, issn = {1664-462X}, abstract = {Pasteuria spp. are endospore forming bacteria which act as natural antagonists to many of the most economically significant plant parasitic nematodes (PPNs). Highly species-specific nematode suppression may be observed in soils containing a sufficiently high density of Pasteuria spp. spores. This suppression is enacted by the bacteria via inhibition of root invasion and sterilization of the nematode host. Molecular methods for the detection of Pasteuria spp. from environmental DNA (eDNA) have been described; however, these methods are limited in both scale and in depth. We report the use of small subunit rRNA gene metabarcoding to profile Pasteuria spp. and nematode communities in parallel. We have investigated Pasteuria spp. population structure in Scottish soils using eDNA from two sources: soil extracted DNA from the second National Soil Inventory of Scotland (NSIS2); and nematode extracted DNA collected from farms in the East Scotland Farm Network (ESFN). We compared the Pasteuria spp. community culture to both nematode community structure and the physiochemical properties of soils. Our results indicate that Pasteuria spp. populations in Scottish soils are broadly dominated by two sequence variants. The first of these aligns with high identity to Pasteuria hartismeri, a species first described parasitizing Meloidogyne ardenensis, a nematode parasite of woody and perennial plants in northern Europe. The second aligns with a Pasteuria-like sequence which was first recovered from a farm near Edinburgh which was found to contain bacterial feeding nematodes and Pratylenchus spp. encumbered by Pasteuria spp. endospores. Further, soil carbon, moisture, bulk density, and pH showed a strong correlation with the Pasteuria spp. community composition. These results indicate that metabarcoding is appropriate for the sensitive, specific, and semi-quantitative profiling of Pasteuria species from eDNA.}, }
@article {pmid32062778, year = {2020}, author = {Nkongolo, KK and Narendrula-Kotha, R}, title = {Advances in monitoring soil microbial community dynamic and function.}, journal = {Journal of applied genetics}, volume = {61}, number = {2}, pages = {249-263}, pmid = {32062778}, issn = {2190-3883}, support = {CRDP-J- 470535-2014//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Bacteria/*genetics/isolation &amp; purification ; *Environmental Monitoring ; High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; Polymorphism, Restriction Fragment Length/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Microorganisms are vital to the overall ecosystem functioning, stability, and sustainability. Soil fertility and health depend on chemical composition and also on the qualitative and quantitative nature of microorganisms inhabiting it. Historically, denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE), single-strand conformation polymorphism, DNA amplification fingerprinting, amplified ribosomal DNA restriction analysis, terminal restriction fragment length polymorphism, length heterogeneity PCR, and ribosomal intergenic spacer analysis were used to assess soil microbial community structure (SMCS), abundance, and diversity. However, these methods had significant shortcomings and limitations for application in land reclamation monitoring. SMCS has been primarily determined by phospholipid fatty acid (PLFA) analysis. This method provides a direct measure of viable biomass in addition to a biochemical profile of the microbial community. PLFA has limitations such as overlap in the composition of microorganisms and the specificity of PLFAs signature. In recent years, high-throughput next-generation sequencing has dramatically increased the resolution and detectable spectrum of diverse microbial phylotypes from environmental samples and it plays a significant role in microbial ecology studies. Next-generation sequencings using 454, Illumina, SOLiD, and Ion Torrent platforms are rapid and flexible. The two methods, PLFA and next-generation sequencing, are useful in detecting changes in microbial community diversity and structure in different ecosystems. Single-molecule real-time (SMRT) and nanopore sequencing technologies represent third-generation sequencing (TGS) platforms that have been developed to address the shortcomings of second-generation sequencing (SGS). Enzymatic and soil respiration analyses are performed to further determine soil quality and microbial activities. Other valuable methods that are being recently applied to microbial function and structures include NanoSIM, GeoChip, and DNA stable staple isotope probing (DNA-SIP) technologies. They are powerful metagenomics tool for analyzing microbial communities, including their structure, metabolic potential, diversity, and their impact on ecosystem functions. This review is a critical analysis of current methods used in monitoring soil microbial community dynamic and functions.}, }
@article {pmid32062526, year = {2020}, author = {Iacumin, L and Osualdini, M and Bovolenta, S and Boscolo, D and Chiesa, L and Panseri, S and Comi, G}, title = {Microbial, chemico-physical and volatile aromatic compounds characterization of Pitina PGI, a peculiar sausage-like product of North East Italy.}, journal = {Meat science}, volume = {163}, number = {}, pages = {108081}, doi = {10.1016/j.meatsci.2020.108081}, pmid = {32062526}, issn = {1873-4138}, mesh = {Animals ; Bacteria/isolation &amp; purification ; Fermentation ; Food Microbiology ; Fusarium/isolation &amp; purification ; Italy ; Meat Products/*analysis/*microbiology ; Penicillium/isolation &amp; purification ; Sheep ; Swine ; Volatile Organic Compounds/*analysis ; }, abstract = {Pitina is a fermented sausage-like produced in the mountainous area of the North-East Italy by artisanal plants without the use of both selected starters and casing (Slow Food Presidium). Originally, Pitina has been a way of preserving meat and it is manifactured by meat from ungulates mixed with pork lard, smoked, dryed and ripened. In this study, microbial ecology, physic-chemical parameters, and volatile aromatic compounds of Pitina SR and LR, which differ by the duration of ripening processes, were investigated. Results showed the good hygienic quality. Staphylococcus xylosus and Lactobacillus sakei were responsible for the ripening. Other Coagulase-negative Catalase-positive Cocci (CNCPC) and LAB species were identified: S. equorum, S. warneri, S. succinus and Carnobacterium divergens, Streptococcus equinus, Kocuria rhizophila. Giberella moniliformis and Penicillium turbatum were the only mould species isolated. Strain characterization demonstrated a high genetic variability. Raw meat, environment and ripening conditions seemed to affect strains distribution, which had an impact on the aromatic profile of the product.}, }
@article {pmid32062264, year = {2020}, author = {Stopelli, E and Duyen, VT and Mai, TT and Trang, PTK and Viet, PH and Lightfoot, A and Kipfer, R and Schneider, M and Eiche, E and Kontny, A and Neumann, T and Glodowska, M and Patzner, M and Kappler, A and Kleindienst, S and Rathi, B and Cirpka, O and Bostick, B and Prommer, H and Winkel, LHE and Berg, M}, title = {Spatial and temporal evolution of groundwater arsenic contamination in the Red River delta, Vietnam: Interplay of mobilisation and retardation processes.}, journal = {The Science of the total environment}, volume = {717}, number = {}, pages = {137143}, doi = {10.1016/j.scitotenv.2020.137143}, pmid = {32062264}, issn = {1879-1026}, abstract = {Geogenic arsenic (As) contamination of groundwater poses a major threat to global health, particularly in Asia. To mitigate this exposure, groundwater is increasingly extracted from low-As Pleistocene aquifers. This, however, disturbs groundwater flow and potentially draws high-As groundwater into low-As aquifers. Here we report a detailed characterisation of the Van Phuc aquifer in the Red River Delta region, Vietnam, where high-As groundwater from a Holocene aquifer is being drawn into a low-As Pleistocene aquifer. This study includes data from eight years (2010-2017) of groundwater observations to develop an understanding of the spatial and temporal evolution of the redox status and groundwater hydrochemistry. Arsenic concentrations were highly variable (0.5-510 μg/L) over spatial scales of <200 m. Five hydro(geo)chemical zones (indicated as A to E) were identified in the aquifer, each associated with specific As mobilisation and retardation processes. At the riverbank (zone A), As is mobilised from freshly deposited sediments where Fe(III)-reducing conditions occur. Arsenic is then transported across the Holocene aquifer (zone B), where the vertical intrusion of evaporative water, likely enriched in dissolved organic matter, promotes methanogenic conditions and further release of As (zone C). In the redox transition zone at the boundary of the two aquifers (zone D), groundwater arsenic concentrations decrease by sorption and incorporations onto Fe(II) carbonates and Fe(II)/Fe(III) (oxyhydr)oxides under reducing conditions. The sorption/incorporation of As onto Fe(III) minerals at the redox transition and in the Mn(IV)-reducing Pleistocene aquifer (zone E) has consistently kept As concentrations below 10 μg/L for the studied period of 2010-2017, and the location of the redox transition zone does not appear to have propagated significantly. Yet, the largest temporal hydrochemical changes were found in the Pleistocene aquifer caused by groundwater advection from the Holocene aquifer. This is critical and calls for detailed investigations.}, }
@article {pmid32061251, year = {2020}, author = {Zhu, X and Campanaro, S and Treu, L and Seshadri, R and Ivanova, N and Kougias, PG and Kyrpides, N and Angelidaki, I}, title = {Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {22}, pmid = {32061251}, issn = {2049-2618}, mesh = {Acetates/metabolism ; Anaerobiosis ; Bacteria/classification/*metabolism ; Bioreactors ; Chemoautotrophic Growth ; Ecosystem ; Gene Expression Profiling ; Hydrogen/metabolism ; *Metabolic Networks and Pathways ; Metagenomics ; Methane/*biosynthesis ; Methanosarcina/metabolism ; *Microbiota ; }, abstract = {Methanogenesis, a biological process mediated by complex microbial communities, has attracted great attention due to its contribution to global warming and potential in biotechnological applications. The current study unveiled the core microbial methanogenic metabolisms in anaerobic vessel ecosystems by applying combined genome-centric metagenomics and metatranscriptomics. Here, we demonstrate that an enriched natural system, fueled only with acetate, could support a bacteria-dominated microbiota employing a multi-trophic methanogenic process. Moreover, significant changes, in terms of microbial structure and function, were recorded after the system was supplemented with additional H2. Methanosarcina thermophila, the predominant methanogen prior to H2 addition, simultaneously performed acetoclastic, hydrogenotrophic, and methylotrophic methanogenesis. The methanogenic pattern changed after the addition of H2, which immediately stimulated Methanomicrobia-activity and was followed by a slow enrichment of Methanobacteria members. Interestingly, the essential genes involved in the Wood-Ljungdahl pathway were not expressed in bacterial members. The high expression of a glycine cleavage system indicated the activation of alternative metabolic pathways for acetate metabolism, which were reconstructed in the most abundant bacterial genomes. Moreover, as evidenced by predicted auxotrophies, we propose that specific microbes of the community were forming symbiotic relationships, thus reducing the biosynthetic burden of individual members. These results provide new information that will facilitate future microbial ecology studies of interspecies competition and symbiosis in methanogenic niches. Video abstract.}, }
@article {pmid32060621, year = {2020}, author = {Walter, JM and Coutinho, FH and Leomil, L and Hargreaves, PI and Campeão, ME and Vieira, VV and Silva, BS and Fistarol, GO and Salomon, PS and Sawabe, T and Mino, S and Hosokawa, M and Miyashita, H and Maruyama, F and van Verk, MC and Dutilh, BE and Thompson, CC and Thompson, FL}, title = {Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {249-265}, doi = {10.1007/s00248-019-01480-x}, pmid = {32060621}, issn = {1432-184X}, support = {BIOCOMP//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; Universal//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (BR)/ ; CNE//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro (BR)/ ; }, mesh = {Atlantic Ocean ; Brazil ; Coral Reefs ; Cyanobacteria/genetics/*physiology ; Genome, Bacterial/*physiology ; Phylogeny ; }, abstract = {Turfs are among the major benthic components of reef systems worldwide. The nearly complete genome sequences, basic physiological characteristics, and phylogenomic reconstruction of two phycobiliprotein-rich filamentous cyanobacteria strains isolated from turf assemblages from the Abrolhos Bank (Brazil) are investigated. Both Adonisia turfae CCMR0081[T] (= CBAS 745[T]) and CCMR0082 contain approximately 8 Mbp in genome size and experiments identified that both strains exhibit chromatic acclimation. Whereas CCMR0081[T] exhibits chromatic acclimation type 3 (CA3) regulating both phycocyanin (PC) and phycoerythrin (PE), CCMR0082 strain exhibits chromatic acclimation type 2 (CA2), in correspondence with genes encoding specific photosensors and regulators for PC and PE. Furthermore, a high number and diversity of secondary metabolite synthesis gene clusters were identified in both genomes, and they were able to grow at high temperatures (28 °C, with scant growth at 30 °C). These characteristics provide insights into their widespread distribution in reef systems.}, }
@article {pmid33447802, year = {2020}, author = {Payne, AT and Davidson, AJ and Kan, J and Peipoch, M and Bier, R and Williamson, K}, title = {Widespread cryptic viral infections in lotic biofilms.}, journal = {Biofilm}, volume = {2}, number = {}, pages = {100016}, pmid = {33447802}, issn = {2590-2075}, abstract = {Viruses have important impacts on aquatic microbial ecology and have been studied at length in the global ocean. However, the roles of bacteriophages in lotic ecosystems, particularly in benthic biofilms, have been largely under-studied. The main goals of this work were to determine whether viruses are consistent members of natural benthic biofilm communities of freshwater streams; whether temperate phages are present and active in such biofilms; and whether community profiling approaches like RAPD-PCR can be adapted to characterize biofilm virus communities. Results from both field and laboratory experiments suggest that viruses are consistent members of lotic biofilm communities. Interestingly, prophage induction was statistically significant but only a small percentage of the total bacterial population appeared to harbor prophage or engaged in induction. Finally, while the use of RAPD-PCR for the community level profiling of biofilm viral communities suggests temporal change in response to biofilm maturity, further refinements are required for broad-scale quantitative application.}, }
@article {pmid33336908, year = {2019}, author = {Cui, J and Lian, Y and Zhao, C and Du, H and Han, Y and Gao, W and Xiao, H and Zheng, J}, title = {Dietary Fibers from Fruits and Vegetables and Their Health Benefits via Modulation of Gut Microbiota.}, journal = {Comprehensive reviews in food science and food safety}, volume = {18}, number = {5}, pages = {1514-1532}, doi = {10.1111/1541-4337.12489}, pmid = {33336908}, issn = {1541-4337}, support = {CAAS-XTCX201605-1&#x223c;6//Collaborative Innovation of Chinese Academy of Agricultural Sciences/ ; 31401581//National Natural Science Foundation of China/ ; 31428017//National Natural Science Foundation of China/ ; }, abstract = {Dietary fibers (DFs) regulate host health through various mechanisms related to their dietary sources, specific physicochemical structures, fermentability, and physiological properties in the gut. Considering the numerous types and sources of DFs and their different physicochemical and physiological properties, it is challenging yet important to establish the key mechanisms for the beneficial health effects of DFs. In this review, the types and structures of DFs from different fruits and vegetables were summarized and the effects of different processing methods on DF properties were discussed. Moreover, the impacts of DFs on gut microbial ecology, host physiology, and health were described. Understanding the complex interaction between different DFs and gut microbiota is vital for personalized nutrition. It is also important to comprehend factors influencing gut microbiota and strategies to regulate the microbiota, thereby augmenting beneficial health responses. The exploration of molecular mechanism linking DFs, gut microbiota, and host physiology may allow for the identification of effective targets to fight against major chronic diseases.}, }
@article {pmid33354438, year = {2018}, author = {Reyes, VC and Merino, N and Gedalanga, PB and Van Nostrand, JD and Keely, SP and De Long, SK and Zhou, J and Mahendra, S}, title = {Differential Sensitivity of Wetland-Derived Nitrogen Cycling Microorganisms to Copper Nanoparticles.}, journal = {ACS sustainable chemistry &amp; engineering}, volume = {6}, number = {9}, pages = {11642-11652}, pmid = {33354438}, issn = {2168-0485}, support = {EPA999999/ImEPA/Intramural EPA/United States ; }, abstract = {Metallic nanoparticles (NPs), the most abundant nanomaterials in consumer and industrial products, are the most probable class to enter the environment. In this study, wetland-derived microcosms were incubated with copper nanoparticles (Cu-NP) and ionic CuCl2 to investigate acute (10 days) and chronic (100 days) exposure towards nitrogen cycling microorganisms. The microbial ecology of wetlands play a crucial role in balancing nitrogen in pristine environments as well as in areas impacted by high nutrient loads (e.g., at wastewater effluent discharges). Gene abundance and expression changes were monitored using the GeoChip 5.0 high throughput functional gene microarray and metatranscriptomic shotgun sequencing (RNA-seq), respectively. After 10 days, the Cu-NP impacted microbial communities experienced structural shifts within microorganisms associated with dissimilatory nitrogen reduction accompanied by lower nitrate removal as compared to the unexposed controls. By day 100, these differences were largely resolved and nitrate removal was similar to the unexposed control. Furthermore, the Cu-NP exposed microcosms tolerated copper and were more resilient and adaptive than the unexposed controls based on the abundance and expression of other functions, including electron transfer, metal homeostasis, and stress response. These findings suggest sudden influxes of Cu-NPs into wetland systems may impair nitrogen removal initially, but long-term microbial shifts and functional redundancy would promote the net flux of total nitrogen out of the wetlands.}, }
@article {pmid32624887, year = {2018}, author = {Tzirita, M and Papanikolaou, S and Chatzifragkou, A and Quilty, B}, title = {Waste fat biodegradation and biomodification by Yarrowia lipolytica and a bacterial consortium composed of Bacillus spp. and Pseudomonas putida.}, journal = {Engineering in life sciences}, volume = {18}, number = {12}, pages = {932-942}, pmid = {32624887}, issn = {1618-0240}, abstract = {Fats, oils, and greases (FOGs) are a particular environmental threat. Biodegradation of FOGs is a challenge and in this study the biodegradation of waste cooking fats, namely butter and olive oil, was studied using a non-conventional yeast, Yarrowia lipolytica strain LFMB 20, and a bioaugmentation product consisting of Bacillus spp. and Pseudomonas putida CP1 strain. The microorganisms were grown aerobically in shake-flask experiments in an enriched medium supplemented with ca 0.85% w/v of waste fat. Analysis of the remaining substrate showed a removal of ca 90% of the fat by the yeast at the end of the incubation, while the bacteria removed ca 95% of both fats. Growth rate, biomass production and biomass yield per unit of fat consumed were all higher for the yeast compared to the bacterial consortium. The bacterial consortium exhibited autolysis and a significant decrease in its DCW value at the late growth phases of both fat substrate cultures. The main fatty acids (FAs) present in both fats were linoleic (Δ9,12C18:2), oleic (Δ9C18:1), palmitic (C16:0), palmitoleic (Δ9C16:1) and stearic (C18:0) acid. Both the bacterial consortium and Y. lipolytica preferentially removed Δ9C18:1 from the medium, while a negative selectivity against C18:0 was reported. Both inocula produced microbial mass that contained intra-cellular lipid quantities, but the bacterial consortium gave significantly higher lipid in DCW values compared with the yeast (maximum values up to ca 63% w/w for the butter and ca 42% w/w for the olive oil while the respective values for both lipids were 22% ± 2% w/w for Y. lipolytica). In all cases, intra-cellular lipids in DCW values decreased during the late growth phases, while their FA composition differed with those of the substrate fat.}, }
@article {pmid32846721, year = {2014}, author = {Yang, LH and Gratton, C}, title = {Insects as drivers of ecosystem processes.}, journal = {Current opinion in insect science}, volume = {2}, number = {}, pages = {26-32}, doi = {10.1016/j.cois.2014.06.004}, pmid = {32846721}, issn = {2214-5753}, abstract = {Insects and other small invertebrates are ubiquitous components of all terrestrial and freshwater food webs, but their cumulative biomass is small relative to plants and microbes. As a result, it is often assumed that these animals make relatively minor contributions to ecosystem processes. Despite their small sizes and cumulative biomass, we suggest that these animals may commonly have important effects on carbon and nutrient cycling by modulating the quality and quantity of resources that enter the detrital food web, with consequences at the ecosystem level. These effects can occur through multiple pathways, including direct inputs of insect biomass, the transformation of detrital biomass, and the indirect effects of predators on herbivores and detritivores. In virtually all cases, the ecosystem effects of these pathways are ultimately mediated through interactions with plants and soil microbes. Merging our understanding of insect, plant and microbial ecology will offer a valuable way to better integrate community-level interactions with ecosystem processes.}, }
@article {pmid33412651, year = {2014}, author = {Clodoveo, ML and Hbaieb, RH and Kotti, F and Mugnozza, GS and Gargouri, M}, title = {Mechanical Strategies to Increase Nutritional and Sensory Quality of Virgin Olive Oil by Modulating the Endogenous Enzyme Activities.}, journal = {Comprehensive reviews in food science and food safety}, volume = {13}, number = {2}, pages = {135-154}, doi = {10.1111/1541-4337.12054}, pmid = {33412651}, issn = {1541-4337}, abstract = {This monograph is a critical review of the biological activities that occur during virgin olive oil (VOO) extraction process. Strategic choices of plant engineering systems and of processing technologies should be made to condition the enzymatic activities, in order to modulate the nutritional and the sensory quality of the product toward the consumer expectations. "Modulation" of the product quality properties has the main aim to predetermine the quantity and the quality of 2 classes of substances: polyphenols and volatile compounds responsible of VOO nutritional and sensory characteristics. In the 1st section, a systematic analysis of the literature has been carried out to investigate the main olive enzymatic activities involved in the complex biotransformation that occurs during the mechanical extraction process. In the 2nd section, a critical and interpretative discussion of the influence of each step of the extraction process on the polyphenols and the volatile compounds has been performed. The effect of the different mechanical devices that are part of the extraction process is analyzed and recommendations, strategies, and possible avenues for future researches are suggested.}, }
@article {pmid32731678, year = {1989}, author = {Corpet, DE}, title = {Microbial ecology of the intestine. In vitro, in vivo and mathematical models.}, journal = {Revue scientifique et technique (International Office of Epizootics)}, volume = {8}, number = {2}, pages = {391-403}, doi = {10.20506/rst.8.2.419}, pmid = {32731678}, issn = {0253-1933}, }
@article {pmid32060494, year = {2020}, author = {Louca, P and Menni, C and Padmanabhan, S}, title = {Genomic Determinants of Hypertension With a Focus on Metabolomics and the Gut Microbiome.}, journal = {American journal of hypertension}, volume = {33}, number = {6}, pages = {473-481}, pmid = {32060494}, issn = {1941-7225}, support = {CS/16/1/31878/BHF_/British Heart Foundation/United Kingdom ; MR/M016560/1/MRC_/Medical Research Council/United Kingdom ; SP/14/8/31352/BHF_/British Heart Foundation/United Kingdom ; RE/18/6/34217/BHF_/British Heart Foundation/United Kingdom ; }, mesh = {Animals ; Bacteria/*metabolism ; *Blood Pressure ; Diet ; Essential Hypertension/*genetics/*microbiology/physiopathology ; *Gastrointestinal Microbiome ; Gene-Environment Interaction ; Genetic Predisposition to Disease ; *Genetic Variation ; Humans ; *Metabolomics ; Risk Factors ; }, abstract = {Epidemiologic and genomic studies have progressively improved our understanding of the causation of hypertension and the complex relationship with diet and environment. The majority of Mendelian forms of syndromic hypotension and hypertension (HTN) have all been linked to mutations in genes whose encoded proteins regulate salt-water balance in the kidney, supporting the primacy of the kidneys in blood pressure regulation. There are more than 1,477 single nucleotide polymorphisms associated with blood pressure and hypertension and the challenge is establishing a causal role for these variants. Hypertension is a complex multifactorial phenotype and it is likely to be influenced by multiple factors including interactions between diet and lifestyle factors, microbiome, and epigenetics. Given the finite genetic variability that is possible in humans, it is likely that incremental gains from single marker analyses have now plateaued and a greater leap in our understanding of the genetic basis of disease will come from integration of other omics and the interacting environmental factors. In this review, we focus on emerging results from the microbiome and metabolomics and discuss how leveraging these findings may facilitate a deeper understanding of the interrelationships between genomics, diet, and microbial ecology in humans in the causation of essential hypertension.}, }
@article {pmid32059463, year = {2020}, author = {Costa, OYA and Zerillo, MM and Zühlke, D and Kielak, AM and Pijl, A and Riedel, K and Kuramae, EE}, title = {Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses.}, journal = {Microorganisms}, volume = {8}, number = {2}, pages = {}, pmid = {32059463}, issn = {2076-2607}, support = {729.004.013//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 202496/2015-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, abstract = {The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined the bacterial transcriptome and proteome under growth in poor medium with a low or high concentration of sugar. We detected the presence of 217 carbohydrate-associated enzymes in the genome of strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that high sugar triggered a stress response. As part of this response, transcripts related to cell wall stress, such as sigma factor σW and toxin-antitoxin (TA) systems, were upregulated, as were several proteins involved in detoxification and repair, including MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of carbon metabolism (especially the pentose phosphate pathway) and the reduction of protein synthesis, carbohydrate metabolism, and cell division, suggesting the arrest of cell activity and growth. In summary, the stress response of Granulicella sp. WH15 induced by the presence of a high sugar concentration in the medium resulted in the intensification of secretion functions to eliminate toxic compounds and the reallocation of resources to cell maintenance instead of growth.}, }
@article {pmid32056227, year = {2020}, author = {Smirnova, E and Puri, P and Muthiah, MD and Daitya, K and Brown, R and Chalasani, N and Liangpunsakul, S and Shah, VH and Gelow, K and Siddiqui, MS and Boyett, S and Mirshahi, F and Sikaroodi, M and Gillevet, P and Sanyal, AJ}, title = {Fecal Microbiome Distinguishes Alcohol Consumption From Alcoholic Hepatitis But Does Not Discriminate Disease Severity.}, journal = {Hepatology (Baltimore, Md.)}, volume = {72}, number = {1}, pages = {271-286}, pmid = {32056227}, issn = {1527-3350}, support = {UL1 TR002649/TR/NCATS NIH HHS/United States ; U01 AA026979/AA/NIAAA NIH HHS/United States ; UO1 AA021891-01/NH/NIH HHS/United States ; U01 AA021891/AA/NIAAA NIH HHS/United States ; T32 DK07150-40/NH/NIH HHS/United States ; CTSA UL1TR002649/NH/NIH HHS/United States ; KL2 TR002648/TR/NCATS NIH HHS/United States ; T32 DK007150/DK/NIDDK NIH HHS/United States ; K23 AA021179/AA/NIAAA NIH HHS/United States ; }, mesh = {Adult ; *Alcohol Drinking ; Diagnosis, Differential ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Hepatitis, Alcoholic/*diagnosis/*microbiology ; Humans ; Male ; Middle Aged ; Severity of Illness Index ; }, abstract = {BACKGROUND AND AIMS: The role of the intestinal microbiome in alcoholic hepatitis is not established. The aims of this study were to (1) characterize the fecal microbial ecology associated with alcoholic hepatitis, (2) relate microbiome changes to disease severity, and (3) infer the functional relevance of shifts in microbial ecology.<br><br>APPROACH AND RESULTS: The fecal microbiome in patients with moderate alcoholic hepatitis (MAH) or severe alcoholic hepatitis (SAH) was compared with healthy controls (HCs) and heavy drinking controls (HDCs). Microbial taxa were identified by 16S pyrosequencing. Functional metagenomics was performed using PICRUSt. Fecal short chain fatty acids (SCFAs) were measured using a liquid chromatography-mass spectrometry platform. A total of 78 participants (HC, n&#xa0;=&#xa0;24; HDC, n&#xa0;=&#xa0;20; MAH, n&#xa0;=&#xa0;10; SAH, n&#xa0;=&#xa0;24) were studied.&#xa0;HDC had a distinct signature compared with HC with depletion of Bacteroidetes (46% vs. 26%; P&#xa0;=&#xa0;0.01). Alcoholic hepatitis was associated with a distinct microbiome signature compared with&#xa0;HDC&#xa0;(area under the curve =&#xa0;0.826); differential abundance of&#xa0;Ruminococcaceae,&#xa0;Veillonellaceae,&#xa0;Lachnospiraceae,&#xa0;Porphyromonadaceae, and&#xa0;Rikenellaceae&#xa0;families were the key contributors to these differences. The beta diversity was significantly different among the groups (permutational multivariate analysis of variance [PERMANOVA] P&#xa0;<&#xa0;0.001). SAH was associated with increased Proteobacteria (SAH 14% vs. HDC 7% and SAH vs. HC 2%, P&#xa0;=&#xa0;0.20 and 0.01, respectively). Firmicutes abundance declined from HDC to MAH to SAH (63% vs. 53% vs. 48%, respectively; P&#xa0;=&#xa0;0.09, HDC vs. SAH). Microbial taxa&#xa0;did not distinguish between MAH and SAH (PERMANOVA P&#xa0;=&#xa0;0.785). SCFAs producing bacteria (Lachnospiraceae and Ruminococcaceae) were decreased in alcoholic hepatitis, and a similar decrease was observed in fecal SCFAs among alcoholic hepatitis patients.<br><br>CONCLUSIONS: There are distinct changes in fecal microbiome associated with the development, but not severity, of alcoholic hepatitis.}, }
@article {pmid32055819, year = {2020}, author = {Marlow, JJ and Colocci, I and Jungbluth, SP and Weber, NM and Gartman, A and Kallmeyer, J}, title = {Mapping metabolic activity at single cell resolution in intact volcanic fumarole sediment.}, journal = {FEMS microbiology letters}, volume = {367}, number = {1}, pages = {}, doi = {10.1093/femsle/fnaa031}, pmid = {32055819}, issn = {1574-6968}, mesh = {*Environmental Microbiology ; Geologic Sediments/chemistry/*microbiology ; *Metabolome ; Microbiota/*physiology ; Minerals/metabolism ; Population Density ; *Single-Cell Analysis ; Volcanic Eruptions ; }, abstract = {Interactions among microorganisms and their mineralogical substrates govern the structure, function and emergent properties of microbial communities. These interactions are predicated on spatial relationships, which dictate metabolite exchange and access to key substrates. To quantitatively assess links between spatial relationships and metabolic activity, this study presents a novel approach to map all organisms, the metabolically active subset and associated mineral grains, all while maintaining spatial integrity of an environmental microbiome. We applied this method at an outgassing fumarole of Vanuatu's Marum Crater, one of the largest point sources of several environmentally relevant gaseous compounds, including H2O, CO2 and SO2. With increasing distance from the sediment-air surface and from mineral grain outer boundaries, organism abundance decreased but the proportion of metabolically active organisms often increased. These protected niches may provide more stable conditions that promote consistent metabolic activity of a streamlined community. Conversely, exterior surfaces accumulate more organisms that may cover a wider range of preferred conditions, implying that only a subset of the community will be active under any particular environmental regime. More broadly, the approach presented here allows investigators to see microbial communities 'as they really are' and explore determinants of metabolic activity across a range of microbiomes.}, }
@article {pmid32055027, year = {2020}, author = {Hatzenpichler, R and Krukenberg, V and Spietz, RL and Jay, ZJ}, title = {Next-generation physiology approaches to study microbiome function at single cell level.}, journal = {Nature reviews. Microbiology}, volume = {18}, number = {4}, pages = {241-256}, pmid = {32055027}, issn = {1740-1534}, support = {80NSSC19K0449/NSSC/Shared Services Center NASA/United States ; }, mesh = {*Bacterial Physiological Phenomena ; Inventions ; Microbiota/*physiology ; Single-Cell Analysis/*methods ; }, abstract = {The function of cells in their native habitat often cannot be reliably predicted from genomic data or from physiology studies of isolates. Traditional experimental approaches to study the function of taxonomically and metabolically diverse microbiomes are limited by their destructive nature, low spatial resolution or low throughput. Recently developed technologies can offer new insights into cellular function in natural and human-made systems and how microorganisms interact with and shape the environments that they inhabit. In this Review, we provide an overview of these next-generation physiology approaches and discuss how the non-destructive analysis of cellular phenotypes, in combination with the separation of the target cells for downstream analyses, provide powerful new, complementary ways to study microbiome function. We anticipate that the widespread application of next-generation physiology approaches will transform the field of microbial ecology and dramatically improve our understanding of how microorganisms function in their native environment.}, }
@article {pmid32054207, year = {2020}, author = {Park, J and Kim, EB}, title = {Differences in microbiome and virome between cattle and horses in the same farm.}, journal = {Asian-Australasian journal of animal sciences}, volume = {33}, number = {6}, pages = {1042-1055}, pmid = {32054207}, issn = {1011-2367}, support = {//National Research Foundation of Korea/ ; 2016R1C1B2016246//Ministry of Education/ ; }, abstract = {OBJECTIVE: The ecosystem of an animal farm is composed of various elements, such as animals, farmers, plants, feed, soil, and microorganisms. A domesticated animal's health is largely connected with the reservoir of bacteria and viruses in animal farms. Although a few studies have focused on exploring the gut microbiome of animals, communities of microbiota and viruses in feedlots have not been thoroughly investigated.<br><br>METHODS: Here, we collected feces and dust samples (4 groups: cattle feces, C_F; horse feces, H_F; cattle dust, C_D; and horse dust, H_D) from cattle and horse farms sharing the same housing and investigated their microbiome/virome communities by Illumina sequencing.<br><br>RESULTS: Dust groups (C_D and H_D) showed higher microbial diversity than feces groups (C_F and H_F) regardless of animal species. From the microbial community analysis, all the samples from the four groups have major phyla such as Proteobacteria (min 37.1% to max 42.8%), Firmicutes (19.1% to 24.9%), Bacteroidetes (10.6% to 22.1%), and Actinobacteria (6.1% to 20.5%). The abundance of Streptococcus, which commonly recognized as equine pathogens, was significantly higher in the horse group (H_D and H_F). Over 99% among the classified virome reads were classified as Caudovirales, a group of tailed bacteriophages, in all four groups. Foot-and-mouth disease virus and equine adenovirus, which cause deadly diseases in cattle and horse, respectively, were not detected.<br><br>CONCLUSION: Our results will provide baseline information to understand different gut and environmental microbial ecology between two livestock species.}, }
@article {pmid32052099, year = {2020}, author = {Nakabachi, A and Malenovský, I and Gjonov, I and Hirose, Y}, title = {16S rRNA Sequencing Detected Profftella, Liberibacter, Wolbachia, and Diplorickettsia from Relatives of the Asian Citrus Psyllid.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {410-422}, doi = {10.1007/s00248-020-01491-z}, pmid = {32052099}, issn = {1432-184X}, support = {KAKENHI grant number 26292174//the Japan Society for the Promotion of Science/ ; NA//Tatematsu Foundation/ ; NA//Nagase Science and Technology Foundation/ ; }, mesh = {Animals ; Bacteria/classification/*isolation &amp; purification ; Female ; France ; Hemiptera/*microbiology ; Male ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Symbiosis ; Wolbachia/isolation &amp; purification ; }, abstract = {The Asian citrus psyllid Diaphorina citri (Hemiptera: Psylloidea) is a serious pest of citrus species worldwide because it transmits Candidatus Liberibacter spp. (Alphaproteobacteria: Rhizobiales), the causative agents of the incurable citrus disease, huanglongbing or greening disease. Diaphorina citri possesses a specialized organ called a bacteriome, which harbors vertically transmitted intracellular mutualists, Ca. Carsonella ruddii (Gammaproteobacteria: Oceanospirillales) and Ca. Profftella armatura (Gammaproteobacteria: Betaproteobacteriales). Whereas Carsonella is a typical nutritional symbiont, Profftella is an unprecedented type of toxin-producing defensive symbiont, unusually sharing organelle-like features with nutritional symbionts. Additionally, many D. citri strains are infected with Wolbachia, which manipulate reproduction in various arthropod hosts. In the present study, in an effort to obtain insights into the evolution of symbioses between Diaphorina and bacteria, microbiomes of psyllids closely related to D. citri were investigated. Bacterial populations of Diaphorina cf. continua and Diaphorina lycii were analyzed using Illumina sequencing of 16S rRNA gene amplicons and compared with data obtained from D. citri. The analysis revealed that all three Diaphorina spp. harbor Profftella as well as Carsonella lineages, implying that Profftella is widespread within the genus Diaphorina. Moreover, the analysis identified Ca. Liberibacter europaeus and Diplorickettsia sp. (Gammaproteobacteria: Diplorickettsiales) in D. cf. continua, and a total of four Wolbachia (Alphaproteobacteria: Rickettsiales) lineages in the three psyllid species. These results provide deeper insights into the interactions among insects, bacteria, and plants, which would eventually help to better manage horticulture.}, }
@article {pmid32051016, year = {2020}, author = {Glendinning, L and Stewart, RD and Pallen, MJ and Watson, KA and Watson, M}, title = {Assembly of hundreds of novel bacterial genomes from the chicken caecum.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {34}, pmid = {32051016}, issn = {1474-760X}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; BBS/E/F/000PR10351/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P013759/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P013732/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/D/20320000/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004243/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Cecum/microbiology ; Chickens/*microbiology ; *Gastrointestinal Microbiome ; *Genome, Bacterial ; *Metagenome ; }, abstract = {BACKGROUND: Chickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short-chain fatty acids, nitrogen recycling, and amino acid production. In this study, we sequence DNA from caecal content samples taken from 24 chickens belonging to either a fast or a slower growing breed consuming either a vegetable-only diet or a diet containing fish meal.<br><br>RESULTS: We utilise 1.6&#x2009;T of Illumina data to construct 469 draft metagenome-assembled bacterial genomes, including 460 novel strains, 283 novel species, and 42 novel genera. We compare our genomes to data from 9 European Union countries and show that these genomes are abundant within European chicken flocks. We also compare the abundance of our genomes, and the carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are both breed- and diet-specific microbiomes, as well as an overlapping core microbiome.<br><br>CONCLUSIONS: This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota.}, }
@article {pmid32050392, year = {2020}, author = {Chai, B and Tsoi, T and Sallach, JB and Liu, C and Landgraf, J and Bezdek, M and Zylstra, G and Li, H and Johnston, CT and Teppen, BJ and Cole, JR and Boyd, SA and Tiedje, JM}, title = {Bioavailability of clay-adsorbed dioxin to Sphingomonas wittichii RW1 and its associated genome-wide shifts in gene expression.}, journal = {The Science of the total environment}, volume = {712}, number = {}, pages = {135525}, doi = {10.1016/j.scitotenv.2019.135525}, pmid = {32050392}, issn = {1879-1026}, mesh = {Biological Availability ; Clay ; Dioxins ; Gene Expression ; Genome, Bacterial ; *Sphingomonas ; }, abstract = {Polychlorinated dibenzo-p-dioxins and dibenzofurans are a group of chemically-related pollutants categorically known as dioxins. Some of their chlorinated congeners are among the most hazardous pollutants that persist in the environment. This persistence is due in part to the limited number of bacteria capable of metabolizing these compounds, but also to their limited bioavailability in soil. We used Sphingomonas wittichii strain RW1 (RW1), one of the few strains able to grow on dioxin, to characterize its ability to respond to and degrade clay-bound dioxin. We found that RW1 grew on and completely degraded dibenzo-p-dioxin (DD) intercalated into the smectite clay saponite (SAP). To characterize the effects of DD sorption on RW1 gene expression, we compared transcriptomes of RW1 grown with either free crystalline DD or DD intercalated clay, i.e. sandwiched between the clay interlayers (DDSAP). Free crystalline DD appeared to cause greater expression of toxicity and stress related functions. Genes coding for heat shock proteins, chaperones, as well as genes involved in DNA repair, and efflux were up-regulated during growth on crystalline dioxin compared to growth on intercalated dioxin. In contrast, growth on intercalated dioxin up-regulated genes that might be important in recognition and uptake mechanisms, as well as surface interaction/attachment/biofilm formation such as extracellular solute-binding protein and LuxR. These differences in gene expression may reflect the underlying adaptive mechanisms by which RW1 cells sense and deploy pathways to access dioxin intercalated into clay. These data show that intercalated DD remains bioavailable to the degrading bacterium with implications for bioremediation alternatives.}, }
@article {pmid32049503, year = {2020}, author = {De Paepe, J and De Pryck, L and Verliefde, ARD and Rabaey, K and Clauwaert, P}, title = {Electrochemically Induced Precipitation Enables Fresh Urine Stabilization and Facilitates Source Separation.}, journal = {Environmental science &amp; technology}, volume = {54}, number = {6}, pages = {3618-3627}, doi = {10.1021/acs.est.9b06804}, pmid = {32049503}, issn = {1520-5851}, mesh = {Ammonia ; *Bathroom Equipment ; Chemical Precipitation ; Hydrolysis ; Recycling ; Urine ; *Wastewater ; }, abstract = {Source separation of urine can enable nutrient recycling, facilitate wastewater management, and conserve water. Without stabilization of the urine, urea is quickly hydrolyzed into ammonia and (bi)carbonate, causing nutrient loss, clogging of collection systems, ammonia volatilization, and odor nuisance. In this study, electrochemically induced precipitation and stabilization of fresh urine was successfully demonstrated. By recirculating the urine over the cathodic compartment of an electrochemical cell, the pH was increased due to the production of hydroxyl ions at the cathode. The pH increased to 11-12, decreasing calcium and magnesium concentrations by >80%, and minimizing scaling and clogging during downstream processing. At pH 11, urine could be stabilized for one week, while an increase to pH 12 allowed urine storage without urea hydrolysis for >18 months. By a smart selection of membranes [anion exchange membrane (AEM) with a cation exchange membrane (CEM) or a bipolar membrane (BPM)], no chemical input was required in the electrochemical cell and an acidic stream was produced that can be used to periodically rinse the electrochemical cell and toilet. On-site electrochemical treatment, close to the toilet, is a promising new concept to minimize clogging in collection systems by forcing controlled precipitation and to inhibit urea hydrolysis during storage until further treatment in more centralized nutrient recovery plants.}, }
@article {pmid32045510, year = {2020}, author = {Boreczek, J and Litwinek, D and Żylińska-Urban, J and Izak, D and Buksa, K and Gawor, J and Gromadka, R and Bardowski, JK and Kowalczyk, M}, title = {Bacterial community dynamics in spontaneous sourdoughs made from wheat, spelt, and rye wholemeal flour.}, journal = {MicrobiologyOpen}, volume = {9}, number = {4}, pages = {e1009}, pmid = {32045510}, issn = {2045-8827}, mesh = {Bacteroidetes/classification/isolation &amp; purification/*metabolism ; Biodiversity ; Bioreactors/microbiology ; Bread/*microbiology ; Fermentation ; Flour/*microbiology ; Food Microbiology ; Lactobacillus/classification/isolation &amp; purification/*metabolism ; Proteobacteria/classification/isolation &amp; purification/*metabolism ; Secale/metabolism ; Triticum/metabolism ; }, abstract = {Sourdough fermentation is a traditional process that is used to improve bread quality. A spontaneous sourdough ecosystem consists of a mixture of flour and water that is fermented by endogenous lactic acid bacteria (LAB) and yeasts. The aim of this study was to identify bacterial diversity during backslopping of spontaneous sourdoughs prepared from wheat, spelt, or rye wholemeal flour. Culture-dependent analyses showed that the number of LAB (10[9] CFU/ml) was higher by three orders of magnitude than the number of yeasts (10[6] CFU/ml), irrespective of the flour type. These results were complemented by next-generation sequencing of the 16S rDNA V3 and V4 variable regions. The dominant phylum in all sourdough samples was Firmicutes, which was represented exclusively by the Lactobacillales order. The two remaining and less abundant phyla were Proteobacteria and Bacteroidetes. The culture-independent approach allowed us to detect changes in microbial ecology during the 72-hr fermentation period. Weissella sp. was the most abundant genus after 24 hr of fermentation of the rye sourdough, but as the process progressed, its abundance decreased in favor of the Lactobacillus genus similarly as in wheat and spelt sourdoughs. The Lactobacillus genus was dominant in all sourdoughs after 72 hr, which was consistent with our results obtained using culture-dependent analyses. This work was carried out to determine the microbial biodiversity of sourdoughs that are made from wheat, spelt, and rye wholemeal flour and can be used as a source of strains for specific starter cultures to produce functional bread.}, }
@article {pmid32043958, year = {2020}, author = {Hofmann, K and Huptas, C and Doll, EV and Scherer, S and Wenning, M}, title = {Pseudomonas haemolytica sp. nov., isolated from raw milk and skimmed milk concentrate.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {70}, number = {4}, pages = {2339-2347}, doi = {10.1099/ijsem.0.004043}, pmid = {32043958}, issn = {1466-5034}, mesh = {Animals ; Bacterial Typing Techniques ; Base Composition ; Cattle ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; *Food Microbiology ; Genes, Bacterial ; Milk/*microbiology ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; Pseudomonas/*classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {Two strains, WS 5063[T] and WS 5067, isolated from raw cow's milk and skimmed milk concentrate, could be affiliated as members of the same, hitherto unknown, Pseudomonas species by 16S rRNA and rpoD gene sequences. Multilocus sequence and average nucleotide identity (ANIm) analyses based on draft genome sequences confirmed the discovery of a novel Pseudomonas species. It was most closely related to Pseudomonas synxantha DSM 18928[T] with an ANIm of 91.4 %. The DNA G+C content of WS 5063[T] was 60.0 mol %. Phenotypic characterizations showed that the isolates are rod-shaped, motile, catalase- and oxidase-positive, and aerobic. Growth occurred at 4-34 °C and at pH values of pH 5.5-8.0. Both strains showed strong β-haemolysis on blood agar. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The dominant quinone was Q-9 (90 %), but noticeable amounts of Q-8 (9 %) and traces of Q-7 were also detected. Fatty acid profiles were typical for Pseudomonas species and exhibited C16 : 0 as a major component. Based on these results, we conclude that both strains belong to a novel species, for which the name Pseudomonas haemolytica sp. nov. is proposed. The type strain is WS 5063[T] (=DSM 108987[T]=LMG 31232[T]) and an additional strain is WS 5067 (=DSM 108988=LMG 31233).}, }
@article {pmid32043954, year = {2020}, author = {Wenning, M and Breitenwieser, F and Huptas, C and Doll, E and Bächler, B and Schulz, A and Dunkel, A and Hofmann, T and von Neubeck, M and Busse, HJ and Scherer, S}, title = {Brevilactibacter flavus gen. nov., sp. nov., a novel bacterium of the family Propionibacteriaceae isolated from raw milk and dairy products and reclassification of Propioniciclava sinopodophylli as Brevilactibacter sinopodophylli comb. nov.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {70}, number = {4}, pages = {2186-2193}, doi = {10.1099/ijsem.0.003909}, pmid = {32043954}, issn = {1466-5034}, mesh = {Animals ; Bacterial Typing Techniques ; Base Composition ; Cell Wall/chemistry ; DNA, Bacterial/genetics ; Dairy Products/*microbiology ; Diaminopimelic Acid/chemistry ; Fatty Acids/chemistry ; Food Microbiology ; Germany ; Glycolipids/chemistry ; Milk/*microbiology ; Peptidoglycan/chemistry ; Phospholipids/chemistry ; *Phylogeny ; Propionibacteriaceae/*classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {Eight facultatively anaerobic rod-shaped bacteria were isolated from raw milk and two other dairy products. Results of phylogenetic analyses based on 16S rRNA gene sequences showed that the isolates are placed in a distinct lineage within the family Propionibacteriaceae with Propioniciclava sinopodophylli and Propioniciclava tarda as the closest relatives (94.6 and 93.5 % similarity, respectively). The cell-wall peptidoglycan contained meso-diaminopimelic acid, alanine and glutamic acid and was of the A1γ type (meso-DAP-direct). The major cellular fatty acid was anteiso-C15 : 0 and the major polar lipids were diphosphatidylglycerol, phosphatidyglycerol and three unidentified glycolipids. The quinone system contained predominantly menaquinone MK-9(H4). The G+C content of the genomic DNA of strain VG341[T] was 67.7 mol%. The whole-cell sugar pattern contained ribose, rhamnose, arabinose and galactose. On the basis of phenotypic and genetic data, eight strains (VG341[T], WS4684, WS4769, WS 4882, WS4883, WS4901, WS4902 and WS4904) are proposed to be classified as members of a novel species in a new genus of the family Propionibacteriaceae, for which the name Brevilactibacter flavus gen. nov., sp. nov. is proposed. The type strain is VG341[T] (=WS4900[T]=DSM 100885[T]=LMG 29089[T]) and seven additional strains are WS4684, WS4769, WS4882, WS4883, WS4901, WS4902 and WS4904. Furthermore, we propose the reclassification of P. sinopodophylli as Brevilactibacter sinopodophylli comb. nov.}, }
@article {pmid32042158, year = {2020}, author = {Zhang, J and Fu, XX and Li, RQ and Zhao, X and Liu, Y and Li, MH and Zwaenepoel, A and Ma, H and Goffinet, B and Guan, YL and Xue, JY and Liao, YY and Wang, QF and Wang, QH and Wang, JY and Zhang, GQ and Wang, ZW and Jia, Y and Wang, MZ and Dong, SS and Yang, JF and Jiao, YN and Guo, YL and Kong, HZ and Lu, AM and Yang, HM and Zhang, SZ and Van de Peer, Y and Liu, ZJ and Chen, ZD}, title = {The hornwort genome and early land plant evolution.}, journal = {Nature plants}, volume = {6}, number = {2}, pages = {107-118}, pmid = {32042158}, issn = {2055-0278}, mesh = {Anthocerotophyta/*genetics ; *Biological Evolution ; *Genome, Plant ; Multigene Family ; Phylogeny ; }, abstract = {Hornworts, liverworts and mosses are three early diverging clades of land plants, and together comprise the bryophytes. Here, we report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan, while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage. Although the Anthoceros genome is small and characterized by minimal redundancy, expansions are observed in gene families related to RNA editing, UV protection and desiccation tolerance. The genome of A. angustus bears the signatures of horizontally transferred genes from bacteria and fungi, in particular of genes operating in stress-response and metabolic pathways. Our study provides insight into the unique features of hornworts and their molecular adaptations to live on land.}, }
@article {pmid32042128, year = {2020}, author = {VanInsberghe, D and Elsherbini, JA and Varian, B and Poutahidis, T and Erdman, S and Polz, MF}, title = {Diarrhoeal events can trigger long-term Clostridium difficile colonization with recurrent blooms.}, journal = {Nature microbiology}, volume = {5}, number = {4}, pages = {642-650}, pmid = {32042128}, issn = {2058-5276}, mesh = {Actinobacteria/genetics/growth &amp; development/isolation &amp; purification ; Animals ; Bacteroidetes/genetics/growth &amp; development/isolation &amp; purification ; Clostridioides difficile/*drug effects/growth &amp; development/*pathogenicity ; Clostridium Infections/complications/*microbiology ; Colony Count, Microbial ; Diarrhea/chemically induced/complications/*microbiology ; Disease Models, Animal ; Feces/microbiology ; Firmicutes/genetics/growth &amp; development/isolation &amp; purification ; Fusobacteria/genetics/growth &amp; development/isolation &amp; purification ; Gastrointestinal Microbiome/*drug effects ; Humans ; Laxatives/*adverse effects ; Male ; Mice ; Polyethylene Glycols/*adverse effects ; Proteobacteria/genetics/growth &amp; development/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Although Clostridium difficile is widely considered an antibiotic- and hospital-associated pathogen, recent evidence indicates that this is an insufficient depiction of the risks and reservoirs. A common thread that links all major risk factors of infection is their association with gastrointestinal disturbances, but this relationship to C. difficile colonization has never been tested directly. Here, we show that disturbances caused by diarrhoeal events trigger susceptibility to C. difficile colonization. Using survey data of the human gut microbiome, we detected C. difficile colonization and blooms in people recovering from food poisoning and Vibrio cholerae infections. Carriers remained colonized for year-long time scales and experienced highly variable patterns of C. difficile abundance, where increased shedding over short periods of 1-2 d interrupted week-long periods in which C. difficile was undetectable. Given that short shedding events were often linked to gastrointestinal disturbances, our results help explain why C. difficile is frequently detected as a co-infecting pathogen in patients with diarrhoea. To directly test the impact of diarrhoea on susceptibility to colonization, we developed a mouse model of variable disturbance intensity, which allowed us to monitor colonization in the absence of disease. As mice exposed to avirulent C. difficile spores ingested increasing quantities of laxatives, more individuals experienced C. difficile blooms. Our results indicate that the likelihood of colonization is highest in the days immediately following acute disturbances, suggesting that this could be an important window during which transmission could be interrupted and the incidence of infection lowered.}, }
@article {pmid32039976, year = {2020}, author = {Burmeister, DM and Johnson, TR and Lai, Z and Scroggins, SR and DeRosa, M and Jonas, RB and Zhu, C and Scherer, E and Stewart, RM and Schwacha, MG and Jenkins, DH and Eastridge, BJ and Nicholson, SE}, title = {The gut microbiome distinguishes mortality in trauma patients upon admission to the emergency department.}, journal = {The journal of trauma and acute care surgery}, volume = {88}, number = {5}, pages = {579-587}, pmid = {32039976}, issn = {2163-0763}, support = {KL2 TR001118/TR/NCATS NIH HHS/United States ; KL2 TR002646/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Aged ; Emergency Service, Hospital/statistics &amp; numerical data ; Feces/microbiology ; Female ; Follow-Up Studies ; Gastrointestinal Microbiome/*physiology ; Hospital Mortality ; Humans ; Injury Severity Score ; Length of Stay/statistics &amp; numerical data ; Male ; Middle Aged ; Prognosis ; Prospective Studies ; Trauma Centers/statistics &amp; numerical data ; Wounds, Nonpenetrating/diagnosis/microbiology/*mortality ; Wounds, Penetrating/diagnosis/microbiology/*mortality ; }, abstract = {BACKGROUND: Traumatic injury can lead to a compromised intestinal epithelial barrier, decreased gut perfusion, and inflammation. While recent studies indicate that the gut microbiome (GM) is altered early following traumatic injury, the impact of GM changes on clinical outcomes remains unknown. Our objective of this follow-up study was to determine if the GM is associated with clinical outcomes in critically injured patients.<br><br>METHODS: We conducted a prospective, observational study in adult patients (N = 67) sustaining severe injury admitted to a level I trauma center. Fecal specimens were collected on admission to the emergency department, and microbial DNA from all samples was analyzed using the Quantitative Insights Into Microbial Ecology pipeline and compared against the Greengenes database. &#x3b1;-Diversity and &#x3b2;-diversity were estimated using the observed species metrics and analyzed with t tests and permutational analysis of variance for overall significance, with post hoc pairwise analyses.<br><br>RESULTS: Our patient population consisted of 63% males with a mean age of 44 years. Seventy-eight percent of the patients suffered blunt trauma with 22% undergoing penetrating injuries. The mean body mass index was 26.9 kg/m. Significant differences in admission &#x3b2;-diversity were noted by hospital length of stay, intensive care unit hospital length of stay, number of days on the ventilator, infections, and acute respiratory distress syndrome (p < 0.05). &#x3b2;-Diversity on admission differed in patients who died compared with patients who lived (mean time to death, 8 days). There were also significantly less operational taxonomic units in samples from patients who died versus those who survived. A number of species were enriched in the GM of injured patients who died, which included some traditionally probiotic species such as Akkermansia muciniphilia, Oxalobacter formigenes, and Eubacterium biforme (p < 0.05).<br><br>CONCLUSION: Gut microbiome diversity on admission in severely injured patients is predictive of a variety of clinically important outcomes. While our study does not address causality, the GM of trauma patients may provide valuable diagnostic and therapeutic targets for the care of injured patients.<br><br>LEVEL OF EVIDENCE: Prognostic and epidemiological, level III.}, }
@article {pmid32038529, year = {2019}, author = {Lee, JY and Haruta, S and Kato, S and Bernstein, HC and Lindemann, SR and Lee, DY and Fredrickson, JK and Song, HS}, title = {Prediction of Neighbor-Dependent Microbial Interactions From Limited Population Data.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {3049}, pmid = {32038529}, issn = {1664-302X}, abstract = {Modulation of interspecies interactions by the presence of neighbor species is a key ecological factor that governs dynamics and function of microbial communities, yet the development of theoretical frameworks explicit for understanding context-dependent interactions are still nascent. In a recent study, we proposed a novel rule-based inference method termed the Minimal Interspecies Interaction Adjustment (MIIA) that predicts the reorganization of interaction networks in response to the addition of new species such that the modulation in interaction coefficients caused by additional members is minimal. While the theoretical basis of MIIA was established through the previous work by assuming the full availability of species abundance data in axenic, binary, and complex communities, its extension to actual microbial ecology can be highly constrained in cases that species have not been cultured axenically (e.g., due to their inability to grow in the absence of specific partnerships) because binary interaction coefficients - basic parameters required for implementing the MIIA - are inestimable without axenic and binary population data. Thus, here we present an alternative formulation based on the following two central ideas. First, in the case where only data from axenic cultures are unavailable, we remove axenic populations from governing equations through appropriate scaling. This allows us to predict neighbor-dependent interactions in a relative sense (i.e., fractional change of interactions between with versus without neighbors). Second, in the case where both axenic and binary populations are missing, we parameterize binary interaction coefficients to determine their values through a sensitivity analysis. Through the case study of two microbial communities with distinct characteristics and complexity (i.e., a three-member community where all members can grow independently, and a four-member community that contains member species whose growth is dependent on other species), we demonstrated that despite data limitation, the proposed new formulation was able to successfully predict interspecies interactions that are consistent with experimentally derived results. Therefore, this technical advancement enhances our ability to predict context-dependent interspecies interactions in a broad range of microbial systems without being limited to specific growth conditions as a pre-requisite.}, }
@article {pmid32036919, year = {2020}, author = {Babaahmadifooladi, M and Jacxsens, L and Van de Wiele, T and Laing, GD}, title = {Gap analysis of nickel bioaccessibility and bioavailability in different food matrices and its impact on the nickel exposure assessment.}, journal = {Food research international (Ottawa, Ont.)}, volume = {129}, number = {}, pages = {108866}, doi = {10.1016/j.foodres.2019.108866}, pmid = {32036919}, issn = {1873-7145}, mesh = {Biological Availability ; Food Analysis/*methods ; *Hypersensitivity ; Nickel/*chemistry/*pharmacokinetics ; Plants/*chemistry ; }, abstract = {The metal nickel is well known to cause nickel allergy in sensitive humans by prolonged dermal contact to materials releasing (high) amounts of nickel. Oral nickel exposure via water and food intake is of potential concern. Nickel is essential to plants and animals and can be naturally found in food products or contamination may occur across the agro-food chain. This gap analysis is an evaluation of nickel as a potential food safety hazard causing a risk for human health. In the first step, the available data regarding the occurrence of nickel and its contamination in food and drinks have been collected through literature review. Subsequently, a discussion is held on the potential risks associated with this contamination. Elevated nickel concentrations were mostly found in plant-based foods, e.g. legumes and nuts in which nickel of natural origin is expected. However, it was observed that dedicated and systematic screening of foodstuffs for the presence of nickel is currently still lacking. In a next step, published studies on exposure of humans to nickel via foods and drinks were critically evaluated. Not including bioaccessibility and/or bioavailability of the metal may lead to an overestimation of the exposure of the body to nickel via food and drinks. This overestimation may be problematic when the measured nickel level in foods is high and bioaccessibility and/or bioavailability of nickel in these products is low. Therefore, this paper analyzes the outcomes of the existing dietary intake and bioaccessibility/bioavailability studies conducted for nickel. Besides, the available gaps in nickel bioaccessibility and/or bioavailability studies have been clarified in this paper. The reported bioaccessibility and bioavailability percentages for different food and drinks were found to vary between <LOD and 83% and between 0 and 30% respectively. This indicates that of the total nickel contained in the foodstuffs only a fraction can be absorbed by the intestinal epithelium cells. This paper provides a unique critical overview on nickel in the human diet starting from factors affecting its occurrence in food until its absorption by the body.}, }
@article {pmid32036914, year = {2020}, author = {Vossen, E and Goethals, S and De Vrieze, J and Boon, N and Van Hecke, T and De Smet, S}, title = {Red and processed meat consumption within two different dietary patterns: Effect on the colon microbial community and volatile metabolites in pigs.}, journal = {Food research international (Ottawa, Ont.)}, volume = {129}, number = {}, pages = {108793}, doi = {10.1016/j.foodres.2019.108793}, pmid = {32036914}, issn = {1873-7145}, mesh = {Animals ; Butyrivibrio/metabolism ; Campylobacter/metabolism ; Chickens ; Clostridium/metabolism ; Colon/metabolism/*microbiology ; DNA, Bacterial/genetics/isolation &amp; purification ; Diet/*veterinary ; Diet, Western ; Enterobacteriaceae/metabolism ; Fermentation ; *Gastrointestinal Microbiome ; Male ; Meat Products/*analysis ; Red Meat/*analysis ; Swine ; Volatile Organic Compounds/*metabolism ; }, abstract = {Pigs were fed either red and processed meat or chicken meat within either a prudent or a Western dietary pattern for four weeks (2 × 2 full factorial design). The colon microbial community and volatile organic compounds were assessed (either quantified or based on their presence). Results show that Lactobacilli were characteristic for the chicken × prudent dietary pattern treatment and Paraprevotella for the red and processed meat × prudent dietary pattern treatment. Enterobacteriaceae and Desulfovibrio were characteristic for the chicken × Western dietary pattern treatment and Butyrivibrio for the red and processed meat × Western dietary pattern treatment. Campylobacter was characteristic for chicken consumption and Clostridium XIVa for red and processed meat, irrespective of the dietary pattern. Ethyl valerate and 1-methylthio-propane were observed more frequently in pigs fed red and processed meat compared to chicken meat. The prevalence of 3-methylbutanal was >80% for pigs receiving a Western dietary pattern, whereas for pigs fed a prudent dietary pattern the prevalence was <35%. The concentration of butanoic acid was significantly higher when the prudent dietary pattern was given, compared to the Western dietary pattern, but no differences for other short chain fatty acids or protein fermentation products were observed.}, }
@article {pmid32034763, year = {2020}, author = {Rombouts, JL and Kranendonk, EMM and Regueira, A and Weissbrodt, DG and Kleerebezem, R and van Loosdrecht, MCM}, title = {Selecting for lactic acid producing and utilising bacteria in anaerobic enrichment cultures.}, journal = {Biotechnology and bioengineering}, volume = {117}, number = {5}, pages = {1281-1293}, pmid = {32034763}, issn = {1097-0290}, support = {024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/International ; FPU14/05457//Spanish Ministry of Education/International ; }, mesh = {Anaerobiosis/*physiology ; Bioreactors/microbiology ; Cell Culture Techniques ; Fermentation/physiology ; Lactic Acid/metabolism ; *Lactobacillales/metabolism/physiology ; }, abstract = {Lactic acid-producing bacteria are important in many fermentations, such as the production of biobased plastics. Insight in the competitive advantage of lactic acid bacteria over other fermentative bacteria in a mixed culture enables ecology-based process design and can aid the development of sustainable and energy-efficient bioprocesses. Here we demonstrate the enrichment of lactic acid bacteria in a controlled sequencing batch bioreactor environment using a glucose-based medium supplemented with peptides and B vitamins. A mineral medium enrichment operated in parallel was dominated by Ethanoligenens species and fermented glucose to acetate, butyrate and hydrogen. The complex medium enrichment was populated by Lactococcus, Lactobacillus and Megasphaera species and showed a product spectrum of acetate, ethanol, propionate, butyrate and valerate. An intermediate peak of lactate was observed, showing the simultaneous production and consumption of lactate, which is of concern for lactic acid production purposes. This study underlines that the competitive advantage for lactic acid-producing bacteria primarily lies in their ability to attain a high biomass specific uptake rate of glucose, which was two times higher for the complex medium enrichment when compared to the mineral medium enrichment. The competitive advantage of lactic acid production in rich media can be explained using a resource allocation theory for microbial growth processes.}, }
@article {pmid32034151, year = {2020}, author = {Kitzinger, K and Marchant, HK and Bristow, LA and Herbold, CW and Padilla, CC and Kidane, AT and Littmann, S and Daims, H and Pjevac, P and Stewart, FJ and Wagner, M and Kuypers, MMM}, title = {Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {767}, pmid = {32034151}, issn = {2041-1723}, abstract = {Nitrification, the oxidation of ammonia via nitrite to nitrate, is a key process in marine nitrogen (N) cycling. Although oceanic ammonia and nitrite oxidation are balanced, ammonia-oxidizing archaea (AOA) vastly outnumber the main nitrite oxidizers, the bacterial Nitrospinae. The ecophysiological reasons for this discrepancy in abundance are unclear. Here, we compare substrate utilization and growth of Nitrospinae to AOA in the Gulf of Mexico. Based on our results, more than half of the Nitrospinae cellular N-demand is met by the organic-N compounds urea and cyanate, while AOA mainly assimilate ammonium. Nitrospinae have, under in situ conditions, around four-times higher biomass yield and five-times higher growth rates than AOA, despite their ten-fold lower abundance. Our combined results indicate that differences in mortality between Nitrospinae and AOA, rather than thermodynamics, biomass yield and cell size, determine the abundances of these main marine nitrifiers. Furthermore, there is no need to invoke yet undiscovered, abundant nitrite oxidizers to explain nitrification rates in the ocean.}, }
@article {pmid32033945, year = {2020}, author = {Heys, C and Cheaib, B and Busetti, A and Kazlauskaite, R and Maier, L and Sloan, WT and Ijaz, UZ and Kaufmann, J and McGinnity, P and Llewellyn, MS}, title = {Neutral Processes Dominate Microbial Community Assembly in Atlantic Salmon, Salmo salar.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {8}, pages = {}, pmid = {32033945}, issn = {1098-5336}, support = {BB/P001203/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Aquaculture ; Bacteria/*genetics ; Gastrointestinal Microbiome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Salmo salar/growth &amp; development/*microbiology ; Stochastic Processes ; }, abstract = {In recent years, a wealth of studies has examined the relationships between a host and its microbiome across diverse taxa. Many studies characterize the host microbiome without considering the ecological processes that underpin microbiome assembly. In this study, the intestinal microbiota of Atlantic salmon, Salmo salar, sampled from farmed and wild environments was first characterized using 16S rRNA gene MiSeq sequencing analysis. We used neutral community models to determine the balance of stochastic and deterministic processes that underpin microbial community assembly and transfer across life cycle stage and between gut compartments. Across gut compartments in farmed fish, neutral models suggest that most microbes are transient with no evidence of adaptation to their environment. In wild fish, we found declining taxonomic and functional microbial community richness as fish mature through different life cycle stages. Alongside neutral community models applied to wild fish, we suggest that declining richness demonstrates an increasing role for the host in filtering microbial communities that is correlated with age. We found a limited subset of gut microflora adapted to the farmed and wild host environment among which Mycoplasma spp. are prominent. Our study reveals the ecological drivers underpinning community assembly in both farmed and wild Atlantic salmon and underlines the importance of understanding the role of stochastic processes, such as random drift and small migration rates in microbial community assembly, before considering any functional role of the gut microbes encountered.IMPORTANCE A growing number of studies have examined variation in the microbiome to determine the role in modulating host health, physiology, and ecology. However, the ecology of host microbial colonization is not fully understood and rarely tested. The continued increase in production of farmed Atlantic salmon, coupled with increased farmed-wild salmon interactions, has accentuated the need to unravel the potential adaptive function of the microbiome and to distinguish resident from transient gut microbes. Between gut compartments in a farmed system, we found a majority of operational taxonomic units (OTUs) that fit the neutral model, with Mycoplasma species among the key exceptions. In wild fish, deterministic processes account for more OTU differences across life stages than those observed across gut compartments. Unlike previous studies, our results make detailed comparisons between fish from wild and farmed environments, while also providing insight into the ecological processes underpinning microbial community assembly in this ecologically and economically important species.}, }
@article {pmid32031212, year = {2020}, author = {Fenske, GJ and Ghimire, S and Antony, L and Christopher-Hennings, J and Scaria, J}, title = {Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {3}, pages = {}, doi = {10.1093/femsec/fiaa022}, pmid = {32031212}, issn = {1574-6941}, mesh = {Animals ; Bacteroidetes/genetics ; *Gastrointestinal Microbiome ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Swine ; }, abstract = {Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.}, }
@article {pmid32030584, year = {2020}, author = {Mariano, C and Mello, IS and Barros, BM and da Silva, GF and Terezo, AJ and Soares, MA}, title = {Mercury alters the rhizobacterial community in Brazilian wetlands and it can be bioremediated by the plant-bacteria association.}, journal = {Environmental science and pollution research international}, volume = {27}, number = {12}, pages = {13550-13564}, pmid = {32030584}, issn = {1614-7499}, support = {409062/2018-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 568258/2014//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa&#xa0;do Estado de&#xa0;Mato Grosso/ ; }, mesh = {Actinobacteria ; Bacillus ; Biodegradation, Environmental ; Brazil ; *Mercury ; Microbacterium ; Soil Microbiology ; *Soil Pollutants ; Wetlands ; }, abstract = {This study examined how soil mercury contamination affected the structure and functionality of rhizobacteria communities from Aeschynomene fluminensis and Polygonum acuminatum and how rhizobacteria mediate metal bioremediation. The strains were isolated using culture-dependent methods, identified through 16S rDNA gene sequencing, and characterized with respect to their functional traits related to plant growth promotion and resistance to metals and antibiotics. The bioremediation capacity of the rhizobacteria was determined in greenhouse using corn plants. The isolated bacteria belonged to the phyla Actinobacteria, Deinococcus-Thermus, Firmicutes, and Proteobacteria, with great abundance of the species Microbacterium trichothecenolyticum. The rhizobacteria abundance, richness, and diversity were greater in mercury-contaminated soils. Bacteria isolated from contaminated environments had higher minimum inhibitory concentration values, presented plasmids and the merA gene, and were multi-resistant to metals and antibiotics. Enterobacter sp._C35 and M. trichothecenolyticum_C34 significantly improved (Dunnett's test, p < 0.05) corn plant growth in mercury-contaminated soil. These bacteria helped to reduce up to 87% of the mercury content in the soil, and increased the mercury bioaccumulation factor by up to 94%. Mercury bioremediation mitigated toxicity of the contaminated substrate. Enterobacter sp._C35, Bacillus megaterium_C28, and Bacillus mycoides_C1 stimulated corn plant growth and could be added to biofertilizers produced in research and related industries.}, }
@article {pmid32027305, year = {2020}, author = {Lee, HJ and Whang, KS}, title = {Elioraea rosea sp. nov., a plant promoting bacterium isolated from floodwater of a paddy field.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {70}, number = {3}, pages = {2132-2136}, doi = {10.1099/ijsem.0.004028}, pmid = {32027305}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Nucleic Acid Hybridization ; Oryza ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Rhodospirillales/*classification/isolation &amp; purification ; Sequence Analysis, DNA ; Ubiquinone/analogs &amp; derivatives/chemistry ; *Water Microbiology ; }, abstract = {A Gram-stain-negative bacterium, designated strain PF-30[T], was isolated from floodwater of a paddy field in South Korea. Strain PF-30[T] was found to be a strictly aerobic, motile and pink-pigmented rods which can grow at 25-40 °C (optimum, 28 °C), at pH 5.0-9.0 (optimum pH 7.0) and at salinities of 0.5-3.0 % NaCl (optimum 0.5 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain PF-30[T] belongs to the genus Elioraea, showing highest sequence similarity to Elioraea tepidiphila TU-7[T] (97.1%) and less than 91.3 % similarity with other members of the family Acetobacteraceae. The average nucleotide identity (ANI) and DNA-DNA relatedness between the strain PF-30[T] and E. tepidiphila TU-7[T] yielded an ANI value of 75.1 % and DNA-DNA relatedness of 11.7±0.7 %, respectively. The major fatty acids were identified as C18 : 0 and C18 : 1 ω7c. The predominant respiratory quinone was identified as Q-10. The DNA G+C content was determined to be 69.9 mol%. The strain PF-30[T] was observed to produce plant-growth-promoting materials such as indole-3-acetic acid (IAA), siderophore and phytase. On the basis of the results from phylogenetic, chemotaxonomic and phenotypic data, we concluded that strain PF-30[T] represents a novel species of the genus Elioraea, for which the name Elioraea rosea sp. nov. is proposed. The type strain is PF-30[T] (=KACC 19985[T]=NBRC 113984[T]).}, }
@article {pmid32025810, year = {2020}, author = {Smichi, N and Messaoudi, Y and Allaf, K and Gargouri, M}, title = {Steam explosion (SE) and instant controlled pressure drop (DIC) as thermo-hydro-mechanical pretreatment methods for bioethanol production.}, journal = {Bioprocess and biosystems engineering}, volume = {43}, number = {6}, pages = {945-957}, doi = {10.1007/s00449-020-02297-6}, pmid = {32025810}, issn = {1615-7605}, mesh = {*Biofuels ; *Bioreactors ; *Biotechnology ; Ethanol/*metabolism ; Steam ; }, abstract = {Lignocellulosic biomass can be considered as one of the largest sources for the production of renewable biofuels (bioethanol). It involves an enzymatic treatment capable of ensuring the depolymerization of cellulose into fermentable sugars, followed by the production of ethanol by appropriate bacteriological fermentation. Proper destruction of the compact natural structure of the biomass would allow an interesting intensification of the operation. Among the most prominent technical approaches, the steam explosion (SE) is the most famous. However, this high pressure-high temperature process implies too high energy consumption while leading to the generation of many non-fermentable molecules. In recent years, many studies have proposed the use of the Instant Controlled Pressure-Drop (DIC) texturing pretreatment as an effective alternative to SE for ethanol production. Therefore, in this manuscript, we propose to compare and discuss the fundamental principles and experimental results of these two operations, as presented in the relevant literature.}, }
@article {pmid32024862, year = {2020}, author = {Snyder, GT and Matsumoto, R and Suzuki, Y and Kouduka, M and Kakizaki, Y and Zhang, N and Tomaru, H and Sano, Y and Takahata, N and Tanaka, K and Bowden, SA and Imajo, T}, title = {Evidence in the Japan Sea of microdolomite mineralization within gas hydrate microbiomes.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {1876}, pmid = {32024862}, issn = {2045-2322}, mesh = {Aquatic Organisms/chemistry/*metabolism ; Bacteroidetes/chemistry/*metabolism ; Biodegradation, Environmental ; Calcium Carbonate/*chemistry ; Fossils ; Geologic Sediments/chemistry/*microbiology ; Magnesium/*chemistry ; Methane/*metabolism ; Microbiota ; Petroleum/metabolism ; Seawater/chemistry/microbiology ; }, abstract = {Over the past 15 years, massive gas hydrate deposits have been studied extensively in Joetsu Basin, Japan Sea, where they are associated primarily with active gas chimney structures. Our research documents the discovery of spheroidal microdolomite aggregates found in association with other impurities inside of these massive gas hydrates. The microdolomites are often conjoined and show dark internal cores occasionally hosting saline fluid inclusions. Bacteroidetes sp. are concentrated on the inner rims of microdolomite grains, where they degrade complex petroleum-macromolecules present as an impurity within yellow methane hydrate. These oils show increasing biodegradation with depth which is consistent with the microbial activity of Bacteroidetes. Further investigation of these microdolomites and their contents can potentially yield insight into the dynamics and microbial ecology of other hydrate localities. If microdolomites are indeed found to be ubiquitous in both present and fossil hydrate settings, the materials preserved within may provide valuable insights into an unusual microhabitat which could have once fostered ancient life.}, }
@article {pmid32023186, year = {2020}, author = {Dhaulaniya, AS and Balan, B and Yadav, A and Jamwal, R and Kelly, S and Cannavan, A and Singh, DK}, title = {Development of an FTIR based chemometric model for the qualitative and quantitative evaluation of cane sugar as an added sugar adulterant in apple fruit juices.}, journal = {Food additives &amp; contaminants. Part A, Chemistry, analysis, control, exposure &amp; risk assessment}, volume = {37}, number = {4}, pages = {539-551}, doi = {10.1080/19440049.2020.1718774}, pmid = {32023186}, issn = {1944-0057}, mesh = {Food Additives/*analysis ; *Food Analysis ; Food Contamination/*analysis ; Fruit and Vegetable Juices/*analysis ; Malus/chemistry ; *Models, Chemical ; Saccharum/chemistry ; Spectroscopy, Fourier Transform Infrared ; }, abstract = {A Fourier Transform Infrared Spectroscopy based chemometric model was evaluated for the rapid identification and estimation of cane sugar as an added sugar adulterant in apple fruit juices. For all the ninety samples, spectra were acquired in the mid-infrared range (4000 cm[-1]-400 cm[-1]). The spectral analysis provided information regarding the distinctive variable region, which lies in the range of 1200cm[-1] to 900cm[-1], designated as fingerprint region for the carbohydrates. A specific peak in the fingerprint region was observed at 997cm[-1] in all the adulterated samples and was undetectable in pure samples. Based on different levels of cane sugar adulteration (5, 10, 15, and 20%), principal component analysis showed the clustering of samples and further helped us in compression of data by selecting wavenumbers with maximum variability based on the loading line plot. Supervised classification methods (SIMCA and LDA) were evaluated based on their classification efficiencies for a test set. Though SIMCA showed 100% classification efficiency (Raw data set), LDA was able to classify the test set with an accuracy of only 96.67% (Raw as well as Transformed data set) between pure and 5% adulterated samples. For the quantitative estimation, calibration models were developed using partial least square regression (PLS-R) and principal component regression method (PCR) methods. PLS-1[st] derivative showed a maximum coefficient of determination (R[2]) with a value of 0.991 for calibration and 0.992 for prediction. The RMSECV, RMSEP, LOD and LOQ observed for PLS-1[st] derivative model were 0.75% w/v, 0.61% w/v, 1.28%w/v and 3.88%w/v, respectively. The coefficient of variation as a measure of precision (repeatability) was also determined for all models, and it ranged from 0.23% to 1.83% (interday), and 0.25% to 1.43% (intraday).}, }
@article {pmid32020257, year = {2020}, author = {Wang, F and Cale, JA and Erbilgin, N}, title = {Induced Defenses of a Novel Host Tree Affect the Growth and Interactions of Bark Beetle-Vectored Fungi.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {181-190}, doi = {10.1007/s00248-020-01490-0}, pmid = {32020257}, issn = {1432-184X}, mesh = {Alberta ; Animals ; Antibiosis ; *Host Microbial Interactions ; Ophiostomatales/*growth &amp; development ; Pinus/*immunology/microbiology ; Plant Diseases/*microbiology ; *Plant Immunity ; Weevils/*microbiology ; }, abstract = {Mountain pine beetle (MPB) has recently expanded its host range to the novel jack pine forests in Alberta. Invasion success of MPB may depend on the outcome of interactions between its symbiotic fungus Grosmannia clavigera and Ophiostoma ips, a fungal associate of a potential competitor Ips pini. However, how the quality of jack pine phloem could influence interactions between the fungi is unknown. We investigated whether introduced concentrations of host nitrogen and monoterpenes affect the growth of and interaction between the fungi. Nitrogen concentrations did not affect the growth rate of either fungus. In the absence of monoterpenes, the presence of O. ips promoted G. clavigera growth. Monoterpenes either promoted or inhibited the growth of both fungi, and altered the outcome of species interactions from facilitation to no-effect. Overall, these results suggest that jack pine phloem quality and the presence of a niche-sharing fungus could influence MPB development.}, }
@article {pmid32019835, year = {2020}, author = {Rodriguez-Gonzalez, RA and Leung, CY and Chan, BK and Turner, PE and Weitz, JS}, title = {Quantitative Models of Phage-Antibiotic Combination Therapy.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, pmid = {32019835}, issn = {2379-5077}, support = {R01 AI146592/AI/NIAID NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; }, abstract = {The spread of multidrug-resistant (MDR) bacteria is a global public health crisis. Bacteriophage therapy (or "phage therapy") constitutes a potential alternative approach to treat MDR infections. However, the effective use of phage therapy may be limited when phage-resistant bacterial mutants evolve and proliferate during treatment. Here, we develop a nonlinear population dynamics model of combination therapy that accounts for the system-level interactions between bacteria, phage, and antibiotics for in vivo application given an immune response against bacteria. We simulate the combination therapy model for two strains of Pseudomonas aeruginosa, one which is phage sensitive (and antibiotic resistant) and one which is antibiotic sensitive (and phage resistant). We find that combination therapy outperforms either phage or antibiotic alone and that therapeutic effectiveness is enhanced given interaction with innate immune responses. Notably, therapeutic success can be achieved even at subinhibitory concentrations of antibiotics, e.g., ciprofloxacin. These in silico findings provide further support to the nascent application of combination therapy to treat MDR bacterial infections, while highlighting the role of innate immunity in shaping therapeutic outcomes.IMPORTANCE This work develops and analyzes a novel model of phage-antibiotic combination therapy, specifically adapted to an in vivo context. The objective is to explore the underlying basis for clinical application of combination therapy utilizing bacteriophage that target antibiotic efflux pumps in Pseudomonas aeruginosa In doing so, the paper addresses three key questions. How robust is combination therapy to variation in the resistance profiles of pathogens? What is the role of immune responses in shaping therapeutic outcomes? What levels of phage and antibiotics are necessary for curative success? As we show, combination therapy outperforms either phage or antibiotic alone, and therapeutic effectiveness is enhanced given interaction with innate immune responses. Notably, therapeutic success can be achieved even at subinhibitory concentrations of antibiotic. These in silico findings provide further support to the nascent application of combination therapy to treat MDR bacterial infections, while highlighting the role of system-level feedbacks in shaping therapeutic outcomes.}, }
@article {pmid32019791, year = {2020}, author = {Tkacz, A and Bestion, E and Bo, Z and Hortala, M and Poole, PS}, title = {Influence of Plant Fraction, Soil, and Plant Species on Microbiota: a Multikingdom Comparison.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {32019791}, issn = {2150-7511}, support = {BB/N013387/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R017859/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/classification ; Fungi/classification ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Plant Leaves/*microbiology ; Plant Roots/*microbiology ; Plants/classification/*microbiology ; RNA, Ribosomal, 16S ; Rhizosphere ; *Soil Microbiology ; }, abstract = {Plant roots influence the soil microbiota via physical interaction, secretion, and plant immunity. However, it is unclear whether the root fraction or soil is more important in determining the structure of the prokaryotic or eukaryotic community and whether this varies between plant species. Furthermore, the leaf (phyllosphere) and root microbiotas have a large overlap; however, it is unclear whether this results from colonization of the phyllosphere by the root microbiota. Soil, rhizosphere, rhizoplane, and root endosphere prokaryote-, eukaryote-, and fungus-specific microbiotas of four plant species were analyzed with high-throughput sequencing. The strengths of factors controlling microbiota structure were determined using permutational multivariate analysis of variance (PERMANOVA) statistics. The origin of the phyllosphere microbiota was investigated using a soil swap experiment. Global microbial kingdom analysis conducted simultaneously on multiple plants shows that cereals, legumes, and Brassicaceae establish similar prokaryotic and similar eukaryotic communities inside and on the root surface. While the bacterial microbiota is recruited from the surrounding soil, its profile is influenced by the root itself more so than by soil or plant species. However, in contrast, the fungal microbiota is most strongly influenced by soil. This was observed in two different soils and for all plant species examined. Microbiota structure is established within 2 weeks of plant growth in soil and remains stable thereafter. A reciprocal soil swap experiment shows that the phyllosphere is colonized from the soil in which the plant is grown.IMPORTANCE Global microbial kingdom analysis conducted simultaneously on multiple plants shows that cereals, legumes, and Brassicaceae establish similar prokaryotic and similar eukaryotic communities inside and on the root surface. While the bacterial microbiota is recruited from the surrounding soil, its profile is influenced by the root fraction more so than by soil or plant species. However, in contrast, the fungal microbiota is most strongly influenced by soil. This was observed in two different soils and for all plant species examined, indicating conserved adaptation of microbial communities to plants. Microbiota structure is established within 2 weeks of plant growth in soil and remains stable thereafter. We observed a remarkable similarity in the structure of a plant's phyllosphere and root microbiotas and show by reciprocal soil swap experiments that both fractions are colonized from the soil in which the plant is grown. Thus, the phyllosphere is continuously colonized by the soil microbiota.}, }
@article {pmid32018979, year = {2020}, author = {Gionchetta, G and Oliva, F and Romaní, AM and Bañeras, L}, title = {Hydrological variations shape diversity and functional responses of streambed microbes.}, journal = {The Science of the total environment}, volume = {714}, number = {}, pages = {136838}, doi = {10.1016/j.scitotenv.2020.136838}, pmid = {32018979}, issn = {1879-1026}, mesh = {Biomass ; Hydrology ; *Microbiota ; Rivers ; }, abstract = {Microbiota inhabiting the intermittent streambeds mediates several in-stream processes that are essential for ecosystem function. Reduced stream discharge caused by the strengthened intermittency and increased duration of the dry phase is a spreading global response to changes in climate. Here, the impacts of a 5-month desiccation, one-week rewetting and punctual storms, which interrupted the dry period, were examined. The genomic composition of total (DNA) and active (RNA) diversity, and the community level physiological profiles (CLPP) were considered as proxies for functional diversity to describe both prokaryotes and eukaryotes inhabiting the surface and hyporheic streambeds. Comparisons between the genomic and potential functional responses helped to understand how and whether the microbial diversity was sensitive to the environmental conditions and resource acquisition, such as water stress and extracellular enzyme activities, respectively. RNA expression showed the strongest relationship with the environmental conditions and resource acquisition, being more responsive to changing conditions compared to DNA diversity, especially in the case of prokaryotes. The DNA results presumably reflected the legacy of the treatments because inactive, dormant, or dead cells were included, suggesting a slow microbial biomass turnover or responses of the microbial communities to changes mainly through physiological acclimation. On the other hand, microbial functional diversity was largely explained by resources acquisition, such as metrics of extracellular enzymes, and appeared vulnerable to the hydrological changes and duration of desiccation. The data highlight the need to improve the functional assessment of stream ecosystems with the application of complementary metrics to better describe the streambed microbial dynamics under dry-rewet stress.}, }
@article {pmid32016609, year = {2020}, author = {Pantigoso, HA and Manter, DK and Vivanco, JM}, title = {Differential Effects of Phosphorus Fertilization on Plant Uptake and Rhizosphere Microbiome of Cultivated and Non-cultivated Potatoes.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {169-180}, doi = {10.1007/s00248-020-01486-w}, pmid = {32016609}, issn = {1432-184X}, mesh = {Bacteria/*metabolism ; Fertilizers/*analysis ; Microbiota ; Phosphorus/*metabolism ; Rhizosphere ; *Soil Microbiology ; Solanum tuberosum/*metabolism/*microbiology ; }, abstract = {There is evidence that shows that phosphorus (P) fertilization has a moderate effect on the rhizosphere microbial composition of cultivated crops. But how this effect is manifested on wild species of the same crop is not clear. This study compares the impact of phosphorus fertilization with rhizosphere bacterial community composition and its predicted functions, related to P-cycling genes, in both cultivated and non-cultivated potato (Solanum sp.) plants. It was found that the biomass of non-cultivated potatoes was more responsive to P fertilization as compared with cultivated plants. Differences in general bacterial community composition patterns under increasing P amendments were subtle for both potato groups. However, potato genotype significantly influenced community composition with several bacterial families being more abundant in the cultivated plants. In addition, the predicted phosphatases had lower abundances in modern cultivars compared with non-cultivated potatoes. In summary, despite higher accumulation of differentially abundant bacteria in the rhizosphere of cultivated plants, the responsiveness of these plants to increase P levels was lower than in non-cultivated plants.}, }
@article {pmid32014077, year = {2020}, author = {Morand, C and De Roos, B and Garcia-Conesa, MT and Gibney, ER and Landberg, R and Manach, C and Milenkovic, D and Rodriguez-Mateos, A and Van de Wiele, T and Tomas-Barberan, F}, title = {Why interindividual variation in response to consumption of plant food bioactives matters for future personalised nutrition.}, journal = {The Proceedings of the Nutrition Society}, volume = {79}, number = {2}, pages = {225-235}, doi = {10.1017/S0029665120000014}, pmid = {32014077}, issn = {1475-2719}, mesh = {Biological Availability ; *Biological Variation, Population ; *Diet ; Female ; Gastrointestinal Microbiome ; Genome, Human ; Heart Disease Risk Factors ; Humans ; Male ; Metabolome ; Nutrigenomics ; *Nutritional Physiological Phenomena ; Nutritive Value ; Phytochemicals/*administration &amp; dosage/*metabolism/pharmacokinetics ; Precision Medicine ; Research ; }, abstract = {Food phytochemicals are increasingly considered to play a key role in the cardiometabolic health effects of plant foods. However, the heterogeneity in responsiveness to their intake frequently observed in clinical trials can hinder the beneficial effects of these compounds in specific subpopulations. A range of factors, including genetic background, gut microbiota, age, sex and health status, could be involved in these interindividual variations; however, the current knowledge is limited and fragmented. The European network, European Cooperation in Science and Technology (COST)-POSITIVe, has analysed, in a systematic way, existing knowledge with the aim to better understand the factors responsible for the interindividual variation in response to the consumption of the major families of plant food bioactives, regarding their bioavailability and bioefficacy. If differences in bioavailability, likely reflecting differences in human subjects' genetics or in gut microbiota composition and functionality, are believed to underpin much of the interindividual variability, the key molecular determinants or microbial species remain to be identified. The systematic analysis of published studies conducted to assess the interindividual variation in biomarkers of cardiometabolic risk suggested some factors (such as adiposity and health status) as involved in between-subject variation. However, the contribution of these factors is not demonstrated consistently across the different compounds and biological outcomes and would deserve further investigations. The findings of the network clearly highlight that the human subjects' intervention studies published so far are not adequate to investigate the relevant determinants of the absorption/metabolism and biological responsiveness. They also emphasise the need for a new generation of intervention studies designed to capture this interindividual variation.}, }
@article {pmid32014020, year = {2020}, author = {Woodhams, DC and Bletz, MC and Becker, CG and Bender, HA and Buitrago-Rosas, D and Diebboll, H and Huynh, R and Kearns, PJ and Kueneman, J and Kurosawa, E and LaBumbard, BC and Lyons, C and McNally, K and Schliep, K and Shankar, N and Tokash-Peters, AG and Vences, M and Whetstone, R}, title = {Host-associated microbiomes are predicted by immune system complexity and climate.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {23}, pmid = {32014020}, issn = {1474-760X}, mesh = {Adaptation, Physiological ; Animals ; *Climate ; Host-Pathogen Interactions/*immunology ; Humans ; *Microbiota ; }, abstract = {BACKGROUND: Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacterial communities have the potential to elucidate global-scale patterns of microbial community structure and function. It is possible that host surface-associated (external) microbiomes respond more strongly to variations in environmental factors, whereas internal microbiomes are more tightly linked to host factors.<br><br>RESULTS: Here, we use the dataset from the Earth Microbiome Project and accumulate data from 50 additional studies totaling 654 host species and over 15,000 samples to examine global-scale patterns of bacterial diversity and function. We analyze microbiomes from non-captive hosts sampled from natural habitats and find patterns with bioclimate and geophysical factors, as well as land use, host phylogeny, and trophic level/diet. Specifically, external microbiomes are best explained by variations in mean daily temperature range and precipitation seasonality. In contrast, internal microbiomes are best explained by host factors such as phylogeny/immune complexity and trophic level/diet, plus climate.<br><br>CONCLUSIONS: Internal microbiomes are predominantly associated with top-down effects, while climatic factors are stronger determinants of microbiomes on host external surfaces. Host immunity may act on microbiome diversity through top-down regulation analogous to predators in non-microbial ecosystems. Noting gaps in geographic and host sampling, this combined dataset represents a global baseline available for interrogation by future microbial ecology studies.}, }
@article {pmid32012657, year = {2020}, author = {Purushotham, N and Jones, E and Monk, J and Ridgway, H}, title = {Community Structure, Diversity and Potential of Endophytic Bacteria in the Primitive New Zealand Medicinal Plant Pseudowintera colorata.}, journal = {Plants (Basel, Switzerland)}, volume = {9}, number = {2}, pages = {}, pmid = {32012657}, issn = {2223-7747}, abstract = {Although the importance of the plant microbiome in commercial plant health has been well established, there are limited studies in native medicinal plants. Pseudowintera colorata (horopito) is a native New Zealand medicinal plant recognized for its antimicrobial properties. Denaturing gradient gel electrophoresis (DGGE) and Illumina MiSeq analysis of P. colorata plants from ten sites across New Zealand showed that tissue type strongly influenced the diversity and richness of endophytic bacteria (PERMANOVA, P < 0.05). In addition, two OTUs belonging to the genus Pseudomonas (Greengenes ID: 646549 and 138914) were found to be present in >75% of all P. colorata leaf, stem and root samples and were identified as the members of the P. colorata "core endomicrobiome". Culture-independent analysis was complemented by the recovery of 405 endophytic bacteria from the tissues of P. colorata. Some of these cultured endophytic bacteria (n = 10) showed high antagonism against four different phytopathogenic fungi tested. The influence of endophytic bacteria on plant growth was assessed by inoculating P. colorata seedlings. The mean shoot height of seedlings treated with Bacillus sp. TP1LA1B were longer (1.83×), had higher shoot dry weight (1.8×) and produced more internodes (1.8×) compared to the control.}, }
@article {pmid32010196, year = {2019}, author = {Mascarenhas, R and Ruziska, FM and Moreira, EF and Campos, AB and Loiola, M and Reis, K and Trindade-Silva, AE and Barbosa, FAS and Salles, L and Menezes, R and Veiga, R and Coutinho, FH and Dutilh, BE and Guimarães, PR and Assis, APA and Ara, A and Miranda, JGV and Andrade, RFS and Vilela, B and Meirelles, PM}, title = {Integrating Computational Methods to Investigate the Macroecology of Microbiomes.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {1344}, pmid = {32010196}, issn = {1664-8021}, abstract = {Studies in microbiology have long been mostly restricted to small spatial scales. However, recent technological advances, such as new sequencing methodologies, have ushered an era of large-scale sequencing of environmental DNA data from multiple biomes worldwide. These global datasets can now be used to explore long standing questions of microbial ecology. New methodological approaches and concepts are being developed to study such large-scale patterns in microbial communities, resulting in new perspectives that represent a significant advances for both microbiology and macroecology. Here, we identify and review important conceptual, computational, and methodological challenges and opportunities in microbial macroecology. Specifically, we discuss the challenges of handling and analyzing large amounts of microbiome data to understand taxa distribution and co-occurrence patterns. We also discuss approaches for modeling microbial communities based on environmental data, including information on biological interactions to make full use of available Big Data. Finally, we summarize the methods presented in a general approach aimed to aid microbiologists in addressing fundamental questions in microbial macroecology, including classical propositions (such as "everything is everywhere, but the environment selects") as well as applied ecological problems, such as those posed by human induced global environmental changes.}, }
@article {pmid32006806, year = {2020}, author = {Trebuch, LM and Oyserman, BO and Janssen, M and Wijffels, RH and Vet, LEM and Fernandes, TV}, title = {Impact of hydraulic retention time on community assembly and function of photogranules for wastewater treatment.}, journal = {Water research}, volume = {173}, number = {}, pages = {115506}, doi = {10.1016/j.watres.2020.115506}, pmid = {32006806}, issn = {1879-2448}, mesh = {Bioreactors ; Netherlands ; Sewage ; *Waste Disposal, Fluid ; *Wastewater ; }, abstract = {Photogranules are dense, spherical agglomerates of cyanobacteria, microalgae and non-phototrophic microorganisms that have considerable advantages in terms of harvesting and nutrient removal rates for light driven wastewater treatment processes. This ecosystem is poorly understood in terms of the microbial community structure and the response of the community to changing abiotic conditions. To get a better understanding, we investigated the effect of hydraulic retention time (HRT) on photogranule formation and community assembly over a period of 148 days. Three laboratory bioreactors were inoculated with field samples from various locations in the Netherlands and operated in sequencing batch mode. The bioreactors were operated at four different HRTs (2.00, 1.00, 0.67, 0.33 days), while retaining the same solid retention time of 7 days. A microbial community with excellent settling characteristics (95-99% separation efficiency) was established within 2-5 weeks. The observed nutrient uptake rates ranged from 24 to 90 mgN L[-1] day[-1] and from 3.1 to 5.4 mgP L[-1] day[-1] depending on the applied HRT. The transition from single-cell suspension culture to floccular agglomeration to granular sludge was monitored by microscopy and 16S/18S sequencing. In particular, two important variables for driving aggregation and granulation, and for the structural integrity of photogranules were identified: 1. Extracellular polymeric substances (EPS) with high protein to polysaccharide ratio and 2. specific microorganisms. The key players were found to be the cyanobacteria Limnothrix and Cephalothrix, the colony forming photosynthetic eukaryotes within Chlamydomonadaceae, and the biofilm producing bacteria Zoogloea and Thauera. Knowing the makeup of the microbial community and the operational conditions influencing granulation and bioreactor function is crucial for successful operation of photogranular systems.}, }
@article {pmid32006032, year = {2020}, author = {De Gruyter, J and Weedon, JT and Bazot, S and Dauwe, S and Fernandez-Garberí, PR and Geisen, S and De La Motte, LG and Heinesch, B and Janssens, IA and Leblans, N and Manise, T and Ogaya, R and Löfvenius, MO and Peñuelas, J and Sigurdsson, BD and Vincent, G and Verbruggen, E}, title = {Patterns of local, intercontinental and interseasonal variation of soil bacterial and eukaryotic microbial communities.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {3}, pages = {}, doi = {10.1093/femsec/fiaa018}, pmid = {32006032}, issn = {1574-6941}, mesh = {Bacteria/genetics ; Eukaryota ; Fungi/genetics ; *Microbiota ; *Soil ; Soil Microbiology ; }, abstract = {Although ongoing research has revealed some of the main drivers behind global spatial patterns of microbial communities, spatio-temporal dynamics of these communities still remain largely unexplored. Here, we investigate spatio-temporal variability of both bacterial and eukaryotic soil microbial communities at local and intercontinental scales. We compare how temporal variation in community composition scales with spatial variation in community composition, and explore the extent to which bacteria, protists, fungi and metazoa have similar patterns of temporal community dynamics. All soil microbial groups displayed a strong correlation between spatial distance and community dissimilarity, which was related to the ratio of organism to sample size. Temporal changes were variable, ranging from equal to local between-sample variation, to as large as that between communities several thousand kilometers apart. Moreover, significant correlations were found between bacterial and protist communities, as well as between protist and fungal communities, indicating that these microbial groups change in tandem, potentially driven by interactions between them. We conclude that temporal variation can be considerable in soil microbial communities, and that future studies need to consider temporal variation in order to reliably capture all drivers of soil microbiome changes.}, }
@article {pmid32001557, year = {2020}, author = {Eichorst, SA and Trojan, D and Huntemann, M and Clum, A and Pillay, M and Palaniappan, K and Varghese, N and Mikhailova, N and Stamatis, D and Reddy, TBK and Daum, C and Goodwin, LA and Shapiro, N and Ivanova, N and Kyrpides, N and Woyke, T and Woebken, D}, title = {One Complete and Seven Draft Genome Sequences of Subdivision 1 and 3 Acidobacteria Isolated from Soil.}, journal = {Microbiology resource announcements}, volume = {9}, number = {5}, pages = {}, pmid = {32001557}, issn = {2576-098X}, abstract = {We report eight genomes from representatives of the phylum Acidobacteria subdivisions 1 and 3, isolated from soils. The genome sizes range from 4.9 to 6.7 Mb. Genomic analysis reveals putative genes for low- and high-affinity respiratory oxygen reductases, high-affinity hydrogenases, and the capacity to use a diverse collection of carbohydrates.}, }
@article {pmid32000682, year = {2020}, author = {De Maayer, P and Pillay, T and Coutinho, TA}, title = {Comparative genomic analysis of the secondary flagellar (flag-2) system in the order Enterobacterales.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {100}, pmid = {32000682}, issn = {1471-2164}, mesh = {Bacterial Proteins/*genetics ; Enterobacteriaceae/*classification/genetics ; Evolution, Molecular ; Flagella/*genetics ; Gene Transfer, Horizontal ; Multigene Family ; Phylogeny ; }, abstract = {BACKGROUND: The order Enterobacterales encompasses a broad range of metabolically and ecologically versatile bacterial taxa, most of which are motile by means of peritrichous flagella. Flagellar biosynthesis has been linked to a primary flagella locus, flag-1, encompassing ~ 50 genes. A discrete locus, flag-2, encoding a distinct flagellar system, has been observed in a limited number of enterobacterial taxa, but its function remains largely uncharacterized.<br><br>RESULTS: Comparative genomic analyses showed that orthologous flag-2 loci are present in 592/4028 taxa belonging to 5/8 and 31/76 families and genera, respectively, in the order Enterobacterales. Furthermore, the presence of only the outermost flag-2 genes in many taxa suggests that this locus was far more prevalent and has subsequently been lost through gene deletion events. The flag-2 loci range in size from ~&#x2009;3.4 to 81.1 kilobases and code for between five and 102 distinct proteins. The discrepancy in size and protein number can be attributed to the presence of cargo gene islands within the loci. Evolutionary analyses revealed a complex evolutionary history for the flag-2 loci, representing ancestral elements in some taxa, while showing evidence of recent horizontal acquisition in other enterobacteria.<br><br>CONCLUSIONS: The flag-2 flagellar system is a fairly common, but highly variable feature among members of the Enterobacterales. Given the energetic burden of flagellar biosynthesis and functioning, the prevalence of a second flagellar system suggests it plays important biological roles in the enterobacteria and we postulate on its potential role as locomotory organ or as secretion system.}, }
@article {pmid31999996, year = {2020}, author = {Ahmad, JI and Liu, G and van der Wielen, PWJJ and Medema, G and Peter van der Hoek, J}, title = {Effects of cold recovery technology on the microbial drinking water quality in unchlorinated distribution systems.}, journal = {Environmental research}, volume = {183}, number = {}, pages = {109175}, doi = {10.1016/j.envres.2020.109175}, pmid = {31999996}, issn = {1096-0953}, mesh = {Bacteria ; Biofilms ; *Cold Temperature ; *Drinking Water ; Water Microbiology ; *Water Quality ; Water Supply ; }, abstract = {Drinking water distribution systems (DWDSs) are used to supply hygienically safe and biologically stable water for human consumption. The potential of thermal energy recovery from drinking water has been explored recently to provide cooling for buildings. Yet, the effects of increased water temperature induced by this "cold recovery" on the water quality in DWDSs are not known. The objective of this study was to investigate the impact of cold recovery from DWDSs on the microbiological quality of drinking water. For this purpose, three pilot distribution systems were operated in parallel for 38 weeks. System 1 has an operational heat exchanger, mimicking the cold recovery system by maintaining the water temperature at 25 °C; system 2 operated with a non-operational heat exchanger and system 3 run without heat exchanger. The results showed no significant effects on drinking water quality: cell numbers and ATP concentrations remained around 3.5 × 10[5] cells/ml and 4 ng ATP/l, comparable observed operational taxonomic units (OTUs) (~470-490) and similar Shannon indices (7.7-8.9). In the system with cold recovery, a higher relative abundance of Pseudomonas spp. and Chryseobacterium spp. was observed in the drinking water microbial community, but only when the cold recovery induced temperature difference (ΔT) was higher than 9 °C. In the 38 weeks' old biofilm, higher ATP concentration (475 vs. 89 pg/cm[2]), lower diversity (observed OTUs: 88 vs. ≥200) and a different bacterial community composition (e.g. higher relative abundance of Novosphingobium spp.) were detected, which did not influence water quality. No impacts were observed for the selected opportunisitic pathogens after introducing cold recovery. It is concluded that cold recovery does not affect bacterial water quality. Further investigation for a longer period is commended to understand the dynamic responses of biofilm to the increased temperature caused by cold recovery.}, }
@article {pmid31999470, year = {2020}, author = {Saavedra-Lavoie, J and de la Porte, A and Piché-Choquette, S and Guertin, C and Constant, P}, title = {Biological H2 and CO oxidation activities are sensitive to compositional change of soil microbial communities.}, journal = {Canadian journal of microbiology}, volume = {66}, number = {4}, pages = {263-273}, doi = {10.1139/cjm-2019-0412}, pmid = {31999470}, issn = {1480-3275}, mesh = {Bacteria/classification/*drug effects/genetics/isolation &amp; purification ; Carbon Dioxide/chemistry/pharmacology ; Carbon Monoxide/*chemistry/pharmacology ; Hydrogen/*chemistry/pharmacology ; Microbiota ; Oxidation-Reduction ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Trace gas uptake by microorganisms controls the oxidative capacity of the troposphere, but little is known about how this important function is affected by changes in soil microbial diversity. This article bridges that knowledge gap by examining the response of the microbial community-level physiological profiles (CLPPs), carbon dioxide (CO2) production, and molecular hydrogen (H2) and carbon monoxide (CO) oxidation activities to manipulation of microbial diversity in soil microcosms. Microbial diversity was manipulated by mixing nonsterile and sterile soil with and without the addition of antibiotics. Nonsterile soil without antibiotics was used as a reference. Species composition changed significantly in soil microcosms as a result of dilution and antibiotic treatments, but there was no difference in species richness, according to PCR amplicon sequencing of the bacterial 16S rRNA gene. The CLPP was 15% higher in all dilution and antibiotic treatments than in reference microcosms, but the dilution treatment had no effect on CO2 production. Soil microcosms with dilution treatments had 58%-98% less H2 oxidation and 54%-99% lower CO oxidation, relative to reference microcosms, but did not differ among the antibiotic treatments. These results indicate that H2 and CO oxidation activities respond to compositional changes of microbial community in soil.}, }
@article {pmid31998352, year = {2019}, author = {Harkes, P and van Steenbrugge, JJM and van den Elsen, SJJ and Suleiman, AKA and de Haan, JJ and Holterman, MHM and Helder, J}, title = {Shifts in the Active Rhizobiome Paralleling Low Meloidogyne chitwoodi Densities in Fields Under Prolonged Organic Soil Management.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {1697}, pmid = {31998352}, issn = {1664-462X}, abstract = {Plants manipulate their rhizosphere community in a species and even a plant life stage-dependent manner. In essence plants select, promote and (de)activate directly the local bacterial and fungal community, and indirectly representatives of the next trophic level, protists and nematodes. By doing so, plants enlarge the pool of bioavailable nutrients and maximize local disease suppressiveness within the boundaries set by the nature of the local microbial community. MiSeq sequencing of specific variable regions of the 16S or 18S ribosomal DNA (rDNA) is widely used to map microbial shifts. As current RNA extraction procedures are time-consuming and expensive, the rRNA-based characterization of the active microbial community is taken along less frequently. Recently, we developed a relatively fast and affordable protocol for the simultaneous extraction of rDNA and rRNA from soil. Here, we investigated the long-term impact of three type of soil management, two conventional and an organic regime, on soil biota in fields naturally infested with the Columbian root-knot nematode Meloidogyne chitwoodi with pea (Pisum sativum) as the main crop. For all soil samples, large differences were observed between resident (rDNA) and active (rRNA) microbial communities. Among the four organismal group under investigation, the bacterial community was most affected by the main crop, and unweighted and weighted UniFrac analyses (explaining respectively 16.4% and 51.3% of the observed variation) pointed at a quantitative rather than a qualitative shift. LEfSe analyses were employed for each of the four organismal groups to taxonomically pinpoint the effects of soil management. Concentrating on the bacterial community in the pea rhizosphere, organic soil management resulted in a remarkable activation of members of the Burkholderiaceae, Enterobacteriaceae, and Pseudomonadaceae. Prolonged organic soil management was also accompanied by significantly higher densities of bacterivorous nematodes, whereas levels of M. chitwoodi had dropped drastically. Though present and active in the fields under investigation Orbiliaceae, a family harboring numerous nematophagous fungi, was not associated with the M. chitwoodi decline. A closer look revealed that a local accumulation and activation of Pseudomonas, a genus that includes a number of nematode-suppressive species, paralleled the lower M. chitwoodi densities. This study underlines the relevance of taking along both resident and active fractions of multiple organismal groups while mapping the impact of e.g. crops and soil management regimes.}, }
@article {pmid31998276, year = {2019}, author = {Eberl, C and Ring, D and Münch, PC and Beutler, M and Basic, M and Slack, EC and Schwarzer, M and Srutkova, D and Lange, A and Frick, JS and Bleich, A and Stecher, B}, title = {Reproducible Colonization of Germ-Free Mice With the Oligo-Mouse-Microbiota in Different Animal Facilities.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2999}, pmid = {31998276}, issn = {1664-302X}, abstract = {The Oligo-Mouse-Microbiota (OMM[12]) is a recently developed synthetic bacterial community for functional microbiome research in mouse models (Brugiroux et al., 2016). To date, the OMM[12] model has been established in several germ-free mouse facilities world-wide and is employed to address a growing variety of research questions related to infection biology, mucosal immunology, microbial ecology and host-microbiome metabolic cross-talk. The OMM[12] consists of 12 sequenced and publically available strains isolated from mice, representing five bacterial phyla that are naturally abundant in the murine gastrointestinal tract (Lagkouvardos et al., 2016). Under germ-free conditions, the OMM[12] colonizes mice stably over multiple generations. Here, we investigated whether stably colonized OMM[12] mouse lines could be reproducibly established in different animal facilities. Germ-free C57Bl/6J mice were inoculated with a frozen mixture of the OMM[12] strains. Within 2 weeks after application, the OMM[12] community reached the same stable composition in all facilities, as determined by fecal microbiome analysis. We show that a second application of the OMM[12] strains after 72 h leads to a more stable community composition than a single application. The availability of such protocols for reliable de novo generation of gnotobiotic rodents will certainly contribute to increasing experimental reproducibility in biomedical research.}, }
@article {pmid31998260, year = {2019}, author = {Rath, S and Rud, T and Pieper, DH and Vital, M}, title = {Potential TMA-Producing Bacteria Are Ubiquitously Found in Mammalia.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2966}, pmid = {31998260}, issn = {1664-302X}, abstract = {Human gut bacteria metabolize dietary components such as choline and carnitine to trimethylamine (TMA) that is subsequently oxidized to trimethylamine-N-oxide (TMAO) by hepatic enzymes. Increased plasma levels of TMAO are associated with the development of cardiovascular and renal disease. In this study, we applied gene-targeted assays in order to quantify (qPCR) and characterize (MiSeq) bacterial genes encoding enzymes responsible for TMA production, namely choline-TMA lyase (CutC), carnitine oxygenase (CntA) and betaine reductase (GrdH) in 89 fecal samples derived from various mammals spanning three dietary groups (carnivores, omnivores and herbivores) and four host orders (Carnivora, Primates, Artiodactyla and Perissodactyla). All samples contained potential TMA-producing bacteria, however, at low abundances (<1.2% of total community). The cutC gene was more abundant in omnivores and carnivores compared with herbivores. CntA was almost absent from herbivores and grdH showed lowest average abundance of all three genes. Bacteria harboring cutC and grdH displayed high diversities where sequence types affiliated with various taxa within Firmicutes dominated, whereas cntA comprised sequences primarily linked to Escherichia. Composition of TMA-forming communities was strongly influenced by diet and host taxonomy and despite their high correlation, both factors contributed uniquely to community structure. Furthermore, Random Forest (RF) models could differentiate between groups at high accuracies. This study gives a comprehensive overview of potential TMA-producing bacteria in the mammalian gut demonstrating that both diet and host taxonomy govern their abundance and composition. It highlights the role of functional redundancy sustaining potential TMA formation in distinct gut environments.}, }
@article {pmid31998259, year = {2019}, author = {Rahi, P and Vaishampayan, P}, title = {Editorial: MALDI-TOF MS Application in Microbial Ecology Studies.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2954}, pmid = {31998259}, issn = {1664-302X}, }
@article {pmid31997534, year = {2020}, author = {van Gestel, NC and Ducklow, HW and Bååth, E}, title = {Comparing temperature sensitivity of bacterial growth in Antarctic marine water and soil.}, journal = {Global change biology}, volume = {26}, number = {4}, pages = {2280-2291}, doi = {10.1111/gcb.15020}, pmid = {31997534}, issn = {1365-2486}, support = {PLR-1440435//National Science Foundation/ ; }, abstract = {The western Antarctic Peninsula is an extreme low temperature environment that is warming rapidly due to global change. Little is known, however, on the temperature sensitivity of growth of microbial communities in Antarctic soils and in the surrounding oceanic waters. This is the first study that directly compares temperature adaptation of adjacent marine and terrestrial bacteria in a polar environment. The bacterial communities in the ocean were adapted to lower temperatures than those from nearby soil, with cardinal temperatures for growth in the ocean being the lowest so far reported for microbial communities. This was reflected in lower minimum (Tmin) and optimum temperatures (Topt) for growth in water (-17 and +20°C, respectively) than in soil (-11 and +27°C), with lower sensitivity to changes in temperature (Q10 ; 0-10°C interval) in Antarctic water (2.7) than in soil (3.9). This is likely due to the more stable low temperature conditions of Antarctic waters than soils, and the fact that maximum in situ temperatures in water are lower than in soils, at least in summer. Importantly, the thermally stable environment of Antarctic marine water makes it feasible to create a single temperature response curve for bacterial communities. This would thus allow for calculations of temperature-corrected growth rates, and thereby quantifying the influence of factors other than temperature on observed growth rates, as well as predicting the effects of future temperature increases on Antarctic marine bacteria.}, }
@article {pmid31996939, year = {2020}, author = {Zhang, Z and Liu, W and Shao, S and Wang, ET and Li, Y}, title = {Diverse Genomic Backgrounds Vs. Highly Conserved Symbiotic Genes in Sesbania-Nodulating Bacteria: Shaping of the Rhizobial Community by Host and Soil Properties.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {158-168}, doi = {10.1007/s00248-020-01489-7}, pmid = {31996939}, issn = {1432-184X}, support = {31600009//National Natural Science Foundation of China/ ; 31800099//National Natural Science Foundation of China/ ; 19273802D//Key Research and Development Program of Hebei province/ ; 2019SYHZ0036//Joint fund of Jilin province and Chinese Academy of Sciences for high-tech industrialization/ ; KFZD-SW-112//Key Deployment Project of Chinese Academy of Sciences/ ; }, mesh = {Biological Evolution ; *Genetic Variation ; *Genotype ; Plant Roots/microbiology ; Rhizobiaceae/genetics/*physiology ; Sesbania/*microbiology ; Soil/chemistry ; *Soil Microbiology ; Symbiosis/*genetics ; }, abstract = {Aiming at investigating the overall diversity, biogeography, and symbiosis gene evolutionary history of the Sesbania cannabina-nodulating rhizobia in China, a total of 874 rhizobial isolates originating from the root nodules of this plant grown at different sites were characterized and compared with those of some reference strains. All of the S. cannabina-nodulating rhizobia were classified into 16 (geno) species, including seven novel genospecies in the genera Ensifer, Rhizobium, Neorhizobium, and Agrobacterium, with Ensifer sesbaniae and Neorhizobium huautlense as the dominant and universal species. Ten of these species were found to nodulate other leguminous hosts or to lack nodulating abilities and were defined as symbiovar sesbania. Biogeographic patterns were observed, for which pH, TN, AK, and AP were the main determinants. The effects of pH were opposite to those of TN and AK, while AP presented effects independently of TN, AK, and pH. Symbiotic genes of these rhizobia showed a common origin, but nodA evolved faster than nifH. Point mutation is the main driving force in the evolution of both nodA and nifH, and lateral transfer of symbiotic genes might play an important role in the formation of diverse S. cannabina-nodulating rhizobial species. S. cannabina only nodulates with Sesbania rhizobia, demonstrating its severe selection on rhizobial symbiosis genes. Soil pH and physiochemical characteristics could affect rhizobial survival and competitive nodulation. This study provides insight into the community shifts and evolution of rhizobia in relation to their host and soil environments.}, }
@article {pmid31996419, year = {2020}, author = {Ghannam, RB and Schaerer, LG and Butler, TM and Techtmann, SM}, title = {Biogeographic Patterns in Members of Globally Distributed and Dominant Taxa Found in Port Microbial Communities.}, journal = {mSphere}, volume = {5}, number = {1}, pages = {}, pmid = {31996419}, issn = {2379-5042}, mesh = {Actinobacteria/*classification ; Asia ; Bacteroidetes/*classification ; *Biodiversity ; Cyanobacteria/*classification ; DNA, Bacterial/genetics ; Europe ; Fresh Water/microbiology ; Machine Learning ; Microbiota ; Phylogeography ; Proteobacteria/*classification ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Ships ; United States ; *Water Microbiology ; }, abstract = {We conducted a global characterization of the microbial communities of shipping ports to serve as a novel system to investigate microbial biogeography. The community structures of port microbes from marine and freshwater habitats house relatively similar phyla, despite spanning large spatial scales. As part of this project, we collected 1,218 surface water samples from 604 locations across eight countries and three continents to catalogue a total of 20 shipping ports distributed across the East and West Coast of the United States, Europe, and Asia to represent the largest study of port-associated microbial communities to date. Here, we demonstrated the utility of machine learning to leverage this robust system to characterize microbial biogeography by identifying trends in biodiversity across broad spatial scales. We found that for geographic locations sharing similar environmental conditions, subpopulations from the dominant phyla of these habitats (Actinobacteria, Bacteroidetes, Cyanobacteria, and Proteobacteria) can be used to differentiate 20 geographic locations distributed globally. These results suggest that despite the overwhelming diversity within microbial communities, members of the most abundant and ubiquitous microbial groups in the system can be used to differentiate a geospatial location across global spatial scales. Our study provides insight into how microbes are dispersed spatially and robust methods whereby we can interrogate microbial biogeography.IMPORTANCE Microbes are ubiquitous throughout the world and are highly diverse. Characterizing the extent of variation in the microbial diversity across large geographic spatial scales is a challenge yet can reveal a lot about what biogeography can tell us about microbial populations and their behavior. Machine learning approaches have been used mostly to examine the human microbiome and, to some extent, microbial communities from the environment. Here, we display how supervised machine learning approaches can be useful to understand microbial biodiversity and biogeography using microbes from globally distributed shipping ports. Our findings indicate that the members of globally dominant phyla are important for differentiating locations, which reduces the reliance on rare taxa to probe geography. Further, this study displays how global biogeographic patterning of aquatic microbial communities (and other systems) can be assessed through populations of the highly abundant and ubiquitous taxa that dominant the system.}, }
@article {pmid31996418, year = {2020}, author = {Bartelme, RP and Custer, JM and Dupont, CL and Espinoza, JL and Torralba, M and Khalili, B and Carini, P}, title = {Influence of Substrate Concentration on the Culturability of Heterotrophic Soil Microbes Isolated by High-Throughput Dilution-to-Extinction Cultivation.}, journal = {mSphere}, volume = {5}, number = {1}, pages = {}, pmid = {31996418}, issn = {2379-5042}, support = {P01 AI118687/AI/NIAID NIH HHS/United States ; }, mesh = {Actinobacteria/growth &amp; development/*isolation &amp; purification ; Alphaproteobacteria/growth &amp; development/*isolation &amp; purification ; Arizona ; Bacteriological Techniques ; Centrifugation ; Culture Media/*chemistry ; Forests ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {The vast majority of microbes inhabiting oligotrophic shallow subsurface soil environments have not been isolated or studied under controlled laboratory conditions. In part, the challenges associated with isolating shallow subsurface microbes may persist because microbes in deeper soils are adapted to low nutrient availability or quality. Here, we use high-throughput dilution-to-extinction culturing to isolate shallow subsurface microbes from a conifer forest in Arizona, USA. We hypothesized that the concentration of heterotrophic substrates in microbiological growth medium would affect which microbial taxa were culturable from these soils. To test this, we diluted cells extracted from soil into one of two custom-designed defined growth media that differed by 100-fold in the concentration of amino acids and organic carbon. Across the two media, we isolated a total of 133 pure cultures, all of which were classified as Actinobacteria or Alphaproteobacteria The substrate availability dictated which actinobacterial phylotypes were culturable but had no significant effect on the culturability of Alphaproteobacteria We isolated cultures that were representative of the most abundant phylotype in the soil microbial community (Bradyrhizobium spp.) and representatives of five of the top 10 most abundant Actinobacteria phylotypes, including Nocardioides spp., Mycobacterium spp., and several other phylogenetically divergent lineages. Flow cytometry of nucleic acid-stained cells showed that cultures isolated on low-substrate medium had significantly lower nucleic acid fluorescence than those isolated on high-substrate medium. These results show that dilution-to-extinction is an effective method to isolate abundant soil microbes and that the concentration of substrates in culture medium influences the culturability of specific microbial lineages.IMPORTANCE Isolating environmental microbes and studying their physiology under controlled conditions are essential aspects of understanding their ecology. Subsurface ecosystems are typically nutrient-poor environments that harbor diverse microbial communities-the majority of which are thus far uncultured. In this study, we use modified high-throughput cultivation methods to isolate subsurface soil microbes. We show that a component of whether a microbe is culturable from subsurface soils is the concentration of growth substrates in the culture medium. Our results offer new insight into technical approaches and growth medium design that can be used to access the uncultured diversity of soil microbes.}, }
@article {pmid31994719, year = {2020}, author = {Yuan, S and Meng, F}, title = {Ecological insights into the underlying evolutionary patterns of biofilm formation from biological wastewater treatment systems: Red or Black Queen Hypothesis?.}, journal = {Biotechnology and bioengineering}, volume = {117}, number = {5}, pages = {1270-1280}, doi = {10.1002/bit.27289}, pmid = {31994719}, issn = {1097-0290}, support = {2017YFE0114300//National Key R&amp;D Program of China/International ; 51622813 and 51878675//National Natural Science Foundation of China/International ; 2017B020216006 and 2015A020215014//Science and Technology Planning Project of Guangdong Province/International ; }, mesh = {*Biofilms ; *Biological Evolution ; Bioreactors ; Microbial Interactions ; *Models, Biological ; Sewage/*microbiology ; *Water Purification ; }, abstract = {Interspecies interactions and phylogenetic distances were studied to reveal the underlying evolutionary adaptations of biofilms sourced from wastewater treatment processes. Based on 380 pairwise cocultures of 40 strains from two microbial aggregates (surface-attached and mobile aggregates [flocs]) at two substrate concentrations (LB broth and 0.1× LB broth), interspecies interactions were explored using biofilm classification schemes. There was a strong source-dependence of biofilm development formed by the monocultures, that is, a higher biofilm formation potential for strains from attached aggregates than for those from sludge flocs at both substrate concentrations. Interestingly, the results showed that total biofilm reduction was dominant in the dual-species biofilm sourced from flocs in both LB broth (67.37%) and 0.1× LB broth (64.21%), indicating high interspecific competition in mobile aggregates and the independence of substrate concentrations. However, biofilm reduction was higher (33.68%) than induction (19.37%) for the biofilms formed by surface-attached aggregates in LB broth, while the opposite trend was apparent in 0.1× LB broth, suggesting the occurrence of indeterministic processes for biofilm formation and important roles of substrate concentrations. In addition, the more closely related phylogenetic relationships of cocultures from mobile aggregates were consistent with higher competition compared with those from surface-attached aggregates. Overall, the underlying evolutionary patterns of biofilms formed from mobile aggregates consistently followed the essence of the "Red Queen Hypothesis," while biofilms developed from surface-attached aggregates were not deterministic. This study advanced our understanding of biofilm-related treatment processes using the principles of microbial ecology.}, }
@article {pmid31992626, year = {2020}, author = {Lennon, JT}, title = {Microbial Life Deep Underfoot.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {31992626}, issn = {2150-7511}, mesh = {Biodiversity ; Ecosystem ; *Microbiota ; North America ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Soil is one of the most diverse microbial habitats on Earth. While the distribution and abundance of microbial taxa in surface soils have been well described, the phylogenetic and functional diversity of bacteria and archaea in deep-soil strata remains unexplored. Brewer et al. (mBio 10:e01318-19, 2019, https://doi.org/10.1128/mBio.01318-19) documented consistent shifts in the composition and genomic attributes of microbial communities as a function of depth in 20 soil pits that spanned a range of ecosystems across North America. The unique microorganisms found in deep soils appear to be adapted to conditions of low energy based on the recovery of genes that code for traits such as internal resource storage, mixotrophy, and dormancy.}, }
@article {pmid31989236, year = {2020}, author = {Zhu, B and Wang, Z and Kanaparthi, D and Kublik, S and Ge, T and Casper, P and Schloter, M and Lueders, T}, title = {Long-Read Amplicon Sequencing of Nitric Oxide Dismutase (nod) Genes Reveal Diverse Oxygenic Denitrifiers in Agricultural Soils and Lake Sediments.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {243-247}, pmid = {31989236}, issn = {1432-184X}, support = {616644//FP7 Ideas: European Research Council/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Bacterial Proteins/*analysis ; China ; Crop Production ; Denitrification ; Geologic Sediments/*microbiology ; Lakes/microbiology ; Nitrogen Cycle ; Oxygenases/*analysis ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Soil Microbiology ; }, abstract = {Microorganisms play an essential role in nitrogen cycling and greenhouse gas emissions in soils and sediments. The recently discovered oxygenic denitrifiers are proposed to reduce nitrate and nitrite via nitric oxide dismutation directly to N2 and O2. So far, the ecological role of these microbes is not well understood. The only available tool for a targeted study of oxygenic denitrifiers is their respective maker gene, nitric oxide dismutase (nod). Here, we established the use of PacBio long-read sequencing of nod gene amplicons to study the diversity and community structure of oxygenic denitrifiers. Two distinct sets of environmental samples, agricultural soil and lake sediment, were investigated as examples. The circular consensus sequences (ca 1.0 kb) obtained covered most substitution characteristic of NO dismutase and allowed for reliable classification of oxygenic denitrifiers. Distinct nod gene pools and community structure were revealed for the different habitats, with most sequence types affiliated to yet unidentified environmental nod lineages. The abundance of nod genes ranged 2.2 × 10[6]-3.2 × 10[7] gene copies g[-1] soil or sediment, accounting for up to 3% of total bacterial 16S rRNA gene counts. This study indicates that nod-gene-targeted long-read sequencing can be a powerful tool for studying the ecology of these novel microbes, and the results also suggest that oxygenic denitrifiers are prevalent and abundant in different terrestrial samples, where they could play an important, but yet overlooked role in nitrogen transformations.}, }
@article {pmid31988316, year = {2020}, author = {Remizovschi, A and Carpa, R and Forray, FL and Chiriac, C and Roba, CA and Beldean-Galea, S and Andrei, A&#x218; and Szekeres, E and Baricz, A and Lupan, I and Rudi, K and Coman, C}, title = {Mud volcanoes and the presence of PAHs.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {1253}, pmid = {31988316}, issn = {2045-2322}, abstract = {A mud volcano (MV) is a naturally hydrocarbon-spiked environment, as indicated by the presence of various quantities of PAHs and aromatic isotopic shifts in its sediments. Recurrent expulsion of various hydrocarbons consolidates the growth of hydrocarbonoclastic bacterial communities in the areas around MVs. In addition to the widely-known availability of biologically malleable alkanes, MVs can represent hotbeds of polyaromatic hydrocarbons (PAHs), as well - an aspect that has not been previously explored. This study measured the availability of highly recalcitrant PAHs and the isotopic signature of MV sediments both by GC-MS and δ[13]C analyses. Subsequently, this study highlighted both the occurrence and distribution of putative PAH-degrading bacterial OTUs using a metabarcoding technique. The putative hydrocarbonoclastic taxa incidence are the following: Enterobacteriaceae (31.5%), Methylobacteriaceae (19.9%), Bradyrhizobiaceae (16.9%), Oxalobacteraceae (10.2%), Comamonadaceae (7.6%) and Sphingomonadaceae (5.5%). Cumulatively, the results of this study indicate that MVs represent polyaromatic hydrocarbonoclastic hotbeds, as defined by both natural PAH input and high incidence of putative PAH-degrading bacterial OTUs.}, }
@article {pmid31987702, year = {2020}, author = {Kalita, M and Małek, W and Coutinho, TA}, title = {Putative novel Bradyrhizobium and Phyllobacterium species isolated from root nodules of Chamaecytisus ruthenicus.}, journal = {Systematic and applied microbiology}, volume = {43}, number = {2}, pages = {126056}, doi = {10.1016/j.syapm.2020.126056}, pmid = {31987702}, issn = {1618-0984}, mesh = {Bacterial Proteins/genetics ; Bradyrhizobium/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Fabaceae/*microbiology ; Genes, Essential/genetics ; Genetic Variation ; Nitrogen Fixation/genetics ; Phyllobacteriaceae/*classification/genetics/isolation &amp; purification ; *Phylogeny ; Plant Root Nodulation/genetics ; Poland ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/microbiology ; Sequence Analysis, DNA ; Symbiosis/genetics ; }, abstract = {In this study, the diversity and the phylogenetic relationships of bacteria isolated from root nodules of Chamaecytisus ruthenicus growing in Poland were investigated using ERIC-PCR fingerprinting and by multilocus sequence analysis (MLSA). Two major clusters comprising 13 and 3 isolates were detected which 16S rRNA gene sequencing identified as Bradyrhizobium and Phyllobacterium. The results of phylogenetic analysis of individual and concatenated atpD, gyrB and recA gene sequences showed that the studied strains may represent novel species in the genera Bradyrhizobium and Phyllobacterium. In the phylogenetic tree based on the atpD-gyrB-recA concatemers, Bradyrhizobium isolates were split into two groups closely related to Bradyrhizobium algeriense STM89[T] and Bradyrhizobium valentinum LmjM3[T]. The genus Phyllobacterium isolates formed a separate cluster close to Phyllobacterium ifriqiyense LMG27887[T] in the atpD-gyrB-recA phylogram. Analysis of symbiotic gene sequences (nodC, nodZ, nifD, and nifH) showed that the Bradyrhizobium isolates were most closely related to Bradyrhizobium algeriense STM89[T], Bradyrhizobium valentinum LmjM3[T] and Bradyrhizobium retamae Ro19[T] belonging to symbiovar retamae. This is the first report on the occurrence of members of symbiovar retamae from outside the Mediterranean region. No symbiosis related genes were amplified from Phyllobacterium strains, which were also unable to induce nodules on C. ruthenicus roots. Based on these findings Phyllobacterium isolates can be regarded as endophytic bacteria inhabitating root nodules of C. ruthenicus.}, }
@article {pmid31985137, year = {2020}, author = {Cramer, N and Fischer, S and Hedtfeld, S and Dorda, M and Tümmler, B}, title = {Intraclonal competitive fitness of longitudinal cystic fibrosis Pseudomonas aeruginosa airway isolates in liquid cultures.}, journal = {Environmental microbiology}, volume = {22}, number = {7}, pages = {2536-2549}, doi = {10.1111/1462-2920.14924}, pmid = {31985137}, issn = {1462-2920}, support = {C-H-P 01/12//Christiane Herzog Stiftung/International ; 82DZL002A1//Deutsche Zentrum f&#xfc;r Lungenforschung/International ; //German Center for Lung Research/International ; //Bundesministerium f&#xfc;r Bildung und Forschung/International ; //Research Foundation/International ; SFB900/3 - 158989968 - A2 and Z1//Deutsche Forschungsgemeinschaft/International ; }, mesh = {Adaptation, Physiological/genetics/*physiology ; Base Sequence ; Cystic Fibrosis/*microbiology ; Evolution, Molecular ; Genomics ; Humans ; Lung/*microbiology ; Phenotype ; Pseudomonas Infections ; Pseudomonas aeruginosa/genetics/*growth &amp; development/isolation &amp; purification/*metabolism ; Sequence Analysis, DNA ; }, abstract = {The metabolically versatile Pseudomonas aeruginosa inhabits biotic and abiotic environments including the niche of cystic fibrosis (CF) airways. This study investigated how the adaptation to CF lungs affects the within-clone fitness of P. aeruginosa to grow and persist in liquid cultures in the presence of the clonal ancestors. Longitudinal clonal P. aeruginosa isolates that had been collected from 12 CF donors since the onset of colonization for up to 30 years was subjected to within-clone competition experiments. The relative quantities of individual strains were determined by marker-free amplicon sequencing of multiplex PCR products of strain-specific nucleotide sequence variants, a novel method that is generally applicable to studies in evolutionary genetics and microbial ecology with real-world strain collections. For 10 of the 12 examined patient courses, P. aeruginosa isolates of the first years of colonization grew faster in the presence of their clonal progeny than alone. Single growth of individual strains showed no temporal trend with colonization time, but in co-culture, the early isolates out-competed their clonal progeny. Irrespective of the genetic make-up of the clone and its genomic microevolution in CF lungs, the early isolates expressed fitness traits to win the within-clone competition that were absent in their progeny.}, }
@article {pmid31984651, year = {2020}, author = {Xu, H and Wang, X and Feng, W and Liu, Q and Zhou, S and Liu, Q and Cai, L}, title = {The gut microbiota and its interactions with cardiovascular disease.}, journal = {Microbial biotechnology}, volume = {13}, number = {3}, pages = {637-656}, pmid = {31984651}, issn = {1751-7915}, mesh = {*Bacteria/metabolism ; *Cardiovascular Diseases/microbiology ; Dysbiosis/microbiology ; *Gastrointestinal Microbiome/physiology ; Humans ; Risk Factors ; }, abstract = {The intestine is colonized by a considerable community of microorganisms that cohabits within the host and plays a critical role in maintaining host homeostasis. Recently, accumulating evidence has revealed that the gut microbial ecology plays a pivotal role in the occurrence and development of cardiovascular disease (CVD). Moreover, the effects of imbalances in microbe-host interactions on homeostasis can lead to the progression of CVD. Alterations in the composition of gut flora and disruptions in gut microbial metabolism are implicated in the pathogenesis of CVD. Furthermore, the gut microbiota functions like an endocrine organ that produces bioactive metabolites, including trimethylamine/trimethylamine N-oxide, short-chain fatty acids and bile acids, which are also involved in host health and disease via numerous pathways. Thus, the gut microbiota and its metabolic pathways have attracted growing attention as a therapeutic target for CVD treatment. The fundamental purpose of this review was to summarize recent studies that have illustrated the complex interactions between the gut microbiota, their metabolites and the development of common CVD, as well as the effects of gut dysbiosis on CVD risk factors. Moreover, we systematically discuss the normal physiology of gut microbiota and potential therapeutic strategies targeting gut microbiota to prevent and treat CVD.}, }
@article {pmid31982930, year = {2020}, author = {Chen, YT and Zeng, Y and Wang, HZ and Zheng, D and Kamagata, Y and Narihiro, T and Nobu, MK and Tang, YQ}, title = {Different Interspecies Electron Transfer Patterns during Mesophilic and Thermophilic Syntrophic Propionate Degradation in Chemostats.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {120-132}, doi = {10.1007/s00248-020-01485-x}, pmid = {31982930}, issn = {1432-184X}, support = {2016YFE0127700//Ministry of Science and Technology of the People's Republic of China/ ; 51678378//National Natural Science Foundation of China/ ; 41701295//National Natural Science Foundation of China/ ; 2018M643480//Postdoctoral Research Foundation of China/ ; 2018SCUH0023//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Anaerobiosis ; Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; Biodegradation, Environmental ; Bioreactors ; Electron Transport ; Genome, Archaeal ; Genome, Bacterial ; Metagenomics ; Propionates/*metabolism ; Temperature ; }, abstract = {Propionate is one of the major intermediates in anaerobic digestion of organic waste to CO2 and CH4. In methanogenic environments, propionate is degraded through a mutualistic interaction between symbiotic propionate oxidizers and methanogens. Although temperature heavily influences the microbial ecology and performance of methanogenic processes, its effect on syntrophic interaction during propionate degradation remains poorly understood. In this study, metagenomics and metatranscriptomics were employed to compare mesophilic and thermophilic propionate degradation communities. Mesophilic propionate degradation involved multiple syntrophic organisms (Syntrophobacter, Smithella, and Syntrophomonas), pathways, interactions, and preference toward formate-based electron transfer to methanogenic partners (i.e., Methanoculleus). In thermophilic propionate degradation, one syntrophic organism predominated (Pelotomaculum), interspecies H2 transfer played a major role, and phylogenetically and metabolically diverse H2-oxidizing methanogens were present (i.e., Methanoculleus, Methanothermobacter, and Methanomassiliicoccus). This study showed that microbial interactions, metabolic pathways, and niche diversity are distinct between mesophilic and thermophilic microbial communities responsible for syntrophic propionate degradation.}, }
@article {pmid31982929, year = {2020}, author = {Tivey, TR and Parkinson, JE and Mandelare, PE and Adpressa, DA and Peng, W and Dong, X and Mechref, Y and Weis, VM and Loesgen, S}, title = {N-Linked Surface Glycan Biosynthesis, Composition, Inhibition, and Function in Cnidarian-Dinoflagellate Symbiosis.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {223-236}, doi = {10.1007/s00248-020-01487-9}, pmid = {31982929}, issn = {1432-184X}, support = {1557804//Division of Integrative Organismal Systems/ ; }, mesh = {Animals ; Anthozoa/*microbiology ; Dinoflagellida/*physiology ; Host Microbial Interactions ; Polysaccharides/biosynthesis/chemistry/*physiology ; *Symbiosis ; }, abstract = {The success of symbioses between cnidarian hosts (e.g., corals and sea anemones) and micro-algal symbionts hinges on the molecular interactions that govern the establishment and maintenance of intracellular mutualisms. As a fundamental component of innate immunity, glycan-lectin interactions impact the onset of marine endosymbioses, but our understanding of the effects of cell surface glycome composition on symbiosis establishment remains limited. In this study, we examined the canonical N-glycan biosynthesis pathway in the genome of the dinoflagellate symbiont Breviolum minutum (family Symbiodiniaceae) and found it to be conserved with the exception of the transferase GlcNAc-TII (MGAT2). Using coupled liquid chromatography-mass spectrometry (LC-MS/MS), we characterized the cell surface N-glycan content of B. minutum, providing the first insight into the molecular composition of surface glycans in dinoflagellates. We then used the biosynthesis inhibitors kifunensine and swainsonine to alter the glycan composition of B. minutum. Successful high-mannose enrichment via kifunensine treatment resulted in a significant decrease in colonization of the model sea anemone Aiptasia (Exaiptasia pallida) by B. minutum. Hybrid glycan enrichment via swainsonine treatment, however, could not be confirmed and did not impact colonization. We conclude that functional Golgi processing of N-glycans is critical for maintaining appropriate cell surface glycan composition and for ensuring colonization success by B. minutum.}, }
@article {pmid31972955, year = {2020}, author = {Lepoutre, A and Faassen, EJ and Zweers, AJ and Lürling, M and Geffard, A and Lance, E}, title = {How the Neurotoxin β-N-Methylamino-l-Alanine Accumulates in Bivalves: Distribution of the Different Accumulation Fractions among Organs.}, journal = {Toxins}, volume = {12}, number = {2}, pages = {}, pmid = {31972955}, issn = {2072-6651}, support = {Bourse Eole//R&#xe9;seau Franco-N&#xe9;erlandais de l'enseignement sup&#xe9;rieur et de la recherche (RFN) and the Nuffic (Netherlands Organization for International Co-operation in Higher Education)./International ; 2015/1/191//Agence Nationale de S&#xe9;curit&#xe9; Sanitaire de l'Alimentation, de l'Environnement et du Travail/International ; }, mesh = {Amino Acids, Diamino/*pharmacokinetics ; Animals ; Cyanobacteria Toxins ; Dreissena/*metabolism ; Gastrointestinal Tract/metabolism ; Gills/metabolism ; Gonads/metabolism ; Hemolymph/metabolism ; Muscles/metabolism ; Neurotoxins/*pharmacokinetics ; Tissue Distribution ; Water Pollutants, Chemical/*pharmacokinetics ; }, abstract = {The environmental neurotoxin β-methylamino-l-alanine (BMAA) may represent a risk for human health. BMAA accumulates in freshwater and marine organisms consumed by humans. However, few data are available about the kinetics of BMAA accumulation and detoxification in exposed organisms, as well as the organ distribution and the fractions in which BMAA is present in tissues (free, soluble bound or precipitated bound cellular fractions). Here, we exposed the bivalve mussel Dreissena polymorpha to 7.5 µg of dissolved BMAA/mussel/3 days for 21 days, followed by 21 days of depuration in clear water. At 1, 3, 8, 14 and 21 days of exposure and depuration, the hemolymph and organs (digestive gland, the gills, the mantle, the gonad and muscles/foot) were sampled. Total BMAA as well as free BMAA, soluble bound and precipitated bound BMAA were quantified by tandem mass spectrometry. Free and soluble bound BMAA spread throughout all tissues from the first day of exposure to the last day of depuration, without a specific target organ. However, precipitated bound BMAA was detected only in muscles and foot from the last day of exposure to day 8 of depuration, at a lower concentration compared to free and soluble bound BMAA. In soft tissues (digestive gland, gonad, gills, mantle and muscles/foot), BMAA mostly accumulated as a free molecule and in the soluble bound fraction, with variations occurring between the two fractions among tissues and over time. The results suggest that the assessment of bivalve contamination by BMAA may require the quantification of total BMAA in whole individuals when possible.}, }
@article {pmid31969867, year = {2019}, author = {Qu, EB and Omelon, CR and Oren, A and Meslier, V and Cowan, DA and Maggs-Kölling, G and DiRuggiero, J}, title = {Trophic Selective Pressures Organize the Composition of Endolithic Microbial Communities From Global Deserts.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2952}, pmid = {31969867}, issn = {1664-302X}, abstract = {Studies of microbial biogeography are often convoluted by extremely high diversity and differences in microenvironmental factors such as pH and nutrient availability. Desert endolithic (inside rock) communities are relatively simple ecosystems that can serve as a tractable model for investigating long-range biogeographic effects on microbial communities. We conducted a comprehensive survey of endolithic sandstones using high-throughput marker gene sequencing to characterize global patterns of diversity in endolithic microbial communities. We also tested a range of abiotic variables in order to investigate the factors that drive community assembly at various trophic levels. Macroclimate was found to be the primary driver of endolithic community composition, with the most striking difference witnessed between hot and polar deserts. This difference was largely attributable to the specialization of prokaryotic and eukaryotic primary producers to different climate conditions. On a regional scale, microclimate and properties of the rock substrate were found to influence community assembly, although to a lesser degree than global hot versus polar conditions. We found new evidence that the factors driving endolithic community assembly differ between trophic levels. While phototrophic taxa, mostly oxygenic photosynthesizers, were rigorously selected for among different sites, heterotrophic taxa were more cosmopolitan, suggesting that stochasticity plays a larger role in heterotroph assembly. This study is the first to uncover the global drivers of desert endolithic diversity using high-throughput sequencing. We demonstrate that phototrophs and heterotrophs in the endolithic community assemble under different stochastic and deterministic influences, emphasizing the need for studies of microorganisms in context of their functional niche in the community.}, }
@article {pmid31969866, year = {2019}, author = {Hao, X and Zhu, YG and Nybroe, O and Nicolaisen, MH}, title = {The Composition and Phosphorus Cycling Potential of Bacterial Communities Associated With Hyphae of Penicillium in Soil Are Strongly Affected by Soil Origin.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2951}, pmid = {31969866}, issn = {1664-302X}, abstract = {Intimate fungal-bacterial interactions are widespread in nature. However the main drivers for the selection of hyphae-associated bacterial communities and their functional traits in soil systems remain elusive. In the present study, baiting microcosms were used to recover hyphae-associated bacteria from two Penicillium species with different phosphorus-solubilizing capacities in five types of soils. Based on amplicon sequencing of 16S rRNA genes, the composition of bacterial communities associated with Penicillium hyphae differed significantly from the soil communities, showing a lower diversity and less variation in taxonomic structure. Furthermore, soil origin had a significant effect on hyphae-associated community composition, whereas the two fungal species used in this study had no significant overall impact on bacterial community structure, despite their different capacities to solubilize phosphorus. However, discriminative taxa and specific OTUs were enriched in hyphae-associated communities of individual Penicillium species indicating that each hyphosphere represented a unique niche for bacterial colonization. Additionally, an increased potential of phosphorus cycling was found in hyphae-associated communities, especially for the gene phnK involved in phosphonate degradation. Altogether, it was established that the two Penicillium hyphae represent unique niches in which microbiome assemblage and phosphorus cycling potential are mainly driven by soil origin, with less impact made by fungal identity with a divergent capacity to utilize phosphorus.}, }
@article {pmid31968298, year = {2020}, author = {Lu, B and Shen, Z and Zhang, Q and Hu, X and Warren, A and Song, W}, title = {Morphology and molecular analyses of four epibiotic peritrichs on crustacean and polychaete hosts, including descriptions of two new species (Ciliophora, Peritrichia).}, journal = {European journal of protistology}, volume = {73}, number = {}, pages = {125670}, doi = {10.1016/j.ejop.2019.125670}, pmid = {31968298}, issn = {1618-0429}, mesh = {Animals ; China ; Crustacea/*parasitology ; DNA, Protozoan/genetics ; Oligohymenophorea/*classification/cytology/genetics ; Phylogeny ; Polychaeta/*parasitology ; Species Specificity ; }, abstract = {Four epibiotic sessilid peritrichs, i.e., Zoothamnium wilberti n. sp., Baikalonis microdiscus n. sp., Epistylis anastatica (Linnaeus, 1767) Ehrenberg, 1830, and Rhabdostyla commensalisMöbius, 1888, were isolated from one syllid polychaete and three crustacean hosts in Qingdao, China. For each species, specimens were observed both in vivo and following silver staining. Their SSU rDNA was also sequenced for phylogenetic analyses. Zoothamnium wilberti n. sp. is characterized by the appearance of its colony, which is up to 350 μm high, and usually has fewer than 16 zooids, and the dichotomously branched stalk with transverse wrinkles, the conspicuously conical peristomial disc, and infundibular polykinety 3 comprising three isometric ciliary rows. Baikalonis microdiscus n. sp. can be recognized by its barrel-shaped zooid, small peristomial disc, smooth and short stalk, and its unusual infundibular polykinety 3 comprising a long inner row and a short outer row. Two poorly known species, i.e., Epistylis anastatica and Rhabdostyla commensalis, are redescribed and redefined. Phylogenetic analyses reveal that: (i) R. commensalis is closely related to the family Astylozoidae rather than to the morphologically similar Epistylididae; (ii) B. microdiscus n. sp. is sister to the family Scyphidiidae; (iii) E. anastatica groups with vorticellids and ophrydiids, which further supports the polyphyly of the genus Epistylis; and (iv) Z. wilberti n. sp. is nested within the Zoothamniidae, as expected.}, }
@article {pmid31967575, year = {2020}, author = {Probst, AJ and Vaishampayan, P}, title = {Are we There Yet? Understanding Interplanetary Microbial Hitchhikers using Molecular Methods.}, journal = {Current issues in molecular biology}, volume = {38}, number = {}, pages = {33-52}, doi = {10.21775/cimb.038.033}, pmid = {31967575}, issn = {1467-3045}, mesh = {Adenosine Triphosphate/chemistry ; Bacteria/growth &amp; development/*isolation &amp; purification ; Cell Survival ; *Ecological Systems, Closed ; *Environmental Microbiology ; Extraterrestrial Environment/*chemistry ; Genomics ; Metagenomics ; Microbiota ; RNA, Ribosomal/chemistry/isolation &amp; purification ; *Space Flight ; Spacecraft/standards ; Spores/isolation &amp; purification ; Sterilization ; United States ; United States National Aeronautics and Space Administration ; Weightlessness ; }, abstract = {Since the early time of space travel, planetary bodies undergoing chemical or biological evolution have been of particular interest for life detection missions. NASA's and ESA's Planetary Protection offices ensure responsible exploration of the solar system and aim at avoiding inadvertent contamination of celestial bodies with biomolecules or even living organisms. Life forms that have the potential to colonize foreign planetary bodies could be a threat to the integrity of science objectives of life detection missions. While standard requirements for assessing the cleanliness of spacecraft are still based on cultivation approaches, several molecular methods have been applied in the past to elucidate the full breadth of (micro)organisms that can be found on spacecraft and in cleanrooms, where the hardware is assembled. Here, we review molecular assays that have been applied in Planetary Protection research and list their significant advantages and disadvantages. By providing a comprehensive summary of the latest molecular methods yet to be applied in this research area, this article will not only aid in designing technological roadmaps for future Planetary Protection endeavors but also help other disciplines in environmental microbiology that deal with low biomass samples.}, }
@article {pmid31965838, year = {2019}, author = {Moens, F and Duysburgh, C and van den Abbeele, P and Morera, M and Marzorati, M}, title = {Lactobacillus rhamnosus GG and Saccharomyces cerevisiae boulardii exert synergistic antipathogenic activity in vitro against enterotoxigenic Escherichia coli.}, journal = {Beneficial microbes}, volume = {10}, number = {8}, pages = {923-935}, doi = {10.3920/BM2019.0064}, pmid = {31965838}, issn = {1876-2891}, mesh = {Adult ; Batch Cell Culture Techniques ; Child, Preschool ; Coculture Techniques ; Colon/metabolism/microbiology ; Dysbiosis/metabolism/microbiology ; Enterotoxigenic Escherichia coli/*drug effects/growth &amp; development/metabolism ; Enterotoxins/metabolism ; Fatty Acids, Volatile/metabolism ; Healthy Volunteers ; Humans ; Intestinal Mucosa/metabolism/microbiology ; Lacticaseibacillus rhamnosus/growth &amp; development/metabolism/*physiology ; Probiotics/*pharmacology ; Saccharomyces cerevisiae/growth &amp; development/metabolism/*physiology ; }, abstract = {Short-term colonic in vitro batch incubations were performed to elucidate the possible synergistic effects of Lactobacillus rhamnosus GG (CNCM-I-4798) and Saccharomyces cerevisiae boulardii (CNCM-I-1079) (associated in Smebiocta/Smectaflora Protect®) on the colonic microbial fermentation process, as well as their antipathogenic activity against enterotoxigenic Escherichia coli (LMG2092) (ETEC). These incubations adequately simulate the native microbiota and environmental conditions of the proximal colon of both adult and toddler donors, including the colonic mucosal layer. Results indicated that both strains were capable of growing together without showing antagonistic effects. Co-cultivation of both strains resulted in increased butyrate (stimulated by L. rhamnosus GG), propionate (stimulated by S. boulardii), and ethanol (produced by S. boulardii) production compared to the control incubations, revealing the additive effect of both strains. After inoculation of ETEC under simulated dysbiotic conditions, a 40 and 46% reduction in the concentration of ETEC was observed upon addition of both strains during the experiments with the adult and toddler donor, respectively. Furthermore, ETEC toxin levels decreased upon S. boulardii inoculation, probably due to proteolytic activity of this strain, with a synergistic effect being observed upon co-cultivation of L. rhamnosus GG and S. boulardii resulting in a reduction of 57 and 46% for the adult and toddler donor, respectively. Altogether, the results suggest that both probiotics together may help microbiota functionality, in both adults and toddlers and under healthy or impaired conditions, which could be of great interest when the colonic microbiota is dysbiotic and therefore sensitive to pathogenic invasion such as during antibiotic treatment.}, }
@article {pmid31965223, year = {2020}, author = {Mina, D and Pereira, JA and Lino-Neto, T and Baptista, P}, title = {Epiphytic and Endophytic Bacteria on Olive Tree Phyllosphere: Exploring Tissue and Cultivar Effect.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {145-157}, doi = {10.1007/s00248-020-01488-8}, pmid = {31965223}, issn = {1432-184X}, support = {PTDC/ASP-PLA/31133/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH-BD-105341/2014//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PRIMA/0002/2018//Horizon 2020 Framework Programme/ ; }, mesh = {Bacteria/classification/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; Endophytes/classification/isolation &amp; purification/physiology ; *Microbiota ; Olea/*microbiology ; Plant Leaves/*microbiology ; Portugal ; }, abstract = {Variation on bacterial communities living in the phyllosphere as epiphytes and endophytes has been attributed to plant host effects. However, there is contradictory or inconclusive evidence regarding the effect of plant genetics (below the species' level) and of plant tissue type on phyllosphere bacterial community assembly, in particular when epiphytes and endophytes are considered simultaneously. Here, both surface and internal bacterial communities of two olive (Olea europaea) cultivars were evaluated in twigs and leaves by molecular identification of cultivable isolates, with an attempt to answer these questions. Overall, Proteobacteria, Actinobacteria and Firmicutes were the dominant phyla, being epiphytes more diverse and abundant than endophytes. Host genotype (at cultivar level) had a structuring effect on the composition of bacterial communities and, in a similar way, for both epiphytes and endophytes. Plant organ (leaf vs. twig) control of the bacterial communities was less evident when compared with plant genotype and with a greater influence on epiphytic than on endophytic community structure. Each olive genotype/plant organ was apparently selective towards specific bacterial operational taxonomic units (OTUs), which may lead to specific feedbacks on fitness of plant genotypes. Bacterial recruitment was observed to happen mainly within epiphytes than in endophytes and in leaves as compared with twigs. Such host specificity suggested that the benefits derived from the plant-bacteria interaction should be considered at genetic levels below the species.}, }
@article {pmid31964728, year = {2020}, author = {Carini, P and Delgado-Baquerizo, M and Hinckley, ES and Holland-Moritz, H and Brewer, TE and Rue, G and Vanderburgh, C and McKnight, D and Fierer, N}, title = {Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {31964728}, issn = {2150-7511}, mesh = {*Metagenome ; *Metagenomics/methods ; Microbial Interactions ; *Microbiota ; RNA, Ribosomal, 16S ; Seasons ; Soil/chemistry ; *Soil Microbiology ; Spatio-Temporal Analysis ; }, abstract = {Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes.IMPORTANCE Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.}, }
@article {pmid31958594, year = {2020}, author = {Vandekerckhove, TGL and Props, R and Carvajal-Arroyo, JM and Boon, N and Vlaeminck, SE}, title = {Adaptation and characterization of thermophilic anammox in bioreactors.}, journal = {Water research}, volume = {172}, number = {}, pages = {115462}, doi = {10.1016/j.watres.2019.115462}, pmid = {31958594}, issn = {1879-2448}, mesh = {*Ammonium Compounds ; Anaerobiosis ; *Bioreactors ; Nitrogen ; Oxidation-Reduction ; RNA, Ribosomal, 16S ; Sewage ; Temperature ; }, abstract = {Anammox, the oxidation of ammonium with nitrite, is a key microbial process in the nitrogen cycle. Under mesophilic conditions (below 40 °C), it is widely implemented to remove nitrogen from wastewaters lacking organic carbon. Despite evidence of the presence of anammox bacteria in high-temperature environments, reports on the cultivation of thermophilic anammox bacteria are limited to a short-term experiment of 2 weeks. This study showcases the adaptation of a mesophilic inoculum to thermophilic conditions, and its characterization. First, an attached growth technology was chosen to obtain the process. In an anoxic fixed-bed biofilm bioreactor (FBBR), a slow linear temperature increase from 38 to over 48 °C (0.05-0.07 °C d[-1]) was imposed to the community over 220 days, after which the reactor was operated at 48 °C for over 200 days. Maximum total nitrogen removal rates reached up to 0.62 g N L[-1] d[-1]. Given this promising performance, a suspended growth system was tested. The obtained enrichment culture served as inoculum for membrane bioreactors (MBR) operated at 50 °C, reaching a maximum total nitrogen removal rate of 1.7 g N L[-1] d[-1] after 35 days. The biomass in the MBR had a maximum specific anammox activity of 1.1 ± 0.1 g NH4[+]-N g[-1] VSS d[-1], and the growth rate was estimated at 0.075-0.19 d[-1]. The thermophilic cultures displayed nitrogen stoichiometry ratios typical for mesophilic anammox: 0.93-1.42 g NO2[-]-Nremoved g[-1] NH4[+]-Nremoved and 0.16-0.35 g NO3[-]-Nproduced g[-1] NH4[+]-Nremoved. Amplicon and Sanger sequencing of the 16S rRNA genes revealed a disappearance of the original "Ca. Brocadia" and "Ca. Jettenia" taxa, yielding Planctomycetes members with only 94-95% similarity to "Ca. Brocadia anammoxidans" and "Ca. B. caroliniensis", accounting for 45% of the bacterial FBBR community. The long-term operation of thermophilic anammox reactors and snapshot views on the nitrogen stoichiometry, kinetics and microbial community open up the development path of thermophilic partial nitritation/anammox. A first economic assessment highlighted that treatment of sludge reject water from thermophilic anaerobic digestion of sewage sludge may become attractive.}, }
@article {pmid31955749, year = {2020}, author = {Gontijo, MTP and Silva, JS and Vidigal, PMP and Martin, JGP}, title = {Phylogenetic distribution of the bacteriocin repertoire of lactic acid bacteria species associated with artisanal cheese.}, journal = {Food research international (Ottawa, Ont.)}, volume = {128}, number = {}, pages = {108783}, doi = {10.1016/j.foodres.2019.108783}, pmid = {31955749}, issn = {1873-7145}, mesh = {Bacteriocins/chemistry/genetics/*metabolism ; Cheese/*microbiology ; Food Microbiology ; Genome, Bacterial ; Lactobacillales/*genetics/*metabolism ; Peptides/chemistry/classification/metabolism/pharmacology ; Phylogeny ; }, abstract = {The microbiota contributes to artisanal cheese bioprotection and biopreservation through inter and intraspecific competition. This work aimed to investigate the phylogenetic distribution of the repertoire of bacteriocin structural genes of model lactic acid bacteria (LAB) in order to investigate its respective role in the artisanal cheeses microenvironment. A phylogenetic analysis of the rRNA 16S gene from 445 model strains of LAB was conducted using bayesian inference and the repertoire of bacteriocin genes was predicted from these strains by BAGEL software. Bacterial strains were clustered in five monophyletic clades (A, B, C, D and E) with high posterior probability values (PP > 0.99). One bacteriocin structural gene was predicted for 88.5% of the analyzed strains. The majority of the species encoded different classes of bacteriocins. Greater diversity of bacteriocin genes was found for strains included in clade A, comprising Lactococcus lactis, Streptococcus agalactiae, Streptococcus thermophilus, Streptococcus macedonicus, Enterococcus faecalis and Enterococcus faecium. In addition, Lactococcus lactis presented higher diversity of bacteriocin classes, encoding glycocins, lanthipeptides, sactipeptides, cyclic and linear azole-containing peptides, included in bacteriocins class I, besides class II and III. The results suggest that the distribution of bacteriocin structural genes is related to the phylogenetic clades of LAB species, with a higher frequency in some specific clades. Information comprised in this study contributes to comprehend the bacterial competition mechanisms in the artisanal cheese microenvironment.}, }
@article {pmid31955225, year = {2020}, author = {Liu, H and Gao, H and Wu, M and Ma, C and Wu, J and Ye, X}, title = {Distribution Characteristics of Bacterial Communities and Hydrocarbon Degradation Dynamics During the Remediation of Petroleum-Contaminated Soil by Enhancing Moisture Content.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {202-211}, doi = {10.1007/s00248-019-01476-7}, pmid = {31955225}, issn = {1432-184X}, support = {No. 21577109//National Natural Science Foundation of China/ ; }, mesh = {Bacteria/*metabolism ; Bacterial Physiological Phenomena ; Biodegradation, Environmental ; Environmental Pollution/*prevention &amp; control ; Environmental Restoration and Remediation ; Humidity ; Hydrocarbons/*metabolism ; *Microbiota ; Soil/*chemistry ; Soil Pollutants/*metabolism ; }, abstract = {Microorganisms are the driver of petroleum hydrocarbon degradation in soil micro-ecological systems. However, the distribution characteristics of microbial communities and hydrocarbon degradation dynamics during the remediation of petroleum-contaminated soil by enhancing moisture content are not clear. In this study, polymerase chain reaction and high-throughput sequencing of soil microbial DNA were applied to investigate the compositions of microorganisms and alpha diversity in the oil-polluted soil, and the hydrocarbon removal also being analyzed using ultrasonic extraction and gravimetric method in a laboratory simulated ex-situ experiment. Results showed the distribution of petroleum hydrocarbon degrading microorganisms in the petroleum-contaminated loessal soil mainly was Proteobacteria phylum (96.26%)-Gamma-proteobacteria class (90.03%)-Pseudomonadales order (89.98%)-Pseudomonadaceae family (89.96%)-Pseudomonas sp. (87.22%). After 15% moisture content treatment, Actinobacteria, Proteobacteria, and Firmicutes still were the predominant phyla, but their relative abundances changed greatly. Also Bacillus sp. and Promicromonospora sp. became the predominant genera. Maintaining 15% moisture content increased the relative abundance of Firmicutes phylum and Bacillus sp. As the moisture-treated time increases, the uniformity and the richness of the soil bacterial community were decreased and increased respectively; the relative abundance of Pseudomonas sp. increased. Petroleum hydrocarbon degradation by enhancing soil moisture accorded with the pseudo-first-order reaction kinetic model (correlation coefficient of 0.81; half-life of 56 weeks). The richness of Firmicutes phylum and Bacillus sp. may be a main reason for promoting the removal of 18% petroleum hydrocarbons responded to 15% moisture treatment. Our results provided some beneficial microbiological information of oil-contaminated soil and will promote the exploration of remediation by changing soil moisture content for increasing petroleum hydrocarbon degradation efficiency.}, }
@article {pmid31954761, year = {2020}, author = {Mongui, A and Lozano, GL and Handelsman, J and Restrepo, S and Junca, H}, title = {Design and validation of a transposon that promotes expression of genes in episomal DNA.}, journal = {Journal of biotechnology}, volume = {310}, number = {}, pages = {1-5}, doi = {10.1016/j.jbiotec.2020.01.007}, pmid = {31954761}, issn = {1873-4863}, mesh = {*DNA Transposable Elements ; DNA-Directed RNA Polymerases/biosynthesis/*genetics ; Escherichia coli/*genetics/metabolism ; *Gene Expression ; Plasmids/*genetics/metabolism ; *Promoter Regions, Genetic ; Viral Proteins/biosynthesis/*genetics ; }, abstract = {Functional metagenomics, or the cloning and expression of DNA isolated directly from environmental samples, represents a source of novel compounds with biotechnological potential. However, attempts to identify such compounds in metagenomic libraries are generally inefficient in part due to lack of expression of heterologous DNA. In this research, the TnC_T7 transposon was developed to supply transcriptional machinery during functional analysis of metagenomic libraries. TnC_T7 contains bidirectional T7 promoters, the gene encoding the T7 RNA polymerase (T7RNAP), and a kanamycin resistance gene. The T7 RNA polymerase gene is regulated by the inducible arabinose promoter (PBAD), thereby facilitating inducible expression of genes adjacent to the randomly integrating transposon. The high processivity of T7RNAP should make this tool particularly useful for obtaining gene expression in long inserts. TnC_T7 functionality was validated by conducting in vitro transposition of pKR-C12 or fosmid pF076_GFPmut3*, carrying metagenomic DNA from soil. We identified transposon insertions that enhanced GFP expression in both vectors, including insertions in which the promoter delivered by the transposon was located as far as 8.7 kb from the GFP gene, indicating the power of the high processivity of the T7 polymerase. The results gathered in this research demonstrate the potential of TnC_T7 to enhance gene expression in functional metagenomic studies.}, }
@article {pmid31954367, year = {2020}, author = {Giri, S and Shitut, S and Kost, C}, title = {Harnessing ecological and evolutionary principles to guide the design of microbial production consortia.}, journal = {Current opinion in biotechnology}, volume = {62}, number = {}, pages = {228-238}, doi = {10.1016/j.copbio.2019.12.012}, pmid = {31954367}, issn = {1879-0429}, mesh = {Bacteria/genetics ; *Biotechnology ; *Microbial Consortia/genetics ; }, abstract = {Bacteria are widely used for commercially producing biomolecules. However, attempts to rationally design production strains and optimize cultivation conditions are frequently counteracted by the emergence of mutants with reduced production characteristics that decrease overall process yield. The reason why these mutants arise is likely because of a mismatch between the ecological conditions under which bacteria evolved in nature and the situation they experience in an industrial setting. Thus, there is a great potential for improving biotechnological production processes by implementing eco-evolutionary knowledge. However, this is often limited by a lack of effective communication between process engineers and microbial ecologists/evolutionary biologists. Here, we highlight recent findings in the field of microbial ecology and evolution and suggest implementation of this knowledge can significantly enhance microbial bioproduction.}, }
@article {pmid31953337, year = {2020}, author = {Tinker, KA and Ottesen, EA}, title = {Phylosymbiosis across Deeply Diverging Lineages of Omnivorous Cockroaches (Order Blattodea).}, journal = {Applied and environmental microbiology}, volume = {86}, number = {7}, pages = {}, pmid = {31953337}, issn = {1098-5336}, support = {R35 GM133789/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Bacterial Physiological Phenomena ; Cockroaches/*microbiology ; *Gastrointestinal Microbiome ; *Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Symbiosis ; }, abstract = {The gut microbiome is shaped by both host diet and host phylogeny. However, separating the relative influence of these two factors over long periods of evolutionary time is often difficult. We conducted a 16S rRNA gene amplicon-based survey of the gut microbiome from 237 individuals and 19 species of omnivorous cockroaches from the order Blattodea. The order Blattodea represents an ancient lineage of insects that emerged over 300 million years ago, have a diverse gut microbiota, and have a typically gregarious lifestyle. All cockroaches shared a broadly similar gut microbiota, with 66 microbial families present across all species and 13 present in every individual examined. Although our network analysis of the cockroach gut microbiome showed a large amount of connectivity, we demonstrated that gut microbiota cluster strongly by host species. We conducted follow-up tests to determine if cockroaches exhibit phylosymbiosis, or the tendency of host-associated microbial communities to parallel the phylogeny of related host species. Across the full data set, gut microbial community similarity was not found to correlate with host phylogenetic distance. However, a weak but significant phylosymbiotic signature was observed using the matching cluster metric, which allows for localized changes within a phylogenetic tree that are more likely to occur over long evolutionary distances. This finding suggests that host phylogeny plays a large role in structuring the cockroach gut microbiome over shorter evolutionary distances and a weak but significant role in shaping the gut microbiome over extended periods of evolutionary time.IMPORTANCE The gut microbiome plays a key role in host health. Therefore, it is important to understand the evolution of the gut microbiota and how it impacts, and is impacted by, host evolution. In this study, we explore the relationship between host phylogeny and gut microbiome composition in omnivorous, gregarious cockroaches within the Blattodea order, an ancient lineage that spans 300 million years of evolutionary divergence. We demonstrate a strong relationship between host species identity and gut microbiome composition and found a weaker but significant role for host phylogeny in determining microbiome similarity over extended periods of evolutionary time. This study advances our understanding of the role of host phylogeny in shaping the gut microbiome over different evolutionary distances.}, }
@article {pmid31952848, year = {2020}, author = {Krishnamoorthy, S and Coetzee, V and Kruger, J and Potgieter, H and Buys, EM}, title = {Dysbiosis Signatures of Fecal Microbiota in South African Infants with Respiratory, Gastrointestinal, and Other Diseases.}, journal = {The Journal of pediatrics}, volume = {218}, number = {}, pages = {106-113.e3}, doi = {10.1016/j.jpeds.2019.11.029}, pmid = {31952848}, issn = {1097-6833}, mesh = {Anti-Bacterial Agents/therapeutic use ; Case-Control Studies ; Child, Preschool ; Dysbiosis/*microbiology ; Feces/microbiology ; Female ; Gastrointestinal Diseases/*microbiology ; *Gastrointestinal Microbiome ; Hospitalization ; Humans ; Infant ; Male ; Principal Component Analysis ; RNA, Ribosomal, 16S/metabolism ; Respiration Disorders/*microbiology ; Software ; South Africa ; Vitamin A/therapeutic use ; }, abstract = {OBJECTIVE: To determine the association between the fecal microbiota diversity of the infants with different disease conditions, and vitamin A supplementation, antibiotic, and deworming therapies.<br><br>STUDY DESIGN: In this case-control study, the bacterial community variations and the potential pathogens were identified through 16S ribosomal RNA gene-based amplicon sequencing and quantitative insights into microbial ecology pipeline in fecal samples. The participants were South African infants (mean age, 16&#xa0;&#xb1;&#xa0;8&#xa0;months; 17 male and 17 female) hospitalized and diagnosed with gastrointestinal, respiratory, and other diseases.<br><br>RESULTS: The top phyla of the infants with respiratory disease were Proteobacteria, followed by Firmicutes, which were equally abundant in gastrointestinal disease. A significant difference in Shannon (alpha) diversity index (95% CI, 2.6-4.4; P&#xa0;=&#xa0;.008), among the microbiota of the fecal samples categorized by disease conditions, was observed. In beta diversity analysis of fecal microbiota, remarkable variations were found within the groups of deworming therapy (95% CI, 0.40-0.90; P&#xa0;=&#xa0;.033), disease conditions (95% CI, 0.44-0.86; P&#xa0;<&#xa0;.012) through unweighted and antibiotic therapy (95% CI, 0.20-0.75; P&#xa0;=&#xa0;.007), vitamin A intake (95% CI, 0.10-0.80; P&#xa0;<&#xa0;.033) and disease conditions (95% CI, 0.10-0.79; P&#xa0;=&#xa0;.006) through weighted UniFrac distances. The candidate pathogen associated with the disease groups were identified through analysis of the composition of microbiomes analysis.<br><br>CONCLUSIONS: This study provides preliminary evidence for the fecal microbiome-derived dysbiosis signature and pathobiome concept that may be observed in young children during illness.}, }
@article {pmid31952472, year = {2020}, author = {Feng, J and Wang, C and Lei, J and Yang, Y and Yan, Q and Zhou, X and Tao, X and Ning, D and Yuan, MM and Qin, Y and Shi, ZJ and Guo, X and He, Z and Van Nostrand, JD and Wu, L and Bracho-Garillo, RG and Penton, CR and Cole, JR and Konstantinidis, KT and Luo, Y and Schuur, EAG and Tiedje, JM and Zhou, J}, title = {Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {3}, pmid = {31952472}, issn = {2049-2618}, mesh = {Carbon/metabolism ; *Carbon Cycle ; *Global Warming ; Methane/metabolism ; *Microbiota ; Permafrost/*microbiology ; RNA, Ribosomal, 16S/genetics ; Seasons ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {BACKGROUND: It is well-known that global warming has effects on high-latitude tundra underlain with permafrost. This leads to a severe concern that decomposition of soil organic carbon (SOC) previously stored in this region, which accounts for about 50% of the world's SOC storage, will cause positive feedback that accelerates climate warming. We have previously shown that short-term warming (1.5 years) stimulates rapid, microbe-mediated decomposition of tundra soil carbon without affecting the composition of the soil microbial community (based on the depth of 42684 sequence reads of 16S rRNA gene amplicons per 3 g of soil sample).<br><br>RESULTS: We show that longer-term (5 years) experimental winter warming at the same site altered microbial communities (p < 0.040). Thaw depth correlated the strongest with community assembly and interaction networks, implying that warming-accelerated tundra thaw fundamentally restructured the microbial communities. Both carbon decomposition and methanogenesis genes increased in relative abundance under warming, and their functional structures strongly correlated (R[2] > 0.725, p < 0.001) with ecosystem respiration or CH4 flux.<br><br>CONCLUSIONS: Our results demonstrate that microbial responses associated with carbon cycling could lead to positive feedbacks that accelerate SOC decomposition in tundra regions, which is alarming because SOC loss is unlikely to subside owing to changes in microbial community composition. Video Abstract.}, }
@article {pmid31951572, year = {2020}, author = {Li, Z and Van de Peer, Y}, title = {"Winter Is Coming": How did Polyploid Plants Survive?.}, journal = {Molecular plant}, volume = {13}, number = {1}, pages = {4-5}, doi = {10.1016/j.molp.2019.12.003}, pmid = {31951572}, issn = {1752-9867}, mesh = {Humans ; *Magnoliopsida ; Plants ; Polyploidy ; Seasons ; }, }
@article {pmid31951190, year = {2020}, author = {Lee, JC and Whang, KS}, title = {Segeticoccus rhizosphaerae gen. nov., sp. nov., an actinobacterium isolated from soil of a farming field.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {70}, number = {3}, pages = {1785-1792}, doi = {10.1099/ijsem.0.003973}, pmid = {31951190}, issn = {1466-5034}, mesh = {Actinobacteria/*classification/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; *Farms ; Fatty Acids/chemistry ; Peptidoglycan/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {A Gram-stain-positive actinobacterial strain, designated YJ01[T], was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ01[T] was aerobic, non-motile, non-spore-forming cocci with diameters of 1.5-1.9 µm, and was able to grow at 10-37 °C (optimum, 28-30 °C), at pH 4.5-9.0 (optimum, pH 7.0-8.0) and at salinities of 0-7.5 % (w/v) NaCl (optimum, 1.0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ01[T] with closely related relatives were in the range 96.2-92.8 %, and the results of phylogenomic analysis indicated that strain YJ01[T] was clearly separated from species of genera in the family Intrasporangiaceae showing average nucleotide identity values of 84.2-83.4 %. The predominant isoprenoid quinone was identified as MK-8(H4) and the major fatty acids were iso-C15 : 0, iso-C16:1 h, iso-C16 : 0 and anteiso-C17 : 1ω9c. The diagnostic diamino acid of the peptidoglycan was ornithine, and the interpeptide bridge was l-Orn-Gly2-d-Glu. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylserine, an unidentified phosphatidylglycolipid, two unidentified phosphoaminolipids and an unidentified phosphoglycoaminolipid. The G+C content of the genome was 70.1 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences, strain YJ01[T] is considered to represent a novel species of a new genus in the family Intrasporangiaceae, for which the name Segeticoccus rhizosphaerae gen. nov. sp. nov. is proposed. The type strain of Segeticoccus rhizosphaerae is YJ01[T] (=KACC 19547[T]=NBRC 113173[T]).}, }
@article {pmid31950228, year = {2020}, author = {Guhr, A and Kircher, S}, title = {Drought-Induced Stress Priming in Two Distinct Filamentous Saprotrophic Fungi.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {27-33}, pmid = {31950228}, issn = {1432-184X}, support = {DFG-GU 1818/1-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Adaptation, Physiological ; Biomass ; *Droughts ; Neurospora crassa/*physiology ; Penicillium chrysogenum/*physiology ; *Stress, Physiological ; }, abstract = {Sessile organisms constantly face environmental fluctuations and especially drought is a common stressor. One adaptive mechanism is "stress priming," the ability to cope with a severe stress ("triggering") by retaining information from a previous mild stress event ("priming"). While plants have been extensively investigated for drought-induced stress priming, no information is available for saprotrophic filamentous fungi, which are highly important for nutrient cycles. Here, we investigated the potential for drought-induced stress priming of one strain each of two ubiquitous species, Neurospora crassa and Penicillium chrysogenum. A batch experiment with 4 treatments was conducted on a sandy soil: exposure to priming and/or triggering as well as non-stressed controls. A priming stress was caused by desiccation to pF 4. The samples were then rewetted and after 1-, 7-, or 14-days of recovery triggered (pF 6). After triggering, fungal biomass, respiration, and β-glucosidase activity were quantified. P. chrysogenum showed positive stress priming effects. After 1 day of recovery, biomass as well as β-glucosidase activity and respiration were 0.5 to 5 times higher during triggering. Effects on biomass and activity decreased with prolonged recovery but lasted for 7 days and minor effects were still detectable after 14 days. Without triggering, stress priming had a temporary negative impact on biomass but this reversed after 14 days. For N. crassa, no stress priming effect was observed on the tested variables. The potential for drought-induced stress priming seems to be species specific with potentially high impact on composition and activity of fungal communities considering the expected increase of drought events.}, }
@article {pmid31948971, year = {2020}, author = {Korotetskiy, IS and Joubert, M and Magabotha, SM and Jumagaziyeva, AB and Shilov, SV and Suldina, NA and Kenesheva, ST and Yssel, A and Reva, ON and Ilin, AI}, title = {Complete Genome Sequence of Collection Strain Acinetobacter baumannii ATCC BAA-1790, Used as a Model To Study the Antibiotic Resistance Reversion Induced by Iodine-Containing Complexes.}, journal = {Microbiology resource announcements}, volume = {9}, number = {3}, pages = {}, pmid = {31948971}, issn = {2576-098X}, abstract = {The strain Acinetobacter baumannii ATCC BAA-1790 was sequenced as a model for nosocomial multidrug-resistant infections. Long-read PacBio sequencing revealed a circular chromosome of 3,963,235 bp with two horizontally transferred genomic islands and a 67,023-bp plasmid. Multiple antibiotic resistance genes and genome methylation patterns were identified.}, }
@article {pmid31947979, year = {2020}, author = {Purkamo, L and Kietäväinen, R and Nuppunen-Puputti, M and Bomberg, M and Cousins, C}, title = {Ultradeep Microbial Communities at 4.4 km within Crystalline Bedrock: Implications for Habitability in a Planetary Context.}, journal = {Life (Basel, Switzerland)}, volume = {10}, number = {1}, pages = {}, pmid = {31947979}, issn = {2075-1729}, support = {2016-2018//Jenny ja Antti Wihurin Rahasto/ ; RENGAS//KYT2018/ ; BIKES//KYT22/ ; C.Cousins//Royal Society of Edinburgh/ ; }, abstract = {The deep bedrock surroundings are an analog for extraterrestrial habitats for life. In this study, we investigated microbial life within anoxic ultradeep boreholes in Precambrian bedrock, including the adaptation to environmental conditions and lifestyle of these organisms. Samples were collected from Pyhäsalmi mine environment in central Finland and from geothermal drilling wells in Otaniemi, Espoo, in southern Finland. Microbial communities inhabiting the up to 4.4 km deep bedrock were characterized with phylogenetic marker gene (16S rRNA genes and fungal ITS region) amplicon and DNA and cDNA metagenomic sequencing. Functional marker genes (dsrB, mcrA, narG) were quantified with qPCR. Results showed that although crystalline bedrock provides very limited substrates for life, the microbial communities are diverse. Gammaproteobacterial phylotypes were most dominant in both studied sites. Alkanindiges -affiliating OTU was dominating in Pyhäsalmi fluids, while different depths of Otaniemi samples were dominated by Pseudomonas. One of the most common OTUs detected from Otaniemi could only be classified to phylum level, highlighting the uncharacterized nature of the deep biosphere in bedrock. Chemoheterotrophy, fermentation and nitrogen cycling are potentially significant metabolisms in these ultradeep environments. To conclude, this study provides information on microbial ecology of low biomass, carbon-depleted and energy-deprived deep subsurface environment. This information is useful in the prospect of finding life in other planetary bodies.}, }
@article {pmid31943686, year = {2020}, author = {Guégan, M and Tran Van, V and Martin, E and Minard, G and Tran, FH and Fel, B and Hay, AE and Simon, L and Barakat, M and Potier, P and Haichar, FEZ and Valiente Moro, C}, title = {Who is eating fructose within the Aedes albopictus gut microbiota?.}, journal = {Environmental microbiology}, volume = {22}, number = {4}, pages = {1193-1206}, doi = {10.1111/1462-2920.14915}, pmid = {31943686}, issn = {1462-2920}, support = {//EC2CO CNRS/International ; ANR-13-EBID-0007-01//ERA-NET BiodivERsA/International ; FWF I-1437//ERA-NET BiodivERsA/International ; DFG KL 2087/6//ERA-NET BiodivERsA/International ; }, mesh = {Aedes/*microbiology ; Animals ; Bacteria/metabolism ; Female ; Fructose/*metabolism ; Fungi/metabolism ; *Gastrointestinal Microbiome ; Male ; Mosquito Vectors ; }, abstract = {The Asian tiger mosquito Aedes albopictus is a major public health concern because of its invasive success and its ability to transmit pathogens. Given the low availability of treatments against mosquito-borne diseases, vector control remains the most suitable strategy. The methods used thus far are becoming less effective, but recent strategies have emerged from the study of mosquito-associated microorganisms. Although the role of the microbiota in insect biology does not require further proof, much remains to be deciphered in mosquitoes, especially the contribution of the microbiota to host nutrient metabolism. Mosquitoes feed on plant nectar, composed of mostly fructose. We used stable isotope probing to identify bacteria and fungi assimilating fructose within the gut of Ae. albopictus. Mosquitoes were fed a [13] C-labelled fructose solution for 24 h. Differences in the active microbial community according to the sex of mosquitoes were highlighted. The bacterium Lelliottia and the fungi Cladosporium and Aspergillus dominated the active microbiota in males, whereas the bacterium Ampullimonas and the yeast Cyberlindnera were the most active in females. This study is the first to investigate trophic interactions between Ae. albopictus and its microbiota, thus underscoring the importance of the microbial component in nectar feeding in mosquitoes.}, }
@article {pmid31942799, year = {2020}, author = {Cakmak, I and Marzorati, M and Van den Abbeele, P and Hora, K and Holwerda, HT and Yazici, MA and Savasli, E and Neri, J and Du Laing, G}, title = {Fate and Bioaccessibility of Iodine in Food Prepared from Agronomically Biofortified Wheat and Rice and Impact of Cofertilization with Zinc and Selenium.}, journal = {Journal of agricultural and food chemistry}, volume = {68}, number = {6}, pages = {1525-1535}, doi = {10.1021/acs.jafc.9b05912}, pmid = {31942799}, issn = {1520-5118}, mesh = {Biofortification ; Bread/analysis ; Cooking ; Fertilizers/analysis ; Flour/analysis ; Food, Fortified/analysis ; Hot Temperature ; Humans ; Iodine/analysis/*metabolism ; Oryza/chemistry/*metabolism ; Seeds/chemistry/metabolism ; Selenium/analysis/*metabolism ; Triticum/chemistry/*metabolism ; Zinc/analysis/*metabolism ; }, abstract = {Enrichment of food crops with iodine is an option to alleviate dietary deficiencies. Therefore, foliar iodine fertilizer was applied on wheat and rice, in the presence and absence of the other micronutrients zinc and selenium. This treatment increased the concentration of iodine, as well as zinc and selenium, in the staple grains. Subsequently, potential iodine losses during preparation of foodstuffs with the enriched grains were studied. Oven-heating did not affect the iodine content in bread. Extraction of bran from flour lowered the iodine in white bread compared to wholegrain bread, but it was still markedly higher compared to the control. During subsequent in vitro gastrointestinal digestion, a higher percentage of iodine was released from foods based on extracted flour (82-92%) compared to wholegrain foods (50-76%). The foliar fertilization of wheat was found to be adequate to alleviate iodine deficiency in a population with a moderate to high intake of bread.}, }
@article {pmid31942666, year = {2021}, author = {Morrison, ES and Thomas, P and Ogram, A and Kahveci, T and Turner, BL and Chanton, JP}, title = {Characterization of Bacterial and Fungal Communities Reveals Novel Consortia in Tropical Oligotrophic Peatlands.}, journal = {Microbial ecology}, volume = {82}, number = {1}, pages = {188-201}, pmid = {31942666}, issn = {1432-184X}, support = {DEB 0841596//National Science Foundation/ ; }, mesh = {Bacteria/genetics ; *Greenhouse Gases ; Humans ; *Microbiota ; *Mycobiome ; Soil ; }, abstract = {Despite their importance for global biogeochemical cycles and carbon sequestration, the microbiome of tropical peatlands remains under-determined. Microbial interactions within peatlands can regulate greenhouse gas production, organic matter turnover, and nutrient cycling. Here we analyze bacterial and fungal communities along a steep P gradient in a tropical peat dome and investigate community level traits and network analyses to better understand the composition and potential interactions of microorganisms in these understudied systems and their relationship to peatland biogeochemistry. We found that both bacterial and fungal community compositions were significantly different along the P gradient, and that the low-P bog plain was characterized by distinct fungal and bacterial families. At low P, the dominant fungal families were cosmopolitan parasites and endophytes, including Clavicipitaceae (19%) in shallow soils (0-4 cm), Hypocreaceae (50%) in intermediate-depth soils (4-8 cm), and Chaetothyriaceae (45%) in deep soils (24-30 cm). In contrast, high- and intermediate-P sites were dominated by saprotrophic families at all depths. Bacterial communities were consistently dominated by the acidophilic Koribacteraceae family, with the exception of the low-P bog site, which was dominated by Acetobacteraceae (19%) and Syntrophaceae (11%). These two families, as well as Rhodospirillaceae, Syntrophobacteraceae, Syntrophorhabdaceae, Spirochaetaceae, and Methylococcaceae appeared within low-P bacterial networks, suggesting the presence of a syntrophic-methanogenic consortium in these soils. Further investigation into the active microbial communities at these sites, when paired with CH4 and CO2 gas exchange, and the quantification of metabolic intermediates will validate these potential interactions and provide insight into microbially driven biogeochemical cycling within these globally important tropical peatlands.}, }
@article {pmid31942051, year = {2020}, author = {Hampton, HG and Watson, BNJ and Fineran, PC}, title = {The arms race between bacteria and their phage foes.}, journal = {Nature}, volume = {577}, number = {7790}, pages = {327-336}, pmid = {31942051}, issn = {1476-4687}, mesh = {Adsorption ; Animals ; Bacteria/growth &amp; development/*immunology/*virology ; Bacteriophages/*immunology/metabolism ; CRISPR-Cas Systems/physiology ; Host Microbial Interactions/*immunology ; Humans ; }, abstract = {Bacteria are under immense evolutionary pressure from their viral invaders-bacteriophages. Bacteria have evolved numerous immune mechanisms, both innate and adaptive, to cope with this pressure. The discovery and exploitation of CRISPR-Cas systems have stimulated a resurgence in the identification and characterization of anti-phage mechanisms. Bacteriophages use an extensive battery of counter-defence strategies to co-exist in the presence of these diverse phage defence mechanisms. Understanding the dynamics of the interactions between these microorganisms has implications for phage-based therapies, microbial ecology and evolution, and the development of new biotechnological tools. Here we review the spectrum of anti-phage systems and highlight their evasion by bacteriophages.}, }
@article {pmid31941815, year = {2020}, author = {De Rudder, C and Calatayud Arroyo, M and Lebeer, S and Van de Wiele, T}, title = {Dual and Triple Epithelial Coculture Model Systems with Donor-Derived Microbiota and THP-1 Macrophages To Mimic Host-Microbe Interactions in the Human Sinonasal Cavities.}, journal = {mSphere}, volume = {5}, number = {1}, pages = {}, pmid = {31941815}, issn = {2379-5042}, mesh = {Coculture Techniques ; Cytokines/immunology ; *Host Microbial Interactions ; Humans ; Latilactobacillus sakei/immunology/physiology ; Macrophages/*microbiology ; *Microbiota ; Nasal Cavity/cytology/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Respiratory Mucosa/immunology/*microbiology ; Staphylococcus aureus/immunology/physiology ; THP-1 Cells ; }, abstract = {The epithelium of the human sinonasal cavities is colonized by a diverse microbial community, modulating epithelial development and immune priming and playing a role in respiratory disease. Here, we present a novel in vitro approach enabling a 3-day coculture of differentiated Calu-3 respiratory epithelial cells with a donor-derived bacterial community, a commensal species (Lactobacillus sakei), or a pathobiont (Staphylococcus aureus). We also assessed how the incorporation of macrophage-like cells could have a steering effect on both epithelial cells and the microbial community. Inoculation of donor-derived microbiota in our experimental setup did not pose cytotoxic stress on the epithelial cell layers, as demonstrated by unaltered cytokine and lactate dehydrogenase release compared to a sterile control. Epithelial integrity of the differentiated Calu-3 cells was maintained as well, with no differences in transepithelial electrical resistance observed between coculture with donor-derived microbiota and a sterile control. Transition of nasal microbiota from in vivo to in vitro conditions maintained phylogenetic richness, and yet a decrease in phylogenetic and phenotypic diversity was noted. Additional inclusion and coculture of THP-1-derived macrophages did not alter phylogenetic diversity, and yet donor-independent shifts toward higher Moraxella and Mycoplasma abundance were observed, while phenotypic diversity was also increased. Our results demonstrate that coculture of differentiated airway epithelial cells with a healthy donor-derived nasal community is a viable strategy to mimic host-microbe interactions in the human upper respiratory tract. Importantly, including an immune component allowed us to study host-microbe interactions in the upper respiratory tract more in depth.IMPORTANCE Despite the relevance of the resident microbiota in sinonasal health and disease and the need for cross talk between immune and epithelial cells in the upper respiratory tract, these parameters have not been combined in a single in vitro model system. We have developed a coculture system of differentiated respiratory epithelium and natural nasal microbiota and incorporated an immune component. As indicated by absence of cytotoxicity and stable cytokine profiles and epithelial integrity, nasal microbiota from human origin appeared to be well tolerated by host cells, while microbial community composition remained representative for that of the human (sino)nasal cavity. Importantly, the introduction of macrophage-like cells enabled us to obtain a differential readout from the epithelial cells dependent on the donor microbial background to which the cells were exposed. We conclude that both model systems offer the means to investigate host-microbe interactions in the upper respiratory tract in a more representative way.}, }
@article {pmid31940957, year = {2020}, author = {Xu, Y and Shen, Z and Gentekaki, E and Xu, J and Yi, Z}, title = {Comparative Transcriptome Analyses during the Vegetative Cell Cycle in the Mono-Cellular Organism Pseudokeronopsis erythrina (Alveolata, Ciliophora).}, journal = {Microorganisms}, volume = {8}, number = {1}, pages = {}, pmid = {31940957}, issn = {2076-2607}, support = {2018SDKJ0406-4//Pilot National Laboratory for Marine Science and Technology (Qingdao)/ ; 31772440//National Natural Science Foundation of China/ ; 31430077//National Natural Science Foundation of China/ ; 31970486//National Natural Science Foundation of China/ ; GDOE2019A23//Guangdong MEPP Fund/ ; }, abstract = {Studies focusing on molecular mechanisms of cell cycles have been lagging in unicellular eukaryotes compared to other groups. Ciliates, a group of unicellular eukaryotes, have complex cell division cycles characterized by multiple events. During their vegetative cell cycle, ciliates undergo macronuclear amitosis, micronuclear mitosis, stomatogenesis and somatic cortex morphogenesis, and cytokinesis. Herein, we used the hypotrich ciliate Pseudokeronopsis erythrina, whose morphogenesis has been well studied, to examine molecular mechanisms of ciliate vegetative cell cycles. Single-cell transcriptomes of the growth (G) and cell division (D) stages were compared. The results showed that (i) More than 2051 significantly differentially expressed genes (DEGs) were detected, among which 1545 were up-regulated, while 256 were down-regulated at the D stage. Of these, 11 randomly picked DEGs were validated by reverse transcription quantitative polymerase chain reaction (RT-qPCR); (ii) Enriched DEGs during the D stage of the vegetative cell cycle of P. erythrina were involved in development, cortex modifications, and several organelle-related biological processes, showing correspondence of molecular evidence to morphogenetic changes for the first time; (iii) Several individual components of molecular mechanisms of ciliate vegetative division, the sexual cell cycle and cellular regeneration overlap; and (iv) The P. erythrina cell cycle and division have the same essential components as other eukaryotes, including cyclin-dependent kinases (CDKs), cyclins, and genes closely related to cell proliferation, indicating the conserved nature of this biological process. Further studies are needed focusing on detailed inventory and gene interactions that regulate specific ciliated cell-phase events.}, }
@article {pmid31937947, year = {2020}, author = {Amaral-Zettler, LA and Zettler, ER and Mincer, TJ}, title = {Ecology of the plastisphere.}, journal = {Nature reviews. Microbiology}, volume = {18}, number = {3}, pages = {139-151}, pmid = {31937947}, issn = {1740-1534}, mesh = {Biodegradation, Environmental ; Environmental Pollutants ; *Microbiota ; *Plastics ; Waste Products ; }, abstract = {The plastisphere, which comprises the microbial community on plastic debris, rivals that of the built environment in spanning multiple biomes on Earth. Although human-derived debris has been entering the ocean for thousands of years, microplastics now numerically dominate marine debris and are primarily colonized by microbial and other microscopic life. The realization that this novel substrate in the marine environment can facilitate microbial dispersal and affect all aquatic ecosystems has intensified interest in the microbial ecology and evolution of this biotope. Whether a 'core' plastisphere community exists that is specific to plastic is currently a topic of intense investigation. This Review provides an overview of the microbial ecology of the plastisphere in the context of its diversity and function, as well as suggesting areas for further research.}, }
@article {pmid31937679, year = {2020}, author = {Weissman, JL and Johnson, PLF}, title = {Network-Based Prediction of Novel CRISPR-Associated Genes in Metagenomes.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, pmid = {31937679}, issn = {2379-5077}, abstract = {A diversity of clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems provide adaptive immunity to bacteria and archaea through recording "memories" of past viral infections. Recently, many novel CRISPR-associated proteins have been discovered via computational studies, but those studies relied on biased and incomplete databases of assembled genomes. We avoided these biases and applied a network theory approach to search for novel CRISPR-associated genes by leveraging subtle ecological cooccurrence patterns identified from environmental metagenomes. We validated our method using existing annotations and discovered 32 novel CRISPR-associated gene families. These genes span a range of putative functions, with many potentially regulating the response to infection.IMPORTANCE Every branch on the tree of life, including microbial life, faces the threat of viral pathogens. Over the course of billions of years of coevolution, prokaryotes have evolved a great diversity of strategies to defend against viral infections. One of these is the CRISPR adaptive immune system, which allows microbes to "remember" past infections in order to better fight them in the future. There has been much interest among molecular biologists in CRISPR immunity because this system can be repurposed as a tool for precise genome editing. Recently, a number of comparative genomics approaches have been used to detect novel CRISPR-associated genes in databases of genomes with great success, potentially leading to the development of new genome-editing tools. Here, we developed novel methods to search for these distinct classes of genes directly in environmental samples ("metagenomes"), thus capturing a more complete picture of the natural diversity of CRISPR-associated genes.}, }
@article {pmid31937676, year = {2020}, author = {Sedlacek, CJ and Giguere, AT and Dobie, MD and Mellbye, BL and Ferrell, RV and Woebken, D and Sayavedra-Soto, LA and Bottomley, PJ and Daims, H and Wagner, M and Pjevac, P}, title = {Transcriptomic Response of Nitrosomonas europaea Transitioned from Ammonia- to Oxygen-Limited Steady-State Growth.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, pmid = {31937676}, issn = {2379-5077}, support = {P 30570/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Ammonia-oxidizing microorganisms perform the first step of nitrification, the oxidation of ammonia to nitrite. The bacterium Nitrosomonas europaea is the best-characterized ammonia oxidizer to date. Exposure to hypoxic conditions has a profound effect on the physiology of N. europaea, e.g., by inducing nitrifier denitrification, resulting in increased nitric and nitrous oxide production. This metabolic shift is of major significance in agricultural soils, as it contributes to fertilizer loss and global climate change. Previous studies investigating the effect of oxygen limitation on N. europaea have focused on the transcriptional regulation of genes involved in nitrification and nitrifier denitrification. Here, we combine steady-state cultivation with whole-genome transcriptomics to investigate the overall effect of oxygen limitation on N. europaea Under oxygen-limited conditions, growth yield was reduced and ammonia-to-nitrite conversion was not stoichiometric, suggesting the production of nitrogenous gases. However, the transcription of the principal nitric oxide reductase (cNOR) did not change significantly during oxygen-limited growth, while the transcription of the nitrite reductase-encoding gene (nirK) was significantly lower. In contrast, both heme-copper-containing cytochrome c oxidases encoded by N. europaea were upregulated during oxygen-limited growth. Particularly striking was the significant increase in transcription of the B-type heme-copper oxidase, proposed to function as a nitric oxide reductase (sNOR) in ammonia-oxidizing bacteria. In the context of previous physiological studies, as well as the evolutionary placement of N. europaea's sNOR with regard to other heme-copper oxidases, these results suggest sNOR may function as a high-affinity terminal oxidase in N. europaea and other ammonia-oxidizing bacteria.IMPORTANCE Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea, growing under oxygen-limited conditions.}, }
@article {pmid31935341, year = {2020}, author = {Bophela, KN and Petersen, Y and Bull, CT and Coutinho, TA}, title = {Identification of Pseudomonas Isolates Associated With Bacterial Canker of Stone Fruit Trees in the Western Cape, South Africa.}, journal = {Plant disease}, volume = {104}, number = {3}, pages = {882-892}, doi = {10.1094/PDIS-05-19-1102-RE}, pmid = {31935341}, issn = {0191-2917}, mesh = {*Fruit ; Phylogeny ; *Plant Diseases ; Pseudomonas syringae ; South Africa ; }, abstract = {Bacterial canker is a common bacterial disease of stone fruit trees. The causal agents responsible for the disease include several pathovars in Pseudomonas syringae sensu lato and newly described Pseudomonas species. Pseudomonad strains were isolated from symptomatic stone fruit trees, namely apricot, peach, and plum trees cultivated in spatially separated orchards in the Western Cape. A polyphasic approach was used to identify and characterize these strains. Using a multilocus sequence typing approach of four housekeeping loci, namely cts, gapA, gyrB, and rpoD, the pseudomonad strains were delineated into two phylogenetic groups within P. syringae sensu lato: P. syringae sensu stricto and Pseudomonas viridiflava. These results were further supported by LOPAT diagnostic assays and analysis of clades in the rep-PCR dendrogram. The pseudomonad strains were pathogenic on both apricot and plum seedlings, indicative of a lack of host specificity between Pseudomonas strains infecting Prunus spp. This is a first report of P. viridiflava isolated from plum trees showing symptoms of bacterial canker. P. viridiflava is considered to be an opportunistic pathogen that causes foliar diseases of vegetable crops, fruit trees, and aromatic herbs, and thus the isolation of pathogenic P. viridiflava from twigs of plum trees showing symptoms of bacterial canker suggests that this bacterial species is a potentially emerging stem canker pathogen of stone fruit trees in South Africa.}, }
@article {pmid31935110, year = {2020}, author = {El Hage, R and Hernandez-Sanabria, E and Calatayud Arroyo, M and Van de Wiele, T}, title = {Supplementation of a propionate-producing consortium improves markers of insulin resistance in an in vitro model of gut-liver axis.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {318}, number = {5}, pages = {E742-E749}, doi = {10.1152/ajpendo.00523.2019}, pmid = {31935110}, issn = {1522-1555}, mesh = {Biomarkers ; Cytokines/metabolism ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*metabolism/microbiology ; Glycogen/metabolism ; Hep G2 Cells ; Hepatocytes/*metabolism ; Humans ; Inflammation/metabolism/microbiology ; Insulin Resistance/*physiology ; Liver/*metabolism/microbiology ; Propionates/*metabolism ; }, abstract = {Gut-liver cross talk is an important determinant of human health with profound effects on energy homeostasis. While gut microbes produce a huge range of metabolites, specific compounds such as short-chain fatty acids (SCFAs) can enter the portal circulation and reach the liver (Brandl K, Schnabl B. Curr Opin Gastroenterol 33: 128-133, 2017), a central organ involved in glucose homeostasis and diabetes control. Propionate is a major SCFA involved in activation of intestinal gluconeogenesis (IGN), thereby regulating food intake, enhancing insulin sensitivity, and leading to metabolic homeostasis. Although microbiome-modulating strategies may target the increased microbial production of propionate, it is not clear whether such an effect spreads through to the hepatic cellular level. Here, we designed a propionate-producing consortium using a selection of commensal gut bacteria, and we investigated how their delivered metabolites impact an in vitro enterohepatic model of insulin resistance. Glycogen storage on hepatocyte-like cells and inflammatory markers associated with insulin resistance were evaluated to understand the role of gut metabolites on gut-liver cross talk in a simulated scenario of insulin resistance. The metabolites produced by our consortium increased glycogen synthesis by ~57% and decreased proinflammatory markers such as IL-8 by 12%, thus elucidating the positive effect of our consortium on metabolic function and low-grade inflammation. Our results suggest that microbiota-derived products can be a promising multipurpose strategy to modulate energy homeostasis, with the potential ability to assist in managing metabolic diseases due to their adaptability.}, }
@article {pmid31932882, year = {2020}, author = {Cleary, DFR and Polónia, ARM and Reijnen, BT and Berumen, ML and de Voogd, NJ}, title = {Prokaryote Communities Inhabiting Endemic and Newly Discovered Sponges and Octocorals from the Red Sea.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {103-119}, doi = {10.1007/s00248-019-01465-w}, pmid = {31932882}, issn = {1432-184X}, support = {PTDC/AAC-AMB/115304/2009//FCT/ ; SFRH/BPD/117563/2016//FCT/ ; }, mesh = {Animals ; Anthozoa/*microbiology ; Archaea/classification/isolation &amp; purification/*physiology ; Bacteria/classification/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Geologic Sediments/*microbiology ; Indian Ocean ; Microbiota ; Porifera/*microbiology ; Saudi Arabia ; Seawater/*microbiology ; }, abstract = {In the present study, we assessed prokaryotic communities of demosponges, a calcareous sponge, octocorals, sediment and seawater in coral reef habitat of the central Red Sea, including endemic species and species new to science. Goals of the study were to compare the prokaryotic communities of demosponges with the calcareous sponge and octocorals and to assign preliminary high microbial abundance (HMA) or low microbial abundance (LMA) status to the sponge species based on compositional trait data. Based on the compositional data, we were able to assign preliminary LMA or HMA status to all sponge species. Certain species, however, had traits of both LMA and HMA species. For example, the sponge Ectyoplasia coccinea, which appeared to be a LMA species, had traits, including a relatively high abundance of Chloroflexi members, that were more typical of HMA species. This included dominant OTUs assigned to two different classes within the Chloroflexi. The calcareous sponge clustered together with seawater, the known LMA sponge Stylissa carteri and other presumable LMA species. The two dominant OTUs of this species were assigned to the Deltaproteobacteria and had no close relatives in the GenBank database. The octocoral species in the present study had prokaryotic communities that were distinct from sediment, seawater and all sponge species. These were characterised by OTUs assigned to the orders Rhodospirillales, Cellvibrionales, Spirochaetales and the genus Endozoicomonas, which were rare or absent in samples from other biotopes.}, }
@article {pmid31932881, year = {2020}, author = {Ruiz-Rodríguez, M and Scheifler, M and Sanchez-Brosseau, S and Magnanou, E and West, N and Suzuki, M and Duperron, S and Desdevises, Y}, title = {Host Species and Body Site Explain the Variation in the Microbiota Associated to Wild Sympatric Mediterranean Teleost Fishes.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {212-222}, doi = {10.1007/s00248-020-01484-y}, pmid = {31932881}, issn = {1432-184X}, support = {SU-16-R-EMR-22-MICROFISH//Universit&#xe9; Sorbonne Paris Cit&#xe9;/ ; }, mesh = {Animals ; Bacteria/classification/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; Fishes/*microbiology ; France ; Gastrointestinal Microbiome ; Gills/microbiology ; *Host Microbial Interactions ; Intestines/microbiology ; Mediterranean Sea ; *Microbiota ; Mucus/microbiology ; Skin/microbiology ; Species Specificity ; }, abstract = {Microorganisms are an important component in shaping the evolution of hosts and as such, the study of bacterial communities with molecular techniques is shedding light on the complexity of symbioses between bacteria and vertebrates. Teleost fish are a heterogeneous group that live in a wide variety of habitats, and thus a good model group to investigate symbiotic interactions and their influence on host biology and ecology. Here we describe the microbiota of thirteen teleostean species sharing the same environment in the Mediterranean Sea and compare bacterial communities among different species and body sites (external mucus, skin, gills, and intestine). Our results show that Proteobacteria is the dominant phylum present in fish and water. However, the prevalence of other bacterial taxa differs between fish and the surrounding water. Significant differences in bacterial diversity are observed among fish species and body sites, with higher diversity found in the external mucus. No effect of sampling time nor species individual was found. The identification of indicator bacterial taxa further supports that each body site harbors its own characteristic bacterial community. These results improve current knowledge and understanding of symbiotic relationships among bacteria and their fish hosts in the wild since the majority of previous studies focused on captive individuals.}, }
@article {pmid31929046, year = {2020}, author = {Obata, O and Salar-Garcia, MJ and Greenman, J and Kurt, H and Chandran, K and Ieropoulos, I}, title = {Development of efficient electroactive biofilm in urine-fed microbial fuel cell cascades for bioelectricity generation.}, journal = {Journal of environmental management}, volume = {258}, number = {}, pages = {109992}, pmid = {31929046}, issn = {1095-8630}, mesh = {*Bioelectric Energy Sources ; Biofilms ; Electricity ; Electrodes ; Sewage ; }, abstract = {The Microbial fuel cell (MFC) technology harnesses the potential of some naturally occurring bacteria for electricity generation. Digested sludge is commonly used as the inoculum to initiate the process. There are, however, health hazards and practical issues associated with the use of digested sludge depending on its origin as well as the location for system deployment. This work reports the development of an efficient electroactive bacterial community within ceramic-based MFCs fed with human urine in the absence of sludge inoculum. The results show the development of a uniform bacterial community with power output levels equal to or higher than those generated from MFCs inoculated with sludge. In this case, the power generation begins within 2 days of the experimental set-up, compared to about 5 days in some sludge-inoculated MFCs, thus significantly reducing the start-up time. The metagenomics analysis of the successfully formed electroactive biofilm (EAB) shows significant shifts between the microbial ecology of the feeding material (fresh urine) and the developed anodic biofilm. A total of 21 bacteria genera were detected in the urine feedstock whilst up to 35 different genera were recorded in the developed biofilm. Members of Pseudomonas (18%) and Anaerolineaceae (17%) dominate the bacterial community of the fresh urine feed while members of Burkholderiaceae (up to 50%) and Tissierella (up to 29%) dominate the anodic EAB. These results highlight a significant shift in the bacterial community of the feedstock towards a selection and adaptation required for the various electrochemical reactions essential for survival through power generation.}, }
@article {pmid31927597, year = {2020}, author = {Sun, F and Wang, C and Chen, H and Zheng, Z}, title = {Metagenomic Analysis of the Effect of Enteromorpha prolifera Bloom on Microbial Community and Function in Aquaculture Environment.}, journal = {Current microbiology}, volume = {77}, number = {5}, pages = {816-825}, pmid = {31927597}, issn = {1432-0991}, support = {2017A020216008//Guangdong Science and Technology Department/ ; 2016I1002//Fujian Provincial Department of Science and Technology/ ; 2017T3010//Fujian Provincial Department of Science and Technology/ ; }, mesh = {Actinomycetales/classification ; *Aquaculture ; *Eutrophication ; Flavobacteriaceae/classification ; *Metagenome ; Metagenomics ; *Microbiota ; Sequence Analysis, DNA ; Ulva/growth &amp; development/*metabolism ; Viruses/classification ; }, abstract = {Enteromorpha prolifera blooms considerably affected coastal environments in recent years. However, the effects of E. prolifera on microbial ecology and function remained unknown. In this study, metagenomic sequencing was used to investigate the effect of E. prolifera bloom on the microbial communities and functional genes in an aquaculture environment. Results showed that E. prolifera bloom could significantly alter the microbial composition and abundance, and heterotrophic bacteria comprised the major groups in the E. prolifera bloom pond, which was dominated by Actinomycetales and Flavobacteriales. The study indicated that viruses played an important role in shaping the microbial community and diversity during E. prolifera bloom. These viruses affected various dominant microbial taxa (such as Rhodobacteraceae, Synechococcus, and Prochlorococcus), which produced an obvious impact on potential nutrient transformation. Functional annotation analysis indicated that E. prolifera bloom would considerably shift the metabolism function by altering the structure and abundance of the microbial community. E. prolifera bloom pond had the low ability of potential metabolic capabilities of nitrogen, sulfur, and phosphate, whereas promoted gene abundance of genetic information processing. These changes in the microbial community and function could produce serious effect on aquaculture ecosystem.}, }
@article {pmid31926392, year = {2020}, author = {Lepoutre, A and Hervieux, J and Faassen, EJ and Zweers, AJ and Lurling, M and Geffard, A and Lance, E}, title = {Usability of the bivalves Dreissena polymorpha and Anodonta anatina for a biosurvey of the neurotoxin BMAA in freshwater ecosystems.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {259}, number = {}, pages = {113885}, doi = {10.1016/j.envpol.2019.113885}, pmid = {31926392}, issn = {1873-6424}, mesh = {*Amino Acids, Diamino/analysis ; Animals ; *Anodonta/chemistry ; Cyanobacteria Toxins ; *Dreissena/chemistry ; Ecosystem ; *Environmental Monitoring/methods/standards ; *Fresh Water/chemistry ; *Water Pollutants, Chemical/analysis ; }, abstract = {The environmental neurotoxin β-methylamino-L-alanine (BMAA) may represent a risk for human health in case of chronic exposure or after short-term exposure during embryo development. BMAA accumulates in freshwater and marine organisms consumed by humans. It is produced by marine and freshwater phytoplankton species, but the range of producers remains unknown. Therefore, analysing the phytoplankton composition is not sufficient to inform about the risk of freshwater contamination by BMAA. Filter-feeders mussels have accumulation capacities and therefore appear to be relevant to monitor various pollutants in aquatic ecosystems. We investigated the suitability of the freshwater mussels Dreissena polymorpha and Anodonta anatina for monitoring BMAA in water. Both species were exposed to 1, 10, and 50 μg of dissolved BMAA/L daily for 21 days, followed by 42 days of depuration in clean water. On days 0, 1, 7, 14, and 21 of exposure and 1, 7, 14, 21 and 42 of depuration, whole D. polymorpha and digestive glands of A. anatina were sampled, and the total BMAA concentration was measured. D. polymorpha accumulated BMAA earlier (from day 1 at all concentrations) and at higher tissue concentrations than A. anatina, which accumulated BMAA from day 14 when exposed to 10 μg BMAA/L and from day 7 when exposed to 50 μg BMAA/L. As BMAA accumulation by D. polymorpha was time and concentration-dependent, with a significant elimination during the depuration period, this species may be able to reflect the levels and dynamics of water contamination by dissolved BMAA. The species A. anatina could be used for monitoring water concentrations above 10 μg BMAA/L.}, }
@article {pmid31925848, year = {2020}, author = {Dove, NC and Safford, HD and Bohlman, GN and Estes, BL and Hart, SC}, title = {High-severity wildfire leads to multi-decadal impacts on soil biogeochemistry in mixed-conifer forests.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {30}, number = {4}, pages = {e02072}, doi = {10.1002/eap.2072}, pmid = {31925848}, issn = {1051-0761}, mesh = {Carbon ; Ecosystem ; Forests ; Soil ; *Tracheophyta ; *Wildfires ; }, abstract = {During the past century, systematic wildfire suppression has decreased fire frequency and increased fire severity in the western United States of America. While this has resulted in large ecological changes aboveground such as altered tree species composition and increased forest density, little is known about the long-term, belowground implications of altered, ecologically novel, fire regimes, especially on soil biological processes. To better understand the long-term implications of ecologically novel, high-severity fire, we used a 44-yr high-severity fire chronosequence in the Sierra Nevada where forests were historically adapted to frequent, low-severity fire, but were fire suppressed for at least 70 yr. High-severity fire in the Sierra Nevada resulted in a long-term (44 +yr) decrease (>50%, P < 0.05) in soil extracellular enzyme activities, basal microbial respiration (56-72%, P < 0.05), and organic carbon (>50%, P < 0.05) in the upper 5 cm compared to sites that had not been burned for at least 115 yr. However, nitrogen (N) processes were only affected in the most recent fire site (4 yr post-fire). Net nitrification increased by over 600% in the most recent fire site (P < 0.001), but returned to similar levels as the unburned control in the 13-yr site. Contrary to previous studies, we did not find a consistent effect of plant cover type on soil biogeochemical processes in mid-successional (10-50 yr) forest soils. Rather, the 44-yr reduction in soil organic carbon (C) quantity correlated positively with dampened C cycling processes. Our results show the drastic and long-term implication of ecologically novel, high-severity fire on soil biogeochemistry and underscore the need for long-term fire ecological experiments.}, }
@article {pmid31924621, year = {2020}, author = {Suttner, B and Johnston, ER and Orellana, LH and Rodriguez-R, LM and Hatt, JK and Carychao, D and Carter, MQ and Cooley, MB and Konstantinidis, KT}, title = {Metagenomics as a Public Health Risk Assessment Tool in a Study of Natural Creek Sediments Influenced by Agricultural and Livestock Runoff: Potential and Limitations.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {6}, pages = {}, pmid = {31924621}, issn = {1098-5336}, mesh = {Agriculture ; Animal Husbandry ; Animals ; California ; Geologic Sediments/*microbiology ; Livestock ; *Metagenomics ; Public Health/*methods ; Risk Assessment/*methods ; Rivers/microbiology ; Shiga-Toxigenic Escherichia coli/*isolation &amp; purification ; Water Pollution ; }, abstract = {Little is known about the public health risks associated with natural creek sediments that are affected by runoff and fecal pollution from agricultural and livestock practices. For instance, the persistence of foodborne pathogens such as Shiga toxin-producing Escherichia coli (STEC) originating from these practices remains poorly quantified. Towards closing these knowledge gaps, the water-sediment interface of two creeks in the Salinas River Valley of California was sampled over a 9-month period using metagenomics and traditional culture-based tests for STEC. Our results revealed that these sediment communities are extremely diverse and have functional and taxonomic diversity comparable to that observed in soils. With our sequencing effort (∼4 Gbp per library), we were unable to detect any pathogenic E. coli in the metagenomes of 11 samples that had tested positive using culture-based methods, apparently due to relatively low abundance. Furthermore, there were no significant differences in the abundance of human- or cow-specific gut microbiome sequences in the downstream impacted sites compared to that in upstream more pristine (control) sites, indicating natural dilution of anthropogenic inputs. Notably, the high number of metagenomic reads carrying antibiotic resistance genes (ARGs) found in all samples was significantly higher than ARG reads in other available freshwater and soil metagenomes, suggesting that these communities may be natural reservoirs of ARGs. The work presented here should serve as a guide for sampling volumes, amount of sequencing to apply, and what bioinformatics analyses to perform when using metagenomics for public health risk studies of environmental samples such as sediments.IMPORTANCE Current agricultural and livestock practices contribute to fecal contamination in the environment and the spread of food- and waterborne disease and antibiotic resistance genes (ARGs). Traditionally, the level of pollution and risk to public health are assessed by culture-based tests for the intestinal bacterium Escherichia coli However, the accuracy of these traditional methods (e.g., low accuracy in quantification, and false-positive signal when PCR based) and their suitability for sediments remain unclear. We collected sediments for a time series metagenomics study from one of the most highly productive agricultural regions in the United States in order to assess how agricultural runoff affects the native microbial communities and if the presence of Shiga toxin-producing Escherichia coli (STEC) in sediment samples can be detected directly by sequencing. Our study provided important information on the potential for using metagenomics as a tool for assessment of public health risk in natural environments.}, }
@article {pmid31924617, year = {2020}, author = {Bai, C and Cai, J and Zhou, L and Jiang, X and Hu, Y and Dai, J and Shao, K and Tang, X and Yang, X and Gao, G}, title = {Geographic Patterns of Bacterioplankton among Lakes of the Middle and Lower Reaches of the Yangtze River Basin, China.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {6}, pages = {}, pmid = {31924617}, issn = {1098-5336}, mesh = {*Bacterial Physiological Phenomena ; China ; Geography ; Lakes/*microbiology ; *Microbiota ; Phytoplankton/*physiology ; Population Density ; Rivers/microbiology ; Seasons ; }, abstract = {The revolution of molecular techniques has revealed that the composition of natural bacterial communities normally includes a few abundant taxa and many rare taxa. Unraveling the mechanisms underlying the spatial assembly process of both abundant and rare bacterial taxa has become a central goal in microbial ecology. Here, we used high-throughput sequencing to explore geographic patterns and the relative importance of ecological processes in the assembly of abundant and rare bacterial subcommunities from 25 lakes across the middle and lower reaches of Yangtze River basin (MLYB), located in Southeast China, where most of the lakes are interconnected by river networks. We found similar biogeographic patterns of abundant and rare subcommunities which could significantly distinguish the community compositions of the two lake groups that were far from each other but which could not distinguish the community compositions of the nearby lakes. Both abundant and rare bacteria followed a strong distance-decay relationship. These findings suggest that the interconnectivity between lakes homogenizes the bacterial communities in local areas, and the abundant and rare taxa therein may be affected by the same ecological process. In addition, based on the measured environmental variables, the deterministic processes explain a small fraction of variation within both abundant and rare subcommunities, while both neutral and null models revealed a high stochasticity ratio for the spatial distribution patterns of both abundant and rare taxa. These findings indicate that the stochastic processes exhibited a greater influence on both abundant and rare bacterial subcommunity assemblies among interconnected lakes.IMPORTANCE The middle and lower Yangtze Plain is a typical floodplain in which many lakes connect with each other, especially in the wet season. More importantly, with the frequent change of regional water level in the wet season, there is a mutual hydrodynamic exchange among these lakes. The microbial biogeography among these interconnected lakes is still poorly understood. This study aims to unravel the mechanisms underlying the assembly process of abundant and rare bacteria among the interconnected lakes in the middle and lower Yangtze Plain. Our findings will provide a deeper understanding of the biogeographic patterns of rare and abundant bacterial taxa and their determined processes among interconnected aquatic habitats.}, }
@article {pmid31924214, year = {2020}, author = {Shuai, Y and Ma, Z and Liu, W and Yu, T and Yan, C and Jiang, H and Tian, S and Xu, T and Shu, Y}, title = {TEAD4 modulated LncRNA MNX1-AS1 contributes to gastric cancer progression partly through suppressing BTG2 and activating BCL2.}, journal = {Molecular cancer}, volume = {19}, number = {1}, pages = {6}, pmid = {31924214}, issn = {1476-4598}, mesh = {Animals ; Apoptosis ; Biomarkers, Tumor/genetics/*metabolism ; Cell Movement ; Cell Proliferation ; DNA-Binding Proteins/genetics/*metabolism ; Disease Progression ; Female ; *Gene Expression Regulation, Neoplastic ; Homeodomain Proteins/antagonists &amp; inhibitors ; Humans ; Immediate-Early Proteins/genetics/*metabolism ; Male ; Mice ; Mice, Nude ; MicroRNAs/genetics ; Middle Aged ; Muscle Proteins/genetics/*metabolism ; Neoplasm Invasiveness ; Prognosis ; Proto-Oncogene Proteins c-bcl-2/genetics/*metabolism ; RNA, Antisense/genetics ; RNA, Long Noncoding/*genetics ; Stomach Neoplasms/genetics/metabolism/*pathology ; Survival Rate ; TEA Domain Transcription Factors ; Transcription Factors/antagonists &amp; inhibitors/genetics/*metabolism ; Tumor Cells, Cultured ; Tumor Suppressor Proteins/genetics/*metabolism ; Xenograft Model Antitumor Assays ; }, abstract = {BACKGROUND: Gastric cancer (GC) is the third leading cause of cancer-related mortality globally. Long noncoding RNAs (lncRNAs) are dysregulated in obvious malignancies including GC and exploring the regulatory mechanisms underlying their expression is an attractive research area. However, these molecular mechanisms require further clarification, especially upstream mechanisms.<br><br>METHODS: LncRNA MNX1-AS1 expression in GC tissue samples was investigated via microarray analysis and further determined in a cohort of GC tissues via quantitative reverse transcription polymerase chain reaction (qRT-PCR) assays. Cell proliferation and flow cytometry assays were performed to confirm the roles of MNX1-AS1 in GC proliferation, cell cycle regulation, and apoptosis. The influence of MNX1-AS1 on GC cell migration and invasion was explored with Transwell assays. A xenograft tumour model was established to verify the effects of MNX1-AS1 on in vivo tumourigenesis. The TEAD4-involved upstream regulatory mechanism of MNX1-AS1 was explored through ChIP and luciferase reporter assays. The mechanistic model of MNX1-AS1 in regulating gene expression was further detected by subcellular fractionation, FISH, RIP, ChIP and luciferase reporter assays.<br><br>RESULTS: It was found that MNX1-AS1 displayed obvious upregulation in GC tissue samples and cell lines, and ectopic expression of MNX1-AS1 predicted poor clinical outcomes for patients with GC. Overexpressed MNX1-AS1 expression promoted proliferation, migration and invasion of GC cells markedly, whereas decreased MNX1-AS1 expression elicited the opposite effects. Consistent with the in vitro results, MNX1-AS1 depletion effectively inhibited the growth of xenograft tumour in vivo. Mechanistically, TEAD4 directly bound the promoter region of MNX1-AS1 and stimulated the transcription of MNX1-AS1. Furthermore, MNX1-AS1 can sponge miR-6785-5p to upregulate the expression of BCL2 in GC cells. Meanwhile, MNX1-AS1 suppressed the transcription of BTG2 by recruiting polycomb repressive complex 2 to BTG2 promoter regions.<br><br>CONCLUSIONS: Our findings demonstrate that MNX1-AS1 may be able to serve as a prognostic indicator in GC patients and that TEAD4-activatd MNX1-AS1 can promote GC progression through EZH2/BTG2 and miR-6785-5p/BCL2 axes, implicating it as a novel and potent target for the treatment of GC.}, }
@article {pmid31924126, year = {2020}, author = {Agudelo-Ochoa, GM and Valdés-Duque, BE and Giraldo-Giraldo, NA and Jaillier-Ramírez, AM and Giraldo-Villa, A and Acevedo-Castaño, I and Yepes-Molina, MA and Barbosa-Barbosa, J and Benítez-Paéz, A}, title = {Gut microbiota profiles in critically ill patients, potential biomarkers and risk variables for sepsis.}, journal = {Gut microbes}, volume = {12}, number = {1}, pages = {1707610}, pmid = {31924126}, issn = {1949-0984}, mesh = {APACHE ; Adult ; Bacteria/*classification/genetics/*isolation &amp; purification ; Biomarkers ; Case-Control Studies ; Critical Care ; Critical Illness ; Female ; Gastrointestinal Microbiome/*genetics/physiology ; Humans ; Inflammation/pathology ; Intestines/*microbiology ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Sepsis/*microbiology/pathology ; Young Adult ; }, abstract = {Critically ill patients are physiologically unstable and recent studies indicate that the intestinal microbiota could be involved in the health decline of such patients during ICU stays. This study aims to assess the intestinal microbiota in critically ill patients with and without sepsis and to determine its impact on outcome variables, such as medical complications, ICU stay time, and mortality. A multi-center study was conducted with a total of 250 peri-rectal swabs obtained from 155 patients upon admission and during ICU stays. Intestinal microbiota was assessed by sequencing the V3-V4 hypervariable regions of the 16S rRNA gene. Linear mixed models were used to integrate microbiota data with more than 40 clinical and demographic variables to detect covariates and minimize the effect of confounding factors. We found that the microbiota of ICU patients with sepsis has an increased abundance of microbes tightly associated with inflammation, such as Parabacteroides, Fusobacterium and Bilophila species. Female sex and aging would represent an increased risk for sepsis possibly because of some of their microbiota features. We also evidenced a remarkable loss of microbial diversity, during the ICU stay. Concomitantly, we detected that the abundance of pathogenic species, such as Enterococcus spp., was differentially increased in sepsis patients who died, indicating these species as potential biomarkers for monitoring during ICU stay. We concluded that particular intestinal microbiota signatures could predict sepsis development in ICU patients. We propose potential biomarkers for evaluation in the clinical management of ICU patients.}, }
@article {pmid31924109, year = {2020}, author = {Triplett, J and Ellis, D and Braddock, A and Roberts, E and Ingram, K and Perez, E and Short, A and Brown, D and Hutzley, V and Webb, C and Soto, A and Chan, V}, title = {Temporal and region-specific effects of sleep fragmentation on gut microbiota and intestinal morphology in Sprague Dawley rats.}, journal = {Gut microbes}, volume = {11}, number = {4}, pages = {706-720}, pmid = {31924109}, issn = {1949-0984}, mesh = {Animals ; Bacterial Adhesion ; Bacterial Physiological Phenomena ; Cecum/microbiology/*pathology ; Colon/microbiology/*pathology ; Cytokines/analysis ; Endotoxins/analysis ; *Gastrointestinal Microbiome ; Hypothalamo-Hypophyseal System/physiology ; Ileum/microbiology/*pathology ; Phylogeny ; Rats ; Rats, Sprague-Dawley ; *Sleep Deprivation/microbiology/pathology/physiopathology ; }, abstract = {Sleep is a fundamental biological process, that when repeatedly disrupted, can result in severe health consequences. Recent studies suggest that both sleep fragmentation (SF) and dysbiosis of the gut microbiome can lead to metabolic disorders, though the underlying mechanisms are largely unclear. To better understand the consequences of SF, we investigated the effects of acute (6 days) and chronic (6 weeks) SF on rats by examining taxonomic profiles of microbiota in the distal ileum, cecum and proximal colon, as well as assessing structural and functional integrity of the gastrointestinal barrier. We further assayed the impact of SF on a host function by evaluating inflammation and immune response. Both acute and chronic SF induced microbial dysbiosis, more dramatically in the distal ileum (compared to other two regions studied), as noted by significant perturbations in alpha- and beta-diversity; though, specific microbial populations were significantly altered throughout each of the three regions. Furthermore, chronic SF resulted in increased crypt depth in the distal ileum and an increase in the number of villi lining both the cecum and proximal colon. Additional changes were noted with chronic SF, including: decreased microbial adhesion and penetration in the distal ileum and cecum, elevation in serum levels of the cytokine KC/GRO, and depressed levels of corticotropin. Importantly, our data show that perturbations to microbial ecology and intestinal morphology intensify in response to prolonged SF and these changes are habitat specific. Together, these results reveal consequences to gut microbiota homeostasis and host response following acute and chronic SF in rats.}, }
@article {pmid31922946, year = {2020}, author = {Studholme, DJ and Wicker, E and Abrare, SM and Aspin, A and Bogdanove, A and Broders, K and Dubrow, Z and Grant, M and Jones, JB and Karamura, G and Lang, J and Leach, J and Mahuku, G and Nakato, GV and Coutinho, T and Smith, J and Bull, CT}, title = {Transfer of Xanthomonas campestris pv. arecae and X. campestris pv. musacearum to X. vasicola (Vauterin) as X. vasicola pv. arecae comb. nov. and X. vasicola pv. musacearum comb. nov. and Description of X. vasicola pv. vasculorum pv. nov.}, journal = {Phytopathology}, volume = {110}, number = {6}, pages = {1153-1160}, doi = {10.1094/PHYTO-03-19-0098-LE}, pmid = {31922946}, issn = {0031-949X}, mesh = {Areca ; *Musa ; Plant Diseases ; *Xanthomonas ; *Xanthomonas campestris ; }, abstract = {We present an amended description of the bacterial species Xanthomonas vasicola to include the causative agent of banana Xanthomonas wilt, as well as strains that cause disease on Areca palm, Tripsacum grass, sugarcane, and maize. Genome-sequence data reveal that these strains all share more than 98% average nucleotide with each other and with the type strain. Our analyses and proposals should help to resolve the taxonomic confusion that surrounds some of these pathogens and help to prevent future use of invalid names.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.}, }
@article {pmid31922546, year = {2020}, author = {Morris, MM and Frixione, NJ and Burkert, AC and Dinsdale, EA and Vannette, RL}, title = {Microbial abundance, composition, and function in nectar are shaped by flower visitor identity.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {3}, pages = {}, doi = {10.1093/femsec/fiaa003}, pmid = {31922546}, issn = {1574-6941}, mesh = {Animals ; Bees ; Birds ; Flowers ; *Microbiota ; *Plant Nectar ; Pollination ; }, abstract = {Microbial dispersal is essential for establishment in new habitats, but the role of vector identity is poorly understood in community assembly and function. Here, we compared microbial assembly and function in floral nectar visited by legitimate pollinators (hummingbirds) and nectar robbers (carpenter bees). We assessed effects of visitation on the abundance and composition of culturable bacteria and fungi and their taxonomy and function using shotgun metagenomics and nectar chemistry. We also compared metagenome-assembled genomes (MAGs) of Acinetobacter, a common and highly abundant nectar bacterium, among visitor treatments. Visitation increased microbial abundance, but robbing resulted in 10× higher microbial abundance than pollination. Microbial communities differed among visitor treatments: robbed flowers were characterized by predominant nectar specialists within Acetobacteraceae and Metschnikowiaceae, with a concurrent loss of rare taxa, and these resulting communities harbored genes relating to osmotic stress, saccharide metabolism and specialized transporters. Gene differences were mirrored in function: robbed nectar contained a higher percentage of monosaccharides. Draft genomes of Acinetobacter revealed distinct amino acid and saccharide utilization pathways in strains isolated from robbed versus pollinated flowers. Our results suggest an unrecognized cost of nectar robbing for pollination and distinct effects of visitor type on interactions between plants and pollinators. Overall, these results suggest vector identity is an underappreciated factor structuring microbial community assembly and function.}, }
@article {pmid31922045, year = {2020}, author = {Chakraborty, A and DasGupta, CK and Bhadury, P}, title = {Diversity of Betaproteobacteria revealed by novel primers suggests their role in arsenic cycling.}, journal = {Heliyon}, volume = {6}, number = {1}, pages = {e03089}, pmid = {31922045}, issn = {2405-8440}, abstract = {High arsenic concentration in groundwater is a severe environmental problem affecting human health, particularly in countries of South and South-East Asia. The Bengal Delta Plain (BDP) distributed within India and Bangladesh is a major arsenic-affected region where groundwater is the primary source of drinking water. Previous studies have indicated that members of the bacterial class Betaproteobacteria constitute a major fraction of the microbial community in many of the aquifers within this region. Bacteria belonging to this class are known to be involved in redox cycling of arsenic as well as other metals such iron and manganese, thereby impacting arsenic mobilization and immobilization. While microbial diversity in arsenic-contaminated environments is generally assessed using universal 16S rRNA gene primers, targeted evaluation of Betaproteobacteria diversity remains poorly constrained. In this study, bacterial diversity was investigated in the groundwater from two shallow aquifers (West Bengal, India) based on 16S rRNA gene clone libraries and sequencing using a custom-designed pair of primers specific to Betaproteobacteria. Specificity of the primers was confirmed in silico as well as by the absence of PCR amplification of other bacterial classes. Four major families (Burkholderiaceae, Comamonadaceae, Gallionellaceae and Rhodocyclaceae) were detected among which members of Burkholderiaceae represented 59% and 71% of the total community in each aquifer. The four OTUs (operational taxonomic units; 97% sequence identity) within Burkholderiaceae were close phylogenetic relatives of bacteria within the genus Burkholderia known to solubilize phosphate minerals. Additionally, the OTUs belonging to Gallionellaceae were closely related to the members of the genera Gallionella and Sideroxydans, known to oxidize iron under microaerophilic conditions. These results suggest that members of Betaproteobacteria can potentially influence iron and phosphorus cycling which can influence biogeochemistry in arsenic-contaminated aquifers of the BDP.}, }
@article {pmid31921433, year = {2020}, author = {Klaps, J and Lievens, B and Álvarez-Pérez, S}, title = {Towards a better understanding of the role of nectar-inhabiting yeasts in plant-animal interactions.}, journal = {Fungal biology and biotechnology}, volume = {7}, number = {}, pages = {1}, pmid = {31921433}, issn = {2054-3085}, abstract = {Flowers offer a wide variety of substrates suitable for fungal growth. However, the mycological study of flowers has only recently begun to be systematically addressed from an ecological point of view. Most research on the topic carried out during the last decade has focused on studying the prevalence and diversity of flower-inhabiting yeasts, describing new species retrieved from floral parts and animal pollinators, and the use of select nectar yeasts as model systems to test ecological hypotheses. In this primer article, we summarize the current state of the art in floral nectar mycology and provide an overview of some research areas that, in our view, still require further attention, such as the influence of fungal volatile organic compounds on the foraging behavior of pollinators and other floral visitors, the analysis of the direct and indirect effects of nectar-inhabiting fungi on the fitness of plants and animals, and the nature and consequences of fungal-bacterial interactions taking place within flowers.}, }
@article {pmid31921095, year = {2019}, author = {Hounmanou, YMG and Leekitcharoenphon, P and Hendriksen, RS and Dougnon, TV and Mdegela, RH and Olsen, JE and Dalsgaard, A}, title = {Corrigendum: Surveillance and Genomics of Toxigenic Vibrio cholerae O1 From Fish, Phytoplankton and Water in Lake Victoria, Tanzania.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2974}, doi = {10.3389/fmicb.2019.02974}, pmid = {31921095}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2019.00901.].}, }
@article {pmid31921014, year = {2019}, author = {Calabrese, F and Voloshynovska, I and Musat, F and Thullner, M and Schlömann, M and Richnow, HH and Lambrecht, J and Müller, S and Wick, LY and Musat, N and Stryhanyuk, H}, title = {Quantitation and Comparison of Phenotypic Heterogeneity Among Single Cells of Monoclonal Microbial Populations.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2814}, pmid = {31921014}, issn = {1664-302X}, abstract = {Phenotypic heterogeneity within microbial populations arises even when the cells are exposed to putatively constant and homogeneous conditions. The outcome of this phenomenon can affect the whole function of the population, resulting in, for example, new "adapted" metabolic strategies and impacting its fitness at given environmental conditions. Accounting for phenotypic heterogeneity becomes thus necessary, due to its relevance in medical and applied microbiology as well as in environmental processes. Still, a comprehensive evaluation of this phenomenon requires a common and unique method of quantitation, which allows for the comparison between different studies carried out with different approaches. Consequently, in this study, two widely applicable indices for quantitation of heterogeneity were developed. The heterogeneity coefficient (HC) is valid when the population follows unimodal activity, while the differentiation tendency index (DTI) accounts for heterogeneity implying outbreak of subpopulations and multimodal activity. We demonstrated the applicability of HC and DTI for heterogeneity quantitation on stable isotope probing with nanoscale secondary ion mass spectrometry (SIP-nanoSIMS), flow cytometry, and optical microscopy datasets. The HC was found to provide a more accurate and precise measure of heterogeneity, being at the same time consistent with the coefficient of variation (CV) applied so far. The DTI is able to describe the differentiation in single-cell activity within monoclonal populations resolving subpopulations with low cell abundance, individual cells with similar phenotypic features (e.g., isotopic content close to natural abundance, as detected with nanoSIMS). The developed quantitation approach allows for a better understanding on the impact and the implications of phenotypic heterogeneity in environmental, medical and applied microbiology, microbial ecology, cell biology, and biotechnology.}, }
@article {pmid31915852, year = {2020}, author = {Baños, I and Montero, MF and Benavides, M and Arístegui, J}, title = {INT Toxicity over Natural Bacterial Assemblages from Surface Oligotrophic Waters: Implications for the Assessment of Respiratory Activity.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {237-242}, doi = {10.1007/s00248-019-01479-4}, pmid = {31915852}, issn = {1432-184X}, support = {BES-2016- 078407//Secretar&#xed;a de Estado de Investigaci&#xf3;n, Desarrollo e Innovaci&#xf3;n/ ; CTM2015-69392-C3-1-R//Secretar&#xed;a de Estado de Investigaci&#xf3;n, Desarrollo e Innovaci&#xf3;n/ ; }, mesh = {Bacteria/*drug effects/metabolism ; Fresh Water/microbiology ; Oxygen Consumption/*drug effects ; Plankton/*drug effects/metabolism ; Seawater/microbiology ; Spain ; Tetrazolium Salts/*toxicity ; }, abstract = {Plankton community respiration (R) is a major component of the carbon flux in aquatic ecosystems. However, current methods to measure actual respiration from oxygen consumption at relevant spatial scales are not sensitive enough in oligotrophic environments where respiration rates are very low. To overcome this drawback, more sensitive indirect enzymatic approaches are commonly used as R proxies. The in vivo electron transport system (ETSvivo) assay, which measures the reduction of (2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyl tetrazolium chloride salt, INT) to INT-formazan in the presence of natural substrate levels, was recently proposed as an indirect reliable estimation of R for natural plankton communities. However, under in vivo conditions, formazan salts could be toxic to the cells. Here, we test the toxicity of 0.2 mM of final INT concentration, widely used for ETSvivo assays, on natural bacterial assemblages collected in coastal and oceanic waters off Gran Canaria (Canary Islands, subtropical North Atlantic), in eight independent experiments. After 0.5 h of incubation, a significant but variable decline in cell viability (14-49%) was observed in all samples inoculated with INT. Moreover, INT also inhibited leucine uptake in less than 90 min of incubation. In the light of these results, we argue that enzymatic respiratory rates obtained with the ETSvivo method need to be interpreted with caution to derive R in oceanic regions where bacteria largely contribute to community respiration. Moreover, the variable toxicity on bacterial assemblages observed in our experiments questions the use of a single R/ETSvivo relationship as a universal proxy for regional studies.}, }
@article {pmid31915217, year = {2020}, author = {Schnizlein, MK and Vendrov, KC and Edwards, SJ and Martens, EC and Young, VB}, title = {Dietary Xanthan Gum Alters Antibiotic Efficacy against the Murine Gut Microbiota and Attenuates Clostridioides difficile Colonization.}, journal = {mSphere}, volume = {5}, number = {1}, pages = {}, pmid = {31915217}, issn = {2379-5042}, support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; T32 DK094775/DK/NIDDK NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*therapeutic use ; Cefoperazone/therapeutic use ; Clostridioides difficile/*drug effects ; Clostridium Infections/microbiology/*prevention &amp; control ; Dietary Fiber/*administration &amp; dosage ; Dietary Supplements ; Disease Susceptibility ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Male ; Mice ; Mice, Inbred C57BL ; Polysaccharides, Bacterial/*administration &amp; dosage ; Specific Pathogen-Free Organisms ; }, abstract = {Dietary fiber provides a variety of microbiota-mediated benefits ranging from anti-inflammatory metabolites to pathogen colonization resistance. A healthy gut microbiota protects against Clostridioides difficile colonization. Manipulation of these microbes through diet may increase colonization resistance to improve clinical outcomes. The primary objective of this study was to identify how the dietary fiber xanthan gum affects the microbiota and C. difficile colonization. We added 5% xanthan gum to the diet of C57BL/6 mice and examined its effect on the microbiota through 16S rRNA gene amplicon sequencing and short-chain fatty acid analysis. Following either cefoperazone or an antibiotic cocktail administration, we challenged mice with C. difficile and measured colonization by monitoring the CFU. Xanthan gum administration is associated with increases in fiber-degrading taxa and short-chain fatty acid concentrations. However, by maintaining both the diversity and absolute abundance of the microbiota during antibiotic treatment, the protective effects of xanthan gum administration on the microbiota were more prominent than the enrichment of these fiber-degrading taxa. As a result, mice that were on the xanthan gum diet experienced limited to no C. difficile colonization. Xanthan gum administration alters mouse susceptibility to C. difficile colonization by maintaining the microbiota during antibiotic treatment. While antibiotic-xanthan gum interactions are not well understood, xanthan gum has previously been used to bind drugs and alter their pharmacokinetics. Thus, xanthan gum may alter the activity of the oral antibiotics used to make the microbiota susceptible. Future research should further characterize how this and other common dietary fibers interact with drugs.IMPORTANCE A healthy gut bacterial community benefits the host by breaking down dietary nutrients and protecting against pathogens. Clostridioides difficile capitalizes on the absence of this community to cause diarrhea and inflammation. Thus, a major clinical goal is to find ways to increase resistance to C. difficile colonization by either supplementing with bacteria that promote resistance or a diet to enrich for those already present in the gut. In this study, we describe an interaction between xanthan gum, a human dietary additive, and the microbiota resulting in an altered gut environment that is protective against C. difficile colonization.}, }
@article {pmid31911465, year = {2020}, author = {Li, P and Li, W and Dumbrell, AJ and Liu, M and Li, G and Wu, M and Jiang, C and Li, Z}, title = {Spatial Variation in Soil Fungal Communities across Paddy Fields in Subtropical China.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, pmid = {31911465}, issn = {2379-5077}, abstract = {Fungi underpin almost all terrestrial ecosystem functions, yet our understanding of their community ecology lags far behind that of other organisms. Here, red paddy soils in subtropical China were collected across a soil depth profile, comprising 0-to-10-cm- (0-10cm-), 10-20cm-, and 20-40cm-deep layers. Using Illumina MiSeq amplicon sequencing of the internal transcribed spacer (ITS) region, distance-decay relationships (DDRs), and ecological models, fungal assemblages and their spatial patterns were investigated from each soil depth. We observed significant spatial variation in fungal communities and found that environmental heterogeneity decreased with soil depth, while spatial variation in fungal communities showed the opposite trend. DDRs occurred only in 0-10cm- and 10-20cm-deep soil layers, not in the 20-40cm layer. Our analyses revealed that the fungal community assembly in the 0-10cm layer was primarily governed by environmental filtering and a high dispersal rate, while in the deeper layer (20-40cm), it was primarily governed by dispersal limitation with minimal environmental filtering. Both environmental filtering and dispersal limitation controlled fungal community assembly in the 10-20cm layer, with dispersal limitation playing the major role. Results demonstrate the decreasing importance of environmental filtering and an increase in the importance of dispersal limitation in structuring fungal communities from shallower to deeper soils. Effectively, "everything is everywhere, but the environment selects," although only in shallower soils that are easily accessible to dispersive fungal propagules. This work highlights that perceived drivers of fungal community assembly are dependent on sampling depth, suggesting that caution is required when interpreting diversity patterns from samples that integrate across depths.IMPORTANCE In this work, Illumina MiSeq amplicon sequencing of the ITS region was used to investigate the spatial variation and assembly mechanisms of fungal communities from different soil layers across paddy fields in subtropical China, and the results demonstrate the decreasing importance of environmental filtering and an increase in the importance of dispersal limitation in structuring fungal communities from shallower to deeper soils. Therefore, the results of this study highlight that perceived drivers of fungal community assembly are dependent on sampling depth and suggest that caution is required when interpreting diversity patterns from samples that integrate across depths. This is the first study focusing on assemblages of fungal communities in different soil layers on a relatively large scale, and we thus believe that this study is of great importance to researchers and readers in microbial ecology, especially in microbial biogeography, because the results can provide sampling guidance in future studies of microbial biogeography.}, }
@article {pmid31909618, year = {2020}, author = {Van den Abbeele, P and Moens, F and Pignataro, G and Schnurr, J and Ribecco, C and Gramenzi, A and Marzorati, M}, title = {Yeast-Derived Formulations Are Differentially Fermented by the Canine and Feline Microbiome As Assessed in a Novel In Vitro Colonic Fermentation Model.}, journal = {Journal of agricultural and food chemistry}, volume = {68}, number = {46}, pages = {13102-13110}, doi = {10.1021/acs.jafc.9b05085}, pmid = {31909618}, issn = {1520-5118}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Cats ; Colon/*microbiology ; Dietary Supplements/analysis ; Dogs ; Fatty Acids, Volatile/*metabolism ; Fermentation ; *Gastrointestinal Microbiome ; Yeasts/*chemistry/metabolism ; }, abstract = {The current study evaluated the effect of five yeast-derived formulations (T1-T5) on microbial metabolism and composition of the canine and feline gut microbiota using a novel in vitro colonic incubation approach. This novel in vitro model allowed for growth of the entire spectrum of dog- and cat-derived bacteria from the inoculum, thus offering an excellent platform to evaluate effects of nutritional interventions on the gut microbiota. Further, yeast-derived ingredients differentially increased production of acetate, propionate, butyrate, ammonium, and branched short-chain fatty acids, with T5 and T1 consistently stimulating propionate and butyrate, respectively. 16S-targeted Illumina sequencing coupled with flow cytometry provided unprecedented high-resolution quantitative insights in canine and feline microbiota modulation by yeast-derived ingredients, revealing that effects on propionate production were related to Prevotellaceae, Tannerellaceae, Bacteroidaceae, and Veillonellaceae members, while effects on butyrate production were related to Erysipelotrichaceae, Lachnospiraceae, Ruminococcaceae, and Fusobacteriaceae. Overall, these findings strengthen the health-promoting potential of yeast-derived ingredients.}, }
@article {pmid31897988, year = {2020}, author = {Zhang, D and Luther, AK and Clauwaert, P and Ciccioli, P and Ronsse, F}, title = {Assessment of carbon recovery from solid organic wastes by supercritical water oxidation for a regenerative life support system.}, journal = {Environmental science and pollution research international}, volume = {27}, number = {8}, pages = {8260-8270}, pmid = {31897988}, issn = {1614-7499}, support = {201406350071//China Sponsorship Council/ ; 4000113452/15/NL/AT//European Space Agency/ ; DOZA/DDC/AM/DL/171b-2015//Universiteit Gent/ ; }, mesh = {Carbon/*analysis/chemistry ; Life Support Systems ; Oxidation-Reduction ; *Solid Waste/analysis ; Waste Disposal, Fluid ; *Water ; }, abstract = {The carbon recovery from organic space waste by supercritical water oxidation (SCWO) was studied to support resource recovery in a regenerative life support system. Resource recovery is of utmost importance in such systems which only have a limited total amount of mass. However, the practical waste treatment strategies for solid space wastes employed today are only storing and disposal without further recovery. This work assesses the performance of SCWO at recovering organic wastes as CO2 and water, to discuss the superiority of SCWO over most present strategies, and to evaluate the different SCWO reactor systems for space application. Experiments were carried out with a batch and a continuous reactor at different reaction conditions. The liquid and gas products distribution were analyzed to understand the conversion of organics in SCWO. Up to 97% and 93% of the feed carbon were recovered as CO2 in the continuous and the batch reactor, respectively. Residual carbon was mostly found as soluble organics in the effluent. Compared with the batch reactor, the continuous reactor system demonstrated a ten times higher capacity within the same reactor volume, while the batch reactor system was capable of handling feeds that contained particulate matter though suffering from poor heat integration (hence low-energy efficiency) and inter-batch variability. It was concluded that SCWO could be a promising technology to treat solid wastes for space applications. A continuous reactor would be more suitable for a regenerative life support system.}, }
@article {pmid31897570, year = {2020}, author = {Donati, I and Cellini, A and Sangiorgio, D and Vanneste, JL and Scortichini, M and Balestra, GM and Spinelli, F}, title = {Pseudomonas syringae pv. actinidiae: Ecology, Infection Dynamics and Disease Epidemiology.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {81-102}, pmid = {31897570}, issn = {1432-184X}, support = {613678//Seventh Framework Programme/ ; }, mesh = {Actinidia/*physiology ; Plant Diseases/*microbiology ; Plant Leaves/microbiology/physiology ; Pseudomonas syringae/*physiology ; }, abstract = {Since 2008, the kiwifruit industry has been devastated by a pandemic outbreak of Pseudomonas syringae pv. actinidiae (Psa), the causal agent of bacterial canker. This disease has become the most significant limiting factor in kiwifruit production. Psa colonizes different organs of the host plant, causing a specific symptomatology on each of them. In addition, the systemic invasion of the plant may quickly lead to plant death. Despite the massive risk that this disease poses to the kiwifruit industry, studies focusing on Psa ecology have been sporadic, and a comprehensive description of the disease epidemiology is still missing. Optimal environmental conditions for infection, dispersal and survival in the environment, or the mechanisms of penetration and colonization of host tissues have not been fully elucidated yet. The present work aims to provide a synthesis of the current knowledge, and a deeper understanding of the epidemiology of kiwifruit bacterial canker based on new experimental data. The pathogen may survive in the environment or overwinter in dormant tissues and be dispersed by wind or rain. Psa was observed in association with several plant structures (stomata, trichomes, lenticels) and wounds, which could represent entry points for apoplast infection. Environmental conditions also affect the bacterial colonization, with lower optimum values of temperature and humidity for epiphytic than for endophytic growth, and disease incidence requiring a combination of mild temperature and leaf wetness. By providing information on Psa ecology, these data sets may contribute to plan efficient control strategies for kiwifruit bacterial canker.}, }
@article {pmid31897569, year = {2020}, author = {Floc'h, JB and Hamel, C and Harker, KN and St-Arnaud, M}, title = {Fungal Communities of the Canola Rhizosphere: Keystone Species and Substantial Between-Year Variation of the Rhizosphere Microbiome.}, journal = {Microbial ecology}, volume = {80}, number = {4}, pages = {762-777}, doi = {10.1007/s00248-019-01475-8}, pmid = {31897569}, issn = {1432-184X}, mesh = {Alberta ; Brassica napus/*microbiology ; *Crop Production/methods ; Fungi/*isolation &amp; purification ; Mycobiome/*physiology ; *Rhizosphere ; Saskatchewan ; Seasons ; }, abstract = {Rhizosphere microbes influence one another, forming extremely complex webs of interactions that may determine plant success. Identifying the key factors that structure the fungal microbiome of the plant rhizosphere is a necessary step in optimizing plant production. In a long-term field experiment conducted at three locations in the Canadian prairies, we tested the following hypotheses: (1) diversification of cropping systems influences the fungal microbiome of the canola (Brassica napus) rhizosphere; (2) the canola rhizosphere has a core fungal microbiome, i.e., a set of fungi always associated with canola; and (3) some taxa within the rhizosphere microbiome of canola are highly interrelated and fit the description of hub taxa. Our results show that crop diversification has a significant effect on the structure of the rhizosphere fungal community but not on fungal diversity. We also discovered and described a canola core microbiome made up of one zero-radius operational taxonomic unit (ZOTU), cf. Olpidium brassicae, and an eco-microbiome found only in 2013 consisting of 47 ZOTUs. Using network analysis, we identified four hub taxa in 2013: ZOTU14 (Acremonium sp.), ZOTU28 (Sordariomycetes sp.), ZOTU45 (Mortierella sp.) and ZOTU179 (cf. Ganoderma applanatum), and one hub taxon, ZOTU17 (cf. Mortierella gamsii) in 2016. None of these most interacting taxa belonged to the core microbiome or eco-microbiome for each year of sampling. This temporal variability puts into question the idea of a plant core fungal microbiome and its stability. Our results provide a basis for the development of ecological engineering strategies for the improvement of canola production systems in Canada.}, }
@article {pmid31896790, year = {2020}, author = {Op De Beeck, M and Troein, C and Siregar, S and Gentile, L and Abbondanza, G and Peterson, C and Persson, P and Tunlid, A}, title = {Regulation of fungal decomposition at single-cell level.}, journal = {The ISME journal}, volume = {14}, number = {4}, pages = {896-905}, pmid = {31896790}, issn = {1751-7370}, mesh = {Agaricales ; Basidiomycota/physiology ; Environmental Microbiology ; Fungi/*physiology ; Hyphae ; Mycelium/physiology ; Mycorrhizae/physiology ; Nutrients ; Soil/chemistry ; }, abstract = {Filamentous fungi play a key role as decomposers in Earth's nutrient cycles. In soils, substrates are heterogeneously distributed in microenvironments. Hence, individual hyphae of a mycelium may experience very different environmental conditions simultaneously. In the current work, we investigated how fungi cope with local environmental variations at single-cell level. We developed a method based on infrared spectroscopy that allows the direct, in-situ chemical imaging of the decomposition activity of individual hyphal tips. Colonies of the ectomycorrhizal Basidiomycete Paxillus involutus were grown on liquid media, while parts of colonies were allowed to colonize lignin patches. Oxidative decomposition of lignin by individual hyphae growing under different conditions was followed for a period of seven days. We identified two sub-populations of hyphal tips: one with low decomposition activity and one with much higher activity. Active cells secreted more extracellular polymeric substances and oxidized lignin more strongly. The ratio of active to inactive hyphae strongly depended on the environmental conditions in lignin patches, but was further mediated by the decomposition activity of entire mycelia. Phenotypic heterogeneity occurring between genetically identical hyphal tips may be an important strategy for filamentous fungi to cope with heterogeneous and constantly changing soil environments.}, }
@article {pmid31896018, year = {2020}, author = {Yuan, W and Tian, T and Yang, Q and Riaz, L}, title = {Transfer potentials of antibiotic resistance genes in Escherichia spp. strains from different sources.}, journal = {Chemosphere}, volume = {246}, number = {}, pages = {125736}, doi = {10.1016/j.chemosphere.2019.125736}, pmid = {31896018}, issn = {1879-1298}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects ; Drug Resistance, Microbial/*genetics ; *Environmental Monitoring ; Escherichia ; *Genes, Bacterial ; Humans ; Livestock ; Manure/microbiology ; Metals, Heavy ; Plasmids ; Wastewater/microbiology ; }, abstract = {Multidrug-resistant Escherichia coli and antibiotic-resistance genes (ARGs) present a danger to public health. However, information on the dissemination potentials of antibiotic resistance among bacteria from different environments is lacking. We isolated multiple antibiotic-resistant Escherichia spp. from animal farms, hospitals, and municipal wastewater-treatment plants (MWWTPs) using culture-based methods, and carried out resistance phenotype and gene analyses. Thirty-five isolates of multiple antibiotic-resistant Escherichia spp. were further screened to detect 61 ARGs, 18 mobile genetic elements (MGEs), and gene cassettes. The isolates from livestock manure and MWWTPs showed greater diversity in plasmid profiling than hospital wastewater. Each Escherichia sp. carried 21-26 ARGs and 8-12 MGEs. In addition, 11 gene cassettes were detected in 34 Escherichia isolates, with greater diversity in livestock manure and MWWTPs than in hospital wastewater. The results indicated that the potential for ARG transfer was higher in livestock manure and MWWTPs compared with human clinical sources, possibly related to the high occurrence of both residual antibiotics and heavy metals in these environments.}, }
@article {pmid31894632, year = {2021}, author = {Baricz, A and Chiriac, CM and Andrei, A&#x218; and Bulzu, PA and Levei, EA and Cadar, O and Battes, KP and Cîmpean, M and Șenilă, M and Cristea, A and Muntean, V and Alexe, M and Coman, C and Szekeres, EK and Sicora, CI and Ionescu, A and Blain, D and O'Neill, WK and Edwards, J and Hallsworth, JE and Banciu, HL}, title = {Spatio-temporal insights into microbiology of the freshwater-to-hypersaline, oxic-hypoxic-euxinic waters of Ursu Lake.}, journal = {Environmental microbiology}, volume = {23}, number = {7}, pages = {3523-3540}, doi = {10.1111/1462-2920.14909}, pmid = {31894632}, issn = {1462-2920}, mesh = {*Bacteria/genetics ; *Lakes ; Sodium Chloride ; Sulfur ; Water Microbiology ; }, abstract = {Ursu Lake is located in the Middle Miocene salt deposit of Central Romania. It is stratified, and the water column has three distinct water masses: an upper freshwater-to-moderately saline stratum (0-3 m), an intermediate stratum exhibiting a steep halocline (3-3.5 m), and a lower hypersaline stratum (4 m and below) that is euxinic (i.e. anoxic and sulphidic). Recent studies have characterized the lake's microbial taxonomy and given rise to intriguing ecological questions. Here, we explore whether the communities are dynamic or stable in relation to taxonomic composition, geochemistry, biophysics, and ecophysiological functions during the annual cycle. We found: (i) seasonally fluctuating, light-dependent communities in the upper layer (≥0.987-0.990 water-activity), a stable but phylogenetically diverse population of heterotrophs in the hypersaline stratum (water activities down to 0.762) and a persistent plate of green sulphur bacteria that connects these two (0.958-0.956 water activity) at 3-3.5 to 4 m; (ii) communities that might be involved in carbon- and sulphur-cycling between and within the lake's three main water masses; (iii) uncultured lineages including Acetothermia (OP1), Cloacimonetes (WWE1), Marinimicrobia (SAR406), Omnitrophicaeota (OP3), Parcubacteria (OD1) and other Candidate Phyla Radiation bacteria, and SR1 in the hypersaline stratum (likely involved in the anaerobic steps of carbon- and sulphur-cycling); and (iv) that species richness and habitat stability are associated with high redox-potentials. Ursu Lake has a unique and complex ecology, at the same time exhibiting dynamic fluctuations and stability, and can be used as a modern analogue for ancient euxinic water bodies and comparator system for other stratified hypersaline systems.}, }
@article {pmid31891451, year = {2020}, author = {Cosetta, CM and Wolfe, BE}, title = {Deconstructing and Reconstructing Cheese Rind Microbiomes for Experiments in Microbial Ecology and Evolution.}, journal = {Current protocols in microbiology}, volume = {56}, number = {1}, pages = {e95}, doi = {10.1002/cpmc.95}, pmid = {31891451}, issn = {1934-8533}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Biofilms ; *Biological Evolution ; Cattle ; Cheese/*microbiology ; Food Microbiology/*methods ; Fungi/classification/genetics/*isolation &amp; purification/physiology ; Microbiological Techniques/*methods ; *Microbiota ; Milk/microbiology ; }, abstract = {Cheese rind microbiomes are useful model systems for identifying the mechanisms that control microbiome diversity. Here, we describe the methods we have optimized to first deconstruct in situ cheese rind microbiome diversity and then reconstruct that diversity in laboratory environments to conduct controlled microbiome manipulations. Most cheese rind microbial species, including bacteria, yeasts, and filamentous fungi, can be easily cultured using standard lab media. Colony morphologies of taxa are diverse and can often be used to distinguish taxa at the phylum and sometimes even genus level. Through the use of cheese curd agar medium, thousands of unique community combinations or microbial interactions can be assessed. Transcriptomic experiments and transposon mutagenesis screens can pinpoint mechanisms of interactions between microbial species. Our general approach of creating a tractable synthetic microbial community from cheese can be easily applied to other fermented foods to develop other model microbiomes. © 2019 by John Wiley &amp; Sons, Inc. Basic Protocol 1: Isolation of cheese rind microbial communities Support Protocol 1: Preparation of plate count agar with milk and salt Basic Protocol 2: Identification of cheese rind bacterial and fungal isolates using 16S and ITS sequences Basic Protocol 3: Preparation of experimental glycerol stocks of yeasts and bacteria Basic Protocol 4: Preparation of experimental glycerol stocks of filamentous fungi Basic Protocol 5: Reconstruction of cheese rind microbial communities in vitro Support Protocol 2: Preparation of lyophilized and powdered cheese curd Support Protocol 3: Preparation of 10% cheese curd agar plates and tubes Basic Protocol 6: Interaction screens using responding lawns Support Protocol 4: Preparation of liquid 2% cheese curd Basic Protocol 7: Experimental evolution Basic Protocol 8: Measuring community function: pH/acidification Basic Protocol 9: Measuring community function: Pigment production Basic Protocol 10: RNA sequencing of cheese rind biofilms.}, }
@article {pmid31889749, year = {2019}, author = {Philips, CA and Phadke, N and Ganesan, K and Rajesh, S and Padsalgi, G and Ahamed, R and John, SK and Valiathan, GC and Augustine, P}, title = {Gut Microbiota in Alcoholic Hepatitis is Disparate from Those in Acute Alcoholic Pancreatitis and Biliary Disease.}, journal = {Journal of clinical and experimental hepatology}, volume = {9}, number = {6}, pages = {690-698}, pmid = {31889749}, issn = {0973-6883}, abstract = {BACKGROUND: Alcoholic hepatitis (AH) is associated with gut dysbiosis. Comparative gut microbial profiles of acute alcoholic pancreatitis (AAP) and acute biliary disease (ABD) are not demonstrated. We aimed to compare gut microbiota of AH, AAP, and ABD patients with each other and with their respective healthy controls (HCs).<br><br>METHODS: From December 2016 to September 2017, consecutive patients with AH, AAP, and ABD (acute cholecystitis, acute biliary pancreatitis, and choledocholithiasis with cholangitis) were included in the study. Qualitative and functional stool microbiota comparative analysis was performed between groups, with AH as the reference comparator.<br><br>RESULTS: Of 3564, 882, and 224 patients with liver disease, pancreatic disease, and biliary disease, respectively, after exclusion, 29 patients with AH and 7 patients each with AAP and ABD&#xa0;and their corresponding HCs were included in the study analysis. The alpha diversity between patients with AH and AAP was found to be significantly different. Significant relative abundance (RA) of Acinetobacter and Moraxella was noted among patients with AAP. Enterobacter, Atopobium, Synergistia, and Devosia were significantly higher in patients with ABD compared to patients with AH, in whom Faecalibacterium and Megamonas were higher. Functional pathways associated with carbohydrate metabolism, phenylpropanoid biosynthesis, and ethylbenzene degradation were significantly higher in AAP when compared to AH. Fatty acid and inositol phosphate metabolism and dioxin degradation were significantly upregulated in patients with ABD while lipid and fatty acid biosynthetic pathways and pathways associated with immune processes were upregulated in patients with AH.<br><br>CONCLUSIONS: Differential gut dysbiosis is evident in both patients with AH, AAP, and ABD and also in comparison to HCs. The differential microbiota among patients with AH and AAP maybe important in promotion and progression of liver or pancreatic disease among alcohol users and may be a potential therapeutic target, which needs to be confirmed in larger multicenter studies.}, }
@article {pmid31889414, year = {2020}, author = {García-Timermans, C and Rubbens, P and Heyse, J and Kerckhof, FM and Props, R and Skirtach, AG and Waegeman, W and Boon, N}, title = {Discriminating Bacterial Phenotypes at the Population and Single-Cell Level: A Comparison of Flow Cytometry and Raman Spectroscopy Fingerprinting.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {97}, number = {7}, pages = {713-726}, doi = {10.1002/cyto.a.23952}, pmid = {31889414}, issn = {1552-4930}, mesh = {*Bacteria ; Escherichia coli/genetics ; Flow Cytometry ; Phenotype ; Single-Cell Analysis ; *Spectrum Analysis, Raman ; }, abstract = {Investigating phenotypic heterogeneity can help to better understand and manage microbial communities. However, characterizing phenotypic heterogeneity remains a challenge, as there is no standardized analysis framework. Several optical tools are available, such as flow cytometry and Raman spectroscopy, which describe optical properties of the individual cell. In this work, we compare Raman spectroscopy and flow cytometry to study phenotypic heterogeneity in bacterial populations. The growth stages of three replicate Escherichia coli populations were characterized using both technologies. Our findings show that flow cytometry detects and quantifies shifts in phenotypic heterogeneity at the population level due to its high-throughput nature. Raman spectroscopy, on the other hand, offers a much higher resolution at the single-cell level (i.e., more biochemical information is recorded). Therefore, it can identify distinct phenotypic populations when coupled with analyses tailored toward single-cell data. In addition, it provides information about biomolecules that are present, which can be linked to cell functionality. We propose a computational workflow to distinguish between bacterial phenotypic populations using Raman spectroscopy and validated this approach with an external data set. We recommend using flow cytometry to quantify phenotypic heterogeneity at the population level, and Raman spectroscopy to perform a more in-depth analysis of heterogeneity at the single-cell level. © 2019 International Society for Advancement of Cytometry.}, }
@article {pmid31887587, year = {2020}, author = {van Dorst, J and Wilkins, D and King, CK and Spedding, T and Hince, G and Zhang, E and Crane, S and Ferrari, B}, title = {Applying microbial indicators of hydrocarbon toxicity to contaminated sites undergoing bioremediation on subantarctic Macquarie Island.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {259}, number = {}, pages = {113780}, doi = {10.1016/j.envpol.2019.113780}, pmid = {31887587}, issn = {1873-6424}, mesh = {*Biodegradation, Environmental ; Humans ; Hydrocarbons/*toxicity ; Islands ; *Petroleum ; Soil ; Soil Microbiology ; *Soil Pollutants ; }, abstract = {Microorganisms are useful biological indicators of toxicity and play a key role in the functioning of healthy soils. In this study, we investigated the residual toxicity of hydrocarbons in aged contaminated soils and determined the extent of microbial community recovery during in-situ bioremediation at subantarctic Macquarie Island. Previously identified microbial indicators of hydrocarbon toxicity were used to understand interactions between hydrocarbon concentrations, soil physicochemical parameters and the microbial community. Despite the complexity of the field sites, which included active fuel storage areas with high levels of soil heterogeneity, multiple spill events and variable fuel sources, we observed consistent microbial community traits associated with exposure to high concentrations of hydrocarbons. These included; reductions in alpha diversity, inhibition of nitrification potential and a reduction in the ratio of oligotrophic to copiotrophic species. These observed responses and the sensitivity of microbial communities in the field, were comparable to sensitivity estimates obtained in a previous lab-based mesocosm study with hydrocarbon spiked soils. This study provides a valuable and often missing link between the quite disparate conditions of controlled lab-based spiking experiments and the complexity presented by 'real-world' contaminated field sites.}, }
@article {pmid31887546, year = {2020}, author = {Carney, RL and Brown, MV and Siboni, N and Raina, JB and Kahlke, T and Mitrovic, SM and Seymour, JR}, title = {Highly heterogeneous temporal dynamics in the abundance and diversity of the emerging pathogens Arcobacter at an urban beach.}, journal = {Water research}, volume = {171}, number = {}, pages = {115405}, doi = {10.1016/j.watres.2019.115405}, pmid = {31887546}, issn = {1879-2448}, mesh = {*Arcobacter ; Bacteria ; DNA, Bacterial ; Humans ; RNA, Ribosomal, 16S ; Real-Time Polymerase Chain Reaction ; }, abstract = {While the significance of Arcobacter in clinical settings grows, the ecological dynamics of potentially pathogenic Arcobacter in coastal marine environments remains unclear. In this study, we monitored the temporal dynamics of Arcobacter at an urban beach subject to significant stormwater input and wet weather sewer overflows (WWSO). Weekly monitoring of bacterial communities over 24 months using 16S rRNA amplicon sequencing revealed large, intermittent peaks in the relative abundance of Arcobacter. Quantitative PCR was subsequently employed to track absolute abundance of Arcobacter 23S rRNA gene copies, revealing peaks in abundance reaching up to 10[8] gene copies L[-1], with these increases statistically correlated with stormwater and WWSO intrusion. Notably, peaks in Arcobacter abundance were poorly correlated with enterococci plate counts, and remained elevated for one week following heavy rainfall. Using oligotyping we discriminated single nucleotide variants (SNVs) within the Arcobacter population, revealing 10 distinct clusters of SNVs that we defined as Arcobacter "ecotypes", with each displaying distinct temporal dynamics. The most abundant ecotype during stormwater and modelled WWSO events displayed 16S rRNA sequence similarity to A. cryaerophilius, a species previously implicated in human illness. Our findings highlight the diverse environmental drivers of Arcobacter abundance within coastal settings and point to a potentially important, yet overlooked exposure risk of these potential pathogens to humans.}, }
@article {pmid31885873, year = {2019}, author = {Pareek, S and Kurakawa, T and Das, B and Motooka, D and Nakaya, S and Rongsen-Chandola, T and Goyal, N and Kayama, H and Dodd, D and Okumura, R and Maeda, Y and Fujimoto, K and Nii, T and Ogawa, T and Iida, T and Bhandari, N and Kida, T and Nakamura, S and Nair, GB and Takeda, K}, title = {Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi.}, journal = {NPJ biofilms and microbiomes}, volume = {5}, number = {1}, pages = {37}, pmid = {31885873}, issn = {2055-5008}, support = {K08 DK110335/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/*growth &amp; development/*metabolism ; Diet/*methods ; Feces/microbiology ; Fungi/classification/*growth &amp; development/*metabolism ; *Gastrointestinal Microbiome ; Humans ; India ; Japan ; Mice ; *Microbial Interactions ; Models, Animal ; Polysaccharides/metabolism ; }, abstract = {The bacterial species living in the gut mediate many aspects of biological processes such as nutrition and activation of adaptive immunity. In addition, commensal fungi residing in the intestine also influence host health. Although the interaction of bacterium and fungus has been shown, its precise mechanism during colonization of the human intestine remains largely unknown. Here, we show interaction between bacterial and fungal species for utilization of dietary components driving their efficient growth in the intestine. Next generation sequencing of fecal samples from Japanese and Indian adults revealed differential patterns of bacterial and fungal composition. In particular, Indians, who consume more plant polysaccharides than Japanese, harbored increased numbers of Prevotella and Candida. Candida spp. showed strong growth responses to the plant polysaccharide arabinoxylan in vitro. Furthermore, the culture supernatants of Candida spp. grown with arabinoxylan promoted rapid proliferation of Prevotella copri. Arabinose was identified as a potential growth-inducing factor in the Candida culture supernatants. Candida spp. exhibited a growth response to xylose, but not to arabinose, whereas P. copri proliferated in response to both xylose and arabinose. Candida spp., but not P. copri, colonized the intestine of germ-free mice. However, P. copri successfully colonized mouse intestine already harboring Candida. These findings demonstrate a proof of concept that fungal members of gut microbiota can facilitate a colonization of the intestine by their bacterial counterparts, potentially mediated by a dietary metabolite.}, }
@article {pmid31885375, year = {2019}, author = {Wein, T and Stücker, FT and Hülter, NF and Dagan, T}, title = {Quantification of Plasmid-Mediated Antibiotic Resistance in an Experimental Evolution Approach.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {154}, pages = {}, doi = {10.3791/60749}, pmid = {31885375}, issn = {1940-087X}, mesh = {Drug Resistance, Microbial/*genetics ; Evolution, Molecular ; *Plasmids ; }, abstract = {Plasmids play a major role in microbial ecology and evolution as vehicles of lateral gene transfer and reservoirs of accessory gene functions in microbial populations. This is especially the case under rapidly changing environments such as fluctuating antibiotics exposure. We recently showed that plasmids maintain antibiotic resistance genes in Escherichia coli without positive selection for the plasmid presence. Here we describe an experimental system that allows following both the plasmid genotype and phenotype in long-term evolution experiments. We use molecular techniques to design a model plasmid that is subsequently introduced to an experimental evolution batch system approach in an E. coli host. We follow the plasmid frequency over time by applying replica plating of the E. coli populations while quantifying the antibiotic resistance persistence. In addition, we monitor the conformation of plasmids in host cells by analyzing the extent of plasmid multimer formation by plasmid nicking and agarose gel electrophoresis. Such an approach allows us to visualize not only the genome size of evolving plasmids but also their topological conformation-a factor highly important for plasmid inheritance. Our system combines molecular strategies with traditional microbiology approaches and provides a set-up to follow plasmids in bacterial populations over a long time. The presented approach can be applied to study a wide range of mobile genetic elements in the future.}, }
@article {pmid31881501, year = {2020}, author = {Favere, J and Buysschaert, B and Boon, N and De Gusseme, B}, title = {Online microbial fingerprinting for quality management of drinking water: Full-scale event detection.}, journal = {Water research}, volume = {170}, number = {}, pages = {115353}, doi = {10.1016/j.watres.2019.115353}, pmid = {31881501}, issn = {1879-2448}, mesh = {Bacteria ; *Drinking Water ; Water Microbiology ; Water Quality ; Water Supply ; }, abstract = {Microbial regrowth during drinking water distribution can result in a variety of problems such as a deviating taste and odor, and may even pose a risk to public health. Frequent monitoring is essential to anticipate events of biological instability, and relevant microbial parameters for operational control of biostability of drinking water should be developed. Here, online flow cytometry and derived biological metrics were used to assess the biological stability of a full-scale drinking water tower during normal and disturbed flow regime. Pronounced operational events, such as switching from drinking water source, and seasonal changes, were detected in the total cell counts, and regrowth was observed despite the short hydraulic residence time of 6-8 h. Based on the flow cytometric fingerprints, the Bray-Curtis dissimilarity was calculated and was developed as unambiguous parameter to indicate or warn for changing microbial drinking water quality during operational events. In the studied water tower, drastic microbial water quality changes were reflected in the Bray-Curtis dissimilarity, which demonstrates its use as an indicator to follow-up and detect microbial quality changes in practice. Hence, the Bray-Curtis dissimilarity can be used in an online setup as a straightforward parameter during full-scale operation of drinking water distribution, and combined with the cell concentration, it serves as an early-warning system for biological instability.}, }
@article {pmid31878322, year = {2019}, author = {Sahu, SK and Liu, M and Yssel, A and Kariba, R and Muthemba, S and Jiang, S and Song, B and Hendre, PS and Muchugi, A and Jamnadass, R and Kao, SM and Featherston, J and Zerega, NJC and Xu, X and Yang, H and Deynze, AV and Peer, YV and Liu, X and Liu, H}, title = {Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis).}, journal = {Genes}, volume = {11}, number = {1}, pages = {}, pmid = {31878322}, issn = {2073-4425}, mesh = {Artocarpus/classification/*genetics ; Genome Size ; Genome, Plant ; Molecular Sequence Annotation ; Whole Genome Sequencing/*methods ; }, abstract = {Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for thousands of years in their native regions. Today they are grown throughout tropical to subtropical areas as an important source of starch and other valuable nutrients. There are hundreds of breadfruit varieties that are native to Oceania, of which the most commonly distributed types are seedless triploids. Jackfruit is likely native to the Western Ghats of India and produces one of the largest tree-borne fruit structures (reaching up to 45 kg). To-date, there is limited genomic information for these two economically important species. Here, we generated 273 Gb and 227 Gb of raw data from jackfruit and breadfruit, respectively. The high-quality reads from jackfruit were assembled into 162,440 scaffolds totaling 982 Mb with 35,858 genes. Similarly, the breadfruit reads were assembled into 180,971 scaffolds totaling 833 Mb with 34,010 genes. A total of 2822 and 2034 expanded gene families were found in jackfruit and breadfruit, respectively, enriched in pathways including starch and sucrose metabolism, photosynthesis, and others. The copy number of several starch synthesis-related genes were found to be increased in jackfruit and breadfruit compared to closely-related species, and the tissue-specific expression might imply their sugar-rich and starch-rich characteristics. Overall, the publication of high-quality genomes for jackfruit and breadfruit provides information about their specific composition and the underlying genes involved in sugar and starch metabolism.}, }
@article {pmid31873774, year = {2020}, author = {Velasco-González, I and Sanchez-Jimenez, A and Singer, D and Murciano, A and Díez-Hermano, S and Lara, E and Martín-Cereceda, M}, title = {Correction to: Rain-Fed Granite Rock Basins Accumulate a High Diversity of Dormant Microbial Eukaryotes.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {248}, doi = {10.1007/s00248-019-01478-5}, pmid = {31873774}, issn = {1432-184X}, abstract = {The original version of this article contained an erratum of omission in the Acknowledgments section.}, }
@article {pmid31873773, year = {2020}, author = {Poret-Peterson, AT and Sayed, N and Glyzewski, N and Forbes, H and González-Orta, ET and Kluepfel, DA}, title = {Temporal Responses of Microbial Communities to Anaerobic Soil Disinfestation.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {191-201}, pmid = {31873773}, issn = {1432-184X}, support = {2032-22000-016-00D//Agricultural Research Service/ ; }, mesh = {Anaerobiosis ; Carbon/analysis ; *Disinfection ; Microbiota/*drug effects ; Soil/*chemistry ; *Soil Microbiology ; Time Factors ; }, abstract = {Anaerobic soil disinfestation (ASD) is an organic amendment-based management tool for controlling soil-borne plant diseases and is increasingly used in a variety of crops. ASD results in a marked decrease in soil redox potential and other physicochemical changes, and a turnover in the composition of the soil microbiome. Mechanisms of ASD-mediated pathogen control are not fully understood, but appear to depend on the carbon source used to initiate the process and involve a combination of biological (i.e., release of volatile organic compounds) and abiotic (i.e., lowered pH, release of metal ions) factors. In this study, we examined how the soil microbiome changes over time in response to ASD initiated with rice bran, tomato pomace, or red grape pomace as amendments using growth chamber mesocosms that replicate ASD-induced field soil redox conditions. Within 2 days, the soil microbiome rapidly shifted from a diverse assemblage of taxa to being dominated by members of the Firmicutes for all ASD treatments, whereas control mesocosms maintained diverse and more evenly distributed communities. Rice bran and tomato pomace amendments resulted in microbial communities with similar compositions and trajectories that were different from red grape pomace communities. Quantitative PCR showed nitrogenase gene abundances were higher in ASD communities and tended to increase over time, suggesting the potential for altering soil nitrogen availability. These results highlight the need for temporal and functional studies to understand how pathogen suppressive microbial communities assemble and function in ASD-treated soils.}, }
@article {pmid31872949, year = {2020}, author = {Harrison, JG and Calder, WJ and Shastry, V and Buerkle, CA}, title = {Dirichlet-multinomial modelling outperforms alternatives for analysis of microbiome and other ecological count data.}, journal = {Molecular ecology resources}, volume = {20}, number = {2}, pages = {481-497}, doi = {10.1111/1755-0998.13128}, pmid = {31872949}, issn = {1755-0998}, support = {EPS-1655726//National Science Foundation/ ; //University of Wyoming/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Bacterial Proteins/genetics ; Humans ; Lung/microbiology ; *Microbiota ; *Models, Statistical ; Monte Carlo Method ; }, abstract = {Molecular ecology regularly requires the analysis of count data that reflect the relative abundance of features of a composition (e.g., taxa in a community, gene transcripts in a tissue). The sampling process that generates these data can be modelled using the multinomial distribution. Replicate multinomial samples inform the relative abundances of features in an underlying Dirichlet distribution. These distributions together form a hierarchical model for relative abundances among replicates and sampling groups. This type of Dirichlet-multinomial modelling (DMM) has been described previously, but its benefits and limitations are largely untested. With simulated data, we quantified the ability of DMM to detect differences in proportions between treatment and control groups, and compared the efficacy of three computational methods to implement DMM-Hamiltonian Monte Carlo (HMC), variational inference (VI), and Gibbs Markov chain Monte Carlo. We report that DMM was better able to detect shifts in relative abundances than analogous analytical tools, while identifying an acceptably low number of false positives. Among methods for implementing DMM, HMC provided the most accurate estimates of relative abundances, and VI was the most computationally efficient. The sensitivity of DMM was exemplified through analysis of previously published data describing lung microbiomes. We report that DMM identified several potentially pathogenic, bacterial taxa as more abundant in the lungs of children who aspirated foreign material during swallowing; these differences went undetected with different statistical approaches. Our results suggest that DMM has strong potential as a statistical method to guide inference in molecular ecology.}, }
@article {pmid31872380, year = {2019}, author = {Mohr, T and Aliyu, H and Biebinger, L and Gödert, R and Hornberger, A and Cowan, D and de Maayer, P and Neumann, A}, title = {Effects of different operating parameters on hydrogen production by Parageobacillus thermoglucosidasius DSM 6285.}, journal = {AMB Express}, volume = {9}, number = {1}, pages = {207}, pmid = {31872380}, issn = {2191-0855}, support = {031B0180//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 109137//National Research Foundation/ ; }, abstract = {Hydrogen gas represents a promising alternative energy source to dwindling fossil fuel reserves, as it carries the highest energy per unit mass and its combustion results in the release of water vapour as only byproduct. The facultatively anaerobic thermophile Parageobacillus thermoglucosidasius is able to produce hydrogen via the water-gas shift reaction catalyzed by a carbon monoxide dehydrogenase-hydrogenase enzyme complex. Here we have evaluated the effects of several operating parameters on hydrogen production, including different growth temperatures, pre-culture ages and inoculum sizes, as well as different pHs and concentrations of nickel and iron in the fermentation medium. All of the tested parameters were observed to have a substantive effect on both hydrogen yield and (specific) production rates. A final experiment incorporating the best scenario for each tested parameter showed a marked increase in the H2 production rate compared to each individual parameter. The optimised parameters serve as a strong basis for improved hydrogen production with a view of commercialisation of this process.}, }
@article {pmid31870202, year = {2020}, author = {Erber, AC and Cetin, H and Berry, D and Schernhammer, ES}, title = {The role of gut microbiota, butyrate and proton pump inhibitors in amyotrophic lateral sclerosis: a systematic review.}, journal = {The International journal of neuroscience}, volume = {130}, number = {7}, pages = {727-735}, doi = {10.1080/00207454.2019.1702549}, pmid = {31870202}, issn = {1563-5279}, mesh = {*Amyotrophic Lateral Sclerosis/drug therapy/metabolism/microbiology ; Animals ; Butyrates/*metabolism ; Disease Progression ; Gastrointestinal Microbiome/*physiology ; Humans ; Proton Pump Inhibitors/*therapeutic use ; }, abstract = {Aim of the study: We conducted a systematic review on existing literature in humans and animals, linking the gut microbiome with amyotrophic lateral sclerosis (ALS). Additionally, we sought to explore the role of the bacterially produced metabolite butyrate as well as of proton pump inhibitors (PPIs) in these associations.Materials and methods: Following PRISMA guidelines for systematic literature reviews, four databases (Medline, Scopus, Embase and Web of Science) were searched and screened by two independent reviewers against defined inclusion criteria. Six studies in humans and six animal studies were identified, summarized and reviewed.Results: Overall, the evidence accrued to date is supportive of changes in the gut microbiome being associated with ALS risk, and potentially progression, though observational studies are small (describing a total of 145 patients with ALS across all published studies), and not entirely conclusive.Conclusions: With emerging studies beginning to apply metagenome sequencing, more clarity regarding the importance and promise of the gut microbiome in ALS can be expected. Future studies may also help establish the therapeutic potential of butyrate, and the role of PPIs in these associations.}, }
@article {pmid31867834, year = {2020}, author = {Kuenen, JG}, title = {Anammox and beyond.}, journal = {Environmental microbiology}, volume = {22}, number = {2}, pages = {525-536}, doi = {10.1111/1462-2920.14904}, pmid = {31867834}, issn = {1462-2920}, mesh = {Ammonium Compounds/*metabolism ; Anaerobiosis ; Bacteria/*metabolism ; Bioreactors/*microbiology ; Environmental Microbiology ; Hydrazines/metabolism ; Nitrates/metabolism ; Nitrites/metabolism ; Nitrogen/metabolism ; Nitrogen Cycle/*physiology ; Organelles/metabolism ; Oxidation-Reduction ; Sulfur/metabolism ; Wastewater/microbiology ; }, abstract = {When looking back and wonder how we did it, I became even more aware of how my wanderings in microbiology are all linked, from the start of my PhD with Hans Veldkamp on sulphur-oxidizing bacteria in chemostats. My interests broadened from obligate chemolithoautotrophic bacteria to facultative organisms and the question about the ecological niches of these different metabolic types. The sulphide oxidizing bacteria also may be used to produce elemental sulphur, which can easily be removed from wastewater. This fitted in a long-standing collaboration with Dimitry Sorokin on the ecophysiology and application of alkaliphilic sulphur bacteria. Then came the denitrifying sulphur-oxidizing bacteria and their application to remove sulphide from wastewater, which lead to our interest in nitrate, nitrite and ammonium removal in general. The big surprise was the serendipitous discovery of the 'anammox'-process, whereby ammonium is anaerobically oxidized to dinitrogen gas with nitrite as electron acceptor. The early days of our anammox research are the main focus of this article, which describes the struggle of growing and identifying the most peculiar bacteria we ever came across. A specialized organelle, the anammoxosome was shown to be responsible for the key ammonium oxidation, whereby a rocket fuel, hydrazine, turned out to be an intermediate. Soon after we became aware that anammox is everywhere and in the marine environment makes up a major portion of the nitrogen cycle. The intense scientific collaboration with Mike Jetten and Mark van Loosdrecht and colleagues led to our further understanding and application of this fascinating process, which is briefly summarized in this article. My broader interest in environmental microbiology and microbial ecology has been a regularly returning theme, taking me all over the world to great collaborations lasting to this very day.}, }
@article {pmid31867463, year = {2019}, author = {Oliveira, M and Rodrigues, CM and Teixeira, P}, title = {Microbiological quality of raw berries and their products: A focus on foodborne pathogens.}, journal = {Heliyon}, volume = {5}, number = {12}, pages = {e02992}, pmid = {31867463}, issn = {2405-8440}, abstract = {Berry samples (n = 316; strawberries, raspberries, blackberries and blueberries) obtained from a fruit processing plant were examined regarding bacteriological quality and their potential public health risk. Three types of berry products were analysed including raw material, product from the mixing step and final product. Escherichia coli, Salmonella spp., Listeria monocytogenes, Bacillus cereus, sulphite-reducing clostridia spores and coagulase-positive staphylococci were the parameters investigated. Salmonella enterica serovar Braenderup and L. monocytogenes were isolated from one fruit sample of raw material each. Two samples harboured E. coli between 0.7 and 0.9 log cfu g[-1], not exceeding the hygienic criteria. Coagulase-positive staphylococci were not detected in the studied samples; however, coagulase-negative staphylococci (CNS) were isolated from a small proportion of samples mainly raspberries. Presumptive B. cereus were isolated from a relatively large proportion of the samples, raspberries and blackberries being the most contaminated fruits. The absence of pathogenic microorganisms in the final product as well as the low prevalence of presumptive B. cereus and CNS indicates proper implementation of good manufacturing and hygiene practices (GMPs/GHPs) by the food industry. Nevertheless, the results indicate that the raw material examined may contain pathogenic bacteria and thereby represent a risk to consumers regarding the manifestation of foodborne diseases.}, }
@article {pmid31866955, year = {2019}, author = {Li, Z and Yao, Q and Guo, X and Crits-Christoph, A and Mayes, MA and Hervey, WJ and Lebeis, SL and Banfield, JF and Hurst, GB and Hettich, RL and Pan, C}, title = {Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using [13]CO2 and [13]C-Methanol.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2706}, pmid = {31866955}, issn = {1664-302X}, abstract = {Stable isotope probing (SIP) enables tracking the nutrient flows from isotopically labeled substrates to specific microorganisms in microbial communities. In proteomic SIP, labeled proteins synthesized by the microbial consumers of labeled substrates are identified with a shotgun proteomics approach. Here, proteomic SIP was combined with targeted metagenomic binning to reconstruct metagenome-assembled genomes (MAGs) of the microorganisms producing labeled proteins. This approach was used to track carbon flows from [13]CO2 to the rhizosphere communities of Zea mays, Triticum aestivum, and Arabidopsis thaliana. Rhizosphere microorganisms that assimilated plant-derived [13]C were capable of metabolic and signaling interactions with their plant hosts, as shown by their MAGs containing genes for phytohormone modulation, quorum sensing, and transport and metabolism of nutrients typical of those found in root exudates. XoxF-type methanol dehydrogenases were among the most abundant proteins identified in the rhizosphere metaproteomes. [13]C-methanol proteomic SIP was used to test the hypothesis that XoxF was used to metabolize and assimilate methanol in the rhizosphere. We detected 7 [13]C-labeled XoxF proteins and identified methylotrophic pathways in the MAGs of 8 [13]C-labeled microorganisms, which supported the hypothesis. These two studies demonstrated the capability of proteomic SIP for functional characterization of active microorganisms in complex microbial communities.}, }
@article {pmid31863131, year = {2020}, author = {Wang, ZB and Sun, YY and Li, Y and Chen, XL and Wang, P and Ding, HT and Chen, B and Zhang, XY and Song, XY and Wang, M and McMinn, A and Zhang, YZ and Qin, QL}, title = {Significant Bacterial Distance-Decay Relationship in Continuous, Well-Connected Southern Ocean Surface Water.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {73-80}, doi = {10.1007/s00248-019-01472-x}, pmid = {31863131}, issn = {1432-184X}, support = {2018YFC1406706//National Key R&amp;D Program of China/ ; U1706207//National Science Foundation of China/ ; 2017ASTCP-OS14//AoShan Talents Cultivation Program/ ; 2009TS079//Taishan Scholars Program of Shandong Province/ ; 2016WLJH36//Young Scholars Program of Shandong University/ ; }, mesh = {Bacteria/*isolation &amp; purification ; Geography ; *Microbiota ; Oceans and Seas ; Seawater/*microbiology ; }, abstract = {Recently, an increasing number of studies have focused on the biogeographic distribution of marine microorganisms. However, the extent to which geographic distance can affect marine microbial communities is still unclear, especially for the microbial communities in well-connected surface seawaters. In this study, the bacterial community compositions of 21 surface seawater samples, that were distributed over a distance of 7800 km, were surveyed to investigate how bacterial community similarity changes with increasing geographical distance. Proteobacteria and Bacteroidetes were the dominant bacterial phyla, with Proteobacteria accounting for 52.6-92.5% and Bacteroidetes comprising 3.5-46.9% of the bacterial communities. A significant bacterial distance-decay relationship was observed in the well-connected Southern Ocean surface seawater. The number of pairwise shared operational taxonomic units (OTUs), and community similarities tended to decrease with increasing geographic distance. Calculation of the similarity indices with all, abundant or rare OTUs did not affect the observed distance-decay relationship. Spatial distance can largely explain the observed bacterial community variation. This study shows that even in well-connected surface waters, bacterial distance-decay patterns can be found as long as the geographical distance is great enough. The biogeographic patterns should then be present for marine microorganisms considering the large size and complexity of the marine ecosystem.}, }
@article {pmid31860060, year = {2020}, author = {Cavichiolli de Oliveira, N and Cônsoli, FL}, title = {Beyond host regulation: Changes in gut microbiome of permissive and non-permissive hosts following parasitization by the wasp Cotesia flavipes.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {2}, pages = {}, doi = {10.1093/femsec/fiz206}, pmid = {31860060}, issn = {1574-6941}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Host-Parasite Interactions/physiology ; Larva/classification/microbiology/parasitology ; Moths/classification/*microbiology/*parasitology/physiology ; Wasps/*physiology ; }, abstract = {Koinobiont parasitoids regulate the physiology of their hosts, possibly interfering with the host gut microbiota and ultimately impacting parasitoid development. We used the parasitoid Cotesia flavipes to investigate if the regulation of the host would also affect the host gut microbiota. We also wondered if the effects of parasitization on the gut microbiota would depend on the host-parasitoid association by testing the permissive Diatraea saccharalis and the non-permissive Spodoptera frugiperda hosts. We determined the structure and potential functional contribution of the gut microbiota of the fore-midgut and hindgut of the hosts at different stages of development of the immature parasitoid. The abundance and diversity of operational taxonomic units of the anteromedial (fore-midgut) gut and posterior (hindgut) region from larvae of the analyzed hosts were affected by parasitization. Changes in the gut microbiota induced by parasitization altered the potential functional contribution of the gut microbiota associated with both hosts. Our data also indicated that the mechanism by which C. flavipes interferes with the gut microbiota of the host does not require a host-parasitoid coevolutionary history. Changes observed in the potential contribution of the gut microbiota of parasitized hosts impact the host's nutritional quality, and could favor host exploitation by C. flavipes.}, }
@article {pmid31858913, year = {2021}, author = {Basilua, JM and Pochart, P}, title = {Cotrimoxazole Prophylaxis is Not Associated with a Higher Occurrence of Atazanavir Treatment Failure: Analysis of Worldwide Pharmacovigilance Data.}, journal = {Infectious disorders drug targets}, volume = {21}, number = {1}, pages = {55-59}, doi = {10.2174/1871526520666191220112416}, pmid = {31858913}, issn = {2212-3989}, mesh = {Africa ; *Anti-HIV Agents/therapeutic use ; Atazanavir Sulfate/therapeutic use ; *HIV Infections/drug therapy ; HIV Protease Inhibitors/*therapeutic use ; Humans ; Pharmacovigilance ; Ritonavir/therapeutic use ; Treatment Failure ; Trimethoprim, Sulfamethoxazole Drug Combination/*therapeutic use ; }, abstract = {UNLABELLED: [Background: Cotrimoxazole is the main antibiotic used in HIV-infected patients for the prophylaxis of opportunistic infections. This antibiotic is prescribed in patients receiving antiretroviral agents (ART) such as Atazanavir (ATV), a protease inhibitor used with other ART classes. The objective of this study was to compare HIV treatment failure (HIVTF) in HIV-infected patients treated concomitantly with ATV and cotrimoxazole to those of patients treated only with ATV.<br><br>MATERIALS AND METHODS: This is a comparative analysis of the safety data of HIVTF available with ATV in the WHO International Pharmacovigilance database "VigiBase&#xae;". We used the SMQ (Standardized MedDRA Querie) to identify all the terms corresponding to HIVTF. We presented results as a percentage or an adjusted Reporting Odds Ratio (aROR) with a 95% confidence interval (95% CI).<br><br>RESULTS: A total of 116 cases of HIVTF (2.2%) were reported with ATV among the 5196 individual case safety reports (ICSR) included in the analysis. The proportion of HIV-infected patients who presented ATV treatment failure (ATVTF) was lower (2.6%, 3/116) when cotrimoxazole was concomitant (aROR was 0.5 with a 95%CI from 0.2 to 1.7). Only 10 of 273 ICSRs (3.7%) were reported from Africa concerning the use of cotrimoxazole prophylaxis concomitantly with ATV.<br><br>CONCLUSION: This study did not show a higher occurrence of ATVTF when cotrimoxazole was concomitant. These results reinforce the place of concomitant use of ATV with cotrimoxazole in the management of HIV treatment.}, }
@article {pmid31854329, year = {2019}, author = {Hewson, I}, title = {Technical pitfalls that bias comparative microbial community analyses of aquatic disease Ian Hewson.}, journal = {Diseases of aquatic organisms}, volume = {137}, number = {2}, pages = {109-124}, doi = {10.3354/dao03432}, pmid = {31854329}, issn = {0177-5103}, mesh = {Animals ; Bias ; *Microbiota ; }, abstract = {The accessibility of high-throughput DNA sequencing technologies has attracted the application of comparative microbial analyses to study diseases. These studies present a window into host microbiome diversity and composition that can be used to address ecological theory in the context of host biology and behavior. Recently, comparative microbiome studies have been used to study non-vertebrate aquatic diseases to elucidate microorganisms potentially involved in disease processes or in disease prevention. These investigations suffer from many well-described biases, especially prior to sequence analyses, that could lead to misleading conclusions. Microbiome-focused studies of aquatic metazoan diseases provide valuable documentation of microbial ecology, although, they are only a starting point for establishing disease etiology, which demands quantitative validation through targeted approaches. The microbiome approach to understanding disease is most useful after laboratory diagnostics guided by pathology have failed to identify a causative agent. This opinion piece presents several technical pitfalls which may affect wider interpretation of microbe-host interactions through comparative microbial community analyses and provides recommendations, based on studies in non-aquatic systems, for incorporation into future aquatic disease research.}, }
@article {pmid31853069, year = {2020}, author = {Zhang, L and Chen, F and Zhang, X and Li, Z and Zhao, Y and Lohaus, R and Chang, X and Dong, W and Ho, SYW and Liu, X and Song, A and Chen, J and Guo, W and Wang, Z and Zhuang, Y and Wang, H and Chen, X and Hu, J and Liu, Y and Qin, Y and Wang, K and Dong, S and Liu, Y and Zhang, S and Yu, X and Wu, Q and Wang, L and Yan, X and Jiao, Y and Kong, H and Zhou, X and Yu, C and Chen, Y and Li, F and Wang, J and Chen, W and Chen, X and Jia, Q and Zhang, C and Jiang, Y and Zhang, W and Liu, G and Fu, J and Chen, F and Ma, H and Van de Peer, Y and Tang, H}, title = {The water lily genome and the early evolution of flowering plants.}, journal = {Nature}, volume = {577}, number = {7788}, pages = {79-84}, pmid = {31853069}, issn = {1476-4687}, support = {/ERC_/European Research Council/International ; }, mesh = {Flowers/genetics/metabolism ; *Genome, Plant ; Nymphaea/*genetics/metabolism ; Odorants/analysis ; *Phylogeny ; }, abstract = {Water lilies belong to the angiosperm order Nymphaeales. Amborellales, Nymphaeales and Austrobaileyales together form the so-called ANA-grade of angiosperms, which are extant representatives of lineages that diverged the earliest from the lineage leading to the extant mesangiosperms[1-3]. Here we report the 409-megabase genome sequence of the blue-petal water lily (Nymphaea colorata). Our phylogenomic analyses support Amborellales and Nymphaeales as successive sister lineages to all other extant angiosperms. The N. colorata genome and 19 other water lily transcriptomes reveal a Nymphaealean whole-genome duplication event, which is shared by Nymphaeaceae and possibly Cabombaceae. Among the genes retained from this whole-genome duplication are homologues of genes that regulate flowering transition and flower development. The broad expression of homologues of floral ABCE genes in N. colorata might support a similarly broadly active ancestral ABCE model of floral organ determination in early angiosperms. Water lilies have evolved attractive floral scents and colours, which are features shared with mesangiosperms, and we identified their putative biosynthetic genes in N. colorata. The chemical compounds and biosynthetic genes behind floral scents suggest that they have evolved in parallel to those in mesangiosperms. Because of its unique phylogenetic position, the N. colorata genome sheds light on the early evolution of angiosperms.}, }
@article {pmid31849864, year = {2019}, author = {Bains, M and Laney, C and Wolfe, AE and Orr, M and Waschek, JA and Ericsson, AC and Dorsam, GP}, title = {Vasoactive Intestinal Peptide Deficiency Is Associated With Altered Gut Microbiota Communities in Male and Female C57BL/6 Mice.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2689}, pmid = {31849864}, issn = {1664-302X}, support = {K01 OD019924/OD/NIH HHS/United States ; P20 GM109024/GM/NIGMS NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; }, abstract = {Vasoactive intestinal peptide (VIP) is crucial for gastrointestinal tract (GIT) health. VIP sustains GIT homeostasis through maintenance of the intestinal epithelial barrier and acts as a potent anti-inflammatory mediator that contributes to gut bacterial tolerance. Based on these biological functions by VIP, we hypothesized that its deficiency would alter gut microbial ecology. To this end, fecal samples from male and female VIP[+/+], VIP[+/-], and VIP[-/-] littermates (n = 47) were collected and 16S rRNA sequencing was conducted. Our data revealed significant changes in bacterial composition, biodiversity, and weight loss from VIP[-/-] mice compared to VIP[+/+] and VIP[+/-] littermates, irrespective of sex. The gut bacteria compositional changes observed in VIP[-/-] mice was consistent with gut microbial structure changes reported for certain inflammatory and autoimmune disorders. Moreover, predicted functional changes by PICRUSt software suggested an energy surplus within the altered microbiota from VIP[-/-] mice. These data support that VIP plays an important role in maintaining microbiota balance, biodiversity, and GIT function, and its genetic removal results in significant gut microbiota restructuring and weight loss.}, }
@article {pmid31849848, year = {2019}, author = {Madigan, AP and Egidi, E and Bedon, F and Franks, AE and Plummer, KM}, title = {Bacterial and Fungal Communities Are Differentially Modified by Melatonin in Agricultural Soils Under Abiotic Stress.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2616}, pmid = {31849848}, issn = {1664-302X}, abstract = {An extensive body of evidence from the last decade has indicated that melatonin enhances plant resistance to a range of biotic and abiotic stressors. This has led to an interest in the application of melatonin in agriculture to reduce negative physiological effects from environmental stresses that affect yield and crop quality. However, there are no reports regarding the effects of melatonin on soil microbial communities under abiotic stress, despite the importance of microbes for plant root health and function. Three agricultural soils associated with different land usage histories (pasture, canola or wheat) were placed under abiotic stress by cadmium (100 or 280 mg kg[-1] soil) or salt (4 or 7 g kg[-1] soil) and treated with melatonin (0.2 and 4 mg kg[-1] soil). Automated Ribosomal Intergenic Spacer Analysis (ARISA) was used to generate Operational Taxonomic Units (OTU) for microbial community analysis in each soil. Significant differences in richness (α diversity) and community structures (β diversity) were observed between bacterial and fungal assemblages across all three soils, demonstrating the effect of melatonin on soil microbial communities under abiotic stress. The analysis also indicated that the microbial response to melatonin is governed by the type of soil and history. The effects of melatonin on soil microbes need to be regarded in potential future agricultural applications.}, }
@article {pmid31848649, year = {2020}, author = {Somers, DJ and Strock, KE and Saros, JE}, title = {Environmental Controls on Microbial Diversity in Arctic Lakes of West Greenland.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {60-72}, doi = {10.1007/s00248-019-01474-9}, pmid = {31848649}, issn = {1432-184X}, support = {1203434//Arctic System Science program of the US National Science Foundation/ ; SFR161//Center for Sustainability Education at Dickinson College/ ; }, mesh = {Arctic Regions ; *Bacterial Physiological Phenomena ; *Ecosystem ; Greenland ; Lakes/*microbiology ; *Microbiota ; }, abstract = {We assessed the microbial community structure of six arctic lakes in West Greenland and investigated relationships to lake physical and chemical characteristics. Lakes from the ice sheet region exhibited the highest species richness, while inland and plateau lakes had lower observed taxonomical diversity. Lake habitat differentiation during summer stratification appeared to alter within lake microbial community composition in only a subset of lakes, while lake variability across regions was a consistent driver of microbial community composition in these arctic lakes. Principal coordinate analysis revealed differentiation of communities along two axes: each reflecting differences in morphometric (lake surface area), geographic (latitude and distance from the ice sheet), physical lake variables (water clarity), and lakewater chemistry (dissolved organic carbon [DOC], dissolved oxygen [DO], total nitrogen [TN], and conductivity). Understanding these relationships between environmental variables and microbial communities is especially important as heterotrophic microorganisms are key to organic matter decomposition, nutrient cycling, and carbon flow through nutrient poor aquatic environments in the Arctic.}, }
@article {pmid31846683, year = {2019}, author = {Moccia, KM and Lebeis, SL}, title = {Microbial Ecology: How to Fight the Establishment.}, journal = {Current biology : CB}, volume = {29}, number = {24}, pages = {R1320-R1323}, doi = {10.1016/j.cub.2019.10.067}, pmid = {31846683}, issn = {1879-0445}, mesh = {*Arabidopsis ; Microbial Consortia ; *Microbiota ; }, abstract = {Creating microbial consortia capable of consistently producing desired qualities requires a detailed understanding of community interactions. A new paper demonstrates the role of historical contingency in Arabidopsis thaliana leaf-microbiome formation using an adaptable experimental approach, which could be applied to other host organisms.}, }
@article {pmid31845419, year = {2020}, author = {Bakker, A and Siegel, JA and Mendell, MJ and Prussin, AJ and Marr, LC and Peccia, J}, title = {Bacterial and fungal ecology on air conditioning cooling coils is influenced by climate and building factors.}, journal = {Indoor air}, volume = {30}, number = {2}, pages = {326-334}, doi = {10.1111/ina.12632}, pmid = {31845419}, issn = {1600-0668}, mesh = {*Air Conditioning ; *Air Microbiology ; Air Pollution, Indoor/*analysis ; Climate ; Ecology ; *Environmental Monitoring ; Fungi/*growth &amp; development ; Microbiota ; }, abstract = {The presence of biofilms on the cooling coils of commercial air conditioning (AC) units can significantly reduce the heat transfer efficiency of the coils and may lead to the aerosolization of microbes into occupied spaces of a building. We investigated how climate and AC operation influence the ecology of microbial communities on AC coils. Forty large-scale commercial ACs were considered with representation from warm-humid and hot-dry climates. Both bacterial and fungal ecologies, including richness and taxa, on the cooling coil surfaces were significantly impacted by outdoor climate, through differences in dew point that result in increased moisture (condensate) on coils, and by the minimum efficiency reporting value (MERV 8 vs MERV 14) of building air filters. Based on targeted qPCR and sequence analysis, low efficiency upstream filters (MERV 8) were associated with a greater abundance of pathogenic bacteria and medically relevant fungi. As the implementation of air conditioning continues to grow worldwide, better understanding of the factors impacting microbial growth and ecology on cooling coils should enable more rational approaches for biofilm control and ultimately result in reduced energy consumption and healthier buildings.}, }
@article {pmid31844910, year = {2020}, author = {Bridier, A and Piard, JC and Briandet, R and Bouchez, T}, title = {Emergence of a Synergistic Diversity as a Response to Competition in Pseudomonas putida Biofilms.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {47-59}, doi = {10.1007/s00248-019-01470-z}, pmid = {31844910}, issn = {1432-184X}, support = {SYSCOMM project DISCO, ANR-09-SYSC-003//French National Research Agency (ANR)/ ; }, mesh = {Adaptation, Physiological ; *Biofilms ; *Microbial Interactions ; Pseudomonas putida/*physiology ; }, abstract = {Genetic diversification through the emergence of variants is one of the known mechanisms enabling the adaptation of bacterial communities. We focused in this work on the adaptation of the model strain Pseudomonas putida KT2440 in association with another P. putida strain (PCL1480) recently isolated from soil to investigate the potential role of bacterial interactions in the diversification process. On the basis of colony morphology, three variants of P. putida KT2440 were obtained from co-culture after 168 h of growth whereas no variant was identified from the axenic KT2440 biofilm. The variants exhibited distinct phenotypes and produced biofilms with specific architecture in comparison with the ancestor. The variants better competed with the P. putida PCL1480 strain in the dual-strain biofilms after 24 h of co-culture in comparison with the ancestor. Moreover, the synergistic interaction of KT2440 ancestor and the variants led to an improved biofilm production and to higher competitive ability versus the PCL1480 strain, highlighting the key role of diversification in the adaptation of P. putida KT2440 in the mixed community. Whole genome sequencing revealed mutations in polysaccharides biosynthesis protein, membrane transporter, or lipoprotein signal peptidase genes in variants.}, }
@article {pmid31844283, year = {2020}, author = {Wang, S and Li, L and Li, H and Sahu, SK and Wang, H and Xu, Y and Xian, W and Song, B and Liang, H and Cheng, S and Chang, Y and Song, Y and Çebi, Z and Wittek, S and Reder, T and Peterson, M and Yang, H and Wang, J and Melkonian, B and Van de Peer, Y and Xu, X and Wong, GK and Melkonian, M and Liu, H and Liu, X}, title = {Genomes of early-diverging streptophyte algae shed light on plant terrestrialization.}, journal = {Nature plants}, volume = {6}, number = {2}, pages = {95-106}, pmid = {31844283}, issn = {2055-0278}, mesh = {*Biological Evolution ; Chlorophyta/*genetics ; *Genome, Plant ; }, abstract = {Mounting evidence suggests that terrestrialization of plants started in streptophyte green algae, favoured by their dual existence in freshwater and subaerial/terrestrial environments. Here, we present the genomes of Mesostigma viride and Chlorokybus atmophyticus, two sister taxa in the earliest-diverging clade of streptophyte algae dwelling in freshwater and subaerial/terrestrial environments, respectively. We provide evidence that the common ancestor of M. viride and C. atmophyticus (and thus of streptophytes) had already developed traits associated with a subaerial/terrestrial environment, such as embryophyte-type photorespiration, canonical plant phytochrome, several phytohormones and transcription factors involved in responses to environmental stresses, and evolution of cellulose synthase and cellulose synthase-like genes characteristic of embryophytes. Both genomes differed markedly in genome size and structure, and in gene family composition, revealing their dynamic nature, presumably in response to adaptations to their contrasting environments. The ancestor of M. viride possibly lost several genomic traits associated with a subaerial/terrestrial environment following transition to a freshwater habitat.}, }
@article {pmid31838570, year = {2020}, author = {Li, XD and Chen, YH and Liu, C and Hong, J and Deng, H and Yu, DJ}, title = {Eutrophication and Related Antibiotic Resistance of Enterococci in the Minjiang River, China.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {1-13}, doi = {10.1007/s00248-019-01464-x}, pmid = {31838570}, issn = {1432-184X}, support = {2016YFD0501310//State Key Development Program during the 13th Five-Year Plan period of China/ ; 31272606//National Natural Science Foundation of China/ ; 31602106//National Natural Science Foundation of China/ ; 2017J01598//Natural Science Foundation of Fujian Province/ ; }, mesh = {Biological Oxygen Demand Analysis ; China ; *Drug Resistance, Microbial ; Enterococcus/*drug effects/isolation &amp; purification/physiology ; *Eutrophication ; Nitrogen/analysis ; Phosphorus/analysis ; Rivers/chemistry/*microbiology ; }, abstract = {Antimicrobial resistance (AMR) in the aquatic environment has received increasing attention in recent years, and growing eutrophication problems may contribute to AMR in aquatic ecosystems. To evaluate whether and how eutrophication affects AMR, 40 surface water samples were collected from the Minjiang River, Fujian Province, China. Total nitrogen (TN), total phosphorus (TP), and chemical oxygen demand (CODMn) were measured as eutrophication factors. Additionally, enterococci species were isolated and their resistance to six common antibiotics was tested. Eutrophication generally showed a trend of increasing with the flow direction of the Minjiang River, with 25 sites (62.5%) having a TN/TP value over the Redfield value (16:1), which indicated that eutrophication in this region was of phosphorus limitation. High nutrition sites were in or near urban areas. Poor quality water was found in the middle and lower reaches of the Minjiang River system. The resistance frequency of 40 enterococci isolates to the six antibiotics tested was as follows: oxytetracycline > erythromycin > ciprofloxacin > chloramphenicol > ampicillin > vancomycin (70, 50, 17.5, 12.5, 2.5, 0%), and the multi-resistant rate reached 50% with eight resistance phenotypes. AMR also increased along the direction of water flow downstream, and most of the sites with the highest AMR were in or near urban areas, as was true for nutrition levels. Positive correlations between AMR and eutrophication factors (TN, TP, and CODMn) were identified using the Pearson's correlation coefficient, and TN/TP generally was negatively related to AMR. These results indicated that eutrophication may induce or selective for resistance of water-borne pathogens to antibiotics, with a high resistance level and a wide resistance spectrum.}, }
@article {pmid31838363, year = {2020}, author = {Chun, SJ and Cui, Y and Lee, JJ and Choi, IC and Oh, HM and Ahn, CY}, title = {Network analysis reveals succession of Microcystis genotypes accompanying distinctive microbial modules with recurrent patterns.}, journal = {Water research}, volume = {170}, number = {}, pages = {115326}, doi = {10.1016/j.watres.2019.115326}, pmid = {31838363}, issn = {1879-2448}, mesh = {*Cyanobacteria ; Genotype ; *Microcystis ; RNA, Ribosomal, 16S ; Republic of Korea ; }, abstract = {Every member of the ecological community is connected via a network of vital and complex relationships, called the web of life. To elucidate the ecological network and interactions among producers, consumers, and decomposers in the Daechung Reservoir, Korea, during cyanobacterial harmful algal blooms (cyanoHAB), especially those involving Microcystis, we investigated the diversity and compositions of the cyanobacterial (16S rRNA gene), including the genotypes of Microcystis (cpcBA-IGS gene), non-cyanobacterial (16S), and eukaryotic (18S) communities through high-throughput sequencing. Microcystis blooms were divided into the Summer Major Bloom and Autumn Minor Bloom with different dominant genotypes of Microcystis. Network analysis demonstrated that the modules involved in the different phases of the Microcystis blooms were categorized into the Pre-Bloom, Bloom, Post-Bloom, and Non-Bloom Groups at all sampling stations. In addition, the non-cyanobacterial components of each Group were classified, while the same Group showed similarity across all stations, suggesting that Microcystis and other microbes were highly interdependent and organized into cyanoHAB-related module units. Importantly, the Microcystis genotype-based sub-network uncovered that Pirellula, Pseudanabaena, and Vampirovibrionales preferred to interact with specific Microcystis genotypes in the Summer Major Bloom than with other genotypes in the Autumn Minor Bloom, while the copepod Skistodiaptomus exhibited the opposite pattern. In conclusion, the transition patterns of cyanoHAB-related modules and their key components could be crucial in the succession of Microcystis genotypes and to enhance the understanding of microbial ecology in an aquatic environment.}, }
@article {pmid31838145, year = {2019}, author = {Mickalide, H and Kuehn, S}, title = {Higher-Order Interaction between Species Inhibits Bacterial Invasion of a Phototroph-Predator Microbial Community.}, journal = {Cell systems}, volume = {9}, number = {6}, pages = {521-533.e10}, doi = {10.1016/j.cels.2019.11.004}, pmid = {31838145}, issn = {2405-4720}, mesh = {Bacteria/metabolism/*pathogenicity ; Bacterial Physiological Phenomena ; Chlamydomonas reinhardtii/metabolism ; Ecology ; Escherichia coli/metabolism ; Microbiota/*physiology ; Population Dynamics ; Tetrahymena thermophila/metabolism ; }, abstract = {The composition of an ecosystem is thought to be important for determining its resistance to invasion. Studies of natural ecosystems, from plant to microbial communities, have found that more diverse communities are more resistant to invasion. In some cases, more diverse communities resist invasion by more completely consuming the resources necessary for the invader. We show that Escherichia coli can successfully invade cultures of the alga Chlamydomonas reinhardtii (phototroph) or the ciliate Tetrahymena thermophila (predator) but cannot invade a community where both are present. The invasion resistance of the algae-ciliate community arises from a higher-order interaction between species (interaction modification) that is unrelated to resource consumption. We show that the mode of this interaction is the algal inhibition of bacterial aggregation, which leaves bacteria vulnerable to predation. This mode requires both the algae and the ciliate to be present and provides an example of invasion resistance through an interaction modification.}, }
@article {pmid31837971, year = {2020}, author = {Böllmann, J and Martienssen, M}, title = {Comparison of different media for the detection of denitrifying and nitrate reducing bacteria in mesotrophic aquatic environments by the most probable number method.}, journal = {Journal of microbiological methods}, volume = {168}, number = {}, pages = {105808}, doi = {10.1016/j.mimet.2019.105808}, pmid = {31837971}, issn = {1872-8359}, mesh = {Bacteria/growth &amp; development/metabolism ; Culture Media/*chemistry ; *Denitrification ; Fresh Water/*microbiology ; *Microbial Consortia ; Nitrates/*metabolism ; Probability ; Statistics as Topic ; Wastewater/*microbiology ; Water Purification ; }, abstract = {The cultivation based characterization of microbial communities and the quantification of certain functional bacterial groups is still an essential part of microbiology and microbial ecology. For plate count methods meanwhile low strength media are recommended, since they cover a broader range of different species and result in higher counts compared to established high strength media. For liquid media, as they are used for most probable number (MPN) quantifications, comparisons between high and low strength media are rare. In this study we compare the performance of different high and low strength media for the MPN quantification of nitrate reducing and denitrifying bacteria in two different fresh water environments. We also calculated the cell specific turnover rates of several denitrifying cultures previously enriched in high and low strength media from three different fresh water environments and a waste water treatment plant. For fresh water samples, our results indicate that high strength media detect higher MPN of denitrifying bacteria and in equal MPN of nitrate reducing bacteria compared to low strength media, which is in contrary to plate count techniques. For sediment samples, high and low strength media performed equal. The cell specific turnover rate was independent from the enrichment media and the media of the performance test. The cause of the lower denitrifyer MPN in low strength media remains, however, unclear. The results are important for further MPN quantifications of bacteria in nutrient poor environments and for calculations of nitrogen turnover rates by kinetical models using the number of metabolic active cells as one parameter.}, }
@article {pmid31836929, year = {2020}, author = {Nyirabuhoro, P and Liu, M and Xiao, P and Liu, L and Yu, Z and Wang, L and Yang, J}, title = {Seasonal Variability of Conditionally Rare Taxa in the Water Column Bacterioplankton Community of Subtropical Reservoirs in China.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {14-26}, pmid = {31836929}, issn = {1432-184X}, support = {91851104//National Natural Science Foundation of China/ ; 31500372//National Natural Science Foundation of China/ ; KFJ-SW-YW036//Program of Field Station Alliance, Chinese Academy of Sciences/ ; 2019J02016//Natural Science Foundation of Fujian Province/ ; }, mesh = {Bacteria/*isolation &amp; purification ; Bacterial Physiological Phenomena ; China ; Lakes/*microbiology ; *Microbiota ; Plankton/*isolation &amp; purification ; Seasons ; Water Supply ; }, abstract = {Conditionally rare bacteria are ubiquitous and perhaps the most diverse of microbial lifeforms, but their temporal dynamics remain largely unknown. High-throughput and deep sequencing of the 16S rRNA gene has allowed us to identify and compare the conditionally rare taxa with other bacterioplankton subcommunities. In this study, we examined the effect of season, water depth, and ecological processes on the fluctuations of bacterial subcommunities (including abundant, conditionally rare, moderate, and rare taxa) from three subtropical reservoirs in China. We discovered that the conditionally rare taxa (CRT) made up 49.7 to 71.8% of the bacterioplankton community richness, and they accounted for 70.6 to 84.4% of the temporal changes in the community composition. Beta-diversity analysis revealed strong seasonal succession patterns among all bacterioplankton subcommunities, suggesting abundant, conditionally rare, moderate, and rare taxa subcommunities have comparable environmental sensitivity. The dominant phyla of CRT were Proteobacteria, Actinobacteria, and Bacteroidetes, whose variations were strongly correlated with environmental variables. Both deterministic and stochastic processes showed strong effect on bacterioplankton community assembly, with deterministic patterns more pronounced for CRT subcommunity. The difference in bacterial community composition was strongly linked with seasonal change rather than water depth. The seasonal patterns of CRT expand our understanding of underlying mechanisms for bacterial community structure and composition. This implies their importance in the function and stability of freshwater ecosystem after environmental disturbance.}, }
@article {pmid31836376, year = {2020}, author = {Ntagia, E and Fiset, E and Truong Cong Hong, L and Vaiopoulou, E and Rabaey, K}, title = {Electrochemical treatment of industrial sulfidic spent caustic streams for sulfide removal and caustic recovery.}, journal = {Journal of hazardous materials}, volume = {388}, number = {}, pages = {121770}, doi = {10.1016/j.jhazmat.2019.121770}, pmid = {31836376}, issn = {1873-3336}, abstract = {Alkaline spent caustic streams (SCS) produced in the petrochemical and chemical manufacturing industry, contain high concentrations of reactive sulfide (HS[-]) and caustic soda (NaOH). Common treatment methods entail high operational costs while not recovering the possible resources that SCS contain. Here we studied the electrochemical treatment of SCS from a chemical manufacturing industry in an electrolysis cell, aiming at anodic HS[-] removal and cathodic NaOH, devoid of sulfide, recovery. Using a synthetic SCS we first evaluated the HS[-] oxidation product distribution over time, as well as the HS[-] removal and the NaOH recovery, as a function of current density. In a second step, we investigated the operational aspects of such treatment for the industrial SCS, under 300 A m[-2] fixed current density. In an electrolysis cell receiving 205 ± 60 g S L[-1] d[-1] HS[-] over 20 days of continuous operation, HS[-] was removed with a 38.0 ± 7.7 % removal and ∼80 % coulombic efficiency, with a concomitant recovery of a ∼12 wt.% NaOH solution. The low cell voltage obtained (1.75 ± 0.12 V), resulted in low energy requirements of 3.7 ± 0.6 kW h kg[-1] S and 6.3 ± 0.4 kW h kg[-1] NaOH and suggests techno-economic viability of this process.}, }
@article {pmid31835452, year = {2019}, author = {Cancello, R and Turroni, S and Rampelli, S and Cattaldo, S and Candela, M and Cattani, L and Mai, S and Vietti, R and Scacchi, M and Brigidi, P and Invitti, C}, title = {Effect of Short-Term Dietary Intervention and Probiotic Mix Supplementation on the Gut Microbiota of Elderly Obese Women.}, journal = {Nutrients}, volume = {11}, number = {12}, pages = {}, pmid = {31835452}, issn = {2072-6643}, support = {RICCOR number: 2015_12_15_03//Ministero della Salute/ ; }, mesh = {Aged ; Aged, 80 and over ; Biodiversity ; Body Weight/drug effects ; *Diet, Mediterranean ; Dietary Supplements ; Dysbiosis/diet therapy ; Feces ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Male ; Obesity/*diet therapy/genetics/*microbiology ; Probiotics/*therapeutic use ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Accumulating literature is providing evidence that the gut microbiota is involved in metabolic disorders, but the question of how to effectively modulate it to restore homeostasis, especially in the elderly, is still under debate. In this study, we profiled the intestinal microbiota of 20 elderly obese women (EO) at the baseline (T0), after 15 days of hypocaloric Mediterranean diet administered as part of a nutritional-metabolic rehabilitation program for obesity (T1), and after a further 15 days of the same diet supplemented with a probiotic mix (T2). Fecal samples were characterized by Illumina MiSeq sequencing of the 16S rRNA gene. The EO microbiota showed the typical alterations found in obesity, namely, an increase in potential pro-inflammatory components (i.e., Collinsella) and a decrease in health-promoting, short-chain fatty acid producers (i.e., Lachnospiraceae and Ruminococcaceae members), with a tendency to reduced biodiversity. After 15 days of the rehabilitation program, weight decreased by (2.7 ± 1.5)% and the gut microbiota dysbiosis was partially reversed, with a decline of Collinsella and an increase in leanness-related taxa. During the next 15 days of diet and probiotics, weight dropped further by (1.2 ± 1.1)%, markers of oxidative stress improved, and Akkermansia, a mucin degrader with beneficial effects on host metabolism, increased significantly. These findings support the relevant role of a correct dietetic approach, even in the short term, to modulate the EO gut microbiota towards a metabolic health-related configuration, counteracting the increased risk of morbidity in these patients.}, }
@article {pmid31835036, year = {2019}, author = {Pachiadaki, MG and Brown, JM and Brown, J and Bezuidt, O and Berube, PM and Biller, SJ and Poulton, NJ and Burkart, MD and La Clair, JJ and Chisholm, SW and Stepanauskas, R}, title = {Charting the Complexity of the Marine Microbiome through Single-Cell Genomics.}, journal = {Cell}, volume = {179}, number = {7}, pages = {1623-1635.e11}, pmid = {31835036}, issn = {1097-4172}, support = {R21 AI134037/AI/NIAID NIH HHS/United States ; }, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Energy Metabolism ; *Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeography ; Plankton ; Seawater/*microbiology ; Single-Cell Analysis/methods ; Transcriptome ; }, abstract = {Marine bacteria and archaea play key roles in global biogeochemistry. To improve our understanding of this complex microbiome, we employed single-cell genomics and a randomized, hypothesis-agnostic cell selection strategy to recover 12,715 partial genomes from the tropical and subtropical euphotic ocean. A substantial fraction of known prokaryoplankton coding potential was recovered from a single, 0.4 mL ocean sample, which indicates that genomic information disperses effectively across the globe. Yet, we found each genome to be unique, implying limited clonality within prokaryoplankton populations. Light harvesting and secondary metabolite biosynthetic pathways were numerous across lineages, highlighting the value of single-cell genomics to advance the identification of ecological roles and biotechnology potential of uncultured microbial groups. This genome collection enabled functional annotation and genus-level taxonomic assignments for >80% of individual metagenome reads from the tropical and subtropical surface ocean, thus offering a model to improve reference genome databases for complex microbiomes.}, }
@article {pmid31832698, year = {2020}, author = {Huang, CL and Sarkar, R and Hsu, TW and Yang, CF and Chien, CH and Chang, WC and Chiang, TY}, title = {Endophytic Microbiome of Biofuel Plant Miscanthus sinensis (Poaceae) Interacts with Environmental Gradients.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {133-144}, doi = {10.1007/s00248-019-01467-8}, pmid = {31832698}, issn = {1432-184X}, support = {106-2621-B-006-001-MY3//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Bacteria/classification/*isolation &amp; purification ; Biofuels ; Ecosystem ; *Ecotype ; *Endophytes ; Metagenomics ; *Microbiota ; Poaceae/*microbiology ; *Rhizosphere ; }, abstract = {Miscanthus in Taiwan occupies a cline along altitude and adapts to diverse environments, e.g., habitats of high salinity and volcanoes. Rhizospheric and endophytic bacteria may help Miscanthus acclimate to those stresses. The relative contributions of rhizosphere vs. endosphere compartments to the adaptation remain unknown. Here, we used targeted metagenomics to compare the microbial communities in the rhizosphere and endosphere among ecotypes of M. sinensis that dwell habitats under different stresses. Proteobacteria and Actinobacteria predominated in the endosphere. Diverse phyla constituted the rhizosphere microbiome, including a core microbiome found consistently across habitats. In endosphere, the predominance of the bacteria colonizing from the surrounding soil suggests that soil recruitment must have subsequently determined the endophytic microbiome in Miscanthus roots. In endosphere, the bacterial diversity decreased with the altitude, likely corresponding to rising limitation to microorganisms according to the species-energy theory. Specific endophytes were associated with different environmental stresses, e.g., Pseudomonas spp. for alpine and Agrobacterium spp. for coastal habitats. This suggests Miscanthus actively recruits an endosphere microbiome from the rhizosphere it influences.}, }
@article {pmid31831078, year = {2019}, author = {Ricci, F and Rossetto Marcelino, V and Blackall, LL and Kühl, M and Medina, M and Verbruggen, H}, title = {Beneath the surface: community assembly and functions of the coral skeleton microbiome.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {159}, pmid = {31831078}, issn = {2049-2618}, mesh = {Animals ; Anthozoa/*microbiology ; Archaea/classification ; Bacteria/classification ; Biodiversity ; *Coral Reefs ; Microbiota/*physiology ; }, abstract = {Coral microbial ecology is a burgeoning field, driven by the urgency of understanding coral health and slowing reef loss due to climate change. Coral resilience depends on its microbiota, and both the tissue and the underlying skeleton are home to a rich biodiversity of eukaryotic, bacterial and archaeal species that form an integral part of the coral holobiont. New techniques now enable detailed studies of the endolithic habitat, and our knowledge of the skeletal microbial community and its eco-physiology is increasing rapidly, with multiple lines of evidence for the importance of the skeletal microbiota in coral health and functioning. Here, we review the roles these organisms play in the holobiont, including nutritional exchanges with the coral host and decalcification of the host skeleton. Microbial metabolism causes steep physico-chemical gradients in the skeleton, creating micro-niches that, along with dispersal limitation and priority effects, define the fine-scale microbial community assembly. Coral bleaching causes drastic changes in the skeletal microbiome, which can mitigate bleaching effects and promote coral survival during stress periods, but may also have detrimental effects. Finally, we discuss the idea that the skeleton may function as a microbial reservoir that can promote recolonization of the tissue microbiome following dysbiosis and help the coral holobiont return to homeostasis.}, }
@article {pmid31828390, year = {2020}, author = {Vick, SHW and Greenfield, P and Willows, RD and Tetu, SG and Midgley, DJ and Paulsen, IT}, title = {Subsurface Stappia: Success Through Defence, Specialisation and Putative Pressure-Dependent Carbon Fixation.}, journal = {Microbial ecology}, volume = {80}, number = {1}, pages = {34-46}, doi = {10.1007/s00248-019-01471-y}, pmid = {31828390}, issn = {1432-184X}, mesh = {Biomass ; *Carbon Cycle ; Coal ; Fresh Water/*microbiology ; *Genome, Bacterial ; Geologic Sediments/*microbiology ; Mining ; New South Wales ; Queensland ; Rhodobacteraceae/genetics/isolation &amp; purification/*physiology ; Species Specificity ; }, abstract = {Diverse microbial communities living in subsurface coal seams are responsible for important geochemical processes including the movement of carbon between the geosphere, biosphere and atmosphere. Microbial conversion of the organic matter in coal to methane involves a complex assemblage of bacteria and archaea working in syntrophic relationships. Despite the importance and value of this microbial process, very few of the microbial taxa have defined metabolic or ecological roles in these environments. Additionally, the genomic features mediating life in this chemically reduced, energy poor, deep subsurface environment are not well characterised. Here we describe the isolation and genomic and catabolic characterisation of three alphaproteobacterial Stappia indica species from three coal basins across Australia. S. indica genomes from coal seams were compared with those from closely related S. indica isolated from diverse surface waters, revealing a coal seam-specific suite of genes associated with life in the subsurface. These genes are linked to processes including viral defence, secondary metabolite production, polyamine metabolism, polypeptide uptake membrane transporters and putative energy neutral pressure-dependent CO2 fixation. This indicates that subsurface Stappia have diverse metabolisms for biomass recycling and pressure-dependent CO2 fixation and require a suite of defensive and competitive strategies relative to their surface-dwelling relatives.}, }
@article {pmid31828389, year = {2020}, author = {Gnanasekaran, G and Lim, JY and Hwang, I}, title = {Disappearance of Quorum Sensing in Burkholderia glumae During Experimental Evolution.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {947-959}, doi = {10.1007/s00248-019-01445-0}, pmid = {31828389}, issn = {1432-184X}, support = {Grant 2010-0018280//National Research Foundation of Korea/ ; }, mesh = {*Biological Evolution ; Burkholderia/genetics/*physiology ; *Genome, Bacterial ; Mutation ; *Quorum Sensing ; Virulence Factors/physiology ; }, abstract = {The plant pathogen Burkholderia glumae uses quorum sensing (QS) that allows bacteria to share information and alter gene expression on the basis of cell density. The wild-type strain of B. glumae produces quorum-sensing signals (autoinducers) to detect their community and upregulate QS-dependent genes across the population for performing social and group behaviors. The model organism B. glumae was selected to investigate adaptation, estimate evolutionary parameters, and test diverse evolutionary hypotheses by using experimental evolution. The wild-type B. glumae virulent strain showed genotypic changes during regular subculture due to oxygen limitation. The laboratory-evolved clones failed to produce the signaling molecule of C8-HSL/C6-HSL for activation of the quorum-sensing system. Further, the laboratory-evolved clones failed to produce catalase and oxalate for protecting themselves from the toxic environment at stationary phase and phytotoxins (toxoflavin) for infecting rice grain, respectively. The laboratory-evolved clones were completely sequenced and compared with the wild-type. Sequencing analysis of the evolved clones revealed that mutations in QS-responsible genes (iclR), sensor genes (shk, mcp), and signaling genes (luxR) were responsible for quorum-sensing activity failure. The experimental results and sequencing analysis revealed quorum-sensing process failure in the laboratory-evolved clones. In conclusion, the wild-type B. glumae strain was often exposed to oxidative stress during regular subculture and evolved as an avirulent strain (quorum-sensing mutant) by losing the phenotypic and genotypic characteristics.}, }
@article {pmid31828388, year = {2020}, author = {Brambilla, S and Soto, G and Odorizzi, A and Arolfo, V and McCormick, W and Primo, E and Giordano, W and Jozefkowicz, C and Ayub, N}, title = {Spontaneous Mutations in the Nitrate Reductase Gene napC Drive the Emergence of Eco-friendly Low-N2O-Emitting Alfalfa Rhizobia in Regions with Different Climates.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {1044-1053}, doi = {10.1007/s00248-019-01473-w}, pmid = {31828388}, issn = {1432-184X}, support = {FVT-39//Fondo de Valorizaci&#xf3;n Tecnol&#xf3;gica/ ; PICT-2017-0674//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; }, mesh = {Amino Acid Sequence ; Argentina ; Bacterial Proteins/chemistry/*genetics/metabolism ; Base Sequence ; *Climate ; *Mutation ; Nitrate Reductases/chemistry/*genetics/metabolism ; Nitrous Oxide/*metabolism ; Phylogeny ; Sequence Alignment ; Sinorhizobium meliloti/genetics/*physiology ; }, abstract = {We have recently shown that commercial alfalfa inoculants (e.g., Sinorhizobium meliloti B399), which are closely related to the denitrifier model strain Sinorhizobium meliloti 1021, have conserved nitrate, nitrite, and nitric oxide reductases associated with the production of the greenhouse gas nitrous oxide (N2O) from nitrate but lost the N2O reductase related to the degradation of N2O to gas nitrogen. Here, we screened a library of nitrogen-fixing alfalfa symbionts originating from different ecoregions and containing N2O reductase genes and identified novel rhizobia (Sinorhizobium meliloti INTA1-6) exhibiting exceptionally low N2O emissions. To understand the genetic basis of this novel eco-friendly phenotype, we sequenced and analyzed the genomes of these strains, focusing on their denitrification genes, and found mutations only in the nitrate reductase structural gene napC. The evolutionary analysis supported that, in these natural strains, the denitrification genes were inherited by vertical transfer and that their defective nitrate reductase napC alleles emerged by independent spontaneous mutations. In silico analyses showed that mutations in this gene occurred in ssDNA loop structures with high negative free energy (-ΔG) and that the resulting mutated stem-loop structures exhibited increased stability, suggesting the occurrence of transcription-associated mutation events. In vivo assays supported that at least one of these ssDNA sites is a mutational hot spot under denitrification conditions. Similar benefits from nitrogen fixation were observed when plants were inoculated with the commercial inoculant B399 and strains INTA4-6, suggesting that the low-N2O-emitting rhizobia can be an ecological alternative to the current inoculants without resigning economic profitability.}, }
@article {pmid31827386, year = {2019}, author = {Zheng, P and Wang, C and Zhang, X and Gong, J}, title = {Community Structure and Abundance of Archaea in a Zostera marina Meadow: A Comparison between Seagrass-Colonized and Bare Sediment Sites.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2019}, number = {}, pages = {5108012}, pmid = {31827386}, issn = {1472-3654}, mesh = {Archaea/classification/genetics/*growth &amp; development/*isolation &amp; purification ; Biodiversity ; Genes, Archaeal ; Genes, rRNA ; Geologic Sediments/*microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Zosteraceae/*growth &amp; development ; }, abstract = {Seagrass colonization alters sediment physicochemical properties by depositing seagrass fibers and releasing organic carbon and oxygen from the roots. How this seagrass colonization-induced spatial heterogeneity affects archaeal community structure and abundance remains unclear. In this study, we investigated archaeal abundance, diversity, and composition in both vegetated and adjacent bare surface sediments of a Zostera marina meadow. High-throughput sequencing of 16S rDNA showed that Woesearchaeota, Bathyarchaeota, and Thaumarchaeota were the most abundant phyla across all samples, accounting for approximately 42%, 21%, and 17% of the total archaeal communities, respectively. In terms of relative abundance, Woesearchaeota and Bathyarchaeota were not significantly different between these two niches; however, specific subclades (Woese-3, Woese-21, Bathy-6, Bathy-18) were significantly enriched in vegetated sediments (P < 0.05), while Thaumarchaeota was favored in unvegetated sites (P = 0.02). The quantification of archaeal 16S rRNA genes showed that the absolute abundance of the whole archaeal community, Bathyarchaeota, and Woese-3, Woese-10, Woese-13, and Woese-21 was significantly more abundant in vegetated sediments than in bare sediments (P < 0.05). Our study expands the available knowledge of the distribution patterns and niche preferences of archaea in seagrass systems, especially for the different subclades of Woesearchaeota and Bathyarchaeota, in terms of both relative proportions and absolute quantities.}, }
@article {pmid31827245, year = {2020}, author = {Hiraoka, S and Hirai, M and Matsui, Y and Makabe, A and Minegishi, H and Tsuda, M and Juliarni,  and Rastelli, E and Danovaro, R and Corinaldesi, C and Kitahashi, T and Tasumi, E and Nishizawa, M and Takai, K and Nomaki, H and Nunoura, T}, title = {Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments.}, journal = {The ISME journal}, volume = {14}, number = {3}, pages = {740-756}, pmid = {31827245}, issn = {1751-7370}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Geologic Sediments/chemistry/*microbiology ; Japan ; *Microbiota ; Nitrates/metabolism ; Pacific Ocean ; }, abstract = {Hadal trench bottom (>6000 m below sea level) sediments harbor higher microbial cell abundance compared with adjacent abyssal plain sediments. This is supported by the accumulation of sedimentary organic matter (OM), facilitated by trench topography. However, the distribution of benthic microbes in different trench systems has not been well explored yet. Here, we carried out small subunit ribosomal RNA gene tag sequencing for 92 sediment subsamples of seven abyssal and seven hadal sediment cores collected from three trench regions in the northwest Pacific Ocean: the Japan, Izu-Ogasawara, and Mariana Trenches. Tag-sequencing analyses showed specific distribution patterns of several phyla associated with oxygen and nitrate. The community structure was distinct between abyssal and hadal sediments, following geographic locations and factors represented by sediment depth. Co-occurrence network revealed six potential prokaryotic consortia that covaried across regions. Our results further support that the OM cycle is driven by hadal currents and/or rapid burial shapes microbial community structures at trench bottom sites, in addition to vertical deposition from the surface ocean. Our trans-trench analysis highlights intra- and inter-trench distributions of microbial assemblages and geochemistry in surface seafloor sediments, providing novel insights into ultradeep-sea microbial ecology, one of the last frontiers on our planet.}, }
@article {pmid31826981, year = {2019}, author = {Klufa, J and Bauer, T and Hanson, B and Herbold, C and Starkl, P and Lichtenberger, B and Srutkova, D and Schulz, D and Vujic, I and Mohr, T and Rappersberger, K and Bodenmiller, B and Kozakova, H and Knapp, S and Loy, A and Sibilia, M}, title = {Hair eruption initiates and commensal skin microbiota aggravate adverse events of anti-EGFR therapy.}, journal = {Science translational medicine}, volume = {11}, number = {522}, pages = {}, doi = {10.1126/scitranslmed.aax2693}, pmid = {31826981}, issn = {1946-6242}, support = {I 2320/FWF_/Austrian Science Fund FWF/Austria ; P 27129/FWF_/Austrian Science Fund FWF/Austria ; P 31113/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Antineoplastic Agents/*adverse effects ; Epidermis/pathology ; ErbB Receptors/*antagonists &amp; inhibitors/deficiency ; Fibroblast Growth Factor 7/metabolism ; Hair/*pathology ; Humans ; Inflammation/pathology ; Keratinocytes/pathology ; MAP Kinase Signaling System ; Membrane Glycoproteins/metabolism ; Mice ; *Microbiota ; Nerve Tissue Proteins/metabolism ; Skin/*microbiology/pathology ; }, abstract = {Epidermal growth factor receptor (EGFR)-targeted anticancer therapy induces stigmatizing skin toxicities affecting patients' quality of life and therapy adherence. The lack of mechanistic details underlying these adverse events hampers their management. We found that EGFR/ERK signaling is required in LRIG1-positive stem cells during de novo hair eruption to secure barrier integrity and prevent the invasion of commensal microbiota and inflammatory skin disease. EGFR-deficient epidermis is permissive for microbiota outgrowth and displays an atopic-like TH2-dominated signature. The opening of the follicular ostia during hair eruption allows invasion of commensal microbiota into the hair follicle, initiating an additional TH1 and TH17 response culminating in chronic folliculitis. Restoration of epidermal ERK signaling via prophylactic FGF7 treatment or transgenic SOS expression rescues the barrier defect in the absence of EGFR, highlighting a therapeutic anchor point. These data reveal that commensal skin microbiota provoke atopic-like inflammatory skin diseases by invading into the follicular opening of erupting hair.}, }
@article {pmid31824766, year = {2019}, author = {Carruthers, LV and Moses, A and Adriko, M and Faust, CL and Tukahebwa, EM and Hall, LJ and Ranford-Cartwright, LC and Lamberton, PHL}, title = {The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e8133}, pmid = {31824766}, issn = {2167-8359}, support = {/WT_/Wellcome Trust/United Kingdom ; BBS/E/F/00044409/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {BACKGROUND: Multiple factors can influence stool sample integrity upon sample collection. Preservation of faecal samples for microbiome studies is therefore an important step, particularly in tropical regions where resources are limited and high temperatures may significantly influence microbiota profiles. Freezing is the accepted standard to preserve faecal samples however, cold chain methods are often unfeasible in fieldwork scenarios particularly in low and middle-income countries and alternatives are required. This study therefore aimed to address the impact of different preservative methods, time-to-freezing at ambient tropical temperatures, and stool heterogeneity on stool microbiome diversity and composition under real-life physical environments found in resource-limited fieldwork conditions.<br><br>METHODS: Inner and outer stool samples collected from one specimen obtained from three children were stored using different storage preservation methods (raw, ethanol and RNAlater) in a Ugandan field setting. Mixed stool was also stored using these techniques and frozen at different time-to-freezing intervals post-collection from 0-32 h. Metataxonomic profiling was used to profile samples, targeting the V1-V2 regions of 16S rRNA with samples run on a MiSeq platform. Reads were trimmed, combined and aligned to the Greengenes database. Microbial diversity and composition data were generated and analysed using Quantitative Insights Into Microbial Ecology and R software.<br><br>RESULTS: Child donor was the greatest predictor of microbiome variation between the stool samples, with all samples remaining identifiable to their child of origin despite the stool being stored under a variety of conditions. However, significant differences were observed in composition and diversity between preservation techniques, but intra-preservation technique variation was minimal for all preservation methods, and across the time-to-freezing range (0-32 h) used. Stool heterogeneity yielded no apparent microbiome differences.<br><br>CONCLUSIONS: Stool collected in a fieldwork setting for comparative microbiome analyses should ideally be stored as consistently as possible using the same preservation method throughout.}, }
@article {pmid31824462, year = {2019}, author = {Liu, D and Zhang, P and Chen, D and Howell, K}, title = {From the Vineyard to the Winery: How Microbial Ecology Drives Regional Distinctiveness of Wine.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2679}, pmid = {31824462}, issn = {1664-302X}, abstract = {Wine production is a complex process from the vineyard to the winery. On this journey, microbes play a decisive role. From the environment where the vines grow, encompassing soil, topography, weather and climate through to management practices in vineyards, the microbes present can potentially change the composition of wine. Introduction of grapes into the winery and the start of winemaking processes modify microbial communities further. Recent advances in next-generation sequencing (NGS) technology have progressed our understanding of microbial communities associated with grapes and fermentations. We now have a finer appreciation of microbial diversity across wine producing regions to begin to understand how diversity can contribute to wine quality and style characteristics. In this review, we highlight literature surrounding wine-related microorganisms and how these affect factors interact with and shape microbial communities and contribute to wine quality. By discussing the geography, climate and soil of environments and viticulture and winemaking practices, we claim microbial biogeography as a new perspective to impact wine quality and regionality. Depending on geospatial scales, habitats, and taxa, the microbial community respond to local conditions. We discuss the effect of a changing climate on local conditions and how this may alter microbial diversity and thus wine style. With increasing understanding of microbial diversity and their effects on wine fermentation, wine production can be optimised with enhancing the expression of regional characteristics by understanding and managing the microbes present.}, }
@article {pmid31823065, year = {2020}, author = {Schultz, J and Rosado, AS}, title = {Extreme environments: a source of biosurfactants for biotechnological applications.}, journal = {Extremophiles : life under extreme conditions}, volume = {24}, number = {2}, pages = {189-206}, pmid = {31823065}, issn = {1433-4909}, mesh = {Bacteria ; Biotechnology ; *Extreme Environments ; Petroleum ; Surface-Active Agents ; }, abstract = {The surfactant industry moves billions of dollars a year and consists of chemically synthesized molecules usually derived from petroleum. Surfactant is a versatile molecule that is widely used in different industrial areas, with an emphasis on the petroleum, biomedical and detergent industries. Recently, interest in environmentally friendly surfactants that are resistant to extreme conditions has increased because of consumers' appeal for sustainable products and industrial processes that often require these characteristics. With this context, the need arises to search for surfactants produced by microorganisms coming from extreme environments and to mine their unique biotechnological potential. The production of biosurfactants is still incipient and presents challenges regarding economic viability due to the high costs of cultivation, production, recovery and purification. Advances can be made by exploring the extreme biosphere and bioinformatics tools. This review focuses on biosurfactants produced by microorganisms from different extreme environments, presenting a complete overview of what information is available in the literature, including the advances, challenges and future perspectives, as well as showing the possible applications of extreme biosurfactants.}, }
@article {pmid31822601, year = {2019}, author = {Sogin, EM and Puskás, E and Dubilier, N and Liebeke, M}, title = {Marine Metabolomics: a Method for Nontargeted Measurement of Metabolites in Seawater by Gas Chromatography-Mass Spectrometry.}, journal = {mSystems}, volume = {4}, number = {6}, pages = {}, pmid = {31822601}, issn = {2379-5077}, abstract = {Microbial communities exchange molecules with their environment, which plays a major role in regulating global biogeochemical cycles and climate. While extracellular metabolites are commonly measured in terrestrial and limnic ecosystems, the presence of salt in marine habitats limits the nontargeted analyses of the ocean exometabolome using mass spectrometry (MS). Current methods require salt removal prior to sample measurements, which can alter the molecular composition of the metabolome and limit the types of compounds detected by MS. To overcome these limitations, we developed a gas chromatography MS (GC-MS) method that avoids sample altering during salt removal and that detects metabolites down to nanomolar concentrations from less than 1 ml of seawater. We applied our method (SeaMet) to explore marine metabolomes in vitro and in vivo First, we measured the production and consumption of metabolites during the culture of a heterotrophic bacterium, Marinobacter adhaerens Our approach revealed successional uptake of amino acids, while sugars were not consumed. These results show that exocellular metabolomics provides insights into nutrient uptake and energy conservation in marine microorganisms. We also applied SeaMet to explore the in situ metabolome of coral reef and mangrove sediment porewaters. Despite the fact that these ecosystems occur in nutrient-poor waters, we uncovered high concentrations of sugars and fatty acids, compounds predicted to play a key role for the abundant and diverse microbial communities in coral reef and mangrove sediments. Our data demonstrate that SeaMet advances marine metabolomics by enabling a nontargeted and quantitative analysis of marine metabolites, thus providing new insights into nutrient cycles in the oceans.IMPORTANCE Nontargeted approaches using metabolomics to analyze metabolites that occur in the oceans is less developed than those for terrestrial and limnic ecosystems. One of the challenges in marine metabolomics is that salt limits metabolite analysis in seawater to methods requiring salt removal. Building on previous sample preparation methods for metabolomics, we developed SeaMet, which overcomes the limitations of salt on metabolite detection. Considering that the oceans contain the largest dissolved organic matter pool on Earth, describing the marine metabolome using nontargeted approaches is critical for understanding the drivers behind element cycles, biotic interactions, ecosystem function, and atmospheric CO2 storage. Our method complements both targeted marine metabolomic investigations as well as other "omics" (e.g., genomics, transcriptomics, and proteomics) approaches by providing an avenue for studying the chemical interaction between marine microbes and their habitats.}, }
@article {pmid31821931, year = {2020}, author = {Sun, H and Mei, R and Zhang, XX and Ren, H and Liu, WT and Ye, L}, title = {Bacterial enrichment in highly-selective acetate-fed bioreactors and its application in rapid biofilm formation.}, journal = {Water research}, volume = {170}, number = {}, pages = {115359}, doi = {10.1016/j.watres.2019.115359}, pmid = {31821931}, issn = {1879-2448}, mesh = {Acetates ; Bacteria ; Biofilms ; *Bioreactors ; RNA, Ribosomal, 16S ; *Sewage ; Waste Disposal, Fluid ; }, abstract = {In this study, we systematically investigated the bacterial community dynamics in highly-selective (strong hydraulic selection pressure and high organic loading rate) bioreactors with acetate as the sole carbon source. 16S rRNA gene high-throughput sequencing and metagenomic sequencing results showed that phenolics-degrading bacteria (PDB), which were mainly Acinetobacter species, in the newly-formed aerobic granules could account for >70% of the total bacteria. Near full-length 16S rRNA gene sequences obtained by cloning suggest that the PDB are potentially novel species because they are distantly related to known Acinetobacter species. However, these PDB only temporarily appeared in the early stage of the granule formation and their abundance quickly decreased along the reactor operation. To retain these PDB, we demonstrated that the newly-formed aerobic granules could accelerate biofilm formation in moving bed biofilm reactors (MBBRs), and the biofilm carriers showed gradually-increased phenol degradation performance in the MBBRs. While, the bacterial community in biofilm significantly changed during the operation process of the MBBRs and the community structure became more complicated than that in the aerobic granules. Collectively, this study provides new insights into the microbial ecology of sludge granulation and biofilm formation process in the wastewater treatment systems for remediating phenolic matters.}, }
@article {pmid31820074, year = {2020}, author = {Tong, Q and Hu, ZF and Du, XP and Bie, J and Wang, HB}, title = {Effects of Seasonal Hibernation on the Similarities Between the Skin Microbiota and Gut Microbiota of an Amphibian (Rana dybowskii).}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {898-909}, doi = {10.1007/s00248-019-01466-9}, pmid = {31820074}, issn = {1432-184X}, mesh = {Animals ; China ; Female ; Gastrointestinal Microbiome ; Hibernation ; High-Throughput Nucleotide Sequencing ; Intestine, Large/*microbiology ; Intestine, Small/*microbiology ; Male ; *Microbiota ; Ranidae/*microbiology ; Seasons ; Sequence Analysis, DNA ; Skin/*microbiology ; }, abstract = {Both the gut and skin microbiotas have important functions for amphibians. The gut microbiota plays an important role in both the health and evolution of the host species, whereas the role of skin microbiota in disease resistance is particularly important for amphibians. Many studies have examined the effects of environmental factors on the skin and gut microbiotas, but no study has yet explored the similarities between the skin and gut microbiotas. In this study, the gut and skin microbiotas of Rana dybowskii in summer and winter were investigated via high-throughput Illumina sequencing. The results showed that the alpha diversity of gut and skin microbiotas decreased significantly from summer to winter. In both seasons, the microbial composition and structure differed significantly between the gut and skin, and the similarities between these microbiotas differed between seasons. The pairwise distances between the gut and skin microbiotas were greater in winter than in summer. The ratio of core OTUs and shared OTUs to the sum of the OTUs in the gut and skin microbiotas in summer was significantly higher than that in winter. The similarities between the gut and skin microbiotas are important for understanding amphibian ecology and life history.}, }
@article {pmid31820073, year = {2020}, author = {Arai, H and Lin, SR and Nakai, M and Kunimi, Y and Inoue, MN}, title = {Closely Related Male-Killing and Nonmale-Killing Wolbachia Strains in the Oriental Tea Tortrix Homona magnanima.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {1011-1020}, doi = {10.1007/s00248-019-01469-6}, pmid = {31820073}, issn = {1432-184X}, mesh = {Animals ; Insect Proteins/analysis ; Larva/genetics/growth &amp; development/microbiology ; Moths/genetics/growth &amp; development/*microbiology ; Phenotype ; Sex Factors ; Sex Ratio ; Symbiosis ; Taiwan ; Wolbachia/genetics/*physiology ; }, abstract = {Wolbachia are inherited intracellular bacteria that cause male-specific death in some arthropods, called male-killing. To date, three Wolbachia strains have been identified in the oriental tea tortrix Homona magnanima (Tortricidae, Lepidoptera); however, none of these caused male-killing in the Japanese population. Here, we describe a male-killing Wolbachia strain in Taiwanese H. magnanima. From field-collected H. magnanima, two female-biased host lines were established, and antibiotic treatments revealed Wolbachia (wHm-t) as the causative agent of male-killing. The wsp and MLST genes in wHm-t are identical to corresponding genes in the nonmale-killing strain wHm-c from the Japanese population, implying a close relationship of the two strains. Crossing the Japanese and Taiwanese H. magnanima revealed that Wolbachia genotype rather than the host genetic background was responsible for the presence of the male-killing phenotype. Quantitative PCR analyses revealed that the density of wHm-t was higher than that of other Wolbachia strains in H. magnanima, including wHm-c. The densities of wHm-t were also heterogeneous between host lines. Notably, wHm-t in the low-density and high-density lines carried identical wsp and MLST genes but had distinct lethal patterns. Furthermore, over 90% of field-collected lines of H. magnanima in Taiwan were infected with wHm-t, although not all host lines harboring wHm-t showed male-killing. The host lines that showed male-killing harbored a high density of Wolbachia compared to the host lines that did not show male-killing. Thus, the differences in the phenotypes appear to be dependent on biological and genetic characteristics of closely related Wolbachia strains.}, }
@article {pmid31820072, year = {2020}, author = {Basili, D and Lutfi, E and Falcinelli, S and Balbuena-Pecino, S and Navarro, I and Bertolucci, C and Capilla, E and Carnevali, O}, title = {Photoperiod Manipulation Affects Transcriptional Profile of Genes Related to Lipid Metabolism and Apoptosis in Zebrafish (Danio rerio) Larvae: Potential Roles of Gut Microbiota.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {933-946}, doi = {10.1007/s00248-019-01468-7}, pmid = {31820072}, issn = {1432-184X}, support = {AGL2014-57974-R//Ministerio de Econom&#xed;a y Competitividad/ ; AGL2017-89436-R//Ministerio de Econom&#xed;a y Competitividad/ ; FA2015//Universit&#xe0; Politecnica delle Marche/ ; FAR2018//Universit&#xe0; degli Studi di Ferrara/ ; FIR2018//Universit&#xe0; degli Studi di Ferrara/ ; }, mesh = {Animals ; *Apoptosis ; Circadian Rhythm ; Fish Proteins/metabolism ; Gastrointestinal Microbiome/*physiology ; *Lipid Metabolism ; *Photoperiod ; Probiotics/administration &amp; dosage ; Real-Time Polymerase Chain Reaction ; *Transcriptome ; Zebrafish/*microbiology/physiology ; }, abstract = {Gut microbiota plays a fundamental role in maintaining host's health by controlling a wide range of physiological processes. Administration of probiotics and manipulation of photoperiod have been suggested as modulators of microbial composition and are currently undergoing an extensive research in aquaculture as a way to improve health and quality of harvested fish. However, our understanding regarding their effects on physiological processes is still limited. In the present study we investigated whether manipulation of photoperiod and/or probiotic administration was able to alter microbial composition in zebrafish larvae at hatching stage. Our findings show that probiotic does not elicit effects while photoperiod manipulation has a significant impact on microbiota composition. Moreover, we successfully predicted lipid biosynthesis and apoptosis to be modulated by microbial communities undergoing continuous darkness. Interestingly, expression levels of caspase 3 gene (casp3) and lipid-related genes (hnf4a, npc1l1, pparγ, srebf1, agpat4 and fitm2) were found to be significantly overexpressed in dark-exposed larvae, suggesting an increase in the occurrence of apoptotic processes and a lipid metabolism impairment, respectively (p < 0.05). Our results provide the evidence that microbial communities in zebrafish at early life stages are not modulated by a short administration of probiotics and highlight the significant effect that dark photoperiod elicits on zebrafish microbiota and potentially on health.}, }
@article {pmid31819142, year = {2019}, author = {Costa, JH and Wassano, CI and Angolini, CFF and Scherlach, K and Hertweck, C and Pacheco Fill, T}, title = {Antifungal potential of secondary metabolites involved in the interaction between citrus pathogens.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {18647}, pmid = {31819142}, issn = {2045-2322}, mesh = {Antifungal Agents/metabolism ; Citrus/genetics/*growth &amp; development/parasitology ; Fruit/microbiology ; Fungal Proteins/*genetics/metabolism ; Fungi/drug effects/pathogenicity ; Fungicides, Industrial/pharmacology ; Mass Spectrometry ; Penicillium/*metabolism/pathogenicity ; Plant Diseases/genetics/*microbiology ; Spores, Fungal/metabolism ; }, abstract = {Numerous postharvest diseases have been reported that cause substantial losses of citrus fruits worldwide. Penicillium digitatum is responsible for up to 90% of production losses, and represent a problem for worldwide economy. In order to control phytopathogens, chemical fungicides have been extensively used. Yet, the use of some artificial fungicides cause concerns about environmental risks and fungal resistance. Therefore, studies focusing on new approaches, such as the use of natural products, are getting attention. Co-culture strategy can be applied to discover new bioactive compounds and to understand microbial ecology. Mass Spectrometry Imaging (MSI) was used to screen for potential antifungal metabolites involved in the interaction between Penicillium digitatum and Penicillium citrinum. MSI revealed a chemical warfare between the fungi: two tetrapeptides, deoxycitrinadin A, citrinadin A, chrysogenamide A and tryptoquialanines are produced in the fungi confrontation zone. Antimicrobial assays confirmed the antifungal activity of the investigated metabolites. Also, tryptoquialanines inhibited sporulation of P. citrinum. The fungal metabolites reported here were never described as antimicrobials until this date, demonstrating that co-cultures involving phytopathogens that compete for the same host is a positive strategy to discover new antifungal agents. However, the use of these natural products on the environment, as a safer strategy, needs further investigation. This paper aimed to contribute to the protection of agriculture, considering health and ecological risks.}, }
@article {pmid31817158, year = {2019}, author = {D'Amico, F and Biagi, E and Rampelli, S and Fiori, J and Zama, D and Soverini, M and Barone, M and Leardini, D and Muratore, E and Prete, A and Gotti, R and Pession, A and Masetti, R and Brigidi, P and Turroni, S and Candela, M}, title = {Enteral Nutrition in Pediatric Patients Undergoing Hematopoietic SCT Promotes the Recovery of Gut Microbiome Homeostasis.}, journal = {Nutrients}, volume = {11}, number = {12}, pages = {}, pmid = {31817158}, issn = {2072-6643}, support = {GR-2013-02357136//Ministero della Salute/ ; }, mesh = {Child ; *Enteral Nutrition ; Fatty Acids, Volatile/analysis/metabolism ; Feces/chemistry ; *Gastrointestinal Microbiome/genetics ; Graft vs Host Disease/prevention &amp; control ; *Hematopoietic Stem Cell Transplantation ; Homeostasis/physiology ; Humans ; *Parenteral Nutrition ; }, abstract = {Hematopoietic stem cell transplantation (HSCT) is the first-line immunotherapy to treat several hematologic disorders, although it can be associated with many complications reducing the survival rate, such as acute graft-versus-host disease (aGvHD) and infections. Given the fundamental role of the gut microbiome (GM) for host health, it is not surprising that a suboptimal path of GM recovery following HSCT may compromise immune homeostasis and/or increase the risk of opportunistic infections, with an ultimate impact in terms of aGvHD onset. Traditionally, the first nutritional approach in post-HSCT patients is parenteral nutrition (PN), which is associated with several clinical adverse effects, supporting enteral nutrition (EN) as a preferential alternative. The aim of the study was to evaluate the impact of EN vs. PN on the trajectory of compositional and functional GM recovery in pediatric patients undergoing HSCT. The GM structure and short-chain fatty acid (SCFA) production profiles were analyzed longitudinally in twenty pediatric patients receiving HSCT-of which, ten were fed post-transplant with EN and ten with total PN. According to our findings, we observed the prompt recovery of a structural and functional eubiotic GM layout post-HSCT only in EN subjects, thus possibly reducing the risk of systemic infections and GvHD onset.}, }
@article {pmid31816089, year = {2019}, author = {Linsmith, G and Rombauts, S and Montanari, S and Deng, CH and Celton, JM and Guérif, P and Liu, C and Lohaus, R and Zurn, JD and Cestaro, A and Bassil, NV and Bakker, LV and Schijlen, E and Gardiner, SE and Lespinasse, Y and Durel, CE and Velasco, R and Neale, DB and Chagné, D and Van de Peer, Y and Troggio, M and Bianco, L}, title = {Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.).}, journal = {GigaScience}, volume = {8}, number = {12}, pages = {}, pmid = {31816089}, issn = {2047-217X}, mesh = {Chromosomes, Plant/*genetics ; Contig Mapping/*methods ; Genome Size ; Haploidy ; Molecular Sequence Annotation ; Plant Breeding ; Pyrus/*genetics ; Sequence Analysis, DNA ; Synteny ; }, abstract = {BACKGROUND: We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII long-read sequencing, Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. The sample selected for sequencing is a double haploid derived from the same "Bartlett" reference pear that was previously sequenced. Sequencing of di-haploid plants makes assembly more tractable in highly heterozygous species such as P. communis.<br><br>FINDINGS: A total of 496.9 Mb corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 pear chromosomes. Approximately 50% (247 Mb) of the genome consists of repetitive sequences. Gene annotation confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.<br><br>CONCLUSIONS: We showed that the use of a doubled-haploid plant is an effective solution to the problems presented by high levels of heterozygosity and duplication for the generation of high-quality genome assemblies. We present a high-quality chromosome-scale assembly of the European pear Pyrus communis and demostrate its high degree of synteny with the genomes of Malus x Domestica and Pyrus x bretschneideri.}, }
@article {pmid31813647, year = {2020}, author = {Sutherland, WJ and Dias, MP and Dicks, LV and Doran, H and Entwistle, AC and Fleishman, E and Gibbons, DW and Hails, R and Hughes, AC and Hughes, J and Kelman, R and Le Roux, X and LeAnstey, B and Lickorish, FA and Maggs, L and Pearce-Higgins, JW and Peck, LS and Pettorelli, N and Pretty, J and Spalding, MD and Tonneijck, FH and Wentworth, J and Thornton, A}, title = {A Horizon Scan of Emerging Global Biological Conservation Issues for 2020.}, journal = {Trends in ecology &amp; evolution}, volume = {35}, number = {1}, pages = {81-90}, doi = {10.1016/j.tree.2019.10.010}, pmid = {31813647}, issn = {1872-8383}, mesh = {*Biodiversity ; *Conservation of Natural Resources ; Ecosystem ; Forecasting ; Forests ; }, abstract = {In this horizon scan, we highlight 15 emerging issues of potential relevance to global conservation in 2020. Seven relate to potentially extensive changes in vegetation or ecological systems. These changes are either relatively new, for example, conversion of kelp forests to simpler macroalgal systems, or may occur in the future, for example, as a result of the derivation of nanocelluose from wood or the rapid expansion of small hydropower schemes. Other topics highlight potential changes in national legislation that may have global effect on international agreements. Our panel of 23 scientists and practitioners selected these issues using a modified version of the Delphi technique from a long-list of 89 potential topics.}, }
@article {pmid31813285, year = {2021}, author = {Ritter, MR and Tempesta de, OM and Makimori, RY and Sereia, AL and Simionato, AS and Chierrito, D and Galdino, AF and Gonçalves de, OA and Brentan da, SD and Novello, CR and Cristina de, MD and Benedito Prado, DF and João Carlos Palazzo de, M}, title = {Dimeric glycosylated flavan-3-ol and antimicrobial in vitro evaluation of Trichilia catigua extracts.}, journal = {Natural product research}, volume = {35}, number = {19}, pages = {3293-3300}, doi = {10.1080/14786419.2019.1698569}, pmid = {31813285}, issn = {1478-6427}, mesh = {Anti-Bacterial Agents/isolation &amp; purification/*pharmacology ; Brazil ; Catechin/isolation &amp; purification ; Flavonoids/isolation &amp; purification/*pharmacology ; *Meliaceae/chemistry ; Phytochemicals/isolation &amp; purification/pharmacology ; Plant Bark/chemistry ; Plant Extracts/pharmacology ; }, abstract = {Trichilia catigua is a tree known as "catuaba", widely distributed in Brazil. Studies carried out with T. catigua barks suggest that plant has antidepressant, antidiabetic, antimicrobial, antioxidant, antiviral, and preventive against brain damage. The aim of this work was to isolate and characterise compounds from the semipurified fraction of T. catigua barks, and to conduct microbiological screening against bacteria and fungi. The crude extract (CE) of "catuaba" was produced by turbo extraction with acetone-water, and later, partitioned to yield ethyl-acetate (EAF) and aqueous (AqF) fractions. From AqF the new catechin-3-O-α-L-rhamnoside-(4α→8)-epicatechin was isolated, identified, and described here for the first time. Regarding antimicrobial activity, the extracts presented impressive results, mainly for Vancomycin Resistant Enterococcus faecium (VREfm) with MIC of 156.5 μg/mL. The results suggest that extract of T. catigua could potentially be used as an adjuvant to treatment and is a promising candidate for the development of new antimicrobial drugs.}, }
@article {pmid31812391, year = {2020}, author = {Rowles, LS and Hossain, AI and Aggarwal, S and Kirisits, MJ and Saleh, NB}, title = {Water quality and associated microbial ecology in selected Alaska Native communities: Challenges in off-the-grid water supplies.}, journal = {The Science of the total environment}, volume = {711}, number = {}, pages = {134450}, doi = {10.1016/j.scitotenv.2019.134450}, pmid = {31812391}, issn = {1879-1026}, mesh = {*Alaska Natives ; Arctic Regions ; *Groundwater ; Humans ; United States ; Water Quality ; Water Supply ; }, abstract = {The availability of safe water for potable purposes in Alaska Native communities is limited due to naturally occurring metals and contaminants released from anthropogenic activities, such as drilling and mining. The impacts of climate change are magnified in the arctic and sub-arctic regions and thus have the potential to mobilize contaminants and exacerbate the water contamination problem. Alaska Native communities are vulnerable to such changes in their water quality because of their remote location and limited access to resources. This study initiates an assessment of water quality, including its microbial ecology, in off-the-grid Alaskan water supplies (i.e., primarily groundwater wells). In particular, water quality data were collected from nine communities (22 ground water wells). Water quality analyses included basic water quality parameters, a suite of metals relevant to human health, and microbial community composition. Results revealed location-specific elevated arsenic concentrations based on the underlying geological formation, particularly in the areas located in the geological formation of the McHugh Complex. Diverse microbial communities were observed, and the grouping appeared to be based on elevation. These findings present evidence of compromised water quality in an understudied area in the United States. The results from this study should be considered as a snapshot in time, which highlight the importance for further systematic studies in similar off-the-grid communities.}, }
@article {pmid31812098, year = {2020}, author = {Neckovic, A and van Oorschot, RAH and Szkuta, B and Durdle, A}, title = {Investigation of direct and indirect transfer of microbiomes between individuals.}, journal = {Forensic science international. Genetics}, volume = {45}, number = {}, pages = {102212}, doi = {10.1016/j.fsigen.2019.102212}, pmid = {31812098}, issn = {1878-0326}, mesh = {DNA, Bacterial/genetics ; Forensic Genetics/methods ; Glass ; Humans ; Microbiota/*genetics ; Paper ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Skin/*microbiology ; Textiles ; *Touch ; }, abstract = {The human microbiome encompasses the fungi, bacteria and viruses that live on, within, and immediately surrounding the body. Microbiomes have potential utility in forensic science as an evidentiary tool to link or exclude persons of interest associated with criminal activities. Research has shown the microbiome is individualised, and that personal microbial signatures can be recovered from surfaces such as phones, shoes and fabrics. Before the human microbiome may be used as an investigative tool, further research is required to investigate the utility and potential limitations surrounding microbial profiling. This includes the detectability of microbial transfer between individuals or items, the associated risks (such as contamination events) and the applicability of microbial profiling for forensic purposes. This research aimed to identify whether an individual's distinguishable microbiome could be transferred to another individual and onto substrates, and vice versa. Paper, cotton, and glass surfaces were chosen to represent a range of substrate matrices. The study involved six participants placed into three pairs; participants took part in two modes of transfer. Transfer Mode 1 involved the pair shaking hands, followed by rubbing a substrate in their right hand. Transfer Mode 2 involved individuals rubbing a substrate in their left hand, swapping substrates with their partner and then rubbing the swapped substrate in their left hand. 16S rRNA sequencing was performed on the extracted microbial DNA from participant and substrate samples. Quantitative Insights into Microbial Ecology 2 (QIIME 2) was used for sequence quality control and beta (between-sample) diversity analyses and taxonomic assignment. Principal Coordinate Analysis (PCoA) based on Jaccard distances was visualised through Emperor software to determine the phylogenetic similarity of bacterial communities between participants and among participant pairs. Statistical testing through PERMANOVA revealed significant differences in the Jaccard distances between each participant pair (P < 0.001), highlighting not only the potential distinguishability of skin microbiomes among individuals, but also the clustering effect observed between participant pairs due to the potential transfer of hand-associated microbiomes between individuals. The study demonstrated that transfer of the human skin microbiome had occurred between all participant pairs, regardless of substrate type or mode of transfer.}, }
@article {pmid31811330, year = {2020}, author = {Wang, L and Xing, P and Li, H and Zhou, L and Wu, QL}, title = {Distinct Intra-lake Heterogeneity of Diazotrophs in a Deep Oligotrophic Mountain Lake.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {840-852}, doi = {10.1007/s00248-019-01461-0}, pmid = {31811330}, issn = {1432-184X}, support = {31730013//National Natural Science Foundation of China (CN)/ ; 41621002//National Natural Science Foundation of China (CN)/ ; QYZDJ-SSW-DQC030//the Key Research Program of Frontier Science, CAS/ ; }, mesh = {Bacteria/*metabolism ; Bacterial Proteins/analysis ; China ; High-Throughput Nucleotide Sequencing ; Lakes/*microbiology ; *Microbiota ; *Nitrogen Fixation ; Polymerase Chain Reaction ; }, abstract = {To date, little is known about the diazotrophs in freshwater ecosystems. In this study, we examined the diversity, abundance, and distribution of the diazotrophic community in the deep oligotrophic Lake Fuxian using high-throughput sequencing and quantitative polymerase chain reaction of nifH genes. Our results showed that the diazotrophs in Lake Fuxian were diverse and were distributed among Proteobacteria, Planctomycetes, Cyanobacteria, Verrucomicrobia, Bacteroidetes, Chloroflexi, and other unclassified environmental sequences. For the first time, it is found that Bacteroidetes and Planctomycetes harbor diazotrophs in freshwater ecosystems. The diazotrophic community compositions were significantly different between the littoral and pelagic zones in the surface layer, and they also changed dramatically along the vertical profile. High diazotrophic abundance and diversity were mostly observed in the surface littoral zone, and overall, a significant relationship between nifH gene richness and abundance was observed. The water turbidity, nitrite, and phosphorus were the most important factors explaining the spatial changes in diversity and abundances of this important functional group. The two most dominant operational taxonomic units belonging to Betaroproteobacteria and Planctomycetes demonstrated opposite distribution patterns in abundance that were driven by non-overlapping environmental factors. This study is by far the first to uncover the high diversity and intra-lake heterogeneity of diazotrophs in a freshwater lake and illuminate the controlling factors. It provides the probability of the co-occurrence of N2 fixation and N-loss in particles.}, }
@article {pmid31811036, year = {2020}, author = {Hinger, I and Ansorge, R and Mussmann, M and Romano, S}, title = {Phylogenomic Analyses of Members of the Widespread Marine Heterotrophic Genus Pseudovibrio Suggest Distinct Evolutionary Trajectories and a Novel Genus, Polycladidibacter gen. nov.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {4}, pages = {}, pmid = {31811036}, issn = {1098-5336}, support = {P 31010/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Biological Evolution ; Genome, Bacterial ; *Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Rhodobacteraceae/*classification/genetics/*physiology ; }, abstract = {Bacteria belonging to the Pseudovibrio genus are widespread, metabolically versatile, and able to thrive as both free-living and host-associated organisms. Although more than 50 genomes are available, a comprehensive comparative genomics study to resolve taxonomic inconsistencies is currently missing. We analyzed all available genomes and used 552 core genes to perform a robust phylogenomic reconstruction. This in-depth analysis revealed the divergence of two monophyletic basal lineages of strains isolated from polyclad flatworm hosts, namely, Pseudovibrio hongkongensis and Pseudovibrio stylochi These strains have reduced genomes and lack sulfur-related metabolisms and major biosynthetic gene clusters, and their environmental distribution appears to be tightly associated with invertebrate hosts. We showed experimentally that the divergent strains are unable to utilize various sulfur compounds that, in contrast, can be utilized by the type strain Pseudovibrio denitrificans Our analyses suggest that the lineage leading to these two strains has been subject to relaxed purifying selection resulting in great gene loss. Overall genome relatedness indices (OGRI) indicate substantial differences between the divergent strains and the rest of the genus. While 16S rRNA gene analyses do not support the establishment of a different genus for the divergent strains, their substantial genomic, phylogenomic, and physiological differences strongly suggest a divergent evolutionary trajectory and the need for their reclassification. Therefore, we propose the novel genus Polycladidibacter gen. nov.IMPORTANCE The genus Pseudovibrio is commonly associated with marine invertebrates, which are essential for ocean health and marine nutrient cycling. Traditionally, the phylogeny of the genus has been based on 16S rRNA gene analysis. The use of the 16S rRNA gene or any other single marker gene for robust phylogenetic placement has recently been questioned. We used a large set of marker genes from all available Pseudovibrio genomes for in-depth phylogenomic analyses. We identified divergent monophyletic basal lineages within the Pseudovibrio genus, including two strains isolated from polyclad flatworms. These strains showed reduced sulfur metabolism and biosynthesis capacities. The phylogenomic analyses revealed distinct evolutionary trajectories and ecological adaptations that differentiate the divergent strains from the other Pseudovibrio members and suggest that they fall into a novel genus. Our data show the importance of widening the use of phylogenomics for better understanding bacterial physiology, phylogeny, and evolution.}, }
@article {pmid31811031, year = {2020}, author = {Song, Y and Jiang, CY and Liang, ZL and Wang, BJ and Jiang, Y and Yin, Y and Zhu, HZ and Qin, YL and Cheng, RX and Liu, ZP and Liu, Y and Jin, T and Corvini, PF and Rabaey, K and Wang, AJ and Liu, SJ}, title = {Casimicrobium huifangae gen. nov., sp. nov., a Ubiquitous "Most-Wanted" Core Bacterial Taxon from Municipal Wastewater Treatment Plants.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {4}, pages = {}, pmid = {31811031}, issn = {1098-5336}, mesh = {Betaproteobacteria/*classification/genetics/*physiology ; Microbiota ; Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sewage/*microbiology ; }, abstract = {Microorganisms in wastewater treatment plants (WWTPs) play a key role in the removal of pollutants from municipal and industrial wastewaters. A recent study estimated that activated sludge from global municipal WWTPs harbors 1 × 10[9] to 2 × 10[9] microbial species, the majority of which have not yet been cultivated, and 28 core taxa were identified as "most-wanted" ones (L. Wu, D. Ning, B. Zhang, Y. Li, et al., Nat Microbiol 4:1183-1195, 2019, https://doi.org/10.1038/s41564-019-0426-5). Cultivation and characterization of the "most-wanted" core bacteria are critical to understand their genetic, physiological, phylogenetic, and ecological traits, as well as to improve the performance of WWTPs. In this study, we isolated a bacterial strain, designated SJ-1, that represents a novel cluster within Betaproteobacteria and corresponds to OTU_16 within the 28 core taxa in the "most-wanted" list. Strain SJ-1 was identified and nominated as Casimicrobium huifangae gen. nov., sp. nov., of a novel family, Casimicrobiaceae. C. huifangae is ubiquitously distributed and is metabolically versatile. In addition to mineralizing various carbon sources (including carbohydrates, aromatic compounds, and short-chain fatty acids), C. huifangae is capable of nitrate reduction and phosphorus accumulation. The population of C. huifangae accounted for more than 1% of the bacterial population of the activated sludge microbiome from the Qinghe WWTP, which showed seasonal dynamic changes. Cooccurrence analysis suggested that C. huifangae was an important module hub in the bacterial network of Qinghe WWTP.IMPORTANCE The activated sludge process is the most widely applied biotechnology and is one of the best ecosystems to address microbial ecological principles. Yet, the cultivation of core bacteria and the exploration of their physiology and ecology are limited. In this study, the core and novel bacterial taxon C. huifangae was cultivated and characterized. This study revealed that C. huifangae functioned as an important module hub in the activated sludge microbiome, and it potentially plays an important role in municipal wastewater treatment plants.}, }
@article {pmid31810817, year = {2020}, author = {Estrella, MJ and Fontana, MF and Cumpa Velásquez, LM and Torres Tejerizo, GA and Diambra, L and Hansen, LH and Pistorio, M and Sannazzaro, AI}, title = {Mesorhizobium intechi sp. nov. isolated from nodules of Lotus tenuis in soils of the Flooding Pampa, Argentina.}, journal = {Systematic and applied microbiology}, volume = {43}, number = {1}, pages = {126044}, doi = {10.1016/j.syapm.2019.126044}, pmid = {31810817}, issn = {1618-0984}, mesh = {Argentina ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Genes, Bacterial/genetics ; Genes, Essential/genetics ; Genome, Bacterial/genetics ; Lotus/*microbiology ; Mesorhizobium/chemistry/*classification/cytology/physiology ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {Three symbiotic nitrogen-fixing bacteria (BD68[T], BD66 and BD73) isolated from root nodules of Lotus tenuis in lowland soils of the Flooding Pampa (Argentina), previously classified as members of the Mesorhizobium genus, were characterized in this study. Phylogenetic analysis of their 16S rRNA gene sequences showed a close relationship to M. japonicum MAFF 303099[T], M. erdmanii USDA 3471[T], M. carmichaelinearum ICMP 18942[T], M. opportunistum WSM 2975[T] and M. jarvisii ATCC 33699[T], with sequence identities of 99.72%-100%. Multilocus sequence analysis of other housekeeping genes revealed that the three isolates belonged to a phylogenetically distinct clade within the genus Mesorhizobium. Strain BD68[T] was designated as the group representative and its genome was fully sequenced. The average nucleotide identity and in silico DNA-DNA hybridization comparisons between BD68[T] and the most related type strains showed values below the accepted threshold for species discrimination. Phenotypic and chemotaxonomic features were also studied. Based on these results, BD68[T], BD66 and BD73 could be considered to represent a novel species of the genus Mesorhizobium, for which the name Mesorhizobium intechi sp. nov. is hereby proposed. The type strain of this species is BD68[T] (=CECT 9304[T]=LMG 30179[T]).}, }
@article {pmid31807860, year = {2020}, author = {Zhao, J and Li, G and Lu, W and Huang, S and Zhang, Z}, title = {Dominant and Subordinate Relationship Formed by Repeated Social Encounters Alters Gut Microbiota in Greater Long-Tailed Hamsters.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {998-1010}, doi = {10.1007/s00248-019-01462-z}, pmid = {31807860}, issn = {1432-184X}, support = {No. XDB11050300//"Strategic Priority Research Program" of the Chinese Academy of Sciences/ ; No. 152111KYSB20160089//International Partnership Program of Chinese Academy of Sciences/ ; No.152111KYSB20150023//External Cooperation Program of BIC, Chinese Academy of Sciences/ ; }, mesh = {Animals ; Bacteria/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Cricetinae/*microbiology/physiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Male ; *Social Dominance ; }, abstract = {Social stress can dramatically influence the health of animals via communication between gut microbiota and the HPA system. However, this effect has been rarely investigated among different social ranked animals after chronic repeated social encounters. In this study, we evaluated changes and differences in microbiota among control, dominant, and subordinate male greater long-tailed hamsters (Tscherskia triton) over 28 successive days of repeated social encounter. Our results indicated that as compared with the control group, short-term repeated social encounters significantly altered fecal microbiota of subordinate hamsters, while chronic repeated social encounters altered colonic mucosa-associated microbiota of both dominant and subordinate hamsters. Fecal microbiota showed a transition in composition and diversity on day 2 for the subordinate group but on day 4 for the control and dominant groups under repeated encounters. Compared with their baseline, genus Lactobacillus increased in both dominant and subordinate groups, while genus Bifidobacterium increased in the subordinate group and genus Adlercreutzia increased in the dominant group. Our results suggest that chronic repeated social encounter can alter diversity and composition of gut microbiota of hamsters in both feces and colonic mucosa, but the latter performed better in reflecting the effects of chronic stress on microbiota in this species. Future studies should focus on elucidating how these microbiota alterations may affect animal behavior and fitness.}, }
@article {pmid31806445, year = {2020}, author = {Qi, Y and Ossowicki, A and Yang, X and Huerta Lwanga, E and Dini-Andreote, F and Geissen, V and Garbeva, P}, title = {Effects of plastic mulch film residues on wheat rhizosphere and soil properties.}, journal = {Journal of hazardous materials}, volume = {387}, number = {}, pages = {121711}, doi = {10.1016/j.jhazmat.2019.121711}, pmid = {31806445}, issn = {1873-3336}, mesh = {Bacteria/drug effects ; Biodegradable Plastics/*pharmacology ; Biomass ; Microplastics/*pharmacology ; Polyethylene/*pharmacology ; *Rhizosphere ; Soil/chemistry ; Soil Pollutants/*pharmacology ; Triticum/*drug effects ; Volatile Organic Compounds/metabolism ; }, abstract = {Plastic residues could accumulate in soils as a consequence of using plastic mulching, which results in a serious environmental concern for agroecosystems. As an alternative, biodegradable plastic films stand as promising products to minimize plastic debris accumulation and reduce soil pollution. However, the effects of residues from traditional and biodegradable plastic films on the soil-plant system are not well studied. In this study, we used a controlled pot experiment to investigate the effects of macro- and micro- sized residues of low-density polyethylene and biodegradable plastic mulch films on the rhizosphere bacterial communities, rhizosphere volatile profiles and soil chemical properties. Interestingly, we identified significant effects of biodegradable plastic residues on the rhizosphere bacterial communities and on the blend of volatiles emitted in the rhizosphere. For example, in treatments with biodegradable plastics, bacteria genera like Bacillus and Variovorax were present in higher relative abundances and volatile compounds like dodecanal were exclusively produced in treatment with biodegradable microplastics. Furthermore, significant differences in soil pH, electrical conductivity and C:N ratio were observed across treatments. Our study provides evidence for both biotic and abiotic impacts of plastic residues on the soil-plant system, suggesting the urgent need for more research examining their environmental impacts on agroecosystems.}, }
@article {pmid31803164, year = {2019}, author = {Yang, Y and Ashworth, AJ and Willett, C and Cook, K and Upadhyay, A and Owens, PR and Ricke, SC and DeBruyn, JM and Moore, PA}, title = {Review of Antibiotic Resistance, Ecology, Dissemination, and Mitigation in U.S. Broiler Poultry Systems.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2639}, pmid = {31803164}, issn = {1664-302X}, abstract = {Since the onset of land application of poultry litter, transportation of microorganisms, antibiotics, and disinfectants to new locations has occurred. While some studies provide evidence that antimicrobial resistance (AMR), an evolutionary phenomenon, could be influenced by animal production systems, other research suggests AMR originates in the environment from non-anthropogenic sources. In addition, AMR impacts the effective prevention and treatment of poultry illnesses and is increasingly a threat to global public health. Therefore, there is a need to understand the dissemination of AMR genes to the environment, particularly those directly relevant to animal health using the One Health Approach. This review focuses on the potential movement of resistance genes to the soil via land application of poultry litter. Additionally, we highlight impacts of AMR on microbial ecology and explore hypotheses explaining gene movement pathways from U.S. broiler operations to the environment. Current approaches for decreasing antibiotic use in U.S. poultry operations are also described in this review.}, }
@article {pmid31803161, year = {2019}, author = {Banerji, A and Jahne, M and Herrmann, M and Brinkman, N and Keely, S}, title = {Bringing Community Ecology to Bear on the Issue of Antimicrobial Resistance.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2626}, pmid = {31803161}, issn = {1664-302X}, abstract = {Antimicrobial resistance (AMR) is a global concern, pertaining not only to human health but also to the health of industry and the environment. AMR research has traditionally focused on genetic exchange mechanisms and abiotic environmental constraints, leaving important aspects of microbial ecology unresolved. The genetic and ecological aspects of AMR, however, not only contribute separately to the problem but also are interrelated. For example, mutualistic associations among microbes such as biofilms can both serve as a barrier to antibiotic penetration and a breeding ground for horizontal exchange of antimicrobial resistance genes (ARGs). In this review, we elucidate how species interactions promote and impede the establishment, maintenance, and spread of ARGs and indicate how management initiatives might benefit from leveraging the principles and tools of community ecology to better understand and manipulate the processes underlying AMR.}, }
@article {pmid31802728, year = {2020}, author = {Fix, J and Chandrashekhar, K and Perez, J and Bucardo, F and Hudgens, MG and Yuan, L and Twitchell, E and Azcarate-Peril, MA and Vilchez, S and Becker-Dreps, S}, title = {Association between Gut Microbiome Composition and Rotavirus Vaccine Response among Nicaraguan Infants.}, journal = {The American journal of tropical medicine and hygiene}, volume = {102}, number = {1}, pages = {213-219}, pmid = {31802728}, issn = {1476-1645}, support = {K24 AI141744/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/classification ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Nicaragua/epidemiology ; Rotavirus Infections/*prevention &amp; control ; Rotavirus Vaccines/*immunology ; Seroconversion ; }, abstract = {Rotavirus is the leading cause of childhood deaths due to diarrhea. Although existing oral rotavirus vaccines are highly efficacious in high-income countries, these vaccines have been demonstrated to have decreased efficacy in low- and middle-income countries. A possible explanation for decreased efficacy is the impact of gut microbiota on the enteric immune system's response to vaccination. We analyzed the gut microbiome of 50 children enrolled in a prospective study evaluating response to oral pentavalent rotavirus vaccination (RV5) to assess associations between relative abundance of bacterial taxa and seroconversion following vaccination. Stool samples were taken before the first RV5 dose, and microbiome composition characterized using 16S rRNA amplicon sequencing and Quantitative Insights Into Microbial Ecology software. Relative abundance of bacterial taxa between seroconverters following the first RV5 dose, those with ≥ 4-fold increase in rotavirus-specific IgA titers, and nonseroconverters were compared using the Wilcoxon-Mann-Whitney test. We identified no significant differences in microbiome composition between infants who did and did not respond to vaccination. Infants who responded to vaccination tended to have higher abundance of Proteobacteria and Eggerthella, whereas those who did not respond had higher abundance of Fusobacteria and Enterobacteriaceae; however, these differences were not statistically significant following a multiple comparison correction. This study suggests a limited impact of gut microbial taxa on response to oral rotavirus vaccination among infants; however, additional research is needed to improve our understanding of the impact of gut microbiome on vaccine response, toward a goal of improving vaccine efficacy and rotavirus prevention.}, }
@article {pmid31802185, year = {2020}, author = {Walker, DM and Hill, AJ and Albecker, MA and McCoy, MW and Grisnik, M and Romer, A and Grajal-Puche, A and Camp, C and Kelehear, C and Wooten, J and Rheubert, J and Graham, SP}, title = {Variation in the Slimy Salamander (Plethodon spp.) Skin and Gut-Microbial Assemblages Is Explained by Geographic Distance and Host Affinity.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {985-997}, doi = {10.1007/s00248-019-01456-x}, pmid = {31802185}, issn = {1432-184X}, mesh = {Animal Distribution ; Animals ; Bacteria/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Fungi/isolation &amp; purification/*physiology ; Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; *Microbiota ; Mycobiome ; Skin/*microbiology ; Southeastern United States ; Spatial Analysis ; Tennessee ; Caudata/*microbiology ; }, abstract = {A multicellular host and its microbial communities are recognized as a metaorganism-a composite unit of evolution. Microbial communities have a variety of positive and negative effects on the host life history, ecology, and evolution. This study used high-throughput amplicon sequencing to characterize the complete skin and gut microbial communities, including both bacteria and fungi, of a terrestrial salamander, Plethodon glutinosus (Family Plethodontidae). We assessed salamander populations, representing nine mitochondrial haplotypes ('clades'), for differences in microbial assemblages across 13 geographic locations in the Southeastern United States. We hypothesized that microbial assemblages were structured by both host factors and geographic distance. We found a strong correlation between all microbial assemblages at close geographic distances, whereas, as spatial distance increases, the patterns became increasingly discriminate. Network analyses revealed that gut-bacterial communities have the highest degree of connectedness across geographic space. Host salamander clade was explanatory of skin-bacterial and gut-fungal assemblages but not gut-bacterial assemblages, unless the latter were analyzed within a phylogenetic context. We also inferred the function of gut-fungal assemblages to understand how an understudied component of the gut microbiome may influence salamander life history. We concluded that dispersal limitation may in part describe patterns in microbial assemblages across space and also that the salamander host may select for skin and gut communities that are maintained over time in closely related salamander populations.}, }
@article {pmid31802184, year = {2020}, author = {Xu, S and Jiang, L and Qiao, G and Chen, J}, title = {The Bacterial Flora Associated with the Polyphagous Aphid Aphis gossypii Glover (Hemiptera: Aphididae) Is Strongly Affected by Host Plants.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {971-984}, pmid = {31802184}, issn = {1432-184X}, support = {2016YFE0203100//National Key R &amp; D Program of China/ ; XDA19050303//Strategic Priority Research Program A of the Chinese Academy of Sciences/ ; 31620103916//National Natural Science Foundation of China/ ; 31430078//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Aphids/*microbiology/physiology ; Bacteria/classification/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Diet ; *Food Chain ; *Microbiota ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA ; }, abstract = {Aphids live in symbiosis with a variety of bacteria, including the obligate symbiont Buchnera aphidicola and diverse facultative symbionts. The symbiotic associations for one aphid species, especially for polyphagous species, often differ across populations. In the present study, by using high-throughput 16S rRNA sequencing, we surveyed in detail the microbiota in natural populations of the cotton aphid Aphis gossypii in China and assessed differences in bacterial diversity with respect to host plant and geography. The microbial community of A. gossypii was dominated by a few heritable symbionts. Arsenophonus was the most dominant secondary symbiont, and Spiroplasma was detected for the first time. Statistical tests and ordination analyses showed that host plants rather than geography seemed to have shaped the associated symbiont composition. Special symbiont communities inhabited the Cucurbitaceae-feeding populations, which supported the ecological specialization of A. gossypii on cucurbits from the viewpoint of symbiotic bacteria. Correlation analysis suggested antagonistic interactions between Buchnera and coexisting secondary symbionts and more complicated interactions between different secondary symbionts. Our findings lend further support to an important role of the host plant in structuring symbiont communities of polyphagous aphids and will improve our understanding of the interactions among phytophagous insects, symbionts, and environments.}, }
@article {pmid31798545, year = {2019}, author = {Harth-Chu, EN and Alves, LA and Theobaldo, JD and Salomão, MF and Höfling, JF and King, WF and Smith, DJ and Mattos-Graner, RO}, title = {PcsB Expression Diversity Influences on Streptococcus mitis Phenotypes Associated With Host Persistence and Virulence.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2567}, pmid = {31798545}, issn = {1664-302X}, abstract = {S. mitis is an abundant member of the commensal microbiota of the oral cavity and pharynx, which has the potential to promote systemic infections. By analyzing a collection of S. mitis strains isolated from the oral cavity at commensal states or from systemic infections (blood strains), we established that S. mitis ubiquitously express the surface immunodominant protein, PcsB (also called GbpB), required for binding to sucrose-derived exopolysaccharides (EPS). Immuno dot blot assays with anti-PcsB antibodies and RT-qPCR transcription analyses revealed strain-specific profiles of PcsB production associated with diversity in pcsB transcriptional activities. Additionally, blood strains showed significantly higher levels of PcsB expression compared to commensal isolates. Because Streptococcus mutans co-colonizes S. mitis dental biofilms, and secretes glucosyltransferases (GtfB/C/D) for the synthesis of highly insoluble EPS from sucrose, profiles of S. mitis binding to EPS, biofilm formation and evasion of the complement system were assessed in sucrose-containing BHI medium supplemented or not with filter-sterilized S. mutans culture supernatants. These analyses showed significant S. mitis binding to EPS and biofilm formation in the presence of S. mutans supernatants supplemented with sucrose, compared to BHI or BHI-sucrose medium. In addition, these phenotypes were abolished if strains were grown in culture supernatants of a gtfBCD-defective S. mutans mutant. Importantly, GtfB/C/D-associated phenotypes were enhanced in high PcsB-expressing strains, compared to low PcsB producers. Increased PcsB expression was further correlated with increased resistance to deposition of C3b/iC3b of the complement system after exposure to human serum, when strains were previously grown in the presence of S. mutans supernatants. Finally, analyses of PcsB polymorphisms and bioinformatic prediction of epitopes with significant binding to MHC class II alleles revealed that blood isolates harbor PcsB polymorphisms in its functionally conserved CHAP-domain, suggesting antigenic variation. These findings reveal important roles of PcsB in S. mitis-host interactions under commensal and pathogenic states, highlighting the need for studies to elucidate mechanisms regulating PcsB expression in this species.}, }
@article {pmid31798544, year = {2019}, author = {Gallardo-Navarro, &#xd3;A and Santillán, M}, title = {Three-Way Interactions in an Artificial Community of Bacterial Strains Directly Isolated From the Environment and Their Effect on the System Population Dynamics.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2555}, pmid = {31798544}, issn = {1664-302X}, abstract = {This work is motivated by previous studies that have analyzed the population ecology of a collection of culturable thermoresistant bacteria, isolated from the Churince lagoon in Cuatro Cienegas, Mexico. In particular, it is aimed at testing a hypothesis from a modeling study, which states that antagonistic and sensitive bacteria co-exist thanks to resistant bacteria that protect sensitive ones by forming physical barriers. We selected three different bacterial strains from the referred collection: one antagonistic, one sensitive, and one resistant, and studied the population dynamics of mixed colonies. Our results show that, although the proposed protective mechanism does not work in this case, the resistant strain confers some kind of protection to sensitive bacteria. Further modeling and experimental results suggest that the presence of resistant bacteria indirectly improves the probability that patches of sensitive bacteria grow in a mixed colony. More precisely, our results suggest that by making antagonistic bacteria produce and secrete an antagonistic substance (with the concomitant metabolic cost and growth rate reduction), resistant bacteria increase the likelihood that sensitive bacteria locally outcompete antagonistic ones.}, }
@article {pmid31796996, year = {2020}, author = {Velasco-González, I and Sanchez-Jimenez, A and Singer, D and Murciano, A and Díez-Hermano, S and Lara, E and Martín-Cereceda, M}, title = {Rain-Fed Granite Rock Basins Accumulate a High Diversity of Dormant Microbial Eukaryotes.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {882-897}, doi = {10.1007/s00248-019-01463-y}, pmid = {31796996}, issn = {1432-184X}, support = {CGL2013-40851-P//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; SNF 31003A_143960//Swiss Re Foundation/ ; }, mesh = {Eukaryota/isolation &amp; purification/*physiology ; Geologic Sediments/*microbiology/*parasitology ; Microbiota ; Mycobiome ; Rain ; *Silicon Dioxide ; Spain ; }, abstract = {Rain fed granite rock basins are ancient geological landforms of worldwide distribution and structural simplicity. They support habitats that can switch quickly from terrestrial to aquatic along the year. Diversity of animals and plants, and the connexion between communities in different basins have been widely explored in these habitats, but hardly any research has been carried out on microorganisms. The aim of this study is to provide the first insights on the diversity of eukaryotic microbial communities from these environments. Due to the ephemeral nature of these aquatic environments, we predict that the granitic basins should host a high proportion of dormant microeukaryotes. Based on an environmental DNA diversity survey, we reveal diverse communities with representatives of all major eukaryotic taxonomic supergroups, mainly composed of a diverse pool of low abundance OTUs. Basin communities were very distinctive, with alpha and beta diversity patterns non-related to basin size or spatial distance respectively. Dissimilarity between basins was mainly characterised by turnover of OTUs. The strong microbial eukaryotic heterogeneity observed among the basins may be explained by a complex combination of deterministic factors (diverging environment in the basins), spatial constraints, and randomness including founder effects. Most interestingly, communities contain organisms that cannot coexist at the same time because of incompatible metabolic requirements, thus suggesting the existence of a pool of dormant organisms whose activity varies along with the changing environment. These organisms accumulate in the pools, which turns granitic rock into high biodiversity microbial islands whose conservation and study deserve further attention.}, }
@article {pmid31796995, year = {2020}, author = {González-Serrano, F and Pérez-Cobas, AE and Rosas, T and Baixeras, J and Latorre, A and Moya, A}, title = {The Gut Microbiota Composition of the Moth Brithys crini Reflects Insect Metamorphosis.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {960-970}, doi = {10.1007/s00248-019-01460-1}, pmid = {31796995}, issn = {1432-184X}, support = {SAF2015-65878-R//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; BFU2015-64322-C2-1-R//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; Prometeo/2018/A/133//Conselleria d'Educaci&#xf3;, Investigaci&#xf3;, Cultura i Esport/ ; Co-finance//Interreg/ ; PGC2018-099344-B-100//Agencia Estatal de Investigaci&#xf3;n/ ; }, mesh = {Animals ; Female ; *Gastrointestinal Microbiome ; Larva/growth &amp; development/microbiology ; Male ; *Metamorphosis, Biological ; Moths/growth &amp; development/*microbiology ; Ovum/growth &amp; development/microbiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA ; }, abstract = {Lepidoptera is a highly diverse insect order with major importance in agriculture as many species are considered pests. The role of the gut microbiota in insect physiology is still poorly understood, despite the research undertaken in recent years. Furthermore, Lepidoptera are holometabolous insects and few studies have addressed the influence of the changes taking place on the gut microbiome composition and diversity during metamorphosis, especially in monophagous species. The V3-V4 region of the 16S rRNA gene was sequenced to investigate the microbiota composition and diversity of the monophagous moth Brithys crini during three different life stages: egg, larvae (midgut and hindgut), and adult (gut). Our results showed that the microbiota composition of B. crini was stage specific, indicating that the developmental stage is a main factor affecting the gut microbiome in composition and potential functions. Moreover, the diversity of the gut microbiome reflected the developmental process, since a drop in diversity occurred between the larval and the adult phase, when the intestine is completely renewed. In spite of the changes in the gut microbiota during metamorphosis, 29 genera were conserved throughout the three developmental stages, mainly belonging to the Proteobacteria phylum, which define the core microbiome of B. crini. These genera seem to contribute to host physiology by participating in food digestion, nutrition, and detoxification mechanisms.}, }
@article {pmid31791792, year = {2020}, author = {Nguyen, LN and Commault, AS and Kahlke, T and Ralph, PJ and Semblante, GU and Johir, MAH and Nghiem, LD}, title = {Genome sequencing as a new window into the microbial community of membrane bioreactors - A critical review.}, journal = {The Science of the total environment}, volume = {704}, number = {}, pages = {135279}, doi = {10.1016/j.scitotenv.2019.135279}, pmid = {31791792}, issn = {1879-1026}, mesh = {Base Sequence ; Bioreactors/*microbiology ; Microbiota ; *Waste Disposal, Fluid ; Wastewater/*microbiology ; }, abstract = {Recent developed sequencing techniques have resulted in a new and unprecedented way to study biological wastewater treatment, in which most organisms are uncultivable. This review provides (i) an insight on state-of-the-art sequencing techniques and their limitations; (ii) a critical assessment of the microbial community in biological reactor and biofouling layer in a membrane bioreactor (MBR). The data from high-throughput sequencing has been used to infer microbial growth conditions and metabolisms of microorganisms present in MBRs at the time of sampling. These data shed new insight to two fundamental questions about a microbial community in the MBR process namely the microbial composition (who are they?) and the functions of each specific microbial assemblage (what are their function?). The results to date also highlight the complexity of the microbial community growing on MBRs. Environmental conditions are dynamic and diverse, and can influence the diversity and structural dynamics of any given microbial community for wastewater treatment. The benefits of understanding the structure of microbial communities on three major aspects of the MBR process (i.e. nutrient removal, biofouling control, and micropollutant removal) were symmetrically delineated. This review also indicates that the deployment of microbial community analysis for a practical engineering context, in terms of process design and system optimization, can be further realized.}, }
@article {pmid31791487, year = {2020}, author = {Mathews, ER and Wood, JL and Phillips, D and Billington, N and Barnett, D and Franks, AE}, title = {Town-scale microbial sewer community and H2S emissions response to common chemical and biological dosing treatments.}, journal = {Journal of environmental sciences (China)}, volume = {87}, number = {}, pages = {133-148}, doi = {10.1016/j.jes.2019.06.011}, pmid = {31791487}, issn = {1001-0742}, mesh = {Hydrogen Sulfide/*analysis/chemistry ; Hydrogen-Ion Concentration ; Microbiota ; Sewage/chemistry/microbiology ; Waste Disposal, Fluid/*methods ; }, abstract = {Controlling hydrogen sulfide (H2S) odors and emissions using a single, effective treatment across a town-scale sewer network is a challenge faced by many water utilities. Implementation of a sewer diversion provided the opportunity to compare the effectiveness of magnesium hydroxide (Mg(OH)2) and two biological dosing compounds (Bioproducts A and B), with different modes of action (MOA), in a field-test across a large sewer network. Mg(OH)2 increases sewer pH allowing suppression of H2S release into the sewer environment while Bioproduct A acts to disrupt microbial communication through quorum sensing (QS), reducing biofilm integrity. Bioproduct B reduces H2S odors by scouring the sewer of fats, oils and grease (FOGs), which provide adhesion points for the microbial biofilm. Results revealed that only Mg(OH)2 altered the microbial community structure and reduced H2S emissions in a live sewer system, whilst Bioproducts A and B did not reduce H2S emissions or have an observable effect on the composition of the microbial community at the dosed site. Study results recommend in situ testing of dosing treatments before implementation across an operational system.}, }
@article {pmid31790889, year = {2020}, author = {Yan, L and Herrmann, M and Kampe, B and Lehmann, R and Totsche, KU and Küsel, K}, title = {Environmental selection shapes the formation of near-surface groundwater microbiomes.}, journal = {Water research}, volume = {170}, number = {}, pages = {115341}, doi = {10.1016/j.watres.2019.115341}, pmid = {31790889}, issn = {1879-2448}, mesh = {Bacteria ; *Groundwater ; *Microbiota ; }, abstract = {Hydrodynamics drives both stochastic and deterministic community assembly in aquatic habitats, by translocating microbes across geographic barriers and generating changes in selective pressures. Thus, heterogeneity of hydrogeological settings and episodic surface inputs from recharge areas might play important roles in shaping and maintaining groundwater microbial communities. Here we took advantage of the Hainich Critical Zone Exploratory to disentangle mechanisms of groundwater microbiome differentiation via a three-year observation in a setting of mixed carbonate-siliciclastic alternations along a hillslope transect. Variation partitioning of all data elucidated significant roles of hydrochemistry (35.0%) and spatial distance (18.6%) but not of time in shaping groundwater microbiomes. Groundwater was dominated by rare species (99.6% of OTUs), accounting for 25.9% of total reads, whereas only 26 OTUs were identified as core species. The proximity to the recharge area gave prominence to high microbial diversity coinciding with high surface inputs. In downstream direction, the abundance of rare OTUs decreased whereas core OTUs abundance increased up to 47% suggesting increasing selection stress with a higher competition cost for colonization. In general, environmental selection was the key mechanism driving the spatial differentiation of groundwater microbiomes, with N-compounds and dissolved oxygen as the major determinants, but it was more prominent in the upper aquifer with low flow velocity. Across the lower aquifer with higher flow velocity, stochastic processes appeared to be additionally important for community assembly. Overall, this study highlights the impact of surface and subsurface conditions, as well as flow regime and related habitat accessibility, on groundwater microbiomes assembly.}, }
@article {pmid31790419, year = {2019}, author = {Díaz-Riaño, J and Posada, L and Acosta, IC and Ruíz-Pérez, C and García-Castillo, C and Reyes, A and Zambrano, MM}, title = {Computational search for UV radiation resistance strategies in Deinococcus swuensis isolated from Paramo ecosystems.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0221540}, pmid = {31790419}, issn = {1932-6203}, mesh = {Adaptation, Physiological/radiation effects ; Deinococcus/genetics/isolation &amp; purification/*physiology/*radiation effects ; *Ecosystem ; Gene Expression Regulation, Bacterial/radiation effects ; RNA, Bacterial/genetics ; *Radiation Tolerance ; Survival Analysis ; *Ultraviolet Rays ; }, abstract = {Ultraviolet radiation (UVR) is widely known as deleterious for many organisms since it can cause damage to biomolecules either directly or indirectly via the formation of reactive oxygen species. The goal of this study was to analyze the capacity of high-mountain Espeletia hartwegiana plant phyllosphere microorganisms to survive UVR and to identify genes related to resistance strategies. A strain of Deinococcus swuensis showed a high survival rate of up to 60% after UVR treatment at 800J/m2 and was used for differential expression analysis using RNA-seq after exposing cells to 400J/m2 of UVR (with >95% survival rate). Differentially expressed genes were identified using the R-Bioconductor package NOISeq and compared with other reported resistance strategies reported for this genus. Genes identified as being overexpressed included transcriptional regulators and genes involved in protection against damage by UVR. Non-coding (nc)RNAs were also differentially expressed, some of which have not been previously implicated. This study characterized the immediate radiation response of D. swuensis and indicates the involvement of ncRNAs in the adaptation to extreme environmental conditions.}, }
@article {pmid31788934, year = {2020}, author = {Hannula, SE and Ma, HK and Pérez-Jaramillo, JE and Pineda, A and Bezemer, TM}, title = {Structure and ecological function of the soil microbiome affecting plant-soil feedbacks in the presence of a soil-borne pathogen.}, journal = {Environmental microbiology}, volume = {22}, number = {2}, pages = {660-676}, pmid = {31788934}, issn = {1462-2920}, support = {865.14.006//Netherlands Organization for Scientific Research NWO VICI/International ; 870.15.080//Netherlands Organization for Scientific Research NWO VICI/International ; }, mesh = {Bacteria/classification/genetics ; Chrysanthemum/*growth &amp; development ; Fabaceae/*microbiology ; Microbiota/genetics ; Mycorrhizae/physiology ; Plant Development/*physiology ; Plant Diseases/microbiology ; Plant Roots/*microbiology ; Plants ; Poaceae/microbiology ; Pythium/*metabolism ; Soil/chemistry ; Soil Microbiology ; Species Specificity ; }, abstract = {Interactions between plants and soil microbes are important for plant growth and resistance. Through plant-soil-feedbacks, growth of a plant is influenced by the previous plant that was growing in the same soil. We performed a plant-soil feedback study with 37 grass, forb and legume species, to condition the soil and then tested the effects of plant-induced changes in soil microbiomes on the growth of the commercially important cut-flower Chrysanthemum in presence and absence of a pathogen. We analysed the fungal and bacterial communities in these soils using next-generation sequencing and examined their relationship with plant growth in inoculated soils with or without the root pathogen, Pythium ultimum. We show that a large part of the soil microbiome is plant species-specific while a smaller part is conserved at the plant family level. We further identified clusters of plant species creating plant growth promoting microbiomes that suppress concomitantly plant pathogens. Especially soil inocula with higher relative abundances of arbuscular mycorrhizal fungi caused positive effects on the Chrysanthemum growth when exposed to the pathogen. We conclude that plants differ greatly in how they influence the soil microbiome and that plant growth and protection against pathogens is associated with a complex soil microbial community.}, }
@article {pmid31787951, year = {2019}, author = {Pelikan, C and Jaussi, M and Wasmund, K and Seidenkrantz, MS and Pearce, C and Kuzyk, ZZA and Herbold, CW and Røy, H and Kjeldsen, KU and Loy, A}, title = {Glacial Runoff Promotes Deep Burial of Sulfur Cycling-Associated Microorganisms in Marine Sediments.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2558}, pmid = {31787951}, issn = {1664-302X}, support = {P 25111/FWF_/Austrian Science Fund FWF/Austria ; P 29426/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Marine fjords with active glacier outlets are hot spots for organic matter burial in the sediments and subsequent microbial mineralization. Here, we investigated controls on microbial community assembly in sub-arctic glacier-influenced (GI) and non-glacier-influenced (NGI) marine sediments in the Godthåbsfjord region, south-western Greenland. We used a correlative approach integrating 16S rRNA gene and dissimilatory sulfite reductase (dsrB) amplicon sequence data over six meters of depth with biogeochemistry, sulfur-cycling activities, and sediment ages. GI sediments were characterized by comparably high sedimentation rates and had "young" sediment ages of <500 years even at 6 m sediment depth. In contrast, NGI stations reached ages of approximately 10,000 years at these depths. Sediment age-depth relationships, sulfate reduction rates (SRR), and C/N ratios were strongly correlated with differences in microbial community composition between GI and NGI sediments, indicating that age and diagenetic state were key drivers of microbial community assembly in subsurface sediments. Similar bacterial and archaeal communities were present in the surface sediments of all stations, whereas only in GI sediments were many surface taxa also abundant through the whole sediment core. The relative abundance of these taxa, including diverse Desulfobacteraceae members, correlated positively with SRRs, indicating their active contributions to sulfur-cycling processes. In contrast, other surface community members, such as Desulfatiglans, Atribacteria, and Chloroflexi, survived the slow sediment burial at NGI stations and dominated in the deepest sediment layers. These taxa are typical for the energy-limited marine deep biosphere and their relative abundances correlated positively with sediment age. In conclusion, our data suggests that high rates of sediment accumulation caused by glacier runoff and associated changes in biogeochemistry, promote persistence of sulfur-cycling activity and burial of a larger fraction of the surface microbial community into the deep subsurface.}, }
@article {pmid31786395, year = {2020}, author = {Xu, R and Zhang, S and Meng, F}, title = {Large-sized planktonic bioaggregates possess high biofilm formation potentials: Bacterial succession and assembly in the biofilm metacommunity.}, journal = {Water research}, volume = {170}, number = {}, pages = {115307}, doi = {10.1016/j.watres.2019.115307}, pmid = {31786395}, issn = {1879-2448}, mesh = {Bacteria ; Biofilms ; Calcium Hydroxide ; *Extracellular Polymeric Substance Matrix ; Hydroxyapatites ; Phylogeny ; *Plankton ; Silicates ; }, abstract = {Wanted and unwanted surface-attached growth of bacteria is ubiquitous in natural and engineered settings. Normally, attachment of planktonic cells to media surfaces initiates biofilm formation and fundamentally regulates biofilm assembly processes. Here, culturing biofilm with planktonic sludge as source community, we found distinct succession profiles of biofilm communities sourced from the size-fractionated sludge flocs (<25; 25-120; >120 μm). Null model analyses revealed that deterministic process dominated in biofilm community assemblies but decreased with decreasing floc size. Additionally, the relative importance of environmental selection increased with increasing floc size of the source sludge, whereas homogenizing dispersal and ecological drift followed opposite trends. Phylogenetic molecular ecological networks (pMENs) indicated that species interactions were intensive in biofilm microbiota developed from large-sized flocs (>120 μm), as evidenced by the low modularity and harmonic geodesic distance and the high average degree. Intriguingly, the keystone taxa in these biofilm ecological networks were controlled by distinct interaction patterns but all showed strong habitat characteristics (e.g., facultative anaerobic, motile, hydrophobic and involved in extracellular polymeric substance metabolism), corroborating the crucial roles of environmental filtering in structuring biofilm community. Taken together, our findings highlight the role of planktonic floc properties in biofilm community assembly and advance our understanding of microbial ecology in biofilm-based systems.}, }
@article {pmid31785367, year = {2020}, author = {Wilson, JM and Platts-Mills, TAE}, title = {α-Gal and other recent findings that have informed our understanding of anaphylaxis.}, journal = {Annals of allergy, asthma &amp; immunology : official publication of the American College of Allergy, Asthma, &amp; Immunology}, volume = {124}, number = {2}, pages = {135-142}, pmid = {31785367}, issn = {1534-4436}, support = {R37 AI020565/AI/NIAID NIH HHS/United States ; }, mesh = {Allergens/*immunology ; Anaphylaxis/*etiology ; Animals ; Food Hypersensitivity/immunology ; Humans ; Immunoglobulin E/immunology ; Immunoglobulin G/immunology ; Microbiota ; alpha-Galactosidase/*immunology ; }, abstract = {OBJECTIVE: To summarize the current understanding of anaphylaxis, with an emphasis on major findings that have been reported within the last 10 years.<br><br>DATA SOURCES: Queries relating to anaphylaxis, immunoglobulin E (IgE), and mast cells were conducted with PubMed and Google Scholar, searching for primary articles and review papers.<br><br>STUDY SELECTIONS: We focused on articles written in English and which were reported in major allergy and immunology journals.<br><br>RESULTS: Anaphylaxis represents an extreme manifestation of a form of allergic immunity that appears to have evolved to protect against "toxic" threats that present at skin and mucosal barriers. The factors that have contributed to a rise in anaphylaxis are increasingly appreciated to relate to changes in hygiene and microbial ecology that have occurred with industrialization. Induction of allergen-specific IgG4 is often part of the allergic response and is associated with protection against anaphylaxis. The recognition of the &#x3b1;-Gal syndrome suggests that carbohydrates can be epitopes that are relevant to anaphylaxis and that IgE-mediated reactions do not always occur "immediately."<br><br>CONCLUSION: Our understanding of anaphylaxis has advanced significantly over the past 10 years. It is anticipated that ongoing research will build on this foundation to further advance our knowledge of anaphylaxis and also translate into clinically meaningful therapies.}, }
@article {pmid31784839, year = {2019}, author = {Chen, J and He, Y and Wang, J and Huang, M and Guo, C}, title = {Dynamics of nitrogen transformation and bacterial community with different aeration depths in malodorous river.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {35}, number = {12}, pages = {196}, pmid = {31784839}, issn = {1573-0972}, support = {41877477//National Natural Science Foundation of China/ ; 16ZR1408800//Natural Science Foundation of Shanghai/ ; 16PJD023//Shanghai Pujiang Talent Program/ ; 18DZ1203806//Shanghai Science and Technology Development Foundation/ ; 1701K005//Research Funds of The Guangxi Key Laboratory of Theory and Technology for Environmental Pollution Control/ ; }, mesh = {Bacteria/classification/genetics/*metabolism ; China ; Geologic Sediments/microbiology ; Microbiota/*physiology ; Nitrogen/*metabolism ; Oxygen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S ; Rivers/*chemistry/*microbiology ; Sulfur/metabolism ; }, abstract = {In this research, the dynamics of nitrogen transformation and bacterial community in malodorous river were investigated with different aeration depths. Computational flow dynamics (CFD) and Reynolds number (Re) were specially used to characterize the hydrodynamics condition under different aeration depths. The results indicated that aeration depth had vital impact on nitrogen transformation and bacterial community structure. It was found that a range of aeration depth (0.20-0.45 m above sediment-water interface) facilitated the removal of NH4[+]-N and TN with Re ranging between 6211 and 8930. Proteobacteria took over Firmicutes to become the predominant phylum (36-78%) under aeration, and the main subdivisions of γ-, β- and δ-Proteobacteria also varied greatly with different aeration depths. Interestingly, there was a marked shift of the inferentially identified dominant functional role within Proteobacteria from organic-matter degradation to nitrogen metabolism and then to sulfur metabolism as well as the coupling of nitrogen and sulfur with the increase of disturbance. The redundancy analysis (RDA) further confirmed the importance of aeration disturbance in shaping bacterial community. These findings help to gain improved understanding of endogenous N-behavior and aquatic microbial ecology, and underline the need for integrating the hydrodynamics factors with microbial community.}, }
@article {pmid31781077, year = {2019}, author = {Glamoclija, M and Ramirez, S and Sirisena, K and Widanagamage, I}, title = {Subsurface Microbial Ecology at Sediment-Groundwater Interface in Sulfate-Rich Playa; White Sands National Monument, New Mexico.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2595}, pmid = {31781077}, issn = {1664-302X}, abstract = {The hypersaline sediment and groundwater of playa lake, Lake Lucero, at the White Sands National Monument in New Mexico were examined for microbial community composition, geochemical gradients, and mineralogy during the dry season along a meter and a half depth profile of the sediment vs. the groundwater interface. Lake Lucero is a highly dynamic environment, strongly characterized by the capillary action of the groundwater, the extreme seasonality of the climate, and the hypersalinity. Sediments are predominantly composed of gypsum with minor quartz, thenardite, halite, quartz, epsomite, celestine, and clays. Geochemical analysis has revealed the predominance of nitrates over ammonium in all of the analyzed samples, indicating oxygenated conditions throughout the sediment column and in groundwater. Conversely, the microbial communities are primarily aerobic, gram-negative, and are largely characterized by their survival adaptations. Halophiles and oligotrophs are ubiquitous for all the samples. The very diverse communities contain methanogens, phototrophs, heterotrophs, saprophytes, ammonia-oxidizers, sulfur-oxidizers, sulfate-reducers, iron-reducers, and nitrifiers. The microbial diversity varied significantly between groundwater and sediment samples as their temperature adaptation inferences that revealed potential psychrophiles inhabiting the groundwater and thermophiles and mesophiles being present in the sediment. The dynamism of this environment manifests in the relatively even character of the sediment hosted microbial communities, where significant taxonomic distinctions were observed. Therefore, sediment and groundwater substrates are considered as separate ecological entities. We hope that the variety of the discussed playa environments and the microorganisms may be considered a useful terrestrial analog providing valuable information to aid future astrobiological explorations.}, }
@article {pmid31781072, year = {2019}, author = {Zhang, Z and Li, D and Xu, W and Tang, R and Li, L}, title = {Microbiome of Co-cultured Fish Exhibits Host Selection and Niche Differentiation at the Organ Scale.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2576}, pmid = {31781072}, issn = {1664-302X}, abstract = {Fish are the most widespread aquaculture species and maintain complex associations with microbial consortiums. However, the ecology of these associations present in multiple microhabitats in fish remains elusive, especially on the microbial assembly in fish external (skin and gill) and internal (stomach and intestine) niches, and the relationship with the rearing environment. To understand host dependence and niche differentiation of organ-specific microbiome signatures using a 16S rRNA gene-based sequencing technique, we systematically provided characterizations of a comparative framework relevant to the microbiome of stomach, regional intestine, skin, and gill in two important farmed fish species, herbivorous grass carp (Ctenopharyngodon idella) and carnivorous southern catfish (Silurus meridionalis), and of the rearing water. The different feeding habits of grass carp and southern catfish showed a significant separation of microbial community structure, with great compositional differences across body sites within each species. Site-driven divergences relied on host species: the same types of microhabitats between grass carp and southern catfish harbored differential microbiome. Additionally, body sites had remarkably distinct communities and displayed lower alpha diversity compared to rearing water. Unexpectedly, the stomach of southern catfish had the highest microbial diversity in the digestive tract of the two co-cultured fish species. For external sites within each species, a higher diversity occurred in gill of grass carp and in skin of southern catfish. Our results unveil different topographical microbiome signatures of the co-cultured species, indicating host selection in individual-level microbial assemblages and niche differentiation at the organ scale. This work represents a foundation for understanding the comprehensive microbial ecology of cohabiting farmed fish, suggesting potential applications associated with fish microbiome that urgently needs to be assessed in polycultured operations in aquaculture.}, }
@article {pmid31780680, year = {2019}, author = {Vivero, RJ and Villegas-Plazas, M and Cadavid-Restrepo, GE and Herrera, CXM and Uribe, SI and Junca, H}, title = {Wild specimens of sand fly phlebotomine Lutzomyia evansi, vector of leishmaniasis, show high abundance of Methylobacterium and natural carriage of Wolbachia and Cardinium types in the midgut microbiome.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17746}, pmid = {31780680}, issn = {2045-2322}, mesh = {Animals ; Bacteroidetes/genetics/*isolation &amp; purification ; Female ; Gastrointestinal Microbiome ; Humans ; Insect Vectors/*microbiology ; Leishmaniasis/*transmission ; Male ; Methylobacterium/genetics/*isolation &amp; purification ; Psychodidae/*microbiology ; RNA, Ribosomal, 16S/genetics ; Wolbachia/genetics/*isolation &amp; purification ; }, abstract = {Phlebotomine sand flies are remarkable vectors of several etiologic agents (virus, bacterial, trypanosomatid Leishmania), posing a heavy health burden for human populations mainly located at developing countries. Their intestinal microbiota is involved in a wide range of biological and physiological processes, and could exclude or facilitate such transmission of pathogens. In this study, we investigated the Eubacterial microbiome from digestive tracts of Lu. evansi adults structure using 16S rRNA gene sequence amplicon high throughput sequencing (Illumina MiSeq) obtained from digestive tracts of Lu. evansi adults. The samples were collected at two locations with high incidence of the disease in humans: peri-urban and forest ecosystems from the department of Sucre, Colombia. 289,068 quality-filtered reads of V4 region of 16S rRNA gene were obtained and clustered into 1,762 operational taxonomic units (OTUs) with 97% similarity. Regarding eubacterial diversity, 14 bacterial phyla and 2 new candidate phyla were found to be consistently associated with the gut microbiome content. Proteobacteria, Firmicutes, and Bacteroidetes were the most abundant phyla in all the samples and the core microbiome was particularly dominated by Methylobacterium genus. Methylobacterium species, are known to have mutualistic relationships with some plants and are involved in shaping the microbial community in the phyllosphere. As a remarkable feature, OTUs classified as Wolbachia spp. were found abundant on peri-urban ecosystem samples, in adult male (OTUs n = 776) and unfed female (OTUs n = 324). Furthermore, our results provide evidence of OTUs classified as Cardinium endosymbiont in relative abundance, notably higher with respect to Wolbachia. The variation in insect gut microbiota may be determined by the environment as also for the type of feeding. Our findings increase the richness of the microbiota associated with Lu. evansi. In this study, OTUs of Methylobacterium found in Lu. evansi was higher in engorged females, suggesting that there are interactions between microbes from plant sources, blood nutrients and the parasites they transmit during the blood intake.}, }
@article {pmid31780241, year = {2020}, author = {Lavergne, C and Bovio-Winkler, P and Etchebehere, C and García-Gen, S}, title = {Towards centralized biogas plants: Co-digestion of sewage sludge and pig manure maintains process performance and active microbiome diversity.}, journal = {Bioresource technology}, volume = {297}, number = {}, pages = {122442}, doi = {10.1016/j.biortech.2019.122442}, pmid = {31780241}, issn = {1873-2976}, mesh = {Anaerobiosis ; Animals ; Biofuels ; Bioreactors ; Manure ; Methane ; *Microbiota ; RNA, Ribosomal, 16S ; *Sewage ; Swine ; }, abstract = {The aim of this study is to assess the performance of anaerobic digestion against co-digestion systems during the start-up stages based on key process parameters and biological indicators. Two parallel experiments treating sewage sludge alone or co-digested with low concentration of pig manure (8% vol., 2-3% in COD basis) were carried out in two lab-scale CSTR at mesophilic conditions. Same inoculant and organic loading rate sequences were applied for two consecutive runs of 79 and 90 days. According to the removal efficiencies achieved, no significant differences were encountered amongst mono-digestion and co-digestion. This observation was reinforced with the analysis of the total/active microbiome, sequencing 16S rRNA genes and transcripts. The addition of a co-substrate at low concentration had a negligible effect on the total/active microbial communities; they evolved following the same pattern. This might be an advantage in order to upgrade existing wastewater treatment plants to become centralized biogas facilities.}, }
@article {pmid31779402, year = {2019}, author = {Taylor, AW and Harris, DM}, title = {Optimized commercial desktop cutter technique for rapid-prototyping of microfluidic devices and application to Taylor dispersion.}, journal = {The Review of scientific instruments}, volume = {90}, number = {11}, pages = {116102}, doi = {10.1063/1.5123130}, pmid = {31779402}, issn = {1089-7623}, abstract = {Microfluidics provides a platform for efficient and transportable microanalysis, catalyzing advancements in fields such as biochemistry, materials science, and microbial ecology. While the analysis is cost-effective, standard device fabrication techniques are disproportionately expensive and specialized. A commercially available desktop cutting plotter provides an accessible method for rapidly fabricating microfluidic devices at extremely low costs. The optimized technique described in the present work enables fabrication of microchannels with dimensions as small as ∼100 μm. Straightness of channel walls is comparable to other common fabrication techniques but achieved here at a fraction of the cost and fabrication time. Solute dispersion experiments are performed using the rapidly prototyped channels to measure the effective dispersion coefficient in laminar flow through rectangular channels. The results of these experiments compare favorably to predictions from classical Taylor-Aris dispersion theory. This note provides all necessary tools for researchers and educators to seamlessly apply the desktop cutter fabrication technique. Materials list, fabrication instructions, and detailed channel characterization results are available in the supplementary material.}, }
@article {pmid31771976, year = {2019}, author = {Janzon, A and Goodrich, JK and Koren, O and ,  and Waters, JL and Ley, RE}, title = {Interactions between the Gut Microbiome and Mucosal Immunoglobulins A, M, and G in the Developing Infant Gut.}, journal = {mSystems}, volume = {4}, number = {6}, pages = {}, pmid = {31771976}, issn = {2379-5077}, support = {U01 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK063863/DK/NIDDK NIH HHS/United States ; HHSN267200700014C/DK/NIDDK NIH HHS/United States ; U01 DK063861/DK/NIDDK NIH HHS/United States ; U01 DK063790/DK/NIDDK NIH HHS/United States ; UL1 TR001082/TR/NCATS NIH HHS/United States ; UL1 TR000064/TR/NCATS NIH HHS/United States ; U01 DK063836/DK/NIDDK NIH HHS/United States ; U01 DK063829/DK/NIDDK NIH HHS/United States ; U01 DK063865/DK/NIDDK NIH HHS/United States ; UC4 DK095300/DK/NIDDK NIH HHS/United States ; UC4 DK063861/DK/NIDDK NIH HHS/United States ; UC4 DK063829/DK/NIDDK NIH HHS/United States ; UC4 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK117483/DK/NIDDK NIH HHS/United States ; UC4 DK063836/DK/NIDDK NIH HHS/United States ; UC4 DK112243/DK/NIDDK NIH HHS/United States ; UC4 DK063865/DK/NIDDK NIH HHS/United States ; U01 DK063863/DK/NIDDK NIH HHS/United States ; UC4 DK106955/DK/NIDDK NIH HHS/United States ; UC4 DK100238/DK/NIDDK NIH HHS/United States ; }, abstract = {Interactions between the gut microbiome and immunoglobulin A (IgA) in the gut during infancy are important for future health. IgM and IgG are also present in the gut; however, their interactions with the microbiome in the developing infant remain to be characterized. Using stool samples sampled 15 times in infancy from 32 healthy subjects at 4 locations in 3 countries, we characterized patterns of microbiome development in relation to fecal levels of IgA, IgG, and IgM. For 8 infants from a single location, we used fluorescence-activated cell sorting of microbial cells from stool by Ig-coating status over 18 months. We used 16S rRNA gene profiling on full and sorted microbiomes to assess patterns of antibody coating in relation to age and other factors. All antibodies decreased in concentration with age but were augmented by breastmilk feeding regardless of infant age. Levels of IgA correlated with relative abundances of operational taxonomic units (OTUs) belonging to the Bifidobacteria and Enterobacteriaceae, which dominated the early microbiome, and IgG levels correlated with Haemophilus The diversity of Ig-coated microbiota was influenced by breastfeeding and age. IgA and IgM coated the same microbiota, which reflected the overall diversity of the microbiome, while IgG targeted a different subset. Blautia generally evaded antibody coating, while members of the Bifidobacteria and Enterobacteriaceae were high in IgA/M. IgA/M displayed similar dynamics, generally coating the microbiome proportionally, and were influenced by breastfeeding status. IgG only coated a small fraction of the commensal microbiota and differed from the proportion targeted by IgA and IgM.IMPORTANCE Antibodies are secreted into the gut and attach to roughly half of the trillions of bacterial cells present. When babies are born, the breastmilk supplies these antibodies until the baby's own immune system takes over this task after a few weeks. The vast majority of these antibodies are IgA, but two other types, IgG and IgM, are also present in the gut. Here, we ask if these three different antibody types target different types of bacteria in the infant gut as the infant develops from birth to 18 months old and how patterns of antibody coating of bacteria change with age. In this study of healthy infant samples over time, we found that IgA and IgM coat the same bacteria, which are generally representative of the diversity present, with a few exceptions that were more or less antibody coated than expected. IgG coated a separate suite of bacteria. These results provide a better understanding of how these antibodies interact with the developing infant gut microbiome.}, }
@article {pmid31769802, year = {2020}, author = {Jiménez, DJ and Wang, Y and Chaib de Mares, M and Cortes-Tolalpa, L and Mertens, JA and Hector, RE and Lin, J and Johnson, J and Lipzen, A and Barry, K and Mondo, SJ and Grigoriev, IV and Nichols, NN and van Elsas, JD}, title = {Defining the eco-enzymological role of the fungal strain Coniochaeta sp. 2T2.1 in a tripartite lignocellulolytic microbial consortium.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {1}, pages = {}, doi = {10.1093/femsec/fiz186}, pmid = {31769802}, issn = {1574-6941}, mesh = {Ascomycota/enzymology/genetics/*metabolism ; Citrobacter freundii/metabolism ; Fungal Proteins/genetics/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Lignin/*metabolism ; *Microbial Consortia ; Sphingobacterium/metabolism ; Triticum/metabolism ; }, abstract = {Coniochaeta species are versatile ascomycetes that have great capacity to deconstruct lignocellulose. Here, we explore the transcriptome of Coniochaeta sp. strain 2T2.1 from wheat straw-driven cultures with the fungus growing alone or as a member of a synthetic microbial consortium with Sphingobacterium multivorum w15 and Citrobacter freundii so4. The differential expression profiles of carbohydrate-active enzymes indicated an onset of (hemi)cellulose degradation by 2T2.1 during the initial 24 hours of incubation. Within the tripartite consortium, 63 transcripts of strain 2T2.1 were differentially expressed at this time point. The presence of the two bacteria significantly upregulated the expression of one galactose oxidase, one GH79-like enzyme, one multidrug transporter, one laccase-like protein (AA1 family) and two bilirubin oxidases, suggesting that inter-kingdom interactions (e.g. amensalism) take place within this microbial consortium. Overexpression of multicopper oxidases indicated that strain 2T2.1 may be involved in lignin depolymerization (a trait of enzymatic synergism), while S. multivorum and C. freundii have the metabolic potential to deconstruct arabinoxylan. Under the conditions applied, 2T2.1 appears to be a better degrader of wheat straw when the two bacteria are absent. This conclusion is supported by the observed suppression of its (hemi)cellulolytic arsenal and lower degradation percentages within the microbial consortium.}, }
@article {pmid31768533, year = {2020}, author = {Duysburgh, C and Ossieur, WP and De Paepe, K and Van den Abbeele, P and Vichez-Vargas, R and Vital, M and Pieper, DH and Van de Wiele, T and Hesta, M and Possemiers, S and Marzorati, M}, title = {Development and validation of the Simulator of the Canine Intestinal Microbial Ecosystem (SCIME)1.}, journal = {Journal of animal science}, volume = {98}, number = {1}, pages = {}, pmid = {31768533}, issn = {1525-3163}, mesh = {Animals ; Bacteria/*classification/isolation &amp; purification ; Dogs/*microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Humans ; Intestines/microbiology ; Lactobacillus/*physiology ; Probiotics/*analysis ; }, abstract = {Whereas a wide variety of in vitro models have been developed and validated to assess the effect of specific food ingredients on the human gut microbiome, such models have only been developed and applied to a limited extent for companion animals. Since the use of pre- and probiotics to improve gut health is an emerging research topic in the field of companion animals and as dogs are often used as laboratory animals in developing and testing of pharmaceuticals, the current study aimed to establish an adequate canine in vitro model. This consisted of a four-stage reactor composed of a stomach and small intestinal compartment followed by a proximal and distal colon. This semi-continuous gastrointestinal tract model allowed a long-term, region-dependent, and pH-controlled simulation of the colon-associated microbial community of dogs. Upon reaching a functional steady state, the simulated canine microbial community composition proved to be representative of the in vivo situation. Indeed, the predominant bacterial phyla present in the in vitro proximal and distal colon corresponded with the main bacterial phyla detected in the fecal material of the dogs, resulting in an average community composition along the simulated canine gastrointestinal tract of 50.5% Firmicutes, 34.5% Bacteroidetes, 7.4% Fusobacteria, 4.9% Actinobacteria, and 2.7% Proteobacteria. A parallel in vivo-in vitro comparison assessing the effects of fructooligosaccharides (FOS) on the canine microbial community composition showed a consistent stimulation of Lactobacillus concentrations in the in vivo fecal samples as well as in the in vitro canine gut model. Furthermore, the in vitro platform provided additional insights about the prebiotic effect of FOS supplementation of dogs, such as a reduced abundance of Megamonas spp. which are only present in very low abundance in in vivo fecal samples, indicating an interesting application potential of the developed canine in vitro model in research related to gastrointestinal health of dogs.}, }
@article {pmid31766265, year = {2019}, author = {Sun, Z and Yu, Z and Wang, B}, title = {Perilla frutescens Leaf Alters the Rumen Microbial Community of Lactating Dairy Cows.}, journal = {Microorganisms}, volume = {7}, number = {11}, pages = {}, pmid = {31766265}, issn = {2076-2607}, support = {31902181//National Natural Science Foundation of China/ ; }, abstract = {Perilla frutescens (L.) Britt., an annual herbaceous plant, has antibacterial, anti-inflammation, and antioxidant properties. To understand the effects of P. frutescens leaf on the ruminal microbial ecology of cattle, Illumina MiSeq 16S rRNA sequencing technology was used. Fourteen cows were used in a randomized complete block design trial. Two diets were fed to these cattle: a control diet (CON); and CON supplemented with 300 g/d P. frutescens leaf (PFL) per cow. Ruminal fluid was sampled at the end of the experiment for microbial DNA extraction. Overall, our findings revealed that supplementation with PFL could increase ruminal fluid pH value. The ruminal bacterial community of cattle was dominated by Bacteroidetes, Firmicutes, and Proteobacteria. The addition of PFL had a positive effect on Firmicutes, Actinobacteria, and Spirochaetes, but had no effect on Bacteroidetes and Proteobacteria compared with the CON. The supplementation with PFL significantly increased the abundance of Marvinbryantia, Acetitomaculum, Ruminococcus gauvreauii, Eubacterium coprostanoligenes, Selenomonas_1, Pseudoscardovia, norank_f__Muribaculaceae, and Sharpea, and decreased the abundance of Treponema_2 compared to CON. Eubacterium coprostanoligenes, and norank_f__Muribaculaceae were positively correlated with ruminal pH value. It was found that norank_f__Muribaculaceae and Acetitomaculum were positively correlated with milk yield, indicating that these different genera are PFL associated bacteria. This study suggests that PFL supplementation could increase the ruminal pH value and induce shifts in the ruminal bacterial composition.}, }
@article {pmid31763752, year = {2020}, author = {Zanne, AE and Abarenkov, K and Afkhami, ME and Aguilar-Trigueros, CA and Bates, S and Bhatnagar, JM and Busby, PE and Christian, N and Cornwell, WK and Crowther, TW and Flores-Moreno, H and Floudas, D and Gazis, R and Hibbett, D and Kennedy, P and Lindner, DL and Maynard, DS and Milo, AM and Nilsson, RH and Powell, J and Schildhauer, M and Schilling, J and Treseder, KK}, title = {Fungal functional ecology: bringing a trait-based approach to plant-associated fungi.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {95}, number = {2}, pages = {409-433}, doi = {10.1111/brv.12570}, pmid = {31763752}, issn = {1469-185X}, mesh = {Animals ; Databases, Factual ; Ecosystem ; Fungi/genetics/*physiology ; Plants/*microbiology ; }, abstract = {Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (Fun[Fun]). Fun[Fun] is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.}, }
@article {pmid31763477, year = {2019}, author = {Anderson, OR}, title = {Atmospheric respiratory CO2 efflux by aquatic suspended particle-bound microbial communities: A laboratory experimental study.}, journal = {Heliyon}, volume = {5}, number = {11}, pages = {e02816}, pmid = {31763477}, issn = {2405-8440}, abstract = {Natural sources of atmospheric CO2 are of increasing interest as possible contributors to global climate warming. This study documents the amount of respiratory CO2 contributed by microbial communities associated with suspended particulates in aquatic water columns. Microcosms containing three different sources of water (pond freshwater, NY East River estuary and Hudson River estuary) were used to experimentally determine the atmospheric respiratory CO2 released from particle-associated microbes. Two different approaches were used. In the first, finely powdered dried cereal leaves (alfalfa) were added to each of the three microcosms as a consistent source of particulate organic matter (POM). In the second, only Hudson River estuary water samples were used with natural densities of POM. Respiration rates associated with two sizes of particles were assessed: 1) ≥ 200 μm and 2) ≥ 50 μm but less than 200 μm. The total respiration rate for the three microcosms with cereal leaf POM ranged from 5.09 to 14.87 μmol CO2 min[-1] L[-1]. Of this, the amount contributed by larger particulates was in the range of 55-63%; and for smaller particulates ranged from 18 to 32 %. Data for microcosms containing water from the Hudson River estuary, with natural particulates, was as follows: total respiration ranged from ∼3 μmol CO2 min[-1] L[-1] to ∼3.73 μmol CO2 min[-1] L[-1]. Larger particulates contributed approximately 40% of total respiration, and that of smaller particulates was substantially less (4-5% of total). Overall, these results indicate that microbial communities associated with particulates in the water column (especially larger particulates) may contribute substantial amounts of CO2 to the atmosphere.}, }
@article {pmid31759643, year = {2020}, author = {Wen, D and Ordonez, D and McKenna, A and Chang, NB}, title = {Fate and transport processes of nitrogen in biosorption activated media for stormwater treatment at varying field conditions of a roadside linear ditch.}, journal = {Environmental research}, volume = {181}, number = {}, pages = {108915}, doi = {10.1016/j.envres.2019.108915}, pmid = {31759643}, issn = {1096-0953}, mesh = {Groundwater ; Nitrates ; *Nitrogen ; *Rain ; Waste Disposal, Fluid/*methods ; Water Purification ; Water Supply ; }, abstract = {Roadside drainage networks can result in changes to watershed hydrology and water quality. By acting as hydrological links between urban development, agricultural fields, and natural streams, roadside ditches may be modified by filling in some green sorption media to control nitrogen pollution. Biosorption activated media (BAM), one of the green sorption media, are composed of sand, tire crumb, and clay, which can remove nitrogen from stormwater and groundwater through integrated hydrological, chemophysical, and microbial processes. The fate and transport processes of interest are complicated by internal microbial processes including ammonification, nitrification, denitrification, and dissimilatory nitrate reduction to ammonium (DNRA), each of which is controlled by different microbial species in addition to some varying field conditions. In this study, BAM was tested in a suite of columns to address site-specific physical, chemical and biological concerns driven by in situ traffic compaction, carbon availability, and animal impact (such as gopher turtles, moles, and ants) all of which impose different impacts on nitrogen fate and transport processes that may be signified by changing dissolved organic nitrogen species (DONs). The traffic compaction condition resulted in the most suitable hydraulic retention time in the hydrological process, which is beneficial for the assimilation of DONs in a long-term carbon rich environment due to biofilm expansion. Denitrifiers were the most predominant microbial population and the microbial species of DNRA were the second most predominant one in all three field conditions. However, the relationship of denitrifiers and DNRA in BAM can be shifted from commensalism to competition or even inhibition after carbon addition in microbial ecology.}, }
@article {pmid31758237, year = {2020}, author = {Wang, Y and Xie, Q and Zhang, Y and Ma, W and Ning, K and Xiang, JY and Cui, J and Xiang, H}, title = {Combination of probiotics with different functions alleviate DSS-induced colitis by regulating intestinal microbiota, IL-10, and barrier function.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {1}, pages = {335-349}, doi = {10.1007/s00253-019-10259-6}, pmid = {31758237}, issn = {1432-0614}, support = {20180201078YY//Science and Technology Development Planning of Jilin/ ; }, mesh = {Animals ; Colitis/chemically induced/*prevention &amp; control ; Colon/*immunology/*microbiology ; Dextran Sulfate ; Disease Models, Animal ; Drugs, Chinese Herbal/administration &amp; dosage ; Dysbiosis ; Gastrointestinal Microbiome ; Inflammation ; Interleukin-10/genetics/*immunology ; Intestinal Mucosa/microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Probiotics/*administration &amp; dosage ; Specific Pathogen-Free Organisms ; Sulfasalazine/administration &amp; dosage ; }, abstract = {The potential of probiotics for treating ulcerative colitis (UC) has attracted increasing attention. However, more studies are still needed to guide physicians on the proper selection and use of probiotics. Here, we propose that combination of multiple probiotics with different functions can reduce intestinal inflammation. In this study, the effects of probiotics (Lactobacillus reuteri, Bacillus coagulans, Bifidobacterium longum, and Clostridium butyricum) on the physiology and histopathology of colon were evaluated in a dextran sulfate sodium (DSS)-induced colitis mouse model. The combined species, as well as the species individually, were tested and compared with sulfasalazine (SASP) and two Chinese herbal therapies. Results show that the functions of the four probiotic strains were different in regulating intestinal immunity and barrier function. The four-species probiotic cocktail was more effective than the species individually and anti-inflammatory drugs in repairing the dysbiosis of mucosal microbial ecology and reducing intestinal inflammation. The multi-strain probiotic mixture increased the proportion of beneficial bacteria and decreased the proportion of pro-inflammatory bacteria in the colonic mucosa. In addition, probiotic mixture significantly enhanced the expression of IL-10 and intestinal barrier function. These results suggest that a combination of multiple probiotics with different functions has synergistic effects and can restore the balance of interactions between microorganisms and immunological niches.}, }
@article {pmid31757825, year = {2020}, author = {Frankel-Bricker, J and Buerki, S and Feris, KP and White, MM}, title = {Influences of a Prolific Gut Fungus (Zancudomyces culisetae) on Larval and Adult Mosquito (Aedes aegypti)-Associated Microbiota.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {3}, pages = {}, pmid = {31757825}, issn = {1098-5336}, support = {P20 GM103408/GM/NIGMS NIH HHS/United States ; P20 GM109095/GM/NIGMS NIH HHS/United States ; P30 GM103324/GM/NIGMS NIH HHS/United States ; }, mesh = {Aedes/growth &amp; development/*microbiology/*physiology ; Animals ; Female ; Fungi/*physiology ; Gastrointestinal Tract/microbiology/physiology ; Larva/growth &amp; development/microbiology/physiology ; Microbiota ; }, abstract = {Adult mosquitoes inherit a bacterial community from larvae via transstadial transmission, an understudied process that may influence host-microbe interactions. Microbes contribute to important host life history traits, and analyzing transmitted microbial communities, the interrelationship between larval and adult-associated microbiota, and factors influencing host-microbe relationships provides targets for research. During its larval stage, the yellow fever mosquito (Aedes aegypti) hosts the trichomycete gut fungus Zancudomyces culisetae, and fungal colonization coincides with environmental perturbations in the digestive tract microecosystem. Natural populations are differentially exposed to fungi, thereby potentially harboring distinct microbiota and experiencing disparate host-microbe interactions. This study's objectives were to characterize larval and initial adult microbiomes, investigate variation in diversity and distribution of microbial communities across individuals, and assess whether larval fungal colonization impacted microbiomes at these developmental stages. Laboratory-based fungal infestation assays, sequencing of 16S rRNA gene amplicons, and bacterial load quantification protocols revealed that initial adult microbiomes varied in diversity and distribution. Larval fungal colonization had downstream effects on initial adult microbiomes, significantly reducing microbial community variation, shifting relative abundances of certain bacterial families, and influencing transstadial transmission outcomes of particular genera. Further, abundances of several families consistently decreased in adults relative to levels in larvae, possibly reflecting impacts of host development on specific bacterial taxa. These findings demonstrated that a prolific gut fungus impacted mosquito-associated microbiota at two developmental stages in an insect connected with global human health.IMPORTANCE Mosquitoes are widespread vectors of numerous human pathogens and harbor microbiota known to affect host phenotypic traits. However, little research has directly investigated how bacterial communities associated with larvae and adults are connected. We characterized whole-body bacterial communities in mosquito larvae preceding pupation and in newly emerged adults, and investigated whether a significant biotic factor, fungal colonization of the larval hindgut, impacted these microbiomes. Results showed that fungal colonization reduced microbial community variation across individuals and differentially impacted the outcomes of transstadial transmission for certain bacterial genera, revealing downstream effects of the fungus on initial adult microbiomes. The importance of our research is in providing a thorough comparative analysis of whole-body microbiota harbored in larvae and adults of the yellow fever mosquito (Aedes aegypti) and in demonstrating the important role a widespread gut fungus played in a host-associated microbiome.}, }
@article {pmid31757758, year = {2020}, author = {Garin-Fernandez, A and Wichels, A}, title = {Looking for the hidden: Characterization of lysogenic phages in potential pathogenic Vibrio species from the North Sea.}, journal = {Marine genomics}, volume = {51}, number = {}, pages = {100725}, doi = {10.1016/j.margen.2019.100725}, pmid = {31757758}, issn = {1876-7478}, mesh = {Lysogeny ; Myoviridae/*physiology ; North Sea ; Vibrio cholerae/*virology ; Vibrio parahaemolyticus/*virology ; }, abstract = {The incidence of potentially pathogenic Vibrio species in the marine environment around Europe, is correlated with the increase of surface seawater temperature. Despite their importance, little is known about the trigger factors of potential outbreak-causing strains in this region. As prophages may compose a major reservoir of virulence traits in marine ecosystems, this study aims to identify and characterize the genomes of lysogenic Vibrio phages exemplarily from the North Sea. Therefore, 31 isolates from potentially pathogenic Vibrio species from the North Sea were screened for inducible prophages with mitomycin C. From them, one V. cholerae isolate and 40% V. parahaemolyticus isolates carried inducible prophages. Three lysogenic phages were selected for genomic characterization. The phage vB_VpaM_VP-3212 (unclassified Myoviridae) has a genome with a length of 36.81 Kbp and 55 CDS were identified. This lysogenic phage of V. parahaemolyticus contains genes related to replicative transposition mechanism, such as transposase and mobile elements similar to Mu-like viruses. The phage vB_VpaP_VP-3220 (Podoviridae, unclassified Nona33virus) has a genome length of 58,14 Kbp and contains 63 CDS. This V. parahaemolyticus phage probably uses a headful (pac) packaging replication mechanism. The phage vB_VchM_VP-3213 (unclassified Myoviridae) has a genome with a length of 41 Kbp and 63 CDS were identified, including integrase and Xer system for lysogenic recombination. This lysogenic phage of V. cholerae has similar genomic features as lambdoid phages. Although no pathogenicity genes were identified, their similarity among other phage genomes indicates that these phages can affect the development of pathogenic Vibrio strains in marine environments.}, }
@article {pmid31757204, year = {2019}, author = {Patuzzi, I and Baruzzo, G and Losasso, C and Ricci, A and Di Camillo, B}, title = {metaSPARSim: a 16S rRNA gene sequencing count data simulator.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 9}, pages = {416}, pmid = {31757204}, issn = {1471-2105}, support = {-//Universit&#xe0; degli Studi di Padova/ ; }, mesh = {Animals ; Computer Simulation ; DNA, Ribosomal/genetics ; Databases, Genetic ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome ; *Metagenomics ; RNA, Ribosomal, 16S/*genetics ; *Software ; }, abstract = {BACKGROUND: In the last few years, 16S rRNA gene sequencing (16S rDNA-seq) has seen a surprisingly rapid increase in election rate as a methodology to perform microbial community studies. Despite the considerable popularity of this technique, an exiguous number of specific tools are currently available for proper 16S rDNA-seq count data preprocessing and simulation. Indeed, the great majority of tools have been developed adapting methodologies previously used for bulk RNA-seq data, with poor assessment of their applicability in the metagenomics field. For such tools and the few ones specifically developed for 16S rDNA-seq data, performance assessment is challenging, mainly due to the complex nature of the data and the lack of realistic simulation models. In fact, to the best of our knowledge, no software thought for data simulation are available to directly obtain synthetic 16S rDNA-seq count tables that properly model heavy sparsity and compositionality typical of these data.<br><br>RESULTS: In this paper we present metaSPARSim, a sparse count matrix simulator intended for usage in development of 16S rDNA-seq metagenomic data processing pipelines. metaSPARSim implements a new generative process that models the sequencing process with a Multivariate Hypergeometric distribution in order to realistically simulate 16S rDNA-seq count table, resembling real experimental data compositionality and sparsity. It provides ready-to-use count matrices and comes with the possibility to reproduce different pre-coded scenarios and to estimate simulation parameters from real experimental data. The tool is made available at http://sysbiobig.dei.unipd.it/?q=Software#metaSPARSimand https://gitlab.com/sysbiobig/metasparsim.<br><br>CONCLUSION: metaSPARSim is able to generate count matrices resembling real 16S rDNA-seq data. The availability of count data simulators is extremely valuable both for methods developers, for which a ground truth for tools validation is needed, and for users who want to assess state of the art analysis tools for choosing the most accurate one. Thus, we believe that metaSPARSim is a valuable tool for researchers involved in developing, testing and using robust and reliable data analysis methods in the context of 16S rRNA gene sequencing.}, }
@article {pmid31757073, year = {2019}, author = {Yssel, AEJ and Kao, SM and Van de Peer, Y and Sterck, L}, title = {ORCAE-AOCC: A Centralized Portal for the Annotation of African Orphan Crop Genomes.}, journal = {Genes}, volume = {10}, number = {12}, pages = {}, pmid = {31757073}, issn = {2073-4425}, mesh = {*Databases, Genetic ; *Genome, Plant ; *Molecular Sequence Annotation ; }, abstract = {ORCAE (Online Resource for Community Annotation of Eukaryotes) is a public genome annotation curation resource. ORCAE-AOCC is a branch that is dedicated to the genomes published as part of the African Orphan Crops Consortium (AOCC). The motivation behind the development of the ORCAE platform was to create a knowledge-based website where the research-community can make contributions to improve genome annotations. All changes to any given gene-model or gene description are stored, and the entire annotation history can be retrieved. Genomes can either be set to "public" or "restricted" mode; anonymous users can browse public genomes but cannot make any changes. Aside from providing a user-&amp;nbsp;friendly interface to view genome annotations, the platform also includes tools and information (such as gene expression evidence) that enables authorized users to edit and validate genome annotations. The ORCAE-AOCC platform will enable various stakeholders from around the world to coordinate their efforts to annotate and study underutilized crops.}, }
@article {pmid31756853, year = {2019}, author = {Suleiman, AKA and Harkes, P and van den Elsen, S and Holterman, M and Korthals, GW and Helder, J and Kuramae, EE}, title = {Organic amendment strengthens interkingdom associations in the soil and rhizosphere of barley (Hordeum vulgare).}, journal = {The Science of the total environment}, volume = {695}, number = {}, pages = {133885}, doi = {10.1016/j.scitotenv.2019.133885}, pmid = {31756853}, issn = {1879-1026}, mesh = {Agriculture ; Bacteria ; Biota ; Ecosystem ; Eukaryota ; Fertilizers ; Food Chain ; Fungi ; *Hordeum ; *Rhizosphere ; Soil ; *Soil Microbiology ; }, abstract = {Anthropogenic modification of soil systems has diverse impacts on food web interactions and ecosystem functioning. To understand the positive, neutral or adverse effects of agricultural practices on the associations of community members of soil microbes and microfaunal biomes, we characterized the effects of different fertilization types (organic, inorganic and a combination of organic and inorganic) on the food web active communities in the bulk soil and rhizosphere compartments in field conditions. We examined the influence of fertilization on (i) individual groups (bacteria, protozoa and fungi as microbe representatives and metazoans as microfauna representatives) and (ii) inter-kingdom interactions (focusing on the interactions between bacteria and eukaryotic groups) both neglecting and considering environmental factors in our analysis in combination with the microbial compositional data. Our results revealed different patterns of biota communities under organic versus inorganic fertilization, which shaped food web associations in both the bulk and rhizosphere compartments. Overall, organic fertilization increased the complexity of microbial-microfaunal ecological associations with inter- and intra- connections among categories of primary decomposers (bacteria and fungi) and predators (protozoa and microfauna) and differences in potential function in the soil food web in both the bulk and rhizosphere compartments. Furthermore, the inter-connections between primary decomposers and predators in bulk soil were more pronounced when environmental factors were considered. We suggest that organic fertilization selects bacterial orders with different potential ecological functions and interactions as survival, predation and cooperation due to more complex environment than those of inorganic or combined fertilization. Our findings support the importance of a comprehensive understanding of trophic food web patterns for soil management systems.}, }
@article {pmid31756842, year = {2019}, author = {Hylling, O and Nikbakht Fini, M and Ellegaard-Jensen, L and Muff, J and Madsen, HT and Aamand, J and Hansen, LH}, title = {A novel hybrid concept for implementation in drinking water treatment targets micropollutant removal by combining membrane filtration with biodegradation.}, journal = {The Science of the total environment}, volume = {694}, number = {}, pages = {133710}, doi = {10.1016/j.scitotenv.2019.133710}, pmid = {31756842}, issn = {1879-1026}, mesh = {*Biodegradation, Environmental ; Drinking Water/*chemistry ; *Filtration ; Water Pollutants, Chemical/*analysis ; Water Purification/*methods ; }, abstract = {Groundwater extracted for drinking water production is commonly treated by aeration and sand filtration. However, this simple treatment is typically unable to remove pesticide residues. As a solution, bioaugmentation of sand filter units (i.e., the addition of specific degrader strains) has been proposed as an alternative "green" technology for targeted pesticide removal. However, the introduced degraders are challenged by (i) micropollutant levels of target residue, (ii) the oligotrophic environment and (iii) competition and predation by the native microorganisms, leading to loss of population and degradation potential. To overcome these challenges, we propose the introduction of a novel hybrid treatment step to the overall treatment process in which reverse osmosis filtration and biodegradation are combined to remove a target micropollutant. Here, the reverse osmosis produces a concentrated retentate that will act as a feed to a dedicated biofilter unit, intended to promote biodegradation potential and stability of an introduced degrader. Subsequently, the purified retentate will be re-mixed with the permeate from reverse osmosis, for re-mineralization and downstream consumption. In our study, we investigated the effect of reverse osmosis retentates on the degradation potential of an introduced degrader. This paper provides the first promising results of this hybrid concept using the 2,6-dichlorobenzamide (BAM)-degrading bacteria Aminobacter sp. MSH1 in batch experiments, spiked with radiolabeled BAM. The results showed an increased degradation potential of MSH1 in retentate waters versus untreated water. Colony-forming units and qPCR showed a stable MSH1 population, despite higher concentrations of salts and metals, and increased growth of native bacteria.}, }
@article {pmid31756831, year = {2019}, author = {Iqbal, A and Shang, Z and Rehman, MLU and Ju, M and Rehman, MMU and Rafiq, MK and Ayub, N and Bai, Y}, title = {Pattern of microbial community composition and functional gene repertoire associated with methane emission from Zoige wetlands, China-A review.}, journal = {The Science of the total environment}, volume = {694}, number = {}, pages = {133675}, doi = {10.1016/j.scitotenv.2019.133675}, pmid = {31756831}, issn = {1879-1026}, mesh = {China ; Methane/*metabolism ; *Microbiota ; *Soil Microbiology ; *Wetlands ; }, abstract = {The Hindu-Kush Himalaya region extends over 4 million km[2] across the eight countries. Knowingly, the Qinghai-Tibetan Plateau (QTP) is considered the principal altitudinal permafrost constituent on earth and is deemed as the third 'pole'. Among which, the Zoige wetlands are located in the northeastern boundary of QTP, wrapping a total area of 6180 km[2] with an average altitude of 3500 m. This entire region is the hotspot for methane emission since the last decade. Given the importance of methane emission, many studies have focused on the effect of environmental fluctuations on the overall methane profile and, more recently on the methanogenic community structure. The current review summarizes recent advancements of the methanogenic community and methane profile and outlines a framework for better understanding of the microbial ecology of the Zoige wetlands, China. Moreover, as microorganisms are indispensable to biogeochemical cycles, especially for methane, they are believed to be the best indicators to identify the condition of wetlands. Hence, we suggest that, underpinning the microbial profile could help understand the status of a wetland.}, }
@article {pmid31754744, year = {2020}, author = {Rajagopala, SV and Singh, H and Yu, Y and Zabokrtsky, KB and Torralba, MG and Moncera, KJ and Frank, B and Pieper, R and Sender, L and Nelson, KE}, title = {Persistent Gut Microbial Dysbiosis in Children with Acute Lymphoblastic Leukemia (ALL) During Chemotherapy.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {1034-1043}, doi = {10.1007/s00248-019-01448-x}, pmid = {31754744}, issn = {1432-184X}, mesh = {Adolescent ; Anti-Bacterial Agents/*administration &amp; dosage ; Antineoplastic Agents/*administration &amp; dosage ; Case-Control Studies ; Child ; Child, Preschool ; Cohort Studies ; Dysbiosis/chemically induced/*microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infant ; Male ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/*drug therapy ; }, abstract = {Prophylactic or therapeutic antibiotic use along with chemotherapy treatment potentially has a long-standing adverse effect on the resident gut microbiota. We have established a case-control cohort of 32 pediatric and adolescent acute lymphoblastic leukemia (ALL) patients and 25 healthy siblings (sibling controls) to assess the effect of chemotherapy as well as antibiotic prophylaxis on the gut microbiota. We observe that the microbiota diversity and richness of the ALL group is significantly lower than that of the control group at diagnosis and during chemotherapy. The microbiota diversity is even lower in antibiotics-exposed ALL patients. Although the gut microbial diversity tends to stabilize after 1-year post-chemotherapy, their abundances were altered because of chemotherapy and prophylactic antibiotic treatments. Specifically, the abundances of mucolytic gram-positive anaerobic bacteria, including Ruminococcus gnavus and Ruminococcus torques, tended to increase during the chemotherapy regimen and continued to be elevated 1 year beyond the initiation of chemotherapy. This dysbiosis may contribute to the development of gastrointestinal complications in ALL children following chemotherapy. These findings set the stage to further understand the role of the gut microbiome dynamics in ALL patients and their potential role in alleviating some of the adverse side effects of chemotherapy and antibiotics use in immunocompromised children.}, }
@article {pmid31753627, year = {2020}, author = {Vázquez-Blanco, R and Arias-Estévez, M and Bååth, E and Fernández-Calviño, D}, title = {Comparison of Cu salts and commercial Cu based fungicides on toxicity towards microorganisms in soil.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {257}, number = {}, pages = {113585}, doi = {10.1016/j.envpol.2019.113585}, pmid = {31753627}, issn = {1873-6424}, mesh = {Copper/*toxicity ; Environmental Pollution ; Fungicides, Industrial/*toxicity ; Salts ; Soil ; *Soil Microbiology ; Soil Pollutants/*toxicity ; }, abstract = {Microbial responses to Cu pollution as a function of Cu sources (Cu salts and commercial Cu fungicides) were assessed in a soil using basal soil respiration, and bacterial and fungal community growth, as endpoints. The soil was amended with different concentrations (0-32 mmol Cu kg[-1]) of Cu nitrate, Cu sulfate, Bordeaux mixture and 3 types of Cu oxychloride. Cu salts decreased soil pH, while this was not found with the other Cu sources. This difference in soil pH effects caused differences in the respiration, bacterial growth and fungal growth response. Basal soil respiration was negatively affected by Cu addition when the soil was spiked with Cu salts, but almost unaffected by commercial Cu fungicides. Bacterial growth was significantly and negatively affected by Cu addition for all the Cu sources, but Cu toxicity was higher for Cu salts than for commercial Cu fungicides. Fungal growth response was also different for Cu salts and commercial Cu fungicides, but only in the long-term. High Cu amendments using Cu salts stimulated fungal growth, whereas for commercial Cu fungicides, these concentrations inhibited fungal growth. Thus, the use of products similar to those used in commercial fungicides is a recommended practice for Cu risk assessments in soil.}, }
@article {pmid31750314, year = {2019}, author = {Gupta, VVSR and Zhang, B and Penton, CR and Yu, J and Tiedje, JM}, title = {Diazotroph Diversity and Nitrogen Fixation in Summer Active Perennial Grasses in a Mediterranean Region Agricultural Soil.}, journal = {Frontiers in molecular biosciences}, volume = {6}, number = {}, pages = {115}, pmid = {31750314}, issn = {2296-889X}, abstract = {Summer-growing perennial grasses such as Panicum coloratum L. cv. Bambatsi (Bambatsi panic), Chloris gayana Kunth cv. Katambora (Rhodes grass) and Digitaria eriantha Steud. cv. Premier (Premier digit grass) growing in the poor fertility sandy soils in the Mediterranean regions of southern Australia and western Australia mainly depend upon soil N and biological N inputs through diazotrophic (free living or associative) N fixation. We investigated the community composition and diversity (nifH-amplicon sequencing), abundance (qPCR) and functional capacity ([15]N incubation assay) of the endophytic diazotrophic community in the below and above ground plant parts of field grown and unfertilized grasses. Results showed a diverse and abundant diazotrophic community inside plant both above and below-ground and there was a distinct diazotrophic assemblage in the different plant parts in all the three grasses. There was a limited difference in the diversity between leaves, stems and roots except that Panicum grass roots harbored greater species richness. Nitrogen fixation potentials ranged between 0.24 and 5.9 mg N kg[-1] day[-1] and N fixation capacity was found in both the above and below ground plant parts. Results confirmed previous reports of plant species-based variation and that Alpha-Proteobacteria were the dominant group of nifH-harboring taxa both in the belowground and aboveground parts of the three grass species. Results also showed a well-structured nifH-harboring community in all plant parts, an example for a functional endophytic community. Overall, the variation in the number and identity of module hubs and connectors among the different plant parts suggests that co-occurrence patterns within the nifH-harboring community specific to individual compartments and local environments of the niches within each plant part may dictate the overall composition of diazotrophs within a plant.}, }
@article {pmid31749830, year = {2019}, author = {Guo, J and Quensen, JF and Sun, Y and Wang, Q and Brown, CT and Cole, JR and Tiedje, JM}, title = {Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {957}, pmid = {31749830}, issn = {1664-8021}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, abstract = {Shotgun metagenomics has greatly advanced our understanding of microbial communities over the last decade. Metagenomic analyses often include assembly and genome binning, computationally daunting tasks especially for big data from complex environments such as soil and sediments. In many studies, however, only a subset of genes and pathways involved in specific functions are of interest; thus, it is not necessary to attempt global assembly. In addition, methods that target genes can be computationally more efficient and produce more accurate assembly by leveraging rich databases, especially for those genes that are of broad interest such as those involved in biogeochemical cycles, biodegradation, and antibiotic resistance or used as phylogenetic markers. Here, we review six gene-targeted assemblers with unique algorithms for extracting and/or assembling targeted genes: Xander, MegaGTA, SAT-Assembler, HMM-GRASPx, GenSeed-HMM, and MEGAN. We tested these tools using two datasets with known genomes, a synthetic community of artificial reads derived from the genomes of 17 bacteria, shotgun sequence data from a mock community with 48 bacteria and 16 archaea genomes, and a large soil shotgun metagenomic dataset. We compared assemblies of a universal single copy gene (rplB) and two N cycle genes (nifH and nirK). We measured their computational efficiency, sensitivity, specificity, and chimera rate and found Xander and MegaGTA, which both use a probabilistic graph structure to model the genes, have the best overall performance with all three datasets, although MEGAN, a reference matching assembler, had better sensitivity with synthetic and mock community members chosen from its reference collection. Also, Xander and MegaGTA are the only tools that include post-assembly scripts tuned for common molecular ecology and diversity analyses. Additionally, we provide a mathematical model for estimating the probability of assembling targeted genes in a metagenome for estimating required sequencing depth.}, }
@article {pmid31749167, year = {2020}, author = {Ferlian, O and Thakur, MP and Castañeda González, A and San Emeterio, LM and Marr, S and da Silva Rocha, B and Eisenhauer, N}, title = {Soil chemistry turned upside down: a meta-analysis of invasive earthworm effects on soil chemical properties.}, journal = {Ecology}, volume = {101}, number = {3}, pages = {e02936}, pmid = {31749167}, issn = {1939-9170}, support = {677232/ERC_/European Research Council/International ; FZT 118//German Research Foundation/International ; 677232//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program/International ; TH 2307/1-1//German Research Foundation/International ; }, mesh = {Animals ; Ecosystem ; Forests ; *Oligochaeta ; Soil ; Soil Microbiology ; }, abstract = {Recent studies have shown that invasive earthworms can dramatically reduce native biodiversity, both above and below the ground. However, we still lack a synthetic understanding of the underlying mechanisms behind these changes, such as whether earthworm effects on soil chemical properties drive such relationships. Here, we investigated the effects of invasive earthworms on soil chemical properties (pH, water content, and the stocks and fluxes of carbon, nitrogen, and phosphorus) by conducting a meta-analysis. Invasive earthworms generally increased soil pH, indicating that the removal of organic layers and the upward transport of more base-rich mineral soil caused a shift in soil pH. Moreover, earthworms significantly decreased soil water content, suggesting that the burrowing activities of earthworms may have increased water infiltration of and/or increased evapotranspiration from soil. Notably, invasive earthworms had opposing effects on organic and mineral soil for carbon and nitrogen stocks, with decreases in organic, and increases in mineral soil. Nitrogen fluxes were higher in mineral soil, whereas fluxes in organic soil were not significantly affected by the presence of invasive earthworms, indicating that earthworms mobilize and redistribute nutrients among soil layers and increase overall nitrogen loss from the soil. Invasive earthworm effects on element stocks increased with ecological group richness only in organic soil. Earthworms further decreased ammonium stocks with negligible effects on nitrate stocks in organic soil, whereas they increased nitrate stocks but not ammonium stocks in mineral soil. Notably, all of these results were consistent across forest and grassland ecosystems underlining the generality of our findings. However, we found some significant differences between studies that were conducted in the field (observational and experimental settings) and in the lab, such as that the effects on soil pH decreased from field to lab settings, calling for a careful interpretation of lab findings. Our meta-analysis provides strong empirical evidence that earthworm invasion may lead to substantial changes in soil chemical properties and element cycling in soil. Furthermore, our results can help explain the dramatic effects of invasive earthworms on native biodiversity, for example, shifts towards the dominance of grass species over herbaceous ones, as shown by recent meta-analyses.}, }
@article {pmid31748246, year = {2019}, author = {Tomkovich, S and Lesniak, NA and Li, Y and Bishop, L and Fitzgerald, MJ and Schloss, PD}, title = {The Proton Pump Inhibitor Omeprazole Does Not Promote Clostridioides difficile Colonization in a Murine Model.}, journal = {mSphere}, volume = {4}, number = {6}, pages = {}, pmid = {31748246}, issn = {2379-5042}, support = {U01 AI124255/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Carrier State/*immunology ; Clostridioides difficile/*growth &amp; development ; Clostridium Infections/*immunology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Disease Models, Animal ; *Disease Susceptibility ; Feces/microbiology ; Mice ; Microbiota/drug effects ; Omeprazole/administration &amp; dosage/*adverse effects ; Phylogeny ; Proton Pump Inhibitors/administration &amp; dosage/*adverse effects ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Proton pump inhibitor (PPI) use has been associated with microbiota alterations and susceptibility to Clostridioides difficile infections (CDIs) in humans. We assessed how PPI treatment alters the fecal microbiota and whether treatment promotes CDIs in a mouse model. Mice receiving a PPI treatment were gavaged with 40 mg of omeprazole per kg of body weight during a 7-day pretreatment phase, the day of C. difficile challenge, and the following 9 days. We found that mice treated with omeprazole were not colonized by C. difficile When omeprazole treatment was combined with a single clindamycin treatment, one cage of mice remained resistant to C. difficile colonization, while the other cage was colonized. Treating mice with only clindamycin followed by challenge resulted in C. difficile colonization. 16S rRNA gene sequencing analysis revealed that omeprazole had minimal impact on the structure of the murine microbiota throughout the 16 days of omeprazole exposure. These results suggest that omeprazole treatment alone is not sufficient to disrupt microbiota resistance to C. difficile infection in mice that are normally resistant in the absence of antibiotic treatment.IMPORTANCE Antibiotics are the primary risk factor for Clostridioides difficile infections (CDIs), but other factors may also increase a person's risk. In epidemiological studies, proton pump inhibitor (PPI) use has been associated with CDI incidence and recurrence. PPIs have also been associated with alterations in the human intestinal microbiota in observational and interventional studies. We evaluated the effects of the PPI omeprazole on the structure of the murine intestinal microbiota and its ability to disrupt colonization resistance to C. difficile We found omeprazole treatment had minimal impact on the murine fecal microbiota and did not promote C. difficile colonization. Further studies are needed to determine whether other factors contribute to the association between PPIs and CDIs seen in humans or whether aspects of murine physiology may limit its utility to test these types of hypotheses.}, }
@article {pmid31743949, year = {2020}, author = {Weber, L and González-Díaz, P and Armenteros, M and Ferrer, VM and Bretos, F and Bartels, E and Santoro, AE and Apprill, A}, title = {Microbial signatures of protected and impacted Northern Caribbean reefs: changes from Cuba to the Florida Keys.}, journal = {Environmental microbiology}, volume = {22}, number = {1}, pages = {499-519}, pmid = {31743949}, issn = {1462-2920}, support = {//Dalio Foundation/International ; 1736288//Division of Ocean Sciences/International ; //National Science Foundation/International ; //Cuban Center for Inspection and Environmental Control/International ; }, mesh = {Animals ; Anthozoa/*microbiology ; Archaea/classification/*genetics/isolation &amp; purification ; Bacteria/classification/*genetics/isolation &amp; purification ; Caribbean Region ; Coral Reefs ; Cuba ; Florida ; Humans ; Microbiota/genetics ; Seawater/*microbiology ; }, abstract = {There are a few baseline reef-systems available for understanding the microbiology of healthy coral reefs and their surrounding seawater. Here, we examined the seawater microbial ecology of 25 Northern Caribbean reefs varying in human impact and protection in Cuba and the Florida Keys, USA, by measuring nutrient concentrations, microbial abundances, and respiration rates as well as sequencing bacterial and archaeal amplicons and community functional genes. Overall, seawater microbial composition and biogeochemistry were influenced by reef location and hydrogeography. Seawater from the highly protected 'crown jewel' offshore reefs in Jardines de la Reina, Cuba had low concentrations of nutrients and organic carbon, abundant Prochlorococcus, and high microbial community alpha diversity. Seawater from the less protected system of Los Canarreos, Cuba had elevated microbial community beta-diversity whereas waters from the most impacted nearshore reefs in the Florida Keys contained high organic carbon and nitrogen concentrations and potential microbial functions characteristic of microbialized reefs. Each reef system had distinct microbial signatures and within this context, we propose that the protection and offshore nature of Jardines de la Reina may preserve the oligotrophic paradigm and the metabolic dependence of the community on primary production by picocyanobacteria.}, }
@article {pmid31742865, year = {2020}, author = {Geesink, P and Wegner, CE and Probst, AJ and Herrmann, M and Dam, HT and Kaster, AK and Küsel, K}, title = {Genome-inferred spatio-temporal resolution of an uncultivated Roizmanbacterium reveals its ecological preferences in groundwater.}, journal = {Environmental microbiology}, volume = {22}, number = {2}, pages = {726-737}, doi = {10.1111/1462-2920.14865}, pmid = {31742865}, issn = {1462-2920}, support = {2016 FGI 0024//Th&#xfc;ringer Ministerium f&#xfc;r Wirtschaft, Wissenschaft und Digitale Gesellschaft/International ; CRC 1076//Collaborative Research Centre AquaDiva/International ; ANR-10-INBS-09//France G&#xe9;nomique and French Bioinformatics Institute/International ; ANR-11-INBS-0013//France G&#xe9;nomique and French Bioinformatics Institute/International ; //LABGeM (CEA/Genoscope &amp; CNRS UMR8030)/International ; SAS-2015-HKI-LWC//Leibniz Research Cluster InfectoOptics/International ; //Ministerium f&#xfc;r Kultur und Wissenschaft des Landes Nordrhein-Westfalen/International ; 41-5507-2016//Strategy and Innovation Grant from the Free State of Thuringia/International ; //Agence Nationale pour la Recherche/International ; //Deutsche Forschungsgemeinschaft/International ; //Friedrich Schiller University Jena/International ; }, mesh = {Bacteria/genetics/*metabolism ; *Bacterial Physiological Phenomena ; Carbon ; Groundwater/*microbiology ; Lactic Acid/*metabolism ; Metagenomics ; Microbial Interactions/*physiology ; Microbiota/genetics/physiology ; RNA, Ribosomal, 16S/genetics ; Spatio-Temporal Analysis ; Symbiosis ; }, abstract = {Subsurface ecosystems like groundwater harbour diverse microbial communities, including small-sized, putatively symbiotic organisms of the Candidate Phyla Radiation, yet little is known about their ecological preferences and potential microbial partners. Here, we investigated a member of the superphylum Microgenomates (Cand. Roizmanbacterium ADI133) from oligotrophic groundwater using mini-metagenomics and monitored its spatio-temporal distribution using 16S rRNA gene analyses. A Roizmanbacteria-specific quantitative PCR assay allowed us to track its abundance over the course of 1 year within eight groundwater wells along a 5.4 km hillslope transect, where Roizmanbacteria reached maximum relative abundances of 2.3%. In-depth genomic analyses suggested that Cand. Roizmanbacterium ADI133 is a lactic acid fermenter, potentially able to utilize a range of complex carbon substrates, including cellulose. We hypothesize that it attaches to host cells using a trimeric autotransporter adhesin and inhibits their cell wall biosynthesis using a toxin-antitoxin system. Network analyses based on correlating Cand. Roizmanbacterium ADI133 abundances with amplicon sequencing-derived microbial community profiles suggested one potential host organism, classified as a member of the class Thermodesulfovibrionia (Nitrospirae). By providing lactate as an electron donor Cand. Roizmanbacterium ADI133 potentially mediates the transfer of carbon to other microorganisms and thereby is an important connector in the microbial community.}, }
@article {pmid31741310, year = {2020}, author = {Alves, KJ and da Silva, MCP and Cotta, SR and Ottoni, JR and van Elsas, JD and de Oliveira, VM and Andreote, FD}, title = {Mangrove soil as a source for novel xylanase and amylase as determined by cultivation-dependent and cultivation-independent methods.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {51}, number = {1}, pages = {217-228}, pmid = {31741310}, issn = {1678-4405}, support = {Finance Code 001.//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {Bacillus/genetics/isolation &amp; purification/metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Bacterial Proteins/genetics ; Cellulose/metabolism ; Endo-1,4-beta Xylanases/*genetics/metabolism ; Genes, Bacterial/genetics ; Metagenomics ; Paenibacillus/genetics/isolation &amp; purification/metabolism ; Planctomycetales/classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S ; *Soil Microbiology ; Starch/metabolism ; *Wetlands ; alpha-Amylases/*genetics/metabolism ; }, abstract = {Xylanase and α-amylase enzymes participate in the degradation of organic matter, acting in hemicellulose and starch mineralization, respectively, and are in high demand for industrial use. Mangroves represent a promising source for bioprospecting enzymes due to their unique characteristics, such as fluctuations in oxic/anoxic conditions and salinity. In this context, the present work aimed to bioprospect xylanases from mangrove soil using cultivation-dependent and cultivation-independent methods. Through screening from a metagenomic library, three potentially xylanolytic clones were obtained and sequenced, and reads were assembled into contigs and annotated. The contig MgrBr135 was affiliated with the Planctomycetaceae family and was one of 30 ORFs selected for subcloning that demonstrated only amylase activity. Through the cultivation method, 38 bacterial isolates with xylanolytic activity were isolated. Isolate 11 showed an enzymatic index of 10.9 using the plate assay method. Isolate 39 achieved an enzyme activity of 0.43 U/mL using the colorimetric method with 3,5-dinitrosalicylic acid. Isolate 39 produced xylanase on culture medium with salinity ranging from 1.25 to 5%. Partial 16S rRNA gene sequencing identified isolates in the Bacillus and Paenibacillus genera. The results of this study highlight the importance of mangroves as an enzyme source and show that bacterial groups can be used for starch and hemicellulose degradation.}, }
@article {pmid31741007, year = {2020}, author = {Hayek, M and Baraquet, C and Lami, R and Blache, Y and Molmeret, M}, title = {The Marine Bacterium Shewanella woodyi Produces C8-HSL to Regulate Bioluminescence.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {865-881}, doi = {10.1007/s00248-019-01454-z}, pmid = {31741007}, issn = {1432-184X}, mesh = {Homoserine/*analogs &amp; derivatives/biosynthesis ; Lactones ; *Luminescence ; *Quorum Sensing ; Shewanella/*physiology ; }, abstract = {Quorum sensing (QS), a cell-to-cell communication system involved in the synchronization of bacterial behavior in a cell-density-dependent manner has been shown to control phenotypes such as luminescence, virulence, and biofilm formation. The marine strain, Shewanella woodyi MS32 has been identified as a luminous bacterium. Very little information is known on this bacterium, in particular if its luminescence and biofilm formation are controlled by QS. In this study, we have demonstrated that S. woodyi MS32 emits luminescence in planktonic and sessile conditions. The putative QS regulatory genes homologous to luxI and luxR identified in the S. woodyi MS32 genome, named swoI and swoR, are divergently transcribed and are not genetically linked to the lux operon in contrast with its closest parent Shewanella hanedai and with Aliivibrio fischeri. Interestingly, the phylogenetic analysis based on the SwoI and SwoR sequences shows that a separate horizontal gene transfer (HGT) occurred for the regulatory genes and for the lux operon. Functional analyses demonstrate that the swoI and swoR mutants were non-luminescent. Expression of lux genes was impaired in the QS regulatory mutants. N-octanoyl-L-homoserine lactone (C8-HSL) identified using liquid chromatography mass spectrometry in the wild-type strain (but not in ΔswoI) can induce S. woodyi luminescence. No significant difference has been detected between the wild-type and mutants on adhesion and biofilm formation in the conditions tested. Therefore, we have demonstrated that the luxCDABEG genes of S. woodyi MS32 are involved in luminescence emission and that the swoR/swoI genes, originated from a separate HGT, regulate luminescence through C8-HSL production.}, }
@article {pmid31737577, year = {2019}, author = {Khan, S and Voordouw, MJ and Hill, JE}, title = {Competition Among Gardnerella Subgroups From the Human Vaginal Microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {374}, pmid = {31737577}, issn = {2235-2988}, mesh = {Biofilms ; Female ; Gardnerella/*physiology ; Gram-Positive Bacterial Infections/*microbiology ; Humans ; Metagenome ; Metagenomics/methods ; *Microbial Interactions ; Microbiota ; RNA, Ribosomal, 16S ; Vagina/*microbiology ; Vaginosis, Bacterial/*microbiology ; }, abstract = {Gardnerella spp. are hallmarks of bacterial vaginosis, a clinically significant dysbiosis of the vaginal microbiome. Gardnerella has four subgroups (A, B, C, and D) based on cpn60 sequences. Multiple subgroups are often detected in individual women, and interactions between these subgroups are expected to influence their population dynamics and associated clinical signs and symptoms of bacterial vaginosis. In the present study, contact-independent and contact-dependent interactions between the four Gardnerella subgroups were investigated in vitro. The cell free supernatants of mono- and co-cultures had no effect on growth rates of the Gardnerella subgroups suggesting that there are no contact-independent interactions (and no contest competition). For contact-dependent interactions, mixed communities of 2, 3, or 4 subgroups were created and the initial (0 h) and final population sizes (48 h) were quantified using subgroup-specific PCR. Compared to the null hypothesis of neutral interactions, most (69.3%) of the mixed communities exhibited competition. Competition reduced the growth rates of subgroups A, B, and C. In contrast, the growth rate of subgroup D increased in the presence of the other subgroups. All subgroups were able to form biofilm alone and in mixed communities. Our study suggests that there is scramble competition among Gardnerella subgroups, which likely contributes to the observed distributions of Gardnerella spp. in vaginal microbiomes and the formation of the multispecies biofilms characteristic of bacterial vaginosis.}, }
@article {pmid31737020, year = {2019}, author = {Del Frari, G and Gobbi, A and Aggerbeck, MR and Oliveira, H and Hansen, LH and Ferreira, RB}, title = {Fungicides and the Grapevine Wood Mycobiome: A Case Study on Tracheomycotic Ascomycete Phaeomoniella chlamydospora Reveals Potential for Two Novel Control Strategies.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {1405}, pmid = {31737020}, issn = {1664-462X}, abstract = {Phaeomoniella chlamydospora is a tracheomycotic fungus that colonizes the xylem of grapevines (Vitis vinifera L.), causing wood discoloration, brown wood streaking, gummosis, and wood necrosis, which negatively affect the overall health, productivity, and life span of vines. Current control strategies to prevent or cope with P. chlamydospora infections are frequently ineffective. Moreover, it is unclear how fungicides commonly applied in vineyards against downy and powdery mildew agents affect the wood mycobiome, including wood pathogens such as P. chlamydospora. In this study, we used next-generation sequencing to assess the effects of foliar spray of grapevines with inorganic (copper oxychloride and sulfur), synthetic (penconazole and fosetyl-aluminum), and natural (Blad) fungicides currently used against the downy and powdery mildews. The subjects of our investigation were (i) the resident wood mycobiome, (ii) the early colonization by a consortium of fungal wood endophytes (ACEA1), (iii) the wood colonization success of P. chlamydospora, and (iv) the in planta interaction between P. chlamydospora and ACEA1, under greenhouse conditions, in rooted grapevine cuttings of cv. Cabernet Sauvignon. The data obtained suggest that the resident mycobiome is affected by different fungicide treatments. In addition, the early colonization success of the endophytes composing ACEA1 varied in response to fungicides, with relative abundances of some taxa being overrepresented or underrepresented when compared with the control. The wood colonization by P. chlamydospora comported significant changes in the mycobiome composition, and in addition, it was greatly affected by the foliar spray with Blad, which decreased the relative abundance of this pathogen 12-fold (4.9%) when compared with the control (60.7%) and other treatments. The presence of the pathogen also decreased considerably when co-inoculated into the plant with ACEA1, reaching relative abundances between 13.9% and 2.0%, depending on the fungicide treatment applied. This study shows that fungicides sprayed to prevent infections of powdery and downy mildews have an effect on non-target fungi that colonize the endosphere of grapevines. We suggest two potential control strategies to fight P. chlamydospora, namely, the foliar spray with Blad and the use of ACEA1. Further studies to confirm these results are required.}, }
@article {pmid31736494, year = {2019}, author = {Villela, HDM and Vilela, CLS and Assis, JM and Varona, N and Burke, C and Coil, DA and Eisen, JA and Peixoto, RS}, title = {Prospecting Microbial Strains for Bioremediation and Probiotics Development for Metaorganism Research and Preservation.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {152}, pages = {}, doi = {10.3791/60238}, pmid = {31736494}, issn = {1940-087X}, mesh = {Animals ; Anthozoa/microbiology ; Bacteria/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Microbial Consortia ; Microbiota ; Probiotics/*pharmacology ; }, abstract = {Pollution affects all biomes. Marine environments have been particularly impacted, especially coral reefs, one of the most sensitive ecosystems on Earth. Globally, 4.5 billion people are economically dependent on the sea, where most of their livelihood is provided by coral reefs. Corals are of great importance and therefore their extinction leads to catastrophic consequences. There are several possible solutions to remediate marine pollutants and local contamination, including bioremediation. Bioremediation is the capacity of organisms to degrade contaminants. The approach presents several advantages, such as sustainability, relatively low cost, and the fact that it can be applied in different ecosystems, causing minimal impacts to the environment. As an extra advantage, the manipulation of endogenous microbiomes, including putative beneficial microorganisms for corals (pBMCs), may have probiotic effects for marine animals. In this context, the use of the two approaches, bioremediation and pBMC inoculation combined, could be promising. This strategy would promote the degradation of specific pollutants that can be harmful to corals and other metaorganisms while also increasing host resistance and resilience to deal with pollution and other threats. This method focuses on the selection of pBMCs to degrade two contaminants: the synthetic estrogen 17a-ethinylestradiol (EE2) and crude oil. Both have been reported to negatively impact marine animals, including corals, and humans. The protocol describes how to isolate and test bacteria capable of degrading the specific contaminants, followed by a description of how to detect some putative beneficial characteristics of these associated microbes to their coral host. The methodologies described here are relatively cheap, easy to perform, and highly adaptable. Almost any kind of soluble target compound can be used instead of EE2 and oil.}, }
@article {pmid31736217, year = {2020}, author = {Paver, SF and Newton, RJ and Coleman, ML}, title = {Microbial communities of the Laurentian Great Lakes reflect connectivity and local biogeochemistry.}, journal = {Environmental microbiology}, volume = {22}, number = {1}, pages = {433-446}, pmid = {31736217}, issn = {1462-2920}, support = {OCE-1830011//Division of Ocean Sciences/International ; NA14OAR170095//Illinois-Indiana Sea Grant/International ; //UChicago Women's Board/International ; }, mesh = {Actinobacteria/classification/genetics/*isolation &amp; purification ; Alphaproteobacteria/classification/genetics/*isolation &amp; purification ; Archaea/classification/genetics/*isolation &amp; purification ; Chloroflexi/classification/genetics/*isolation &amp; purification ; Lakes/*microbiology ; Michigan ; Microbiota/*genetics ; Phylogeny ; Plankton/classification/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The Laurentian Great Lakes are a vast, interconnected freshwater system spanning strong physicochemical gradients, thus constituting a powerful natural laboratory for addressing fundamental questions about microbial ecology and evolution. We present a comparative analysis of pelagic microbial communities across all five Laurentian Great Lakes, focusing on Bacterial and Archaeal picoplankton characterized via 16S rRNA amplicon sequencing. We collected samples throughout the water column from the major basins of each lake in spring and summer over 2 years. Two oligotypes, classified as LD12 (Alphaproteobacteria) and acI-B1 (Actinobacteria), were among the most abundant in every sample. At the same time, microbial communities showed distinct patterns with depth during summer stratification. Deep hypolimnion samples were frequently dominated by a Chloroflexi oligotype that reached up to 19% relative abundance. Stratified surface communities differed between the colder, less productive upper lakes (Superior, Michigan, Huron) and warmer, more productive lower lakes (Erie, Ontario), in part due to an Actinobacteria oligotype (acI-C2) that averaged 7.7% of sequences in the lower lakes but <0.2% in the upper lakes. Together, our findings suggest that both hydrologic connectivity and local selective pressures shape microbial communities in the Great Lakes and establish a framework for future investigations.}, }
@article {pmid31734636, year = {2020}, author = {Sikder, MNA and Xu, H}, title = {Seasonal variations in colonization dynamics of periphytic protozoa in coastal waters of the Yellow Sea, northern China.}, journal = {European journal of protistology}, volume = {72}, number = {}, pages = {125643}, doi = {10.1016/j.ejop.2019.125643}, pmid = {31734636}, issn = {1618-0429}, mesh = {*Biodiversity ; China ; Ciliophora/*physiology ; Environmental Monitoring ; Logistic Models ; *Seasons ; Seawater/*parasitology ; }, abstract = {The colonization features of periphytic protozoa have proved to be a useful tool for indicating water quality status in aquatic ecosystems. In order to reveal the seasonal variations in colonization dynamics of the protozoa, a 1-year baseline survey was carried out in coastal waters of the Yellow Sea, northern China. Using glass slides as artificial substrates, a total of 240 slides were collected at a depth of 1 m in four seasons after colonization periods of 3, 7, 10, 14, 21, and 28 days. A total of 122 ciliate species were identified with 21 dominant species. The colonization dynamics of the protozoa were well fitted to the MacArthur-Wilson and logistic models in all four seasons (P < 0.05). However, the equilibrium species numbers (Seq), colonization rates (G), and the time to 90% Seq (T90%) represented a clear seasonal variability: (1) more or less similar levels in spring and autumn (Seq = 29/23; G = 0.301/0.296; T90%=7.650/7.779); (2) with a significant difference in summer and winter (Seq = 32/121; G = 0.708/0.005; T90% = 3.252/479.705). Multivariate approaches demonstrated that the exposure time for the species composition and community structure of the protozoa to an equilibrium period were 10-14 days in spring and autumn, but less and more time periods were needed in summer and winter, respectively. Based on the results, we suggest that the colonization dynamics of periphytic protozoa were different within four seasons, and an optimal sampling strategy for monitoring surveys should be modified during different seasons in marine ecosystems.}, }
@article {pmid31734395, year = {2020}, author = {Clauwaert, P and De Paepe, J and Jiang, F and Alonso-Fariñas, B and Vaiopoulou, E and Verliefde, A and Rabaey, K}, title = {Electrochemical tap water softening: A zero chemical input approach.}, journal = {Water research}, volume = {169}, number = {}, pages = {115263}, doi = {10.1016/j.watres.2019.115263}, pmid = {31734395}, issn = {1879-2448}, mesh = {Electrodes ; Ion Exchange ; *Water Purification ; *Water Softening ; }, abstract = {Electrochemical water softening was proposed as a sustainable alternative for ion exchange softening, avoiding the input of salt to drinking water and the production of a concentrated brine. Here we demonstrated two novel modes of operation combining an electrochemical cell with a fluidized bed crystallizer. The first approach relied on an electrochemical cell consisting of an anode and cathode separated by a cation or anion exchange membrane. The feed water was first directed into a crystallizer where it was blended with alkaline cathode effluent. The effluent of the crystallizer, softened water, was in part recirculated to the cathode to generate alkalinity, in part to the anode compartment, where the pH was again decreased. Average removal efficiencies for calcium and magnesium of 75-86% and 7-21% respectively, could be sustainably reached, at a specific energy consumption of 7.0-10.1 kWh kg[-1] CaCO3 (0.86-1.39 kWh m[-3] water). This configuration allowed reagent-free water softening, albeit with an effluent with a pH between 3.0 and 3.6. In a second mode of operation, the process influent to soften was also directed to the crystallizer and recirculated over the cathode, which was separated from the anode using an anion exchange membrane. In this mode of operation, the cathode effluent was sent through the crystallizing unit, and the anode compartment was operated in closed-loop. Average calcium and magnesium removal efficiencies of 73-78% and 40-44% were obtained at specific energy consumptions of 5.8-7.5 kWh kg[-1] CaCO3 (0.77-0.88 kWh m[-3] water). Although the softened water had an elevated pH (∼9.4), the advantage of this configuration is concomitant removal of anions and the formation of acids/disinfectant in the anode compartment. Both methods of operation thus showed reagent-free water softening at a relatively low specific energy consumption. These novel methods of softening could be used in remote locations where access to chemicals or discharge of ion exchange brines proves to be difficult, or in case addition of chemicals for softening is unwanted. Further research is needed to further decrease the specific energy consumption during long-term operation.}, }
@article {pmid31732938, year = {2019}, author = {Dutzan, N and Abusleme, L}, title = {T Helper 17 Cells as Pathogenic Drivers of Periodontitis.}, journal = {Advances in experimental medicine and biology}, volume = {1197}, number = {}, pages = {107-117}, doi = {10.1007/978-3-030-28524-1_9}, pmid = {31732938}, issn = {0065-2598}, mesh = {Animals ; Cell Differentiation ; Disease Models, Animal ; Humans ; Inflammation ; Interleukin-17/immunology ; *Periodontitis/physiopathology ; *Th17 Cells/cytology/immunology ; }, abstract = {T helper 17 (Th17) cells were first described as a T helper subset involved in the pathogenesis of experimental autoimmune inflammation. Since then, these cells have been described as orchestrators of immunopathology in several human inflammatory conditions including psoriasis, rheumatoid arthritis, and inflammatory bowel disease. More recently, the crucial role of Th17 cells in the regulation of immunity and protection of barrier sites has been unveiled. In the present work, we review the available evidence regarding Th17 cells in health and disease with a focus on the oral mucosa and their role in periodontitis pathogenesis. Recent mechanistic studies in animal models have demonstrated that interleukin-17A (IL-17A) and Th17 cells are critical mediators for alveolar bone destruction during periodontal inflammation. Observations in a cohort of patients with naturally occurring impaired Th17 cell differentiation supported these findings. However, interventional studies are needed to conclusively implicate Th17 cells in the immunopathogenesis of human alveolar bone and tissue destruction that characterize periodontitis.}, }
@article {pmid31732575, year = {2020}, author = {Custer, GF and van Diepen, LTA and Stump, WL}, title = {Structural and Functional Dynamics of Soil Microbes following Spruce Beetle Infestation.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {3}, pages = {}, pmid = {31732575}, issn = {1098-5336}, mesh = {Animals ; Bacterial Physiological Phenomena ; Fungi/physiology ; *Herbivory ; *Microbiota ; Mycobiome ; Picea/*physiology ; *Soil Microbiology ; Weevils/*physiology ; Wyoming ; }, abstract = {As the range of bark beetles expands into new forests and woodlands, the need to understand their effects on multiple trophic levels becomes increasingly important. To date, much attention has been paid to the aboveground processes affected by bark beetle infestation, with a focus on photoautotrophs and ecosystem level processes. However, indirect effects of bark beetle on belowground processes, especially the structure and function of soil microbiota remains largely a black box. Our study examined the impacts of bark beetle-induced tree mortality on soil microbial community structure and function using high-throughput sequencing of the soil bacterial and fungal communities and measurements of extracellular enzyme activities. The results suggest bark beetle infestation affected edaphic conditions through increased soil water content, pH, electrical conductivity, and carbon/nitrogen ratio and altered bulk and rhizosphere soil microbial community structure and function. Finally, increased enzymatic activity suggests heightened microbial decomposition following bark beetle infestation. With this increase in enzymatic activity, nutrients trapped in organic substrates may become accessible to seedlings and potentially alter the trajectory of forest regeneration. Our results indicate the need for incorporation of microbial processes into ecosystem level models.IMPORTANCE Belowground impacts of bark beetle infestation have not been explored as thoroughly as their aboveground counterparts. In order to accurately model impacts of bark beetle-induced tree mortality on carbon and nutrient cycling and forest regeneration, the intricacies of soil microbial communities must be examined. In this study, we investigated the structure and function of soil bacterial and fungal communities following bark beetle infestation. Our results show bark beetle infestation to impact soil conditions, as well as soil microbial community structure and function.}, }
@article {pmid31732073, year = {2019}, author = {Lee, M and Song, JH and Park, JM and Chang, JY}, title = {Bacterial diversity in Korean temple kimchi fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {126}, number = {}, pages = {108592}, doi = {10.1016/j.foodres.2019.108592}, pmid = {31732073}, issn = {1873-7145}, mesh = {Animals ; Bacteria/*classification/genetics ; Cell Survival ; *Fermentation ; Fermented Foods/classification/*microbiology ; *Food Microbiology ; Hydrogen-Ion Concentration ; Lactobacillales ; RNA, Ribosomal, 16S ; Republic of Korea ; Salts ; Vegans ; Vegetables/microbiology ; }, abstract = {Kimchi is manufactured using salted vegetables and various seasonings, including garlic, scallion, and jeotgal (fermented seafood). However, similar to vegan diets, Korean temple food does not contain animal products (meat- and seafood-free) and is restricted to five pungent herbs: garlic, scallion, leek, onions, and chives. In this study, we investigated the fermentation characteristics of 25 kimchi samples from traditional Korean temples or commercial sources using Illumina MiSeq sequencing. The initial pH of the kimchi samples ranged from 5.05 to 5.95 and the bacterial diversity-index showed a significantly high value in temple-style kimchi. Moreover, differences in microbial community were significantly reflected in kimchi types using non-metric multidimensional scaling plots and analysis of similarity. Additionally, the distribution patterns of the core bacterial genera differed according to kimchi type, especially during early phases of fermentation. These findings offer novel insights into the microbial ecology and quality characteristics of kimchi lacking vital ingredients, which are generally reported based on the origin of the microorganisms.}, }
@article {pmid31731161, year = {2020}, author = {Ma, W and Li, J and Gao, Y and Xing, F and Sun, S and Zhang, T and Zhu, X and Chen, C and Li, Z}, title = {Responses of soil extracellular enzyme activities and microbial community properties to interaction between nitrogen addition and increased precipitation in a semi-arid grassland ecosystem.}, journal = {The Science of the total environment}, volume = {703}, number = {}, pages = {134691}, doi = {10.1016/j.scitotenv.2019.134691}, pmid = {31731161}, issn = {1879-1026}, mesh = {China ; Ecosystem ; Grassland ; *Microbiota ; Nitrogen ; *Soil ; Soil Microbiology ; }, abstract = {Both atmospheric nitrogen (N) deposition and precipitation can strongly impact below-ground biogeochemical processes. Soil extracellular enzymes activities (EEAs) and microorganisms are considered as the key agents in ecosystem nutrient cycling. However, how the interaction between increasing N deposition and precipitation may affect soil EEAs and microbes remain poorly understood. In a 5-year field experiment in a meadow steppe in northern China, we tested the effects of N addition (N0, 0; N1, 5; N2, 10 g N m[-2] yr[-1]) and increased precipitation (W0, ambient precipitation; W1, increase of 15% ambient precipitation; W2, increase of 30% ambient precipitation) on soil EEAs, microbial and chemical properties. Results showed that their interaction significantly affected all hydrolase activities, except for β-1,4-xylosidase (βX). Furthermore, increased precipitation and N addition interactively affected bacterial gene copies (P ≤ 0.05), and increased precipitation comparatively had a stronger effects. The results on the combination of N addition and increased precipitation showed that increased precipitation alleviated the positive effects of N addition on soil EEAs. This implies that the effects of either treatment alone on grassland biogeochemical processes may be alleviated by their simultaneous occurrence. Our results suggested that soil EEAs were mainly controlled by the content of N and phosphorus (P), and the ratio of C: N and C: P. Therefore, soil element content and stoichiometry could better explain the responses of EEAs to global changes. Moreover, soil microbial communities were mainly controlled by soil P content. Overall, our study highlights that the interaction between N deposition and precipitation may play a vital role in predicting the responses of soil enzyme activities to global changes in grassland ecosystems.}, }
@article {pmid31730850, year = {2019}, author = {Salazar, G and Paoli, L and Alberti, A and Huerta-Cepas, J and Ruscheweyh, HJ and Cuenca, M and Field, CM and Coelho, LP and Cruaud, C and Engelen, S and Gregory, AC and Labadie, K and Marec, C and Pelletier, E and Royo-Llonch, M and Roux, S and Sánchez, P and Uehara, H and Zayed, AA and Zeller, G and Carmichael, M and Dimier, C and Ferland, J and Kandels, S and Picheral, M and Pisarev, S and Poulain, J and ,  and Acinas, SG and Babin, M and Bork, P and Bowler, C and de Vargas, C and Guidi, L and Hingamp, P and Iudicone, D and Karp-Boss, L and Karsenti, E and Ogata, H and Pesant, S and Speich, S and Sullivan, MB and Wincker, P and Sunagawa, S}, title = {Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome.}, journal = {Cell}, volume = {179}, number = {5}, pages = {1068-1083.e21}, pmid = {31730850}, issn = {1097-4172}, mesh = {*Gene Expression Regulation ; Geography ; *Metagenome ; Microbiota/genetics ; Molecular Sequence Annotation ; *Oceans and Seas ; RNA, Messenger/genetics/metabolism ; Seawater/microbiology ; Temperature ; Transcriptome/*genetics ; }, abstract = {Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. VIDEO ABSTRACT.}, }
@article {pmid31730030, year = {2020}, author = {Hofmann, K and Huptas, C and Doll, EV and Scherer, S and Wenning, M}, title = {Pseudomonas saxonica sp. nov., isolated from raw milk and skimmed milk concentrate.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {70}, number = {2}, pages = {935-943}, doi = {10.1099/ijsem.0.003851}, pmid = {31730030}, issn = {1466-5034}, mesh = {Animals ; Bacterial Typing Techniques ; Base Composition ; Cattle ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Female ; *Food Microbiology ; Genes, Bacterial ; Germany ; Milk/*microbiology ; Multilocus Sequence Typing ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; Pseudomonas/*classification/isolation &amp; purification ; Quinones/chemistry ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {A polyphasic approach was used to investigate the taxonomic status of two bacterial strains, WS 5072[T] and WS 5092, isolated from skimmed milk concentrate and raw cow's milk. The 16S rRNA and rpoD gene sequences affiliated the strains to the same, hitherto unknown, Pseudomonas species. Further examinations of the draft genomes based on multilocus sequence analysis and average nucleotide identity confirmed the presence of a novel Pseudomonas species. It was most closely related to Pseudomonas fragi DSM 3456[T] with 86.3 % ANIm. The DNA G+C content of strain WS 5072[T] was 56.3 mol%. Cells were aerobic, Gram-negative, catalase and oxidase positive, rod-shaped and motile. Growth occurred at 4-34 °C, pH 5.5-8.0 and with salt concentrations of up to 7 %. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The dominating quinone was Q-9 with 94 %, with noticeable amounts of Q-8 (5 %) and traces of Q-7 and Q-10. Fatty acid profiles showed a composition common for Pseudomonas with the major component C16 : 0. Based on these results, the novel species Pseudomonas saxonica sp. nov. is proposed, with the type strain WS 5072[T] (=DSM 108989[T]=LMG 31234[T]) and the additional strain WS 5092 (=DSM 108990=LMG 31235).}, }
@article {pmid31728602, year = {2020}, author = {Quero, GM and Celussi, M and Relitti, F and Kovačević, V and Del Negro, P and Luna, GM}, title = {Inorganic and Organic Carbon Uptake Processes and Their Connection to Microbial Diversity in Meso- and Bathypelagic Arctic Waters (Eastern Fram Strait).}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {823-839}, doi = {10.1007/s00248-019-01451-2}, pmid = {31728602}, issn = {1432-184X}, mesh = {Arctic Regions ; Autotrophic Processes ; Bacteria/metabolism ; Carbon/*metabolism ; *Carbon Cycle ; Heterotrophic Processes ; *Microbiota ; Oceans and Seas ; Seawater/*chemistry ; Svalbard ; }, abstract = {The deep Arctic Ocean is increasingly vulnerable to climate change effects, yet our understanding of its microbial processes is limited. We collected samples from shelf waters, mesopelagic Atlantic Waters (AW) and bathypelagic Norwegian Sea Deep Waters (NSDW) in the eastern Fram Strait, along coast-to-offshore transects off Svalbard during boreal summer. We measured community respiration, heterotrophic carbon production (HCP), and dissolved inorganic carbon utilization (DICu) together with prokaryotic abundance, diversity, and metagenomic predictions. In deep samples, HCP was significantly faster in AW than in NSDW, while we observed no differences in DICu rates. Organic carbon uptake was higher than its inorganic counterpart, suggesting a major reliance of deep microbial Arctic communities on heterotrophic metabolism. Community structure and spatial distribution followed the hydrography of water masses. Distinct from other oceans, the most abundant OTU in our deep samples was represented by the archaeal MG-II. To address the potential biogeochemical role of each water mass-specific microbial community, as well as their link with the measured rates, PICRUSt-based predicted metagenomes were built. The results showed that pathways of auto- and heterotrophic carbon utilization differed between the deep water masses, although this was not reflected in measured DICu rates. Our findings provide new insights to understand microbial processes and diversity in the dark Arctic Ocean and to progress toward a better comprehension of the biogeochemical cycles and their trends in light of climate changes.}, }
@article {pmid31728601, year = {2020}, author = {Chen, H and Wang, L and Wang, X and Wang, X and Liu, H and Yin, Y}, title = {Distribution and Strain Diversity of Immunoregulating Segmented Filamentous Bacteria in Human Intestinal Lavage Samples.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {1021-1033}, doi = {10.1007/s00248-019-01441-4}, pmid = {31728601}, issn = {1432-184X}, mesh = {Adolescent ; Bacteria/classification/*isolation &amp; purification ; Child ; Child, Preschool ; China ; Female ; Flagellin/analysis ; *Gastrointestinal Microbiome ; Humans ; Ileum/*microbiology/ultrastructure ; Infant ; Male ; Microscopy, Electron, Scanning ; }, abstract = {Segmented filamentous bacteria (SFB) are well known for their functions in the immunoregulation of hosts including the promotion of Th17 cell differentiation, B cell maturation, and immune system development. However, most analyses of SFB have focused on animal models, and thus, investigation of SFB prevalence in humans and their roles in human immunoregulation and health is needed. Although little is known overall of SFB prevalence in humans, they are characteristically abundant in animals during weaning. In this study, SFB-like bacteria were detected in ileal lavage samples from human children that were aged between 1 to 17 years old by scanning electron microscopy (SEM) analysis, and their insertion into the mucosa was also observed. In addition, the expression of SFB flagellin at the human bacterial interface was observed by immunohistochemistry (IHC) and western blot. Moreover, two pairs of primers specific for SFB, but targeting different genes, were used to detect SFB in human intestinal lavage samples. These analyses indicated that SFB were present in over 50% of patient ileal samples independent of age. High-throughput gene sequencing indicated that different SFB strains were detected among samples. Between nine and 23 SFB flagellin gene operational taxonomic units were identified. In addition to evaluating the prevalence of SFB in human samples, correlations between SFB presence and chief complaints of clinical symptoms were evaluated, as well as the relationship between SFB and patient serum immunoglobulin concentrations. SFB prevalence was significantly higher in hematochezia patients (68%) than in abdominal pain (56.10%) and diarrhea (43.75%) patients. Furthermore, the concentrations of serum IgA, IgM, and IgE, were similar between SFB-positive and SFB-negative patient groups, although IgG concentrations were significantly higher in the SFB-negative group.}, }
@article {pmid31728526, year = {2020}, author = {Corrêa, FB and Saraiva, JP and Stadler, PF and da Rocha, UN}, title = {TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes.}, journal = {Nucleic acids research}, volume = {48}, number = {D1}, pages = {D626-D632}, pmid = {31728526}, issn = {1362-4962}, mesh = {Computational Biology/*methods ; Data Mining ; *Databases, Genetic ; Ecology ; Ecosystem ; Genome, Bacterial ; Geography ; Internet ; *Metadata ; *Metagenome ; Soil Microbiology ; User-Computer Interface ; }, abstract = {Microbiome studies focused on the genetic potential of microbial communities (metagenomics) became standard within microbial ecology. MG-RAST and the Sequence Read Archive (SRA), the two main metagenome repositories, contain over 202 858 public available metagenomes and this number has increased exponentially. However, mining databases can be challenging due to misannotated, misleading and decentralized data. The main goal of TerrestrialMetagenomeDB is to make it easier for scientists to find terrestrial metagenomes of interest that could be compared with novel datasets in meta-analyses. We defined terrestrial metagenomes as those that do not belong to marine environments. Further, we curated the database using text mining to assign potential descriptive keywords that better contextualize environmental aspects of terrestrial metagenomes, such as biomes and materials. TerrestrialMetagenomeDB release 1.0 includes 15 022 terrestrial metagenomes from SRA and MG-RAST. Together, the downloadable data amounts to 68 Tbp. In total, 199 terrestrial terms were divided into 14 categories. These metagenomes span 83 countries, 30 biomes and 7 main source materials. The TerrestrialMetagenomeDB is publicly available at https://webapp.ufz.de/tmdb.}, }
@article {pmid31728072, year = {2019}, author = {Wu, L and Ning, D and Zhang, B and Li, Y and Zhang, P and Shan, X and Zhang, Q and Brown, MR and Li, Z and Van Nostrand, JD and Ling, F and Xiao, N and Zhang, Y and Vierheilig, J and Wells, GF and Yang, Y and Deng, Y and Tu, Q and Wang, A and ,  and Zhang, T and He, Z and Keller, J and Nielsen, PH and Alvarez, PJJ and Criddle, CS and Wagner, M and Tiedje, JM and He, Q and Curtis, TP and Stahl, DA and Alvarez-Cohen, L and Rittmann, BE and Wen, X and Zhou, J}, title = {Author Correction: Global diversity and biogeography of bacterial communities in wastewater treatment plants.}, journal = {Nature microbiology}, volume = {4}, number = {12}, pages = {2579}, doi = {10.1038/s41564-019-0617-0}, pmid = {31728072}, issn = {2058-5276}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid31727695, year = {2019}, author = {Aremu, BR and Prigent-Combaret, C and Babalola, OO}, title = {Draft Genome Sequence of Bacillus velezensis Strain ZeaDK315Endo16.}, journal = {Microbiology resource announcements}, volume = {8}, number = {46}, pages = {}, pmid = {31727695}, issn = {2576-098X}, abstract = {Here, we report the draft genome sequence of the endophytic Bacillus velezensis strain ZeaDK315Endo16, isolated from DK315 maize from Lyon, France. B. velezensis ZeaDK315Endo16 exhibits a suppressive ability toward Fusarium graminearum, a widely known threat to maize production and quality.}, }
@article {pmid31727118, year = {2019}, author = {Werner, J and Géron, A and Kerssemakers, J and Matallana-Surget, S}, title = {mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation.}, journal = {Biology direct}, volume = {14}, number = {1}, pages = {21}, pmid = {31727118}, issn = {1745-6150}, mesh = {*Databases, Protein ; Molecular Sequence Annotation/*methods ; *Proteome ; Proteomics/*methods ; }, abstract = {Metaproteomics allows to decipher the structure and functionality of microbial communities. Despite its rapid development, crucial steps such as the creation of standardized protein search databases and reliable protein annotation remain challenging. To overcome those critical steps, we developed a new program named mPies (metaProteomics in environmental sciences). mPies allows the creation of protein databases derived from assembled or unassembled metagenomes, and/or public repositories based on taxon IDs, gene or protein names. For the first time, mPies facilitates the automatization of reliable taxonomic and functional consensus annotations at the protein group level, minimizing the well-known protein inference issue, which is commonly encountered in metaproteomics. mPies' workflow is highly customizable with regards to input data, workflow steps, and parameter adjustment. mPies is implemented in Python 3/Snakemake and freely available on GitHub: https://github.com/johanneswerner/mPies/. REVIEWER: This article was reviewed by Dr. Wilson Wen Bin Goh.}, }
@article {pmid31726596, year = {2020}, author = {Boada, E and Santos-Clotas, E and Bertran, S and Cabrera-Codony, A and Martín, MJ and Bañeras, L and Gich, F}, title = {Potential use of Methylibium sp. as a biodegradation tool in organosilicon and volatile compounds removal for biogas upgrading.}, journal = {Chemosphere}, volume = {240}, number = {}, pages = {124908}, doi = {10.1016/j.chemosphere.2019.124908}, pmid = {31726596}, issn = {1879-1298}, mesh = {Anaerobiosis ; Biodegradation, Environmental ; Biofuels/*analysis ; Bioreactors/*microbiology ; Burkholderiales/*growth &amp; development ; Organosilicon Compounds/*analysis ; Volatile Organic Compounds/*analysis ; Water Purification/methods ; }, abstract = {Organosilicon compounds are the most undesirable compounds for the energy recovery of biogas. These compounds are still resistant to biodegradation when biotechnologies are considered for biogas purification. Herein we isolated 52 bacterial species from anaerobic batch enrichment cultures (BEC) saturated with D4 and from an anaerobic lab-scale biotrickling filter (BTF) fed with a gas flow containing D4 as unique carbon source. Among those Methylibium sp. and Pseudomonas aeruginosa showed the highest capacity to remove D4 (53.04% ± 0.03 and 24.42% ± 0.02, respectively). Contrarily, co-culture evaluation treatment for the biodegradation of siloxanes together with volatile organic compounds removed a lower concentration of D4 compared to toluene and limonene, which were completely removed. Remarkably, the siloxane D5 proved to be more biodegradable than D4. Substrates removal values achieved by Methylibium sp. suggested that this bacterial isolate could be used in biological removal technologies of siloxanes.}, }
@article {pmid31726031, year = {2019}, author = {Rolhion, N and Chassaing, B and Nahori, MA and de Bodt, J and Moura, A and Lecuit, M and Dussurget, O and Bérard, M and Marzorati, M and Fehlner-Peach, H and Littman, DR and Gewirtz, AT and Van de Wiele, T and Cossart, P}, title = {A Listeria monocytogenes Bacteriocin Can Target the Commensal Prevotella copri and Modulate Intestinal Infection.}, journal = {Cell host &amp; microbe}, volume = {26}, number = {5}, pages = {691-701.e5}, pmid = {31726031}, issn = {1934-6069}, support = {TL1 TR001447/TR/NCATS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteriocins/*pharmacology ; Female ; Gastrointestinal Microbiome/*drug effects/genetics/physiology ; Germ-Free Life ; Humans ; Inflammation/prevention &amp; control ; Listeria monocytogenes/*metabolism ; Listeriosis/microbiology/*prevention &amp; control ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Prevotella/drug effects/*growth &amp; development ; }, abstract = {Understanding the role of the microbiota components in either preventing or favoring enteric infections is critical. Here, we report the discovery of a Listeria bacteriocin, Lmo2776, which limits Listeria intestinal colonization. Oral infection of conventional mice with a Δlmo2776 mutant leads to a thinner intestinal mucus layer and higher Listeria loads both in the intestinal content and deeper tissues compared to WT Listeria. This latter difference is microbiota dependent, as it is not observed in germ-free mice. Strikingly, it is phenocopied by pre-colonization of germ-free mice before Listeria infection with Prevotella copri, an abundant gut-commensal bacteria, but not with the other commensals tested. We further show that Lmo2776 targets P. copri and reduces its abundance. Together, these data unveil a role for P.copri in exacerbating intestinal infection, highlighting that pathogens such as Listeria may selectively deplete microbiota bacterial species to avoid excessive inflammation.}, }
@article {pmid31723261, year = {2019}, author = {Schada von Borzyskowski, L and Severi, F and Krüger, K and Hermann, L and Gilardet, A and Sippel, F and Pommerenke, B and Claus, P and Cortina, NS and Glatter, T and Zauner, S and Zarzycki, J and Fuchs, BM and Bremer, E and Maier, UG and Amann, RI and Erb, TJ}, title = {Marine Proteobacteria metabolize glycolate via the β-hydroxyaspartate cycle.}, journal = {Nature}, volume = {575}, number = {7783}, pages = {500-504}, pmid = {31723261}, issn = {1476-4687}, mesh = {Alcohol Oxidoreductases/metabolism ; Aldehyde-Lyases/metabolism ; Aquatic Organisms/enzymology/*metabolism ; Aspartic Acid/*analogs &amp; derivatives/metabolism ; Biocatalysis ; Glycolates/*metabolism ; Glyoxylates/metabolism ; Hydro-Lyases/metabolism ; Kinetics ; *Metabolic Networks and Pathways ; Oxidoreductases/metabolism ; Phytoplankton/enzymology/metabolism ; Proteobacteria/enzymology/*metabolism ; Transaminases/metabolism ; }, abstract = {One of the most abundant sources of organic carbon in the ocean is glycolate, the secretion of which by marine phytoplankton results in an estimated annual flux of one petagram of glycolate in marine environments[1]. Although it is generally accepted that glycolate is oxidized to glyoxylate by marine bacteria[2-4], the further fate of this C2 metabolite is not well understood. Here we show that ubiquitous marine Proteobacteria are able to assimilate glyoxylate via the β-hydroxyaspartate cycle (BHAC) that was originally proposed 56 years ago[5]. We elucidate the biochemistry of the BHAC and describe the structure of its key enzymes, including a previously unknown primary imine reductase. Overall, the BHAC enables the direct production of oxaloacetate from glyoxylate through only four enzymatic steps, representing-to our knowledge-the most efficient glyoxylate assimilation route described to date. Analysis of marine metagenomes shows that the BHAC is globally distributed and on average 20-fold more abundant than the glycerate pathway, the only other known pathway for net glyoxylate assimilation. In a field study of a phytoplankton bloom, we show that glycolate is present in high nanomolar concentrations and taken up by prokaryotes at rates that allow a full turnover of the glycolate pool within one week. During the bloom, genes that encode BHAC key enzymes are present in up to 1.5% of the bacterial community and actively transcribed, supporting the role of the BHAC in glycolate assimilation and suggesting a previously undescribed trophic interaction between autotrophic phytoplankton and heterotrophic bacterioplankton.}, }
@article {pmid31722990, year = {2019}, author = {Dominguez-Mirazo, M and Jin, R and Weitz, JS}, title = {Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in "Candidatus Liberibacter asiaticus".}, journal = {mSphere}, volume = {4}, number = {6}, pages = {}, pmid = {31722990}, issn = {2379-5042}, mesh = {Citrus/microbiology ; Computational Biology ; *Genomics ; Plant Diseases/microbiology ; Prophages/*genetics ; Rhizobiaceae/genetics/*growth &amp; development/isolation &amp; purification/*virology ; Virulence ; }, abstract = {Huanglongbing disease (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen "Candidatus Liberibacter asiaticus" is an alphaproteobacterium of the Rhizobiaceae family that has been identified as the causative agent of HLB. The virulence of "Ca. Liberibacter asiaticus" has been attributed, in part, to prophage-carried genes. Prophage and prophage-like elements have been identified in 12 of the 15 available "Ca. Liberibacter asiaticus" genomes and are classified into three prophage types. Here, we reexamined all 15 "Ca. Liberibacter asiaticus" genomes using a de novo prediction approach and expanded the number of prophage-like elements from 16 to 33. Further, we found that all of the "Ca. Liberibacter asiaticus" genomes contained at least one prophage-like sequence. Comparative analysis revealed a prevalent, albeit previously unknown, prophage-like sequence type that is a remnant of an integrated prophage. Notably, this remnant prophage is found in the Ishi-1 "Ca. Liberibacter asiaticus" strain that had previously been reported as lacking prophages. Our findings provide both a resource for data and new insights into the evolutionary relationship between phage and "Ca. Liberibacter asiaticus" pathogenicity.IMPORTANCE Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is "Candidatus Liberibacter asiaticus." Prior work using mapping-based approaches identified prophage-like sequences in some "Ca. Liberibacter asiaticus" genomes but not all. Here, we utilized a de novo approach that expands the number of prophage-like elements found in "Ca. Liberibacter asiaticus" from 16 to 33 and identified at least one prophage-like sequence in all "Ca. Liberibacter asiaticus" strains. Furthermore, we identified a prophage-like sequence type that is a remnant of an integrated prophage-expanding the number of prophage types in "Ca. Liberibacter asiaticus" from 3 to 4. Overall, the findings will help researchers investigate the role of prophage in the ecology, evolution, and pathogenicity of "Ca. Liberibacter asiaticus."}, }
@article {pmid31721471, year = {2020}, author = {Tyc, O and Putra, R and Gols, R and Harvey, JA and Garbeva, P}, title = {The ecological role of bacterial seed endophytes associated with wild cabbage in the United Kingdom.}, journal = {MicrobiologyOpen}, volume = {9}, number = {1}, pages = {e00954}, pmid = {31721471}, issn = {2045-8827}, mesh = {Actinobacteria/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/*metabolism ; Brassica/*growth &amp; development/microbiology ; Endophytes/classification/genetics/*metabolism ; Firmicutes/classification/genetics/isolation &amp; purification ; Germination/drug effects ; Proteobacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Seeds/*growth &amp; development/microbiology ; United Kingdom ; Volatile Organic Compounds/metabolism/*pharmacology ; }, abstract = {Endophytic bacteria are known for their ability in promoting plant growth and defense against biotic and abiotic stress. However, very little is known about the microbial endophytes living in the spermosphere. Here, we isolated bacteria from the seeds of five different populations of wild cabbage (Brassica oleracea L) that grow within 15 km of each other along the Dorset coast in the UK. The seeds of each plant population contained a unique microbiome. Sequencing of the 16S rRNA genes revealed that these bacteria belong to three different phyla (Actinobacteria, Firmicutes, and Proteobacteria). Isolated endophytic bacteria were grown in monocultures or mixtures and the effects of bacterial volatile organic compounds (VOCs) on the growth and development on B. oleracea and on resistance against a insect herbivore was evaluated. Our results reveal that the VOCs emitted by the endophytic bacteria had a profound effect on plant development but only a minor effect on resistance against an herbivore of B. oleracea. Plants exposed to bacterial VOCs showed faster seed germination and seedling development. Furthermore, seed endophytic bacteria exhibited activity via volatiles against the plant pathogen F. culmorum. Hence, our results illustrate the ecological importance of the bacterial seed microbiome for host plant health and development.}, }
@article {pmid31721347, year = {2020}, author = {Scheepers, M and Spielmann, J and Boulanger, M and Carnol, M and Bosman, B and De Pauw, E and Goormaghtigh, E and Motte, P and Hanikenne, M}, title = {Intertwined metal homeostasis, oxidative and biotic stress responses in the Arabidopsis frd3 mutant.}, journal = {The Plant journal : for cell and molecular biology}, volume = {102}, number = {1}, pages = {34-52}, doi = {10.1111/tpj.14610}, pmid = {31721347}, issn = {1365-313X}, mesh = {Arabidopsis/genetics/metabolism/*physiology ; Arabidopsis Proteins/*genetics/physiology ; Cell Wall/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Homeostasis ; Hydrogen Peroxide/metabolism ; Iron/metabolism ; Membrane Transport Proteins/*genetics/physiology ; Metals/metabolism ; Oxidative Stress/genetics ; Plant Roots/metabolism ; Spectroscopy, Fourier Transform Infrared ; Stress, Physiological ; Zinc/metabolism ; }, abstract = {FRD3 (FERRIC REDUCTASE DEFECTIVE 3) plays a major role in iron (Fe) and zinc (Zn) homeostasis in Arabidopsis. It transports citrate, which enables metal distribution in the plant. An frd3 mutant is dwarf and chlorotic and displays a constitutive Fe-deficiency response and strongly altered metal distribution in tissues. Here, we have examined the interaction between Fe and Zn homeostasis in an frd3 mutant exposed to varying Zn supply. Detailed phenotyping using transcriptomic, ionomic, histochemical and spectroscopic approaches revealed the full complexity of the frd3 mutant phenotype, which resulted from altered transition metal homeostasis, manganese toxicity, and oxidative and biotic stress responses. The cell wall played a key role in these processes, as a site for Fe and hydrogen peroxide accumulation, and displayed modified structure in the mutant. Finally, we showed that Zn excess interfered with these mechanisms and partially restored root growth of the mutant, without reverting the Fe-deficiency response. In conclusion, the frd3 mutant molecular phenotype is more complex than previously described and illustrates how the response to metal imbalance depends on multiple signaling pathways.}, }
@article {pmid31721121, year = {2020}, author = {Kreth, J and Abdelrahman, YM and Merritt, J}, title = {Multiplex Imaging of Polymicrobial Communities-Murine Models to Study Oral Microbiome Interactions.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2081}, number = {}, pages = {107-126}, pmid = {31721121}, issn = {1940-6029}, support = {R01 DE021726/DE/NIDCR NIH HHS/United States ; R01 DE029492/DE/NIDCR NIH HHS/United States ; R35 DE028252/DE/NIDCR NIH HHS/United States ; R56 DE021726/DE/NIDCR NIH HHS/United States ; }, mesh = {Animals ; Biofilms ; Disease Models, Animal ; Gene Expression ; Genes, Reporter ; Luminescent Measurements/methods ; Mice ; *Microbial Interactions ; *Microbiota ; Mouth/*microbiology ; Optical Imaging/*methods ; }, abstract = {Similar to other mucosal surfaces of the body, the oral cavity hosts a diverse microbial flora that live in polymicrobial biofilm communities. It is the ecology of these communities that are the primary determinants of oral health (symbiosis) or disease (dysbiosis). As such, both symbiosis and dysbiosis are inherently polymicrobial phenomena. In an effort to facilitate studies of polymicrobial communities within rodent models, we developed a suite of synthetic luciferases suitable for multiplexed in situ analyses of microbial ecology and specific gene expression. Using this approach, it is feasible to noninvasively measure multiple luciferase signals in vivo with both spatial and temporal resolution. In the following chapter, we describe the relevant details and protocols used to establish a biophotonic imaging platform for the study of experimental polymicrobial oral biofilms and abscesses in mice. The protocols described here are specifically tailored for use with oral streptococci, but the general strategies are adaptable for a wide range of polymicrobial infection studies using other species.}, }
@article {pmid31720799, year = {2020}, author = {Thomas, P and Shaik, SP}, title = {Molecular Profiling on Surface-Disinfected Tomato Seeds Reveals High Diversity of Cultivation-Recalcitrant Endophytic Bacteria with Low Shares of Spore-Forming Firmicutes.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {910-924}, doi = {10.1007/s00248-019-01440-5}, pmid = {31720799}, issn = {1432-184X}, support = {AMAAS Project//National Bureau of Agriculturally Important Microorganisms/ ; }, mesh = {Bacteria/*isolation &amp; purification ; Disinfectants/*administration &amp; dosage ; Endophytes/*isolation &amp; purification ; Firmicutes/isolation &amp; purification ; India ; Solanum lycopersicum/*microbiology ; *Microbiota ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Seeds/microbiology ; }, abstract = {Seeds are known to harbor diverse microorganisms offering protective effects on them with the prospects of quick root colonization at germination, selective recruitment as endophytes, and possible vertical transmission. The study was undertaken to assess the gross seed-internal bacterial community in tomato and to confirm if spore-forming Firmicutes constituted major seed endophytes adopting cultivation versus molecular approach on surface-sterilized seeds. Testing the initial seed wash solutions of "Arka Vikas" and "Arka Abha" cultivars showed > 1000 bacterial cfu per dry seed, largely Bacillus spp. Tissue homogenates from surface-disinfected seeds did not show any cultivable bacteria on enriched media for 1-2 weeks, while 16S rRNA V3-V4 taxonomic profiling revealed a huge bacterial diversity (10-16 phyla per cultivar). Proteobacteria formed the dominant phylum (65.7-69.6% OTUs) followed by Firmicutes, Actinobacteria, Bacteroidetes, and a notable share of Euryarchaeota (1.1-3.1%). Five more phyla appeared common to both cultivars in minor shares (Acidobacteria, Planctomycetes, Chloroflexi, Spirochaetes, Verrucomicrobia) with the ten phyla together constituting 99.6-99.9% OTUs. Class level and family level, the cultivars displayed elevated bacterial diversity, but similar taxonomic profiles. Arka Vikas and Arka Abha showed 114 and 107 genera, respectively, with 63 common genera constituting 96-97% OTUs. Psychrobacter formed the dominant genus. Bacillus and related genera constituted only negligible OTU share (0.16-0.28%). KEGG functional analysis showed metabolism as the major bacterial community role. One-month-old in vitro seedlings showed the activation of some originally uncultivable bacteria uninfluenced by the OTU share. The study reveals a high diversity of cultivation-recalcitrant endophytic bacteria prevailing in tomato seeds with possible vertical transmission and significant roles in plant biology.}, }
@article {pmid31720759, year = {2020}, author = {Liu, L and Wang, S and Chen, J}, title = {Hysteretic response of Microbial Eukaryotic Communities to Gradually Decreased Nutrient Concentrations in Eutrophic Water.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {815-822}, doi = {10.1007/s00248-019-01457-w}, pmid = {31720759}, issn = {1432-184X}, support = {FZHJ15//Oceans and Fisheries Bureau of Fuzhou, China/ ; 31500372//National Natural Science Foundation of China/ ; 31971469//National Natural Science Foundation of China/ ; XRC-17024//Special Foundation for Yong Scientists of Fuzhou University/ ; }, mesh = {Chlorophyta/metabolism/*physiology ; Ciliophora/metabolism/*physiology ; Eukaryota ; Eutrophication ; Fresh Water/*chemistry ; Fungi/metabolism/*physiology ; Microbiota ; Mycobiome/physiology ; Nitrogen/deficiency ; Nutrients/*deficiency ; Phosphorus/deficiency ; }, abstract = {External environments to microbial eukaryotic communities often change gradually with time. However, whether the responses of microbial eukaryotic communities to these gradually changed environments are continuous or hysteretic and the mechanisms underlying these responses are largely unknown. Here, we used a microcosm to investigate the temporal variation of microbial eukaryotic communities with the gradually decreased nutrient concentrations (nitrogen and phosphorus). We found the differences of microbial eukaryotic community composition and species richness between the control and treatment groups were low during the days 0 to 12, although the nutrient concentrations decreased rapidly during this period in treatment group. However, these differences were clear during the days 14 to 18, although the nutrient concentrations decreased slowly during this period in treatment group. The mechanisms for these results are that the strong homogenous selection (perhaps due to the biotic factors) during the days 8 to 10 in treatment group might enhance the stability of microbial eukaryotic communities. However, the continuously decreased nutrient concentrations weakened the homogenous selection and promoted the strength of environmental filtering, and therefore resulted in the distinct change of microbial eukaryotic communities during the days 14 to 18 in treatment group. Fungi, Chlorophyta and Chrysophyta which associated with the nutrient removal played important roles in this hysteretic change of microbial eukaryotic communities. Overall, our findings suggest that disentangling the non-linear response of communities to gradual environmental changes is essential for understanding ecosystem restoration and degradation in future.}, }
@article {pmid31719226, year = {2019}, author = {DAS, B and Nair, GB}, title = {Homeostasis and dysbiosis of the gut microbiome in health and disease.}, journal = {Journal of biosciences}, volume = {44}, number = {5}, pages = {}, pmid = {31719226}, issn = {0973-7138}, mesh = {*Gastrointestinal Microbiome ; *Homeostasis ; Humans ; }, abstract = {The human gastrointestinal tract (GIT) harbors taxonomically and functionally complex microbial ecosystem. The composition of the microbial species in the GIT ecosystem varies among individuals and throughout development. Both environmental factors as well as host genetics influence the composition and homeostasis of GIT microbiome. Intrinsic GIT microbiome can be characterized in terms of diversity, richness, dynamics and resilience. In healthy individual, microbial communities maintain homeostatic equilibrium and are resistant against perturbations. The resilience and resistance to perturbations of the GIT microbial ecosystem are robust but not absolute. Several factors can affect the homeostatic equilibrium of GIT microbiome and lead to dysbiotic microbiome configuration. Taxonomic and/or functional dysbiosis in the GIT microbiome is associated with numerous health disorders like inflammatory bowel disease (IBD), malnutrition, metabolic disorders, asthma and neurodegenerative diseases. In this review, we discuss our current understanding of homeostasis and dysbiosis of the microbial ecology in the human gut and health disorders that are associated with the microbiome dysbiosis.}, }
@article {pmid31719222, year = {2019}, author = {Senapati, T and Kothidar, A and Banerjee, SK and DAS, B}, title = {Insights into the gastrointestinal tract microbiomes of Indian population.}, journal = {Journal of biosciences}, volume = {44}, number = {5}, pages = {}, pmid = {31719222}, issn = {0973-7138}, mesh = {Ecosystem ; *Gastrointestinal Microbiome ; Humans ; India ; Pharmaceutical Preparations ; Species Specificity ; Vaccines ; }, abstract = {Trillions of microbes living in the gastrointestinal tract (GIT) of the human body finely tune homeostatic equilibrium in the GIT ecosystem and encode key functionalities that play crucial role in host metabolic functions, synthesis of macro- and micronutrients, xenobiotics metabolisms, development of innate and adaptive immune systems, tissue and organ developments and resistance against invasion of enteric pathogens. The microbial diversity and richness of GIT ecosystem varies greatly between individuals and over time. Extent of taxonomic and functional variations in GIT ecosystem is linked with dietary habit, pharmaceuticals usages, age, sex, body mass index, ethnicity, geography, altitude and civilization. Understanding a holistic picture of GIT microbiome of healthy people living across geography and identifying population specific 'keystone' taxa is of immense importance for identifying microbial species that may provide protection against chronic and metabolic diseases. Knowledge on geographic or ethnicity specific microbial signatures may also help us to understand the varied efficacy of different drugs and vaccines in different population. India is the home of more than 1.36 billion people belonging to 2000 human communities residing in well distinct geography. In the present review, we discuss the microbial signatures in health and diseases of the rural and urban Indians living in sea level and high altitude areas.}, }
@article {pmid31717367, year = {2019}, author = {An, B and Sam, C and Dries, V and Ruben, S and Christel, V and Mik, VB and Bart, L and Leen, VC}, title = {Comparison of Six Commercial Meat Starter Cultures for the Fermentation of Yellow Mealworm (Tenebrio molitor) Paste.}, journal = {Microorganisms}, volume = {7}, number = {11}, pages = {}, pmid = {31717367}, issn = {2076-2607}, abstract = {In this study, six commercial meat starters, each consisting of a pure strain of a lactic acid-fermenting bacterium (including Lactococcus lactis, Lactobacillus curvatus, L. farciminis, L. plantarum, L. sakei, and Pediococcus acidilactici), were tested for their ability to ferment a paste produced from the yellow mealworm (Tenebrio molitor). During fermentation, microbial counts, pH, and the bacterial community composition were determined. In addition, UPLC-MS was applied to monitor the consumption of glucose and the production of glutamic (Glu) and aspartic (Asp) acid. All tested starters were able to ferment the mealworm paste, judged by a pH reduction from 6.68 to 4.60-4.95 within 72 h. Illumina amplicon sequencing showed that all starters were able to colonize the substrate eciently. Moreover, the introduction of the starter cultures led to the disappearance of Bacillus and Clostridium species, which were the dominant microorganisms in un-inoculated samples. Of the six cultures tested, Lactobacillus farciminis was most promising as its application resulted in the largest increase (±25 mg/100 g of paste) in the content of free glutamic and aspartic acid. These amino acids are responsible for the appreciated umami flavour in fermented food products and might stimulate the acceptance of insects and their consumption.}, }
@article {pmid31715086, year = {2019}, author = {Saiman, L}, title = {Improving outcomes of infections in cystic fibrosis in the era of CFTR modulator therapy.}, journal = {Pediatric pulmonology}, volume = {54 Suppl 3}, number = {}, pages = {S18-S26}, doi = {10.1002/ppul.24522}, pmid = {31715086}, issn = {1099-0496}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Chloride Channel Agonists/*therapeutic use ; Combined Modality Therapy ; Cystic Fibrosis/*drug therapy/microbiology ; Cystic Fibrosis Transmembrane Conductance Regulator/*therapeutic use ; Humans ; Treatment Outcome ; }, abstract = {Currently, available single and dual-combination cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapies have favorably altered the life course of individuals with cystic fibrosis (CF) by decreasing morbidities and increasing survival. However, even with CFTR modulator use, questions and challenges remain to optimize the management of lung infections. This review (a) identifies these ongoing challenges and discusses the current understanding of the potential impact of CFTR modulator therapy on infections; (b) describes ongoing research to optimize detection, diagnosis, and treatment of CF microorganisms; and (c) discusses strategies to develop new anti-infective therapies. The CF Foundation has launched the Infection Research Initiative to fund research that will improve our understanding of the complex microbial ecology within the CF lung, improve detection of CF pathogens, optimize current treatment, including long-term chronic therapies, and develop new anti-infective therapies. Ongoing clinical trials to determine the optimal duration of treatment of pulmonary exacerbations and to diagnose and treat nontuberculous mycobacteria represent clinical research paradigms that could be used to answer other complex treatment questions. The anti-infective pipeline includes both existing anti-infective and non-anti-infective agents, many of which are proposed to have unique mechanisms of action in CF. Future studies plan to evaluate short- and long-term clinical effectiveness and impact on infections, of the next generation of CFTR modulator therapy, the highly effective triple-combination therapy, for individuals with CF, homozygous or heterozygous for F508del.}, }
@article {pmid31712738, year = {2020}, author = {De Paepe, K and Verspreet, J and Courtin, CM and Van de Wiele, T}, title = {Microbial succession during wheat bran fermentation and colonisation by human faecal microbiota as a result of niche diversification.}, journal = {The ISME journal}, volume = {14}, number = {2}, pages = {584-596}, pmid = {31712738}, issn = {1751-7370}, mesh = {*Bacteria/classification/genetics/growth &amp; development/metabolism ; Biofilms ; Butyrates/metabolism ; Diet ; Dietary Fiber/metabolism ; Ecosystem ; Fatty Acids, Volatile/metabolism ; Feces/*microbiology ; Fermentation ; *Gastrointestinal Microbiome/genetics/physiology ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The human gut can be viewed as a flow-through system with a short residence time, a high turnover rate and a spatial gradient of physiological conditions. As a consequence, the gut microbiota is exposed to highly fluctuating environmental determinants presented by the host and diet. Here, we assessed the fermentation and colonisation of insoluble wheat bran by faecal microbiota of three individuals at an unprecedented sampling intensity. Time-resolved 16S rRNA gene amplicon sequencing, revealed a dynamic microbial community, characterised by abrupt shifts in composition, delimiting states with a more constant community, giving rise to a succession of bacterial taxa alternately dominating the community over a 72 h timespan. Early stages were dominated by Enterobacteriaceae and Fusobacterium species, growing on the carbohydrate-low, protein rich medium to which wheat bran was supplemented. The onset of wheat bran fermentation, marked by a spike in short chain fatty acid production with an increasing butyrate proportion and an increased endo-1,4-β-xylanase activity, corresponded to donor-dependent proportional increases of Bacteroides ovatus/stercoris, Prevotella copri and Firmicutes species, which were strongly enriched in the bran-attached community. Literature and database searches provided novel insights into the metabolic and growth characteristics underlying the observed succession and colonisation, illustrating the potency of a time-resolved analysis to increase our understanding of gut microbiota dynamics upon dietary modulations.}, }
@article {pmid31712278, year = {2020}, author = {Bencivenga-Barry, NA and Lim, B and Herrera, CM and Trent, MS and Goodman, AL}, title = {Genetic Manipulation of Wild Human Gut Bacteroides.}, journal = {Journal of bacteriology}, volume = {202}, number = {3}, pages = {}, pmid = {31712278}, issn = {1098-5530}, support = {R35 GM118159/GM/NIGMS NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 DK114793/DK/NIDDK NIH HHS/United States ; R01 AI138576/AI/NIAID NIH HHS/United States ; R56 AI076322/AI/NIAID NIH HHS/United States ; R01 AI129940/AI/NIAID NIH HHS/United States ; R01 AI076322/AI/NIAID NIH HHS/United States ; U01 AI124275/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Bacteroides/drug effects/*genetics ; Bacteroides fragilis/drug effects/genetics ; Gastrointestinal Microbiome/drug effects/genetics ; Gastrointestinal Tract/microbiology ; Humans ; Microbiota/drug effects/genetics ; Polymyxin B/pharmacology ; }, abstract = {Bacteroides is one of the most prominent genera in the human gut microbiome, and study of this bacterial group provides insights into gut microbial ecology and pathogenesis. In this report, we introduce a negative selection system for rapid and efficient allelic exchange in wild Bacteroides species that does not require any alterations to the genetic background or a nutritionally defined culture medium. In this approach, dual antibacterial effectors normally delivered via type VI secretion are targeted to the bacterial periplasm under the control of tightly regulated anhydrotetracycline (aTC)-inducible promoters. Introduction of aTC selects for recombination events producing the desired genetic modification, and the dual effector design allows for broad applicability across strains that may have immunity to one counterselection effector. We demonstrate the utility of this approach across 21 human gut Bacteroides isolates representing diverse species, including strains isolated directly from human donors. We use this system to establish that antimicrobial peptide resistance in Bacteroides vulgatus is determined by the product of a gene that is not included in the genomes of previously genetically tractable members of the human gut microbiome.IMPORTANCE Human gut Bacteroides species exhibit strain-level differences in their physiology, ecology, and impact on human health and disease. However, existing approaches for genetic manipulation generally require construction of genetically modified parental strains for each microbe of interest or defined medium formulations. In this report, we introduce a robust and efficient strategy for targeted genetic manipulation of diverse wild-type Bacteroides species from the human gut. This system enables genetic investigation of members of human and animal microbiomes beyond existing model organisms.}, }
@article {pmid31710600, year = {2019}, author = {Wilkins, LGE and Leray, M and O'Dea, A and Yuen, B and Peixoto, RS and Pereira, TJ and Bik, HM and Coil, DA and Duffy, JE and Herre, EA and Lessios, HA and Lucey, NM and Mejia, LC and Rasher, DB and Sharp, KH and Sogin, EM and Thacker, RW and Vega Thurber, R and Wcislo, WT and Wilbanks, EG and Eisen, JA}, title = {Host-associated microbiomes drive structure and function of marine ecosystems.}, journal = {PLoS biology}, volume = {17}, number = {11}, pages = {e3000533}, pmid = {31710600}, issn = {1545-7885}, mesh = {Animals ; Aquatic Organisms/*microbiology ; Bacteria/classification ; Ecosystem ; Host Microbial Interactions/physiology ; Humans ; Microbiota/*physiology ; Symbiosis/*physiology ; }, abstract = {The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to the ecosystem level and underpins the health of Earth's most threatened marine ecosystems. Despite rapid growth in research on host-associated microbes, from individual microbial symbionts to host-associated consortia of significantly relevant taxa, little is known about their interactions with the vast majority of marine host species. We outline research priorities to strengthen our current knowledge of host-microbiome interactions and how they shape marine ecosystems. We argue that such advances in research will help predict responses of species, communities, and ecosystems to stressors driven by human activity and inform future management strategies.}, }
@article {pmid31710301, year = {2019}, author = {Bai, J and Jhaney, I and Wells, J}, title = {Developing a Reproducible Microbiome Data Analysis Pipeline Using the Amazon Web Services Cloud for a Cancer Research Group: Proof-of-Concept Study.}, journal = {JMIR medical informatics}, volume = {7}, number = {4}, pages = {e14667}, pmid = {31710301}, issn = {2291-9694}, support = {K99 NR017897/NR/NINR NIH HHS/United States ; }, abstract = {BACKGROUND: Cloud computing for microbiome data sets can significantly increase working efficiencies and expedite the translation of research findings into clinical practice. The Amazon Web Services (AWS) cloud provides an invaluable option for microbiome data storage, computation, and analysis.<br><br>OBJECTIVE: The goals of this study were to develop a microbiome data analysis pipeline by using AWS cloud and to conduct a proof-of-concept test for microbiome data storage, processing, and analysis.<br><br>METHODS: A multidisciplinary team was formed to develop and test a reproducible microbiome data analysis pipeline with multiple AWS cloud services that could be used for storage, computation, and data analysis. The microbiome data analysis pipeline developed in AWS was tested by using two data sets: 19 vaginal microbiome samples and 50 gut microbiome samples.<br><br>RESULTS: Using AWS features, we developed a microbiome data analysis pipeline that included Amazon Simple Storage Service for microbiome sequence storage, Linux Elastic Compute Cloud (EC2) instances (ie, servers) for data computation and analysis, and security keys to create and manage the use of encryption for the pipeline. Bioinformatics and statistical tools (ie, Quantitative Insights Into Microbial Ecology 2 and RStudio) were installed within the Linux EC2 instances to run microbiome statistical analysis. The microbiome data analysis pipeline was performed through command-line interfaces within the Linux operating system or in the Mac operating system. Using this new pipeline, we were able to successfully process and analyze 50 gut microbiome samples within 4 hours at a very low cost (a c4.4xlarge EC2 instance costs $0.80 per hour). Gut microbiome findings regarding diversity, taxonomy, and abundance analyses were easily shared within our research team.<br><br>CONCLUSIONS: Building a microbiome data analysis pipeline with AWS cloud is feasible. This pipeline is highly reliable, computationally powerful, and cost effective. Our AWS-based microbiome analysis pipeline provides an efficient tool to conduct microbiome data analysis.}, }
@article {pmid31709856, year = {2020}, author = {Joshipura, K and Muñoz-Torres, F and Fernández-Santiago, J and Patel, RP and Lopez-Candales, A}, title = {Over-the-counter mouthwash use, nitric oxide and hypertension risk.}, journal = {Blood pressure}, volume = {29}, number = {2}, pages = {103-112}, pmid = {31709856}, issn = {1651-1999}, support = {U54 MD007600/MD/NIMHD NIH HHS/United States ; U54 MD007587/MD/NIMHD NIH HHS/United States ; P30 DK079626/DK/NIDDK NIH HHS/United States ; S21 MD001830/MD/NIMHD NIH HHS/United States ; R01 DE020111/DE/NIDCR NIH HHS/United States ; R01 DE028195/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Aged ; Bacteria/*drug effects/metabolism ; *Blood Pressure ; Female ; Humans ; Hypertension/diagnosis/*epidemiology/physiopathology ; Incidence ; Longitudinal Studies ; Male ; Middle Aged ; Mouth/*microbiology ; Mouthwashes/*adverse effects ; Nitric Oxide/*metabolism ; Puerto Rico ; Risk Assessment ; Risk Factors ; Time Factors ; }, abstract = {Purpose: Mouthwash is used by a large population. Short-term clinical trials have shown that antibacterial mouthwash deplete oral nitrate-reducing bacteria, and decrease systemic nitric oxide bioavailability. Our previous publication from the San Juan Overweight Adults Longitudinal Study (SOALS) was the first to show frequent over-the-counter mouthwash use was independently associated with increased risk of prediabetes/diabetes. This manuscript evaluates whether over-the-counter mouthwash was associated with increased risk of hypertension.Materials and methods: SOALS recruited 40-65 year old overweight/obese individuals; baseline evaluations started in 2011 and the 3-year follow-up exam was completed by 2016. From the 1028 participants (76%) who completed follow-up, we excluded people with reported physician diagnosis of hypertension or systolic or diastolic BP at or above the hypertension cut-offs (n = 481), missing smoking (n = 1), missing physical activity (n = 1) and missing alcohol intake (n = 5) at baseline; 540 participants were included. The primary exposure was mouthwash use twice daily or more. The primary outcome for this manuscript is self-reported physician-diagnosed hypertension over the follow-up. We used Poisson regression controlling for age, sex, smoking, physical activity, waist circumference, alcohol intake, systolic blood pressure, pre-diabetes/diabetes status and cardiac medication use. We additionally evaluated other mouthwash use categorizations.Results: Twelve percent (66/540) developed hypertension over follow-up. People who used mouthwash twice/day or more had higher incidence of hypertension compared to less frequent users (Incidence Rate Ratio = 1.85; 95% Confidence Interval: 1.17, 2.94), and compared to non-users (IRR = 2.17; 95% CI: 1.27, 3.71). Several additional potential confounders evaluated did not impact these associations. Associations persisted among never smokers. Additional outcomes including BP assessed at a single study visit did not show associations.Conclusion: In this study, frequent regular use of over-the-counter mouthwash was associated with increased risk of hypertension, independent of major risk factors for hypertension and several other potential confounders.}, }
@article {pmid31709616, year = {2020}, author = {Crone, S and Vives-Flórez, M and Kvich, L and Saunders, AM and Malone, M and Nicolaisen, MH and Martínez-García, E and Rojas-Acosta, C and Catalina Gomez-Puerto, M and Calum, H and Whiteley, M and Kolter, R and Bjarnsholt, T}, title = {The environmental occurrence of Pseudomonas aeruginosa.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {128}, number = {3}, pages = {220-231}, doi = {10.1111/apm.13010}, pmid = {31709616}, issn = {1600-0463}, mesh = {Animals ; Environment ; Environmental Microbiology ; Humans ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/*genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Pseudomonas aeruginosa is generally described as ubiquitous in natural settings, such as soil and water. However, because anecdotal observations and published reports have questioned whether or not this description is true, we undertook a rigorous study using three methods to investigate the occurrence of P. aeruginosa: We investigated environmental samples, analyzed 16S rRNA data, and undertook a systematic review and meta-analysis of published data. The environmental sample screening identified P. aeruginosa as significantly associated with hydrocarbon and pesticide-contaminated environments and feces, as compared to uncontaminated environments in which its prevalence was relatively low. The 16S rRNA data analysis showed that P. aeruginosa sequences were present in all habitats but were most abundant in samples from human and animals. Similarly, the meta-analysis revealed that samples obtained from environments with intense human contact had a higher prevalence of P. aeruginosa compared to those with less human contact. Thus, we found a clear tendency of P. aeruginosa to be present in places closely linked with human activity. Although P. aeruginosa may be ubiquitous in nature, it is usually scarce in pristine environments. Thus, we suggest that P. aeruginosa should be described as a bacterium largely found in locations associated with human activity.}, }
@article {pmid31708901, year = {2019}, author = {Navarro, MOP and Simionato, AS and Pérez, JCB and Barazetti, AR and Emiliano, J and Niekawa, ETG and Andreata, MFL and Modolon, F and Dealis, ML and Araújo, EJA and Carlos, TM and Scarpelim, OJ and da Silva, DB and Chryssafidis, AL and Bruheim, P and Andrade, G}, title = {Fluopsin C for Treating Multidrug-Resistant Infections: In vitro Activity Against Clinically Important Strains and in vivo Efficacy Against Carbapenemase-Producing Klebsiella pneumoniae.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2431}, pmid = {31708901}, issn = {1664-302X}, abstract = {The increasing emergence of multidrug-resistant (MDR) organisms in hospital infections is causing a global public health crisis. The development of drugs with effective antibiotic action against such agents is of the highest priority. In the present study, the action of Fluopsin C against MDR clinical isolates was evaluated under in vitro and in vivo conditions. Fluopsin C was produced in cell suspension culture of Pseudomonas aeruginosa LV strain, purified by liquid adsorption chromatography and identified by mass spectrometric analysis. Bioactivity, bacterial resistance development risk against clinically important pathogenic strains and toxicity in mammalian cell were initially determined by in vitro models. In vivo toxicity was evaluated in Tenebrio molitor larvae and mice. The therapeutic efficacy of intravenous Fluopsin C administration was evaluated in a murine model of Klebsiella pneumoniae (KPC) acute sepsis, using six different treatments. The in vitro results indicated MIC and MBC below 2 μg/mL and low bacterial resistance development frequency. Electron microscopy showed that Fluopsin C may have altered the exopolysaccharide matrix and caused disruption of the cell wall of MDR bacteria. Best therapeutic results were achieved in mice treated with a single dose of 2 mg/kg and in mice treated with two doses of 1 mg/kg, 8 h apart. Furthermore, acute and chronic histopathological studies demonstrated absent nephrotoxicity and moderate hepatotoxicity. The results demonstrated the efficacy of Fluopsin C against MDR organisms in in vitro and in vivo models, and hence it can be a novel therapeutic agent for the control of severe MDR infections.}, }
@article {pmid31708885, year = {2019}, author = {Géron, A and Werner, J and Wattiez, R and Lebaron, P and Matallana-Surget, S}, title = {Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2395}, pmid = {31708885}, issn = {1664-302X}, abstract = {Unraveling the complex structure and functioning of microbial communities is essential to accurately predict the impact of perturbations and/or environmental changes. From all molecular tools available today to resolve the dynamics of microbial communities, metaproteomics stands out, allowing the establishment of phenotype-genotype linkages. Despite its rapid development, this technology has faced many technical challenges that still hamper its potential power. How to maximize the number of protein identification, improve quality of protein annotation, and provide reliable ecological interpretation are questions of immediate urgency. In our study, we used a robust metaproteomic workflow combining two protein fractionation approaches (gel-based versus gel-free) and four protein search databases derived from the same metagenome to analyze the same seawater sample. The resulting eight metaproteomes provided different outcomes in terms of (i) total protein numbers, (ii) taxonomic structures, and (iii) protein functions. The characterization and/or representativeness of numerous proteins from ecologically relevant taxa such as Pelagibacterales, Rhodobacterales, and Synechococcales, as well as crucial environmental processes, such as nutrient uptake, nitrogen assimilation, light harvesting, and oxidative stress response, were found to be particularly affected by the methodology. Our results provide clear evidences that the use of different protein search databases significantly alters the biological conclusions in both gel-free and gel-based approaches. Our findings emphasize the importance of diversifying the experimental workflow for a comprehensive metaproteomic study.}, }
@article {pmid31708883, year = {2019}, author = {Del Campo, J and Heger, TJ and Rodríguez-Martínez, R and Worden, AZ and Richards, TA and Massana, R and Keeling, PJ}, title = {Assessing the Diversity and Distribution of Apicomplexans in Host and Free-Living Environments Using High-Throughput Amplicon Data and a Phylogenetically Informed Reference Framework.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2373}, pmid = {31708883}, issn = {1664-302X}, abstract = {Apicomplexans are a group of microbial eukaryotes that contain some of the most well-studied parasites, including the causing agents of toxoplasmosis and malaria, and emergent diseases like cryptosporidiosis or babesiosis. Decades of research have illuminated the pathogenic mechanisms, molecular biology, and genomics of model apicomplexans, but we know little about their diversity and distribution in natural environments. In this study we analyze the distribution of apicomplexans across a range of both host-associated and free-living environments. Using publicly available small subunit (SSU) rRNA gene databases, high-throughput environmental sequencing (HTES) surveys, and our own generated HTES data, we developed an apicomplexan reference database, which includes the largest apicomplexan SSU rRNA tree available to date and encompasses comprehensive sampling of this group and their closest relatives. This tree allowed us to identify and correct incongruences in the molecular identification of apicomplexan sequences. Analyzing the diversity and distribution of apicomplexans in HTES studies with this curated reference database also showed a widespread, and quantitatively important, presence of apicomplexans across a variety of free-living environments. These data allow us to describe a remarkable molecular diversity of this group compared with our current knowledge, especially when compared with that identified from described apicomplexan species. This is most striking in marine environments, where potentially the most diverse apicomplexans apparently exist, but have not yet been formally recognized. The new database will be useful for microbial ecology and epidemiological studies, and provide valuable reference for medical and veterinary diagnosis especially in cases of emerging, zoonotic, and cryptic infections.}, }
@article {pmid31708882, year = {2019}, author = {Smyth, EM and Chattopadhyay, S and Babik, K and Reid, M and Chopyk, J and Malayil, L and Kulkarni, P and Hittle, LE and Clark, PI and Sapkota, AR and Mongodin, EF}, title = {The Bacterial Communities of Little Cigars and Cigarillos Are Dynamic Over Time and Varying Storage Conditions.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2371}, pmid = {31708882}, issn = {1664-302X}, support = {P50 CA180523/CA/NCI NIH HHS/United States ; }, abstract = {Despite their potential importance with regard to tobacco-related health outcomes, as well as their hypothesized role in the production of tobacco-specific N-nitrosamines, bacterial constituents of tobacco products lack characterization. Specifically, to our knowledge, there has been no comprehensive characterization of the effects of storage conditions on the bacterial communities associated with little cigars and cigarillos. To address this knowledge gap, we characterized the bacterial community composition of the tobacco and wrapper components of the following four products: Swisher Sweets Original; Swisher Sweets, Sweet Cherry; Cheyenne Cigars Full Flavor 100's; and Cheyenne Menthol Box. Each product was stored under three different conditions of temperature and relative humidity to mimic different user storage conditions: room (20°C 50% RH), refrigerator (5°C 18% RH) and pocket (25°C 30% RH). On days 0, 5, 9 and 14, subsamples were collected, the wrapper and tobacco were separated, and their total DNA was extracted separately and purified. Resulting DNA was then used in PCR assays targeting the V3 V4 region of the bacterial 16S rRNA gene, followed by sequencing using Illumina HiSeq 300bp PE. Resulting sequences were processed using the Quantitative Insights Into Microbial Ecology (QIIME) software package, followed by analyses in R using the Phyloseq and Vegan packages. A single bacterial phylum, Firmicutes, dominated in the wrapper subsamples whereas the tobacco subsamples were dominated by Proteobacteria. Cheyenne Menthol Box (CMB) samples were characterized by significant differential abundances for 23 bacterial operational taxonomic units (OTUs) in tobacco subsamples and 27 OTUs in the wrapper subsamples between day 0 and day 14 under all conditions. OTUs from the genera Acinetobacter and Bacillus significantly increased in the CMB tobacco subsamples, and OTUs from Bacillus, Streptococcus, Lactobacillus, and Enterococcus significantly increased in the CMB wrapper subsamples over time. These initial results suggest that the bacterial communities of little cigars and cigarillos are dynamic over time and varying storage conditions.}, }
@article {pmid31707464, year = {2020}, author = {Polonca, S}, title = {Environment Shapes the Intra-species Diversity of Bacillus subtilis Isolates.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {853-864}, doi = {10.1007/s00248-019-01455-y}, pmid = {31707464}, issn = {1432-184X}, support = {US/18-19-091//Javna Agencija za Raziskovalno Dejavnost RS/ ; J4-8228//Javna Agencija za Raziskovalno Dejavnost RS/ ; P4-0116//Javna Agencija za Raziskovalno Dejavnost RS/ ; J4-9302//Javna Agencija za Raziskovalno Dejavnost RS/ ; }, mesh = {Bacillus subtilis/genetics/*physiology ; *Biofilms ; California ; *Ecosystem ; Environment ; *Genetic Variation ; Slovenia ; Soil Microbiology ; Spatial Analysis ; }, abstract = {Cosmopolitan bacteria are those that are found practically everywhere in the world. One of them is Bacillus subtilis, which can travel around the world through dust storms rising from various deserts. Upon landing, bacterial survival is determined by the ability to adjust to the heterogonous environments and bacteria isolated from extremely different environments, such as desert and riverbank soil, are expected to be less related due to the environmental pressure of each region. However, little is known about the influence of soil and habitat on B. subtilis evolution. Here, we show that desert and riverbank B. subtilis strains differ in genetic relatedness and physiological traits, such as biofilm morphology and utilisation of carbon sources. Desert strains showed more diversity at the genetic level and were able to utilise more carbon sources than riverbank strains which were highly genetically conserved. Biofilm morphologies of desert and riverbank strains generally segregated and both groups formed different morphology clusters despite the astonishing diversity observed among riverbank strains. We also show that relatedness of B. subtilis strains does not decrease with distance inside the same habitat, which, together with diversity data implies that the difference in environmental selection pressures plays a fundamental role in the evolution of this species.}, }
@article {pmid31705383, year = {2020}, author = {Queiroz, LL and Costa, MS and de Abreu Pereira, A and de Paula Avila, M and Costa, PS and Nascimento, AMA and Lacorte, GA}, title = {Dynamics of microbial contaminants is driven by selection during ethanol production.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {51}, number = {1}, pages = {303-312}, pmid = {31705383}, issn = {1678-4405}, support = {156/2013//Instituto Federal de Minas Gerais/ ; }, mesh = {Bacteria/genetics/isolation &amp; purification ; Brazil ; *Ethanol ; *Fermentation ; Industrial Microbiology ; *Lactobacillus/genetics/isolation &amp; purification ; Microbial Interactions ; Microbiota ; RNA, Ribosomal, 16S/genetics ; *Saccharum/metabolism/microbiology ; Yeasts/isolation &amp; purification ; }, abstract = {Brazil is the second largest ethanol producer in the world and largest using sugarcane feedstock. Bacteria contamination is one of the most important issues faced by ethanol producers that seek to increase production efficiency. Each step of production is a selection event due to the environmental and biological changes that occur. Therefore, we evaluated the influence of the selection arising from the ethanol production process on diversity and composition of bacteria. Our objectives were to test two hypotheses, (1) that species richness will decrease during the production process and (2) that lactic acid bacteria will become dominant with the advance of ethanol production. Bacterial community assemblage was accessed using 16S rRNA gene sequencing from 19 sequential samples. Temperature is of great importance in shaping microbial communities. Species richness increased between the decanter and must steps of the process. Low Simpson index values were recorded at the fermentation step, indicating a high dominance of Lactobacillus. Interactions between Lactobacillus and yeast may be impairing the efficiency of industrial ethanol production.}, }
@article {pmid31705158, year = {2020}, author = {Jeong, SY and Choi, JY and Kim, TG}, title = {Coordinated Metacommunity Assembly and Spatial Distribution of Multiple Microbial Kingdoms within a Lake.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {801-814}, doi = {10.1007/s00248-019-01453-0}, pmid = {31705158}, issn = {1432-184X}, support = {2018R1D1A1B07048872//National research foundation of Korea/ ; }, mesh = {Animals ; Bacteria/isolation &amp; purification ; Fungi/isolation &amp; purification ; Lakes/*microbiology/parasitology ; *Microbiota ; Republic of Korea ; Spatial Analysis ; }, abstract = {Freshwater planktonic communities comprise a tremendous diversity of microorganisms. This study investigated the distribution patterns of microbial kingdoms (bacteria, fungi, protists, and microbial metazoans) within a lake ecosystem. Water samples were collected from 50 sites along the shoreline in a lake during an early eutrophication period, and MiSeq sequencing was performed with different marker genes. Metacommunity analyses revealed a bimodal occupancy-frequency distribution and a Clementsian gradient persisting throughout all microbial kingdoms, suggesting similar regional processes in all kingdoms. Variation partitioning revealed that environmental characteristics, macrophyte/macroinvertebrate composition, space coordinates, and distance-based Moran's eigenvector maps (dbMEM) together could explain up to 29% of the community variances in microbial kingdoms. Kingdom synchrony results showed strong couplings between kingdoms (R[2] ≥ 0.31), except between Fungi and Metazoa (R[2] = 0.09). Another variation partitioning revealed that microbial kingdoms could well explain their community variances up to 73%. Interestingly, the kingdom Protista was best synchronized with the other kingdoms. A correlation network showed that positive associations between kingdoms outnumbered the negative ones and that the kingdom Protista acted as a hub among kingdoms. Module analysis showed that network modules included multi-kingdom associations that were prevalent. Our findings suggest that protists coordinate community assembly and distribution of other kingdoms, and inter-kingdom interactions are a key determinant in shaping their community structures in a freshwater lake.}, }
@article {pmid31704994, year = {2019}, author = {Fu, S and Hao, J and Yang, Q and Lan, R and Wang, Y and Ye, S and Liu, Y and Li, R}, title = {Long-distance transmission of pathogenic Vibrio species by migratory waterbirds: a potential threat to the public health.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {16303}, pmid = {31704994}, issn = {2045-2322}, mesh = {*Animal Migration ; Animals ; Birds/*microbiology ; Fisheries ; Food Contamination ; Genome, Bacterial ; Genomics/methods ; Geography ; Phylogeny ; Phylogeography ; Public Health Surveillance ; Rivers ; *Vibrio/classification/genetics/pathogenicity ; Vibrio Infections/epidemiology/*microbiology/*transmission ; }, abstract = {A potential mechanism for the global distribution of waterborne pathogens is through carriage by the migratory waterbirds. However, this mode of transmission has yet been confirmed epidemiologically. Here, we conducted whole genome sequencing of Vibrio spp. collected from waterbirds, sediments, and mollusks in the estuary of the Liaohe River in China to investigate this transmission mode. We found that a V. parahaemolyticus strain isolated from a waterbird was clonally related to the other V. parahaemolyticus strains obtained from the sediments and mollusks, and three V. mimicus strains isolated from bird feces were genomically related to those found in the mollusks and upstream groundwater, suggesting that the bird-carried Vibrio strains were acquired through the direct predation of the local mollusks. Surprisingly, two bird-carried V. parahaemolyticus strains belonging to the same clone were identified in Panjin and Shanghai, which are over 1,150 km apart, and another two were found at two locations 50 km apart, further supporting that waterbirds are capable of carrying and disseminating these pathogens over long distances. Our results provide the first evidence of direct transmission from mollusks to waterbirds and confirm that waterbirds act as disseminating vehicles of waterborne pathogens. Effective surveillance of migratory waterbirds along their routes will be valuable for predicting future epidemics of infectious diseases.}, }
@article {pmid31704678, year = {2020}, author = {Schloss, PD}, title = {Reintroducing mothur: 10 Years Later.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {2}, pages = {}, pmid = {31704678}, issn = {1098-5336}, mesh = {*Environmental Microbiology ; Sequence Analysis/*methods ; Software ; }, abstract = {More than 10 years ago, we published the paper describing the mothur software package in Applied and Environmental Microbiology Our goal was to create a comprehensive package that allowed users to analyze amplicon sequence data using the most robust methods available. mothur has helped lead the community through the ongoing sequencing revolution and continues to provide this service to the microbial ecology community. Beyond its success and impact on the field, mothur's development exposed a series of observations that are generally translatable across science. Perhaps the observation that stands out the most is that all science is done in the context of prevailing ideas and available technologies. Although it is easy to criticize choices that were made 10 years ago through a modern lens, if we were to wait for all of the possible limitations to be solved before proceeding, science would stall. Even preceding the development of mothur, it was necessary to address the most important problems and work backwards to other problems that limited access to robust sequence analysis tools. At the same time, we strive to expand mothur's capabilities in a data-driven manner to incorporate new ideas and accommodate changes in data and desires of the research community. It has been edifying to see the benefit that a simple set of tools can bring to so many other researchers.}, }
@article {pmid31704461, year = {2020}, author = {Coggins, LX and Larma, I and Hinchliffe, A and Props, R and Ghadouani, A}, title = {Flow cytometry for rapid characterisation of microbial community dynamics in waste stabilisation ponds.}, journal = {Water research}, volume = {169}, number = {}, pages = {115243}, doi = {10.1016/j.watres.2019.115243}, pmid = {31704461}, issn = {1879-2448}, mesh = {Flow Cytometry ; *Microbiota ; *Ponds ; Waste Disposal, Fluid ; Wastewater ; }, abstract = {Algal and bacterial communities play a major role in the treatment performance and efficiency of waste stabilisation ponds (WSPs); however, the study of these WSP microbial communities has been challenging. Flow cytometry (FCM) has been used widely as a rapid, culture-independent method of characterising algae and/or bacteria in a range of freshwater and marine environments, and in conventional wastewater treatment processes, but its application to WSP wastewater has been underexplored. In this study, a method for the characterisation of both algal and bacterial microbial populations in WSP wastewater is presented and standardised, using cultures and field samples. We show that SYTO 16 dye is more effective than SYBR Green I for the concurrent detection of both algae and bacteria in samples. Through gating and phenotypic diversity analysis, the FCM results show both spatial and temporal shifts in pond microbial communities. The ability to rapidly determine the spatiotemporal shifts in pond populations is not only important for the improvement of pond operation and monitoring strategies, but also for the planning and management. Flow cytometry has the potential to become a diagnostic tool for ponds to assess treatment performance and determine the most optimal operating conditions.}, }
@article {pmid31703886, year = {2020}, author = {Aldrete-Tapia, JA and Escalante-Minakata, P and Martínez-Peniche, RA and Tamplin, ML and Hernández-Iturriaga, M}, title = {Yeast and bacterial diversity, dynamics and fermentative kinetics during small-scale tequila spontaneous fermentation.}, journal = {Food microbiology}, volume = {86}, number = {}, pages = {103339}, doi = {10.1016/j.fm.2019.103339}, pmid = {31703886}, issn = {1095-9998}, mesh = {Agave/chemistry/microbiology ; Alcoholic Beverages/analysis/*microbiology ; Bacteria/chemistry/genetics/isolation &amp; purification/*metabolism ; Biodiversity ; Ethanol/metabolism ; Fermentation ; Kinetics ; Limosilactobacillus fermentum/chemistry/metabolism ; Saccharomyces cerevisiae/chemistry/metabolism ; Yeasts/chemistry/genetics/*isolation &amp; purification/metabolism ; }, abstract = {The study of microbial communities associated with spontaneous fermentation of agave juice for tequila production is required to develop starter cultures that improve both yield and quality of the final product. Quantification by HPLC of primary metabolites produced during the fermentations was determined. A polyphasic approach using plate count, isolation and identification of microorganisms, denaturing gradient gel electrophoresis and next generation sequencing was carried out to describe the diversity and dynamics of yeasts and bacteria during small-scale spontaneous fermentations of agave juice from two-year samplings. High heterogeneity in microbial populations and fermentation parameters were observed, with bacteria showing higher diversity than yeast. The core microorganisms identified were Saccharomyces cerevisiae and Lactobacillus fermentum. Practices in tequila production changed during the two-year period, which affected microbial community structure and the time to end fermentation. Bacterial growth and concomitant lactic acid production were associated with low ethanol production, thus bacteria could be defined as contaminants in tequila fermentation and efforts to control them should be implemented.}, }
@article {pmid31702484, year = {2019}, author = {Basilua, JM and Sawoo, O and Mangin, I and Dossou-Yovo, F and Boussard, A and Chevillard, L and Lutete, GT and Eto, B and Peytavin, G and Pochart, P}, title = {Higher Atazanavir Plasma Exposure in Rats is Associated with Gut Microbiota Changes Induced by Cotrimoxazole.}, journal = {Current drug metabolism}, volume = {20}, number = {11}, pages = {898-906}, doi = {10.2174/1389200220666191023105609}, pmid = {31702484}, issn = {1875-5453}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Atazanavir Sulfate/blood/*pharmacokinetics ; *Gastrointestinal Microbiome ; HIV Protease Inhibitors/blood/*pharmacokinetics ; Humans ; Intestines/*microbiology ; Male ; Rats ; Rats, Wistar ; Trimethoprim, Sulfamethoxazole Drug Combination/*pharmacology ; }, abstract = {BACKGROUND: Cotrimoxazole (TMP-SMX) is concomitantly used as a primary prophylaxis of opportunistic infections with antiretroviral agents, such as Atazanavir (ATV). Results from an ex vivo study showed changes in intestinal absorption of ATV when rats were pretreated with TMP-SMX. The objective of this in vivo study is to determine the effect of TMP-SMX on the pharmacokinetics of ATV in rats. We also studied changes in gut microbiota induced by TMP-SMX.<br><br>METHODS: We used the non-compartment analysis to compare the pharmacokinetics of ATV in a parallel group of rats treated with a low or therapeutic dose of TMP-SMX for nine days to untreated control rats. Gut microbiota was characterized using qPCR and High Throughput Sequencing of 16S rDNA.<br><br>RESULTS: Rats treated with TMP-SMX showed a much broader exposure to ATV compared to the control group (AUC0-8h (ng.mL-1.h), 25975.9&#xb1;4048.7 versus 2587.6&#xb1;546.9, p=0.001). The main observation regarding the gut microbiota was a lower proportion of enterobacteria related to the administration of TMP-SMX. Moreover, the Total Gastrointestinal Transit Time (TGTT) was longer in the TMP-SMX treated group.<br><br>CONCLUSION: Concomitant administration of TMP-SMX and ATV significantly increased ATV exposure in rats. This increase could be the result of a prolonged TGTT leading to an increase in the intestinal residence time of ATV favoring its absorption. Gut microbiota changes induced by TMP-SMX could be at the origin of this prolonged TGTT. If demonstrated in humans, this potential interaction could be accompanied by an increase in the adverse effects of ATV.}, }
@article {pmid31701171, year = {2020}, author = {Ni, J and Hatori, S and Wang, Y and Li, YY and Kubota, K}, title = {Uncovering Viable Microbiome in Anaerobic Sludge Digesters by Propidium Monoazide (PMA)-PCR.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {925-932}, doi = {10.1007/s00248-019-01449-w}, pmid = {31701171}, issn = {1432-184X}, support = {NA//Strategic International Collaborative Research Program/ ; NA//Ministry of Land, Infrastructure, Transport and Tourism/ ; KAKENHI Grant Number JP18H01564//Japan Society for the Promotion of Science/ ; }, mesh = {Anaerobiosis ; Azides/*chemistry ; Fluorescent Dyes/*chemistry ; Japan ; *Microbial Viability ; *Microbiota ; Polymerase Chain Reaction/*veterinary ; Propidium/*analogs &amp; derivatives/chemistry ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, RNA ; Sewage/*microbiology ; Staining and Labeling/*methods ; }, abstract = {Use of anaerobic sludge digester is a common practice around the world for solids digestion and methane generation from municipal sewage sludge. Understanding microbial community structure is vital to get better insight into the anaerobic digestion process and to gain better process control. However, selective analysis of viable microorganisms is limited by DNA-based assays. In this study, propidium monoazide (PMA)-PCR with 16S rRNA gene sequencing analysis was used to distinguish live and dead microorganisms based on cell membrane integrity. Microbial community structures of PMA-treated and PMA-untreated anaerobic digester sludge samples were compared. Quantitative PCR revealed that 5-30% of the rRNA genes were derived from inactive or dead cells in anaerobic sludge digesters. This caused a significant decrease in the numbers of operational taxonomic units and Chao1 and Shannon indices compared with that of the PMA-untreated sludge. Microbial community analysis showed that majority of the viable microbiome consisted of Euryarchaeota, Bacteroidetes, Deltaproteobacteria, Chloroflexi, Firmicutes, WWE1, Spirochaetes, Synergistetes, and Caldiserica. On the other hand, after the PMA treatment, numbers of Alphaproteobacteria and Betaproteobacteria declined. These were considered residual microbial members. The network analysis also revealed a relationship among the OTUs belonging to WWE1 and Bacteroidales. PMA-PCR-based 16S rRNA gene sequencing analysis is an effective tool for uncovering viable microbiome in complex environmental samples.}, }
@article {pmid31701033, year = {2019}, author = {Testa, S and Berger, S and Piccardi, P and Oechslin, F and Resch, G and Mitri, S}, title = {Spatial structure affects phage efficacy in infecting dual-strain biofilms of Pseudomonas aeruginosa.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {405}, pmid = {31701033}, issn = {2399-3642}, mesh = {Biofilms/*growth &amp; development ; Host Microbial Interactions/physiology ; Microscopy, Electron, Transmission ; Models, Biological ; Pseudomonas Phages/*pathogenicity/ultrastructure ; Pseudomonas aeruginosa/classification/physiology/*virology ; Species Specificity ; }, abstract = {Bacterial viruses, or phage, are key members of natural microbial communities. Yet much research on bacterial-phage interactions has been conducted in liquid cultures involving single bacterial strains. Here we explored how bacterial diversity affects the success of lytic phage in structured communities. We infected a sensitive Pseudomonas aeruginosa strain PAO1 with a lytic phage Pseudomonas 352 in the presence versus absence of an insensitive P. aeruginosa strain PA14, in liquid culture versus colonies on agar. We found that both in liquid and in colonies, inter-strain competition reduced resistance evolution in the susceptible strain and decreased phage population size. However, while all sensitive bacteria died in liquid, bacteria in colonies could remain sensitive yet escape phage infection, due mainly to reduced growth in colony centers. In sum, spatial structure can protect bacteria against phage infection, while the presence of competing strains reduces the evolution of resistance to phage.}, }
@article {pmid31700900, year = {2019}, author = {Han, MM and Zhu, XY and Peng, YF and Lin, H and Liu, DC and Li, L}, title = {The alterations of gut microbiota in mice with chronic pancreatitis.}, journal = {Annals of translational medicine}, volume = {7}, number = {18}, pages = {464}, pmid = {31700900}, issn = {2305-5839}, abstract = {BACKGROUND: The changes of intestinal microbiome are associated with inflammatory, metabolic, and malignant disorders, and there are no studies assessing the intestinal microbiota of mice with chronic pancreatitis (CP). Thus, we aim to investigate the variations in diversity, composition and function of intestinal microbiota in CP mice.<br><br>METHODS: Sixteen male C57BL/6 mice were randomly selected, and divided into two groups, treated intraperitoneally with saline (normal control group, CT group) or ethanol + cerulein (experimental group, CP group) for 6 weeks. Body weight as measured in entire processes. Histopathological examination of CP index was conducted to verify the CP induction. Extracted DNA from colon samples was used for Illumina HiSeq sequencing of the bacterial V4 region of 16S rRNA gene and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Functional profiling of microbial communities was predicted with BugBase.<br><br>RESULTS: Significant alterations of the gut microbiota were found in the CP mice compared to CT groups, as revealed by significant decrease in bacterial richness and diversity, declined the relative abundance of Lachnospiraceae_NK4A136, Ruminiclostridium and Roseburia, and increased the relative abundances of Bacteroides and Alloprevotella genera. Analysis of microbial community-level phenotypes revealed significant differences in nine phenotypes (aerobic, anaerobic, containing mobile elements, facultatively anaerobic, biofilm forming, gram-negative, gram-positive, potentially pathogenic, and stress tolerant) between CP group and CT group.<br><br>CONCLUSIONS: This study indicated that mice with CP had a distinct microbiota profile.}, }
@article {pmid31700196, year = {2019}, author = {Zheng, Q and Hu, Y and Zhang, S and Noll, L and Böckle, T and Dietrich, M and Herbold, CW and Eichorst, SA and Woebken, D and Richter, A and Wanek, W}, title = {Soil multifunctionality is affected by the soil environment and by microbial community composition and diversity.}, journal = {Soil biology &amp; biochemistry}, volume = {136}, number = {}, pages = {107521}, pmid = {31700196}, issn = {0038-0717}, support = {636928/ERC_/European Research Council/International ; P 28037/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Microorganisms are critical in mediating carbon (C) and nitrogen (N) cycling processes in soils. Yet, it has long been debated whether the processes underlying biogeochemical cycles are affected by the composition and diversity of the soil microbial community or not. The composition and diversity of soil microbial communities can be influenced by various environmental factors, which in turn are known to impact biogeochemical processes. The objectives of this study were to test effects of multiple edaphic drivers individually and represented as the multivariate soil environment interacting with microbial community composition and diversity, and concomitantly on multiple soil functions (i.e. soil enzyme activities, soil C and N processes). We employed high-throughput sequencing (Illumina MiSeq) to analyze bacterial/archaeal and fungal community composition by targeting the 16S rRNA gene and the ITS1 region of soils collected from three land uses (cropland, grassland and forest) deriving from two bedrock forms (silicate and limestone). Based on this data set we explored single and combined effects of edaphic variables on soil microbial community structure and diversity, as well as on soil enzyme activities and several soil C and N processes. We found that both bacterial/archaeal and fungal communities were shaped by the same edaphic factors, with most single edaphic variables and the combined soil environment representation exerting stronger effects on bacterial/archaeal communities than on fungal communities, as demonstrated by (partial) Mantel tests. We also found similar edaphic controls on the bacterial/archaeal/fungal richness and diversity. Soil C processes were only directly affected by the soil environment but not affected by microbial community composition. In contrast, soil N processes were significantly related to bacterial/archaeal community composition and bacterial/archaeal/fungal richness/diversity but not directly affected by the soil environment. This indicates direct control of the soil environment on soil C processes and indirect control of the soil environment on soil N processes by structuring the microbial communities. The study further highlights the importance of edaphic drivers and microbial communities (i.e. composition and diversity) on important soil C and N processes.}, }
@article {pmid31700119, year = {2020}, author = {Avalos, M and Garbeva, P and Raaijmakers, JM and van Wezel, GP}, title = {Production of ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces species.}, journal = {The ISME journal}, volume = {14}, number = {2}, pages = {569-583}, pmid = {31700119}, issn = {1751-7370}, mesh = {Ammonia/*metabolism ; Anti-Bacterial Agents/metabolism/*pharmacology ; Antibiosis ; Drug Resistance, Microbial/physiology ; Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Gram-Negative Bacteria/drug effects ; Gram-Positive Bacteria/drug effects ; Microbial Interactions ; Soil Microbiology ; Streptomyces/*metabolism ; }, abstract = {Soil-inhabiting streptomycetes are nature's medicine makers, producing over half of all known antibiotics and many other bioactive natural products. However, these bacteria also produce many volatiles, molecules that disperse through the soil matrix and may impact other (micro)organisms from a distance. Here, we show that soil- and surface-grown streptomycetes have the ability to kill bacteria over long distances via air-borne antibiosis. Our research shows that streptomycetes do so by producing surprisingly high amounts of the low-cost volatile ammonia, dispersing over long distances to inhibit the growth of Gram-positive and Gram-negative bacteria. Glycine is required as precursor to produce ammonia, and inactivation of the glycine cleavage system nullified ammonia biosynthesis and concomitantly air-borne antibiosis. Reduced expression of the porin master regulator OmpR and its cognate kinase EnvZ is used as a resistance strategy by E. coli cells to survive ammonia-mediated antibiosis. Finally, ammonia was shown to enhance the activity of canonical antibiotics, suggesting that streptomycetes adopt a low-cost strategy to sensitize competitors for antibiosis from a distance.}, }
@article {pmid31699144, year = {2019}, author = {Park, R and Dzialo, MC and Spaepen, S and Nsabimana, D and Gielens, K and Devriese, H and Crauwels, S and Tito, RY and Raes, J and Lievens, B and Verstrepen, KJ}, title = {Microbial communities of the house fly Musca domestica vary with geographical location and habitat.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {147}, pmid = {31699144}, issn = {2049-2618}, mesh = {Animals ; Bacteria/*classification/genetics ; Belgium ; Houseflies/*microbiology ; *Microbiota ; *Phylogeography ; Rwanda ; }, abstract = {House flies (Musca domestica) are widespread, synanthropic filth flies commonly found on decaying matter, garbage, and feces as well as human food. They have been shown to vector microbes, including clinically relevant pathogens. Previous studies have demonstrated that house flies carry a complex and variable prokaryotic microbiota, but the main drivers underlying this variability and the influence of habitat on the microbiota remain understudied. Moreover, the differences between the external and internal microbiota and the eukaryotic components have not been examined. To obtain a comprehensive view of the fly microbiota and its environmental drivers, we sampled over 400 flies from two geographically distinct countries (Belgium and Rwanda) and three different environments-farms, homes, and hospitals. Both the internal as well as external microbiota of the house flies were studied, using amplicon sequencing targeting both bacteria and fungi. Results show that the house fly's internal bacterial community is very diverse yet relatively consistent across geographic location and habitat, dominated by genera Staphylococcus and Weissella. The external bacterial community, however, varies with geographic location and habitat. The fly fungal microbiota carries a distinct signature correlating with the country of sampling, with order Capnodiales and genus Wallemia dominating Belgian flies and genus Cladosporium dominating Rwandan fly samples. Together, our results reveal an intricate country-specific pattern for fungal communities, a relatively stable internal bacterial microbiota and a variable external bacterial microbiota that depends on geographical location and habitat. These findings suggest that vectoring of a wide spectrum of environmental microbes occurs principally through the external fly body surface, while the internal microbiome is likely more limited by fly physiology.}, }
@article {pmid31699041, year = {2019}, author = {Yuen, B and Polzin, J and Petersen, JM}, title = {Organ transcriptomes of the lucinid clam Loripes orbiculatus (Poli, 1791) provide insights into their specialised roles in the biology of a chemosymbiotic bivalve.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {820}, pmid = {31699041}, issn = {1471-2164}, support = {VRG14-021//Vienna Science and Technology Fund/ ; }, mesh = {Animals ; Apoptosis/genetics ; Bacterial Physiological Phenomena ; Bivalvia/cytology/*genetics/immunology/microbiology ; Environment ; Foot/physiology ; *Gene Expression Profiling ; Immunity, Innate/genetics ; Nutrients/metabolism ; *Symbiosis ; }, abstract = {BACKGROUND: The lucinid clam Loripes orbiculatus lives in a nutritional symbiosis with sulphur-oxidizing bacteria housed in its gills. Although our understanding of the lucinid endosymbiont physiology and metabolism has made significant progress, relatively little is known about how the host regulates the symbiosis at the genetic and molecular levels. We generated transcriptomes from four L. orbiculatus organs (gills, foot, visceral mass, and mantle) for differential expression analyses, to better understand this clam's physiological adaptations to a chemosymbiotic lifestyle, and how it regulates nutritional and immune interactions with its symbionts.<br><br>RESULTS: The transcriptome profile of the symbiont-housing gill suggests the regulation of apoptosis and innate immunity are important processes in this organ. We also identified many transcripts encoding ion transporters from the solute carrier family that possibly allow metabolite exchange between host and symbiont. Despite the clam holobiont's clear reliance on chemosynthesis, the clam's visceral mass, which contains the digestive tract, is characterised by enzymes involved in digestion, carbohydrate recognition and metabolism, suggesting that L. orbiculatus has a mixotrophic diet. The foot transcriptome is dominated by the biosynthesis of glycoproteins for the construction of mucus tubes, and receptors that mediate the detection of chemical cues in the environment.<br><br>CONCLUSIONS: The transcriptome profiles of gills, mantle, foot and visceral mass provide insights into the molecular basis underlying the functional specialisation of bivalve organs adapted to a chemosymbiotic lifestyle.}, }
@article {pmid31698527, year = {2020}, author = {Roesch, LFW and Dobbler, PT and Pylro, VS and Kolaczkowski, B and Drew, JC and Triplett, EW}, title = {pime: A package for discovery of novel differences among microbial communities.}, journal = {Molecular ecology resources}, volume = {20}, number = {2}, pages = {415-428}, doi = {10.1111/1755-0998.13116}, pmid = {31698527}, issn = {1755-0998}, support = {//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 5R21AI120195-02/GF/NIH HHS/United States ; 1-INO-2018-637-A-N//JDRF/United States ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Computational Biology/*methods ; DNA, Bacterial/genetics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The data used for profiling microbial communities is usually sparse with some microbes having high abundance in a few samples and being nearly absent in others. However, current bioinformatics tools able to deal with this sparsity are lacking. pime (Prevalence Interval for Microbiome Evaluation) was designed to remove those taxa that may be high in relative abundance in just a few samples but have a low prevalence overall. The reliability and robustness of pime were compared against existing methods and tested using 16S rRNA independent data sets. pime filters microbial taxa not shared in a per treatment prevalence interval started at 5% prevalence with increasing increments of 5% at each filtering step. For each prevalence interval, hundreds of decision trees were calculated to predict the likelihood of detecting differences in treatments. The best prevalence-filtered data set was user-selected by choosing the prevalence interval that kept a large portion of the 16S rRNA sequences in the data set while also showing the lowest error rate. To obtain the likelihood of introducing type I error while building prevalence-filtered data sets, an error detection step based was also included. A pime reanalysis of published data sets uncovered other expected microbial associations than previously reported, which may be masked when only relative abundance was considered.}, }
@article {pmid31693956, year = {2020}, author = {Burges, A and Fievet, V and Oustriere, N and Epelde, L and Garbisu, C and Becerril, JM and Mench, M}, title = {Long-term phytomanagement with compost and a sunflower - Tobacco rotation influences the structural microbial diversity of a Cu-contaminated soil.}, journal = {The Science of the total environment}, volume = {700}, number = {}, pages = {134529}, doi = {10.1016/j.scitotenv.2019.134529}, pmid = {31693956}, issn = {1879-1026}, mesh = {*Biodegradation, Environmental ; Composting ; Copper/analysis/*metabolism ; Helianthus/*physiology ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/analysis/*metabolism ; Nicotiana/*physiology ; }, abstract = {At a former wood preservation site contaminated with Cu, various phytomanagement options have been assessed in the last decade through physicochemical, ecotoxicological and biological assays. In a field trial at this site, phytomanagement with a crop rotation based on tobacco and sunflower, combined with the incorporation of compost and dolomitic limestone, has proved to be efficient in Cu-associated risk mitigation, ecological soil functions recovery and net gain of economic and social benefits. To demonstrate the long-term effectiveness and sustainability of phytomanagement, we assessed here the influence of this remediation option on the diversity, composition and structure of microbial communities over time, through a metabarcoding approach. After 9 years of phytomanagement, no overall effect was identified on microbial diversity; the soil amendments, notably the repeated compost application, led to shifts in soil microbial populations. This phytomanagement option induced changes in the composition of soil microbial communities, promoting the growth of microbial groups belonging to Alphaproteobacteria, many being involved in N cycling. Populations of Nitrososphaeria, which are crucial in nitrification, as well as taxa from phyla Planctomycetacia, Chloroflexi and Gemmatimonadetes, which are tolerant to metal contamination and adapted to oligotrophic soil conditions, decreased in amended phytomanaged plots. Our study provides an insight into population dynamics within soil microbial communities under long-term phytomanagement, in line with the assessment of soil ecological functions and their recovery.}, }
@article {pmid31692676, year = {2019}, author = {Vera-Gutiérrez, T and García-Muñoz, MC and Otálvaro-Alvarez, AM and Mendieta-Menjura, O}, title = {Effect of processing technology and sugarcane varieties on the quality properties of unrefined non-centrifugal sugar.}, journal = {Heliyon}, volume = {5}, number = {10}, pages = {e02667}, pmid = {31692676}, issn = {2405-8440}, abstract = {In this research, the unrefined non-centrifugal sugar (UNCS) quality obtained from two sugarcane varieties (RD 7511 and CC 8475) and using two types of technologies (traditional and Ward-Cimpa production facilities) were evaluated. The parameters monitored through the process were impurities, total soluble solids, acidity, pH, and temperature profile. Microbiological analyses were carried out on beating, molding, packing, and storage operations; and finally, an organoleptic analysis was carried out on the final UNCS product. Results showed that the UNCS obtained from variety CC 8475 had higher consumer acceptance; meanwhile, the technologies assessed did not show significant differences in final product quality. However, these technologies showed significant differences in the highest temperature, syrup, and juice properties. Microbiological analyses highlighted beating and molding as the critical points in UNCS production safety. Finally, it was evident that the implementation of new technologies or the improvement of the furnace, as in the Ward-Cimpa production facility, is not enough to achieve food safety requirements, as many other conditions affect the microbiological quality of the product. Although the temperatures reached on the Ward-Cimpa furnace are higher than those reached with the traditional furnace and thus, enough to kill all the harmful microorganisms, contamination in downstream operations still occurs.}, }
@article {pmid31690886, year = {2020}, author = {Pernice, M and Raina, JB and Rädecker, N and Cárdenas, A and Pogoreutz, C and Voolstra, CR}, title = {Down to the bone: the role of overlooked endolithic microbiomes in reef coral health.}, journal = {The ISME journal}, volume = {14}, number = {2}, pages = {325-334}, pmid = {31690886}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/metabolism/*microbiology ; Archaea/metabolism ; Bacteria/metabolism ; *Coral Reefs ; Fungi/metabolism ; Microalgae ; *Microbiota ; Symbiosis ; }, abstract = {Reef-building corals harbour an astonishing diversity of microorganisms, including endosymbiotic microalgae, bacteria, archaea, and fungi. The metabolic interactions within this symbiotic consortium are fundamental to the ecological success of corals and the unique productivity of coral reef ecosystems. Over the last two decades, scientific efforts have been primarily channelled into dissecting the symbioses occurring in coral tissues. Although easily accessible, this compartment is only 2-3 mm thick, whereas the underlying calcium carbonate skeleton occupies the vast internal volume of corals. Far from being devoid of life, the skeleton harbours a wide array of algae, endolithic fungi, heterotrophic bacteria, and other boring eukaryotes, often forming distinct bands visible to the bare eye. Some of the critical functions of these endolithic microorganisms in coral health, such as nutrient cycling and metabolite transfer, which could enable the survival of corals during thermal stress, have long been demonstrated. In addition, some of these microorganisms can dissolve calcium carbonate, weakening the coral skeleton and therefore may play a major role in reef erosion. Yet, experimental data are wanting due to methodological limitations. Recent technological and conceptual advances now allow us to tease apart the complex physical, ecological, and chemical interactions at the heart of coral endolithic microbial communities. These new capabilities have resulted in an excellent body of research and provide an exciting outlook to further address the functional microbial ecology of the "overlooked" coral skeleton.}, }
@article {pmid31690591, year = {2019}, author = {Maslov, S and Sneppen, K}, title = {Regime Shifts in a Phage-Bacterium Ecosystem and Strategies for Its Control.}, journal = {mSystems}, volume = {4}, number = {6}, pages = {}, pmid = {31690591}, issn = {2379-5077}, abstract = {The competition between bacteria often involves both nutrients and phage predators and may give rise to abrupt regime shifts between the alternative stable states characterized by different species compositions. While such transitions have been previously studied in the context of competition for nutrients, the case of phage-induced bistability between competing bacterial species has not been considered yet. Here we demonstrate a possibility of regime shifts in well-mixed phage-bacterium ecosystems. In one of the bistable states, the fast-growing bacteria competitively exclude the slow-growing ones by depleting their common nutrient. Conversely, in the second state, the slow-growing bacteria with a large burst size generate such a large phage population that the other species cannot survive. This type of bistability can be realized as the competition between a strain of bacteria protected from phage by abortive infection and another strain with partial resistance to phage. It is often desirable to reliably control the state of microbial ecosystems, yet bistability significantly complicates this task. We discuss successes and limitations of one control strategy in which one adds short pulses to populations of individual species. Our study proposes a new type of phage therapy, where introduction of the phage is supplemented by the addition of a partially resistant host bacteria.IMPORTANCE Phage-microbe communities play an important role in human health as well as natural and industrial environments. Here we show that these communities can assume several alternative species compositions separated by abrupt regime shifts. Our model predicts these regime shifts in the competition between bacterial strains protected by two different phage defense mechanisms: abortive infection/CRISPR and partial resistance. The history dependence caused by regime shifts greatly complicates the task of manipulation and control of a community. We propose and study a successful control strategy via short population pulses aimed at inducing the desired regime shifts. In particular, we predict that a fast-growing pathogen could be eliminated by a combination of its phage and a slower-growing susceptible host.}, }
@article {pmid31689403, year = {2019}, author = {Wood, K}, title = {Microbial Ecology: Complex Bacterial Communities Reduce Selection for Antibiotic Resistance.}, journal = {Current biology : CB}, volume = {29}, number = {21}, pages = {R1143-R1145}, doi = {10.1016/j.cub.2019.09.017}, pmid = {31689403}, issn = {1879-0445}, support = {MR/N007174/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Anti-Bacterial Agents ; Bacteria/drug effects ; Drug Resistance, Bacterial ; Ecology ; *Microbiota ; }, abstract = {Competition between antibiotic-resistant and -susceptible bacteria is well studied in single-species communities, but less is known about selection for resistance in more complex ecologies. A new experiment shows natural microbial communities can hinder selection by increasing the fitness costs of resistance or by offering protection to drug-sensitive strains.}, }
@article {pmid31688899, year = {2019}, author = {Wong, YY and Lee, CW and Bong, CW and Lim, JH and Narayanan, K and Sim, EUH}, title = {Environmental control of Vibrio spp. abundance and community structure in tropical waters.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {11}, pages = {}, doi = {10.1093/femsec/fiz176}, pmid = {31688899}, issn = {1574-6941}, mesh = {Chlorophyll A/metabolism ; *Environmental Microbiology ; Estuaries ; Malaysia ; Salinity ; Vibrio/*growth &amp; development ; }, abstract = {We measured Vibrio spp. distribution and community profile in the tropical estuary of Port Klang and coastal water of Port Dickson, Malaysia. Vibrio spp. abundance ranged from 15 to 2395 colony forming units mL-1, and was driven by salinity and chlorophyll a (Chl a) concentration. However, the effect of salinity was pronounced only when salinity was <20 ppt. A total of 27 Vibrio spp. were identified, and theVibrio spp. community at Port Dickson was more diverse (H' = 1.94 ± 0.21). However species composition between Port Dickson and Port Klang were similar. Two frequently occurring Vibrio spp. were V. owensii and V. rotiferianus, which exhibited relatively higher growth rates (ANCOVA: F > 4.338, P < 0.05). Co-culture experiments between fast- and slow-growing Vibrio spp. revealed that fast-growing Vibrio spp. (r-strategists) were overwhelmed by slower-growing Vibrio spp. (K-strategists) when nutrient conditions were set towards oligotrophy. In response to resource availability, the intrinsic growth strategy of each Vibrio spp. determined its occurrence and the development of Vibrio spp. community composition.}, }
@article {pmid31686026, year = {2020}, author = {McCall, LI and Callewaert, C and Zhu, Q and Song, SJ and Bouslimani, A and Minich, JJ and Ernst, M and Ruiz-Calderon, JF and Cavallin, H and Pereira, HS and Novoselac, A and Hernandez, J and Rios, R and Branch, OH and Blaser, MJ and Paulino, LC and Dorrestein, PC and Knight, R and Dominguez-Bello, MG}, title = {Home chemical and microbial transitions across urbanization.}, journal = {Nature microbiology}, volume = {5}, number = {1}, pages = {108-115}, pmid = {31686026}, issn = {2058-5276}, support = {P41 GM103484/GM/NIGMS NIH HHS/United States ; R25 GM061151/GM/NIGMS NIH HHS/United States ; S10 RR029121/RR/NCRR NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; *Biodiversity ; Environmental Exposure/*analysis ; Environmental Microbiology ; Fungi/classification/genetics/isolation &amp; purification ; Household Products/*analysis ; Housing ; Humans ; Microbiota ; Rainforest ; South America ; *Urbanization ; }, abstract = {Urbanization represents a profound shift in human behaviour, and has considerable cultural and health-associated consequences[1,2]. Here, we investigate chemical and microbial characteristics of houses and their human occupants across an urbanization gradient in the Amazon rainforest, from a remote Peruvian Amerindian village to the Brazilian city of Manaus. Urbanization was found to be associated with reduced microbial outdoor exposure, increased contact with housing materials, antimicrobials and cleaning products, and increased exposure to chemical diversity. The degree of urbanization correlated with changes in the composition of house bacterial and microeukaryotic communities, increased house and skin fungal diversity, and an increase in the relative abundance of human skin-associated fungi and bacteria in houses. Overall, our results indicate that urbanization has large-scale effects on chemical and microbial exposures and on the human microbiota.}, }
@article {pmid31684148, year = {2019}, author = {Gomes, A and Oudot, C and Macià, A and Foito, A and Carregosa, D and Stewart, D and Van de Wiele, T and Berry, D and Motilva, MJ and Brenner, C and Dos Santos, CN}, title = {Berry-Enriched Diet in Salt-Sensitive Hypertensive Rats: Metabolic Fate of (Poly)Phenols and the Role of Gut Microbiota.}, journal = {Nutrients}, volume = {11}, number = {11}, pages = {}, pmid = {31684148}, issn = {2072-6643}, support = {ANR-13-ISV1-0001-01//Agence Nationale de la Recherche/ ; ANR-11-IDEX-0003-01//Agence Nationale de la Recherche/ ; FCTANR/BEX-BCM/0001/2013//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; SFRH/BD/103155/2014//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; IF/01097/2013//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; FWF P26127-B20//Austrian Science Fund/ ; FunKeyGut 741623/ERC_/European Research Council/International ; Rural &amp; Environment Science &amp; Analytical Services//Scottish Government/ ; LISBOA-01-0145-FEDER-007344//iNOVA4Health Research Unit/ ; }, mesh = {Animals ; Diet ; Dysbiosis/metabolism ; Feces/microbiology ; *Fruit ; Gastrointestinal Microbiome/genetics/*physiology ; Glycosides/metabolism ; Male ; Phenols/analysis/*metabolism ; Phytochemicals/analysis/metabolism ; Rats ; Rats, Inbred Dahl ; Sodium, Dietary ; }, abstract = {Diets rich in (poly)phenols are associated with a reduced reduction in the incidence of cardiovascular disorders. While the absorption and metabolism of (poly)phenols has been described, it is not clear how their metabolic fate is affected under pathological conditions. This study evaluated the metabolic fate of berry (poly)phenols in an in vivo model of hypertension as well as the associated microbiota response. Dahl salt-sensitive rats were fed either a low-salt diet (0.26% NaCl) or a high-salt diet (8% NaCl), with or without a berry mixture (blueberries, blackberries, raspberries, Portuguese crowberry and strawberry tree fruit) for 9 weeks. The salt-enriched diet promoted an increase in the urinary excretion of berry (poly)phenol metabolites, while the abundance of these metabolites decreased in faeces, as revealed by UPLC-MS/MS. Moreover, salt and berries modulated gut microbiota composition as demonstrated by 16S rRNA analysis. Some changes in the microbiota composition were associated with the high-salt diet and revealed an expansion of the families Proteobacteria and Erysipelotrichaceae. However, this effect was mitigated by the dietary supplementation with berries. Alterations in the metabolic fate of (poly)phenols occur in parallel with the modulation of gut microbiota in hypertensive rats. Thus, beneficial effects of (poly)phenols could be related with these interlinked modifications, between metabolites and microbiota environments.}, }
@article {pmid31682986, year = {2020}, author = {Brackmann, M and Leib, SL and Tonolla, M and Schürch, N and Wittwer, M}, title = {Antimicrobial resistance classification using MALDI-TOF-MS is not that easy: lessons from vancomycin-resistant Enterococcus faecium.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {26}, number = {3}, pages = {391-393}, doi = {10.1016/j.cmi.2019.10.027}, pmid = {31682986}, issn = {1469-0691}, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; *Drug Resistance, Bacterial ; Enterococcus faecium/*drug effects ; Gram-Positive Bacterial Infections/diagnosis/drug therapy/microbiology ; Humans ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Vancomycin/*pharmacology/therapeutic use ; }, }
@article {pmid31681511, year = {2019}, author = {Kobayashi, K and Aoyagi, H}, title = {Microbial community structure analysis in Acer palmatum bark and isolation of novel bacteria IAD-21 of the candidate division FBP.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e7876}, pmid = {31681511}, issn = {2167-8359}, abstract = {BACKGROUND: The potential of unidentified microorganisms for academic and other applications is limitless. Plants have diverse microbial communities associated with their biomes. However, few studies have focused on the microbial community structure relevant to tree bark.<br><br>METHODS: In this report, the microbial community structure of bark from the broad-leaved tree Acer palmatum was analyzed. Both a culture-independent approach using polymerase chain reaction (PCR) amplification and next generation sequencing, and bacterial isolation and sequence-based identification methods were used to explore the bark sample as a source of previously uncultured microorganisms. Molecular phylogenetic analyses based on PCR-amplified 16S rDNA sequences were performed.<br><br>RESULTS: At the phylum level, Proteobacteria and Bacteroidetes were relatively abundant in the A. palmatum bark. In addition, microorganisms from the phyla Acidobacteria, Gemmatimonadetes, Verrucomicrobia, Armatimonadetes, and candidate division FBP, which contain many uncultured microbial species, existed in the A. palmatum bark. Of the 30 genera present at relatively high abundance in the bark, some genera belonging to the phyla mentioned were detected. A total of 70 isolates could be isolated and cultured using the low-nutrient agar media DR2A and PE03. Strains belonging to the phylum Actinobacteria were isolated most frequently. In addition, the newly identified bacterial strain IAP-33, presumed to belong to Acidobacteria, was isolated on PE03 medium. Of the isolated bacteria, 44 strains demonstrated less than 97% 16S rDNA sequence-similarity with type strains. Molecular phylogenetic analysis of IAD-21 showed the lowest similarity (79%), and analyses suggested it belongs to candidate division FBP. Culture of the strain IAD-21 was deposited in Japan Collection of Microorganisms (JCM) and Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) as JCM 32665 and DSM 108248, respectively.<br><br>DISCUSSION: Our results suggest that a variety of uncultured microorganisms exist in A. palmatum bark. Microorganisms acquirable from the bark may prove valuable for academic pursuits, such as studying microbial ecology, and the bark might be a promising source of uncultured bacterial isolates.}, }
@article {pmid31681249, year = {2019}, author = {He, H and Fu, L and Liu, Q and Fu, L and Bi, N and Yang, Z and Zhen, Y}, title = {Community Structure, Abundance and Potential Functions of Bacteria and Archaea in the Sansha Yongle Blue Hole, Xisha, South China Sea.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2404}, pmid = {31681249}, issn = {1664-302X}, abstract = {The Sansha Yongle Blue Hole is the deepest blue hole in the world and exhibits unique environmental characteristics. In this paper, Illumina sequencing and qPCR analysis were conducted to obtain the microbial information in this special ecosystem. The results showed that the richness and diversity of bacterial communities in the hole was greater than those of archaeal communities, and bacterial and archaeal communities were dominated by Proteobacteria and Euryarchaeota, respectively. Temperature and nitrate concentration significantly contributed to the heterogeneous distribution of major bacterial clades; salinity explained most variations of the archaeal communities, but not significant. A sudden increase of bacterial 16S rRNA, archaeal 16S rRNA, ANAMMOX 16S rRNA, nirS and dsrB gene was noticed from 90 to 100 m in the hole probably due to more phytoplankton at this depth. Sulfur oxidation and nitrate reduction were the most abundant predicted ecological functions in the hole, while lots of archaea were predicted to be involved in aerobic ammonia oxidation and methanogenesis. The co-occurrence network analysis illustrated that a synergistic effect between sulfate reduction and sulfur oxidation, and between nitrogen fixation and denitrification, a certain degree of coupling between sulfur and nitrogen cycle was also observed in the hole. The comparisons of bacterial and archaeal communities between the hole and other caves in the world (or other areas of the South China Sea) suggest that similar conditions are hypothesized to give rise to similar microbial communities, and environmental conditions may contribute significantly to the bacterial and archaeal communities.}, }
@article {pmid31680681, year = {2019}, author = {Temkin, MI and Carlson, CM and Stubbendieck, AL and Currie, CR and Stubbendieck, RM}, title = {High Throughput Co-culture Assays for the Investigation of Microbial Interactions.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {152}, pages = {}, pmid = {31680681}, issn = {1940-087X}, support = {T15 LM007359/LM/NLM NIH HHS/United States ; U19 AI109673/AI/NIAID NIH HHS/United States ; }, mesh = {Actinobacteria/*isolation &amp; purification/*metabolism ; Biological Assay/*methods ; Coculture Techniques/methods ; Humans ; Microbial Interactions/*physiology ; Microbiota/physiology ; Nasal Cavity/microbiology ; }, abstract = {The study of interactions between microorganisms has led to numerous discoveries, from novel antimicrobials to insights in microbial ecology. Many approaches used for the study of microbial interactions require specialized equipment and are expensive and time intensive. This paper presents a protocol for co-culture interaction assays that are inexpensive, scalable to large sample numbers, and easily adaptable to numerous experimental designs. Microorganisms are cultured together, with each well representing one pairwise combination of microorganisms. A test organism is cultured on one side of each well and first incubated in monoculture. Subsequently, target organisms are simultaneously inoculated onto the opposite side of each well using a 3D-printed inoculation stamp. After co-culture, the completed assays are scored for visual phenotypes, such as growth or inhibition. These assays can be used to confirm phenotypes or identify patterns among isolates of interest. Using this simple and effective method, users can analyze combinations of microorganisms rapidly and efficiently. This co-culture approach is applicable to antibiotic discovery as well as culture-based microbiome research and has already been successfully applied to both applications.}, }
@article {pmid31679006, year = {2020}, author = {González-Hourcade, M and Braga, MR and Del Campo, EM and Ascaso, C and Patiño, C and Casano, LM}, title = {Ultrastructural and biochemical analyses reveal cell wall remodelling in lichen-forming microalgae submitted to cyclic desiccation-rehydration.}, journal = {Annals of botany}, volume = {125}, number = {3}, pages = {459-469}, pmid = {31679006}, issn = {1095-8290}, mesh = {Cell Wall ; Desiccation ; Fluid Therapy ; *Lichens ; *Microalgae ; }, abstract = {BACKGROUND AND AIMS: One of the most distinctive features of desiccation-tolerant plants is their high cell wall (CW) flexibility. Most lichen microalgae can tolerate drastic dehydration-rehydration (D/R) conditions; however, their mechanisms of D/R tolerance are scarcely understood. We tested the hypothesis that D/R-tolerant microalgae would have flexible CWs due to species-specific CW ultrastructure and biochemical composition, which could be remodelled by exposure to cyclic D/R.<br><br>METHODS: Two lichen microalgae, Trebouxia sp. TR9 (TR9, adapted to rapid D/R cycles) and Coccomyxa simplex (Csol, adapted to seasonal dry periods) were exposed to no or four cycles of desiccation [25-30 % RH (TR9) or 55-60 % RH (Csol)] and 16 h of rehydration (100 % RH). Low-temperature SEM, environmental SEM and freeze-substitution TEM were employed to visualize structural alterations induced by D/R. In addition, CWs were extracted and sequentially fractionated with hot water and KOH, and the gel permeation profile of polysaccharides was analysed in each fraction. The glycosyl composition and linkage of the main polysaccharides of each CW fraction were analysed by GC-MS.<br><br>KEY RESULTS: All ultrastructural analyses consistently showed that desiccation caused progressive cell shrinkage and deformation in both microalgae, which could be rapidly reversed when water availability increased. Notably, the plasma membrane of TR9 and Csol remained in close contact with the deformed CW. Exposure to D/R strongly altered the size distribution of TR9 hot-water-soluble polysaccharides, composed mainly of a &#x3b2;-3-linked rhamnogalactofuranan and Csol KOH-soluble &#x3b2;-glucans.<br><br>CONCLUSIONS: Cyclic D/R induces biochemical remodelling of the CW that could increase CW flexibility, allowing regulated shrinkage and expansion of D/R-tolerant microalgae.}, }
@article {pmid31678751, year = {2020}, author = {Contreras-Dávila, CA and Carrión, VJ and Vonk, VR and Buisman, CNJ and Strik, DPBTB}, title = {Consecutive lactate formation and chain elongation to reduce exogenous chemicals input in repeated-batch food waste fermentation.}, journal = {Water research}, volume = {169}, number = {}, pages = {115215}, doi = {10.1016/j.watres.2019.115215}, pmid = {31678751}, issn = {1879-2448}, mesh = {Bioreactors ; Butyrates ; Fatty Acids ; Fermentation ; *Food ; *Refuse Disposal ; }, abstract = {The production of biochemicals from renewables through biorefinery processes is important to reduce the anthropogenic impact on the environment. Chain elongation processes based on microbiomes have been successfully developed to produce medium-chain fatty acids (MCFA) from organic waste streams. Yet, the sustainability of chain elongation can still be improved by reducing the use of electron donors and additional chemicals. This work aimed to couple lactate production and subsequent chain elongation to decrease chemicals input such as electron donors and hydroxide for pH control in repeated-batch food waste fermentation. Food waste with adjusted pH was used as substrate and fermentation proceeded without pH control. During fermentation, lactate was first formed through the homolactic pathway and then converted to fatty acids (FA), mainly n-butyrate and n-caproate. The highest n-caproate carbon selectivities (mmol C/mmol CFA) and production rates were 38% and 4.2 g COD/L-d, respectively. Hydroxide input was reduced over time to a minimum of 0.47 mol OH[-]/mol MCFA or 0.79 mol OH[-]/kg CODFA. Lactate was a key electron donor for chain elongation and its conversion was observed at pH as low as 4.3. The microbiome enriched in this work was dominated by Lactobacillus spp. and Caproiciproducens spp. The high abundance of Caproiciproducens spp. and their co-occurrence with Lactobacillus spp. suggest Caproiciproducens spp. used lactate as electron donor for chain elongation. This work shows the production of n-caproate from food waste with decreased use of hydroxide and no use of exogenous electron donors.}, }
@article {pmid31677344, year = {2020}, author = {Dumack, K and Fiore-Donno, AM and Bass, D and Bonkowski, M}, title = {Making sense of environmental sequencing data: Ecologically important functional traits of the protistan groups Cercozoa and Endomyxa (Rhizaria).}, journal = {Molecular ecology resources}, volume = {20}, number = {2}, pages = {398-403}, doi = {10.1111/1755-0998.13112}, pmid = {31677344}, issn = {1755-0998}, support = {BO 1907/13-2//Deutsche Forschungsgemeinschaft/ ; BO 1907/18-1//Deutsche Forschungsgemeinschaft/ ; Priority Program 1374//Deutsche Forschungsgemeinschaft/ ; NE/H000887/1//NERC Science of the Environment/ ; NE/H009426/1//NERC Science of the Environment/ ; }, mesh = {Cercozoa/classification/genetics ; DNA, Environmental/genetics ; Databases, Genetic ; Ecosystem ; Phenotype ; Phylogeny ; Rhizaria/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {We have compiled a database of functional traits for two widespread and ecologically important groups of protists, Cercozoa and Endomyxa (Rhizaria). The functional traits of microorganisms are crucially important for interpreting results from environmental sequencing surveys. Linking morphological and ecological traits to environmental factors is common practice in studies involving micro- and macroorganisms, but is rarely applied to protists. Our database provides functional and ecologically significant traits linked to morphology, nutrition, locomotion and habitats. We discuss how the use of functional traits may help to unveil underlying ecosystem processes. This database is intended as a common reference for the molecular ecology community and will boost the understanding of ecosystem functions, especially those driven by biological interactions.}, }
@article {pmid31676992, year = {2020}, author = {Kublanovskaya, A and Solovchenko, A and Fedorenko, T and Chekanov, K and Lobakova, E}, title = {Natural Communities of Carotenogenic Chlorophyte Haematococcus lacustris and Bacteria from the White Sea Coastal Rock Ponds.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {785-800}, doi = {10.1007/s00248-019-01437-0}, pmid = {31676992}, issn = {1432-184X}, support = {18-29-25050//&#x420;&#x43e;&#x441;&#x441;&#x438;&#x439;&#x441;&#x43a;&#x438;&#x439; &#x424;&#x43e;&#x43d;&#x434; &#x424;&#x443;&#x43d;&#x434;&#x430;&#x43c;&#x435;&#x43d;&#x442;&#x430;&#x43b;&#x44c;&#x43d;&#x44b;&#x445; &#x418;&#x441;&#x441;&#x43b;&#x435;&#x434;&#x43e;&#x432;&#x430;&#x43d;&#x438;&#x439; (&#x420;&#x424;&#x424;&#x418;)/ ; }, mesh = {Bacteria/classification/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; Chlorophyta/*microbiology ; *Microbiota ; Oceans and Seas ; Russia ; Seawater/*microbiology ; }, abstract = {Haematococcus lacustris is a biotechnologically important green unicellular alga producing widely used keta-karotenoid astaxanthin. In natural habitats, it exists in the form of algal-bacterial community, and under laboratory conditions, it is also accompanied by bacteria. The issue of the bacterial composition of industrial algal cultures is widely recognized as important. However, there is a dearth of information about bacterial composition of H. lacustris communities. In current work, we analyze the composition of natural H. lacustris communities from the White Sea coastal temporal rock ponds. For the first time, a 16S rRNA gene-based metagenome of natural H. lacustris bacterial communities has been generated. Main results of its analysis are as follow. Bacterial families Comamonadaceae, Cytophagaceae, Xanthomonadaceae, Acetobacteraceae, Rhodobacteraceae, and Rhodocyclaceae were observed in all studied H. lacustris natural communities. They also contained genera Hydrogenophaga and Cytophaga. Bacteria from the Hydrogenophaga genus were present in H. lacustris cultures after their isolation under the conditions of laboratory cultivation. Similar to other planktonic microalgae, H. lacustris forms a phycosphere around the cells. In this zone, bacteria attached to the algal surface. The contact between H. lacustris and bacteria is maintained even after sample drying. The study provides information about possible members of H. lacustris core microbiome, which can be presented in the industrial and laboratory cultures of the microalga.}, }
@article {pmid31676479, year = {2020}, author = {Dyer, SW and Needoba, JA}, title = {Use of High-Resolution Pressure Nephelometry To Measure Gas Vesicle Collapse as a Means of Determining Growth and Turgor Changes in Planktonic Cyanobacteria.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {2}, pages = {}, pmid = {31676479}, issn = {1098-5336}, mesh = {Cyanobacteria/growth &amp; development/*physiology ; Harmful Algal Bloom/*physiology ; Microcystis/*physiology ; Nephelometry and Turbidimetry/instrumentation/*methods ; Phytoplankton/*physiology ; }, abstract = {Previous work has demonstrated that the physical properties of intracellular bacterial gas vesicles (GVs) can be analyzed in vivo using pressure nephelometry. In analyzing the buoyant state of GV-containing cyanobacteria, hydrostatic pressure within a sample cell is increased in a stepwise manner, where the concomitant collapse of GVs due to pressure and the resultant decrease in suspended cells are detected by changes in nephelometric scattering. As the relative pressure at which GVs collapse is a function of turgor pressure and cellular osmotic gradients, pressure nephelometry is a powerful tool for assaying changes in metabolism that affect turgor, such as photosynthetic and osmoregulatory processes. We have developed an updated and automated pressure nephelometer that utilizes visible-infrared (Vis-IR) spectra to accurately quantify GV critical collapse pressure, critical collapse pressure distribution, and cell turgor pressure. Here, using the updated pressure nephelometer and axenic cultures of Microcystis aeruginosa PCC7806, we demonstrate that GV critical collapse pressure is stable during mid-exponential growth phase, introduce pressure-sensitive turbidity as a robust metric for the abundance of gas-vacuolate cyanobacteria, and demonstrate that pressure-sensitive turbidity is a more accurate proxy for abundance and growth than photopigment fluorescence. As cyanobacterium-dominated harmful algal bloom (cyanoHAB) formation is dependent on the constituent cells possessing gas vesicles, characterization of environmental cyanobacteria populations via pressure nephelometry is identified as an underutilized monitoring method. Applications of this instrument focus on physiological and ecological studies of cyanobacteria, for example, cyanoHAB dynamics and the drivers associated with cyanotoxin production in aquatic ecosystems.IMPORTANCE The increased prevalence of bloom-forming cyanobacteria and associated risk of exposure to cyanobacterial toxins through drinking water utilities and recreational waterways are growing public health concerns. Cost-effective, early-detection methodologies specific to cyanobacteria are crucial for mitigating these risks, with a gas vesicle-specific signal offering a number of benefits over photopigment fluorescence, including improved detection limits and discrimination against non-gas-vacuolate phototrophs. Here, we present a multiplexed instrument capable of quantifying the relative abundance of cyanobacteria based on the signal generated from the presence of intracellular gas vesicles specific to bloom-forming cyanobacteria. Additionally, as cell turgor can be measured in vivo via pressure nephelometry, the measurement furnishes information about the internal osmotic pressure of gas-vacuolate cyanobacteria, which relates to the metabolic state of the cell. Together these advances may improve routine waterway monitoring and the mitigation of human health threats due to cyanobacterial blooms.}, }
@article {pmid31676478, year = {2019}, author = {Oh, JH and Lin, XB and Zhang, S and Tollenaar, SL and Özçam, M and Dunphy, C and Walter, J and van Pijkeren, JP}, title = {Prophages in Lactobacillus reuteri Are Associated with Fitness Trade-Offs but Can Increase Competitiveness in the Gut Ecosystem.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {1}, pages = {}, pmid = {31676478}, issn = {1098-5336}, mesh = {Animals ; *Bacteriophages/genetics/physiology ; Chickens ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology/virology ; Genome, Bacterial ; Genome, Viral ; Humans ; Limosilactobacillus reuteri/genetics/*virology ; *Lysogeny/genetics/physiology ; Mice ; Microbial Interactions/*genetics ; Prophages/*genetics ; Rats ; Swine ; Virus Activation/physiology ; }, abstract = {The gut microbiota harbors a diverse phage population that is largely derived from lysogens, which are bacteria that contain dormant phages in their genome. While the diversity of phages in gut ecosystems is getting increasingly well characterized, knowledge is limited on how phages contribute to the evolution and ecology of their host bacteria. Here, we show that biologically active prophages are widely distributed in phylogenetically diverse strains of the gut symbiont Lactobacillus reuteri Nearly all human- and rodent-derived strains, but less than half of the tested strains of porcine origin, contain active prophages, suggesting different roles of phages in the evolution of host-specific lineages. To gain insight into the ecological role of L. reuteri phages, we developed L. reuteri strain 6475 as a model to study its phages. After administration to mice, L. reuteri 6475 produces active phages throughout the intestinal tract, with the highest number detected in the distal colon. Inactivation of recA abolished in vivo phage production, which suggests that activation of the SOS response drives phage production in the gut. In conventional mice, phage production reduces bacterial fitness as fewer wild-type bacteria survive gut transit compared to the mutant lacking prophages. However, in gnotobiotic mice, phage production provides L. reuteri with a competitive advantage over a sensitive host. Collectively, we uncovered that the presence of prophages, although associated with a fitness trade-off, can be advantageous for a gut symbiont by killing a competitor strain in its intestinal niche.IMPORTANCE Bacteriophages derived from lysogens are abundant in gut microbiomes. Currently, mechanistic knowledge is lacking on the ecological ramifications of prophage carriage yet is essential to explain the abundance of lysogens in the gut. An extensive screen of the bacterial gut symbiont Lactobacillus reuteri revealed that biologically active prophages are widely distributed in this species. L. reuteri 6475 produces phages throughout the mouse intestinal tract, but phage production is associated with reduced fitness of the lysogen. However, phage production provides a competitive advantage in direct competition with a nonlysogenic strain of L. reuteri that is sensitive to these phages. This combination of increased competition with a fitness trade-off provides a potential explanation for the domination of lysogens in gut ecosystem and how lysogens can coexist with sensitive hosts.}, }
@article {pmid31672892, year = {2019}, author = {Carrión, VJ and Perez-Jaramillo, J and Cordovez, V and Tracanna, V and de Hollander, M and Ruiz-Buck, D and Mendes, LW and van Ijcken, WFJ and Gomez-Exposito, R and Elsayed, SS and Mohanraju, P and Arifah, A and van der Oost, J and Paulson, JN and Mendes, R and van Wezel, GP and Medema, MH and Raaijmakers, JM}, title = {Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome.}, journal = {Science (New York, N.Y.)}, volume = {366}, number = {6465}, pages = {606-612}, doi = {10.1126/science.aaw9285}, pmid = {31672892}, issn = {1095-9203}, mesh = {Bacteria/classification ; Bacterial Physiological Phenomena ; Bacteroidetes/physiology ; Beta vulgaris/*microbiology ; Biodiversity ; Chitinases/genetics ; Disease Resistance ; Endophytes/*physiology ; Flavobacterium/physiology ; Genes, Bacterial ; Genome, Bacterial ; Metagenome ; *Microbiota ; Mutagenesis, Site-Directed ; Peptide Synthases/genetics ; Plant Diseases/*microbiology ; Plant Roots/*microbiology ; Polyketide Synthases/genetics ; Rhizoctonia/*pathogenicity ; Soil Microbiology ; }, abstract = {Microorganisms living inside plants can promote plant growth and health, but their genomic and functional diversity remain largely elusive. Here, metagenomics and network inference show that fungal infection of plant roots enriched for Chitinophagaceae and Flavobacteriaceae in the root endosphere and for chitinase genes and various unknown biosynthetic gene clusters encoding the production of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). After strain-level genome reconstruction, a consortium of Chitinophaga and Flavobacterium was designed that consistently suppressed fungal root disease. Site-directed mutagenesis then revealed that a previously unidentified NRPS-PKS gene cluster from Flavobacterium was essential for disease suppression by the endophytic consortium. Our results highlight that endophytic root microbiomes harbor a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out.}, }
@article {pmid31670141, year = {2019}, author = {Ouoba, LII and Vouidibio Mbozo, AB and Anyogu, A and Obioha, PI and Lingani-Sawadogo, H and Sutherland, JP and Jespersen, L and Ghoddusi, HB}, title = {Environmental heterogeneity of Staphylococcus species from alkaline fermented foods and associated toxins and antimicrobial resistance genetic elements.}, journal = {International journal of food microbiology}, volume = {311}, number = {}, pages = {108356}, doi = {10.1016/j.ijfoodmicro.2019.108356}, pmid = {31670141}, issn = {1879-3460}, mesh = {Anti-Bacterial Agents/pharmacology ; Burkina Faso ; Coagulase/genetics ; Congo ; DNA-Directed RNA Polymerases/genetics ; Drug Resistance, Bacterial/genetics ; Enterotoxins/*genetics ; Erythromycin/pharmacology ; Fermented Foods/*microbiology ; Genotype ; Microbial Sensitivity Tests ; Phenotype ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; *Staphylococcus/classification/drug effects/genetics/isolation &amp; purification ; Tetracycline/pharmacology ; }, abstract = {Different samples of three products including Bikalga and Soumbala from Burkina Faso (West Africa) and Ntoba Mbodi from Congo-Brazzaville (Central Africa) were evaluated. The bacteria (400) were phenotyped and genotypically characterized by Rep-PCR, PFGE, 16S rRNA and rpoB gene sequencing and spa typing. Their PFGE profiles were compared with those of 12,000 isolates in the Center for Disease Control (CDC, USA) database. They were screened for the production of enterotoxins, susceptibility to 19 antimicrobials, presence of 12 staphylococcal toxin and 38 AMR genes and the ability to transfer erythromycin and tetracycline resistance genes to Enterococcus faecalis JH2-2. Fifteen coagulase negative (CoNS) and positive (CoPS) species characterized by 25 Rep-PCR/PFGE clusters were identified: Staphylococcus arlettae, S. aureus, S. cohnii, S. epidermidis, S. gallinarum, S. haemolyticus, S. hominis, S. pasteuri, S. condimenti, S. piscifermentans, S. saprophyticus, S. sciuri, S. simulans, S. warneri and Macrococcus caseolyticus. Five species were specific to Soumbala, four to Bikalga and four to Ntoba Mbodi. Two clusters of S. gallinarum and three of S. sciuri were particular to Burkina Faso. The S. aureus isolates exhibited a spa type t355 and their PFGE profiles did not match any in the CDC database. Bacteria from the same cluster displayed similar AMR and toxin phenotypes and genotypes, whereas clusters peculiar to a product or a location generated distinct profiles. The toxin genes screened were not detected and the bacteria did not produce the staphylococcal enterotoxins A, B, C and D. AMR genes including blazA, cat501, dfr(A), dfr(G), mecA, mecA1, msr(A) and tet(K) were identified in CoNS and CoPS. Conjugation experiments produced JH2-2 isolates that acquired resistance to erythromycin and tetracycline, but no gene transfer was revealed by PCR. The investigation of the heterogeneity of Staphylococcus species from alkaline fermented foods, their relationship with clinical and environmental isolates and their safety in relation to antimicrobial resistance (AMR) and toxin production is anticipated to contribute to determining the importance of staphylococci in alkaline fermented foods, especially in relation to the safety of the consumers.}, }
@article {pmid31666490, year = {2020}, author = {Sharma, NC and Kumar, D and Sarkar, A and Chowdhury, G and Mukhopadhyay, AK and Ramamurthy, T}, title = {Prevalence of Multidrug Resistant Salmonellae with Increasing Frequency of Salmonella enterica Serovars Kentucky and Virchow among Hospitalized Diarrheal Cases in and around Delhi, India.}, journal = {Japanese journal of infectious diseases}, volume = {73}, number = {2}, pages = {119-123}, doi = {10.7883/yoken.JJID.2019.063}, pmid = {31666490}, issn = {1884-2836}, mesh = {Anti-Bacterial Agents/pharmacology ; Child ; Child, Preschool ; Diarrhea/*epidemiology/microbiology ; *Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Humans ; India/epidemiology ; Kentucky ; Prevalence ; Salmonella Infections/*epidemiology ; Salmonella enterica/classification/*drug effects ; Serogroup ; }, abstract = {Non-typhoidal salmonellae (NTS) are a major cause of acute diarrhea with characteristic multidrug resistance (MDR). In a hospital-based study, 81 NTS were isolated and tested for serotypes and antimicrobial resistance (AMR). Salmonella enterica isolates were classified into 7 different typable serovars, however, 19 (23%) isolates remained untypable. The most common serovars were S. Kentucky (48%), and S. Virchow (22%). Most of the NTS isolates displayed resistance to nalidixic acid (NA) (73%), ciprofloxacin (CIP) (48%), ampicillin (AM) and norfloxacin (NOR) (36% each), and gentamicin (CN) (31%). The AMR profiles for CN and NA; and AM, CIP, NA and NOR, were found to be high in S. Virchow (83%) and S. Kentucky (43%), respectively. Analysis of the pulsed-field gel electrophoresis patterns of S. Kentucky revealed 3 clusters. S. Kentucky has clones closely related to become prominent in recent years in Delhi. The AMR appears to be consistent with the change in MDR patterns during 2014-2017. The observed prevalence of S. Kentucky and S. Virchow in large numbers of diarrheal cases is novel. The NTS are mostly resistant to fluoroquinolones, which is the current drug of choice for treating diarrheal cases. MDR is very common among clonally related S. Kentucky.}, }
@article {pmid31665274, year = {2020}, author = {Wuyts, K and Smets, W and Lebeer, S and Samson, R}, title = {Green infrastructure and atmospheric pollution shape diversity and composition of phyllosphere bacterial communities in an urban landscape.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {1}, pages = {}, doi = {10.1093/femsec/fiz173}, pmid = {31665274}, issn = {1574-6941}, mesh = {*Air Pollution ; Bacteria/classification/genetics/isolation &amp; purification ; Belgium ; Biodiversity ; Ecosystem ; *Microbiota ; Plant Leaves/*microbiology ; RNA, Ribosomal, 16S/genetics ; Trees/microbiology ; *Urbanization ; }, abstract = {The microbial habitat on leaf surfaces, also called the phyllosphere, is a selective environment for bacteria, harbouring specific phyllosphere bacterial communities (PBCs). These communities influence plant health, plant-community diversity, ecosystem functioning and ecosystem services. Host plants in an urban environment accommodate different PBCs than those in non-urban environments, but previous studies did not address individual urban factors. In this study, the PBC composition and diversity of 55 London plane (Platanus x acerifolia) trees throughout an urban landscape (Antwerp, Belgium) were determined using 16S rRNA amplicon sequencing. An increasing proportion of green infrastructure in the surrounding of the trees, and subsequently decreasing proportion of anthropogenic land use, was linked with taxa loss, expressed in lower phyllosphere alpha diversity and higher abundances of typical phyllosphere bacteria such as Hymenobacter, Pseudomonas and Beijerinckia. Although air pollution exposure, as assessed by leaf magnetic analysis, did not link with alpha diversity, it correlated with shifts in PBC composition in form of turnover, an equilibrium of taxa gain and taxa loss. We found that both urban landscape composition and air pollution exposure - each in their own unique way - influence bacterial communities in the urban tree phyllosphere.}, }
@article {pmid31665056, year = {2019}, author = {Kieran, TJ and Arnold, KMH and Thomas, JC and Varian, CP and Saldaña, A and Calzada, JE and Glenn, TC and Gottdenker, NL}, title = {Regional biogeography of microbiota composition in the Chagas disease vector Rhodnius pallescens.}, journal = {Parasites &amp; vectors}, volume = {12}, number = {1}, pages = {504}, pmid = {31665056}, issn = {1756-3305}, support = {DGE-1545433//National Science Foundation/ ; COL11-043//Secretar&#xed;a Nacional de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; }, mesh = {Actinobacteria/classification/genetics ; Analysis of Variance ; Animals ; Bacteria/*classification/genetics ; Bacteroidetes/classification/genetics ; Biodiversity ; Chagas Disease/*transmission ; DNA Barcoding, Taxonomic ; Ecosystem ; Firmicutes/classification/genetics ; Gene Library ; Humans ; Insect Vectors/*microbiology/physiology ; *Microbiota ; Panama ; Phylogeography ; Polymerase Chain Reaction ; Proteobacteria/classification/genetics ; RNA, Ribosomal, 16S/chemistry ; Rhodnius/*microbiology/physiology ; }, abstract = {BACKGROUND: Triatomine bugs are vectors of the protozoan parasite Trypanosoma cruzi, which causes Chagas disease. Rhodnius pallescens is a major vector of Chagas disease in Panama. Understanding the microbial ecology of disease vectors is important in the development of vector management strategies that target vector survival and fitness. In this study we examined the whole-body microbial composition of R. pallescens from three locations in Panama.<br><br>METHODS: We collected 89 R. pallescens specimens using Noireau traps in Attalea butyracea palms. We then extracted total DNA from whole-bodies of specimens and amplified bacterial microbiota using 16S rRNA metabarcoding PCR. The 16S libraries were sequenced on an Illumina MiSeq and analyzed using QIIME2 software.<br><br>RESULTS: We found Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes to be the most abundant bacterial phyla across all samples. Geographical location showed the largest difference in microbial composition with northern Veraguas Province having the most diversity and Panama Oeste Province localities being most similar to each other. Wolbachia was detected in high abundance (48-72%) at Panama Oeste area localities with a complete absence of detection in Veraguas Province. No significant differences in microbial composition were detected between triatomine age class, primary blood meal source, or T. cruzi infection status.<br><br>CONCLUSIONS: We found biogeographical regions differ in microbial composition among R. pallescens populations in Panama. While overall the microbiota has bacterial taxa consistent with previous studies in triatomine microbial ecology, locality differences are an important observation for future studies. Geographical heterogeneity in microbiomes of vectors is an important consideration for future developments that leverage microbiomes for disease control.}, }
@article {pmid31664477, year = {2020}, author = {Kolátková, V and Čepička, I and Gargiulo, GM and Vohník, M}, title = {Enigmatic Phytomyxid Parasite of the Alien Seagrass Halophila stipulacea: New Insights into Its Ecology, Phylogeny, and Distribution in the Mediterranean Sea.}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {631-643}, pmid = {31664477}, issn = {1432-184X}, support = {1308218//Grantov&#xe1; Agentura, Univerzita Karlova (CZ)/ ; }, mesh = {Cercozoa/classification/genetics/*physiology ; Hydrocharitaceae/*parasitology ; Introduced Species ; Italy ; Mediterranean Sea ; Phylogeny ; Plant Leaves/*parasitology ; RNA, Protozoan/analysis ; RNA, Ribosomal, 18S/analysis ; *Symbiosis ; }, abstract = {Marine phytomyxids represent often overlooked obligate biotrophic parasites colonizing diatoms, brown algae, and seagrasses. An illustrative example of their enigmatic nature is the phytomyxid infecting the seagrass Halophila stipulacea (a well-known Lessepsian migrant from the Indo-Pacific to the Mediterranean Sea). In the Mediterranean, the occurrence of this phytomyxid was first described in 1995 in the Strait of Messina (southern Italy) and the second time in 2017 in the Aegean coast of Turkey. Here we investigated, using scuba diving, stereomicroscopy, light and scanning electron microscopy, and molecular methods, whether the symbiosis is still present in southern Italy, its distribution in this region and its relation to the previous reports. From the total of 16 localities investigated, the symbiosis has only been found at one site. A seasonal pattern was observed with exceptionally high abundance (> 40% of the leaf petioles colonized) in September 2017, absence of the symbiosis in May/June 2018, and then again high infection rates (~ 30%) in September 2018. In terms of anatomy and morphology as well as resting spore dimensions and arrangement, the symbiosis seems to be identical to the preceding observations in the Mediterranean. According to the phylogenetic analyses of the 18S rRNA gene, the phytomyxid represents the first characterized member of the environmental clade "TAGIRI-5". Our results provide new clues about its on-site ecology (incl. possible dispersal mechanisms), hint that it is rare but established in the Mediterranean, and encourage further research into its distribution, ecophysiology, and taxonomy.}, }
@article {pmid31662456, year = {2019}, author = {Chase, AB and Arevalo, P and Brodie, EL and Polz, MF and Karaoz, U and Martiny, JBH}, title = {Maintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial Bacteria.}, journal = {mBio}, volume = {10}, number = {5}, pages = {}, pmid = {31662456}, issn = {2150-7511}, mesh = {Actinobacteria/genetics ; Bacteria/classification/*genetics ; Ecology ; Ecosystem ; Gene Flow ; Genetic Variation ; Genome, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil ; *Soil Microbiology ; }, abstract = {For free-living bacteria and archaea, the equivalent of the biological species concept does not exist, creating several obstacles to the study of the processes contributing to microbial diversification. These obstacles are particularly high in soil, where high bacterial diversity inhibits the study of closely related genotypes and therefore the factors structuring microbial populations. Here, we isolated strains within a single Curtobacterium ecotype from surface soil (leaf litter) across a regional climate gradient and investigated the phylogenetic structure, recombination, and flexible gene content of this genomic diversity to infer patterns of gene flow. Our results indicate that microbial populations are delineated by gene flow discontinuities, with distinct populations cooccurring at multiple sites. Bacterial population structure was further delineated by genomic features allowing for the identification of candidate genes possibly contributing to local adaptation. These results suggest that the genetic structure within this bacterium is maintained both by ecological specialization in localized microenvironments (isolation by environment) and by dispersal limitation between geographic locations (isolation by distance).IMPORTANCE Due to the promiscuous exchange of genetic material and asexual reproduction, delineating microbial species (and, by extension, populations) remains challenging. Because of this, the vast majority of microbial studies assessing population structure often compare divergent strains from disparate environments under varied selective pressures. Here, we investigated the population structure within a single bacterial ecotype, a unit equivalent to a eukaryotic species, defined as highly clustered genotypic and phenotypic strains with the same ecological niche. Using a combination of genomic and computational analyses, we assessed the phylogenetic structure, extent of recombination, and flexible gene content of this genomic diversity to infer patterns of gene flow. To our knowledge, this study is the first to do so for a dominant soil bacterium. Our results indicate that bacterial soil populations, similarly to those in other environments, are structured by gene flow discontinuities and exhibit distributional patterns consistent with both isolation by distance and isolation by environment. Thus, both dispersal limitation and local environments contribute to the divergence among closely related soil bacteria as observed in macroorganisms.}, }
@article {pmid31662077, year = {2019}, author = {Madison, JD and Ouellette, SP and Schmidt, EL and Kerby, JL}, title = {Serratia marcescens shapes cutaneous bacterial communities and influences survival of an amphibian host.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1914}, pages = {20191833}, pmid = {31662077}, issn = {1471-2954}, support = {P20 GM103443/GM/NIGMS NIH HHS/United States ; }, mesh = {Amphibians/*microbiology ; Animals ; Chytridiomycota/physiology ; Microbiota ; Mycoses/microbiology ; Serratia marcescens/*physiology ; Skin/microbiology ; }, abstract = {Ongoing investigations into the interactions between microbial communities and their associated hosts are changing how emerging diseases are perceived and ameliorated. Of the numerous host-microbiome-disease systems of study, the emergence of chytridiomycosis (caused by Batrachochytrium dendrobatidis, hereafter Bd) has been implicated in ongoing declines and extinction events of amphibians worldwide. Interestingly, there has been differential survival among amphibians in resisting Bd infection and subsequent disease. One factor thought to contribute to this resistance is the host-associated cutaneous microbiota. This has raised the possibility of using genetically modified probiotics to restructure the host-associated microbiota for desired anti-fungal outcomes. Here, we use a previously described strain of Serratia marcescens (Sm) for the manipulation of amphibian cutaneous microbiota. Sm was genetically altered to have a dysfunctional pathway for the production of the extracellular metabolite prodigiosin. This genetically altered strain (Δpig) and the functional prodigiosin producing strain (wild-type, WT) were compared for their microbial community and anti-Bd effects both in vitro and in vivo. In vitro, Bd growth was significantly repressed in the presence of prodigiosin. In vivo, the inoculation of both Sm strains was shown to significantly influence amphibian microbiota diversity with the Δpig-Sm treatment showing increasing alpha diversity, and the WT-Sm having no temporal effect on diversity. Differences were also seen in host mortality with Δpig-Sm treatments exhibiting significantly decreased survival probability when compared with WT-Sm in the presence of Bd. These results are an important proof-of-concept for linking the use of genetically modified probiotic bacteria to host microbial community structure and disease outcomes, which in the future may provide a way to ameliorate disease and address critical frontiers in disease and microbial ecology.}, }
@article {pmid31660948, year = {2019}, author = {Waters, JL and Ley, RE}, title = {The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {83}, pmid = {31660948}, issn = {1741-7007}, support = {R01 DK093595/DK/NIDDK NIH HHS/United States ; }, mesh = {Clostridiales/genetics/*physiology ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {The Christensenellaceae, a recently described family in the phylum Firmicutes, is emerging as an important player in human health. The relative abundance of Christensenellaceae in the human gut is inversely related to host body mass index (BMI) in different populations and multiple studies, making its relationship with BMI the most robust and reproducible link between the microbial ecology of the human gut and metabolic disease reported to date. The family is also related to a healthy status in a number of other different disease contexts, including obesity and inflammatory bowel disease. In addition, Christensenellaceae is highly heritable across multiple populations, although specific human genes underlying its heritability have so far been elusive. Further research into the microbial ecology and metabolism of these bacteria should reveal mechanistic underpinnings of their host-health associations and enable their development as therapeutics.}, }
@article {pmid31659049, year = {2019}, author = {Gusareva, ES and Acerbi, E and Lau, KJX and Luhung, I and Premkrishnan, BNV and Kolundžija, S and Purbojati, RW and Wong, A and Houghton, JNI and Miller, D and Gaultier, NE and Heinle, CE and Clare, ME and Vettath, VK and Kee, C and Lim, SBY and Chénard, C and Phung, WJ and Kushwaha, KK and Nee, AP and Putra, A and Panicker, D and Yanqing, K and Hwee, YZ and Lohar, SR and Kuwata, M and Kim, HL and Yang, L and Uchida, A and Drautz-Moses, DI and Junqueira, ACM and Schuster, SC}, title = {Microbial communities in the tropical air ecosystem follow a precise diel cycle.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {46}, pages = {23299-23308}, pmid = {31659049}, issn = {1091-6490}, mesh = {*Air Microbiology ; Air Pollutants/analysis ; Circadian Rhythm ; Ecosystem ; Metagenome ; *Microbiota ; Models, Biological ; Singapore ; *Tropical Climate ; }, abstract = {The atmosphere is vastly underexplored as a habitable ecosystem for microbial organisms. In this study, we investigated 795 time-resolved metagenomes from tropical air, generating 2.27 terabases of data. Despite only 9 to 17% of the generated sequence data currently being assignable to taxa, the air harbored a microbial diversity that rivals the complexity of other planetary ecosystems. The airborne microbial organisms followed a clear diel cycle, possibly driven by environmental factors. Interday taxonomic diversity exceeded day-to-day and month-to-month variation. Environmental time series revealed the existence of a large core of microbial taxa that remained invariable over 13 mo, thereby underlining the long-term robustness of the airborne community structure. Unlike terrestrial or aquatic environments, where prokaryotes are prevalent, the tropical airborne biomass was dominated by DNA from eukaryotic phyla. Specific fungal and bacterial species were strongly correlated with temperature, humidity, and CO2 concentration, making them suitable biomarkers for studying the bioaerosol dynamics of the atmosphere.}, }
@article {pmid31657947, year = {2019}, author = {Ilgrande, C and Defoirdt, T and Vlaeminck, SE and Boon, N and Clauwaert, P}, title = {Media Optimization, Strain Compatibility, and Low-Shear Modeled Microgravity Exposure of Synthetic Microbial Communities for Urine Nitrification in Regenerative Life-Support Systems.}, journal = {Astrobiology}, volume = {19}, number = {11}, pages = {1353-1362}, doi = {10.1089/ast.2018.1981}, pmid = {31657947}, issn = {1557-8070}, mesh = {Ammonia/metabolism ; Bioreactors/*microbiology ; *Ecological Systems, Closed ; Heterotrophic Processes ; Humans ; Hydrolysis ; Microbiota/*physiology ; Nitrates/metabolism ; Nitrification ; Oxidation-Reduction ; Space Flight/*instrumentation ; Urea/metabolism ; Urine/*chemistry ; Weightlessness ; }, abstract = {Urine is a major waste product of human metabolism and contains essential macro- and micronutrients to produce edible microorganisms and crops. Its biological conversion into a stable form can be obtained through urea hydrolysis, subsequent nitrification, and organics removal, to recover a nitrate-enriched stream, free of oxygen demand. In this study, the utilization of a microbial community for urine nitrification was optimized with the focus for space application. To assess the role of selected parameters that can impact ureolysis in urine, the activity of six ureolytic heterotrophs (Acidovorax delafieldii, Comamonas testosteroni, Cupriavidus necator, Delftia acidovorans, Pseudomonas fluorescens, and Vibrio campbellii) was tested at different salinities, urea, and amino acid concentrations. The interaction of the ureolytic heterotrophs with a nitrifying consortium (Nitrosomonas europaea ATCC 19718 and Nitrobacter winogradskyi ATCC 25931) was also tested. Lastly, microgravity was simulated in a clinostat utilizing hardware for in-flight experiments with active microbial cultures. The results indicate salt inhibition of the ureolysis at 30 mS cm[-1], while amino acid nitrogen inhibits ureolysis in a strain-dependent manner. The combination of the nitrifiers with C. necator and V. campbellii resulted in a complete halt of the urea hydrolysis process, while in the case of A. delafieldii incomplete nitrification was observed, and nitrite was not oxidized further to nitrate. Nitrate production was confirmed in all the other communities; however, the other heterotrophic strains most likely induced oxygen competition in the test setup, and nitrite accumulation was observed. Samples exposed to low-shear modeled microgravity through clinorotation behaved similarly to the static controls. Overall, nitrate production from urea was successfully demonstrated with synthetic microbial communities under terrestrial and simulated space gravity conditions, corroborating the application of this process in space.}, }
@article {pmid31656973, year = {2020}, author = {Otto-Hanson, LK and Kinkel, LL}, title = {Densities and inhibitory phenotypes among indigenous Streptomyces spp. vary across native and agricultural habitats.}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {694-705}, pmid = {31656973}, issn = {1432-184X}, support = {9977907//National Science Foundation/ ; 2006-35319-17445//U.S. Department of Agriculture/ ; }, mesh = {*Ecosystem ; Minnesota ; Phenotype ; Soil/*chemistry ; *Soil Microbiology ; Streptomyces/*physiology ; }, abstract = {Streptomyces spp. perform vital roles in natural and agricultural soil ecosystems including in decomposition and nutrient cycling, promotion of plant growth and fitness, and plant disease suppression. Streptomyces densities can vary across the landscape, and inhibitory phenotypes are often a result of selection mediated by microbial competitive interactions in soil communities. Diverse environmental factors, including those specific to habitat, are likely to determine microbial densities in the soil and the outcomes of microbial species interactions. Here, we characterized indigenous Streptomyces densities and inhibitory phenotypes from soil samples (n = 82) collected in 6 distinct habitats across the Cedar Creek Ecosystem Science Reserve (CCESR; agricultural, prairie, savanna, wetland, wet-woodland, and forest). Significant variation in Streptomyces density and the frequency of antagonistic Streptomyces were observed among habitats. There was also significant variation in soil chemical properties among habitats, including percent carbon, percent nitrogen, available phosphorus, extractable potassium, and pH. Density and frequency of antagonists were significantly correlated with one or more environmental parameters across all habitats, though relationships with some parameters differed among habitats. In addition, we found that habitat rather than spatial proximity was a better predictor of variation in Streptomyces density and inhibitory phenotypes. Moreover, habitats least conducive for Streptomyces growth and proliferation, as determined by population density, had increased frequencies of inhibitory phenotypes. Identifying environmental parameters that structure variation in density and frequency of antagonistic Streptomyces can provide insight for determining factors that mediate selection for inhibitory phenotypes across the landscape.}, }
@article {pmid31656023, year = {2020}, author = {Farias, GC and Nunes, KG and Soares, MA and de Siqueira, KA and Lima, WC and Neves, ALR and de Lacerda, CF and Filho, EG}, title = {Dark septate endophytic fungi mitigate the effects of salt stress on cowpea plants.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {51}, number = {1}, pages = {243-253}, pmid = {31656023}, issn = {1678-4405}, mesh = {Ascomycota/*isolation &amp; purification ; Calcium/metabolism ; Chlorine/metabolism ; Endophytes/*isolation &amp; purification ; Mycorrhizae ; Myrtales/microbiology ; Photosynthesis ; Plant Leaves/metabolism ; Plant Roots/microbiology ; Plants/microbiology ; Potassium/metabolism ; Salinity ; *Salt Stress ; Sodium/metabolism ; Vigna/growth &amp; development/metabolism/*microbiology ; }, abstract = {The association of plant with microorganisms, such as dark septate endophytic fungi, has mitigated the harmful effects of chemical, physical, and biological agents on the host. The objective of this work was to evaluate the interaction of the dark septate endophytic fungi with cowpea plants under salt stress. Endophytic fungi were isolated from Vochysia divergens root system, and molecular identification of fungi was performed by sequencing the ITS region. We selected and identified Sordariomycetes sp1-B'2 and Melanconiella elegans-21W2 for their ability to infect V. divergens root in vitro with development of typical dark septate fungi structures. Cowpea plants-inoculated or not inoculated with Sordariomycetes sp1-B'2 and M. elegans 21W2-were cultivated in 5-L pots under greenhouse conditions and submitted to four different electrical conductivities of irrigation water (1.2, 2.2, 3.6, and 5.0 dS m[-1]). The salinity caused decrease in leaf concentration of K and increased leaf concentration of calcium, sodium, and chlorine; and no influence of dark septate endophytic fungi was observed in these responses. On the other hand, root colonization with Sordariomycetes sp1-B'2 and M. elegans 21W2 resulted in improved nutrition with N and P in cowpea under salt stress, favoring the growth and rate of liquid photosynthesis. However, such positive responses were evident only at moderate levels of salinity.}, }
@article {pmid31655872, year = {2020}, author = {Biedunkiewicz, A and Sucharzewska, E and Kulesza, K and Nowacka, K and Kubiak, D}, title = {Phyllosphere of Submerged Plants in Bathing Lakes as a Reservoir of Fungi-Potential Human Pathogens.}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {552-561}, pmid = {31655872}, issn = {1432-184X}, support = {12.610.009-300//Uniwersytet Warmi&#x144;sko-Mazurski w Olsztynie/ ; }, mesh = {Environmental Monitoring ; Lakes/*microbiology ; Plant Leaves/*microbiology ; Poland ; Yeasts/*isolation &amp; purification ; }, abstract = {This study analysed whether the littoral zone in the immediate vicinity of bathing sites retains potentially pathogenic yeasts on the phyllosphere surface and to what extent the species composition of microfungi in the phyllosphere and in surface waters is similar. The research was carried out in selected lakes located within the administrative boundaries of the city of Olsztyn, the largest city in the Masurian Lake District (NE Poland). The experiment was conducted in three summer seasons near bathing sites in three lakes, which are the most popular as recreational sites (Lake Kortowskie, Lake Tyrsko, and Lake Skanda). Microfungi isolated from the phyllosphere of 13 plant species of the littoral zone from dropped leaves of coast plants with no disease symptoms were used as the study material. The isolated fungi were identified in accordance with the accepted diagnostic procedures applied in mycological laboratories. A total of 36 yeast species of 16 genera were identified. Fungi found earlier at the bathing sites of the lakes were identified in 60% of the cases. Nine species were categorised as class BSL-2 fungi. This study provides a valuable complement of data concerning the natural composition of the littoral microbiota.}, }
@article {pmid31654911, year = {2019}, author = {Masteling, R and Lombard, L and de Boer, W and Raaijmakers, JM and Dini-Andreote, F}, title = {Harnessing the microbiome to control plant parasitic weeds.}, journal = {Current opinion in microbiology}, volume = {49}, number = {}, pages = {26-33}, pmid = {31654911}, issn = {1879-0364}, mesh = {Crops, Agricultural ; Host Microbial Interactions ; Microbial Interactions ; *Microbiota ; Plant Diseases/*parasitology ; Plant Roots/*microbiology/physiology ; Plant Weeds/*microbiology ; Signal Transduction ; *Soil Microbiology ; }, abstract = {Microbiomes can significantly expand the genomic potential of plants, contributing to nutrient acquisition, plant growth promotion and tolerance to (a)biotic stresses. Among biotic stressors, root parasitic weeds (RPWs), mainly of the genera Orobanche, Phelipanche and Striga, are major yield-limiting factors of a wide range of staple crops, particularly in developing countries. Here, we provide a conceptual synthesis of putative mechanisms by which soil and plant microbiomes could be harnessed to control RPWs. These mechanisms are partitioned in direct and indirect modes of action and discussed in the context of past and present studies on microbe-mediated suppression of RPWs. Specific emphasis is given to the large but yet unexplored potential of root-associated microorganisms to interfere with the chemical signalling cascade between the host plant and the RPWs. We further provide concepts and ideas for future research directions and prospective designs of novel control strategies.}, }
@article {pmid31654107, year = {2020}, author = {Reyns, W and Rineau, F and Spaak, JW and Franken, O and Berg, MP and Van Der Plas, F and Bardgett, RD and Beenaerts, N and De Laender, F}, title = {Food Web Uncertainties Influence Predictions of Climate Change Effects on Soil Carbon Sequestration in Heathlands.}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {686-693}, pmid = {31654107}, issn = {1432-184X}, support = {BOF15DOCNA02//Bijzonder Onderzoeksfonds/ ; }, mesh = {*Carbon Cycle ; *Carbon Sequestration ; *Climate Change ; *Ecosystem ; Food Chain ; Models, Biological ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {Carbon cycling models consider soil carbon sequestration a key process for climate change mitigation. However, these models mostly focus on abiotic soil processes and, despite its recognized critical mechanistic role, do not explicitly include interacting soil organisms. Here, we use a literature study to show that even a relatively simple soil community (heathland soils) contains large uncertainties in temporal and spatial food web structure. Next, we used a Lotka-Volterra-based food web model to demonstrate that, due to these uncertainties, climate change can either increase or decrease soil carbon sequestration to varying extents. Both the strength and direction of changes strongly depend on (1) the main consumer's (enchytraeid worms) feeding preferences and (2) whether decomposers (fungi) or enchytraeid worms are more sensitive to stress. Hence, even for a soil community with a few dominant functional groups and a simulation model with a few parameters, filling these knowledge gaps is a critical first step towards the explicit integration of soil food web dynamics into carbon cycling models in order to better assess the role soils play in climate change mitigation.}, }
@article {pmid31654106, year = {2020}, author = {Schappe, T and Albornoz, FE and Turner, BL and Jones, FA}, title = {Co-occurring Fungal Functional Groups Respond Differently to Tree Neighborhoods and Soil Properties Across Three Tropical Rainforests in Panama.}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {675-685}, pmid = {31654106}, issn = {1432-184X}, support = {DEB 1542681//National Science Foundation/ ; NA//Smithsonian Tropical Research Institute/ ; }, mesh = {Fungi/*physiology ; Mycorrhizae/physiology ; Panama ; *Rainforest ; Soil/*chemistry ; *Soil Microbiology ; Trees/*growth &amp; development ; }, abstract = {Abiotic and biotic drivers of co-occurring fungal functional guilds across regional-scale environmental gradients remain poorly understood. We characterized fungal communities using Illumina sequencing from soil cores collected across three Neotropical rainforests in Panama that vary in soil properties and plant community composition. We classified each fungal OTU into different functional guilds, namely plant pathogens, saprotrophs, arbuscular mycorrhizal (AM), or ectomycorrhizal (ECM). We measured soil properties and nutrients within each core and determined the tree community composition and richness around each sampling core. Canonical correspondence analyses showed that soil pH and moisture were shared potential drivers of fungal communities for all guilds. However, partial the Mantel tests showed different strength of responses of fungal guilds to composition of trees and soils. Plant pathogens and saprotrophs were more strongly correlated with soil properties than with tree composition; ECM fungi showed a stronger correlation with tree composition than with soil properties; and AM fungi were correlated with soil properties, but not with trees. In conclusion, we show that co-occurring fungal guilds respond differently to abiotic and biotic environmental factors, depending on their ecological function. This highlights the joint role that abiotic and biotic factors play in determining composition of fungal communities, including those associated with plant hosts.}, }
@article {pmid31653831, year = {2019}, author = {Sonner, JK and Keil, M and Falk-Paulsen, M and Mishra, N and Rehman, A and Kramer, M and Deumelandt, K and Röwe, J and Sanghvi, K and Wolf, L and von Landenberg, A and Wolff, H and Bharti, R and Oezen, I and Lanz, TV and Wanke, F and Tang, Y and Brandao, I and Mohapatra, SR and Epping, L and Grill, A and Röth, R and Niesler, B and Meuth, SG and Opitz, CA and Okun, JG and Reinhardt, C and Kurschus, FC and Wick, W and Bode, HB and Rosenstiel, P and Platten, M}, title = {Dietary tryptophan links encephalogenicity of autoreactive T cells with gut microbial ecology.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4877}, pmid = {31653831}, issn = {2041-1723}, mesh = {Animals ; Autoimmunity/*immunology ; *Diet ; Dietary Proteins ; Disease Models, Animal ; Encephalomyelitis, Autoimmune, Experimental/*immunology/microbiology ; Gastrointestinal Microbiome/genetics/*immunology ; Mice ; Multiple Sclerosis ; RNA, Ribosomal, 16S/genetics ; T-Lymphocytes/*immunology ; *Tryptophan ; }, abstract = {The interaction between the mammalian host and its resident gut microbiota is known to license adaptive immune responses. Nutritional constituents strongly influence composition and functional properties of the intestinal microbial communities. Here, we report that omission of a single essential amino acid - tryptophan - from the diet abrogates CNS autoimmunity in a mouse model of multiple sclerosis. Dietary tryptophan restriction results in impaired encephalitogenic T cell responses and is accompanied by a mild intestinal inflammatory response and a profound phenotypic shift of gut microbiota. Protective effects of dietary tryptophan restriction are abrogated in germ-free mice, but are independent of canonical host sensors of intracellular tryptophan metabolites. We conclude that dietary tryptophan restriction alters metabolic properties of gut microbiota, which in turn have an impact on encephalitogenic T cell responses. This link between gut microbiota, dietary tryptophan and adaptive immunity may help to develop therapeutic strategies for protection from autoimmune neuroinflammation.}, }
@article {pmid31653789, year = {2019}, author = {Kleyer, H and Tecon, R and Or, D}, title = {Rapid Shifts in Bacterial Community Assembly under Static and Dynamic Hydration Conditions in Porous Media.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {1}, pages = {}, pmid = {31653789}, issn = {1098-5336}, support = {320499/ERC_/European Research Council/International ; }, mesh = {*Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; Metagenomics ; Microbial Interactions ; Microbiota/*genetics ; Phylogeny ; Porosity ; RNA, Ribosomal, 16S ; Soil/chemistry ; *Soil Microbiology ; Water ; }, abstract = {The complexity of natural soils presents a challenge to the systematic identification and disentanglement of governing processes that shape natural bacterial communities. Studies have highlighted the critical role of the soil aqueous phase in shaping interactions among soil bacterial communities. To quantify and improve the attributability of soil aqueous-phase effects, we introduced a synthetic and traceable bacterial community to simple porous microcosms and subjected the community to constant or dynamic hydration conditions. The results were expressed in terms of absolute abundance and show species-specific responses to hydration and nutrient conditions. Hydration dynamics exerted a significant influence on the fraction of less-abundant species, especially after extended incubation periods. Phylogenetic relationships did not explain the group of most abundant species. The ability to quantify species-level dynamics in a bacterial community offers an important step toward deciphering the links between community composition and functions in dynamic terrestrial environments.IMPORTANCE The composition and activity of soil bacteria are central to various ecosystem services and soil biogeochemical cycles. A key factor for soil bacterial activity is soil hydration, which is in a constant state of change due to rainfall, drainage, plant water uptake, and evaporation. These dynamic changes in soil hydration state affect the structure and function of soil bacterial communities in complex ways often unobservable in natural soil. We designed an experimental system that retains the salient features of hydrated soil yet enables systematic evaluation of changes in a representative bacterial community in response to cycles of wetting and drying. The study shows that hydration cycles affect community abundance, yet most changes in composition occur with the less-abundant species (while the successful ones remain dominant). This research offers a new path for an improved understanding of bacterial community assembly in natural environments, including bacterial growth, maintenance, and death, with a special focus on the role of hydrological factors.}, }
@article {pmid31650676, year = {2020}, author = {Bennett, JA and Koch, AM and Forsythe, J and Johnson, NC and Tilman, D and Klironomos, J}, title = {Resistance of soil biota and plant growth to disturbance increases with plant diversity.}, journal = {Ecology letters}, volume = {23}, number = {1}, pages = {119-128}, doi = {10.1111/ele.13408}, pmid = {31650676}, issn = {1461-0248}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Biota ; *Ecosystem ; Plants ; *Soil ; Soil Microbiology ; }, abstract = {Plant diversity is critical to the functioning of ecosystems, potentially mediated in part by interactions with soil biota. Here, we characterised multiple groups of soil biota across a plant diversity gradient in a long-term experiment. We then subjected soil samples taken along this gradient to drought, freezing and a mechanical disturbance to test how plant diversity affects the responses of soil biota and growth of a focal plant to these disturbances. High plant diversity resulted in soils that were dominated by fungi and associated soil biota, including increased arbuscular mycorrhizal fungi and reduced plant-feeding nematodes. Disturbance effects on the soil biota were reduced when plant diversity was high, resulting in higher growth of the focal plant in all but the frozen soils. These results highlight the importance of plant diversity for soil communities and their resistance to disturbance, with potential feedback effects on plant productivity.}, }
@article {pmid31649246, year = {2019}, author = {Wagg, C and Schlaeppi, K and Banerjee, S and Kuramae, EE and van der Heijden, MGA}, title = {Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4841}, pmid = {31649246}, issn = {2041-1723}, mesh = {*Bacteria ; *Biodiversity ; Ecology ; *Ecosystem ; *Fungi ; *Grassland ; Microbial Consortia ; *Microbiota ; *Soil Microbiology ; }, abstract = {The soil microbiome is highly diverse and comprises up to one quarter of Earth's diversity. Yet, how such a diverse and functionally complex microbiome influences ecosystem functioning remains unclear. Here we manipulated the soil microbiome in experimental grassland ecosystems and observed that microbiome diversity and microbial network complexity positively influenced multiple ecosystem functions related to nutrient cycling (e.g. multifunctionality). Grassland microcosms with poorly developed microbial networks and reduced microbial richness had the lowest multifunctionality due to fewer taxa present that support the same function (redundancy) and lower diversity of taxa that support different functions (reduced functional uniqueness). Moreover, different microbial taxa explained different ecosystem functions pointing to the significance of functional diversity in microbial communities. These findings indicate the importance of microbial interactions within and among fungal and bacterial communities for enhancing ecosystem performance and demonstrate that the extinction of complex ecological associations belowground can impair ecosystem functioning.}, }
@article {pmid31648128, year = {2020}, author = {Tortosa, G and Torralbo, F and Maza-Márquez, P and Aranda, E and Calvo, C and González-Murua, C and Bedmar, EJ}, title = {Assessment of the diversity and abundance of the total and active fungal population and its correlation with humification during two-phase olive mill waste (''alperujo") composting.}, journal = {Bioresource technology}, volume = {295}, number = {}, pages = {122267}, doi = {10.1016/j.biortech.2019.122267}, pmid = {31648128}, issn = {1873-2976}, mesh = {*Ascomycota ; *Basidiomycota ; *Composting ; *Olea ; Soil ; }, abstract = {Metagenomic and transcriptomic techniques applied to composting could increase our understanding of the overall microbial ecology and could help us to optimise operational conditions which are directly related with economic interest. In this study, the fungal diversity and abundance of two-phase olive mill waste ("alperujo") composting was studied using Illumina MiSeq sequencing and quantitative PCR, respectively. The results showed an increase of the fungal diversity during the process, with Ascomycota being the predominant phylum. Penicillium was the main genera identified at the mesophilic and maturation phases, with Debaryomyces and Sarocladium at the thermophilic phase, respectively. The fungal abundance was increased during composting, which confirms their important role during thermophilic and maturation phases. Some Basidiomycota showed an increased during the process, which showed a positive correlation with the humification parameters. According to that, the genus Cystofilobasidium could be used as a potential fungal biomarker to assess alperujo compost maturation.}, }
@article {pmid31642982, year = {2019}, author = {Landberg, R and Manach, C and Kerckhof, FM and Minihane, AM and Saleh, RNM and De Roos, B and Tomas-Barberan, F and Morand, C and Van de Wiele, T}, title = {Future prospects for dissecting inter-individual variability in the absorption, distribution and elimination of plant bioactives of relevance for cardiometabolic endpoints.}, journal = {European journal of nutrition}, volume = {58}, number = {Suppl 2}, pages = {21-36}, pmid = {31642982}, issn = {1436-6215}, support = {FA1403//EU - COST Action FA-1403 (2014-2018)/ ; }, mesh = {Biological Variation, Population/*physiology ; Cardiovascular System/*metabolism ; Diet, Vegetarian/*methods/trends ; Humans ; Metabolomics/*methods ; Phytochemicals/administration &amp; dosage/*pharmacokinetics ; Plants, Edible/*metabolism ; }, abstract = {PURPOSE: The health-promoting potential of food-derived plant bioactive compounds is evident but not always consistent across studies. Large inter-individual variability may originate from differences in digestion, absorption, distribution, metabolism and excretion (ADME). ADME can be modulated by age, sex, dietary habits, microbiome composition, genetic variation, drug exposure and many other factors. Within the recent COST Action POSITIVe, large-scale literature surveys were undertaken to identify the reasons and extent of inter-individual variability in ADME of selected plant bioactive compounds of importance to cardiometabolic health. The aim of the present review is to summarize the findings and suggest a framework for future studies designed to investigate the etiology of inter-individual variability in plant bioactive ADME and bioefficacy.<br><br>RESULTS: Few studies have reported individual data on the ADME of bioactive compounds and on determinants such as age, diet, lifestyle, health status and medication, thereby limiting a mechanistic understanding of the main drivers of variation in ADME processes observed across individuals. Metabolomics represent crucial techniques to decipher inter-individual variability and to stratify individuals according to metabotypes reflecting the intrinsic capacity to absorb and metabolize bioactive compounds.<br><br>CONCLUSION: A methodological framework was developed to decipher how the contribution from genetic variants or microbiome variants to ADME of bioactive compounds can be predicted. Future study design should include (1) a larger number of study participants, (2) individual and full profiling of all possible determinants of internal exposure, (3) the presentation of individual ADME data and (4) incorporation of omics platforms, such as genomics, microbiomics and metabolomics in ADME and efficacy studies.}, }
@article {pmid31642672, year = {2019}, author = {Yuan, Y and Zheng, Y and Zhou, J and Geng, Y and Zou, P and Li, Y and Zhang, C}, title = {Polyphenol-Rich Extracts from Brown Macroalgae Lessonia trabeculate Attenuate Hyperglycemia and Modulate Gut Microbiota in High-Fat Diet and Streptozotocin-Induced Diabetic Rats.}, journal = {Journal of agricultural and food chemistry}, volume = {67}, number = {45}, pages = {12472-12480}, doi = {10.1021/acs.jafc.9b05118}, pmid = {31642672}, issn = {1520-5118}, mesh = {Animals ; Blood Glucose/metabolism ; Diabetes Mellitus, Experimental/*drug therapy/metabolism/microbiology ; Diet, High-Fat/adverse effects ; Gastrointestinal Microbiome/*drug effects ; Humans ; Hyperglycemia/*drug therapy/metabolism/microbiology ; Hypoglycemic Agents/*administration &amp; dosage ; Male ; Mice, Inbred C57BL ; Phaeophyceae/*chemistry ; Plant Extracts/*administration &amp; dosage ; Polyphenols/*administration &amp; dosage ; Rats ; Seaweed/*chemistry ; Streptozocin/adverse effects ; }, abstract = {Brown macroalgae are an important source of polyphenols with multiple health functions. In this work, polyphenol extracts from Lessonia trabeculate were purified and investigated for the antidiabetic activity in vitro and in vivo. The purified polyphenol extracts exhibited good antioxidant activities, α-glucosidase and lipase inhibition activities (IC50 < 0.25 mg/mL). The HPLC-DAD-ESI-MS/MS analysis indicated that the compounds in polyphenol extracts were mainly phlorotannin derivatives, phenolic acid derivatives, and gallocatechin derivatives. In vivo, C57BL/6J rats treated with polyphenol extracts for 4 weeks had lower fasting blood glucose levels, insulin levels, as well as better serum lipid profiles and antioxidant stress parameters, compared with the diabetic control (DC) group. Histopathology revealed that polyphenol extracts preserved the architecture and function of the liver. Short-chain fatty acid contents in rats' fecal samples with polyphenols administration were significantly recovered as compared with the DC group. Furthermore, the gut microflora of rats was investigated with high-throughput 16S rRNA gene sequencing and results indicated that polyphenol extracts had a positive effect on regulating the dysbiosis of the microbial ecology in diabetic rats. All of the results from the study provided a scientific reference of the potentially beneficial effects of L. trabeculate polyphenols on diabetes management.}, }
@article {pmid31642093, year = {2019}, author = {Deepika, S and Mittal, A and Kothamasi, D}, title = {HCN-producing Pseudomonas protegens CHA0 affects intraradical viability of Rhizophagus irregularis in Sorghum vulgare roots.}, journal = {Journal of basic microbiology}, volume = {59}, number = {12}, pages = {1229-1237}, doi = {10.1002/jobm.201900364}, pmid = {31642093}, issn = {1521-4028}, mesh = {Biomass ; Glomeromycota/*physiology ; Hydrogen Cyanide/*metabolism ; *Microbial Interactions ; Mycorrhizae/*physiology ; Nutrients/metabolism ; Plant Growth Regulators/genetics/*metabolism ; Plant Roots/metabolism/microbiology ; Pseudomonas/genetics/*metabolism ; Rhizosphere ; Soil Microbiology ; Sorghum/metabolism/*microbiology ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria inhabit the plant rhizosphere. Both functional groups can influence plant community structures, and interactions between them can vary from being synergistic to antagonistic. HCN-producing Pseudomonas protegens CHA0 is a plant growth-promoting rhizobacterium. P. protegens CHA0 has been shown to weakly attach to AMF hyphae. Here, we analyze the effect of P. protegens CHA0 on the viability of intraradical AMF hyphae. Using pot experiments, we have grown mycorrhizal and nonmycorrhizal Sorghum vulgare var. M35 with P. protegens CHA0 or HCN[-] mutant P. protegens CHA77, which did not produce HCN. Mycorrhizal and nonmycorrhizal Sorghum grown without CHA0 or CHA77 served as the control. While metabolically active AMF was not detected in mycorrhizal plants grown with HCN[+] CHA0, the percentage of root colonization of metabolically active AMF in plants grown with HCN[-] CHA77 was lower than in the control. Root phosphorus was highest in mycorrhizal plants grown with HCN[+] CHA0, but root Fe was higher in plants grown with the bacterial strains. Our results indicate that HCN-producing P. protegens can affect the viability of intraradical AMF.}, }
@article {pmid31640813, year = {2019}, author = {Chen, S and Waghmode, TR and Sun, R and Kuramae, EE and Hu, C and Liu, B}, title = {Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {136}, pmid = {31640813}, issn = {2049-2618}, mesh = {Agriculture/*methods ; Bacteria/classification/growth &amp; development ; Crops, Agricultural/microbiology ; Fertilizers/*microbiology ; Fungi/classification/growth &amp; development ; Microbiota/*physiology ; Mycobiome/physiology ; Plant Development/physiology ; Plant Roots/*microbiology ; *Rhizosphere ; Soil/chemistry ; Soil Microbiology ; *Triticum/metabolism/microbiology ; }, abstract = {BACKGROUND: Plant roots assemble microbial communities both inside the roots and in the rhizosphere, and these root-associated microbiomes play pivotal roles in plant nutrition and productivity. Although it is known that increased synthetic fertilizer input in Chinese farmlands over the past 50 years has resulted in not only increased yields but also environmental problems, we lack a comprehensive understanding of how crops under elevated nutrient input shape root-associated microbial communities, especially through adjusting the quantities and compositions of root metabolites and exudates.<br><br>METHODS: The compositions of bacterial and fungal communities from the roots and rhizosphere of wheat (Triticum aestivum L.) under four levels of long-term&#xa0;inorganic nitrogen (N) fertilization were characterized at the tillering, jointing and ripening stages. The root-released organic carbon (ROC), organic acids in the root exudates and soil organic carbon (SOC) and soil active carbon (SAC) in the rhizosphere were quantified.<br><br>RESULTS: ROC levels varied dramatically across wheat&#xa0;growth stages and correlated&#xa0;more with the bacterial community than with the fungal community. Rhizosphere SOC and SAC levels were elevated by long-term N fertilization but varied only slightly across growth stages. Variation in the microbial community structure across plant growth stages showed a decreasing trend with N fertilization level in the rhizosphere. In addition, more bacterial and fungal genera were significantly correlated in the jointing and ripening stages than in the tillering stage in the root samples. A number of bacterial genera that shifted in response to N fertilization, including Arthrobacter, Bacillus and Devosia, correlated&#xa0;significantly with acetic acid, oxalic acid, succinic acid and tartaric acid levels.<br><br>CONCLUSIONS: Our results indicate that both plant growth status and N input drive changes in the microbial community structure in the root zone of wheat. Plant growth stage&#xa0;demostrated a stronger&#xa0;influence on bacterial than on fungal community composition. A number of bacterial genera that have been described as plant growth-promoting rhizobacteria (PGPR) responded&#xa0;positively to N fertilization, and their abundance correlated&#xa0;significantly with the organic acid level, suggesting that the secretion of organic acids may be a strategy developed by plants to recruit beneficial microbes in the root zone to cope with high N input. These results provide novel insight into the associations among increased N input, altered carbon availability, and shifts in microbial communities in the plant roots and rhizosphere of intensive agricultural ecosystems.}, }
@article {pmid31640783, year = {2019}, author = {Chen, W and Ren, K and Isabwe, A and Chen, H and Liu, M and Yang, J}, title = {Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {138}, pmid = {31640783}, issn = {2049-2618}, mesh = {*Biodiversity ; China ; Ecosystem ; Environmental Monitoring ; High-Throughput Nucleotide Sequencing/methods ; *Plankton/classification/microbiology ; Rivers/*microbiology ; *Seasons ; Stochastic Processes ; *Water Microbiology ; }, abstract = {BACKGROUND: The deep mechanisms (deterministic and/or stochastic processes) underlying community assembly are a central challenge in microbial ecology. However, the relative importance of these processes in shaping riverine microeukaryotic biogeography is still poorly understood. Here, we compared the spatiotemporal and biogeographical patterns of microeukaryotic community using high-throughput sequencing of 18S rRNA gene and multivariate statistical analyses from a subtropical river during wet and dry seasons.<br><br>RESULTS: Our results provide the first description of biogeographical patterns of microeukaryotic communities in the Tingjiang River, the largest river in the west of Fujian province, southeastern China. The results showed that microeukaryotes from both wet and dry seasons exhibited contrasting community compositions, which might be owing to planktonic microeukaryotes having seasonal succession patterns. Further, all components of the microeukaryotic communities (including total, dominant, always rare, and conditionally rare taxa) exhibited a significant distance-decay pattern in both seasons, and these communities had a stronger distance-decay relationship during the dry season, especially for the conditionally rare taxa. Although several variables had a significant influence on the microeukaryotic communities, the environmental and spatial factors showed minor roles in shaping the communities. Importantly, these microeukaryotic communities were strongly driven by stochastic processes, with 89.9%, 88.5%, and 89.6% of the community variation explained by neutral community model during wet, dry, and both seasons, respectively. The neutral community model also explained a large fraction of the community variation across different taxonomic groups and levels. Additionally, the microeukaryotic taxa, which were above and below the neutral prediction, were ecologically and taxonomically distinct groups, which might be interactively structured by deterministic and stochastic processes.<br><br>CONCLUSIONS: This study demonstrated that stochastic processes are sufficient in shaping substantial variation in river microeukaryotic metacommunity across different hydrographic regimes, thereby providing a better understanding of spatiotemporal patterns, processes, and mechanisms of microeukaryotic community in waters.}, }
@article {pmid31640497, year = {2019}, author = {Brunner, JD and Chia, N}, title = {Metabolite-mediated modelling of microbial community dynamics captures emergent behaviour more effectively than species-species modelling.}, journal = {Journal of the Royal Society, Interface}, volume = {16}, number = {159}, pages = {20190423}, pmid = {31640497}, issn = {1742-5662}, support = {R01 CA179243/CA/NCI NIH HHS/United States ; }, mesh = {Gastrointestinal Microbiome/*physiology ; *Models, Biological ; Species Specificity ; }, abstract = {Personalized models of the gut microbiome are valuable for disease prevention and treatment. For this, one requires a mathematical model that predicts microbial community composition and the emergent behaviour of microbial communities. We seek a modelling strategy that can capture emergent behaviour when built from sets of universal individual interactions. Our investigation reveals that species-metabolite interaction (SMI) modelling is better able to capture emergent behaviour in community composition dynamics than direct species-species modelling. Using publicly available data, we examine the ability of species-species models and species-metabolite models to predict trio growth experiments from the outcomes of pair growth experiments. We compare quadratic species-species interaction models and quadratic SMI models and conclude that only species-metabolite models have the necessary complexity to explain a wide variety of interdependent growth outcomes. We also show that general species-species interaction models cannot match the patterns observed in community growth dynamics, whereas species-metabolite models can. We conclude that species-metabolite modelling will be important in the development of accurate, clinically useful models of microbial communities.}, }
@article {pmid31640295, year = {2019}, author = {Giuliani, C and Marzorati, M and Daghio, M and Franzetti, A and Innocenti, M and Van de Wiele, T and Mulinacci, N}, title = {Effects of Olive and Pomegranate By-Products on Human Microbiota: A Study Using the SHIME[®] in Vitro Simulator.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {20}, pages = {}, pmid = {31640295}, issn = {1420-3049}, support = {DD6107/2013//Tuscany Region/ ; CRF 2016.959//Foundation CR of Florence/ ; }, mesh = {Ammonium Compounds/metabolism ; Bifidobacterium/classification/drug effects/isolation &amp; purification ; DNA, Bacterial/analysis ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/*drug effects ; High-Throughput Nucleotide Sequencing ; Humans ; Lactobacillaceae/classification/drug effects/isolation &amp; purification ; Olea/*chemistry ; Phenols/*administration &amp; dosage/chemistry/pharmacology ; Phylogeny ; Polysaccharides/*administration &amp; dosage/chemistry/pharmacology ; Pomegranate/*chemistry ; }, abstract = {Two by-products containing phenols and polysaccharides, a "pâté" (OP) from the extra virgin olive oil milling process and a decoction of pomegranate mesocarp (PM), were investigated for their effects on human microbiota using the SHIME[®] system. The ability of these products to modulate the microbial community was studied simulating a daily intake for nine days. Microbial functionality, investigated in terms of short chain fatty acids (SCFA) and NH4[+], was stable during the treatment. A significant increase in Lactobacillaceae and Bifidobacteriaceae at nine days was induced by OP mainly in the proximal tract. Polyphenol metabolism indicated the formation of tyrosol from OP mainly in the distal tract, while urolithins C and A were produced from PM, identifying the human donor as a metabotype A. The results confirm the SHIME[®] system as a suitable in vitro tool to preliminarily investigate interactions between complex botanicals and human microbiota before undertaking more challenging human studies.}, }
@article {pmid31637799, year = {2020}, author = {Dedysh, SN and Henke, P and Ivanova, AA and Kulichevskaya, IS and Philippov, DA and Meier-Kolthoff, JP and Göker, M and Huang, S and Overmann, J}, title = {100-year-old enigma solved: identification, genomic characterization and biogeography of the yet uncultured Planctomyces bekefii.}, journal = {Environmental microbiology}, volume = {22}, number = {1}, pages = {198-211}, doi = {10.1111/1462-2920.14838}, pmid = {31637799}, issn = {1462-2920}, support = {16-04-00290//Russian Foundation for Basic Research/International ; }, mesh = {Genomics ; High-Throughput Nucleotide Sequencing ; In Situ Hybridization, Fluorescence ; Lakes/microbiology ; Metabolic Networks and Pathways/genetics ; Metagenome ; Phylogeny ; Phylogeography ; Planctomycetales/*classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The first representative of the phylum Planctomycetes, Planctomyces bekefii, was described nearly one century ago. This morphologically conspicuous freshwater bacterium is a rare example of as-yet-uncultivated prokaryotes with validly published names and unknown identity. We report the results of molecular identification of this elusive bacterium, which was detected in a eutrophic boreal lake in Northern Russia. By using high-performance cell sorting, P. bekefii-like cell rosettes were selectively enriched from lake water. The retrieved 16S rRNA gene sequence was nearly identical to those in dozens of metagenomes assembled from freshwater lakes during cyanobacterial blooms and was phylogenetically placed within a large group of environmental sequences originating from various freshwater habitats worldwide. In contrast, 16S rRNA gene sequence similarity to all currently described members of the order Planctomycetales was only 83%-92%. The metagenome assembled for P. bekefii reached 43% genome coverage and showed the potential for degradation of peptides, pectins, and sulfated polysaccharides. Tracing the seasonal dynamics of P. bekefii by Illumina paired-end sequencing of 16S rRNA gene fragments and by fluorescence in situ hybridization revealed that these bacteria only transiently surpass the detection limit, with a characteristic population peak of up to 10[4] cells ml[-1] following cyanobacterial blooms.}, }
@article {pmid31637492, year = {2019}, author = {Zhu, X and Wang, J and De Belie, N and Boon, N}, title = {Complementing urea hydrolysis and nitrate reduction for improved microbially induced calcium carbonate precipitation.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {21-22}, pages = {8825-8838}, doi = {10.1007/s00253-019-10128-2}, pmid = {31637492}, issn = {1432-0614}, support = {File No. 201706140108//Distinguished International Students Scholarship/ ; reference code: 01SC4918//Universiteit Gent/ ; }, mesh = {Calcium Carbonate/*metabolism ; Chemical Precipitation ; Construction Materials/microbiology ; Cupriavidus necator/enzymology/*metabolism ; Hydrolysis ; Nitrates/*metabolism ; Urea/*metabolism ; }, abstract = {Microbial-induced CaCO3 precipitation has been widely applied in bacterial-based self-healing concrete. However, the limited biogenetic CaCO3 production by bacteria after they were introduced into the incompatible concrete matrix is a major challenge of this technology. In the present study, the potential of combining two metabolic pathways, urea hydrolysis and nitrate reduction, simultaneously in one bacteria strain for improving the bacterial CaCO3 yield has been investigated. One bacterial strain, Ralstonia eutropha H16, which has the highest Ca[2+] tolerance and is capable of performing both urea hydrolysis and nitrate reduction in combined media was selected among three bacterial candidates based on the enzymatic examinations. Results showed that H16 does not need oxygen for urea hydrolysis and urease activity was determined primarily by cell concentration. However, the additional urea in the combined medium slowed down the nitrate reduction rate to 7 days until full NO3[-] decomposition. Moreover, the nitrate reduction of H16 was significantly restricted by an increased Ca[2+] ion concentration in the media. Nevertheless, the overall CaCO3 precipitation yield can be improved by 20 to 30% after optimization through the combination of two metabolic pathways. The highest total CaCO3 precipitation yield achieved in an orthogonal experiment was 14 g/L. It can be concluded that Ralstonia eutropha H16 is a suitable bacterium for simultaneous activation of urea hydrolysis and nitrate reduction for improving the CaCO3 precipitation and it can be studied later, on activation of multiple metabolic pathways in bacteria-based self-healing concrete.}, }
@article {pmid31637468, year = {2019}, author = {de Roos, B and Aura, AM and Bronze, M and Cassidy, A and Conesa, MG and Gibney, ER and Greyling, A and Kaput, J and Kerem, Z and Knežević, N and Kroon, P and Landberg, R and Manach, C and Milenkovic, D and Rodriguez-Mateos, A and Tomás-Barberán, FA and van de Wiele, T and Morand, C}, title = {Targeting the delivery of dietary plant bioactives to those who would benefit most: from science to practical applications.}, journal = {European journal of nutrition}, volume = {58}, number = {Suppl 2}, pages = {65-73}, pmid = {31637468}, issn = {1436-6215}, support = {FA 1403//European Cooperation in Science and Technology/ ; }, mesh = {Cardiovascular Diseases/*prevention &amp; control ; Diet, Vegetarian/*methods ; Health Promotion/*methods ; Humans ; Metabolic Diseases/*prevention &amp; control ; Phytochemicals/*administration &amp; dosage ; }, abstract = {BACKGROUND: A healthy diet and optimal lifestyle choices are amongst the most important actions for the prevention of cardiometabolic diseases. Despite this, it appears difficult to convince consumers to select more nutritious foods. Furthermore, the development and production of healthier foods do not always lead to economic profits for the agro-food sector. Most dietary recommendations for the general population represent a "one-size-fits-all approach" which does not necessarily ensure that everyone has adequate exposure to health-promoting constituents of foods. Indeed, we now know that individuals show a high variability in responses when exposed to specific nutrients, foods, or diets.<br><br>PURPOSE: This review aims to highlight our current understanding of inter-individual variability in response to dietary bioactives, based on the integration of findings of the COST Action POSITIVe. We also evaluate opportunities for translation of scientific knowledge on inter-individual variability in response to dietary bioactives, once it becomes available, into practical applications for stakeholders, such as the agro-food industry. The potential impact from such applications will form an important impetus for the food industry to develop and market new high quality and healthy foods for specific groups of consumers in the future. This may contribute to a decrease in the burden of diet-related chronic diseases.}, }
@article {pmid31635887, year = {2019}, author = {Čanković, M and Žučko, J and Radić, ID and Janeković, I and Petrić, I and Ciglenečki, I and Collins, G}, title = {Microbial diversity and long-term geochemical trends in the euxinic zone of a marine, meromictic lake.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {6}, pages = {126016}, doi = {10.1016/j.syapm.2019.126016}, pmid = {31635887}, issn = {1618-0984}, mesh = {Archaea/classification/genetics/isolation &amp; purification/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Biodiversity ; Climate Change ; Databases, Chemical ; Ireland ; Lakes/chemistry/*microbiology ; *Microbiota/genetics ; Oxygen/analysis/*metabolism ; RNA, Ribosomal, 16S/genetics ; Seasons ; Water Microbiology ; }, abstract = {Hypoxic and anoxic niches of meromictic lakes are important sites for studying the microbial ecology of conditions resembling ancient Earth. The expansion and increasing global distribution of such environments also means that information about them serves to understand future phenomena. In this study, a long-term chemical dataset (1996-2015) was explored together with seasonal (in 2015) information on the diversity and abundance of bacterial and archaeal communities residing in the chemocline, monimolimnion and surface sediment of the marine meromictic Rogoznica Lake. The results of quantitative PCR assays, and high-throughput sequencing, targeting 16S rRNA genes and transcripts, revealed a clear vertical structure of the microbial community with Gammaproteobacteria (Halochromatium) and cyanobacteria (Synechococcus spp.) dominating the chemocline, Deltaproteobacteria and Bacteroidetes dominating the monimolimnion, and significantly more abundant archaeal populations in the surface sediment, most of which affiliated to Nanoarchaeota. Seasonal changes in the community structure and abundance were not pronounced. Diversity in Rogoznica Lake was found to be high, presumably as a consequence of stable environmental conditions accompanied by high dissolved carbon and nutrient concentrations. Long-term data indicated that Rogoznica Lake exhibited climate changes that could alter its physico-chemical features and, consequently, induce structural and physiological changes within its microbial community.}, }
@article {pmid31633390, year = {2019}, author = {Baker, JL and He, X and Shi, W}, title = {Precision Reengineering of the Oral Microbiome for Caries Management.}, journal = {Advances in dental research}, volume = {30}, number = {2}, pages = {34-39}, pmid = {31633390}, issn = {1544-0737}, support = {F32 DE026947/DE/NIDCR NIH HHS/United States ; R01 DE020102/DE/NIDCR NIH HHS/United States ; R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 DE026186/DE/NIDCR NIH HHS/United States ; }, mesh = {Biofilms ; *Dental Caries ; *Dental Plaque ; Humans ; *Microbiota ; Streptococcus mutans ; }, abstract = {Technological advancements have revolutionized our understanding of the complexity and importance of the human microbiome. This progress has also emphasized the need for precision therapeutics, as it has underscored the dilemmas, such as dysbiosis and increasing antibiotic resistance, associated with current, broad-spectrum treatment modalities. Dental caries remains the most common chronic disease worldwide, accompanied by a tremendous financial and social burden, despite widespread and efficacious fluoride and hygienic regimens. Over the past several decades, various precision approaches to combat dental caries, including vaccines, probiotics, and antimicrobial compounds, have been pursued. Despite the distinct overall conceptual strengths of each approach, for various reasons, there are currently no approved precision antibiotic therapeutics to prevent dental caries. Specifically targeted antimicrobial peptides (STAMPs) are synthetic molecules that combine the antibiotic moiety of a traditional antimicrobial peptide with a targeting domain to provide specificity against a particular organism. Conjoining the killing domain from the antimicrobial, novispirin G10, and a targeting domain derived from the Streptococcus mutans pheromone, CSP, the STAMP C16G2 was designed to provide targeted killing of S. mutans, widely considered the keystone species in dental caries pathogenesis. C16G2 was able to selectively eliminate S. mutans from complex ecosystems while leaving closely related, yet health-associated, oral species unharmed. This remodeling of the dental plaque community is expected to have significant advantages compared to conventional broad-spectrum mouthwashes, as the intact, surviving community is apt to prevent reinfection by pathogens. Following successful phase I clinical trials that evaluated the safety and basic microbiology of C16G2 treatments, the phase II trials of several C16G2 formulations are currently in progress. C16G2 represents an exciting advance in precision therapeutics, and the STAMP platform provides vast opportunities for both the development of additional therapeutics and the overall study of microbial ecology.}, }
@article {pmid31633060, year = {2019}, author = {Krych, &#x141; and Castro-Mejía, JL and Forero-Junco, LM and Moesby, DN and Mikkelsen, MB and Rasmussen, MA and Sykulski, M and Nielsen, DS}, title = {DNA enrichment and tagmentation method for species-level identification and strain-level differentiation using ON-rep-seq.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {369}, pmid = {31633060}, issn = {2399-3642}, mesh = {Bacillus cereus/genetics ; *DNA, Bacterial ; High-Throughput Nucleotide Sequencing/economics/*methods ; Listeria monocytogenes/genetics ; Microbiological Techniques/economics/*methods ; Salmonella enterica/genetics ; Sequence Analysis, DNA/economics/*methods ; Species Specificity ; Time Factors ; }, abstract = {Despite the massive developments within culture-independent methods for detection of microorganisms during the last decade, culture-based methods remain a cornerstone in microbiology. Yet, the problem of rapid, accurate and inexpensive identification of bacterial isolates down to species/strain level remains unresolved. We have developed a new method for bacterial DNA enrichment and tagmentation allowing fast (<24 h) and cost-effective species level identification and strain level differentiation using the MinION portable sequencing platform (ON-rep-seq). DNA library preparation for 96 isolates takes less than 5 h and ensures highly reproducible distribution of reads that can be used to generate strain level specific read length counts profiles (LCp). We have developed a pipeline that by correcting reads error within peaks of LCp generates a set of high quality (>99%) consensus reads. Whereas, the information from high quality reads is used to retrieve species level taxonomy, comparison of LCp allows for strain level differentiation.}, }
@article {pmid31632370, year = {2019}, author = {Mendes, LW and de Chaves, MG and Fonseca, MC and Mendes, R and Raaijmakers, JM and Tsai, SM}, title = {Resistance Breeding of Common Bean Shapes the Physiology of the Rhizosphere Microbiome.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2252}, pmid = {31632370}, issn = {1664-302X}, abstract = {The taxonomically diverse rhizosphere microbiome contributes to plant nutrition, growth and health, including protection against soil-borne pathogens. We previously showed that breeding for Fusarium-resistance in common bean changed the rhizosphere microbiome composition and functioning. Here, we assessed the impact of Fusarium-resistance breeding in common bean on microbiome physiology. Combined with metatranscriptome data, community-level physiological profiling by Biolog EcoPlate analyses revealed that the rhizosphere microbiome of the Fusarium-resistant accession was distinctly different from that of the Fusarium-susceptible accession, with higher consumption of amino acids and amines, higher metabolism of xylanase and sialidase, and higher expression of genes associated with nitrogen, phosphorus and iron metabolism. The resistome analysis indicates higher expression of soxR, which is involved in protecting bacteria against oxidative stress induced by a pathogen invasion. These results further support our hypothesis that breeding for resistance has unintentionally shaped the assembly and activity of the rhizobacterial community toward a higher abundance of specific rhizosphere competent bacterial taxa that can provide complementary protection against fungal root infections.}, }
@article {pmid31630686, year = {2019}, author = {Kavagutti, VS and Andrei, A&#x15e; and Mehrshad, M and Salcher, MM and Ghai, R}, title = {Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {135}, pmid = {31630686}, issn = {2049-2618}, mesh = {Actinobacteria/*virology ; Bacteriophages/genetics/*isolation &amp; purification ; Czech Republic ; Ecology ; Ecosystem ; Fresh Water/*microbiology ; Genome, Viral ; Metagenome/*genetics ; Metagenomics ; Phylogeny ; *Water Microbiology ; }, abstract = {The persistent inertia in the ability to culture environmentally abundant microbes from aquatic ecosystems represents an obstacle in disentangling the complex web of ecological interactions spun by a diverse assortment of participants (pro- and eukaryotes and their viruses). In aquatic microbial communities, the numerically most abundant actors, the viruses, remain the most elusive, and especially in freshwaters their identities and ecology remain unknown. Here, using ultra-deep metagenomic sequencing from pelagic freshwater habitats, we recovered complete genomes of > 2000 phages, including small "miniphages" and large "megaphages" infecting iconic freshwater prokaryotic lineages. For instance, abundant freshwater Actinobacteria support infection by a very broad size range of phages (13-200 Kb). We describe many phages encoding genes that likely afford protection to their host from reactive oxygen species (ROS) in the aquatic environment and in the oxidative burst in protist phagolysosomes (phage-mediated ROS defense). Spatiotemporal abundance analyses of phage genomes revealed evanescence as the primary dynamic in upper water layers, where they displayed short-lived existences. In contrast, persistence was characteristic for the deeper layers where many identical phage genomes were recovered repeatedly. Phage and host abundances corresponded closely, with distinct populations displaying preferential distributions in different seasons and depths, closely mimicking overall stratification and mixis.}, }
@article {pmid31624348, year = {2020}, author = {Gwak, JH and Jung, MY and Hong, H and Kim, JG and Quan, ZX and Reinfelder, JR and Spasov, E and Neufeld, JD and Wagner, M and Rhee, SK}, title = {Archaeal nitrification is constrained by copper complexation with organic matter in municipal wastewater treatment plants.}, journal = {The ISME journal}, volume = {14}, number = {2}, pages = {335-346}, pmid = {31624348}, issn = {1751-7370}, mesh = {Ammonia/metabolism ; Archaea/*growth &amp; development/metabolism ; Bacteria/growth &amp; development/metabolism ; *Copper ; *Nitrification ; Oxidation-Reduction ; Sewage/microbiology ; Wastewater/*microbiology ; Water Purification ; }, abstract = {Consistent with the observation that ammonia-oxidizing bacteria (AOB) outnumber ammonia-oxidizing archaea (AOA) in many eutrophic ecosystems globally, AOB typically dominate activated sludge aeration basins from municipal wastewater treatment plants (WWTPs). In this study, we demonstrate that the growth of AOA strains inoculated into sterile-filtered wastewater was inhibited significantly, in contrast to uninhibited growth of a reference AOB strain. In order to identify possible mechanisms underlying AOA-specific inhibition, we show that complex mixtures of organic compounds, such as yeast extract, were highly inhibitory to all AOA strains but not to the AOB strain. By testing individual organic compounds, we reveal strong inhibitory effects of organic compounds with high metal complexation potentials implying that the inhibitory mechanism for AOA can be explained by the reduced bioavailability of an essential metal. Our results further demonstrate that the inhibitory effect on AOA can be alleviated by copper supplementation, which we observed for pure AOA cultures in a defined medium and for AOA inoculated into nitrifying sludge. Our study offers a novel mechanistic explanation for the relatively low abundance of AOA in most WWTPs and provides a basis for modulating the composition of nitrifying communities in both engineered systems and naturally occurring environments.}, }
@article {pmid31624166, year = {2019}, author = {Schultz, J and Kallies, R and Nunes da Rocha, U and Rosado, AS}, title = {Draft Genome Sequence of Geobacillus sp. Strain LEMMJ02, a Thermophile Isolated from Deception Island, an Active Volcano in Antarctica.}, journal = {Microbiology resource announcements}, volume = {8}, number = {42}, pages = {}, pmid = {31624166}, issn = {2576-098X}, abstract = {The thermophilic Geobacillus sp. strain LEMMJ02 was isolated from Fumarole Bay sediment on Deception Island, an active Antarctic volcano. Here, we report the draft genome of LEMMJ02, which consists of 3,160,938 bp with 52.8% GC content and 3,523 protein-coding genes.}, }
@article {pmid31623889, year = {2019}, author = {Christiaens, MER and De Paepe, J and Ilgrande, C and De Vrieze, J and Barys, J and Teirlinck, P and Meerbergen, K and Lievens, B and Boon, N and Clauwaert, P and Vlaeminck, SE}, title = {Urine nitrification with a synthetic microbial community.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {6}, pages = {126021}, doi = {10.1016/j.syapm.2019.126021}, pmid = {31623889}, issn = {1618-0984}, mesh = {Ammonia/metabolism ; Bioreactors/*microbiology ; Comamonadaceae/metabolism ; Delftia acidovorans/metabolism ; *Microbiota ; *Nitrification ; Nitrites/metabolism ; Nitrobacter/metabolism ; Nitrosomonas europaea/metabolism ; Pseudomonas fluorescens/metabolism ; Urea/metabolism ; Urine/*chemistry ; Waste Disposal, Fluid/*methods ; }, abstract = {During long-term extra-terrestrial missions, food is limited and waste is generated. By recycling valuable nutrients from this waste via regenerative life support systems, food can be produced in space. Astronauts' urine can, for instance, be nitrified by micro-organisms into a liquid nitrate fertilizer for plant growth in space. Due to stringent conditions in space, microbial communities need to be be defined (gnotobiotic); therefore, synthetic rather than mixed microbial communities are preferred. For urine nitrification, synthetic communities face challenges, such as from salinity, ureolysis, and organics. In this study, a synthetic microbial community containing an AOB (Nitrosomonas europaea), NOB (Nitrobacter winogradskyi), and three ureolytic heterotrophs (Pseudomonas fluorescens, Acidovorax delafieldii, and Delftia acidovorans) was compiled and evaluated for these challenges. In reactor 1, salt adaptation of the ammonium-fed AOB and NOB co-culture was possible up to 45mScm[-1], which resembled undiluted nitrified urine, while maintaining a 44±10mgNH4[+]-NL[-1]d[-1] removal rate. In reactor 2, the nitrifiers and ureolytic heterotrophs were fed with urine and achieved a 15±6mg NO3[-]-NL[-1]d[-1] production rate for 1% and 10% synthetic and fresh real urine, respectively. Batch activity tests with this community using fresh real urine even reached 29±3mgNL[-1]d[-1]. Organics removal in the reactor (69±15%) should be optimized to generate a nitrate fertilizer for future space applications.}, }
@article {pmid31623169, year = {2019}, author = {García-Mantrana, I and Calatayud, M and Romo-Vaquero, M and Espín, JC and Selma, MV and Collado, MC}, title = {Urolithin Metabotypes Can Determine the Modulation of Gut Microbiota in Healthy Individuals by Tracking Walnuts Consumption over Three Days.}, journal = {Nutrients}, volume = {11}, number = {10}, pages = {}, pmid = {31623169}, issn = {2072-6643}, support = {RTI2018-097982-B-I00//Spanish Ministry of Science, Innovation and Universities (MICINN)/ ; ERC starting grant, n&#xb0; 639226/ERC_/European Research Council/International ; }, mesh = {Adult ; Bacteria/classification/genetics/*metabolism ; Biomarkers/urine ; Coumarins/*urine ; Fatty Acids/*metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Hydrolyzable Tannins/*metabolism ; Juglans/*metabolism ; Male ; Middle Aged ; Nuts/*metabolism ; Time Factors ; }, abstract = {Walnuts are rich in polyphenols ellagitannins, modulate gut microbiota (GM), and exert health benefits after long-term consumption. The metabolism of ellagitannins to urolithins via GM depends on urolithin metabotypes (UM-A, -B, or -0), which have been reported to predict host responsiveness to a polyphenol-rich intervention. This study aims to assess whether UMs were associated with differential GM modulation after short-term walnut consumption. In this study, 27 healthy individuals consumed 33 g of peeled raw walnuts over three days. GM profiling was determined using 16S rRNA illumina sequencing and specific real-time quantitative polymerase chain reactions (qPCRs), as well as microbial activity using short-chain fatty acids analysis in stool samples. UMs stratification of volunteers was assessed using ultra performance liquid chromatography-electro spray ionization-quadrupole time of flight-mass spectrometry (UPLC-ESI-QTOF-MS) analysis of urolithins in urine samples. The gut microbiota associated with UM-B was more sensitive to the walnut intervention. Blautia, Bifidobacterium, and members of the Coriobacteriaceae family, including Gordonibacter, increased exclusively in UM-B subjects, while some members of the Lachnospiraceae family decreased in UM-A individuals. Coprococcus and Collinsella increased in both UMs and higher acetate and propionate production resulted after walnuts intake. Our results show that walnuts consumption after only three days modulates GM in a urolithin metabotype-depending manner and increases the production of short-chain fatty acids (SCFA).}, }
@article {pmid31622236, year = {2020}, author = {Cho, GY and Whang, KS}, title = {Aliifodinibius saliphilus sp. nov., a moderately halophilic bacterium isolated from sediment of a crystallizing pond of a saltern.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {70}, number = {1}, pages = {358-363}, doi = {10.1099/ijsem.0.003765}, pmid = {31622236}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Bacteroides/*classification/isolation &amp; purification ; Base Composition ; Chlorobi/*classification/isolation &amp; purification ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Phospholipids/chemistry ; *Phylogeny ; Ponds/*microbiology ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Salinity ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry ; Water Microbiology ; }, abstract = {Two Gram-stain-negative, moderately halophilic bacteria, designated strains ECH52[T] and KHM46, were isolated from the sediment of a grey saltern located in Sinui island at Shinan, Korea. The isolates were aerobic, non-motile, short rods and grew at 15-45 °C (optimum, 37 °C), at pH 6.0-10.0 (optimum, pH 8.0) and with 3-25 % (w/v) NaCl (optimum, 10 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains ECH52[T] and KHM46 belonged to the genus Aliifodinibius in the family Balneolaceae with sequence similarities of 94.3-98.6 % and showed the highest sequence similarity to Aliifodinibius halophilus 2W32[T] (98.6 %), A. sediminis YIM J21[T] (94.7%), A. salicampi KHM44[T] (94.6 %) and A. roseus YIM D15[T] (94.3 %). The DNA G+C content of the genomic DNA of strain ECH52[T] was 40.8 mol%. The predominant isoprenoid quinone was menaquinone-7 (MK-7) and the major cellular fatty acids were iso-C17 : 1ω9c, iso-C15 : 0, and C16 : 1ω7c and/or iso-C15 : 0 2-OH. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified glycolipids and four unidentified lipids. Based on the phylogenetic, phenotypic and chemotaxonomic data, strains ECH52[T] and KHM46 are considered to represent a novel species of the genus Aliifodinibius , for which the name Aliifodinibius saliphilus sp. nov. is proposed. The type strain is ECH52[T] (=KACC 19126[T]=NBRC 112664[T]).}, }
@article {pmid31615877, year = {2019}, author = {Deng, J and Auchtung, JM and Konstantinidis, KT and Brettar, I and Höfle, MG and Tiedje, JM}, title = {Genomic Variations Underlying Speciation and Niche Specialization of Shewanella baltica.}, journal = {mSystems}, volume = {4}, number = {5}, pages = {}, pmid = {31615877}, issn = {2379-5077}, abstract = {Shewanella baltica was the dominant culturable nitrate-reducing bacterium in the eutrophic and strongly stratified Baltic Sea in the 1980s, where it primarily inhabited the oxic-anoxic transition zone. The genomic structures of 46 of these isolates were investigated through comparative genomic hybridization (CGH), which revealed a gradient of genomic similarity, ranging from 65% to as high as 99%. The core genome of the S. baltica species was enriched in anaerobic respiration-associated genes. Auxiliary genes, most of which locate within a few genomic islands (GIs), were nonuniformly distributed among the isolates. Specifically, hypothetical and mobile genetic element (MGE)-associated genes dominated intraclade gene content differences, whereas gain/loss of functional genes drove gene content differences among less related strains. Among the major S. baltica clades, gene signatures related to specific redox-driven and spatial niches within the water column were identified. For instance, genes involved in anaerobic respiration of sulfur compounds may provide key adaptive advantages for clade A strains in anoxic waters where sulfur-containing electron acceptors are present. Genes involved in cell motility, in particular, a secondary flagellar biosynthesis system, may be associated with the free-living lifestyle by clade E strains. Collectively, this study revealed characteristics of genome variations present in the water column and active speciation of S. baltica strains, driven by niche partitioning and horizontal gene transfer (HGT).IMPORTANCE Speciation in nature is a fundamental process driving the formation of the vast microbial diversity on Earth. In the central Baltic Sea, the long-term stratification of water led to formation of a large-scale vertical redoxcline that provided a gradient of environmental niches with respect to the availability of electron acceptors and donors. The region was home to Shewanella baltica populations, which composed the dominant culturable nitrate-reducing bacteria, particularly in the oxic-anoxic transition zone. Using the collection of S. baltica isolates as a model system, genomic variations showed contrasting gene-sharing patterns within versus among S. baltica clades and revealed genomic signatures of S. baltica clades related to redox niche specialization as well as particle association. This study provides important insights into genomic mechanisms underlying bacterial speciation within this unique natural redoxcline.}, }
@article {pmid31613739, year = {2020}, author = {Dumolin, C and Peeters, C and Ehsani, E and Tahon, G and De Canck, E and Cnockaert, M and Boon, N and Vandamme, P}, title = {Achromobacter veterisilvae sp. nov., from a mixed hydrogen-oxidizing bacteria enrichment reactor for microbial protein production.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {70}, number = {1}, pages = {530-536}, doi = {10.1099/ijsem.0.003786}, pmid = {31613739}, issn = {1466-5034}, mesh = {Achromobacter/*classification/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; Belgium ; Bioreactors/*microbiology ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Forests ; Hydrogen ; Multilocus Sequence Typing ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Strain LMG 30378[T] was isolated from a hydrogen-oxidizing bacteria enrichment reactor inoculated with forest soil. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Achromobacter. Multilocus sequence analysis combined with sequence analysis of a 765 bp nrd A gene fragment both showed Achromobacter agilis LMG 3411[T] and Achromobacter denitrificans LMG 1231[T] to be the closest-related neighbours to strain LMG 30378[T]. Genome sequence analysis revealed a draft genome of 6.81 Mb with a G+C content of 67.2 mol%. In silico DNA-DNA hybridization with A. denitrificans LMG 1231[T] and A. agilis LMG 3411[T] showed 42.7 and 42.5% similarity, respectively, confirming that strain LMG 30378[T] represented a novel Achromobacter species. Phenotypic and metabolic characterization revealed acid phosphatase activity and the absence of phosphoamidase activity as distinctive features. The draft genome composes all necessary metabolic components to fix carbon dioxide and to oxidize molecular hydrogen, suggesting that strain LMG 30378[T] is a key organism in the enrichment reactor. Together, these data demonstrate that strain LMG 30378[T] represents a novel species of the genus Achromobacter, for which the name Achromobacter veterisilvae sp. nov. is proposed. The type strain is LMG 30378[T] (=CCUG 71558[T]).}, }
@article {pmid31612608, year = {2019}, author = {Seto, M and Iwasa, Y}, title = {The fitness of chemotrophs increases when their catabolic by-products are consumed by other species.}, journal = {Ecology letters}, volume = {22}, number = {12}, pages = {1994-2005}, pmid = {31612608}, issn = {1461-0248}, support = {19K06853//Japan Society for the Promotion of Science Grant-in-Aid for Scientific Research (C)/ ; }, mesh = {Biomass ; *Ecology ; *Ecosystem ; Symbiosis ; }, abstract = {Chemotrophic microorganisms synthesise biomass by utilising energy obtained from a set of chemical reactions that convert resources to by-products, forming catabolic interactions. The amount of energy obtained per catabolic reaction decreases with the abundance of the by-product named as the 'abundant resource premium'. Consider two species, Species 1 and 2, Species 1 obtains energy from a reaction that converts resource A to by-product B. Species 2 then utilises B as its resource, extracting energy from a reaction that converts B to C. Thus, the presence of Species 2 reduces the abundance of B, which improves the fitness of Species 1 by increasing the energy acquisition per reaction of A to B. We discuss the population dynamic implication of this effect and its importance in expanding a realised niche, boosting material flow through the ecosystem and providing mutualistic interactions among species linked by the material flow. Introducing thermodynamics into population ecology could offer us fundamental ecological insights into understanding the ecology of chemotrophic microorganisms dominating the subsurface realm.}, }
@article {pmid31612601, year = {2019}, author = {Simonsen, AK and Barrett, LG and Thrall, PH and Prober, SM}, title = {Novel model-based clustering reveals ecologically differentiated bacterial genomes across a large climate gradient.}, journal = {Ecology letters}, volume = {22}, number = {12}, pages = {2077-2086}, doi = {10.1111/ele.13389}, pmid = {31612601}, issn = {1461-0248}, support = {//OCE Postdoctoral Fellowship,&#xa0;Australian Research Council/ ; }, mesh = {*Climate ; Ecotype ; *Genome, Bacterial ; Phylogeny ; Soil Microbiology ; }, abstract = {A pervasive challenge in microbial ecology is understanding the genetic level where ecological units can be differentiated. Ecological differentiation often occurs at fine genomic levels, yet it is unclear how to utilise ecological information to define ecotypes given the breadth of environmental variation among microbial taxa. Here, we present an analytical framework that infers clusters along genome-based microbial phylogenies according to shared environmental responses. The advantage of our approach is the ability to identify genomic clusters that best fit complex environmental information whilst characterising cluster niches through model predictions. We apply our method to determine climate-associated ecotypes in populations of nitrogen-fixing symbionts using whole genomes, explicitly sampled to detect climate differentiation across a heterogeneous landscape. Although soil and plant host characteristics strongly influence distribution patterns of inferred ecotypes, our flexible statistical method enabled us to identify climate-associated genomic clusters using environmental data, providing solid support for ecological specialisation in soil symbionts.}, }
@article {pmid31612432, year = {2020}, author = {Rattes de Almeida Couto, C and Catharine de Assis Leite, D and Jurelevicius, D and van Elsas, JD and Seldin, L}, title = {Chemical and biological dispersants differently affect the bacterial communities of uncontaminated and oil-contaminated marine water.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {51}, number = {2}, pages = {691-700}, pmid = {31612432}, issn = {1678-4405}, support = {01//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; -//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; }, mesh = {Bacteria/classification/metabolism ; Biodegradation, Environmental ; Brazil ; Metagenome ; *Microbiota ; Petroleum/metabolism ; Petroleum Pollution ; Seawater/analysis/*microbiology ; Surface-Active Agents/classification/*metabolism ; *Water Microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The use of dispersants in marine environments is a common practice worldwide for oil spill remediation. While the effects of chemical dispersants have been extensively studied, those of biosurfactants, mainly surfactin that is considered one of the most effective surfactants produced by bacteria, have been less considered. We constructed microcosms containing marine water collected from Grumari beach (W_GB, Brazil) and from Schiermonnikoog beach (W_SI, The Netherlands) with the addition of oil (WO), Ultrasperse II plus oil (WOS), surfactin plus oil (WOB), and both dispersants (WS or WB) individually. In these treatments, the composition of bacterial communities and their predictive biodegradation potential were determined over time. High-throughput sequencing of the rrs gene encoding bacterial 16S rRNA revealed that Bacteroidetes (Flavobacteria class) and Proteobacteria (mainly Gammaproteobacteria and Alphaproteobacteria classes) were the most abundant phyla found among the W_GB and W_SI microbiomes, and the relative abundance of the bacterial types in the different microcosms varied based on the treatment applied. Non-metrical multidimensional scaling (NMDS) revealed a clear clustering based on the addition of oil and on the dispersant type added to the GB or SI microcosms, i.e., WB and WOB were separated from WS and WOS in both marine ecosystems studied. The potential presence of diverse enzymes involved in oil degradation was indicated by predictive bacterial metagenome reconstruction. The abundance of predicted genes for degradation of petroleum hydrocarbons increased more in surfactin-treated microcosms than those treated with Ultrasperse II, mainly in the marine water samples from Grumari beach.}, }
@article {pmid31612324, year = {2020}, author = {Norte, AC and Lopes de Carvalho, I and Núncio, MS and Araújo, PM and Matthysen, E and Albino Ramos, J and Sprong, H and Heylen, D}, title = {Getting under the birds' skin: tissue tropism of Borrelia burgdorferi s.l. in naturally and experimentally infected avian hosts.}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {756-769}, pmid = {31612324}, issn = {1432-184X}, support = {MARE - UID/MAR/04292/2013//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BPD/108197/2015//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; na//Portuguese National Institute of Health Doutor Ricardo Jorge/ ; Marie 544 Sklodowska-Curie Actions, Individual Global Fellowship, project n&#xb0; 545 799609//European Union - Horizon2020/ ; G0.049.10//Fund for Scientific Research - Flanders/ ; na//Bill and Melinda Gates Foundation/ ; }, mesh = {Animals ; Bird Diseases/*microbiology ; Borrelia burgdorferi Group/*physiology ; Disease Reservoirs/microbiology/*veterinary ; Disease Vectors ; Female ; Lyme Disease/microbiology/*veterinary ; Male ; *Songbirds ; }, abstract = {Wild birds are frequently exposed to the zoonotic tick-borne bacteria Borrelia burgdorferi sensu lato (s.l.), and some bird species act as reservoirs for some Borrelia genospecies. Studying the tropism of Borrelia in the host, how it is sequestered in different organs, and whether it is maintained in circulation and/or in the host's skin is important to understand pathogenicity, infectivity to vector ticks and reservoir competency.We evaluated tissue dissemination of Borrelia in blackbirds (Turdus merula) and great tits (Parus major), naturally and experimentally infected with Borrelia genospecies from enzootic foci. We collected both minimally invasive biological samples (feathers, skin biopsies and blood) and skin, joint, brain and visceral tissues from necropsied birds. Infectiousness of the host was evaluated through xenodiagnoses and infection rates in fed and moulted ticks. Skin biopsies were the most reliable method for assessing avian hosts' Borrelia infectiousness, which was supported by the agreement of infection status results obtained from the analysis of chin and lore skin samples from necropsied birds and of their xenodiagnostic ticks, including a significant correlation between the estimated concentration of Borrelia genome copies in the skin and the Borrelia infection rate in the xenodiagnostic ticks. This confirms a dermatropism of Borrelia garinii, B. valaisiana and B. turdi in its avian hosts. However, time elapsed from exposure to Borrelia and interaction between host species and Borrelia genospecies may affect the reliability of skin biopsies. The blood was not useful to assess infectiousness of birds, even during the period of expected maximum spirochetaemia. From the tissues sampled (foot joint, liver, spleen, heart, kidney, gut and brain), Borrelia was detected only in the gut, which could be related with infection mode, genospecies competition, genospecies-specific seasonality and/or excretion processes.}, }
@article {pmid31611655, year = {2020}, author = {Jiao, S and Yang, Y and Xu, Y and Zhang, J and Lu, Y}, title = {Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China.}, journal = {The ISME journal}, volume = {14}, number = {1}, pages = {202-216}, pmid = {31611655}, issn = {1751-7370}, mesh = {*Agriculture ; Archaea/genetics/isolation &amp; purification ; Bacteria/genetics/isolation &amp; purification ; China ; Ecosystem ; Fungi/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Oryza ; *Soil Microbiology ; Zea mays ; }, abstract = {Revealing the linkages between community assembly and species coexistence, which is crucial for the understanding of ecosystem diversity and functioning, is a fundamental but rarely investigated subject in microbial ecology. Here we examined archaeal, bacterial, and fungal community assembly in adjacent pairs of maize (water-unsaturated) and rice (water-saturated) fields across different habitats and regions throughout Eastern China. The high-throughput sequencing dataset was analyzed by variation partitioning, null model, and neutral community model analyses. We demonstrated that microbial community assembly was governed more by species sorting than by dispersal limitation in maize fields, and to a lesser extent in rice fields. The relative importance of species sorting in maize soils was greater at low latitudes than at high latitudes, while rice soils exhibited an opposite trend. Microbial co-occurrence associations tended to be higher when communities were primarily driven by dispersal limitation relative to species sorting. There were greater community dissimilarities between maize and rice soils in low-latitude regions, which was consistent with the higher proportion of negative edges in the correlation networks. The results indicate that a balance between species sorting and dispersal limitation mediates species coexistence in soil microbiomes. This study enhances our understanding of contemporary coexistence theory in microbial ecosystems.}, }
@article {pmid31611646, year = {2019}, author = {Ansorge, R and Romano, S and Sayavedra, L and Porras, M&#xc1;G and Kupczok, A and Tegetmeyer, HE and Dubilier, N and Petersen, J}, title = {Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels.}, journal = {Nature microbiology}, volume = {4}, number = {12}, pages = {2487-2497}, pmid = {31611646}, issn = {2058-5276}, mesh = {Animals ; Bacteria/classification/*genetics ; Base Sequence ; Biodiversity ; Bivalvia/metabolism/*microbiology ; Ecosystem ; Genetic Heterogeneity ; Hydrogenase/genetics ; Hydrothermal Vents ; Metagenome ; Microbiota/genetics ; Mytilidae/metabolism/microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; *Symbiosis ; Transcriptome ; }, abstract = {Genetic diversity of closely related free-living microorganisms is widespread and underpins ecosystem functioning, but most evolutionary theories predict that it destabilizes intimate mutualisms. Accordingly, strain diversity is assumed to be highly restricted in intracellular bacteria associated with animals. Here, we sequenced metagenomes and metatranscriptomes of 18 Bathymodiolus mussel individuals from four species, covering their known distribution range at deep-sea hydrothermal vents in the Atlantic. We show that as many as 16 strains of intracellular, sulfur-oxidizing symbionts coexist in individual Bathymodiolus mussels. Co-occurring symbiont strains differed extensively in key functions, such as the use of energy and nutrient sources, electron acceptors and viral defence mechanisms. Most strain-specific genes were expressed, highlighting their potential to affect fitness. We show that fine-scale diversity is pervasive in Bathymodiolus sulfur-oxidizing symbionts, and hypothesize that it may be widespread in low-cost symbioses where the environment, rather than the host, feeds the symbionts.}, }
@article {pmid31608034, year = {2019}, author = {Cai, Y and Cao, Y and Tang, C}, title = {Evidence for the Primary Role of Phytoplankton on Nitrogen Cycle in a Subtropical Reservoir: Reflected by the Stable Isotope Ratios of Particulate Nitrogen and Total Dissolved Nitrogen.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2202}, pmid = {31608034}, issn = {1664-302X}, abstract = {Knowledge about the primary factor controlling stable isotope ratios of particulate nitrogen (δ[15]NPN) and total dissolved nitrogen (δ[15]NTDN) in a subtropical reservoir can improve the understanding of regional and global nitrogen cycles. Taking Lianhe Reservoir as a representative subtropical reservoir, we studied the spatial and temporal distributions of δ[15]NPN andδ[15]NTDN and their relationships with the surrounding physicochemical factors and phytoplankton. The results showed that variations in δ[15]NPN and δ[15]NTDN followed seasonal thermal cycles. The values of δ[15]NTDN were inversely proportional to those of δ[15]NPN. PCA showed that phytoplankton cell density and pH were the primary drivers of the variation of δ[15]NPN (45.2%). The primary factors influencing δ[15]NTDN were Chl a and phytoplankton cell density, which both indicated phytoplankton biomass. We also determined that the dominant species was Microcystis densa during the thermal stratification period and Staurodesmus aristiferus during the mixing period. Laboratory experiments showed that δ[15]NPN values in both M. densa (from 19.5 to 14.6‰) and S. aristiferus (from 19.4 to 16.0 ‰) media decreased significantly as the algal cells grew. Furthermore, the δ[15]NTDN values increased from 4.9 to 7.9‰ and from 4.7 to 6.9‰ in M. densa and S. aristiferus media, respectively, when the δ[15]NPN values decreased. These experimental results were consistent with field investigation results and indicated that variations in δ[15]NPN and δ[15]NTDN were mainly controlled by phytoplankton cell density, especially the cell density of the dominant species, in both the thermal stratification and mixing periods. The results also suggested that cell density, not phytoplankton species, was the key factor regulating the distribution of nitrogen stable isotopes. These results together indicated that phytoplankton cell density is the primary factor in the regulation of nitrogen stable isotope composition and that its influence is greater than that of other physical and chemical factors. This study provided detailed information supporting the primary role of phytoplankton in the nitrogen geochemical cycle and improved the understanding of biochemical processes in natural subtropical reservoirs.}, }
@article {pmid31605197, year = {2020}, author = {Hess, AL and Benítez-Páez, A and Blædel, T and Larsen, LH and Iglesias, JR and Madera, C and Sanz, Y and Larsen, TM and , }, title = {The effect of inulin and resistant maltodextrin on weight loss during energy restriction: a randomised, placebo-controlled, double-blinded intervention.}, journal = {European journal of nutrition}, volume = {59}, number = {6}, pages = {2507-2524}, pmid = {31605197}, issn = {1436-6215}, support = {613979//Seventh Framework Programme/ ; }, mesh = {Blood Pressure/drug effects ; *Caloric Restriction ; Double-Blind Method ; Energy Intake ; Female ; Gastrointestinal Microbiome/drug effects ; Glucose/metabolism ; Humans ; Inulin/*pharmacology ; Male ; Middle Aged ; Polysaccharides/*pharmacology ; Weight Loss/*drug effects ; }, abstract = {PURPOSE: The objective of this study was to investigate the additive effects of combining energy restriction with dietary fibres on change in body weight and gut microbiota composition.<br><br>METHODS: The study was a 12-week randomised, placebo-controlled, double-blinded, parallel intervention trial. A total of 116 overweight or obese participants were assigned randomly either to 10&#xa0;g inulin plus 10&#xa0;g resistant maltodextrin or to 20&#xa0;g of placebo supplementation through 400&#xa0;mL of milk a day, while on a -&#x2009;500&#xa0;kcal/day energy restricted diet.<br><br>RESULTS: Altogether, 86 participants completed the intervention. There were no significant differences in weight loss or body composition between the groups. The fibre supplement reduced systolic (5.35&#x2009;&#xb1;&#x2009;2.4&#xa0;mmHg, p&#x2009;=&#x2009;0.043) and diastolic (2.82&#x2009;&#xb1;&#x2009;1.3&#xa0;mmHg, p&#x2009;=&#x2009;0.047) blood pressure to a larger extent than placebo. Furthermore, a larger decrease in serum insulin was observed in the placebo group compared to the fibre group (-&#x2009;26.0&#x2009;&#xb1;&#x2009;9.2&#xa0;pmol/L, p&#x2009;=&#x2009;0.006). The intake of fibre induced changes in the composition of gut microbiota resulting in higher abundances of Parabacteroides and Bifidobacteria, compared to placebo. The effects on blood pressure and glucose metabolism were mainly observed in women, and could be attributed to a higher gut microbiota diversity after intervention. Finally, the fibre group experienced a higher degree of gastrointestinal symptoms, which attenuated over time.<br><br>CONCLUSIONS: Supplementation of inulin and resistant maltodextrin did not provide an additional weight loss during an energy-restricted diet, but reduced both systolic and diastolic blood pressure. Furthermore, the fibre supplement did stimulate the growth of potentially beneficial bacteria genera.<br><br>CLINICAL TRIAL REGISTRY: The study was registered at http://www.clinicaltrials.gov , NCT03135041.}, }
@article {pmid31600966, year = {2019}, author = {Lin, X and Gao, D and Lu, K and Li, X}, title = {Bacterial Community Shifts Driven by Nitrogen Pollution in River Sediments of a Highly Urbanized City.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {20}, pages = {}, pmid = {31600966}, issn = {1660-4601}, mesh = {Bacteria/*classification/*drug effects ; China ; Cities ; Geologic Sediments/microbiology ; Nitrogen/chemistry/*toxicity ; Rivers/*microbiology ; Urbanization ; Water Pollutants, Chemical/chemistry/*toxicity ; }, abstract = {Effects of nitrogen pollution on bacterial community shifts in river sediments remain barely understood. Here, we investigated the bacterial communities in sediments of urban and suburban rivers in a highly urbanized city, Shanghai. Sediment nitrate (NO3[-]) and ammonia (NH4[+]) were highly accumulated in urban river. Operation Taxonomic Units (OTUs), Abundance-based Coverage Estimators (ACEs) and Chao 1 estimator in urban rivers were slightly lower than those in suburban rivers, while Shannon and Simpson indices were higher in urban rivers than those in suburban rivers. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant bacterial phylum communities, accounting for 68.5-84.9% of all communities. In particular, the relative abundances of Firmicutes and Nitrospirae were significantly higher in suburban rivers than in urban rivers, while relative abundances of Bacteroidetes, Verrucomicrobia, and Spirochaetes were significantly lower in suburban rivers than in urban rivers. NH4[+] was significantly and negatively correlated with abundances of Firmicutes, Nitrospirae, and Actinobacteria. Importantly, the significant and negative effects of sediment NH4[+] on bacterial richness and diversity suggested that nitrogen pollution likely contribute to the decrease in the bacterial richness and diversity. The results highlight that nitrogen enrichment could drive the shifts of bacterial abundance and diversity in the urban river sediments where are strongly influenced by human activities under the rapid urbanization stress.}, }
@article {pmid31599931, year = {2019}, author = {Cavaco, MA and St Louis, VL and Engel, K and St Pierre, KA and Schiff, SL and Stibal, M and Neufeld, JD}, title = {Freshwater microbial community diversity in a rapidly changing High Arctic watershed.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {11}, pages = {}, doi = {10.1093/femsec/fiz161}, pmid = {31599931}, issn = {1574-6941}, mesh = {Arctic Regions ; Climate Change ; Ecosystem ; Fresh Water/*microbiology ; Lakes/microbiology ; *Microbiota ; Nunavut ; RNA, Ribosomal, 16S ; Rivers/microbiology ; Seasons ; Soil ; Soil Microbiology ; *Water Microbiology ; }, abstract = {Current models predict increases in High Arctic temperatures and precipitation that will have profound impacts on the Arctic hydrological cycle, including enhanced glacial melt and thawing of active layer soils. However, it remains uncertain how these changes will impact the structure of downstream resident freshwater microbial communities and ensuing microbially driven freshwater ecosystem services. Using the Lake Hazen watershed (Nunavut, Canada; 82°N, 71°W) as a sentinel system, we related microbial community composition (16S rRNA gene sequencing) to physicochemical parameters (e.g. dissolved oxygen and nutrients) over an annual hydrological cycle in three freshwater compartments within the watershed: (i) glacial rivers; (ii) active layer thaw-fed streams and waterbodies and (iii) Lake Hazen, into which (i) and (ii) drain. Microbial communities throughout these freshwater compartments were strongly interconnected, hydrologically, and often correlated with the presence of melt-sourced chemicals (e.g. dissolved inorganic carbon) as the melt season progressed. Within Lake Hazen itself, water column microbial communities were generally stable over spring and summer, despite fluctuating lake physicochemistry, indicating that these communities and the potential ecosystem services they provide therein may be resilient to environmental change. This work helps to establish a baseline understanding of how microbial communities and the ecosystem services they provide in Arctic watersheds might respond to future climate change.}, }
@article {pmid31598761, year = {2020}, author = {Brunel, C and Beifen, Y and Pouteau, R and Li, J and van Kleunen, M}, title = {Responses of Rhizospheric Microbial Communities of Native and Alien Plant Species to Cuscuta Parasitism.}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {617-630}, pmid = {31598761}, issn = {1432-184X}, support = {2016YFC1201100//Chinese National Key Research and Development Program/ ; 15-2//International Science and Technology Cooperation Programme/ ; 30800133//National Natural Science Foundation of China/ ; }, mesh = {Bacteria/genetics ; Cuscuta/*physiology ; DNA, Bacterial/analysis ; Introduced Species ; Magnoliopsida/*microbiology/parasitology ; *Microbiota ; *Rhizosphere ; Symbiosis ; }, abstract = {Parasitic plants have major impacts on host fitness. In the case of species of the holoparasitic Cuscuta genus, these impacts were shown to be particularly strong in some invasive alien plants, which has raised interest in the underlying mechanism. We hypothesized that Cuscuta parasitization may exert strong influence in shaping the diversity patterns in the host rhizosphere microbiome and that this may vary between native (coevolved) and alien (non-coevolved) plants. Here, we report on a field study exploring the effect of parasitization by Cuscuta australis on the rhizosphere microbiota (16S and ITS rDNA) of four plant species sharing and three plant species not sharing the parasite's native range. Despite a predominant role of the host species in shaping the rhizosphere microbiota, the role of host origin and of parasitization still appeared important in structuring microbial communities and their associated functions. Bacterial communities were more strongly influenced than fungi by the native range of the host plant, while fungi were slightly more affected than bacteria by parasitization. About 7% of bacterial phylotypes and 11% of fungal phylotypes were sensitive to Cuscuta parasitization. Parasitization also reduced the abundance of arbuscular mycorrhizal fungi by ca. 18% and of several genes related to plant growth promoting functions (e.g., nitrogen metabolism and quorum sensing). Both fungi and bacteria differentially responded to host parasitization depending on host origin, and the extent of these shifts suggests that they may have more dramatic consequences for alien than for native plants.}, }
@article {pmid31598755, year = {2020}, author = {Sodhi, KK and Kumar, M and Balan, B and Dhaulaniya, AS and Singh, DK}, title = {Isolation and characterization of amoxicillin-resistant bacteria and amoxicillin-induced alteration in its protein profiling and RNA yield.}, journal = {Archives of microbiology}, volume = {202}, number = {2}, pages = {225-232}, doi = {10.1007/s00203-019-01737-6}, pmid = {31598755}, issn = {1432-072X}, support = {(NASF/CA-6030/2017-18)//Indian Council of Agricultural Research/ ; }, mesh = {Amoxicillin/*metabolism/pharmacology ; Anti-Bacterial Agents/*metabolism/pharmacology ; Bacterial Proteins/genetics ; Biodegradation, Environmental ; Chromatography, Liquid ; DNA, Bacterial/genetics ; DNA-Directed RNA Polymerases/genetics/*metabolism ; Penicillin Resistance/genetics ; Phylogeny ; Plasmids/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil Microbiology ; Stenotrophomonas/*drug effects/genetics/*metabolism ; Tandem Mass Spectrometry ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Amoxicillin-resistant bacteria were isolated using selective enrichment procedure. The morphological, biochemical and molecular characterization based on 16S rRNA gene sequencing and phylogenetic analysis of the bacterial strain WA5 confirmed that the strain belongs to the genus Stenotrophomonas. The bacteria were named as Stenotrophomonas sp. strain WA5 (MK110499). Substantial growth was seen in M9 minimal media supplemented with 5 mg L[-1] of amoxicillin as a sole source of carbon and energy. RNA yield was also observed to be decreased in the presence of amoxicillin. Amoxicillin (5 mg L[-1])-induced alteration is seen on bacterial protein profile and unique polypeptide bands were seen to be induced in the presence of amoxicillin, the bands were subjected to trypsin digestion, and LC-MS/MS analysis showed that the bands belong to the family of DNA-dependent RNA polymerase subunit β (rpoC). Plasmid DNA isolation indicated the presence of antibiotic-resistant genes being harboured by the plasmid.}, }
@article {pmid31598633, year = {2020}, author = {Baruzzo, G and Patuzzi, I and Di Camillo, B}, title = {SPARSim single cell: a count data simulator for scRNA-seq data.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {5}, pages = {1468-1475}, doi = {10.1093/bioinformatics/btz752}, pmid = {31598633}, issn = {1367-4811}, mesh = {Gene Expression Profiling ; RNA-Seq ; Sequence Analysis, RNA ; *Single-Cell Analysis ; *Software ; }, abstract = {MOTIVATION: Single cell RNA-seq (scRNA-seq) count data show many differences compared with bulk RNA-seq count data, making the application of many RNA-seq pre-processing/analysis methods not straightforward or even inappropriate. For this reason, the development of new methods for handling scRNA-seq count data is currently one of the most active research fields in bioinformatics. To help the development of such new methods, the availability of simulated data could play a pivotal role. However, only few scRNA-seq count data simulators are available, often showing poor or not demonstrated similarity with real data.<br><br>RESULTS: In this article we present SPARSim, a scRNA-seq count data simulator based on a Gamma-Multivariate Hypergeometric model. We demonstrate that SPARSim allows to generate count data that resemble real data in terms of count intensity, variability and sparsity, performing comparably or better than one of the most used scRNA-seq simulator, Splat. In particular, SPARSim simulated count matrices well resemble the distribution of zeros across different expression intensities observed in real count data.<br><br>SPARSim R package is freely available at http://sysbiobig.dei.unipd.it/? q=SPARSim and at https://gitlab.com/sysbiobig/sparsim.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid31595680, year = {2019}, author = {Wepking, C and Badgley, B and Barrett, JE and Knowlton, KF and Lucas, JM and Minick, KJ and Ray, PP and Shawver, SE and Strickland, MS}, title = {Prolonged exposure to manure from livestock-administered antibiotics decreases ecosystem carbon-use efficiency and alters nitrogen cycling.}, journal = {Ecology letters}, volume = {22}, number = {12}, pages = {2067-2076}, doi = {10.1111/ele.13390}, pmid = {31595680}, issn = {1461-0248}, support = {1832888//NSF/ ; 2013-67019-21363//USDA-NIFA/ ; }, mesh = {Animals ; Anti-Bacterial Agents ; Carbon ; Cattle ; *Ecosystem ; Livestock ; *Manure ; Nitrogen ; Soil ; Soil Microbiology ; }, abstract = {Microbial communities drive soil ecosystem function but are also susceptible to environmental disturbances. We investigated whether exposure to manure sourced from cattle either administered or not administered antibiotics affected microbially mediated terrestrial ecosystem function. We quantified changes in microbial community composition via amplicon sequencing, and terrestrial elemental cycling via a stable isotope pulse-chase. Exposure to manure from antibiotic-treated cattle caused: (i) changes in microbial community structure; and (ii) alterations in elemental cycling throughout the terrestrial system. This exposure caused changes in fungal : bacterial ratios, as well as changes in bacterial community structure. Additionally, exposure to manure from cattle treated with pirlimycin resulted in an approximate two-fold increase in ecosystem respiration of recently fixed-carbon, and a greater proportion of recently added nitrogen in plant and soil pools compared to the control manure. Manure from antibiotic-treated cattle therefore affects terrestrial ecosystem function via the soil microbiome, causing decreased ecosystem carbon use efficiency, and altered nitrogen cycling.}, }
@article {pmid31595328, year = {2020}, author = {Li, F and Li, P and Hua, H and Hou, M and Wang, F}, title = {Diversity, Tissue Localization, and Infection Pattern of Bacterial Symbionts of the White-Backed Planthopper, Sogatella furcifera (Hemiptera: Delphacidae).}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {720-730}, pmid = {31595328}, issn = {1432-184X}, support = {2018YFD0200300//National Key R&amp;D Project of China/ ; 31371951//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bacteria/classification ; DNA, Bacterial/analysis ; Female ; Hemiptera/*microbiology ; In Situ Hybridization, Fluorescence ; Male ; Microbiota/*physiology ; RNA, Ribosomal, 16S/analysis ; Symbiosis ; }, abstract = {The white-backed planthopper (WBPH), Sogatella furcifera (Horváth), is a destructive pest of rice. Bacterial symbionts play an important role in insect hosts, especially hemipteran hosts. This study was designed to examine the bacterial symbionts of the WBPH using 16S rDNA high-throughput sequencing. A total of 63 and 177 operational taxonomic units (OTUs) were identified in females and males of three WBPH populations, respectively. These OTUs included bacteria of 75 genera from 11 phyla, where Wolbachia, Cardinium, and Asaia were the dominant genera, accounting for over 97.99% of all the symbiotic bacteria. Fluorescence in situ hybridization detected Wolbachia, Cardinium, and Asaia in the salivary glands, guts, testes, and eggs of the WBPH, indicating the potential for both horizontal and vertical transmission. Moreover, the infection pattern of the three dominant bacterial symbionts was detected in six WBPH populations. The frequencies of Wolbachia infection of females and Cardinium infection of both sexes were over 96.7%. Wolbachia infection of males ranged between 46.7 and 63.3%, which was significantly lower than that observed for females. Asaia infection of both sexes varied substantially among the populations. These results indicate that the complex host-symbiotic bacteria interaction is influenced by host sex and geographical origin and potentially by the transmission modes of the symbionts.}, }
@article {pmid31595008, year = {2019}, author = {Soffe, R and Bernach, M and Remus-Emsermann, MNP and Nock, V}, title = {Replicating Arabidopsis Model Leaf Surfaces for Phyllosphere Microbiology.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {14420}, pmid = {31595008}, issn = {2045-2322}, mesh = {Arabidopsis/*microbiology/ultrastructure ; Bacteria/pathogenicity/*ultrastructure ; Dimethylpolysiloxanes/chemistry ; Microscopy ; Plant Leaves/*microbiology/ultrastructure ; Surface Properties ; Waxes/chemistry ; }, abstract = {Artificial surfaces are commonly used in place of leaves in phyllosphere microbiology to study microbial behaviour on plant leaf surfaces. These surfaces enable a reductionist approach to be undertaken, to enable individual environmental factors influencing microorganisms to be studied. Commonly used artificial surfaces include nutrient agar, isolated leaf cuticles, and reconstituted leaf waxes. Recently, replica surfaces mimicking the complex topography of leaf surfaces for phyllosphere microbiology studies are appearing in literature. Replica leaf surfaces have been produced in agar, epoxy, polystyrene, and polydimethylsiloxane (PDMS). However, none of these protocols are suitable for replicating fragile leaves such as of the model plant Arabidopsis thaliana. This is of importance, as A. thaliana is a model system for molecular plant genetics, molecular plant biology, and microbial ecology. To overcome this limitation, we introduce a versatile replication protocol for replicating fragile leaf surfaces into PDMS. Here we demonstrate the capacity of our replication process using optical microscopy, atomic force microscopy (AFM), and contact angle measurements to compare living and PDMS replica A. thaliana leaf surfaces. To highlight the use of our replica leaf surfaces for phyllosphere microbiology, we visualise bacteria on the replica leaf surfaces in comparison to living leaf surfaces.}, }
@article {pmid31593911, year = {2020}, author = {Prévoteau, A and Carvajal-Arroyo, JM and Ganigué, R and Rabaey, K}, title = {Microbial electrosynthesis from CO2: forever a promise?.}, journal = {Current opinion in biotechnology}, volume = {62}, number = {}, pages = {48-57}, doi = {10.1016/j.copbio.2019.08.014}, pmid = {31593911}, issn = {1879-0429}, mesh = {*Carbon Dioxide ; Electrodes ; Fermentation ; }, abstract = {Microbial electrosynthesis (MES) is an electrochemical process used to drive microbial metabolism for bio-production, such as the reduction of CO2 into industrially relevant organic products as an alternative to current fossil-fuel-derived commodities. After a decade of research on MES from CO2, figures of merit have increased significantly but are plateauing yet far from those expected to allow competitiveness for synthesis of commodity chemicals. Here we discuss the substantial technological shortcomings still associated with MES and evoke possible ways to mitigate them. It appears particularly challenging to obtain both relevant production rates (driven by high current densities) and energy conversion efficiency (i.e. low cell voltage) in microbial-compatible electrolytes. More competitive processes could arise by decoupling effective abiotic electroreductions (e.g. CO2 to CO or ethanol; H2 evolution) with subsequent fermentation processes.}, }
@article {pmid31593527, year = {2020}, author = {Tabima, JF and Søndreli, KL and Keriö, S and Feau, N and Sakalidis, ML and Hamelin, RC and LeBoldus, JM}, title = {Population Genomic Analyses Reveal Connectivity via Human-Mediated Transport across Populus Plantations in North America and an Undescribed Subpopulation of Sphaerulina musiva.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {33}, number = {2}, pages = {189-199}, doi = {10.1094/MPMI-05-19-0131-R}, pmid = {31593527}, issn = {0894-0282}, mesh = {*Ascomycota/genetics ; Canada ; Genetic Variation ; Humans ; *Metagenomics ; North America ; Plant Diseases/microbiology ; *Populus/microbiology ; }, abstract = {Domestication of plant species has affected the evolutionary dynamics of plant pathogens in agriculture and forestry. A model system for studying the consequences of plant domestication on the evolution of an emergent plant disease is the fungal pathogen Sphaerulina musiva. This ascomycete causes leaf spot and stem canker disease of Populus spp. and their hybrids. A population genomics approach was used to determine the degree of population structure and evidence for selection on the North American population of S. musiva. In total, 122 samples of the fungus were genotyped identifying 120,016 single-nucleotide polymorphisms after quality filtering. In North America, S. musiva has low to moderate degrees of differentiation among locations. Three main genetic clusters were detected: southeastern United States, midwestern United States and Canada, and a new British Columbia cluster (BC2). Population genomics suggest that BC2 is a novel genetic cluster from central British Columbia, clearly differentiated from previously reported S. musiva from coastal British Columbia, and the product of a single migration event. Phenotypic measurements from greenhouse experiments indicate lower aggressiveness of BC2 on Populus trichocarpa. In summary, S. musiva has geographic structure across broad regions indicative of gene flow among clusters. The interconnectedness of the North American S. musiva populations across large geographic distances further supports the hypothesis of anthropogenic-facilitated transport of the pathogen.}, }
@article {pmid31591493, year = {2020}, author = {Ben Maamar, S and Hu, J and Hartmann, EM}, title = {Implications of indoor microbial ecology and evolution on antibiotic resistance.}, journal = {Journal of exposure science &amp; environmental epidemiology}, volume = {30}, number = {1}, pages = {1-15}, pmid = {31591493}, issn = {1559-064X}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics/*physiology ; Ecology ; Gene Transfer, Horizontal ; Humans ; }, abstract = {The indoor environment is an important source of microbial exposures for its human occupants. While we naturally want to favor positive health outcomes, built environment design and operation may counter-intuitively favor negative health outcomes, particularly with regard to antibiotic resistance. Indoor environments contain microbes from both human and non-human origins, providing a unique venue for microbial interactions, including horizontal gene transfer. Furthermore, stressors present in the built environment could favor the exchange of genetic material in general and the retention of antibiotic resistance genes in particular. Intrinsic and acquired antibiotic resistance both pose a potential threat to human health; these phenomena need to be considered and controlled separately. The presence of both environmental and human-associated microbes, along with their associated antibiotic resistance genes, in the face of stressors, including antimicrobial chemicals, creates a unique opportunity for the undesirable spread of antibiotic resistance. In this review, we summarize studies and findings related to various interactions between human-associated bacteria, environmental bacteria, and built environment conditions, and particularly their relation to antibiotic resistance, aiming to guide "healthy" building design.}, }
@article {pmid31590609, year = {2020}, author = {Diaz, PI and Valm, AM}, title = {Microbial Interactions in Oral Communities Mediate Emergent Biofilm Properties.}, journal = {Journal of dental research}, volume = {99}, number = {1}, pages = {18-25}, pmid = {31590609}, issn = {1544-0591}, support = {R03 DE028042/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria ; *Biofilms ; *Microbial Interactions ; *Microbiota ; Virulence ; }, abstract = {Oral microbial communities are extraordinarily complex in taxonomic composition and comprise interdependent biological systems. The bacteria, archaea, fungi, and viruses that thrive within these communities engage in extensive cell-cell interactions, which are both beneficial and antagonistic. Direct physical interactions among individual cells mediate large-scale architectural biofilm arrangements and provide spatial proximity for chemical communication and metabolic cooperation. In this review, we summarize recent work in identifying specific molecular components that mediate cell-cell interactions and describe metabolic interactions, such as cross-feeding and exchange of electron acceptors and small molecules, that modify the growth and virulence of individual species. We argue, however, that although pairwise interaction models have provided useful information, complex community-like systems are needed to study the properties of oral communities. The networks of multiple synergistic and antagonistic interactions within oral biofilms give rise to the emergent properties of persistence, stability, and long-range spatial structure, with these properties mediating the dysbiotic transitions from health to oral diseases. A better understanding of the fundamental properties of interspecies networks will lead to the development of effective strategies to manipulate oral communities.}, }
@article {pmid31589437, year = {2020}, author = {Syrpas, M and Bukauskaitė, J and Ramanauskienė, K and Karosienė, JR and Majienė, D and Bašinskienė, L and Venskutonis, PR}, title = {Ultrasound-Assisted Extraction and Assessment of Biological Activity of Phycobiliprotein-Rich Aqueous Extracts from Wild Cyanobacteria (Aphanizomenon flos-aquae).}, journal = {Journal of agricultural and food chemistry}, volume = {68}, number = {7}, pages = {1896-1909}, doi = {10.1021/acs.jafc.9b05483}, pmid = {31589437}, issn = {1520-5118}, mesh = {Antioxidants/chemistry/isolation &amp; purification/pharmacology ; Aphanizomenon/*chemistry/growth &amp; development ; Bacterial Proteins/chemistry/*isolation &amp; purification/*pharmacology ; Cell Line, Tumor ; Cell Survival/drug effects ; Humans ; Phycobiliproteins/chemistry/*isolation &amp; purification/*pharmacology ; Ultrasonics ; }, abstract = {Cyanobacteria are photosynthetic microorganisms that are considered as an important source of bioactive metabolites, among which phycobiliproteins (PBPs) are a class of water-soluble macromolecules of cyanobacteria with a wide range of applications. Massive proliferation of cyanobacteria can lead to excessive surface water blooms, of which removal, as a management measure, should be prioritized. In this study, the utilization of wild cyanobacteria biomass (Aphanizomenon flos-aquae) for extraction of phycobiliproteins is reported. Extraction of phycobiliproteins by conventional methods, such as homogenization, freeze-thaw cycles, and solid-liquid extraction, were optimized prior to ultrasound-assisted extraction. Standardization of ultrasonication for different parameters, such as ultrasonication amplitude (38, 114, and 190 μm) and ultrasonication time (1, 5.5, and 10 min), was carried out using a central composite design and response surface methodology for each of the primary techniques. A substantial increase on the individual and total phycobiliprotein yields was observed after ultrasonic treatment. The highest total PBP yield (115.37 mg/g of dry weight) was observed with samples treated with a homogenizer (30 min, 30 °C, and 1 cycle) combined with ultrasound treatment (8.7 min at 179 μm). Moreover, in vitro antioxidant capacity was observed for the obtained extracts in the Folin-Ciocalteu and ABTS[*] [+] assays. In addition, a cytotoxic effect against C6 glioma cells was observed for A. flos-aquae PBPs. Conclusively, wild cyanobacteria could be considered as an alternative feedstock for recovery of PBPs.}, }
@article {pmid31588957, year = {2020}, author = {Le, D and Nguyen, P and Nguyen, D and Dierckens, K and Boon, N and Lacoere, T and Kerckhof, FM and De Vrieze, J and Vadstein, O and Bossier, P}, title = {Gut Microbiota of Migrating Wild Rabbit Fish (Siganus guttatus) Larvae Have Low Spatial and Temporal Variability.}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {539-551}, pmid = {31588957}, issn = {1432-184X}, support = {ZIUS2015AP026//VLIR-IUC/ ; }, mesh = {Animal Migration ; Animals ; Bacteria/genetics ; *Gastrointestinal Microbiome ; Perciformes/*microbiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, RNA ; Vietnam ; }, abstract = {We investigated the gut microbiota of rabbit fish larvae at three locations in Vietnam (ThuanAn-northern, QuangNam-intermediate, BinhDinh-southern sampling site) over a three-year period. In the wild, the first food for rabbit fish larvae remains unknown, while the juveniles and adults are herbivores, forming schools near the coasts, lagoons, and river mouths, and feeding mainly on filamentous algae. This is the first study on the gut microbiota of the wild fish larvae and with a large number of individuals analyzed spatially and temporally. The Clostridiales order was the most predominant in the gut, and location-by-location alpha diversity showed significant differences in Chao-1, Hill number 1, and evenness. Analysis of beta diversity indicated that the location, not year, had an effect on the composition of the microbiota. In 2014, the gut microbiota of fish from QuangNam was different from that in BinhDinh; in 2015, the gut microbiota was different for all locations; and, in 2016, the gut microbiota in ThuanAn was different from that in the other locations. There was a time-dependent trend in the north-south axis for the gut microbiota, which is considered to be tentative awaiting larger datasets. We found limited variation in the gut microbiota geographically and in time and strong indications for a core microbiome. Five and fifteen OTUs were found in 100 and 99% of the individuals, respectively. This suggests that at this life stage the gut microbiota is under strong selection due to a combination of fish-microbe and microbe-microbe interactions.}, }
@article {pmid31587650, year = {2019}, author = {Sebastián, M and Gasol, JM}, title = {Visualization is crucial for understanding microbial processes in the ocean.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1786}, pages = {20190083}, pmid = {31587650}, issn = {1471-2970}, mesh = {Genomics ; Oceans and Seas ; Prokaryotic Cells/*physiology ; Seawater/*microbiology ; Single-Cell Analysis/*methods ; }, abstract = {Recent developments in community and single-cell genomic approaches have provided an unprecedented amount of information on the ecology of microbes in the aquatic environment. However, linkages between each specific microbe's identity and their in situ level of activity (be it growth, division or just metabolic activity) are much more scarce. The ultimate goal of marine microbial ecology is to understand how the environment determines the types of different microbes in nature, their function, morphology and cell-to-cell interactions and to do so we should gather three levels of information, the genomic (including identity), the functional (activity or growth), and the morphological, and for as many individual cells as possible. We present a brief overview of methodologies applied to address single-cell activity in marine prokaryotes, together with a discussion of the difficulties in identifying and categorizing activity and growth. We then provide and discuss some examples showing how visualization has been pivotal for challenging established paradigms and for understanding the role of microbes in the environment, unveiling processes and interactions that otherwise would have been overlooked. We conclude by stating that more effort should be directed towards integrating visualization in future approaches if we want to gain a comprehensive insight into how microbes contribute to the functioning of ecosystems. This article is part of a discussion meeting issue 'Single cell ecology'.}, }
@article {pmid31585384, year = {2019}, author = {Wang, D and Tooker, NB and Srinivasan, V and Li, G and Fernandez, LA and Schauer, P and Menniti, A and Maher, C and Bott, CB and Dombrowski, P and Barnard, JL and Onnis-Hayden, A and Gu, AZ}, title = {Side-stream enhanced biological phosphorus removal (S2EBPR) process improves system performance - A full-scale comparative study.}, journal = {Water research}, volume = {167}, number = {}, pages = {115109}, doi = {10.1016/j.watres.2019.115109}, pmid = {31585384}, issn = {1879-2448}, mesh = {Bioreactors ; *Phosphorus ; Polyphosphates ; *Rivers ; Sewage ; Wastewater ; }, abstract = {To address the common challenges in enhanced biological phosphorus removal (EBPR) related to stability and unfavorable influent carbon to phosphorus ratio, a side-stream EBPR (S2EBPR) process that involves a side-stream anaerobic biological sludge hydrolysis and fermentation reactor was proposed as an emerging alternative. In this study, a full-scale pilot testing was performed with side-by-side operation of a conventional anaerobic-anoxic-aerobic (A2O) process versus a S2EBPR process. A comparison of the performance, activity and microbial community between the two configurations was performed. The results demonstrated that, with the same influent wastewater characteristics, S2EBPR configuration showed improved P removal performance and stability than the conventional A2O configuration, especially when the mixers in the side-stream anaerobic reactor were operated intermittently. Mass balance analysis illustrated that both denitrification and EBPR were enhanced in S2EBPR configuration, where return activated sludge was diverted into the anaerobic zone to promote fermentation and enrichment of polyphosphate accumulating organisms (PAOs), and the influent was bypassed to the anoxic zone for enhancing denitrification. A relatively higher PAO activity and total PAO abundance were observed in S2EBPR than in A2O configuration, accompanied by a higher degree of dependence on glycolysis pathway than tricarboxylic acid cycle. No significant difference in the relative abundances of putative PAOs, including Ca. Accumulibacter and Tetrasphaera, were observed between the two configurations. However, higher microbial community diversity indices were observed in S2EBPR configuration than in conventional one. In addition, consistently lower relative abundance of known glycogen accumulating organisms (GAOs) was observed in S2EBPR system. Extended anaerobic retention time and conditions that generate continuous and more complex volatile fatty acids in the side-stream anaerobic reactor of S2EBPR process likely give more competitive advantage for PAOs over GAOs. PAOs exhibited sustained EBPR activity and delayed decay under extended anaerobic condition, likely due to their versatile metabolic pathways depending on the availability and utilization of multiple intracellular polymers. This study provided new insights into the effects of implementing side-stream EBPR configuration on microbial populations, EBPR activity profiles and resulted system performance.}, }
@article {pmid31584168, year = {2020}, author = {Browne, PD and Kot, W and Jørgensen, TS and Hansen, LH}, title = {The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2075}, number = {}, pages = {253-264}, doi = {10.1007/978-1-4939-9877-7_18}, pmid = {31584168}, issn = {1940-6029}, mesh = {Computational Biology/methods ; *DNA Transposable Elements ; DNA, Circular ; Databases, Genetic ; Escherichia coli/genetics ; Gene Library ; Gene Transfer, Horizontal ; *Metagenome ; *Metagenomics/methods ; Plasmids/*genetics ; Viruses/*genetics ; }, abstract = {Isolation, sequencing, and analysis of circular genetic elements bring new insights to mobile genetic elements related to microbial ecology. One method used to study circular plasmids, viruses, and other elements is called the mobilome method. The mobilome method presented here is an unamplified mobilome approach allowing fast isolation of circular DNA elements from a variety of samples followed by directly building unamplified Illumina-compatible sequencing libraries using enzymatic tagging and fragmentation. Several methods for bioinformatic analysis of mobilome data are also suggested.}, }
@article {pmid31582458, year = {2019}, author = {Schultz, J and Kallies, R and Nunes da Rocha, U and Rosado, AS}, title = {Draft Genome Sequence of Brevibacillus sp. Strain LEMMJ03, Isolated from an Antarctic Volcano.}, journal = {Microbiology resource announcements}, volume = {8}, number = {40}, pages = {}, pmid = {31582458}, issn = {2576-098X}, abstract = {Here, we announce the draft genome sequence of Brevibacillus sp. strain LEMMJ03, isolated from Whalers Bay sediment (Deception Island, Antarctica). In total, 4,500 coding sequences (CDS), among those 102 coding for tRNAs and 5 for noncoding RNAs (ncRNAs), were predicted from the 4.64-Mb genome. Predicted functions were for bacteriocin and degradation of aromatic compounds.}, }
@article {pmid31580006, year = {2020}, author = {Li, X and Garbeva, P and Liu, X and Klein Gunnewiek, PJA and Clocchiatti, A and Hundscheid, MPJ and Wang, X and de Boer, W}, title = {Volatile-mediated antagonism of soil bacterial communities against fungi.}, journal = {Environmental microbiology}, volume = {22}, number = {3}, pages = {1025-1035}, pmid = {31580006}, issn = {1462-2920}, support = {BK20190040//Excellent Youth Foundation of Jiangsu Province/International ; 41671306//National Natural Science Foundation of China/International ; 2017YFD0200604//National Key Research and Development Program of China/International ; }, mesh = {Agriculture ; Antibiosis/*physiology ; *Bacterial Physiological Phenomena ; Fungi/drug effects/*physiology ; Microbiota ; *Soil Microbiology ; }, abstract = {Competition is a major type of interaction between fungi and bacteria in soil and is also an important factor in suppression of plant diseases caused by soil-borne fungal pathogens. There is increasing attention for the possible role of volatiles in competitive interactions between bacteria and fungi. However, knowledge on the actual role of bacterial volatiles in interactions with fungi within soil microbial communities is lacking. Here, we examined colonization of sterile agricultural soils by fungi and bacteria from non-sterile soil inoculums during exposure to volatiles emitted by soil-derived bacterial communities. We found that colonization of soil by fungi was negatively affected by exposure to volatiles emitted by bacterial communities whereas that of bacteria was barely changed. Furthermore, there were strong effects of bacterial community volatiles on the assembly of fungal soil colonizers. Identification of volatile composition produced by bacterial communities revealed several compounds with known fungistatic activity. Our results are the first to reveal a collective volatile-mediated antagonism of soil bacteria against fungi. Given the better exploration abilities of filamentous fungi in unsaturated soils, this may be an important strategy for bacteria to defend occupied nutrient patches against invading fungi. Another implication of our research is that bacterial volatiles in soil atmospheres can have a major contribution to soil fungistasis.}, }
@article {pmid31579614, year = {2019}, author = {Benucci, GMN and Longley, R and Zhang, P and Zhao, Q and Bonito, G and Yu, F}, title = {Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e7744}, pmid = {31579614}, issn = {2167-8359}, support = {T32 GM110523/GM/NIGMS NIH HHS/United States ; }, abstract = {Morels (Morchella spp.) are iconic edible mushrooms with a long history of human consumption. Some microbial taxa are hypothesized to be important in triggering the formation of morel primordia and development of fruiting bodies, thus, there is interest in the microbial ecology of these fungi. To identify and compare fungal and prokaryotic communities in soils where Morchella sextelata is cultivated in outdoor greenhouses, ITS and 16S rDNA high throughput amplicon sequencing and microbiome analyses were performed. Pedobacter, Pseudomonas, Stenotrophomonas, and Flavobacterium were found to comprise the core microbiome of M. sextelata ascocarps. These bacterial taxa were also abundant in the soil beneath growing fruiting bodies. A total of 29 bacterial taxa were found to be statistically associated to Morchella fruiting bodies. Bacterial community network analysis revealed high modularity with some 16S rDNA operational taxonomic unit clusters living in specialized fungal niches (e.g., pileus, stipe). Other fungi dominating the soil mycobiome beneath morels included Morchella, Phialophora, and Mortierella. This research informs understanding of microbial indicators and potential facilitators of Morchella ecology and fruiting body production.}, }
@article {pmid31578554, year = {2020}, author = {An, SQ and Potnis, N and Dow, M and Vorhölter, FJ and He, YQ and Becker, A and Teper, D and Li, Y and Wang, N and Bleris, L and Tang, JL}, title = {Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas.}, journal = {FEMS microbiology reviews}, volume = {44}, number = {1}, pages = {1-32}, pmid = {31578554}, issn = {1574-6976}, support = {BB/R012415/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adaptation, Physiological/*genetics ; Genome, Bacterial/genetics ; Host-Pathogen Interactions/*physiology ; Plant Diseases/*microbiology ; Plants/*microbiology ; Virulence/genetics ; Xanthomonas/genetics/*pathogenicity/*physiology ; }, abstract = {Xanthomonas is a well-studied genus of bacterial plant pathogens whose members cause a variety of diseases in economically important crops worldwide. Genomic and functional studies of these phytopathogens have provided significant understanding of microbial-host interactions, bacterial virulence and host adaptation mechanisms including microbial ecology and epidemiology. In addition, several strains of Xanthomonas are important as producers of the extracellular polysaccharide, xanthan, used in the food and pharmaceutical industries. This polymer has also been implicated in several phases of the bacterial disease cycle. In this review, we summarise the current knowledge on the infection strategies and regulatory networks controlling virulence and adaptation mechanisms from Xanthomonas species and discuss the novel opportunities that this body of work has provided for disease control and plant health.}, }
@article {pmid31575762, year = {2019}, author = {Brewer, TE and Aronson, EL and Arogyaswamy, K and Billings, SA and Botthoff, JK and Campbell, AN and Dove, NC and Fairbanks, D and Gallery, RE and Hart, SC and Kaye, J and King, G and Logan, G and Lohse, KA and Maltz, MR and Mayorga, E and O'Neill, C and Owens, SM and Packman, A and Pett-Ridge, J and Plante, AF and Richter, DD and Silver, WL and Yang, WH and Fierer, N}, title = {Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons.}, journal = {mBio}, volume = {10}, number = {5}, pages = {}, pmid = {31575762}, issn = {2150-7511}, mesh = {Archaea/classification/growth &amp; development/*isolation &amp; purification ; Bacteria/classification/growth &amp; development/*isolation &amp; purification ; Metagenomics ; *Soil Microbiology ; }, abstract = {While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.}, }
@article {pmid31574348, year = {2019}, author = {Carney, RL and Labbate, M and Siboni, N and Tagg, KA and Mitrovic, SM and Seymour, JR}, title = {Urban beaches are environmental hotspots for antibiotic resistance following rainfall.}, journal = {Water research}, volume = {167}, number = {}, pages = {115081}, doi = {10.1016/j.watres.2019.115081}, pmid = {31574348}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; *Bacteria ; Drug Resistance, Microbial ; Genes, Bacterial ; Humans ; RNA, Ribosomal, 16S ; Tetracycline ; *Wastewater ; }, abstract = {To reveal the occurrence and mechanisms for dispersal of antibiotic resistance (AbR) among the microbial assemblages inhabiting impacted coastal environments, we performed a weekly, two-year duration time-series study at two urban beaches between 2014 and 2016. We combined quantitative PCR and multiplex PCR/reverse line blot techniques to track patterns in the occurrence of 31 AbR genes, including genes that confer resistance to antibiotics that are critically important antimicrobials for human medicine. Patterns in the abundance of these genes were linked to specific microbial groups and environmental parameters by coupling qPCR and 16S rRNA amplicon sequencing data with network analysis. Up to 100-fold increases in the abundance of several AbR genes, including genes conferring resistance to quinolones, trimethoprim, sulfonamides, tetracycline, vancomycin and carbapenems, occurred following storm-water and modelled wet-weather sewer overflow events. The abundance of AbR genes strongly and significantly correlated with several potentially pathogenic bacterial OTUs regularly associated with wastewater infrastructure, such as Arcobacter, Acinetobacter, Aeromonas and Cloacibacterium. These high-resolution observations provide clear links between storm-water discharge and sewer overflow events and the occurrence of AbR in the coastal microbial assemblages inhabiting urban beaches, highlighting a direct mechanism for potentially significant AbR exposure risks to humans.}, }
@article {pmid31572496, year = {2019}, author = {Mondo, SJ and Jiménez, DJ and Hector, RE and Lipzen, A and Yan, M and LaButti, K and Barry, K and van Elsas, JD and Grigoriev, IV and Nichols, NN}, title = {Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery.}, journal = {Biotechnology for biofuels}, volume = {12}, number = {}, pages = {229}, pmid = {31572496}, issn = {1754-6834}, abstract = {BACKGROUND: Particular species of the genus Coniochaeta (Sordariomycetes) exhibit great potential for bioabatement of furanic compounds and have been identified as an underexplored source of novel lignocellulolytic enzymes, especially Coniochaeta ligniaria. However, there is a lack of information about their genomic features and metabolic capabilities. Here, we report the first in-depth genome/transcriptome survey of a Coniochaeta species (strain 2T2.1).<br><br>RESULTS: The genome of Coniochaeta sp. strain 2T2.1 has a size of 74.53 Mbp and contains 24,735 protein-encoding genes. Interestingly, we detected a genome expansion event, resulting&#x2009;~&#x2009;98% of the assembly being duplicated with 91.9% average nucleotide identity between the duplicated regions. The lack of gene loss, as well as the&#xa0;high divergence and strong genome-wide signatures of purifying selection between copies indicates that this is likely a recent duplication, which arose through hybridization between two related Coniochaeta-like species (allopolyploidization). Phylogenomic analysis revealed that 2T2.1 is related Coniochaeta sp. PMI546 and Lecythophora sp. AK0013, which both occur endophytically. Based on carbohydrate-active enzyme (CAZy) annotation, we observed that even after in silico removal of its duplicated content, the&#xa0;2T2.1 genome contains exceptional lignocellulolytic machinery. Moreover, transcriptomic data reveal the overexpression of proteins affiliated to CAZy families GH11, GH10 (endoxylanases), CE5, CE1 (xylan esterases), GH62, GH51 (&#x3b1;-l-arabinofuranosidases), GH12, GH7 (cellulases), and AA9 (lytic polysaccharide monoxygenases) when the fungus was grown on wheat straw compared with glucose as the sole carbon source.<br><br>CONCLUSIONS: We provide data that suggest that&#xa0;a recent hybridization between the genomes of&#xa0;related species may have given rise to Coniochaeta sp. 2T2.1. Moreover, our results reveal that the degradation of arabinoxylan, xyloglucan and cellulose are key metabolic processes in strain&#xa0;2T2.1 growing on wheat straw. Different genes for key lignocellulolytic enzymes&#xa0;were identified, which can be starting points for production, characterization and/or supplementation of enzyme cocktails used in saccharification of agricultural residues. Our findings represent first steps that enable a better understanding of the reticulate evolution and "eco-enzymology" of lignocellulolytic Coniochaeta species.}, }
@article {pmid31572347, year = {2019}, author = {Dagher, DJ and de la Providencia, IE and Pitre, FE and St-Arnaud, M and Hijri, M}, title = {Plant Identity Shaped Rhizospheric Microbial Communities More Strongly Than Bacterial Bioaugmentation in Petroleum Hydrocarbon-Polluted Sediments.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2144}, pmid = {31572347}, issn = {1664-302X}, abstract = {Manipulating the plant-root microbiota has the potential to reduce plant stress and promote their growth and production in harsh conditions. Community composition and activity of plant-roots microbiota can be either beneficial or deleterious to plant health. Shifting this equilibrium could then strongly affect plant productivity in anthropized areas. In this study, we tested whether repeated bioaugmentation with Proteobacteria influenced plant productivity and the microbial communities associated with the rhizosphere of four plant species growing in sediments contaminated with petroleum hydrocarbons (PHCs). A mesocosm experiment was performed in randomized block design with two factors: (1) presence or absence of four plants species collected from a sedimentation basin of a former petrochemical plant, and (2) bioaugmentation or not with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over 4 months. MiSeq amplicon sequencing, targeting the bacterial 16S rRNA gene and the fungal ITS, was used to assess microbial community structures of sediments from planted or unplanted microcosms. Our results showed that while bioaugmentation caused a significant shift in microbial communities, presence of plant and their species identity had a stronger influence on the structure of the microbiome in PHCs contaminated sediments. The outcome of this study provides knowledge on the diversity and behavior of rhizosphere microbes associated with indigenous plants following repeated bioaugmentation, underlining the importance of plant selection in order to facilitate their efficient management, in order to accelerate processes of land reclamation.}, }
@article {pmid31572346, year = {2019}, author = {Schweitzer-Natan, O and Ofek-Lalzar, M and Sher, D and Sukenik, A}, title = {Particle-Associated Microbial Community in a Subtropical Lake During Thermal Mixing and Phytoplankton Succession.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2142}, pmid = {31572346}, issn = {1664-302X}, abstract = {Ecosystem dynamics in monomictic lakes are characterized by seasonal thermal mixing and stratification. These physical processes bring about seasonal variations in nutrients and organic matter fluxes, affecting the biogeochemical processes that occur in the water column. Physical and chemical dynamics are generally reflected in seasonal structural changes in the phytoplankton and bacterio-plankton community. In this study, we analyzed, using 16S rRNA amplicon sequencing, the structure of the bacterial community associated with large particles (>20 μm) in Lake Kinneret (Sea of Galilee, Israel), and its associations to phytoplankton populations. The study was carried out during late winter and early spring, a highly dynamic period in terms of thermal mixing, nutrient availability, and shifts in phytoplankton composition. Structural changes in the bacterioplankton population corresponded with limnological variations in the lake. In terms of the entire heterotrophic community, the structural patterns of particle-associated bacteria were mainly correlated with abiotic factors such as pH, ammonia, water temperature and nitrate. However, analysis of microbial taxon-specific correlations with phytoplankton species revealed a strong potential link between specific bacterial populations and the presence of different phytoplankton species, such as the cyanobacterium Microcystis, as well as the dinoflagellates Peridinium and Peridiniopsis. We found that Brevundimonas, a common freshwater genus, and Bdellovibrio, a well-known Gram-negative bacteria predator, were positively associated to Microcystis, suggesting a potentially important role of these three taxa in the microbial ecology of the lake. Our results show that the dynamics of environmental abiotic conditions, rather than specific phytoplankton assemblages, are the main factors positively correlated with changes in the community structure as a whole. Nevertheless, some specific bacteria may interact and be linked with specific phytoplankton, which may potentially control the dynamic patterns of the microbial community.}, }
@article {pmid31572315, year = {2019}, author = {Shin, GY and Schachterle, JK and Shyntum, DY and Moleleki, LN and Coutinho, TA and Sundin, GW}, title = {Functional Characterization of a Global Virulence Regulator Hfq and Identification of Hfq-Dependent sRNAs in the Plant Pathogen Pantoea ananatis.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2075}, pmid = {31572315}, issn = {1664-302X}, abstract = {To successfully infect plant hosts, the collective regulation of virulence factors in a bacterial pathogen is crucial. Hfq is an RNA chaperone protein that facilitates the small RNA (sRNA) regulation of global gene expression at the post-transcriptional level. In this study, the functional role of Hfq in a broad host range phytopathogen Pantoea ananatis was determined. Inactivation of the hfq gene in P. ananatis LMG 2665[T] resulted in the loss of pathogenicity and motility. In addition, there was a significant reduction of quorum sensing signal molecule acyl-homoserine lactone (AHL) production and biofilm formation. Differential sRNA expression analysis between the hfq mutant and wild-type strains of P. ananatis revealed 276 sRNAs affected in their abundance by the loss of hfq at low (OD600 = 0.2) and high cell (OD600 = 0.6) densities. Further analysis identified 25 Hfq-dependent sRNAs, all showing a predicted Rho-independent terminator of transcription and mapping within intergenic regions of the P. ananatis genome. These included known sRNAs such as ArcZ, FnrS, GlmZ, RprA, RyeB, RyhB, RyhB2, Spot42, and SsrA, and 16 novel P. ananatis sRNAs. The current study demonstrated that Hfq is an important component of the collective regulation of virulence factors and sets a foundation for understanding Hfq-sRNA mediated regulation in the phytopathogen P. ananatis.}, }
@article {pmid31566612, year = {2019}, author = {Šimek, K and Sirova, D}, title = {Fluorescently Labeled Bacteria as a Tracer to Reveal Novel Pathways of Organic Carbon Flow in Aquatic Ecosystems.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {151}, pages = {}, doi = {10.3791/59903}, pmid = {31566612}, issn = {1940-087X}, mesh = {Animals ; Bacteria/*metabolism ; Carbon/*metabolism ; Czech Republic ; Eukaryota ; *Food Chain ; *Microbiota ; *Predatory Behavior ; Rivers ; Tetrahymena/*physiology ; *Water Microbiology ; }, abstract = {Elucidating trophic interactions, such as predation and its effects, is a frequent task for many researchers in ecology. The study of microbial communities has many limitations, and determining a predator, prey, and predatory rates is often difficult. Presented here is an optimized method based on the addition of fluorescently labelled prey as a tracer, which allows for reliable quantitation of the grazing rates in aquatic predatory eukaryotes and estimation of nutrient transfer to higher trophic levels.}, }
@article {pmid31565058, year = {2019}, author = {Ahmed, EH and Hassan, HM and El-Sherbiny, NM and Soliman, AMA}, title = {Bacteriological Monitoring of Inanimate Surfaces and Equipment in Some Referral Hospitals in Assiut City, Egypt.}, journal = {International journal of microbiology}, volume = {2019}, number = {}, pages = {5907507}, pmid = {31565058}, issn = {1687-918X}, abstract = {Hospital-acquired infections represent a serious public health problem in all countries. It is clear that monitoring of the hospital environment is an essential element in the control and a part of the policy for preventing nosocomial infections. It allows a better understanding of the microbial ecology for the purpose of conducting preventive and corrective actions. The aims of this work were to determine the percentage of bacterial contamination of environmental samples and to identify potential nosocomial pathogens isolated from environments of seven referral hospitals from 2009 to 2015. By using the swab technique, 12863 samples were collected. Qualitative and quantitative cultures were performed. The organisms were primarily identified by colony morphology, microscopy of Gram stain, and standard biochemical tests. 25.6% of total samples showed contamination (93% was monomicrobial and 7.0% was polymicrobial). The predominant species was coagulase-negative staphylococcus (CNS) (32%), followed by methicillin-resistant S. aureus (MRSA) (26%) and then K. pneumonia (10.6%). The percentage of contamination varied among the covered hospitals and according to the year of monitoring with highly statistically significant difference (p value < 0.001). Direct contact with environmental surfaces or equipment transmits the majority of nosocomial infection. Major nosocomial pathogens have been identified. Hospital managers and healthcare bodies must be aware of the reality of the concept of environmental bacterial tanks and the need for respect of biocleaning procedures and choice of biocleaning tools.}, }
@article {pmid31563048, year = {2019}, author = {Villegas-Plazas, M and Sanabria, J and Junca, H}, title = {A composite taxonomical and functional framework of microbiomes under acid mine drainage bioremediation systems.}, journal = {Journal of environmental management}, volume = {251}, number = {}, pages = {109581}, doi = {10.1016/j.jenvman.2019.109581}, pmid = {31563048}, issn = {1095-8630}, mesh = {Acids ; Biodegradation, Environmental ; Bioreactors ; *Microbiota ; *Mining ; }, abstract = {Mining-industry is one of the most important activities in the economic development of many countries and produces highly significant alterations on the environment, mainly due to the release of a strong acidic metal-rich wastewater called acid mine drainage (AMD). Consequently, the establishment of multiple wastewater treatment strategies remains as a fundamental challenge in AMD research. Bioremediation, as a constantly-evolving multidisciplinary endeavor had been complemented during the last decades by novel tools of increasingly higher resolution such as those based on omics approaches, which are providing detailed insights into the ecology, evolution and mechanisms of microbial communities acting in bioremediation processes. This review specifically addresses, reanalyzes and reexamines in a composite comparative manner, the available sequence information and associated metadata available in public databases about AMD impacted microbial communities; summarizing our understanding of its composition and functions, and proposing potential genetic enhancements for improved bioremediation strategies. 16 S rRNA gene-targeted sequencing data from 9 studies previously published including AMD systems reported and studied around the world, were collected and reanalyzed to compare and identify the core and most abundant genera in four distinct AMD ecosystems: surface biofilm, water, impacted soils/sediments and bioreactor microbiomes. We determined that the microbial communities of bioreactors were the most diverse in bacterial types detected. The metabolic pathways predicted strongly suggest the key role of syntrophic communities with denitrification, methanogenesis, manganese, sulfate and iron reduction. The perspectives to explore the dynamics of engineering systems by high-throughput sequencing and biochemical techniques are discussed and foreseen application of synthetic biology and omics exploration on improved AMD biotransformation are proposed.}, }
@article {pmid31562384, year = {2020}, author = {Assié, A and Leisch, N and Meier, DV and Gruber-Vodicka, H and Tegetmeyer, HE and Meyerdierks, A and Kleiner, M and Hinzke, T and Joye, S and Saxton, M and Dubilier, N and Petersen, JM}, title = {Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria).}, journal = {The ISME journal}, volume = {14}, number = {1}, pages = {104-122}, pmid = {31562384}, issn = {1751-7370}, mesh = {Animals ; Bivalvia/microbiology ; Carbon Cycle ; Citric Acid Cycle ; Epsilonproteobacteria/classification/genetics/*metabolism ; Gammaproteobacteria/genetics ; *Photosynthesis ; Phylogeny ; Symbiosis ; }, abstract = {Most autotrophs use the Calvin-Benson-Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts ("Candidatus Thiobarba") of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cycle genes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that "Ca. Thiobarba" switched from the rTCA cycle to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated "Ca. Thiobarba". Direct stable isotope fingerprinting showed that "Ca. Thiobarba" has typical CBB signatures, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment.}, }
@article {pmid31562166, year = {2019}, author = {Joyce, RE and Lavender, H and Farrar, J and Werth, JT and Weber, CF and D'Andrilli, J and Vaitilingom, M and Christner, BC}, title = {Biological Ice-Nucleating Particles Deposited Year-Round in Subtropical Precipitation.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {23}, pages = {}, pmid = {31562166}, issn = {1098-5336}, mesh = {Atmosphere ; *Bacterial Physiological Phenomena ; Freezing ; *Ice ; Louisiana ; *Rain ; Seasons ; Temperature ; }, abstract = {Airborne bacteria that nucleate ice at relatively warm temperatures (>-10°C) can interact with cloud water droplets, affecting the formation of ice in clouds and the residency time of the cells in the atmosphere. We sampled 65 precipitation events in southeastern Louisiana over 2 years to examine the effect of season, meteorological conditions, storm type, and ecoregion source on the concentration and type of ice-nucleating particles (INPs) deposited. INPs sensitive to heat treatment were inferred to be biological in origin, and the highest concentrations of biological INPs (∼16,000 INPs liter[-1] active at ≥-10°C) were observed in snow and sleet samples from wintertime nimbostratus clouds with cloud top temperatures as warm as -7°C. Statistical analysis revealed three temperature classes of biological INPs (INPs active from -5 to -10°C, -11 to -12°C, and -13 to -14°C) and one temperature class of INPs that were sensitive to lysozyme (i.e., bacterial INPs, active from -5 to -10°C). Significant correlations between the INP data and abundances of taxa in the Bacteroidetes, Firmicutes, and unclassified bacterial divisions implied that certain members of these phyla may possess the ice nucleation phenotype. The interrelation between the INP classes and fluorescent dissolved organic matter, major ion concentrations (Na[+], Cl[-], SO4[2-], and NO3[-]), and backward air mass trajectories indicated that the highest concentrations of INPs were sourced from high-latitude North American and Asian continental environments, whereas the lowest values were observed when air was sourced from marine ecoregions. The intra- and extracontinental regions identified as sources of biological INPs in precipitation deposited in the southeastern United States suggests that these bioaerosols can disperse and affect meteorological conditions thousands of kilometers from their terrestrial points of origin.IMPORTANCE The particles most effective at inducing the freezing of water in the atmosphere are microbiological in origin; however, information on the species harboring this phenotype, their environmental distribution, and ecological sources are very limited. Analysis of precipitation collected over 2 years in Louisiana showed that INPs active at the warmest temperatures were sourced from terrestrial ecosystems and displayed behaviors that implicated specific bacterial taxa as the source of the ice nucleation activity. The abundance of biological INPs was highest in precipitation from winter storms and implied that their in-cloud concentrations were sufficient to affect the formation of ice and precipitation in nimbostratus clouds.}, }
@article {pmid31559142, year = {2019}, author = {Zheng, P and Li, Y and Wu, J and Zhang, H and Huang, Y and Tan, X and Pan, J and Duan, J and Liang, W and Yin, B and Deng, F and Perry, SW and Wong, ML and Licinio, J and Wei, H and Yu, G and Xie, P}, title = {Perturbed Microbial Ecology in Myasthenia Gravis: Evidence from the Gut Microbiome and Fecal Metabolome.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {6}, number = {18}, pages = {1901441}, pmid = {31559142}, issn = {2198-3844}, abstract = {Myasthenia gravis (MG) is a devastating acquired autoimmune disease. Emerging evidence indicates that the gut microbiome plays a key role in maintaining immune system homeostasis. This work reports that MG is characterized by decreased α-phylogenetic diversity, and significantly disturbed gut microbiome and fecal metabolome. The altered gut microbial composition is associated with fecal metabolome changes, with 38.75% of altered bacterial operational taxonomic units showing significant correlations with a range of metabolite biomarkers. Some microbes are particularly linked with MG severity. Moreover, a combination of microbial makers and their correlated metabolites enable discriminating MG from healthy controls (HCs) with 100% accuracy. To investigate whether disturbed gut mcirobiome might contribute to the onset of MG, germ-free (GF) mice are initially colonized with MG microbiota (MMb) or healthy microbiota (HMb), and then immunized in a classic mouse model of MG. The MMb mice demonstrate substantially impaired locomotion ability compared with the HMb mice. This effect could be reversed by cocolonizing GF mice with both MMb and HMb. The MMb mice also exhibit similar disturbances of fecal metabolic pathways as found in MG. Together these data demonstrate disturbances in microbiome composition and activity that are likely to be relevant to the pathogenesis of MG.}, }
@article {pmid31557953, year = {2019}, author = {Zhang, Z and Mocanu, V and Cai, C and Dang, J and Slater, L and Deehan, EC and Walter, J and Madsen, KL}, title = {Impact of Fecal Microbiota Transplantation on Obesity and Metabolic Syndrome-A Systematic Review.}, journal = {Nutrients}, volume = {11}, number = {10}, pages = {}, pmid = {31557953}, issn = {2072-6643}, support = {./CAPMC/CIHR/Canada ; }, mesh = {*Fecal Microbiota Transplantation ; Humans ; Metabolic Syndrome/*therapy ; Obesity/*therapy ; }, abstract = {Fecal microbiota transplantation (FMT) is a gut microbial-modulation strategy that has been investigated for the treatment of a variety of human diseases, including obesity-associated metabolic disorders. This study appraises current literature and provides an overview of the effectiveness and limitations of FMT as a potential therapeutic strategy for obesity and metabolic syndrome (MS). Five electronic databases and two gray literature sources were searched up to 10 December 2018. All interventional and observational studies that contained information on the relevant population (adult patients with obesity and MS), intervention (receiving allogeneic FMT) and outcomes (metabolic parameters) were eligible. From 1096 unique citations, three randomized placebo-controlled studies (76 patients with obesity and MS, body mass index = 34.8 ± 4.1 kg/m[2], fasting plasma glucose = 5.8 ± 0.7 mmol/L) were included for review. Studies reported mixed results with regards to improvement in metabolic parameters. Two studies reported improved peripheral insulin sensitivity (rate of glucose disappearance, RD) at 6 weeks in patients receiving donor FMT versus patients receiving the placebo control. In addition, one study observed lower HbA1c levels in FMT patients at 6 weeks. No differences in fasting plasma glucose, hepatic insulin sensitivity, body mass index (BMI), or cholesterol markers were observed between two groups across all included studies. While promising, the influence of FMT on long-term clinical endpoints needs to be further explored. Future studies are also required to better understand the mechanisms through which changes in gut microbial ecology and engraftment of microbiota affect metabolic outcomes for patients with obesity and MS. In addition, further research is needed to better define the optimal fecal microbial preparation, dosing, and method of delivery.}, }
@article {pmid31557655, year = {2019}, author = {Wang, Y and Lin, Z and He, L and Huang, W and Zhou, J and He, Q}, title = {Simultaneous partial nitrification, anammox and denitrification (SNAD) process for nitrogen and refractory organic compounds removal from mature landfill leachate: Performance and metagenome-based microbial ecology.}, journal = {Bioresource technology}, volume = {294}, number = {}, pages = {122166}, doi = {10.1016/j.biortech.2019.122166}, pmid = {31557655}, issn = {1873-2976}, mesh = {Bioreactors ; Denitrification ; Metagenome ; *Nitrification ; Nitrogen ; Oxidation-Reduction ; *Water Pollutants, Chemical ; }, abstract = {In this study, a simultaneous partial nitrification, Anammox and denitrification (SNAD) bioreactor was constructed for mature landfill leachate treatment, which exhibited favorable NH4[+]-N (98.9-99.9%), TN (90.7-94.9%) and bio-refractory organic compounds (46.2-67.7%) removal efficiencies. Stoichiometric analysis demonstrated that the synergy of ammonium-oxidizing bacteria and Anammox bacteria dominated TN removal (96.1-97.2%). NO3[-]-N produced in Anammox could be further reduced through (partial) denitrification and dissimilatory nitrate reduction to ammonium (DNRA). The results highlighted that humic-like and their intermediates might serve as the electron donor for these (partial) denitrifiers and DNRA bacteria to remove NO3[-]-N, and could be effectively removed from mature landfill leachate in SNAD bioreactor. Metagenomic characterization further demonstrated that phyla Chloroflexi, Chlorobi and genera Nitrosomonas, Ignavibacterium and Aminiphilus might be responsible for such humic-like degradation. Overall, this work offers new insights into the metagenome-based bioinformatic roles for the previously understudied microorganisms in SNAD bioreactor for mature landfill leachate treatment.}, }
@article {pmid31557445, year = {2020}, author = {Þorsteinsdóttir, GV and Blischke, A and Sigurbjörnsdóttir, MA and Òskarsson, F and Arnarson, &#xde;S and Magnússon, KP and Vilhelmsson, O}, title = {Gas seepage pockmark microbiomes suggest the presence of sedimentary coal seams in the Öxarfjörður graben of northeastern Iceland.}, journal = {Canadian journal of microbiology}, volume = {66}, number = {1}, pages = {25-38}, doi = {10.1139/cjm-2019-0081}, pmid = {31557445}, issn = {1480-3275}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Bioprospecting ; Coal/analysis/*microbiology ; Geologic Sediments/chemistry/*microbiology ; Hydrocarbons/analysis ; Iceland ; Methane/analysis ; *Microbiota/genetics ; Natural Gas/analysis/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Natural gas seepage pockmarks are found off- and onshore in the Öxarfjörður graben, Iceland. The bacterial communities of two onshore seepage sites were analysed by 16S rRNA gene amplicon sequencing; the geochemical characteristics, hydrocarbon content, and the carbon isotope composition of the sites were also determined. While one site was found to be characterised by biogenic origin of methane gas, with a carbon isotope ratio (δ[13]C (‰)) of -63.2, high contents of organic matter and complex hydrocarbons, the other site showed a mixed origin of the methane gas (δ[13]C (‰) = -26.6) with geothermal characteristics and lower organic matter content. While both sites harboured Proteobacteria as the most abundant bacterial phyla, the Deltaproteobacteria were more abundant at the geothermal site and the Alphaproteobacteria at the biogenic site. The Dehalococcoidia class of phylum Chloroflexi was abundant at the geothermal site while the Anaerolineae class was more abundant at the biogenic site. Bacterial strains from the seepage pockmarks were isolated on a variety of selective media targeting bacteria with bioremediation potential. A total of 106 strains were isolated and characterised, including representatives from the phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. This article describes the first microbial study on gas seepage pockmarks in Iceland.}, }
@article {pmid31556187, year = {2020}, author = {Tang, HC and Sieo, CC and Abdullah, N and Chong, CW and Gan, HM and Mohd Asrore, MS and Yong, CY and Omar, AR and Ho, YW}, title = {Effects of supplementing freeze-dried Mitsuokella jalaludinii phytase on the growth performance and gut microbial diversity of broiler chickens.}, journal = {Journal of animal physiology and animal nutrition}, volume = {104}, number = {1}, pages = {116-125}, doi = {10.1111/jpn.13208}, pmid = {31556187}, issn = {1439-0396}, support = {06-01-04-SF1376//eScience Fund/ ; }, mesh = {6-Phytase/metabolism/*pharmacology ; Animals ; Bacteria/genetics ; Chickens/*growth &amp; development/*microbiology ; Dietary Supplements ; Firmicutes/*enzymology ; Freeze Drying ; Gastrointestinal Microbiome/*drug effects ; Male ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Weight Gain/drug effects ; }, abstract = {Inclusion of phytase in animal feedstuff is a common practice to enhance nutrients availability. However, little is known about the effects of phytase supplementation on the microbial ecology of the gastrointestinal tract. In this study, freeze-dried Mitsuokella jalaludinii phytase (MJ) was evaluated in a feeding trial with broilers fed a low available phosphorus (aP) diet. A total of 180 male broiler chicks (day-old Cobb) were assigned into three dietary treatments: Control fed with 0.4% (w/w) of available phosphorus (aP); Group T1 fed low aP [0.2% (w/w)] supplemented with MJ; and T2 fed low aP and deactivated MJ. The source of readily available P, dicalcium phosphate (DCP), was removed from low aP diet, whereby additional limestone was provided to replace the amount of Ca normally found in DCP. For each treatment, 4 replicate pens were used, where each pen consisted of 15 animals. The animals' energy intake and caecal bacterial community were monitored weekly for up to 3 weeks. The apparent metabolizable energy (AME) and apparent digestibility of dry matter (ADDM) of broilers fed with different diets were determined. In addition, the caecal microbial diversities of broilers were assessed using high-throughput next-generation sequencing targeting the V3-V4 region of bacterial 16S rRNA. The results showed that broilers fed with T1 diet have better feed conversion ratio (FCR) when compared to the Control (p < .05) and T2 diets (p < .05), demonstrating the efficiency of MJ as a supplement to low aP diet. Nevertheless, MJ did not significantly affect the microbial population and diversity in broilers' caeca, which mainly consists of members from Bacteroidetes, Firmicutes, and Proteobacteria. Regardless, significant variations in the caecal bacterial composition were observed over time, probably due to succession as the broilers aged. This is the first reported study on the effect of MJ on the microbial diversity of broiler's caeca.}, }
@article {pmid31555253, year = {2019}, author = {Sarkar, A and Morita, D and Ghosh, A and Chowdhury, G and Mukhopadhyay, AK and Okamoto, K and Ramamurthy, T}, title = {Altered Integrative and Conjugative Elements (ICEs) in Recent Vibrio cholerae O1 Isolated From Cholera Cases, Kolkata, India.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2072}, pmid = {31555253}, issn = {1664-302X}, abstract = {The self-transferring integrative and conjugative elements (ICEs) are large genomic segments carrying several bacterial adaptive functions including antimicrobial resistance (AMR). SXT/R391 family is one of the ICEs extensively studied in cholera-causing pathogen Vibrio cholerae. The genetic characteristics of ICE-SXT/R391 in V. cholerae are dynamic and region-specific. These ICEs in V. cholerae are strongly correlated with resistance to several antibiotics such as tetracycline, streptomycin and trimethoprim-sulfamethoxazole. We screened V. cholerae O1 strains isolated from cholera patients in Kolkata, India from 2008 to 2015 for antibiotic susceptibility and the presence of ICEs, and subsequently sequenced their conserved genes. Resistance to tetracycline, streptomycin and trimethoprim-sulfamethoxazole was detected in strains isolated during 2008-2010 and 2014-2015. The genes encoding resistance to tetracycline (tetA), trimethoprim-sulfamethoxazole (dfrA1 and sul2), streptomycin (strAB), and chloramphenicol (floR) were detected in the ICEs of these strains. There was a decrease in overall drug resistance in V. cholerae associated with the ICEs in 2011. DNA sequence analysis also showed that AMR in these strains was conferred mainly by two types of ICEs, i.e., ICE[TET] (comprising tetA, strAB, sul2, and dfrA1) and ICE[GEN] (floR, strAB, sul2, and dfrA1). Based on the genetic structure, Kolkata strains of V. cholerae O1 had distinct genetic traits different from the ICEs reported in other cholera endemic regions. Transfer of AMR was confirmed by conjugation with sodium azide resistant Escherichia coli J53. In addition to the acquired resistance to streptomycin and trimethoprim-sulfamethoxazole, the conjugally transferred (CT) E. coli J53 with ICE showed higher resistance to chloramphenicol and tetracycline than the donor V. cholerae. Pulsed-field gel electrophoresis (PFGE) based clonal analysis revealed that the V. cholerae strains could be grouped based on their ICEs and AMR patterns. Our findings demonstrate the epidemiological importance of ICEs and their role in the emergence of multidrug resistance (MDR) in El Tor vibrios.}, }
@article {pmid31555238, year = {2019}, author = {Pires, ES and Hardoim, CCP and Miranda, KR and Secco, DA and Lobo, LA and de Carvalho, DP and Han, J and Borchers, CH and Ferreira, RBR and Salles, JF and Domingues, RMCP and Antunes, LCM}, title = {The Gut Microbiome and Metabolome of Two Riparian Communities in the Amazon.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2003}, pmid = {31555238}, issn = {1664-302X}, abstract = {During the last decades it has become increasingly clear that the microbes that live on and in humans are critical for health. The communities they form, termed microbiomes, are involved in fundamental processes such as the maturation and constant regulation of the immune system. Additionally, they constitute a strong defense barrier to invading pathogens, and are also intricately linked to nutrition. The parameters that affect the establishment and maintenance of these microbial communities are diverse, and include the genetic background, mode of birth, nutrition, hygiene, and host lifestyle in general. Here, we describe the characterization of the gut microbiome of individuals living in the Amazon, and the comparison of these microbial communities to those found in individuals from an urban, industrialized setting. Our results showed striking differences in microbial communities from these two types of populations. Additionally, we used high-throughput metabolomics to study the chemical ecology of the gut environment and found significant metabolic changes between the two populations. Although we cannot point out a single cause for the microbial and metabolic changes observed between Amazonian and urban individuals, they are likely to include dietary differences as well as diverse patterns of environmental exposure. To our knowledge, this is the first description of gut microbial and metabolic profiles in Amazonian populations, and it provides a starting point for thorough characterizations of the impact of individual environmental conditions on the human microbiome and metabolome.}, }
@article {pmid31554820, year = {2019}, author = {Riva, A and Kuzyk, O and Forsberg, E and Siuzdak, G and Pfann, C and Herbold, C and Daims, H and Loy, A and Warth, B and Berry, D}, title = {A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4366}, pmid = {31554820}, issn = {2041-1723}, support = {I 2320/FWF_/Austrian Science Fund FWF/Austria ; P 26127/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Colon/*microbiology ; *Diet ; Dietary Fiber/*deficiency ; Gastrointestinal Microbiome/genetics/*physiology ; Intestinal Mucosa/microbiology ; Metagenomics/methods ; Mice, Inbred C57BL ; Microbiota/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Compartmentalization of the gut microbiota is thought to be important to system function, but the extent of spatial organization in the gut ecosystem remains poorly understood. Here, we profile the murine colonic microbiota along longitudinal and lateral axes using laser capture microdissection. We found fine-scale spatial structuring of the microbiota marked by gradients in composition and diversity along the length of the colon. Privation of fiber reduces the diversity of the microbiota and disrupts longitudinal and lateral gradients in microbiota composition. Both mucus-adjacent and luminal communities are influenced by the absence of dietary fiber, with the loss of a characteristic distal colon microbiota and a reduction in the mucosa-adjacent community, concomitant with depletion of the mucus layer. These results indicate that diet has not only global but also local effects on the composition of the gut microbiota, which may affect function and resilience differently depending on location.}, }
@article {pmid31554088, year = {2019}, author = {Vissenaekens, H and Grootaert, C and Rajkovic, A and De Schutter, K and Raes, K and Smagghe, G and Van de Wiele, T and Van Camp, J}, title = {Cell line-dependent increase in cellular quercetin accumulation upon stress induced by valinomycin and lipopolysaccharide, but not by TNF-α.}, journal = {Food research international (Ottawa, Ont.)}, volume = {125}, number = {}, pages = {108596}, doi = {10.1016/j.foodres.2019.108596}, pmid = {31554088}, issn = {1873-7145}, mesh = {Antioxidants/pharmacology ; Caco-2 Cells ; Cell Line ; Cell Proliferation/drug effects ; Endothelial Cells/drug effects/metabolism ; Flavonoids/pharmacology ; HCT116 Cells ; Humans ; Intestinal Mucosa/cytology/drug effects/metabolism ; Lipopolysaccharides/*toxicity ; Quercetin/*pharmacology ; Stress, Physiological/*drug effects ; Tumor Necrosis Factor-alpha/*metabolism ; Valinomycin/*toxicity ; }, abstract = {As the interface between the luminal and internal environment, the intestinal epithelium is strongly exposed to food-related, host-related and microbial stress. Furthermore, the endothelial stress response plays an important role in vascular disease development, which may be improved upon consumption of dietary bioactives such as polyphenols. The impact of the latter, however, is largely individual-dependent and effects are, in most cases, only observed under mild diseased conditions. Here, it is hypothesized that the individual's stressor levels may contribute to this variable response. To this end, the impact of the stressors (i) valinomycin (as model for cereulide, food-related microbial metabolite), (ii) TNF-α (host-related) and (iii) lipopolysaccharide (gram-negative bacterial cell related) on flavonoid accumulation was investigated in several intestinal and endothelial cell lines. Flow cytometry, confocal microscopy and an in-house developed, robust and high-throughput spectrofluorometric method, showed that quercetin accumulated in all tested cell lines in a dose-dependent manner. Upon stress induced by valinomycin and to a lesser extent by lipopolysaccharide, but not by TNF-α, an increased quercetin accumulation was observed in proliferating intestinal and endothelial cells and not in differentiated intestinal or quiescent endothelial cells. Therefore, flavonoid accumulation may be a potential cellular stress response mechanism which strongly depends on the applied stressor, flavonoid, cell line and even growth conditions. This opens perspectives for further understanding the mechanisms by which cellular stress may shape the individual's response to bioactive compounds.}, }
@article {pmid31553939, year = {2019}, author = {Zhang, Y and Shen, Z and Zhang, F and Yu, Y and Li, J and Lin, X}, title = {Taxonomy and phylogeny of Pseudovorticella littoralis sp. n. and P. alani sp. n. (Ciliophora: Peritrichia) from coastal waters of southern China.}, journal = {European journal of protistology}, volume = {71}, number = {}, pages = {125635}, doi = {10.1016/j.ejop.2019.125635}, pmid = {31553939}, issn = {1618-0429}, mesh = {China ; Oligohymenophorea/*classification/cytology/genetics ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; Seawater/*parasitology ; Species Specificity ; }, abstract = {The morphology, infraciliature, and silverline system of two peritrich ciliates, Pseudovorticella littoralis sp. n. and P. alani sp. n., isolated from coastal waters of southern China, were investigated based on both living and silver-stained specimens. Pseudovorticella littoralis sp. n. is characterized by the following combination of characters: cell inverted cone-shaped; contractile vacuole ventral; J-shaped macronucleus; infundibular polykinety 3 with two kinetosome rows of equal length; 19-26 silverlines from peristome to trochal band and 5-14 from trochal band to scopula. Pseudovorticella alani sp. n. is characterized by: cell inverted bell-shaped; contractile vacuole ventral; J-shaped macronucleus recurved almost forming a loop; infundibular polykinety 3 with three kinetosome rows, outer two rows longer than inner one; 48-61 silverlines between peristome and aboral trochal band, and 12-20 between aboral trochal band and scopula. The SSU rDNA sequences of both new species are reported and their genetic distances with congeners and phylogenetic relationships are investigated. Pseudovorticella and Epicarchesium cluster into two subclades with low support values. One subclade contains nearly all the available sequences of Pseudovorticella and Epicarchesium. Another one contains P. monilata and E. pectinatum. This calls on the need of a generic re-classification of Pseudovorticella and Epicarchesium based on more morphological and molecular data.}, }
@article {pmid31553931, year = {2019}, author = {Subirats, J and Di Cesare, A and Varela Della Giustina, S and Fiorentino, A and Eckert, EM and Rodriguez-Mozaz, S and Borrego, CM and Corno, G}, title = {High-quality treated wastewater causes remarkable changes in natural microbial communities and intI1 gene abundance.}, journal = {Water research}, volume = {167}, number = {}, pages = {114895}, doi = {10.1016/j.watres.2019.114895}, pmid = {31553931}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; Genes, Bacterial ; Integrases ; Integrons ; *Microbiota ; *Wastewater ; }, abstract = {We carry out a mesocosms experiment to assess the impact of high-quality treated wastewater intended for agricultural reuse (HQWR) on freshwater bacteria seldom exposed to anthropogenic pollution. Effects were assessed by comparing the abundance and composition of bacterial communities as well as their resistance profile under control (source water from an unpolluted lake) and treatment conditions (source water mixed 1:1 with HQWR, with and without 5 μg L[-1] of cefotaxime). We investigated the effect of the different conditions on the abundance of genes encoding resistance to β-lactams and carbapenems (blaTEM, blaCTX-M, blaOXA, and blaKPC), fluoroquinolones (qnrS), tetracyclines (tetA), sulfonamides (sul2), macrolides (ermB), arsenic and cadmium (arsB and czcA, respectively), and on the gene encoding the Class 1 integron integrase (intI1). Bacterial communities exposed to HQWR showed a significant higher abundance of tetA, arsB, czcA, and intI1 genes, whereas those exposed to Cefotaxime-amended HQWR did not. Genes conferring resistance to carbapenems, β-lactams, fluoroquinolones, and macrolides were below detection limit in all treatments. Besides, the higher availability of nutrients under treatment conditions favored bacterial growth in comparison to those exposed to control conditions. Particularly, Acinetobacter spp. and Pseudomonas spp. were significantly enriched after 22 days of treatment exposure. The presence of cefotaxime (a third generation cephalosporine) in the feeding medium caused an enrichment of bacterial communities in sequences affiliated to Acinetobacter thus suggesting that these resistant forms may possess resistance genes other than those studied here (blaCTX-M, blaOXA, and blaKPC). Although derived from a mesocosm experiment in continuous cultures, our results call attention to the need of refined regulations regarding the use of reclaimed water in agriculture since even high-quality treated wastewater may lead to undesired effects on receiving bacterial communities in terms of composition and dissemination of antibiotic resistance genes.}, }
@article {pmid31553930, year = {2019}, author = {Regnery, J and Parrhysius, P and Schulz, RS and Möhlenkamp, C and Buchmeier, G and Reifferscheid, G and Brinke, M}, title = {Wastewater-borne exposure of limnic fish to anticoagulant rodenticides.}, journal = {Water research}, volume = {167}, number = {}, pages = {115090}, doi = {10.1016/j.watres.2019.115090}, pmid = {31553930}, issn = {1879-2448}, mesh = {Animals ; Anticoagulants ; Environmental Monitoring ; Germany ; Retrospective Studies ; *Rodenticides ; Wastewater ; *Water Pollutants, Chemical ; }, abstract = {The recent emergence of second-generation anticoagulant rodenticides (AR) in the aquatic environment emphasizes the relevance and impact of aquatic exposure pathways during rodent control. Pest control in municipal sewer systems of urban and suburban areas is thought to be an important emission pathway for AR to reach wastewater and municipal wastewater treatment plants (WWTP), respectively. To circumstantiate that AR will enter streams via effluent discharges and bioaccumulate in aquatic organisms despite very low predicted environmental emissions, we conducted a retrospective biological monitoring of fish tissue samples from different WWTP fish monitoring ponds exclusively fed by municipal effluents in Bavaria, Germany. At the same time, information about rodent control in associated sewer systems was collected by telephone survey to assess relationships between sewer baiting and rodenticide residues in fish. In addition, mussel and fish tissue samples from several Bavarian surface waters with different effluent impact were analyzed to evaluate the prevalence of anticoagulants in indigenous aquatic organisms. Hepatic AR residues were detected at 12 out of 25 WWTP sampling sites in the low μg/kg range, thereof six sites with one or more second-generation AR (i.e., brodifacoum, difenacoum, bromadiolone). 14 of 18 surveyed sites confirmed sewer baiting with AR and detected hepatic residues matched the reported active ingredients used for sewer baiting at six sites. Furthermore, second-generation AR were detected in more than 80% of fish liver samples from investigated Bavarian streams. Highest total hepatic AR concentrations in these fish were 9.1 and 8.5 μg/kg wet weight, respectively and were observed at two riverine sampling sites characterized by close proximity to upstream WWTP outfalls. No anticoagulant residues were found in fish liver samples from two lakes without known influences of effluent discharges. The findings of our study clearly show incomplete removal of anticoagulants during conventional wastewater treatment and confirm exposure of aquatic organisms via municipal effluents. Based on the demonstrated temporal and spatial coherence between sewer baiting and hepatic AR residues in effluent-exposed fish, sewer baiting in combined sewer systems contributes to the release of active ingredients into the aquatic environment.}, }
@article {pmid31552450, year = {2019}, author = {Wagner, AO and Praeg, N and Illmer, P}, title = {Spiking a Silty-Sand Reference Soil with Bacterial DNA: Limits and Pitfalls in the Discrimination of Live and Dead Cells When Applying Ethidium Monoazide (EMA) Treatment.}, journal = {Current microbiology}, volume = {76}, number = {12}, pages = {1425-1434}, pmid = {31552450}, issn = {1432-0991}, support = {P 22815/FWF_/Austrian Science Fund FWF/Austria ; P 22815//Austrian Science Fund/ ; }, mesh = {Affinity Labels/*chemistry ; Azides/*chemistry ; Bacteriological Techniques/*methods ; Colony Count, Microbial ; DNA, Bacterial/*chemistry/genetics/isolation &amp; purification ; Listeria monocytogenes/genetics/isolation &amp; purification/*physiology ; *Microbial Viability ; Polymerase Chain Reaction ; Soil Microbiology ; }, abstract = {In the present study, EMA (ethidium monoazide) treatment was applied to a silty-sand reference soil prior to DNA extraction to enable a differentiation between dead and living cells. For this purpose, a reference soil was spiked with Listeria monocytogenes cells or cell equivalents, respectively. With the purpose of evaluating optimum treatment conditions, different EMA concentrations have been tested. However, the results remained largely inconclusive. Furthermore, varied dark incubation periods allowing EMA to penetrate dead cells did not allow the selective removal of DNA from membrane-compromised cells in downstream analyses. In contrast to undiluted soil, an effect of EMA treatment during DNA extraction could be observed when using a 1:10 dilution of the reference soil; however, the effect has not been sufficiently selective to act on heat-treated cells only. Although the application of EMA to soil requires further evaluation, the procedure harbors future potential for improving DNA-based approaches in microbial ecology studies.}, }
@article {pmid31551063, year = {2019}, author = {Keiser, CN and Hammer, TJ and Pruitt, JN}, title = {Social spider webs harbour largely consistent bacterial communities across broad spatial scales.}, journal = {Biology letters}, volume = {15}, number = {9}, pages = {20190436}, pmid = {31551063}, issn = {1744-957X}, mesh = {Animals ; Bacteria ; Predatory Behavior ; *Silk ; *Spiders ; }, abstract = {Social animals that live in domiciles constructed from biomaterials may facilitate microbial growth. Spider webs are one of the most conspicuous biomaterials in nature, yet almost nothing is known about the potential for webs to harbour microbes, even in social spiders that live in dense, long-term aggregations. Here, we tested whether the dominant bacteria present in social spider webs vary across sampling localities and whether the more permanent retreat web harbours compositionally distinct microbes from the more ephemeral capture webs in the desert social spider, Stegodyphus dumicola. We also sampled spider cuticles and prey items in a subset of colonies. We found that spider colonies across large spatial scales harboured similar web-associated bacterial communities. We also found substantial overlap in bacterial community composition between spider cuticle, prey and web samples. These data suggest that social spider webs can harbour characteristic microbial communities and potentially facilitate microbial transmission among individuals, and this study serves as the first step towards understanding the microbial ecology of these peculiar animal societies.}, }
@article {pmid31550548, year = {2020}, author = {De Vrieze, J and Verbeeck, K and Pikaar, I and Boere, J and Van Wijk, A and Rabaey, K and Verstraete, W}, title = {The hydrogen gas bio-based economy and the production of renewable building block chemicals, food and energy.}, journal = {New biotechnology}, volume = {55}, number = {}, pages = {12-18}, doi = {10.1016/j.nbt.2019.09.004}, pmid = {31550548}, issn = {1876-4347}, mesh = {Bacterial Proteins/metabolism ; Biofuels/*economics ; Food/*economics ; Hydrogen/*chemistry ; Methane/metabolism ; Renewable Energy/*economics ; }, abstract = {The carrying capacity of the planet is being exceeded, and there is an urgent need to bring forward revolutionary approaches, particularly in terms of energy supply, carbon emissions and nitrogen inputs into the biosphere. Hydrogen gas, generated by means of renewable energy through water electrolysis, can be a platform molecule to drive the future bioeconomy and electrification in the 21[st] century. The potential to use hydrogen gas in microbial metabolic processes is highly versatile, and this opens a broad range of opportunities for novel biotechnological developments and applications. A first approach concerns the central role of hydrogen gas in the production of bio-based building block chemicals using the methane route, thus, bypassing the inherent low economic value of methane towards higher-value products. Second, hydrogen gas can serve as a key carbon-neutral source to produce third-generation proteins, i.e. microbial protein for food applications, whilst simultaneously enabling carbon capture and nutrient recovery, directly at their point of emission. Combining both approaches to deal with the intermittent nature of renewable energy sources maximises the ability for efficient use of renewable resources.}, }
@article {pmid31550268, year = {2019}, author = {Mahjoubi, M and Aliyu, H and Cappello, S and Naifer, M and Souissi, Y and Cowan, DA and Cherif, A}, title = {The genome of Alcaligenes aquatilis strain BU33N: Insights into hydrocarbon degradation capacity.}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0221574}, pmid = {31550268}, issn = {1932-6203}, mesh = {Alcaligenes/*genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Environmental Pollutants/metabolism ; Genome, Bacterial ; Geologic Sediments/microbiology ; Humans ; Hydrocarbons/*metabolism ; Metabolic Networks and Pathways/genetics ; Multigene Family ; Phylogeny ; Species Specificity ; Surface-Active Agents/metabolism ; }, abstract = {Environmental contamination with hydrocarbons though natural and anthropogenic activities is a serious threat to biodiversity and human health. Microbial bioremediation is considered as the effective means of treating such contamination. This study describes a biosurfactant producing bacterium capable of utilizing crude oil and various hydrocarbons as the sole carbon source. Strain BU33N was isolated from hydrocarbon polluted sediments from the Bizerte coast (northern Tunisia) and was identified as Alcaligenes aquatilis on the basis of 16S rRNA gene sequence analysis. When grown on crude oil and phenanthrene as sole carbon and energy sources, isolate BU33N was able to degrade ~86%, ~56% and 70% of TERHc, n-alkanes and phenanthrene, respectively. The draft genome sequence of the A. aquatilis strain BU33N was assembled into one scaffold of 3,838,299 bp (G+C content of 56.1%). Annotation of the BU33N genome resulted in 3,506 protein-coding genes and 56 rRNA genes. A large repertoire of genes related to the metabolism of aromatic compounds including genes encoding enzymes involved in the complete degradation of benzoate were identified. Also genes associated with resistance to heavy metals such as copper tolerance and cobalt-zinc-cadmium resistance were identified in BU33N. This work provides insight into the genomic basis of biodegradation capabilities and bioremediation/detoxification potential of A. aquatilis BU33N.}, }
@article {pmid31548611, year = {2019}, author = {Soares-Castro, P and Araújo-Rodrigues, H and Godoy-Vitorino, F and Ferreira, M and Covelo, P and López, A and Vingada, J and Eira, C and Santos, PM}, title = {Microbiota fingerprints within the oral cavity of cetaceans as indicators for population biomonitoring.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13679}, pmid = {31548611}, issn = {2045-2322}, support = {U54 MD007600/MD/NIMHD NIH HHS/United States ; }, mesh = {Animals ; Biological Monitoring/*methods ; Cetacea/*microbiology ; DNA Barcoding, Taxonomic ; Microbiota/*physiology ; Mouth/*microbiology ; }, abstract = {The composition of mammalian microbiota has been related with the host health status. In this study, we assessed the oral microbiome of 3 cetacean species most commonly found stranded in Iberian Atlantic waters (Delphinus delphis, Stenella coeruleoalba and Phocoena phocoena), using 16S rDNA-amplicon metabarcoding. All oral microbiomes were dominated by Proteobacteria, Firmicutes, Bacteroidetes and Fusobacteria bacteria, which were also predominant in the oral cavity of Tursiops truncatus. A Constrained Canonical Analysis (CCA) showed that the major factors shaping the composition of 38 oral microbiomes (p-value < 0.05) were: (i) animal species and (ii) age class, segregating adults and juveniles. The correlation analysis also grouped the microbiomes by animal stranding location and health status. Similar discriminatory patterns were detected using the data from a previous study on Tursiops truncatus, indicating that this correlation approach may facilitate data comparisons between different studies on several cetacean species. This study identified a total of 15 bacterial genera and 27 OTUs discriminating between the observed CCA groups, which can be further explored as microbiota fingerprints to develop (i) specific diagnostic assays for cetacean population conservation and (ii) bio-monitoring approaches to assess the health of marine ecosystems from the Iberian Atlantic basin, using cetaceans as bioindicators.}, }
@article {pmid31548387, year = {2019}, author = {Petersen, J and Vollmers, J and Ringel, V and Brinkmann, H and Ellebrandt-Sperling, C and Spröer, C and Howat, AM and Murrell, JC and Kaster, AK}, title = {A marine plasmid hitchhiking vast phylogenetic and geographic distances.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {41}, pages = {20568-20573}, pmid = {31548387}, issn = {1091-6490}, mesh = {Bacterial Proteins/*genetics ; *Environment ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Geography ; Phylogeny ; Plasmids/*genetics ; Recombination, Genetic ; Roseobacter/classification/*genetics ; }, abstract = {Horizontal gene transfer (HGT) plays an important role in bacterial evolution and serves as a driving force for bacterial diversity and versatility. HGT events often involve mobile genetic elements like plasmids, which can promote their own dissemination by associating with adaptive traits in the gene pool of the so-called mobilome. Novel traits that evolve through HGT can therefore lead to the exploitation of new ecological niches, prompting an adaptive radiation of bacterial species. In this study, we present phylogenetic, biogeographic, and functional analyses of a previously unrecognized RepL-type plasmid found in diverse members of the marine Roseobacter group across the globe. Noteworthy, 100% identical plasmids were detected in phylogenetically and geographically distant bacteria, revealing a so-far overlooked, but environmentally highly relevant vector for HGT. The genomic and functional characterization of this plasmid showed a completely conserved backbone dedicated to replication, stability, and mobilization as well as an interchangeable gene cassette with highly diverse, but recurring motifs. The majority of the latter appear to be involved in mechanisms coping with toxins and/or pollutants in the marine environment. Furthermore, we provide experimental evidence that the plasmid has the potential to be transmitted across bacterial orders, thereby increasing our understanding of evolution and microbial niche adaptation in the environment.}, }
@article {pmid31547186, year = {2019}, author = {Messal, M and Slippers, B and Naidoo, S and Bezuidt, O and Kemler, M}, title = {Active Fungal Communities in Asymptomatic Eucalyptus grandis Stems Differ between a Susceptible and Resistant Clone.}, journal = {Microorganisms}, volume = {7}, number = {10}, pages = {}, pmid = {31547186}, issn = {2076-2607}, abstract = {Fungi represent a common and diverse part of the microbial communities that associate with plants. They also commonly colonise various plant parts asymptomatically. The molecular mechanisms of these interactions are, however, poorly understood. In this study we use transcriptomic data from Eucalyptus grandis, to demonstrate that RNA-seq data are a neglected source of information to study fungal-host interactions, by exploring the fungal transcripts they inevitably contain. We identified fungal transcripts from E. grandis data based on their sequence dissimilarity to the E. grandis genome and predicted biological functions. Taxonomic classifications identified, amongst other fungi, many well-known pathogenic fungal taxa in the asymptomatic tissue of E. grandis. The comparison of a clone of E. grandis resistant to Chrysoporthe austroafricana with a susceptible clone revealed a significant difference in the number of fungal transcripts, while the number of fungal taxa was not substantially affected. Classifications of transcripts based on their respective biological functions showed that the fungal communities of the two E. grandis clones associate with fundamental biological processes, with some notable differences. To shield the greater host defence machinery in the resistant E. grandis clone, fungi produce more secondary metabolites, whereas the environment for fungi associated with the susceptible E. grandis clone is more conducive for building fungal cellular structures and biomass growth. Secreted proteins included carbohydrate active enzymes that potentially are involved in fungal-plant and fungal-microbe interactions. While plant transcriptome datasets cannot replace the need for designed experiments to probe plant-microbe interactions at a molecular level, they clearly hold potential to add to the understanding of the diversity of plant-microbe interactions.}, }
@article {pmid31547035, year = {2019}, author = {Wang, J and Sun, Y and Tao, D and Wang, S and Li, C and Zheng, F and Wu, Z}, title = {Reduction of Escherichia coli O157:H7, Listeria monocytogenes, and Naturally Present Microbe Counts on Lettuce using an Acid Mixture of Acetic and Lactic Acid.}, journal = {Microorganisms}, volume = {7}, number = {10}, pages = {}, pmid = {31547035}, issn = {2076-2607}, abstract = {Lactic acid (LA) and acetic acid (AA) are independently used to disinfect fresh leaf vegetables. LA has a higher efficacy but costs more than AA. Herein, we compared the disinfection efficacy of LA, AA, and their mixture on lettuce to determine whether the cheaper acid mixture shows similar or more efficacy than LA. Quality analysis indicated that the acid mixture and individual acids did not cause additional loss of instrument color and polyphenolic content compared with that of the control; however, visible defects were observed at AA concentrations exceeding 0.8%. Analysis of Escherichia coli O157:H7, Listeria monocytogenes, and naturally present microbes (aerobic mesophilic and psychrotrophic bacteria, coliforms, molds, and yeasts) showed that the acid mixture led to the highest reduction in microbial count during storage. 16S rRNA sequencing was further employed to understand the effects of the acid mixture and individual acids on lettuce microbial ecology. During storage, the acid mixture and individual acids significantly decreased the abundance of Massilia spp. and Alkanindiges spp. but there was a marked increase in Escherichia-Shigella abundance (LA: 0.003-58.82%; AA: 0.01-55.34%; acid mixture: undetected to 50.71%; control: 0.007-33.09%), indicating that acid disinfection altered the microbial ecology to stimulate Escherichia-Shigella growth. These results enhance our understanding of the relationship between lettuce disinfection and ecological changes.}, }
@article {pmid31546184, year = {2020}, author = {Pietro-Souza, W and de Campos Pereira, F and Mello, IS and Stachack, FFF and Terezo, AJ and Cunha, CND and White, JF and Li, H and Soares, MA}, title = {Mercury resistance and bioremediation mediated by endophytic fungi.}, journal = {Chemosphere}, volume = {240}, number = {}, pages = {124874}, doi = {10.1016/j.chemosphere.2019.124874}, pmid = {31546184}, issn = {1879-1298}, mesh = {*Biodegradation, Environmental ; Fungi/*chemistry ; Mercury/*chemistry ; }, abstract = {The present study proposes the use of endophytic fungi for mercury bioremediation in in vitro and host-associated systems. We examined mercury resistance in 32 strains of endophytic fungi grown in culture medium supplemented with toxic metal concentrations. The residual mercury concentrations were quantified after mycelial growth. Aspergillus sp. A31, Curvularia geniculata P1, Lindgomycetaceae P87, and Westerdykella sp. P71 were selected and further tested for mercury bioremediation and bioaccumulation in vitro, as well as for growth promotion of Aeschynomene fluminensis and Zea mays in the presence or absence of the metal. Aspergillus sp. A31, C. geniculata P1, Lindgomycetaceae P87 and Westerdykella sp. P71 removed up to 100% of mercury from the culture medium in a species-dependent manner and they promoted A. fluminensis and Z. mays growth in substrates containing mercury or not (Dunnett's test, p < 0.05). Lindgomycetaceae P87 and C. geniculata P1 are dark septate endophytic fungi that endophytically colonize root cells of their host plants. The increase of host biomass correlated with the reduction of soil mercury concentration due to the metal bioaccumulation in host tissues and its possible volatilization. The soil mercury concentration was decreased by 7.69% and 57.14% in A. fluminensis plants inoculated with Lindgomycetaceae P87 + Aspergillus sp. A31 and Lindgomycetaceae P87, respectively (Dunnet's test, p < 0.05). The resistance mechanisms of mercury volatilization and bioaccumulation in plant tissues mediated by these endophytic fungi can contribute to bioremediation programs. The biochemical and genetic mechanisms involved in bioaccumulation and volatilization need to be elucidated in the future.}, }
@article {pmid31546029, year = {2019}, author = {Pikaar, I and Flugen, M and Lin, HW and Salehin, S and Li, J and Donose, BC and Dennis, PG and Bethke, L and Johnson, I and Rabaey, K and Yuan, Z}, title = {Full-scale investigation of in-situ iron and alkalinity generation for efficient sulfide control.}, journal = {Water research}, volume = {167}, number = {}, pages = {115032}, doi = {10.1016/j.watres.2019.115032}, pmid = {31546029}, issn = {1879-2448}, mesh = {*Hydrogen Sulfide ; *Iron ; Sewage ; Sulfides ; Wastewater ; }, abstract = {Hydrogen sulfide induced corrosion of concrete sewer pipes is a major issue for wastewater utilities globally. One of the most commonly used methods to combat hydrogen sulfide is the addition of ferric chloride. While a reliable and effective method, ferric chloride is acidic causing OH&amp;S concerns as well as alkalinity consumption in sewage. This study investigates, under full-scale field conditions, an alternative method for sulfide control by in-situ electrochemical generation of iron ions using sacrificial iron electrodes. This method concomitantly produces alkalinity through cathodic OH[-] generation, rather than consumption. The gaseous hydrogen sulfide concentrations at the discharge wet well of a real-life rising main (length: ∼1 km in, diameter: 150 mm) decreased from 173 ppm to 43 ppm (90 percentile of peak values), when a current of 0.86 A/m[3] of sewage was applied. The 90 percentile peak H2S value was further reduced to 6.6 ppm when the applied current was increased to 1.14 A/m[3] sewage. Moreover, methane generation was almost completely inhibited from 25.3 ± 1.46 mg COD/L to 0.06 ± 0.04 mg COD/L. The overall cell voltage remained constant throughout the experimental period clearly showing the stability of the process. Detailed characterization of the down-stream sewer pipe biofilm revealed the complexity of the iron chemistry as the in-situ produced iron ions undergo transformation into a variety of iron species. Overall, this study demonstrates that in-situ generation of iron and alkalinity is an effective alternative method for hydrogen sulfide control in sewers.}, }
@article {pmid31545283, year = {2019}, author = {Huang, X and Chen, W and Yan, C and Yang, R and Chen, Q and Xu, H and Huang, Y}, title = {Gypenosides improve the intestinal microbiota of non-alcoholic fatty liver in mice and alleviate its progression.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {118}, number = {}, pages = {109258}, doi = {10.1016/j.biopha.2019.109258}, pmid = {31545283}, issn = {1950-6007}, mesh = {Animals ; Biodiversity ; Body Weight/drug effects ; Diet, High-Fat ; *Disease Progression ; Down-Regulation/drug effects ; Gastrointestinal Microbiome/*drug effects ; Gynostemma/chemistry ; Hyperlipidemias/complications/drug therapy ; Insulin Resistance ; Intestines/drug effects/pathology ; Lipid Metabolism/drug effects ; Liver/drug effects/pathology ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/blood/complications/*drug therapy/*microbiology ; Organ Size/drug effects ; Plant Extracts/chemistry/pharmacology/therapeutic use ; }, abstract = {Gypenosides (GP) are a type of traditional Chinese medicine (TCM) extracted from plants and commonly applied for treatment of metabolic diseases. This study aims to explore the effects of GP extracts on alleviating non-alcoholic fatty liver disease (NAFLD). In this experiment, C57BL/6 J mice were randomly assigned into normal diet control (ND), HFHC (high-fat and high-cholesterol) and HFHC + GP (GP) groups. Mice in HFHC group were fed HFHC diet combined with fructose drinking water for 12 weeks to induce the animal model of NAFLD, followed by ordinary drinking water until the end of the experiment. In the HFHC + GP group, mice were fed HFHC diet combined with fructose drinking water for 12 weeks, followed by GP-containing drinking water till the end. Mouse body weight was measured weekly. After animal procedures, mouse liver and serum samples were collected. It is shown that GP administration reduced body weight, enhanced the sensitivity to insulin resistance (IR) and decreased serum levels of ALT, AST and TG in NAFLD mice. In addition, GP treatment alleviated steatohepatitis, and downregulated ACC1, PPARγ, CD36, APOC3 and MTTP levels in mice fed with HFHC diet. Furthermore, GP treatment markedly improved intestinal microbiota, and reduced relative abundance ratio of Firmicutes / Bacteroidetes in the feces of NAFLD mice. Our results suggested that GP alleviated NAFLD in mice through improving intestinal microbiota.}, }
@article {pmid31543873, year = {2019}, author = {Alviz-Gazitua, P and Fuentes-Alburquenque, S and Rojas, LA and Turner, RJ and Guiliani, N and Seeger, M}, title = {Corrigendum: The Response of Cupriavidus metallidurans CH34 to Cadmium Involves Inhibition of the Initiation of Biofilm Formation, Decrease in Intracellular c-di-GMP Levels, and a Novel Metal Regulated Phosphodiesterase.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2014}, doi = {10.3389/fmicb.2019.02014}, pmid = {31543873}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2019.01499.].}, }
@article {pmid31541814, year = {2019}, author = {Petrin, S and Patuzzi, I and Di Cesare, A and Tiengo, A and Sette, G and Biancotto, G and Corno, G and Drigo, M and Losasso, C and Cibin, V}, title = {Evaluation and quantification of antimicrobial residues and antimicrobial resistance genes in two Italian swine farms.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {255}, number = {Pt 1}, pages = {113183}, doi = {10.1016/j.envpol.2019.113183}, pmid = {31541814}, issn = {1873-6424}, mesh = {Agriculture ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics ; Drug Resistance, Bacterial/*genetics ; Feces/chemistry ; Female ; *Genes, Bacterial ; Italy ; Male ; Manure/microbiology ; Plasmids ; Swine/*microbiology ; }, abstract = {Antimicrobial resistance genes (ARGs) are considered emerging environmental pollutants, posing potential risks for human and animal health: the misuse of antimicrobials in food-producing animals could favour the maintenance and spread of resistances in bacteria. The occurrence of ARGs in Italian swine farming - which has specific characteristics - was investigated in order to explore resistance spread dynamics. Two farrow-to-finish pig farms were longitudinally monitored: faecal samples from animals and environmental samples were collected. DNA was extracted and tetA, ermB, qnrS and mcr1 ARGs were analysed by qPCR for their ability to confer resistance to highly or critically important antimicrobials (CIAs). Moreover, 16SrDNA gene was analysed to assess bacterial abundance. ermB and tetA genes were found in animal samples and manure samples. On the contrary, mcr1 was exclusively found in weaners, while qnrS occurred in all animal categories but sows and finishers. Among the analysed genes, ermB and tetA showed the highest absolute and relative abundances. Our results indicate that ermB and tetA ARGs are widely disseminated in the explored farms, suggesting efficient maintenance among bacteria and persistence in the environment. Interestingly, the presence of qnrS and mcr1, limited to just a few animal categories, highlights inefficient dissemination of these genes in the farm environment, in particular for mcr1, a stable plasmid gene conferring resistance to the last-resort antimicrobial, colistin. Paying close attention only to the finishing phase would have hampered the discovery of resistances to CIAs at farm level, which we instead identified thanks to an intensive longitudinal monitoring programme.}, }
@article {pmid31539855, year = {2019}, author = {Santos-Clotas, E and Cabrera-Codony, A and Boada, E and Gich, F and Muñoz, R and Martín, MJ}, title = {Efficient removal of siloxanes and volatile organic compounds from sewage biogas by an anoxic biotrickling filter supplemented with activated carbon.}, journal = {Bioresource technology}, volume = {294}, number = {}, pages = {122136}, doi = {10.1016/j.biortech.2019.122136}, pmid = {31539855}, issn = {1873-2976}, mesh = {*Biofuels ; Bioreactors ; Charcoal ; Filtration ; Sewage ; Siloxanes ; *Volatile Organic Compounds ; }, abstract = {The removal of siloxanes (D4 and D5) and volatile organic contaminants (hexane, toluene and limonene) typically found in sewage biogas was investigated in a lab-scale biotrickling filter (BTF) packed with lava rock under anoxic conditions. Complete removal efficiencies for toluene and limonene were recorded at all empty bed residence time (EBRT) tested. The influence of EBRT was remarkable on the abatement of D5, whose removal decreased from 37% at 14.5 min to 16% at 4 min, while the removal of D4 and hexane remained below 16%. The packing material was supplemented with 20% of activated carbon aiming at increasing the mass transfer of the most hydrophobic pollutants. This strategy supported high removal efficiencies of 43 and 45% for hexane and D5 at the lowest EBRT. CO2 and silica were identified as mineralization products along with the presence of metabolites in the trickling solution such as dimethylsilanediol, 2-carene and α-terpinene.}, }
@article {pmid31538807, year = {2019}, author = {Tomar, SL}, title = {Oral Health Effects of Tobacco Products: Science and Regulatory Policy.}, journal = {Advances in dental research}, volume = {30}, number = {1}, pages = {2-3}, doi = {10.1177/0022034519872481}, pmid = {31538807}, issn = {1544-0737}, support = {R13 FD006142/FD/FDA HHS/United States ; }, mesh = {*Health Policy ; Humans ; *Oral Health ; Science ; *Tobacco Products/legislation &amp; jurisprudence ; Tobacco Use Disorder ; }, }
@article {pmid31536878, year = {2019}, author = {Lambrecht, E and Van Coillie, E and Van Meervenne, E and Boon, N and Heyndrickx, M and Van de Wiele, T}, title = {Commensal E. coli rapidly transfer antibiotic resistance genes to human intestinal microbiota in the Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME).}, journal = {International journal of food microbiology}, volume = {311}, number = {}, pages = {108357}, doi = {10.1016/j.ijfoodmicro.2019.108357}, pmid = {31536878}, issn = {1879-3460}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Cefotaxime/pharmacology ; Chickens/microbiology ; *Computer Simulation ; Conjugation, Genetic/*genetics ; Drug Resistance, Bacterial/*genetics ; Ecosystem ; Escherichia coli/drug effects/*genetics ; Gastrointestinal Microbiome/drug effects/genetics ; Gene Transfer, Horizontal/*genetics ; Humans ; Intestinal Mucosa/*microbiology ; Intestines/microbiology ; Plasmids/genetics ; }, abstract = {Food-producing animals are indicated as a reservoir of antibiotic resistance genes and a potential vector for transmission of plasmid-encoded antibiotic resistance genes by conjugation to the human intestinal microbiota. In this study, transfer of an antibiotic resistance plasmid from a commensal E. coli originating from a broiler chicken towards the human intestinal microbiota was assessed by using a Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME). This in vitro model mimics the human intestinal ecosystem and received a single dose of 10[9]E. coli MB6212, which harbors a plasmid known to confer resistance towards several antibiotics including tetracycline, sulfamethoxazole and cefotaxime. Since the degree of stress imposed by stomach pH and bile acids vary with the consumed meal size, the effect of meal size on E. coli donor survival and on plasmid transfer towards lumen and mucosal coliforms and anaerobes was determined. The administered commensal E. coli strain survived stomach acid and bile salt stress and was able to grow in the colon environment during the timeframe of the experiment (72 h). Transfer of antibiotic resistance was observed rapidly since cultivable transconjugant coliforms and anaerobes were already detected in the lumen and mucosa after 2 h in the simulated proximal colon. The presence of the resistance plasmid in the transconjugants was confirmed by PCR. Differences in meal size and adapted digestion had neither a detectable impact on antibiotic resistance transfer, nor on the survival of the E. coli donor strain, nor on short chain fatty acid profiles. The median number of resistant indigenous coliforms in the lumen of the inoculated colon vessels was 5.00 × 10[5] cfu/ml [min - max: 3.47 × 10[4]-3.70 × 10[8] cfu/ml], and on the mucosa 1.44 × 10[7] cfu/g [min-max: 4.00 × 10[3]-4.00 × 10[8] cfu/g]. Exact quantification of the anaerobic transconjugants was difficult, as (intrinsic) resistant anaerobic background microbiota were present. QPCR data supported the observation of plasmid transfer in the simulated colon. Moreover, inoculation of E. coli MB6212 had no significant impact on the microbial diversity in the lumen as determined by 16 S ribosomal gene based next generation sequencing on lumen samples. This study demonstrates that a commensal, antibiotic resistant E. coli strain present in food can transfer its antibiotic resistance plasmid relatively quickly to intestinal microbiota in the M-SHIME. The spread and persistence of antibiotic resistance genes and resistant bacteria in our intestinal system is an alarming scenario which might present clinical challenges, since it implies a potential reservoir for dissemination to pathogenic bacteria.}, }
@article {pmid31535335, year = {2020}, author = {Contador, CA and Veas-Castillo, L and Tapia, E and Antipán, M and Miranda, N and Ruiz-Tagle, B and García-Araya, J and Andrews, BA and Marin, M and Dorador, C and Asenjo, JA}, title = {Atacama Database: a platform of the microbiome of the Atacama Desert.}, journal = {Antonie van Leeuwenhoek}, volume = {113}, number = {2}, pages = {185-195}, doi = {10.1007/s10482-019-01328-x}, pmid = {31535335}, issn = {1572-9699}, support = {FB0001//Comisi&#xf3;n Nacional de Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; }, mesh = {Archaea/genetics/physiology ; Bacteria/genetics ; Biotechnology ; *Databases, Factual ; Desert Climate ; Microbiota/physiology ; Soil Microbiology ; }, abstract = {The Atacama Desert is one of the oldest and driest places on Earth. In the last decade, microbial richness and diversity has been acknowledged as an important biological resource of this region. Owing to the value of the microbial diversity apparent in potential biotechnology applications and conservation purposes, it is necessary to catalogue these microbial communities to promote research activities and help to preserve the wide range of ecological niches of the Atacama region. A prototype Atacama Database has been designed and it provides a description of the rich microbial diversity of the Atacama Desert, and helps to visualise available literature resources. Data has been collected, curated, and organised into several categories to generate a single record for each organism in the database that covers classification, isolation metadata, morphology, physiology, genome and metabolism information. The current version of Atacama Database contains 2302 microorganisms and includes cultured and uncultured organisms retrieved from different environments within the desert between 1984 and 2016. These organisms are distributed in bacterial, archaeal or eukaryotic domains, along with those that are unclassified taxonomically. The initial prototype of the Atacama Database includes a basic search and taxonomic and advanced search tools to allow identification and comparison of microbial populations, and space distribution within this biome. A geolocation search was implemented to visualise the microbial diversity of the ecological niches defined by sectors and extract general information of the sampling sites. This effort will aid understanding of the microbial ecology of the desert, microbial population dynamics, seasonal behaviour, impact of climate change over time, and reveal further biotechnological applications of these microorganisms. The Atacama Database is freely available at: https://www.atacamadb.cl.}, }
@article {pmid31534146, year = {2019}, author = {Harkes, P and Suleiman, AKA and van den Elsen, SJJ and de Haan, JJ and Holterman, M and Kuramae, EE and Helder, J}, title = {Conventional and organic soil management as divergent drivers of resident and active fractions of major soil food web constituents.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13521}, pmid = {31534146}, issn = {2045-2322}, mesh = {Agriculture/*methods ; Bacteria/genetics ; Biodiversity ; Carbon Cycle ; Ecosystem ; Eukaryota ; Fertilizers/*analysis ; Food Chain ; Fungi/genetics ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {Conventional agricultural production systems, typified by large inputs of mineral fertilizers and pesticides, reduce soil biodiversity and may negatively affect ecosystem services such as carbon fixation, nutrient cycling and disease suppressiveness. Organic soil management is thought to contribute to a more diverse and stable soil food web, but data detailing this effect are sparse and fragmented. We set out to map both the resident (rDNA) and the active (rRNA) fractions of bacterial, fungal, protozoan and metazoan communities under various soil management regimes in two distinct soil types with barley as the main crop. Contrasts between resident and active communities explained 22%, 14%, 21% and 25% of the variance within the bacterial, fungal, protozoan, and metazoan communities. As the active fractions of organismal groups define the actual ecological functioning of soils, our findings underline the relevance of characterizing both resident and active pools. All four major organismal groups were affected by soil management (p < 0.01), and most taxa showed both an increased presence and an enlarged activity under the organic regime. Hence, a prolonged organic soil management not only impacts the primary decomposers, bacteria and fungi, but also major representatives of the next trophic level, protists and metazoa.}, }
@article {pmid31533344, year = {2019}, author = {Zwart, MP and Ali, G and Strien, EAV and Schijlen, EGWM and Wang, M and Werf, WV and Vlak, JM}, title = {Identification of Loci Associated with Enhanced Virulence in Spodoptera litura Nucleopolyhedrovirus Isolates Using Deep Sequencing.}, journal = {Viruses}, volume = {11}, number = {9}, pages = {}, pmid = {31533344}, issn = {1999-4915}, mesh = {Animals ; China ; Genetic Loci/*genetics ; High-Throughput Nucleotide Sequencing ; Nucleopolyhedroviruses/*genetics/pathogenicity ; Open Reading Frames ; Pakistan ; Pest Control, Biological ; Spodoptera/*virology ; *Virulence ; }, abstract = {Spodoptera litura is an emerging pest insect in cotton and arable crops in Central Asia. To explore the possibility of using baculoviruses as biological control agents instead of chemical pesticides, in a previous study we characterized a number of S. litura nucleopolyhedrovirus (SpltNPV) isolates from Pakistan. We found significant differences in speed of kill, an important property of a biological control agent. Here we set out to understand the genetic basis of these differences in speed of kill, by comparing the genome of the fast-killing SpltNPV-Pak-TAX1 isolate with that of the slow-killing SpltNPV-Pak-BNG isolate. These two isolates and the SpltNPV-G2 reference strain from China were deep sequenced with Illumina. As expected, the two Pakistani isolates were closely related with >99% sequence identity, whereas the Chinese isolate was more distantly related. We identified two loci that may be associated with the fast action of the SpltNPV-Pak-TAX1 isolate. First, an analysis of rates of synonymous and non-synonymous mutations identified neutral to positive selection on open reading frame (ORF) 122, encoding a viral fibroblast growth factor (vFGF) that is known to affect virulence in other baculoviruses. Second, the homologous repeat region hr17, a putative enhancer of transcription and origin of replication, is absent in SpltNPV-Pak-TAX1 suggesting it may also affect virulence. Additionally, we found there is little genetic variation within both Pakistani isolates, and we identified four genes under positive selection in both isolates that may have played a role in adaptation of SpltNPV to conditions in Central Asia. Our results contribute to the understanding of the enhanced activity of SpltNPV-Pak-TAX1, and may help to select better SpltNPV isolates for the control of S. litura in Pakistan and elsewhere.}, }
@article {pmid31528722, year = {2019}, author = {Tiwari, UP and Singh, AK and Jha, R}, title = {Fermentation characteristics of resistant starch, arabinoxylan, and β-glucan and their effects on the gut microbial ecology of pigs: A review.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {5}, number = {3}, pages = {217-226}, pmid = {31528722}, issn = {2405-6383}, abstract = {Dietary fibers (DF) contain an abundant amount of energy, although the mammalian genome does not encode most of the enzymes required to degrade them. However, a mutual dependence is developed between the host and symbiotic microbes, which has the potential to extract the energy present in these DF. Dietary fibers escape digestion in the foregut and are fermented in the hindgut, producing short-chain fatty acids (SCFA) that alter the microbial ecology in the gastrointestinal tract (GIT) of pigs. Most of the carbohydrates are fermented in the proximal part, allowing protein fermentation in the distal part, resulting in colonic diseases. The structures of resistant starch (RS), arabinoxylan (AX), and β-glucan (βG) are complex; hence, makes their way into the hindgut where these are fermented and provide energy substrates for the colonic epithelial cells. Different microbes have different preferences of binding to different substrates. The RS, AX and βG act as a unique substrate for the microbes and modify the relative composition of the gut microbial community. The granule dimension and surface area of each substrate are different, which influences the penetration capacity of microbes. Arabinose and xylan are 2 different hemicelluloses, but arabinose is substituted on the xylan backbone and occurs in the form of AX. Fermentation of xylan produces butyrate primarily in the small intestine, whereas arabinose produces butyrate in the large intestine. Types of RS and forms of βG also exert beneficial effects by producing different metabolites and modulating the intestinal microbiota. Therefore, it is important to have information of different types of RS, AX and βG and their roles in microbial modulation to get the optimum benefits of fiber fermentation in the gut. This review provides relevant information on the similarities and differences that exist in the way RS, AX, and βG are fermented, and their positive and negative effects on SCFA production and gut microbial ecology of pigs. These insights will help nutritionists to develop dietary strategies that can modulate specific SCFA production and promote beneficial microbiota in the GIT of swine.}, }
@article {pmid31527408, year = {2019}, author = {Connor, R and Brister, R and Buchmann, JP and Deboutte, W and Edwards, R and Martí-Carreras, J and Tisza, M and Zalunin, V and Andrade-Martínez, J and Cantu, A and D'Amour, M and Efremov, A and Fleischmann, L and Forero-Junco, L and Garmaeva, S and Giluso, M and Glickman, C and Henderson, M and Kellman, B and Kristensen, D and Leubsdorf, C and Levi, K and Levi, S and Pakala, S and Peddu, V and Ponsero, A and Ribeiro, E and Roy, F and Rutter, L and Saha, S and Shakya, M and Shean, R and Miller, M and Tully, B and Turkington, C and Youens-Clark, K and Vanmechelen, B and Busby, B}, title = {NCBI's Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements.}, journal = {Genes}, volume = {10}, number = {9}, pages = {}, pmid = {31527408}, issn = {2073-4425}, support = {R35 CA220523/CA/NCI NIH HHS/United States ; }, mesh = {Big Data ; Cloud Computing/*standards ; Genome, Human ; *Genome, Viral ; Humans ; *Metagenome ; Metagenomics/*methods/standards ; Software ; }, abstract = {A wealth of viral data sits untapped in publicly available metagenomic data sets when it might be extracted to create a usable index for the virological research community. We hypothesized that work of this complexity and scale could be done in a hackathon setting. Ten teams comprised of over 40 participants from six countries, assembled to create a crowd-sourced set of analysis and processing pipelines for a complex biological data set in a three-day event on the San Diego State University campus starting 9 January 2019. Prior to the hackathon, 141,676 metagenomic data sets from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) were pre-assembled into contiguous assemblies (contigs) by NCBI staff. During the hackathon, a subset consisting of 2953 SRA data sets (approximately 55 million contigs) was selected, which were further filtered for a minimal length of 1 kb. This resulted in 4.2 million (Mio) contigs, which were aligned using BLAST against all known virus genomes, phylogenetically clustered and assigned metadata. Out of the 4.2 Mio contigs, 360,000 contigs were labeled with domains and an additional subset containing 4400 contigs was screened for virus or virus-like genes. The work yielded valuable insights into both SRA data and the cloud infrastructure required to support such efforts, revealing analysis bottlenecks and possible workarounds thereof. Mainly: (i) Conservative assemblies of SRA data improves initial analysis steps; (ii) existing bioinformatic software with weak multithreading/multicore support can be elevated by wrapper scripts to use all cores within a computing node; (iii) redesigning existing bioinformatic algorithms for a cloud infrastructure to facilitate its use for a wider audience; and (iv) a cloud infrastructure allows a diverse group of researchers to collaborate effectively. The scientific findings will be extended during a follow-up event. Here, we present the applied workflows, initial results, and lessons learned from the hackathon.}, }
@article {pmid31526457, year = {2019}, author = {de Los Santos Villalobos, S and Robles, RI and Parra Cota, FI and Larsen, J and Lozano, P and Tiedje, JM}, title = {Bacillus cabrialesii sp. nov., an endophytic plant growth promoting bacterium isolated from wheat (Triticum turgidum subsp. durum) in the Yaqui Valley, Mexico.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {69}, number = {12}, pages = {3939-3945}, doi = {10.1099/ijsem.0.003711}, pmid = {31526457}, issn = {1466-5034}, mesh = {Bacillus/*classification/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Endophytes/classification/isolation &amp; purification ; Fatty Acids/chemistry ; Mexico ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Triticum/*microbiology ; }, abstract = {Strain TE3[T], an endophytic plant growth promoting bacterium, was isolated from wheat (Triticumturgidum subsp. durum) sampled in the Yaqui Valley, Mexico. Biochemical, phenotypic and genotypic approaches were used to clarify the taxonomic affiliation of this strain. Based on analysis of its full-length 16S rRNA gene, strain TE3[T] was assigned to the genus Bacillus (similarity ≥98.7 %). This finding was supported by morphological and metabolic characteristics, such as rod shape, strictly aerobic metabolism, spore formation, Gram-positive staining, catalase-positive activity, reduction of nitrate to nitrite, starch and casein hydrolysis, growth in presence of lysozyme and 2 % NaCl, citrate utilization, growth pH from 6.0 to 8.0, and acid and indole production from glucose and tryptophan, respectively. The whole-genome phylogenetic relationship showed that TE3[T] formed an individual clade with Bacillus tequilensis KCTC 13622[T], distant from that generated by all Bacillus subtilis subspecies. The maximum values for average nucleotide identity and in silico DNA-DNA hybridization were 93.85 and 54.30 %, respectively, related to Bacillus subtilissubsp. inaquosorum KCTC 13429[T]. Analysis of its fatty acid content showed the ability of strain TE3[T] to bio-synthetize fatty acids that are not present in closely related Bacillus species, such as C12 : 0, C12 : 0 2OH, C12 : 0 3OH, C17 : 0, iso-C17 : 0 3OH and C18 : 1ω9c. These results provide evidence that strain TE3[T] is a novel species of the genus Bacillus, for which the name Bacilluscabrialesii sp. nov. is proposed. The type strain of Bacilluscabrialesii is TE3[T] (CM-CNRG TB54[T]=CCStamb A1[T]).}, }
@article {pmid31523442, year = {2019}, author = {Koga, Y and Ohtsu, T and Kimura, K and Asami, Y}, title = {Probiotic L. gasseri strain (LG21) for the upper gastrointestinal tract acting through improvement of indigenous microbiota.}, journal = {BMJ open gastroenterology}, volume = {6}, number = {1}, pages = {e000314}, pmid = {31523442}, issn = {2054-4774}, abstract = {OBJECTIVE: To describe probiotics including a Lactobacillus gasseri strain LG21 used for the upper gastrointestinal tract, which are considered to act through improvement of indigenous microbiota inhabiting there.<br><br>BACKGROUND AND DESIGN: Because the early definition of probiotics emphasized their effects on improving the intestinal microbial ecology, their effects on the intestinal tract and its immunity have been considered common general benefits associated with probiotics. This conclusion was also based on a body of successful clinical trials whose endpoints were the prevention or treatment of intestinal diseases. In contrast to intestinal microbiota, our understanding of the role of gastric microbiota in human health and physiology remains poor, as the bacterial load in the stomach is considered too small to exert a significant effect due to the highly acidic environment of the human stomach. Therefore, the intervention using probiotics in the stomach is still limited at present.Results:In this article using representative 38 quoted articles, we first describe the gastric microbiota, as the indigenous microbiota in the stomach is thought to be significantly involved in the pathophysiology of this organ, since probiotics exert their beneficial effects through improving the resident microbiota. We then review the present status and future prospects of probiotics for the treatment of upper gastrointestinal diseases by quoting representative published articles, including our basic and clinical data.<br><br>CONCLUSIONS: Probiotics have been demonstrated to suppress Helicobacter pylori in the stomach, and are also expected to improve functional dyspepsia through the correction of dysbiotic gastric microbiota.}, }
@article {pmid31520875, year = {2019}, author = {Wichmann, S and Ardern, Z}, title = {Optimality in the standard genetic code is robust with respect to comparison code sets.}, journal = {Bio Systems}, volume = {185}, number = {}, pages = {104023}, doi = {10.1016/j.biosystems.2019.104023}, pmid = {31520875}, issn = {1872-8324}, mesh = {Algorithms ; Amino Acids/*genetics ; Codon/*genetics ; Codon, Terminator/genetics ; Evolution, Molecular ; Genetic Code/*genetics ; Models, Genetic ; Mutation ; Open Reading Frames/*genetics ; Protein Biosynthesis ; Selection, Genetic ; }, abstract = {The genetic code and its evolution have been studied by many different approaches. One approach is to compare the properties of the standard genetic code (SGC) to theoretical alternative codes in order to determine how optimal it is and from this infer whether or not it is likely that it has undergone a selective evolutionary process. Many different properties have been studied in this way in the literature. Less focus has been put on the alternative code sets which are used as a comparison to the standard code. Each implicitly represents an evolutionary hypothesis and the sets used differ greatly across the literature. Here we determine the influence of the comparison set on the results of the optimality calculation by using codes based upon different sub-structures of the SGC. With these results we can generalize the results to different evolutionary hypotheses. We find that the SGC's optimality is very robust, as no code set with no optimised properties is found. We therefore conclude that the optimality of the SGC is a robust feature across all evolutionary hypotheses. Our results provide important information for any future studies on the evolution of the standard genetic code. We also studied properties of the SGC concerning overlapping genes, which have recently been found to be more widespread than often believed. Although our results are not conclusive yet we find additional intriguing structures in the SGC that need explanation.}, }
@article {pmid31518408, year = {2019}, author = {Bugge Harder, C and Nyrop Albers, C and Rosendahl, S and Aamand, J and Ellegaard-Jensen, L and Ekelund, F}, title = {Successional trophic complexity and biogeographical structure of eukaryotic communities in waterworks' rapid sand filters.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {11}, pages = {}, doi = {10.1093/femsec/fiz148}, pmid = {31518408}, issn = {1574-6941}, mesh = {Bacteria/isolation &amp; purification ; DNA Primers ; Denmark ; Eukaryota/classification/*isolation &amp; purification ; Filtration/*instrumentation ; Groundwater/*microbiology ; Humans ; *Microbiota ; Sand ; Water Purification ; }, abstract = {As groundwater-fed waterworks clean their raw inlet water with sand filters, a variety of pro- and eukaryotic microbial communities develop on these filters. While several studies have targeted the prokaryotic sand filter communities, little is known about the eukaryotic communities, despite the obvious need for knowledge of microorganisms that get in contact with human drinking water. With a new general eukaryotic primer set (18S, V1-V3 region), we performed FLX-454 sequencing of material from 21 waterworks' sand filters varying in age (3-40 years) and geographical location on a 250 km east-west axis in Denmark, and put the data in context of their previously published prokaryotic communities. We find that filters vary highly in trophic complexity depending on age, from simple systems with bacteria and protozoa (3-6 years) to complex, mature systems with nematodes, rotifers and turbellarians as apex predators (40 years). Unlike the bacterial communities, the eukaryotic communities display a clear distance-decay relationship that predominates over environmental variations, indicating that the underlying aquifers feeding the filters harbor distinct eukaryotic communities with limited dispersal in between. Our findings have implications for waterworks' filter management, and offer a window down to the largely unexplored eukaryotic microbiology of groundwater aquifers.}, }
@article {pmid31517286, year = {2019}, author = {Duysburgh, C and Van den Abbeele, P and Krishnan, K and Bayne, TF and Marzorati, M}, title = {A synbiotic concept containing spore-forming Bacillus strains and a prebiotic fiber blend consistently enhanced metabolic activity by modulation of the gut microbiome in vitro.}, journal = {International journal of pharmaceutics: X}, volume = {1}, number = {}, pages = {100021}, pmid = {31517286}, issn = {2590-1567}, abstract = {A standardized in vitro simulation of the human gastrointestinal tract (M-SHIME®) was used to assess the effect of repeated daily administration of a synbiotic formulation, containing five spore-forming Bacillus strains and a prebiotic fiber blend, on the microbial activity and composition of three simulated human subjects. Firstly, while confirming recent findings, deeper phylogenetic insight was obtained in the resident M-SHIME® microbiota, demonstrating that the model maintains a diverse and representative, colon region-specific luminal and mucosal microbial community. Supplementation of the synbiotic concept increased microbial diversity in the distal colon areas, whereas specific enhancement of Bacillaceae levels was observed in the ascending colon suggesting a successful engraftment of the Bacillus spores, which probably resulted in a stimulatory effect on, among others, Bifidobacteriaceae, Lactobacillaceae, Prevotellaceae, Tannerellaceae and Faecalibacterium prausnitzii contributing directly or indirectly to stimulation of acetate, propionate and butyrate production. When compared with a previous study investigating the Bacillus strains, the generated data suggest a synergistic effect on the intestinal microbiota for the synbiotic formulation. Given the fact that the probiotic strains have been shown to impact post-prandial metabolic endotoxemia in human individuals, it might be interesting to further investigate the efficacy of the synbiotic concept in protecting against obesity-related disorders.}, }
@article {pmid31515652, year = {2020}, author = {Lee, HJ and Shin, SY and Whang, KS}, title = {Paenibacillus pinistramenti sp. nov., isolated from pine litter.}, journal = {Antonie van Leeuwenhoek}, volume = {113}, number = {2}, pages = {155-163}, doi = {10.1007/s10482-019-01325-0}, pmid = {31515652}, issn = {1572-9699}, mesh = {Base Composition/genetics/physiology ; DNA, Bacterial/metabolism ; Diaminopimelic Acid/metabolism ; Glycolipids/metabolism ; Hydrogen-Ion Concentration ; Paenibacillus/classification/*genetics ; Phosphatidylethanolamines/metabolism ; Phosphatidylglycerols/metabolism ; Phylogeny ; Sodium Chloride ; }, abstract = {A Gram-stain-positive bacterium, designated strain ASL46[T], was isolated from litter layer of a pine forest located in Anmyondo, Korea. Strain ASL46[T] was found to be an aerobic, motile, endospore-forming rod which can grow at 20-45 °C (optimum, 37 °C), at pH 6.0-11.0 (optimum, pH 7.0) and at salinities of 0-2% (w/v) NaCl (optimum, 1% NaCl). Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain ASL46[T] belongs to the genus Paenibacillus, showing highest sequence similarity to P. yonginensis DCY84[T] (98.3%), P. physcomitrella XB[T] (97.4%) and P. faecis CIP 101062[T] (96.6%). The average nucleotide identity (ANI) and DNA-DNA relatedness between the strain ASL46[T] and P. physcomitrella XB[T] and P. yonginensis DCY84[T] yielded ANI values of 84.6 and 84.5% and DNA-DNA relatedness of 11.7 ± 0.7 and 10.9 ± 0.2%, respectively. The DNA G+C content of the genomic DNA of strain ASL46[T] was 52.1 mol%. The predominant isoprenoid quinone was identified as menaquinone-7 and the major cellular fatty acids were determined to be anteiso-C15:0, C16:0 and iso-C16:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, five unidentified aminophospholipids, an unidentified phospholipid and an unidentified glycolipid. The whole-cell sugar was found to be ribose and cell wall peptidoglycan contained meso-diaminopimelic acid. On the basis of phylogenetic analyses, and phenotypic and chemotaxonomic characteristics, strain ASL46[T] represents a novel species of the genus Paenibacillus, for which the name Paenibacillus pinistramenti sp. nov. is proposed. The type strain is ASL46[T] (= KACC 18701[T] = NBRC 111876[T]).}, }
@article {pmid31512011, year = {2020}, author = {Sekhohola-Dlamini, L and Tekere, M}, title = {Microbiology of municipal solid waste landfills: a review of microbial dynamics and ecological influences in waste bioprocessing.}, journal = {Biodegradation}, volume = {31}, number = {1-2}, pages = {1-21}, doi = {10.1007/s10532-019-09890-x}, pmid = {31512011}, issn = {1572-9729}, mesh = {Biodegradation, Environmental ; Ecosystem ; *Refuse Disposal ; Solid Waste/*analysis ; Waste Disposal Facilities ; }, abstract = {Municipal solid waste landfills are widely used as a waste management tool and landfill microbiology is at the core of waste degradation in these ecosystems. This review investigates the microbiology of municipal solid waste landfills, focusing on the current state of knowledge pertaining to microbial diversity and functions facilitating in situ waste bioprocessing, as well as ecological factors influencing microbial dynamics in landfills. Bioprocessing of waste in municipal landfills emanates from substrate metabolism and co-metabolism by several syntrophic microorganisms, resulting in partial transformation of complex substrates into simpler polymeric compounds and complete mineralisation into inorganic salts, water and gases including the biofuel gas methane. The substrate decomposition is characterised by evolution and interactions of different bacterial, archaeal and fungal groups due to prevailing biotic and abiotic conditions in the landfills, allowing for hydrolytic, fermentative, acetogenic and methanogenic processes to occur. Application of metagenomics studies based on high throughput Next Generation Sequencing technique has advanced research on profiling of the microbial communities in municipal solid waste landfills. However, functional diversity and bioprocess dynamics, as well as key factors influencing the in situ bioprocesses involved in landfill waste degradation; the very elements that are key in determining the efficiency of municipal landfills as tools of waste management, remain ambiguous. Such gaps also hinder progressive understanding of fundamentals that underlie technology development based on waste biodegradation, and exploration of municipal waste as a bioresource.}, }
@article {pmid31511911, year = {2020}, author = {Wang, L and Han, M and Li, X and Ginawi, A and Ning, K and Yan, Y}, title = {Niche and Neutrality Work Differently in Microbial Communities in Fluidic and Non-fluidic Ecosystems.}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {527-538}, pmid = {31511911}, issn = {1432-184X}, mesh = {Archaea/classification/genetics/*physiology ; Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; China ; *Ecosystem ; *Microbiota ; Models, Biological ; Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Rivers/*microbiology ; }, abstract = {This data-intensive study investigated the delicate balance of niche and neutrality underlying microbial communities in freshwater ecosystems through comprehensive application of high-throughput sequencing, species abundance distribution (SAD), and the neutral community model (NCM), combined with species diversity and phylogenetic measures, which unite the traditional and microbial ecology. On the genus level, 45.10% and 41.18% of the water samples could be explained by the log-normal and Volkov model respectively, among which 31.37% could fit both models. Meanwhile, 55.56% of the sediment samples could be depicted by the log-normal model, and Volkov-fitted samples comprised only 13.33%. Besides, operational taxonomic units (OTUs) from water samples fit Sloan's neutral model significantly better than those in sediment. Therefore, it was concluded that deterministic processes played a great role in both water and sediment ecosystems, whereas neutrality was much more involved in water assemblages than in non-fluidic sediment ecosystems. Secondly, log-normal fitted samples had lower phylogenetic species variability (PSV) than Volkov-fitted ones, indicating that niche-based communities were more phylogenetically clustered than neutrally assembled counterparts. Additionally, further testing showed that the relative richness of rare species was vital to SAD modeling, either niche-based or neutral, and communities containing fewer rare species were more easily captured by theoretical SAD models.}, }
@article {pmid31511558, year = {2019}, author = {Makarchuk, S and Braz, VC and Araújo, NAM and Ciric, L and Volpe, G}, title = {Enhanced propagation of motile bacteria on surfaces due to forward scattering.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4110}, pmid = {31511558}, issn = {2041-1723}, mesh = {Computer Simulation ; Escherichia coli/*cytology ; Movement ; Probability ; Surface Properties ; }, abstract = {How motile bacteria move near a surface is a problem of fundamental biophysical interest and is key to the emergence of several phenomena of biological, ecological and medical relevance, including biofilm formation. Solid boundaries can strongly influence a cell's propulsion mechanism, thus leading many flagellated bacteria to describe long circular trajectories stably entrapped by the surface. Experimental studies on near-surface bacterial motility have, however, neglected the fact that real environments have typical microstructures varying on the scale of the cells' motion. Here, we show that micro-obstacles influence the propagation of peritrichously flagellated bacteria on a flat surface in a non-monotonic way. Instead of hindering it, an optimal, relatively low obstacle density can significantly enhance cells' propagation on surfaces due to individual forward-scattering events. This finding provides insight on the emerging dynamics of chiral active matter in complex environments and inspires possible routes to control microbial ecology in natural habitats.}, }
@article {pmid31507553, year = {2019}, author = {Durán-Viseras, A and Andrei, AS and Ghai, R and Sánchez-Porro, C and Ventosa, A}, title = {New Halonotius Species Provide Genomics-Based Insights Into Cobalamin Synthesis in Haloarchaea.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1928}, pmid = {31507553}, issn = {1664-302X}, abstract = {Hypersaline aquatic and terrestrial ecosystems display a cosmopolitan distribution. These environments teem with microbes and harbor a plethora of prokaryotic lineages that evaded ecological characterization due to the prior inability to cultivate them or to access their genomic information. In order to close the current knowledge gap, we performed two sampling and isolation campaigns in the saline soils of the Odiel Saltmarshes and the salterns of Isla Cristina (Huelva, Spain). From the isolated haloarchaeal strains subjected to high-throughput phylogenetic screening, two were chosen (F15B[T] and F9-27[T]) for physiological and genomic characterization due of their relatedness to the genus Halonotius. Comparative genomic analyses were carried out between the isolated strains and the genomes of previously described species Halonotius pteroides CECT 7525[T], Halonotius aquaticus F13-13[T] and environmentaly recovered metagenome-assembled representatives of the genus Halonotius. The topology of the phylogenomic tree showed agreement with the phylogenetic ones based on 16S rRNA and rpoB' genes, and together with average amino acid and nucleotide identities suggested the two strains as novel species within the genus. We propose the names Halonotius terrestris sp. nov. (type strain F15B[T] = CECT 9688[T] = CCM 8954[T]) and Halonotius roseus sp. nov. (type strain F9-27[T] = CECT 9745[T] = CCM 8956[T]) for these strains. Comparative genomic analyses within the genus highlighted a typical salt-in signature, characterized by acidic proteomes with low isoelectric points, and indicated heterotrophic aerobic lifestyles. Genome-scale metabolic reconstructions revealed that the newly proposed species encode all the necessary enzymatic reactions involved in cobalamin (vitamin B12) biosynthesis. Based on the worldwide distribution of the genus and its abundance in hypersaline habitats we postulate that its members perform a critical function by being able to provide "expensive" commodities (i.e., vitamin B12) to the halophilic microbial communities at large.}, }
@article {pmid31507541, year = {2019}, author = {Bates, KA and Shelton, JMG and Mercier, VL and Hopkins, KP and Harrison, XA and Petrovan, SO and Fisher, MC}, title = {Captivity and Infection by the Fungal Pathogen Batrachochytrium salamandrivorans Perturb the Amphibian Skin Microbiome.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1834}, pmid = {31507541}, issn = {1664-302X}, support = {MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {The emerging fungal pathogen, Batrachochytrium salamandrivorans (Bsal) is responsible for the catastrophic decline of European salamanders and poses a threat to amphibians globally. The amphibian skin microbiome can influence disease outcome for several host-pathogen systems, yet little is known of its role in Bsal infection. In addition, many experimental in-vivo amphibian disease studies to date have relied on specimens that have been kept in captivity for long periods without considering the influence of environment on the microbiome and how this may impact the host response to pathogen exposure. We characterized the impact of captivity and exposure to Bsal on the skin bacterial and fungal communities of two co-occurring European newt species, the smooth newt, Lissotriton vulgaris and the great-crested newt, Triturus cristatus. We show that captivity led to significant losses in bacterial and fungal diversity of amphibian skin, which may be indicative of a decline in microbe-mediated protection. We further demonstrate that in both L. vulgaris and T. cristatus, Bsal infection was associated with changes in the composition of skin bacterial communities with possible negative consequences to host health. Our findings advance current understanding of the role of host-associated microbiota in Bsal infection and highlight important considerations for ex-situ amphibian conservation programmes.}, }
@article {pmid31506821, year = {2019}, author = {Callejas, C and Fernández, A and Passeggi, M and Wenzel, J and Bovio, P and Borzacconi, L and Etchebehere, C}, title = {Microbiota adaptation after an alkaline pH perturbation in a full-scale UASB anaerobic reactor treating dairy wastewater.}, journal = {Bioprocess and biosystems engineering}, volume = {42}, number = {12}, pages = {2035-2046}, doi = {10.1007/s00449-019-02198-3}, pmid = {31506821}, issn = {1615-7605}, mesh = {Anaerobiosis ; Archaea/metabolism ; Bacteria, Anaerobic/classification ; Biofuels ; Bioreactors/*microbiology ; Clostridium/classification ; Dairying ; Euryarchaeota/metabolism ; Firmicutes/classification ; Hydrogen-Ion Concentration ; Methane/metabolism ; Microbiota ; Proteobacteria/classification ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; *Waste Disposal, Fluid ; Wastewater ; *Water Microbiology ; *Water Purification ; }, abstract = {The aim of this study was to understand how the microbial community adapted to changes, including a pH perturbation, occurring during the start-up and operation processes in a full-scale methanogenic UASB reactor designed to treat dairy wastewater. The reactor performance, prokaryotic community, and lipid degradation capacity were monitored over a 9-month period. The methanogenic community was studied by mcrA/mrtA gene copy-number quantification and methanogenic activity tests. A diverse prokaryotic community characterized the seeding sludge as assessed by sequencing the V4 region of the 16S rRNA gene. As the feeding began, the bacterial community was dominated by Firmicutes, Synergistetes, and Proteobacteria phyla. After an accidental pH increase that affected the microbial community structure, a sharp increase in the relative abundance of Clostridia and a decrease in the mcrA/mrtA gene copy number and methanogenic activity were observed. After a recovery period, the microbial population regained diversity and methanogenic activity. Alkaline shocks are likely to happen in dairy wastewater treatment because of the caustic soda usage. In this work, the plasticity of the prokaryotic community was key to surviving changes to the external environment and supporting biogas production in the reactor.}, }
@article {pmid31506760, year = {2020}, author = {Lamei, S and Stephan, JG and Nilson, B and Sieuwerts, S and Riesbeck, K and de Miranda, JR and Forsgren, E}, title = {Feeding Honeybee Colonies with Honeybee-Specific Lactic Acid Bacteria (Hbs-LAB) Does Not Affect Colony-Level Hbs-LAB Composition or Paenibacillus larvae Spore Levels, Although American Foulbrood Affected Colonies Harbor a More Diverse Hbs-LAB Community.}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {743-755}, pmid = {31506760}, issn = {1432-184X}, support = {222-2013-423//Svenska Forskningsr&#xe5;det Formas/ ; }, mesh = {Animal Feed/analysis ; Animals ; Bees/*microbiology ; Diet ; Lactobacillales/*chemistry ; Larva/microbiology ; *Microbiota ; Paenibacillus larvae/*physiology ; Spores, Bacterial/*physiology ; }, abstract = {The main current methods for controlling American Foulbrood (AFB) in honeybees, caused by the bacterial pathogen Paenibacillus larvae, are enforced incineration or prophylactic antibiotic treatment, neither of which is fully satisfactory. This has led to an increased interest in the natural relationships between the pathogenic and mutualistic microorganisms of the honeybee microbiome, in particular, the antagonistic effects of Honeybee-Specific Lactic Acid Bacteria (hbs-LAB) against P. larvae. We investigated whether supplemental administration of these bacteria affected P. larvae infection at colony level over an entire flowering season. Over the season, the supplements affected neither colony-level hbs-LAB composition nor naturally subclinical or clinical P. larvae spore levels. The composition of hbs-LAB in colonies was, however, more diverse in apiaries with a history of clinical AFB, although this was also unrelated to P. larvae spore levels. During the experiments, we also showed that qPCR could detect a wider range of hbs-LAB, with higher specificity and sensitivity than mass spectrometry. Honeybee colonies are complex super-organisms where social immune defenses, natural homeostatic mechanisms, and microbiome diversity and function play a major role in disease resistance. This means that observations made at the individual bee level cannot be simply extrapolated to infer similar effects at colony level. Although individual laboratory larval assays have clearly demonstrated the antagonistic effects of hbs-LAB on P. larvae infection, the results from the experiments presented here indicate that direct conversion of such practice to colony-level administration of live hbs-LAB is not effective.}, }
@article {pmid31506516, year = {2019}, author = {Bridier, A and Le Grandois, P and Moreau, MH and Prénom, C and Le Roux, A and Feurer, C and Soumet, C}, title = {Impact of cleaning and disinfection procedures on microbial ecology and Salmonella antimicrobial resistance in a pig slaughterhouse.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12947}, pmid = {31506516}, issn = {2045-2322}, mesh = {Abattoirs ; Animals ; Anti-Bacterial Agents/*pharmacology ; Disinfection/*methods ; *Drug Resistance, Bacterial ; Microbial Sensitivity Tests ; Salmonella/*drug effects ; Salmonella Infections, Animal/*drug therapy/epidemiology/microbiology ; Swine ; Swine Diseases/epidemiology/microbiology/*prevention &amp; control ; }, abstract = {To guarantee food safety, a better deciphering of ecology and adaptation strategies of bacterial pathogens such as Salmonella in food environments is crucial. The role of food processing conditions such as cleaning and disinfection procedures on antimicrobial resistance emergence should especially be investigated. In this work, the prevalence and antimicrobial resistance of Salmonella and the microbial ecology of associated surfaces communities were investigated in a pig slaughterhouse before and after cleaning and disinfection procedures. Salmonella were detected in 67% of samples and isolates characterization revealed the presence of 15 PFGE-patterns belonging to five serotypes: S.4,5,12:i:-, Rissen, Typhimurium, Infantis and Derby. Resistance to ampicillin, sulfamethoxazole, tetracycline and/or chloramphenicol was detected depending on serotypes. 16S rRNA-based bacterial diversity analyses showed that Salmonella surface associated communities were highly dominated by the Moraxellaceae family with a clear site-specific composition suggesting a persistent colonization of the pig slaughterhouse. Cleaning and disinfection procedures did not lead to a modification of Salmonella susceptibility to antimicrobials in this short-term study but they tended to significantly reduce bacterial diversity and favored some genera such as Rothia and Psychrobacter. Such data participate to the construction of a comprehensive view of Salmonella ecology and antimicrobial resistance emergence in food environments in relation with cleaning and disinfection procedures.}, }
@article {pmid31506265, year = {2019}, author = {Zhang, CJ and Pan, J and Duan, CH and Wang, YM and Liu, Y and Sun, J and Zhou, HC and Song, X and Li, M}, title = {Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes.}, journal = {mSystems}, volume = {4}, number = {5}, pages = {}, pmid = {31506265}, issn = {2379-5077}, abstract = {Mangroves, as a blue carbon reservoir, provide an environment for a variety of microorganisms. Mangroves lie in special locations connecting coastal and estuarine areas and experience fluctuating conditions, which are expected to intensify with climate change, creating a need to better understand the relative roles of stochastic and deterministic processes in shaping microbial community assembly. Here, a study of microbial communities inhabiting mangrove sediments across southeastern China, spanning mangroves in six nature reserves, was conducted. We performed high-throughput DNA sequencing of these samples and compared them with data of 1,370 sediment samples collected from the Earth Microbiome Project (EMP) to compare the microbial diversity of mangroves with that of other biomes. Our results showed that prokaryotic alpha diversity in mangroves was significantly higher than that in other biomes and that microbial beta diversity generally clustered according to biome types. The core operational taxonomic units (OTUs) in mangroves were mostly assigned to Gammaproteobacteria, Deltaproteobacteria, Chloroflexi, and Euryarchaeota The majority of beta nearest-taxon index values were higher than 2, indicating that community assembly in mangroves was better explained through a deterministic process than through a stochastic process. Mean annual precipitation (MAP) and total organic carbon (TOC) were main deterministic factors explaining variation in the microbial community. This study fills a gap in addressing the unique microbial diversity of mangrove ecosystems and their microbial community assembly mechanisms.IMPORTANCE Understanding the underlying mechanisms of microbial community assembly patterns is a vital issue in microbial ecology. Mangroves, as an important and special ecosystem, provide a unique environment for examining the relative importance of stochastic and deterministic processes. We made the first global-scale comparison and found that microbial diversity was significantly different in mangrove sediments compared to that of other biomes. Furthermore, our results suggest that a deterministic process is more important in shaping microbial community assembly in mangroves.}, }
@article {pmid31506264, year = {2019}, author = {Dumolin, C and Aerts, M and Verheyde, B and Schellaert, S and Vandamme, T and Van der Jeugt, F and De Canck, E and Cnockaert, M and Wieme, AD and Cleenwerck, I and Peiren, J and Dawyndt, P and Vandamme, P and Carlier, A}, title = {Introducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry Data.}, journal = {mSystems}, volume = {4}, number = {5}, pages = {}, pmid = {31506264}, issn = {2379-5077}, abstract = {The isolation of microorganisms from microbial community samples often yields a large number of conspecific isolates. Increasing the diversity covered by an isolate collection entails the implementation of methods and protocols to minimize the number of redundant isolates. Matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry methods are ideally suited to this dereplication problem because of their low cost and high throughput. However, the available software tools are cumbersome and rely either on the prior development of reference databases or on global similarity analyses, which are inconvenient and offer low taxonomic resolution. We introduce SPeDE, a user-friendly spectral data analysis tool for the dereplication of MALDI-TOF mass spectra. Rather than relying on global similarity approaches to classify spectra, SPeDE determines the number of unique spectral features by a mix of global and local peak comparisons. This approach allows the identification of a set of nonredundant spectra linked to operational isolation units. We evaluated SPeDE on a data set of 5,228 spectra representing 167 bacterial strains belonging to 132 genera across six phyla and on a data set of 312 spectra of 78 strains measured before and after lyophilization and subculturing. SPeDE was able to dereplicate with high efficiency by identifying redundant spectra while retrieving reference spectra for all strains in a sample. SPeDE can identify distinguishing features between spectra, and its performance exceeds that of established methods in speed and precision. SPeDE is open source under the MIT license and is available from https://github.com/LM-UGent/SPeDEIMPORTANCE Estimation of the operational isolation units present in a MALDI-TOF mass spectral data set involves an essential dereplication step to identify redundant spectra in a rapid manner and without sacrificing biological resolution. We describe SPeDE, a new algorithm which facilitates culture-dependent clinical or environmental studies. SPeDE enables the rapid analysis and dereplication of isolates, a critical feature when long-term storage of cultures is limited or not feasible. We show that SPeDE can efficiently identify sets of similar spectra at the level of the species or strain, exceeding the taxonomic resolution of other methods. The high-throughput capacity, speed, and low cost of MALDI-TOF mass spectrometry and SPeDE dereplication over traditional gene marker-based sequencing approaches should facilitate adoption of the culturomics approach to bacterial isolation campaigns.}, }
@article {pmid31506260, year = {2019}, author = {Rubbens, P and Schmidt, ML and Props, R and Biddanda, BA and Boon, N and Waegeman, W and Denef, VJ}, title = {Randomized Lasso Links Microbial Taxa with Aquatic Functional Groups Inferred from Flow Cytometry.}, journal = {mSystems}, volume = {4}, number = {5}, pages = {}, pmid = {31506260}, issn = {2379-5077}, abstract = {High-nucleic-acid (HNA) and low-nucleic-acid (LNA) bacteria are two operational groups identified by flow cytometry (FCM) in aquatic systems. A number of reports have shown that HNA cell density correlates strongly with heterotrophic production, while LNA cell density does not. However, which taxa are specifically associated with these groups, and by extension, productivity has remained elusive. Here, we addressed this knowledge gap by using a machine learning-based variable selection approach that integrated FCM and 16S rRNA gene sequencing data collected from 14 freshwater lakes spanning a broad range in physicochemical conditions. There was a strong association between bacterial heterotrophic production and HNA absolute cell abundances (R [2] = 0.65), but not with the more abundant LNA cells. This solidifies findings, mainly from marine systems, that HNA and LNA bacteria could be considered separate functional groups, the former contributing a disproportionately large share of carbon cycling. Taxa selected by the models could predict HNA and LNA absolute cell abundances at all taxonomic levels. Selected operational taxonomic units (OTUs) ranged from low to high relative abundance and were mostly lake system specific (89.5% to 99.2%). A subset of selected OTUs was associated with both LNA and HNA groups (12.5% to 33.3%), suggesting either phenotypic plasticity or within-OTU genetic and physiological heterogeneity. These findings may lead to the identification of system-specific putative ecological indicators for heterotrophic productivity. Generally, our approach allows for the association of OTUs with specific functional groups in diverse ecosystems in order to improve our understanding of (microbial) biodiversity-ecosystem functioning relationships.IMPORTANCE A major goal in microbial ecology is to understand how microbial community structure influences ecosystem functioning. Various methods to directly associate bacterial taxa to functional groups in the environment are being developed. In this study, we applied machine learning methods to relate taxonomic data obtained from marker gene surveys to functional groups identified by flow cytometry. This allowed us to identify the taxa that are associated with heterotrophic productivity in freshwater lakes and indicated that the key contributors were highly system specific, regularly rare members of the community, and that some could possibly switch between being low and high contributors. Our approach provides a promising framework to identify taxa that contribute to ecosystem functioning and can be further developed to explore microbial contributions beyond heterotrophic production.}, }
@article {pmid31504446, year = {2019}, author = {Blackwell, N and Perkins, W and Palumbo-Roe, B and Bearcock, J and Lloyd, JR and Edwards, A}, title = {Seasonal blooms of neutrophilic Betaproteobacterial Fe(II) oxidizers and Chlorobi in iron-rich coal mine drainage sediments.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {10}, pages = {}, doi = {10.1093/femsec/fiz140}, pmid = {31504446}, issn = {1574-6941}, mesh = {Betaproteobacteria/classification/genetics/isolation &amp; purification/*metabolism ; Chlorobi/genetics/isolation &amp; purification/*metabolism ; Coal/analysis ; Coal Mining ; Environmental Pollution ; Ferrous Compounds/*metabolism ; Geologic Sediments/*microbiology ; Iron/*metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Seasons ; }, abstract = {Waters draining from flooded and abandoned coal mines in the South Wales Coalfield (SWC) are substantial sources of pollution to the environment characterized by circumneutral pH and elevated dissolved iron concentrations (>1 mg L-1). The discharged Fe precipitates to form Fe(III) (oxyhydr)oxides which sustain microbial communities. However, while several studies have investigated the geochemistry of mine drainage in the SWC, less is known about the microbial ecology of the sites presenting a gap in our understanding of biogeochemical cycling and pollutant turnover. This study investigated the biogeochemistry of the Ynysarwed mine adit in the SWC. Samples were collected from nine locations within sediment at the mine entrance from the upper and lower layers three times over one year for geochemical and bacterial 16S rRNA gene sequence analysis. During winter, members of the Betaproteobacteria bloomed in relative abundance (>40%) including the microaerophilic Fe(II)-oxidizing genus Gallionella. A concomitant decrease in Chlorobi-associated bacteria occurred, although by summer the community composition resembled that observed in the previous autumn. Here, we provide the first insights into the microbial ecology and seasonal dynamics of bacterial communities of Fe(III)-rich deposits in the SWC and demonstrate that neutrophilic Fe(II)-oxidizing bacteria are important and dynamic members of these communities.}, }
@article {pmid31499451, year = {2019}, author = {Chen, S and Smith, AL}, title = {Performance and microbial ecology of methane-driven microbial fuel cells at temperatures ranging from 25 to 5 °C.}, journal = {Water research}, volume = {166}, number = {}, pages = {115036}, doi = {10.1016/j.watres.2019.115036}, pmid = {31499451}, issn = {1879-2448}, mesh = {*Bioelectric Energy Sources ; Electrodes ; *Geobacter ; Methane ; RNA, Ribosomal, 16S ; Temperature ; }, abstract = {The effluent of mainstream anaerobic processes is saturated with dissolved methane, representing a lost energy source and potent greenhouse gas emission if left unmanaged. This study investigated the impact of operational temperature on methane-driven microbial fuel cells (MFCs) designed for continuous operation to mitigate dissolved methane emissions in anaerobic effluents. Two bench-scale, single-chamber MFCs were operated sequentially at 25, 20, 15, 10 and 5 °C. Voltage production from both MFCs ranged from approximately 0.463 to 0.512 V over 1 kΩ resistance at temperatures ≥15 °C, but abruptly dropped as temperature decreased to 10 and 5 °C, averaging just 0.156 and 0.190 V for the replicate systems. Dissolved methane removal efficiency remained relatively stable across all operational temperatures, ranging from 53.0% to 63.6%. High-throughput sequencing of 16S rRNA genes and reverse transcription quantitative polymerase chain reaction indicated distinct distribution of methanotrophs (e.g., Methylomonas) and exoelectrogens (e.g., Geobacter) on the cathode and anode, respectively. Spearman's rank correlation suggested that an indirect interaction between methanotrophs and exoelectrogens via fermentative bacteria (e.g., Acetobacterium) may play a role in system function. Notably, diversity of the anode microbial community was positively correlated with both voltage production and Coulombic efficiency, suggesting overall diversity, as opposed to abundance or activity of exoelectrogens, was the primary factor governing performance at varying temperatures.}, }
@article {pmid31497590, year = {2019}, author = {Ramamurthy, T and Mutreja, A and Weill, FX and Das, B and Ghosh, A and Nair, GB}, title = {Corrigendum: Revisiting the Global Epidemiology of Cholera in Conjunction With the Genomics of Vibrio cholerae.}, journal = {Frontiers in public health}, volume = {7}, number = {}, pages = {237}, doi = {10.3389/fpubh.2019.00237}, pmid = {31497590}, issn = {2296-2565}, abstract = {[This corrects the article DOI: 10.3389/fpubh.2019.00203.].}, }
@article {pmid31494089, year = {2019}, author = {Hsu, RH and Clark, RL and Tan, JW and Ahn, JC and Gupta, S and Romero, PA and Venturelli, OS}, title = {Microbial Interaction Network Inference in Microfluidic Droplets.}, journal = {Cell systems}, volume = {9}, number = {3}, pages = {229-242.e4}, pmid = {31494089}, issn = {2405-4720}, support = {T32 GM130550/GM/NIGMS NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/metabolism ; Biodiversity ; Host-Pathogen Interactions ; Humans ; Lipid Droplets/*microbiology ; Microbial Consortia/*physiology ; Microbial Interactions/*physiology ; Microfluidics/*methods ; Microscopy, Fluorescence ; }, abstract = {Microbial interactions are major drivers of microbial community dynamics and functions but remain challenging to identify because of limitations in parallel culturing and absolute abundance quantification of community members across environments and replicates. To this end, we developed Microbial Interaction Network Inference in microdroplets (MINI-Drop). Fluorescence microscopy coupled to computer vision techniques were used to rapidly determine the absolute abundance of each strain in hundreds to thousands of droplets per condition. We showed that MINI-Drop could accurately infer pairwise and higher-order interactions in synthetic consortia. We developed a stochastic model of community assembly to provide insight into the heterogeneity in community states across droplets. Finally, we elucidated the complex web of interactions linking antibiotics and different species in a synthetic consortium. In sum, we demonstrated a robust and generalizable method to infer microbial interaction networks by random encapsulation of sub-communities into microfluidic droplets.}, }
@article {pmid31493988, year = {2019}, author = {Calatayud, M and Koren, O and Collado, MC}, title = {Maternal Microbiome and Metabolic Health Program Microbiome Development and Health of the Offspring.}, journal = {Trends in endocrinology and metabolism: TEM}, volume = {30}, number = {10}, pages = {735-744}, doi = {10.1016/j.tem.2019.07.021}, pmid = {31493988}, issn = {1879-3061}, support = {//CIHR/Canada ; }, mesh = {Female ; Humans ; Infant, Newborn ; Lactation/physiology ; Metabolic Syndrome/metabolism/microbiology ; Microbiota/*physiology ; Obesity/*metabolism/*microbiology ; Pregnancy ; }, abstract = {Maternal nutritional, metabolic, and physiological states, as well as exposure to various environmental factors during conception, gestation, and lactation, have a fundamental role in the health programming of the offspring. Therefore, alterations affecting the maternal microbiota might indirectly influence fetal development. In addition, such alterations could be transmitted to the progeny at different stages of infant development (e.g., preconception, prenatal, or postnatal), thereby favoring the development of an altered microbiota in the neonate. Microbial changes of this kind have been linked to an increased risk of non-communicable diseases (NCDs), including obesity and metabolic syndrome, allergy-related problems, and diabetes. In this review, we summarize the relevance of the maternal microbiota to fetal-neonatal health programming, with a focus on maternal nutritional and metabolic states.}, }
@article {pmid31492977, year = {2020}, author = {Expósito, JR and Coello, AJ and Barreno, E and Casano, LM and Catalá, M}, title = {Endogenous NO Is Involved in Dissimilar Responses to Rehydration and Pb(NO3)2 in Ramalina farinacea Thalli and Its Isolated Phycobionts.}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {604-616}, pmid = {31492977}, issn = {1432-184X}, support = {PROMETEOIII /2017/039 GVA//Generalitat Valenciana/ ; CGL2016-79158-P//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; CGL2016-40058-P//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; }, mesh = {Air Pollutants/*metabolism ; Ascomycota/drug effects/*metabolism ; Chlorophyta/drug effects/*metabolism ; Desiccation ; Energy Metabolism ; Lead/*metabolism ; Lichens/drug effects/*metabolism ; Nitrates/*metabolism ; Nitric Oxide/*metabolism ; Oxidative Stress ; }, abstract = {Lichens undergo desiccation/rehydration cycles and are permeable to heavy metals, which induce free radicals. Nitrogen monoxide (NO) regulates important cellular functions, but the research on lichen NO is still very scarce. In Ramalina farinacea thalli, NO seems to be involved in the peroxidative damage caused by air pollution, antioxidant defence and regulation of lipid peroxidation and photosynthesis. Our hypothesis is that NO also has a critical role during the rehydration and in the responses to lead of its isolated phycobionts (Trebouxia sp. TR9 and Trebouxia jamesii). Therefore, we studied the intracellular reactive oxygen species (ROS) production, lipid peroxidation and chlorophyll autofluorescence during rehydration of thalli and isolated microalgae in the presence of a NO scavenger and Pb(NO3)2. During rehydration, NO scavenging modulates free radical release and chlorophyll autofluorescence but not lipid peroxidation in both thalli and phycobionts. Pb(NO3)2 reduced free radical release (hormetic effect) both in the whole thallus and in microalgae. However, only in TR9, the ROS production, chlorophyll autofluorescence and lipid peroxidation were dependent on NO. In conclusion, Pb hormetic effect seems to depend on NO solely in TR9, while is doubtful for T. jamesii and the whole thalli.}, }
@article {pmid31489900, year = {2019}, author = {Jaswal, R and Pathak, A and Chauhan, A}, title = {Metagenomic Evaluation of Bacterial and Fungal Assemblages Enriched within Diffusion Chambers and Microbial Traps Containing Uraniferous Soils.}, journal = {Microorganisms}, volume = {7}, number = {9}, pages = {}, pmid = {31489900}, issn = {2076-2607}, support = {DE-AC09-08SR22470//Savannah River National Laboratory/ ; }, abstract = {Despite significant technological advancements in the field of microbial ecology, cultivation and subsequent isolation of the vast majority of environmental microorganisms continues to pose challenges. Isolation of the environmental microbiomes is prerequisite to better understand a myriad of ecosystem services they provide, such as bioremediation of contaminants. Towards this end, in this culturomics study, we evaluated the colonization of soil bacterial and fungal communities within diffusion chambers (DC) and microbial traps (MT) established using uraniferous soils collected from a historically contaminated soil from Aiken, USA. Microbial assemblages were compared between the DC and MT relative to the native soils using amplicon based metagenomic and bioinformatic analysis. The overall rationale of this study is that DC and MT growth chambers provide the optimum conditions under which desired microbiota, identified in a previous study to serve as the "core" microbiomes, will proliferate, leading to their successful isolation. Specifically, the core microbiomes consisted of assemblages of bacteria (Burkholderia spp.) and fungi (Penicillium spp.), respectively. The findings from this study further supported previous data such that the abundance and diversity of the desired "core" microbiomes significantly increased as a function of enrichments over three consecutive generations of DC and MT, respectively. Metagenomic analysis of the DC/MT generations also revealed that enrichment and stable populations of the desired "core" bacterial and fungal microbiomes develop within the first 20 days of incubation and the practice of subsequent transfers for second and third generations, as is standard in previous studies, may be unnecessary. As a cost and time cutting measure, this study recommends running the DC/MT chambers for only a 20-day time period, as opposed to previous studies, which were run for months. In summation, it was concluded that, using the diffusion chamber-based enrichment techniques, growth of desired microbiota possessing environmentally relevant functions can be achieved in a much shorter time frame than has been previously shown.}, }
@article {pmid31488068, year = {2019}, author = {Pereira-Flores, E and Glöckner, FO and Fernandez-Guerra, A}, title = {Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data.}, journal = {BMC bioinformatics}, volume = {20}, number = {1}, pages = {453}, pmid = {31488068}, issn = {1471-2105}, support = {57129354//Deutscher Akademischer Austauschdienst/ ; POS_EXT_2012_1_10105//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n/ ; 634486//Horizon 2020 Framework Programme/ ; }, mesh = {Benchmarking ; DNA Copy Number Variations ; Databases, Genetic ; *Gene Dosage ; *Genome Size ; Metagenome/*genetics ; Metagenomics/*methods ; Oceans and Seas ; RNA, Ribosomal, 16S/*genetics ; Time Factors ; }, abstract = {BACKGROUND: Metagenomics caused a quantum leap in microbial ecology. However, the inherent size and complexity of metagenomic data limit its interpretation. The quantification of metagenomic traits in metagenomic analysis workflows has the potential to improve the exploitation of metagenomic data. Metagenomic traits are organisms' characteristics linked to their performance. They are measured at the genomic level taking a random sample of individuals in a community. As such, these traits provide valuable information to uncover microorganisms' ecological patterns. The Average Genome Size (AGS) and the 16S rRNA gene Average Copy Number (ACN) are two highly informative metagenomic traits that reflect microorganisms' ecological strategies as well as the environmental conditions they inhabit.<br><br>RESULTS: Here, we present the ags.sh and acn.sh tools, which analytically derive the AGS and ACN metagenomic traits. These tools represent an advance on previous approaches to compute the AGS and ACN traits. Benchmarking shows that ags.sh is up to 11 times faster than state-of-the-art tools dedicated to the estimation AGS. Both ags.sh and acn.sh show comparable or higher accuracy than existing tools used to estimate these traits. To exemplify the applicability of both tools, we analyzed the 139 prokaryotic metagenomes of TARA Oceans and revealed the ecological strategies associated with different water layers.<br><br>CONCLUSION: We took advantage of recent advances in gene annotation to develop the ags.sh and acn.sh tools to combine easy tool usage with fast and accurate performance. Our tools compute the AGS and ACN metagenomic traits on unassembled metagenomes and allow researchers to improve their metagenomic data analysis to gain deeper insights into microorganisms' ecology. The ags.sh and acn.sh tools are publicly available using Docker container technology at https://github.com/pereiramemo/AGS-and-ACN-tools .}, }
@article {pmid31487597, year = {2019}, author = {Griffero, L and Alcántara-Durán, J and Alonso, C and Rodríguez-Gallego, L and Moreno-González, D and García-Reyes, JF and Molina-Díaz, A and Pérez-Parada, A}, title = {Basin-scale monitoring and risk assessment of emerging contaminants in South American Atlantic coastal lagoons.}, journal = {The Science of the total environment}, volume = {697}, number = {}, pages = {134058}, doi = {10.1016/j.scitotenv.2019.134058}, pmid = {31487597}, issn = {1879-1026}, abstract = {Emerging contaminants (ECs) such as pharmaceuticals, personal care products, drugs of abuse and polar pesticides are under particular attention due to their high consumption, frequent detection in the environment and reported ecotoxicological risk. This study investigates the occurrence and distribution of multiclass of ECs in surface waters at basin scale of two Atlantic coastal lagoons of Uruguay, South America. For this purpose, a target screening approach covering up to 362 compounds was employed using nanoflow liquid chromatography - high resolution mass spectrometry (nanoLC/HRMS). 56 compounds were identified including five banned pesticides in the European Union: atrazine, carbendazim, chlorpyrifos ethyl, diazinon, and ethion. Pharmaceuticals, hormones and drugs of abuse showed maximum detection frequencies and concentrations downstream cities. The highest occurrence of pesticides was found in lagoons and streams with neighboring agricultural activity. ECs were also found in coastal sea. Environmental risk assessment revealed that the hormones 17α-ethinylestradiol and 17-β-estradiol showed the highest risk to aquatic organisms in these basins. This study represents the first basin- scale monitoring of ECs in superficial waters encompassing streams, lagoons, and coastal seas in Uruguay, South America.}, }
@article {pmid31487593, year = {2019}, author = {Field, HR and Whitaker, AH and Henson, JA and Duckworth, OW}, title = {Sorption of copper and phosphate to diverse biogenic iron (oxyhydr)oxide deposits.}, journal = {The Science of the total environment}, volume = {697}, number = {}, pages = {134111}, doi = {10.1016/j.scitotenv.2019.134111}, pmid = {31487593}, issn = {1879-1026}, mesh = {Adsorption ; Copper/*chemistry ; Iron/*chemistry ; Models, Chemical ; Organic Chemicals ; Oxidation-Reduction ; Oxides ; Phosphates/*chemistry ; }, abstract = {Iron (Fe) transformations partially control the biogeochemical cycling of biologically and environmentally important elements, such as carbon (C), nitrogen (N), phosphorus (P), and trace metals. In marine and freshwater environments, iron oxidizing bacteria commonly promote the oxidation of ferrous iron (Fe(II)) at circumneutral oxic-anoxic interfaces, resulting in the formation of mineral-organic composites known as biogenic Fe(III) (oxyhydr)oxides (BIOS). Previous studies have examined the microbial ecology, composition, morphology, and sorption reactivity of BIOS. However, a broad survey of BIOS properties and sorption reactivity is lacking. To further explore these relationships, this study utilized X-ray absorption spectroscopy (XAS) to characterize the Fe mineral species, acid digestions and elemental analysis to determine composition, Brunauer-Emmett-Teller (BET) analysis to measure specific surface area, and copper (Cu) and phosphorus (P) adsorption experiments at concentrations designed to measure maximum sorption to evaluate reactivity of BIOS samples collected in lakes and streams of the North Carolina Piedmont. Sample composition varied widely, with Fe and C content ranging from 6.3 to 34% and 3.4-13%, respectively. XAS spectra were best fit with 42-100% poorly crystalline Fe (oxyhydr)oxides, with the remainder composed of crystalline Fe minerals and organic complexes. On a sorbent mass basis, Cu and P sorption varied by a factor of two and 15, respectively. Regression analyses reveal interrelationships between physicochemical properties, and suggest that differences in P binding are driven by sorption to Fe(III) (oxyhydr)oxide surfaces. In total, results suggest that the physical and chemical characteristics of organic and Fe(III) (oxyhydr)oxide phases in BIOS interplay to control the sorption of solutes, and thus influence nutrient and contaminant cycling in soil and natural waters.}, }
@article {pmid31486865, year = {2020}, author = {Hernández-Del Amo, E and Ramió-Pujol, S and Gich, F and Trias, R and Bañeras, L}, title = {Changes in the Potential Activity of Nitrite Reducers and the Microbial Community Structure After Sediment Dredging and Plant Removal in the Empuriabrava FWS-CW.}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {588-603}, pmid = {31486865}, issn = {1432-184X}, support = {IF-UDG2013//Universitat de Girona/ ; (MPCUdG2016/121//Universitat de Girona/ ; CGL2009-08338/BOS//Ministerio de Educaci&#xf3;n, Cultura y Deporte/ ; 2017SGR-548//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; }, mesh = {Bacteria/*metabolism ; *Conservation of Water Resources ; Geologic Sediments/*microbiology ; *Microbiota ; Nitrites/*metabolism ; Oxidation-Reduction ; Spain ; Waste Disposal, Fluid ; *Wetlands ; }, abstract = {In constructed wetlands (CW), denitrification usually accounts for > 60% of nitrogen removal and is supposedly affected by wetland management practices, such as dredging (and plant removal). These practices cause an impact in sediment properties and microbial communities living therein. We have quantified the effects of a sediment dredging event on dissimilatory nitrite reduction by analysing the structure and activities of the microbial community before and after the event. Potential rates for nitrate reduction to ammonia and denitrification were in accordance with changes in the physicochemical conditions. Denitrification was the predominant pathway for nitrite removal (> 60%) and eventually led to the complete removal of nitrate. On the contrary, dissimilatory nitrite reduction to ammonia (DNRA) increased from 5 to 18% after the dredging event. Both actual activities and abundances of 16S rRNA, nirK and nirS significantly decreased after sediment dredging. However, genetic potential for denitrification (qnirS + qnirK/q16S rRNA) remained unchanged. Analyses of the 16S rRNA gene sequences revealed the importance of vegetation in shaping microbial community structures, selecting specific phylotypes potentially contributing to the nitrogen cycle. Overall, we confirmed that sediment dredging and vegetation removal exerted a measurable effect on the microbial community, but not on potential nitrite + nitrate removal rates. According to redundancy analysis, nitrate concentration and pH were the main variables affecting sediment microbial communities in the Empuriabrava CWs. Our results highlight a high recovery of the functionality of an ecosystem service after a severe intervention and point to metabolic redundancy of denitrifiers. We are confident these results will be taken into account in future management strategies in CWs.}, }
@article {pmid31483625, year = {2019}, author = {Cruz, H and Law, YY and Guest, JS and Rabaey, K and Batstone, D and Laycock, B and Verstraete, W and Pikaar, I}, title = {Mainstream Ammonium Recovery to Advance Sustainable Urban Wastewater Management.}, journal = {Environmental science &amp; technology}, volume = {53}, number = {19}, pages = {11066-11079}, doi = {10.1021/acs.est.9b00603}, pmid = {31483625}, issn = {1520-5851}, mesh = {*Ammonium Compounds ; Ecosystem ; Sewage ; Waste Disposal, Fluid ; *Wastewater ; }, abstract = {Throughout the 20th century, the prevailing approach toward nitrogen management in municipal wastewater treatment was to remove ammonium by transforming it into dinitrogen (N2) using biological processes such as conventional activated sludge. While this has been a very successful strategy for safeguarding human health and protecting aquatic ecosystems, the conversion of ammonium into its elemental form is incompatible with the developing circular economy of the 21st century. Equally important, the activated sludge process and other emerging ammonium removal pathways have several environmental and technological limitations. Here, we assess that the theoretical energy embedded in ammonium in domestic wastewater represents roughly 38-48% of the embedded chemical energy available in the whole of the discharged bodily waste. The current routes for ammonium removal not only neglect the energy embedded in ammonium, but they can also produce N2O, a very strong greenhouse gas, with such emissions comprising the equivalent of 14-26% of the overall carbon footprint of wastewater treatment plants. N2O emissions often exceed the carbon emissions related to the electricity consumption for the process requirements of WWTPs. Considering these limitations, there is a need to develop alternative ammonium management approaches that center around recovery of ammonium from domestic wastewater rather than deal with its "destruction" into elemental dinitrogen. Current ammonium recovery techniques are applicable only at orders of magnitude above domestic wastewater strength, and so new techniques based on physicochemical adsorption are of particular interest. A new pathway is proposed that allows for mainstream ammonium recovery from wastewater based on physicochemical adsorption through development of polymer-based adsorbents. Provided adequate adsorbents corresponding to characteristics outlined in this paper are designed and brought to industrial production, this adsorption-based approach opens perspectives for mainstream continuous adsorption coupled with side-stream recovery of ammonium with minimal chemical requirements. This proposed pathway can bring forward an effective resource-oriented approach to upgrade the fate of ammonium in urban water management without generating hidden externalized environmental costs.}, }
@article {pmid31482748, year = {2019}, author = {Arias-Borrego, A and Callejón-Leblic, B and Calatayud, M and Gómez-Ariza, JL and Collado, MC and García-Barrera, T}, title = {Insights into cancer and neurodegenerative diseases through selenoproteins and the connection with gut microbiota - current analytical methodologies.}, journal = {Expert review of proteomics}, volume = {16}, number = {10}, pages = {805-814}, doi = {10.1080/14789450.2019.1664292}, pmid = {31482748}, issn = {1744-8387}, mesh = {Body Fluids/metabolism ; Dietary Supplements ; Gastrointestinal Microbiome/*genetics ; Humans ; Neoplasms/diet therapy/*genetics/microbiology ; Neurodegenerative Diseases/diet therapy/*genetics/microbiology ; Selenium/metabolism/therapeutic use ; Selenoproteins/*genetics/isolation &amp; purification/metabolism ; }, abstract = {Introduction: Selenium plays many key roles in health especially in connection with cancer and neurodegenerative diseases. However, it needs to be appreciated that the essentiality/toxicity of selenium depends on both, a narrow range of concentration and the chemical specie involved. In this context, selenoproteins are essential biomolecules against these disorders, mainly due to its antioxidant action. To this end, analytical methodologies may allow identifying and quantifying individual selenospecies in human biofluids and tissues. Areas covered: This review focus on the role of selenoproteins in medicine, with special emphasis in cancer and neurodegenerative diseases, considering the possible link with gut microbiota. In particular, this article reviews the analytical techniques and procedures recently developed for the absolute quantification of selenoproteins and selenometabolites in human biofluids and tissues. Expert commentary: The beneficial role of selenium in human health has been extensively studied and reviewed. However, several challenges remain unsolved as discussed in this article: (i) speciation of selenium (especially selenoproteins) in cancer and neurodegenerative disease patients; (ii) supplementation of selenium in humans using functional foods and nutraceuticals; (iii) the link between selenium and selenoproteins expression and the gut microbiota and (iv) analytical methods and pitfalls for the absolute quantification of selenoproteins and selenometabolites.}, }
@article {pmid31482287, year = {2020}, author = {Veach, AM and Zeglin, LH}, title = {Historical Drought Affects Microbial Population Dynamics and Activity During Soil Drying and Re-Wet.}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {662-674}, pmid = {31482287}, issn = {1432-184X}, support = {EPS-0903806//Kansas NSF-EPSCoR First Award/ ; }, mesh = {*Bacterial Physiological Phenomena ; Biomass ; Desiccation ; *Droughts ; Kansas ; *Microbiota ; Population Dynamics ; *Soil Microbiology ; }, abstract = {A history of drought exposure promoted by variable precipitation regimes can select for drought-tolerant soil microbial taxa, but the mechanisms of survival and death of microbial populations through the selective stresses of soil drying and re-wet are not well understood. We subjected soils collected from a 15-year field drought experiment ("Altered" precipitation history with extended dry periods, versus the "Ambient" field control) to a laboratory drying/re-wetting experiment, to learn whether selective population survival, death, or maintenance of protein synthesis potential and microbial respiration through variable soil water conditions was affected by field drought legacy. Microbial community composition, as measured by Illumina MiSeq sequencing of the 16S rRNA and 16S rRNA gene, shifted with laboratory drying/re-wet and field drought treatments. In Ambient soils, there was a higher proportion of reduced OTU abundance (indicative of mortality) during re-wet, whereas Altered soils had a greater proportion of stable OTU populations that did not change in abundance (indicative of survival) through drying/re-wet. Altered soils also had a lower proportion of rRNA:rRNA genes (lower protein synthesis potential) during dry-down, a greater weighted mean rRNA operon number (potential growth rate and r-selection) which was associated with higher abundance of Firmicutes (order Bacillales), and lower average microbial respiration rates. These data demonstrate that soils with a weaker historical drought legacy exhibit a higher prevalence of microbial water-stress mortality and differential survival and death at OTU levels following short-term dryingand re-wetting, concurrent with higher carbon loss potential. This work provides novel insight into the mechanisms and consequences of soil microbial changes resulting from extended drought conditions.}, }
@article {pmid31482282, year = {2019}, author = {Ehsani, E and Dumolin, C and Arends, JBA and Kerckhof, FM and Hu, X and Vandamme, P and Boon, N}, title = {Enriched hydrogen-oxidizing microbiomes show a high diversity of co-existing hydrogen-oxidizing bacteria.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {19}, pages = {8241-8253}, doi = {10.1007/s00253-019-10082-z}, pmid = {31482282}, issn = {1432-0614}, support = {Geconcerteerde Onderzoeksactie (GOA) of Ghent University (BOF15/GOA/006)//Universiteit Gent/ ; Geconcerteerde Onderzoeksactie (GOA) of Ghent University (BOF15/GOA/006)//Universiteit Gent/ ; }, mesh = {Ammonium Compounds/metabolism ; Bacteria/*classification/genetics/*metabolism ; Bacteriological Techniques ; Carbon Dioxide/metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Hydrogen/*metabolism ; Metagenomics ; Oxidation-Reduction ; Oxygen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {While numerous reports exist on the axenic culturing of different hydrogen-oxidizing bacteria (HOB), knowledge about the enrichment of microbial communities growing on hydrogen, oxygen, and carbon dioxide as sole carbon and energy sources remains negligible. We want to elucidate if in such enrichments, most enriched populations are HOBs or heterotrophic organisms. In the present study, bacteria enriched from a soil sample and grown over 5 transfers using a continuous supply of hydrogen, oxygen, and carbon dioxide to obtain an enriched autotrophic hydrogen-oxidizing microbiome. The success of the enrichment was evaluated by monitoring ammonium consumption and biomass concentration for 120 days. The shift in the microbial composition of the original soil inoculum and all transfers was observed based on 16S rRNA amplicon sequencing. The hydrogen-oxidizing facultative chemolithoautotroph Hydrogenophaga electricum was isolated and found to be one of the abundant species in most transfers. Moreover, Achromobacter was isolated both under heterotrophic and autotrophic conditions, which was characterized as a hydrogen-oxidizing bacterium. The HOB enrichment condition constructed in this study provided an environment for HOB to develop and conquer in all transfers. In conclusion, we showed that enrichments on hydrogen, oxygen, and carbon dioxide as sole carbon and energy sources contain a diverse mixture of HOB and heterotrophs that resulted in a collection of culturable isolates. These isolates can be useful for further investigation for industrial applications.}, }
@article {pmid31482007, year = {2019}, author = {Keshvardoust, P and Huron, VAA and Clemson, M and Constancias, F and Barraud, N and Rice, SA}, title = {Biofilm formation inhibition and dispersal of multi-species communities containing ammonia-oxidising bacteria.}, journal = {NPJ biofilms and microbiomes}, volume = {5}, number = {1}, pages = {22}, pmid = {31482007}, issn = {2055-5008}, mesh = {Ammonium Compounds/metabolism ; Biofilms/*growth &amp; development ; Carbon/metabolism ; Culture Media/chemistry ; *Microbial Interactions ; *Microbiota ; Nitrification ; Nitrosomonas europaea/*growth &amp; development/metabolism ; Organic Chemicals/metabolism ; }, abstract = {Despite considerable research, the biofilm-forming capabilities of Nitrosomonas europaea are poorly understood for both mono and mixed-species communities. This study combined biofilm assays and molecular techniques to demonstrate that N. europaea makes very little biofilm on its own, and relies on the activity of associated heterotrophic bacteria to establish a biofilm. However, N. europaea has a vital role in the proliferation of mixed-species communities under carbon-limited conditions, such as in drinking water distribution systems, through the provision of organic carbon via ammonia oxidation. Results show that the addition of nitrification inhibitors to mixed-species nitrifying cultures under carbon-limited conditions disrupted biofilm formation and caused the dispersal of pre-formed biofilms. This dispersal effect was not observed when an organic carbon source, glucose, was included in the medium. Interestingly, inhibition of nitrification activity of these mixed-species biofilms in the presence of added glucose resulted in increased total biofilm formation compared to controls without the addition of nitrification inhibitors, or with only glucose added. This suggests that active AOB partially suppress or limit the overall growth of the heterotrophic bacteria. The experimental model developed here provides evidence that ammonia-oxidising bacteria (AOB) are involved in both the formation and maintenance of multi-species biofilm communities. The results demonstrate that the activity of the AOB not only support the growth and biofilm formation of heterotrophic bacteria by providing organic carbon, but also restrict and limit total biomass in mixed community systems.}, }
@article {pmid31475212, year = {2019}, author = {Godoy-Vitorino, F}, title = {Human microbial ecology and the rising new medicine.}, journal = {Annals of translational medicine}, volume = {7}, number = {14}, pages = {342}, pmid = {31475212}, issn = {2305-5839}, abstract = {The first life forms on earth were Prokaryotic, and the evolution of all Eukaryotic life occurred with the help of bacteria. Animal-associated microbiota also includes members of the archaea, fungi, protists, and viruses. The genomes of this host-associated microbial life are called the microbiome. Across the mammalian tree, microbiomes guarantee the development of immunity, physiology, and resistance to pathogens. In humans, all surfaces and cavities are colonized by a microbiome, maintained by a careful balance between the host response and its colonizers-thus humans are considered now supraorganisms. These microbiomes supply essential ecosystem services that benefit health through homeostasis, and the loss of the indigenous microbiota leads to dysbiosis, which can have significant consequences to disease. This educational review aims to describe the importance of human microbial ecology, explain the ecological terms applied to the study of the human microbiome, developments within the cutting-edge microbiome field, and implications to diagnostic and treatment.}, }
@article {pmid31469487, year = {2019}, author = {Overholt, WA and Schwing, P and Raz, KM and Hastings, D and Hollander, DJ and Kostka, JE}, title = {The core seafloor microbiome in the Gulf of Mexico is remarkably consistent and shows evidence of recovery from disturbance caused by major oil spills.}, journal = {Environmental microbiology}, volume = {21}, number = {11}, pages = {4316-4329}, doi = {10.1111/1462-2920.14794}, pmid = {31469487}, issn = {1462-2920}, support = {C-IMAGE II//Gulf of Mexico Research Initiative/International ; C-IMAGE III//Gulf of Mexico Research Initiative/International ; 2013172310//National Science Foundation/International ; }, mesh = {Environmental Monitoring/methods ; Geologic Sediments/*microbiology ; Gulf of Mexico ; *Microbiota ; *Petroleum Pollution ; }, abstract = {The microbial ecology of oligotrophic deep ocean sediments is understudied relative to their shallow counterparts, and this lack of understanding hampers our ability to predict responses to current and future perturbations. The Gulf of Mexico has experienced two of the largest accidental marine oil spills, the 1979 Ixtoc-1 blowout and the 2010 Deepwater Horizon (DWH) discharge. Here, microbial communities were characterized for 29 sites across multiple years in > 700 samples. The composition of the seafloor microbiome was broadly consistent across the region and was well approximated by the overlying water depth and depth within the sediment column, while geographic distance played a limited role. Biogeographical distributions were employed to generate predictive models for over 4000 OTU that leverage easy-to-obtain geospatial variables which are linked to measured sedimentary oxygen profiles. Depth stratification and putative niche diversification are evidenced by the distribution of taxa that mediate the microbial nitrogen cycle. Furthermore, these results demonstrate that sediments impacted by the DWH spill had returned to near baseline conditions after 2 years. The distributions of benthic microorganisms in the Gulf can be constrained, and moreover, deviations from these predictions may pinpoint impacted sites and aid in future response efforts or long-term stability studies.}, }
@article {pmid31466158, year = {2019}, author = {Zhang, L and Shen, Z and Fang, W and Gao, G}, title = {Composition of bacterial communities in municipal wastewater treatment plant.}, journal = {The Science of the total environment}, volume = {689}, number = {}, pages = {1181-1191}, doi = {10.1016/j.scitotenv.2019.06.432}, pmid = {31466158}, issn = {1879-1026}, mesh = {Bacteria/classification ; Bacteroidetes/genetics ; China ; Firmicutes ; *Microbiota ; Phylogeny ; Proteobacteria/genetics ; Sewage/microbiology ; *Waste Disposal, Fluid ; Wastewater/*microbiology ; }, abstract = {Efforts to understand the environmental and biological factors that influence the dynamics of microbial communities have received substantial attention in microbial ecology. In this study, Illumina MiSeq high-throughput sequencing technology was used to examine the microbial community structure of activated sludge in municipal wastewater treatment systems (Chuzhou city, China). Overall, Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were the most dominant phyla in the five activated sludge samples. However, the community structure of nitrifying bacteria was relatively simple, and diversity was low; only AOB (Nitrosomonas) and NOB (Nitrospira) were detected. The dominant bacteria in the anaerobic sludge, anoxic sludge and oxic sludge were the same, and each bacterial species was relatively uniform, with differences only in proportions. Redundancy analysis indicated that pH, TP and COD were strong environmental factors influencing the bacterial community distribution. PICRUSt was used to describe the metabolic and functional abilities of the activated sludge bacterial communities. The results emphasized the vast genetic diversity of these organisms, which are involved in various essential processes such as amino acid transport and metabolism, energy production and conversion, cell wall/membrane/envelope/biogenesis, signal transduction mechanisms, and carbohydrate transport and metabolism. Activated sludge of municipal wastewater treatment systems can be ranked in the following order based on the 16S rRNA gene copy numbers of the detected phylotypes: S1 > S2 > S4 > S5 > S3. This study provides basic data and a theoretical analysis of the optimal design and operation in wastewater treatment plants.}, }
@article {pmid31466157, year = {2019}, author = {Xu, M and Stedtfeld, RD and Wang, F and Hashsham, SA and Song, Y and Chuang, Y and Fan, J and Li, H and Jiang, X and Tiedje, JM}, title = {Composting increased persistence of manure-borne antibiotic resistance genes in soils with different fertilization history.}, journal = {The Science of the total environment}, volume = {689}, number = {}, pages = {1172-1180}, doi = {10.1016/j.scitotenv.2019.06.376}, pmid = {31466157}, issn = {1879-1026}, mesh = {*Composting ; Drug Resistance, Microbial/*genetics ; Farms ; Fertilizers ; *Genes, Bacterial ; Manure/*microbiology ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Different long-term fertilization regimes may change indigenous microorganism diversity in the arable soil and thus might influence the persistence and transmission of manure-born antibiotic resistance genes (ARGs). Different manure origins and composting techniques might affect the fate of introduced ARGs in farmland. A four-month microcosm experiment was performed using two soils, which originated from the same field and applied with the same chemical fertilizer or swine manure for 26 years, to investigate the dynamics of ARGs in soil amended with manure or compost from the farm and an agro-technology company. High throughput qPCR and sequencing were applied to quantify ARGs using 144 primer sets and microorganism in soil. Fertilization history had little effect on dynamics of manure-borne ARGs in soil regardless of manure origin or composting. Very different half-lives of ARGs and mobile genetic elements from farm manure and commercial manure were observed in both soils. Composting decreased abundance of most ARGs in manure, but increased the persistence of manure-introduced ARGs in soil irrespective of fertilization history, especially for those from farm manure. These findings help understanding the fate of ARGs in manured soil and may inform techniques to mitigate ARGs transmission.}, }
@article {pmid31463982, year = {2020}, author = {Elghandour, MMY and Khusro, A and Adegbeye, MJ and Tan, Z and Abu Hafsa, SH and Greiner, R and Ugbogu, EA and Anele, UY and Salem, AZM}, title = {Dynamic role of single-celled fungi in ruminal microbial ecology and activities.}, journal = {Journal of applied microbiology}, volume = {128}, number = {4}, pages = {950-965}, doi = {10.1111/jam.14427}, pmid = {31463982}, issn = {1365-2672}, mesh = {Animal Feed/analysis ; Animal Nutritional Physiological Phenomena/*physiology ; Animals ; Diet/veterinary ; Dietary Supplements/*microbiology ; Fermentation ; Fungi/metabolism/*physiology ; Rumen/chemistry/*microbiology ; Ruminants/microbiology/*physiology ; Saccharomyces cerevisiae/metabolism/physiology ; }, abstract = {In ruminants, high fermentation capacity is necessary to develop more efficient ruminant production systems. Greater level of production depends on the ability of the microbial ecosystem to convert organic matter into precursors of milk and meat. This has led to increased interest by animal nutritionists, biochemists and microbiologists in evaluating different strategies to manipulate the rumen biota to improve animal performance, production efficiency and animal health. One of such strategies is the use of natural feed additives such as single-celled fungi yeast. The main objectives of using yeasts as natural additives in ruminant diets include; (i) to prevent rumen microflora disorders, (ii) to improve and sustain higher production of milk and meat, (iii) to reduce rumen acidosis and bloat which adversely affect animal health and performance, (iv) to decrease the risk of ruminant-associated human pathogens and (v) to reduce the excretion of nitrogenous-based compounds, carbon dioxide and methane. Yeast, a natural feed additive, has the potential to enhance feed degradation by increasing the concentration of volatile fatty acids during fermentation processes. In addition, microbial growth in the rumen is enhanced in the presence of yeast leading to the delivery of a greater amount of microbial protein to the duodenum and high nitrogen retention. Single-celled fungi yeast has demonstrated its ability to increase fibre digestibility and lower faecal output of organic matter due to improved digestion of organic matter, which subsequently improves animal productivity. Yeast also has the ability to alter the fermentation process in the rumen in a way that reduces methane formation. Furthermore, yeast inclusion in ruminant diets has been reported to decrease toxins absorption such as mycotoxins and promote epithelial cell integrity. This review article provides information on the impact of single-celled fungi yeast as a feed supplement on ruminal microbiota and its function to improve the health and productive longevity of ruminants.}, }
@article {pmid31463664, year = {2020}, author = {Erni-Cassola, G and Wright, RJ and Gibson, MI and Christie-Oleza, JA}, title = {Early Colonization of Weathered Polyethylene by Distinct Bacteria in Marine Coastal Seawater.}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {517-526}, pmid = {31463664}, issn = {1432-184X}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; NE/S005501/1//Natural Environment Research Council/ ; NE/K009044/1//Natural Environment Research Council/ ; BB/M01116X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; CENTA//Natural Environment Research Council/ ; }, mesh = {Bacteria/classification/genetics/*metabolism ; Biodegradation, Environmental ; Polyethylene/*metabolism ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Seawater/*microbiology ; *Waste Products ; }, abstract = {Plastic debris in aquatic environments is rapidly colonized by a diverse community of microorganisms, often referred to as the "Plastisphere." Given that common plastics are derived from fossil fuels, one would expect that Plastispheres should be enriched with obligate hydrocarbon-degrading bacteria (OHCB). So far, though, different polymer types do not seem to exert a strong effect on determining the composition of the Plastisphere, and putative biodegrading bacteria are only found as rare taxa within these biofilms. Here, we show through 16S rRNA gene sequencing that the enrichment of a prominent OHCB member on weathered and non-weathered polyethylene only occurred at early stages of colonization (i.e., after 2 days of incubation in coastal marine water; 5.8% and 3.7% of relative abundance, respectively, vs. 0.6% on glass controls). As biofilms matured, these bacteria decreased in relative abundance on all materials (< 0.3% after 9 days). Apart from OHCB, weathered polyethylene strongly enriched for other distinct organisms during early stages of colonization, such as a specific member of the Roseobacter group and a member of the genus Aestuariibacter (median 26.9% and 1.8% of the community, respectively), possibly as a consequence of the availability of short-oxidized chains generated from weathering. Our results demonstrate that Plastispheres can vary in accordance with the weathering state of the material and that very early colonizing communities are enriched with taxa that can potentially degrade hydrocarbons. Given the lack of persistent enrichment and overall community convergence between materials over time, common non-hydrolysable polymers might not serve as an important source of carbon for mature Plastispheres once the labile substrates generated from weathering have been depleted.}, }
@article {pmid31463663, year = {2020}, author = {Baselga-Cervera, B and García-Balboa, C and Díaz-Alejo, HM and Costas, E and López-Rodas, V}, title = {Rapid Colonization of Uranium Mining-Impacted Waters, the Biodiversity of Successful Lineages of Phytoplankton Extremophiles.}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {576-587}, pmid = {31463663}, issn = {1432-184X}, support = {CTM-2013-44366-R.//Spanish Secretar&#xed;a de Estado, Investigaci&#xf3;n, Desarrollo e Innovaci&#xf3;n/ ; BES-2014-067580.//Secretar&#xed;a de Estado, Investigaci&#xf3;n, Desarrollo e Innovaci&#xf3;n/ ; }, mesh = {Biodiversity ; Chlamydomonas reinhardtii/physiology/radiation effects ; Chlorophyta/*physiology/radiation effects ; Extremophiles/*physiology/radiation effects ; Mining ; Phytoplankton/*physiology/radiation effects ; Portugal ; Spain ; Uranium/*analysis ; Water Pollutants, Radioactive/*analysis ; }, abstract = {Anthropogenic extreme environments are emphasized as interesting sites for the study of evolutionary pathways, biodiversity, and extremophile bioprospection. Organisms that grow under these conditions are usually regarded as extremophiles; however, the extreme novelty of these environments may have favor adaptive radiations of facultative extremophiles. At the Iberian Peninsula, uranium mining operations have rendered highly polluted extreme environments in multiple locations. In this study, we examined the phytoplankton diversity, community structure, and possible determining factors in separate uranium mining-impacted waters. Some of these human-induced extreme environments may be able to sustain indigenous facultative extremophile phytoplankton species, as well as alleged obligate extremophiles. Therefore, we investigated the adaptation capacity of three laboratory strains, two Chlamydomonas reinhardtii and a Dictyosphaerium chlorelloides, to uranium-polluted waters. The biodiversity among the sampled waters was very low, and despite presenting unique taxonomic records, ecological patterns can be identified. The microalgae adaptation experiments indicated a gradient of ecological novelty and different phenomena of adaptation, from acclimation in some waters to non-adaptation in the harshest anthropogenic environment. Certainly, phytoplankton extremophiles might have been often overlooked, and the ability to flourish in extreme environments might be a functional feature in some neutrophilic species. Evolutionary biology and microbial biodiversity can benefit the study of recently evolved systems such as uranium-polluted waters. Moreover, anthropogenic extremophiles can be harnessed for industrial applications.}, }
@article {pmid31462415, year = {2019}, author = {McGonigle, JM and Bernau, JA and Bowen, BB and Brazelton, WJ}, title = {Robust Archaeal and Bacterial Communities Inhabit Shallow Subsurface Sediments of the Bonneville Salt Flats.}, journal = {mSphere}, volume = {4}, number = {4}, pages = {}, pmid = {31462415}, issn = {2379-5042}, mesh = {Archaea/*classification ; Bacteria/*classification ; DNA, Bacterial/genetics ; Ecosystem ; *Genetic Variation ; Lakes/chemistry/microbiology ; *Microbiota ; Nevada ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salt Tolerance ; Utah ; }, abstract = {We report the first census of natural microbial communities of the Bonneville Salt Flats (BSF), a perennial salt pan at the Utah-Nevada border. Environmental DNA sequencing of archaeal and bacterial 16S rRNA genes was conducted on samples from multiple evaporite sediment layers collected from the upper 30 cm of the surface salt crust. Our results show that at the time of sampling (September 2016), BSF hosted a robust microbial community dominated by diverse halobacteria and Salinibacter species. Sequences identical to Geitlerinema sp. strain PCC 9228, an anoxygenic cyanobacterium that uses sulfide as the electron donor for photosynthesis, are also abundant in many samples. We identified taxonomic groups enriched in each layer of the salt crust sediment and revealed that the upper gypsum sediment layer found immediately under the uppermost surface halite contains a robust microbial community. In these sediments, we found an increased presence of Thermoplasmatales, Hadesarchaeota, Nanoarchaeaeota, Acetothermia, Desulfovermiculus, Halanaerobiales, Bacteroidetes, and Rhodovibrio This study provides insight into the diversity, spatial heterogeneity, and geologic context of a surprisingly complex microbial ecosystem within this macroscopically sterile landscape.IMPORTANCE Pleistocene Lake Bonneville, which covered a third of Utah, desiccated approximately 13,000 years ago, leaving behind the Bonneville Salt Flats (BSF) in the Utah West Desert. The potash salts that saturate BSF basin are extracted and sold as an additive for agricultural fertilizers. The salt crust is a well-known recreational and economic commodity, but the biological interactions with the salt crust have not been studied. This study is the first geospatial analysis of microbially diverse populations at this site using cultivation-independent environmental DNA sequencing methods. Identification of the microbes present within this unique, dynamic, and valued sedimentary evaporite environment is an important step toward understanding the potential consequences of perturbations to the microbial ecology on the surrounding landscape and ecosystem.}, }
@article {pmid31456784, year = {2019}, author = {Gogulancea, V and González-Cabaleiro, R and Li, B and Taniguchi, D and Jayathilake, PG and Chen, J and Wilkinson, D and Swailes, D and McGough, AS and Zuliani, P and Ofiteru, ID and Curtis, TP}, title = {Individual Based Model Links Thermodynamics, Chemical Speciation and Environmental Conditions to Microbial Growth.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1871}, pmid = {31456784}, issn = {1664-302X}, abstract = {Individual based Models (IbM) must transition from research tools to engineering tools. To make the transition we must aspire to develop large, three dimensional and physically and biologically credible models. Biological credibility can be promoted by grounding, as far as possible, the biology in thermodynamics. Thermodynamic principles are known to have predictive power in microbial ecology. However, this in turn requires a model that incorporates pH and chemical speciation. Physical credibility implies plausible mechanics and a connection with the wider environment. Here, we propose a step toward that ideal by presenting an individual based model connecting thermodynamics, pH and chemical speciation and environmental conditions to microbial growth for 5·10[5] individuals. We have showcased the model in two scenarios: a two functional group nitrification model and a three functional group anaerobic community. In the former, pH and connection to the environment had an important effect on the outcomes simulated. Whilst in the latter pH was less important but the spatial arrangements and community productivity (that is, methane production) were highly dependent on thermodynamic and reactor coupling. We conclude that if IbM are to attain their potential as tools to evaluate the emergent properties of engineered biological systems it will be necessary to combine the chemical, physical, mechanical and biological along the lines we have proposed. We have still fallen short of our ideals because we cannot (yet) calculate specific uptake rates and must develop the capacity for longer runs in larger models. However, we believe such advances are attainable. Ideally in a common, fast and modular platform. For future innovations in IbM will only be of use if they can be coupled with all the previous advances.}, }
@article {pmid31455798, year = {2019}, author = {Park, CH and Lee, JG and Lee, AR and Eun, CS and Han, DS}, title = {Network construction of gastric microbiome and organization of microbial modules associated with gastric carcinogenesis.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12444}, pmid = {31455798}, issn = {2045-2322}, mesh = {Adult ; *Bacteria/classification/genetics ; *Carcinogenesis ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metaplasia ; Middle Aged ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; *Stomach Neoplasms/genetics/microbiology ; }, abstract = {In addition to Helicobacter pylori infection, nitrosating/nitrate-reducing bacteria and type IV secretion system (T4SS) protein gene-contributing bacteria have been proposed as potential causes of gastric cancer development. However, bacterial modules related with gastric carcinogenesis have not been clarified. In this study, we analyzed gastric microbiome using the gastric mucosal samples obtained from the Hanyang University Gastric Microbiome Cohort by 16S rRNA gene sequencing. Weighted correlation network analysis was performed to construct a microbiome network and to identify microbial modules associated with gastric carcinogenesis. At the family level, 420 bacterial taxa were identified in the gastric microbiome of 83 participants. Through network analysis, 18 microbial modules were organized. Among them, two modules-pink and brown-were positively correlated with a higher-risk of gastric cancer development such as intestinal metaplasia with no current H. pylori infection (correlation coefficient [γ]: pink module, 0.31 [P = 0.004], brown module, 0.26 [P = 0.02]). At the family level, twenty-two and thirty-two bacterial taxa belonged to the pink and brown modules, respectively. They included nitrosating/nitrate-reducing bacteria, T4SS protein gene-contributing bacteria, and various other bacteria, including Gordoniaceae, Tsukamurellaceae, Prevotellaceae, Cellulomonadaceae, Methylococcaceae, and Procabacteriaceae. The blue module, which included H. pylori, was correlated negatively with intestinal metaplasia (γ = -0.49 [P < 0.001]). In conclusion, intragastric bacterial taxa associated with gastric carcinogenesis can be classified by network analysis. Microbial modules may provide an integrative view of the microbial ecology relevant to precancerous lesions in the stomach.}, }
@article {pmid31454177, year = {2019}, author = {Goulart, MC and Cueva-Yesquén, LG and Hidalgo Martinez, KJ and Attili-Angelis, D and Fantinatti-Garboggini, F}, title = {Comparison of specific endophytic bacterial communities in different developmental stages of Passiflora incarnata using culture-dependent and culture-independent analysis.}, journal = {MicrobiologyOpen}, volume = {8}, number = {10}, pages = {e896}, pmid = {31454177}, issn = {2045-8827}, mesh = {Bacteria/*classification/genetics/growth &amp; development/isolation &amp; purification ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Endophytes/*classification/genetics/growth &amp; development/isolation &amp; purification ; *Microbiota ; Passiflora/*growth &amp; development/*microbiology ; Phylogeny ; Plant Development ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Plants and endophytic microorganisms have coevolved unique relationships over many generations. Plants show a specific physiological status in each developmental stage, which may determine the occurrence and dominance of specific endophytic populations with a predetermined ecological role. This study aimed to compare and determine the structure and composition of cultivable and uncultivable bacterial endophytic communities in vegetative and reproductive stages (RS) of Passiflora incarnata. To that end, the endophytic communities were assessed by plating and Illumina-based 16S rRNA gene amplicon sequencing. Two hundred and four cultivable bacterial strains were successfully isolated. From the plant's RS, the isolated strains were identified mainly as belonging to the genera Sphingomonas, Curtobacterium, and Methylobacterium, whereas Bacillus was the dominant genus isolated from the vegetative stage (VS). From a total of 133,399 sequences obtained from Illumina-based sequencing, a subset of 25,092 was classified in operational taxonomy units (OTUs). Four hundred and sixteen OTUs were obtained from the VS and 66 from the RS. In the VS, the most abundant families were Pseudoalteromonadaceae and Alicyclobacillaceae, while in the RS, Enterobacteriaceae and Bacillaceae were the most abundant families. The exclusive abundance of specific bacterial populations for each developmental stage suggests that plants may modulate bacterial endophytic community structure in response to different physiological statuses occurring at the different plant developmental stages.}, }
@article {pmid31451772, year = {2019}, author = {Adam, PS and Borrel, G and Gribaldo, S}, title = {An archaeal origin of the Wood-Ljungdahl H4MPT branch and the emergence of bacterial methylotrophy.}, journal = {Nature microbiology}, volume = {4}, number = {12}, pages = {2155-2163}, pmid = {31451772}, issn = {2058-5276}, mesh = {Archaea/*classification ; Bacteria/*classification/enzymology ; Carbon/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genome, Archaeal ; Genome, Bacterial ; Methane/*metabolism ; Phylogeny ; Pterins/*metabolism ; Wood/metabolism ; }, abstract = {The tetrahydromethanopterin (H4MPT) methyl branch of the Wood-Ljungdahl pathway is shared by archaeal and bacterial metabolisms that greatly contribute to the global carbon budget and greenhouse gas fluxes: methanogenesis and methylotrophy, including methanotrophy[1-3]. It has been proposed that the H4MPT branch dates back to the last universal common ancestor[4-6]. Interestingly, it has been identified in numerous recently sequenced and mostly uncultured non-methanogenic and non-methylotrophic archaeal and bacterial lineages, where its function remains unclear[5,7]. Here, we have examined the distribution and phylogeny of the enzymes involved in the H4MPT branch and the biosynthesis of its cofactors in over 6,400 archaeal and bacterial genomes. We find that a full Wood-Ljungdahl H4MPT pathway is widespread in Archaea and is likely ancestral to this domain, whereas this is not the case for Bacteria. Moreover, the inclusion of recently sequenced lineages leads to an important shortening of the branch separating Archaea and Bacteria with respect to previous phylogenies of the H4MPT branch. Finally, the genes for the pathway are colocalized in many of the recently sequenced archaeal lineages, similar to bacteria. Together, these results weaken the last universal common ancestor hypothesis and rather favour an origin of the H4MPT branch in Archaea and its subsequent transfer to Bacteria. We propose a scenario for its potential initial role in the first bacterial recipients and its evolution up to the emergence of aerobic methylotrophy. Finally, we discuss how an ancient horizontal transfer not only triggered the emergence of key metabolic processes but also important transitions in Earth's history.}, }
@article {pmid31451346, year = {2019}, author = {Voulgari-Kokota, A and McFrederick, QS and Steffan-Dewenter, I and Keller, A}, title = {Drivers, Diversity, and Functions of the Solitary-Bee Microbiota.}, journal = {Trends in microbiology}, volume = {27}, number = {12}, pages = {1034-1044}, doi = {10.1016/j.tim.2019.07.011}, pmid = {31451346}, issn = {1878-4380}, mesh = {Animals ; Bees/*microbiology/*physiology ; *Biodiversity ; Environment ; Female ; Male ; *Microbiota ; *Social Behavior ; Social Isolation ; Symbiosis ; }, abstract = {Accumulating reports of global bee declines have drawn much attention to the bee microbiota and its importance. Most research has focused on social bees, while solitary species have received scant attention despite their enormous biodiversity, ecological importance, and agroeconomic value. We review insights from several recent studies on diversity, function, and drivers of the solitary-bee microbiota, and compare these factors with those relevant to the social-bee microbiota. Despite basic similarities, the social-bee model, with host-specific core microbiota and social transmission, is not representative of the vast majority of bee species. The solitary-bee microbiota exhibits greater variability and biodiversity, with a strong impact of environmental acquisition routes. Our synthesis identifies outstanding questions that will build understanding of these interactions, responses to environmental threats, and consequences for health.}, }
@article {pmid31450207, year = {2020}, author = {He, Q and Song, J and Zhang, W and Gao, S and Wang, H and Yu, J}, title = {Enhanced simultaneous nitrification, denitrification and phosphorus removal through mixed carbon source by aerobic granular sludge.}, journal = {Journal of hazardous materials}, volume = {382}, number = {}, pages = {121043}, doi = {10.1016/j.jhazmat.2019.121043}, pmid = {31450207}, issn = {1873-3336}, mesh = {Acetates/*metabolism ; Aerobiosis ; Carbon/metabolism ; Denitrification ; Nitrification ; Phosphorus/*metabolism ; Sewage ; Succinic Acid/*metabolism ; Waste Disposal, Fluid/*methods ; Wastewater ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Aerobic granular sludge-based simultaneous nitrification, denitrification and phosphorus removal (SNDPR) systems were configured for the treatment of low-strength municipal wastewater. Granular characteristics, process performance, and the corresponding microbial ecology dynamics were comprehensively explored with sodium acetate and succinate as mixed carbon source. Results revealed that aerobic granules kept structural and functional resilience, while mixed carbon source largely altered and balanced the growth and competition of phosphorus/glycogen accumulating organisms (PAOs/GAOs). Appropriate ratio of mixed carbon source was vital for superb physiochemical behaviors and reliable removal performance by aerobic granules. Therefore, the aerobic granular SNDPR system could achieve deep-level nutrients removal through enhancing the anaerobic carbon uptake rate and strengthening the carbon usage efficiency. The present work could add some guiding sight into the application of aerobic granular SNDPR system for wastewater treatment.}, }
@article {pmid31449563, year = {2019}, author = {Kim, JG and Gwak, JH and Jung, MY and An, SU and Hyun, JH and Kang, S and Rhee, SK}, title = {Distinct temporal dynamics of planktonic archaeal and bacterial assemblages in the bays of the Yellow Sea.}, journal = {PloS one}, volume = {14}, number = {8}, pages = {e0221408}, pmid = {31449563}, issn = {1932-6203}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Biodiversity ; China ; *Environmental Monitoring ; Fresh Water/microbiology ; Humans ; Nitrogen/metabolism ; Oceans and Seas ; *Phylogeny ; Plankton/classification/genetics ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Seawater/microbiology ; Tidal Waves ; }, abstract = {The Yellow Sea features unique characteristics due to strong tides and nutrient-enriched freshwater outflows from China and Korea. The coupling of archaeal and bacterial assemblages associated with environmental factors at two bay areas in the Yellow Sea was investigated. Temporal variations of the archaeal and bacterial assemblages were shown to be greater than the spatial variations based on an analysis of the 16S rRNA gene sequences. Distinct temporal dynamics of both planktonic archaeal and bacterial assemblages was associated with temperature, NO2-, and chlorophyll a ([chl-a]) concentrations in the bays of the Yellow Sea. The [chl-a] was the prime predictor of bacterial abundance, and some taxa were clearly correlated with [chl-a]. Bacteroidetes and Alpha-proteobacteria dominated at high [chl-a] stations while Gamma-proteobacteria (esp. SAR86 clade) and Actinobacteria (Candidatus Actinomarina clade) were abundant at low [chl-a] stations. The archaeal abundance was comparable with the bacterial abundance in most of the October samples. Co-dominance of Marine Group II (MGII) and Candidatus Nitrosopumilus suggests that the assimilation of organic nitrogen by MGII could be coupled with nitrification by ammonia-oxidizing archaea. The distinct temporal dynamics of the archaeal and bacterial assemblages might be attributable to the strong tides and the inflow of nutrient-rich freshwater.}, }
@article {pmid31448388, year = {2020}, author = {Rojas, EC and Sapkota, R and Jensen, B and Jørgensen, HJL and Henriksson, T and Jørgensen, LN and Nicolaisen, M and Collinge, DB}, title = {Fusarium Head Blight Modifies Fungal Endophytic Communities During Infection of Wheat Spikes.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {397-408}, pmid = {31448388}, issn = {1432-184X}, support = {674964//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; }, mesh = {Endophytes/*physiology ; Fusarium/*physiology ; Mycobiome/*physiology ; Plant Diseases/*microbiology ; Triticum/*microbiology ; }, abstract = {Fusarium head blight (FHB) is a devastating disease of wheat heads. It is caused by several species from the genus Fusarium. Several endophytic fungi also colonize wheat spikes asymptomatically. Pathogenic and commensal fungi share and compete for the same niche and thereby influence plant performance. Understanding the natural dynamics of the fungal community and how the pre-established species react to pathogen attack can provide useful information on the disease biology and the potential use of some of these endophytic organisms in disease control strategies. Fungal community composition was assessed during anthesis as well as during FHB attack in wheat spikes during 2016 and 2017 in two locations. Community metabarcoding revealed that endophyte communities are dominated by basidiomycete yeasts before anthesis and shift towards a more opportunistic ascomycete-rich community during kernel development. These dynamics are interrupted when Fusarium spp. colonize wheat spikes. The Fusarium pathogens appear to exclude other fungi from floral tissues as they are associated with a reduction in community diversity, especially in the kernel which they colonize rapidly. Similarly, the presence of several endophytes was negatively correlated with Fusarium spp. and linked with spikes that stayed healthy despite exposure to the pathogen. These endophytes belonged to the genera Cladosporium, Itersonillia and Holtermanniella. These findings support the hypothesis that some naturally occurring endophytes could outcompete or prevent FHB and represent a source of potential biological control agents in wheat.}, }
@article {pmid31448296, year = {2019}, author = {Rothrock, MJ and Locatelli, A and Feye, KM and Caudill, AJ and Guard, J and Hiett, K and Ricke, SC}, title = {A Microbiomic Analysis of a Pasture-Raised Broiler Flock Elucidates Foodborne Pathogen Ecology Along the Farm-To-Fork Continuum.}, journal = {Frontiers in veterinary science}, volume = {6}, number = {}, pages = {260}, pmid = {31448296}, issn = {2297-1769}, abstract = {While conventionally grown poultry continues to dominate the U. S. poultry industry, there is an increasing demand for locally-grown, "all natural" alternatives. The use of next generation sequencing allows for not only the gross (e.g., community structure) but also fine-scale (e.g., taxa abundances) examination of these complex microbial communities. This data provides a better understanding of how a pasture flock's microbiome changes throughout the production life cycle and how that change in microbial ecology changes foodborne pathogens in alternative poultry production systems. In order to understand this ecology better, pooled broiler samples were taken during the entire flock life cycle, from pre-hatch gastrointestinal samples (N = 12) to fecal samples from the brood (N = 5), and pasture (N = 10) periods. Additional samples were taken during processing, including skin and feather rinsates (N = 12), ceca (N = 12), and whole carcass rinses (N = 12), and finally whole carcasss rinsates of final products (N = 3). Genomic DNA was extracted, 16S rDNA microbiome sequencing was conducted (Illumina MiSeq), and microbiomes were analyzed and compared using QIIME 1.9.1 to determine how microbiomes shifted throughout production continuum, as well as what environmental factors may be influencing these shifts. Significant microbiome shifts occurred during the life cycle of the pasture broiler flock, with the brood and pasture fecal samples and cecal samples being very distinct from the other pre-hatch, processing, and final product samples. Throughout these varied microbiomes, there was a stable core microbiome containing 13 taxa. Within this core microbiome, five taxa represented known foodborne pathogens (Salmonella, Campylobacter) or potential/emerging pathogens (Pseudomonas, Enterococcus, Acinetobacter) whose relative abundances varied throughout the farm-to-fork continuum, although all were more prevalent in the fecal samples. Additionally, of the 25 physiochemical and nutrient variables measured from the fecal samples, the carbon to nitrogen ratio was one of the most significant variables to warrant further investigations because it impacted both general fecal microbial ecology and Campylobacter and Enterococcus taxa within the core fecal microbiomes. These findings demonstrate the need for further longitudinal, farm-to-fork studies to understand the ecology of the microbial ecology of pasture production flocks to improve animal, environmental, and public health.}, }
@article {pmid31446647, year = {2019}, author = {Lemos, LN and Medeiros, JD and Dini-Andreote, F and Fernandes, GR and Varani, AM and Oliveira, G and Pylro, VS}, title = {Genomic signatures and co-occurrence patterns of the ultra-small Saccharimonadia (phylum CPR/Patescibacteria) suggest a symbiotic lifestyle.}, journal = {Molecular ecology}, volume = {28}, number = {18}, pages = {4259-4271}, doi = {10.1111/mec.15208}, pmid = {31446647}, issn = {1365-294X}, support = {BB/P027849/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/*genetics ; Base Sequence ; Gene Regulatory Networks ; *Genome, Bacterial ; *Genomics ; Metabolic Networks and Pathways/genetics ; Metagenome ; Microbiota/genetics ; Mining ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Symbiosis/*genetics ; }, abstract = {The size of bacterial genomes is often associated with organismal metabolic capabilities determining ecological breadth and lifestyle. The recently proposed Candidate Phyla Radiation (CPR)/Patescibacteria encompasses mostly unculturable bacterial taxa with relatively small genome sizes with potential for co-metabolism interdependencies. As yet, little is known about the ecology and evolution of CPR, particularly with respect to how they might interact with other taxa. Here, we reconstructed two novel genomes (namely, Candidatus Saccharibacter sossegus and Candidatus Chaer renensis) of taxa belonging to the class Saccharimonadia within the CPR/Patescibacteria using metagenomes obtained from acid mine drainage (AMD). By testing the hypothesis of genome streamlining or symbiotic lifestyle, our results revealed clear signatures of gene losses in these genomes, such as those associated with de novo biosynthesis of essential amino acids, nucleotides, fatty acids and cofactors. In addition, co-occurrence analysis provided evidence supporting potential symbioses of these organisms with Hydrotalea sp. in the AMD system. Together, our findings provide a better understanding of the ecology and evolution of CPR/Patescibacteria and highlight the importance of genome reconstruction for studying metabolic interdependencies between unculturable Saccharimonadia representatives.}, }
@article {pmid31446448, year = {2020}, author = {Wise, BR and Roane, TM and Mosier, AC}, title = {Community Composition of Nitrite Reductase Gene Sequences in an Acid Mine Drainage Environment.}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {562-575}, pmid = {31446448}, issn = {1432-184X}, mesh = {Bacteria/classification/*enzymology/genetics ; Colorado ; Denitrification ; *Genes, Bacterial ; Geologic Sediments/*microbiology ; Hydrogen-Ion Concentration ; Microbiota ; *Mining ; Nitrite Reductases/*analysis ; }, abstract = {Denitrifying microbial communities play a central role in the nitrogen cycle, contribute to greenhouse gas production, and provide ecosystem services through the mitigation of nitrogen pollution. The impacts of human-induced acid mine drainage (AMD) and naturally occurring acid rock drainage (ARD), both characterized by low pH and high metal concentrations, on denitrifying microbial communities is not well understood. This study examined denitrifying microbes within sediments impacted by acidic and metal-rich AMD or ARD in the Iron Springs Mining District (10 sites across four regions over four time points) located in Southwest Colorado, USA. Denitrification functional gene sequences (nirS and nirK coding for nitrite reductase) had a high number of observed OTUs (260 for nirS and 253 for nirK) and were observed at sites with pH as low as 3.5 and metals > 2 mg/L (including aluminum, iron, manganese, strontium, and zinc). A majority of the nirK and nirS OTUs (> 60%) were present in only one sampling region. Approximately 8% of the nirK and nirS OTUs had a more cosmopolitan distribution with presence in three or more regions. Phylogenetically related OTUs were found across sites with very different chemistry. The overall community structure for nirK and nirS genes was correlated to conductivity and calcium (respectively), which may suggest that conductivity may play an important role in shaping the distribution of nirK- and nirS-type denitrifiers. Overall, these findings improve upon our understanding of the potential for denitrification within an ecosystem impacted by AMD or ARD and provide a foundation for future research to understand the rates and physiology of denitrifying organisms in these systems.}, }
@article {pmid31444524, year = {2020}, author = {Zhang, G and Bai, J and Zhao, Q and Jia, J and Wang, W and Wang, X}, title = {Bacterial Succession in Salt Marsh Soils Along a Short-term Invasion Chronosequence of Spartina alterniflora in the Yellow River Estuary, China.}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {644-661}, pmid = {31444524}, issn = {1432-184X}, support = {2017YFC0505906//National Key R &amp; D Program of China/ ; 310430001//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Bacterial Physiological Phenomena ; China ; Estuaries ; Introduced Species ; *Microbiota ; Poaceae/*growth &amp; development ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Soil Microbiology ; }, abstract = {As an exotic plant species, Spartina alterniflora seriously threatens native ecosystem function in Chinese coastal regions. Unveiling the dynamics of soil bacteria community during its invasion is essential for a better understanding of related biogeochemical processes, while the shift in soil bacterial community over invasive time remains unclear. A short-term chronosequence was identified to assess the impacts of Spartina alterniflora invasion on soil nutrients and bacterial community composition and structure (using 16S rRNA gene high-throughput sequencing) over the time of invasion (i.e., (1) at least 10 years, (2) nearly 5 years, (3) less than 2 years, and (4) in native salt marshes or 0 years) in the Yellow River Estuary. The results exhibited an orderly change in the soil physicochemical properties and bacterial community composition over the invasion time. Soil pH showed a significant decrease with the accumulation of soil organic matter (SOM), whereas soil nutrients such as soil dissolved organic carbon (DOC), total nitrogen (TN), nitrate (NO3[-]), ammonium (NH4[+]), K[+], and Mg[2+] were generally increased with the age of the invasion. The number of operational taxonomic units (OTUs, 97% similarity level) exhibited a decreasing trend, which suggested a decline in bacterial diversity with the invasion age. The dominant groups at the phylum level were Proteobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, and Gemmatimonadetes (the sum of relative abundance was > 70% across all samples). The relative abundances of Chloroflexi and Gemmatimonadetes steadily decreased, while the abundance of Bacteroidetes significantly increased with the plant invasion. The distribution pattern of the soil bacteria was clearly separated according to the principal coordinate analysis (PCoA) and canonical correspondence analysis (CCA) in native and invaded salt marshes. The variation in the soil bacterial community was tightly associated with the soil physicochemical properties (Mantel test, P < 0.05). Variance partitioning analysis (VPA) showed that plant traits explained 4.95% of the bacterial community variation, and soil variables explained approximately 26.96% of the variation. Network analysis also revealed that plant invasion strengthens the interaction among soil bacterial communities. Overall, our findings highlight the bacterial community succession during the Spartina alterniflora invasion in coastal salt marsh soils, which can provide insight regarding the association between soil development and invasive plant.}, }
@article {pmid31444200, year = {2019}, author = {Campa, MF and Techtmann, SM and Ladd, MP and Yan, J and Patterson, M and Garcia de Matos Amaral, A and Carter, KE and Ulrich, N and Grant, CJ and Hettich, RL and Lamendella, R and Hazen, TC}, title = {Surface Water Microbial Community Response to the Biocide 2,2-Dibromo-3-Nitrilopropionamide, Used in Unconventional Oil and Gas Extraction.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {21}, pages = {}, pmid = {31444200}, issn = {1098-5336}, mesh = {Disinfectants/*pharmacology ; Ecology ; Hydraulic Fracking/methods ; Microbiota/*drug effects/genetics ; Nitriles/*pharmacology ; RNA, Ribosomal, 16S/genetics ; Rivers ; Wastewater/analysis ; Water Microbiology ; Water Pollutants, Chemical/analysis ; Water Purification ; }, abstract = {Production of unconventional oil and gas continues to rise, but the effects of high-density hydraulic fracturing (HF) activity near aquatic ecosystems are not fully understood. A commonly used biocide in HF, 2,2-dibromo-3-nitrilopropionamide (DBNPA), was studied in microcosms of HF-impacted (HF+) versus HF-unimpacted (HF-) surface water streams to (i) compare the microbial community response, (ii) investigate DBNPA degradation products based on past HF exposure, and (iii) compare the microbial community response differences and similarities between the HF biocides DBNPA and glutaraldehyde. The microbial community responded to DBNPA differently in HF-impacted versus HF-unimpacted microcosms in terms of the number of 16S rRNA gene copies quantified, alpha and beta diversity, and differential abundance analyses of microbial community composition through time. The differences in microbial community changes affected degradation dynamics. HF-impacted microbial communities were more sensitive to DBNPA, causing the biocide and by-products of the degradation to persist for longer than in HF-unimpacted microcosms. A total of 17 DBNPA by-products were detected, many of them not widely known as DBNPA by-products. Many of the brominated by-products detected that are believed to be uncharacterized may pose environmental and health impacts. Similar taxa were able to tolerate glutaraldehyde and DBNPA; however, DBNPA was not as effective for microbial control, as indicated by a smaller overall decrease of 16S rRNA gene copies/ml after exposure to the biocide, and a more diverse set of taxa was able to tolerate it. These findings suggest that past HF activity in streams can affect the microbial community response to environmental perturbation such as that caused by the biocide DBNPA.IMPORTANCE Unconventional oil and gas activity can affect pH, total organic carbon, and microbial communities in surface water, altering their ability to respond to new environmental and/or anthropogenic perturbations. These findings demonstrate that 2,2-dibromo-3-nitrilopropionamide (DBNPA), a common hydraulic fracturing (HF) biocide, affects microbial communities differently as a consequence of past HF exposure, persisting longer in HF-impacted (HF+) waters. These findings also demonstrate that DBNPA has low efficacy in environmental microbial communities regardless of HF impact. These findings are of interest, as understanding microbial responses is key for formulating remediation strategies in unconventional oil and gas (UOG)-impacted environments. Moreover, some DBNPA degradation by-products are even more toxic and recalcitrant than DBNPA itself, and this work identifies novel brominated degradation by-products formed.}, }
@article {pmid31443509, year = {2019}, author = {Hernández-Arriaga, A and Baumann, A and Witte, OW and Frahm, C and Bergheim, I and Camarinha-Silva, A}, title = {Changes in Oral Microbial Ecology of C57BL/6 Mice at Different Ages Associated with Sampling Methodology.}, journal = {Microorganisms}, volume = {7}, number = {9}, pages = {}, pmid = {31443509}, issn = {2076-2607}, support = {CA 1708/1-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {The mouth is an important niche for bacterial colonization. Previous research used mouth microbiota to predict diseases like colon cancer and inflammatory bowel disease (IBD). It is still unclear how the sampling methodology influences microbial characterization. Our aim was to determine if the sampling methods, e.g., cotton swab or tissue biopsy, and the age influence the oral microbial composition of mice. Microbial DNA was extracted using a commercial kit and characterized targeting the 16s rRNA gene from mouth swabs and tissue biopsies from 2 and 15 months old C57BL/6 male mice kept in the same SPF facility. Our results show statistical different microbial community of the different ages, type of sampling, and the two fixed factors age x type of sample (p-value <0.05). At the genus level, we identified that the genera Actinobacillus, Neisseria, Staphylococcus, and Streptococcus either increase or decrease in abundance depending on sampling and age. Additionally, the abundance of Streptococcus danieliae, Moraxella osloensis, and some unclassified Streptococcus was affected by the sampling method. While swab and tissue biopsies both identified the common colonizers of oral microbiota, cotton swabbing is a low-cost and practical method, validating the use of the swab as the preferred oral sampling approach.}, }
@article {pmid31441243, year = {2019}, author = {Smessaert, J and Van Geel, M and Verreth, C and Crauwels, S and Honnay, O and Keulemans, W and Lievens, B}, title = {Temporal and spatial variation in bacterial communities of "Jonagold" apple (Malus x domestica Borkh.) and "Conference" pear (Pyrus communis L.) floral nectar.}, journal = {MicrobiologyOpen}, volume = {8}, number = {12}, pages = {e918}, pmid = {31441243}, issn = {2045-8827}, mesh = {*Bacteria/classification/genetics ; Biodiversity ; DNA Barcoding, Taxonomic ; Fruit/microbiology ; Malus/*microbiology ; *Microbiota ; *Plant Nectar ; Pyrus/*microbiology ; }, abstract = {Production of many agricultural crops and fruits strongly depends on pollinators. For instance, pome fruits such as apple and pear are highly dependent on pollination for fruit set, fruit quality, and yield. Nectar is often inhabited by microbes, most often yeasts and bacteria, which may change nectar quality and therefore also affect plant-pollinator interactions. Here, we used high-throughput 16S ribosomal RNA gene amplicon sequencing to investigate the temporal and spatial variation in bacterial communities in floral nectar of apple and pear. We sampled 15 apple (Malus x domestica Borkh.) and 15 pear (Pyrus communis L.) orchards distributed over the eastern part of Belgium over a timespan of seven days. Nectar bacterial community composition differed strongly among fruit species. Nectar of pear was dominated by Actinobacteria, followed by Proteobacteria and Firmicutes. Apple nectar was strongly enriched in Bacteroidetes, a phylum which until now has been found to be rarely associated with floral nectar. Nectar was dominated by only a few bacterial species, with Brevibacterium (Actinobacteria) and Undibacterium (Proteobacteria) as the most abundant bacteria in pear and apple nectar, respectively. Bacterial richness and diversity were found to fluctuate during flowering, likely due to changing environmental conditions. Additionally, spatial structure in nectar bacterial community composition was found in apple orchards, while this was not the case for pear. Differences in nectar bacterial communities between apple and pear nectar may differently affect the chemical and nutritional composition of the nectar, influencing pollinator attraction and visitation, and thus pollination efficacy in general.}, }
@article {pmid31438955, year = {2019}, author = {Vavourakis, CD and Mehrshad, M and Balkema, C and van Hall, R and Andrei, A&#x15e; and Ghai, R and Sorokin, DY and Muyzer, G}, title = {Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {69}, pmid = {31438955}, issn = {1741-7007}, support = {322551/ERC_/European Research Council/International ; }, mesh = {Archaea/*classification/genetics/*metabolism ; Bacteria/*classification/genetics/*metabolism ; Hydrogen-Ion Concentration ; Lakes/chemistry/*microbiology ; Metagenome ; Oxidation-Reduction ; Phylogeny ; Salinity ; Salts/chemistry ; Siberia ; Sulfur/analysis/*metabolism ; }, abstract = {BACKGROUND: The planetary sulfur cycle is a complex web of chemical reactions that can be microbial-mediated or can occur spontaneously in the environment, depending on the temperature and pH. Inorganic sulfur compounds can serve as energy sources for specialized prokaryotes and are important substrates for microbial growth in general. Here, we investigate dissimilatory sulfur cycling in the brine and sediments of a southwestern Siberian soda lake characterized by an extremely high pH and salinity, combining meta-omics analyses of its uniquely adapted highly diverse prokaryote communities with biogeochemical profiling to identify key microbial players and expand our understanding of sulfur cycling under haloalkaline conditions.<br><br>RESULTS: Peak microbial activity was found in the top 4&#x2009;cm of the sediments, a layer with a steep drop in oxygen concentration and redox potential. The majority of sulfur was present as sulfate or iron sulfide. Thiosulfate was readily oxidized by microbes in the presence of oxygen, but oxidation was partially inhibited by light. We obtained 1032 metagenome-assembled genomes, including novel population genomes of characterized colorless sulfur-oxidizing bacteria (SOB), anoxygenic purple sulfur bacteria, heterotrophic SOB, and highly active lithoautotrophic sulfate reducers. Surprisingly, we discovered the potential for nitrogen fixation in a new genus of colorless SOB, carbon fixation in a new species of phototrophic Gemmatimonadetes, and elemental sulfur/sulfite reduction in the "Candidatus Woesearchaeota." Polysulfide/thiosulfate and tetrathionate reductases were actively transcribed by various (facultative) anaerobes.<br><br>CONCLUSIONS: The recovery of over 200 genomes that encoded enzymes capable of catalyzing key reactions in the inorganic sulfur cycle indicates complete cycling between sulfate and sulfide at moderately hypersaline and extreme alkaline conditions. Our results suggest that more taxonomic groups are involved in sulfur dissimilation than previously assumed.}, }
@article {pmid31435691, year = {2020}, author = {Damjanovic, K and Menéndez, P and Blackall, LL and van Oppen, MJH}, title = {Early Life Stages of a Common Broadcast Spawning Coral Associate with Specific Bacterial Communities Despite Lack of Internalized Bacteria.}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {706-719}, pmid = {31435691}, issn = {1432-184X}, support = {DP160101468//Australian Research Council/ ; Holsworth Wildlife Endowment//Ecological Society of Australia/ ; }, mesh = {Animals ; Anthozoa/growth &amp; development/*microbiology ; *Bacterial Physiological Phenomena ; Embryo, Nonmammalian/microbiology ; In Situ Hybridization, Fluorescence ; Larva/microbiology ; *Life Cycle Stages ; Male ; Microbiota/*physiology ; Ovum/microbiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Reproduction ; Spermatozoa/microbiology ; }, abstract = {Coral-associated bacteria are critical for the well-being of their host and may play essential roles during ontogeny, as suggested by the vertical transmission of some bacteria in brooding corals. Bacterial acquisition patterns in broadcast spawners remain uncertain, as 16S rRNA gene metabarcoding of coral early life stages suggests the presence of bacterial communities, which have not been detected by microscopic examinations. Here, we combined 16S rRNA gene metabarcoding with fluorescence in situ hybridization (FISH) microscopy to analyze bacterial assemblages in Acropora tenuis egg-sperm bundles, embryos, and larvae following a spawning event. Metabarcoding results indicated that A. tenuis offspring ≤ 4-day-old were associated with diverse and dynamic bacterial microbiomes, dominated by Rhodobacteraceae, Alteromonadaceae, and Oceanospirillaceae. While FISH analyses confirmed the lack of internalized bacteria in A. tenuis offspring, metabarcoding showed that even the earliest life stages examined (egg-sperm bundles and two-cell stages) were associated with a diverse bacterial community, suggesting the bacteria were confined to the mucus layer. These results can be explained by vertical transmission of certain taxa (mainly Endozoicomonas) in the mucus surrounding the gametes within bundles, or by horizontal bacterial transmission through the release of bacteria by spawning adults into the water column.}, }
@article {pmid31435492, year = {2019}, author = {Onywera, H and Williamson, AL and Mbulawa, ZZA and Coetzee, D and Meiring, TL}, title = {Factors associated with the composition and diversity of the cervical microbiota of reproductive-age Black South African women: a retrospective cross-sectional study.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e7488}, pmid = {31435492}, issn = {2167-8359}, abstract = {BACKGROUND: Lactobacillus spp. are common bacteria in the cervical and vaginal microbiota (CVM) and are thought to represent a "healthy" cervicovaginal state. Several studies have found an independent association between ethnicity/race and cervical and vaginal microbiota (CVM) composition. Women of sub-Saharan African descent appear to be significantly more likely to have non-Lactobacillus-dominated CVM compared to women of European descent. The factors contributing to these differences remain to be fully elucidated. The CVM of Black South African women and factors influencing their CVM remain understudied. In this study, we characterized the cervical microbiota of reproductive-age South African women and assessed the associations of these microbiota with participants' metadata.<br><br>METHODS: The cervical microbiota from cervical DNA of 62 reproductive-age women were profiled by Ion Torrent sequencing the V4 hypervariable region of the bacterial 16S ribosomal RNA (rRNA) gene and analyzed with the Quantitative Insights Into Microbial Ecology (QIIME), UPARSE, and metagenomeSeq tools. Associations between cervical microbiota and participants' metadata were assessed using GraphPad Prism, R packages and an in-house script.<br><br>RESULTS: The cervical microbiota clustered into three distinct community state types (CSTs): Lactobacillus iners-dominated cervical microbiota (CST I (38.7%, 24/62)), unclassified Lactobacillus-dominated cervical microbiota (CST II (4.8%, 3/62)), and diverse cervical microbiota (CST III (56.5%, 35/62)) with an array of heterogeneous bacteria, predominantly the bacterial vaginosis (BV)-associated Gardnerella, Prevotella, Sneathia, and Shuttleworthia. CST III was associated with BV (p&#xa0;=&#xa0;0.001). Women in CST I were more likely to be on hormonal contraception, especially progestin-based, compared to women in CST III (odds ratio: 5.2 (95% CI [1.6-17.2]); p&#xa0;=&#xa0;0.005). Women on hormonal contraception had a significantly lower alpha (Shannon indices: 0.9 (0.2-1.9) versus 2.3 (0.6-2.3); p&#xa0;=&#xa0;0.025) and beta (permutational multivariate analysis of variance (PERMANOVA) pseudo-F statistic&#xa0;=4.31, p&#xa0;=&#xa0;0.019) diversity compared to non-users. There was no significant difference in the alpha (Shannon indices: 1.0 (0.3-2.2) versus 1.9 (0.3-2.2); p&#xa0;=&#xa0;0.483) and beta (PERMANOVA pseudo-F statistic = 0.89, p&#xa0;=&#xa0;0.373) diversity in women with versus without human papillomavirus infection.<br><br>CONCLUSIONS: The majority of Black women in our study had non-Lactobacillus-dominated cervical microbiota. Additional studies are needed to examine whether such microbiota represent abnormal, intermediate or variant states of health. Lastly, the association of hormonal contraception with L. iners dominance requires further in-depth research to confirm this association, determine its biological mechanism and whether it has a beneficial effect on the cervicovaginal health.}, }
@article {pmid31434790, year = {2019}, author = {Weiner, BG and Posfai, A and Wingreen, NS}, title = {Spatial ecology of territorial populations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {36}, pages = {17874-17879}, pmid = {31434790}, issn = {1091-6490}, support = {R01 GM082938/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biodiversity ; *Ecology ; *Ecosystem ; Models, Theoretical ; Population Dynamics ; }, abstract = {Many ecosystems, from vegetation to biofilms, are composed of territorial populations that compete for both nutrients and physical space. What are the implications of such spatial organization for biodiversity? To address this question, we developed and analyzed a model of territorial resource competition. In the model, all species obey trade-offs inspired by biophysical constraints on metabolism; the species occupy nonoverlapping territories, while nutrients diffuse in space. We find that the nutrient diffusion time is an important control parameter for both biodiversity and the timescale of population dynamics. Interestingly, fast nutrient diffusion allows the populations of some species to fluctuate to zero, leading to extinctions. Moreover, territorial competition spontaneously gives rise to both multistability and the Allee effect (in which a minimum population is required for survival), so that small perturbations can have major ecological effects. While the assumption of trade-offs allows for the coexistence of more species than the number of nutrients-thus violating the principle of competitive exclusion-overall biodiversity is curbed by the domination of "oligotroph" species. Importantly, in contrast to well-mixed models, spatial structure renders diversity robust to inequalities in metabolic trade-offs. Our results suggest that territorial ecosystems can display high biodiversity and rich dynamics simply due to competition for resources in a spatial community.}, }
@article {pmid31432245, year = {2020}, author = {Sun, Y and Liu, Y and Pan, J and Wang, F and Li, M}, title = {Perspectives on Cultivation Strategies of Archaea.}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {770-784}, pmid = {31432245}, issn = {1432-184X}, support = {31622002//NSFC/ ; 91851105//NSFC/ ; }, mesh = {Archaea/*growth &amp; development ; Bacteriological Techniques/instrumentation/*methods ; }, abstract = {Archaea have been recognized as a major domain of life since the 1970s and occupy a key position in the tree of life. Recent advances in culture-independent approaches have greatly accelerated the research son Archaea. However, many hypotheses concerning the diversity, physiology, and evolution of archaea are waiting to be confirmed by culture-base experiments. Consequently, archaeal isolates are in great demand. On the other hand, traditional approaches of archaeal cultivation are rarely successful and require urgent improvement. Here, we review the current practices and applicable microbial cultivation techniques, to inform on potential strategies that could improve archaeal cultivation in the future. We first summarize the current knowledge on archaeal diversity, with an emphasis on cultivated and uncultivated lineages pertinent to future research. Possible causes for the low success rate of the current cultivation practices are then discussed to propose future improvements. Finally, innovative insights for archaeal cultivation are described, including (1) medium refinement for selective cultivation based on the genetic and transcriptional information; (2) consideration of the up-to-date archaeal culturing skills; and (3) application of multiple cultivation techniques, such as co-culture, direct interspecies electron transfer (DIET), single-cell isolation, high-throughput culturing (HTC), and simulation of the natural habitat. Improved cultivation efforts should allow successful isolation of as yet uncultured archaea, contributing to the much-needed physiological investigation of archaea.}, }
@article {pmid31432244, year = {2020}, author = {Nasser, NA and Gregory, BRB and Steele, RE and Patterson, RT and Galloway, JM}, title = {Behind the Organic Veil: Assessing the Impact of Chemical Deflocculation on Organic Content Reduction and Lacustrine Arcellinida (Testate Amoebae) Analysis.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {443-458}, pmid = {31432244}, issn = {1432-184X}, mesh = {*Flocculation ; Geologic Sediments/*parasitology ; Lakes/parasitology ; Lobosea/*isolation &amp; purification ; Microbiological Techniques/*instrumentation ; Northwest Territories ; Parasitology/methods ; }, abstract = {Arcellinida (testate lobose amoebae) are widely used as bio-indicators of lacustrine environmental change. Too much obscuring organic material in a gridded wet Petri dish preparation makes it difficult to observe all specimens present and slows quantification as the organic material has to be carefully worked through with a dissection probe. Chemical deflocculation using soda ash (Na2CO3·H2O), potassium hydroxide (KOH), or sodium hexametaphosphate ((NaPO3)6) has previously been shown to disaggregate and reduce organic content in lake sediments, but to date, no attempt has been made to comparatively evaluate the efficiency of these deflocculants in disaggregating organic content and their impact on Arcellinida analysis in lacustrine sediments. Here, we assess the effectiveness of soda ash, potassium hydroxide, and sodium hexametaphosphate treatments on removing organic content and the impact of those digestions on Arcellinida preservation in 126 sample aliquots subdivided from three sediment samples (YK-20, YK-25, and YK-57) collected from three lakes near Yellowknife, Northwest Territories, Canada. Following treatment, cluster analysis and Bray-Curtis dissimilarity matrix (BCDM) were utilized to determine whether treatments resulted in dissolution-driven changes in Arcellinida assemblage composition. Observed Arcellinida tests in aliquots increased drastically after treatment of organic-rich samples (47.5-452.7% in organic-rich aliquots and by 14.8% in aliquots with less organic matter). The BCDM results revealed that treatment with 5% KOH resulted in the highest reduction in observed organic content without significantly affecting Arcellinida assemblage structure, while soda ash and sodium hexametaphosphate treatments resulted in marginal organic matter reduction and caused severe damage to the arcellinidan tests.}, }
@article {pmid31431510, year = {2019}, author = {Taroni, JN}, title = {Making Workshops Work: Insights from EDAMAME.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, pmid = {31431510}, issn = {2379-5077}, abstract = {Microbiology, like many areas of life science research, is increasingly data-intensive. As such, bioinformatics and data science skills have become essential to leverage microbiome sequencing data for discovery. Short intensive courses have sprung up as formal computational training opportunities at individual institutions fail to meet demands. In this issue, Shade et al. (A. Shade, T. K. Dunivin, J. Choi, T. K. Teal, et al., mSystems 4:e00297-19, 2019, https://doi.org/10.1128/mSystems.00297-19) share their experience and approach in executing the annual, weeklong Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology (EDAMAME) workshop from 2014 to 2018. EDAMAME introduced learners to general scientific computing concepts and domain-specific data analysis approaches. Workshop learners self-reported appreciable gains in understanding and ability. This report on the EDAMAME workshop strategy and lessons learned will help others in the life sciences to plan, execute, and assess short hands-on computing-intensive courses that support research in a particular domain.}, }
@article {pmid31431509, year = {2019}, author = {Shade, A and Dunivin, TK and Choi, J and Teal, TK and Howe, AC}, title = {Strategies for Building Computing Skills To Support Microbiome Analysis: a Five-Year Perspective from the EDAMAME Workshop.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, pmid = {31431509}, issn = {2379-5077}, support = {R25 GM115335/GM/NIGMS NIH HHS/United States ; }, abstract = {Here, we report our educational approach and learner evaluations of the first 5 years of the Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology (EDAMAME) workshop, held annually at Michigan State University's Kellogg Biological Station from 2014 to 2018. We hope this information will be useful for others who want to organize computing-intensive workshops and will encourage quantitative skill development among microbiologists.IMPORTANCE High-throughput sequencing and related statistical and bioinformatic analyses have become routine in microbiology in the past decade, but there are few formal training opportunities to develop these skills. A weeklong workshop can offer sufficient time for novices to become introduced to best computing practices and common workflows in sequence analysis. We report our experiences in executing such a workshop targeted to professional learners (graduate students, postdoctoral scientists, faculty, and research staff).}, }
@article {pmid31431508, year = {2019}, author = {Sun, Z and Huang, S and Zhu, P and Yue, F and Zhao, H and Yang, M and Niu, Y and Jing, G and Su, X and Li, H and Callewaert, C and Knight, R and Liu, J and Smith, E and Wei, K and Xu, J}, title = {A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, pmid = {31431508}, issn = {2379-5077}, abstract = {A quantitative and objective indicator for skin health via the microbiome is of great interest for personalized skin care, but differences among skin sites and across human populations can make this goal challenging. A three-city (two Chinese and one American) comparison of skin microbiota from atopic dermatitis (AD) and healthy pediatric cohorts revealed that, although city has the greatest effect size (the skin microbiome can predict the originated city with near 100% accuracy), a microbial index of skin health (MiSH) based on 25 bacterial genera can diagnose AD with 83 to ∼95% accuracy within each city and 86.4% accuracy across cities (area under the concentration-time curve [AUC], 0.90). Moreover, nonlesional skin sites across the bodies of AD-active children (which include shank, arm, popliteal fossa, elbow, antecubital fossa, knee, neck, and axilla) harbor a distinct but lesional state-like microbiome that features relative enrichment of Staphylococcus aureus over healthy individuals, confirming the extension of microbiome dysbiosis across body surface in AD patients. Intriguingly, pretreatment MiSH classifies children with identical AD clinical symptoms into two host types with distinct microbial diversity and treatment effects of corticosteroid therapy. These findings suggest that MiSH has the potential to diagnose AD, assess risk-prone state of skin, and predict treatment response in children across human populations.IMPORTANCE MiSH, which is based on the skin microbiome, can quantitatively assess pediatric skin health across cohorts from distinct countries over large geographic distances. Moreover, the index can identify a risk-prone skin state and compare treatment effect in children, suggesting applications in diagnosis and patient stratification.}, }
@article {pmid31428833, year = {2020}, author = {Tang, Y and Dai, T and Su, Z and Hasegawa, K and Tian, J and Chen, L and Wen, D}, title = {A Tripartite Microbial-Environment Network Indicates How Crucial Microbes Influence the Microbial Community Ecology.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {342-356}, pmid = {31428833}, issn = {1432-184X}, support = {51678003//National Natural Science Foundation of China/ ; 51678334//National Natural Science Foundation of China/ ; }, mesh = {Archaea/*physiology ; *Bacterial Physiological Phenomena ; Bays/*microbiology ; China ; Geologic Sediments/*microbiology ; *Microbial Consortia ; Microbiological Techniques/*methods ; }, abstract = {Current technologies could identify the abundance and functions of specific microbes, and evaluate their individual effects on microbial ecology. However, these microbes interact with each other, as well as environmental factors, in the form of complex network. Determination of their combined ecological influences remains a challenge. In this study, we developed a tripartite microbial-environment network (TMEN) analysis method that integrates microbial abundance, metabolic function, and environmental data as a tripartite network to investigate the combined ecological effects of microbes. Applying TMEN to analyzing the microbial-environment community structure in the sediments of Hangzhou Bay, one of the most seriously polluted coastal areas in China, we found that microbes were well-organized into 4 bacterial communities and 9 archaeal communities. The total organic carbon, sulfate, chemical oxygen demand, salinity, and nitrogen-related indexes were detected as crucial environmental factors in the microbial-environmental network. With close interactions with these environmental factors, Nitrospirales and Methanimicrococcu were identified as hub microbes with connection advantage. Our TMEN method could close the gap between lack of efficient statistical and computational approaches and the booming of large-scale microbial genomic and environmental data. Based on TMEN, we discovered a potential microbial ecological mechanism that crucial species with significant influence on the microbial community ecology would possess one or two of the community advantages for enhancing their ecological status and essentiality, including abundance advantage and connection advantage.}, }
@article {pmid31420342, year = {2019}, author = {In 't Zandt, MH and Kip, N and Frank, J and Jansen, S and van Veen, JA and Jetten, MSM and Welte, CU}, title = {High-Level Abundances of Methanobacteriales and Syntrophobacterales May Help To Prevent Corrosion of Metal Sheet Piles.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {20}, pages = {}, pmid = {31420342}, issn = {1098-5336}, mesh = {Corrosion ; Deltaproteobacteria/*metabolism ; Iron/*metabolism ; Methanobacteriales/*metabolism ; Netherlands ; }, abstract = {Iron sheet piles are widely used in flood protection, dike construction, and river bank reinforcement. Their corrosion leads to gradual deterioration and often makes replacement necessary. Natural deposit layers on these sheet piles can prevent degradation and significantly increase their life span. However, little is known about the mechanisms of natural protective layer formation. Here, we studied the microbially diverse populations of corrosion-protective deposit layers on iron sheet piles at the Gouderak pumping station in Zuid-Holland, the Netherlands. Deposit layers, surrounding sediment and top sediment samples were analyzed for soil physicochemical parameters, microbially diverse populations, and metabolic potential. Methanogens appeared to be enriched 18-fold in the deposit layers. After sequencing, metagenome assembly and binning, we obtained four nearly complete draft genomes of microorganisms (Methanobacteriales, two Coriobacteriales, and Syntrophobacterales) that were highly enriched in the deposit layers, strongly indicating a potential role in corrosion protection. Coriobacteriales and Syntrophobacterales could be part of a microbial food web degrading organic matter to supply methanogenic substrates. Methane-producing Methanobacteriales could metabolize iron, which may initially lead to mild corrosion but potentially stimulates the formation of a carbonate-rich protective deposit layer in the long term. In addition, Methanobacteriales and Coriobacteriales have the potential to interact with metal surfaces via direct interspecies or extracellular electron transfer. In conclusion, our study provides valuable insights into microbial populations involved in iron corrosion protection and potentially enables the development of novel strategies for in situ screening of iron sheet piles in order to reduce risks and develop more sustainable replacement practices.IMPORTANCE Iron sheet piles are widely used to reinforce dikes and river banks. Damage due to iron corrosion poses a significant safety risk and has significant economic impact. Different groups of microorganisms are known to either stimulate or inhibit the corrosion process. Recently, natural corrosion-protective deposit layers were found on sheet piles. Analyses of the microbial composition indicated a potential role for methane-producing archaea. However, the full metabolic potential of the microbial communities within these protective layers has not been determined. The significance of this work lies in the reconstruction of the microbial food web of natural corrosion-protective layers isolated from noncorroding metal sheet piles. With this work, we provide insights into the microbiological mechanisms that potentially promote corrosion protection in freshwater ecosystems. Our findings could support the development of screening protocols to assess the integrity of iron sheet piles to decide whether replacement is required.}, }
@article {pmid31420340, year = {2019}, author = {Bale, NJ and Palatinszky, M and Rijpstra, WIC and Herbold, CW and Wagner, M and Sinninghe Damsté, JS}, title = {Membrane Lipid Composition of the Moderately Thermophilic Ammonia-Oxidizing Archaeon "Candidatus Nitrosotenuis uzonensis" at Different Growth Temperatures.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {20}, pages = {}, pmid = {31420340}, issn = {1098-5336}, mesh = {Ammonia/metabolism ; Archaea/*chemistry/growth &amp; development ; Cell Membrane/*chemistry ; Glyceryl Ethers/analysis ; Membrane Lipids/*analysis ; Oxidation-Reduction ; *Temperature ; }, abstract = {"Candidatus Nitrosotenuis uzonensis" is the only cultured moderately thermophilic member of the thaumarchaeotal order Nitrosopumilales (NP) that contains many mesophilic marine strains. We examined its membrane lipid composition at different growth temperatures (37°C, 46°C, and 50°C). Its lipids were all membrane-spanning glycerol dialkyl glycerol tetraethers (GDGTs), with 0 to 4 cyclopentane moieties. Crenarchaeol (cren), the characteristic thaumarchaeotal GDGT, and its isomer (cren') were present in high abundance (30 to 70%). The GDGT polar headgroups were mono-, di-, and trihexoses and hexose/phosphohexose. The ratio of glycolipid to phospholipid GDGTs was highest in the cultures grown at 50°C. With increasing growth temperatures, the relative contributions of cren and cren' increased, while those of GDGT-0 to GDGT-4 (including isomers) decreased. TEX86 (tetraether index of tetraethers consisting of 86 carbons)-derived temperatures were much lower than the actual growth temperatures, further demonstrating that TEX86 does not accurately reflect the membrane lipid adaptation of thermophilic Thaumarchaeota As the temperature increased, specific GDGTs changed relative to their isomers, possibly representing temperature adaption-induced changes in cyclopentane ring stereochemistry. Comparison of a wide range of thaumarchaeotal core lipid compositions revealed that the "Ca Nitrosotenuis uzonensis" cultures clustered separately from other members of the NP order and the Nitrososphaerales (NS) order. While phylogeny generally seems to have a strong influence on GDGT distribution, our analysis of "Ca Nitrosotenuis uzonensis" demonstrates that its terrestrial, higher-temperature niche has led to a lipid composition that clearly differentiates it from other NP members and that this difference is mostly driven by its high cren' content.IMPORTANCE For Thaumarchaeota, the ratio of their glycerol dialkyl glycerol tetraether (GDGT) lipids depends on growth temperature, a premise that forms the basis of the widely applied TEX86 paleotemperature proxy. A thorough understanding of which GDGTs are produced by which Thaumarchaeota and what the effect of temperature is on their GDGT composition is essential for constraining the TEX86 proxy. "Ca Nitrosotenuis uzonensis" is a moderately thermophilic thaumarchaeote enriched from a thermal spring, setting it apart in its environmental niche from the other marine mesophilic members of its order. Indeed, we found that the GDGT composition of "Ca Nitrosotenuis uzonensis" cultures was distinct from those of other members of its order and was more similar to those of other thermophilic, terrestrial Thaumarchaeota This suggests that while phylogeny has a strong influence on GDGT distribution, the environmental niche that a thaumarchaeote inhabits also shapes its GDGT composition.}, }
@article {pmid31418250, year = {2019}, author = {Jiang, Y and Xu, ZW and Wang, RZ and Li, H and Zhang, YG}, title = {[Effects of long-term fertilization and water addition on soil properties and plant community characteristics in a semiarid grassland.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {30}, number = {7}, pages = {2470-2480}, doi = {10.13287/j.1001-9332.201907.034}, pmid = {31418250}, issn = {1001-9332}, mesh = {*Agriculture ; China ; Ecosystem ; *Fertilizers ; *Grassland ; Nitrogen ; Plants ; *Soil ; Water ; }, abstract = {We summarized the effects of fertilization and water addition on some soil properties and plant community characteristics in a long-term field experiment established in 2005 in a degraded grassland in Duolun, Inner Mongolia, China. The results showed that nitrogen (N) addition resulted in surface soil acidification and decreased acid buffering capacity, increased the availability of carbon (C), N, phosphorus (P), sulfur (S) and DTPA-extractable iron (Fe), manganese (Mn), and copper (Cu) contents, depleted the sum of base cations calcium (Ca), magnesium (Mg), potassium (K) and sodium (Na), decreased the diversity of soil microbial community. Nitrogen addition enhanced the uptake of N, P, S, K, Mn, Cu and Zn by plants, while inhibited plant Fe uptake, but with no effect on the uptake of Ca or Mg. Nitrogen addition increased aboveground net primary productivity (ANPP) but declined plant species diversity and community stability. Phosphorus addition alone increased total P and Olsen-P contents and fungal abundance in the surface soil, and improved N, P and S uptake by leaves, but had no significant influence on other soil basic chemical properties, ANPP, and plant species diversity. Water addition could improve the resistance of plant community, but its contribution to ANPP was limited by soil N availa-bility. Water addition could buffer soil acidification and the decline of microbial and plant diversity induced by N addition. Under the treatments of N and water addition or P and water addition, the diversity and function of soil microorganisms were affected by plant community structure and function. Long-term controlled field experiments were useful for understanding ecosystem structure and functions of grasslands. However, to uncover the underlying mechanisms in grassland ecosystem ecology, single-site experiments should be incorporated with multiple-site controlled field experiments in different regions. More attentions should be paid to the linkage of above- and below-ground ecological processes.}, }
@article {pmid31415965, year = {2019}, author = {Deng, Y and Ruan, Y and Ma, B and Timmons, MB and Lu, H and Xu, X and Zhao, H and Yin, X}, title = {Multi-omics analysis reveals niche and fitness differences in typical denitrification microbial aggregations.}, journal = {Environment international}, volume = {132}, number = {}, pages = {105085}, doi = {10.1016/j.envint.2019.105085}, pmid = {31415965}, issn = {1873-6750}, mesh = {Bacteria/*metabolism ; *Biofilms ; *Bioreactors ; Carbon ; *Denitrification ; Salinity ; Wastewater/*chemistry/microbiology ; *Water Purification ; }, abstract = {Suspended floc and fixed biofilm are two commonly applied strategies for heterotrophic denitrification in wastewater treatment. These two strategies use different carbon sources and reside within different ecological niches for microbial aggregation, which were hypothesized to show distinct microbial structures and metabolic fitness. We surveyed three floc reactors and three biofilm reactors for denitrification and determined if there were distinct microbial aggregations. Multiple molecular omics approaches were used to determine the microbial community composition, co-occurrence network and metabolic pathways. Proteobacteria was the dominating and most active phylum among all samples. Carbon source played an important role in shaping the microbial community composition while the distribution of functional protein was largely influenced by salinity. We found that the topological network features had different ecological patterns and that the microorganisms in the biofilm reactors had more nodes but less interactions than those in floc reactors. The large niche differences in the biofilm reactors explained the observed high microbial diversity, functional redundancy and resulting high system stability. We also observed a lower proportion of denitrifiers and higher resistance to oxygen and salinity perturbation in the biofilm reactors than the floc reactors. Our findings support our hypothesis that niche differences caused a distinct microbial structure and increased microbial ecology distribution, which has the potential to improve system efficiency and stability.}, }
@article {pmid31412927, year = {2019}, author = {Pérez-Jaramillo, JE and de Hollander, M and Ramírez, CA and Mendes, R and Raaijmakers, JM and Carrión, VJ}, title = {Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {114}, pmid = {31412927}, issn = {2049-2618}, mesh = {Bacteria/*isolation &amp; purification ; Colombia ; *Domestication ; *Microbiota ; Phaseolus/*microbiology ; Plant Roots/*microbiology ; Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {BACKGROUND: Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood.<br><br>RESULTS: Here, we investigated if the transition from a native to an agricultural soil affected rhizobacterial community assembly of wild and modern common bean (Phaseolus vulgaris) and if this led to a depletion of rhizobacterial diversity. The impact of the bean genotype on rhizobacterial assembly was more prominent in the agricultural soil than in the native soil. Although only 113 operational taxonomic units (OTUs) out of a total of 15,925 were shared by all eight bean accessions grown in native and agricultural soils, this core microbiome represented a large fraction (25.9%) of all sequence reads. More OTUs were exclusively found in the rhizosphere of common bean in the agricultural soil as compared to the native soil and in the rhizosphere of modern bean accessions as compared to wild accessions. Co-occurrence analyses further showed a reduction in complexity of the interactions in the bean rhizosphere microbiome in the agricultural soil as compared to the native soil.<br><br>CONCLUSIONS: Collectively, these results suggest that habitat expansion of common bean from its native soil environment to an agricultural context had an unexpected overall positive effect on rhizobacterial diversity and led to a stronger bean genotype-dependent effect on rhizosphere microbiome assembly.}, }
@article {pmid31409850, year = {2019}, author = {Posada-Perlaza, CE and Ramírez-Rojas, A and Porras, P and Adu-Oppong, B and Botero-Coy, AM and Hernández, F and Anzola, JM and Díaz, L and Dantas, G and Reyes, A and Zambrano, MM}, title = {Bogotá River anthropogenic contamination alters microbial communities and promotes spread of antibiotic resistance genes.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11764}, pmid = {31409850}, issn = {2045-2322}, mesh = {Colombia ; Drug Resistance, Microbial/*genetics ; Geologic Sediments/microbiology ; *Human Activities ; Humans ; Microbiota/*drug effects ; Rivers ; *Water Microbiology ; Water Pollutants, Chemical/*toxicity ; }, abstract = {The increase in antibiotic resistant bacteria has raised global concern regarding the future effectiveness of antibiotics. Human activities that influence microbial communities and environmental resistomes can generate additional risks to human health. In this work, we characterized aquatic microbial communities and their resistomes in samples collected at three sites along the Bogotá River and from wastewaters at three city hospitals, and investigated community profiles and antibiotic resistance genes (ARGs) as a function of anthropogenic contamination. The presence of antibiotics and other commonly used drugs increased in locations highly impacted by human activities, while the diverse microbial communities varied among sites and sampling times, separating upstream river samples from more contaminated hospital and river samples. Clinically relevant antibiotic resistant pathogens and ARGs were more abundant in contaminated water samples. Tracking of resistant determinants to upstream river waters and city sources suggested that human activities foster the spread of ARGs, some of which were co-localized with mobile genetic elements in assembled metagenomic contigs. Human contamination of this water ecosystem changed both community structure and environmental resistomes that can pose a risk to human health.}, }
@article {pmid31409661, year = {2019}, author = {Small, CM and Currey, M and Beck, EA and Bassham, S and Cresko, WA}, title = {Highly Reproducible 16S Sequencing Facilitates Measurement of Host Genetic Influences on the Stickleback Gut Microbiome.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, pmid = {31409661}, issn = {2379-5077}, support = {F32 GM122419/GM/NIGMS NIH HHS/United States ; P50 GM098911/GM/NIGMS NIH HHS/United States ; R24 RR032670/RR/NCRR NIH HHS/United States ; }, abstract = {Multicellular organisms interact with resident microbes in important ways, and a better understanding of host-microbe interactions is aided by tools such as high-throughput 16S sequencing. However, rigorous evaluation of the veracity of these tools in a different context from which they were developed has often lagged behind. Our goal was to perform one such critical test by examining how variation in tissue preparation and DNA isolation could affect inferences about gut microbiome variation between two genetically divergent lines of threespine stickleback fish maintained in the same laboratory environment. Using careful experimental design and intensive sampling of individuals, we addressed technical and biological sources of variation in 16S-based estimates of microbial diversity. After employing a two-tiered bead beating approach that comprised tissue homogenization followed by microbial lysis in subsamples, we found an extremely minor effect of DNA isolation protocol relative to among-host microbial diversity differences. Abundance estimates for rare operational taxonomic units (OTUs), however, showed much lower reproducibility. Gut microbiome composition was highly variable across fish-even among cohoused siblings-relative to technical replicates, but a subtle effect of host genotype (stickleback line) was nevertheless detected for some microbial taxa.IMPORTANCE Our findings demonstrate the importance of appropriately quantifying biological and technical variance components when attempting to understand major influences on high-throughput microbiome data. Our focus was on understanding among-host (biological) variance in community metrics and its magnitude in relation to within-host (technical) variance, because meaningful comparisons among individuals are necessary in addressing major questions in host-microbe ecology and evolution, such as heritability of the microbiome. Our study design and insights should provide a useful example for others desiring to quantify microbiome variation at biological levels in the face of various technical factors in a variety of systems.}, }
@article {pmid31407303, year = {2019}, author = {Kröber, E and Eyice, &#xd6;}, title = {Profiling of Active Microorganisms by Stable Isotope Probing-Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2046}, number = {}, pages = {151-161}, doi = {10.1007/978-1-4939-9721-3_12}, pmid = {31407303}, issn = {1940-6029}, mesh = {Cluster Analysis ; Ecosystem ; Isotope Labeling/methods ; Metabolic Networks and Pathways/genetics ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics/physiology ; Software ; }, abstract = {Stable isotope probing (SIP) provides researchers a culture-independent method to retrieve nucleic acids from active microbial populations performing a specific metabolic activity in complex ecosystems. In recent years, the use of the SIP method in microbial ecology studies has been accelerated. This is partly due to the advances in sequencing and bioinformatics tools, which enable fast and reliable analysis of DNA and RNA from the SIP experiments. One of these sequencing tools, metagenomics, has contributed significantly to the body of knowledge by providing data not only on taxonomy but also on the key functional genes in specific metabolic pathways and their relative abundances. In this chapter, we provide a general background on the application of the SIP-metagenomics approach in microbial ecology and a workflow for the analysis of metagenomic datasets using the most up-to-date bioinformatics tools.}, }
@article {pmid31407302, year = {2019}, author = {Finley, BK and Hayer, M and Mau, RL and Purcell, AM and Koch, BJ and van Gestel, NC and Schwartz, E and Hungate, BA}, title = {Microbial Taxon-Specific Isotope Incorporation with DNA Quantitative Stable Isotope Probing.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2046}, number = {}, pages = {137-149}, doi = {10.1007/978-1-4939-9721-3_11}, pmid = {31407302}, issn = {1940-6029}, mesh = {Carbon Isotopes/analysis/metabolism ; Classification ; DNA Probes/*metabolism ; DNA, Bacterial/*genetics/metabolism ; Environmental Microbiology ; Isotope Labeling/*methods ; Microbiota/*genetics ; Nitrogen Isotopes/analysis/metabolism ; Oxygen Isotopes/analysis/metabolism ; }, abstract = {Quantitative stable isotope probing (qSIP) measures rates of taxon-specific element assimilation in intact microbial communities, utilizing substrates labeled with a heavy isotope.The laboratory protocol for qSIP is nearly identical to that for conventional stable isotope probing, with two key additions: (1) in qSIP, qPCR measurements are conducted on each density fraction recovered after isopycnic separation, and (2) in qSIP, multiple density fractions are sequenced spanning the entire range of densities over which nucleic acids were recovered. qSIP goes beyond identifying taxa assimilating a substrate, as it also allows for measuring that assimilation for each taxon within a given microbial community. Here, we describe an analysis process necessary to determine atom fraction excess of a heavy stable isotope added to an environmental sample for a given taxon's DNA.}, }
@article {pmid31407297, year = {2019}, author = {Mayali, X and Weber, PK and Nuccio, E and Lietard, J and Somoza, M and Blazewicz, SJ and Pett-Ridge, J}, title = {Chip-SIP: Stable Isotope Probing Analyzed with rRNA-Targeted Microarrays and NanoSIMS.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2046}, number = {}, pages = {71-87}, doi = {10.1007/978-1-4939-9721-3_6}, pmid = {31407297}, issn = {1940-6029}, mesh = {Bacteria/genetics ; Carbon Isotopes/analysis/metabolism ; Classification ; DNA, Bacterial/*genetics ; Isotope Labeling/*methods ; Mass Spectrometry ; Microarray Analysis ; Microbiota/*genetics ; Nitrogen Isotopes/analysis/metabolism ; Oxygen Isotopes/analysis/metabolism ; Phylogeny ; RNA, Ribosomal/*genetics/metabolism ; Software ; }, abstract = {Chip-SIP is a stable isotope probing (SIP) method for linking microbial identity and function in mixed communities and is capable of analyzing multiple isotopes ([13]C, [15]N, and [18]O) simultaneously. This method uses a high-density microarray to separate taxon-specific 16S (or 18S) rRNA genes and a high sensitivity magnetic sector secondary ion mass spectrometer (SIMS) to determine the relative isotope incorporation of the rRNA at each probe location. Using a maskless array synthesizer (MAS), we synthesize multiple unique sequences to target hundreds of taxa at the ribosomal operational taxonomic unit (OTU) level on an array surface, and then analyze it with a NanoSIMS 50, using its high-spatial resolution imaging capability to generate isotope ratios for individual probes. The Chip-SIP method has been used in diverse systems, including surface marine and estuarine water, rhizosphere, and peat soils, to quantify taxon-specific relative incorporation of different substrates in complex microbial communities. Depending on the hypothesis and experimental design, Chip-SIP allows the user to compare the same community incorporating different substrates, different communities incorporating the same substrate(s), or quantify how a community responds to treatment effects, such as temperature or nutrient concentrations.}, }
@article {pmid31407296, year = {2019}, author = {Taubert, M}, title = {SIP-Metaproteomics: Linking Microbial Taxonomy, Function, and Activity.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2046}, number = {}, pages = {57-69}, doi = {10.1007/978-1-4939-9721-3_5}, pmid = {31407296}, issn = {1940-6029}, mesh = {Biomarkers/chemistry/*metabolism ; Carbon Isotopes ; Classification/methods ; Isotope Labeling/*methods ; Mass Spectrometry ; Microbiota/*genetics/physiology ; Phylogeny ; Proteins/chemistry/isolation &amp; purification/metabolism ; Proteolysis ; Proteome/chemistry/*metabolism ; Proteomics/*methods ; Workflow ; }, abstract = {Stable isotope probing combined with metaproteomics enables the detection and characterization of active key species in microbial populations under near-natural conditions, which greatly helps to understand the metabolic functions of complex microbial communities. This is achieved by providing growth substrates labeled with heavy isotopes such as [13]C, which will be assimilated into microbial biomass. After subsequent extraction of proteins and proteolytic cleavage into peptides, the heavy isotope enrichment can be detected by high-resolution mass spectrometric analysis, and linked to the functional and taxonomic characterization of these biomarkers. Here we provide protocols for obtaining isotopically labeled proteins and for downstream SIP-metaproteomics analysis.}, }
@article {pmid31407294, year = {2019}, author = {Ghori, NU and Moreira-Grez, B and Vuong, P and Waite, I and Morald, T and Wise, M and Whiteley, AS}, title = {RNA Stable Isotope Probing (RNA-SIP).}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2046}, number = {}, pages = {31-44}, doi = {10.1007/978-1-4939-9721-3_3}, pmid = {31407294}, issn = {1940-6029}, mesh = {Carbon Isotopes/chemistry ; Centrifugation, Density Gradient/instrumentation/methods ; DNA, Bacterial/genetics/metabolism ; Isotope Labeling/*methods ; Microbiota/genetics ; RNA/isolation &amp; purification/metabolism ; RNA Probes/genetics/*metabolism ; RNA, Ribosomal, 16S/metabolism ; Spectrum Analysis, Raman ; Workflow ; }, abstract = {Stable isotope probing is a combined molecular and isotopic technique used to probe the identity and function of uncultivated microorganisms within environmental samples. Employing stable isotopes of common elements such as carbon and nitrogen, RNA-SIP exploits an increase in the buoyant density of RNA caused by the active metabolism and incorporation of heavier mass isotopes into the RNA after cellular utilization of labeled substrates pulsed into the community. Labeled RNAs are subsequently separated from unlabeled RNAs by density gradient centrifugation followed by identification of the RNAs by sequencing. Therefore, RNA stable isotope probing is a culture-independent technique that provides simultaneous information about microbiome community, composition and function. This chapter presents the detailed protocol for performing an RNA-SIP experiment, including the formation, ultracentrifugation, and fractional analyses of stable isotope-labeled RNAs extracted from environmental samples.}, }
@article {pmid31407021, year = {2020}, author = {Bockoven, AA and Bondy, EC and Flores, MJ and Kelly, SE and Ravenscraft, AM and Hunter, MS}, title = {What Goes Up Might Come Down: the Spectacular Spread of an Endosymbiont Is Followed by Its Decline a Decade Later.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {482-494}, pmid = {31407021}, issn = {1432-184X}, support = {DEB-1020460//Division of Environmental Biology/ ; IOS-1256905//Division of Integrative Organismal Systems/ ; }, mesh = {Animals ; Arizona ; Genetic Fitness ; Hemiptera/genetics/*microbiology/*physiology ; *Microbiota ; Rickettsia/*physiology ; Sex Ratio ; *Symbiosis ; }, abstract = {Facultative, intracellular bacterial symbionts of arthropods may dramatically affect host biology and reproduction. The length of these symbiont-host associations may be thousands to millions of years, and while symbiont loss is predicted, there have been very few observations of a decline of symbiont infection rates. In a population of the sweet potato whitefly species (Bemisia tabaci MEAM1) in Arizona, USA, we documented the frequency decline of a strain of Rickettsia in the Rickettsia bellii clade from near-fixation in 2011 to 36% of whiteflies infected in 2017. In previous studies, Rickettsia had been shown to increase from 1 to 97% from 2000 to 2006 and remained at high frequency for at least five years. At that time, Rickettsia infection was associated with both fitness benefits and female bias. In the current study, we established matrilines of whiteflies from the field (2016, Rickettsia infection frequency = 58%) and studied (a) Rickettsia vertical transmission, (b) fitness and sex ratios associated with Rickettsia infection, (c) symbiont titer, and (d) bacterial communities within whiteflies. The vertical transmission rate was high, approximately 98%. Rickettsia infection in the matrilines was not associated with fitness benefits or sex ratio bias and appeared to be slightly costly, as more Rickettsia-infected individuals produced non-hatching eggs. Overall, the titer of Rickettsia in the matrilines was lower in 2016 than in the whiteflies collected in 2011, but the titer distribution appeared bimodal, with high- and low-titer lines, and constancy of the average titer within lines over three generations. We found neither association between Rickettsia titer and fitness benefits or sex ratio bias nor evidence that Rickettsia was replaced by another secondary symbiont. The change in the interaction between symbiont and host in 2016 whiteflies may explain the drop in symbiont frequency we observed.}, }
@article {pmid31402530, year = {2020}, author = {Onnis-Hayden, A and Srinivasan, V and Tooker, NB and Li, G and Wang, D and Barnard, JL and Bott, C and Dombrowski, P and Schauer, P and Menniti, A and Shaw, A and Stinson, B and Stevens, G and Dunlap, P and Takács, I and McQuarrie, J and Phillips, H and Lambrecht, A and Analla, H and Russell, A and Gu, AZ}, title = {Survey of full-scale sidestream enhanced biological phosphorus removal (S2EBPR) systems and comparison with conventional EBPRs in North America: Process stability, kinetics, and microbial populations.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {92}, number = {3}, pages = {403-417}, doi = {10.1002/wer.1198}, pmid = {31402530}, issn = {1554-7531}, support = {U1R13//Water Environment &amp; Reuse Foundation/ ; //Hampton Roads Sanitation District/ ; //Woodard &amp; Curran, Inc./ ; }, mesh = {*Bioreactors ; Kinetics ; North America ; *Phosphorus ; Phylogeny ; Polyphosphates ; RNA, Ribosomal, 16S ; Surveys and Questionnaires ; }, abstract = {Sidestream EBPR (S2EBPR) is an emerging alternative process to address common challenges in EBPR related to weak wastewater influent and may improve EBPR process stability. A systematic evaluation and comparison of the process performance and microbial community structure was conducted between conventional and S2EBPR facilities in North America. The statistical analysis suggested higher performance stability in S2EBPR than conventional EBPR, although possible bias associated with other plant-specific factors might have affected the comparison. Variations in stoichiometric values related to EBPR activity and discrepancies between the observed values and current model predictions suggested a varying degree of metabolic versatility of PAOs in S2EBPR systems that warrant further investigation. Microbial community analysis using various techniques suggested comparable known candidate PAO relative abundances in S2EBPR and conventional EBPR systems, whereas the relative abundance of known candidate GAOs seemed to be consistently lower in S2EBPR facilities than conventional EBPR facilities. 16S rRNA gene sequencing analysis revealed differences in the community phylogenetic fingerprints between S2EBPR and conventional facilities and indicated statistically higher microbial diversity index values in S2EBPR facilities than those in conventional EBPRs. PRACTITIONER POINTS: Sidestream EBPR (S2EBPR) can be implemented with varying and flexible configurations, and they offer advantages over conventional configurations for addressing the common challenges in EBPR related to weak wastewater influent and may improve EBPR process stability. Survey of S2EBPR plants in North America suggested statistically more stable phosphorus removal performance in S2EBPR plants than conventional EBPRs, although possible bias might affect the comparison due to other plant-specific factors. The EBPR kinetics and stoichiometry of the S2EBPR facilities seemed to vary and are associated with metabolic versatility of PAOs in S2EBPR systems that warrant further investigation. The abundance of known candidate PAOs in S2EBPR plants was similar to those in conventional EBPRs, and the abundance of known candidate GAOs was generally lower in S2EBPR than conventional EBPR facilities. Further finer-resolution analysis of PAOs and GAOs, as well as identification of other unknown PAOs and GAOs, is needed. Microbial diversity is higher in S2EBPR facilities compared with conventional ones, implying that S2EBPR microbial communities could show better resilience to perturbations due to potential functional redundancy.}, }
@article {pmid31399723, year = {2019}, author = {Bolyen, E and Rideout, JR and Dillon, MR and Bokulich, NA and Abnet, CC and Al-Ghalith, GA and Alexander, H and Alm, EJ and Arumugam, M and Asnicar, F and Bai, Y and Bisanz, JE and Bittinger, K and Brejnrod, A and Brislawn, CJ and Brown, CT and Callahan, BJ and Caraballo-Rodríguez, AM and Chase, J and Cope, EK and Da Silva, R and Diener, C and Dorrestein, PC and Douglas, GM and Durall, DM and Duvallet, C and Edwardson, CF and Ernst, M and Estaki, M and Fouquier, J and Gauglitz, JM and Gibbons, SM and Gibson, DL and Gonzalez, A and Gorlick, K and Guo, J and Hillmann, B and Holmes, S and Holste, H and Huttenhower, C and Huttley, GA and Janssen, S and Jarmusch, AK and Jiang, L and Kaehler, BD and Kang, KB and Keefe, CR and Keim, P and Kelley, ST and Knights, D and Koester, I and Kosciolek, T and Kreps, J and Langille, MGI and Lee, J and Ley, R and Liu, YX and Loftfield, E and Lozupone, C and Maher, M and Marotz, C and Martin, BD and McDonald, D and McIver, LJ and Melnik, AV and Metcalf, JL and Morgan, SC and Morton, JT and Naimey, AT and Navas-Molina, JA and Nothias, LF and Orchanian, SB and Pearson, T and Peoples, SL and Petras, D and Preuss, ML and Pruesse, E and Rasmussen, LB and Rivers, A and Robeson, MS and Rosenthal, P and Segata, N and Shaffer, M and Shiffer, A and Sinha, R and Song, SJ and Spear, JR and Swafford, AD and Thompson, LR and Torres, PJ and Trinh, P and Tripathi, A and Turnbaugh, PJ and Ul-Hasan, S and van der Hooft, JJJ and Vargas, F and Vázquez-Baeza, Y and Vogtmann, E and von Hippel, M and Walters, W and Wan, Y and Wang, M and Warren, J and Weber, KC and Williamson, CHD and Willis, AD and Xu, ZZ and Zaneveld, JR and Zhang, Y and Zhu, Q and Knight, R and Caporaso, JG}, title = {Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.}, journal = {Nature biotechnology}, volume = {37}, number = {9}, pages = {1091}, doi = {10.1038/s41587-019-0252-6}, pmid = {31399723}, issn = {1546-1696}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid31399193, year = {2019}, author = {Xu, X and Zhu, X and Wang, C and Li, Y and Fan, C and Kao, X}, title = {microRNA-650 promotes inflammation induced apoptosis of intestinal epithelioid cells by targeting NLRP6.}, journal = {Biochemical and biophysical research communications}, volume = {517}, number = {4}, pages = {551-556}, doi = {10.1016/j.bbrc.2019.06.077}, pmid = {31399193}, issn = {1090-2104}, mesh = {Animals ; Apoptosis/*genetics ; Base Sequence ; Caco-2 Cells ; Cell Line ; Colitis, Ulcerative/genetics/pathology ; Epithelioid Cells/metabolism/*pathology ; Gene Expression Regulation ; Humans ; Inflammation/*genetics/*pathology ; Intestines/*pathology ; Intracellular Signaling Peptides and Proteins/*metabolism ; Male ; Mice ; MicroRNAs/genetics/*metabolism ; Rats ; }, abstract = {Ulcerative colitis (UC), a serious threat to public health, is one of the main forms of inflammatory bowel disease, whereas the molecular mechanisms underlying ulcerative colitis induced by inflammation still remain elusive. NPLR6 gene is previously shown to regulate intestinal homeostasis and regulate the colonic microbial ecology. Here, we report that microRNA-650 (miR-650) plays an important role in the pathogenesis of UC as an upstream regulator of NPLR6 gene. MiR-650 is proved overexpressed in the inflamed mucosa of patients with ulcerative colitis and the DSS induced colitis model mice by qRT-PCR. Over-expression of miR-650 leads to increased apoptosis of Caco-2 and IEC-6 cells, and the DSS-induced mice aggravation, while knock-down of miR-650 shows opposite effects. Through constructing luciferase reporter genes containing 3'-untranslated regions of NLRP6, we further demonstrate that miR-650 inhibits NLRP6 through binding to its 3'-untranslated regions. Overexpression of NLRP6 in Caco-2 and IEC-6 cells suppress the increase apoptosis induced by miR-650 overexpression. Overall, the findings of this study indicate the role of miR-650 in ulcerative colitis, which provides a new target for therapeutic treatment.}, }
@article {pmid31398879, year = {2019}, author = {Hassan, Z and Sultana, M and Khan, SI and Braster, M and Röling, WFM and Westerhoff, HV}, title = {Ample Arsenite Bio-Oxidation Activity in Bangladesh Drinking Water Wells: A Bonanza for Bioremediation?.}, journal = {Microorganisms}, volume = {7}, number = {8}, pages = {}, pmid = {31398879}, issn = {2076-2607}, support = {W01.65.324.00/project 4//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NFRADEV-4-2014-2015 #654248//Corbel: EU-H2020/ ; EU-H2020 MSCA-ITN-2014-ETN: Marie Sk&#x142;odowska-Curie Innovative Training Networks (ITN-ETN) #642691, BBSRC China: BB/J020060/1//Epipredict/ ; }, abstract = {Millions of people worldwide are at risk of arsenic poisoning from their drinking water. In Bangladesh the problem extends to rural drinking water wells, where non-biological solutions are not feasible. In serial enrichment cultures of water from various Bangladesh drinking water wells, we found transfer-persistent arsenite oxidation activity under four conditions (aerobic/anaerobic; heterotrophic/autotrophic). This suggests that biological decontamination may help ameliorate the problem. The enriched microbial communities were phylogenetically at least as diverse as the unenriched communities: they contained a bonanza of 16S rRNA gene sequences. These related to Hydrogenophaga, Acinetobacter, Dechloromonas, Comamonas, and Rhizobium/Agrobacterium species. In addition, the enriched microbiomes contained genes highly similar to the arsenite oxidase (aioA) gene of chemolithoautotrophic (e.g., Paracoccus sp. SY) and heterotrophic arsenite-oxidizing strains. The enriched cultures also contained aioA phylotypes not detected in the previous survey of uncultivated samples from the same wells. Anaerobic enrichments disclosed a wider diversity of arsenite oxidizing aioA phylotypes than did aerobic enrichments. The cultivatable chemolithoautotrophic and heterotrophic arsenite oxidizers are of great interest for future in or ex-situ arsenic bioremediation technologies for the detoxification of drinking water by oxidizing arsenite to arsenate that should then precipitates with iron oxides. The microbial activities required for such a technology seem present, amplifiable, diverse and hence robust.}, }
@article {pmid31398339, year = {2019}, author = {Arevalo, P and VanInsberghe, D and Elsherbini, J and Gore, J and Polz, MF}, title = {A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations.}, journal = {Cell}, volume = {178}, number = {4}, pages = {820-834.e14}, doi = {10.1016/j.cell.2019.06.033}, pmid = {31398339}, issn = {1097-4172}, mesh = {Adaptation, Physiological/genetics ; Alleles ; Clostridiales/*genetics ; Colitis, Ulcerative/microbiology ; Crohn Disease/microbiology ; *Gene Flow ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Microbiota/*genetics ; Models, Genetic ; Mutation Rate ; Phylogeny ; Polymorphism, Single Nucleotide ; Prochlorococcus/genetics ; Sulfolobus/genetics ; Vibrio/genetics ; }, abstract = {Delineating ecologically meaningful populations among microbes is important for identifying their roles in environmental and host-associated microbiomes. Here, we introduce a metric of recent gene flow, which when applied to co-existing microbes, identifies congruent genetic and ecological units separated by strong gene flow discontinuities from their next of kin. We then develop a pipeline to identify genome regions within these units that show differential adaptation and allow mapping of populations onto environmental variables or host associations. Using this reverse ecology approach, we show that the human commensal bacterium Ruminococcus gnavus breaks up into sharply delineated populations that show different associations with health and disease. Defining populations by recent gene flow in this way will facilitate the analysis of bacterial and archaeal genomes using ecological and evolutionary theory developed for plants and animals, thus allowing for testing unifying principles across all biology.}, }
@article {pmid31397240, year = {2019}, author = {Lv, Y and Qin, X and Jia, H and Chen, S and Sun, W and Wang, X}, title = {The association between gut microbiota composition and BMI in Chinese male college students, as analysed by next-generation sequencing.}, journal = {The British journal of nutrition}, volume = {122}, number = {9}, pages = {986-995}, doi = {10.1017/S0007114519001909}, pmid = {31397240}, issn = {1475-2662}, mesh = {Asian People ; Bacteria/*genetics ; Biodiversity ; *Body Mass Index ; China ; Gastrointestinal Microbiome/*genetics ; *High-Throughput Nucleotide Sequencing ; Humans ; Male ; Overweight/*microbiology ; Young Adult ; }, abstract = {Altered gut microbial ecology contributes to the development of metabolic diseases including obesity. However, studies based on different populations have generated conflicting results due to diet, environment, methodologies, etc. The aim of our study was to explore the association between gut microbiota and BMI in Chinese college students. The 16S next-generation sequencing (NGS) was used to test the gut microbiota of nine lean, nine overweight/obesity and ten normal-weight male college students. The differences in gut microbiota distribution among three groups were compared, and the relationship between the richness, diversity, composition of gut microbiota and BMI were analysed. The predominant phyla Bacteroidetes and Firmicutes were further confirmed by real-time PCR. Metagenomic biomarker discovery was conducted by linear discriminant analysis (LDA) effect size (LEfSe). NGS revealed that gut microbiota composition was different among three groups, but there was no difference in the abundance ratio of Firmicutes:Bacteroidetes. Several bacterial taxa were in linear relationship with BMI (positive relationship: uncultured bacterium (Bacteroides genus); negative relationship: Porphyromonadaceae, Acidaminococcaceae, Rikenellaceae, Desulfovibrionaceae, Blautia, Anaerotruncus, Parabacteroides, Alistipes). Moreover, gut microbiota diversity decreased with the increase in BMI. And LEfSe analysis indicated that Blautia, Anaerotruncus and its uncultured species were significantly enriched in the lean group (LDA score ≥ 3), Parasuterella and its uncultured species were significantly enriched in the overweight/obese groups (LDA score ≥ 3). In general, gut microbiota composition and microbial diversity were associated with BMI in Chinese male college students. Our results might enrich the understanding between gut microbiota and obesity.}, }
@article {pmid31396501, year = {2019}, author = {Ramamurthy, T and Mutreja, A and Weill, FX and Das, B and Ghosh, A and Nair, GB}, title = {Revisiting the Global Epidemiology of Cholera in Conjuction With the Genomics of Vibrio cholerae.}, journal = {Frontiers in public health}, volume = {7}, number = {}, pages = {203}, pmid = {31396501}, issn = {2296-2565}, abstract = {Toxigenic Vibrio cholerae is responsible for 1.4 to 4.3 million cases with about 21,000-143,000 deaths per year. Dominance of O1 and O139 serogroups, classical and El tor biotypes, alterations in CTX phages and the pathogenicity Islands are some of the major features of V. cholerae isolates that are responsible for cholera epidemics. Whole-genome sequencing (WGS) based analyses of single-nucleotide polymorphisms (SNPs) and other infrequent genetic variants provide a robust phylogenetic framework. Recent studies on the global transmission of pandemic V. cholerae O1 strains have shown the existence of eight different phyletic lineages. In these, the classical and El Tor biotype strains were separated as two distinctly evolved lineages. The frequency of SNP accumulation and the temporal and geographical distribution supports the perception that the seventh cholera pandemic (7CP) has spread from the Bay of Bengal region in three independent but overlapping waves. The 2010 Haitian outbreak shared a common ancestor with South-Asian wave-3 strains. In West Africa and East/Southern Africa, cholera epidemics are caused by single expanded lineage, which has been introduced several times since 1970. The Latin American epidemics that occurred in 1991 and 2010 were the result of introductions of two 7CP sublineages. Sublineages representing wave-3 have caused huge outbreaks in Haiti and Yemen. The Ogawa-Inaba serotype switchover in several cholera epidemics are believed to be due to the involvement of certain selection mechanism(s) rather than due to random events. V. cholerae O139 serogroup is phylogenetically related to the 7CP El Tor, and almost all these isolates belonged to the multilocus sequence type-69. Additional phenotypic and genotypic information have been generated to understand the pathogenicity of classical and El Tor vibrios. Presence of integrative conjugative elements (ICE) with antibiotic resistance gene cassettes, clustered regularly interspaced short palindromic repeats-associated protein system and ctxAB promoter based ToxRS expression of cholera toxin (CT) separates classical and El Tor biotypes. With the availability of WGS information, several important applications including, molecular typing, antimicrobial resistance, new diagnostics, and vaccination strategies could be generated.}, }
@article {pmid31396176, year = {2019}, author = {Fernández-Martínez, M&#xc1; and Dos Santos Severino, R and Moreno-Paz, M and Gallardo-Carreño, I and Blanco, Y and Warren-Rhodes, K and García-Villadangos, M and Ruiz-Bermejo, M and Barberán, A and Wettergreen, D and Cabrol, N and Parro, V}, title = {Prokaryotic Community Structure and Metabolisms in Shallow Subsurface of Atacama Desert Playas and Alluvial Fans After Heavy Rains: Repairing and Preparing for Next Dry Period.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1641}, pmid = {31396176}, issn = {1664-302X}, abstract = {The Atacama Desert, the oldest and driest desert on Earth, displays significant rains only once per decade. To investigate how microbial communities take advantage of these sporadic wet events, we carried out a geomicrobiological study a few days after a heavy rain event in 2015. Different physicochemical and microbial community analyses were conducted on samples collected from playas and an alluvial fan from surface, 10, 20, 50, and 80 cm depth. Gravimetric moisture content peaks were measured in 10 and 20 cm depth samples (from 1.65 to 4.1% w/w maximum values) while, in general, main anions such as chloride, nitrate, and sulfate concentrations increased with depth, with maximum values of 13-1,125; 168-10,109; and 9,904-30,952 ppm, respectively. Small organic anions such as formate and acetate had maximum concentrations from 2.61 to 3.44 ppm and 6.73 to 28.75 ppm, respectively. Microbial diversity inferred from DNA analysis showed Actinobacteria and Alphaproteobacteria as the most abundant and widespread bacterial taxa among the samples, followed by Chloroflexi and Firmicutes at specific sites. Archaea were mainly dominated by Nitrososphaerales, Methanobacteria, with the detection of other groups such as Halobacteria. Metaproteomics showed a high and even distribution of proteins involved in primary metabolic processes such as energy production and biosynthetic pathways, and a limited but remarkable presence of proteins related to resistance to environmental stressors such as radiation, oxidation, or desiccation. The results indicated that extra humidity in the system allows the microbial community to repair, and prepare for the upcoming hyperarid period. Additionally, it supplies biomarkers to the medium whose preservation potential could be high under strong desiccation conditions and relevant for planetary exploration.}, }
@article {pmid31395953, year = {2019}, author = {Cardini, U and Bartoli, M and Lücker, S and Mooshammer, M and Polzin, J and Lee, RW and Micić, V and Hofmann, T and Weber, M and Petersen, JM}, title = {Chemosymbiotic bivalves contribute to the nitrogen budget of seagrass ecosystems.}, journal = {The ISME journal}, volume = {13}, number = {12}, pages = {3131-3134}, pmid = {31395953}, issn = {1751-7370}, mesh = {Animals ; Bivalvia/*metabolism ; Carbon/metabolism ; Carbon Cycle ; Chemoautotrophic Growth ; Ecology ; Ecosystem ; Nitrogen/*metabolism ; Plants/*metabolism ; Symbiosis ; }, abstract = {In many seagrass sediments, lucinid bivalves and their sulfur-oxidizing symbionts are thought to underpin key ecosystem functions, but little is known about their role in nutrient cycles, particularly nitrogen. We used natural stable isotopes, elemental analyses, and stable isotope probing to study the ecological stoichiometry of a lucinid symbiosis in spring and fall. Chemoautotrophy appeared to dominate in fall, when chemoautotrophic carbon fixation rates were up to one order of magnitude higher as compared with the spring, suggesting a flexible nutritional mutualism. In fall, an isotope pool dilution experiment revealed carbon limitation of the symbiosis and ammonium excretion rates up to tenfold higher compared with fluxes reported for nonsymbiotic marine bivalves. These results provide evidence that lucinid bivalves can contribute substantial amounts of ammonium to the ecosystem. Given the preference of seagrasses for this nitrogen source, lucinid bivalves' contribution may boost productivity of these important blue carbon ecosystems.}, }
@article {pmid31393934, year = {2019}, author = {Barone, M and Turroni, S and Rampelli, S and Soverini, M and D'Amico, F and Biagi, E and Brigidi, P and Troiani, E and Candela, M}, title = {Gut microbiome response to a modern Paleolithic diet in a Western lifestyle context.}, journal = {PloS one}, volume = {14}, number = {8}, pages = {e0220619}, pmid = {31393934}, issn = {1932-6203}, mesh = {Bile/microbiology ; *Diet, Mediterranean ; *Diet, Paleolithic ; Diet, Western ; Dietary Fats/metabolism ; *Gastrointestinal Microbiome ; Humans ; Life Style ; }, abstract = {The modern Paleolithic diet (MPD), featured by the consumption of vegetables, fruit, nuts, seeds, eggs, fish and lean meat, while excluding grains, dairy products, salt and refined sugar, has gained substantial public attention in recent years because of its potential multiple health benefits. However, to date little is known about the actual impact of this dietary pattern on the gut microbiome (GM) and its implications for human health. In the current scenario where Western diets, low in fiber while rich in industrialized and processed foods, are considered one of the leading causes of maladaptive GM changes along human evolution, likely contributing to the increasing incidence of chronic non-communicable diseases, we hypothesize that the MPD could modulate the Western GM towards a more "ancestral" configuration. In an attempt to shed light on this, here we profiled the GM structure of urban Italian subjects adhering to the MPD, and compared data with other urban Italians following a Mediterranean Diet (MD), as well as worldwide traditional hunter-gatherer populations from previous publications. Notwithstanding a strong geography effect on the GM structure, our results show an unexpectedly high degree of biodiversity in MPD subjects, which well approximates that of traditional populations. The GM of MPD individuals also shows some peculiarities, including a high relative abundance of bile-tolerant and fat-loving microorganisms. The consumption of plant-based foods-albeit with the exclusion of grains and pulses-along with the minimization of the intake of processed foods, both hallmarks of the MPD, could therefore contribute to partially rewild the GM but caution should be taken in adhering to this dietary pattern in the long term.}, }
@article {pmid31392355, year = {2020}, author = {Gray, L and Kernaghan, G}, title = {Fungal Succession During the Decomposition of Ectomycorrhizal Fine Roots.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {271-284}, pmid = {31392355}, issn = {1432-184X}, support = {rgpin-2015-04323//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Abies/*microbiology ; *Mycobiome ; Mycorrhizae/*physiology ; Nova Scotia ; Picea/*microbiology ; Plant Roots/*microbiology ; Seedlings/microbiology ; }, abstract = {Ectomycorrhizal (ECM) fine roots account for a substantial proportion of forest production and their decomposition releases large amounts of nutrients to the soil ecosystem. However, little is known about the fungi involved in ECM decomposition, including assemblages of fungal saprotrophs, endophytes, and the ECM fungi themselves. To follow fungal succession during the degradation of senescing fine roots, understory seedlings of Abies balsamea and Picea rubens at two sites in the Acadian forest of Nova Scotia were either severed at the root collar or left as controls. Root systems were collected sequentially over two growing seasons and assessed for fine root loss and ECM mantle integrity. ECM were identified by ITS-PCR and grouped into broad morphological categories. Fungal communities colonizing the senescing fine roots were also monitored by systematically constructing clone libraries over the course of the experiment. ECM with cottony, weakly pigmented mantles (e.g., Cortinarius) degraded within the first year. Those with cottony, but intensely pigmented mantles (Piloderma), and smooth mantles with weak pigmentation (Russulaceae) degraded more slowly. Smooth, melanized ECM (Cenococcum and Tomentella) generally maintained integrity over the course of the experiment. Rates of fine root loss and changes in ECM mantle integrity were positively correlated with soil temperature. ECM DNA was detected throughout the experiment, and was not replaced by that of saprotrophic species during the two seasons sampled. However, fungal root endophytes (e.g., Helotiaceae) initially increased in abundance and then decreased as mantles degraded, suggesting a possible role in ECM decomposition.}, }
@article {pmid31391302, year = {2019}, author = {Ning, D and Deng, Y and Tiedje, JM and Zhou, J}, title = {A general framework for quantitatively assessing ecological stochasticity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {34}, pages = {16892-16898}, pmid = {31391302}, issn = {1091-6490}, mesh = {*Algorithms ; *Ecosystem ; *Models, Biological ; Stochastic Processes ; }, abstract = {Understanding the community assembly mechanisms controlling biodiversity patterns is a central issue in ecology. Although it is generally accepted that both deterministic and stochastic processes play important roles in community assembly, quantifying their relative importance is challenging. Here we propose a general mathematical framework to quantify ecological stochasticity under different situations in which deterministic factors drive the communities more similar or dissimilar than null expectation. An index, normalized stochasticity ratio (NST), was developed with 50% as the boundary point between more deterministic (<50%) and more stochastic (>50%) assembly. NST was tested with simulated communities by considering abiotic filtering, competition, environmental noise, and spatial scales. All tested approaches showed limited performance at large spatial scales or under very high environmental noise. However, in all of the other simulated scenarios, NST showed high accuracy (0.90 to 1.00) and precision (0.91 to 0.99), with averages of 0.37 higher accuracy (0.1 to 0.7) and 0.33 higher precision (0.0 to 1.8) than previous approaches. NST was also applied to estimate stochasticity in the succession of a groundwater microbial community in response to organic carbon (vegetable oil) injection. Our results showed that community assembly was shifted from more deterministic (NST = 21%) to more stochastic (NST = 70%) right after organic carbon input. As the vegetable oil was consumed, the community gradually returned to be more deterministic (NST = 27%). In addition, our results demonstrated that null model algorithms and community similarity metrics had strong effects on quantifying ecological stochasticity.}, }
@article {pmid31388702, year = {2020}, author = {Moss, JA and Henriksson, NL and Pakulski, JD and Snyder, RA and Jeffrey, WH}, title = {Oceanic Microplankton Do Not Adhere to the Latitudinal Diversity Gradient.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {511-515}, pmid = {31388702}, issn = {1432-184X}, mesh = {Archaea/classification/*isolation &amp; purification ; Bacteria/classification/*isolation &amp; purification ; *Biodiversity ; Eukaryota/classification/*isolation &amp; purification ; *Microbiota ; Pacific Ocean ; Plankton/classification/*isolation &amp; purification ; Seawater/microbiology ; }, abstract = {A latitudinal biodiversity gradient has captivated ecologists for years, and has become a widely recognized pattern in biogeography, manifest as an increase in biodiversity from the poles to the tropics. Oceanographers have attempted to discern whether these distribution patterns are shared with marine biota, and a lively debate has emerged concerning the global distribution of microbes. Limitations in sampling resolution for such large-scale assessments have often prohibited definitive conclusions. We evaluated microbial planktonic communities along a ~ 15,400-km Pacific Ocean transect with DNA from samples acquired every 2 degrees of latitude within a 3-month period between late August and early November 2003. Next-generation sequencing targeting the Bacteria, Archaea, and Eukarya yielded ~ 10.8 million high-quality sequences. Beta-analysis revealed geographic patterns of microbial communities, primarily the Bacteria and Archaea domains. None of the domains exhibited a unimodal pattern of alpha-diversity with respect to latitude. Bacteria communities increased in richness from Arctic to Antarctic waters, whereas Archaea and Eukarya communities showed no latitudinal or polar trends. Based on our analyses, environmental factors related to latitude thought to influence various macrofauna may not define microplankton diversity patterns of richness in the global ocean.}, }
@article {pmid31387934, year = {2019}, author = {Ziels, RM and Nobu, MK and Sousa, DZ}, title = {Elucidating Syntrophic Butyrate-Degrading Populations in Anaerobic Digesters Using Stable-Isotope-Informed Genome-Resolved Metagenomics.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, pmid = {31387934}, issn = {2379-5077}, support = {323009/ERC_/European Research Council/International ; }, abstract = {Linking the genomic content of uncultivated microbes to their metabolic functions remains a critical challenge in microbial ecology. Resolving this challenge has implications for improving our management of key microbial interactions in biotechnologies such as anaerobic digestion, which relies on slow-growing syntrophic and methanogenic communities to produce renewable methane from organic waste. In this study, we combined DNA stable-isotope probing (SIP) with genome-centric metagenomics to recover the genomes of populations enriched in [13]C after growing on [[13]C]butyrate. Differential abundance analysis of recovered genomic bins across the SIP metagenomes identified two metagenome-assembled genomes (MAGs) that were significantly enriched in heavy [[13]C]DNA. Phylogenomic analysis assigned one MAG to the genus Syntrophomonas and the other MAG to the genus Methanothrix. Metabolic reconstruction of the annotated genomes showed that the Syntrophomonas genome encoded all the enzymes for beta-oxidizing butyrate, as well as several mechanisms for interspecies electron transfer via electron transfer flavoproteins, hydrogenases, and formate dehydrogenases. The Syntrophomonas genome shared low average nucleotide identity (<95%) with any cultured representative species, indicating that it is a novel species that plays a significant role in syntrophic butyrate degradation within anaerobic digesters. The Methanothrix genome contained the complete pathway for acetoclastic methanogenesis, indicating that it was enriched in [13]C from syntrophic acetate transfer. This study demonstrates the potential of stable-isotope-informed genome-resolved metagenomics to identify in situ interspecies metabolic cooperation within syntrophic consortia important to anaerobic waste treatment as well as global carbon cycling.IMPORTANCE Predicting the metabolic potential and ecophysiology of mixed microbial communities remains a major challenge, especially for slow-growing anaerobes that are difficult to isolate. Unraveling the in situ metabolic activities of uncultured species may enable a more descriptive framework to model substrate transformations by microbiomes, which has broad implications for advancing the fields of biotechnology, global biogeochemistry, and human health. Here, we investigated the in situ function of mixed microbiomes by combining stable-isotope probing with metagenomics to identify the genomes of active syntrophic populations converting butyrate, a C4 fatty acid, into methane within anaerobic digesters. This approach thus moves beyond the mere presence of metabolic genes to resolve "who is doing what" by obtaining confirmatory assimilation of the labeled substrate into the DNA signature. Our findings provide a framework to further link the genomic identities of uncultured microbes with their ecological function within microbiomes driving many important biotechnological and global processes.}, }
@article {pmid31387904, year = {2019}, author = {Su, X and Jing, G and McDonald, D and Wang, H and Wang, Z and Gonzalez, A and Sun, Z and Huang, S and Navas, J and Knight, R and Xu, J}, title = {Reply to Sun et al., "Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy".}, journal = {mBio}, volume = {10}, number = {4}, pages = {}, pmid = {31387904}, issn = {2150-7511}, mesh = {*Microbiota ; RNA, Ribosomal, 16S ; Solar System ; }, }
@article {pmid31384980, year = {2020}, author = {Siddiqee, MH and Henry, R and Deletic, A and Bulach, DM and Coleman, RA and McCarthy, DT}, title = {Salmonella from a Microtidal Estuary Are Capable of Invading Human Intestinal Cell Lines.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {259-270}, pmid = {31384980}, issn = {1432-184X}, support = {LP120100718//Australian Research Council/ ; LP120100718//Melbourne Water/ ; }, mesh = {Caco-2 Cells/*microbiology ; Cities ; Estuaries ; Feces/*microbiology ; Humans ; Intestines/microbiology ; Salmonella/*isolation &amp; purification/*physiology ; Seasons ; Victoria ; Virulence ; }, abstract = {Faecal contamination poses health risks for the recreational users of urban estuaries. However, our understanding of the potential pathogenicity of faecal microbes in these environments is limited. To this end, a study was conducted to understand the spatial and seasonal distribution of Salmonella in water and sediments of the Yarra River estuary, Melbourne, Australia. Among 210 samples in total, culturable Salmonella were recovered from 27%, 17%, and 19% of water, bank, and bed sediment samples, respectively. The combined detection increased from 15% in winter to 32% in summer (p < 0.05) indicating seasonal variation as potential part of public health risk assessments. Further, pathogenic potential of the Salmonella isolates was characterised via the quantification of attachment and invasion capacity using human epithelial colorectal cell line Caco-2 on a subset of isolates (n = 62). While all of these isolates could attach and invade Caco-2 cells, 52% and 13% of these showed greater attachment and invasiveness, respectively, than the corresponding mean values for S. Typhimurium ATCC14028 control. Isolates from winter were on average more invasive (seven out of eight isolates with the highest invasiveness recovered from the colder sampling period) than the isolates from summer, and Salmonella collected during summer showed lower invasion (p < 0.05) compared with the control. Similar low invasion compared with the same control was observed for isolates recovered from bank sediment (p < 0.05). While the higher prevalence in summer may imply higher risks during these peak recreational periods, it is essential that this information is used in combination with quantitative microbial risk assessments to fully understand the health risks posed by Salmonella in microtidal estuaries.}, }
@article {pmid31384013, year = {2019}, author = {Hale, L and Feng, W and Yin, H and Guo, X and Zhou, X and Bracho, R and Pegoraro, E and Penton, CR and Wu, L and Cole, J and Konstantinidis, KT and Luo, Y and Tiedje, JM and Schuur, EAG and Zhou, J}, title = {Tundra microbial community taxa and traits predict decomposition parameters of stable, old soil organic carbon.}, journal = {The ISME journal}, volume = {13}, number = {12}, pages = {2901-2915}, pmid = {31384013}, issn = {1751-7370}, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Carbon/*analysis/metabolism ; Climate Change ; Fungi/classification/genetics/*isolation &amp; purification ; *Microbiota ; Permafrost/microbiology ; Soil/chemistry ; *Soil Microbiology ; Tundra ; }, abstract = {The susceptibility of soil organic carbon (SOC) in tundra to microbial decomposition under warmer climate scenarios potentially threatens a massive positive feedback to climate change, but the underlying mechanisms of stable SOC decomposition remain elusive. Herein, Alaskan tundra soils from three depths (a fibric O horizon with litter and course roots, an O horizon with decomposing litter and roots, and a mineral-organic mix, laying just above the permafrost) were incubated. Resulting respiration data were assimilated into a 3-pool model to derive decomposition kinetic parameters for fast, slow, and passive SOC pools. Bacterial, archaeal, and fungal taxa and microbial functional genes were profiled throughout the 3-year incubation. Correlation analyses and a Random Forest approach revealed associations between model parameters and microbial community profiles, taxa, and traits. There were more associations between the microbial community data and the SOC decomposition parameters of slow and passive SOC pools than those of the fast SOC pool. Also, microbial community profiles were better predictors of model parameters in deeper soils, which had higher mineral contents and relatively greater quantities of old SOC than in surface soils. Overall, our analyses revealed the functional potential of microbial communities to decompose tundra SOC through a suite of specialized genes and taxa. These results portray divergent strategies by which microbial communities access SOC pools across varying depths, lending mechanistic insights into the vulnerability of what is considered stable SOC in tundra regions.}, }
@article {pmid31383901, year = {2019}, author = {Andrade-Martínez, JS and Moreno-Gallego, JL and Reyes, A}, title = {Defining a Core Genome for the Herpesvirales and Exploring their Evolutionary Relationship with the Caudovirales.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11342}, pmid = {31383901}, issn = {2045-2322}, mesh = {Caudovirales/*genetics ; Evolution, Molecular ; *Genome, Viral ; Herpesviridae/*genetics ; Herpesviridae Infections/virology ; Humans ; Phylogeny ; Viral Proteins/genetics ; }, abstract = {The order Herpesvirales encompasses a wide variety of important and broadly distributed human pathogens. During the last decades, similarities in the viral cycle and the structure of some of their proteins with those of the order Caudovirales, the tailed bacterial viruses, have brought speculation regarding the existence of an evolutionary relationship between these clades. To evaluate such hypothesis, we used over 600 Herpesvirales and 2000 Caudovirales complete genomes to search for the presence or absence of clusters of orthologous protein domains and constructed a dendrogram based on their compositional similarities. The results obtained strongly suggest an evolutionary relationship between the two orders. Furthermore, they allowed to propose a core genome for the Herpesvirales, composed of 4 proteins, including the ATPase subunit of the DNA-packaging terminase, the only protein with previously verified conservation. Accordingly, a phylogenetic tree constructed with sequences derived from the clusters associated to these proteins grouped the Herpesvirales strains accordingly to the established families and subfamilies. Overall, this work provides results supporting the hypothesis that the two orders are evolutionarily related and contributes to the understanding of the history of the Herpesvirales.}, }
@article {pmid31379798, year = {2019}, author = {Vigneron, A and Lovejoy, C and Cruaud, P and Kalenitchenko, D and Culley, A and Vincent, WF}, title = {Contrasting Winter Versus Summer Microbial Communities and Metabolic Functions in a Permafrost Thaw Lake.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1656}, pmid = {31379798}, issn = {1664-302X}, abstract = {Permafrost thawing results in the formation of thermokarst lakes, which are biogeochemical hotspots in northern landscapes and strong emitters of greenhouse gasses to the atmosphere. Most studies of thermokarst lakes have been in summer, despite the predominance of winter and ice-cover over much of the year, and the microbial ecology of these waters under ice remains poorly understood. Here we first compared the summer versus winter microbiomes of a subarctic thermokarst lake using DNA- and RNA-based 16S rRNA amplicon sequencing and qPCR. We then applied comparative metagenomics and used genomic bin reconstruction to compare the two seasons for changes in potential metabolic functions in the thermokarst lake microbiome. In summer, the microbial community was dominated by Actinobacteria and Betaproteobacteria, with phototrophic and aerobic pathways consistent with the utilization of labile and photodegraded substrates. The microbial community was strikingly different in winter, with dominance of methanogens, Planctomycetes, Chloroflexi and Deltaproteobacteria, along with various taxa of the Patescibacteria/Candidate Phyla Radiation (Parcubacteria, Microgenomates, Omnitrophica, Aminicenantes). The latter group was underestimated or absent in the amplicon survey, but accounted for about a third of the metagenomic reads. The winter lineages were associated with multiple reductive metabolic processes, fermentations and pathways for the mobilization and degradation of complex organic matter, along with a strong potential for syntrophy or cross-feeding. The results imply that the summer community represents a transient stage of the annual cycle, and that carbon dioxide and methane production continue through the prolonged season of ice cover via a taxonomically distinct winter community and diverse mechanisms of permafrost carbon transformation.}, }
@article {pmid31379789, year = {2019}, author = {Osorio, H and Mettert, E and Kiley, P and Dopson, M and Jedlicki, E and Holmes, DS}, title = {Identification and Unusual Properties of the Master Regulator FNR in the Extreme Acidophile Acidithiobacillus ferrooxidans.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1642}, pmid = {31379789}, issn = {1664-302X}, support = {R01 GM045844/GM/NIGMS NIH HHS/United States ; R01 GM115894/GM/NIGMS NIH HHS/United States ; }, abstract = {The ability to conserve energy in the presence or absence of oxygen provides a metabolic versatility that confers an advantage in natural ecosystems. The switch between alternative electron transport systems is controlled by the fumarate nitrate reduction transcription factor (FNR) that senses oxygen via an oxygen-sensitive [4Fe-4S][2+] iron-sulfur cluster. Under O2 limiting conditions, FNR plays a key role in allowing bacteria to transition from aerobic to anaerobic lifestyles. This is thought to occur via transcriptional activation of genes involved in anaerobic respiratory pathways and by repression of genes involved in aerobic energy production. The Proteobacterium Acidithiobacillus ferrooxidans is a model species for extremely acidophilic microorganisms that are capable of aerobic and anaerobic growth on elemental sulfur coupled to oxygen and ferric iron reduction, respectively. In this study, an FNR-like protein (FNRAF) was discovered in At. ferrooxidans that exhibits a primary amino acid sequence and major motifs and domains characteristic of the FNR family of proteins, including an effector binding domain with at least three of the four cysteines known to coordinate an [4Fe-4S][2+] center, a dimerization domain, and a DNA binding domain. Western blotting with antibodies against Escherichia coli FNR (FNREC) recognized FNRAF. FNRAF was able to drive expression from the FNR-responsive E. coli promoter PnarG, suggesting that it is functionally active as an FNR-like protein. Upon air exposure, FNRAF demonstrated an unusual lack of sensitivity to oxygen compared to the archetypal FNREC. Comparison of the primary amino acid sequence of FNRAF with that of other natural and mutated FNRs, including FNREC, coupled with an analysis of the predicted tertiary structure of FNRAF using the crystal structure of the related FNR from Aliivibrio fisheri as a template revealed a number of amino acid changes that could potentially stabilize FNRAF in the presence of oxygen. These include a truncated N terminus and amino acid changes both around the putative Fe-S cluster coordinating cysteines and also in the dimer interface. Increased O2 stability could allow At. ferrooxidans to survive in environments with fluctuating O2 concentrations, providing an evolutionary advantage in natural, and engineered environments where oxygen gradients shape the bacterial community.}, }
@article {pmid31379773, year = {2019}, author = {Gupta, VVSR and Bramley, RGV and Greenfield, P and Yu, J and Herderich, MJ}, title = {Vineyard Soil Microbiome Composition Related to Rotundone Concentration in Australian Cool Climate 'Peppery' Shiraz Grapes.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1607}, pmid = {31379773}, issn = {1664-302X}, abstract = {Soil microbial communities have an integral association with plants and play an important role in shaping plant nutrition, health, crop productivity and product quality. The influence of bacteria and fungi on wine fermentation is well known. However, little is known about the role of soil microbes, other than microbial pathogens, on grape composition or their role in vintage or site (terroir) impacts on grape composition. In this study, we used an amplicon sequencing approach to investigate the potential relationships between soil microbes and inherent spatial variation in grape metabolite composition - specifically, the concentration of the 'impact aroma compound' rotundone in Shiraz grapes (Vitis vinifera L.) grown in a 6.1 ha vineyard in the Grampians region of Victoria, Australia. Previous work had demonstrated temporal stability in patterns of within-vineyard spatial variation in rotundone concentration, enabling identification of defined 'zones' of inherently 'low' or 'high' concentration of this grape metabolite. 16S rRNA and ITS region-amplicon sequencing analysis of microbial communities in the surface soils collected from these zones indicated marked differences between zones in the genetic diversity and composition of the soil bacterial and fungal microbiome. Soils in the High rotundone zone exhibited higher diversity of bacteria, but lower diversity of fungi, compared to the soils in the Low rotundone zone. In addition, the network analysis of the microbial community in the High rotundone zone soils appeared well structured, especially with respect to the bacterial community, compared to that in the Low rotundone zone soils. The key differences in the microbial community structure between the rotundone zones are obvious for taxa/groups of both bacteria and fungi, particularly for bacteria belonging to Acidobacteria-GP4 and GP7, Rhizobiales, Gaiellaceae, Alphaproteobacteria and the Nectriaceae and Tremellaceae families of fungi. Although mulching in some parts of the vineyard caused changes in bacterial and fungal composition and overall microbial catabolic diversity and activity, its effects did not mask the rotundone zone-based variation. This finding of a systematic rotundone zone-based variation in soil microbiomes suggests an opportunity to bring together understanding of microbial ecology, plant biochemistry, and viticultural management for improved management of grape metabolism, composition and wine flavor.}, }
@article {pmid31377832, year = {2020}, author = {Frankel-Bricker, J and Song, MJ and Benner, MJ and Schaack, S}, title = {Variation in the Microbiota Associated with Daphnia magna Across Genotypes, Populations, and Temperature.}, journal = {Microbial ecology}, volume = {79}, number = {3}, pages = {731-742}, pmid = {31377832}, issn = {1432-184X}, support = {MCB-1150213//National Science Foundation/ ; none//M.J. Murdock Charitable Trust/ ; }, mesh = {Animals ; Bacteria/classification ; *Bacterial Physiological Phenomena ; Daphnia/genetics/*microbiology ; Finland ; *Genotype ; Geography ; Germany ; *Host Microbial Interactions ; Israel ; *Microbiota ; Temperature ; }, abstract = {Studies of how the microbiome varies among individuals, populations, and abiotic conditions are critical for understanding this key component of an organism's biology and ecology. In the case of Daphnia, aquatic microcrustaceans widely used in population/community ecology and environmental science studies, understanding factors that influence microbiome shifts among individuals is useful for both basic and applied research contexts. In this study, we assess differences in the microbiome among genotypes of D. magna collected from three regions along a large latitudinal gradient (Finland, Germany, and Israel). After being reared in the lab for many years, we sought to characterize any differences in genotype- or population-specific microbial communities, and to assess whether the microbiota varied among temperatures. Our study is similar to a recent comparison of the microbial communities among D. magna genotypes raised in different temperatures published by Sullam et al. (Microb Ecol 76(2):506-517, 2017), and as such represents one of the first examples of a reproducible result in microbiome research. Like the previous study, we find evidence for a strong effect of temperature on the microbiome of D. magna, although across a much smaller temperature range representing potential near-future climates. In addition, we find evidence that the microbiomes of D. magna genotypes from different regions are distinct, even years after being brought into the laboratory. Finally, our results highlight a potentially common finding in the expanding area of microbiome research-differences among treatments are not necessarily observed in the most abundant taxonomic groups. This highlights the importance of considering sampling scheme and depth of coverage when characterizing the microbiome, as different experimental designs can significantly impact taxon-specific results, even when large-scale effects are reproduced.}, }
@article {pmid31376000, year = {2020}, author = {Cowan, DA and Hopkins, DW and Jones, BE and Maggs-Kölling, G and Majewska, R and Ramond, JB}, title = {Microbiomics of Namib Desert habitats.}, journal = {Extremophiles : life under extreme conditions}, volume = {24}, number = {1}, pages = {17-29}, pmid = {31376000}, issn = {1433-4909}, mesh = {Bacteria ; Desert Climate ; *Ecosystem ; Soil ; Soil Microbiology ; }, abstract = {The Namib Desert is one of the world's only truly coastal desert ecosystem. Until the end of the 1st decade of the twenty-first century, very little was known of the microbiology of this southwestern African desert, with the few reported studies being based solely on culture-dependent approaches. However, from 2010, an intense research program was undertaken by researchers from the University of the Western Cape Institute for Microbial Biotechnology and Metagenomics, and subsequently the University of Pretoria Centre for Microbial Ecology and Genomics, and their collaborators, led to a more detailed understanding of the ecology of the indigenous microbial communities in many Namib Desert biotopes. Namib Desert soils and the associated specialized niche communities are inhabited by a wide array of prokaryotic, lower eukaryotic and virus/phage taxa. These communities are highly heterogeneous on both small and large spatial scales, with community composition impacted by a range of macro- and micro-environmental factors, from water regime to soil particle size. Community functionality is also surprisingly non-homogeneous, with some taxa retaining functionality even under hyper-arid soil conditions, and with subtle changes in gene expression and phylotype abundances even on diel timescales. Despite the growing understanding of the structure and function of Namib Desert microbiomes, there remain enormous gaps in our knowledge. We have yet to quantify many of the processes in these soil communities, from regional nutrient cycling to community growth rates. Despite the progress that has been made, we still have little knowledge of either the role of phages in microbial community dynamics or inter-species interactions. Furthermore, the intense research efforts of the past decade have highlighted the immense scope for future microbiological research in this dynamic, enigmatic and charismatic region of Africa.}, }
@article {pmid31375480, year = {2019}, author = {Lawley, B and Otal, A and Moloney-Geany, K and Diana, A and Houghton, L and Heath, AM and Taylor, RW and Tannock, GW}, title = {Fecal Microbiotas of Indonesian and New Zealand Children Differ in Complexity and Bifidobacterial Taxa during the First Year of Life.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {19}, pages = {}, pmid = {31375480}, issn = {1098-5336}, mesh = {Age Factors ; Bifidobacterium/*classification ; Breast Feeding ; Cohort Studies ; DNA, Bacterial/genetics ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Indonesia ; Infant ; Milk, Human/microbiology ; New Zealand ; RNA, Ribosomal, 16S/genetics ; Randomized Controlled Trials as Topic ; Rural Population ; Urban Population ; }, abstract = {The biological succession that occurs during the first year of life in the gut of infants in Western countries is broadly predictable in terms of the increasing complexity of the composition of microbiotas. Less information is available about microbiotas in Asian countries, where environmental, nutritional, and cultural influences may differentially affect the composition and development of the microbial community. We compared the fecal microbiotas of Indonesian (n = 204) and New Zealand (NZ) (n = 74) infants 6 to 7 months and 12 months of age. Comparisons were made by analysis of 16S rRNA gene sequences and derivation of community diversity metrics, relative abundances of bacterial families, enterotypes, and cooccurrence correlation networks. Abundances of Bifidobacterium longum subsp. infantis and B. longum subsp. longum were determined by quantitative PCR. All observations supported the view that the Indonesian and NZ infant microbiotas developed in complexity over time, but the changes were much greater for NZ infants. B. longum subsp. infantis dominated the microbiotas of Indonesian children, whereas B. longum subsp. longum was dominant in NZ children. Network analysis showed that the niche model (in which trophic adaptation results in preferential colonization) of the assemblage of microbiotas was supported in Indonesian infants, whereas the neutral (stochastic) model was supported by the development of the microbiotas of NZ infants. The results of the study show that the development of the fecal microbiota is not the same for infants in all countries, and they point to the necessity of obtaining a better understanding of the factors that control the colonization of the gut in early life.IMPORTANCE This study addresses the microbiology of a natural ecosystem (the infant bowel) for children in a rural setting in Indonesia and in an urban environment in New Zealand. Analysis of DNA sequences generated from the microbial community (microbiota) in the feces of the infants during the first year of life showed marked differences in the composition and complexity of the bacterial collections. The differences were most likely due to differences in the prevalence and duration of breastfeeding of infants in the two countries. These kinds of studies are essential for developing concepts of microbial ecology related to the influence of nutrition and environment on the development of the gut microbiota and for determining the long-term effects of microbiological events in early life on human health and well-being.}, }
@article {pmid31374443, year = {2019}, author = {Zhu, YG and Zhao, Y and Zhu, D and Gillings, M and Penuelas, J and Ok, YS and Capon, A and Banwart, S}, title = {Soil biota, antimicrobial resistance and planetary health.}, journal = {Environment international}, volume = {131}, number = {}, pages = {105059}, doi = {10.1016/j.envint.2019.105059}, pmid = {31374443}, issn = {1873-6750}, mesh = {Animals ; Anti-Bacterial Agents ; *Drug Resistance, Bacterial ; *Ecosystem ; *Health ; Humans ; *Soil Microbiology ; }, abstract = {The concept of planetary health acknowledges the links between ecosystems, biodiversity and human health and well-being. Soil, the critical component of the interconnected ecosystem, is the most biodiverse habitat on Earth, and soil microbiomes play a major role in human health and well-being through ecosystem services such as nutrient cycling, pollutant remediation and synthesis of bioactive compounds such as antimicrobials. Soil is also a natural source of antimicrobial resistance, which is often termed intrinsic resistance. However, increasing use and misuse of antimicrobials in humans and animals in recent decades has increased both the diversity and prevalence of antimicrobial resistance in soils, particularly in areas affected by human and animal wastes, such as organic manures and reclaimed wastewater, and also by air transmission. Antimicrobials and antimicrobial resistance are two sides of the sword, while antimicrobials are essential in health care; globally, antimicrobial resistance is jeopardizing the effectiveness of antimicrobial drugs, thus threatening human health. Soil is a crucial pathway through which humans are exposed to antimicrobial resistance determinants, including those harbored by human pathogens. In this review, we use the nexus of antimicrobials and antimicrobial resistance as a focus to discuss the role of soil in planetary health and illustrate the impacts of soil microbiomes on human health and well-being. This review examines the sources and dynamics of antimicrobial resistance in soils and uses the perspective of planetary health to track the movement of antimicrobial-resistance genes between environmental compartments, including soil, water, food and air.}, }
@article {pmid31374141, year = {2019}, author = {Jakob, F and Quintero, Y and Musacchio, A and Estrada-de Los Santos, P and Hernández, L and Vogel, RF}, title = {Acetic acid bacteria encode two levansucrase types of different ecological relationship.}, journal = {Environmental microbiology}, volume = {21}, number = {11}, pages = {4151-4165}, doi = {10.1111/1462-2920.14768}, pmid = {31374141}, issn = {1462-2920}, support = {2816IP001//German Federal Ministry of Food and Agriculture (BMEL) through the Federal Office of Agriculture and Food (BLE)/International ; }, mesh = {Animals ; *Ecosystem ; Hexosyltransferases/classification/*genetics/*metabolism ; Insecta/microbiology ; Plants/microbiology ; Proteobacteria/*enzymology/genetics ; }, abstract = {Acetic acid bacteria (AAB) are associated with plants and insects. Determinants for the targeting and occupation of these widely different environments are unknown. However, most of these natural habitats share plant-derived sucrose, which can be metabolized by some AAB via polyfructose building levansucrases (LS) known to be involved in biofilm formation. Here, we propose two LS types (T) encoded by AAB as determinants for habitat selection, which emerged from vertical (T1) and horizontal (T2) lines of evolution and differ in their genetic organization, structural features and secretion mechanism, as well as their occurrence in proteobacteria. T1-LS are secreted by plant-pathogenic α- and γ-proteobacteria, while T2-LS genes are common in diazotrophic, plant-growth-promoting α-, β- and γ-proteobacteria. This knowledge may be exploited for a better understanding of microbial ecology, plant health and biofilm formation by sucrase-secreting proteobacteria in eukaryotic hosts.}, }
@article {pmid31373372, year = {2019}, author = {Brink, LR and Matazel, K and Piccolo, BD and Bowlin, AK and Chintapalli, SV and Shankar, K and Yeruva, L}, title = {Neonatal Diet Impacts Bioregional Microbiota Composition in Piglets Fed Human Breast Milk or Infant Formula.}, journal = {The Journal of nutrition}, volume = {149}, number = {12}, pages = {2236-2246}, pmid = {31373372}, issn = {1541-6100}, support = {P20 GM121293/GM/NIGMS NIH HHS/United States ; }, mesh = {*Animal Feed ; Animals ; *Animals, Newborn ; *Gastrointestinal Microbiome ; Humans ; *Infant Formula ; *Milk, Human ; Swine ; }, abstract = {BACKGROUND: Early infant diet influences postnatal gut microbial development, which in turn can modulate the developing immune system.<br><br>OBJECTIVES: The aim of this study was to characterize diet-specific bioregional microbiota differences in piglets fed either human breast milk (HM) or infant formula.<br><br>METHODS: Male piglets (White Dutch Landrace Duroc) were raised on HM or cow milk formula (MF) from postnatal day (PND) 2 to PND 21 and weaned to an ad libitum diet until PND 51. Piglets were euthanized on either PND 21 or PND 51, and the gastrointestinal contents were collected for 16s RNA sequencing. Data were analyzed using the Quantitative Insight into Microbial Ecology. Diversity measurements (Chao1 and Shannon) and the Wald test were used to determine relative abundance.<br><br>RESULTS: At PND 21, the ileal luminal region of HM-fed piglets showed lower Chao1 operational taxonomic unit diversity, while Shannon diversity was lower in cecal, proximal colon (PC), and distal colon (DC) luminal regions, relative to MF-fed piglets. In addition, at PND 51, the HM-fed piglets had lower genera diversity within the jejunum, ileum, PC, and DC luminal regions, relative to MF-fed piglets. At PND 21, Turicibacter was 4- to 5-fold lower in the HM-fed piglets' ileal, cecal, PC, and DC luminal regions, relative to the MF-fed piglets. Campylobacter is 3- to 6-fold higher in HM-fed piglets duodenal, ileal, cecal, PC, and DC luminal regions, in comparison to MF-fed piglets. Furthermore, the large intestine (cecum, PC, and rectum) luminal region of HM-fed piglets showed 4- to 7-fold higher genera that belong to class Bacteroidia, in comparison to MF-fed piglets at PND 21. In addition, at PND 51 distal colon lumen of HM-fed piglets showed 1.5-fold higher genera from class Bacteroidia than the MF-fed piglets.<br><br>CONCLUSIONS: In the large intestinal regions (cecum, PC, and rectum), MF diet alters microbiota composition, relative to HM diet, with sustained effects after weaning from the neonatal diet. These microbiota changes could impact immune system and health outcomes later in life.}, }
@article {pmid31372752, year = {2019}, author = {Mosina, NL and Schubert, WD and Cowan, DA}, title = {Characterization and homology modelling of a novel multi-modular and multi-functional Paenibacillus mucilaginosus glycoside hydrolase.}, journal = {Extremophiles : life under extreme conditions}, volume = {23}, number = {6}, pages = {681-686}, pmid = {31372752}, issn = {1433-4909}, mesh = {Bacterial Proteins/*chemistry/genetics ; Glycoside Hydrolases/*chemistry/genetics ; Hot Temperature ; Hydrogen-Ion Concentration ; *Models, Molecular ; Paenibacillus/*enzymology/genetics ; Protein Domains ; Protein Structure, Secondary ; }, abstract = {Glycoside hydrolases, particularly cellulases, xylanases and mannanases, are essential for the depolymerisation of lignocellulosic substrates in various industrial bio-processes. In the present study, a novel glycoside hydrolase from Paenibacillus mucilaginosus (PmGH) was expressed in E. coli, purified and characterised. Functional analysis indicated that PmGH is a 130 kDa thermophilic multi-modular and multi-functional enzyme, comprising a GH5, a GH6 and two CBM3 domains and exhibiting cellulase, mannanase and xylanase activities. The enzyme displayed optimum hydrolytic activities at pH 6 and 60 °C and moderate thermostability. Homology modelling of the full-length protein highlighted the structural and functional novelty of native PmGH, with no close structural homologs identified. However, homology modelling of the individual GH5, GH6 and the two CBM3 domains yielded excellent models based on related structures from the Protein Data Bank. The catalytic GH5 and GH6 domains displayed a (β/α)8 and a distorted seven stranded (β/α) fold, respectively. The distinct homology at the domain level but low homology of the full-length protein suggests that this protein evolved by exogenous gene acquisition and recombination.}, }
@article {pmid31372686, year = {2020}, author = {Bonner, MTL and Allen, DE and Brackin, R and Smith, TE and Lewis, T and Shoo, LP and Schmidt, S}, title = {Tropical Rainforest Restoration Plantations Are Slow to Restore the Soil Biological and Organic Carbon Characteristics of Old Growth Rainforest.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {432-442}, pmid = {31372686}, issn = {1432-184X}, support = {Soil Carbon Research Program (SCaRP)//Commonwealth Scientific and Industrial Research Organisation/ ; Student Research Award//Ecological Society of Australia/ ; Australian Postgraduate Award//Australian Federal Government/ ; }, mesh = {*Carbon Cycle ; *Conservation of Natural Resources ; Queensland ; *Rainforest ; Soil/*chemistry ; *Soil Microbiology ; Tropical Climate ; }, abstract = {Widespread and continuing losses of tropical old-growth forests imperil global biodiversity and alter global carbon (C) cycling. Soil organic carbon (SOC) typically declines with land use change from old-growth forest, but the underlying mechanisms are poorly understood. Ecological restoration plantations offer an established means of restoring aboveground biomass, structure and diversity of forests, but their capacity to recover the soil microbial community and SOC is unknown due to limited empirical data and consensus on the mechanisms of SOC formation. Here, we examine soil microbial community response and SOC in tropical rainforest restoration plantings, comparing them with the original old-growth forest and the previous land use (pasture). Two decades post-reforestation, we found a statistically significant but small increase in SOC in the fast-turnover particulate C fraction. Although the δ[13]C signature of the more stable humic organic C (HOC) fraction indicated a significant compositional turnover in reforested soils, from C4 pasture-derived C to C3 forest-derived C, this did not translate to HOC gains compared with the pasture baseline. Matched old-growth rainforest soils had significantly higher concentrations of HOC than pasture and reforested soils, and soil microbial enzyme efficiency and the ratio of gram-positive to gram-negative bacteria followed the same pattern. Restoration plantings had unique soil microbial composition and function, distinct from baseline pasture but not converging on target old growth rainforest within the examined timeframe. Our results suggest that tropical reforestation efforts could benefit from management interventions beyond re-establishing tree cover to realize the ambition of early recovery of soil microbial communities and stable SOC.}, }
@article {pmid31372685, year = {2020}, author = {Cania, B and Vestergaard, G and Kublik, S and Köhne, JM and Fischer, T and Albert, A and Winkler, B and Schloter, M and Schulz, S}, title = {Biological Soil Crusts from Different Soil Substrates Harbor Distinct Bacterial Groups with the Potential to Produce Exopolysaccharides and Lipopolysaccharides.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {326-341}, pmid = {31372685}, issn = {1432-184X}, support = {SCHU 2907/4-1//Deutsche Forschungsgemeinschaft/ ; TRR 38/2 2011 B04//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Bacteria/genetics/*metabolism ; Lipopolysaccharides/metabolism ; Microbiota/*genetics ; Polysaccharides, Bacterial/*metabolism ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Biological soil crusts (biocrusts) play an important role in improving soil stability and resistance to erosion by promoting aggregation of soil particles. During initial development, biocrusts are dominated by bacteria. Some bacterial members of the biocrusts can contribute to the formation of soil aggregates by producing exopolysaccharides and lipopolysaccharides that act as "glue" for soil particles. However, little is known about the dynamics of "soil glue" producers during the initial development of biocrusts. We hypothesized that different types of initial biocrusts harbor distinct producers of adhesive polysaccharides. To investigate this, we performed a microcosm experiment, cultivating biocrusts on two soil substrates. High-throughput shotgun sequencing was used to obtain metagenomic information on microbiomes of bulk soils from the beginning of the experiment, and biocrusts sampled after 4 and 10 months of incubation. We discovered that the relative abundance of genes involved in the biosynthesis of exopolysaccharides and lipopolysaccharides increased in biocrusts compared with bulk soils. At the same time, communities of potential "soil glue" producers that were highly similar in bulk soils underwent differentiation once biocrusts started to develop. In the bulk soils, the investigated genes were harbored mainly by Betaproteobacteria, whereas in the biocrusts, the major potential producers of adhesive polysaccharides were, aside from Alphaproteobacteria, either Cyanobacteria or Chloroflexi and Acidobacteria. Overall, our results indicate that the potential to form exopolysaccharides and lipopolysaccharides is an important bacterial trait for initial biocrusts and is maintained despite the shifts in bacterial community composition during biocrust development.}, }
@article {pmid31372543, year = {2019}, author = {Ayala-Usma, DA and Lozano-Gutiérrez, RE and González Arango, C}, title = {Wood anatomy of two species of the genus Chrysochlamys (Clusiaceae: Clusioideae: Clusieae) from the northern Andes of Colombia.}, journal = {Heliyon}, volume = {5}, number = {7}, pages = {e02078}, pmid = {31372543}, issn = {2405-8440}, abstract = {Chrysochlamys is a genus of neotropical angiosperms distributed in wet and riparian forests from Bolivia to Mexico in altitudes from near sea-level to close to 3000 m. The wood anatomy of two species of the genus was investigated. Branches of mature stems were collected in a secondary wet forest in Colombian Northern Andes. Slides were obtained and visualized using light microscopy. Gelatinous fiber bands were found and described in C. colombiana and C. dependens. There was a higher amount of septate fibers in the latter. Average ray height and pigment deposit content in ray cells was greater in C. colombiana relative to C. dependens, but rays were commonly wider in the second one. The diversity of vessel-ray pit shapes in C. dependens is greater than in C. colombiana. In both cases rays are considered to be paedomorphic type I. Scanty to absent axial and apotracheal parenchyma was found for both species. We discuss the similarities and differences of the two species in order to establish diagnostic wood features. Also we include brief notes in comparative anatomy with other members of the Clusieaceae family, emphasizing in the incongruences found with previous reports for the genus. This is the first descriptive work in wood anatomy of C. colombiana and C. dependens.}, }
@article {pmid31371535, year = {2019}, author = {Hausmann, B and Vandieken, V and Pjevac, P and Schreck, K and Herbold, CW and Loy, A}, title = {Draft Genome Sequence of Desulfosporosinus fructosivorans Strain 63.6F[T], Isolated from Marine Sediment in the Baltic Sea.}, journal = {Microbiology resource announcements}, volume = {8}, number = {31}, pages = {}, pmid = {31371535}, issn = {2576-098X}, support = {P 31996/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Desulfosporosinus fructosivorans strain 63.6F[T] is a strictly anaerobic, spore-forming, sulfate-reducing bacterium isolated from marine sediment in the Baltic Sea. Here, we report the draft genome sequence of D. fructosivorans 63.6F[T].}, }
@article {pmid31368886, year = {2019}, author = {Wuyts, S and Allonsius, CN and Wittouck, S and Thys, S and Lievens, B and Weckx, S and De Vuyst, L and Sarah, L}, title = {Comparative genome analysis of Lactobacillus mudanjiangensis, an understudied member of the Lactobacillus plantarum group.}, journal = {Microbial genomics}, volume = {5}, number = {9}, pages = {}, pmid = {31368886}, issn = {2057-5858}, mesh = {Bacterial Proteins/genetics ; Cellulase/genetics ; Cellulose/metabolism ; Conjugation, Genetic ; *Genome, Bacterial ; Lactobacillus/classification/*genetics/isolation &amp; purification ; Lactobacillus plantarum/classification/*genetics ; Microscopy, Electron, Scanning ; Phylogeny ; Whole Genome Sequencing ; }, abstract = {The genus Lactobacillus is known to be extremely diverse and consists of different phylogenetic groups that show a diversity that is roughly equal to the expected diversity of a typical bacterial genus. One of the most prominent phylogenetic groups within this genus is the Lactobacillus plantarum group, which contains the understudied Lactobacillus mudanjiangensis species. Before this study, only one L. mudanjiangensis strain, DSM 28402[T], had been described, but without whole-genome analysis. In this study, three strains classified as L. mudanjiangensis were isolated from three different carrot juice fermentations and their whole-genome sequence was determined, together with the genome sequence of the type strain. The genomes of all four strains were compared with publicly available L. plantarum group genome sequences. This analysis showed that L. mudanjiangensis harboured the second largest genome size and gene count of the whole L. plantarum group. In addition, all members of this species showed the presence of a gene coding for a cellulose-degrading enzyme. Finally, three of the four L. mudanjiangensis strains studied showed the presence of pili on scanning electron microscopy (SEM) images, which were linked to conjugative gene regions, coded on a plasmid in at least two of the strains studied.}, }
@article {pmid31368488, year = {2019}, author = {Sapriel, G and Brosch, R}, title = {Shared Pathogenomic Patterns Characterize a New Phylotype, Revealing Transition toward Host-Adaptation Long before Speciation of Mycobacterium tuberculosis.}, journal = {Genome biology and evolution}, volume = {11}, number = {8}, pages = {2420-2438}, pmid = {31368488}, issn = {1759-6653}, mesh = {Adaptation, Physiological/*genetics ; Bacterial Proteins/genetics ; *Evolution, Molecular ; *Genome, Bacterial ; Humans ; Mycobacterium tuberculosis/classification/*genetics/*pathogenicity ; *Phylogeny ; Tuberculosis/*microbiology ; Virulence Factors/genetics ; }, abstract = {Tuberculosis remains one of the deadliest infectious diseases of humanity. To better understand the evolutionary history of host-adaptation of tubercle bacilli (MTB), we sought for mycobacterial species that were more closely related to MTB than the previously used comparator species Mycobacterium marinum and Mycobacterium kansasii. Our phylogenomic approach revealed some recently sequenced opportunistic mycobacterial pathogens, Mycobacterium decipiens, Mycobacterium lacus, Mycobacterium riyadhense, and Mycobacterium shinjukuense, to constitute a common clade with MTB, hereafter called MTB-associated phylotype (MTBAP), from which MTB have emerged. Multivariate and clustering analyses of genomic functional content revealed that the MTBAP lineage forms a clearly distinct cluster of species that share common genomic characteristics, such as loss of core genes, shift in dN/dS ratios, and massive expansion of toxin-antitoxin systems. Consistently, analysis of predicted horizontal gene transfer regions suggests that putative functions acquired by MTBAP members were markedly associated with changes in microbial ecology, for example adaption to intracellular stress resistance. Our study thus considerably deepens our view on MTB evolutionary history, unveiling a decisive shift that promoted conversion to host-adaptation among ancestral founders of the MTBAP lineage long before Mycobacterium tuberculosis has adapted to the human host.}, }
@article {pmid31366993, year = {2019}, author = {Kiersztyn, B and Chróst, R and Kaliński, T and Siuda, W and Bukowska, A and Kowalczyk, G and Grabowska, K}, title = {Structural and functional microbial diversity along a eutrophication gradient of interconnected lakes undergoing anthropopressure.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11144}, pmid = {31366993}, issn = {2045-2322}, mesh = {Bacteria/*genetics ; Biodiversity ; Carbon/metabolism ; Eutrophication/*physiology ; Geologic Sediments/microbiology ; Lakes/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {We present the results of an analysis of the 16S rRNA-based taxonomical structure of bacteria together with an analysis of carbon source utilization ability using EcoPlate (Biolog, USA) metabolic fingerprinting assessment against the backdrop of physicochemical parameters in fifteen interconnected lakes. The lakes exhibit a wide spectrum of trophic gradients and undergo different intensities of anthropopressure. Sequences of V3-V4 16S rRNA genes binned by taxonomic assignment to family indicated that bacterial communities in the highly eutrophicated lakes were distinctly different from the bacterial communities in the meso-eutrophic lakes (ANOSIM r = 0.99, p = 0.0002) and were characterized by higher richness and more diverse taxonomical structure. Representatives of the Actinobacteria, Proteobacteria, Cyanobacteria, Planctomycetes, Verrucomicrobia, Bacteroides phyla predominated. In most cases their relative abundance was significantly correlated with lake trophic state. We found no similar clear relationship of community-level physiological profiling with lake trophic state. However, we found some significant links between the taxonomic and metabolic structure of the microbes in the studied lakes (Mantel's correlation r = 0.22, p = 0.006). The carbon source utilization ability of the studied microorganisms was affected not only by the taxonomic groups present in the lakes but also by various characteristics like a high PO4[3-] concentration inhibiting the utilization of phosphorylated carbon.}, }
@article {pmid31366952, year = {2019}, author = {Otte, JM and Blackwell, N and Ruser, R and Kappler, A and Kleindienst, S and Schmidt, C}, title = {N2O formation by nitrite-induced (chemo)denitrification in coastal marine sediment.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {10691}, pmid = {31366952}, issn = {2045-2322}, abstract = {Nitrous oxide (N2O) is a potent greenhouse gas that also contributes to stratospheric ozone depletion. Besides microbial denitrification, abiotic nitrite reduction by Fe(II) (chemodenitrification) has the potential to be an important source of N2O. Here, using microcosms, we quantified N2O formation in coastal marine sediments under typical summer temperatures. Comparison between gamma-radiated and microbially-active microcosm experiments revealed that at least 15-25% of total N2O formation was caused by chemodenitrification, whereas 75-85% of total N2O was potentially produced by microbial N-transformation processes. An increase in (chemo)denitrification-based N2O formation and associated Fe(II) oxidation caused an upregulation of N2O reductase (typical nosZ) genes and a distinct community shift to potential Fe(III)-reducers (Arcobacter), Fe(II)-oxidizers (Sulfurimonas), and nitrate/nitrite-reducing microorganisms (Marinobacter). Our study suggests that chemodenitrification contributes substantially to N2O formation from marine sediments and significantly influences the N- and Fe-cycling microbial community.}, }
@article {pmid31366612, year = {2019}, author = {McBain, AJ and O'Neill, CA and Amezquita, A and Price, LJ and Faust, K and Tett, A and Segata, N and Swann, JR and Smith, AM and Murphy, B and Hoptroff, M and James, G and Reddy, Y and Dasgupta, A and Ross, T and Chapple, IL and Wade, WG and Fernandez-Piquer, J}, title = {Consumer Safety Considerations of Skin and Oral Microbiome Perturbation.}, journal = {Clinical microbiology reviews}, volume = {32}, number = {4}, pages = {}, pmid = {31366612}, issn = {1098-6618}, mesh = {*Consumer Product Safety ; Cosmetics/*standards ; Education ; Humans ; Microbiota/*physiology ; Mouth/*microbiology ; Skin/*microbiology ; }, abstract = {Microbiomes associated with human skin and the oral cavity are uniquely exposed to personal care regimes. Changes in the composition and activities of the microbial communities in these environments can be utilized to promote consumer health benefits, for example, by reducing the numbers, composition, or activities of microbes implicated in conditions such as acne, axillary odor, dandruff, and oral diseases. It is, however, important to ensure that innovative approaches for microbiome manipulation do not unsafely disrupt the microbiome or compromise health, and where major changes in the composition or activities of the microbiome may occur, these require evaluation to ensure that critical biological functions are unaffected. This article is based on a 2-day workshop held at SEAC Unilever, Sharnbrook, United Kingdom, involving 31 specialists in microbial risk assessment, skin and oral microbiome research, microbial ecology, bioinformatics, mathematical modeling, and immunology. The first day focused on understanding the potential implications of skin and oral microbiome perturbation, while approaches to characterize those perturbations were discussed during the second day. This article discusses the factors that the panel recommends be considered for personal care products that target the microbiomes of the skin and the oral cavity.}, }
@article {pmid31365541, year = {2019}, author = {Yao, Y and Carretero-Paulet, L and Van de Peer, Y}, title = {Using digital organisms to study the evolutionary consequences of whole genome duplication and polyploidy.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0220257}, pmid = {31365541}, issn = {1932-6203}, mesh = {*Evolution, Molecular ; *Gene Duplication ; Gene Regulatory Networks/genetics ; Genome ; *Models, Genetic ; Polyploidy ; }, abstract = {The potential role of whole genome duplication (WGD) in evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary 'dead end', there is growing evidence that the long-term establishment of polyploidy might be linked to environmental change, stressful conditions, or periods of extinction. However, despite much research, the mechanistic underpinnings of why and how polyploids might be able to outcompete non-polyploids at times of environmental upheaval remain indefinable. Here, we improved our recently developed bio-inspired framework, combining an artificial genome with an agent-based system, to form a population of so-called Digital Organisms (DOs), to examine the impact of WGD on evolution under different environmental scenarios mimicking extinction events of varying strength and frequency. We found that, under stable environments, DOs with non-duplicated genomes formed the majority, if not all, of the population, whereas the numbers of DOs with duplicated genomes increased under dramatically challenging environments. After tracking the evolutionary trajectories of individual genomes in terms of sequence and encoded gene regulatory networks (GRNs), we propose that duplicated GRNs might provide polyploids with better chances to acquire the drastic changes necessary to adapt to challenging conditions, thus endowing DOs with increased adaptive potential under extinction events. In contrast, under stable environments, random mutations might easily render the GRN less well adapted to such environments, a phenomenon that is exacerbated in duplicated, more complex GRNs. We believe that our results provide some additional insights into how genome duplication and polyploidy might help organisms to compete for novel niches and survive ecological turmoil, and confirm the usefulness of our computational simulation in studying the role of WGD in evolution and adaptation, helping to overcome some of the traditional limitations of evolution experiments with model organisms.}, }
@article {pmid31364812, year = {2020}, author = {Boll, M and Geiger, R and Junghare, M and Schink, B}, title = {Microbial degradation of phthalates: biochemistry and environmental implications.}, journal = {Environmental microbiology reports}, volume = {12}, number = {1}, pages = {3-15}, doi = {10.1111/1758-2229.12787}, pmid = {31364812}, issn = {1758-2229}, support = {//University of Konstanz/International ; BO 1565/16-1//German research council/International ; }, mesh = {Bacteria/enzymology/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Environmental Pollutants/chemistry/metabolism ; Phthalic Acids/chemistry/*metabolism ; Plastics/chemistry/*metabolism ; }, abstract = {The environmentally relevant xenobiotic esters of phthalic acid (PA), isophthalic acid (IPA) and terephthalic acid (TPA) are produced on a million ton scale annually and are predominantly used as plastic polymers or plasticizers. Degradation by microorganisms is considered as the most effective means of their elimination from the environment and proceeds via hydrolysis to the corresponding PA isomers and alcohols under oxic and anoxic conditions. Further degradation of PA, IPA and TPA differs fundamentally between anaerobic and aerobic microorganisms. The latter introduce hydroxyl functionalities by dioxygenases to facilitate subsequent decarboxylation by either aromatizing dehydrogenases or cofactor-free decarboxylases. In contrast, anaerobic bacteria activate the PA isomers to the respective thioesters using CoA ligases or CoA transferases followed by decarboxylation to the central intermediate benzoyl-CoA. Decarboxylases acting on the three PA CoA thioesters belong to the UbiD enzyme family that harbour a prenylated flavin mononucleotide (FMN) cofactor to achieve the mechanistically challenging decarboxylation. Capture of the extremely instable PA-CoA intermediate is accomplished by a massive overproduction of phthaloyl-CoA decarboxylase and a balanced production of PA-CoA forming/decarboxylating enzymes. The strategy of anaerobic phthalate degradation probably represents a snapshot of an ongoing evolution of a xenobiotic degradation pathway via a short-lived reaction intermediate.}, }
@article {pmid31363029, year = {2019}, author = {Richardson, M and Gottel, N and Gilbert, JA and Lax, S}, title = {Microbial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial Signatures.}, journal = {mBio}, volume = {10}, number = {4}, pages = {}, pmid = {31363029}, issn = {2150-7511}, mesh = {Entropy ; Genetic Markers/genetics ; Humans ; Microbiota/*physiology ; Phylogeny ; Students/*statistics &amp; numerical data ; }, abstract = {The microbiota of the built environment is an amalgamation of both human and environmental sources. While human sources have been examined within single-family households or in public environments, it is unclear what effect a large number of cohabitating people have on the microbial communities of their shared environment. We sampled the public and private spaces of a college dormitory, disentangling individual microbial signatures and their impact on the microbiota of common spaces. We compared multiple methods for marker gene sequence clustering and found that minimum entropy decomposition (MED) was best able to distinguish between the microbial signatures of different individuals and was able to uncover more discriminative taxa across all taxonomic groups. Further, weighted UniFrac- and random forest-based graph analyses uncovered two distinct spheres of hand- or shoe-associated samples. Using graph-based clustering, we identified spheres of interaction and found that connection between these clusters was enriched for hands, implicating them as a primary means of transmission. In contrast, shoe-associated samples were found to be freely interacting, with individual shoes more connected to each other than to the floors they interact with. Individual interactions were highly dynamic, with groups of samples originating from individuals clustering freely with samples from other individuals, while all floor and shoe samples consistently clustered together.IMPORTANCE Humans leave behind a microbial trail, regardless of intention. This may allow for the identification of individuals based on the "microbial signatures" they shed in built environments. In a shared living environment, these trails intersect, and through interaction with common surfaces may become homogenized, potentially confounding our ability to link individuals to their associated microbiota. We sought to understand the factors that influence the mixing of individual signatures and how best to process sequencing data to best tease apart these signatures.}, }
@article {pmid31363014, year = {2019}, author = {Chevrette, MG and Bratburd, JR and Currie, CR and Stubbendieck, RM}, title = {Experimental Microbiomes: Models Not to Scale.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, pmid = {31363014}, issn = {2379-5077}, support = {P41 RR002301/RR/NCRR NIH HHS/United States ; T32 GM008505/GM/NIGMS NIH HHS/United States ; T15 LM007359/LM/NLM NIH HHS/United States ; T32 AI055397/AI/NIAID NIH HHS/United States ; U19 TW009872/TW/FIC NIH HHS/United States ; }, abstract = {Low-cost, high-throughput nucleic acid sequencing ushered the field of microbial ecology into a new era in which the microbial composition of nearly every conceivable environment on the planet is under examination. However, static "screenshots" derived from sequence-only approaches belie the underlying complexity of the microbe-microbe and microbe-host interactions occurring within these systems. Reductionist experimental models are essential to identify the microbes involved in interactions and to characterize the molecular mechanisms that manifest as complex host and environmental phenomena. Herein, we focus on three models (Bacillus-Streptomyces, Aliivibrio fischeri-Hawaiian bobtail squid, and gnotobiotic mice) at various levels of taxonomic complexity and experimental control used to gain molecular insight into microbe-mediated interactions. We argue that when studying microbial communities, it is crucial to consider the scope of questions that experimental systems are suited to address, especially for researchers beginning new projects. Therefore, we highlight practical applications, limitations, and tradeoffs inherent to each model.}, }
@article {pmid31361544, year = {2019}, author = {Cerdó, T and Diéguez, E and Campoy, C}, title = {Early nutrition and gut microbiome: interrelationship between bacterial metabolism, immune system, brain structure, and neurodevelopment.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {317}, number = {4}, pages = {E617-E630}, doi = {10.1152/ajpendo.00188.2019}, pmid = {31361544}, issn = {1522-1555}, mesh = {Animals ; Bacteria/*metabolism ; Brain/*physiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Immune System/*physiology ; Liver/*physiology ; Nervous System/*growth &amp; development ; }, abstract = {Disturbances of diet during pregnancy and early postnatal life may impact colonization of gut microbiota during early life, which could influence infant health, leading to potential long-lasting consequences later in life. This is a nonsystematic review that explores the recent scientific literature to provide a general perspective of this broad topic. Several studies have shown that gut microbiota composition is related to changes in metabolism, energy balance, and immune system disturbances through interaction between microbiota metabolites and host receptors by the gut-brain axis. Moreover, recent clinical studies suggest that an intestinal dysbiosis in gut microbiota may result in cognitive disorders and behavioral problems. Furthermore, recent research in the field of brain imaging focused on the study of the relationship between gut microbial ecology and large-scale brain networks, which will help to decipher the influence of the microbiome on brain function and potentially will serve to identify multiple mediators of the gut-brain axis. Thus, knowledge about optimal nutrition by modulating gut microbiota-brain axis activity will allow a better understanding of the molecular mechanisms involved in the crosstalk between gut microbiota and the developing brain during critical windows. In addition, this knowledge will open new avenues for developing novel microbiota-modulating based diet interventions during pregnancy and early life to prevent metabolic disorders, as well as neurodevelopmental deficits and brain functional disorders.}, }
@article {pmid31359073, year = {2020}, author = {Cellini, A and Donati, I and Fiorentini, L and Vandelle, E and Polverari, A and Venturi, V and Buriani, G and Vanneste, JL and Spinelli, F}, title = {N-Acyl Homoserine Lactones and Lux Solos Regulate Social Behaviour and Virulence of Pseudomonas syringae pv. actinidiae.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {383-396}, pmid = {31359073}, issn = {1432-184X}, support = {613678//FP7-KBBE/ ; }, mesh = {Acyl-Butyrolactones/*metabolism ; Bacterial Proteins/*metabolism ; *Microbial Interactions/genetics ; Plant Diseases/microbiology ; Pseudomonas syringae/*genetics/*pathogenicity ; Repressor Proteins/*metabolism ; Trans-Activators/*metabolism ; Transcription Factors/*metabolism ; Virulence ; }, abstract = {The phyllosphere is a complex environment where microbes communicate through signalling molecules in a system, generally known as quorum sensing (QS). One of the most common QS systems in Gram-negative proteobacteria is based on the production of N-acyl homoserine lactones (AHLs) by a LuxI synthase and their perception by a LuxR sensor. Pseudomonas syringae pv. actinidiae (Psa), the aetiological agent of the bacterial canker of kiwifruit, colonises plant phyllosphere before penetrating via wounds and natural openings. Since Psa genome encodes three LuxR solos without a cognate LuxI, this bacterium may perceive diffusible signals, but it cannot produce AHLs, displaying a non-canonical QS system. The elucidation of the mechanisms underlying the perception of environmental cues in the phyllosphere by this pathogen and their influence on the onset of pathogenesis are of crucial importance for a long-lasting and sustainable management of the bacterial canker of kiwifruit. Here, we report the ability of Psa to sense its own population density and the presence of surrounding bacteria. Moreover, we show that Psa can perceive AHLs, indicating that AHL-producing neighbouring bacteria may regulate Psa virulence in the host. Our results suggest that the ecological environment is important in determining Psa fitness and pathogenic potential. This opens new perspectives in the use of more advanced biochemical and microbiological tools for the control of bacterial canker of kiwifruit.}, }
@article {pmid31357043, year = {2019}, author = {Cagnetta, C and Saerens, B and Meerburg, FA and Decru, SO and Broeders, E and Menkveld, W and Vandekerckhove, TGL and De Vrieze, J and Vlaeminck, SE and Verliefde, ARD and De Gusseme, B and Weemaes, M and Rabaey, K}, title = {High-rate activated sludge systems combined with dissolved air flotation enable effective organics removal and recovery.}, journal = {Bioresource technology}, volume = {291}, number = {}, pages = {121833}, doi = {10.1016/j.biortech.2019.121833}, pmid = {31357043}, issn = {1873-2976}, mesh = {Biofuels ; Flocculation ; *Sewage ; Waste Disposal, Fluid ; }, abstract = {High-rate activated sludge (HRAS) systems typically generate diluted sludge which requires further thickening prior to anaerobic digestion (AD), besides the need to add considerable coagulant and flocculant for the solids separation. As an alternative to conventional gravitational settling, a dissolved air flotation (DAF) unit was coupled to a HRAS system or a high-rate contact stabilization (HiCS) system. The HRAS-DAF system allowed up to 78% removal of the influent solids, and the HiCS-DAF 67%. Both were within the range of values typically obtained for HRAS-settler systems, albeit at a lower chemical requirement. The separated sludge had a high concentration of up to 47 g COD L[-1], suppressing the need of further thickening before AD. Methanation tests showed a biogas yield of up to 68% on a COD basis. The use of a DAF separation system can thus enable direct organics removal at high sludge concentration and with low chemical needs.}, }
@article {pmid31355925, year = {2019}, author = {Shao, D and Vogtmann, E and Liu, A and Qin, J and Chen, W and Abnet, CC and Wei, W}, title = {Microbial characterization of esophageal squamous cell carcinoma and gastric cardia adenocarcinoma from a high-risk region of China.}, journal = {Cancer}, volume = {125}, number = {22}, pages = {3993-4002}, pmid = {31355925}, issn = {1097-0142}, support = {31570116//National Natural Science Foundation of China/International ; 2016YFC0901400//National Key Research and Development Program of precision medicine, China/International ; 2016-I2M-3-001//Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences (CIFMS)/International ; //Intramural Research Program of the National Cancer Institute of the National Institutes of Health/International ; Z99 CA999999/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Adenocarcinoma/*epidemiology/*etiology ; Adult ; Aged ; Bacterial Infections/*complications ; Cardia ; China/epidemiology ; Disease Susceptibility ; Esophageal Squamous Cell Carcinoma/*epidemiology/*etiology ; Female ; Humans ; Male ; Microbiota ; Middle Aged ; Population Surveillance ; Risk Assessment ; Risk Factors ; Stomach Neoplasms/*epidemiology/*etiology ; }, abstract = {BACKGROUND: Little is known about the microbiota and upper gastrointestinal tumors. Esophageal squamous cell carcinoma (ESCC) and gastric cardia adenocarcinoma (GCA) occur in adjacent organs, co-occur geographically, and share many risk factors despite being of different tissue types.<br><br>METHODS: This study characterized the microbial communities of paired tumor and nontumor samples from 67 patients with ESCC and 36 patients with GCA in Henan, China. DNA was extracted with the MoBio PowerSoil kit. The V4 region of the 16S ribosomal RNA gene was sequenced with MiniSeq and was processed with Quantitative Insights Into Microbial Ecology 1. The linear discriminant analysis effect size method was used to identify differentially abundant microbes, the Wilcoxon rank-sum test was used to test &#x3b1; diversity differences, and permutational multivariate analysis of variance was used to test for differences in &#x3b2; diversity.<br><br>RESULTS: The microbial environments of ESCC and GCA tissues were all composed primarily of Firmicutes, Bacteroidetes, and Proteobacteria. ESCC tumor tissues contained more Fusobacterium (3.2% vs 1.3%) and less Streptococcus (12.0% vs 30.2%) than nontumor tissues. GCA nontumor tissues had a greater abundance of Helicobacter (60.5% vs 11.8%), which may have been linked to the lower &#x3b1; diversity (58.0 vs 102.5; P&#xa0;=&#xa0;.0012) in comparison with tumor tissues. A comparison of ESCC and GCA nontumor tissues showed that the microbial composition (P&#xa0;=&#xa0;.0040) and the &#x3b1; diversity (87.0 vs 58.0; P&#xa0;=&#xa0;.00052) were significantly different. No significant differences were detected for &#x3b1; diversity within ESCC and GCA tumor tissues.<br><br>CONCLUSIONS: This study showed differences in the microbial compositions of paired ESCC and GCA tumor and nontumor tissues and differences by organ site. Large-scale, prospective cohort studies are needed to confirm these findings.}, }
@article {pmid31354777, year = {2019}, author = {Del Frari, G and Gobbi, A and Aggerbeck, MR and Oliveira, H and Hansen, LH and Ferreira, RB}, title = {Characterization of the Wood Mycobiome of Vitis vinifera in a Vineyard Affected by Esca. Spatial Distribution of Fungal Communities and Their Putative Relation With Leaf Symptoms.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {910}, pmid = {31354777}, issn = {1664-462X}, abstract = {Esca is a disease complex belonging to the grapevine trunk diseases cluster. It comprises five syndromes, three main fungal pathogenic agents and several symptoms, both internal (i.e., affecting woody tissue) and external (e.g., affecting leaves and bunches). The etiology and epidemiology of this disease complex remain, in part, unclear. Some of the points that are still under discussion concern the sudden rise in disease incidence, the simultaneous presence of multiple wood pathogens in affected grapevines, the causal agents and the discontinuity in time of leaf symptoms manifestation. The standard approach to the study of esca has been mostly through culture-dependent studies, yet, leaving many questions unanswered. In this study, we used Illumina[®] next-generation amplicon sequencing to investigate the mycobiome of grapevines wood in a vineyard with history of esca. We characterized the wood mycobiome composition, investigated the spatial dynamics of the fungal communities in different areas of the stem and in canes, and assessed the putative link between mycobiome and leaf symptoms. An unprecedented diversity of fungi is presented (289 taxa), including five genera reported for the first time in association with grapevines wood (Debaryomyces, Trematosphaeria, Biatriospora, Lopadostoma, and Malassezia) and numerous hitherto unreported species. Esca-associated fungi Phaeomoniella chlamydospora and Fomitiporia sp. dominate the fungal community, and numerous other fungi associated with wood syndromes are also encountered (e.g., Eutypa spp., Inonotus hispidus). The spatial analysis revealed differences in diversity, evenness and taxa abundances, the unique presence of certain fungi in specific areas of the plants, and tissue specificity. Lastly, the mycobiome composition of the woody tissue in proximity to leaves manifesting 'tiger stripes' symptoms of esca, as well as in leaf-symptomatic canes, was highly similar to that of plants not exhibiting any leaf symptomatology. This observation supports the current understanding that leaf symptoms are not directly linked with the fungal communities in the wood. This work builds to the understanding of the microbial ecology of the grapevines wood, offering insights and a critical view on the current knowledge of the etiology of esca.}, }
@article {pmid31354673, year = {2019}, author = {Chen, C and He, R and Cheng, Z and Han, M and Zha, Y and Yang, P and Yao, Q and Zhou, H and Zhong, C and Ning, K}, title = {The Seasonal Dynamics and the Influence of Human Activities on Campus Outdoor Microbial Communities.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1579}, pmid = {31354673}, issn = {1664-302X}, abstract = {Large-scale campus resembles a small "semi-open community," harboring disturbances from the exchanges of people and vehicles, wherein stressors such as temperature and population density differ among the ground surfaces of functional partitions. Therefore, it represents a special ecological niche for the study on microbial ecology in the process of urbanization. In this study, we investigated outdoor microbial communities in four campuses in Wuhan, China. We obtained 284 samples from 55 sampling sites over six seasons, as well as their matching climatic and environmental records. The structure of campus outdoor microbial communities which influenced by multiple climatic factors featured seasonality. The dispersal influence of human activities on microbial communities also contributed to this seasonal pattern non-negligibly. However, despite the microbial composition alteration in response to multiple stressors, the overall predicted function of campus outdoor microbial communities remained stable across campuses. The spatial-temporal dynamic patterns on campus outdoor microbial communities and its predicted functions have bridged the gap between microbial and macro-level ecosystems, and provided hints toward a better understanding of the effects of climatic factors and human activities on campus micro-environments.}, }
@article {pmid31347068, year = {2019}, author = {Mihăşan, M and Babii, C and Aslebagh, R and Channaveerappa, D and Dupree, EJ and Darie, CC}, title = {Exploration of Nicotine Metabolism in Paenarthrobacter nicotinovorans pAO1 by Microbial Proteomics.}, journal = {Advances in experimental medicine and biology}, volume = {1140}, number = {}, pages = {515-529}, doi = {10.1007/978-3-030-15950-4_30}, pmid = {31347068}, issn = {0065-2598}, mesh = {Micrococcaceae/*metabolism ; Nicotine/*metabolism ; Plasmids ; *Proteomics ; *Tandem Mass Spectrometry ; }, abstract = {Proteomics, or the large-scale study of proteins, is a post-genomics field that, together with transcriptomics and metabolomics, has moved the study of bacteria to a new era based on system-wide understanding of bacterial metabolic and regulatory networks. The study of bacterial proteins or microbial proteomics has found a wide array of applications in many fields of microbiology, from food, clinical, and industrial microbiology to microbial ecology and physiology. The current chapter makes a brief technical introduction into the available approaches for the large-scale study of bacterial proteins using mass-spectrometry. Furthermore, the advantages and disadvantages of using bacteria for proteomics studies are indicated as well as several example studies where MS-based bacterial proteomics had a fundamental role in deciphering the scientific question. Finally, the proteomics study of nicotine catabolism in Paenarthrobacter nicotinovorans pAO1 using nanoLC-MS/MS is given as an in-depth example for possible applications of microbial proteomics.The nicotine degradation pathway functioning in Paenarthrobacter nicotinovorans is encoded by the catabolic megaplasmid pAO1 that contains about 40 nicotine-related genes making out the nic-gens cluster. Despite the promising biotechnological potential for the production of green-chemicals, only half of the nic-genes have been experimentally linked to nicotine. In an attempt to systematically identify all the proteins involved in nicotine degradation, a gel-based proteomics approach was used to identify a total of 801 proteins when Paenarthrobacter nicotinovorans was grown on three carbon sources: citrate, nicotine and nicotine and citrate. The differences in protein abundance showed that the bacterium is able to switch between deamination and demethylation in the lower nicotine pathway based on the available C source. Several pAO1 putative genes including a hypothetical polyketide cyclase have been shown to have a nicotine-dependent expression and we hypothesize that the polyketide cyclase would hydrolyze the N1-C6 bond from the pyridine ring with the formation of alpha-keto-glutaramate. Two chromosomal proteins, a malate dehydrogenase, and a D-3-phosphoglycerate dehydrogenase were shown to be strongly upregulated when nicotine was the sole carbon source and could be related to the production of the alpha-keto-glutaramate by the polyketide cyclase.}, }
@article {pmid31346687, year = {2020}, author = {Jha, PN and Gomaa, AB and Yanni, YG and El-Saadany, AY and Stedtfeld, TM and Stedtfeld, RD and Gantner, S and Chai, B and Cole, J and Hashsham, SA and Dazzo, FB}, title = {Alterations in the Endophyte-Enriched Root-Associated Microbiome of Rice Receiving Growth-Promoting Treatments of Urea Fertilizer and Rhizobium Biofertilizer.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {367-382}, pmid = {31346687}, issn = {1432-184X}, support = {INT 0211267//National Science Foundation/ ; BIO10-001-011 Contract #303//US-Eqypt Science &amp; Technology Joint Fund/ ; 3852 [58-3148-1-140//US-Egypt Scientific and Technology Joint Fund/ ; DE-FG02-99ER62848//US Dept. of Energy/ ; F-5 20/2013[IC}//University Grants Commission (IN)/ ; MICLO 2346//Michigan State University / Hatch (US)/ ; }, mesh = {Endophytes/drug effects/*physiology ; *Fertilizers ; Microbiota/drug effects/*physiology ; Oryza/drug effects/metabolism/*microbiology ; Plant Roots/drug effects/metabolism/*microbiology ; Rhizobiaceae/chemistry ; Rhizosphere ; Soil Microbiology ; Urea/administration &amp; dosage/*metabolism ; }, abstract = {We examined the bacterial endophyte-enriched root-associated microbiome within rice (Oryza sativa) 55 days after growth in soil with and without urea fertilizer and/or biofertilization with a growth-promotive bacterial strain (Rhizobium leguminosarum bv. trifolii E11). After treatment to deplete rhizosphere/rhizoplane communities, washed roots were macerated and their endophyte-enriched communities were analyzed by 16S ribosomal DNA 454 amplicon pyrosequencing. This analysis clustered 99,990 valid sequence reads into 1105 operational taxonomic units (OTUs) with 97% sequence identity, 133 of which represented a consolidated core assemblage representing 12.04% of the fully detected OTU richness. Taxonomic affiliations indicated Proteobacteria as the most abundant phylum (especially α- and γ-Proteobacteria classes), followed by Firmicutes, Bacteroidetes, Verrucomicrobia, Actinobacteria, and several other phyla. Dominant genera included Rheinheimera, unclassified Rhodospirillaceae, Pseudomonas, Asticcacaulis, Sphingomonas, and Rhizobium. Several OTUs had close taxonomic affiliation to genera of diazotrophic rhizobacteria, including Rhizobium, unclassified Rhizobiales, Azospirillum, Azoarcus, unclassified Rhizobiaceae, Bradyrhizobium, Azonexus, Mesorhizobium, Devosia, Azovibrio, Azospira, Azomonas, and Azotobacter. The endophyte-enriched microbiome was restructured within roots receiving growth-promoting treatments. Compared to the untreated control, endophyte-enriched communities receiving urea and/or biofertilizer treatments were significantly reduced in OTU richness and relative read abundances. Several unique OTUs were enriched in each of the treatment communities. These alterations in structure of root-associated communities suggest dynamic interactions in the host plant microbiome, some of which may influence the well-documented positive synergistic impact of rhizobial biofertilizer inoculation plus low doses of urea-N fertilizer on growth promotion of rice, considered as one of the world's most important food crops.}, }
@article {pmid31342100, year = {2020}, author = {Long, XE and Yao, H}, title = {Phosphorus Input Alters the Assembly of Rice (Oryza sativa L.) Root-Associated Communities.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {357-366}, pmid = {31342100}, issn = {1432-184X}, support = {41525002//National Natural Science Foundation of China (CN)/ ; 41773079//National Natural Science Foundation of China/ ; XDB15020303//Strategic Priority Research Program of Chinese Academy of Sciences/ ; }, mesh = {Archaea/drug effects/physiology ; Bacterial Physiological Phenomena/drug effects ; Dose-Response Relationship, Drug ; Fungi/drug effects/physiology ; Microbiota/*drug effects ; Oryza/*microbiology ; Phosphorus/administration &amp; dosage/*metabolism ; Plant Roots/*microbiology ; Rhizosphere ; *Soil Microbiology ; }, abstract = {Rice root-associated microbial community play an important role in plant nutrient acquisition, biomass production, and stress tolerance. Herein, root-associated community assembly was investigated under different phosphate input levels in phosphorus (P)-deficient paddy soil. Rice was grown in a long-term P-depleted paddy soil with 0 (P0), 50 (PL), or 200 (PH) mg P2O5 kg[-1] application. DNA from root endophytes was isolated after 46 days, and PCR amplicons from archaea, bacteria, and fungi were sequenced by an Illumina Miseq PE300 platform, respectively. P application had no significant effect on rice root endophytic archaea, which were dominated by ammonia-oxidizing Candidatus Nitrososphaera. By contrast, rice root endophytic community structure of the bacteria and fungi was affected by soil P. Low P input increased endophytic bacterial diversity, whereas high P input increased rhizosphere fungi diversity. Bacillus and Pleosporales, associated with phosphate solubilization and P uptake, dominated in P0 and PH treatments, and Pseudomonas were more abundant in the PL treatment than in the P0 and PH treatments. Co-occurrence network analysis revealed a close interaction between endophytic bacteria and fungi. Soil P application affected both the rice root endosphere and soil rhizosphere microbial community and interaction between rice root endophytic bacteria, and fungi, especially species related to P cycling.}, }
@article {pmid31341288, year = {2019}, author = {Bolyen, E and Rideout, JR and Dillon, MR and Bokulich, NA and Abnet, CC and Al-Ghalith, GA and Alexander, H and Alm, EJ and Arumugam, M and Asnicar, F and Bai, Y and Bisanz, JE and Bittinger, K and Brejnrod, A and Brislawn, CJ and Brown, CT and Callahan, BJ and Caraballo-Rodríguez, AM and Chase, J and Cope, EK and Da Silva, R and Diener, C and Dorrestein, PC and Douglas, GM and Durall, DM and Duvallet, C and Edwardson, CF and Ernst, M and Estaki, M and Fouquier, J and Gauglitz, JM and Gibbons, SM and Gibson, DL and Gonzalez, A and Gorlick, K and Guo, J and Hillmann, B and Holmes, S and Holste, H and Huttenhower, C and Huttley, GA and Janssen, S and Jarmusch, AK and Jiang, L and Kaehler, BD and Kang, KB and Keefe, CR and Keim, P and Kelley, ST and Knights, D and Koester, I and Kosciolek, T and Kreps, J and Langille, MGI and Lee, J and Ley, R and Liu, YX and Loftfield, E and Lozupone, C and Maher, M and Marotz, C and Martin, BD and McDonald, D and McIver, LJ and Melnik, AV and Metcalf, JL and Morgan, SC and Morton, JT and Naimey, AT and Navas-Molina, JA and Nothias, LF and Orchanian, SB and Pearson, T and Peoples, SL and Petras, D and Preuss, ML and Pruesse, E and Rasmussen, LB and Rivers, A and Robeson, MS and Rosenthal, P and Segata, N and Shaffer, M and Shiffer, A and Sinha, R and Song, SJ and Spear, JR and Swafford, AD and Thompson, LR and Torres, PJ and Trinh, P and Tripathi, A and Turnbaugh, PJ and Ul-Hasan, S and van der Hooft, JJJ and Vargas, F and Vázquez-Baeza, Y and Vogtmann, E and von Hippel, M and Walters, W and Wan, Y and Wang, M and Warren, J and Weber, KC and Williamson, CHD and Willis, AD and Xu, ZZ and Zaneveld, JR and Zhang, Y and Zhu, Q and Knight, R and Caporaso, JG}, title = {Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.}, journal = {Nature biotechnology}, volume = {37}, number = {8}, pages = {852-857}, pmid = {31341288}, issn = {1546-1696}, support = {R35 GM133420/GM/NIGMS NIH HHS/United States ; U54 MD012388/MD/NIMHD NIH HHS/United States ; U54 CA143925/CA/NCI NIH HHS/United States ; T32 ES015459/ES/NIEHS NIH HHS/United States ; Z99 CA999999/ImNIH/Intramural NIH HHS/United States ; }, mesh = {*Computational Biology ; *Data Science ; Databases, Factual ; Humans ; *Microbiota ; *Software ; }, }
@article {pmid31339480, year = {2019}, author = {Lee, JC and Whang, KS}, title = {Aquibacillus sediminis sp. nov., a moderately halophilic bacterium isolated from saltern soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {69}, number = {10}, pages = {3121-3127}, doi = {10.1099/ijsem.0.003599}, pmid = {31339480}, issn = {1466-5034}, mesh = {Bacillaceae/*classification/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Diaminopimelic Acid/chemistry ; Fatty Acids/chemistry ; Geologic Sediments/microbiology ; Peptidoglycan/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Salinity ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {A Gram-stain-positive, moderately halophilic bacterium, designated strain BH258[T], was isolated from solar saltern sediment sampled at Shinan in the Republic of Korea. Cells of strain BH258[T] were found to be strictly aerobic, motile, endospore-forming rods which could grow at 15-45 °C (optimum, 35 °C), at pH 5.5-9.0 (pH 7.0) and at salinities of 0.5-20 % (w/v) NaCl (7-10%). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BH258[T] belongs to the genus Aquibacillus, showing highest sequence similarity to Aquibacillus koreensis BH30097[T] (96.1 %), Aquibacillus albus YIM 93624[T] (95.9 %), Aquibacillus halophilus B6B[T] (95.6 %) and Aquibacillus salifodinae WSY08-1[T] (95.1 %). The predominant isoprenoid quinone was identified as menaquinone-7, and the cell-wall peptidoglycan was found to contain meso-diaminopimelic acid as the diagnostic diamino acid. The major fatty acids were identified as anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C15 : 0. The major polar lipids were identified as phosphatidylglycerol, diphosphatidylglycerol and three unidentified phospholipids. The DNA G+C content of this novel isolate was determined to be 37.35 mol%. On the basis of the results of phylogenetic, phenotypic and chemotaxonomic analyses in this study, strain BH258[T] is considered to represent a novel species of the genus Aquibacillus, for which the name Aquibacillus sediminis sp. nov. is proposed. The type strain is BH258[T] (=KACC 18680[T]=NBRC 111875[T]).}, }
@article {pmid31338843, year = {2019}, author = {Vincent, Q and Chartin, C and Krüger, I and Van Wesemael, B and Carnol, M}, title = {CARBIOSOL: Biological indicators of soil quality and organic carbon in grasslands and croplands in Wallonia, Belgium.}, journal = {Ecology}, volume = {100}, number = {11}, pages = {e02843}, doi = {10.1002/ecy.2843}, pmid = {31338843}, issn = {1939-9170}, abstract = {The protection of agricultural soil quality is critical to environmental sustainability and requires relevant indicators. Total soil organic carbon (SOC) is of importance for soil quality but its slow dynamic and inherent variability do not allow early detection of changes. The project CARBIOSOL provides a data set from agricultural soils in Wallonia (Southern Belgium), of total SOC, SOC fractions and biological indicators, selected for their relevance as indicators of soil quality. Two land uses (sampled in 2013), five agricultural regions (2015), seasonal variability in croplands (2016) and four management types (2017) were studied. Soil organic carbon content (total, stable fine fraction <20 μm, labile coarse fraction >20 μm), cold and hot water extractable carbon and nitrogen contents, total nitrogen, pHKC l , pHH 2O , potential respiration, microbial biomass carbon and nitrogen, net nitrogen mineralization, metabolic potential of soil bacteria, earthworm density and biomass, and two ecophysiological quotients (metabolic and microbial quotient) were measured for a total of 415 samples. The present data set provides an important contribution for establishing a reference system of soil quality in Wallonia and eventually for large-scale studies through its integration into a global database. Moreover, the present data set could be used to support the interpretation of measurements of fractions of SOC and biological indicators by soil analyses laboratories, which will be useful for farmers and decision makers to evaluate the effect of different management practices. Information contained in this publication or product may be reproduced, in part or in whole, and by any means for personal or public non-commercial uses, without charge or further permission, unless otherwise specified. Users are required to exercise due diligence in ensuring the accuracy of the material reproduced, indicate the complete title of the material produced and refer to this publication (including author names), indicate that the reproduction is a copy/uses official work financed by the SPW-DGO3. Commercial reproduction and distribution is prohibited, except with written permission from SPW-DGO3 and publication authors.}, }
@article {pmid31338076, year = {2019}, author = {Alviz-Gazitua, P and Fuentes-Alburquenque, S and Rojas, LA and Turner, RJ and Guiliani, N and Seeger, M}, title = {The Response of Cupriavidus metallidurans CH34 to Cadmium Involves Inhibition of the Initiation of Biofilm Formation, Decrease in Intracellular c-di-GMP Levels, and a Novel Metal Regulated Phosphodiesterase.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1499}, pmid = {31338076}, issn = {1664-302X}, abstract = {Cadmium is a highly toxic heavy metal for biological systems. Cupriavidus metallidurans CH34 is a model strain to study heavy metal resistance and bioremediation as it is able to deal with high heavy metal concentrations. Biofilm formation by bacteria is mediated by the second messenger bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP). The aim of this study was to characterize the response of C. metallidurans CH34 planktonic and biofilm cells to cadmium including their c-di-GMP regulatory pathway. Inhibition of the initiation of biofilm formation and EPS production by C. metallidurans CH34 correlates with increased concentration of cadmium. Planktonic and biofilm cells showed similar tolerance to cadmium. During exposure to cadmium an acute decrease of c-di-GMP levels in planktonic and biofilm cells was observed. Transcription analysis by RT-qPCR showed that cadmium exposure to planktonic and biofilm cells induced the expression of the urf2 gene and the mercuric reductase encoding merA gene, which belong to the Tn501/Tn21 mer operon. After exposure to cadmium, the cadA gene involved in cadmium resistance was equally upregulated in both lifestyles. Bioinformatic analysis and complementation assays indicated that the protein encoded by the urf2 gene is a functional phosphodiesterase (PDE) involved in the c-di-GMP metabolism. We propose to rename the urf2 gene as mrp gene for metal regulated PDE. An increase of the second messenger c-di-GMP content by the heterologous expression of the constitutively active diguanylate cyclase PleD correlated with an increase in biofilm formation and cadmium susceptibility. These results indicate that the response to cadmium in C. metallidurans CH34 inhibits the initiation of biofilm lifestyle and involves a decrease in c-di-GMP levels and a novel metal regulated PDE.}, }
@article {pmid31337729, year = {2019}, author = {Rath, KM and Maheshwari, A and Rousk, J}, title = {Linking Microbial Community Structure to Trait Distributions and Functions Using Salinity as an Environmental Filter.}, journal = {mBio}, volume = {10}, number = {4}, pages = {}, pmid = {31337729}, issn = {2150-7511}, mesh = {Bacteria/classification/growth &amp; development ; *Ecosystem ; Fungi/classification/growth &amp; development ; *Microbiota ; RNA, Ribosomal, 16S ; *Salinity ; Salt Tolerance ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {The structure and function of microbial communities vary along environmental gradients; however, interlinking the two has been challenging. In this study, salinity was used as an environmental filter to study how it could shape trait distributions, community structures, and the resulting functions of soil microbes. The environmental filter was applied by salinizing nonsaline soil (0 to 22 mg NaCl g[-1]). Our targeted community trait distribution (salt tolerance) was determined with dose-response relationships between bacterial growth and salinity. The bacterial community structure responses were resolved with Illumina 16S rRNA gene amplicon sequencing, and the microbial functions determined were respiration and bacterial and fungal growth. Salt exposure quickly resulted in filtered trait distributions, and stronger filters resulted in larger shifts. The filtered trait distributions correlated well with community composition differences, suggesting that trait distribution shifts were driven at least partly by species turnover. While salt exposure decreased respiration, microbial growth responses appeared to be characterized by competitive interactions. Fungal growth was highest when bacterial growth was inhibited by the highest salinity, and it was lowest when the bacterial growth rate peaked at intermediate salt levels. These findings corroborated a higher potential for fungal salt tolerance than bacterial salt tolerance for communities derived from a nonsaline soil. In conclusion, by using salt as an environmental filter, we could interlink the targeted trait distribution with both the community structure and resulting functions of soil microbes.IMPORTANCE Understanding the role of ecological communities in maintaining multiple ecosystem processes is a central challenge in ecology. Soil microbial communities perform vital ecosystem functions, such as the decomposition of organic matter to provide plant nutrition. However, despite the functional importance of soil microorganisms, attribution of ecosystem function to particular constituents of the microbial community has been impeded by a lack of information linking microbial processes to community composition and structure. Here, we apply a conceptual framework to determine how microbial communities influence ecosystem processes, by applying a "top-down" trait-based approach. By determining the dependence of microbial processes on environmental factors (e.g., the tolerance to salinity), we can define the aggregate response trait distribution of the community, which then can be linked to the community structure and the resulting function performed by the microbial community.}, }
@article {pmid31336252, year = {2019}, author = {Shen, Y and Stedtfeld, RD and Guo, X and Bhalsod, GD and Jeon, S and Tiedje, JM and Li, H and Zhang, W}, title = {Pharmaceutical exposure changed antibiotic resistance genes and bacterial communities in soil-surface- and overhead-irrigated greenhouse lettuce.}, journal = {Environment international}, volume = {131}, number = {}, pages = {105031}, doi = {10.1016/j.envint.2019.105031}, pmid = {31336252}, issn = {1873-6750}, mesh = {Bacteria/drug effects ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; Lactuca/chemistry/*microbiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Soil Microbiology ; Soil Pollutants/*analysis ; Water Pollutants/*analysis ; }, abstract = {New classes of emerging contaminants such as pharmaceuticals, antibiotic resistant bacteria (ARB), and antibiotic resistance genes (ARGs) have received increasing attention due to rapid increases of their abundance in agroecosystems. As food consumption is a direct exposure pathway of pharmaceuticals, ARB, and ARGs to humans, it is important to understand changes of bacterial communities and ARG profiles in food crops produced with contaminated soils and waters. This study examined the level and type of ARGs and bacterial community composition in soil, and lettuce shoots and roots under soil-surface or overhead irrigation with pharmaceuticals-contaminated water, using high throughput qPCR and 16S rRNA amplicon sequencing techniques, respectively. In total 52 ARG subtypes were detected in the soil, lettuce shoot and root samples, with mobile genetic elements (MGEs), and macrolide-lincosamide-streptogramin B (MLSB) and multidrug resistance (MDR) genes as dominant types. The overall abundance and diversity of ARGs and bacteria associated with lettuce shoots under soil-surface irrigation were lower than those under overhead irrigation, indicating soil-surface irrigation may have lower risks of producing food crops with high abundance of ARGs. ARG profiles and bacterial communities were sensitive to pharmaceutical exposure, but no consistent patterns of changes were observed. MGE intl1 was consistently more abundant with pharmaceutical exposure than in the absence of pharmaceuticals. Pharmaceutical exposure enriched Proteobacteria (specifically Methylophilaceae) and decreased bacterial alpha diversity. Finally, there were significant interplays among bacteria community, antibiotic concentrations, and ARG abundance possibly involving hotspots including Sphingomonadaceae, Pirellulaceae, and Chitinophagaceae, MGEs (intl1 and tnpA_1) and MDR genes (mexF and oprJ).}, }
@article {pmid31333629, year = {2019}, author = {Yuan, H and Mei, R and Liao, J and Liu, WT}, title = {Nexus of Stochastic and Deterministic Processes on Microbial Community Assembly in Biological Systems.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1536}, pmid = {31333629}, issn = {1664-302X}, abstract = {Microbial community assembly in engineered biological systems is often simultaneously influenced by stochastic and deterministic processes, and the nexus of these two mechanisms remains to be further investigated. Here, three lab-scale activated sludge reactors were seeded with identical inoculum and operated in parallel under eight different sludge retention time (SRT) by sequentially reducing the SRT from 15 days to 1 day. Using 16S rRNA gene amplicon sequencing data, the microbial populations at the start-up (15-day SRT) and SRT-driven (≤10-day SRT) phases were observed to be noticeably different. Clustering results demonstrated ecological succession at the start-up phase with no consistent successional steps among the three reactors, suggesting that stochastic processes played an important role in the community assembly during primary succession. At the SRT-driven phase, the three reactors shared 31 core operational taxonomic units (OTUs). Putative primary acetate utilizers and secondary metabolizers were proposed based on K-means clustering, network and synchrony analysis. The shared core populations accounted for 65% of the total abundance, indicating that the microbial communities at the SRT-driven phase were shaped predominantly by deterministic processes. Sloan's Neutral model and a null model analysis were performed to disentangle and quantify the relative influence of stochastic and deterministic processes on community assembly. The increased estimated migration rate in the neutral community model and the higher percentage of stochasticity in the null model implied that stochastic community assembly was intensified by strong deterministic factors. This was confirmed by the significantly different α- and β-diversity indices at SRTs shorter than 2 days and the observation that over half of the core OTUs were unshared or unsynchronized. Overall, this study provided quantitative insights into the nexus of stochastic and deterministic processes on microbial community assembly in a biological process.}, }
@article {pmid31330399, year = {2019}, author = {Lippens, C and De Vrieze, J}, title = {Exploiting the unwanted: Sulphate reduction enables phosphate recovery from energy-rich sludge during anaerobic digestion.}, journal = {Water research}, volume = {163}, number = {}, pages = {114859}, doi = {10.1016/j.watres.2019.114859}, pmid = {31330399}, issn = {1879-2448}, mesh = {Anaerobiosis ; Biofuels ; *Bioreactors ; Methane ; Phosphates ; *Sewage ; Sulfates ; }, abstract = {Anaerobic digestion is shifting from a single-purpose technology for renewable energy recovery from organic waste streams to a process for integrated resource recovery. The valorisation of high-rate energy- and phosphorus-rich sludge creates the opportunity for their combined recovery. This phosphate is present in a precipitated form in the sludge, and its release into the liquid phase is an important issue before recovery can be achieved. The objective of this research was to exploit the "unwanted" sulphate reduction process for the release of phosphate into the liquid phase during anaerobic digestion, thus, making it available for recovery. Two different treatments were considered, i.e., a control digester and a digester to which sulphate was added, each operated in triplicate for a period of 119 days. The control digester showed stable methane production at 628 ± 103 mL CH4 L[-1] d[-1], with a feedstock COD (chemical oxygen demand) conversion efficiency of 89.5 ± 14.6%. In contrast, the digester with sulphate addition showed a 29.9 ± 15.3% decrease in methane production, reaching an "inhibited steady state", but phosphate release into the liquid phase increased to 58.7 ± 12.9% of total P, a factor 4.5 higher than the control digester. This inhibited steady state coincided with a clear shift from a Methanosaetaceae to a Methanosarcinaceae dominated methanogenic community. Overall, the sulphate reduction process allows phosphate release during the anaerobic digestion process, yet, at the cost of a reduced methane production rate.}, }
@article {pmid31329319, year = {2020}, author = {Onnis-Hayden, A and Majed, N and Li, Y and Rahman, SM and Drury, D and Risso, L and Gu, AZ}, title = {Impact of solid residence time (SRT) on functionally relevant microbial populations and performance in full-scale enhanced biological phosphorus removal (EBPR) systems.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {92}, number = {3}, pages = {389-402}, doi = {10.1002/wer.1185}, pmid = {31329319}, issn = {1554-7531}, mesh = {*Bioreactors ; Glycogen ; *Phosphorus ; Polyphosphates ; }, abstract = {Investigations of the impact of solid residence time (SRT) on microbial ecology and performance of enhanced biological phosphorus removal (EBPR) process in full-scale systems have been scarce due to the challenges in isolating and examining the SRT from other complex plant-specific factors. This study performed a comprehensive evaluation of the influence of SRT on polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs) dynamics and on P removal performance at Clark County Water Reclamation District Facility in Las Vegas, USA. Five parallel treatment trains with separated clarifiers were operated with five different SRTs ranging from 6 to 40 days. Microbial community analysis using multiple molecular and Raman techniques suggested that the relative abundances and diversity of PAOs and GAOs in EBPR systems are highly affected by the SRT. The resultant EBPR system stability and performance can be potentially controlled and optimized by manipulating the system SRT, and shorter SRT (<10 days) seems to be preferred. PRACTITIONER POINTS: Phosphorus removal performance and kinetics are highly affected by the operational solid residence time (SRT), with lower and more stable effluent P level achieved at SRT < 10 days. Excessive long SRTs above that needed for nitrification may harm EBPR performance; additionally, excessive long SRT may favor GAOs to dominate over PAOs and thus further reducing efficient use of rbCOD for EBPR. Microbial population abundance and diversity, especially those functionally relevant PAOs and GAOs, can impact the P removal performances, and they are highly dependent on the operational solid residence time. EBPR performance can be potentially controlled and optimized by manipulating the system SRT, and shorter SRT (≤10 days) seems to be preferred at the influent rbCOD/P ratio and environmental conditions as in the plant studied.}, }
@article {pmid31328364, year = {2019}, author = {Colangelo-Lillis, J and Pelikan, C and Herbold, CW and Altshuler, I and Loy, A and Whyte, LG and Wing, BA}, title = {Diversity decoupled from sulfur isotope fractionation in a sulfate-reducing microbial community.}, journal = {Geobiology}, volume = {17}, number = {6}, pages = {660-675}, doi = {10.1111/gbi.12356}, pmid = {31328364}, issn = {1472-4669}, support = {P 25111/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/classification/*metabolism ; Mexico ; Microbiota ; Oxidation-Reduction ; Ponds/*microbiology ; Sulfates/*metabolism ; Sulfur Isotopes/*metabolism ; }, abstract = {The extent of fractionation of sulfur isotopes by sulfate-reducing microbes is dictated by genomic and environmental factors. A greater understanding of species-specific fractionations may better inform interpretation of sulfur isotopes preserved in the rock record. To examine whether gene diversity influences net isotopic fractionation in situ, we assessed environmental chemistry, sulfate reduction rates, diversity of putative sulfur-metabolizing organisms by 16S rRNA and dissimilatory sulfite reductase (dsrB) gene amplicon sequencing, and net fractionation of sulfur isotopes along a sediment transect of a hypersaline Arctic spring. In situ sulfate reduction rates yielded minimum cell-specific sulfate reduction rates < 0.3 × 10[-15] moles cell[-1] day[-1] . Neither 16S rRNA nor dsrB diversity indices correlated with relatively constant (38‰-45‰) net isotope fractionation (ε[34] Ssulfide-sulfate). Measured ε[34] S values could be reproduced in a mechanistic fractionation model if 1%-2% of the microbial community (10%-60% of Deltaproteobacteria) were engaged in sulfate respiration, indicating heterogeneous respiratory activity within sulfate-reducing populations. This model indicated enzymatic kinetic diversity of Apr was more likely to correlate with sulfur fractionation than DsrB. We propose that, above a threshold Shannon diversity value of 0.8 for dsrB, the influence of the specific composition of the microbial community responsible for generating an isotope signal is overprinted by the control exerted by environmental variables on microbial physiology.}, }
@article {pmid31325575, year = {2019}, author = {Kumar, KV and Pal, A and Bai, P and Kour, A and E, S and P, R and Kausar, A and Chatterjee, M and Prasad, G and Balayan, S and Dutta, P and Wijesekera, K}, title = {Co-aggregation of bacterial flora isolated from the human skin surface.}, journal = {Microbial pathogenesis}, volume = {135}, number = {}, pages = {103630}, doi = {10.1016/j.micpath.2019.103630}, pmid = {31325575}, issn = {1096-1208}, mesh = {Adolescent ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Adhesion/*physiology ; Bacterial Physiological Phenomena ; Ecology ; Host Microbial Interactions/physiology ; Humans ; Microbiota/*physiology ; RNA, Ribosomal, 16S/genetics ; Skin/*microbiology ; }, abstract = {Human hands play a prominent role in the intra and interpersonal transmission of microbes that constantly connect one's microbiome to other individuals and the environment. Along with beneficial bacteria, an individual may harbor pathogenic organisms which may get transferred to others. Thus, understanding the transmission mechanism and interaction among microbiota is crucial in preventing infection. In the present study, the ability of skin microbes, isolated from different individuals, to physically interact (coaggregate) intergenically was assessed. The bacterial flora from the hands (palm area) of similar age group students was isolated. The predominant isolates were selected and identified using 16s rRNA gene sequencing. Further, these isolates were subjected to visual coaggregation assay. A total of 27 bacteria were isolated from the human skin (palm area-fingers) of 10 individuals. These isolates belong to seven bacterial genera and 10 different species. Among 123 combinational visual coaggregation positive reactions; 53.66% showed a reaction score of +1, while 32.52%, 11.38% and 2.44% showed a score of +2, +3, and +4 respectively. Among 27 isolates, Staphylococcus haemolyticus had highest coaggregation partners of 17 followed by Acinetobacter spp. and Pseudomonas spp. with 15 partners each. The present study is the first report demonstrating the coaggregation potential of microbiota harboring the skin surface of the human hand. The study indicates that few microbes have high potential to influence coaggregation among distinct genera isolated from the skin. However, further studies are needed to understand the ability of these bacteria to coaggregate, their influence in interpersonal transmission and shaping of microbial ecology of the host skin.}, }
@article {pmid31324234, year = {2019}, author = {Ling, S and Hui, L}, title = {Evaluation of the complexity of indoor air in hospital wards based on PM2.5, real-time PCR, adenosine triphosphate bioluminescence assay, microbial culture and mass spectrometry.}, journal = {BMC infectious diseases}, volume = {19}, number = {1}, pages = {646}, pmid = {31324234}, issn = {1471-2334}, support = {2018J12SN084//Scientific and Technological Innovation of Dalian/ ; }, mesh = {Adenosine Triphosphate/analysis ; *Air Microbiology ; Air Pollution, Indoor/*analysis ; Bacterial Load/methods ; China ; Colony Count, Microbial/methods ; *Hospitals ; Humans ; Luminescent Measurements/*methods ; Particulate Matter/analysis ; Real-Time Polymerase Chain Reaction/*methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Staphylococcus ; }, abstract = {BACKGROUND: The aim of this study was to establish a set of assessment methods suitable for evaluating the complex indoor environment of hospital wards and to ascertain the composition of bacteria and microbial ecology of hospital wards.<br><br>METHODS: Colony-forming units (CFUs), PM2.5 detection, real-time PCR, and adenosine triphosphate (ATP) bioluminescence assay were employed to evaluate the complexity of indoor air in 18 wards of nine departments in a hospital and two student dormitories in a university. Subsequently, the microbial samples were quantified and identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS).<br><br>RESULTS: Although the studied indices were relatively independent, the PM2.5 content was correlated with bacterial CFUs determined by passive sedimentation method, bacterial and fungal counts measured by real-time PCR, and ATP bioluminescence assay. The composition of microorganisms in the air of hospital wards differed from that in the air of student dormitories. The dominant genera in hospital wards were Staphylococcus (39.4%), Micrococcus (21.9%), Corynebacterium (11.7%), Kocuria (4.4%), Bacillus (2.9%), Streptococcus (1.6%), Moraxella (1.6%), and Enterococcus (1.3%), and the microbial ecology differed between Respiration Dept. III and other hospital departments. Additionally, 11.1 and 27.3% of bacteria in hospital wards and student dormitories were not identified, respectively.<br><br>CONCLUSIONS: Assessment of environmental quality of hospital wards should be based on comprehensive analysis with multiple indicators. There may be imbalances in the microbial diversity in the hospital wards, therefore, monitoring of the environmental quality of hospitals is important in the prevention of nosocomial infections.}, }
@article {pmid31323513, year = {2019}, author = {Zamorano-López, N and Borrás, L and Giménez, JB and Seco, A and Aguado, D}, title = {Acclimatised rumen culture for raw microalgae conversion into biogas: Linking microbial community structure and operational parameters in anaerobic membrane bioreactors (AnMBR).}, journal = {Bioresource technology}, volume = {290}, number = {}, pages = {121787}, doi = {10.1016/j.biortech.2019.121787}, pmid = {31323513}, issn = {1873-2976}, mesh = {Anaerobiosis ; Animals ; Biofuels ; Bioreactors ; Methane ; *Microalgae ; *Microbiota ; RNA, Ribosomal, 16S ; Rumen ; Waste Disposal, Fluid ; }, abstract = {Ruminal fluid was inoculated in an Anaerobic Membrane Reactor (AnMBR) to produce biogas from raw Scenedesmus. This work explores the microbial ecology of the system during stable operation at different solids retention times (SRT). The 16S rRNA amplicon analysis revealed that the acclimatised community was mainly composed of Anaerolineaceae, Spirochaetaceae, Lentimicrobiaceae and Cloacimonetes fermentative and hydrolytic members. During the highest biodegradability achieved in the AnMBR (62%) the dominant microorganisms were Fervidobacterium and Methanosaeta. Different microbial community clusters were observed at different SRT conditions. Interestingly, syntrophic bacteria Gelria and Smithella were enhanced after increasing 2-fold the organic loading rate, suggesting their importance in continuous systems producing biogas from raw microalgae.}, }
@article {pmid31321764, year = {2019}, author = {Xie, M and An, F and Wu, J and Liu, Y and Shi, H and Wu, R}, title = {Meta-omics reveal microbial assortments and key enzymes in bean sauce mash, a traditional fermented soybean product.}, journal = {Journal of the science of food and agriculture}, volume = {99}, number = {14}, pages = {6522-6534}, doi = {10.1002/jsfa.9932}, pmid = {31321764}, issn = {1097-0010}, support = {31470538//Natural Science Foundation of China/ ; 31471713//Natural Science Foundation of China/ ; RC170212//Shenyang Youth Science and Technology Innovation Talent Project/ ; 17-189-9-00//Liaoning BaiQianWan Talents Program Project, Shenyang Science and Technology Project/ ; XLYC1807040//LiaoNing Revitalization Talents Program/ ; }, mesh = {Bacteria/classification/*enzymology/genetics/isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; China ; Fermentation ; Fermented Foods/*microbiology ; Fungal Proteins/genetics/metabolism ; Fungi/classification/*enzymology/genetics/isolation &amp; purification ; *Microbiota ; Glycine max/metabolism/*microbiology ; }, abstract = {BACKGROUND: Dajiang is fermented based on the metabolism of microbial communities in bean sauce mash, a traditional fermented soybean product in China. The current study first investigated the metaproteome of bean sauce mash. This was followed by an analysis of its biological functions and its microbial community to reveal information about strains and about the expressed proteins to better understand the roles of the microbiota in bean sauce mash.<br><br>RESULTS: The metaproteomic results demonstrated that a total of 1415 microbial protein clusters were expressed mainly by members of the Penicillium and Rhizopus genera and were classified into 100 cellular components, 238 biological processes, and 220 molecular function categories by gene ontology (GO) annotation. Enzymes associated with glycolysis metabolic pathways were also identified. These can provide the energy required for microbial fermentation. Illumina MiSeq sequencing technology results showed that the microorganism communities of bean sauce mash exhibited a high level of diversity. Microbiological analysis demonstrated that the Penicillium, Mucor, Fusarium, Aspergillus, and Rhizopus fungi, and Lactobacillus, Enterococcus, Fructobacillus, Staphylococcus, Carnobacterium genera were predominant 22 samples.<br><br>CONCLUSION: The profiles and insights in the current study are important for research on bean sauce mash and related products in terms of their food microbial ecology. The information obtained from this study will help the development of stable sufu starter cultures with unique sensory qualities. &#xa9; 2019 Society of Chemical Industry.}, }
@article {pmid31320430, year = {2019}, author = {Hausmann, B and Pjevac, P and Huemer, M and Herbold, CW and Pester, M and Loy, A}, title = {Draft Genome Sequence of Desulfosporosinus sp. Strain Sb-LF, Isolated from an Acidic Peatland in Germany.}, journal = {Microbiology resource announcements}, volume = {8}, number = {29}, pages = {}, pmid = {31320430}, issn = {2576-098X}, abstract = {Desulfosporosinus sp. strain Sb-LF was isolated from an acidic peatland in Bavaria, Germany. Here, we report the draft genome sequence of the sulfate-reducing and lactate-utilizing strain Sb-LF.}, }
@article {pmid31316095, year = {2019}, author = {Mailloux, BJ and Kim, C and Kichuk, T and Nguyen, K and Precht, C and Wang, S and Jewell, TNM and Karaoz, U and Brodie, EL and Williams, KH and Beller, HR and Buchholz, BA}, title = {Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {10370}, pmid = {31316095}, issn = {2045-2322}, support = {P42 ES010349/ES/NIEHS NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; S10 RR027303/RR/NCRR NIH HHS/United States ; P41 GM103483/GM/NIGMS NIH HHS/United States ; }, mesh = {*Autotrophic Processes ; Bacteria/genetics/isolation &amp; purification/*metabolism ; Base Sequence ; Carbon Cycle ; Carbon Radioisotopes/analysis ; Colorado ; Escherichia coli/metabolism ; Groundwater/*microbiology ; Iron/metabolism ; Phylogeny ; RNA, Bacterial/*analysis/genetics ; RNA, Ribosomal, 16S/*analysis/genetics ; Radiometric Dating ; Sequence Analysis, RNA ; Sulfur/metabolism ; *Water Microbiology ; }, abstract = {Determining the carbon sources for active microbial populations in the subsurface is a challenging but highly informative component of subsurface microbial ecology. This work developed a method to provide ecological insights into groundwater microbial communities by characterizing community RNA through its radiocarbon and ribosomal RNA (rRNA) signatures. RNA was chosen as the biomolecule of interest because rRNA constitutes the majority of RNA in prokaryotes, represents recently active organisms, and yields detailed taxonomic information. The method was applied to a groundwater filter collected from a shallow alluvial aquifer in Colorado. RNA was extracted, radiometrically dated, and the 16S rRNA was analyzed by RNA-Seq. The RNA had a radiocarbon signature (Δ[14]C) of -193.4 ± 5.6‰. Comparison of the RNA radiocarbon signature to those of potential carbon pools in the aquifer indicated that at least 51% of the RNA was derived from autotrophy, in close agreement with the RNA-Seq data, which documented the prevalence of autotrophic taxa, such as Thiobacillus and Gallionellaceae. Overall, this hybrid method for RNA analysis provided cultivation-independent information on the in-situ carbon sources of active subsurface microbes and reinforced the importance of autotrophy and the preferential utilization of dissolved over sedimentary organic matter in alluvial aquifers.}, }
@article {pmid31314939, year = {2019}, author = {Ranchou-Peyruse, M and Auguet, JC and Mazière, C and Restrepo-Ortiz, CX and Guignard, M and Dequidt, D and Chiquet, P and Cézac, P and Ranchou-Peyruse, A}, title = {Geological gas-storage shapes deep life.}, journal = {Environmental microbiology}, volume = {21}, number = {10}, pages = {3953-3964}, doi = {10.1111/1462-2920.14745}, pmid = {31314939}, issn = {1462-2920}, support = {//Storengy and Ter&#xe9;ga/International ; }, mesh = {Archaea/*metabolism ; Deltaproteobacteria/*metabolism ; Desulfotomaculum/*metabolism ; Firmicutes/*metabolism ; Geologic Sediments/chemistry/*microbiology ; Geology ; Groundwater/microbiology ; Microbiota ; *Natural Gas ; RNA, Ribosomal, 16S/genetics ; Sulfates/metabolism ; }, abstract = {Around the world, several dozen deep sedimentary aquifers are being used for storage of natural gas. Ad hoc studies of the microbial ecology of some of them have suggested that sulfate reducing and methanogenic microorganisms play a key role in how these aquifers' communities function. Here, we investigate the influence of gas storage on these two metabolic groups by using high-throughput sequencing and show the importance of sulfate-reducing Desulfotomaculum and a new monophyletic methanogenic group. Aquifer microbial diversity was significantly related to the geological level. The distance to the stored natural gas affects the ratio of sulfate-reducing Firmicutes to deltaproteobacteria. In only one aquifer, the methanogenic archaea dominate the sulfate-reducers. This aquifer was used to store town gas (containing at least 50% H2) around 50 years ago. The observed decrease of sulfates in this aquifer could be related to stimulation of subsurface sulfate-reducers. These results suggest that the composition of the microbial communities is impacted by decades old transient gas storage activity. The tremendous stability of these gas-impacted deep subsurface microbial ecosystems suggests that in situ biotic methanation projects in geological reservoirs may be sustainable over time.}, }
@article {pmid31314103, year = {2019}, author = {Stres, B and Kronegger, L}, title = {Shift in the paradigm towards next-generation microbiology.}, journal = {FEMS microbiology letters}, volume = {366}, number = {15}, pages = {}, pmid = {31314103}, issn = {1574-6968}, mesh = {Artificial Intelligence ; *Meta-Analysis as Topic ; Microbiology/standards/*trends ; Publications ; Software ; *Systems Biology ; }, abstract = {In this work, the position of contemporary microbiology is considered from the perspective of scientific success, and a list of historical points and lessons learned from the fields of medical microbiology, microbial ecology and systems biology is presented. In addition, patterns in the development of top-down research topics that emerged over time as well as overlapping ideas and personnel, which are the first signs of trans-domain research activities in the fields of metagenomics, metaproteomics, metatranscriptomics and metabolomics, are explored through analysis of the publication networks of 28 654 papers using the computer programme Pajek. The current state of affairs is defined, and the need for meta-analyses to leverage publication biases in the field of microbiology is put forward as a very important emerging field of microbiology, especially since microbiology is progressively dealing with multi-scale systems. Consequently, the need for cross-fertilisation with other fields/disciplines instead of 'more microbiology' is needed to advance the field of microbiology as such. The reader is directed to consider how novel technologies, the introduction of big data approaches and artificial intelligence have transformed microbiology into a multi-scale field and initiated a shift away from its history of mostly manual work and towards a largely technology-, data- and statistics-driven discipline that is often coupled with automation and modelling.}, }
@article {pmid31314089, year = {2019}, author = {Paterson, JS and Smith, RJ and McKerral, JC and Dann, LM and Launer, E and Goonan, P and Kleinig, T and Fuhrman, JA and Mitchell, JG}, title = {A hydrocarbon-contaminated aquifer reveals a Piggyback-the-Persistent viral strategy.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {8}, pages = {}, doi = {10.1093/femsec/fiz116}, pmid = {31314089}, issn = {1574-6941}, mesh = {Bacteria/growth &amp; development/metabolism/*virology ; Biodegradation, Environmental ; Biomass ; Ecosystem ; Groundwater/*microbiology ; Hydrocarbons/metabolism ; Trichloroethylene/*metabolism ; Viral Load ; Virus Physiological Phenomena/*drug effects ; Viruses/*growth &amp; development ; }, abstract = {Subsurface environments hold the largest reservoir of microbes in the biosphere. They play essential roles in transforming nutrients, degrading contaminants and recycling organic matter. Here, we propose a previously unrecognised fundamental microbial process that influences aquifer bioremediation dynamics and that applies to all microbial communities. In contrast to previous models, our proposed Piggyback-the-Persistent (PtP) mechanism occurs when viruses become more dominated by those exhibiting temperate rather than lytic lifestyles driven by persistent chemicals (in our case chlorinated-hydrocarbon pollutants) that provide long-term carbon sources and that refocus the aquifer carbon cycle, thus altering the microbial community. In this ultra-oligotrophic system, the virus:microbial ratio (VMR) ranges from below the detection limit of 0.0001 to 0.6, well below the common aquatic range of 3-10. Shortest-average-path network analysis revealed VMR and trichlorethene (TCE) as nodes through which ecosystem information and biomass most efficiently pass. Novel network rearrangement revealed a hierarchy of Kill-the-Winner (KtW), Piggyback-the-Winner (PtW) and PtP nodes. We propose that KtW, PtW and PtP occur simultaneously as competing strategies, with their relative importance depending on conditions at a particular time and location with unusual nutrient sources, such as TCE, appearing to contribute to a shift in this balance between viral mechanisms.}, }
@article {pmid31313962, year = {2019}, author = {Moye, ZD and Woolston, J and Abbeele, PVD and Duysburgh, C and Verstrepen, L and DAS, CR and Marzorati, M and Sulakvelidze, A}, title = {A Bacteriophage Cocktail Eliminates Salmonella Typhimurium from the Human Colonic Microbiome while Preserving Cytokine Signaling and Preventing Attachment to and Invasion of Human Cells by Salmonella In Vitro.}, journal = {Journal of food protection}, volume = {82}, number = {8}, pages = {1336-1349}, doi = {10.4315/0362-028X.JFP-18-587}, pmid = {31313962}, issn = {1944-9097}, mesh = {*Bacteriophages/physiology ; Caco-2 Cells ; Colon/microbiology ; Cytokines/metabolism ; *Gastrointestinal Microbiome ; Humans ; In Vitro Techniques ; *Salmonella typhimurium/virology ; Signal Transduction ; }, abstract = {Nontyphoidal Salmonella strains continue to be a major cause of foodborne illness globally. One intriguing approach to reducing the risk of salmonellosis is the direct ingestion of phages targeting Salmonella to enhance natural gut resilience and provide protection during foodborne disease outbreaks. We evaluated the ability of a prophylactically administered bacteriophage cocktail, the foodborne outbreak pill (FOP) targeting Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella, to resolve a Salmonella infection in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME), a simulated gut platform populated by the human intestinal microbiome of healthy donors. The FOP preparation eliminated Salmonella enterica serovar Typhimurium from the colon compartment of the SHIME platform but health-associated metabolites, such as short-chain fatty acids and lactate, remained stable or increased in a donor-dependent manner. In studies of human intestinal cells, pretreatment of Salmonella Typhimurium with the FOP cocktail preserved lipopolysaccharide-stimulated signaling in a Caco-2-THP-1 Transwell system and prevented destruction of the Caco-2 monolayer by Salmonella. Adhesion and invasion of intestinal epithelial cells by Salmonella-a critical factor in Salmonella pathogenesis-was blunted when the bacteria were incubated with the FOP preparation before addition to the monolayer. The FOP phage cocktail was effective for (i) eliminating Salmonella from a simulated human gut without disturbing the indigenous microbiota and (ii) reducing the risk of invasion by Salmonella into the intestinal epithelia. These results suggest that the FOP preparation may be of value for reducing the risk of salmonellosis in humans, e.g., during foodborne disease outbreaks.}, }
@article {pmid31312870, year = {2020}, author = {Shih, JL and Selph, KE and Wall, CB and Wallsgrove, NJ and Lesser, MP and Popp, BN}, title = {Trophic Ecology of the Tropical Pacific Sponge Mycale grandis Inferred from Amino Acid Compound-Specific Isotopic Analyses.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {495-510}, pmid = {31312870}, issn = {1432-184X}, support = {NA14OAR4170071//Hawai'i Sea Grant, University of Hawai'i/ ; }, mesh = {Amino Acids/chemistry/*metabolism ; Animals ; Bacteria/*metabolism ; Isotopes/analysis ; Microbiota/*physiology ; Nutrients/metabolism ; Porifera/*metabolism/*microbiology ; }, abstract = {Many sponges host abundant and active microbial communities that may play a role in the uptake of dissolved organic matter (DOM) by the sponge holobiont, although the mechanism of DOM uptake and metabolism is uncertain. Bulk and compound-specific isotopic analysis of whole sponge, isolated sponge cells, and isolated symbiotic microbial cells of the shallow water tropical Pacific sponge Mycale grandis were used to elucidate the trophic relationships between the host sponge and its associated microbial community. δ[15]N and δ[13]C values of amino acids in M. grandis isolated sponge cells are not different from those of its bacterial symbionts. Consequently, there is no difference in trophic position of the sponge and its symbiotic microbes indicating that M. grandis sponge cell isolates do not display amino acid isotopic characteristics typical of metazoan feeding. Furthermore, both the isolated microbial and sponge cell fractions were characterized by a similarly high ΣV value-a measure of bacterial-re-synthesis of organic matter calculated from the sum of variance among individual δ[15]N values of trophic amino acids. These high ΣV values observed in the sponge suggest that M. grandis is not reliant on translocated photosynthate from photosymbionts or feeding on water column picoplankton, but obtains nutrition through the uptake of amino acids of bacterial origin. Our results suggest that direct assimilation of bacterially synthesized amino acids from its symbionts, either in a manner similar to translocation observed in the coral holobiont or through phagotrophic feeding, is an important if not primary pathway of amino acid acquisition for M. grandis.}, }
@article {pmid31309868, year = {2019}, author = {Pantoja-Feliciano, IG and Soares, JW and Doherty, LA and Karl, JP and McClung, HL and Armstrong, NJ and Branck, TA and Arcidiacono, S}, title = {Acute stressor alters inter-species microbial competition for resistant starch-supplemented medium.}, journal = {Gut microbes}, volume = {10}, number = {4}, pages = {439-446}, pmid = {31309868}, issn = {1949-0984}, mesh = {Adolescent ; Adult ; Bacteria/classification/genetics/growth &amp; development/metabolism ; Culture Media/chemistry ; DNA, Bacterial/genetics ; Feces/microbiology ; Fermentation ; Gastrointestinal Microbiome/*drug effects/genetics ; Humans ; Lactobacillus/genetics/growth &amp; development/metabolism ; Male ; Middle Aged ; Military Personnel ; RNA, Ribosomal, 16S/genetics ; Ruminococcus/genetics/growth &amp; development/metabolism ; Starch/chemistry/metabolism/*pharmacology ; Young Adult ; }, abstract = {Gut microbiome community dynamics are maintained by complex microbe-microbe and microbe-host interactions, which can be disturbed by stress. In vivo studies on the dynamics and manipulation of those interactions are costly and slow, but can be accelerated using in vitro fermentation. Herein, in vitro fermentation was used to determine how an acute stressor, a sudden change in diet, impacts inter-bacterial species competition for resistant starch-supplemented medium (RSM). Fermentation vessels were seeded with fecal samples collected from 10 individuals consuming a habitual diet or U.S. military rations for 21 days. Lactobacillus spp. growth in response to RSM was attenuated following ration consumption, whereas growth of Ruminococcus bromii was enhanced. These differences were not evident in the pre-fermentation samples. Findings demonstrate how incorporating in vitro fermentation into clinical studies can increase understanding of stress-induced changes in nutrient-microbiome dynamics, and suggest that sudden changes in diet may impact inter-species competition for substrates.}, }
@article {pmid31304521, year = {2019}, author = {Migliara, G and Di Paolo, C and Barbato, D and Baccolini, V and Salerno, C and Nardi, A and Alessandri, F and Giordano, A and Tufi, D and Marinelli, L and Cottarelli, A and De Giusti, M and Marzuillo, C and De Vito, C and Antonelli, G and Venditti, M and Tellan, G and Ranieri, MV and Villari, P}, title = {Multimodal surveillance of healthcare associated infections in an intensive care unit of a large teaching hospital.}, journal = {Annali di igiene : medicina preventiva e di comunita}, volume = {31}, number = {5}, pages = {399-413}, doi = {10.7416/ai.2019.2302}, pmid = {31304521}, issn = {3035-5559}, mesh = {Adult ; Aged ; Catheter-Related Infections/*epidemiology/microbiology/prevention &amp; control ; Cross Infection/*epidemiology/microbiology/prevention &amp; control ; Female ; Guideline Adherence ; Hospitals, Teaching ; Humans ; Incidence ; Intensive Care Units ; Italy/epidemiology ; Male ; Middle Aged ; Personnel, Hospital/standards ; Pneumonia, Ventilator-Associated/*epidemiology/microbiology/prevention &amp; control ; Practice Guidelines as Topic ; Urinary Tract Infections/*epidemiology/microbiology/prevention &amp; control ; }, abstract = {BACKGROUND: Healthcare-associated infections (HAIs), or nosocomial infections, represent a significant burden in terms of mortality, morbidity, length of stay and costs for patients hospitalized in intensive care units (ICUs). Surveillance systems are recommended by national and international institutions to gather data on HAIs in order to develop and evaluate interventions that reduce the risk of HAIs.<br><br>STUDY DESIGN: Here we describe the methodology and the results of the surveillance system implemented in the ICU of the Policlinico Umberto I, a large teaching hospital in Rome, from April 2016 to October 2018.<br><br>METHODS: The multimodal infection surveillance system integrates four different approaches: i) active surveillance of inpatients; ii) environmental microbiological surveillance; iii) surveillance of isolated microorganisms; and iv) behavioral surveillance of healthcare personnel. Data were collected on catheter-related bloodstream infections, ventilation-associated pneumonia, catheter-associated urinary tract infections and primary bloodstream infections that developed in patients after 48 h in the ICU. For environmental surveillance 14 points were selected for sampling (i.e. bed edges, medication carts, PC keyboards, sink faucets). The system of active surveillance of HAIs also included surveillance of microorganisms, consisting of the molecular genotyping of bacterial isolates by pulsed-field gel electrophoresis (PFGE). From 1 November 2016, monitoring of compliance with guidelines for hand hygiene (HH) and proper glove or gown use by healthcare personnel was included in the surveillance system. After the first six months (baseline phase), a multimodal intervention to improve adherence to guidelines by healthcare personnel was conducted with the ICU staff.<br><br>RESULTS: Overall, 773 patients were included in the active surveillance. The overall incidence rate of device-related HAIs was 14.1 (95% CI: 12.2-16.3) per 1000 patient-days. The monthly device-related HAI incident rate showed a decreasing trend over time, with peaks of incidence becoming progressively lower. The most common bacterial isolates were Klebsiella pneumoniae (20.7%), Acinetobacter baumannii (17.2%), Pseudomonas aeruginosa (13.4%) and Staphylococcus aureus (5.4%). Acinetobacter baumannii and Klebsiella pneumoniae showed the highest proportion of isolates with a multidrug-resistant profile. A total of 819 environmental samples were collected, from which 305 bacterial isolates were retrieved. The most frequent bacterial isolates were Acinetobacter baumannii (27.2%), Staphylococcus aureus (12.1%), Enterococcus faecalis (11.1%), Klebsiella pneumoniae (5.2%) and Pseudomonas aeruginosa (4.7%). All Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae environmental isolates were at least multidrug-resistant. Genotyping showed a limited number of major PFGE patterns for both clinical and environmental isolates of Klebsiella pneumoniae and Acinetobacter baumannii. Behavioral compliance rates significantly improved from baseline to post-intervention phase.<br><br>CONCLUSIONS: By integrating information gathered from active surveillance, environmental microbiological surveillance, surveillance of bacterial isolates and behavioral surveillance of healthcare personnel, the multimodal infection surveillance system returned a precise and detailed view of the infectious risk and microbial ecology of the ICU.}, }
@article {pmid31303186, year = {2020}, author = {Garcia-Mazcorro, JF and Ishaq, SL and Rodriguez-Herrera, MV and Garcia-Hernandez, CA and Kawas, JR and Nagaraja, TG}, title = {Review: Are there indigenous Saccharomyces in the digestive tract of livestock animal species? Implications for health, nutrition and productivity traits.}, journal = {Animal : an international journal of animal bioscience}, volume = {14}, number = {1}, pages = {22-30}, doi = {10.1017/S1751731119001599}, pmid = {31303186}, issn = {1751-732X}, mesh = {Animals ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology/*physiology ; Livestock/*microbiology ; Probiotics/therapeutic use ; Saccharomyces/*physiology ; }, abstract = {All livestock animal species harbour complex microbial communities throughout their digestive tract that support vital biochemical processes, thus sustaining health and productivity. In part as a consequence of the strong and ancient alliance between the host and its associated microbes, the gut microbiota is also closely related to productivity traits such as feed efficiency. This phenomenon can help researchers and producers develop new and more effective microbiome-based interventions using probiotics, also known as direct-fed microbials (DFMs), in Animal Science. Here, we focus on one type of such beneficial microorganisms, the yeast Saccharomyces. Saccharomyces is one of the most widely used microorganisms as a DFM in livestock operations. Numerous studies have investigated the effects of dietary supplementation with different species, strains and doses of Saccharomyces (mostly Saccharomyces cerevisiae) on gut microbial ecology, health, nutrition and productivity traits of several livestock species. However, the possible existence of Saccharomyces which are indigenous to the animals' digestive tract has received little attention and has never been the subject of a review. We for the first time provide a comprehensive review, with the objective of shedding light into the possible existence of indigenous Saccharomyces of the digestive tract of livestock. Saccharomyces cerevisiae is a nomadic yeast able to survive in a broad range of environments including soil, grass and silages. Therefore, it is very likely that cattle and other animals have been in direct contact with this and other types of Saccharomyces throughout their entire existence. However, to date, the majority of animal scientists seem to agree that the presence of Saccharomyces in any section of the gut only reflects dietary contamination; in other words, these are foreign organisms that are only transiently present in the gut. Importantly, this belief (i.e. that Saccharomyces come solely from the diet) is often not well grounded and does not necessarily hold for all the many other groups of microbes in the gut. In addition to summarizing the current body of literature involving Saccharomyces in the digestive tract, we discuss whether the beneficial effects associated with the consumption of Saccharomyces may be related to its foreign origin, though this concept may not necessarily satisfy the theories that have been proposed to explain probiotic efficacy in vivo. This novel review may prove useful for biomedical scientists and others wishing to improve health and productivity using Saccharomyces and other beneficial microorganisms.}, }
@article {pmid31303107, year = {2019}, author = {Houldcroft, CJ and Rifkin, RF and Underdown, SJ}, title = {Human biology and ancient DNA: exploring disease, domestication and movement.}, journal = {Annals of human biology}, volume = {46}, number = {2}, pages = {95-98}, doi = {10.1080/03014460.2019.1629536}, pmid = {31303107}, issn = {1464-5033}, mesh = {Archaeology ; *Biological Evolution ; DNA, Ancient/*analysis ; Domestication ; Genetic Predisposition to Disease/*etiology/history ; History, Ancient ; Human Migration/*history ; Humans ; }, }
@article {pmid31300838, year = {2020}, author = {White, JA and Styer, A and Rosenwald, LC and Curry, MM and Welch, KD and Athey, KJ and Chapman, EG}, title = {Endosymbiotic Bacteria Are Prevalent and Diverse in Agricultural Spiders.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {472-481}, pmid = {31300838}, issn = {1432-184X}, support = {0224651//U.S. Department of Agriculture/ ; 148-502-16-377//Kentucky Science and Engineering Foundation/ ; 148-502-10-261//Kentucky Science and Engineering Foundation/ ; }, mesh = {Animals ; Bacteria/classification/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Bacteriological Techniques/*methods ; Entomology/*methods ; Food Deprivation ; High-Throughput Nucleotide Sequencing ; Kentucky ; *Microbiota/genetics ; Polymerase Chain Reaction ; Spiders/*microbiology ; Symbiosis/*physiology ; }, abstract = {Maternally inherited bacterial endosymbionts are common in arthropods, but their distribution and prevalence are poorly characterized in many host taxa. Initial surveys have suggested that vertically transmitted symbionts may be particularly common in spiders (Araneae). Here, we used diagnostic PCR and high-throughput sequencing to evaluate symbiont infection in 267 individual spiders representing 14 species (3 families) of agricultural spiders. We found 27 operational taxonomic units (OTUs) that are likely endosymbiotic, including multiple strains of Wolbachia, Rickettsia, and Cardinium, which are all vertically transmitted and frequently associated with reproductive manipulation of arthropod hosts. Additional strains included Rickettsiella, Spiroplasma, Rhabdochlamydia, and a novel Rickettsiales, all of which could range from pathogenic to mutualistic in their effects upon their hosts. Seventy percent of spider species had individuals that tested positive for one or more endosymbiotic OTUs, and specimens frequently contained multiple symbiotic strain types. The most symbiont-rich species, Idionella rugosa, had eight endosymbiotic OTUs, with as many as five present in the same specimen. Individual specimens within infected spider species had a variety of symbiotypes, differing from one another in the presence or absence of symbiotic strains. Our sample included both starved and unstarved specimens, and dominant bacterial OTUs were consistent per host species, regardless of feeding status. We conclude that spiders contain a remarkably diverse symbiotic microbiota. Spiders would be an informative group for investigating endosymbiont population dynamics in time and space, and unstarved specimens collected for other purposes (e.g., food web studies) could be used, with caution, for such investigations.}, }
@article {pmid31299565, year = {2019}, author = {Mahon, BM and Brehony, C and Cahill, N and McGrath, E and O'Connor, L and Varley, A and Cormican, M and Ryan, S and Hickey, P and Keane, S and Mulligan, M and Ruane, B and Jolley, KA and Maiden, MC and Brisse, S and Morris, D}, title = {Detection of OXA-48-like-producing Enterobacterales in Irish recreational water.}, journal = {The Science of the total environment}, volume = {690}, number = {}, pages = {1-6}, doi = {10.1016/j.scitotenv.2019.06.480}, pmid = {31299565}, issn = {1879-1026}, mesh = {Enterobacteriaceae/isolation &amp; purification/*physiology ; Environmental Monitoring ; Recreation ; *Water Microbiology ; beta-Lactamases/metabolism ; }, abstract = {The rapid dissemination of carbapenemase-producing Enterobacterales (CPE) is a major public health concern. The role that the aquatic environment plays in this dissemination is underexplored. This study aimed to examine seawater as a reservoir for CPE. Seawater sampling took place at a bathing site throughout the 2017 bathing season. Each 30 L sample (n = 6) was filtered using the CapE filtration system. Wastewater samples (200 mL) (pre-treatment (n = 3) and post-treatment (n = 3)) were obtained from a nearby secondary wastewater treatment plant, during the same time period. All samples were examined for CPE. Whole genome sequencing of confirmed CPE was carried out using Illumina sequencing. Isolate genomes were hosted in corresponding BIGSdb databases and analyses were performed using multiple web-based tools. CPE was detected in 2/6 seawater samples. It was not detected in any wastewater samples. OXA-48-like-producing ST131 Escherichia coli (Ec_BM707) was isolated from a seawater sample collected in May 2017 and OXA-48-like-producing ST101 Klebsiella pneumoniae (Kp_BM758) was isolated from a seawater sample collected in August 2017. The genomes of the environmental isolates were compared to a collection of previously described Irish clinical OXA-48-like-producing Enterobacterales (n = 105). Ec_BM707 and Kp_BM758 harboured blaOXA-48 on similar mobile genetic elements to those identified in the clinical collection (pOXA-48 fragment in Ec_BM707 and IncL(pOXA-48) plasmid in Kp_BM758). Genetic similarities were observed between Ec_BM707 and several of the clinical ST131 E. coli, with allele matches at up to 98.2% of 2513 core genome multilocus sequence type (cgMLST) loci. In contrast, Kp_BM758 and the 34 clinical K. pneumoniae were genetically distant. The source of the CPE at this site was not identified. The detection of OXA-48-like-producing ST131 E. coli and OXA-48-like-producing ST101 K. pneumoniae in Irish recreational water is a concern. The potential for contamination of the aquatic environment to contribute to dissemination of CPE in Europe warrants further study.}, }
@article {pmid31299167, year = {2020}, author = {Mayali, X}, title = {NanoSIMS: Microscale Quantification of Biogeochemical Activity with Large-Scale Impacts.}, journal = {Annual review of marine science}, volume = {12}, number = {}, pages = {449-467}, doi = {10.1146/annurev-marine-010419-010714}, pmid = {31299167}, issn = {1941-0611}, mesh = {Aquatic Organisms/*growth &amp; development/metabolism ; Environmental Monitoring/instrumentation/*methods ; Isotope Labeling ; *Microbiota/drug effects ; *Seawater/chemistry/microbiology ; Spectrometry, Mass, Secondary Ion/methods ; *Water Microbiology ; Water Pollutants, Chemical/toxicity ; }, abstract = {One major objective of aquatic microbial ecology is to understand the distribution of microbial populations over space and time and in response to environmental factors. Perhaps more importantly, it is crucial to quantify how those microbial cells affect biogeochemical processes of interest, such as primary production, nitrogen cycling, or the breakdown of pollutants. One valuable approach to link microbial identity to activity is to carry out incubations with stable-isotope-labeled substrates and then quantify the isotope incorporation by individual microbial cells using nanoscale secondary ion mass spectrometry (NanoSIMS). This review summarizes recent efforts in this field, highlights novel methods, describes studies investigating rare metabolisms as well as widespread microbial activity, and hopes to provide a framework to increase the use and capabilities of NanoSIMS for microbial biogeochemical studies in the future.}, }
@article {pmid31299137, year = {2019}, author = {Pjevac, P and Dyksma, S and Goldhammer, T and Mujakić, I and Koblížek, M and Mußmann, M and Amann, R and Orlić, S}, title = {In situ abundance and carbon fixation activity of distinct anoxygenic phototrophs in the stratified seawater lake Rogoznica.}, journal = {Environmental microbiology}, volume = {21}, number = {10}, pages = {3896-3908}, doi = {10.1111/1462-2920.14739}, pmid = {31299137}, issn = {1462-2920}, support = {//Croatian Science Foundation/International ; }, mesh = {Carbon Cycle ; Chlorobium/isolation &amp; purification/*metabolism ; Chromatiaceae/isolation &amp; purification/*metabolism ; Croatia ; Lakes/*microbiology ; Photosynthesis ; Seawater/microbiology ; Sulfides/*metabolism ; Sulfur/*metabolism ; }, abstract = {Sulphide-driven anoxygenic photosynthesis is an ancient microbial metabolism that contributes significantly to inorganic carbon fixation in stratified, sulphidic water bodies. Methods commonly applied to quantify inorganic carbon fixation by anoxygenic phototrophs, however, cannot resolve the contributions of distinct microbial populations to the overall process. We implemented a straightforward workflow, consisting of radioisotope labelling and flow cytometric cell sorting based on the distinct autofluorescence of bacterial photopigments, to discriminate and quantify contributions of co-occurring anoxygenic phototrophic populations to in situ inorganic carbon fixation in environmental samples. This allowed us to assign 89.3% ± 7.6% of daytime inorganic carbon fixation by anoxygenic phototrophs in Lake Rogoznica (Croatia) to an abundant chemocline-dwelling population of green sulphur bacteria (dominated by Chlorobium phaeobacteroides), whereas the co-occurring purple sulphur bacteria (Halochromatium sp.) contributed only 1.8% ± 1.4%. Furthermore, we obtained two metagenome assembled genomes of green sulphur bacteria and one of a purple sulphur bacterium which provides the first genomic insights into the genus Halochromatium, confirming its high metabolic flexibility and physiological potential for mixo- and heterotrophic growth.}, }
@article {pmid31297747, year = {2019}, author = {Costa, FS and Macedo, MWFS and Araújo, ACM and Rodrigues, CA and Kuramae, EE and de Barros Alcanfor, SK and Pessoa-Filho, M and Barreto, CC}, title = {Assessing nickel tolerance of bacteria isolated from serpentine soils.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {50}, number = {3}, pages = {705-713}, pmid = {31297747}, issn = {1678-4405}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Brazil ; Nickel/*metabolism ; Phylogeny ; Secologanin Tryptamine Alkaloids/*analysis/metabolism ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Serpentine soils present unique characteristics such as a low Ca/Mg ratio, low concentration of nutrients, and a high concentration of heavy metals, especially nickel. Soil bacterial isolates from an ultramafic complex located in the tropical savanna known as the Brazilian Cerrado were studied. Nickel-tolerant bacteria were obtained, and their ability to remove nickel from a culture medium was assessed. Bacterial isolates presented higher tolerance to nickel salts than previously reported for bacteria obtained from serpentine environments in other regions of the world. In addition, the quantification of nickel in cell pellets indicated that at least four isolates may adsorb soluble forms of nickel. It is expected that information gathered in this study will support future efforts to exploit serpentine soil bacteria for biotechnological processes involving nickel decontamination from environmental samples.}, }
@article {pmid31296406, year = {2019}, author = {Lajoie, G and Kembel, SW}, title = {Making the Most of Trait-Based Approaches for Microbial Ecology.}, journal = {Trends in microbiology}, volume = {27}, number = {10}, pages = {814-823}, doi = {10.1016/j.tim.2019.06.003}, pmid = {31296406}, issn = {1878-4380}, mesh = {Biodiversity ; Ecological and Environmental Phenomena ; *Ecology ; Ecosystem ; Microbiota/*physiology ; *Phenotype ; }, abstract = {There is an increasing interest in applying trait-based approaches to microbial ecology, but the question of how and why to do it is still lagging behind. By anchoring our discussion of these questions in a framework derived from epistemology, we broaden the scope of trait-based approaches to microbial ecology from one oriented mostly around explanation towards one inclusive of the predictive and integrative potential of these approaches. We use case studies from macro-organismal ecology to concretely show how these goals for knowledge development can be fulfilled and propose clear directions, adapted to the biological reality of microbes, to make the most of recent advancements in the measurement of microbial phenotypes and traits.}, }
@article {pmid31295324, year = {2019}, author = {Defoirdt, T}, title = {Amino acid-derived quorum sensing molecules controlling the virulence of vibrios (and beyond).}, journal = {PLoS pathogens}, volume = {15}, number = {7}, pages = {e1007815}, pmid = {31295324}, issn = {1553-7374}, mesh = {Amino Acids/metabolism ; Animals ; Dipeptides/metabolism ; Humans ; Indoles/metabolism ; Peptides, Cyclic/metabolism ; Pyrazoles/metabolism ; Quorum Sensing/*physiology ; Vibrio/*pathogenicity/*physiology ; Virulence/physiology ; Virulence Factors/metabolism ; }, }
@article {pmid31294971, year = {2019}, author = {Han, P and Yu, Y and Zhou, L and Tian, Z and Li, Z and Hou, L and Liu, M and Wu, Q and Wagner, M and Men, Y}, title = {Specific Micropollutant Biotransformation Pattern by the Comammox Bacterium Nitrospira inopinata.}, journal = {Environmental science &amp; technology}, volume = {53}, number = {15}, pages = {8695-8705}, doi = {10.1021/acs.est.9b01037}, pmid = {31294971}, issn = {1520-5851}, mesh = {Ammonia ; Archaea ; Bacteria ; Biotransformation ; *Nitrification ; Oxidation-Reduction ; Phylogeny ; *Soil Microbiology ; }, abstract = {The recently discovered complete ammonia-oxidizing (comammox) bacteria occur in various environments, including wastewater treatment plants. To better understand their role in micropollutant biotransformation in comparison with ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), we investigated the biotransformation capability of Nitrospira inopinata (the only comammox isolate) for 17 micropollutants. Asulam, fenhexamid, mianserin, and ranitidine were biotransformed by N. inopinata, Nitrososphaera gargensis (AOA), and Nitrosomonas nitrosa Nm90 (AOB). More distinctively, carbendazim, a benzimidazole fungicide, was exclusively biotransformed by N. inopinata. The biotransformation of carbendazim only occurred when N. inopinata was supplied with ammonia but not nitrite as the energy source. The exclusive biotransformation of carbendazim by N. inopinata was likely enabled by an enhanced substrate promiscuity of its unique AMO and its much higher substrate (for ammonia) affinity compared with the other two ammonia oxidizers. One major plausible transformation product (TP) of carbendazim is a hydroxylated form at the aromatic ring, which is consistent with the function of AMO. These findings provide fundamental knowledge on the micropollutant degradation potential of a comammox bacterium to better understand the fate of micropollutants in nitrifying environments.}, }
@article {pmid31293665, year = {2019}, author = {Martín-Sánchez, L and Singh, KS and Avalos, M and van Wezel, GP and Dickschat, JS and Garbeva, P}, title = {Phylogenomic analyses and distribution of terpene synthases among Streptomyces.}, journal = {Beilstein journal of organic chemistry}, volume = {15}, number = {}, pages = {1181-1193}, pmid = {31293665}, issn = {1860-5397}, abstract = {Terpene synthases are widely distributed among microorganisms and have been mainly studied in members of the genus Streptomyces. However, little is known about the distribution and evolution of the genes for terpene synthases. Here, we performed whole-genome based phylogenetic analysis of Streptomyces species, and compared the distribution of terpene synthase genes among them. Overall, our study revealed that ten major types of terpene synthases are present within the genus Streptomyces, namely those for geosmin, 2-methylisoborneol, epi-isozizaene, 7-epi-α-eudesmol, epi-cubenol, caryolan-1-ol, cyclooctat-9-en-7-ol, isoafricanol, pentalenene and α-amorphene. The Streptomyces species divide in three phylogenetic groups based on their whole genomes for which the distribution of the ten terpene synthases was analysed. Geosmin synthases were the most widely distributed and were found to be evolutionary positively selected. Other terpene synthases were found to be specific for one of the three clades or a subclade within the genus Streptomyces. A phylogenetic analysis of the most widely distributed classes of Streptomyces terpene synthases in comparison to the phylogenomic analysis of this genus is discussed.}, }
@article {pmid31292537, year = {2019}, author = {Salcher, MM and Schaefle, D and Kaspar, M and Neuenschwander, SM and Ghai, R}, title = {Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae.}, journal = {The ISME journal}, volume = {13}, number = {11}, pages = {2764-2777}, pmid = {31292537}, issn = {1751-7370}, mesh = {Adaptation, Physiological ; *Ecosystem ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome Size ; *Genome, Bacterial ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; Methylophilaceae/classification/*genetics/isolation &amp; purification/physiology ; Phylogeny ; Seawater/*microbiology ; }, abstract = {The most abundant aquatic microbes are small in cell and genome size. Genome-streamlining theory predicts gene loss caused by evolutionary selection driven by environmental factors, favouring superior competitors for limiting resources. However, evolutionary histories of such abundant, genome-streamlined microbes remain largely unknown. Here we reconstruct the series of steps in the evolution of some of the most abundant genome-streamlined microbes in freshwaters ("Ca. Methylopumilus") and oceans (marine lineage OM43). A broad genomic spectrum is visible in the family Methylophilaceae (Betaproteobacteria), from sediment microbes with medium-sized genomes (2-3 Mbp genome size), an occasionally blooming pelagic intermediate (1.7 Mbp), and the most reduced pelagic forms (1.3 Mbp). We show that a habitat transition from freshwater sediment to the relatively oligotrophic pelagial was accompanied by progressive gene loss and adaptive gains. Gene loss has mainly affected functions not necessarily required or advantageous in the pelagial or is encoded by redundant pathways. Likewise, we identified genes providing adaptations to oligotrophic conditions that have been transmitted horizontally from pelagic freshwater microbes. Remarkably, the secondary transition from the pelagial of lakes to the oceans required only slight modifications, i.e., adaptations to higher salinity, gained via horizontal gene transfer from indigenous microbes. Our study provides first genomic evidence of genome reduction taking place during habitat transitions. In this regard, the family Methylophilaceae is an exceptional model for tracing the evolutionary history of genome streamlining as such a collection of evolutionarily related microbes from different habitats is rare in the microbial world.}, }
@article {pmid31292259, year = {2019}, author = {Chuang, JS and Frentz, Z and Leibler, S}, title = {Homeorhesis and ecological succession quantified in synthetic microbial ecosystems.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {30}, pages = {14852-14861}, pmid = {31292259}, issn = {1091-6490}, mesh = {Chlamydomonas reinhardtii/*physiology ; *Ecosystem ; *Homeostasis ; Symbiosis ; Tetrahymena thermophila/*physiology ; }, abstract = {The dynamics of ecological change following a major perturbation, known as succession, are influenced by random processes. Direct quantitation of the degree of contingency in succession requires chronological study of replicate ecosystems. We previously found that population dynamics in carefully controlled, replicated synthetic microbial ecosystems were strongly deterministic over several months. Here, we present simplified, two-species microbial ecosystems consisting of algae and ciliates, imaged in toto at single-cell resolution with fluorescence microscopy over a period of 1 to 2 weeks. To directly study succession in these ecosystems, we deliberately varied the initial cell abundances over replicates and quantified the ensuing dynamics. The distribution of abundance trajectories rapidly converged to a nearly deterministic path, with small fluctuations, despite variations in initial conditions, environmental perturbations, and intrinsic noise, indicative of homeorhesis. Homeorhesis was also observed for certain phenotypic variables, such as partitioning of the ciliates into distinct size classes and clumping of the algae. Although the mechanism of homeorhesis observed in these synthetic ecosystems remains to be elucidated, it is clear that it must emerge from the ways each species controls its own internal states, with respect to a diverse set of environmental conditions and ecological interactions.}, }
@article {pmid31292233, year = {2019}, author = {Moeller, AH and Gomes-Neto, JC and Mantz, S and Kittana, H and Segura Munoz, RR and Schmaltz, RJ and Ramer-Tait, AE and Nachman, MW}, title = {Experimental Evidence for Adaptation to Species-Specific Gut Microbiota in House Mice.}, journal = {mSphere}, volume = {4}, number = {4}, pages = {}, pmid = {31292233}, issn = {2379-5042}, support = {R01 GM074245/GM/NIGMS NIH HHS/United States ; R01 GM127468/GM/NIGMS NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Animals ; Bacteria/*classification ; Female ; *Gastrointestinal Microbiome ; Germ-Free Life ; *Host Microbial Interactions ; *Host Specificity ; Male ; Metagenome ; Mice ; Mice, Inbred C57BL ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {The gut microbial communities of mammals have codiversified with host species, and changes in the gut microbiota can have profound effects on host fitness. Therefore, the gut microbiota may drive adaptation in mammalian species, but this possibility is underexplored. Here, we show that the gut microbiota has codiversified with mice in the genus Mus over the past ∼6 million years, and we present experimental evidence that the gut microbiota has driven adaptive evolution of the house mouse, Mus musculusdomesticus Phylogenetic analyses of metagenome-assembled bacterial genomic sequences revealed that gut bacterial lineages have been retained within and diversified alongside Mus species over evolutionary time. Transplantation of gut microbiotas from various Mus species into germfree M. m. domesticus showed that foreign gut microbiotas slowed growth rate and upregulated macrophage inflammatory protein in hosts. These results suggest adaptation by M. m. domesticus to its gut microbiota since it diverged from other Mus species.IMPORTANCE The communities of bacteria that reside within mammalian guts are deeply integrated with their hosts, but the impact of this gut microbiota on mammalian evolution remains poorly understood. Experimental transplantation of the gut microbiota between mouse species revealed that foreign gut microbiotas lowered the host growth rate and upregulated the expression of an immunomodulating cytokine. In addition, foreign gut microbiotas increased host liver sizes and attenuated sex-specific differences in host muscle and fat content. These results suggest that the house mouse has adapted to its species-specific gut microbiota.}, }
@article {pmid31289346, year = {2019}, author = {Schmidt, R and Ulanova, D and Wick, LY and Bode, HB and Garbeva, P}, title = {Microbe-driven chemical ecology: past, present and future.}, journal = {The ISME journal}, volume = {13}, number = {11}, pages = {2656-2663}, pmid = {31289346}, issn = {1751-7370}, mesh = {Bacteria/*chemistry/classification/*metabolism ; Ecology ; *Ecosystem ; *Microbial Interactions ; Microbiota ; }, abstract = {In recent years, research in the field of Microbial Ecology has revealed the tremendous diversity and complexity of microbial communities across different ecosystems. Microbes play a major role in ecosystem functioning and contribute to the health and fitness of higher organisms. Scientists are now facing many technological and methodological challenges in analyzing these complex natural microbial communities. The advances in analytical and omics techniques have shown that microbial communities are largely shaped by chemical interaction networks mediated by specialized (water-soluble and volatile) metabolites. However, studies concerning microbial chemical interactions need to consider biotic and abiotic factors on multidimensional levels, which require the development of new tools and approaches mimicking natural microbial habitats. In this review, we describe environmental factors affecting the production and transport of specialized metabolites. We evaluate their ecological functions and discuss approaches to address future challenges in microbial chemical ecology (MCE). We aim to emphasize that future developments in the field of MCE will need to include holistic studies involving organisms at all levels and to consider mechanisms underlying the interactions between viruses, micro-, and macro-organisms in their natural environments.}, }
@article {pmid31289280, year = {2019}, author = {De Tender, C and Mesuere, B and Van der Jeugt, F and Haegeman, A and Ruttink, T and Vandecasteele, B and Dawyndt, P and Debode, J and Kuramae, EE}, title = {Peat substrate amended with chitin modulates the N-cycle, siderophore and chitinase responses in the lettuce rhizobiome.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {9890}, pmid = {31289280}, issn = {2045-2322}, mesh = {Bacteria/*isolation &amp; purification/metabolism ; Chitin/*metabolism ; Chitinases/*metabolism ; Lactuca/*metabolism/microbiology ; Nitrogen/*metabolism ; Nitrogen Cycle ; Rhizobium ; Siderophores/*metabolism ; Soil/*chemistry ; Substrate Specificity ; }, abstract = {Chitin is a valuable peat substrate amendment by increasing lettuce growth and reducing the survival of the zoonotic pathogen Salmonella enterica on lettuce leaves. The production of chitin-catabolic enzymes (chitinases) play a crucial role and are mediated through the microbial community. A higher abundance of plant-growth promoting microorganisms and genera involved in N and chitin metabolism are present in a chitin-enriched substrate. In this study, we hypothesize that chitin addition to peat substrate stimulates the microbial chitinase production. The degradation of chitin leads to nutrient release and the production of small chitin oligomers that are related to plant growth promotion and activation of the plant's defense response. First a shotgun metagenomics approach was used to decipher the potential rhizosphere microbial functions then the nutritional content of the peat substrate was measured. Our results show that chitin addition increases chitin-catabolic enzymes, bacterial ammonium oxidizing and siderophore genes. Lettuce growth promotion can be explained by a cascade degradation of chitin to N-acetylglucosamine and eventually ammonium. The occurrence of increased ammonium oxidizing bacteria, Nitrosospira, and amoA genes results in an elevated concentration of plant-available nitrate. In addition, the increase in chitinase and siderophore genes may have stimulated the plant's systemic resistance.}, }
@article {pmid31286860, year = {2019}, author = {Meola, M and Rifa, E and Shani, N and Delbès, C and Berthoud, H and Chassard, C}, title = {DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {560}, pmid = {31286860}, issn = {1471-2164}, mesh = {Classification/*methods ; Dairy Products/*microbiology ; *Databases, Genetic ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {BACKGROUND: Reads assignment to taxonomic units is a key step in microbiome analysis pipelines. To date, accurate taxonomy annotation of 16S reads, particularly at species rank, is still challenging due to the short size of read sequences and differently curated classification databases. The close phylogenetic relationship between species encountered in dairy products, however, makes it crucial to annotate species accurately to achieve sufficient phylogenetic resolution for further downstream ecological studies or for food diagnostics. Curated databases dedicated to the environment of interest are expected to improve the accuracy and resolution of taxonomy annotation.<br><br>RESULTS: We provide a manually curated database composed of 10'290 full-length 16S rRNA gene sequences from prokaryotes tailored for dairy products analysis (https://github.com/marcomeola/DAIRYdb). The performance of the DAIRYdb was compared with the universal databases Silva, LTP, RDP and Greengenes. The DAIRYdb significantly outperformed all other databases independently of the classification algorithm by enabling higher accurate taxonomy annotation down to the species rank. The DAIRYdb accurately annotates over 90% of the sequences of either single or paired hypervariable regions automatically. The manually curated DAIRYdb strongly improves taxonomic annotation accuracy for microbiome studies in dairy environments. The DAIRYdb is a practical solution that enables automatization of this key step, thus facilitating the routine application of NGS microbiome analyses for microbial ecology studies and diagnostics in dairy products.}, }
@article {pmid31286170, year = {2020}, author = {Puentes-Téllez, PE and Salles, JF}, title = {Dynamics of Abundant and Rare Bacteria During Degradation of Lignocellulose from Sugarcane Biomass.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {312-325}, pmid = {31286170}, issn = {1432-184X}, support = {729004006//FAPESP-NWO/ ; }, mesh = {Bacteria/*metabolism ; Brazil ; Cellulose/chemistry ; Lignin/*metabolism ; *Microbiota ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Saccharum/chemistry ; Silage ; *Soil Microbiology ; }, abstract = {Microorganisms play a crucial role in lignocellulosic degradation. Many enriched microbial communities have demonstrated to reach functional and structural stability with effective degrading capacities of industrial interest. These microbial communities are typically composed by only few dominant species and a high number of usually overlooked rare species. Here, we used two sources of lignocellulose (sugarcane bagasse and straw) in order to obtain lignocellulose-degrading bacteria through an enriched process, followed the selective trajectory of both abundant and rare bacterial communities by 16S rRNA gene amplification and analyzed the outcomes of selection in terms of capacities and specialization. We verified the importance of pre-selection by using two sources of microbial inoculum: soil samples from a sugarcane field with history of straw addition (St15) and control samples, from the same field, without amendments (St0). We found similitudes in terms of stabilization between the abundant and rare fractions. We also found positive correlations of both abundant and rare taxa (like Caulobacteraceae and Alcaligenaceae) and the degradation of lignocellulosic fractions. Differences in the inocula's initial diversity rapidly decreased during the enrichment resulting in comparable richness levels at the end of the process; however, the legacy of the St15 inoculum and its specialization positively influenced the degradation capacities of the community. Analysis of specialization of the final communities revealed increased straw degradation capacity in the communities enriched in bagasse, which could be potentially used as a strategy for improving lignocellulose waste degradation on the sugarcane fields. This work highlights the importance of including the rare fraction of bacterial communities during investigations involving the screening and assessment of effective degrading communities.}, }
@article {pmid31286169, year = {2020}, author = {Cutler, NA and Arróniz-Crespo, M and Street, LE and Jones, DL and Chaput, DL and DeLuca, TH}, title = {Correction to: Long-Term Recovery of Microbial Communities in the Boreal Bryosphere Following Fire Disturbance.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {516}, doi = {10.1007/s00248-019-01408-5}, pmid = {31286169}, issn = {1432-184X}, abstract = {The original version of this article contained an error in the Molecular Analysis subsection of the Methods.}, }
@article {pmid31285347, year = {2019}, author = {Johnston, ER and Hatt, JK and He, Z and Wu, L and Guo, X and Luo, Y and Schuur, EAG and Tiedje, JM and Zhou, J and Konstantinidis, KT}, title = {Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {30}, pages = {15096-15105}, pmid = {31285347}, issn = {1091-6490}, mesh = {Alaska ; Arctic Regions ; Carbon/*chemistry/metabolism ; Carbon Cycle ; Carbon Dioxide/*chemistry/metabolism ; Climate Change/statistics &amp; numerical data ; Microbiota/*genetics ; *Models, Statistical ; Permafrost/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Temperature ; *Tundra ; }, abstract = {Northern-latitude tundra soils harbor substantial carbon (C) stocks that are highly susceptible to microbial degradation with rising global temperatures. Understanding the magnitude and direction (e.g., C release or sequestration) of the microbial responses to warming is necessary to accurately model climate change. In this study, Alaskan tundra soils were subjected to experimental in situ warming by ∼1.1 °C above ambient temperature, and the microbial communities were evaluated using metagenomics after 4.5 years, at 2 depths: 15 to 25 cm (active layer at outset of the experiment) and 45 to 55 cm (transition zone at the permafrost/active layer boundary at the outset of the experiment). In contrast to small or insignificant shifts after 1.5 years of warming, 4.5 years of warming resulted in significant changes to the abundances of functional traits and the corresponding taxa relative to control plots (no warming), and microbial shifts differed qualitatively between the two soil depths. At 15 to 25 cm, increased abundances of carbohydrate utilization genes were observed that correlated with (increased) measured ecosystem carbon respiration. At the 45- to 55-cm layer, increased methanogenesis potential was observed, which corresponded with a 3-fold increase in abundance of a single archaeal clade of the Methanosarcinales order, increased annual thaw duration (45.3 vs. 79.3 days), and increased CH4 emissions. Collectively, these data demonstrate that the microbial responses to warming in tundra soil are rapid and markedly different between the 2 critical soil layers evaluated, and identify potential biomarkers for the corresponding microbial processes that could be important in modeling.}, }
@article {pmid31285337, year = {2019}, author = {Greenlon, A and Chang, PL and Damtew, ZM and Muleta, A and Carrasquilla-Garcia, N and Kim, D and Nguyen, HP and Suryawanshi, V and Krieg, CP and Yadav, SK and Patel, JS and Mukherjee, A and Udupa, S and Benjelloun, I and Thami-Alami, I and Yasin, M and Patil, B and Singh, S and Sarma, BK and von Wettberg, EJB and Kahraman, A and Bukun, B and Assefa, F and Tesfaye, K and Fikre, A and Cook, DR}, title = {Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {30}, pages = {15200-15209}, pmid = {31285337}, issn = {1091-6490}, mesh = {Biological Evolution ; Cicer/*microbiology ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Mesorhizobium/classification/*genetics ; Metagenomics/methods ; Microbial Consortia/*genetics ; Nitrogen Fixation/physiology ; Phylogeny ; Phylogeography ; Soil/classification ; Soil Microbiology ; Symbiosis/genetics ; }, abstract = {Although microorganisms are known to dominate Earth's biospheres and drive biogeochemical cycling, little is known about the geographic distributions of microbial populations or the environmental factors that pattern those distributions. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of the nitrogen-fixing bacterial symbionts of the crop chickpea, generating 1,027 draft whole-genome sequences at the level of bacterial populations, including 14 high-quality PacBio genomes from a phylogenetically representative subset. We find that diverse Mesorhizobium taxa perform symbiosis with chickpea and have largely overlapping global distributions. However, sampled locations cluster based on the phylogenetic diversity of Mesorhizobium populations, and diversity clusters correspond to edaphic and environmental factors, primarily soil type and latitude. Despite long-standing evolutionary divergence and geographic isolation, the diverse taxa observed to nodulate chickpea share a set of integrative conjugative elements (ICEs) that encode the major functions of the symbiosis. This symbiosis ICE takes 2 forms in the bacterial chromosome-tripartite and monopartite-with tripartite ICEs confined to a broadly distributed superspecies clade. The pairwise evolutionary relatedness of these elements is controlled as much by geographic distance as by the evolutionary relatedness of the background genome. In contrast, diversity in the broader gene content of Mesorhizobium genomes follows a tight linear relationship with core genome phylogenetic distance, with little detectable effect of geography. These results illustrate how geography and demography can operate differentially on the evolution of bacterial genomes and offer useful insights for the development of improved technologies for sustainable agriculture.}, }
@article {pmid31285190, year = {2019}, author = {Wörner, S and Pester, M}, title = {Microbial Succession of Anaerobic Chitin Degradation in Freshwater Sediments.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {18}, pages = {}, pmid = {31285190}, issn = {1098-5336}, mesh = {Anaerobiosis ; Bacteria/classification/*metabolism ; Biodegradation, Environmental ; Chitin/*metabolism ; Geologic Sediments/*microbiology ; Germany ; Lakes/*microbiology ; Microbiota ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Chitin is massively produced by freshwater plankton species as a structural element of their exoskeleton or cell wall. At the same time, chitin does not accumulate in the predominantly anoxic sediments, underlining its importance as carbon and nitrogen sources for sedimentary microorganisms. We studied chitin degradation in littoral sediment of Lake Constance, Central Europe's third largest lake. Turnover of the chitin analog methyl-umbelliferyl-N,N-diacetylchitobioside (MUF-DC) was highest in the upper oxic sediment layer, with 5.4 nmol MUF-DC h[-1] (g sediment [dry weight])[-1] In the underlying anoxic sediment layers, chitin hydrolysis decreased with depth from 1.1 to 0.08 nmol MUF-DC h[-1] (g sediment [dry weight])[-1] Bacteria involved in chitin degradation were identified by 16S rRNA (gene) amplicon sequencing of anoxic microcosms incubated in the presence of chitin compared to microcosms amended either with N-acetylglucosamine as the monomer of chitin or no substrate. Chitin degradation was driven by a succession of bacteria responding specifically to chitin only. The early phase (0 to 9 days) was dominated by Chitinivibrio spp. (Fibrobacteres). The intermediate phase (9 to 21 days) was characterized by a higher diversity of chitin responders, including, besides Chitinivibrio spp., also members of the phyla Bacteroidetes, Proteobacteria, Spirochaetes, and Chloroflexi In the late phase (21 to 43 days), the Chitinivibrio populations broke down with a parallel strong increase of Ruminiclostridium spp. (formerly Clostridium cluster III, Firmicutes), which became the dominating chitin responders. Our study provides quantitative insights into anaerobic chitin degradation in lake sediments and linked this to a model of microbial succession associated with this activity.IMPORTANCE Chitin is the most abundant biopolymer in aquatic environments, with a direct impact on the carbon and nitrogen cycles. Despite its massive production as a structural element of crustaceans, insects, or algae, it does not accumulate in sediments. Little is known about its turnover in predominantly anoxic freshwater sediments and the responsible microorganisms. We proved that chitin is readily degraded under anoxic conditions and linked this to a succession of the members of the responsible microbial community over a 43-day period. While Fibrobacteres and Firmicutes members were driving the early and late phases of chitin degradation, respectively, a more diverse community was involved in chitin degradation in the intermediate phase. Entirely different microorganisms responded toward the chitin monomer N-acetylglucosamine, which underscores that soluble monomers are poor and misleading substrates to study polymer-utilizing microorganisms. Our study provides quantitative insights into the microbial ecology driving anaerobic chitin degradation in freshwater sediments.}, }
@article {pmid31284214, year = {2019}, author = {Lorenz, C and Roscher, L and Meyer, MS and Hildebrandt, L and Prume, J and Löder, MGJ and Primpke, S and Gerdts, G}, title = {Spatial distribution of microplastics in sediments and surface waters of the southern North Sea.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {252}, number = {Pt B}, pages = {1719-1729}, doi = {10.1016/j.envpol.2019.06.093}, pmid = {31284214}, issn = {1873-6424}, mesh = {Environmental Monitoring/*methods ; Geologic Sediments/*chemistry ; North Sea ; Plastics/*analysis ; Polypropylenes/analysis ; Polyurethanes/analysis ; Seawater/chemistry ; Spatial Analysis ; Water Pollutants, Chemical/*analysis ; }, abstract = {Microplastic pollution within the marine environment is of pressing concern globally. Accordingly, spatial monitoring of microplastic concentrations, composition and size distribution may help to identify sources and entry pathways, and hence allow initiating focused mitigation. Spatial distribution patterns of microplastics were investigated in two compartments of the southern North Sea by collecting sublittoral sediment and surface water samples from 24 stations. Large microplastics (500-5000 μm) were detected visually and identified using attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy. The remaining sample was digested enzymatically, concentrated onto filters and analyzed for small microplastics (11-500 μm) using Focal Plane Array (FPA) FTIR imaging. Microplastics were detected in all samples with concentrations ranging between 2.8 and 1188.8 particles kg[-1] for sediments and 0.1-245.4 particles m[-3] for surface waters. On average 98% of microplastics were <100 μm in sediments and 86% in surface waters. The most prevalent polymer types in both compartments were polypropylene, acrylates/polyurethane/varnish, and polyamide. However, polymer composition differed significantly between sediment and surface water samples as well as between the Frisian Islands and the English Channel sites. These results show that microplastics are not evenly distributed, in neither location nor size, which is illuminating regarding the development of monitoring protocols.}, }
@article {pmid31283892, year = {2020}, author = {Philip, N and Leishman, SJ and Bandara, HMHN and Healey, DL and Walsh, LJ}, title = {Randomized Controlled Study to Evaluate Microbial Ecological Effects of CPP-ACP and Cranberry on Dental Plaque.}, journal = {JDR clinical and translational research}, volume = {5}, number = {2}, pages = {118-126}, doi = {10.1177/2380084419859871}, pmid = {31283892}, issn = {2380-0852}, mesh = {Australia ; Caseins ; Corynebacterium ; *Dental Caries ; *Dental Plaque ; Humans ; Neisseria ; Plant Extracts ; Tooth Remineralization ; *Vaccinium macrocarpon ; Veillonella ; }, abstract = {INTRODUCTION: Ecological approaches to dental caries prevention play a key role in attaining long-term control over the disease and maintaining a symbiotic oral microbiome.<br><br>OBJECTIVES: This study aimed to investigate the microbial ecological effects of 2 interventional dentifrices: a casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) dentifrice and the same dentifrice supplemented with a polyphenol-rich cranberry extract.<br><br>METHODS: The interventional toothpastes were compared with each other and with an active control fluoride dentifrice in a double-blinded randomized controlled trial. Real-time quantitative polymerase chain reaction (qPCR) analysis was used to determine changes in the bacterial loads of 14 key bacterial species (8 caries associated and 6 health associated) in the dental plaque of trial participants after they used the dentifrices for 5 to 6 wk.<br><br>RESULTS: From the baseline to the recall visit, significant differences were observed between the treatment groups in the bacterial loads of 2 caries-associated bacterial species (Streptococcus mutans [P < 0.001] and Veillonella parvula [P < 0.001]) and 3 health-associated bacterial species (Corynebacterium durum [P = 0.008], Neisseria flavescens [P = 0.005], and Streptococcus sanguinis [P < 0.001]). Compared to the fluoride control dentifrice, the CPP-ACP dentifrice demonstrated significant differences for S. mutans (P = 0.032), C. durum (P = 0.007), and S. sanguinis (P < 0.001), while combination CPP-ACP-cranberry dentifrice showed significant differences for S. mutans (P < 0.001), V. parvula (P < 0.001), N. flavescens (P = 0.003), and S. sanguinis (P < 0.001). However, no significant differences were observed in the bacterial load comparisons between the CPP-ACP and combination dentifrices for any of the targeted bacterial species (P > 0.05).<br><br>CONCLUSIONS: Overall, the results indicate that dentifrices containing CPP-ACP and polyphenol-rich cranberry extracts can influence a species-level shift in the ecology of the oral microbiome, resulting in a microbial community less associated with dental caries (Australian New Zealand Clinical Trial Registry ANZCTR 12618000095268).<br><br>KNOWLEDGE TRANSFER STATEMENT: The results of this randomized controlled trial indicate that dentifrices containing casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) and polyphenol-rich cranberry extracts were able to beneficially modulate the microbial ecology of dental plaque in a group of high caries-risk patients. This could contribute toward lowering the risk of developing new caries lesions, an important goal sought by patients, clinicians, and policy makers.}, }
@article {pmid31280333, year = {2019}, author = {Ghosh, A and Bhadury, P}, title = {Vibrio chemaguriensis sp. nov., from Sundarbans, Bay of Bengal.}, journal = {Current microbiology}, volume = {76}, number = {10}, pages = {1118-1127}, pmid = {31280333}, issn = {1432-0991}, mesh = {Bays/*microbiology ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Genes, Bacterial/genetics ; Genome, Bacterial/genetics ; India ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Vibrio/chemistry/*classification/genetics/growth &amp; development ; }, abstract = {A new species of Vibrio (annotated as SBOTS_Iso1) was isolated in August 2014 from the Stn1 located in Chemaguri creek of Sundarbans mangrove ecoregion and taxonomically characterized using a polyphasic approach. Phenotypic analysis including biochemical tests and growth across a wide range of salinities indicated the typical estuarine characteristics of this new species. The bacterium was Gram negative, rod-shaped, oxidase and catalase negative and grows in the presence of NaCl. FAME analysis indicated 31.7% of the cellular fatty acids to be made up of 16:1 ω7c/16:1 ω6c. Amplification and sequencing of 16S rRNA and multilocus sequence analysis of four loci (2040 bp; rpoA, topA, mreB, pyrH) and additional sequence data of ftsZ, atpD, ompW and rpoB genes showed this isolate to be a member of Harveyi clade of the genus Vibrio. The closest phylogenetic neighbour was Vibrio alginolyticus ATCC 17749[T] with 96.8% similarity. Whole-genome sequence data indicates the presence of ~ 5 Mbp genome. GGDC, orthoANIu and AAI indicated 45%, 92% and 0.962 identity respectively with genome of Vibrio alginolyticus ATCC 17749[T]. The isolate SBOTS_Iso1 has been named Vibrio chemaguriensis sp. nov. on the name of the site from where it was first isolated.}, }
@article {pmid31280331, year = {2020}, author = {Chen, H and Li, C and Liu, T and Chen, S and Xiao, H}, title = {A Metagenomic Study of Intestinal Microbial Diversity in Relation to Feeding Habits of Surface and Cave-Dwelling Sinocyclocheilus Species.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {299-311}, pmid = {31280331}, issn = {1432-184X}, support = {31560111//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bacteria/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Caves ; Cyprinidae/*microbiology/*physiology ; *Ecosystem ; *Feeding Behavior ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Species Specificity ; }, abstract = {Light is completely absent in cave habitats, causing a shortage or lack of autochthonous photosynthesis. Thus, understanding the mechanisms underlying the ability of organisms to adapt to the unique cave habitat is of great interest. We used high-throughput sequencing of the 16S ribosomal RNA gene of intestinal microorganisms from 11 Sinocyclocheilus (Cypriniformes: Cyprinidae) species, to explore the characteristics of intestinal microorganisms and the adaptive mechanisms of Sinocyclocheilus cavefish and surface fish. We found that the α-diversity and richness of the intestinal microbiome were much higher in cavefish than in surface fish. Principal coordinate analysis showed that cavefish and surface fish formed three clusters because of different dominant gut microorganisms which are generated by different habitats. Based on PICRUSt-predicted functions, harmful substance degradation pathways were much more common in cavefish intestinal microorganisms than in those from surface fish. The intestinal microbiota of surface fish group 1 had a higher capacity for carbohydrate metabolism, whereas protein and amino acid metabolism and digestive pathways were more abundant in microorganisms from the cavefish group and surface fish group 2. Combined analysis of the intestinal microbial composition and functional predictions further revealed the structures and functions of intestinal microbial communities in Sinocyclocheilus cave and surface species. Moreover, based on their habits and intestinal microbial composition and intestinal microbial functional predictions, we inferred that the three fish groups were all omnivorous; however, surface fish group 1 preferred feeding on plants, while surface fish group 2 and cavefish preferred meat. This study improves our understanding of mechanisms of adaptation in cave habitats and may contribute to the protection of these habitats from water pollution.}, }
@article {pmid31279253, year = {2019}, author = {Gros, M and Marti, E and Balcázar, JL and Boy-Roura, M and Busquets, A and Colón, J and Sànchez-Melsió, A and Lekunberri, I and Borrego, CM and Ponsá, S and Petrovic, M}, title = {Fate of pharmaceuticals and antibiotic resistance genes in a full-scale on-farm livestock waste treatment plant.}, journal = {Journal of hazardous materials}, volume = {378}, number = {}, pages = {120716}, doi = {10.1016/j.jhazmat.2019.05.109}, pmid = {31279253}, issn = {1873-3336}, mesh = {*Agriculture ; Anaerobiosis ; Animals ; DNA/isolation &amp; purification ; Drug Residues/*analysis ; Drug Resistance, Microbial/*genetics ; *Livestock ; Osmosis ; Sewage ; Veterinary Drugs/*analysis ; *Waste Disposal, Fluid ; Wastewater ; }, abstract = {This study investigated, for the first time, the distribution and fate of 28 multiple-class veterinary pharmaceuticals and antibiotics (PhACs), and their corresponding antibiotic resistance genes (ARGs), in a full-scale on-farm livestock waste treatment plant. The plant relies on several technologies, including: anaerobic digestion (AD), solid-liquid separation, and two stages reverse osmosis (RO) of the liquid digestate. Tetracycline, fluoroquinolone, lincosamide and pleuromutilin antibiotics, together with anti-helmintic (flubendazole) and anti-inflammatory (flunixin) drugs were the most frequently detected compounds in livestock waste and in slaughterhouse sludge. This last fraction is used as co-substrate in the AD process and showed to be an important input source of PhACs and ARGs. In terms of treatment performance, AD exhibited moderate to low PhACs and ARGs reduction, while a large fraction (<50%) of the PhACs present in the digestate were distributed onto the solid fraction, after solid-liquid separation. Both solid and liquid digestates had relatively high copy numbers of ARGs. Finally, RO showed high rejection percentages for all PhACs (<90%), with concentrations in the low ng L[-1] range in permeates, for most target PhACs. Nevertheless, moderate copy numbers of ARGs were detected in permeates.}, }
@article {pmid31275291, year = {2019}, author = {Lukumbuzya, M and Schmid, M and Pjevac, P and Daims, H}, title = {A Multicolor Fluorescence in situ Hybridization Approach Using an Extended Set of Fluorophores to Visualize Microorganisms.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1383}, pmid = {31275291}, issn = {1664-302X}, support = {P 27319/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes is a key method for the detection of (uncultured) microorganisms in environmental and medical samples. A major limitation of standard FISH protocols, however, is the small number of phylogenetically distinct target organisms that can be detected simultaneously. In this study, we introduce a multicolor FISH approach that uses eight fluorophores with distinct spectral properties, which can unambiguously be distinguished by confocal laser scanning microscopy combined with white light laser technology. Hybridization of rRNA-targeted DNA oligonucleotide probes, which were mono-labeled with these fluorophores, to Escherichia coli cultures confirmed that the fluorophores did not affect probe melting behavior. Application of the new multicolor FISH method enabled the differentiation of seven (potentially up to eight) phylogenetically distinct microbial populations in an artificial community of mixed pure cultures (five bacteria, one archaeon, and one yeast strain) and in activated sludge from a full-scale wastewater treatment plant. In contrast to previously published multicolor FISH approaches, this method does not rely on combinatorial labeling of the same microorganisms with different fluorophores, which is prone to biases. Furthermore, images acquired by this method do not require elaborate post-processing prior to analysis. We also demonstrate that the newly developed multicolor FISH method is compatible with an improved cell fixation protocol for FISH targeting Gram-negative bacterial populations. This fixation approach uses agarose embedding during formaldehyde fixation to better preserve the three-dimensional structure of spatially complex samples such as biofilms and activated sludge flocs. The new multicolor FISH approach should be highly suitable for studying structural and functional aspects of microbial communities in virtually all types of samples that can be analyzed by conventional FISH methods.}, }
@article {pmid31273405, year = {2020}, author = {Kerfahi, D and Ogwu, MC and Ariunzaya, D and Balt, A and Davaasuren, D and Enkhmandal, O and Purevsuren, T and Batbaatar, A and Tibbett, M and Undrakhbold, S and Boldgiv, B and Adams, JM}, title = {Metal-Tolerant Fungal Communities Are Delineated by High Zinc, Lead, and Copper Concentrations in Metalliferous Gobi Desert Soils.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {420-431}, pmid = {31273405}, issn = {1432-184X}, support = {NRF 2013-031400//National Research Foundation/ ; }, mesh = {Copper/analysis ; Desert Climate ; Fungi/classification/isolation &amp; purification ; Lead/analysis ; Mongolia ; Mycobiome/*drug effects ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants/*analysis ; Zinc/analysis ; }, abstract = {The soil fungal ecology of the southern Gobi region of Mongolia has been little studied. We utilized the ITS1 region from soil DNA to study possible influences soil metal concentrations on soil fungal community variation. In the sample network, a distinctive fungal community was closely associated with high zinc (Zn), lead (Pb), and copper (Cu) concentrations. The pattern of occurrence suggests that high metal concentrations are natural and not a product of mining activities. The metal-associated fungal community differs little from the "normal" community in its major OTUs, and in terms of major fungal guilds and taxa, and its distinctiveness depends on a combination of many less common OTUs. The fungal community in the sites with high metal concentrations is no less diverse than that in areas with normal background levels. Overall, these findings raise interesting questions of the evolutionary origin and functional characteristics of this apparently "metal-tolerant" community, and of the associated soil biota in general. It is possible that rehabilitation of metal-contaminated mined soils from spoil heaps could benefit from the incorporation of fungi derived from these areas.}, }
@article {pmid31272871, year = {2020}, author = {Pant, A and Das, B and Bhadra, RK}, title = {CTX phage of Vibrio cholerae: Genomics and applications.}, journal = {Vaccine}, volume = {38 Suppl 1}, number = {}, pages = {A7-A12}, doi = {10.1016/j.vaccine.2019.06.034}, pmid = {31272871}, issn = {1873-2518}, mesh = {Bacteriophages/*genetics/physiology ; Cholera ; Cholera Toxin/genetics ; Chromosomes, Bacterial ; Genome, Viral ; Genomics ; Humans ; Vibrio cholerae/genetics/*virology ; *Virus Integration ; }, abstract = {The bipartite genome of Vibrio cholerae is divided into two circular non-homologous chromosomes, which harbor several genetic elements like phages, plasmids, transposons, integrative conjugative elements, and pathogenic islands that encode functions responsible for disease development, antimicrobial resistance, and subsistence in hostile environments. These elements are highly heterogeneous, mobile in nature, and encode their own mobility functions or exploit host-encoded enzymes for intra- and inter-cellular movements. The key toxin of V. cholerae responsible for the life-threatening diarrheal disease cholera, the cholera toxin, is coded by part of the genome of a filamentous phage, CTXϕ. The replicative genome of CTXϕ is divided into two distinct modular structures and has adopted a unique strategy for its irreversible integration into the V. cholerae chromosomes. CTXϕ exploits two host-encoded tyrosine recombinases, XerC and XerD, for its integration in the highly conserved dimer resolution site (dif) of V. cholerae chromosomes. CTXϕ can replicate only in the limited number of Vibrio species. In contrast, the phage integration into the bacterial chromosome does not rely on its replication and could integrate to the dif site of large numbers of gram-negative bacteria. Recent pangenomic analysis revealed that like CTXϕ, the bacterial dif site is the integration spot for several other mobile genetic elements such as plasmids and genomic islands. In this review we discuss about current molecular insights into CTXϕ genomics and its replication and integration mechanisms into hosts. Particular emphasis has been given on the exploitation of CTXϕ genomics knowledge in developing genetic tools and designing environmentally safe recombinant live oral cholera vaccine strains.}, }
@article {pmid31272870, year = {2020}, author = {Das, B and Verma, J and Kumar, P and Ghosh, A and Ramamurthy, T}, title = {Antibiotic resistance in Vibrio cholerae: Understanding the ecology of resistance genes and mechanisms.}, journal = {Vaccine}, volume = {38 Suppl 1}, number = {}, pages = {A83-A92}, doi = {10.1016/j.vaccine.2019.06.031}, pmid = {31272870}, issn = {1873-2518}, mesh = {Anti-Bacterial Agents/pharmacology ; *Cholera/epidemiology/microbiology ; *DNA Transposable Elements ; Drug Resistance, Multiple, Bacterial/*genetics ; Humans ; Integrons ; Plasmids ; *Vibrio cholerae/drug effects/genetics ; }, abstract = {The unique genetic makeup and remarkable competency of Vibrio cholerae are the key factors that help the cholera pathogen adapt rapidly to adverse environmental conditions and resist the detrimental effect of antimicrobial agents. In the last few decades, V. cholerae that causes acute watery diarrhoeal disease cholera has emerged as a notorious multidrug resistant (MDR) enteric pathogen. Although chromosomal mutations can contribute to antimicrobial resistance (AMR), the frequent acquisition of extrachromosomal mobile genetic elements (MGEs) from closely/distantly related bacterial species are major players in V. cholerae drug resistance. Whole genome sequence analysis of clinical and environmental V. cholerae strains revealed that the genome of most of the recent isolates harbour integrating conjugative elements (ICEs), plasmids, superintegron, transposable elements and insertion sequences, which are the key carriers of genetic traits encoding antimicrobial resistance function. Different antimicrobial resistance genes identified in V. cholerae can contribute in antibiotic resistance by facilitating one of the following three mechanisms; (i) reduced permeability or active efflux of the antibiotics, (ii) alteration of the antibiotic targets by introducing post-transcriptional/translational modifications and (iii) hydrolysis or chemical modification of antibiotics. Here, we present an overview of the present insights on the emergence and mechanisms of AMR in V. cholerae.}, }
@article {pmid31271506, year = {2019}, author = {Moeller, FU and Webster, NS and Herbold, CW and Behnam, F and Domman, D and Albertsen, M and Mooshammer, M and Markert, S and Turaev, D and Becher, D and Rattei, T and Schweder, T and Richter, A and Watzka, M and Nielsen, PH and Wagner, M}, title = {Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta.}, journal = {Environmental microbiology}, volume = {21}, number = {10}, pages = {3831-3854}, pmid = {31271506}, issn = {1462-2920}, support = {FP7-PEOPLE-2010-ITM Symbiomics//Marie Curie Initial Training Networks/International ; Research grants 15510; 16578//VILLUM FONDEN/International ; Advanced Grant project NITRICARE 294343/ERC_/European Research Council/International ; /MCCC_/Marie Curie/United Kingdom ; }, mesh = {Ammonia/*metabolism ; Animals ; Archaea/*genetics/isolation &amp; purification/*metabolism ; Chemoautotrophic Growth/physiology ; In Situ Hybridization, Fluorescence ; Nitrification/physiology ; Nitrites/metabolism ; Oxidation-Reduction ; Phylogeny ; Porifera/*microbiology ; Soil Microbiology ; }, abstract = {Marine sponges represent one of the few eukaryotic groups that frequently harbour symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia-oxidizers in many environments. However, in most studies, direct demonstration of ammonia-oxidation by these archaea within sponges is lacking, and little is known about sponge-specific adaptations of ammonia-oxidizing archaea (AOA). Here, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and isotope-based functional assays. 'Candidatus Nitrosospongia ianthellae' is only distantly related to cultured AOA. It is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbour nitrite-oxidizing microbes. Furthermore, this AOA is equipped with an expanded set of extracellular subtilisin-like proteases, a metalloprotease unique among archaea, as well as a putative branched-chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge-associated, but not in free-living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic-like proteins, and a DNA-phosporothioation system, represent important adaptations of AOA to life within these ancient filter-feeding animals.}, }
@article {pmid31271413, year = {2019}, author = {Dann, LM and Clanahan, M and Paterson, JS and Mitchell, JG}, title = {Distinct niche partitioning of marine and freshwater microbes during colonisation.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {8}, pages = {}, doi = {10.1093/femsec/fiz098}, pmid = {31271413}, issn = {1574-6941}, mesh = {Animals ; Bacteria/classification/*growth &amp; development/*isolation &amp; purification ; Fresh Water/*microbiology/virology ; Microbiota ; Seawater/*microbiology/virology ; Viruses ; Water Microbiology ; }, abstract = {Bacteria are ubiquitous on the Earth, and many use chemotaxis to colonise favourable microenvironments. The colonisation process is continuous, where animals, plants, protists, viruses and chemical and physical factors frequently remove bacteria from wide volume ranges. Colonisation processes are poorly understood in natural communities. Here, we investigated niche partitioning during colonisation in aquatic microbial communities using bands of bacterial chemotaxis in petri dishes from mixed-species communities. The community partitioned into loiterers, primary and secondary colonisers, each having distinct abundances and taxonomy. Within marine samples, Shewanella dominated the primary colonisers, whilst Enterobacteriaceae dominated this group within the freshwater samples. Whether the success of these specific groups translates to what occurs within natural communities is uncertain, but here we show these taxa have the capacity to colonise new, unexplored environments. A strong negative association existed between the primary colonisers and viral abundance, suggesting that successful colonisers simultaneously move toward areas of heightened resources, which correlated with lower virus-like particles. Here, we show that microbial communities constantly sort themselves into distinct taxonomic groups as they move into new environments. This sorting during colonisation may be fundamental to microbial ecology, industry, technology, and disease development by setting the initial conditions that determine the winners as a community develops.}, }
@article {pmid31267158, year = {2020}, author = {Stirling, E and Macdonald, LM and Smernik, RJ and Cavagnaro, TR}, title = {Soil Microbial Community Responses After Amendment with Thermally Altered Pinus radiata Needles.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {409-419}, pmid = {31267158}, issn = {1432-184X}, mesh = {*Fires ; *Microbiota ; Pinus/chemistry ; Plant Leaves/*chemistry ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Post-fire litter layers are composed of leaves and woody debris that predominantly fall during or soon after the fire event. These layers are distinctly different to pre-fire litters due to their common origin and deposition time. However, heterogeneity can arise from the variable thermal conditions in the canopy during fire. Therefore, in this study, we used thermally altered pine needles (heated to 40 °C, 150 °C, 260 °C and 320 °C for 1 h) in a laboratory incubation study for 43 days. These samples were measured for respiration throughout and extracted for DNA at the experiment's end; soil ribosomal RNA was analysed using Illumina sequencing (16S and internal transcribed spacer amplicons). The addition of pine needles heated to 40 °C or 150 °C caused a substantial shift in community structure, decreased alpha diversity and significantly increased soil respiration relative to the control treatment. In contrast, pine needles heated to 260 °C or 320 °C had little effect on microbial community structure or soil respiration. These results indicate that highly thermally altered needles are not microbially decomposed during the first 43 days of exposure and therefore that biomass temperature may have significant effects on post-fire litter decomposition and carbon flux. This research outlines an important knowledge gap in forest fire responses that may affect post-fire carbon emission estimates.}, }
@article {pmid31267157, year = {2020}, author = {Ou, L and Qin, X and Shi, X and Feng, Q and Zhang, S and Lu, S and Qi, Y}, title = {Alkaline phosphatase activities and regulation in three harmful Prorocentrum species from the coastal waters of the East China Sea.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {459-471}, pmid = {31267157}, issn = {1432-184X}, support = {41776121, 41176087, 41466001//National Natural Science Foundation of China/ ; }, mesh = {Alkaline Phosphatase/*metabolism ; China ; Dinoflagellida/*enzymology ; *Harmful Algal Bloom ; Phosphorus/*deficiency ; Phytoplankton/*enzymology ; Species Specificity ; }, abstract = {Harmful blooms of Prorocentrum donghaiense occur annually in the phosphorus-scarce coastal waters of the East China Sea (ECS). The enzymatic activities of alkaline phosphatase (AP) and its regulation by external phosphorus were studied during a P. donghaiense bloom in this area. The AP characteristics of P. donghaiense was further compared with Prorocentrum minimum and Prorocentrum micans in monocultures with both bulk and single-cell enzyme-labeled fluorescence AP assays. Concentrations of dissolved inorganic phosphorus (DIP) varied between 0.04 and 0.73 μmol l[-1], with more than half recording stations registering concentrations below 0.10 μmol l[-1]. Concentrations of dissolved organic phosphorus (DOP) were comparable or even higher than those of DIP. P. donghaiense suffered phosphorus stress and expressed abundant AP, especially when DIP was lower than 0.10 μmol l[-1]. The AP activities showed a negative correlation with DIP but a positive correlation with DOP. The AP activities were also regulated by internal phosphorus pool. The sharp increase in AP activities was observed until cellular phosphorus was exhausted. Most AP of P. donghaiense was located on the cell surface and some were released into the water with time. Compared with P. minimum and P. micans, P. donghaiense showed a higher AP affinity for organic phosphorus substrates, a more efficient and energy-saving AP expression quantity as a response to phosphorus deficiency. The unique AP characteristic of P. donghaiense suggests that it benefits from the efficient utilization of DOP, and outcompete other species in the phosphorus-scarce ECS.}, }
@article {pmid31266970, year = {2019}, author = {Grunert, O and Robles-Aguilar, AA and Hernandez-Sanabria, E and Schrey, SD and Reheul, D and Van Labeke, MC and Vlaeminck, SE and Vandekerckhove, TGL and Mysara, M and Monsieurs, P and Temperton, VM and Boon, N and Jablonowski, ND}, title = {Tomato plants rather than fertilizers drive microbial community structure in horticultural growing media.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {9561}, pmid = {31266970}, issn = {2045-2322}, mesh = {Ammonia/chemistry/metabolism ; Biomass ; Culture Media ; *Fertilizers ; Hydrogen-Ion Concentration ; Solanum lycopersicum/*growth &amp; development/*microbiology ; *Microbiota ; Oxidation-Reduction ; Plant Development ; *Soil Microbiology ; }, abstract = {Synthetic fertilizer production is associated with a high environmental footprint, as compounds typically dissolve rapidly leaching emissions to the atmosphere or surface waters. We tested two recovered nutrients with slower release patterns, as promising alternatives for synthetic fertilizers: struvite and a commercially available organic fertilizer. Using these fertilizers as nitrogen source, we conducted a rhizotron experiment to test their effect on plant performance and nutrient recovery in juvenile tomato plants. Plant performance was significantly improved when organic fertilizer was provided, promoting higher shoot biomass. Since the microbial community influences plant nitrogen availability, we characterized the root-associated microbial community structure and functionality. Analyses revealed distinct root microbial community structure when different fertilizers were supplied. However, plant presence significantly increased the similarity of the microbial community over time, regardless of fertilization. Additionally, the presence of the plant significantly reduced the potential ammonia oxidation rates, implying a possible role of the rhizosheath microbiome or nitrification inhibition by the plant. Our results indicate that nitrifying community members are impacted by the type of fertilizer used, while tomato plants influenced the potential ammonia-oxidizing activity of nitrogen-related rhizospheric microbial communities. These novel insights on interactions between recovered fertilizers, plant and associated microbes can contribute to develop sustainable crop production systems.}, }
@article {pmid31266879, year = {2019}, author = {Sze, MA and Topçuoğlu, BD and Lesniak, NA and Ruffin, MT and Schloss, PD}, title = {Fecal Short-Chain Fatty Acids Are Not Predictive of Colonic Tumor Status and Cannot Be Predicted Based on Bacterial Community Structure.}, journal = {mBio}, volume = {10}, number = {4}, pages = {}, pmid = {31266879}, issn = {2150-7511}, support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; R01 CA215574/CA/NCI NIH HHS/United States ; UL1 TR002240/TR/NCATS NIH HHS/United States ; }, mesh = {Adenoma/*diagnosis/pathology ; Bacteria/classification/genetics ; Carcinoma/*diagnosis/pathology ; Clinical Decision Rules ; Colonic Neoplasms/*diagnosis/pathology ; Fatty Acids, Volatile/*analysis ; Feces/*chemistry/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; United States ; }, abstract = {Colonic bacterial populations are thought to have a role in the development of colorectal cancer with some protecting against inflammation and others exacerbating inflammation. Short-chain fatty acids (SCFAs) have been shown to have anti-inflammatory properties and are produced in large quantities by colonic bacteria that produce SCFAs by fermenting fiber. We assessed whether there was an association between fecal SCFA concentrations and the presence of colonic adenomas or carcinomas in a cohort of individuals using 16S rRNA gene and metagenomic shotgun sequence data. We measured the fecal concentrations of acetate, propionate, and butyrate within the cohort and found that there were no significant associations between SCFA concentration and tumor status. When we incorporated these concentrations into random forest classification models trained to differentiate between people with healthy colons and those with adenomas or carcinomas, we found that they did not significantly improve the ability of 16S rRNA gene or metagenomic gene sequence-based models to classify individuals. Finally, we generated random forest regression models trained to predict the concentration of each SCFA based on 16S rRNA gene or metagenomic gene sequence data from the same samples. These models performed poorly and were able to explain at most 14% of the observed variation in the SCFA concentrations. These results support the broader epidemiological data that questions the value of fiber consumption for reducing the risks of colorectal cancer. Although other bacterial metabolites may serve as biomarkers to detect adenomas or carcinomas, fecal SCFA concentrations have limited predictive power.IMPORTANCE Considering that colorectal cancer is the third leading cancer-related cause of death within the United States, it is important to detect colorectal tumors early and to prevent the formation of tumors. Short-chain fatty acids (SCFAs) are often used as a surrogate for measuring gut health and for being anticarcinogenic because of their anti-inflammatory properties. We evaluated the fecal SCFA concentrations of a cohort of individuals with different colonic tumor burdens who were previously analyzed to identify microbiome-based biomarkers of tumors. We were unable to find an association between SCFA concentration and tumor burden or use SCFAs to improve our microbiome-based models of classifying people based on their tumor status. Furthermore, we were unable to find an association between the fecal community structure and SCFA concentrations. Our results indicate that the association between fecal SCFAs, the gut microbiome, and tumor burden is weak.}, }
@article {pmid31265069, year = {2019}, author = {de Boer, W and Li, X and Meisner, A and Garbeva, P}, title = {Pathogen suppression by microbial volatile organic compounds in soils.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {8}, pages = {}, doi = {10.1093/femsec/fiz105}, pmid = {31265069}, issn = {1574-6941}, mesh = {Biological Control Agents/analysis/*pharmacology ; Fungi/*drug effects/pathogenicity ; Microbial Interactions ; Microbiota ; Plant Diseases/microbiology ; Soil/chemistry ; *Soil Microbiology ; Volatile Organic Compounds/analysis/*pharmacology ; }, abstract = {There is increasing evidence that microbial volatile organic compounds (mVOCs) play an important role in interactions between microbes in soils. In this minireview, we zoom in on the possible role of mVOCs in the suppression of plant-pathogenic soil fungi. In particular, we have screened the literature to see what the actual evidence is that mVOCs in soil atmospheres can contribute to pathogen suppression. Furthermore, we discuss biotic and abiotic factors that influence the production of suppressive mVOCs in soils. Since microbes producing mVOCs in soils are part of microbial communities, community ecological aspects such as diversity and assembly play an important role in the composition of produced mVOC blends. These aspects have not received much attention so far. In addition, the fluctuating abiotic conditions in soils, such as changing moisture contents, influence mVOC production and activity. The biotic and abiotic complexity of the soil environment hampers the extrapolation of the production and suppressing activity of mVOCs by microbial isolates on artificial growth media. Yet, several pathogen suppressive mVOCs produced by pure cultures do also occur in soil atmospheres. Therefore, an integration of lab and field studies on the production of mVOCs is needed to understand and predict the composition and dynamics of mVOCs in soil atmospheres. This knowledge, together with the knowledge of the chemistry and physical behaviour of mVOCs in soils, forms the basis for the development of sustainable management strategies to enhance the natural control of soil-borne pathogens with mVOCs. Possibilities for the mVOC-based control of soil-borne pathogens are discussed.}, }
@article {pmid31263981, year = {2020}, author = {Yi, Y and Wang, H and Chen, Y and Gou, M and Xia, Z and Hu, B and Nie, Y and Tang, Y}, title = {Identification of Novel Butyrate- and Acetate-Oxidizing Bacteria in Butyrate-Fed Mesophilic Anaerobic Chemostats by DNA-Based Stable Isotope Probing.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {285-298}, pmid = {31263981}, issn = {1432-184X}, support = {2016YFE0127700//Ministry of Science and Technology of the People's Republic of China/ ; 51678378//National Natural Science Foundation of China/ ; 31200068//National Natural Science Foundation of China/ ; }, mesh = {Acetates/*metabolism ; Anaerobiosis ; Bacteria/*metabolism ; Bioreactors/*microbiology ; Butyrates/*metabolism ; High-Throughput Nucleotide Sequencing ; Isotope Labeling ; Oxidation-Reduction ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Butyrate is one of the most important intermediates during anaerobic digestion of protein wastewater, and its oxidization is considered as a rate-limiting step during methane production. However, information on syntrophic butyrate-oxidizing bacteria (SBOB) is limited due to the difficulty in isolation of pure cultures. In this study, two anaerobic chemostats fed with butyrate as the sole carbon source were operated at different dilution rates (0.01/day and 0.05/day). Butyrate- and acetate-oxidizing bacteria in both chemostats were investigated, combining DNA-Stable Isotope Probing (DNA-SIP) and 16S rRNA gene high-throughput sequencing. The results showed that, in addition to known SBOB, Syntrophomonas, other species of unclassified Syntrophomonadaceae were putative butyrate-oxidizing bacteria. Species of Mesotoga, Aminivibrio, Acetivibrio, Desulfovibrio, Petrimonas, Sedimentibacter, unclassified Anaerolineae, unclassified Synergistaceae, unclassified Spirochaetaceae, and unclassified bacteria may contribute to acetate oxidation from butyrate metabolism. Among them, the ability of butyrate oxidation was unclear for species of Sedimentibacter, unclassified Synergistaceae, unclassified Spirochaetaceae, and unclassified bacteria. These results suggested that more unknown species participated in the degradation of butyrate. However, the corresponding function and pathway for butyrate or acetate oxidization of these labeled species need to be further investigated.}, }
@article {pmid31263456, year = {2019}, author = {Song, HS and Lee, JY and Haruta, S and Nelson, WC and Lee, DY and Lindemann, SR and Fredrickson, JK and Bernstein, HC}, title = {Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1264}, pmid = {31263456}, issn = {1664-302X}, abstract = {An intriguing aspect in microbial communities is that pairwise interactions can be influenced by neighboring species. This creates context dependencies for microbial interactions that are based on the functional composition of the community. Context dependent interactions are ecologically important and clearly present in nature, yet firmly established theoretical methods are lacking from many modern computational investigations. Here, we propose a novel network inference method that enables predictions for interspecies interactions affected by shifts in community composition and species populations. Our approach first identifies interspecies interactions in binary communities, which is subsequently used as a basis to infer modulation in more complex multi-species communities based on the assumption that microbes minimize adjustments of pairwise interactions in response to neighbor species. We termed this rule-based inference minimal interspecies interaction adjustment (MIIA). Our critical assessment of MIIA has produced reliable predictions of shifting interspecies interactions that are dependent on the functional role of neighbor organisms. We also show how MIIA has been applied to a microbial community composed of competing soil bacteria to elucidate a new finding that - in many cases - adding fewer competitors could impose more significant impact on binary interactions. The ability to predict membership-dependent community behavior is expected to help deepen our understanding of how microbiomes are organized in nature and how they may be designed and/or controlled in the future.}, }
@article {pmid31257772, year = {2019}, author = {Hu, K and Tao, JP and He, DN and Huang, K and Wang, W}, title = {[Effects of root growth on dynamics of microbes and enzyme activities during litter decomposition.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {30}, number = {6}, pages = {1993-2001}, doi = {10.13287/j.1001-9332.201906.022}, pmid = {31257772}, issn = {1001-9332}, mesh = {Bacteria ; Biomass ; Ecosystem ; *Forests ; *Microbiota ; Plant Leaves ; Plant Roots/*growth &amp; development ; *Soil Microbiology ; }, abstract = {To understand the influence of roots of understory plant entering litter layer on litter decomposition in forest ecosystems, we examined the effects of different treatments of Lolium multiflorum root biomass on microorganisms and enzyme activities during leaf litter decomposition of Symplocos setchuensis, a dominant species in a mid-subtropical evergreen broad-leaved forest, through a litter bag simulation experiment. Results showed that diversity index of bacterial and fungal communities of leaf litter surface under three treatments, i.e. no root (N), less roots (L), more roots (M), in a 240-day decomposition process showed the following pattern: M > L > N. The effects of these different root biomass treatments on the composition and quantity of fungal community were more significant than those on bacterial community. The biomass of living roots growing in the litter bag gradually decreased at the end of the growing season of L. multiflorum. The impacts of root growth on the composition of the fungal community gradually decreased during decomposition. At the same decomposition stage, the activities of acid phosphatase, β-glucosidase, polyphenol oxidase, and peroxidase on the litter surface were higher in the treatments with roots than that without roots. These results indicated that root growth could change the composition and quantity of microbial communities and increase the extracellular enzyme activities of microbes, and thus stimulating litter decomposition.}, }
@article {pmid31253856, year = {2019}, author = {Carr, A and Diener, C and Baliga, NS and Gibbons, SM}, title = {Use and abuse of correlation analyses in microbial ecology.}, journal = {The ISME journal}, volume = {13}, number = {11}, pages = {2647-2655}, pmid = {31253856}, issn = {1751-7370}, mesh = {Computational Biology/methods ; Correlation of Data ; *Ecosystem ; *Environmental Microbiology ; Humans ; *Microbial Interactions ; }, abstract = {Correlation analyses are often included in bioinformatic pipelines as methods for inferring taxon-taxon interactions. In this perspective, we highlight the pitfalls of inferring interactions from covariance and suggest methods, study design considerations, and additional data types for improving high-throughput interaction inferences. We conclude that correlation, even when augmented by other data types, almost never provides reliable information on direct biotic interactions in real-world ecosystems. These bioinformatically inferred associations are useful for reducing the number of potential hypotheses that we might test, but will never preclude the necessity for experimental validation.}, }
@article {pmid31252032, year = {2020}, author = {Callewaert, C and Nakatsuji, T and Knight, R and Kosciolek, T and Vrbanac, A and Kotol, P and Ardeleanu, M and Hultsch, T and Guttman-Yassky, E and Bissonnette, R and Silverberg, JI and Krueger, J and Menter, A and Graham, NMH and Pirozzi, G and Hamilton, JD and Gallo, RL}, title = {IL-4Rα Blockade by Dupilumab Decreases Staphylococcus aureus Colonization and Increases Microbial Diversity in Atopic Dermatitis.}, journal = {The Journal of investigative dermatology}, volume = {140}, number = {1}, pages = {191-202.e7}, pmid = {31252032}, issn = {1523-1747}, support = {R01 AR076082/AR/NIAMS NIH HHS/United States ; }, mesh = {Antibodies, Monoclonal, Humanized/*therapeutic use ; Cytokines/metabolism ; Dermatitis, Atopic/*drug therapy ; Disease Progression ; Double-Blind Method ; Female ; Follow-Up Studies ; Humans ; Immunotherapy/*methods ; Male ; Placebos ; RNA, Ribosomal, 16S/genetics ; Receptors, Interleukin-4/antagonists &amp; inhibitors ; Skin/drug effects/*microbiology ; Staphylococcal Infections/*drug therapy ; Staphylococcus aureus/*physiology ; Th2 Cells/*immunology ; }, abstract = {Dupilumab is a fully human antibody to interleukin-4 receptor α that improves the signs and symptoms of moderate to severe atopic dermatitis (AD). To determine the effects of dupilumab on Staphylococcus aureus colonization and microbial diversity on the skin, bacterial DNA was analyzed from swabs collected from lesional and nonlesional skin in a double-blind, placebo-controlled study of 54 patients with moderate to severe AD randomized (1:1) and treated with either dupilumab (200 mg weekly) or placebo for 16 weeks. Microbial diversity and relative abundance of Staphylococcus were assessed by DNA sequencing of 16S ribosomal RNA, and absolute S. aureus abundance was measured by quantitative PCR. Before treatment, lesional skin had lower microbial diversity and higher overall abundance of S. aureus than nonlesional skin. During dupilumab treatment, microbial diversity increased and the abundance of S. aureus decreased. Pronounced changes were seen in nonlesional and lesional skin. Decreased S. aureus abundance during dupilumab treatment correlated with clinical improvement of AD and biomarkers of type 2 immunity. We conclude that clinical improvement of AD that is mediated by interleukin-4 receptor α inhibition and the subsequent suppression of type 2 inflammation is correlated with increased microbial diversity and reduced abundance of S. aureus.}, }
@article {pmid31250077, year = {2020}, author = {Goss-Souza, D and Mendes, LW and Rodrigues, JLM and Tsai, SM}, title = {Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {110-122}, pmid = {31250077}, issn = {1432-184X}, support = {2008/58114-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2014/50320-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 140317/2014-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (BR)/ ; 311008/2016-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Agriculture ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Forests ; *Microbiota ; Phylogeny ; Rhizosphere ; *Soil Microbiology ; Glycine max/growth &amp; development ; Trees/growth &amp; development ; }, abstract = {Forest-to-agriculture conversion has been identified as a major threat to soil biodiversity and soil processes resilience, although the consequences of long-term land use change to microbial community assembly and ecological processes have been often neglected. Here, we combined metagenomic approach with a large environmental dataset, to (i) identify the microbial assembly patterns and, (ii) to evaluate the ecological processes governing microbial assembly, in bulk soil and soybean rhizosphere, along a long-term forest-to-agriculture conversion chronosequence, in Eastern Amazon. We hypothesized that (i) microbial communities in bulk soil and rhizosphere have different assembly patterns and (ii) the weight of the four ecological processes governing assembly differs between bulk soil and rhizosphere and along the chronosequence in the same fraction. Community assembly in bulk soil fitted most the zero-sum multinomial (ZSM) neutral-based model, regardless of time. Low to intermediate dispersal was observed. Decreasing influence of abiotic factors was counterbalanced by increasing influence of biotic factors, as the chronosequence advanced. Undominated ecological processes of dispersal limitation and variable selection governing community assembly were observed in this soil fraction. For soybean rhizosphere, community assembly fitted most the lognormal niche-based model in all chronosequence areas. High dispersal and an increasing influence of abiotic factors coupled with a decreasing influence of biotic factors were found along the chronosequence. Thus, we found a dominant role of dispersal process governing microbial assembly with a secondary effect of homogeneous selection process, mainly driven by decreasing aluminum and increased cations saturation in soil solution, due to long-term no-till cropping. Together, our results indicate that long-term no-till lead community abundances in bulk soil to be in a transient and conditional state, while for soybean rhizosphere, community abundances reach a periodic and permanent distribution state. Dominant dispersal process in rhizosphere, coupled with homogeneous selection, brings evidences that soybean root system selects microbial taxa via trade-offs in order to keep functional resilience of soil processes.}, }
@article {pmid31250076, year = {2020}, author = {Jeong, SY and Lee, CH and Yi, T and Kim, TG}, title = {Effects of Quorum Quenching on Biofilm Metacommunity in a Membrane Bioreactor.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {84-97}, pmid = {31250076}, issn = {1432-184X}, support = {2018R1D1A1B07048872//Ministry of Education/ ; }, mesh = {Bacteria/classification/genetics/growth &amp; development ; Bacterial Physiological Phenomena ; *Biofilms ; Bioreactors/*microbiology ; Fungi/classification/genetics/growth &amp; development/*physiology ; Membranes, Artificial ; *Quorum Sensing ; }, abstract = {Quorum quenching (QQ) has received attention for the control of biofilms, e.g., biofilms that cause biofouling in membrane bioreactors (MBRs). Despite the efficacy of QQ on biofouling, it is elusive how QQ influences biofilm formation on membranes. A pilot-scale QQ-MBR and non-QQ-MBR were identically operated for 4 days and 8 days to destructively sample the membranes. QQ prolonged the membrane filterability by 43% with no harmful influence on MBR performance. qPCR showed no effect of QQ on microbial density during either of these time periods. Community comparisons revealed that QQ influenced the bacterial and fungal community structures, and the fungal structure corresponded with the bacterial structure. Metacommunity and spatial analyses showed that QQ induced structural variation rather than compositional variation of bacteria and fungi. Moreover, QQ considerably enhanced the bacterial dispersal across membrane during the early development. As the dispersal enhancement by QQ counteracted the ecological drift, it eliminated the distance-decay relationship, reflecting a neutral theory archetype of metacommunity. Network analyses showed that QQ substantially reduced the amount and magnitude of interactions, e.g., competition and cooperation, for bacteria and fungi, and weakened their network structures, irrespective of time. Additionally, QQ suppressed the growth of specific microbial species (e.g., Acinetobacter), abundant and widespread at the early stage. These findings suggest that QQ influenced the community dynamics at the regional and local levels, correspondingly the ecological selection and dispersal processes, during the biofilm development.}, }
@article {pmid31250075, year = {2020}, author = {Lee, J and Han, G and Kim, JW and Jeon, CO and Hyun, S}, title = {Taxon-Specific Effects of Lactobacillus on Drosophila Host Development.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {241-251}, pmid = {31250075}, issn = {1432-184X}, mesh = {Animals ; Drosophila melanogaster/genetics/*growth &amp; development/microbiology ; Female ; Lactobacillus/*classification/genetics/isolation &amp; purification ; Larva/growth &amp; development/*microbiology ; Male ; Phylogeny ; Species Specificity ; }, abstract = {Commensal microbiota heavily influence metazoan host physiology. Drosophila melanogaster has been proven a valuable animal model for studying many aspects of host-microbiota interaction. Lactobacillus are the most common human probiotics and are also one of the major symbiotic bacteria in Drosophila. Although the beneficial effects of Lactobacillus on fly development and physiology have been recognized, how broadly these effects are observed across the Lactobacillus taxa remains largely unknown. In this study, four Lactobacillus species including five strains of L. plantarum were examined for their effects on fly larval development. Monoassociation of germ-free flies with L. rhamnosus (GG) most strongly accelerated fly larval development. Monoassociation with L. plantarum moderately accelerated fly development, but monoassociation with L. reuteri or L. sakei had marginal effects, despite similar bacterial loads in the host gut. An L. plantarum strain previously isolated from our lab rarely enhanced larval development, confirming the strain-specific effects of L. plantarum. The correlation between development-promoting effects and protein digestion activity in the host gut was found only among the members of L. plantarum species. Moreover, the cytoprotective response in the host gut known to be induced by L. plantarum was not correlated with development-promoting effects among any of the bacteria tested. Our results suggest that a broad range of Lactobacillus taxa are able to reside in the fly gut, but their ability to enhance host larval development is highly varied. This study may aid our understanding of the basic principles underlying the beneficial effects of probiotic commensal bacteria on metazoan development.}, }
@article {pmid31249384, year = {2019}, author = {Frau, A and Kenny, JG and Lenzi, L and Campbell, BJ and Ijaz, UZ and Duckworth, CA and Burkitt, MD and Hall, N and Anson, J and Darby, AC and Probert, CSJ}, title = {DNA extraction and amplicon production strategies deeply inf luence the outcome of gut mycobiome studies.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {9328}, pmid = {31249384}, issn = {2045-2322}, mesh = {DNA Primers/genetics ; DNA, Fungal/genetics/*isolation &amp; purification ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Microbial ecology studies are often performed through extraction of metagenomic DNA followed by amplification and sequencing of a marker. It is known that each step may bias the results. These biases have been explored for the study of bacterial communities, but rarely for fungi. Our aim was therefore to evaluate methods for the study of the gut mycobiome. We first evaluated DNA extraction methods in fungal cultures relevant to the gut. Afterwards, to assess how these methods would behave with an actual sample, stool from a donor was spiked with cells from the same cultures. We found that different extraction kits favour some species and bias against others. In terms of amplicon sequencing, we evaluated five primer sets, two for ITS2 and one for ITS1, 18S and 28S rRNA. Results showed that 18S rRNA outperformed the other markers: it was able to amplify all the species in the mock community and to discriminate among them. ITS primers showed both amplification and sequencing biases, the latter related to the variable length of the product. We identified several biases in the characterisation of the gut mycobiome and showed how crucial it is to be aware of these before drawing conclusions from the results of these studies.}, }
@article {pmid31248111, year = {2019}, author = {Richardson, E and Dacks, JB}, title = {Microbial Eukaryotes in Oil Sands Environments: Heterotrophs in the Spotlight.}, journal = {Microorganisms}, volume = {7}, number = {6}, pages = {}, pmid = {31248111}, issn = {2076-2607}, support = {RES0021028, RES0043758, RES0046091//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Hydrocarbon extraction and exploitation is a global, trillion-dollar industry. However, for decades it has also been known that fossil fuel usage is environmentally detrimental; the burning of hydrocarbons results in climate change, and environmental damage during extraction and transport can also occur. Substantial global efforts into mitigating this environmental disruption are underway. The global petroleum industry is moving more and more into exploiting unconventional oil reserves, such as oil sands and shale oil. The Albertan oil sands are one example of unconventional oil reserves; this mixture of sand and heavy bitumen lying under the boreal forest of Northern Alberta represent one of the world's largest hydrocarbon reserves, but extraction also requires the disturbance of a delicate northern ecosystem. Considerable effort is being made by various stakeholders to mitigate environmental impact and reclaim anthropogenically disturbed environments associated with oil sand extraction. In this review, we discuss the eukaryotic microbial communities associated with the boreal ecosystem and how this is affected by hydrocarbon extraction, with a particular emphasis on the reclamation of tailings ponds, where oil sands extraction waste is stored. Microbial eukaryotes, or protists, are an essential part of every global ecosystem, but our understanding of how they affect reclamation is limited due to our fledgling understanding of these organisms in anthropogenically hydrocarbon-associated environments and the difficulties of studying them. We advocate for an environmental DNA sequencing-based approach to determine the microbial communities of oil sands associated environments, and the importance of studying the heterotrophic components of these environments to gain a full understanding of how these environments operate and thus how they can be integrated with the natural watersheds of the region.}, }
@article {pmid31244886, year = {2019}, author = {Azarian, T and Ridgway, JP and Yin, Z and David, MZ}, title = {Long-Term Intrahost Evolution of Methicillin Resistant Staphylococcus aureus Among Cystic Fibrosis Patients With Respiratory Carriage.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {546}, pmid = {31244886}, issn = {1664-8021}, support = {K23 AI095361/AI/NIAID NIH HHS/United States ; }, abstract = {Staphylococcus aureus is the most commonly identified airway colonizer of cystic fibrosis (CF) patients, and infections with methicillin-resistant S. aureus (MRSA) are associated with poor outcomes. Yet, little is known about the intrahost evolution of S. aureus among CF patients. We investigated convergent evolution and adaptation of MRSA among four CF patients with long-term respiratory carriage. For each patient, we performed whole-genome sequencing on an average of 21 isolates (range: 19-23) carried for a mean of 1,403 days (range: 903-1,679), including 25 pairs of isolates collected on the same day. We assessed intrahost diversity, population structure, evolutionary history, evidence of switched intergenic regions (IGRs), and signatures of adaptation in the context of patient age, antibiotic treatment, and co-colonizing microbes. Phylogenetic analysis delineated distinct multilocus sequence type ST5 (n = 3) and ST72 (n = 1) clonal populations in addition to sporadic, non-clonal isolates, and uncovered a putative transmission event. Variation in antibiotic resistance was observed within clonal populations, even among isolates collected on the same day. Rates of molecular evolution ranged from 2.21 to 8.64 nucleotide polymorphisms per year, and lineage ages were consistent with acquisition of colonization in early childhood followed by subsequent persistence of multiple sub-populations. Selection analysis of 1,622 core genes present in all four clonal populations (n = 79) found 11 genes variable in three subjects - most notably, ATP-dependent protease clpX, 2-oxoglutarate dehydrogenase odhA, fmtC, and transcription-repair coupling factor mfd. Only one gene, staphylococcal protein A (spa), was found to have evidence of gene-wide diversifying selection. We identified three instances of intrahost IGR switching events, two of which flanked genes related to quorum sensing. The complex microbial ecology of the CF airway poses challenges for management. We illustrate appreciable intrahost diversity as well as persistence of a dominant lineage. We also show that intrahost adaptation is a continual process, despite purifying selective pressure, and provide targets that should be investigated further for their function in CF adaptation.}, }
@article {pmid31243077, year = {2019}, author = {McNamara, PJ}, title = {mSphere of Influence: Engineering Microbes.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, pmid = {31243077}, issn = {2379-5042}, mesh = {Bacteria/drug effects/genetics ; Disinfection ; Drinking Water/*microbiology ; Genetic Engineering ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Water Purification ; }, abstract = {Patrick J. McNamara works in the field of environmental engineering. In this mSphere of Influence article, he reflects on how the papers "Bacterial community structure in the drinking water microbiome is governed by filtration processes" (A. J. Pinto, C. Xi, and L. Raskin, Environ Sci Technol 46:8851-8859, 2012, https://doi.org/10.1021/es302042t) and "Differential resistance of drinking water bacterial populations to monochloramine disinfection" (T. Chiao, T. M. Clancy, A. Pinto, C. Xi, and L. Raskin, Environ Sci Technol 48:4038-4047, 2014, https://doi.org/10.1021/es4055725) by Lutgarde Raskin and colleagues made an impact on him by providing a foundation for the study of microbial ecology in engineering drinking water treatment plants and drinking water distribution systems.}, }
@article {pmid31239395, year = {2019}, author = {Bayer, B and Pelikan, C and Bittner, MJ and Reinthaler, T and Könneke, M and Herndl, GJ and Offre, P}, title = {Proteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic Alphaproteobacterium.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, pmid = {31239395}, issn = {2379-5077}, support = {P 28781/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Ammonia-oxidizing archaea (AOA) play an important role in the nitrogen cycle and account for a considerable fraction of the prokaryotic plankton in the ocean. Most AOA lack the hydrogen peroxide (H2O2)-detoxifying enzyme catalase, and some AOA have been shown to grow poorly under conditions of exposure to H2O2 However, differences in the degrees of H2O2 sensitivity of different AOA strains, the physiological status of AOA cells exposed to H2O2, and their molecular response to H2O2 remain poorly characterized. Further, AOA might rely on heterotrophic bacteria to detoxify H2O2, and yet the extent and variety of costs and benefits involved in these interactions remain unclear. Here, we used a proteomics approach to compare the protein profiles of three Nitrosopumilus strains grown in the presence and absence of catalase and in coculture with the heterotrophic alphaproteobacterium Oceanicaulis alexandrii We observed that most proteins detected at a higher relative abundance in H2O2-exposed Nitrosopumilus cells had no known function in oxidative stress defense. Instead, these proteins were putatively involved in the remodeling of the extracellular matrix, which we hypothesize to be a strategy limiting the influx of H2O2 into the cells. Using RNA-stable isotope probing, we confirmed that O. alexandrii cells growing in coculture with the Nitrosopumilus strains assimilated Nitrosopumilus-derived organic carbon, suggesting that AOA could recruit H2O2-detoxifying bacteria through the release of labile organic matter. Our results contribute new insights into the response of AOA to H2O2 and highlight the potential ecological importance of their interactions with heterotrophic free-living bacteria in marine environments.IMPORTANCE Ammonia-oxidizing archaea (AOA) are the most abundant chemolithoautotrophic microorganisms in the oxygenated water column of the global ocean. Although H2O2 appears to be a universal by-product of aerobic metabolism, genes encoding the hydrogen peroxide (H2O2)-detoxifying enzyme catalase are largely absent in genomes of marine AOA. Here, we provide evidence that closely related marine AOA have different degrees of sensitivity to H2O2, which may contribute to niche differentiation between these organisms. Furthermore, our results suggest that marine AOA rely on H2O2 detoxification during periods of high metabolic activity and release organic compounds, thereby potentially attracting heterotrophic prokaryotes that provide this missing function. In summary, this report provides insights into the metabolic interactions between AOA and heterotrophic bacteria in marine environments and suggests that AOA play an important role in the biogeochemical carbon cycle by making organic carbon available for heterotrophic microorganisms.}, }
@article {pmid31238848, year = {2019}, author = {Dimitriu, T and Marchant, L and Buckling, A and Raymond, B}, title = {Bacteria from natural populations transfer plasmids mostly towards their kin.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1905}, pages = {20191110}, pmid = {31238848}, issn = {1471-2954}, support = {MR/N013824/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacteria/genetics ; Bacterial Physiological Phenomena ; Conjugation, Genetic ; Escherichia coli/*genetics ; Gene Transfer, Horizontal ; *Plasmids ; }, abstract = {Plasmids play a key role in microbial ecology and evolution, yet the determinants of plasmid transfer rates are poorly understood. Particularly, interactions between donor hosts and potential recipients are understudied. Here, we investigate the importance of genetic similarity between naturally co-occurring Escherichia coli isolates in plasmid transfer. We uncover extensive variability, spanning over five orders of magnitude, in the ability of isolates to donate and receive two different plasmids, R1 and RP4. Overall, transfer is strongly biased towards clone-mates, but not correlated to genetic distance when donors and recipients are not clone-mates. Transfer is limited by the presence of a functional restriction-modification system in recipients, suggesting sharing of strain-specific defence systems contributes to bias towards kin. Such restriction of transfer to kin sets the stage for longer-term coevolutionary interactions leading to mutualism between plasmids and bacterial hosts in natural communities.}, }
@article {pmid31236844, year = {2019}, author = {Kunath, BJ and Minniti, G and Skaugen, M and Hagen, LH and Vaaje-Kolstad, G and Eijsink, VGH and Pope, PB and Arntzen, M&#xd8;}, title = {Metaproteomics: Sample Preparation and Methodological Considerations.}, journal = {Advances in experimental medicine and biology}, volume = {1073}, number = {}, pages = {187-215}, doi = {10.1007/978-3-030-12298-0_8}, pmid = {31236844}, issn = {0065-2598}, mesh = {*Metagenomics ; *Microbial Consortia ; Proteins ; *Proteomics ; Specimen Handling/*methods ; }, abstract = {Meta-omic techniques have progressed rapidly in the past decade and are frequently used in microbial ecology to study microorganisms in their natural ecosystems independent from culture restrictions. Metaproteomics, in combination with metagenomics, enables quantitative assessment of expressed proteins and pathways from individual members of the consortium. Together, metaproteomics and metagenomics can provide a detailed understanding of which organisms occupy specific metabolic niches, how they interact, and how they utilize nutrients, and these insights can be obtained directly from environmental samples. Here, we outline key aspects of sample preparation, database generation, and other methodological considerations that are required for successful quantitative metaproteomic analyses and we describe case studies on the integration with metagenomics for enhanced functional output.}, }
@article {pmid31236611, year = {2020}, author = {Fiałkowska, E and Fiałkowski, W and Pajdak-Stós, A}, title = {The Relations Between Predatory Fungus and Its Rotifer Preys as a Noteworthy Example of Intraguild Predation (IGP).}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {73-83}, pmid = {31236611}, issn = {1432-184X}, mesh = {Animals ; Ecosystem ; Feeding Behavior ; Food Chain ; Fungi/growth &amp; development/*physiology ; Mycelium/growth &amp; development/physiology ; Predatory Behavior ; Rotifera/*physiology ; Spores, Fungal/growth &amp; development/physiology ; }, abstract = {Intraguild predation (IGP) is a widespread interaction combining predation and competition. We investigated a unique IGP example among predacious fungus Zoophagus sp. and two rotifers, the predacious Cephalodella gibba and the common prey Lecane inermis. We checked the influence of the fungus on its competitor C. gibba and their joint influence on shared prey L. inermis, and the impact of the competitive predator on the growth of predacious fungus. The experiment on grown mycelium showed that Zoophagus strongly, negatively influences the growth of C. gibba (intermediate consumer) whose number did not increase throughout the experiment. The intermediate consumer was also trapped by Zoophagus and become extinct when it was its only prey, whereas in the absence of the fungus and with unlimited access to prey, its number grew quickly. As only few C. gibba were trapped by fungi when common preys were present, competition for food seems to have stronger effect on intermediate consumer population than predation. The experiment with conidia of the fungus showed that intermediate consumer significantly limits the growth of Zoophagus by reducing the number of available prey. It was observed that although the fungus can trap C. gibba, the latter does not support its growth. Trapping the intermediate consumer might serve to eliminate a competitor rather than to find a source of food. The chances of survival for L. inermis under the pressure of the two competing predators are scarce. It is the first example of IGP involving representatives of two kingdoms: Fungi and Animalia.}, }
@article {pmid31234491, year = {2019}, author = {Kraemer, SA and Ramachandran, A and Perron, GG}, title = {Antibiotic Pollution in the Environment: From Microbial Ecology to Public Policy.}, journal = {Microorganisms}, volume = {7}, number = {6}, pages = {}, pmid = {31234491}, issn = {2076-2607}, abstract = {The ability to fight bacterial infections with antibiotics has been a longstanding cornerstone of modern medicine. However, wide-spread overuse and misuse of antibiotics has led to unintended consequences, which in turn require large-scale changes of policy for mitigation. In this review, we address two broad classes of corollaries of antibiotics overuse and misuse. Firstly, we discuss the spread of antibiotic resistance from hotspots of resistance evolution to the environment, with special concerns given to potential vectors of resistance transmission. Secondly, we outline the effects of antibiotic pollution independent of resistance evolution on natural microbial populations, as well as invertebrates and vertebrates. We close with an overview of current regional policies tasked with curbing the effects of antibiotics pollution and outline areas in which such policies are still under development.}, }
@article {pmid31233889, year = {2019}, author = {Forger, LV and Woolf, MS and Simmons, TL and Swall, JL and Singh, B}, title = {A eukaryotic community succession based method for postmortem interval (PMI) estimation of decomposing porcine remains.}, journal = {Forensic science international}, volume = {302}, number = {}, pages = {109838}, doi = {10.1016/j.forsciint.2019.05.054}, pmid = {31233889}, issn = {1872-6283}, mesh = {Animals ; Biodiversity ; Eukaryota/genetics/*physiology ; Forensic Pathology ; High-Throughput Nucleotide Sequencing ; *Postmortem Changes ; RNA, Ribosomal, 18S ; Swine ; }, abstract = {Recent, short-term studies on porcine and human models (albeit with few replicates) demonstrated that the succession of the microbial community of remains may be used to estimate time since death. Using a porcine model (N=6) over an extended period of time (1703 ADD, or two months), this study characterized the eukaryote community of decomposing remains. Skin microbial samples were collected from the torso of each set of remains every day during the first week, on alternate days during the second week, and once a week for the remainder of the 60-day period; all collection intervals were recorded in accumulated degree days (ADD). The eukaryote community of each sample was determined using 18S ribosomal DNA (rDNA) MiSeq high throughput sequencing; data were analyzed in the Mothur pipeline (v1.39.5) and in IBM SPSS and R statistical packages. The relative abundance of eukaryote taxa across ADD/Days and an Analysis of Molecular Variance (AMOVA) indicated similarities between sequential ADD/Days, but significant differences in the eukaryote communities as broad stage 'milestones' of decomposition were reached. Fresh remains (0-57 ADD/0-2 Days; exhibiting a total body score (TBS) of 0-10) were characterized by the combined presence of Saccharomycetaceae, Debaryomycetaceae, Trichosporonaceae, Rhabditida, and Trichostomatia. During bloat and active decay (87-209 ADD/3-7 Days; exhibiting TBS of 11-20), Diptera was the most abundant eukaryotic taxa. During advanced decay stage (267-448 ADD/9-15 Days; exhibiting TBS of 21-25), Rhabditida was the most dominant eukaryote. Dry/skeletal remains (734-1703 ADD/26-61 Days; TBS≥26) were dominated by fungal families Dipodascaceae, Debaryomycetaceae, Trichosporonaceae, and Sporidiobolaceae. Using the family-level eukaryote taxonomic data for the entire study, random forest modelling explained 89.58% of the variation in ADD/Days, with a root mean square error (RMSE) of 177.55 ADD (≈6 days). Overall, these results highlight the importance of the microbial eukaryote community during the process of decomposition and in estimation of PMI.}, }
@article {pmid31233284, year = {2019}, author = {Zealand, AM and Mei, R and Roskilly, AP and Liu, W and Graham, DW}, title = {Molecular microbial ecology of stable versus failing rice straw anaerobic digesters.}, journal = {Microbial biotechnology}, volume = {12}, number = {5}, pages = {879-891}, pmid = {31233284}, issn = {1751-7915}, mesh = {Anaerobiosis ; Archaea/classification/*genetics/metabolism ; Bacteria/classification/genetics/*growth &amp; development/metabolism ; Biofuels/microbiology ; Bioreactors/*microbiology ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Industrial Waste ; *Microbiota ; Organic Chemicals/metabolism ; Oryza/*metabolism ; Phylogeny ; Plant Stems/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Waste rice straw (RS) is generated in massive quantities around the world and is often burned, creating greenhouse gas and air quality problems. Anaerobic digestion (AD) may be a better option for RS management, but RS is presumed to be comparatively refractory under anaerobic conditions without pre-treatment or co-substrates. However, this presumption assumes frequent reactor feeding regimes but less frequent feeding may be better for RS due to slow hydrolysis rates. Here, we assess how feeding frequency (FF) and organic loading rate (OLR) impacts microbial communities and biogas production in RS AD reactors. Using 16S rDNA amplicon sequencing and bioinformatics, microbial communities from five bench-scale bioreactors were characterized. At low OLR (1.0 g VS l[-1] day[-1]), infrequently fed units (once every 21 days) had higher specific biogas yields than more frequent feeding (five in 7 days), although microbial community diversities were statistically similar (P > 0.05; ANOVA with Tukey comparison). In contrast, an increase in OLR to 2.0 g VS l[-1] day[-1] significantly changed Archaeal and fermenting Eubacterial sub-communities and the least frequency fed reactors failed. 'Stable' reactors were dominated by Methanobacterium, Methanosarcina and diverse Bacteroidetes, whereas 'failed' reactors saw shifts towards Clostridia and Christensenellaceae among fermenters and reduced methanogen abundances. Overall, OLR impacted RS AD microbial communities more than FF. However, combining infrequent feeding and lower OLRs may be better for RS AD because of higher specific yields.}, }
@article {pmid31232323, year = {2019}, author = {Zhong, X and Xu, G and Min, GS and Kim, S and Xu, H}, title = {Can tidal events influence monitoring surveys using periphytic ciliates based on biological trait analysis in marine ecosystems?.}, journal = {Marine pollution bulletin}, volume = {142}, number = {}, pages = {452-456}, doi = {10.1016/j.marpolbul.2019.04.005}, pmid = {31232323}, issn = {1879-3363}, mesh = {Ciliophora/*physiology ; Ecosystem ; Environmental Monitoring/instrumentation/*methods ; Multivariate Analysis ; Phenotype ; Republic of Korea ; *Seawater ; }, abstract = {To identify the influence of tidal events on community functioning of periphytic ciliates for monitoring program and community research using biological trait analysis, a 3-month baseline survey was conducted in Korean coastal waters using the polyurethane foam enveloped slide system (PFES) and conventional slide system (CS). Although the periphytic ciliate communities had similar biological trait categories, they represented considerable differences in community functioning and functional diversity measures within the PFES and CS systems. Multivariate analyses revealed different ways of the temporal shift in community functioning of the ciliates in both systems. The dispersion analysis demonstrated that the CS system was sensitive to the strong disturbance of tidal current and circulation compared to the PFES system. These findings suggest that the strong tidal event may significantly influence the output of analysis on community functioning of periphytic ciliates for bioassessment in marine ecosystems.}, }
@article {pmid31229831, year = {2019}, author = {Souza, FFC and Rissi, DV and Pedrosa, FO and Souza, EM and Baura, VA and Monteiro, RA and Balsanelli, E and Cruz, LM and Souza, RAF and Andreae, MO and Reis, RA and Godoi, RHM and Huergo, LF}, title = {Uncovering prokaryotic biodiversity within aerosols of the pristine Amazon forest.}, journal = {The Science of the total environment}, volume = {688}, number = {}, pages = {83-86}, doi = {10.1016/j.scitotenv.2019.06.218}, pmid = {31229831}, issn = {1879-1026}, mesh = {Aerosols/*analysis ; *Air Microbiology ; Biodiversity ; Brazil ; Environmental Monitoring ; *Forests ; }, abstract = {Biological aerosols (bioaerosol) are atmospheric particles that act as a dispersion unit of living organisms across the globe thereby affecting the biogeographic distribution of organisms. Despite their importance, there is virtually no knowledge about bioaerosols emitted by pristine forests. Here we provide the very first survey of the prokaryotic community of a bioaerosol collected inside pristine Amazon forest at 2 m above ground. Total atmospheric particles were collected at the Amazon Tall Tower Observatory, subjected to metagenomic DNA extraction and the prokaryotic diversity was determined by 16S rRNA gene amplicon sequencing. A total of 271,577 reads of 250 bp of the 16S rRNA gene amplicon were obtained. Only 27% of the reads could be classified using the 16S SILVA database. Most belonged to Proteobacteria, Actinobacteria and Firmicutes which is in good agreement with other bioaerosol studies. Further inspection of the reads using Blast searches and the 18S SILVA database revealed that most of the dataset was composed of Fungi sequences. The identified microbes suggest that the atmosphere may act as an important gateway to interchange bacteria between plants, soil and water ecosystems.}, }
@article {pmid31229570, year = {2019}, author = {Boyle, MA and Kearney, A and Carling, PC and Humphreys, H}, title = {'Off the rails': hospital bed rail design, contamination, and the evaluation of their microbial ecology.}, journal = {The Journal of hospital infection}, volume = {103}, number = {1}, pages = {e16-e22}, doi = {10.1016/j.jhin.2019.06.008}, pmid = {31229570}, issn = {1532-2939}, mesh = {Beds/*microbiology ; Cross Infection/transmission ; Disease Transmission, Infectious ; *Equipment Contamination ; *Hospitals ; Humans ; }, abstract = {Microbial contamination of the near-patient environment is an acknowledged reservoir for nosocomial pathogens. The hospital bed and specifically bed rails have been shown to be frequently and heavily contaminated in observational and interventional studies. Whereas the complexity of bed rail design has evolved over the years, the microbial contamination of these surfaces has been incompletely evaluated. In many published studies, key design variables are not described, compromising the extrapolation of results to other settings. This report reviews the evolving structure of hospital beds and bed rails, the possible impact of different design elements on microbial contamination and their role in pathogen transmission. Our findings support the need for clearly defined standardized assessment protocols to accurately assess bed rail and similar patient zone surface levels of contamination, as part of environmental hygiene investigations.}, }
@article {pmid31227816, year = {2019}, author = {Jung, MY and Gwak, JH and Rohe, L and Giesemann, A and Kim, JG and Well, R and Madsen, EL and Herbold, CW and Wagner, M and Rhee, SK}, title = {Indications for enzymatic denitrification to N2O at low pH in an ammonia-oxidizing archaeon.}, journal = {The ISME journal}, volume = {13}, number = {10}, pages = {2633-2638}, pmid = {31227816}, issn = {1751-7370}, mesh = {Ammonia/*metabolism ; Archaea/classification/*enzymology/genetics/*metabolism ; Archaeal Proteins/genetics/*metabolism ; Denitrification ; Ecosystem ; Hydrogen-Ion Concentration ; Nitrites/metabolism ; Nitrosomonas europaea ; Nitrous Oxide/*metabolism ; Oxidation-Reduction ; Soil Microbiology ; }, abstract = {Nitrous oxide (N2O) is a key climate change gas and nitrifying microbes living in terrestrial ecosystems contribute significantly to its formation. Many soils are acidic and global change will cause acidification of aquatic and terrestrial ecosystems, but the effect of decreasing pH on N2O formation by nitrifiers is poorly understood. Here, we used isotope-ratio mass spectrometry to investigate the effect of acidification on production of N2O by pure cultures of two ammonia-oxidizing archaea (AOA; Nitrosocosmicus oleophilus and Nitrosotenuis chungbukensis) and an ammonia-oxidizing bacterium (AOB; Nitrosomonas europaea). For all three strains acidification led to increased emission of N2O. However, changes of [15]N site preference (SP) values within the N2O molecule (as indicators of pathways for N2O formation), caused by decreasing pH, were highly different between the tested AOA and AOB. While acidification decreased the SP value in the AOB strain, SP values increased to a maximum value of 29‰ in N. oleophilus. In addition, [15]N-nitrite tracer experiments showed that acidification boosted nitrite transformation into N2O in all strains, but the incorporation rate was different for each ammonia oxidizer. Unexpectedly, for N. oleophilus more than 50% of the N2O produced at pH 5.5 had both nitrogen atoms from nitrite and we demonstrated that under these conditions expression of a putative cytochrome P450 NO reductase is strongly upregulated. Collectively, our results indicate that N. oleophilus might be able to enzymatically denitrify nitrite to N2O at low pH.}, }
@article {pmid31227556, year = {2019}, author = {Webster, TM and Fierer, N}, title = {Microbial Dynamics of Biosand Filters and Contributions of the Microbial Food Web to Effective Treatment of Wastewater-Impacted Water Sources.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {17}, pages = {}, pmid = {31227556}, issn = {1098-5336}, mesh = {*Bacterial Physiological Phenomena ; *Filtration ; Food Chain ; Sand/*microbiology ; Wastewater/*microbiology ; Water Purification/*instrumentation ; }, abstract = {Biosand filtration systems are widely used for drinking water treatment, from household-level, intermittently operated filters to large-scale continuous municipal systems. While it is well-established that microbial activity within the filter is essential for the removal of potential pathogens and other contaminants, the microbial ecology of these systems and how microbial succession relates to their performance remain poorly resolved. We determined how different source waters influence the composition, temporal dynamics, and performance of microbial communities in intermittently operated biosand filters. We operated lab-scale biosand filters, adding daily inputs from two contrasting water sources with differing nutrient concentrations and found that total coliform removal increased and became less variable after 4 weeks, regardless of water source. Total effluent biomass was also lower than total influent biomass for both water sources. Bacterial community composition, assessed via cultivation-independent DNA sequencing, varied by water source, sample type (influent, effluent, or sand), and time. Despite these differences, we identified specific taxa that were consistently removed, including common aquatic and wastewater bacteria. In contrast, taxa consistently more abundant in the sand and effluent included predatory, intracellular, and symbiotic bacteria.IMPORTANCE Although microbial activities are known to contribute to the effectiveness of biosand filtration for drinking water treatment, we have a limited understanding of what microbial groups are most effectively removed, colonize the sand, or make it through the filter. This study tracked the microbial communities in the influent, sand, and effluent of lab-scale, intermittently operated biosand filters over 8 weeks. These results represent the most detailed and time-resolved investigation of the microbial communities in biosand filters typical of those implemented at the household level in many developing countries. We show the importance of the microbial food web in biosand filtration, and we identified taxa that are preferentially removed from wastewater-impacted water sources. We found consistent patterns in filter effectiveness from source waters with differing nutrient loads and, likewise, identified specific bacterial taxa that were consistently more abundant in effluent waters, taxa that are important targets for further study and posttreatment.}, }
@article {pmid31226149, year = {2019}, author = {Wang, S and Zheng, X and Xia, H and Shi, D and Fan, J and Wang, P and Yan, Z}, title = {Archaeal community variation in the Qinhuangdao coastal aquaculture zone revealed by high-throughput sequencing.}, journal = {PloS one}, volume = {14}, number = {6}, pages = {e0218611}, pmid = {31226149}, issn = {1932-6203}, mesh = {Animals ; *Aquaculture ; Archaea/classification/*genetics ; *Biodiversity ; DNA, Archaeal/analysis/genetics ; *Ecosystem ; Geologic Sediments/*analysis/microbiology ; High-Throughput Nucleotide Sequencing ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/analysis/genetics ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; }, abstract = {The differences in archaeal diversity and community composition in the sediments and waters of the Qinhuangdao coastal aquaculture zone were investigated. Furthermore, the associations between dominant archaeal taxa with geographic and environmental variables were evaluated. High-throughput sequencing of archaeal 16S rRNA genes yielded a total of 176,211 quality-filtered reads and 1,178 operational taxonomic units (OTUs) overall. The most abundant phylum and class among all communities were Thaumarchaeota and Nitrososphaeria, respectively. Beta diversity analysis indicated that community composition was divided into two groups according to the habitat type (i.e., sediments or waters). Only 9.8% OTUs were shared by communities from the two habitats, while 73.9% and 16.3% of the OTUs were unique to sediment or water communities, respectively. Furthermore, the relative abundances of the dominant OTUs differed with habitat type. Investigations of relationships between dominant OTUs and environmental variables indicated that some dominant OTUs were more sensitive to variation in environmental factors, which could be due to individual taxonomic differences in lifestyles and biological processes. Overall, the investigation of archaeal community variation within the Qinhuangdao coastal aquaculture zone provides an important baseline understanding of the microbial ecology in this important ecosystem.}, }
@article {pmid31226029, year = {2020}, author = {Hellweger, FL}, title = {Combining Molecular Observations and Microbial Ecosystem Modeling: A Practical Guide.}, journal = {Annual review of marine science}, volume = {12}, number = {}, pages = {267-289}, doi = {10.1146/annurev-marine-010419-010829}, pmid = {31226029}, issn = {1941-0611}, mesh = {Biomass ; Chlorophyll A ; *Ecosystem ; Microbiota/*genetics ; *Models, Biological ; *Oceans and Seas ; }, abstract = {Advances in technologies for molecular observation are leading to novel types of data, including gene, transcript, protein, and metabolite levels, which are fundamentally different from the types traditionally compared with microbial ecosystem models, such as biomass (e.g., chlorophyll a) and nutrient concentrations. A grand challenge is to use these data to improve predictive models and use models to explain observed patterns. This article presents a framework that aligns observations and models along the dimension of abstraction or biological organization-from raw sequences to ecosystem patterns for observations, and from sequence simulators to ecological theory for models. It then reviews 16 studies that compared model results with molecular observations. Molecular data can and are being combined with microbial ecosystem models, but to keep up with and take advantage of the full scope of observations, models need to become more mechanistically detailed and complex, which is a technical and cultural challenge for the ecological modeling community.}, }
@article {pmid31225613, year = {2019}, author = {Brehony, C and McGrath, E and Brennan, W and Tuohy, A and Whyte, T and Brisse, S and Maiden, M and Jolley, K and Morris, D and Cormican, M}, title = {An MLST approach to support tracking of plasmids carrying OXA-48-like carbapenemase.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {74}, number = {7}, pages = {1856-1862}, pmid = {31225613}, issn = {1460-2091}, mesh = {Bacterial Proteins/*genetics ; Carbapenem-Resistant Enterobacteriaceae/classification/enzymology/genetics/*isolation &amp; purification ; *Disease Outbreaks ; Enterobacteriaceae Infections/*epidemiology/microbiology ; *Genotype ; Humans ; Ireland/epidemiology ; Molecular Epidemiology/methods ; Multilocus Sequence Typing/*methods ; Plasmids/*analysis ; Prevalence ; Sequence Analysis, DNA ; beta-Lactamases/*genetics ; }, abstract = {OBJECTIVES: The prevalence of infections caused by OXA-48-like carbapenemase-producing organisms in Ireland has increased dramatically since 2011 and is an urgent public health issue. Genome-based high-resolution genotyping was used to analyse clinical isolates submitted to the Irish Carbapenemase-Producing Enterobacteriaceae Reference Laboratory Service for a 13 month period (2016-17).<br><br>METHODS: A total of 109 OXA-48-producing non-duplicate clinical isolates from 16 submitting centres were sequenced. Using a gene-by-gene approach, isolate genomes were characterized by MLST and core genome MLST, and the presence of antimicrobial resistance determinants was determined. Reference mapping and a novel plasmid MLST-type approach was applied to determine plasmid background.<br><br>RESULTS: The OXA-48-like-producing isolates were Escherichia coli (n&#x205f;=&#x205f;56), Klebsiella spp. (n&#x205f;=&#x205f;46) and Enterobacter cloacae (n&#x205f;=&#x205f;7). Amongst the E. coli isolates there were 37 different STs and amongst the Klebsiella spp. isolates there were 27 different STs. blaOXA-48 was present in 105/109 (96.3%) of isolates. Based on mapping analysis and detection of the pOXA-48 IncL-type plasmid replicon and backbone genes, a pOXA-48-like plasmid was identified in 93/109 isolates (85.3%). The remaining isolates (n&#x205f;=&#x205f;16; 14.7%) harboured blaOXA-48-like genes in unknown environments. Using a gene-by-gene approach two pOXA-48-like plasmid groups with 2/71 pOXA-48-like locus differences between them were identified.<br><br>CONCLUSIONS: In Ireland we found a diversity of genotypes associated with OXA-48-like-producing clinical isolates with the IncL pOXA-48 plasmid type predominating as the blaOXA-48 genetic environment. A plasmid MLST approach can rapidly identify plasmids associated with outbreaks and monitor spread of types temporally and geographically.}, }
@article {pmid31222757, year = {2019}, author = {Hammerbacher, A and Coutinho, TA and Gershenzon, J}, title = {Roles of plant volatiles in defence against microbial pathogens and microbial exploitation of volatiles.}, journal = {Plant, cell &amp; environment}, volume = {42}, number = {10}, pages = {2827-2843}, doi = {10.1111/pce.13602}, pmid = {31222757}, issn = {1365-3040}, mesh = {Anti-Infective Agents/pharmacology ; Bacteria/drug effects ; Biosynthetic Pathways ; Disease Resistance ; Fungi/drug effects ; Herbivory ; Microbial Interactions/drug effects ; Plant Diseases/*immunology/microbiology/prevention &amp; control ; Plants/*immunology/*metabolism ; Terpenes ; Viruses/drug effects ; Volatile Organic Compounds/immunology/*pharmacology ; }, abstract = {Plants emit a large variety of volatile organic compounds during infection by pathogenic microbes, including terpenes, aromatics, nitrogen-containing compounds, and fatty acid derivatives, as well as the volatile plant hormones, methyl jasmonate, and methyl salicylate. Given the general antimicrobial activity of plant volatiles and the timing of emission following infection, these compounds have often been assumed to function in defence against pathogens without much solid evidence. In this review, we critically evaluate current knowledge on the toxicity of volatiles to fungi, bacteria, and viruses and their role in plant resistance as well as how they act to induce systemic resistance in uninfected parts of the plant and in neighbouring plants. We also discuss how microbes can detoxify plant volatiles and exploit them as nutrients, attractants for insect vectors, and inducers of volatile emissions, which stimulate immune responses that make plants more susceptible to infection. Although much more is known about plant volatile-herbivore interactions, knowledge of volatile-microbe interactions is growing and it may eventually be possible to harness plant volatiles to reduce disease in agriculture and forestry. Future research in this field can be facilitated by making use of the analytical and molecular tools generated by the prolific research on plant-herbivore interactions.}, }
@article {pmid31220587, year = {2020}, author = {Trifi, H and Najjari, A and Achouak, W and Barakat, M and Ghedira, K and Mrad, F and Saidi, M and Sghaier, H}, title = {Metataxonomics of Tunisian phosphogypsum based on five bioinformatics pipelines: Insights for bioremediation.}, journal = {Genomics}, volume = {112}, number = {1}, pages = {981-989}, doi = {10.1016/j.ygeno.2019.06.014}, pmid = {31220587}, issn = {1089-8646}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; *Calcium Sulfate/chemistry/metabolism ; Computational Biology ; High-Throughput Nucleotide Sequencing ; Microbiota ; *Phosphorus/chemistry/metabolism ; Sequence Analysis, DNA ; Software ; Tunisia ; }, abstract = {Phosphogypsum (PG) is an acidic by-product from the phosphate fertilizer industry and it is characterized by a low nutrient availability and the presence of radionuclides and heavy metals which pose a serious problem in its management. Here, we have applied Illumina MiSeq sequencing technology and five bioinformatics pipelines to explore the phylogenetic communities in Tunisian PG. Taking One Codex as a reference method, we present the results of 16S-rDNA-gene-based metataxonomics abundances with four other alternative bioinformatics pipelines (MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST), mothur, MICrobial Community Analysis (MICCA) and Quantitative Insights into Microbial Ecology (QIIME)), when analyzing the Tunisian PG. Importantly, based on 16S rDNA datasets, the functional capabilities of microbial communities of PG were deciphered. They suggested the presence of PG autochthonous bacteria valorizable into (1) removal of radioactive elements and toxic heavy metals, (2) promotion of plant growth, (3) oxidation and (4) reduction of sulfate. These bacteria can be explored further for applications in the bioremediation of by-products, like PG, by different processes.}, }
@article {pmid31219789, year = {2019}, author = {Myer, PR}, title = {Bovine Genome-Microbiome Interactions: Metagenomic Frontier for the Selection of Efficient Productivity in Cattle Systems.}, journal = {mSystems}, volume = {4}, number = {3}, pages = {}, pmid = {31219789}, issn = {2379-5077}, abstract = {The mutualistic, commensal, and parasitic microorganisms that reside in the rumen and lower gastrointestinal tract of cattle and other ruminants exert enormous influence over animal physiology and performance. Because these microbial communities are critical for host nutrient utilization and contribute to the metabolic capacity of the rumen, past research has aimed to define host-microbe symbioses in cattle by examining the rumen and lower gut microbiomes with respect to production phenotypes, such as feed efficiency. However, as the field of bovine gut microbial ecology progresses, multidisciplinary approaches must be employed, combining host genomics and other omics-based techniques to understand the complex host-microbe network. In this perspective, I discuss the direction of the field of bovine gut microbial ecology with regard to feed efficiency and explore how the grand challenge of such research will be to maintain host-efficient gut microbiomes in cattle production through manipulations of genome-microbiome interactions.}, }
@article {pmid31219680, year = {2019}, author = {Tedersoo, L and Anslan, S}, title = {Towards PacBio-based pan-eukaryote metabarcoding using full-length ITS sequences.}, journal = {Environmental microbiology reports}, volume = {11}, number = {5}, pages = {659-668}, doi = {10.1111/1758-2229.12776}, pmid = {31219680}, issn = {1758-2229}, mesh = {DNA Barcoding, Taxonomic/*methods ; DNA Primers/genetics ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/*genetics ; Eukaryota/*genetics ; Fungi/genetics ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Development of high-throughput sequencing techniques has greatly benefited our understanding about microbial ecology, yet the methods producing short reads suffer from species-level resolution and uncertainty of identification. Here, we optimize Pacific Biosciences-based metabarcoding protocols covering the internal transcribed spacer (ITS region) and partial small subunit of the rRNA gene for species-level identification of all eukaryotes, with a specific focus on Fungi (including Glomeromycota) and Stramenopila (particularly Oomycota). Based on tests on composite soil samples and mock communities, we propose best suitable degenerate primers, ITS9munngs + ITS4ngsUni for eukaryotes and selected groups therein and discuss the pros and cons of long read-based identification of eukaryotes.}, }
@article {pmid31218384, year = {2020}, author = {Della Mónica, IF and Godeas, AM and Scervino, JM}, title = {In Vivo Modulation of Arbuscular Mycorrhizal Symbiosis and Soil Quality by Fungal P Solubilizers.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {21-29}, pmid = {31218384}, issn = {1432-184X}, support = {PICT 2012 0285//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; }, mesh = {Agricultural Inoculants/classification/*physiology ; Glomeromycota/classification/*physiology ; Mycorrhizae/classification/*physiology ; Phosphorus/*metabolism ; Plant Roots/growth &amp; development/microbiology/physiology ; Rhizosphere ; Soil/*chemistry ; Soil Microbiology ; *Symbiosis ; Triticum/growth &amp; development/*microbiology/physiology ; }, abstract = {Phosphorus (P) is an essential nutrient with low bioavailability in soils for plant growth. The use of P solubilization fungi (PSF) has arisen as an eco-friendly strategy to increase this nutrient's bioavailability. The effect of PSF inoculation and its combination with P-transporting organisms (arbuscular mycorrhizal fungi, AMF) on plant growth has been previously studied. However, these studies did not evaluate the combined effect of PSF and AMF inoculation on plant growth, symbiosis, and soil quality. Therefore, the aim of this study is to assess the impact of PSF on the AMF-wheat symbiosis establishment and efficiency, considering the effect on plant growth and soil quality. We performed a greenhouse experiment with wheat under different treatments (+/-AMF: Rhizophagus irregularis; +/-PSF strains: Talaromyces flavus, T. helicus L7B, T. helicus N24, and T. diversus) and measured plant growth, AMF root colonization, symbiotic efficiency, and soil quality indicators. No interaction between PSF and R. irregularis was found in wheat growth, showcasing that their combination is not better than single inoculation. T. helicus strains did not interfere with the AMF-wheat symbiosis establishment, while T. diversus and T. flavus decreased it. The symbiotic efficiency was increased by T. flavus and T. helicus N24, and unchanged with T. helicus L7B and T. diversus inoculation. The soil quality indicators were higher with microbial co-inoculation, particularly the alkaline phosphatases parameter, showing the beneficial role of fungi in soil. This work highlights the importance of microbial interactions in the rhizosphere for crop sustainability and soil quality improvement, assessing the effects of PSF on AMF-wheat symbiosis.}, }
@article {pmid31217455, year = {2019}, author = {Fan, Z and Lu, S and Liu, S and Guo, H and Wang, T and Zhou, J and Peng, X}, title = {Changes in Plant Rhizosphere Microbial Communities under Different Vegetation Restoration Patterns in Karst and Non-karst Ecosystems.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {8761}, pmid = {31217455}, issn = {2045-2322}, mesh = {*Bacteria/classification/growth &amp; development ; *Ecosystem ; *Microbiota ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Understanding how patterns of recovery and geological conditions affect microbial communities is important for determining the stability of karst ecosystems. Here, we investigated the diversity and composition of microorganisms in karst and non-karst environments under natural restoration and artificial rehabilitation conditions. The results showed no significant differences in soil microbial diversity, but the microbial communities associated with geological conditions and tree species differed significantly. Variation partitioning analysis (VPA) showed that a total of 77.3% of the variation in bacteria and a total of 69.3% of the variation in fungi could be explained by vegetation type and geological background. There were significant differences in six bacterial classes (Actinobacteria, Alphaproteobacteria, Ktedonobacteria, TK10, Gammaproteobacteria, and Anaerolineae) and nine fungal classes (Eurotiomycetes, Agaricomycetes, unclassified _p_Ascomycota, Sordariomycetes, Tremellomycetes, norank_k_Fungi, Pezizomycetes, Leotiomycetes and Archaeorhizomycetes) among the soils collected from six plots. A Spearman correlation heatmap showed that the microbial community was affected by the major soil properties. Principal coordinates analysis indicated that the microbial community of Pinus yunnanensis in the artificial forest, which was established for the protection of the environment was most similar to that in the natural secondary forest in the karst ecosystem. These findings further our understanding of microbial responses to vegetation restoration and geological conditions.}, }
@article {pmid31214149, year = {2019}, author = {Hounmanou, YMG and Mdegela, RH and Dougnon, TV and Madsen, H and Withey, JH and Olsen, JE and Dalsgaard, A}, title = {Tilapia (Oreochromis niloticus) as a Putative Reservoir Host for Survival and Transmission of Vibrio cholerae O1 Biotype El Tor in the Aquatic Environment.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1215}, pmid = {31214149}, issn = {1664-302X}, support = {R01 AI127390/AI/NIAID NIH HHS/United States ; }, abstract = {Studies have reported the occurrence of Vibrio cholerae in fish but little is known about the interaction between fish and toxigenic V. cholerae as opposed to phytoplankton, which are well-established aquatic reservoirs for V. cholerae. The present study determined the role of tilapia (Oreochromis niloticus) as a reservoir host for survival and transmission of V. cholerae in aquatic environments. Three experiments were performed with one repetition each, where O. niloticus (∼2 g) kept in beakers were inoculated with four V. cholerae strains (5 × 10[7] cfu/mL). Firstly, infected tilapia were kept in stagnant water and fed live brine shrimp (Artemia salina) larvae daily. Secondly, infected tilapia were kept without feeding and water was changed every 24 h. Thirdly, infected tilapia were fed and water was renewed daily. Infected tilapia and non-infected controls were sacrificed on days 1, 2, 3, 7, and 14 post-inoculation and V. cholerae were enumerated in intestinal content and water. Another experiment assessed the transmission of V. cholerae from infected to non-infected tilapia. The study revealed that El Tor biotype V. cholerae O1 and V. cholerae non-O1 colonized tilapia intestines and persisted at stable concentrations during the second week of the experiment whereas the Classical biotype was undetectable after 1 week. In stagnant water with feeding, V. cholerae counts dropped to 10[5] cfu/ml in water and from 10[7] to 10[4] cfu/intestine in fish after 14 days. When water was renewed, counts in water decreased from 10[7] to 10[3] cfu/ml and intestinal counts went from 10[6] to 10[2] cfu/intestine regardless of feeding. All strains were transmitted from infected to naïve fish after 24 h of cohabitation. Tilapia like other fish may play an essential role in the survival and dissemination of V. cholerae O1 in aquatic environments, e.g., the seventh pandemic strains mostly. In this study, tilapia were exposed to high concentrations of V. cholerae to ensure initial uptake and follow-up studies with lower doses resembling natural concentrations of V. cholerae in the aquatic environment are needed to confirm our findings.}, }
@article {pmid31214145, year = {2019}, author = {El Hage, R and Hernandez-Sanabria, E and Calatayud Arroyo, M and Props, R and Van de Wiele, T}, title = {Propionate-Producing Consortium Restores Antibiotic-Induced Dysbiosis in a Dynamic in vitro Model of the Human Intestinal Microbial Ecosystem.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1206}, pmid = {31214145}, issn = {1664-302X}, abstract = {Metabolic syndrome is a growing public health concern. Efforts at searching for links with the gut microbiome have revealed that propionate is a major fermentation product in the gut with several health benefits toward energy homeostasis. For instance, propionate stimulates satiety-inducing hormones, leading to lower energy intake and reducing weight gain and associated risk factors. In (disease) scenarios where microbial dysbiosis is apparent, gut microbial production of propionate may be decreased. Here, we investigated the effect of a propionogenic bacterial consortium composed of Lactobacillus plantarum, Bacteroides thetaiotaomicron, Ruminococcus obeum, Coprococcus catus, Bacteroides vulgatus, Akkermansia muciniphila, and Veillonella parvula for its potential to restore in vitro propionate concentrations upon antibiotic-induced microbial dysbiosis. Using the mucosal simulator of the human intestinal microbial ecosystem (M-SHIME), we challenged the simulated colon microbiome with clindamycin. Addition of the propionogenic consortium resulted in successful colonization and subsequent restoration of propionate levels, while a positive effect on the mitochondrial membrane potential (ΔΨm) was observed in comparison with the controls. Our results support the development and application of next generation probiotics, which are composed of multiple bacterial strains with diverse functionality and phylogenetic background.}, }
@article {pmid31214144, year = {2019}, author = {Dai, D and Wang, T and Wu, S and Gao, NL and Chen, WH}, title = {Metabolic Dependencies Underlie Interaction Patterns of Gut Microbiota During Enteropathogenesis.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1205}, pmid = {31214144}, issn = {1664-302X}, abstract = {In recent decades, increasing evidence has strongly suggested that gut microbiota play an important role in many intestinal diseases including inflammatory bowel disease (IBD) and colorectal cancer (CRC). The composition of gut microbiota is thought to be largely shaped by interspecies competition for available resources and also by cooperative interactions. However, to what extent the changes could be attributed to external factors such as diet of choice and internal factors including mutual relationships among gut microbiota, respectively, are yet to be elucidated. Due to the advances of high-throughput sequencing technologies, flood of (meta)-genome sequence information and high-throughput biological data are available for gut microbiota and their association with intestinal diseases, making it easier to gain understanding of microbial physiology at the systems level. In addition, the newly developed genome-scale metabolic models that cover significant proportion of known gut microbes enable researchers to analyze and simulate the system-level metabolic response in response to different stimuli in the gut, providing deeper biological insights. Using metabolic interaction network based on pair-wise metabolic dependencies, we found the same interaction pattern in two IBD datasets and one CRC datasets. We report here for the first time that the growth of significantly enriched bacteria in IBD and CRC patients could be boosted by other bacteria including other significantly increased ones. Conversely, the growth of probiotics could be strongly inhibited from other species, including other probiotics. Therefore, it is very important to take the mutual interaction of probiotics into consideration when developing probiotics or "microbial based therapies." Together, our metabolic interaction network analysis can predict majority of the changes in terms of the changed directions in the gut microbiota during enteropathogenesis. Our results thus revealed unappreciated interaction patterns between species could underlie alterations in gut microbiota during enteropathogenesis, and between probiotics and other microbes. Our methods provided a new framework for studying interactions in gut microbiome and their roles in health and disease.}, }
@article {pmid31214131, year = {2019}, author = {You, YA and Yoo, JY and Kwon, EJ and Kim, YJ}, title = {Blood Microbial Communities During Pregnancy Are Associated With Preterm Birth.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1122}, pmid = {31214131}, issn = {1664-302X}, abstract = {Microbial infection of the placenta, amniotic fluid, vaginal canal, and oral cavity is known to significantly contribute to preterm birth (PTB). Although microbes can be translocated into the blood, little is known regarding the blood microbiota during pregnancy. To assess changes in the microbiome during pregnancy, blood samples were obtained 2 or 3 times during pregnancy from a cohort of 45 pregnant women enrolled between 2008 and 2010. To analyze the association with PTB, we conducted a case-control study involving 41 pregnant women upon admission for preterm labor and rupture of membrane (20 with term delivery; 21 with PTB). Bacterial diversity was assessed in number and composition between the first, second, and third trimesters in term delivered women according to 16S rRNA gene amplicon sequencing, and data were analyzed using Quantitative Insight Into Microbial Ecology (QIIME). Taxonomy was assigned using the GreenGenes 8.15.13 database. Dominant microorganisms at the phylum level in all pregnant women were identified as Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. However, the number and composition of bacteria in women with PTB differed from that in women with term delivery. Firmicutes and Bacteroidetes were more abundant in women with PTB than in women with term delivery, while Proteobacteria was less prevalent in women with PTB. At the genus level, Bacteroides, Lactobacillus, Sphingomonas, Fastidiosipila, Weissella, and Butyricicoccus were enriched in PTB samples. These observational results suggest that several taxa in the maternal blood microbiome are associated with PTB. Further studies are needed to confirm the composition of the blood microbiota in women with PTB. Additionally, the mechanism by which pathogenic microbes in maternal blood cause infection and PTB requires further analysis.}, }
@article {pmid31207046, year = {2019}, author = {Czechowska, K and Lannigan, J and Wang, L and Arcidiacono, J and Ashhurst, TM and Barnard, RM and Bauer, S and Bispo, C and Bonilla, DL and Brinkman, RR and Cabanski, M and Chang, HD and Chakrabarti, L and Chojnowski, G and Cotleur, B and Degheidy, H and Dela Cruz, GV and Eck, S and Elliott, J and Errington, R and Filby, A and Gagnon, D and Gardner, R and Green, C and Gregory, M and Groves, CJ and Hall, C and Hammes, F and Hedrick, M and Hoffman, R and Icha, J and Ivaska, J and Jenner, DC and Jones, D and Kerckhof, FM and Kukat, C and Lanham, D and Leavesley, S and Lee, M and Lin-Gibson, S and Litwin, V and Liu, Y and Molloy, J and Moore, JS and Müller, S and Nedbal, J and Niesner, R and Nitta, N and Ohlsson-Wilhelm, B and Paul, NE and Perfetto, S and Portat, Z and Props, R and Radtke, S and Rayanki, R and Rieger, A and Rogers, S and Rubbens, P and Salomon, R and Schiemann, M and Sharpe, J and Sonder, SU and Stewart, JJ and Sun, Y and Ulrich, H and Van Isterdael, G and Vitaliti, A and van Vreden, C and Weber, M and Zimmermann, J and Vacca, G and Wallace, P and Tárnok, A}, title = {Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2018 Conference Workshops.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {95}, number = {6}, pages = {598-644}, doi = {10.1002/cyto.a.23777}, pmid = {31207046}, issn = {1552-4930}, mesh = {Aptamers, Nucleotide ; Biomarkers ; Databases as Topic ; Flow Cytometry/instrumentation/standards/*trends ; Genomics ; Humans ; Mass Spectrometry/instrumentation/methods ; Microbiota/genetics ; Microscopy, Fluorescence ; Reproducibility of Results ; Single-Cell Analysis/*methods ; Software ; Validation Studies as Topic ; }, }
@article {pmid31205409, year = {2019}, author = {Yao, R and Xu, L and Lu, G and Zhu, L}, title = {Evaluation of the Function of Wild Animal Gut Microbiomes Using Next-Generation Sequencing and Bioinformatics and its Relevance to Animal Conservation.}, journal = {Evolutionary bioinformatics online}, volume = {15}, number = {}, pages = {1176934319848438}, pmid = {31205409}, issn = {1176-9343}, abstract = {The relationship between animal conservation and the animal gut microbiome is a hot topic in current microbial ecology research. Our group has recently revealed that the occurrence of diverse combinations of gut microbial compositions and functions (metagenomics) in Père David's deer (Elaphurus davidianus) populations is likely to lead to increased evolutionary potential and resilience in response to environmental changes. Thus, considering the effects of diet on the gut microbiome and the importance of a stable gut microbial community to host health, we suggest that a transitional buffer period (with feeding on a regular diet and a diet from the translocation habitat) is needed before animal translocation. When the gut microbiome enters into relatively stable stages and adapts to the new diet from the translocation site, the time is suitable for translocation. Long-term monitoring of the gut microbiomes of translocated animals (by collecting fresh feces and carrying out next-generation sequencing) is still necessary after their translocation.}, }
@article {pmid31204896, year = {2021}, author = {Tian, H and Hui, M and Pan, P and Huang, J and Chen, L and Zhao, J}, title = {Performance and microbial ecology of biofilms adhering on aerated membrane with distinctive conditions for the treatment of domestic sewage.}, journal = {Environmental technology}, volume = {42}, number = {3}, pages = {459-467}, doi = {10.1080/09593330.2019.1631890}, pmid = {31204896}, issn = {1479-487X}, mesh = {Biofilms ; *Bioreactors ; Denitrification ; Nitrogen ; Nitrosomonas ; *Sewage ; Waste Disposal, Fluid ; Wastewater ; }, abstract = {When used to treat domestic wastewater, biofilms adhering to oxygen-permeable membranes are generally altered by environmental conditions. In this study, the effect of common conditions, including salinity, temperature, air-supplying pressure, flow velocity, influent COD, and NH4-N on the biofilm structure were determined. Principal component analysis revealed that archaeal community was more easily affected by the changing conditions than bacteria. The subsequent redundancy analysis showed that salinity had the most influence on bacteria, followed by temperature, influent COD, flow velocity, pressure, and influent NH4-N. In archaea, temperature had the highest effect, followed by flow velocity, salinity, influent NH4-N, pressure, and influent COD. The key bacterial class Anaerolineae was not easily influenced by the above conditions, but the population probably contributed to the nitrogen removal. Gammaproteobacteria was promoted significantly by influent NH4-N concentration, salinity, and pressure. Betaproteobacteria and Deltaproteobacteria were apparently inhibited by the high salinity and contributed to the organic compound degradation. Flow velocity primarily promoted the growth of Alphaproteobacteria. Candidatus Nitrososphaera had a higher tolerance for salinity but lower tolerance for influent NH4-N than Nitrosomonas. The former probably played a more crucial role in ammoxidation. Methanomethylovorans might disrupt nitrogen removal because it could consume the carbon source for denitrification.}, }
@article {pmid31202406, year = {2019}, author = {Wedel, C and Wenning, M and Dettling, A and Scherer, S and Hinrichs, J}, title = {Resistance of thermophilic spore formers isolated from milk and whey products towards cleaning-in-place conditions: Influence of pH, temperature and milk residues.}, journal = {Food microbiology}, volume = {83}, number = {}, pages = {150-158}, doi = {10.1016/j.fm.2019.05.002}, pmid = {31202406}, issn = {1095-9998}, mesh = {Acids/*pharmacology ; Alkalies/*pharmacology ; Animals ; Colony Count, Microbial ; Dairying ; Drug Resistance, Bacterial ; Hydrogen-Ion Concentration ; Kinetics ; Microbial Viability/*drug effects ; Milk/*microbiology ; Powders ; Spores, Bacterial/*drug effects ; *Temperature ; Whey Proteins/metabolism ; }, abstract = {The occurrence of thermophilic spore formers in dairy powders is a major concern for producers worldwide. This study aims to investigate the resistance of thermophilic endospores towards cleaning solutions typically used for cleaning-in-place in dairy manufacturing plants. From eleven tested strains, all were able to survive an alkaline treatment (NaOH) at 65 °C for 10 min (0.5%), whereas at concentrations of 2% eight strains withstood the treatment. Acid solutions were more sporicidal. At 0.5% of HNO3, only three strains survived the treatment. Milk impurities reduced the inactivation effect of the NaOH solutions towards thermophilic spore formers. For two selected strains, a detailed kinetic inactivation in NaOH and HNO3 solutions at different temperatures was performed and non-log-linear inactivation curves were observed. This study highlights the risk of reusing cleaning solutions in dairies.}, }
@article {pmid31202277, year = {2019}, author = {Soverini, M and Turroni, S and Biagi, E and Brigidi, P and Candela, M and Rampelli, S}, title = {HumanMycobiomeScan: a new bioinformatics tool for the characterization of the fungal fraction in metagenomic samples.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {496}, pmid = {31202277}, issn = {1471-2164}, mesh = {Animals ; Fungi/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Mycobiome/*genetics ; *Software ; }, abstract = {BACKGROUND: Modern metagenomic analysis of complex microbial communities produces large amounts of sequence data containing information on the microbiome in terms of bacterial, archaeal, viral and eukaryotic composition. The bioinformatics tools available are mainly devoted to profiling the bacterial and viral fractions and only a few software packages consider fungi. As the human fungal microbiome (human mycobiome) can play an important role in the onset and progression of diseases, a comprehensive description of host-microbiota interactions cannot ignore this component.<br><br>RESULTS: HumanMycobiomeScan is a bioinformatics tool for the taxonomic profiling of the mycobiome directly from raw data of next-generation sequencing. The tool uses hierarchical databases of fungi in order to unambiguously assign reads to fungal species more accurately and&#x2009;>&#x2009;10,000 times faster than other comparable approaches. HumanMycobiomeScan was validated using in silico generated synthetic communities and then applied to metagenomic data, to characterize the intestinal fungal components in subjects adhering to different subsistence strategies.<br><br>CONCLUSIONS: Although blind to unknown species, HumanMycobiomeScan allows the characterization of the fungal fraction of complex microbial ecosystems with good performance in terms of sample denoising from reads belonging to other microorganisms. HumanMycobiomeScan is most appropriate for well-studied microbiomes, for which most of the fungal species have been fully sequenced. This released version is functionally implemented to work with human-associated microbiota samples. In combination with other microbial profiling tools, HumanMycobiomeScan is a frugal and efficient tool for comprehensive characterization of microbial ecosystems through shotgun metagenomics sequencing.}, }
@article {pmid31201518, year = {2019}, author = {Moisan, K and Cordovez, V and van de Zande, EM and Raaijmakers, JM and Dicke, M and Lucas-Barbosa, D}, title = {Volatiles of pathogenic and non-pathogenic soil-borne fungi affect plant development and resistance to insects.}, journal = {Oecologia}, volume = {190}, number = {3}, pages = {589-604}, pmid = {31201518}, issn = {1432-1939}, mesh = {Animals ; Fungi ; Insecta ; *Plant Development ; Soil ; *Volatile Organic Compounds ; }, abstract = {Plants are ubiquitously exposed to a wide diversity of (micro)organisms, including mutualists and antagonists. Prior to direct contact, plants can perceive microbial organic and inorganic volatile compounds (hereafter: volatiles) from a distance that, in turn, may affect plant development and resistance. To date, however, the specificity of plant responses to volatiles emitted by pathogenic and non-pathogenic fungi and the ecological consequences of such responses remain largely elusive. We investigated whether Arabidopsis thaliana plants can differentiate between volatiles of pathogenic and non-pathogenic soil-borne fungi. We profiled volatile organic compounds (VOCs) and measured CO2 emission of 11 fungi. We assessed the main effects of fungal volatiles on plant development and insect resistance. Despite distinct differences in VOC profiles between the pathogenic and non-pathogenic fungi, plants did not discriminate, based on plant phenotypic responses, between pathogenic and non-pathogenic fungi. Overall, plant growth was promoted and flowering was accelerated upon exposure to fungal volatiles, irrespectively of fungal CO2 emission levels. In addition, plants became significantly more susceptible to a generalist insect leaf-chewing herbivore upon exposure to the volatiles of some of the fungi, demonstrating that a prior fungal volatile exposure can negatively affect plant resistance. These data indicate that plant development and resistance can be modulated in response to exposure to fungal volatiles.}, }
@article {pmid31201356, year = {2019}, author = {Szafrański, SP and Kilian, M and Yang, I and Bei der Wieden, G and Winkel, A and Hegermann, J and Stiesch, M}, title = {Diversity patterns of bacteriophages infecting Aggregatibacter and Haemophilus species across clades and niches.}, journal = {The ISME journal}, volume = {13}, number = {10}, pages = {2500-2522}, pmid = {31201356}, issn = {1751-7370}, mesh = {Aggregatibacter/classification/*virology ; Bacteriophages/classification/genetics/isolation &amp; purification/*physiology ; Base Composition ; Biodiversity ; Genome, Viral ; Genomics ; Haemophilus/classification/*virology ; Host Specificity ; Humans ; Lysogeny ; Metagenome ; Phylogeny ; Prophages/classification/genetics/isolation &amp; purification/physiology ; }, abstract = {Aggregatibacter and Haemophilus species are relevant human commensals and opportunistic pathogens. Consequently, their bacteriophages may have significant impact on human microbial ecology and pathologies. Our aim was to reveal the prevalence and diversity of bacteriophages infecting Aggregatibacter and Haemophilus species that colonize the human body. Genome mining with comparative genomics, screening of clinical isolates, and profiling of metagenomes allowed characterization of 346 phages grouped in 52 clusters and 18 superclusters. Less than 10% of the identified phage clusters were represented by previously characterized phages. Prophage diversity patterns varied significantly for different phage types, host clades, and environmental niches. A more diverse phage community lysogenizes Haemophilus influenzae and Haemophilus parainfluenzae strains than Aggregatibacter actinomycetemcomitans and "Haemophilus ducreyi". Co-infections occurred more often in "H. ducreyi". Phages from Aggregatibacter actinomycetemcomitans preferably lysogenized strains of specific serotype. Prophage patterns shared by subspecies clades of different bacterial species suggest similar ecoevolutionary drivers. Changes in frequencies of DNA uptake signal sequences and guanine-cytosine content reflect phage-host long-term coevolution. Aggregatibacter and Haemophilus phages were prevalent at multiple oral sites. Together, these findings should help exploring the ecoevolutionary forces shaping virus-host interactions in the human microbiome. Putative lytic phages, especially phiKZ-like, may provide new therapeutic options.}, }
@article {pmid31195956, year = {2019}, author = {Hirano, H and Takemoto, K}, title = {Difficulty in inferring microbial community structure based on co-occurrence network approaches.}, journal = {BMC bioinformatics}, volume = {20}, number = {1}, pages = {329}, pmid = {31195956}, issn = {1471-2105}, support = {JP17H04703//Japan Society for the Promotion of Science/ ; }, mesh = {*Ecosystem ; *Microbiota ; Models, Biological ; }, abstract = {BACKGROUND: Co-occurrence networks-ecological associations between sampled populations of microbial communities inferred from taxonomic composition data obtained from high-throughput sequencing techniques-are widely used in microbial ecology. Several co-occurrence network methods have been proposed. Co-occurrence network methods only infer ecological associations and are often used to discuss species interactions. However, validity of this application of co-occurrence network methods is currently debated. In particular, they simply evaluate using parametric statistical models, even though microbial compositions are determined through population dynamics.<br><br>RESULTS: We comprehensively evaluated the validity of common methods for inferring microbial ecological networks through realistic simulations. We evaluated how correctly nine widely used methods describe interaction patterns in ecological communities. Contrary to previous studies, the performance of the co-occurrence network methods on compositional data was almost equal to or less than that of classical methods (e.g., Pearson's correlation). The methods described the interaction patterns in dense and/or heterogeneous networks rather inadequately. Co-occurrence network performance also depended upon interaction types; specifically, the interaction patterns in competitive communities were relatively accurately predicted while those in predator-prey (parasitic) communities were relatively inadequately predicted.<br><br>CONCLUSIONS: Our findings indicated that co-occurrence network approaches may be insufficient in interpreting species interactions in microbiome studies. However, the results do not diminish the importance of these approaches. Rather, they highlight the need for further careful evaluation of the validity of these much-used methods and the development of more suitable methods for inferring microbial ecological networks.}, }
@article {pmid31194939, year = {2019}, author = {Johnson, AJ and Vangay, P and Al-Ghalith, GA and Hillmann, BM and Ward, TL and Shields-Cutler, RR and Kim, AD and Shmagel, AK and Syed, AN and ,  and Walter, J and Menon, R and Koecher, K and Knights, D}, title = {Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans.}, journal = {Cell host &amp; microbe}, volume = {25}, number = {6}, pages = {789-802.e5}, doi = {10.1016/j.chom.2019.05.005}, pmid = {31194939}, issn = {1934-6069}, mesh = {Adult ; *Diet ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Young Adult ; }, abstract = {Diet is a key determinant of human gut microbiome variation. However, the fine-scale relationships between daily food choices and human gut microbiome composition remain unexplored. Here, we used multivariate methods to integrate 24-h food records and fecal shotgun metagenomes from 34 healthy human subjects collected daily over 17 days. Microbiome composition depended on multiple days of dietary history and was more strongly associated with food choices than with conventional nutrient profiles, and daily microbial responses to diet were highly personalized. Data from two subjects consuming only meal replacement beverages suggest that a monotonous diet does not induce microbiome stability in humans, and instead, overall dietary diversity associates with microbiome stability. Our work provides key methodological insights for future diet-microbiome studies and suggests that food-based interventions seeking to modulate the gut microbiota may need to be tailored to the individual microbiome. Trial Registration: ClinicalTrials.gov: NCT03610477.}, }
@article {pmid31194515, year = {2019}, author = {Ali, M and Wang, Z and Salam, KW and Hari, AR and Pronk, M and van Loosdrecht, MCM and Saikaly, PE}, title = {Importance of Species Sorting and Immigration on the Bacterial Assembly of Different-Sized Aggregates in a Full-Scale Aerobic Granular Sludge Plant.}, journal = {Environmental science &amp; technology}, volume = {53}, number = {14}, pages = {8291-8301}, doi = {10.1021/acs.est.8b07303}, pmid = {31194515}, issn = {1520-5851}, mesh = {Aerobiosis ; Bacteria ; *Bioreactors ; Ecosystem ; Emigration and Immigration ; *Sewage ; Waste Disposal, Fluid ; }, abstract = {In aerobic granular sludge (AGS) systems, different-sized microbial aggregates having different solids retention time (SRT) coexist in the same reactor compartment and are subjected to the same influent wastewater. Thus, the AGS system provides a unique ecosystem to study the importance of local (species sorting) and regional (immigration) processes in bacterial community assembly. The microbial communities of different-sized aggregates (flocs <0.2 mm, small granules (0.2-1.0 mm) and large granules >1.0 mm), influent wastewater, excess sludge and effluent of a full-scale AGS plant were characterized over a steady-state operation period of 6 months. Amplicon sequencing was integrated with mass balance to determine the SRT and net growth rate of operational taxonomic units (OTUs). We found strong evidence of species sorting as opposed to immigration, which was significantly higher at short SRT (i.e., flocs and small granules) than that at long SRT (large granules). Rare OTUs in wastewater belonging to putative functional groups responsible for nitrogen and phosphorus removal were progressively enriched with an increase in microbial aggregates size. In contrast, fecal- and sewage infrastructure-derived microbes progressively decreased in relative abundance with increase in microbial aggregate size. These findings highlight the importance of AGS as a unique model ecosystem to study fundamental microbial ecology concepts.}, }
@article {pmid31191599, year = {2019}, author = {Zhang, B and Xu, S and Xu, W and Chen, Q and Chen, Z and Yan, C and Fan, Y and Zhang, H and Liu, Q and Yang, J and Yang, J and Xiao, C and Xu, H and Ren, J}, title = {Leveraging Fecal Bacterial Survey Data to Predict Colorectal Tumors.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {447}, pmid = {31191599}, issn = {1664-8021}, abstract = {Colorectal cancer (CRC) ranks second in cancer-associated mortality and third in the incidence worldwide. Most of CRC follow adenoma-carcinoma sequence, and have more than 90% chance of survival if diagnosed at early stage. But the recommended screening by colonoscopy is invasive, expensive, and poorly adhered to. Recently, several studies reported that the fecal bacteria might provide non-invasive biomarkers for CRC and precancerous tumors. Therefore, we collected and uniformly re-analyzed these published fecal 16S rDNA sequencing datasets to verify the association and identify biomarkers to classify and predict colorectal tumors by random forest method. A total of 1674 samples (330 CRC, 357 advanced adenoma, 141 adenoma, and 846 control) from 7 studies were analyzed in this study. By random effects model and fixed effects model, we observed significant differences in alpha-diversity and beta-diversity between individuals with CRC and the normal colon, but not between adenoma and the normal. We identified various bacterial genera with significant odds ratios for colorectal tumors at different stages. Through building random forest model with 10-fold cross-validation as well as new test datasets, we classified individuals with CRC, advanced adenoma, adenoma and normal colon. All approaches obtained comparable performance at entire OTU level, entire genus level, and the common genus level as measured using AUC. When combined all samples, the AUC of random forest model based on 12 common genera reached 0.846 for CRC, although the predication performed poorly for advance adenoma and adenoma.}, }
@article {pmid31191490, year = {2019}, author = {Chronopoulou, PM and Salonen, I and Bird, C and Reichart, GJ and Koho, KA}, title = {Metabarcoding Insights Into the Trophic Behavior and Identity of Intertidal Benthic Foraminifera.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1169}, pmid = {31191490}, issn = {1664-302X}, abstract = {Foraminifera are ubiquitous marine protists with an important role in the benthic carbon cycle. However, morphological observations often fail to resolve their exact taxonomic placement and there is a lack of field studies on their particular trophic preferences. Here, we propose the application of metabarcoding as a tool for the elucidation of the in situ feeding behavior of benthic foraminifera, while also allowing the correct taxonomic assignment of the feeder, using the V9 region of the 18S (small subunit; SSU) rRNA gene. Living foraminiferal specimens were collected from two intertidal mudflats of the Wadden Sea and DNA was extracted from foraminiferal individuals and from the surrounding sediments. Molecular analysis allowed us to confirm that our foraminiferal specimens belong to three genetic types: Ammonia sp. T6, Elphidium sp. S5 and Haynesina sp. S16. Foraminiferal intracellular eukaryote communities reflected to an extent those of the surrounding sediments but at different relative abundances. Unlike sediment eukaryote communities, which were largely determined by the sampling site, foraminiferal intracellular eukaryote communities were driven by foraminiferal species, followed by sediment depth. Our data suggests that Ammonia sp. T6 can predate on metazoan classes, whereas Elphidium sp. S5 and Haynesina sp. S16 are more likely to ingest diatoms. These observations, alongside the use of metabarcoding in similar ecological studies, significantly contribute to our overall understanding of the ecological roles of these protists in intertidal benthic environments and their position and function in the benthic food webs.}, }
@article {pmid31189482, year = {2019}, author = {Bouslimani, A and da Silva, R and Kosciolek, T and Janssen, S and Callewaert, C and Amir, A and Dorrestein, K and Melnik, AV and Zaramela, LS and Kim, JN and Humphrey, G and Schwartz, T and Sanders, K and Brennan, C and Luzzatto-Knaan, T and Ackermann, G and McDonald, D and Zengler, K and Knight, R and Dorrestein, PC}, title = {The impact of skin care products on skin chemistry and microbiome dynamics.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {47}, pmid = {31189482}, issn = {1741-7007}, support = {R21 AR071731/AR/NIAMS NIH HHS/United States ; }, mesh = {Adult ; Cosmetics/*adverse effects/classification ; Female ; Humans ; Male ; Microbiota/*drug effects ; Skin/chemistry/*drug effects/microbiology ; Skin Care/*adverse effects ; }, abstract = {BACKGROUND: Use of skin personal care products on a regular basis is nearly ubiquitous, but their effects on molecular and microbial diversity of the skin are unknown. We evaluated the impact of four beauty products (a facial lotion, a moisturizer, a foot powder, and a deodorant) on 11 volunteers over 9 weeks.<br><br>RESULTS: Mass spectrometry and 16S rRNA inventories of the skin revealed decreases in chemical as well as in bacterial and archaeal diversity on halting deodorant use. Specific compounds from beauty products used before the study remain detectable with half-lives of 0.5-1.9&#x2009;weeks. The deodorant and foot powder increased molecular, bacterial, and archaeal diversity, while arm and face lotions had little effect on bacterial and archaeal but increased chemical diversity. Personal care product effects last for weeks and produce highly individualized responses, including alterations in steroid and pheromone levels and in bacterial and archaeal ecosystem structure and dynamics.<br><br>CONCLUSIONS: These findings may lead to next-generation precision beauty products and therapies for skin disorders.}, }
@article {pmid31187884, year = {2019}, author = {Vissenaekens, H and Grootaert, C and Rajkovic, A and Van De Wiele, T and Calatayud, M}, title = {The response of five intestinal cell lines to anoxic conditions in vitro.}, journal = {Biology of the cell}, volume = {111}, number = {9}, pages = {232-244}, doi = {10.1111/boc.201800076}, pmid = {31187884}, issn = {1768-322X}, support = {BOF (01B04212)//Universiteit Gent/ ; 1S18417N//Fonds Wetenschappelijk Onderzoek/ ; FWO/12R2717N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {Caco-2 Cells ; Cell Hypoxia ; Glutathione/*metabolism ; HCT116 Cells ; HT29 Cells ; Humans ; Hypoxia/*metabolism ; Intestinal Mucosa/*metabolism ; Oxidation-Reduction ; Oxidative Stress ; Oxygen/*metabolism ; Reactive Oxygen Species/*metabolism ; }, abstract = {BACKGROUND INFORMATION: In vivo oxygen levels in tissues range from 1% to 15%, while mechanistic cell culture studies employ an atmospheric oxygen level of 21% to grow cells. These oxygen concentrations are therefore not representative for conditions where the cell response is dependent on oxygen partial pressure. In pathological situation, such as (colon) cancer or chronic inflammation, tissue oxygenation is severely affected, and even under physiological conditions a steep oxygen gradient is present in the large intestine, where epithelial cells co-exist with microbial species, resulting in almost anoxia at the midpoint of the lumen. In these situations, a better characterisation of the essential cellular behaviour under hypoxia or anoxia is required.<br><br>RESULTS: We have characterised the cellular response of commonly used cell cultures for the study of intestinal epithelial processes and colon cancer development (Caco-2, HT-29, SW480, HCT 116 and LoVo) under conventional normoxic conditions (21% O2) and in an anoxic (<0.1% O2) environment generated in an anaerobic chamber. In general, anoxic conditions led to lower levels of oxidative stress, a reduction in reduced glutathione/oxidised glutathione (GSH/GSSG) ratio, the shift of the redox status to oxidised glutathione levels, reduced cell proliferation, decreased barrier function and higher glycolysis rates at the expense of oxidative respiration.<br><br>CONCLUSIONS: Continuous exposure to anoxic conditions, such as occurring at the host-microbe interface in the intestine, may create an adaptive metabolic cellular response of the cells.<br><br>SIGNIFICANCE: Considering adequate oxygen levels is essential for creating more physiologically relevant models for the study of host-microbe interactions and colon cancer development.}, }
@article {pmid31187177, year = {2020}, author = {Johnke, J and Fraune, S and Bosch, TCG and Hentschel, U and Schulenburg, H}, title = {Bdellovibrio and Like Organisms Are Predictors of Microbiome Diversity in Distinct Host Groups.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {252-257}, pmid = {31187177}, issn = {1432-184X}, support = {CRC 1182, project A4//Deutsche Forschungsgemeinschaft (DE)/ ; CRC 1182, project B2//Deutsche Forschungsgemeinschaft (DE)/ ; CRC 1182, project B2//Deutsche Forschungsgemeinschaft (DE)/ ; CRC 1182, project A4//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; Bdellovibrio/classification/genetics/isolation &amp; purification/*physiology ; Biodiversity ; Caenorhabditis elegans/*microbiology ; DNA, Bacterial/genetics ; Drosophila melanogaster/*microbiology ; Host Specificity ; Hydra/*microbiology ; *Microbiota ; Phylogeny ; Porifera/classification/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Biodiversity is generally believed to be a main determinant of ecosystem functioning. This principle also applies to the microbiome and could consequently contribute to host health. According to ecological theory, communities are shaped by top predators whose direct and indirect interactions with community members cause stability and diversity. Bdellovibrio and like organisms (BALOs) are a neglected group of predatory bacteria that feed on Gram-negative bacteria and can thereby influence microbiome composition. We asked whether BALOs can predict biodiversity levels in microbiomes from distinct host groups and environments. We demonstrate that genetic signatures of BALOs are commonly found within the 16S rRNA reads from diverse host taxa. In many cases, their presence, abundance, and especially richness are positively correlated with overall microbiome diversity. Our findings suggest that BALOs can act as drivers of microbial alpha-diversity and should therefore be considered candidates for the restoration of microbiomes and the prevention of dysbiosis.}, }
@article {pmid31187139, year = {2019}, author = {Pacheco, AR and Segrè, D}, title = {A multidimensional perspective on microbial interactions.}, journal = {FEMS microbiology letters}, volume = {366}, number = {11}, pages = {}, pmid = {31187139}, issn = {1574-6968}, support = {R01 GM121950/GM/NIGMS NIH HHS/United States ; T32 GM100842/GM/NIGMS NIH HHS/United States ; P30 DK036836/DK/NIDDK NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Ecology/methods ; Humans ; Microbial Interactions/*physiology ; Microbiota/physiology ; Systems Biology/*methods ; }, abstract = {Beyond being simply positive or negative, beneficial or inhibitory, microbial interactions can involve a diverse set of mechanisms, dependencies and dynamical properties. These more nuanced features have been described in great detail for some specific types of interactions, (e.g. pairwise metabolic cross-feeding, quorum sensing or antibiotic killing), often with the use of quantitative measurements and insight derived from modeling. With a growing understanding of the composition and dynamics of complex microbial communities for human health and other applications, we face the challenge of integrating information about these different interactions into comprehensive quantitative frameworks. Here, we review the literature on a wide set of microbial interactions, and explore the potential value of a formal categorization based on multidimensional vectors of attributes. We propose that such an encoding can facilitate systematic, direct comparisons of interaction mechanisms and dependencies, and we discuss the relevance of an atlas of interactions for future modeling and rational design efforts.}, }
@article {pmid31186361, year = {2019}, author = {Kehe, J and Kulesa, A and Ortiz, A and Ackerman, CM and Thakku, SG and Sellers, D and Kuehn, S and Gore, J and Friedman, J and Blainey, PC}, title = {Massively parallel screening of synthetic microbial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {26}, pages = {12804-12809}, pmid = {31186361}, issn = {1091-6490}, support = {F32 CA236425/CA/NCI NIH HHS/United States ; T32 GM087237/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/isolation &amp; purification ; Bacteriological Techniques/*methods ; High-Throughput Screening Assays/*methods ; *Microbial Consortia ; Microbial Interactions ; Microfluidics/methods ; *Soil Microbiology ; }, abstract = {Microbial communities have numerous potential applications in biotechnology, agriculture, and medicine. Nevertheless, the limited accuracy with which we can predict interspecies interactions and environmental dependencies hinders efforts to rationally engineer beneficial consortia. Empirical screening is a complementary approach wherein synthetic communities are combinatorially constructed and assayed in high throughput. However, assembling many combinations of microbes is logistically complex and difficult to achieve on a timescale commensurate with microbial growth. Here, we introduce the kChip, a droplets-based platform that performs rapid, massively parallel, bottom-up construction and screening of synthetic microbial communities. We first show that the kChip enables phenotypic characterization of microbes across environmental conditions. Next, in a screen of ∼100,000 multispecies communities comprising up to 19 soil isolates, we identified sets that promote the growth of the model plant symbiont Herbaspirillum frisingense in a manner robust to carbon source variation and the presence of additional species. Broadly, kChip screening can identify multispecies consortia possessing any optically assayable function, including facilitation of biocontrol agents, suppression of pathogens, degradation of recalcitrant substrates, and robustness of these functions to perturbation, with many applications across basic and applied microbial ecology.}, }
@article {pmid31186282, year = {2019}, author = {Biancalani, T and Gore, J}, title = {Disentangling bacterial invasiveness from lethality in an experimental host-pathogen system.}, journal = {Molecular systems biology}, volume = {15}, number = {6}, pages = {e8707}, pmid = {31186282}, issn = {1744-4292}, support = {DP2 AG044279/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*pathogenicity ; Bacterial Infections/*mortality/veterinary ; Caenorhabditis elegans/*microbiology ; Host-Pathogen Interactions ; Mortality ; Pseudomonas aeruginosa/pathogenicity ; Salmonella enterica/pathogenicity ; Serratia marcescens/pathogenicity ; Virulence ; }, abstract = {Quantifying virulence remains a central problem in human health, pest control, disease ecology, and evolutionary biology. Bacterial virulence is typically quantified by the LT50 (i.e., the time taken to kill 50% of infected hosts); however, such an indicator cannot account for the full complexity of the infection process, such as distinguishing between the pathogen's ability to colonize versus kill the hosts. Indeed, the pathogen needs to breach the primary defenses in order to colonize, find a suitable environment to replicate, and finally express the virulence factors that cause disease. Here, we show that two virulence attributes, namely pathogen lethality and invasiveness, can be disentangled from the survival curves of a laboratory population of Caenorhabditis elegans nematodes exposed to three bacterial pathogens: Pseudomonas aeruginosa, Serratia marcescens, and Salmonella enterica We first show that the host population eventually experiences a constant mortality rate, which quantifies the lethality of the pathogen. We then show that the time necessary to reach this constant mortality rate regime depends on the pathogen growth rate and colonization rate, and thus determines the pathogen invasiveness. Our framework reveals that Serratia marcescens is particularly good at the initial colonization of the host, whereas Salmonella enterica is a poor colonizer yet just as lethal once established. Pseudomonas aeruginosa, on the other hand, is both a good colonizer and highly lethal after becoming established. The ability to quantitatively characterize the ability of different pathogens to perform each of these steps has implications for treatment and prevention of disease and for the evolution and ecology of pathogens.}, }
@article {pmid31180804, year = {2019}, author = {Mark Welch, JL and Dewhirst, FE and Borisy, GG}, title = {Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis.}, journal = {Annual review of microbiology}, volume = {73}, number = {}, pages = {335-358}, pmid = {31180804}, issn = {1545-3251}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R37 DE016937/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; Mouth/*microbiology ; Spatial Analysis ; }, abstract = {Microbial communities are complex and dynamic, composed of hundreds of taxa interacting across multiple spatial scales. Advances in sequencing and imaging technology have led to great strides in understanding both the composition and the spatial organization of these complex communities. In the human mouth, sequencing results indicate that distinct sites host microbial communities that not only are distinguishable but to a meaningful degree are composed of entirely different microbes. Imaging suggests that the spatial organization of these communities is also distinct. Together, the literature supports the idea that most oral microbes are site specialists. A clear understanding of microbiota structure at different sites in the mouth enables mechanistic studies, informs the generation of hypotheses, and strengthens the position of oral microbiology as a model system for microbial ecology in general.}, }
@article {pmid31178845, year = {2019}, author = {Berlanas, C and Berbegal, M and Elena, G and Laidani, M and Cibriain, JF and Sagües, A and Gramaje, D}, title = {The Fungal and Bacterial Rhizosphere Microbiome Associated With Grapevine Rootstock Genotypes in Mature and Young Vineyards.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1142}, pmid = {31178845}, issn = {1664-302X}, abstract = {The microbiota colonizing the rhizosphere and the endorhizosphere contribute to plant growth, productivity, carbon sequestration, and phytoremediation. Several studies suggested that different plants types and even genotypes of the same plant species harbor partially different microbiomes. Here, we characterize the rhizosphere bacterial and fungal microbiota across five grapevine rootstock genotypes cultivated in the same soil at two vineyards and sampling dates over 2 years by 16S rRNA gene and ITS high-throughput amplicon sequencing. In addition, we use quantitative PCR (qPCR) approach to measure the relative abundance and dynamic changes of fungal pathogens associated with black-foot disease. The objectives were to (1) unravel the effects of rootstock genotype on microbial communities in the rhizosphere of grapevine and (2) to compare the relative abundances of sequence reads and DNA amount of black-foot disease pathogens. Host genetic control of the microbiome was evident in the rhizosphere of the mature vineyard. Microbiome composition also shifted as year of sampling, and fungal diversity varied with sampling moments. Linear discriminant analysis identified specific bacterial (i.e., Bacillus) and fungal (i.e., Glomus) taxa associated with grapevine rootstocks. Host genotype did not predict any summary metrics of rhizosphere α- and β-diversity in the young vineyard. Regarding black-foot associated pathogens, a significant correlation between sequencing reads and qPCR was observed. In conclusion, grapevine rootstock genotypes in the mature vineyard were associated with different rhizosphere microbiomes. The latter could also have been affected by age of the vineyard, soil properties or field management practices. A more comprehensive study is needed to decipher the cause of the rootstock microbiome selection and the mechanisms by which grapevines are able to shape their associated microbial community. Understanding the vast diversity of bacteria and fungi in the rhizosphere and the interactions between microbiota and grapevine will facilitate the development of future strategies for grapevine protection.}, }
@article {pmid31177395, year = {2020}, author = {Liu, H and Wu, M and Liu, J and Qu, Y and Gao, Y and Ren, A}, title = {Tripartite Interactions Between Endophytic Fungi, Arbuscular Mycorrhizal Fungi, and Leymus chinensis.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {98-109}, pmid = {31177395}, issn = {1432-184X}, support = {31570433//National Natural Science Foundation of China/ ; 2016YFC0500702//National Key Research and Development Program/ ; }, mesh = {Endophytes/*physiology ; Glomeromycota/*physiology ; Mycorrhizae/*physiology ; Plant Roots/growth &amp; development/microbiology ; Poaceae/growth &amp; development/*microbiology ; Symbiosis ; }, abstract = {Grasses often establish multiple simultaneous symbiotic associations with endophytic fungi and arbuscular mycorrhizal fungi (AMF). Many studies have examined pair-wise interactions between plants and endophytic fungi or between plants and AMF, overlooking the interplays among multiple endosymbionts and their combined impacts on hosts. Here, we examined both the way in which each symbiont affects the other symbionts and the tripartite interactions between leaf endophytic fungi, AMF, and Leymus chinensis. As for AMF, different species (Glomus etunicatum, GE; Glomus mosseae, GM; Glomus claroideum, GC; and Glomus intraradices, GI) and AMF richness (no AMF, single AMF taxa, double AMF mixtures, triple AMF mixtures, and all four together) were considered. Our results showed that significant interactions were observed between endophytes and AMF, with endophytes interacting antagonistically with GM but synergistically with GI. No definitive interactions were observed between the endophytes and GE or GC. Additionally, the concentration of endophytes in the leaf sheath was positively correlated with the concentration of AMF in the roots under low AMF richness. The shoot biomass of L. chinensis was positively related to both endophyte concentration and AMF concentration, with only endophytes contributing to shoot biomass more than AMF. Endophytes and AMF increased shoot growth by contributing to phosphorus uptake. The interactive effects of endophytes and AMF on host growth were affected by the identity of AMF species. The beneficial effect of the endophytes decreased in response to GM but increased in response to GI. However, no influences were observed with other GC and GE. In addition, endophyte presence can alter the response of host plants to AMF richness. When leaf endophytes were absent, shoot biomass increased with higher AMF richness, only the influence of AMF species identity outweighed that of AMF richness. However, when leaf endophytes were present, no significant association was observed between AMF richness and shoot biomass. AMF species identity rather than AMF richness promoted shoot growth. The results of this study demonstrate that the outcomes of interspecific symbiotic interactions are very complex and vary with partner identity such that the effects of simultaneous symbioses cannot be generalized and highlight the need for studies to evaluate fitness response of all three species, as the interactive effects may not be the same for each partner.}, }
@article {pmid31176264, year = {2019}, author = {Patel, R and Kunjadia, P and Koringa, P and Joshi, C and Kunjadiya, A}, title = {Microbiological profiles in clinical and subclinical cases of mastitis in milking Jafarabadi buffalo.}, journal = {Research in veterinary science}, volume = {125}, number = {}, pages = {94-99}, doi = {10.1016/j.rvsc.2019.05.012}, pmid = {31176264}, issn = {1532-2661}, mesh = {Animals ; Bacteria/*classification ; *Buffaloes ; DNA, Bacterial/*analysis ; DNA, Ribosomal/analysis ; Dairying ; Female ; India ; Mastitis/microbiology/*veterinary ; Microbiota/*physiology ; Milk/*microbiology ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Mastitis is one of the important diseases affecting the dairy industry across the globe. Identification of bacterial pathogens associated with mastitis becomes essential in order to understand the etiology of disease which in turn will help to new strategies to control it. Microbial diversity analysis using pyrosequencing is widely studied for mastitis pathogens in dairy cows. However it is unexplored in case of buffalo. In the present study 16SrDNA gene pyrosequencing was used to characterize microbiota associated with clinical and subclinical mastitis in 28 Jafarabadi buffalo. The obtained sequencing data were analyzed by Quantitative Insights into Microbial Ecology (QIIME) and statistical analysis was done using Paleontological Statistics (PAST). Pyrosequencing produced 47.3 million base pairs reads. Phylogenetic profiles using ribosomal database revealed differences in abundance of Staphylococcus (25.95%, 10.09% and 0.03%), Enterococcus (10.80%, 8.72% and 0.36%), Escherichia (8.88%, 0.38% and 0.00%), Streptococcus (3.97%, 0.42% and 0.00%), Lactococcus (3.73%, 23.96% and 0.01%), and Ralstonia (0.54%, 12.72% and 0.00%), genera in clinical, subclinical and healthy samples, respectively. Different microbial profiles in clinical and subclinical mastitis in buffalo suggest the composition of bacteria in the milk is more diverse and complex hence single therapeutic regimes cannot be applied.}, }
@article {pmid31175190, year = {2019}, author = {Schmidt, JE and Vannette, RL and Igwe, A and Blundell, R and Casteel, CL and Gaudin, ACM}, title = {Effects of Agricultural Management on Rhizosphere Microbial Structure and Function in Processing Tomato Plants.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {16}, pages = {}, pmid = {31175190}, issn = {1098-5336}, support = {R25 GM056765/GM/NIGMS NIH HHS/United States ; }, mesh = {Agriculture ; Bacteria/classification/genetics/isolation &amp; purification ; Fungi/classification/genetics/isolation &amp; purification ; Solanum lycopersicum/*growth &amp; development/microbiology ; Microbiota ; Phylogeny ; Plant Roots/growth &amp; development/microbiology ; Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Agricultural management practices affect bulk soil microbial communities and the functions they carry out, but it remains unclear how these effects extend to the rhizosphere in different agroecosystem contexts. Given close linkages between rhizosphere processes and plant nutrition and productivity, understanding how management practices impact this critical zone is of great importance to optimize plant-soil interactions for agricultural sustainability. A comparison of six paired conventional-organic processing tomato farms was conducted to investigate relationships between management, soil physicochemical parameters, and rhizosphere microbial community composition and functions. Organically managed fields were higher in soil total N and NO3-N, total and labile C, plant Ca, S, and Cu, and other essential nutrients, while soil pH was higher in conventionally managed fields. Differential abundance, indicator species, and random forest analyses of rhizosphere communities revealed compositional differences between organic and conventional systems and identified management-specific microbial taxa. Phylogeny-based trait prediction showed that these differences translated into more abundant pathogenesis-related gene functions in conventional systems. Structural equation modeling revealed a greater effect of soil biological communities than physicochemical parameters on plant outcomes. These results highlight the importance of rhizosphere-specific studies, as plant selection likely interacts with management in regulating microbial communities and functions that impact agricultural productivity.IMPORTANCE Agriculture relies, in part, on close linkages between plants and the microorganisms that live in association with plant roots. These rhizosphere bacteria and fungi are distinct from microbial communities found in the rest of the soil and are even more important to plant nutrient uptake and health. Evidence from field studies shows that agricultural management practices such as fertilization and tillage shape microbial communities in bulk soil, but little is known about how these practices affect the rhizosphere. We investigated how agricultural management affects plant-soil-microbe interactions by comparing soil physical and chemical properties, plant nutrients, and rhizosphere microbial communities from paired fields under organic and conventional management. Our results show that human management effects extend even to microorganisms living in close association with plant roots and highlight the importance of these bacteria and fungi to crop nutrition and productivity.}, }
@article {pmid31173081, year = {2019}, author = {Roodt, D and Li, Z and Van de Peer, Y and Mizrachi, E}, title = {Loss of Wood Formation Genes in Monocot Genomes.}, journal = {Genome biology and evolution}, volume = {11}, number = {7}, pages = {1986-1996}, pmid = {31173081}, issn = {1759-6653}, mesh = {Genes, Plant ; Genome, Plant/*genetics ; Magnoliopsida/*genetics/growth &amp; development/*metabolism ; Wood/*metabolism ; }, abstract = {Woodiness (secondary xylem derived from vascular cambium) has been gained and lost multiple times in the angiosperms, but has been lost ancestrally in all monocots. Here, we investigate the conservation of genes involved in xylogenesis in fully sequenced angiosperm genomes, hypothesizing that monocots have lost some essential orthologs involved in this process. We analyzed the conservation of genes preferentially expressed in the developing secondary xylem of two eudicot trees in the sequenced genomes of 26 eudicot and seven monocot species, and the early diverging angiosperm Amborella trichopoda. We also reconstructed a regulatory model of early vascular cambial cell identity and differentiation and investigated the conservation of orthologs across the angiosperms. Additionally, we analyzed the genome of the aquatic seagrass Zostera marina for additional losses of genes otherwise essential to, especially, secondary cell wall formation. Despite almost complete conservation of orthology within the early cambial differentiation gene network, we show a clear pattern of loss of genes preferentially expressed in secondary xylem in the monocots that are highly conserved across eudicot species. Our study provides candidate genes that may have led to the loss of vascular cambium in the monocots, and, by comparing terrestrial angiosperms to an aquatic monocot, highlights genes essential to vasculature on land.}, }
@article {pmid31171824, year = {2019}, author = {Verspecht, T and Rodriguez Herrero, E and Khodaparast, L and Khodaparast, L and Boon, N and Bernaerts, K and Quirynen, M and Teughels, W}, title = {Development of antiseptic adaptation and cross-adapatation in selected oral pathogens in vitro.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {8326}, pmid = {31171824}, issn = {2045-2322}, mesh = {Adaptation, Biological ; Aggregatibacter actinomycetemcomitans/drug effects ; Anti-Infective Agents, Local/*pharmacology ; Biological Transport ; Cell Membrane/metabolism ; Cetylpyridinium/*pharmacology ; Chlorhexidine/*pharmacology ; Disinfectants/pharmacology ; Drug Resistance, Microbial ; *Drug Resistance, Multiple, Bacterial ; Fusobacterium nucleatum/drug effects ; Hydrophobic and Hydrophilic Interactions ; Mass Spectrometry ; Microbial Sensitivity Tests ; Oxidative Stress ; Porphyromonas gingivalis/drug effects ; Prevotella intermedia/drug effects ; Protein Domains ; Streptococcus mutans/drug effects ; Streptococcus sobrinus/drug effects ; Virulence ; }, abstract = {There is evidence that pathogenic bacteria can adapt to antiseptics upon repeated exposure. More alarming is the concomitant increase in antibiotic resistance that has been described for some pathogens. Unfortunately, effects of adaptation and cross-adaptation are hardly known for oral pathogens, which are very frequently exposed to antiseptics. Therefore, this study aimed to determine the in vitro increase in minimum inhibitory concentrations (MICs) in oral pathogens after repeated exposure to chlorhexidine or cetylpyridinium chloride, to examine if (cross-)adaptation to antiseptics/antibiotics occurs, if (cross-)adaptation is reversible and what the potential underlying mechanisms are. When the pathogens were exposed to antiseptics, their MICs significantly increased. This increase was in general at least partially conserved after regrowth without antiseptics. Some of the adapted species also showed cross-adaptation, as shown by increased MICs of antibiotics and the other antiseptic. In most antiseptic-adapted bacteria, cell-surface hydrophobicity was increased and mass-spectrometry analysis revealed changes in expression of proteins involved in a wide range of functional domains. These in vitro data shows the adaptation and cross-adaptation of oral pathogens to antiseptics and antibiotics. This was related to changes in cell surface hydrophobicity and in expression of proteins involved in membrane transport, virulence, oxidative stress protection and metabolism.}, }
@article {pmid31171429, year = {2019}, author = {Raskin, L and Nielsen, PH}, title = {Editorial overview: Integrating biotechnology and microbial ecology in urban water infrastructure through a microbiome continuum viewpoint.}, journal = {Current opinion in biotechnology}, volume = {57}, number = {}, pages = {iii-vi}, doi = {10.1016/j.copbio.2019.05.001}, pmid = {31171429}, issn = {1879-0429}, }
@article {pmid31167950, year = {2019}, author = {Ghashghavi, M and Belova, SE and Bodelier, PLE and Dedysh, SN and Kox, MAR and Speth, DR and Frenzel, P and Jetten, MSM and Lücker, S and Lüke, C}, title = {Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, pmid = {31167950}, issn = {2379-5042}, mesh = {Adaptation, Physiological ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Fresh Water/*microbiology ; Genome, Bacterial ; Methane/*metabolism ; Methylococcaceae/*classification/isolation &amp; purification/physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Methane-oxidizing microorganisms perform an important role in reducing emissions of the greenhouse gas methane to the atmosphere. To date, known bacterial methanotrophs belong to the Proteobacteria, Verrucomicrobia, and NC10 phyla. Within the Proteobacteria phylum, they can be divided into type Ia, type Ib, and type II methanotrophs. Type Ia and type II are well represented by isolates. Contrastingly, the vast majority of type Ib methanotrophs have not been able to be cultivated so far. Here, we compared the distributions of type Ib lineages in different environments. Whereas the cultivated type Ib methanotrophs (Methylococcus and Methylocaldum) are found in landfill and upland soils, lineages that are not represented by isolates are mostly dominant in freshwater environments, such as paddy fields and lake sediments. Thus, we observed a clear niche differentiation within type Ib methanotrophs. Our subsequent isolation attempts resulted in obtaining a pure culture of a novel type Ib methanotroph, tentatively named "Methylotetracoccus oryzae" C50C1. Strain C50C1 was further characterized to be an obligate methanotroph, containing C16:1ω9c as the major membrane phospholipid fatty acid, which has not been found in other methanotrophs. Genome analysis of strain C50C1 showed the presence of two pmoCAB operon copies and XoxF5-type methanol dehydrogenase in addition to MxaFI. The genome also contained genes involved in nitrogen and sulfur cycling, but it remains to be demonstrated if and how these help this type Ib methanotroph to adapt to fluctuating environmental conditions in freshwater ecosystems.IMPORTANCE Most of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study focused on the diversity and adaptation of aerobic methane-oxidizing bacteria in different environments by comparing their phenotypic and genotypic properties. We used lab-scale microcosms to create a countergradient of oxygen and methane for preenrichment, followed by classical isolation techniques to obtain methane-oxidizing bacteria from a freshwater environment. This resulted in the discovery and isolation of a novel methanotroph with interesting physiological and genomic properties that could possibly make this bacterium able to cope with fluctuating environmental conditions.}, }
@article {pmid31166992, year = {2019}, author = {Weinroth, MD and Britton, BC and McCullough, KR and Martin, JN and Geornaras, I and Knight, R and Belk, KE and Metcalf, JL}, title = {Ground beef microbiome changes with antimicrobial decontamination interventions and product storage.}, journal = {PloS one}, volume = {14}, number = {6}, pages = {e0217947}, pmid = {31166992}, issn = {1932-6203}, mesh = {Anti-Infective Agents/*pharmacology ; Antioxidants/pharmacology ; Bacteria/drug effects/growth &amp; development ; Biodiversity ; Biomass ; Colony Count, Microbial ; *Decontamination ; *Food Preservation ; *Microbiota/drug effects ; Phylogeny ; Red Meat/*microbiology ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Ground beef makes up more than half of the beef consumed in the U.S. market. Although numerous studies have been conducted on microbial safety and shelf life of ground beef limited work has been done using a culture-independent approach. While past studies have allowed for the evaluation of a few organisms of interest, there is limited work on the microbial community associated with fresh ground beef. In order to have a more complete picture of the microbial ecology of the product, a culture-independent approach utilizing 16S rRNA gene amplicon sequencing was used. The objectives of this study were to characterize the fresh ground beef microbiome and the effect that antimicrobial interventions and antioxidants, applied to beef trim before grinding, and product storage have on community composition using 16S rRNA gene amplicon sequencing. Beef trimmings were treated with antimicrobials and an antioxidant. Samples were ground, loafed, and overwrapped before being packaged in modified-atmosphere packaging. Samples were in dark storage for 21 days followed by five days in retail display. Periodically during storage, samples were collected for microbiological analysis and DNA isolation. Due to low microbial biomass, only 52 of 210 samples were included in the final analysis. These samples represented two antimicrobial treatments (peroxyacetic acid, and a sulfuric acid and sodium sulfate blend) and a control, from day-15 of dark storage and day-5 of retail display. As sample age increased, so did the number of raw reads (P < 0.001) and aerobic plate counts (P < 0.001), which were correlated (r = 0.94, P = 0.017). Across all samples, lactic acid bacteria were most abundant followed by Enterobacteriaceae; several rare taxa were also identified (namely Geobacillus, Thermus, and Sporosarcina). Antimicrobial treatment altered the bacterial alpha (P < 0.001) and beta (P = 0.001) diversity, while storage day altered alpha (P = 0.001) diversity. Enterobacteriaceae relative abundance differed (P < 0.05) among treatments and was highest in control samples. In addition to confirming previously described dominant microbial differences in culture-dependent results, these data identified genera not typically associated with ground beef and allowed for study of shifts in the entire microbiome and not just a subset of indicator organisms.}, }
@article {pmid31166650, year = {2019}, author = {Maaroufi, NI and Nordin, A and Palmqvist, K and Hasselquist, NJ and Forsmark, B and Rosenstock, NP and Wallander, H and Gundale, MJ}, title = {Anthropogenic nitrogen enrichment enhances soil carbon accumulation by impacting saprotrophs rather than ectomycorrhizal fungal activity.}, journal = {Global change biology}, volume = {25}, number = {9}, pages = {2900-2914}, doi = {10.1111/gcb.14722}, pmid = {31166650}, issn = {1365-2486}, mesh = {Carbon ; *Mycorrhizae ; *Nitrogen ; Soil ; Soil Microbiology ; Sweden ; }, abstract = {There is evidence that anthropogenic nitrogen (N) deposition enhances carbon (C) sequestration in boreal forest soils. However, it is unclear how free-living saprotrophs (bacteria and fungi, SAP) and ectomycorrhizal (EM) fungi responses to N addition impact soil C dynamics. Our aim was to investigate how SAP and EM communities are impacted by N enrichment and to estimate whether these changes influence decay of litter and humus. We conducted a long-term experiment in northern Sweden, maintained since 2004, consisting of ambient, low N additions (0, 3, 6, and 12 kg N ha[-1] year[-1]) simulating current N deposition rates in the boreal region, as well as a high N addition (50 kg N ha[-1] year[-1]). Our data showed that long-term N enrichment impeded mass loss of litter, but not of humus, and only in response to the highest N addition treatment. Furthermore, our data showed that EM fungi reduced the mass of N and P in both substrates during the incubation period compared to when only SAP organisms were present. Low N additions had no effect on microbial community structure, while the high N addition decreased fungal and bacterial biomasses and altered EM fungi and SAP community composition. Actinomycetes were the only bacterial SAP to show increased biomass in response to the highest N addition. These results provide a mechanistic understanding of how anthropogenic N enrichment can influence soil C accumulation rates and suggest that current N deposition rates in the boreal region (≤12 kg N ha[-1] year[-1]) are likely to have a minor impact on the soil microbial community and the decomposition of humus and litter.}, }
@article {pmid31165188, year = {2020}, author = {Li, Y and Guo, Q and He, F and Li, Y and Xue, Q and Lai, H}, title = {Biocontrol of Root Diseases and Growth Promotion of the Tuberous Plant Aconitum carmichaelii Induced by Actinomycetes Are Related to Shifts in the Rhizosphere Microbiota.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {134-147}, pmid = {31165188}, issn = {1432-184X}, support = {31600407//Youth Fund of the National Natural Science Foundation of China/ ; Z109021616//Fundamental Research Funds for the Central Universities of China/ ; 2012BAD14B11//National Key Technology R&amp;D Program of China/ ; }, mesh = {Aconitum/growth &amp; development/*microbiology ; Agricultural Inoculants/*physiology ; Antibiosis ; *Basidiomycota ; Fusarium/physiology ; Microbiota ; Plant Diseases/*microbiology/prevention &amp; control ; Plant Tubers/*growth &amp; development/microbiology ; Rhizosphere ; Soil Microbiology ; Streptomyces/*physiology ; }, abstract = {Soil Actinomycetes have been used as biocontrol agents against soil-borne plant diseases, yet little is known about their effects on the structure of the rhizosphere microbiota and the long-term effects on crop yield and disease intensity after the application of Actinomycetes is stopped. Here, we conducted 3-year plot experiments to investigate the roles of two Actinomycetes strains (Streptomyces pactum Act12 and Streptomyces rochei D74) in the biocontrol of soil-borne root diseases and growth promotion of monkhood (Aconitum carmichaelii). We also examined their long-term effects after soil application of a mixed Actinomycetes preparation (spore powder) was completed. High-throughput sequencing was used to analyze shifts in the rhizosphere microbiota. The antifungal activity and root colonization ability of the two Actinomycetes were also tested. Disease severity of southern blight and root rot decreased following application of the Actinomycetes preparation, whereas biomass yield of tubers increased compared with the control group. Significant effects of disease control and plant growth promotion were also observed after application was stopped. The Actinomycetes preparation induced marked increases in the abundance of beneficial microbes and decreases in the abundance of harmful microbes in rhizosphere soil. Adding cell-free culture filtrates of both strains Act12 and D74 inhibited the growth of fungal pathogens capable of causing southern blight (Sclerotium rolfsii) and root rot (Fusarium oxysporum) in A. carmichaelii. A GFP-labeled strain was used to show that D74 can colonize roots of A. carmichaelii. In conclusion, a preparation of two Actinomycetes plays a role in the biocontrol of root diseases and growth promotion of A. carmichaelii by inhibiting pathogen growth and shaping the rhizosphere microbiota.}, }
@article {pmid31165187, year = {2020}, author = {Kruger, A}, title = {Functional Redundancy of Batrachochytrium dendrobatidis Inhibition in Bacterial Communities Isolated from Lithobates clamitans Skin.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {231-240}, pmid = {31165187}, issn = {1432-184X}, mesh = {Animals ; *Antibiosis ; Bacteria/classification/genetics/*growth &amp; development/isolation &amp; purification ; Chytridiomycota/*physiology ; *Microbiota ; Mycoses/microbiology/*veterinary ; Phylogeny ; Rana clamitans/*microbiology ; Skin/*microbiology ; }, abstract = {The cutaneous microbial community can influence the health of amphibians exposed to Batrachochytrium dendrobatidis (Bd), a fungal pathogen that has contributed to recent amphibian declines. Resistance to Bd in amphibian populations is correlated with the presence of anti-Bd cutaneous microbes, which confer disease resistance by inhibiting Bd growth. I aimed to determine if green frogs (Lithobates clamitans), an abundant and widely distributed species in New Jersey, harbored bacteria that inhibit Bd and whether the presence and identity of these microbes varied among sites. I used in vitro challenge assays to determine if bacteria isolated from green frog skin could inhibit or enhance the growth of Bd. I found that green frogs at all sites harbored anti-Bd bacteria. However, there were differences in Bd inhibition capabilities among bacterial isolates identified as the same operational taxonomic unit (OTU), lending support to the idea that phylogenetic relatedness does not always predict Bd inhibition status. Additionally, anti-Bd bacterial richness did not vary by site, but the composition of anti-Bd bacterial taxa was distinct at each site. This suggests that there is functional redundancy of Bd inhibition across unique communities of anti-Bd symbionts found on frogs at different sites. These findings highlight the need to better elucidate the structure-function relationship of microbiomes and their role in disease resistance.}, }
@article {pmid31164870, year = {2019}, author = {Guarcello, R and Gaglio, R and Todaro, A and Alfonzo, A and Schicchi, R and Cirlincione, F and Moschetti, G and Francesca, N}, title = {Insights Into the Cultivable Microbial Ecology of "Manna" Ash Products Extracted From Fraxinus angustifolia (Oleaceae) Trees in Sicily, Italy.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {984}, pmid = {31164870}, issn = {1664-302X}, abstract = {Microbial communities characterizing a specific food matrix, generally, strongly contribute to both its composition, and properties for food applications. To our knowledge, this is the first study to investigate the cultivable microbial ecology of Sicilian "Manna" ash products in order to acquire new information on the hygienic quality, shelf-life and potential application of this traditional food. To this purpose, several manna samples belonging to different commercial categories were collected and subjected to the analysis of bacteria, yeasts, and filamentous fungi. Furthermore, an investigation of the sugar content and physicochemical parameters was performed. The results of our study followed the trend generally reported for other sugary foods. Conversely, as regards microbiological analyses, in the present study, the presence of microorganisms at high levels confirmed their survival in stressing conditions characterizing this food matrix in a viable and cultivable form. Most species were osmophilic, endophytic bacteria, antagonistic of fungi pathogen of plants. Yeasts were the most abundant microbial populations and a total of six species were identified: Candida aaseri, Candida lactis-condensi, Citeromyces matritensis, Lachancea thermotolerans, Saccharomyces cerevisiae, and Zygosaccharomyces bailii. Filamentous fungi included five genera, which were considered common contaminants of honey and of other foods due to their xerophilic characteristics. Interestingly, our results suggest that the strains of L. thermotolerans isolated in this study might be evaluated for their potential to act as starters either singly or in multi-combination for food applications.}, }
@article {pmid31164404, year = {2019}, author = {Bik, HM}, title = {Microbial Metazoa Are Microbes Too.}, journal = {mSystems}, volume = {4}, number = {3}, pages = {}, pmid = {31164404}, issn = {2379-5077}, abstract = {Microbial metazoa inhabit a certain "Goldilocks zone," where conditions are just right for the continued ignorance of these taxa. These microscopic animal species have body sizes of <1 mm and include diverse groups such as nematodes, tardigrades, kinorhynchs, loriciferans, and platyhelminths. The majority of species are too large to be considered in single-cell genomics approaches, yet too small to be wrapped into international genome sequencing initiatives. Other microbial eukaryote groups (namely the fungal and protist communities) have gained significant momentum in recent years, driven by a strong community of researchers united behind a common goal of culturing and sequencing new representatives. However, due to historical factors and difficult taxonomy, persistent research silos still exist for most microbial metazoan groups, and public molecular databases remain sparsely populated. Here, I argue that small metazoa should be embraced as a key component of microbial ecology studies, promoting a holistic and cutting-edge view of natural ecosystems.}, }
@article {pmid31163430, year = {2019}, author = {Philip, N and Leishman, SJ and Bandara, HMHN and Walsh, LJ}, title = {Casein Phosphopeptide-Amorphous Calcium Phosphate Attenuates Virulence and Modulates Microbial Ecology of Saliva-Derived Polymicrobial Biofilms.}, journal = {Caries research}, volume = {53}, number = {6}, pages = {643-649}, doi = {10.1159/000499869}, pmid = {31163430}, issn = {1421-976X}, mesh = {Actinobacteria/drug effects ; Bacterial Load ; Biofilms/*drug effects ; Calcium Phosphates/*pharmacology ; Caseins/*pharmacology ; Humans ; In Vitro Techniques ; Phosphopeptides ; Prevotella/drug effects ; Saliva/*microbiology ; Streptococcus/drug effects ; *Tooth Remineralization ; Virulence ; }, abstract = {BACKGROUND: Casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) acts as a salivary biomimetic that provides bioavailable calcium and phosphate ions to augment fluoride-mediated remineralisation of early caries lesions. However, there are indications that it may also have beneficial ecological effects on the oral microbiome.<br><br>OBJECTIVE: This in vitro study investigated whether CPP-ACP could influence microbial counts, acidogenicity, and the relative abundance of specific caries- and health-associated bacterial -species in polymicrobial biofilms.<br><br>METHODS: Saliva-derived polymicrobial biofilms were grown for 96 h in a cariogenic environment and treated every 12 h with 2% CPP-ACP or vehicle control. Colony forming units (CFUs) and acidogenicity were estimated from the treated biofilms. Microbial ecological effects of CPP-ACP were assessed based on the relative abundance of 14 specific caries- and health-associated -bacterial species using a real-time quantitative PCR assay. -Results: CPP-ACP-treated biofilms showed relatively modest, but significant, reductions in microbial CFUs (21% reduction, p = 0.008) and acidogenicity (33% reduction, p < 0.001), compared to the control-treated biofilms. The CPP-ACP treated biofilms also exhibited significantly lower bacterial loads of cariogenic Scardovia wiggsiae (fold change 0.017, p < 0.001) and Prevotella denticola(fold change 0.005, p < 0.001), and higher bacterial loads of commensal Streptococcus sanguinis(fold change 30.22, p < 0.001), S. mitis/oralis(fold change 9.66, p = 0.012), and S. salivarius/thermophilus(fold change 89.35, p < 0.001) than the control-treated biofilms.<br><br>CONCLUSIONS: The results indicate that CPP-ACP has virulence-attenuating attributes that can influence a beneficial microbial ecological change in the biofilm.}, }
@article {pmid31163257, year = {2019}, author = {Momper, L and Hu, E and Moore, KR and Skoog, EJ and Tyler, M and Evans, AJ and Bosak, T}, title = {Metabolic versatility in a modern lineage of cyanobacteria from terrestrial hot springs.}, journal = {Free radical biology &amp; medicine}, volume = {140}, number = {}, pages = {224-232}, doi = {10.1016/j.freeradbiomed.2019.05.036}, pmid = {31163257}, issn = {1873-4596}, mesh = {Cyanobacteria/*genetics/metabolism ; Hot Springs/chemistry ; Oxygen/metabolism ; Photosynthesis/*genetics ; *Phylogeny ; Sulfides/metabolism ; }, abstract = {The extent of oxygenated environments on the early Earth was much lower than today, and cyanobacteria were critical players in Earth's shift from widespread anoxia to oxygenated surface environments. Extant cyanobacteria that aggregate into cones, tufts and ridges are used to understand the long record of photosynthesis and microbe-mineral interactions during times when oxygen was much lower, i.e., the Archean and the Proterozoic. To better understand the metabolic versatility and physiological properties of these organisms, we examined publicly available genomes of cyanobacteria from modern terrestrial hydrothermal systems and a newly sequenced genome of a cyanobacterium isolated from conical and ridged microbialites that grow in occasionally sulfidic hydrothermal springs in Yellowstone National Park, USA. Phylogenomic analyses reveal that cyanobacteria from globally distributed terrestrial and shallow marine hydrothermal systems form a monophyletic clade within the Cyanobacteria phylum. Comparative genomics of this clade reveals the genetic capacity for oxygenic photosynthesis that uses photosystems I and II, and anoxygenic photosynthesis that uses a putative sulfide quinone reductase to oxidize sulfide and bypass photosystem II. Surprisingly large proportions of the newly sequenced genome from Yellowstone National Park are also dedicated to secondary metabolite production (15.1-15.6%), of which ∼6% can be attributed to antibiotic production and resistance genes. All this may be advantageous to benthic, mat-forming photosynthesizers that have to compete for light and nutrients in sporadically or permanently sulfidic environments, and may have also improved the tolerance of ancient counterparts of these cyanobacteria to sulfidic conditions in benthic communities that colonized the coastal margins in the Archean and the Proterozoic.}, }
@article {pmid31162610, year = {2019}, author = {Etienne-Mesmin, L and Chassaing, B and Desvaux, M and De Paepe, K and Gresse, R and Sauvaitre, T and Forano, E and de Wiele, TV and Schüller, S and Juge, N and Blanquet-Diot, S}, title = {Experimental models to study intestinal microbes-mucus interactions in health and disease.}, journal = {FEMS microbiology reviews}, volume = {43}, number = {5}, pages = {457-489}, doi = {10.1093/femsre/fuz013}, pmid = {31162610}, issn = {1574-6976}, support = {BBS/E/F/00044452/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/*physiology ; Homeostasis ; Host Microbial Interactions ; Humans ; In Vitro Techniques ; Intestinal Mucosa/microbiology ; Mice ; *Microbial Interactions ; Models, Animal ; Mucins/chemistry/metabolism ; Mucus/*microbiology ; Rats ; }, abstract = {A close symbiotic relationship exists between the intestinal microbiota and its host. A critical component of gut homeostasis is the presence of a mucus layer covering the gastrointestinal tract. Mucus is a viscoelastic gel at the interface between the luminal content and the host tissue that provides a habitat to the gut microbiota and protects the intestinal epithelium. The review starts by setting up the biological context underpinning the need for experimental models to study gut bacteria-mucus interactions in the digestive environment. We provide an overview of the structure and function of intestinal mucus and mucins, their interactions with intestinal bacteria (including commensal, probiotics and pathogenic microorganisms) and their role in modulating health and disease states. We then describe the characteristics and potentials of experimental models currently available to study the mechanisms underpinning the interaction of mucus with gut microbes, including in vitro, ex vivo and in vivo models. We then discuss the limitations and challenges facing this field of research.}, }
@article {pmid31161957, year = {2019}, author = {Ilgrande, C and Mastroleo, F and Christiaens, MER and Lindeboom, REF and Prat, D and Van Hoey, O and Ambrozova, I and Coninx, I and Heylen, W and Pommerening-Roser, A and Spieck, E and Boon, N and Vlaeminck, SE and Leys, N and Clauwaert, P}, title = {Reactivation of Microbial Strains and Synthetic Communities After a Spaceflight to the International Space Station: Corroborating the Feasibility of Essential Conversions in the MELiSSA Loop.}, journal = {Astrobiology}, volume = {19}, number = {9}, pages = {1167-1176}, doi = {10.1089/ast.2018.1973}, pmid = {31161957}, issn = {1557-8070}, mesh = {Autotrophic Processes ; Bacteria/*metabolism ; *Exobiology ; Feasibility Studies ; Microbial Viability ; Nitrification ; *Space Flight ; *Spacecraft ; Temperature ; Urea/metabolism ; }, abstract = {To sustain human deep space exploration or extra-terrestrial settlements where no resupply from the Earth or other planets is possible, technologies for in situ food production, water, air, and waste recovery need to be developed. The Micro-Ecological Life Support System Alternative (MELiSSA) is such a Regenerative Life Support System (RLSS) and it builds on several bacterial bioprocesses. However, alterations in gravity, temperature, and radiation associated with the space environment can affect survival and functionality of the microorganisms. In this study, representative strains of different carbon and nitrogen metabolisms with application in the MELiSSA were selected for launch and Low Earth Orbit (LEO) exposure. An edible photoautotrophic strain (Arthrospira sp. PCC 8005), a photoheterotrophic strain (Rhodospirillum rubrum S1H), a ureolytic heterotrophic strain (Cupriavidus pinatubonensis 1245), and combinations of C. pinatubonensis 1245 and autotrophic ammonia and nitrite oxidizing strains (Nitrosomonas europaea ATCC19718, Nitrosomonas ureae Nm10, and Nitrobacter winogradskyi Nb255) were sent to the International Space Station (ISS) for 7 days. There, the samples were exposed to 2.8 mGy, a dose 140 times higher than on the Earth, and a temperature of 22°C ± 1°C. On return to the Earth, the cultures were reactivated and their growth and activity were compared with terrestrial controls stored under refrigerated (5°C ± 2°C) or room temperature (22°C ± 1°C and 21°C ± 0°C) conditions. Overall, no difference was observed between terrestrial and ISS samples. Most cultures presented lower cell viability after the test, regardless of the type of exposure, indicating a harsher effect of the storage and sample preparation than the spaceflight itself. Postmission analysis revealed the successful survival and proliferation of all cultures except for Arthrospira, which suffered from the premission depressurization test. These observations validate the possibility of launching, storing, and reactivating bacteria with essential functionalities for microbial bioprocesses in RLSS.}, }
@article {pmid31161232, year = {2020}, author = {Mojica, KDA and Carlson, CA and Behrenfeld, MJ}, title = {Regulation of Low and High Nucleic Acid Fluorescent Heterotrophic Prokaryote Subpopulations and Links to Viral-Induced Mortality Within Natural Prokaryote-Virus Communities.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {213-230}, pmid = {31161232}, issn = {1432-184X}, support = {NNX15AF30G/NASA/NASA/United States ; 1537943//National Science Foundation/ ; }, mesh = {Archaea/chemistry/*genetics/metabolism/virology ; Bacteria/chemistry/*genetics/metabolism/virology ; Carbon/metabolism ; Flow Cytometry ; Fluorescence ; Heterotrophic Processes ; Host-Pathogen Interactions ; Nucleic Acids/chemistry/genetics ; Prokaryotic Cells/chemistry/*metabolism/*virology ; *Virus Physiological Phenomena ; Viruses/genetics/growth &amp; development ; }, abstract = {Flow cytometric analysis of marine prokaryotes routinely reveals two distinct clusters of heterotrophic cells referred to as high nucleic acid fluorescent (HNA) and low nucleic acid fluorescent (LNA) populations. Evidence suggests that these may represent physiologically and ecologically distinct prokaryote populations. According to the "kill the winner" hypothesis, viral lysis reduces the efficiency of the microbial loop by decreasing the biomass and activity of the most abundant and active members of a population (i.e., competition specialist). Thus, viral-induced mortality may vary according to the physiology of HNA and LNA cells, with implications for the marine carbon cycle. Here, the abundance and production of heterotrophic prokaryotic populations were assessed in the North Atlantic during two phases of the annual plankton cycle and related to bottom-up (i.e., organic carbon variability) and top-down processes (i.e., viral abundance and lytic production). Our results demonstrate that the relative abundance of HNA and LNA heterotrophic cells and heterotrophic prokaryote production vary according to organic carbon variability in the water column, which can be strongly influenced by the physical eddy field (i.e., type of eddy: cyclonic, anticyclonic, or no eddy). In addition, the abundance and lytic production of virus subpopulations were correlated with the cellular production and abundance of heterotrophic HNA and LNA prokaryote communities. Our data suggest group- and activity-specific linkages between hosts and viruses (i.e., HNA-V1 and LNA-V2). Specifically, V1 had a greater contribution to total viral production (i.e., 2.6-fold higher than V2 viruses), similar to their putative host. Finally, we explore potential implications of group- and activity-specific linkages between host and virus groups on the flux of carbon through the microbial food web.}, }
@article {pmid31159875, year = {2019}, author = {Wright, RJ and Gibson, MI and Christie-Oleza, JA}, title = {Understanding microbial community dynamics to improve optimal microbiome selection.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {85}, pmid = {31159875}, issn = {2049-2618}, mesh = {Bacteria/*classification/enzymology ; *Bacterial Physiological Phenomena ; Chitin/metabolism ; Chitinases/metabolism ; *Microbiota ; }, abstract = {BACKGROUND: Artificial selection of microbial communities that perform better at a desired process has seduced scientists for over a decade, but the method has not been systematically optimised nor the mechanisms behind its success, or failure, determined. Microbial communities are highly dynamic and, hence, go through distinct and rapid stages of community succession, but the consequent effect this may have on artificially selected communities is unknown.<br><br>RESULTS: Using chitin as a case study, we successfully selected for microbial communities with enhanced chitinase activities but found that continuous optimisation of incubation times between selective transfers was of utmost importance. The analysis of the community composition over the entire selection process revealed fundamental aspects in microbial ecology: when incubation times between transfers were optimal, the system was dominated by Gammaproteobacteria (i.e. main bearers of chitinase enzymes and drivers of chitin degradation), before being succeeded by cheating, cross-feeding and grazing organisms.<br><br>CONCLUSIONS: The selection of microbiomes to enhance a desired process is widely used, though the success of artificially selecting microbial communities appears to require optimal incubation times in order to avoid the loss of the desired trait as a consequence of an inevitable community succession. A comprehensive understanding of microbial community dynamics will improve the success of future community selection studies.}, }
@article {pmid31158321, year = {2019}, author = {Jaba, A and Dagher, F and Hamidi Oskouei, AM and Guertin, C and Constant, P}, title = {Physiological traits and relative abundance of species as explanatory variables of co-occurrence pattern of cultivable bacteria associated with chia seeds.}, journal = {Canadian journal of microbiology}, volume = {65}, number = {9}, pages = {668-680}, doi = {10.1139/cjm-2019-0052}, pmid = {31158321}, issn = {1480-3275}, mesh = {Bacteria/*classification/genetics ; *Bacterial Physiological Phenomena ; Fungi/classification/genetics/*physiology ; *Microbiota ; Phylogeny ; Salvia/*microbiology ; }, abstract = {Deciphering the rules defining microbial community assemblage is envisioned as a promising strategy to improve predictions of pathogens colonization and proliferation in food. Despite the increasing number of studies reporting microbial co-occurrence patterns, only a few attempts have been made to challenge them in experimental or theoretical frameworks. Here, we tested the hypothesis that observed variations in co-occurrence patterns can be explained by taxonomy, relative abundance, and physiological traits of microbial species. We used PCR amplicon sequencing of taxonomic markers to assess distribution and co-occurrence patterns of bacterial and fungal species found in 25 chia (Salvia hispanica L.) samples originating from eight different sources. The use of nutrient-rich and oligotrophic media enabled isolation of 71 strains encompassing 16 bacterial species, of which five corresponded to phylotypes represented in the molecular survey. Tolerance to different growth inhibitors and antibiotics was tested to assess the physiological traits of these isolates. Divergence of physiological traits and relative abundance of each pair of species explained 69% of the co-occurrence profile displayed by cultivable bacterial phylotypes in chia. Validation of this ecological network conceptualization approach to more food products is required to integrate microbial species co-occurrence patterns in predictive microbiology.}, }
@article {pmid31156569, year = {2019}, author = {Joyner, JL and Kerwin, J and Deeb, M and Lozefski, G and Prithiviraj, B and Paltseva, A and McLaughlin, J and Groffman, P and Cheng, Z and Muth, TR}, title = {Green Infrastructure Design Influences Communities of Urban Soil Bacteria.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {982}, pmid = {31156569}, issn = {1664-302X}, abstract = {The importance of natural ecosystem processes is often overlooked in urban areas. Green Infrastructure (GI) features have been constructed in urban areas as elements to capture and treat excess urban runoff while providing a range of ancillary benefits, e.g., ecosystem processes mediated by microorganisms that improve air and water quality, in addition to the associations with plant and tree rhizospheres. The objective of this study was to characterize the bacterial community and diversity in engineered soils (Technosols) of five types of GI in New York City; vegetated swales, right of way bioswales (ROWB; including street-side infiltration systems and enhanced tree pits), and an urban forest. The design of ROWB GI features directly connects with the road to manage street runoff, which can increase the Technosol saturation and exposure to urban contaminants washed from the street and carried into the GI feature. This GI design specifically accommodates dramatic pulses of water that influence the bacterial community composition and diversity through the selective pressure of contaminants or by disturbance. The ROWB had the highest biodiversity, but no significant correlation with levels of soil organic matter and microbially-mediated biogeochemical functions. Another important biogeochemical parameter for soil bacterial communities is pH, which influenced the bacterial community composition, consistent with studies in non-urban soils. Bacterial community composition in GI features showed signs of anthropogenic disturbance, including exposure to animal feces and chemical contaminants, such as petroleum products. Results suggest the overall design and management of GI features with a channeled connection with street runoff, such as ROWB, have a comprehensive effect on soil parameters (particularly organic matter) and the bacterial community. One key consideration for future assessments of GI microbial community would be to determine the source of organic matter and elucidate the relationship between vegetation, Technosol, and bacteria in the designed GI features.}, }
@article {pmid31154270, year = {2019}, author = {Yue, SJ and Liu, J and Wang, WX and Wang, AT and Yang, XY and Guan, HS and Wang, CY and Yan, D}, title = {Berberine treatment-emergent mild diarrhea associated with gut microbiota dysbiosis.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {116}, number = {}, pages = {109002}, doi = {10.1016/j.biopha.2019.109002}, pmid = {31154270}, issn = {1950-6007}, mesh = {Animals ; Berberine/*adverse effects ; Biodiversity ; Cecum/pathology ; Colon/drug effects/pathology/physiopathology ; Diarrhea/*chemically induced/*microbiology/physiopathology ; Dysbiosis/*complications/*microbiology/physiopathology ; Fatty Acids/metabolism ; Feces/chemistry ; *Gastrointestinal Microbiome/drug effects ; Gastrointestinal Transit/drug effects ; Male ; Organ Size ; Rats, Wistar ; Statistics, Nonparametric ; }, abstract = {Berberine (BBR) is a non-prescription drug to treat various bacteria-associated diarrheas. However, BBR has also been reported to cause diarrhea in clinic, with underlying mechanisms poorly understood. Because altered gut microbial ecology is a potential basis for diarrhea, this study was conducted to investigate the impact of BBR on gut microbiota of treatment-emergent diarrhea. BBR treatment (200 mg/kg, i.g.) in normal rats exhibited no significant changes in serum biochemical parameters but mild diarrhea occurred, accompanied with the decreased gastrointestinal transit time and increased fecal moisture, suggestive of the local effects of BBR in the intestine. Colon histology revealed the decreased abundance of mucus-filled goblet cells in BBR group. Although BBR-treated rats had the enlarged cecum with watery caecal digesta, short-chain fatty acids concentration was significantly lower than control group. Additionally, BBR caused gut microbiota dysbiosis by evaluating the decreased observed species number and Shannon index. BBR increased the relative abundances of families Porphyromonadaceae and Prevotellaceae as well as genera Parabacteroides, Prevotellaceae_UCG-001 and Prevotellaceae_NK3B31_group. Spearman's correlation analysis revealed family Prevotellaceae and genus Prevotellaceae_UCG-001 as the most prominent drivers of the BBR treatment-emergent diarrhea, correlating positively with fecal moisture but negatively with gastrointestinal transit time. This study therefore demonstrated that the treatment-emergent mild diarrhea of BBR was most likely due to the dysbiosis of the gut microbiota.}, }
@article {pmid31152013, year = {2019}, author = {Herlemann, DPR and Markert, S and Meeske, C and Andersson, AF and de Bruijn, I and Hentschker, C and Unfried, F and Becher, D and Jürgens, K and Schweder, T}, title = {Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {15}, pages = {}, pmid = {31152013}, issn = {1098-5336}, mesh = {Bacterial Load/statistics &amp; numerical data ; *Bacterial Physiological Phenomena ; Bacterial Proteins/*physiology ; Oceans and Seas ; *Proteome ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Salinity ; Seawater/*microbiology ; Sweden ; Time Factors ; }, abstract = {Enclosure experiments are frequently used to investigate the impact of changing environmental conditions on microbial assemblages. Yet, how the incubation itself challenges complex bacterial communities is thus far unknown. In this study, metaproteomic profiling, 16S rRNA gene analyses, and cell counts were combined to evaluate bacterial communities derived from marine, mesohaline, and oligohaline conditions after long-term batch incubations. Early in the experiment, the three bacterial communities were highly diverse and differed significantly in their compositions. Manipulation of the enclosures with terrigenous dissolved organic carbon resulted in notable differences compared to the control enclosures at this early phase of the experiment. However, after 55 days, bacterial communities in the manipulated and the control enclosures under marine and mesohaline conditions were all dominated by gammaproteobacterium Spongiibacter In the oligohaline enclosures, actinobacterial cluster I of the hgc group (hgc-I) remained abundant in the late phase of the incubation. Metaproteome analyses suggested that the ability to use outer membrane-based internal energy stores, in addition to the previously described grazing resistance, may enable the gammaproteobacterium Spongiibacter to prevail in long-time incubations. Under oligohaline conditions, the utilization of external recalcitrant carbon appeared to be more important (hgc-I). Enclosure experiments with complex natural microbial communities are important tools to investigate the effects of manipulations. However, species-specific properties, such as individual carbon storage strategies, can cause manipulation-independent effects and need to be considered when interpreting results from enclosures.IMPORTANCE In microbial ecology, enclosure studies are often used to investigate the effect of single environmental factors on complex bacterial communities. However, in addition to the manipulation, unintended effects ("bottle effect") may occur due to the enclosure itself. In this study, we analyzed the bacterial communities that originated from three different salinities of the Baltic Sea, comparing their compositions and physiological activities both at the early stage and after 55 days of incubation. Our results suggested that internal carbon storage strategies impact the success of certain bacterial species, independent of the experimental manipulation. Thus, while enclosure experiments remain valid tools in environmental research, microbial community composition shifts must be critically followed. This investigation of the metaproteome during long-term batch enclosures expanded our current understanding of the so-called "bottle effect," which is well known to occur during enclosure experiments.}, }
@article {pmid31150591, year = {2019}, author = {Gleason, ML and Zhang, R and Batzer, JC and Sun, G}, title = {Stealth Pathogens: The Sooty Blotch and Flyspeck Fungal Complex.}, journal = {Annual review of phytopathology}, volume = {57}, number = {}, pages = {135-164}, doi = {10.1146/annurev-phyto-082718-100237}, pmid = {31150591}, issn = {1545-2107}, mesh = {*Ascomycota ; Fruit ; *Malus ; Phylogeny ; Plant Diseases ; }, abstract = {Sooty blotch and flyspeck (SBFS) fungi produce superficial, dark-colored colonies on fruits, stems, and leaves of many plant genera. These blemishes are economically damaging on fruit, primarily apple and pear, because they reduce the sale price of fresh fruit. Fungicide spray programs can control SBFS but are costly and impair human and environmental health; thus, less chemically intensive management strategies are needed. Although the scientific study of SBFS fungi began nearly 200 years ago, recent DNA-driven studies revealed an unexpectedly diverse complex: more than 100 species in 30 genera of Ascomycota and Basidiomycota. Analysis of evolutionary phylogenetics and phylogenomics indicates that the evolution of SBFS fungi from plant-penetrating ancestors to noninvasive ectophytic parasites was accompanied by a massive contraction of pathogenicity-related genes, including plant cell wall-degrading enzymes and effectors, and an expansion of cuticle-degradation genes. This article reviews progress in understanding SBFS taxonomy and ecology and improving disease management. We also highlight recent breakthroughs in reconstructing the evolutionary origins of these unusual plant pathogens and delineating adaptations to their ectophytic niche.}, }
@article {pmid31147731, year = {2020}, author = {Arias, A and Saiz, E and Calbet, A}, title = {Towards an Understanding of Diel Feeding Rhythms in Marine Protists: Consequences of Light Manipulation.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {64-72}, pmid = {31147731}, issn = {1432-184X}, support = {FERMI (CGL2014-59227-R)//MINECO/FEDER, UE/ ; FPI (BES-2015-074092)//MINECO/ ; }, mesh = {Cell Division/radiation effects ; Ciliophora/*physiology/radiation effects ; Dinoflagellida/*physiology/radiation effects ; Heterotrophic Processes ; Light ; }, abstract = {Temporal programs synchronised with the daily cycle are of adaptive importance for organisms exposed to periodic fluctuations. This study deepens into several aspects of the exogenous and endogenous nature of microbial grazers. We investigated the diel rhythms of cell division and feeding activity of four marine protists under different light regimes. In particular, we tested if the feeding cycle of protistan grazers could be mediated by a light-aided enhancement of prey digestion, and also explored the consequences of cell division on diel feeding rhythms. Cell division occurred at night for the heterotrophic dinoflagellates Gyrodinium dominans and Oxyrrhis marina. In contrast, the mixotrophic dinoflagellate Karlodinium armiger and the ciliate Strombidium sp. mostly divided during the day. Additionally, a significant diurnal feeding rhythm was observed in all species. When exposed to continuous darkness, nearly all species maintained the cell division rhythm, but lost the feeding cycle within several hours/days (with the exception of O. marina that kept the rhythm for 9.5 days). Additional feeding experiments under continuous light also showed the same pattern. We conclude that the feeding rhythms of protistan grazers are generally regulated not by cell division nor by the enhancement of digestion by light. Our study, moreover, indicates that the cell division cycle is under endogenous control, whereas an external trigger is required to maintain the feeding rhythm, at least for most of the species studied here.}, }
@article {pmid31145076, year = {2019}, author = {Farfour, E and Henry, A and Razillard, A and Cardot, E and Limousin, L and Cahen, P and Jolly, E and Vasse, M and Mathonnet, D}, title = {Rapid identification of Escherichia coli colonies from clinical sample inoculated on CHROMagar Orientation media (Becton Dickinson).}, journal = {Annales de biologie clinique}, volume = {77}, number = {3}, pages = {350-352}, doi = {10.1684/abc.2019.1446}, pmid = {31145076}, issn = {1950-6112}, mesh = {Bacteriological Techniques/*methods ; Blood Culture/methods ; Chromogenic Compounds/*chemistry ; Culture Media/*chemistry ; Escherichia coli/*isolation &amp; purification ; Humans ; Microbial Sensitivity Tests ; Reproducibility of Results ; Sensitivity and Specificity ; }, abstract = {CHROMmagar Orientation media (Becton Dickinson) was developed and validated for the culture of urinary samples. It allows a direct identification of E. coli colonies without additional tests. As CHROMmagar Orientation media is superior to non-chromogenic media for the distinction of enterobacterial colonies, it is used for the inoculation of a large variety of samples in clinical laboratories. Direct identification of E. coli colonies cultured from these samples is not validated by the manufacturer. The difference in microbial ecology and the nature of the sample may impact CHROMagar Orientation performances for this use. We evaluated these media for the direct identification of E. coli colonies from 410 samples (excluding urine). Its sensitivity of 99% allows a direct identification of E. coli colonies cultured from a wide variety of samples. On-site testing using a large number of representative samples, allows laboratories to assess agar media performance and adapt their uses. Suppliers who are aware of frequent and non-recommended use of their culture media should perform tests and if conclusive, adapt their technical instructions.}, }
@article {pmid31144710, year = {2019}, author = {Villa-Rodriguez, JA and Ifie, I and Gonzalez-Aguilar, GA and Roopchand, DE}, title = {The Gastrointestinal Tract as Prime Site for Cardiometabolic Protection by Dietary Polyphenols.}, journal = {Advances in nutrition (Bethesda, Md.)}, volume = {10}, number = {6}, pages = {999-1011}, pmid = {31144710}, issn = {2156-5376}, support = {K01 AT008829/AT/NCCIH NIH HHS/United States ; R01 AT010242/AT/NCCIH NIH HHS/United States ; }, mesh = {AMP-Activated Protein Kinases/metabolism ; Cardiovascular Diseases/*prevention &amp; control ; *Diet ; Energy Metabolism ; Gastrointestinal Microbiome/drug effects/physiology ; Gastrointestinal Tract/*drug effects/metabolism/microbiology ; Glucagon-Like Peptide 1/metabolism ; Glucose/metabolism ; Humans ; Intestinal Absorption/drug effects ; Metabolic Diseases/*prevention &amp; control ; Polyphenols/*administration &amp; dosage ; }, abstract = {Substantial evidence from nutritional epidemiology links polyphenol-rich diets with reduced incidence of chronic disorders; however, biological mechanisms underlying polyphenol-disease relations remain enigmatic. Emerging evidence is beginning to unmask the contribution of the gastrointestinal tract on whole-body energy homeostasis, suggesting that the intestine may be a prime target for intervention and a fundamental site for the metabolic actions of polyphenols. During their transit through the gastrointestinal tract, polyphenols may activate enteric nutrient sensors ensuing appropriate responses from other peripheral organs to regulate metabolic homeostasis. Furthermore, polyphenols can modulate the absorption of glucose, attenuating exaggerated hormonal responses and metabolic imbalances. Polyphenols that escape absorption are metabolized by the gut microbiota and the resulting catabolites may act locally, activating nuclear receptors that control enteric functions such as intestinal permeability. Finally, polyphenols modulate gut microbial ecology, which can have profound effects on cardiometabolic health.}, }
@article {pmid31144004, year = {2020}, author = {Clairmont, LK and Slawson, RM}, title = {Contrasting Water Quality Treatments Result in Structural and Functional Changes to Wetland Plant-Associated Microbial Communities in Lab-Scale Mesocosms.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {50-63}, pmid = {31144004}, issn = {1432-184X}, support = {GR-RGPGP 2014-00060-R//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada/ ; 471103-2015, PGSD//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; *Microbiota ; Ontario ; Phalaris/*microbiology ; Rivers/*chemistry/*microbiology ; Veronica/*microbiology ; Water Pollutants, Chemical/chemistry/metabolism ; Water Purification ; Water Quality ; Wetlands ; }, abstract = {The impact of contrasting water quality treatments on wetland plant-associated microbial communities was investigated in this study using 12 lab-scale wetland mesocosms (subsurface flow design) planted with reed canary grass (Phalaris arundinacea) or water speedwell (Veronica anagallis-aquatica) over a 13-week period. Mesocosms received water collected from two sites along the Grand River (Ontario, Canada) designated as having either high or poor water quality according to Grand River Conservation Authority classifications. All mesocosms were established using sediment collected from the high water quality site and received water from this source pre-treatment. Resulting changes to microbial community structure were assessed using PCR-denaturing gel gradient electrophoresis (DGGE) on microbial 16S rDNA sequences extracted from rhizoplane, rhizosphere, and water samples before and after exposure to water quality treatments. Functional community changes were determined using Biolog™ EcoPlates which assess community-level carbon source utilization profiles. Wetland mesocosm removal of inorganic nutrients (N, P) and fecal coliforms was also determined, and compared among treatments. Treatment-specific effects were assessed using a repeated measures restricted maximum likelihood (REML) analysis. Structural and functional characteristics of rhizoplane microbial communities were significantly influenced by the interaction between plant species and water treatment (P = 0.04, P = 0.01). Plant species-specific effects were observed for rhizosphere structural diversity (P = 0.01) and wetland water community metabolic diversity (P = 0.03). The effect of water treatment alone was significant for structural diversity measurements in wetland water communities (P = 0.03). The effect of plant species, water quality treatment, and the interaction between the two is dependent on the microhabitat type (rhizoplane, rhizosphere, or water). Rhizoplane communities appear to be more sensitive to water quality-specific environmental changes and may be a good candidate for microbial community-based monitoring of wetland ecosystems.}, }
@article {pmid31144003, year = {2020}, author = {Han, D and Kang, HY and Kang, CK and Unno, T and Hur, HG}, title = {Seasonal Mixing-Driven System in Estuarine-Coastal Zone Triggers an Ecological Shift in Bacterial Assemblages Involved in Phytoplankton-Derived DMSP Degradation.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {12-20}, pmid = {31144003}, issn = {1432-184X}, support = {Long-term Marine Ecosystem Research//Ministry of Oceans and Fisheries/ ; NRF-2016R1A6A3A11931896//National Research Foundation of Korea/ ; }, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Estuaries ; Phylogeny ; Phytoplankton/chemistry/*metabolism ; Republic of Korea ; Seasons ; Seawater/chemistry/microbiology ; Sulfonium Compounds/*metabolism ; }, abstract = {The coastal zone has distinguishable but tightly connected ecosystems from rivers to the ocean and globally contributes to nutrient cycling including phytoplankton-derived organic matter. Particularly, bacterial contributions to phytoplankton-derived dimethylsulfoniopropionate (DMSP) degradation have been recently evaluated by using advanced sequencing technologies to understand their role in the marine microbial food web. Here, we surveyed the bacterial diversity and community composition under seasonal water mixing in the bay of Gwangyang (GW), a semi-enclosed estuary at the southern tip of the Korea Peninsula. We detected phylogenetic dissimilarities among season-specific habitats in GW and their specific bacterial taxa. Additionally, bacterial contribution to degradation of phytoplankton-derived DMSP from estuarine to coastal waters at euphotic depths in GW was investigated as the presence or absence of DMSP demethylation gene, encoded by dmdA. Among the operational taxonomic units (OTUs) in GW bacterial communities, the most dominant and ubiquitous OTU1 was affiliated with the SAR11 clade (SAR11-OTU). The population dynamics of SAR11-OTU in dmdA-detected GW waters suggest that water mass mixing plays a major role in shaping bacterial communities involved in phytoplankton-derived DMSP demethylation.}, }
@article {pmid31144002, year = {2020}, author = {Bittar, C and Machado, RRG and Comelis, MT and Bueno, LM and Beguelini, MR and Morielle-Versute, E and Nogueira, ML and Rahal, P}, title = {Alphacoronavirus Detection in Lungs, Liver, and Intestines of Bats from Brazil.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {203-212}, pmid = {31144002}, issn = {1432-184X}, support = {2015/09704-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 165802/2015-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Alphacoronavirus/classification/genetics/*isolation &amp; purification ; Animals ; Biological Evolution ; Brazil ; Chiroptera/*virology ; Genome, Viral ; Intestines/virology ; Liver/virology ; Lung/virology ; Phylogeny ; }, abstract = {Bats are flying mammals distributed worldwide known to host several types of Coronavirus (CoV). Since they were reported as the probable source of spillover of highly pathogenic CoV into the human population, investigating the circulation of this virus in bats around the world became of great importance. We analyzed samples from 103 bats from two distinct regions in Brazil. Coronavirus from the Alphacoronavirus genus was detected in 12 animals, 11 from São José do Rio Preto-SP region and 1 from Barreiras-BA region, resulting in a prevalence of 17.18% and 2.56% respectively. The virus was detected not only in intestines but also in lungs and liver. Phylogenetic analysis based on nsP12 genomic region suggests that the sequences group according to host family and sampling location. Studies on the circulation of these viruses in bats remain important to understand the ecology and evolutionary relationship of these pathogens.}, }
@article {pmid31143408, year = {2019}, author = {Conrads, G and Wendt, LK and Hetrodt, F and Deng, ZL and Pieper, D and Abdelbary, MMH and Barg, A and Wagner-Döbler, I and Apel, C}, title = {Deep sequencing of biofilm microbiomes on dental composite materials.}, journal = {Journal of oral microbiology}, volume = {11}, number = {1}, pages = {1617013}, pmid = {31143408}, issn = {2000-2297}, abstract = {Background: The microbiome on dental composites has not been studied in detail before. It has not been conclusively clarified whether restorative materials influence the oral microbiome. Methods: We used Illumina Miseq next-generation sequencing of the 16S V1-V2 region to compare the colonisation patterns of bovine enamel (BE) and the composite materials Grandio Flow (GF) and Grandio Blocs (GB) after 48 h in vivo in 14 volunteers. Applying a new method to maintain the oral microbiome ex vivo for 48 h also, we compared the microbiome on GF alone and with the new antimicrobial substance carolacton (GF+C). Results: All in vitro biofilm communities showed a higher diversity and richness than those grown in vivo but the very different atmospheric conditions must be considered. Contrary to expectations, there were only a few significant differences between BE and the composite materials GB and GF either in vivo or in vitro: Oribacterium, Peptostreptococcaceae [XI][G-1] and Streptococcus mutans were more prevalent and Megasphaera, Prevotella oulorum, Veillonella atypica, V. parvula, Gemella morbillorum, and Fusobacterium periodonticum were less prevalent on BE than on composites. In vivo, such preferences were only significant for Granulicatella adiacens (more prevalent on BE) and Fusobacterium nucleatum subsp. animalis (more prevalent on composites). On DNA sequence level, there were no significant differences between the biofilm communities on GF and GF+C. Conclusion: We found that the oral microbiome showed an increased richness when grown on various composites compared to BE in vitro, but otherwise changed only slightly independent of the in vivo or in vitro condition. Our new ex vivo biofilm model might be useful for pre-clinical testing of preventive strategies.}, }
@article {pmid31143165, year = {2019}, author = {Miller, JI and Techtmann, S and Fortney, J and Mahmoudi, N and Joyner, D and Liu, J and Olesen, S and Alm, E and Fernandez, A and Gardinali, P and GaraJayeva, N and Askerov, FS and Hazen, TC}, title = {Oil Hydrocarbon Degradation by Caspian Sea Microbial Communities.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {995}, pmid = {31143165}, issn = {1664-302X}, abstract = {The Caspian Sea, which is the largest landlocked body of water on the planet, receives substantial annual hydrocarbon input from anthropogenic sources (e.g., industry, agriculture, oil exploration, and extraction) and natural sources (e.g., mud volcanoes and oil seeps). The Caspian Sea also receives substantial amounts of runoff from agricultural and municipal sources, containing nutrients that have caused eutrophication and subsequent hypoxia in the deep, cold waters. The effect of decreasing oxygen saturation and cold temperatures on oil hydrocarbon biodegradation by a microbial community is not well characterized. The purpose of this study was to investigate the effect of oxic and anoxic conditions on oil hydrocarbon biodegradation at cold temperatures by microbial communities derived from the Caspian Sea. Water samples were collected from the Caspian Sea for study in experimental microcosms. Major taxonomic orders observed in the ambient water samples included Flavobacteriales, Actinomycetales, and Oceanospirillales. Microcosms were inoculated with microbial communities from the deepest waters and amended with oil hydrocarbons for 17 days. Hydrocarbon degradation and shifts in microbial community structure were measured. Surprisingly, oil hydrocarbon biodegradation under anoxic conditions exceeded that under oxic conditions; this was particularly evident in the degradation of aromatic hydrocarbons. Important microbial taxa associated with the anoxic microcosms included known oil degraders such as Oceanospirillaceae. This study provides knowledge about the ambient community structure of the Caspian Sea, which serves as an important reference point for future studies. Furthermore, this may be the first report in which anaerobic biodegradation of oil hydrocarbons exceeds aerobic biodegradation.}, }
@article {pmid31143163, year = {2019}, author = {Kuramae, EE and Leite, MFA and Suleiman, AKA and Gough, CM and Castillo, BT and Faller, L and Franklin, RB and Syring, J}, title = {Wood Decay Characteristics and Interspecific Interactions Control Bacterial Community Succession in Populus grandidentata (Bigtooth Aspen).}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {979}, pmid = {31143163}, issn = {1664-302X}, abstract = {Few studies have investigated bacterial community succession and the role of bacterial decomposition over a continuum of wood decay. Here, we identified how (i) the diversity and abundance of bacteria changed along a chronosequence of decay in Populus grandidentata (bigtooth aspen); (ii) bacterial community succession was dependent on the physical and chemical characteristics of the wood; (iii) interspecific bacterial interactions may mediate community structure. Four hundred and fifty-nine taxa were identified through Illumina sequencing of 16S rRNA amplicons from samples taken along a continuum of decay, representing standing dead trees, downed wood, and soil. Community diversity increased as decomposition progressed, peaking in the most decomposed trees. While a small proportion of taxa displayed a significant pattern in regards to decay status of the host log, many bacterial taxa followed a stochastic distribution. Changes in the water availability and chemical composition of standing dead and downed trees and soil were strongly coupled with shifts in bacterial communities. Nitrogen was a major driver of succession and nitrogen-fixing taxa of the order Rhizobiales were abundant early in decomposition. Recently downed logs shared 65% of their bacterial abundance with the microbiomes of standing dead trees while only sharing 16% with soil. As decay proceeds, bacterial communities appear to respond less to shifting resource availability and more to interspecific bacterial interactions - we report an increase in both the proportion (+9.3%) and the intensity (+62.3%) of interspecific interactions in later stages of decomposition, suggesting the emergence of a more complex community structure as wood decay progresses.}, }
@article {pmid31139578, year = {2019}, author = {Castillo, DJ and Rifkin, RF and Cowan, DA and Potgieter, M}, title = {The Healthy Human Blood Microbiome: Fact or Fiction?.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {148}, pmid = {31139578}, issn = {2235-2988}, mesh = {Bacteria/*classification/genetics ; Blood/*microbiology ; Blood-Borne Pathogens/classification ; Dysbiosis ; Humans ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The blood that flows perpetually through our veins and arteries performs numerous functions essential to our survival. Besides distributing oxygen, this vast circulatory system facilitates nutrient transport, deters infection and dispenses heat throughout our bodies. Since human blood has traditionally been considered to be an entirely sterile environment, comprising only blood-cells, platelets and plasma, the detection of microbes in blood was consistently interpreted as an indication of infection. However, although a contentious concept, evidence for the existence of a healthy human blood-microbiome is steadily accumulating. While the origins, identities and functions of these unanticipated micro-organisms remain to be elucidated, information on blood-borne microbial phylogeny is gradually increasing. Given recent advances in microbial-hematology, we review current literature concerning the composition and origin of the human blood-microbiome, focusing on bacteria and their role in the configuration of both the diseased and healthy human blood-microbiomes. Specifically, we explore the ways in which dysbiosis in the supposedly innocuous blood-borne bacterial microbiome may stimulate pathogenesis. In addition to exploring the relationship between blood-borne bacteria and the development of complex disorders, we also address the matter of contamination, citing the influence of contaminants on the interpretation of blood-derived microbial datasets and urging the routine analysis of laboratory controls to ascertain the taxonomic and metabolic characteristics of environmentally-derived contaminant-taxa.}, }
@article {pmid31139170, year = {2019}, author = {León-Sobrino, C and Ramond, JB and Maggs-Kölling, G and Cowan, DA}, title = {Nutrient Acquisition, Rather Than Stress Response Over Diel Cycles, Drives Microbial Transcription in a Hyper-Arid Namib Desert Soil.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1054}, pmid = {31139170}, issn = {1664-302X}, abstract = {Hot desert surface soils are characterized by extremely low water activities for large parts of any annual cycle. It is widely assumed that microbial processes in such soils are very limited. Here we present the first metatranscriptomic survey of microbial community function in a low water activity hyperarid desert soil. Sequencing of total mRNA revealed a diverse and active community, dominated by Actinobacteria. Metatranscriptomic analysis of samples taken at different times over 3 days indicated that functional diel variations were limited at the whole community level, and mostly affected the eukaryotic subpopulation which was induced during the cooler night hours. High levels of transcription of chemoautotrophic carbon fixation genes contrasted with limited expression of photosynthetic genes, indicating that chemoautotrophy is an important alternative to photosynthesis for carbon cycling in desiccated desert soils. Analysis of the transcriptional levels of key N-cycling genes provided strong evidence that soil nitrate was the dominant nitrogen input source. Transcriptional network analyses and taxon-resolved functional profiling suggested that nutrient acquisition processes, and not diurnal environmental variation, were the main drivers of community activity in hyperarid Namib Desert soil. While we also observed significant levels of expression of common stress response genes, these genes were not dominant hubs in the co-occurrence network.}, }
@article {pmid31138723, year = {2019}, author = {Emerson, JB}, title = {Soil Viruses: A New Hope.}, journal = {mSystems}, volume = {4}, number = {3}, pages = {}, pmid = {31138723}, issn = {2379-5077}, abstract = {As abundant members of microbial communities, viruses impact microbial mortality, carbon and nutrient cycling, and food web dynamics. Although most of our information about viral communities comes from marine systems, evidence is mounting to suggest that viruses are similarly important in soil. Here I outline soil viral metagenomic approaches and the current state of soil viral ecology as a field, and then I highlight existing knowledge gaps that we can begin to fill. We are poised to elucidate soil viral contributions to terrestrial ecosystem processes, considering: the full suite of potential hosts across trophic scales, the ecological impacts of different viral replication strategies, links to economically relevant outcomes like crop productivity, and measurable in situ virus-host population dynamics across spatiotemporal scales and environmental conditions. Soon, we will learn how soil viruses contribute to food webs linked to organic matter decomposition, carbon and nutrient cycling, greenhouse gas emissions, and agricultural productivity.}, }
@article {pmid31138673, year = {2019}, author = {Benítez-Páez, A and Kjølbæk, L and Gómez Del Pulgar, EM and Brahe, LK and Astrup, A and Matysik, S and Schött, HF and Krautbauer, S and Liebisch, G and Boberska, J and Claus, S and Rampelli, S and Brigidi, P and Larsen, LH and Sanz, Y}, title = {A Multi-omics Approach to Unraveling the Microbiome-Mediated Effects of Arabinoxylan Oligosaccharides in Overweight Humans.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, pmid = {31138673}, issn = {2379-5077}, abstract = {Long-term consumption of dietary fiber is generally considered beneficial for weight management and metabolic health, but the results of interventions vary greatly depending on the type of dietary fibers involved. This study provides a comprehensive evaluation of the effects of a specific dietary fiber consisting of a wheat-bran extract enriched in arabinoxylan-oligosaccharides (AXOS) in a human intervention trial. An integrated multi-omics analysis has been carried out to evaluate the effects of an intervention trial with an AXOS-enriched diet in overweight individuals with indices of metabolic syndrome. Microbiome analyses were performed by shotgun DNA sequencing in feces; in-depth metabolomics using nuclear magnetic resonance in fecal, urine, and plasma samples; and massive lipid profiling using mass spectrometry in fecal and serum/plasma samples. In addition to their bifidogenic effect, we observed that AXOS boost the proportion of Prevotella species. Metagenome analysis showed increases in the presence of bacterial genes involved in vitamin/cofactor production, glycan metabolism, and neurotransmitter biosynthesis as a result of AXOS intake. Furthermore, lipidomics analysis revealed reductions in plasma ceramide levels. Finally, we observed associations between Prevotella abundance and short-chain fatty acids (SCFAs) and succinate concentration in feces and identified a potential protective role of Eubacterium rectale against metabolic disease given that its abundance was positively associated with plasma phosphatidylcholine levels, thus hypothetically reducing bioavailability of choline for methylamine biosynthesis. The metagenomics, lipidomics, and metabolomics data integration indicates that sustained consumption of AXOS orchestrates a wide variety of changes in the gut microbiome and the host metabolism that collectively would impact on glucose homeostasis. (This study has been registered at ClinicalTrials.gov under identifier NCT02215343)IMPORTANCE The use of dietary fiber food supplementation as a strategy to reduce the burden of diet-related diseases is a matter of study given its cost-effectiveness and the positive results demonstrated in clinical trials. This multi-omics assessment, on different biological samples of overweight subjects with signs of metabolic syndrome, sheds light on the early and less evident effects of short-term AXOS intake on intestinal microbiota and host metabolism. We observed a deep influence of AXOS on gut microbiota beyond their recognized bifidogenic effect by boosting concomitantly a wide diversity of butyrate producers and Prevotella copri, a microbial species abundant in non-Westernized populations with traditional lifestyle and diets enriched in fresh unprocessed foods. A comprehensive evaluation of hundreds of metabolites unveiled new benefits of the AXOS intake, such as reducing the plasma ceramide levels. Globally, we observed that multiple effects of AXOS consumption seem to converge in reversing the glucose homeostasis impairment.}, }
@article {pmid31132623, year = {2019}, author = {Liu, L and Wu, L and Knauth, S and Eickhorst, T}, title = {Degradation of transgenic Bt-rice straw incorporated with two different paddy soils.}, journal = {Journal of environmental management}, volume = {244}, number = {}, pages = {415-421}, doi = {10.1016/j.jenvman.2019.05.075}, pmid = {31132623}, issn = {1095-8630}, mesh = {Bacteria ; *Oryza ; *Soil ; Soil Microbiology ; }, abstract = {Transgenic Bt-rice is rice that has been genetically modified to produce insecticidal proteins (Cry1Ab/Ac) within the plant. Rice straw is incorporated into paddy soils after harvest for fertilization or to improve the soil structure. The incorporation of straw from transgenic Bt-rice may pose risks to the paddy soil system. The decomposition of Bt-rice straw and degradation of Cry1Ab/Ac proteins from the straw were investigated under laboratory conditions. In addition, effects of the incorporation with chopped rice straw on microbial communities in differently textured paddy soils were studied. The results indicated that the incorporation of straw from transgenic Bt-rice might have a slight influence on soil respiration and CH4 emissions in two paddy soils, i.e. the Silt Loam soil and the Silty Clay soil. Differences were also observed in the cumulative emissions of CO2 between the two amended paddy soils in addition to the well-known increase in emissions of both CO2 and CH4 due to straw incorporation. The Cry1Ab/Ac proteins from straw of transgenic Bt-rice were degraded in paddy soils. The rate of decline in the concentration of Cry1Ab/Ac proteins was different in the two soils. After 29 d of incubation, 61% and 42% of initial Cry1Ab/Ac proteins were detected in the silt loam and silty clay, respectively. As a result of the presence of the rice straw, the abundance of bacteria, archaea, and total cells were increased in two soils. The numbers of bacteria and total cells were 6.4% and 11.5% higher in the silt loam amended with straw of Bt-rice than non-Bt-rice, respectively. The silty clay displayed a similar trend as the silt loam.}, }
@article {pmid31130935, year = {2019}, author = {Cramm, MA and Chakraborty, A and Li, C and Ruff, SE and Jørgensen, BB and Hubert, CRJ}, title = {Freezing Tolerance of Thermophilic Bacterial Endospores in Marine Sediments.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {945}, pmid = {31130935}, issn = {1664-302X}, abstract = {Dormant endospores of anaerobic, thermophilic bacteria found in cold marine sediments offer a useful model for studying microbial biogeography, dispersal, and survival. The dormant endospore phenotype confers resistance to unfavorable environmental conditions, allowing dispersal to be isolated and studied independently of other factors such as environmental selection. To study the resilience of thermospores to conditions relevant for survival in extreme cold conditions, their viability following different freezing treatments was tested. Marine sediment was frozen at either -80°C or -20°C for 10 days prior to pasteurization and incubation at +50°C for 21 days to assess thermospore viability. Sulfate reduction commenced at +50°C following both freezing pretreatments indicating persistence of thermophilic endospores of sulfate-reducing bacteria. The onset of sulfate reduction at +50°C was delayed in -80°C pretreated microcosms, which exhibited more variability between triplicates, compared to -20°C pretreated microcosms and parallel controls that were not frozen in advance. Microbial communities were evaluated by 16S rRNA gene amplicon sequencing, revealing an increase in the relative sequence abundance of thermophilic endospore-forming Firmicutes in all microcosms. Different freezing pretreatments (-80°C and -20°C) did not appreciably influence the shift in overall bacterial community composition that occurred during the +50°C incubations. Communities that had been frozen prior to +50°C incubation showed an increase in the relative sequence abundance of operational taxonomic units (OTUs) affiliated with the class Bacilli, relative to unfrozen controls. These results show that freezing impacts but does not obliterate thermospore populations and their ability to germinate and grow under appropriate conditions. Indeed the majority of the thermospore OTUs detected in this study (21 of 22) could be observed following one or both freezing treatments. These results are important for assessing thermospore viability in frozen samples and following cold exposure such as the very low temperatures that would be encountered during panspermia.}, }
@article {pmid31129882, year = {2019}, author = {Huh, YJ and Seo, JY and Nam, J and Yang, J and McDowell, A and Kim, YK and Lee, JH}, title = {Bariatric/Metabolic Surgery Induces Noticeable Changes of Microbiota and Their Secreting Extracellular Vesicle Composition in the Gut.}, journal = {Obesity surgery}, volume = {29}, number = {8}, pages = {2470-2484}, pmid = {31129882}, issn = {1708-0428}, mesh = {Animals ; Bacteria/classification/isolation &amp; purification ; Bacterial Typing Techniques ; Bariatric Surgery/*methods ; Diabetes Mellitus, Experimental/metabolism/microbiology/*surgery ; Diabetes Mellitus, Type 2/metabolism/microbiology/surgery ; Diet, High-Fat ; Extracellular Vesicles/*metabolism ; Feces/microbiology ; Gastrectomy ; Gastric Bypass ; *Gastrointestinal Microbiome ; Male ; Metagenomics/methods ; Obesity/metabolism/microbiology/*surgery ; Postoperative Period ; Rats ; Rats, Wistar ; }, abstract = {INTRODUCTION: Microbial ecology is reported to be an important regulator of energy homeostasis and glucose metabolism. Microbes secrete extracellular vesicles (EVs) during their proliferation and death to communicate with other cells. To investigate the roles of gut microbiota in glucose metabolism, we analyzed serial changes of gut microbe and microbial EV composition before and after bariatric/metabolic surgery (BMS).<br><br>METHODS: Twenty-eight Wistar rats were fed on high-fat diet (HFD) to induce obesity and diabetes. Five of them compared with 5 rats fed on regular chow diet (RCD). Among the remaining 23 rats, Roux-en-Y gastric bypass (RYGB) (n&#x2009;=&#x2009;10), sleeve gastrectomy (SG) (n&#x2009;=&#x2009;10), or sham operation (n&#x2009;=&#x2009;3) was randomly performed. Gut microbiota and EVs from fecal samples were analyzed by 16S rDNA amplicon sequencing.<br><br>RESULTS: The present study showed that microbial diversity was decreased in HFD-fed rats versus RCD-fed rats. In addition, BMS reversed glucose intolerance and microbial richness which were induced by HFD. In terms of microbiota and microbial EV composition, both RYGB and SG enhance the composition of phyla Proteobacteria, Verrucomicrobia, and their secreting EVs, but decrease phylum Firmicutes and its EVs. We tried to demonstrate specific genera showed a significant compositional difference in obesity/diabetes-induced rats compared with normal rats and then restored similarly toward normal rats' level after BMS. At the genus level, Lactococcus, Ruminococcus, Dorea in Firmicutes(p), Psychrobacter in Proteobacteria(p), and Akkermansia in Verrucomicrobia(p) fit these conditions after BMS.<br><br>CONCLUSION: We suggest that these genera are the candidates contributing to obesity and diabetes improvement mechanism after BMS.}, }
@article {pmid31129376, year = {2019}, author = {Meng, Y and Zhou, Z and Meng, F}, title = {Impacts of diel temperature variations on nitrogen removal and metacommunity of anammox biofilm reactors.}, journal = {Water research}, volume = {160}, number = {}, pages = {1-9}, doi = {10.1016/j.watres.2019.05.021}, pmid = {31129376}, issn = {1879-2448}, mesh = {Anaerobiosis ; Biofilms ; Bioreactors ; *Denitrification ; Ecosystem ; *Nitrogen ; Oxidation-Reduction ; RNA, Ribosomal, 16S ; Temperature ; }, abstract = {The influence of diel temperature variations (DTVs) on nitrogen removal and bacterial communities was investigated in two parallel anammox reactors (i.e., control and DTV reactors). The control reactor was operated at a constant temperature of 30 °C, whereas the DTV reactor was operated in a temperature fluctuation mode with a cycle of 12/12 h of high/low temperatures. Nine water temperature variations for the day/night periods were set from 30/30 °C (i.e., Δ0 °C) to 38/22 °C (i.e., Δ16 °C). An increase in DTVs from Δ8 °C (34/26 °C) to Δ16 °C (38/22 °C) caused a significant decline in reactor performance and a shift in bacterial diversity. Compared to the control reactor, for instance, nitrogen removal efficiency decreased (P < 0.05) when temperature fluctuations exceeded Δ8 °C in the DTV reactor with a decreasing ΔNO3[-]/ΔNH4[+] ratio (from 0.21 ± 0.15 to 0.16 ± 0.04). The results of 16S rRNA gene sequencing showed that the initial disturbance of temperature variations led to increased levels of bacterial diversity (i.e., alpha diversity) and decreased community levels of anammox consortia whereas they slightly recovered at the end of each DTV phase. Notably, Candidatus Jettenia was more sensitive to strong water temperature fluctuations, with the lower relative abundance at Δ14 °C (17.11 ± 5.01%) and Δ16 °C (17.83 ± 7.22%) than at Δ4 °C (39.82 ± 0.01%). In contrast, Ca. Brocadia and Ca. Kuenenia had higher relative abundance at Δ14 °C (i.e., 0.24 ± 0.07% and 0.09 ± 0.02%, respectively) and Δ16 °C (i.e., 0.28 ± 0.05% and 0.12 ± 0.03%, respectively) compared to that at Δ4 °C (i.e., 0.15 ± 0.04% and 0.04 ± 0.01%, respectively). Nitrifiers (i.e., unidentified_Nitrospiraceae and Nitrosomonas) and denitrifiers (i.e., Denitratisoma) were also capable of tolerating high temperature perturbations. Overall this study furthers our knowledge of responses of the microbial ecology of anammox bacteria to DTVs in anammox processes, which could aid us in optimizing anammox-related wastewater treatment systems and in understanding the nitrogen cycles of natural ecosystems.}, }
@article {pmid31128471, year = {2019}, author = {Tsao, HF and Scheikl, U and Herbold, C and Indra, A and Walochnik, J and Horn, M}, title = {The cooling tower water microbiota: Seasonal dynamics and co-occurrence of bacterial and protist phylotypes.}, journal = {Water research}, volume = {159}, number = {}, pages = {464-479}, pmid = {31128471}, issn = {1879-2448}, support = {TRP 209/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Humans ; *Legionella ; *Legionnaires' Disease ; *Microbiota ; Seasons ; Water ; Water Microbiology ; }, abstract = {Cooling towers for heating, ventilation and air conditioning are ubiquitous in the built environment. Often located on rooftops, their semi-open water basins provide a suitable environment for microbial growth. They are recognized as a potential source of bacterial pathogens and have been associated with disease outbreaks such as Legionnaires' disease. While measures to minimize public health risks are in place, the general microbial and protist community structure and dynamics in these systems remain largely elusive. In this study, we analysed the microbiome of the bulk water from the basins of three cooling towers by 16S and 18S rRNA gene amplicon sequencing over the course of one year. Bacterial diversity in all three towers was broadly comparable to other freshwater systems, yet less diverse than natural environments; the most abundant taxa are also frequently found in freshwater or drinking water. While each cooling tower had a pronounced site-specific microbial community, taxa shared among all locations mainly included groups generally associated with biofilm formation. We also detected several groups related to known opportunistic pathogens, such as Legionella, Mycobacterium, and Pseudomonas species, albeit at generally low abundance. Although cooling towers represent a rather stable environment, microbial community composition was highly dynamic and subject to seasonal change. Protists are important members of the cooling tower water microbiome and known reservoirs for bacterial pathogens. Co-occurrence analysis of bacteria and protist taxa successfully captured known interactions between amoeba-associated bacteria and their hosts, and predicted a large number of additional relationships involving ciliates and other protists. Together, this study provides an unbiased and comprehensive overview of microbial diversity of cooling tower water basins, establishing a framework for investigating and assessing public health risks associated with these man-made freshwater environments.}, }
@article {pmid31125804, year = {2019}, author = {Zhou, LJ and Han, P and Yu, Y and Wang, B and Men, Y and Wagner, M and Wu, QL}, title = {Cometabolic biotransformation and microbial-mediated abiotic transformation of sulfonamides by three ammonia oxidizers.}, journal = {Water research}, volume = {159}, number = {}, pages = {444-453}, doi = {10.1016/j.watres.2019.05.031}, pmid = {31125804}, issn = {1879-2448}, mesh = {*Ammonia ; Archaea ; Biotransformation ; *Nitrification ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; Sulfonamides ; }, abstract = {The abilities of three phylogenetically distant ammonia oxidizers, Nitrososphaera gargensis, an ammonia-oxidizing archaeon (AOA); Nitrosomomas nitrosa Nm90, an ammonia-oxidizing bacterium (AOB); and Nitrospira inopinata, the only complete ammonia oxidizer (comammox) available as a pure culture, to biotransform seven sulfonamides (SAs) were investigated. The removals and protein-normalized biotransformation rate constants indicated that the AOA strain N. gargensis exhibited the highest SA biotransformation rates, followed by N. inopinata and N. nitrosa Nm90. The transformation products (TPs) of sulfadiazine (SDZ), sulfamethazine (SMZ) and sulfamethoxazole (SMX) and the biotransformation mechanisms were evaluated. Based on the analysis of the TP formulas and approximate structures, it was found that during biotransformation, i) the AOA strain carried out SA deamination, hydroxylation, and nitration; ii) the AOB strain mainly performed SA deamination; and iii) the comammox isolate participated only in deamination reactions. It is proposed that deamination was catalyzed by deaminases while hydroxylation and nitration were mediated by nonspecific activities of the ammonia monooxygenase (AMO). Additionally, it was demonstrated that among the three ammonia oxidizers, only AOB contributed to the formation of pterin-SA conjugates. The biotransformation of SDZ, SMZ and SMX occurred only when ammonia oxidation was active, suggesting a cometabolic transformation mechanism. Interestingly, SAs could also be transformed by hydroxylamine, an intermediate of ammonia oxidation, suggesting that in addition to enzymatic conversions, a microbially induced abiotic mechanism contributes to SA transformation during ammonia oxidation. Overall, using experiments with pure cultures, this study provides important insights into the roles played by ammonia oxidizers in SA biotransformation.}, }
@article {pmid31120557, year = {2019}, author = {Dove, NC and Stark, JM and Newman, GS and Hart, SC}, title = {Carbon control on terrestrial ecosystem function across contrasting site productivities: the carbon connection revisited.}, journal = {Ecology}, volume = {100}, number = {7}, pages = {e02695}, doi = {10.1002/ecy.2695}, pmid = {31120557}, issn = {1939-9170}, support = {92-37101-7976//U.S. Department of Agriculture Co-operative State Research Service/International ; }, mesh = {Biomass ; *Carbon ; *Ecosystem ; Nitrogen ; Oregon ; Soil ; Soil Microbiology ; }, abstract = {Understanding how altered soil organic carbon (SOC) availability affects microbial communities and their function is imperative in predicting impacts of global change on soil carbon (C) storage and ecosystem function. However, the response of soil microbial communities and their function to depleted C availability in situ is unclear. We evaluated the role of soil C inputs in controlling microbial biomass, community composition, physiology, and function by (1) experimentally excluding plant C inputs in situ for 9 yr in four temperate forest ecosystems along a productivity gradient in Oregon, USA; and (2) integrating these findings with published data from similar C-exclusion studies into a global meta-analysis. Excluding plant C inputs for 9 yr resulted in a 13% decrease in SOC across the four Oregon sites and an overall shift in the microbial community composition, with a 45% decrease in the fungal : bacterial ratio and a 13% increase in Gram-positive : Gram-negative bacterial ratio. Although gross N mineralization decreased under C exclusion, decreases in gross N immobilization were greater, resulting in increased net N mineralization rates in all but the lowest-productivity site. Microbial biomass showed a variable response to C exclusion that was method dependent; however, we detected a 29% decrease in C-use efficiency across the sites, with greater declines occurring in less-productive sites. Although extracellular enzyme activity increased with C exclusion, C exclusion resulted in a 31% decrease in microbial respiration across all sites. Our meta-analyses of published data with similar C-exclusion treatments were largely consistent with our experimental results, showing decreased SOC, fungal : bacterial ratios, and microbial respiration, and increased Gram-positive : Gram-negative bacterial ratio following exclusion of C inputs to soil. Effect sizes of SOC and respiration correlated negatively with the duration of C exclusion; however, there were immediate effects of C exclusion on microbial community composition and biomass that were unaltered by duration of treatment. Our field-based experimental results and analyses demonstrate unequivocally the dominant control of C availability on soil microbial biomass, community composition, and function, and provide additional insight into the mechanisms for these effects in forest ecosystems.}, }
@article {pmid31119088, year = {2019}, author = {Roux, S and Trubl, G and Goudeau, D and Nath, N and Couradeau, E and Ahlgren, NA and Zhan, Y and Marsan, D and Chen, F and Fuhrman, JA and Northen, TR and Sullivan, MB and Rich, VI and Malmstrom, RR and Eloe-Fadrosh, EA}, title = {Optimizing de novo genome assembly from PCR-amplified metagenomes.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6902}, pmid = {31119088}, issn = {2167-8359}, abstract = {BACKGROUND: Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes.<br><br>METHODS: Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs &#x2265; 10 kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes.<br><br>RESULTS: Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs &#x2265;10 kb by 10 to 100-fold for low input metagenomes.<br><br>CONCLUSIONS: PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.}, }
@article {pmid31118299, year = {2019}, author = {Sze, MA and Schloss, PD}, title = {The Impact of DNA Polymerase and Number of Rounds of Amplification in PCR on 16S rRNA Gene Sequence Data.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, pmid = {31118299}, issn = {2379-5042}, support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; R01 CA215574/CA/NCI NIH HHS/United States ; UL1 TR002240/TR/NCATS NIH HHS/United States ; }, mesh = {Bacteria/genetics ; DNA, Bacterial/genetics ; DNA-Directed DNA Polymerase/genetics/*standards ; Feces/microbiology ; Humans ; *Microbiota ; Polymerase Chain Reaction/methods/*standards ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*standards ; }, abstract = {PCR amplification of 16S rRNA genes is a critical yet underappreciated step in the generation of sequence data to describe the taxonomic composition of microbial communities. Numerous factors in the design of PCR can impact the sequencing error rate, the abundance of chimeric sequences, and the degree to which the fragments in the product represent their abundance in the original sample (i.e., bias). We compared the performance of high fidelity polymerases and various numbers of rounds of amplification when amplifying a mock community and human stool samples. Although it was impossible to derive specific recommendations, we did observe general trends. Namely, using a polymerase with the highest possible fidelity and minimizing the number of rounds of PCR reduced the sequencing error rate, fraction of chimeric sequences, and bias. Evidence of bias at the sequence level was subtle and could not be ascribed to the fragments' fraction of bases that were guanines or cytosines. When analyzing mock community data, the amount that the community deviated from the expected composition increased with the number of rounds of PCR. This bias was inconsistent for human stool samples. Overall, the results underscore the difficulty of comparing sequence data that are generated by different PCR protocols. However, the results indicate that the variation in human stool samples is generally larger than that introduced by the choice of polymerase or number of rounds of PCR.IMPORTANCE A steep decline in sequencing costs drove an explosion in studies characterizing microbial communities from diverse environments. Although a significant amount of effort has gone into understanding the error profiles of DNA sequencers, little has been done to understand the downstream effects of the PCR amplification protocol. We quantified the effects of the choice of polymerase and number of PCR cycles on the quality of downstream data. We found that these choices can have a profound impact on the way that a microbial community is represented in the sequence data. The effects are relatively small compared to the variation in human stool samples; however, care should be taken to use polymerases with the highest possible fidelity and to minimize the number of rounds of PCR. These results also underscore that it is not possible to directly compare sequence data generated under different PCR conditions.}, }
@article {pmid31117021, year = {2019}, author = {Beinart, RA}, title = {The Significance of Microbial Symbionts in Ecosystem Processes.}, journal = {mSystems}, volume = {4}, number = {3}, pages = {}, pmid = {31117021}, issn = {2379-5077}, abstract = {It is increasingly accepted that the microbial symbionts of eukaryotes can have profound effects on host ecology and evolution. However, the relative contribution that they make directly to ecosystem processes, like energy and nutrient flows, is less explicitly acknowledged and, in many cases, only poorly constrained. Here, I explore the idea that, in some habitats, host-associated microbes may have an outsized role in ecosystem processes relative to functionally equivalent free-living microbes due to key aspects of the physiology, ecology, and evolution of symbiotic interactions. My research quantifying symbiont metabolism has shown that microbial symbionts have the potential to make a substantial impact on carbon and sulfur cycling. It is my perspective that direct measurement of symbiont activity and comparison to free-living counterparts will expand our understanding of the significance of microbial symbioses and, more broadly, the role of microbial processes in ecosystems.}, }
@article {pmid31114556, year = {2019}, author = {Hounmanou, YMG and Leekitcharoenphon, P and Hendriksen, RS and Dougnon, TV and Mdegela, RH and Olsen, JE and Dalsgaard, A}, title = {Surveillance and Genomics of Toxigenic Vibrio cholerae O1 From Fish, Phytoplankton and Water in Lake Victoria, Tanzania.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {901}, pmid = {31114556}, issn = {1664-302X}, abstract = {The occurrence of toxigenic Vibrio cholerae O1 during a non- outbreak period in Lake Victoria was studied and genetic characteristics for environmental persistence and relatedness to pandemic strains were assessed. We analyzed 360 samples of carps, phytoplankton and water collected in 2017 during dry and rainy seasons in the Tanzanian basin of Lake Victoria. Samples were tested using PCR (ompW and ctxA) with DNA extracted from bacterial isolates and samples enriched in alkaline peptone water. Isolates were screened with polyvalent antiserum O1 followed by antimicrobial susceptibility testing. Whole genome sequencing and bioinformatics tools were employed to investigate the genomic characteristics of the isolates. More V. cholerae positive samples were recovered by PCR when DNA was obtained from enriched samples than from isolates (69.0% vs. 21.3%, p < 0.05), irrespectively of season. We identified ten V. cholerae O1 among 22 ctxA-positive isolates. Further studies are needed to serotype the remaining ctxA-positive non-O1 strains. Sequenced strains belonged to El Tor atypical biotype of V. cholerae O1 of MLST ST69 harboring the seventh pandemic gene. Major virulence genes, ctxA, ctxB, zot, ace, tcpA, hlyA, rtxA, ompU, toxR, T6SS, alsD, makA and pathogenicity islands VPI-1, VPI-2, VSP-1, and VSP-2 were found in all strains. The strains contained Vibrio polysaccharide biosynthesis enzymes, the mshA gene and two-component response regulator proteins involved in stress response and autoinducers for quorum sensing and biofilm formation. They carried the SXT integrative conjugative element with phenotypic and genotypic resistance to aminoglycoside, sulfamethoxazole, trimethoprim, phenicol, and quinolones. Strains contained a multidrug efflux pump component and were resistant to toxic compounds with copper homeostasis and cobalt-zinc-cadmium resistance proteins. The environmental strains belonged to the third wave of the seventh pandemic and most are genetically closely related to recent outbreak strains from Tanzania, Kenya, and Uganda with as low as three SNPs difference. Some strains have persisted longer in the environment and were more related to older outbreak strains in the region. V. cholerae O1 of outbreak potential seem to persist in Lake Victoria through interactions with fish and phytoplankton supported by the optimum water parameters and intrinsic genetic features enhancing survival in the aquatic environment.}, }
@article {pmid31114015, year = {2019}, author = {Worrich, A and Musat, N and Harms, H}, title = {Associational effects in the microbial neighborhood.}, journal = {The ISME journal}, volume = {13}, number = {9}, pages = {2143-2149}, pmid = {31114015}, issn = {1751-7370}, mesh = {Ecology ; Metagenome ; *Microbiota ; Plant Development ; Plants/*microbiology ; }, abstract = {Even though "perfect" metagenomes or metatranscriptomes are close at hand, the implicit assumption of spatial homogeneity in the "omic" approaches makes it difficult if not impossible to relate those data to ecological processes occurring in natural and man-made ecosystems. In fact, the distribution of microbes in their habitats is far from being uniform and random. Microbial communities show a high degree of spatial organization that stems from environmental gradients and local interactions. These interactions can be very complex and may involve multiple species. Several studies highlighted the importance of indirect interactions for community stability, but the absence of a theoretical framework for microbial ecology restricts the possibilities to strike a balance between the investigation of simple communities with purely pairwise interactions and the attempts to understand interaction patterns in whole communities based on meta-omics studies. Here we suggest adapting the concept of Associational Effects (AE) from plant ecology, to better understand the link between ecological interactions, spatial arrangement, and stability in microbial communities. By bringing together a conceptual framework developed for plants and observations made for microbes, this perspective article fosters synthesis of related disciplines to yield novel insights into the advancing field of spatial microbial ecology. To promote the integration into microbial ecology, we (i) outline the theoretical background of AE, (ii) collect underlying mechanisms by literature synthesis, (iii) propose a three-point roadmap for the investigation of AE in microbial communities, and (iv) discuss its implications for microbial ecology research.}, }
@article {pmid31112792, year = {2019}, author = {Michels, N and Van de Wiele, T and Fouhy, F and O'Mahony, S and Clarke, G and Keane, J}, title = {Gut microbiome patterns depending on children's psychosocial stress: Reports versus biomarkers.}, journal = {Brain, behavior, and immunity}, volume = {80}, number = {}, pages = {751-762}, doi = {10.1016/j.bbi.2019.05.024}, pmid = {31112792}, issn = {1090-2139}, mesh = {Adolescent ; Adverse Childhood Experiences ; Biomarkers ; Child ; Emotions/physiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Hair/chemistry ; Heart Rate/physiology ; Humans ; Hydrocortisone/analysis ; Male ; Psychology/methods ; Stress, Psychological/*metabolism/microbiology/*physiopathology ; }, abstract = {AIM: Chronic stress increases disease vulnerability factors including inflammation, a pathological characteristic potentially regulated by the gut microbiota. We checked the association between the gut microbiome and psychosocial stress in children/adolescents and investigated which stress parameter (negative versus positive emotion, self-report versus parental report, events versus emotions, biomarker cortisol versus parasympathetic activity) is the most relevant indicator herein.<br><br>METHODS: Gut microbiome sequencing was completed in fecal samples from 93 Belgian 8-16y olds. Stress measures included negative events, negative emotions, emotional problems reported by parents, happiness, hair cortisol and heart rate variability (pnn50 parameter reflecting parasympathetic activity). Alpha diversity, beta diversity and linear discriminant analysis were the unadjusted analyses. Age, sex, socio-economic status, diet, physical activity, sleep and weight status were adjusted for via a redundancy analysis and differential abundance via zero-inflated negative binomial regression.<br><br>RESULTS: High stress as reflected by low pnn50 and more negative events were associated with a lower alpha diversity as indicated by the Simpson index. Happiness and pnn50 showed significant differences between high and low stress groups based on weighted UniFrac distance, and this remained significant after confounder adjustment. Adjusted and unadjusted taxonomic differences were also most pronounced for happiness and pnn50 being associated respectively with 24 OTU (=11.8% of bacterial counts) and 31 OTU (=13.0%). As a general pattern, high stress was associated with lower Firmicutes at the phylum level and higher Bacteroides, Parabacteroides, Rhodococcus, Methanobrevibacter and Roseburia but lower Phascolarctobacterium at genus level. Several genera gave conflicting results between different stress measures e.g. Ruminococcaceae UCG014, Tenericutes, Eubacterium coprostanoligenes, Prevotella 9 and Christensenellaceae R7. Differential results in preadolescents versus adolescents were also evident.<br><br>CONCLUSION: Even in this young healthy population, stress parameters were cross-sectionally associated with gut microbial composition but this relationship was instrument specific. Positive emotions and parasympathetic activity appeared the strongest parameters and should be integrated in future microbiota projects amongst other stress measures.}, }
@article {pmid31111178, year = {2020}, author = {Mesquita, MCB and Prestes, ACC and Gomes, AMA and Marinho, MM}, title = {Direct Effects of Temperature on Growth of Different Tropical Phytoplankton Species.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {1-11}, pmid = {31111178}, issn = {1432-184X}, support = {478440/2011-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Biomass ; Chlorophyta/*growth &amp; development/radiation effects ; Climate ; Diatoms/*growth &amp; development/radiation effects ; Light ; Microcystis/*growth &amp; development/radiation effects ; Phytoplankton/*growth &amp; development/radiation effects ; Temperature ; }, abstract = {Temperature increase may influence competition among phytoplankton species, potentially intensifying cyanobacteria blooms that can be favored by direct and indirect effects of temperature. In this study, we aimed to clarify how cyanobacteria can be favored by the direct effects of increased temperature compared to diatoms and chlorophytes. Strains of the most representative species of a eutrophic coastal lagoon (Microcystis aeruginosa, Planktothrix agardhii, Desmodesmus communis, and Cyclotella meneghiniana) were used to test the hypothesis that cyanobacteria would be favored by the direct effect of temperature increase. First, we evaluated the effect of temperature increase on growth in monocultures (batch and chemostats) at 25 and 30 °C and after in mixed cultures (chemostats). In batch monocultures, the cyanobacteria showed higher growth rates in 30 °C than in 25 °C. However, in continuous culture experiments (chemostats), growth rates of M. aeruginosa and P. agardhii were not affected by temperature, but the strains showed higher biovolume in steady-state with the temperature increase. In continuous mixed cultures, M. aeruginosa was always dominant and C. meneghiniana was excluded, regardless of temperature tested. D. communis was able to coexist with lower biomass. This study shows that rising temperatures can be detrimental to diatoms, even for a tropical strain. Although some studies indicate that the dominance of cyanobacteria in warmer climates may be due to the indirect effect of warming that will promote physical conditions in the environment more favorable to cyanobacteria, the outcomes of mixed cultures demonstrate that the direct effect of temperature can also favor the dominance of cyanobacteria.}, }
@article {pmid31110670, year = {2019}, author = {Silva, DP and Duarte, G and Villela, HDM and Santos, HF and Rosado, PM and Rosado, JG and Rosado, AS and Ferreira, EM and Soriano, AU and Peixoto, RS}, title = {Adaptable mesocosm facility to study oil spill impacts on corals.}, journal = {Ecology and evolution}, volume = {9}, number = {9}, pages = {5172-5185}, pmid = {31110670}, issn = {2045-7758}, abstract = {Although numerous studies have been carried out on the impacts of oil spills on coral physiology, most have relied on laboratory assays. This scarcity is partly explained by the difficulty of reproducing realistic conditions in a laboratory setting or of performing experiments with toxic compounds in the field. Mesocosm systems provide the opportunity to carry out such studies with safe handling of contaminants while reproducing natural conditions required by living organisms. The mesocosm design is crucial and can lead to the development of innovative technologies to mitigate environmental impacts. Therefore, this study aimed to develop a mesocosm system for studies simulating oil spills with several key advantages, including true replication and the use of gravity to control flow-through that reduces reliance on pumps that can clog thereby decreasing errors and costs. This adaptable system can be configured to (a) have continuous flow-through; (b) operate as an open or closed system; (c) be fed by gravity; (d) have separate mesocosm sections that can be used for individual and simultaneous experiments; and (e) simulate the migration of oil from ocean oil spills to the nearby reefs. The mesocosm performance was assessed with two experiments using the hydrocoral Millepora alcicornis and different configurations to simulate two magnitudes of oil spills. With few exceptions, physical and chemical parameters remained stable within replicates and within treatments throughout the experiments. Physical and chemical parameters that expressed change during the experiment were still within the range of natural conditions observed in Brazilian marine environments. The photosynthetic potential (Fv/Fm) of the algae associated with M. alcicornis decreased in response to an 1% crude-oil contamination, suggesting a successful delivery of the toxic contaminant to the targeted replicates. This mesocosm is customizable and adjustable for several types of experiments and proved to be effective for studies of oil spills.}, }
@article {pmid31109532, year = {2019}, author = {Qi, H and Wei, Z and Zhang, J and Zhao, Y and Wu, J and Gao, X and Liu, Z and Li, Y}, title = {Effect of MnO2 on biotic and abiotic pathways of humic-like substance formation during composting of different raw materials.}, journal = {Waste management (New York, N.Y.)}, volume = {87}, number = {}, pages = {326-334}, doi = {10.1016/j.wasman.2019.02.022}, pmid = {31109532}, issn = {1879-2456}, mesh = {Animals ; *Composting ; Humic Substances ; Manure ; Soil ; Zea mays ; }, abstract = {The humic-like substances (HLS) are proposed to be formed by biotic and abiotic pathways. The abiotic pathways were neglected in existed composting studies. The present study aims to accelerate the abiotic pathways, and to investigate how MnO2 drives the HLS transformation via changing the contribution of abiotic and biotic pathways during composting with different materials. Parallel factor analysis model (PARAFAC), hetero two-dimensional correlation spectra (hetero-2DCOS) and variance partitioning were used to identify the effects of MnO2 on the formation of humic acid (HA) and fluvic acid (FA) during composting of chicken manure (CM) and corn straw (CS). The addition of MnO2 could change the structures of HLS during CS and CM composting, mainly promoting the formation of complex components in HA and FA during CS composting, as well as the complex components of FA during CM composting. Meanwhile, the addition of MnO2 could reshape the microbial ecology, which enhanced the correlation between microbes and complex components formation during composting, especially in CM composting. Variance partitioning showed that both abiotic and biotic pathways were stimulated in conversion of HLS components after adding MnO2 during CS composting, especially for the abiotic pathways. During CM composting, the MnO2 promoted biotic effects on the conversion of HLS components. Above all, the addition of MnO2 could stimulate pathways of biotic, abiotic or both of them to improve the humification degree of HLS by changing microbial ecology, which could be a promising way for promoting the application value of composting products.}, }
@article {pmid31105660, year = {2019}, author = {Jørgensen, BB and Findlay, AJ and Pellerin, A}, title = {The Biogeochemical Sulfur Cycle of Marine Sediments.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {849}, pmid = {31105660}, issn = {1664-302X}, abstract = {Microbial dissimilatory sulfate reduction to sulfide is a predominant terminal pathway of organic matter mineralization in the anoxic seabed. Chemical or microbial oxidation of the produced sulfide establishes a complex network of pathways in the sulfur cycle, leading to intermediate sulfur species and partly back to sulfate. The intermediates include elemental sulfur, polysulfides, thiosulfate, and sulfite, which are all substrates for further microbial oxidation, reduction or disproportionation. New microbiological discoveries, such as long-distance electron transfer through sulfide oxidizing cable bacteria, add to the complexity. Isotope exchange reactions play an important role for the stable isotope geochemistry and for the experimental study of sulfur transformations using radiotracers. Microbially catalyzed processes are partly reversible whereby the back-reaction affects our interpretation of radiotracer experiments and provides a mechanism for isotope fractionation. We here review the progress and current status in our understanding of the sulfur cycle in the seabed with respect to its microbial ecology, biogeochemistry, and isotope geochemistry.}, }
@article {pmid31100891, year = {2019}, author = {Jeong, Y and Kim, JW and You, HJ and Park, SJ and Lee, J and Ju, JH and Park, MS and Jin, H and Cho, ML and Kwon, B and Park, SH and Ji, GE}, title = {Gut Microbial Composition and Function Are Altered in Patients with Early Rheumatoid Arthritis.}, journal = {Journal of clinical medicine}, volume = {8}, number = {5}, pages = {}, pmid = {31100891}, issn = {2077-0383}, support = {NRF-2017M3A9F3041045//National Research Foundation/ ; NRF-2017M3A9F3041747//National Research Foundation/ ; }, abstract = {Rheumatoid arthritis (RA) is an autoimmune disease characterized by synovial inflammation of the joints and extra-articular manifestations. Recent studies have shown that microorganisms affect RA pathogenesis. However, few studies have examined the microbial distribution of early RA patients, particularly female patients. In the present study, we investigated the gut microbiome profile and microbial functions in early RA female patients, including preclinical and clinically apparent RA cases. Changes in microbiological diversity, composition, and function in each group were analyzed using quantitative insights into microbial ecology (QIIME) and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt). The results revealed the dysbiosis due to decreased diversity in the early RA patients compared with healthy subjects. There were significant differences in the microbial distribution of various taxa from phylum to genus levels between healthy subjects and early RA patients. Phylum Bacteroidetes was enriched in early RA patients, while Actinobacteria, including the genus Collinsella, was enriched in healthy subjects. Functional analysis based on clusters of orthologous groups revealed that the genes related to the biosynthesis of menaquinone, known to be derived from gram-positive bacteria, were enriched in healthy subjects, while iron transport-related genes were enriched in early RA patients. Genes related to the biosynthesis of lipopolysaccharide, the gram-negative bacterial endotoxin, were enriched in clinically apparent RA patients. The obvious differences in microbial diversity, taxa, and associated functions of the gut microbiota between healthy subjects and early RA patients highlight the involvement of the gut microbiome in the early stages of RA.}, }
@article {pmid31100615, year = {2019}, author = {Bautista-de Los Santos, QM and Chavarria, KA and Nelson, KL}, title = {Understanding the impacts of intermittent supply on the drinking water microbiome.}, journal = {Current opinion in biotechnology}, volume = {57}, number = {}, pages = {167-174}, doi = {10.1016/j.copbio.2019.04.003}, pmid = {31100615}, issn = {1879-0429}, mesh = {Disinfection ; Drinking Water/*microbiology ; *Microbiota ; *Water Microbiology ; Water Quality ; *Water Supply ; }, abstract = {Increasing access to piped water in low-income and middle-income countries combined with the many factors that threaten our drinking water supply infrastructure mean that intermittent water supply (IWS) will remain a common practice around the world. Common features of IWS include water stagnation, pipe drainage, intrusion, backflow, first flush events, and household storage. IWS has been shown to cause degradation as measured by traditional microbial water quality indicators. In this review, we build on new insights into the microbial ecology of continuous water supply systems revealed by sequencing methods to speculate about how intermittent supply conditions may further influence the drinking water microbiome, and identify priorities for future research.}, }
@article {pmid31099963, year = {2019}, author = {Nguyen, B and Rubbens, P and Kerckhof, FM and Boon, N and De Baets, B and Waegeman, W}, title = {Learning Single-Cell Distances from Cytometry Data.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {95}, number = {7}, pages = {782-791}, doi = {10.1002/cyto.a.23792}, pmid = {31099963}, issn = {1552-4930}, mesh = {Algorithms ; Bacteria/cytology ; Blood Cells/cytology ; Cluster Analysis ; Flow Cytometry/*methods ; Humans ; *Machine Learning ; Microbiota ; Pattern Recognition, Automated/*methods ; Single-Cell Analysis ; }, abstract = {Recent years have seen an increased interest in employing data analysis techniques for the automated identification of cell populations in the field of cytometry. These techniques highly depend on the use of a distance metric, a function that quantifies the distances between single-cell measurements. In most cases, researchers simply use the Euclidean distance metric. In this article, we exploit the availability of single-cell labels to find an optimal Mahalanobis distance metric derived from the data. We show that such a Mahalanobis distance metric results in an improved identification of cell populations compared with the Euclidean distance metric. Once determined, it can be used for the analysis of multiple samples that were measured under the same experimental setup. We illustrate this approach for cytometry data from two different origins, that is, flow cytometry applied to microbial cells and mass cytometry for the analysis of human blood cells. We also illustrate that such a distance metric results in an improved identification of cell populations when clustering methods are employed. Generally, these results imply that the performance of data analysis techniques can be improved by using a more advanced distance metric. © 2019 International Society for Advancement of Cytometry.}, }
@article {pmid31098412, year = {2019}, author = {Sato, Y and Hori, T and Koike, H and Navarro, RR and Ogata, A and Habe, H}, title = {Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {179}, pmid = {31098412}, issn = {2399-3642}, mesh = {Biodegradation, Environmental ; Bioreactors/microbiology ; Carbon/*metabolism ; Gene Expression Profiling ; Industrial Oils ; Metagenomics ; Microbiota/genetics/*physiology ; Models, Biological ; Nitrification/genetics/*physiology ; Sewage/*microbiology ; Waste Disposal, Fluid/methods ; Wastewater/microbiology ; }, abstract = {Although metagenomics researches have illuminated microbial diversity in numerous biospheres, understanding individual microbial functions is yet difficult due to the complexity of ecosystems. To address this issue, we applied a metagenome-independent, de novo assembly-based metatranscriptomics to a complex microbiome, activated sludge, which has been used for wastewater treatment for over a century. Even though two bioreactors were operated under the same conditions, their performances differed from each other with unknown causes. Metatranscriptome profiles in high- and low-performance reactors demonstrated that denitrifiers contributed to the anaerobic degradation of heavy oil; however, no marked difference in the gene expression was found. Instead, gene expression-based nitrification activities that fueled the denitrifiers by providing the respiratory substrate were notably high in the high-performance reactor only. Nitrifiers-small minorities with relative abundances of <0.25%-governed the heavy-oil degradation performances of the reactors, unveiling an unexpected linkage of carbon- and nitrogen-metabolisms of the complex microbiome.}, }
@article {pmid31097577, year = {2019}, author = {Brumley, DR and Carrara, F and Hein, AM and Yawata, Y and Levin, SA and Stocker, R}, title = {Bacteria push the limits of chemotactic precision to navigate dynamic chemical gradients.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {22}, pages = {10792-10797}, pmid = {31097577}, issn = {1091-6490}, mesh = {*Bacteria/drug effects/metabolism ; Chemotactic Factors/pharmacology ; Chemotaxis/*physiology ; Computer Simulation ; Environment ; *Models, Biological ; Signal-To-Noise Ratio ; Vibrio/drug effects/physiology ; }, abstract = {Ephemeral aggregations of bacteria are ubiquitous in the environment, where they serve as hotbeds of metabolic activity, nutrient cycling, and horizontal gene transfer. In many cases, these regions of high bacterial concentration are thought to form when motile cells use chemotaxis to navigate to chemical hotspots. However, what governs the dynamics of bacterial aggregations is unclear. Here, we use an experimental platform to create realistic submillimeter-scale nutrient pulses with controlled nutrient concentrations. By combining experiments, mathematical theory, and agent-based simulations, we show that individual Vibrio ordalii bacteria begin chemotaxis toward hotspots of dissolved organic matter (DOM) when the magnitude of the chemical gradient rises sufficiently far above the sensory noise that is generated by stochastic encounters with chemoattractant molecules. Each DOM hotspot is surrounded by a dynamic ring of chemotaxing cells, which congregate in regions of high DOM concentration before dispersing as DOM diffuses and gradients become too noisy for cells to respond to. We demonstrate that V. ordalii operates close to the theoretical limits on chemotactic precision. Numerical simulations of chemotactic bacteria, in which molecule counting noise is explicitly taken into account, point at a tradeoff between nutrient acquisition and the cost of chemotactic precision. More generally, our results illustrate how limits on sensory precision can be used to understand the location, spatial extent, and lifespan of bacterial behavioral responses in ecologically relevant environments.}, }
@article {pmid31095604, year = {2019}, author = {Di Lonardo, DP and de Boer, W and Zweers, H and van der Wal, A}, title = {Effect of the amount of organic trigger compounds, nitrogen and soil microbial biomass on the magnitude of priming of soil organic matter.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0216730}, pmid = {31095604}, issn = {1932-6203}, mesh = {*Biomass ; Carbon Dioxide/analysis ; Nitrogen/*analysis ; Organic Chemicals/*analysis ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Priming effects (PEs) are defined as short-term changes in the turnover of soil organic matter (SOM) caused by the addition of easily degradable organic compounds to the soil. PEs are ubiquitous but the direction (acceleration or retardation of SOM decomposition) and magnitude are not easy to predict. It has been suggested that the ratio between the amount of added PE-triggering substrate to the size of initial soil microbial biomass is an important factor influencing PEs. However, this is mainly based on comparison of different studies and not on direct experimentation. The aim of the current study is to examine the impact of glucose-to-microbial biomass ratios on PEs for three different ecosystems. We did this by adding three different amounts of 13C-glucose with or without addition of mineral N (NH4NO3) to soils collected from arable lands, grasslands and forests. The addition of 13C-glucose was equivalent to 15%, 50% and 200% of microbial biomass C. After one month of incubation, glucose had induced positive PEs for almost all the treatments, with differences in magnitude related to the soil origin and the amount of glucose added. For arable and forest soils, the primed C increased with increasing amount of glucose added, whereas for grassland soils this relationship was negative. We found positive correlations between glucose-derived C and primed C and the strength of these correlations was different among the three ecosystems considered. Generally, additions of mineral N next to glucose (C:N = 15:1) had little effect on the flux of substrate-derived C and primed C. Overall, our study does not support the hypothesis that the trigger-substrate to microbial biomass ratio can be an important predictor of PEs. Rather our results indicate that the amount of energy obtained from decomposing trigger substrates is an important factor for the magnitude of PEs.}, }
@article {pmid31093727, year = {2020}, author = {Woodhams, DC and Rollins-Smith, LA and Reinert, LK and Lam, BA and Harris, RN and Briggs, CJ and Vredenburg, VT and Patel, BT and Caprioli, RM and Chaurand, P and Hunziker, P and Bigler, L}, title = {Probiotics Modulate a Novel Amphibian Skin Defense Peptide That Is Antifungal and Facilitates Growth of Antifungal Bacteria.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {192-202}, pmid = {31093727}, issn = {1432-184X}, support = {0640373//National Science Foundation/ ; 1121758//National Science Foundation/ ; 31-125099//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {Amino Acid Sequence ; Animals ; Antifungal Agents/chemistry/metabolism/*pharmacology ; Chytridiomycota/drug effects/growth &amp; development ; Microbiota/drug effects ; Peptides/chemistry/genetics/metabolism/*pharmacology ; Probiotics/*pharmacology ; Ranidae/metabolism/*microbiology ; Skin/*metabolism/microbiology ; }, abstract = {Probiotics can ameliorate diseases of humans and wildlife, but the mechanisms remain unclear. Host responses to interventions that change their microbiota are largely uncharacterized. We applied a consortium of four natural antifungal bacteria to the skin of endangered Sierra Nevada yellow-legged frogs, Rana sierrae, before experimental exposure to the pathogenic fungus Batrachochytrium dendrobatidis (Bd). The probiotic microbes did not persist, nor did they protect hosts, and skin peptide sampling indicated immune modulation. We characterized a novel skin defense peptide brevinin-1Ma (FLPILAGLAANLVPKLICSITKKC) that was downregulated by the probiotic treatment. Brevinin-1Ma was tested against a range of amphibian skin cultures and found to inhibit growth of fungal pathogens Bd and B. salamandrivorans, but enhanced the growth of probiotic bacteria including Janthinobacterium lividum, Chryseobacterium ureilyticum, Serratia grimesii, and Pseudomonas sp. While commonly thought of as antimicrobial peptides, here brevinin-1Ma showed promicrobial function, facilitating microbial growth. Thus, skin exposure to probiotic bacterial cultures induced a shift in skin defense peptide profiles that appeared to act as an immune response functioning to regulate the microbiome. In addition to direct microbial antagonism, probiotic-host interactions may be a critical mechanism affecting disease resistance.}, }
@article {pmid31093726, year = {2020}, author = {Hernández-Gómez, O and Wuerthner, V and Hua, J}, title = {Amphibian Host and Skin Microbiota Response to a Common Agricultural Antimicrobial and Internal Parasite.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {175-191}, pmid = {31093726}, issn = {1432-184X}, support = {1655190//Division of Environmental Biology/ ; 1708926//Directorate for Biological Sciences/ ; }, mesh = {Amphibians/*microbiology/*parasitology ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/genetics/growth &amp; development ; Microbiota/*drug effects ; Phylogeny ; Skin/*microbiology ; Trematoda/*physiology ; }, abstract = {Holistic approaches that simultaneously characterize responses of both microbial symbionts and their hosts to environmental shifts are imperative to understanding the role of microbiotas on host health. Using the northern leopard frog (Lithobates pipiens) as our model, we investigated the effects of a common trematode (family Echinostomatidae), a common agricultural antimicrobial (Sulfadimethoxine; SDM), and their interaction on amphibian skin microbiota and amphibian health (growth metrics and susceptibility to parasites). In the trematode-exposed individuals, we noted an increase in alpha diversity and a shift in microbial communities. In the SDM-treated individuals, we found a change in the composition of the skin microbiota similar to those induced by the trematode treatment. Groups treated with SDM, echinostomes, or a combination of SDM and echinostomes, had higher relative abundances of OTUs assigned to Flavobacterium and Acinetobacter. Both of these genera have been associated with infectious disease in amphibians and the production of anti-pathogen metabolites. Similar changes in microbial community composition between SDM and trematode exposed individuals may have resulted from stress-related disruption of host immunity. Despite changes in the microbiota, we found no effect of echinostomes and SDM on host health. Given the current disease- and pollution-related threats facing amphibians, our study highlights the need to continue to evaluate the influence of natural and anthropogenic stressors on host-associated microbial communities.}, }
@article {pmid31091418, year = {2019}, author = {Cordovez, V and Dini-Andreote, F and Carrión, VJ and Raaijmakers, JM}, title = {Ecology and Evolution of Plant Microbiomes.}, journal = {Annual review of microbiology}, volume = {73}, number = {}, pages = {69-88}, doi = {10.1146/annurev-micro-090817-062524}, pmid = {31091418}, issn = {1545-3251}, mesh = {*Host Microbial Interactions ; *Microbiota ; Plants/*microbiology ; }, abstract = {Microorganisms colonizing plant surfaces and internal tissues provide a number of life-support functions for their host. Despite increasing recognition of the vast functional capabilities of the plant microbiome, our understanding of the ecology and evolution of the taxonomically hyperdiverse microbial communities is limited. Here, we review current knowledge of plant genotypic and phenotypic traits as well as allogenic and autogenic factors that shape microbiome composition and functions. We give specific emphasis to the impact of plant domestication on microbiome assembly and how insights into microbiomes of wild plant relatives and native habitats can contribute to reinstate or enrich for microorganisms with beneficial effects on plant growth, development, and health. Finally, we introduce new concepts and perspectives in plant microbiome research, in particular how community ecology theory can provide a mechanistic framework to unravel the interplay of distinct ecological processes-i.e., selection, dispersal, drift, diversification-that structure the plant microbiome.}, }
@article {pmid31088922, year = {2019}, author = {König, L and Wentrup, C and Schulz, F and Wascher, F and Escola, S and Swanson, MS and Buchrieser, C and Horn, M}, title = {Symbiont-Mediated Defense against Legionella pneumophila in Amoebae.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, pmid = {31088922}, issn = {2150-7511}, support = {I 1628/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Acanthamoeba castellanii/*microbiology/physiology ; Chlamydiales/*physiology ; Gene Expression ; Humans ; Legionella pneumophila/*pathogenicity ; *Symbiosis ; Virulence ; }, abstract = {Legionella pneumophila is an important opportunistic pathogen for which environmental reservoirs are crucial for the infection of humans. In the environment, free-living amoebae represent key hosts providing nutrients and shelter for highly efficient intracellular proliferation of L. pneumophila, which eventually leads to lysis of the protist. However, the significance of other bacterial players for L. pneumophila ecology is poorly understood. In this study, we used a ubiquitous amoeba and bacterial endosymbiont to investigate the impact of this common association on L. pneumophila infection. We demonstrate that L. pneumophila proliferation was severely suppressed in Acanthamoeba castellanii harboring the chlamydial symbiont Protochlamydia amoebophila The amoebae survived the infection and were able to resume growth. Different environmental amoeba isolates containing the symbiont were equally well protected as different L. pneumophila isolates were diminished, suggesting ecological relevance of this symbiont-mediated defense. Furthermore, protection was not mediated by impaired L. pneumophila uptake. Instead, we observed reduced virulence of L. pneumophila released from symbiont-containing amoebae. Pronounced gene expression changes in the presence of the symbiont indicate that interference with the transition to the transmissive phase impedes the L. pneumophila infection. Finally, our data show that the defensive response of amoebae harboring P. amoebophila leaves the amoebae with superior fitness reminiscent of immunological memory. Given that mutualistic associations between bacteria and amoebae are widely distributed, P. amoebophila and potentially other amoeba endosymbionts could be key in shaping environmental survival, abundance, and virulence of this important pathogen, thereby affecting the frequency of human infection.IMPORTANCE Bacterial pathogens are generally investigated in the context of disease. To prevent outbreaks, it is essential to understand their lifestyle and interactions with other microbes in their natural environment. Legionella pneumophila is an important human respiratory pathogen that survives and multiplies in biofilms or intracellularly within protists, such as amoebae. Importantly, transmission to humans occurs from these environmental sources. Legionella infection generally leads to rapid host cell lysis. It was therefore surprising to observe that amoebae, including fresh environmental isolates, were well protected during Legionella infection when the bacterial symbiont Protochlamydia amoebophila was also present. Legionella was not prevented from invading amoebae but was impeded in its ability to develop fully virulent progeny and were ultimately cleared in the presence of the symbiont. This study highlights how ecology and virulence of an important human pathogen is affected by a defensive amoeba symbiont, with possibly major consequences for public health.}, }
@article {pmid31087742, year = {2019}, author = {Geiger, RA and Junghare, M and Mergelsberg, M and Ebenau-Jehle, C and Jesenofsky, VJ and Jehmlich, N and von Bergen, M and Schink, B and Boll, M}, title = {Enzymes involved in phthalate degradation in sulphate-reducing bacteria.}, journal = {Environmental microbiology}, volume = {21}, number = {10}, pages = {3601-3612}, doi = {10.1111/1462-2920.14681}, pmid = {31087742}, issn = {1462-2920}, support = {BO 1565/16-1//German research council/International ; }, mesh = {Anaerobiosis ; Deltaproteobacteria/classification/genetics/*metabolism ; Oxidation-Reduction ; Phthalic Acids/*metabolism ; Proteome/metabolism ; Sulfates/*metabolism ; }, abstract = {The complete degradation of the xenobiotic and environmentally harmful phthalate esters is initiated by hydrolysis to alcohols and o-phthalate (phthalate) by esterases. While further catabolism of phthalate has been studied in aerobic and denitrifying microorganisms, the degradation in obligately anaerobic bacteria has remained obscure. Here, we demonstrate a previously overseen growth of the δ-proteobacterium Desulfosarcina cetonica with phthalate/sulphate as only carbon and energy sources. Differential proteome and CoA ester pool analyses together with in vitro enzyme assays identified the genes, enzymes and metabolites involved in phthalate uptake and degradation in D. cetonica. Phthalate is initially activated to the short-lived phthaloyl-CoA by an ATP-dependent phthalate CoA ligase (PCL) followed by decarboxylation to the central intermediate benzoyl-CoA by an UbiD-like phthaloyl-CoA decarboxylase (PCD) containing a prenylated flavin cofactor. Genome/metagenome analyses predicted phthalate degradation capacity also in the sulphate-reducing Desulfobacula toluolica, strain NaphS2, and other δ-proteobacteria. Our results suggest that phthalate degradation proceeds in all anaerobic bacteria via the labile phthaloyl-CoA that is captured and decarboxylated by highly abundant PCDs. In contrast, two alternative strategies have been established for the formation of phthaloyl-CoA, the possibly most unstable CoA ester in biology.}, }
@article {pmid31086312, year = {2019}, author = {Wu, L and Ning, D and Zhang, B and Li, Y and Zhang, P and Shan, X and Zhang, Q and Brown, MR and Li, Z and Van Nostrand, JD and Ling, F and Xiao, N and Zhang, Y and Vierheilig, J and Wells, GF and Yang, Y and Deng, Y and Tu, Q and Wang, A and ,  and Zhang, T and He, Z and Keller, J and Nielsen, PH and Alvarez, PJJ and Criddle, CS and Wagner, M and Tiedje, JM and He, Q and Curtis, TP and Stahl, DA and Alvarez-Cohen, L and Rittmann, BE and Wen, X and Zhou, J}, title = {Global diversity and biogeography of bacterial communities in wastewater treatment plants.}, journal = {Nature microbiology}, volume = {4}, number = {7}, pages = {1183-1195}, pmid = {31086312}, issn = {2058-5276}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/genetics ; Geography ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; Water Purification/statistics &amp; numerical data ; }, abstract = {Microorganisms in wastewater treatment plants (WWTPs) are essential for water purification to protect public and environmental health. However, the diversity of microorganisms and the factors that control it are poorly understood. Using a systematic global-sampling effort, we analysed the 16S ribosomal RNA gene sequences from ~1,200 activated sludge samples taken from 269 WWTPs in 23 countries on 6 continents. Our analyses revealed that the global activated sludge bacterial communities contain ~1 billion bacterial phylotypes with a Poisson lognormal diversity distribution. Despite this high diversity, activated sludge has a small, global core bacterial community (n = 28 operational taxonomic units) that is strongly linked to activated sludge performance. Meta-analyses with global datasets associate the activated sludge microbiomes most closely to freshwater populations. In contrast to macroorganism diversity, activated sludge bacterial communities show no latitudinal gradient. Furthermore, their spatial turnover is scale-dependent and appears to be largely driven by stochastic processes (dispersal and drift), although deterministic factors (temperature and organic input) are also important. Our findings enhance our mechanistic understanding of the global diversity and biogeography of activated sludge bacterial communities within a theoretical ecology framework and have important implications for microbial ecology and wastewater treatment processes.}, }
@article {pmid31079748, year = {2019}, author = {López, JC and Porca, E and Collins, G and Clifford, E and Quijano, G and Muñoz, R}, title = {Ammonium influences kinetics and structure of methanotrophic consortia.}, journal = {Waste management (New York, N.Y.)}, volume = {89}, number = {}, pages = {345-353}, doi = {10.1016/j.wasman.2019.04.028}, pmid = {31079748}, issn = {1879-2456}, mesh = {*Ammonium Compounds ; Kinetics ; Methane ; *Methylococcaceae ; Oxidation-Reduction ; Soil Microbiology ; }, abstract = {The literature is conflicted on the influence of ammonium on the kinetics and microbial ecology of methanotrophy. In this study, methanotrophic cultures were enriched, under ammonium concentrations ranging from 0 to 200 mM, from an inoculum comprising leachate and top-cover soil from a landfill. Specific CH4 biodegradation rates were highest (7.8 × 10[-4] ± 6.0 × 10[-5] gCH4 gX[-1] h[-1]) in cultures enriched at 4 mM NH4[+], which were mainly dominated by type II methanotrophs belonging to Methylocystis spp. Lower specific CH4 oxidation rates (average values of 1.8-3.6 × 10[-4] gCH4 gX[-1] h[-1]) were achieved by cultures enriched at higher NH4[+] concentrations (20 and 80 mM), and had higher affinity for CH4 compared to 4 mM enrichments. These lower affinities were attributed to lower diversity dominated by type I methanotrophs, of the Methylosarcina, Methylobacter and Methylomicrobium genera, encountered with increasing concentrations of NH4[+]. The study indicates that CH4 oxidation biotechnologies applied at low NH4[+] concentrations can support efficient abatement of CH4 and high diversity of methanotrophic consortia, whilst enriching type II methanotrophs.}, }
@article {pmid31079198, year = {2020}, author = {Wanner, M and Birkhofer, K and Fischer, T and Shimizu, M and Shimano, S and Puppe, D}, title = {Soil Testate Amoebae and Diatoms as Bioindicators of an Old Heavy Metal Contaminated Floodplain in Japan.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {123-133}, pmid = {31079198}, issn = {1432-184X}, support = {PU 626/2-1//Deutsche Forschungsgemeinschaft/ ; S16738//Japan Society for the Promotion of Science/ ; Kakenhi 15H02858//Japan Society for the Promotion of Science/ ; }, mesh = {Amoeba/*growth &amp; development/metabolism ; Copper/analysis/metabolism ; Diatoms/*growth &amp; development/metabolism ; Environmental Biomarkers ; Environmental Monitoring ; Floods ; Japan ; Lead/analysis/metabolism ; Metals, Heavy/analysis/*metabolism ; Soil/*chemistry/parasitology ; Soil Pollutants/analysis/*metabolism ; Zinc/analysis/metabolism ; }, abstract = {Soil protists are rarely included in ecotoxicological investigations, despite their fundamental role in ecological processes. Moreover, testate amoebae and diatoms contribute considerably to silicon fluxes in soils. We investigated the effects of heavy metals on testate amoebae (species and individual densities) and diatoms (individual densities) in aged soils of a floodplain (Watarase retarding basin, Japan) taking soil samples from two unpolluted reference sites and two polluted sites. The total concentrations of Cu, Pb, and Zn in soil were higher at the polluted sites as compared with the reference sites. The available concentrations of Co, Cu, and Zn in CaCl2 extracts were higher at the polluted sites but available Pb was not detectable. Testate amoeba taxonomic richness was higher in the reference sites (45/38 taxa) than in the polluted sites (36/27 taxa). The reference sites had higher diatom and amoeba densities than the polluted sites. There was a significant negative correlation between total testate amoeba density and heavy metal concentration (available Co), while significant negative correlations were found between diatom density and Co, Cu, and Zn (available and total concentration). Densities of Cyclopyxis kahli cyclostoma, Centropyxis spp., and Trinema complanatum were negatively correlated to concentrations of available heavy metals. The observed decrease in individual numbers due to heavy metal pollution resulted in a considerable decline in protozoic (testate amoebae) and protophytic (pennate diatoms) silicon pools. Our data suggest that heavy metal pollution affects biogeochemical cycling in this system.}, }
@article {pmid31079197, year = {2020}, author = {Pillot, G and Davidson, S and Auria, R and Combet-Blanc, Y and Godfroy, A and Liebgott, PP}, title = {Production of Current by Syntrophy Between Exoelectrogenic and Fermentative Hyperthermophilic Microorganisms in Heterotrophic Biofilm from a Deep-Sea Hydrothermal Chimney.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {38-49}, pmid = {31079197}, issn = {1432-184X}, support = {PEPS-ExoMod 2016//Institut National des Sciences de l'Univers, Centre National de la Recherche Scientifique/ ; 1166-39417//European Regional Development Fund/ ; }, mesh = {Acetates/metabolism ; Archaea/*chemistry/classification/genetics/*physiology ; Biofilms ; Electricity ; Electrodes/microbiology ; Fermentation ; Hydrogen/metabolism ; Hydrothermal Vents/*microbiology ; Oxidation-Reduction ; Pyruvic Acid/metabolism ; }, abstract = {To study the role of exoelectrogens within the trophic network of deep-sea hydrothermal vents, we performed successive subcultures of a hyperthermophilic community from a hydrothermal chimney sample on a mix of electron donors in a microbial fuel cell system. Electrode (the electron acceptor) was swapped every week to enable fresh development from spent media as inoculum. The MFC at 80 °C yielded maximum current production increasing from 159 to 247 mA m[-2] over the subcultures. The experiments demonstrated direct production of electric current from acetate, pyruvate, and H2 and indirect production from yeast extract and peptone through the production of H2 and acetate from fermentation. The microorganisms found in on-electrode communities were mainly affiliated to exoelectrogenic Archaeoglobales and Thermococcales species, whereas in liquid media, the communities were mainly affiliated to fermentative Bacillales and Thermococcales species. The work shows interactions between fermentative microorganisms degrading complex organic matter into fermentation products that are then used by exoelectrogenic microorganisms oxidizing these reduced compounds while respiring on a conductive support. The results confirmed that with carbon cycling, the syntrophic relations between fermentative microorganisms and exoelectrogens could enable some microbes to survive as biofilm in extremely unstable conditions. Graphical Abstract Schematic representation of cross-feeding between fermentative and exoelectrogenic microbes on the surface of the conductive support. B, Bacillus/Geobacillus spp.; Tc, Thermococcales; Gg, Geoglobus spp.; Py, pyruvate; Ac, acetate.}, }
@article {pmid31074596, year = {2019}, author = {Feng, M and Tripathi, BM and Shi, Y and Adams, JM and Zhu, YG and Chu, H}, title = {Interpreting distance-decay pattern of soil bacteria via quantifying the assembly processes at multiple spatial scales.}, journal = {MicrobiologyOpen}, volume = {8}, number = {9}, pages = {e00851}, pmid = {31074596}, issn = {2045-8827}, mesh = {Bacteria/*classification/*genetics ; China ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; *Microbiota ; *Soil Microbiology ; *Spatial Analysis ; Zea mays/*growth &amp; development ; }, abstract = {It has been widely accepted that there is a distance-decay pattern in the soil microbiome. However, few studies have attempted to interpret the microbial distance-decay pattern from the perspective of quantifying underlying processes. In this study, we examined the processes governing bacterial community assembly at multiple spatial scales in maize fields of Northeast China using Illumina MiSeq sequencing. Results showed that the processes governing spatial turnover in bacterial community composition shifted regularly with spatial scale, with homogenizing dispersal dominating at small spatial scales and variable selection dominating at larger scales, which in turn explained the distance-decay pattern that closer located sites tended to have higher community similarity. Together, homogenizing dispersal and dispersal limitation resulting from geographic factors governed about 33% of spatial turnover in bacterial community composition. Deterministic selection processes had the strongest influence, at 57%, with biotic factors and abiotic environmental filtering (mainly imposed by soil pH) respectively contributing about 37% and 63% of variation. Our results provided a novel and comprehensive way to explain the distance-decay pattern of soil microbiome via quantifying the assembly processes at multiple spatial scales, as well as the method to quantify the influence of abiotic, biotic, and geographic factors in shaping microbial community structure, thus enabling understanding of widely acknowledged microbial biogeographic patterns and microbial ecology.}, }
@article {pmid31065700, year = {2019}, author = {Mohammed, AA and Jiang, S and Jacobs, JA and Cheng, HW}, title = {Effect of a synbiotic supplement on cecal microbial ecology, antioxidant status, and immune response of broiler chickens reared under heat stress.}, journal = {Poultry science}, volume = {98}, number = {10}, pages = {4408-4415}, doi = {10.3382/ps/pez246}, pmid = {31065700}, issn = {1525-3171}, mesh = {Animal Nutritional Physiological Phenomena/drug effects ; Animals ; Antioxidants/*metabolism ; Cecum/microbiology/physiology ; Chickens/immunology/*metabolism/microbiology ; Dose-Response Relationship, Drug ; Gastrointestinal Microbiome/*drug effects/physiology ; Hot Temperature/*adverse effects ; Immunity, Innate/*drug effects ; Male ; Random Allocation ; Stress, Physiological ; Synbiotics/*administration &amp; dosage ; }, abstract = {The aim of this study was to examine the effect of a dietary synbiotic supplement on the cecal microflora, antioxidant status, and immune response of broiler chickens under heat stress (HS). A total of 360 one-day-old male Ross 708 broiler chicks were randomly distributed among 3 dietary treatments containing a synbiotic (PoultryStar consists of Bifidobacterium animalis, Enterococcus faecium, Lactobacillus reuteri, Pediococcus acidilactici, and fructooligosaccharides) at 0 (control), 0.5 (0.5X), and 1.0 (1.0X) g/kg. Each treatment contained 8 replicates of 15 birds each housed in floor pens. Heat stimulation was at 32°C for 9 h daily from day 15 to 42. Heat stress-induced changes of cecal bacteria were detected using bacteria-specific agars, and spleen protein concentration and mRNA expression of interleukins and antioxidants were examined using ELISA and real-time PCR, respectively. Under the HS condition, synbiotic fed broilers regardless of dose had lower cecal enumerations of Escherichia coli and coliforms, and a lower heterophil/lymphocyte (H/L) ratio (P < 0.05) compared to controls. 1.0X group also had higher cecal enumerations of Bifidobacterium spp. and Lactobacillus spp., spleen glutathione peroxidase (GPx), and plasma nuclear factor erythroid 2-related factor 2 (Nrf-2), and a lower H/L ratio compared to both control and 0.5X groups (P < 0.05). However, there were no treatment effects on the levels of Enterococcus spp., the circulating monocytes, eosinophils, and basophils, Toll like receptor-4 (TLR-4), interleukin-6 (IL-6), interlukin-10 (IL-10), and their mRNA expression, as well as plasma Kelch-like ECH-associated protein 1 (Keap-1) (P > 0.05). These results suggest that the synbiotic could inhibit the negative effects of HS on broiler health through the reduction of cecal pathogens, regulation of stress reactions, and improvement of antioxidant status.}, }
@article {pmid31064055, year = {2019}, author = {Pineda-Quiroga, C and Borda-Molina, D and Chaves-Moreno, D and Ruiz, R and Atxaerandio, R and Camarinha-Silva, A and García-Rodríguez, A}, title = {Microbial and Functional Profile of the Ceca from Laying Hens Affected by Feeding Prebiotics, Probiotics, and Synbiotics.}, journal = {Microorganisms}, volume = {7}, number = {5}, pages = {}, pmid = {31064055}, issn = {2076-2607}, support = {LIFE11/ENV/ES/000639//LIFE program of the European Union/ ; PRE/2013/1/1077//Department of Education, Language Policy and Culture, Scholarship, , Basque Government, Vitoria-Gasteiz, Spain/ ; }, abstract = {Diet has an essential influence in the establishment of the cecum microbial communities in poultry, so its supplementation with safe additives, such as probiotics, prebiotics, and synbiotics might improve animal health and performance. This study showed the ceca microbiome modulations of laying hens, after feeding with dry whey powder as prebiotics, Pediococcus acidilactici as probiotics, and the combination of both as synbiotics. A clear grouping of the samples induced per diet was observed (p < 0.05). Operational taxonomic units (OTUs) identified as Olsenella spp., and Lactobacillus crispatus increased their abundance in prebiotic and synbiotic treatments. A core of the main functions was shared between all metagenomes (45.5%), although the genes encoding for the metabolism of butanoate, propanoate, inositol phosphate, and galactose were more abundant in the prebiotic diet. The results indicated that dietary induced-changes in microbial composition did not imply a disturbance in the principal biological roles, while the specific functions were affected.}, }
@article {pmid31063726, year = {2019}, author = {Lindemann, SR}, title = {Microbial Ecology: Functional 'Modules' Drive Assembly of Polysaccharide-Degrading Marine Microbial Communities.}, journal = {Current biology : CB}, volume = {29}, number = {9}, pages = {R330-R332}, doi = {10.1016/j.cub.2019.03.056}, pmid = {31063726}, issn = {1879-0445}, mesh = {*Bacteria ; Ecology ; *Microbiota ; Polysaccharides ; }, abstract = {Although ecological principles governing the competition of microbes for simple substrates are well-understood, less is known about how complex, structured substrates influence ecological outcomes in microbial communities. A new study sheds light on how marine microbial communities assemble on polysaccharide particles modeling marine snow.}, }
@article {pmid31060399, year = {2019}, author = {Panebianco, C and Pazienza, V}, title = {Body site-dependent variations of microbiota in pancreatic cancer pathophysiology.}, journal = {Critical reviews in clinical laboratory sciences}, volume = {56}, number = {4}, pages = {260-273}, doi = {10.1080/10408363.2019.1615407}, pmid = {31060399}, issn = {1549-781X}, mesh = {Animals ; Gastrointestinal Microbiome ; Humans ; *Microbiota ; Organ Specificity ; Pancreatic Neoplasms/*microbiology/*physiopathology ; }, abstract = {Lack of specific symptoms and reliable biomarkers, along with aggressive nature and resistance to therapies makes pancreatic cancer (PC) one of the leading causes of death from cancer worldwide. The search for new diagnostic, prognostic, predictive, and therapeutic tools that could improve clinical outcomes of patients has led, in recent years, to the investigation of potential roles for the microbiota in the pathogenesis of this disease. The human microbiota encompasses trillions of microorganisms residing within several body tissues and organs, where they provide beneficial functions for host homeostasis and health. Derangements of the microbial ecology in different anatomic districts have been described in PC, as in many other diseases, both in patients and in animal models. In detail, infection from the gastric pathogen Helicobacter pylori and changes in composition and diversity of oral, intestinal, and pancreatic microbiota have been found to associate with PC. Future research should assess how to potentially exploit such differences in microbiota composition as diagnostic, prognostic, or predictive biomarkers, and as targets for therapeutic interventions, in the hope of improving the dismal prognosis of this insidious cancer.}, }
@article {pmid31058277, year = {2018}, author = {Photos-Jones, E}, title = {From mine to apothecary: an archaeo-biomedical approach to the study of the Greco-Roman lithotherapeutics industry.}, journal = {World archaeology}, volume = {50}, number = {3}, pages = {418-433}, pmid = {31058277}, issn = {0043-8243}, abstract = {Western biomedicine has only partially developed its own tradition of mineral medicinals (lithotherapeutics), at least compared to botanicals. This is perhaps because these minerals were site-specific, and fundamental information associated with the empirical processes of mineral extraction, beneficiation, storage, trade and preparation was not widely available. In other words, there are many and serious breaks in the multi-link chain from mine to apothecary. This long-term investigation aims to rebuild this chain, on a mineral-by-mineral basis, by pulling together the extant documentary record, material culture, mineralogy, geochemistry and microbial ecology, as well as by testing against known pathogens as an indicator of their antimicrobial activity. Critical to understanding the nature and efficacy of lithotherapeutics is the recognition that these materials need to be investigated simultaneously at two levels: the empirical (ancient sources and practices); and the biomedical (application of physical and biological sciences). Both approaches require the same starting point, namely the field (mine or quarry) and in particular the 'point of contact' (relationship) between minerals and their microbiome.}, }
@article {pmid31055618, year = {2020}, author = {Ben Yahia, H and Chairat, S and Gharsa, H and Alonso, CA and Ben Sallem, R and Porres-Osante, N and Hamdi, N and Torres, C and Ben Slama, K}, title = {First Report of KPC-2 and KPC-3-Producing Enterobacteriaceae in Wild Birds in Africa.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {30-37}, pmid = {31055618}, issn = {1432-184X}, mesh = {Africa ; Animals ; Animals, Wild/classification/*microbiology ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Birds/classification/*microbiology ; Drug Resistance, Bacterial ; Enterobacteriaceae/classification/*drug effects/genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Phylogeny ; beta-Lactamases/genetics/*metabolism ; }, abstract = {The increased incidence of antibiotic-resistant Enterobacteriaceae is a public health problem worldwide. The aim of this study was to analyze the potential role of wild birds, given their capacity of migrating over long distances, in the spreading of carbapenemase, extended-spectrum β-lactamase (ESBL), and acquired-AmpC beta-lactamase-producing Enterobacteriaceae in the environment. Fecal and pellet samples were recovered from 150 wild birds in seven Tunisian regions and were inoculated in MacConkey-agar plates for Enterobacteriaceae recovery (one isolate/animal). Ninety-nine isolates were obtained and acquired resistance mechanisms were characterized in the five detected imipenem-resistant and/or cefotaxime-resistant isolates, by PCR and sequencing. The following ESBL, carbapenemase, and acquired-AmpC beta-lactamase genes were detected: blaCTX-M-15 (two Escherichia fergusonii and one Klebsiella oxytoca isolates), blaKPC-2 (one K. oxytoca), blaKPC-3 (one E. fergusonii), blaACT-36, and blaACC-2 (two K. oxytoca, four E. fergusonii, and two E. coli). The IncFIIs, IncF, IncFIB, IncK, IncP, and IncX replicons were detected among these beta-lactamase Enterobacteriaceae producers. The blaKPC-2, tetA, sul3, qnrB, and cmlA determinants were co-transferred by conjugation from K. oxytoca strain to E. coli J153, in association with IncK and IncF replicons. Our results support the implication of wild birds as a biological vector for carbapenemase, ESBL, and acquired-AmpC-producing Enterobacteriaceae.}, }
@article {pmid31054240, year = {2019}, author = {Ma, S and De Frenne, P and Boon, N and Brunet, J and Cousins, SAO and Decocq, G and Kolb, A and Lemke, I and Liira, J and Naaf, T and Orczewska, A and Plue, J and Wulf, M and Verheyen, K}, title = {Plant species identity and soil characteristics determine rhizosphere soil bacteria community composition in European temperate forests.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {6}, pages = {}, doi = {10.1093/femsec/fiz063}, pmid = {31054240}, issn = {1574-6941}, mesh = {Acidobacteria/classification/isolation &amp; purification ; Actinobacteria/classification/isolation &amp; purification ; Bacteria/classification/*isolation &amp; purification ; Europe ; *Forests ; Nitrogen ; Poaceae/*microbiology ; Proteobacteria/classification/isolation &amp; purification ; *Rhizosphere ; *Soil/chemistry ; *Soil Microbiology ; Stachys/*microbiology ; }, abstract = {Soil bacteria and understorey plants interact and drive forest ecosystem functioning. Yet, knowledge about biotic and abiotic factors that affect the composition of the bacterial community in the rhizosphere of understorey plants is largely lacking. Here, we assessed the effects of plant species identity (Milium effusum vs. Stachys sylvatica), rhizospheric soil characteristics, large-scale environmental conditions (temperature, precipitation and nitrogen (N) deposition), and land-use history (ancient vs. recent forests) on bacterial community composition in rhizosphere soil in temperate forests along a 1700 km latitudinal gradient in Europe. The dominant bacterial phyla in the rhizosphere soil of both plant species were Acidobacteria, Actinobacteria and Proteobacteria. Bacterial community composition differed significantly between the two plant species. Within plant species, soil chemistry was the most important factor determining soil bacterial community composition. More precisely, soil acidity correlated with the presence of multiple phyla, e.g. Acidobacteria (negatively), Chlamydiae (negatively) and Nitrospirae (positively), in both plant species. Large-scale environmental conditions were only important in S. sylvatica and land-use history was not important in either of the plant species. The observed role of understorey plant species identity and rhizosphere soil characteristics in determining soil bacterial community composition extends our understanding of plant-soil bacteria interactions in forest ecosystem functioning.}, }
@article {pmid31053974, year = {2020}, author = {Krstin, L and Katanić, Z and Repar, J and Ježić, M and Kobaš, A and Ćurković-Perica, M}, title = {Genetic Diversity of Cryphonectria hypovirus 1, a Biocontrol Agent of Chestnut Blight, in Croatia and Slovenia.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {148-163}, pmid = {31053974}, issn = {1432-184X}, support = {IZ73Z0_152525/1//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; IZIP-2016-54//Sveu&#x10d;ili&#x161;te Josipa Jurja Strossmayera u Osijeku/ ; }, mesh = {Ascomycota/*physiology/*virology ; Croatia ; Fagaceae/*microbiology ; Fungal Viruses/classification/*genetics/physiology ; Genetic Variation ; Phylogeny ; Plant Diseases/*microbiology/prevention &amp; control ; Slovenia ; }, abstract = {Transmissible hypovirulence associated with Cryphonectria hypovirus 1 (CHV1) has been used for biological control of chestnut blight, devastating disease of chestnut caused by the fungus Cryphonectria parasitica. The main aims of this study were to provide molecular characterization of CHV1 from Croatia and Slovenia and to reveal its genetic variability, phylogeny, and diversification of populations. Fifty-one CHV1 haplotypes were detected among 54 partially sequenced CHV1 isolates, all belonging to Italian subtype (I). Diversity was mainly generated by point mutations while evidence of recombination was not found. The level of conservation over analyzed parts of ORF-A proteins p29 and p40 varied, but functional sites were highly conserved. Phylogenetic analysis revealed close relatedness and intermixing of Croatian and Slovenian CHV1 populations. Our CHV1 isolates were also related to Swiss and Bosnian hypoviruses supporting previously suggested course of CHV1 invasion in Europe. Overall, this study indicates that phylogeny of CHV1 subtype I in Europe is complex and characterized with frequent point mutations resulting in many closely related variants of the virus. Possible association between variations within CHV1 ORF-A and growth of the hypovirulent fungal isolates is tested and presented.}, }
@article {pmid31050730, year = {2019}, author = {Moraïs, S and Mizrahi, I}, title = {Islands in the stream: from individual to communal fiber degradation in the rumen ecosystem.}, journal = {FEMS microbiology reviews}, volume = {43}, number = {4}, pages = {362-379}, pmid = {31050730}, issn = {1574-6976}, mesh = {Anaerobiosis ; Animal Nutritional Physiological Phenomena ; Animals ; Dietary Fiber/*metabolism ; *Ecosystem ; Rumen/*microbiology ; Ruminants/metabolism/microbiology ; }, abstract = {The herbivore rumen ecosystem constitutes an extremely efficient degradation machinery for the intricate chemical structure of fiber biomass, thus, enabling the hosting animal to digest its feed. The challenging task of deconstructing and metabolizing fiber is performed by microorganisms inhabiting the rumen. Since most of the ingested feed is comprised of plant fiber, these fiber-degrading microorganisms are of cardinal importance to the ecology of the rumen microbial community and to the hosting animal, and have a great impact on our environment and food sustainability. We summarize herein the enzymological fundamentals of fiber degradation, how the genes encoding these enzymes are spread across fiber-degrading microbes, and these microbes' interactions with other members of the rumen microbial community and potential effect on community structure. An understanding of these concepts has applied value for agriculture and our environment, and will also contribute to a better understanding of microbial ecology and evolution in anaerobic ecosystems.}, }
@article {pmid31050668, year = {2019}, author = {Melo-Bolívar, JF and Ruiz Pardo, RY and Hume, ME and Nisbet, DJ and Rodríguez-Villamizar, F and Alzate, JF and Junca, H and Villamil Díaz, LM}, title = {Establishment and characterization of a competitive exclusion bacterial culture derived from Nile tilapia (Oreochromis niloticus) gut microbiomes showing antibacterial activity against pathogenic Streptococcus agalactiae.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0215375}, pmid = {31050668}, issn = {1932-6203}, mesh = {Animals ; Bacteria/*classification/isolation &amp; purification ; Bacterial Load ; Bacteriological Techniques ; Cichlids/*microbiology ; Colombia ; Fusobacteria/isolation &amp; purification/physiology ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/*veterinary ; Lactococcus/isolation &amp; purification/physiology ; Microbial Viability ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Streptococcus agalactiae/*growth &amp; development ; }, abstract = {This study reports the characterization of the microbial community composition, and the establishment and dynamics of a continuous-flow competitive exclusion culture (CFCEC) derived from gut microbiomes of Nile tilapia (Oreochromis niloticus) specimens reared on aquaculture farms in Colombia. 16S rRNA gene amplicon Illumina sequencing was used to identify taxonomical changes in the CFCEC microbial community over time. The CFCEC was developed from adult tilapia from two farms in Colombia, and CFCEC samples were collected over two months. The pH varied from 6.25 to 6.35 throughout culturing, while anaerobic and aerobic cell counts stabilized at day 9, at 109 CFU mL-1 and were maintained to day 68. A variation in the CFCEC bacterial composition was observed over time. Cetobacterium was the most abundant in the first two days and coincided with a higher CFCEC supernatant antimicrobial effect against the fish pathogen Streptococcus agalactiae. Antimicrobial activity against S. agalactiae disappeared by day 3. Changes in bacterial composition continued to day 33 with Lactococcus spp. becoming the most abundant member of the community. In conclusion, the study of the CFCEC from intestinal tract of Nile tilapia (Oreochromis niloticus) by 16S rRNA gene sequencing allowed identification of predominant bacterial genera in the continuous-flow competitive exclusion culture exhibiting antibacterial activity against the fish pathogen Streptococcus agalactiae.}, }
@article {pmid31049616, year = {2020}, author = {Ma, GC and Worthing, KA and Ward, MP and Norris, JM}, title = {Commensal Staphylococci Including Methicillin-Resistant Staphylococcus aureus from Dogs and Cats in Remote New South Wales, Australia.}, journal = {Microbial ecology}, volume = {79}, number = {1}, pages = {164-174}, pmid = {31049616}, issn = {1432-184X}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cats/*microbiology ; Disease Reservoirs/microbiology/veterinary ; Dogs/*microbiology ; Methicillin/pharmacology ; Methicillin-Resistant Staphylococcus aureus/classification/drug effects/genetics/*isolation &amp; purification ; Microbial Sensitivity Tests ; New South Wales ; Pets/*microbiology ; }, abstract = {Staphylococci are important opportunistic pathogens in human and veterinary medicine in addition to being part of the normal flora of the skin and mucous membranes of mammals and birds. The rise of antimicrobial resistance amongst staphylococci warrants closer investigation of the diversity of skin commensal organisms-including coagulase-negative staphylococci (CoNS)-due to their potential as a source of resistance genes. This study is aimed at characterising the commensal staphylococci-including methicillin-resistant Staphylococcus species (spp.)-from mucocutaneous sites of dogs and cats from remote New South Wales (NSW), Australia. Pet dogs and cats were recruited from participants in a community companion animal health programme in six communities in western NSW. Three swabs were collected from each animal (anterior nares, oropharynx, and perineum) and from skin lesions or wounds if present and cultured on selective media for Staphylococcus spp. In total, 383 pets (303 dogs, 80 cats) were enrolled. Staphylococcus spp. were isolated from 67.3% of dogs and 73.8% of cats (494 isolates). The diversity of CoNS was high (20 species) whilst only three coagulase-positive spp. were isolated (S. pseudintermedius, S. aureus, S. intermedius). The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) carriage in dogs was high (2.6%) relative to other studies but was only a small proportion of overall commensal staphylococci. No cats carried MRSA and no MRSP was isolated from either species. Dogs were significantly more likely to carry coagulase-positive staphylococci than cats (P < 0.001). Amongst dogs, males and those with skin lesions were more likely to carry S. pseudintermedius. This study highlights important differences in the diversity and patterns of carriage of commensal staphylococci between dogs and cats in remote NSW, Australia.}, }
@article {pmid31049565, year = {2019}, author = {Samba-Louaka, A and Delafont, V and Rodier, MH and Cateau, E and Héchard, Y}, title = {Free-living amoebae and squatters in the wild: ecological and molecular features.}, journal = {FEMS microbiology reviews}, volume = {43}, number = {4}, pages = {415-434}, doi = {10.1093/femsre/fuz011}, pmid = {31049565}, issn = {1574-6976}, mesh = {Amoeba/genetics/*physiology/virology ; Bacteria/*classification/virology ; Bacterial Physiological Phenomena ; Biological Evolution ; *Ecosystem ; Genetic Variation ; }, abstract = {Free-living amoebae are protists frequently found in water and soils. They feed on other microorganisms, mainly bacteria, and digest them through phagocytosis. It is accepted that these amoebae play an important role in the microbial ecology of these environments. There is a renewed interest for the free-living amoebae since the discovery of pathogenic bacteria that can resist phagocytosis and of giant viruses, underlying that amoebae might play a role in the evolution of other microorganisms, including several human pathogens. Recent advances, using molecular methods, allow to bring together new information about free-living amoebae. This review aims to provide a comprehensive overview of the newly gathered insights into (1) the free-living amoeba diversity, assessed with molecular tools, (2) the gene functions described to decipher the biology of the amoebae and (3) their interactions with other microorganisms in the environment.}, }
@article {pmid31048756, year = {2019}, author = {Schwank, K and Bornemann, TLV and Dombrowski, N and Spang, A and Banfield, JF and Probst, AJ}, title = {An archaeal symbiont-host association from the deep terrestrial subsurface.}, journal = {The ISME journal}, volume = {13}, number = {8}, pages = {2135-2139}, pmid = {31048756}, issn = {1751-7370}, mesh = {Archaea/*genetics/isolation &amp; purification/physiology ; Ecosystem ; Genome, Archaeal/*genetics ; Groundwater ; In Situ Hybridization, Fluorescence ; *Metagenome ; Nanoarchaeota/*genetics/isolation &amp; purification/physiology ; Phylogeny ; *Symbiosis ; Utah ; }, abstract = {DPANN archaea have reduced metabolic capacities and are diverse and abundant in deep aquifer ecosystems, yet little is known about their interactions with other microorganisms that reside there. Here, we provide evidence for an archaeal host-symbiont association from a deep aquifer system at the Colorado Plateau (Utah, USA). The symbiont, Candidatus Huberiarchaeum crystalense, and its host, Ca. Altiarchaeum hamiconexum, show a highly significant co-occurrence pattern over 65 metagenome samples collected over six years. The physical association of the two organisms was confirmed with genome-informed fluorescence in situ hybridization depicting small cocci of Ca. H. crystalense attached to Ca. A. hamiconexum cells. Based on genomic information, Ca. H. crystalense potentially scavenges vitamins, sugars, nucleotides, and reduced redox-equivalents from its host and thus has a similar metabolism as Nanoarchaeum equitans. These results provide insight into host-symbiont interactions among members of two uncultivated archaeal phyla that thrive in a deep subsurface aquifer.}, }
@article {pmid31048390, year = {2019}, author = {Bryce, C and Blackwell, N and Straub, D and Kleindienst, S and Kappler, A}, title = {Draft Genome Sequence of Chlorobium sp. Strain N1, a Marine Fe(II)-Oxidizing Green Sulfur Bacterium.}, journal = {Microbiology resource announcements}, volume = {8}, number = {18}, pages = {}, pmid = {31048390}, issn = {2576-098X}, abstract = {Here, we present the draft genome sequence of the halotolerant photoferrotroph Chlorobium sp. strain N1. This draft genome provides insights into the genomic potential of the only marine Fe(II)-oxidizing green sulfur bacterium (GSB) available in culture and expands our views on the metabolic capabilities of Fe(II)-oxidizing GSB more generally.}, }
@article {pmid31046835, year = {2019}, author = {Sharma, A and Richardson, M and Cralle, L and Stamper, CE and Maestre, JP and Stearns-Yoder, KA and Postolache, TT and Bates, KL and Kinney, KA and Brenner, LA and Lowry, CA and Gilbert, JA and Hoisington, AJ}, title = {Longitudinal homogenization of the microbiome between both occupants and the built environment in a cohort of United States Air Force Cadets.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {70}, pmid = {31046835}, issn = {2049-2618}, mesh = {Bacteria/classification/isolation &amp; purification ; *Built Environment ; Cohort Studies ; Diet ; *Environmental Microbiology ; Female ; Gastrointestinal Microbiome ; *Housing ; Humans ; Longitudinal Studies ; Male ; *Microbiota ; *Military Personnel ; RNA, Ribosomal, 16S ; Skin/microbiology ; United States ; Young Adult ; }, abstract = {BACKGROUND: The microbiome of the built environment has important implications for human health and wellbeing; however, bidirectional exchange of microbes between occupants and surfaces can be confounded by lifestyle, architecture, and external environmental exposures. Here, we present a longitudinal study of United States Air Force Academy cadets (n = 34), which have substantial homogeneity in lifestyle, diet, and age, all factors that influence the human microbiome. We characterized bacterial communities associated with (1) skin and gut samples from roommate pairs, (2) four built environment sample locations inside the pairs' dormitory rooms, (3) four built environment sample locations within shared spaces in the dormitory, and (4) room-matched outdoor samples from the window ledge of their rooms.<br><br>RESULTS: We analyzed 2,170 samples, which generated 21,866 unique amplicon sequence variants. Linear convergence of microbial composition and structure was observed between an occupants' skin and the dormitory surfaces that were only used by that occupant (i.e., desk). Conversely, bacterial community beta diversity (weighted Unifrac) convergence between the skin of both roommates and the shared dormitory floor between the two cadet's beds was not seen across the entire study population. The sampling period included two semester breaks in which the occupants vacated their rooms; upon their return, the beta diversity similarity between their skin and the surfaces had significantly decreased compared to before the break (p&#x2009;<&#x2009;0.05). There was no apparent convergence between the gut and building microbiota, with the exception of communal bathroom door-handles, which suggests that neither co-occupancy, diet, or lifestyle homogenization had a significant impact on gut microbiome similarity between these cadets over the observed time frame. As a result, predictive classifier models were able to identify an individual more accurately based on the gut microbiota (74%) compared to skin (51%).<br><br>CONCLUSIONS: To the best of our knowledge, this is the first study to show an increase in skin microbial similarity of two individuals who start living together for the first time and who are not genetically related or romantically involved. Cohabitation was significantly associated with increased skin microbiota similarity but did not significantly influence the gut microbiota. Following a departure from the occupied space of several weeks, the skin microbiota, but not the gut microbiota, showed a significant reduction in similarity relative to the building. Overall, longitudinal observation of these dynamics enables us to dissect the influence of occupation, diet, and lifestyle factors on occupant and built environment microbial ecology.}, }
@article {pmid31040329, year = {2019}, author = {Engel, F and Attermeyer, K and Ayala, AI and Fischer, H and Kirchesch, V and Pierson, DC and Weyhenmeyer, GA}, title = {Phytoplankton gross primary production increases along cascading impoundments in a temperate, low-discharge river: Insights from high frequency water quality monitoring.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6701}, pmid = {31040329}, issn = {2045-2322}, abstract = {Damming alters carbon processing along river continua. Estimating carbon transport along rivers intersected by multiple dams requires an understanding of the effects of cascading impoundments on the riverine metabolism. We analyzed patterns of riverine metabolism and phytoplankton biomass (chlorophyll a; Chla) along a 74.4-km river reach intersected by six low-head navigation dams. Calculating gross primary production (GPP) from continuous measurements of dissolved oxygen concentration, we found a maximum increase in the mean GPP by a factor of 3.5 (absolute difference of 0.45 g C m[-3] d[-1]) along the first 26.5 km of the study reach, while Chla increased over the entire reach by a factor of 2.9 (8.7 µg l[-1]). In the intermittently stratified section of the deepest impoundment the mean GPP between the 1 and 4 m water layer differed by a factor of 1.4 (0.31 g C m[-3] d[-1]). Due to the strong increase in GPP, the river featured a wide range of conditions characteristic of low- to medium-production rivers. We suggest that cascading impoundments have the potential to stimulate riverine GPP, and conclude that phytoplankton CO2 uptake is an important carbon flux in the river Saar, where a considerable amount of organic matter is of autochthonous origin.}, }
@article {pmid31038352, year = {2019}, author = {Dong, Y and Sanford, RA and Inskeep, WP and Srivastava, V and Bulone, V and Fields, CJ and Yau, PM and Sivaguru, M and Ahrén, D and Fouke, KW and Weber, J and Werth, CR and Cann, IK and Keating, KM and Khetani, RS and Hernandez, AG and Wright, C and Band, M and Imai, BS and Fried, GA and Fouke, BW}, title = {Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats.}, journal = {Astrobiology}, volume = {19}, number = {12}, pages = {1442-1458}, pmid = {31038352}, issn = {1557-8070}, mesh = {Bacteria/genetics/isolation &amp; purification/metabolism ; *Biodiversity ; Carbon Cycle ; DNA, Bacterial/isolation &amp; purification ; Extremophiles/isolation &amp; purification/*physiology ; Fimbriae Proteins/genetics/metabolism ; Fossils/microbiology ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Geologic Sediments/microbiology ; Hot Springs/*microbiology ; Microbiota/*physiology ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfur/metabolism ; }, abstract = {The evolutionarily ancient Aquificales bacterium Sulfurihydrogenibium spp. dominates filamentous microbial mat communities in shallow, fast-flowing, and dysoxic hot-spring drainage systems around the world. In the present study, field observations of these fettuccini-like microbial mats at Mammoth Hot Springs in Yellowstone National Park are integrated with geology, geochemistry, hydrology, microscopy, and multi-omic molecular biology analyses. Strategic sampling of living filamentous mats along with the hot-spring CaCO3 (travertine) in which they are actively being entombed and fossilized has permitted the first direct linkage of Sulfurihydrogenibium spp. physiology and metabolism with the formation of distinct travertine streamer microbial biomarkers. Results indicate that, during chemoautotrophy and CO2 carbon fixation, the 87-98% Sulfurihydrogenibium-dominated mats utilize chaperons to facilitate enzyme stability and function. High-abundance transcripts and proteins for type IV pili and extracellular polymeric substances (EPSs) are consistent with their strong mucus-rich filaments tens of centimeters long that withstand hydrodynamic shear as they become encrusted by more than 5 mm of travertine per day. Their primary energy source is the oxidation of reduced sulfur (e.g., sulfide, sulfur, or thiosulfate) and the simultaneous uptake of extremely low concentrations of dissolved O2 facilitated by bd-type cytochromes. The formation of elevated travertine ridges permits the Sulfurihydrogenibium-dominated mats to create a shallow platform from which to access low levels of dissolved oxygen at the virtual exclusion of other microorganisms. These ridged travertine streamer microbial biomarkers are well preserved and create a robust fossil record of microbial physiological and metabolic activities in modern and ancient hot-spring ecosystems.}, }
@article {pmid31037377, year = {2019}, author = {Wu, C and Kan, J and Liu, H and Pujari, L and Guo, C and Wang, X and Sun, J}, title = {Heterotrophic Bacteria Dominate the Diazotrophic Community in the Eastern Indian Ocean (EIO) during Pre-Southwest Monsoon.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {804-819}, pmid = {31037377}, issn = {1432-184X}, support = {41276124//the National Natural Science Foundation of China/ ; 41676112//the National Natural Science Foundation of China/ ; NORC2017-10//NSFC open research cruises/ ; TD12-5003//the Science Fund for University Creative Research Groups in Tianjin/ ; 41876134//Foundation for the Author of National Excellent Doctoral Dissertation of the People's Republic of China (CN)/ ; }, mesh = {Bacteria/classification/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Indian Ocean ; *Microbiota ; Phylogeny ; Seasons ; Seawater/*microbiology ; }, abstract = {The diazotrophic communities play an important role in sustaining primary productivity through adding new nitrogen to oligotrophic marine ecosystems. Yet, their composition in the oligotrophic Indian Ocean is poorly understood. Here, we report the first observation of phylogenetic diversity and distribution of diazotrophs in the Eastern Indian Ocean (EIO) surface water (to 200 m) during the pre-southwest monsoon period. Through high throughput sequencing of nifH genes, we identified diverse groups of diazotrophs in the EIO including both non-cyanobacterial and cyanobacterial phylotypes. Proteobacteria (mainly Alpha-, Beta-, and Gamma-proteobacteria) were the most diverse and abundant groups within all the diazotrophs, which accounted for more than 86.9% of the total sequences. Cyanobacteria were also retrieved, and they were dominated by the filamentous non-heterocystous cyanobacteria Trichodesmium spp. Other cyanobacteria such as unicellular diazotrophic cyanobacteria were detected sporadically. Interestingly, our qPCR analysis demonstrated that the depth-integrated gene abundances of the diazotrophic communities exhibited spatial heterogeneity with Trichodesmium spp. appeared to be more abundant in the Bay of Bengal (p < 0.05), while Sagittula castanea (Alphaproteobacteria) was found to be more dominating in the equatorial region and offshores (p < 0.05). Non-metric multidimensional scaling analysis (NMDS) further confirmed distinct vertical and horizontal spatial variations in the EIO. Canonical correspondence analysis (CCA) indicated that temperature, salinity, and phosphate were the major environmental factors driving the distribution of the diazotroph communities. Overall, our study provides the first insight into the diversity and distribution of the diazotrophic communities in EIO. The findings from this study highlight distinct contributions of both non-cyanobacteria and cyanobacteria to N2 fixation. Moreover, our study reveals information that is critical for understanding spatial heterogeneity and distribution of diazotrophs, and their vital roles in nitrogen and carbon cycling.}, }
@article {pmid31037376, year = {2019}, author = {Robledo-Mahón, T and Silva-Castro, GA and Kuhar, U and Jamnikar-Ciglenečki, U and Barlič-Maganja, D and Aranda, E and Calvo, C}, title = {Effect of Composting Under Semipermeable Film on the Sewage Sludge Virome.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {895-903}, pmid = {31037376}, issn = {1432-184X}, mesh = {*Composting/methods ; Sewage/*virology ; *Soil Microbiology ; Spain ; Virus Physiological Phenomena ; Viruses/classification/*isolation &amp; purification ; }, abstract = {The addition of compost from sewage sludge to soils represents a sustainable option from an environmental and economic point of view, which involves the valorisation of these wastes. However, before their use as a soil amendment, compost has to reach the quality levels according to the normative, including microbial parameters. Viruses are not included in this regulation and they can produce agricultural problems and human diseases if the compost is not well sanitised. In this study, we carried out the analysis of the viral populations during a composting process with sewage sludge at an industrial scale, using semipermeable cover technology. Viral community was characterised by the presence of plant viruses and bacteriophages of enteric bacteria. The phytopathogen viruses were the group with the highest relative abundance in the sewage sludge sample and at 70 days of the composting process. The diversity of bacterial viruses and their specificity, with respect to the more abundant bacterial taxa throughout the process, highlights the importance of the interrelations between viral and bacterial communities in the control of pathogenic communities. These results suggest the possibility of using them as a tool to predict the effectiveness of the process.}, }
@article {pmid31031958, year = {2019}, author = {Collins, GE and Hogg, ID and Baxter, JR and Maggs-Kölling, G and Cowan, DA}, title = {Ancient landscapes of the Namib Desert harbor high levels of genetic variability and deeply divergent lineages for Collembola.}, journal = {Ecology and evolution}, volume = {9}, number = {8}, pages = {4969-4979}, pmid = {31031958}, issn = {2045-7758}, support = {U54 ES030246/ES/NIEHS NIH HHS/United States ; }, abstract = {AIM: To assess spatial patterns of genetic and species-level diversity for Namib Desert Collembola using mitochondrial DNA cytochrome c oxidase subunit I (COI) gene sequences.<br><br>LOCATION: Namib Desert gravel plains.<br><br>TAXON: Collembola (springtails).<br><br>METHODS: A total of 77 soil samples were collected along NE-SW (60&#xa0;km) and E-W (160&#xa0;km) transects from within a 4,000&#xa0;km[2] area of the Namib Desert gravel plains. We extracted 434 springtails from the 37 samples which contained Collembola and sequenced them at the COI gene locus. In the absence of specific taxonomic keys and previous genetic data for these taxa, we used Generalized Mixed Yule Coalescent (GMYC) analyses to provide putative species-level designations.<br><br>RESULTS: We obtained 341 successful COI sequences, 175 of which were unique haplotypes. GMYC analyses identified 30 putative species, with up to 28% sequence divergence (uncorrected p-distance). The distribution of genetic variants was disjunct, with 97% of haplotypes and 70% of "GMYC species" found only at single sites.<br><br>MAIN CONCLUSIONS: Dispersal events, although rare, may be facilitated by environmental events such as prevailing onshore winds or occasional flow of rainwater to the coast. We conclude that the high genetic diversity we observed is the result of ancient springtail lineages, patchy distribution of suitable habitats, and limited dispersal (gene flow) among habitable locations.}, }
@article {pmid31031435, year = {2019}, author = {Gomes, J and Khandeparker, R and Meena, RM and Ramaiah, N}, title = {Bacterial Community Composition Markedly Altered by Coastal Hypoxia.}, journal = {Indian journal of microbiology}, volume = {59}, number = {2}, pages = {200-208}, pmid = {31031435}, issn = {0046-8991}, abstract = {Monsoonal upwelling along south and central west coast of India leads to intense biological productivity. As a consequence of excess organic matter production following upwelling during June-October and low dissolved oxygen in the upwelled waters, denitrification occurs in the near shore waters. Implicitly, these processes ought to bring alterations in microbial communities. Therefore, diversity and community structure of bacteria from subsurface layers of a tropical region experiencing intense seasonal lows of oxygen were analyzed through sequencing of 16S rRNA gene clones. The overall diversity was more during hypoxic period of Fall intermonsoon (FIM, October) compared either to Spring intermonsoon (SIM, March) or summer monsoon (SuM, June) months. As many as 14 lineages of bacterial domains: Gammaproteobacteria (37%), Alphaproteobacteria (21%), Cyanobacteria (20%), Deltaproteobacteria (3%), Firmicutes (3%), Betaproteobacteria (2%), Acidobacteria (2%), Actinobacteria (7%), Marinimicrobia (2%), Bacteroidetes (1%), Verrucomicrobia (1%), Planctomycetes (0.4%), Chloroflexi (0.2%) and Omnitrophica bacterium (0.2%), were recognized from our coastal location. Notably, sequences of Planctomycetes, Chloroflexi and Omnitrophica bacterium were found exclusively during FIM. A generally higher representation of sequences of Betaproteobacteria during SuM and of Actinobacteria and Firmicutes during SIM was discernible. This study is thus useful to recognize that microbial community might undergo strong temporal shifts in the monsoon affected tropical coastal ecosystems.}, }
@article {pmid31031118, year = {2019}, author = {Enke, TN and Datta, MS and Schwartzman, J and Cermak, N and Schmitz, D and Barrere, J and Pascual-García, A and Cordero, OX}, title = {Modular Assembly of Polysaccharide-Degrading Marine Microbial Communities.}, journal = {Current biology : CB}, volume = {29}, number = {9}, pages = {1528-1535.e6}, doi = {10.1016/j.cub.2019.03.047}, pmid = {31031118}, issn = {1879-0445}, support = {T32 GM087237/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification ; *Bacterial Physiological Phenomena ; Massachusetts ; Microbiota/*physiology ; Seawater/*microbiology ; }, abstract = {Understanding the principles that govern the assembly of microbial communities across earth's biomes is a major challenge in modern microbial ecology. This pursuit is complicated by the difficulties of mapping functional roles and interactions onto communities with immense taxonomic diversity and of identifying the scale at which microbes interact [1]. To address this challenge, here, we focused on the bacterial communities that colonize and degrade particulate organic matter in the ocean [2-4]. We show that the assembly of these communities can be simplified as a linear combination of functional modules. Using synthetic polysaccharide particles immersed in natural bacterioplankton assemblages [1, 5], we showed that successional particle colonization dynamics are driven by the interaction of two types of modules: a first type made of narrowly specialized primary degraders, whose dynamics are controlled by particle polysaccharide composition, and a second type containing substrate-independent taxa whose dynamics are controlled by interspecific interactions-in particular, cross-feeding via organic acids, amino acids, and other metabolic byproducts. We show that, as a consequence of this trophic structure, communities can assemble modularly-i.e., by a simple sum of substrate-specific primary degrader modules, one for each complex polysaccharide in the particle, connected to a single broad-niche range consumer module. Consistent with this model, a linear combination of the communities on single-polysaccharide particles accurately predicts community composition on mixed-polysaccharide particles. Our results suggest that the assembly of heterotrophic communities that degrade complex organic materials follows simple design principles that could be exploited to engineer heterotrophic microbiomes.}, }
@article {pmid31031092, year = {2019}, author = {Hull, NM and Ling, F and Pinto, AJ and Albertsen, M and Jang, HG and Hong, PY and Konstantinidis, KT and LeChevallier, M and Colwell, RR and Liu, WT}, title = {Drinking Water Microbiome Project: Is it Time?.}, journal = {Trends in microbiology}, volume = {27}, number = {8}, pages = {670-677}, doi = {10.1016/j.tim.2019.03.011}, pmid = {31031092}, issn = {1878-4380}, mesh = {Drinking Water/*microbiology ; Humans ; *Microbiota ; Water Microbiology ; }, abstract = {Now is an opportune time to foster collaborations across sectors and geographical boundaries to enable development of best practices for drinking water (DW) microbiome research, focusing on accuracy and reproducibility of meta-omic techniques (while learning from past microbiome projects). A large-scale coordinated effort that builds on this foundation will enable the urgently needed comprehensive spatiotemporal understanding and control of DW microbiomes by engineering interventions to protect public health. This opinion paper highlights the need to initiate and conduct a large-scale coordinated DW microbiome project by addressing key knowledge gaps and recommends a roadmap for this effort.}, }
@article {pmid31030239, year = {2019}, author = {Omae, K and Fukuyama, Y and Yasuda, H and Mise, K and Yoshida, T and Sako, Y}, title = {Diversity and distribution of thermophilic hydrogenogenic carboxydotrophs revealed by microbial community analysis in sediments from multiple hydrothermal environments in Japan.}, journal = {Archives of microbiology}, volume = {201}, number = {7}, pages = {969-982}, pmid = {31030239}, issn = {1432-072X}, support = {16J11269//Grant-in-Aid from the Japan Society for the Promotion of Science (JSPS) Fellows/ ; 25252038//Japan Society for the Promotion of Science/ ; 16H06381//Japan Society for the Promotion of Science/ ; }, mesh = {Aldehyde Oxidoreductases/metabolism ; *Biodiversity ; Carbon Monoxide/metabolism ; Firmicutes/physiology ; Geologic Sediments/*microbiology ; Hot Springs/*microbiology ; Hydrogenase/*genetics/metabolism ; Japan ; Microbiota/genetics/*physiology ; Multienzyme Complexes/metabolism ; Multigene Family/genetics ; }, abstract = {In hydrothermal environments, carbon monoxide (CO) utilisation by thermophilic hydrogenogenic carboxydotrophs may play an important role in microbial ecology by reducing toxic levels of CO and providing H2 for fuelling microbial communities. We evaluated thermophilic hydrogenogenic carboxydotrophs by microbial community analysis. First, we analysed the correlation between carbon monoxide dehydrogenase (CODH)-energy-converting hydrogenase (ECH) gene cluster and taxonomic affiliation by surveying an increasing genomic database. We identified 71 genome-encoded CODH-ECH gene clusters, including 46 whose owners were not reported as hydrogenogenic carboxydotrophs. We identified 13 phylotypes showing > 98.7% identity with these taxa as potential hydrogenogenic carboxydotrophs in hot springs. Of these, Firmicutes phylotypes such as Parageobacillus, Carboxydocella, Caldanaerobacter, and Carboxydothermus were found in different environmental conditions and distinct microbial communities. The relative abundance of the potential thermophilic hydrogenogenic carboxydotrophs was low. Most of them did not show any symbiotic networks with other microbes, implying that their metabolic activities might be low.}, }
@article {pmid31026580, year = {2019}, author = {Han, M and Dsouza, M and Zhou, C and Li, H and Zhang, J and Chen, C and Yao, Q and Zhong, C and Zhou, H and Gilbert, JA and Wang, Z and Ning, K}, title = {Agricultural Risk Factors Influence Microbial Ecology in Honghu Lake.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {17}, number = {1}, pages = {76-90}, pmid = {31026580}, issn = {2210-3244}, mesh = {*Agriculture ; Animals ; Anti-Bacterial Agents/*analysis ; China ; Eutrophication ; Geologic Sediments/chemistry/microbiology ; Lakes/chemistry/*microbiology ; *Microbiota ; Risk Factors ; Water Pollutants, Chemical/*analysis ; }, abstract = {Agricultural activities, including stock-farming, planting industry, and fish aquaculture, can affect the physicochemical and biological characters of freshwater lakes. However, the effects of pollution producing by agricultural activities on microbial ecosystem of lakes remain unclear. Hence, in this work, we selected Honghu Lake as a typical lake that is influenced by agriculture activities. We collected water and sediment samples from 18 sites, which span a wide range of areas from impacted and less-impacted areas. We performed a geospatial analysis on the composition of microbial communities associated with physicochemical properties and antibiotic pollution of samples. The co-occurrence networks of water and sediment were also built and analyzed. Our results showed that the microbial communities of impacted and less-impacted samples of water were largely driven by the concentrations of TN, TP, NO3[-]-N, and NO2[-]-N, while those of sediment were affected by the concentrations of Sed-OM and Sed-TN. Antibiotics have also played important roles in shaping these microbial communities: the concentrations of oxytetracycline and tetracycline clearly reflected the variance in taxonomic diversity and predicted functional diversity between impacted and less-impacted sites in water and sediment samples, respectively. Furthermore, for samples from both water and sediment, large differences of network topology structures between impacted and less-impacted were also observed. Our results provide compelling evidence that the microbial community can be used as a sentinel of eutrophication and antibiotics pollution risk associated with agricultural activity; and that proper monitoring of this environment is vital to maintain a sustainable environment in Honghu Lake.}, }
@article {pmid31025063, year = {2019}, author = {Negi, A and Sarethy, IP}, title = {Microbial Biodeterioration of Cultural Heritage: Events, Colonization, and Analyses.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {1014-1029}, pmid = {31025063}, issn = {1432-184X}, mesh = {Architecture ; *Bacterial Physiological Phenomena ; Biofilms/*growth &amp; development ; Construction Materials/*microbiology ; Microbiota/*physiology ; }, abstract = {Geochemical cycles result in the chemical, physical, and mineralogical modification of rocks, eventually leading to formation of soil. However, when the stones and rocks are a part of historic buildings and monuments, the effects are deleterious. In addition, microorganisms also colonize these monuments over a period of time, resulting in formation of biofilms; their metabolites lead to physical weakening and discoloration of stone eventually. This process, known as biodeterioration, leads to a significant loss of cultural heritage. For formulating effective conservation strategies to prevent biodeterioration and restore monuments, it is important to know which microorganisms are colonizing the substrate and the different energy sources they consume to sustain themselves. With this view in scope, this review focuses on studies that have attempted to understand the process of biodeterioration, the mechanisms by which they colonize and affect the monuments, the techniques used for assessment of biodeterioration, and conservation strategies that aim to preserve the original integrity of the monuments. This review also includes the "omics" technologies that have started playing a large role in elucidating the nature of microorganisms, and how they can play a role in hastening the formulation of effective conservation strategies.}, }
@article {pmid31025062, year = {2019}, author = {Zhao, Z and Zhang, X and Cheng, M and Song, X and Zhang, Y and Zhong, X}, title = {Influences of Iron Compounds on Microbial Diversity and Improvements in Organic C, N, and P Removal Performances in Constructed Wetlands.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {792-803}, pmid = {31025062}, issn = {1432-184X}, support = {D-8005-18-0068-1/2//China Postdoctoral Science Foundation/ ; 51679041//National Natural Science Foundation of China/ ; A2-0203-00-100356//Shanghai Ocean University Ph. D Start-Up Fund/ ; 2017B020236002//program of. science and technology in Guangdong Province/ ; }, mesh = {Bacteria/classification/*metabolism ; Biodegradation, Environmental ; Carbon/*metabolism ; Iron Compounds ; *Microbiota ; Nitrogen/*metabolism ; Phosphorus/*metabolism ; *Waste Disposal, Fluid ; Water Pollutants, Chemical/metabolism ; Water Pollution, Chemical/analysis ; Wetlands ; }, abstract = {The effects of various combinations of iron compounds on the contaminant removal performance in constructed wetlands (CWs) were explored under various initial iron concentrations, contaminant concentrations, different hydraulic retention time (HRT), and different temperatures. The Combo 6 (nanoscale zero-valent iron combined with Fe[3+]) in CW treatments showed the highest pollutant removal performance under the conditions of C2 initial iron dosage concentration (total iron 0.2 mM) and I2 initial contaminant concentration (COD:TN:TP = 60 mg/L:60 mg/L:1 mg/L) in influent after 72-h HRT. These results were directly verified by two different microbial tests (Biolog test and high-throughput pyrosequencing) and microbial community analysis (principal component analysis of community-level physiological profile, biodiversity index, cluster tree, relative abundance at order of taxonomy level). Specific bacteria related to significant improvements in contaminant removal were domesticated by various combinations of iron compounds. Iron dosage was advised as a green, new, and effective option for wastewater treatment. Graphical Abstract .}, }
@article {pmid31024771, year = {2019}, author = {Cipriano, MAP and Suleiman, AKA and da Silveira, APD and do Carmo, JB and Kuramae, EE}, title = {Bacterial community composition and diversity of two different forms of an organic residue of bioenergy crop.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6768}, pmid = {31024771}, issn = {2167-8359}, abstract = {The use of residue of sugarcane ethanol industry named vinasse in fertirrigation is an established and widespread practice in Brazil. Both non-concentrated vinasse (NCV) and concentrated vinasse (CV) are used in fertirrigation, particularly to replace the potassium fertilizer. Although studies on the chemical and organic composition of vinasse and their impact on nitrous oxide emissions when applied in soil have been carried out, no studies have evaluated the microbial community composition and diversity in different forms of vinasse. We assessed the bacterial community composition of NCV and CV by non-culturable and culturable approaches. The non-culturable bacterial community was assessed by next generation sequencing of the 16S rRNA gene and culturable community by isolation of bacterial strains and molecular and biochemical characterization. Additionally, we assessed in the bacterial strains the presence of genes of nitrogen cycle nitrification and denitrification pathways. The microbial community based on 16S rRNA sequences of NCV was overrepresented by Bacilli and Negativicutes while CV was mainly represented by Bacilli class. The isolated strains from the two types of vinasse belong to class Bacilli, similar to Lysinibacillus, encode for nirK gene related to denitrification pathway. This study highlights the bacterial microbial composition particularly in CV what residue is currently recycled and recommended as a sustainable practice in sugarcane cultivation in the tropics.}, }
@article {pmid31024471, year = {2019}, author = {Lacerda-Júnior, GV and Noronha, MF and Cabral, L and Delforno, TP and de Sousa, STP and Fernandes-Júnior, PI and Melo, IS and Oliveira, VM}, title = {Land Use and Seasonal Effects on the Soil Microbiome of a Brazilian Dry Forest.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {648}, pmid = {31024471}, issn = {1664-302X}, abstract = {Drylands occupy approximately 41% of the Earth's terrestrial surface. Climate change and land use practices are expected to affect biogeochemical cycling by the soil microbiome in these ecosystems. Understanding how soil microbial community might respond to these drivers is extremely important to mitigate the processes of land degradation and desertification. The Caatinga, an exclusively Brazilian biome composed of an extensive seasonal tropical dry forest, is exposed to variable spatiotemporal rainfall patterns as well as strong human-driven pressures. Herein, an integrated analysis of shotgun metagenomics approach coupled to meteorological data was employed to unravel the impact of seasonality and land use change on soil microbiome from preserved and agriculture-affected experimental fields in Caatinga drylands. Multivariate analysis suggested that microbial communities of preserved soils under seasonal changes were shaped primarily by water deficit, with a strong increase of Actinobacteria and Proteobacteria members in the dry and rainy seasons, respectively. In contrast, nutrient availability notably played a critical role in driving the microbial community in agriculture-affected soils. The strong enrichment of bacterial genera belonging to the poorly-known phylum Acidobacteria ('Candidatus Solibacter' and 'Candidatus Koribacter') in soils from dry season affected by ferti-irrigation practices presupposes a contrasting copiotrophic lifestyle and ecological role in mitigating the impact of chemical fertilization. Functional analyses identify overrepresented genes related to osmotic stress response (synthesis of osmoprotectant compounds, accumulation of potassium ions) and preferential carbon and nitrogen utilization when comparing the microbiome of preserved soils under seasonal changes, reflecting differences in the genetic potential for nutrient cycling and C acquisition in the environment. However, the prevalence of nitrosative stress and denitrification functions in irrigation/fertilization-affected soils of the dry season clearly suggest that nutrient input and disruption of natural water regime may impact biogeochemical cycles linked to the microbial processes, with potential impacts on the ecosystem functionality. These findings help to better understand how natural seasonality and agricultural management differentially affect soil microbial ecology from dry forests, providing support for the development of more sustainable land management in dryland ecosystems.}, }
@article {pmid31021624, year = {2019}, author = {Mani, T and Primpke, S and Lorenz, C and Gerdts, G and Burkhardt-Holm, P}, title = {Microplastic Pollution in Benthic Midstream Sediments of the Rhine River.}, journal = {Environmental science &amp; technology}, volume = {53}, number = {10}, pages = {6053-6062}, doi = {10.1021/acs.est.9b01363}, pmid = {31021624}, issn = {1520-5851}, mesh = {Environmental Monitoring ; Geologic Sediments ; *Plastics ; Rivers ; *Water Pollutants, Chemical ; }, abstract = {Rivers are major transport vectors for microplastics (MP) toward the sea. However, there is evidence that MP can temporarily or permanently be inhibited from migrating downstream by retention in sediments or ingestion by organisms. MP concentrations, compositions, and fate within the different compartments of the fluvial environment are poorly understood. Here, benthic, midstream sediments of two undammed, open-flowing stretches were investigated in the Rhine River, one of the world's busiest inland waterways. Twenty-five samples were collected at ten sites via riverbed access through a diving bell or dredging. We performed the first comprehensive analysis of riverbed sediment aliquots that avoids visual selection bias using state-of-the art automated micro-Fourier-transform infrared spectroscopy (μFTIR) imaging. MP numbers ranged between 0.26 ± 0.01 and 11.07 ± 0.6 × 10[3] MP kg[-1] while MP particles <75 μm accounted for a mean numerical proportion ± SD of 96 ± 6%. MP concentrations decreased with sediment depth. Eighteen polymers were identified in the size range of 11-500 μm; the acrylates/polyurethane/varnish (APV) cluster was found at all sites (mean numerical proportion, 70 ± 19%), possibly indicating particulate pollution from ship antifouling paint. Overall, polymers denser than freshwater (>1 g cm[-3]) dominated (85 ± 18%), which contrasts the large proportions of low-density polymers previously reported in near-surface compartments of the Rhine.}, }
@article {pmid31019271, year = {2019}, author = {Averill, C and Cates, LL and Dietze, MC and Bhatnagar, JM}, title = {Spatial vs. temporal controls over soil fungal community similarity at continental and global scales.}, journal = {The ISME journal}, volume = {13}, number = {8}, pages = {2082-2093}, pmid = {31019271}, issn = {1751-7370}, mesh = {Climate ; Ecology ; Ecosystem ; Fungi/genetics/*physiology ; Geography ; Mycobiome/genetics/*physiology ; Seasons ; *Soil Microbiology ; Surveys and Questionnaires ; Time Factors ; }, abstract = {Large-scale environmental sequencing efforts have transformed our understanding of the spatial controls over soil microbial community composition and turnover. Yet, our knowledge of temporal controls is comparatively limited. This is a major uncertainty in microbial ecology, as there is increasing evidence that microbial community composition is important for predicting microbial community function in the future. Here, we use continental- and global-scale soil fungal community surveys, focused within northern temperate latitudes, to estimate the relative contribution of time and space to soil fungal community turnover. We detected large intra-annual temporal differences in soil fungal community similarity, where fungal communities differed most among seasons, equivalent to the community turnover observed over thousands of kilometers in space. inter-annual community turnover was comparatively smaller than intra-annual turnover. Certain environmental covariates, particularly climate covariates, explained some spatial-temporal effects, though it is unlikely the same mechanisms drive spatial vs. temporal turnover. However, these commonly measured environmental covariates could not fully explain relationships between space, time and community composition. These baseline estimates of fungal community turnover in time provide a starting point to estimate the potential duration of legacies in microbial community composition and function.}, }
@article {pmid31016338, year = {2019}, author = {Nappi, J and Soldi, E and Egan, S}, title = {Diversity and Distribution of Bacteria Producing Known Secondary Metabolites.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {885-894}, pmid = {31016338}, issn = {1432-184X}, support = {FT130100828//Australian Research Council/ ; }, mesh = {Bacteria/classification/isolation &amp; purification/*metabolism ; Environmental Microbiology ; Genes, Bacterial ; Microbiota/*physiology ; New South Wales ; Seawater/*microbiology ; }, abstract = {There is an increasing interest in the utilisation of marine bioactive compounds as novel biopharmaceuticals and agrichemicals; however, little is known about the environmental distribution for many of these molecules. Here, we aimed to elucidate the environmental distribution and to detect the biosynthetic gene clusters in environmental samples of four bioactive compounds, namely violacein, tropodithietic acid (TDA), tambjamine and the antibacterial protein AlpP. Our database analyses revealed high bacterial diversity for AlpP and violacein producers, while TDA-producing bacteria were mostly associated with marine surfaces and all belonged to the roseobacter group. In contrast, the tambjamine cluster was only found in the genomes of two Pseudoalteromonas species and in one terrestrial species belonging to the Cupriavidus genus. Using a PCR-based screen of different marine samples, we detected TDA and violacein genes associated with the microbiome of Ulva and Protohyale niger and tambjamine genes associated with Nodilittorina unifasciata; however, alpP was not detected. These results highlight the variable distribution of the genes encoding these four bioactive compounds, including their detection from the surface of multiple marine eukaryotic hosts. Determining the natural distribution of these gene clusters will help to understand the ecological importance of these metabolites and the bacteria that produce them.}, }
@article {pmid31015413, year = {2019}, author = {Kits, KD and Jung, MY and Vierheilig, J and Pjevac, P and Sedlacek, CJ and Liu, S and Herbold, C and Stein, LY and Richter, A and Wissel, H and Brüggemann, N and Wagner, M and Daims, H}, title = {Low yield and abiotic origin of N2O formed by the complete nitrifier Nitrospira inopinata.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1836}, pmid = {31015413}, issn = {2041-1723}, support = {P 30570/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Ammonia/*metabolism ; Archaea/metabolism ; Bacteria/drug effects/*metabolism ; Climate Change ; Cyclic N-Oxides/pharmacology ; Imidazoles/pharmacology ; Metabolic Networks and Pathways/drug effects/physiology ; Nitric Oxide/*metabolism ; Nitrification/drug effects/physiology ; Nitrous Oxide/*metabolism ; Oxidation-Reduction ; Soil Microbiology ; }, abstract = {Nitrous oxide (N2O) and nitric oxide (NO) are atmospheric trace gases that contribute to climate change and affect stratospheric and ground-level ozone concentrations. Ammonia oxidizing bacteria (AOB) and archaea (AOA) are key players in the nitrogen cycle and major producers of N2O and NO globally. However, nothing is known about N2O and NO production by the recently discovered and widely distributed complete ammonia oxidizers (comammox). Here, we show that the comammox bacterium Nitrospira inopinata is sensitive to inhibition by an NO scavenger, cannot denitrify to N2O, and emits N2O at levels that are comparable to AOA but much lower than AOB. Furthermore, we demonstrate that N2O formed by N. inopinata formed under varying oxygen regimes originates from abiotic conversion of hydroxylamine. Our findings indicate that comammox microbes may produce less N2O during nitrification than AOB.}, }
@article {pmid31015324, year = {2019}, author = {Easton, AV and Quiñones, M and Vujkovic-Cvijin, I and Oliveira, RG and Kepha, S and Odiere, MR and Anderson, RM and Belkaid, Y and Nutman, TB}, title = {The Impact of Anthelmintic Treatment on Human Gut Microbiota Based on Cross-Sectional and Pre- and Postdeworming Comparisons in Western Kenya.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, pmid = {31015324}, issn = {2150-7511}, support = {MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anthelmintics/*administration &amp; dosage ; Ascariasis/*drug therapy ; Bacteria/*classification/genetics ; Child ; Child, Preschool ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Kenya ; Metagenomics ; Microbiota/*drug effects ; Middle Aged ; Necatoriasis/*drug therapy ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Rural Population ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Murine studies suggest that the presence of some species of intestinal helminths is associated with changes in host microbiota composition and diversity. However, studies in humans have produced varied conclusions, and the impact appears to vary widely depending on the helminth species present. To demonstrate how molecular approaches to the human gut microbiome can provide insights into the complex interplay among disparate organisms, DNA was extracted from cryopreserved stools collected from residents of 5 rural Kenyan villages prior to and 3 weeks and 3 months following albendazole (ALB) therapy. Samples were analyzed by quantitative PCR (qPCR) for the presence of 8 species of intestinal parasites and by MiSeq 16S rRNA gene sequencing. Based on pretreatment results, the presence of neither Ascaris lumbricoides nor Necator americanus infection significantly altered the overall diversity of the microbiota in comparison with age-matched controls. Following ALB therapy and clearance of soil-transmitted helminths (STH), there were significant increases in the proportion of the microbiota made up by Clostridiales (P = 0.0002; average fold change, 0.57) and reductions in the proportion made up by Enterobacteriales (P = 0.0004; average fold change, -0.58). There was a significant posttreatment decrease in Chao1 richness, even among individuals who were uninfected pretreatment, suggesting that antimicrobial effects must be considered in any posttreatment setting. Nevertheless, the helminth-associated changes in Clostridiales and Enterobacteriales suggest that clearance of STH, and of N. americanus in particular, alters the gut microbiota.IMPORTANCE The gut microbiome is an important factor in human health. It is affected by what we eat, what medicines we take, and what infections we acquire. In turn, it affects the way we absorb nutrients and whether we have excessive intestinal inflammation. Intestinal worms may have an important impact on the composition of the gut microbiome. Without a complete understanding of the impact of mass deworming programs on the microbiome, it is impossible to accurately calculate the cost-effectiveness of such public health interventions and to guard against any possible deleterious side effects. Our research examines this question in a "real-world" setting, using a longitudinal cohort, in which individuals with and without worm infections are treated with deworming medication and followed up at both three weeks and three months posttreatment. We quantify the impact of roundworms and hookworms on gut microbial composition, suggesting that the impact is small, but that treatment of hookworm infection results in significant changes. This work points to the need for follow-up studies to further examine the impact of hookworm on the gut microbiota and determine the health consequences of the observed changes.}, }
@article {pmid31015144, year = {2019}, author = {Corno, G and Yang, Y and Eckert, EM and Fontaneto, D and Fiorentino, A and Galafassi, S and Zhang, T and Di Cesare, A}, title = {Effluents of wastewater treatment plants promote the rapid stabilization of the antibiotic resistome in receiving freshwater bodies.}, journal = {Water research}, volume = {158}, number = {}, pages = {72-81}, doi = {10.1016/j.watres.2019.04.031}, pmid = {31015144}, issn = {1879-2448}, mesh = {*Anti-Bacterial Agents ; Drug Resistance, Microbial ; Fresh Water ; Genes, Bacterial ; Humans ; *Wastewater ; }, abstract = {Treated wastewater discharged into the environment acts as a disturbance of the natural microbial communities in terms of taxonomic composition and of functional gene pool, including antibiotic resistance genes. We tested whether stochastic and heterogeneous site-specific trajectories or generalities, potentially driven by deterministic processes, control the fate of allochthonous bacteria from anthropogenic sources and the persistence of their functional traits in freshwater. Finding generalities would allow the identification of wastewater treatments that could be effective in abating determinants of antibiotic resistance. We analysed the short-term response of native bacterial communities in waters exposed to the disturbance of wastewater at different dilutions, using a metagenomic approach that revealed both microbial community composition and the scope and abundance of the resistome that can pose indirect risks to human health. We found that the taxonomic composition of the communities after the disturbance was driven by case-specific stochastic processes, whereas the resistome had a deterministic trajectory, rapidly stabilising its functional traits with higher proportions of wastewater effluents, regardless of differences in taxonomic composition, richness of antibiotic resistance genes and of bacterial taxa, phenotypic features of the bacterial communities, and type of wastewater treatment. The observed deterministic proliferation of resistomes in freshwater bodies receiving wastewater effluents, suggests that this process may contribute to the global propagation of antibiotic resistance, and thus calls for new legislations promoting alternative tertiary treatments for the wastewater reuse, and targeting bacterial functional traits and not only bacterial abundances.}, }
@article {pmid31009873, year = {2019}, author = {Lin, S and Wang, TY and Xu, HR and Zhang, XN and Wang, Q and Liu, R and Li, Q and Bi, KS}, title = {A systemic combined nontargeted and targeted LC-MS based metabolomic strategy of plasma and liver on pathology exploration of alpha-naphthylisothiocyanate induced cholestatic liver injury in mice.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {171}, number = {}, pages = {180-192}, doi = {10.1016/j.jpba.2019.04.009}, pmid = {31009873}, issn = {1873-264X}, mesh = {1-Naphthylisothiocyanate/toxicity ; Animals ; Biomarkers/blood/metabolism ; *Chemical and Drug Induced Liver Injury/blood/pathology ; Chromatography, Liquid/*methods ; Liver/drug effects/*metabolism ; Male ; Metabolome ; Metabolomics/*methods ; Mice, Inbred C57BL ; Tandem Mass Spectrometry/*methods ; }, abstract = {The pathology of cholestatic liver injury (CLI) was complicated, which has limited the development of anti-cholestatic drugs for a long period. Metabolomic researches focused on global and dynamic changes of the organism could shed some light on mechanism investigation. In order to characterize and validate metabolite alterations of alpha-naphthylisothiocyanate (ANIT) induced CLI in C57BL/6 mice, a systemic metabolomic approach combining nontargeted HPLC-ESI-QTOF-MS and targeted UFLC-ESI-MS/MS technologies were developed innovatively. Multivariate data analysis was applied to determine the changes of metabolites in processed plasma and liver samples between control and model groups. Afterwards, 38 potential plasma biomarkers and 17 potential liver biomarkers involved in bile acid (BA) biosynthesis, phospholipid biosynthesis, sphingolipid metabolism, alpha linolenic acid and linoleic acid metabolism, as well as arachidonic acid metabolism were found and attributed as potential biomarkers and influential pathways of cholestasis. Based on correlation analysis, BA biosynthesis played the most important role in ANIT induced CLI, thereinto, major BAs were carried out with quantitative analysis. Targeted metabolomic results showed that the increase of BAs might have an impact on intestinal microbial ecology which could aggravate liver injury probably, among which cholic acid (CA) and taurocholic acid (TCA) were the most sensitive indicators of ANIT induced CLI in both plasma and liver. In conclusion, CLI might correlate significantly with hepatocyte necrosis, metabolic disorders and imbalance of intestinal microbiome ecology triggered by BA accumulation.}, }
@article {pmid31005840, year = {2019}, author = {Qian, X and Gu, J and Sun, W and Wang, X and Li, H}, title = {Effects of passivators on antibiotic resistance genes and related mechanisms during composting of copper-enriched pig manure.}, journal = {The Science of the total environment}, volume = {674}, number = {}, pages = {383-391}, doi = {10.1016/j.scitotenv.2019.04.197}, pmid = {31005840}, issn = {1879-1026}, mesh = {Animals ; Charcoal/chemistry ; Composting/*methods ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; Manure/microbiology ; Zeolites/chemistry ; }, abstract = {Due to the intensive use of feed additives in livestock farming, animal manure has become a hotspot for antibiotics, heavy metals, and antibiotic resistance genes (ARGs). Unlike antibiotics, heavy metals cannot be degraded during composting and thus could pose a persistent co-selective pressure in the proliferation of antibiotic resistance. Passivators are commonly applied to immobilize metals and improve the safety of compost. However, little is known about the effects of various passivators on ARGs and mobile genetic elements (MGEs) during composting and the underlying mechanisms involved. Thus, three typical passivators (biochar, fly ash, and zeolite) were applied during the composting of copper-enriched pig manure, and their effects on ARGs, copper resistance genes, MGEs, and the bacterial communities were examined. Compared to the control, all passivator treatments reduced the abundances of at least six ARGs (tetC, tetG, tetQ, tetX, sul1, and ermB) by 0.23-1.09 logs and of two MGEs (intI1 and ISCR1) by 26-85% after composting. Biochar and fly ash also significantly reduced the abundances of intI2 and Tn914/1545. In contrast, abundances of copper resistance genes were not reduced by passivators, implying that the decreased co-selective pressure may not be a major contributor to ARG reductions in this study. Procrustes analysis and redundancy analysis demonstrated that shifts in the bacterial community determined the changes in the abundances of ARGs, and the variation in MGEs and DTPA-Cu can also partially explain the ARG variance. Overall, all of three passivators can be used to reduce the health risks associated with ARGs in livestock manure, and biochar performed the best at reducing ARGs and MGEs.}, }
@article {pmid31001657, year = {2019}, author = {Mastan, A and Bharadwaj, R and Kushwaha, RK and Vivek Babu, CS}, title = {Functional Fungal Endophytes in Coleus forskohlii Regulate Labdane Diterpene Biosynthesis for Elevated Forskolin Accumulation in Roots.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {914-926}, pmid = {31001657}, issn = {1432-184X}, mesh = {Ascomycota/*physiology ; Colforsin/*metabolism ; Diterpenes/*metabolism ; Endophytes ; Fusarium/*physiology ; Hypocreales/physiology ; Plant Roots/metabolism ; Plectranthus/*metabolism/*microbiology ; Xylariales/physiology ; }, abstract = {Coleus forskohlii is a perennial medicinal shrub cultivated mainly for its forskolin content. The plant has been used since ancient times in ayurvedic traditional medicines for the treatment of hypertension, glaucoma, asthma, congestive heart failures, obesity, and cancer. Use of endophytic microorganisms presents a special interest for the development of value-added bioactive compounds through agriculture. Limited investigations have been undertaken on in planta enhancement of forskolin content using endophytic fungus in sustainable agriculture. Here we report specific roles of three fungal endophytes, Fusarium redolens (RF1), Phialemoniopsis cornearis (SF1), and Macrophomina pseudophaseolina (SF2), functionally acting as plant probiotic fungus, regulating secondary metabolite (forskolin) biosynthesis in C. forskohlii. The root endophyte, RF1, and shoot endophytes, SF1 and SF2, were found to enhance forskolin content by 52 to 88% in pot and 60 to 84% in field experiments as compared to uninoculated control plants. The three endophytes also enhanced total biomass owing to plant growth promoting properties. The expression of diterpene synthases (CfTPSs) like CfTPS1, CfTPS2, CfTPS3, and CfTPS4 were significantly upregulated in endophyte-treated C. forskohlii plants. Elevated expression of key diterpene synthases (CfTPS2) in the forskolin biosynthesis pathway, exclusively present in the root cork of C. forskohlii, was observed following SF2 endophyte treatment. Furthermore, endophyte treatments conferred a variety of antagonistic activity against nematode galls (80%) and plant pathogens like Fusarium oxysporum, Colletotricum gloeosporioides, and Sclerotium rolfsii. RF1 and SF1 fungal endophytes showed positive for IAA production; however, SF1 also indicated phosphate solubilization activity. Overall, the qualitative and quantitative improvement of in planta forskolin enhancement represents an area of high commercial interest, and hence, our work focused on novel insights for the application of three fungal endophytes for in planta enhancement of forskolin content for C. forskohlii cultivation by a sustainable approach.}, }
@article {pmid31000488, year = {2019}, author = {Ladau, J and Eloe-Fadrosh, EA}, title = {Spatial, Temporal, and Phylogenetic Scales of Microbial Ecology.}, journal = {Trends in microbiology}, volume = {27}, number = {8}, pages = {662-669}, doi = {10.1016/j.tim.2019.03.003}, pmid = {31000488}, issn = {1878-4380}, mesh = {*Ecology/methods ; *Microbiota ; Phylogeny ; Spatio-Temporal Analysis ; }, abstract = {Microbial communities play a major role in disease, biogeochemical cycling, agriculture, and bioremediation. However, identifying the ecological processes that govern microbial community assembly and disentangling the relative impacts of those processes has proven challenging. Here, we propose that this discord is due to microbial systems being studied at different spatial, temporal, and phylogenetic scales. We argue that different processes dominate at different scales, and that through a more explicit consideration of spatial, temporal, and phylogenetic grains and extents (the two components of scale) a more accurate, clear, and useful understanding of microbial community assembly can be developed. We demonstrate the value of applying ecological concepts of scale to microbiology, specifically examining their application to nestedness, legacy effects, and taxa-area relationships of microbial systems. These proposed considerations of scale will help resolve long-standing debates in microbial ecology regarding the processes determining the assembly of microbial communities, and provide organizing principles around which hypotheses and theories can be developed.}, }
@article {pmid30993370, year = {2019}, author = {Li, W and Wang, M and Burgaud, G and Yu, H and Cai, L}, title = {Fungal Community Composition and Potential Depth-Related Driving Factors Impacting Distribution Pattern and Trophic Modes from Epi- to Abyssopelagic Zones of the Western Pacific Ocean.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {820-831}, pmid = {30993370}, issn = {1432-184X}, mesh = {DNA Barcoding, Taxonomic ; DNA, Fungal/analysis ; DNA, Ribosomal Spacer/analysis ; Fungi/classification/*isolation &amp; purification ; *Mycobiome ; Pacific Ocean ; Seawater/*microbiology ; }, abstract = {Fungi play an important role in cycling organic matter and nutrients in marine ecosystems. However, the distribution of fungal communities in the ocean, especially the vertical distribution along depth in the water column, remained poorly understood. Here, we assess the depth-related distribution pattern of fungal communities along the water column from epi- to abyssopelagic zones of the Western Pacific Ocean using internal transcribed spacer 2 (ITS2) metabarcoding. Majority of the assigned OTUs were affiliated to Ascomycota, followed by three other minor phyla (Basidiomycota, Chytridiomycota, and Mucoromycota). The epipelagic zone harbored a higher OTU richness with distinct fungal communities as compared with meso-, bathy-, and abyssopelagic zones. Across the whole water column, depth appears as a key parameter for both fungal α- and β-diversity. However, when the dataset was split into the upper (5-500 m) and deeper (below 500 m) layers, no significant correlation was observed between depth and community compositions. In the upper layer, temperature and dissolved oxygen were recognized as the primary environmental factors shaping fungal α- and β- diversity. By parsing fungal OTUs into ecological categories, multi-trophic mode of nutrition was found to be more prevalent with increasing depth, suggesting a potential adaptation to the extreme conditions of the deep sea. This study provides new and meaningful information on the depth-stratified fungal diversity, community structure, and putative ecological roles in the open sea.}, }
@article {pmid30992445, year = {2019}, author = {Lax, S and Cardona, C and Zhao, D and Winton, VJ and Goodney, G and Gao, P and Gottel, N and Hartmann, EM and Henry, C and Thomas, PM and Kelley, ST and Stephens, B and Gilbert, JA}, title = {Microbial and metabolic succession on common building materials under high humidity conditions.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1767}, pmid = {30992445}, issn = {2041-1723}, support = {T32 EB009412/EB/NIBIB NIH HHS/United States ; U19 AI135964/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/genetics/isolation &amp; purification/*metabolism ; Construction Materials/*microbiology ; Environmental Monitoring/*methods ; Fungi/genetics/isolation &amp; purification/*metabolism ; Humidity ; Phylogeny ; RNA, Ribosomal, 16S/isolation &amp; purification ; Viruses/genetics/isolation &amp; purification/*metabolism ; }, abstract = {Despite considerable efforts to characterize the microbial ecology of the built environment, the metabolic mechanisms underpinning microbial colonization and successional dynamics remain unclear, particularly at high moisture conditions. Here, we applied bacterial/viral particle counting, qPCR, amplicon sequencing of the genes encoding 16S and ITS rRNA, and metabolomics to longitudinally characterize the ecological dynamics of four common building materials maintained at high humidity. We varied the natural inoculum provided to each material and wet half of the samples to simulate a potable water leak. Wetted materials had higher growth rates and lower alpha diversity compared to non-wetted materials, and wetting described the majority of the variance in bacterial, fungal, and metabolite structure. Inoculation location was weakly associated with bacterial and fungal beta diversity. Material type influenced bacterial and viral particle abundance and bacterial and metabolic (but not fungal) diversity. Metabolites indicative of microbial activity were identified, and they too differed by material.}, }
@article {pmid30989355, year = {2019}, author = {Nilsson, LKJ and de Oliveira, MR and Marinotti, O and Rocha, EM and Håkansson, S and Tadei, WP and de Souza, AQL and Terenius, O}, title = {Characterization of Bacterial Communities in Breeding Waters of Anopheles darlingi in Manaus in the Amazon Basin Malaria-Endemic Area.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {781-791}, pmid = {30989355}, issn = {1432-184X}, support = {348-2012-622//Vetenskapsr&#xe5;det/ ; }, mesh = {*Animal Distribution ; Animals ; Anopheles/*physiology ; Bacteria/classification/*isolation &amp; purification ; Brazil ; Ecosystem ; Fresh Water/*microbiology ; Malaria ; *Microbiota ; Mosquito Vectors/physiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Reproduction ; }, abstract = {The microbiota in mosquito breeding waters can affect ovipositing mosquitoes, have effects on larval development, and can modify adult mosquito-gut bacterial composition. This, in turn, can affect transmission of human pathogens such as malaria parasites. Here, we explore the microbiota of four breeding sites for Anopheles darlingi, the most important malaria vector in Latin America. The sites are located in Manaus in the Amazon basin in Brazil, an area of active malaria transmission. Using 16S rRNA gene sequencing by MiSeq, we found that all sites were dominated by Proteobacteria and Firmicutes and that 94% of the total number of reads belonged to 36 operational taxonomic units (OTUs) identified in all sites. Of these, the most common OTUs belonged to Escherichia/Shigella, Staphylococcus, and Pseudomonas. Of the remaining 6% of the reads, the OTUs found to differentiate between the four sites belonged to the orders Burkholderiales, Actinomycetales, and Clostridiales. We conclude that An. darlingi can develop in breeding waters with different surface-water bacteria, but that the common microbiota found in all breeding sites might indicate or contribute to a suitable habitat for this important malaria vector.}, }
@article {pmid30989354, year = {2019}, author = {Newsham, KK and Tripathi, BM and Dong, K and Yamamoto, N and Adams, JM and Hopkins, DW}, title = {Bacterial Community Composition and Diversity Respond to Nutrient Amendment but Not Warming in a Maritime Antarctic Soil.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {974-984}, pmid = {30989354}, issn = {1432-184X}, support = {NE/D00893X/1//Natural Environment Research Council/ ; 2018R1C1B6007755//National Research Foundation of Korea/ ; }, mesh = {Antarctic Regions ; Bacteria/*classification ; *Bacterial Physiological Phenomena ; Fertilizers/*analysis ; Global Warming ; *Hot Temperature ; *Microbiota/drug effects ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Soil Microbiology ; }, abstract = {A resumption of climate warming in maritime Antarctica, arising from continued greenhouse gas emissions to the atmosphere, is predicted to lead to further expansions of plant populations across the region, with consequent increases in nutrient inputs to soils. Here, we test the main and interactive effects of warming, applied with open top chambers (OTCs), and nutrient amendment with tryptic soy broth (TSB), an artificial growth substrate, on bacterial community composition and diversity using Illumina sequencing of 16S rRNA genes in soil from a field experiment in the southern maritime Antarctic. Substantial effects of TSB application on bacterial communities were identified after 49 months, including reduced diversity, altered phylogenetic community assembly processes, increased Proteobacteria-to-Acidobacteria ratios and significant divergence in community composition, notably increases in the relative abundances of the gram-positive genera Arthrobacter, Paeniglutamicibacter and Planococcus. Contrary to previous observations from other maritime Antarctic field warming experiments, we recorded no effects of warming with OTCs, or interactive effects of OTCs and TSB application, on bacterial community composition or diversity. Based on these findings, we conclude that further warming of the maritime Antarctic is unlikely to influence soil bacterial community composition or diversity directly, but that increased nutrient inputs arising from enhanced plant growth across the region may affect the composition of soil bacterial communities, with possible effects on ecosystem productivity.}, }
@article {pmid30988401, year = {2019}, author = {Tanaka, SE and Dayi, M and Maeda, Y and Tsai, IJ and Tanaka, R and Bligh, M and Takeuchi-Kaneko, Y and Fukuda, K and Kanzaki, N and Kikuchi, T}, title = {Stage-specific transcriptome of Bursaphelenchus xylophilus reveals temporal regulation of effector genes and roles of the dauer-like stages in the lifecycle.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6080}, pmid = {30988401}, issn = {2045-2322}, mesh = {Animal Distribution ; Animals ; *Gene Expression Regulation, Developmental ; Genes, Helminth/genetics ; Helminth Proteins/genetics/metabolism ; Life Cycle Stages/*genetics ; Pinus/*parasitology ; Plant Diseases/*parasitology ; RNA-Seq ; Tylenchida/*genetics/pathogenicity ; }, abstract = {The pine wood nematode Bursaphelenchus xylophilus is the causal agent of pine wilt disease, one of the most devastating forest diseases in East Asian and West European countries. The lifecycle of B. xylophilus includes four propagative larval stages and gonochoristic adults which are involved in the pathogenicity, and two stages of dispersal larvae involved in the spread of the disease. To elucidate the ecological roles of each developmental stage in the pathogenic life cycle, we performed a comprehensive transcriptome analysis using RNA-seq generated from all developmental stages of B. xylophilus and compared transcriptomes between stages. We found more than 9000 genes are differentially expressed in at least one stage of the life cycle including genes involved in general nematode biology such as reproduction and moulting but also effector genes likely to be involved in parasitism. The dispersal-stage transcriptome revealed its analogy to C. elegans dauer and the distinct roles of the two larval stages from each other regarding survival and transmission. This study provides important insights and resources to understand B. xylophilus parasitic biology.}, }
@article {pmid30980672, year = {2019}, author = {Pratama, AA and van Elsas, JD}, title = {Gene mobility in microbiomes of the mycosphere and mycorrhizosphere -role of plasmids and bacteriophages.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {5}, pages = {}, doi = {10.1093/femsec/fiz053}, pmid = {30980672}, issn = {1574-6941}, mesh = {Bacteriophages/*genetics ; Burkholderiaceae/*genetics ; Fungi/*genetics ; Gene Transfer, Horizontal ; Microbiota ; Plasmids/*genetics ; Prophages/genetics ; *Soil Microbiology ; }, abstract = {Microbial activity in soil, including horizontal gene transfer (HGT), occurs in soil hot spots and at "hot moments". Given their capacities to explore soil for nutrients, soil fungi (associated or not with plant roots) can act as (1) selectors of myco(rrhizo)sphere-adapted organisms and (2) accelerators of HGT processes across the cell populations that are locally present. This minireview critically examines our current understanding of the drivers of gene mobility in the myco(rrhizo)sphere. We place a special focus on the role of two major groups of gene mobility agents, i.e. plasmids and bacteriophages. With respect to plasmids, there is mounting evidence that broad-host-range (IncP-1β and PromA group) plasmids are prominent drivers of gene mobility across mycosphere inhabitants. A role of IncP-1β plasmids in Fe uptake processes has been revealed. Moreover, a screening of typical mycosphere-inhabiting Paraburkholderia spp. revealed carriage of integrated plasmids, next to prophages, that presumably confer fitness enhancements. In particular, functions involved in biofilm formation and nutrient uptake were thus identified. The potential of the respective gene mobility agents to promote the movement of such genes is critically examined.}, }
@article {pmid30980101, year = {2019}, author = {Ogwu, MC and Srinivasan, S and Dong, K and Ramasamy, D and Waldman, B and Adams, JM}, title = {Community Ecology of Deinococcus in Irradiated Soil.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {855-872}, pmid = {30980101}, issn = {1432-184X}, support = {2016E1D1A1B03930385//National Research Foundation Korea/ ; 2017R1D1A1B03035583//National Foundation foundation Korea/ ; }, mesh = {Deinococcus/physiology/*radiation effects ; Dose-Response Relationship, Radiation ; Gamma Rays/*adverse effects ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Republic of Korea ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Deinococcus is a genus of soil bacteria known for radiation resistance. However, the effects of radiation exposure on its community structure are unknown. We exposed soil to three levels of gamma radiation, 0.1 kGy/h (low), 1 kGy/h (medium), and 3 kGy/h (high), once a week for 6 weeks and then extracted soil DNA for 16S rRNA amplicon sequencing. We found the following: (1) Increasing radiation dose produced a major increase in relative abundance of Deinococcus, reaching ~ 80% of reads at the highest doses. Differing abundances of the various Deinococcus species in relation to exposure levels indicate distinct "radiation niches." At 3 kGy/h, a single OTU identified as D. ficus overwhelmingly dominated the mesocosms. (2) Corresponding published genome data show that the dominant species at 3 kGy/h, D. ficus, has a larger and more complex genome than other Deinococcus species with a greater proportion of genes related to DNA and nucleotide metabolism, cell wall, membrane, and envelope biogenesis as well as more cell cycle control, cell division, and chromosome partitioning-related genes. Deinococcus ficus also has a higher guanine-cytosine ratio than most other Deinococcus. These features may be linked to genome stability and may explain its greater abundance in this apparently competitive system, under high-radiation exposures. (3) Genomic analysis suggests that Deinococcus, including D. ficus, are capable of utilizing diverse carbon sources derived from both microbial cells killed by the radiation (including C5-C12-containing compounds, like arabinose, lactose, N-acetyl-D-glucosamine) and plant-derived organic matter in the soil (e.g., cellulose and hemicellulose). (4) Overall, based on its metagenome, even the most highly irradiated (3 kGy/h) soil possesses a wide range of the activities necessary for a functional soil system. Future studies may consider the resilience and sustainability of such soils in a high-radiation environment.}, }
@article {pmid30980037, year = {2019}, author = {Lee, KS and Palatinszky, M and Pereira, FC and Nguyen, J and Fernandez, VI and Mueller, AJ and Menolascina, F and Daims, H and Berry, D and Wagner, M and Stocker, R}, title = {Publisher Correction: An automated Raman-based platform for the sorting of live cells by functional properties.}, journal = {Nature microbiology}, volume = {4}, number = {5}, pages = {902-903}, doi = {10.1038/s41564-019-0446-1}, pmid = {30980037}, issn = {2058-5276}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid30977724, year = {2019}, author = {Gralka, M and Hallatschek, O}, title = {Environmental heterogeneity can tip the population genetics of range expansions.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {30977724}, issn = {2050-084X}, support = {R01 GM115851/GM/NIGMS NIH HHS/United States ; }, mesh = {*Adaptation, Biological ; Biological Evolution ; Computer Simulation ; *Environmental Exposure ; Escherichia coli/genetics/*growth &amp; development ; Genetic Drift ; *Genetics, Population ; *Population Dynamics ; Selection, Genetic ; Time-Lapse Imaging ; }, abstract = {The population genetics of most range expansions is thought to be shaped by the competition between Darwinian selection and random genetic drift at the range margins. Here, we show that the evolutionary dynamics during range expansions is highly sensitive to additional fluctuations induced by environmental heterogeneities. Tracking mutant clones with a tunable fitness effect in bacterial colonies grown on randomly patterned surfaces we found that environmental heterogeneity can dramatically reduce the efficacy of selection. Time-lapse microscopy and computer simulations suggest that this effect arises generically from a local 'pinning' of the expansion front, whereby stretches of the front are slowed down on a length scale that depends on the structure of the environmental heterogeneity. This pinning focuses the range expansion into a small number of 'lucky' individuals with access to expansion paths, altering the neutral evolutionary dynamics and increasing the importance of chance relative to selection.}, }
@article {pmid30976843, year = {2019}, author = {Salerno, C and Berardi, G and Laera, G and Pollice, A}, title = {Functional Response of MBR Microbial Consortia to Substrate Stress as Revealed by Metaproteomics.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {873-884}, pmid = {30976843}, issn = {1432-184X}, mesh = {Bacterial Physiological Phenomena ; Bacterial Proteins/analysis ; *Bioreactors ; Microbial Consortia/*physiology ; Proteome/*analysis ; Sewage/*analysis ; *Waste Disposal, Fluid ; }, abstract = {Bacterial consortia have a primary role in the biological degradations occurring in activated sludge for wastewater treatment, for their capacities to metabolize the polluting matter. Therefore, the knowledge of the main metabolic pathways for the degradation of pollutants becomes critical for a correct design and operation of wastewater treatment plants. The metabolic activity of the different bacterial groups in activated sludge is commonly investigated through respirometry. Furthermore, in the last years, the development of "omic" approaches has offered more opportunities to integrate or substitute the conventional microbiological assays and to deeply understand the taxonomy and dynamics of complex microbial consortia. In the present work, an experimental membrane bioreactor (MBR) was set up and operated for the treatment of municipal wastewater, and the effects of a sudden decrease of the organic supply on the activated sludge were investigated. Both respirometric and metaproteomic approaches revealed a resistance of autotrophic bacteria to the substrate stress, and particularly of nitrifying bacteria. Furthermore, metaproteomics allowed the identification of the taxonomy of the microbial consortium based on its protein expression, unveiling the prevalence of Sorangium and Nitrosomonas genera both before and after the organic load decrease. Moreover, it confirmed the results obtained through respirometry and revealed a general expression of proteins involved in metabolism and transport of nitrogen, or belonging to nitrifying species like Nitrosomonas europeae, Nitrosomonas sp. AL212, or Nitrospira defluvii.}, }
@article {pmid30976842, year = {2019}, author = {Vieira, LC and da Silva, DKA and de Melo, MAC and Escobar, IEC and Oehl, F and da Silva, GA}, title = {Edaphic Factors Influence the Distribution of Arbuscular Mycorrhizal Fungi Along an Altitudinal Gradient of a Tropical Mountain.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {904-913}, pmid = {30976842}, issn = {1432-184X}, mesh = {Altitude ; Brazil ; Mycobiome/*physiology ; Mycorrhizae/classification/*isolation &amp; purification/physiology ; *Soil Microbiology ; Tropical Climate ; }, abstract = {Changes in relief in montane areas, with increasing altitude, provide different biotic and abiotic conditions, acting on the species of arbuscular mycorrhizal fungi (AMF). The objective of this work was to determine the influence of altitude, edaphic factors, and vegetation on the AMF species in a mountainous area. The list of AMF species was obtained from morphological identification of the spores, with 72 species recovered from field samples and trap cultures. Lower levels of Shannon's diversity occurred only at lower altitude; however, there was no difference in AMF richness. The structure of the AMF assembly between the two highest altitudes was similar and differed in relation to the lower altitude. There was variation in the distribution of AMF species, which was related to soil texture and chemical factors along the altitude gradient. Some species, genera, and families were indicative of a certain altitude, showing the preference of fungi for certain environmental conditions, which may aid in decisions to conserve montane ecosystems.}, }
@article {pmid30976841, year = {2019}, author = {Sedlacek, CJ and McGowan, B and Suwa, Y and Sayavedra-Soto, L and Laanbroek, HJ and Stein, LY and Norton, JM and Klotz, MG and Bollmann, A}, title = {A Physiological and Genomic Comparison of Nitrosomonas Cluster 6a and 7 Ammonia-Oxidizing Bacteria.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {985-994}, pmid = {30976841}, issn = {1432-184X}, support = {1120443//National Science Foundation/ ; 0541797//National Science Foundation/ ; 0541797//National Science Foundation/ ; }, mesh = {Ammonia/metabolism ; Genome, Bacterial/*physiology ; Nitrosomonas/genetics/*physiology ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Ammonia-oxidizing bacteria (AOB) within the genus Nitrosomonas perform the first step in nitrification, ammonia oxidation, and are found in diverse aquatic and terrestrial environments. Nitrosomonas AOB were grouped into six defined clusters, which correlate with physiological characteristics that contribute to adaptations to a variety of abiotic environmental factors. A fundamental physiological trait differentiating Nitrosomonas AOB is the adaptation to either low (cluster 6a) or high (cluster 7) ammonium concentrations. Here, we present physiological growth studies and genome analysis of Nitrosomonas cluster 6a and 7 AOB. Cluster 6a AOB displayed maximum growth rates at ≤ 1 mM ammonium, while cluster 7 AOB had maximum growth rates at ≥ 5 mM ammonium. In addition, cluster 7 AOB were more tolerant of high initial ammonium and nitrite concentrations than cluster 6a AOB. Cluster 6a AOB were completely inhibited by an initial nitrite concentration of 5 mM. Genomic comparisons were used to link genomic traits to observed physiological adaptations. Cluster 7 AOB encode a suite of genes related to nitrogen oxide detoxification and multiple terminal oxidases, which are absent in cluster 6a AOB. Cluster 6a AOB possess two distinct forms of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and select species encode genes for hydrogen or urea utilization. Several, but not all, cluster 6a AOB can utilize urea as a source of ammonium. Hence, although Nitrosomonas cluster 6a and 7 AOB have the capacity to fulfill the same functional role in microbial communities, i.e., ammonia oxidation, differentiating species-specific and cluster-conserved adaptations is crucial in understanding how AOB community succession can affect overall ecosystem function.}, }
@article {pmid30975748, year = {2019}, author = {Baker, JL and Hendrickson, EL and Tang, X and Lux, R and He, X and Edlund, A and McLean, JS and Shi, W}, title = {Klebsiella and Providencia emerge as lone survivors following long-term starvation of oral microbiota.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {17}, pages = {8499-8504}, pmid = {30975748}, issn = {1091-6490}, support = {F32 DE026947/DE/NIDCR NIH HHS/United States ; R00 DE024543/DE/NIDCR NIH HHS/United States ; R01 DE020102/DE/NIDCR NIH HHS/United States ; R01 DE026186/DE/NIDCR NIH HHS/United States ; }, mesh = {Gastrointestinal Microbiome/*physiology ; Humans ; Klebsiella/*physiology ; *Microbial Viability ; Mouth/*microbiology ; Providencia/*physiology ; Saliva/microbiology ; }, abstract = {It is well-understood that many bacteria have evolved to survive catastrophic events using a variety of mechanisms, which include expression of stress-response genes, quiescence, necrotrophy, and metabolic advantages obtained through mutation. However, the dynamics of individuals leveraging these abilities to gain a competitive advantage in an ecologically complex setting remain unstudied. In this study, we observed the saliva microbiome throughout the ecological perturbation of long-term starvation, allowing only the species best equipped to access and use the limited resources to survive. During the first several days, the community underwent a death phase that resulted in a ∼50-100-fold reduction in the number of viable cells. Interestingly, after this death phase, only three species, Klebsiella pneumoniae, Klebsiella oxytoca, and Providencia alcalifaciens, all members of the family Enterobacteriaceae, appeared to be transcriptionally active and recoverable. Klebsiella are significant human pathogens, frequently resistant to multiple antibiotics, and recently, ectopic colonization of the gut by oral Klebsiella was documented to induce dysbiosis and inflammation. MetaOmics analyses provided several leads for further investigation regarding the ecological success of the Enterobacteriaceae. The isolates accumulated single nucleotide polymorphisms in known growth advantage in stationary phase alleles and produced natural products closely resembling antimicrobial cyclic depsipeptides. The results presented in this study suggest that pathogenic Enterobacteriaceae persist much longer than their more benign neighbors in the salivary microbiome when faced with starvation. This is particularly significant, given that hospital surfaces contaminated with oral fluids, especially sinks and drains, are well-established sources of outbreaks of drug-resistant Enterobacteriaceae.}, }
@article {pmid30974353, year = {2019}, author = {Cahill, N and O'Connor, L and Mahon, B and Varley, &#xc1; and McGrath, E and Ryan, P and Cormican, M and Brehony, C and Jolley, KA and Maiden, MC and Brisse, S and Morris, D}, title = {Hospital effluent: A reservoir for carbapenemase-producing Enterobacterales?.}, journal = {The Science of the total environment}, volume = {672}, number = {}, pages = {618-624}, pmid = {30974353}, issn = {1879-1026}, mesh = {Bacterial Proteins/*analysis/metabolism ; Enterobacteriaceae/*growth &amp; development ; Hospitals ; Wastewater/*microbiology ; *Water Microbiology ; Water Pollutants/analysis/*metabolism ; beta-Lactamases/*analysis/metabolism ; }, abstract = {Antimicrobial resistance is a major public health concern. Carbapenemase-producing Enterobacterales (CPE) represent a significant health threat as some strains are resistant to almost all available antibiotics. The aim of this research was to examine hospital effluent and municipal wastewater in an urban area in Ireland for CPE. Samples of hospital effluent (n = 5), municipal wastewater before (n = 5) and after (n = 4) the hospital effluent stream joined the municipal wastewater stream were collected over a nine-week period (May-June 2017). All samples were examined for CPE by direct plating onto Brilliance CRE agar. Isolates were selected for susceptibility testing to 15 antimicrobial agents in accordance with EUCAST criteria. Where relevant, isolates were tested for carbapenemase-encoding genes by real-time PCR. CPE were detected in five samples of hospital effluent, one sample of pre-hospital wastewater and three samples of post-hospital wastewater. Our findings suggest hospital effluent is a major contributor to CPE in municipal wastewater. Monitoring of hospital effluent for CPE could have important applications in detection and risk management of unrecognised dissemination of CPE in both the healthcare setting and the environment.}, }
@article {pmid30973888, year = {2019}, author = {Nakato, GV and Fuentes Rojas, JL and Verniere, C and Blondin, L and Coutinho, T and Mahuku, G and Wicker, E}, title = {A new Multi Locus Variable Number of Tandem Repeat Analysis Scheme for epidemiological surveillance of Xanthomonas vasicola pv. musacearum, the plant pathogen causing bacterial wilt on banana and enset.}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0215090}, pmid = {30973888}, issn = {1932-6203}, mesh = {DNA, Bacterial/analysis/*genetics ; Ethiopia ; *Genetics, Population ; Genomics ; *Minisatellite Repeats ; Molecular Epidemiology ; Musaceae/classification/*microbiology ; Plant Diseases/*genetics/microbiology ; *Population Surveillance ; Xanthomonas/classification/*genetics/pathogenicity ; }, abstract = {Xanthomonas vasicola pv. musacearum (Xvm) which causes Xanthomonas wilt (XW) on banana (Musa accuminata x balbisiana) and enset (Ensete ventricosum), is closely related to the species Xanthomonas vasicola that contains the pathovars vasculorum (Xvv) and holcicola (Xvh), respectively pathogenic to sugarcane and sorghum. Xvm is considered a monomorphic bacterium whose intra-pathovar diversity remains poorly understood. With the sudden emergence of Xvm within east and central Africa coupled with the unknown origin of one of the two sublineages suggested for Xvm, attention has shifted to adapting technologies that focus on identifying the origin and distribution of the genetic diversity within this pathogen. Although microbiological and conventional molecular diagnostics have been useful in pathogen identification. Recent advances have ushered in an era of genomic epidemiology that aids in characterizing monomorphic pathogens. To unravel the origin and pathways of the recent emergence of XW in Eastern and Central Africa, there was a need for a genotyping tool adapted for molecular epidemiology. Multi-Locus Variable Number of Tandem Repeat Analysis (MLVA) is able to resolve the evolutionary patterns and invasion routes of a pathogen. In this study, we identified microsatellite loci from nine published Xvm genome sequences. Of the 36 detected microsatellite loci, 21 were selected for primer design and 19 determined to be highly typeable, specific, reproducible and polymorphic with two- to four- alleles per locus on a sub-collection. The 19 markers were multiplexed and applied to genotype 335 Xvm strains isolated from seven countries over several years. The microsatellite markers grouped the Xvm collection into three clusters; with two similar to the SNP-based sublineages 1 and 2 and a new cluster 3, revealing an unknown diversity in Ethiopia. Five of the 19 markers had alleles present in both Xvm and Xanthomonas vasicola pathovars holcicola and vasculorum, supporting the phylogenetic closeliness of these three pathovars. Thank to the public availability of the haplotypes on the MLVABank database, this highly reliable and polymorphic genotyping tool can be further used in a transnational surveillance network to monitor the spread and evolution of XW throughout Africa.. It will inform and guide management of Xvm both in banana-based and enset-based cropping systems. Due to the suitability of MLVA-19 markers for population genetic analyses, this genotyping tool will also be used in future microevolution studies.}, }
@article {pmid30973887, year = {2019}, author = {Perona-Vico, E and Blasco-Gómez, R and Colprim, J and Puig, S and Bañeras, L}, title = {[NiFe]-hydrogenases are constitutively expressed in an enriched Methanobacterium sp. population during electromethanogenesis.}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0215029}, pmid = {30973887}, issn = {1932-6203}, mesh = {Archaeal Proteins/genetics/*metabolism ; *Bioelectric Energy Sources ; Carbon Dioxide ; *Electrodes ; Hydrogenase/genetics/*metabolism ; Methane/*metabolism ; Methanobacterium/*enzymology/genetics/growth &amp; development ; }, abstract = {Electromethanogenesis is the bioreduction of carbon dioxide (CO2) to methane (CH4) utilizing an electrode as electron donor. Some studies have reported the active participation of Methanobacterium sp. in electron capturing, although no conclusive results are available. In this study, we aimed at determining short-time changes in the expression levels of [NiFe]-hydrogenases (Eha, Ehb and Mvh), heterodisulfide reductase (Hdr), coenzyme F420-reducing [NiFe]-hydrogenase (Frh), and hydrogenase maturation protein (HypD), according to the electron flow in independently connected carbon cloth cathodes poised at- 800 mV vs. standard hydrogen electrode (SHE). Amplicon massive sequencing of cathode biofilm confirmed the presence of an enriched Methanobacterium sp. population (>70% of sequence reads), which remained in an active state (78% of cDNA reads), tagging this archaeon as the main methane producer in the system. Quantitative RT-PCR determinations of ehaB, ehbL, mvhA, hdrA, frhA, and hypD genes resulted in only slight (up to 1.5 fold) changes for four out of six genes analyzed when cells were exposed to open (disconnected) or closed (connected) electric circuit events. The presented results suggested that suspected mechanisms for electron capturing were not regulated at the transcriptional level in Methanobacterium sp. for short time exposures of the cells to connected-disconnected circuits. Additional tests are needed in order to confirm proteins that participate in electron capturing in Methanobacterium sp.}, }
@article {pmid30972435, year = {2019}, author = {Wei, W and Wang, N and Cai, L and Zhang, C and Jiao, N and Zhang, R}, title = {Impacts of Freshwater and Seawater Mixing on the Production and Decay of Virioplankton in a Subtropical Estuary.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {843-854}, pmid = {30972435}, issn = {1432-184X}, support = {41522603//National Natural Science Foundation of China/ ; 31570172//National Natural Science Foundation of China/ ; 91428308//National Natural Science Foundation of China/ ; 41673073//National Natural Science Foundation of China/ ; 41861144018//National Natural Science Foundation of China/ ; QNLM2016ORP0303//Qingdao National Laboratory for Marine Science and Technology/ ; }, mesh = {China ; Estuaries ; Fresh Water/*virology ; Plankton/*physiology ; Seawater/*virology ; *Virus Physiological Phenomena ; *Water Microbiology ; }, abstract = {Virioplankton is an important component of the aquatic ecosystem and plays multiple ecological and biogeochemical roles. Although the spatial and temporal distributions and dynamics of virioplankton have been well investigated in riverine and marine environments, little is known about the dynamics and environmental controlling mechanisms of virioplankton in estuaries. In this study, viral abundance, production and decay were examined in the Pearl River Estuary (PRE), one of the largest estuaries in China. The influences of freshwater and seawater mixing on viral ecological dynamics were evaluated with several cross-transplant experiments. In PRE, viral abundance, production and decay rates varied from 2.72 ± 0.09 to 27.5 ± 1.07 × 10[6] viruses ml[-1], 7.98 ± 2.33 to 16.27 ± 2.85% h[-1] and 0.80 ± 0.23 to 3.74 ± 0.98% h[-1], respectively. When the riverine and marine microbial community were transferred into simulated brackish water, viral production rates were markedly inhibited by 83.8% and 47.3%, respectively. The decay of riverine and marine virioplankton was inhibited by 21.1% and 34.2%, respectively, in simulated brackish water. These results indicate change of estuarine environmental factors significantly alters the dynamics of riverine and marine virioplankton. In addition, the effects of mixing on viral production and decay differed between high- and low-fluorescence viruses. High-fluorescence viruses seemed more resistant to decay than low-fluorescence viruses, whereas the production of marine low-fluorescence viruses seemed more resistant to inhibition than that of marine high-fluorescence viruses. Together, these results provide new insights into the ecological dynamics of virioplankton in estuarine environments.}, }
@article {pmid30967122, year = {2019}, author = {Ai, D and Li, X and Pan, H and Chen, J and Cram, JA and Xia, LC}, title = {Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis.}, journal = {BMC genomics}, volume = {20}, number = {Suppl 2}, pages = {185}, pmid = {30967122}, issn = {1471-2164}, support = {R01 HG006137/HG/NHGRI NIH HHS/United States ; }, mesh = {*Algorithms ; Bacteria/*classification/genetics ; Biodiversity ; Computational Biology/*methods ; *Metagenome ; *Microbial Interactions ; *Microbiota ; *Software ; }, abstract = {BACKGROUND: Discovering the key microbial species and environmental factors of microbial community and characterizing their relationships with other members are critical to ecosystem studies. The microbial co-occurrence patterns across a variety of environmental settings have been extensively characterized. However, previous studies were limited by their restriction toward pairwise relationships, while there was ample evidence of third-party mediated co-occurrence in microbial communities.<br><br>METHODS: We implemented and applied the triplet-based liquid association analysis in combination with the local similarity analysis procedure to microbial ecology data. We developed an intuitive scheme to visualize those complex triplet associations along with pairwise correlations. Using a time series from the marine microbial ecosystem as example, we identified pairs of operational taxonomic units (OTUs) where the strength of their associations appeared to relate to the values of a third "mediator" variable. These "mediator" variables appear to modulate the associations between pairs of bacteria.<br><br>RESULTS: Using this analysis, we were able to assess the OTUs' ability to regulate its functional partners in the community, typically not manifested in the pairwise correlation patterns. For example, we identified Flavobacteria as a multifaceted player in the marine microbial ecosystem, and its clades were involved in mediating other OTU pairs. By contrast, SAR11 clades were not active mediators of the community, despite being abundant and highly correlated with other OTUs. Our results suggested that Flavobacteria are more likely to respond to situations where particles and unusual sources of dissolved organic material are prevalent, such as after a plankton bloom. On the other hand, SAR11s are oligotrophic chemoheterotrophs with inflexible metabolisms, and their relationships with other organisms may be less governed by environmental or biological factors.<br><br>CONCLUSIONS: By integrating liquid association with local similarity analysis to explore the mediated co-varying dynamics, we presented a novel perspective and a useful toolkit to analyze and interpret time series data from microbial community. Our augmented association network analysis is thus more representative of the true underlying dynamic structure of the microbial community. The analytic software in this study was implemented as new functionalities of the ELSA (Extended local similarity analysis) tool, which is available for free download (http://bitbucket.org/charade/elsa).}, }
@article {pmid30963868, year = {2019}, author = {Barbaro, L and Allan, E and Ampoorter, E and Castagneyrol, B and Charbonnier, Y and De Wandeler, H and Kerbiriou, C and Milligan, HT and Vialatte, A and Carnol, M and Deconchat, M and De Smedt, P and Jactel, H and Koricheva, J and Le Viol, I and Muys, B and Scherer-Lorenzen, M and Verheyen, K and van der Plas, F}, title = {Biotic predictors complement models of bat and bird responses to climate and tree diversity in European forests.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1894}, pages = {20182193}, pmid = {30963868}, issn = {1471-2954}, mesh = {Animals ; *Biodiversity ; *Birds ; *Chiroptera ; Environment ; Europe ; *Forests ; Models, Biological ; }, abstract = {Bats and birds are key providers of ecosystem services in forests. How climate and habitat jointly shape their communities is well studied, but whether biotic predictors from other trophic levels may improve bird and bat diversity models is less known, especially across large bioclimatic gradients. Here, we achieved multi-taxa surveys in 209 mature forests replicated in six European countries from Spain to Finland, to investigate the importance of biotic predictors (i.e. the abundance or activity of defoliating insects, spiders, earthworms and wild ungulates) for bat and bird taxonomic and functional diversity. We found that nine out of 12 bird and bat diversity metrics were best explained when biotic factors were added to models including climate and habitat variables, with a mean gain in explained variance of 38% for birds and 15% for bats. Tree functional diversity was the most important habitat predictor for birds, while bats responded more to understorey structure. The best biotic predictors for birds were spider abundance and defoliating insect activity, while only bat functional evenness responded positively to insect herbivory. Accounting for potential biotic interactions between bats, birds and other taxa of lower trophic levels will help to understand how environmental changes along large biogeographical gradients affect higher-level predator diversity in forest ecosystems.}, }
@article {pmid30962365, year = {2019}, author = {Tveit, AT and Hestnes, AG and Robinson, SL and Schintlmeister, A and Dedysh, SN and Jehmlich, N and von Bergen, M and Herbold, C and Wagner, M and Richter, A and Svenning, MM}, title = {Widespread soil bacterium that oxidizes atmospheric methane.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {17}, pages = {8515-8524}, pmid = {30962365}, issn = {1091-6490}, mesh = {Bacterial Proteins/metabolism ; *Beijerinckiaceae/classification/enzymology/genetics/physiology ; Greenhouse Gases/*metabolism ; Methane/*metabolism ; Oxidation-Reduction ; Oxygenases/metabolism ; Soil Microbiology ; }, abstract = {The global atmospheric level of methane (CH4), the second most important greenhouse gas, is currently increasing by ∼10 million tons per year. Microbial oxidation in unsaturated soils is the only known biological process that removes CH4 from the atmosphere, but so far, bacteria that can grow on atmospheric CH4 have eluded all cultivation efforts. In this study, we have isolated a pure culture of a bacterium, strain MG08 that grows on air at atmospheric concentrations of CH4 [1.86 parts per million volume (p.p.m.v.)]. This organism, named Methylocapsa gorgona, is globally distributed in soils and closely related to uncultured members of the upland soil cluster α. CH4 oxidation experiments and [13]C-single cell isotope analyses demonstrated that it oxidizes atmospheric CH4 aerobically and assimilates carbon from both CH4 and CO2 Its estimated specific affinity for CH4 (a[0]s) is the highest for any cultivated methanotroph. However, growth on ambient air was also confirmed for Methylocapsa acidiphila and Methylocapsa aurea, close relatives with a lower specific affinity for CH4, suggesting that the ability to utilize atmospheric CH4 for growth is more widespread than previously believed. The closed genome of M. gorgona MG08 encodes a single particulate methane monooxygenase, the serine cycle for assimilation of carbon from CH4 and CO2, and CO2 fixation via the recently postulated reductive glycine pathway. It also fixes dinitrogen and expresses the genes for a high-affinity hydrogenase and carbon monoxide dehydrogenase, suggesting that atmospheric CH4 oxidizers harvest additional energy from oxidation of the atmospheric trace gases carbon monoxide (0.2 p.p.m.v.) and hydrogen (0.5 p.p.m.v.).}, }
@article {pmid30961521, year = {2019}, author = {Dos Santos, HRM and Argolo, CS and Argôlo-Filho, RC and Loguercio, LL}, title = {A 16S rDNA PCR-based theoretical to actual delta approach on culturable mock communities revealed severe losses of diversity information.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {74}, pmid = {30961521}, issn = {1471-2180}, mesh = {Bacteria/classification/growth &amp; development ; Cacao/microbiology ; DNA Fingerprinting ; DNA Primers ; DNA, Bacterial/genetics ; DNA, Ribosomal/*genetics ; Endophytes/*classification ; *Genetic Variation ; *Microbiota ; *Models, Theoretical ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Stem Cells ; }, abstract = {BACKGROUND: Subunits of ribosomal RNA genes (rDNAs) characterized by PCR-based protocols have been the proxy for studies in microbial taxonomy, phylogenetics, evolution and ecology. However, relevant factors have shown to interfere in the experimental outputs in a variety of systems. In this work, a 'theoretical' to 'actual' delta approach was applied to data on culturable mock bacterial communities (MBCs) to study the levels of losses in operational taxonomic units (OTUs) detectability. Computational and lab-bench strategies based on 16S rDNA amplification by 799F and U1492R primers were employed, using a fingerprinting method with highly improved detectability of fragments as a case-study tool. MBCs were of two major types: in silico MBCs, assembled with database-retrieved sequences, and in vitro MBCs, with AluI digestions of PCR data generated from culturable endophytes isolated from cacao trees.<br><br>RESULTS: Interfering factors for the 16&#x2009;s rDNA amplifications, such as the type of template, direct and nested PCR, proportion of chloroplast DNA from a tropical plant source (Virola officinalis), and biased-amplification by the primers resulted in altered bacterial 16S rDNA amplification, both on MBCs and V. officinalis leaf-extracted DNA. For the theoretical data, the maximum number of fragments for in silico and in vitro cuts were not significantly different from each other. Primers' preferences for certain sequences were detected, depending on the MBCs' composition prior to PCR. The results indicated overall losses from 2.3 up to 8.2 times in the number of OTUs detected from actual AluI digestions of MBCs when compared to in silico and in vitro theoretical data.<br><br>CONCLUSIONS: Due to all those effects, the final amplification profile of the bacterial community assembled was remarkably simplified when compared to the expected number of detectable fragments known to be present in the MBC. From these findings, the scope of hypotheses generation and conclusions from experiments based on PCR amplifications of bacterial communities was discussed.}, }
@article {pmid30961507, year = {2019}, author = {Joe, MB and Roland, L and Laurent, C and Patrick, LM and Sawoo, O and Gaston, TL and Bruno, E and Gilles, P and Philippe, P}, title = {Concomitant Use of Cotrimoxazole and Atazanavir in HIV-infected Patients: A Therapeutic Drug Monitoring and Pharmacovigilance Based Dual Approach.}, journal = {Current clinical pharmacology}, volume = {14}, number = {3}, pages = {214-223}, doi = {10.2174/1574884714666190405160612}, pmid = {30961507}, issn = {2212-3938}, mesh = {Adult ; Aged ; Atazanavir Sulfate/*administration &amp; dosage/adverse effects/blood ; *Drug Monitoring ; Drug Therapy, Combination ; Female ; HIV Infections/*drug therapy ; Humans ; Male ; Middle Aged ; *Pharmacovigilance ; Trimethoprim, Sulfamethoxazole Drug Combination/*administration &amp; dosage/adverse effects/blood ; }, abstract = {BACKGROUND: Cotrimoxazole is the main antibiotic used in primary prophylaxis for opportunistic infections in advanced HIV infection. This drug can inhibit one of the metabolic pathways of atazanavir (ATV), such as the cytochromes P450 (CYP) 2C8/2C9 and could interfere with its safety and efficacy.<br><br>OBJECTIVE: We studied the drug-drug interaction (DDI) between cotrimoxazole and ATV by using therapeutic drug monitoring (TDM) and pharmacovigilance (PV) approaches.<br><br>METHODS: We compared a group of patients treated with cotrimoxazole and receiving an ATV-based regimen to controls. This historical cohort analysis used data from Dat'AIDS in HIV-infected patients who had at least two lowest plasma concentrations (C-trough) of ATV during their outpatient follow-up. Likewise, we used the international pharmacovigilance data from VigiBase to evaluate the notifications of hyperbilirubinemia reported with ATV.<br><br>RESULTS: In the TDM analysis, the two groups of patients (treated with cotrimoxazole and controls) were almost homogeneous concerning the main baseline features. After at least six months of ATVbased regimen, there was no significant difference in the safety threshold of the ATV C-trough [with an adjusted odds ratio (aOR) of 1.4 (95% CI: 0.5 - 4.4)] compared to controls. We observed similar results with the efficacy thresholds of ATV C-trough. Regarding the PV analysis, there was no difference in hyperbilirubinemia occurring with ATV when cotrimoxazole was concomitant, with an adjusted reporting odds ratio (aROR) of 0.9 (95% CI: 0.6 to 1.2).<br><br>CONCLUSION: This study showed a relevant concomitant use between Cotrimoxazole and ATV based on TDM and PV approaches.}, }
@article {pmid30958642, year = {2019}, author = {Kim, J and Gómez-Pastora, J and Weigand, M and Potgieter, M and A Walters, N and Reátegui, E and F Palmer, A and Yazer, M and Zborowski, M and Chalmers, JJ}, title = {A Subpopulation of Monocytes in Normal Human Blood Has Significant Magnetic Susceptibility: Quantification and Potential Implications.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {95}, number = {5}, pages = {478-487}, pmid = {30958642}, issn = {1552-4930}, support = {P30 CA016058/CA/NCI NIH HHS/United States ; R01 HL131720/HL/NHLBI NIH HHS/United States ; R21 GM126543/GM/NIGMS NIH HHS/United States ; }, mesh = {Blood/*metabolism ; Cell Separation ; Cell Size ; Cell Tracking ; Centrifugation, Density Gradient ; Flow Cytometry ; Humans ; Image Processing, Computer-Assisted ; *Magnetic Phenomena ; Monocytes/*cytology ; }, abstract = {The presence of iron in circulating monocytes is well known as they play essential roles in iron recycling. Also, the storage of this metal as well as its incorrect uptake and/or release are important data to diagnose different pathologies. It has been demonstrated that iron storage in human blood cells can be measured through their magnetic behavior with high accuracy; however, the magnetic characteristics of monocytes have not been reported so far to the best of our knowledge. Therefore, in this work, we report, for the first time, the physical and magnetic properties of human monocytes, along with plasma platelets, oxyhemoglobin red blood cells (oxyHb-RBCs), and methemoglobin red blood cells (metHb-RBCs). The different cell populations were separated by Ficoll-density gradient centrifugation, followed by a flow sorting step to isolate monocytes from peripheral blood mononuclear cells. The different fractions were analyzed by Coulter Counter (for determining the size distribution and concentration) and the sorted monocytes were qualitatively analyzed on ImageStream, a state-of-the-art imaging cytometer. The analysis of the Coulter Counter and ImageStream data suggests that although there exists contamination in the monocyte fraction, the integrity of the sorted monocytes appears to be intact and the concentration was high enough to precisely measure their magnetic velocity by Cell Tracking Velocimetry. Surprisingly, monocytes reported the highest magnetic mobility from the four fractions under analysis, with an average magnetic velocity 7.8 times higher than MetHb-RBCs, which is the only type of cells with positive magnetic velocities. This value is equivalent to a susceptibility 2.5 times higher than the value reported by fresh MetHb-RBCs. It should be noted that this is the first study that reports that a subpopulation of human monocytes is much more magnetic than MetHb-RBCs, opening the door to the possible isolation of human monocytes by label-free magnetic techniques. Further, it is suggested that these magnetic monocytes could "contaminate" positively selected, immunomagnetically labeled blood cells (i.e., during a process using magnetically conjugated antibodies targeting cells, such as CD34 positive cells). Conversely, these magnetic monocytes could be inadvertently removed from a desired blood population when one is using a negative magnetic isolation technique to target cells for removal. © 2019 International Society for Advancement of Cytometry.}, }
@article {pmid30957419, year = {2019}, author = {Fanin, N and Kardol, P and Farrell, M and Kempel, A and Ciobanu, M and Nilsson, MC and Gundale, MJ and Wardle, DA}, title = {Effects of plant functional group removal on structure and function of soil communities across contrasting ecosystems.}, journal = {Ecology letters}, volume = {22}, number = {7}, pages = {1095-1103}, doi = {10.1111/ele.13266}, pmid = {30957419}, issn = {1461-0248}, support = {//Vetenskapsr&#xe5;det/ ; }, mesh = {*Biodiversity ; *Ecosystem ; Islands ; Plants ; Soil ; *Soil Microbiology ; Sweden ; }, abstract = {Loss of plant diversity has an impact on ecosystems worldwide, but we lack a mechanistic understanding of how this loss may influence below-ground biota and ecosystem functions across contrasting ecosystems in the long term. We used the longest running biodiversity manipulation experiment across contrasting ecosystems in existence to explore the below-ground consequences of 19 years of plant functional group removals for each of 30 contrasting forested lake islands in northern Sweden. We found that, against expectations, the effects of plant removals on the communities of key groups of soil organisms (bacteria, fungi and nematodes), and organic matter quality and soil ecosystem functioning (decomposition and microbial activity) were relatively similar among islands that varied greatly in productivity and soil fertility. This highlights that, in contrast to what has been shown for plant productivity, plant biodiversity loss effects on below-ground functions can be relatively insensitive to environmental context or variation among widely contrasting ecosystems.}, }
@article {pmid30956127, year = {2020}, author = {Abad, ED and Ferreira, DC and Cavalcante, FS and Saintive, S and Goudouris, E and Prado, EA and Hofer, C and Ribeiro, M and da Silva, AMP and Rosado, AS and van Elsas, JD and Dos Santos, KRN}, title = {High incidence of acquiring methicillin-resistant Staphylococcus aureus in Brazilian children with Atopic Dermatitis and associated risk factors.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {53}, number = {5}, pages = {724-730}, doi = {10.1016/j.jmii.2018.12.014}, pmid = {30956127}, issn = {1995-9133}, mesh = {Adolescent ; Anti-Bacterial Agents/pharmacology ; Brazil/epidemiology ; Child ; Child, Preschool ; Cohort Studies ; Cyclosporine ; Dermatitis, Atopic/*epidemiology/*microbiology ; Female ; Histamine Antagonists ; Humans ; Incidence ; Infant ; Male ; Methicillin-Resistant Staphylococcus aureus/drug effects/isolation &amp; purification ; Multivariate Analysis ; Prospective Studies ; Protective Factors ; Risk Factors ; Staphylococcal Infections/*epidemiology/*microbiology ; }, abstract = {BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) colonization in Atopic Dermatitis (AD) patients can contribute to worsening their clinical condition.<br><br>OBJECTIVE: A cohort study was carried out to determine the incidence of MRSA acquisition and its risk factors in AD children.<br><br>METHODS: Patients with AD (2 months-14 years old) were followed up for about 1&#xa0;year at a reference center for AD treatment in Rio de Janeiro, Brazil, from September 2011 to February 2014. Nasal swabs from patients and contacts were collected every 2 months. The SCORAD system assessed the severity of the AD. S. aureus isolates were evaluated to determine the methicillin resistance and the clonal lineages.<br><br>RESULTS: Among 117 AD patients, 97 (82.9%) were already colonized with S. aureus and 26 (22.2%) had MRSA at the first evaluation. The incidence of MRSA acquisition in the cohort study was 27.47% (n&#xa0;=&#xa0;25). The SCORAD assessments were: mild (46.15%), moderate (37.36%) or severe (16.48%). Risk factors were: colonized MRSA contacts (HR&#xa0;=&#xa0;2.27; 95% CI: 1.16-7.54), use of cyclosporine (HR&#xa0;=&#xa0;5.84; 95% CI: 1.70-19.98), moderate or severe AD (HR&#xa0;=&#xa0;3.26; 95% CI: 1.13-9.37). Protective factors were: availability of running water (HR&#xa0;=&#xa0;0.21; 95% CI: 0.049-0.96) and use of antihistamines (HR&#xa0;=&#xa0;0.21; 95% IC: 0.64-0.75). MRSA isolates carried the SCCmec type IV and most of them were typed as USA800/ST5.<br><br>CONCLUSIONS: The high incidence of MRSA acquisition found among AD patients and the risk factors associated show that an effective surveillance of MRSA colonization in these patients is needed.}, }
@article {pmid30955771, year = {2019}, author = {Cotta, SR and Cadete, LL and van Elsas, JD and Andreote, FD and Dias, ACF}, title = {Exploring bacterial functionality in mangrove sediments and its capability to overcome anthropogenic activity.}, journal = {Marine pollution bulletin}, volume = {141}, number = {}, pages = {586-594}, doi = {10.1016/j.marpolbul.2019.03.001}, pmid = {30955771}, issn = {1879-3363}, mesh = {Bacteria/genetics/metabolism ; Biodiversity ; Brazil ; Carbon/metabolism ; Ecosystem ; Gene Transfer, Horizontal ; Geologic Sediments/*microbiology ; Metagenomics ; *Microbiota/genetics ; Sulfur/metabolism ; *Wetlands ; }, abstract = {Mangrove forests are highly productive yet vulnerable ecosystems that act as important carbon sinks ("blue carbon"). The objective of this work was to analyze the impact of anthropogenic activities on microbiome structure and functioning. The metagenomic analysis revealed that the taxonomic compositions were grossly similar across all mangrove microbiomes. Remarkably, these microbiomes, along the gradient of anthropogenic impact, showed fluctuations in the relative abundances of bacterial taxa predicted to be involved in sulfur cycling processes. Functions involved in sulfur metabolism, such as APS pathways (associated with sulfate reduction and sulfur oxidation processes) were prevalent across the microbiomes, being sox and dsrAB genes highly expressed on anthropogenically-impacted areas. Apparently, the oil-impacted microbiomes were more affected in taxonomic than in functional terms, as high functional redundancies were noted across them. The microbial gene diversity found was typical for a functional system, even following the previous disturbance.}, }
@article {pmid30953090, year = {2019}, author = {Stamou, GP and Monokrousos, N and Gwynn-Jones, D and Whitworth, DE and Papatheodorou, EM}, title = {A Polyphasic Approach for Assessing Eco-System Connectivity Demonstrates that Perturbation Remodels Network Architecture in Soil Microcosms.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {949-960}, pmid = {30953090}, issn = {1432-184X}, support = {No. Project 89434//Research Committee, Aristotle University of Thessaloniki/ ; }, mesh = {Bacteria/*drug effects ; Dose-Response Relationship, Drug ; Ecosystem ; Mentha spicata/chemistry ; Microbiota/*drug effects ; Mycorrhizae/*physiology ; Oils, Volatile/administration &amp; dosage/*chemistry ; Soil ; *Soil Microbiology ; }, abstract = {Network analysis was used to show changes in network attributes by analyzing the relations among the main soil microbial groups in a potted tomato soil inoculated with arbuscular mycorrhizal fungus, treated with low doses of Mentha spicata essential oil, or both, and then exposed to tenfold higher oil addition (stress pulse). Pretreatments were chosen since they can induce changes in the composition of the microbial community. Cellular phospholipid fatty acids (PLFAs) and the activity of six soil enzymes, mainly involved in the N-cycle were measured. Networks were constructed based on correlated changes in PLFA abundances. The values of all parameters were significantly different from those of random networks indicating modular architecture. Networks ranked from the lowest to highest modularity: control, non-pretreated and stressed, inoculated and stressed, oil treated and stressed, inoculated and treated with oil and stressed. The high values of network density and 1st/2nd eigenvalue ratio are related to arylamidase activity while N-acetyl-glucosaminidase, acid phosphomoesterase, and asparaginase activities related to high values of the clustering coefficient index. We concluded that modularity may be an efficient indicator of changes in the network of interactions among the members of the soil microbial community and the modular structure of the network may be related to the activity of specific enzymes. Communities that were stressed without a pretreatment were relatively resistant but prone to sudden transition towards instability, while oil or inoculation pretreatments gave networks which could be considered adaptable and susceptible to gradual change.}, }
@article {pmid30953089, year = {2019}, author = {Han, J and Wang, S and Fan, D and Guo, Y and Liu, C and Zhu, Y}, title = {Time-Dependent Hormetic Response of Soil Alkaline Phosphatase Induced by Cd and the Association with Bacterial Community Composition.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {961-973}, pmid = {30953089}, issn = {1432-184X}, support = {No. 41375149//National Natural Science Foundation of China/ ; No. 41471191//National Natural Science Foundation of China/ ; }, mesh = {Alkaline Phosphatase/*analysis ; Bacteria/*classification/drug effects ; Cadmium/*adverse effects ; *Hormesis ; Microbiota/drug effects ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/*adverse effects ; }, abstract = {Hormetic dose-response that involved Cd in soils is increasingly paid attentions for risk assessment of Cd toxicity, but insufficient studies were conducted to define the temporary modification of soil enzyme and the potential microbial responses. The present study chooses soil alkaline phosphatase (ALP) as endpoint to uncover the time-dependent hormetic responses to low doses of Cd and its association with bacterial community composition. The results showed that addition of 0.01-3.0 mg kg[-1] Cd significantly increased ALP's activities with maximum stimulatory magnitude of 11.4-27.2%, indicating a typical hormesis. The response started at 12 h after Cd addition and maintained about 24 h. This demonstrated that the hormetic response is time-dependent and transient. Changes of soil bacterial community composition showed that, at 6 h, relative abundances (RAs) of Proteobacteria and Firmicutes at phylum and Pontibacter, Bacillaceae-Bacillus, Bacillaceae1-Bacillus, and Paenisporosarcina at genus significantly correlated with ALP's activities at 12-36 h (P < 0.05). This suggests that soil bacteria likely showed an earlier response to Cd and potentially contributes to the subsequent soil enzyme's hormesis. In addition, it was found that Gram-negative bacteria other than Gram-positive bacteria are prone to exhibiting a hormetic response under Cd stress. Our findings provide much insight into ecotoxicological risk assessment for soil Cd pollution.}, }
@article {pmid30952994, year = {2019}, author = {Martiny, AC}, title = {High proportions of bacteria are culturable across major biomes.}, journal = {The ISME journal}, volume = {13}, number = {8}, pages = {2125-2128}, pmid = {30952994}, issn = {1751-7370}, mesh = {Bacteria/genetics/*growth &amp; development/isolation &amp; purification ; *Microbiota ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The paradigm that only 1% of microbes are culturable has had a profound impact on our understanding of microbial ecology and is still a major motivation for mostly using molecular tools to characterize microbial communities. However, this point is often expressed vaguely, suggesting that some scientists have different interpretations of the paradigm. In addition, there have been substantial advances in cultivation techniques suggesting that this paradigm may no longer be correct. To quantify bacterial culturability across six major biomes, I found that the median 16S rRNA similarity of bacteria to known cultured relatives was 97.3 ± 2.3% (s.d.). Furthermore, 52.0 ± 24% of sequences and 34.9 ± 23% of taxa (defined as >97% similar) had a closely related cultured relative. Thus, many cells and taxa across environments are culturable with known techniques, suggesting that the 1% paradigm is no longer correct.}, }
@article {pmid30952863, year = {2019}, author = {Wilschut, RA and van der Putten, WH and Garbeva, P and Harkes, P and Konings, W and Kulkarni, P and Martens, H and Geisen, S}, title = {Root traits and belowground herbivores relate to plant-soil feedback variation among congeners.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1564}, pmid = {30952863}, issn = {2041-1723}, mesh = {Animals ; Geranium/genetics/microbiology/*physiology ; Herbivory/*physiology ; Microbiota ; Nematoda/physiology ; Phylogeny ; Plant Roots/genetics/microbiology/physiology ; Rhizosphere ; *Soil ; }, abstract = {Plant-soil feedbacks contribute to vegetation dynamics by species-specific interactions between plants and soil biota. Variation in plant-soil feedbacks can be predicted by root traits, successional position, and plant nativeness. However, it is unknown whether closely related plant species develop more similar plant-soil feedbacks than more distantly related species. Where previous comparisons included plant species from distant phylogenetic positions, we studied plant-soil feedbacks of congeneric species. Using eight intra-continentally range-expanding and native Geranium species, we tested relations between phylogenetic distances, chemical and structural root traits, root microbiomes, and plant-soil feedbacks. We show that root chemistry and specific root length better predict bacterial and fungal community composition than phylogenetic distance. Negative plant-soil feedback strength correlates with root-feeding nematode numbers, whereas microbiome dissimilarity, nativeness, or phylogeny does not predict plant-soil feedbacks. We conclude that root microbiome variation among congeners is best explained by root traits, and that root-feeding nematode abundances predict plant-soil feedbacks.}, }
@article {pmid30951891, year = {2019}, author = {Philip, N and Bandara, HMHN and Leishman, SJ and Walsh, LJ}, title = {Effect of polyphenol-rich cranberry extracts on cariogenic biofilm properties and microbial composition of polymicrobial biofilms.}, journal = {Archives of oral biology}, volume = {102}, number = {}, pages = {1-6}, doi = {10.1016/j.archoralbio.2019.03.026}, pmid = {30951891}, issn = {1879-1506}, mesh = {*Biofilms ; *Dental Caries ; Humans ; Plant Extracts ; Polyphenols ; Streptococcus mutans ; *Vaccinium macrocarpon ; }, abstract = {OBJECTIVE: To investigate the effect of cranberry extracts on saliva-derived polymicrobial biofilms with regards to biofilm biomass, acidogenicity, exopolysaccharide (EPS)/microbial biovolumes, colony forming unit (CFU) counts, and the relative abundance of specific caries- and health-associated bacteria.<br><br>METHODS: Saliva-derived polymicrobial biofilms were grown for 96&#x2009;h in a cariogenic environment and treated for 2&#x2009;min every 12&#x2009;h over the entire biofilm growth period with 500&#x2009;&#x3bc;g/mL cranberry extract or vehicle control. The effect of the cranberry extract on biofilm behaviour was evaluated using different assays and its influence on key cariogenic and health-associated bacterial populations was assessed with a microarray real-time quantitative PCR method.<br><br>RESULTS: Cranberry-treated biofilms showed significant drops in biomass (38% reduction, P&#x2009;<&#x2009; 0.001), acidogenicity (44% reduction, P&#x2009;<&#x2009; 0.001), EPS/microbial biovolume ratios (P&#x2009;=&#x2009; 0.033), and CFU counts (51% reduction, P&#x2009;=&#x2009; 0.001). Furthermore, the cranberry extracts effected a significantly lower relative abundance of caries-associated Streptococcus sobrinus (fold change 0.004, P&#x2009;=&#x2009; 0.002) and Provotella denticola (0.002, P&#x2009;<&#x2009; 0.001), and a significantly higher relative abundance of the health-associated Streptococcus sanguinis (fold change 90.715, P&#x2009;=&#x2009; 0.001).<br><br>CONCLUSIONS: The cranberry extract lowered biofilm biomass, acidogenicity, EPS/microbial biovolumes, CFU counts, and modulated a beneficial microbial ecological change in saliva-derived polymicrobial biofilms.}, }
@article {pmid30949751, year = {2019}, author = {Hughey, MC and Sokol, ER and Walke, JB and Becker, MH and Belden, LK}, title = {Ecological Correlates of Large-Scale Turnover in the Dominant Members of Pseudacris crucifer Skin Bacterial Communities.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {832-842}, pmid = {30949751}, issn = {1432-184X}, support = {DEB-1136640//National Science Foundation/ ; D10ZO-028//Morris Animal Foundation/ ; }, mesh = {Animals ; Anura/*microbiology ; Bacteria/classification/*isolation &amp; purification ; *Microbiota ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Skin/*microbiology ; Virginia ; }, abstract = {Animals host a wide diversity of symbiotic microorganisms that contribute important functions to host health, and our knowledge of what drives variation in the composition of these complex communities continues to grow. Microbiome studies at larger spatial scales present opportunities to evaluate the contribution of large-scale factors to variation in the microbiome. We conducted a large-scale field study to assess variation in the bacterial symbiont communities on adult frog skin (Pseudacris crucifer), characterized using 16S rRNA gene amplicon sequencing. We found that skin bacterial communities on frogs were less diverse than, and structurally distinct from, the surrounding habitat. Frog skin was typically dominated by one of two bacterial OTUs: at western sites, a Proteobacteria dominated the community, whereas eastern sites were dominated by an Actinobacteria. Using a metacommunity framework, we then sought to identify factors explaining small- and large-scale variation in community structure-that is, among hosts within a pond, and among ponds spanning the study transect. We focused on the presence of a fungal skin pathogen, Batrachochytrium dendrobatidis (Bd) as one potential driver of variation. We found no direct link between skin bacterial community structure and Bd infection status of individual frog hosts. Differences in pond-level community structure, however, were explained by Bd infection prevalence. Importantly, Bd infection prevalence itself was correlated with numerous other environmental factors; thus, skin bacterial diversity may be influenced by a complex suite of extrinsic factors. Our findings indicate that large-scale factors and processes merit consideration when seeking to understand microbiome diversity.}, }
@article {pmid30949750, year = {2019}, author = {Lan, S and Thomas, AD and Tooth, S and Wu, L and Hu, C}, title = {Small-Scale Spatial Heterogeneity of Photosynthetic Fluorescence Associated with Biological Soil Crust Succession in the Tengger Desert, China.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {936-948}, pmid = {30949750}, issn = {1432-184X}, support = {31670456 and 31300322//National Natural Science Foundation of China/ ; 2017385//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 663830//European Union's Horizon 2020 research and innovation programme under the Marie Sk&#x142;odowska-Curie Grant/ ; }, mesh = {Bryophyta/*physiology ; China ; Cyanobacteria/*physiology ; *Desert Climate ; Fluorescence ; Lichens/*physiology ; *Photosynthesis ; *Soil Microbiology ; }, abstract = {In dryland regions, biological soil crusts (BSCs) have numerous important ecosystem functions. Crust species and functions are, however, highly spatially heterogeneous and remain poorly understood at a range of scales. In this study, chlorophyll fluorescence imaging was used to quantify millimeter-scale patterns in the distribution and activity of photosynthetic organisms in BSCs of different successional stages (including cyanobacterial, lichen, moss three main successional stages and three intermixed transitional stages) from the Tengger Desert, China. Chlorophyll fluorescence images derived from the Imaging PAM (Pulse Amplitude Modulation) showed that with the succession from cyanobacterial to lichen and to moss crusts, crust photosynthetic efficiency (including the maximum and effective photosynthetic efficiency, respectively) and fluorescence coverage increased significantly (P < 0.05), and that increasing photosynthetically active radiation (PAR) reduced the effective photosynthetic efficiency (Yield). The distribution of photosynthetic organisms in crusts determined Fv/Fm (ratio of variable fluorescence to maximum fluorescence) frequency pattern, although the photosynthetic heterogeneity (SHI index) was not significantly different (P > 0.05) between cyanobacterial and moss crusts, and showed a unimodal pattern of Fv/Fm values. In contrast, photosynthetic heterogeneity was significantly higher in lichen, cyanobacteria-moss and lichen-moss crusts (P < 0.05), with a bimodal pattern of Fv/Fm values. Point pattern analysis showed that the distribution pattern of chlorophyll fluorescence varied at different spatial scales and also among the different crust types. These new results provide a detailed (millimeter-scale) insight into crust photosynthetic mechanisms and spatial distribution patterns associated with their community types. Collectively, this information provides an improved theoretical basis for crust maintenance and management in dryland regions.}, }
@article {pmid30948795, year = {2019}, author = {D'Amico, F and Soverini, M and Zama, D and Consolandi, C and Severgnini, M and Prete, A and Pession, A and Barone, M and Turroni, S and Biagi, E and Brigidi, P and Masetti, R and Rampelli, S and Candela, M}, title = {Gut resistome plasticity in pediatric patients undergoing hematopoietic stem cell transplantation.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5649}, pmid = {30948795}, issn = {2045-2322}, mesh = {Adolescent ; Anti-Bacterial Agents/adverse effects ; Child ; Drug Resistance, Microbial/*genetics ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Graft vs Host Disease/etiology ; Hematopoietic Stem Cell Transplantation/methods ; Hematopoietic Stem Cells/*metabolism ; Humans ; Male ; Metagenomics/methods ; Transplantation, Homologous/adverse effects ; }, abstract = {The gut microbiome of pediatric patients undergoing allo-hematopoietic stem cell transplantation (HSCT) has recently been considered as a potential reservoir of antimicrobial resistance, with important implications in terms of patient mortality rate. By means of shotgun metagenomics, here we explored the dynamics of the gut resistome - i.e. the pattern of antibiotic resistance genes provided by the gut microbiome - in eight pediatric patients undergoing HSCT, half of whom developed acute Graft-versus-Host Disease (aGvHD). According to our findings, the patients developing aGvHD are characterized by post-HSCT expansion of their gut resistome, involving the acquisition of new resistances, as well as the consolidation of those already present before HSCT. Interestingly, the aGvHD-associated bloom in resistome diversity is not limited to genes coding for resistance to the antibiotics administered along the therapeutic course, but rather involves a broad pattern of different resistance classes, including multidrug resistance, as well as resistance to macrolides, aminoglycosides, tetracyclines and beta-lactams. Our data stress the relevance of mapping the gut resistome in HSCT pediatric patients to define the most appropriate anti-infective treatment post HSCT.}, }
@article {pmid30945554, year = {2020}, author = {Miclotte, L and Van de Wiele, T}, title = {Food processing, gut microbiota and the globesity problem.}, journal = {Critical reviews in food science and nutrition}, volume = {60}, number = {11}, pages = {1769-1782}, doi = {10.1080/10408398.2019.1596878}, pmid = {30945554}, issn = {1549-7852}, mesh = {Diet ; Dietary Fiber ; *Food Handling ; *Gastrointestinal Microbiome ; Humans ; Noncommunicable Diseases/*epidemiology ; Obesity/*epidemiology/*microbiology ; }, abstract = {In the context of diseases of affluence, western diets have in the past years mainly been studied on their fat and sugar content and lack of dietary fiber. Yet, the more general aspect of food processing has recently sparked scientific interest as well. In addition, the gut microbiota have been put forward as an important link between diet, obesity and non-communicable diseases (NCD). Western dietary patterns, containing large amounts of processed foods might create an imbalance in the gut system by affecting gut bacteria and their metabolism. Here we discuss what has been already published regarding the relationship between several recently researched features of processed foods and the etiology of obesity and NCD. The addressed features concern micronutrient and energy density, several types of food additives and the generation of advanced glycation end products by thermal treatment during food processing. Overall, literature indicates that all discussed aspects can be linked to western ailments and that they can have a potential negative impact on human microbiota. Therefore, we propose that the thesis that a distressed gut microbiota is a mechanism that might explain how food processing features could harm human health is gaining empirical evidence. Future research will need to address the question whether the alteration of the gut microbiota is a direct or an indirect (via the host) effect. These conclusions are important assets in the fight against the continuing worldwide upsurge of obesity and NCD.}, }
@article {pmid30944882, year = {2019}, author = {Jiao, S and Xu, Y and Zhang, J and Hao, X and Lu, Y}, title = {Core Microbiota in Agricultural Soils and Their Potential Associations with Nutrient Cycling.}, journal = {mSystems}, volume = {4}, number = {2}, pages = {}, pmid = {30944882}, issn = {2379-5077}, abstract = {Revealing the ecological roles of the core microbiota in community maintaining and soil nutrient cycling is crucial for understanding ecosystem function, yet there is a dearth of continental-scale studies on this fundamental topic in microbial ecology. Here, we collected 251 soil samples from adjacent pairs of maize and rice fields at a continental scale in eastern China. We revealed the major ecological roles of the core microbiota in maintaining complex connections between bacterial taxa and their associations with belowground multinutrient cycling. By identifying the habitat preferences of the core microbiota, we built a continental atlas for mapping the spatial distributions of bacteria in agro-soils, which helps forecast the responses of agricultural ecosystems to anthropogenic disturbance. The multinutrient cycling index for maize and rice soils was related to bacterial α-diversity and β-diversity, respectively. Rice soils exhibited higher bacterial diversity and closer bacterial cooccurrence relationships than maize soils. In contrast to the macro- or microecological latitudinal richness patterns in natural terrestrial ecosystems, the bacteria in maize soils showed higher richness at high latitudes; however, this trend was not observed in rice soils. This study provides a new perspective on the distinct bacterial biogeographic patterns to predict the ecological roles of the core microbiota in agro-soils and thus helps manage soil bacterial communities for better provisioning of key ecosystem services. IMPORTANCE Disentangling the roles of the core microbiota in community maintaining and soil nutrient cycling is an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the spatial atlas and ecological roles of the core microbiota. A systematic, continental-scale survey was conducted using agro-soils in adjacent pairs of maize (dryland) and rice (wetland) fields across eastern China. The results indicate that the core microbiota play major ecological roles in maintaining complex connections between bacterial taxa and are associated with belowground multinutrient cycling. A continental atlas was built for mapping the bacterial spatial distributions in agro-soils through identifying their habitat preferences. This study represents a significant advance in forecasting the responses of agricultural ecosystems to anthropogenic disturbance and thus helps manage soil bacterial communities for better provisioning of key ecosystem services-the ultimate goal of microbial ecology.}, }
@article {pmid30944878, year = {2019}, author = {Tong, X and Leung, MHY and Wilkins, D and Cheung, HHL and Lee, PKH}, title = {Neutral Processes Drive Seasonal Assembly of the Skin Mycobiome.}, journal = {mSystems}, volume = {4}, number = {2}, pages = {}, pmid = {30944878}, issn = {2379-5077}, abstract = {The importance of microorganisms to human skin health has led to a growing interest in the temporal stability of skin microbiota. Here we investigated the dynamics and assembly of skin fungal communities (mycobiomes) with amplicon sequencing of samples collected from multiple sites on 24 healthy Chinese individuals across four seasons (in the order of winter, spring, summer, and autumn in a calendar year). We found a significant difference in community compositions between individuals, and intrapersonal community variation increased over time at all body sites. Within each season, the frequency of occurrence of most operational taxonomic units (OTUs) was well fitted by a neutral model, highlighting the importance of stochastic forces such as passive dispersal and ecological drift in skin community assembly. Despite the significant richness contributed by neutrally distributed OTUs, skin coassociation networks were dominated by taxa well-adapted to multiple body sites (forehead, forearm, and palm), although hub species were disproportionately rare. Taken together, these results suggest that while skin mycobiome assembly is a predominantly neutral process, taxa that could be under the influence of selective forces (e.g., host selection) are potentially key to the structure of a community network. IMPORTANCE Fungi are well recognized members of the human skin microbiota and are crucial to cutaneous health. Common cutaneous diseases such as seborrheic dermatitis and dermatophytes are linked to fungal species. Most studies related to skin microbial community dynamics have focused on Western subjects, while non-Western individuals are understudied. In this study, we explore the seasonal changes of the skin mycobiome in a healthy Chinese cohort and identify ecological processes that could possibly give rise to such variations. Our work reveals the dynamic nature of host skin fungal community, highlighting the dominant roles neutral forces play in the seasonal assembly of skin mycobiome. This study provides insight into the microbial ecology of the human skin microbiome and fills a knowledge gap in the literature regarding the dynamics of skin fungal community.}, }
@article {pmid30944853, year = {2019}, author = {Pärnänen, KMM and Narciso-da-Rocha, C and Kneis, D and Berendonk, TU and Cacace, D and Do, TT and Elpers, C and Fatta-Kassinos, D and Henriques, I and Jaeger, T and Karkman, A and Martinez, JL and Michael, SG and Michael-Kordatou, I and O'Sullivan, K and Rodriguez-Mozaz, S and Schwartz, T and Sheng, H and Sørum, H and Stedtfeld, RD and Tiedje, JM and Giustina, SVD and Walsh, F and Vaz-Moreira, I and Virta, M and Manaia, CM}, title = {Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence.}, journal = {Science advances}, volume = {5}, number = {3}, pages = {eaau9124}, pmid = {30944853}, issn = {2375-2548}, mesh = {Anti-Bacterial Agents/metabolism/*pharmacology ; Drug Resistance, Microbial/*genetics ; Environmental Monitoring/methods ; Europe/epidemiology ; Genes, Bacterial/*genetics ; Geography ; Humans ; Population Surveillance/methods ; Prevalence ; Wastewater/*microbiology ; Water Purification/*methods ; }, abstract = {Integrated antibiotic resistance (AR) surveillance is one of the objectives of the World Health Organization global action plan on antimicrobial resistance. Urban wastewater treatment plants (UWTPs) are among the most important receptors and sources of environmental AR. On the basis of the consistent observation of an increasing north-to-south clinical AR prevalence in Europe, this study compared the influent and final effluent of 12 UWTPs located in seven countries (Portugal, Spain, Ireland, Cyprus, Germany, Finland, and Norway). Using highly parallel quantitative polymerase chain reaction, we analyzed 229 resistance genes and 25 mobile genetic elements. This first trans-Europe surveillance showed that UWTP AR profiles mirror the AR gradient observed in clinics. Antibiotic use, environmental temperature, and UWTP size were important factors related with resistance persistence and spread in the environment. These results highlight the need to implement regular surveillance and control measures, which may need to be appropriate for the geographic regions.}, }
@article {pmid30941803, year = {2019}, author = {Björk, JR and Dasari, M and Grieneisen, L and Archie, EA}, title = {Primate microbiomes over time: Longitudinal answers to standing questions in microbiome research.}, journal = {American journal of primatology}, volume = {81}, number = {10-11}, pages = {e22970}, pmid = {30941803}, issn = {1098-2345}, support = {R01 AG053330/AG/NIA NIH HHS/United States ; R01 AG071684/AG/NIA NIH HHS/United States ; R21 AG055777/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Ecosystem ; Feces/microbiology ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; Longitudinal Studies ; Primates/*microbiology ; Social Environment ; }, abstract = {To date, most insights into the processes shaping vertebrate gut microbiomes have emerged from studies with cross-sectional designs. While this approach has been valuable, emerging time series analyses on vertebrate gut microbiomes show that gut microbial composition can change rapidly from 1 day to the next, with consequences for host physical functioning, health, and fitness. Hence, the next frontier of microbiome research will require longitudinal perspectives. Here we argue that primatologists, with their traditional focus on tracking the lives of individual animals and familiarity with longitudinal fecal sampling, are well positioned to conduct research at the forefront of gut microbiome dynamics. We begin by reviewing some of the most important ecological processes governing microbiome change over time, and briefly summarizing statistical challenges and approaches to microbiome time series analysis. We then introduce five questions of general interest to microbiome science where we think field-based primate studies are especially well positioned to fill major gaps: (a) Do early life events shape gut microbiome composition in adulthood? (b) Do shifting social landscapes cause gut microbial change? (c) Are gut microbiome phenotypes heritable across variable environments? (d) Does the gut microbiome show signs of host aging? And (e) do gut microbiome composition and dynamics predict host health and fitness? For all of these questions, we highlight areas where primatologists are uniquely positioned to make substantial contributions. We review preliminary evidence, discuss possible study designs, and suggest future directions.}, }
@article {pmid30941446, year = {2019}, author = {Johansen, R and Albright, M and Gallegos-Graves, V and Lopez, D and Runde, A and Yoshida, T and Dunbar, J}, title = {Tracking Replicate Divergence in Microbial Community Composition and Function in Experimental Microcosms.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {1035-1039}, pmid = {30941446}, issn = {1432-184X}, support = {SFA 2015F260//U.S. Department of Energy/ ; }, mesh = {Bacteria/*classification ; *Bacterial Physiological Phenomena ; Fungi/*classification ; *Microbiota ; Mycobiome ; *Soil Microbiology ; }, abstract = {The study of microbial community functions necessitates replicating microbial communities. Variation in community development over time renders this an imperfect process. Thus, anticipating the likely degree of variation among replicate communities may aid in experimental design. We examined divergence in replicate community composition and function among 128 naturally assembled starting communities obtained from soils, each replicated three times, following a 30-day microcosm incubation period. Bacterial and fungal communities diverged in both composition and function among replicates, but remained much more similar to each other than to communities from different starting inocula. Variation in bacterial community composition among replicates was, however, correlated with variation in dissolved organic carbon production. A smaller-scale experiment testing nine starting communities showed that divergence was similar whether replicates were incubated on sterile or non-sterile pine litter, suggesting the impact of a pre-existing community on replicate divergence is minor. However, replicates in this experiment which were incubated for 114 days diverged more than those incubated for 30 days, suggesting experiments that run over long time periods will likely see greater variation among replicate community composition. These results suggest that while replicates diverge at a community level, such divergence is unlikely to severely impede the study of community function.}, }
@article {pmid30937143, year = {2019}, author = {Chiu, CY and Chan, YL and Tsai, MH and Wang, CJ and Chiang, MH and Chiu, CC}, title = {Gut microbial dysbiosis is associated with allergen-specific IgE responses in young children with airway allergies.}, journal = {The World Allergy Organization journal}, volume = {12}, number = {3}, pages = {100021}, pmid = {30937143}, issn = {1939-4551}, abstract = {BACKGROUND: There is increasing evidence linking alterations of the gut microbial composition during early infancy to the development of atopic diseases and asthma. However, few studies have addressed the association of dysbiotic gut microbiota with allergic reactions through evaluation of feces in young children with allergic airway diseases.<br><br>METHODS: We sought to evaluate relationships among gut microbiota, total fecal immunoglobulin E (IgE) levels, serum allergic sensitization, and their relevance to childhood allergic rhinitis and asthma. Microbial composition and diversity were analyzed with Illumina-based 16S rRNA gene sequencing of 89 stool samples collected from children with asthma (n&#xa0;=&#xa0;35) and allergic rhinitis (n&#xa0;=&#xa0;28), and from healthy controls (n&#xa0;=&#xa0;26). Data analysis was performed using Quantitative Insights into Microbial Ecology (QIIME) software.<br><br>RESULTS: A significantly lower abundance of organisms of the phylum Firmicutes were found in children with asthma and allergic rhinitis than in the healthy controls. Relatively lower Chao1 and Shannon indices were also found in children with allergic airway diseases but without any significant difference. Total fecal IgE levels in early childhood were strongly correlated with serum D.&#xa0;pteronyssinus- and D.&#xa0;farinae-specific IgE but not with food-specific IgE levels. In comparison with healthy controls, the genus Dorea was less abundant and negatively correlated with total fecal IgE levels in children with rhinitis, whereas the genus Clostridium was abundant and positively correlated with fecal IgE levels in children with asthma.<br><br>CONCLUSIONS: An interaction between particular subsets of gut microbial dysbiosis and IgE-mediated responses to allergens may contribute to the susceptibility to allergic rhinitis and asthma in early childhood.}, }
@article {pmid30936485, year = {2019}, author = {Bulzu, PA and Andrei, A&#x15e; and Salcher, MM and Mehrshad, M and Inoue, K and Kandori, H and Beja, O and Ghai, R and Banciu, HL}, title = {Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche.}, journal = {Nature microbiology}, volume = {4}, number = {7}, pages = {1129-1137}, pmid = {30936485}, issn = {2058-5276}, mesh = {Aerobiosis ; Anaerobiosis ; Archaea/*classification/genetics/*metabolism ; Ecosystem ; Evolution, Molecular ; Genome, Archaeal/genetics ; Metabolic Networks and Pathways ; *Phylogeny ; RNA, Ribosomal/genetics ; Rhodopsins, Microbial/classification/genetics ; }, abstract = {Recent advances in phylogenomic analyses and increased genomic sampling of uncultured prokaryotic lineages have brought compelling evidence in support of the emergence of eukaryotes from within the archaeal domain of life (eocyte hypothesis)[1,2]. The discovery of Asgardarchaeota and its supposed position at the base of the eukaryotic tree of life[3,4] provided cues about the long-awaited identity of the eocytic lineage from which the nucleated cells (Eukaryota) emerged. While it is apparent that Asgardarchaeota encode a plethora of eukaryotic-specific proteins (the highest number identified yet in prokaryotes)[5], the lack of genomic information and metabolic characterization has precluded inferences about their lifestyles and the metabolic landscape that favoured the emergence of the protoeukaryote ancestor. Here, we use advanced phylogenetic analyses for inferring the deep ancestry of eukaryotes, and genome-scale metabolic reconstructions for shedding light on the metabolic milieu of Asgardarchaeota. In doing so, we: (1) show that Heimdallarchaeia (the closest eocytic lineage to eukaryotes to date) are likely to have a microoxic niche, based on their genomic potential, with aerobic metabolic pathways that are unique among Archaea (that is, the kynurenine pathway); (2) provide evidence of mixotrophy within Asgardarchaeota; and (3) describe a previously unknown family of rhodopsins encoded within the recovered genomes.}, }
@article {pmid30929045, year = {2019}, author = {Hogue, SR and Gomez, MF and da Silva, WV and Pierce, CM}, title = {A Customized At-Home Stool Collection Protocol for Use in Microbiome Studies Conducted in Cancer Patient Populations.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {1030-1034}, pmid = {30929045}, issn = {1432-184X}, support = {P30 CA076292/CA/NCI NIH HHS/United States ; 02-25999-18-46//Florida Academic Cancer Center Alliance/ ; P30-CA076292//H. Lee Moffitt Cancer Center and Research Institute/ ; }, mesh = {Feces/*microbiology ; Humans ; *Microbiota ; Neoplasms/*microbiology ; Specimen Handling/instrumentation/*methods ; }, abstract = {Fecal specimen collection in the clinical setting is often unfeasible for large population studies, especially because cancer patients on immunotherapy often experience constipation. A method for constructing and using an at-home stool collection kit designed for epidemiological studies in cancer patients is presented. Participation and compliance rates of the collection kit among late-stage cancer patients from an ongoing, longitudinal study are also discussed. The kit includes three different media on which samples are introduced. Using one stool sample, patients collect specimens by smearing stool onto a fecal occult blood test (FOBT) card, containing three slides for collection. Additional specimens from the same stool sample are added to one tube containing 8 mL of RNAlater preservative and one tube containing 8 mL of 95% ethanol. Stool specimens are stored at room temperature and returned to researchers within 3 days of collection. The purpose of this kit is to yield stool specimens on a variety of media that can be preserved for extended periods of time at room temperature and are compatible with multi-omics approaches for specimen analysis. According to leading microbiome researchers and published literature, each collection method is considered optimal for use in large epidemiological studies. Moreover, the kit is comprised of various components that make stool collection easy, so as not to burden the patient and hence maximize overall compliance. Use of this kit in a study of late-stage lung cancer patients had a participation rate of 83% and baseline compliance rate of 58%.}, }
@article {pmid30929044, year = {2019}, author = {Semenec, L and Vergara, IA and Laloo, AE and Mathews, ER and Bond, PL and Franks, AE}, title = {Correction to: Enhanced Growth of Pilin-Deficient Geobacter sulfurreducens Mutants in Carbon Poor and Electron Donor Limiting Conditions.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {1040-1041}, doi = {10.1007/s00248-019-01370-2}, pmid = {30929044}, issn = {1432-184X}, abstract = {The published version of this article contained an old version of Fig. 2.}, }
@article {pmid30926316, year = {2019}, author = {Brown, MR and Hands, CL and Coello-Garcia, T and Sani, BS and Ott, AIG and Smith, SJ and Davenport, RJ}, title = {A flow cytometry method for bacterial quantification and biomass estimates in activated sludge.}, journal = {Journal of microbiological methods}, volume = {160}, number = {}, pages = {73-83}, doi = {10.1016/j.mimet.2019.03.022}, pmid = {30926316}, issn = {1872-8359}, mesh = {Bacteria/*isolation &amp; purification ; *Environmental Microbiology ; Sewage/*microbiology ; Water Purification/methods ; }, abstract = {Absolute bacterial quantification receives little serious attention in the literature compared to sequencing, conceivably because it is considered unimportant and facile, or because existing methods are tedious, laborious and/or biased in nature. This is particularly true in engineered systems, including activated sludge, where such information underpins their design and operation. To overcome these limitations we built upon existing work and optimised and comprehensively validated, through comparison with epifluorescence microscopy (EFM), a rapid and precise flow cytometric protocol to enumerate total bacterial numbers in activated sludge. Insights into potential biases were evaluated using appropriate statistical analyses on this comparison, which spanned four orders of magnitude, as well as comparing volatile suspended solid (VSS) concentrations. The results suggest flow cytometry (FCM) is a rapid, reproducible and economical technique for quantifying total bacterial numbers and biomass concentrations in activated sludge, despite within order of magnitude discrepancies with EFM counts, which had inherent and evidently greater errors and biases than FCM. The use of FCM for routine monitoring over both EFM and VSS should help further understanding of the microbial ecology in, and the operation of, engineered systems.}, }
@article {pmid30923872, year = {2019}, author = {Wu, RN and Meng, H and Wang, YF and Gu, JD}, title = {Functional dominance and community compositions of ammonia-oxidizing archaea in extremely acidic soils of natural forests.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {10}, pages = {4229-4240}, doi = {10.1007/s00253-019-09721-2}, pmid = {30923872}, issn = {1432-0614}, support = {31470562//National Natural Science Foundation of China/ ; }, mesh = {Ammonia/*metabolism ; Archaea/*classification/enzymology/genetics/*metabolism ; *Forests ; Hydrogen-Ion Concentration ; *Microbiota ; Oxidation-Reduction ; Oxidoreductases/analysis/genetics ; RNA, Messenger/analysis/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Extremely acidic soils of natural forests in Nanling National Nature Reserve have been previously investigated and revisited in two successive years to reveal the active ammonia oxidizers. Ammonia-oxidizing archaea (AOA) rather than ammonia-oxidizing bacteria (AOB) were found more functionally important in the extremely acidic soils of the natural forests in Nanling National Nature Reserve. The relative abundances of Nitrosotalea, Nitrososphaera sister group, and Nitrososphaera lineages recovered by ammonia monooxygenase subunit A (amoA) transcripts were reassessed and compared to AOA communities formerly detected by genomic DNA. Nitrosotalea, previously found the most abundant AOA, were the second-most-active lineage after Nitrososphaera sister group. Our field study results, therefore, propose the acidophilic AOA, Nitrosotalea, can better reside in extremely acidic soils while they may not contribute to nitrification proportionately according to their abundances or they are less functionally active. In contrast, the functional importance of Nitrososphaera sister group may be previously underestimated and the functional dominance further extends their ecological distribution as little has been reported. Nitrososphaera gargensis-like AOA, the third abundant lineage, were more active in summer. The analyses of AOA community composition and its correlation with environmental parameters support the previous observations of the potential impact of organic matter on AOA composition. Al[3+], however, did not show a strong adverse correlation with the abundances of functional AOA unlike in the DNA-based study. The new data further emphasize the functional dominance of AOA in extremely acidic soils, and unveil the relative contributions of AOA lineages to nitrification and their community transitions under the environmental influences.}, }
@article {pmid30923814, year = {2019}, author = {Tiedje, JM}, title = {Editorial: Environmental aspects of antibiotic resistance.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {4}, pages = {}, doi = {10.1093/femsec/fiz019}, pmid = {30923814}, issn = {1574-6941}, }
@article {pmid30919752, year = {2020}, author = {Cabezas, A and Bovio, P and Etchebehere, C}, title = {Commercial formulation amendment transiently affects the microbial composition but not the biogas production of a full scale methanogenic UASB reactor.}, journal = {Environmental technology}, volume = {41}, number = {24}, pages = {3119-3133}, doi = {10.1080/09593330.2019.1600042}, pmid = {30919752}, issn = {1479-487X}, mesh = {Anaerobiosis ; Biofuels ; Bioreactors ; *Euryarchaeota ; Methane ; RNA, Ribosomal, 16S ; *Sewage ; }, abstract = {The treatment of dairy wastewater in methanogenic reactors cause several problems due to their high lipid content. One strategy to overcome these problems is the use of commercial formulations. Here we studied the effect of adding a commercial formulation, designed to improve fat degradation, on both the microbial community composition and reactor performance. Samples from two full-scale Up-flow Anaerobic Sludge Blanket (UASB) reactors in parallel arrangement were analysed. The commercial product was added to one of the reactors while the other was used as control. The amendment increased significantly the fat removal but an accumulation of volatile fatty acids was detected. Nevertheless, no significant differences were observed in the total Chemical Oxygen Demand (COD) removal and biogas production between reactors. A significant change in the bacterial community was not detected by 16S rRNA gene Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis probably due to the limitation of the technique. A strong change in the composition of the phylum Firmicutes was detected with 16S rRNA gene amplicon sequencing; however, it didn't persist during the whole operation period. The relative abundance of minor Operational Taxonomic Units (OTUs) with sequences related to syntrophic bacteria increased with the amendment. Although a better hydrolytic capacity was obtained when adding the commercial product, the overall process did not improve and no increase in biogas production was detected. Alternative strategies could be applied to avoid the accumulation of intermediary products and improve biogas production as intermittent addition of the commercial product or batch operation of reactors.}, }
@article {pmid30918994, year = {2019}, author = {Klima, CL and Holman, DB and Ralston, BJ and Stanford, K and Zaheer, R and Alexander, TW and McAllister, TA}, title = {Lower Respiratory Tract Microbiome and Resistome of Bovine Respiratory Disease Mortalities.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {446-456}, pmid = {30918994}, issn = {1432-184X}, support = {2015R025R//Alberta Livestock and Meat Agency/ ; 001//Growing Forward II/ ; 001//Genomics Research Initiative/ ; }, mesh = {Alberta ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics/*isolation &amp; purification ; Bacterial Infections/microbiology/mortality/*veterinary ; Cattle ; Cattle Diseases/*microbiology/mortality ; *Drug Resistance, Bacterial ; *Microbiota ; Respiratory System/*microbiology ; Respiratory Tract Diseases/microbiology/mortality/*veterinary ; }, abstract = {Bovine respiratory disease (BRD) continues to be a serious health problem in beef cattle production. A multifactorial condition, BRD encompasses several types of pneumonia that are associated with multiple viral and bacterial agents. Comprehensive identification of microbes associated with BRD fatalities could enhance our understanding of the range of pathogens that contribute to the disease and identify new therapeutic targets. This study used metagenomic analysis to describe the lower respiratory tract microbiome and resistome of 15 feedlot cattle BRD and 3 non-BRD mortalities along with any affiliated integrative and conjugative elements (ICEs). Known bacterial pathogens associated with BRD, including Histophilus somni, Mannheimia haemolytica, and Mycoplasma bovis, were relatively abundant (> 5%) in most, but not all samples. Other relatively abundant genera (> 1%) included Acinetobacter, Bacillus, Bacteroides, Clostridium, Enterococcus, and Pseudomonas. Antimicrobial resistance genes (ARGs) comprised up to 0.5% of sequences and many of these genes were associated with ICEs previously described within the Pasteurellaceae family. A total of 20 putative ICEs were detected among 16 samples. These results document the wide diversity of microorganisms in the lower respiratory tract of cattle that have succumbed to BRD. The data also strongly suggest that antimicrobial-resistant Pasteurellaceae strains are prevalent in BRD cases in Alberta and that the resistance observed is associated with ICEs. The presence of ICEs harboring a wide array of ARGs holds significant consequence for the effectiveness of drug therapies for the control of BRD in beef cattle.}, }
@article {pmid30915518, year = {2019}, author = {Kolasa, M and Ścibior, R and Mazur, MA and Kubisz, D and Dudek, K and Kajtoch, &#x141;}, title = {How Hosts Taxonomy, Trophy, and Endosymbionts Shape Microbiome Diversity in Beetles.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {995-1013}, pmid = {30915518}, issn = {1432-184X}, support = {DEC-2013/11/D/NZ8/00583//National Science Centre, Poland/ ; small grants for young researchers//Polish Ministry of Science and Higher Education/ ; }, mesh = {Animals ; Bacteria/*classification ; Bacterial Physiological Phenomena ; Coleoptera/classification/*microbiology/*physiology ; Feeding Behavior ; Microbiota/*physiology ; Phylogeny ; *Symbiosis ; }, abstract = {Bacterial communities play a crucial role in the biology, ecology, and evolution of multicellular organisms. In this research, the microbiome of 24 selected beetle species representing five families (Carabidae, Staphylinidae, Curculionidae, Chrysomelidae, Scarabaeidae) and three trophic guilds (carnivorous, herbivorous, detrivorous) was examined using 16S rDNA sequencing on the Illumina platform. The aim of the study was to compare diversity within and among species on various levels of organization, including evaluation of the impact of endosymbiotic bacteria. Collected data showed that beetles possess various bacterial communities and that microbiota of individuals of particular species hosts are intermixed. The most diverse microbiota were found in Carabidae and Scarabaeidae; the least diverse, in Staphylinidae. On higher organization levels, the diversity of bacteria was more dissimilar between families, while the most distinct with respect to their microbiomes were trophic guilds. Moreover, eight taxa of endosymbiotic bacteria were detected including common genera such as Wolbachia, Rickettsia, and Spiroplasma, as well as the rarely detected Cardinium, Arsenophonus, Buchnera, Sulcia, Regiella, and Serratia. There were no correlations among the abundance of the most common Wolbachia and Rickettsia; a finding that does not support the hypothesis that these bacteria occur interchangeably. The abundance of endosymbionts only weakly and negatively correlates with diversity of the whole microbiome in beetles. Overall, microbiome diversity was found to be more dependent on host phylogeny than on the abundance of endosymbionts. This is the first study in which bacteria diversity is compared between numerous species of beetles in a standardized manner.}, }
@article {pmid30915517, year = {2019}, author = {Neupane, S and Modry, D and Pafčo, B and Zurek, L}, title = {Correction to: Bacterial Community of the Digestive Tract of the European Medicinal Leech (Hirudo verbana) from the Danube River.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {1091}, doi = {10.1007/s00248-019-01363-1}, pmid = {30915517}, issn = {1432-184X}, abstract = {The original published version of this article had mistakes in figure legends. Correct figure legends are presented below.}, }
@article {pmid30915050, year = {2019}, author = {Wang, W and Luo, X and Chen, Y and Ye, X and Wang, H and Cao, Z and Ran, W and Cui, Z}, title = {Succession of Composition and Function of Soil Bacterial Communities During Key Rice Growth Stages.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {421}, pmid = {30915050}, issn = {1664-302X}, abstract = {Elucidating the succession of soil microbial communities and microbial functions at key plant growth stages is a major goal of microbial ecology research. In this study, we investigated the succession of soil bacteria during four fertilizer treatments (control, NPK, NPK + pig manure, and NPK + straw) and at three crucial rice growth stages (tillering, heading, and ripening) in paddy soil from a rice-wheat cropping system over a 10-year period. The results showed that the bacterial community and function composition of the control treatment was significantly different from that of the other treatments with NPK fertilizers, and S1 from others stages (ANOSIM, p < 0.05). The application of pig manure could reduce the effects of applying NPK fertilizers on bacterial communities in heading and ripening stages, but the effects of straw returning is not obvious. Variance partitioning analyses (VPA) suggested that pH, OM, and AK appeared to be key factors responsible for the microbial community changes observed in all the treatments or stages. The correlation results showed the bacterial families different between S1 and other stages such as Micromonosporaceae, Nocardioidaceae, Gaiellaceae, and Anaerolineaceae etc., were correlated with bacterial KEGG metabolic pathways. In addition, the topological of the soil bacterial community network with more nodes, links and higher Maximal degree at the heading stage and maintained relatively similar topological structures at the heading and ripening stages. However, the topological of the functional networks at the ripening stage were a small yet complicated co-occurring network with 209 nodes, 789 links, higher Average connectivity (avgK), and Maximal degree. These results suggest an obvious succession of soil bacteria and bacterial function at the key rice growth stages, but the topological of functional network structure of bacteria changes a little in the early and middle stages of rice, while its changes significantly in the ripening stage of rice growth.}, }
@article {pmid30914267, year = {2019}, author = {Zhang, X and Fan, L and Wu, J and Xu, H and Leung, WY and Fu, K and Wu, J and Liu, K and Man, K and Yang, X and Han, J and Ren, J and Yu, J}, title = {Macrophage p38α promotes nutritional steatohepatitis through M1 polarization.}, journal = {Journal of hepatology}, volume = {71}, number = {1}, pages = {163-174}, doi = {10.1016/j.jhep.2019.03.014}, pmid = {30914267}, issn = {1600-0641}, mesh = {Animals ; Cell Polarity ; Chemokine CXCL10/*metabolism ; Diet, High-Fat ; Disease Models, Animal ; Disease Progression ; Drug Discovery ; Hepatocytes/*metabolism ; Humans ; Interleukin-6/*metabolism ; Macrophage Activation ; Macrophages/*metabolism ; Mice ; Mice, Knockout ; *Non-alcoholic Fatty Liver Disease/immunology/metabolism/pathology ; Tumor Necrosis Factor-alpha/*metabolism ; *p38 Mitogen-Activated Protein Kinases/antagonists &amp; inhibitors/metabolism ; }, abstract = {BACKGROUND &amp; AIMS: p38 mitogen-activated protein kinases are important inflammatory factors. p38α alteration has been implicated in both human and mouse inflammatory disease models. Therefore, we aimed to characterize the cell type-specific role of p38α in non-alcoholic steatohepatitis (NASH).<br><br>METHODS: Human liver tissues were obtained from 27 patients with non-alcoholic fatty liver disease (NAFLD) and 20 control individuals. NASH was established and compared between hepatocyte-specific p38&#x3b1; knockout (p38&#x3b1;[&#x394;Hep]), macrophage-specific p38&#x3b1; knockout (p38&#x3b1;[&#x394;M&#x3a6;]) and wild-type (p38&#x3b1;[fl/fl]) mice fed with high-fat diet (HFD), high-fat/high-cholesterol diet (HFHC), or methionine-and choline-deficient diet (MCD). p38 inhibitors were administered to HFHC-fed wild-type mice for disease treatment.<br><br>RESULTS: p38&#x3b1; was significantly upregulated in the liver tissues of patients with NAFLD. Compared to p38&#x3b1;[fl/fl] littermates, p38&#x3b1;[&#x394;Hep] mice developed significant nutritional steatohepatitis induced by HFD, HFHC or MCD. Meanwhile, p38&#x3b1;[&#x394;M&#x3a6;] mice exhibited less severe steatohepatitis and insulin resistance than p38&#x3b1;[fl/fl] mice in response to a HFHC or MCD. The effect of macrophage p38&#x3b1; in promoting steatohepatitis was mediated by the induction of pro-inflammatory factors (CXCL2, IL-1&#x3b2;, CXCL10 and IL-6) secreted by M1 macrophages and associated signaling pathways. p38&#x3b1;[&#x394;M&#x3a6;] mice exhibited M2 anti-inflammatory polarization as demonstrated by increased CD45[+]F4/80[+]CD11b[+]CD206[+] M2 macrophages and enhanced arginase activity in liver tissues. Primary hepatocytes from p38&#x3b1;[&#x394;M&#x3a6;] mice showed decreased steatosis and inflammatory damage. In a co-culture system, p38&#x3b1; deleted macrophages attenuated steatohepatitic changes in hepatocytes through decreased secretion of pro-inflammatory cytokines (TNF-&#x3b1;, CXCL10 and IL-6), which mediate M1 macrophage polarization in p38&#x3b1;[&#x394;M&#x3a6;] mice. Restoration of TNF-&#x3b1;, CXCL10 or IL-6 induced lipid accumulation and inflammatory responses in p38&#x3b1;[fl/fl] hepatocytes co-cultured with p38&#x3b1;[&#x394;M&#x3a6;] macrophages. Moreover, pharmacological p38 inhibitors suppressed HFHC-induced steatohepatitis.<br><br>CONCLUSIONS: Macrophage p38&#x3b1; promotes the progression of steatohepatitis by inducing pro-inflammatory cytokine secretion and M1 polarization. p38 inhibition protects against steatohepatitis. LAY SUMMARY: p38 mitogen-activated protein kinases are important inflammatory factors. In the present study, we demonstrated that p38&#x3b1; is upregulated in liver tissues of patients with non-alcoholic fatty liver diseases. Genetic deletion of p38&#x3b1; in macrophages led to ameliorated nutritional steatohepatitis in mice through decreased pro-inflammatory cytokine secretion and increased M2 macrophage polarization.}, }
@article {pmid30912268, year = {2019}, author = {Timmis, K and Cavicchioli, R and Garcia, JL and Nogales, B and Chavarría, M and Stein, L and McGenity, TJ and Webster, N and Singh, BK and Handelsman, J and de Lorenzo, V and Pruzzo, C and Timmis, J and Martín, JLR and Verstraete, W and Jetten, M and Danchin, A and Huang, W and Gilbert, J and Lal, R and Santos, H and Lee, SY and Sessitsch, A and Bonfante, P and Gram, L and Lin, RTP and Ron, E and Karahan, ZC and van der Meer, JR and Artunkal, S and Jahn, D and Harper, L}, title = {The urgent need for microbiology literacy in society.}, journal = {Environmental microbiology}, volume = {21}, number = {5}, pages = {1513-1528}, doi = {10.1111/1462-2920.14611}, pmid = {30912268}, issn = {1462-2920}, }
@article {pmid30911770, year = {2019}, author = {Pan, Y and Wu, Y and Li, X and Zeng, J and Lin, X}, title = {Continuing Impacts of Selective Inhibition on Bacterial and Fungal Communities in an Agricultural Soil.}, journal = {Microbial ecology}, volume = {78}, number = {4}, pages = {927-935}, pmid = {30911770}, issn = {1432-184X}, support = {41671266//National Natural Science Foundation of China/ ; }, mesh = {Agriculture ; Anti-Bacterial Agents/*adverse effects ; Bacteria/*drug effects ; Captan/adverse effects ; China ; Cycloheximide/adverse effects ; Fungi/*drug effects ; Fungicides, Industrial/*adverse effects ; Microbiota/*drug effects ; Mycobiome/drug effects ; Propylene Glycols/adverse effects ; *Soil Microbiology ; Streptomycin/adverse effects ; }, abstract = {Selective inhibition (SI) has been routinely used to differentiate the contributions of bacteria and fungi to soil ecological processes. SI experiments typically measured rapid responses within hours since the addition of inhibitor, but the long-term effects of selective biocides on microbial community composition and function were largely unknown. In this study, a microcosm experiment was performed with an agricultural soil to explore the effectiveness of two bactericides (bronopol, streptomycin) and two fungicides (cycloheximide, captan), which were applied at two different concentrations (2 and 10 mg g[-1]). The microcosms were incubated for 6 weeks. A radiolabeled substrate, [1,2,3,4,4a,9a-[14]C] anthracene, was spiked to all microcosms, and the derived CO2 was monitored during the incubation. The abundance and composition of bacteria and fungi were assessed by qPCR and Miseq sequencing of ribosomal rRNA genes. It was demonstrated that only 2 mg g[-1] bronopol and cycloheximide significantly changed the bacteria to fungi ratio without apparent non-target inhibition on the abundances; however, community shifts were observed in all treatments after 6 weeks incubation. The enrichment of specific taxa implicated a selection of resistant or adapted microbes by these biocides. Mineralization of anthracene was continuingly suppressed in all SI microcosms, which may result in biased estimate of bacterial and fungal contributions to pollutant degradation. These findings highlight the risks of long-term application of selective inhibition, and a preliminary assessment of biocide selection and concentration is highly recommended.}, }
@article {pmid30911147, year = {2019}, author = {Guo, X and Zhou, X and Hale, L and Yuan, M and Ning, D and Feng, J and Shi, Z and Li, Z and Feng, B and Gao, Q and Wu, L and Shi, W and Zhou, A and Fu, Y and Wu, L and He, Z and Van Nostrand, JD and Qiu, G and Liu, X and Luo, Y and Tiedje, JM and Yang, Y and Zhou, J}, title = {Climate warming accelerates temporal scaling of grassland soil microbial biodiversity.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {4}, pages = {612-619}, doi = {10.1038/s41559-019-0848-8}, pmid = {30911147}, issn = {2397-334X}, mesh = {Bacteria/genetics/isolation &amp; purification ; *Biodiversity ; *Climate Change ; DNA, Bacterial/analysis ; DNA, Fungal/analysis ; Fungi/genetics/isolation &amp; purification ; *Grassland ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Determining the temporal scaling of biodiversity, typically described as species-time relationships (STRs), in the face of global climate change is a central issue in ecology because it is fundamental to biodiversity preservation and ecosystem management. However, whether and how climate change affects microbial STRs remains unclear, mainly due to the scarcity of long-term experimental data. Here, we examine the STRs and phylogenetic-time relationships (PTRs) of soil bacteria and fungi in a long-term multifactorial global change experiment with warming (+3 °C), half precipitation (-50%), double precipitation (+100%) and clipping (annual plant biomass removal). Soil bacteria and fungi all exhibited strong STRs and PTRs across the 12 experimental conditions. Strikingly, warming accelerated the bacterial and fungal STR and PTR exponents (that is, the w values), yielding significantly (P < 0.001) higher temporal scaling rates. While the STRs and PTRs were significantly shifted by altered precipitation, clipping and their combinations, warming played the predominant role. In addition, comparison with the previous literature revealed that soil bacteria and fungi had considerably higher overall temporal scaling rates (w = 0.39-0.64) than those of plants and animals (w = 0.21-0.38). Our results on warming-enhanced temporal scaling of microbial biodiversity suggest that the strategies of soil biodiversity preservation and ecosystem management may need to be adjusted in a warmer world.}, }
@article {pmid30910952, year = {2019}, author = {Penn, JL and Weber, T and Chang, BX and Deutsch, C}, title = {Microbial ecosystem dynamics drive fluctuating nitrogen loss in marine anoxic zones.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {15}, pages = {7220-7225}, pmid = {30910952}, issn = {1091-6490}, mesh = {Ammonia/metabolism ; Aquatic Organisms/*physiology ; Bacteria, Anaerobic/*physiology ; *Climate ; Denitrification/physiology ; *Ecosystem ; Microbial Consortia/*physiology ; Nitrogen/*metabolism ; Oxygen/metabolism ; }, abstract = {The dynamics of nitrogen (N) loss in the ocean's oxygen-deficient zones (ODZs) are thought to be driven by climate impacts on ocean circulation and biological productivity. Here we analyze a data-constrained model of the microbial ecosystem in an ODZ and find that species interactions drive fluctuations in local- and regional-scale rates of N loss, even in the absence of climate variability. By consuming O2 to nanomolar levels, aerobic nitrifying microbes cede their competitive advantage for scarce forms of N to anaerobic denitrifying bacteria. Because anaerobes cannot sustain their own low-O2 niche, the physical O2 supply restores competitive advantage to aerobic populations, resetting the cycle. The resulting ecosystem oscillations induce a unique geochemical signature within the ODZ-short-lived spikes of ammonium that are found in measured profiles. The microbial ecosystem dynamics also give rise to variable ratios of anammox to heterotrophic denitrification, providing a mechanism for the unexplained variability of these pathways observed in the ocean.}, }
@article {pmid30904989, year = {2019}, author = {Yoo, K and Han, I and Ko, KS and Lee, TK and Yoo, H and Khan, MI and Tiedje, JM and Park, J}, title = {Bacillus-Dominant Airborne Bacterial Communities Identified During Asian Dust Events.}, journal = {Microbial ecology}, volume = {78}, number = {3}, pages = {677-687}, pmid = {30904989}, issn = {1432-184X}, support = {2018R1A6A1A08025348//National Research Foundation of Korea/ ; }, mesh = {*Air Microbiology ; Bacillus/classification/genetics/*isolation &amp; purification ; Dust/*analysis ; Ecosystem ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Multilocus Sequence Typing ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Asian dust (AD) events have received significant attention due to their adverse effects on ecosystems and human health. However, detailed information about airborne pathogens associated with AD events is limited. This study monitored airborne bacterial communities and identified AD-specific bacteria and the potential hazards associated with these bacteria during AD events. Over a 33-month period, 40 air samples were collected under normal atmospheric conditions (non-AD events; n = 34) and during AD events (n = 6). The airborne bacterial communities in the air samples collected during non-AD events (non-AD sample) and AD events (AD sample) were evaluated using both culture-dependent and culture-independent methods. The bacterial diversity increased significantly, along with the 16S rRNA gene copy number, in AD samples (p < 0.05) and was positively correlated with PM10 concentration. High throughput sequencing of the 16S rRNA gene revealed that the relative abundance of the phylum Firmicutes increased substantially in AD samples (44.3 ± 5.0%) compared with non-AD samples (27.8 ± 4.3%). Within the phylum Firmicutes, AD samples included a greater abundance of Bacillus species (almost 23.8%) than non-AD samples (almost 13.3%). Both culture-dependent and culture-independent methods detected common predominant species closely related to Bacillus cereus during AD events. Subsequent multilocus sequence typing (MLST) and enterotoxin gene assays confirmed the presence of virulence factors in B. cereus isolates from AD samples. Furthermore, the abundance of bceT, encoding enterotoxin in B. cereus, was significantly higher in AD samples (p < 0.05). The systematic characterization of airborne bacterial communities in AD samples in this study suggests that B. cereus pose risks to public health.}, }
@article {pmid30904709, year = {2019}, author = {Vandekerckhove, TGL and Kerckhof, FM and De Mulder, C and Vlaeminck, SE and Boon, N}, title = {Determining stoichiometry and kinetics of two thermophilic nitrifying communities as a crucial step in the development of thermophilic nitrogen removal.}, journal = {Water research}, volume = {156}, number = {}, pages = {34-45}, doi = {10.1016/j.watres.2019.03.008}, pmid = {30904709}, issn = {1879-2448}, mesh = {Ammonia ; *Denitrification ; Kinetics ; Nitrification ; Nitrites ; *Nitrogen ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Nitrification and denitrification, the key biological processes for thermophilic nitrogen removal, have separately been established in bioreactors at 50 °C. A well-characterized set of kinetic parameters is essential to integrate these processes while safeguarding the autotrophs performing nitrification. Knowledge on thermophilic nitrifying kinetics is restricted to isolated or highly enriched batch cultures, which do not represent bioreactor conditions. This study characterized the stoichiometry and kinetics of two thermophilic (50 °C) nitrifying communities. The most abundant ammonia oxidizing archaea (AOA) were related to the Nitrososphaera genus, clustering relatively far from known species Nitrososphaera gargensis (95.5% 16S rRNA gene sequence identity). The most abundant nitrite oxidizing bacteria (NOB) were related to Nitrospira calida (97% 16S rRNA gene sequence identity). The nitrification biomass yield was 0.20-0.24 g VSS g[-1] N, resulting mainly from a high AOA yield (0.16-0.20 g VSS g[-1] N), which was reflected in a high AOA abundance in the community (57-76%) compared to NOB (5-11%). Batch-wise determination of decay rates (AOA: 0.23-0.29 d[-1]; NOB: 0.32-0.43 d[-1]) rendered an overestimation compared to in situ estimations of overall decay rate (0.026-0.078 d[-1]). Possibly, the inactivation rate rather than the actual decay rate was determined in batch experiments. Maximum growth rates of AOA and NOB were 0.12-0.15 d[-1] and 0.13-0.33 d[-1] respectively. NOB were susceptible to nitrite, opening up opportunities for shortcut nitrogen removal. However, NOB had a similar growth rate and oxygen affinity (0.15-0.55 mg O2 L[-1]) as AOA and were resilient towards free ammonia (IC50 > 16 mg NH3-N L[-1]). This might complicate NOB outselection using common practices to establish shortcut nitrogen removal (SRT control; aeration control; free ammonia shocks). Overall, the obtained insights can assist in integrating thermophilic conversions and facilitate single-sludge nitrification/denitrification.}, }
@article {pmid30904186, year = {2020}, author = {Delzenne, NM and Olivares, M and Neyrinck, AM and Beaumont, M and Kjølbæk, L and Larsen, TM and Benítez-Páez, A and Romaní-Pérez, M and Garcia-Campayo, V and Bosscher, D and Sanz, Y and van der Kamp, JW}, title = {Nutritional interest of dietary fiber and prebiotics in obesity: Lessons from the MyNewGut consortium.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {39}, number = {2}, pages = {414-424}, doi = {10.1016/j.clnu.2019.03.002}, pmid = {30904186}, issn = {1532-1983}, mesh = {Dietary Fiber/*therapeutic use ; Gastrointestinal Microbiome/*drug effects ; Humans ; *Nutritional Status ; Obesity/*diet therapy/microbiology ; Prebiotics/*administration &amp; dosage ; }, abstract = {The aim of EU project MyNewGut is to contribute to future public health-related recommendations supported by new insight in gut microbiome and nutrition-host relationship. In this Opinion Paper, we first revisit the concept of dietary fiber, taking into account their interaction with the gut microbiota. This paper also summarizes the main effects of dietary fibers with prebiotic properties in intervention studies in humans, with a particular emphasis on the effects of arabinoxylans and arabinoxylo-oligosaccharides on metabolic alterations associated with obesity. Based on the existing state of the art and future development, we elaborate the steps required to propose dietary guidelines related to dietary fibers, taking into account their interaction with the gut microbiota.}, }
@article {pmid30903203, year = {2019}, author = {Hu, J and Liu, S and Yang, W and He, Z and Wang, J and Liu, H and Zheng, P and Xi, C and Ma, F and Hu, B}, title = {Ecological Success of the Nitrosopumilus and Nitrosospira Clusters in the Intertidal Zone.}, journal = {Microbial ecology}, volume = {78}, number = {3}, pages = {555-564}, pmid = {30903203}, issn = {1432-184X}, support = {No.41773074//National Natural Science Foundation of China/ ; No. 31828001//National Natural Science Foundation of China/ ; No.41641031//National Natural Science Foundation of China/ ; No. QAK201714//Open Project of State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology/ ; }, mesh = {Ammonia/metabolism ; Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Betaproteobacteria/classification/genetics/*isolation &amp; purification/metabolism ; China ; Ecosystem ; Geologic Sediments/*microbiology ; Islands ; Nitrification ; Oxidation-Reduction ; Phylogeny ; }, abstract = {The intertidal zone is an important buffer and a nitrogen sink between land and sea. Ammonia oxidation is the rate-limiting step of nitrification, conducted by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, it remains a debatable issue regarding dominant ammonia oxidizers in this region, and environmental factors driving their spatiotemporal niche differentiation have yet to be identified. In this study, intertidal and subtidal zones of Zhoushan Islands were selected for seasonal sampling. Ammonia-oxidizing activity, quantitative PCR, and 454 high-throughput sequencing were performed to study the nitrification potential, abundance, and community structure of ammonia-oxidizing archaea and bacteria. AOA and AOB amoA abundance (10[7]-10[8]amoA gene copies/g dry weight sediment) varied spatiotemporally independently of environmental factors. AOA surpassed AOB in most samples, driven by sediment temperature, moisture, and total nitrogen. The diversity of both AOA and AOB differed spatiotemporally. The Nitrosopumilus and Nitrosospira clusters accounted for an absolutely dominant percentage of AOA (> 99%) and AOB (> 99%) respectively, indicating a negligible contribution of other clusters to ammonia oxidation. However, there was no significant correlation between nitrification potential and the abundance of AOA or AOB. Overall, the present study showed that AOA dominated over AOB spatiotemporally in the intertidal zone of Zhoushan Islands due to fluctuations in environmental factors, and the Nitrosopumilus and Nitrosospira clusters ecologically succeeded in the intertidal zone of Zhoushan Islands.}, }
@article {pmid30903202, year = {2019}, author = {Borg Dahl, M and Brejnrod, AD and Russel, J and Sørensen, SJ and Schnittler, M}, title = {Different Degrees of Niche Differentiation for Bacteria, Fungi, and Myxomycetes Within an Elevational Transect in the German Alps.}, journal = {Microbial ecology}, volume = {78}, number = {3}, pages = {764-780}, pmid = {30903202}, issn = {1432-184X}, support = {RTG2010//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; DNA, Protozoan/genetics ; Fungi/classification/genetics/*isolation &amp; purification ; Germany ; Myxomycetes/genetics/*isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Soil/*parasitology ; Soil Microbiology ; }, abstract = {We used direct DNA amplification from soil extracts to analyze microbial communities from an elevational transect in the German Alps by parallel metabarcoding of bacteria (16S rRNA), fungi (ITS2), and myxomycetes (18S rRNA). For the three microbial groups, 5710, 6133, and 261 operational taxonomic units (OTU) were found. For the latter group, we can relate OTUs to barcodes from fruit bodies sampled over a 4-year period. The alpha diversity of myxomycetes was positively correlated with that of bacteria. Vegetation type was found to be the main explanatory parameter for the community composition of all three groups and a substantial species turnover with elevation was observed. Bacteria and fungi display similar community responses, driven by symbiont species and plant substrate quality. Myxamoebae show a more patchy distribution, though still clearly stratified between taxa, which seems to be a response to both structural properties of the habitat and interaction with specific bacterial and fungal taxa. Finally, we report a high number of myxomycete OTUs not represented in a reference database from fructifications, which might represent novel species.}, }
@article {pmid30901846, year = {2019}, author = {Horniblow, RD and Mistry, P and Quraishi, MN and Beggs, AD and Van de Wiele, T and Iqbal, TH and Tselepis, C}, title = {The Safety and Tolerability of a Potential Alginate-Based Iron Chelator; Results of A Healthy Participant Study.}, journal = {Nutrients}, volume = {11}, number = {3}, pages = {}, pmid = {30901846}, issn = {2072-6643}, support = {EME/13/179/01/DH_/Department of Health/United Kingdom ; MR/M009157/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Alginates/*pharmacology ; Bacteria/metabolism ; Colon/metabolism/microbiology ; *Dietary Supplements ; Dysbiosis/metabolism ; Feasibility Studies ; Female ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/metabolism/microbiology ; Healthy Volunteers ; Humans ; Inflammatory Bowel Diseases/microbiology ; Iron/metabolism ; Iron Chelating Agents/*pharmacology ; Male ; Middle Aged ; *Prebiotics ; }, abstract = {Evidence supporting the ferro-toxic nature of iron in the progression of inflammatory bowel disease (IBD) is becoming well established. A microbial dysbiosis is observed in IBD patients, and intra-luminal colonic-iron is able to support a more pathogenic community of bacteria; whether this is attributed to the development of IBD and how iron could be mediating these microbial changes is still unknown. Dietary fibres are commonly used in pre-biotic supplements to beneficially affect the host by improving the viability of bacterial communities within the colon. Alginates are a class of biopolymers considered as prebiotics due to their fibre-like composition and are able to bind metal cations, in particular, iron. Considering that iron excess is able to negatively alter the microbiome, the use of alginate as a food supplement could be useful in colonic-iron chelation. As such, this first-in-man study aimed to assess whether the use of alginate as a dietary iron chelator was both safe and well tolerated. In addition, the impact of alginate on the microbiome and iron levels was assessed by using an intestinal model SHIME (Simulation of the Human Intestinal Microbial Ecosystem). Alginate was supplemented into the diets (3 g/day) of healthy volunteers (n = 17) for 28 days. Results from this study suggest that daily ingestion of 3 g alginate was well tolerated with very minor side effects. There were no detrimental changes in a variety of haematological parameters or the intestinal microbiome. The bacterial communities within the SHIME model were also not influenced by iron and or alginate; it is possible that alginate may be susceptible to bacterial or enzymatic degradation within the gastro-intestinal tract.}, }
@article {pmid30900038, year = {2019}, author = {Procópio, L and Pádula, M and van Elsas, JD and Seldin, L}, title = {Oxidative damage induced by H2O2 reveals SOS adaptive transcriptional response of Dietzia cinnamea strain P4.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {35}, number = {4}, pages = {53}, pmid = {30900038}, issn = {1573-0972}, mesh = {Actinomycetales/*drug effects/enzymology/genetics/*metabolism ; Bacterial Proteins/genetics ; Catalase/classification/genetics ; DNA Damage/drug effects ; DNA Helicases/genetics ; Gene Expression Regulation, Bacterial/drug effects ; Genes, Bacterial ; Glutathione/genetics ; Hydrogen Peroxide/*adverse effects ; Kinetics ; *Oxidative Stress ; Peroxidases/genetics ; Peroxiredoxins/genetics ; Phylogeny ; RNA, Messenger/metabolism ; Rec A Recombinases/genetics ; SOS Response, Genetics/genetics/*physiology ; Sequence Analysis ; Serine Endopeptidases/genetics ; Superoxide Dismutase/genetics ; Thioredoxins/genetics ; Time Factors ; Up-Regulation/drug effects ; }, abstract = {The oxidative stress response of the highly resistant actinomycete Dietzia cinnamea P4 after treatment with hydrogen peroxide (H2O2) was assessed in order to depict the possible mechanisms underlying its intrinsic high resistance to DNA damaging agents. We used transcriptional profiling to monitor the magnitude and kinetics of changes in the mRNA levels after exposure to different concentrations of H2O2 at 10 min and 1 h following the addition of the stressor. Catalase and superoxide dismutase genes were induced in different ways, according to the condition applied. Moreover, alkyl hydroperoxide reductase ahpCF, thiol peroxidase, thioredoxin and glutathione genes were upregulated in the presence of H2O2. Expression of peroxidase genes was not detected during the experiment. Overall results point to an actinomycete strain endowed with a set of enzymatic defenses against oxidative stress and with the main genes belonging to a functional SOS system (lexA, recA, uvrD), including suppression of lexA repressor, concomitantly to recA and uvrD gene upregulation upon H2O2 challenge.}, }
@article {pmid30899980, year = {2019}, author = {Jabiol, J and Lecerf, A and Lamothe, S and Gessner, MO and Chauvet, E}, title = {Litter Quality Modulates Effects of Dissolved Nitrogen on Leaf Decomposition by Stream Microbial Communities.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {959-966}, pmid = {30899980}, issn = {1432-184X}, support = {ANR-14-CE01-0009-01//Agence Nationale de la Recherche/ ; }, mesh = {Fungi/*physiology ; *Microbiota ; Nitrogen/*metabolism ; Plant Leaves/*microbiology ; Rivers/*microbiology ; }, abstract = {Rates of leaf litter decomposition in streams are strongly influenced both by inorganic nutrients dissolved in stream water and by litter traits such as lignin, nitrogen (N) and phosphorus (P) concentrations. As a result, decomposition rates of different leaf species can show contrasting responses to stream nutrient enrichment resulting from human activities. It is unclear, however, whether the root cause of such discrepancies in field observations is the interspecific variation in either litter nutrient or litter lignin concentrations. To address this question, we conducted a controlled laboratory experiment with a known fungal community to determine decomposition rates of 38 leaf species exhibiting contrasting litter traits (N, P and lignin concentrations), which were exposed to 8 levels of dissolved N concentrations representative of field conditions across European streams (0.07 to 8.96 mg N L[-1]). The effect of N enrichment on decomposition rate was modelled using Monod kinetics to quantify N effects across litter species. Lignin concentration was the most important litter trait determining decomposition rates and their response to N enrichment. In particular, increasing dissolved N supply from 0.1 to 3.0 mg N L[-1] accelerated the decomposition of lignin-poor litter (e.g. < 10% of lignin, 2.9× increase ± 1.4 SD, n = 14) more strongly than that of litter rich in lignin (e.g. > 15% of lignin, 1.4× increase ± 0.2 SD, n = 9). Litter nutrient concentrations were less important, with a slight positive effect of P on decomposition rates and no effect of litter N. These results indicate that shifts in riparian vegetation towards species characterized by high litter lignin concentrations could alleviate the stimulation of C turnover by stream nutrient enrichment.}, }
@article {pmid30895363, year = {2019}, author = {Hýsek, J and Vavera, R and Růžek, P}, title = {Cultivation Intensity in Combination with Other Ecological Factors as Limiting Ones for the Abundance of Phytopathogenic Fungi on Wheat.}, journal = {Microbial ecology}, volume = {78}, number = {3}, pages = {565-574}, pmid = {30895363}, issn = {1432-184X}, support = {MZe-RO0418//Ministry of Agriculture/ ; }, mesh = {Ascomycota/classification/genetics/growth &amp; development/*isolation &amp; purification ; Basidiomycota/classification/genetics/growth &amp; development/*isolation &amp; purification ; Ecosystem ; Plant Diseases/*microbiology ; Temperature ; Triticum/*microbiology ; }, abstract = {In field and laboratory experiments during 2014-2017, we investigated the influence of lower and higher cultivation intensity of wheat and ecological factors (weather-temperature and rainfalls, year) on the occurrence of phytopathogenic fungi on the leaves of winter wheat. The prevailing fungi in those years were Mycosphaerella graminicola (Fuckel) J. Schrott and Pyrenophora tritici-repentis (Died.) Drechsler. Using cluster analysis, we statistically evaluated interrelationships of known factors on the abundance of the fungi on leaf surfaces. Our results showed strongest correlation with Mycosphaerella graminicola and Pyrenophora tritici-repentis abundance to be with lower cultivation intensity and year done by the temperature and the rainfalls. The two pathogens-Puccinia tritici Oerst and Hymenula cerealis Ellis &amp; Everh. occurred only very sparsely in some years and had little positive or negative correlation with named factors. The semi-early and semi-late winter wheat varieties Matchball, Annie, Fakir, and Tobak were used for our experiments. Higher cultivation intensity had protective effect against leaf phytopathogenic fungi.}, }
@article {pmid30894691, year = {2019}, author = {Fernando, EY and McIlroy, SJ and Nierychlo, M and Herbst, FA and Petriglieri, F and Schmid, MC and Wagner, M and Nielsen, JL and Nielsen, PH}, title = {Resolving the individual contribution of key microbial populations to enhanced biological phosphorus removal with Raman-FISH.}, journal = {The ISME journal}, volume = {13}, number = {8}, pages = {1933-1946}, pmid = {30894691}, issn = {1751-7370}, mesh = {Actinobacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Betaproteobacteria/classification/genetics/isolation &amp; purification/metabolism ; Biodegradation, Environmental ; Bioreactors/microbiology ; In Situ Hybridization, Fluorescence/*methods ; Phosphorus/*metabolism ; Sewage/microbiology ; Spectrum Analysis, Raman/*methods ; }, abstract = {Enhanced biological phosphorus removal (EBPR) is a globally important biotechnological process and relies on the massive accumulation of phosphate within special microorganisms. Candidatus Accumulibacter conform to the classical physiology model for polyphosphate accumulating organisms and are widely believed to be the most important player for the process in full-scale EBPR systems. However, it was impossible till now to quantify the contribution of specific microbial clades to EBPR. In this study, we have developed a new tool to directly link the identity of microbial cells to the absolute quantification of intracellular poly-P and other polymers under in situ conditions, and applied it to eight full-scale EBPR plants. Besides Ca. Accumulibacter, members of the genus Tetrasphaera were found to be important microbes for P accumulation, and in six plants they were the most important. As these Tetrasphaera cells did not exhibit the classical phenotype of poly-P accumulating microbes, our entire understanding of the microbiology of the EBPR process has to be revised. Furthermore, our new single-cell approach can now also be applied to quantify storage polymer dynamics in individual populations in situ in other ecosystems and might become a valuable tool for many environmental microbiologists.}, }
@article {pmid30894042, year = {2019}, author = {Bor, B and Bedree, JK and Shi, W and McLean, JS and He, X}, title = {Saccharibacteria (TM7) in the Human Oral Microbiome.}, journal = {Journal of dental research}, volume = {98}, number = {5}, pages = {500-509}, pmid = {30894042}, issn = {1544-0591}, support = {F32 DE025548/DE/NIDCR NIH HHS/United States ; K99 DE027719/DE/NIDCR NIH HHS/United States ; R01 DE020102/DE/NIDCR NIH HHS/United States ; R00 DE027719/DE/NIDCR NIH HHS/United States ; R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 DE026186/DE/NIDCR NIH HHS/United States ; T90 DE022734/DE/NIDCR NIH HHS/United States ; F31 DE026057/DE/NIDCR NIH HHS/United States ; }, mesh = {Animals ; Bacteria ; Bacterial Physiological Phenomena ; Humans ; *Microbiota ; Mouth ; RNA, Ribosomal, 16S ; }, abstract = {Bacteria from the Saccharibacteria phylum (formerly known as TM7) are ubiquitous members of the human oral microbiome and are part of the Candidate Phyla Radiation. Recent studies have revealed remarkable 16S rRNA diversity in environmental and mammalian host-associated members across this phylum, and their association with oral mucosal infectious diseases has been reported. However, due to their recalcitrance to conventional cultivation, TM7's physiology, lifestyle, and role in health and diseases remain elusive. The recent cultivation and characterization of Nanosynbacter lyticus type strain TM7x (HMT_952)-the first Saccharibacteria strain coisolated as an ultrasmall obligate parasite with its bacterial host from the human oral cavity-provide a rare glimpse into the novel symbiotic lifestyle of these enigmatic human-associated bacteria. TM7x is unique among all bacteria: it has an ultrasmall size and lives on the surface of its host bacterium. With a highly reduced genome, it lacks the ability to synthesize any of its own amino acids, vitamins, or cell wall precursors and must parasitize other oral bacteria. TM7x displays a highly dynamic interaction with its bacterial hosts, as reflected by the reciprocal morphologic and physiologic changes in both partners. Furthermore, depending on environmental conditions, TM7x can exhibit virulent killing of its host bacterium. Thus, Saccharibacteria potentially affect oral microbial ecology by modulating the oral microbiome structure hierarchy and functionality through affecting the bacterial host's physiology, inhibiting the host's growth dynamics, or affecting the relative abundance of the host via direct killing. At this time, several other uncharacterized members of this phylum have been detected in various human body sites at high prevalence. In the oral cavity alone, at least 6 distinct groups vary widely in relative abundance across anatomic sites. Here, we review the current knowledge on the diversity and unique biology of this recently uncovered group of ultrasmall bacteria.}, }
@article {pmid30891612, year = {2019}, author = {Cockerham, S and Lee, B and Orben, RA and Suryan, RM and Torres, LG and Warzybok, P and Bradley, R and Jahncke, J and Young, HS and Ouverney, C and Shaffer, SA}, title = {Microbial Ecology of the Western Gull (Larus occidentalis).}, journal = {Microbial ecology}, volume = {78}, number = {3}, pages = {665-676}, pmid = {30891612}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; California ; Charadriiformes/*microbiology ; Cloaca/microbiology ; DNA, Bacterial/genetics ; *Microbiota ; Oregon ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Avian species host diverse communities of microorganisms which have important roles in the life of birds, including increased metabolism, protection from disease, and immune system development. Along with high human populations and a diversity of human uses of coastal zones, anthropogenic food sources are becoming increasingly available to some species, including gulls. Anthropogenic associations increase the likelihood of encountering foreign or pathogenic bacteria. Diseases in birds caused by bacteria are a substantial source of avian mortality; therefore, it is essential to characterize the microbiome of seabirds. Here, we determined both core and environmentally derived microbial communities of breeding western gulls (Larus occidentalis) from six colonies in California and Oregon. Using DNA extracted from bacterial swabs of the bill, cloaca, and feet of gulls, 16S rRNA gene sequencing was performed targeting the V4 region. We identified a total of 8542 operational taxonomic units (OTUs) from 75 gulls. Sixty-eight OTUs were identified in gulls from all six colonies with the greatest representation from phyla's of Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. Overall, microbial richness based on Chao's Abundance-based Coverage Estimator (ACE) index was similar for all colonies (mean = 2347 OTUs) with the smallest coastal colonies having the highest richness (mean = 2626 OTUs) and the largest colonies, located farther off-shore, having the lowest (mean = 2068 OTUs). This survey represents the most in-depth assessment to date of microbes associated with western gulls, and the first study to identify both species-specific and environmentally derived bacteria across multiple populations.}, }
@article {pmid30886359, year = {2019}, author = {Lee, KS and Palatinszky, M and Pereira, FC and Nguyen, J and Fernandez, VI and Mueller, AJ and Menolascina, F and Daims, H and Berry, D and Wagner, M and Stocker, R}, title = {An automated Raman-based platform for the sorting of live cells by functional properties.}, journal = {Nature microbiology}, volume = {4}, number = {6}, pages = {1035-1048}, pmid = {30886359}, issn = {2058-5276}, mesh = {Animals ; Bacteria/genetics ; Colon ; Female ; Flow Cytometry ; Genomics ; Isotope Labeling/*methods ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Microfluidics/instrumentation/*methods ; Models, Biological ; Mucins/metabolism ; Seawater/microbiology ; Single-Cell Analysis/methods ; Soil Microbiology ; Spectrum Analysis, Raman/instrumentation/*methods ; }, abstract = {Stable-isotope probing is widely used to study the function of microbial taxa in their natural environment, but sorting of isotopically labelled microbial cells from complex samples for subsequent genomic analysis or cultivation is still in its early infancy. Here, we introduce an optofluidic platform for automated sorting of stable-isotope-probing-labelled microbial cells, combining microfluidics, optical tweezing and Raman microspectroscopy, which yields live cells suitable for subsequent single-cell genomics, mini-metagenomics or cultivation. We describe the design and optimization of this Raman-activated cell-sorting approach, illustrate its operation with four model bacteria (two intestinal, one soil and one marine) and demonstrate its high sorting accuracy (98.3 ± 1.7%), throughput (200-500 cells h[-1]; 3.3-8.3 cells min[-1]) and compatibility with cultivation. Application of this sorting approach for the metagenomic characterization of bacteria involved in mucin degradation in the mouse colon revealed a diverse consortium of bacteria, including several members of the underexplored family Muribaculaceae, highlighting both the complexity of this niche and the potential of Raman-activated cell sorting for identifying key players in targeted processes.}, }
@article {pmid30884680, year = {2019}, author = {Hamdouche, Y and Meile, JC and Lebrun, M and Guehi, T and Boulanger, R and Teyssier, C and Montet, D}, title = {Impact of turning, pod storage and fermentation time on microbial ecology and volatile composition of cocoa beans.}, journal = {Food research international (Ottawa, Ont.)}, volume = {119}, number = {}, pages = {477-491}, doi = {10.1016/j.foodres.2019.01.001}, pmid = {30884680}, issn = {1873-7145}, mesh = {Bacteria/genetics/isolation &amp; purification ; Cacao/*chemistry/*microbiology ; Chocolate/analysis ; *Fermentation ; Food Handling/methods ; Food Microbiology ; Food Storage/*methods ; Fungi/genetics/isolation &amp; purification ; Gas Chromatography-Mass Spectrometry ; *Microbiota/genetics ; Time Factors ; Volatile Organic Compounds/*isolation &amp; purification ; }, abstract = {Cocoa quality depends on several parameters, such as cocoa variety, environmental growth conditions, cultivation technique, and post-harvest treatments applied to coca beans. In this work, we studied the impact of cocoa post-harvest processing on both microbial communities structure and volatile composition. Cocoa beans samples were fermented in wooden boxes in Ivory Coast at different time intervals with turning and without turning, and derived from pods stored for two different duration times. Cocoa beans were analyzed using a molecular fingerprinting method (PCR-DGGE) in order to detect variations in microbial communities' structure; this global analysis was coupled to SPME-GC-MS for assessing cocoa volatile profiles. The results showed that the main parameter that influenced microbial communities structure was fermentation time, followed by turning, whereas, pods storage duration had a minor impact. Similar results were obtained for aromatic profile, except for pods storage duration that significantly affected volatile compound production. Global statistical analysis using Canonical Correspondence Analysis (CCA), showed the relationship between microbial communities and volatile composition. Furthermore, this study allowed the identification of discriminating microbial and chemical markers of cocoa post-harvest processing.}, }
@article {pmid30881924, year = {2019}, author = {Tribble, GD and Angelov, N and Weltman, R and Wang, BY and Eswaran, SV and Gay, IC and Parthasarathy, K and Dao, DV and Richardson, KN and Ismail, NM and Sharina, IG and Hyde, ER and Ajami, NJ and Petrosino, JF and Bryan, NS}, title = {Frequency of Tongue Cleaning Impacts the Human Tongue Microbiome Composition and Enterosalivary Circulation of Nitrate.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {39}, pmid = {30881924}, issn = {2235-2988}, mesh = {Anti-Bacterial Agents/*administration &amp; dosage ; Blood Pressure/drug effects ; Chlorhexidine/*administration &amp; dosage ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Healthy Volunteers ; Humans ; Microbiota/*drug effects ; Mouthwashes/administration &amp; dosage ; Nitrates/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tongue/*microbiology ; }, abstract = {The oral microbiome has the potential to provide an important symbiotic function in human blood pressure physiology by contributing to the generation of nitric oxide (NO), an essential cardiovascular signaling molecule. NO is produced by the human body via conversion of arginine to NO by endogenous nitric oxide synthase (eNOS) but eNOS activity varies by subject. Oral microbial communities are proposed to supplement host NO production by reducing dietary nitrate to nitrite via bacterial nitrate reductases. Unreduced dietary nitrate is delivered to the oral cavity in saliva, a physiological process termed the enterosalivary circulation of nitrate. Previous studies demonstrated that disruption of enterosalivary circulation via use of oral antiseptics resulted in increases in systolic blood pressure. These previous studies did not include detailed information on the oral health of enrolled subjects. Using 16S rRNA gene sequencing and analysis, we determined whether introduction of chlorhexidine antiseptic mouthwash for 1 week was associated with changes in tongue bacterial communities and resting systolic blood pressure in healthy normotensive individuals with documented oral hygiene behaviors and free of oral disease. Tongue cleaning frequency was a predictor of chlorhexidine-induced changes in systolic blood pressure and tongue microbiome composition. Twice-daily chlorhexidine usage was associated with a significant increase in systolic blood pressure after 1 week of use and recovery from use resulted in an enrichment in nitrate-reducing bacteria on the tongue. Individuals with relatively high levels of bacterial nitrite reductases had lower resting systolic blood pressure. These results further support the concept of a symbiotic oral microbiome contributing to human health via the enterosalivary nitrate-nitrite-NO pathway. These data suggest that management of the tongue microbiome by regular cleaning together with adequate dietary intake of nitrate provide an opportunity for the improvement of resting systolic blood pressure.}, }
@article {pmid30877120, year = {2019}, author = {Wang, T and Tian, Z and Tunlid, A and Persson, P}, title = {Influence of Ammonium on Formation of Mineral-Associated Organic Carbon by an Ectomycorrhizal Fungus.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {10}, pages = {}, pmid = {30877120}, issn = {1098-5336}, mesh = {Agaricales/*metabolism ; Ammonium Compounds/*metabolism ; Carbon/*metabolism ; Minerals/metabolism ; Mycorrhizae/*metabolism ; Nitrogen/*metabolism ; Soil/chemistry ; Soil Microbiology ; }, abstract = {The interactions between dissolved organic matter (DOM) and mineral particles are critical for the stabilization of soil organic matter (SOM) in terrestrial ecosystems. The processing of DOM by ectomycorrhizal fungi contributes to the formation of mineral-stabilized SOM by two contrasting pathways: the extracellular transformation of DOM (ex vivo pathway) and the secretion of mineral-surface-reactive metabolites (in vivo pathway). In this study, we examined how changes in nitrogen (N) availability affected the formation of mineral-associated carbon (C) from these two pathways. DOM was extracted from forest soils. The processing of this DOM by the ectomycorrhizal fungus Paxillus involutus was examined in laboratory-scale studies with different levels of ammonium. At low levels of ammonium (i.e., under N-limited conditions), the DOM components were slightly oxidized, and fungal C metabolites with iron-reducing activity were secreted. Ammonium amendments decreased the amount of C metabolites, and no additional oxidation of the organic matter was detected. In contrast, the hydrolytic activity and the secretion of N-containing compounds increased, particularly when high levels of ammonium were added. Under these conditions, C, but not N, limited fungal growth. Although the overall production of mineral-associated organic C was not affected by ammonium concentrations, the observed shifts in the activities of the ex vivo and in vivo pathways affected the composition of organic matter adsorbed onto the mineral particles. Such changes will affect the properties of organic matter-mineral associations and, thus, ultimately, the stabilization of SOM.IMPORTANCE Nitrogen (N) availability plays a critical role in the cycling and storage of soil organic matter (SOM). However, large uncertainties remain in predicting the net effect of N addition on soil organic carbon (C) storage due to the complex interactions between organic matter, microbial activity, and mineral particles that determine the formation of stable SOM. Here, we attempted to disentangle the effects of ammonium on these interactions in controlled microcosm experiments including the ectomycorrhizal fungus P.involutus and dissolved organic matter extracted from forest soils. Increased ammonium levels affected the fungal processing of the organic material as well as the secretion of extracellular metabolites. Although ammonium additions did not increase the net production of mineral-adsorbed C, changes in the decomposition and secretion pathways altered the composition of the adsorbed organic matter. These changes may influence the properties of the organic matter-mineral associations and, thus, the stabilization of SOM.}, }
@article {pmid30875864, year = {2019}, author = {Uritskiy, G and DiRuggiero, J}, title = {Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome.}, journal = {Genes}, volume = {10}, number = {3}, pages = {}, pmid = {30875864}, issn = {2073-4425}, support = {T32 GM007231/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics ; Base Composition ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; Sequence Analysis, RNA/methods ; Whole Genome Sequencing/*methods ; }, abstract = {In the past decades, the study of microbial life through shotgun metagenomic sequencing has rapidly expanded our understanding of environmental, synthetic, and clinical microbial communities. Here, we review how shotgun metagenomics has affected the field of halophilic microbial ecology, including functional potential reconstruction, virus[-]host interactions, pathway selection, strain dispersal, and novel genome discoveries. However, there still remain pitfalls and limitations from conventional metagenomic analysis being applied to halophilic microbial communities. Deconvolution of halophilic metagenomes has been difficult due to the high G + C content of these microbiomes and their high intraspecific diversity, which has made both metagenomic assembly and binning a challenge. Halophiles are also underrepresented in public genome databases, which in turn slows progress. With this in mind, this review proposes experimental and analytical strategies to overcome the challenges specific to the halophilic microbiome, from experimental designs to data acquisition and the computational analysis of metagenomic sequences. Finally, we speculate about the potential applications of other next-generation sequencing technologies in halophilic communities. RNA sequencing, long-read technologies, and chromosome conformation assays, not initially intended for microbiomes, are becoming available in the study of microbial communities. Together with recent analytical advancements, these new methods and technologies have the potential to rapidly advance the field of halophile research.}, }
@article {pmid30875367, year = {2019}, author = {Cougoul, A and Bailly, X and Vourc'h, G and Gasqui, P}, title = {Rarity of microbial species: In search of reliable associations.}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0200458}, pmid = {30875367}, issn = {1932-6203}, mesh = {Animals ; Computational Biology ; Computer Simulation ; Ecosystem ; Humans ; *Microbial Interactions ; *Microbiota ; Models, Biological ; }, abstract = {The role of microbial interactions in defining the properties of microbiota is a topic of key interest in microbial ecology. Microbiota contain hundreds to thousands of operational taxonomic units (OTUs), most of them rare. This feature of community structure can lead to methodological difficulties: simulations have shown that methods for detecting pairwise associations between OTUs, which presumably reflect interactions, yield problematic results. The performance of association detection tools is impaired when there is a high proportion of zeros in OTU tables. Our goal was to understand the impact of OTU rarity on the detection of associations. We explored the utility of common statistics for testing associations; the sensitivity of alternative association measures; and the performance of network inference tools. We found that a large proportion of pairwise associations, especially negative associations, cannot be reliably tested. This constraint could hamper the identification of candidate biological agents that could be used to control rare pathogens. Identifying testable associations could serve as an objective method for filtering datasets in lieu of current empirical approaches. This trimming strategy could significantly reduce the computational time needed to infer networks and network inference quality. Different possibilities for improving the analysis of associations within microbiota are discussed.}, }
@article {pmid30874727, year = {2019}, author = {Hädrich, A and Taillefert, M and Akob, DM and Cooper, RE and Litzba, U and Wagner, FE and Nietzsche, S and Ciobota, V and Rösch, P and Popp, J and Küsel, K}, title = {Microbial Fe(II) oxidation by Sideroxydans lithotrophicus ES-1 in the presence of Schlöppnerbrunnen fen-derived humic acids.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {4}, pages = {}, doi = {10.1093/femsec/fiz034}, pmid = {30874727}, issn = {1574-6941}, mesh = {Ferric Compounds/chemistry/metabolism ; Ferrous Compounds/*metabolism ; Gallionellaceae/growth &amp; development/*metabolism ; Humic Substances/*analysis ; Iron/chemistry/metabolism ; Minerals/chemistry/metabolism ; Oxidation-Reduction ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Controlled laboratory experiments were combined with field measurements to better understand the interactions between dissolved organic matter (DOM) and reduced iron in organic-rich peatlands. Addition of peat-derived humic acid extract (HA) to Sideroxydans lithotrophicus ES-1 liquid cultures led to higher cell numbers and up to 1.4 times higher Fe(II) oxidation rates compared to chemical controls. This effect was positively correlated with increasing HA concentrations. Similar Fe(III) (oxyhydr)oxide mineralogies were formed both abiotically and biotically irrespective of HA amendment, but minerals formed in the presence of ES-1 and HA were smaller. ES-1 growth with HA promoted aggregation of Fe(III) products in agarose-stabilized gradient tubes as shown by voltammetric profiling. In situ voltammetry in an acidic, iron-rich peatland revealed a gap between oxygen penetration and iron reduction that may reflect active Fe(II)-oxidizing microorganisms. The highest abundance of Fe(II) oxidizers Sideroxydans (4.9 × 107 gene copies gww-1) and Gallionella (1.5 × 107 gene copies gww-1) in the upper peat layer coincided with small-sized minerals resembling nanoparticulate ferrihydrite or goethite. Our results suggest that microbially mediated Fe(II) oxidation dominates in the presence of DOM leading to the formation of nano-sized biogenic Fe(III) (oxyhydr)oxides that might be readily bioavailable and likely important to iron and carbon cycling.}, }
@article {pmid30873129, year = {2019}, author = {Hanson, CA and Müller, AL and Loy, A and Dona, C and Appel, R and Jørgensen, BB and Hubert, CRJ}, title = {Historical Factors Associated With Past Environments Influence the Biogeography of Thermophilic Endospores in Arctic Marine Sediments.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {245}, pmid = {30873129}, issn = {1664-302X}, support = {P 20185/FWF_/Austrian Science Fund FWF/Austria ; P 25111/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Selection by the local, contemporary environment plays a prominent role in shaping the biogeography of microbes. However, the importance of historical factors in microbial biogeography is more debatable. Historical factors include past ecological and evolutionary circumstances that may have influenced present-day microbial diversity, such as dispersal and past environmental conditions. Diverse thermophilic sulfate-reducing Desulfotomaculum are present as dormant endospores in marine sediments worldwide where temperatures are too low to support their growth. Therefore, they are dispersed to here from elsewhere, presumably a hot, anoxic habitat. While dispersal through ocean currents must influence their distribution in cold marine sediments, it is not clear whether even earlier historical factors, related to the source habitat where these organisms were once active, also have an effect. We investigated whether these historical factors may have influenced the diversity and distribution of thermophilic endospores by comparing their diversity in 10 Arctic fjord surface sediments. Although community composition varied spatially, clear biogeographic patterns were only evident at a high level of taxonomic resolution (>97% sequence similarity of the 16S rRNA gene) achieved with oligotyping. In particular, the diversity and distribution of oligotypes differed for the two most prominent OTUs (defined using a standard 97% similarity cutoff). One OTU was dominated by a single ubiquitous oligotype, while the other OTU consisted of ten more spatially localized oligotypes that decreased in compositional similarity with geographic distance. These patterns are consistent with differences in historical factors that occurred when and where the taxa were once active, prior to sporulation. Further, the influence of history on biogeographic patterns was only revealed by analyzing microdiversity within OTUs, suggesting that populations within standard OTU-level groupings do not necessarily share a common ecological and evolutionary history.}, }
@article {pmid30872712, year = {2019}, author = {Oh, S and Choi, D and Cha, CJ}, title = {Ecological processes underpinning microbial community structure during exposure to subinhibitory level of triclosan.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4598}, pmid = {30872712}, issn = {2045-2322}, mesh = {Biodiversity ; Ecology ; Metagenome ; Metagenomics/methods ; Microbiota/*drug effects ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; Triclosan/*pharmacology ; }, abstract = {Ecological processes shaping the structure and diversity of microbial communities are of practical importance for managing the function and resilience of engineered biological ecosystems such as activated sludge processes. This study systematically evaluated the ecological processes acting during continuous exposure to a subinhibitory level of antimicrobial triclosan (TCS) as an environmental stressor. 16S rRNA gene-based community profiling revealed significant perturbations on the community structure and dramatic reduction (by 20-30%) in species diversity/richness compared to those under the control conditions. In addition, community profiling determined the prevalence of the deterministic processes overwhelming the ecological stochasticity. Analysis of both community composition and phenotypes in the TCS-exposed communities suggested the detailed deterministic mechanism: selection of TCS degrading (Sphingopyxis) and resistant (Pseudoxanthomonas) bacterial populations. The analysis also revealed a significant reduction of core activated sludge members, Chitinophagaceae (e.g., Ferruginibacter) and Comamonadaceae (e.g., Acidovorax), potentially affecting ecosystem functions (e.g., floc formation and nutrient removal) directly associated with system performance (i.e., wastewater treatment efficiency and effluent quality). Overall, our study provides new findings that inform the mechanisms underlying the community structure and diversity of activated sludge, which not only advances the current understanding of microbial ecology in activated sludge, but also has practical implications for the design and operation of environmental bioprocesses for treatment of antimicrobial-bearing waste streams.}, }
@article {pmid30872659, year = {2019}, author = {Johnston, J and LaPara, T and Behrens, S}, title = {Composition and Dynamics of the Activated Sludge Microbiome during Seasonal Nitrification Failure.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4565}, pmid = {30872659}, issn = {2045-2322}, mesh = {Metagenome ; Metagenomics/methods ; *Microbiota ; Minnesota ; *Nitrification ; RNA, Ribosomal, 16S/genetics ; *Seasons ; Sewage/*microbiology ; Waste Management ; }, abstract = {Wastewater treatment plants in temperate climate zones frequently undergo seasonal nitrification failure in the winter month yet maintain removal efficiency for other contaminants. We tested the hypothesis that nitrification failure can be correlated to shifts in the nitrifying microbial community. We monitored three parallel, full-scale sequencing batch reactors over the course of a year with respect to reactor performance, microbial community composition via 16S rRNA gene amplicon sequencing, and functional gene abundance using qPCR. All reactors demonstrated similar changes to their core microbiome, and only subtle variations among seasonal and transient taxa. We observed a decrease in species richness during the winter, with a slow recovery of the activated sludge community during spring. Despite the change in nitrification performance, ammonia monooxygenase gene abundances remained constant throughout the year, as did the relative sequence abundance of Nitrosomonadacae. This suggests that nitrification failure at colder temperatures might result from different reaction kinetics of nitrifying taxa, or that other organisms with strong seasonal shifts in population abundance, e.g. an uncultured lineage of Saprospiraceae, affect plant performance in the winter. This research is a comprehensive analysis of the seasonal microbial community dynamics in triplicate full-scale sequencing batch reactors and ultimately strengthens our basic understanding of the microbial ecology of activated sludge communities by revealing seasonal succession patterns of individual taxa that correlate with nutrient removal efficiency.}, }
@article {pmid30869196, year = {2019}, author = {Liu, YS and Wang, LF and Cheng, XS and Huo, YN and Ouyang, XM and Liang, LY and Lin, Y and Wu, JF and Ren, JL and Guleng, B}, title = {The pattern-recognition molecule mindin binds integrin Mac-1 to promote macrophage phagocytosis via Syk activation and NF-κB p65 translocation.}, journal = {Journal of cellular and molecular medicine}, volume = {23}, number = {5}, pages = {3402-3416}, pmid = {30869196}, issn = {1582-4934}, mesh = {Animals ; Base Sequence ; Cell Nucleus/metabolism ; Extracellular Matrix Proteins/*metabolism ; HEK293 Cells ; Humans ; Macrophage-1 Antigen/chemistry/*metabolism ; Macrophages/*cytology/*metabolism ; Mice ; Mice, Knockout ; *Phagocytosis ; Phosphorylation ; Protein Binding ; Protein Domains ; Protein Transport ; RAW 264.7 Cells ; Receptors, Pattern Recognition/*metabolism ; Syk Kinase/*metabolism ; Transcription Factor RelA/*metabolism ; }, abstract = {Mindin has a broad spectrum of roles in the innate immune system, including in macrophage migration, antigen phagocytosis and cytokine production. Mindin functions as a pattern-recognition molecule for microbial pathogens. However, the underlying mechanisms of mindin-mediated phagocytosis and its exact membrane receptors are not well established. Herein, we generated mindin-deficient mice using the CRISPR-Cas9 system and show that peritoneal macrophages from mindin-deficient mice were severely defective in their ability to phagocytize E coli. Phagocytosis was enhanced when E coli or fluorescent particles were pre-incubated with mindin, indicating that mindin binds directly to bacteria or non-pathogen particles and promotes phagocytosis. We defined that [131] I-labelled mindin binds with integrin Mac-1 (CD11b/CD18), the F-spondin (FS)-fragment of mindin binds with the αM -I domain of Mac-1 and that mindin serves as a novel ligand of Mac-1. Blockade of the αM -I domain of Mac-1 using either a neutralizing antibody or si-Mac-1 efficiently blocked mindin-induced phagocytosis. Furthermore, mindin activated the Syk and MAPK signalling pathways and promoted NF-κB entry into the nucleus. Our data indicate that mindin binds with the integrin Mac-1 to promote macrophage phagocytosis through Syk activation and NF-κB p65 translocation, suggesting that the mindin/Mac-1 axis plays a critical role during innate immune responses.}, }
@article {pmid30868207, year = {2019}, author = {Brown, SP and Jumpponen, A}, title = {Microbial Ecology of Snow Reveals Taxa-Specific Biogeographical Structure.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {946-958}, pmid = {30868207}, issn = {1432-184X}, mesh = {*Bacterial Physiological Phenomena ; Colorado ; Fungi/*physiology ; Microalgae/*physiology ; Microbiota ; Scandinavian and Nordic Countries ; Snow/*microbiology ; }, abstract = {Snows that persist late into the growing season become colonized with numerous metabolically active microorganisms, yet underlying mechanisms of community assembly and dispersal remain poorly known. We investigated (Illumina MiSeq) snow-borne bacterial, fungal, and algal communities across a latitudinal gradient in Fennoscandia and inter-continental distribution between northern Europe and North America. Our data indicate that bacterial communities are ubiquitous regionally (across Fennoscandia), whereas fungal communities are regionally heterogeneous. Both fungi and bacteria are biogeographically heterogeneous inter-continentally. Snow algae, generally thought to occur in colorful algae blooms (red, green, or yellow) on the snow surface, are molecularly described here as an important component of snows even in absence of visible algal growth. This suggests that snow algae are a previously underestimated major biological component of visually uncolonized snows. In contrast to fungi and bacteria, algae exhibit no discernible inter-continental or regional community structure and exhibit little endemism. These results indicate that global and regional snow microbial communities and their distributions may be dictated by a combination of size-limited propagule dispersal potential and restrictions (bacteria and fungi) and homogenization of ecologically specialized taxa (snow algae) across the globe. These results are among the first to compare inter-continental snow microbial communities and highlight how poorly understood microbial communities in these threatened ephemeral ecosystems are.}, }
@article {pmid30867308, year = {2019}, author = {Chong, R and Shi, M and Grueber, CE and Holmes, EC and Hogg, CJ and Belov, K and Barrs, VR}, title = {Fecal Viral Diversity of Captive and Wild Tasmanian Devils Characterized Using Virion-Enriched Metagenomics and Metatranscriptomics.}, journal = {Journal of virology}, volume = {93}, number = {11}, pages = {}, pmid = {30867308}, issn = {1098-5514}, mesh = {Animals ; Animals, Wild ; Animals, Zoo ; Australia ; Endangered Species ; Feces/*virology ; Gene Expression Profiling/methods ; Marsupialia/*virology ; Metagenomics/methods ; Transcriptome/genetics ; Virion ; }, abstract = {The Tasmanian devil is an endangered carnivorous marsupial threatened by devil facial tumor disease (DFTD). While research on DFTD has been extensive, little is known about viruses in devils and whether any are of potential conservation relevance for this endangered species. Using both metagenomics based on virion enrichment and sequence-independent amplification (virion-enriched metagenomics) and metatranscriptomics based on bulk RNA sequencing, we characterized and compared the fecal viromes of captive and wild devils. A total of 54 fecal samples collected from two captive and four wild populations were processed for virome characterization using both approaches. In total, 24 novel marsupial-related viruses, comprising a sapelovirus, astroviruses, rotaviruses, picobirnaviruses, parvoviruses, papillomaviruses, polyomaviruses, and a gammaherpesvirus, were identified, as well as known mammalian pathogens such as rabbit hemorrhagic disease virus 2. Captive devils showed significantly lower viral diversity than wild devils. Comparison of the two virus discovery approaches revealed substantial differences in the number and types of viruses detected, with metatranscriptomics better suited for RNA viruses and virion-enriched metagenomics largely identifying more DNA viruses. Thus, the viral communities revealed by virion-enriched metagenomics and metatranscriptomics were not interchangeable and neither approach was able to detect all viruses present. An integrated approach using both virion-enriched metagenomics and metatranscriptomics constitutes a powerful tool for obtaining a complete overview of both the taxonomic and functional profiles of viral communities within a sample.IMPORTANCE The Tasmanian devil is an iconic Australian marsupial that has suffered an 80% population decline due to a contagious cancer, devil facial tumor disease, along with other threats. Until now, viral discovery in this species has been confined to one gammaherpesvirus (dasyurid herpesvirus 2 [DaHV-2]), for which captivity was identified as a significant risk factor. Our discovery of 24 novel marsupial-associated RNA and DNA viruses, and that viral diversity is lower in captive than in wild devils, has greatly expanded our knowledge of gut-associated viruses in devils and provides important baseline information that will contribute to the conservation and captive management of this endangered species. Our results also revealed that a combination of virion-enriched metagenomics and metatranscriptomics may be a more comprehensive approach for virome characterization than either method alone. Our results thus provide a springboard for continuous improvements in the way we study complex viral communities.}, }
@article {pmid30867296, year = {2019}, author = {Verma, J and Bag, S and Saha, B and Kumar, P and Ghosh, TS and Dayal, M and Senapati, T and Mehra, S and Dey, P and Desigamani, A and Kumar, D and Rana, P and Kumar, B and Maiti, TK and Sharma, NC and Bhadra, RK and Mutreja, A and Nair, GB and Ramamurthy, T and Das, B}, title = {Genomic plasticity associated with antimicrobial resistance in Vibrio cholerae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {13}, pages = {6226-6231}, pmid = {30867296}, issn = {1091-6490}, mesh = {Anti-Bacterial Agents/pharmacology ; Cholera/*microbiology ; Conjugation, Genetic/genetics ; DNA Transposable Elements/genetics ; Diarrhea/microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Evolution, Molecular ; Feces/microbiology ; *Gene Transfer, Horizontal ; Genetic Variation ; Genome, Bacterial/*genetics ; Genomic Islands/genetics ; Humans ; Imipenem/pharmacology ; India ; Interspersed Repetitive Sequences/genetics ; Phenotype ; Plasmids/genetics ; Prophages/genetics ; Proteome ; Vibrio cholerae/drug effects/*genetics/isolation &amp; purification/pathogenicity ; Vibrio cholerae O1/genetics/isolation &amp; purification/pathogenicity ; Whole Genome Sequencing ; }, abstract = {The Bay of Bengal is known as the epicenter for seeding several devastating cholera outbreaks across the globe. Vibrio cholerae, the etiological agent of cholera, has extraordinary competency to acquire exogenous DNA by horizontal gene transfer (HGT) and adapt them into its genome for structuring metabolic processes, developing drug resistance, and colonizing the human intestine. Antimicrobial resistance (AMR) in V. cholerae has become a global concern. However, little is known about the identity of the resistance traits, source of AMR genes, acquisition process, and stability of the genetic elements linked with resistance genes in V. cholerae Here we present details of AMR profiles of 443 V. cholerae strains isolated from the stool samples of diarrheal patients from two regions of India. We sequenced the whole genome of multidrug-resistant (MDR) and extensively drug-resistant (XDR) V. cholerae to identify AMR genes and genomic elements that harbor the resistance traits. Our genomic findings were further confirmed by proteome analysis. We also engineered the genome of V. cholerae to monitor the importance of the autonomously replicating plasmid and core genome in the resistance profile. Our findings provided insights into the genomes of recent cholera isolates and identified several acquired traits including plasmids, transposons, integrative conjugative elements (ICEs), pathogenicity islands (PIs), prophages, and gene cassettes that confer fitness to the pathogen. The knowledge generated from this study would help in better understanding of V. cholerae evolution and management of cholera disease by providing clinical guidance on preferred treatment regimens.}, }
@article {pmid30861385, year = {2019}, author = {Rodriguez-Sanchez, A and Muñoz-Palazon, B and Hurtado-Martinez, M and Maza-Marquez, P and Gonzalez-Lopez, J and Vahala, R and Gonzalez-Martinez, A}, title = {Microbial ecology dynamics of a partial nitritation bioreactor with Polar Arctic Circle activated sludge operating at low temperature.}, journal = {Chemosphere}, volume = {225}, number = {}, pages = {73-82}, doi = {10.1016/j.chemosphere.2019.03.012}, pmid = {30861385}, issn = {1879-1298}, mesh = {Ammonium Compounds/analysis ; Biomass ; Bioreactors/*microbiology ; *Cold Temperature ; Nitrites/*analysis ; Scandinavian and Nordic Countries ; Sewage/*microbiology ; Trichosporon/metabolism ; Water Purification/*methods ; Xanthomonadaceae/metabolism ; }, abstract = {A lab-scale partial nitritation SBR was operated at 11 °C for 300 days used for the treatment of high-ammonium wastewater, which was inoculated with activated sludge from Rovaniemi WWTP (located in Polar Arctic Circle) in order to evaluate the influence the temperature on the performance, stability and dynamics of its microbial community. The partial nitritation achieved steady-state long-term operation and granulation process was not affected despite the low temperature and high ammonia concentration. The steady conditions were reached after 60 days of operation where the granular biomass was fully-formed and the 50%-50% of ammonium-nitrite effluent was successful achieved. Inoculation with cold adapted inoculum showed to yield bigger, denser granules with faster start-up without necessity of low temperature adaptation period. Next-generation sequences techniques showed that Trichosporonaceae and Xanthomonadaceae were the dominant OTUs in the mature granules. Our study could be useful in the implementation of full-scale partial nitritation reactors in cold regions such as Nordic countries for treating wastewater with high concentration of ammonium.}, }
@article {pmid30857548, year = {2019}, author = {Kim, SJ and Kim, JG and Lee, SH and Park, SJ and Gwak, JH and Jung, MY and Chung, WH and Yang, EJ and Park, J and Jung, J and Hahn, Y and Cho, JC and Madsen, EL and Rodriguez-Valera, F and Hyun, JH and Rhee, SK}, title = {Correction to: Genomic and metatranscriptomic analyses of carbon remineralization in an Antarctic polynya.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {38}, pmid = {30857548}, issn = {2049-2618}, abstract = {Following publication of the original article [1], the authors identified wrong citations in the maintext.}, }
@article {pmid30856427, year = {2019}, author = {Prévoteau, A and Clauwaert, P and Kerckhof, FM and Rabaey, K}, title = {Oxygen-reducing microbial cathodes monitoring toxic shocks in tap water.}, journal = {Biosensors &amp; bioelectronics}, volume = {132}, number = {}, pages = {115-121}, doi = {10.1016/j.bios.2019.02.037}, pmid = {30856427}, issn = {1873-4235}, mesh = {Biofilms/drug effects/growth &amp; development ; Biosensing Techniques/*instrumentation/methods ; Drinking Water/analysis ; Electric Conductivity ; Electrochemical Techniques/instrumentation/methods ; Electrodes/*microbiology ; Environmental Monitoring/instrumentation/methods ; Equipment Design ; Formaldehyde/analysis/metabolism ; Gammaproteobacteria/drug effects/*physiology ; Metals, Heavy/analysis/metabolism ; Oxidation-Reduction ; Oxygen/*metabolism ; Water Pollutants, Chemical/*analysis/metabolism ; }, abstract = {Electroactive biofilms (EABs) have recently attracted considerable research interest for their possible use as amperometric biosensors in environmental or bioprocess monitoring, for example for in situ detection of toxic compounds. Almost exclusively, corresponding research has focused on heterotrophic, anodic EABs. These biofilms require sufficiently high organic loads and anoxic conditions to deliver a stable baseline current. Conversely, electroautotrophic O2-reducing EABs have recently been proposed to monitor toxic shocks in oxic solutions that are poor or devoid of organic substrate. This was done in optimal media and only assessed for formaldehyde as a model toxic compound. Here we show that O2-reducing EABs can grow in unamended tap water on carbon electrodes at + 0.2 V vs. Ag/AgCl. They retained substantial electroactivity for at least eight months without adding exogenous compounds. The most represented operational taxonomic units were assigned to the phylum Gammaproteobacteria (25 ± 15%, n = 5 electrodes). Cyclic voltammograms showed a reproducible nernstian behavior for O2 reduction with a mid-wave potential at + 0.27 V and variable plateau current densities ranging from - 1 to - 22 µA cm[-2] (n = 10 electrodes). The biocatalytic current was substantially impacted by the addition of either of three tested heavy metals (Hg(II), Cr(VI) or Pb(II)) or by organic pollutants (formaldehyde, 2,4-dichlorophenol, benzalkonium chloride), with limits of detection ranging from 0.5 to 10 mg L[-1] (2.5-61 µmol L[-1]). Response times were typically around 1 min. Comparison with previous reports suggests that O2-reducing microbial cathodes may be more sensitive to toxic shocks than anodic, heterotrophic EABs.}, }
@article {pmid30855669, year = {2019}, author = {Horton, DJ and Theis, KR and Uzarski, DG and Learman, DR}, title = {Microbial community structure and microbial networks correspond to nutrient gradients within coastal wetlands of the Laurentian Great Lakes.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {4}, pages = {}, pmid = {30855669}, issn = {1574-6941}, mesh = {Great Lakes Region ; Human Activities ; Humans ; Microbial Consortia/genetics ; *Microbiota/genetics ; Nutrients/*analysis ; Soil/*chemistry ; *Soil Microbiology ; *Wetlands ; }, abstract = {Microbial communities within the soil of Laurentian Great Lakes coastal wetlands drive biogeochemical cycles and provide several other ecosystem services. However, there exists a lack of understanding of how microbial communities respond to nutrient gradients and human activity in these systems. This research sought to address the lack of understanding through exploration of relationships among nutrient gradients, microbial community diversity, and microbial networks. Significant differences in microbial community structure were found among coastal wetlands within the western basin of Lake Erie and all other wetlands studied (three regions within Saginaw Bay and one region in the Beaver Archipelago). These diversity differences coincided with higher nutrient levels within the Lake Erie region. Site-to-site variability also existed within the majority of the regions studied, suggesting site-scale heterogeneity may impact microbial community structure. Several subnetworks of microbial communities and individual community members were related to chemical gradients among wetland regions, revealing several candidate indicator communities and taxa that may be useful for Great Lakes coastal wetland management. This research provides an initial characterization of microbial communities among Great Lakes coastal wetlands and demonstrates that microbial communities could be negatively impacted by anthropogenic activities.}, }
@article {pmid30854582, year = {2019}, author = {Sun, W and Xiao, E and Krumins, V and Dong, Y and Li, B and Deng, J and Wang, Q and Xiao, T and Liu, J}, title = {Comparative Analyses of the Microbial Communities Inhabiting Coal Mining Waste Dump and an Adjacent Acid Mine Drainage Creek.}, journal = {Microbial ecology}, volume = {78}, number = {3}, pages = {651-664}, pmid = {30854582}, issn = {1432-184X}, support = {41771301//National Natural Science Foundation of China/ ; 41420104007//National Natural Science Foundation of China/ ; }, mesh = {Acids/analysis/metabolism ; Bacteria/classification/genetics/*isolation &amp; purification ; Coal Mining ; Geologic Sediments/*microbiology ; Hydrogen-Ion Concentration ; Iron/metabolism ; *Microbiota ; Nitrogen/metabolism ; Phylogeny ; Sulfides/metabolism ; Waste Disposal Facilities ; Wastewater/analysis/*microbiology ; }, abstract = {Microbial communities inhabiting the acid mine drainage (AMD) have been extensively studied, but the microbial communities in the coal mining waste dump that may generate the AMD are still relatively under-explored. In this study, we characterized the microbial communities within these under-explored extreme habitats and compared with those in the downstream AMD creek. In addition, the interplay between the microbiota and the environmental parameters was statistically investigated. A Random Forest ensemble model indicated that pH was the most important environmental parameter influencing microbial community and diversity. Parameters associated with nitrogen cycling were also critical factors, with positive effects on microbial diversity, while S-related parameters had negative effects. The microbial community analysis also indicated that the microbial assemblage was driven by pH. Various taxa were enriched in different pH ranges: Sulfobacillus was the indicator genus in samples with pH < 3 while Acidobacteriaceae-affiliated bacteria prevailed in samples with 3 < pH < 3.5. The detection of some lineages that are seldom reported in mining areas suggested the coal mining dumps may be a reservoir of phylogenetic novelty. For example, potential nitrogen fixers, autotrophs, and heterotrophs may form diverse communities that actively self-perpetuate pyrite dissolution and acidic waste generation, suggesting unique ecological strategies adopted by these innate microorganisms. In addition, co-occurrence network analyses suggest that members of Acidimicrobiales play important roles in interactions with other taxa, especially Fe- and S-oxidizing bacteria such as Sulfobacillus spp.}, }
@article {pmid30853950, year = {2019}, author = {Mareš, J and Strunecký, O and Bučinská, L and Wiedermannová, J}, title = {Evolutionary Patterns of Thylakoid Architecture in Cyanobacteria.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {277}, pmid = {30853950}, issn = {1664-302X}, abstract = {While photosynthetic processes have become increasingly understood in cyanobacterial model strains, differences in the spatial distribution of thylakoid membranes among various lineages have been largely unexplored. Cyanobacterial cells exhibit an intriguing diversity in thylakoid arrangements, ranging from simple parietal to radial, coiled, parallel, and special types. Although metabolic background of their variability remains unknown, it has been suggested that thylakoid patterns are stable in certain phylogenetic clades. For decades, thylakoid arrangements have been used in cyanobacterial classification as one of the crucial characters for definition of taxa. The last comprehensive study addressing their evolutionary history in cyanobacteria was published 15 years ago. Since then both DNA sequence and electron microscopy data have grown rapidly. In the current study, we map ultrastructural data of >200 strains onto the SSU rRNA gene tree, and the resulting phylogeny is compared to a phylogenomic tree. Changes in thylakoid architecture in general follow the phylogeny of housekeeping loci. Parietal arrangement is resolved as the original thylakoid organization, evolving into complex arrangement in the most derived group of heterocytous cyanobacteria. Cyanobacteria occupying intermediate phylogenetic positions (greater filamentous, coccoid, and baeocytous types) exhibit fascicular, radial, and parallel arrangements, partly tracing the reconstructed course of phylogenetic branching. Contrary to previous studies, taxonomic value of thylakoid morphology seems very limited. Only special cases such as thylakoid absence or the parallel arrangement could be used as taxonomically informative apomorphies. The phylogenetic trees provide evidence of both paraphyly and reversion from more derived architectures in the simple parietal thylakoid pattern. Repeated convergent evolution is suggested for the radial and fascicular architectures. Moreover, thylakoid arrangement is constrained by cell size, excluding the occurrence of complex architectures in cyanobacteria smaller than 2 μm in width. It may further be dependent on unknown (eco)physiological factors as suggested by recurrence of the radial type in unrelated but morphologically similar cyanobacteria, and occurrence of special features throughout the phylogeny. No straightforward phylogenetic congruences have been found between proteins involved in photosynthesis and thylakoid formation, and the thylakoid patterns. Remarkably, several postulated thylakoid biogenesis factors are partly or completely missing in cyanobacteria, challenging their proposed essential roles.}, }
@article {pmid30853948, year = {2019}, author = {Coclet, C and Garnier, C and Durrieu, G and Omanović, D and D'Onofrio, S and Le Poupon, C and Mullot, JU and Briand, JF and Misson, B}, title = {Changes in Bacterioplankton Communities Resulting From Direct and Indirect Interactions With Trace Metal Gradients in an Urbanized Marine Coastal Area.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {257}, pmid = {30853948}, issn = {1664-302X}, abstract = {Unraveling the relative importance of both environmental conditions and ecological processes regulating bacterioplankton communities is a central goal in microbial ecology. Marine coastal environments are among the most urbanized areas and as a consequence experience environmental pressures. The highly anthropized Toulon Bay (France) was considered as a model system to investigate shifts in bacterioplankton communities along natural and anthropogenic physicochemical gradients during a 1-month survey. In depth geochemical characterization mainly revealed strong and progressive Cd, Zn, Cu, and Pb contamination gradients between the entrance of the Bay and the north-western anthropized area. On the other hand, low-amplitude natural gradients were observed for other environmental variables. Using 16S rRNA gene sequencing, we observed strong spatial patterns in bacterioplankton taxonomic and predicted function structure along the chemical contamination gradient. Variation partitioning analysis demonstrated that multiple metallic contamination explained the largest part of the spatial biological variations observed, but DOC and salinity were also significant contributors. Network analysis revealed that biotic interactions were far more numerous than direct interactions between microbial groups and environmental variables. This suggests indirect effects of the environment, and especially trace metals, on the community through a few taxonomic groups. These spatial patterns were also partially found for predicted bacterioplankton functions, thus indicating a limited functional redundancy. All these results highlight both potential direct influences of trace metals contamination on coastal bacterioplankton and indirect forcing through biotic interactions and cascading.}, }
@article {pmid30853940, year = {2019}, author = {Jaiswal, S and Singh, DK and Shukla, P}, title = {Gene Editing and Systems Biology Tools for Pesticide Bioremediation: A Review.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {87}, pmid = {30853940}, issn = {1664-302X}, abstract = {Bioremediation is the degradation potential of microorganisms to dissimilate the complex chemical compounds from the surrounding environment. The genetics and biochemistry of biodegradation processes in datasets opened the way of systems biology. Systemic biology aid the study of interacting parts involved in the system. The significant keys of system biology are biodegradation network, computational biology, and omics approaches. Biodegradation network consists of all the databases and datasets which aid in assisting the degradation and deterioration potential of microorganisms for bioremediation processes. This review deciphers the bio-degradation network, i.e., the databases and datasets (UM-BBD, PAN, PTID, etc.) aiding in assisting the degradation and deterioration potential of microorganisms for bioremediation processes, computational biology and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation experiments. Besides, the present review also describes the gene editing tools like CRISPR Cas, TALEN, and ZFNs which can possibly make design microbe with functional gene of interest for degradation of particular recalcitrant for improved bioremediation.}, }
@article {pmid30852639, year = {2019}, author = {Haro, S and Brodersen, KE and Bohórquez, J and Papaspyrou, S and Corzo, A and Kühl, M}, title = {Radiative Energy Budgets in a Microbial Mat Under Different Irradiance and Tidal Conditions.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {852-865}, pmid = {30852639}, issn = {1432-184X}, support = {CTM2013-43857-R//Ministerio de Econom&#xed;a y Competitividad/ ; DFF-1323-00065B//Ministeriet for Forskning Innovation og Videreg&#xe5;ende Uddannelser/ ; postdoctoral fellowship//Carlsbergfondet (DK)/ ; PU-2014-043-FPI//Universidad de C&#xe1;diz/ ; }, mesh = {*Bacterial Physiological Phenomena ; Denmark ; Geologic Sediments/*microbiology ; Seawater/*microbiology ; *Sunlight ; *Tidal Waves ; }, abstract = {Irradiance and temperature variations during tidal cycles modulate microphytobenthic primary production potentially by changing the radiative energy balance of photosynthetic mats between immersion and emersion and thus sediment daily net metabolism. To test the effect of tidal stages on the radiative energy budget, we used microsensor measurements of oxygen, temperature, and scalar irradiance to estimate the radiative energy budget in a coastal photosynthetic microbial mat during immersion (constant water column of 2 cm) and emersion under increasing irradiance. Total absorbed light energy was higher in immersion than emersion, due to a lower reflectance of the microbial mat, while most (> 97%) of the absorbed light energy was dissipated as heat irrespective of tidal conditions. During immersion, the upward heat flux was higher than the downward one, whereas the opposite occurred during emersion. At highest photon irradiance (800 μmol photon m[-2] s[-1]), the sediment temperature increased ~ 2.5 °C after changing the conditions from immersion to emersion. The radiative energy balance showed that less than 1% of the incident light energy (PAR, 400-700 nm) was conserved by photosynthesis under both tidal conditions. At low to moderate incident irradiances, the light use efficiency was similar during the tidal stages. In contrast, we found an ~ 30% reduction in the light use efficiency during emersion as compared to immersion under the highest irradiance likely due to the rapid warming of the sediment during emersion and increased non-photochemical quenching. These changes in the photosynthetic efficiency and radiative energy budget could affect both primary producers and temperature-dependent bacterial activity and consequently daily net metabolism rates having important ecological consequences.}, }
@article {pmid30852638, year = {2019}, author = {Castle, SC and Samac, DA and Sadowsky, MJ and Rosen, CJ and Gutknecht, JLM and Kinkel, LL}, title = {Impacts of Sampling Design on Estimates of Microbial Community Diversity and Composition in Agricultural Soils.}, journal = {Microbial ecology}, volume = {78}, number = {3}, pages = {753-763}, pmid = {30852638}, issn = {1432-184X}, support = {12108463//Agricultural Research Service/ ; }, mesh = {Agriculture ; Bacteria/classification/genetics/*isolation &amp; purification ; Fungi/classification/genetics/*isolation &amp; purification ; *Microbiota ; Minnesota ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Soil microbiota play important and diverse roles in agricultural crop nutrition and productivity. Yet, despite increasing efforts to characterize soil bacterial and fungal assemblages, it is challenging to disentangle the influences of sampling design on assessments of communities. Here, we sought to determine whether composite samples-often analyzed as a low cost and effort alternative to replicated individual samples-provide representative summary estimates of microbial communities. At three Minnesota agricultural research sites planted with an oat cover crop, we conducted amplicon sequencing for soil bacterial and fungal communities (16SV4 and ITS2) of replicated individual or homogenized composite soil samples. We compared soil microbiota from within and among plots and then among agricultural sites using both sampling strategies. Results indicated that single or multiple replicated individual samples, or a composite sample from each plot, were sufficient for distinguishing broad site-level macroecological differences among bacterial and fungal communities. Analysis of a single sample per plot captured only a small fraction of the distinct OTUs, diversity, and compositional variability detected in the analysis of multiple individual samples or a single composite sample. Likewise, composite samples captured only a fraction of the diversity represented by the six individual samples from which they were formed, and, on average, analysis of two or three individual samples offered greater compositional coverage (i.e., greater number of OTUs) than a single composite sample. We conclude that sampling design significantly impacts estimates of bacterial and fungal communities even in homogeneously managed agricultural soils, and our findings indicate that while either strategy may be sufficient for broad macroecological investigations, composites may be a poor substitute for replicated samples at finer spatial scales.}, }
@article {pmid30850431, year = {2019}, author = {Schreiber, L and Fortin, N and Tremblay, J and Wasserscheid, J and Elias, M and Mason, J and Sanschagrin, S and Cobanli, S and King, T and Lee, K and Greer, CW}, title = {Potential for Microbially Mediated Natural Attenuation of Diluted Bitumen on the Coast of British Columbia (Canada).}, journal = {Applied and environmental microbiology}, volume = {85}, number = {10}, pages = {}, pmid = {30850431}, issn = {1098-5336}, mesh = {Bacteria/*metabolism ; Biodegradation, Environmental ; British Columbia ; Hydrocarbons/*analysis ; Petroleum Pollution/*analysis ; Seawater/analysis ; Water Pollutants, Chemical/*analysis ; }, abstract = {Western Canada produces large amounts of bitumen, a heavy, highly weathered crude oil. Douglas Channel and Hecate Strait on the coast of British Columbia are two water bodies that may be impacted by a proposed pipeline and marine shipping route for diluted bitumen (dilbit). This study investigated the potential of microbial communities from these waters to mitigate the impacts of a potential dilbit spill. Microcosm experiments were set up with water samples representing different seasons, years, sampling stations, and dilbit blends. While the alkane fraction of the tested dilbit blends was almost completely degraded after 28 days, the majority of the polycyclic aromatic hydrocarbons (PAHs) remained. The addition of the dispersant Corexit 9500A most often had either no effect or an enhancing effect on dilbit degradation. Dilbit-degrading microbial communities were highly variable between seasons, years, and stations, with dilbit type having little impact on community trajectories. Potential oil-degrading genera showed a clear succession pattern and were for the most part recruited from the "rare biosphere." At the community level, dispersant appeared to stimulate an accelerated enrichment of genera typically associated with hydrocarbon degradation, even in dilbit-free controls. This suggests that dispersant-induced growth of hydrocarbon degraders (and not only increased bioavailability of oil-associated hydrocarbons) contributes to the degradation-enhancing effect previously reported for Corexit 9500A.IMPORTANCE Western Canada hosts large petroleum deposits, which ultimately enter the market in the form of dilbit. Tanker-based shipping represents the primary means to transport dilbit to international markets. With anticipated increases in production to meet global energy needs, the risk of a dilbit spill is expected to increase. This study investigated the potential of microbial communities naturally present in the waters of a potential dilbit shipping lane to mitigate the effects of a spill. Here we show that microbial degradation of dilbit was mostly limited to n-alkanes, while the overall concentration of polycyclic aromatic hydrocarbons, which represent the most toxic fraction of dilbit, decreased only slightly within the time frame of our experiments. We further investigated the effect of the oil dispersant Corexit 9500A on microbial dilbit degradation. Our results highlight the fact that dispersant-associated growth stimulation, and not only increased bioavailability of hydrocarbons and inhibition of specific genera, contributes to the overall effect of dispersant addition.}, }
@article {pmid30847110, year = {2019}, author = {Sharma, RS and Karmakar, S and Kumar, P and Mishra, V}, title = {Application of filamentous phages in environment: A tectonic shift in the science and practice of ecorestoration.}, journal = {Ecology and evolution}, volume = {9}, number = {4}, pages = {2263-2304}, pmid = {30847110}, issn = {2045-7758}, abstract = {Theories in soil biology, such as plant-microbe interactions and microbial cooperation and antagonism, have guided the practice of ecological restoration (ecorestoration). Below-ground biodiversity (bacteria, fungi, invertebrates, etc.) influences the development of above-ground biodiversity (vegetation structure). The role of rhizosphere bacteria in plant growth has been largely investigated but the role of phages (bacterial viruses) has received a little attention. Below the ground, phages govern the ecology and evolution of microbial communities by affecting genetic diversity, host fitness, population dynamics, community composition, and nutrient cycling. However, few restoration efforts take into account the interactions between bacteria and phages. Unlike other phages, filamentous phages are highly specific, nonlethal, and influence host fitness in several ways, which make them useful as target bacterial inocula. Also, the ease with which filamentous phages can be genetically manipulated to express a desired peptide to track and control pathogens and contaminants makes them useful in biosensing. Based on ecology and biology of filamentous phages, we developed a hypothesis on the application of phages in environment to derive benefits at different levels of biological organization ranging from individual bacteria to ecosystem for ecorestoration. We examined the potential applications of filamentous phages in improving bacterial inocula to restore vegetation and to monitor changes in habitat during ecorestoration and, based on our results, recommend a reorientation of the existing framework of using microbial inocula for such restoration and monitoring. Because bacterial inocula and biomonitoring tools based on filamentous phages are likely to prove useful in developing cost-effective methods of restoring vegetation, we propose that filamentous phages be incorporated into nature-based restoration efforts and that the tripartite relationship between phages, bacteria, and plants be explored further. Possible impacts of filamentous phages on native microflora are discussed and future areas of research are suggested to preclude any potential risks associated with such an approach.}, }
@article {pmid30846975, year = {2019}, author = {Zorz, J and Willis, C and Comeau, AM and Langille, MGI and Johnson, CL and Li, WKW and LaRoche, J}, title = {Drivers of Regional Bacterial Community Structure and Diversity in the Northwest Atlantic Ocean.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {281}, pmid = {30846975}, issn = {1664-302X}, abstract = {The fundamental role of bacteria in global biogeochemical cycles warrants a thorough understanding of the factors controlling bacterial community structure. In this study, the integrated effect of seasonal differences and spatial distribution on bacterial community structure and diversity were investigated at the regional scale. We conducted a comprehensive bacterial survey, with 451 samples of the Scotian Shelf sector of the Northwest Atlantic Ocean during spring and fall of 2014 and 2016, to analyze the effects of physicochemical gradients on bacterial community structure. Throughout the region, Pelagibacteraceae and Rhodobacteraceae were the most common in the free-living fraction, while Flavobacteriia and Deltaproteobacteria were more abundant in the particle-associated fraction. Overall, there was strong covariation of the microbial community diversity from the two size fractions. This relationship existed despite the statistically significant difference in community structure between the free-living and particle-associated size fractions. In both size fractions, distribution patterns of bacterial taxa, and species within taxa, displayed temporal and spatial preferences. Distinct bacterial assemblages specific to season and depth in the water column were identified. These distinct assemblages, consistent for both 2014 and 2016, suggested replicable patterns in microbial communities for spring and fall in this region. Over all sites, temperature and oxygen values were highly correlated with community similarity, and salinity and oxygen values were the most strongly positively- and negatively correlated with alpha diversity, respectively. However, the strengths of these correlations depended on the depth and season sampled. The bathymetry of the Scotian Shelf, the abrupt shelf break to the Scotian Slope and the major ocean currents dominating in the region led to the formation of distinct on-shelf and off-shelf bacterial communities both in spring and fall. The highest species richness was observed at the shelf break, where water masses from the two major currents meet. Our study establishes the baseline for assessing future changes in the bacterial community of the Scotian Shelf waters, a rapidly changing sector of the Atlantic Ocean.}, }
@article {pmid30837968, year = {2019}, author = {Hinzke, T and Kouris, A and Hughes, RA and Strous, M and Kleiner, M}, title = {More Is Not Always Better: Evaluation of 1D and 2D-LC-MS/MS Methods for Metaproteomics.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {238}, pmid = {30837968}, issn = {1664-302X}, abstract = {Metaproteomics, the study of protein expression in microbial communities, is a versatile tool for environmental microbiology. Achieving sufficiently high metaproteome coverage to obtain a comprehensive picture of the activities and interactions in microbial communities is one of the current challenges in metaproteomics. An essential step to maximize the number of identified proteins is peptide separation via liquid chromatography (LC) prior to mass spectrometry (MS). Thorough optimization and comparison of LC methods for metaproteomics are, however, currently lacking. Here, we present an extensive development and test of different 1D and 2D-LC approaches for metaproteomic peptide separations. We used fully characterized mock community samples to evaluate metaproteomic approaches with very long analytical columns (50 and 75 cm) and long gradients (up to 12 h). We assessed a total of over 20 different 1D and 2D-LC approaches in terms of number of protein groups and unique peptides identified, peptide spectrum matches (PSMs) generated, the ability to detect proteins of low-abundance species, the effect of technical replicate runs on protein identifications and method reproducibility. We show here that, while 1D-LC approaches are faster and easier to set up and lead to more identifications per minute of runtime, 2D-LC approaches allow for a higher overall number of identifications with up to >10,000 protein groups identified. We also compared the 1D and 2D-LC approaches to a standard GeLC workflow, in which proteins are pre-fractionated via gel electrophoresis. This method yielded results comparable to the 2D-LC approaches, however with the drawback of a much increased sample preparation time. Based on our results, we provide recommendations on how to choose the best LC approach for metaproteomics experiments, depending on the study aims.}, }
@article {pmid30834960, year = {2019}, author = {Kerdraon, L and Balesdent, MH and Barret, M and Laval, V and Suffert, F}, title = {Crop Residues in Wheat-Oilseed Rape Rotation System: a Pivotal, Shifting Platform for Microbial Meetings.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {931-945}, pmid = {30834960}, issn = {1432-184X}, support = {634179//Horizon 2020 Framework Programme/ ; }, mesh = {Bacteria/*classification ; Brassica/growth &amp; development ; Crop Production/*methods ; Crops, Agricultural/*growth &amp; development ; DNA Barcoding, Taxonomic ; Fungi/*classification ; *Microbiota ; Seasons ; *Soil Microbiology ; Triticum/growth &amp; development ; }, abstract = {Crop residues are a crucial ecological niche with a major biological impact on agricultural ecosystems. In this study, we used a combined diachronic and synchronic field experiment based on wheat-oilseed rape rotations to test the hypothesis that plant is a structuring factor of microbial communities in crop residues, and that this effect decreases over time with their likely progressive degradation and colonisation by other microorganisms. We characterised an entire fungal and bacterial community associated with 150 wheat and oilseed rape residue samples at a plurennial scale by metabarcoding. The impact of plant species on the residue microbiota decreased over time and our data revealed turnover, with the replacement of oligotrophs, often plant-specific genera (such as pathogens) by copiotrophs, belonging to more generalist genera. Within a single cropping season, the plant-specific genera and species were gradually replaced by taxa that are likely to originate from the soil. These changes occurred more rapidly for bacteria than for fungi, known to degrade complex compounds. Overall, our findings suggest that crop residues constitute a key fully-fledged microbial ecosystem. Taking into account this ecosystem, that has been neglected for too long, is essential, not only to improve the quantitative management of residues, the presence of which can be detrimental to crop health, but also to identify groups of beneficial microorganisms. Our findings are of particular importance, because the wheat-oilseed rape rotation, in which no-till practices are frequent, is particularly widespread in the European arable cropping systems.}, }
@article {pmid30834332, year = {2019}, author = {Dunivin, TK and Choi, J and Howe, A and Shade, A}, title = {RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids.}, journal = {mSystems}, volume = {4}, number = {1}, pages = {}, pmid = {30834332}, issn = {2379-5077}, abstract = {Plasmids harbor transferable genes that contribute to the functional repertoire of microbial communities, yet their contributions to metagenomes are often overlooked. Environmental plasmids have the potential to spread antibiotic resistance to clinical microbial strains. In soils, high microbiome diversity and high variability in plasmid characteristics present a challenge for studying plasmids. To improve the understanding of soil plasmids, we present RefSoil+, a database containing plasmid sequences from 922 soil microorganisms. Soil plasmids were larger than other described plasmids, which is a trait associated with plasmid mobility. There was a weak relationship between chromosome size and plasmid size and no relationship between chromosome size and plasmid number, suggesting that these genomic traits are independent in soil. We used RefSoil+ to inform the distributions of antibiotic resistance genes among soil microorganisms compared to those among nonsoil microorganisms. Soil-associated plasmids, but not chromosomes, had fewer antibiotic resistance genes than other microorganisms. These data suggest that soils may offer limited opportunity for plasmid-mediated transfer of described antibiotic resistance genes. RefSoil+ can serve as a reference for the diversity, composition, and host associations of plasmid-borne functional genes in soil, a utility that will be enhanced as the database expands. Our study improves the understanding of soil plasmids and provides a resource for assessing the dynamics of the genes that they carry, especially genes conferring antibiotic resistances. IMPORTANCE Soil-associated plasmids have the potential to transfer antibiotic resistance genes from environmental to clinical microbial strains, which is a public health concern. A specific resource is needed to aggregate the knowledge of soil plasmid characteristics so that the content, host associations, and dynamics of antibiotic resistance genes can be assessed and then tracked between the environment and the clinic. Here, we present RefSoil+, a database of soil-associated plasmids. RefSoil+ presents a contemporary snapshot of antibiotic resistance genes in soil that can serve as a reference as novel plasmids and transferred antibiotic resistances are discovered. Our study broadens our understanding of plasmids in soil and provides a community resource of important plasmid-associated genes, including antibiotic resistance genes.}, }
@article {pmid30834183, year = {2019}, author = {Tormoehlen, K and Johnson-Walker, YJ and Lankau, EW and Myint, MS and Herrmann, JA}, title = {Considerations for studying transmission of antimicrobial resistant enteric bacteria between wild birds and the environment on intensive dairy and beef cattle operations.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6460}, pmid = {30834183}, issn = {2167-8359}, abstract = {BACKGROUND: Wild birds using livestock facilities for food and shelter may contribute to dissemination of enteric pathogens or antimicrobial resistant bacteria. However, drivers of microbial exchange among wildlife and livestock are not well characterized. Predisposition for acquiring and retaining environmental bacteria may vary among species because of physiologic or behavioral differences, complicating selection of a bacterial model that can accurately characterize microbial connections among hosts of interest. This study compares the prevalence and antibiotic resistance phenotypes of two potential model bacterial organisms isolated from wild birds and their environments.<br><br>METHODS: We compared prevalence and resistance profiles of Escherichia coli and Enterococcus species isolated from environmental swabs and bird feces on a residential control site, a confinement dairy, a pasture-based beef farm, and a confinement beef farm.<br><br>RESULTS: Bird feces at all sites had low-to-moderate prevalence of Escherichia coli (range: 17-47%), despite potential for exposure on farms (range: 63-97%). Few Escherichia coli were isolated from the control environment. Enterococcus faecalis was dominant in birds at both beef farms (62% and 81% of Enterococcus isolates) and low-to-moderately prevalent at the dairy and control sites (29% and 23% of isolates, respectively). Antimicrobial resistance prevalence was higher in farm samples compared to those from the residential control, but distribution of resistant isolates varied between the bacterial genera. Birds on all farms carried resistant Enterococcus at similar rates to that of the environment, but resistance was less common in bird-associated Escherichia coli despite presence of resistant isolates in the farm environment.<br><br>DISCUSSION: Bacterial species studied may affect how readily bacterial exchange among populations is detected. Selection of microbial models must carefully consider both the questions being posed and how findings might influence resulting management decisions.}, }
@article {pmid30834012, year = {2019}, author = {El-Sayed, H and Aly, Y and Elgamily, H and Nagy, MM}, title = {A Promising Probiotic Irrigant: An In Vitro Study.}, journal = {Open access Macedonian journal of medical sciences}, volume = {7}, number = {3}, pages = {407-411}, pmid = {30834012}, issn = {1857-9655}, abstract = {AIM: The present study aimed to investigate the inhibitory effect of Lactobacillus rhamnosus (B-445) as a probiotics irrigant on the growth of Enterococcus faecalis.<br><br>METHODS: Forty-two extracted single human canal anterior teeth were prepared with rotary instrumentation and sterilised. Teeth were divided into 3 groups according to the type of irrigant, N = 14. Three experimental groups were inoculated with E. faecalis and cultured for 21 days before use; Group 1 was 2.5% NaOCl (positive control), Group 2 was saline (negative control), Group 3 was the experimental probiotic irrigant. Paper point sampling of the canals of each group was obtained before irrigation (S1), immediately after irrigation (S2) and after 24 hours (post irrigation samples) (S3) to determine remaining colony forming units for E. faecalis. Also, Colony counts for L. rhamnosus in Group 3 after immediate irrigation, as well as 24 hours post irrigation, was performed to determine the survival profile of these bacteria in infected root canal with E. faecalis.<br><br>RESULTS: The NaOCl irrigant group had the lowest mean value of (log 10 CFU/mL) of E. faecalis after immediate irrigation and after 24 hrs post irrigation followed by the probiotic group, while the highest mean value was the saline group (P &#x2264; 0.001). The survival profile for L. rhamnosus in Group 3 after immediate irrigation and post-irrigation were slightly higher than for E. faecalis (P &#x2264; 0.001).<br><br>CONCLUSION: Lactobacillus rhamnosus which revealed a potential inhibitory effect on the growth of Enterococcus faecalis, could be used as a new natural, safe probiotic irrigant agent.}, }
@article {pmid30833723, year = {2019}, author = {Archer, SDJ and Lee, KC and Caruso, T and Maki, T and Lee, CK and Cary, SC and Cowan, DA and Maestre, FT and Pointing, SB}, title = {Airborne microbial transport limitation to isolated Antarctic soil habitats.}, journal = {Nature microbiology}, volume = {4}, number = {6}, pages = {925-932}, pmid = {30833723}, issn = {2058-5276}, mesh = {*Air Microbiology ; Antarctic Regions ; Biodiversity ; Climate Change ; *Ecosystem ; Microbiota/genetics ; Phylogeny ; Sequence Analysis, DNA ; Soil ; *Soil Microbiology ; }, abstract = {Dispersal is a critical yet poorly understood factor underlying macroecological patterns in microbial communities[1]. Airborne microbial transport is assumed to occupy a central role in determining dispersal outcomes[2,3], and extra-range dispersal has important implications for predicting ecosystem resilience and response to environmental change[4]. One of the most pertinent biomes in this regard is Antarctica, given its geographic isolation and vulnerability to climate change and human disturbance[5]. Here, we report microbial diversity in near-ground and high-altitude air above the largest ice-free Antarctic habitat, as well as that of underlying soil microbial communities. We found that persistent local airborne inputs were unable to fully explain Antarctic soil community assembly. Comparison with airborne microbial diversity from high-altitude and non-polar sources suggests that strong selection occurs during long-range atmospheric transport. The influence of selection during airborne transit and at sink locations varied between microbial phyla. Overall, the communities from this isolated Antarctic ecosystem displayed limited connectivity to the non-polar microbial pool, and alternative sources of recruitment are necessary to fully explain extant soil diversity. Our findings provide critical insights into the role of airborne transport limitation in determining microbial biogeographic patterns.}, }
@article {pmid30832740, year = {2019}, author = {Song, W and Wemheuer, B and Zhang, S and Steensen, K and Thomas, T}, title = {MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {36}, pmid = {30832740}, issn = {2049-2618}, mesh = {Bacteria/classification/*genetics ; Computational Biology/*methods ; Databases, Genetic ; Drug Resistance, Bacterial ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Metagenomics ; Phylogeny ; Soil Microbiology ; }, abstract = {BACKGROUND: Metagenomic datasets provide an opportunity to study horizontal gene transfer (HGT) on the level of a microbial community. However, current HGT detection methods cannot be applied to community-level datasets or require reference genomes. Here, we present MetaCHIP, a pipeline for reference-independent HGT identification at the community level.<br><br>RESULTS: Assessment of MetaCHIP's performance on simulated datasets revealed that it can predict HGTs with various degrees of genetic divergence from metagenomic datasets. The results also indicated that the detection of very recent gene transfers (i.e. those with low levels of genetic divergence) from metagenomics datasets is largely affected by the read assembly step. Comparison of MetaCHIP with a previous analysis on soil bacteria showed a high level of consistency for the prediction of recent HGTs and revealed a large number of additional non-recent gene transfers, which can provide new biological and ecological insight. Assessment of MetaCHIP's performance on real metagenomic datasets confirmed the role of HGT in the spread of genes related to antibiotic resistance in the human gut microbiome. Further testing also showed that functions related to energy production and conversion as well as carbohydrate transport and metabolism are frequently transferred among free-living microorganisms.<br><br>CONCLUSION: MetaCHIP provides an opportunity to study HGTs among members of a microbial community and therefore has several applications in the field of microbial ecology and evolution. MetaCHIP is implemented in Python and freely available at https://github.com/songweizhi/MetaCHIP .}, }
@article {pmid30827722, year = {2020}, author = {Kjølbæk, L and Benítez-Páez, A and Gómez Del Pulgar, EM and Brahe, LK and Liebisch, G and Matysik, S and Rampelli, S and Vermeiren, J and Brigidi, P and Larsen, LH and Astrup, A and Sanz, Y}, title = {Arabinoxylan oligosaccharides and polyunsaturated fatty acid effects on gut microbiota and metabolic markers in overweight individuals with signs of metabolic syndrome: A randomized cross-over trial.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {39}, number = {1}, pages = {67-79}, doi = {10.1016/j.clnu.2019.01.012}, pmid = {30827722}, issn = {1532-1983}, mesh = {Adolescent ; Adult ; Cross-Over Studies ; Diet/methods ; Dietary Fiber/*pharmacology ; Fatty Acids, Unsaturated/*pharmacology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Male ; Metabolic Syndrome/*metabolism/microbiology ; Middle Aged ; Oligosaccharides ; Overweight/*metabolism/microbiology ; Xylans/*pharmacology ; Young Adult ; }, abstract = {BACKGROUND &amp; AIMS: Gut microbiota composition is linked to obesity and metabolic syndrome. The nutrients and doses required to modulate the gut microbiota towards beneficially influence components of the metabolic syndrome are unclear. This study aimed to investigate diet-induced effects on the gut microbiota and metabolic markers in overweight individuals with indices of the metabolic syndrome.<br><br>METHODS: A twelve-week randomized cross-over trial was conducted with two intervention periods separated by a washout period. The dietary intakes of interest were wheat bran extract, rich in arabinoxylan oligosaccharides (AXOS) (10.4&#xa0;g/d AXOS) and polyunsaturated fatty acids (PUFA) (3.6&#xa0;g/d n-3 PUFA). Dietary records, fecal and blood samples, as well as anthropometric data, were collected before and after intervention. Anthropometry and gastrointestinal symptoms were evaluated weekly. Gut microbiota composition was analyzed by massive sequencing of 16S ribosomal RNA gene V3V4 amplicons.<br><br>RESULTS: Twenty-seven participants completed the study (90%). Intake of AXOS induced an expected bifidogenic effect on gut microbiota (p&#xa0;<&#xa0;0.01) and increased butyrate-producing bacterial species as well (p&#xa0;<&#xa0;0.05). Beta-diversity analysis indicated that the structure of the gut microbiota only changed as a result of the AXOS intervention (Permanova&#xa0;=&#xa0;1.90, p&#xa0;<&#xa0;0.02) and no changes in metabolic markers were observed after any of the interventions.<br><br>CONCLUSIONS: AXOS intake has a bifidogenic effect and also increases butyrate producers in the gut microbiota; even though this type of dietary fiber did not modulate lipid or glucose metabolic parameters related to metabolic syndrome. Four-week PUFA intake did not induce any notable effect on the gut microbiota composition or metabolic risk markers.<br><br>REGISTRATION: Registered under ClinicalTrials.gov Identifier no. NCT02215343.<br><br>CLINICAL TRIAL REGISTRATION: Registered at https://www.clinicaltrials.gov/ (NCT02215343).<br><br>ETHICAL COMMITTEE: H-4-2014-052.<br><br>2013-54-0522.}, }
@article {pmid30823725, year = {2019}, author = {Wang, LZ and Zhao, ZD and Jiang, J and Guo, BH and Wang, X and Huang, ZG and Lai, YC}, title = {A model for meme popularity growth in social networking systems based on biological principle and human interest dynamics.}, journal = {Chaos (Woodbury, N.Y.)}, volume = {29}, number = {2}, pages = {023136}, doi = {10.1063/1.5085009}, pmid = {30823725}, issn = {1089-7682}, mesh = {Humans ; *Internet ; *Models, Theoretical ; *Social Behavior ; *Social Media ; *Social Networking ; }, abstract = {We analyze five big data sets from a variety of online social networking (OSN) systems and find that the growth dynamics of meme popularity exhibit characteristically different behaviors. For example, there is linear growth associated with online recommendation and sharing platforms, a plateaued (or an "S"-shape) type of growth behavior in a web service devoted to helping users to collect bookmarks, and an exponential increase on the largest and most popular microblogging website in China. Does a universal mechanism with a common set of dynamical rules exist, which can explain these empirically observed, distinct growth behaviors? We provide an affirmative answer in this paper. In particular, inspired by biomimicry to take advantage of cell population growth dynamics in microbial ecology, we construct a base growth model for meme popularity in OSNs. We then take into account human factors by incorporating a general model of human interest dynamics into the base model. The final hybrid model contains a small number of free parameters that can be estimated purely from data. We demonstrate that our model is universal in the sense that, with a few parameters estimated from data, it can successfully predict the distinct meme growth dynamics. Our study represents a successful effort to exploit principles in biology to understand online social behaviors by incorporating the traditional microbial growth model into meme popularity. Our model can be used to gain insights into critical issues such as classification, robustness, optimization, and control of OSN systems.}, }
@article {pmid30822632, year = {2019}, author = {Ahmed, M and Lin, O and Saup, CM and Wilkins, MJ and Lin, LS}, title = {Effects of Fe/S ratio on the kinetics and microbial ecology of an Fe(III)-dosed anaerobic wastewater treatment system.}, journal = {Journal of hazardous materials}, volume = {369}, number = {}, pages = {593-600}, doi = {10.1016/j.jhazmat.2019.02.062}, pmid = {30822632}, issn = {1873-3336}, support = {OIA-1458952//National Science Foundation/International ; }, mesh = {Anaerobiosis ; Biological Oxygen Demand Analysis ; Bioreactors ; Desulfovibrio ; Fermentation ; Ferric Compounds/*analysis ; Geobacter ; Kinetics ; Oxidation-Reduction ; Sewage/analysis ; Sulfides/*analysis ; Waste Disposal, Fluid/*methods ; Wastewater/*analysis/*microbiology ; Water Microbiology ; }, abstract = {Effects of Fe(III)/sulfate (Fe/S) ratio on organic carbon oxidation kinetics and microbial ecology of a novel Fe(III)-dosed anaerobic wastewater treatment system were investigated in this study. Fixed-film batch bioreactors under three Fe/S molar ratios (1, 2, and 3) yielded COD oxidation rates that increased with the Fe/S ratio, and estimated Michaelis-Menten model parameters Vmax ranging in 0.47-1.09 mg/L⋅min and Km in 2503-3267 mg/L. Both iron and sulfate reducing bacteria contributed to the organics oxidation, and the produced sludge materials contained both biomass (32-45 wt.%) and inorganic precipitates from biogenic ferrous iron and sulfide (68-55 wt.%). Spectroscopic and chemical elemental analyses indicated that the inorganic fraction of the sludge materials contained both FeS and FeS2, and had Fe/S stoichiometric ratios close to 1. Microbiological analyses of the biofilm samples revealed that the major putative iron- and sulfate reducers were Geobacter sp. and Desulfovibrio sp. along with noticeable N-fixing and fermentative bacteria. The COD oxidation rate had a positive correlation with the relative abundance of iron reducers, and both increased with the Fe/S ratio. A conceptual framework was proposed to illustrate the effects of Fe/S ratio on organics oxidation rate, microbial ecology and their interplays.}, }
@article {pmid30820035, year = {2019}, author = {Callieri, C and Slabakova, V and Dzhembekova, N and Slabakova, N and Peneva, E and Cabello-Yeves, PJ and Di Cesare, A and Eckert, EM and Bertoni, R and Corno, G and Salcher, MM and Kamburska, L and Bertoni, F and Moncheva, S}, title = {The mesopelagic anoxic Black Sea as an unexpected habitat for Synechococcus challenges our understanding of global "deep red fluorescence".}, journal = {The ISME journal}, volume = {13}, number = {7}, pages = {1676-1687}, pmid = {30820035}, issn = {1751-7370}, mesh = {Black Sea ; Chlorophyll A/metabolism ; Ecosystem ; Fluorescence ; Genome, Bacterial ; Oceans and Seas ; Photosynthesis ; Phycoerythrin/metabolism ; Phylogeny ; Synechococcus/*chemistry/classification/*isolation &amp; purification/metabolism ; }, abstract = {The Black Sea is the largest meromictic sea with a reservoir of anoxic water extending from 100 to 1000 m depth. These deeper layers are characterised by a poorly understood fluorescence signal called "deep red fluorescence", a chlorophyll a- (Chl a) like signal found in deep dark oceanic waters. In two cruises, we repeatedly found up to 10[3] cells ml[-1] of picocyanobacteria at 750 m depth in these waters and isolated two phycoerythrin-rich Synechococcus sp. strains (BS55D and BS56D). Tests on BS56D revealed its high adaptability, involving the accumulation of Chl a in anoxic/dark conditions and its capacity to photosynthesise when re-exposed to light. Whole-genome sequencing of the two strains showed the presence of genes that confirms the putative ability of our strains to survive in harsh mesopelagic environments. This discovery provides new evidence to support early speculations associating the "deep red fluorescence" signal to viable picocyanobacteria populations in the deep oxygen-depleted oceans, suggesting a reconsideration of the ecological role of a viable stock of Synechococcus in dark deep waters.}, }
@article {pmid30818756, year = {2019}, author = {Dong, X and Lv, L and Wang, W and Liu, Y and Yin, C and Xu, Q and Yan, H and Fu, J and Liu, X}, title = {Differences in Distribution of Potassium-Solubilizing Bacteria in Forest and Plantation Soils in Myanmar.}, journal = {International journal of environmental research and public health}, volume = {16}, number = {5}, pages = {}, pmid = {30818756}, issn = {1660-4601}, mesh = {Bacteria/classification/isolation &amp; purification/*metabolism ; Biodiversity ; Fertilizers ; *Forests ; Hevea/growth &amp; development/metabolism/*microbiology ; Myanmar ; Potassium/*metabolism ; Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Potassium (K) has been recognized as an essential element in intensive agricultural production systems, and deficiency of K usually results in a decrease in crop yields. The utilization of potassium-solubilizing bacteria (KSB) to increase the soluble K content in soil has been regarded as a desirable pathway to increase plant yields. Following the inoculation of KSB in the soil, potassium can be released (in the form of K[+]) and consumed by plants. This study aims to investigate and compare the distribution characteristics of potassium-solubilizing bacteria between forest and plantation soils in Myanmar. In this study, 14 KSB strains were isolated from rhizosphere samples collected from forest soil, as well as fertilized rubber tree rhizosphere soil and fertilized bare soil from a plantation. Broadleaf forests with high levels of canopy cover mainly comprised the forest environment, and rubber trees were planted in the plantation environment. The Chao and abundance-based coverage estimator (ACE) indices showed that the microbial abundance of the plantation soil was higher than that of the forest soil. According to the Illumina MiSeq sequencing analysis results, the Shannon index of the forest soil was lower while the Simpson index was higher, which demonstrated that the microbial diversity of the forest soil was higher than that of the plantation soil. Potassium-solubilizing test results showed that the strains E, I, M, and N were the most effective KSB under liquid cultivation conditions. Additionally, KSB only accounted for less than 5.47% of the total bacteria detected in either of the sample types, and the distribution of dominant KSB varied with the soil samples. As another result, the abundance of Pseudomonas spp. in S1 was higher than in S2 and S3, indicating a negative impact on the growth of Pseudomonas in the fertilized rubber tree rhizosphere soil. The significance of our research is that it proves that the increasing use of KSB for restoring soil is a good way to reduce the use of chemical fertilizers, which could further provide a relatively stable environment for plant growth.}, }
@article {pmid30814983, year = {2019}, author = {Vandekerckhove, TGL and Bodé, S and De Mulder, C and Vlaeminck, SE and Boon, N}, title = {[13]C Incorporation as a Tool to Estimate Biomass Yields in Thermophilic and Mesophilic Nitrifying Communities.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {192}, pmid = {30814983}, issn = {1664-302X}, abstract = {Current methods determining biomass yield require sophisticated sensors for in situ measurements or multiple steady-state reactor runs. Determining the yield of specific groups of organisms in mixed cultures in a fast and easy manner remains challenging. This study describes a fast method to estimate the maximum biomass yield (Ymax), based on [13]C incorporation during activity measurements. It was applied to mixed cultures containing ammonia oxidizing bacteria (AOB) or archaea (AOA) and nitrite oxidizing bacteria (NOB), grown under mesophilic (15-28°C) and thermophilic (50°C) conditions. Using this method, no distinction could be made between AOB and AOA co-existing in a community. A slight overestimation of the nitrifier biomass due to [13]C redirection via SMP to heterotrophs could occur, meaning that this method determines the carbon fixation activity of the autotrophic microorganisms rather than the actual nitrifier biomass yield. Thermophilic AOA yields exceeded mesophilic AOB yields (0.22 vs. 0.06-0.11 g VSS g[-1] N), possibly linked to a more efficient pathway for CO2 incorporation. NOB thermophilically produced less biomass (0.025-0.028 vs. 0.048-0.051 g VSS g[-1] N), conceivably attributed to higher maintenance requirement, rendering less energy available for biomass synthesis. Interestingly, thermophilic nitrification yield was higher than its mesophilic counterpart, due to the dominance of AOA over AOB at higher temperatures. An instant temperature increase impacted the mesophilic AOB yield, corroborating the effect of maintenance requirement on production capacity. Model simulations of two realistic nitrification/denitrification plants were robust toward changing nitrifier yield in predicting effluent ammonium concentrations, whereas sludge composition was impacted. Summarized, a fast, precise and easily executable method was developed determining Ymax of ammonia and nitrite oxidizers in mixed communities.}, }
@article {pmid30811315, year = {2019}, author = {Ganin, H and Kemper, N and Meir, S and Rogachev, I and Ely, S and Massalha, H and Mandaby, A and Shanzer, A and Keren-Paz, A and Meijler, MM and Malitsky, S and Aharoni, A and Kolodkin-Gal, I}, title = {Indole Derivatives Maintain the Status Quo Between Beneficial Biofilms and Their Plant Hosts.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {32}, number = {8}, pages = {1013-1025}, doi = {10.1094/MPMI-12-18-0327-R}, pmid = {30811315}, issn = {0894-0282}, mesh = {*Bacillus subtilis/physiology ; Bacterial Proteins/genetics ; *Biofilms ; Host-Pathogen Interactions/drug effects/physiology ; *Indoles/chemistry/pharmacology ; Plant Roots/microbiology ; *Plants/microbiology ; }, abstract = {Biofilms formed by bacteria on plant roots play an important role in maintaining an optimal rhizosphere environment that supports plant growth and fitness. Bacillus subtilis is a potent plant growth promoter, forming biofilms that play a key role in protecting the host from fungal and bacterial infections. In this work, we demonstrate that the development of B. subtilis biofilms is antagonized by specific indole derivatives that accumulate during symbiotic interactions with plant hosts. Indole derivatives are more potent signals when the plant polysaccharide xylan serves as a carbon source, a mechanism to sustain beneficial biofilms at a biomass that can be supported by the plant. Moreover, B. subtilis biofilms formed by mutants resistant to indole derivatives become deleterious to the plants due to their capacity to consume and recycle plant polysaccharides. These results demonstrate how a dynamic metabolite-based dialogue can promote homeostasis between plant hosts and their beneficial biofilm communities.}, }
@article {pmid30809693, year = {2019}, author = {Zhang, Y and Zhang, LT and Li, ZD and Xin, CX and Li, XQ and Wang, X and Deng, YL}, title = {Microbiomes of China's Space Station During Assembly, Integration, and Test Operations.}, journal = {Microbial ecology}, volume = {78}, number = {3}, pages = {631-650}, pmid = {30809693}, issn = {1432-184X}, support = {31600404//National Natural Science Foundation of China/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; China ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Spacecraft/*statistics &amp; numerical data ; }, abstract = {Sufficient evidence indicates that orbiting space stations contain diverse microbial populations, which may threaten astronaut health and equipment reliability. Understanding the composition of microbial communities in space stations will facilitate further development of targeted biological safety prevention and maintenance practices. Therefore, this study systematically investigated the microbial community of China's Space Station (CSS). Air and surface samples from 46 sites on the CSS and Assembly Integration and Test (AIT) center were collected, from which 40 bacteria strains were isolated and identified. Most isolates were cold- and desiccation-resistant and adapted to oligotrophic conditions. Bacillus was the dominant bacterial genus detected by both cultivation-based and Illumina MiSeq amplicon sequencing methods. Microbial contamination on the CSS was correlated with encapsulation staff activities. Analysis by spread plate and qPCR revealed that the CSS surface contained 2.24 × 10[3]-5.47 × 10[3] CFU/100 cm[2] culturable bacteria and 9.32 × 10[5]-5.64 × 10[6] 16S rRNA gene copies/100cm[2]; BacLight™ analysis revealed that the viable/total bacterial cell ratio was 1.98-13.28%. This is the first study to provide important systematic insights into the microbiome of the CSS during assembly that describes the pre-launch microbial diversity of the space station. Our findings revealed the following. (1) Bacillus strains and staff activities should be considered major concerns for future biological safety. (2) Autotrophic and multi-resistant microbial communities were widespread in the AIT environment. Although harsh cleaning methods reduced the number of microorganisms, stress-resistant strains were not completely removed. (3) Sampling, storage and analytical methods for the space station were thoroughly optimized, and are expected to be applicable to low-biomass environments in general. Microbiology-related future works will follow up to comprehensively understand the changing characteristics of microbial communities in CSS.}, }
@article {pmid30809205, year = {2019}, author = {Marco, DE and Abram, F}, title = {Editorial: Using Genomics, Metagenomics and Other "Omics" to Assess Valuable Microbial Ecosystem Services and Novel Biotechnological Applications.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {151}, pmid = {30809205}, issn = {1664-302X}, }
@article {pmid30809011, year = {2019}, author = {Bouma-Gregson, K and Olm, MR and Probst, AJ and Anantharaman, K and Power, ME and Banfield, JF}, title = {Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network.}, journal = {The ISME journal}, volume = {13}, number = {6}, pages = {1618-1634}, pmid = {30809011}, issn = {1751-7370}, support = {S10 OD018174/OD/NIH HHS/United States ; }, mesh = {California ; Cyanobacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Cyanobacteria Toxins ; Lakes/microbiology ; Metagenomics ; Nitrogen/metabolism ; Phosphorus/metabolism ; Phylogeny ; Rivers/chemistry/*microbiology ; Tropanes/*metabolism ; }, abstract = {Blooms of planktonic cyanobacteria have long been of concern in lakes, but more recently, harmful impacts of riverine benthic cyanobacterial mats been recognized. As yet, we know little about how various benthic cyanobacteria are distributed in river networks, or how environmental conditions or other associated microbes in their consortia affect their biosynthetic capacities. We performed metagenomic sequencing for 22 Oscillatoriales-dominated (Cyanobacteria) microbial mats collected across the Eel River network in Northern California and investigated factors associated with anatoxin-a producing cyanobacteria. All microbial communities were dominated by one or two cyanobacterial species, so the key mat metabolisms involve oxygenic photosynthesis and carbon oxidation. Only a few metabolisms fueled the growth of the mat communities, with little evidence for anaerobic metabolic pathways. We genomically defined four cyanobacterial species, all which shared <96% average nucleotide identity with reference Oscillatoriales genomes and are potentially novel species in the genus Microcoleus. One of the Microcoleus species contained the anatoxin-a biosynthesis genes, and we describe the first anatoxin-a gene cluster from the Microcoleus clade within Oscillatoriales. Occurrence of these four Microcoleus species in the watershed was correlated with total dissolved nitrogen and phosphorus concentrations, and the species that contains the anatoxin-a gene cluster was found in sites with higher nitrogen concentrations. Microbial assemblages in mat samples with the anatoxin-a gene cluster consistently had a lower abundance of Burkholderiales (Betaproteobacteria) species than did mats without the anatoxin-producing genes. The associations of water nutrient concentrations and certain co-occurring microbes with anatoxin-a producing Microcoleus motivate further exploration for their roles as potential controls on the distributions of toxigenic benthic cyanobacteria in river networks.}, }
@article {pmid30808753, year = {2019}, author = {Ramírez-Flandes, S and González, B and Ulloa, O}, title = {Redox traits characterize the organization of global microbial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {9}, pages = {3630-3635}, pmid = {30808753}, issn = {1091-6490}, mesh = {Ecology ; *Ecosystem ; Humans ; *Metagenomics ; Microbiota/*genetics ; *Oxidation-Reduction ; Soil Microbiology ; }, abstract = {The structure of biological communities is conventionally described as profiles of taxonomic units, whose ecological functions are assumed to be known or, at least, predictable. In environmental microbiology, however, the functions of a majority of microorganisms are unknown and expected to be highly dynamic and collectively redundant, obscuring the link between taxonomic structure and ecosystem functioning. Although genetic trait-based approaches at the community level might overcome this problem, no obvious choice of gene categories can be identified as appropriate descriptive units in a general ecological context. We used 247 microbial metagenomes from 18 biomes to determine which set of genes better characterizes the differences among biomes on the global scale. We show that profiles of oxidoreductase genes support the highest biome differentiation compared with profiles of other categories of enzymes, general protein-coding genes, transporter genes, and taxonomic gene markers. Based on oxidoreductases' description of microbial communities, the role of energetics in differentiation and particular ecosystem function of different biomes become readily apparent. We also show that taxonomic diversity is decoupled from functional diversity, e.g., grasslands and rhizospheres were the most diverse biomes in oxidoreductases but not in taxonomy. Considering that microbes underpin biogeochemical processes and nutrient recycling through oxidoreductases, this functional diversity should be relevant for a better understanding of the stability and conservation of biomes. Consequently, this approach might help to quantify the impact of environmental stressors on microbial ecosystems in the context of the global-scale biome crisis that our planet currently faces.}, }
@article {pmid30808694, year = {2019}, author = {Feng, J and Penton, CR and He, Z and Van Nostrand, JD and Yuan, MM and Wu, L and Wang, C and Qin, Y and Shi, ZJ and Guo, X and Schuur, EAG and Luo, Y and Bracho, R and Konstantinidis, KT and Cole, JR and Tiedje, JM and Yang, Y and Zhou, J}, title = {Long-Term Warming in Alaska Enlarges the Diazotrophic Community in Deep Soils.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, pmid = {30808694}, issn = {2150-7511}, mesh = {Alaska ; *Biota ; *Global Warming ; Metagenomics ; Microarray Analysis ; *Nitrogen Fixation ; Oxidoreductases/genetics ; Plant Development ; *Soil Microbiology ; Tundra ; }, abstract = {Tundra ecosystems are typically carbon (C) rich but nitrogen (N) limited. Since biological N2 fixation is the major source of biologically available N, the soil N2-fixing (i.e., diazotrophic) community serves as an essential N supplier to the tundra ecosystem. Recent climate warming has induced deeper permafrost thaw and adversely affected C sequestration, which is modulated by N availability. Therefore, it is crucial to examine the responses of diazotrophic communities to warming across the depths of tundra soils. Herein, we carried out one of the deepest sequencing efforts of nitrogenase gene (nifH) to investigate how 5 years of experimental winter warming affects Alaskan soil diazotrophic community composition and abundance spanning both the organic and mineral layers. Although soil depth had a stronger influence on diazotrophic community composition than warming, warming significantly (P < 0.05) enhanced diazotrophic abundance by 86.3% and aboveground plant biomass by 25.2%. Diazotrophic composition in the middle and lower organic layers, detected by nifH sequencing and a microarray-based tool (GeoChip), was markedly altered, with an increase of α-diversity. Changes in diazotrophic abundance and composition significantly correlated with soil moisture, soil thaw duration, and plant biomass, as shown by structural equation modeling analyses. Therefore, more abundant diazotrophic communities induced by warming may potentially serve as an important mechanism for supplementing biologically available N in this tundra ecosystem.IMPORTANCE With the likelihood that changes in global climate will adversely affect the soil C reservoir in the northern circumpolar permafrost zone, an understanding of the potential role of diazotrophic communities in enhancing biological N2 fixation, which constrains both plant production and microbial decomposition in tundra soils, is important in elucidating the responses of soil microbial communities to global climate change. A recent study showed that the composition of the diazotrophic community in a tundra soil exhibited no change under a short-term (1.5-year) winter warming experiment. However, it remains crucial to examine whether the lack of diazotrophic community responses to warming is persistent over a longer time period as a possibly important mechanism in stabilizing tundra soil C. Through a detailed characterization of the effects of winter warming on diazotrophic communities, we showed that a long-term (5-year) winter warming substantially enhanced diazotrophic abundance and altered community composition, though soil depth had a stronger influence on diazotrophic community composition than warming. These changes were best explained by changes in soil moisture, soil thaw duration, and plant biomass. These results provide crucial insights into the potential factors that may impact future C and N availability in tundra regions.}, }
@article {pmid30806729, year = {2019}, author = {Neupane, S and Modry, D and Pafčo, B and Zurek, L}, title = {Bacterial Community of the Digestive Tract of the European Medicinal Leech (Hirudo verbana) from the Danube River.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {1082-1090}, pmid = {30806729}, issn = {1432-184X}, mesh = {Animals ; Bacteria/*classification/genetics ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Leeches/*microbiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Rivers ; Romania ; }, abstract = {The digestive tract of medicinal leeches from commercial suppliers has been investigated previously and comprises of a relatively simple bacterial community. However, the microbiome of medicinal leeches collected directly from the natural habitat has not been examined. In this study, we characterized the bacterial community in the digestive tract (anterior crop, posterior crop, and intestine) of the European medicinal leech, Hirudo verbana, collected from the Danube river using culture-independent and culture-dependent approaches. Culture-independent approach confirmed that the digestive tract of H. verbana carries a relatively simple bacterial community with species richness in the individual samples ranging from 43 to164. The dominant bacterial taxon was Mucinivorans sp. (49.7% of total reads), followed by Aeromonas sp. (18.7% of total reads). Several low abundance taxa, new for H. verbana, such as Phreatobacter, Taibaiella, Fluviicola, Aquabacterium, Burkholderia, Hydrogenophaga, Wolinella, and unidentified Chitinophagia, were also detected. The aerobic culturing approach showed Aeromonas veronii (Proteobacteria), the known leech symbiont, as the most dominant taxon followed by several Pseudomonas and Acidovorax spp. No significant differences in the bacterial community composition were detected among different parts of the digestive tract of individual leeches. However, the overall composition of the bacterial community among individual specimen varied significantly and this is possibly due to differences in leech age, feeding status, and blood source. Our results showed that the core bacterial community of H. verbana collected from the natural habitat is similar to that reported from the digestive tract of commercially supplied leeches maintained in the laboratory.}, }
@article {pmid30804920, year = {2019}, author = {Luo, Z and Liu, J and Zhao, P and Jia, T and Li, C and Chai, B}, title = {Biogeographic Patterns and Assembly Mechanisms of Bacterial Communities Differ Between Habitat Generalists and Specialists Across Elevational Gradients.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {169}, pmid = {30804920}, issn = {1664-302X}, abstract = {A core issue in microbial ecology is the need to elucidate the ecological processes and underlying mechanisms involved in microbial community assembly. However, the extent to which these mechanisms differ in importance based on traits of taxa with different niche breadth is poorly understood. Here, we used high-throughput sequencing to examine the relative importance of environmental selection and stochastic processes in shaping soil bacterial sub-communities with different niche breadth (including habitat generalists, specialists and other taxa) across elevational gradients on the subalpine slope of Mount Wutai, Northern China. Our findings suggested that the composition of soil bacterial communities differed significantly different among elevational gradients. According to the niche breadth index, 10.9% of OTUs were defined as habitat generalists (B-value >8.7) and 10.0% of OTUs were defined as habitat specialists (B-value <1.5). Generalists and specialists differed distinctly in diversity and biogeographic patterns across elevational gradients. Environmental selection (deterministic processes) and spatial factors (stochastic processes) seemed to determine the assembly and biogeography of habitat generalists. However, for specialists, deterministic processes strongly influenced the distribution, while stochastic processes were not at play. Environmental drivers for generalists and specialists differed, as did their importance. Elevation, total nitrogen and pH were the main factors determining habitat generalists, and soil water content, nitrate nitrogen and pH had the strongest impacts on specialists. Moreover, variation partitioning analysis revealed that environmental selection had a much greater impact on both generalists (17.7% of pure variance was explained) and specialists (3.6%) than spatial factors. However, generalists had a much stronger response to spatial factors (2.3%) than specialists (0.3%). More importantly, null models of β-diversity suggested that specialists deviated significantly from non-neutral assembly mechanisms (relative null deviation= 0.64-0.74) relative to generalists (0.16-0.65) (P < 0.05). These results indicate that generalists and specialists are governed by different assembly mechanisms and present distinct biogeographical patterns. The large proportion of unexplained variation in specialists (93.3%) implies that very complex assembly mechanisms exist in the assembly of specialists across elevational gradients on the subalpine slope of Mount Wutai. It is essential to understand the microbial community assembly at a more refined level, and to expand the current understanding of microbial ecological mechanisms.}, }
@article {pmid30804907, year = {2019}, author = {Ghosh, P and Sinha, R and Samanta, P and Saha, DR and Koley, H and Dutta, S and Okamoto, K and Ghosh, A and Ramamurthy, T and Mukhopadhyay, AK}, title = {Haitian Variant Vibrio cholerae O1 Strains Manifest Higher Virulence in Animal Models.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {111}, pmid = {30804907}, issn = {1664-302X}, abstract = {Vibrio cholerae causes fatal diarrheal disease cholera in humans due to consumption of contaminated water and food. To instigate the disease, the bacterium must evade the host intestinal innate immune system; penetrate the mucus layer of the small intestine, adhere and multiply on the surface of microvilli and produce toxin(s) through the action of virulence associated genes. V. cholerae O1 that has caused a major cholera outbreak in Haiti contained several unique genetic signatures. These novel traits are used to differentiate them from the canonical El Tor strains. Several studies reported the spread of these Haitian variant strains in different parts of the world including Asia and Africa, but there is a paucity of information on the clinical consequence of these genetic changes. To understand the impact of these changes, we undertook a study involving mice and rabbit models to evaluate the pathogenesis. The colonization ability of Haitian variant strain in comparison to canonical El Tor strain was found to be significantly more in both suckling mice and rabbit model. Adult mice also displayed the same results. Besides that, infection patterns of Haitian variant strains showed a completely different picture. Increased mucosal damaging, colonization, and inflammatory changes were observed through hematoxylin-eosin staining and transmission electron microscopy. Fluid accumulation ability was also significantly higher in rabbit model. Our study indicated that these virulence features of the Haitian variant strain may have some association with the severe clinical outcome of the cholera patients in different parts of the world.}, }
@article {pmid30804904, year = {2019}, author = {Filippidou, S and Junier, T and Wunderlin, T and Kooli, WM and Palmieri, I and Al-Dourobi, A and Molina, V and Lienhard, R and Spangenberg, JE and Johnson, SL and Chain, PSG and Dorador, C and Junier, P}, title = {Adaptive Strategies in a Poly-Extreme Environment: Differentiation of Vegetative Cells in Serratia ureilytica and Resistance to Extreme Conditions.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {102}, pmid = {30804904}, issn = {1664-302X}, abstract = {Poly-extreme terrestrial habitats are often used as analogs to extra-terrestrial environments. Understanding the adaptive strategies allowing bacteria to thrive and survive under these conditions could help in our quest for extra-terrestrial planets suitable for life and understanding how life evolved in the harsh early earth conditions. A prime example of such a survival strategy is the modification of vegetative cells into resistant resting structures. These differentiated cells are often observed in response to harsh environmental conditions. The environmental strain (strain Lr5/4) belonging to Serratia ureilytica was isolated from a geothermal spring in Lirima, Atacama Desert, Chile. The Atacama Desert is the driest habitat on Earth and furthermore, due to its high altitude, it is exposed to an increased amount of UV radiation. The geothermal spring from which the strain was isolated is oligotrophic and the temperature of 54°C exceeds mesophilic conditions (15 to 45°C). Although the vegetative cells were tolerant to various environmental insults (desiccation, extreme pH, glycerol), a modified cell type was formed in response to nutrient deprivation, UV radiation and thermal shock. Scanning (SEM) and Transmission Electron Microscopy (TEM) analyses of vegetative cells and the modified cell structures were performed. In SEM, a change toward a circular shape with reduced size was observed. These circular cells possessed what appears as extra coating layers under TEM. The resistance of the modified cells was also investigated, they were resistant to wet heat, UV radiation and desiccation, while vegetative cells did not withstand any of those conditions. A phylogenomic analysis was undertaken to investigate the presence of known genes involved in dormancy in other bacterial clades. Genes related to spore-formation in Myxococcus and Firmicutes were found in S. ureilytica Lr5/4 genome; however, these genes were not enough for a full sporulation pathway that resembles either group. Although, the molecular pathway of cell differentiation in S. ureilytica Lr5/4 is not fully defined, the identified genes may contribute to the modified phenotype in the Serratia genus. Here, we show that a modified cell structure can occur as a response to extremity in a species that was previously not known to deploy this strategy. This strategy may be widely spread in bacteria, but only expressed under poly-extreme environmental conditions.}, }
@article {pmid30803810, year = {2019}, author = {Puozaa, DK and Jaiswal, SK and Dakora, FD}, title = {Phylogeny and distribution of Bradyrhizobium symbionts nodulating cowpea (Vigna unguiculata L. Walp) and their association with the physicochemical properties of acidic African soils.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {3}, pages = {403-414}, pmid = {30803810}, issn = {1618-0984}, mesh = {Bradyrhizobium/*classification/genetics/*growth &amp; development/physiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Genes, Essential/genetics ; Genetic Variation ; Ghana ; Hydrogen-Ion Concentration ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; South Africa ; *Symbiosis/genetics ; Vigna/*microbiology ; }, abstract = {In the N2-fixing symbiosis, the choice of a symbiotic partner is largely influenced by the host plant, the rhizobial symbiont, as well as soil factors. Understanding the soil environment conducive for the survival and multiplication of root-nodule bacteria is critical for microbial ecology. In this study, we collected cowpea-nodules from acidic soils in Ghana and South Africa, and nodule DNA isolates were characterized using 16S-23S rRNA-RFLP, phylogenetic analysis of housekeeping and symbiotic genes, and bradyrhizobial community structure through canonical correspondence analysis (CCA). The CCA ordination plot results showed that arrow of soil pH was overlapping on CCA2 axis and was the most important to the ordination. The test nodule DNA isolates from Ghana were positively influenced by soil Zn, Na and K while nodule DNA isolates from South Africa were influenced by P. The amplified 16S-23S rRNA region yielded single polymorphic bands of varying lengths (573-1298bp) that were grouped into 28 ITS types. The constructed ITS-dendrogram placed all the nodule DNA isolates in five major clusters at low cut-off of approx. 0.1 Jaccard's similarity coefficient. The phylogenetic analysis of 16S rRNA and housekeeping genes (glnII, gyrB, and atpD) formed distinct Bradyrhizobium groups in the phylogenetic trees. It revealed the presence of highly diverse bradyrhizobia (i.e. Bradyrhizobium vignae, Bradyrhizobium elkanii, Bradyrhizobium iriomotense, Bradyrhizobium pachyrhizi, and Bradyrhizobium yuanmingense) together with novel/unidentified bradyrhizobia in the acidic soils from Ghana and South Africa. Discrepancies noted in the phylogenies of some nodule DNA isolates could be attributed to horizontal gene transfer or recombination.}, }
@article {pmid30802335, year = {2019}, author = {Sáenz, JS and Roldan, F and Junca, H and Arbeli, Z}, title = {Effect of the extraction and purification of soil DNA and pooling of PCR amplification products on the description of bacterial and archaeal communities.}, journal = {Journal of applied microbiology}, volume = {126}, number = {5}, pages = {1454-1467}, doi = {10.1111/jam.14231}, pmid = {30802335}, issn = {1365-2672}, support = {//Pontificia Universidad Javeriana/ ; }, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *DNA, Archaeal/genetics/isolation &amp; purification ; *DNA, Bacterial/genetics/isolation &amp; purification ; Polymerase Chain Reaction ; *Soil Microbiology ; }, abstract = {AIMS: This study evaluated the effects of DNA extraction method, DNA purification and pooling of PCR amplification products on the description of bacterial and archaeal diversity.<br><br>METHODS AND RESULTS: Soil DNA was extracted by the Power Soil DNA extraction kit and a customized Griffiths' protocol. Both methods are based on cell disruption by bead beating. In total, we used three soils and six independent extractions from each soil obtained by each of the two methods. Then, three of the six extracts of each treatment were further purified by spin columns filled with Sepharose 2B and polyvinylpolypyrrolidone (PVPP). The V4 hypervariable region of the 16S rRNA gene was amplified from each extract using the 515F/806R primer pair in four independent reactions. Three amplification products were combined and sequenced as a pooled sample, while the additional amplification product was sequenced individually. The resulting 72 amplification products were sequenced by Illumina MiSeq platform. DNA extraction method had a statistically significant effect on the estimation of the composition of microbial communities that might overwhelm differences in microbial communities from distinct soils. On the other hand, a further DNA purification step or pooling of PCR amplification products had a minor effect on the description of bacterial and archaeal communities.<br><br>CONCLUSIONS: DNA extraction had the strongest effect on the description of bacterial and archaeal communities; low concentration of impurities, which allow PCR amplification, can still generate a minor additional bias, while PCR stochastic variability had the lowest effect.<br><br>Although it is well known that methodological factors affect the description of microbial communities, the relative importance of each step is still unknown. The present study determined that of the factors tested, the DNA extraction method had the strongest effects on the description of bacterial and archaeal communities.}, }
@article {pmid30800101, year = {2019}, author = {Dang, H and Klotz, MG and Lovell, CR and Sievert, SM}, title = {Editorial: The Responses of Marine Microorganisms, Communities and Ecofunctions to Environmental Gradients.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {115}, pmid = {30800101}, issn = {1664-302X}, }
@article {pmid30797477, year = {2019}, author = {Singh, NS and Sharma, R and Singh, DK}, title = {Identification of enzyme(s) capable of degrading endosulfan and endosulfan sulfate using in silico techniques.}, journal = {Enzyme and microbial technology}, volume = {124}, number = {}, pages = {32-40}, doi = {10.1016/j.enzmictec.2019.01.003}, pmid = {30797477}, issn = {1879-0909}, mesh = {Bacillus subtilis/enzymology/metabolism ; Bacterial Proteins/metabolism ; Basidiomycota/enzymology/growth &amp; development/*metabolism ; Biodegradation, Environmental ; Databases, Protein ; Endosulfan/*analogs &amp; derivatives/*metabolism ; Fungal Proteins/metabolism ; Insecticides/*metabolism ; Laccase/metabolism ; Mixed Function Oxygenases/antagonists &amp; inhibitors/*metabolism ; *Molecular Docking Simulation ; }, abstract = {Endosulfan is one of the most widely used organochlorine cyclodiene insecticides. Microbial oxidation of endosulfan forms endosulfan sulfate, which is more or less toxic and persistent as endosulfan. Due to lack of specificity and efficiency of microbial bioremediation technique in the field conditions, enzymatic bioremediation is receiving huge attention to clean-up the environment. In the present study, X-ray crystal structures of enzymes from Brookhaven Protein Data Bank were screened for their potential to degrade endosulfan and endosulfan sulfate using molecular docking and molecular dynamics simulation techniques. A phenol hydroxylase, 1PN0 from Trichosporon cutaneum was found to have the potential to degrade both α-endosulfan and endosulfan sulfate while a bacterial CotA laccase, 3ZDW from Bacillus subtilis has the potential to degrade α-endosulfan. The in silico result correlate with in vitro degradation study using two different strains of Trichosporon cutaneum. In vitro degradation study found that the fungal strain was capable of degrading 60.36% α-endosulfan, 70.73% β-endosulfan, and 52.08% endosulfan sulfate. The presence of phenol hydroxylase inhibitor in the sulfur-free medium with endosulfan and endosulfan sulfate as sole sulfur source inhibits the growth of both the fungal strains. Such in silico techniques can provide an easy and reliable way to speed up the development of bioremediation processes through rapid identification of potential enzymes and microbes to counter the ever-increasing number of toxic compounds in the environment.}, }
@article {pmid30796503, year = {2020}, author = {Lebre, PH and Cowan, DA}, title = {Genomics of Alkaliphiles.}, journal = {Advances in biochemical engineering/biotechnology}, volume = {172}, number = {}, pages = {135-155}, doi = {10.1007/10_2018_83}, pmid = {30796503}, issn = {0724-6145}, mesh = {Archaea ; Bacteria ; *Extremophiles/genetics ; *Genomics ; *Microbiota ; }, abstract = {Alkalinicity presents a challenge for life due to a "reversed" proton gradient that is unfavourable to many bioenergetic processes across the membranes of microorganisms. Despite this, many bacteria, archaea, and eukaryotes, collectively termed alkaliphiles, are adapted to life in alkaline ecosystems and are of great scientific and biotechnological interest due to their niche specialization and ability to produce highly stable enzymes. Advances in next-generation sequencing technologies have propelled not only the genomic characterization of many alkaliphilic microorganisms that have been isolated from nature alkaline sources but also our understanding of the functional relationships between different taxa in microbial communities living in these ecosystems. In this review, we discuss the genetics and molecular biology of alkaliphiles from an "omics" point of view, focusing on how metagenomics and transcriptomics have contributed to our understanding of these extremophiles. Graphical Abstract.}, }
@article {pmid30796467, year = {2019}, author = {Schlatter, DC and Paul, NC and Shah, DH and Schillinger, WF and Bary, AI and Sharratt, B and Paulitz, TC}, title = {Biosolids and Tillage Practices Influence Soil Bacterial Communities in Dryland Wheat.}, journal = {Microbial ecology}, volume = {78}, number = {3}, pages = {737-752}, pmid = {30796467}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Fertilizers/analysis ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; Triticum/growth &amp; development/*microbiology ; Washington ; }, abstract = {Class B biosolids are used in dryland wheat (Triticum aestivum L.) production in eastern Washington as a source of nutrients and to increase soil organic matter, but little is known about their effects on bacterial communities and potential for harboring human pathogens. Moreover, conservation tillage is promoted to reduce erosion and soil degradation. We explored the impacts of biosolids or synthetic fertilizer in combination with traditional (conventional) or conservation tillage on soil bacterial communities. Bacterial communities were characterized from fresh biosolids, biosolid aggregates embedded in soil, and soil after a second application of biosolids using high-throughput amplicon sequencing. Biosolid application significantly affected bacterial communities, even 4 years after their application. Bacteria in the families Clostridiaceae, Norcardiaceae, Anaerolinaceae, Dietziaceae, and Planococcaceae were more abundant in fresh biosolids, biosolid aggregates, and soils treated with biosolids than in synthetically fertilized soils. Taxa identified as Turcibacter, Dietzia, Clostridiaceae, and Anaerolineaceae were highly abundant in biosolid aggregates in the soil and likely originated from the biosolids. In contrast, Oxalobacteriaceae, Streptomyceteaceae, Janthinobacterium, Pseudomonas, Kribbella, and Bacillus were rare in the fresh biosolids, but relatively abundant in biosolid aggregates in the soil, and probably originated from the soil to colonize the substrate. However, tillage had relatively minor effects on bacterial communities, with only a small number of taxa differing in relative abundance between traditional and conventional tillage. Although biosolid-associated bacteria persisted in soil, potentially pathogenic taxa were extremely rare and no toxin genes for key groups (Salmonella, Clostridium) were detectable, suggesting that although fecal contamination was apparent via indicator taxa, pathogen populations had declined to low levels. Thus, biosolid amendments had profound effects on soil bacterial communities both by introducing gut- or digester-derived bacteria and by enriching potentially beneficial indigenous soil populations.}, }
@article {pmid30796063, year = {2019}, author = {Heyse, J and Buysschaert, B and Props, R and Rubbens, P and Skirtach, AG and Waegeman, W and Boon, N}, title = {Coculturing Bacteria Leads to Reduced Phenotypic Heterogeneities.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {8}, pages = {}, pmid = {30796063}, issn = {1098-5336}, mesh = {*Axenic Culture ; Bacteria/genetics/*growth &amp; development ; *Bacterial Physiological Phenomena ; Biodiversity ; *Coculture Techniques ; DNA, Bacterial ; Ecosystem ; Enterobacter/genetics/growth &amp; development/physiology ; Environment ; Environmental Microbiology ; Flow Cytometry ; Genetic Heterogeneity ; Microbial Interactions/*physiology ; Phenotype ; Pseudomonas/genetics/growth &amp; development/physiology ; Virulence ; }, abstract = {Isogenic bacterial populations are known to exhibit phenotypic heterogeneity at the single-cell level. Because of difficulties in assessing the phenotypic heterogeneity of a single taxon in a mixed community, the importance of this deeper level of organization remains relatively unknown for natural communities. In this study, we have used membrane-based microcosms that allow the probing of the phenotypic heterogeneity of a single taxon while interacting with a synthetic or natural community. Individual taxa were studied under axenic conditions, as members of a coculture with physical separation, and as a mixed culture. Phenotypic heterogeneity was assessed through both flow cytometry and Raman spectroscopy. Using this setup, we investigated the effect of microbial interactions on the individual phenotypic heterogeneities of two interacting drinking water isolates. Through flow cytometry we have demonstrated that interactions between these bacteria lead to a reduction of their individual phenotypic diversities and that this adjustment is conditional on the bacterial taxon. Single-cell Raman spectroscopy confirmed a taxon-dependent phenotypic shift due to the interaction. In conclusion, our data suggest that bacterial interactions may be a general driver of phenotypic heterogeneity in mixed microbial populations.IMPORTANCE Laboratory studies have shown the impact of phenotypic heterogeneity on the survival and functionality of isogenic populations. Because phenotypic heterogeneity plays an important role in pathogenicity and virulence, antibiotic resistance, biotechnological applications, and ecosystem properties, it is crucial to understand its influencing factors. An unanswered question is whether bacteria in mixed communities influence the phenotypic heterogeneity of their community partners. We found that coculturing bacteria leads to a reduction in their individual phenotypic heterogeneities, which led us to the hypothesis that the individual phenotypic diversity of a taxon is dependent on the community composition.}, }
@article {pmid30793041, year = {2019}, author = {Lee, CK and Laughlin, DC and Bottos, EM and Caruso, T and Joy, K and Barrett, JE and Brabyn, L and Nielsen, UN and Adams, BJ and Wall, DH and Hopkins, DW and Pointing, SB and McDonald, IR and Cowan, DA and Banks, JC and Stichbury, GA and Jones, I and Zawar-Reza, P and Katurji, M and Hogg, ID and Sparrow, AD and Storey, BC and Allan Green, TG and Cary, SC}, title = {Biotic interactions are an unexpected yet critical control on the complexity of an abiotically driven polar ecosystem.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {62}, pmid = {30793041}, issn = {2399-3642}, mesh = {Animals ; Antarctic Regions ; Arthropods/classification/*physiology ; Biodiversity ; Cyanobacteria/classification/*physiology ; Ecosystem ; Fungi/classification/*physiology ; Models, Statistical ; Nematoda/classification/*physiology ; Rotifera/classification/*physiology ; Tardigrada/classification/*physiology ; }, abstract = {Abiotic and biotic factors control ecosystem biodiversity, but their relative contributions remain unclear. The ultraoligotrophic ecosystem of the Antarctic Dry Valleys, a simple yet highly heterogeneous ecosystem, is a natural laboratory well-suited for resolving the abiotic and biotic controls of community structure. We undertook a multidisciplinary investigation to capture ecologically relevant biotic and abiotic attributes of more than 500 sites in the Dry Valleys, encompassing observed landscape heterogeneities across more than 200 km[2]. Using richness of autotrophic and heterotrophic taxa as a proxy for functional complexity, we linked measured variables in a parsimonious yet comprehensive structural equation model that explained significant variations in biological complexity and identified landscape-scale and fine-scale abiotic factors as the primary drivers of diversity. However, the inclusion of linkages among functional groups was essential for constructing the best-fitting model. Our findings support the notion that biotic interactions make crucial contributions even in an extremely simple ecosystem.}, }
@article {pmid30792823, year = {2019}, author = {Wu, CH and Ko, JL and Liao, JM and Huang, SS and Lin, MY and Lee, LH and Chang, LY and Ou, CC}, title = {D-methionine alleviates cisplatin-induced mucositis by restoring the gut microbiota structure and improving intestinal inflammation.}, journal = {Therapeutic advances in medical oncology}, volume = {11}, number = {}, pages = {1758835918821021}, pmid = {30792823}, issn = {1758-8340}, abstract = {BACKGROUND: There are close links between chemotherapy-induced intestinal mucositis and microbiota dysbiosis. Previous studies indicated that D-methionine was an excellent candidate for a chemopreventive agent. Here, we investigated the effects of D-methionine on cisplatin-induced mucositis.<br><br>MATERIALS AND METHODS: Male Wistar rats (176-200 g, 6 weeks old) were given cisplatin (5 mg/kg) and treated with D-methionine (300 mg/kg). Histopathological, digestive enzymes activity, oxidative/antioxidant status, proinflammatory/anti-inflammatory cytokines in intestinal tissues were measured. Next-generation sequencing technologies were also performed to investigate the gut microbial ecology.<br><br>RESULTS: D-methionine administration increased villus length and crypt depth and improved digestive enzyme (leucine aminopeptidase, sucrose and alkaline phosphatase) activities in the brush-border membrane of cisplatin-treated rats (p < 0.05). Furthermore, D-methionine significantly attenuated oxidative stress and inflammatory reaction and increased interleukin-10 levels in cisplatin-induced intestinal mucositis (p < 0.05). Cisplatin administration resulted in high relative abundances of Deferribacteres and Proteobacteria and a low diversity of the microbiota when compared with control groups, D-methionine only and cisplatin plus D-methionine. Cisplatin markedly increased comparative abundances of Bacteroides caccae, Escherichia coli, Mucispirillum schaedleri, Bacteroides uniformis and Desulfovibrio C21-c20, while Lactobacillus was almost completely depleted, compared with the control group. There were higher abundances of Lactobacillus, Lachnospiraceae, and Clostridium butyrium in cisplatin plus D-methionine rats than in cisplatin rats. D-methionine treatment alone significantly increased the number of Lactobacillus reuteri.<br><br>CONCLUSION: D-methionine protects against cisplatin-induced intestinal damage through antioxidative and anti-inflammatory effects. By enhancing growth of beneficial bacteria (Lachnospiraceae and Lactobacillus), D-methionine attenuates gut microbiome imbalance caused by cisplatin and maintains gut homeostasis.}, }
@article {pmid30792705, year = {2019}, author = {Trigodet, F and Larché, N and Morrison, HG and Jebbar, M and Thierry, D and Maignien, L}, title = {Electroactive Bacteria Associated With Stainless Steel Ennoblement in Seawater.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {170}, pmid = {30792705}, issn = {1664-302X}, abstract = {Microorganisms can increase the open-circuit potential of stainless steel immersed in seawater of several hundred millivolts in a phenomenon called ennoblement. It raises the chance of corrosion as the open-circuit potential may go over the pitting corrosion potential. Despite the large impact of the ennoblement, no unifying mechanisms have been described as responsible for the phenomenon. Here we show that the strict electrotroph bacterium "Candidatus Tenderia electrophaga" is detected as an ennoblement biomarker and is only present at temperatures at which we observe ennoblement. This bacterium was previously enriched in biocathode systems. Our results suggest that "Candidatus Tenderia electrophaga," and its previously described extracellular electron transfer metabolism coupled to oxygen reduction activity, could play a central role in modulating stainless steel open-circuit potential and consequently mediating ennoblement.}, }
@article {pmid30792076, year = {2019}, author = {Álvarez-Pérez, S and Lievens, B and Fukami, T}, title = {Yeast-Bacterium Interactions: The Next Frontier in Nectar Research.}, journal = {Trends in plant science}, volume = {24}, number = {5}, pages = {393-401}, doi = {10.1016/j.tplants.2019.01.012}, pmid = {30792076}, issn = {1878-4372}, mesh = {Bacteria ; *Flowers ; *Plant Nectar ; Pollination ; Yeasts ; }, abstract = {Beyond its role as a reward for pollinators, floral nectar also provides a habitat for specialized and opportunistic yeasts and bacteria. These microbes modify nectar chemistry, often altering mutualistic relationships between plants and pollinators in ways that we are only beginning to understand. Many studies on this multi-partite system have focused on either yeasts or bacteria without consideration of yeast-bacterium interactions, but recent evidence suggests that such interactions drive the assembly of nectar microbial communities and its consequences for pollination. Unexplored potential mechanisms of yeast-bacterium interactions include the formation of physical complexes, nutritional interactions, antibiosis, signaling-based interactions, and horizontal gene transfer. We argue that studying these mechanisms can elucidate how nectar microbial communities are established and affect plant fitness via pollinators.}, }
@article {pmid30789995, year = {2019}, author = {Martinez, AFC and de Almeida, LG and Moraes, LAB and Cônsoli, FL}, title = {Microbial Diversity and Chemical Multiplicity of Culturable, Taxonomically Similar Bacterial Symbionts of the Leaf-Cutting Ant Acromyrmex coronatus.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {1067-1081}, pmid = {30789995}, issn = {1432-184X}, support = {2011/50877-0//Funda??o de Amparo ? Pesquisa do Estado de S?o Paulo/ ; 2014/21584-3//Funda??o de Amparo ? Pesquisa do Estado de S?o Paulo/ ; }, mesh = {Animals ; Ants/*microbiology ; Bacteria/*chemistry/*classification ; Bacterial Physiological Phenomena ; Brazil ; Chromatography, Liquid ; *Microbiota ; *Symbiosis ; Tandem Mass Spectrometry ; }, abstract = {Insects are a highly diverse group, exploit a wide range of habitats, and harbor bacterial symbionts of largely unknown diversity. Insect-associated bacterial symbionts are underexplored but promising sources of bioactive compounds. The community of culturable bacteria associated with the leaf-cutting ant Acromyrmex coronatus (Fabricius) and the diversity of their metabolites produced were investigated. Forty-six phylotypes belonging to Actinobacteria, Firmicutes, and Proteobacteria were identified. The chemical profiles of 65 isolates were further analyzed by LC-MS/MS, and principal components analysis (PCA) was used to group the isolates according to their chemical profiles. Historically, selection of bacterial strains for drug discovery has been based on phenotypic and/or genotypic traits. Use of such traits may well impede the discovery of new compounds; in this study, several indistinguishable phylotypes cultured in identical nutritional and environmental conditions produced completely different chemical profiles. Our data also demonstrated the wide chemical diversity to be explored in insect-associated symbionts.}, }
@article {pmid30787397, year = {2019}, author = {Mansfeldt, C and Achermann, S and Men, Y and Walser, JC and Villez, K and Joss, A and Johnson, DR and Fenner, K}, title = {Microbial residence time is a controlling parameter of the taxonomic composition and functional profile of microbial communities.}, journal = {The ISME journal}, volume = {13}, number = {6}, pages = {1589-1601}, pmid = {30787397}, issn = {1751-7370}, support = {614768/ERC_/European Research Council/International ; }, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Bioreactors/microbiology ; DNA, Bacterial/genetics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; Wastewater/microbiology ; }, abstract = {A remaining challenge within microbial ecology is to understand the determinants of richness and diversity observed in environmental microbial communities. In a range of systems, including activated sludge bioreactors, the microbial residence time (MRT) has been previously shown to shape the microbial community composition. However, the physiological and ecological mechanisms driving this influence have remained unclear. Here, this relationship is explored by analyzing an activated sludge system fed with municipal wastewater. Using a model designed in this study based on Monod-growth kinetics, longer MRTs were shown to increase the range of growth parameters that enable persistence, resulting in increased richness and diversity in the modeled community. In laboratory experiments, six sequencing batch reactors treating domestic wastewater were operated in parallel at MRTs between 1 and 15 days. The communities were characterized using both 16S ribosomal RNA and non-target messenger RNA sequencing (metatranscriptomic analysis), and model-predicted monotonic increases in richness were confirmed in both profiles. Accordingly, taxonomic Shannon diversity also increased with MRT. In contrast, the diversity in enzyme class annotations resulting from the metatranscriptomic analysis displayed a non-monotonic trend over the MRT gradient. Disproportionately high abundances of transcripts encoding for rarer enzymes occur at longer MRTs and lead to the disconnect between taxonomic and functional diversity profiles.}, }
@article {pmid30786927, year = {2019}, author = {Kim, SJ and Kim, JG and Lee, SH and Park, SJ and Gwak, JH and Jung, MY and Chung, WH and Yang, EJ and Park, J and Jung, J and Hahn, Y and Cho, JC and Madsen, EL and Rodriguez-Valera, F and Hyun, JH and Rhee, SK}, title = {Genomic and metatranscriptomic analyses of carbon remineralization in an Antarctic polynya.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {29}, pmid = {30786927}, issn = {2049-2618}, mesh = {Bacterial Proteins/genetics/metabolism ; Bacteroidetes/classification/genetics/isolation &amp; purification/metabolism ; Carbon/*metabolism ; Diatoms/growth &amp; development/metabolism/microbiology ; Gammaproteobacteria/classification/genetics/isolation &amp; purification/metabolism ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Bacterial ; Haptophyta/*growth &amp; development/metabolism/microbiology ; Metagenomics/*methods ; Phylogeny ; Phytoplankton/metabolism/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Polynyas in the Southern Ocean are regions of intense primary production, mainly by Phaeocystis antarctica. Carbon fixed by phytoplankton in the water column is transferred to higher trophic levels, and finally, to the deep ocean. However, in the Amundsen Sea, most of this organic carbon does not reach the sediment but is degraded in the water column due to high bacterial heterotrophic activity.<br><br>RESULTS: We reconstructed 12 key bacterial genomes from different phases of bloom and analyzed the expression of genes involved in organic carbon remineralization. A high correlation of gene expression between the peak and decline phases was observed in an individual genome bin-based pairwise comparison of gene expression. Polaribacter belonging to Bacteroidetes was found to be dominant in the peak phase, and its transcriptional activity was high (48.9% of the total mRNA reads). Two dominant Polaribacter bins had the potential to utilize major polymers in P. antarctica, chrysolaminarin and xylan, with a distinct set of glycosyl hydrolases. In the decline phase, Gammaproteobacteria (Ant4D3, SUP05, and SAR92), with the potential to utilize low molecular weight-dissolved organic matter (LMW-DOM) including compatible solutes, was increased. The versatility of Gammaproteobacteria may contribute to their abundance in organic carbon-rich polynya waters, while the SAR11 clade was found to be predominant in the sea ice-covered oligotrophic ocean. SAR92 clade showed transcriptional activity for utilization of both polysaccharides and LMW-DOM; this may account for their abundance both in the peak and decline phases. Ant4D3 clade was dominant in all phases of the polynya bloom, implicating the crucial roles of this clade in LMW-DOM remineralization in the Antarctic polynyas.<br><br>CONCLUSIONS: Genomic reconstruction and in situ gene expression analyses revealed the unique metabolic potential of dominant bacteria of the Antarctic polynya at a finer taxonomic level. The information can be used to predict temporal community succession linked to the availability of substrates derived from the P. antarctica bloom. Global warming has resulted in compositional changes in phytoplankton from P. antarctica to diatoms, and thus, repeated parallel studies in various polynyas are required to predict global warming-related changes in carbon remineralization.}, }
@article {pmid30785932, year = {2019}, author = {Han, SH and Yi, J and Kim, JH and Lee, S and Moon, HW}, title = {Composition of gut microbiota in patients with toxigenic Clostridioides (Clostridium) difficile: Comparison between subgroups according to clinical criteria and toxin gene load.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0212626}, pmid = {30785932}, issn = {1932-6203}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacterial Toxins/genetics ; Clostridioides difficile/*genetics/isolation &amp; purification ; Clostridium Infections/*microbiology ; Diarrhea/microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Genetic Load ; Humans ; Male ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Data concerning the human microbiota composition during Clostridioides (Clostridium) difficile infection (CDI) using next-generation sequencing are still limited. We aimed to confirm key features indicating tcdB positive patients and compare the microbiota composition between subgroups based on toxin gene load (tcdB gene) and presence of significant diarrhea. Ninety-nine fecal samples from 79 tcdB positive patients and 20 controls were analyzed using 16S rRNA gene sequencing. Chao1 index for alpha diversity were calculated and principal coordinate analysis was performed for beta diversity using Quantitative Insights into Microbial Ecology (QIIME) pipeline. The mean relative abundance in each group was compared at phylum, family, and genus levels. There were significant alterations in alpha and beta diversity in tcdB positive patients (both colonizer and CDI) compared with those in the control. The mean Chao1 index of tcdB positive patients was significantly lower than the control group (P<0.001), whereas there was no significant difference between tcdB groups and between colonizer and CDI. There were significant differences in microbiota compositions between tcdB positive patients and the control at phylum, family, and genus levels. Several genera such as Phascolarctobacterium, Lachnospira, Butyricimonas, Catenibacterium, Paraprevotella, Odoribacter, and Anaerostipes were not detected in most CDI cases. We identified several changes in the microbiota of CDI that could be further evaluated as predictive markers. Microbiota differences between clinical subgroups of CDI need to be further studied in larger controlled studies.}, }
@article {pmid30785875, year = {2019}, author = {Rosa, E and Minard, G and Lindholm, J and Saastamoinen, M}, title = {Moderate plant water stress improves larval development, and impacts immunity and gut microbiota of a specialist herbivore.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0204292}, pmid = {30785875}, issn = {1932-6203}, mesh = {Animals ; Butterflies/*growth &amp; development/*immunology/microbiology ; Dehydration ; *Droughts ; Gastrointestinal Microbiome ; Gene Expression Regulation ; *Herbivory ; Insect Proteins/metabolism ; Larva/growth &amp; development/immunology/microbiology ; *Plantago/physiology ; *Stress, Physiological ; Survival Rate ; }, abstract = {While host plant drought is generally viewed as a negative phenomenon, its impact on insect herbivores can vary largely depending on the species involved and on the intensity of the drought. Extreme drought killing host plants can clearly reduce herbivore fitness, but the impact of moderate host plant water stress on insect herbivores can vary, and may even be beneficial. The populations of the Finnish Glanville fritillary butterfly (Melitaea cinxia) have faced reduced precipitation in recent years, with impacts even on population dynamics. Whether the negative effects of low precipitation are solely due to extreme desiccation killing the host plant or whether moderate drought reduces plant quality for the larvae remains unknown. We assessed the performance of larvae fed on moderately water-stressed Plantago lanceolata in terms of growth, survival, and immune response, and additionally were interested to assess whether the gut microbial composition of the larvae changed due to modification of the host plant. We found that larvae fed on water-stressed plants had increased growth, with no impact on survival, up-regulated the expression of one candidate immune gene (pelle), and had a more heterogeneous bacterial community and a shifted fungal community in the gut. Most of the measured traits showed considerable variation due to family structure. Our data suggest that in temperate regions moderate host plant water stress can positively shape resource acquisition of this specialized insect herbivore, potentially by increasing nutrient accessibility or concentration. Potentially, the better larval performance may be mediated by a shift of the microbiota on water-stressed plants, calling for further research especially on the understudied gut fungal community.}, }
@article {pmid30782553, year = {2019}, author = {Díaz Nieto, CH and Palacios, NA and Verbeeck, K and Prévoteau, A and Rabaey, K and Flexer, V}, title = {Membrane electrolysis for the removal of Mg[2+] and Ca[2+] from lithium rich brines.}, journal = {Water research}, volume = {154}, number = {}, pages = {117-124}, doi = {10.1016/j.watres.2019.01.050}, pmid = {30782553}, issn = {1879-2448}, mesh = {Calcium Compounds ; Electrolysis ; *Lithium ; *Salts ; }, abstract = {Lithium is today an essential raw material for renewable energy technologies and electric mobility. Continental brines as present in the Lithium Triangle are the most abundant and the easiest to exploit lithium sources. Lithium is present in diluted concentrations together with different ions, and it is imperative to fully remove both magnesium and calcium before lithium carbonate can be precipitated. Here we use membrane electrolysis as a novel method to generate hydroxyl groups in situ in a two-chamber electrochemical cell with a side crystallizer, omitting the need for chemical addition and not leading to substantial loss of lithium rich brine. Batch electrolysis experiments fully removed more than 99.99% of both Mg[2+] and Ca[2+] for three different native South-American brines treated at current densities ranging from 27 to 350 A m[-2] (final concentrations were below ICP detection limit: < 0.05 mg L[-1]). For a brine containing 3090 mg L[-1] of Mg[2+] and 685 mg L[-1] of Ca[2+], 62 kWh m[-3] are needed for the full removal of both cations when a current density of 223 A m[-2] is employed. Most importantly, the Li[+] concentration in the brine is not affected. The removed cations are precipitated as Mg(OH)2 and Ca(OH)2. Our process has the potential to simultaneously recover lithium, magnesium, and calcium compounds, minimizing waste production.}, }
@article {pmid30778376, year = {2019}, author = {Zeng, X and Gao, X and Peng, Y and Wu, Q and Zhu, J and Tan, C and Xia, G and You, C and Xu, R and Pan, S and Zhou, H and He, Y and Yin, J}, title = {Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {4}, pmid = {30778376}, issn = {2235-2988}, mesh = {Aged ; Aged, 80 and over ; Butyrates/*analysis ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Dysbiosis/*complications ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; *Microbiota ; Middle Aged ; Phylogeny ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Risk Assessment ; Sequence Analysis, DNA ; Stroke/*epidemiology ; }, abstract = {Objective: Gut microbiota is a newly identified risk factor for stroke, and there are no large prospective studies linking the baseline gut microbiome to long-term risk of stroke. We present here the correlation between the gut microbiota and stroke risk in people with no prior stroke history. Methods: A total of 141 participants aged ≥60 years without prior history of stroke were recruited and divided into low-risk, medium-risk, and high-risk groups based on known risk factors and whether they were suffering from chronic diseases. The composition of their gut microbiomes was compared using 16S rRNA gene amplicon next-generation-sequencing and Quantitative Insights into Microbial Ecology (QIIME) analysis. Levels of fecal short-chain fatty acids were measured using gas chromatography. Results: We found that opportunistic pathogens (e.g., Enterobacteriaceae and Veillonellaceae) and lactate-producing bacteria (e.g., Bifidobacterium and Lactobacillus) were enriched, while butyrate-producing bacteria (e.g., Lachnospiraceae and Ruminococcaceae) were depleted, in the high-risk group compared to the low-risk group. Butyrate concentrations were also lower in the fecal samples obtained from the high-risk group than from the low-risk group. The concentrations of other short-chain fatty acids (e.g., acetate, propionate, isobutyrate, isovalerate, and valerate) in the gut were comparable among the three groups. Conclusion: Participants at high risk of stroke were characterized by the enrichment of opportunistic pathogens, low abundance of butyrate-producing bacteria, and reduced concentrations of fecal butyrate. More researches into the gut microbiota as a risk factor in stroke should be carried out in the near future.}, }
@article {pmid30775415, year = {2018}, author = {Photos-Jones, E and Knapp, CW and Venieri, D and Christidis, GE and Elgy, C and Valsami-Jones, E and Gounaki, I and Andriopoulou, NC}, title = {Greco-Roman mineral (litho)therapeutics and their relationship to their microbiome: The case of the red pigment miltos.}, journal = {Journal of archaeological science, reports}, volume = {22}, number = {}, pages = {179-192}, pmid = {30775415}, issn = {2352-409X}, support = {//Wellcome Trust/United Kingdom ; }, abstract = {This paper introduces a holistic approach to the study of Greco-Roman (G-R) lithotherapeutics. These are the minerals or mineral combinations that appear in the medical and scientific literature of the G-R world. It argues that they can best be described not simply in terms of their bulk chemistry/mineralogy but also their ecological microbiology and nanofraction component. It suggests that each individual attribute may have underpinned the bioactivity of the lithotherapeutic as an antibacterial, antifungal or other. We focus on miltos, the highly prized, naturally fine, red iron oxide-based mineral used as a pigment, in boat maintenance, agriculture and medicine. Five samples (four geological (from Kea, N. Cyclades) and one archaeological (from Lemnos, NE Aegean)) of miltos were analyzed with physical and biological science techniques. We show that: a. Kean miltos and Lemnian earth/miltos must have been chemically and mineralogically different; b. Lemnian miltos must have been more effective as an antibacterial against specific pathogens (Gram + and Gram - bacteria) than its Kean counterpart; c. two samples of Kean miltos, although similar, chemically, mineralogically and eco-microbiologically (phylum/class level), nevertheless, displayed different antibacterial action. We suggest that this may constitute proof of microbial ecology playing an important role in effecting bioactivity and, interestingly, at the more specific genus/species level. From the perspective of the historian of G-R science, we suggest that it may have been on account of its bioactivity, rather than simply its 'red-staining' effect, that miltos gained prominent entry into the scientific and medical literature of the G-R world.}, }
@article {pmid30772540, year = {2019}, author = {Reid, T and Droppo, IG and Chaganti, SR and Weisener, CG}, title = {Microbial metabolic strategies for overcoming low-oxygen in naturalized freshwater reservoirs surrounding the Athabasca Oil Sands: A proxy for End-Pit Lakes?.}, journal = {The Science of the total environment}, volume = {665}, number = {}, pages = {113-124}, doi = {10.1016/j.scitotenv.2019.02.032}, pmid = {30772540}, issn = {1879-1026}, mesh = {Alberta ; Ecosystem ; *Environmental Monitoring ; Eutrophication ; Lakes/*chemistry/microbiology ; Mining ; *Oil and Gas Fields ; *Water Microbiology ; Water Pollutants, Chemical/*analysis ; }, abstract = {The success and sustainability of aquatic ecosystems are driven by the complex, cooperative metabolism of microbes. Ecological engineering strategies often strive to harness this syntrophic synergy of microbial metabolism for the reclamation of contaminated environments worldwide. Currently, there is a significant knowledge gap in our understanding of how the natural microbial ecology overcomes thermodynamic limitations in recovering contaminated environments. Here, we used in-situ metatranscriptomics and associated metataxonomic analyses on sediments collected from naturalized freshwater man-made reservoirs within the Athabasca Oil Sands region of Alberta, Canada. These reservoirs are unique since they are untouched by industrial mining processes and serve as representative endpoints for model landscape reconstruction. Results indicate that a microbial syntrophic cooperation has been established represented by the oxygenic and anoxygenic phototrophs, sustained through the efficient use of novel cellular mechanistic adaptations tailored to these unique thermodynamic conditions. Specifically, chemotaxis transcripts (cheY &amp; MCPs-methyl-accepting chemotaxis proteins) were highly expressed, suggesting a highly active microbial response to gradients in environmental stimuli, resulting indirectly from hydrocarbon compound alteration. A high expression of photosynthetic activity, likely sustaining nutrient delivery to the similarly highly expressed methanogenic community acting in syntrophy during the breakdown of organics. Overall the more diversified functionality within sub-oxic sample locations indicates an ability to maintain efficient metabolism under thermodynamic constraints. This is the first study to holistically identify and characterize these types of in-situ, metabolic processes and address their thermodynamic feasibility within a global context for large landscape reconstruction. These characterizations of regional, natural landscapes surrounding the oil sands mining operation are severely lacking, but truly provide invaluable insight into end-point goals and targets for reclamation procedures.}, }
@article {pmid30771735, year = {2019}, author = {Petersen, C and Wankhade, UD and Bharat, D and Wong, K and Mueller, JE and Chintapalli, SV and Piccolo, BD and Jalili, T and Jia, Z and Symons, JD and Shankar, K and Anandh Babu, PV}, title = {Dietary supplementation with strawberry induces marked changes in the composition and functional potential of the gut microbiome in diabetic mice.}, journal = {The Journal of nutritional biochemistry}, volume = {66}, number = {}, pages = {63-69}, pmid = {30771735}, issn = {1873-4847}, support = {R01 HL141540/HL/NHLBI NIH HHS/United States ; R03 AG052848/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Diabetes Mellitus, Experimental/diet therapy/*microbiology ; Dietary Supplements ; *Fragaria ; Gastrointestinal Microbiome/*physiology ; Male ; Metabolic Networks and Pathways ; Mice, Inbred C57BL ; Mice, Mutant Strains ; Receptors, Leptin/genetics ; }, abstract = {Gut microbiota contributes to the biological activities of berry anthocyanins by transforming them into bioactive metabolites, and anthocyanins support the growth of specific bacteria, indicating a two-way relationship between anthocyanins and microbiota. In the present study, we tested the hypothesis that strawberry supplementation alters gut microbial ecology in diabetic db/db mice. Control (db/+) and diabetic (db/db) mice (7 weeks old) consumed standard diet or diet supplemented with 2.35% freeze-dried strawberry (db/db + SB) for 10 weeks. Colon contents were used to isolate bacterial DNA. V4 variable region of 16S rRNA gene was amplified. Data analyses were performed using standardized pipelines (QIIME 1.9 and R packages). Differences in predictive metagenomics function were identified by PICRUSt. Principal coordinate analyses confirmed that the microbial composition was significantly influenced by both host genotype and strawberry consumption. Further, α-diversity indices and β-diversity were different at the phylum and genus levels, and genus and operational taxonomical units levels, respectively (P<.05). At the phylum level, strawberry supplementation decreased the abundance of Verrucomicrobia in db/db + SB vs. db/db mice (P<.05). At the genus level, db/db mice exhibited a decrease in the abundance of Bifidobacterium, and strawberry supplementation increased Bifidobacterium in db/db + SB vs. db/db mice (P<.05). PICRUSt revealed significant differences in 45 predicted metabolic functions among the 3 groups. Our study provides evidence for marked changes in the composition and functional potential of the gut microbiome with strawberry supplementation in diabetic mice. Importantly, strawberry supplementation increased the abundance of beneficial bacteria Bifidobacterium which play a pivotal role in the metabolism of anthocyanins.}, }
@article {pmid30770943, year = {2019}, author = {Lewis, RW and Islam, A and Opdahl, L and Davenport, JR and Sullivan, TS}, title = {Comparative Genomics, Siderophore Production, and Iron Scavenging Potential of Root Zone Soil Bacteria Isolated from 'Concord' Grape Vineyards.}, journal = {Microbial ecology}, volume = {78}, number = {3}, pages = {699-713}, pmid = {30770943}, issn = {1432-184X}, support = {3319-3259//Washington State Concord Grape Research Council/ ; 3019-8894/3387//Washington State University Center for Sustaining Agriculture and Natural Resources/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Carbon/metabolism ; Farms ; Iron/*metabolism ; Nitrogen/metabolism ; Phylogeny ; Rhizosphere ; Siderophores/*metabolism ; *Soil Microbiology ; Vitis/growth &amp; development ; Washington ; }, abstract = {Iron (Fe) deficiency in crop production is a worldwide problem which often results in chlorosis in grapevines, particularly in calcareous soils. Siderophores secreted by microorganisms and Strategy II plants can chelate Fe and other metals in soil solution, and siderophore-Fe complexes can then be utilized by plants and microbes. Plants may also shift rhizosphere conditions to favor siderophore-producing microbes, which can increase plant available Fe. Between-row cover crops (barley, rye, wheat, wheat/vetch) were planted as living mulch to address grapevine chlorosis by enhancing soil health in two vineyards in central Washington. The objectives of the current study were to (1) enrich for siderophore-producing organisms from within the indigenous rooting zone community of 'Concord' grapevines, and (2) perform comparative genomics on putative siderophore producing organisms to assess potentially important Fe acquisition-related functional domains and protein families. A high-throughput, chrome azurol S (CAS)-based enrichment assay was used to select siderophore-producing microbes from 'Concord' grapevine root zone soil. Next-generation whole genome sequencing allowed the assembly and annotation of ten full genomes. Phylogenetic analysis revealed two distinct clades among the genomes using the 40 nearest neighbors available in the public database, all of which were of the Pseudomonas genus. Significant differences in functional domain abundances were observed between the clades including iron acquisition and metabolism of amino acids, carbon, nitrogen, phosphate, and sulfur. Diverse mechanisms of Fe uptake and siderophore production/uptake were identified in the protein families of the genomes. The sequenced organisms are likely pseudomonads which are well-suited for iron scavenging, suggesting a potential role in Fe turnover in vineyard systems.}, }
@article {pmid30769104, year = {2019}, author = {Conrads, G and Abdelbary, MMH}, title = {Challenges of next-generation sequencing targeting anaerobes.}, journal = {Anaerobe}, volume = {58}, number = {}, pages = {47-52}, doi = {10.1016/j.anaerobe.2019.02.006}, pmid = {30769104}, issn = {1095-8274}, mesh = {Archaea/*genetics ; Bacteria, Anaerobic/*genetics ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {Next-generation sequencing allows for investigating the composition of microbiomes that are associated with infection (clinical microbiology) or dysbiosis (microbial ecology). The most commonly applied short-read sequencing technologies are Illumina MiSeq/HiSeq and Ion Torrent PGM, however, other platforms that generate long-reads are under way and optimized. A pre-condition for representative results is an appropriate method for contamination-free collection, homogenization, storage of specimens and a subsequent efficient DNA extraction protocol. As some of the anaerobes such as Clostridia or anaerobe Archaea are robust while others of the same environment, such as spirochetes, possess a very thin cell wall, a chemico-mechanical lysing strategy is recommended but with some precautions to avoid DNA-sheering and overheating. For amplicon sequencing, the Silva-TestPrime online tool helps to find the optimal 16S directed primers for individual studies. For metagenome profiling, the classifier tool has to be selected with helpful decision trees available but a combination based on different strategies seems to be indispensable. Further development of both hard- and software is needed before microbiome results become free of a substantial technology-dependent bias.}, }
@article {pmid30768364, year = {2019}, author = {Kain, V and Van Der Pol, W and Mariappan, N and Ahmad, A and Eipers, P and Gibson, DL and Gladine, C and Vigor, C and Durand, T and Morrow, C and Halade, GV}, title = {Obesogenic diet in aging mice disrupts gut microbe composition and alters neutrophil:lymphocyte ratio, leading to inflamed milieu in acute heart failure.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {33}, number = {5}, pages = {6456-6469}, pmid = {30768364}, issn = {1530-6860}, support = {UL1 TR003096/TR/NCATS NIH HHS/United States ; R01 HL132989/HL/NHLBI NIH HHS/United States ; R00 AT006704/AT/NCCIH NIH HHS/United States ; P30 AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR001417/TR/NCATS NIH HHS/United States ; K99 AT006704/AT/NCCIH NIH HHS/United States ; }, mesh = {Acute Disease ; Aging/drug effects/*metabolism/pathology ; Animals ; Diet, High-Fat/adverse effects ; Dietary Fats/*adverse effects/pharmacology ; Firmicutes/classification/*metabolism ; *Gastrointestinal Microbiome ; Heart Failure/chemically induced/*metabolism/pathology ; Inflammation/chemically induced/metabolism/pathology ; Lymphocytes/*metabolism ; Male ; Mice ; Neutrophils/*metabolism/pathology ; *Obesity/chemically induced/metabolism/microbiology/pathology ; }, abstract = {Calorie-dense obesogenic diet (OBD) is a prime risk factor for cardiovascular disease in aging. However, increasing age coupled with changes in the diet can affect the interaction of intestinal microbiota influencing the immune system, which can lead to chronic inflammation. How age and calorie-enriched OBD interact with microbial flora and impact leukocyte profiling is currently under investigated. Here, we tested the interorgan hypothesis to determine whether OBD in young and aging mice alters the gut microbe composition and the splenic leukocyte profile in acute heart failure (HF). Young (2-mo-old) and aging (18-mo-old) mice were supplemented with standard diet (STD, ∼4% safflower oil diet) and OBD (10% safflower oil) for 2 mo and then subjected to coronary artery ligation to induce myocardial infarction. Fecal samples were collected pre- and post-diet intervention, and the microbial flora were analyzed using 16S variable region 4 rRNA gene DNA sequencing and Quantitative Insights Into Microbial Ecology informatics. The STD and OBD in aging mice resulted in an expansion of the genus Allobaculum in the fecal microbiota. However, we found a pathologic change in the neutrophil:lymphocyte ratio in aging mice in comparison with their young counterparts. Thus, calorie-enriched OBD dysregulated splenic leukocytes by decreasing immune-responsive F4/80[+] and CD169[+] macrophages in aging mice. OBD programmed neutrophil swarming with an increase in isoprostanoid levels, with dysregulation of lipoxygenases, cytokines, and metabolite-sensing receptor expression. In summary, calorie-dense OBD in aging mice disrupted the composition of the gut microbiome, which correlates with the development of integrative and system-wide nonresolving inflammation in acute HF.-Kain, V., Van Der Pol, W., Mariappan, N., Ahmad, A., Eipers, P., Gibson, D. L., Gladine, C., Vigor, C., Durand, T., Morrow, C., Halade, G. V. Obesogenic diet in aging mice disrupts gut microbe composition and alters neutrophil:lymphocyte ratio, leading to inflamed milieu in acute heart failure.}, }
@article {pmid30767956, year = {2019}, author = {Bai, J and Jhaney, I and Daniel, G and Watkins Bruner, D}, title = {Pilot Study of Vaginal Microbiome Using QIIME 2™ in Women With Gynecologic Cancer Before and After Radiation Therapy.}, journal = {Oncology nursing forum}, volume = {46}, number = {2}, pages = {E48-E59}, doi = {10.1188/19.ONF.E48-E59}, pmid = {30767956}, issn = {1538-0688}, support = {K99 NR017897/NR/NINR NIH HHS/United States ; }, mesh = {Adult ; Aged ; Female ; Genital Neoplasms, Female/*microbiology/*radiotherapy ; Georgia ; Humans ; Microbiota/*genetics/*radiation effects ; Middle Aged ; Pilot Projects ; RNA, Ribosomal, 16S/*analysis ; Vagina/*microbiology ; }, abstract = {OBJECTIVES: To characterize the vaginal microbiome using QIIME 2™ (Quantitative Insights Into Microbial Ecology 2) in women with gynecologic cancer.<br><br>SAMPLE &amp;AMP; SETTING: 19 women with gynecologic cancer before and after radiation therapy at a comprehensive cancer center in Atlanta, Georgia.<br><br>METHODS &amp;AMP; VARIABLES: This pilot study analyzed vaginal microbiome communities using a microbiome analysis pipeline, beginning with 16S rRNA gene sequencing and processing through use of a bioinformatics pipeline to downstream microbial statistical analysis.<br><br>RESULTS: The findings showed the methods to be robust, and most women with gynecologic cancer showed depletion of Lactobacillus. Compared to those pre-radiation therapy, women post-radiation therapy showed higher abundances of Mobiluncus, Atopobium, and Prevotella but lower abundances of Lactobacillus, Gardnerella, and Peptostreptococcus, which are associated with bacterial vaginosis.<br><br>IMPLICATIONS FOR NURSING: This study presents the fundamentals of human microbiome data collection and analysis methods to inform nursing science. Assessing the vaginal microbiome provides a potential pathway to develop interventions to ameliorate dysbiosis of the vaginal microbiome.}, }
@article {pmid30762095, year = {2019}, author = {Martínez-Rodríguez, P and Rolán-Alvarez, E and Del Mar Pérez-Ruiz, M and Arroyo-Yebras, F and Carpena-Catoira, C and Carvajal-Rodríguez, A and Bella, JL}, title = {Geographic and Temporal Variation of Distinct Intracellular Endosymbiont Strains of Wolbachia sp. in the Grasshopper Chorthippus parallelus: a Frequency-Dependent Mechanism?.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {1036-1047}, pmid = {30762095}, issn = {1432-184X}, support = {CGL2016-75482-P//Ministerio de Ciencia y Tecnolog?a/ ; BFU2013-44635//Ministerio de Econom?a, Industria y Competitividad, Gobierno de Espa?a/ ; }, mesh = {Animals ; Biological Coevolution ; Computer Simulation ; Geography ; Grasshoppers/*microbiology ; Linear Models ; *Polymorphism, Genetic ; Seasons ; *Symbiosis ; Wolbachia/genetics/*physiology ; }, abstract = {Wolbachia is an intracellular endosymbiont that can produce a range of effects on host fitness, but the temporal dynamics of Wolbachia strains have rarely been experimentally evaluated. We compare interannual strain frequencies along a geographical region for understanding the forces that shape Wolbachia strain frequency in natural populations of its host, Chorthippus parallelus (Orthoptera, Acrididae). General linear models show that strain frequency changes significantly across geographical and temporal scales. Computer simulation allows to reject the compatibility of the observed patterns with either genetic drift or sampling errors. We use consecutive years to estimate total Wolbachia strain fitness. Our estimation of Wolbachia fitness is significant in most cases, within locality and between consecutive years, following a negatively frequency-dependent trend. Wolbachia spp. B and F strains show a temporal pattern of variation that is compatible with a negative frequency-dependent natural selection mechanism. Our results suggest that such a mechanism should be at least considered in future experimental and theoretical research strategies that attempt to understand Wolbachia biodiversity.}, }
@article {pmid30761424, year = {2019}, author = {Parera-Valadez, Y and Yam-Puc, A and López-Aguiar, LK and Borges-Argáez, R and Figueroa-Saldivar, MA and Cáceres-Farfán, M and Márquez-Velázquez, NA and Prieto-Davó, A}, title = {Ecological Strategies Behind the Selection of Cultivable Actinomycete Strains from the Yucatan Peninsula for the Discovery of Secondary Metabolites with Antibiotic Activity.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {839-851}, pmid = {30761424}, issn = {1432-184X}, support = {CVU223481//Consejo Nacional de Ciencia y Tecnolog?a/ ; PNC//Consejo Nacional de Ciencia y Tecnolog?a/ ; TA200212, TA200415//Direcci?n General de Asuntos del Personal Acad?mico, Universidad Nacional Aut?noma de M?xico/ ; }, mesh = {Actinobacteria/*chemistry ; Anti-Bacterial Agents/*analysis ; Biological Products/*analysis ; Drug Discovery/*methods ; Mexico ; Seawater/*analysis ; }, abstract = {The quest for novel natural products has recently focused on the marine environment as a source for novel microorganisms. Although isolation of marine-derived actinomycete strains is now common, understanding their distribution in the oceans and their adaptation to this environment can be helpful in the selection of isolates for further novel secondary metabolite discovery. This study explores the taxonomic diversity of marine-derived actinomycetes from distinct environments in the coastal areas of the Yucatan Peninsula and their adaptation to the marine environment as a first step towards novel natural product discovery. The use of simple ecological principles, for example, phylogenetic relatedness to previously characterized actinomycetes or seawater requirements for growth, to recognize isolates with adaptations to the ocean in an effort to select for marine-derived actinomycete to be used for further chemical studies. Marine microbial environments are an important source of novel bioactive natural products and, together with methods such as genome mining for detection of strains with biotechnological potential, ecological strategies can bring useful insights in the selection and identification of marine-derived actinomycetes for novel natural product discovery.}, }
@article {pmid30761423, year = {2019}, author = {Purahong, W and Kahl, T and Krüger, D and Buscot, F and Hoppe, B}, title = {Home-Field Advantage in Wood Decomposition Is Mainly Mediated by Fungal Community Shifts at "Home" Versus "Away".}, journal = {Microbial ecology}, volume = {78}, number = {3}, pages = {725-736}, pmid = {30761423}, issn = {1432-184X}, support = {KR 3587/1-1, KR 3587/3-2//Deutsche Forschungsgemeinschaft/ ; BU 941/17-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Biodegradation, Environmental ; DNA, Fungal/genetics ; Fagus/*microbiology ; Fungi/classification/genetics/*isolation &amp; purification/*metabolism ; *Mycobiome ; Nitrogen/metabolism ; Picea/*microbiology ; RNA, Ribosomal, 16S/genetics ; Trees/microbiology ; Wood/*microbiology ; }, abstract = {The home-field advantage (HFA) hypothesis has been used intensively to study leaf litter decomposition in various ecosystems. However, the HFA in woody substrates is still unexplored. Here, we reanalyzed and integrated existing datasets on various groups of microorganisms collected from natural deadwood of two temperate trees, Fagus sylvatica and Picea abies, from forests in which one or other of these species dominates but where both are present. Our aims were (i) to test the HFA hypothesis on wood decomposition rates of these two temperate tree species, and (ii) to investigate if HFA hypothesis can be explained by diversity and community composition of bacteria and in detail N-fixing bacteria (as determined by molecular 16S rRNA and nifH gene amplification) and fungi (as determined by molecular ITS rRNA amplification and sporocarp surveys). Our results showed that wood decomposition rates were accelerated at "home" versus "away" by 38.19% ± 20.04% (mean ± SE). We detected strong changes in fungal richness (increase 36-50%) and community composition (RANOSIM = 0.52-0.60, P < 0.05) according to HFA hypothesis. The changes of fungi were much stronger than for total bacteria and nitrogen fixing for both at richness and community composition levels. In conclusion, our results support the HFA hypothesis in deadwood: decomposition rate is accelerated at home due to specialization of fungal communities produced by the plant community above them. Furthermore, the higher richness of fungal sporocarps and nitrogen-fixing bacteria (nifH) may stimulate or at least stabilize wood decomposition rates at "home" versus "away."}, }
@article {pmid30759613, year = {2019}, author = {Wang, X and Li, X and Yu, L and Huang, L and Xiu, J and Lin, W and Zhang, Y}, title = {Characterizing the microbiome in petroleum reservoir flooded by different water sources.}, journal = {The Science of the total environment}, volume = {653}, number = {}, pages = {872-885}, doi = {10.1016/j.scitotenv.2018.10.410}, pmid = {30759613}, issn = {1879-1026}, mesh = {Betaproteobacteria/genetics/*metabolism ; China ; Environmental Monitoring ; Gammaproteobacteria/genetics/*metabolism ; Metagenomics ; *Microbiota/genetics ; Oil and Gas Fields/*microbiology ; Petroleum/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S ; Water Microbiology ; *Water Resources/supply &amp; distribution ; }, abstract = {Petroleum reservoir is an unusual subsurface biosphere, where indigenous microbes lived and evolved for million years. However, continual water injection changed the situation by introduction of new electron acceptors, donors and exogenous microbes. In this study, 16S-rRNA gene sequencing, comparative metagenomics and genomic bins reconstruction were employed to investigate the microbial community and metabolic potential in three typical water-flooded blocks of the Shen84 oil reservoir in Liaohe oil field, China. The results showed significant difference of microbial community compositions and metabolic characteristics existed between the injected water and the produced water/oil mixtures; however, there was considerable uniformity between the produced samples in different blocks. Microbial communities in the produced fluids were dominated by exogenous facultative microbes such as Pseudomonas and Thauera members from Proteobacteria phylum. Metabolic potentials for O2-dependent hydrocarbon degradation, dissimilarly nitrate reduction, and thiosulfate‑sulfur oxidation were much more abundant, whereas genes involved in dissimilatory sulfate reduction, anaerobic hydrocarbon degradation and methanogenesis were less abundant in the oil reservoir. Statistical analysis indicated the water composition had an obvious influence on microbial community composition and metabolic potential. The water-flooding process accompanied with introduction of nitrate or nitrite, and dissolved oxygen promoted the alteration of microbiome in oil reservoir from slow-growing anaerobic indigenous microbes (such as Thermotoga, Clostridia, and Syntrophobacter) to fast-growing opportunists as Beta- and Gama- Proteobacteria. The findings of this study shed light on the microbial ecology change in water flooded petroleum reservoir.}, }
@article {pmid30759269, year = {2019}, author = {Semenec, L and Vergara, IA and Laloo, AE and Mathews, ER and Bond, PL and Franks, AE}, title = {Enhanced Growth of Pilin-Deficient Geobacter sulfurreducens Mutants in Carbon Poor and Electron Donor Limiting Conditions.}, journal = {Microbial ecology}, volume = {78}, number = {3}, pages = {618-630}, pmid = {30759269}, issn = {1432-184X}, support = {N626909-13-1-N259//Office of Naval Research Global/ ; FA2386-14-1-4032//Asian Office of Aerospace Research and Development/ ; LP140100459//Australian Research Council/ ; }, mesh = {Carbon/*metabolism ; Cytochromes/metabolism ; Electron Transport ; Electrons ; Fimbriae Proteins/chemistry/deficiency/*genetics ; Fimbriae, Bacterial/chemistry/genetics/metabolism ; Geobacter/chemistry/genetics/*growth &amp; development/metabolism ; Mass Spectrometry ; Mutation ; Proteomics ; }, abstract = {Geobacter sulfurreducens pili enable extracellular electron transfer and play a role in secretion of c-type cytochromes such as OmcZ. PilA-deficient mutants of G. sulfurreducens have previously been shown to accumulate cytochromes within their membranes. This cytochrome retaining phenotype allowed for enhanced growth of PilA-deficient mutants in electron donor and carbon-limited conditions where formate and fumarate are provided as the sole electron donor and acceptor with no supplementary carbon source. Conversely, wild-type G. sulfurreducens, which has normal secretion of cytochromes, has comparative limited growth in these conditions. This growth is further impeded for OmcZ-deficient and OmcS-deficient mutants. A PilB-deficient mutant which prevents pilin production but allows for secretion of OmcZ had moderate growth in these conditions, indicating a role for cytochrome localization to enabling survival in the electron donor and carbon-limited conditions. To determine which pathways enhanced growth using formate, Sequential Window Acquisition of all Theoretical Mass Spectra mass spectrometry (SWATH-MS) proteomics of formate adapted PilA-deficient mutants and acetate grown wild type was performed. PilA-deficient mutants had an overall decrease in tricarboxylic acid (TCA) cycle enzymes and significant upregulation of electron transport chain associated proteins including many c-type cytochromes and [NiFe]-hydrogenases. Whole genome sequencing of the mutants shows strong convergent evolution and emergence of genetic subpopulations during adaptation to growth on formate. The results described here suggest a role for membrane constrained c-type cytochromes to the enhancement of survival and growth in electron donor and carbon-limited conditions.}, }
@article {pmid30759084, year = {2019}, author = {Hawinkel, S and Kerckhof, FM and Bijnens, L and Thas, O}, title = {A unified framework for unconstrained and constrained ordination of microbiome read count data.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0205474}, pmid = {30759084}, issn = {1932-6203}, mesh = {Algorithms ; Bacteria/genetics ; Computer Simulation ; *Data Visualization ; Humans ; Microbiota/*genetics ; Monte Carlo Method ; Neoplasms/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Explorative visualization techniques provide a first summary of microbiome read count datasets through dimension reduction. A plethora of dimension reduction methods exists, but many of them focus primarily on sample ordination, failing to elucidate the role of the bacterial species. Moreover, implicit but often unrealistic assumptions underlying these methods fail to account for overdispersion and differences in sequencing depth, which are two typical characteristics of sequencing data. We combine log-linear models with a dispersion estimation algorithm and flexible response function modelling into a framework for unconstrained and constrained ordination. The method is able to cope with differences in dispersion between taxa and varying sequencing depths, to yield meaningful biological patterns. Moreover, it can correct for observed technical confounders, whereas other methods are adversely affected by these artefacts. Unlike distance-based ordination methods, the assumptions underlying our method are stated explicitly and can be verified using simple diagnostics. The combination of unconstrained and constrained ordination in the same framework is unique in the field and facilitates microbiome data exploration. We illustrate the advantages of our method on simulated and real datasets, while pointing out flaws in existing methods. The algorithms for fitting and plotting are available in the R-package RCM.}, }
@article {pmid30758801, year = {2019}, author = {Kiewra, D and Czułowska, A and Dyczko, D and Zieliński, R and Plewa-Tutaj, K}, title = {First record of Haemaphysalis concinna (Acari: Ixodidae) in Lower Silesia, SW Poland.}, journal = {Experimental &amp; applied acarology}, volume = {77}, number = {3}, pages = {449-454}, pmid = {30758801}, issn = {1572-9702}, mesh = {*Animal Distribution ; Animals ; Female ; Forests ; Grassland ; Ixodidae/growth &amp; development/*physiology ; Larva/physiology ; Male ; Nymph/physiology ; Poland ; }, abstract = {Haemaphysalis concinna Koch is one of 19 species of the genus Haemaphysalis which has been reported in the Palearctic region. In Europe, the presence of H. concinna ticks has been reported in numerous countries. In Poland, to date, the precise occurrence of H. concinna was known only from one site in the north-western region. This paper shows that H. concinna ticks can be considered a typical example of the tick fauna occurring in Lower Silesia, SW Poland. Tick monitoring was conducted using a standard flagging method in 24 sites in the various forest types of Lower Silesia. Among 1622 host-seeking ticks collected, H. concinna accounted for 2.7%. From the collected H. concinna there were: 25 (58.1%) larvae, 15 (34.9%) nymphs, 1 (2.3%) female, and 2 (4.7%) males. The presence of H. concinna was confirmed in 6 out of 24 tested sites in fresh mixed broadleaf forests, fresh mixed coniferous forests and in pastures.}, }
@article {pmid30756135, year = {2019}, author = {Singer, D and Metz, S and Unrein, F and Shimano, S and Mazei, Y and Mitchell, EAD and Lara, E}, title = {Contrasted Micro-Eukaryotic Diversity Associated with Sphagnum Mosses in Tropical, Subtropical and Temperate Climatic Zones.}, journal = {Microbial ecology}, volume = {78}, number = {3}, pages = {714-724}, pmid = {30756135}, issn = {1432-184X}, support = {310003A//Schweizerischer Nationalfonds zur F?rderung der Wissenschaftlichen Forschung/ ; 143960//Schweizerischer Nationalfonds zur F?rderung der Wissenschaftlichen Forschung/ ; ASTF 520 - 2015//European Molecular Biology Organization/ ; FONCyT PICT-2014-1290//Consejo Nacional de Investigaciones Cient?ficas y T?cnicas/ ; }, mesh = {*Biodiversity ; Climate ; Ecosystem ; Eukaryota/classification/genetics/*isolation &amp; purification ; Phylogeny ; Sphagnopsida/*parasitology ; Temperature ; }, abstract = {Sphagnum-dominated ecosystem plays major roles as carbon sinks at the global level. Associated microbial communities, in particular, eukaryotes, play significant roles in nutrient fixation and turnover. In order to understand better the ecological processes driven by these organisms, the first step is to characterise these associated organisms. We characterised the taxonomic diversity, and from this, inferred the functional diversity of microeukaryotes in Sphagnum mosses in tropical, subtropical and temperate climatic zones through an environmental DNA diversity metabarcoding survey of the V9 region of the gene coding for the RNA of the small subunit of the ribosomes (SSU rRNA). As microbial processes are strongly driven by temperatures, we hypothesised that saprotrophy would be highest in warm regions, whereas mixotrophy, an optimal strategy in oligotrophic environments, would peak under colder climates. Phylotype richness was higher in tropical and subtropical climatic zones than in the temperate region, mostly due to a higher diversity of animal parasites (i.e. Apicomplexa). Decomposers, and especially opportunistic yeasts and moulds, were more abundant under warmer climates, while mixotrophic organisms were more abundant under temperate climates. The dominance of decomposers, suggesting a higher heterotrophic activity under warmer climates, is coherent with the generally observed faster nutrient cycling at lower latitudes; this phenomenon is likely enhanced by higher inputs of nutrients most probably brought in the system by Metazoa, such as arthropods.}, }
@article {pmid30755506, year = {2019}, author = {Hausmann, B and Pelikan, C and Rattei, T and Loy, A and Pester, M}, title = {Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, pmid = {30755506}, issn = {2150-7511}, support = {P 23117/FWF_/Austrian Science Fund FWF/Austria ; P 25111/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacterial Load ; Biomass ; Gene Expression Profiling ; Genome, Bacterial ; Metagenomics ; Peptococcaceae/*genetics/*growth &amp; development ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Soil Microbiology ; *Transcription, Genetic ; }, abstract = {Microbial diversity in the environment is mainly concealed within the rare biosphere (all species with <0.1% relative abundance). While dormancy explains a low-abundance state very well, the mechanisms leading to rare but active microorganisms remain elusive. We used environmental systems biology to genomically and transcriptionally characterize "Candidatus Desulfosporosinus infrequens," a low-abundance sulfate-reducing microorganism cosmopolitan to freshwater wetlands, where it contributes to cryptic sulfur cycling. We obtained its near-complete genome by metagenomics of acidic peat soil. In addition, we analyzed anoxic peat soil incubated under in situ-like conditions for 50 days by Desulfosporosinus-targeted qPCR and metatranscriptomics. The Desulfosporosinus population stayed at a constant low abundance under all incubation conditions, averaging 1.2 × 10[6] 16S rRNA gene copies per cm[3] soil. In contrast, transcriptional activity of "Ca. Desulfosporosinus infrequens" increased at day 36 by 56- to 188-fold when minor amendments of acetate, propionate, lactate, or butyrate were provided with sulfate, compared to the no-substrate-control. Overall transcriptional activity was driven by expression of genes encoding ribosomal proteins, energy metabolism, and stress response but not by expression of genes encoding cell growth-associated processes. Since our results did not support growth of these highly active microorganisms in terms of biomass increase or cell division, they had to invest their sole energy for maintenance, most likely counterbalancing acidic pH conditions. This finding explains how a rare biosphere member can contribute to a biogeochemically relevant process while remaining in a zero-growth state over a period of 50 days.IMPORTANCE The microbial rare biosphere represents the largest pool of biodiversity on Earth and constitutes, in sum of all its members, a considerable part of a habitat's biomass. Dormancy or starvation is typically used to explain the persistence of low-abundance microorganisms in the environment. We show that a low-abundance microorganism can be highly transcriptionally active while remaining in a zero-growth state for at least 7 weeks. Our results provide evidence that this zero growth at a high cellular activity state is driven by maintenance requirements. We show that this is true for a microbial keystone species, in particular a cosmopolitan but permanently low-abundance sulfate-reducing microorganism in wetlands that is involved in counterbalancing greenhouse gas emissions. In summary, our results provide an important step forward in understanding time-resolved activities of rare biosphere members relevant for ecosystem functions.}, }
@article {pmid30747342, year = {2019}, author = {Faulkner, M and Zhao, LS and Barrett, S and Liu, LN}, title = {Self-Assembly Stability and Variability of Bacterial Microcompartment Shell Proteins in Response to the Environmental Change.}, journal = {Nanoscale research letters}, volume = {14}, number = {1}, pages = {54}, pmid = {30747342}, issn = {1931-7573}, support = {UF120411//Royal Society/ ; RG130442//Royal Society/ ; URF\R\180030//Royal Society/ ; RGF\EA\180233//Royal Society/ ; BB/M024202/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R003890/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Bacterial microcompartments (BMCs) are proteinaceous self-assembling organelles that are widespread among the prokaryotic kingdom. By segmenting key metabolic enzymes and pathways using a polyhedral shell, BMCs play essential roles in carbon assimilation, pathogenesis, and microbial ecology. The BMC shell is composed of multiple protein homologs that self-assemble to form the defined architecture. There is tremendous interest in engineering BMCs to develop new nanobioreactors and molecular scaffolds. Here, we report the quantitative characterization of the formation and self-assembly dynamics of BMC shell proteins under varying pH and salt conditions using high-speed atomic force microscopy (HS-AFM). We show that 400-mM salt concentration is prone to result in larger single-layered shell patches formed by shell hexamers, and a higher dynamic rate of hexamer self-assembly was observed at neutral pH. We also visualize the variability of shell proteins from hexameric assemblies to fiber-like arrays. This study advances our knowledge about the stability and variability of BMC protein self-assemblies in response to microenvironmental changes, which will inform rational design and construction of synthetic BMC structures with the capacity of remodeling their self-assembly and structural robustness. It also offers a powerful toolbox for quantitatively assessing the self-assembly and formation of BMC-based nanostructures in biotechnology applications.}, }
@article {pmid30746494, year = {2019}, author = {Tecon, R and Mitri, S and Ciccarese, D and Or, D and van der Meer, JR and Johnson, DR}, title = {Bridging the Holistic-Reductionist Divide in Microbial Ecology.}, journal = {mSystems}, volume = {4}, number = {1}, pages = {}, pmid = {30746494}, issn = {2379-5077}, abstract = {Microbial communities are inherently complex systems. To address this complexity, microbial ecologists are developing new, more elaborate laboratory models at an ever-increasing pace. These model microbial communities and habitats have opened up the exploration of new territories that lie between the simplicity and controllability of "synthetic" systems and the convolution and complexity of natural environments. Here, we discuss this classic methodological divide, we propose a conceptual perspective that integrates new research developments, and we sketch a 3-point possible roadmap to cross the divide between controllability and complexity in microbial ecology.}, }
@article {pmid30745899, year = {2018}, author = {Eveillard, D and Bouskill, NJ and Vintache, D and Gras, J and Ward, BB and Bourdon, J}, title = {Probabilistic Modeling of Microbial Metabolic Networks for Integrating Partial Quantitative Knowledge Within the Nitrogen Cycle.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3298}, pmid = {30745899}, issn = {1664-302X}, abstract = {Understanding the interactions between microbial communities and their environment sufficiently to predict diversity on the basis of physicochemical parameters is a fundamental pursuit of microbial ecology that still eludes us. However, modeling microbial communities is problematic, because (i) communities are complex, (ii) most descriptions are qualitative, and (iii) quantitative understanding of the way communities interact with their surroundings remains incomplete. One approach to overcoming such complications is the integration of partial qualitative and quantitative descriptions into more complex networks. Here we outline the development of a probabilistic framework, based on Event Transition Graph (ETG) theory, to predict microbial community structure across observed chemical data. Using reverse engineering, we derive probabilities from the ETG that accurately represent observations from experiments and predict putative constraints on communities within dynamic environments. These predictions can feedback into the future development of field experiments by emphasizing the most important functional reactions, and associated microbial strains, required to characterize microbial ecosystems.}, }
@article {pmid30743865, year = {2018}, author = {Pikaar, I and de Vrieze, J and Rabaey, K and Herrero, M and Smith, P and Verstraete, W}, title = {Carbon emission avoidance and capture by producing in-reactor microbial biomass based food, feed and slow release fertilizer: Potentials and limitations.}, journal = {The Science of the total environment}, volume = {644}, number = {}, pages = {1525-1530}, doi = {10.1016/j.scitotenv.2018.07.089}, pmid = {30743865}, issn = {1879-1026}, mesh = {Biomass ; *Bioreactors ; Carbon ; Carbon Cycle ; *Carbon Sequestration ; Climate Change ; *Fertilizers ; }, abstract = {To adhere to the Paris Agreement of 2015, we need to store several Gigatonnes (Gt) of carbon annually. In the last years, a variety of technologies for carbon capture and storage (CCS) and carbon capture and usage (CCU) have been demonstrated. While conventional CCS and CCU are techno-economically feasible, their climate change mitigation potentials are limited, due to limited amount of CO2 that can be captured. Hence, there is an urgent need to explore other CCS and CCU routes. Here we discuss an interesting alternative route for capture of carbon dioxide from industrial point sources, using CO2-binding, so-called autotrophic aerobic bacteria to produce microbial biomass as a C-storage product. The produced microbial biomass is often referred to as microbial protein (MP) because it has a crude protein content of ~70-75%. Depending on the industrial production process and final quality of the produced MP, it can be used for human consumption as meat replacement, protein supplement in animal diets, or slow-release organic fertilizer thus providing both organic nitrogen and carbon to agricultural soils. Here, we discuss the potentials and limitations of this so far unexplored CCU approach. A preliminary assessment of the economic feasibility of the different routes for CO2 carbon avoidance, capture and utilization indicates that the value chain to food is becoming attractive and that the other end-points warrant close monitoring over the coming years.}, }
@article {pmid30742313, year = {2019}, author = {Noor, NM and Defoirdt, T and Alipiah, N and Karim, M and Daud, H and Natrah, I}, title = {Quorum sensing is required for full virulence of Vibrio campbellii towards tiger grouper (Epinephelus fuscoguttatus) larvae.}, journal = {Journal of fish diseases}, volume = {42}, number = {4}, pages = {489-495}, doi = {10.1111/jfd.12946}, pmid = {30742313}, issn = {1365-2761}, support = {BOF-UGent//Universiteit Gent/ ; GP-HIP/2018/9598400//Universiti Putra Malaysia/ ; //Malaysian Ministry of Education/ ; }, mesh = {4-Butyrolactone/analogs &amp; derivatives/genetics ; Animals ; Bass/*microbiology ; Fish Diseases/*microbiology ; Homoserine/analogs &amp; derivatives/genetics ; Lactones ; Larva/microbiology ; Mutation ; *Quorum Sensing ; Vibrio/genetics/*metabolism/*pathogenicity ; Virulence ; }, abstract = {The link between quorum sensing in Vibrio campbellii and its virulence towards tiger grouper (Epinephelus fuscoguttatus) was investigated using V. campbellii wild type and quorum-sensing mutants with inactive quorum sensing or constitutively maximal quorum-sensing activity, and signal molecule synthase mutants. The results showed that wild-type V. campbellii is pathogenic to grouper larvae, causing more than 50% mortality after 4 days of challenge. Furthermore, the mortality of larvae challenged with the mutant with maximally active quorum sensing was significantly higher than that of larvae challenged with the wild type, whereas a higher survival was observed in the larvae challenged to the mutant with a completely inactive quorum-sensing system. Grouper larvae challenged with either the signal molecule synthase triple mutant, the harveyi autoinducer-1 (HAI-1) synthase mutant and the autoinducer-2 (AI-2) synthase mutant showed higher survival than larvae challenged with the wild type. In contrast, larvae challenged with the cholerae autoinducer-1 (CAI-1) synthase mutant showed high mortality. This indicates that HAI-1 and AI-2, but not CAI-1, are required for full virulence of V. campbellii towards grouper larvae. Our data suggest that quorum-sensing inhibition could be an effective strategy to control V. campbellii infections in tiger grouper.}, }
@article {pmid30740279, year = {2019}, author = {Lee, KM and Adams, M and Klassen, JL}, title = {Evaluation of DESS as a storage medium for microbial community analysis.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6414}, pmid = {30740279}, issn = {2167-8359}, abstract = {Microbial ecology research requires sampling strategies that accurately represent the microbial community under study. These communities must typically be transported from the collection location to the laboratory and then stored until they can be processed. However, there is a lack of consensus on how best to preserve microbial communities during transport and storage. Here, we evaluated dimethyl sulfoxide, ethylenediamine tetraacetic acid, saturated salt (DESS) solution as a broadly applicable preservative for microbial ecology experiments. We stored fungus gardens grown by the ant Trachymyrmex septentrionalis in DESS, 15% glycerol, and phosphate buffered saline (PBS) to test their impact on the fungus garden microbial community. Variation in microbial community structure due to differences in preservative type was minimal when compared to variation between ant colonies. Additionally, DESS preserved the structure of a defined mock community more faithfully than either 15% glycerol or PBS. DESS is inexpensive, easy to transport, and effective in preserving microbial community structure. We therefore conclude that DESS is a valuable preservative for use in microbial ecology research.}, }
@article {pmid30739147, year = {2019}, author = {Pastor, A and Freixa, A and Skovsholt, LJ and Wu, N and Romaní, AM and Riis, T}, title = {Microbial Organic Matter Utilization in High-Arctic Streams: Key Enzymatic Controls.}, journal = {Microbial ecology}, volume = {78}, number = {3}, pages = {539-554}, pmid = {30739147}, issn = {1432-184X}, support = {CF16-0325//Carlsbergfondet/ ; Postgraduate studies program//Fundaci?n Ram?n Areces/ ; }, mesh = {Arctic Regions ; Bacteria/classification/*enzymology/genetics/isolation &amp; purification ; Bacterial Proteins/genetics/*metabolism ; Biofilms ; Ecosystem ; Greenland ; Humic Substances/*analysis/microbiology ; Nitrogen/metabolism ; Phosphorus/metabolism ; Rivers/*microbiology ; Soil/chemistry ; Soil Microbiology ; }, abstract = {In the Arctic, climate changes contribute to enhanced mobilization of organic matter in streams. Microbial extracellular enzymes are important mediators of stream organic matter processing, but limited information is available on enzyme processes in this remote area. Here, we studied the variability of microbial extracellular enzyme activity in high-Arctic fluvial biofilms. We evaluated 12 stream reaches in Northeast Greenland draining areas exhibiting different geomorphological features with contrasting contents of soil organic matter to cover a wide range of environmental conditions. We determined stream nitrogen, phosphorus, and dissolved organic carbon concentrations, quantified algal biomass and bacterial density, and characterized the extracellular enzyme activities involved in catalyzing the cleavage of a range of organic matter compounds (e.g., β-glucosidase, phosphatase, β-xylosidase, cellobiohydrolase, and phenol oxidase). We found significant differences in microbial organic matter utilization among the study streams draining contrasting geomorphological features, indicating a strong coupling between terrestrial and stream ecosystems. Phosphatase and phenol oxidase activities were higher in solifluction areas than in alluvial areas. Besides dissolved organic carbon, nitrogen availability was the main driver controlling enzyme activities in the high-Arctic, which suggests enhanced organic matter mineralization at increased nutrient availability. Overall, our study provides novel information on the controls of organic matter usage by high-Arctic stream biofilms, which is of high relevance due to the predicted increase of nutrient availability in high-Arctic streams in global climate change scenarios.}, }
@article {pmid30739041, year = {2019}, author = {Camacho-Montealegre, CM and Rodrigues, EM and Tótola, MR}, title = {Microbial diversity and bioremediation of rhizospheric soils from Trindade Island - Brazil.}, journal = {Journal of environmental management}, volume = {236}, number = {}, pages = {358-364}, doi = {10.1016/j.jenvman.2019.02.013}, pmid = {30739041}, issn = {1095-8630}, mesh = {Biodegradation, Environmental ; Brazil ; Hydrocarbons ; Islands ; *Petroleum ; Soil ; Soil Microbiology ; *Soil Pollutants ; }, abstract = {Pristine environments may harbor complex microbial communities with metabolic potential for use in bioremediation of organic pollutants. This study aimed to evaluate crude oil biodegradation by microbial communities present in rhizospheric soils of Bulbostylis nesiotis and Cyperus atlanticus on Trindade Island and the compositional structure of these communities. After 60 days under aerobic conditions, Total Petroleum Hydrocarbon biodegradation ranged from 66 to 75%, depending on the plant species and the origin of the soil samples. There was no response of petroleum biodegradation to fertilization with N:P:K (80:160:80 mg dm[-3]). Soil contamination with crude oil did not necessarily reduce microbial diversity. The richness and diversity increased in contaminated soils in some specific situations. We conclude that microbial communities from pristine soils have the ability to remove hydrocarbons through biodegradation and that Bulbostylis nesiotis and Cyperus atlanticus inhabiting Trindade Island harbor rhizospheric microbial communities with potential for application in rhizoremediation.}, }
@article {pmid30738110, year = {2019}, author = {Mateus-Barros, E and Meneghine, AK and Bagatini, IL and Fernandes, CC and Kishi, LT and Vieira, AAH and Sarmento, H}, title = {Comparison of two DNA extraction methods widely used in aquatic microbial ecology.}, journal = {Journal of microbiological methods}, volume = {159}, number = {}, pages = {12-17}, doi = {10.1016/j.mimet.2019.02.005}, pmid = {30738110}, issn = {1872-8359}, mesh = {Bacteria/chemistry/genetics/*isolation &amp; purification ; Biodiversity ; Chemical Fractionation/*methods ; DNA, Bacterial/genetics/*isolation &amp; purification ; Hydrobiology ; Lakes/*microbiology ; Microbiota ; }, abstract = {In recent years, the rapid advances of culture-independent methods and new molecular tools have revolutionized our understanding of microbial biodiversity and ecological functions. DNA extraction from microbial communities is a critical step in this process and several methods have been proposed and used, but the influence of the extraction method on the outcome and ultimately on ecological inferences from the results is not yet precisely determined. Here, we compared two of the most commonly used extraction methods in aquatic microbial ecology, and investigated whether the two methods yielded comparable results for community ecology analyses. We extracted DNA from 15 different shallow lakes with phenol:chloroform, a classical and widely used extraction method, and with the PowerSoil DNA isolation Kit, often suggested as the standard DNA extraction method, with some adaptations for aquatic environments. We found that although only 5% of all OTUs showed significant differences in pairwise comparisons (using the 15 lakes as replicates), these OTUs accounted for >35% (on average) of the relative abundance. Diversity and richness did not differ significantly between the two extraction methods, but the beta-dispersion of the communities indicated that the organic extraction yielded more homogeneous communities, while the kit extraction generated variability. Consequently, we conclude that despite the small number of OTUs with significant differences, their impact on the community composition obtained was not negligible, and therefore the results from these two extraction methods were not comparable.}, }
@article {pmid30735594, year = {2019}, author = {Ferguson, RMW and Garcia-Alcega, S and Coulon, F and Dumbrell, AJ and Whitby, C and Colbeck, I}, title = {Bioaerosol biomonitoring: Sampling optimization for molecular microbial ecology.}, journal = {Molecular ecology resources}, volume = {19}, number = {3}, pages = {672-690}, pmid = {30735594}, issn = {1755-0998}, support = {NE/M010813/1//Natural Environment Research Council/ ; }, mesh = {*Aerosols ; *Air Microbiology ; Bacteria/*classification/*isolation &amp; purification ; Environmental Monitoring/*methods ; }, abstract = {Bioaerosols (or biogenic aerosols) have largely been overlooked by molecular ecologists. However, this is rapidly changing as bioaerosols play key roles in public health, environmental chemistry and the dispersal ecology of microbes. Due to the low environmental concentrations of bioaerosols, collecting sufficient biomass for molecular methods is challenging. Currently, no standardized methods for bioaerosol collection for molecular ecology research exist. Each study requires a process of optimization, which greatly slows the advance of bioaerosol science. Here, we evaluated air filtration and liquid impingement for bioaerosol sampling across a range of environmental conditions. We also investigated the effect of sampling matrices, sample concentration strategies and sampling duration on DNA yield. Air filtration using polycarbonate filters gave the highest recovery, but due to the faster sampling rates possible with impingement, we recommend this method for fine -scale temporal/spatial ecological studies. To prevent bias for the recovery of Gram-positive bacteria, we found that the matrix for impingement should be phosphate-buffered saline. The optimal method for bioaerosol concentration from the liquid matrix was centrifugation. However, we also present a method using syringe filters for rapid in-field recovery of bioaerosols from impingement samples, without compromising microbial diversity for high -throughput sequencing approaches. Finally, we provide a resource that enables molecular ecologists to select the most appropriate sampling strategy for their specific research question.}, }
@article {pmid30735001, year = {2019}, author = {Cassman, NA and Soares, JR and Pijl, A and Lourenço, KS and van Veen, JA and Cantarella, H and Kuramae, EE}, title = {Nitrification inhibitors effectively target N2 O-producing Nitrosospira spp. in tropical soil.}, journal = {Environmental microbiology}, volume = {21}, number = {4}, pages = {1241-1254}, pmid = {30735001}, issn = {1462-2920}, support = {//NWO-FAPESP/International ; NWO-729.004.003//Netherlands Organization for Scientific Research/International ; FAPESP-2013/50365-5)//Sao Paulo State foundation/International ; }, mesh = {Ammonia/metabolism ; Archaea/*drug effects/genetics ; Bacteria/drug effects/genetics ; Fertilizers/analysis ; Guanidines/*pharmacology ; Nitrification/drug effects ; Nitrosomonadaceae/*drug effects/genetics ; Nitrous Oxide/*metabolism ; Oxidation-Reduction ; Pyrazoles/pharmacology ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Tropical Climate ; }, abstract = {The nitrification inhibitors (NIs) 3,4-dimethylpyrazole (DMPP) and dicyandiamide (DCD) can effectively reduce N2 O emissions; however, which species are targeted and the effect of these NIs on the microbial nitrifier community is still unclear. Here, we identified the ammonia oxidizing bacteria (AOB) species linked to N2 O emissions and evaluated the effects of urea and urea with DCD and DMPP on the nitrifying community in a 258 day field experiment under sugarcane. Using an amoA AOB amplicon sequencing approach and mining a previous dataset of 16S rRNA sequences, we characterized the most likely N2 O-producing AOB as a Nitrosospira spp. and identified Nitrosospira (AOB), Nitrososphaera (archaeal ammonia oxidizer) and Nitrospira (nitrite-oxidizer) as the most abundant, present nitrifiers. The fertilizer treatments had no effect on the alpha and beta diversities of the AOB communities. Interestingly, we found three clusters of co-varying variables with nitrifier operational taxonomic units (OTUs): the N2 O-producing AOB Nitrosospira with N2 O, NO3 [-] , NH4 [+] , water-filled pore space (WFPS) and pH; AOA Nitrososphaera with NO3 [-] , NH4 [+] and pH; and AOA Nitrososphaera and NOB Nitrospira with NH4 [+] , which suggests different drivers. These results support the co-occurrence of non-N2 O-producing Nitrososphaera and Nitrospira in the unfertilized soils and the promotion of N2 O-producing Nitrosospira under urea fertilization. Further, we suggest that DMPP is a more effective NI than DCD in tropical soil under sugarcane.}, }
@article {pmid30729265, year = {2019}, author = {Bernard, C and Escalas, A and Villeriot, N and Agogué, H and Hugoni, M and Duval, C and Carré, C and Got, P and Sarazin, G and Jézéquel, D and Leboulanger, C and Grossi, V and Ader, M and Troussellier, M}, title = {Very Low Phytoplankton Diversity in a Tropical Saline-Alkaline Lake, with Co-dominance of Arthrospira fusiformis (Cyanobacteria) and Picocystis salinarum (Chlorophyta).}, journal = {Microbial ecology}, volume = {78}, number = {3}, pages = {603-617}, pmid = {30729265}, issn = {1432-184X}, support = {ANR-13-BS06-0001//Agence Nationale de la Recherche/ ; }, mesh = {Biodiversity ; Biomass ; Chlorophyll A/metabolism ; Chlorophyta/*growth &amp; development/metabolism ; Ecosystem ; Indian Ocean ; Islands ; Lakes/*microbiology ; Phytoplankton/genetics/*growth &amp; development ; Seasons ; Spirulina/*growth &amp; development/metabolism ; }, abstract = {Lake Dziani Dzaha (Mayotte Island, Indian Ocean) is a tropical thalassohaline lake which geochemical and biological conditions make it a unique aquatic ecosystem considered as a modern analogue of Precambrian environments. In the present study, we focused on the diversity of phytoplanktonic communities, which produce very high and stable biomass (mean2014-2015 = 652 ± 179 μg chlorophyll a L[-1]). As predicted by classical community ecology paradigms, and as observed in similar environments, a single species is expected to dominate the phytoplanktonic communities. To test this hypothesis, we sampled water column in the deepest part of the lake (18 m) during rainy and dry seasons for two consecutive years. Phytoplanktonic communities were characterized using a combination of metagenomic, microscopy-based and flow cytometry approaches, and we used statistical modeling to identify the environmental factors determining the abundance of dominant organisms. As hypothesized, the overall diversity of the phytoplanktonic communities was very low (15 OTUs), but we observed a co-dominance of two, and not only one, OTUs, viz., Arthrospira fusiformis (Cyanobacteria) and Picocystis salinarum (Chlorophyta). We observed a decrease in the abundance of these co-dominant taxa along the depth profile and identified the adverse environmental factors driving this decline. The functional traits measured on isolated strains of these two taxa (i.e., size, pigment composition, and concentration) are then compared and discussed to explain their capacity to cope with the extreme environmental conditions encountered in the aphotic, anoxic, and sulfidic layers of the water column of Lake Dziani Dzaha.}, }
@article {pmid30728279, year = {2019}, author = {Props, R and Monsieurs, P and Vandamme, P and Leys, N and Denef, VJ and Boon, N}, title = {Gene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic Conditions.}, journal = {mSphere}, volume = {4}, number = {1}, pages = {}, pmid = {30728279}, issn = {2379-5042}, mesh = {Adaptation, Physiological/*genetics ; Carbon/metabolism ; Comamonadaceae/*classification/genetics/metabolism ; DNA, Bacterial/genetics ; Fresh Water/chemistry/microbiology ; *Genome, Bacterial ; Genomics ; Metagenomics ; Nuclear Reactors ; Phosphorus/metabolism ; Phylogeny ; *Selection, Genetic ; }, abstract = {We examined the genomic adaptations of prevalent bacterial taxa in a highly nutrient- and ion-depleted freshwater environment located in the secondary cooling water system of a nuclear research reactor. Using genome-centric metagenomics, we found that none of the prevalent bacterial taxa were related to typical freshwater bacterial lineages. We also did not identify strong signatures of genome streamlining, which has been shown to be one of the ecoevolutionary forces shaping the genome characteristics of bacterial taxa in nutrient-depleted environments. Instead, focusing on the dominant taxon, a novel Ramlibacter sp. which we propose to name Ramlibacter aquaticus, we detected extensive positive selection on genes involved in phosphorus and carbon scavenging pathways. These genes were involved in the high-affinity phosphate uptake and storage into polyphosphate granules, metabolism of nitrogen-rich organic matter, and carbon/energy storage into polyhydroxyalkanoate. In parallel, comparative genomics revealed a high number of paralogs and an accessory genome significantly enriched in environmental sensing pathways (i.e., chemotaxis and motility), suggesting extensive gene expansions in R. aquaticus The type strain of R. aquaticus (LMG 30558[T]) displayed optimal growth kinetics and productivity at low nutrient concentrations, as well as substantial cell size plasticity. Our findings with R. aquaticus LMG 30558[T] demonstrate that positive selection and gene expansions may represent successful adaptive strategies to oligotrophic environments that preserve high growth rates and cellular productivity.IMPORTANCE By combining a genome-centric metagenomic approach with a culture-based approach, we investigated the genomic adaptations of prevalent populations in an engineered oligotrophic freshwater system. We found evidence for widespread positive selection on genes involved in phosphorus and carbon scavenging pathways and for gene expansions in motility and environmental sensing to be important genomic adaptations of the abundant taxon in this system. In addition, microscopic and flow cytometric analysis of the first freshwater representative of this population (Ramlibacter aquaticus LMG 30558[T]) demonstrated phenotypic plasticity, possibly due to the metabolic versatility granted by its larger genome, to be a strategy to cope with nutrient limitation. Our study clearly demonstrates the need for the use of a broad set of genomic tools combined with culture-based physiological characterization assays to investigate and validate genomic adaptations.}, }
@article {pmid30726948, year = {2019}, author = {Achouak, W and Abrouk, D and Guyonnet, J and Barakat, M and Ortet, P and Simon, L and Lerondelle, C and Heulin, T and Haichar, FEZ}, title = {Plant hosts control microbial denitrification activity.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {3}, pages = {}, doi = {10.1093/femsec/fiz021}, pmid = {30726948}, issn = {1574-6941}, mesh = {Bacteria/classification/genetics/metabolism ; *Denitrification/genetics ; Host Microbial Interactions ; Microbiota/genetics/*physiology ; Plant Exudates ; Plant Roots/chemistry/classification/microbiology ; Plants/chemistry/classification/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {In the rhizosphere, complex and dynamic interactions occur between plants and microbial networks that are primarily mediated by root exudation. Plants exude various metabolites that may influence the rhizosphere microbiota. However, few studies have sought to understand the role of root exudation in shaping the functional capacities of the microbiota. In this study, we aimed to determine the impact of plants on the diversity of active microbiota and their ability to denitrify via root exudates. For that purpose, we grew four plant species, Triticum aestivum, Brassica napus, Medicago truncatula and Arabidopsis thaliana separately in the same soil. We extracted RNA from the root-adhering soil and the root tissues, and we analysed the bacterial diversity by using 16S rRNA metabarcoding. We measured denitrification activity and denitrification gene expression (nirK and nirS) from each root-adhering soil sample and the root tissues using gas chromatography and quantitative PCR, respectively. We demonstrated that plant species shape denitrification activity and modulate the diversity of the active microbiota through root exudation. We observed a positive effect of T. aestivum and A. thaliana on denitrification activity and nirK gene expression on the root systems. Together, our results underscore the potential power of host plants in controlling microbial activities.}, }
@article {pmid30726571, year = {2019}, author = {Laforest-Lapointe, I and Whitaker, BK}, title = {Decrypting the phyllosphere microbiota: progress and challenges.}, journal = {American journal of botany}, volume = {106}, number = {2}, pages = {171-173}, doi = {10.1002/ajb2.1229}, pmid = {30726571}, issn = {1537-2197}, mesh = {*Climate Change ; Ecosystem ; Environmental Microbiology ; *Microbiota ; Plant Leaves/*microbiology ; }, }
@article {pmid30725170, year = {2019}, author = {Sun, X and Li, B and Han, F and Xiao, E and Xiao, T and Sun, W}, title = {Impacts of Arsenic and Antimony Co-Contamination on Sedimentary Microbial Communities in Rivers with Different Pollution Gradients.}, journal = {Microbial ecology}, volume = {78}, number = {3}, pages = {589-602}, pmid = {30725170}, issn = {1432-184X}, support = {41771301//National Natural Science Foundation of China/ ; 41420104007//National Natural Science Foundation of China/ ; }, mesh = {Antimony/*analysis/pharmacology ; Arsenic/*analysis/pharmacology ; Bacteria/classification/drug effects/genetics/*isolation &amp; purification ; China ; Geologic Sediments/analysis/*microbiology ; *Microbiota ; Rivers/chemistry/*microbiology ; Water Pollutants, Chemical/*analysis/pharmacology ; Water Pollution/analysis ; }, abstract = {Arsenic (As) and antimony (Sb) are both toxic metalloids that are of primary concern for human health. Mining activity has introduced elevated levels of arsenic and antimony into the rivers and has increased the risks of drinking water contamination in China. Due to their mobility, the majority of the metalloids originating from mining activities are deposited in the river sediments. Thus, depending on various geochemical conditions, sediment could either be a sink or source for As and Sb in the water column. Microbes are key mediators for biogeochemical transformation and can both mobilize or precipitate As and Sb. To further understand the microbial community responses to As and Sb contamination, sediment samples with different contamination levels were collected from three rivers. The result of the study suggested that the major portions of As and Sb were in strong association with the sediment matrix and considered nonbioavailable. These fractions, however, were also suggested to have profound influences on the microbial community composition. As and Sb contamination caused strong reductions in microbial diversity in the heavily contaminated river sediments. Microorganisms were more sensitive to As comparing to Sb, as revealed by the co-occurrence network and random forest predictions. Operational taxonomic units (OTUs) that were potentially involved in As and Sb metabolism, such as Anaerolinea, Sphingomonas, and Opitutus, were enriched in the heavily contaminated samples. In contrast, many keystone taxa, including members of the Hyphomicrobiaceae and Bradyrhizobiaceae families, were inhibited by metalloid contamination, which could further impair crucial environmental services provided by these members.}, }
@article {pmid30724437, year = {2019}, author = {Ma, Y and Zilles, JL and Kent, AD}, title = {An evaluation of primers for detecting denitrifiers via their functional genes.}, journal = {Environmental microbiology}, volume = {21}, number = {4}, pages = {1196-1210}, doi = {10.1111/1462-2920.14555}, pmid = {30724437}, issn = {1462-2920}, support = {//U.S. Department of Agriculture/International ; 2015-67019-23584//National Institute of Food and Agriculture/International ; }, mesh = {Base Sequence ; DNA Primers/genetics/*standards ; Denitrification/*genetics ; Ecosystem ; Metagenome ; Microbiota/*genetics ; Nitrogen ; Soil ; *Soil Microbiology ; }, abstract = {Microbial populations provide nitrogen cycling ecosystem services at the nexus of agriculture, environmental quality and climate change. Denitrification, in particular, impacts socio-environmental systems in both positive and negative ways, through reduction of aquatic and atmospheric nitrogen pollution, but also reduction of soil fertility and production of greenhouse gases. However, denitrification rates are quite variable in time and space, and therefore difficult to model. Microbial ecology is working to improve the predictive ecology of denitrifiers by quantifying and describing the diversity of microbial functional groups. However, metagenomic sequencing has revealed previously undescribed diversity within these functional groups, and highlighted a need to reevaluate coverage of existing DNA primers for denitrification functional genes. We provide here a comprehensive in silico evaluation of primer sets that target diagnostic genes in the denitrification pathway. This analysis makes use of current DNA sequence data available for each functional gene. It contributes a comparative analysis of the strengths and limitations of each primer set for describing denitrifier functional groups. This analysis identifies genes for which development of new tools is needed, and aids in interpretation of existing datasets, both of which will facilitate application of molecular methods to further develop the predictive ecology of denitrifiers.}, }
@article {pmid30721227, year = {2019}, author = {Marsland, R and Cui, W and Goldford, J and Sanchez, A and Korolev, K and Mehta, P}, title = {Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities.}, journal = {PLoS computational biology}, volume = {15}, number = {2}, pages = {e1006793}, pmid = {30721227}, issn = {1553-7358}, support = {R35 GM119461/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology ; Databases, Factual ; *Ecosystem ; Energy Metabolism/*physiology ; Microbial Consortia/*physiology ; Models, Biological ; Stochastic Processes ; Thermodynamics ; }, abstract = {A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences between the microbes and their chemical environment through the consumption and production of metabolites. By analyzing a generalized consumer resource model that explicitly includes cross-feeding, stochastic colonization, and thermodynamics, we show that complex microbial communities generically exhibit a transition as a function of available energy fluxes from a "resource-limited" regime where community structure and stability is shaped by energetic and metabolic considerations to a diverse regime where the dominant force shaping microbial communities is the overlap between species' consumption preferences. These two regimes have distinct species abundance patterns, different functional profiles, and respond differently to environmental perturbations. Our model reproduces large-scale ecological patterns observed across multiple experimental settings such as nestedness and differential beta diversity patterns along energy gradients. We discuss the experimental implications of our results and possible connections with disorder-induced phase transitions in statistical physics.}, }
@article {pmid30719551, year = {2019}, author = {Margesin, R and Collins, T}, title = {Microbial ecology of the cryosphere (glacial and permafrost habitats): current knowledge.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {6}, pages = {2537-2549}, pmid = {30719551}, issn = {1432-0614}, support = {IF/01635/2014//Investigador FCT Programme/ ; }, mesh = {*Biodiversity ; Biota ; Climate Change ; Cold Temperature ; Ice Cover/*microbiology ; *Microbiota ; Permafrost/*microbiology ; }, abstract = {Microorganisms in cold ecosystems play a key ecological role in their natural habitats. Since these ecosystems are especially sensitive to climate changes, as indicated by the worldwide retreat of glaciers and ice sheets as well as permafrost thawing, an understanding of the role and potential of microbial life in these habitats has become crucial. Emerging technologies have added significantly to our knowledge of abundance, functional activity, and lifestyles of microbial communities in cold environments. The current knowledge of microbial ecology in glacial habitats and permafrost, the most studied habitats of the cryosphere, is reported in this review.}, }
@article {pmid30715579, year = {2019}, author = {Kivlin, SN and Kazenel, MR and Lynn, JS and Lee Taylor, D and Rudgers, JA}, title = {Plant Identity Influences Foliar Fungal Symbionts More Than Elevation in the Colorado Rocky Mountains.}, journal = {Microbial ecology}, volume = {78}, number = {3}, pages = {688-698}, pmid = {30715579}, issn = {1432-184X}, support = {DEB1354972//Directorate for Biological Sciences/ ; }, mesh = {Climate Change ; Colorado ; Ecosystem ; Endophytes/classification/genetics/isolation &amp; purification/physiology ; Fungi/classification/genetics/*isolation &amp; purification/physiology ; Mycobiome ; Phylogeny ; Plant Leaves/classification/*microbiology/physiology ; Plant Physiological Phenomena ; Poaceae/classification/*microbiology/physiology ; *Symbiosis ; }, abstract = {Despite colonizing nearly every plant on Earth, foliar fungal symbionts have received little attention in studies on the biogeography of host-associated microbes. Evidence from regional scale studies suggests that foliar fungal symbiont distributions are influenced both by plant hosts and environmental variation in climate and soil resources. However, previous surveys have focused on either one plant host across an environmental gradient or one gradient and multiple plant hosts, making it difficult to disentangle the influence of host identity from the influence of the environment on foliar endophyte communities. We used a culture-based approach to survey fungal symbiont composition in the leaves of nine C3 grass species along replicated elevation gradients in grasslands of the Colorado Rocky Mountains. In these ecosystems, the taxonomic richness and composition of foliar fungal symbionts were mostly structured by the taxonomic identity of the plant host rather than by variation in climate. Plant traits related to size (height and leaf length) were the best predictors of foliar fungal symbiont composition and diversity, and composition did not vary predictably with plant evolutionary history. The largest plants had the most diverse and distinctive fungal communities. These results suggest that across the ~ 300 m elevation range that we sampled, foliar fungal symbionts may indirectly experience climate change by tracking the shifting distributions of plant hosts rather than tracking climate directly.}, }
@article {pmid30715272, year = {2019}, author = {McAllister, SM and Moore, RM and Gartman, A and Luther, GW and Emerson, D and Chan, CS}, title = {The Fe(II)-oxidizing Zetaproteobacteria: historical, ecological and genomic perspectives.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {4}, pages = {}, pmid = {30715272}, issn = {1574-6941}, support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics ; Ecosystem ; Ferrous Compounds/*metabolism ; Genome, Bacterial/genetics ; Hydrothermal Vents/microbiology ; Oxidation-Reduction ; Phylogeny ; Proteobacteria/classification/*genetics/isolation &amp; purification/*metabolism ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; }, abstract = {The Zetaproteobacteria are a class of bacteria typically associated with marine Fe(II)-oxidizing environments. First discovered in the hydrothermal vents at Loihi Seamount, Hawaii, they have become model organisms for marine microbial Fe(II) oxidation. In addition to deep sea and shallow hydrothermal vents, Zetaproteobacteria are found in coastal sediments, other marine subsurface environments, steel corrosion biofilms and saline terrestrial springs. Isolates from a range of environments all grow by autotrophic Fe(II) oxidation. Their success lies partly in their microaerophily, which enables them to compete with abiotic Fe(II) oxidation at Fe(II)-rich oxic/anoxic transition zones. To determine the known diversity of the Zetaproteobacteria, we have used 16S rRNA gene sequences to define 59 operational taxonomic units (OTUs), at 97% similarity. While some Zetaproteobacteria taxa appear to be cosmopolitan, others are enriched by specific habitats. OTU networks show that certain Zetaproteobacteria co-exist, sharing compatible niches. These niches may correspond with adaptations to O2, H2 and nitrate availability, based on genomic analyses of metabolic potential. Also, a putative Fe(II) oxidation gene has been found in diverse Zetaproteobacteria taxa, suggesting that the Zetaproteobacteria evolved as Fe(II) oxidation specialists. In all, studies suggest that Zetaproteobacteria are widespread, and therefore may have a broad influence on marine and saline terrestrial Fe cycling.}, }
@article {pmid30712793, year = {2019}, author = {Raabis, S and Li, W and Cersosimo, L}, title = {Effects and immune responses of probiotic treatment in ruminants.}, journal = {Veterinary immunology and immunopathology}, volume = {208}, number = {}, pages = {58-66}, pmid = {30712793}, issn = {1873-2534}, support = {T32 OD010423/OD/NIH HHS/United States ; }, mesh = {Animals ; Cell Line ; Gastrointestinal Microbiome/immunology ; Gastrointestinal Tract/immunology ; Immunity, Innate ; Probiotics/*therapeutic use ; Ruminants/*immunology/*microbiology ; }, abstract = {Gut microbial colonization and establishment are vital to ruminant health and production. This review article focuses on current knowledge and methods used to understand and manipulate the gut microbial community in ruminant animals, with a special focus on probiotics treatment. This review highlights the most promising of studies in this area, including gut microbial colonization and establishment, effect of gastrointestinal tract microbial community on host mucosal innate immune function, impact of feeding strategies on gut microbial community, current probiotic treatments in ruminants, methods to manipulate the gut microbiota and associated antimicrobial compounds, and models and cell lines used in understanding the host immune response to probiotic treatments. As a lot of work in this area was done in humans and mice, this review article also includes up-to-date knowledge from relevant studies in human and mouse models. This review is a useful resource for scientists working in the areas of ruminant nutrition and health, and to researchers investigating the microbial ecology and its relation to animal health.}, }
@article {pmid30706113, year = {2019}, author = {Ávila, MP and Oliveira-Junior, ES and Reis, MP and Hester, ER and Diamantino, C and Veraart, AJ and Lamers, LPM and Kosten, S and Nascimento, AMA}, title = {The Water Hyacinth Microbiome: Link Between Carbon Turnover and Nutrient Cycling.}, journal = {Microbial ecology}, volume = {78}, number = {3}, pages = {575-588}, pmid = {30706113}, issn = {1432-184X}, support = {APQ 01673/16//Funda??o de Amparo ? Pesquisa do Estado de Minas Gerais/ ; 306774/2016-0//Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico (BR)/ ; BEX 13607/13-8//Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior/ ; 8631(2012)//Boeing/ ; 2017//Erasmus plus program/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Carbon/*metabolism ; DNA, Bacterial/genetics ; Ecosystem ; Eichhornia/*microbiology ; *Microbiota ; Nutrients/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Water hyacinth (WH), a large floating plant, plays an important role in the biogeochemistry and ecology of many freshwaters globally. Its biogeochemical impact on wetland functioning is strongly mediated by the microbiome associated with its roots. However, little is known about the structure and function of this WH rhizobiome and its relation to wetland ecosystem functioning. Here, we unveil the core and transient rhizobiomes of WH and their key biogeochemical functions in two of the world's largest wetlands: the Amazon and the Pantanal. WH hosts a highly diverse microbial community shaped by spatiotemporal changes. Proteobacteria lineages were most common, followed by Actinobacteria and Planctomycetes. Deltaproteobacteria and Sphingobacteriia predominated in the core microbiome, potentially associated with polysaccharide degradation and fermentation of plant-derived carbon. Conversely, a plethora of lineages were transient, including highly abundant Acinetobacter, Acidobacteria subgroup 6, and methanotrophs, thus assuring diverse taxonomic signatures in the two different wetlands. Our findings point out that methanogenesis is a key driver of, and proxy for, community structure, especially during seasonal plant decline. We provide ecologically relevant insights into the WH microbiome, which is a key element linking plant-associated carbon turnover with other biogeochemical fluxes in tropical wetlands.}, }
@article {pmid30706112, year = {2019}, author = {Song, Y and Mao, G and Gao, G and Bartlam, M and Wang, Y}, title = {Structural and Functional Changes of Groundwater Bacterial Community During Temperature and pH Disturbances.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {428-445}, pmid = {30706112}, issn = {1432-184X}, support = {No.31670498 and 31322012//National Natural Science Foundation of China/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Biodiversity ; Denitrification ; Flow Cytometry ; Groundwater/*chemistry/*microbiology ; Hydrogen-Ion Concentration ; Nitrification ; Nitrogen/metabolism ; Phylogeny ; Temperature ; }, abstract = {In this study, we report the characteristics of a microbial community in sampled groundwater and elucidate the effects of temperature and pH disturbances on bacterial structure and nitrogen-cycling functions. The predominant phyla of candidate OD1, candidate OP3, and Proteobacteria represented more than half of the total bacteria, which clearly manifested as a "low nucleic acid content (LNA) bacteria majority" type via flow cytometric fingerprint. The results showed that LNA bacteria were more tolerant to rapid changes in temperature and pH, compared to high nucleic acid content (HNA) bacteria. A continuous temperature increase test demonstrated that the LNA bacterial group was less competitive than the HNA bacterial group in terms of maintaining their cell intactness and growth potential. In contrast, the percentage of intact LNA bacteria was maintained at nearly 70% with pH decrease, despite a 50% decrease in total intact cells. Next-generation sequencing results revealed strong resistance and growth potential of phylum Proteobacteria when the temperature increased or the pH decreased in groundwater, especially for subclasses α-, β-, and γ-Proteobacteria. In addition, relative abundance of nitrogen-related functional genes by qPCR showed no difference in nitrifiers or denitrifiers within 0.45 μm-captured and 0.45 μm-filterable bacteria due to phylogenetic diversity. One exception was the monophyletic anammox bacteria that belong to the phylum Planctomycetes, which were mostly captured on a 0.45-μm filter. Furthermore, we showed that both temperature increase and pH decrease could enhance the denitrification potential, whereas the nitrification and anammox potentials were weakened.}, }
@article {pmid30704595, year = {2019}, author = {Kamimura, BA and De Filippis, F and Sant'Ana, AS and Ercolini, D}, title = {Large-scale mapping of microbial diversity in artisanal Brazilian cheeses.}, journal = {Food microbiology}, volume = {80}, number = {}, pages = {40-49}, doi = {10.1016/j.fm.2018.12.014}, pmid = {30704595}, issn = {1095-9998}, mesh = {Animals ; *Biodiversity ; Brazil ; Cheese/*microbiology ; Cluster Analysis ; DNA, Bacterial/genetics ; *Food Microbiology ; Geography ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Brazilian artisanal cheeses are characterized by the use of raw milk and in some cases, natural starter cultures, known as "pingo", as well as following simple and traditional manufacturing technology. In this study, a large-scale screening of the microbial ecology of 11 different types of artisanal cheeses produced in five geographical areas of Brazil was performed. Besides, the specific origin-related microbial signatures were identified. Clear geography- and technology-based differences in the microbiota were observed. Lactic acid bacteria dominated in all cheeses although Enterobacteriaceae and Staphylococcus also occurred in North, Northeast and Central cheeses. Differences in the lactic acid bacteria patterns were also highlighted: Streptococcus, Leuconostoc, Lactococcus and Lactobacillus were differently combined in terms of relative abundance according to product type and region of production. This study provides a comprehensive, unprecedented microbiological mapping of Brazilian cheeses, highlighting the impact of geographical origin and mode of production on microbial diversity. The results obtained will help to plan an evaluation of microbial contamination sources that will need to be studied for the improvement of cheese quality and safety.}, }
@article {pmid30701285, year = {2019}, author = {Ely, CS and Smets, BF}, title = {Guild Composition of Root-Associated Bacteria Changes with Increased Soil Contamination.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {416-427}, pmid = {30701285}, issn = {1432-184X}, support = {R829405//U.S. Environmental Protection Agency/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Biodegradation, Environmental ; DNA, Bacterial/genetics ; Plant Roots/*microbiology ; Plants/microbiology ; Polycyclic Aromatic Hydrocarbons/*analysis/metabolism ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/*analysis/metabolism ; }, abstract = {The interaction of plants and root-associated bacteria encourage the removal of soil contaminants. Engineers and scientists have looked at this phenomenon as a possible means of soil treatment (rhizodegradation). In this study, root-associated bacteria were isolated and selected for growth on a model soil contaminant: polycyclic aromatic hydrocarbons. Isolates were compared genetically to see how plant-bacteria interactions change with soil contamination levels. Characterization of root-associated bacteria was performed using REP-PCR genetic fingerprinting and 16s rRNA gene alignments for identification. Genomic fingerprinting indicated that the composition of PAH-metabolizing bacteria ("guild") was similar among plant species at each treatment level. However, guild composition changed with contamination level and differed from that of bulk soils, suggesting a common rhizosphere effect among plant species related to PAH contamination. PAH-metabolizing bacteria were identified through 16s rRNA gene alignment as members of the α-, β-, and γ-proteobacteria, Actinobacteria, and Bacilli classes. Burkholderia and Pseudomonas spp. were the only genera of bacteria isolated from all plant types in uncontaminated controls. Bacterial species found at the highest treatment included Achromobacter xylosoxidans, Rhodococcus spp., members of the Microbacteriae, Stenotrophomonas rhizophilia, as well as other members of the alpha-proteobacteria. Given their ability to grow on PAHs and inhabit highly contaminated rhizospheres, these bacteria appear good candidates for the promotion of rhizodegradation.}, }
@article {pmid30701133, year = {2019}, author = {De Paepe, K and Verspreet, J and Rezaei, MN and Hidalgo Martinez, S and Meysman, F and Van de Walle, D and Dewettinck, K and Raes, J and Courtin, C and Van de Wiele, T}, title = {Isolation of wheat bran-colonizing and metabolizing species from the human fecal microbiota.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6293}, pmid = {30701133}, issn = {2167-8359}, abstract = {Undigestible, insoluble food particles, such as wheat bran, are important dietary constituents that serve as a fermentation substrate for the human gut microbiota. The first step in wheat bran fermentation involves the poorly studied solubilization of fibers from the complex insoluble wheat bran structure. Attachment of bacteria has been suggested to promote the efficient hydrolysis of insoluble substrates, but the mechanisms and drivers of this microbial attachment and colonization, as well as subsequent fermentation remain to be elucidated. We have previously shown that an individually dependent subset of gut bacteria is able to colonize the wheat bran residue. Here, we isolated these bran-attached microorganisms, which can then be used to gain mechanistic insights in future pure culture experiments. Four healthy fecal donors were screened to account for inter-individual differences in gut microbiota composition. A combination of a direct plating and enrichment method resulted in the isolation of a phylogenetically diverse set of species, belonging to the Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria phyla. A comparison with 16S rRNA gene sequences that were found enriched on wheat bran particles in previous studies, however, showed that the isolates do not yet cover the entire diversity of wheat-bran colonizing species, comprising among others a broad range of Prevotella, Bacteroides and Clostridium cluster XIVa species. We, therefore, suggest several modifications to the experiment set-up to further expand the array of isolated species.}, }
@article {pmid30698709, year = {2019}, author = {Janssens, TKS and Tyc, O and Besselink, H and de Boer, W and Garbeva, P}, title = {Biological activities associated with the volatile compound 2,5-bis(1-methylethyl)-pyrazine.}, journal = {FEMS microbiology letters}, volume = {366}, number = {3}, pages = {}, doi = {10.1093/femsle/fnz023}, pmid = {30698709}, issn = {1574-6968}, mesh = {Anti-Infective Agents/*pharmacology/toxicity ; Bacteria/*drug effects ; Burkholderia/physiology ; Cell Line ; Cell Survival/*drug effects ; Cell Wall/drug effects ; Coculture Techniques ; Escherichia coli/genetics ; Fungi/*drug effects ; Microbial Interactions/physiology ; Paenibacillus/*chemistry/*metabolism ; Pyrazines/*pharmacology/toxicity ; }, abstract = {Pyrazines are 1,4-diazabenzene-based volatile organic compounds and known for their broad-spectrum antimicrobial activity. In the present study, we assessed the antimicrobial activity of 2,5-bis(1-methylethyl)-pyrazine, produced by Paenibacillus sp. AD87 during co-culture with Burkholderia sp. AD24. In addition, we were using transcriptional reporter assays in E. coli and mammalian cells to decipher the possible mode of action. Bacterial and mammalian luciferase reporter strains were deployed to elucidate antimicrobial and toxicological effects of 2,5-bis(1-methylethyl)-pyrazine. At high levels of exposure, 2,5-bis(1-methylethyl)-pyrazine exerted strong DNA damage response. At lower concentrations, cell-wall damage response was observed. The activity was corroborated by a general toxicity reporter assay in E. coli ΔampD, defective in peptidoglycan turnover. The maximum E. coli cell-wall stress activity was measured at a concentration close to the onset of the mammalian cytotoxicity, while other adverse outcome pathways, such as the activation of aryl hydrocarbon and estrogenic receptor, the p53 tumour suppressor and the oxidative stress-related Nrf2 transcription factor, were induced at elevated concentrations compared to the response of mammalian cells. Because of its broad-spectrum antimicrobial activity at lower concentrations and the relatively low mammalian toxicity, 2,5-bis(1-methylethyl)-pyrazine is a potential bio-based fumigant with possible applications in food industry, agriculture or logistics.}, }
@article {pmid30697889, year = {2019}, author = {Eckert, EM and Quero, GM and Di Cesare, A and Manfredini, G and Mapelli, F and Borin, S and Fontaneto, D and Luna, GM and Corno, G}, title = {Antibiotic disturbance affects aquatic microbial community composition and food web interactions but not community resilience.}, journal = {Molecular ecology}, volume = {28}, number = {5}, pages = {1170-1182}, doi = {10.1111/mec.15033}, pmid = {30697889}, issn = {1365-294X}, support = {Call 2014 - Molecular Biodiversity of invasive spe//LifeWatch-Italy/International ; 655537//Marie Sk&#x142;odowska-Curie Actions Individual Fellowship/International ; Program 2013-15//CIPAIS - International Commission for the Protection of Italian-Swiss Waters/International ; 655537//Horizon 2020/International ; 2015//Horizon 2020/International ; 2017//Horizon 2020/International ; 2//Horizon 2020/International ; }, mesh = {Anti-Bacterial Agents/adverse effects ; Bacteria/*drug effects/genetics ; Biodiversity ; *Ecosystem ; Food Chain ; Microbiota/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Notwithstanding the fundamental role that environmental microbes play for ecosystem functioning, data on how microbes react to disturbances are still scarce, and most factors that confer stability to microbial communities are unknown. In this context, antibiotic discharge into the environment is considered a worldwide threat for ecosystems with potential risks to human health. We therefore tested resilience of microbial communities challenged by the presence of an antibiotic. In a continuous culture experiment, we compared the abundance, composition and diversity of microbial communities undisturbed or disturbed by the constant addiction of tetracycline in low (10 µg/L) or intermediate (100 µg/L) concentration (press disturbance). Further, the bacterial communities in the three treatments had to face the sudden pulse disturbance of adding an allochthonous bacterium (Escherichia coli). Tetracycline, even at low concentrations, affected microbial communities by changing their phylogenetic composition and causing cell aggregation. This, however, did not coincide with a reduced microbial diversity, but was mainly caused by a shift in dominance of specific bacterial families. Moreover, the less disturbed community (10 µg/L tetracycline) was sometimes more similar to the control and sometimes more similar to heavily disturbed community (100 µg/L tetracycline). All in all, we could not see a pattern where the communities disturbed with antibiotics were less resilient to a second disturbance introducing E. coli, but they seemed to be able to buffer the input of the allochthonous strain in a similar manner as the control.}, }
@article {pmid30694508, year = {2019}, author = {Pérez-Cobas, AE and Buchrieser, C}, title = {Analysis of the Pulmonary Microbiome Composition of Legionella pneumophila-Infected Patients.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1921}, number = {}, pages = {429-443}, doi = {10.1007/978-1-4939-9048-1_27}, pmid = {30694508}, issn = {1940-6029}, mesh = {Computational Biology/methods ; DNA, Ribosomal Spacer ; Data Interpretation, Statistical ; High-Throughput Nucleotide Sequencing ; Humans ; Legionella pneumophila/*physiology ; Legionnaires' Disease/*microbiology ; *Microbiota ; Molecular Sequence Annotation ; Pneumonia, Bacterial/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; }, abstract = {The analysis of the lung microbiome composition is a field of research that recently emerged. It gained great interest in pulmonary diseases such as pneumonia since the microbiome seems to be involved in host immune responses, inflammation, and protection against pathogens. Thus, it is possible that the microbial communities living in the lungs play a role in the outcome and severity of lung infections such as Legionella-caused pneumonia and in the response to antibiotic therapy. In this chapter, all steps necessary for the characterization of the bacterial and fungal fraction of the lung microbiome using high-throughput sequencing approaches are explained, starting from the selection of clinical samples to the analysis of the taxonomic composition, diversity, and ecology of the microbiome.}, }
@article {pmid30694341, year = {2019}, author = {Ruiz-Ripa, L and Gómez, P and Alonso, CA and Camacho, MC and de la Puente, J and Fernández-Fernández, R and Ramiro, Y and Quevedo, MA and Blanco, JM and Zarazaga, M and Höfle, U and Torres, C}, title = {Detection of MRSA of Lineages CC130-mecC and CC398-mecA and Staphylococcus delphini-lnu(A) in Magpies and Cinereous Vultures in Spain.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {409-415}, pmid = {30694341}, issn = {1432-184X}, support = {SAF2016-76571-R//Ministerio de Econom?a, Industria y Competitividad, Gobierno de Espa?a/ ; }, mesh = {Animals ; Animals, Wild/*microbiology ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Falconiformes/*microbiology ; Methicillin-Resistant Staphylococcus aureus/classification/drug effects/genetics/*isolation &amp; purification ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Penicillin-Binding Proteins/genetics/metabolism ; Spain ; Tetracycline/pharmacology ; Virulence Factors/genetics/metabolism ; }, abstract = {The aim of this study was to determine the carriage rate of coagulase-positive staphylococci (CoPS) in wild birds and to characterize recovered isolates. Tracheal samples from 324 wild birds, obtained in different Spanish regions during 2015-2016, were screened for CoPS carriage. The antimicrobial resistance profile and the virulence gene content were investigated. Molecular typing was performed by spa, agr, MLST, SCCmec, and S. delphini group classification. CoPS were recovered from 26 samples of wild birds (8.3%), and 27 isolates were further characterized. Two CoPS species were detected: S. aureus (n = 15; eight cinereous vultures and seven magpies) and S. delphini (n = 12; 11 cinereous vultures and one red kite). Thirteen S. aureus were methicillin-resistant (MRSA) and the remaining two strains were methicillin-susceptible (MSSA). Twelve MRSA were mecC-positive, typed as t843-ST1583/ST1945/ST1581/ST1571 (n = 11) and t1535-ST1945 (n = 1) (all of clonal-complex CC130); they were susceptible to the non-β-lactams tested. The remaining MRSA strain carried the mecA gene, was typed as t011-ST398-CC398-agrI-SCCmec-V, and showed a multiresistance phenotype. MSSA isolates were ascribed to lineages ST97-CC97 and ST425-CC425. All S. aureus lacked the studied virulence genes (lukS/F-PV, tst, eta, etb, and etd), and the IEC type E (with scn and sak genes) was detected in four mecC-positive and one MSSA isolates. S. delphini strains were methicillin-susceptible but showed resistance to at least one of the antimicrobials tested, with high penicillin (75%, with blaZ gene) and tetracycline [58%, with tet(K)± tet(L)] resistance rates. All S. delphini isolates presented the virulence genes lukS-I, siet, and se-int, and four carried the clindamycin-resistance lnu(A) gene.}, }
@article {pmid30689848, year = {2019}, author = {Xu, CQ and Liu, H and Zhou, SS and Zhang, DX and Zhao, W and Wang, S and Chen, F and Sun, YQ and Nie, S and Jia, KH and Jiao, SQ and Zhang, RG and Yun, QZ and Guan, W and Wang, X and Gao, Q and Bennetzen, JL and Maghuly, F and Porth, I and Van de Peer, Y and Wang, XR and Ma, Y and Mao, JF}, title = {Genome sequence of Malania oleifera, a tree with great value for nervonic acid production.}, journal = {GigaScience}, volume = {8}, number = {2}, pages = {}, pmid = {30689848}, issn = {2047-217X}, mesh = {*Genome, Plant ; Molecular Sequence Annotation ; Olacaceae/*genetics ; Phylogeny ; *Sequence Analysis, RNA ; *Whole Genome Sequencing ; }, abstract = {BACKGROUND: Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools.<br><br>FINDINGS: We generated 51 Gb and 135&#xa0;Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10&#xd7; Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51&#xa0;Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10&#xd7; Genomics reads. Identified repeats constituted &#x223c;82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long-chain fatty acid were identified and studied in detail.<br><br>CONCLUSIONS: Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology and for the functional genomics of nervonic acid biosynthesis.}, }
@article {pmid30689307, year = {2019}, author = {Wackett, LP}, title = {Evolutionary microbial ecology: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology.}, journal = {Environmental microbiology reports}, volume = {11}, number = {1}, pages = {48-49}, doi = {10.1111/1758-2229.12734}, pmid = {30689307}, issn = {1758-2229}, mesh = {*Biological Evolution ; Databases, Factual ; *Environmental Microbiology ; *Internet ; }, }
@article {pmid30689286, year = {2019}, author = {Berg, JS and Pjevac, P and Sommer, T and Buckner, CRT and Philippi, M and Hach, PF and Liebeke, M and Holtappels, M and Danza, F and Tonolla, M and Sengupta, A and Schubert, CJ and Milucka, J and Kuypers, MMM}, title = {Dark aerobic sulfide oxidation by anoxygenic phototrophs in anoxic waters.}, journal = {Environmental microbiology}, volume = {21}, number = {5}, pages = {1611-1626}, doi = {10.1111/1462-2920.14543}, pmid = {30689286}, issn = {1462-2920}, support = {//Deutsche Forschungsgemeinschaft/International ; Cross Disciplinary Fellowship, LT000993/2014-C//Human Frontier Science Program/International ; //International Max Planck Research School of Marine Microbiology/International ; //Max Planck Society/International ; }, mesh = {Aerobiosis ; Chromatiaceae/genetics/growth &amp; development/*metabolism/radiation effects ; Lakes/analysis/*microbiology ; Light ; Oxidation-Reduction ; Oxygen/analysis/*metabolism ; Phototrophic Processes ; Sulfides/*metabolism ; }, abstract = {Anoxygenic phototrophic sulfide oxidation by green and purple sulfur bacteria (PSB) plays a key role in sulfide removal from anoxic shallow sediments and stratified waters. Although some PSB can also oxidize sulfide with nitrate and oxygen, little is known about the prevalence of this chemolithotrophic lifestyle in the environment. In this study, we investigated the role of these phototrophs in light-independent sulfide removal in the chemocline of Lake Cadagno. Our temporally resolved, high-resolution chemical profiles indicated that dark sulfide oxidation was coupled to high oxygen consumption rates of ~9 μM O2 ·h[-1] . Single-cell analyses of lake water incubated with [13] CO2 in the dark revealed that Chromatium okenii was to a large extent responsible for aerobic sulfide oxidation and it accounted for up to 40% of total dark carbon fixation. The genome of Chr. okenii reconstructed from the Lake Cadagno metagenome confirms its capacity for microaerophilic growth and provides further insights into its metabolic capabilities. Moreover, our genomic and single-cell data indicated that other PSB grow microaerobically in these apparently anoxic waters. Altogether, our observations suggest that aerobic respiration may not only play an underappreciated role in anoxic environments but also that organisms typically considered strict anaerobes may be involved.}, }
@article {pmid30687882, year = {2019}, author = {Liu, J and Tu, T and Gao, G and Bartlam, M and Wang, Y}, title = {Biogeography and Diversity of Freshwater Bacteria on a River Catchment Scale.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {324-335}, pmid = {30687882}, issn = {1432-184X}, support = {2015CB459000//Ministry of Science and Technology of the People's Republic of China/ ; 31670498//National Natural Science Foundation of China/ ; 31322012//National Natural Science Foundation of China/ ; }, mesh = {Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; *Biodiversity ; Geography ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Rivers/*microbiology ; Water Microbiology ; }, abstract = {To illustrate how freshwater bacterial community changes with geographic gradient, we investigated the spatial changes of bacterial abundance and community structures from over 200 samples on a catchment scale in the Songhua River using heterotrophic plate counts, flow cytometry, denaturing gradient gel electrophoresis, and pyrosequencing analysis. The results showed that the mainstream had higher cultivable bacteria and total bacterial concentration than tributaries in the Songhua River catchment. Response model analysis demonstrated that the bacterial community exhibits a biogeographical signature even in an interconnected river network system, and the total bacterial concentration and biodiversity were significantly correlated to latitude (p < 0.001) and longitude (p < 0.001). Multivariate redundancy analysis indicated that temperature was the most important factor driving bacterial community structure in the Songhua River, which accounts for 35.30% variance of communities, then dissolved oxygen (17.60%), latitude (17.60%), longitude (11.80%), and pH (5.88%). High-throughput pyrosequencing revealed that at the phylum level, Proteobacteria was numerically dominant (89.6%) in river catchment, followed by Bacteroidetes (8.1%) and Cyanobacteria (1.2%). The overall results revealed that the bacterial community was driven by geographical distance regardless of the continuum of the river on a catchment scale.}, }
@article {pmid30687755, year = {2018}, author = {Kuang, X and Chen, V and Xu, X}, title = {Novel Approaches to the Control of Oral Microbial Biofilms.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {6498932}, pmid = {30687755}, issn = {2314-6141}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology/*therapeutic use ; Bacterial Infections/*drug therapy ; Biofilms/*drug effects ; Dental Cements/pharmacology/therapeutic use ; Humans ; Mouth/*microbiology ; Virulence/drug effects ; }, abstract = {Effective management of biofilm-related oral infectious diseases is a global challenge. Oral biofilm presents increased resistance to antimicrobial agents and elevated virulence compared with planktonic bacteria. Antimicrobial agents, such as chlorhexidine, have proven effective in the disruption/inhibition of oral biofilm. However, the challenge of precisely and continuously eliminating the specific pathogens without disturbing the microbial ecology still exists, which is a major factor in determining the virulence of a multispecies microbial consortium and the consequent development of oral infectious diseases. Therefore, several novel approaches are being developed to inhibit biofilm virulence without necessarily inducing microbial dysbiosis of the oral cavity. Nanoparticles, such as pH-responsive enzyme-mimic nanoparticles, have been developed to specifically target the acidic niches within the oral biofilm where tooth demineralization readily occurs, in effect controlling dental caries. Quaternary ammonium salts (QAS) such as dimethylaminododecyl methacrylate (DMADDM), when incorporated into dental adhesives or resin composite, have also shown excellent and durable antimicrobial activity and thus could effectively inhibit the occurrence of secondary caries. In addition, custom-designed small molecules, natural products and their derivatives, as well as basic amino acids such as arginine, have demonstrated ecological effects by modulating the virulence of the oral biofilm without universally killing the commensal bacteria, indicating a promising approach to the management of oral infectious diseases such as dental caries and periodontal diseases. This article aims to introduce these novel approaches that have shown potential in the control of oral biofilm. These methods may be utilized in the near future to effectively promote the clinical management of oral infectious diseases and thus benefit oral health.}, }
@article {pmid30687262, year = {2018}, author = {Zhou, C and Ontiveros-Valencia, A and Nerenberg, R and Tang, Y and Friese, D and Krajmalnik-Brown, R and Rittmann, BE}, title = {Hydrogenotrophic Microbial Reduction of Oxyanions With the Membrane Biofilm Reactor.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3268}, pmid = {30687262}, issn = {1664-302X}, abstract = {Oxyanions, such as nitrate, perchlorate, selenate, and chromate are commonly occurring contaminants in groundwater, as well as municipal, industrial, and mining wastewaters. Microorganism-mediated reduction is an effective means to remove oxyanions from water by transforming oxyanions into harmless and/or immobilized forms. To carry out microbial reduction, bacteria require a source of electrons, called the electron-donor substrate. Compared to organic electron donors, H2 is not toxic, generates minimal secondary contamination, and can be readily obtained in a variety of ways at reasonable cost. However, the application of H2 through conventional delivery methods, such as bubbling, is untenable due to H2's low water solubility and combustibility. In this review, we describe the membrane biofilm reactor (MBfR), which is a technological breakthrough that makes H2 delivery to microorganisms efficient, reliable, and safe. The MBfR features non-porous gas-transfer membranes through which bubbleless H2 is delivered on-demand to a microbial biofilm that develops naturally on the outer surface of the membranes. The membranes serve as an active substratum for a microbial biofilm able to biologically reduce oxyanions in the water. We review the development of the MBfR technology from bench, to pilot, and to commercial scales, and we elucidate the mechanisms that control MBfR performance, particularly including methods for managing the biofilm's structure and function. We also give examples of MBfR performance for cases of treating single and co-occurring oxyanions in different types of contaminated water. In summary, the MBfR is an effective and reliable technology for removing oxyanion contaminants by accurately providing a biofilm with bubbleless H2 on demand. Controlling the H2 supply in accordance to oxyanion surface loading and managing the accumulation and activity of biofilm are the keys for process success.}, }
@article {pmid30685711, year = {2019}, author = {Vick, SHW and Greenfield, P and Pinetown, KL and Sherwood, N and Gong, S and Tetu, SG and Midgley, DJ and Paulsen, IT}, title = {Succession Patterns and Physical Niche Partitioning in Microbial Communities from Subsurface Coal Seams.}, journal = {iScience}, volume = {12}, number = {}, pages = {152-167}, pmid = {30685711}, issn = {2589-0042}, abstract = {The subsurface represents a largely unexplored frontier in microbiology. Here, coal seams present something of an oasis for microbial life, providing moisture, warmth, and abundant fossilized organic material. Microbes in coal seams are thought to syntrophically mobilize fossilized carbon from the geosphere to the biosphere. Despite the environmental and economic importance of this process, little is known about the microbial ecology of coal seams. In the current study, ecological succession and spatial niche partitioning are explored in three coal seam microbial communities. Scanning electron microscopic visualization and 16S rRNA sequencing track changes in microbial communities over time, revealing distinct attached and planktonic communities displaying patterns of ecological succession. Attachment to the coal surface is biofilm mediated on Surat coal, whereas microbes on Sydney and Gunnedah coal show different attachment processes. This study demonstrates that coal seam microbial communities undergo spatial niche partitioning during periods of succession as microbes colonize coal environments.}, }
@article {pmid30684803, year = {2019}, author = {Kumar, M and Jaiswal, S and Sodhi, KK and Shree, P and Singh, DK and Agrawal, PK and Shukla, P}, title = {Antibiotics bioremediation: Perspectives on its ecotoxicity and resistance.}, journal = {Environment international}, volume = {124}, number = {}, pages = {448-461}, doi = {10.1016/j.envint.2018.12.065}, pmid = {30684803}, issn = {1873-6750}, mesh = {Animals ; Anti-Bacterial Agents/*metabolism/*pharmacology ; Bacteria/*drug effects ; *Biodegradation, Environmental ; *Drug Resistance, Bacterial ; Environmental Pollutants/*metabolism ; Humans ; }, abstract = {Antibiotic is one of the most significant discoveries and have brought a revolution in the field of medicine for human therapy. In addition to the medical uses, antibiotics have broad applications in agriculture and animal husbandry. In developing nations, antibiotics use have helped to increase the life expectancy by lowering the deaths due to bacterial infections, but the risks associated with antibiotics pollution is largely affecting people. Since antibiotics are released partially degraded and undegraded into environment creating antibiotic pollution, and its bioremediation is a challenging task. In the present review, we have discussed the primary antibiotic sources like hospitals, dairy, and agriculture causing antibiotic pollution and their innovative detection methods. The strong commitment towards the resistance prevention and participation, nations through strict policies and their implementations now come to fight against the antibiotic resistance under WHO. The review also deciphers the bacterial evolution based strategies to overcome the effects of antibiotics, so the antibiotic degradation and elimination from the environment and its health benefits. The present review focuses on the environmental sources of antibiotics, it's possible degradation mechanisms, health effects, and bacterial antibiotics resistance mechanisms.}, }
@article {pmid30683748, year = {2019}, author = {Burkert, A and Douglas, TA and Waldrop, MP and Mackelprang, R}, title = {Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {7}, pages = {}, pmid = {30683748}, issn = {1098-5336}, mesh = {Actinobacteria/genetics/isolation &amp; purification ; Alaska ; Bacillaceae/genetics/isolation &amp; purification ; Carbon/metabolism ; Clostridiaceae/genetics/isolation &amp; purification ; DNA, Bacterial/genetics/isolation &amp; purification ; Ecology ; Freezing ; Metagenomics ; Microbiota/genetics/*physiology ; Permafrost/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; Spores, Bacterial/physiology ; Temperature ; }, abstract = {Permafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the class Bacilli were more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of the Clostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous "relic" DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost.IMPORTANCE Permafrost soils store more than half of Earth's soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171-179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.}, }
@article {pmid30680433, year = {2019}, author = {Goetghebuer, L and Bonal, M and Faust, K and Servais, P and George, IF}, title = {The Dynamic of a River Model Bacterial Community in Two Different Media Reveals a Divergent Succession and an Enhanced Growth of Most Strains Compared to Monocultures.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {313-323}, pmid = {30680433}, issn = {1432-184X}, support = {T.1037.14//Fonds De La Recherche Scientifique - FRS-FNRS (BE)/ ; }, mesh = {Bacteria/genetics/*growth &amp; development/isolation &amp; purification/metabolism ; Biodiversity ; Culture Media/*chemistry/metabolism ; Models, Biological ; Rivers/*microbiology ; Water Microbiology ; }, abstract = {The dynamic of a community of 20 bacterial strains isolated from river water was followed in R2 broth and in autoclaved river water medium for 27 days in batch experiments. At an early stage of incubation, a fast-growing specialist strain, Acinetobater sp., dominated the community in both media. Later on, the community composition in both media diverged but was highly reproducible across replicates. In R2, several strains previously reported to degrade multiple simple carbon sources prevailed. In autoclaved river water, the community was more even and became dominated by several strains growing faster or exclusively in that medium. Those strains have been reported in the literature to degrade complex compounds. Their growth rate in the community was 1.5- to 7-fold greater than that observed in monoculture. Furthermore, those strains developed simultaneously in the community. Together, our results suggest the existence of cooperative interactions within the community incubated in autoclaved river water.}, }
@article {pmid30678814, year = {2019}, author = {Lavefve, L and Marasini, D and Carbonero, F}, title = {Microbial Ecology of Fermented Vegetables and Non-Alcoholic Drinks and Current Knowledge on Their Impact on Human Health.}, journal = {Advances in food and nutrition research}, volume = {87}, number = {}, pages = {147-185}, doi = {10.1016/bs.afnr.2018.09.001}, pmid = {30678814}, issn = {1043-4526}, mesh = {Bacteria/classification/metabolism ; Beverages/*microbiology ; *Fermented Foods ; *Food Microbiology ; Humans ; Probiotics ; Vegetables/*microbiology ; }, abstract = {Fermented foods are currently experiencing a re-discovery, largely driven by numerous health benefits claims. While fermented dairy, beer, and wine (and other alcoholic fermented beverages) have been the subject of intensive research, other plant-based fermented foods that are in some case widely consumed (kimchi/sauerkraut, pickles, kombucha) have received less scientific attention. In this chapter, the current knowledge on the microbiology and potential health benefits of such plant-based fermented foods are presented. Kimchi is the most studied, characterized by primarily acidic fermentation by lactic acid bacteria. Anti-obesity and anti-hypertension properties have been reported for kimchi and other pickled vegetables. Kombucha is the most popular non-alcoholic fermented drink. Kombucha's microbiology is remarkable as it involves all fermenters described in known fermented foods: lactic acid bacteria, acetic acid bacteria, fungi, and yeasts. While kombucha is often hyped as a "super-food," only antioxidant and antimicrobial properties toward foodborne pathogens are well established; and it is unknown if these properties incur beneficial impact, even in vitro or in animal models. The mode of action that has been studied and demonstrated the most is the probiotic one. However, it can be expected that fermentation metabolites may be prebiotic, or influence host health directly. To conclude, plant-based fermented foods and drinks are usually safe products; few negative reports can be found, but more research, especially human dietary intervention studies, are warranted to substantiate any health claim.}, }
@article {pmid30678161, year = {2019}, author = {Snelson, M and Coughlan, MT}, title = {Dietary Advanced Glycation End Products: Digestion, Metabolism and Modulation of Gut Microbial Ecology.}, journal = {Nutrients}, volume = {11}, number = {2}, pages = {}, pmid = {30678161}, issn = {2072-6643}, mesh = {Animals ; *Diet ; Digestion/*drug effects ; Food ; Gastrointestinal Microbiome/*drug effects ; Glycation End Products, Advanced/*metabolism/*pharmacology ; Humans ; }, abstract = {The formation of advanced glycation end products (AGEs) in foods is accelerated with heat treatment, particularly within foods that are cooked at high temperatures for long periods of time using dry heat. The modern processed diet is replete with AGEs, and excessive AGE consumption is thought to be associated with a number of negative health effects. Many dietary AGEs have high molecular weight and are not absorbed in the intestine, and instead pass through to the colon, where they are available for metabolism by the colonic bacteria. Recent studies have been conducted to explore the effects of AGEs on the composition of the gut microbiota as well as the production of beneficial microbial metabolites, in particular, short-chain fatty acids. However, there is conflicting evidence regarding the impact of dietary AGEs on gut microbiota reshaping, which may be due, in part, to the formation of alternate compounds during the thermal treatment of foods. This review summarises the current evidence regarding dietary sources of AGEs, their gastrointestinal absorption and role in gut microbiota reshaping, provides a brief overview of the health implications of dietary AGEs and highlights knowledge gaps and avenues for future study.}, }
@article {pmid30677885, year = {2019}, author = {Young, JM and Skvortsov, T and Kelleher, BP and Mahaney, WC and Somelar, P and Allen, CCR}, title = {Effect of soil horizon stratigraphy on the microbial ecology of alpine paleosols.}, journal = {The Science of the total environment}, volume = {657}, number = {}, pages = {1183-1193}, doi = {10.1016/j.scitotenv.2018.11.442}, pmid = {30677885}, issn = {1879-1026}, mesh = {Bacteria/classification/genetics ; Biodiversity ; France ; High-Throughput Nucleotide Sequencing ; Metals/analysis ; Microbial Consortia/genetics ; Principal Component Analysis ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {There is remarkable potential for research at the interface between the earth sciences and environmental microbiology that may lead to advances in our understanding of the role of bacterial communities in the surface or subsurface environment of our planet. One mainstay of sedimentary classification is the concept of differential soil and/or paleosol horizons being the result of primarily physical and chemical weathering, with relatively little understanding of how microbial communities between these stratified horizons differ, if at all. In this study we evaluate the differences in microbial community taxonomy and biogeochemical functional potential between stratified soil horizons in an alpine paleosol environment using next-generation sequencing (NGS) shotgun sequencing. Paleosols represent a unique environment to study the effect of differences soil horizon environments on the microbial community due to their relative isolation, and the fact that three distinct stratified soil horizons can be identified within the top 30 cm of the soil. This enables us to assess variation in microbial community composition that will be relatively distinct from variation due to distance alone. We test the hypothesis that variation in soil community composition is linked to variation in the physical and chemical parameters that define stratigraphy. Multivariate statistical analysis of sequencing reads from soil horizons across five sampling sites revealed that 1223 microbial genera vary significantly and consistently in abundance across stratified soil horizons at class level. Specifically Ktedonobacter, Bacilli and Betaproteobacteria responded most strongly to soil depth. Alpha diversity showed a positive correlation with soil depth. Beta diversity, however, did not differ significantly between horizons. Genes involved in carbohydrate and nitrogen metabolism were found to be more abundant in Ah horizon samples. Closer inspection of carbohydrate metabolism genes revealed that genes involved in CO2 fixation, fermentation and saccharide metabolism decreased in abundance with depth while one‑carbon metabolism increased down profile.}, }
@article {pmid30674322, year = {2019}, author = {Adela, R and Reddy, PNC and Ghosh, TS and Aggarwal, S and Yadav, AK and Das, B and Banerjee, SK}, title = {Serum protein signature of coronary artery disease in type 2 diabetes mellitus.}, journal = {Journal of translational medicine}, volume = {17}, number = {1}, pages = {17}, pmid = {30674322}, issn = {1479-5876}, mesh = {Adult ; Aged ; Algorithms ; Area Under Curve ; Biomarkers/blood ; Blood Proteins/*metabolism ; Case-Control Studies ; Coronary Artery Disease/*blood/*complications ; Diabetes Mellitus, Type 2/*blood/*complications ; Female ; Humans ; Machine Learning ; Male ; Middle Aged ; Principal Component Analysis ; Signal Transduction ; }, abstract = {BACKGROUND: Coronary artery disease (CAD) is the leading cause of morbidity and mortality in patients with type 2 diabetes mellitus (T2DM). The purpose of the present study was to discriminate the Indian CAD patients with or without T2DM by using multiple pathophysiological biomarkers.<br><br>METHODS: Using sensitive multiplex protein assays, we assessed 46 protein markers including cytokines/chemokines, metabolic hormones, adipokines and apolipoproteins for evaluating different pathophysiological conditions of control, T2DM, CAD and T2DM with CAD patients (T2DM_CAD). Network analysis was performed to create protein-protein interaction networks by using significantly (p&#x2009;<&#x2009;0.05) altered protein markers in each disease using STRING 10.5 database. We used two supervised analysis methods i.e., between class analysis (BCA) and principal component analysis (PCA) to reveals distinct biomarkers profiles. Further, random forest classification (RF) was used to classify the diseases by the panel of markers.<br><br>RESULTS: Our two supervised analysis methods BCA and PCA revealed a distinct biomarker profiles and high degree of variability in the marker profiles for T2DM_CAD and CAD. Thereafter, the present study identified multiple potential biomarkers to differentiate T2DM, CAD, and T2DM_CAD patients based on their relative abundance in serum. RF classified T2DM based on the abundance patterns of nine markers i.e., IL-1&#x3b2;, GM-CSF, glucagon, PAI-I, rantes, IP-10, resistin, GIP and Apo-B; CAD by 14 markers i.e., resistin, PDGF-BB, PAI-1, lipocalin-2, leptin, IL-13, eotaxin, GM-CSF, Apo-E, ghrelin, adipsin, GIP, Apo-CII and IP-10; and T2DM _CAD by 12 markers i.e., insulin, resistin, PAI-1, adiponectin, lipocalin-2, GM-CSF, adipsin, leptin, Apo-AII, rantes, IL-6 and ghrelin with respect to the control subjects. Using network analysis, we have identified several cellular network proteins like PTPN1, AKT1, INSR, LEPR, IRS1, IRS2, IL1R2, IL6R, PCSK9 and MYD88, which are responsible for regulating inflammation, insulin resistance, and atherosclerosis.<br><br>CONCLUSION: We have identified three distinct sets of serum markers for diabetes, CAD and diabetes associated with CAD in Indian patients using nonparametric-based machine learning approach. These multiple marker classifiers may be useful for monitoring progression from a healthy person to T2DM and T2DM to T2DM_CAD. However, these findings need to be further confirmed in the future studies with large number of samples.}, }
@article {pmid30668615, year = {2019}, author = {Snelson, M and Kellow, NJ and Coughlan, MT}, title = {Modulation of the Gut Microbiota by Resistant Starch as a Treatment of Chronic Kidney Diseases: Evidence of Efficacy and Mechanistic Insights.}, journal = {Advances in nutrition (Bethesda, Md.)}, volume = {10}, number = {2}, pages = {303-320}, pmid = {30668615}, issn = {2156-5376}, mesh = {Animals ; *Dietary Supplements ; Disease Models, Animal ; Disease Progression ; Dysbiosis/*therapy ; Gastrointestinal Microbiome/*drug effects ; Humans ; Kidney/microbiology ; *Prebiotics ; Renal Insufficiency, Chronic/*microbiology ; Starch/*pharmacology ; }, abstract = {Chronic kidney disease (CKD) has been associated with changes in gut microbial ecology, or "dysbiosis," which may contribute to disease progression. Recent studies have focused on dietary approaches to favorably alter the composition of the gut microbial communities as a treatment method in CKD. Resistant starch (RS), a prebiotic that promotes proliferation of gut bacteria such as Bifidobacteria and Lactobacilli, increases the production of metabolites including short-chain fatty acids, which confer a number of health-promoting benefits. However, there is a lack of mechanistic insight into how these metabolites can positively influence renal health. Emerging evidence shows that microbiota-derived metabolites can regulate the incretin axis and mitigate inflammation via expansion of regulatory T cells. Studies from animal models and patients with CKD show that RS supplementation attenuates the concentrations of uremic retention solutes, including indoxyl sulfate and p-cresyl sulfate. Here, we present the current state of knowledge linking the microbiome to CKD, we explore the efficacy of RS in animal models of CKD and in humans with the condition, and we discuss how RS supplementation could be a promising dietary approach for slowing CKD progression.}, }
@article {pmid30666369, year = {2019}, author = {Zhou, D and Feng, H and Schuelke, T and De Santiago, A and Zhang, Q and Zhang, J and Luo, C and Wei, L}, title = {Rhizosphere Microbiomes from Root Knot Nematode Non-infested Plants Suppress Nematode Infection.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {470-481}, pmid = {30666369}, issn = {1432-184X}, support = {31601685//National Natural Science Foundation of China/ ; CARS-24-C-01//Agriculture Research System of China/ ; 201403032//Special Fund for Agro-scientific Research in the Public Interest/ ; 4921701//Key Research and Development Program of Jiangsu Province/ ; }, mesh = {Animals ; *Antibiosis ; Bacteria/classification/genetics/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; DNA, Bacterial/genetics ; Solanum lycopersicum/microbiology/*parasitology ; *Microbiota ; Plant Diseases/*parasitology ; Plant Roots/*microbiology/parasitology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil Microbiology ; Tylenchoidea/*physiology ; }, abstract = {Root knot nematodes (RKN, Meloidogyne spp.) are serious pathogens of numerous crops worldwide. Understanding the roles plant rhizosphere soil microbiome play during RKN infection is very important. The current study aims at investigating the impacts of soil microbiome on the activity of RKN. In this study, the 16S rRNA genes of the bacterial communities from nematode-infested and non-infested rhizosphere soils from four different plants were sequenced on the Illumina Hi-Seq platform. The soil microbiome effects on RKN infection were tested in a greenhouse assay. The non-infested soils had more microbial diversity than the infested soils from all plant rhizospheres, and both soil types had exclusive microbial communities. The inoculation of the microbiomes from eggplant and cucumber non-infested soils to tomato plants significantly alleviated the RKN infection, while the microbiome from infested soil showed increased the RKN infection. Furthermore, bacteria Pseudomonas sp. and Bacillus sp. were screened out from non-infested eggplant soil and exhibited biocontrol activity to RKN on tomato. Our findings suggest that microbes may regulate RKN infection in plants and are involved in biocontrol of RKN.}, }
@article {pmid30666368, year = {2019}, author = {Clifford, EL and Varela, MM and De Corte, D and Bode, A and Ortiz, V and Herndl, GJ and Sintes, E}, title = {Taurine Is a Major Carbon and Energy Source for Marine Prokaryotes in the North Atlantic Ocean off the Iberian Peninsula.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {299-312}, pmid = {30666368}, issn = {1432-184X}, support = {I486-B09//Austrian Science Fund/ ; Z194-B17//Austrian Science Fund/ ; 10MMA604024PR, 2010-2012//Xunta de Galicia/ ; P27696-B22//Austrian Science Fund/ ; CTM2011-24008//Ministerio de Econom?a y Competitividad/ ; 268595//FP7 Ideas: European Research Council (FP7/2007-2013)/ ; Z 194/FWF_/Austrian Science Fund FWF/Austria ; I 486/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Amino Acids/metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Atlantic Ocean ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Carbon/analysis/metabolism ; Seawater/chemistry/*microbiology ; Taurine/*metabolism ; }, abstract = {Taurine, an amino acid-like compound, acts as an osmostress protectant in many marine metazoans and algae and is released via various processes into the oceanic dissolved organic matter pool. Taurine transporters are widespread among members of the marine prokaryotic community, tentatively indicating that taurine might be an important substrate for prokaryotes in the ocean. In this study, we determined prokaryotic taurine assimilation and respiration throughout the water column along two transects in the North Atlantic off the Iberian Peninsula. Taurine assimilation efficiency decreased from the epipelagic waters from 55 ± 14% to 27 ± 20% in the bathypelagic layers (means of both transects). Members of the ubiquitous alphaproteobacterial SAR11 clade accounted for a large fraction of cells taking up taurine, especially in surface waters. Archaea (Thaumarchaeota + Euryarchaeota) were also able to take up taurine in the upper water column, but to a lower extent than Bacteria. The contribution of taurine assimilation to the heterotrophic prokaryotic carbon biomass production ranged from 21% in the epipelagic layer to 16% in the bathypelagic layer. Hence, we conclude that dissolved free taurine is a significant carbon and energy source for prokaryotes throughout the oceanic water column being utilized with similar efficiencies as dissolved free amino acids.}, }
@article {pmid30666243, year = {2018}, author = {Zhang, F and Xu, X and Huo, Y and Xiao, Y}, title = {Trichoderma-Inoculation and Mowing Synergistically Altered Soil Available Nutrients, Rhizosphere Chemical Compounds and Soil Microbial Community, Potentially Driving Alfalfa Growth.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3241}, pmid = {30666243}, issn = {1664-302X}, abstract = {Trichoderma spp. are proposed as major plant growth-promoting fungi (PGPF) to increase plants growth and productivity. Mowing can stimulate aboveground regrowth to improve plant biomass and nutritional quality. However, the synergistic effects of Trichoderma and mowing on plants growth, particularly the underlying microbial mechanisms mediated by rhizosphere soil chemical compounds, have rarely been reported. In the present study, we employed Trichoderma harzianum T-63 and conducted a pot experiment to investigate the synergistic effect of Trichoderma-inoculation and mowing on alfalfa growth, and the potential soil microbial ecological mechanisms were also explored. Alfalfa treated with Trichoderma-inoculation and/or mowing (T, M, and TM) had significant (P < 0.05) increases in plant shoot and root dry weights and soil available nutrients (N, P, and K), compared with those of the control (CK). Non-metric multidimensional scaling (NMDS) demonstrated that the rhizosphere chemical compounds and soil bacterial and fungal communities were, respectively, separated according to different treatments. There was a clear significant (P < 0.05) positive correlation between alfalfa biomass and the relative abundance of Trichoderma (R[2] = 0.3451, P = 0.045). However, Pseudomonas, Flavobacterium, Arthrobacter, Bacillus, Agrobacterium, and Actinoplanes were not significantly correlated with alfalfa biomass. According to structure equation modeling (SEM), Trichoderma abundance and available P served as primary contributors to alfalfa growth promotion. Additionally, Trichoderma-inoculation and mowing altered rhizosphere soil chemical compounds to drive the soil microbial community, indirectly influencing alfalfa growth. Our research provides a basis for promoting alfalfa growth from a soil microbial ecology perspective and may provide a scientific foundation for guiding the farming of alfalfa.}, }
@article {pmid30666239, year = {2018}, author = {Dinakaran, V and Mandape, SN and Shuba, K and Pratap, S and Sakhare, SS and Tabatabai, MA and Smoot, DT and Farmer-Dixon, CM and Kesavalu, LN and Adunyah, SE and Southerland, JH and Gangula, PR}, title = {Identification of Specific Oral and Gut Pathogens in Full Thickness Colon of Colitis Patients: Implications for Colon Motility.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3220}, pmid = {30666239}, issn = {1664-302X}, support = {U54 CA163069/CA/NCI NIH HHS/United States ; G12 MD007586/MD/NIMHD NIH HHS/United States ; U54 MD007586/MD/NIMHD NIH HHS/United States ; U54 MD007593/MD/NIMHD NIH HHS/United States ; SC1 GM121282/GM/NIGMS NIH HHS/United States ; }, abstract = {Impaired colon motility is one of the leading problems associated with inflammatory bowel disease (IBD). An expanding body of evidence supports the role of microbiome in normal gut function and in progression of IBD. The objective of this work is to determine whether diseased full thickness colon specimens, including the neuromuscular region (critical for colon motility function), contain specific oral and gut pathogens. In addition, we compared the differences in colon microbiome between Caucasians (CA) and African Americans (AA). Thirty-nine human full thickness colon (diseased colon and adjacent healthy colon) specimens were collected from Crohn's Colitis (CC) or Ulcerative Colitis (UC) patients while they underwent elective colon surgeries. We isolated and analyzed bacterial ribosomal RNA (rRNA) from colon specimens by amplicon sequencing of the 16S rRNA gene region. The microbiome proportions were quantified into Operational Taxonomic Units (OTUs) by analysis with Quantitative Insights Into Microbial ecology (QIIME) platform. Two hundred twenty-eight different bacterial species were identified by QIIME analysis. However, we could only decipher the species name of fifty-three bacteria. Our results show that proportion of non-detrimental bacteria in CC or UC colon samples were altered compared to adjacent healthy colon specimens. We further show, for the first time in full thickness colon specimens, that microbiome of CC and UC diseased specimens is dominated by putative oral pathogens belonging to the Phyla Firmicutes (Streptococcus, Staphylococcus, Peptostreptococcus), and Fusobacteria (Fusobacterium). In addition, we have identified patterns of differences in microbiome levels between CA and AA specimens with potential implications for health disparities research. Overall, our results suggest a significant association between oral and gut microbes in the modulation of colon motility in colitis patients.}, }
@article {pmid30661111, year = {2019}, author = {Plotnikov, AO and Balkin, AS and Gogoleva, NE and Lanzoni, O and Khlopko, YA and Cherkasov, SV and Potekhin, AA}, title = {High-Throughput Sequencing of the 16S rRNA Gene as a Survey to Analyze the Microbiomes of Free-Living Ciliates Paramecium.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {286-298}, pmid = {30661111}, issn = {1432-184X}, support = {16-14-10157//Russian Science Foundation/ ; 14-04-01796//Russian Foundation for Basic Research/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Paramecium/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Ciliates are the largest group of ubiquitous aquatic bacterivorous protists, and many species are easily cultivated. However, only few studies reported prokaryotic communities naturally associated with ciliate cells. Herein, we analyzed the microbiome composition of several strains of Paramecium (Ciliophora) originating from different locations and belonging to two morpho-species by high-throughput sequencing (HTS) of the 16S rRNA gene. Possible reasons of HTS results bias were addressed comparing DNA libraries obtained using different primers and different number of ciliate cells. Microbiomes associated with ciliates and their environments were always significantly different by prokaryotic taxonomic composition and bacterial richness. There were also pronounced differences between Paramecium strains. Interestingly, potentially pathogenic bacteria were revealed in Paramecium microbiomes.}, }
@article {pmid30658982, year = {2019}, author = {Jiao, S and Chen, W and Wei, G}, title = {Resilience and Assemblage of Soil Microbiome in Response to Chemical Contamination Combined with Plant Growth.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {6}, pages = {}, pmid = {30658982}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Biodiversity ; Fabaceae/*growth &amp; development/*microbiology ; Metagenomics ; Metals/analysis/metabolism ; *Microbiota ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/analysis/*metabolism ; }, abstract = {A lack of knowledge of the microbial responses to environmental change at the species and functional levels hinders our ability to understand the intrinsic mechanisms underlying the maintenance of microbial ecosystems. Here, we present results from temporal microcosms that introduced inorganic and organic contaminants into agro-soils for 90 days, with three common legume plants. Temporal dynamics and assemblage of soil microbial communities and functions in response to contamination under the influence of growth of different plants were explored via sequencing of the 16S rRNA amplicon and by shotgun metagenomics. Soil microbial alpha diversity and structure at the taxonomic and functional levels exhibited resilience patterns. Functional profiles showed greater resilience than did taxonomic ones. Different legume plants imposed stronger selection on taxonomic profiles than on functional ones. Network and random forest analyses revealed that the functional potential of soil microbial communities was fostered by various taxonomic groups. Betaproteobacteria were important predictors of key functional traits such as amino acid metabolism, nucleic acid metabolism, and hydrocarbon degradation. Our study reveals the strong resilience of the soil microbiome to chemical contamination and sensitive responses of taxonomic rather than functional profiles to selection processes induced by different legume plants. This is pivotal to develop approaches and policies for the protection of soil microbial diversity and functions in agro-ecosystems with different response strategies from global environmental drivers, such as soil contamination and plant invasion.IMPORTANCE Exploring the microbial responses to environmental disturbances is a central issue in microbial ecology. Understanding the dynamic responses of soil microbial communities to chemical contamination and the microbe-soil-plant interactions is essential for forecasting the long-term changes in soil ecosystems. Nevertheless, few studies have applied multi-omics approaches to assess the microbial responses to soil contamination and the microbe-soil-plant interactions at the taxonomic and functional levels simultaneously. Our study reveals clear succession and resilience patterns of soil microbial diversity and structure in response to chemical contamination. Different legume plants exerted stronger selection processes on taxonomic than on functional profiles in contaminated soils, which could benefit plant growth and fitness as well as foster the potential abilities of hydrocarbon degradation and metal tolerance. These results provide new insight into the resilience and assemblage of soil microbiome in response to environmental disturbances in agro-ecosystems at the species and functional levels.}, }
@article {pmid30655101, year = {2019}, author = {Wolters, M and Ahrens, J and Romaní-Pérez, M and Watkins, C and Sanz, Y and Benítez-Páez, A and Stanton, C and Günther, K}, title = {Dietary fat, the gut microbiota, and metabolic health - A systematic review conducted within the MyNewGut project.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {38}, number = {6}, pages = {2504-2520}, doi = {10.1016/j.clnu.2018.12.024}, pmid = {30655101}, issn = {1532-1983}, mesh = {Adult ; Aged ; *Diet/methods/statistics &amp; numerical data ; *Dietary Fats ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Middle Aged ; Young Adult ; }, abstract = {BACKGROUND AND AIMS: Studies indicate that dietary fat quantity and quality influence the gut microbiota composition which may as a consequence impact metabolic health. This systematic review aims to summarize the results of available studies in humans on dietary fat intake (quantity and quality), the intestinal microbiota composition and related cardiometabolic health outcomes.<br><br>METHODS: We performed a systematic review (CRD42018088685) following PRISMA guidelines and searched for literature in Medline, EMBASE, and Cochrane databases.<br><br>RESULTS: From 796 records, 765 records were excluded based on title or abstract. After screening of 31 full-text articles six randomized controlled trials (RCT) and nine cross-sectional observational studies were included. Our results of interventional trials do not suggest strong effects of different amounts and types of dietary fat on the intestinal microbiota composition or on metabolic health outcomes while observational studies indicate associations with the microbiota and health outcomes. High intake of fat and saturated fatty acids (SFA) may negatively affect microbiota richness and diversity and diets high in monounsaturated fatty acids (MUFA) may decrease total bacterial numbers whereas dietary polyunsaturated fatty acids (PUFA) had no effect on richness and diversity.<br><br>CONCLUSIONS: High fat and high SFA diets can exert unfavorable effects on the gut microbiota and are associated with an unhealthy metabolic state. Also high MUFA diets may negatively affect gut microbiota whereas PUFA do not seem to negatively affect the gut microbiota or metabolic health outcomes. However, data are not consistent and most RCT and observational studies showed risks of bias.}, }
@article {pmid30654982, year = {2019}, author = {Mandalakis, M and Gavriilidou, A and Polymenakou, PN and Christakis, CA and Nomikou, P and Medvecký, M and Kilias, SP and Kentouri, M and Kotoulas, G and Magoulas, A}, title = {Microbial strains isolated from CO2-venting Kolumbo submarine volcano show enhanced co-tolerance to acidity and antibiotics.}, journal = {Marine environmental research}, volume = {144}, number = {}, pages = {102-110}, doi = {10.1016/j.marenvres.2019.01.002}, pmid = {30654982}, issn = {1879-0291}, mesh = {Acids/*pharmacology ; Anti-Bacterial Agents/*pharmacology ; Carbon Dioxide ; *Ecosystem ; Hydrogen-Ion Concentration ; Hydrothermal Vents/*microbiology ; Oceans and Seas ; Pseudomonas/classification/*drug effects/isolation &amp; purification ; Seawater/microbiology ; }, abstract = {As ocean acidification intensifies, there is growing global concern about the impacts that future pH levels are likely to have on marine life and ecosystems. By analogy, a steep decrease of seawater pH with depth is encountered inside the Kolumbo submarine volcano (northeast Santorini) as a result of natural CO2 venting, making this system ideal for ocean acidification research. Here, we investigated whether the increase of acidity towards deeper layers of Kolumbo crater had any effect on relevant phenotypic traits of bacterial isolates. A total of 31 Pseudomonas strains were isolated from both surface- (SSL) and deep-seawater layers (DSL), with the latter presenting a significantly higher acid tolerance. In particular, the DSL strains were able to cope with H[+] levels that were 18 times higher. Similarly, the DSL isolates exhibited a significantly higher tolerance than SSL strains against six commonly used antibiotics and As(III). More importantly, a significant positive correlation was revealed between antibiotics and acid tolerance across the entire set of SSL and DSL isolates. Our findings imply that Pseudomonas species with higher resilience to antibiotics could be favored by the prospect of acidifying oceans. Further studies are required to determine if this feature is universal across marine bacteria and to assess potential ecological impacts.}, }
@article {pmid30653351, year = {2019}, author = {Alvarez-Ordóñez, A and Coughlan, LM and Briandet, R and Cotter, PD}, title = {Biofilms in Food Processing Environments: Challenges and Opportunities.}, journal = {Annual review of food science and technology}, volume = {10}, number = {}, pages = {173-195}, doi = {10.1146/annurev-food-032818-121805}, pmid = {30653351}, issn = {1941-1421}, mesh = {*Biofilms ; Fermented Foods ; *Food Handling ; *Food Microbiology ; }, abstract = {This review examines the impact of microbial communities colonizing food processing environments in the form of biofilms on food safety and food quality. The focus is both on biofilms formed by pathogenic and spoilage microorganisms and on those formed by harmless or beneficial microbes, which are of particular relevance in the processing of fermented foods. Information is presented on intraspecies variability in biofilm formation, interspecies relationships of cooperativism or competition within biofilms, the factors influencing biofilm ecology and architecture, and how these factors may influence removal. The effect on the biofilm formation ability of particular food components and different environmental conditions that commonly prevail during food processing is discussed. Available tools for the in situ monitoring and characterization of wild microbial biofilms in food processing facilities are explored. Finally, research on novel agents or strategies for the control of biofilm formation or removal is summarized.}, }
@article {pmid30647456, year = {2019}, author = {Junghare, M and Spiteller, D and Schink, B}, title = {Anaerobic degradation of xenobiotic isophthalate by the fermenting bacterium Syntrophorhabdus aromaticivorans.}, journal = {The ISME journal}, volume = {13}, number = {5}, pages = {1252-1268}, pmid = {30647456}, issn = {1751-7370}, mesh = {Acyl Coenzyme A/metabolism ; Anaerobiosis ; Bacterial Proteins/genetics/metabolism ; Benzoates/metabolism ; Carboxy-Lyases/genetics/metabolism ; Deltaproteobacteria/classification/genetics/isolation &amp; purification/*metabolism ; Fermentation ; Phthalic Acids/*metabolism ; Phylogeny ; Proteomics ; Xenobiotics/*metabolism ; }, abstract = {Syntrophorhabdus aromaticivorans is a syntrophically fermenting bacterium that can degrade isophthalate (3-carboxybenzoate). It is a xenobiotic compound which has accumulated in the environment for more than 50 years due to its global industrial usage and can cause negative effects on the environment. Isophthalate degradation by the strictly anaerobic S. aromaticivorans was investigated to advance our understanding of the degradation of xenobiotics introduced into nature, and to identify enzymes that might have ecological significance for bioremediation. Differential proteome analysis of isophthalate- vs benzoate-grown cells revealed over 400 differentially expressed proteins of which only four were unique to isophthalate-grown cells. The isophthalate-induced proteins include a phenylacetate:CoA ligase, a UbiD-like decarboxylase, a UbiX-like flavin prenyltransferase, and a hypothetical protein. These proteins are encoded by genes forming a single gene cluster that putatively codes for anaerobic conversion of isophthalate to benzoyl-CoA. Subsequently, benzoyl-CoA is metabolized by the enzymes of the anaerobic benzoate degradation pathway that were identified in the proteomic analysis. In vitro enzyme assays with cell-free extracts of isophthalate-grown cells indicated that isophthalate is activated to isophthalyl-CoA by an ATP-dependent isophthalate:CoA ligase (IPCL), and subsequently decarboxylated to benzoyl-CoA by a UbiD family isophthalyl-CoA decarboxylase (IPCD) that requires a prenylated flavin mononucleotide (prFMN) cofactor supplied by UbiX to effect decarboxylation. Phylogenetic analysis revealed that IPCD is a novel member of the functionally diverse UbiD family (de)carboxylases. Homologs of the IPCD encoding genes are found in several other bacteria, such as aromatic compound-degrading denitrifiers, marine sulfate-reducers, and methanogenic communities in a terephthalate-degrading reactor. These results suggest that metabolic strategies adapted for degradation of isophthalate and other phthalate are conserved between microorganisms that are involved in the anaerobic degradation of environmentally relevant aromatic compounds.}, }
@article {pmid30640580, year = {2019}, author = {Cornut, J and De Respinis, S and Tonolla, M and Petrini, O and Bärlocher, F and Chauvet, E and Bruder, A}, title = {Rapid characterization of aquatic hyphomycetes by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.}, journal = {Mycologia}, volume = {111}, number = {1}, pages = {177-189}, doi = {10.1080/00275514.2018.1528129}, pmid = {30640580}, issn = {1557-2536}, mesh = {Cluster Analysis ; France ; Fungal Proteins/*analysis ; Mitosporic Fungi/chemistry/*classification ; *Phylogeny ; Proteomics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Water Microbiology ; }, abstract = {Protein fingerprinting using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI--TOF MS) is a rapid, reliable, and economical method to characterize isolates of terrestrial fungi and other microorganisms. The objective of our study was to evaluate the suitability of MALDI-TOF MS for the identification of aquatic hyphomycetes, a polyphyletic group of fungi that play crucial roles in stream ecosystems. To this end, we used 34 isolates of 21 aquatic hyphomycete species whose identity was confirmed by spore morphology and internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) nuc rDNA sequencing. We tested the efficiency of three protein extraction methods, including chemical and mechanical treatments using 13 different protocols, with the objective of producing high-quality MALDI-TOF mass spectra. In addition to extraction protocols, mycelium age was identified as a key parameter affecting protein extraction efficiency. The dendrogram based on mass-spectrum similarity indicated good and relevant taxonomic discrimination; the tree structure was comparable to that of the phylogram based on ITS sequences. Consequently, MALDI-TOF MS could reliably identify the isolates studied and provided greater taxonomic accuracy than classical morphological methods. MALDI-TOF MS seems suited for rapid characterization and identification of aquatic hyphomycete species.}, }
@article {pmid31186603, year = {2018}, author = {Saha, M and Goecke, F and Bhadury, P}, title = {Correction to: Minireview: algal natural compounds and extracts as antifoulants.}, journal = {Journal of applied phycology}, volume = {30}, number = {3}, pages = {1875}, doi = {10.1007/s10811-018-1424-3}, pmid = {31186603}, issn = {0921-8971}, abstract = {[This corrects the article DOI: 10.1007/s10811-017-1322-0.].}, }
@article {pmid31294162, year = {2017}, author = {Valverde, A and González-Tirante, M and Medina-Sierra, M and Rivas, R and Santa-Regina, I and Igual, JM}, title = {Culturable bacterial diversity from the chestnut (Castanea sativa Mill.) phyllosphere and antagonism against the fungi causing the chestnut blight and ink diseases.}, journal = {AIMS microbiology}, volume = {3}, number = {2}, pages = {293-314}, pmid = {31294162}, issn = {2471-1888}, abstract = {The phyllosphere supports a large and complex bacterial community that varies both across plant species and geographical locations. Phyllosphere bacteria can have important effects on plant health. The sweet chestnut (Castanea sativa Mill.) is an economically important tree species affected worldwide by the fungal pathogens Cryphonectria parasitica and Phytophthora cinnamomi. We examined the culturable phyllosphere bacterial community of the sweet chestnut at two nearby locations in Central Spain in order to know its geographical variability and to explore its potential as source of biological control agents against these two pathogenic fungi. The bacterial diversity at strain level was high but it varied significantly between locations; however, phylotype richness and diversity were more comparable. The isolates were affiliated with the phyla Actinobacteria, Firmicutes and Proteobacteria. Most of them were members of recognized bacterial species, with a notable proportion of representative of the genera Dietzia and Lonsdalea, but a small fraction of the strains revealed the existence of several potential novel species or even genera. Antagonism tests showed the occurrence in the chestnut phyllosphere of bacterial strains potentially useful as biological control agents against the two pathogenic fungi, some of which belong to species never before described as fungal antagonists. Chestnut phyllosphere, therefore, contains a great diversity of culturable bacteria and may represent an untapped source of potential biocontrol agents against the fungi causing blight and ink diseases of this tree species.}, }
@article {pmid30918626, year = {2016}, author = {Ramiro-Garcia, J and Hermes, GDA and Giatsis, C and Sipkema, D and Zoetendal, EG and Schaap, PJ and Smidt, H}, title = {NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes.}, journal = {F1000Research}, volume = {5}, number = {}, pages = {1791}, pmid = {30918626}, issn = {2046-1402}, abstract = {Background: Massive high-throughput sequencing of short, hypervariable segments of the 16S ribosomal RNA (rRNA) gene has transformed the methodological landscape describing microbial diversity within and across complex biomes. However, several studies have shown that the methodology rather than the biological variation is responsible for the observed sample composition and distribution. This compromises meta-analyses, although this fact is often disregarded. Results: To facilitate true meta-analysis of microbiome studies, we developed NG-Tax, a pipeline for 16S rRNA gene amplicon sequence analysis that was validated with different mock communities and benchmarked against QIIME as a frequently used pipeline. The microbial composition of 49 independently amplified mock samples was characterized by sequencing two variable 16S rRNA gene regions, V4 and V5-V6, in three separate sequencing runs on Illumina's HiSeq2000 platform. This allowed for the evaluation of important causes of technical bias in taxonomic classification: 1) run-to-run sequencing variation, 2) PCR-error, and 3) region/primer specific amplification bias. Despite the short read length (~140 nt) and all technical biases, the average specificity of the taxonomic assignment for the phylotypes included in the mock communities was 97.78%. On average 99.95% and 88.43% of the reads could be assigned to at least family or genus level, respectively, while assignment to 'spurious genera' represented on average only 0.21% of the reads per sample. Analysis of α- and β-diversity confirmed conclusions guided by biology rather than the aforementioned methodological aspects, which was not achieved with QIIME. Conclusions: Different biological outcomes are commonly observed due to 16S rRNA region-specific performance. NG-Tax demonstrated high robustness against choice of region and other technical biases associated with 16S rRNA gene amplicon sequencing studies, diminishing their impact and providing accurate qualitative and quantitative representation of the true sample composition. This will improve comparability between studies and facilitate efforts towards standardization.}, }
@article {pmid30703910, year = {2014}, author = {Zablocki, ODJ and Rybicki, EP and Cowan, DA}, title = {First Report of a Potyvirus Infecting Albuca rautanenii in the Namib Desert.}, journal = {Plant disease}, volume = {98}, number = {12}, pages = {1749}, doi = {10.1094/PDIS-07-14-0737-PDN}, pmid = {30703910}, issn = {0191-2917}, abstract = {Chlorotic, streak-like symptoms were observed in April 2013 on a single specimen of Albuca rautanenii (Schinz) J.C.Manning &amp; Goldblatt (Family: Hyacinthaceae) found among other plants near Homeb in the Namib Desert, Namibia. No potential insect vectors (e.g., aphids) were observed on or around the infected plant. An extract from symptomatic leaves was assessed by transmission electron microscopy (leaf dip method) to ascertain if the symptoms were viral in origin. Long, flexuous threadlike particles 687 to 825 nm in length and 12.5 nm in diameter were observed. The morphology and size of the particles were indicative of a putative member of the taxonomic family Potyviridae. To confirm this, RT-PCR using universal potyvirus primers which amplify part of the nuclear inclusion b gene (NIb) was conducted (1) on total RNA extracted from leaf tissue (Qiagen RNeasy Plant Mini Kit). The triplicated reaction yielded amplicons of the expected size (~350 bp), which were cloned into the pJET 1.2 vector (Thermo Scientific, Waltham, MA) according to manufacturer's instructions. The sequences of 10 clones were trimmed to remove vector and primer ends and were deposited in the EBI database under the accession numbers LK995422 to LK995431. Curated sequences were used to search the GenBank database using BLASTn and tBLASTx, as well as for phylogenetic analysis. Intra-clonal nucleotide sequence similarity ranged from 97.99 to 99.72%. BLASTn searches showed all clones were 72% identical to Papaya ringspot virus isolate 1 accession JQ314105.1 (87% coverage), followed by Bean yellow mosaic virus clone Brn167 accession JF707769.1 (72% identity with 86% sequence coverage). The translated peptide fragment was most similar to Sugarcane mosaic virus isolate Beijing (AY042184.1), with a query cover of 98% and a similarity of 81%. Phylogenetic analysis was performed with a set of 57 reference potyvirus genomes, with their NIb regions aligned with the cloned nucleotide sequences according to the parameters used previously (1). The clones formed a distinct cluster, at a node with Cocksfoot streak virus (CSV) (NC_003742.1). An identity matrix of the aligned NIb clones and CSV showed a nucleotide identity range of 68.79 to 70.23%. These results suggest that the virus isolate belongs to the family Potyviridae, genus Potyvirus, supported by the characteristic morphological features of the virion and its relatedness to CSV. Moreover, the clustering of all sequences at a single node suggests a homogeneous viral population, without significant strain variation. Genetic distance inferred by phylogenetic analysis further suggests that the isolate is a novel species within the genus, which we tentatively name Albuca mosaic virus, AlbMV. To our knowledge, this is the first report of any plant virus infection in the native Namib Desert ecosystem. This is particularly relevant due to the scarcity and uniqueness of plant life in this hyperarid desert environment, and additional monitoring of this virus infection and other desert plant species is encouraged. Reference: (1) L. Zheng et al. Plant Pathol. 59:211, 2010.}, }
@article {pmid30727523, year = {2012}, author = {Rosenzweig, N and Tiedje, JM and Quensen, JF and Meng, Q and Hao, JJ}, title = {Microbial Communities Associated with Potato Common Scab-Suppressive Soil Determined by Pyrosequencing Analyses.}, journal = {Plant disease}, volume = {96}, number = {5}, pages = {718-725}, doi = {10.1094/PDIS-07-11-0571}, pmid = {30727523}, issn = {0191-2917}, abstract = {Potato common scab, caused by Streptomyces spp., is an annual production problem for potato growers, and not effectively controlled by current methods. A field with naturally occurring common scab suppression has been identified in Michigan, and confirmed to have a biological basis for this disease suppression. This field and an adjacent scab nursery conducive to disease were studied using pyrosequencing to compare the two microbial communities. Total DNA was extracted from both the disease-conducive and -suppressive soils. A phylogenetically taxon-informative region of the 16S rRNA gene was used to establish operational taxonomic units (OTUs) to characterize bacterial community richness and diversity. In total, 1,124 OTUs were detected and 565 OTUs (10% dissimilarity) were identified in disease-conducive soil and 859 in disease-suppressive soil, including 300 shared both between sites. Common phyla based on relative sequence abundance were Acidobacteria, Proteobacteria, and Firmicutes. Sequences of Lysobacter were found in significantly higher numbers in the disease-suppressive soil, as were sequences of group 4 and group 6 Acidobacteria. The relative abundance of sequences identified as the genus Bacillus was significantly higher by an order of magnitude in the disease-conducive soil.}, }
@article {pmid31195556, year = {1997}, author = {Giraffa, G and Carminati, D and Neviani, E}, title = {Enterococci Isolated from Dairy Products: A Review of Risks and Potential Technological Use.}, journal = {Journal of food protection}, volume = {60}, number = {6}, pages = {732-738}, doi = {10.4315/0362-028X-60.6.732}, pmid = {31195556}, issn = {1944-9097}, abstract = {Enterococci are ubiquitous bacteria which frequently occur in large numbers in dairy and other food products. Although they share a number of biotechnological traits (e.g., bacteriocin production, probiotic characteristics, usefulness in dairy technology), there is no consensus on whether enterococci pose a threat as foodborne pathogens, The potential pathogenicity of lactic acid bacteria (LAB), including enterococci, in human clinical infections and their association with endocarditis have recently become a matter of controversy, in spite of the fact that foods containing enterococci have a long history of safe use. This article provides literature data available on microbial ecology, biochemical properties, production of anti- Listeria bacteriocins, and potential pathogenic traits of enterococci isolated from different dairy products.}, }
@article {pmid31084167, year = {1993}, author = {Fapohunda, AO and McMILLIN, KW and Marshall, DL and Waites, WM}, title = {A Simple and Effective Method for Obtaining Aseptic Raw Beef Tissues [1].}, journal = {Journal of food protection}, volume = {56}, number = {6}, pages = {543-544}, doi = {10.4315/0362-028X-56.6.543}, pmid = {31084167}, issn = {1944-9097}, abstract = {The need for gnotoxenic studies (defined microflora) in beef to better understand the microbial ecology of spoilage and pathogenic organisms necessitates the development of a simple and rapid method devoid of obvious disadvantages of existing ones. The aseptic technique described here is an improvement on the flaming and hot-iron searing methods already in use. It involved the use of a Sensa-Temp Heat Control Electric Frier (West Bend, IN) at 232°C to destroy practically all surface microflora on top round meat blocks of freshly slaughtered, healthy beef cattle, before aseptically removing the cooked exterior to a depth of approximately 1 cm. In two separate trials, 95 and 90%, respectively, of the total number of samples removed were sterile. We recommend this method to procure sterile samples suitable for inoculation with defined microflora and for other studies. The method seems applicable to a wide variety of muscle food types, including fish.}, }
@article {pmid31018335, year = {1990}, author = {Parish, ME and Higgins, DP}, title = {Investigation of the Microbial Ecology of Commercial Grapefruit Sections [1].}, journal = {Journal of food protection}, volume = {53}, number = {8}, pages = {685-688}, doi = {10.4315/0362-028X-53.8.685}, pmid = {31018335}, issn = {1944-9097}, abstract = {Commercially prepared grapefruit sections were qualitatively surveyed for microorganisms prior to heat processing. The micro flora included 7 genera of yeasts (Candida , Cryptococcus , Hansenula , Rhodotorula , Saccharomyces , Torulaspora , Trichosporon , Zygosaccharomyces), 12 genera of molds (Aspergillus , Aureobasidium pullulans , Byssochlamys , Cladosporium , Fonseceae , Fusarium , Geotrichum , Mucor , Penicillium , Rhizopus , Trichoderma , Trichophyton), and 2 of bacteria (Lactobacillus and Leuconostoc). A quantitative analysis of the native microflora indicated that the overall microbial population was capable of significant growth (p ≥ 0.05) at 25°C within 2 to 4 h in the unprocessed product.}, }
@article {pmid30812118, year = {1979}, author = {Kushner, L and Rosenzweig, WD and Stotzky, G}, title = {Effects of Salts, Sugars, and Salt-Sugar Combinations on Growth and Sporulation of an Isolate of Eurotium rubrum from Pancake Syrup.}, journal = {Journal of food protection}, volume = {42}, number = {9}, pages = {706-711}, doi = {10.4315/0362-028X-42.9.706}, pmid = {30812118}, issn = {1944-9097}, abstract = {An osmoduric-saccharophilic fungus, identified as a strain of Eurotium rubrum Konig, Speikermann and Bremer and isolated from a bottle of syrup, showed optimum growth (i.e., increase in colony diameter) on Sabouraud's agar amended with 60% (w/v) sucrose (calculated aw = 0.964) and still grew near optimally at 110% (aw = 0.927). On glucose, fructose or arabinose, optimum growth occurred at 40% (w/v) (aw = 0.962, 0.962, and 0.954, respectively), but glucose supported better growth than did fructose or arabinose. In the presence of glycerol, optimum growth (i.e., increase in dry weight of mycelium) occurred at a 10% (v/v) concentration (aw = 0.972) and no growth occurred above 35% (aw = 0.878). In general, growth was better with 12-C > 6-C > 5-C > 3-C compounds. The fungus did not grow on concentrations of inorganic salts above 30%; growth on salts was best with (on a w/v basis) 10% KCl (aw = 0.957), 5% NaCl (aw = 0.972) or 10% CaCl2, (aw = 0.965). In the absence of either organic or inorganic solutes, there was essentially no growth. When sucrose and either KCl or NaCl were added together, growth was greater on a salt/sugar mixture than on the same concentration of salt alone, and, at equivalent calculated osmotic pressures and aw, sucrose alone supported better growth than did any salt/sugar mixture. These data indicate that the fungus has a requirement for, and a tolerance to, high solute concentrations. At equivalent osmotic pressures and aw, however, sugars supported greater growth than did inorganic salts.}, }
@article {pmid30636276, year = {2019}, author = {Zak, DR and Pellitier, PT and Argiroff, W and Castillo, B and James, TY and Nave, LE and Averill, C and Beidler, KV and Bhatnagar, J and Blesh, J and Classen, AT and Craig, M and Fernandez, CW and Gundersen, P and Johansen, R and Koide, RT and Lilleskov, EA and Lindahl, BD and Nadelhoffer, KJ and Phillips, RP and Tunlid, A}, title = {Exploring the role of ectomycorrhizal fungi in soil carbon dynamics.}, journal = {The New phytologist}, volume = {223}, number = {1}, pages = {33-39}, doi = {10.1111/nph.15679}, pmid = {30636276}, issn = {1469-8137}, mesh = {Carbon/*metabolism ; Mycorrhizae/*physiology ; Nitrogen/metabolism ; Phylogeny ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {The extent to which ectomycorrhizal (ECM) fungi enable plants to access organic nitrogen (N) bound in soil organic matter (SOM) and transfer this growth-limiting nutrient to their plant host, has important implications for our understanding of plant-fungal interactions, and the cycling and storage of carbon (C) and N in terrestrial ecosystems. Empirical evidence currently supports a range of perspectives, suggesting that ECM vary in their ability to provide their host with N bound in SOM, and that this capacity can both positively and negatively influence soil C storage. To help resolve the multiplicity of observations, we gathered a group of researchers to explore the role of ECM fungi in soil C dynamics, and propose new directions that hold promise to resolve competing hypotheses and contrasting observations. In this Viewpoint, we summarize these deliberations and identify areas of inquiry that hold promise for increasing our understanding of these fundamental and widespread plant symbionts and their role in ecosystem-level biogeochemistry.}, }
@article {pmid30635381, year = {2019}, author = {Yao, Z and Du, S and Liang, C and Zhao, Y and Dini-Andreote, F and Wang, K and Zhang, D}, title = {Bacterial Community Assembly in a Typical Estuarine Marsh with Multiple Environmental Gradients.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {6}, pages = {}, pmid = {30635381}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Ecosystem ; Estuaries ; Geologic Sediments/microbiology ; *Microbiota ; Nitrogen/metabolism ; Phosphorus/metabolism ; Phylogeny ; Wetlands ; }, abstract = {Bacterial communities play essential roles in estuarine marsh ecosystems, but the interplay of ecological processes underlying their community assembly is poorly understood. Here, we studied the sediment bacterial communities along a linear gradient extending from the water-land junction toward a high marsh, using 16S rRNA gene amplicon sequencing. Bacterial community compositions differed significantly between sediment transects. Physicochemical properties, particularly sediment nutrient levels (i.e., total nitrogen [TN] and available phosphorus [AP]), as well as sediment physical structure and pH (P < 0.05), were strongly associated with the overall community variations. In addition, the topological properties of bacterial cooccurrence networks varied with distance to the water-land junction. Both node- and network-level topological features revealed that the bacterial network of sediments farthest from the junction was less intense in complexity and interactions than other sediments. Phylogenetic null modeling analysis showed a progressive transition from stochastic to deterministic community assembly for the water-land junction sites toward the emerging terrestrial system. Taken together, data from this study provide a detailed outline of the distribution pattern of the sediment bacterial community across an estuarine marsh and inform the mechanisms and processes mediating bacterial community assembly in marsh soils.IMPORTANCE Salt marshes represent highly dynamic ecosystems where the atmosphere, continents, and the ocean interact. The bacterial distribution in this ecosystem is of great ecological concern, as it provides essential functions acting on ecosystem services. However, ecological processes mediating bacterial assembly are poorly understood for salt marshes, especially the ones located in estuaries. In this study, the distribution and assembly of bacterial communities in an estuarine marsh located in south Hangzhou Bay were investigated. The results revealed an intricate interplay between stochastic and deterministic processes mediating the assembly of bacterial communities in the studied gradient system. Collectively, our findings illustrate the main drivers of community assembly, taking into consideration changes in sediment abiotic variables and potential biotic interactions. Thus, we offer new insights into estuarine bacterial communities and illustrate the interplay of ecological processes shaping the assembly of bacterial communities in estuarine marsh ecosystems.}, }
@article {pmid30633563, year = {2019}, author = {Tomás-Barberán, FA and Espín, JC}, title = {Effect of Food Structure and Processing on (Poly)phenol-Gut Microbiota Interactions and the Effects on Human Health.}, journal = {Annual review of food science and technology}, volume = {10}, number = {}, pages = {221-238}, doi = {10.1146/annurev-food-032818-121615}, pmid = {30633563}, issn = {1941-1421}, mesh = {*Food ; *Gastrointestinal Microbiome ; Humans ; Polyphenols/metabolism ; Prebiotics ; }, abstract = {The two-way interaction of food (poly)phenols with the human gut microbiota has been studied throughout the past ten years. Research has shown that this interaction can be relevant to explain the health effects of these phytochemicals. The effect of the food matrix and food processing on this interaction has only been partially studied. In this article, the studies within this field have been critically reviewed, with a special focus on the following groups of phenolic metabolites: citrus flavanones, pomegranate ellagitannins, and cocoa proanthocyanidins. The available research shows that both the food matrix and food processing can be relevant factors for gut microbiota reshaping to reach a healthier microbial ecology and for the conversion of polyphenols to bioactive and bioavailable metabolites. There are, however, some research gaps that indicate a more comprehensive research approach is needed to reach valid conclusions regarding the gut microbiota-mediated effects of polyphenols on human health.}, }
@article {pmid30629579, year = {2019}, author = {Miranda-CasoLuengo, R and Lu, J and Williams, EJ and Miranda-CasoLuengo, AA and Carrington, SD and Evans, ACO and Meijer, WG}, title = {Delayed differentiation of vaginal and uterine microbiomes in dairy cows developing postpartum endometritis.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0200974}, pmid = {30629579}, issn = {1932-6203}, mesh = {Animals ; *Bacteria/classification/genetics ; Cattle ; *Cattle Diseases/microbiology/pathology ; *Endometritis/microbiology/pathology ; Female ; Microbiota/*genetics ; *Postpartum Period ; Pregnancy ; *Uterus/microbiology/pathology ; *Vagina/microbiology/pathology ; }, abstract = {Bacterial overgrowth in the uterus is a normal event after parturition. In contrast to the healthy cow, animals unable to control the infection within 21 days after calving develop postpartum endometritis. Studies on the Microbial Ecology of the bovine reproductive tract have focused on either vaginal or uterine microbiomes. This is the first study that compares both microbiomes in the same animals. Terminal Restriction Fragment Length Polymorphism of the 16S rRNA gene showed that despite large differences associated to individuals, a shared community exist in vagina and uterus during the postpartum period. The largest changes associated with development of endometritis were observed at 7 days postpartum, a time when vaginal and uterine microbiomes were most similar. 16S rRNA pyrosequencing of the vaginal microbiome at 7 days postpartum showed at least three different microbiome types that were associated with later development of postpartum endometritis. All three microbiome types featured reduced bacterial diversity. Taken together, the above findings support a scenario where disruption of the compartmentalization of the reproductive tract during parturition results in the dispersal and mixing of the vaginal and uterine microbiomes, which subsequently are subject to differentiation. This differentiation was observed early postpartum in the healthy cow. In contrast, loss of bacterial diversity and dominance of the microbiome by few bacterial taxa were related to a delayed succession at 7DPP in cows that at 21 DPP or later were diagnosed with endometritis.}, }
@article {pmid30627762, year = {2019}, author = {Treichel, NS and Prevoršek, Z and Mrak, V and Kostrić, M and Vestergaard, G and Foesel, B and Pfeiffer, S and Stres, B and Schöler, A and Schloter, M}, title = {Effect of the Nursing Mother on the Gut Microbiome of the Offspring During Early Mouse Development.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {517-527}, pmid = {30627762}, issn = {1432-184X}, mesh = {Animals ; Animals, Inbred Strains ; Animals, Outbred Strains ; Bacteria/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Mice ; Milk, Human/*microbiology ; Mothers/statistics &amp; numerical data ; Obesity/*microbiology ; Pedigree ; RNA, Ribosomal, 16S/genetics ; Thinness/*microbiology ; }, abstract = {The development of the gut microbiome is influenced by several factors. It is acquired during and after birth and involves both maternal and environmental factors as well as the genetic disposition of the offspring. However, it is unclear if the microbiome development is directly triggered by the mode of delivery and very early contact with the mother or mostly at later stages of initial development mainly by breast milk provided by the mother. To investigate to what extent the gut microbiome composition of the offspring is determined by the nursing mother, providing breast milk, compared to the birth mother during early development, a cross-fostering experiment involving two genetically different mouse lines was developed, being prone to be obese or lean, respectively. The microbiome of the colon was analyzed by high-throughput 16S rRNA gene sequencing, when the mice were 3 weeks old. The nursing mother affected both α- and β-diversity of the offspring's gut microbiome and shaped its composition. Especially bacterial families directly transferred by breast milk, like Streptococcaceae, or families which are strongly influenced by the quality of the breast milk like Rikenellaceae, showed a strong response. The core microbiome transferred from the obese nursing mother showed a higher robustness in comparison to the microbiome transferred from the lean nursing mother. Overall, the nursing mother impacts the gut microbial composition of the offspring during early development and might play an important role for health and disease of the animals at later stages of life.}, }
@article {pmid30627761, year = {2019}, author = {Fokin, SI and Serra, V and Ferrantini, F and Modeo, L and Petroni, G}, title = {"Candidatus Hafkinia simulans" gen. nov., sp. nov., a Novel Holospora-Like Bacterium from the Macronucleus of the Rare Brackish Water Ciliate Frontonia salmastra (Oligohymenophorea, Ciliophora): Multidisciplinary Characterization of the New Endosymbiont and Its Host.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {1092-1106}, pmid = {30627761}, issn = {1432-184X}, support = {PRA_2018_63//Universit&#xe0; di Pisa/ ; }, mesh = {Holosporaceae/classification/genetics/*physiology/ultrastructure ; Italy ; Macronucleus/microbiology ; Microscopy, Electron, Transmission ; Peniculina/*microbiology/physiology ; Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; RNA, Ribosomal, 18S/analysis ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {We characterized a novel Holospora-like bacterium (HLB) (Alphaproteobacteria, Holosporales) living in the macronucleus of the brackish water ciliate Frontonia salmastra. This bacterium was morphologically and ultrastructurally investigated, and its life cycle and infection capabilities were described. We also obtained its 16S rRNA gene sequence and performed in situ hybridization experiments with a specifically-designed probe. A new taxon, "Candidatus Hafkinia simulans", was established for this HLB. The phylogeny of the family Holosporaceae based on 16S rRNA gene sequences was inferred, adding to the already available data both the sequence of the novel bacterium and those of other Holospora and HLB species recently characterized. Our phylogenetic analysis provided molecular support for the monophyly of HLBs and placed the new endosymbiont as the sister genus of Holospora. Additionally, the host ciliate F. salmastra, recorded in Europe for the first time, was concurrently described through a multidisciplinary study. Frontonia salmastra's phylogenetic position in the subclass Peniculia and the genus Frontonia was assessed according to 18S rRNA gene sequencing. Comments on the biodiversity of this genus were added according to past and recent literature.}, }
@article {pmid30625192, year = {2019}, author = {Ramírez-Fernández, L and Trefault, N and Carú, M and Orlando, J}, title = {Seabird and pinniped shape soil bacterial communities of their settlements in Cape Shirreff, Antarctica.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0209887}, pmid = {30625192}, issn = {1932-6203}, mesh = {Animals ; Antarctic Regions ; Bacteria ; *Birds ; *Caniformia ; *Ecosystem ; Nitrogen/analysis ; Phosphorus/analysis ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Seabirds and pinnipeds play an important role in biogeochemical cycling by transferring nutrients from aquatic to terrestrial environments. Indeed, soils rich in animal depositions have generally high organic carbon, nitrogen and phosphorus contents. Several studies have assessed bacterial diversity in Antarctic soils influenced by marine animals; however most have been conducted in areas with significant human impact. Thus, we chose Cape Shirreff, Livingston Island, an Antarctic Specially Protected Area designated mainly to protect the diversity of marine vertebrate fauna, and selected sampling sites with different types of animals coexisting in a relatively small space, and where human presence and impact are negligible. Using 16S rRNA gene analyses through massive sequencing, we assessed the influence of animal concentrations, via their modification of edaphic characteristics, on soil bacterial diversity and composition. The nutrient composition of soils impacted by Antarctic fur seals and kelp gulls was more similar to that of control soils (i.e. soils without visible presence of plants or animals), which may be due to the more active behaviour of these marine animals compared to other species. Conversely, the soils from concentrations of southern elephant seals and penguins showed greater differences in soil nutrients compared to the control. In agreement with this, the bacterial communities of the soils associated with these animals were most different from those of the control soils, with the soils of penguin colonies also possessing the lowest bacterial diversity. However, all the soils influenced by the presence of marine animals were dominated by bacteria belonging to Gammaproteobacteria, particularly those of the genus Rhodanobacter. Therefore, we conclude that the modification of soil nutrient composition by marine vertebrates promotes specific groups of bacteria, which could play an important role in the recycling of nutrients in terrestrial Antarctic ecosystems.}, }
@article {pmid30625112, year = {2019}, author = {Brooks, LE and Kaze, M and Sistrom, M}, title = {Where the plasmids roam: large-scale sequence analysis reveals plasmids with large host ranges.}, journal = {Microbial genomics}, volume = {5}, number = {1}, pages = {}, pmid = {30625112}, issn = {2057-5858}, mesh = {Corynebacterium/*genetics ; *Databases, Nucleic Acid ; Enterobacteriaceae/*genetics ; Plasmids/*genetics ; }, abstract = {Describing the role of plasmids and their contribution to the exchange of genetic material among bacteria is essential for understanding the fields of plasmid epidemiology, microbial ecology, and commercial and synthetic microbiology. Broad-host-range (BHR) plasmids are those that are found not only in a single bacterial species, but in members of different taxonomic groups and are of significant interest to researchers in many fields. We applied a novel approach to computationally identify new BHR plasmids, in which we searched for highly similar cognate plasmids within a comprehensive plasmid database. After identifying 125 plasmid groups with highly similar cognates found in multiple taxa, we closely examined BHR plasmids found in multiple families. The majority of our identified BHR plasmids are found in members of the Enterobacteriaceae and closely related taxa, while three BHR plasmids of potential commercial significance were found in two species of Cyanobacteria. One plasmid with an exceptionally broad host range was found in both Gram-positive and Gram-negative bacterial species. This analysis demonstrates the utility of this method in identifying new BHR plasmids while highlighting unknown ranges of previously documented plasmids.}, }
@article {pmid30625109, year = {2019}, author = {van der Aart, LT and Nouioui, I and Kloosterman, A and Igual, JM and Willemse, J and Goodfellow, M and van Wezel, GP}, title = {Polyphasic classification of the gifted natural product producer Streptomyces roseifaciens sp. nov.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {69}, number = {4}, pages = {899-908}, doi = {10.1099/ijsem.0.003215}, pmid = {30625109}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; Biological Products ; China ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Genes, Bacterial ; Multilocus Sequence Typing ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; Pigmentation ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Streptomyces/*classification/isolation &amp; purification ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {A polyphasic study was designed to establish the taxonomic status of a Streptomyces strain isolated from soil from the QinLing Mountains, Shaanxi Province, China, and found to be the source of known and new specialized metabolites. Strain MBT76[T] was found to have chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Streptomyces. The strain formed a distinct branch in the Streptomyces16S rRNA gene tree and was closely related to the type strains of Streptomyces hiroshimensis and Streptomycesmobaraerensis. Multi-locus sequence analyses based on five conserved house-keeping gene alleles showed that strain MBT76[T] is closely related to the type strain of S. hiroshimensis, as was the case in analysis of a family of conserved proteins. The organism was also distinguished from S. hiroshimensis using cultural and phenotypic features. Average nucleotide identity and digital DNA-DNA hybridization values between the genomes of strain MBT76[T] and S. hiroshimensis DSM 40037[T] were 88.96 and 28.4±2.3%, respectively, which is in line with their assignment to different species. On the basis of this wealth of data it is proposed that strain MBT76[T] (=DSM 106196[T]=NCCB 100637[T]), be classified as a new species, Streptomycesroseifaciens sp. nov.}, }
@article {pmid30624643, year = {2019}, author = {Baldrian, P}, title = {The known and the unknown in soil microbial ecology.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {2}, pages = {}, doi = {10.1093/femsec/fiz005}, pmid = {30624643}, issn = {1574-6941}, mesh = {Bacteria/*classification/enzymology/genetics ; Ecology ; Ecosystem ; Fungi/*classification/enzymology/genetics ; Metabolomics ; Metagenomics ; Microbiota/*genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {The methodical developments in the fields of molecular biology and analytical chemistry significantly increased the level of detail that we achieve when exploring soils and their microbial inhabitants. High-resolution description of microbial communities, detection of taxa with minor abundances, screening of gene expression or the detailed characterization of metabolomes are nowadays technically feasible. Despite all of this, our understanding of soil is limited in many ways. The imperfect tools to describe microbial communities and limited possibilities to assign traits to community members make it difficult to link microbes to functions. Also the analysis of processes exemplified by enzyme activity measurements is still imperfect. In the future, it is important to look at soil at a finer detail to obtain a better picture on the properties of individual microbes, their in situ interactions, metabolic rates and activity at a scale relevant to individual microbes. Scaling up is needed as well to get answers at ecosystem or biome levels and to enable global modelling. The recent development of novel tools including metabolomics, identification of genomes in metagenomics sequencing datasets or collection of trait data have the potential to bring soil ecology further. It will, however, always remain a highly demanding scientific discipline.}, }
@article {pmid30623643, year = {2019}, author = {Evert, C and Loesekann, T and Bhat, G and Shajahan, A and Sonon, R and Azadi, P and Hunter, RC}, title = {Generation of [13]C-Labeled MUC5AC Mucin Oligosaccharides for Stable Isotope Probing of Host-Associated Microbial Communities.}, journal = {ACS infectious diseases}, volume = {5}, number = {3}, pages = {385-393}, pmid = {30623643}, issn = {2373-8227}, support = {R01 HL136919/HL/NHLBI NIH HHS/United States ; S10 OD018530/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Carbon Isotopes ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/chemistry/metabolism/microbiology ; Glucose/chemistry/metabolism ; Humans ; Isotope Labeling/*methods ; Microbiota ; Mucin 5AC/*chemistry/metabolism ; Oligosaccharides/*chemistry/metabolism ; }, abstract = {Stable isotope probing (SIP) has emerged as a powerful tool to address key questions about microbiota structure and function. To date, diverse isotopically labeled substrates have been used to characterize in situ growth activity of specific bacterial taxa and have revealed the flux of bioavailable substrates through microbial communities associated with health and disease. A major limitation to the growth of the field is the dearth of biologically relevant "heavy" labeled substrates. Mucin glycoproteins, for example, comprise an abundant source of carbon in the gut, oral cavity, respiratory tract, and other mucosal surfaces but are not commercially available. Here, we describe a method to incorporate a [13]C-labeled monosaccharide into MUC5AC, a predominant mucin in both gastrointestinal and airway environments. Using the lung adenocarcinoma cell line, Calu-3, polarized cell cultures grown in [13]C-labeled d-glucose resulted in liberal mucin production on the apical surface. Mucins were isolated by size-exclusion chromatography, and O-linked glycans were released by β-elimination, permethylated, and analyzed by electrospray ionization tandem mass spectrometry (ESI-MS/MS) and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) techniques. We demonstrate a 98.7% incorporation of [13]C in the heterogeneous O-linked oligosaccharides that make up >80% of mucin dry weight. These "heavy" labeled glycoproteins represent a valuable tool for probing in vivo activity of host-associated bacterial communities and their interactions with the mucosal barrier. The continued expansion of labeled substrates for use in SIP will eventually allow bacterial taxa that degrade host compounds to be identified, with long-term potential for improved health and disease management.}, }
@article {pmid30623212, year = {2019}, author = {de Sousa, AGG and Tomasino, MP and Duarte, P and Fernández-Méndez, M and Assmy, P and Ribeiro, H and Surkont, J and Leite, RB and Pereira-Leal, JB and Torgo, L and Magalhães, C}, title = {Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {388-408}, pmid = {30623212}, issn = {1432-184X}, support = {244646//Research Council of Norway/ ; NORTE-01-0145-FEDER-000031//Structured Program of R&amp;D&amp;I MarInfo/ ; Arktis 2030//Norwegian Ministries of Foreign Affairs and Climate and Environment/ ; NITROLIMIT - PTDC 2017 - PTDC/CTA-AMB/30997/2017//Funda??o para a Ci?ncia e a Tecnologia/ ; }, mesh = {Arctic Regions ; Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Eukaryota/classification/genetics/*isolation &amp; purification ; Ice Cover/chemistry/*microbiology/*parasitology ; Phylogeny ; Seasons ; Seawater/chemistry/microbiology/parasitology ; Svalbard ; }, abstract = {One of the most prominent manifestations of climate change is the changing Arctic sea-ice regime with a reduction in the summer sea-ice extent and a shift from thicker, perennial multiyear ice towards thinner, first-year ice. These changes in the physical environment are likely to impact microbial communities, a key component of Arctic marine food webs and biogeochemical cycles. During the Norwegian young sea ICE expedition (N-ICE2015) north of Svalbard, seawater samples were collected at the surface (5 m), subsurface (20 or 50 m), and mesopelagic (250 m) depths on 9 March, 27 April, and 16 June 2015. In addition, several physical and biogeochemical data were recorded to contextualize the collected microbial communities. Through the massively parallel sequencing of the small subunit ribosomal RNA amplicon and metagenomic data, this work allows studying the Arctic's microbial community structure during the late winter to early summer transition. Results showed that, at compositional level, Alpha- (30.7%) and Gammaproteobacteria (28.6%) are the most frequent taxa across the prokaryotic N-ICE2015 collection, and also the most phylogenetically diverse. Winter to early summer trends were quite evident since there was a high relative abundance of thaumarchaeotes in the under-ice water column in late winter while this group was nearly absent during early summer. Moreover, the emergence of Flavobacteria and the SAR92 clade in early summer might be associated with the degradation of a spring bloom of Phaeocystis. High relative abundance of hydrocarbonoclastic bacteria, particularly Alcanivorax (54.3%) and Marinobacter (6.3%), was also found. Richness showed different patterns along the depth gradient for prokaryotic (highest at mesopelagic depth) and protistan communities (higher at subsurface depths). The microbial N-ICE2015 collection analyzed in the present study provides comprehensive new knowledge about the pelagic microbiota below drifting Arctic sea-ice. The higher microbial diversity found in late winter/early spring communities reinforces the need to continue with further studies to properly characterize the winter microbial communities under the pack-ice.}, }
@article {pmid30620427, year = {2019}, author = {Pasulka, A and Hu, SK and Countway, PD and Coyne, KJ and Cary, SC and Heidelberg, KB and Caron, DA}, title = {SSU-rRNA Gene Sequencing Survey of Benthic Microbial Eukaryotes from Guaymas Basin Hydrothermal Vent.}, journal = {The Journal of eukaryotic microbiology}, volume = {66}, number = {4}, pages = {637-653}, doi = {10.1111/jeu.12711}, pmid = {30620427}, issn = {1550-7408}, mesh = {Alveolata/genetics/*isolation &amp; purification ; Beggiatoa/physiology ; Cercozoa/genetics/*isolation &amp; purification ; Hydrothermal Vents/*microbiology ; Mexico ; *Microbiota ; RNA, Protozoan/analysis ; RNA, Ribosomal, 18S/analysis ; Seawater/*microbiology ; }, abstract = {Microbial eukaryotes have important roles in marine food webs, but their diversity and activities in hydrothermal vent ecosystems are poorly characterized. In this study, we analyzed microbial eukaryotic communities associated with bacterial (Beggiatoa) mats in the 2,000 m deep-sea Guaymas Basin hydrothermal vent system using 18S rRNA gene high-throughput sequencing of the V4 region. We detected 6,954 distinct Operational Taxonomic Units (OTUs) across various mat systems. Of the sequences that aligned with known protistan phylotypes, most were affiliated with alveolates (especially dinoflagellates and ciliates) and cercozoans. OTU richness and community structure differed among sediment habitats (e.g. different mat types and cold sediments away from mats). Additionally, full-length 18S rRNA genes amplified and cloned from single cells revealed the identities of some of the most commonly encountered, active ciliates in this hydrothermal vent ecosystem. Observations and experiments were also conducted to demonstrate that ciliates were trophically active and ingesting fluorescent bacteria or Beggiatoa trichomes. Our work suggests that the active and diverse protistan community at the Guaymas Basin hydrothermal vent ecosystem likely consumes substantial amounts of bacterial biomass, and that the different habitats, often defined by distances of just a few 10s of cm, select for particular assemblages and levels of diversity.}, }
@article {pmid30619557, year = {2018}, author = {Duplouy, A and Minard, G and Lähteenaro, M and Rytteri, S and Saastamoinen, M}, title = {Silk properties and overwinter survival in gregarious butterfly larvae.}, journal = {Ecology and evolution}, volume = {8}, number = {24}, pages = {12443-12455}, pmid = {30619557}, issn = {2045-7758}, abstract = {All organisms are challenged by encounters with parasites, which strongly select for efficient escape strategies in the host. The threat is especially high for gregarious species entering immobile periods, such as diapause. Larvae of the Glanville fritillary butterfly, Melitaea cinxia, spend the winter in diapause in groups of conspecifics each sheltered in a silk nest. Despite intensive monitoring of the population, we have little understanding of the ecological factors influencing larval survival over the winter in the field. We tested whether qualitative and quantitative properties of the silk nest contribute to larval survival over diapause. We used comparative proteomics, metabarcoding analyses, microscopic imaging, and in vitro experiments to compare protein composition of the silk, community composition of the silk-associated microbiota, and silk density from both wild-collected and laboratory-reared families, which survived or died in the field. Although most traits assessed varied across families, only silk density was correlated with overwinter survival in the field. The silk nest spun by gregarious larvae before the winter acts as an efficient breathable physical shield that positively affects larval survival during diapause. Such benefit may explain how this costly trait is conserved across populations of this butterfly species and potentially across other silk-spinning insect species.}, }
@article {pmid30619545, year = {2018}, author = {Alessi, AM and Redeker, KR and Chong, JPJ}, title = {A practical introduction to microbial molecular ecology through the use of isolation chips.}, journal = {Ecology and evolution}, volume = {8}, number = {24}, pages = {12286-12298}, pmid = {30619545}, issn = {2045-7758}, abstract = {In the context of antimicrobial resistance as one of the most serious issues faced globally by health providers, we explored a practical introduction to molecular microbial ecology. We designed field work and practical experiments for third year members of a 4 year undergraduate Masters Program, in which the students employed traditional and novel isolation techniques to identify antimicrobial activities from soil dwelling microorganisms. Students gained experience in isolating DNA from complex microbial communities, amplifying 16S rRNA genes and applied richness/diversity indices as well as principal coordinate analyses to the interpretation of the data they obtained from high throughput sequencing. Our results confirmed that isolation chips facilitate the growth of a greater diversity and different species subset from the complex soil microorganism community than traditional plate spreading techniques. However, rarefaction of 16S rRNA amplicon sequencing data showed that the majority of observed species in soil remain unculturable by current methods. Based on the written reports produced by the students carrying out the work, we concluded that the described protocols are robust and informative, that these activities provide a good practical introduction to the theories and practice of molecular ecology and can be easily deployed to groups of six or more students in a cost-effective manner.}, }
@article {pmid30619197, year = {2018}, author = {Dyksma, S and Lenk, S and Sawicka, JE and Mußmann, M}, title = {Uncultured Gammaproteobacteria and Desulfobacteraceae Account for Major Acetate Assimilation in a Coastal Marine Sediment.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3124}, pmid = {30619197}, issn = {1664-302X}, abstract = {Acetate is a key intermediate in anaerobic mineralization of organic matter in marine sediments. Its turnover is central to carbon cycling, however, the relative contribution of different microbial populations to acetate assimilation in marine sediments is unknown. To quantify acetate assimilation by in situ abundant bacterial populations, we incubated coastal marine sediments with [14]C-labeled acetate and flow-sorted cells that had been labeled and identified by fluorescence in situ hybridization. Subsequently, scintillography determined the amount of [14]C-acetate assimilated by distinct populations. This approach fostered a high-throughput quantification of acetate assimilation by phylogenetically identified populations. Acetate uptake was highest in the oxic-suboxic surface layer for all sorted bacterial populations, including deltaproteobacterial sulfate-reducing bacteria (SRB), which accounted for up to 32% of total bacterial acetate assimilation. We show that the family Desulfobulbaceae also assimilates acetate in marine sediments, while the more abundant Desulfobacteraceae dominated acetate assimilation despite lower uptake rates. Unexpectedly, members of Gammaproteobacteria accounted for the highest relative acetate assimilation in all sediment layers with up to 31-62% of total bacterial acetate uptake. We also show that acetate is used to build up storage compounds such as polyalkanoates. Together, our findings demonstrate that not only the usual suspects SRB but a diverse bacterial community may substantially contribute to acetate assimilation in marine sediments. This study highlights the importance of quantitative approaches to reveal the roles of distinct microbial populations in acetate turnover.}, }
@article {pmid30619181, year = {2018}, author = {Simonin, M and Cantarel, AAM and Crouzet, A and Gervaix, J and Martins, JMF and Richaume, A}, title = {Negative Effects of Copper Oxide Nanoparticles on Carbon and Nitrogen Cycle Microbial Activities in Contrasting Agricultural Soils and in Presence of Plants.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3102}, pmid = {30619181}, issn = {1664-302X}, abstract = {Metal-oxide nanoparticles (NPs) such as copper oxide (CuO) NPs offer promising perspectives for the development of novel agro-chemical formulations of pesticides and fertilizers. However, their potential impact on agro-ecosystem functioning still remains to be investigated. Here, we assessed the impact of CuO-NPs (0.1, 1, and 100 mg/kg dry soil) on soil microbial activities involved in the carbon and nitrogen cycles in five contrasting agricultural soils in a microcosm experiment over 90 days. Additionally, in a pot experiment, we evaluated the influence of plant presence on the toxicity of CuO-NPs on soil microbial activities. CuO-NPs caused significant reductions of the three microbial activities measured (denitrification, nitrification, and soil respiration) at 100 mg/kg dry soil, but the low concentrations (0.1 and 1 mg/kg) had limited effects. We observed that denitrification was the most sensitive microbial activity to CuO-NPs in most soil types, while soil respiration and nitrification were mainly impacted in coarse soils with low organic matter content. Additionally, large decreases in heterotrophic microbial activities were observed in soils planted with wheat, even at 1 mg/kg for soil substrate-induced respiration, indicating that plant presence did not mitigate or compensate CuO-NP toxicity for microorganisms. These two experiments show that CuO-NPs can have detrimental effects on microbial activities in soils with contrasting physicochemical properties and previously exposed to various agricultural practices. Moreover, we observed that the negative effects of CuO-NPs increased over time, indicating that short-term studies (hours, days) may underestimate the risks posed by these contaminants in soils.}, }
@article {pmid30619134, year = {2018}, author = {Porcar, M and Louie, KB and Kosina, SM and Van Goethem, MW and Bowen, BP and Tanner, K and Northen, TR}, title = {Microbial Ecology on Solar Panels in Berkeley, CA, United States.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3043}, pmid = {30619134}, issn = {1664-302X}, abstract = {Solar panels can be found practically all over the world and represent a standard surface that can be colonized by microbial communities that are resistant to harsh environmental conditions, including high irradiation, temperature fluctuations and desiccation. These properties make them not only ideal sources of stress-resistant bacteria, but also standard devices to study the microbial communities and their colonization process from different areas of Earth. We report here a comprehensive description of the microbial communities associated with solar panels in Berkeley, CA, United States. Cultivable bacteria were isolated to characterize their adhesive capabilities, and UV- and desiccation-resistance properties. Furthermore, a parallel culture-independent metagenomic and metabolomic approach has allowed us to gain insight on the taxonomic and functional nature of these communities. Metagenomic analysis was performed using the Illumina HiSeq2500 sequencing platform, revealing that the bacterial population of the Berkeley solar panels is composed mainly of Actinobacteria, Bacteroidetes and Proteobacteria, as well as lower amounts of Deinococcus-Thermus and Firmicutes. Furthermore, a clear predominance of Hymenobacter sp. was also observed. A functional analysis revealed that pathways involved in the persistence of microbes on solar panels (i.e., stress response, capsule development, and metabolite repair) and genes assigned to carotenoid biosynthesis were common to all metagenomes. On the other hand, genes involved in photosynthetic pathways and general autotrophic subsystems were rare, suggesting that these pathways are not critical for persistence on solar panels. Metabolomics was performed using a liquid chromatography tandem mass spectrometry (LC-MS/MS) approach. When comparing the metabolome of the solar panels from Berkeley and from Valencia (Spain), a very similar composition in polar metabolites could be observed, although some metabolites appeared to be differentially represented (for example, trigonelline, pantolactone and 5-valerolactone were more abundant in the samples from Valencia than in the ones from Berkeley). Furthermore, triglyceride metabolites were highly abundant in all the solar panel samples, and both locations displayed similar profiles. The comparison of the taxonomic profile of the Californian solar panels with those previously described in Spain revealed striking similarities, highlighting the central role of both selective pressures and the ubiquity of microbial populations in the colonization and establishment of microbial communities.}, }
@article {pmid30619117, year = {2018}, author = {López-García, A and Pineda-Quiroga, C and Atxaerandio, R and Pérez, A and Hernández, I and García-Rodríguez, A and González-Recio, O}, title = {Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3010}, pmid = {30619117}, issn = {1664-302X}, abstract = {Background: Microbiome studies need to analyze massive sequencing data, which requires the use of sophisticated bioinformatics pipelines. Up to date, several tools are available, although the literature is scarce on studies that compare the performance of different bioinformatics pipelines on rumen microbiota when 16S rRNA amplicons are analyzed. The impact of the pipeline on the outcome of the results is also unknown, mainly in terms of the output from studies using these tools as an intermediate phenotype (pseudophenotypes). This study compares two commonly used software (Quantitative Insights Into Microbial Ecology) (QIIME) and mothur, and two microbial gene data bases (GreenGenes and SILVA) for 16S rRNA gene analysis, using metagenome read data collected from rumen content of a cohort of dairy cows. Results: We compared the relative abundance (RA) of the identified OTUs at the genus level. Both tools presented a high degree of agreement at identifying the most abundant genera: Bifidobacterium, Butyrivibrio, Methanobrevibacter, Prevotella, and Succiniclasticum (RA > 1%), regardless the database. There were no statistical differences between mothur and QIIME (P > 0.05) at estimating the overall RA of the most abundant (RA > 10%) genera, either using SILVA or GreenGenes. However, differences were found at RA < 10% (P < 0.05) when using GreenGenes as database, with mothur assigning OTUs to a larger number of genera and in larger RA for these less frequent microorganisms. With this database mothur resulted in larger richness (P < 0.05), more favorable rarefaction curves and a larger analytic sensitivity. These differences caused significant and relevant differences between tools at identifying the dissimilarity of microbiotas between pairs of animals. However, these differences were attenuated, but not erased, when SILVA was used as the reference database. Conclusion: The findings showed that the SILVA database seemed a preferred reference dataset for classifying OTUs from rumen microbiota. If this database was used, both QIIME and mothur produced comparable richness and diversity, and also in the RA of most common rumen microbes. However, important differences were found for less common microorganisms which impacted on the beta diversity calculated between pipelines. This may have relevant implications at studying global rumen microbiota.}, }
@article {pmid30618066, year = {2019}, author = {Flores-Uribe, J and Hevroni, G and Ghai, R and Pushkarev, A and Inoue, K and Kandori, H and Béjà, O}, title = {Heliorhodopsins are absent in diderm (Gram-negative) bacteria: Some thoughts and possible implications for activity.}, journal = {Environmental microbiology reports}, volume = {11}, number = {3}, pages = {419-424}, doi = {10.1111/1758-2229.12730}, pmid = {30618066}, issn = {1758-2229}, support = {545/17//Israel Science Foundation/International ; }, mesh = {Fresh Water/microbiology/virology ; Gram-Negative Bacteria/classification/*genetics ; Metagenome ; Models, Biological ; Oceans and Seas ; Open Reading Frames ; Seawater/microbiology/virology ; Sensory Rhodopsins/*genetics/metabolism ; }, abstract = {Microbial heliorhodopsins are a new type of rhodopsins, currently believed to engage in light sensing, with an opposite membrane topology compared to type-1 and type-2 rhodopsins. We determined heliorhodopsins presence/absence is monoderms and diderms representatives from the Tara Oceans and freshwater metagenomes as well as metagenome assembled genome collections. Heliorhodopsins are absent in diderms, confirming our previous observations in cultured Proteobacteria. We do not rule out the possibility that heliorhodopsins serve as light sensors. However, this does not easily explain their absence from diderms. Based on these observations, we speculate on the putative role of heliorhodopsins in light-driven transport of amphiphilic molecules.}, }
@article {pmid30613848, year = {2019}, author = {Ye, S and Bhattacharjee, M and Siemann, E}, title = {Thermal Tolerance in Green Hydra: Identifying the Roles of Algal Endosymbionts and Hosts in a Freshwater Holobiont Under Stress.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {537-545}, pmid = {30613848}, issn = {1432-184X}, mesh = {Animals ; Chlorophyta/*physiology ; Fresh Water/chemistry/parasitology ; Hot Temperature ; Hydra/*parasitology/physiology ; Stress, Physiological ; *Symbiosis ; }, abstract = {It has been proposed that holobionts (host-symbiont units) could swap endosymbionts, rapidly alter the hologenome (host plus symbiont genome), and increase their stress tolerance. However, experimental tests of individual and combined contributions of hosts and endosymbionts to holobiont stress tolerance are needed to test this hypothesis. Here, we used six green hydra (Hydra viridissima) strains to tease apart host (hydra) and symbiont (algae) contributions to thermal tolerance. Heat shock experiments with (1) hydra with their original symbionts, (2) aposymbiotic hydra (algae removed), (3) novel associations (a single hydra strain hosting different algae individually), and (4) control hydra (aposymbiotic hydra re-associated with their original algae) showed high variation in thermal tolerance in each group. Relative tolerances of strains were the same within original, aposymbiotic, and control treatments, but reversed in the novel associations group. Aposymbiotic hydra had similar or higher thermal tolerance than hydra with algal symbionts. Selection on the holobiont appears to be stronger than on either partner alone, suggesting endosymbiosis could become an evolutionary trap under climate change. Our results suggest that green hydra thermal tolerance is strongly determined by the host, with a smaller, non-positive role for the algal symbiont. Once temperatures exceed host tolerance limits, swapping symbionts is unlikely to allow these holobionts to persist. Rather, increases in host tolerance through in situ adaptation or migration of pre-adapted host strains appear more likely to increase local thermal tolerance. Overall, our results indicate green hydra is a valuable system for studying aquatic endosymbiosis under changing environmental conditions, and demonstrate how the host and the endosymbiont contribute to holobiont stress tolerance.}, }
@article {pmid30612185, year = {2019}, author = {Murphy, AE and Kolkmeyer, R and Song, B and Anderson, IC and Bowen, J}, title = {Bioreactivity and Microbiome of Biodeposits from Filter-Feeding Bivalves.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {343-357}, pmid = {30612185}, issn = {1432-184X}, support = {OCE 1062882//National Science Foundation/ ; OCE 1233801//National Science Foundation/ ; LTER 0080381//National Science Foundation/ ; NA10OAR4170085//Virginia Sea Grant, Virginia Institute of Marine Science/ ; }, mesh = {Ammonium Compounds/metabolism ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Bivalvia/metabolism/*microbiology ; Carbon/metabolism ; Crassostrea/metabolism/microbiology ; Eutrophication ; Geologic Sediments/chemistry/microbiology ; Mercenaria/metabolism/microbiology ; *Microbiota ; Phylogeny ; Seawater/chemistry/microbiology ; }, abstract = {Bivalves serve an important ecosystem function in delivering organic matter from pelagic to benthic zones and are important in mediating eutrophication. However, the fate of this organic matter (i.e., biodeposits) is an important consideration when assessing the ecological roles of these organisms in coastal ecosystems. In addition to environmental conditions, the processing of biodeposits is dependent on its composition and the metabolic capacity of the associated microbial community. The objectives of this study were to compare the biological reactivity, potential denitrification rates, and microbial communities of biodeposits sourced from different bivalve species: hard clam (Mercenaria mercenaria), eastern oyster (Crassostrea virginica), and ribbed mussel (Geukensia demissa). To our knowledge, this is the first study to investigate and compare the microbiome of bivalve biodeposits using high-throughput sequencing and provide important insight into the mechanisms by which bivalves may alter sediment microbial communities and benthic biogeochemical cycles. We show that clam biodeposits had significantly higher bioreactivity compared to mussel and oyster biodeposits, as reflected in higher dissolved inorganic carbon and ammonium production rates in controlled incubations. Potential denitrification rates were also significantly higher for clam biodeposits compared to oyster and mussel biodeposits. The microbial communities associated with the biodeposits were significantly different across bivalve species, with significantly greater abundances of Alteromonadales, Chitinophagales, Rhodobacterales, and Thiotrichales associated with the clam biodeposits. These bioreactivity and microbial differences across bivalve species are likely due to differences in bivalve physiology and feeding behavior and should be considered when evaluating the effects of bivalves on water quality and ecosystem function.}, }
@article {pmid30612184, year = {2019}, author = {Pan, J and Chen, Y and Wang, Y and Zhou, Z and Li, M}, title = {Vertical Distribution of Bathyarchaeotal Communities in Mangrove Wetlands Suggests Distinct Niche Preference of Bathyarchaeota Subgroup 6.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {417-428}, pmid = {30612184}, issn = {1432-184X}, support = {41506163,31622002,91851105//National Natural Science Foundation of China/ ; 31600093//National Natural Science Foundation of China/ ; }, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Carbon Cycle ; DNA, Archaeal/genetics ; Geologic Sediments/analysis/microbiology ; High-Throughput Nucleotide Sequencing ; Lakes/analysis/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/analysis/microbiology ; Wetlands ; }, abstract = {Bathyarchaeota is a diverse, abundant, and widespread archaeal phylum that may play an important role in global carbon cycling. The vertical distribution of Bathyarchaeota and environmental impact on bathyarchaeotal community in deep-sea and lake sediments are known; however, little information is available on Bathyarchaeota in eutrophic and brackish environments, such as mangrove wetlands. In the current study, we investigated the bathyarchaeotal community in the mangrove ecosystem of Futian Nature Reserve, Shenzhen. By slicing the profile into 2-cm layers from the surface to bottom, 110 sediment samples were obtained from three mangrove and three mud flat profiles. High-throughput sequencing of archaeal 16S rRNA genes, quantification of bathyarchaeotal 16S rRNA genes with optimized quantitative primers, and the ensuing statistical analyses revealed the vertical distribution of Bathyarchaeota in the mangrove ecosystem, indicating that Bathyarchaeota was the dominant archaeal phylum therein, with Bathyarchaeota subgroups 6, 8, 15, and 17 as the most abundant subgroups. The abundance of Bathyarchaeota was higher in the mangrove than in the mud flat and other oligotrophic or freshwater habitats. Total organic carbon (TOC) and nitric oxide were significantly correlated with the abundance of Bathyarchaeota, and pH was the major factor shaping the community composition. Further, the data suggested that Bathyarchaeota subgroup 6 preferentially dwelled in slightly acidic, high TOC, and subsurface environments, indicating a potentially distinct role in the global geochemical cycle. These findings expand the knowledge of the distribution and niche preference of Bathyarchaeota, emphasizing the need for continuous characterization of bathyarchaeotal subgroups.}, }
@article {pmid30612183, year = {2019}, author = {Ding, W and Zhang, W and Alikunhi, NM and Batang, Z and Pei, B and Wang, R and Chen, L and Al-Suwailem, A and Qian, PY}, title = {Metagenomic Analysis of Zinc Surface-Associated Marine Biofilms.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {406-416}, pmid = {30612183}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; Biodiversity ; *Biofilms ; Indian Ocean ; Metagenomics ; Phylogeny ; Seawater/analysis/*microbiology ; Zinc/analysis/*metabolism ; }, abstract = {Biofilms are a significant source of marine biofouling. Marine biofilm communities are established when microorganisms adhere to immersed surfaces. Despite the microbe-inhibiting effect of zinc surfaces, microbes can still attach to the surface and form biofilms. However, the diversity of biofilm-forming microbes that can attach to zinc surfaces and their common functional features remain elusive. Here, by analyzing 9,000,000 16S rRNA gene amplicon sequences and 270 Gb of metagenomic data, we comprehensively explored the taxa and functions related to biofilm formation in subtidal zones of the Red Sea. A clear difference was observed between the biofilm and adjacent seawater microbial communities in terms of the taxonomic structure at phylum and genus levels, and a huge number of genera were only present in the biofilms. Saturated alpha-diversity curves suggested the existence of more than 14,000 operational taxonomic units in one biofilm sample, which is much higher than previous estimates. Remarkably, the biofilms contained abundant and diverse transposase genes, which were localized along microbial chromosomal segments and co-existed with genes related to metal ion transport and resistance. Genomic analyses of two cyanobacterial strains that were abundant in the biofilms revealed a variety of metal ion transporters and transposases. Our analyses revealed the high diversity of biofilm-forming microbes that can attach to zinc surfaces and the ubiquitous role of transposase genes in microbial adaptation to toxic metal surfaces.}, }
@article {pmid30612083, year = {2019}, author = {Zhu, X and Campanaro, S and Treu, L and Kougias, PG and Angelidaki, I}, title = {Novel ecological insights and functional roles during anaerobic digestion of saccharides unveiled by genome-centric metagenomics.}, journal = {Water research}, volume = {151}, number = {}, pages = {271-279}, doi = {10.1016/j.watres.2018.12.041}, pmid = {30612083}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Bioreactors ; Metagenome ; *Metagenomics ; Microbial Consortia ; }, abstract = {In typical anaerobic digestion (AD) systems, the microbial functional assertion is hampered by synchronised versatile metabolism required for heterogeneous substrates degradation. Thus, the intricate methanogenic process from organic compounds remains an enigma after decades of empirical operation. In this study, simplified AD microbial communities were obtained with substrate specifications and continuous reactor operation. Genome-centric metagenomic approach was followed to holistically investigate the metabolic pathways of the AD and the microbial synergistic networks. In total, 63 metagenome assembled genomes (MAGs) were assembled from 8 metagenomes acquired in specific methanogenic niches. The metabolic pathways were reconstructed from the annotated genes and their dynamicity under experimental conditions. The results show that the methanogenic niches nourish unique metabolism beyond current knowledge acquired from cultivation-based methods. A novel glucose mineralization model without acetate formation was proposed and asserted in a pair of syntrophs: Clostridiaceae sp. and Methanoculleus thermophilus. Moreover, the catabolic pathway was elucidated in uncharacterized syntrophic acetate oxidizers, Synergistaceae spp. A remarkable evolutionary insight is the discovery that electron transport and energy conservation mechanisms impose selective pressure on syntrophic partners. Overall, the functional roles of the individual microbes tightly rely on the catabolic pathways and cannot always be physiologically defined in accordance with conventional four-step AD concept. The substrate-specific systems provided a traceable microbial community to dissecting the AD process. The genome-centric metagenomics successfully constructed genomes of microbes that have not been previously isolated and illustrated metabolic pathways that beyond the current knowledge of AD process. This study provides new perspectives to unravel the AD microbial ecology and suggests more attention should be paid on uncharacterized metabolism specifically harboured by AD microbial communities.}, }
@article {pmid30610256, year = {2019}, author = {Mikhailov, IS and Zakharova, YR and Bukin, YS and Galachyants, YP and Petrova, DP and Sakirko, MV and Likhoshway, YV}, title = {Correction to: Co-occurrence Networks Among Bacteria and Microbial Eukaryotes of Lake Baikal During a Spring Phytoplankton Bloom.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {558}, doi = {10.1007/s00248-018-1307-9}, pmid = {30610256}, issn = {1432-184X}, abstract = {The original version of this article unfortunately contained mistakes in the legends of figures.}, }
@article {pmid30610255, year = {2019}, author = {Xia, X and Cheung, S and Endo, H and Suzuki, K and Liu, H}, title = {Latitudinal and Vertical Variation of Synechococcus Assemblage Composition Along 170° W Transect From the South Pacific to the Arctic Ocean.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {333-342}, pmid = {30610255}, issn = {1432-184X}, support = {JPMJCR11A5//JST CREST program/ ; 24121004//JSPS Grant-in-Aid for Scientific Research on Innovative Areas/ ; 16128416 and 16101917//Research Grant Council of Hong Kong/ ; }, mesh = {Arctic Regions ; Biodiversity ; Pacific Ocean ; Phylogeny ; Seawater/chemistry/*microbiology ; Synechococcus/*classification/genetics/*isolation &amp; purification ; Temperature ; }, abstract = {Synechococcus is one of the most widely distributed and abundant picocyanobacteria in the global oceans. Although latitudinal variation of Synechococcus assemblage in marine surface waters has been observed, few studies compared Synechococcus assemblage composition in surface and subsurface waters at the basin scale. Here, we report marine Synechococcus diversity in the surface and deep chlorophyll maximum (DCM) layers along 170° W from the South Pacific to the Arctic Ocean in summer. Along the transect, spatial niche partitioning of Synechococcus lineages in the surface waters was clearly observed. Species richness of surface Synechococcus assemblage was positively correlated with water temperature. Clade CRD1 was dominant in the areas (15° S-10° N and 35-40° N) associated with upwelling, and there were 3 different subclades with distinct distribution. CRD1-A was restricted in the North Equatorial Current (5-10° N), CRD1-B dominated in the equatorial upwelling region (15° S-0.17° N), and CRD1-C was only distributed in the North Pacific Current (35-40° N). Similarities between the Synechococcus assemblages in the surface and DCM layers were high at the upwelling regions and areas where the mixed layer was deep, while low in the Subtropical Gyres with strong stratification. Clade I, CRD1-B, and CRD1-C were major Synechococcus lineages in the DCM layer. In particular, clade I, which is composed of 7 subclades with distinct thermal niches, was widely distributed in the DCM layer. Overall, our results provide new insights into not only the latitudinal distribution of Synechococcus assemblages, but also their vertical variation in the central Pacific.}, }
@article {pmid30610231, year = {2019}, author = {Andrei, A&#x15e; and Salcher, MM and Mehrshad, M and Rychtecký, P and Znachor, P and Ghai, R}, title = {Niche-directed evolution modulates genome architecture in freshwater Planctomycetes.}, journal = {The ISME journal}, volume = {13}, number = {4}, pages = {1056-1071}, pmid = {30610231}, issn = {1751-7370}, mesh = {Bacteria/classification/*genetics ; Ecosystem ; *Evolution, Molecular ; Fresh Water/*microbiology ; *Genome, Bacterial ; Genomics ; Phylogeny ; }, abstract = {Freshwater environments teem with microbes that do not have counterparts in culture collections or genetic data available in genomic repositories. Currently, our apprehension of evolutionary ecology of freshwater bacteria is hampered by the difficulty to establish organism models for the most representative clades. To circumvent the bottlenecks inherent to the cultivation-based techniques, we applied ecogenomics approaches in order to unravel the evolutionary history and the processes that drive genome architecture in hallmark freshwater lineages from the phylum Planctomycetes. The evolutionary history inferences showed that sediment/soil Planctomycetes transitioned to aquatic environments, where they gave rise to new freshwater-specific clades. The most abundant lineage was found to have the most specialised lifestyle (increased regulatory genetic circuits, metabolism tuned for mineralization of proteinaceous sinking aggregates, psychrotrophic behaviour) within the analysed clades and to harbour the smallest freshwater Planctomycetes genomes, highlighting a genomic architecture shaped by niche-directed evolution (through loss of functions and pathways not needed in the newly acquired freshwater niche).}, }
@article {pmid30607437, year = {2019}, author = {Lupatini, M and Suleiman, AKA and Jacques, RJS and Lemos, LN and Pylro, VS and Van Veen, JA and Kuramae, EE and Roesch, LFW}, title = {Moisture Is More Important than Temperature for Assembly of Both Potentially Active and Whole Prokaryotic Communities in Subtropical Grassland.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {460-470}, pmid = {30607437}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; Grassland ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; Temperature ; Water/*analysis/metabolism ; }, abstract = {Moisture and temperature play important roles in the assembly and functioning of prokaryotic communities in soil. However, how moisture and temperature regulate the function of niche- versus neutral-based processes during the assembly of these communities has not been examined considering both the total microbial community and the sole active portion with potential for growth in native subtropical grassland. We set up a well-controlled microcosm-based experiment to investigate the individual and combined effects of moisture and temperature on soil prokaryotic communities by simulating subtropical seasons in grassland. The prokaryotic populations with potential for growth and the total prokaryotic community were assessed by 16S rRNA transcript and 16S rRNA gene analyses, respectively. Moisture was the major factor influencing community diversity and structure, with a considerable effect of this factor on the total community. The prokaryotic populations with potential for growth and the total communities were influenced by the same assembly rules, with the niche-based mechanism being more influential in communities under dry condition. Our results provide new information regarding moisture and temperature in microbial communities of soil and elucidate how coexisting prokaryotic populations, under different physiological statuses, are shaped in native subtropical grassland soil.}, }
@article {pmid30604790, year = {2019}, author = {De Paepe, K and Verspreet, J and Rezaei, MN and Martinez, SH and Meysman, F and Van de Walle, D and Dewettinck, K and Courtin, CM and Van de Wiele, T}, title = {Modification of wheat bran particle size and tissue composition affects colonisation and metabolism by human faecal microbiota.}, journal = {Food &amp; function}, volume = {10}, number = {1}, pages = {379-396}, doi = {10.1039/c8fo01272e}, pmid = {30604790}, issn = {2042-650X}, mesh = {Adult ; Bacteria/classification/genetics/growth &amp; development/*metabolism ; Dietary Fiber/analysis/*metabolism ; Fatty Acids, Volatile/metabolism ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Particle Size ; Triticum/chemistry/*metabolism ; Young Adult ; }, abstract = {Dietary modulation can alter the gut microbiota composition and activity, in turn affecting health. Particularly, dietary fibre rich foods, such as wheat bran, are an important nutrient source for the gut microbiota. Several processing methods have been developed to modify the functional, textural and breadmaking properties of wheat bran, which can affect the gut microbiota. We therefore studied the effect of enzyme treatment, particle size reduction and wheat kernel pearling on the faecal microbiota of ten healthy individuals. The most commonly studied health marker, associated to the gut microbiota activity is Short Chain Fatty Acid (SCFA) production. This study shows that modifying wheat bran physicochemical properties allows control over the extent and the rate of SCFA production by the faecal microbiota. Wheat bran pericarp fractions, depleted in starch and enriched in cellulose and highly branched arabinoxylans, were poorly fermentable compared to unmodified wheat bran, thus resulting in a reduced SCFA production with up to 20 mM. The nature of the SCFA, however, largely depends on the donor and can be linked to the individual's gut microbiota composition. The latter changed in an individually dependent manner in response to wheat bran modification. Some product dependent significant differences could still be identified across the ten donors. This product effect is more pronounced in the microbial community attached to the wheat bran residue as compared to the luminal microbial community. Generally, we find lower levels of Firmicutes, Bacteroidetes and Bifidobacterium and a higher abundance of Proteobacteria in the pericarp enriched wheat bran fractions, compared to unmodified wheat bran.}, }
@article {pmid30603770, year = {2019}, author = {Ishizawa, H and Kuroda, M and Inoue, K and Inoue, D and Morikawa, M and Ike, M}, title = {Colonization and Competition Dynamics of Plant Growth-Promoting/Inhibiting Bacteria in the Phytosphere of the Duckweed Lemna minor.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {440-450}, pmid = {30603770}, issn = {1432-184X}, support = {JPJMAL1108//Advanced Low Carbon Technology Research and Development Program/ ; JP18J10181//Japan Society for the Promotion of Science/ ; }, mesh = {Agricultural Inoculants/classification/genetics/growth &amp; development/*isolation &amp; purification ; Araceae/*growth &amp; development/microbiology ; Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Biodiversity ; Plant Roots/growth &amp; development/*microbiology ; }, abstract = {Despite the considerable role of aquatic plant-associated bacteria in host plant growth and nutrient cycling in aquatic environments, the mode of their plant colonization has hardly been understood. This study examined the colonization and competition dynamics of a plant growth-promoting bacterium (PGPB) and two plant growth-inhibiting bacteria (PGIB) in the aquatic plant Lemna minor (common duckweed). When inoculated separately to L. minor, each bacterial strain quickly colonized at approximately 10[6] cells per milligram (plant fresh weight) and kept similar populations throughout the 7-day cultivation time. The results of two-membered co-inoculation assays revealed that the PGPB strain Aquitalea magnusonii H3 consistently competitively excluded the PGIB strain Acinetobacter ursingii M3, and strain H3 co-existed at almost 1:1 proportion with another PGIB strain, Asticcacaulis excentricus M6, regardless of the inoculation ratios (99:1-1:99) and inoculation order. We also found that A. magnusonii H3 exerted its growth-promoting effect over the negative effects of the two PGIB strains even when only a small amount was inoculated, probably due to its excellent competitive colonization ability. These experimental results demonstrate that there is a constant ecological equilibrium state involved in the bacterial colonization of aquatic plants.}, }
@article {pmid30603713, year = {2018}, author = {Nakato, GV and Wicker, E and Coutinho, TA and Mahuku, G and Studholme, DJ}, title = {A highly specific tool for identification of Xanthomonas vasicola pv. musacearum based on five Xvm-specific coding sequences.}, journal = {Heliyon}, volume = {4}, number = {12}, pages = {e01080}, pmid = {30603713}, issn = {2405-8440}, abstract = {Xanthomonas vasicola pv. musacearum (Xvm) is a bacterial pathogen responsible for the economically important Xanthomonas wilt disease on banana and enset crops in Sub-Saharan Africa. Given that the symptoms are similar to those of other diseases, molecular diagnosis is essential to unambiguously identify this pathogen and distinguish it from closely related strains not pathogenic on these hosts. Currently, Xvm identification is based on polymerase chain reaction (PCR) with GspDm primers, targeting the gene encoding general secretory protein D. Experimental results and examination of genomic sequences revealed poor specificity of the GspDm PCR. Here, we present and validate five new Xvm-specific primers amplifying only Xvm strains.}, }
@article {pmid30602082, year = {2018}, author = {Jeon, SJ and Galvão, KN}, title = {An Advanced Understanding of Uterine Microbial Ecology Associated with Metritis in Dairy Cows.}, journal = {Genomics &amp; informatics}, volume = {16}, number = {4}, pages = {e21}, pmid = {30602082}, issn = {1598-866X}, abstract = {Metritis, the inflammation of the uterus caused by polymicrobial infections, is a prevalent and costly disease to the dairy industry as it decreases milk yield, survival, and the welfare of dairy cows. Although the antibiotic ceftiofur is widely used for the treatment of metritis, endometrium and ovary function is compromised, resulting in subfertility and infertility. According to culture-dependent studies, uterine pathogens include Escherichia coli, Trueperella pyogenes, Fusobacterium necrophorum, and Prevotella melaninogenica. Recent studies using high-throughput sequencing claimed that metritis is a microbiota-associated disease. Herein, we propose that metritis is associated with uterine microbiota with high abundance of Bacteroides, Porphyromonas, and Fusobacterium, but rare bacteria such as Escherichia coli and Helcococcus ovis cannot be ignored.}, }
@article {pmid30599206, year = {2019}, author = {Zwaenepoel, A and Li, Z and Lohaus, R and Van de Peer, Y}, title = {Finding Evidence for Whole Genome Duplications: A Reappraisal.}, journal = {Molecular plant}, volume = {12}, number = {2}, pages = {133-136}, doi = {10.1016/j.molp.2018.12.019}, pmid = {30599206}, issn = {1752-9867}, mesh = {Evolution, Molecular ; *Gene Duplication ; Genome ; *Magnoliopsida ; }, }
@article {pmid30598728, year = {2019}, author = {Rafeek, R and Carrington, CVF and Gomez, A and Harkins, D and Torralba, M and Kuelbs, C and Addae, J and Moustafa, A and Nelson, KE}, title = {Xylitol and sorbitol effects on the microbiome of saliva and plaque.}, journal = {Journal of oral microbiology}, volume = {11}, number = {1}, pages = {1536181}, pmid = {30598728}, issn = {2000-2297}, abstract = {Chewing gum containing xylitol may help prevent caries by reducing levels of mutans streptococci (MS) and lactobacilli in saliva and plaque. Very little is known about other species which are possibly beneficial to oral health. In this study, we employed high-throughput sequencing of the 16S rRNA gene to profile microbial communities of saliva and plaque following short-term consumption of xylitol and sorbitol containing chewing gum. Participants (n = 30) underwent a washout period and were randomly assigned to one of two groups. Each group chewed either xylitol or sorbitol gum for three weeks, before undergoing a second four-week washout period after which they switched to the alternate gum for three weeks. Analysis of samples collected before and after each intervention identified distinct plaque and saliva microbial communities that altered dependent on the order in which gum treatments were given. Neither the xylitol nor sorbitol treatments significantly affected the bacterial composition of plaque. Lactobacilli were undetected and the number of Streptococcus mutans sequence reads was very low and unaffected by either xylitol or sorbitol. However, sorbitol affected several other streptococcal species in saliva including increasing the abundance of S. cristatus, an oral commensal shown to inhibit bacteria associated with chronic periodontitis.}, }
@article {pmid30595029, year = {2019}, author = {Tian, L and Tan, Y and Chen, G and Wang, G and Sun, J and Ou, S and Chen, W and Bai, W}, title = {Metabolism of anthocyanins and consequent effects on the gut microbiota.}, journal = {Critical reviews in food science and nutrition}, volume = {59}, number = {6}, pages = {982-991}, doi = {10.1080/10408398.2018.1533517}, pmid = {30595029}, issn = {1549-7852}, mesh = {Anthocyanins/*metabolism/*pharmacokinetics ; Biological Availability ; Diet ; Dietary Supplements ; Fruit/chemistry ; Gastric Absorption ; Gastrointestinal Microbiome/*drug effects/*physiology ; Humans ; Insurance Benefits ; Intestinal Absorption ; Oral Mucosal Absorption ; Oxidative Stress/drug effects ; Polyphenols ; Vegetables/chemistry ; }, abstract = {Anthocyanins are natural water-soluble polyphenols present in fruits and vegetables. Health-promoting effects attributed to anthocyanins are mainly associated with oxidative stress inhibition and gut microbiota modulation. Dietary anthocyanins undergo a complex metabolism after ingestion and interact with endogenous and microbial enzymes, leading to the production of a large number of circulating and excreted anthocyanin metabolites and catabolic products. To date, the bioavailability and health benefits of anthocyanins have been widely documented. Although there are several papers that illustrated the metabolism of anthocyanins, the effects of dietary anthocyanins on the modulation of the gut microbial ecology and on the growth of certain microbial species are still poorly understood. The present paper summarizes the recent data on the absorption of anthocyanins in the upper gastrointestine and the metabolism of anthocyanins by gut microbiota. The modulatory effects of anthocyanins from different sources on gut microbiota are also discussed.}, }
@article {pmid30594092, year = {2019}, author = {Garner, E and Inyang, M and Garvey, E and Parks, J and Glover, C and Grimaldi, A and Dickenson, E and Sutherland, J and Salveson, A and Edwards, MA and Pruden, A}, title = {Impact of blending for direct potable reuse on premise plumbing microbial ecology and regrowth of opportunistic pathogens and antibiotic resistant bacteria.}, journal = {Water research}, volume = {151}, number = {}, pages = {75-86}, doi = {10.1016/j.watres.2018.12.003}, pmid = {30594092}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; *Drinking Water ; *Legionella ; RNA, Ribosomal, 16S ; Sanitary Engineering ; Water Microbiology ; }, abstract = {Little is known about how introducing recycled water intended for direct potable reuse (DPR) into distribution systems and premise plumbing will affect water quality at the point of use, particularly with respect to effects on microbial communities and regrowth. The examination of potential growth of opportunistic pathogens (OPs) and spread of antibiotic resistance genes (ARGs), each representing serious and growing public health concerns, by introducing DPR water has not previously been evaluated. In this study, the impact of blending purified DPR water with traditional drinking water sources was investigated with respect to treatment techniques, blending location, and blending ratio. Water from four U.S. utility partners was treated in bench- and pilot-scale treatment trains to simulate DPR with blending. Water was incubated in simulated premise plumbing rigs made of PVC pipe containing brass coupons to measure regrowth of total bacteria (16S rRNA genes, heterotrophic plate count), OPs (Legionella spp., Mycobacterium spp., Pseudomonas aeruginosa), ARGs (qnrA, vanA), and an indicator of horizontal gene transfer and multi-drug resistance (intI1). The microbial community composition was profiled and the resistome (i.e., all ARGs present) was characterized in select samples using next generation sequencing. While regrowth of total bacteria (16S rRNA genes) from the start of the incubation through week eight consistently occurred across tested scenarios (Wilcoxon, p ≤ 0.0001), total bacteria were not more abundant in the water or biofilm of any DPR scenario than in the corresponding conventional potable condition (p ≥ 0.0748). Regrowth of OP marker genes, qnrA, vanA, and intI1 were not significantly greater in water or biofilm for any DPR blends treated with advanced oxidation compared to corresponding potable water (p ≥ 0.1047). This study of initial bacteria colonizing pipes after introduction of blended DPR water revealed little evidence (i.e., one target in one water type) of exacerbated regrowth of total bacteria, OPs, or ARGs in premise plumbing.}, }
@article {pmid30593603, year = {2019}, author = {Bachran, M and Kluge, S and Lopez-Fernandez, M and Cherkouk, A}, title = {Microbial Diversity in an Arid, Naturally Saline Environment.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {494-505}, pmid = {30593603}, issn = {1432-184X}, mesh = {Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Desert Climate ; Ecosystem ; High-Throughput Nucleotide Sequencing ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sodium Chloride/analysis/metabolism ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {The Arava Valley in is a rock desert within the Great African Rift valley. Soil from this area is covered with a salt crust. Here, we report microbial diversity from arid, naturally saline samples collected near Ein Yahav from the Arava Valley by culture-independent as well as culture-dependent analysis. High-throughput sequencing of the hypervariable region V4 of the 16S rRNA gene revealed that the microbial community consists of halophiles from the domain Bacteria as well as Archaea. Bacterial diversity was mainly represented by the genus Salinimicrobium of the order Flavobacteriales within the phylum Bacteroidetes, from the gammaproteobacterial orders Alteromonadales and Oceanospirillales as well as representatives from the order Bacillales of the phylum Firmicutes. Archaeal diversity was dominated by euryarchaeal Halobacteria from the orders Halobacteriales, Haloferacales, and Natrialbales. But more than 40% of the sequences affiliated with Archaea were assigned to unknown or unclassified archaea. Even if taxonomic resolution of the 16S rRNA gene V4 region for Archaea is limited, this study indicates the need of further and more detailed studies of Archaea. By using culture-dependent analysis, bacteria of the order Bacillales as well as archaea from all three halobacterial orders Halobacteriales, Haloferacales, and Natrialbales including potentially novel species from the genera Halorubrum and Haloparvum were isolated.}, }
@article {pmid30593565, year = {2019}, author = {Vallespir Lowery, N and Ursell, T}, title = {Structured environments fundamentally alter dynamics and stability of ecological communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {2}, pages = {379-388}, pmid = {30593565}, issn = {1091-6490}, support = {P50 GM098911/GM/NIGMS NIH HHS/United States ; }, mesh = {*Computer Simulation ; Microbial Consortia/*physiology ; *Models, Biological ; }, abstract = {The dynamics and stability of ecological communities are intimately linked with the specific interactions-like cooperation or predation-between constituent species. In microbial communities, like those found in soils or the mammalian gut, physical anisotropies produced by fluid flow and chemical gradients impact community structure and ecological dynamics, even in structurally isotropic environments. Although natural communities existing in physically unstructured environments are rare, the role of environmental structure in determining community dynamics and stability remains poorly studied. To address this gap, we used modified Lotka-Volterra simulations of competitive microbial communities to characterize the effects of surface structure on community dynamics. We find that environmental structure has profound effects on communities, in a manner dependent on the specific pattern of interactions between community members. For two mutually competing species, eventual extinction of one competitor is effectively guaranteed in isotropic environments. However, addition of environmental structure enables long-term coexistence of both species via local "pinning" of competition interfaces, even when one species has a significant competitive advantage. In contrast, while three species competing in an intransitive loop (as in a game of rock-paper-scissors) coexist stably in isotropic environments, structural anisotropy disrupts the spatial patterns on which coexistence depends, causing chaotic population fluctuations and subsequent extinction cascades. These results indicate that the stability of microbial communities strongly depends on the structural environment in which they reside. Therefore, a more complete ecological understanding, including effective manipulation and interventions in natural communities of interest, must account for the physical structure of the environment.}, }
@article {pmid30586832, year = {2019}, author = {Yang, S and Zheng, Q and Yuan, M and Shi, Z and Chiariello, NR and Docherty, KM and Dong, S and Field, CB and Gu, Y and Gutknecht, J and Hungate, BA and Le Roux, X and Ma, X and Niboyet, A and Yuan, T and Zhou, J and Yang, Y}, title = {Long-term elevated CO2 shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentials.}, journal = {The Science of the total environment}, volume = {652}, number = {}, pages = {1474-1481}, doi = {10.1016/j.scitotenv.2018.10.353}, pmid = {30586832}, issn = {1879-1026}, mesh = {California ; Carbon Dioxide/*analysis/toxicity ; Climate Change ; Desert Climate ; Environmental Monitoring/*methods ; *Grassland ; *Microbiota/genetics ; *Nitrogen Fixation/genetics ; Poaceae/*drug effects/growth &amp; development/metabolism ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The continuously increasing concentration of atmospheric CO2 has considerably altered ecosystem functioning. However, few studies have examined the long-term (i.e. over a decade) effect of elevated CO2 on soil microbial communities. Using 16S rRNA gene amplicons and a GeoChip microarray, we investigated soil microbial communities from a Californian annual grassland after 14 years of experimentally elevated CO2 (275 ppm higher than ambient). Both taxonomic and functional gene compositions of the soil microbial community were modified by elevated CO2. There was decrease in relative abundance for taxa with higher ribosomal RNA operon (rrn) copy number under elevated CO2, which is a functional trait that responds positively to resource availability in culture. In contrast, taxa with lower rrn copy number were increased by elevated CO2. As a consequence, the abundance-weighted average rrn copy number of significantly changed OTUs declined from 2.27 at ambient CO2 to 2.01 at elevated CO2. The nitrogen (N) fixation gene nifH and the ammonium-oxidizing gene amoA significantly decreased under elevated CO2 by 12.6% and 6.1%, respectively. Concomitantly, nitrifying enzyme activity decreased by 48.3% under elevated CO2, albeit this change was not significant. There was also a substantial but insignificant decrease in available soil N, with both nitrate (NO3[-]) (-27.4%) and ammonium (NH4[+]) (-15.4%) declining. Further, a large number of microbial genes related to carbon (C) degradation were also affected by elevated CO2, whereas those related to C fixation remained largely unchanged. The overall changes in microbial communities and soil N pools induced by long-term elevated CO2 suggest constrained microbial N decomposition, thereby slowing the potential maximum growth rate of the microbial community.}, }
@article {pmid30585386, year = {2019}, author = {Cholet, F and Ijaz, UZ and Smith, CJ}, title = {Differential ratio amplicons (Ramp) for the evaluation of RNA integrity extracted from complex environmental samples.}, journal = {Environmental microbiology}, volume = {21}, number = {2}, pages = {827-844}, pmid = {30585386}, issn = {1462-2920}, support = {//Univeristy of Glasgow, School of Engineering Doctoral Scholarship/International ; NE/L011956/1//NERC IRF/International ; RCSRF1718643//Royal Academy of Engineering under the Research Chairs and Senior Research Fellowships scheme/International ; }, mesh = {Bacteria/classification/*genetics/metabolism ; Computational Biology ; Environmental Microbiology ; Geologic Sediments/analysis/*microbiology ; Humans ; RNA Stability ; RNA, Bacterial/*genetics/metabolism ; RNA, Messenger/genetics/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {Reliability and reproducibility of transcriptomics-based studies are dependent on RNA integrity. In microbial ecology, microfluidics-based techniques, such as the Ribosomal Integrity Number (RIN), targeting rRNA are currently the only approaches to evaluate RNA integrity. However, the relationship between rRNA and mRNA integrity is unknown. Here, we present an integrity index, the Ratio Amplicon, Ramp , adapted from human clinical studies, to directly monitor mRNA integrity from complex environmental samples. We show, in a suite of experimental degradations of RNA extracted from sediment, that while the RIN generally reflected the degradation status of RNA the Ramp mapped mRNA degradation better. Furthermore, we examined the effect of degradation on transcript community structure by amplicon sequencing of 16S rRNA, amoA and glnA transcripts. We successfully sequenced transcripts for all three targets even from highly-degraded RNA samples. While RNA degradation changed the community structure of the mRNA profiles, no changes were observed for the 16S rRNA transcript profiles. Since both RT-Q-PCR and sequencing results were obtained, even from highly degraded samples, we strongly recommend evaluating RNA integrity prior to downstream processing to ensure meaningful results. For this, both the RIN and Ramp are useful, with the Ramp better evaluating mRNA integrity in this study.}, }
@article {pmid30581429, year = {2018}, author = {Brenzinger, K and Drost, SM and Korthals, G and Bodelier, PLE}, title = {Organic Residue Amendments to Modulate Greenhouse Gas Emissions From Agricultural Soils.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3035}, pmid = {30581429}, issn = {1664-302X}, abstract = {Organic fertilizers have been shown to stimulate CH4 uptake from agricultural soils. Managing fertilizer application to maximize this effect and to minimize emission of other greenhouse gasses offers possibilities to increase sustainability of agriculture. To tackle this challenge, we incubated an agricultural soil with different organic amendments (compost, sewage sludge, digestate, cover crop residues mixture), either as single application or in a mixture and subjected it to different soil moisture concentrations using different amounts of organic amendments. GHG fluxes and in vitro CH4 oxidation rates were measured repeatedly, while changes in organic matter and abundance of GHG relevant microbial groups (nitrifiers, denitrifiers, methanotrophs, methanogens) were measured at the end of the incubation. Overall the dynamics of the analyzed GHGs differed significantly. While CO2 and N2O differed considerably between the treatments, CH4 fluxes remained stable. In contrast, in vitro CH4 oxidation showed a clear increase for all amendments over time. CO2 fluxes were mostly dependent on the amount of organic residue that was used, while N2O fluxes were affected more by soil moisture. Several combinations of amendments led to reductions of CO2, CH4, and/or N2O emissions compared to un-amended soil. Most optimal GHG balance was obtained by compost amendments, which resulted in a similar overall GHG balance as compared to the un-amended soil. However, compost is not very nutrient rich potentially leading to lower crop yield when applied as single fertilizer. Hence, the combination of compost with one of the more nutrient rich organic amendments (sewage sludge, digestate) provides a trade-off between maintaining crop yield and minimizing GHG emissions. Additionally, we could observe a strong increase in microbial communities involved in GHG consumption in all amendments, with the strongest increase associated with cover crop residue mixtures. Future research should focus on the interrelation of plants, soil, and microbes and their impact on the global warming potential in relation to applied organic amendments.}, }
@article {pmid30580396, year = {2019}, author = {Williams, MR and Hashsham, SA}, title = {Direct or DNA Extraction-Free Amplification and Quantification of Foodborne Pathogens.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1918}, number = {}, pages = {21-33}, doi = {10.1007/978-1-4939-9000-9_2}, pmid = {30580396}, issn = {1940-6029}, mesh = {Animals ; DNA, Bacterial ; Escherichia coli/genetics ; Food Microbiology/*methods ; Foodborne Diseases/diagnosis/*microbiology ; Humans ; *Nucleic Acid Amplification Techniques ; Polymerase Chain Reaction ; Salmonella/genetics ; Sensitivity and Specificity ; }, abstract = {The use of direct nucleic acid amplification of pathogens from food matrices has the potential to reduce time to results over DNA extraction-based approaches as well as traditional culture-based approaches. Here we describe protocols for assay design and experiments for direct amplification of foodborne pathogens in food sample matrices using loop-mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR). The examples provided include the detection Escherichia coli in milk samples and Salmonella in pork meat samples. This protocol includes relevant reagents and methods including obtaining target sequences, assay design, sample processing, and amplification. These methods, though used for specific example matrices, could be applied to many other foodborne pathogens and sample types.}, }
@article {pmid30579209, year = {2019}, author = {Bains, W and Petkowski, JJ and Sousa-Silva, C and Seager, S}, title = {New environmental model for thermodynamic ecology of biological phosphine production.}, journal = {The Science of the total environment}, volume = {658}, number = {}, pages = {521-536}, doi = {10.1016/j.scitotenv.2018.12.086}, pmid = {30579209}, issn = {1879-1026}, mesh = {Bacteria/*metabolism ; *Environment ; Models, Chemical ; Oxidation-Reduction ; Phosphines/analysis/*metabolism ; Thermodynamics ; }, abstract = {We present a new model for the biological production of phosphine (PH3). Phosphine is found globally, in trace amounts, in the Earth's atmosphere. It has been suggested as a key molecule in the phosphorus cycle, linking atmospheric, lithospheric and biological phosphorus chemistry. Phosphine's production is strongly associated with marshes, swamps and other sites of anaerobic biology. However the mechanism of phosphine's biological production has remained controversial, because it has been believed that reduction of phosphate to phosphine is endergonic. In this paper we show through thermodynamic calculations that, in specific environments, the combined action of phosphate reducing and phosphite disproportionating bacteria can produce phosphine. Phosphate-reducing bacteria can capture energy from the reduction of phosphate to phosphite through coupling phosphate reduction to NADH oxidation. Our hypothesis describes how the phosphate chemistry in an environmental niche is coupled to phosphite generation in ground water, which in turn is coupled to the phosphine production in water and atmosphere, driven by a specific microbial ecology. Our hypothesis provides clear predictions on specific complex environments where biological phosphine production could be widespread. We propose tests of our hypothesis in fieldwork.}, }
@article {pmid30577137, year = {2019}, author = {Abreu-Junior, CH and de Lima Brossi, MJ and Monteiro, RT and Cardoso, PHS and da Silva Mandu, T and Nogueira, TAR and Ganga, A and Filzmoser, P and de Oliveira, FC and Firme, LP and He, Z and Capra, GF}, title = {Effects of sewage sludge application on unfertile tropical soils evaluated by multiple approaches: A field experiment in a commercial Eucalyptus plantation.}, journal = {The Science of the total environment}, volume = {655}, number = {}, pages = {1457-1467}, doi = {10.1016/j.scitotenv.2018.11.334}, pmid = {30577137}, issn = {1879-1026}, mesh = {Eucalyptus/*drug effects/growth &amp; development/physiology ; Fertilizers/*analysis ; Forestry ; Sewage/*adverse effects ; Soil/chemistry ; Soil Pollutants/*toxicity ; }, abstract = {Sewage sludge (SS) reuse in forest plantation as soil fertilizer/amendment has tremendously increased in recent years. However, SS may have high concentrations of potentially toxic elements (PTE), representing a potential risk for soil and the whole ecosystem. This paper was aimed to assess the toxicity of PTE in unfertile tropical soils amended with SS in a commercial Eucalyptus plantation, with an integrated multiple approaches combining: i) the use of a battery of bioassays (Daphnia magna, Pseudokcrichirella subcapitata, Lactuca sativa, and Allium cepa); and ii) the evaluation of some PTE (Cd, Cr, Cu, Fe, Mn, Ni, Pb, and Zn) and their availability into the pedoenvironment. Differences in total and available PTE between SS doses and time of treatments were evaluated using ANOVA; correlations between PTE and bioassays by a sparse partial robust M-regression (SPRM), while multiple correlations among parameters were performed by principal factor analysis (PFA). Results show that PTE contents in soils tended to increase with SS application doses. However this cannot be assumed as a general rule since in all the investigated treatments the PTE concentrations were consistently below both soil natural background concentrations and quality reference values. Bioassays showed a generalized low eco- and genotoxicity of SS with an increase in toxicity at increasing SS doses but with a clear decreasing trend as time went by. A. cepa was the most sensitive bioassay followed by P. subcapitata > D. magna > L. sativa. Overall, the results indicate that in realistic open field conditions SS risk may be lower than expected due to dynamic decrease in PTE toxicity with time after application. This study has an important implication that open-field trials should be strongly encouraged for evaluating environmental risk of SS application in forestry.}, }
@article {pmid30577127, year = {2019}, author = {Wang, D and Li, T and Huang, K and He, X and Zhang, XX}, title = {Roles and correlations of functional bacteria and genes in the start-up of simultaneous anammox and denitrification system for enhanced nitrogen removal.}, journal = {The Science of the total environment}, volume = {655}, number = {}, pages = {1355-1363}, doi = {10.1016/j.scitotenv.2018.11.321}, pmid = {30577127}, issn = {1879-1026}, mesh = {Ammonia/metabolism ; Bacteria/*metabolism ; *Bioreactors ; Denitrification ; Nitrogen/*metabolism ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Waste Disposal, Fluid ; }, abstract = {Simultaneous anammox and denitrification (SAD) is a newly developed wastewater treatment process efficient in nitrogen removal, but its underlying microbiological mechanisms during start-up remains unknown. This study investigated the changing patterns of functional bacteria and genes, as well as their correlation during the start-up (260 d) of the SAD systems in two lab-scale up-flow anaerobic sludge blanket bioreactors separately inoculated with anaerobic granular sludge (R1) and aerobic floccular sludge (R2). Results showed that high total nitrogen removal was achieved in the SAD systems of both R1 (88.25%) and R2 (89.42%). High-throughput sequencing of 16S rRNA gene amplicons revealed that Armatimonadetes phylum had a high abundance (44.34%) in R2, while was not detectable in R1 during the anammox stage. However, the SAD bioreactors retained inherent microbial community and the inoculation with different sludge showed less notable effects on their microbial composition. In the SAD systems, Candidatus Brocadia had high abundance in R1 (2.93%) and R2 (4.64%) and played important role in anammox. Network analysis indicated that Denitratisoma and Dokdonella were positively correlated with nitrite reductase genes nirS and nirK (p < 0.05), while Thermomonas and Pseudomonas showing a positive correlation with nitrate reductase gene narG (p < 0.05) were mainly responsible for the nitrate reduction in the SAD systems. Moreover, the overwhelming dominance of narG v.s. napA revealed the crucial roles of respiratory nitrate reduction in the bioreactors. The results extend our knowledge regarding the microbial ecology of the SAD system, which might be practically helpful for application of the process in wastewater treatment.}, }
@article {pmid30574135, year = {2018}, author = {Vander Roost, J and Daae, FL and Steen, IH and Thorseth, IH and Dahle, H}, title = {Distribution Patterns of Iron-Oxidizing Zeta- and Beta-Proteobacteria From Different Environmental Settings at the Jan Mayen Vent Fields.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3008}, pmid = {30574135}, issn = {1664-302X}, abstract = {Iron oxidizers are widespread in marine environments and play an important role in marine iron cycling. However, little is known about the overall distribution of iron oxidizers within hydrothermal systems, including settings with little hydrothermal activity. Moreover, the extent to which different phylogenetic groups of iron oxidizers exhibit niche specialization toward different environmental settings, remains largely unknown. Obtaining such knowledge is critical to unraveling the impact of the activity of iron oxidizers and how they are adapted. Here, we used 16S rRNA sequencing to characterize the distribution of iron oxidizers in different environmental settings within the Jan Mayen hydrothermal vent fields (JMVFs). Putative iron oxidizers affiliated to Zetaproteobacteria and Betaproteobacteria were detected within iron mounds, bottom seawater, basalt surfaces, and surface layers of sediments. The detected iron oxidizers were compared to sequence types previously observed in patchily distributed iron mats associated with diffuse venting at the JMVFs. Most OTUs of iron oxidizers reoccurred under different environmental settings, suggesting a limited degree of niche specialization. Consequently, most of the detected iron oxidizers seem to be generalists with a large habitat range. Our study highlights the importance of gathering information about the overall distribution of iron oxidizers in hydrothermal systems to fully understand the role of this metabolic group regarding cycling of iron. Furthermore, our results provide further evidence of the presence of iron-oxidizing members of Betaproteobacteria in marine environments.}, }
@article {pmid30572962, year = {2018}, author = {Du Preez, S and Corbitt, M and Cabanas, H and Eaton, N and Staines, D and Marshall-Gradisnik, S}, title = {A systematic review of enteric dysbiosis in chronic fatigue syndrome/myalgic encephalomyelitis.}, journal = {Systematic reviews}, volume = {7}, number = {1}, pages = {241}, pmid = {30572962}, issn = {2046-4053}, mesh = {Dietary Supplements ; *Dysbiosis ; Fatigue Syndrome, Chronic/*physiopathology ; *Gastrointestinal Microbiome ; Humans ; Probiotics ; Quality of Life/*psychology ; }, abstract = {BACKGROUND: Chronic fatigue syndrome or myalgic encephalomyelitis (CFS/ME) is an illness characterised by profound and pervasive fatigue in addition to a heterogeneous constellation of symptoms. The aetiology of this condition remains unknown; however, it has been previously suggested that enteric dysbiosis is implicated in the pathogenesis of CFS/ME. This review examines the evidence currently available for the presence of abnormal microbial ecology in CFS/ME in comparison to healthy controls, with one exception being probiotic-supplemented CFS/ME patients, and whether the composition of the microbiome plays a role in symptom causation.<br><br>METHODS: EMBASE, Medline (via EBSCOhost), Pubmed and Scopus were systematically searched from 1994 to March 2018. All studies that investigated the gut microbiome composition of CFS/ME patients were initially included prior to the application of specific exclusion criteria. The association between these findings and patient-centred outcomes (fatigue, quality of life, gastrointestinal symptoms, psychological wellbeing) are also reported.<br><br>RESULTS: Seven studies that met the inclusion criteria were included in the review. The microbiome composition of CFS/ME patients was compared with healthy controls, with the exception of one study that compared to probiotic-supplemented CFS/ME patients. Differences were reported in each study; however, only three were considered statistically significant, and the findings across all studies were inconsistent. The quality of the studies included in this review scored between poor (<&#x2009;54%), fair (54-72%) and good (94-100%) using the Downs and Black checklist.<br><br>CONCLUSIONS: There is currently insufficient evidence for enteric dysbiosis playing a significant role in the pathomechanism of CFS/ME. Recommendations for future research in this field include the use of consistent criteria for the diagnosis of CFS/ME, reduction of confounding variables by controlling factors that influence microbiome composition prior to sample collection and including more severe cases of CFS/ME.}, }
@article {pmid30568671, year = {2018}, author = {Bardin, M and Leyronas, C and Troulet, C and Morris, CE}, title = {Striking Similarities Between Botrytis cinerea From Non-agricultural and From Agricultural Habitats.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1820}, pmid = {30568671}, issn = {1664-462X}, abstract = {Investigations into life history of microorganisms that cause plant diseases have been limited mostly to contexts where they are in interaction with plants, and with cropped or otherwise managed vegetation. Therefore, knowledge about the diversity of plant pathogens, about potential reservoirs of inoculum and about the processes that contribute to their survival and adaptation is limited to these contexts. The agro-centric perspective of plant pathogen life histories is incoherent with respect to the capacity of many of them to persist as saprophytes on various substrates. In this context we have investigated the ubiquity of the broad host range necrotrophic fungus Botrytis cinerea, outside of agricultural settings and have determined if the populations in these natural habitats can be distinguished phenotypically and phylogenetically from populations isolated from diseased crops. Over a period of 5 years, we isolated B. cinerea from 235 samples of various substrates collected in France including rainfall, snowpack, river, and lake water, epilithic biofilms in mountain streams, leaf litter and plant debris, rock surfaces, bird feathers and healthy wild plants from outside of agricultural fields. All substrates except rock surfaces harbored B. cinerea leading us to establish a collection of purified strains that were compared to B. cinerea from diseased tomato, grapes and various other crops in France. Phylogenetic comparisons of 321 strains from crop plants and 100 strains from environmental substrates based on sequences of 9 microsatellite markers revealed that strains from crops and the environment could not be distinguished. Furthermore, the genetic diversity of strains outside of agriculture was just as broad as within agriculture. In tests to determine the aggressiveness of strains on tomato stems, the mean disease severity caused by strains from environmental substrates was statistically identical to the severity of disease caused by strains from tomato, but was significantly greater than the severity caused by strains from grape or other crops. Our results suggest that highly diverse populations of this plant pathogen persist outside of agriculture in association with substrates other than plants and that this part of their life history is compatible with its capacity to maintain its potential as plant pathogen.}, }
@article {pmid30565880, year = {2019}, author = {Thorn, CE and Bergesch, C and Joyce, A and Sambrano, G and McDonnell, K and Brennan, F and Heyer, R and Benndorf, D and Abram, F}, title = {A robust, cost-effective method for DNA, RNA and protein co-extraction from soil, other complex microbiomes and pure cultures.}, journal = {Molecular ecology resources}, volume = {19}, number = {2}, pages = {439-455}, doi = {10.1111/1755-0998.12979}, pmid = {30565880}, issn = {1755-0998}, support = {//NUI Galway/ ; }, mesh = {Cost-Benefit Analysis ; DNA/genetics/*isolation &amp; purification ; Metagenomics/economics/*methods ; *Microbiota ; Proteins/analysis/*isolation &amp; purification ; Proteomics/economics/*methods ; RNA/genetics/*isolation &amp; purification ; *Soil Microbiology ; }, abstract = {The soil microbiome is inherently complex with high biological diversity, and spatial heterogeneity typically occurring on the submillimetre scale. To study the microbial ecology of soils, and other microbiomes, biomolecules, that is, nucleic acids and proteins, must be efficiently and reliably co-recovered from the same biological samples. Commercial kits are currently available for the co-extraction of DNA, RNA and proteins but none has been developed for soil samples. We present a new protocol drawing on existing phenol-chloroform-based methods for nucleic acids co-extraction but incorporating targeted precipitation of proteins from the phenol phase. The protocol is cost-effective and robust, and easily implemented using reagents commonly available in laboratories. The method is estimated to be eight times cheaper than using disparate commercial kits for the isolation of DNA and/or RNA, and proteins, from soil. The method is effective, providing good quality biomolecules from a diverse range of soil types, with clay contents varying from 9.5% to 35.1%, which we successfully used for downstream, high-throughput gene sequencing and metaproteomics. Additionally, we demonstrate that the protocol can also be easily implemented for biomolecule co-extraction from other complex microbiome samples, including cattle slurry and microbial communities recovered from anaerobic bioreactors, as well as from Gram-positive and Gram-negative pure cultures.}, }
@article {pmid30565684, year = {2019}, author = {Wang, JC and Bergeron, M and Andersen, H and Tikhtman, R and Haslam, D and Hunter, T and Herr, AB and de Alarcon, A}, title = {Feasibility of shotgun metagenomics to assess microbial ecology of pediatric tracheostomy tubes.}, journal = {The Laryngoscope}, volume = {129}, number = {2}, pages = {317-323}, doi = {10.1002/lary.27356}, pmid = {30565684}, issn = {1531-4995}, mesh = {Biofilms/*growth &amp; development ; Child ; Child, Preschool ; Equipment Contamination ; Feasibility Studies ; Female ; Humans ; Infant ; Male ; Metagenomics/*methods ; Tracheostomy/*instrumentation ; }, abstract = {OBJECTIVE: Biofilm formation on medical devices such as tracheostomy tubes (TTs) is a serious problem. The clinical impact of biofilms on the airway is still unclear. Biofilms may play a role in granulation tissue development, recurrent airway infections, and failure of laryngotracheal reconstructions. The microbial ecology on TTs has yet to be elucidated. The purpose of this study was to determine the feasibility of shotgun metagenomics to assess the biodistribution of microorganisms on TTs.<br><br>METHODS: Four TTs were collected from pediatric patients (1.4-10.2 years) with (n&#x2009;=&#x2009;2) and without (n&#x2009;=&#x2009;2) granulation tissue formation. Duration of TT placement prior to retrieval from patients ranged from 5 to 365 days. DNA extraction was performed using the MO BIO UltraClean Microbial Isolation (Mo Bio Laboratories, Carlsbad, CA). Library generation using Nextera XT adapters (Illumina Inc., San Diego, CA) and metagenomic shotgun sequencing was performed using the Illumina NextSeq500 (Illumina Inc, San Diego, CA). Salinibacter ruber, a species not found in mammalian microbiome communities, was used as a DNA standard and represented 0.7% to 5.7% of the microbiome, ensuring good quality and abundance of sample DNA.<br><br>RESULTS: Metagenomic shotgun sequencing was successful for all patients. In TTs associated with granuloma, Fusobacterium nucleatum, Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae were predominant, most of which are considered pathogens. From TTs without granulomas, Neisseria mucosa, Neisseria sicca, Acinetobacter baumannii, and Haemophilus parainfluenzae were identified, primarily consistent with respiratory microbiome.<br><br>CONCLUSION: This study reveals that metagenomic shotgun sequencing of biofilms formed on pediatric TTs is feasible with an apparent difference in microbiome for patients with granulation tissue. Further studies are necessary to elucidate the pathogenesis of microbial ecology and its role in airway disease in patients with TTs.<br><br>LEVEL OF EVIDENCE: 2c Laryngoscope, 129:317-323, 2019.}, }
@article {pmid30565024, year = {2019}, author = {Lee, JC and Song, JS and Whang, KS}, title = {Sphingobium pinisoli sp. nov., isolated from the rhizosphere soil of a Korean native pine tree.}, journal = {Antonie van Leeuwenhoek}, volume = {112}, number = {6}, pages = {815-825}, doi = {10.1007/s10482-018-01215-x}, pmid = {30565024}, issn = {1572-9699}, support = {PJ01287601//Department of Agriculture and Rural Development/ ; }, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry/metabolism ; Phylogeny ; Pinus/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Rhizosphere ; *Soil Microbiology ; Sphingomonadaceae/classification/genetics/*isolation &amp; purification/metabolism ; }, abstract = {A Gram-stain negative, aromatic compound degrading bacterium, designated strain ASA28[T], was isolated from the rhizosphere soil of a pine tree at Anmyon island, Taean in Korea. Strain ASA28[T] was found to be strictly aerobic, non-motile, short rods which can grow at 15-28 °C (optimum, 25-28 °C), at pH 5.0-11.0 (optimum, pH 7.0) and at salinities of 0-1.0% (w/v) NaCl (optimum, 0% NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain ASA28[T] belongs to the genus Sphingobium, showing high sequence similarity to Sphingobium scionense WP01[T] (97.8%), Sphingobium vermicocomposti VC-230[T] (96.8%), Sphingobium yanoikuyae ATCC 51230[T] (96.5%) and Sphingobium herbicidovorans MH[T] (95.6%). The predominant ubiquinone and polyamine components were identified as Q-10 and spermidine, respectively. The major fatty acids were identified as C18:1ω7c, C16:0, C14:0 2-OH and C16:1ω7c and/or C15:0 iso 2-OH. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, sphingoglycolipid, phosphoglycolipid, four unidentified aminophospholipids, an unidentified aminolipid, two unidentified phospholipids and six unidentified lipids. The DNA G+C content of this novel isolate was determined to be 63.0 mol%. DNA-DNA relatedness between strain ASA28[T] and S. herbicidovorans KCTC 2939[T], S. vermicocomposti DSM 21299[T] and S. scionense DSM 19371[T] was determined to be 32 ± 5%, 30 ± 4% and 25 ± 5%, respectively. On the basis of the phylogenetic, phenotypic and chemotaxonomic analyses in this study, strain ASA28[T] is considered to represent a novel species of the genus Sphingobium, for which the name Sphingobium pinisoli sp. nov. is proposed. The type strain is ASA28[T] (= KACC 18700[T] = NBRC 112246[T]).}, }
@article {pmid30564217, year = {2018}, author = {Ramírez, GA and Jørgensen, SL and Zhao, R and D'Hondt, S}, title = {Minimal Influence of Extracellular DNA on Molecular Surveys of Marine Sedimentary Communities.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2969}, pmid = {30564217}, issn = {1664-302X}, abstract = {Extracellular DNA has been reported to comprise a large fraction of total DNA in near-seafloor sediment. However, the potential effect of extracellular DNA, arising from dead or moribund cells, on sequencing surveys is a critical concern that has largely not been addressed for marine sedimentary habitats. To address this concern, we interrogated freshly collected Arctic and Pacific sediment for extracellular 16S rRNA genes using the photoactive DNA-binding dye Propidium Monoazide. Significant differences between relative abundances of total (intracellular + extracellular) Bacterial 16S rRNA genes and relative abundances of intracellular Bacterial 16S rRNA genes are only detected in three of twelve shallow [10 cm below seafloor (cmbsf)] samples. Relative abundances of total Bacterial 16S rRNA genes are statistically indistinguishable from relative abundances of intracellular Bacterial 16S rRNA genes in all interrogated samples from depths greater than 10 cmbsf. 16S rRNA gene sequencing shows that even where significantly higher abundances of extracellular genes are detected, they have little or no influence on prokaryote community composition. Taxon-level analyses suggest that extracellular DNA, arising from in situ death, may be sourced from different organisms in sediment of different ages. However, the overall effect of extracellular genes on sequencing surveys of marine sedimentary prokaryotes is minimal.}, }
@article {pmid30564202, year = {2018}, author = {Too, CC and Keller, A and Sickel, W and Lee, SM and Yule, CM}, title = {Microbial Community Structure in a Malaysian Tropical Peat Swamp Forest: The Influence of Tree Species and Depth.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2859}, pmid = {30564202}, issn = {1664-302X}, abstract = {Tropical peat swamp forests sequester globally significant stores of carbon in deep layers of waterlogged, anoxic, acidic and nutrient-depleted peat. The roles of microbes in supporting these forests through the formation of peat, carbon sequestration and nutrient cycling are virtually unknown. This study investigated physicochemical peat properties and microbial diversity between three dominant tree species: Shorea uliginosa (Dipterocarpaceae), Koompassia malaccensis (legumes associated with nitrogen-fixing bacteria), Eleiodoxa conferta (palm) and depths (surface, 45 and 90 cm) using microbial 16S rRNA gene amplicon sequencing. Water pH, oxygen, nitrogen, phosphorus, total phenolic contents and C/N ratio differed significantly between depths, but not tree species. Depth also strongly influenced microbial diversity and composition, while both depth and tree species exhibited significant impact on the archaeal communities. Microbial diversity was highest at the surface, where fresh leaf litter accumulates, and nutrient supply is guaranteed. Nitrogen was the core parameter correlating to microbial communities, but the interactive effects from various environmental variables displayed significant correlation to relative abundance of major microbial groups. Proteobacteria was the dominant phylum and the most abundant genus, Rhodoplanes, might be involved in nitrogen fixation. The most abundant methanogens and methanotrophs affiliated, respectively, to families Methanomassiliicoccaceae and Methylocystaceae. Our results demonstrated diverse microbial communities and provide valuable insights on microbial ecology in these extreme ecosystems.}, }
@article {pmid30562060, year = {2019}, author = {Arora, T and Rudenko, O and Egerod, KL and Husted, AS and Kovatcheva-Datchary, P and Akrami, R and Kristensen, M and Schwartz, TW and Bäckhed, F}, title = {Microbial fermentation of flaxseed fibers modulates the transcriptome of GPR41-expressing enteroendocrine cells and protects mice against diet-induced obesity.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {316}, number = {3}, pages = {E453-E463}, doi = {10.1152/ajpendo.00391.2018}, pmid = {30562060}, issn = {1522-1555}, mesh = {Animals ; Bifidobacterium ; Cecum/microbiology ; Cellulose ; Colon/cytology ; Diet, High-Fat ; Dietary Fiber ; Enteroendocrine Cells/*metabolism ; Fatty Acids, Volatile/*metabolism ; Female ; *Fermentation ; Firmicutes ; Flax/*metabolism ; *Gastrointestinal Microbiome ; Ileum/cytology ; Lactobacillus ; Male ; Mice ; Obesity/*metabolism ; Receptors, G-Protein-Coupled/metabolism ; *Transcriptome ; Verrucomicrobia ; }, abstract = {Dietary fibers, an integral part of the human diet, require the enzymatic activity of the gut microbiota for complete metabolism into short-chain fatty acids (SCFAs). SCFAs are important modulators of host metabolism and physiology and act in part as signaling molecules by activating G protein-coupled receptors (GPCRs), such as GPR41. Flaxseed fibers improve metabolism in rodents and mice, but their fermentation profiles, effects on enteroendocrine cells, and associated metabolic benefits are unknown. We fed GPR41-red fluorescent protein mice, an enteroendocrine reporter mouse strain, chow, high-fat diet (HFD), or HFD supplemented either with 10% nonfermentable fiber cellulose or fermentable flaxseed fibers for 12 wk to assess changes in cecal gut microbiota, enteroendocrine cell transcriptome in the ileum and colon, and physiological parameters. We observed that flaxseed fibers restructured the gut microbiota and promoted proliferation of the genera Bifidobacterium and Akkermansia compared with HFD. The shifts in cecal bacterial composition restored levels of the SCFAs butyrate similar to the chow diet, resulting in colonic but not ileal enteroendocrine cell transcriptional changes in genes related to cell cycle, mRNA, and protein transport compared with HFD. Consistent with the effects on enteroendocrine functions, flaxseed fibers also protected mice from diet-induced obesity, potentially by preventing a reduction in energy expenditure induced by an HFD. Our study shows that flaxseed fibers alter cecal microbial ecology, are fermented to SCFAs in the cecum, and modulate enteroendocrine cell transcriptome in the colon, which may contribute to their metabolically favorable phenotype.}, }
@article {pmid30559748, year = {2018}, author = {Guyonnet, JP and Guillemet, M and Dubost, A and Simon, L and Ortet, P and Barakat, M and Heulin, T and Achouak, W and Haichar, FEZ}, title = {Plant Nutrient Resource Use Strategies Shape Active Rhizosphere Microbiota Through Root Exudation.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1662}, pmid = {30559748}, issn = {1664-462X}, abstract = {Plant strategies for soil nutrient uptake have the potential to strongly influence plant-microbiota interactions, due to the competition between plants and microorganisms for soil nutrient acquisition and/or conservation. In the present study, we investigate whether these plant strategies could influence rhizosphere microbial activities via root exudation, and contribute to the microbiota diversification of active bacterial communities colonizing the root-adhering soil (RAS) and inhabiting the root tissues. We applied a DNA-based stable isotope probing (DNA-SIP) approach to six grass species distributed along a gradient of plant nutrient resource strategies, from conservative species, characterized by low nitrogen (N) uptake, a long lifespans and low root exudation level, to exploitative species, characterized by high rates of photosynthesis, rapid rates of N uptake and high root exudation level. We analyzed their (i) associated microbiota composition involved in root exudate assimilation and soil organic matter (SOM) degradation by 16S-rRNA-based metabarcoding. (ii) We determine the impact of root exudation level on microbial activities (denitrification and respiration) by gas chromatography. Measurement of microbial activities revealed an increase in denitrification and respiration activities for microbial communities colonizing the RAS of exploitative species. This increase of microbial activities results probably from a higher exudation rate and more diverse metabolites by exploitative plant species. Furthermore, our results demonstrate that plant nutrient resource strategies have a role in shaping active microbiota. We present evidence demonstrating that plant nutrient use strategies shape active microbiota involved in root exudate assimilation and SOM degradation via root exudation.}, }
@article {pmid30555445, year = {2018}, author = {Ilgrande, C and Leroy, B and Wattiez, R and Vlaeminck, SE and Boon, N and Clauwaert, P}, title = {Metabolic and Proteomic Responses to Salinity in Synthetic Nitrifying Communities of Nitrosomonas spp. and Nitrobacter spp.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2914}, pmid = {30555445}, issn = {1664-302X}, abstract = {Typically, nitrification is a two-stage microbial process and is key in wastewater treatment and nutrient recovery from waste streams. Changes in salinity represent a major stress factor that can trigger response mechanisms, impacting the activity and the physiology of bacteria. Despite its pivotal biotechnological role, little information is available on the specific response of nitrifying bacteria to varying levels of salinity. In this study, synthetic communities of ammonia-oxidizing bacteria (AOB Nitrosomonas europaea and/or Nitrosomonas ureae) and nitrite-oxidizing bacteria (NOB Nitrobacter winogradskyi and/or Nitrobacter vulgaris) were tested at 5, 10, and 30 mS cm[-1] by adding sodium chloride to the mineral medium (0, 40, and 200 mM NaCl, respectively). Ammonia oxidation activity was less affected by salinity than nitrite oxidation. AOB, on their own or in combination with NOB, showed no significant difference in the ammonia oxidation rate among the three conditions. However, N. winogradskyi improved the absolute ammonia oxidation rate of both N. europaea and N. ureae. N. winogradskyi's nitrite oxidation rate decreased to 42% residual activity upon exposure to 30 mS cm[-1], also showing a similar behavior when tested with Nitrosomonas spp. The nitrite oxidation rate of N. vulgaris, as a single species, was not affected when adding sodium chloride up to 30 mS cm[-1], however, its activity was completely inhibited when combined with Nitrosomonas spp. in the presence of ammonium/ammonia. The proteomic analysis of a co-culture of N. europaea and N. winogradskyi revealed the production of osmolytes, regulation of cell permeability and an oxidative stress response in N. europaea and an oxidative stress response in N. winogradskyi, as a result of increasing the salt concentration from 5 to 30 mS cm[-1]. A specific metabolic response observed in N. europaea suggests the role of carbon metabolism in the production of reducing power, possibly to meet the energy demands of the stress response mechanisms, induced by high salinity. For the first time, metabolic modifications and response mechanisms caused by the exposure to salinity were described, serving as a tool toward controllability and predictability of nitrifying systems exposed to salt fluctuations.}, }
@article {pmid30555443, year = {2018}, author = {Tanaka, K and Yokoe, S and Igarashi, K and Takashino, M and Ishikawa, M and Hori, K and Nakanishi, S and Kato, S}, title = {Extracellular Electron Transfer via Outer Membrane Cytochromes in a Methanotrophic Bacterium Methylococcus capsulatus (Bath).}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2905}, pmid = {30555443}, issn = {1664-302X}, abstract = {Electron exchange reactions between microbial cells and solid materials, referred to as extracellular electron transfer (EET), have attracted attention in the fields of microbial physiology, microbial ecology, and biotechnology. Studies of model species of iron-reducing, or equivalently, current-generating bacteria such as Geobacter spp. and Shewanella spp. have revealed that redox-active proteins, especially outer membrane c-type cytochromes (OMCs), play a pivotal role in the EET process. Recent (meta)genomic analyses have revealed that diverse microorganisms that have not been demonstrated to have EET ability also harbor OMC-like proteins, indicating that EET via OMCs could be more widely preserved in microorganisms than originally thought. A methanotrophic bacterium Methylococcus capsulatus (Bath) was reported to harbor multiple OMC genes whose expression is elevated by Cu starvation. However, the physiological role of these genes is unknown. Therefore, in this study, we explored whether M. capsulatus (Bath) displays EET abilities via OMCs. In electrochemical analysis, M. capsulatus (Bath) generated anodic current only when electron donors such as formate were available, and could reduce insoluble iron oxides in the presence of electron donor compounds. Furthermore, the current-generating and iron-reducing activities of M. capsulatus (Bath) cells that were cultured in a Cu-deficient medium, which promotes high levels of OMC expression, were higher than those cultured in a Cu-supplemented medium. Anodic current production by the Cu-deficient cells was significantly suppressed by disruption of MCA0421, a highly expressed OMC gene, and by treatment with carbon monoxide (CO) gas (an inhibitor of c-type cytochromes). Our results provide evidence of EET in M. capsulatus (Bath) and demonstrate the pivotal role of OMCs in this process. This study raises the possibility that EET to solid compounds is a novel survival strategy of methanotrophic bacteria.}, }
@article {pmid30554808, year = {2019}, author = {Sutherland, WJ and Broad, S and Butchart, SHM and Clarke, SJ and Collins, AM and Dicks, LV and Doran, H and Esmail, N and Fleishman, E and Frost, N and Gaston, KJ and Gibbons, DW and Hughes, AC and Jiang, Z and Kelman, R and LeAnstey, B and le Roux, X and Lickorish, FA and Monk, KA and Mortimer, D and Pearce-Higgins, JW and Peck, LS and Pettorelli, N and Pretty, J and Seymour, CL and Spalding, MD and Wentworth, J and Ockendon, N}, title = {A Horizon Scan of Emerging Issues for Global Conservation in 2019.}, journal = {Trends in ecology &amp; evolution}, volume = {34}, number = {1}, pages = {83-94}, doi = {10.1016/j.tree.2018.11.001}, pmid = {30554808}, issn = {1872-8383}, mesh = {Biodiversity ; *Conservation of Natural Resources/trends ; *Forecasting ; }, abstract = {We present the results of our tenth annual horizon scan. We identified 15 emerging priority topics that may have major positive or negative effects on the future conservation of global biodiversity, but currently have low awareness within the conservation community. We hope to increase research and policy attention on these areas, improving the capacity of the community to mitigate impacts of potentially negative issues, and maximise the benefits of issues that provide opportunities. Topics include advances in crop breeding, which may affect insects and land use; manipulations of natural water flows and weather systems on the Tibetan Plateau; release of carbon and mercury from melting polar ice and thawing permafrost; new funding schemes and regulations; and land-use changes across Indo-Malaysia.}, }
@article {pmid30554770, year = {2019}, author = {Cordier, T and Lanzén, A and Apothéloz-Perret-Gentil, L and Stoeck, T and Pawlowski, J}, title = {Embracing Environmental Genomics and Machine Learning for Routine Biomonitoring.}, journal = {Trends in microbiology}, volume = {27}, number = {5}, pages = {387-397}, doi = {10.1016/j.tim.2018.10.012}, pmid = {30554770}, issn = {1878-4380}, mesh = {Bacteria/*classification ; DNA Barcoding, Taxonomic ; Ecosystem ; Environmental Microbiology ; Environmental Monitoring/*methods ; Genetic Variation ; *Machine Learning ; *Metagenomics ; Microbiota ; }, abstract = {Genomics is fast becoming a routine tool in medical diagnostics and cutting-edge biotechnologies. Yet, its use for environmental biomonitoring is still considered a futuristic ideal. Until now, environmental genomics was mainly used as a replacement of the burdensome morphological identification, to screen known morphologically distinguishable bioindicator taxa. While prokaryotic and eukaryotic microbial diversity is of key importance in ecosystem functioning, its implementation in biomonitoring programs is still largely unappreciated, mainly because of difficulties in identifying microbes and limited knowledge of their ecological functions. Here, we argue that the combination of massive environmental genomics microbial data with machine learning algorithms can be extremely powerful for biomonitoring programs and pave the way to fill important gaps in our understanding of microbial ecology.}, }
@article {pmid30554323, year = {2019}, author = {Jiang, N and Liu, H and Wang, P and Huang, J and Han, H and Wang, Q}, title = {Illumina MiSeq Sequencing Investigation of Microbiota in Bronchoalveolar Lavage Fluid and Cecum of the Swine Infected with PRRSV.}, journal = {Current microbiology}, volume = {76}, number = {2}, pages = {222-230}, pmid = {30554323}, issn = {1432-0991}, support = {No. 81172777//the National Natural Science Foundation of China under Grant/ ; No. 2014B11NC096//the Dalian Science and Technological Project under Grant/ ; }, mesh = {Animals ; Antibodies, Viral/blood ; Bacteria/genetics/*isolation &amp; purification/pathogenicity ; Bronchoalveolar Lavage Fluid/*microbiology ; Cecum/*microbiology ; Coinfection/microbiology/*veterinary/virology ; Dysbiosis/microbiology ; Feces/microbiology ; High-Throughput Nucleotide Sequencing ; Lung/microbiology ; Microbiota ; Mucous Membrane/microbiology ; Porcine Reproductive and Respiratory Syndrome/*microbiology ; Porcine respiratory and reproductive syndrome virus/genetics ; Swine ; }, abstract = {Porcine reproductive and respiratory syndrome virus (PRRSV) causes significant animal morbidity and mortality and economic losses worldwide. In this study, we analyzed the microbiota in bronchoalveolar lavage fluid (BAL), mucosa, and feces in cecum of the PRRSV-challenged pigs using the Illumina MiSeq sequencing platform, to investigate the role of microbiota in the pathogenesis and development of porcine reproductive and respiratory syndrome (PRRS). Quantitative insights into microbial ecology analyses indicated that the dominant bacterial groups in the lung from the PRRSV-challenged pigs were Haemophilus parasuis and Mycoplasma hyorhinis, with a relative abundance of 35-48% and 27-41%, respectively. Our results were consistent with the clinical observation that the PRRSV-infected pigs are always co-infected with other bacteria, such as Haemophilus and Mycoplasma. On the other hand, Campylobacter and Clostridium became the two most abundant bacteria in the mucosal and luminal microbiota of the cecum of the PRRSV-challenged pigs, and the relative abundance was four times higher than that in the healthy pigs. This suggested that Campylobacter and Clostridium might be associated with the pathogenesis of diarrhea in PRRS. Linear discriminant analysis effect size reveals significant microbial dysbiosis of BAL, mucosa, and feces in cecum of the PRRSV-challenged pigs. We have identified a structural imbalance of the microbiota, characterized by a reduced diversity of microbiota and abundance alterations of certain bacteria in the PRRSV-challenged pigs. The observed microbiota dysbiosis in this study provides insight into the roles of the microbiota in the complications of the PRRSV infection.}, }
@article {pmid30552443, year = {2019}, author = {Rothman, JA and Andrikopoulos, C and Cox-Foster, D and McFrederick, QS}, title = {Floral and Foliar Source Affect the Bee Nest Microbial Community.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {506-516}, pmid = {30552443}, issn = {1432-184X}, support = {NNX15AP99A//National Aeronautics and Space Administration/ ; 2018-67011-28123//National Institute of Food and Agriculture/ ; CA-R-ENT-5109-H//National Institute of Food and Agriculture/ ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bees/*microbiology/physiology ; Fungi/classification/genetics/*isolation &amp; purification ; Larva/microbiology ; Medicago sativa/microbiology ; *Microbiota ; Phylogeny ; Pollen/microbiology ; Pollination ; RNA, Ribosomal, 16S ; }, abstract = {Managed pollinators such as the alfalfa leafcutting bee, Megachile rotundata, are essential to the production of a wide variety of agricultural crops. These pollinators encounter a diverse array of microbes when foraging for food and nest-building materials on various plants. To test the hypothesis that food and nest-building source affects the composition of the bee-nest microbiome, we exposed M. rotundata adults to treatments that varied both floral and foliar source in a 2 × 2 factorial design. We used 16S rRNA gene and internal transcribed spacer (ITS) sequencing to capture the bacterial and fungal diversity of the bee nests. We found that nest microbial communities were significantly different between treatments, indicating that bee nests become inoculated with environmentally derived microbes. We did not find evidence of interactions between the fungi and bacteria within our samples. Furthermore, both the bacterial and fungal communities were quite diverse and contained numerous exact sequence variants (ESVs) of known plant and bee pathogens that differed based on treatment. Our research indicates that bees deposit plant-associated microbes into their nests, including multiple plant pathogens such as smut fungi and bacteria that cause blight and wilt. The presence of plant pathogens in larval pollen provisions highlights the potential for bee nests to act as disease reservoirs across seasons. We therefore suggest that future research should investigate the ability of bees to transmit pathogens from nest to host plant.}, }
@article {pmid30547761, year = {2018}, author = {Morales-Cruz, A and Figueroa-Balderas, R and García, JF and Tran, E and Rolshausen, PE and Baumgartner, K and Cantu, D}, title = {Profiling grapevine trunk pathogens in planta: a case for community-targeted DNA metabarcoding.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {214}, pmid = {30547761}, issn = {1471-2180}, mesh = {Ascomycota/classification/genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Mycological Typing Techniques/*methods ; Plant Diseases/*microbiology ; Vitis/*microbiology ; }, abstract = {BACKGROUND: DNA metabarcoding, commonly used in exploratory microbial ecology studies, is a promising method for the simultaneous in planta-detection of multiple pathogens associated with disease complexes, such as the grapevine trunk diseases. Profiling of pathogen communities associated with grapevine trunk diseases is particularly challenging, due to the presence within an individual wood lesion of multiple co-infecting trunk pathogens and other wood-colonizing fungi, which span a broad range of taxa in the fungal kingdom. As such, we designed metabarcoding primers, using as template the ribosomal internal transcribed spacer of grapevine trunk-associated ascomycete fungi (GTAA) and compared them to two universal primer widely used in microbial ecology.<br><br>RESULTS: We first performed in silico simulations and then tested the primers by high-throughput amplicon sequencing of (i) multiple combinations of mock communities, (ii) time-course experiments with controlled inoculations, and (iii) diseased field samples from vineyards under natural levels of infection. All analyses showed that GTAA had greater affinity and sensitivity, compared to those of the universal primers. Importantly, with GTAA, profiling of mock communities and comparisons with shotgun-sequencing metagenomics of field samples gave an accurate representation of genera of important trunk pathogens, namely Phaeomoniella, Phaeoacremonium, and Eutypa, the abundances of which were over- or under-estimated with universal primers.<br><br>CONCLUSIONS: Overall, our findings not only demonstrate that DNA metabarcoding gives qualitatively and quantitatively accurate results when applied to grapevine trunk diseases, but also that primer customization and testing are crucial to ensure the validity of DNA metabarcoding results.}, }
@article {pmid30547194, year = {2019}, author = {Visvalingam, J and Zhang, P and Ells, TC and Yang, X}, title = {Dynamics of Biofilm Formation by Salmonella Typhimurium and Beef Processing Plant Bacteria in Mono- and Dual-Species Cultures.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {375-387}, pmid = {30547194}, issn = {1432-184X}, support = {A-1603 and A-1637//Agriculture and Agri-Food Canada/ ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Biodiversity ; *Biofilms ; Cattle ; Food Handling ; Red Meat/analysis/*microbiology ; Salmonella typhimurium/genetics/isolation &amp; purification/*physiology ; }, abstract = {This study aimed to determine the impact of bacteria from a beef plant conveyor belt on the biofilm formation of Salmonella in dual-species cultures. Beef plant isolates (50) including 18 Gram-negative aerobes (GNA), 8 Gram-positive aerobes (GPA), 5 lactic acid bacteria (LAB), 9 Enterobacteriaceae (EB), and 10 generic Escherichia coli (GEC) were included for developing biofilms in mono- and co-culture with S. Typhimurium at 15 °C for 6 days. Five selected cultures in planktonic form and in biofilms were tested for susceptibility to two commonly used sanitizers (i.e. E-San and Perox-E Plus). In mono-cultures, ≥ 80, 67, 61, 20, and 13% of GEC, EB, GNA, LAB, and GPA, respectively, developed measurable biofilms after 2 days, while all co-culture pairings with S. Typhimurium achieved some level of biofilm production. The predominant effect of EB and only effect of GEC strains on the biofilm formation of S. Typhimurium was antagonistic, while that of Gram-positive bacteria was synergistic, with the effect being more prominent on day 6. The effect was highly variable for the GNA isolates. Six aerobic isolates that formed moderate/strong biofilms by day 2 greatly boosted the co-culture biofilm formation. Seven Gram-negative bacteria were antagonistic against the biofilm formation of the co-cultures. Both sanitizers completely inactivated the selected planktonic cultures, but were largely ineffective against biofilms. In conclusion, all beef plant isolates assessed formed biofilms when paired with S. Typhimurium. Aerobic biofilm formers may create a more favorable condition for Salmonella biofilm formation, while some beef plant isolates have potential as a biocontrol strategy for Salmonella biofilms.}, }
@article {pmid30545051, year = {2018}, author = {Haro, C and Villatoro, M and Vaquero, L and Pastor, J and Giménez, MJ and Ozuna, CV and Sánchez-León, S and García-Molina, MD and Segura, V and Comino, I and Sousa, C and Vivas, S and Landa, BB and Barro, F}, title = {The Dietary Intervention of Transgenic Low-Gliadin Wheat Bread in Patients with Non-Celiac Gluten Sensitivity (NCGS) Showed No Differences with Gluten Free Diet (GFD) but Provides Better Gut Microbiota Profile.}, journal = {Nutrients}, volume = {10}, number = {12}, pages = {}, pmid = {30545051}, issn = {2072-6643}, support = {Projects AGL2013-48946-C3-1-R, AGL2013-48946-C and AGL2016-80566-P//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a/ ; }, mesh = {Adult ; Diet, Gluten-Free/*statistics &amp; numerical data ; Feces/chemistry/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Gliadin/*adverse effects/*analysis ; High-Throughput Nucleotide Sequencing ; Humans ; Malabsorption Syndromes/*diet therapy ; Male ; Middle Aged ; Plants, Genetically Modified/genetics ; Triticum/genetics ; }, abstract = {The study evaluated the symptoms, acceptance, and digestibility of bread made from transgenic low-gliadin wheat, in comparison with gluten free bread, in Non-coeliac gluten sensitivity (NCGS) patients, considering clinical/sensory parameters and gut microbiota composition. This study was performed in two phases of seven days each, comprising a basal phase with gluten free bread and an E82 phase with low-gliadin bread. Gastrointestinal clinical symptoms were evaluated using the Gastrointestinal Symptom Rating Scale (GSRS) questionnaire, and stool samples were collected for gluten immunogenic peptides (GIP) determination and the extraction of gut microbial DNA. For the basal and E82 phases, seven and five patients, respectively, showed undetectable GIPs content. The bacterial 16S rRNA gene V1-V2 hypervariable regions were sequenced using the Illumina MiSeq platform and downstream analysis was done using a Quantitative Insights into Microbial Ecology (QIIME) pipeline. No significant differences in the GSRS questionnaires were observed between the two phases. However, we observed a significantly lower abundance of some gut genera Oscillospira, Dorea, Blautia, Bacteroides, Coprococcus, and Collinsella, and a significantly higher abundance of Roseburia and Faecalibacterium genera during the E82 phase compared with the basal phase. The consumption of low-gliadin bread E82 by NCGS subjects induced potentially positive changes in the gut microbiota composition, increasing the butyrate-producing bacteria and favoring a microbial profile that is suggested to have a key role in the maintenance or improvement of gut permeability.}, }
@article {pmid30544668, year = {2018}, author = {Kaboré, WAD and Dembélé, R and Bagré, TS and Konaté, A and Boisramé, S and Chevalier, V and Konsem, T and Traoré, AS and Barro, N}, title = {Characterization and Antimicrobial Susceptibility of Lactococcus lactis Isolated from Endodontic Infections in Ouagadougou, Burkina Faso.}, journal = {Dentistry journal}, volume = {6}, number = {4}, pages = {}, pmid = {30544668}, issn = {2304-6767}, abstract = {BACKGROUND: This study aimed to characterize and test the antimicrobial susceptibility of Lactococcus lactis isolated in endodontic infections in Burkina Faso.<br><br>MATERIAL AND METHODS: This was a prospective study conducted at the Municipal Oral Health Center of Ouagadougou, Burkina Faso, from June to October 2014. Clinical data were collected using a questionnaire form. The method of streaking on selective medium was used to isolate bacteria. Identification was made using the API 20 Strep gallery. Antibiotic susceptibility was performed by the diffusion method on solid medium.<br><br>RESULTS: One hundred and twenty-five (125) patients were received with a significant proportion from the age group of 19 to 40 years (55.2%). Apical periodontitis accounted for 50.4% and cellulitis for 49.6% of cases. Lactococcus lactis ssp. lactis was identified in five exudate samples. Isolates were 100% resistant to cefixime and metronidazole, 80% to ceftriaxone, cefuroxime, cefotaxime, chloramphenicol and 60% to penicillin G, amoxicillin, amoxicillin clavulanic acid. A multidrug resistance of more than three families of antibiotics was noticed. No strains produced extended spectrum &#xdf;-lactamases.<br><br>CONCLUSION: Lactococcus lactis is part of endodontic biofilm. The reported strong antibiotic resistance involving endodontic therapy will focus on the effect of the disinfectant solution and the mechanical action of the canal instruments.}, }
@article {pmid30544592, year = {2018}, author = {Bosmans, L and Pozo, MI and Verreth, C and Crauwels, S and Wäckers, F and Jacquemyn, H and Lievens, B}, title = {Hibernation Leads to Altered Gut Communities in Bumblebee Queens (Bombus terrestris).}, journal = {Insects}, volume = {9}, number = {4}, pages = {}, pmid = {30544592}, issn = {2075-4450}, abstract = {Many reptiles, amphibians, mammals, and insects practice some form of hibernation during which their metabolic rate is drastically reduced. This allows them to conserve energy and survive the harsh winter conditions with little or no food. While it can be expected that a reduction in host metabolism has a substantial influence on the gut microbial community, little is known about the effects of hibernation on the composition of the microbial gut community, especially for insects. In this study, we assessed and compared the bacterial gut community composition within the midgut and ileum of indoor-reared queens of Bombus terrestris before and after an artificial hibernation period of 16 weeks. Deep sequencing of 16S ribosomal RNA gene amplicons and clustering of sequence reads into operational taxonomic units (OTUs) at a similarity threshold of 97% revealed several bacterial taxa that are known to be strongly associated with corbiculate bees. Bacterial community composition after hibernation compared to before hibernation was characterized by higher OTU richness and evenness, with decreased levels of the core bacteria Gilliamella (Proteobacteria, Orbaceae) and Snodgrassella (Proteobacteria, Neisseriaceae), and increased relative abundance of non-core bacteria, including several psychrophilic and psychrotrophic taxa.}, }
@article {pmid30544159, year = {2019}, author = {Pedrinho, A and Mendes, LW and Merloti, LF and da Fonseca, MC and Cannavan, FS and Tsai, SM}, title = {Forest-to-pasture conversion and recovery based on assessment of microbial communities in Eastern Amazon rainforest.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {3}, pages = {}, doi = {10.1093/femsec/fiy236}, pmid = {30544159}, issn = {1574-6941}, mesh = {Agriculture ; Biodiversity ; *Conservation of Natural Resources ; Ecosystem ; *Environmental Restoration and Remediation ; Metagenome ; Microbiota/*genetics ; *Rainforest ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Amazon rainforest has been subjected to particularly high rates of deforestation caused mainly by the expansion of cattle pasture and agriculture. A commonly observed response to land-use change is a negative impact on biodiversity of plant and animal species. However, its effect on the soil microbial community and ecosystem functioning is still poorly understood. Here, we used a DNA metagenomic sequencing approach to investigate the impact of land-use change on soil microbial community composition and its potential functions in three land-use systems (primary forest, pasture and secondary forest) in the Amazon region. In general, the microbial community structure was influenced by changes in soil physicochemical properties. Aluminum and water-holding capacity significantly correlated to overall community structure and most of microbial phyla. Taxonomic changes were followed by potential functional changes in the soil microbial community, with pasture presenting the most distinct profile in comparison with other sites. Although taxonomic structure was very distinct among sites, we observed a recovery of the potential functions in secondary forest after pasture abandonment. Our findings elucidate a significant shift in belowground microbial taxonomic and potential functional diversity following natural forest re-establishment and have implications for ecological restoration programs in tropical and sub-tropical ecosystems.}, }
@article {pmid30542336, year = {2018}, author = {Okazaki, Y and Salcher, MM and Callieri, C and Nakano, SI}, title = {The Broad Habitat Spectrum of the CL500-11 Lineage (Phylum Chloroflexi), a Dominant Bacterioplankton in Oxygenated Hypolimnia of Deep Freshwater Lakes.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2891}, pmid = {30542336}, issn = {1664-302X}, abstract = {CL500-11 (phylum Chloroflexi) is one of the most ubiquitous and abundant bacterioplankton lineages in deep freshwater lakes inhabiting the oxygenated hypolimnion. While metagenomics predicted possible eco-physiological characteristics of this uncultured lineage, no consensus on their ecology has so far been reached, partly because their niche is not clearly understood due to a limited number of quantitative field observations. This study investigated the abundance and distribution of CL500-11 in seven deep perialpine lakes using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Samples were taken vertically (5-12 depths in each lake) and temporally (in two lakes) at the deepest point of the lakes located in Switzerland, Italy, and Austria with varying depth, trophic state, mixing regime, and water retention time. The results showed a dominance of CL500-11 in all the lakes; their proportion to total prokaryotes ranged from 4.3% (Mondsee) to 24.3% (Lake Garda) and their abundance ranged from 0.65 × 10[5] (Mondsee) to 1.77 × 10[5] (Lake Garda) cells mL[-1]. By summarizing available information on CL500-11 occurrence to date, we demonstrated their broad habitat spectrum, ranging from ultra-oligotrophic to meso-eutrophic lakes, while low abundances or complete absence was observed in lakes with shallow depth, low pH, and/or short water retention time (<1 year). Together with available metagenomic and geochemical evidences from literatures, here we reviewed potential substrates supporting growth of CL500-11. Overall, the present study further endorsed ubiquity and quantitative significance of CL500-11 in deep freshwater systems and narrowed the focus on their physiological characteristics and ecological importance.}, }
@article {pmid30542078, year = {2019}, author = {Scoma, A and Heyer, R and Rifai, R and Dandyk, C and Marshall, I and Kerckhof, FM and Marietou, A and Boshker, HTS and Meysman, FJR and Malmos, KG and Vosegaard, T and Vermeir, P and Banat, IM and Benndorf, D and Boon, N}, title = {Reduced TCA cycle rates at high hydrostatic pressure hinder hydrocarbon degradation and obligate oil degraders in natural, deep-sea microbial communities.}, journal = {The ISME journal}, volume = {13}, number = {4}, pages = {1004-1018}, pmid = {30542078}, issn = {1751-7370}, mesh = {Bacteria/*metabolism ; *Citric Acid Cycle ; Geologic Sediments/*microbiology ; Hydrocarbons/*metabolism ; Hydrostatic Pressure ; *Microbiota ; Petroleum/*metabolism ; Seawater ; }, abstract = {Petroleum hydrocarbons reach the deep-sea following natural and anthropogenic factors. The process by which they enter deep-sea microbial food webs and impact the biogeochemical cycling of carbon and other elements is unclear. Hydrostatic pressure (HP) is a distinctive parameter of the deep sea, although rarely investigated. Whether HP alone affects the assembly and activity of oil-degrading communities remains to be resolved. Here we have demonstrated that hydrocarbon degradation in deep-sea microbial communities is lower at native HP (10 MPa, about 1000 m below sea surface level) than at ambient pressure. In long-term enrichments, increased HP selectively inhibited obligate hydrocarbon-degraders and downregulated the expression of beta-oxidation-related proteins (i.e., the main hydrocarbon-degradation pathway) resulting in low cell growth and CO2 production. Short-term experiments with HP-adapted synthetic communities confirmed this data, revealing a HP-dependent accumulation of citrate and dihydroxyacetone. Citrate accumulation suggests rates of aerobic oxidation of fatty acids in the TCA cycle were reduced. Dihydroxyacetone is connected to citrate through glycerol metabolism and glycolysis, both upregulated with increased HP. High degradation rates by obligate hydrocarbon-degraders may thus be unfavourable at increased HP, explaining their selective suppression. Through lab-scale cultivation, the present study is the first to highlight a link between impaired cell metabolism and microbial community assembly in hydrocarbon degradation at high HP. Overall, this data indicate that hydrocarbons fate differs substantially in surface waters as compared to deep-sea environments, with in situ low temperature and limited nutrients availability expected to further prolong hydrocarbons persistence at deep sea.}, }
@article {pmid30524385, year = {2018}, author = {Rilling, JI and Acuña, JJ and Sadowsky, MJ and Jorquera, MA}, title = {Putative Nitrogen-Fixing Bacteria Associated With the Rhizosphere and Root Endosphere of Wheat Plants Grown in an Andisol From Southern Chile.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2710}, pmid = {30524385}, issn = {1664-302X}, abstract = {Acidic ash derived volcanic soils (Andisols) support 50% of cereal production in Chile. Nitrogen (N) is essential for cereal crops and commonly added as urea with consequent environmental concerns due to leaching. Despite the relevance of N to plant growth, few studies have focused on understanding the application, management and ecological role of N2-fixing bacterial populations as tool for improve the N nutrition of cereal crops in Chile. It is known that N2-fixing bacteria commonly inhabits diverse plant compartments (e.g., rhizosphere and root endosphere) where they can supply N for plant growth. Here, we used culture-independent and dependent approaches to characterize and compare the putative N2-fixing bacteria associated with the rhizosphere and root endosphere of wheat plants grown in an Andisol from southern Chile. Our results showed significantly greater bacterial loads in the rhizosphere than the root endosphere. Quantitative PCR results indicated that the copy number of the 16S rRNA gene ranged from 10[12]~10[13] and 10[7]~10[8] g[-1] sample in rhizosphere and root endosphere, respectively. The nifH gene copy number ranged from 10[5]~10[6] and 10[5] g[-1] sample in rhizosphere and root endosphere, respectively. The total culturable bacteria number ranged from 10[9]~10[10] and 10[7]~10[8] CFU g[-1] sample in rhizosphere and 10[4]~10[5] and 10[4] CFU g[-1] sample in root endosphere using LB and NM-1 media, respectively. Indirect counts of putative N2-fixing bacteria were 10[3] and 10[2]~10[3] CFU g[-1] sample in rhizosphere and root endosphere using NFb medium, respectively. Sequencing of 16S rRNA genes from randomly selected putative N2-fixing bacteria revealed the presence of members of Proteobacteria (Bosea and Roseomonas), Actinobacteria (Georgenia, Mycobacterium, Microbacterium, Leifsonia, and Arthrobacter), Bacteroidetes (Chitinophaga) and Firmicutes (Bacillus and Psychrobacillus) taxa. Differences in 16S rRNA and putative nifH-containing bacterial communities between rhizosphere and root endosphere were shown by denaturing gradient gel electrophoresis (DGGE). This study shows a compartmentalization between rhizosphere and root endosphere for both the abundance and diversity of total (16S rRNA) and putative N2-fixing bacterial communities on wheat plants grown in Chilean Andisols. This information can be relevant for the design and application of agronomic strategies to enhance sustainable N-utilization in cereal crops in Chile.}, }
@article {pmid30522433, year = {2018}, author = {Mohr, T and Aliyu, H and Küchlin, R and Zwick, M and Cowan, D and Neumann, A and de Maayer, P}, title = {Comparative genomic analysis of Parageobacillus thermoglucosidasius strains with distinct hydrogenogenic capacities.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {880}, pmid = {30522433}, issn = {1471-2164}, support = {031B0180//Bundesministerium f&#xfc;r Bildung und Forschung/ ; }, mesh = {Bacterial Proteins/genetics ; Base Sequence ; Carbon Monoxide/chemistry/metabolism ; *Comparative Genomic Hybridization ; Genetic Loci ; *Genome, Bacterial ; Geobacillus/*genetics ; Hydrogen/*metabolism ; Hydrogenase/genetics ; INDEL Mutation ; Multienzyme Complexes/genetics ; Sequence Alignment ; }, abstract = {BACKGROUND: The facultatively anaerobic thermophile Parageobacillus thermoglucosidasius produces hydrogen gas (H2) by coupling CO oxidation to proton reduction in the water-gas shift (WGS) reaction via a carbon monoxide dehydrogenase-hydrogenase enzyme complex. Although little is known about the hydrogenogenic capacities of different strains of this species, these organisms offer a potentially viable process for the synthesis of this alternative energy source.<br><br>RESULTS: The WGS-catalyzed H2 production capacities of four distinct P. thermoglucosidasius strains were determined by cultivation and gas analysis. Three strains (DSM 2542[T], DSM 2543 and DSM 6285) were hydrogenogenic, while the fourth strain (DSM 21625) was not. Furthermore, in one strain (DSM 6285) H2 production commenced earlier in the cultivation than the other hydrogenogenic strains. Comparative genomic analysis of the four strains identified extensive differences in the protein complement encoded on the genomes, some of which are postulated to contribute to the different hydrogenogenic capacities of the strains. Furthermore, polymorphisms and deletions in the CODH-NiFe hydrogenase loci may also contribute towards this variable phenotype.<br><br>CONCLUSIONS: Disparities in the hydrogenogenic capacities of different P. thermoglucosidasius strains were identified, which may be correlated to variability in their global proteomes and genetic differences in their CODH-NiFe hydrogenase loci. The data from this study may contribute towards an improved understanding of WGS-catalysed hydrogenogenesis by P. thermoglucosidasius.}, }
@article {pmid30538275, year = {2019}, author = {Nicolás, C and Martin-Bertelsen, T and Floudas, D and Bentzer, J and Smits, M and Johansson, T and Troein, C and Persson, P and Tunlid, A}, title = {The soil organic matter decomposition mechanisms in ectomycorrhizal fungi are tuned for liberating soil organic nitrogen.}, journal = {The ISME journal}, volume = {13}, number = {4}, pages = {977-988}, pmid = {30538275}, issn = {1751-7370}, support = {//CIHR/Canada ; }, mesh = {Ascomycota/*metabolism ; Basidiomycota/*metabolism ; Carbon/metabolism ; Ecosystem ; Forests ; Fungi/*metabolism ; Gene Expression Regulation ; Mycorrhizae/genetics/*metabolism ; Nitrogen/*metabolism ; Soil/chemistry ; *Soil Microbiology ; Symbiosis ; Transcription, Genetic ; }, abstract = {Many trees form ectomycorrhizal symbiosis with fungi. During symbiosis, the tree roots supply sugar to the fungi in exchange for nitrogen, and this process is critical for the nitrogen and carbon cycles in forest ecosystems. However, the extents to which ectomycorrhizal fungi can liberate nitrogen and modify the soil organic matter and the mechanisms by which they do so remain unclear since they have lost many enzymes for litter decomposition that were present in their free-living, saprotrophic ancestors. Using time-series spectroscopy and transcriptomics, we examined the ability of two ectomycorrhizal fungi from two independently evolved ectomycorrhizal lineages to mobilize soil organic nitrogen. Both species oxidized the organic matter and accessed the organic nitrogen. The expression of those events was controlled by the availability of glucose and inorganic nitrogen. Despite those similarities, the decomposition mechanisms, including the type of genes involved as well as the patterns of their expression, differed markedly between the two species. Our results suggest that in agreement with their diverse evolutionary origins, ectomycorrhizal fungi use different decomposition mechanisms to access organic nitrogen entrapped in soil organic matter. The timing and magnitude of the expression of the decomposition activity can be controlled by the below-ground nitrogen quality and the above-ground carbon supply.}, }
@article {pmid30536130, year = {2019}, author = {Wilpiszeski, RL and Zhang, Z and House, CH}, title = {Biogeography of thermophiles and predominance of Thermus scotoductus in domestic water heaters.}, journal = {Extremophiles : life under extreme conditions}, volume = {23}, number = {1}, pages = {119-132}, pmid = {30536130}, issn = {1433-4909}, support = {NAI Cooperative agreement #NNA09DA76A//National Aeronautics and Space Administration/ ; }, mesh = {Drinking Water/microbiology ; Heating/*instrumentation ; *Microbiota ; Phylogeography ; RNA, Ribosomal, 16S/genetics ; Thermus/classification/genetics/*isolation &amp; purification ; *Water Microbiology ; }, abstract = {Built systems such as water heaters can harbor extremophiles similar to those residing in natural hot springs, but the extent of colonization is not well understood. To address this, we conducted a survey of thermophilic microorganisms in household water heaters across the United States. Filter samples and inoculated cultures were collected by citizen-scientists from 101 homes. Draft genomes were assembled from cultured isolates and 16S rRNA genes were sequenced from filter samples. 28% of households harbored communities with unambiguous DNA signatures of thermophilic organisms, 36% of households provided viable inocula, and 21% of households had both. All of the recovered cultures as well as the community sequencing results revealed Thermus scotoductus to be the dominant thermophile in domestic water heaters, with a minority of water heaters also containing Meiothermus species and a few containing Aquificae. Sequence distance comparisons show that allopatric speciation does not appear to be a strong control on T. scotoductus distribution. Our results demonstrate that thermophilic organisms are widespread in hot tap water, and that Thermus scotoductus preferentially colonizes water heaters at the expense of local environmental Thermus strains.}, }
@article {pmid30535916, year = {2019}, author = {Albecker, MA and Belden, LK and McCoy, MW}, title = {Comparative Analysis of Anuran Amphibian Skin Microbiomes Across Inland and Coastal Wetlands.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {348-360}, pmid = {30535916}, issn = {1432-184X}, support = {DEB 1136640//National Science Foundation/ ; Project No. 2014-R/14-HCE-3//North Carolina SeaGrant/ ; }, mesh = {Animals ; Anura/classification/*microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Ecosystem ; Islands ; *Microbiota ; Skin/*microbiology ; Wetlands ; }, abstract = {Amphibians host a community of microbes on their skin that helps resist infectious disease via the dual influence of anti-pathogenic microbial species and emergent community dynamics. Many frogs rely on freshwater habitats, but salinization is rapidly increasing saltwater concentrations in wetlands around the globe, increasing the likelihood that frogs will come into contact with salt-contaminated habitats. Currently, we know little about how increased salt exposure will affect the symbiotic relationship between the skin microbes and frog hosts. To better understand how salt exposure in a natural context affects the frog skin microbiome, we use Hyla cinerea, a North American treefrog species that can inhabit brackish wetlands, to explore three questions. First, we determine the extent that microbial communities in the environment and on frog skin are similar across populations. Second, we assess the microbial species richness and relative abundance on frogs from habitats with different salinity levels to determine how salinity affects the microbiome. Third, we test whether the relative abundances of putatively pathogen-resistant bacterial species differ between frogs from inland and coastal environments. We found that the frog microbiome is more similar among frogs than to the microbial communities found in surface water and soil, but there is overlap between frog skin and the environmental samples. Skin microbial community richness did not differ among populations, but the relative abundances of microbes were different across populations and salinities. We found no differences in the relative abundances of the anti-fungal bacteria Janthinobacterium lividum, the genus Pseudomonas, and Serratia marcescens, suggesting that environmental exposure to saltwater has a limited influence on these putatively beneficial bacterial taxa.}, }
@article {pmid30535915, year = {2019}, author = {Chamizo, S and Adessi, A and Mugnai, G and Simiani, A and De Philippis, R}, title = {Soil Type and Cyanobacteria Species Influence the Macromolecular and Chemical Characteristics of the Polysaccharidic Matrix in Induced Biocrusts.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {482-493}, pmid = {30535915}, issn = {1432-184X}, support = {706351//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; }, mesh = {Cyanobacteria/classification/genetics/isolation &amp; purification/*metabolism ; Desert Climate ; Polysaccharides, Bacterial/*chemistry/*metabolism ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Inoculation of soils with cyanobacteria is proposed as a sustainable biotechnological technique for restoration of degraded areas in drylands due to the important role that cyanobacteria and their exopolysaccharides (EPS) play in the environment. So far, few studies have analyzed the macromolecular and chemical characteristics of the polysaccharidic matrix in induced cyanobacterial biocrusts and the scarce existing studies have mainly focused on sandy soil textures. However, the characteristics of the cyanobacterial polysaccharidic matrix may greatly depend on soil type. The objective of this study was to examine the macromolecular distribution and monosaccharidic composition of the polysaccharidic matrix induced by inoculation of two cyanobacterial species common in arid environments, Phormidium ambiguum (non N-fixing) and Scytonema javanicum (N-fixing) in different soil types. S. javanicum promoted a higher release in the soil of the more soluble and less condensed EPS fraction (i.e., the loosely bound EPS fraction, LB-EPS), while P. ambiguum showed a higher release of the less soluble and more condensed EPS fraction (i.e., the tightly bound EPS fraction, TB-EPS). LB-EPSs were mainly composed of low MW molecules (< 50 kDa), while TB-EPSs were mainly composed of high MW molecules (1100-2000 kDa). The two EPS fractions showed a complex monosaccharidic composition (from 11 to 12 different types of monosaccharides), with glucose as the most abundant monosaccharide, in particular in the poorer soils characterized by lower organic C contents. In more C-rich soils, high abundances of galactose, mannose, and xylose were also found. Low abundance of uronic acids and hydrophobic monosaccharides, such as fucose and rhamnose, was found in the EPS extracted from the inoculated soils. Our results point to the influence of soil type on the macromolecular distribution and monosaccharide composition of the polysaccharidic matrix in induced biocrusts, which is likely to affect biocrust development and their role in soil structure and nutrient cycling in restored dryland soils.}, }
@article {pmid30535914, year = {2019}, author = {Muthukrishnan, T and Al Khaburi, M and Abed, RMM}, title = {Fouling Microbial Communities on Plastics Compared with Wood and Steel: Are They Substrate- or Location-Specific?.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {361-374}, pmid = {30535914}, issn = {1432-184X}, support = {SQU-GCC/CL/17/02//Sultan Qaboos University/ ; }, mesh = {Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Biofouling ; *Microbiota ; Plastics/*chemistry ; Polyethylene Terephthalates/chemistry ; Species Specificity ; Steel/*chemistry ; Wood/*microbiology ; }, abstract = {Although marine biofouling has been widely studied on different substrates, information on biofouling on plastics in the Arabian Gulf is limited. Substrate- and location-specific effects were investigated by comparing the microbial communities developed on polyethylene terephthalate (PET) and polyethylene (PE) with those on steel and wood, at two locations in the Sea of Oman. Total biomass was lower on PET and PE than on steel and wood. PET had the highest bacterial abundance at both locations, whereas chlorophyll a concentrations did not vary between substrates. MiSeq 16S ribosomal RNA sequencing revealed comparable operational taxonomic unit (OTU) richness on all substrates at one location but lower numbers on PET and PE at the other location. Non-metric multidimensional scaling (NMDS) showed distinct clusters of the bacterial communities based on substrate (analysis of similarity (ANOSIM), R = 0.45-0.97, p < 0.03) and location (ANOSIM, R = 0.56, p < 0.0001). The bacterial genera Microcystis and Hydrogenophaga and the diatoms Licmophora and Mastogloia were specifically detected on plastics. Desulfovibrio and Pseudomonas spp. exhibited their highest abundance on steel and Corynebacterium spp. on wood. Scanning electron microscopy (SEM) revealed fissure formation on PET and PE, indicating physical degradation. The presence of free radicals on PET and carbonyl bonds (C=O) on PE, as revealed by Fourier transform infrared (FTIR) spectroscopy, indicated abiotic degradation while hydroxyl groups and spectral peaks for proteins and polysaccharides on PE indicated biotic degradation. We conclude that fouling microbial communities are not only substrate-specific but also location-specific and microbes developing on plastics could potentially contribute to their degradation in the marine environment.}, }
@article {pmid30535652, year = {2019}, author = {Whittle, A and Amesbury, MJ and Charman, DJ and Hodgson, DA and Perren, BB and Roberts, SJ and Gallego-Sala, AV}, title = {Salt-Enrichment Impact on Biomass Production in a Natural Population of Peatland Dwelling Arcellinida and Euglyphida (Testate Amoebae).}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {534-538}, pmid = {30535652}, issn = {1432-184X}, support = {NE/L002434/1//Natural Environment Research Council/ ; }, mesh = {Antarctic Regions ; Biodiversity ; Cercozoa/*growth &amp; development/metabolism ; Ecosystem ; Lobosea/*growth &amp; development/metabolism ; Salinity ; Sodium Chloride/analysis/metabolism ; Soil/chemistry/parasitology ; }, abstract = {Unicellular free-living microbial eukaryotes of the order Arcellinida (Tubulinea; Amoebozoa) and Euglyphida (Cercozoa; SAR), commonly termed testate amoebae, colonise almost every freshwater ecosystem on Earth. Patterns in the distribution and productivity of these organisms are strongly linked to abiotic conditions-particularly moisture availability and temperature-however, the ecological impacts of changes in salinity remain poorly documented. Here, we examine how variable salt concentrations affect a natural community of Arcellinida and Euglyphida on a freshwater sub-Antarctic peatland. We principally report that deposition of wind-blown oceanic salt-spray aerosols onto the peatland surface corresponds to a strong reduction in biomass and to an alteration in the taxonomic composition of communities in favour of generalist taxa. Our results suggest novel applications of this response as a sensitive tool to monitor salinisation of coastal soils and to detect salinity changes within peatland palaeoclimate archives. Specifically, we suggest that these relationships could be used to reconstruct millennial scale variability in salt-spray deposition-a proxy for changes in wind-conditions-from sub-fossil communities of Arcellinida and Euglyphida preserved in exposed coastal peatlands.}, }
@article {pmid30535561, year = {2019}, author = {Rydzanicz, K and Golab, E and Rozej-Bielicka, W and Masny, A}, title = {Screening of mosquitoes for filarioid helminths in urban areas in south western Poland-common patterns in European Setaria tundra xenomonitoring studies.}, journal = {Parasitology research}, volume = {118}, number = {1}, pages = {127-138}, pmid = {30535561}, issn = {1432-1955}, mesh = {Aedes/*parasitology/physiology ; Animals ; Culex/*parasitology/physiology ; Dirofilaria immitis/genetics/*isolation &amp; purification ; Dirofilaria repens/genetics/*isolation &amp; purification ; Dirofilariasis/epidemiology/parasitology/*transmission ; Humans ; Mosquito Vectors/*parasitology/physiology ; Poland/epidemiology ; Setaria Nematode/genetics/*isolation &amp; purification ; Setariasis/epidemiology/parasitology/*transmission ; }, abstract = {In recent years, numerous studies screening mosquitoes for filarioid helminths (xenomonitoring) have been performed in Europe. The entomological monitoring of filarial nematode infections in mosquitoes by molecular xenomonitoring might serve as the measure of the rate at which humans and animals expose mosquitoes to microfilariae and the rate at which animals and humans are exposed to the bites of the infected mosquitoes. We hypothesized that combining the data obtained from molecular xenomonitoring and phenological studies of mosquitoes in the urban environment would provide insights into the transmission risk of filarial diseases. In our search for Dirofilaria spp.-infected mosquitoes, we have found Setaria tundra-infected ones instead, as in many other European studies. We have observed that cross-reactivity in PCR assays for Dirofilaria repens, Dirofilaria immitis, and S. tundra COI gene detection was the rule rather than the exception. S. tundra infections were mainly found in Aedes mosquitoes. The differences in the diurnal rhythm of Aedes and Culex mosquitoes did not seem a likely explanation for the lack of S. tundra infections in Culex mosquitoes. The similarity of S. tundra COI gene sequences found in Aedes vexans and Aedes caspius mosquitoes and in roe deer in many European studies, supported by data on Ae. vexans biology, suggested host preference as the most likely cause of the mosquito genus-biased infections. High diversity of the COI gene sequences isolated in the city of Wroclaw in south western Poland and the presence of identical or almost identical sequences in mosquitoes and roe deer across Europe suggests that S. tundra has been established in most of Europe for a very long time.}, }
@article {pmid30535196, year = {2019}, author = {Kolora, SRR and Weigert, A and Saffari, A and Kehr, S and Walter Costa, MB and Spröer, C and Indrischek, H and Chintalapati, M and Lohse, K and Doose, G and Overmann, J and Bunk, B and Bleidorn, C and Grimm-Seyfarth, A and Henle, K and Nowick, K and Faria, R and Stadler, PF and Schlegel, M}, title = {Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation.}, journal = {GigaScience}, volume = {8}, number = {2}, pages = {}, pmid = {30535196}, issn = {2047-217X}, mesh = {Animals ; *Evolution, Molecular ; Female ; *Genome ; Genomics ; Lizards/*genetics ; Male ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; }, abstract = {BACKGROUND: Lacerta viridis and Lacerta bilineata are sister species of European green lizards (eastern and western clades, respectively) that, until recently, were grouped together as the L. viridis complex. Genetic incompatibilities were observed between lacertid populations through crossing experiments, which led to the delineation of two separate species within the L. viridis complex. The population history of these sister species and processes driving divergence are unknown. We constructed the first high-quality de novo genome assemblies for both L. viridis and L. bilineata through Illumina and PacBio sequencing, with annotation support provided from transcriptome sequencing of several tissues. To estimate gene flow between the two species and identify factors involved in reproductive isolation, we studied their evolutionary history, identified genomic rearrangements, detected signatures of selection on non-coding RNA, and on protein-coding genes.<br><br>FINDINGS: Here we show that gene flow was primarily unidirectional from L. bilineata to L. viridis after their split at least 1.15 million years ago. We detected positive selection of the non-coding repertoire; mutations in transcription factors; accumulation of divergence through inversions; selection on genes involved in neural development, reproduction, and behavior, as well as in ultraviolet-response, possibly driven by sexual selection, whose contribution to reproductive isolation between these lacertid species needs to be further evaluated.<br><br>CONCLUSION: The combination of short and long sequence reads resulted in one of the most complete lizard genome assemblies. The characterization of a diverse array of genomic features provided valuable insights into the demographic history of divergence among European green lizards, as well as key species differences, some of which are candidates that could have played a role in speciation. In addition, our study generated valuable genomic resources that can be used to address conservation-related issues in lacertids.}, }
@article {pmid30534614, year = {2018}, author = {Rampelli, S and Guenther, K and Turroni, S and Wolters, M and Veidebaum, T and Kourides, Y and Molnár, D and Lissner, L and Benitez-Paez, A and Sanz, Y and Fraterman, A and Michels, N and Brigidi, P and Candela, M and Ahrens, W}, title = {Pre-obese children's dysbiotic gut microbiome and unhealthy diets may predict the development of obesity.}, journal = {Communications biology}, volume = {1}, number = {}, pages = {222}, pmid = {30534614}, issn = {2399-3642}, abstract = {It is widely accepted that the intestinal microbiome is connected to obesity, as key mediator of the diet impact on the host metabolic and immunological status. To investigate whether the individual gut microbiome has a potential in predicting the onset and progression of diseases, here we characterized the faecal microbiota of 70 children in a two-time point prospective study, within a four-year window. All children had normal weight at the beginning of this study, but 36 of them gained excessive weight at the subsequent check-up. Microbiome data were analysed together with the hosts' diet information, physical activity, and inflammatory parameters. We find that the gut microbiota structures were stratified into a discrete number of groups, characterized by different biodiversity that correlates with inflammatory markers and dietary habits, regardless of age, gender, and body weight. Collectively, our data underscore the importance of the microbiome-host-diet configuration as a possible predictor of obesity.}, }
@article {pmid30534120, year = {2018}, author = {Heijboer, A and de Ruiter, PC and Bodelier, PLE and Kowalchuk, GA}, title = {Modulation of Litter Decomposition by the Soil Microbial Food Web Under Influence of Land Use Change.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2860}, pmid = {30534120}, issn = {1664-302X}, abstract = {Soil microbial communities modulate soil organic matter (SOM) dynamics by catalyzing litter decomposition. However, our understanding of how litter-derived carbon (C) flows through the microbial portion of the soil food web is far from comprehensive. This information is necessary to facilitate reliable predictions of soil C cycling and sequestration in response to a changing environment such as land use change in the form of agricultural abandonment. To examine the flow of litter-derived C through the soil microbial food web and it's response to land use change, we carried out an incubation experiment with soils from six fields; three recently abandoned and three long term abandoned fields. In these soils, the fate of [13]C-labeled plant litter was followed by analyzing phospholipid fatty acids (PLFA) over a period of 56 days. The litter-amended soils were sampled over time to measure [13]CO2 and mineral N dynamics. Microbial [13]C-incorporation patterns revealed a clear succession of microbial groups during litter decomposition. Fungi were first to incorporate [13]C-label, followed by G[-] bacteria, G[+] bacteria, actinomycetes and micro-fauna. The order in which various microbial groups responded to litter decomposition was similar across all the fields examined, with no clear distinction between recent and long-term abandoned soils. Although the microbial biomass was initially higher in long-term abandoned soils, the net amount of [13]C-labeled litter that was incorporated by the soil microbial community was ultimately comparable between recent and long-term abandoned fields. In relative terms, this means there was a higher efficiency of litter-derived [13]C-incorporation in recent abandoned soil microbial communities compared to long-term abandoned soils, most likely due to a net shift from SOM-derived C toward root-derived C input in the soil microbial food web following land-abandonment.}, }
@article {pmid30533919, year = {2018}, author = {Kim, SJ and Park, SJ and Kim, JG and Jung, MY and Gwak, JH and Rhee, SK}, title = {Draft Genome Sequence of "Candidatus Izimaplasma sp." Strain ZiA1, Obtained from a Toluene-Degrading and Iron-Reducing Enrichment Culture.}, journal = {Microbiology resource announcements}, volume = {7}, number = {8}, pages = {}, pmid = {30533919}, issn = {2576-098X}, abstract = {Here, we report the draft genome sequence of "Candidatus Izimaplasma sp." strain ZiA1 (1.88 Mb and 29.6% G+C content). Strain ZiA1 was cocultured with iron-reducing and toluene-degrading bacteria in an enrichment culture from tidal flat sediment. Like the genomes of other strains of "Ca. Izimaplasma," the ZiA1 genome contained genes required for anaerobic fermentation.}, }
@article {pmid30532956, year = {2019}, author = {Zhao, Y and Su, JQ and Ye, J and Rensing, C and Tardif, S and Zhu, YG and Brandt, KK}, title = {AsChip: A High-Throughput qPCR Chip for Comprehensive Profiling of Genes Linked to Microbial Cycling of Arsenic.}, journal = {Environmental science &amp; technology}, volume = {53}, number = {2}, pages = {798-807}, doi = {10.1021/acs.est.8b03798}, pmid = {30532956}, issn = {1520-5851}, mesh = {*Arsenic ; Humans ; Oligonucleotide Array Sequence Analysis ; RNA, Ribosomal, 16S ; Real-Time Polymerase Chain Reaction ; }, abstract = {Arsenic (As) is a ubiquitous toxic element adversely affecting human health. Microbe-mediated cycling of As is largely mediated by detoxification and energy metabolism in microorganisms. We here report the development of a novel high-throughput qPCR (HT-qPCR) chip (AsChip) for comprehensive profiling of genes involved in microbial As cycling (here collectively termed "As genes"). AsChip contained 81 primer sets targeting 19 As genes and the 16S rRNA gene as a reference gene. Gene amplicon sequencing showed high identity (>96%) of newly designed primers corresponding to their targets. AsChip displayed high sensitivity (plasmid template serial dilution test; r = -0.99), with more than 96% of all PCR assays yielding true positive signals. R[2] coefficients for standard curves and PCR amplification efficiencies averaged 0.98 and 0.99, respectively. A high correlation between CT values obtained by AsChip and conventional qPCR was obtained (r = 0.962, P < 0.001). Finally, we successfully applied AsChip on soil samples from a chromium-copper-arsenic-contaminated field site and identified diverse As genes with total abundance average of 0.4 As gene copies per 16S rRNA. Our results indicate that AsChip constitutes a robust tool for comprehensive quantitative profiling of As genes in environmental samples.}, }
@article {pmid30532746, year = {2018}, author = {Bachmann, J and Heimbach, T and Hassenrück, C and Kopprio, GA and Iversen, MH and Grossart, HP and Gärdes, A}, title = {Environmental Drivers of Free-Living vs. Particle-Attached Bacterial Community Composition in the Mauritania Upwelling System.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2836}, pmid = {30532746}, issn = {1664-302X}, abstract = {Saharan dust input and seasonal upwelling along North-West Africa provide a model system for studying microbial processes related to the export and recycling of nutrients. This study offers the first molecular characterization of prokaryotic particle-attached (PA; >3.0 μm) and free-living (FL; 0.2-3.0 μm) players in this important ecosystem during August 2016. Environmental drivers for alpha-diversity, bacterial community composition, and differences between FL and PA fractions were identified. The ultra-oligotrophic waters off Senegal were dominated by Cyanobacteria while higher relative abundances of Alphaproteobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes (known particle-degraders) occurred in the upwelling area. Temperature, proxy for different water masses, was the best predictor for changes in FL communities. PA community variation was best explained by temperature and ammonium. Bray Curtis dissimilarities between FL and PA were generally very high and correlated with temperature and salinity in surface waters. Greatest similarities between FL and PA occurred at the deep chlorophyll maximum, where bacterial substrate availability was likely highest. This indicates that environmental drivers do not only influence changes among FL and PA communities but also differences between them. This could provide an explanation for contradicting results obtained by different studies regarding the dissimilarity/similarity between FL and PA communities and their biogeochemical functions.}, }
@article {pmid30532651, year = {2018}, author = {Haruta, S and Yamamoto, K}, title = {Model Microbial Consortia as Tools for Understanding Complex Microbial Communities.}, journal = {Current genomics}, volume = {19}, number = {8}, pages = {723-733}, pmid = {30532651}, issn = {1389-2029}, abstract = {A major biological challenge in the postgenomic era has been untangling the composition and functions of microbes that inhabit complex communities or microbiomes. Multi-omics and modern bioinformatics have provided the tools to assay molecules across different cellular and community scales; however, mechanistic knowledge over microbial interactions often remains elusive. This is due to the immense diversity and the essentially undiminished volume of not-yet-cultured microbes. Simplified model communities hold some promise in enabling researchers to manage complexity so that they can mechanistically understand the emergent properties of microbial community interactions. In this review, we surveyed several approaches that have effectively used tractable model consortia to elucidate the complex behavior of microbial communities. We go further to provide some perspectives on the limitations and new opportunities with these approaches and highlight where these efforts are likely to lead as advances are made in molecular ecology and systems biology.}, }
@article {pmid30532562, year = {2018}, author = {Eze, EC and Chenia, HY and El Zowalaty, ME}, title = {Acinetobacter baumannii biofilms: effects of physicochemical factors, virulence, antibiotic resistance determinants, gene regulation, and future antimicrobial treatments.}, journal = {Infection and drug resistance}, volume = {11}, number = {}, pages = {2277-2299}, pmid = {30532562}, issn = {1178-6973}, abstract = {Acinetobacter baumannii is a leading cause of nosocomial infections due to its increased antibiotic resistance and virulence. The ability of A. baumannii to form biofilms contributes to its survival in adverse environmental conditions including hospital environments and medical devices. A. baumannii has undoubtedly propelled the interest of biomedical researchers due to its broad range of associated infections especially in hospital intensive care units. The interplay among microbial physicochemistry, alterations in the phenotype and genotypic determinants, and the impact of existing ecological niche and the chemistry of antimicrobial agents has led to enhanced biofilm formation resulting in limited access of drugs to their specific targets. Understanding the triggers to biofilm formation is a step towards limiting and containing biofilm-associated infections and development of biofilm-specific countermeasures. The present review therefore focused on explaining the impact of environmental factors, antimicrobial resistance, gene alteration and regulation, and the prevailing microbial ecology in A. baumannii biofilm formation and gives insights into prospective anti-infective treatments.}, }
@article {pmid30530706, year = {2019}, author = {Holman, DB and Bearson, BL and Allen, HK and Shippy, DC and Loving, CL and Kerr, BJ and Bearson, SMD and Brunelle, BW}, title = {Chlortetracycline Enhances Tonsil Colonization and Fecal Shedding of Multidrug-Resistant Salmonella enterica Serovar Typhimurium DT104 without Major Alterations to the Porcine Tonsillar and Intestinal Microbiota.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {4}, pages = {}, pmid = {30530706}, issn = {1098-5336}, mesh = {Animal Feed ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Shedding/*drug effects ; Cecum/microbiology ; Chlortetracycline/*pharmacology ; Drug Resistance, Multiple, Bacterial/*drug effects ; Feces/*microbiology ; Gastrointestinal Microbiome/*drug effects ; Palatine Tonsil/*microbiology ; Salmonella Infections, Animal/drug therapy/microbiology/prevention &amp; control ; Salmonella enterica/*drug effects ; Serogroup ; Swine ; Swine Diseases/drug therapy/microbiology/prevention &amp; control ; }, abstract = {Salmonella spp. are estimated to cause 1.2 million cases of human foodborne illness each year in the United States, and pigs can often be asymptomatically colonized with Salmonella spp. (>50% of farms). Recent reports state that 18.3% of Salmonella enterica serovar Typhimurium isolates are resistant to ≥3 antimicrobial classes, and multidrug-resistant (MDR) strains are associated with an increased hospitalization rate and other complications. Chlortetracycline is commonly used in swine production to prevent/treat various diseases; therefore, chlortetracycline treatment of pigs unknowingly colonized with MDR Salmonella may have collateral effects on Salmonella spp. (and other gut bacteria). In this study, we determined the effect of in-feed chlortetracycline (400 g/ton) on shedding and colonization of pigs challenged with the MDR S Typhimurium strain DT104 (n = 11/group). We also assessed the impact on the fecal microbiota over the 12-day experimental period and on the ileum, cecum, and tonsil microbiota at 7 days postinoculation (dpi). In MDR S Typhimurium-inoculated pigs, chlortetracycline administration significantly increased fecal shedding at 2 dpi (+1.4 log10 CFU/g; P < 0.001) and enhanced tonsil colonization (+3.1 log10 CFU/g; P < 0.001). There were few major alterations detected in the gut or tonsillar microbiota of pigs treated with MDR S Typhimurium and/or chlortetracycline. The tonsillar transcriptome was largely unaffected despite increased colonization by MDR S Typhimurium following inoculation of the chlortetracycline-treated pigs. These results highlight the idea that chlortetracycline administration can enhance shedding and colonization of MDR S Typhimurium in pigs, which could increase the risk of environmental dissemination of MDR Salmonella strains.IMPORTANCESalmonella spp. are an important cause of foodborne illness in North America, and pork products are associated with sporadic cases and outbreaks of human salmonellosis. Isolates of Salmonella may be resistant to multiple antibiotics, and infections with multidrug-resistant (MDR) Salmonella spp. are more difficult to treat, leading to increased hospitalization rates. Swine operations commonly use antimicrobials, such as chlortetracycline, to prevent/treat infections, which may have collateral effects on pig microbial populations. Recently, we demonstrated that chlortetracycline induces the expression of genes associated with pathogenesis and invasion in MDR Salmonella enterica serovar Typhimurium in vitro In our current study, we show increased tonsillar colonization and fecal shedding of the MDR S Typhimurium strain DT104 from pigs administered chlortetracycline. Therefore, pigs unknowingly colonized with multidrug-resistant Salmonella spp. and receiving chlortetracycline for an unrelated infection may be at a greater risk for disseminating MDR Salmonella spp. to other pigs and to humans through environmental or pork product contamination.}, }
@article {pmid30530153, year = {2019}, author = {Macintosh, KA and Chin, J and Jacobs, B and Cordell, D and McDowell, RW and Butler, P and Haygarth, PM and Williams, P and Quinn, JP and O'Flaherty, V and McGrath, JW}, title = {Transforming phosphorus use on the island of Ireland: A model for a sustainable system.}, journal = {The Science of the total environment}, volume = {656}, number = {}, pages = {852-861}, doi = {10.1016/j.scitotenv.2018.11.389}, pmid = {30530153}, issn = {1879-1026}, abstract = {Phosphorus is an essential part of the world food web and a non-substitutable nutrient in all biological systems. Losses of phosphorus occur along the food-supply chain and cause environmental degradation and eutrophication. A key global challenge is to meet rising worldwide food demand while protecting water and environmental quality, and seeking to manage uncertainty around potential future phosphorus price or supply shocks. This paper presents a stakeholder-generated conceptual model of potential transformative change for implementing phosphorus sustainability on the island of Ireland via an 'All-Island Phosphorus Sustainability' workshop. Key transition pathways identified by stakeholders included: incentivising phosphorus recovery, developing collaborative networks to facilitate change, developing markets and value chains for recovered products; implementing data-informed practices on-farm to prevent losses and increase efficiencies, and harmonisation of technologies with end-user needs. A comparable model was previously produced for the North American region. We describe consensus and differences around key priorities between the two regions' conceptual models, and assess how the model produced for the island of Ireland can effect system-wide change and policy moving forward. Many of the transitional pathways and future aspirations presented in both models resonate globally and are highly pertinent to other jurisdictions.}, }
@article {pmid30530129, year = {2019}, author = {Christiaens, MER and Udert, KM and Arends, JBA and Huysman, S and Vanhaecke, L and McAdam, E and Rabaey, K}, title = {Membrane stripping enables effective electrochemical ammonia recovery from urine while retaining microorganisms and micropollutants.}, journal = {Water research}, volume = {150}, number = {}, pages = {349-357}, doi = {10.1016/j.watres.2018.11.072}, pmid = {30530129}, issn = {1879-2448}, mesh = {*Ammonia ; Bioreactors ; Denitrification ; *Escherichia coli ; Nitrification ; Nitrogen ; }, abstract = {Ammonia recovery from urine avoids the need for nitrogen removal through nitrification/denitrification and re-synthesis of ammonia (NH3) via the Haber-Bosch process. Previously, we coupled an alkalifying electrochemical cell to a stripping column, and achieved competitive nitrogen removal and energy efficiencies using only electricity as input, compared to other technologies such as conventional column stripping with air. Direct liquid-liquid extraction with a hydrophobic gas membrane could be an alternative to increase nitrogen recovery from urine into the absorbent while minimizing energy requirements, as well as ensuring microbial and micropollutant retention. Here we compared a column with a membrane stripping reactor, each coupled to an electrochemical cell, fed with source-separated urine and operated at 20 A m[-2]. Both systems achieved similar nitrogen removal rates, 0.34 ± 0.21 and 0.35 ± 0.08 mol N L[-1] d[-1], and removal efficiencies, 45.1 ± 18.4 and 49.0 ± 9.3%, for the column and membrane reactor, respectively. The membrane reactor improved nitrogen recovery to 0.27 ± 0.09 mol N L[-1] d[-1] (38.7 ± 13.5%) while lowering the operational (electrochemical and pumping) energy to 6.5 kWhe kg N[-1] recovered, compared to the column reactor, which reached 0.15 ± 0.06 mol N L[-1] d[-1] (17.2 ± 8.1%) at 13.8 kWhe kg N[-1]. Increased cell concentrations of an autofluorescent E. coli MG1655 + prpsM spiked in the urine influent were observed in the absorbent of the column stripping reactor after 24 h, but not for the membrane stripping reactor. None of six selected micropollutants spiked in the urine were found in the absorbent of both technologies. Overall, the membrane stripping reactor is preferred as it improved nitrogen recovery with less energy input and generated an E. coli- and micropollutant-free product for potential safe reuse. Nitrogen removal rate and efficiency can be further optimized by increasing the NH3 vapor pressure gradient and/or membrane surface area.}, }
@article {pmid30529486, year = {2019}, author = {Labarthe, S and Polizzi, B and Phan, T and Goudon, T and Ribot, M and Laroche, B}, title = {A mathematical model to investigate the key drivers of the biogeography of the colon microbiota.}, journal = {Journal of theoretical biology}, volume = {462}, number = {}, pages = {552-581}, doi = {10.1016/j.jtbi.2018.12.009}, pmid = {30529486}, issn = {1095-8541}, mesh = {Animals ; Chemotaxis ; Colon/anatomy &amp; histology/*microbiology ; Dietary Fiber/metabolism ; Epithelial Cells/cytology ; Epithelium ; *Gastrointestinal Microbiome ; Humans ; *Models, Theoretical ; Spatio-Temporal Analysis ; }, abstract = {The gut microbiota, mainly located in the colon, is engaged in a complex dialogue with the large intestinal epithelium through which important regulatory processes for the health and well-being of the host take place. Imbalances of the microbial populations, called dysbiosis, are related to several pathological status, emphasizing the importance of understanding the gut bacterial ecology. Among the ecological drivers of the microbiota, the spatial structure of the colon is of special interest: spatio-temporal mechanisms can lead to the constitution of spatial interactions among the bacterial populations and of environmental niches that impact the overall colonization of the colon. In the present study, we introduce a mathematical model of the colon microbiota in its fluid environment, based on the explicit coupling of a population dynamics model of microbial populations involved in fibre degradation with a fluid dynamics model of the luminal content. This modeling framework is used to study the main drivers of the spatial structure of the microbiota, specially focusing on the dietary fibre inflow, the epithelial motility, the microbial active swimming and viscosity gradients in the digestive track. We found 1) that the viscosity gradients allow the creation of favorable niches in the vicinity of the mucus layer; 2) that very low microbial active swimming in the radial direction is enough to promote bacterial growth, which sheds a new light on microbial motility in the colon and 3) that dietary fibres are the main driver of the spatial structure of the microbiota in the distal bowel whereas epithelial motility is preponderant for the colonization of the proximal colon; in the transverse colon, fibre levels and chemotaxis have the strongest impact on the distribution of the microbial communities.}, }
@article {pmid30521380, year = {2019}, author = {Calatayud, M and Dezutter, O and Hernandez-Sanabria, E and Hidalgo-Martinez, S and Meysman, FJR and Van de Wiele, T}, title = {Development of a host-microbiome model of the small intestine.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {33}, number = {3}, pages = {3985-3996}, doi = {10.1096/fj.201801414R}, pmid = {30521380}, issn = {1530-6860}, mesh = {Caco-2 Cells ; Chemokine CXCL16/genetics/metabolism ; Escherichia coli/pathogenicity ; *Gastrointestinal Microbiome ; HT29 Cells ; *Host-Pathogen Interactions ; Humans ; Interleukin-6/genetics/metabolism ; Interleukin-8/genetics/metabolism ; Intestinal Mucosa/metabolism/*microbiology ; Lipopolysaccharides/metabolism ; Primary Cell Culture/*methods ; Toll-Like Receptor 2/genetics/metabolism ; Toll-Like Receptor 4/genetics/metabolism ; Tumor Necrosis Factor-alpha/genetics/metabolism ; Veillonella/pathogenicity ; }, abstract = {The intestinal epithelium plays an essential role in the balance between tolerant and protective immune responses to infectious agents. In vitro models do not typically consider the innate immune response and gut microbiome in detail, so these models do not fully mimic the physiologic aspects of the small intestine. We developed and characterized a long-term in vitro model containing enterocyte, goblet, and immune-like cells exposed to a synthetic microbial community representative of commensal inhabitants of the small intestine. This model showed differential responses toward a synthetic microbial community of commensal bacterial inhabitants of the small intestine in the absence or presence of LPS from Escherichia coli O111:B4. Simultaneous exposure to LPS and microbiota induced impaired epithelial barrier function; increased production of IL-8, IL-6, TNF-α, and C-X-C motif chemokine ligand 16; and augmented differentiation and adhesion of macrophage-like cells and the overexpression of dual oxidase 2 and TLR-2 and -4 mRNA. In addition, the model demonstrated the ability to assess the adhesion of specific bacterial strains from the synthetic microbial community-more specifically, Veillonella parvula-to the simulated epithelium. This novel in vitro model may assist in overcoming sampling and retrieval difficulties when studying host-microbiome interactions in the small intestine.-Calatayud, M., Dezutter, O., Hernandez-Sanabria, E., Hidalgo-Martinez, S., Meysman, F. J. R., Van de Wiele, T. Development of a host-microbiome model of the small intestine.}, }
@article {pmid30520189, year = {2019}, author = {Andeta, AF and Vandeweyer, D and Teffera, EF and Woldesenbet, F and Verreth, C and Crauwels, S and Lievens, B and Vancampenhout, K and Van Campenhout, L}, title = {Effect of fermentation system on the physicochemical and microbial community dynamics during enset (Ensete ventricosum) fermentation.}, journal = {Journal of applied microbiology}, volume = {126}, number = {3}, pages = {842-853}, doi = {10.1111/jam.14173}, pmid = {30520189}, issn = {1365-2672}, support = {VLIR-TEAM ZEIN2015PR407//Vlaamse Interuniversitaire Raad voor Universitaire Ontwikkelingssamen werking' (VLIR-UOS)/ ; }, mesh = {*Fermentation ; *Fermented Foods ; Food Technology/*methods ; *Microbiota ; *Musaceae ; }, abstract = {AIMS: The present study was conducted to assess the effect of three different fermentation systems on fermentation of enset into kocho.<br><br>METHODS AND RESULTS: Nine enset plants were processed, mixed and fermented in either a pit, a bamboo basket or a sauerkraut jar. Samples were taken on days 1, 7, 15, 31, 60 and 90. Moisture content and pH generally decreased and titratable acidity increased during fermentation. Total viable aerobic counts were generally high for all samples and Enterobacteriaceae counts were reduced to below the detectable level after day 1 for the pits and jars and after day 7 for the baskets. Illumina MiSeq sequencing of 16S ribosomal RNA genes revealed that Leuconostoc and Lactococcus spp. were the most abundant lactic acid bacteria in the initial phases of the fermentation. Later on, Lactobacillus, Weissella and Bifidobacterium dominated.<br><br>CONCLUSIONS: The type of fermentation system used had an effect on the microbial dynamics and the effect increased towards the end of fermentation.<br><br>Millions of people in Ethiopia daily consume kocho prepared in either a pit or a basket. These systems show practical problems, but this study shows that fermentation is also possible in a sauerkraut jar.}, }
@article {pmid30518818, year = {2019}, author = {Rosado, PM and Leite, DCA and Duarte, GAS and Chaloub, RM and Jospin, G and Nunes da Rocha, U and P Saraiva, J and Dini-Andreote, F and Eisen, JA and Bourne, DG and Peixoto, RS}, title = {Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation.}, journal = {The ISME journal}, volume = {13}, number = {4}, pages = {921-936}, pmid = {30518818}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*microbiology ; *Coral Reefs ; Gammaproteobacteria/*classification/*metabolism ; Humans ; Microbiota ; Polymerase Chain Reaction ; Probiotics/administration &amp; dosage ; Seawater/chemistry/*microbiology ; Temperature ; }, abstract = {Although the early coral reef-bleaching warning system (NOAA/USA) is established, there is no feasible treatment that can minimize temperature bleaching and/or disease impacts on corals in the field. Here, we present the first attempts to extrapolate the widespread and well-established use of bacterial consortia to protect or improve health in other organisms (e.g., humans and plants) to corals. Manipulation of the coral-associated microbiome was facilitated through addition of a consortium of native (isolated from Pocillopora damicornis and surrounding seawater) putatively beneficial microorganisms for corals (pBMCs), including five Pseudoalteromonas sp., a Halomonas taeanensis and a Cobetia marina-related species strains. The results from a controlled aquarium experiment in two temperature regimes (26 °C and 30 °C) and four treatments (pBMC; pBMC with pathogen challenge - Vibrio coralliilyticus, VC; pathogen challenge, VC; and control) revealed the ability of the pBMC consortium to partially mitigate coral bleaching. Significantly reduced coral-bleaching metrics were observed in pBMC-inoculated corals, in contrast to controls without pBMC addition, especially challenged corals, which displayed strong bleaching signs as indicated by significantly lower photopigment contents and Fv/Fm ratios. The structure of the coral microbiome community also differed between treatments and specific bioindicators were correlated with corals inoculated with pBMC (e.g., Cobetia sp.) or VC (e.g., Ruegeria sp.). Our results indicate that the microbiome in corals can be manipulated to lessen the effect of bleaching, thus helping to alleviate pathogen and temperature stresses, with the addition of BMCs representing a promising novel approach for minimizing coral mortality in the face of increasing environmental impacts.}, }
@article {pmid30506480, year = {2019}, author = {Ascunce, MS and Shin, K and Huguet-Tapia, JC and Poudel, R and Garrett, KA and van Bruggen, AHC and Goss, EM}, title = {Penicillin Trunk Injection Affects Bacterial Community Structure in Citrus Trees.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {457-469}, pmid = {30506480}, issn = {1432-184X}, support = {N/A//Florida Department of Agriculture and Consumer Services/ ; N/A//Institute of Food and Agricultural Sciences/ ; N/A//Esther B. O'Keeffe Foundation/ ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/genetics/isolation &amp; purification ; Citrus/drug effects/*microbiology ; Microbiota/*drug effects ; Penicillins/*pharmacology ; Plant Diseases/*microbiology ; Plant Roots/drug effects/microbiology ; Trees/drug effects/microbiology ; }, abstract = {Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus (CLas), an uncultured α-proteobacterium, is the most destructive disease of citrus trees worldwide. In previous studies, trunk injections of penicillin reduced CLas titers and HLB symptoms in citrus. However, antibiotic effects on the whole plant microbial community, which include effects on taxa that interact with CLas, have not yet been addressed. In this study, we investigated the effects of penicillin injection (0, 1000, and 6000 mg L[-1]) on rhizospheric and endophytic bacterial communities of grapefruit trees in field and greenhouse experiments through culture-independent high-throughput sequencing. DNA extractions from petioles and roots were subjected to 16S rRNA high-throughput sequencing, and reads were clustered by sequence similarity into operational taxonomic units (OTUs). Principal coordinates analysis based on weighted-UniFrac distances did not reveal differences in bacterial communities among treatments in any of the sample sources. However, pairwise linear discriminant analysis indicated significant differences in relative abundance of some taxa (including CLas) among treatments. Network analysis showed that penicillin produced major changes in root bacterial community structure by affecting interspecific microbial associations. This study provides new knowledge of the effect of antimicrobial treatments on interspecific relationships in citrus microbial communities.}, }
@article {pmid30505703, year = {2018}, author = {Ellis, S and Ritz, K}, title = {A modified high-throughput analysis of PLFAs in soil.}, journal = {MethodsX}, volume = {5}, number = {}, pages = {1491-1497}, pmid = {30505703}, issn = {2215-0161}, abstract = {Microbial community profiling via phospholipid fatty-acid (PLFA) analysis is an insightful technique which elucidates the phenotypic structure of microbial assemblages within soil. Previous iterations of PLFA analysis have used large quantities of chemicals and can take extended periods of time to perform. Another barrier to the implementation of this method is the cost and availability of specialised machinery. We report on a high-throughput method which reduces both the time to extract PLFAs from soil and reduces the quantity of chemicals required.}, }
@article {pmid30504896, year = {2019}, author = {Aguilar-Trigueros, CA and Hempel, S and Powell, JR and Cornwell, WK and Rillig, MC}, title = {Bridging reproductive and microbial ecology: a case study in arbuscular mycorrhizal fungi.}, journal = {The ISME journal}, volume = {13}, number = {4}, pages = {873-884}, pmid = {30504896}, issn = {1751-7370}, mesh = {Biological Evolution ; Glomeromycota/*physiology ; Mycorrhizae/*physiology ; Phenotype ; Phylogeny ; Reproduction ; Spores, Fungal/*cytology ; }, abstract = {Offspring size is a key trait for understanding the reproductive ecology of species, yet studies addressing the ecological meaning of offspring size have so far been limited to macro-organisms. We consider this a missed opportunity in microbial ecology and provide what we believe is the first formal study of offspring-size variation in microbes using reproductive models developed for macro-organisms. We mapped the entire distribution of fungal spore size in the arbuscular mycorrhizal (AM) fungi (subphylum Glomeromycotina) and tested allometric expectations of this trait to offspring (spore) output and body size. Our results reveal a potential paradox in the reproductive ecology of AM fungi: while large spore-size variation is maintained through evolutionary time (independent of body size), increases in spore size trade off with spore output. That is, parental mycelia of large-spored species produce fewer spores and thus may have a fitness disadvantage compared to small-spored species. The persistence of the large-spore strategy, despite this apparent fitness disadvantage, suggests the existence of advantages to large-spored species that could manifest later in fungal life history. Thus, we consider that solving this paradox opens the door to fruitful future research establishing the relationship between offspring size and other AM life history traits.}, }
@article {pmid30504213, year = {2019}, author = {Zinke, LA and Glombitza, C and Bird, JT and Røy, H and Jørgensen, BB and Lloyd, KG and Amend, JP and Reese, BK}, title = {Microbial Organic Matter Degradation Potential in Baltic Sea Sediments Is Influenced by Depositional Conditions and In Situ Geochemistry.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {4}, pages = {}, pmid = {30504213}, issn = {1098-5336}, mesh = {Biodegradation, Environmental ; Carbohydrate Metabolism ; Carbon/metabolism ; *Carbon Cycle ; Ecology ; Fatty Acids, Volatile/analysis ; Fermentation ; Food Chain ; Geologic Sediments/*chemistry/*microbiology ; Heterotrophic Processes ; Metabolic Networks and Pathways/genetics ; Metagenome ; Microbiota/genetics/*physiology ; Multivariate Analysis ; Open Reading Frames/genetics ; Seawater/*chemistry/*microbiology ; }, abstract = {Globally, marine sediments are a vast repository of organic matter, which is degraded through various microbial pathways, including polymer hydrolysis and monomer fermentation. The sources, abundances, and quality (i.e., labile or recalcitrant) of the organic matter and the composition of the microbial assemblages vary between sediments. Here, we examine new and previously published sediment metagenomes from the Baltic Sea and the nearby Kattegat region to determine connections between geochemistry and the community potential to degrade organic carbon. Diverse organic matter hydrolysis encoding genes were present in sediments between 0.25 and 67 meters below seafloor and were in higher relative abundances in those sediments that contained more organic matter. New analysis of previously published metatranscriptomes demonstrated that many of these genes were transcribed in two organic-rich Holocene sediments. Some of the variation in deduced pathways in the metagenomes correlated with carbon content and depositional conditions. Fermentation-related genes were found in all samples and encoded multiple fermentation pathways. Notably, genes involved in alcohol metabolism were amongst the most abundant of these genes, indicating that this is an important but underappreciated aspect of sediment carbon cycling. This study is a step towards a more complete understanding of microbial food webs and the impacts of depositional facies on present sedimentary microbial communities.IMPORTANCE Sediments sequester organic matter over geologic time scales and impact global climate regulation. Microbial communities in marine sediments drive organic matter degradation, but the factors controlling their assemblages and activities, which in turn impact their role in organic matter degradation, are not well understood. Hence, determining the role of microbial communities in carbon cycling in various sediment types is necessary for predicting future sediment carbon cycling. We examined microbial communities in Baltic Sea sediments, which were deposited across various climatic and geographical regimes to determine the relationship between microbial potential for breakdown of organic matter and abiotic factors, including geochemistry and sediment lithology. The findings from this study will contribute to our understanding of carbon cycling in the deep biosphere and how microbial communities live in deeply buried environments.}, }
@article {pmid30503875, year = {2018}, author = {Vega, NM and Gore, J}, title = {Simple organizing principles in microbial communities.}, journal = {Current opinion in microbiology}, volume = {45}, number = {}, pages = {195-202}, doi = {10.1016/j.mib.2018.11.007}, pmid = {30503875}, issn = {1879-0364}, mesh = {Animals ; Bacteria/genetics ; Bacterial Infections/microbiology ; *Bacterial Physiological Phenomena ; Humans ; *Microbiota ; Models, Animal ; }, abstract = {There is a great deal of interest in discovering the principles that organize microbial communities, to better understand the structure and diversity of these communities in the natural world. Recent conceptual and technical advances have shown how simple organizing principles can give rise to surprising diversity and complex patterns in these consortia. Understanding competition, cooperation, and communication among microbes has provided novel insights into the structure and behavior of microbial collectives, and the use of simple animal models has advanced our understanding of microbial ecology in the host. These multidisciplinary efforts to understand and predict the properties of microbial communities will be critical in the development of microbial ecology as an applied science.}, }
@article {pmid30502541, year = {2019}, author = {Pannekens, M and Kroll, L and Müller, H and Mbow, FT and Meckenstock, RU}, title = {Oil reservoirs, an exceptional habitat for microorganisms.}, journal = {New biotechnology}, volume = {49}, number = {}, pages = {1-9}, pmid = {30502541}, issn = {1876-4347}, mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; *Ecosystem ; Hydrogen-Ion Concentration ; Oil and Gas Fields/*microbiology/virology ; Phylogeny ; Salinity ; }, abstract = {Microorganisms are present in oil reservoirs around the world where they degrade oil and lead to changes in oil quality. Unfortunately, our knowledge about processes in deep oil reservoirs is limited due to the lack of undisturbed samples. In this review, we discuss the distribution of microorganisms at the oil-water transition zone as well as in water saturated parts of the oil leg and their possible physiological adaptations to abiotic and biotic ecological factors such as temperature, salinity and viruses. We show the importance of studying the water phase within the oil, because small water inclusions and pockets within the oil leg provide an exceptional habitat for microorganisms within a natural oil reservoir and concurrently enlarge the zone of oil biodegradation. Environmental factors such as temperature and salinity control oil biodegradation. Temperature determines the type of microorganisms which are able to inhabit the reservoir. Proteobacteria and Euryarchaeota, are ubiquitous in oil reservoirs over all temperature ranges, whereas some others are tied to specific temperatures. It is proposed that biofilm formation is the dominant way of life within oil reservoirs, enhancing nutrient uptake, syntrophic interactions and protection against environmental stress. Literature shows that viruses are abundant in oil reservoirs and the possible impact on microbial community composition due to control of microbial activity and function is discussed.}, }
@article {pmid30515182, year = {2018}, author = {Gil-Martínez, M and López-García, &#xc1; and Domínguez, MT and Navarro-Fernández, CM and Kjøller, R and Tibbett, M and Marañón, T}, title = {Ectomycorrhizal Fungal Communities and Their Functional Traits Mediate Plant-Soil Interactions in Trace Element Contaminated Soils.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1682}, pmid = {30515182}, issn = {1664-462X}, abstract = {There is an increasing consensus that microbial communities have an important role in mediating ecosystem processes. Trait-based ecology predicts that the impact of the microbial communities on ecosystem functions will be mediated by the expression of their traits at community level. The link between the response of microbial community traits to environmental conditions and its effect on plant functioning is a gap in most current microbial ecology studies. In this study, we analyzed functional traits of ectomycorrhizal fungal species in order to understand the importance of their community assembly for the soil-plant relationships in holm oak trees (Quercus ilex subsp. ballota) growing in a gradient of exposure to anthropogenic trace element (TE) contamination after a metalliferous tailings spill. Particularly, we addressed how the ectomycorrhizal composition and morphological traits at community level mediate plant response to TE contamination and its capacity for phytoremediation. Ectomycorrhizal fungal taxonomy and functional diversity explained a high proportion of variance of tree functional traits, both in roots and leaves. Trees where ectomycorrhizal fungal communities were dominated by the abundant taxa Hebeloma cavipes and Thelephora terrestris showed a conservative root economics spectrum, while trees colonized by rare taxa presented a resource acquisition strategy. Conservative roots presented ectomycorrhizal functional traits characterized by high rhizomorphs formation and low melanization which may be driven by resource limitation. Soil-to-root transfer of TEs was explained substantially by the ectomycorrhizal fungal species composition, with the highest transfer found in trees whose roots were colonized by Hebeloma cavipes. Leaf phosphorus was related to ectomycorrhizal species composition, specifically higher leaf phosphorus was related to the root colonization by Thelephora terrestris. These findings support that ectomycorrhizal fungal community composition and their functional traits mediate plant performance in metal-contaminated soils, and have a high influence on plant capacity for phytoremediation of contaminants. The study also corroborates the overall effects of ectomycorrhizal fungi on ecosystem functioning through their mediation over the plant economics spectrum.}, }
@article {pmid30514367, year = {2018}, author = {Marasco, R and Mosqueira, MJ and Fusi, M and Ramond, JB and Merlino, G and Booth, JM and Maggs-Kölling, G and Cowan, DA and Daffonchio, D}, title = {Rhizosheath microbial community assembly of sympatric desert speargrasses is independent of the plant host.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {215}, pmid = {30514367}, issn = {2049-2618}, mesh = {Actinobacteria/classification/genetics/isolation &amp; purification ; Alphaproteobacteria/classification/genetics/isolation &amp; purification ; Ascomycota/classification/genetics/isolation &amp; purification ; Bacteria/classification/*isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; Desert Climate ; Fungi/classification/*isolation &amp; purification ; Metagenomics/*methods ; Phylogeny ; Plant Roots/microbiology ; Poaceae/*microbiology ; Rhizosphere ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {BACKGROUND: The rhizosheath-root system is an adaptive trait of sandy-desert speargrasses in response to unfavourable moisture and nutritional conditions. Under the deserts' polyextreme conditions, plants interact with edaphic microorganisms that positively affect their fitness and resistance. However, the trophic simplicity and environmental harshness of desert ecosystems have previously been shown to strongly influence soil microbial community assembly. We hypothesize that sand-driven ecological filtering constrains the microbial recruitment processes in the speargrass rhizosheath-root niche, prevailing over the plant-induced selection.<br><br>METHODS: Bacterial and fungal communities from the rhizosheath-root compartments (endosphere root tissues, rhizosheath and rhizosphere) of three Namib Desert speargrass species (Stipagrostis sabulicola, S. seelyae and Cladoraphis spinosa) along with bulk sand have been studied to test our hypothesis. To minimize the variability determined by edaphic and climatic factors, plants living in a single dune were studied. We assessed the role of plant species vs the sandy substrate on the recruitment and selection, phylogenetic diversity and co-occurrence microbial networks of the rhizosheath-root system microbial communities.<br><br>RESULTS: Microorganisms associated with the speargrass rhizosheath-root system were recruited from the surrounding bulk sand population and were significantly enriched in the rhizosheath compartments (10[5] and 10[4] of bacterial 16S rRNA and fungal ITS copies per gram of sand to up to 10[8] and 10[7] copies per gram, respectively). Furthermore, each rhizosheath-root system compartment hosted a specific microbial community demonstrating strong niche-partitioning. The rhizosheath-root systems of the three speargrass species studied were dominated by desert-adapted Actinobacteria and Alphaproteobacteria (e.g. Lechevalieria, Streptomyces and Microvirga) as well as saprophytic Ascomycota fungi (e.g. Curvularia, Aspergillus and Thielavia). Our results clearly showed a random phylogenetic turnover of rhizosheath-root system associated microbial communities, independent of the plant species, where stochastic factors drive neutral assembly. Co-occurrence network analyses also indicated that the bacterial and fungal community members of the rhizosheath-root systems established a higher number of interactions than those in the barren bulk sand, suggesting that the former are more stable and functional than the latter.<br><br>CONCLUSION: Our study demonstrates that the rhizosheath-root system microbial communities of desert dune speargrasses are stochastically assembled and host-independent. This finding supports the concept that the selection determined by the desert sand prevails over that imposed by the genotype of the different plant species.}, }
@article {pmid30512194, year = {2019}, author = {Petrovich, ML and Rosenthal, AF and Griffin, JS and Wells, GF}, title = {Spatially resolved abundances of antibiotic resistance genes and intI1 in wastewater treatment biofilms.}, journal = {Biotechnology and bioengineering}, volume = {116}, number = {3}, pages = {543-554}, doi = {10.1002/bit.26887}, pmid = {30512194}, issn = {1097-0290}, mesh = {Bacteria/genetics ; *Biofilms ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial/*genetics ; Integrases/*genetics ; Wastewater/*microbiology ; }, abstract = {Attached growth bioprocesses that use biofilms to remove organic matter or nutrients from wastewater are known to harbor antibiotic resistance genes (ARGs). Biofilms in these processes are spatially heterogeneous, but little is known about depth stratification of ARGs in complex, mixed culture biofilms. To address this knowledge gap, we used an experimental approach combining cryosectioning and quantitative polymerase chain reaction to quantify the spatial distribution of three ARGs (sul1, ermB, and qnrS) and the class 1 integron-integrase gene intI1 in biofilms from a lab-scale rotating annular reactor fed with synthetic wastewater. We also used high throughput 16S ribosomal RNA (rRNA) gene sequencing to characterize community structure with depth in biofilms. The ARG sul1 and the integron-integrase gene intI1 were found in higher abundances in upper layers of biofilm near the fluid-biofilm interface than in lower layers and exhibited significant correlations between the distance from substratum and gene abundances. The genes ermB and qnrS were present in comparatively low relative abundances. Microbial community structure varied significantly by date of sampling and distance from the substratum. These findings highlight the genetic and taxonomic heterogeneity with distance from substratum in wastewater treatment biofilms and show that sul1 and intI1 are particularly abundant near fluid-biofilm interfaces where cells are most likely to detach and flow into downstream portions of treatment systems and can ultimately be released into the environment through effluent.}, }
@article {pmid30502606, year = {2019}, author = {Xiong, Z and Hussain, A and Lee, J and Lee, HS}, title = {Food waste fermentation in a leach bed reactor: Reactor performance, and microbial ecology and dynamics.}, journal = {Bioresource technology}, volume = {274}, number = {}, pages = {153-161}, doi = {10.1016/j.biortech.2018.11.066}, pmid = {30502606}, issn = {1873-2976}, mesh = {Bioreactors/microbiology ; Ecosystem ; Fatty Acids, Volatile/biosynthesis ; *Fermentation ; *Food ; Hydrogen-Ion Concentration ; Refuse Disposal/methods ; }, abstract = {Food waste fermentation was investigated in a leach bed reactor operated at acidic, neutral and alkaline conditions. Highest solids reduction of 87% was obtained at pH 7 in 14 days of reaction time with minimum mixing. The concentration of volatile fatty acids increased to 28.6 g COD/L under pH 7, while the highest butyric acid of 16 g COD/L was obtained at pH 6. Bacterial community structure was narrowed down to Bifidobacterium and Clostridium at pH 6, while Bacteroides and Dysgonomonas were identified as main players at both pH 7 and 8. Bacterial populations in the food residue generally reflected those in the leachate, but some bacteria were selectively enriched in the leachate or the food residue. Bacterial community dynamics suggested that biodegradable food waste was first fermented by one of dominant players (e.g., Clostridium) and the other degraded resistant dietary fibers later (e.g., Bifidobacterium, Bacteroides, Dysgonomonas).}, }
@article {pmid30500479, year = {2019}, author = {Kothamasi, D and Wannijn, J and Van Hees, M and Nauts, R and Van Gompel, A and Vanhoudt, N and Vandenhove, H}, title = {Exposure to ionizing radiation affects the growth of ectomycorrhizal fungi and induces increased melanin production and increased capacities of reactive oxygen species scavenging enzymes.}, journal = {Journal of environmental radioactivity}, volume = {197}, number = {}, pages = {16-22}, doi = {10.1016/j.jenvrad.2018.11.005}, pmid = {30500479}, issn = {1879-1700}, mesh = {Basidiomycota ; Cesium Radioisotopes ; Ecosystem ; Fungi ; Melanins/*metabolism ; Mycorrhizae/enzymology/growth &amp; development/*radiation effects ; *Radiation, Ionizing ; Reactive Oxygen Species/metabolism ; }, abstract = {Ectomycorrhizal (EM) fungi form symbioses with dominant tree families in boreal, temperate and tropical ecosystems and are important drivers of ecosystem function. EM fungal hyphae extend over a large area making them susceptible to enhanced radiation levels from naturally occurring or anthropogenically originating radioisotopes in the rhizosphere. In this study, the in-vitro effects of ionizing radiation on the growth and biomass of EM fungi Suillus luteus, S. bovinus and Rhizopogon luteolus were investigated. EM fungal cultures were exposed to gamma radiation from a [137]Cs source for 137 h in darkness at 21 °C at dose rates of 404, 108.5 and 54.9 mGy h[-1] resulting in total absorbed doses of 55.21, 14.82 and 7.50 Gy respectively. Cultures grown in the dark at 21 °C but not exposed to the [137]Cs source served as the control. Our results show that EM fungi vary in their sensitivity to ionizing radiation. EM fungi used in this study produced melanin and reactive oxygen species scavenging enzymes such as catalase and superoxide dismutase as a response to ionizing radiation.}, }
@article {pmid30499007, year = {2019}, author = {Maillard, F and Leduc, V and Bach, C and de Moraes Gonçalves, JL and Androte, FD and Saint-André, L and Laclau, JP and Buée, M and Robin, A}, title = {Microbial Enzymatic Activities and Community-Level Physiological Profiles (CLPP) in Subsoil Layers Are Altered by Harvest Residue Management Practices in a Tropical Eucalyptus grandis Plantation.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {528-533}, pmid = {30499007}, issn = {1432-184X}, mesh = {Bacteria/classification/*enzymology/genetics/isolation &amp; purification ; Bacterial Proteins/analysis/*metabolism ; Brazil ; Crop Production/*methods ; Eucalyptus/*chemistry/growth &amp; development ; Microbiota ; Plant Stems/chemistry ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Harvest residue management is a key issue for the sustainability of Eucalyptus plantations established on poor soils. Soil microbial communities contribute to soil fertility by the decomposition of the organic matter (OM), but little is known about the effect of whole-tree harvesting (WTH) in comparison to stem only harvesting (SOH) on soil microbial functional diversity in Eucalyptus plantations. We studied the effects of harvest residue management (branches, leaves, bark) of Eucalyptus grandis trees on soil enzymatic activities and community-level physiological profiles in a Brazilian plantation. We measured soil microbial enzymatic activities involved in OM decomposition and we compared the community level physiological profiles (CLPP) of the soil microbes in WTH and SOH plots. WTH decreased enzyme activities and catabolic potential of the soil microbial community. Furthermore, these negative effects on soil functional diversity were mainly observed below the 0-5 cm layer (5-10 and 10-20 cm), suggesting that WTH can be harmful to the soil health in these plantations.}, }
@article {pmid30498637, year = {2018}, author = {Honeyman, AS and Day, ML and Spear, JR}, title = {Regional fresh snowfall microbiology and chemistry are driven by geography in storm-tracked events, Colorado, USA.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5961}, pmid = {30498637}, issn = {2167-8359}, abstract = {Snowfall is a global phenomenon highly integrated with hydrology and ecology. Forays into studying bioaerosols and their dependence on aeolian movement are largely constrained to either precipitation-independent analyses or in silico models. Though snowpack and glacial microbiological studies have been conducted, little is known about the biological component of meteoric snow. Through culture-independent phylogenetic and geochemical analyses, we show that the geographical location at which snow precipitates determines snowfall's geochemical and microbiological composition. Storm-tracking, furthermore, can be used as a valuable environmental indicator to trace down what factors are influencing bioaerosols. We estimate annual aeolian snowfall deposits of up to ∼10 kg of bacterial/archaeal biomass per hectare along our study area of the eastern Front Range in Colorado. The dominant kinds of microbiota captured in an analysis of seven snow events at two different locations, one urban, one rural, across the winter of 2016/2017 included phyla Proteobacteria, Bacteroidetes, Firmicutes, and Acidobacteria, though a multitude of different kinds of organisms were found in both. Taxonomically, Bacteroidetes were more abundant in Golden (urban plain) snow while Proteobacteria were more common in Sunshine (rural mountain) samples. Chemically, Golden snowfall was positively correlated with some metals and anions. The work also hints at better informing the "everything is everywhere" hypotheses of the microbial world and that atmospheric transport of microbiota is not only common, but is capable of disseminating vast amounts of microbiota of different physiologies and genetics that then affect ecosystems globally. Snowfall, we conclude, is a significant repository of microbiological material with strong implications for both ecosystem genetic flux and general bio-aerosol theory.}, }
@article {pmid30498561, year = {2018}, author = {Sakoula, D and Nowka, B and Spieck, E and Daims, H and Lücker, S}, title = {The draft genome sequence of "Nitrospira lenta" strain BS10, a nitrite oxidizing bacterium isolated from activated sludge.}, journal = {Standards in genomic sciences}, volume = {13}, number = {}, pages = {32}, pmid = {30498561}, issn = {1944-3277}, support = {339880/ERC_/European Research Council/International ; P 24101/FWF_/Austrian Science Fund FWF/Austria ; P 25231/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {The genus Nitrospira is considered to be the most widespread and abundant group of nitrite-oxidizing bacteria in many natural and man-made ecosystems. However, the ecophysiological versatility within this phylogenetic group remains highly understudied, mainly due to the lack of pure cultures and genomic data. To further expand our understanding of this biotechnologically important genus, we analyzed the high quality draft genome of "Nitrospira lenta" strain BS10, a sublineage II Nitrospira that was isolated from a municipal wastewater treatment plant in Hamburg, Germany. The genome of "N. lenta" has a size of 3,756,190 bp and contains 3968 genomic objects, of which 3907 are predicted protein-coding sequences. Thorough genome annotation allowed the reconstruction of the "N. lenta" core metabolism for energy conservation and carbon fixation. Comparative analyses indicated that most metabolic features are shared with N. moscoviensis and "N. defluvii", despite their ecological niche differentiation and phylogenetic distance. In conclusion, the genome of "N. lenta" provides important insights into the genomic diversity of the genus Nitrospira and provides a foundation for future comparative genomic studies that will generate a better understanding of the nitrification process.}, }
@article {pmid30498480, year = {2018}, author = {Zäncker, B and Cunliffe, M and Engel, A}, title = {Bacterial Community Composition in the Sea Surface Microlayer Off the Peruvian Coast.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2699}, pmid = {30498480}, issn = {1664-302X}, abstract = {The sea surface microlayer (SML) is located at the air-sea interface, with microorganisms and organic matter in the SML influencing air-sea exchange processes. Yet understanding of the SML bacterial (bacterioneuston) community composition and assembly remains limited. Availability of organic matter, UV radiation and wind speed have previously been suggested to influence the community composition of bacterioneuston. Another mechanism potentially controlling bacterioneuston dynamics is bacterioplankton attached to gel-like particles that ascend through the water column into the SML. We analyzed the bacterial community composition, Transparent Exopolymer Particles (TEP) abundance and nutrient concentrations in the surface waters of the Peruvian upwelling region. The bacterioneuston and bacterioplankton communities were similar, suggesting a close spatial coupling. Four Bacteroidetes families were significantly enriched in the SML, two of them, the Flavobacteriaceae and Cryomorphaceae, were found to comprise the majority of SML-enriched operational taxonomic units (OTUs). The enrichment of these families was controlled by a variety of environmental factors. The SML-enriched bacterial families were negatively correlated with water temperature and wind speed in the SML and positively correlated with nutrient concentrations, salinity and TEP in the underlying water (ULW). The correlations with nutrient concentrations and salinity suggest that the enriched bacterial families were more abundant at the upwelling stations.}, }
@article {pmid30497363, year = {2018}, author = {Sperlea, T and Füser, S and Boenigk, J and Heider, D}, title = {SEDE-GPS: socio-economic data enrichment based on GPS information.}, journal = {BMC bioinformatics}, volume = {19}, number = {Suppl 15}, pages = {440}, pmid = {30497363}, issn = {1471-2105}, mesh = {Algorithms ; Biodiversity ; *Geographic Information Systems ; Lakes ; Machine Learning ; Microbiota ; Socioeconomic Factors ; }, abstract = {BACKGROUND: Microbes are essentail components of all ecosystems because they drive many biochemical processes and act as primary producers. In freshwater ecosystems, the biodiversity in and the composition of microbial communities can be used as indicators for environmental quality. Recently, some environmental features have been identified that influence microbial ecosystems. However, the impact of human action on lake microbiomes is not well understood. This is, in part, due to the fact that environmental data is, albeit theoretically accessible, not easily available.<br><br>RESULTS: In this work, we present SEDE-GPS, a tool that gathers data that are relevant to the environment of an user-provided GPS coordinate. To this end, it accesses a list of public and corporate databases and aggregates the information in a single file, which can be used for further analysis. To showcase the use of SEDE-GPS, we enriched a lake microbial ecology sequencing dataset with around 18,000 socio-economic, climate, and geographic features. The sources of SEDE-GPS are public databases such as Eurostat, the Climate Data Center, and OpenStreetMap, as well as corporate sources such as Twitter. Using machine learning and feature selection methods, we were able to identify features in the data provided by SEDE-GPS that can be used to predict lake microbiome alpha diversity.<br><br>CONCLUSION: The results presented in this study show that SEDE-GPS is a handy and easy-to-use tool for comprehensive data enrichment for studies of ecology and other processes that are affected by environmental features. Furthermore, we present lists of environmental, socio-economic, and climate features that are predictive for microbial biodiversity in lake ecosystems. These lists indicate that human action has a major impact on lake microbiomes. SEDE-GPS and its source code is available for download at http://SEDE-GPS.heiderlab.de.}, }
@article {pmid30496195, year = {2018}, author = {Calderoli, PA and Espínola, FJ and Dionisi, HM and Gil, MN and Jansson, JK and Lozada, M}, title = {Predominance and high diversity of genes associated to denitrification in metagenomes of subantarctic coastal sediments exposed to urban pollution.}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0207606}, pmid = {30496195}, issn = {1932-6203}, mesh = {Archaea/*genetics/isolation &amp; purification ; Archaeal Proteins/classification/genetics/metabolism ; Argentina ; Bacteria/*genetics/isolation &amp; purification ; Bacterial Proteins/classification/genetics/metabolism ; Bays ; Cluster Analysis ; DNA/chemistry/isolation &amp; purification/metabolism ; Denitrification/*genetics ; *Genetic Variation ; Geologic Sediments/*microbiology ; *Metagenomics ; Nitrous Oxide/metabolism ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The aim of this work was to characterize the microbial nitrogen cycling potential in sediments from Ushuaia Bay, a subantarctic environment that has suffered a recent explosive demographic growth. Subtidal sediment samples were retrieved in triplicate from two urban points in the Bay, and analyzed through metagenomic shotgun sequencing. Sequences assigned to genes related to nitrification, nitrate reduction and denitrification were predominant in this environment with respect to metagenomes from other environments, including other marine sediments. The nosZ gene, responsible for nitrous oxide transformation into di-nitrogen, presented a high diversity. The majority of NosZ sequences were classified as Clade II (atypical) variants affiliated to different bacterial lineages such as Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, Verrucomicrobia, as well as to Archaea. The analysis of a fosmid metagenomic library from the same site showed that the genomic context of atypical variants was variable, and was accompanied by distinct regulatory elements, suggesting the evolution of differential ecophysiological roles. This work increases our understanding of the microbial ecology of nitrogen transformations in cold coastal environments and provides evidence of an enhanced denitrification potential in impacted sediment microbial communities. In addition, it highlights the role of yet overlooked populations in the mitigation of environmentally harmful forms of nitrogen.}, }
@article {pmid30487782, year = {2018}, author = {Vadstein, O and Attramadal, KJK and Bakke, I and Olsen, Y}, title = {K-Selection as Microbial Community Management Strategy: A Method for Improved Viability of Larvae in Aquaculture.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2730}, pmid = {30487782}, issn = {1664-302X}, abstract = {Aquaculture has the potential to become a major food supplier in a world with an increasing human population, and increased consumption of fish will likely have positive health implications. For marine aquaculture, the production of high quality juveniles is a bottleneck. Survival until the juvenile stage is typically as low as 10-15% for many species, which indicates suboptimal rearing conditions. Substantial evidence indicates that the poor performance and viability of larvae is largely due to detrimental larvae-microbiota interactions. This emphasises the need for microbial management strategies in the cultivation of marine fish larvae. Disinfection and probiotics are the most studied microbial management methods so far. However, most studies on these methods overlooked the role of mutualistic relationships between microbes and hosts, and have not proposed or examined methods steering toward such relationships. Based on ecological theory and a number of experiments, we find support for the hypothesis that current practise in aquaculture generally selects for r-strategic, opportunistic microbes, which results in detrimental host-microbiota interactions. Thus, the challenge is to develop technology and methods for microbial management at the ecosystem level that creates a K-selected microbial community, and by this mean select against r-strategic opportunists. Here we summarise experiments done during 25 years and with marine larvae of five different species showing that: (1) K-selection strategies result in different water microbiota with less opportunists, (2) this influences the microbiota of the fish larvae, and (3) the larvae cultivated in water inhabited by a K-selected microbiota perform better. Improved performance of larvae includes improved appetite, earlier onset of and faster growth, increased survival, and increased robustness to stress. K-selection as a method for management of the microbial community is a robust approach that allows steering of host-microbiota interactions in larviculture toward mutualism. It could also be applicable for young stages of other domesticated animals. Our review illustrates that a change from a "beat-them" to a "join-them" strategy for microbial management in larval rearing can lead to a more sustainable aquaculture industry.}, }
@article {pmid30483839, year = {2019}, author = {Zakharenko, AS and Galachyants, YP and Morozov, IV and Shubenkova, OV and Morozov, AA and Ivanov, VG and Pimenov, NV and Krasnopeev, AY and Zemskaya, TI}, title = {Bacterial Communities in Areas of Oil and Methane Seeps in Pelagic of Lake Baikal.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {269-285}, pmid = {30483839}, issn = {1432-184X}, support = {17-29-05040//ofi-m RFBR/ ; 0345-2016-0007//State Task for Limnological Institute SB RAS/ ; 18-34-00442//a-mol RFBR/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; DNA, Bacterial/genetics ; Geologic Sediments/chemistry/microbiology ; Lakes/chemistry/*microbiology ; Methane/analysis/*metabolism ; Oils/analysis/*metabolism ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {We have assessed the diversity of bacteria near oil-methane (area I) and methane (area II) seeps in the pelagic zone of Lake Baikal using massive parallel sequencing of 16S rRNA, pmoA, and mxaF gene fragments amplified from total DNA. At depths from the surface to 100 m, sequences belonging to Cyanobacteria dominated. In the communities to a depth of 200 m of the studied areas, Proteobacteria dominated the deeper layers of the water column. Alphaproteobacteria sequences were predominant in the community near the oil-methane seep, while the community near the methane seep was characterized by the prevalence of Alpha- and Gammaproteobacteria. Among representatives of these classes, type I methanotrophs prevailed in the 16S rRNA gene libraries from the near-bottom area, and type II methanotrophs were detected in minor quantities at different depths. In the analysis of the libraries of the pmoA and mxaF functional genes, we observed the different taxonomic composition of methanotrophic bacteria in the surface and deep layers of the water column. All pmoA sequences from area I were type II methanotrophs and were detected at a depth of 300 m, while sequences of type I methanotrophs were the most abundant in deep layers of the water column of area II. All mxaF gene sequences belonged to Methylobacterium representatives. Based on comparative analyses of 16S rRNA, pmoA, and mxaF gene fragment libraries, we suggest that there must be a wider spectrum of functional genes facilitating methane oxidation that were not detected with the primers used.}, }
@article {pmid30482830, year = {2018}, author = {Espinoza, JL and Harkins, DM and Torralba, M and Gomez, A and Highlander, SK and Jones, MB and Leong, P and Saffery, R and Bockmann, M and Kuelbs, C and Inman, JM and Hughes, T and Craig, JM and Nelson, KE and Dupont, CL}, title = {Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, pmid = {30482830}, issn = {2150-7511}, support = {R01 DE019665/DE/NIDCR NIH HHS/United States ; R01 GM120624/GM/NIGMS NIH HHS/United States ; }, mesh = {Australia ; Bacteria/*classification/*genetics ; Child ; Child, Preschool ; Dental Caries/*microbiology ; Dental Plaque/*microbiology ; Humans ; Metabolic Networks and Pathways/genetics ; Metagenomics ; *Microbiota ; Sequence Analysis, DNA ; }, abstract = {To address the question of how microbial diversity and function in the oral cavities of children relates to caries diagnosis, we surveyed the supragingival plaque biofilm microbiome in 44 juvenile twin pairs. Using shotgun sequencing, we constructed a genome encyclopedia describing the core supragingival plaque microbiome. Caries phenotypes contained statistically significant enrichments in specific genome abundances and distinct community composition profiles, including strain-level changes. Metabolic pathways that are statistically associated with caries include several sugar-associated phosphotransferase systems, antimicrobial resistance, and metal transport. Numerous closely related previously uncharacterized microbes had substantial variation in central metabolism, including the loss of biosynthetic pathways resulting in auxotrophy, changing the ecological role. We also describe the first complete Gracilibacteria genomes from the human microbiome. Caries is a microbial community metabolic disorder that cannot be described by a single etiology, and our results provide the information needed for next-generation diagnostic tools and therapeutics for caries.IMPORTANCE Oral health has substantial economic importance, with over $100 billion spent on dental care in the United States annually. The microbiome plays a critical role in oral health, yet remains poorly classified. To address the question of how microbial diversity and function in the oral cavities of children relate to caries diagnosis, we surveyed the supragingival plaque biofilm microbiome in 44 juvenile twin pairs. Using shotgun sequencing, we constructed a genome encyclopedia describing the core supragingival plaque microbiome. This unveiled several new previously uncharacterized but ubiquitous microbial lineages in the oral microbiome. Caries is a microbial community metabolic disorder that cannot be described by a single etiology, and our results provide the information needed for next-generation diagnostic tools and therapeutics for caries.}, }
@article {pmid30481288, year = {2019}, author = {Khan, MAW and Bohannan, BJM and Nüsslein, K and Tiedje, JM and Tringe, SG and Parlade, E and Barberán, A and Rodrigues, JLM}, title = {Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {2}, pages = {}, pmid = {30481288}, issn = {1574-6941}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Conservation of Natural Resources ; Denitrification ; Forests ; Microbiota/genetics/*physiology ; Nitrification ; Nitrogen Cycle ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Co-occurrence networks allow for the identification of potential associations among species, which may be important for understanding community assembly and ecosystem functions. We employed this strategy to examine prokaryotic co-occurrence patterns in the Amazon soils and the response of these patterns to land use change to pasture, with the hypothesis that altered microbial composition due to deforestation will mirror the co-occurrence patterns across prokaryotic taxa. In this study, we calculated Spearman correlations between operational taxonomic units (OTUs) as determined by 16S rRNA gene sequencing, and only robust correlations were considered for network construction (-0.80 ≥ P ≥ 0.80, adjusted P < 0.01). The constructed network represents distinct forest and pasture components, with altered compositional and topological features. A comparative analysis between two representative modules of these contrasting ecosystems revealed novel information regarding changes to metabolic pathways related to nitrogen cycling. Our results showed that soil physicochemical properties such as temperature, C/N and H++Al3+ had a significant impact on prokaryotic communities, with alterations to network topologies. Taken together, changes in co-occurrence patterns and physicochemical properties may contribute to ecosystem processes including nitrification and denitrification, two important biogeochemical processes occurring in tropical forest systems.}, }
@article {pmid30479328, year = {2018}, author = {de Bruijn, I and Verhoeven, KJF}, title = {Cross-species interference of gene expression.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5019}, pmid = {30479328}, issn = {2041-1723}, mesh = {Epigenesis, Genetic ; *Gene Expression Regulation ; RNA/genetics ; Species Specificity ; }, abstract = {Microbes can contribute to protection of animals and plants against diseases. A recent study reveals a mechanism by which a bacterium controls fungal infection in wheat, involving secretion of a metabolite that affects histone acetyltransferase activity of a plant pathogenic fungus.}, }
@article {pmid30478730, year = {2019}, author = {Dhaulaniya, AS and Balan, B and Kumar, M and Agrawal, PK and Singh, DK}, title = {Cold survival strategies for bacteria, recent advancement and potential industrial applications.}, journal = {Archives of microbiology}, volume = {201}, number = {1}, pages = {1-16}, doi = {10.1007/s00203-018-1602-3}, pmid = {30478730}, issn = {1432-072X}, support = {NASF/CA-6030/2017-18//National Agriculture Science Fund/ ; }, mesh = {Adaptation, Physiological/*physiology ; Bacteria/*enzymology/*metabolism ; Biodegradation, Environmental ; *Cold Temperature ; Ecosystem ; Food Microbiology ; Humans ; Hydrocarbons/metabolism ; }, abstract = {Microorganisms have evolved themselves to thrive under various extreme environmental conditions such as extremely high or low temperature, alkalinity, and salinity. These microorganisms adapted several metabolic processes to survive and reproduce efficiently under such extreme environments. As the major proportion of earth is covered with the cold environment and is exploited by human beings, these sites are not pristine anymore. Human interventions are a great reason for disturbing the natural biogeochemical cycles in these regions. The survival strategies of these organisms have shown great potential for helping us to restore these pristine sites and the use of isolated cold-adapted enzymes from these organisms has also revolutionized various industrial products. This review gives you the insight of psychrophilic enzyme adaptations and their industrial applications.}, }
@article {pmid30478232, year = {2019}, author = {Liang, C and Huang, Y and Wang, H}, title = {pahE, a Functional Marker Gene for Polycyclic Aromatic Hydrocarbon-Degrading Bacteria.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {3}, pages = {}, pmid = {30478232}, issn = {1098-5336}, mesh = {Bacteria/classification/enzymology/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Biodegradation, Environmental ; Dioxygenases/genetics/*metabolism ; Geologic Sediments/microbiology ; Microbiota ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/*metabolism ; }, abstract = {The characterization of native polycyclic aromatic hydrocarbon (PAH)-degrading bacteria is significant for understanding the PAH degradation process in the natural environment and developing effective remediation technologies. Most previous investigations of PAH-degrading bacteria in environmental samples employ pahAc, which encodes the α-subunit of PAH ring-hydroxylating dioxygenase, as a functional marker gene. However, the poor phylogenetic resolution and nonspecificity of pahAc result in a misestimation of PAH-degrading bacteria. Here, we propose a PAH hydratase-aldolase-encoding gene, pahE, as a superior biomarker for PAH-degrading bacteria. Comparative phylogenetic analysis of the key enzymes involved in the upper pathway of PAH degradation indicated that pahE evolved dependently from a common ancestor. A phylogenetic tree constructed based on PahE is largely congruent with PahAc-based phylogenies, except for the dispersion of several clades of other non-PAH-degrading aromatic hydrocarbon dioxygenases present in the PahAc tree. Analysis of pure strains by PCR confirmed that pahE can specifically distinguish PAH-degrading bacteria, while pahAc cannot. Illumina sequencing of pahE and pahAc amplicons showed more genotypes and higher specificity and resolution for pahE Novel reads were also discovered among the pahE amplicons, suggesting the presence of novel PAH-degrading populations. These results suggest that pahE is a more powerful biomarker for exploring the ecological role and degradation potential of PAH-degrading bacteria in ecosystems, which is significant to the bioremediation of PAH pollution and environmental microbial ecology.IMPORTANCE PAH contamination has become a worldwide environmental issue because of the potential toxic effects on natural ecosystems and human health. Biotransformation and biodegradation are considered the main natural elimination forms of PAHs from contaminated sites. Therefore, the knowledge of the degradation potential of the microbial community in contaminated sites is crucial for PAH pollution bioremediation. However, the nonspecificity of pahAc as a functional marker of PAH-degrading bacteria has resulted neither in a reliable prediction of PAH degradation potential nor an accurate assessment of degradation. Here, we introduced pahE encoding the PAH hydratase-aldolase as a new and better functional marker gene of PAH-degrading bacteria. This study provides a powerful molecular tool to more effectively explore the ecological role and degradation potential of PAH-degrading bacteria in ecosystems, which is significant to the bioremediation of PAH pollution.}, }
@article {pmid30477264, year = {2018}, author = {Almendras, K and García, J and Carú, M and Orlando, J}, title = {Nitrogen-Fixing Bacteria Associated with Peltigera Cyanolichens and Cladonia Chlorolichens.}, journal = {Molecules (Basel, Switzerland)}, volume = {23}, number = {12}, pages = {}, pmid = {30477264}, issn = {1420-3049}, support = {11100381 and 1181510//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; }, mesh = {Analysis of Variance ; Ascomycota/classification/*physiology ; Molecular Typing/methods ; Nitrogen-Fixing Bacteria/*physiology ; RNA, Ribosomal, 28S/genetics ; Symbiosis ; }, abstract = {Lichens have been extensively studied and described; however, recent evidence suggests that members of the bacterial community associated with them could contribute new functions to the symbiotic interaction. In this work, we compare the nitrogen-fixing guild associated with bipartite terricolous lichens with different types of photobiont: Peltigera cyanolichens and Cladonia chlorolichens. Since cyanobacteria contribute nitrogen to the symbiosis, we propose that chlorolichens have more diverse bacteria with the ability to fix nitrogen compared to cyanolichens. In addition, since part of these bacteria could be recruited from the substrate where lichens grow, we propose that thalli and substrates share some bacteria in common. The structure of the nitrogen-fixing guild in the lichen and substrate bacterial communities of both lichens was determined by terminal restriction fragment length polymorphism (TRFLP) of the nifH gene. Multivariate analyses showed that the nitrogen-fixing bacteria associated with both types of lichen were distinguishable from those present in their substrates. Likewise, the structure of the nitrogen-fixing bacteria present in the cyanolichens was different from that of chlorolichens. Finally, the diversity of this bacterial guild calculated using the Shannon index confirms the hypothesis that chlorolichens have a higher diversity of nitrogen-fixing bacteria than cyanolichens.}, }
@article {pmid30476032, year = {2019}, author = {Nierychlo, M and Milobedzka, A and Petriglieri, F and McIlroy, B and Nielsen, PH and McIlroy, SJ}, title = {The morphology and metabolic potential of the Chloroflexi in full-scale activated sludge wastewater treatment plants.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {2}, pages = {}, doi = {10.1093/femsec/fiy228}, pmid = {30476032}, issn = {1574-6941}, mesh = {Biomass ; Chloroflexi/classification/genetics/*isolation &amp; purification ; Fermentation ; In Situ Hybridization, Fluorescence ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; *Waste Disposal, Fluid ; *Water Purification ; }, abstract = {Filamentous bacteria belonging to the phylum Chloroflexi have received considerable attention in wastewater treatment systems for their suggested role in the operational problem of impaired sludge settleability known as bulking. Their consistently high abundance in full-scale systems, even in the absence of bulking, indicates that they make a substantial contribution to the nutrient transformations during wastewater treatment. In this study, extensive 16S rRNA amplicon surveys of Danish wastewater treatment plants (WWTPs) with nutrient removal were screened to identify numerically important Chloroflexi genera. Fluorescence in situ hybridization probes were designed for their in situ characterization. All abundant Chloroflexi phylotypes were putatively identified as facultative anaerobic chemoorganotrophs involved in sugar fermentation. They were all filamentous but differed in their morphology and spatial arrangement. 'Candidatus Villigracilis' was predominantly located within the activated sludge flocs, where they possibly have structural importance, and their abundance was relatively stable. Conversely, the abundance of 'Candidatus Amarolinea' was highly dynamic, relative to other genera, sometimes reaching abundances in excess of 30% of the biovolume, suggesting their likely role in bulking episodes. This study gives an important insight into the role of Chloroflexi in WWTPs, thus contributing to the broader goal of understanding the ecology of these biotechnologically important systems.}, }
@article {pmid30474807, year = {2019}, author = {Wu, H and Chen, H and Jin, C and Tang, C and Zhang, Y}, title = {The chirality of imazethapyr herbicide selectively affects the bacterial community in soybean field soil.}, journal = {Environmental science and pollution research international}, volume = {26}, number = {3}, pages = {2531-2546}, pmid = {30474807}, issn = {1614-7499}, support = {41071314//National Natural Science Foundation of China/ ; }, mesh = {Bacteria/classification/*drug effects/genetics/isolation &amp; purification ; China ; Herbicides/chemistry/*pharmacology ; Nicotinic Acids/chemistry/*pharmacology ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/chemistry/pharmacology ; Glycine max/*growth &amp; development ; Stereoisomerism ; }, abstract = {The chiral herbicide imazethapyr (IM) is frequently used to control weeds in soybean fields in northeast China. However, the impact of IM enantiomers on microbial communities in soil is still unknown. Genetic markers (16S rRNA V3-V4 regions) were used to characterize and evaluate the variation of the bacterial communities potentially effected by IM enantiomers. Globally, the bacterial community structure based on the OTU profiles in (-)-R-IM-treated soils was significantly different from those in (+)-S-IM-treated soils, and the differences were enlarged with the treatment dose increasing. Interestingly, the Rhizobiaceae family and several other beneficial bacteria, including Bradyrhizobium, Methylobacterium, and Paenibacillus, were strongly enriched in (-)-R-IM treatment compared to (+)-S-IM treatment. In contrast, the pathogenic bacteria, including Erwinia, Pseudomonas, Burkholderia, Streptomyces, and Agrobacterium, were suppressed in the presence of (-)-R-IM compared to (+)-S-IM. Furthermore, we also observed that the bacterial community structure in (-)-R-IM-treated soils was more quickly restored to its original state compared with those in (+)-S-IM-treated soils. These findings unveil a new role of chiral herbicide in the development of soil microbial ecology and provide theoretical support for the application of low-persistence, high-efficiency, and eco-friendly optical rotatory (-)-R-IM.}, }
@article {pmid30474731, year = {2019}, author = {Hosseinzadeh, S and Shams-Bakhsh, M and Mann, M and Fattah-Hosseini, S and Bagheri, A and Mehrabadi, M and Heck, M}, title = {Distribution and Variation of Bacterial Endosymbiont and "Candidatus Liberibacter asiaticus" Titer in the Huanglongbing Insect Vector, Diaphorina citri Kuwayama.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {206-222}, pmid = {30474731}, issn = {1432-184X}, support = {5300-163//California Citrus Research Board/ ; 2016-70016-24779//National Institute of Food and Agriculture/ ; 8062-22410-006-00-D//Agricultural Research Service/ ; }, mesh = {Animals ; Citrus/*microbiology/parasitology ; Endophytes/genetics/isolation &amp; purification/*physiology ; Female ; Hemiptera/*microbiology/physiology ; Insect Vectors/microbiology/physiology ; Male ; Plant Diseases/*microbiology ; Rhizobiaceae/genetics/isolation &amp; purification/*physiology ; *Symbiosis ; Wolbachia/genetics/isolation &amp; purification/physiology ; }, abstract = {The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama, is an economic insect pest in most citrus-growing regions and the vector of 'Candidatus Liberibacter asiaticus' (CLas), one of at least three known bacteria associated with Huanglongbing (HLB or citrus greening disease). D. citri harbors bacterial endosymbionts, including Wolbachia pipientis (strain Wolbachia wDi), 'Candidatus Carsonella ruddii,' and 'Candidatus Profftella armatura.' Many important functions of these bacteria can be inferred from their genome sequences, but their interactions with each other, CLas, and their D. citri host are poorly understood. In the present study, the titers of the endosymbionts in different tissues, in each sex, and in insects reared on healthy citrus (referred to as unexposed) and CLas-infected citrus (referred to as CLas-exposed) D. citri were investigated using real-time, quantitative PCR (qPCR) using two different quantitative approaches. Wolbachia and CLas were detected in all insect tissues. The titer of Wolbachia was higher in heads of CLas-exposed males as compared to unexposed males. In males and females, Wolbachia titer was highest in the Malpighian tubules. The highest titer of CLas was observed in the gut. Profftella and Carsonella titers were significantly reduced in the bacteriome of CLas-exposed males compared with that of unexposed males, but this effect was not observed in females. In ovaries of CLas-exposed females, the Profftella and Carsonella titers were increased as compared to non-exposed females. CLas appeared to influence the overall levels of the symbionts but did not drastically perturb the overall microbial community structure. In all the assessed tissues, CLas titer in males was significantly higher than that of females using absolute quantification. These data provide a better understanding of multi-trophic interactions regulating symbiont dynamics in the HLB pathosystem.}, }
@article {pmid30474730, year = {2019}, author = {Lima, BP and Hu, LI and Vreeman, GW and Weibel, DB and Lux, R}, title = {The Oral Bacterium Fusobacterium nucleatum Binds Staphylococcus aureus and Alters Expression of the Staphylococcal Accessory Regulator sarA.}, journal = {Microbial ecology}, volume = {78}, number = {2}, pages = {336-347}, pmid = {30474730}, issn = {1432-184X}, support = {R01 DE021108/DE/NIDCR NIH HHS/United States ; DE021108/DE/NIDCR NIH HHS/United States ; DMR-1121288//National Science Foundation/ ; }, mesh = {Adhesins, Bacterial/genetics/metabolism ; Bacterial Proteins/*genetics/*metabolism ; Biofilms ; Fusobacterium nucleatum/genetics/*metabolism ; Humans ; *Microbiota ; Mouth/*microbiology ; Protein Binding ; Staphylococcus aureus/genetics/*metabolism ; Trans-Activators/*genetics/*metabolism ; }, abstract = {Staphylococcus aureus, an opportunistic pathogen member of the nasal and skin microbiota, can also be found in human oral samples and has been linked to infectious diseases of the oral cavity. As the nasal and oral cavities are anatomically connected, it is currently unclear whether S. aureus can colonize the oral cavity and become part of the oral microbiota, or if its presence in the oral cavity is simply transient. To start addressing this question, we assessed S. aureus ability to directly bind selected members of the oral microbiota as well as its ability to integrate into a human-derived complex oral microbial community in vitro. Our data show that S. aureus forms aggregates with Fusobacterium nucleatum and Porphyromonas gingivalis and that it can incorporate into the human-derived in vitro oral community. Further analysis of the F. nucleatum-S. aureus interaction revealed that the outer-membrane adhesin RadD is partially involved in aggregate formation and that the RadD-mediated interaction leads to an increase in expression of the staphylococcal global regulator gene sarA. Our findings lend support to the notion that S. aureus can become part of the complex microbiota of the human mouth, which could serve as a reservoir for S. aureus. Furthermore, direct interaction with key members of the oral microbiota could affect S. aureus pathogenicity contributing to the development of several S. aureus associated oral infections.}, }
@article {pmid30474350, year = {2019}, author = {Cox, TL and Gan, HM and Moreau, JW}, title = {Seawater recirculation through subducting sediments sustains a deeply buried population of sulfate-reducing bacteria.}, journal = {Geobiology}, volume = {17}, number = {2}, pages = {172-184}, doi = {10.1111/gbi.12324}, pmid = {30474350}, issn = {1472-4669}, mesh = {Bacteria/classification/*metabolism ; Geologic Sediments/*microbiology ; Oxidation-Reduction ; Pacific Ocean ; Phylogeny ; Seawater/*analysis ; Sequence Analysis, Protein ; Sulfates/*metabolism ; }, abstract = {Subseafloor sulfate concentrations typically decrease with depth as this electron acceptor is consumed by respiring microorganisms. However, studies show that seawater can flow through hydraulically conductive basalt to deliver sulfate upwards into deeply buried overlying sediments. Our previous work on IODP Site C0012A (Nankai Trough, Japan) revealed that recirculation of sulfate through the subducting Philippine Sea Plate stimulated microbial activity near the sediment-basement interface (SBI). Here, we describe the microbial ecology, phylogeny, and energetic requirements of population of aero-tolerant sulfate-reducing bacteria in the deep subseafloor. We identified dissimilatory sulfite reductase gene (dsr) sequences 93% related to oxygen-tolerant Desulfovibrionales species across all reaction zones while no SRB were detected in drilling fluid control samples. Pore fluid chemistry revealed low concentrations of methane (<0.25 mM), while hydrogen levels were consistent with active bacterial sulfate reduction (0.51-1.52 nM). Solid phase total organic carbon (TOC) was also considerably low in these subseafloor sediments. Our results reveal the phylogenetic diversity, potential function, and physiological tolerance of a community of sulfate-reducing bacteria living at ~480 m below subducting seafloor.}, }
@article {pmid30471620, year = {2018}, author = {Gutiérrez, S and Zwart, MP}, title = {Population bottlenecks in multicomponent viruses: first forays into the uncharted territory of genome-formula drift.}, journal = {Current opinion in virology}, volume = {33}, number = {}, pages = {184-190}, doi = {10.1016/j.coviro.2018.09.001}, pmid = {30471620}, issn = {1879-6265}, mesh = {*Evolution, Molecular ; Genetics, Population ; *Genome, Viral ; Viruses/*genetics/*growth &amp; development ; }, abstract = {Multicomponent viral systems face specific challenges when enduring population bottlenecks. These systems can lose coding information due to the lack of co-encapsidation of all the genetic information, at least in a proportion of the capsids in a population. Moreover, bottlenecks can also impact one of the main potential advantages of multicomponent systems: the regulation of gene expression through changes in gene copy frequencies at the population level. How these systems cope with population bottlenecks is far from being clear. Here, two non-exclusive scenarios are described. In the first scenario, population bottlenecks during host infection allow for the isolation of within-host populations with different gene frequencies, leaving the door opened for the selection of populations with adaptive gene frequencies. The second scenario postulates that viruses could influence bottleneck size, at least at certain steps of their life cycle, to limit random changes in gene frequencies. Examples of viral mechanism impacting bottleneck size at cell infection are available and, intriguingly, they can lead to either increases or reductions in bottleneck size. This situation opens the way for putative trade-offs on both gene frequencies and bottleneck sizes that could differ among multicomponent systems.}, }
@article {pmid30470844, year = {2019}, author = {Lizoňová, Z and Zhai, M and Bojková, J and Horsák, M}, title = {Small-scale Variation of Testate Amoeba Assemblages: the Effect of Site Heterogeneity and Empty Shell Inclusion.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {1014-1024}, pmid = {30470844}, issn = {1432-184X}, support = {P505/16-03881S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; }, mesh = {Bryophyta/growth &amp; development ; Czech Republic ; Lobosea/classification/*physiology ; *Microbiota ; Soil/*chemistry ; Wetlands ; }, abstract = {Studies on testate amoeba species distribution at small scales (i.e., single peatland sites) are rare and mostly focus on bogs or mineral-poor Sphagnum fens, leaving spatial patterns within mineral-rich fens completely unexplored. In this study, two mineral-rich fen sites of contrasting groundwater chemistry and moss layer composition were selected for the analysis of testate amoeba compositional variance within a single site. At each study site, samples from 20 randomly chosen moss-dominated plots were collected with several environmental variables being measured at each sampling spot. We also distinguished between empty shells and living individuals to evaluate the effect of empty shell inclusion on recorded species distribution. At the heterogeneous-rich Sphagnum-fen, a clear composition turnover in testate amoebae between Sphagnum-dominated and brown moss-dominated samples was closely related to water pH, temperature and redox potential. We also found notable species composition variance within the homogeneous calcareous fen, yet it was not as high as for the former site and the likely drivers of community assembly remained unidentified. The exclusion of empty shells provided more accurate data on species distribution as well as their relationship with some environmental variables, particularly moisture. Small-scale variability in species composition of communities seems to be a worthwhile aspect in testate amoeba research and should be considered in future sampling strategies along with a possible empty shell bias for more precise understanding of testate amoeba ecology and paleoecology.}, }
@article {pmid30469475, year = {2018}, author = {Chi, H and Yang, L and Yang, W and Li, Y and Chen, Z and Huang, L and Chao, Y and Qiu, R and Wang, S}, title = {Variation of the Bacterial Community in the Rhizoplane Iron Plaque of the Wetland Plant Typha latifolia.}, journal = {International journal of environmental research and public health}, volume = {15}, number = {12}, pages = {}, pmid = {30469475}, issn = {1660-4601}, mesh = {Bacteria/*isolation &amp; purification ; Environmental Monitoring ; Iron/*chemistry ; Plant Roots/*chemistry/*microbiology ; *Rhizosphere ; Soil Microbiology ; Soil Pollutants/*chemistry ; Typhaceae/*chemistry ; Wetlands ; }, abstract = {The survival of wetland plants in iron, sulfur and heavy metals-rich mine tailing ponds has been commonly attributed to the iron plaque (IP) on the root surface that acts as a protective barrier. However, the contribution of bacteria potentially regulates the iron-sulfur cycle and heavy metal exclusion at the root surface has not been studied in depth, particularly from a microbial ecology perspective. In this study, a pot experiment using Typha latifolia, a typical wetland plant, in non-polluted soil (NP) and tailing soil (T) was conducted. Samples from four zones, comprising non-rhizosphere soil (NR), rhizosphere soil (R) and internal (I) and external (E) layers of iron plaque, were collected from the NP and T and analyzed by 16S rRNA sequencing. Simpson index of the genus level showed greater diversities of bacterial community in the NP and its I zone is the most important part of the rhizosphere. PICRUSt predicted that the I zones in both NP and T harbored most of the functional genes. Specifically, functional genes related to sulfur relay and metabolism occurred more in the I zone in the T, whereas those related to iron acquisition and carbon and nitrogen circulation occurred more in the I zone in the NP. Analysis of dominant bacterial communities at genus level showed highest abundance of heavy metal resistant genus Burkholderia in the E zones in both soils, indicating that heavy metal resistance of Typha latifolia driven by Burkholderia mainly occurred at the external layer of IP. Moreover, many bacterial genera, such as Acidithiobacillus, Ferritrophicum, Thiomonas, Metallibacterium and Sideroxydans, involved in iron and sulfur metabolisms were found in the T and most showed higher abundance in the I zone than in the other zones. This work, as the first endeavor to separate the iron plaque into external and internal layers and investigate the variations of the bacterial communities therein, can provide an insight for further understanding the survival strategy of wetland plants, e.g., Typha latifolia, in extreme environment.}, }
@article {pmid30467715, year = {2019}, author = {Lemmel, F and Maunoury-Danger, F and Fanesi, A and Leyval, C and Cébron, A}, title = {Soil Properties and Multi-Pollution Affect Taxonomic and Functional Bacterial Diversity in a Range of French Soils Displaying an Anthropisation Gradient.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {993-1013}, pmid = {30467715}, issn = {1432-184X}, support = {ANR-13-JSV7-000701//Agence Nationale de la Recherche/ ; EC2CO- Biohefect/Ecodyn//Dril/MicrobiEen (EcobioS project)//Institut National des Sciences de l'Univers, Centre National de la Recherche Scientifique/ ; traitMic project//OSU-Otelo/ ; }, mesh = {Bacteria/*classification/drug effects ; *Carbon Cycle ; DNA, Bacterial/analysis ; France ; Industrial Waste ; *Microbiota ; RNA, Ribosomal, 16S/analysis ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants/*analysis ; }, abstract = {The intensive industrial activities of the twentieth century have left behind highly contaminated wasteland soils. It is well known that soil parameters and the presence of pollutants shape microbial communities. But in such industrial waste sites, the soil multi-contamination with organic (polycyclic aromatic hydrocarbons, PAH) and metallic (Zn, Pb, Cd) pollutants and long-term exposure may induce a selection pressure on microbial communities that may modify soil functioning. The aim of our study was to evaluate the impact of long-term multi-contamination and soil characteristics on bacterial taxonomic and functional diversity as related to the carbon cycle. We worked on 10 soils from northeast of France distributed into three groups (low anthropised controls, slag heaps, and settling ponds) based on their physico-chemical properties (texture, C, N) and pollution level. We assessed bacterial taxonomic diversity by 16S rDNA Illumina sequencing, and functional diversity using Biolog® and MicroResp™ microtiter plate tools. Although taxonomic diversity at the phylum level was not different among the soil groups, many operational taxonomic units were influenced by metal or PAH pollution, and by soil texture and total nitrogen content. Functional diversity was not influenced by PAH contamination while metal pollution selected microbial communities with reduced metabolic functional diversity but more tolerant to zinc. Limited microbial utilisation of carbon substrates in metal-polluted soils was mainly due to the nitrogen content. Based on these two observations, we hypothesised that reduced microbial activity and lower carbon cycle-related functional diversity may have contributed to the accumulation of organic matter in the soils that exhibited the highest levels of metal pollution.}, }
@article {pmid30467714, year = {2019}, author = {Ellison, S and Rovito, S and Parra-Olea, G and Vásquez-Almazán, C and Flechas, SV and Bi, K and Vredenburg, VT}, title = {The Influence of Habitat and Phylogeny on the Skin Microbiome of Amphibians in Guatemala and Mexico.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {257-267}, pmid = {30467714}, issn = {1432-184X}, support = {IOS-1258133//National Science Foundation/ ; 1633948//National Science Foundation/ ; DEB-1026396//National Science Foundation/ ; ICER-1633948//National Science Foundation/ ; CN-13-614//University of California Institute for Mexico and the United States/ ; }, mesh = {Amphibians/classification/*microbiology ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Guatemala ; Mexico ; *Microbiota ; *Phylogeny ; Skin/*microbiology ; }, abstract = {Microbial symbionts are increasingly recognized as playing a critical role in organismal health across a wide range of hosts. Amphibians are unique hosts in that their skin helps to regulate the exchange of water, ions, and gases, and it plays an active role in defense against pathogens through the synthesis of anti-microbial peptides. The microbiome of amphibian skin includes a diverse community of bacteria known to defend against pathogens, including the global pandemic lineage of Batrachochytrium dendrobatidis associated with mass amphibian die-offs. The relative influence of host phylogeny and environment in determining the composition of the amphibian skin microbiome remains poorly understood. We collected skin swabs from montane amphibians in Mexico and Guatemala, focusing on two genera of plethodontid salamanders and one genus of frogs. We used high throughput sequencing to characterize the skin bacterial microbiome and tested the impact of phylogeny and habitat on bacterial diversity. Our results show that phylogenetic history strongly influences the diversity and community structure of the total bacterial microbiome at higher taxonomic levels (between orders), but on lower scales (within genera and species), the effect of habitat predominates. These results add to a growing consensus that habitat exerts a strong effect on microbiome structure and composition, particularly at shallow phylogenetic scales.}, }
@article {pmid30467713, year = {2019}, author = {Ribière, C and Hegarty, C and Stephenson, H and Whelan, P and O'Toole, PW}, title = {Gut and Whole-Body Microbiota of the Honey Bee Separate Thriving and Non-thriving Hives.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {195-205}, pmid = {30467713}, issn = {1432-184X}, support = {SFI/12/RC/2273//Science Foundation Ireland/Ireland ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bees/*microbiology/*physiology ; Behavior, Animal ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; *Microbiota ; Phylogeny ; Pollination ; }, abstract = {The recent worldwide decline of honey bee colonies is a major ecological problem which also threatens pollinated crop production. Several interacting stressors such as environmental pressures and pathogens are suspected. Recently, the gut microbiota has emerged as a critical factor affecting bee health and fitness. We profiled the bacterial communities associated with the gut and whole body of worker bees to assess whether non-thriving colonies could be separated from thriving hives based on their microbial signature. The microbiota of thriving colonies was characterised by higher diversity and higher relative abundance of bacterial taxa involved in sugar degradation that were previously associated with healthy bees (e.g. Commensalibacter sp. and Bartonella apis). In contrast, the microbiota of non-thriving bees was depleted in health-associated species (e.g. Lactobacillus apis), and bacterial taxa associated with disease states (e.g. Gilliamella apicola) and pollen degradation (e.g. G. apicola and Bifidobacterium asteroides) were present in higher abundance compared to thriving colonies. Gut and whole-body microbiota shared a similar dominant core but their comparison showed differences in composition and relative abundance. More differences in taxon relative abundance between gut and whole body were observed in non-thriving bees, suggesting that microbiota associated with other bee organs might also be different. Thus, microbiota profiling could be used as a diagnostic tool in beekeeping practices to predict hive health and guide hive management.}, }
@article {pmid30467310, year = {2018}, author = {Pollock, FJ and McMinds, R and Smith, S and Bourne, DG and Willis, BL and Medina, M and Thurber, RV and Zaneveld, JR}, title = {Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4921}, pmid = {30467310}, issn = {2041-1723}, mesh = {Animals ; Anthozoa/classification/*genetics/*microbiology ; Archaea/classification/*genetics ; Australia ; Bacteria/classification/*genetics ; Coral Reefs ; DNA, Mitochondrial/genetics ; Geography ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Scleractinian corals' microbial symbionts influence host health, yet how coral microbiomes assembled over evolution is not well understood. We survey bacterial and archaeal communities in phylogenetically diverse Australian corals representing more than 425 million years of diversification. We show that coral microbiomes are anatomically compartmentalized in both modern microbial ecology and evolutionary assembly. Coral mucus, tissue, and skeleton microbiomes differ in microbial community composition, richness, and response to host vs. environmental drivers. We also find evidence of coral-microbe phylosymbiosis, in which coral microbiome composition and richness reflect coral phylogeny. Surprisingly, the coral skeleton represents the most biodiverse coral microbiome, and also shows the strongest evidence of phylosymbiosis. Interactions between bacterial and coral phylogeny significantly influence the abundance of four groups of bacteria-including Endozoicomonas-like bacteria, which divide into host-generalist and host-specific subclades. Together these results trace microbial symbiosis across anatomy during the evolution of a basal animal lineage.}, }
@article {pmid30465731, year = {2020}, author = {Beji, O and Adouani, N and Poncin, S and Hamdi, M and Li, HZ}, title = {Mineral pollutants removal through immobilized microalgae-bacterial flocs in a multitrophic microreactor.}, journal = {Environmental technology}, volume = {41}, number = {15}, pages = {1912-1922}, doi = {10.1080/09593330.2018.1551939}, pmid = {30465731}, issn = {1479-487X}, mesh = {Bacteria ; *Environmental Pollutants ; *Microalgae ; Minerals ; Wastewater ; }, abstract = {Microalgae-bacterial flocs (MaB-flocs) immobilization technique using polyvinyl alcohol (PVA) crosslinked with sodium alginate represent a novel approach for sustainable pollutants removal. The present work was performed to evaluate the performance of a multitrophic batch reactor at microscale for treating two synthetic wastewater solutions prepared with two different initial Chemical Oxygen Demand (COD): 200 mg.L[-1] and 450 mg.L[-1], respectively. Three MaB-flocs concentrations were entrapped into PVA-alginate beads: C1 (2%, v/v), C2 (5%, v/v) and C3 (10%, v/v), without O2 supply, during three periods 2, 4 and 6 days of batch incubation. PVA-alginate beads containing the highest concentration C3 of MaB-flocs improved the performance of the microreactor to remove significantly NH4[+] and PO4[3-] of about 61% and 82%, respectively, from wastewater more than two other concentrations used. This result confirms that C3 of MaB-flocs displays not only a good potential for nutrients removals but also the highest MaB-flocs morphological progression after 6 days of treatment with the highest COD of 450 mg.L[-1]. The feasibility of the PVA-alginate for cells immobilization, investigated through microscopy analysis, reveals that the evolution of multicellularity in MaB-flocs, for all experiments.}, }
@article {pmid30465068, year = {2019}, author = {Hubert, J and Nesvorna, M and Kopecky, J and Erban, T and Klimov, P}, title = {Population and Culture Age Influence the Microbiome Profiles of House Dust Mites.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {1048-1066}, pmid = {30465068}, issn = {1432-184X}, support = {17-12068S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; (No. 6.1933.2014/K Project Code 1933//Ministry of Education and Science of the Russian Federation/ ; No. 15-04-0s5185-a//the Russian Foundation for Basic Research/ ; }, mesh = {Animals ; *Bacteria/classification ; DNA Barcoding, Taxonomic ; *Fungi/classification ; *Microbiota ; Population Dynamics ; Pyroglyphidae/*microbiology/*physiology ; RNA, Bacterial/analysis ; RNA, Fungal/analysis ; RNA, Ribosomal, 16S/analysis ; RNA, Ribosomal, 18S/analysis ; Real-Time Polymerase Chain Reaction ; Species Specificity ; }, abstract = {Interactions with microorganisms might enable house dust mites (HDMs) to derive nutrients from difficult-to-digest structural proteins and to flourish in human houses. We tested this hypothesis by investigating the effects of changes in the mite culture growth and population of two HDM species on HDM microbiome composition and fitness. Growing cultures of laboratory and industrial allergen-producing populations of Dermatophagoides farinae (DFL and DFT, respectively) and Dermatophagoides pteronyssinus (DPL and DPT, respectively) were sampled at four time points. The symbiotic microorganisms of the mites were characterized by DNA barcode sequencing and quantified by qPCR using universal/specific primers. The population growth of mites and nutrient contents of mite bodies were measured and correlated with the changes in bacteria in the HDM microbiome. The results showed that both the population and culture age significantly influenced the microbiome profiles. Cardinium formed 93% and 32% of the total sequences of the DFL and DFT bacterial microbiomes, respectively, but this bacterial species was less abundant in the DPL and DPT microbiomes. Staphylococcus abundance was positively correlated with increased glycogen contents in the bodies of mites, and increased abundances of Aspergillus, Candida, and Kocuria were correlated with increased lipid contents in the bodies of mites. The xerophilic fungus Wallemia accounted for 39% of the fungal sequences in the DPL microbiome, but its abundance was low in the DPT, DFL, and DFT microbiomes. With respect to the mite culture age, we made three important observations: the mite population growth from young cultures was 5-8-fold higher than that from old cultures; specimens from old cultures had greater abundances of fungi and bacteria in their bodies; and yeasts predominated in the gut contents of specimens from young cultures, whereas filamentous mycelium prevailed in specimens from old cultures. Our results are consistent with the hypothesis that mites derive nutrients through associations with microorganisms.}, }
@article {pmid30460544, year = {2019}, author = {Koosha, M and Vatandoost, H and Karimian, F and Choubdar, N and Oshaghi, MA}, title = {Delivery of a Genetically Marked Serratia AS1 to Medically Important Arthropods for Use in RNAi and Paratransgenic Control Strategies.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {185-194}, pmid = {30460544}, issn = {1432-184X}, support = {30353//Tehran University of Medical Sciences and Health Services/ ; 33613//Tehran University of Medical Sciences and Health Services/ ; }, mesh = {Animals ; Arthropod Vectors/*microbiology/physiology ; Culicidae/*microbiology/physiology ; Female ; Ixodidae/*microbiology/physiology ; Larva/microbiology/physiology ; Male ; Pest Control, Biological/instrumentation/*methods ; Phlebotomus/*microbiology/physiology ; *RNA Interference ; Serratia/*genetics/physiology ; }, abstract = {Understanding how arthropod vectors acquire their bacteria is essential for implementation of paratransgenic and RNAi strategies using genetically modified bacteria to control vector-borne diseases. In this study, a genetically marked Serratia AS1 strain expressing the mCherry fluorescent protein (mCherry-Serratia) was used to test various acquisition routes in six arthropod vectors including Anopheles stephensi, Culex pipiens, Cx. quinquefaciatus, Cx. theileri, Phlebotomus papatasi, and Hyalomma dromedarii. Depending on the species, the bacteria were delivered to (i) mosquito larval breeding water, (ii) host skin, (iii) sugar bait, and (iv) males (paratransgenic). The arthropods were screened for the bacteria in their guts or other tissues. All the hematophagous arthropods were able to take the bacteria from the skin of their hosts while taking blood meal. The mosquitoes were able to take up the bacteria from the water at larval stages and to transfer them transstadially to adults and finally to transfer them to the water they laid eggs in. The mosquitoes were also able to acquire the bacteria from male sperm. The level of bacterial acquisition was influenced by blood feeding time and strategies (pool or vessel feeding), dipping in water and resting time of newly emerged adult mosquitoes, and the disseminated tissue/organ. Transstadial, vertical, and venereal bacterial acquisition would increase the sustainability of the modified bacteria in vector populations and decrease the need for supplementary release experiments whereas release of paratransgenic males that do not bite has fewer ethical issues. Furthermore, this study is required to determine if the modified bacteria can be introduced to arthropods in the same routes in nature.}, }
@article {pmid30459201, year = {2018}, author = {Hannigan, GD and Duhaime, MB and Ruffin, MT and Koumpouras, CC and Schloss, PD}, title = {Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, pmid = {30459201}, issn = {2150-7511}, support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; T32 AI007528/AI/NIAID NIH HHS/United States ; U01 CA086400/CA/NCI NIH HHS/United States ; }, mesh = {Bacteria/genetics/virology ; Bacteriophages/*genetics/isolation &amp; purification ; Cohort Studies ; Colorectal Neoplasms/*diagnosis/microbiology/*virology ; Feces/microbiology/virology ; Humans ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Viruses/*genetics ; }, abstract = {Human viruses (those that infect human cells) have been associated with many cancers, largely due to their mutagenic and functionally manipulative abilities. Despite this, cancer microbiome studies have focused almost exclusively on bacteria instead of viruses. We began evaluating the cancer virome by focusing on colorectal cancer, a primary cause of morbidity and mortality throughout the world and a cancer linked to altered colonic bacterial community compositions but with an unknown association with the gut virome. We used 16S rRNA gene, whole shotgun metagenomic, and purified virus metagenomic sequencing of stool to evaluate the differences in human colorectal cancer virus and bacterial community composition. Through random forest modeling, we identified differences in the healthy and colorectal cancer viromes. The cancer-associated virome consisted primarily of temperate bacteriophages that were also predicted to be bacterium-virus community network hubs. These results provide foundational evidence that bacteriophage communities are associated with colorectal cancer and potentially impact cancer progression by altering the bacterial host communities.IMPORTANCE Colorectal cancer is a leading cause of cancer-related death in the United States and worldwide. Its risk and severity have been linked to colonic bacterial community composition. Although human-specific viruses have been linked to other cancers and diseases, little is known about colorectal cancer virus communities. We addressed this knowledge gap by identifying differences in colonic virus communities in the stool of colorectal cancer patients and how they compared to bacterial community differences. The results suggested an indirect role for the virome in impacting colorectal cancer by modulating the associated bacterial community. These findings both support the idea of a biological role for viruses in colorectal cancer and provide a new understanding of basic colorectal cancer etiology.}, }
@article {pmid30456756, year = {2019}, author = {Jung, MY and Kang, MS and Lee, KE and Lee, EY and Park, SJ}, title = {Paraburkholderia dokdonella sp. nov., isolated from a plant from the genus Campanula.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {57}, number = {2}, pages = {107-112}, pmid = {30456756}, issn = {1976-3794}, mesh = {Bacterial Typing Techniques ; Base Composition ; Benzoquinones ; Burkholderiaceae/*classification/genetics/*isolation &amp; purification/physiology ; Campanulaceae/*microbiology ; DNA, Bacterial/analysis ; Fatty Acids/analysis ; Islands ; Nucleic Acid Hybridization ; Phosphatidylethanolamines/analysis ; Phosphatidylglycerols/analysis ; Phospholipids/analysis ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; Soil Microbiology ; Species Specificity ; Temperature ; Ubiquinone ; }, abstract = {The novel Gram-stain-negative, rod-shaped, aerobic bacterial strain DCR-13[T] was isolated from a native plant belonging to the genus Campanula on Dokdo, an island in the Republic of Korea. Comparative analysis of the 16S rRNA gene sequence indicated that this strain is closely related to Paraburkholderia peleae PP52-1[T] (98.43% 16S rRNA gene sequence similarity), Paraburkholderia oxyphila NBRC 105797[T] (98.42%), Paraburkholderia sacchari IPT 101[T] (98.28%), Paraburkholderia mimosarum NBRC 106338[T] (97.80%), Paraburkholderia denitrificans KIS30-44[T] (97.46%), and Paraburkholderia paradise WA[T] (97.45%). This analysis of the 16S rRNA gene sequence also suggested that DCR-13[T] and the six closely related strains formed a clade within the genus Paraburkholderia, but that DCR-13[T] was clearly separated from the established species. DCR-13[T] had ubiquinone 8 as its predominant respiratory quinone, and its genomic DNA G + C content was 63.9 mol%. The isolated strain grew at a pH of 6.0-8.0 (with an optimal pH of 6.5), 0-4% w/v NaCl (with an optimal level of 0%), and a temperature of 18-42°C (with an optimal temperature of 30°C). The predominant fatty acids were C16:0, summed feature 8 (C18:1ω7c/C18:1ω6c), C17:0 cyclo, C19:0 cyclo ω8c, summed feature 3 (C16:1ω6c/C16:1ω7c) and summed feature 2 (C12:0 aldehyde), and the major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. On the basis of polyphasic evidence, it is proposed that strain DCR-13[T] (= KCTC 62811[T] = LMG 30889[T]) represents the type strain of a novel species, Paraburkholderia dokdonella sp. nov.}, }
@article {pmid30455213, year = {2018}, author = {Daru, BH and Bowman, EA and Pfister, DH and Arnold, AE}, title = {A novel proof of concept for capturing the diversity of endophytic fungi preserved in herbarium specimens.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1763}, pages = {}, pmid = {30455213}, issn = {1471-2970}, mesh = {Endophytes/*classification/physiology ; Ericaceae/*microbiology ; Fungi/*classification/physiology ; Ledum/microbiology ; *Microbiota ; *Museums ; Specimen Handling/*methods ; }, abstract = {Herbarium specimens represent important records of morphological and genetic diversity of plants that inform questions relevant to global change, including species distributions, phenology and functional traits. It is increasingly appreciated that plant microbiomes can influence these aspects of plant biology, but little is known regarding the historic distribution of microbes associated with plants collected in the pre-molecular age. If microbiomes can be observed reliably in herbarium specimens, researchers will gain a new lens with which to examine microbial ecology, evolution, species interactions. Here, we describe a method for accessing historical plant microbiomes from preserved herbarium specimens, providing a proof of concept using two plant taxa from the imperiled boreal biome (Andromeda polifolia and Ledum palustre subsp. groenlandicum, Ericaceae). We focus on fungal endophytes, which occur within symptomless plant tissues such as leaves. Through a three-part approach (i.e. culturing, cloning and next-generation amplicon sequencing via the Illumina MiSeq platform, with extensive controls), we examined endophyte communities in dried, pressed leaves that had been processed as regular herbarium specimens and stored at room temperature in a herbarium for four years. We retrieved only one endophyte in culture, but cloning and especially the MiSeq analysis revealed a rich community of foliar endophytes. The phylogenetic distribution and diversity of endophyte assemblages, especially among the Ascomycota, resemble endophyte communities from fresh plants collected in the boreal biome. We could distinguish communities of endophytes in each plant species and differentiate likely endophytes from fungi that could be surface contaminants. Taxa found by cloning were observed in the larger MiSeq dataset, but species richness was greater when subsets of the same tissues were evaluated with the MiSeq approach. Our findings provide a proof of concept for capturing endophyte DNA from herbarium specimens, supporting the importance of herbarium records as roadmaps for understanding the dynamics of plant-associated microbial biodiversity in the Anthropocene.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.}, }
@article {pmid30453516, year = {2018}, author = {Sharma, L and Oliveira, I and Raimundo, F and Torres, L and Marques, G}, title = {Soil Chemical Properties Barely Perturb the Abundance of Entomopathogenic Fusarium oxysporum: A Case Study Using a Generalized Linear Mixed Model for Microbial Pathogen Occurrence Count Data.}, journal = {Pathogens (Basel, Switzerland)}, volume = {7}, number = {4}, pages = {}, pmid = {30453516}, issn = {2076-0817}, support = {UID/MULTI/04621/2013 ; UID/AGR/04033/2013 ; POCI-01-0145-FEDER-006958//National Funds by FCT - Portuguese Foundation for Science and Technology; EcoVitis project; FEDER/COMPETE/POCI - Operacional Competitiveness and Internationalization Programme/ ; }, abstract = {Fusarium oxysporum exhibits insect pathogenicity-however, generalized concerns of releasing phytopathogens within agroecosystems marred its entomopathogenicity-related investigations. In a previous study, soils were sampled from Douro vineyards and adjacent hedgerows. In this study, 80 of those soils were analyzed for their chemical properties and were subsequently co-related with the abundance of entomopathogenic F. oxysporum, after insect baiting of soils with Galleria mellonella and Tenebrio molitor larvae. The soil chemical properties studied were organic matter content; total organic carbon; total nitrogen; available potassium; available phosphorus; exchangeable cations, such as K[+], Na[+], Ca[2+], and Mg[2+]; pH; total acidity; degree of base saturation; and effective cation exchange capacity. Entomopathogenic F. oxysporum was found in 48 soils, i.e., 60% ± 5.47%, of the total soil samples. Out of the 1280 insect larvae used, 93, i.e., 7.26% ± 0.72%, were found dead by entomopathogenic F. oxysporum. Stepwise deletion of non-significant variables using a generalized linear model was followed by a generalized linear mixed model (GLMM). A higher C:N (logarithmized) (p < 0.001) and lower exchangeable K[+] (logarithmized) (p = 0.008) were found significant for higher fungal abundance. Overall, this study suggests that entomopathogenic F. oxysporum is robust with regard to agricultural changes, and GLMM is a useful statistical tool for count data in ecology.}, }
@article {pmid30451146, year = {2019}, author = {Matsuyama, M and Gomez-Arango, LF and Fukuma, NM and Morrison, M and Davies, PSW and Hill, RJ}, title = {Breastfeeding: a key modulator of gut microbiota characteristics in late infancy.}, journal = {Journal of developmental origins of health and disease}, volume = {10}, number = {2}, pages = {206-213}, doi = {10.1017/S2040174418000624}, pmid = {30451146}, issn = {2040-1752}, mesh = {Anti-Bacterial Agents/administration &amp; dosage ; Australia ; *Breast Feeding ; Cohort Studies ; DNA, Bacterial/isolation &amp; purification ; Feces/microbiology ; Female ; Firmicutes/genetics/isolation &amp; purification ; Gastrointestinal Microbiome/drug effects/*physiology ; Healthy Volunteers ; Humans ; Infant ; Male ; Milk, Human ; RNA, Ribosomal, 16S/genetics ; Time Factors ; Veillonella/genetics/isolation &amp; purification ; }, abstract = {The objective of this study was to investigate the impact of the most commonly cited factors that may have influenced infants' gut microbiota profiles at one year of age: mode of delivery, breastfeeding duration and antibiotic exposure. Barcoded V3/V4 amplicons of bacterial 16S-rRNA gene were prepared from the stool samples of 52 healthy 1-year-old Australian children and sequenced using the Illumina MiSeq platform. Following the quality checks, the data were processed using the Quantitative Insights Into Microbial Ecology pipeline and analysed using the Calypso package for microbiome data analysis. The stool microbiota profiles of children still breastfed were significantly different from that of children weaned earlier (P<0.05), independent of the age of solid food introduction. Among children still breastfed, Veillonella spp. abundance was higher. Children no longer breastfed possessed a more 'mature' microbiota, with notable increases of Firmicutes. The microbiota profiles of the children could not be differentiated by delivery mode or antibiotic exposure. Further analysis based on children's feeding patterns found children who were breastfed alongside solid food had significantly different microbiota profiles compared to that of children who were receiving both breastmilk and formula milk alongside solid food. This study provided evidence that breastfeeding continues to influence gut microbial community even at late infancy when these children are also consuming table foods. At this age, any impacts from mode of delivery or antibiotic exposure did not appear to be discernible imprints on the microbial community profiles of these healthy children.}, }
@article {pmid30450083, year = {2018}, author = {Meisner, A and de Boer, W}, title = {Strategies to Maintain Natural Biocontrol of Soil-Borne Crop Diseases During Severe Drought and Rainfall Events.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2279}, pmid = {30450083}, issn = {1664-302X}, abstract = {In many parts of the world, agricultural ecosystems are increasingly exposed to severe drought, and rainfall events due to climate changes. This coincides with a higher vulnerability of crops to soil-borne diseases, which is mostly ascribed to decreased resistance to pathogen attacks. However, loss of the natural capacity of soil microbes to suppress soil-borne plant pathogens may also contribute to increased disease outbreaks. In this perspectives paper, we will discuss the effect of extreme weather events on pathogen-antagonist interactions during drought and rainfall events and upon recovery. We will focus on diseases caused by root-infecting fungi and oomycetes. In addition, we will explore factors that affect restoration of the balance between pathogens and other soil microbes. Finally, we will indicate potential future avenues to improve the resistance and/or recovery of natural biocontrol during, and after water stresses. As such, our perspective paper will highlight a knowledge gap that needs to be bridged to adapt agricultural ecosystems to changing climate scenarios.}, }
@article {pmid30449244, year = {2019}, author = {Sterlin, D and Fieschi, C and Malphettes, M and Larsen, M and Gorochov, G and Fadlallah, J}, title = {Immune/microbial interface perturbation in human IgA deficiency.}, journal = {Gut microbes}, volume = {10}, number = {3}, pages = {429-433}, pmid = {30449244}, issn = {1949-0984}, mesh = {Bacteria/classification/genetics/immunology ; Biodiversity ; Common Variable Immunodeficiency/immunology/microbiology ; Gastrointestinal Microbiome/genetics/*immunology ; Humans ; IgA Deficiency/*immunology/*microbiology ; Immunoglobulin A/*immunology/metabolism ; Immunoglobulin M/immunology/metabolism ; }, abstract = {In a recently published article we report the metagenomic analysis of human gut microbiomes evolved in the absence of immunoglobulin A (IgA). We show that human IgA deficiency is not associated with massive quantitative perturbations of gut microbial ecology. While our study underlines a rather expected pathobiont expansion, we at the same time highlight a less expected depletion in some typically beneficial symbionts. We also show that IgM partially supply IgA deficiency, explaining the relatively mild clinical phenotype associated with the early steps of this condition. Microbiome studies in patients should consider potential issues such as cohort size, human genetic polymorphism and treatments. In this commentary, we discuss how such issues were taken into account in our own study.}, }
@article {pmid30448922, year = {2019}, author = {De Corte, D and Paredes, G and Yokokawa, T and Sintes, E and Herndl, GJ}, title = {Differential Response of Cafeteria roenbergensis to Different Bacterial and Archaeal Prey Characteristics.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {1-5}, pmid = {30448922}, issn = {1432-184X}, support = {268595/ERC_/European Research Council/International ; P 28781/FWF_/Austrian Science Fund FWF/Austria ; Z194-B17//Austrian Science Fund/ ; P16085//Japan Society for the Promotion of Science/ ; Z 194/FWF_/Austrian Science Fund FWF/Austria ; PIEF-GA-2011-299860//FP7 People: Marie-Curie Actions/ ; P28781-B21//Austrian Science Fund/ ; P27696-B22//Austrian Science Fund/ ; }, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Feeding Behavior ; Food Chain ; Heterotrophic Processes ; Seawater/microbiology/parasitology ; Stramenopiles/classification/growth &amp; development/*physiology ; }, abstract = {In the marine environment, the abundance of Bacteria and Archaea is either controlled bottom-up via nutrient availability or top-down via grazing. Heterotrophic nanoflagellates (HNF) are mainly responsible for prokaryotic grazing losses besides viral lysis. However, the grazing specificity of HNF on specific bacterial and archaeal taxa is under debate. Bacteria and Archaea might have different nutritive values and surface properties affecting the growth rates of HNF. In this study, we offered different bacterial and archaeal strains with different morphologic and physiologic characteristics to Cafeteria roenbergensis, one of the most abundant and ubiquitous species of HNF in the ocean. Two Nitrosopumilus maritimus-related strains isolated from the northern Adriatic Sea (Nitrosopumilus adriaticus, Nitrosopumilus piranensis), two Nitrosococcus strains, and two fast growing marine Bacteria (Pseudoalteromonas sp. and Marinobacter sp.) were fed to Cafeteria cultures. Cafeteria roenbergensis exhibited high growth rates when feeding on Pseudoalteromonas sp., Marinobacter sp., and Nitrosopumilus adriaticus, while the addition of the other strains resulted in minimal growth. Taken together, our data suggest that the differences in growth of Cafeteria roenbergensis associated to grazing on different thaumarchaeal and bacterial strains are likely due to the subtle metabolic, cell size, and physiological differences between different bacterial and thaumarchaeal taxa. Moreover, Nitrosopumilus adriaticus experienced a similar grazing pressure by Cafeteria roenbergensis as compared to the other strains, suggesting that other HNF may also prey on Archaea which might have important consequences on the global biogeochemical cycles.}, }
@article {pmid30447886, year = {2019}, author = {Maayer, P and Aliyu, H and Cowan, DA}, title = {Reorganising the order Bacillales through phylogenomics.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {2}, pages = {178-189}, doi = {10.1016/j.syapm.2018.10.007}, pmid = {30447886}, issn = {1618-0984}, mesh = {Bacillaceae/*classification ; DNA, Bacterial/genetics ; Genomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bacterial classification at higher taxonomic ranks such as the order and family levels is currently reliant on phylogenetic analysis of 16S rRNA and the presence of shared phenotypic characteristics. However, these may not be reflective of the true genotypic and phenotypic relationships of taxa. This is evident in the order Bacillales, members of which are defined as aerobic, spore-forming and rod-shaped bacteria. However, some taxa are anaerobic, asporogenic and coccoid. 16S rRNA gene phylogeny is also unable to elucidate the taxonomic positions of several families incertae sedis within this order. Whole genome-based phylogenetic approaches may provide a more accurate means to resolve higher taxonomic levels. A suite of phylogenomic approaches were applied to re-evaluate the taxonomy of 80 representative taxa of eight families (and six family incertae sedis taxa) within the order Bacillales. This showed several anomalies in the current family and order level classifications including the existence of four Bacillaceae and two Paenibacillaceae "family" clades. Furthermore, the families Staphylococcaceae and Listeriaceae belong to the sister order Lactobacillales. Finally, we propose a consensus phylogenomic approach which may diminish algorithmic biases associated with single approaches and facilitate more accurate classification of a broad range of taxa at the higher taxonomic levels.}, }
@article {pmid30446738, year = {2019}, author = {Fernandez, VI and Yawata, Y and Stocker, R}, title = {A Foraging Mandala for Aquatic Microorganisms.}, journal = {The ISME journal}, volume = {13}, number = {3}, pages = {563-575}, pmid = {30446738}, issn = {1751-7370}, mesh = {Adaptation, Physiological ; *Bacteria ; Bacterial Physiological Phenomena ; Ecosystem ; *Hydrobiology ; *Microbial Interactions ; Phytoplankton/*physiology ; }, abstract = {Aquatic environments harbor a great diversity of microorganisms, which interact with the same patchy, particulate, or diffuse resources by means of a broad array of physiological and behavioral adaptations, resulting in substantially different life histories and ecological success. To date, efforts to uncover and understand this diversity have not been matched by equivalent efforts to identify unifying frameworks that can provide a degree of generality and thus serve as a stepping stone to scale up microscale dynamics to predict their ecosystem-level consequences. In particular, evaluating the ecological consequences of different resource landscapes and of different microbial adaptations has remained a major challenge in aquatic microbial ecology. Here, inspired by Ramon Margalef's mandala for phytoplankton, we propose a foraging mandala for microorganisms in aquatic environments, which accounts for both the local environment and individual adaptations. This biophysical framework distills resource acquisition into two fundamental parameters: the search time for a new resource and the growth return obtained from encounter with a resource. We illustrate the foraging mandala by considering a broad range of microbial adaptations and environmental characteristics. The broad applicability of the foraging mandala suggests that it could be a useful framework to compare disparate microbial strategies in aquatic environments and to reduce the vast complexity of microbe-environment interactions into a minimal number of fundamental parameters.}, }
@article {pmid30446737, year = {2019}, author = {Rath, KM and Fierer, N and Murphy, DV and Rousk, J}, title = {Linking bacterial community composition to soil salinity along environmental gradients.}, journal = {The ISME journal}, volume = {13}, number = {3}, pages = {836-846}, pmid = {30446737}, issn = {1751-7370}, mesh = {Bacteria/*drug effects/growth &amp; development ; Bacterial Physiological Phenomena ; Dose-Response Relationship, Drug ; Environment ; Hydrogen-Ion Concentration ; Microbiota/*drug effects/physiology ; Phenotype ; Salinity ; Salt Tolerance ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Salinization is recognized as a threat to soil fertility worldwide. A challenge in understanding the effects of salinity on soil microbial communities is the fact that it can be difficult to disentangle the effects of salinity from those of other variables that may co-vary with salinity. Here we use a trait-based approach to identify direct effects of salinity on soil bacterial communities across two salinity gradients. Through dose-response relationships between salinity and bacterial growth, we quantified distributions of the trait salt tolerance within the communities. Community salt tolerance was closely correlated with soil salinity, indicating a strong filtering effect of salinity on the bacterial communities. Accompanying the increases in salt tolerance were consistent shifts in bacterial community composition. We identified specific bacterial taxa that increased in relative abundances with community salt tolerance, which could be used as bioindicators for high community salt tolerance. A strong filtering effect was also observed for pH across the gradients, with pH tolerance of bacterial communities correlated to soil pH. We propose phenotypic trait distributions aggregated at the community level as a useful approach to study the role of environmental factors as filters of microbial community composition.}, }
@article {pmid30445447, year = {2019}, author = {Philips, J and Monballyu, E and Georg, S and De Paepe, K and Prévoteau, A and Rabaey, K and Arends, JBA}, title = {An Acetobacterium strain isolated with metallic iron as electron donor enhances iron corrosion by a similar mechanism as Sporomusa sphaeroides.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {2}, pages = {}, doi = {10.1093/femsec/fiy222}, pmid = {30445447}, issn = {1574-6941}, mesh = {Acetobacterium/*isolation &amp; purification/*metabolism ; Corrosion ; Electron Transport/*physiology ; Electrons ; Firmicutes/metabolism ; Hydrogen ; Iron/*metabolism ; }, abstract = {Sporomusa sphaeroides related strains are to date the only homoacetogens known to increase metallic iron corrosion. The goal of this work was to isolate additional homoacetogenic bacteria capable of using Fe(0) as electron donor and to explore their extracellular electron transfer mechanism. Enrichments were started from anoxic corrosion products and yielded Acetobacterium as main homoacetogenic genus. Isolations were performed with a new procedure using plates with a Fe(0) powder top layer. An Acetobacterium strain, closely related to A. malicum and A. wieringae, was isolated, in addition to a S. sphaeroides strain. The Acetobacterium isolate significantly increased Fe(0) corrosion ((1.44 ± 0.16)-fold) compared to abiotic controls. The increase of corrosion by type strains ranged from (1.28 ± 0.13)-fold for A. woodii to (2.03 ± 0.22)-fold for S. sphaeroides. Hydrogen mediated the electron uptake from Fe(0) by the acetogenic isolates and tested type strains. Exchange of the medium and SEM imaging suggested that cells were attached to Fe(0). The corrosion enhancement mechanism is for all tested strains likely related to free extracellular components catalyzing hydrogen formation on the Fe(0) surface, or to the maintenance of low hydrogen concentrations on the Fe(0) surface by attached cells thereby thermodynamically favoring hydrogen formation.}, }
@article {pmid30443991, year = {2019}, author = {Schneider, S and Schintlmeister, A and Becana, M and Wagner, M and Woebken, D and Wienkoop, S}, title = {Sulfate is transported at significant rates through the symbiosome membrane and is crucial for nitrogenase biosynthesis.}, journal = {Plant, cell &amp; environment}, volume = {42}, number = {4}, pages = {1180-1189}, pmid = {30443991}, issn = {1365-3040}, support = {W 1257-820/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Gas Chromatography-Mass Spectrometry ; Lotus/metabolism ; Membrane Transport Proteins/*metabolism ; Microscopy, Electron, Transmission ; Nitrogenase/*biosynthesis ; Reverse Transcriptase Polymerase Chain Reaction ; Rhizobiaceae/metabolism ; Root Nodules, Plant/metabolism/ultrastructure ; Sulfates/*metabolism ; Symbiosis ; }, abstract = {Legume-rhizobia symbioses play a major role in food production for an ever growing human population. In this symbiosis, dinitrogen is reduced ("fixed") to ammonia by the rhizobial nitrogenase enzyme complex and is secreted to the plant host cells, whereas dicarboxylic acids derived from photosynthetically produced sucrose are transported into the symbiosomes and serve as respiratory substrates for the bacteroids. The symbiosome membrane contains high levels of SST1 protein, a sulfate transporter. Sulfate is an essential nutrient for all living organisms, but its importance for symbiotic nitrogen fixation and nodule metabolism has long been underestimated. Using chemical imaging, we demonstrate that the bacteroids take up 20-fold more sulfate than the nodule host cells. Furthermore, we show that nitrogenase biosynthesis relies on high levels of imported sulfate, making sulfur as essential as carbon for the regulation and functioning of symbiotic nitrogen fixation. Our findings thus establish the importance of sulfate and its active transport for the plant-microbe interaction that is most relevant for agriculture and soil fertility.}, }
@article {pmid30443603, year = {2018}, author = {Paver, SF and Muratore, D and Newton, RJ and Coleman, ML}, title = {Reevaluating the Salty Divide: Phylogenetic Specificity of Transitions between Marine and Freshwater Systems.}, journal = {mSystems}, volume = {3}, number = {6}, pages = {}, pmid = {30443603}, issn = {2379-5077}, abstract = {Marine and freshwater microbial communities are phylogenetically distinct, and transitions between habitat types are thought to be infrequent. We compared the phylogenetic diversity of marine and freshwater microorganisms and identified specific lineages exhibiting notably high or low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA gene tag-sequencing data sets. As expected, marine and freshwater microbial communities differed in the relative abundance of major phyla and contained habitat-specific lineages. At the same time, and contrary to expectations, many shared taxa were observed in both habitats. Based on several metrics, we found that Gammaproteobacteria, Alphaproteobacteria, Bacteroidetes, and Betaproteobacteria contained the highest number of closely related marine and freshwater sequences, suggesting comparatively recent habitat transitions in these groups. Using the abundant alphaproteobacterial group SAR11 as an example, we found evidence that new lineages, beyond the recognized LD12 clade, are detected in freshwater at low but reproducible abundances; this evidence extends beyond the 16S rRNA locus to core genes throughout the genome. Our results suggest that shared taxa are numerous, but tend to occur sporadically and at low relative abundance in one habitat type, leading to an underestimation of transition frequency between marine and freshwater habitats. Rare taxa with abundances near or below detection, including lineages that appear to have crossed the salty divide relatively recently, may possess adaptations enabling them to exploit opportunities for niche expansion when environments are disturbed or conditions change. IMPORTANCE The distribution of microbial diversity across environments yields insight into processes that create and maintain this diversity as well as potential to infer how communities will respond to future environmental changes. We integrated data sets from dozens of freshwater lake and marine samples to compare diversity across open water habitats differing in salinity. Our novel combination of sequence-based approaches revealed lineages that likely experienced a recent transition across habitat types. These taxa are promising targets for studying physiological constraints on salinity tolerance. Our findings contribute to understanding the ecological and evolutionary controls on microbial distributions, and open up new questions regarding the plasticity and adaptability of particular lineages.}, }
@article {pmid30442907, year = {2019}, author = {Zhou, W and Chow, KH and Fleming, E and Oh, J}, title = {Selective colonization ability of human fecal microbes in different mouse gut environments.}, journal = {The ISME journal}, volume = {13}, number = {3}, pages = {805-823}, pmid = {30442907}, issn = {1751-7370}, support = {DP2 GM126893/GM/NIGMS NIH HHS/United States ; K22 AI119231/AI/NIAID NIH HHS/United States ; 1 DP2 GM126893-01//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/International ; }, mesh = {Animals ; Bacteroides/growth &amp; development/*physiology ; Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Genotype ; Humans ; *Metagenomics ; Mice ; Mice, Inbred C57BL ; }, abstract = {Mammalian hosts constantly interact with diverse exogenous microbes, but only a subset of the microbes manage to colonize due to selective colonization resistance exerted by host genetic factors as well as the native microbiota of the host. An important question in microbial ecology and medical science is if such colonization resistance can discriminate closely related microbial species, or even closely related strains of the same species. Using human-mouse fecal microbiota transplantation and metagenomic shotgun sequencing, we reconstructed colonization patterns of human fecal microbes in mice with different genotypes (C57BL6/J vs. NSG) and with or without an intact gut microbiota. We found that mouse genotypes and the native mouse gut microbiota both exerted different selective pressures on exogenous colonizers: human fecal Bacteroides successfully established in the mice gut, however, different species of Bacteroides selectively enriched under different gut conditions, potentially due to a multitude of functional differences, ranging from versatility in nutrient acquisition to stress responses. Additionally, different clades of Bacteroides cellulosilyticus strains were selectively enriched in different gut conditions, suggesting that the fitness of conspecific microbial strains in a novel host environment could differ.}, }
@article {pmid30442070, year = {2019}, author = {Barnett, JA and Gibson, DL}, title = {H2Oh No! The importance of reporting your water source in your in vivo microbiome studies.}, journal = {Gut microbes}, volume = {10}, number = {3}, pages = {261-269}, pmid = {30442070}, issn = {1949-0984}, mesh = {Animals ; Drinking Water/adverse effects/chemistry/*standards ; Gastrointestinal Microbiome/drug effects/*physiology ; Hydrogen-Ion Concentration ; Mice ; Models, Animal ; Reproducibility of Results ; Research Report/*standards ; Water/*standards ; Water Purification ; }, abstract = {Water is a fundamental part of any in vivo microbiome experiment however, it is also one of the most overlooked and underreported variables within the literature. Currently there is no established standard for drinking water quality set by the Canadian Council on Animal Care. Most water treatment methods focus on inhibiting bacterial growth within the water while prolonging the shelf-life of bottles once poured. When reviewing the literature, it is clear that some water treatment methods, such as water acidification, alter the gut microbiome of experimental animals resulting in dramatic differences in disease phenotype progression. Furthermore, The Jackson Lab, one of the world's leading animal vendors, provides acidified water to their in-house animals and is often cited in the literature as having a dramatically different gut microbiome than animals acquired from either Charles River or Taconic. While we recognize that it is impossible to standardize water across all animal facilities currently conducting microbiome research, we hope that by drawing attention to the issue in this commentary, researchers will consider water source as an experimental variable and report their own water sources to facilitate experimental reproducibility. Moreover, researchers should be cognisant of potential phenotypic differences observed between commercial animal vendors due to changes in the gut microbiome as a result of various sources of water used.}, }
@article {pmid30430196, year = {2019}, author = {Wynants, E and Frooninckx, L and Crauwels, S and Verreth, C and De Smet, J and Sandrock, C and Wohlfahrt, J and Van Schelt, J and Depraetere, S and Lievens, B and Van Miert, S and Claes, J and Van Campenhout, L}, title = {Assessing the Microbiota of Black Soldier Fly Larvae (Hermetia illucens) Reared on Organic Waste Streams on Four Different Locations at Laboratory and Large Scale.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {913-930}, pmid = {30430196}, issn = {1432-184X}, support = {RT 15/9 EDINCO//FOD Volksgezondheid, Veiligheid van de Voedselketen en Leefmilieu/ ; }, mesh = {Animal Feed/analysis/*microbiology ; Animals ; Belgium ; Diptera/growth &amp; development/*microbiology ; Larva/growth &amp; development/microbiology ; *Microbiota ; Solid Waste ; }, abstract = {This study aimed to gain insight into the microbial quality, safety and bacterial community composition of black soldier fly larvae (Hermetia illucens) reared at different facilities on a variety of organic waste streams. For seven rearing cycles, both on laboratory-scale and in large-scale facilities at several locations, the microbiota of the larvae was studied. Also samples of the substrate used and the residue (= leftover substrate after rearing, existing of non-consumed substrate, exuviae and faeces) were investigated. Depending on the sample, it was subjected to plate counting, Illumina Miseq sequencing and/or detection of specific food pathogens. The results revealed that the substrates applied at the various locations differed substantially in microbial numbers as well as in the bacterial community composition. Furthermore, little similarity was observed between the microbiota of the substrate and that of the larvae reared on that substrate. Despite substantial differences between the microbiota of larvae reared at several locations, 48 species-level operational taxonomic units (OTUs) were shared by all larvae, among which most belonged to the phyla Firmicutes and Proteobacteria. Although the substrate is assumed to be an important source of bacteria, our results suggest that a variety of supposedly interacting factors-both abiotic and biotic-are likely to affect the microbiota in the larvae. In some larvae and/or residue samples, potential foodborne pathogens such as Salmonella and Bacillus cereus were detected, emphasising that decontamination technologies are required when the larvae are used in feed, just as for other feed ingredients, or eventually in food.}, }
@article {pmid30429840, year = {2018}, author = {Mas-Carrió, E and Dini-Andreote, F and Brossi, MJL and Salles, JF and Olff, H}, title = {Organic Amendment Under Increasing Agricultural Intensification: Effects on Soil Bacterial Communities and Plant Productivity.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2612}, pmid = {30429840}, issn = {1664-302X}, abstract = {The soil microbiome is a complex living network that plays essential roles in agricultural systems, regardless of the level of intensification. However, the effects of agricultural management on the soil microbiome and the association with plant productivity remain largely unclear. Here, we studied the responses of three soil systems displaying distinct levels of agriculture intensiveness (i.e., natural, organic, and conventional soil management regimes) to experimentally manipulated organic farming amendments (i.e., dung and earthworms). We aimed at (i) identifying the effect on plant productivity and (ii) elucidating the degree of shifts in bacterial communities in response to the applied organic amendments. We found plant productivity to be lower with increasing agricultural intensification. Bacterial communities shifted distinctively for each soil management regime to the organic amendments applied. In brief, greater changes were observed in the Conventional management comparatively to the Organic and Natural management, an effect largely driven by dung addition. Moreover, we found evidence that the level of agricultural intensiveness also affects the timespan for these shifts. For instance, while the Natural system reached a relatively stable community composition before the end of the experiment, treatments on the conventional soil management regime did not. Random forest analyses further revealed an increasing impact of introduced taxa from dung addition aligned with increasing agricultural intensification. These analyses suggested that earthworms regulate the introduction of species from dung into the soil bacterial community. Collectively, our results contribute to a better understanding of the outcomes of organic amendments on soils under distinct levels of agriculture intensiveness, with implications for further development in soil restorations practices.}, }
@article {pmid30429832, year = {2018}, author = {Bruno, A and Sandionigi, A and Bernasconi, M and Panio, A and Labra, M and Casiraghi, M}, title = {Changes in the Drinking Water Microbiome: Effects of Water Treatments Along the Flow of Two Drinking Water Treatment Plants in a Urbanized Area, Milan (Italy).}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2557}, pmid = {30429832}, issn = {1664-302X}, abstract = {While safe and of high quality, drinking water can host an astounding biodiversity of microorganisms, dismantling the belief of its "biological simplicity." During the very few years, we are witnessing an exponential growth in scientific publications, exploring the ecology hidden in drinking water treatment plants (DWTPs) and drinking water distribution system (DWDS). We focused on what happens to the microbial communities from source water (groundwater) throughout the main steps of the potabilization process of a DWTP, located in an urbanized area in Northern Italy. Samples were processed by a stringent water filtration to retain even the smallest environmental bacteria and then analyzed with High-Throughput DNA Sequencing (HTS) techniques. We showed that carbon filters harbored a microbial community seeding and shaping water microbiota downstream, introducing a significant variation on incoming (groundwater) microbial community. Chlorination did not instantly affect the altered microbiota. We were also able to correctly predict (through machine learning analysis) samples belonging to groundwater (overall accuracy was 0.71), but the assignation was not reliable with carbon filter samples, which were incorrectly predicted as chlorination samples. The presence and abundance of specific microorganisms allowed us to hypothesize their role as indicators. In particular, Candidatus Adlerbacteria (Parcubacteria), together with microorganisms belonging to Alphaproteobacteria and Gammaproteobacteria, characterized treated water, but not raw water. An exception, confirming our hypothesis, is given by the samples downstream the filters renewal, which had a composition resembling groundwater. Volatility analysis illustrated how carbon filters represented an ecosystem that is stable over time, probably bearing the environmental conditions that promote the survival and growth of this peculiar microbial community.}, }
@article {pmid30429514, year = {2018}, author = {De Vrieze, J and Ijaz, UZ and Saunders, AM and Theuerl, S}, title = {Terminal restriction fragment length polymorphism is an "old school" reliable technique for swift microbial community screening in anaerobic digestion.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16818}, pmid = {30429514}, issn = {2045-2322}, mesh = {*Anaerobiosis ; Archaea/isolation &amp; purification/metabolism ; Bacteria/isolation &amp; purification/metabolism ; Hydrogen-Ion Concentration ; *Microbiota ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/*analysis ; Temperature ; Waste Management/*methods/standards ; }, abstract = {The microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades. In the last decade, high-throughput 16S rRNA gene amplicon sequencing has replaced these techniques, but the time-consuming and complex nature of high-throughput techniques is a potential bottleneck for full-scale anaerobic digestion application, when monitoring community dynamics. Here, the bacterial and archaeal TRFLP profiles were compared with 16S rRNA gene amplicon profiles (Illumina platform) of 25 full-scale anaerobic digestion plants. The α-diversity analysis revealed a higher richness based on Illumina data, compared with the TRFLP data. This coincided with a clear difference in community organisation, Pareto distribution, and co-occurrence network statistics, i.e., betweenness centrality and normalised degree. The β-diversity analysis showed a similar clustering profile for the Illumina, bacterial TRFLP and archaeal TRFLP data, based on different distance measures and independent of phylogenetic identification, with pH and temperature as the two key operational parameters determining microbial community composition. The combined knowledge of temporal dynamics and projected clustering in the β-diversity profile, based on the TRFLP data, distinctly showed that TRFLP is a reliable technique for swift microbial community dynamics screening in full-scale anaerobic digestion plants.}, }
@article {pmid30427665, year = {2018}, author = {Dang, H and Kanitkar, YH and Stedtfeld, RD and Hatzinger, PB and Hashsham, SA and Cupples, AM}, title = {Abundance of Chlorinated Solvent and 1,4-Dioxane Degrading Microorganisms at Five Chlorinated Solvent Contaminated Sites Determined via Shotgun Sequencing.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {23}, pages = {13914-13924}, doi = {10.1021/acs.est.8b04895}, pmid = {30427665}, issn = {1520-5851}, mesh = {Biodegradation, Environmental ; *Chloroflexi ; Dioxanes ; *Groundwater ; Solvents ; *Water Pollutants, Chemical ; }, abstract = {Shotgun sequencing was used for the quantification of taxonomic and functional biomarkers associated with chlorinated solvent bioremediation in 20 groundwater samples (five sites), following bioaugmentation with SDC-9. The analysis determined the abundance of (1) genera associated with chlorinated solvent degradation, (2) reductive dehalogenase (RDases) genes, (3) genes associated with 1,4-dioxane removal, (4) genes associated with aerobic chlorinated solvent degradation, and (5) D. mccartyi genes associated with hydrogen and corrinoid metabolism. The taxonomic analysis revealed numerous genera previously linked to chlorinated solvent degradation, including Dehalococcoides, Desulfitobacterium, and Dehalogenimonas. The functional gene analysis indicated vcrA and tceA from D. mccartyi were the RDases with the highest relative abundance. Reads aligning with both aerobic and anaerobic biomarkers were observed across all sites. Aerobic solvent degradation genes, etnC or etnE, were detected in at least one sample from each site, as were pmoA and mmoX. The most abundant 1,4-dioxane biomarker detected was Methylosinus trichosporium OB3b mmoX. Reads aligning to thmA or Pseudonocardia were not found. The work illustrates the importance of shotgun sequencing to provide a more complete picture of the functional abilities of microbial communities. The approach is advantageous over current methods because an unlimited number of functional genes can be quantified.}, }
@article {pmid30426401, year = {2019}, author = {Ver Heul, A and Planer, J and Kau, AL}, title = {The Human Microbiota and Asthma.}, journal = {Clinical reviews in allergy &amp; immunology}, volume = {57}, number = {3}, pages = {350-363}, pmid = {30426401}, issn = {1559-0267}, support = {K08 AI113184/AI/NIAID NIH HHS/United States ; T32 DK077653/DK/NIDDK NIH HHS/United States ; 5T32DK077653-27/DK/NIDDK NIH HHS/United States ; }, mesh = {Allergens/immunology ; Asthma/*etiology/metabolism/therapy ; Disease Management ; *Disease Susceptibility ; Environmental Exposure/adverse effects ; Gastrointestinal Microbiome/immunology ; Humans ; *Microbiota/immunology ; Respiratory Mucosa/immunology/metabolism/microbiology ; }, abstract = {Over the last few decades, advances in our understanding of microbial ecology have allowed us to appreciate the important role of microbial communities in maintaining human health. While much of this research has focused on gut microbes, microbial communities in other body sites and from the environment are increasingly recognized in human disease. Here, we discuss recent advances in our understanding of host-microbiota interactions in the development and manifestation of asthma focusing on three distinct microbial compartments. First, environmental microbes originating from house dust, pets, and farm animals have been linked to asthma pathogenesis, which is often connected to their production of bioactive molecules such as lipopolysaccharide. Second, respiratory microbial communities, including newly appreciated populations of microbes in the lung have been associated with allergic airway inflammation. Current evidence suggests that the presence of particular microbes, especially Streptococcus, Haemophilus, and Morexella species within the airway may shape local immune responses and alter the severity and manifestations of airway inflammation. Third, the gut microbiota has been implicated in both experimental models and clinical studies in predisposing to asthma. There appears to be a "critical window" of colonization that occurs during early infancy in which gut microbial communities shape immune maturation and confer susceptibility to allergic airway inflammation. The mechanisms by which gut microbial communities influence lung immune responses and physiology, the "gut-lung axis," are still being defined but include the altered differentiation of immune cell populations important in asthma and the local production of metabolites that affect distal sites. Together, these findings suggest an intimate association of microbial communities with host immune development and the development of allergic airway inflammation. Improved understanding of these relationships raises the possibility of microbiota-directed therapies to improve or prevent asthma.}, }
@article {pmid30425147, year = {2018}, author = {Su, X and Jing, G and McDonald, D and Wang, H and Wang, Z and Gonzalez, A and Sun, Z and Huang, S and Navas, J and Knight, R and Xu, J}, title = {Identifying and Predicting Novelty in Microbiome Studies.}, journal = {mBio}, volume = {9}, number = {6}, pages = {}, pmid = {30425147}, issn = {2150-7511}, mesh = {*Computational Biology ; *Databases, Factual ; Humans ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {With the expansion of microbiome sequencing globally, a key challenge is to relate new microbiome samples to the existing space of microbiome samples. Here, we present Microbiome Search Engine (MSE), which enables the rapid search of query microbiome samples against a large, well-curated reference microbiome database organized by taxonomic similarity at the whole-microbiome level. Tracking the microbiome novelty score (MNS) over 8 years of microbiome depositions based on searching in more than 100,000 global 16S rRNA gene amplicon samples, we detected that the structural novelty of human microbiomes is approaching saturation and likely bounded, whereas that in environmental habitats remains 5 times higher. Via the microbiome focus index (MFI), which is derived from the MNS and microbiome attention score (MAS), we objectively track and compare the structural-novelty and attracted-attention scores of individual microbiome samples and projects, and we predict future trends in the field. For example, marine and indoor environments and mother-baby interactions are likely to receive disproportionate additional attention based on recent trends. Therefore, MNS, MAS, and MFI are proposed "alt-metrics" for evaluating a microbiome project or prospective developments in the microbiome field, both of which are done in the context of existing microbiome big data.IMPORTANCE We introduce two concepts to quantify the novelty of a microbiome. The first, the microbiome novelty score (MNS), allows identification of microbiomes that are especially different from what is already sequenced. The second, the microbiome attention score (MAS), allows identification of microbiomes that have many close neighbors, implying that considerable scientific attention is devoted to their study. By computing a microbiome focus index based on the MNS and MAS, we objectively track and compare the novelty and attention scores of individual microbiome samples and projects over time and predict future trends in the field; i.e., we work toward yielding fundamentally new microbiomes rather than filling in the details. Therefore, MNS, MAS, and MFI can serve as "alt-metrics" for evaluating a microbiome project or prospective developments in the microbiome field, both of which are done in the context of existing microbiome big data.}, }
@article {pmid30423502, year = {2019}, author = {Ntagia, E and Fiset, E and da Silva Lima, L and Pikaar, I and Zhang, X and Jeremiasse, AW and Prévoteau, A and Rabaey, K}, title = {Anode materials for sulfide oxidation in alkaline wastewater: An activity and stability performance comparison.}, journal = {Water research}, volume = {149}, number = {}, pages = {111-119}, doi = {10.1016/j.watres.2018.11.004}, pmid = {30423502}, issn = {1879-2448}, mesh = {Electrodes ; Oxidation-Reduction ; Oxides ; *Sulfides ; *Wastewater ; }, abstract = {Electrochemical sulfide removal can be attractive as a zero-chemical-input approach for treatment of waste streams such as spent caustics coupled to caustic recovery. A key concern is possible decline in catalytic activity, due to passivation from deposited elemental sulfur (S[0]) on the anode surface and stability limitation, due to sulfide oxidation under highly alkaline conditions. In this study, six commercially available electrode materials (Ir Mixed Metal Oxide (MMO), Ru MMO, Pt/IrOx, Pt, PbOx and TiO2/IrTaO2 coated titanium-based electrodes) were tested to investigate the impact of the electrocatalyst on the process efficiency in terms of sulfide removal and final product of sulfide oxidation, as well as to determine the stability of the electrocatalyst under high sulfide concentrations (50 mM Na2S) and high alkalinity (pH > 12). Short-term experiments showed that the catalyst type impacts the anode potential and the sulfide oxidation reaction products. Longer-term experiments under current densities up to 200 A m[-2] showed a high differentiation in stability performance among the catalysts. Ru MMO was the most active towards sulfide oxidation with a coulombic efficiency of 63.2 ± 0.5% at an average anode potential of 0.92 ± 0.17 V vs SHE. Ir MMO was the most stable, preserving 100% of its original catalyst loading during the tests. The results demonstrated that Ru MMO and Ir MMO were the most suitable electrode materials for sulfide oxidation under highly alkaline conditions, while the need for establishing a good trade-off between activity, stability and cost still persists.}, }
@article {pmid30423115, year = {2018}, author = {Romano, S and Ansorge, R}, title = {Scientific communication strategies of microbiologists in the era of social media.}, journal = {FEMS microbiology letters}, volume = {365}, number = {23}, pages = {}, doi = {10.1093/femsle/fny264}, pmid = {30423115}, issn = {1574-6968}, mesh = {Biomedical Research/*methods ; Humans ; Interviews as Topic ; *Microbiology ; Preprints as Topic ; Research Personnel/*psychology ; Scholarly Communication/*statistics &amp; numerical data ; Social Media/*statistics &amp; numerical data ; }, abstract = {Over the last decades, the world of communication underwent drastic changes, and internet and social media emerged as essential vehicles for exchanging information. Following these trends, it is important that scientists adapt to changes and adopt optimal strategies to communicate with colleagues, lay people and institutions. We conducted an online survey to investigate the communication strategies of microbiologists and their colleagues from other disciplines. We collected data from 527 scholars from 57 countries, with ∼42% of them being microbiologists. We focused particularly on social media and found that >80% of participants used them for work, and that ∼50% of interviewed actively shared and gathered scientific contents from social media. Compared to colleagues from other fields, microbiologists were less averse to use social media for work and were also less accustomed to use pre-prints as a source and vehicle of information. However, a large proportion of microbiologists declared to have planned pre-print publications in the future. Surprisingly, our data revealed that age is a poor predictor of social media usage, but it is strongly associated with the type of social media used, the activity undertaken on them and the attitude towards pre-print publications. Considering the kaleidoscopic variety of scientific communication tools, our data might help to optimize the scientific promotion strategies among microbiologists.}, }
@article {pmid30421114, year = {2019}, author = {Chung, YA and Jumpponen, A and Rudgers, JA}, title = {Divergence in Diversity and Composition of Root-Associated Fungi Between Greenhouse and Field Studies in a Semiarid Grassland.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {122-135}, pmid = {30421114}, issn = {1432-184X}, support = {1601210//Division of Environmental Biology/ ; 1456955//Division of Environmental Biology/ ; 1748133//National Science Foundation/ ; 1440478//National Science Foundation/ ; }, mesh = {*Biodiversity ; Crop Production/*instrumentation ; Fungi/classification/genetics/*isolation &amp; purification ; Grassland ; Mycobiome ; Plant Roots/*microbiology ; Poaceae/microbiology ; Soil Microbiology ; Species Specificity ; }, abstract = {Investigations of plant-soil feedbacks (PSF) and plant-microbe interactions often rely exclusively on greenhouse experiments, yet we have little understanding of how, and when, results can be extrapolated to explain phenomena in nature. A systematic comparison of microbial communities using the same host species across study environments can inform the generalizability of such experiments. We used Illumina MiSeq sequencing to characterize the root-associated fungi of two foundation grasses from a greenhouse PSF experiment, a field PSF experiment, field monoculture stands, and naturally occurring resident plants in the field. A core community consisting < 10% of total fungal OTU richness but > 50% of total sequence abundance occurred in plants from all study types, demonstrating the ability of field and greenhouse experiments to capture the dominant component of natural communities. Fungal communities were plant species-specific across the study types, with the core community showing stronger host specificity than peripheral taxa. Roots from the greenhouse and field PSF experiments had lower among sample variability in community composition and higher diversity than those from naturally occurring, or planted monoculture plants from the field. Core and total fungal composition differed substantially across study types, and dissimilarity between fungal communities did not predict plant-soil feedbacks measured in experiments. These results suggest that rhizobiome assembly mechanisms in nature differ from the dynamics of short-term, inoculation studies. Our results validate the efficacy of common PSF experiment designs to test soil inoculum effects, and highlight the challenges of scaling the underlying microbial mechanisms of plant responses from whole-community inoculation experiments to natural ecosystems.}, }
@article {pmid30421109, year = {2019}, author = {La, A and Perré, P and Taidi, B}, title = {Process for symbiotic culture of Saccharomyces cerevisiae and Chlorella vulgaris for in situ CO2 mitigation.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {2}, pages = {731-745}, doi = {10.1007/s00253-018-9506-3}, pmid = {30421109}, issn = {1432-0614}, mesh = {Carbon Dioxide/*metabolism ; Chlorella vulgaris/*growth &amp; development/*metabolism ; Coculture Techniques/*methods ; Culture Media/chemistry ; Saccharomyces cerevisiae/*growth &amp; development/*metabolism ; *Symbiosis ; }, abstract = {Industrial biotechnology relies heavily on fermentation processes that release considerable amounts of CO2. Apart from the fact that this CO2 represents a considerable part of the organic substrate, it has a negative impact on the environment. Microalgae cultures have been suggested as potential means of capturing the CO2 with further applications in high-value compounds production or directly for feed applications. We developed a sustainable process based on a mixed co-dominant culture of Saccharomyces cerevisiae and Chlorella vulgaris where the CO2 production and utilization controlled the microbial ecology of the culture. By mixing yeast and microalga in the same culture, the CO2 is produced in dissolved form and is available to the microalga avoiding degassing and dissolution phenomena. With this process, the CO2 production and utilization rates were balanced and a mutual symbiosis between the yeast and the microalga was set up in the culture. In this study, the reutilization of CO2 and growth of C. vulgaris was demonstrated. The two organism populations were balanced at approximately 20 × 10[6] cells ml[-1] and almost all the CO2 produced by yeast was reutilized by microalga within 168 h of culture. The C. vulgaris inoculum preparation played a key role in establishing co-dominance of the two organisms. Other key factors in establishing symbiosis were the inoculum ratio of the two organisms and the growth medium design. A new method allowed the independent enumeration of each organism in a mixed culture. This study could provide a basis for the development of green processes of low environmental impact.}, }
@article {pmid30419469, year = {2019}, author = {Miao, Y and Johnson, NW and Gedalanga, PB and Adamson, D and Newell, C and Mahendra, S}, title = {Response and recovery of microbial communities subjected to oxidative and biological treatments of 1,4-dioxane and co-contaminants.}, journal = {Water research}, volume = {149}, number = {}, pages = {74-85}, doi = {10.1016/j.watres.2018.10.070}, pmid = {30419469}, issn = {1879-2448}, mesh = {Biodegradation, Environmental ; Dioxanes ; Hydrogen Peroxide ; *Microbiota ; Oxidative Stress ; *Water Pollutants, Chemical ; }, abstract = {Microbial community dynamics were characterized following combined oxidation and biodegradation treatment trains for mixtures of 1,4-dioxane and chlorinated volatile organic compounds (CVOCs) in laboratory microcosms. Bioremediation is generally inhibited by co-contaminate CVOCs; with only a few specific bacterial taxa reported to metabolize or cometabolize 1,4-dioxane being unaffected. Chemical oxidation by hydrogen peroxide (H2O2) as a non-selective treatment demonstrated 50-80% 1,4-dioxane removal regardless of the initial CVOC concentrations. Post-oxidation bioaugmentation with 1,4-dioxane metabolizer Pseudonocardia dioxanivorans CB1190 removed the remaining 1,4-dioxane. The intrinsic microbial population, biodiversity, richness, and biomarker gene abundances decreased immediately after the brief oxidation phase, but recovery of cultivable microbiomes and a more diverse community were observed during the subsequent 9-week biodegradation phase. Results generated from the Illumina Miseq sequencing and bioinformatics analyses established that generally oxidative stress tolerant genus Ralstonia was abundant after the oxidation step, and Cupriavidus, Pseudolabrys, Afipia, and Sphingomonas were identified as dominant genera after aerobic incubation. Multidimensional analysis elucidated the separation of microbial populations as a function of time under all conditions, suggesting that temporal succession is a determining factor that is independent of 1,4-dioxane and CVOCs mixtures. Network analysis highlighted the potential interspecies competition or commensalism, and dynamics of microbiomes during the biodegradation phase, in line with the shifts of predominant genera and various developing directions during different steps of the treatment train. Collectively, this study demonstrated that chemical oxidation followed by bioaugmentation is effective for treating 1,4-dioxane, even in the presence of high levels of CVOC mixtures and residual peroxide, a disinfectant, and enhanced our understanding of microbial ecological impacts of the treatment train. These results will be valuable for predicting treatment synergies that lead to cost savings and improved remedial outcomes in short-term active remediation as well as long-term changes to the environmental microbial communities.}, }
@article {pmid30418580, year = {2019}, author = {Lekeux, G and Crowet, JM and Nouet, C and Joris, M and Jadoul, A and Bosman, B and Carnol, M and Motte, P and Lins, L and Galleni, M and Hanikenne, M}, title = {Homology modeling and in vivo functional characterization of the zinc permeation pathway in a heavy metal P-type ATPase.}, journal = {Journal of experimental botany}, volume = {70}, number = {1}, pages = {329-341}, pmid = {30418580}, issn = {1460-2431}, mesh = {Adenosine Triphosphatases/*genetics/metabolism ; Arabidopsis/enzymology/*genetics/metabolism ; Arabidopsis Proteins/*genetics/metabolism ; Biological Transport ; Models, Genetic ; Structural Homology, Protein ; Zinc/*metabolism ; }, abstract = {The P1B ATPase heavy metal ATPase 4 (HMA4) is responsible for zinc and cadmium translocation from roots to shoots in Arabidopsis thaliana. It couples ATP hydrolysis to cytosolic domain movements, enabling metal transport across the membrane. The detailed mechanism of metal permeation by HMA4 through the membrane remains elusive. Here, homology modeling of the HMA4 transmembrane region was conducted based on the crystal structure of a ZntA bacterial homolog. The analysis highlighted amino acids forming a metal permeation pathway, whose importance was subsequently investigated functionally through mutagenesis and complementation experiments in plants. Although the zinc pathway displayed overall conservation among the two proteins, significant differences were observed, especially in the entrance area with altered electronegativity and the presence of a ionic interaction/hydrogen bond network. The analysis also newly identified amino acids whose mutation results in total or partial loss of the protein function. In addition, comparison of zinc and cadmium accumulation in shoots of A. thaliana complemented lines revealed a number of HMA4 mutants exhibiting different abilities in zinc and cadmium translocation. These observations could be instrumental to design low cadmium-accumulating crops, hence decreasing human cadmium exposure.}, }
@article {pmid30418043, year = {2018}, author = {Muleviciene, A and D'Amico, F and Turroni, S and Candela, M and Jankauskiene, A}, title = {Iron deficiency anemia-related gut microbiota dysbiosis in infants and young children: A pilot study.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {65}, number = {4}, pages = {551-564}, doi = {10.1556/030.65.2018.045}, pmid = {30418043}, issn = {1217-8950}, mesh = {Anemia, Iron-Deficiency/*complications ; Bacteria/classification/genetics ; Child ; Child, Preschool ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Metagenomics ; *Microbiota ; Phylogeny ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Nutritional iron deficiency (ID) causes not only anemia but also malfunction of the entire human organism. Recently, a role of the gut microbiota has been hypothesized, but limited data are available especially in infants. Here, we performed a pilot study to explore the gut microbiota in 10 patients with iron deficiency anemia (IDA) and 10 healthy controls aged 6-34 months. Fresh stool samples were collected from diapers, and the fecal microbiota was profiled by next-generation sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Except for diet diversity, the breastfeeding status at the enrollment, the exclusive breastfeeding duration, and the introduction of complementary foods did not differ between groups. Distinct microbial signatures were found in IDA patients, with increased relative abundance of Enterobacteriaceae (mean relative abundance, patients vs. controls, 4.4% vs. 3.0%) and Veillonellaceae (13.7% vs. 3.6%), and reduced abundance of Coriobacteriaceae (3.5% vs. 8.8%) compared to healthy controls. A decreased Bifidobacteriaceae/Enterobacteriaceae ratio was observed in IDA patients. Notwithstanding the low sample size, our data highlight microbiota dysbalance in IDA worth for further investigations, aimed at unraveling the ID impact on the microbiome trajectory in early life, and the possible long-term consequences.}, }
@article {pmid30418019, year = {2018}, author = {Shan, Y and Harms, H and Wick, LY}, title = {Electric Field Effects on Bacterial Deposition and Transport in Porous Media.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {24}, pages = {14294-14301}, doi = {10.1021/acs.est.8b03648}, pmid = {30418019}, issn = {1520-5851}, mesh = {Bacteria ; *Ecosystem ; *Electricity ; Electrophoresis ; Porosity ; }, abstract = {Bacterial deposition and transport are key to microbial ecology and biotechnological applications. We therefore tested whether electrokinetic forces (electroosmotic shear force (FEOF), electrophoretic drag force (FEP)) acting on bacteria may be used to control bacterial deposition during transport in laboratory percolation columns exposed to external direct current (DC) electric fields. For different bacteria, yet similar experimental conditions we observed that DC fields either enhanced or reduced bacterial deposition efficiencies (α) relative to DC-free controls. By calculating the DLVO force of colloidal interactions, FEOF, FEP, and the hydraulic shear forces acting on single cells at a collector surface we found that DC-induced changes of α correlated to | FEOF| to | FEP| ratios: If | FEOF| > | FEP|, α was clearly increased and if | FEOF| < | FEP| α was clearly decreased. Our findings allow for better prediction of the forces acting on a bacterium at collector surface and, hence, the electrokinetic control of microbial deposition in natural and manmade ecosystems.}, }
@article {pmid30417222, year = {2019}, author = {Zhang, FG and Bell, T and Zhang, QG}, title = {Experimental Testing of Dispersal Limitation in Soil Bacterial Communities with a Propagule Addition Approach.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {905-912}, pmid = {30417222}, issn = {1432-184X}, support = {31700434//National Natural Science Foundation of China/ ; 31725006 and 31670376//National Natural Science Foundation of China/ ; }, mesh = {Bacteria/*isolation &amp; purification ; Bacteriological Techniques/*methods ; China ; Environmental Monitoring/*methods ; Grassland ; *Soil Microbiology ; }, abstract = {The role of dispersal in the assembly of microbial communities remains contentious. This study tested the importance of dispersal limitation for the structuring of local soil bacterial communities using an experimental approach of propagule addition. Microbes extracted from soil pooled from samples collected at 20 localities across ~ 400 km in a temperate steppe were added to microcosms of local soils at three sites; the microcosms were then incubated in situ for 3 months. We then assessed the composition and diversity of bacterial taxa in the soils using 16S rRNA gene amplicon sequencing. The addition of the regional microbial pool did not cause significant changes in the overall composition or diversity of the total bacterial community, although a very small number of individual taxa may have been affected by the addition treatment. Our results suggest a negligible role of dispersal limitation in structuring soil bacterial communities in our study area.}, }
@article {pmid30417111, year = {2018}, author = {Minich, JJ and Humphrey, G and Benitez, RAS and Sanders, J and Swafford, A and Allen, EE and Knight, R}, title = {High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity.}, journal = {mSystems}, volume = {3}, number = {6}, pages = {}, pmid = {30417111}, issn = {2379-5077}, abstract = {Next-generation sequencing technologies have enabled many advances across biology, with microbial ecology benefiting primarily through expanded sample sizes. Although the cost of running sequencing instruments has decreased substantially over time, the price of library preparation methods has largely remained unchanged. In this study, we developed a low-cost miniaturized (5-µl volume) high-throughput (384-sample) amplicon library preparation method with the Echo 550 acoustic liquid handler. Our method reduces costs of library preparation to $1.42 per sample, a 58% reduction compared to existing automated methods and a 21-fold reduction from commercial kits, without compromising sequencing success or distorting the microbial community composition analysis. We further validated the optimized method by sampling five body sites from 46 Pacific chub mackerel fish caught across 16 sampling events over seven months from the Scripps Institution of Oceanography pier in La Jolla, CA. Fish microbiome samples were processed with the miniaturized 5-µl reaction volume with 0.2 µl of genomic DNA (gDNA) and the standard 25-µl reaction volume with 1 µl of gDNA. Between the two methods, alpha diversity was highly correlated (R 2 > 0.95), while distances of technical replicates were much lower than within-body-site variation (P < 0.0001), further validating the method. The cost savings of implementing the miniaturized library preparation (going from triplicate 25-µl reactions to triplicate 5-µl reactions) are large enough to cover a MiSeq sequencing run for 768 samples while preserving accurate microbiome measurements. IMPORTANCE Reduced costs of sequencing have tremendously impacted the field of microbial ecology, allowing scientists to design more studies with larger sample sizes that often exceed 10,000 samples. Library preparation costs have not kept pace with sequencing prices, although automated liquid handling robots provide a unique opportunity to bridge this gap while also decreasing human error. Here, we take advantage of an acoustic liquid handling robot to develop a high-throughput miniaturized library preparation method of a highly cited and broadly used 16S rRNA gene amplicon reaction. We evaluate the potential negative effects of reducing the PCR volume along with varying the amount of gDNA going into the reaction. Our optimized method reduces sample-processing costs while continuing to generate a high-quality microbiome readout that is indistinguishable from the original method.}, }
@article {pmid30413836, year = {2019}, author = {Villegas-Plazas, M and Wos-Oxley, ML and Sanchez, JA and Pieper, DH and Thomas, OP and Junca, H}, title = {Variations in Microbial Diversity and Metabolite Profiles of the Tropical Marine Sponge Xestospongia muta with Season and Depth.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {243-256}, pmid = {30413836}, issn = {1432-184X}, support = {KBBE-2009-245226//MAGICPAH/ ; 652-2014//EcosNord-Colciencias/ ; JI-2012//J&#xf3;ven Investigador - Colciencias/ ; MSc scholarship//Universidad de los Andes/ ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Biodiversity ; Caribbean Region ; Coral Reefs ; *Microbiota ; Panama ; Phylogeny ; Seasons ; Seawater/*chemistry/microbiology ; Symbiosis ; Xestospongia/*microbiology/physiology ; }, abstract = {Xestospongia muta is among the most emblematic sponge species inhabiting coral reefs of the Caribbean Sea. Besides being the largest sponge species growing in the Caribbean, it is also known to produce secondary metabolites. This study aimed to assess the effect of depth and season on the symbiotic bacterial dynamics and major metabolite profiles of specimens of X. muta thriving in a tropical marine biome (Portobelo Bay, Panamá), which allow us to determine whether variability patterns are similar to those reported for subtropical latitudes. The bacterial assemblages were characterized using Illumina deep-sequencing and metabolomic profiles using UHPLC-DAD-ELSD from five depths (ranging 9-28 m) across two seasons (spring and autumn). Diverse symbiotic communities, representing 24 phyla with a predominance of Proteobacteria and Chloroflexi, were found. Although several thousands of OTUs were determined, most of them belong to the rare biosphere and only 23 to a core community. There was a significant difference between the structure of the microbial communities in respect to season (autumn to spring), with a further significant difference between depths only in autumn. This was partially mirrored in the metabolome profile, where the overall metabolite composition did not differ between seasons, but a significant depth gradient was observed in autumn. At the phyla level, Cyanobacteria, Firmicutes, Actinobacteria, and Spirochaete showed a mild-moderate correlation with the metabolome profile. The metabolomic profiles were mainly characterized by known brominated polyunsaturated fatty acids. This work presents findings about the composition and dynamics of the microbial assemblages of X. muta expanding and confirming current knowledge about its remarkable diversity and geographic variability as observed in this tropical marine biome.}, }
@article {pmid30413475, year = {2019}, author = {Zerfaß, C and Christie-Oleza, JA and Soyer, OS}, title = {Manganese Oxide Biomineralization Provides Protection against Nitrite Toxicity in a Cell-Density-Dependent Manner.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {2}, pages = {}, pmid = {30413475}, issn = {1098-5336}, support = {BB/K003240/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M017982/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biomineralization ; Manganese Compounds/*chemistry ; Nitrites/*toxicity ; Oxides/*chemistry ; Population Growth ; Roseobacter/*drug effects/physiology ; }, abstract = {Manganese biomineralization is a widespread process among bacteria and fungi. To date, there is no conclusive experimental evidence for how and if this process impacts microbial fitness in the environment. Here, we show how a model organism for manganese oxidation is growth inhibited by nitrite, and that this inhibition is mitigated in the presence of manganese. We show that such manganese-mediated mitigation of nitrite inhibition is dependent on the culture inoculum size, and that manganese oxide (MnOX) forms granular precipitates in the culture, rather than sheaths around individual cells. We provide evidence that MnOX protection involves both its ability to catalyze nitrite oxidation into (nontoxic) nitrate under physiological conditions and its potential role in influencing processes involving reactive oxygen species (ROS). Taken together, these results demonstrate improved microbial fitness through MnOX deposition in an ecological setting, i.e., mitigation of nitrite toxicity, and point to a key role of MnOX in handling stresses arising from ROS.IMPORTANCE We present here a direct fitness benefit (i.e., growth advantage) for manganese oxide biomineralization activity in Roseobacter sp. strain AzwK-3b, a model organism used to study this process. We find that strain AzwK-3b in a laboratory culture experiment is growth inhibited by nitrite in manganese-free cultures, while the inhibition is considerably relieved by manganese supplementation and manganese oxide (MnOX) formation. We show that biogenic MnOX interacts directly with nitrite and possibly with reactive oxygen species and find that its beneficial effects are established through formation of dispersed MnOX granules in a manner dependent on the population size. These experiments raise the possibility that manganese biomineralization could confer protection against nitrite toxicity to a population of cells. They open up new avenues of interrogating this process in other species and provide possible routes to their biotechnological applications, including in metal recovery, biomaterials production, and synthetic community engineering.}, }
@article {pmid30411190, year = {2019}, author = {Rossi, A and Bellone, A and Fokin, SI and Boscaro, V and Vannini, C}, title = {Detecting Associations Between Ciliated Protists and Prokaryotes with Culture-Independent Single-Cell Microbiomics: a Proof-of-Concept Study.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {232-242}, pmid = {30411190}, issn = {1432-184X}, support = {565-60%2016//University of Pisa/ ; 565-60%2017//University of Pisa/ ; 565-FFABR 2017//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Biological Evolution ; Ciliophora/genetics/isolation &amp; purification/*microbiology/physiology ; Ecosystem ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; Pilot Projects ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Symbioses between prokaryotes and microbial eukaryotes, particularly ciliated protists, have been studied for a long time. Nevertheless, researchers have focused only on a few host genera and species, mainly due to difficulties in cultivating the hosts, and usually have considered a single symbiont at a time. Here, we present a pilot study using a single-cell microbiomic approach to circumvent these issues. Unicellular ciliate isolation followed by simultaneous amplification of eukaryotic and prokaryotic markers was used. Our preliminary test gave reliable and satisfactory results both on samples collected from different habitats (marine and freshwater) and on ciliates belonging to different taxonomic groups. Results suggest that, as already assessed for many macro-organisms like plants and metazoans, ciliated protists harbor distinct microbiomes. The applied approach detected new potential symbionts as well as new hosts for previously described ones, with relatively low time and cost effort and without culturing. When further developed, single-cell microbiomics for ciliates could be applied to a large number of studies aiming to unravel the evolutionary and ecological meaning of these symbiotic systems.}, }
@article {pmid30411189, year = {2019}, author = {Dror, H and Novak, L and Evans, JS and López-Legentil, S and Shenkar, N}, title = {Core and Dynamic Microbial Communities of Two Invasive Ascidians: Can Host-Symbiont Dynamics Plasticity Affect Invasion Capacity?.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {170-184}, pmid = {30411189}, issn = {1432-184X}, support = {2014025//United States - Israel Binational Science Foundation/ ; 2014025//United States - Israel Binational Science Foundation/ ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Phylogeny ; Predatory Behavior ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; Urochordata/microbiology/*physiology ; }, abstract = {Ascidians (Chordata, Ascidiacea) are considered to be prominent marine invaders, able to tolerate highly polluted environments and fluctuations in salinity and temperature. Here, we examined the seasonal and spatial dynamics of the microbial communities in the inner-tunic of two invasive ascidians, Styela plicata (Lesueur 1823) and Herdmania momus (Savigny 1816), in order to investigate the changes that occur in the microbiome of non-indigenous ascidians in different environments. Microbial communities were characterized using next-generation sequencing of partial (V4) 16S rRNA gene sequences. A clear differentiation between the ascidian-associated microbiome and bacterioplankton was observed, and two distinct sets of operational taxonomic units (OTUs), one core and the other dynamic, were recovered from both species. The relative abundance of the dynamic OTUs in H. momus was higher than in S. plicata, for which core OTU structure was maintained independently of location. Ten and seventeen core OTUs were identified in S. plicata and H. momus, respectively, including taxa with reported capabilities of carbon fixing, ammonia oxidization, denitrification, and heavy-metal processing. The ascidian-sourced dynamic OTUs clustered in response to site and season but significantly differed from the bacterioplankton community structure. These findings suggest that the associations between invasive ascidians and their symbionts may enhance host functionality while maintaining host adaptability to changing environmental conditions.}, }
@article {pmid30411188, year = {2019}, author = {Liu, PY and Cheng, AC and Huang, SW and Chang, HW and Oshida, T and Yu, HT}, title = {Variations in Gut Microbiota of Siberian Flying Squirrels Correspond to Seasonal Phenological Changes in Their Hokkaido Subarctic Forest Ecosystem.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {223-231}, pmid = {30411188}, issn = {1432-184X}, support = {MOST 103-2311-B-002-001//Ministry of Science and Technology, Taiwan/ ; MOST 106-2633-B-006-004//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Animals ; Animals, Wild/microbiology ; Arctic Regions ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Ecosystem ; Forests ; *Gastrointestinal Microbiome ; Intestines/*microbiology ; Phylogeny ; Sciuridae/*microbiology ; Seasons ; }, abstract = {Gut microbial communities of animals are influenced by diet and seasonal weather changes. Since foraging strategies of wild animals are affected by phenological changes, gut microbial communities would differ among seasons. However, interactions of plant-animal-microbiota with seasonal changes have not been well characterized. Here, we surveyed gut microbial diversity of Siberian flying squirrels (Pteromys volans orii) from a natural forest in Hokkaido during spring and summer of 2013 and 2014. Additionally, we compared microbial diversity to temperature changes and normalized difference vegetation index (NDVI). Changes in both seasonal temperature and phenology were significantly associated with alterations in gut microbiota. There were two clusters of OTUs, below and above 20 °C that were significantly correlated with low and high temperatures, respectively. Low-temperature cluster OTUs belonged to various phyla, whereas the high-temperature cluster was only constituted by Firmicutes. In conclusion, gut microbiota of Siberian flying squirrels varied with environmental changes on an ecological scale.}, }
@article {pmid30411009, year = {2018}, author = {Van den Abbeele, P and Kamil, A and Fleige, L and Chung, Y and De Chavez, P and Marzorati, M}, title = {Different Oat Ingredients Stimulate Specific Microbial Metabolites in the Gut Microbiome of Three Human Individuals in Vitro.}, journal = {ACS omega}, volume = {3}, number = {10}, pages = {12446-12456}, pmid = {30411009}, issn = {2470-1343}, abstract = {We used a standardized in vitro simulation of the intestinal environment of three human donors to investigate the effect of six oat ingredients, which were produced by the application of different processing techniques, on the gut microbial community. Fructooligosaccharide was used as the positive control. Consistent changes in pH and gas production, on average -0.4 pH units and +32 kPa, indicated the high fermentability of the oat ingredients, and the resulting increased production of metabolites that are considered as beneficial for human health. These metabolites included acetate and lactate, but mostly propionate (+13.6 mM on average). All oat ingredients resulted in increased bifidobacteria levels with an average increase of 0.73 log. Moreover, a decreased production of proteolytic markers was observed, including branched short-chain fatty acids and ammonium. The results were donor-specific and product-specific. The results suggested an association between the total amounts of dietary fiber and the prebiotic potentials of different ingredients. Furthermore, as mechanical processing of oat products has previously been linked to increased extractability of dietary fibers, the obtained results suggest that different processing techniques might have impacted the potential functional properties of the final ingredients.}, }
@article {pmid30405584, year = {2018}, author = {Godoy-Vitorino, F and Romaguera, J and Zhao, C and Vargas-Robles, D and Ortiz-Morales, G and Vázquez-Sánchez, F and Sanchez-Vázquez, M and de la Garza-Casillas, M and Martinez-Ferrer, M and White, JR and Bittinger, K and Dominguez-Bello, MG and Blaser, MJ}, title = {Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2533}, pmid = {30405584}, issn = {1664-302X}, support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; S21 MD001830/MD/NIMHD NIH HHS/United States ; U54 MD007587/MD/NIMHD NIH HHS/United States ; U54 MD007600/MD/NIMHD NIH HHS/United States ; }, abstract = {The human cervicovaginal microbiota resides at an interface between the host and the environment and may affect susceptibility to disease. Puerto Rican women have high human papillomavirus (HPV) infection and cervical cancer rates. We hypothesized that the population structure of the cervicovaginal bacterial and fungal biota changed with cervical squamous intraepithelial lesions and HPV infections. DNA was extracted from cervix, introitus, and anal sites of 62 patients attending high-risk San Juan clinics. The 16S rRNA V4 region and ITS-2 fungal regions were amplified and sequenced using Illumina technology. HPV genotyping was determined by reverse hybridization with the HPV SPF10-LiPA25 kit. HPV prevalence was 84% of which ∼44% subjects were infected with high-risk HPV, ∼35% were co-infected with as many as 9 HPV types and ∼5% were infected with exclusively low-risk HPV types. HPV diversity did not change with cervical dysplasia. Cervical bacteria were more diverse in patients with CIN3 pre-cancerous lesions. We found enrichment of Atopobium vaginae and Gardnerella vaginalis in patients with CIN3 lesions. We found no significant bacterial biomarkers associated with HPV infections. Fungal diversity was significantly higher in cervical samples with high-risk HPV and introitus samples of patients with Atypical Squamous Cells of Undetermined Significance (ASCUS). Fungal biomarker signatures for vagina and cervix include Sporidiobolaceae and Sacharomyces for ASCUS, and Malassezia for high-risk HPV infections. Our combined data suggests that specific cervicovaginal bacterial and fungal populations are related to the host epithelial microenvironment, and could play roles in cervical dysplasia.}, }
@article {pmid30405571, year = {2018}, author = {Biagi, E and Aceti, A and Quercia, S and Beghetti, I and Rampelli, S and Turroni, S and Soverini, M and Zambrini, AV and Faldella, G and Candela, M and Corvaglia, L and Brigidi, P}, title = {Microbial Community Dynamics in Mother's Milk and Infant's Mouth and Gut in Moderately Preterm Infants.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2512}, pmid = {30405571}, issn = {1664-302X}, abstract = {Mother's own milk represents the optimal source for preterm infant nutrition, as it promotes immune defenses and gastrointestinal function, protects against necrotizing enterocolitis, improves long-term clinical outcome and is hypothesized to drive gut microbiota assembly. Preterm infants at birth usually do not receive their mother's milk directly from the breast, because active suckling and coordination between suckling, swallowing and breathing do not develop until 32-34 weeks gestational age, but actual breastfeeding is usually possible as they grow older. Here, we enrolled moderately preterm infants (gestational age 32-34 weeks) to longitudinally characterize mothers' milk and infants' gut and oral microbiomes, up to more than 200 days after birth, through 16S rRNA sequencing. This peculiar population offers the chance to disentangle the differential contribution of human milk feeding per se vs. actual breastfeeding in the development of infant microbiomes, that have both been acknowledged as crucial contributors to short and long-term infant health status. In this cohort, the milk microbiome composition seemed to change following the infant's latching to the mother's breast, shifting toward a more diverse microbial community dominated by typical oral microbes, i.e., Streptococcus and Rothia. Even if all infants in the present study were fed human milk, features typical of healthy, full term, exclusively breastfed infants, i.e., high percentages of Bifidobacterium and low abundances of Pseudomonas in fecal and oral samples, respectively, were detected in samples taken after actual breastfeeding started. These findings underline the importance of encouraging not only human milk feeding, but also an early start of actual breastfeeding in preterm infants, since the infant's latching to the mother's breast might constitute an independent factor helping the health-promoting assembly of the infant gut microbiome.}, }
@article {pmid30405545, year = {2018}, author = {Mehner-Breitfeld, D and Rathmann, C and Riedel, T and Just, I and Gerhard, R and Overmann, J and Brüser, T}, title = {Evidence for an Adaptation of a Phage-Derived Holin/Endolysin System to Toxin Transport in Clostridioides difficile.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2446}, pmid = {30405545}, issn = {1664-302X}, abstract = {The pathogenicity locus (PaLoc) of Clostridioides difficile usually comprises five genes (tcdR, tcdB, tcdE, tcdA, tcdC). While the proteins TcdA and TcdB represent the main toxins of this pathogen, TcdR and TcdC are involved in the regulation of their production. TcdE is a holin family protein, members of which are usually involved in the transport of cell wall-degrading enzymes (endolysins) for phage-induced lysis. In the past, TcdE has been shown to contribute to the release of TcdA and TcdB, but it is unclear whether it mediates a specific transport or rather a lysis of cells. TcdE of C. difficile strains analyzed so far can be produced in three isoforms that are initiated from distinct N-terminal ATG codons. When produced in Escherichia coli, we found that the longest TcdE isoform had a moderate effect on cell growth, whereas the shortest isoform strongly induced lysis. The effect of the longest isoform was inhibitory for cell lysis, implying a regulatory function of the N-terminal 24 residues. We analyzed the PaLoc sequence of 44 C. difficile isolates and found that four of these apparently encode only the short TcdE isoforms, and the most closely related holins from C. difficile phages only possess one of these initiation codons, indicating that an N-terminal extension of TcdE evolved in C. difficile. All PaLoc sequences comprised also a conserved gene encoding a short fragment of an endolysin remnant of a phage holin/endolysin pair. We could produce this peptide, which we named TcdL, and demonstrated by bacterial two-hybrid analysis a self-interaction and an interaction with TcdB that might serve to mediate TcdE-dependent transport.}, }
@article {pmid30405201, year = {2018}, author = {Wankhade, UD and Zhong, Y and Kang, P and Alfaro, M and Chintapalli, SV and Piccolo, BD and Mercer, KE and Andres, A and Thakali, KM and Shankar, K}, title = {Maternal High-Fat Diet Programs Offspring Liver Steatosis in a Sexually Dimorphic Manner in Association with Changes in Gut Microbial Ecology in Mice.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16502}, pmid = {30405201}, issn = {2045-2322}, mesh = {Animals ; Bile Acids and Salts/metabolism ; Biodiversity ; Biomarkers ; Diet, High-Fat/*adverse effects ; Fatty Liver/*etiology/*metabolism/pathology ; Female ; *Gastrointestinal Microbiome ; Lipid Metabolism ; Male ; Maternal Exposure/*adverse effects ; Metabolic Networks and Pathways ; Metagenome ; Metagenomics/methods ; Mice ; Phylogeny ; Sex Characteristics ; Weight Gain ; }, abstract = {The contributions of maternal diet and obesity in shaping offspring microbiome remain unclear. Here we employed a mouse model of maternal diet-induced obesity via high-fat diet feeding (HFD, 45% fat calories) for 12 wk prior to conception on offspring gut microbial ecology. Male and female offspring were provided access to control or HFD from weaning until 17 wk of age. Maternal HFD-associated programming was sexually dimorphic, with male offspring from HFD dams showing hyper-responsive weight gain to postnatal HFD. Likewise, microbiome analysis of offspring cecal contents showed differences in α-diversity, β-diversity and higher Firmicutes in male compared to female mice. Weight gain in offspring was significantly associated with abundance of Lachnospiraceae and Clostridiaceae families and Adlercreutzia, Coprococcus and Lactococcus genera. Sex differences in metagenomic pathways relating to lipid metabolism, bile acid biosynthesis and immune response were also observed. HFD-fed male offspring from HFD dams also showed worse hepatic pathology, increased pro-inflammatory cytokines, altered expression of bile acid regulators (Cyp7a1, Cyp8b1 and Cyp39a1) and serum bile acid concentrations. These findings suggest that maternal HFD alters gut microbiota composition and weight gain of offspring in a sexually dimorphic manner, coincident with fatty liver and a pro-inflammatory state in male offspring.}, }
@article {pmid30403856, year = {2018}, author = {Calatayud, M and Xiong, C and Du Laing, G and Raber, G and Francesconi, K and van de Wiele, T}, title = {Salivary and Gut Microbiomes Play a Significant Role in in Vitro Oral Bioaccessibility, Biotransformation, and Intestinal Absorption of Arsenic from Food.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {24}, pages = {14422-14435}, pmid = {30403856}, issn = {1520-5851}, support = {I 2412/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Arsenic ; Biological Availability ; Biotransformation ; *Gastrointestinal Microbiome ; *Gastrointestinal Tract ; Humans ; Intestinal Absorption ; }, abstract = {The release of a toxicant from a food matrix during the gastrointestinal digestion is a crucial determinant of the toxicant's oral bioavailability. We present a modified setup of the human simulator of the gut microbial ecosystem (SHIME), with four sequential gastrointestinal reactors (oral, stomach, small intestine, and colon), including the salivary and colonic microbiomes. Naturally arsenic-containing rice, mussels, and nori seaweed were digested in the presence of microorganisms and in vitro oral bioaccessibility, bioavailability, and metabolism of arsenic species were evaluated following analysis by using HPLC/mass spectrometry. When food matrices were digested with salivary bacteria, the soluble arsenic in the gastric digestion stage increased for mussel and nori samples, but no coincidence impact was found in the small intestinal and colonic digestion stages. However, the simulated small intestinal absorption of arsenic was increased in all food matrices (1.2-2.7 fold higher) following digestion with salivary microorganisms. No significant transformation of the arsenic species occurred except for the arsenosugars present in mussels and nori. In those samples, conversions between the oxo arsenosugars were observed in the small intestinal digestion stage whereupon the thioxo analogs became major metabolites. These results expand our knowledge on the likely metabolism and oral bioavailabiltiy of arsenic during human digestion, and provide valuable information for future risk assessments of dietary arsenic.}, }
@article {pmid30402724, year = {2019}, author = {Veresoglou, SD and Verbruggen, E and Makarova, O and Mansour, I and Sen, R and Rillig, MC}, title = {Arbuscular Mycorrhizal Fungi Alter the Community Structure of Ammonia Oxidizers at High Fertility via Competition for Soil NH4.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {147-158}, pmid = {30402724}, issn = {1432-184X}, support = {300298//FP7 People: Marie-Curie Actions ()/ ; }, mesh = {Ammonia/*metabolism ; Bacteria/isolation &amp; purification/metabolism ; Biodiversity ; Ecosystem ; Fungi/isolation &amp; purification/*metabolism ; Mycorrhizae/isolation &amp; purification/*metabolism ; Nitrification ; Nitrogen/metabolism ; Oxidation-Reduction ; Plantago/growth &amp; development/microbiology ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {Nitrification represents a central process in the cycling of nitrogen (N) which in high-fertility habitats can occasionally be undesirable. Here, we explore how arbuscular mycorrhiza (AM) impacts nitrification when N availability is not limiting to plant growth. We wanted to test which of the mechanisms that have been proposed in the literature best describes how AM influences nitrification. We manipulated the growth settings of Plantago lanceolata so that we could control the mycorrhizal state of our plants. AM induced no changes in the potential nitrification rates or the estimates of ammonium oxidizing (AO) bacteria. However, we could observe a moderate shift in the community of ammonia-oxidizers, which matched the shift we saw when comparing hyphosphere to rhizosphere soil samples and mirrored well changes in the availability of ammonium in soil. We interpret our results as support that it is competition for N that drives the interaction between AM and AO. Our experiment sheds light on an understudied interaction which is pertinent to typical management practices in agricultural systems.}, }
@article {pmid30397796, year = {2019}, author = {Kraus, C and Voegele, RT and Fischer, M}, title = {Temporal Development of the Culturable, Endophytic Fungal Community in Healthy Grapevine Branches and Occurrence of GTD-Associated Fungi.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {866-876}, pmid = {30397796}, issn = {1432-184X}, support = {FKZ 031A349D//Bundesministerium f&#xfc;r Bildung und Forschung/ ; }, mesh = {Endophytes/*growth &amp; development ; Fungi/*growth &amp; development ; *Mycobiome ; Plant Diseases/*microbiology ; Plant Stems/microbiology ; Vitis/*microbiology ; }, abstract = {Endophytic fungi play an important role in the life of grapevine, either as beneficial microorganisms or as pathogens. Many surveys concerning the fungal grapevine community have been conducted. Nevertheless, exactly how the fungal community arises within the plant and develops from young shoots to mature vines is still unknown. Therefore, it was the aim of this study to investigate the early development of endophytic fungal communities in healthy grapevine branches from 2 months to 8 years old. More than 3800 fungi belonging to 86 operational taxonomic units (OTUs) were isolated from wood samples and assigned to eight age groups. The community composition within the age groups changed and significant differences between young (≤ 1 year) and old (> 1 year) branches were found. The former were primarily dominated by ubiquitous, fast-growing fungi like Alternaria spp., Aureobasidium pullulans, Cladosporium spp., or Epicoccum nigrum, while communities of perennial branches additionally harbored many grapevine trunk disease (GTD)-associated fungi such as Diplodia seriata or Eutypa lata. This work gives an insight into the early development of fungal communities in grapevine, the nature and composition of primary settlers and core communities, as well as the emergence of GTD-associated fungi in perennial wood. This information may help grapevine growers to better estimate the risk in relation to the applied training system, producing mainly old branches or young shoots.}, }
@article {pmid30397795, year = {2019}, author = {Palacios, OA and Lopez, BR and Bashan, Y and de-Bashan, LE}, title = {Early Changes in Nutritional Conditions Affect Formation of Synthetic Mutualism Between Chlorella sorokiniana and the Bacterium Azospirillum brasilense.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {980-992}, pmid = {30397795}, issn = {1432-184X}, support = {251102//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 284562//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; }, mesh = {Azospirillum brasilense/*physiology ; Chlorella/*physiology ; Indoleacetic Acids/metabolism ; Microalgae/physiology ; Population Growth ; Starch/metabolism ; *Symbiosis ; Tryptophan/metabolism ; }, abstract = {The effect of three different nutritional conditions during the initial 12 h of interaction between the microalgae Chlorella sorokiniana UTEX 2714 and the plant growth-promoting bacterium Azospirillum brasilense Cd on formation of synthetic mutualism was assessed by changes in population growth, production of signal molecules tryptophan and indole-3-acetic acid, starch accumulation, and patterns of cell aggregation. When the interaction was supported by a nutrient-rich medium, production of both signal molecules was detected, but not when this interaction began with nitrogen-free (N-free) or carbon-free (C-free) media. Overall, populations of bacteria and microalgae were larger when co-immobilized. However, the highest starch production was measured in C. sorokiniana immobilized alone and growing continuously in a C-free mineral medium. In this interaction, the initial nutritional condition influenced the time at which the highest accumulation of starch occurred in Chlorella, where the N-free medium induced faster starch production and the richer medium delayed its accumulation. Formation of aggregates made of microalgae and bacteria occurred in all nutritional conditions, with maximum at 83 h in mineral medium, and coincided with declining starch content. This study demonstrates that synthetic mutualism between C. sorokiniana and A. brasilense can be modulated by the initial nutritional condition, mainly by the presence or absence of nitrogen and carbon in the medium in which they are interacting.}, }
@article {pmid30397794, year = {2019}, author = {Lau, NS and Zarkasi, KZ and Md Sah, ASR and Shu-Chien, AC}, title = {Diversity and Coding Potential of the Microbiota in the Photic and Aphotic Zones of Tropical Man-Made Lake with Intensive Aquaculture Activities: a Case Study on Temengor Lake, Malaysia.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {20-32}, pmid = {30397794}, issn = {1432-184X}, mesh = {Aquaculture ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Biodiversity ; DNA, Bacterial/genetics ; Ecosystem ; Lakes/chemistry/*microbiology ; Malaysia ; Metagenomics ; *Microbiota ; Nitrogen/analysis/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfur/analysis/metabolism ; }, abstract = {Although freshwater biomes cover less than 1% of the Earth's surface, they have disproportionate ecological significances. Attempts to study the taxonomy and function of freshwater microbiota are currently limited to samples collected from temperate lakes. In this study, we investigated samples from the photic and aphotic of an aquaculture site (disturbed) of Temengor Lake, a tropical lake in comparison with the undisturbed site of the lake using 16S rRNA amplicon and shotgun metagenomic approaches. Vertical changes in bacterial community composition and function of the Temengor Lake metagenomes were observed. The photic water layer of Temengor Lake was dominated by typical freshwater assemblages consisting of Proteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, and Cyanobacteria lineages. On the other hand, the aphotic water featured in addition to Proteobacteria, Bacteroidetes, Verrucomicrobia, and two more abundant bacterial phyla that are typically ubiquitous in anoxic habitats (Chloroflexi and Firmicutes). The aphotic zone of Temengor Lake exhibited genetic potential for nitrogen and sulfur metabolisms for which terminal electron acceptors other than oxygen are used in the reactions. The aphotic water of the disturbed site also showed an overrepresentation of genes associated with the metabolism of carbohydrates, likely driven by the enrichment of nutrient resulting from aquaculture activities at the site. The results presented in this study can serve as a basis for understanding the structure and functional capacity of the microbial communities in the photic and aphotic zones/water layers of tropical man-made lakes.}, }
@article {pmid30397546, year = {2018}, author = {Md Zoqratt, MZH and Eng, WWH and Thai, BT and Austin, CM and Gan, HM}, title = {Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5826}, pmid = {30397546}, issn = {2167-8359}, abstract = {Aquaculture production of the Pacific white shrimp is the largest in the world for crustacean species. Crucial to the sustainable global production of this important seafood species is a fundamental understanding of the shrimp gut microbiota and its relationship to the microbial ecology of shrimp pond. This is especially true, given the recently recognized role of beneficial microbes in promoting shrimp nutrient intake and in conferring resistance against pathogens. Unfortunately, aquaculture-related microbiome studies are scarce in Southeast Asia countries despite the severe impact of early mortality syndrome outbreaks on shrimp production in the region. In this study, we employed the 16S rRNA amplicon (V3-V4 region) sequencing and amplicon sequence variants (ASV) method to investigate the microbial diversity of shrimp guts and pond water samples collected from aquaculture farms located in Malaysia and Vietnam. Substantial differences in the pond microbiota were observed between countries with the presence and absence of several taxa extending to the family level. Microbial diversity of the shrimp gut was found to be generally lower than that of the pond environments with a few ubiquitous genera representing a majority of the shrimp gut microbial diversity such as Vibrio and Photobacterium, indicating host-specific selection of microbial species. Given the high sequence conservation of the 16S rRNA gene, we assessed its veracity at distinguishing Vibrio species based on nucleotide alignment against type strain reference sequences and demonstrated the utility of ASV approach in uncovering a wider diversity of Vibrio species compared to the conventional OTU clustering approach.}, }
@article {pmid30391860, year = {2019}, author = {van der Waals, MJ and Plugge, C and Meima-Franke, M and de Waard, P and Bodelier, PLE and Smidt, H and Gerritse, J}, title = {Ethyl tert-butyl ether (EtBE) degradation by an algal-bacterial culture obtained from contaminated groundwater.}, journal = {Water research}, volume = {148}, number = {}, pages = {314-323}, doi = {10.1016/j.watres.2018.10.050}, pmid = {30391860}, issn = {1879-2448}, mesh = {Biodegradation, Environmental ; *Chlorella ; Ethyl Ethers ; *Groundwater ; Humans ; *Methyl Ethers ; Phylogeny ; tert-Butyl Alcohol ; }, abstract = {EtBE is a fuel oxygenate that is synthesized from (bio)ethanol and fossil-based isobutylene, and replaces the fossil-based MtBE. Biodegradation of EtBE to harmless metabolites or end products can reduce the environmental and human health risks after accidental release. In this study, an algal-bacterial culture enriched from contaminated groundwater was used to (i) assess the potential for EtBE degradation, (ii) resolve the EtBE degradation pathway and (iii) characterize the phylogenetic composition of the bacterial community involved in EtBE degradation in contaminated groundwater. In an unamended microcosm, algal growth was observed after eight weeks when exposed to a day-night light cycle. In the fed-batch reactor, oxygen produced by the algae Scenedesmus and Chlorella was used by bacteria to degrade 50 μM EtBE replenishments with a cumulative total of 1250 μM in a day/night cycle (650 lux), over a period of 913 days. The microbial community in the fed-batch reactor degraded EtBE, using a P450 monooxygenase and 2-hydroxyisobutyryl-CoA mutase, to tert-butyl alcohol (TBA), ethanol and CO2 as determined using [13]C nuclear magnetic resonance spectroscopy (NMR) and gas chromatography. Stable isotope probing (SIP) with [13]C6 labeled EtBE in a fed-batch vessel showed no significant difference in community profiles of the [13]C and [12]C enriched DNA fractions, with representatives of the families Halomonadaceae, Shewanellaceae, Rhodocyclaceae, Oxalobacteraceae, Comamonadaceae, Sphingomonadaceae, Hyphomicrobiaceae, Candidatus Moranbacteria, Omnitrophica, Anaerolineaceae, Nocardiaceae, and Blastocatellaceae. This is the first study describing micro-oxic degradation of EtBE by an algal-bacterial culture. This algal-bacterial culture has advantages compared with conventional aerobic treatments: (i) a lower risk of EtBE evaporation and (ii) no need for external oxygen supply in the presence of light. This study provides novel leads towards future possibilities to implement algal-bacterial consortia in field-scale groundwater or wastewater treatment.}, }
@article {pmid30390579, year = {2019}, author = {Gómez-Sagasti, MT and Epelde, L and Anza, M and Urra, J and Alkorta, I and Garbisu, C}, title = {The impact of nanoscale zero-valent iron particles on soil microbial communities is soil dependent.}, journal = {Journal of hazardous materials}, volume = {364}, number = {}, pages = {591-599}, doi = {10.1016/j.jhazmat.2018.10.034}, pmid = {30390579}, issn = {1873-3336}, mesh = {Bacteria/drug effects/growth &amp; development ; Biomass ; Clay ; Environmental Restoration and Remediation ; Iron/*toxicity ; Metal Nanoparticles/*toxicity ; Microbiota/*drug effects ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The application of nanoscale zero-valent iron particles (nZVI) for the remediation of contaminated sites is very promising. However, information concerning the ecotoxicity of nZVI on soil microbial communities and, hence, soil quality, is still scarce. We carried out a three-month experiment to evaluate the impact of the application of different concentrations of nZVI (from 1 to 20 mg g DW soil[-1]) on soil microbial properties in a clay-loam versus a sandy-loam soil. Data on microbial biomass (total bacteria and fungi by qPCR, microbial biomass carbon), activity (β-glucosidase, arylsulphatase and urease activities), and functional (Biolog Ecoplates[™]) and structural (ARISA, 16S rRNA amplicon sequencing) diversity evidenced that the sandy-loam soil was more vulnerable to the presence of nZVI than the clay-loam soil. In the sandy-loam soil, arylsulphatase activity and bacterial abundance, richness and diversity were susceptible to the presence of nZVI. The high content of clay and organic matter present in the clay-loam soil may explain the observed negligible effects of nZVI on soil microbial properties. It was concluded that the impact of nZVI on soil microbial communities and, hence, soil quality, is soil dependent.}, }
@article {pmid30388523, year = {2019}, author = {Zhang, Y and Hua, ZS and Lu, H and Oehmen, A and Guo, J}, title = {Elucidating functional microorganisms and metabolic mechanisms in a novel engineered ecosystem integrating C, N, P and S biotransformation by metagenomics.}, journal = {Water research}, volume = {148}, number = {}, pages = {219-230}, doi = {10.1016/j.watres.2018.10.061}, pmid = {30388523}, issn = {1879-2448}, mesh = {*Bioreactors ; Biotransformation ; Ecosystem ; *Metagenomics ; Phosphorus ; }, abstract = {Denitrifying sulfur conversion-associated enhanced biological phosphorous removal (DS-EBPR) system is not only a novel wastewater treatment process, but also an ideal model for microbial ecology in a community context. However, it exists the knowledge gap on the roles and interactions of functional microorganisms in the DS-EBPR system for carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) bioconversions. We use genome-resolved metagenomics to build up an ecological model of microbial communities in a lab-scale DS-EBPR system with stable operation for more than 400 days. Our results yield 11 near-complete draft genomes that represent a substantial portion of the microbial community (39.4%). Sulfate-reducing bacteria (SRB) and sulfide-oxidizing bacteria (SOB) promote complex metabolic processes and interactions for C, N, P and S conversions. Bins 1-4 and 10 are considered as new potential polyphosphate-accumulating organisms (PAOs), in which Bins 1-4 can be considered as S-related PAOs (S-PAOs) with no previously cultivated or reported members. Our findings give an insight into a new ecological system with C, N, P and S simultaneous bioconversions and improve the understanding of interactions among SRB, SOB, denitrifiers and PAOs within a community context.}, }
@article {pmid30387912, year = {2019}, author = {de Nijs, EA and Hicks, LC and Leizeaga, A and Tietema, A and Rousk, J}, title = {Soil microbial moisture dependences and responses to drying-rewetting: The legacy of 18 years drought.}, journal = {Global change biology}, volume = {25}, number = {3}, pages = {1005-1015}, doi = {10.1111/gcb.14508}, pmid = {30387912}, issn = {1365-2486}, mesh = {Acclimatization/*physiology ; Bacteria/growth &amp; development ; Carbon/analysis ; Climate Change ; *Droughts ; Seasons ; Soil/*chemistry ; *Soil Microbiology ; Water/*analysis ; }, abstract = {Climate change will alter precipitation patterns with consequences for soil C cycling. An understanding of how fluctuating soil moisture affects microbial processes is therefore critical to predict responses to future global change. We investigated how long-term experimental field drought influences microbial tolerance to lower moisture levels ("resistance") and ability to recover when rewetted after drought ("resilience"), using soils from a heathland which had been subjected to experimental precipitation reduction during the summer for 18 years. We tested whether drought could induce increased resistance, resilience, and changes in the balance between respiration and bacterial growth during perturbation events, by following a two-tiered approach. We first evaluated the effects of the long-term summer drought on microbial community functioning to drought and drying-rewetting (D/RW), and second tested the ability to alter resistance and resilience through additional perturbation cycles. A history of summer drought in the field selected for increased resilience but not resistance, suggesting that rewetting after drought, rather than low moisture levels during drought, was the selective pressure shaping the microbial community functions. Laboratory D/RW cycles also selected for communities with a higher resilience rather than increased resistance. The ratio of respiration to bacterial growth during D/RW perturbation was lower for the field drought-exposed communities and decreased for both field treatments during the D/RW cycles. This suggests that cycles of D/RW also structure microbial communities to respond quickly and efficiently to rewetting after drought. Our findings imply that microbial communities can adapt to changing climatic conditions and that this might slow the rate of soil C loss predicted to be induced by future cyclic drought.}, }
@article {pmid30386315, year = {2018}, author = {Florez, AM and Suarez-Barrera, MO and Morales, GM and Rivera, KV and Orduz, S and Ochoa, R and Guerra, D and Muskus, C}, title = {Toxic Activity, Molecular Modeling and Docking Simulations of Bacillus thuringiensis Cry11 Toxin Variants Obtained via DNA Shuffling.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2461}, pmid = {30386315}, issn = {1664-302X}, abstract = {The Cry11 family belongs to a large group of δ-endotoxins that share three distinct structural domains. Among the dipteran-active toxins referred to as three-domain Cry11 toxins, the Cry11Aa protein from Bacillus thuringiensis subsp. israelensis (Bti) has been the most extensively studied. Despite the potential of Bti as an effective biological control agent, the understanding of Cry11 toxins remains incomplete. In this study, five Cry11 variants obtained via DNA shuffling displayed toxic activity against Aedes aegypti and Culex quinquefasciatus. Three of these Cry11 variants (8, 23, and 79) were characterized via 3D modeling and analysis of docking with ALP1. The relevant mutations in these variants, such as deletions, insertions and point mutations, are discussed in relation to their structural domains, toxic activities and toxin-receptor interactions. Importantly, deletion of the N-terminal segment in domain I was not associated with any change in toxic activity, and domain III exhibited higher sequence variability than domains I and II. Variant 8 exhibited up to 3.78- and 6.09-fold higher toxicity to A. aegypti than Cry11Bb and Cry11Aa, respectively. Importantly, variant 79 showed an α-helix conformation at the C-terminus and formed crystals retaining toxic activity. These findings indicate that five Cry11 variants were preferentially reassembled from the cry11Aa gene during DNA shuffling. The mutations described in loop 2 and loop 3 of domain II provide valuable information regarding the activity of Cry11 toxins against A. aegypti and C. quinquefasciatus larvae and reveal new insights into the application of directed evolution strategies to study the genetic variability of specific domains in cry11 family genes.}, }
@article {pmid30384950, year = {2018}, author = {Ihekweazu, FD and Versalovic, J}, title = {Development of the Pediatric Gut Microbiome: Impact on Health and Disease.}, journal = {The American journal of the medical sciences}, volume = {356}, number = {5}, pages = {413-423}, pmid = {30384950}, issn = {1538-2990}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; U01 CA170930/CA/NCI NIH HHS/United States ; }, mesh = {Adolescent ; Brain/*growth &amp; development ; Child ; Child, Preschool ; Disease/*etiology ; Dysbiosis/*etiology ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; }, abstract = {The intestinal microbiota are important in human growth and development. Microbial composition may yield insights into the temporal development of microbial communities and vulnerabilities to disorders of microbial ecology such as recurrent Clostridium difficile infection. Discoveries of key microbiome features of carbohydrate and amino acid metabolism are lending new insights into possible therapies or preventative strategies for inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS). In this review, we summarize the current understanding of the development of the pediatric gastrointestinal microbiome, the influence of the microbiome on the developing brain through the gut-brain axis, and the impact of dysbiosis on disease development. Dysbiosis is explored in the context of pediatric allergy and asthma, recurrent C. difficile infection, IBD, IBS, and metabolic disorders. The central premise is that the human intestinal microbiome plays a vital role in health and disease, beginning in the prenatal period and extending throughout childhood.}, }
@article {pmid30379400, year = {2019}, author = {Van Hecke, T and De Vrieze, J and Boon, N and De Vos, WH and Vossen, E and De Smet, S}, title = {Combined Consumption of Beef-Based Cooked Mince and Sucrose Stimulates Oxidative Stress, Cardiac Hypertrophy, and Colonic Outgrowth of Desulfovibrionaceae in Rats.}, journal = {Molecular nutrition &amp; food research}, volume = {63}, number = {2}, pages = {e1800962}, doi = {10.1002/mnfr.201800962}, pmid = {30379400}, issn = {1613-4133}, mesh = {Animals ; C-Reactive Protein/analysis ; Cardiomegaly/*etiology ; Cattle ; Colon/*microbiology ; Desulfovibrionaceae/*growth &amp; development ; Gastrointestinal Microbiome ; Glutathione/metabolism ; Male ; *Oxidative Stress ; Rats ; Rats, Sprague-Dawley ; *Red Meat ; Sucrose/*pharmacology ; Thiobarbituric Acid Reactive Substances/analysis ; }, abstract = {SCOPE: High red meat and sucrose consumption increases the epidemiological risk for chronic diseases. Mechanistic hypotheses include alterations in oxidative status, gut microbiome, fat deposition, and low-grade inflammation.<br><br>METHODS AND RESULTS: For 2 weeks, 40 rats consumed a diet high in white or red meat (chicken-based or beef-based cooked mince, respectively), and containing corn starch or sucrose in a 2 &#xd7; 2 factorial design. Lard was mixed with lean chicken or beef to obtain comparable dietary fatty acid profiles. Beef (vs chicken)-fed rats had higher lipid oxidation products (malondialdehyde, 4-hydroxy-2-nonenal, and hexanal) in stomach content and blood, and lower blood glutathione. Sucrose (vs corn starch)-fed rats showed increased blood lipid oxidation products and glutathione peroxidase activity, higher liver weight and malondialdehyde concentrations, and mesenterial and retroperitoneal fat accumulation. Beef-sucrose-fed rats had increased cardiac weight, suggesting pathophysiological effects on the cardiovascular system. The colonic microbiome of beef-sucrose-fed rats showed an outgrowth of the sulfate-reducing family of the Desulfovibrionaceae, and lower abundance of the Lactobacillus genus, indicating intestinal dysbiosis. Blood C-reactive protein, a marker for inflammation, was not different among groups.<br><br>CONCLUSIONS: Consumption of a cooked beef-based meat product with sucrose increased oxidative stress parameters and promoted cardiac hypertrophy and intestinal dysbiosis.}, }
@article {pmid30376889, year = {2018}, author = {Hale, VL and Jeraldo, P and Chen, J and Mundy, M and Yao, J and Priya, S and Keeney, G and Lyke, K and Ridlon, J and White, BA and French, AJ and Thibodeau, SN and Diener, C and Resendis-Antonio, O and Gransee, J and Dutta, T and Petterson, XM and Sung, J and Blekhman, R and Boardman, L and Larson, D and Nelson, H and Chia, N}, title = {Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers.}, journal = {Genome medicine}, volume = {10}, number = {1}, pages = {78}, pmid = {30376889}, issn = {1756-994X}, support = {R01 CA179243/CA/NCI NIH HHS/United States ; R01 CA170357/CA/NCI NIH HHS/United States ; P30 DK084567/DK/NIDDK NIH HHS/United States ; R01CA170357/NH/NIH HHS/United States ; U24 DK100469/DK/NIDDK NIH HHS/United States ; R01CA179243/NH/NIH HHS/United States ; P30DK084567/DK/NIDDK NIH HHS/United States ; U24DK100469//Mayo Clinic Metabolomics Resource Core/International ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteroides/growth &amp; development/physiology ; Colorectal Neoplasms/*metabolism/*microbiology ; *DNA Mismatch Repair ; Female ; Humans ; Hydrogen Sulfide/metabolism ; Male ; *Metabolome ; *Microbiota ; Middle Aged ; Young Adult ; }, abstract = {BACKGROUND: Links between colorectal cancer (CRC) and the gut microbiome have been established, but the specific microbial species and their role in carcinogenesis remain an active area of inquiry. Our understanding would be enhanced by better accounting for tumor subtype, microbial community interactions, metabolism, and ecology.<br><br>METHODS: We collected paired colon tumor and normal-adjacent tissue and mucosa samples from 83 individuals who underwent partial or total colectomies for CRC. Mismatch repair (MMR) status was determined in each tumor sample and classified as either deficient MMR (dMMR) or proficient MMR (pMMR) tumor subtypes. Samples underwent 16S rRNA gene sequencing and a subset of samples from 50 individuals were submitted for targeted metabolomic analysis to quantify amino acids and short-chain fatty acids. A PERMANOVA was used to identify the biological variables that explained variance within the microbial communities. dMMR and pMMR microbial communities were then analyzed separately using a generalized linear mixed effects model that accounted for MMR status, sample location, intra-subject variability, and read depth. Genome-scale metabolic models were then used to generate microbial interaction networks for dMMR and pMMR microbial communities. We assessed global network properties as well as the metabolic influence of each microbe within the dMMR and pMMR networks.<br><br>RESULTS: We demonstrate distinct roles for microbes in dMMR and pMMR CRC. Bacteroides fragilis and sulfidogenic Fusobacterium nucleatum were significantly enriched in dMMR CRC, but not pMMR CRC. These findings were further supported by metabolic modeling and metabolomics indicating suppression of B. fragilis in pMMR CRC and increased production of amino acid proxies for hydrogen sulfide in dMMR CRC.<br><br>CONCLUSIONS: Integrating tumor biology and microbial ecology highlighted distinct microbial, metabolic, and ecological properties unique to dMMR and pMMR CRC. This approach could critically improve our ability to define, predict, prevent, and treat colorectal cancers.}, }
@article {pmid30375646, year = {2019}, author = {Philip, N and Walsh, L}, title = {The potential ecological effects of casein phosphopeptide-amorphous calcium phosphate in dental caries prevention.}, journal = {Australian dental journal}, volume = {64}, number = {1}, pages = {66-71}, doi = {10.1111/adj.12661}, pmid = {30375646}, issn = {1834-7819}, mesh = {Calcium Phosphates ; Cariostatic Agents/*pharmacology ; *Caseins/pharmacology ; *Dental Caries/prevention &amp; control ; Dental Enamel ; Humans ; Phosphopeptides ; Tooth Remineralization ; }, abstract = {Contemporary caries prevention protocols recommend not only effective remineralizing agents but also ecological measures to reverse the dental plaque dysbiosis responsible for the disease pathogenesis. There is a high-level of evidence supporting the remineralizing efficacy of casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) from studies around the world. Evidence is now emerging that CPP-ACP may also have a beneficial influence on the dental plaque microbial ecology and homeostasis. The ecological cariostatic effects of CPP-ACP are believed to be mediated predominantly through its anti-adhesion, buffering and biofilm disrupting actions. This review principally discusses the ecological mechanisms of CPP-ACP and presents the current evidence for its effects on the oral microbiome ecology.}, }
@article {pmid30374168, year = {2018}, author = {Reese, AT and Pereira, FC and Schintlmeister, A and Berry, D and Wagner, M and Hale, LP and Wu, A and Jiang, S and Durand, HK and Zhou, X and Premont, RT and Diehl, AM and O'Connell, TM and Alberts, SC and Kartzinel, TR and Pringle, RM and Dunn, RR and Wright, JP and David, LA}, title = {Microbial nitrogen limitation in the mammalian large intestine.}, journal = {Nature microbiology}, volume = {3}, number = {12}, pages = {1441-1450}, pmid = {30374168}, issn = {2058-5276}, support = {P 26127/FWF_/Austrian Science Fund FWF/Austria ; P 27831/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Carbon/metabolism ; Diet ; Dietary Proteins ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Host Microbial Interactions/physiology ; Intestine, Large/*metabolism/*microbiology ; Mammals/*microbiology ; Mice ; Nitrogen/*metabolism ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Resource limitation is a fundamental factor governing the composition and function of ecological communities. However, the role of resource supply in structuring the intestinal microbiome has not been established and represents a challenge for mammals that rely on microbial symbionts for digestion: too little supply might starve the microbiome while too much might starve the host. We present evidence that microbiota occupy a habitat that is limited in total nitrogen supply within the large intestines of 30 mammal species. Lowering dietary protein levels in mice reduced their faecal concentrations of bacteria. A gradient of stoichiometry along the length of the gut was consistent with the hypothesis that intestinal nitrogen limitation results from host absorption of dietary nutrients. Nitrogen availability is also likely to be shaped by host-microbe interactions: levels of host-secreted nitrogen were altered in germ-free mice and when bacterial loads were reduced via experimental antibiotic treatment. Single-cell spectrometry revealed that members of the phylum Bacteroidetes consumed nitrogen in the large intestine more readily than other commensal taxa did. Our findings support a model where nitrogen limitation arises from preferential host use of dietary nutrients. We speculate that this resource limitation could enable hosts to regulate microbial communities in the large intestine. Commensal microbiota may have adapted to nitrogen-limited settings, suggesting one reason why excess dietary protein has been associated with degraded gut-microbial ecosystems.}, }
@article {pmid30372571, year = {2019}, author = {Nottingham, AT and Bååth, E and Reischke, S and Salinas, N and Meir, P}, title = {Adaptation of soil microbial growth to temperature: Using a tropical elevation gradient to predict future changes.}, journal = {Global change biology}, volume = {25}, number = {3}, pages = {827-838}, pmid = {30372571}, issn = {1365-2486}, support = {FP7-2012-329360//European Research Council/International ; }, mesh = {Adaptation, Physiological/*physiology ; Altitude ; Carbon Cycle ; Climate Change ; Forests ; *Models, Biological ; Soil/chemistry ; *Soil Microbiology ; *Temperature ; *Tropical Climate ; }, abstract = {Terrestrial biogeochemical feedbacks to the climate are strongly modulated by the temperature response of soil microorganisms. Tropical forests, in particular, exert a major influence on global climate because they are the most productive terrestrial ecosystem. We used an elevation gradient across tropical forest in the Andes (a gradient of 20°C mean annual temperature, MAT), to test whether soil bacterial and fungal community growth responses are adapted to long-term temperature differences. We evaluated the temperature dependency of soil bacterial and fungal growth using the leucine- and acetate-incorporation methods, respectively, and determined indices for the temperature response of growth: Q10 (temperature sensitivity over a given 10oC range) and Tmin (the minimum temperature for growth). For both bacterial and fungal communities, increased MAT (decreased elevation) resulted in increases in Q10 and Tmin of growth. Across a MAT range from 6°C to 26°C, the Q10 and Tmin varied for bacterial growth (Q10-20 = 2.4 to 3.5; Tmin = -8°C to -1.5°C) and fungal growth (Q10-20 = 2.6 to 3.6; Tmin = -6°C to -1°C). Thus, bacteria and fungi did not differ significantly in their growth temperature responses with changes in MAT. Our findings indicate that across natural temperature gradients, each increase in MAT by 1°C results in increases in Tmin of microbial growth by approximately 0.3°C and Q10-20 by 0.05, consistent with long-term temperature adaptation of soil microbial communities. A 2°C warming would increase microbial activity across a MAT gradient of 6°C to 26°C by 28% to 15%, respectively, and temperature adaptation of microbial communities would further increase activity by 1.2% to 0.3%. The impact of warming on microbial activity, and the related impact on soil carbon cycling, is thus greater in regions with lower MAT. These results can be used to predict future changes in the temperature response of microbial activity over different levels of warming and over large temperature ranges, extending to tropical regions.}, }
@article {pmid30370317, year = {2018}, author = {Cooper, R and Tsimring, L and Hasty, J}, title = {Microfluidics-Based Analysis of Contact-dependent Bacterial Interactions.}, journal = {Bio-protocol}, volume = {8}, number = {16}, pages = {}, pmid = {30370317}, issn = {2331-8325}, support = {P50 GM085764/GM/NIGMS NIH HHS/United States ; }, abstract = {Bacteria in nature live in complex communities with multiple cell types and spatially-dependent interactions. Studying cells in well-mixed environments such as shaking culture tubes or flasks cannot capture these spatial dynamics, but cells growing in full-fledged biofilms are difficult to observe in real time. We present here a protocol for observing time-resolved, multi-species interactions at single-cell resolution. The protocol involves growing bacterial cells in a near monolayer in a microfluidic device. As a demonstration, we describe in particular observing the dynamic interactions between E. coli and Acinetobacter baylyi. In this case, the protocol is capable of observing both contact-dependent lysis of E. coli by A. baylyi via the Type VI Secretion System (T6SS) and subsequent functional horizontal gene transfer (HGT) of genes from E. coli to A. baylyi.}, }
@article {pmid30369284, year = {2018}, author = {Braga, RM and Padilla, G and Araújo, WL}, title = {The biotechnological potential of Epicoccum spp.: diversity of secondary metabolites.}, journal = {Critical reviews in microbiology}, volume = {44}, number = {6}, pages = {759-778}, doi = {10.1080/1040841X.2018.1514364}, pmid = {30369284}, issn = {1549-7828}, mesh = {Animals ; Anti-Infective Agents/metabolism ; Antineoplastic Agents/metabolism ; Ascomycota/chemistry/genetics/*metabolism ; Biotechnology/*methods ; Humans ; *Secondary Metabolism ; }, abstract = {Epicoccum is a genus of ubiquitous fungi typically found in air, in soil, and on decaying vegetation. They also commonly display an endophytic lifestyle and are isolated from diverse plant tissues. The fungi from the genus Epicoccum are mainly known for their use as biocontrol agents against phytopathogens and for their ability to produce many secondary metabolites with potential biotechnological applications, such as antioxidant, anticancer,r and antimicrobial compounds. Among the bioactive compounds produced by Epicoccum spp., epicocconone is a commercially available fluorophore, D8646-2-6 is a patented telomerase inhibitor, and taxol is an anticancer drug originally isolated from Taxus brevifolia. Epicoccum spp. also produces epicolactone, an antimicrobial compound with a unique and complex structure that has aroused considerable interest in the chemical-synthesis community. The main goal of the present review is to discuss the diversity of secondary metabolites produced by Epicoccum spp., their biotechnological applications, and proposed hypothetical biosynthesis. In addition, the use of Epicoccum spp. as biocontrol agents and the pigments produced by these fungi are also discussed.}, }
@article {pmid30368967, year = {2018}, author = {Feng, Y and Chen, R and Stegen, JC and Guo, Z and Zhang, J and Li, Z and Lin, X}, title = {Two key features influencing community assembly processes at regional scale: Initial state and degree of change in environmental conditions.}, journal = {Molecular ecology}, volume = {27}, number = {24}, pages = {5238-5251}, doi = {10.1111/mec.14914}, pmid = {30368967}, issn = {1365-294X}, support = {//US Department of Energy/International ; 41430859//National Natural Science Foundation of China/International ; 41671267//National Natural Science Foundation of China/International ; KFZD-SW-112-03-04//CAS Strategic Priority Research Program/International ; XDB15010103//CAS Strategic Priority Research Program/International ; XDB15020103//CAS Strategic Priority Research Program/International ; 2014CB954500//National Basic Research Program/International ; 2016YFD0200306//National Key R&amp;D Program/International ; 2014271//Youth Innovation Promotion Association of the Chinese Academy of Sciences/International ; ISSASIP1639//Knowledge Innovation Program of Chinese Academy of Sciences/International ; //Subsurface Biogeochemical Research Program's Scientific Focus Area/International ; //Office of Biological and Environmental Research/International ; }, mesh = {Bacteria/*classification ; China ; DNA, Bacterial/genetics ; Ecology ; *Ecosystem ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Belowground microbial communities strongly influence ecosystem function such that predicting function may rely on understanding ecological processes that assemble communities. Uncertainty remains, however, in what governs the relative contributions of different ecological processes. To help fill this knowledge gap, we test the general hypothesis that both initial state and degree of change in environmental conditions govern the relative contributions of different ecological assembly processes. To do so, we leveraged regional-scale nutrient and organic matter addition experiments and used soil organic matter (SOM) as a proxy of integrated soil environmental conditions. Consistent with our hypothesis, we found that both the initial amount of SOM and the degree of change in SOM-in response to nutrient addition-influenced the relative contributions of different ecological assembly processes. These influences were most clearly observed at the regional scale, suggesting potential scale dependence. More specifically, nutrient additions homogenized bacterial community composition due to enhanced influences of homogenizing dispersal when SOM content was initially high. In contrast, nutrient additions led to divergence in community composition due to variable selection when initial SOM was low and/or when SOM increased significantly in response to nutrient additions. Our findings indicate important connections among initial conditions, degree of change in environmental variables and microbial community assembly processes that may influence ecosystem processes. These conceptual inferences highlight a need to strengthen connections between ecological theory and biogeochemical modelling.}, }
@article {pmid30368524, year = {2019}, author = {Li, X and Jousset, A and de Boer, W and Carrión, VJ and Zhang, T and Wang, X and Kuramae, EE}, title = {Legacy of land use history determines reprogramming of plant physiology by soil microbiome.}, journal = {The ISME journal}, volume = {13}, number = {3}, pages = {738-751}, pmid = {30368524}, issn = {1751-7370}, mesh = {Agriculture ; Arachis/*microbiology/physiology ; Crops, Agricultural ; *Metagenome ; Microbiota/genetics/*physiology ; Plant Roots/microbiology/physiology ; Rhizosphere ; *Soil Microbiology ; }, abstract = {Microorganisms associated with roots are thought to be part of the so-called extended plant phenotypes with roles in the acquisition of nutrients, production of growth hormones, and defense against diseases. Since the crops selectively enrich most rhizosphere microbes out of the bulk soil, we hypothesized that changes in the composition of bulk soil communities caused by agricultural management affect the extended plant phenotype. In the current study, we performed shotgun metagenome sequencing of the rhizosphere microbiome of the peanut (Arachis hypogaea) and metatranscriptome analysis of the roots of peanut plants grown in the soil with different management histories, peanut monocropping and crop rotation. We found that the past planting record had a significant effect on the assembly of the microbial community in the peanut rhizosphere, indicating a soil memory effect. Monocropping resulted in a reduction of the rhizosphere microbial diversity, an enrichment of several rare species, and a reduced representation of traits related to plant performance, such as nutrients metabolism and phytohormone biosynthesis. Furthermore, peanut plants in monocropped soil exhibited a significant reduction in growth coinciding with a down-regulation of genes related to hormone production, mainly auxin and cytokinin, and up-regulation of genes related to the abscisic acid, salicylic acid, jasmonic acid, and ethylene pathways. These findings suggest that land use history affects crop rhizosphere microbiomes and plant physiology.}, }
@article {pmid30367681, year = {2018}, author = {Lian, Y and Yang, J and Lian, Y and Xiao, C and Hu, X and Xu, H}, title = {DUXAP8, a pseudogene derived lncRNA, promotes growth of pancreatic carcinoma cells by epigenetically silencing CDKN1A and KLF2.}, journal = {Cancer communications (London, England)}, volume = {38}, number = {1}, pages = {64}, pmid = {30367681}, issn = {2523-3548}, support = {81602052//the National Natural Science Foundation of China/International ; 8160100460//the National Natural Science Foundation of China/International ; 8157040399//the National Natural Science Foundation of China/International ; }, mesh = {Aged ; Animals ; Cell Line, Tumor ; Cell Proliferation/genetics ; Cyclin-Dependent Kinase Inhibitor p21/genetics/*metabolism ; Down-Regulation ; Epigenesis, Genetic ; Female ; Heterografts ; Humans ; Kruppel-Like Transcription Factors/genetics/*metabolism ; Male ; Mice ; Mice, Nude ; Pseudogenes ; RNA, Long Noncoding/genetics/*metabolism ; Transfection ; }, abstract = {BACKGROUND: Recent studies highlight pseudogene derived long non-coding RNAs (lncRNAs) as key regulators of cancer biology. However, few of them have been well characterized in pancreatic cancer. Here, we aimed to identify the association between pseudogene derived lncRNA DUXAP8 and growth of pancreatic cancer cells.<br><br>METHODS: We screened for pseudogene derived lncRNAs associated with human pancreatic cancer by comparative analysis of three independent datasets from GEO. Quantitative real-time reverse transcription polymerase chain reaction was used to assess the relative expression of DUXAP8 in pancreatic cancer tissues and cells. Loss-of-function approaches were used to investigate the potential functional roles of DUXAP8 in pancreatic cancer cell proliferation and apoptosis in vitro and in vivo. RNA immunoprecipitation, chromosome immunoprecipitation assay and rescue experiments were performed to analyze the association of DUXAP8 with target proteins and genes in pancreatic cancer cells.<br><br>RESULTS: Pancreatic cancer tissues had significantly higher DUXAP8 levels than paired adjacent normal tissues. High DUXAP8 expression was associated with a larger tumor size, advanced pathological stage and shorter overall survival of pancreatic cancer patients. Moreover, silencing DUXAP8 expression by siRNA or shRNA inhibited pancreatic cancer cell proliferation and promoted apoptosis in vitro and in vivo. Mechanistic analyses indicated that DUXAP8 regulates PC cell proliferation partly through downregulation of tumor suppressor CDKN1A and KLF2 expression.<br><br>CONCLUSION: Our results suggest that tumor expression of pseudogene derived lncRNA DUXAP8 plays an important role in pancreatic cancer progression. DUXAP8 may serve as a candidate biomarker and represent a novel therapeutic target of pancreatic cancer.}, }
@article {pmid30367007, year = {2019}, author = {Ren, L and Song, X and He, D and Wang, J and Tan, M and Xia, X and Li, G and Tan, Y and Wu, QL}, title = {Bacterioplankton Metacommunity Processes across Thermal Gradients: Weaker Species Sorting but Stronger Niche Segregation in Summer than in Winter in a Subtropical Bay.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {2}, pages = {}, pmid = {30367007}, issn = {1098-5336}, mesh = {*Bacterial Physiological Phenomena ; Bays/microbiology ; China ; Ecosystem ; High-Throughput Nucleotide Sequencing ; *Hot Temperature ; Microbiota/*physiology ; Phytoplankton/*physiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Seasons ; }, abstract = {Thermal effluents from nuclear power plants greatly change the environmental and ecological conditions of the receiving marine water body, but knowledge about their impact on microbial ecology is limited. Here we used high-throughput sequencing of the 16S rRNA gene to examine marine bacterioplankton metacommunity assembly across thermal gradients in two representative seasons (i.e., winter and summer) in a subtropical bay located on the northern coast of the South China Sea. We found high heterogeneity in bacterioplankton community compositions (BCCs) across thermal gradients and between seasons. The spatially structured temperature gradient created by thermal effluents was the key determinant of BCCs, but its influence differed by season. Using a metacommunity approach, we found that in the thermal discharge area, i.e., where water is frequently exchanged with surrounding seawater and thermal effluent water, the BCC spatial patterns were shaped by species sorting rather than by mass effects from surrounding seawater or by dilution of thermal effluent water by surrounding seawater. However, this effect of species sorting was weaker in summer than in winter seawater. In both seasons, the bacterioplankton community structure was predominately determined by niche sharing; however, the relative importance of niche segregation was enhanced in summer seawater. Our findings suggest that for the seasonal differences in metacommunity processes, the BCCs of subtropical summer seawater were more sensitive to temperature and were more difficult to predict than those of winter seawater in the face of different intensities of thermal impacts.IMPORTANCE Understanding the mechanisms of bacterial community assembly across environmental gradients is one of the major goals of marine microbial ecology. Thermal effluents from two nuclear power plants have been present in the subtropical Daya Bay for more than 20 years and have generated a comparatively stable and long thermal gradient (a temperature increase from 0 to 10°C). The environmental patches across thermal gradients are heterogeneous and very strongly interconnected on a microbial scale; thus, this is a useful model for the study of the metacommunity processes (i.e., patch dynamics, species sorting, mass effects, and neutral processes) that underlie marine bacterioplankton assembly. The significance of our research is to reveal how environmental conditions and dispersal-related processes interact to influence bacterioplankton metacommunity processes and their seasonal differences across thermal gradients. Our results may advance the understanding of marine microbial ecology under future conditions of global warming.}, }
@article {pmid30367000, year = {2019}, author = {Šulčius, S and Šimoliūnas, E and Alzbutas, G and Gasiūnas, G and Jauniškis, V and Kuznecova, J and Miettinen, S and Nilsson, E and Meškys, R and Roine, E and Paškauskas, R and Holmfeldt, K}, title = {Genomic Characterization of Cyanophage vB_AphaS-CL131 Infecting Filamentous Diazotrophic Cyanobacterium Aphanizomenon flos-aquae Reveals Novel Insights into Virus-Bacterium Interactions.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {1}, pages = {}, pmid = {30367000}, issn = {1098-5336}, mesh = {Aphanizomenon/*virology ; Base Sequence ; Clustered Regularly Interspaced Short Palindromic Repeats ; DNA, Viral/analysis ; Genome, Viral/*genetics ; Lithuania ; Phylogeny ; Siphoviridae/classification/*genetics ; }, abstract = {While filamentous cyanobacteria play a crucial role in food web dynamics and biogeochemical cycling of many aquatic ecosystems around the globe, the knowledge regarding the phages infecting them is limited. Here, we describe the complete genome of the virulent cyanophage vB_AphaS-CL131 (here, CL 131), a Siphoviridae phage that infects the filamentous diazotrophic bloom-forming cyanobacterium Aphanizomenon flos-aquae in the brackish Baltic Sea. CL 131 features a 112,793-bp double-stranded DNA (dsDNA) genome encompassing 149 putative open reading frames (ORFs), of which the majority (86%) lack sequence homology to genes with known functions in other bacteriophages or bacteria. Phylogenetic analysis revealed that CL 131 possibly represents a new evolutionary lineage within the group of cyanophages infecting filamentous cyanobacteria, which form a separate cluster from phages infecting unicellular cyanobacteria. CL 131 encodes a putative type V-U2 CRISPR-Cas system with one spacer (out of 10) targeting a DNA primase pseudogene in a cyanobacterium and a putative type II toxin-antitoxin system, consisting of a GNAT family N-acetyltransferase and a protein of unknown function containing the PRK09726 domain (characteristic of HipB antitoxins). Comparison of CL 131 proteins to reads from Baltic Sea and other available fresh- and brackish-water metagenomes and analysis of CRISPR-Cas arrays in publicly available A. flos-aquae genomes demonstrated that phages similar to CL 131 are present and dynamic in the Baltic Sea and share a common history with their hosts dating back at least several decades. In addition, different CRISPR-Cas systems within individual A. flos-aquae genomes targeted several sequences in the CL 131 genome, including genes related to virion structure and morphogenesis. Altogether, these findings revealed new genomic information for exploring viral diversity and provide a model system for investigation of virus-host interactions in filamentous cyanobacteria.IMPORTANCE The genomic characterization of novel cyanophage vB_AphaS-CL131 and the analysis of its genomic features in the context of other viruses, metagenomic data, and host CRISPR-Cas systems contribute toward a better understanding of aquatic viral diversity and distribution in general and of brackish-water cyanophages infecting filamentous diazotrophic cyanobacteria in the Baltic Sea in particular. The results of this study revealed previously undescribed features of cyanophage genomes (e.g., self-excising intein-containing putative dCTP deaminase and putative cyanophage-encoded CRISPR-Cas and toxin-antitoxin systems) and can therefore be used to predict potential interactions between bloom-forming cyanobacteria and their cyanophages.}, }
@article {pmid30366996, year = {2019}, author = {De Filippis, F and La Storia, A and Villani, F and Ercolini, D}, title = {Strain-Level Diversity Analysis of Pseudomonas fragi after In Situ Pangenome Reconstruction Shows Distinctive Spoilage-Associated Metabolic Traits Clearly Selected by Different Storage Conditions.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {1}, pages = {}, pmid = {30366996}, issn = {1098-5336}, mesh = {Food Packaging/*methods ; Food Storage/*methods ; *Genes, Bacterial ; Genome, Bacterial ; Metabolic Networks and Pathways ; Metagenome ; Metagenomics ; Pseudomonas fragi/*genetics/metabolism ; Red Meat/*microbiology ; }, abstract = {Microbial spoilage of raw meat causes huge economic losses every year. An understanding of the microbial ecology associated with the spoilage and its dynamics during the refrigerated storage of meat can help in preventing and delaying the spoilage-related activities. The raw meat microbiota is usually complex, but only a few members will develop during storage and cause spoilage upon the pressure from several external factors, such as temperature and oxygen availability. We characterized the metagenome of beef packed aerobically or under vacuum during refrigerated storage to explore how different packaging conditions may influence the microbial composition and potential spoilage-associated activities. Different population dynamics and spoilage-associated genomic repertoires occurred in beef stored aerobically or in vacuum packaging. Moreover, the pangenomes of Pseudomonas fragi strains were extracted from metagenomes. We demonstrated the presence of specific, storage-driven strain-level profiles of Pseudomonas fragi, characterized by different gene repertoires and thus potentially able to act differently during meat spoilage. The results provide new knowledge on strain-level microbial ecology associated with meat spoilage and may be of value for future strategies of spoilage prevention and food waste reduction.IMPORTANCE This work provides insights on the mechanisms involved in raw beef spoilage during refrigerated storage and on the selective pressure exerted by the packaging conditions. We highlighted the presence of different microbial metagenomes during the spoilage of beef packaged aerobically or under vacuum. The packaging condition was able to select specific Pseudomonas fragi strains with distinctive genomic repertoires. This study may help in deciphering the behavior of different biomes directly in situ in food and in understanding the specific contribution of different strains to food spoilage.}, }
@article {pmid30366260, year = {2019}, author = {Sharma, S and Tripathi, P}, title = {Gut microbiome and type 2 diabetes: where we are and where to go?.}, journal = {The Journal of nutritional biochemistry}, volume = {63}, number = {}, pages = {101-108}, doi = {10.1016/j.jnutbio.2018.10.003}, pmid = {30366260}, issn = {1873-4847}, mesh = {Animals ; Anti-Bacterial Agents/adverse effects ; Carbohydrate Metabolism ; Diabetes Mellitus, Type 2/diet therapy/*microbiology ; Diet ; Gastrointestinal Microbiome/*physiology ; Humans ; Obesity/microbiology ; Probiotics/therapeutic use ; }, abstract = {Type 2 diabetes mellitus (T2D) is a highly prevalent metabolic disorder characterized by an imbalance in blood glucose level, altered lipid profile and high blood pressure. Genetic constituents, high-fat and high-energy dietary habits, and a sedentary lifestyle are three major factors that contribute to high risk of T2D. Several studies have reported gut microbiome dysbiosis as a factor in rapid progression of insulin resistance in T2D that accounts for about 90% of all diabetes cases worldwide. The gut microbiome dysbiosis may reshape intestinal barrier functions and host metabolic and signaling pathways, which are directly or indirectly related to the insulin resistance in T2D. Thousands of the metabolites derived from microbes interact with the epithelial, hepatic and cardiac cell receptors that modulate host physiology. Xenobiotics including dietary components, antibiotics and nonsteroidal anti-inflammatory drugs strongly affect the gut microbial composition and can promote dysbiosis. Any change in the gut microbiota can shift the host metabolism towards increased energy harvest during diabetes and obesity. However, the exact mechanisms behind the dynamics of gut microbes and their impact on host metabolism at the molecular level are yet to be deciphered. We reviewed the published literature for better understanding of the dynamics of gut microbiota, factors that potentially induce gut microbiome dysbiosis and their relation to the progression of T2D. Special emphasis was also given to understand the gut microbiome induced breaching of intestinal barriers and/or tight junctions and their relation to insulin resistance.}, }
@article {pmid30362214, year = {2019}, author = {Götz, F and Pjevac, P and Markert, S and McNichol, J and Becher, D and Schweder, T and Mussmann, M and Sievert, SM}, title = {Transcriptomic and proteomic insight into the mechanism of cyclooctasulfur- versus thiosulfate-oxidation by the chemolithoautotroph Sulfurimonas denitrificans.}, journal = {Environmental microbiology}, volume = {21}, number = {1}, pages = {244-258}, doi = {10.1111/1462-2920.14452}, pmid = {30362214}, issn = {1462-2920}, support = {OCE-1559198//NSF/International ; //The Investment in Science Fund at WHOI/International ; //Institute of Marine Biotechnology e.V./International ; }, mesh = {Chemoautotrophic Growth ; Gene Expression Regulation, Bacterial ; Helicobacteraceae/*genetics/*metabolism ; Oxidation-Reduction ; *Proteome ; Proteomics ; Sulfur/*metabolism ; Thiosulfates/*metabolism ; *Transcriptome ; }, abstract = {Chemoautotrophic bacteria belonging to the genus Sulfurimonas (class Campylobacteria) were previously identified as key players in the turnover of zero-valence sulfur, a central intermediate in the marine sulfur cycle. S. denitrificans was further shown to be able to oxidize cyclooctasulfur (S8). However, at present the mechanism of activation and metabolism of cyclooctasulfur is not known. Here, we assessed the transcriptome and proteome of S. denitrificans grown with either thiosulfate or S8 as the electron donor. While the overall expression profiles under the two growth conditions were rather similar, distinct differences were observed that could be attributed to the utilization of S8 . This included a higher abundance of expressed genes related to surface attachment in the presence of S8 , and the differential regulation of the sulfur-oxidation multienzyme complex (SOX), which in S. denitrificans is encoded in two gene clusters: soxABXY 1 Z 1 and soxCDY 2 Z 2 . While the proteins of both clusters were present with thiosulfate, only proteins of the soxCDY 2 Z 2 were detected at significant levels with S8 . Based on these findings a model for the oxidation of S8 is proposed. Our results have implications for interpreting metatranscriptomic and -proteomic data and for the observed high level of diversification of soxY 2 Z 2 among sulfur-oxidizing Campylobacteria.}, }
@article {pmid30362076, year = {2019}, author = {Almeida, OGG and De Martinis, ECP}, title = {Bioinformatics tools to assess metagenomic data for applied microbiology.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {1}, pages = {69-82}, doi = {10.1007/s00253-018-9464-9}, pmid = {30362076}, issn = {1432-0614}, support = {17/13759-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 6762/2006-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (BR)/ ; }, mesh = {Biodiversity ; Computational Biology/*methods ; Gene Library ; High-Throughput Nucleotide Sequencing/methods ; Industrial Microbiology/*methods ; Metagenomics/*methods/statistics &amp; numerical data ; Phylogeny ; Quality Control ; }, abstract = {The reduction of the price of DNA sequencing has resulted in the emergence of large data sets to handle and analyze, especially in microbial ecosystems, which are characterized by high taxonomic and functional diversities. To assess the properties of these complex ecosystems, a conceptual background of the application of NGS technology and bioinformatics analysis to metagenomics is required. Accordingly, this article presents an overview of the evolution of knowledge of microbial ecology from traditional culture-dependent methods to culture-independent methods and the last frontier in knowledge, metagenomics. Topics that will be covered include sample preparation for NGS, starting with total DNA extraction and library preparation, followed by a brief discussion of the chemistry of NGS to help provide an understanding of which bioinformatics pipeline approach may be helpful for achieving a researcher's goals. The importance of selecting appropriate sequencing coverage and depth parameters to obtain a suitable measure of microbial diversity is discussed. As all DNA sequencing processes produce base-calling errors that compromise data analysis, including genome assembly and microbial functional analysis, dedicated software is presented and conceptually discussed with regard to potential applications in the general microbial ecology field.}, }
@article {pmid30359366, year = {2018}, author = {Bosmans, L and Pozo, MI and Verreth, C and Crauwels, S and Wilberts, L and Sobhy, IS and Wäckers, F and Jacquemyn, H and Lievens, B}, title = {Habitat-specific variation in gut microbial communities and pathogen prevalence in bumblebee queens (Bombus terrestris).}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0204612}, pmid = {30359366}, issn = {1932-6203}, mesh = {Animals ; Bacteria/isolation &amp; purification/pathogenicity ; Bees/*microbiology ; Biodiversity ; Crithidia/isolation &amp; purification/pathogenicity ; *Ecosystem ; Female ; Fungi/isolation &amp; purification ; Gastrointestinal Microbiome ; Nosema/isolation &amp; purification/pathogenicity ; Prevalence ; }, abstract = {Gut microbial communities are critical for the health of many insect species. However, little is known about how gut microbial communities respond to anthropogenic changes and how such changes affect host-pathogen interactions. In this study, we used deep sequencing to investigate and compare the composition of gut microbial communities within the midgut and ileum (both bacteria and fungi) in Bombus terrestris queens collected from natural (forest) and urbanized habitats. Additionally, we investigated whether the variation in gut microbial communities under each habitat affected the prevalence of two important bumblebee pathogens that have recently been associated with Bombus declines (Crithidia bombi and Nosema bombi). Microbial community composition differed strongly among habitat types, both for fungi and bacteria. Fungi were almost exclusively associated with bumblebee queens from the forest habitats, and were not commonly detected in bumblebee queens from the urban sites. Further, gut bacterial communities of urban B. terrestris specimens were strongly dominated by bee-specific core bacteria like Snodgrassella (Betaproteobacteria) and Gilliamella (Gammaproteobacteria), whereas specimens from the forest sites contained a huge fraction of environmental bacteria. Pathogen infection was very low in urban populations and infection by Nosema was only observed in specimens collected from forest habitats. No significant relationship was found between pathogen prevalence and microbial gut diversity. However, there was a significant and negative relationship between prevalence of Nosema and relative abundance of the core resident Snodgrassella, supporting its role in pathogen defense. Overall, our results indicate that land-use change may lead to different microbial gut communities in bumblebees, which may have implications for bumblebee health, survival and overall fitness.}, }
@article {pmid30357428, year = {2019}, author = {Kamitani, M and Nagano, AJ and Honjo, MN and Kudoh, H}, title = {A Survey on Plant Viruses in Natural Brassicaceae Communities Using RNA-Seq.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {113-121}, pmid = {30357428}, issn = {1432-184X}, support = {JP26221106//KAKENHI/ ; 16H06171//KAKENHI/ ; JP16H01473//KAKENHI/ ; JPMJCR15O1//Core Research for Evolutional Science and Technology/ ; JPMJCR15O2//Core Research for Evolutional Science and Technology/ ; 15J00628//Grant-in-Aid for JSPS Fellows/ ; }, mesh = {Brassicaceae/classification/*virology ; Genome, Viral ; Phylogeny ; Plant Diseases/*virology ; Plant Viruses/classification/genetics/*isolation &amp; purification ; Sequence Analysis, RNA ; }, abstract = {Studies on plant viruses are biased towards crop diseases and little is known about viruses in natural vegetation. We conducted extensive surveys of plant viruses in wild Brassicaceae plants occurring in three local plant communities in central Japan. We applied RNA-Seq with selective depletion of rRNA, which allowed us to detect infections of all genome-reported viruses simultaneously. Infections of Turnip mosaic virus (TuMV), Cucumber mosaic virus (CMV), Brassica yellows virus, Pelargonium zonate spot virus, and Arabidopsis halleri partitivirus 1 were detected from the two perennial species, Arabidopsis halleri subsp. gemmifera and Rorippa indica. De novo assembly further detected partial sequences of a putative novel virus in Arabis fragellosa. Virus species composition and infection rate differed depending on site and plant species. Viruses were most frequently detected from the perennial clonal plant, A. halleri, in which a high clonal transmission rate of viruses across multiple years was confirmed. Phylogenetic analysis of TuMV and CMV showed that virus strains from wild Brassicaceae were included as a major clade of these viruses with other reported strains from crop plants, suggesting that viruses were shared among wild plants and crops. Our studies indicated that distribution of viruses in natural plant populations are determined by the combinations of life histories of viruses and hosts. Revealing viral distribution in the natural plant communities improves our knowledge on the ecology of plant viruses.}, }
@article {pmid30357425, year = {2019}, author = {Li, CX and Fan, YF and Luan, W and Dai, Y and Wang, MX and Wei, CM and Wang, Y and Tao, X and Mao, P and Ma, XR}, title = {Titanium Ions Inhibit the Bacteria in Vase Solutions of Freshly Cut Gerbera jamesonii and Extend the Flower Longevity.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {967-979}, pmid = {30357425}, issn = {1432-184X}, support = {2017YFD0201301//National Key Research and Development Program of China/ ; 2018NA0027//Key Research and Development Program of Sichuan/ ; }, mesh = {Asteraceae/growth &amp; development ; Bacteria/classification/drug effects/*metabolism ; Flowers/growth &amp; development ; Ions/metabolism ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Titanium/*metabolism ; *Water Microbiology ; }, abstract = {Titanium ions significantly promote plant growth, but the mechanism is still unclear. Cut flowers are ideal materials for the study of plant growth and senescence. In this study, freshly cut Gerbera jamesonii were used to study the effects of titanium ions (8 mg/L) on the flower longevity. Flowering observation showed that the gerbera vase life was significantly prolonged in the presence of titanium ions. Plate colony counts showed that the amounts of bacteria in the vase solution of the control group were approximately 1700 times more than that of titanium ion treatment group. High-throughput sequencing was used to determine the sequences of 16S rRNA gene V3-V4 variable regions of the vase solutions to analyze bacterial species, their average proportions, and absolute abundance. The results showed that the titanium ions reduced the entire bacterial counts as well as altered the absolute abundance of different bacterial species in the vase solution. The most prevalent bacteria were mainly Enterobacteriaceae, Pseudomonas veronii, Pseudomonas sp., Delftia sp., Agrobacterium sp., Sphingobacterium multivorum, Acinetobacter johnsonii, and Clostridiaceae. In combination with plate colony counts, we demonstrated that all the bacterial growths were significantly inhibited by titanium ions, regardless of their average proportions increased or decreased. These results showed that titanium ions could extend effectively the longevity of gerberas and possess the broad-spectrum antibacterial properties. This study provides a basis for further mechanism exploration of titanium ions action and its applications in cut flower preservation and agricultural production.}, }
@article {pmid30355963, year = {2018}, author = {Almendras, K and Leiva, D and Carú, M and Orlando, J}, title = {Carbon Consumption Patterns of Microbial Communities Associated with Peltigera Lichens from a Chilean Temperate Forest.}, journal = {Molecules (Basel, Switzerland)}, volume = {23}, number = {11}, pages = {}, pmid = {30355963}, issn = {1420-3049}, support = {11100381 and 1181510//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; }, mesh = {Carbon/*metabolism ; Chile ; *Forests ; Lichens/*metabolism/*microbiology ; Metabolome ; Metabolomics ; *Microbiota ; }, abstract = {Lichens are a symbiotic association between a fungus and a green alga or a cyanobacterium, or both. They can grow in practically any terrestrial environment and play crucial roles in ecosystems, such as assisting in soil formation and degrading soil organic matter. In their thalli, they can host a wide diversity of non-photoautotrophic microorganisms, including bacteria, which play important functions and are considered key components of the lichens. In this work, using the BioLog[®] EcoPlate system, we studied the consumption kinetics of different carbon-sources by microbial communities associated with the thallus and the substrate of Peltigera lichens growing in a Chilean temperate rain forest dominated by Nothofagus pumilio. Based on the similarity of the consumption of 31 carbon-sources, three groups were formed. Among them, one group clustered the microbial metabolic profiles of almost all the substrates from one of the sampling sites, which exhibited the highest levels of consumption of the carbon-sources, and another group gathered the microbial metabolic profiles from the lichen thalli with the most abundant mycobiont haplotypes. These results suggest that the lichen thallus has a higher impact on the metabolism of its microbiome than on the microbial community of its substrate, with the latter being more diverse in terms of the metabolized sources and whose activity level is probably related to the availability of soil nutrients. However, although significant differences were detected in the microbial consumption of several carbon-sources when comparing the lichen thallus and the underlying substrate, d-mannitol, l-asparagine, and l-serine were intensively metabolized by both communities, suggesting that they share some microbial groups. Likewise, some communities showed high consumption of 2-hydroxybenzoic acid, d-galacturonic acid, and itaconic acid; these could serve as suitable sources of microorganisms as bioresources of novel bioactive compounds with biotechnological applications.}, }
@article {pmid30355662, year = {2018}, author = {Hird, SM and Ganz, H and Eisen, JA and Boyce, WM}, title = {The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, pmid = {30355662}, issn = {2379-5042}, support = {HHSN266200700010C/AI/NIAID NIH HHS/United States ; HHSN272201400008C/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bird Diseases/*virology ; Cloaca/*microbiology ; Disease Reservoirs ; Ducks/*microbiology/*virology ; Influenza A virus ; Influenza in Birds/*microbiology/virology ; *Microbiota ; }, abstract = {Waterfowl, especially ducks of the genus Anas, are natural reservoir species for influenza A virus (IAV). Duck populations contain nearly all the known diversity of IAVs, and the birds are asymptomatic to infection. Previous work established that IAV infection status is correlated with changes in the cloacal microbiome in juvenile mallards. Here, we analyze five Anas species to determine whether these duck species have similar IAV[+] and IAV[-] cloacal microbiomes, or if the relationships among a host, influenza virus, and the microbiome are species specific. We assessed taxonomic composition of the microbiome, alpha diversity, and beta diversity and found very few patterns related to microbiome and infection status across species, while detecting strong differences within species. A host species-specific signal was stronger in IAV[-] ducks than IAV[+] ducks, and the effect size of host species on the microbiome was three times higher in IAV[-] birds than IAV[+] birds. The mallards and the northern shovelers, the species with highest sample sizes but also with differing feeding ecology, showed especially contrasting patterns in microbiome composition, alpha diversity, and beta diversity. Our results indicate that the microbiome may have a unique relationship with influenza virus infection at the species level.IMPORTANCE Waterfowl are natural reservoir species for influenza A virus (IAV). Thus, they maintain high levels of pathogen diversity, are asymptomatic to the infection, and also contribute to the risk of a global influenza pandemic. An individual's microbiome is a critical part in how a vertebrate manages pathogens and illness. Here, we describe the cloacal microbiome of 300 wild ducks, from five species (four with previously undescribed microbiomes), including both IAV-negative and IAV-positive individuals. We demonstrate that there is not one consistent "flu-like" microbiome or response to flu across species. Individual duck species appear to have unique relationships between their microbiomes and IAV, and IAV-negative birds have a stronger tie to host species than the IAV-positive birds. In a broad context, understanding the role of the microbiome in IAV reservoir species may have future implications for avian disease management.}, }
@article {pmid30355348, year = {2018}, author = {Tackmann, J and Arora, N and Schmidt, TSB and Rodrigues, JFM and von Mering, C}, title = {Ecologically informed microbial biomarkers and accurate classification of mixed and unmixed samples in an extensive cross-study of human body sites.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {192}, pmid = {30355348}, issn = {2049-2618}, mesh = {Bacteria/*classification/*genetics ; Biomarkers/analysis ; DNA, Bacterial/*genetics ; Genome, Bacterial/*genetics ; Human Body ; Humans ; Machine Learning ; Microbiota/*genetics ; }, abstract = {BACKGROUND: The identification of body site-specific microbial biomarkers and their use for classification tasks have promising applications in medicine, microbial ecology, and forensics. Previous studies have characterized site-specific microbiota and shown that sample origin can be accurately predicted by microbial content. However, these studies were usually restricted to single datasets with consistent experimental methods and conditions, as well as comparatively small sample numbers. The effects of study-specific biases and statistical power on classification performance and biomarker identification thus remain poorly understood. Furthermore, reliable detection in mixtures of different body sites or with noise from environmental contamination has rarely been investigated thus far. Finally, the impact of ecological associations between microbes on biomarker discovery was usually not considered in previous work.<br><br>RESULTS: Here we present the analysis of one of the largest cross-study sequencing datasets of microbial communities from human body sites (15,082 samples from 57 publicly available studies). We show that training a Random Forest Classifier on this aggregated dataset increases prediction performance for body sites by 35% compared to a single-study classifier. Using simulated datasets, we further demonstrate that the source of different microbial contributions in mixtures of different body sites or with soil can be detected starting at 1% of the total microbial community. We apply a biomarker selection method that excludes indirect environmental associations driven by microbe-microbe associations, yielding a parsimonious set of highly predictive taxa including novel biomarkers and excluding many previously reported taxa. We find a considerable fraction of unclassified biomarkers ("microbial dark matter") and observe that negatively associated taxa have a surprisingly high impact on classification performance. We further detect a significant enrichment of rod-shaped, motile, and sporulating taxa for feces biomarkers, consistent with a highly competitive environment.<br><br>CONCLUSIONS: Our machine learning model shows strong body site classification performance, both in single-source samples and mixtures, making it promising for tasks requiring high accuracy, such as forensic applications. We report a core set of ecologically informed biomarkers, inferred across a wide range of experimental protocols and conditions, providing the most concise, general, and least biased overview of body site-associated microbes to date.}, }
@article {pmid30353678, year = {2019}, author = {Tan, CK and Natrah, I and Suyub, IB and Edward, MJ and Kaman, N and Samsudin, AA}, title = {Comparative study of gut microbiota in wild and captive Malaysian Mahseer (Tor tambroides).}, journal = {MicrobiologyOpen}, volume = {8}, number = {5}, pages = {e00734}, pmid = {30353678}, issn = {2045-8827}, mesh = {Animals ; Bacteria/*classification/*genetics ; Cluster Analysis ; Cyprinidae/*microbiology ; DNA, Ribosomal/chemistry/genetics ; *Gastrointestinal Microbiome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {AIMS: The aim of this study was to identify and compare the gut microbial community of wild and captive Tor tambroides through 16S rDNA metagenetic sequencing followed by functions prediction.<br><br>METHODS AND RESULTS: The library of 16S rDNA V3-V4 hypervariable regions of gut microbiota was amplified and sequenced using Illumina MiSeq. The sequencing data were analyzed using Quantitative Insights into Microbial Ecology (QIIME) pipeline and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). The most abundant bacterial phyla in both wild and captive T.&#xa0;tambroides were Firmicutes, Proteobacteria, Fusobacteria and Bacteroidetes. Cetobacterium spp., Peptostreptococcaceae family, Bacteroides spp., Phosphate solubilizing bacteria PSB-M-3, and Vibrio spp. were five most abundant OTU in wild T.&#xa0;tambroides as compared to Cetobacterium spp., Citrobacter spp., Aeromonadaceae family, Peptostreptococcaceae family and Turicibacter spp. in captive T.&#xa0;tambroides.<br><br>CONCLUSION: In this study, the specimens of the wild T.&#xa0;tambroides contain more diverse gut microbiota than of the captive ones. The results suggested that Cetobacterium spp. is one of the core microbiota in guts of T.&#xa0;tambroides. Besides, high abundant Bacteroides spp., Citrobacter spp., Turicibacter spp., and Bacillus spp. may provide important functions in T.&#xa0;tambroides guts.<br><br>The results of this study provide significant information of T.&#xa0;tambroides gut microbiota for further understanding of their physiological functions including growth and disease resistance.}, }
@article {pmid30352731, year = {2019}, author = {De Vrieze, J and Colica, G and Pintucci, C and Sarli, J and Pedizzi, C and Willeghems, G and Bral, A and Varga, S and Prat, D and Peng, L and Spiller, M and Buysse, J and Colsen, J and Benito, O and Carballa, M and Vlaeminck, SE}, title = {Resource recovery from pig manure via an integrated approach: A technical and economic assessment for full-scale applications.}, journal = {Bioresource technology}, volume = {272}, number = {}, pages = {582-593}, doi = {10.1016/j.biortech.2018.10.024}, pmid = {30352731}, issn = {1873-2976}, mesh = {Anaerobiosis ; Animals ; Composting ; *Manure ; Swine ; }, abstract = {Intensive livestock farming cannot be uncoupled from the massive production of manure, requiring adequate management to avoid environmental damage. The high carbon, nitrogen and phosphorus content of pig manure enables targeted resource recovery. Here, fifteen integrated scenarios for recovery of water, nutrients and energy are compared in terms of technical feasibility and economic viability. The recovery of refined nutrients with a higher market value and quality, i.e., (NH4)2SO4 for N and struvite for P, coincided with higher net costs, compared to basic composting. The inclusion of anaerobic digestion promoted nutrient recovery efficiency, and enabled energy recovery through electricity production. Co-digestion of the manure with carbon-rich waste streams increased electricity production, but did not result in lower process costs. Overall, key drivers for the selection of the optimal manure treatment scenario will include the market demand for more refined (vs. separated or concentrated) products, and the need for renewable electricity production.}, }
@article {pmid30352325, year = {2019}, author = {Christiaens, MER and De Vrieze, J and Clinckemaillie, L and Ganigué, R and Rabaey, K}, title = {Anaerobic ureolysis of source-separated urine for NH3 recovery enables direct removal of divalent ions at the toilet.}, journal = {Water research}, volume = {148}, number = {}, pages = {97-105}, doi = {10.1016/j.watres.2018.10.021}, pmid = {30352325}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Bathroom Equipment ; Bioreactors ; Hydrolysis ; Ions ; Sewage ; }, abstract = {Source-separated urine is of interest for nutrient recovery. Most nitrogen recovery technologies rely on ammonia (NH3) as input, which requires ureolysis. As urease positive bacteria are widespread, source-separated urine is unstable, not only leading to NH3 release but also loss, odor nuisance, and downstream scaling. Hence, ureolysis ideally occurs in a closed controlled environment close to the toilet. We characterized microbial-induced ureolysis, subsequent divalent cation precipitation, and fermentation in anaerobic sequencing batch reactors (SBRs) at 15 °C and 28 °C. Temperatures were a proxy for urine hydrolysis in a wet well at street level or in the toilet, respectively. The need for inoculation and the metabolic stability was assessed by inoculation with autofermented urine or a mixture of anaerobic digestion and fermentation sludge. The highest specific ureolysis rates in the SBRs were achieved at 28 °C: 2107 ± 395 and 1948 ± 1121 mg N g VSS[-1] d[-1], for the mixed and autofermented inoculum, respectively. For Ca[2+] and Mg[2+] precipitation, and organics fermentation, autofermented urine at 28 °C performed best with 47.9 ± 16.4 mg Ca[2+] g VSS[-1] d[-1], 8.2 ± 4.6 mg Mg[2+] g VSS[-1] d[-1], and 623 ± 129 mg VFA-COD g VSS[-1] d[-1], respectively. This indicates the hydrolysis reactor should be close to the toilet. The selected inoculum did not impact ureolysis, whereas both Ca[2+] and Mg[2+] precipitation and fermentation were better in the SBRs with autofermented urine. Ureolysis was identified as the only process significantly impacting the microbial community, indicating external inoculation would not be required. A urine hydrolysis reactor in the toilet without external inoculation could thus serve as a controlled environment to release NH3 and remove divalent cations to prevent scaling in downstream transport and processing. For practical implementation in a household toilet, the reactor should be designed for user-friendly precipitate discharge and odor control.}, }
@article {pmid30350953, year = {2018}, author = {Cabernard, L and Roscher, L and Lorenz, C and Gerdts, G and Primpke, S}, title = {Comparison of Raman and Fourier Transform Infrared Spectroscopy for the Quantification of Microplastics in the Aquatic Environment.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {22}, pages = {13279-13288}, doi = {10.1021/acs.est.8b03438}, pmid = {30350953}, issn = {1520-5851}, mesh = {Environmental Monitoring ; North Sea ; *Plastics ; Spectroscopy, Fourier Transform Infrared ; *Water Pollutants, Chemical ; }, abstract = {Microplastics (MPs, <5 mm) have been reported as emerging environmental contaminants, but reliable data are still lacking. We compared the two most promising techniques for MP analysis, namely, Raman and Fourier transform infrared (FTIR) spectroscopy, by analyzing MPs extracted from North Sea surface waters. Microplastics >500 μm were visually sorted and manually analyzed by μ-Raman and attenuated total reflection (ATR)-FTIR spectroscopy. Microplastics ≤500 μm were concentrated on gold-coated filters and analyzed by automated single-particle exploration coupled to μ-Raman (ASPEx-μ-Raman) and FTIR imaging (reflection mode). The number of identified MPs >500 μm was slightly higher for μ-Raman (+23%) than ATR-FTIR analysis. Concerning MPs ≤500 μm, ASPEx-μ-Raman quantified two-times higher MP numbers but required a four-times higher analysis time compared to FTIR imaging. Because ASPEx-μ-Raman revealed far higher MP concentrations (38-2621 particles m[-3]) compared to the results of previous water studies (0-559 particles m[-3]), the environmental concentration of MPs ≤500 μm may have been underestimated until now. This may be attributed to the exceptional increase in concentration with decreasing MP size found in this work. Our results demonstrate the need for further research to enable time-efficient routine application of ASPEx-μ-Raman for reliable MP counting down to 1 μm.}, }
@article {pmid30349964, year = {2019}, author = {Gonzalez-Escobedo, R and Briones-Roblero, CI and López, MF and Rivera-Orduña, FN and Zúñiga, G}, title = {Changes in the Microbial Community of Pinus arizonica Saplings After Being Colonized by the Bark Beetle Dendroctonus rhizophagus (Curculionidae: Scolytinae).}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {102-112}, pmid = {30349964}, issn = {1432-184X}, support = {SIP 20180686//Secretar&#xed;a de Investigaci&#xf3;n y Posgrado, Instituto Polit&#xe9;cnico Nacional/ ; }, mesh = {Animals ; Arizona ; Bacteria/classification/genetics/*isolation &amp; purification ; Coleoptera/growth &amp; development/*physiology ; Feeding Behavior ; Fungi/classification/genetics/*isolation &amp; purification ; Life Cycle Stages ; *Microbiota ; Mycobiome ; Pinus/*microbiology/parasitology ; Plant Diseases/*parasitology ; Trees/microbiology/parasitology ; }, abstract = {The death of trees is an ecological process that promotes regeneration, organic matter recycling, and the structure of communities. However, diverse biotic and abiotic factors can disturb this process. Dendroctonus bark beetles (Curculionidae: Scolytinae) are natural inhabitants of pine forests, some of which produce periodic outbreaks, killing thousands of trees in the process. These insects spend almost their entire life cycle under tree bark, where they reproduce and feed on phloem. Tunneling and feeding of the beetles result in the death of the tree and an alteration of the resident microbiota as well as the introduction of microbes that the beetles vector. To understand how microbial communities in subcortical tissues of pines change after they are colonized by the bark beetle Dendroctonus rhizophagus, we compare both the bacterial and fungal community structures in two colonization stages of Pinus arizonica (Arizona pine) employing Illumina MiSeq. Our findings showed significant differences in diversity and the dominance of bacterial community in the two colonization stages with Shannon (P = 0.004) and Simpson (P = 0.0006) indices, respectively, but not in species richness with Chao1 (P = 0.19). In contrast, fungal communities in both stages showed significant differences in species richness with Chao1 (P = 0.0003) and a diversity with Shannon index (P = 0.038), but not in the dominance with the Simpson index (P = 0.12). The β-diversity also showed significant changes in the structure of bacterial and fungal communities along the colonization stages, maintaining the dominant members in both cases. Our results suggest that microbial communities present in the Arizona pine at the tree early colonization stage by bark beetle change predictably over time.}, }
@article {pmid30348833, year = {2019}, author = {Zeng, L and Burne, RA}, title = {Essential Roles of the sppRA Fructose-Phosphate Phosphohydrolase Operon in Carbohydrate Metabolism and Virulence Expression by Streptococcus mutans.}, journal = {Journal of bacteriology}, volume = {201}, number = {2}, pages = {}, pmid = {30348833}, issn = {1098-5530}, support = {R01 DE012236/DE/NIDCR NIH HHS/United States ; }, mesh = {Biofilms/growth &amp; development ; Cations, Divalent/metabolism ; Enzyme Activators ; Enzyme Inhibitors ; Fructose/*metabolism ; Fructose-Bisphosphatase/genetics/*metabolism ; Gene Deletion ; Gene Expression Regulation, Bacterial ; Magnesium/metabolism ; Manganese/metabolism ; *Operon ; Recombinant Proteins/genetics/metabolism ; Repressor Proteins/genetics/*metabolism ; Sodium Fluoride/metabolism ; Streptococcus mutans/*enzymology/genetics/growth &amp; development/metabolism ; Virulence Factors/*biosynthesis ; }, abstract = {The dental caries pathogen Streptococcus mutans can ferment a variety of sugars to produce organic acids. Exposure of S. mutans to certain nonmetabolizable carbohydrates, such as xylitol, impairs growth and can cause cell death. Recently, the presence of a sugar-phosphate stress in S. mutans was demonstrated using a mutant lacking 1-phosphofructokinase (FruK) that accumulates fructose-1-phosphate (F-1-P). Here, we studied an operon in S. mutans, sppRA, which was highly expressed in the fruK mutant. Biochemical characterization of a recombinant SppA protein indicated that it possessed hexose-phosphate phosphohydrolase activity, with preferences for F-1-P and, to a lesser degree, fructose-6-phosphate (F-6-P). SppA activity was stimulated by Mg[2+] and Mn[2+] but inhibited by NaF. SppR, a DeoR family regulator, repressed the expression of the sppRA operon to minimum levels in the absence of the fructose-derived metabolite F-1-P and likely also F-6-P. The accumulation of F-1-P, as a result of growth on fructose, not only induced sppA expression, but it significantly altered biofilm maturation through increased cell lysis and enhanced extracellular DNA release. Constitutive expression of sppA, via a plasmid or by deleting sppR, greatly alleviated fructose-induced stress in a fruK mutant, enhanced resistance to xylitol, and reversed the effects of fructose on biofilm formation. Finally, by identifying three additional putative phosphatases that are capable of promoting sugar-phosphate tolerance, we show that S. mutans is capable of mounting a sugar-phosphate stress response by modulating the levels of certain glycolytic intermediates, functions that are interconnected with the ability of the organism to manifest key virulence behaviors.IMPORTANCEStreptococcus mutans is a major etiologic agent for dental caries, primarily due to its ability to form biofilms on the tooth surface and to convert carbohydrates into organic acids. We have discovered a two-gene operon in S. mutans that regulates fructose metabolism by controlling the levels of fructose-1-phosphate, a potential signaling compound that affects bacterial behaviors. With fructose becoming increasingly common and abundant in the human diet, we reveal the ways that fructose may alter bacterial development, stress tolerance, and microbial ecology in the oral cavity to promote oral diseases.}, }
@article {pmid30344635, year = {2018}, author = {Lavoie, C and Courcelle, M and Redivo, B and Derome, N}, title = {Structural and compositional mismatch between captive and wild Atlantic salmon (Salmo salar) parrs' gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods.}, journal = {Evolutionary applications}, volume = {11}, number = {9}, pages = {1671-1685}, pmid = {30344635}, issn = {1752-4571}, abstract = {Stocking methods are used in the Province of Quebec to restore Salmo salar populations. However, Atlantic salmon stocked juveniles show higher mortality rates than wild ones when introduced into nature. Hatchery environment, which greatly differs from the natural environment, is identified as the main driver of the phenotypic mismatch between captive and wild parrs. The latter is also suspected to impact the gut microbiota composition, which can be associated with essential metabolic functions for their host. We hypothesized that hatchery-raised parrs potentially recruit gut microbial communities that are different from those recruited in the wild. This study evaluated the impacts of artificial rearing on gut microbiota composition in 0+ parrs meant for stocking in two distinct Canadian rivers: Rimouski and Malbaie (Quebec, Canada). Striking differences between hatchery and wild-born parrs' gut microbiota suggest that microbiota could be another factor that could impact their survival in the targeted river, because the microbiome is narrowly related to host physiology. For instance, major commensals belonging to Enterobacteriaceae and Clostridiacea from wild parrs' gut microbiota were substituted in captive parrs by lactic acid bacteria from the Lactobacillaceae family. Overall, captive parrs host a generalist bacterial community whereas wild parrs' microbiota is much more specialized. This is the very first study demonstrating extensive impact of captive rearing on intestinal microbiota composition in Atlantic salmon intended for wild population stocking. Our results strongly suggest the need to implement microbial ecology concepts into conservation management of endangered salmon stocks supplemented with hatchery-reared parrs.}, }
@article {pmid30343437, year = {2019}, author = {Li, T and Qi, M and Gatesoupe, FJ and Tian, D and Jin, W and Li, J and Lin, Q and Wu, S and Li, H}, title = {Adaptation to Fasting in Crucian Carp (Carassius auratus): Gut Microbiota and Its Correlative Relationship with Immune Function.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {6-19}, pmid = {30343437}, issn = {1432-184X}, support = {lzujbky-2018-68//Fundamental Research Funds for the Central Universities/ ; LY18E090010//Zhejiang Provincial Natural Science Foundation of China/ ; }, mesh = {Adaptation, Physiological ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Carps/*immunology/metabolism/*microbiology ; Fasting ; *Gastrointestinal Microbiome ; Intestines/immunology/*microbiology ; }, abstract = {Fasting influences the overall physiology of fish, and the knowledge how the gut microbiota, growth performances, and immune function in response to intermittent and long-term fasting is still insufficient. Here, we characterized the effects of fasting on the host-gut microbiota in crucian carp, which would enhance our insight into physiological adaptation to fasting. To achieve this, we investigated the gut microbial communities of crucian carp with different fasting stress, and corresponding immune and growth parameters. The gut microbial communities were structured into four clusters according to different fasting stress, namely one control group (feed regularly), two intermittent fasting groups (fasting period and re-feeding period, respectively), and one long-term fasting group. Intermittent fasting significantly improved the activity of superoxide dismutase (SOD) and lysozyme (LZM) (ANOVA, p < 0.05) and significantly increased alpha diversity and ecosystem stability of gut microbiota (ANOVA, p < 0.05). Gut length (GL) and condition factor (CF) showed no significant difference between the control group (CG) and intermittent fasting group under re-feeding period (RIF) (ANOVA, p = 0.11), but relative gut length (RGL) in group RIF was higher than that in the CG (ANOVA, p = 0.00). The bacterial genera Bacteroides, Akkermansia, and Erysipelotrichaceae were enriched in fishes under intermittent fasting. Two Bacteroides OTUs (OTU50 and OTU1292) correlated positively with immune (SOD, complement, and LZM) and growth (GL and RGL) parameters. These results highlight the possible interplay between growth performances, immune function, and gut microbiota in response to fasting.}, }
@article {pmid30342721, year = {2018}, author = {Free, A and McDonald, MA and Pagaling, E}, title = {Diversity-Function Relationships in Natural, Applied, and Engineered Microbial Ecosystems.}, journal = {Advances in applied microbiology}, volume = {105}, number = {}, pages = {131-189}, doi = {10.1016/bs.aambs.2018.07.002}, pmid = {30342721}, issn = {0065-2164}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Ecosystem ; Industrial Microbiology/*methods/trends ; *Metabolism ; *Microbial Consortia ; }, abstract = {The connection between ecosystem function and taxonomic diversity has been of interest and relevance to macroecologists for decades. After many years of lagging behind due to the difficulty of assigning both taxonomy and function to poorly distinguishable microscopic cells, microbial ecology now has access to a suite of powerful molecular tools which allow its practitioners to generate data relating to diversity and function of a microbial community on an unprecedented scale. Instead, the problem facing today's microbial ecologists is coupling the ease of generation of these datasets with the formulation and testing of workable hypotheses relating the diversity and function of environmental, host-associated, and engineered microbial communities. Here, we review the current state of knowledge regarding the links between taxonomic alpha- and beta-diversity and ecosystem function, comparing our knowledge in this area to that obtained by macroecologists who use more traditional techniques. We consider the methodologies that can be applied to study these properties and how successful they are at linking function to diversity, using examples from the study of model microbial ecosystems, methanogenic bioreactors (anaerobic digesters), and host-associated microbiota. Finally, we assess ways in which our newly acquired understanding might be used to manipulate diversity in ecosystems of interest in order to improve function for the benefit of us or the environment in general through the provision of ecosystem services.}, }
@article {pmid30341500, year = {2019}, author = {Deja-Sikora, E and Gołębiewski, M and Kalwasińska, A and Krawiec, A and Kosobucki, P and Walczak, M}, title = {Comamonadaceae OTU as a Remnant of an Ancient Microbial Community in Sulfidic Waters.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {85-101}, pmid = {30341500}, issn = {1432-184X}, support = {1919-B//Uniwersytet Mikolaja Kopernika w Toruniu/ ; }, mesh = {Archaea/classification/genetics/isolation &amp; purification/metabolism ; Comamonadaceae/*classification/genetics/*isolation &amp; purification/metabolism ; DNA, Bacterial/genetics ; Fresh Water/chemistry/*microbiology ; Geologic Sediments/chemistry/microbiology ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfides/*analysis/metabolism ; Sulfur/analysis/metabolism ; Water Microbiology ; }, abstract = {Intraterrestrial waters harbor microbial communities being extensively studied to understand microbial processes underlying subsurface ecosystem functioning. This paper provides the results of an investigation on the microbiomes of unique, subsurface sulfidic waters associated with Upper Jurassic, Cretaceous, and Miocene sediments. We used high-throughput 16S rDNA amplicon sequencing to reveal the structure of bacterial and archaeal communities in water samples differing in sulfide content (20-960 mg/dm[3]), salinity (1.3-3.2%), and depth of extraction (60-660 m below ground level). Composition of the bacterial communities strongly varied across the samples; however, the bacteria participating in the sulfur cycle were common in all sulfidic waters. The shallowest borehole water (60 m bgl) was dominated by sulfur-oxidizing Epsilonproteobacteria (Sulfurimonas, Sulfurovum). In the waters collected from greater depths (148-300 m bgl), the prevalence of Betaproteobacteria (Comamonadaceae) and sulfate/sulfur-reducing Deltaproteobacteria (Desulfopila, Desulfomicrobium, MSBL7) was observed. Sulfate reducers (members of Clostridia: Candidatus Desulforudis) were the most abundant bacteria in the deepest borehole water (660 m bgl). Out of 850 bacterial OTUs, only one, affiliated with the Comamonadaceae family, was found abundant (> 1% of total bacterial sequences) in all samples. Contribution of Archaea to the whole microbial communities was lower than 0.5%. Archaeal communities did not differ across the samples and they consisted of Halobacteriaceae. Out of 372 archaeal OTUs, five, belonging to the four genera Natronomonas, Halorubrum, Halobellus, and Halorhabdus, were the most numerous.}, }
@article {pmid30341452, year = {2019}, author = {Amberkar, U and Khandeparker, R and Parab, P}, title = {Nitrate Reductase Gene Expression in Idiomarina Strain cos21 Obtained from Oxygen Minimum Zone of Arabian Sea.}, journal = {Current microbiology}, volume = {76}, number = {1}, pages = {63-69}, pmid = {30341452}, issn = {1432-0991}, mesh = {Adaptation, Physiological/*genetics/physiology ; Alteromonadaceae/*enzymology/*genetics/isolation &amp; purification ; Anaerobiosis/physiology ; Denitrification/physiology ; Indian Ocean ; Nitrate Reductase/*biosynthesis/*genetics ; Nitrates/metabolism ; Nitrites/metabolism ; Oxygen/analysis ; RNA, Messenger/genetics ; }, abstract = {This study analyses the induction and repression of nitrate reduction activity in a batch culture of Idiomarina strain cos21. On a change from aerobic to anaerobic respiration, the culture entered a stationary phase. The onset of this phase showed 3.75 fold increase in mRNA levels for the nitrate reductase enzyme. mRNA accumulated very rapidly during a short period, after which its overall concentration declined to reach a lower value. The level of nitrite reductase protein reached a maximum value at 36 h of growth when the oxygen concentration dropped below 10 µM. The data set provided here confer new insights into the understanding of the physiological response of Idiomarina strain cos21 to change in oxygen concentration allowing the bacterium to survive and adapt to a new environment by dissimilatory reduction of nitrate to nitrite, which serves to provide energy as the bacteria adapt to anaerobiosis. Main strategy used here is to induce, measure, and track the expression of microbial genes, while they grow in culture conditions to better mimic interaction in a natural environment. This study will help us with a better understanding of the nitrate reduction process in the oxygen minimum zone.}, }
@article {pmid30340417, year = {2018}, author = {Van Houdt, R and Provoost, A and Van Assche, A and Leys, N and Lievens, B and Mijnendonckx, K and Monsieurs, P}, title = {Cupriavidus metallidurans Strains with Different Mobilomes and from Distinct Environments Have Comparable Phenomes.}, journal = {Genes}, volume = {9}, number = {10}, pages = {}, pmid = {30340417}, issn = {2073-4425}, support = {C90356//Federaal Wetenschapsbeleid/ ; }, abstract = {Cupriavidus metallidurans has been mostly studied because of its resistance to numerous heavy metals and is increasingly being recovered from other environments not typified by metal contamination. They host a large and diverse mobile gene pool, next to their native megaplasmids. Here, we used comparative genomics and global metabolic comparison to assess the impact of the mobilome on growth capabilities, nutrient utilization, and sensitivity to chemicals of type strain CH34 and three isolates (NA1, NA4 and H1130). The latter were isolated from water sources aboard the International Space Station (NA1 and NA4) and from an invasive human infection (H1130). The mobilome was expanded as prophages were predicted in NA4 and H1130, and a genomic island putatively involved in abietane diterpenoids metabolism was identified in H1130. An active CRISPR-Cas system was identified in strain NA4, providing immunity to a plasmid that integrated in CH34 and NA1. No correlation between the mobilome and isolation environment was found. In addition, our comparison indicated that the metal resistance determinants and properties are conserved among these strains and thus maintained in these environments. Furthermore, all strains were highly resistant to a wide variety of chemicals, much broader than metals. Only minor differences were observed in the phenomes (measured by phenotype microarrays), despite the large difference in mobilomes and the variable (shared by two or three strains) and strain-specific genomes.}, }
@article {pmid30327827, year = {2019}, author = {Kowalec, M and Szewczyk, T and Welc-Falęciak, R and Siński, E and Karbowiak, G and Bajer, A}, title = {Rickettsiales Occurrence and Co-occurrence in Ixodes ricinus Ticks in Natural and Urban Areas.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {890-904}, pmid = {30327827}, issn = {1432-184X}, support = {NN404795240//Ministerstwo Nauki i Szkolnictwa Wy&#x17c;szego/ ; The study was financially supported by the Ministry of Science and Higher Education through the Faculty of Biology, University of Warsaw intramural grant DSM #501/86 - 104911//Ministerstwo Nauki i Szkolnictwa Wy&#x17c;szego/ ; The study was financially supported by the Ministry of Science and Higher Education through the Faculty of Biology, University of Warsaw intramural grant DSM #501/86 - 107422//Ministerstwo Nauki i Szkolnictwa Wy&#x17c;szego/ ; }, mesh = {Animals ; Borrelia/*isolation &amp; purification/physiology ; Forests ; Ixodes/*microbiology ; Parks, Recreational ; Poland ; Rickettsiales/*isolation &amp; purification/physiology ; }, abstract = {Bacteria of Rickettsiaceae and Anaplasmataceae families include disease agents spread by Ixodes ricinus ticks, the most common tick vector in Europe. The aim of the study was to compare the prevalence and co-infection prevalence of particular tick-transmitted Rickettsiales members: Rickettsia spp. (further referred as Rs), Anaplasma phagocytophilum (Ap), and "Candidatus Neoehrlichia mikurensis" (CNM) in I. ricinus ticks in two types of areas, different in terms of human impact: natural and urban. Using additional data, we aimed at investigating co-occurrence of these Rickettsiales with Borreliella spp. A total of 4189 tick specimens, 2363 from the urban area (Warsaw park and forests) and 1826 from the natural area (forests and park in the vicinity of National Parks), were tested for the presence of Rickettsiales DNA by PCRs. The prevalence of selected Rickettsiales was twice higher in urban than natural areas (13.2% vs. 6.9%, respectively). In total ticks, the prevalence of Rs, Ap, and CNM was 6.5%, 5.3%, and 3.6% in urban areas vs. 4.4%, 1.1%, and 2.1% in natural areas, respectively. Co-infections of Rickettsiales were also more prevalent in urban areas (2.6% vs. 0.3%, respectively). The most common Rs was R. helvetica; also R. monacensis and novel "Candidatus Rickettsia mendelii" were detected. Positive association between Ap and CNM infections was discovered. Rickettsiales bacteria occurrence was not associated with Borreliella occurrence, but co-infections with these two groups were more common in ticks in urban areas. In conclusion, three groups of Rickettsiales constituted the important part of the tick pathogen community in Poland, especially in the urbanized central Poland (Mazovia). In the Warsaw agglomeration, there is a greater risk of encountering the I. ricinus tick infected with Rickettsiales and co-infected with Lyme spirochaetes, in comparison to natural areas. This finding raises the question whether cities might in fact be the hot spots for TBDs.}, }
@article {pmid30326440, year = {2019}, author = {Van Winckel, T and Liu, X and Vlaeminck, SE and Takács, I and Al-Omari, A and Sturm, B and Kjellerup, BV and Murthy, SN and De Clippeleir, H}, title = {Overcoming floc formation limitations in high-rate activated sludge systems.}, journal = {Chemosphere}, volume = {215}, number = {}, pages = {342-352}, doi = {10.1016/j.chemosphere.2018.09.169}, pmid = {30326440}, issn = {1879-1298}, mesh = {Flocculation ; Polymers/analysis ; Proteins/analysis ; Sewage/*chemistry/microbiology ; Waste Disposal, Fluid/*methods ; Wastewater/chemistry ; Water Purification/methods ; }, abstract = {High-rate activated sludge (HRAS) is an essential cornerstone of the pursuit towards energy positive sewage treatment through maximizing capture of organics. The capture efficiency heavily relies on the degree of solid separation achieved in the clarifiers. Limitations in the floc formation process commonly emerge in HRAS systems, with detrimental consequences for the capture of organics. This study pinpointed and overcame floc formation limitations present in full-scale HRAS reactors. Orthokinetic flocculation tests were performed with varying shear, sludge concentration, and coagulant or flocculant addition. These were analyzed with traditional and novel settling parameters and extracellular polymeric substances (EPS) measurements. HRAS was limited by insufficient collision efficiency and occurred because the solids retention time (SRT) was short and colloid loading was high. The limitation was predominantly caused by impaired flocculation rather than coagulation. In addition, the collision efficiency limitation was driven by EPS composition (low protein over polysaccharide ratio) instead of total EPS amount. Collision efficiency limitation was successfully overcome by bio-augmenting sludge from a biological nutrient removal reactor operating at long SRT which did not show any floc formation limitations. However, this action brought up a floc strength limitation. The latter was not correlated with EPS composition, but rather EPS amount and hindered settling parameters, which determined floc morphology. With this, an analysis toolkit was proposed that will enable design engineers and operators to tackle activated solid separation challenges found in HRAS systems and maximize the recovery potential of the process.}, }
@article {pmid30325958, year = {2018}, author = {Lee, YM and Kor, CT and Zhou, D and Lai, HC and Chang, CC and Ma, WL}, title = {Impact of age at appendectomy on development of type 2 diabetes: A population-based cohort study.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0205502}, pmid = {30325958}, issn = {1932-6203}, mesh = {Adult ; Age Factors ; Aged ; Aged, 80 and over ; *Appendectomy ; Diabetes Mellitus, Type 2/*epidemiology ; Female ; Follow-Up Studies ; Humans ; Incidence ; Male ; Middle Aged ; Retrospective Studies ; Risk Factors ; Taiwan ; Young Adult ; }, abstract = {AIM: Diabetes is a complex metabolic disease characterized by chronic low-grade inflammation in which genetic and environmental factors are involved. Growing evidence implicates that alterations of the gut microbiota potentially contribute to the emergence of metabolic diseases. The human appendix has more recently been recognized as a microbial reservoir for repopulating the gastrointestinal tract and an important part of the immune system. Thus, appendectomy may influence microbial ecology and immune function. This study investigated the association between appendectomy and type 2 diabetes risk.<br><br>METHODS: We analyzed a cohort of 10954 patients who underwent appendectomy between 1998 and 2013 based on the Taiwan National Health Insurance Program database. A comparison cohort of 43815 persons without appendectomy was selected randomly and matched by sex, age, comorbidities, and index year. To ensure reliability of the results, a sensitivity analysis using a propensity score-matched study was performed. We observed the subsequent development of type 2 diabetes in both cohorts.<br><br>RESULTS: Although the overall incidence of type 2 diabetes in the appendectomy patients was 7.9% higher than that in the non-appendectomy patients, it was not statistically significant (95% confidence interval [CI], 0.997-1.168) after the adjustment of confounding factors. Multivariate regression analysis revealed that the adjusted hazard ratio (HR) of type 2 diabetes was 1.347 for appendectomy patients < 30 years of age (95% CI, 1.009-1.798) compared to non-appendectomy patients. The incidence of type 2 diabetes was higher within 3 years of post-appendectomy follow-up than for non-appendectomy patients (HR, 2.017; 95% CI, 1.07-3.802). Age impacted the association between appendectomy and type 2 diabetes risk (Pinteraction = 0.002); in contrast, sex did not affect the association between appendectomy and type 2 diabetes risk (Pinteraction = 0.88).<br><br>CONCLUSIONS: Our study results suggest that appendectomy increases type 2 diabetes risk, particularly when performed prior to middle age.}, }
@article {pmid30324255, year = {2018}, author = {Szczepańska, A and Kiewra, D and Guz-Regner, K}, title = {Sensitivity of Ixodes ricinus (L., 1758) and Dermacentor reticulatus (Fabr., 1794) ticks to Bacillus thuringiensis isolates: preliminary study.}, journal = {Parasitology research}, volume = {117}, number = {12}, pages = {3897-3902}, pmid = {30324255}, issn = {1432-1955}, support = {0420/2308/17//Uniwersytet Wroc&#x142;awski/ ; }, mesh = {Animals ; Bacillus thuringiensis/*pathogenicity ; *Biological Control Agents ; Dermacentor/*microbiology ; Female ; Ixodes/*microbiology ; Male ; Pest Control, Biological/*methods ; Tick Infestations/prevention &amp; control ; }, abstract = {Bacillus thuringiensis is a highly specific entomopathogenic microorganism. Although defined as having properties which work against insects, its role in the control of tick populations is still insufficiently known. In our bioassay, four environmental strains of B. thuringiensis, along with one commercially available product (Vectobac), have been used against ticks. Vectobac turned out to be ineffective in the biocontrol of ticks; however, two of environmental B. thuringiensis strains proved to be efficient against both Ixodes ricinus and Dermacentor reticulatus. In those cases, the mortality rate for ticks was assessed as being up to 80%, and LC50 ranged between 9.1 × 10[6] and 1.3 × 10[15] (cfu/ml). Dermacentor reticulatus males were the most sensitive to bacteria. The similarity between the most and least efficient B. thuringiensis strains in enzymatic profiles-including lipases, phosphatases, proteases, and chitinases-may indicate a limited role of detected enzymes in the pathogenicity profile of bacterial strains against ticks.}, }
@article {pmid30321727, year = {2019}, author = {Liu, K and Liu, Y and Han, BP and Xu, B and Zhu, L and Ju, J and Jiao, N and Xiong, J}, title = {Bacterial community changes in a glacial-fed Tibetan lake are correlated with glacial melting.}, journal = {The Science of the total environment}, volume = {651}, number = {Pt 2}, pages = {2059-2067}, doi = {10.1016/j.scitotenv.2018.10.104}, pmid = {30321727}, issn = {1879-1026}, mesh = {Actinobacteria/classification/isolation &amp; purification ; Bacteria/classification/*isolation &amp; purification ; Bacteroidetes/classification/isolation &amp; purification ; Climate Change ; *Global Warming ; Ice Cover ; Lakes/*microbiology ; *Microbiota ; Proteobacteria/classification/isolation &amp; purification ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Seasons ; Tibet ; }, abstract = {Climate change-induced glacial melting is a global phenomenon. The effects of climate change-induced melting on the microbial ecology in different glacial-fed aquatic systems have been well illuminated, but the resolution of seasonal dynamics was still limited. Here, we studied bacterial community composition and diversity in a glacial-fed Tibetan lake, Lake Ranwu, to elucidate how glacial-fed aquatic ecosystems respond to the seasonal glacial melting. Obvious seasonal variations of bacterial dominant groups were found in Lake Ranwu and inlet rivers. In April, the majority of OTUs belonged to the Bacteroidetes, Actinobacteria and Proteobacteria. The Proteobacteria increased to the most abundant phylum in July and November, while the Bacteroidetes and Actinobacteria decreased about 50% over seasons. Most key discriminant taxa of each season's community strongly associated with specific environmental variables, suggesting their adaptation to seasonal environments. Bacterial alpha diversity varied among seasons and exhibited strongly negative correlations with conductivity. Conductivity was the major driving force in determining the seasonal variation of bacterial community composition. Fluctuated conductivity was one of the consequences of seasonal melting of glaciers. This study offered evidence for the unique seasonal dynamics pattern of bacterial communities responding to glacial melting. Moreover, this study may provide a reference for assessing the long-term effects of glacial retreat on glacial-fed aquatic ecosystems.}, }
@article {pmid30320221, year = {2018}, author = {Stegen, JC and Goldman, AE}, title = {WHONDRS: a Community Resource for Studying Dynamic River Corridors.}, journal = {mSystems}, volume = {3}, number = {5}, pages = {}, doi = {10.1128/mSystems.00151-18}, pmid = {30320221}, issn = {2379-5077}, abstract = {The Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) aims to galvanize a global community to provide the scientific basis for improved management of dynamic river corridors. WHONDRS is a global research consortium working to understand connections among dynamic hydrology, biogeochemistry, and microbiology in river corridors from local to global scales. WHONDRS ascribes to the perspective that resources, knowledge, and data belong to the community as a whole and that science advances more rapidly and more robustly through community ownership. As such, WHONDRS provides free access to novel instrumentation, molecular analysis, and well-curated data associated with river corridor hydrology, biogeochemistry, and microbiology. There are a number of ways to be involved in WHONDRS, ranging from one-time surface water sampling to installation of WHONDRS-developed multiparameter sensors for continuous monitoring. WHONDRS hinges on broad involvement, and we encourage all interested parties to contact us and become part of the consortium.}, }
@article {pmid30320215, year = {2018}, author = {Trubl, G and Jang, HB and Roux, S and Emerson, JB and Solonenko, N and Vik, DR and Solden, L and Ellenbogen, J and Runyon, AT and Bolduc, B and Woodcroft, BJ and Saleska, SR and Tyson, GW and Wrighton, KC and Sullivan, MB and Rich, VI}, title = {Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing.}, journal = {mSystems}, volume = {3}, number = {5}, pages = {}, pmid = {30320215}, issn = {2379-5077}, abstract = {Rapidly thawing permafrost harbors ∼30 to 50% of global soil carbon, and the fate of this carbon remains unknown. Microorganisms will play a central role in its fate, and their viruses could modulate that impact via induced mortality and metabolic controls. Because of the challenges of recovering viruses from soils, little is known about soil viruses or their role(s) in microbial biogeochemical cycling. Here, we describe 53 viral populations (viral operational taxonomic units [vOTUs]) recovered from seven quantitatively derived (i.e., not multiple-displacement-amplified) viral-particle metagenomes (viromes) along a permafrost thaw gradient at the Stordalen Mire field site in northern Sweden. Only 15% of these vOTUs had genetic similarity to publicly available viruses in the RefSeq database, and ∼30% of the genes could be annotated, supporting the concept of soils as reservoirs of substantial undescribed viral genetic diversity. The vOTUs exhibited distinct ecology, with different distributions along the thaw gradient habitats, and a shift from soil-virus-like assemblages in the dry palsas to aquatic-virus-like assemblages in the inundated fen. Seventeen vOTUs were linked to microbial hosts (in silico), implicating viruses in infecting abundant microbial lineages from Acidobacteria, Verrucomicrobia, and Deltaproteobacteria, including those encoding key biogeochemical functions such as organic matter degradation. Thirty auxiliary metabolic genes (AMGs) were identified and suggested virus-mediated modulation of central carbon metabolism, soil organic matter degradation, polysaccharide binding, and regulation of sporulation. Together, these findings suggest that these soil viruses have distinct ecology, impact host-mediated biogeochemistry, and likely impact ecosystem function in the rapidly changing Arctic. IMPORTANCE This work is part of a 10-year project to examine thawing permafrost peatlands and is the first virome-particle-based approach to characterize viruses in these systems. This method yielded >2-fold-more viral populations (vOTUs) per gigabase of metagenome than vOTUs derived from bulk-soil metagenomes from the same site (J. B. Emerson, S. Roux, J. R. Brum, B. Bolduc, et al., Nat Microbiol 3:870-880, 2018, https://doi.org/10.1038/s41564-018-0190-y). We compared the ecology of the recovered vOTUs along a permafrost thaw gradient and found (i) habitat specificity, (ii) a shift in viral community identity from soil-like to aquatic-like viruses, (iii) infection of dominant microbial hosts, and (iv) carriage of host metabolic genes. These vOTUs can impact ecosystem carbon processing via top-down (inferred from lysing dominant microbial hosts) and bottom-up (inferred from carriage of auxiliary metabolic genes) controls. This work serves as a foundation which future studies can build upon to increase our understanding of the soil virosphere and how viruses affect soil ecosystem services.}, }
@article {pmid30320131, year = {2018}, author = {Ziadi, M and Bouzaiene, T and M'Hir, S and Zaafouri, K and Mokhtar, F and Hamdi, M and Boisset-Helbert, C}, title = {Evaluation of the Efficiency of Ethanol Precipitation and Ultrafiltration on the Purification and Characteristics of Exopolysaccharides Produced by Three Lactic Acid Bacteria.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {1896240}, pmid = {30320131}, issn = {2314-6141}, mesh = {Ethanol/*chemistry ; Lactobacillus plantarum/*chemistry ; Lactococcus lactis/*chemistry ; Leuconostoc mesenteroides/*chemistry ; Polysaccharides, Bacterial/chemistry/*isolation &amp; purification ; Ultrafiltration/methods ; }, abstract = {Exopolysaccharides (EPS) produced by three Lactic Acid Bacteria strains, Lactococcus lactis SLT10, Lactobacillus plantarum C7, and Leuconostoc mesenteroides B3, were isolated using two methods: ethanol precipitation (EPS-ETOH) and ultrafiltration (EPS-UF) through a 10 KDa cut-off membrane. EPS recovery by ultrafiltration was higher than ethanol precipitation for Lactococcus lactis SLT10 and Lactobacillus plantarum C7. However, it was similar with both methods for Leuconostoc mesenteroides B3. The monomer composition of the EPS fractions revealed differences in structures and molar ratios between the two studied methods. EPS isolated from Lactococcus lactis SLT10 are composed of glucose and mannose for EPS-ETOH against glucose, mannose, and rhamnose for EPS-UF. EPS extracted from Lactobacillus plantarum C7 and Leuconostoc mesenteroides B3 showed similar composition (glucose and mannose) but different molar ratios. The molecular weights of the different EPS fractions ranged from 11.6±1.83 to 62.4±2.94 kDa. Molecular weights of EPS-ETOH fractions were higher than those of EPS-UF fractions. Fourier transform infrared (FTIR) analysis revealed a similarity in the distribution of the functional groups (O-H, C-H, C=O, -COO, and C-O-C) between the EPS isolated from the three strains.}, }
@article {pmid30319569, year = {2018}, author = {D'Amico, F and Candela, M and Turroni, S and Biagi, E and Brigidi, P and Bega, A and Vancini, D and Rampelli, S}, title = {The Rootstock Regulates Microbiome Diversity in Root and Rhizosphere Compartments of Vitis vinifera Cultivar Lambrusco.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2240}, pmid = {30319569}, issn = {1664-302X}, abstract = {Plants belonging to Vitis vinifera varieties are usually grafted on different rootstocks to enhance the plant defenses against pathogens and increase productivity under harsh environmental conditions. Particularly, in Emilia-Romagna region (Italy), Vitis vinifera cultivar Lambrusco can be grafted on a hybrid of V. berlandieri × V. riparia (5BB) or V. berlandieri × V. rupestris (1103P). However, the latter shows potassium absorption problems, with a consequent reduction in grapevine production. Since it has recently been demonstrated that the rootstock has the potential to select for different microorganisms at the root-soil interface, here we hypothesized that the potassium deficiency of 1103P could be partially accounted for by the peculiarities of the rootstock microbiome. We thus employed 16S rRNA sequencing to compare root and rhizosphere microbiomes in plants of V. vinifera cultivar Lambrusco grafted on the two aforementioned rootstocks. According to our findings, 1103P shows a reduced diversity in root and rhizosphere microbiomes, including members of potassium-solubilizing microorganisms, possibly explaining the inadequate potassium absorption of this hybrid. Besides confirming the importance of the rootstock as a determinant of the composition of plant microbiomes, our data indicate the relevance of rootstock-selected microbiomes as possible regulators of potassium absorption by V. vinifera.}, }
@article {pmid30318762, year = {2019}, author = {Van Assche, A and Crauwels, S and De Brabanter, J and Willems, KA and Lievens, B}, title = {Characterization of the bacterial community composition in water of drinking water production and distribution systems in Flanders, Belgium.}, journal = {MicrobiologyOpen}, volume = {8}, number = {5}, pages = {e00726}, pmid = {30318762}, issn = {2045-8827}, mesh = {Bacteria/*classification/*genetics ; Belgium ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Drinking Water/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Purification ; }, abstract = {The quality of drinking water is influenced by its chemical and microbial composition which in turn may be affected by the source water and the different processes applied in drinking water purification systems. In this study, we investigated the bacterial diversity in different water samples from the production and distribution chain of thirteen drinking water production and distribution systems from Flanders (Belgium) that use surface water or groundwater as source water. Water samples were collected over two seasons from the source water, the processed drinking water within the production facility and out of the tap in houses along its distribution network. 454-pyrosequencing of 16S ribosomal RNA gene sequences revealed a total of 1,570 species-level bacterial operational taxonomic units. Strong differences in community composition were found between processed drinking water samples originating from companies that use surface water and other that use groundwater as source water. Proteobacteria was the most abundant phylum in all samples. Yet, several phyla including Actinobacteria were significantly more abundant in surface water while Cyanobacteria were more abundant in surface water and processed water originating from surface water. Gallionella, Acinetobacter, and Pseudomonas were the three most abundant genera detected. Members of the Acinetobacter genus were even found at a relative read abundance of up to 47.5% in processed water samples, indicating a general occurrence of Acinetobacter in drinking water (systems).}, }
@article {pmid30318710, year = {2018}, author = {Liu, Y and Qin, Q and Defoirdt, T}, title = {Does quorum sensing interference affect the fitness of bacterial pathogens in the real world?.}, journal = {Environmental microbiology}, volume = {20}, number = {11}, pages = {3918-3926}, doi = {10.1111/1462-2920.14446}, pmid = {30318710}, issn = {1462-2920}, support = {//Special Research Fund of Ghent University/International ; 218043//Scientific Research Startup Fund of South China Agricultural University/International ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects ; *Bacterial Physiological Phenomena ; Humans ; *Quorum Sensing/drug effects ; Virulence ; }, abstract = {Many bacterial pathogens rely on quorum sensing to control virulence gene expression. Based on numerous experiments conducted under well-defined conditions, quorum sensing interference is considered as a promising strategy to tackle infections and thus might have the potential to (partially) replace antibiotics. Despite the promising results in well-defined (artificial) laboratory experiments, there still is a lack of knowledge with respect to the impact of quorum sensing interference on the fitness of pathogens in more realistic scenarios, including interactions with a host, the external environment and complex microbial communities. In this article, we critically evaluate the current knowledge with respect to these three facets of the real world that can affect the fitness of quorum sensing bacterial pathogens. We argue that further research is needed in order to determine how these factors interplay with quorum sensing and to what extent they can influence the selective pressure that might be exerted by quorum sensing interference (and thus determine the risk of resistance development against quorum sensing interference). This kind of information is indispensable in order to optimize quorum sensing interference-based therapeutic strategies.}, }
@article {pmid30317429, year = {2019}, author = {Mania, I and Gorra, R and Colombo, N and Freppaz, M and Martin, M and Anesio, AM}, title = {Prokaryotic Diversity and Distribution in Different Habitats of an Alpine Rock Glacier-Pond System.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {70-84}, pmid = {30317429}, issn = {1432-184X}, support = {NE/J02399X/1//Natural Environment Research Council/ ; }, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Ecosystem ; Ice Cover/chemistry/*microbiology ; Italy ; Microbiota ; Ponds/analysis/*microbiology ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Rock glaciers (RG) are assumed to influence the biogeochemistry of downstream ecosystems because of the high ratio of rock:water in those systems, but no studies have considered the effects of a RG inflow on the microbial ecology of sediments in a downstream pond. An alpine RG-pond system, located in the NW Italian Alps has been chosen as a model, and Bacteria and Archaea 16S rRNA genes abundance, distribution and diversity have been assessed by qPCR and Illumina sequencing, coupled with geochemical analyses on sediments collected along a distance gradient from the RG inflow. RG surface material and neighbouring soil have been included in the analysis to better elucidate relationships among different habitats.Our results showed that different habitats harboured different, well-separated microbial assemblages. Across the pond, the main variations in community composition (e.g. Thaumarchaeota and Cyanobacteria relative abundance) and porewater geochemistry (pH, DOC, TDN and NH4[+]) were not directly linked to RG proximity, but to differences in water depth. Some microbial markers potentially linked to the presence of meltwater inputs from the RG have been recognised, although the RG seems to have a greater influence on the pond microbial communities due to its contribution in terms of sedimentary material.}, }
@article {pmid30314008, year = {2018}, author = {Sen, A and Saha, R and Sivakumar, K and Bhadury, P}, title = {Inventorizing the modern benthic foraminiferal assemblage from marginal marine environments across the North West coast of Bay of Bengal.}, journal = {Zootaxa}, volume = {4441}, number = {2}, pages = {245-260}, doi = {10.11646/zootaxa.4441.2.3}, pmid = {30314008}, issn = {1175-5334}, mesh = {Animals ; Bays ; Environmental Monitoring ; *Foraminifera ; *Geologic Sediments ; Indian Ocean ; }, abstract = {Modern benthic foraminiferal assemblages are instrumental in providing information regarding changes in relative sea level as well as prevailing environmental conditions in marine environments. Marginal marine environments are coastal environments that are in most cases characterized by high influx of terrestrially originated nutrients. Inventorizing of modern benthic foraminiferal assemblages from such habitats can act as biotic indicators of water quality variations along with any changes in relative sea level. The present study documents the modern benthic foraminiferal assemblage from three major marginal marine habitats located along the North West coast of Bay of Bengal, in the Indian Ocean. Sediment samples for the purpose were thus collected from the Indian Sundarbans Delta, Chilika lagoon and the Gautami Godavari estuarine zone which encompasses the Kakinada bay. A total of 32 species of benthic foraminifera were documented during the study. The present observations were compared with previous reports of benthic foraminiferal diversity from these habitats and exhibited variability.}, }
@article {pmid30312413, year = {2018}, author = {Van Geel, M and Yu, K and Ceulemans, T and Peeters, G and van Acker, K and Geerts, W and Ramos, MA and Serafim, C and Kastendeuch, P and Najjar, G and Ameglio, T and Ngao, J and Saudreau, M and Waud, M and Lievens, B and Castro, PM and Somers, B and Honnay, O}, title = {Variation in ectomycorrhizal fungal communities associated with Silver linden (Tilia tomentosa) within and across urban areas.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {12}, pages = {}, doi = {10.1093/femsec/fiy207}, pmid = {30312413}, issn = {1574-6941}, mesh = {Belgium ; Biodiversity ; Ecosystem ; France ; Geography ; Metals, Heavy/toxicity ; Mycobiome/*physiology ; Mycorrhizae/*classification/*growth &amp; development ; Portugal ; Soil ; Soil Microbiology ; Symbiosis ; Tilia/*microbiology ; Trees/*microbiology ; Urban Population ; Urbanization ; }, abstract = {Trees in urban areas face harsh environmental conditions. Ectomycorrhizal fungi (EcM) form a symbiosis with many tree species and provide a range of benefits to their host through their extraradical hyphal network. Although our understanding of the environmental drivers and large scale geographical variation of EcM communities in natural ecosystems is growing, our knowledge of EcM communities within and across urban areas is still limited. Here, we characterized EcM communities using Illumina miseq sequencing on 175 root samples of the urban tree Tilia tomentosa from three European cities, namely Leuven (Belgium), Strasbourg (France) and Porto (Portugal). We found strong differences in EcM richness and community composition between cities. Soil acidity, organic matter and moisture content were significantly associated with EcM community composition. In agreement, the explained variability in EcM communities was mostly attributed to general soil characteristics, whereas very little variation was explained by city and heavy metal pollution. Overall, our results suggest that EcM communities in urban areas are significantly associated with soil characteristics, while heavy metal pollution and biogeography had little or no impact. These findings deliver new insights into EcM distribution patterns in urban areas and contribute to specific inoculation strategies to improve urban tree vitality.}, }
@article {pmid30310241, year = {2017}, author = {Eisenhauer, N and Powell, JR}, title = {Plant trait effects on soil organisms and functions.}, journal = {Pedobiologia}, volume = {65}, number = {}, pages = {1-4}, pmid = {30310241}, issn = {0031-4056}, support = {677232/ERC_/European Research Council/International ; }, abstract = {Global change alters the composition and functioning of ecosystems by creating novel environmental conditions and thereby selecting for specific traits of organisms. Thus, trait-based approaches are promising tools to more mechanistically understand compositional and functional shifts in ecological communities as well as the dependency of response and effect traits upon global change. Such approaches have been particularly successful for the study of plant communities in terrestrial ecosystems. However, given the intimate linkages between aboveground and belowground compartments as well as the significance of plants as integrating organisms across those compartments, the role of plant traits in affecting soils communities has been understudied. This special issue contains empirical studies and reviews of plant trait effects on soil organisms and functions. Based on those contributions, we discuss here plasticity in trait expression, the context-dependency of plant trait effects, time lags in soil biotic responses to trait expression, and limitations of measured plant traits. We conclude that plant trait-based approaches are an important tool to advance soil ecological research, but also identify critical limitations and next steps.}, }
@article {pmid30310127, year = {2018}, author = {Cuer, CA and Rodrigues, RAR and Balieiro, FC and Jesus, J and Silva, EP and Alves, BJR and Rachid, CTCC}, title = {Short-term effect of Eucalyptus plantations on soil microbial communities and soil-atmosphere methane and nitrous oxide exchange.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {15133}, pmid = {30310127}, issn = {2045-2322}, mesh = {Atmosphere/*chemistry ; Brazil ; Environmental Monitoring ; *Eucalyptus ; Forests ; Metagenomics/methods ; Methane/*analysis ; Microbiota ; Nitrous Oxide/*analysis ; RNA, Ribosomal, 16S ; Soil/*chemistry ; *Soil Microbiology ; Time Factors ; }, abstract = {Soil greenhouse gas (GHG) emissions are a significant environmental problem resulting from microbially-mediated nitrogen (N) and carbon (C) cycling. This study aimed to investigate the impact of Eucalyptus plantations on the structure and function of a soil microbial community, and how resulting alterations may be linked to GHG fluxes. We sampled and monitored two adjacent Eucalyptus plantations-a recently logged site that harbored new seedlings and an adult plantation-and compared them to a site hosting native vegetation. We used 16S rRNA gene sequencing and qPCR amplifications of key nitrogen and methane cycle genes to characterize microbial structure and functional gene abundance and compared our data with soil parameters and GHG fluxes. Both microbial community attributes were significantly affected by land use and logging of Eucalyptus plantations. The genes nosZ and archaeal amoA were significantly more abundant in native forest than in either young or old Eucalyptus plantations. Statistical analyses suggest that land use type has a greater impact on microbial community structure and functional gene abundance than Eucalyptus rotation. There was no correlation between GHG fluxes and shifts in microbial community, suggesting that microbial community structure and functional gene abundance are not the main drivers of GHG fluxes in this system.}, }
@article {pmid30308860, year = {2019}, author = {Karmakar, R and Bindiya, S and Hariprasad, P}, title = {Convergent evolution in bacteria from multiple origins under antibiotic and heavy metal stress, and endophytic conditions of host plant.}, journal = {The Science of the total environment}, volume = {650}, number = {Pt 1}, pages = {858-867}, doi = {10.1016/j.scitotenv.2018.09.078}, pmid = {30308860}, issn = {1879-1026}, mesh = {Adaptation, Physiological/physiology ; Anti-Bacterial Agents/*toxicity ; Bacteria/*genetics ; *Biological Evolution ; Endophytes ; Integrons ; Metals, Heavy/*toxicity ; Plants/*microbiology ; Soil Pollutants/*toxicity ; }, abstract = {The focus of this work is to study the convergent evolution in bacteria from multiple origins under antibiotic and heavy metal stress, and endophytic conditions of host plant cultivated on the Yamuna river bank. Forty-one endophytic bacteria (EB) were isolated from green leafy vegetables (GLV's) and were found to be resistant to a wide range of antibiotics (AB) and heavy metals (HM) tested. Further, they showed susceptibility to Quinolones group of antibiotics, and the HM, Cadmium, Chromium, and Mercury. Twenty-seven percent of these bacteria endowed with Class I integron. The probability of co-existence of HM resistance with β‑lactams was higher, whereas quinolones group of AB recorded lesser values. These EB owned a wide array of beneficial traits, through which they improved the plant health under HM and salt stress conditions. Bacterial identity revealed the association of both plant beneficial and human pathogenic bacteria as an endophyte with GLV's. Principal component analysis showed a pattern of convergent evolution irrespective of their origin. In conclusion, under the selection pressure of AB and HM, the susceptible EB population may reduce with time and the resistant native/introduced bacteria might survive. The vertical and horizontal gene transfer between introduced and native bacteria is the crucial factor in enhancing their fitness along with the host plant to survive under abiotic stress conditions.}, }
@article {pmid30308834, year = {2019}, author = {Lourenço, KS and Rossetto, R and Vitti, AC and Montezano, ZF and Soares, JR and Sousa, RM and do Carmo, JB and Kuramae, EE and Cantarella, H}, title = {Strategies to mitigate the nitrous oxide emissions from nitrogen fertilizer applied with organic fertilizers in sugarcane.}, journal = {The Science of the total environment}, volume = {650}, number = {Pt 1}, pages = {1476-1486}, doi = {10.1016/j.scitotenv.2018.09.037}, pmid = {30308834}, issn = {1879-1026}, abstract = {Vinasse is a major byproduct of the sugarcane biofuel industry, recycled in the fields. However, there is evidence that the application of vinasse with mineral nitrogen (N) fertilizers in sugarcane enhances the emission of greenhouse gases (GHGs). Therefore, strategies are needed to decrease the environmental impacts caused by both inputs. We carried out three sugarcane field experiments by applying N fertilizer (ammonium nitrate) with types of vinasses (concentrated-CV and standard-V) in different combinations (vinasses with N fertilizer and vinasses one month before or after mineral N fertilization). The gases nitrous oxide (N2O), carbon dioxide (CO2), and methane (CH4) were measured in one experiment fertilized in the beginning (fall/winter = dry season) and two experiments fertilized in the end (spring = rainy season) of the harvest season. Sugarcane fields were sinks rather than sources of CH4, while total carbon emitted as CO2 was similar between seasons and treatments. The effect of mineral fertilization and vinasses (CV and V) on N2O emissions was highly dependent on soil moisture (rain events). The N2O-N fertilizer emission factor (EF) varied from 0.07% to 0.51%, whereas the average EF of V and CV were 0.66% and 0.34%, respectively. On average across the three experiments, the combination of vinasse (CV or V) with N fertilizer increased the N2O emissions 2.9-fold compared to that of N fertilizer alone. For CV + N, the EF was 0.94% of the applied N and 0.23% of the ammonium nitrate-N, and for V + N (EF = 0.47%), increased emissions were observed in two out of three experiments. The strategy of anticipating or postponing vinasse application by one month with respect to mineral N reduced the N2O emissions by 51% for CV, but not for V. Therefore, to avoid boosting N2O emissions, we suggest applying vinasses (CV and V) before or after mineral N fertilization.}, }
@article {pmid30308248, year = {2018}, author = {Hessler, T and Harrison, STL and Huddy, RJ}, title = {Stratification of microbial communities throughout a biological sulphate reducing up-flow anaerobic packed bed reactor, revealed through 16S metagenomics.}, journal = {Research in microbiology}, volume = {169}, number = {10}, pages = {543-551}, doi = {10.1016/j.resmic.2018.09.003}, pmid = {30308248}, issn = {1769-7123}, mesh = {Anaerobiosis ; Bacteria/classification/*genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Biodiversity ; Bioreactors/*microbiology ; DNA, Bacterial/genetics ; Genome, Bacterial ; Metagenomics ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sulfur Compounds/*metabolism ; }, abstract = {Biological sulphate reduction (BSR) is a promising low-cost treatment of acid rock drainage effluents. In this paper, the system performance and microbial ecology of a lactate supplemented BSR up-flow anaerobic packed bed reactor (UAPBR) are evaluated across reactor height and compared to a continuous stirred tank reactor (CSTR). The biomass concentrations of planktonic and biofilm communities were quantified and subsequently characterised by 16S rRNA gene amplicon sequencing. The defined microbial communities were shown to correlate with differing availability of lactate, volatile fatty acids produced from lactate degradation and sulphate concentration. The UAPBR was able to achieve near complete sulphate conversion at a 4-day hydraulic residence time (HRT) at a sulphate feed concentration of 10.41 mM (1 g/L). The high volumetric sulphate reduction rate of 0.184 mM/L.h achieved in the first third of the reactor was attributed to OTUs present in the planktonic and biofilm communities. While the scavenging of sulphate within the final third of the UAPBR was attributed to an acetate oxidising genus of SRB which was not detected in the lactate-fed CSTR. The detailed analyses of the microbial communities throughout the UAPBR and CSTR contribute to the growing understanding of the impact of the microbial communities of BSR reactors on system performance.}, }
@article {pmid30305843, year = {2018}, author = {Cassman, NA and Lourenço, KS and do Carmo, JB and Cantarella, H and Kuramae, EE}, title = {Correction to: Genome-resolved metagenomics of sugarcane vinasse bacteria.}, journal = {Biotechnology for biofuels}, volume = {11}, number = {}, pages = {270}, pmid = {30305843}, issn = {1754-6834}, abstract = {[This corrects the article DOI: 10.1186/s13068-018-1036-9.].}, }
@article {pmid30303297, year = {2019}, author = {Ghosh, A and Bhadury, P}, title = {Exploring biogeographic patterns of bacterioplankton communities across global estuaries.}, journal = {MicrobiologyOpen}, volume = {8}, number = {5}, pages = {e00741}, pmid = {30303297}, issn = {2045-8827}, mesh = {Bacteria/*classification/*genetics ; *Estuaries ; *Microbiota ; *Phylogeography ; Plankton/*microbiology ; }, abstract = {Estuaries provide an ideal niche to study structure and function of bacterioplankton communities owing to the presence of a multitude of environmental stressors. Bacterioplankton community structures from nine global estuaries were compared to understand their broad-scale biogeographic patterns. Bacterioplankton community structure from four estuaries of Sundarbans, namely Mooriganga, Thakuran, Matla, and Harinbhanga, was elucidated using Illumina sequencing. Bacterioplankton communities from these estuaries were compared against available bacterioplankton sequence data from Columbia, Delaware, Jiulong, Pearl, and Hangzhou estuaries. All nine estuaries were dominated by Proteobacteria. Other abundant phyla included Bacteroidetes, Firmicutes, Acidobacteria, Actinobacteria, Cyanobacteria, Planctomycetes, and Verrucomicrobia. The abundant bacterial phyla showed a ubiquitous presence across the estuaries. At class level, the overwhelming abundance of Gammaproteobacteria in the estuaries of Sundarbans and Columbia estuary clearly stood out amidst high abundance of Alphaproteobacteria observed in the other estuaries. Abundant bacterial families including Rhodobacteriaceae, Shingomonadaceae, Acidobacteriaceae, Vibrionaceae, and Xanthomondaceae also showed ubiquitous presence in the studied estuaries. However, rare taxa including Chloroflexi, Tenericutes, Nitrospirae, and Deinococcus-Thermus showed clear site-specific distribution patterns. Such distribution patterns were also reinstated by nMDS ordination plots. Such clustering patterns could hint toward the potential role of environmental parameters and substrate specificity which could result in distinct bacterioplankton communities at specific sites. The ubiquitous presence of abundant bacterioplankton groups along with their strong correlation with surface water temperature and dissolved nutrient concentrations indicates the role of such environmental parameters in shaping bacterioplankton community structure in estuaries. Overall, studies on biogeographic patters of bacterioplankton communities can provide interesting insights into ecosystem functioning and health of global estuaries.}, }
@article {pmid30301807, year = {2018}, author = {Weber, Y and Sinninghe Damsté, JS and Zopfi, J and De Jonge, C and Gilli, A and Schubert, CJ and Lepori, F and Lehmann, MF and Niemann, H}, title = {Redox-dependent niche differentiation provides evidence for multiple bacterial sources of glycerol tetraether lipids in lakes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {43}, pages = {10926-10931}, pmid = {30301807}, issn = {1091-6490}, mesh = {Bacteria/*metabolism ; Biomass ; Carbon/metabolism ; Carbon Isotopes/metabolism ; Ecology ; Geologic Sediments/microbiology ; Glycerol/*metabolism ; Lakes/*microbiology ; Lipids/*chemistry ; Methane/metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S/metabolism ; }, abstract = {Terrestrial paleoclimate archives such as lake sediments are essential for our understanding of the continental climate system and for the modeling of future climate scenarios. However, quantitative proxies for the determination of paleotemperatures are sparse. The relative abundances of certain bacterial lipids, i.e., branched glycerol dialkyl glycerol tetraethers (brGDGTs), respond to changes in environmental temperature, and thus have great potential for climate reconstruction. Their application to lake deposits, however, is hampered by the lack of fundamental knowledge on the ecology of brGDGT-producing microbes in lakes. Here, we show that brGDGTs are synthesized by multiple groups of bacteria thriving under contrasting redox regimes in a deep meromictic Swiss lake (Lake Lugano). This niche partitioning is evidenced by highly distinct brGDGT inventories in oxic vs. anoxic water masses, and corresponding vertical patterns in bacterial 16S rRNA gene abundances, implying that sedimentary brGDGT records are affected by temperature-independent changes in the community composition of their microbial producers. Furthermore, the stable carbon isotope composition (δ[13]C) of brGDGTs in Lake Lugano and 34 other (peri-)Alpine lakes attests to the widespread heterotrophic incorporation of [13]C-depleted, methane-derived biomass at the redox transition zone of mesotrophic to eutrophic lake systems. The brGDGTs produced under such hypoxic/methanotrophic conditions reflect near-bottom water temperatures, and are characterized by comparatively low δ[13]C values. Depending on climate zone and water depth, lake sediment archives predominated by deeper water/low-[13]C brGDGTs may provide more reliable records of climate variability than those where brGDGTs derive from terrestrial and/or aquatic sources with distinct temperature imprints.}, }
@article {pmid30298251, year = {2018}, author = {Hall, M and Beiko, RG}, title = {16S rRNA Gene Analysis with QIIME2.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1849}, number = {}, pages = {113-129}, doi = {10.1007/978-1-4939-8728-3_8}, pmid = {30298251}, issn = {1940-6029}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Biodiversity ; Computational Biology/methods ; *Genetic Markers ; High-Throughput Nucleotide Sequencing/*methods ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; *Software ; }, abstract = {Microbial marker-gene sequence data can be used to generate comprehensive taxonomic profiles of the microorganisms present in a given community and for other community diversity analyses. The process of going from raw gene sequences to taxonomic profiles or diversity measures involves a series of data transformations performed by numerous computational tools. This includes tools for sequence quality checking, denoising, taxonomic classification, alignment, and phylogenetic tree building. In this chapter, we demonstrate how the Quantitative Insights Into Microbial Ecology version 2 (QIIME2) software suite can simplify 16S rRNA marker-gene analysis. We walk through an example data set extracted from the guts of bumblebees in order to show how QIIME2 can transform raw sequences into taxonomic bar plots, phylogenetic trees, principal co-ordinates analyses, and other visualizations of microbial diversity.}, }
@article {pmid30297403, year = {2018}, author = {García, FC and Bestion, E and Warfield, R and Yvon-Durocher, G}, title = {Changes in temperature alter the relationship between biodiversity and ecosystem functioning.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {43}, pages = {10989-10994}, pmid = {30297403}, issn = {1091-6490}, mesh = {*Biodiversity ; Biomass ; *Ecosystem ; Introduced Species ; Models, Biological ; Temperature ; }, abstract = {Global warming and the loss of biodiversity through human activities (e.g., land-use change, pollution, invasive species) are two of the most profound threats to the functional integrity of the Earth's ecosystems. These factors are, however, most frequently investigated separately, ignoring the potential for synergistic effects of biodiversity loss and environmental warming on ecosystem functioning. Here we use high-throughput experiments with microbial communities to investigate how changes in temperature affect the relationship between biodiversity and ecosystem functioning. We found that changes in temperature systematically altered the relationship between biodiversity and ecosystem functioning. As temperatures departed from ambient conditions the exponent of the diversity-functioning relationship increased, meaning that more species were required to maintain ecosystem functioning under thermal stress. This key result was driven by two processes linked to variability in the thermal tolerance curves of taxa. First, more diverse communities had a greater chance of including species with thermal traits that enabled them to maintain productivity as temperatures shifted from ambient conditions. Second, we found a pronounced increase in the contribution of complementarity to the net biodiversity effect at high and low temperatures, indicating that changes in species interactions played a critical role in mediating the impacts of temperature change on the relationship between biodiversity and ecosystem functioning. Our results highlight that if biodiversity loss occurs independently of species' thermal tolerance traits, then the additional impacts of environmental warming will result in sharp declines in ecosystem function.}, }
@article {pmid30297041, year = {2019}, author = {Ssepuuya, G and Wynants, E and Verreth, C and Crauwels, S and Lievens, B and Claes, J and Nakimbugwe, D and Van Campenhout, L}, title = {Microbial characterisation of the edible grasshopper Ruspolia differens in raw condition after wild-harvesting in Uganda.}, journal = {Food microbiology}, volume = {77}, number = {}, pages = {106-117}, doi = {10.1016/j.fm.2018.09.005}, pmid = {30297041}, issn = {1095-9998}, mesh = {Animals ; Bacteria/*classification/genetics/*isolation &amp; purification ; Bacterial Load ; Biodiversity ; DNA, Bacterial/analysis ; Food Safety ; Foodborne Diseases/microbiology ; Grasshoppers/*microbiology ; Hydrogen-Ion Concentration ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; Uganda ; Yeasts ; }, abstract = {This research aimed at establishing the chemical intrinsic properties and the microbial quality of an edible grasshopper Ruspolia differens and the effect of its source (geographical area) in Uganda, trading point, swarming season and plucking on these parameters. The intrinsic properties of the grasshopper can support the growth of a wide variety of microorganisms. High counts of total aerobic microbes, Enterobacteriaceae, lactic acid bacteria, total aerobic spores, and yeasts and moulds were obtained. Metagenetic analyses yielded 1793 Operational Taxonomic Units (OTUs) belonging to 24 phyla. Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria and Proteobacteria were the most abundant phyla, while members of the genera Acinetobacter, Buttiauxella, Lactococcus, Staphylococcus and Undibacterium were the most abundant OTUs. A number of genera harbouring potential pathogens (Acinetobacter, Bacillus, Buttiauxella, Campylobacter, Clostridium, Staphylococcus, Pseudomonas and Neisseria) were identified. The geographical area, trading point, swarming season and plucking significantly influenced microbial counts and bacterial diversity. The high microbial counts predispose R. differens to fast microbial spoilage, while the presence of Clostridium and Campylobacter makes this grasshopper a potential source of food borne diseases. Further research should identify the specific spoilage microorganisms of R. differens and assess the characteristics of this grasshopper that support growth of food pathogens.}, }
@article {pmid30294625, year = {2018}, author = {Urra, J and Alkorta, I and Mijangos, I and Garbisu, C}, title = {Data on links between structural and functional prokaryotic diversity in long-term sewage sludge amended soil.}, journal = {Data in brief}, volume = {20}, number = {}, pages = {1787-1796}, pmid = {30294625}, issn = {2352-3409}, abstract = {The application of sewage sludge to agricultural soil induces co-exposure of prokaryotic populations to antibiotics and heavy metals, thus exerting a selection pressure that may lead to the development of antibiotic resistance. Here, soil samples from a long-term factorial field experiment in which sewage sludge was applied to agricultural soil, at different rates (40 and 80 t ha[-1]) and frequencies (every 1, 2 and 4 years) of application, were studied to assess: (i) the effect of sewage sludge application on prokaryotic community composition, (ii) the links between prokaryotic community composition and antibiotic resistance profiles, and (iii) the links between antibiotic resistance and metal(oid) concentrations in amended soil. We found no significant impact of sewage sludge on prokaryotic community composition. Some antibiotic resistance genes (ARGs) correlated positively with particular prokaryotic taxa, being Gemmatimonadetes the taxon with the greatest number of positive correlations at phylum level. No positive correlation was found between prokaryotic taxa and genes encoding resistance to sulfonamides and FCA. All metal(oid)s showed positive correlations with, at least, one ARG. Metal(oid) concentrations in soil also showed positive correlations with mobile genetic element genes, particularly with the gene tnpA-07. These data provide useful information on the links between soil prokaryotic composition and resistome profiles, and between antibiotic resistance and metal(oid) concentrations, in agricultural soils amended with sewage sludge.}, }
@article {pmid30294306, year = {2018}, author = {Purahong, W and Wubet, T and Lentendu, G and Hoppe, B and Jariyavidyanont, K and Arnstadt, T and Baber, K and Otto, P and Kellner, H and Hofrichter, M and Bauhus, J and Weisser, WW and Krüger, D and Schulze, ED and Kahl, T and Buscot, F}, title = {Determinants of Deadwood-Inhabiting Fungal Communities in Temperate Forests: Molecular Evidence From a Large Scale Deadwood Decomposition Experiment.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2120}, pmid = {30294306}, issn = {1664-302X}, abstract = {Despite the important role of wood-inhabiting fungi (WIF) in deadwood decomposition, our knowledge of the factors shaping the dynamics of their species richness and community composition is scarce. This is due to limitations regarding the resolution of classical methods used for characterizing WIF communities and to a lack of well-replicated long-term experiments with sufficient numbers of tree species. Here, we used a large scale experiment with logs of 11 tree species at an early stage of decomposition, distributed across three regions of Germany, to identify the factors shaping WIF community composition and Operational Taxonomic Unit (OTU) richness using next generation sequencing. We found that tree species identity was the most significant factor, corresponding to (P < 0.001) and explaining 10% (representing 48% of the explainable variance) of the overall WIF community composition. The next important group of variables were wood-physicochemical properties, of which wood pH was the only factor that consistently corresponded to WIF community composition. For overall WIF richness patterns, we found that approximately 20% of the total variance was explained by wood N content, location, tree species identity and wood density. It is noteworthy that the importance of determinants of WIF community composition and richness appeared to depend greatly on tree species group (broadleaved vs. coniferous) and it differed between the fungal phyla Ascomycota and Basidiomycota.}, }
@article {pmid30290356, year = {2019}, author = {Cipullo, S and Negrin, I and Claveau, L and Snapir, B and Tardif, S and Pulleyblank, C and Prpich, G and Campo, P and Coulon, F}, title = {Linking bioavailability and toxicity changes of complex chemicals mixture to support decision making for remediation endpoint of contaminated soils.}, journal = {The Science of the total environment}, volume = {650}, number = {Pt 2}, pages = {2150-2163}, doi = {10.1016/j.scitotenv.2018.09.339}, pmid = {30290356}, issn = {1879-1026}, mesh = {Biological Availability ; Charcoal/*administration &amp; dosage ; *Composting ; Decision Making ; England ; Environmental Biomarkers ; Environmental Restoration and Remediation/*methods ; Hydrocarbons, Aromatic/analysis ; Metalloids/analysis ; Metals, Heavy/analysis ; Risk Assessment ; Soil Pollutants/*analysis ; Tars/*analysis ; }, abstract = {A six-month laboratory scale study was carried out to investigate the effect of biochar and compost amendments on complex chemical mixtures of tar, heavy metals and metalloids in two genuine contaminated soils. An integrated approach, where organic and inorganic contaminants bioavailability and distribution changes, along with a range of microbiological indicators and ecotoxicological bioassays, was used to provide multiple lines of evidence to support the risk characterisation and assess the remediation end-point. Both compost and biochar amendment (p = 0.005) as well as incubation time (p = 0.001) significantly affected the total and bioavailable concentrations of the total petroleum hydrocarbons (TPH) in the two soils. Specifically, TPH concentration decreased by 46% and 30% in Soil 1 and Soil 2 amended with compost. These decreases were accompanied by a reduction of 78% (Soil 1) and 6% (Soil 2) of the bioavailable hydrocarbons and the most significant decrease was observed for the medium to long chain aliphatic compounds (EC16-35) and medium molecular weight aromatic compounds (EC16-21). Compost amendment enhanced the degradation of both the aliphatic and aromatic fractions in the two soils, while biochar contributed to lock the hydrocarbons in the contaminated soils. Neither compost nor biochar affected the distribution and behaviour of the heavy metals (HM) and metalloids in the different soil phases, suggesting that the co-presence of heavy metals and metalloids posed a low risk. Strong negative correlations were observed between the bioavailable hydrocarbon fractions and the ecotoxicological assays suggesting that when bioavailable concentrations decreased, the toxicity also decreased. This study showed that adopting a combined diagnostic approach can significantly help to identify optimal remediation strategies and contribute to change the over-conservative nature of the current risk assessments thus reducing the costs associated with remediation endpoint.}, }
@article {pmid30288545, year = {2019}, author = {Benucci, GMN and Bonito, V and Bonito, G}, title = {Fungal, Bacterial, and Archaeal Diversity in Soils Beneath Native and Introduced Plants in Fiji, South Pacific.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {136-146}, pmid = {30288545}, issn = {1432-184X}, support = {project MICL02416//Michigan State University AgBioResearch NIFA/ ; DEB1737898//National Science Foundation/ ; }, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Ecosystem ; Fiji ; Fungi/classification/genetics/*isolation &amp; purification ; Introduced Species ; Phylogeny ; Plants/microbiology ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The Fiji Islands is an archipelago of more than 330 islands located in the tropics of the South Pacific Ocean. Microbial diversity and biogeography in this region is still not understood. Here, we present the first molecular characterization of fungal, bacterial, and archaeal communities in soils from different habitats within the largest Fijian island, Viti Levu. Soil samples were collected from under native vegetation in maritime-, forest-, stream-, grassland-, and casuarina-dominated habitats, as well as from under the introduced agricultural crops sugarcane, cassava, pine, and mahogany. Soil microbial diversity was analyzed through MiSeq amplicon sequencing of 16S (for prokaryotes), ITS, LSU ribosomal DNA (for fungi). Prokaryotic communities were dominated by Proteobacteria (~ 25%), Acidobacteria (~ 19%), and Actinobacteria (~ 17%), and there were no indicator species associated with particular habitats. ITS and LSU were congruent in β-diversity patterns of fungi, and fungal communities were dominated by Ascomycota (~ 57-64%), followed by Basidiomycota (~ 20-23%) and Mucoromycota (~ 10%) according to ITS, or Chytridiomycota (~ 9%) according to LSU. Indicator species analysis of fungi found statistical associations of Cenococcum, Wilcoxina, and Rhizopogon to Pinus caribaea. We hypothesize these obligate biotrophic fungi were co-introduced with their host plant. Entoloma was statistically associated with grassland soils, and Fusarium and Lecythophora with soils under cassava. Observed richness varied from 65 (casuarina) to 404 OTUs (cassava) for fungi according to ITS region, and from 1268 (pine) to 2931 OTUs (cassava) for bacteria and archaea. A major finding of this research is that nearly 25% of the fungal OTUs are poorly classified, indicative of novel biodiversity in this region. This preliminary survey provides important baseline data on fungal, bacterial, and archaeal diversity and biogeography in the Fiji Islands.}, }
@article {pmid30288544, year = {2019}, author = {Peters, MJ and Suwannapong, G and Pelin, A and Corradi, N}, title = {Genetic and Genome Analyses Reveal Genetically Distinct Populations of the Bee Pathogen Nosema ceranae from Thailand.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {877-889}, pmid = {30288544}, issn = {1432-184X}, support = {ER13-09-190//Ministry of Research, Innovation and Science/ ; }, mesh = {Animals ; Bees/*microbiology ; *Genome, Fungal ; Genomics ; Nosema/*genetics ; Polymerase Chain Reaction ; *Polymorphism, Single Nucleotide ; Thailand ; }, abstract = {The recent global decline in Western honeybee (Apis mellifera) populations is of great concern for pollination and honey production worldwide. Declining honeybee populations are frequently infected by the microsporidian pathogen Nosema ceranae. This species was originally described in the Asiatic honeybee (Apis cerana), and its identification in global A. mellifera hives could result from a recent host transfer. Recent genome studies have found that global populations of this parasite are polyploid and that humans may have fueled their global expansion. To better understand N. ceranae biology, we investigated its genetic diversity within part of their native range (Thailand) and among different hosts (A. mellifera, A. cerana) using both PCR and genome-based methods. We find that Thai N. ceranae populations share many SNPs with other global populations and appear to be clonal. However, in stark contrast with previous studies, we found that these populations also carry many SNPs not found elsewhere, indicating that these populations have evolved in their current geographic location for some time. Our genome analyses also indicate the potential presence of diploidy within Thai populations of N. ceranae.}, }
@article {pmid30288176, year = {2018}, author = {Walker, TWN and Kaiser, C and Strasser, F and Herbold, CW and Leblans, NIW and Woebken, D and Janssens, IA and Sigurdsson, BD and Richter, A}, title = {Microbial temperature sensitivity and biomass change explain soil carbon loss with warming.}, journal = {Nature climate change}, volume = {8}, number = {10}, pages = {885-889}, pmid = {30288176}, issn = {1758-678X}, support = {294343/ERC_/European Research Council/International ; 610028/ERC_/European Research Council/International ; 636928/ERC_/European Research Council/International ; }, abstract = {Soil microorganisms control carbon losses from soils to the atmosphere1-3, yet their responses to climate warming are often short-lived and unpredictable4-7. Two mechanisms, microbial acclimation and substrate depletion, have been proposed to explain temporary warming effects on soil microbial activity8-10. However, empirical support for either mechanism is unconvincing. Here we used geothermal temperature gradients (> 50 years of field warming)11 and a short-term experiment to show that microbial activity (gross rates of growth, turnover, respiration and carbon uptake) is intrinsically temperature sensitive and does not acclimate to warming (+ 6 ºC) over weeks or decades. Permanently accelerated microbial activity caused carbon loss from soil. However, soil carbon loss was temporary because substrate depletion reduced microbial biomass and constrained the influence of microbes over the ecosystem. A microbial biogeochemical model12-14 showed that these observations are reproducible through a modest, but permanent, acceleration in microbial physiology. These findings reveal a mechanism by which intrinsic microbial temperature sensitivity and substrate depletion together dictate warming effects on soil carbon loss via their control over microbial biomass. We thus provide a framework for interpreting the links between temperature, microbial activity and soil carbon loss on timescales relevant to Earth's climate system.}, }
@article {pmid30287354, year = {2018}, author = {Staley, C and Sadowsky, MJ}, title = {Practical considerations for sampling and data analysis in contemporary metagenomics-based environmental studies.}, journal = {Journal of microbiological methods}, volume = {154}, number = {}, pages = {14-18}, doi = {10.1016/j.mimet.2018.09.020}, pmid = {30287354}, issn = {1872-8359}, mesh = {Algorithms ; Biodiversity ; Biostatistics/methods ; Computational Biology/methods ; DNA/analysis/isolation &amp; purification ; *Data Analysis ; Ecology ; Ecosystem ; Environment ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenome ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeography ; Sequence Analysis, DNA/methods ; Specimen Handling/*methods ; }, abstract = {Recent advancements in metagenomic-based studies, especially analyses of amplicon-based DNA sequencing targeting taxonomic marker genes, has led to an unprecedented characterization of microbial communities from diverse ecosystems around the world. While originally constrained by a lack of appropriate analytical tools and sequencing depth, new technologies and computational and statistical algorithms have been developed to handle highly dimensional, next-generation sequencing datasets. Both these tools allow for the robust analysis of structural and distributional patterns of microbiota essential for the understanding of microbial ecology and biogeography. Furthermore, consortia of individual laboratories working on large interdisciplinary research programs, like the Human and Earth Microbiome Projects, have developed standardized protocols for DNA extraction, sequencing pipelines, and bioinformatics. These approaches provide large repositories of publicly available data to serve as references for on-going and future, hypothesis-driven studies to better characterize the roles of microbial communities in diverse ecosystems. In this review, we outline the currently available statistical approaches and tools to aid in statistically powered study designs and analyses. Given what is now known about the enormous diversity and variability of the microbial communities in aquatic and terrestrial habitats, we also discuss practical considerations for sample collection. Due to the extensive advances made in the field of metagenomics over the last decade, rigorous, well replicated, hypothesis-driven studies are: 1) needed, 2) now possible, and 3) essential to make best use of sequencing-based technologies to characterize the roles of microbial communities in the structure and function of diverse ecosystems.}, }
@article {pmid30285851, year = {2018}, author = {Mehrshad, M and Salcher, MM and Okazaki, Y and Nakano, SI and Šimek, K and Andrei, AS and Ghai, R}, title = {Hidden in plain sight-highly abundant and diverse planktonic freshwater Chloroflexi.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {176}, pmid = {30285851}, issn = {2049-2618}, mesh = {Chloroflexi/*classification/genetics/isolation &amp; purification ; Czech Republic ; DNA, Bacterial/genetics ; Ecosystem ; Genome, Bacterial/genetics ; Lakes/*microbiology ; Metagenome/*genetics ; Phylogeny ; Plankton/*classification/genetics ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Representatives of the phylum Chloroflexi, though reportedly highly abundant in the extensive deep water habitats of both marine (SAR202 up to 30% of total prokaryotes) and freshwater (CL500-11 up to 26% of total prokaryotes), remain uncultivated and uncharacterized. There are few metagenomic studies on marine Chloroflexi representatives, while the pelagic freshwater Chloroflexi community is largely unknown except for a single metagenome-assembled genome of CL500-11.<br><br>RESULTS: Here, we provide the first extensive examination of the community composition of this cosmopolitan phylum in a range of pelagic habitats (176 datasets) and highlight the impact of salinity and depth on their phylogenomic composition. Reconstructed genomes (53 in total) provide a perspective on the phylogeny, metabolism, and distribution of three novel classes and two family-level taxa within the phylum Chloroflexi. We unraveled a remarkable genomic diversity of pelagic freshwater Chloroflexi representatives that thrive not only in the hypolimnion as previously suspected, but also in the epilimnion. Our results suggest that the lake hypolimnion provides a globally stable habitat reflected in lower species diversity among hypolimnion-specific CL500-11 and TK10 clusters in distantly related lakes compared to a higher species diversity of the epilimnion-specific SL56 cluster. Cell volume analyses show that the CL500-11 are among the largest prokaryotic cells in the water column of deep lakes and with a biomass to abundance ratio of two they significantly contribute to the deep lake carbon flow. Metabolic insights indicate participation of JG30-KF-CM66 representatives in the global cobalamin production via cobinamide to cobalamin salvage pathway.<br><br>CONCLUSIONS: Extending phylogenomic comparisons to brackish and marine habitats suggests salinity as the major influencer of the community composition of the deep-dwelling Chloroflexi in marine (SAR202) and freshwater (CL500-11) habitats as both counterparts thrive in intermediate brackish salinity; however, freshwater habitats harbor the most phylogenetically diverse community of pelagic Chloroflexi representatives that reside both in epi- and hypolimnion.}, }
@article {pmid30285747, year = {2018}, author = {Lebre, PH and Aliyu, H and De Maayer, P and Cowan, DA}, title = {In silico characterization of the global Geobacillus and Parageobacillus secretome.}, journal = {Microbial cell factories}, volume = {17}, number = {1}, pages = {156}, pmid = {30285747}, issn = {1475-2859}, mesh = {Genome, Bacterial/*genetics ; Geobacillus/*genetics ; }, abstract = {BACKGROUND: Geobacillus and Parageobacillus are two ecologically diverse thermophilic genera within the phylum Firmicutes. These taxa have long been of biotechnological interest due to their ability to secrete thermostable enzymes and other biomolecules that have direct applications in various industrial and clinical fields. Despite the commercial and industrial interest in these microorganisms, the full scope of the secreted protein, i.e. the secretome, of Geobacillus and Parageobacillus species remains largely unexplored, with most studies focusing on single enzymes. A genome-wide exploration of the global secretome can provide a platform for understanding the extracellular functional "protein cloud" and the roles that secreted proteins play in the survival and adaptation of these biotechnologically relevant organisms.<br><br>RESULTS: In the present study, the global secretion profile of 64 Geobacillus and Parageobacillus strains, comprising 772 distinct proteins, was predicted using comparative genomic approaches. Thirty-one of these proteins are shared across all strains used in this study and function in cell-wall/membrane biogenesis as well as transport and metabolism of carbohydrates, amino acids and inorganic ions. An analysis of the clustering patterns of the secretomes of the 64 strains according to shared functional orthology revealed a correlation between the secreted profiles of different strains and their phylogeny, with Geobacillus and Parageobacillus species forming two distinct functional clades.<br><br>CONCLUSIONS: The in silico characterization of the global secretome revealed a metabolically diverse set of secreted proteins, which include proteases, glycoside hydrolases, nutrient binding proteins and toxins.}, }
@article {pmid30284602, year = {2019}, author = {Lin, X and Hetharua, B and Lin, L and Xu, H and Zheng, T and He, Z and Tian, Y}, title = {Mangrove Sediment Microbiome: Adaptive Microbial Assemblages and Their Routed Biogeochemical Processes in Yunxiao Mangrove National Nature Reserve, China.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {57-69}, pmid = {30284602}, issn = {1432-184X}, support = {2017YFC05061001//National Key Research and Development Program of China/ ; }, mesh = {Ammonium Compounds/metabolism ; Bacteria/*classification/genetics/*isolation &amp; purification/metabolism ; Biodiversity ; China ; Conservation of Natural Resources ; DNA, Bacterial/genetics ; Geologic Sediments/chemistry/*microbiology ; *Microbiota ; Nitrates/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfur/metabolism ; Wetlands ; }, abstract = {Microorganisms play important roles in mangrove ecosystems. However, we know little about the ecological implications of mangrove microbiomes for high productivity and the efficient circulation of elements in mangrove ecosystems. Here, we focused on mangrove sediments located at the Yunxiao National Mangrove Reserve in southeast China, uncovering the mangrove microbiome using the 16S rRNA gene and shotgun metagenome sequencing approaches. Physicochemical assays characterized the Yunxiao mangrove sediments as carbon (C)-rich, sulfur (S)-rich, and nitrogen (N)-limited environment. Then phylogenetic analysis profiling a distinctive microbiome with an unexpected high frequency of Chloroflexi and Nitrospirae appeared to be an adaptive characteristic of microbial structure in S-rich habitat. Metagenome sequencing analysis revealed that the metabolic pathways of N and S cycling at the community-level were routed through ammonification and dissimilatory nitrate reduction to ammonium for N conservation in this N-limited habitat, and dissimilatory sulfate reduction along with polysulfide formation for generating bioavailable S resource avoiding the biotoxicity of sulfide in mangrove sediments. In addition, methane metabolism acted as a bridge to connect C cycling to N and S cycling. Further identification of possible biogeochemical linkers suggested Syntrophobacter, Sulfurovum, Nitrospira, and Anaerolinea potentially drive the coupling of C, N, and S cycling. These results highlighting the adaptive routed metabolism flow, a previously undescribed property of mangrove sediment microbiome, appears to be a defining characteristic of this habitat and may significantly contribute to the high productivity of mangrove ecosystems, which could be used as indicators for the health and biodiversity of mangrove ecosystems.}, }
@article {pmid30283424, year = {2018}, author = {El-Chakhtoura, J and Saikaly, PE and van Loosdrecht, MCM and Vrouwenvelder, JS}, title = {Impact of Distribution and Network Flushing on the Drinking Water Microbiome.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2205}, pmid = {30283424}, issn = {1664-302X}, abstract = {We sampled the tap water of seven unique, full-scale drinking water distribution systems at different locations as well as the corresponding treatment plant effluents to evaluate the impact of distribution and the potential presence of a core drinking water microbiome. The water was also sampled during network flushing to examine its effect on the microbial ecology. While a core microbiome dominated by Gammaproteobacteria was found using 16S rRNA gene pyrosequencing, an increase in biomass was detected in the networks, especially during flushing. Water age did not significantly impact the microbiology. Irrespective of differences in treatment plants, tap water bacterial communities in the distinct networks converged and highly resembled the flushed water communities. Piping biofilm and sediment communities therefore largely determine the final tap water microbial quality, attenuating the impact of water source and treatment strategy and highlighting the fundamental role of local physicochemical conditions and microbial processes within infrastructure micro-niches.}, }
@article {pmid30283421, year = {2018}, author = {Durán, P and Tortella, G and Viscardi, S and Barra, PJ and Carrión, VJ and Mora, ML and Pozo, MJ}, title = {Microbial Community Composition in Take-All Suppressive Soils.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2198}, pmid = {30283421}, issn = {1664-302X}, abstract = {Gaeumannomyces graminis var. tritici (Ggt) is the main soilborne factor that affects wheat production around the world. Recently we reported the occurrence of six suppressive soils in monoculture areas from indigenous "Mapuche" communities, and evidenced that the suppression relied on the biotic component of those soils. Here, we compare the rhizosphere and endosphere microbial community structure (total bacteria, actinomycetes, total fungi, and ascomycetes) of wheat plants grown in suppressive and conducive soils. Our results suggested that Ggt suppression could be mediated mostly by bacterial endophytes, rather than rhizosphere microorganisms, since the community structure was similar in all suppressive soils as compared with conducive. Interestingly, we found that despite the lower incidence of take-all disease in suppressive soils, the Ggt concentration in roots was not significantly reduced in all suppressive soils compared to those growing in conducive soil. Therefore, the disease suppression is not always related to a reduction of the pathogen biomass. Furthermore, we isolated endophytic bacteria from wheat roots growing in suppressive soils. Among them we identified Serratia spp. and Enterobacter spp. able to inhibit Ggt growth in vitro. Since the disease, but not always pathogen amount, was reduced in the suppressive soils, we propose that take all disease suppressiveness is not only related to direct antagonism to the pathogen.}, }
@article {pmid30283052, year = {2018}, author = {Boers, SA and Prest, EI and Taučer-Kapteijn, M and Knezev, A and Schaap, PG and Hays, JP and Jansen, R}, title = {Monitoring of microbial dynamics in a drinking water distribution system using the culture-free, user-friendly, MYcrobiota platform.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14727}, pmid = {30283052}, issn = {2045-2322}, mesh = {Bacteria/genetics/isolation &amp; purification ; DNA, Bacterial/classification/*genetics/isolation &amp; purification ; Disinfection ; Drinking Water/*microbiology/standards ; High-Throughput Nucleotide Sequencing ; Humans ; Microbiological Techniques ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Water Purification/methods ; Water Quality/*standards ; }, abstract = {Drinking water utilities currently rely on a range of microbiological detection techniques to evaluate the quality of their drinking water (DW). However, microbiota profiling using culture-free 16S rRNA gene next-generation sequencing (NGS) provides an opportunity for improved monitoring of the microbial ecology and quality of DW. Here, we evaluated the utility of a previously validated microbiota profiling platform (MYcrobiota) to investigate the microbial dynamics of a full-scale, non-chlorinated DW distribution system (DWDS). In contrast to conventional methods, we observed spatial and temporal bacterial genus changes (expressed as operational taxonomic units - OTUs) within the DWDS. Further, a small subset of bacterial OTUs dominated with abundances that shifted across the length of the DWDS, and were particularly affected by a post-disinfection step. We also found seasonal variation in OTUs within the DWDS and that many OTUs could not be identified, even though MYcrobiota is specifically designed to reduce potential PCR sequencing artefacts. This suggests that our current knowledge about the microbial ecology of DW communities is limited. Our findings demonstrate that the user-friendly MYcrobiota platform facilitates culture-free, standardized microbial dynamics monitoring and has the capacity to facilitate the introduction of microbiota profiling into the management of drinking water quality.}, }
@article {pmid30281902, year = {2019}, author = {Sollai, M and Villanueva, L and Hopmans, EC and Reichart, GJ and Sinninghe Damsté, JS}, title = {A combined lipidomic and 16S rRNA gene amplicon sequencing approach reveals archaeal sources of intact polar lipids in the stratified Black Sea water column.}, journal = {Geobiology}, volume = {17}, number = {1}, pages = {91-109}, pmid = {30281902}, issn = {1472-4669}, mesh = {Archaea/*metabolism ; Black Sea ; Lipids/*analysis ; RNA, Bacterial/*analysis ; RNA, Ribosomal, 16S/*analysis ; Seawater/*chemistry ; }, abstract = {Archaea are important players in marine biogeochemical cycles, and their membrane lipids are useful biomarkers in environmental and geobiological studies. However, many archaeal groups remain uncultured and their lipid composition unknown. Here, we aim to expand the knowledge on archaeal lipid biomarkers and determine the potential sources of those lipids in the water column of the euxinic Black Sea. The archaeal community was evaluated by 16S rRNA gene amplicon sequencing and by quantitative PCR. The archaeal intact polar lipids (IPLs) were investigated by ultra-high-pressure liquid chromatography coupled to high-resolution mass spectrometry. Our study revealed both a complex archaeal community and large changes with water depth in the IPL assemblages. In the oxic/upper suboxic waters (<105 m), the archaeal community was dominated by marine group (MG) I Thaumarchaeota, coinciding with a higher relative abundance of hexose phosphohexose crenarchaeol, a known marker for Thaumarchaeota. In the suboxic waters (80-110 m), MGI Nitrosopumilus sp. dominated and produced predominantly monohexose glycerol dibiphytanyl glycerol tetraethers (GDGTs) and hydroxy-GDGTs. Two clades of MGII Euryarchaeota were present in the oxic and upper suboxic zones in much lower abundances, preventing the detection of their specific IPLs. In the deep sulfidic waters (>110 m), archaea belonging to the DPANN Woesearchaeota, Bathyarchaeota, and ANME-1b clades dominated. Correlation analyses suggest that the IPLs GDGT-0, GDGT-1, and GDGT-2 with two phosphatidylglycerol (PG) head groups and archaeol with a PG, phosphatidylethanolamine, and phosphatidylserine head groups were produced by ANME-1b archaea. Bathyarchaeota represented 55% of the archaea in the deeper part of the euxinic zone and likely produces archaeol with phospho-dihexose and hexose-glucuronic acid head groups.}, }
@article {pmid30280234, year = {2019}, author = {Boixel, AL and Delestre, G and Legeay, J and Chelle, M and Suffert, F}, title = {Phenotyping Thermal Responses of Yeasts and Yeast-like Microorganisms at the Individual and Population Levels: Proof-of-Concept, Development and Application of an Experimental Framework to a Plant Pathogen.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {42-56}, pmid = {30280234}, issn = {1432-184X}, support = {ANR-11-LABX-0034//Agence Nationale de la Recherche/ ; }, mesh = {Adaptation, Physiological ; Ascomycota/growth &amp; development/*physiology ; Biological Evolution ; Hot Temperature ; Phenotype ; Plant Diseases/*microbiology ; Triticum/*microbiology ; Yeasts/growth &amp; development/*physiology ; }, abstract = {Deciphering the responses of microbial populations to spatiotemporal changes in their thermal environment is instrumental in improving our understanding of their eco-evolutionary dynamics. Recent studies have shown that current phenotyping protocols do not adequately address all dimensions of phenotype expression. Therefore, these methods can give biased assessments of sensitivity to temperature, leading to misunderstandings concerning the ecological processes underlying thermal plasticity. We describe here a new robust and versatile experimental framework for the accurate investigation of thermal performance and phenotypic diversity in yeasts and yeast-like microorganisms, at the individual and population levels. In addition to proof-of-concept, the application of this framework to the fungal wheat pathogen Zymoseptoria tritici resulted in detailed characterisations for this yeast-like microorganism of (i) the patterns of temperature-dependent changes in performance for four fitness traits; (ii) the consistency in thermal sensitivity rankings of strains between in planta and in vitro growth assessments; (iii) significant interindividual variation in thermal responses, with four principal thermotypes detected in a sample of 66 strains; and (iv) the ecological consequences of this diversity for population-level processes through pairwise competition experiments highlighting temperature-dependent outcomes. These findings extend our knowledge and ability to quantify and categorise the phenotypic heterogeneity of thermal responses. As such, they lay the foundations for further studies elucidating local adaptation patterns and the effects of temperature variations on eco-evolutionary and epidemiological processes.}, }
@article {pmid30280026, year = {2018}, author = {Li, J and Lin, J and Pei, C and Lai, K and Jeffries, TC and Tang, G}, title = {Variation of soil bacterial communities along a chronosequence of Eucalyptus plantation.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5648}, pmid = {30280026}, issn = {2167-8359}, abstract = {Eucalyptus is harvested for wood and fiber production in many tropical and sub-tropical habitats globally. Plantation has been controversial because of its influence on the surrounding environment, however, the influence of massive Eucalyptus planting on soil microbial communities is unclear. Here we applied high-throughput sequencing of the 16S rRNA gene to assess the microbial community composition and diversity of planting chronosequences, involving two, five and ten years of Eucalyptus plantation, comparing to that of secondary-forest in South China. We found that significant changes in the composition of soil bacteria occurred when the forests were converted from secondary-forest to Eucalyptus. The bacterial community structure was clearly distinct from control and five year samples after Eucalyptus was grown for 2 and 10 years, highlighting the influence of this plantation on local soil microbial communities. These groupings indicated a cycle of impact (2 and 10 year plantations) and low impact (5-year plantations) in this chronosequence of Eucalyptus plantation. Community patterns were underpinned by shifts in soil properties such as pH and phosphorus concentration. Concurrently, key soil taxonomic groups such as Actinobacteria showed abundance shifts, increasing in impacted plantations and decreasing in low impacted samples. Shifts in taxonomy were reflected in a shift in metabolic potential, including pathways for nutrient cycles such as carbon fixation, which changed in abundance over time following Eucalyptus plantation. Combined these results confirm that Eucalyptus plantation can change the community structure and diversity of soil microorganisms with strong implications for land-management and maintaining the health of these ecosystems.}, }
@article {pmid30279438, year = {2018}, author = {Quintanilla, E and Ramírez-Portilla, C and Adu-Oppong, B and Walljasper, G and Glaeser, SP and Wilke, T and Muñoz, AR and Sánchez, JA}, title = {Local confinement of disease-related microbiome facilitates recovery of gorgonian sea fans from necrotic-patch disease.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14636}, pmid = {30279438}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/*genetics ; Microbiota/*genetics ; Pacific Ocean ; Phylogeny ; RNA, Bacterial ; RNA, Ribosomal, 16S ; Symbiosis ; }, abstract = {Microbiome disruptions triggering disease outbreaks are increasingly threatening corals worldwide. In the Tropical Eastern Pacific, a necrotic-patch disease affecting gorgonian corals (sea fans, Pacifigorgia spp.) has been observed in recent years. However, the composition of the microbiome and its disease-related disruptions remain unknown in these gorgonian corals. Therefore, we analysed 16S rRNA gene amplicons from tissues of healthy colonies (n = 19) and from symptomatic-asymptomatic tissues of diseased colonies (n = 19) of Pacifigorgia cairnsi (Gorgoniidae: Octocorallia) in order to test for disease-related changes in the bacterial microbiome. We found that potential endosymbionts (mostly Endozoicomonas spp.) dominate the core microbiome in healthy colonies. Moreover, healthy tissues differed in community composition and functional profile from those of the symptomatic tissues but did not show differences to asymptomatic tissues of the diseased colonies. A more diverse set of bacteria was observed in symptomatic tissues, together with the decline in abundance of the potential endosymbionts from the healthy core microbiome. Furthermore, according to a comparative taxonomy-based functional profiling, these symptomatic tissues were characterized by the increase in heterotrophic, ammonia oxidizer and dehalogenating bacteria and by the depletion of nitrite and sulphate reducers. Overall, our results suggest that the bacterial microbiome associated with the disease behaves opportunistically and is likely in a state of microbial dysbiosis. We also conclude that the confinement of the disease-related consortium to symptomatic tissues may facilitate colony recovery.}, }
@article {pmid30276419, year = {2019}, author = {Renoz, F and Pons, I and Vanderpoorten, A and Bataille, G and Noël, C and Foray, V and Pierson, V and Hance, T}, title = {Evidence for Gut-Associated Serratia symbiotica in Wild Aphids and Ants Provides New Perspectives on the Evolution of Bacterial Mutualism in Insects.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {159-169}, pmid = {30276419}, issn = {1432-184X}, support = {1.E074.14//Fonds pour la Formation &#xe0; la Recherche dans l'Industrie et dans l'Agriculture/ ; }, mesh = {Animals ; Animals, Wild/microbiology/physiology ; Ants/*microbiology/physiology ; Aphids/classification/genetics/*microbiology/physiology ; Bacterial Proteins/genetics/metabolism ; Biological Evolution ; *Gastrointestinal Microbiome ; Intestines/microbiology/physiology ; Phylogeny ; Serratia/genetics/*physiology ; *Symbiosis ; }, abstract = {Many insects engage in symbiotic associations with diverse assemblages of bacterial symbionts that can deeply impact on their ecology and evolution. The intraspecific variation of symbionts remains poorly assessed while phenotypic effects and transmission behaviors, which are key processes for the persistence and evolution of symbioses, may differ widely depending on the symbiont strains. Serratia symbiotica is one of the most frequent symbiont species in aphids and a valuable model to assess this intraspecific variation since it includes both facultative and obligate symbiotic strains. Despite evidence that some facultative S. symbiotica strains exhibit a free-living capacity, the presence of these strains in wild aphid populations, as well as in insects with which they maintain regular contact, has never been demonstrated. Here, we examined the prevalence, diversity, and tissue tropism of S. symbiotica in wild aphids and associated ants. We found a high occurrence of S. symbiotica infection in ant populations, especially when having tended infected aphid colonies. We also found that the S. symbiotica diversity includes strains found located within the gut of aphids and ants. In the latter, this tissue tropism was found restricted to the proventriculus. Altogether, these findings highlight the extraordinary diversity and versatility of an insect symbiont and suggest the existence of novel routes for symbiont acquisition in insects.}, }
@article {pmid30274898, year = {2019}, author = {Blachier, F and Beaumont, M and Portune, KJ and Steuer, N and Lan, A and Audebert, M and Khodorova, N and Andriamihaja, M and Airinei, G and Benamouzig, R and Davila, AM and Armand, L and Rampelli, S and Brigidi, P and Tomé, D and Claus, SP and Sanz, Y}, title = {High-protein diets for weight management: Interactions with the intestinal microbiota and consequences for gut health. A position paper by the my new gut study group.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {38}, number = {3}, pages = {1012-1022}, doi = {10.1016/j.clnu.2018.09.016}, pmid = {30274898}, issn = {1532-1983}, mesh = {Body Weight/physiology ; *Diet ; *Diet, High-Protein ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/microbiology/physiology ; Intestine, Large/microbiology/physiology ; *Weight Loss ; }, abstract = {BACKGROUND &amp; AIMS: This review examines to what extent high-protein diets (HPD), which may favor body weight loss and improve metabolic outcomes in overweight and obese individuals, may also impact the gut environment, shaping the microbiota and the host-microbe (co)metabolic pathways and products, possibly affecting large intestine mucosa homeostasis.<br><br>METHODS: PubMed-referenced publications were analyzed with an emphasis on dietary intervention studies involving human volunteers in order to clarify the beneficial vs. deleterious effects of HPD in terms of both metabolic and gut-related health parameters; taking into account the interactions with the gut microbiota.<br><br>RESULTS: HPD generally decrease body weight and improve blood metabolic parameters, but also modify the fecal and urinary contents in various bacterial metabolites and co-metabolites. The effects of HPD on the intestinal microbiota composition appear rather heterogeneous depending on the type of dietary intervention. Recently, HPD consumption was shown to modify the expression of genes playing key roles in homeostatic processes in the rectal mucosa, without evidence of intestinal inflammation. Importantly, the effects of HPD on the gut were dependent on the protein source (i.e. from plant or animal sources), a result which should be considered for further investigations.<br><br>CONCLUSION: Although HPD appear to be efficient for weight loss, the effects of HPD on microbiota-derived metabolites and gene expression in the gut raise new questions on the impact of HPD on the large intestine mucosa homeostasis leading the authors to recommend some caution regarding the utilization of HPD, notably in a recurrent and/or long-term ways.}, }
@article {pmid30273809, year = {2018}, author = {De Vrieze, J and Arends, JBA and Verbeeck, K and Gildemyn, S and Rabaey, K}, title = {Interfacing anaerobic digestion with (bio)electrochemical systems: Potentials and challenges.}, journal = {Water research}, volume = {146}, number = {}, pages = {244-255}, doi = {10.1016/j.watres.2018.08.045}, pmid = {30273809}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Biofuels ; Bioreactors ; *Methane ; }, abstract = {For over a century, anaerobic digestion has been a key technology in stabilizing organic waste streams, while at the same time enabling the recovery of energy. The anticipated transition to a bio-based economy will only increase the quantity and diversity of organic waste streams to be treated, and, at the same time, increase the demand for additional and effective resource recovery schemes for nutrients and organic matter. The performance of anaerobic digestion can be supported and enhanced by (bio)electrochemical systems in a wide variety of hybrid technologies. Here, the possible benefits of combining anaerobic digestion with (bio)electrochemical systems were reviewed in terms of (1) process monitoring, control, and stabilization, (2) nutrient recovery, (3) effluent polishing, and (4) biogas upgrading. The interaction between microorganisms and electrodes with respect to niche creation is discussed, and the potential impact of this interaction on process performance is evaluated. The strength of combining anaerobic digestion with (bio)electrochemical technologies resides in the complementary character of both technologies, and this perspective was used to distinguish transient trends from schemes with potential for full-scale application. This is supported by an operational costs assessment, showing that the economic potential of combining anaerobic digestion with a (bio)electrochemical system is highly case-specific, and strongly depends on engineering challenges with respect to full-scale applications.}, }
@article {pmid30273364, year = {2018}, author = {Tam, J and Hoffmann, T and Fischer, S and Bornstein, S and Gräßler, J and Noack, B}, title = {Obesity alters composition and diversity of the oral microbiota in patients with type 2 diabetes mellitus independently of glycemic control.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0204724}, pmid = {30273364}, issn = {1932-6203}, mesh = {Aged ; Blood Glucose/*metabolism ; Cross-Sectional Studies ; Diabetes Mellitus, Type 2/metabolism/*microbiology ; Female ; Glycated Hemoglobin/metabolism ; Humans ; Longitudinal Studies ; Male ; Microbiota/*physiology ; Mouth/*microbiology ; Obesity/metabolism/*microbiology ; Periodontitis/metabolism/microbiology ; Prospective Studies ; }, abstract = {BACKGROUND AND OBJECTIVE: The involvement of the oral microbiota as a possible link between periodontitis, type 2 diabetes mellitus and obesity is still not well understood. The objective of the study was to investigate if glycemic control and obesity play a role in modulating the composition and diversity of the oral microbial ecology.<br><br>MATERIAL AND METHODS: A cohort of patients with type 2 diabetes mellitus (n = 18) was recruited. Participants demonstrating improved glycemic control after 3 months (n = 6) were included in a second examination. A full mouth examination was performed to estimate periodontitis severity followed by sample collection (subgingival plaque and saliva). Generation of large sequence libraries was performed using the high-throughput Illumina MiSeq sequencing platform.<br><br>RESULTS: The majority of participants (94.4%, n = 17) presented with moderate or severe forms of periodontitis. Differences in microbial composition and diversity between obese (BMI &#x2265; 30 kg/m2) and non-obese (BMI < 30 kg/m2) groups were statistically significant. Cross-sectional and longitudinal approaches failed to reveal statistically significant associations between HbA1c level and species composition or diversity.<br><br>CONCLUSIONS: Obesity was significantly associated with the oral microbial composition. The impact of glycemic control on oral microbiota, however, could not be assured statistically.}, }
@article {pmid30272014, year = {2018}, author = {de Araujo, ASF and Mendes, LW and Lemos, LN and Antunes, JEL and Beserra, JEA and de Lyra, MDCCP and Figueiredo, MDVB and Lopes, &#xc2;CA and Gomes, RLF and Bezerra, WM and Melo, VMM and de Araujo, FF and Geisen, S}, title = {Protist species richness and soil microbiome complexity increase towards climax vegetation in the Brazilian Cerrado.}, journal = {Communications biology}, volume = {1}, number = {}, pages = {135}, pmid = {30272014}, issn = {2399-3642}, abstract = {Biodiversity underlies ecosystem functioning. While aboveground biodiversity is often well studied, the belowground microbiome, in particular protists, remains largely unknown. Indeed, holistic insights into soil microbiome structures in natural soils, especially in hyperdiverse biomes such as the Brazilian Cerrado, remain unexplored. Here, we study the soil microbiome across four major vegetation zones of the Cerrado, ranging from grass-dominated to tree-dominated vegetation with a focus on protists. We show that protist taxon richness increases towards the tree-dominated climax vegetation. Early successional habitats consisting of primary grass vegetation host most potential plant pathogens and least animal parasites. Using network analyses combining protist with prokaryotic and fungal sequences, we show that microbiome complexity increases towards climax vegetation. Together, this suggests that protists are key microbiome components and that vegetation succession towards climax vegetation is stimulated by higher loads of animal and plant pathogens. At the same time, an increase in microbiome complexity towards climax vegetation might enhance system stability.}, }
@article {pmid30269410, year = {2019}, author = {Bovio, P and Cabezas, A and Etchebehere, C}, title = {Preliminary analysis of Chloroflexi populations in full-scale UASB methanogenic reactors.}, journal = {Journal of applied microbiology}, volume = {126}, number = {2}, pages = {667-683}, doi = {10.1111/jam.14115}, pmid = {30269410}, issn = {1365-2672}, mesh = {Biomass ; Bioreactors/*microbiology ; Chloroflexi/classification/cytology/genetics/*isolation &amp; purification ; In Situ Hybridization, Fluorescence ; Methane/metabolism ; Phylogeny ; Sewage/microbiology ; Wastewater/microbiology ; }, abstract = {AIMS: The phylum Chloroflexi is frequently found in high abundance in methanogenic reactors, but their role is still unclear as most of them remain uncultured and understudied. Hence, a detailed analysis was performed in samples from five up-flow anaerobic sludge blanket (UASB) full-scale reactors fed different industrial wastewaters.<br><br>METHODS AND RESULTS: Quantitative PCR show that the phylum Chloroflexi was abundant in all UASB methanogenic reactors, with higher abundance in the reactors operated for a long period of time, which presented granular biomass. Both terminal restriction fragment length polymorphism and 16S rRNA gene amplicon sequencing revealed diverse Chloroflexi populations apparently determined by the different inocula. According to the phylogenetic analysis, the sequences from the dominant Chloroflexi were positioned in branches where no sequences of the cultured representative strains were placed. Fluorescent in&#xa0;situ hybridization analysis performed in two of the reactors showed filamentous morphology of the hybridizing cells.<br><br>CONCLUSIONS: While members of the Anaerolineae class within phylum Chloroflexi were predominant, their diversity is still poorly described in anaerobic reactors. Due to their filamentous morphology, Chloroflexi may have a key role in the granulation in methanogenic UASB reactors.<br><br>Our results bring new insights about the diversity, stability, dynamics and abundance of this phylum in full-scale UASB reactors which aid in understanding their function within the reactor biomass. However, new methodological approaches and analysis of bulking biomass are needed to completely unravel their role in these reactors. Combining all this knowledge with reactor operational parameters will allow to understand their participation in granulation and bulking episodes and design strategies to prevent Chloroflexi overgrowth.}, }
@article {pmid30267172, year = {2018}, author = {Staley, C and Kaiser, T and Khoruts, A}, title = {Clinician Guide to Microbiome Testing.}, journal = {Digestive diseases and sciences}, volume = {63}, number = {12}, pages = {3167-3177}, pmid = {30267172}, issn = {1573-2568}, mesh = {*Dysbiosis/diagnosis/microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Microbiological Phenomena ; Microbiological Techniques/methods/trends ; }, abstract = {Recent recognition that the intestinal microbiome plays potential roles in the pathogenesis of multiple common diseases has led to a growing interest in personalized microbiome analysis among clinical investigators and patients. Permissibility of direct access testing has allowed the emergence of commercial companies offering microbiome analysis to patients seeking to gain a better understanding of their symptoms and disease conditions. In turn, physicians are often asked to help with interpretation of such tests or even requested by their patients to order them. Therefore, physicians need to have a basic understanding of the current state of microbiome science. This review examines how the perspective of microbial ecology, which is fundamental to understanding the microbiome, updates the classical version of the germ theory of disease. We provide the essential vocabulary of microbiome science and describe its current limitations. We look forward to the future when microbiome diagnostics may live up to its potential of becoming integral to clinical care that will become increasingly individualized, and microbiome analysis may become incorporated into that future paradigm. However, we caution patients and providers that the current microbiome tests, given the state of knowledge and technology, do not provide much value in clinical decisions. Considerable research remains to be carried out to make this objective a reality.}, }
@article {pmid30267129, year = {2019}, author = {Miller, SR and Carvey, D}, title = {Ecological Divergence with Gene Flow in a Thermophilic Cyanobacterium.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {33-41}, pmid = {30267129}, issn = {1432-184X}, support = {EF-0801999//National Science Foundation/ ; }, mesh = {Ecology ; Ecosystem ; *Gene Flow ; Genomics ; Hot Springs/chemistry/*microbiology ; Hot Temperature ; Phylogeny ; Recombination, Genetic ; Synechococcus/chemistry/*genetics/growth &amp; development/isolation &amp; purification ; }, abstract = {How ecological diversity is maintained and distributed within populations is a longstanding question in microbial ecology. In the thermophilic cyanobacterium Synechococcus B', high observed levels of recombination are predicted to maintain ecological variation despite the simultaneous action of diverse selective pressures on different regions of the genome. To investigate ecological diversity in these bacteria, we directly isolated laboratory strains of Synechococcus B' from samples collected along the thermal gradients of two geothermal environments in Yellowstone National Park. Extensive recombination was evident for a multi-locus sequence data set, and, consequently, our sample did not exhibit the sequence clustering expected for distinct ecotypes evolving by periodic clonal selection. Evidence for local selective sweeps at specific loci suggests that sweeps may be common but that recombination is effective for maintaining diversity of unlinked genomic regions. Thermal performance for strain growth was positively associated with the temperature of the environment, indicating that Synechococcus B' populations consist of locally adapted ecological specialists that occupy specific thermal niches. Because this ecological differentiation is observed despite the absence of dispersal barriers among sites, we conclude that these bacteria may freely exchange much of the genome but that barriers to gene flow exist for loci under direct temperature selection.}, }
@article {pmid30266729, year = {2018}, author = {Vital, M and Howe, A and Bergeron, N and Krauss, RM and Jansson, JK and Tiedje, JM}, title = {Metagenomic Insights into the Degradation of Resistant Starch by Human Gut Microbiota.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {23}, pages = {}, pmid = {30266729}, issn = {1098-5336}, support = {RC1 DK086472/DK/NIDDK NIH HHS/United States ; UH3 DK083993/DK/NIDDK NIH HHS/United States ; UL1 TR000004/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; Bacteria/classification/*genetics/*isolation &amp; purification/metabolism ; Diabetes Mellitus, Type 2/diet therapy/metabolism/*microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Phylogeny ; Starch/analysis/*metabolism ; }, abstract = {Several studies monitoring alterations in the community structure upon resistant starch (RS) interventions are available, although comprehensive function-based analyses are lacking. Recently, a multiomics approach based on 16S rRNA gene sequencing, metaproteomics, and metabolomics on fecal samples from individuals subjected to high and low doses of type 2 RS (RS2; 48 g and 3 g/2,500 kcal, respectively, daily for 2 weeks) in a crossover intervention experiment was performed. In the present study, we did pathway-based metagenomic analyses on samples from a subset of individuals (n = 12) from that study to obtain additional detailed insights into the functional structure at high resolution during RS2 intervention. A mechanistic framework based on obtained results is proposed where primary degradation was governed by Firmicutes, with Ruminococcus bromii as a major taxon involved, providing fermentation substrates and increased acetate concentrations for the growth of various major butyrate producers exhibiting the enzyme butyryl-coenzyme A (CoA):acetate CoA-transferase. H2-scavenging sulfite reducers and acetogens concurrently increased. Individual responses of gut microbiota were noted, where seven of the 12 participants displayed all features of the outlined pattern, whereas four individuals showed mixed behavior and one subject was unresponsive. Intervention order did not affect the outcome, emphasizing a constant substrate supply for maintaining specific functional communities.IMPORTANCE Manipulation of gut microbiota is increasingly recognized as a promising approach to reduce various noncommunicable diseases, such as obesity and type 2 diabetes. Specific dietary supplements, including resistant starches (RS), are often a focus, yet comprehensive insights into functional responses of microbiota are largely lacking. Furthermore, unresponsiveness in certain individuals is poorly understood. Our data indicate that distinct parts of microbiota work jointly to degrade RS and successively form health-promoting fermentation end products. It highlights the need to consider both primary degraders and specific more-downstream-acting bacterial groups in order to achieve desired intervention outcomes. The gained insights will assist the design of personalized treatment strategies based on an individual's microbiota.}, }
@article {pmid30266244, year = {2018}, author = {Miller, ET and Svanbäck, R and Bohannan, BJM}, title = {Microbiomes as Metacommunities: Understanding Host-Associated Microbes through Metacommunity Ecology.}, journal = {Trends in ecology &amp; evolution}, volume = {33}, number = {12}, pages = {926-935}, doi = {10.1016/j.tree.2018.09.002}, pmid = {30266244}, issn = {1872-8383}, support = {P01 GM125576/GM/NIGMS NIH HHS/United States ; P50 GM098911/GM/NIGMS NIH HHS/United States ; R01 CA176579/CA/NCI NIH HHS/United States ; }, mesh = {*Biological Evolution ; Ecology ; *Microbiota ; Models, Biological ; }, abstract = {Interest in host-associated microbiomes has skyrocketed recently, yet our ability to explain microbiome variation has remained stubbornly low. Considering scales of interaction beyond the level of the individual host could lead to new insights. Metacommunity theory has many of the tools necessary for modeling multiscale processes and has been successfully applied to host microbiomes. However, the biotic nature of the host requires an expansion of theory to incorporate feedback between the habitat patch (host) and their local (microbial) community. This feedback can have unexpected effects, is predicted to be common, and can arise through a variety of mechanisms, including developmental, ecological, and evolutionary processes. We propose a new way forward for both metacommunity theory and host microbiome research that incorporates this feedback.}, }
@article {pmid30265892, year = {2018}, author = {Fiorentino, A and Cucciniello, R and Di Cesare, A and Fontaneto, D and Prete, P and Rizzo, L and Corno, G and Proto, A}, title = {Disinfection of urban wastewater by a new photo-Fenton like process using Cu-iminodisuccinic acid complex as catalyst at neutral pH.}, journal = {Water research}, volume = {146}, number = {}, pages = {206-215}, doi = {10.1016/j.watres.2018.08.024}, pmid = {30265892}, issn = {1879-2448}, mesh = {Amino Acids ; Disinfection ; Escherichia coli ; Hydrogen Peroxide ; Hydrogen-Ion Concentration ; Iron ; Oxidation-Reduction ; Succinates ; Ultraviolet Rays ; *Wastewater ; *Water Purification ; }, abstract = {Photo-Fenton process is among the most effective advanced oxidation processes (AOPs) in urban wastewater treatment and disinfection, but its application as tertiary treatment at full scale has not been a feasible/attractive option so far because optimum conditions are typically achieved under acidic pH. In this work a new photo Fenton like process (UV-C/H2O2/IDS-Cu) using iminodisuccinic acid (IDS)-Cu complex as catalyst, was compared to other processes (UV-C/H2O2/Cu, UV-C/H2O2/Fe, H2O2 and UV-C) in urban wastewater disinfection. Since this is the first time that IDS-Cu complex was isolated and used as catalyst, preliminary tests to evaluate the mineralization of a model compound (phenol, 25 mg L[-1] initial concentration) in water by UV-C/H2O2/IDS-Cu were carried out. Almost complete mineralization of phenol (95%) was observed after 60 min treatment, being the process more effective than all other investigated AOPs (Fenton and photo-Fenton processes). This process was also proven to be more effective in the inactivation of E. coli (complete inactivation (3.5 log units) in 10 min) at natural pH (7.8 ± 0.5) in real wastewater, than the other processes investigated. Unlike of what observed for E. coli inactivation, the investigated processes only partially inactivated total bacterial population (from 18% for UV-C to 43% for UV-C/H2O2/Cu), according to flow cytometry measurements. In particular, Cu based photo-Fenton processes resulted in the higher percentage of inactivated total cells, thus being consistent with the results of E. coli inactivation. It is worthy to note that, as H2O2 was decreased, UV-C/H2O2/Cu-IDS was more effective than UV-C/H2O2/Cu process. Moreover, the formation of small and large clusters decreased in the presence of Cu and Cu-IDS complex, and process efficiency improved accordingly; these results show that Cu based AOPs can more effectively disaggregate clusters, thus making disinfection process more effective than Fe based AOPs.}, }
@article {pmid30262203, year = {2019}, author = {Tomuschat, C and Virbel, CR and O'Donnell, AM and Puri, P}, title = {Reduced expression of the NLRP6 inflammasome in the colon of patients with Hirschsprung's disease.}, journal = {Journal of pediatric surgery}, volume = {54}, number = {8}, pages = {1573-1577}, doi = {10.1016/j.jpedsurg.2018.08.059}, pmid = {30262203}, issn = {1531-5037}, mesh = {*Colon/chemistry/metabolism/pathology ; Enterocolitis ; *Hirschsprung Disease/metabolism/pathology ; Humans ; Inflammasomes/*metabolism ; Intracellular Signaling Peptides and Proteins/*metabolism ; }, abstract = {PURPOSE: Hirschsprung's associated enterocolitis (HAEC) is the most common cause of morbidity and mortality in Hirschsprung's Disease (HSCR). The pathogenesis of HAEC remains unsatisfactorily understood. Mounting evidence of an altered microbiome in patients with HSCR adds a new angle to the pathogenesis of HAEC. NLRP6 is a member of the nucleotide-binding domain, leucine-rich-repeat-containing (NLR) innate immune receptor family, a multiprotein complex that functions as a sensor of damage-associated molecular patterns. Known as inflammasomes they have been implicated in the regulation of colonic microbial ecology and by alteration, regulators of inflammation. We designed this study to test the hypothesis that NLRP6 expression is altered in the colon of patients with HSCR.<br><br>METHODS: We investigated NLPR6 protein expression in both the aganglionic and ganglionic regions of HSCR patients (n&#x202f;=&#x202f;10) versus healthy control colon (n&#x202f;=&#x202f;10). Protein distribution was assessed by using immunofluorescence and confocal microscopy. Gene and protein expressions were quantified using quantitative real-time polymerase chain reaction (qPCR), Western blot analysis, and densitometry.<br><br>MAIN RESULTS: qPCR and Western blot analysis revealed that NLRP6 is expressed in the colon of patients with HSCR. NLRP6 expression was significantly decreased (p&#x202f;<&#x202f;0.003) in the ganglionic and aganglionic bowel in HSCR compared to controls. Confocal microscopy revealed that NLRP6 expression in colonic epithelium was markedly decreased in HSCR specimens compared to controls.<br><br>CONCLUSION: We demonstrate for the first time the expression and distribution of NLRP6 in patients with HSCR. The observed decreased expression of NLRP6 may contribute to an altered colonic microbiome in patients with HSCR and increases the susceptibility to develop HAEC.}, }
@article {pmid30261358, year = {2018}, author = {Friedman, L and Mamane, H and Avisar, D and Chandran, K}, title = {The role of influent organic carbon-to-nitrogen (COD/N) ratio in removal rates and shaping microbial ecology in soil aquifer treatment (SAT).}, journal = {Water research}, volume = {146}, number = {}, pages = {197-205}, doi = {10.1016/j.watres.2018.09.014}, pmid = {30261358}, issn = {1879-2448}, mesh = {Ammonia ; Biological Oxygen Demand Analysis ; Bioreactors ; Carbon ; Denitrification ; *Groundwater ; Nitrification ; *Nitrogen ; Soil ; }, abstract = {Soil columns simulating soil aquifer treatment (SAT), fed with synthetic secondary effluent by intermittent infiltration of flooding/drying cycles, were characterized for nitrogen and organic carbon removal, and microbial ecology and biokinetics. The columns differed in the concentration ratio of chemical oxygen demand (COD) to the summed NH4[+], NO2[-] and organic nitrogen-2 (C/N2) or 5 (C/N5). Chemical profiles along the column demonstrated a preference for COD oxidation over nitrification and coupled denitrification, with higher nitrogen loss (57% vs. 16%) in the C/N5 column. Unexpectedly, significant dominance of the genus Nitrospira over the genus Nitrobacter and ammonia-oxidizing bacteria (AOB) was strongly correlated at column depths where NH4[+] removal occurred. Moreover, the Nitrospira profile had the strongest correlation to the profile of NH4[+] (positive) and NO3[-] (negative), strongly indicating complete ammonia oxidation. 16S sequencing analysis of the topsoil in C/N2 vs. C/N5 columns revealed double the abundance of microbial aerobic potential (64% vs. 32%) vs. one-third the denitrification potential (13% vs. 31%). The concentrations and degradability levels of organic carbon were the most influential parameters shaping community structure. Niche differentiation within the biofilm attached to the soil is suggested to have an important role in the process's anoxic activity and nitrogen removal.}, }
@article {pmid30259511, year = {2018}, author = {Pimentel, SP and Fontes, M and Ribeiro, FV and Corrêa, MG and Nishii, D and Cirano, FR and Casati, MZ and Casarin, RCV}, title = {Smoking habit modulates peri-implant microbiome: A case-control study.}, journal = {Journal of periodontal research}, volume = {53}, number = {6}, pages = {983-991}, doi = {10.1111/jre.12597}, pmid = {30259511}, issn = {1600-0765}, mesh = {Actinomyces/genetics/isolation &amp; purification ; Adult ; *Biofilms ; Capnocytophaga/genetics/isolation &amp; purification ; Case-Control Studies ; DNA, Bacterial/genetics/isolation &amp; purification ; Dental Implants/*microbiology ; Fusobacterium/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Microbiota/genetics ; Middle Aged ; Peri-Implantitis/*etiology/*microbiology ; Periodontitis/microbiology ; RNA, Ribosomal, 16S/genetics ; Smoking/*adverse effects ; Tannerella forsythia/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND AND OBJECTIVE: Smoking is a recognized risk factor for peri-implant disease and leads to microbiological changes in mucositis and peri-implantitis. However, there is no knowledge about the impact of smoking in healthy peri-implant tissue. The aim of the study was to evaluate the microbiome in a peri-implant environment in smokers with healthy peri-implant conditions.<br><br>METHODS: Peri-implant biofilm was collected around single clinically healthy, screwed-retained, teeth-surrounded implants in 12 non-smoker (NSMK) and 12 smoker (SMK) non-periodontitis subjects (no bleeding and probing depth <4&#xa0;mm). Bacterial DNA was isolated and 16S ribosomal RNA gene libraries were sequenced using pyrosequencing, targeting the V3-V4 region. Datasets were processed using the Quantitative Insights into Microbial Ecology, Greengenes and the Human Oral Microbiome Database databases.<br><br>RESULTS: An evident difference in the SMK peri-implant microbiome was observed compared to the NSMK microbiome, with a large abundance of species, even with a healthy peri-implant. The SMK core-microbiome showed an abundance of Fusobacterium, Tannerella and Mogibacterium, while the NSMK core revealed an abundance of Actinomyces, Capnocytophaga and Streptococcus, genera that are usually related to periodontal health. The microbiome inter-relationship was shown to be more inter-generic in SMK then in NSMK, indicating different microbiome cohesion.<br><br>CONCLUSION: Smoking negatively affected the peri-implant microbiome, leading to a disease-associated state, even in clinically healthy individuals.}, }
@article {pmid30259168, year = {2019}, author = {Cardinale, M and Suarez, C and Steffens, D and Ratering, S and Schnell, S}, title = {Effect of Different Soil Phosphate Sources on the Active Bacterial Microbiota Is Greater in the Rhizosphere than in the Endorhiza of Barley (Hordeum vulgare L.).}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {689-700}, pmid = {30259168}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Hordeum/*microbiology ; *Microbiota ; Phosphates/*analysis/metabolism ; Phylogeny ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; Tunisia ; }, abstract = {Phosphate is a macronutrient and often the limiting growing factor of many ecosystems. The aim of this work was to assess the effect of various phosphate sources on the active bacterial microbiota of barley rhizosphere and endorhiza. Barley was grown on poor soil supplemented with either Ca(H2PO4)2 (CaP), Gafsa rock phosphate (Gafsa), sodium hexaphytate (NaHex), or not amended (P0). RNA was extracted and cDNA synthesized via reverse transcription from both rhizosphere and endorhiza of barley roots; the obtained 16S rRNA cDNA was sequenced by Ion Torrent and analyzed with QIIME and co-occurrence network analysis. Phosphatase activity was measured in the rhizosphere. The phosphate source significantly affected alpha- and beta-diversities of the active microbiota, especially in the rhizosphere. CaP enriched the relative abundance of a broad range of taxa, while NaHex and Gafsa specifically enriched one dominant Massilia-related OTU. Co-occurrence network analysis showed that the most abundant OTUs were affected by phosphate source and, at the same time, were low connected to other OTUs (thus they were relatively "independent" from other bacteria); this indicates a successful adaptation to the specific abiotic conditions. In the rhizosphere, the phosphatase activities were correlated to several OTUs. Moreover, the phosphodiesterase/alk. phosphomonoesterase ratio was highly correlated to the dominance index of the microbiota and to the relative abundance of the dominant Massilia OTU. This study shows the differential response of the rhizosphere- and endorhiza bacterial microbiota of barley to various phosphate sources in soil, thus providing insights onto this largely unknown aspect of the soil microbiome ecology and plant-microbe interactions.}, }
@article {pmid30258074, year = {2018}, author = {Cheung, MK and Wong, CK and Chu, KH and Kwan, HS}, title = {Community Structure, Dynamics and Interactions of Bacteria, Archaea and Fungi in Subtropical Coastal Wetland Sediments.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14397}, pmid = {30258074}, issn = {2045-2322}, mesh = {Archaea/*growth &amp; development ; Ascomycota/*growth &amp; development ; Bacteria/*growth &amp; development ; Microbial Consortia/*physiology ; *Models, Biological ; *Tropical Climate ; *Wetlands ; }, abstract = {Bacteria, archaea and fungi play crucial roles in wetland biogeochemical processes. However, little is known about their community structure, dynamics and interactions in subtropical coastal wetlands. Here, we examined communities of the three kingdoms in mangrove and mudflat sediments of a subtropical coastal wetland using Ion Torrent amplicon sequencing and co-occurrence network analysis. Bacterial, archaeal and fungal communities comprised mainly of members from the phyla Proteobacteria and Bacteroidetes, Bathyarchaeota and Euryarchaeota, and Ascomycota, respectively. Species richness and Shannon diversity were highest in bacteria, followed by archaea and were lowest in fungi. Distinct spatiotemporal patterns were observed, with bacterial and fungal communities varying, to different extent, between wet and dry seasons and between mangrove and mudflat, and archaeal community remaining relatively stable between seasons and regions. Redundancy analysis revealed temperature as the major driver of the seasonal patterns of bacterial and fungal communities but also highlighted the importance of interkingdom biotic factors in shaping the community structure of all three kingdoms. Potential ecological interactions and putative keystone taxa were identified based on co-occurrence network analysis. These findings facilitate current understanding of the microbial ecology of subtropical coastal wetlands and provide a basis for better modelling of ecological processes in this important ecosystem.}, }
@article {pmid30255115, year = {2018}, author = {Anza, M and Salazar, O and Epelde, L and Garbisu, C}, title = {Data on the selection of biostimulating agents for the bioremediation of soil simultaneously contaminated with lindane and zinc.}, journal = {Data in brief}, volume = {20}, number = {}, pages = {1371-1377}, pmid = {30255115}, issn = {2352-3409}, abstract = {The bioremediation of contaminated soil often involves the addition of organic/inorganic amendments and mobilizing agents (e.g. surfactants, detergents), in order to stimulate the growth and degrading activity of soil microbial populations and increase contaminant bioavailability. For this data article we carried out an experiment to select biostimulating agents for the bioremediation of soil simultaneously contaminated with lindane (HCH, 10 mg kg[-][1] DW soil) and Zinc (Zn, 1500 mg kg[-1] DW soil). To this purpose, a factorial design was used to test the effect of three organic amendments (i.e. hen manure, composted horse manure, cow slurry) and three mobilizing agents (i.e. sodium dodecylbenzenesulfonate (SDS), rhamnolipids and Tween-80) on the reduction of total HCH and bioavailable Zn concentration in soil. Similarly, the effect of the addition of cyclohexane, as chemical inducer of HCH degradation, was also studied. The addition of SDS, rhamnolipids and Tween-80 significantly reduced HCH concentration in soil, regardless of the presence of other biostimulating agents. When added individually, the three organic amendments (hen manure, composted horse manure, cow slurry) significantly reduced bioavailable Zn concentration in soil. These data provide useful information for the bioremediation, through biostimulation, of soils simultaneously contaminated with HCH and Zn.}, }
@article {pmid30254509, year = {2018}, author = {Krzmarzick, MJ and Taylor, DK and Fu, X and McCutchan, AL}, title = {Diversity and Niche of Archaea in Bioremediation.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2018}, number = {}, pages = {3194108}, pmid = {30254509}, issn = {1472-3654}, mesh = {Archaea/*growth &amp; development/*metabolism ; *Biodegradation, Environmental ; Environmental Pollutants/*metabolism ; Hydrocarbons/metabolism ; }, abstract = {Bioremediation is the use of microorganisms for the degradation or removal of contaminants. Most bioremediation research has focused on processes performed by the domain Bacteria; however, Archaea are known to play important roles in many situations. In extreme conditions, such as halophilic or acidophilic environments, Archaea are well suited for bioremediation. In other conditions, Archaea collaboratively work alongside Bacteria during biodegradation. In this review, the various roles that Archaea have in bioremediation is covered, including halophilic hydrocarbon degradation, acidophilic hydrocarbon degradation, hydrocarbon degradation in nonextreme environments such as soils and oceans, metal remediation, acid mine drainage, and dehalogenation. Research needs are addressed in these areas. Beyond bioremediation, these processes are important for wastewater treatment (particularly industrial wastewater treatment) and help in the understanding of the natural microbial ecology of several Archaea genera.}, }
@article {pmid30252869, year = {2018}, author = {Chen, X and Liu, X and Du, Y and Wang, B and Zhao, N and Geng, Z}, title = {Green forage and fattening duration differentially modulate cecal microbiome of Wanxi white geese.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0204210}, pmid = {30252869}, issn = {1932-6203}, mesh = {Adipose Tissue/*growth &amp; development ; Animal Feed ; Animals ; Cecum/*microbiology ; Fatty Acids/metabolism ; Female ; Geese ; Mammary Glands, Animal/metabolism ; *Microbiota/genetics ; Muscles/metabolism ; }, abstract = {Gut microbial ecology is responsible for fatty acid metabolism in ruminants. The cecal microbiota composition of geese and their adaptation to fiber inclusion and feeding timeswere investigated in this study. A total of 116 Wanxi white geese were randomly selected at 70 days old. Eight geese were subjected to cecal sampling at 70 d of age, and the remaining 108 geese were divided into four groups with three replicates each (9 geese in each replicate). The geese in the four groups were fed 0, 15, 30, and 45% green forage (relative to dry matter), respectively. Three birds from each replicate were selected for cecal sampling at 80, 90, and 100 days old. All samples were subjected to 16S rRNA gene sequencing using the Illumina Ion Personal Genome Machine platform. Bacterial abundance was analyzed using two-way ANOVA analysis, and the relationship between the relative abundance of bacteria (phylum level) and fatty acids was analyzed using acanonical correspondence analysis. Cecal microbiota in geese were mainly composed of Bacteroidetes (68.46%), Firmicutes (20.04%), and Proteobacteria (7.89%). Dietary treatments had no significant effect on the α-diversity indices of the cecal bacterial community (P > 0.05), but a numerical increase occurred with increased fattening duration and green forage inclusion. The Selenomonadales order (P = 0.024), Negativicutes class (P = 0.026), and Megamonas (P = 0.012) and Oscillospira (P = 0.042) genera were affected by green forageinclusion level, and microflora abundance was mainly influenced by the fattening duration. Bacteria phyla were mostly set along the line of linolenic acid and oleic acid. Finally, Bacteroidales might be an intestinal promoter that improves unsaturated fatty acid synthesis in geese.}, }
@article {pmid30251120, year = {2019}, author = {Oh, S and Choi, D}, title = {Microbial Community Enhances Biodegradation of Bisphenol A Through Selection of Sphingomonadaceae.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {631-639}, pmid = {30251120}, issn = {1432-184X}, support = {NRF-2017R1C1B5076367//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIP; Ministry of Science, ICT &amp; Future Planning)/ ; }, mesh = {Benzhydryl Compounds/*metabolism ; Biodegradation, Environmental ; Bioreactors/microbiology ; Microbiota ; Phenols/*metabolism ; Sphingomonadaceae/genetics/isolation &amp; purification/*metabolism ; }, abstract = {Bisphenol A (BPA) is a common ingredient in plastic wares and epoxy resins that are essential for our daily life. Despite the obvious benefits, BPA may act as an environmental endocrine disruptor, causing metabolic, reproductive, and/or developmental consequences and diseases in humans and other organisms. Although previous studies have yielded progress toward the microbial breakdown of BPA, the work has primarily been focused on pure cultures rather than complex microbial communities. In this study, we examined microbial communities in bioreactors that control the fate of BPA at various levels (up to 5000 μg L[-1]). Microbial communities rapidly increased removal rates of 500-5000 μg L[-1] BPA from 23-29 to 89-99% during the first 2 weeks of the acclimation period, after which > 90% stable removal rates were maintained over 3 months. Biochemical assays demonstrated that BPA was removed by biodegradation, rather than other abiotic removal routes (e.g., adsorption and volatilization). The 16S rRNA gene-based community analysis revealed that 50-5000 μg L[-1] of BPA exposure systematically selected for three Sphingomonadaceae species (Sphingobium, Novosphingobium, and Sphingopyxis). The Sphingomonadaceae-enriched communities acclimated to BPA showed a 7.0-L gVSS[-1] day[-1] BPA degradation rate constant, which is comparable to that (4.1-6.3) of Sphingomonadaceae isolates and is higher than other potential BPA degraders. Taken together, our results advanced the understanding of how microbial communities acclimate to environmentally relevant levels of BPA, gradually enhancing BPA degradation via selective enrichment of a few Sphingomonadaceae populations with higher BPA metabolic activity.}, }
@article {pmid30251018, year = {2019}, author = {Sanchis-Chordà, J and Del Pulgar, EMG and Carrasco-Luna, J and Benítez-Páez, A and Sanz, Y and Codoñer-Franch, P}, title = {Bifidobacterium pseudocatenulatum CECT 7765 supplementation improves inflammatory status in insulin-resistant obese children.}, journal = {European journal of nutrition}, volume = {58}, number = {7}, pages = {2789-2800}, pmid = {30251018}, issn = {1436-6215}, support = {AGL2014-52101-P//Spanish Ministry of Economy and Competitiveness/ ; FPU13/03753//Spanish Training University Lecturers Programme/ ; No. 613979//EU Project MyNewGut/ ; }, mesh = {Adolescent ; *Bifidobacterium pseudocatenulatum ; Child ; Dietary Supplements ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Inflammation/*drug therapy/physiopathology ; *Insulin Resistance ; Male ; Obesity/*physiopathology ; Probiotics/administration &amp; dosage/*pharmacology ; Prospective Studies ; }, abstract = {PURPOSE: The relationships between gut microbiota and obesity-related co-morbidities have been increasingly recognized. Low-grade inflammation may be the main factor in the pathogenesis of such disorders. We investigated the effect of the potential probiotic Bifidobacterium pseudocatenulatum CECT 7765 on cardiometabolic risk factors, inflammatory cytokines and gut microbiota composition in obese children with insulin resistance.<br><br>METHODS: The study included 48 obese children (10-15&#xa0;years old) with insulin resistance. They received dietary advice and were assigned to take the capsules with or without probiotic (10[9-10]&#xa0;CFU) daily for 13&#xa0;weeks. Clinical, biochemical and gut microbiome measurements were made at baseline and at the end of the intervention.<br><br>RESULTS: There was a significant improvement in body mass index in all children after the intervention, suggesting that weight changes are related to the dietary advice. A significant decrease in circulating high-sensitive C-reactive protein (P&#x2009;=&#x2009;0.026) and monocyte chemoattractant protein-1 (P&#x2009;=&#x2009;0.032) and an increase in high-density lipoprotein cholesterol (P&#x2009;=&#x2009;0.035) and omentin-1 (P&#x2009;=&#x2009;0.023) in children receiving probiotic supplementation were observed compared to the control group. Regarding gut microbiota, probiotic administration significantly increased the proportion of the Rikenellaceae family members, particularly of the Alistipes genus.<br><br>CONCLUSIONS: The beneficial effects of the intervention on inflammatory markers and lipid profile suggest that B. pseudocatenulatum CECT 7765 intake together with dietary recommendations can improve inflammatory status in children with obesity and insulin resistance. These effects are parallel to increases in bacterial groups associated with a lean phenotype. The modulation of gut microbiota with probiotic supplementation can be considered an effective tool to ameliorate some obesity-related disorders in children.}, }
@article {pmid30250249, year = {2018}, author = {Takano, Y and Chikaraishi, Y and Imachi, H and Miyairi, Y and Ogawa, NO and Kaneko, M and Yokoyama, Y and Krüger, M and Ohkouchi, N}, title = {Insight into anaerobic methanotrophy from [13]C/[12]C- amino acids and [14]C/[12]C-ANME cells in seafloor microbial ecology.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14070}, pmid = {30250249}, issn = {2045-2322}, mesh = {Amino Acids/*metabolism ; Anaerobiosis ; Archaea/*metabolism ; Biomass ; Black Sea ; Carbon/metabolism ; *Carbon Cycle ; Carbon Isotopes/metabolism ; Carbon Radioisotopes/metabolism ; Geologic Sediments/*microbiology ; Lipids/biosynthesis ; Methane/metabolism ; Nitrogen Isotopes/metabolism ; Oxidation-Reduction ; Seawater/microbiology ; Terpenes/metabolism ; }, abstract = {Oceanic methane from global deep-sea sediment is largely consumed through microbially mediated sulfate-coupled oxidation, resulting in [13]C-depleted cell biomass of anaerobic methanotrophic archaea (ANME). The general ecological importance of subseafloor ANME has been well recognized in the last two decades. However, the crucial biochemical pathways for the overall anaerobic oxidation of methane (AOM) still remain enigmatic. Here, methanotrophic pathways were analyzed to trace [13]C-depleted amino acid biosynthesis in two clades of ANME (ANME-1 and ANME-2) from the Black Sea. Compound-specific analysis of ANME-dominated microbial mats showed a significant [13]C-depletion trend in association with increasing carbon numbers in protein-derived amino acid families (e.g., the pyruvate family in the order of alanine, valine, isoleucine and leucine was down to -114‰). This result indicates a stepwise elongation of [13]C-depleted carbon during amino acid biosynthesis. The overall results suggest that intracellular protein amino acids and the most [13]C-depleted signature of leucine, which has a specific branched-chain structure, are potentially propagated as isoprenoid precursor molecules into archaeal biosynthesis, resulting in the extremely [13]C- and [14]C-depleted nature of ANME cells in the deep microbial oasis.}, }
@article {pmid30250138, year = {2018}, author = {Ventorino, V and Pascale, A and Adamo, P and Rocco, C and Fiorentino, N and Mori, M and Faraco, V and Pepe, O and Fagnano, M}, title = {Comparative assessment of autochthonous bacterial and fungal communities and microbial biomarkers of polluted agricultural soils of the Terra dei Fuochi.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14281}, pmid = {30250138}, issn = {2045-2322}, support = {LIFE11/ENV/IT/275//European Commission (EC)/International ; LIFE11/ENV/IT/275//European Commission (EC)/International ; LIFE11/ENV/IT/275//European Commission (EC)/International ; LIFE11/ENV/IT/275//European Commission (EC)/International ; LIFE11/ENV/IT/275//European Commission (EC)/International ; LIFE11/ENV/IT/275//European Commission (EC)/International ; LIFE11/ENV/IT/275//European Commission (EC)/International ; LIFE11/ENV/IT/275//European Commission (EC)/International ; LIFE11/ENV/IT/275//European Commission (EC)/International ; }, mesh = {*Agriculture ; Bacteria/classification/*growth &amp; development ; Biodiversity ; Biomarkers/*metabolism ; Fungi/classification/*growth &amp; development ; Inorganic Chemicals/analysis ; Italy ; *Microbiota ; Organic Chemicals/analysis ; Phylogeny ; Principal Component Analysis ; Soil Pollutants/*analysis ; }, abstract = {Organic and inorganic xenobiotic compounds can affect the potential ecological function of the soil, altering its biodiversity. Therefore, the response of microbial communities to environmental pollution is a critical issue in soil ecology. Here, a high-throughput sequencing approach was used to investigate the indigenous bacterial and fungal community structure as well as the impact of pollutants on their diversity and richness in contaminated and noncontaminated soils of a National Interest Priority Site of Campania Region (Italy) called "Terra dei Fuochi". The microbial populations shifted in the polluted soils via their mechanism of adaptation to contamination, establishing a new balance among prokaryotic and eukaryotic populations. Statistical analyses showed that the indigenous microbial communities were most strongly affected by contamination rather than by site of origin. Overabundant taxa and Actinobacteria were identified as sensitive biomarkers for assessing soil pollution and could provide general information on the health of the environment. This study has important implications for microbial ecology in contaminated environments, increasing our knowledge of the capacity of natural ecosystems to develop microbiota adapted to polluted soil in sites with high agricultural potential and providing a possible approach for modeling pollution indicators for bioremediation purposes.}, }
@article {pmid30249184, year = {2018}, author = {Byloos, B and Monsieurs, P and Mysara, M and Leys, N and Boon, N and Van Houdt, R}, title = {Characterization of the bacterial communities on recent Icelandic volcanic deposits of different ages.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {122}, pmid = {30249184}, issn = {1471-2180}, mesh = {Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Biodiversity ; Carbon/analysis/metabolism ; DNA, Bacterial/genetics ; Iceland ; Nitrogen/analysis/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Volcanic Eruptions/analysis ; }, abstract = {BACKGROUND: Basalt is the most common igneous rock on the Earth's surface covering. Basalt-associated microorganisms drive the cycling and sequestration of different elements such as nitrogen, carbon and other nutrients, which facilitate subsequent pioneer and plant development, impacting long-term regulation of the Earth's temperature and biosphere. The initial processes of colonization and subsequent rock weathering by microbial communities are still poorly understood and relatively few data are available on the diversity and richness of the communities inhabiting successive and chronological lava flows. In this study, the bacterial communities present on lava deposits from different eruptions of the 1975-84 Krafla Fires (32-, 35- and 39-year old, respectively) at the Krafla, Iceland, were determined.<br><br>RESULTS: Three sites were sampled for each deposit (32-, 35- and 39-year old), two proximal sites (at 10&#xa0;m distance) and one more distant site (at 100&#xa0;m from the two other sites). The determined chemical composition and metal concentrations were similar for the three basalt deposits. No significant differences were observed in the total number of cells in each flow. 16S rRNA gene amplicon sequencing showed that the most abundant classified phylum across the 3 flows was Proteobacteria, although predominance of Acidobacteria, Actinobacteria and Firmicutes was observed for some sampling sites. In addition, a considerable fraction of the operational taxonomic units remained unclassified. Alpha diversity (Shannon, inverse Simpson and Chao), HOMOVA and AMOVA only showed a significant difference for Shannon between the 32- and 39-year old flow (p&#xa0;<&#x2009;0.05). Nonmetric multidimensional scaling (NMDS) analysis showed that age significantly (p&#xa0;=&#x2009;0.026) influenced the leftward movement along NMDS axis 1.<br><br>CONCLUSIONS: Although NMDS indicated that the (relatively small) age difference of the deposits appeared to impact the bacterial community, this analysis was not consistent with AMOVA and HOMOVA, indicating no significant difference in community structure. The combined results drive us to conclude that the (relatively small) age differences of the deposits do not appear to be the main factor shaping the microbial communities. Probably other factors such as spatial heterogeneity, associated carbon content, exogenous rain precipitations and wind also affect the diversity and dynamics.}, }
@article {pmid30249049, year = {2018}, author = {Sivakumar, G and Uccella, NA and Gentile, L}, title = {Probing Downstream Olive Biophenol Secoiridoids.}, journal = {International journal of molecular sciences}, volume = {19}, number = {10}, pages = {}, pmid = {30249049}, issn = {1422-0067}, mesh = {Food Handling/*methods ; Glucosides/*metabolism ; Humans ; Iridoids/*chemistry/*metabolism ; Olea/*chemistry ; }, abstract = {Numerous bioactive biophenol secoiridoids (BPsecos) are found in the fruit, leaves, and oil of olives. These BPsecos play important roles in both the taste of food and human health. The main BPseco bioactive from green olive fruits, leaves, and table olives is oleuropein, while olive oil is rich in oleuropein downstream pathway molecules. The aim of this study was to probe olive BPseco downstream molecular pathways that are alike in biological and olive processing systems at different pHs and reaction times. The downstream molecular pathway were analyzed by high performance liquid chromatography coupled with electrospray ionization mass spectrometry (HPLC-ESI/MS) and typed neglected of different overlap (TNDO) computational methods. Our study showed oleuropein highest occupied molecular orbital (HOMO) and HOMO-1 triggered the free radical processes, while HOMO-2 and lowest unoccupied molecular orbital (LUMO) were polar reactions of glucoside and ester groups. Olive BPsecos were found to be stable under acid and base catalylic experiments. Oleuropein aglycone opened to diales and rearranged to hydroxytyrosil-elenolate under strong reaction conditions. The results suggest that competition among olive BPseco HOMOs could induce glucoside hydrolysis during olive milling due to native olive β-glucosidases. The underlined olive BPsecos downstream molecular mechanism herein could provide new insights into the olive milling process to improve BPseco bioactives in olive oil and table olives, which would enhance both the functional food and the nutraceuticals that are produced from olives.}, }
@article {pmid30248830, year = {2018}, author = {Qi, Y and Yang, X and Pelaez, AM and Huerta Lwanga, E and Beriot, N and Gertsen, H and Garbeva, P and Geissen, V}, title = {Macro- and micro- plastics in soil-plant system: Effects of plastic mulch film residues on wheat (Triticum aestivum) growth.}, journal = {The Science of the total environment}, volume = {645}, number = {}, pages = {1048-1056}, doi = {10.1016/j.scitotenv.2018.07.229}, pmid = {30248830}, issn = {1879-1026}, mesh = {Agriculture ; Animals ; *Environmental Monitoring ; Plastics/*analysis ; Poaceae ; Soil/*chemistry ; *Soil Pollutants ; Triticum/chemistry/*drug effects ; }, abstract = {Plastic residues have become a serious environmental problem in the regions with intensive use of plastic mulching. Even though plastic mulch is widely used, the effects of macro- and micro- plastic residues on the soil-plant system and the agroecosystem are largely unknown. In this study, low density polyethylene and one type of starch-based biodegradable plastic mulch film were selected and used as examples of macro- and micro- sized plastic residues. A pot experiment was performed in a climate chamber to determine what effect mixing 1% concentration of residues of these plastics with sandy soil would have on wheat growth in the presence and absence of earthworms. The results showed that macro- and micro- plastic residues affected both above-ground and below-ground parts of the wheat plant during both vegetative and reproductive growth. The type of plastic mulch films used had a strong effect on wheat growth with the biodegradable plastic mulch showing stronger negative effects as compared to polyethylene. The presence of earthworms had an overall positive effect on the wheat growth and chiefly alleviated the impairments made by plastic residues.}, }
@article {pmid30247566, year = {2018}, author = {Otte, JM and Blackwell, N and Soos, V and Rughöft, S and Maisch, M and Kappler, A and Kleindienst, S and Schmidt, C}, title = {Sterilization impacts on marine sediment---Are we able to inactivate microorganisms in environmental samples?.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {12}, pages = {}, doi = {10.1093/femsec/fiy189}, pmid = {30247566}, issn = {1574-6941}, mesh = {Bacteria/*drug effects/growth &amp; development/*radiation effects ; Biota/physiology ; Gamma Rays ; Geologic Sediments/*microbiology ; Hot Temperature ; Sodium Azide ; Sterilization/*methods ; }, abstract = {To distinguish between biotic and abiotic processes in laboratory experiments with environmental samples, an effective sterilization method is required that prevents biological activity but does not change physico-geochemical properties of samples. We compared standard sterilization methods with respect to their impact on microbial abundance and activity. We exposed marine sediment to (i) autoclaving, (ii) gamma-radiation or (iii) sodium azide (NaN3) and determined how nucleic acids, microbial productivity, colony forming units (CFUs) and community composition of microorganisms, fungi, unicellular protists and protozoa were affected. In autoclaved and gamma-sterilized sediments, only few colonies formed within 16 days. After addition of NaN3 to the sediment, numerous CFUs (>50) but lower 3H-leucine incorporation rates, i.e. lower protein biosynthesis rates, were found compared to the other two sterilization techniques. Extractable RNA was detected immediately after all sterilization treatments (0.2-17.9 ng/g dry sediment) but decreased substantially by 84%-98% after 16 days of incubation. The total organic carbon content increased from 18 mg L-1 to 220 mg L-1 (autoclaving) and 150 mg L-1 (gamma-radiation) after sterilization. We compare advantages and disadvantages for each tested sterilization method and provide a helpful decision-making resource for choosing the appropriate sterilization technique for environmental studies, particularly for marine sediments.}, }
@article {pmid30247563, year = {2018}, author = {Cieplak, T and Wiese, M and Nielsen, S and Van de Wiele, T and van den Berg, F and Nielsen, DS}, title = {The Smallest Intestine (TSI)-a low volume in vitro model of the small intestine with increased throughput.}, journal = {FEMS microbiology letters}, volume = {365}, number = {21}, pages = {}, doi = {10.1093/femsle/fny231}, pmid = {30247563}, issn = {1574-6968}, mesh = {*Bioreactors ; Duodenum/microbiology/physiology ; Gastrointestinal Tract/microbiology/*physiology ; High-Throughput Screening Assays ; Humans ; Hydrogen-Ion Concentration ; Intestine, Small/microbiology/*physiology ; Lactobacillus/*metabolism ; Microbial Viability ; Models, Biological ; *Probiotics ; }, abstract = {There is a growing interest in understanding the fate and behaviour of probiotic microorganisms and bioactive compounds during passage of the human gastrointestinal tract (GIT). Here, we report the development of a small volume in vitro model called The smallest Intestine (TSI) with increased throughput focusing on simulating passage through the stomach and small intestine (SI). The basic TSI module consists of five reactors, with a working volume of 12 ml each. During the simulated passage through the SI, bile is absorbed and pH is adjusted to physiologically relevant values for duodenum, jejunum and ileum. A consortium of seven representative bacterial members of the ileum microbiota is included in the ileal stage of the model. The behaviour of three putative probiotic Lactobacillus strains during in vitro simulated upper GIT passage was tested in the model and results were compared to previous studies describing probiotic survival. It was found, that probiotic persistence is strongly related to whether food was ingested, but also to presence of the ileal microbiota, which significantly impacted probiotic survival. In conclusion, TSI allows testing a substantial number of samples, at low cost and short time, and is thus suitable as an in vitro screening platform.}, }
@article {pmid30245683, year = {2018}, author = {Hernandez-Agreda, A and Leggat, W and Ainsworth, TD}, title = {A Comparative Analysis of Microbial DNA Preparation Methods for Use With Massive and Branching Coral Growth Forms.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2146}, pmid = {30245683}, issn = {1664-302X}, abstract = {In the last two decades, over 100 studies have investigated the structure of the coral microbiome. However, as yet there are no standardized methods applied to sample preservation and preparation, with different studies using distinct methods. There have also been several comparisons made of microbiome data generated across different studies, which have not addressed the influence of the methodology employed over each of the microbiome datasets. Here, we assess three different preservation methods; salt saturated dimethyl sulfoxide (DMSO) - EDTA, snap freezing with liquid nitrogen and 4% paraformaldehyde solution, and two different preparation methodologies; bead beating and crushing, that have been applied to study the coral microbiome. We compare the resultant bacterial assemblage data for two coral growth forms, the massive coral Goniastrea edwardsi and the branching coral Isopora palifera. We show that microbiome datasets generated from differing preservation and processing protocols are comparable in composition (presence/absence). Significant discrepancies between preservation and homogenization methods are observed in structure (relative abundance), and in the occurrence and dominance of taxa, with rare (low abundance and low occurrence) phylotypes being the most variable fraction of the microbial community. Finally, we provide evidence to support chemical preservation with DMSO as effective as snap freezing samples for generating reliable and robust microbiome datasets. In conclusion, we recommend where possible a standardized preservation and extraction method be taken up by the field to provide the best possible practices for detailed assessments of symbiotic and conserved bacterial associations.}, }
@article {pmid30245425, year = {2019}, author = {Li, B and Cao, Y and Guan, X and Li, Y and Hao, Z and Hu, W and Chen, L}, title = {Microbial assessments of soil with a 40-year history of reclaimed wastewater irrigation.}, journal = {The Science of the total environment}, volume = {651}, number = {Pt 1}, pages = {696-705}, doi = {10.1016/j.scitotenv.2018.09.193}, pmid = {30245425}, issn = {1879-1026}, mesh = {*Agricultural Irrigation ; Bacteria/*classification/drug effects ; China ; Cucumis sativus/growth &amp; development ; Environmental Monitoring ; Solanum lycopersicum/growth &amp; development ; *Microbiota/drug effects ; RNA, Archaeal/analysis ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Seasons ; *Soil Microbiology ; Solanum melongena/growth &amp; development ; Wastewater/*analysis ; }, abstract = {The long-term effects on soil microorganisms from 40 years of irrigating soil with reclaimed wastewater was investigated by determining the quantity, composition, and inter-species connection of microorganisms. No significant difference in microbial quantity and composition were identified in the reclaimed wastewater- and groundwater-irrigated soils. The dominant bacterial phylum in both irrigation water sources and soils was Proteobacteria, which commonly exists in soil. From the analysis of four (4) alpha diversity metrics, including the observed number of operational taxonomic units (OTUs), Chao1, and the Shannon and Simpson diversity, there was no significant difference between the reclaimed wastewater- and groundwater-irrigated soils. Three zones (shallow, medium and deep) were identified in the reclaimed wastewater- and groundwater-irrigated soils based on the taxonomic networks and clusters generated by graphical lasso and random walk algorithm. The cluster profiles (shallow, medium and deep zones) appear to be different in the reclaimed wastewater- and groundwater-irrigated soils. Soil irrigated with reclaimed wastewater showed less depth of clustered profile in medium zone than that in soil irrigated with groundwater (20-60 cm of reclaimed wastewater-irrigated soil compared to 20-100 cm of groundwater-irrigated soil), although the significance of such a variance (the depth of medium zone of reclaimed wastewater-irrigated soil decreased 40 cm than that of groundwater-irrigated soil) is not clear at this time. Positive influence has been identified in the growth and yield of eggplant, tomato and cucumber between the reclaimed wastewater- and groundwater-irrigated soils, suggesting that reclaimed wastewater irrigation can potentially substitute groundwater irrigation, despite the variance in inter-species clustering profiles in soil microbes in certain soil zones. Nevertheless, the possible negative influence of pathogens, organic compounds and pharmaceuticals should be seriously considered during the reclaimed wastewater irrigation.}, }
@article {pmid30244277, year = {2019}, author = {Shteindel, N and Yankelev, D and Gerchman, Y}, title = {High-Throughput Quantitative Measurement of Bacterial Attachment Kinetics on Seconds Time Scale.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {726-735}, pmid = {30244277}, issn = {1432-184X}, mesh = {Bacteria/*chemistry ; *Bacterial Adhesion ; Bacterial Physiological Phenomena ; Biofilms ; High-Throughput Screening Assays/*methods ; Kinetics ; Staining and Labeling ; }, abstract = {Surface attachment is an important factor in the life of many microbial species. Late stages of attachment (i.e., mature biofilms) are rigorously studied, but data on the very early stages is scarce. The lack of robust research methods may go a long way in explaining this situation. We have developed a method that allows the rapid kinetic measurement of bacterial attachment, with seconds to minute's temporal resolution, in a high-throughput setting. The method requires the use of a commercially available microtiter plate reader capable of fluorescence measurement from the bottom, standard microtiter plates, fluorescently tagged bacteria, and a common dye. The high temporal resolution reveals nuanced, fast, and dynamic behaviors in the very early phases of attachment. To demonstrate potential applications, we tested the effect of various conditions on attachment kinetics-specie, substratum, salt concentration, and culture density. Results are in good agreement with crystal violet staining (correlation R[2] > 0.95 in all cases) and reproducing published data but show much greater detail and fidelity.}, }
@article {pmid30244124, year = {2018}, author = {Podduturi, R and Jørgensen, NOG}, title = {Conidia-based fluorescence quantification of Streptomyces.}, journal = {Journal of microbiological methods}, volume = {153}, number = {}, pages = {104-107}, doi = {10.1016/j.mimet.2018.09.010}, pmid = {30244124}, issn = {1872-8359}, mesh = {Benzothiazoles ; DNA, Bacterial/*isolation &amp; purification ; Diamines ; *Fluorescence ; Organic Chemicals ; Quinolines ; Real-Time Polymerase Chain Reaction ; Spores, Fungal/*isolation &amp; purification ; Staining and Labeling ; Streptomyces/*isolation &amp; purification ; }, abstract = {Determination of cell numbers in filamentous bacteria, such as Streptomyces, is challenging due to the tangled and twisted structure of the filaments and formation of cell clumps in liquid cultures. Here, we developed a conidia-based approach, in which fluorescence of conidia, after staining with the DNA-binding stain SYBR Green 1, was related to SYBR Green 1 fluorescence of DNA in Streptomyces. When cell number in Streptomyces filaments, determined by the conidia assay, was compared to number obtained by a qPCR assay, 34 to 62% of cells in the Streptomyces filaments were recovered. The difference in numbers probably reflects an insufficient extraction of DNA from the Gram-positive bacteria, rather than underestimation of the actual cell number by the conidia-based determination. The conidia-based approach appears to be a fast and reliable procedure for counting cell numbers in Streptomyces filaments but it can also be used for other filamentous bacteria, if proper standard curves can be made.}, }
@article {pmid30243206, year = {2018}, author = {Wen, D and Chang, NB and Wanielista, MP}, title = {Comparative copper toxicity impact and enzymatic cascade effect on Biosorption Activated Media and woodchips for nutrient removal in stormwater treatment.}, journal = {Chemosphere}, volume = {213}, number = {}, pages = {403-413}, doi = {10.1016/j.chemosphere.2018.09.062}, pmid = {30243206}, issn = {1879-1298}, mesh = {Copper/*toxicity ; Denitrification ; Metals, Heavy/*chemistry ; Oxidoreductases ; Wastewater/*chemistry ; }, abstract = {Copper, a commonly occurring heavy metal in stormwater runoff, was tested for its inhibitory effects on key nitrogen cycle bacteria in Biosorption Activated Media (BAM) and woodchip. The information in this paper is used to show that copper can enhance the denitrification process through enzyme cascade reactions since nitrous reductase is the enzyme responsible for the last step of denitrification and is largely dependent on copper as its cofactor. However, media characteristics are critical for assessing multi-enzymatic cascade reactions from the microbial ecology point of view. Moreover, both media showed significant copper removal through various mechanisms at 30 cm depth. The bioactivity evaluation indicates that other bacteria (fermentative bacteria, etc.) can be largely depressed with the presence of copper, hence the biofilm structure would be more vulnerable under shearing effects, which may result in holistic depression on the microbial community.}, }
@article {pmid30241680, year = {2018}, author = {Mergoni, G and Percudani, D and Lodi, G and Bertani, P and Manfredi, M}, title = {Prevalence of Candida Species in Endodontic Infections: Systematic Review and Meta-analysis.}, journal = {Journal of endodontics}, volume = {44}, number = {11}, pages = {1616-1625.e9}, doi = {10.1016/j.joen.2018.07.016}, pmid = {30241680}, issn = {1878-3554}, mesh = {Candida/*isolation &amp; purification ; *Candidiasis ; *Dental Pulp Cavity/microbiology ; Humans ; Periapical Periodontitis/*epidemiology/*microbiology ; Prevalence ; }, abstract = {INTRODUCTION: Candida in endodontic infections has been investigated in a large number of studies, but its role as an endodontic pathogen is still debatable. The aim of this study was to systematically review the literature on the prevalence of Candida species in root canal infections.<br><br>METHODS: Extensive literature research was performed in the most important electronic biomedical databases, and additional studies have been identified from references from relevant articles. Studies were critically appraised using a modified version of the Joanna Briggs Institute Critical Appraisal Checklist.<br><br>RESULTS: From 2225 unique records, 2118 were excluded on the basis of title and abstract. Of the remaining 107 studies, 50 were excluded after full-text review, and 57 were included for qualitative and quantitative analysis. The overall prevalence of Candida spp. in root canal infections was 8.20% (95% confidence interval, 5.56%-11.21%). Candida albicans was the most frequently isolated species. Significant heterogeneity among studies was observed (P&#xa0;<&#xa0;.001, I[2]&#xa0;=&#xa0;86.07%). Subgroup analyses revealed a higher prevalence of Candida spp. from African samples. All studies considered, a high or unclear risk of bias was prevalent regarding 6 out of the 8 items considered in the critical appraisal.<br><br>CONCLUSIONS: Candida spp. occurred in a small proportion of root canal infections. Further and better designed research is needed to investigate the real contribution of Candida spp. to the microbial ecology in infected root canals.}, }
@article {pmid30239657, year = {2018}, author = {Van Herreweghen, F and De Paepe, K and Roume, H and Kerckhof, FM and Van de Wiele, T}, title = {Mucin degradation niche as a driver of microbiome composition and Akkermansia muciniphila abundance in a dynamic gut model is donor independent.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {12}, pages = {}, doi = {10.1093/femsec/fiy186}, pmid = {30239657}, issn = {1574-6941}, mesh = {Colon/microbiology ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/*genetics ; Humans ; Intestines/*microbiology ; Mucin-1/*metabolism ; Propionates/metabolism ; Verrucomicrobia/*isolation &amp; purification/*metabolism ; }, abstract = {Akkermansia muciniphila, an abundant mucin degrading intestinal bacterium, has been correlated with human health in various studies. The in vitro SHIME model was used to reach a mechanistic understanding of A. muciniphila's colonization preferences and its response to environmental parameters such as colon pH and mucins. These insight can help to identify the optimal conditions for successful in vivo application. After a period of mucin deprivation, we found that mucin supplementation resulted in significantly different microbial communities, with more Akkermansia, Bacteroides and Ruminococcus. Mucin treatment accounted for 26% of the observed variation in the microbial community at OTU level (P = 0.001), whereas the donor effect was limited (8%) (P = 0.035), indicating mucins to constitute an important ecological niche shaping the microbiota composition. The effect of colonic pH had a less profound impact on the microbiome with both pH and donor origin explaining around 10% of the variability in the dataset. Yet, higher simulated colonic pH had a positive impact on Akkermansia abundance while short chain fatty acid analysis displayed a preference for propionate production with higher colonic pH. Our results show that mucins as nutritional resource are a more important modulator of the gut microbiome than colon pH as environmental factor.}, }
@article {pmid30238141, year = {2018}, author = {Roussel, C and Galia, W and Leriche, F and Chalancon, S and Denis, S and Van de Wiele, T and Blanquet-Diot, S}, title = {Comparison of conventional plating, PMA-qPCR, and flow cytometry for the determination of viable enterotoxigenic Escherichia coli along a gastrointestinal in vitro model.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {22}, pages = {9793-9802}, doi = {10.1007/s00253-018-9380-z}, pmid = {30238141}, issn = {1432-0614}, mesh = {Colony Count, Microbial/*methods ; Enterotoxigenic Escherichia coli/genetics/*growth &amp; development/isolation &amp; purification ; Flow Cytometry/*methods ; Gastrointestinal Tract/*microbiology ; Humans ; Microbial Viability ; Models, Biological ; Real-Time Polymerase Chain Reaction/*methods ; }, abstract = {Recent technological advances for bacterial viability assessment using molecular methods or flow cytometry can provide meaningful interest for the demarcation between live and dead microorganisms. Nonetheless, these methods have been scarcely applied to foodborne pathogens and never for directly assessing their viability within the human digestive environment. The purpose of this study was to compare two methods based on membrane integrity (propidium monoazide (PMA) q-PCR and Live/Dead flow cytometry) and the classical plate-count method to determine the viability of a common foodborne pathogen, enterotoxigenic Escherichia coli (ETEC), during its transit trough simulated human gastrointestinal environment. Viable ETEC counts in the gastric and small intestinal compartments of the gastrointestinal TIM model indicated a consensus between the three tested methods (PMA-qPCR, flow cytometry, and plate counts). In a further step, flow cytometry analysis appeared as the preferred method to elucidate ETEC physiological states in the in vitro digestive environment by discriminating four subpopulations, while PMA-qPCR can only distinguish two. The defined viable/altered ETEC population was found during all in vitro digestions, but mainly in the gastric compartment. Being able to discriminate the particular physiological states of pathogenic microorganisms in the digestive environment is of high interest, because if some cells are not observable on culture media, they might keep their ability to express virulence functions.}, }
@article {pmid30237506, year = {2018}, author = {Erşan, Y&#xc7; and Van Tittelboom, K and Boon, N and De Belie, N}, title = {Nitrite producing bacteria inhibit reinforcement bar corrosion in cementitious materials.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14092}, pmid = {30237506}, issn = {2045-2322}, mesh = {Bacteria/*metabolism ; Construction Materials ; Corrosion ; Nitrites/*metabolism ; }, abstract = {Chemicals and synthetic coatings are widely used to protect steel against corrosion. Bio-based corrosion inhibition strategies can be an alternative in the arising bioeconomy era. To maintain the good state of steel reinforcement in cracked concrete, microbe-based self-healing cementitious composites (MSCC) have been developed. Yet, proposed strategies involve reasonably slow crack filling by biomineralization and thus risk the possible rebar corrosion during crack healing. Here we upgrade the rebar protection to a higher level by combining MSCC with microbial induced corrosion inhibition. Presented NO3[-] reducing bacterial granules inhibit rebar corrosion by producing the anodic corrosion inhibitor NO2[-] and meanwhile heal a 300-µm-wide crack in 28 days. During 120 days exposure to 0.5 M Cl[-] solution, the rebars in cracked MSCC keep showing open circuit potentials above the critical value of -250 mV and they lose less than 2% of the total rebar material which corresponds to half the material loss in cracked plain mortar. Overall, the obtained rebar protection performance is comparable with that of uncracked mortar and mortar containing chemical inhibitor, hence the microbe-based system becomes an alternative to the traditional methods.}, }
@article {pmid30235606, year = {2019}, author = {Fiorentino, A and Di Cesare, A and Eckert, EM and Rizzo, L and Fontaneto, D and Yang, Y and Corno, G}, title = {Impact of industrial wastewater on the dynamics of antibiotic resistance genes in a full-scale urban wastewater treatment plant.}, journal = {The Science of the total environment}, volume = {646}, number = {}, pages = {1204-1210}, doi = {10.1016/j.scitotenv.2018.07.370}, pmid = {30235606}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Drug Resistance, Microbial/*genetics ; Environmental Monitoring ; *Genes, Bacterial ; Integrons ; Waste Disposal, Fluid/*methods ; Wastewater/*microbiology ; }, abstract = {Urban Wastewater Treatment Plants (UWTPs) treating mixed urban sewage and industrial wastewater are among the major hotspots for the spread of Antibiotic Resistance Genes (ARGs) into the environment. This study addresses the impact of the wastewater origin on ARG dynamics in a full-scale UWTP (15,000 Population Equivalent, PE) by operating the plant with and without industrial wastewater. Composite samples (4 L) from different treatment points were characterized for their chemical composition, bacterial abundance and for the abundance of four resistance genes against tetracycline, sulfonamides, erythromycin, and quinolones (tetA, sul2, ermB, and qnrS), and of the class 1 integrons (intI1). Although the chemical composition of the outflow significantly differed when the plant operated with or without industrial wastewater, the system efficiency in the removal of bacterial cells, ARGs, and intI1 was constant. The final disinfection by peracetic acid (PAA) did not affect the removal of ARGs, independently of the wastewater origin and the chemical characteristics of the inflows. Our results demonstrated that a well-functioning small size UWTP could treat a significant amount of industrial wastewater mixed in the urban sewage without affecting the overall ARGs and class 1 integrons released into the environment.}, }
@article {pmid30234420, year = {2019}, author = {De Mulder, T and Rasschaert, G and Van Coillie, E and Van den Meersche, T and Haegeman, A and Ruttink, T and de Wiele, TV and Heyndrickx, M}, title = {Impact of Cross-Contamination Concentrations of Doxycycline Hyclate on the Microbial Ecosystem in an Ex Vivo Model of the Pig's Cecum.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {25}, number = {2}, pages = {304-315}, doi = {10.1089/mdr.2018.0034}, pmid = {30234420}, issn = {1931-8448}, mesh = {Animal Feed/*analysis ; Animals ; Anti-Bacterial Agents/*analysis/*pharmacology ; Cecum/*drug effects/*microbiology ; Doxycycline/*analysis/*pharmacology ; Drug Resistance, Bacterial/genetics ; Escherichia coli/drug effects/genetics ; Fatty Acids/metabolism ; *Food Contamination ; Microbiota ; Polymerase Chain Reaction ; Sus scrofa ; Swine ; Tetracycline Resistance/*genetics ; }, abstract = {AIMS: Cross-contamination of feed with antibiotics causes pigs to become unintentionally exposed to low concentrations of antibiotics. This study investigates the effect of residues of doxycycline hyclate (DOX) in an ex vivo model of the intestinal tract of pigs, focusing on the microbial community, microbial activity, and the enrichment of resistant bacteria and resistance genes.<br><br>RESULTS: The effect of three concentrations DOX were tested; 1 and 4&#x2009;mg/L correspond to the intestinal concentrations when pigs are fed a compound feed containing 3% of a therapeutic dose, and a reference concentration of 16&#x2009;mg/L. These were continuously administered to a chemostat, simulating the microbial ecosystem of the pig cecum and inoculated with cecal content of organically grown pigs. The administration of even the lowest DOX concentration caused a significant decrease in bacterial activity, while the microbial community profile appeared to remain unaffected by any of the concentrations. A concentration of 1&#x2009;mg/L DOX caused minor selection pressure for tetracycline-resistant Escherichia coli but no other groups enumerated with plate cultivation, while 4&#x2009;mg/L induced major enrichment of tetracycline-resistant E. coli, Enterobacteriaceae and total anaerobes. High abundances of tet(Q), tet(M), tet(W), tet(O), and tet(B) were detected in the inoculum and also before antibiotic administration in the chemostat and did not significantly increase during administration of 1 and 4&#x2009;mg/L DOX. Only 16&#x2009;mg/L DOX caused minor enrichments.<br><br>CONCLUSIONS: Cross-contamination concentrations of doxycycline, as a result of cross-contamination, cause a selection pressure for resistant bacteria and negatively affect microbial activity.}, }
@article {pmid30233537, year = {2018}, author = {Teurlincx, S and Heijboer, A and Veraart, AJ and Kowalchuk, GA and Declerck, SAJ}, title = {Local Functioning, Landscape Structuring: Drivers of Soil Microbial Community Structure and Function in Peatlands.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2060}, pmid = {30233537}, issn = {1664-302X}, abstract = {Agricultural peatlands are essential for a myriad of ecosystem functions and play an important role in the global carbon (C) cycle through C sequestration. Management of these agricultural peatlands takes place at different spatial scales, ranging from local to landscape management, and drivers of soil microbial community structure and function may be scale-dependent. Effective management for an optimal biogeochemical functioning thus requires knowledge of the drivers on soil microbial community structure and functioning, as well as the spatial scales upon which they are influenced. During two field campaigns, we examined the importance of different drivers (i.e., soil characteristics, nutrient management, vegetation composition) at two spatial scales (local vs. landscape) for, respectively, the soil microbial community structure (determined by PLFA) and soil microbial community functional capacity (as assessed by CLPP) in agricultural peatlands. First, we show by an analysis of PLFA profiles that the total microbial biomass changes with soil moisture and relative C:P nutrient availability. Secondly, we showed that soil communities are controlled by a distinct set of drivers at the local, as opposed to landscape, scale. Community structure was found to be markedly different between areas, in contrast to community function which showed high variability within areas. We further found that microbial structure appears to be controlled more at a landscape scale by nutrient-related variables, whereas microbial functional capacity is driven locally through plant community feedbacks. Optimal management strategies within such peatlands should therefore consider the scale-dependent action of soil microbial community drivers, for example by first optimizing microbial structure at the landscape scale by targeted areal management, and then optimizing soil microbial function by local vegetation management.}, }
@article {pmid30232167, year = {2018}, author = {Ingala, MR and Simmons, NB and Perkins, SL}, title = {Bats Are an Untapped System for Understanding Microbiome Evolution in Mammals.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, pmid = {30232167}, issn = {2379-5042}, mesh = {Animals ; Chiroptera/*microbiology ; *Diet ; Ecology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; *Metagenomics ; Phylogeny ; }, abstract = {Mammals evolved in a microbial world, and consequently, microbial symbionts have played a role in their evolution. An exciting new subdiscipline of metagenomics considers the ways in which microbes, particularly those found in the gut, have facilitated the ecological and phylogenetic radiation of mammals. However, the vast majority of such studies focus on domestic animals, laboratory models, or charismatic megafauna (e.g., pandas and chimpanzees). The result is a plethora of studies covering few taxa across the mammal tree of life, leaving broad patterns of microbiome function and evolution unclear. Wildlife microbiome research urgently needs a model system in which to test hypotheses about metagenomic involvement in host ecology and evolution. We propose that bats (Order: Chiroptera) represent a model system ideal for comparative microbiome research, affording opportunities to examine host phylogeny, diet, and other natural history characteristics in relation to the evolution of the gut microbiome.}, }
@article {pmid30231985, year = {2018}, author = {Malik, A and Sharma, D and Malireddi, RKS and Guy, CS and Chang, TC and Olsen, SR and Neale, G and Vogel, P and Kanneganti, TD}, title = {SYK-CARD9 Signaling Axis Promotes Gut Fungi-Mediated Inflammasome Activation to Restrict Colitis and Colon Cancer.}, journal = {Immunity}, volume = {49}, number = {3}, pages = {515-530.e5}, pmid = {30231985}, issn = {1097-4180}, support = {R01 AI101935/AI/NIAID NIH HHS/United States ; R01 AI124346/AI/NIAID NIH HHS/United States ; P30 CA021765/CA/NCI NIH HHS/United States ; R01 CA163507/CA/NCI NIH HHS/United States ; R37 AI101935/AI/NIAID NIH HHS/United States ; R01 AR056296/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; CARD Signaling Adaptor Proteins/genetics/*metabolism ; Cells, Cultured ; Colitis/chemically induced/*immunology ; Colonic Neoplasms/*immunology ; Disease Models, Animal ; Fungi/*immunology ; Gastrointestinal Microbiome/*immunology ; Humans ; Inflammasomes/*metabolism ; Inflammatory Bowel Diseases/*immunology ; Interleukin-18/metabolism ; Intestinal Mucosa/*physiology ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Myeloid Cells/*physiology ; Signal Transduction ; Sodium Dodecyl Sulfate ; Syk Kinase/genetics/*metabolism ; }, abstract = {Fungi represent a significant proportion of the gut microbiota. Aberrant immune responses to fungi are frequently observed in inflammatory bowel diseases (IBD) and colorectal cancer (CRC), and mutations in the fungal-sensing pathways are associated with the pathogenesis of IBD. Fungal recognition receptors trigger downstream signaling via the common adaptor protein CARD9 and the kinase SYK. Here we found that commensal gut fungi promoted inflammasome activation during AOM-DSS-induced colitis. Myeloid cell-specific deletion of Card9 or Syk reduced inflammasome activation and interleukin (IL)-18 maturation and increased susceptibility to colitis and CRC. IL-18 promoted epithelial barrier restitution and interferon-γ production by intestinal CD8[+] T cells. Supplementation of IL-18 or transfer of wild-type myeloid cells reduced tumor burden in AOM-DSS-treated Card9[-/-] and Syk[fl/fl]LysM[Cre/+] mice, whereas treatment with anti-fungal agents exacerbated colitis and CRC. CARD9 deletion changes the gut microbial landscape, suggesting that SYK-CARD9 signaling maintains a microbial ecology that promotes inflammasome activation and thereby restrains colitis and colon tumorigenesis.}, }
@article {pmid30231921, year = {2018}, author = {Vavourakis, CD and Andrei, AS and Mehrshad, M and Ghai, R and Sorokin, DY and Muyzer, G}, title = {A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {168}, pmid = {30231921}, issn = {2049-2618}, support = {322551/ERC_/European Research Council/International ; }, mesh = {Bacteria/classification/*genetics/isolation &amp; purification/metabolism ; Carbon Cycle ; Genetic Variation ; Genome, Bacterial ; Geologic Sediments/analysis/*microbiology ; Lakes/analysis/*microbiology ; Metagenome ; Metagenomics ; Microbiota ; Nitrogen Cycle ; Phylogeny ; Sodium Chloride/analysis ; }, abstract = {BACKGROUND: Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages.<br><br>RESULTS: We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH&#xa0;10 and a salt content between 70 and 400&#xa0;g&#xa0;L[-1]. The recovered 16S rRNA gene sequences were mostly from Bacteria, even in the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria.<br><br>CONCLUSIONS: Our first sequencing effort of hypersaline soda lake sediment metagenomes led to two important advances. First, we showed the existence and obtained the first genomes of haloalkaliphilic members of the CPR and several hundred other novel prokaryote lineages. The soda lake CPR is a functionally diverse group, but the most abundant organisms in this study are likely fermenters with a possible role in primary carbon degradation. Second, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducers, and methanogens. Since only few environmental metagenomics studies have targeted sediment microbial communities and never to this extent, we expect that our findings are relevant not only for the understanding of haloalkaline environments but can also be used to set targets for future studies on marine and freshwater sediments.}, }
@article {pmid30231187, year = {2018}, author = {Wu, T and Grootaert, C and Pitart, J and Vidovic, NK and Kamiloglu, S and Possemiers, S and Glibetic, M and Smagghe, G and Raes, K and Van de Wiele, T and Van Camp, J}, title = {Aronia (Aronia melanocarpa) Polyphenols Modulate the Microbial Community in a Simulator of the Human Intestinal Microbial Ecosystem (SHIME) and Decrease Secretion of Proinflammatory Markers in a Caco-2/endothelial Cell Coculture Model.}, journal = {Molecular nutrition &amp; food research}, volume = {62}, number = {22}, pages = {e1800607}, doi = {10.1002/mnfr.201800607}, pmid = {30231187}, issn = {1613-4133}, mesh = {Biomarkers/metabolism ; Caco-2 Cells ; Chemokine CCL2/metabolism ; Coculture Techniques ; Fatty Acids, Volatile/metabolism ; Fruit and Vegetable Juices ; Gastrointestinal Microbiome/*physiology ; Glutathione/metabolism ; Humans ; Inflammation/drug therapy/metabolism ; Intercellular Adhesion Molecule-1/metabolism ; Interleukin-8/metabolism ; Photinia/*chemistry ; Polyphenols/*pharmacology ; Vascular Endothelial Growth Factor A/metabolism ; }, abstract = {SCOPE: To explore the mechanisms behind the health effects of Aronia (Aronia melanocarpa), the microbial community modulating and anti-inflammatory effects of Aronia polyphenols are investigated by combining the similutor of the human intestinal microbial ecosystem (SHIME) with a coculture of intestinal and endothelial cells.<br><br>RESULTS: Administration of Aronia juice (6.5g L[-1]) to the SHIME for 2 weeks increases the abundance of firmicutes to 92% in the ascending colon (AC), 85% in the transverse colon (TC), and 82% in the descending colon (DC; p&#xa0;<&#xa0;0.001), proteobacteria (6.7% in AC, p&#xa0;<&#xa0;0.001), and Akkermansia (14% in TC and 18% in DC, p&#xa0;<&#xa0;0.001) and decreases the abundance of Bifidobacterium species, associated with a decrease of acetate and increase of propionate and butyrate, whereas no significant difference is observed upon placebo juice treatment. After addition of the digests to TNF-&#x3b1; challenged Caco-2/endothelial cocultures, intercellular adhesion molecule (ICAM)-1, IL-8, and monocyte chemoattractant protein-1 levels are significantly downregulated. Interestingly, Aronia juice treats digests from each colon compartment resulting in a stronger decrease of the ICAM-1 secretion (up to 73%, p&#xa0;<&#xa0;0.001) compared to their corresponding placebo treated digests, thereby pointing to a polyphenol-dependent effect.<br><br>CONCLUSIONS: Aronia polyphenols modulate intestinal microbial composition, induce beneficial short chain fatty acid production, and prevent inflammatory stress in endothelial cells. This opens perspectives for the use of Aronia polyphenols as prebiotics in the context of intestinal and cardiovascular health.}, }
@article {pmid30229264, year = {2018}, author = {Ziller, A and Fraissinet-Tachet, L}, title = {Metallothionein diversity and distribution in the tree of life: a multifunctional protein.}, journal = {Metallomics : integrated biometal science}, volume = {10}, number = {11}, pages = {1549-1559}, doi = {10.1039/c8mt00165k}, pmid = {30229264}, issn = {1756-591X}, mesh = {Eukaryotic Cells/*metabolism ; *Metabolic Networks and Pathways ; Metallothionein/*metabolism ; Metals/*metabolism ; }, abstract = {MTs are small cysteine-rich proteins that chelate metal ions such as Cu+ and Zn2+, and are widely distributed in several life domains, in particular the eukaryotic one. They are present in the following phyla: Opisthokonta (mainly Fungi and Metazoa), Chloroplastida, Alveolata (ciliates) and Excavata (Trichomonas) for Eukaryota and Cyanobacteria, Actinobacteria, Proteobacteria and Firmicutes for Bacteria. However, their absence in some phyla underlines that MTs are far from being fully known. The MT amino acid sequences show a great diversity of sizes and structures both in terms of cysteine motifs and organization of these motifs. This review also highlights the different oxidized, apoprotein and metalated forms of MTs, the diversity of interactions they can establish with different molecules and their central and multifunctional cellular role. We present MTs as a protein system that could be a hub in molecular interaction networks. Studying MTs as a hub in cellular interaction networks should provide new insights for a better understanding of MT functioning and cellular processes.}, }
@article {pmid30228802, year = {2018}, author = {Gacesa, R and Baranasic, D and Starcevic, A and Diminic, J and Korlević, M and Najdek, M and Blažina, M and Oršolić, D and Kolesarić, D and Long, PF and Cullum, J and Hranueli, D and Orlic, S and Zucko, J}, title = {Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from Northern Adriatic Sea Sediments.}, journal = {Food technology and biotechnology}, volume = {56}, number = {2}, pages = {270-277}, pmid = {30228802}, issn = {1330-9862}, support = {MC_EX_MR/S300007/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Three metagenomic libraries were constructed using surface sediment samples from the northern Adriatic Sea. Two of the samples were taken from a highly polluted and an unpolluted site respectively. The third sample from a polluted site had been enriched using crude oil. The results of the metagenome analyses were incorporated in the REDPET relational database (http://redpet.bioinfo.pbf.hr/REDPET), which was generated using the previously developed MEGGASENSE platform. The database includes taxonomic data to allow the assessment of the biodiversity of metagenomic libraries and a general functional analysis of genes using hidden Markov model (HMM) profiles based on the KEGG database. A set of 22 specialised HMM profiles was developed to detect putative genes for hydrocarbon-degrading enzymes. Use of these profiles showed that the metagenomic library generated after selection on crude oil had enriched genes for aerobic n-alkane degradation. The use of this system for bioprospecting was exemplified using potential alkB and almA genes from this library.}, }
@article {pmid30228389, year = {2018}, author = {Mechmeche, M and Kachouri, F and Ksontini, H and Setti, K and Hamdi, M}, title = {Bioprocess development and preservation of functional food from tomato seed isolate fermented by kefir culture mixture.}, journal = {Journal of food science and technology}, volume = {55}, number = {10}, pages = {3911-3921}, pmid = {30228389}, issn = {0022-1155}, abstract = {The aim of this work was to explore the use of protein isolate from tomato seed enriched with the sucrose and the ascorbic acid as a medium for the growth of kefir mixture culture to develop a new non-dairy functional food. Unstructured mathematical and logistic models were proposed to describe cell growth, kefiran production, nutriment consumption and antioxidant activity. It was found that the maximal cell mass in the culture reached 8.38 g L[-1] after 24 h of fermentation. A significant amount of kefiran was also produced (0.65 g L[-1]). The kefir culture growth significantly decreased protein content and enhanced the antioxidant activity during varied fermentation through the production of bio active peptides. After 24 h of fermentation, IC50 value for protein isolate was estimated to be about 10.48 µg mL[-1]. The proposed models adequately described the changes during fermentation and as observed as a promising approach for the formulation of tomato seed-based functional foods. The preservation of the isolate was also investigated through a spray-drying process. The effect of spray-drying on the viability of lactic acid bacteria and stability of protein content and the antioxidant activity of the powder was also carried out. Results showed that the spray-drying method has great potential for the synthesis of powder from the fermented isolate that are rich in desirable properties. However, it was appropriate to preserve the powder for 10 days at 37 °C for the preservation of protein functionality.}, }
@article {pmid30223892, year = {2018}, author = {Sitaraman, R}, title = {Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {163}, pmid = {30223892}, issn = {2049-2618}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; *Biological Evolution ; *Gene Transfer, Horizontal ; Humans ; *Microbiota ; *Symbiosis ; }, abstract = {The ubiquity of horizontal gene transfer in the living world, especially among prokaryotes, raises interesting and important scientific questions regarding its effects on the human holobiont i.e., the human and its resident bacterial communities considered together as a unit of selection. Specifically, it would be interesting to determine how particular gene transfer events have influenced holobiont phenotypes in particular ecological niches and, conversely, how specific holobiont phenotypes have influenced gene transfer events. In this synthetic review, we list some notable and recent discoveries of horizontal gene transfer among the prokaryotic component of the human microbiota, and analyze their potential impact on the holobiont from an ecological-evolutionary viewpoint. Finally, the human-Helicobacter pylori association is presented as an illustration of these considerations, followed by a delineation of unresolved questions and avenues for future research.}, }
@article {pmid30218926, year = {2018}, author = {Zhang, X and Prévoteau, A and Louro, RO and Paquete, CM and Rabaey, K}, title = {Periodic polarization of electroactive biofilms increases current density and charge carriers concentration while modifying biofilm structure.}, journal = {Biosensors &amp; bioelectronics}, volume = {121}, number = {}, pages = {183-191}, doi = {10.1016/j.bios.2018.08.045}, pmid = {30218926}, issn = {1873-4235}, mesh = {Bioelectric Energy Sources ; *Biofilms ; *Biosensing Techniques ; Electrodes/*microbiology ; *Electrophysiological Phenomena ; Geobacter/*physiology ; }, abstract = {Anodic electroactive biofilms (EABs) need to overcome low current densities for applications such as microbial fuel cells or biosensors. EABs can store charge in self-produced redox proteins when temporarily left in open circuit, and discharge them once the electrode is appropriately repolarized, thus behaving as pseudocapacitors. Here we investigated the effect of such periodic polarization on the intrinsic nature of the EABs during their entire growth (i.e. starting from inoculation and for 10 days) on glassy carbon electrodes. An optimal periodic polarization (half-period of 10 s) greatly increased the maximum steady-state current density delivered by the Geobacter-dominated EABs (up to 1.10 ± 0.02 mA cm[-2], n = 3 electrodes) when compared to continuously polarized EABs (0.41 ± 0.04 mA cm[-2]); and increased the amount of electric charges produced per hour by 69 ± 17% even taking into account the half-periods of open circuit. This enhancement was highly correlated with a substantial increase in charge carriers concentration (10.6 ± 0.5 mMe- vs. 2.9 ± 0.6 mMe-), allowing higher charge storage capacity and higher electron mobility across the EABs. Our results suggest that appropriate periodic polarizations may upregulate the expression of heme-containing redox proteins associated with the matrix, such as c-type cytochromes. The EABs grown under periodic polarization presented mushroom-like structures on their top layers, while EABs grown under continuous polarization were flat.}, }
@article {pmid30218130, year = {2019}, author = {Bernasconi, R and Stat, M and Koenders, A and Huggett, MJ}, title = {Global Networks of Symbiodinium-Bacteria Within the Coral Holobiont.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {794-807}, pmid = {30218130}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/classification/*microbiology/physiology ; Bacteria/classification/genetics/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; Coral Reefs ; Microbiota ; Phylogeny ; *Symbiosis ; }, abstract = {Scleractinian corals form the framework of coral reefs and host abundant and diverse microbial communities that are fundamental to their success. A very limited number of studies have examined the co-occurrence of multiple partners within the coral 'holobiont' and their pattern of specificity over different geographical scales. In this study, we explored two molecular sequence datasets representing associations between corals and dinoflagellates in the genus Symbiodinium and between corals and bacteria, across the globe. Through a network theory approach, we characterised patterns of co-occurrences between bacteria and Symbiodinium with 13 coral genera across six water basins. The majority of the bacteria-Symbiodinium co-occurrences were specific to either a coral genus or water basin, emphasising both coral host and environment as important factors driving the diversity of coral assemblages. Yet, results also identified bacteria and Symbiodinium that were shared by multiple coral genera across several water basins. The analyses indicate that shared co-occurrences are independent of the phylogenetic and biogeographic relationship of coral hosts.}, }
@article {pmid30218129, year = {2019}, author = {Biswas, S and Mukherjee, P and Manna, T and Dutta, K and Guchhait, KC and Karmakar, A and Karmakar, M and Dua, P and Panda, AK and Ghosh, C}, title = {Quorum Sensing Autoinducer(s) and Flagellum Independently Mediate EPS Signaling in Vibrio cholerae Through LuxO-Independent Mechanism.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {616-630}, pmid = {30218129}, issn = {1432-184X}, support = {SR/SO/HS-43/2006//Department of Science and Technology/ ; BT/PR3802/BRB/10/981/2011//Department of Biotechnology , Ministry of Science and Technology/ ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; Biofilms ; Flagella/genetics/metabolism ; Flagellin/genetics/*metabolism ; *Gene Expression Regulation, Bacterial ; Homoserine/analogs &amp; derivatives/metabolism ; Ketones/metabolism ; Lactones/metabolism ; Polysaccharides, Bacterial/*metabolism ; *Quorum Sensing ; Signal Transduction ; Vibrio cholerae/genetics/*physiology ; }, abstract = {Vibrio cholerae, the Gram-negative bacterium causing lethal diarrheal disease cholera, forms biofilm on solid surfaces to gain adaptive advantage for successful survival in aquatic reservoirs. Expression of exopolysaccharide (EPS), an extracellular matrix material, has been found critical for biofilm-based environmental persistence. In a subset of epidemic-causing V. cholerae, absence of flagellum but not motility was identified to induce elevated exopolysaccharide expression. Identification of the role played by quorum sensing autoinducer molecules, i.e., cholera autoinducer 1 (CAI-1) and autoinducer 2 (AI-2) as well as central regulator LuxO on EPS expression in the subset was explored. Deletion mutations were introduced in vital genes responsible for synthesizing CAI-1 (cqsA), AI-2 (luxS), flagellum (flaA), LuxO (luxO), flagellar motor (motX), and VpsR (vpsR) in the model strain MO10. Subsequent phenotypic alterations in terms of colony morphology, EPS expression, biofilm formation, and transcription level of relevant genes were analyzed. Autoinducer cross-feeding experiment confirmed the role of autoinducers in EPS signaling. Results reveal that autoinducers and flagellum are the two major EPS signaling units in this subset where one unit becomes predominant for EPS production in absence of the other. Moreover, either unit exerts negative influence on EPS induction by the other. Both the EPS signaling cascades are independent of LuxO contribution and essentially involve sodium-driven flagellar motor and VpsR. A cell density and flagellum-mediated, but LuxO-independent, EPS signaling mechanism is considered to be functional in these organisms that confers their survival fitness.}, }
@article {pmid30217851, year = {2018}, author = {Stough, JMA and Kolton, M and Kostka, JE and Weston, DJ and Pelletier, DA and Wilhelm, SW}, title = {Diversity of Active Viral Infections within the Sphagnum Microbiome.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {23}, pages = {}, pmid = {30217851}, issn = {1098-5336}, mesh = {Bacteriophages/classification/genetics/*isolation &amp; purification/metabolism ; Biodiversity ; Biomass ; Capsid Proteins/genetics ; Carbon Dioxide/metabolism ; *Microbiota ; Phylogeny ; Sphagnopsida/growth &amp; development/metabolism/*virology ; Viruses/classification/genetics/*isolation &amp; purification/metabolism ; }, abstract = {Sphagnum-dominated peatlands play an important role in global carbon storage and represent significant sources of economic and ecological value. While recent efforts to describe microbial diversity and metabolic potential of the Sphagnum microbiome have demonstrated the importance of its microbial community, little is known about the viral constituents. We used metatranscriptomics to describe the diversity and activity of viruses infecting microbes within the Sphagnum peat bog. The vegetative portions of six Sphagnum plants were obtained from a peatland in northern Minnesota, and the total RNA was extracted and sequenced. Metatranscriptomes were assembled and contigs were screened for the presence of conserved virus marker genes. Using bacteriophage capsid protein gp23 as a marker for phage diversity, we identified 33 contigs representing undocumented phages that were active in the community at the time of sampling. Similarly, RNA-dependent RNA polymerase and the nucleocytoplasmic large DNA virus (NCLDV) major capsid protein were used as markers for single-stranded RNA (ssRNA) viruses and NCLDV, respectively. In total, 114 contigs were identified as originating from undescribed ssRNA viruses, 22 of which represent nearly complete genomes. An additional 64 contigs were identified as being from NCLDVs. Finally, 7 contigs were identified as putative virophage or polinton-like viruses. We developed co-occurrence networks with these markers in relation to the expression of potential-host housekeeping gene rpb1 to predict virus-host relationships, identifying 13 groups. Together, our approach offers new tools for the identification of virus diversity and interactions in understudied clades and suggests that viruses may play a considerable role in the ecology of the Sphagnum microbiome.IMPORTANCESphagnum-dominated peatlands play an important role in maintaining atmospheric carbon dioxide levels by modifying conditions in the surrounding soil to favor the growth of Sphagnum over that of other plant species. This lowers the rate of decomposition and facilitates the accumulation of fixed carbon in the form of partially decomposed biomass. The unique environment produced by Sphagnum enriches for the growth of a diverse microbial consortia that benefit from and support the moss's growth, while also maintaining the hostile soil conditions. While a growing body of research has begun to characterize the microbial groups that colonize Sphagnum, little is currently known about the ecological factors that constrain community structure and define ecosystem function. Top-down population control by viruses is almost completely undescribed. This study provides insight into the significant viral influence on the Sphagnum microbiome and identifies new potential model systems to study virus-host interactions in the peatland ecosystem.}, }
@article {pmid30217848, year = {2018}, author = {Mbareche, H and Veillette, M and Bilodeau, GJ and Duchaine, C}, title = {Bioaerosol Sampler Choice Should Consider Efficiency and Ability of Samplers To Cover Microbial Diversity.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {23}, pages = {}, pmid = {30217848}, issn = {1098-5336}, mesh = {Aerosols/*chemistry ; *Air Microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Environmental Monitoring/instrumentation/*methods ; Fungi/classification/genetics/*isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Static Electricity ; }, abstract = {Bioaerosol studies aim to describe the microbial content and increase understanding of the aerosolization processes linked to diseases. Air samplers are used to collect, identify, and quantify bioaerosols. Studies comparing the performances of air samplers have typically used a culture approach or have targeted a specific microorganism in laboratory settings. The objective of this study was to use environmental field samples to compare the efficiencies of 3 high-airflow-rate samplers for describing bioaerosol diversity using a next-generation sequencing approach. Two liquid cyclonic impactors and one electrostatic filter dry sampler were used in four wastewater treatment plants to target bacterial diversity and in five dairy farms to target fungal diversity. The dry electrostatic sampler was consistently more powerful in collecting more fungal and bacterial operational taxonomic units (OTUs). Substantial differences in OTU abundances between liquid and dry sampling were revealed. The majority of the diversity revealed by dry electrostatic sampling was not identified using the cyclonic liquid impactors. The findings from this work suggest that the choice of a bioaerosol sampler should include information about the efficiency and ability of samplers to cover microbial diversity. Although these results suggest that electrostatic filters result in better coverage of the microbial diversity among the tested air samplers, further studies are needed to confirm this hypothesis. While it is difficult to determine a single universally optimal air sampler, this work provides an in-depth look at some of the considerations that are essential when choosing an air sampler for studying the microbial ecology of bioaerosols.IMPORTANCE Associating bioaerosol exposure and health problems is challenging, and adequate exposure monitoring is a priority for scientists in the field. Conclusions that can be drawn from bioaerosol exposure studies are highly dependent on the design of the study and the methodologies used. The air sampling strategy is the first methodological step leading to an accurate interpretation of what is present in the air. Applying new molecular approaches to evaluate the efficiencies of the different types of samplers used in the field is necessary in order to circumvent traditional approaches and the biases they introduce to such studies. The results and conclusions provided in this paper should be taken in consideration when conducting a bioaerosol study.}, }
@article {pmid30214003, year = {2018}, author = {Lindeboom, REF and Ilgrande, C and Carvajal-Arroyo, JM and Coninx, I and Van Hoey, O and Roume, H and Morozova, J and Udert, KM and Sas, B and Paille, C and Lasseur, C and Ilyin, V and Clauwaert, P and Leys, N and Vlaeminck, SE}, title = {Nitrogen cycle microorganisms can be reactivated after Space exposure.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {13783}, pmid = {30214003}, issn = {2045-2322}, mesh = {Ammonia/metabolism ; Archaea/*metabolism/radiation effects ; Bacteria/*metabolism/radiation effects ; Bioreactors/*microbiology ; Denitrification/physiology ; Nitrites/metabolism ; Nitrogen Cycle/*physiology ; Oxidation-Reduction ; *Space Flight ; Spacecraft ; *Weightlessness ; }, abstract = {Long-term human Space missions depend on regenerative life support systems (RLSS) to produce food, water and oxygen from waste and metabolic products. Microbial biotechnology is efficient for nitrogen conversion, with nitrate or nitrogen gas as desirable products. A prerequisite to bioreactor operation in Space is the feasibility to reactivate cells exposed to microgravity and radiation. In this study, microorganisms capable of essential nitrogen cycle conversions were sent on a 44-days FOTON-M4 flight to Low Earth Orbit (LEO) and exposed to 10[-3]-10[-4] g (gravitational constant) and 687 ± 170 µGy (Gray) d[-1] (20 ± 4 °C), about the double of the radiation prevailing in the International Space Station (ISS). After return to Earth, axenic cultures, defined and reactor communities of ureolytic bacteria, ammonia oxidizing archaea and bacteria, nitrite oxidizing bacteria, denitrifiers and anammox bacteria could all be reactivated. Space exposure generally yielded similar or even higher nitrogen conversion rates as terrestrial preservation at a similar temperature, while terrestrial storage at 4 °C mostly resulted in the highest rates. Refrigerated Space exposure is proposed as a strategy to maximize the reactivation potential. For the first time, the combined potential of ureolysis, nitritation, nitratation, denitrification (nitrate reducing activity) and anammox is demonstrated as key enabler for resource recovery in human Space exploration.}, }
@article {pmid30213542, year = {2018}, author = {Lee, K and Yu, H and Zhang, X and Choo, KH}, title = {Quorum sensing and quenching in membrane bioreactors: Opportunities and challenges for biofouling control.}, journal = {Bioresource technology}, volume = {270}, number = {}, pages = {656-668}, doi = {10.1016/j.biortech.2018.09.019}, pmid = {30213542}, issn = {1873-2976}, mesh = {Biofilms ; *Biofouling ; *Bioreactors/microbiology ; *Quorum Sensing ; Wastewater/microbiology ; }, abstract = {Membrane biofouling, due to biofilm growth after planktonic bacteria attachment to a membrane, is a major bottleneck limiting the energy-efficient operation and maintenance of membrane bioreactors (MBRs). Microbial communications, known as quorum sensing (QS), are responsible for this biofouling behavior. Novel strategies for stopping this communication, known as quorum quenching (QQ), appear to be successful for biofouling control in MBRs used for wastewater treatment. This review describes recent information regarding the signal molecules and mechanisms responsible for QS behaviors, promising approaches for QQ (enzymatic, bacterial, fungal, photocatalytic, mimicking, and biostimulating methods), and efficient fabrication and use of QQ media for MBR applications. We discuss the opportunities and challenges of QQ techniques for their further improvement and practical use in MBRs.}, }
@article {pmid30210468, year = {2018}, author = {Nguyen, NL and Yu, WJ and Gwak, JH and Kim, SJ and Park, SJ and Herbold, CW and Kim, JG and Jung, MY and Rhee, SK}, title = {Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1982}, pmid = {30210468}, issn = {1664-302X}, abstract = {Soil acidification is accelerated by anthropogenic and agricultural activities, which could significantly affect global methane cycles. However, detailed knowledge of the genomic properties of methanotrophs adapted to acidic soils remains scarce. Using metagenomic approaches, we analyzed methane-utilizing communities enriched from acidic forest soils with pH 3 and 4, and recovered near-complete genomes of proteobacterial methanotrophs. Novel methanotroph genomes designated KS32 and KS41, belonging to two representative clades of methanotrophs (Methylocystis of Alphaproteobacteria and Methylobacter of Gammaproteobacteria), were dominant. Comparative genomic analysis revealed diverse systems of membrane transporters for ensuring pH homeostasis and defense against toxic chemicals. Various potassium transporter systems, sodium/proton antiporters, and two copies of proton-translocating F1F0-type ATP synthase genes were identified, which might participate in the key pH homeostasis mechanisms in KS32. In addition, the V-type ATP synthase and urea assimilation genes might be used for pH homeostasis in KS41. Genes involved in the modification of membranes by incorporation of cyclopropane fatty acids and hopanoid lipids might be used for reducing proton influx into cells. The two methanotroph genomes possess genes for elaborate heavy metal efflux pumping systems, possibly owing to increased heavy metal toxicity in acidic conditions. Phylogenies of key genes involved in acid adaptation, methane oxidation, and antiviral defense in KS41 were incongruent with that of 16S rRNA. Thus, the detailed analysis of the genome sequences provides new insights into the ecology of methanotrophs responding to soil acidification.}, }
@article {pmid30209587, year = {2019}, author = {Hernández-Gómez, O and Briggler, JT and Williams, RN}, title = {Captivity-Induced Changes in the Skin Microbial Communities of Hellbenders (Cryptobranchus alleganiensis).}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {782-793}, pmid = {30209587}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Female ; Male ; *Microbiota ; Missouri ; Phylogeny ; Skin/*microbiology ; Caudata/growth &amp; development/*microbiology ; }, abstract = {Variation in environmental conditions can result in disparate associations between hosts and microbial symbionts. As such, it is imperative to evaluate how environmental variables (e.g., habitat quality) can influence host-associated microbiome composition. Within wildlife conservation programs, captive conditions can negatively influence the establishment and maintenance of "wild-type" microbiotas within a host. Alternative microbial communities can result in the proliferation of disease among captive stock or upon reintroduction. Hellbenders (Cryptobranchus alleganiensis) are a threatened salamander for which extensive captive management is currently employed. Using metabarcoding, we characterized the skin microbiota of wild and captive hellbenders from two subspecies in the state of Missouri, the eastern (C. a. alleganiensis) and the Ozark hellbender (C. a. bishopi). Both subspecies in our study included wild adults and captive juveniles that were collected from the wild as eggs. Our objectives were to investigate differences in the skin microbial communities' richness/diversity, composition, and functional profiles of microbes between wild and captive individuals. Captive eastern hellbenders possessed richer communities than wild cohorts, whereas the opposite pattern was observed within the Ozark subspecies. We found significant microbial community structure between wild and captive populations of both subspecies. Microbiota structure translated into differences in the predicted metagenome of wild and captive individuals as well. As such, we can expect captive hellbenders to experience alternative microbial structure and function upon reintroduction into the wild. Our study provides a baseline for the effect of captivity on the skin microbial communities of hellbenders, and highlights the need to incorporate microbiota management in current captive-rearing programs.}, }
@article {pmid30209586, year = {2019}, author = {Manjunatha, BS and Paul, S and Aggarwal, C and Bandeppa, S and Govindasamy, V and Dukare, AS and Rathi, MS and Satyavathi, CT and Annapurna, K}, title = {Diversity and Tissue Preference of Osmotolerant Bacterial Endophytes Associated with Pearl Millet Genotypes Having Differential Drought Susceptibilities.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {676-688}, pmid = {30209586}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Droughts ; Endophytes/classification/genetics/*isolation &amp; purification ; Genotype ; Pennisetum/genetics/*microbiology/physiology ; Phylogeny ; Plant Leaves/genetics/microbiology/physiology ; Plant Roots/genetics/microbiology/physiology ; }, abstract = {Genetic and functional diversity of osmotolerant bacterial endophytes colonizing the root, stem, and leaf tissues of pearl millet genotypes differing in their drought susceptibility was assessed. Two genotypes of pearl millet, viz., the drought tolerant genotype TT-1 and the drought susceptible genotype PPMI-69, were used in the present study. Diazotrophs were found to be the predominant colonizers, followed by the Gram positive bacteria in most of the tissues of both the genotypes. Higher proportion of bacterial endophytes obtained from the drought tolerant genotype was found to be osmotolerant. Results of 16S rRNA gene-ARDRA analysis grouped 50 of the highly osmotolerant isolates into 16 clusters, out of which nine clusters had only one isolate each, indicating their uniqueness. One cluster had 21 isolates and remaining clusters were represented by isolates ranging from two to four. The representative isolates from each cluster were identified, and Bacillus was found to be the most prevalent osmotolerant genera with many different species. Other endophytic bacteria belonged to Pseudomonas sp., Stenotrophomonas sp., and Macrococcus caseolyticus. High phylogenetic diversity was observed in the roots of the drought tolerant genotype while different tissues of the drought susceptible genotype showed less diversity. Isolates of Bacillus axarquiensis were present in all the tissues of both the genotypes of pearl millet. However, most of the other endophytic bacteria showed tissue/genotype specificity. With the exception of B. axarquiensis and B. thuringiensis, rest all the species of Bacillus were found colonizing only the drought-tolerant genotype; while M. caseolyticus colonized all the tissues of only the drought susceptible genotype. There was high incidence of IAA producers and low incidence of ACC deaminase producers among the isolates from the root tissues of the drought-tolerant genotype while reverse was the case for the drought-susceptible genotype. Thus, host played an important role in the selection of endophytes based on both phylogenetic and functional traits.}, }
@article {pmid30209585, year = {2019}, author = {Houfani, AA and Větrovský, T and Navarrete, OU and Štursová, M and Tláskal, V and Beiko, RG and Boucherba, N and Baldrian, P and Benallaoua, S and Jorquera, MA}, title = {Cellulase-Hemicellulase Activities and Bacterial Community Composition of Different Soils from Algerian Ecosystems.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {713-725}, pmid = {30209585}, issn = {1432-184X}, support = {LM2015055//Ministry of Education, Youth and Sports of the Czech Republic/ ; 1160302//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; }, mesh = {Algeria ; Bacteria/classification/*enzymology/genetics/isolation &amp; purification ; Bacterial Proteins/genetics/*metabolism ; Cellulase/genetics/*metabolism ; Ecosystem ; Forests ; Glycoside Hydrolases/genetics/*metabolism ; Phylogeny ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Soil microorganisms are important mediators of carbon cycling in nature. Although cellulose- and hemicellulose-degrading bacteria have been isolated from Algerian ecosystems, the information on the composition of soil bacterial communities and thus the potential of their members to decompose plant residues is still limited. The objective of the present study was to describe and compare the bacterial community composition in Algerian soils (crop, forest, garden, and desert) and the activity of cellulose- and hemicellulose-degrading enzymes. Bacterial communities were characterized by high-throughput 16S amplicon sequencing followed by the in silico prediction of their functional potential. The highest lignocellulolytic activity was recorded in forest and garden soils whereas activities in the agricultural and desert soils were typically low. The bacterial phyla Proteobacteria (in particular classes α-proteobacteria, δ-proteobacteria, and γ-proteobacteria), Firmicutes, and Actinobacteria dominated in all soils. Forest and garden soils exhibited higher diversity than agricultural and desert soils. Endocellulase activity was elevated in forest and garden soils. In silico analysis predicted higher share of genes assigned to general metabolism in forest and garden soils compared with agricultural and arid soils, particularly in carbohydrate metabolism. The highest potential of lignocellulose decomposition was predicted for forest soils, which is in agreement with the highest activity of corresponding enzymes.}, }
@article {pmid30209011, year = {2018}, author = {Shade, A and Dunn, RR and Blowes, SA and Keil, P and Bohannan, BJM and Herrmann, M and Küsel, K and Lennon, JT and Sanders, NJ and Storch, D and Chase, J}, title = {Macroecology to Unite All Life, Large and Small.}, journal = {Trends in ecology &amp; evolution}, volume = {33}, number = {10}, pages = {731-744}, doi = {10.1016/j.tree.2018.08.005}, pmid = {30209011}, issn = {1872-8383}, mesh = {*Biodiversity ; Ecology/classification/*methods ; }, abstract = {Macroecology is the study of the mechanisms underlying general patterns of ecology across scales. Research in microbial ecology and macroecology have long been detached. Here, we argue that it is time to bridge the gap, as they share a common currency of species and individuals, and a common goal of understanding the causes and consequences of changes in biodiversity. Microbial ecology and macroecology will mutually benefit from a unified research agenda and shared datasets that span the entirety of the biodiversity of life and the geographic expanse of the Earth.}, }
@article {pmid30206025, year = {2019}, author = {Kispal, ZF and Vajda, P and Kardos, D and Klymiuk, I and Moissl-Eichinger, C and Castellani, C and Singer, G and Till, H}, title = {The local microbiome after pediatric bladder augmentation: intestinal segments and the native urinary bladder host similar mucosal microbiota.}, journal = {Journal of pediatric urology}, volume = {15}, number = {1}, pages = {30.e1-30.e7}, doi = {10.1016/j.jpurol.2018.07.028}, pmid = {30206025}, issn = {1873-4898}, mesh = {Adolescent ; Child ; Colon/*microbiology/*transplantation ; Female ; Gastrointestinal Microbiome ; Humans ; Ileum/*microbiology/*transplantation ; Intestinal Mucosa/microbiology ; Male ; *Microbiota ; Retrospective Studies ; Urinary Bladder/*surgery ; Urinary Reservoirs, Continent/*microbiology ; Urologic Surgical Procedures/methods ; }, abstract = {INTRODUCTION: Next-generation sequencing (NGS) techniques have provided novel insights into the microbiome of the urinary bladder (UB). In children after bladder augmentation using either ileum (ileocystoplasty, ICP) or colon (colocystoplasty, CCP), the fate of the mucosal microbiome introduced into the urinary tract remains unknown.<br><br>OBJECTIVE: The aim was to compare the mucosal microbiome of the native UB vs the augmented intestinal segment (IS) using NGS.<br><br>STUDY DESIGN: Twelve children after bladder augmentation (ICP n&#xa0;=&#xa0;6, CCP n&#xa0;=&#xa0;6) were included. Biopsies were taken during routine postoperative cystoscopy from the native UB and the IS. Specimens underwent whole-genome DNA extraction, 16S rRNA gene amplification, NGS, and Quantitative Insights Into Microbial Ecology (QIIME) data analysis. Downstream statistical data analyses were performed in Calypso.<br><br>RESULTS: Patients' median age at the time of surgery was 11 years (6-17 years), and the median interval between augmentation and sampling was 7 years (4-13 years). &#x3b1;-Diversity (Shannon diversity index) was not significantly different between IS vs UB, ICP vs CCP, and male vs female. No general differences in the overall bacterial pattern (&#x3b2;-diversity) were found between IS, UB, ICP, and CCP groups. The groups overlapped in principal coordinate analysis (PCoA) and non-metric multidimensional scaling (NMDS) analysis (Figure). Age at sampling had a statistically significant influence on &#x3b2;-diversity at the genus level. Corynebacterium, Pseudoxanthomonas, Lactobacillus, Flavobacterium, and Micrococcus were the most dominating taxa detected over all samples. There was an obvious dominance of the genus Corynebacterium in the samples taken from the UB and IS in both ICP and CCP patients. Limitations of this study include the relatively small number of patients.<br><br>CONCLUSION: After bladder augmentation, the native UB and augmented ISs (ICP and CCP) host similar microbiota despite their distinct differences of originating mucosal anatomy.}, }
@article {pmid30204767, year = {2018}, author = {Lee, JZ and Everroad, RC and Karaoz, U and Detweiler, AM and Pett-Ridge, J and Weber, PK and Prufert-Bebout, L and Bebout, BM}, title = {Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0202792}, pmid = {30204767}, issn = {1932-6203}, mesh = {Bacteria/*classification/genetics ; Bacteroidetes/classification/genetics ; California ; Cyanobacteria/classification/genetics ; Evolution, Molecular ; Gammaproteobacteria/classification/genetics ; Metagenomics/*methods ; Molecular Sequence Annotation ; Photosynthesis ; Phylogeny ; Proteobacteria/classification/genetics ; Whole Genome Sequencing/*methods ; }, abstract = {Hypersaline photosynthetic microbial mats are stratified microbial communities known for their taxonomic and metabolic diversity and strong light-driven day-night environmental gradients. In this study of the upper photosynthetic zone of hypersaline microbial mats of Elkhorn Slough, California (USA), we show how metagenome sequencing can be used to meaningfully assess microbial ecology and genetic partitioning in these complex microbial systems. Mapping of metagenome reads to the dominant Cyanobacteria observed in the system, Coleofasciculus (Microcoleus) chthonoplastes, was used to examine strain variants within these metagenomes. Highly conserved gene subsystems indicated a core genome for the species, and a number of variant genes and subsystems suggested strain level differentiation, especially for nutrient utilization and stress response. Metagenome sequence coverage binning was used to assess ecosystem partitioning of remaining microbes to both reconstruct the model organisms in silico and identify their ecosystem functions as well as to identify novel clades and propose their role in the biogeochemical cycling of mats. Functional gene annotation of these bins (primarily of Proteobacteria, Bacteroidetes, and Cyanobacteria) recapitulated the known biogeochemical functions in microbial mats using a genetic basis, and revealed significant diversity in the Bacteroidetes, presumably in heterotrophic cycling. This analysis also revealed evidence of putative phototrophs within the Gemmatimonadetes and Gammaproteobacteria residing in microbial mats. This study shows that metagenomic analysis can produce insights into the systems biology of microbial ecosystems from a genetic perspective and to suggest further studies of novel microbes.}, }
@article {pmid30199845, year = {2018}, author = {Dolan, JR}, title = {The Villefranche Strombidium sulcatum: A review.}, journal = {European journal of protistology}, volume = {66}, number = {}, pages = {68-76}, doi = {10.1016/j.ejop.2018.08.002}, pmid = {30199845}, issn = {1618-0429}, mesh = {Aquatic Organisms/*classification/*physiology ; Ciliophora/*classification/*physiology ; Marine Biology/*standards/trends ; Plankton ; }, abstract = {The marine oligotrich ciliate Strombidium sulcatum, the best known marine oligotrich of the marine microozoplankton, was first cultured in Villefranche-sur-Mer 35 years ago. Cultures were maintained from 1983 to 2003 and used in 22 studies investigating a very wide variety of questions. Here we review the major findings of these studies and underline their contributions to our knowledge of planktonic ciliate ecology and microbial ecology in general. We conclude with the observation that while ecophysiology has apparently fallen out of fashion, culture work will likely return as an invaluable resource in our present 'omics' era.}, }
@article {pmid30199026, year = {2018}, author = {Couper, L and Swei, A}, title = {Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {138}, pages = {}, pmid = {30199026}, issn = {1940-087X}, mesh = {Animals ; High-Throughput Nucleotide Sequencing/*methods ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; Ticks/*genetics ; }, abstract = {In recent decades, vector-borne diseases have re-emerged and expanded at alarming rates, causing considerable morbidity and mortality worldwide. Effective and widely available vaccines are lacking for a majority of these diseases, necessitating the development of novel disease mitigation strategies. To this end, a promising avenue of disease control involves targeting the vector microbiome, the community of microbes inhabiting the vector. The vector microbiome plays a pivotal role in pathogen dynamics, and manipulations of the microbiome have led to reduced vector abundance or pathogen transmission for a handful of vector-borne diseases. However, translating these findings into disease control applications requires a thorough understanding of vector microbial ecology, historically limited by insufficient technology in this field. The advent of next-generation sequencing approaches has enabled rapid, highly parallel sequencing of diverse microbial communities. Targeting the highly-conserved 16S rRNA gene has facilitated characterizations of microbes present within vectors under varying ecological and experimental conditions. This technique involves amplification of the 16S rRNA gene, sample barcoding via PCR, loading samples onto a flow cell for sequencing, and bioinformatics approaches to match sequence data with phylogenetic information. Species or genus-level identification for a high number of replicates can typically be achieved through this approach, thus circumventing challenges of low detection, resolution, and output from traditional culturing, microscopy, or histological staining techniques. Therefore, this method is well-suited for characterizing vector microbes under diverse conditions but cannot currently provide information on microbial function, location within the vector, or response to antibiotic treatment. Overall, 16S next-generation sequencing is a powerful technique for better understanding the identity and role of vector microbes in disease dynamics.}, }
@article {pmid30197411, year = {2018}, author = {Mise, K and Fujita, K and Kunito, T and Senoo, K and Otsuka, S}, title = {Phosphorus-mineralizing Communities Reflect Nutrient-Rich Characteristics in Japanese Arable Andisols.}, journal = {Microbes and environments}, volume = {33}, number = {3}, pages = {282-289}, pmid = {30197411}, issn = {1347-4405}, mesh = {Alkaline Phosphatase/*genetics/metabolism ; Bacteria/classification/enzymology/genetics/*metabolism ; Bacterial Proteins/*genetics/metabolism ; Biodiversity ; Computational Biology ; DNA, Bacterial/genetics ; Genes, Bacterial/genetics ; Geography ; Japan ; Metagenome/genetics ; Phosphorus/analysis/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Elucidating the soil phosphorus cycle driven by soil microbes is a vital question in soil microbial ecology. The Japanese arable Andisols, occupying half of the Japanese cropland, are known for their high phosphorus sorption capacity. However, limited information is currently available on microbially driven phosphorus mineralization in arable Andisols. We herein report that the phosphorus-mineralizing community in the Japanese arable Andisols showed characteristic distribution and composition patterns, from those in other types of soils. We performed a chemical analysis and microbial community analysis of 43 arable Andisols along the Japanese archipelago. Soil phosphomonoesterase activities measured at pH 11 were approximately 70% of those at pH 6.5, which indicates that alkaline phosphatase contributes to phosphorus cycling, although most soil samples were acidic. Functional gene predictions based on 16S rRNA gene sequencing indicated that the alkaline phosphatase gene phoD was more abundant than other alkaline phosphatase genes and, thus, plays major roles. Hence, amplicon sequencing targeting phoD was performed and the results obtained showed that alphaproteobacterial phoD was dominant. This is in contrast to previously reported phoD compositions in other soils and may be attributed to the nutrient conditions in arable Andisols, which favor copiotrophic Alphaproteobacteria. Furthermore, the composition of phoD correlated with soil pH and bioavailable phosphorus concentrations rather than carbon or nitrogen concentrations. These results were partly different from previous findings, varying in the soil types and geographic ranges of sampling sites. Collectively, the present results indicate that the phosphorus-mineralizing community in the Japanese arable Andisols is regulated differently from those in other soil types.}, }
@article {pmid30196926, year = {2018}, author = {Šulčius, S and Mazur-Marzec, H and Vitonytė, I and Kvederavičiūtė, K and Kuznecova, J and Šimoliūnas, E and Holmfeldt, K}, title = {Insights into cyanophage-mediated dynamics of nodularin and other non-ribosomal peptides in Nodularia spumigena.}, journal = {Harmful algae}, volume = {78}, number = {}, pages = {69-74}, doi = {10.1016/j.hal.2018.07.004}, pmid = {30196926}, issn = {1878-1470}, mesh = {Bacteriophages/*physiology ; Biodegradation, Environmental ; Chromatography, Liquid ; Cyanobacteria/*metabolism/*virology ; Environmental Monitoring ; Peptides/metabolism ; Peptides, Cyclic/*metabolism ; Population Density ; Tandem Mass Spectrometry ; }, abstract = {The effect of cyanophage infection and lysis on the dynamics of the hepatotoxin nodularin (NOD) and other non-ribosomal peptides (NRPs) produced by cyanobacteria is poorly understood. In this study, changes in concentration of NOD and other NRPs during cyanophage infection of the filamentous cyanobacteria Nodularia spumigena were assessed using incubation experiments. Viral infection and lysis were associated with a significant reduction (93% at the 96 h post infection) of N. spumigena cell density. While no correlation between N. spumigena abundance and total concentration of NOD (ng mL[-1]) within the infected cells was observed, cellular NOD quota (ng cell[-1]) gradually increased in the remaining cyanophage resistant N. spumigena subpopulation. Lysis of N. spumigena cells resulted in a substantial increase (>57 times) of dissolved NOD concentration in the culture medium. The relative concentration of other cyclic (anabaenopeptins) and linear (aeruginosins, spumigins) NRPs produced by N. spumigena also increased in response to cyanophage addition. This study highlights the importance of cyanophage infection on the population toxicity of filamentous cyanobacteria and demonstrates a significant contribution of virus-mediated cell lysis on the conversion of NOD from the particulate to dissolved phase.}, }
@article {pmid30196314, year = {2019}, author = {Ullah, A and Akbar, A and Luo, Q and Khan, AH and Manghwar, H and Shaban, M and Yang, X}, title = {Microbiome Diversity in Cotton Rhizosphere Under Normal and Drought Conditions.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {429-439}, pmid = {30196314}, issn = {1432-184X}, support = {2016YFD0101006//National Key Project of Research and Development Plan/ ; 2016ZX08005-004-002//Transgenic Crops of Transgenic Crops of Ministry of Science and Technology of China/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Droughts ; Fungi/classification/genetics/*isolation &amp; purification/metabolism ; Gossypium/growth &amp; development/*microbiology ; *Microbiota ; Plant Roots/growth &amp; development/microbiology ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; Water/analysis/metabolism ; }, abstract = {Climate change contributes to drought stress and subsequently affects crop growth, development, and yield. The microbial community, such as fungi and bacteria in the rhizosphere, is of special importance to plant productivity. In this study, soil collected from a cotton research field was used to grow cotton plants (Gossypium hirsutum cv. Jin668) under controlled environment conditions. Drought stress was applied at flowering stage, while control plants were regularly watered. At the same time, the soil without plants was also subjected to drought, while control pots were regularly watered. The soil was collected in sterilized tubes and microbial DNA was isolated and high-throughput sequencing of 16S rRNA genes was carried out. The alpha diversity of bacteria community significantly increased in the soil with cotton plants compared to the soil without cotton plants. Taxonomic analysis revealed that the bacterial community structure of the cotton rhizosphere predominantly consisted of the phyla Proteobacteria (31.7%), Actinobacteria (29.6%), Gemmatimonadetes (9.8%), Chloroflexi (9%), Cyanobacteria (5.6%), and Acidobacteria. In the drought-treated rhizosphere, Chloroflexi and Gemmatimonadetes were the dominant phyla. This study reveals that the cotton rhizosphere has a rich pool of bacterial communities even under drought stress, and which may improve drought tolerance in plants. These data will underpin future improvement of drought tolerance of cotton via the soil microbial community.}, }
@article {pmid30195549, year = {2018}, author = {Jamar, G and Santamarina, AB and Dias, GC and Masquio, DCL and de Rosso, VV and Pisani, LP}, title = {Relationship between fatty acids intake and Clostridium coccoides in obese individuals with metabolic syndrome.}, journal = {Food research international (Ottawa, Ont.)}, volume = {113}, number = {}, pages = {86-92}, doi = {10.1016/j.foodres.2018.07.002}, pmid = {30195549}, issn = {1873-7145}, mesh = {Adult ; Body Mass Index ; Clostridium/*isolation &amp; purification ; *Diet ; Dietary Fats/administration &amp; dosage ; Dyslipidemias/etiology ; Fatty Acids/*administration &amp; dosage ; Fatty Acids, Monounsaturated/administration &amp; dosage ; Fatty Acids, Unsaturated/administration &amp; dosage ; Feces/microbiology ; Feeding Behavior ; Female ; Gastrointestinal Microbiome/drug effects ; Humans ; Male ; Metabolic Syndrome/complications/*microbiology/physiopathology ; Middle Aged ; Obesity/complications/*microbiology/physiopathology ; Risk Factors ; }, abstract = {Dietary habits exert a strong influence on gut microbial composition and may result in an imbalance of gut microbes, representing a predisposition to obesity and metabolic disorders. We aimed to investigate a potential relationship between gut bacterial species and metabolic parameters and dietary intake. Bacterial DNA was extracted from feces of 34 obese subjects with and without metabolic syndrome (MS and n-MS group, respectively). We then used real-time polymerase chain reaction (qPCR) for quantifying specific sequences to Akkermansia muciniphila, Bifidobacterium spp., Clostridium coccoides, and Lactobacillus spp. and analyzed them with respect to clinical characteristics. Our data showed that the MS group had a 6.7-fold higher level of C. coccoides in their stool samples than the n-MS group. The abundance of C. coccoides was positively correlated with a high intake of monounsaturated fatty acids (MUFA) and polyunsaturated fatty acids. Furthermore, an excessive dietary level of MUFA was identified as a predictor of C. coccoides abundance. Alterations in the gut microbial ecology were positively correlated with levels of triacylglycerol in obese individuals. Therefore, the type and quantity of dietary fat may alter the gut microbial ecology in obese individuals with MS and may predispose them to dyslipidemia.}, }
@article {pmid30195522, year = {2018}, author = {Nash, V and Ranadheera, CS and Georgousopoulou, EN and Mellor, DD and Panagiotakos, DB and McKune, AJ and Kellett, J and Naumovski, N}, title = {The effects of grape and red wine polyphenols on gut microbiota - A systematic review.}, journal = {Food research international (Ottawa, Ont.)}, volume = {113}, number = {}, pages = {277-287}, doi = {10.1016/j.foodres.2018.07.019}, pmid = {30195522}, issn = {1873-7145}, mesh = {Adult ; Aged ; Bacteria/drug effects/metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/drug effects/physiology ; Humans ; Male ; Middle Aged ; *Plant Extracts/chemistry/pharmacology ; *Polyphenols/chemistry/metabolism/pharmacology ; Vitis/*chemistry ; Wine/*analysis ; Young Adult ; }, abstract = {There is a growing body of evidence implicating the gut 'microbiome' role in overall human health. Bacterial species belonging to the genera Lactobacillus and Bifidobacterium are generally considered to be beneficial and are commonly used in probiotic applications, whereas increases in some genera including Clostridum, Eubacterium and Bacteroides are implicated in negative health outcomes. Dietary polyphenols are bioactive compounds that have been found to increase the numbers of beneficial bacteria and antimicrobial actions against pathogenic bacteria, however most studies have been conducted in animal models or in-vitro colonic models. The aim of this systematic review was to provide an overview of recent trials on the effect of dietary grape and red wine polyphenols on the gut microbiota in humans. Following PRISMA guidelines, a systematic review was conducted of electronic databases (PubMed, CINAHL, Cochrane Library, Wed of Science and Scopus) to identify human intervention trials examining the effect of grape or wine polyphenols on gut microbiota. Seven trials met the inclusion criteria. One study looked at changes in gut microbiota following the ingestion of de-alcoholised red wine or red wine, and six studies referred to gut microbiota as intermediates in formation of phenolic metabolites. All studies confirmed that ingested polyphenols from grape and red wine, were modulated by gut microbiota, increasing numbers of polyphenolic metabolites which were found in blood, urine, ileal fluid and faeces. Intake of polyphenols derived from grape and red wine can modulate gut microbiota and contribute to beneficial microbial ecology that can enhance human health benefits. Additionally, grape and red wine polyphenols were modulated by the gut microbiota and there is a potential for a two-way relationship between the gut microbiota and polyphenolic compounds. Nevertheless, additional research is required to fully understand the complex relationship between gut microbiota and dietary polyphenols before any health claims can be made in relation to human health.}, }
@article {pmid30195437, year = {2018}, author = {Medlock, GL and Carey, MA and McDuffie, DG and Mundy, MB and Giallourou, N and Swann, JR and Kolling, GL and Papin, JA}, title = {Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota.}, journal = {Cell systems}, volume = {7}, number = {3}, pages = {245-257.e7}, pmid = {30195437}, issn = {2405-4712}, support = {R01 GM108501/GM/NIGMS NIH HHS/United States ; S06 GM008136/GM/NIGMS NIH HHS/United States ; T32 GM008136/GM/NIGMS NIH HHS/United States ; T32 LM012416/LM/NLM NIH HHS/United States ; }, mesh = {Animals ; Clostridium/*physiology ; Coculture Techniques ; Computer Simulation ; Eubacterium/*physiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Lactobacillus/*physiology ; Metabolic Networks and Pathways ; Metabolome ; Mice ; *Microbial Interactions ; Models, Biological ; Models, Theoretical ; Principal Component Analysis ; }, abstract = {The diversity and number of species present within microbial communities create the potential for a multitude of interspecies metabolic interactions. Here, we develop, apply, and experimentally test a framework for inferring metabolic mechanisms associated with interspecies interactions. We perform pairwise growth and metabolome profiling of co-cultures of strains from a model mouse microbiota. We then apply our framework to dissect emergent metabolic behaviors that occur in co-culture. Based on one of the inferences from this framework, we identify and interrogate an amino acid cross-feeding interaction and validate that the proposed interaction leads to a growth benefit in vitro. Our results reveal the type and extent of emergent metabolic behavior in microbial communities composed of gut microbes. We focus on growth-modulating interactions, but the framework can be applied to interspecies interactions that modulate any phenotype of interest within microbial communities.}, }
@article {pmid30194506, year = {2019}, author = {da Silveira, APD and Iório, RPF and Marcos, FCC and Fernandes, AO and de Souza, SACD and Kuramae, EE and Cipriano, MAP}, title = {Exploitation of new endophytic bacteria and their ability to promote sugarcane growth and nitrogen nutrition.}, journal = {Antonie van Leeuwenhoek}, volume = {112}, number = {2}, pages = {283-295}, doi = {10.1007/s10482-018-1157-y}, pmid = {30194506}, issn = {1572-9699}, support = {2008/56147-1//FAPESP/ ; 456420/2013-4//CNPq/NWO/ ; 729.004.013//NWO/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Endophytes/classification/genetics/*isolation &amp; purification/metabolism ; Nitrogen/*metabolism ; Phylogeny ; Saccharum/*growth &amp; development/metabolism/*microbiology ; Siderophores/metabolism ; }, abstract = {Few studies have evaluated endophytic bacteria in relation to plant growth promotion, nitrogen uptake and biological control. The aim of this study was to molecularly and physiologically characterize thirteen endophytic bacteria strains, evaluate their biological control properties and their ability to promote plant growth and plant N nutrition. All the strains produced indole acetic acid and promoted increase of plant biomass, N accumulative amount and N-use efficiency index. None of the strains carries the nifH gene. Four strains stimulated plant nitrate reductase activity, four solubilized phosphate, nine produced siderophores and none produced HCN. Seven strains inhibited Bipolaris sacchari growth and one was antagonistic to Ceratocystis paradoxa. The pathogens were inhibited by the production of diffusible and volatile metabolites by the bacterial strains. Moreover, this is the first study to demonstrate the effect of Delftia acidovorans on sugarcane plant growth, nitrogen metabolism improvement and antagonism to B. sacchari. The most efficient strains in promoting plant growth and exhibiting antagonistic activities towards fungal pathogens were Herbaspirillum frinsingense (IAC-BECa-152) and three Pantoea dispersa strains (IAC-BECa-128, IAC-BECa-129, and IAC-BECa-132). These bacteria show potential to be used as inoculants for sustainable agricultural management, mainly at the seedling production phase.}, }
@article {pmid30194484, year = {2019}, author = {Szubert-Kruszyńska, A and Stańczak, J and Cieniuch, S and Podsiadły, E and Postawa, T and Michalik, J}, title = {Correction to: Bartonella and Rickettsia Infections in Haematophagous Spinturnix myoti Mites (Acari: Mesostigmata) and their Bat Host, Myotis myotis (Yangochiroptera: Vespertilionidae), from Poland.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {769}, doi = {10.1007/s00248-018-1259-0}, pmid = {30194484}, issn = {1432-184X}, abstract = {The original version of this article published online (27 August 2018) unfortunately contained a mistake regarding an affiliation of Dr. Edyta Podsiadły, one of the authors.}, }
@article {pmid30194483, year = {2019}, author = {Eichmeier, A and Kiss, T and Necas, T and Penazova, E and Tekielska, D and Bohunicka, M and Valentova, L and Cmejla, R and Morais, D and Baldrian, P}, title = {High-Throughput Sequencing Analysis of the Bacterial Community in Stone Fruit Phloem Tissues Infected by "Candidatus Phytoplasma prunorum".}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {664-675}, pmid = {30194483}, issn = {1432-184X}, support = {QJ1510352//Ministry of Agriculture of the Czech Republic/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; LM2015042//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Fruit/microbiology ; High-Throughput Nucleotide Sequencing ; Phloem/*microbiology ; Phytoplasma/*physiology ; Plant Diseases/*microbiology ; Prunus/*microbiology ; }, abstract = {"Candidatus Phytoplasma prunorum" (CPp) is a highly destructive phytopathogenic agent in many stone fruit-growing regions in Europe and the surrounding countries. In this work, we focused on documenting entire bacterial community in the phloem tissues of 60 stone fruit trees. Nested PCR and two real-time PCR assays were used to select CPp-positive (group A) and CPp-negative samples (group B). Afterwards, high-throughput amplicon sequencing was performed to assess bacterial community compositions in phloem tissues. The bacterial composition in phloem tissue consisted of 118 distinct genera, represented mainly by Pseudomonas, Acinetobacter, Methylobacterium, Sphingomonas, and Rhizobium. Statistics showed that CPp influenced the bacterial composition of infected plants (group A) and that the bacterial community depended on the geographical origin of the sample. This is the first work focusing on an analysis of the influence of CPp on the bacteria coexisting in the phloem tissues of stone fruit trees.}, }
@article {pmid30194105, year = {2018}, author = {Cordovez, V and Schop, S and Hordijk, K and Dupré de Boulois, H and Coppens, F and Hanssen, I and Raaijmakers, JM and Carrión, VJ}, title = {Priming of Plant Growth Promotion by Volatiles of Root-Associated Microbacterium spp.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {22}, pages = {}, pmid = {30194105}, issn = {1098-5336}, mesh = {Actinobacteria/genetics/isolation &amp; purification/*metabolism ; Arabidopsis/growth &amp; development/*microbiology ; Lactuca/growth &amp; development/*microbiology ; Solanum lycopersicum/growth &amp; development/*microbiology ; Mass Spectrometry ; Nitrogen/metabolism ; Seedlings/growth &amp; development/microbiology ; Sulfur Compounds/chemistry/*metabolism ; Volatile Organic Compounds/chemistry/*metabolism ; }, abstract = {Volatile compounds produced by plant-associated microorganisms represent a diverse resource to promote plant growth and health. Here, we investigated the effect of volatiles from root-associated Microbacterium species on plant growth and development. Volatiles of eight strains induced significant increases in shoot and root biomass of Arabidopsis but differed in their effects on root architecture. Microbacterium strain EC8 also enhanced root and shoot biomass of lettuce and tomato. Biomass increases were also observed for plants exposed only briefly to volatiles from EC8 prior to transplantation of the seedlings to soil. These results indicate that volatiles from EC8 can prime plants for growth promotion without direct and prolonged contact. We further showed that the induction of plant growth promotion is tissue specific; that is, exposure of roots to volatiles from EC8 led to an increase in plant biomass, whereas shoot exposure resulted in no or less growth promotion. Gas chromatography-quadrupole time of flight mass spectometry (GC-QTOF-MS) analysis revealed that EC8 produces a wide array of sulfur-containing compounds, as well as ketones. Bioassays with synthetic sulfur volatile compounds revealed that the plant growth response to dimethyl trisulfide was concentration-dependent, with a significant increase in shoot weight at 1 μM and negative effects on plant biomass at concentrations higher than 1 mM. Genome-wide transcriptome analysis of volatile-exposed Arabidopsis seedlings showed upregulation of genes involved in assimilation and transport of sulfate and nitrate. Collectively, these results show that root-associated Microbacterium primes plants, via the roots, for growth promotion, most likely via modulation of sulfur and nitrogen metabolism.IMPORTANCE In the past decade, various studies have described the effects of microbial volatiles on other (micro)organisms in vitro, but their broad-spectrum activity in vivo and the mechanisms underlying volatile-mediated plant growth promotion have not been addressed in detail. Here, we revealed that volatiles from root-associated bacteria of the genus Microbacterium can enhance the growth of different plant species and can prime plants for growth promotion without direct and prolonged contact between the bacterium and the plant. Collectively, these results provide new opportunities for sustainable agriculture and horticulture by exposing roots of plants only briefly to a specific blend of microbial volatile compounds prior to transplantation of the seedlings to the greenhouse or field. This strategy has no need for large-scale introduction or root colonization and survival of the microbial inoculant.}, }
@article {pmid30192223, year = {2018}, author = {Borel, N and Bavoil, P and Greub, G and Horn, M}, title = {International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Chlamydiae. Minutes of the closed meeting, 9 April 2017, Charlotte, USA.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {68}, number = {1}, pages = {3369-3370}, doi = {10.1099/ijsem.0.003010}, pmid = {30192223}, issn = {1466-5034}, }
@article {pmid30191255, year = {2019}, author = {Tarnecki, AM and Brennan, NP and Schloesser, RW and Rhody, NR}, title = {Shifts in the Skin-Associated Microbiota of Hatchery-Reared Common Snook Centropomus undecimalis During Acclimation to the Wild.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {770-781}, pmid = {30191255}, issn = {1432-184X}, support = {R/LR-A-54//Florida Sea Grant, University of Florida/ ; }, mesh = {Acclimatization ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; *Microbiota ; Perciformes/*microbiology/*physiology ; Phylogeny ; Skin/*microbiology ; }, abstract = {The skin-associated microbiota of fish competes against pathogens for space and nutrients, preventing colonization by harmful bacteria encountered during environmental transitions such as those faced during stock enhancement. Thus, alterations in bacterial community structure during release of cultured fish have important implications for health of these individuals. This study investigated microbiota structure during acclimation of juvenile hatchery-reared common snook Centropomus undecimalis to the wild by comparing skin-associated microflora among snook in captivity, after 48 h of acclimation at release sites, and from the wild. After two days of acclimation, the microbiota of hatchery-reared snook mirrored that observed on wild snook. Relative abundances of potential pathogens were higher in captive fish, whereas acclimated and wild fish harbored bacterial taxa influenced by geographical factors and water quality at release sites. Predicted microbiota function of acclimated and wild fish showed higher production of protective amino acids and antimicrobials, identifying a mechanism for microbial supplementation of the immune defense of these fish. The two-day transition to wild-type microbiota suggests a temporal scale of hours associated with bacterial succession indicating that the microbiota, whose structure is vital to fish health, aids in acclimation of fish to new environments during stock enhancement efforts.}, }
@article {pmid30190715, year = {2018}, author = {Safonov, AV and Babich, TL and Sokolova, DS and Grouzdev, DS and Tourova, TP and Poltaraus, AB and Zakharova, EV and Merkel, AY and Novikov, AP and Nazina, TN}, title = {Microbial Community and in situ Bioremediation of Groundwater by Nitrate Removal in the Zone of a Radioactive Waste Surface Repository.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1985}, pmid = {30190715}, issn = {1664-302X}, abstract = {The goal of the present work was to investigate the physicochemical and radiochemical conditions and the composition of the microbial community in the groundwater of a suspended surface repository for radioactive waste (Russia) and to determine the possibility of in situ groundwater bioremediation by removal of nitrate ions. Groundwater in the repository area (10-m depth) had elevated concentrations of strontium, tritium, nitrate, sulfate, and bicarbonate ions. High-throughput sequencing of the V3-V4/V4 region of the 16S rRNA gene revealed the presence of members of the phyla Proteobacteria (genera Acidovorax, Simplicispira, Thermomonas, Thiobacillus, Pseudomonas, Brevundimonas, and uncultured Oxalobacteraceae), Firmicutes (genera Bacillus and Paenibacillus), and Actinobacteria (Candidatus Planktophila, Gaiella). Canonical correspondence analysis suggested that major contaminant - nitrate, uranium, and sulfate shaped the composition of groundwater microbial community. Groundwater samples contained culturable aerobic organotrophic, as well as anaerobic fermenting, iron-reducing, and denitrifying bacteria. Pure cultures of 33 bacterial strains belonging to 15 genera were isolated. Members of the genera Pseudomonas, Rhizobium, Cupriavidus, Shewanella, Ensifer, and Thermomonas reduced nitrate to nitrite and/or dinitrogen. Application of specific primers revealed the nirS and nirK genes encoding nitrite reductases in bacteria of the genera Pseudomonas, Rhizobium, and Ensifer. Nitrate reduction by pure bacterial cultures resulted in decreased ambient Eh. Among the organic substrates tested, sodium acetate and milk whey were the best for stimulation of denitrification by the microcosms with groundwater microorganisms. Injection of these substrates into the subterranean horizon (single-well push-pull test) resulted in temporary removal of nitrate ions in the area of the suspended radioactive waste repository and confirmed the possibility for in situ application of this method for bioremediation.}, }
@article {pmid30190707, year = {2018}, author = {Hicks, N and Liu, X and Gregory, R and Kenny, J and Lucaci, A and Lenzi, L and Paterson, DM and Duncan, KR}, title = {Temperature Driven Changes in Benthic Bacterial Diversity Influences Biogeochemical Cycling in Coastal Sediments.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1730}, pmid = {30190707}, issn = {1664-302X}, abstract = {Marine sediments are important sites for global biogeochemical cycling, mediated by macrofauna and microalgae. However, it is the microorganisms that drive these key processes. There is strong evidence that coastal benthic habitats will be affected by changing environmental variables (rising temperature, elevated CO2), and research has generally focused on the impact on macrofaunal biodiversity and ecosystem services. Despite their importance, there is less understanding of how microbial community assemblages will respond to environmental changes. In this study, a manipulative mesocosm experiment was employed, using next-generation sequencing to assess changes in microbial communities under future environmental change scenarios. Illumina sequencing generated over 11 million 16S rRNA gene sequences (using a primer set biased toward bacteria) and revealed Bacteroidetes and Proteobacteria dominated the total bacterial community of sediment samples. In this study, the sequencing coverage and depth revealed clear changes in species abundance within some phyla. Bacterial community composition was correlated with simulated environmental conditions, and species level community composition was significantly influenced by the mean temperature of the environmental regime (p = 0.002), but not by variation in CO2 or diurnal temperature variation. Species level changes with increasing mean temperature corresponded with changes in NH4 concentration, suggesting there is no functional redundancy in microbial communities for nitrogen cycling. Marine coastal biogeochemical cycling under future environmental conditions is likely to be driven by changes in nutrient availability as a direct result of microbial activity.}, }
@article {pmid30188995, year = {2018}, author = {Shibl, AA and Ngugi, DK and Talarmin, A and Thompson, LR and Blom, J and Stingl, U}, title = {The genome of a novel isolate of Prochlorococcus from the Red Sea contains transcribed genes for compatible solute biosynthesis.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {12}, pages = {}, doi = {10.1093/femsec/fiy182}, pmid = {30188995}, issn = {1574-6941}, mesh = {Genome, Bacterial/*genetics ; Genomics ; Glucosides/biosynthesis/genetics ; Indian Ocean ; Microscopy, Electron, Transmission ; Phylogeny ; Prochlorococcus/*classification/*genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Salinity ; Synechococcus/genetics ; }, abstract = {Marine microbes possess genomic and physiological adaptations to cope with varying environmental conditions. So far, the effects of high salinity on the most abundant marine photoautotrophic organism, Prochlorococcus, in marine oligotrophic environments, are mostly unknown. Here, we report the isolation of a new Prochlorococcus strain (RSP50) belonging to high-light (HL) clade II from the Red Sea, one of the warmest and most saline bodies of water in the global oceans. A comparative genomic analysis identified a set of 59 genes that were exclusive to RSP50 relative to currently available Prochlorococcus genomes, the majority of which (70%) encode for hypothetical proteins of unknown function. However, three of the unique genes encode for a complete pathway for the biosynthesis of the compatible solute glucosylglycerol, and are homologous to enzymes found in the sister lineage Synechococcus. Metatranscriptomic analyses of this metabolic pathway in the water column of the Red Sea revealed that the corresponding genes were constitutively transcribed, independent of depth and light, suggesting that osmoregulation using glucosylglycerol is a general feature of HL II Prochlorococcus in the Red Sea.}, }
@article {pmid30188282, year = {2018}, author = {Coats, ER and Eyre, K and Bryant, C and Woodland, T and Brinkman, CK}, title = {Assessing the Effects of RAS Fermentation on EBPR Performance and Associated Microbial Ecology.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {90}, number = {7}, pages = {659-671}, doi = {10.2175/106143017X15131012153130}, pmid = {30188282}, issn = {1061-4303}, mesh = {Anaerobiosis ; Carbon/metabolism ; Fatty Acids, Volatile/metabolism ; Fermentation ; Glycogen/metabolism ; Nitrates/metabolism ; Phosphorus/*metabolism ; Sewage/chemistry/*microbiology ; Waste Disposal, Fluid/*methods ; }, abstract = {Enhanced biological phosphorus removal (EBPR) is an engineered water resource recovery facility (WRRF) process configuration that can produce effluent P < 0.5 mg/L. To consistently achieve low effluent P concentrations, EBPR requires volatile fatty acids (VFAs) to induce requisite biochemical reactions. Moreover, returned activated sludge (RAS) nitrate concentrations must be minimized. Returned activated sludge fermentation can potentially address process needs. However, research detailed herein highlights concerns with RAS fermentation integrated with EBPR. Under 2 and 4 hours of RAS fermentation periods, no consequential VFA production was observed; similar results were observed in batch tests with RAS from a full-scale EBPR WRRF. More critically, EBPR performance was poor, with average effluent concentrations of 1.0 to 2.4 mg/L. Furthermore, the glycogen accumulating organism (GAO) fraction under RAS fermentation was 4.3 to 8.7 times higher than in a conventional EBPR mixed microbial consortium (MMC). Integrated RAS fermentation-EBPR only performed well under "high" RAS nitrate; thus, should RAS fermentation be implemented, careful control to prevent anaerobic conditions in the fermentation zone is required.}, }
@article {pmid30187987, year = {2019}, author = {Hooper, R and Brealey, JC and van der Valk, T and Alberdi, A and Durban, JW and Fearnbach, H and Robertson, KM and Baird, RW and Bradley Hanson, M and Wade, P and Gilbert, MTP and Morin, PA and Wolf, JBW and Foote, AD and Guschanski, K}, title = {Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin.}, journal = {Molecular ecology}, volume = {28}, number = {2}, pages = {484-502}, pmid = {30187987}, issn = {1365-294X}, support = {//Lindblad Expeditions/National Geographic Conservation Fund/International ; ERCStG-336536//European Research Council/International ; DNRF94//Danish National Research Foundation/International ; //Antarctic Science Bursary/International ; //Welsh Government and Higher Education Funding Council for Wales through the S&#xea;r Cymru National Research Network for Low Carbon, Energy and Environment/International ; 663830//European Union's Horizon 2020 research and innovation programme under the Marie Sk&#x142;odowska-Curie/International ; SR17/1227//British Ecological Society/International ; 2016-00835//FORMAS/International ; 5051-00033//Danish Council for Independent Research-DFF/International ; R250-2017-1351//Lundbeckfonden/International ; }, mesh = {Animals ; Antarctic Regions ; Diatoms/genetics ; Geography ; *Metagenomics ; Microbiota/*genetics ; Skin/*microbiology ; Whale, Killer/*microbiology/parasitology ; }, abstract = {Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.}, }
@article {pmid30187089, year = {2019}, author = {Chan, YF and Chiang, KP and Ku, Y and Gong, GC}, title = {Abiotic and Biotic Factors Affecting the Ingestion Rates of Mixotrophic Nanoflagellates (Haptophyta).}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {607-615}, pmid = {30187089}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Feeding Behavior ; Haptophyta/chemistry/*physiology/radiation effects ; Kinetics ; Light ; Pacific Ocean ; }, abstract = {Mixotrophic haptophytes comprise one of several important groups of mixotrophic nanoflagellates in the pelagic environment. This study aimed to investigate if phagotrophy in mixotrophic haptophytes is regulated by light or other factors in the surface (SE) and bottom (BE) of the euphotic zone in the subtropical northwestern Pacific Ocean. We estimated the rates of bacterial ingestion by haptophytes using fluorescently labeled bacteria (FLBs) and fluorescence in situ hybridization. Haptophyte diversity and abundance were also investigated in the same sampling area. The annual mean abundance of haptophytes was 419 ± 85.6 cells mL[-1] in both SE and BE. Cells 3-5 μm in size were the dominant group in all haptophytes and accounted for majority of bacteria standing stock removed by haptophytes (53%). Most haptophyte ingestion rates (IRs) were not significantly different between the two layers (average SE ingestion rate: 12.5 ± 2.29 bac Hap[-1] h[-1]; BE: 14.7 ± 3.03 bac Hap[-1] h[-1]). Furthermore, the haptophyte IRs were negatively correlated with nitrate concentrations in the SE and positively correlated with bacterial abundances in the BE, which accounts for the significantly high IRs in August 2012 and 2013. These findings imply that mixotrophic haptophytes in this region had different factors affecting phagotrophy to adapt to the ambient light intensity alterations between SE and BE.}, }
@article {pmid30187088, year = {2019}, author = {Vallesi, A and Sjödin, A and Petrelli, D and Luporini, P and Taddei, AR and Thelaus, J and Öhrman, C and Nilsson, E and Di Giuseppe, G and Gutiérrez, G and Villalobo, E}, title = {A New Species of the γ-Proteobacterium Francisella, F. adeliensis Sp. Nov., Endocytobiont in an Antarctic Marine Ciliate and Potential Evolutionary Forerunner of Pathogenic Species.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {587-596}, pmid = {30187088}, issn = {1432-184X}, mesh = {Antarctic Regions ; DNA Transposable Elements ; Euplotes/*microbiology/physiology ; Francisella/classification/genetics/*isolation &amp; purification/physiology ; Genome, Bacterial ; Phylogeny ; Seawater/microbiology ; Symbiosis ; }, abstract = {The study of the draft genome of an Antarctic marine ciliate, Euplotes petzi, revealed foreign sequences of bacterial origin belonging to the γ-proteobacterium Francisella that includes pathogenic and environmental species. TEM and FISH analyses confirmed the presence of a Francisella endocytobiont in E. petzi. This endocytobiont was isolated and found to be a new species, named F. adeliensis sp. nov.. F. adeliensis grows well at wide ranges of temperature, salinity, and carbon dioxide concentrations implying that it may colonize new organisms living in deeply diversified habitats. The F. adeliensis genome includes the igl and pdp gene sets (pdpC and pdpE excepted) of the Francisella pathogenicity island needed for intracellular growth. Consistently with an F. adeliensis ancient symbiotic lifestyle, it also contains a single insertion-sequence element. Instead, it lacks genes for the biosynthesis of essential amino acids such as cysteine, lysine, methionine, and tyrosine. In a genome-based phylogenetic tree, F. adeliensis forms a new early branching clade, basal to the evolution of pathogenic species. The correlations of this clade with the other clades raise doubts about a genuine free-living nature of the environmental Francisella species isolated from natural and man-made environments, and suggest to look at F. adeliensis as a pioneer in the Francisella colonization of eukaryotic organisms.}, }
@article {pmid30186247, year = {2018}, author = {Olivares, M and Schüppel, V and Hassan, AM and Beaumont, M and Neyrinck, AM and Bindels, LB and Benítez-Páez, A and Sanz, Y and Haller, D and Holzer, P and Delzenne, NM}, title = {The Potential Role of the Dipeptidyl Peptidase-4-Like Activity From the Gut Microbiota on the Host Health.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1900}, pmid = {30186247}, issn = {1664-302X}, abstract = {The Dipeptidyl peptidase-4 (DPP-4) activity influences metabolic, behavioral and intestinal disorders through the cleavage of key hormones and peptides. Some studies describe the existence of human DPP-4 homologs in commensal bacteria, for instance in Prevotella or Lactobacillus. However, the role of the gut microbiota as a source of DPP-4-like activity has never been investigated. Through the comparison of the DPP-4 activity in the cecal content of germ-free mice (GFM) and gnotobiotic mice colonized with the gut microbiota of a healthy subject, we bring the proof of concept that a significant DPP-4-like activity occurs in the microbiota. By analyzing the existing literature, we propose that DPP-4-like activity encoded by the intestinal microbiome could constitute a novel mechanism to modulate protein digestion as well as host metabolism and behavior.}, }
@article {pmid30185512, year = {2018}, author = {Rohwer, RR and Hamilton, JJ and Newton, RJ and McMahon, KD}, title = {TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution.}, journal = {mSphere}, volume = {3}, number = {5}, pages = {}, pmid = {30185512}, issn = {2379-5042}, mesh = {Algorithms ; Animals ; Bacteria/*classification ; DNA, Bacterial/genetics ; Databases as Topic ; *Databases, Genetic ; Ecosystem ; Fresh Water/*microbiology ; *Metagenomics ; Mice ; *Microbial Consortia ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Taxonomy assignment of freshwater microbial communities is limited by the minimally curated phylogenies used for large taxonomy databases. Here we introduce TaxAss, a taxonomy assignment workflow that classifies 16S rRNA gene amplicon data using two taxonomy reference databases: a large comprehensive database and a small ecosystem-specific database rigorously curated by scientists within a field. We applied TaxAss to five different freshwater data sets using the comprehensive SILVA database and the freshwater-specific FreshTrain database. TaxAss increased the percentage of the data set classified compared to using only SILVA, especially at fine-resolution family to species taxon levels, while across the freshwater test data sets classifications increased by as much as 11 to 40% of total reads. A similar increase in classifications was not observed in a control mouse gut data set, which was not expected to contain freshwater bacteria. TaxAss also maintained taxonomic richness compared to using only the FreshTrain across all taxon levels from phylum to species. Without TaxAss, most organisms not represented in the FreshTrain were unclassified, but at fine taxon levels, incorrect classifications became significant. We validated TaxAss using simulated amplicon data derived from full-length clone libraries and found that 96 to 99% of test sequences were correctly classified at fine resolution. TaxAss splits a data set's sequences into two groups based on their percent identity to reference sequences in the ecosystem-specific database. Sequences with high similarity to sequences in the ecosystem-specific database are classified using that database, and the others are classified using the comprehensive database. TaxAss is free and open source and is available at https://www.github.com/McMahonLab/TaxAssIMPORTANCE Microbial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon data sets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at the phylum, class, and order levels lump ecologically distinct organisms together. To avoid this, many researchers define operational taxonomic units (OTUs) based on clustered sequences, sequence variants, or unique sequences. These fine-resolution groupings are more ecologically relevant, but OTU definitions are data set dependent and cannot be compared between data sets. Microbial ecologists studying freshwater have curated a small, ecosystem-specific taxonomy database to provide consistent and up-to-date terminology. We created TaxAss, a workflow that leverages this database to assign taxonomy. We found that TaxAss improves fine-resolution taxonomic classifications (family, genus, and species). Fine taxonomic groupings are more ecologically relevant, so they provide an alternative to OTU-based analyses that is consistent and comparable between data sets.}, }
@article {pmid30184128, year = {2018}, author = {Mangin, I and Dossou-Yovo, F and Lévêque, C and Dessoy, MV and Sawoo, O and Suau, A and Pochart, P}, title = {Oral administration of viable Bifidobacterium pseudolongum strain Patronus modified colonic microbiota and increased mucus layer thickness in rat.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {11}, pages = {}, doi = {10.1093/femsec/fiy177}, pmid = {30184128}, issn = {1574-6941}, mesh = {Administration, Oral ; Animals ; *Bifidobacterium/genetics/isolation &amp; purification ; Colon/*microbiology ; *Gastrointestinal Microbiome ; Male ; Mucus/*cytology ; RNA, Ribosomal, 16S/genetics ; Rats ; Verrucomicrobia/genetics/isolation &amp; purification ; }, abstract = {This study aimed at evaluating the alteration of the colonic microbiota and the changes in the mucus layer thickness induced by oral administration of living bifidobacteria in rats. The study was performed on rats fed with Bifidobacterium pseudolongum strain Patronus (1010 bacteria per day for 7 days). This bacterial administration led to a large increase of mucus thickness (57%, P < 0.05). Both quantitative PCR and high-throughput sequencing of bacterial 16S rRNA gene revealed a significant increase of the amount of the Bifidobacterium genus in the microbiota of rats fed with the strain Patronus, associated with a decrease of Akkermansia muciniphila. The increase in mucus thickness could be due to an increase of the bifidobacteria per se or via the decrease of A. muciniphila, a major mucin-degrading species. As the mucus layer plays an essential role in gut protection, our data enlighten the importance of studying mucus-degrading bacteria for understanding the underlying etiology of diseases such as intestinal bowel diseases and to implement new therapeutic strategies.}, }
@article {pmid30181663, year = {2018}, author = {Castelle, CJ and Brown, CT and Anantharaman, K and Probst, AJ and Huang, RH and Banfield, JF}, title = {Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {10}, pages = {629-645}, doi = {10.1038/s41579-018-0076-2}, pmid = {30181663}, issn = {1740-1534}, mesh = {Anaerobiosis ; *Archaea/genetics/metabolism/physiology ; *Bacteria/genetics/metabolism ; Bacteria, Anaerobic ; Bacterial Physiological Phenomena/*genetics ; Cell Size ; Genome, Archaeal/genetics/physiology ; Genome, Bacterial/genetics/physiology ; Phylogeny ; Symbiosis ; }, abstract = {Candidate phyla radiation (CPR) bacteria and DPANN (an acronym of the names of the first included phyla) archaea are massive radiations of organisms that are widely distributed across Earth's environments, yet we know little about them. Initial indications are that they are consistently distinct from essentially all other bacteria and archaea owing to their small cell and genome sizes, limited metabolic capacities and often episymbiotic associations with other bacteria and archaea. In this Analysis, we investigate their biology and variations in metabolic capacities by analysis of approximately 1,000 genomes reconstructed from several metagenomics-based studies. We find that they are not monolithic in terms of metabolism but rather harbour a diversity of capacities consistent with a range of lifestyles and degrees of dependence on other organisms. Notably, however, certain CPR and DPANN groups seem to have exceedingly minimal biosynthetic capacities, whereas others could potentially be free living. Understanding of these microorganisms is important from the perspective of evolutionary studies and because their interactions with other organisms are likely to shape natural microbiome function.}, }
@article {pmid30180359, year = {2019}, author = {Evans, SE and Dueker, ME and Logan, JR and Weathers, KC}, title = {The biology of fog: results from coastal Maine and Namib Desert reveal common drivers of fog microbial composition.}, journal = {The Science of the total environment}, volume = {647}, number = {}, pages = {1547-1556}, doi = {10.1016/j.scitotenv.2018.08.045}, pmid = {30180359}, issn = {1879-1026}, mesh = {*Air Microbiology ; *Desert Climate ; Environmental Monitoring ; Fungi/*growth &amp; development ; Maine ; Namibia ; Soil Microbiology ; *Weather ; }, abstract = {Fog supplies water and nutrients to systems ranging from coastal forests to inland deserts. Fog droplets can also contain bacterial and fungal aerosols, but our understanding of fog biology is limited. Using metagenomic tools and culturing, we provide a unique look at fungal and bacterial communities in fog at two fog-dominated sites: coastal Maine (USA) and the Namib Desert (Namibia). Microbial communities in the fog at both sites were diverse, distinct from clear aerosols, and influenced by both soil and marine sources. Fog from both sites contained Actinobacteria and Firmicutes, commonly soil- and air-associated phyla, but also contained bacterial taxa associated with marine environments including Cyanobacteria, Oceanospirillales, Novosphingobium, Pseudoalteromonas, and Bradyrhizobiaceae. Marine influence on fog communities was greatest near the coast, but still evident in Namib fogs 50 km inland. In both systems, differences between pre- and post-fog aerosol communities suggest that fog events can significantly alter microbial aerosol diversity and composition. Fog is likely to enhance viability of transported microbes and facilitate their deposition, making fog biology ecologically important in fog-dominated environments. Fog may introduce novel species to terrestrial ecosystems, including human and plant pathogens, warranting further work on the drivers of this important and underrecognized aerobiological transfer between marine and terrestrial systems.}, }
@article {pmid30180347, year = {2019}, author = {Urra, J and Alkorta, I and Mijangos, I and Epelde, L and Garbisu, C}, title = {Application of sewage sludge to agricultural soil increases the abundance of antibiotic resistance genes without altering the composition of prokaryotic communities.}, journal = {The Science of the total environment}, volume = {647}, number = {}, pages = {1410-1420}, doi = {10.1016/j.scitotenv.2018.08.092}, pmid = {30180347}, issn = {1879-1026}, mesh = {Agriculture/*methods ; Anti-Bacterial Agents ; Drug Resistance, Microbial/*genetics ; Humans ; Metals, Heavy ; Sewage ; Soil ; *Soil Microbiology ; Soil Pollutants ; Waste Disposal, Fluid/*methods ; }, abstract = {The application of sewage sludge as soil amendment is a common agricultural practice. However, wastewater treatment plants, sewage sludge and sewage sludge-amended soils have been reported as hotspots for the appearance and dissemination of antibiotic resistance, driven, among other factors, by selection pressure exerted by co-exposure to antibiotics and heavy metals. To address this threat to environmental and human health, soil samples from a long-term (24 years) field experiment, carried out to study the impact of thermally dried and anaerobically digested sewage sludge (at different doses and frequencies of application) on agricultural soil quality, were investigated for the presence of genes encoding antibiotic resistance (ARGs) and mobile genetic elements (MGEs). Sewage sludge-induced changes in specific soil physicochemical and microbial properties, as indicators of soil quality, were also investigated. The application of sewage sludge increased the total concentration of copper and zinc in amended soils, but without affecting the bioavailability of these metals, possibly due to the high values of soil pH and organic matter content. Soil microbal quality, as reflected by the value of the Soil Quality Index, was higher in sewage sludge-amended soils. Similarly, the application of sewage sludge increased soil microbial activity and biomass, as well as the abundance of ARGs and MGE genes, posing a risk of dissemination of antibiotic resistance. In contrast, the composition of soil prokaryotic communities was not significantly altered by the application of sewage sludge. We found correlation between soil Cu and Zn concentrations and the abundance of ARGs and MGE genes. It was concluded that sewage sludge-derived amendments must be properly treated and managed if they are to be applied to agricultural soil.}, }
@article {pmid30179784, year = {2018}, author = {Perez, S and Czerner, M and Patat, ML and Zaritzky, NE and Murialdo, SE and Yeannes, MI}, title = {Monitoring the characteristics of cultivable halophilic microbial community during salted-ripened anchovy (Engraulis anchoita) production.}, journal = {International journal of food microbiology}, volume = {286}, number = {}, pages = {179-189}, doi = {10.1016/j.ijfoodmicro.2018.08.013}, pmid = {30179784}, issn = {1879-3460}, mesh = {Animals ; Bacteria/*growth &amp; development ; Bacterial Load/*drug effects ; Fishes/*microbiology ; Hydrogen Sulfide/metabolism ; Indoles/metabolism ; Salts/*pharmacology ; Sodium Chloride/*pharmacology ; }, abstract = {The halophilic microbial community of the salted-ripened anchovy process was studied. Samples from raw materials (salt and fresh anchovies) and from the stages of brining and ripening were collected and analyzed for their bacterial counts at 15 and 20% NaCl. No halophilic colonies were found in fresh anchovy and counts of about 10[3] CFU/g were determined in salt samples. A fluctuation of bacterial counts during the process was found. At the end of brining, ~10[4] CFU/g were determined in anchovy samples and this value was reduced to not detectable counts at the beginning of the ripening stage. After one month, counts increased to ~10[4] CFU/g and remained stable until the end of the process. From each sample, colonies having different morphotypes were isolated and submitted to a macro and microscopic characterization, a study of salt requirement for growth, and biochemical and phenotypic tests. The results were submitted to Univariate, Bivariate and Multiple Correspondence Factorial Analysis (MCFA). A total of 79 colonies were isolated during the salting-ripening anchovy process. Among the isolates, about 40-50% was positive for indole production and lipolytic activity and a 25% showed ability to produce H2S and proteolytic capacity. Proteolytic and lipolytic activities were well balanced along the process and resulted independent from the isolation stage, which is a desirable condition due to the contribution of microbial proteolysis and lipolysis to the development of texture and final aroma, respectively. H2S and indole producers practically were not detected during ripening. This fact is important because indole and H2S are associated with the development of off-flavors and spoilage in salted fish products. MFCA and Cluster Analyses complemented the Bivariate Analyses. The factor map showed proximity between the isolates from salt samples and from ripening. Isolates were statistically clustered in two groups. Cluster 1 grouped non-desirable activities (H2S and indole production) with cultures proceeding from brining whereas Cluster 2 related isolates mainly from salt samples and during ripening with some desirable microbial capacities (Cytochrome oxidase activity and non-H2S and non-indole production). These results would indicate that during the ripening process of salted anchovies, a natural selection of beneficial microorganisms for the development of the typical product sensory attributes occurred.}, }
@article {pmid30179231, year = {2018}, author = {Berube, PM and Biller, SJ and Hackl, T and Hogle, SL and Satinsky, BM and Becker, JW and Braakman, R and Collins, SB and Kelly, L and Berta-Thompson, J and Coe, A and Bergauer, K and Bouman, HA and Browning, TJ and De Corte, D and Hassler, C and Hulata, Y and Jacquot, JE and Maas, EW and Reinthaler, T and Sintes, E and Yokokawa, T and Lindell, D and Stepanauskas, R and Chisholm, SW}, title = {Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180154}, pmid = {30179231}, issn = {2052-4463}, mesh = {Archaea/*genetics ; *Genome, Archaeal ; *Genome, Bacterial ; *Genome, Viral ; Prochlorococcus/*genetics ; Seawater ; Single-Cell Analysis ; Synechococcus/*genetics ; Viruses/*genetics ; Water Microbiology ; }, abstract = {Prochlorococcus and Synechococcus are the dominant primary producers in marine ecosystems and perform a significant fraction of ocean carbon fixation. These cyanobacteria interact with a diverse microbial community that coexists with them. Comparative genomics of cultivated isolates has helped address questions regarding patterns of evolution and diversity among microbes, but the fraction that can be cultivated is miniscule compared to the diversity in the wild. To further probe the diversity of these groups and extend the utility of reference sequence databases, we report a data set of single cell genomes for 489 Prochlorococcus, 50 Synechococcus, 9 extracellular virus particles, and 190 additional microorganisms from a diverse range of bacterial, archaeal, and viral groups. Many of these uncultivated single cell genomes are derived from samples obtained on GEOTRACES cruises and at well-studied oceanographic stations, each with extensive suites of physical, chemical, and biological measurements. The genomic data reported here greatly increases the number of available Prochlorococcus genomes and will facilitate studies on evolutionary biology, microbial ecology, and biological oceanography.}, }
@article {pmid30178561, year = {2018}, author = {Kilian, M}, title = {The oral microbiome - friend or foe?.}, journal = {European journal of oral sciences}, volume = {126 Suppl 1}, number = {}, pages = {5-12}, doi = {10.1111/eos.12527}, pmid = {30178561}, issn = {1600-0722}, mesh = {Dysbiosis/microbiology ; Humans ; *Microbiota/physiology ; Mouth/*microbiology ; Streptococcus/metabolism ; }, abstract = {The microbiome and the human body constitute an integrated superorganism, which is the result of millions of years of coevolution with mutual adaptation and functional integration, and confers significant benefits for both parties. This evolutionary process has resulted in a highly diverse oral microbiome, which covers the full spectrum of acidogenic, aciduric, inflammatory, and anti-inflammatory properties. The relative proportions of members of the microbiome are affected by factors associated with modern life, such as general diet patterns, sugar consumption, tobacco smoking, oral hygiene, use of antibiotics and other antimicrobials, and vaccines. A perturbed balance in the oral microbiome may result in caries, periodontal disease, or candidiasis, and oral bacteria passively transferred to normally sterile parts of the body may cause extra-oral infections. Nevertheless, it should never be our goal to eliminate the oral microbiome, but rather we have to develop ways to re-establish a harmonious coexistence that is lost because of the modern lifestyle. With regard to oral diseases, this goal can normally be achieved by optimal oral hygiene, exposure to fluoride, reduction of sucrose consumption, stimulation of our innate immune defense, smoking cessation, and control of diabetes.}, }
@article {pmid30178387, year = {2019}, author = {Xu, WF and Ren, HS and Ou, T and Lei, T and Wei, JH and Huang, CS and Li, T and Strobel, G and Zhou, ZY and Xie, J}, title = {Genomic and Functional Characterization of the Endophytic Bacillus subtilis 7PJ-16 Strain, a Potential Biocontrol Agent of Mulberry Fruit Sclerotiniose.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {651-663}, pmid = {30178387}, issn = {1432-184X}, support = {31601678//National Natural Science Foundation of China/ ; XDJK2018D020//Fundamental Research Funds for the Central Universities/ ; cstc2015jcyjys80001//Natural Science Foundation of Chongqing/ ; }, mesh = {*Antibiosis ; Ascomycota/physiology ; Bacillus subtilis/*genetics/physiology ; Bacteriocins/genetics/metabolism ; Biological Control Agents/isolation &amp; purification/metabolism ; Endophytes/*genetics/isolation &amp; purification/physiology ; Fruit/microbiology ; Genome, Bacterial ; Genomics ; Morus/*microbiology ; Peptides, Cyclic/genetics/metabolism ; Plant Diseases/microbiology/*prevention &amp; control ; }, abstract = {Bacillus sp. 7PJ-16, an endophytic bacterium isolated from a healthy mulberry stem and previously identified as Bacillus tequilensis 7PJ-16, exhibits strong antifungal activity and has the capacity to promote plant growth. This strain was studied for its effectiveness as a biocontrol agent to reduce mulberry fruit sclerotiniose in the field and as a growth-promoting agent for mulberry in the greenhouse. In field studies, the cell suspension and supernatant of strain 7PJ-16 exhibited biocontrol efficacy and the lowest disease incidence was reduced down to only 0.80%. In greenhouse experiments, the cell suspension (1.0 × 10[6] and 1.0 × 10[5] CFU/mL) and the cell-free supernatant (100-fold and 1000-fold dilution) stimulated mulberry seed germination and promoted mulberry seedling growth. In addition, to accurately identify the 7PJ-16 strain and further explore the mechanisms of its antifungal and growth-promoting properties, the complete genome of this strain was sequenced and annotated. The 7PJ-16 genome is comprised of two circular plasmids and a 4,209,045-bp circular chromosome, containing 4492 protein-coding genes and 116 RNA genes. This strain was ultimately designed as Bacillus subtilis based on core genome sequence analyses using a phylogenomic approach. In this genome, we identified a series of gene clusters that function in the synthesis of non-ribosomal peptides (surfactin, fengycin, bacillibactin, and bacilysin) as well as the ribosome-dependent synthesis of tasA and bacteriocins (subtilin, subtilosin A), which are responsible for the biosynthesis of numerous antimicrobial metabolites. Additionally, several genes with function that promote plant growth, such as indole-3-acetic acid biosynthesis, the production of volatile substances, and siderophores synthesis, were also identified. The information described in this study has established a good foundation for understanding the beneficial interactions between endophytes and host plants, and facilitates the further application of B. subtilis 7PJ-16 as an agricultural biofertilizer and biocontrol agent.}, }
@article {pmid30175237, year = {2018}, author = {Coenen, AR and Weitz, JS}, title = {Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities.}, journal = {mSystems}, volume = {3}, number = {4}, pages = {}, pmid = {30175237}, issn = {2379-5077}, abstract = {Microbes are present in high abundances in the environment and in human-associated microbiomes, often exceeding 1 million per ml. Viruses of microbes are present in even higher abundances and are important in shaping microbial populations, communities, and ecosystems. Given the relative specificity of viral infection, it is essential to identify the functional linkages between viruses and their microbial hosts, particularly given dynamic changes in virus and host abundances. Multiple approaches have been proposed to infer infection networks from time series of in situ communities, among which correlation-based approaches have emerged as the de facto standard. In this work, we evaluate the accuracy of correlation-based inference methods using an in silico approach. In doing so, we compare predicted networks to actual networks to assess the self-consistency of correlation-based inference. At odds with assumptions underlying its widespread use, we find that correlation is a poor predictor of interactions in the context of viral infection and lysis of microbial hosts. The failure to predict interactions holds for methods that leverage product-moment, time-lagged, and relative-abundance-based correlations. In closing, we discuss alternative inference methods, particularly model-based methods, as a means to infer interactions in complex microbial communities with viruses. IMPORTANCE Inferring interactions from population time series is an active and ongoing area of research. It is relevant across many biological systems-particularly in virus-microbe communities, but also in gene regulatory networks, neural networks, and ecological communities broadly. Correlation-based inference-using correlations to predict interactions-is widespread. However, it is well-known that "correlation does not imply causation." Despite this, many studies apply correlation-based inference methods to experimental time series without first assessing the potential scope for accurate inference. Here, we find that several correlation-based inference methods fail to recover interactions within in silico virus-microbe communities, raising questions on their relevance when applied in situ.}, }
@article {pmid30175122, year = {2018}, author = {Asses, N and Ayed, L and Hkiri, N and Hamdi, M}, title = {Congo Red Decolorization and Detoxification by Aspergillus niger: Removal Mechanisms and Dye Degradation Pathway.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {3049686}, pmid = {30175122}, issn = {2314-6141}, mesh = {*Aspergillus niger ; Azo Compounds ; *Biodegradation, Environmental ; Coloring Agents ; Congo Red/*metabolism ; Water Purification ; }, abstract = {Congo red is one of the best known and used azo dyes which has two azo bonds (-N=N-) chromophore in its molecular structure. Its structural stability makes it highly toxic and resistant to biodegradation. The objective of this study was to assess the congo red biodegradation and detoxification by Aspergillus niger. The effects of pH, initial dye concentration, temperature, and shaking speed on the decolorization rate and enzymes production were studied. The maximum decolorization was correlated with lignin peroxidase and manganese peroxidase production. Above 97% were obtained when 2 g mycelia were incubated at pH 5, in presence of 200 mg/L of dye during 6 days at 28°C and under 120 to 150 rpm shaking speed. The degraded metabolites were characterized by using LC-MS/MS analyses and the biodegradation mechanism was also studied. Congo red bioconversion formed degradation metabolites mainly by peroxidases activities, i.e., the sodium naphthalene sulfonate (m/z = 227) and the cycloheptadienylium (m/z = 91). Phytotoxicity and microtoxicity tests confirmed that degradation metabolites were less toxic than original dye.}, }
@article {pmid30175029, year = {2018}, author = {Li, Y and Jiang, W and Gao, R and Cai, Y and Guan, Z and Liao, X}, title = {Fe(III)-based immobilized metal-affinity chromatography (IMAC) method for the separation of the catechol siderophore from Bacillus tequilensis CD36.}, journal = {3 Biotech}, volume = {8}, number = {9}, pages = {392}, pmid = {30175029}, issn = {2190-572X}, abstract = {Catechol siderophore plays an important role in microbial ecology, agriculture, and medicine, but its research is often limited by the difficulty in acquisition of it in large quantities. Based on evidence from the coordination chemistry and chemical biology, catechol siderophore could chelate Fe[3+] with high affinity. Therefore, Fe(III)-based immobilized metal-affinity chromatography (IMAC) was applied to capture siderophore from the culture filtrate of Bacillus tequilensis CD36. The ethanol-precipitated sample and the separated sample from Fe(III)-based IMAC were analyzed by liquid chromatography-mass spectrometry. According to the result, the pure siderophore DHB-Gly-Thr could be extracted from the ethanol-precipitated sample. Compared with other purifications, Fe(III)-based IMAC was convenient and had fewer steps. In addition, it also reduced the use of toxic chemical solvents in some traditional extraction process, such as extraction and ion exchange chromatography. Fe(III)-based IMAC was successfully used in separation of the catechol siderophore from B. tequilensis CD36. The results revealed that Fe(III)-based IMAC was an efficient and environmentally friendly method for the separation and purification of catechol siderophore.}, }
@article {pmid30172443, year = {2019}, author = {Gänzle, MG and Zheng, J}, title = {Lifestyles of sourdough lactobacilli - Do they matter for microbial ecology and bread quality?.}, journal = {International journal of food microbiology}, volume = {302}, number = {}, pages = {15-23}, doi = {10.1016/j.ijfoodmicro.2018.08.019}, pmid = {30172443}, issn = {1879-3460}, mesh = {Bread/*microbiology/*standards ; Edible Grain/microbiology ; *Fermentation ; *Food Microbiology ; Lactobacillus/metabolism/*physiology ; Life Style ; Microbiota ; Triticum/microbiology ; }, abstract = {Sourdough is used in production of (steamed) bread as leavening agent (type I sourdoughs) or as baking improver to enhance flavour, texture, and shelf life of bread (type II sourdoughs). The long-term propagation of sourdoughs eliminates dispersal limitation and consistently leads to sourdough microbiota that are composed of host adapted lactobacilli. In contrast, community assembly in spontaneous cereal fermentations is limited by dispersal and nomadic or environmental lactic acid bacteria are the first colonizers of these sourdoughs. Propagation of sourdoughs for use as sole leavening agent (type I sourdoughs) dictates fermentation conditions that select for rapid growth. Type I wheat- and rye sourdoughs are consistently populated by insect-adapted lactobacilli, particularly Lactobacillus sanfranciscensis, which is characterized by a small genome size and a restricted metabolic potential. The diverse fermentation conditions employed in industrial or artisanal Type II sourdough fermentation processes also result in a more diverse microbiota. Nevertheless, type II sourdoughs are typically populated by vertebrate host adapted lactobacilli of the L. delbrueckii and L. reuteri groups. Metabolic traits of host-adapted lactobacilli that enhance competitiveness in intestinal ecosystems also provide technological functionality in bread making. Examples include formation of exopolysaccharides, arginine-, glutamine- and glutamate based mechanisms of acid resistance, and glycosyl hydrolases that reduce FODMAP levels in sourdough and sourdough bread. In conclusion, consideration of the lifestyle of sourdough lactobacilli facilitates the selection of competitive and functional sourdough starter cultures.}, }
@article {pmid30172137, year = {2019}, author = {Macintosh, KA and Doody, DG and Withers, PJA and McDowell, RW and Smith, DR and Johnson, LT and Bruulsema, TW and O'Flaherty, V and McGrath, JW}, title = {Transforming soil phosphorus fertility management strategies to support the delivery of multiple ecosystem services from agricultural systems.}, journal = {The Science of the total environment}, volume = {649}, number = {}, pages = {90-98}, doi = {10.1016/j.scitotenv.2018.08.272}, pmid = {30172137}, issn = {1879-1026}, mesh = {Agriculture/*methods ; Crop Production/methods ; *Ecosystem ; Fertilizers/*analysis ; Phosphorus/*administration &amp; dosage ; Soil/*chemistry ; }, abstract = {Despite greater emphasis on holistic phosphorus (P) management, current nutrient advice delivered at farm-scale still focuses almost exclusively on agricultural production. This limits our ability to address national and international strategies for the delivery of multiple ecosystem services (ES). Currently there is no operational framework in place to manage P fertility for multiple ES delivery and to identify the costs of potentially sacrificing crop yield and/or quality. As soil P fertility plays a central role in ES delivery, we argue that soil test phosphorus (STP) concentration provides a suitable common unit of measure by which delivering multiple ES can be economically valued relative to maximum potential yield, in $ ha[-1] yr[-1] units. This value can then be traded, or payments made against one another, at spatio-temporal scales relevant for farmer and national policy objectives. Implementation of this framework into current P fertility management strategies would allow for the integration and interaction of different stakeholder interests in ES delivery on-farm and in the wider landscape. Further progress in biophysical modeling of soil P dynamics is needed to inform its adoption across diverse landscapes.}, }
@article {pmid30171270, year = {2019}, author = {Szafranek-Nakonieczna, A and Wolińska, A and Zielenkiewicz, U and Kowalczyk, A and Stępniewska, Z and Błaszczyk, M}, title = {Activity and Identification of Methanotrophic Bacteria in Arable and No-Tillage Soils from Lublin Region (Poland).}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {701-712}, pmid = {30171270}, issn = {1432-184X}, support = {DEC-2013/09/D/NZ9/02482//Narodowe Centrum Nauki/ ; }, mesh = {Autotrophic Processes ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; DNA, Bacterial/genetics ; Methane/chemistry/*metabolism ; Oxidation-Reduction ; Phylogeny ; Poland ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Methanotrophic bacteria are able to use methane (CH4) as a sole carbon and energy source. Photochemical oxidation of methane takes place in the stratosphere, whereas in the troposphere, this process is carried out by methanotrophic bacteria. On the one hand, it is known that the efficiency of biological CH4 oxidation is dependent on the mode of land use but, on the other hand, the knowledge of this impact on methanotrophic activity (MTA) is still limited. Thus, the aim of the study was to determine the CH4 oxidation ability of methanotrophic bacteria inhabiting selected arable and no-tillage soils from the Lublin region (Albic Luvisol, Brunic Arenosol, Haplic Chernozem, Calcaric Cambisol) and to identify bacteria involved in this process. MTA was determined based on incubation of soils in air with addition of methane at the concentrations of 0.002, 0.5, 1, 5, and 10%. The experiment was conducted in a temperature range of 10-30 °C. Methanotrophs in soils were identified by next-generation sequencing (NGS). MTA was confirmed in all investigated soils (in the entire range of the tested methane concentrations and temperatures, except for the arable Albic Luvisol). Importantly, the MTA values in the no-tillage soil were nearly two-fold higher than in the cultivated soils. Statistical analysis indicated a significant influence of land use, type of soil, temperature, and especially methane concentration (p < 0.05) on MTA. Metagenomic analysis confirmed the presence of methanotrophs from the genus Methylocystis (Alphaproteobacteria) in the studied soils (except for the arable Albic Luvisol). Our results also proved the ability of methanotrophic bacteria to oxidize methane although they constituted only up to 0.1% of the total bacterial community.}, }
@article {pmid30168107, year = {2018}, author = {Xu, G and Abdullah Al, M and Sikder, MNA and Warren, A and Xu, H}, title = {Identifying indicator redundancy of biofilm-dwelling protozoa for bioassessment in marine ecosystems.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {30}, pages = {30441-30450}, pmid = {30168107}, issn = {1614-7499}, mesh = {Aquatic Organisms ; Biofilms ; Ciliophora/*physiology ; *Ecosystem ; Environmental Monitoring/methods ; Seasons ; Seawater ; *Water Quality ; }, abstract = {A multivariate peeling method of data analysis was applied to determine indicator redundancy and for identifying indicator units (IUs) among biofilm-dwelling ciliate communities used for bioassessment of marine water quality. Samples were taken monthly over a 1-year period at four stations in coastal waters of the Yellow Sea: one heavily polluted, one moderately polluted, one intermittently polluted, and one unpolluted. Four IUs (IU1-4) were identified consisting of 22, 13, 14, and 17 species, respectively, out of a total of 144 species. The IUs showed significant correlation with temporal and spatial variations in environmental variables. The redundancy levels of IUs were interchangeable in time and space. However, IU1 and IU2 generally dominated the communities in moderately and intermittently polluted areas during cool (e.g., early spring, late autumn, and winter) and warm (late spring and early autumn) seasons; IU3 dominated in warm seasons (e.g., late spring to autumn) in the heavily polluted area; and IU4 mainly dominated the samples in the unpolluted and moderately polluted areas during the late summer and early autumn. Furthermore, different trophic-functional groupings were represented within the four IUs and these were generally associated with water quality status. These findings suggest that there is high indicator redundancy in marine biofilm-dwelling ciliate communities subjected to different levels of water quality.}, }
@article {pmid30166150, year = {2018}, author = {Houngbédji, M and Johansen, P and Padonou, SW and Akissoé, N and Arneborg, N and Nielsen, DS and Hounhouigan, DJ and Jespersen, L}, title = {Occurrence of lactic acid bacteria and yeasts at species and strain level during spontaneous fermentation of mawè, a cereal dough produced in West Africa.}, journal = {Food microbiology}, volume = {76}, number = {}, pages = {267-278}, doi = {10.1016/j.fm.2018.06.005}, pmid = {30166150}, issn = {1095-9998}, mesh = {Candida/isolation &amp; purification/metabolism ; Edible Grain/*microbiology ; *Fermentation ; Fermented Foods/*microbiology ; Food Microbiology ; Lactic Acid/analysis ; Lactobacillaceae/classification/*isolation &amp; purification/metabolism ; Limosilactobacillus fermentum/isolation &amp; purification ; Pichia/isolation &amp; purification/metabolism ; Saccharomyces cerevisiae/isolation &amp; purification/metabolism ; Yeasts/classification/*isolation &amp; purification/metabolism ; }, abstract = {Mawè is a West African spontaneous fermented cereal-based dough. Different types of mawè exist varying in type of cereal and/or production condition, with fermentations lasting 24-48 h. With the aim of obtaining a comprehensive understanding of the microbial ecology of mawè processing, a microbiological characterisation was performed for four mawè types, produced at eight sites in Benin. At the onset of the fermentations lactic acid bacteria (LAB) and yeast counts were on average 7.5 ± 1.03 and 4.8 ± 0.79 Log10 cfu/g, which increased to 9.2 ± 0.38 and 7.4 ± 0.42 Log10 cfu/g, respectively, at the end of the fermentations. LAB (n = 321) and yeasts (n = 298), isolated during the fermentations, were identified. The predominant LAB and yeast species were Lactobacillus fermentum and Pichia kudriavzevii, respectively, followed by Kluyveromyces marxianus, all present throughout the mawè fermentations. Further, microbial successions took place with Weissella confusa occurring mostly at the onset, while Pediococcus acidilactici and Saccharomyces cerevisiae were mainly associated with the end of the fermentations. Species diversity was influenced both by type of cereal and production condition. The dominating strain clusters of L. fermentum and P. kudriavzevii were ubiquitous and strain diversities were influenced by type of cereal and production site.}, }
@article {pmid30158906, year = {2018}, author = {Mackelprang, R and Grube, AM and Lamendella, R and Jesus, EDC and Copeland, A and Liang, C and Jackson, RD and Rice, CW and Kapucija, S and Parsa, B and Tringe, SG and Tiedje, JM and Jansson, JK}, title = {Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1775}, pmid = {30158906}, issn = {1664-302X}, abstract = {The North American prairie covered about 3.6 million-km[2] of the continent prior to European contact. Only 1-2% of the original prairie remains, but the soils that developed under these prairies are some of the most productive and fertile in the world, containing over 35% of the soil carbon in the continental United States. Cultivation may alter microbial diversity and composition, influencing the metabolism of carbon, nitrogen, and other elements. Here, we explored the structure and functional potential of the soil microbiome in paired cultivated-corn (at the time of sampling) and never-cultivated native prairie soils across a three-states transect (Wisconsin, Iowa, and Kansas) using metagenomic and 16S rRNA gene sequencing and lipid analysis. At the Wisconsin site, we also sampled adjacent restored prairie and switchgrass plots. We found that agricultural practices drove differences in community composition and diversity across the transect. Microbial biomass in prairie samples was twice that of cultivated soils, but alpha diversity was higher with cultivation. Metagenome analyses revealed denitrification and starch degradation genes were abundant across all soils, as were core genes involved in response to osmotic stress, resource transport, and environmental sensing. Together, these data indicate that cultivation shifted the microbiome in consistent ways across different regions of the prairie, but also suggest that many functions are resilient to changes caused by land management practices - perhaps reflecting adaptations to conditions common to tallgrass prairie soils in the region (e.g., soil type, parent material, development under grasses, temperature and rainfall patterns, and annual freeze-thaw cycles). These findings are important for understanding the long-term consequences of land management practices to prairie soil microbial communities and their genetic potential to carry out key functions.}, }
@article {pmid30155556, year = {2019}, author = {Ma, ZS}, title = {Sketching the Human Microbiome Biogeography with DAR (Diversity-Area Relationship) Profiles.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {821-838}, pmid = {30155556}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Humans ; Metagenomics ; *Microbiota ; Models, Biological ; }, abstract = {SAR (species area relationship) is a classic ecological theory that has been extensively investigated and applied in the studies of global biogeography and biodiversity conservation in macro-ecology. It has also found important applications in microbial ecology in recent years thanks to the breakthroughs in metagenomic sequencing technology. Nevertheless, SAR has a serious limitation for practical applications-ignoring the species abundance and treating all species as equally abundant. This study aims to explore the biogeography discoveries of human microbiome over 18 sites of 5 major microbiome habitats, establish the baseline DAR (diversity-area scaling relationship) parameters, and perform comparisons with the classic SAR. The extension from SAR to DAR by adopting the Hill numbers as diversity measures not only overcomes the previously mentioned flaw of SAR but also allows for obtaining a series of important findings on the human microbiome biodiversity and biogeography. Specifically, two types of DAR models were built, the traditional power law (PL) and power law with exponential cutoff (PLEC), using comprehensive datasets from the HMP (human microbiome project). Furthermore, the biogeography "maps" for 18 human microbiome sites using their DAR profiles for assessing and predicting the diversity scaling across individuals, PDO profiles (pair-wise diversity overlap) for measuring diversity overlap (similarity), and MAD profile (for predicting the maximal accrual diversity in a population) were sketched out. The baseline biogeography maps for the healthy human microbiome diversity can offer guidelines for conserving human microbiome diversity and investigating the health implications of the human microbiome diversity and heterogeneity.}, }
@article {pmid30154827, year = {2018}, author = {Cairns, J and Jokela, R and Hultman, J and Tamminen, M and Virta, M and Hiltunen, T}, title = {Construction and Characterization of Synthetic Bacterial Community for Experimental Ecology and Evolution.}, journal = {Frontiers in genetics}, volume = {9}, number = {}, pages = {312}, pmid = {30154827}, issn = {1664-8021}, abstract = {Experimental microbial ecology and evolution have yielded foundational insights into ecological and evolutionary processes using simple microcosm setups and phenotypic assays with one- or two-species model systems. The fields are now increasingly incorporating more complex systems and exploration of the molecular basis of observations. For this purpose, simplified, manageable and well-defined multispecies model systems are required that can be easily investigated using culturing and high-throughput sequencing approaches, bridging the gap between simpler and more complex synthetic or natural systems. Here we address this need by constructing a completely synthetic 33 bacterial strain community that can be cultured in simple laboratory conditions. We provide whole-genome data for all the strains as well as metadata about genomic features and phenotypic traits that allow resolving individual strains by amplicon sequencing and facilitate a variety of envisioned mechanistic studies. We further show that a large proportion of the strains exhibit coexistence in co-culture over serial transfer for 48 days in the absence of any experimental manipulation to maintain diversity. The constructed bacterial community can be a valuable resource in future experimental work.}, }
@article {pmid30154761, year = {2018}, author = {Plominsky, AM and Henríquez-Castillo, C and Delherbe, N and Podell, S and Ramirez-Flandes, S and Ugalde, JA and Santibañez, JF and van den Engh, G and Hanselmann, K and Ulloa, O and De la Iglesia, R and Allen, EE and Trefault, N}, title = {Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1800}, pmid = {30154761}, issn = {1664-302X}, abstract = {Hypersaline environments represent some of the most challenging settings for life on Earth. Extremely halophilic microorganisms have been selected to colonize and thrive in these extreme environments by virtue of a broad spectrum of adaptations to counter high salinity and osmotic stress. Although there is substantial data on microbial taxonomic diversity in these challenging ecosystems and their primary osmoadaptation mechanisms, less is known about how hypersaline environments shape the genomes of microbial inhabitants at the functional level. In this study, we analyzed the microbial communities in five ponds along the discontinuous salinity gradient from brackish to salt-saturated environments and sequenced the metagenome of the salt (halite) precipitation pond in the artisanal Cáhuil Solar Saltern system. We combined field measurements with spectrophotometric pigment analysis and flow cytometry to characterize the microbial ecology of the pond ecosystems, including primary producers and applied metagenomic sequencing for analysis of archaeal and bacterial taxonomic diversity of the salt crystallizer harvest pond. Comparative metagenomic analysis of the Cáhuil salt crystallizer pond against microbial communities from other salt-saturated aquatic environments revealed a dominance of the archaeal genus Halorubrum and showed an unexpectedly low abundance of Haloquadratum in the Cáhuil system. Functional comparison of 26 hypersaline microbial metagenomes revealed a high proportion of sequences associated with nucleotide excision repair, helicases, replication and restriction-methylation systems in all of them. Moreover, we found distinctive functional signatures between the microbial communities from salt-saturated (>30% [w/v] total salinity) compared to sub-saturated hypersaline environments mainly due to a higher representation of sequences related to replication, recombination and DNA repair in the former. The current study expands our understanding of the diversity and distribution of halophilic microbial populations inhabiting salt-saturated habitats and the functional attributes that sustain them.}, }
@article {pmid30153641, year = {2018}, author = {Xie, H and Wang, H and Ji, F and Liang, Y and Song, M and Zhang, J}, title = {Tetrabromobisphenol A alters soil microbial community via selective antibacterial activity.}, journal = {Ecotoxicology and environmental safety}, volume = {164}, number = {}, pages = {597-603}, doi = {10.1016/j.ecoenv.2018.08.053}, pmid = {30153641}, issn = {1090-2414}, mesh = {Anti-Bacterial Agents/*toxicity ; Bacteria/*drug effects ; Biodiversity ; Environment ; Environmental Pollution ; Flame Retardants/*toxicity ; Polybrominated Biphenyls/*toxicity ; *Soil Microbiology ; Soil Pollutants/*toxicity ; }, abstract = {Tetrabromobisphenol A (TBBPA) is the most widely used brominated flame retardant. Most studies regarding TBBPA have concentrated on its occurrence, distribution, toxicity and degradation in the environment. However, little is known about its ecological effects on soil microbial communities. In this study, we investigated the effect of TBBPA on soil microbial community. Overall, the data suggested that the growth and composition of soil microorganisms were correlated to the TBBPA concentration and exposure time. Phospholipid-derived fatty acid analysis (PLFAs) showed that significant microbial growth inhibitions were 46.1% and 46.9% in 40 mg/kg TBBPA-treated soils after 45-day incubation under aerobic and anaerobic conditions, respectively. Results of PLFAs and llumina sequencing indicated that TBBPA mainly inhibited Gram-positive bacteria, but not Gram-negative bacteria. The selective antibacterial activity of TBBPA toward Gram-positive bacteria was further confirmed in pure bacteria cultures. These data suggested that, in addition to their effect on microbial growth and composition, TBBPA may affect the microbial ecology. Additional research should be carried out to identify the ecological risk of TBBPA in soil.}, }
@article {pmid30153548, year = {2018}, author = {Vandekerckhove, TGL and De Mulder, C and Boon, N and Vlaeminck, SE}, title = {Temperature impact on sludge yield, settleability and kinetics of three heterotrophic conversions corroborates the prospect of thermophilic biological nitrogen removal.}, journal = {Bioresource technology}, volume = {269}, number = {}, pages = {104-112}, doi = {10.1016/j.biortech.2018.08.012}, pmid = {30153548}, issn = {1873-2976}, mesh = {*Bioreactors ; *Denitrification ; Kinetics ; Nitrogen ; *Sewage ; Temperature ; Waste Disposal, Fluid ; }, abstract = {In specific municipal and industrial cases, thermophilic wastewater treatment (>45 °C) might bring cost advantages over commonly applied mesophilic processes (10-35 °C). To develop such a novel process, one needs sound parameters on kinetics, sludge yield and sludge settleability of three heterotrophic conversions: aerobic carbon removal, denitritation and denitrification. These features were evaluated in acetate-fed sequencing batch reactors (30, 40, 50 and 60 °C). Higher temperatures were accompanied by lower sludge production and maximum specific removal rates, resulting mainly from lower maximum growth rates. Thermophilic denitritation was demonstrated for the first time, with lower sludge production (18-26%), higher nitrogen removal rates (24-92%) and lower carbon requirement (40%) compared to denitrification. Acceptable settling of thermophilic aerobic (60 °C) and anoxic biomass (50 and 60 °C) was obtained. Overall, this parameter set may catalyze the establishment of thermophilic nitrogen removal, once nitritation and nitratation are characterized. Furthermore, waters with low COD/N ratio might benefit from thermophilic nitritation/denitritation.}, }
@article {pmid30152425, year = {2018}, author = {Samanta, A and Patra, A and Mandal, S and Roy, S and Das, K and Kar, S and Nandi, DK}, title = {Hypoxia: A cause of acute renal failure and alteration of gastrointestinal microbial ecology.}, journal = {Saudi journal of kidney diseases and transplantation : an official publication of the Saudi Center for Organ Transplantation, Saudi Arabia}, volume = {29}, number = {4}, pages = {879-888}, doi = {10.4103/1319-2442.239653}, pmid = {30152425}, issn = {1319-2442}, mesh = {*Acute Kidney Injury/metabolism/physiopathology ; Animals ; Atmospheric Pressure ; Blood Urea Nitrogen ; Creatinine/blood ; Gastrointestinal Microbiome/*physiology ; *Hypoxia/metabolism/physiopathology ; Male ; Malondialdehyde/blood ; Oxidative Stress/physiology ; Oxygen/blood/metabolism ; Rats ; Rats, Wistar ; }, abstract = {Oxygen is very important to the existence of life. Oxygen deficiency, defined as hypoxia, elicits adaptive responses in cells and tissues. Lower oxygen concentration can cause the alteration of renal function, affects the maintenance of a balance of the body fluids, electrolytes, pH, and blood pressure homeostasis. Impaired fluid regulation could, in addition, contribute to the precipitation of pulmonary edema and exacerbate hypoxemia which may accelerate the progression of chronic kidney disease. In this context, the present study attempted to evaluate the association of renal injury and oxidative stress at different atmospheric pressures (1829, 3657, and 5486 m). Limited fecal analysis of experimental animals was also done to evaluate the impact of hypobaric hypoxia on the composition of dominant gastrointestinal microbiota. The study was performed on 24 male Wister strain rats and divided into four groups (C, HA-I, HA-II, and HA-III), and exposure was carried out for seven days period. In hypoxic exposure rats, plasma urea, creatinine, electrolytes and malonaldehyde level elevated and catalase and superoxide dismutase level diminished significantly compared to the controls. Increase in blood uremia profile, toxicity markers, and lipid peroxidation marker enzymes indicated that hypoxia causes renal failure. Histological structures of the kidney of group HA-II and HA-III animals showed severe disorganization of glomerulus and dilation of renal tubules. These results indicate nephrotoxicity or acute renal failure can occur at hypobaric hypoxia and it also affected the gut microbial population. This alteration was observed significantly above 3000 m.}, }
@article {pmid30152327, year = {2018}, author = {Bittleston, LS and Wolock, CJ and Yahya, BE and Chan, XY and Chan, KG and Pierce, NE and Pringle, A}, title = {Convergence between the microcosms of Southeast Asian and North American pitcher plants.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {30152327}, issn = {2050-084X}, support = {NSF Graduate Fellowship and Doctoral Dissertation Improvement Grant DEB-1400982//National Science Foundation/International ; Foundational Questions In Evolutionary Biology//John Templeton Foundation/International ; Putnam Expedition Grant//Harvard University Museum of Comparative Zoology/International ; High Impact Research Grant, UM-MOHE HIR Grant UM.C/625/1/HIR/MOHE/CHAN/14/1//Universiti Malaya/International ; SES-0750480//National Science Foundation/International ; High Impact Research Grant, H-50001-A000027//Universiti Malaya/International ; High Impact Research Grant, A-000001-50001//Universiti Malaya/International ; Foundational Questions In Evolutionary Biology//Templeton Foundation/International ; Putnam Grant//Harvard University Museum of Comparative Zoology Putnam Expedition Grant/International ; UM-MOHE HIR Grant UM.C/625/1/HIR/MOHE/CHAN/14/1//University of Malaya High Impact Research Grant/International ; H-50001-A000027//University of Malaya High Impact Research Grant/International ; A-000001-50001//University of Malaya High Impact Research Grant/International ; }, mesh = {Asia, Southeastern ; Biodiversity ; Chitinases/metabolism ; DNA, Plant/genetics ; *Ecosystem ; Genes, Plant ; Geography ; Microbiota ; Nitrogen/metabolism ; North America ; Phylogeny ; Sarraceniaceae/genetics/*physiology ; Species Specificity ; }, abstract = {The 'pitchers' of carnivorous pitcher plants are exquisite examples of convergent evolution. An open question is whether the living communities housed in pitchers also converge in structure or function. Using samples from more than 330 field-collected pitchers of eight species of Southeast Asian Nepenthes and six species of North American Sarracenia, we demonstrate that the pitcher microcosms, or miniature ecosystems with complex communities, are strikingly similar. Compared to communities from surrounding habitats, pitcher communities house fewer species. While communities associated with the two genera contain different microbial organisms and arthropods, the species are predominantly from the same phylogenetic clades. Microbiomes from both genera are enriched in degradation pathways and have high abundances of key degradation enzymes. Moreover, in a manipulative field experiment, Nepenthes pitchers placed in a North American bog assembled Sarracenia-like communities. An understanding of the convergent interactions in pitcher microcosms facilitates identification of selective pressures shaping the communities.}, }
@article {pmid30152021, year = {2018}, author = {Peyyala, R and Emecen-Huja, P and Ebersole, JL}, title = {Environmental lead effects on gene expression in oral epithelial cells.}, journal = {Journal of periodontal research}, volume = {53}, number = {6}, pages = {961-971}, doi = {10.1111/jre.12594}, pmid = {30152021}, issn = {1600-0765}, support = {GM103538//National Institute of General Medical Sciences/ ; //Center for Oral Health Research in the University of Kentucky College of Dentistry/ ; }, mesh = {*Biofilms ; CD59 Antigens/genetics/metabolism ; Cell Line ; Chemokine CCL20/genetics/metabolism ; Environmental Exposure/*adverse effects ; Epithelial Cells/*immunology/*metabolism/microbiology ; Gene Expression/*drug effects ; Humans ; Hyaluronan Receptors/genetics/metabolism ; Interleukin-8/genetics/metabolism ; Interleukins/genetics/metabolism ; Lead/*adverse effects ; Mouth Mucosa/cytology/immunology/*microbiology ; NF-KappaB Inhibitor alpha/genetics/metabolism ; beta Catenin/genetics/metabolism ; }, abstract = {BACKGROUND AND OBJECTIVE: Host responses in periodontitis span a range of local and emigrating cell types and biomolecules. Accumulating evidence regarding the expression of this disease across the population suggests some component of genetic variation that controls onset and severity of disease, in concert with the qualitative and quantitative parameters of the oral microbiome at sites of disease. However, there remains little information regarding the capacity of accruing environmental stressors or modifiers over a lifespan at both the host genetic and microbial ecology levels to understand fully the population variation in disease. This study evaluated the impact of environmental lead exposure on the responses of oral epithelial cells to challenge with a model pathogenic oral biofilm.<br><br>METHODS AND RESULTS: Using NanoString technology to quantify gene expression profiles of an array of 511 host response-associated genes in the epithelial cells, we identified an interesting primary panel of basal responses of the cells with numerous genes not previously considered as major response markers for epithelial cells, eg, interleukin (IL)-32, CTNNB1, CD59, MIF, CD44 and CD99. Even high levels of environment lead had little effect on these constitutive responses. Challenge of the cells with the biofilms (Streptococcus gordonii/Fusobacterium nucleatum/Porphyromonas gingivalis) resulted in significant increases in an array of host immune-related genes (134 of 511). The greatest magnitude in differential expression was observed with many genes not previously described as major response genes in epithelial cells, including IL-32, CD44, NFKBIA, CTSC, TNFAIP3, IL-1A, IL-1B, IL-8 and CCL20. The effects of environmental lead on responses to the biofilms were mixed, although levels of IL-8, CCL20 and CD70 were significantly decreased at lead concentrations of 1 and/or 5&#xa0;&#x3bc;mol/L.<br><br>CONCLUSION: The results provided new information on a portfolio of genes expressed by oral epithelial cells, targeted substantial increases in an array of immune-related genes post-biofilm challenge, and a focused impact of environmental lead on these induced responses.}, }
@article {pmid30151669, year = {2019}, author = {Szubert-Kruszyńska, A and Stańczak, J and Cieniuch, S and Podsiadły, E and Postawa, T and Michalik, J}, title = {Bartonella and Rickettsia Infections in Haematophagous Spinturnix myoti Mites (Acari: Mesostigmata) and their Bat Host, Myotis myotis (Yangochiroptera: Vespertilionidae), from Poland.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {759-768}, pmid = {30151669}, issn = {1432-184X}, support = {N N303819640//Ministerstwo Nauki i Szkolnictwa Wy&#x17c;szego/ ; }, mesh = {Animals ; Bartonella/classification/genetics/*isolation &amp; purification ; Caves ; Chiroptera/*microbiology ; Mites/*microbiology ; Phylogeny ; Poland ; Rickettsia/classification/genetics/*isolation &amp; purification ; }, abstract = {Hematophagous Spinturnix myoti mites and their host, the greater mouse-eared bat (Myotis myotis), were tested for the presence of Bartonella spp., Rickettsia spp., and Anaplasma phagocytophilum. In total, Bartonella spp. DNA was amplified in 28% of 134 mite pools and in 25% of 59 bats tested by PCR targeting a fragment of citrate synthase gltA gen. Adult mites were at least threefold more frequently infected compared to immature stages. The overall infection prevalence among mite pools from cave-dwelling bats was higher than for those collected from attic shelters. Three distinct genotypes were detected. The most prevalent genotype in mites and bats matched closely with Candidatus Bartonella hemsundetiensis identified in bats from Finland and was relatively distant from bat-borne Bartonella strains described in the UK and France. Importantly, most sequences were close to those reported in forest workers from Poland. The presence of identical genotype among S. myoti samples and M. myotis bats suggests that bartonellae can be shared between mites and their bat hosts. In this case, wing mites could serve as vectors, whereas their hosts as reservoirs. One blood sample was positive by PCR for the msp2 gene of A. phagocytophilum. Two mite pools yielded Rickettsia spp. DNA. Both sequences were distinct from any known species but can be classified as spotted fever group Rickettsia spp. Our findings expanded our knowledge on the role of spinturnicid mites in the ecology and epidemiology of bacterial infections associated with vespertilionid bats, especially regarding the genus Bartonella.}, }
@article {pmid30150233, year = {2018}, author = {Perault, AI and Cotter, PA}, title = {Three Distinct Contact-Dependent Growth Inhibition Systems Mediate Interbacterial Competition by the Cystic Fibrosis Pathogen Burkholderia dolosa.}, journal = {Journal of bacteriology}, volume = {200}, number = {22}, pages = {}, pmid = {30150233}, issn = {1098-5530}, support = {R01 GM121110/GM/NIGMS NIH HHS/United States ; R21 AI112764/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Biofilms/growth &amp; development ; Burkholderia Infections/microbiology ; Burkholderia cepacia complex/*growth &amp; development/*pathogenicity ; Coinfection/microbiology ; Cystic Fibrosis/*microbiology ; Humans ; *Microbial Interactions ; Signal Transduction ; }, abstract = {The respiratory tracts of individuals afflicted with cystic fibrosis (CF) harbor complex polymicrobial communities. By an unknown mechanism, species of the Gram-negative Burkholderia cepacia complex, such as Burkholderia dolosa, can displace other bacteria in the CF lung, causing cepacia syndrome, which has a poor prognosis. The genome of Bdolosa strain AU0158 (BdAU0158) contains three loci that are predicted to encode contact-dependent growth inhibition (CDI) systems. CDI systems function by translocating the toxic C terminus of a large exoprotein directly into target cells, resulting in growth inhibition or death unless the target cells produce a cognate immunity protein. We demonstrate here that each of the three bcpAIOB loci in BdAU0158 encodes a distinct CDI system that mediates interbacterial competition in an allele-specific manner. While only two of the three bcpAIOB loci were expressed under the in vitro conditions tested, the third conferred immunity under these conditions due to the presence of an internal promoter driving expression of the bcpI gene. One BdAU0158 bcpAIOB allele is highly similar to bcpAIOB in Burkholderia thailandensis strain E264 (BtE264), and we showed that their BcpI proteins are functionally interchangeable, but contact-dependent signaling (CDS) phenotypes were not observed in BdAU0158. Our findings suggest that the CDI systems of BdAU0158 may provide this pathogen an ecological advantage during polymicrobial infections of the CF respiratory tract.IMPORTANCE Human-associated polymicrobial communities can promote health and disease, and interbacterial interactions influence the microbial ecology of such communities. Polymicrobial infections of the cystic fibrosis respiratory tract impair lung function and lead to the death of individuals suffering from this disorder; therefore, a greater understanding of these microbial communities is necessary for improving treatment strategies. Bacteria utilize contact-dependent growth inhibition systems to kill neighboring competitors and maintain their niche within multicellular communities. Several cystic fibrosis pathogens have the potential to gain an ecological advantage during infection via contact-dependent growth inhibition systems, including Burkholderia dolosa Our research is significant, as it has identified three functional contact-dependent growth inhibition systems in Bdolosa that may provide this pathogen a competitive advantage during polymicrobial infections.}, }
@article {pmid30149801, year = {2018}, author = {Bascuñán, P and Niño-Garcia, JP and Galeano-Castañeda, Y and Serre, D and Correa, MM}, title = {Factors shaping the gut bacterial community assembly in two main Colombian malaria vectors.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {148}, pmid = {30149801}, issn = {2049-2618}, mesh = {Animals ; Anopheles/*microbiology/physiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Colombia ; DNA, Bacterial/genetics ; Feeding Behavior ; Female ; *Gastrointestinal Microbiome ; Humans ; Malaria/transmission ; Mosquito Vectors/*microbiology/physiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The understanding of the roles of gut bacteria in the fitness and vectorial capacity of mosquitoes that transmit malaria, is improving; however, the factors shaping the composition and structure of such bacterial communities remain elusive. In this study, a high-throughput 16S rRNA gene sequencing was conducted to understand the effect of developmental stage, feeding status, species, and geography on the composition of the gut bacterial microbiota of two main Colombian malaria vectors, Anopheles nuneztovari and Anopheles darlingi.<br><br>RESULTS: The results revealed that mosquito developmental stage, followed by geographical location, are more important determinants of the gut bacterial composition than mosquito species or adult feeding status. Further, they showed that mosquito gut is a major filter for environmental bacteria colonization.<br><br>CONCLUSIONS: The sampling design and analytical approach of this study allowed to untangle the influence of factors that are simultaneously shaping the microbiota composition of two Latin-American malaria vectors, essential aspect for the design of vector biocontrol strategies.}, }
@article {pmid30146914, year = {2019}, author = {Papathanasiou, P and Erdmann, S and Leon-Sobrino, C and Sharma, K and Urlaub, H and Garrett, RA and Peng, X}, title = {Stable maintenance of the rudivirus SIRV3 in a carrier state in Sulfolobus islandicus despite activation of the CRISPR-Cas immune response by a second virus SMV1.}, journal = {RNA biology}, volume = {16}, number = {4}, pages = {557-565}, pmid = {30146914}, issn = {1555-8584}, mesh = {CRISPR-Cas Systems/*genetics ; Coinfection/virology ; DNA, Viral/genetics ; Genome, Viral ; Heterozygote ; Host-Pathogen Interactions/genetics ; *Immunity ; Proteome/metabolism ; RNA, Messenger/genetics/metabolism ; Rudiviridae/*genetics ; Sulfolobus/*genetics/growth &amp; development/*immunology ; Viral Proteins/metabolism ; }, abstract = {Carrier state viral infection constitutes an equilibrium state in which a limited fraction of a cellular population is infected while the remaining cells are transiently resistant to infection. This type of infection has been characterized for several bacteriophages but not, to date, for archaeal viruses. Here we demonstrate that the rudivirus SIRV3 can produce a host-dependent carrier state infection in the model crenarchaeon Sulfolobus. SIRV3 only infected a fraction of a Sulfolobus islandicus REY15A culture over several days during which host growth was unimpaired and no chromosomal DNA degradation was observed. CRISPR spacer acquisition from SIRV3 DNA was induced by coinfecting with the monocaudavirus SMV1 and it was coincident with increased transcript levels from subtype I-A adaptation and interference cas genes. However, this response did not significantly affect the carrier state infection of SIRV3 and both viruses were maintained in the culture over 12 days during which SIRV3 anti-CRISPR genes were shown to be expressed. Transcriptome and proteome analyses demonstrated that most SIRV3 genes were expressed at varying levels over time whereas SMV1 gene expression was generally low. The study yields insights into the basis for the stable infection of SIRV3 and the resistance to the different host CRISPR-Cas interference mechanisms. It also provides a rationale for the commonly observed coinfection of archaeal cells by different viruses in natural environments.}, }
@article {pmid30145477, year = {2018}, author = {Daghio, M and Vaiopoulou, E and Aulenta, F and Sherry, A and Head, I and Franzetti, A and Rabaey, K}, title = {Anode potential selection for sulfide removal in contaminated marine sediments.}, journal = {Journal of hazardous materials}, volume = {360}, number = {}, pages = {498-503}, doi = {10.1016/j.jhazmat.2018.08.016}, pmid = {30145477}, issn = {1873-3336}, abstract = {Sulfate reducing microorganisms are typically involved in hydrocarbon biodegradation in the sea sediment, with their metabolism resulting in the by-production of toxic sulfide. In this context, it is of utmost importance identifying the optimal value for anodic potential which ensures efficient toxic sulfide removal. Along this line, in this study the (bio)electrochemical removal of sulfide was tested at anodic potentials of -205 mV, +195 mV and +300 mV (vs Ag/AgCl), also in the presence of a pure culture of the sulfur-oxidizing bacterium Desulfobulbus propionicus. Current production, sulfide concentration and sulfate concentration were monitored over time. At the end of the experiment sulfur deposition on the electrodes and the microbial communities were characterized by SEM-EDS and by next generation sequencing of the 16S rRNA gene respectively. Results confirmed that current production was linked to sulfide removal and D. propionicus promoted back oxidation of deposited sulfur to sulfate. The highest electron recovery was observed at +195 mV vs Ag/AgCl, and the lowest sulfur deposition was obtained at -205 mV vs Ag/AgCl anode polarization.}, }
@article {pmid30145102, year = {2018}, author = {Chen, L and Xu, W and Lee, A and He, J and Huang, B and Zheng, W and Su, T and Lai, S and Long, Y and Chu, H and Chen, Y and Wang, L and Wang, K and Si, J and Chen, S}, title = {The impact of Helicobacter pylori infection, eradication therapy and probiotic supplementation on gut microenvironment homeostasis: An open-label, randomized clinical trial.}, journal = {EBioMedicine}, volume = {35}, number = {}, pages = {87-96}, pmid = {30145102}, issn = {2352-3964}, support = {KL2 TR002241/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; *Dietary Supplements ; *Disease Eradication ; Female ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Helicobacter Infections/microbiology/*prevention &amp; control/*therapy ; Helicobacter pylori/classification/*physiology ; *Homeostasis ; Humans ; Male ; Probiotics/*administration &amp; dosage ; }, abstract = {BACKGROUND: Helicobacter pylori (H. pylori) infection is associated with remodeling of gastric microbiota. However, comprehensive analyses of the impact of H. pylori infection, eradication therapy and probiotic supplementation on gut microbiota are still lacking. We aimed to provide evidence for clinical decision making.<br><br>METHODS: Seventy H. pylori-positive and 35 H. pylori-negative patients (group C) were enrolled. H. pylori-positive patients were randomly assigned to group A (14-day bismuth-containing quadruple therapy) and group B (quadruple therapy supplemented with Clostridium butyricum). Stool samples of group A and B were collected on day 0, 14 and 56 while stool samples of group C were collected on day 0. Gut microbiota was investigated by 16S rRNA sequencing.<br><br>FINDINGS: The Sobs index (richness estimator) was significantly higher in H. pylori-positive samples than H. pylori-negative samples (p&#x202f;<&#x202f;.05). Several metabolic pathways were more abundant in H. pylori-positive communities while some disease-associated pathways had higher potential in H. pylori-negative community through KEGG pathway analysis. Abundances of most butyrate-producing bacteria significantly decreased, while several detrimental bacteria increased after eradication therapy. Probiotic supplementation was associated with improved gastrointestinal symptoms as well as increased Bacteroidetes:Firmicutes ratio.<br><br>INTERPRETATION: While H. pylori infection may not be necessarily detrimental in all patients, eradication of H. pylori was associated with widespread changes in gut microbial ecology and structure. Probiotic supplementation could relieve more gastrointestinal symptoms by inducing alterations in gut microbiota and host immune responses. As such, the decision to eradicate H. pylori should be based on comprehensive analysis of individual patients.}, }
@article {pmid30143799, year = {2018}, author = {Hall, EK and Bernhardt, ES and Bier, RL and Bradford, MA and Boot, CM and Cotner, JB and Del Giorgio, PA and Evans, SE and Graham, EB and Jones, SE and Lennon, JT and Locey, KJ and Nemergut, D and Osborne, BB and Rocca, JD and Schimel, JP and Waldrop, MP and Wallenstein, MD}, title = {Understanding how microbiomes influence the systems they inhabit.}, journal = {Nature microbiology}, volume = {3}, number = {9}, pages = {977-982}, doi = {10.1038/s41564-018-0201-z}, pmid = {30143799}, issn = {2058-5276}, mesh = {Bacteria/classification/*growth &amp; development/*metabolism ; *Ecosystem ; Microbiota/*physiology ; }, abstract = {Translating the ever-increasing wealth of information on microbiomes (environment, host or built environment) to advance our understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes that they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here, we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system-level processes that they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted using constituent taxa (community-aggregated traits) from those properties that cannot currently be predicted using constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these three categories of microbial characteristics and connect them with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.}, }
@article {pmid30143666, year = {2018}, author = {Benicio, LM and Simionato, AS and Novello, CR and Guimarães, JR and Felicidade, I and de Oliveira, AG and de Mello, JCP and Mantovani, MS and Chryssafidis, AL and Andrade, G and de Syllos Colus, IM and de Oliveira, MT}, title = {RNAm expression profile of cancer marker genes in HepG2 cells treated with different concentrations of a new indolin-3-one from Pseudomonas aeruginosa.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12781}, pmid = {30143666}, issn = {2045-2322}, mesh = {Biomarkers, Tumor/*genetics/metabolism ; Cell Death/drug effects ; Cell Survival/drug effects ; Doxorubicin/pharmacology ; Erythrocytes/drug effects ; *Gene Expression Profiling ; Gene Expression Regulation, Neoplastic/drug effects ; *Genes, Neoplasm ; Genes, Tumor Suppressor ; Hemolysis/drug effects ; Hep G2 Cells ; Humans ; Indoles/chemistry/isolation &amp; purification/*pharmacology ; Pseudomonas aeruginosa/*chemistry ; }, abstract = {The present study tested the effects of a newly identified indolin-3-one compound (compound 1), produced by Pseudomonas aeruginosa, on HepG2 cells. The MTT assays demonstrated decreased metabolic activities in HepG2 cells treated with compound 1, with dose- and time-dependent intensifying effect, starting at a concentration of 40 µM. The IC50 after 24, 48, 72, and 96 h treatments were 41.35, 52.7, 92.79 and 66.65 μM of compound 1, respectively. Below 80 µM, no significative damage on erythrocytes membranes was observed by the hemolytic assays. The RT-qPCR revealed that the compound modulated key genes involved in carcinogenesis process, indicating possible indolin-3-one mechanisms of action. The data showed that gene expression alterations promoted by compound 1, in concentrations up to 60 μM after 48 h, led to a decrease in cellular progression and there was no direct cellular damage. In addition, non-cytotoxic concentrations of compound 1 halved the concentration of the chemotherapeutic doxorubicin, maintaining similar therapeutic effect against HepG2 cells. The novelty of the molecule and the biological activities observed in the present study emphasize the potential of the compound 1 in cancer therapy research.}, }
@article {pmid30142153, year = {2018}, author = {Pace, NR}, title = {The small things can matter.}, journal = {PLoS biology}, volume = {16}, number = {8}, pages = {e3000009}, pmid = {30142153}, issn = {1545-7885}, mesh = {Bacteria ; Humans ; Metagenomics ; Microbiology/*trends ; }, abstract = {In the context of biology as a whole and of our own personal lives, seemingly small things can prove surprisingly influential. Here, I consider the powerful impact of small organisms-the inhabitants of the microbial world-and the small events that shaped my own development as a scientist. I reflect on the early days of the fields of molecular biology and microbial ecology and my own role in the origin story of what we now call "metagenomics".}, }
@article {pmid30141128, year = {2019}, author = {Li, H and Mishra, M and Ding, S and Miyamoto, MM}, title = {Diversity and Dynamics of "Candidatus Endobugula" and Other Symbiotic Bacteria in Chinese Populations of the Bryozoan, Bugula neritina.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {243-256}, pmid = {30141128}, issn = {1432-184X}, support = {201205024-2//Public Welfare Project of the State Oceanic Administration/ ; 2013FY110700//National Basic Research Foundation of China/ ; }, mesh = {Animals ; Biodiversity ; Bryostatins/metabolism ; Bryozoa/growth &amp; development/*microbiology ; China ; DNA, Bacterial/isolation &amp; purification ; Ecology ; Gammaproteobacteria/*classification/genetics/*isolation &amp; purification/*metabolism ; Geography ; Larva/microbiology ; Life Cycle Stages ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; }, abstract = {Bugula neritina is a common invasive cosmopolitan bryozoan that harbors (like many sessile marine invertebrates) a symbiotic bacterial (SB) community. Among the SB of B. neritina, "Candidatus Endobugula sertula" continues to receive the greatest attention, because it is the source of bryostatins. The bryostatins are potent bioactive polyketides, which have been investigated for their therapeutic potential to treat various cancers, Alzheimer's disease, and AIDS. In this study, we compare the metagenomics sequences for the 16S ribosomal RNA gene of the SB communities from different geographic and life cycle samples of Chinese B. neritina. Using a variety of approaches for estimating alpha/beta diversity and taxonomic abundance, we find that the SB communities vary geographically with invertebrate and fish mariculture and with latitude and environmental temperature. During the B. neritina life cycle, we find that the diversity and taxonomic abundances of the SB communities change with the onset of host metamorphosis, filter feeding, colony formation, reproduction, and increased bryostatin production. "Ca. Endobugula sertula" is confirmed as the symbiont of the Chinese "Ca. Endobugula"/B. neritina symbiosis. Our study extends our knowledge about B. neritina symbiosis from the New to the Old World and offers new insights into the environmental and life cycle factors that can influence its SB communities, "Ca. Endobugula," and bryostatins more globally.}, }
@article {pmid30141127, year = {2019}, author = {Choi, Y and Banerjee, A and McNish, S and Couch, KS and Torralba, MG and Lucas, S and Tovchigrechko, A and Madupu, R and Yooseph, S and Nelson, KE and Shanmugam, VK and Chan, AP}, title = {Co-occurrence of Anaerobes in Human Chronic Wounds.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {808-820}, pmid = {30141127}, issn = {1432-184X}, support = {R01NR013888//National Institute of Nursing Research/ ; UL1 TR000075//National Center for Advancing Translational Sciences/ ; }, mesh = {Adult ; Aged ; Bacteria, Anaerobic/classification/genetics/*isolation &amp; purification ; Bacterial Infections/*microbiology/physiopathology ; Chronic Disease ; Female ; Humans ; Male ; Middle Aged ; Phylogeny ; Wound Healing ; Wounds and Injuries/*microbiology/physiopathology ; Young Adult ; }, abstract = {Chronic wounds are wounds that have failed to heal after 3 months of appropriate wound care. Previous reports have identified a diverse collection of bacteria in chronic wounds, and it has been postulated that bacterial profile may contribute to delayed healing. The purpose of this study was to perform a microbiome assessment of the Wound Healing and Etiology (WE-HEAL) Study cohort, including underlying comorbidities less commonly studied in the context of chronic wounds, such as autoimmune diseases, and investigate possible relationships of the wound microbiota with clinical healing trends. We examined chronic wound specimens from 60 patients collected through the WE-HEAL Study using 16S ribosomal RNA gene sequencing. A group of co-occurring obligate anaerobes was identified from taxonomic analysis guided by Dirichlet multinomial mixtures (DMM) modeling. The group includes members of the Gram-positive anaerobic cocci (GPAC) of the Clostridia class (i.e., Anaerococcus, Finegoldia, and Peptoniphilus) and additional strict anaerobes (i.e., Porphyromonas and Prevotella). We showed that the co-occurring group of obligate anaerobes not only co-exists with commonly identified wound species (such as Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas, Corynebacterium, and Streptococcus), but importantly, they could also predominate the wound microbiota. Furthermore, examination of clinical comorbidities of the WE-HEAL specimens showed that specific obligate and facultative anaerobes were significantly reduced in wounds presented with autoimmune disease. With respect to future healing trends, no association with the wound microbiome community or the abundance of individual wound species could be established. In conclusion, we identified a co-occurring obligate anaerobic community type that predominated some human chronic wounds and underrepresentation of anaerobes in wounds associated with autoimmune diseases. Possible elucidation of host environments or key factors that influence anaerobe colonization warrants further investigation in a larger cohort.}, }
@article {pmid30138752, year = {2018}, author = {Zeineldin, M and Barakat, R and Elolimy, A and Salem, AZM and Elghandour, MMY and Monroy, JC}, title = {Synergetic action between the rumen microbiota and bovine health.}, journal = {Microbial pathogenesis}, volume = {124}, number = {}, pages = {106-115}, doi = {10.1016/j.micpath.2018.08.038}, pmid = {30138752}, issn = {1096-1208}, mesh = {Animals ; Cattle ; *Health ; *Host Microbial Interactions ; *Microbiota ; Rumen/*microbiology ; }, abstract = {Host-rumen-microbe interactions are essential components of many physiological processes, and therefore can affect ruminant health. Classical knowledge of rumen microbiology is based on culture-dependent methodologies, which only account for 10-20% of the rumen bacterial communities. While, the advancement in DNA sequencing and bioinformatics platforms provide novel approaches to investigate the composition and dynamics of the rumen microbiota. Recent studies demonstrated that the ruminal ecosystem is highly diverse and harbors numerous microbial communities. The composition of these microbial communities are affected by various environmental factors such as nutrition and different management strategies. Disturbance in the microbial ecology of the rumen is associated with the development of various diseases. Despite the flow of recent rumen-based studies, rumen microbiota is still not fully characterized. This review provides an overview of recent efforts to characterize rumen microbiota and its potential role in rumen health and disease. Moreover, the recent effects of dietary interventions and probiotics on rumen microbiota are discussed.}, }
@article {pmid30137564, year = {2018}, author = {Lekeux, G and Laurent, C and Joris, M and Jadoul, A and Jiang, D and Bosman, B and Carnol, M and Motte, P and Xiao, Z and Galleni, M and Hanikenne, M}, title = {di-Cysteine motifs in the C-terminus of plant HMA4 proteins confer nanomolar affinity for zinc and are essential for HMA4 function in vivo.}, journal = {Journal of experimental botany}, volume = {69}, number = {22}, pages = {5547-5560}, pmid = {30137564}, issn = {1460-2431}, mesh = {Adenosine Triphosphatases/*genetics/metabolism ; Amino Acid Motifs ; Arabidopsis/*genetics/metabolism ; Arabidopsis Proteins/*genetics/metabolism ; Cysteine/*metabolism ; Species Specificity ; Zinc/*metabolism ; }, abstract = {The PIB ATPase heavy metal ATPase 4 (HMA4) has a central role in the zinc homeostasis network of Arabidopsis thaliana. This membrane protein loads metal from the pericycle cells into the xylem in roots, thereby allowing root to shoot metal translocation. Moreover, HMA4 is key for zinc hyperaccumulation as well as zinc and cadmium hypertolerance in the pseudometallophyte Arabidopsis halleri. The plant-specific cytosolic C-terminal extension of HMA4 is rich in putative metal-binding residues and has substantially diverged between A. thaliana and A. halleri. To clarify the function of the domain in both species, protein variants with truncated C-terminal extension, as well as with mutated di-Cys motifs and/or a His-stretch, were functionally characterized. We show that di-Cys motifs, but not the His-stretch, contribute to high affinity zinc binding and function in planta. We suggest that the HMA4 C-terminal extension is at least partly responsible for protein targeting to the plasma membrane. Finally, we reveal that the C-terminal extensions of both A. thaliana and A. halleri HMA4 proteins share similar function, despite marginally different zinc-binding capacity.}, }
@article {pmid30137345, year = {2018}, author = {Luk, AW and Beckmann, S and Manefield, M}, title = {Dependency of DNA extraction efficiency on cell concentration confounds molecular quantification of microorganisms in groundwater.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {10}, pages = {}, doi = {10.1093/femsec/fiy146}, pmid = {30137345}, issn = {1574-6941}, mesh = {Archaea/*cytology/genetics ; Bacteria/*cytology/genetics ; DNA, Archaeal/analysis/genetics ; DNA, Bacterial/analysis/genetics ; Environmental Monitoring/*methods ; Groundwater/*microbiology ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction/standards ; Sequence Analysis, DNA/standards ; *Water Microbiology ; }, abstract = {Quantification of microbes in water systems is essential to industrial practices ranging from drinking water and wastewater treatment to groundwater remediation. While quantification using DNA-based molecular methods is precise, the accuracy is dependent on DNA extraction efficiencies. We show that the DNA yield is strongly impacted by the cell concentration in groundwater samples (r = -0.92, P < 0.0001). This has major implications for industrial applications using quantitative polymerase chain reaction (qPCR) to determine cell concentrations in water, including bioremediation. We propose a simple normalization method using a DNA recovery ratio, calculated with the total cell count and DNA yield. Application of this method to enumeration of bacteria and archaea in groundwater samples targeting phylogenetic markers (16S rRNA) demonstrated an increased goodness of fit after normalization (7.04 vs 0.94 difference in Akaike's information criteria). Furthermore, normalization was applied to qPCR quantification of functional genes and combined with DNA sequencing of archaeal and bacterial 16S rRNA genes to monitor changes in abundance of methanogenic archaea and sulphate-reducing bacteria in groundwater. The integration of qPCR and DNA sequencing with appropriate normalization enables high-throughput quantification of microbial groups using increasingly affordable and accessible techniques. This research has implications for microbial ecology and engineering research as well as industrial practice.}, }
@article {pmid30137328, year = {2018}, author = {Geesink, P and Tyc, O and Küsel, K and Taubert, M and van de Velde, C and Kumar, S and Garbeva, P}, title = {Growth promotion and inhibition induced by interactions of groundwater bacteria.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {11}, pages = {}, doi = {10.1093/femsec/fiy164}, pmid = {30137328}, issn = {1574-6941}, mesh = {Anti-Bacterial Agents/*metabolism ; Bacteria/*growth &amp; development/isolation &amp; purification/metabolism ; Bacteroidetes/metabolism ; Escherichia coli/growth &amp; development ; Firmicutes/metabolism ; Groundwater/*microbiology ; *Microbial Interactions ; Proteobacteria/metabolism ; Staphylococcus aureus/growth &amp; development ; }, abstract = {Microorganisms can produce a plethora of secondary metabolites, some acting as signaling compounds and others as suppressing agents. As yet, the potential of groundwater microbes to produce antimicrobial compounds to increase their competitiveness against other bacteria has not been examined. In this study, we developed an AlamarBlue® based high-throughput screening method that allowed for a fast and highly standardized evaluation of both growth-inhibiting and -promoting metabolites. With this technique, 149 screened bacterial isolates were grown in monocultures and in 1402 co-cultures. Co-cultivation did not increase the frequency of growth inhibition against the two tested model organisms (Staphylococcus aureus 533R4 and Escherichia coli WA321) compared to monocultures. Mainly co-cultivation of Proteobacteria induced growth inhibition of both model organisms. Only slightly increased growth promotion of S. aureus 533R4 was observed. Growth-promoting effects on E. coli WA321 were observed by supernatants from co-cultures between Bacteroidetes and Firmicutes. With the standardized screening for both growth-inhibiting and -promoting effects, this method will enable further studies to elaborate and better understand complex inter-specific interactions and networks in aquatic communities as well as in other environments.}, }
@article {pmid30135980, year = {2019}, author = {Vikström, K and Wikner, J}, title = {Importance of Bacterial Maintenance Respiration in a Subarctic Estuary: a Proof of Concept from the Field.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {574-586}, pmid = {30135980}, issn = {1432-184X}, mesh = {Bacteria/classification/growth &amp; development/isolation &amp; purification/*metabolism ; Biomass ; Carbon Dioxide/metabolism ; Cell Respiration ; Ecosystem ; Estuaries ; Oxygen/metabolism ; Phosphorus/metabolism ; Rivers/chemistry/microbiology ; }, abstract = {Bacterial respiration contributes to atmospheric carbon dioxide accumulation and development of hypoxia and is a critical, often overlooked, component of ecosystem function. This study investigates the concept that maintenance respiration is a significant proportion of bacterial respiration at natural nutrient levels in the field, advancing our understanding of bacterial living conditions and energy strategies. Two river-sea transects of respiration and specific growth rates were analyzed representing low- and high-productivity conditions (by in situ bacterial biomass production) in a subarctic estuary, using an established ecophysiological linear model (the Pirt model) estimating maintenance respiration. The Pirt model was applicable to field conditions during high, but not low, bacterial biomass production. However, a quadratic model provided a better fit to observed data, accounting for the maintained respiration at low μ. A first estimate of maintenance respiration was 0.58 fmol O2 day[-1] cell[-1] by the quadratic model. Twenty percent to nearly all of the bacterial respiration was due to maintenance respiration over the observed range of μ (0.21-0.002 day[-1]). In the less productive condition, bacterial specific respiration was high and without dependence on μ, suggesting enhanced bacterial energy expenditure during starvation. Annual maintenance respiration accounted for 58% of the total bacterioplankton respiration based on μ from monitoring data. Phosphorus availability occasionally, but inconsistently, explained some of the remaining variation in bacterial specific respiration. Bacterial maintenance respiration can constitute a large share of pelagic respiration and merit further study to understand bacterial energetics and oxygen dynamics in the aquatic environment.}, }
@article {pmid30131799, year = {2018}, author = {Seugendo, M and Janssen, I and Lang, V and Hasibuan, I and Bohne, W and Cooper, P and Daniel, R and Gunka, K and Kusumawati, RL and Mshana, SE and von Müller, L and Okamo, B and Ortlepp, JR and Overmann, J and Riedel, T and Rupnik, M and Zimmermann, O and Groß, U}, title = {Prevalence and Strain Characterization of Clostridioides (Clostridium) difficile in Representative Regions of Germany, Ghana, Tanzania and Indonesia - A Comparative Multi-Center Cross-Sectional Study.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1843}, pmid = {30131799}, issn = {1664-302X}, abstract = {Clostridioides (Clostridium) difficile infections (CDI) are considered worldwide as emerging health threat. Uptake of C. difficile spores may result in asymptomatic carrier status or lead to CDI that could range from mild diarrhea, eventually developing into pseudomembranous colitis up to a toxic megacolon that often results in high mortality. Most epidemiological studies to date have been performed in middle- and high income countries. Beside others, the use of antibiotics and the composition of the microbiome have been identified as major risk factors for the development of CDI. We therefore postulate that prevalence rates of CDI and the distribution of C. difficile strains differ between geographical regions depending on the regional use of antibiotics and food habits. A total of 593 healthy control individuals and 608 patients suffering from diarrhea in communities in Germany, Ghana, Tanzania and Indonesia were selected for a comparative multi-center cross-sectional study. The study populations were screened for the presence of C. difficile in stool samples. Cultured C. difficile strains (n = 84) were further subtyped and characterized using PCR-ribotyping, determination of toxin production, and antibiotic susceptibility testing. Prevalence rates of C. difficile varied widely between the countries. Whereas high prevalence rates were observed in symptomatic patients living in Germany and Indonesia (24.0 and 14.7%), patients from Ghana and Tanzania showed low detection rates (4.5 and 6.4%). Differences were also obvious for ribotype distribution and toxin repertoires. Toxin A[+]/B[+] ribotypes 001/072 and 078 predominated in Germany, whereas most strains isolated from Indonesian patients belonged to toxin A[+]/B[+] ribotype SLO160 and toxin A[-]/B[+] ribotype 017. With 42.9-73.3%, non-toxigenic strains were most abundant in Africa, but were also found in Indonesia at a rate of 18.2%. All isolates were susceptible to vancomycin and metronidazole. Mirroring the antibiotic use, however, moxifloxacin resistance was absent in African C. difficile isolates but present in Indonesian (24.2%) and German ones (65.5%). This study showed that CDI is a global health threat with geographically different prevalence rates which might reflect distinct use of antibiotics. Significant differences for distributions of ribotypes, toxin production, and antibiotic susceptibilities were observed.}, }
@article {pmid30130114, year = {2018}, author = {Eshrati, M and Amadei, F and Van de Wiele, T and Veschgini, M and Kaufmann, S and Tanaka, M}, title = {Biopolymer-Based Minimal Formulations Boost Viability and Metabolic Functionality of Probiotics Lactobacillus rhamnosus GG through Gastrointestinal Passage.}, journal = {Langmuir : the ACS journal of surfaces and colloids}, volume = {34}, number = {37}, pages = {11167-11175}, doi = {10.1021/acs.langmuir.8b01915}, pmid = {30130114}, issn = {1520-5827}, mesh = {Administration, Oral ; Alginates/chemistry ; Gastrointestinal Tract/*metabolism ; Lacticaseibacillus rhamnosus/*metabolism ; Microbial Viability ; Particle Size ; Polyelectrolytes/chemistry ; Polysaccharides, Bacterial/chemistry ; Probiotics/administration &amp; dosage/*chemistry/metabolism ; Technology, Pharmaceutical/methods ; }, abstract = {The delivery of probiotic microorganisms as food additives via oral administration is a straightforward strategy to improve the intestinal microbiota. To protect probiotics from the harsh environments in the stomach and small intestine, it is necessary to formulate them in biocompatible carriers, which finally release them in the ileum and colon without losing their viability and functions. Despite major progresses in various polymer-based formulations, many of them are highly heterogeneous and too large in size and hence often "felt" by the tongue. In this study, we established a new formulation for probiotics Lactobacillus rhamnosus GG (LGG) and systematically correlated the physicochemical properties of formulations with the functions of probiotics after the delivery to different gastrointestinal compartments. By reducing the stirring speed by 1 order of magnitude during the emulsification of polyalginate in the presence of xanthan gum, we fabricated microparticles with a size well below the limit of human oral sensory systems. To improve the chemical stability, we deposited chitosan and polyalginate layers on particle surfaces and found that the deposition of a 20 nm-thick layer is already sufficient to perfectly sustain the viability of all LGG. Compared to free LGG, the colony-forming units of LGG in these formulations were by factors of 10[7] larger in stomach fluid and 10[4] larger in small intestine fluid. The metabolic functionality of LGG in polymer formulations was assessed by measuring the amount of lactate produced by LGG in a human gastrointestinal simulator, showing 5 orders of magnitude larger values compared to free LGG. The obtained results have demonstrated that the minimal formulation of LGG established here boosts not only the viability but also the metabolic functionality of probiotics throughout oral uptake, passage through the gastrointestinal tract, and delivery to the ileum and colon.}, }
@article {pmid30128178, year = {2018}, author = {Wallace, J and Laforest-Lapointe, I and Kembel, SW}, title = {Variation in the leaf and root microbiome of sugar maple (Acer saccharum) at an elevational range limit.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5293}, pmid = {30128178}, issn = {2167-8359}, abstract = {BACKGROUND: Bacteria, archaea, viruses and fungi live in various plant compartments including leaves and roots. These plant-associated microbial communities have many effects on host fitness and function. Global climate change is impacting plant species distributions, a phenomenon that will affect plant-microbe interactions both directly and indirectly. In order to predict plant responses to global climate change, it will be crucial to improve our understanding of plant-microbe interactions within and at the edge of plant species natural ranges. While microbes affect their hosts, in turn the plant's attributes and the surrounding environment drive the structure and assembly of the microbial communities themselves. However, the patterns and dynamics of these interactions and their causes are poorly understood.<br><br>METHODS: In this study, we quantified the microbial communities of the leaves and roots of seedlings of the deciduous tree species sugar maple (Acer saccharum Marshall) within its natural range and at the species' elevational range limit at Mont-M&#xe9;gantic, Quebec. Using high-throughput DNA sequencing, we quantified the bacterial and fungal community structure in four plant compartments: the epiphytes and endophytes of leaves and roots. We also quantified endophytic fungal communities in roots.<br><br>RESULTS: The bacterial and fungal communities of A. saccharum seedlings differ across elevational range limits for all four plant compartments. Distinct microbial communities colonize each compartment, although the microbial communities inside a plant's structure (endophytes) were found to be a subset of the communities found outside the plant's structure (epiphytes). Plant-associated bacterial communities were dominated by the phyla Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes while the main fungal taxa present were Ascomycota.<br><br>DISCUSSION: We demonstrate that microbial communities associated with sugar maple seedlings at the edge of the species' elevational range differ from those within the natural range. Variation in microbial communities differed among plant components, suggesting the importance of each compartment's exposure to changes in biotic and abiotic conditions in determining variability in community structure. These findings provide a greater understanding of the ecological processes driving the structure and diversity of plant-associated microbial communities within and at the edge of a plant species range, and suggest the potential for biotic interactions between plants and their associated microbiota to influence the dynamics of plant range edge boundaries and responses to global change.}, }
@article {pmid30127345, year = {2018}, author = {Gilbert, JA and Stephens, B}, title = {Microbiology of the built environment.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {11}, pages = {661-670}, doi = {10.1038/s41579-018-0065-5}, pmid = {30127345}, issn = {1740-1534}, mesh = {Adaptation, Biological ; Animals ; Archaea/*genetics ; Bacteria/*genetics ; Biological Evolution ; *Built Environment ; Ecology ; Ecosystem ; Fungi/*genetics ; Humans ; *Microbiology ; *Microbiota ; Public Health ; Viruses/*genetics ; }, abstract = {The built environment comprises all structures built by humans, including our homes, workplaces, schools and vehicles. As in any ecosystem on Earth, microorganisms have been found in every part of the built environment that has been studied. They exist in the air, on surfaces and on building materials, usually dispersed by humans, animals and outdoor sources. Those microbial communities and their metabolites have been implied to cause (or exacerbate) and prevent (or mitigate) human disease. In this Review, we outline the history of the field of microbiology of the built environment and discuss recent insights that have been gained into microbial ecology, adaptation and evolution of this ecosystem. Finally, we consider the implications of this research, specifically, how it is changing the types of materials we use in buildings and how our built environments affect human health.}, }
@article {pmid30126070, year = {2018}, author = {De Paepe, K and Verspreet, J and Verbeke, K and Raes, J and Courtin, CM and Van de Wiele, T}, title = {Introducing insoluble wheat bran as a gut microbiota niche in an in vitro dynamic gut model stimulates propionate and butyrate production and induces colon region specific shifts in the luminal and mucosal microbial community.}, journal = {Environmental microbiology}, volume = {20}, number = {9}, pages = {3406-3426}, doi = {10.1111/1462-2920.14381}, pmid = {30126070}, issn = {1462-2920}, support = {IWT130028//Fonds Wetenschappelijk Onderzoek/International ; }, mesh = {Adult ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Bacteroides ; Bifidobacterium ; Butyrates/*metabolism ; Colon/metabolism/*microbiology ; Diet ; Dietary Fiber/*metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/metabolism/*microbiology ; Male ; Microbiota ; Middle Aged ; Mucous Membrane ; Prevotella ; Propionates/*metabolism ; Young Adult ; }, abstract = {The spatial organization of gut microorganisms is important with respect to their functional role in the gut ecosystem. Regional differences in the longitudinal and lateral direction are, however, not frequently studied, given the difficulty to sample these human gut regions in vivo. Particularly the insoluble food particle-associated microbiota is poorly studied. Therefore, the long-term effects of insoluble wheat bran supplementation on the composition and functionality of the gut microbial community derived from six individuals were explored in the Dietary Particle-Mucosal-Simulator of the Human Intestinal Microbial Ecosystem in vitro model. Wheat bran stimulated propionate and butyrate production and induced shifts in the luminal and mucosal microbial community composition. The insoluble wheat bran residue and the mucus layer were identified as crucial platforms in sustaining diversity by selectively enriching species, which are not thriving in the luminal environment, including Lactobacillus, Bifidobacterium and Dialister species, Roseburia faecis, Prevotella copri and Bacteroides ovatus. Despite the evident habitat preference, some parallels could be drawn between the enrichment of taxa on bran platforms and their stimulation in the luminal and mucosal communities. Removing wheat bran during the wash-out period reversed the functional effects and gave rise to a blooming of some taxa that are considered opportunistic pathogens.}, }
@article {pmid30124400, year = {2018}, author = {Jung, MY and Islam, MA and Gwak, JH and Kim, JG and Rhee, SK}, title = {Nitrosarchaeum koreense gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon member of the phylum Thaumarchaeota isolated from agricultural soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {68}, number = {10}, pages = {3084-3095}, doi = {10.1099/ijsem.0.002926}, pmid = {30124400}, issn = {1466-5034}, mesh = {Agriculture ; Ammonia/*metabolism ; Archaea/*classification/genetics/isolation &amp; purification ; Base Composition ; Genes, Archaeal ; Glyceryl Ethers/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {A mesophilic, chemolithoautotrophic, neutrophilic and aerobic ammonia-oxidizing archaeon, designated strain MY1[T], was isolated from agricultural soil. Microscopic observation revealed short, rod-shaped cells with a diameter of 0.3-0.5 µm and length of 0.6-1.0 µm. The isolate had no flagella and pili, and possessed no genes associated with archaeal flagella synthesis. The major membrane lipids consisted mainly of the glycerol dibiphytanyl glycerol tetraether (GDGT) lipids GDGT-0 to GDGT-4 and crenarchaeol. The major intact polar lipids (IPLs) were determined as hexose plus phosphohexose IPL and dihexose IPL. Strain MY1[T] obtains energy by aerobically oxidizing ammonia and carbon by fixing CO2. An optimal growth was observed at 25 °C, at pH 7 and with 0.2-0.4 % (w/v) salinity that corresponds with its terrestrial habitat. The addition of α-keto acids was necessary to stimulate growth. The strain tolerated ammonium and nitrite concentrations up to 10 and 5 mM, respectively. The MY1[T] genome has a DNA G+C content of 32.7 mol%. Phylogenetic analysis based on the 16S rRNA gene showed that strain MY1[T] belongs to the family Nitrosopumilaceaeof the phylum Thaumarchaeota, sharing the highest 16S rRNA gene sequence similarity (96.6-97.1 %) with marine isolates of the genus Nitrosopumilus. The average nucleotide identity was 78 % between strain MY1[T] and Nitrosopumilus maritimus SCM1[T], indicating distant relatedness. Based on the phenotypic, phylogenetic and genomic analyses, it was concluded that strain MY1[T] belongs to the novel genus Nitrosarchaeum, under which the name Nitrosarchaeum koreense sp. nov. is proposed as the type species. The type strain is MY1[T] (=JCM 31640[T]=KCTC 4249[T]).}, }
@article {pmid30123820, year = {2018}, author = {Williamson, IA and Arnold, JW and Samsa, LA and Gaynor, L and DiSalvo, M and Cocchiaro, JL and Carroll, I and Azcarate-Peril, MA and Rawls, JF and Allbritton, NL and Magness, ST}, title = {A High-Throughput Organoid Microinjection Platform to Study Gastrointestinal Microbiota and Luminal Physiology.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {6}, number = {3}, pages = {301-319}, pmid = {30123820}, issn = {2352-345X}, support = {UL1 TR001111/TR/NCATS NIH HHS/United States ; R01 DK091427/DK/NIDDK NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; R01 DK081426/DK/NIDDK NIH HHS/United States ; R01 DK109559/DK/NIDDK NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; UL1 TR001117/TR/NCATS NIH HHS/United States ; }, mesh = {Animals ; Bifidobacterium adolescentis/genetics/growth &amp; development/isolation &amp; purification ; Colon/anatomy &amp; histology/*cytology ; Escherichia coli/genetics/growth &amp; development ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*physiology ; Humans ; Male ; Mice ; Microinjections/*methods ; Organoids/anatomy &amp; histology/*cytology ; Single-Cell Analysis ; Video Recording ; Yersinia pseudotuberculosis/genetics/growth &amp; development ; }, abstract = {BACKGROUND &amp; AIMS: The human gut microbiota is becoming increasingly recognized as a key factor in homeostasis and disease. The lack of physiologically relevant in vitro models to investigate host-microbe interactions is considered a substantial bottleneck for microbiota research. Organoids represent an attractive model system because they are derived from primary tissues and embody key properties of the native gut lumen; however, access to the organoid lumen for experimental perturbation is challenging. Here, we report the development and validation of a high-throughput organoid microinjection system for cargo delivery to the organoid lumen and high-content sampling.<br><br>METHODS: A microinjection platform was engineered using off-the-shelf and 3-dimensional printed components. Microinjection needles were modified for vertical trajectories and reproducible injection volumes. Computer vision (CVis) and microfabricated CellRaft Arrays (Cell Microsystems, Research Triangle Park, NC) were used to increase throughput and enable high-content sampling of mock bacterial communities. Modeling preformed using the COMSOL Multiphysics platform predicted a hypoxic luminal environment that was functionally validated by transplantation of fecal-derived microbial communities and monocultures of a nonsporulating anaerobe.<br><br>RESULTS: CVis identified and logged locations of organoids suitable for injection. Reproducible loads of 0.2 nL could be&#xa0;microinjected into the organoid lumen at approximately 90 organoids/h. CVis analyzed and confirmed retention of injected cargos in approximately 500 organoids over 18 hours and showed the requirement to normalize for organoid growth for accurate assessment of barrier function. CVis&#xa0;analyzed growth dynamics of a mock community of green fluorescent protein- or Discosoma sp. red fluorescent protein-expressing bacteria, which grew within the organoid lumen even in the presence of antibiotics to control media contamination. Complex microbiota communities from fecal samples survived and grew in the colonoid lumen without appreciable changes in&#xa0;complexity.<br><br>CONCLUSIONS: High-throughput microinjection into organoids represents a next-generation in&#xa0;vitro approach to investigate gastrointestinal luminal physiology and the gastrointestinal microbiota.}, }
@article {pmid30121434, year = {2018}, author = {Props, R and Rubbens, P and Besmer, M and Buysschaert, B and Sigrist, J and Weilenmann, H and Waegeman, W and Boon, N and Hammes, F}, title = {Detection of microbial disturbances in a drinking water microbial community through continuous acquisition and advanced analysis of flow cytometry data.}, journal = {Water research}, volume = {145}, number = {}, pages = {73-82}, doi = {10.1016/j.watres.2018.08.013}, pmid = {30121434}, issn = {1879-2448}, mesh = {Bacteria ; *Drinking Water ; Flow Cytometry ; *Microbiota ; Staining and Labeling ; }, abstract = {Detecting disturbances in microbial communities is an important aspect of managing natural and engineered microbial communities. Here, we implemented a custom-built continuous staining device in combination with real-time flow cytometry (RT-FCM) data acquisition, which, combined with advanced FCM fingerprinting methods, presents a powerful new approach to track and quantify disturbances in aquatic microbial communities. Through this new approach we were able to resolve various natural community and single-species microbial contaminations in a flow-through drinking water reactor. Next to conventional FCM metrics, we applied metrics from a recently developed fingerprinting technique in order to gain additional insight into the microbial dynamics during these contamination events. Importantly, we found that multiple community FCM metrics based on different statistical approaches were required to fully characterize all contaminations. Furthermore we found that for accurate cell concentration measurements and accurate inference from the FCM metrics (coefficient of variation ≤ 5%), at least 1000 cells should be measured, which makes the achievable temporal resolution a function of the prevalent bacterial concentration in the system-of-interest. The integrated RT-FCM acquisition and analysis approach presented herein provides a considerable improvement in the temporal resolution by which microbial disturbances can be observed and simultaneously provides a multi-faceted toolset to characterize such disturbances.}, }
@article {pmid30121040, year = {2019}, author = {Petersen, NB and Madsen, T and Glaring, MA and Dobbs, FC and Jørgensen, NOG}, title = {Ballast water treatment and bacteria: Analysis of bacterial activity and diversity after treatment of simulated ballast water by electrochlorination and UV exposure.}, journal = {The Science of the total environment}, volume = {648}, number = {}, pages = {408-421}, doi = {10.1016/j.scitotenv.2018.08.080}, pmid = {30121040}, issn = {1879-1026}, mesh = {Bacteria/*drug effects/*radiation effects ; Electrochemical Techniques ; *Halogenation ; *Photolysis ; Ultraviolet Rays ; Waste Disposal, Fluid/*methods ; Wastewater/*analysis ; }, abstract = {Effects of ballast water (BW) treatment by ultra-violet (UV) light and electrochlorination (EC) on survival, activity and diversity of marine bacterioplankton and release of organic matter from cell damage were examined at discharge in a large-scale BW test facility (250 m[3] tanks) at Hundested harbour, Denmark. The tests were performed in accordance with the requirements for type approval testing by International Maritime Organization (IMO) and US Coast Guard. After treatment, the water was held in the tanks for one day (EC) before discharge, or 6 days (UV, including also a final UV re-treatment) before discharge. In the discharged and treated water, numbers of viable bacteria and bacterial growth rate had decreased significantly relative to the untreated water, but the total number of bacteria only was reduced in the EC-treated water. After additional storage for up to 10 days in small-scale laboratory incubations, significant regrowth of bacteria was observed after either treatment. Sequencing of 16S rRNA gene amplicons demonstrated that α-Proteobacteria initially were dominant, but γ-Proteobacteria dominated after regrowth. Bacteria used to document BW treatment efficiency (E. coli, Vibrio spp., enterococci) survived both treatments; neither treatment reduced the risk of pathogen dispersal. Concentrations of amino acids in the water were used as indicators of treatment-induced cell damage and demonstrated higher concentrations at discharge, but only after the EC treatments. Our results indicate that activity of bacteria, rather than their abundances, should be used when examining effects by ballast water treatment on microorganisms and that none of the examined treatment technologies could eliminate pathogenic bacteria.}, }
@article {pmid30117593, year = {2018}, author = {Ngo, TTN and Senior, AM and Culina, A and Santos, ESA and Vlak, JM and Zwart, MP}, title = {Quantitative analysis of the dose-response of white spot syndrome virus in shrimp.}, journal = {Journal of fish diseases}, volume = {41}, number = {11}, pages = {1733-1744}, doi = {10.1111/jfd.12877}, pmid = {30117593}, issn = {1365-2761}, mesh = {Animals ; Penaeidae/*virology ; *Viral Load ; *Virus Replication ; White spot syndrome virus 1/*physiology ; }, abstract = {White spot syndrome virus (WSSV) is an important cause of mortality and economic losses in shrimp farming. Although WSSV-induced mortality is virus dose dependent and WSSV infection does not necessarily lead to mortality, the relationships between virus-particle dose, infection and mortality have not been analysed quantitatively. Here, we explored WSSV dose-response by a combination of experiments, modelling and meta-analysis. We performed dose-response experiments in Penaeus vannamei postlarvae, recorded host mortality and detected WSSV infection. When we fitted infection models to these data, two models-differing in whether they incorporated heterogeneous host susceptibility to the virus or not-were supported for two independent experiments. To determine the generality of these results, we reanalysed published data sets and then performed a meta-analysis. We found that WSSV dose-response kinetics is indeed variable over experiments. We could not clearly identify which specific infection model has the most support by meta-analysis, but we argue that these results also are most concordant with a model incorporating varying levels of heterogeneous host susceptibility to WSSV. We have identified suitable models for analysing WSSV dose-response, which can elucidate the most basic virus-host interactions and help to avoid underestimating WSSV infection at low virus doses.}, }
@article {pmid30115327, year = {2018}, author = {Zimudzi, J and van der Waals, JE and Coutinho, TA and Cowan, DA and Valverde, A}, title = {Temporal shifts of fungal communities in the rhizosphere and on tubers in potato fields.}, journal = {Fungal biology}, volume = {122}, number = {9}, pages = {928-934}, doi = {10.1016/j.funbio.2018.05.008}, pmid = {30115327}, issn = {1878-6146}, mesh = {Agriculture ; Biodiversity ; Fungi/*classification/*genetics ; Mycobiome ; *Rhizosphere ; Sequence Analysis, DNA ; Soil Microbiology ; Solanum tuberosum/*microbiology ; }, abstract = {Soil fungal communities perform important ecological roles determining, at least in part, agricultural productivity. This study aimed at examining the fungal community dynamics in the potato rhizosphere across different development stages in two consecutive growing seasons (winter and summer). Microbial fingerprinting of rhizosphere soil samples collected at pre-planting, tuber initiation, flowering and at senescence was performed using ARISA in conjunction with Next Generation Sequencing (Illumina MiSeq). The epiphytic fungal communities on tubers at harvest were also investigated. Alpha-diversity was stable over time within and across the two seasons. In contrast, rhizospheric fungal community structure and composition were different between the two seasons and in the different plant growth stages within a given season, indicating the significance of the rhizosphere in shaping microbial communities. The phylum Ascomycota was dominant in the potato fungal rhizosphere, with Operational Taxonomic Units (OTUs) belonging to the genus Peyronellaea being the most abundant in all samples. Important fungal pathogens of potato, together with potential biological control agents and saprophytic species, were identified as indicator OTUs at different plant growth stages. These findings indicate that potato rhizosphere fungal communities are functionally diverse, which may contribute to soil health.}, }
@article {pmid30115122, year = {2018}, author = {Pérez-Jaramillo, JE and Carrión, VJ and de Hollander, M and Raaijmakers, JM}, title = {The wild side of plant microbiomes.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {143}, pmid = {30115122}, issn = {2049-2618}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Domestication ; Microbiota ; Phylogeny ; Plant Roots/*microbiology ; Plants/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, }
@article {pmid30110640, year = {2018}, author = {Kearney, SM and Gibbons, SM and Erdman, SE and Alm, EJ}, title = {Orthogonal Dietary Niche Enables Reversible Engraftment of a Gut Bacterial Commensal.}, journal = {Cell reports}, volume = {24}, number = {7}, pages = {1842-1851}, pmid = {30110640}, issn = {2211-1247}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacterial Load ; Bacteroides/isolation &amp; purification/*physiology ; Diet/*methods ; Eating/physiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Mice ; Mice, Inbred C57BL ; Seaweed/*chemistry ; Symbiosis/*physiology ; Verrucomicrobia/isolation &amp; purification/physiology ; }, abstract = {Interest in manipulating the gut microbiota to treat disease has led to a need for understanding how organisms can establish themselves when introduced into a host with an intact microbial community. Here, we employ the concept of orthogonal niche engineering: a resource typically absent from the diet, seaweed, creates a customized niche for an introduced organism. In the short term, co-introduction of this resource at 1% in the diet along with an organism with exclusive access to this resource, Bacteroides plebeius DSM 17135, enables it to colonize at a median abundance of 1% and frequently up to 10 or more percent, both on pulsed and constant seaweed diets. In a two-month follow-up after the initial treatment period, B. plebeius stops responding to seaweed in mice initially on the constant seaweed diet, suggesting treatment regime will affect controllability. These results offer potential for diet-based intervention to introduce and control target organisms.}, }
@article {pmid30108568, year = {2018}, author = {van Kruistum, H and Bodelier, PLE and Ho, A and Meima-Franke, M and Veraart, AJ}, title = {Resistance and Recovery of Methane-Oxidizing Communities Depends on Stress Regime and History; A Microcosm Study.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1714}, pmid = {30108568}, issn = {1664-302X}, abstract = {Although soil microbes are responsible for important ecosystem functions, and soils are under increasing environmental pressure, little is known about their resistance and resilience to multiple stressors. Here, we test resistance and recovery of soil methane-oxidizing communities to two different, repeated, perturbations: soil drying, ammonium addition and their combination. In replicated soil microcosms we measured methane oxidation before and after perturbations, while monitoring microbial abundance and community composition using quantitative PCR assays for the bacterial 16S rRNA and pmoA gene, and sequencing of the bacterial 16S rRNA gene. Although microbial community composition changed after soil drying, methane oxidation rates recovered, even after four desiccation events. Moreover, microcosms subjected to soil drying recovered significantly better from ammonium addition compared to microcosms not subjected to soil drying. Our results show the flexibility of microbial communities, even if abundances of dominant populations drop, ecosystem functions can recover. In addition, a history of stress may induce changes in community composition and functioning, which may in turn affect its future tolerance to different stressors.}, }
@article {pmid30106224, year = {2018}, author = {Otwell, AE and López García de Lomana, A and Gibbons, SM and Orellana, MV and Baliga, NS}, title = {Systems biology approaches towards predictive microbial ecology.}, journal = {Environmental microbiology}, volume = {20}, number = {12}, pages = {4197-4209}, doi = {10.1111/1462-2920.14378}, pmid = {30106224}, issn = {1462-2920}, support = {//Washington Research Foundation/International ; //Office of Science/International ; //U.S. Department of Energy/International ; //Lawrence Berkeley National Laboratory/International ; //National Science Foundation/International ; }, mesh = {*Ecosystem ; *Environmental Microbiology ; Environmental Monitoring/methods ; Nitrogen Cycle ; Nitrous Oxide/metabolism ; *Systems Biology ; }, abstract = {Through complex interspecies interactions, microbial processes drive nutrient cycling and biogeochemistry. However, we still struggle to predict specifically which organisms, communities and biotic and abiotic processes are determining ecosystem function and how environmental changes will alter their roles and stability. While the tools to create such a predictive microbial ecology capability exist, cross-disciplinary integration of high-resolution field measurements, detailed laboratory studies and computation is essential. In this perspective, we emphasize the importance of pursuing a multiscale, systems approach to iteratively link ecological processes measured in the field to testable hypotheses that drive high-throughput laboratory experimentation. Mechanistic understanding of microbial processes gained in controlled lab systems will lead to the development of theory that can be tested back in the field. Using N2 O production as an example, we review the current status of field and laboratory research and layout a plausible path to the kind of integration that is needed to enable prediction of how N-cycling microbial communities will respond to environmental changes. We advocate for the development of realistic and predictive gene regulatory network models for environmental responses that extend from single-cell resolution to ecosystems, which is essential to understand how microbial communities involved in N2 O production and consumption will respond to future environmental conditions.}, }
@article {pmid30105506, year = {2019}, author = {Hotaling, S and Quackenbush, CR and Bennett-Ponsford, J and New, DD and Arias-Rodriguez, L and Tobler, M and Kelley, JL}, title = {Bacterial Diversity in Replicated Hydrogen Sulfide-Rich Streams.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {559-573}, pmid = {30105506}, issn = {1432-184X}, support = {IOS-1557860//National Science Foundation/ ; IOS-1557795//National Science Foundation/ ; W911NF-15-1-0175//United States Army Research Office/ ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; Ecosystem ; Eukaryota/classification/genetics/isolation &amp; purification ; Hydrogen Sulfide/analysis/*metabolism ; Mexico ; Phylogeny ; Rivers/chemistry/*microbiology ; }, abstract = {Extreme environments typically require costly adaptations for survival, an attribute that often translates to an elevated influence of habitat conditions on biotic communities. Microbes, primarily bacteria, are successful colonizers of extreme environments worldwide, yet in many instances, the interplay between harsh conditions, dispersal, and microbial biogeography remains unclear. This lack of clarity is particularly true for habitats where extreme temperature is not the overarching stressor, highlighting a need for studies that focus on the role other primary stressors (e.g., toxicants) play in shaping biogeographic patterns. In this study, we leveraged a naturally paired stream system in southern Mexico to explore how elevated hydrogen sulfide (H2S) influences microbial diversity. We sequenced a portion of the 16S rRNA gene using bacterial primers for water sampled from three geographically proximate pairings of streams with high (> 20 μM) or low (~ 0 μM) H2S concentrations. After exploring bacterial diversity within and among sites, we compared our results to a previous study of macroinvertebrates and fish for the same sites. By spanning multiple organismal groups, we were able to illuminate how H2S may differentially affect biodiversity. The presence of elevated H2S had no effect on overall bacterial diversity (p = 0.21), a large effect on community composition (25.8% of variation explained, p < 0.0001), and variable influence depending upon the group-whether fish, macroinvertebrates, or bacteria-being considered. For bacterial diversity, we recovered nine abundant operational taxonomic units (OTUs) that comprised a core H2S-rich stream microbiome in the region. Many H2S-associated OTUs were members of the Epsilonproteobacteria and Gammaproteobacteria, which both have been implicated in endosymbiotic relationships between sulfur-oxidizing bacteria and eukaryotes, suggesting the potential for symbioses that remain to be discovered in these habitats.}, }
@article {pmid30105505, year = {2019}, author = {Castelli, M and Serra, V and Senra, MVX and Basuri, CK and Soares, CAG and Fokin, SI and Modeo, L and Petroni, G}, title = {The Hidden World of Rickettsiales Symbionts: "Candidatus Spectririckettsia obscura," a Novel Bacterium Found in Brazilian and Indian Paramecium caudatum.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {748-758}, pmid = {30105505}, issn = {1432-184X}, support = {247658//FP7 People: Marie-Curie Actions/ ; PRA_2016_58//Universit&#xe0; di Pisa/ ; }, mesh = {Brazil ; DNA, Bacterial/genetics ; India ; Paramecium caudatum/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rickettsiales/genetics/isolation &amp; purification/*physiology ; *Symbiosis ; }, abstract = {Symbioses between bacteria and eukaryotes are widespread and may have significant impact on the evolutionary history of symbiotic partners. The order Rickettsiales is a lineage of intracellular Alphaproteobacteria characterized by an obligate association with a wide range of eukaryotic hosts, including several unicellular organisms, such as ciliates and amoebas. In this work, we characterized the Rickettsiales symbionts associated with two different genotypes of the freshwater ciliate Paramecium caudatum originated from freshwater environments in distant geographical areas. Phylogenetic analyses based on 16S rRNA gene showed that the two symbionts are closely related to each other (99.4% identity), belong to the family Rickettsiaceae, but are far-related with respect to previously characterized Rickettsiales. Consequently, they were assigned to a new species of a novel genus, namely "Candidatus Spectririckettsia obscura." Screening on a database of short reads from 16S rRNA gene amplicon-based profiling studies confirmed that bacterial sequences related to the new symbiont are preferentially retrieved from freshwater environments, apparently with extremely scarce occurrence (< 0.1% positive samples). The present work provides new information on the still under-explored biodiversity of Rickettsiales, in particular those associated to ciliate host cells.}, }
@article {pmid30105504, year = {2019}, author = {Albright, MBN and Timalsina, B and Martiny, JBH and Dunbar, J}, title = {Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {597-606}, pmid = {30105504}, issn = {1432-184X}, support = {F260LANL2018//U.S. Department of Energy, Office of Science, Biological and Environmental Research Division/ ; Graduate Student Research (SCGSR) Fellowship//U.S. Department of Energy, Office of Science/ ; }, mesh = {Archaea/*genetics/metabolism ; Archaeal Proteins/*genetics/metabolism ; Bacteria/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Ecosystem ; Genome, Archaeal ; Genome, Bacterial ; Genomics ; Nitrogen/*metabolism ; Nitrogen Cycle ; }, abstract = {Despite the explosion of metagenomic sequencing data, using -omics data to predict environmental biogeochemistry remains a challenge. One or a few genes (referred to as marker genes) in a metabolic pathway of interest in meta-omic data are typically used to represent the prevalence of a biogeochemical reaction. This approach often fails to demonstrate a consistent relationship between gene abundance and an ecosystem process rate. One reason this may occur is if a marker gene is not a good representative of a complete pathway. Here, we map the presence of 11 nitrogen (N)-cycling pathways in over 6000 complete bacterial and archaeal genomes using the Integrated Microbial Genomes database. Incomplete N-cycling pathways occurred in 39% of surveyed archaeal and bacterial species revealing a weakness in current marker-gene analyses. Furthermore, we found that most organisms have limited ability to utilize inorganic N in multiple oxidation states. This suggests that inter-organism exchange of inorganic N compounds is common, highlighting the importance of both community composition and spatial structure in determining the extent of recycling versus loss in an ecosystem.}, }
@article {pmid30105011, year = {2018}, author = {Doster, E and Rovira, P and Noyes, NR and Burgess, BA and Yang, X and Weinroth, MD and Lakin, SM and Dean, CJ and Linke, L and Magnuson, R and Jones, KI and Boucher, C and Ruiz, J and Belk, KE and Morley, PS}, title = {Investigating Effects of Tulathromycin Metaphylaxis on the Fecal Resistome and Microbiome of Commercial Feedlot Cattle Early in the Feeding Period.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1715}, pmid = {30105011}, issn = {1664-302X}, support = {T32 OD012201/OD/NIH HHS/United States ; }, abstract = {The objective was to examine effects of treating commercial beef feedlot cattle with therapeutic doses of tulathromycin, a macrolide antimicrobial drug, on changes in the fecal resistome and microbiome using shotgun metagenomic sequencing. Two pens of cattle were used, with all cattle in one pen receiving metaphylaxis treatment (800 mg subcutaneous tulathromycin) at arrival to the feedlot, and all cattle in the other pen remaining unexposed to parenteral antibiotics throughout the study period. Fecal samples were collected from 15 selected cattle in each group just prior to treatment (Day 1), and again 11 days later (Day 11). Shotgun sequencing was performed on isolated metagenomic DNA, and reads were aligned to a resistance and a taxonomic database to identify alignments to antimicrobial resistance (AMR) gene accessions and microbiome content. Overall, we identified AMR genes accessions encompassing 9 classes of AMR drugs and encoding 24 unique AMR mechanisms. Statistical analysis was used to identify differences in the resistome and microbiome between the untreated and treated groups at both timepoints, as well as over time. Based on composition and ordination analyses, the resistome and microbiome were not significantly different between the two groups on Day 1 or on Day 11. However, both the resistome and microbiome changed significantly between these two sampling dates. These results indicate that the transition into the feedlot-and associated changes in diet, geography, conspecific exposure, and environment-may exert a greater influence over the fecal resistome and microbiome of feedlot cattle than common metaphylactic antimicrobial drug treatment.}, }
@article {pmid30103819, year = {2018}, author = {Lourenço, KS and Suleiman, AKA and Pijl, A and van Veen, JA and Cantarella, H and Kuramae, EE}, title = {Resilience of the resident soil microbiome to organic and inorganic amendment disturbances and to temporary bacterial invasion.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {142}, pmid = {30103819}, issn = {2049-2618}, mesh = {Bacteria/classification/drug effects/*growth &amp; development/isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Metagenomics ; Nitrogen/adverse effects ; RNA, Ribosomal, 16S/genetics ; Recycling/methods ; Saccharum/chemistry/*growth &amp; development ; Soil Microbiology ; Solid Waste/*adverse effects ; }, abstract = {BACKGROUND: Vinasse, a by-product of sugarcane ethanol production, is recycled by sugarcane plantations as a fertilizer due to its rich nutrient content. However, the impacts of the chemical and microbial composition of vinasse on soil microbiome dynamics are unknown. Here, we evaluate the recovery of the native soil microbiome after multiple disturbances caused by the application of organic vinasse residue, inorganic nitrogen, or a combination of both during the sugarcane crop-growing season (389 days). Additionally, we evaluated the resistance of the resident soil microbial community to the vinasse microbiome.<br><br>RESULTS: Vinasse applied alone or 30&#xa0;days prior to N resulted in similar changes in the soil microbial community. Furthermore, the impact of the application of vinasse together with N fertilizer on the soil microbial community differed from that of N fertilizer alone. Organic vinasse is a source of microbes, nutrients, and organic matter, and the combination of these factors drove the changes in the resident soil microbial community. However, these changes were restricted to a short period of time due to the capacity of the soil community to recover. The invasive bacteria present in the vinasse microbiome were unable to survive in the soil conditions and disappeared after 31&#xa0;days, with the exception of the Acetobacteraceae (native in the soil) and Lactobacillaceae families.<br><br>CONCLUSION: Our analysis showed that the resident soil microbial community was not resistant to vinasse and inorganic N application but was highly resilient.}, }
@article {pmid30101801, year = {2018}, author = {Muys, M and Coppens, J and Boon, N and Vlaeminck, SE}, title = {Photosynthetic oxygenation for urine nitrification.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {78}, number = {1-2}, pages = {183-194}, doi = {10.2166/wst.2018.200}, pmid = {30101801}, issn = {0273-1223}, mesh = {Humans ; Microalgae/metabolism ; Models, Biological ; *Nitrification ; *Photobioreactors ; Photosynthesis ; Scenedesmus/metabolism ; Sewage ; Urine/*chemistry ; *Water Purification ; }, abstract = {Human urine accounts for only a fraction of the sewage volume, but it contains the majority of valuable nutrient load in wastewater. In this study, synthetic urine was nitrified in a closed photo-bioreactor through photosynthetic oxygenation by means of a consortium of microalgae and nitrifying bacteria. In situ production of oxygen by photosynthetic organisms has the potential to reduce the energy costs linked to conventional aeration. This energy-efficient strategy results in stable urine for further nutrient recovery, while part of the nutrients are biologically recovered in the form of valuable biomass. In this study, urine was nitrified for the first time without conventional aeration at a maximum photosynthetic oxygenation rate of 160 mg O2 gVSS[-1] d[-1] (VSS: volatile suspended solids). A maximum volumetric nitrification rate of 67 mg N L[-1] d[-1] was achieved on 12% diluted synthetic urine. Chemical oxygen demand (COD) removal efficiencies were situated between 44% and 83% at a removal rate of 24 mg COD gVSS[-1] d[-1]. After 180 days, microscopic observations revealed that Scenedesmus sp. was the dominant microalga. Overall, photosynthetic oxygenation for urine nitrification is promising as a highly electricity efficient approach for further nutrient recovery.}, }
@article {pmid30098679, year = {2018}, author = {Kroon, SJ and Ravel, J and Huston, WM}, title = {Cervicovaginal microbiota, women's health, and reproductive outcomes.}, journal = {Fertility and sterility}, volume = {110}, number = {3}, pages = {327-336}, doi = {10.1016/j.fertnstert.2018.06.036}, pmid = {30098679}, issn = {1556-5653}, support = {R01 NR014826/NR/NINR NIH HHS/United States ; R01 NR014784/NR/NINR NIH HHS/United States ; R01 AI116799/AI/NIAID NIH HHS/United States ; }, mesh = {Cervix Uteri/microbiology/*physiology ; Dysbiosis/complications/diagnosis/microbiology ; Female ; Humans ; Infertility, Female/diagnosis/etiology/microbiology ; Lactobacillus/isolation &amp; purification/physiology ; Microbiota/*physiology ; Pregnancy ; Reproduction/*physiology ; Vagina/microbiology/*physiology ; *Women's Health/trends ; }, abstract = {The human microbiome project has shown a remarkable diversity of microbial ecology within the human body. The vaginal microbiota is unique in that in many women it is most often dominated by Lactobacillus species. However, in some women it lacks Lactobacillus spp. and is comprised of a wide array of strict and facultative anaerobes, a state that broadly correlates with increased risk for infection, disease, and poor reproductive and obstetric outcomes. Interestingly, the level of protection against infection can also vary by species and strains of Lactobacillus, and some species although dominant are not always optimal. This factors into the risk of contracting sexually transmitted infections and possibly influences the occurrence of resultant adverse reproductive outcomes such as tubal factor infertility. The composition and function of the vaginal microbiota appear to play an important role in pregnancy and fertility treatment outcomes and future research in this field will shed further translational mechanistic understanding onto the interplay of the vaginal microbiota with women's health and reproduction.}, }
@article {pmid30097682, year = {2019}, author = {Green, TJ and Siboni, N and King, WL and Labbate, M and Seymour, JR and Raftos, D}, title = {Simulated Marine Heat Wave Alters Abundance and Structure of Vibrio Populations Associated with the Pacific Oyster Resulting in a Mass Mortality Event.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {736-747}, pmid = {30097682}, issn = {1432-184X}, support = {9201300681//Macquarie University/ ; FT130100218//Australian Research Council/ ; LP160101785//Australian Research Council/ ; }, mesh = {Animals ; Aquaculture ; Climate Change ; Crassostrea/growth &amp; development/*microbiology/physiology ; Hot Temperature ; Microbiota ; Seawater/chemistry/*microbiology ; Vibrio/genetics/*growth &amp; development/metabolism ; }, abstract = {Marine heat waves are predicted to become more frequent and intense due to anthropogenically induced climate change, which will impact global production of seafood. Links between rising seawater temperature and disease have been documented for many aquaculture species, including the Pacific oyster Crassostrea gigas. The oyster harbours a diverse microbial community that may act as a source of opportunistic pathogens during temperature stress. We rapidly raised the seawater temperature from 20 °C to 25 °C resulting in an oyster mortality rate of 77.4%. Under the same temperature conditions and with the addition of antibiotics, the mortality rate was only 4.3%, strongly indicating a role for bacteria in temperature-induced mortality. 16S rRNA amplicon sequencing revealed a change in the oyster microbiome when the temperature was increased to 25 °C, with a notable increase in the proportion of Vibrio sequences. This pattern was confirmed by qPCR, which revealed heat stress increased the abundance of Vibrio harveyi and Vibrio fortis by 324-fold and 10-fold, respectively. Our findings indicate that heat stress-induced mortality of C. gigas coincides with an increase in the abundance of putative bacterial pathogens in the oyster microbiome and highlights the negative consequences of marine heat waves on food production from aquaculture.}, }
@article {pmid30097447, year = {2018}, author = {Burns, AS and Padilla, CC and Pratte, ZA and Gilde, K and Regensburger, M and Hall, E and Dove, ADM and Stewart, FJ}, title = {Broad Phylogenetic Diversity Associated with Nitrogen Loss through Sulfur Oxidation in a Large Public Marine Aquarium.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {20}, pages = {}, pmid = {30097447}, issn = {1098-5336}, mesh = {Bacteria/*classification/metabolism ; Biodiversity ; Bioreactors/microbiology ; *Denitrification ; *Genetic Variation ; Georgia ; Metagenomics ; Microbiota ; Nitrogen/*metabolism ; Oxidation-Reduction ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sulfur/*metabolism ; Wastewater ; }, abstract = {Denitrification by sulfur-oxidizing bacteria is an effective nitrate removal strategy in engineered aquatic systems. However, the community taxonomic and metabolic diversity of sulfur-driven denitrification (SDN) systems, as well as the relationship between nitrate removal and SDN community structure, remains underexplored. This is particularly true for SDN reactors applied to marine aquaria, despite the increasing use of this technology to supplement filtration. We applied 16S rRNA gene, metagenomic, and metatranscriptomic analyses to explore the microbial basis of SDN reactors operating on Georgia Aquarium's Ocean Voyager, the largest indoor closed-system seawater exhibit in the United States. The exhibit's two SDN systems vary in water retention time and nitrate removal efficiency. The systems also support significantly different microbial communities. These communities contain canonical SDN bacteria, including a strain related to Thiobacillus thioparus that dominates the system with the higher water retention time and nitrate removal but is effectively absent from the other system. Both systems contain a wide diversity of other microbes whose metagenome-assembled genomes contain genes of SDN metabolism. These include hundreds of strains of the epsilonproteobacterium Sulfurimonas, as well as gammaproteobacterial sulfur oxidizers of the Thiotrichales and Chromatiales, and a relative of Sedimenticolathiotaurini with complete denitrification potential. The SDN genes are transcribed and the taxonomic richness of the transcript pool varies markedly among the enzymatic steps, with some steps dominated by transcripts from noncanonical SDN taxa. These results indicate complex and variable SDN communities that may involve chemical dependencies among taxa as well as the potential for altering community structure to optimize nitrate removal.IMPORTANCE Engineered aquatic systems such as aquaria and aquaculture facilities have large societal value. Ensuring the health of animals in these systems requires understanding how microorganisms contribute to chemical cycling and waste removal. Focusing on the largest seawater aquarium in the United States, we explore the microbial communities in specialized reactors designed to remove excess nitrogen through the metabolic activity of sulfur-consuming microbes. We show that the diversity of microbes in these reactors is both high and highly variable, with distinct community types associated with significant differences in nitrogen removal rate. We also show that the genes encoding the metabolic steps of nitrogen removal are distributed broadly throughout community members, suggesting that the chemical transformations in this system are likely a result of microbes relying on other microbes. These results provide a framework for future studies exploring the contributions of different community members, both in waste removal and in structuring microbial biodiversity.}, }
@article {pmid30094615, year = {2019}, author = {Ren, F and Kovalchuk, A and Mukrimin, M and Liu, M and Zeng, Z and Ghimire, RP and Kivimäenpää, M and Holopainen, JK and Sun, H and Asiegbu, FO}, title = {Tissue Microbiome of Norway Spruce Affected by Heterobasidion-Induced Wood Decay.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {640-650}, pmid = {30094615}, issn = {1432-184X}, support = {276862//Academy of Finland/ ; 278424//Academy of Finland/ ; 165010015//Jiangsu Specially-Appointed Professor, China/ ; }, mesh = {Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Basidiomycota/*physiology ; *Microbiota ; Monoterpenes/analysis/metabolism ; Norway ; Picea/chemistry/metabolism/*microbiology ; Plant Diseases/*microbiology ; Wood/chemistry/metabolism/microbiology ; }, abstract = {Plants live in close association with microbial symbionts, which may affect the host fitness, productivity, and tolerance against biotic and abiotic stressors. The composition of plant microbial communities is influenced by many biotic and abiotic factors, but little is known about the effect of plant pathogens on the structure of these communities. In this study, we investigated the structure of bacterial communities associated with different tissues of asymptomatic and symptomatic (Heterobasidion-rotten) Norway spruce (Picea abies (L.) Karst.) trees. Our results demonstrated that each of the investigated anatomic tissues (root, bark, down stem, upper stem, and needles) harbored a unique bacterial assemblage. However, the health status of the host trees had little effect on the structure of bacterial communities, as the only significant differences among asymptomatic and symptomatic trees were found in the composition of the bacterial communities of needles. Proteobacteria was predominant in all anatomic regions with the highest abundance in needles (86.7%), whereas Actinobacteria showed an opposite trend, being more abundant in the woody tissues than in needles. Additionally, we performed profiling of terpenoid compounds present in spruce xylem and phloem. Total concentrations of monoterpenes and sesquiterpenes were considerably higher in asymptomatic trees. However, we found no significant correlations between terpenoid profiles of spruce trees and the composition of their bacterial communities. Our results provide an insight into the diversity of bacteria associated with Norway spruce tree tissues. At the same time, the health status and terpenoid content of host trees had a limited effect on the composition of bacterial communities in our survey.}, }
@article {pmid30093611, year = {2018}, author = {Liang, J and Zhou, Z and Huo, C and Shi, Z and Cole, JR and Huang, L and Konstantinidis, KT and Li, X and Liu, B and Luo, Z and Penton, CR and Schuur, EAG and Tiedje, JM and Wang, YP and Wu, L and Xia, J and Zhou, J and Luo, Y}, title = {More replenishment than priming loss of soil organic carbon with additional carbon input.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {3175}, pmid = {30093611}, issn = {2041-1723}, support = {DE SC00114085//U.S. Department of Energy (DOE)/International ; DE SC0004601//U.S. Department of Energy (DOE)/International ; DE SC0010715//U.S. Department of Energy (DOE)/International ; OIA-1301789//National Science Foundation (NSF)/International ; }, abstract = {Increases in carbon (C) inputs to soil can replenish soil organic C (SOC) through various mechanisms. However, recent studies have suggested that the increased C input can also stimulate the decomposition of old SOC via priming. Whether the loss of old SOC by priming can override C replenishment has not been rigorously examined. Here we show, through data-model synthesis, that the magnitude of replenishment is greater than that of priming, resulting in a net increase in SOC by a mean of 32% of the added new C. The magnitude of the net increase in SOC is positively correlated with the nitrogen-to-C ratio of the added substrates. Additionally, model evaluation indicates that a two-pool interactive model is a parsimonious model to represent the SOC decomposition with priming and replenishment. Our findings suggest that increasing C input to soils likely promote SOC accumulation despite the enhanced decomposition of old C via priming.}, }
@article {pmid30092404, year = {2018}, author = {Lian, Y and Yan, C and Xu, H and Yang, J and Yu, Y and Zhou, J and Shi, Y and Ren, J and Ji, G and Wang, K}, title = {A Novel lncRNA, LINC00460, Affects Cell Proliferation and Apoptosis by Regulating KLF2 and CUL4A Expression in Colorectal Cancer.}, journal = {Molecular therapy. Nucleic acids}, volume = {12}, number = {}, pages = {684-697}, pmid = {30092404}, issn = {2162-2531}, abstract = {Emerging evidence has proven that long noncoding RNAs (lncRNAs) play important roles in human colorectal cancer (CRC) biology, although few lncRNAs have been characterized in CRC. Therefore, the functional significance of lncRNAs in the malignant progression of CRC still needs to be further explored. In this study, through analyzing TCGA RNA sequencing data and other publicly available microarray data, we found a novel lncRNA, LINC00460, whose expression was significantly upregulated in CRC tissues compared to adjacent normal tissues. Consistently, real-time qPCR results also verified that LINC00460 was overexpressed in CRC tissues and cells. Furthermore, high LINC00460 expression levels in CRC specimens were correlated with larger tumor size, advanced tumor stage, lymph node metastasis and shorter overall survival. In vitro and in vivo assays of LINC00460 alterations revealed a complex integrated phenotype affecting cell growth and apoptosis. Mechanistically, LINC00460 repressed Krüppel-like factor 2 (KLF2) transcription by binding to enhancer of zeste homolog 2 (EZH2). LINC00460 also functioned as a molecular sponge for miR-149-5p, antagonizing its ability to repress cullin 4A (CUL4A) protein translation. Taken together, our findings support a model in which the LINC00460/EZH2/KLF2 and LINC00460/miR-149-5p/CUL4A crosstalk serve as critical effectors in CRC tumorigenesis and progression, suggesting new therapeutic directions in CRC.}, }
@article {pmid30088464, year = {2018}, author = {Gil-Pulido, B and Tarpey, E and Finnegan, W and Zhan, X and Dobson, AD and O'Leary, N}, title = {Dominance of the genus Polaromonas in the microbial ecology of an Intermittently Aerated Sequencing Batch Reactor (IASBR) treating dairy processing wastewater under varying aeration rates.}, journal = {The Journal of dairy research}, volume = {85}, number = {3}, pages = {388-390}, doi = {10.1017/S0022029918000572}, pmid = {30088464}, issn = {1469-7629}, mesh = {Comamonadaceae/classification/isolation &amp; purification/*physiology ; DNA, Bacterial/analysis ; *Dairy Products ; Food-Processing Industry/*methods ; Oxygen/*administration &amp; dosage ; Sewage/microbiology ; Wastewater/*microbiology ; Water Purification/*instrumentation/methods ; }, abstract = {In this Research Communication we investigate potential correlations between key bacterial groups and nutrient removal efficiency in an Intermittently Aerated Sequencing Batch Reactor (IASBR) treating synthetic dairy processing wastewater. Reactor aeration rates of 0·6 and 0·4 litre per minute (LPM) were applied to an 8 l laboratory scale system and the relative impacts on IASBR microbial community structure and orthophosphate (PO4-P) and ammonium (NH4-N) removal efficiencies compared. Aeration at 0·6 LPM over several sludge retention times (SRTs) resulted in approximately 92% removal efficiencies for both PO4-P and NH4-N. Biomass samples subjected to next-generation sequencing (NGS), 16S rRNA profiling revealed a concomitant enrichment of Polaromonas under 0·6 LPM conditions, up to ~50% relative abundance within the reactor biomass. The subsequent shift in reactor aeration to 0·4 LPM, over a period of 3 SRTs, resulted in markedly reduced nutrient removal efficiencies for PO4-P (50%) and NH4-N (45%). An 85·7% reduction in the genus level relative abundance of Polaromonas was observed under 0·4 LPM aeration conditions over the same period.}, }
@article {pmid30088023, year = {2019}, author = {Polano, C and Martini, M and Savian, F and Moruzzi, S and Ermacora, P and Firrao, G}, title = {Genome Sequence and Antifungal Activity of Two Niche-Sharing Pseudomonas protegens Related Strains Isolated from Hydroponics.}, journal = {Microbial ecology}, volume = {77}, number = {4}, pages = {1025-1035}, pmid = {30088023}, issn = {1432-184X}, support = {2370 - STAYFRESH//Ager - Agroalimentare e Ricerca/ ; }, mesh = {Antifungal Agents/chemistry/*pharmacology ; *Genome, Bacterial ; Hydroponics ; Pseudomonas/*chemistry/*genetics ; Pythium/*drug effects/growth &amp; development ; Rhizoctonia/*drug effects/growth &amp; development ; }, abstract = {This work reports the comparison of the genome sequence and the ability to inhibit fungal growth of two Pseudomonas protegens related strains that were isolated from the same hydroponic culture of lamb's lettuce. The two strains were very similar in their core genome but one strain, Pf4, contained three gene clusters for the production of secondary metabolites, i.e., pyoluteorin (plt), pyrrolnitrin (prn), and rhizoxin (rzx), that were missing in the other strain, Pf11. The difference between the two strains was not due to simple insertion events, but to a relatively complex differentiation focused on the accessory genomes. In dual culture assays, both strains inhibited nearly all tested fungal strains, yet Pf4 exerted a significantly stronger fungal growth inhibition than Pf11. In addition to the differences in the secondary metabolite production associated genes abundance, the genome of Pf4 was more stable, smaller in size and with a lower number of transposons. The preservation of a dynamic equilibrium within natural populations of different strains comprised in the same species but differing in their secondary metabolite repertoire and in their genome stability may be functional to the adaptation to environmental changes.}, }
@article {pmid30087659, year = {2018}, author = {Trivedi, CB and Lau, GE and Grasby, SE and Templeton, AS and Spear, JR}, title = {Low-Temperature Sulfidic-Ice Microbial Communities, Borup Fiord Pass, Canadian High Arctic.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1622}, pmid = {30087659}, issn = {1664-302X}, abstract = {A sulfur-dominated supraglacial spring system found at Borup Fiord Pass (BFP), Ellesmere Island, Nunavut, Canada, is a unique sulfur-on-ice system expressed along the toe of a glacier. BFP has an intermittent flowing, subsurface-derived, glacial spring that creates a large white-yellow icing (aufeis) that extends down-valley. Over field campaigns in 2014, 2016, and 2017, numerous samples were collected and analyzed for both microbial community composition and aqueous geochemistry. Samples were collected from multiple site types: spring discharge fluid, aufeis (spring-derived ice), melt pools with sedimented cryoconite material, and mineral precipitate scrapings, to probe how microbial communities differed between site types in a dynamic freeze/thaw sulfur-rich system. Dissolved sulfate varied between 0.07 and 11.6 mM and was correlated with chloride concentrations, where the fluids were saltiest among spring fluids. The highest sulfate samples exhibited high dissolved sulfide values between 0.22 and 2.25 mM. 16S rRNA gene sequencing from melt pool and aufeis samples from the 2014 campaign were highly abundant in operational taxonomic units (OTUs) closely related to sulfur-oxidizing microorganisms (SOM; Sulfurimonas, Sulfurovum, and Sulfuricurvum). Subsequent sampling 2 weeks later had fewer SOMs and showed an increased abundance of the genus Flavobacterium. Desulfocapsa, an organism that specializes in the disproportionation of inorganic sulfur compounds was also found. Samples from 2016 and 2017 revealed that microorganisms present were highly similar in community composition to 2014 samples, primarily echoed by the continued presence of Flavobacterium sp. Results suggest that while there may be acute events where sulfur cycling organisms dominate, a basal community structure appears to dominate over time and site type. These results further enhance our knowledge of low-temperature sulfur systems on Earth, and help to guide the search for potential life on extraterrestrial worlds, such as Europa, where similar low-temperature sulfur-rich conditions may exist.}, }
@article {pmid30087358, year = {2018}, author = {Chaib De Mares, M and Jiménez, DJ and Palladino, G and Gutleben, J and Lebrun, LA and Muller, EEL and Wilmes, P and Sipkema, D and van Elsas, JD}, title = {Expressed protein profile of a Tectomicrobium and other microbial symbionts in the marine sponge Aplysina aerophoba as evidenced by metaproteomics.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {11795}, pmid = {30087358}, issn = {2045-2322}, support = {607786//EC | Seventh Framework Programme (European Union Seventh Framework Programme)/International ; 607786//EC | Seventh Framework Programme (European Union Seventh Framework Programme)/International ; 607786//EC | Seventh Framework Programme (European Union Seventh Framework Programme)/International ; 607786//EC | Seventh Framework Programme (European Union Seventh Framework Programme)/International ; }, mesh = {Animals ; *Aquatic Organisms/metabolism/microbiology ; Bacteria/*metabolism ; Bacterial Proteins/*biosynthesis ; Gene Expression Regulation/*physiology ; Porifera/*microbiology ; Proteomics ; Symbiosis/*physiology ; }, abstract = {Aplysina aerophoba is an emerging model marine sponge, with a well-characterized microbial community in terms of diversity and structure. However, little is known about the expressed functional capabilities of its associated microbes. Here, we present the first metaproteomics-based study of the microbiome of A. aerophoba. We found that transport and degradation of halogenated and chloroaromatic compounds are common active processes in the sponge microbiomes. Our data further reveal that the highest number of proteins were affiliated to a sponge-associated Tectomicrobium, presumably from the family Entotheonellaceae, as well as to the well-known symbiont "Candidatus Synechococcus spongiarium", suggesting a high metabolic activity of these two microorganisms in situ. Evidence for nitric oxide (NO) conversion to nitrous oxide was consistently observed for Tectomicrobia across replicates, by production of the NorQ protein. Moreover, we found a potential energy-yielding pathway through CO oxidation by putative Chloroflexi bacteria. Finally, we observed expression of enzymes that may be involved in the transformation of chitin, glycoproteins, glycolipids and glucans into smaller molecules, consistent with glycosyl hydrolases predicted from analyses of the genomes of Poribacteria sponge symbionts. Thus, this study provides crucial links between expressed proteins and specific members of the A. aerophoba microbiome.}, }
@article {pmid30086814, year = {2018}, author = {Yurchenko, V and Lukeš, J}, title = {Parasites and their (endo)symbiotic microbes.}, journal = {Parasitology}, volume = {145}, number = {10}, pages = {1261-1264}, doi = {10.1017/S0031182018001257}, pmid = {30086814}, issn = {1469-8161}, mesh = {Animals ; Biological Evolution ; Organelles ; Parasites/*microbiology ; *Symbiosis ; }, abstract = {Thanks to modern molecular biology methods, our understanding of the impact of (endo)symbiotic bacteria on parasitic protists and helminths is growing fast. In this issue, 9 papers have been brought together that describe various facets of the relationships between these microorganisms, reveal their range and high frequency, as well as their capacity to create novel biological complexity. Comparative analyses of these host-endosymbiont interactions indicate that there may be no discrete types of relationships but rather a continuum ranging from a dispensable endosymbiont minimally integrated within the host cell to organelles, such as mitochondria and plastids that evolved into an indispensable, deeply integrated components of the cell. We hope that this series of studies on parasites and (endo)symbiotic bacteria will increase awareness about these relationships and their representation in microbial ecology models.}, }
@article {pmid30084932, year = {2018}, author = {Cantos-Parra, E and Ramió-Pujol, S and Colprim, J and Puig, S and Bañeras, L}, title = {Specific detection of "Clostridium autoethanogenum", Clostridium ljungdahlii and Clostridium carboxidivorans in complex bioreactor samples.}, journal = {FEMS microbiology letters}, volume = {365}, number = {18}, pages = {}, doi = {10.1093/femsle/fny191}, pmid = {30084932}, issn = {1574-6968}, mesh = {Bioreactors/*microbiology ; Clostridium/*classification/genetics/*isolation &amp; purification ; DNA Gyrase/*genetics ; DNA Primers/genetics ; Membrane Transport Proteins/*genetics ; Polymerase Chain Reaction/*methods ; }, abstract = {The high genetic similarity between some carboxydotrophic bacteria does not allow for the use of common sequencing techniques targeting the 16S rRNA gene for species identification. 16S rRNA sequencing fails to discriminate among Clostridium ljungdahlii and 'Clostridium autoethanogenum', despite this two species exhibit significant differences in CO2 assimilation and alcohol production. In this work we designed PCR primers targeting for the DNA gyrase subunit A (gyrA) and a putative formate/nitrite transporter (fnt) to specifically detect the presence of 'C. autoethanogenum', C. ljungdahlii or Clostridium carboxidivorans. We could confirm the simultaneous presence of C. ljungdahlii and 'C. autoethanogenum' in different bioreactors, and a preference of the latter for high CO2 content.}, }
@article {pmid30083828, year = {2019}, author = {Bai, M and Sen, B and Wang, Q and Xie, Y and He, Y and Wang, G}, title = {Molecular Detection and Spatiotemporal Characterization of Labyrinthulomycete Protist Diversity in the Coastal Waters Along the Pearl River Delta.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {394-405}, pmid = {30083828}, issn = {1432-184X}, support = {31670044//National Natural Science Foundation of China/ ; 91751115//National Natural Science Foundation of China/ ; 2017YFC1404500//National Key R&amp;D program of China/ ; }, mesh = {*Biodiversity ; Nitrogen/analysis/metabolism ; Phosphates/analysis/metabolism ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Rivers/chemistry/*parasitology ; Seawater/chemistry/*parasitology ; Stramenopiles/classification/genetics/*isolation &amp; purification/metabolism ; }, abstract = {The heterotrophic labyrinthulomycete protists have long been known to play an important role in the nutrient cycling of coastal seawater. Yet, their spatiotemporal abundance and diversity in polluted coastal waters remain poorly discussed, due in part to the paucity of a rapid detection method. To this end, we developed a qPCR detection method based on a newly designed primer pair targeting their 18S rRNA gene. Using this method, we studied the population dynamics of labyrinthulomycete protists in nutrient-rich (Shenzhen Bay) and low-nutrient (Daya) coastal habitats along the Pearl River Delta. We found a significantly (P < 0.05) higher abundance of Labyrinthulomycetes in the Shenzhen bay (average 3455 gene copies mL[-1]) than that in Daya Bay (average 378 gene copies mL[-1]). Their abundance gradient positively correlated (P < 0.05) with the levels of inorganic nitrogen and phosphates. Further characterization of the molecular diversity of these protists in Shenzhen Bay using different primer sets revealed the presence of several genera besides a large number of unclassified OTUs. Regardless of the primer biases, our results show significant (P < 0.05) spatiotemporal changes in the molecular abundance and diversity of these heterotrophic protists. Overall, this study provides a rapid molecular detection tool for Labyrinthulomycetes and expands our current understanding of their dynamics controlled by physicochemical gradients in coastal waters.}, }
@article {pmid30083827, year = {2019}, author = {Weinisch, L and Kirchner, I and Grimm, M and Kühner, S and Pierik, AJ and Rosselló-Móra, R and Filker, S}, title = {Correction to: Glycine Betaine and Ectoine Are the Major Compatible Solutes Used by Four Different Halophilic Heterotrophic Ciliates.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {332}, doi = {10.1007/s00248-018-1241-x}, pmid = {30083827}, issn = {1432-184X}, abstract = {The original version of this article unfortunately contained mistakes in the author affiliation, the references given in two tables and in a figure legend.}, }
@article {pmid30083145, year = {2018}, author = {Costa, OYA and Raaijmakers, JM and Kuramae, EE}, title = {Microbial Extracellular Polymeric Substances: Ecological Function and Impact on Soil Aggregation.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1636}, pmid = {30083145}, issn = {1664-302X}, abstract = {A wide range of microorganisms produce extracellular polymeric substances (EPS), highly hydrated polymers that are mainly composed of polysaccharides, proteins, and DNA. EPS are fundamental for microbial life and provide an ideal environment for chemical reactions, nutrient entrapment, and protection against environmental stresses such as salinity and drought. Microbial EPS can enhance the aggregation of soil particles and benefit plants by maintaining the moisture of the environment and trapping nutrients. In addition, EPS have unique characteristics, such as biocompatibility, gelling, and thickening capabilities, with industrial applications. However, despite decades of research on the industrial potential of EPS, only a few polymers are widely used in different areas, especially in agriculture. This review provides an overview of current knowledge on the ecological functions of microbial EPSs and their application in agricultural soils to improve soil particle aggregation, an important factor for soil structure, health, and fertility.}, }
@article {pmid30083144, year = {2018}, author = {Kroeger, ME and Delmont, TO and Eren, AM and Meyer, KM and Guo, J and Khan, K and Rodrigues, JLM and Bohannan, BJM and Tringe, SG and Borges, CD and Tiedje, JM and Tsai, SM and Nüsslein, K}, title = {New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1635}, pmid = {30083144}, issn = {1664-302X}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; }, abstract = {Deforestation in the Brazilian Amazon occurs at an alarming rate, which has broad effects on global greenhouse gas emissions, carbon storage, and biogeochemical cycles. In this study, soil metagenomes and metagenome-assembled genomes (MAGs) were analyzed for alterations to microbial community composition, functional groups, and putative physiology as it related to land-use change and tropical soil. A total of 28 MAGs were assembled encompassing 10 phyla, including both dominant and rare biosphere lineages. Amazon Acidobacteria subdivision 3, Melainabacteria, Microgenomates, and Parcubacteria were found exclusively in pasture soil samples, while Candidatus Rokubacteria was predominant in the adjacent rainforest soil. These shifts in relative abundance between land-use types were supported by the different putative physiologies and life strategies employed by the taxa. This research provides unique biological insights into candidate phyla in tropical soil and how deforestation may impact the carbon cycle and affect climate change.}, }
@article {pmid30081136, year = {2018}, author = {Losasso, C and Di Cesare, A and Mastrorilli, E and Patuzzi, I and Cibin, V and Eckert, EM and Fontaneto, D and Vanzo, A and Ricci, A and Corno, G}, title = {Assessing antimicrobial resistance gene load in vegan, vegetarian and omnivore human gut microbiota.}, journal = {International journal of antimicrobial agents}, volume = {52}, number = {5}, pages = {702-705}, doi = {10.1016/j.ijantimicag.2018.07.023}, pmid = {30081136}, issn = {1872-7913}, mesh = {Bacteria/classification/*genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Diet/*methods ; *Drug Resistance, Bacterial ; *Gastrointestinal Microbiome ; *Genes, Bacterial ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Vegetarians ; }, abstract = {Massive antimicrobial use in animal farming is considered as the greatest contributor to the presence of antimicrobial-resistant bacteria (ARB) in food of animal origin. Nevertheless, sewage from treated animals may impact on vegetables grown on fertilised fields, but it is largely unknown whether and to what extent ARB are transferred to vegetables and the human gut. It could be hypothesised that food of animal and vegetal origin have a different role in ARB transfer to the human gut and that different diets could be characterised by different antimicrobial resistance gene (ARG) loads. This study included three groups comprising vegans (n = 26), vegetarians (n = 32) and omnivores (n = 43). Metadata regarding food consumption and anthropometric parameters were collected. Gut microbial communities were investigated by 16S rDNA analysis. Four ARGs (sul2, tetA, blaTEM and strB) were quantified by qPCR. The results showed a lower total load of investigated ARGs in vegan diet (pairwise comparison adjusted results: omnivorous-vegan, P = 0.0119; omnivorous-vegetarian, P = 0.7416; and vegan-vegetarian, P = 0.0119). No significant differences in abundance of each gene separately were found between the three groups. Neither the amount of animal protein nor the occurrence of ARGs was significant in explaining differences in the gut microbial community of individuals, and a large proportion of the differences between community composition (PERMANOVA, 46.87%) was not explained by the analysed variables. The results support the role of omnivorous and vegetarian diets in accumulating ARGs, suggesting a possible role for animal-derived food consumption.}, }
@article {pmid30078567, year = {2018}, author = {Cordero, RJB and Robert, V and Cardinali, G and Arinze, ES and Thon, SM and Casadevall, A}, title = {Impact of Yeast Pigmentation on Heat Capture and Latitudinal Distribution.}, journal = {Current biology : CB}, volume = {28}, number = {16}, pages = {2657-2664.e3}, pmid = {30078567}, issn = {1879-0445}, support = {R01 AI052733/AI/NIAID NIH HHS/United States ; }, mesh = {*Acclimatization ; *Body Temperature Regulation ; Candida/*physiology ; Cryptococcus neoformans/*physiology ; Hot Temperature ; Pigmentation/*physiology ; }, abstract = {Pigmentation is a fundamental characteristic of living organisms that is used to absorb radiation energy and to regulate temperature. Since darker pigments absorb more radiation than lighter ones, they stream more heat, which can provide an adaptive advantage at higher latitudes and a disadvantage near the Tropics, because of the risk of overheating. This intuitive process of color-mediated thermoregulation, also known as the theory of thermal melanism (TTM), has been only tested in ectothermic animal models [1-8]. Here, we report an association between yeast pigmentation and their latitude of isolation, with dark-pigmented isolates being more frequent away from the Tropics. To measure the impact of microbial pigmentation in energy capture from radiation, we generated 20 pigmented variants of Cryptococcus neoformans and Candida spp. Infrared thermography revealed that dark-pigmented yeasts heated up faster and reached higher temperatures (up to 2-fold) than lighter ones following irradiation. Melanin-pigmented C. neoformans exhibited a growth advantage relative to non-melanized yeasts when incubated under the light at 4°C but increased thermal susceptibility at 25°C ambient temperatures. Our results extend the TTM to microbiology and suggest pigmentation as an ancient adaptation mechanism for gaining thermal energy from radiation. The contribution of microbial pigmentation in heat absorption is relevant to microbial ecology and for estimating global temperatures. The color variations available in yeasts provide new opportunities in chromatology to quantify radiative heat transfer and validate biophysical models of heat flow [9] that are not possible with plants or animals.}, }
@article {pmid30077912, year = {2018}, author = {Seuntjens, D and Carvajal-Arroyo, JM and Ruopp, M and Bunse, P and De Mulder, CP and Lochmatter, S and Agrawal, S and Boon, N and Lackner, S and Vlaeminck, SE}, title = {High-resolution mapping and modeling of anammox recovery from recurrent oxygen exposure.}, journal = {Water research}, volume = {144}, number = {}, pages = {522-531}, doi = {10.1016/j.watres.2018.07.024}, pmid = {30077912}, issn = {1879-2448}, mesh = {Ammonium Compounds/metabolism ; Autotrophic Processes ; Bacteria/*metabolism ; Bioreactors/*microbiology ; *Models, Theoretical ; Nitrogen ; Oxygen/*metabolism ; Waste Disposal, Fluid/instrumentation/*methods ; }, abstract = {Oxygen inhibits anammox, a bioconversion executed by anoxic ammonium oxidizing bacteria (AnAOB). Nonetheless, oxygen is mostly found in the proximity of AnAOB in nitrogen removal applications, being a substrate for nitritation. The experiments performed to date were mostly limited to batch activity tests where AnAOB activity is estimated during oxygen exposure. However, little attention has been paid to the recovery and reversibility of activity following aerobic conditions, of direct relevance for bioreactor operation. In this work, anoxic and autotrophic reactor cultivation at 20 °C yielded an enriched microbial community in AnAOB, consisting for 75% of a member of the genus Brocadia. High-resolution kinetic data were obtained with online ammonium measurements and further processed with a newly developed Python data pipeline. The experimentally obtained AnAOB response showed complete inhibition until micro-aerobic conditions were reached again (<0.02 mg O2 L[-1]). After oxygen inhibition, AnAOB recovered gradually, with recovery times of 5-37 h to reach a steady-state activity, dependent on the perceived inhibition. The recovery immediately after inhibition was lowest when exposed to higher oxygen concentrations (range: 0.5-8 mg O2 L[-1]) with long contact times (range: 9-24 h). The experimental data did not fit well with a conventional 'instant recovery' Monod-type inhibition model. Yet, the fit greatly improved by incorporating a dynamic growth rate formula accurately describing gradual activity recovery. With the upgraded model, long-term kinetic simulations for partial nitritation/anammox (PN/A) with intermittent aeration showed a decrease in growth rate compared to the instant recovery mode. These results indicate that recovery of AnAOB after oxygen exposure was previously overlooked. It is recommended to account for this effect in the intensification of partial nitritation/anammox.}, }
@article {pmid30077104, year = {2018}, author = {Zhou, L and Xu, X and Xia, S}, title = {Effects of sulfate on simultaneous nitrate and selenate removal in a hydrogen-based membrane biofilm reactor for groundwater treatment: Performance and biofilm microbial ecology.}, journal = {Chemosphere}, volume = {211}, number = {}, pages = {254-260}, doi = {10.1016/j.chemosphere.2018.07.092}, pmid = {30077104}, issn = {1879-1298}, mesh = {Biofilms/*drug effects ; Bioreactors/*microbiology ; Groundwater/*chemistry ; Hydrogen/*chemistry ; Nitrates/*chemistry ; Selenic Acid/*chemistry ; Sulfates/*chemistry ; }, abstract = {Effects of sulfate on simultaneous nitrate and selenate removal in a hydrogen-based membrane biofilm reactor (MBfR) for groundwater treatment was identified with performance and biofilm microbial ecology. In whole operation, MBfR had almost 100% removal of nitration even with 50 mg mL[-1] sulfate. Moreover, selenate degradation increased from 95% to approximate 100% with sulfate addition, indicating that sulfate had no obvious effects on nitrate degradation, and even partly promoted selenate removal. Short-term sulfate effect experiment further showed that Gibbs free energy of reduction (majority) and abiotic sulfide oxidation (especially between sulfate and selenate) contributed to degradable performance with sulfate. Microbial ecology showed that high percentage of Hydrogenophaga (≥75%) was one of the contributors for the stable and efficient nitrate degradation. Chemoheterotrophy (ratio>0.3) and dark hydrogen oxidation (ratio>0.3) were the majority of functional profile for biofilm in MBfR, and sulfate led to profiles of sulfate respiration and respiration of sulfur compounds in biofilm. Additionally, no special bacteria for selenate degradation was identified in biofilm microbial ecology, and selenate degradation was relied on Hydrogenophaga (75% of ecology percentage with sulfate addition) and Desulfovibrionaceae (4% of ecology percentage with sulfate addition). But with overloading sulfate, Desulfovibrionaceae was prior to sulfate degradation for energy supply and thus inhibited selenate removal.}, }
@article {pmid30076592, year = {2018}, author = {Nottingham, AT and Fierer, N and Turner, BL and Whitaker, J and Ostle, NJ and McNamara, NP and Bardgett, RD and Leff, JW and Salinas, N and Silman, MR and Kruuk, LEB and Meir, P}, title = {Microbes follow Humboldt: temperature drives plant and soil microbial diversity patterns from the Amazon to the Andes.}, journal = {Ecology}, volume = {99}, number = {11}, pages = {2455-2466}, pmid = {30076592}, issn = {0012-9658}, support = {NE/G018278/1//UK Natural Environment Research Council (NERC)/International ; NE/N006852/1//UK Natural Environment Research Council (NERC)/International ; DP170104091//Australian Research Council (ARC)/International ; FT1110100453//Australian Research Council (ARC)/International ; FP7-2012-329360//European Union Marie-Curie Fellowship/International ; }, mesh = {Biodiversity ; Ecosystem ; Fungi/classification ; Soil/*chemistry ; *Soil Microbiology ; Temperature ; }, abstract = {More than 200 years ago, Alexander von Humboldt reported that tropical plant species richness decreased with increasing elevation and decreasing temperature. Surprisingly, coordinated patterns in plant, bacterial, and fungal diversity on tropical mountains have not yet been observed, despite the central role of soil microorganisms in terrestrial biogeochemistry and ecology. We studied an Andean transect traversing 3.5 km in elevation to test whether the species diversity and composition of tropical forest plants, soil bacteria, and fungi follow similar biogeographical patterns with shared environmental drivers. We found coordinated changes with elevation in all three groups: species richness declined as elevation increased, and the compositional dissimilarity among communities increased with increased separation in elevation, although changes in plant diversity were larger than in bacteria and fungi. Temperature was the dominant driver of these diversity gradients, with weak influences of edaphic properties, including soil pH. The gradients in microbial diversity were strongly correlated with the activities of enzymes involved in organic matter cycling, and were accompanied by a transition in microbial traits towards slower-growing, oligotrophic taxa at higher elevations. We provide the first evidence of coordinated temperature-driven patterns in the diversity and distribution of three major biotic groups in tropical ecosystems: soil bacteria, fungi, and plants. These findings suggest that interrelated and fundamental patterns of plant and microbial communities with shared environmental drivers occur across landscape scales. These patterns are revealed where soil pH is relatively constant, and have implications for tropical forest communities under future climate change.}, }
@article {pmid30070653, year = {2019}, author = {Winkelmann, T and Smalla, K and Amelung, W and Baab, G and Grunewaldt-Stöcker, G and Kanfra, X and Meyhöfer, R and Reim, S and Schmitz, M and Vetterlein, D and Wrede, A and Zühlke, S and Grunewaldt, J and Weiß, S and Schloter, M}, title = {Apple Replant Disease: Causes and Mitigation Strategies.}, journal = {Current issues in molecular biology}, volume = {30}, number = {}, pages = {89-106}, doi = {10.21775/cimb.030.089}, pmid = {30070653}, issn = {1467-3045}, mesh = {Bacteria ; *Disease Susceptibility ; Fungi ; Host-Pathogen Interactions ; Malus/*physiology ; Microbial Interactions ; Microbiota ; Plant Diseases/*microbiology ; Plant Roots/microbiology/physiology ; Soil Microbiology ; }, abstract = {After replanting apple (Malus domestica Borkh.) on the same site severe growth suppressions, and a decline in yield and fruit quality are observed in all apple producing areas worldwide. The causes of this complex phenomenon, called apple replant disease (ARD), are only poorly understood up to now which is in part due to inconsistencies in terms and methodologies. Therefore we suggest the following definition for ARD: ARD describes a harmfully disturbed physiological and morphological reaction of apple plants to soils that faced alterations in their (micro-) biome due to the previous apple cultures. The underlying interactions likely have multiple causes that extend beyond common analytical tools in microbial ecology. They are influenced by soil properties, faunal vectors, and trophic cascades, with genotype-specific effects on plant secondary metabolism, particularly phytoalexin biosynthesis. Yet, emerging tools allow to unravel the soil and rhizosphere (micro-) biome, to characterize alterations of habitat quality, and to decipher the plant reactions. Thereby, deep insights into the reactions taking place at the root rhizosphere interface will be gained. Counteractions are suggested, taking into account that culture management should emphasize on improving soil microbial and faunal diversity as well as habitat quality rather than focus on soil disinfection.}, }
@article {pmid30069710, year = {2019}, author = {McFrederick, QS and Rehan, SM}, title = {Wild Bee Pollen Usage and Microbial Communities Co-vary Across Landscapes.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {513-522}, pmid = {30069710}, issn = {1432-184X}, support = {CA-R-ENT-5109-H//National Institute of Food and Agriculture/ ; NC1173//National Institute of Food and Agriculture/ ; 1638728//Directorate for Biological Sciences/ ; 1456296//Directorate for Biological Sciences/ ; 9659-15//National Geographic Society/ ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bees/*physiology ; Flowers/classification/microbiology ; Fungi/classification/genetics/*isolation &amp; purification ; *Microbiota ; Phylogeny ; Pollen/classification/*microbiology ; }, abstract = {Bees forage for pollen and nectar at flowers but simultaneously acquire pathogenic, commensal, and likely beneficial microbes from these same flowers. Characterizing pollen usage of wild bees is therefore crucial to their conservation yet remains a challenging task. To understand pollen usage across landscapes and how this affects microbial communities found in the pollen provisions collected from flowers, we studied the generalist small carpenter bee Ceratina australensis. We collected C. australensis nests from three different climatic zones across eastern and southern Australia. To characterize the plant, fungal, and bacterial composition of these pollen provisions, we used a metabarcoding and next-generation sequencing approach. We found that the species richness of plant types, fungi, and bacteria was highest in a subtropical zone compared to a temperate or a grassland zone. The composition of these communities also differentiated by zone, particularly in pollen composition and fungal communities. Moreover, pollen composition strongly correlated with fungal community composition, suggesting that variation in pollen usage across landscapes results in variation in microbial communities. While how these pollen usage and microbial community patterns affect bee health merits additional work, these data further our understanding of how flowering plant community composition affects not only the pollen usage of a generalist bee but also its associated microbial communities.}, }
@article {pmid30065892, year = {2018}, author = {Schlemper, TR and Dimitrov, MR and Silva Gutierrez, FAO and van Veen, JA and Silveira, APD and Kuramae, EE}, title = {Effect of Burkholderia tropica and Herbaspirillum frisingense strains on sorghum growth is plant genotype dependent.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5346}, pmid = {30065892}, issn = {2167-8359}, abstract = {Sorghum is a multipurpose crop that is cultivated worldwide. Plant growth-promoting bacteria (PGPB) have important roles in enhancing sorghum biomass and nutrient uptake and suppressing plant pathogens. The aim of this research was to test the effects of the endophytic bacterial species Kosakonia radicincitans strain IAC/BECa 99, Enterobacter asburiae strain IAC/BECa 128, Pseudomonas fluorescens strain IAC/BECa 141, Burkholderia tropica strain IAC/BECa 135 and Herbaspirillum frisingense strain IAC/BECa 152 on the growth and root architecture of four sorghum cultivars (SRN-39, Shanqui-Red, BRS330, BRS509), with different uses and strigolactone profiles. We hypothesized that the different bacterial species would trigger different growth plant responses in different sorghum cultivars. Burkholderia tropica and H. frisingense significantly increased the plant biomass of cultivars SRN-39 and BRS330. Moreover, cultivar BRS330 inoculated with either strain displayed isolates significant decrease in average root diameter. This study shows that Burkholderia tropica strain IAC/BECa 135 and H. frisingense strain IAC/BECa 152 are promising PGPB strains for use as inocula for sustainable sorghum cultivation.}, }
@article {pmid30065353, year = {2018}, author = {Rahlff, J and Ribas-Ribas, M and Brown, SM and Mustaffa, NIH and Renz, J and Peck, MA and Bird, K and Cunliffe, M and Melkonian, K and Zappa, CJ}, title = {Blue pigmentation of neustonic copepods benefits exploitation of a prey-rich niche at the air-sea boundary.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {11510}, pmid = {30065353}, issn = {2045-2322}, support = {GA336408//EC | European Research Council (ERC)/International ; GA336408//EC | European Research Council (ERC)/International ; GA336408//EC | European Research Council (ERC)/International ; }, abstract = {The sea-surface microlayer (SML) at the air-sea interface is a distinct, under-studied habitat compared to the subsurface and copepods, important components of ocean food webs, have developed key adaptations to exploit this niche. By using automated SML sampling, high-throughput sequencing and unmanned aerial vehicles, we report on the distribution and abundance of pontellid copepods in relation to the unique biophysicochemical signature of the SML. We found copepods in the SML even during high exposure to sun-derived ultraviolet radiation and their abundance was significantly correlated to increased algal biomass. We additionally investigated the significance of the pontellids' blue pigmentation and found that the reflectance peak of the blue pigment matched the water-leaving spectral radiance of the ocean surface. This feature could reduce high visibility at the air-sea boundary and potentially provide camouflage of copepods from their predators.}, }
@article {pmid30063956, year = {2018}, author = {Thompson, HF and Lesaulnier, C and Pelikan, C and Gutierrez, T}, title = {Visualisation of the obligate hydrocarbonoclastic bacteria Polycyclovorans algicola and Algiphilus aromaticivorans in co-cultures with micro-algae by CARD-FISH.}, journal = {Journal of microbiological methods}, volume = {152}, number = {}, pages = {73-79}, doi = {10.1016/j.mimet.2018.07.016}, pmid = {30063956}, issn = {1872-8359}, mesh = {Bacteria/*genetics ; Biodegradation, Environmental ; Coculture Techniques/*methods ; Gammaproteobacteria/genetics/growth &amp; development/*isolation &amp; purification/*metabolism ; Hydrocarbons/*metabolism ; In Situ Hybridization, Fluorescence/*methods ; Microalgae/growth &amp; development/*metabolism ; Oligonucleotide Probes ; Petroleum/metabolism ; Phenanthrenes/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; }, abstract = {Some studies have described the isolation and 16S rRNA gene sequence-based identification of hydrocarbon-degrading bacteria living associated with marine eukaryotic phytoplankton, and thus far the direct visual observation of these bacteria on micro-algal cell surfaces ('phycosphere') has not yet been reported. Here, we developed two new 16S rRNA-targeted oligonucleotide probes, PCY223 and ALGAR209, to respectively detect and enumerate the obligate hydrocarbonoclastic bacteria Polycyclovorans algicola and Algiphilus aromaticivorans by Catalyzed Reporter Deposition Fluorescence in situ Hybridization (CARD-FISH). To enhance the hybridization specificity with the ALGAR209 probe, a competitor probe was developed. These probes were tested and optimized using pure cultures, and then used in enrichment experiments with laboratory cultures of micro-algae exposed to phenanthrene, and with coastal water enriched with crude oil. Microscopic analysis revealed these bacteria are found in culture with the micro-algal cells, some of which were found attached to algal cells, and whose abundance increased after phenanthrene or crude oil enrichment. These new probes are a valuable tool for identifying and studying the ecology of P. algicola and A. aromaticivorans in laboratory and field samples of micro-algae, as well as opening new fields of research that could harness their ability to enhance the bioremediation of contaminated sites.}, }
@article {pmid30061909, year = {2018}, author = {Sobhy, IS and Baets, D and Goelen, T and Herrera-Malaver, B and Bosmans, L and Van den Ende, W and Verstrepen, KJ and Wäckers, F and Jacquemyn, H and Lievens, B}, title = {Sweet Scents: Nectar Specialist Yeasts Enhance Nectar Attraction of a Generalist Aphid Parasitoid Without Affecting Survival.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1009}, pmid = {30061909}, issn = {1664-462X}, abstract = {Floral nectar is commonly inhabited by microorganisms, mostly yeasts and bacteria, which can have a strong impact on nectar chemistry and scent. Yet, little is known about the effects of nectar microbes on the behavior and survival of insects belonging to the third trophic level such as parasitoids. Here, we used five nectar-inhabiting yeast species to test the hypothesis that yeast species that almost solely occur in nectar, and therefore substantially rely on floral visitors for dispersal, produce volatile compounds that enhance insect attraction without compromising insect life history parameters, such as survival. Experiments were performed using two nectar specialist yeasts (Metschnikowia gruessii and M. reukaufii) and three generalist species (Aureobasidium pullulans, Hanseniaspora uvarum, and Sporobolomyces roseus). Saccharomyces cerevisiae was included as a reference yeast. We compared olfactory responses of the generalist aphid parasitoid Aphidius ervi (Haliday) (Hymenoptera: Braconidae) when exposed to these microorganisms inoculated in synthetic nectar. Nectar-inhabiting yeasts had a significant impact on nectar chemistry and produced distinct volatile blends, some of which were attractive, while others were neutral or repellent. Among the different yeast species tested, the nectar specialists M. gruessii and M. reukaufii were the only species that produced a highly attractive nectar to parasitoid females, which simultaneously had no adverse effects on longevity and survival of adults. By contrast, parasitoids that fed on nectars fermented with the reference strain, A. pullulans, H. uvarum or S. roseus showed shortest longevity and lowest survival. Additionally, nectars fermented by A. pullulans or S. roseus were consumed significantly less, suggesting a lack of important nutrients or undesirable changes in the nectar chemical profiles. Altogether our results indicate that nectar-inhabiting yeasts play an important, but so far largely overlooked, role in plant-insect interactions by modulating the chemical composition of nectar, and may have important ecological consequences for plant pollination and biological control of herbivorous insects.}, }
@article {pmid30061657, year = {2018}, author = {Butler, S and O'Dwyer, JP}, title = {Stability criteria for complex microbial communities.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2970}, pmid = {30061657}, issn = {2041-1723}, mesh = {Algorithms ; Computational Biology ; *Ecology ; *Microbiota ; Models, Biological ; Software ; *Symbiosis ; }, abstract = {Competition and mutualism are inevitable processes in microbial ecology, and a central question is which and how many taxa will persist in the face of these interactions. Ecological theory has demonstrated that when direct, pairwise interactions among a group of species are too numerous, or too strong, then the coexistence of these species will be unstable to any slight perturbation. Here, we refine and to some extent overturn that understanding, by considering explicitly the resources that microbes consume and produce. In contrast to more complex organisms, microbial cells consume primarily abiotic resources, and mutualistic interactions are often mediated through the mechanism of crossfeeding. We show that if microbes consume, but do not produce resources, then any positive equilibrium will always be stable to small perturbations. We go on to show that in the presence of crossfeeding, stability is no longer guaranteed. However, positive equilibria remain stable whenever mutualistic interactions are either sufficiently weak, or when all pairs of taxa reciprocate each other's assistance.}, }
@article {pmid30061355, year = {2018}, author = {van der Aart, LT and Spijksma, GK and Harms, A and Vollmer, W and Hankemeier, T and van Wezel, GP}, title = {High-Resolution Analysis of the Peptidoglycan Composition in Streptomyces coelicolor.}, journal = {Journal of bacteriology}, volume = {200}, number = {20}, pages = {}, pmid = {30061355}, issn = {1098-5530}, mesh = {Bacterial Proteins/*chemistry ; Cell Wall/chemistry ; Chromatography, Liquid ; Hydrolysis ; Hyphae/growth &amp; development ; Peptidoglycan/*chemistry ; Spores, Bacterial/growth &amp; development ; Streptomyces coelicolor/*chemistry ; Tandem Mass Spectrometry ; }, abstract = {The bacterial cell wall maintains cell shape and protects against bursting by turgor. A major constituent of the cell wall is peptidoglycan (PG), which is continuously modified to enable cell growth and differentiation through the concerted activity of biosynthetic and hydrolytic enzymes. Streptomycetes are Gram-positive bacteria with a complex multicellular life style alternating between mycelial growth and the formation of reproductive spores. This involves cell wall remodeling at apical sites of the hyphae during cell elongation and autolytic degradation of the vegetative mycelium during the onset of development and antibiotic production. Here, we show that there are distinct differences in the cross-linking and maturation of the PGs between exponentially growing vegetative hyphae and the aerial hyphae that undergo sporulation. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis identified over 80 different muropeptides, revealing that major PG hydrolysis takes place over the course of mycelial growth. Half of the dimers lacked one of the disaccharide units in transition-phase cells, most likely due to autolytic activity. The deacetylation of MurNAc to MurN was particularly pronounced in spores and strongly reduced in sporulation mutants with a deletion of bldD or whiG, suggesting that MurN is developmentally regulated. Altogether, our work highlights the dynamic and growth phase-dependent changes in the composition of the PG in StreptomycesIMPORTANCE Streptomycetes are bacteria with a complex lifestyle and are model organisms for bacterial multicellularity. From a single spore, a large multigenomic multicellular mycelium is formed, which differentiates to form spores. Programmed cell death is an important event during the onset of morphological differentiation. In this work, we provide new insights into the changes in the peptidoglycan composition and over time, highlighting changes over the course of development and between growing mycelia and spores. This revealed dynamic changes in the peptidoglycan when the mycelia aged, with extensive peptidoglycan hydrolysis and, in particular, an increase in the proportion of 3-3 cross-links. Additionally, we identified a muropeptide that accumulates predominantly in the spores and may provide clues toward spore development.}, }
@article {pmid30060765, year = {2018}, author = {Seal, BS and Drider, D and Oakley, BB and Brüssow, H and Bikard, D and Rich, JO and Miller, S and Devillard, E and Kwan, J and Bertin, G and Reeves, S and Swift, SM and Raicek, M and Gay, CG}, title = {Microbial-derived products as potential new antimicrobials.}, journal = {Veterinary research}, volume = {49}, number = {1}, pages = {66}, pmid = {30060765}, issn = {1297-9716}, mesh = {Animal Diseases/prevention &amp; control ; *Animal Husbandry ; Animals ; Anti-Infective Agents/*analysis ; Bacteriocins ; Bacteriophages ; CRISPR-Cas Systems ; *Drug Discovery ; France ; Livestock ; }, abstract = {Due to the continuing global concerns involving antibiotic resistance, there is a need for scientific forums to assess advancements in the development of antimicrobials and their alternatives that might reduce development and spread of antibiotic resistance among bacterial pathogens. The objectives of the 2[nd] International Symposium on Alternatives to Antibiotics were to highlight promising research results and novel technologies that can provide alternatives to antibiotics for use in animal health and production, assess challenges associated with their authorization and commercialization for use, and provide actionable strategies to support their development. The session on microbial-derived products was directed at presenting novel technologies that included exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials, probiotics development via fecal microbiome transplants among monogastric production animals such as chickens and mining microbial sources such as bacteria or yeast to identify new antimicrobial compounds. Other research has included continuing development of antimicrobial peptides such as newly discovered bacteriocins as alternatives to antibiotics, use of bacteriophages accompanied by development of unique lytic proteins with specific cell-wall binding domains and novel approaches such as microbial-ecology guided discovery of anti-biofilm compounds discovered in marine environments. The symposium was held at the Headquarters of the World Organisation for Animal Health (OIE) in Paris, France during 12-15 December 2016.}, }
@article {pmid30058041, year = {2018}, author = {Farhat, A and Miladi, B and Hamdi, M and Bouallagui, H}, title = {Fermentative hydrogen and methane co-production from anaerobic co-digestion of organic wastes at high loading rate coupling continuously and sequencing batch digesters.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {28}, pages = {27945-27958}, pmid = {30058041}, issn = {1614-7499}, mesh = {Anaerobiosis ; Animals ; Biofuels ; *Bioreactors/microbiology ; Cattle ; *Fermentation ; Hydrogen/*analysis ; Manure/*analysis ; Methane/*analysis ; Tunisia ; Waste Products/*analysis ; }, abstract = {The anaerobic co-digestion of the most abundant organic wastes was investigated for enhancing biogas production rate and quality. The used feedstock was composed of fruit and vegetable waste (FVW), waste-activated sludge (WAS), olive mill wastewater (OMW) and cattle manure (CM). A considerable methane yield of 340 L/kg volatile solid (VS) inlet was obtained using single-stage anaerobic sequencing batch reactors (ASBRs). However, VS biodegradation becomes difficult at high organic loading rate (OLR). Therefore, a continuously stirred tank reactor (CSTR) was integrated to the ASBR for waste pre-digestion. The dark fermentation leads to the improvement of organic matter solubilisation and bio-hydrogen productivity, reaching 0.73 L/L/day (H2 content of 49.8%) when pH decreased to 5.8. Therefore, methane productivity increased from 0.6 to 1.86 L/L/day in the methanogenic reactor with a better VS biodegradation (91.1%) at high OLR. Furthermore, the bio-hythane production was performed through a controlled biogas recirculation from the dark fermentation stage into the methaniser to reach 842.4 L/kg VS inlet. The produced biogas was composed of 8% H2, 28.5% CO2 and 63.5% CH4. Therefore, two-stage anaerobic co-digestion with coupled CH4 and H2 recuperation may be an important contribution for pollution control and high-rate bioenergy recovery (21.1 kJ/g VS inlet) from organic wastes.}, }
@article {pmid30056833, year = {2018}, author = {Mercer, F and Johnson, PJ}, title = {Trichomonas vaginalis: Pathogenesis, Symbiont Interactions, and Host Cell Immune Responses.}, journal = {Trends in parasitology}, volume = {34}, number = {8}, pages = {683-693}, pmid = {30056833}, issn = {1471-5007}, support = {F32 AI122643/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Immunity, Cellular/*immunology ; *Symbiosis ; Trichomonas Infections/*immunology/*pathology ; Trichomonas vaginalis/*immunology ; }, abstract = {The parasite Trichomonas vaginalis (Tv) causes a highly prevalent sexually transmitted infection. As an extracellular pathogen, the parasite mediates adherence to epithelial cells to colonize the human host. In addition, the parasite interfaces with the host immune system and the vaginal microbiota. Modes of Tv pathogenesis include damage to host tissue mediated by parasite killing of host cells, disruption of steady-state vaginal microbial ecology, and eliciting inflammation by activating the host immune response. Recent Tv research has uncovered new players that contribute to multifactorial mechanisms of host-parasite adherence and killing, and has examined the relationship between Tv and vaginal bacteria. Mechanisms that may lead to parasite recognition and killing, or the evasion of host immune cells, have also been revealed.}, }
@article {pmid30056235, year = {2019}, author = {Lupatini, M and Korthals, GW and Roesch, LFW and Kuramae, EE}, title = {Long-term farming systems modulate multi-trophic responses.}, journal = {The Science of the total environment}, volume = {646}, number = {}, pages = {480-490}, doi = {10.1016/j.scitotenv.2018.07.323}, pmid = {30056235}, issn = {1879-1026}, abstract = {Soil microbiome and multi-trophic relationships are essential for the stability and functioning of agroecosystems. However, little is known about how farming systems and alternative methods for controlling plant pathogens modulate microbial communities, soil mesofauna and plant productivity. In this study, we assessed the composition of eukaryotic microbial groups using a high-throughput sequencing approach (18S rRNA gene marker), the populations of parasitic and free-living nematodes, plant productivity and their inter-relationships in long-term conventional and organic farming systems. The diversity of the fungal community increased in the organic farming system compared to the conventional farming system, whereas the diversity of the protist community was similar between the two farming systems. Compared to conventional farming, organic farming increased the population of free-living nematodes and suppressed plant parasitic nematodes belonging to Meloidogynidae and Pratylenchidae. Fungal diversity and community structure appeared to be related to nematode suppression in the system receiving organic fertilizer, which was characterized by component microbial groups known to be involved in the suppression of soil pathogens. Unraveling the microbiome and multi-trophic interactions in different farming systems may permit the management of the soil environment toward more sustainable control of plant pathogens.}, }
@article {pmid30056005, year = {2018}, author = {Bankevich, A and Pevzner, PA}, title = {Joint Analysis of Long and Short Reads Enables Accurate Estimates of Microbiome Complexity.}, journal = {Cell systems}, volume = {7}, number = {2}, pages = {192-200.e3}, doi = {10.1016/j.cels.2018.06.009}, pmid = {30056005}, issn = {2405-4712}, mesh = {Algorithms ; Bacteria/genetics ; *Gastrointestinal Microbiome ; Genetic Variation ; *Genome, Bacterial ; Humans ; Metagenome ; Metagenomics/*methods ; Sequence Analysis, DNA ; }, abstract = {Reduced microbiome diversity has been linked to several diseases. However, estimating the diversity of bacterial communities-the number and the total length of distinct genomes within a metagenome-remains an open problem in microbial ecology. Here, we describe an algorithm for estimating the microbial diversity in a metagenomic sample based on a joint analysis of short and long reads. Unlike previous approaches, the algorithm does not make any assumptions on the distribution of the frequencies of genomes within a metagenome (as in parametric methods) and does not require a large database that covers the total diversity (as in non-parametric methods). We estimate that genomes comprising a human gut metagenome have total length varying from 1.3 to 3.5 billion nucleotides, with genomes responsible for 50% of total abundance having total length varying from only 25 to 61 million nucleotides. In contrast, genomes comprising an aquifer sediment metagenome have more than two orders of magnitude larger total length (≈840 billion nucleotides).}, }
@article {pmid30055451, year = {2018}, author = {Mayta-Apaza, AC and Pottgen, E and De Bodt, J and Papp, N and Marasini, D and Howard, L and Abranko, L and Van de Wiele, T and Lee, SO and Carbonero, F}, title = {Impact of tart cherries polyphenols on the human gut microbiota and phenolic metabolites in vitro and in vivo.}, journal = {The Journal of nutritional biochemistry}, volume = {59}, number = {}, pages = {160-172}, doi = {10.1016/j.jnutbio.2018.04.001}, pmid = {30055451}, issn = {1873-4847}, mesh = {Adult ; Bifidobacterium/drug effects/genetics ; Female ; Fermentation ; Fruit and Vegetable Juices ; Gastrointestinal Microbiome/*drug effects/genetics/*physiology ; Humans ; Male ; Phenols/metabolism ; Polyphenols/analysis/pharmacokinetics/*pharmacology ; Prunus avium/*chemistry ; }, abstract = {Tart cherries have been reported to exert potential health benefits attributed to their specific and abundant polyphenol content. However, there is a need to study the impact and fate of tart cherries polyphenols in the gut microbiota. Here, tart cherries, pure polyphenols (and apricots) were submitted to in vitro bacterial fermentation assays and assessed through 16S rRNA gene sequence sequencing and metabolomics. A short-term (5 days, 8 oz. daily) human dietary intervention study was also conducted for microbiota analyses. Tart cherry concentrate juices were found to contain expected abundances of anthocyanins (cyanidin-glycosylrutinoside) and flavonoids (quercetin-rutinoside) and high amounts of chlorogenic and neochlorogenic acids. Targeted metabolomics confirmed that gut microbes were able to degrade those polyphenols mainly to 4-hydroxyphenylpropionic acids and to lower amounts of epicatechin and 4-hydroxybenzoic acids. Tart cherries were found to induce a large increase of Bacteroides in vitro, likely due to the input of polysaccharides, but prebiotic effect was also suggested by Bifidobacterium increase from chlorogenic acid. In the human study, two distinct and inverse responses to tart cherry consumption were associated with initial levels of Bacteroides. High-Bacteroides individuals responded with a decrease in Bacteroides and Bifidobacterium, and an increase of Lachnospiraceae, Ruminococcus and Collinsella. Low-Bacteroides individuals responded with an increase in Bacteroides or Prevotella and Bifidobacterium, and a decrease of Lachnospiraceae, Ruminococcus and Collinsella. These data confirm that gut microbiota metabolism, in particular the potential existence of different metabotypes, needs to be considered in studies attempting to link tart cherries consumption and health.}, }
@article {pmid30055017, year = {2018}, author = {Lemay, MA and Martone, PT and Hind, KR and Lindstrom, SC and Wegener Parfrey, L}, title = {Alternate life history phases of a common seaweed have distinct microbial surface communities.}, journal = {Molecular ecology}, volume = {27}, number = {17}, pages = {3555-3568}, doi = {10.1111/mec.14815}, pmid = {30055017}, issn = {1365-294X}, mesh = {Bacteria/*classification ; British Columbia ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Rhodophyta/growth &amp; development/*microbiology ; Seaweed/growth &amp; development/*microbiology ; Species Specificity ; }, abstract = {Macroalgal life histories are complex, often involving the alternation of distinct free-living life history phases that differ in morphology, longevity and ploidy. The surfaces of marine macroalgae support diverse microbial biofilms, yet the degree of microbial variation between alternate phases is unknown. We quantified bacterial (16S rRNA gene) and microeukaryote (18S rRNA gene) communities on the surface of the common intertidal seaweed, Mastocarpus spp., which alternates between gametophyte (foliose, haploid) and sporophyte (encrusting, diploid) life history phases. A large portion (97%) of bacterial taxa on the surface Mastocarpus was also present in samples from the environment, indicating that macroalgal surface communities are largely assembled from the surrounding seawater. Still, changes in the relative abundance of bacterial taxa result in significantly different communities on alternate Mastocarpus life history phases, rocky substrate and seawater at all intertidal elevations. For microeukaryote assemblages, only high intertidal samples had significant differences between life history phases although sporophytes were not different from the rocky substrate at this elevation; gametophytes and sporophytes did not differ in microeukaryote communities in the mid and low zones. By sequencing three host genes, we identified three cryptic species of Mastocarpus in our data set, which co-occur in the mid-to-low intertidal zone. In these samples, M. alaskensis sporophytes harboured distinct bacterial communities compared to M. agardhii and M. intermedius sporophytes, which were not distinguishable. Conversely, microeukaryote communities did not differ among species.}, }
@article {pmid30054367, year = {2018}, author = {Endo, A and Maeno, S and Tanizawa, Y and Kneifel, W and Arita, M and Dicks, L and Salminen, S}, title = {Fructophilic Lactic Acid Bacteria, a Unique Group of Fructose-Fermenting Microbes.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {19}, pages = {}, pmid = {30054367}, issn = {1098-5336}, mesh = {Alcohol Dehydrogenase/genetics/metabolism ; Aldehyde Oxidoreductases/genetics/metabolism ; Animals ; Bacterial Proteins/genetics/metabolism ; Bees ; Fermentation ; Flowers/microbiology ; Fructose/*metabolism ; Fruit/microbiology ; Glucose/metabolism ; Insecta/microbiology ; Lactobacillales/genetics/metabolism ; Lactobacillus/classification/genetics/isolation &amp; purification/*metabolism ; Leuconostocaceae/classification/genetics/isolation &amp; purification/*metabolism ; Phylogeny ; Wine/microbiology ; }, abstract = {Fructophilic lactic acid bacteria (FLAB) are a recently discovered group, consisting of a few Fructobacillus and Lactobacillus species. Because of their unique characteristics, including poor growth on glucose and preference of oxygen, they are regarded as "unconventional" lactic acid bacteria (LAB). Their unusual growth characteristics are due to an incomplete gene encoding a bifunctional alcohol/acetaldehyde dehydrogenase (adhE). This results in the imbalance of NAD/NADH and the requirement of additional electron acceptors to metabolize glucose. Oxygen, fructose, and pyruvate are used as electron acceptors. FLAB have significantly fewer genes for carbohydrate metabolism than other LAB, especially due to the lack of complete phosphotransferase system (PTS) transporters. They have been isolated from fructose-rich environments, including flowers, fruits, fermented fruits, and the guts of insects that feed on plants rich in fructose, and are separated into two groups on the basis of their habitats. One group is associated with flowers, grapes, wines, and insects, and the second group is associated with ripe fruits and fruit fermentations. Species associated with insects may play a role in the health of their host and are regarded as suitable vectors for paratransgenesis in honey bees. Besides their impact on insect health, FLAB may be promising candidates for the promotion of human health. Further studies are required to explore their beneficial properties in animals and humans and their applications in the food industry.}, }
@article {pmid30054363, year = {2018}, author = {Philips, J and Van den Driessche, N and De Paepe, K and Prévoteau, A and Gralnick, JA and Arends, JBA and Rabaey, K}, title = {A Novel Shewanella Isolate Enhances Corrosion by Using Metallic Iron as the Electron Donor with Fumarate as the Electron Acceptor.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {20}, pages = {}, pmid = {30054363}, issn = {1098-5336}, mesh = {Anaerobiosis ; Corrosion ; *Electrons ; Fumarates/*metabolism ; Hydrogen/analysis/metabolism ; Iron/*metabolism ; Oxidation-Reduction ; Shewanella/*metabolism ; }, abstract = {The involvement of Shewanella spp. in biocorrosion is often attributed to their Fe(III)-reducing properties, but they could also affect corrosion by using metallic iron as an electron donor. Previously, we isolated Shewanella strain 4t3-1-2LB from an acetogenic community enriched with Fe(0) as the sole electron donor. Here, we investigated its use of Fe(0) as an electron donor with fumarate as an electron acceptor and explored its corrosion-enhancing mechanism. Without Fe(0), strain 4t3-1-2LB fermented fumarate to succinate and CO2, as was shown by the reaction stoichiometry and pH. With Fe(0), strain 4t3-1-2LB completely reduced fumarate to succinate and increased the Fe(0) corrosion rate (7.0 ± 0.6)-fold in comparison to that of abiotic controls (based on the succinate-versus-abiotic hydrogen formation rate). Fumarate reduction by strain 4t3-1-2LB was, at least in part, supported by chemical hydrogen formation on Fe(0). Filter-sterilized spent medium increased the hydrogen generation rate only 1.5-fold, and thus extracellular hydrogenase enzymes appear to be insufficient to explain the enhanced corrosion rate. Electrochemical measurements suggested that strain 4t3-1-2LB did not excrete dissolved redox mediators. Exchanging the medium and scanning electron microscopy (SEM) imaging indicated that cells were attached to Fe(0). It is possible that strain 4t3-1-2LB used a direct mechanism to withdraw electrons from Fe(0) or favored chemical hydrogen formation on Fe(0) through maintaining low hydrogen concentrations. In coculture with an Acetobacterium strain, strain 4t3-1-2LB did not enhance acetogenesis from Fe(0). This work describes a strong corrosion enhancement by a Shewanella strain through its use of Fe(0) as an electron donor and provides insights into its corrosion-enhancing mechanism.IMPORTANCEShewanella spp. are frequently found on corroded metal structures. Their role in microbial influenced corrosion has been attributed mainly to their Fe(III)-reducing properties and, therefore, has been studied with the addition of an electron donor (lactate). Shewanella spp., however, can also use solid electron donors, such as cathodes and potentially Fe(0). In this work, we show that the electron acceptor fumarate supported the use of Fe(0) as the electron donor by Shewanella strain 4t3-1-2LB, which caused a (7.0 ± 0.6)-fold increase of the corrosion rate. The corrosion-enhancing mechanism likely involved cell surface-associated components in direct contact with the Fe(0) surface or maintenance of low hydrogen levels by attached cells, thereby favoring chemical hydrogen formation by Fe(0). This work sheds new light on the role of Shewanella spp. in biocorrosion, while the insights into the corrosion-enhancing mechanism contribute to the understanding of extracellular electron uptake processes.}, }
@article {pmid30054356, year = {2018}, author = {Peng, M and Salaheen, S and Buchanan, RL and Biswas, D}, title = {Alterations of Salmonella enterica Serovar Typhimurium Antibiotic Resistance under Environmental Pressure.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {19}, pages = {}, pmid = {30054356}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; *Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Genome, Bacterial ; Microbial Sensitivity Tests ; Phylogeny ; Plasmids/genetics/metabolism ; Salmonella Infections, Animal/microbiology ; Salmonella typhimurium/classification/*drug effects/*genetics/isolation &amp; purification ; Selection, Genetic ; Soil Microbiology ; Tetracycline/pharmacology ; }, abstract = {Microbial horizontal gene transfer is a continuous process that shapes bacterial genomic adaptation to the environment and the composition of concurrent microbial ecology. This includes the potential impact of synthetic antibiotic utilization in farm animal production on overall antibiotic resistance issues; however, the mechanisms behind the evolution of microbial communities are not fully understood. We explored potential mechanisms by experimentally examining the relatedness of phylogenetic inference between multidrug-resistant Salmonella enterica serovar Typhimurium isolates and pathogenic Salmonella Typhimurium strains based on genome-wide single-nucleotide polymorphism (SNP) comparisons. Antibiotic-resistant S Typhimurium isolates in a simulated farm environment barely lost their resistance, whereas sensitive S Typhimurium isolates in soils gradually acquired higher tetracycline resistance under antibiotic pressure and manipulated differential expression of antibiotic-resistant genes. The expeditious development of antibiotic resistance and the ensuing genetic alterations in antimicrobial resistance genes in S Typhimurium warrant effective actions to control the dissemination of Salmonella antibiotic resistance.IMPORTANCE Antibiotic resistance is attributed to the misuse or overuse of antibiotics in agriculture, and antibiotic resistance genes can also be transferred to bacteria under environmental stress. In this study, we report a unidirectional alteration in antibiotic resistance from susceptibility to increased resistance. Highly sensitive Salmonella enterica serovar Typhimurium isolates from organic farm systems quickly acquired tetracycline resistance under antibiotic pressure in simulated farm soil environments within 2 weeks, with expression of antibiotic resistance-related genes that was significantly upregulated. Conversely, originally resistant S Typhimurium isolates from conventional farm systems lost little of their resistance when transferred to environments without antibiotic pressure. Additionally, multidrug-resistant S Typhimurium isolates genetically shared relevancy with pathogenic S Typhimurium isolates, whereas susceptible isolates clustered with nonpathogenic strains. These results provide detailed discussion and explanation about the genetic alterations and simultaneous acquisition of antibiotic resistance in S Typhimurium in agricultural environments.}, }
@article {pmid30052926, year = {2018}, author = {Stedtfeld, RD and Guo, X and Stedtfeld, TM and Sheng, H and Williams, MR and Hauschild, K and Gunturu, S and Tift, L and Wang, F and Howe, A and Chai, B and Yin, D and Cole, JR and Tiedje, JM and Hashsham, SA}, title = {Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {9}, pages = {}, pmid = {30052926}, issn = {1574-6941}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; DNA Primers/*genetics ; Drug Resistance, Microbial/*genetics ; Interspersed Repetitive Sequences/*genetics ; Real-Time Polymerase Chain Reaction/*methods ; }, abstract = {The high-throughput antibiotic resistance gene (ARG) qPCR array, initially published in 2012, is increasingly used to quantify resistance and mobile determinants in environmental matrices. Continued utility of the array; however, necessitates improvements such as removing or redesigning questionable primer sets, updating targeted genes and coverage of available sequences. Towards this goal, a new primer design tool (EcoFunPrimer) was used to aid in identification of conserved regions of diverse genes. The total number of assays used for diverse genes was reduced from 91 old primer sets to 52 new primer sets, with only a 10% loss in sequence coverage. While the old and new array both contain 384 primer sets, a reduction in old primer sets permitted 147 additional ARGs and mobile genetic elements to be targeted. Results of validating the updated array with a mock community of strains resulted in over 98% of tested instances incurring true positive/negative calls. Common queries related to sensitivity, quantification and conventional data analysis (e.g. Ct cutoff value, and estimated genomic copies without standard curves) were also explored. A combined list of new and previously used primer sets is provided with a recommended set based on redesign of primer sets and results of validation.}, }
@article {pmid30051940, year = {2018}, author = {Averill, C and Dietze, MC and Bhatnagar, JM}, title = {Continental-scale nitrogen pollution is shifting forest mycorrhizal associations and soil carbon stocks.}, journal = {Global change biology}, volume = {24}, number = {10}, pages = {4544-4553}, doi = {10.1111/gcb.14368}, pmid = {30051940}, issn = {1365-2486}, support = {//National Oceanic and Atmospheric Administration/International ; 1638577//National Science Foundation/International ; //Peter Paul Professorship/International ; }, mesh = {Carbon/*metabolism ; Climate Change ; *Forests ; Mycorrhizae/*drug effects/metabolism ; Nitrogen/*toxicity ; Plant Roots/microbiology ; Soil/*chemistry ; Soil Microbiology ; Soil Pollutants/*toxicity ; Symbiosis ; Trees/microbiology ; }, abstract = {Most tree roots on Earth form a symbiosis with either ecto- or arbuscular mycorrhizal fungi. Nitrogen fertilization is hypothesized to favor arbuscular mycorrhizal tree species at the expense of ectomycorrhizal species due to differences in fungal nitrogen acquisition strategies, and this may alter soil carbon balance, as differences in forest mycorrhizal associations are linked to differences in soil carbon pools. Combining nitrogen deposition data with continental-scale US forest data, we show that nitrogen pollution is spatially associated with a decline in ectomycorrhizal vs. arbuscular mycorrhizal trees. Furthermore, nitrogen deposition has contrasting effects on arbuscular vs. ectomycorrhizal demographic processes, favoring arbuscular mycorrhizal trees at the expense of ectomycorrhizal trees, and is spatially correlated with reduced soil carbon stocks. This implies future changes in nitrogen deposition may alter the capacity of forests to sequester carbon and offset climate change via interactions with the forest microbiome.}, }
@article {pmid30051650, year = {2018}, author = {Müller, AL and Pelikan, C and de Rezende, JR and Wasmund, K and Putz, M and Glombitza, C and Kjeldsen, KU and Jørgensen, BB and Loy, A}, title = {Bacterial interactions during sequential degradation of cyanobacterial necromass in a sulfidic arctic marine sediment.}, journal = {Environmental microbiology}, volume = {20}, number = {8}, pages = {2927-2940}, pmid = {30051650}, issn = {1462-2920}, support = {P 25111/FWF_/Austrian Science Fund FWF/Austria ; P 29426/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Arctic Regions ; Bacteria/*classification/*metabolism ; *Bacterial Physiological Phenomena ; Fatty Acids, Volatile/metabolism ; Geologic Sediments/*microbiology ; In Situ Hybridization, Fluorescence ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Sulfates/*metabolism ; Sulfides/*metabolism ; }, abstract = {Seafloor microorganisms impact global carbon cycling by mineralizing vast quantities of organic matter (OM) from pelagic primary production, which is predicted to increase in the Arctic because of diminishing sea ice cover. We studied microbial interspecies-carbon-flow during anaerobic OM degradation in arctic marine sediment using stable isotope probing. We supplemented sediment incubations with [13] C-labeled cyanobacterial necromass (spirulina), mimicking fresh OM input, or acetate, an important OM degradation intermediate and monitored sulfate reduction rates and concentrations of volatile fatty acids (VFAs) during substrate degradation. Sequential 16S rRNA gene and transcript amplicon sequencing and fluorescence in situ hybridization combined with Raman microspectroscopy revealed that only few bacterial species were the main degraders of [13] C-spirulina necromass. Psychrilyobacter, Psychromonas, Marinifilum, Colwellia, Marinilabiaceae and Clostridiales species were likely involved in the primary hydrolysis and fermentation of spirulina. VFAs, mainly acetate, produced from spirulina degradation were mineralized by sulfate-reducing bacteria and an Arcobacter species. Cellular activity of Desulfobacteraceae and Desulfobulbaceae species during acetoclastic sulfate reduction was largely decoupled from relative 16S rRNA gene abundance shifts. Our findings provide new insights into the identities and physiological constraints that determine the population dynamics of key microorganisms during complex OM degradation in arctic marine sediments.© 2018 Society for Applied Microbiology and John Wiley &amp; Sons Ltd.}, }
@article {pmid30051173, year = {2019}, author = {Weinisch, L and Kirchner, I and Grimm, M and Kühner, S and Pierik, AJ and Rosselló-Móra, R and Filker, S}, title = {Glycine Betaine and Ectoine Are the Major Compatible Solutes Used by Four Different Halophilic Heterotrophic Ciliates.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {317-331}, pmid = {30051173}, issn = {1432-184X}, mesh = {Amino Acids, Diamino/*metabolism ; Betaine/*metabolism ; Ciliophora/genetics/isolation &amp; purification/*metabolism/ultrastructure ; Heterotrophic Processes ; Microscopy, Electrochemical, Scanning ; Osmotic Pressure ; Ponds/chemistry/microbiology ; Salinity ; Sodium Chloride/*metabolism ; }, abstract = {One decisive factor controlling the distribution of organisms in their natural habitats is the cellular response to environmental factors. Compared to prokaryotes, our knowledge about salt adaptation strategies of microbial eukaryotes is very limited. We, here, used a recently introduced approach (implementing proton nuclear magnetic resonance spectroscopy) to investigate the presence of compatible solutes in halophilic, heterotrophic ciliates. Therefore, we isolated four ciliates from solar salterns, which were identified as Cyclidium glaucoma, Euplotes sp., Fabrea salina, and Pseudocohnilembus persalinus based on their 18S rRNA gene signatures and electron microscopy. The results of [1]H-NMR spectroscopy revealed that all four ciliates employ the "low-salt-in" strategy by accumulating glycine betaine and ectoine as main osmoprotectants. We recorded a linear increase of these compatible solutes with increasing salinity of the external medium. Ectoine in particular stands out as its use as compatible solute was thought to be exclusive to prokaryotes. However, our findings and those recently made on two other heterotroph species call for a re-evaluation of this notion. The observation of varying relative proportions of compatible solutes within the four ciliates points to slight differences in haloadaptive strategies by regulatory action of the ciliates. Based on this finding, we provide an explanatory hypothesis for the distribution of protistan diversity along salinity gradients.}, }
@article {pmid30050987, year = {2018}, author = {Zumstein, MT and Schintlmeister, A and Nelson, TF and Baumgartner, R and Woebken, D and Wagner, M and Kohler, HE and McNeill, K and Sander, M}, title = {Biodegradation of synthetic polymers in soils: Tracking carbon into CO2 and microbial biomass.}, journal = {Science advances}, volume = {4}, number = {7}, pages = {eaas9024}, pmid = {30050987}, issn = {2375-2548}, mesh = {Agriculture ; *Biodegradation, Environmental ; *Biomass ; Carbon/chemistry ; Carbon Dioxide/chemistry/metabolism ; Carbon Isotopes/chemistry ; Fungi/metabolism ; Lipase/metabolism ; Polyesters/chemistry/metabolism ; Polymers/chemistry/*metabolism ; *Soil Microbiology ; Spectrometry, Mass, Secondary Ion ; }, abstract = {Plastic materials are widely used in agricultural applications to achieve food security for the growing world population. The use of biodegradable instead of nonbiodegradable polymers in single-use agricultural applications, including plastic mulching, promises to reduce plastic accumulation in the environment. We present a novel approach that allows tracking of carbon from biodegradable polymers into CO2 and microbial biomass. The approach is based on [13]C-labeled polymers and on isotope-specific analytical methods, including nanoscale secondary ion mass spectrometry (NanoSIMS). Our results unequivocally demonstrate the biodegradability of poly(butylene adipate-co-terephthalate) (PBAT), an important polyester used in agriculture, in soil. Carbon from each monomer unit of PBAT was used by soil microorganisms, including filamentous fungi, to gain energy and to form biomass. This work advances both our conceptual understanding of polymer biodegradation and the methodological capabilities to assess this process in natural and engineered environments.}, }
@article {pmid30048866, year = {2018}, author = {Beganskas, S and Gorski, G and Weathers, T and Fisher, AT and Schmidt, C and Saltikov, C and Redford, K and Stoneburner, B and Harmon, R and Weir, W}, title = {A horizontal permeable reactive barrier stimulates nitrate removal and shifts microbial ecology during rapid infiltration for managed recharge.}, journal = {Water research}, volume = {144}, number = {}, pages = {274-284}, doi = {10.1016/j.watres.2018.07.039}, pmid = {30048866}, issn = {1879-2448}, mesh = {Bacteria/*metabolism ; California ; Carbon/analysis ; Denitrification ; Groundwater/*chemistry/*microbiology ; Hydrology/*methods ; *Nitrates/analysis ; Soil/chemistry ; Wood ; }, abstract = {We present results from field experiments linking hydrology, geochemistry, and microbiology during infiltration at a field site that is used for managed aquifer recharge (MAR). These experiments measured how a horizontal permeable reactive barrier (PRB) made of woodchips impacted subsurface nitrate removal and microbial ecology. Concentrations of dissolved organic carbon consistently increased in infiltrating water below the PRB, but not in un-amended native soil. The average nitrate removal rate in soils below the PRB was 1.5 g/m[2]/day NO3-N, despite rapid infiltration (up to 1.9 m/d) and a short fluid residence time within the woodchips (≤6 h). In contrast, 0.09 g/m[2]/day NO3-N was removed on average in native soil. Residual nitrate in infiltrating water below the PRB was enriched in δ[15]N and δ[18]O, with low and variable isotopic enrichment factors that are consistent with denitrification during rapid infiltration. Many putative denitrifying bacteria were significantly enhanced in the soil below a PRB; Methylotenera mobilis and genera Microbacterium, Polaromonas, and Novosphingobium had log2 fold-changes of +4.9, +5.6, +7.2, and +11.8, respectively. These bacteria were present before infiltration and were not enhanced in native soil. It appears that the woodchip PRB contributed to favorable conditions in the underlying soil for enhanced nitrate removal, quantitatively shifting soil microbial ecology. These results suggest that using a horizontal PRB could improve water quality during rapid infiltration for MAR.}, }
@article {pmid30047254, year = {2019}, author = {Biagi, E and D'Amico, F and Soverini, M and Angelini, V and Barone, M and Turroni, S and Rampelli, S and Pari, S and Brigidi, P and Candela, M}, title = {Faecal bacterial communities from Mediterranean loggerhead sea turtles (Caretta caretta).}, journal = {Environmental microbiology reports}, volume = {11}, number = {3}, pages = {361-371}, doi = {10.1111/1758-2229.12683}, pmid = {30047254}, issn = {1758-2229}, support = {LIFE12 NAT/IT/000937//LIFE-EU project TartaLife/International ; }, mesh = {Animals ; Bacteria/classification/genetics ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Mediterranean Sea ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Turtles/*microbiology ; Water Microbiology ; }, abstract = {The loggerhead sea turtle (Caretta caretta) is the most widespread sea turtle species in the Mediterranean Sea and a relevant pollution 'flagship species'. Here, we profiled the faecal microbiota from 29 C. caretta from a rescue centre, and explored the impact of several variables linked to both the animal itself and the environment (i.e., tank water ecosystem). We show that loggerhead turtles share more gut microbiota features with carnivorous marine mammals, than with phylogenetically close, but herbivorous, turtles, as a confirmation of the gut microbiota adaptive function to diet and environment. We also highlight a relation between the microbiota composition and the size (and consequently the age) of the turtles. Finally, we point out that the gut microbiota of sea turtles shows unexpectedly low exchange of microbes with the aquatic environment and is resilient to the stress induced by short-time captivity.}, }
@article {pmid30047191, year = {2018}, author = {Ma, X and Coleman, ML and Waldbauer, JR}, title = {Distinct molecular signatures in dissolved organic matter produced by viral lysis of marine cyanobacteria.}, journal = {Environmental microbiology}, volume = {20}, number = {8}, pages = {3001-3011}, doi = {10.1111/1462-2920.14338}, pmid = {30047191}, issn = {1462-2920}, support = {3305//Gordon and Betty Moore Foundation/International ; }, mesh = {Bacteriophages/*physiology ; Biomass ; Organic Chemicals/*chemistry ; Peptides/chemistry ; Phytoplankton/chemistry/growth &amp; development/virology ; Seawater/*chemistry/microbiology/virology ; Synechococcus/*chemistry/growth &amp; development/*virology ; }, abstract = {Dissolved organic matter (DOM) plays a central role in the microbial ecology and biogeochemistry of aquatic environments, yet little is known about how the mechanism of DOM release from its ultimate source, primary producer biomass, affects the molecular composition of the inputs to the dissolved pool. Here we used a model marine phytoplankton, the picocyanobacterium Synechococcus WH7803, to compare the composition of DOM released by three mechanisms: exudation, mechanical cell lysis and infection by the lytic phage S-SM1. A broad, untargeted analytical approach reveals the complexity of this freshly sourced DOM, and comparative analysis between DOM produced by the different mechanisms suggests that exudation and viral lysis are sources of unsaturated, oxygen-rich and possibly novel biomolecules. Furthermore, viral lysis of WH7803 by S-SM1 releases abundant peptides derived from specific proteolysis of the major light-harvesting protein phycoerythrin, raising the possibility that phage infection of these abundant cyanobacteria could be a significant source of high molecular weight dissolved organic nitrogen compounds.}, }
@article {pmid30046860, year = {2019}, author = {Zhang, H and Feng, J and Chen, S and Zhao, Z and Li, B and Wang, Y and Jia, J and Li, S and Wang, Y and Yan, M and Lu, K and Hao, H}, title = {Geographical Patterns of nirS Gene Abundance and nirS-Type Denitrifying Bacterial Community Associated with Activated Sludge from Different Wastewater Treatment Plants.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {304-316}, pmid = {30046860}, issn = {1432-184X}, support = {2016YFC0400706//the National Key Research and Development Program of China/ ; CSC No. 201708610028//Foundation of China Scholarship Council/ ; 2018KW-011//International Science and Technology Cooperation Program/ ; }, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/*genetics/metabolism ; Denitrification ; Ecosystem ; Gene Dosage ; Nitrite Reductases/*genetics/metabolism ; Phylogeny ; Sewage/*microbiology ; Wastewater/*microbiology ; Water Purification/instrumentation ; }, abstract = {Denitrifying bacteria is a driver of nitrogen removal process in wastewater treatment ecosystem. However, the geographical characteristics of denitrifying bacterial communities associated with activated sludge from diverse wastewater treatment plants (WWTPs) are still unclear. Here, quantitative PCR and next-generation sequencing of the nirS gene were applied to characterize the abundance and denitrifying bacterial communities from 18 geographically distributed WWTPs. The results showed that the nirS abundance ranged from 4.6 × 10[2] to 2.4 × 10[3] copies per ng DNA, while nirS-type denitrifying bacterial populations were diverse and distinct from activated sludge communities. Among WWTPs, total nitrogen removal efficiencies varied from 25.8 to 84%, which was positively correlated with diversity indices, whereas abundance-based coverage estimator index decreased with an increase in latitude. The dominant phyla across all samples were proteobacteria, accounting for 46.23% (ranging from 17.98 to 87.07%) of the sequences. Eight of the 22 genera detected were dominant: Thauera sp., Alicycliphilus sp., and Pseudomonas sp., etc. Based on network analysis, the coexistence and interaction between dominant genera may be vital for regulating the nitrogen and carbon removal behaviors. Multivariate statistical analysis revealed that both geographic location and wastewater factors concurrently govern the distribution patterns of nirS-type denitrifying bacterial community harbored in WWTPs. Taking together, these results from the present study provide novel insights into the nirS gene abundance and nirS-type denitrifying bacterial community composition in geographically distributed WWTPs. Moreover, the knowledge gained will improve the operation and management of WWTPs for nitrogen removal.}, }
@article {pmid30045954, year = {2018}, author = {Van den Bergh, B and Swings, T and Fauvart, M and Michiels, J}, title = {Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {82}, number = {3}, pages = {}, pmid = {30045954}, issn = {1098-5557}, mesh = {*Adaptation, Physiological ; Animals ; *Bacteria ; Biodiversity ; *Biological Evolution ; Genes ; Humans ; Mutation ; Population Dynamics ; *Research Design ; *Selection, Genetic ; *Viruses ; *Yeasts ; }, abstract = {In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.}, }
@article {pmid30045558, year = {2018}, author = {Djukic, I and Kepfer-Rojas, S and Schmidt, IK and Larsen, KS and Beier, C and Berg, B and Verheyen, K and , }, title = {Early stage litter decomposition across biomes.}, journal = {The Science of the total environment}, volume = {628-629}, number = {}, pages = {1369-1394}, doi = {10.1016/j.scitotenv.2018.01.012}, pmid = {30045558}, issn = {1879-1026}, abstract = {Through litter decomposition enormous amounts of carbon is emitted to the atmosphere. Numerous large-scale decomposition experiments have been conducted focusing on this fundamental soil process in order to understand the controls on the terrestrial carbon transfer to the atmosphere. However, previous studies were mostly based on site-specific litter and methodologies, adding major uncertainty to syntheses, comparisons and meta-analyses across different experiments and sites. In the TeaComposition initiative, the potential litter decomposition is investigated by using standardized substrates (Rooibos and Green tea) for comparison of litter mass loss at 336 sites (ranging from -9 to +26 °C MAT and from 60 to 3113 mm MAP) across different ecosystems. In this study we tested the effect of climate (temperature and moisture), litter type and land-use on early stage decomposition (3 months) across nine biomes. We show that litter quality was the predominant controlling factor in early stage litter decomposition, which explained about 65% of the variability in litter decomposition at a global scale. The effect of climate, on the other hand, was not litter specific and explained <0.5% of the variation for Green tea and 5% for Rooibos tea, and was of significance only under unfavorable decomposition conditions (i.e. xeric versus mesic environments). When the data were aggregated at the biome scale, climate played a significant role on decomposition of both litter types (explaining 64% of the variation for Green tea and 72% for Rooibos tea). No significant effect of land-use on early stage litter decomposition was noted within the temperate biome. Our results indicate that multiple drivers are affecting early stage litter mass loss with litter quality being dominant. In order to be able to quantify the relative importance of the different drivers over time, long-term studies combined with experimental trials are needed.}, }
@article {pmid30043185, year = {2018}, author = {Mörkl, S and Lackner, S and Meinitzer, A and Mangge, H and Lehofer, M and Halwachs, B and Gorkiewicz, G and Kashofer, K and Painold, A and Holl, AK and Bengesser, SA and Müller, W and Holzer, P and Holasek, SJ}, title = {Gut microbiota, dietary intakes and intestinal permeability reflected by serum zonulin in women.}, journal = {European journal of nutrition}, volume = {57}, number = {8}, pages = {2985-2997}, pmid = {30043185}, issn = {1436-6215}, support = {A16 - 028180/2009/0143//Stadt Graz/ ; }, mesh = {Adolescent ; Adult ; Biomarkers/blood ; Body Mass Index ; Cholera Toxin/*blood ; Cholesterol/blood ; *Diet ; Dietary Carbohydrates ; Dietary Fats/administration &amp; dosage ; Dietary Proteins/administration &amp; dosage ; Electric Impedance ; Female ; *Gastrointestinal Microbiome ; Haptoglobins ; Humans ; Intestines/*microbiology ; Nutrition Assessment ; Obesity/blood/microbiology ; Overweight/blood/microbiology ; Permeability ; Protein Precursors ; Triglycerides/blood ; Young Adult ; }, abstract = {PURPOSE: Increased gut permeability causes the trespass of antigens into the blood stream which leads to inflammation. Gut permeability reflected by serum zonulin and diversity of the gut microbiome were investigated in this cross-sectional study involving female study participants with different activity and BMI levels.<br><br>METHODS: 102 women were included (BMI range 13.24-46.89&#xa0;kg&#xa0;m[-2]): Anorexia nervosa patients (n&#x2009;=&#x2009;17), athletes (n&#x2009;=&#x2009;20), normal weight (n&#x2009;=&#x2009;25), overweight (n&#x2009;=&#x2009;21) and obese women (n&#x2009;=&#x2009;19). DNA was extracted from stool samples and subjected to 16S rRNA gene analysis (V1-V2). Quantitative Insights Into Microbial Ecology (QIIME) was used to analyze data. Zonulin was measured with ELISA. Nutrient intake was assessed by repeated 24-h dietary recalls. We used the median of serum zonulin concentration to divide our participants into a "high-zonulin" (>&#x2009;53.64&#xa0;ng/ml) and "low-zonulin" (<&#x2009;53.64&#xa0;ng/ml) group.<br><br>RESULTS: The alpha-diversity (Shannon Index, Simpson Index, equitability) and beta-diversity (unweighted and weighted UniFrac distances) of the gut microbiome were not significantly different between the groups. Zonulin concentrations correlated significantly with total calorie-, protein-, carbohydrate-, sodium- and vitamin B12 intake. Linear discriminant analysis effect size (LEfSe) identified Ruminococcaceae (LDA&#x2009;=&#x2009;4.163, p&#x2009;=&#x2009;0.003) and Faecalibacterium (LDA&#x2009;=&#x2009;4.151, p&#x2009;=&#x2009;0.0002) as significantly more abundant in the low zonulin group.<br><br>CONCLUSION: Butyrate-producing gut bacteria such as Faecalibacteria could decrease gut permeability and lower inflammation. The diversity of the gut microbiota in women does not seem to be correlated with the serum zonulin concentration. Further interventional studies are needed to investigate gut mucosal permeability and the gut microbiome in the context of dietary factors.}, }
@article {pmid30042197, year = {2018}, author = {Murray, AK and Zhang, L and Yin, X and Zhang, T and Buckling, A and Snape, J and Gaze, WH}, title = {Novel Insights into Selection for Antibiotic Resistance in Complex Microbial Communities.}, journal = {mBio}, volume = {9}, number = {4}, pages = {}, pmid = {30042197}, issn = {2150-7511}, support = {BB/L502509/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Cefotaxime/*pharmacology ; *Cephalosporin Resistance ; Cephalosporinase/genetics/metabolism ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Metagenomics ; Microbiota/*drug effects ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Selection, Genetic ; Sequence Analysis, DNA ; Sewage/*microbiology ; }, abstract = {Recent research has demonstrated that selection for antibiotic resistance occurs at very low antibiotic concentrations in single-species experiments, but the relevance of these findings when species are embedded in complex microbial communities is unclear. We show that the strength of selection for naturally occurring resistance alleles in a complex community remains constant from low subinhibitory to above clinically relevant concentrations. Selection increases with antibiotic concentration before reaching a plateau where selection remains constant over a 2-order-magnitude concentration range. This is likely to be due to cross protection of the susceptible bacteria in the community following rapid extracellular antibiotic degradation by the resistant population, shown experimentally through a combination of chemical quantification and bacterial growth experiments. Metagenome and 16S rRNA analyses of sewage-derived bacterial communities evolved under cefotaxime exposure show preferential enrichment for blaCTX-M genes over all other beta-lactamase genes, as well as positive selection and co-selection for antibiotic resistant, opportunistic pathogens. These findings have far-reaching implications for our understanding of the evolution of antibiotic resistance, by challenging the long-standing assumption that selection occurs in a dose-dependent manner.IMPORTANCE Antibiotic resistance is one of the greatest global issues facing society. Still, comparatively little is known about selection for resistance at very low antibiotic concentrations. We show that the strength of selection for clinically important resistance genes within a complex bacterial community can remain constant across a large antibiotic concentration range (wide selective space). Therefore, largely understudied ecological compartments could be just as important as clinical environments for selection of antibiotic resistance.}, }
@article {pmid30041461, year = {2018}, author = {Romano, S and Jackson, SA and Patry, S and Dobson, ADW}, title = {Extending the "One Strain Many Compounds" (OSMAC) Principle to Marine Microorganisms.}, journal = {Marine drugs}, volume = {16}, number = {7}, pages = {}, pmid = {30041461}, issn = {1660-3397}, mesh = {Animals ; Aquatic Organisms/*genetics ; Biological Products/metabolism ; Genome/*genetics ; Humans ; Multigene Family/genetics ; Secondary Metabolism/genetics ; }, abstract = {Genomic data often highlights an inconsistency between the number of gene clusters identified using bioinformatic approaches as potentially producing secondary metabolites and the actual number of chemically characterized secondary metabolites produced by any given microorganism. Such gene clusters are generally considered as "silent", meaning that they are not expressed under laboratory conditions. Triggering expression of these "silent" clusters could result in unlocking the chemical diversity they control, allowing the discovery of novel molecules of both medical and biotechnological interest. Therefore, both genetic and cultivation-based techniques have been developed aimed at stimulating expression of these "silent" genes. The principles behind the cultivation based approaches have been conceptualized in the "one strain many compounds" (OSMAC) framework, which underlines how a single strain can produce different molecules when grown under different environmental conditions. Parameters such as, nutrient content, temperature, and rate of aeration can be easily changed, altering the global physiology of a microbial strain and in turn significantly affecting its secondary metabolism. As a direct extension of such approaches, co-cultivation strategies and the addition of chemical elicitors have also been used as cues to activate "silent" clusters. In this review, we aim to provide a focused and comprehensive overview of these strategies as they pertain to marine microbes. Moreover, we underline how changes in some parameters which have provided important results in terrestrial microbes, but which have rarely been considered in marine microorganisms, may represent additional strategies to awaken "silent" gene clusters in marine microbes. Unfortunately, the empirical nature of the OSMAC approach forces scientists to perform extensive laboratory experiments. Nevertheless, we believe that some computation and experimental based techniques which are used in other disciplines, and which we discuss; could be effectively employed to help streamline the OSMAC based approaches. We believe that natural products discovery in marine microorganisms would be greatly aided through the integration of basic microbiological approaches, computational methods, and technological innovations, thereby helping unearth much of the as yet untapped potential of these microorganisms.}, }
@article {pmid30040385, year = {2018}, author = {Garner, E and McLain, J and Bowers, J and Engelthaler, DM and Edwards, MA and Pruden, A}, title = {Microbial Ecology and Water Chemistry Impact Regrowth of Opportunistic Pathogens in Full-Scale Reclaimed Water Distribution Systems.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {16}, pages = {9056-9068}, doi = {10.1021/acs.est.8b02818}, pmid = {30040385}, issn = {1520-5851}, mesh = {*Drinking Water ; *Legionella ; RNA, Ribosomal, 16S ; Water Microbiology ; *Water Purification ; }, abstract = {Need for global water security has spurred growing interest in wastewater reuse to offset demand for municipal water. While reclaimed (i.e., nonpotable) microbial water quality regulations target fecal indicator bacteria, opportunistic pathogens (OPs), which are subject to regrowth in distribution systems and spread via aerosol inhalation and other noningestion routes, may be more relevant. This study compares the occurrences of five OP gene markers (Acanthamoeba spp., Legionella spp., Mycobacterium spp., Naegleria fowleri, Pseudomonas aeruginosa) in reclaimed versus potable water distribution systems and characterizes factors potentially contributing to their regrowth. Samples were collected over four sampling events at the point of compliance for water exiting treatment plants and at five points of use at four U.S. utilities bearing both reclaimed and potable water distribution systems. Reclaimed water systems harbored unique water chemistry (e.g., elevated nutrients), microbial community composition, and OP occurrence patterns compared to potable systems examined here and reported in the literature. Legionella spp. genes, Mycobacterium spp. genes, and total bacteria, represented by 16S rRNA genes, were more abundant in reclaimed than potable water distribution system samples (p ≤ 0.0001). This work suggests that further consideration should be given to managing reclaimed water distribution systems with respect to nonpotable exposures to OPs.}, }
@article {pmid30039872, year = {2018}, author = {De Bodt, J and Defoirdt, T}, title = {Impact of the organic load on the efficacy of chlorine disinfection against acute hepatopancreatic necrosis disease-causing Vibrio parahaemolyticus.}, journal = {Journal of fish diseases}, volume = {41}, number = {10}, pages = {1609-1612}, doi = {10.1111/jfd.12866}, pmid = {30039872}, issn = {1365-2761}, mesh = {Animals ; Aquaculture ; Biofilms ; Chlorine/*chemistry ; *Disinfectants ; Disinfection/*methods ; Organic Chemicals/*chemistry ; Penaeidae/microbiology ; *Vibrio parahaemolyticus ; Water Purification/methods ; }, }
@article {pmid30038663, year = {2018}, author = {Calusinska, M and Goux, X and Fossépré, M and Muller, EEL and Wilmes, P and Delfosse, P}, title = {A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems.}, journal = {Biotechnology for biofuels}, volume = {11}, number = {}, pages = {196}, pmid = {30038663}, issn = {1754-6834}, abstract = {BACKGROUND: Anaerobic digestion (AD) is a microbe-driven process of biomass decomposition to CH4 and CO2. In addition to renewable and cost-effective energy production, AD has emerged in the European Union as an environmentally friendly model of bio-waste valorisation and nutrient recycling. Nevertheless, due to the high diversity of uncharacterised microbes, a typical AD microbiome is still considered as "dark matter".<br><br>RESULTS: Using the high-throughput sequencing of small rRNA gene, and a monthly monitoring of the physicochemical parameters for 20 different mesophilic full-scale bioreactors over 1&#xa0;year, we generated a detailed view of AD microbial ecology towards a better understanding of factors that influence and shape these communities. By studying the broadly distributed OTUs present in over 80% of analysed samples, we identified putatively important core bacteria and archaea to the AD process that accounted for over 70% of the whole microbial community relative abundances. AD reactors localised at the wastewater treatment plants were shown to operate with distinct core microbiomes than the agricultural and bio-waste treating biogas units. We also showed that both the core microbiomes were composed of low (with average community abundance &#x2264;&#x2009;1%) and highly abundant microbial populations; the vast majority of which remains yet uncharacterised, e.g. abundant candidate Cloacimonetes. Using non-metric multidimensional scaling, we observed microorganisms grouping into clusters that well reflected the origin of the samples, e.g. wastewater versus agricultural and bio-waste treating biogas units. The calculated diversity patterns differed markedly between the different community clusters, mainly due to the presence of highly diverse and dynamic transient species. Core microbial communities appeared relatively stable over the monitoring period.<br><br>CONCLUSIONS: In this study, we characterised microbial communities in different AD systems that were monitored over a 1-year period. Evidences were shown to support the concept of a core community driving the AD process, whereas the vast majority of dominant microorganisms remain yet to be characterised.}, }
@article {pmid30035767, year = {2018}, author = {Calatayud Arroyo, M and Van de Wiele, T and Hernandez-Sanabria, E}, title = {Assessing the Viability of a Synthetic Bacterial Consortium on the In Vitro Gut Host-microbe Interface.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {137}, pages = {}, pmid = {30035767}, issn = {1940-087X}, mesh = {Gastrointestinal Microbiome/*physiology ; Humans ; Intestines/*microbiology ; }, abstract = {The interplay between host and microbiota has been long recognized and extensively described. The mouth is similar to other sections of the gastrointestinal tract, as resident microbiota occurs and prevents colonisation by exogenous bacteria. Indeed, more than 600 species of bacteria are found in the oral cavity, and a single individual may carry around 100 different at any time. Oral bacteria possess the ability to adhere to the various niches in the oral ecosystem, thus becoming integrated within the resident microbial communities, and favouring growth and survival. However, the flow of bacteria into the gut during swallowing has been proposed to disturb the balance of the gut microbiota. In fact, oral administration of P. gingivalis shifted bacterial composition in the ileal microflora. We used a synthetic community as a simplified representation of the natural oral ecosystem, to elucidate the survival and viability of oral bacteria subjected to simulated gastrointestinal transit conditions. Fourteen species were selected, subjected to in vitro salivary, gastric, and intestinal digestion processes, and presented to a multicompartment cell model containing Caco-2 and HT29-MTX cells to simulate the gut mucosal epithelium. This model served to unravel the impact of swallowed bacteria on cells involved in the enterohepatic circulation. Using synthetic communities allows for controllability and reproducibility. Thus, this methodology can be adapted to assess pathogen viability and subsequent inflammation-associated changes, colonization capacity of probiotic mixtures, and ultimately, potential bacterial impact on the presystemic circulation.}, }
@article {pmid30033973, year = {2018}, author = {Choi, HJ and Jeong, TY and Yoon, H and Oh, BY and Han, YS and Hur, MJ and Kang, S and Kim, JG}, title = {Comparative microbial communities in tidal flats sediment on Incheon, South Korea.}, journal = {The Journal of general and applied microbiology}, volume = {64}, number = {5}, pages = {232-239}, doi = {10.2323/jgam.2017.12.007}, pmid = {30033973}, issn = {1349-8037}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/genetics ; *Environmental Microbiology ; Geologic Sediments/*microbiology ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Republic of Korea ; Seawater/microbiology ; }, abstract = {Coastal ecosystems, play critical ecological roles of which tidal flats are a significant component of coastal wetlands, such as habitat and nutrient cycling in aquatic biology. Microbial communities in tidal flats are known to play vital roles of self-purification. And the microbial ecology of the sediment is easily affected by human activities and pollution. In this paper, we applied pyrosequencing technology to investigate microbial communities in three different tidal flats (Ganghwa Island, Ongnyeon land region and Yeongjong Island) on the Incheon, Korea peninsula. A total of 16,906 sequences were obtained. We used these sequences to identify the dominant phyla in the three tidal flats: Proteobacteria, Chloroflexi, Actinobacteria, and Bacteroidetes. The composition of the bacterial community of Ganghwa Island and the Ongnyeon region were more similar to each other than they were to the bacterial community of Yeongjong Island. Simpson's dominance index of Yeongjong Island was higher than that of the other regions, and the Shannon diversity index of this region was the lowest. Previous research of samples in these regions indicated that the three tidal flats had similar geochemical characteristics. However, their bacterial communities were rather distinct. This might be because the analysis of microbial communities and physiochemical analysis have different perspectives. Therefore, the pyrosequencing of a bacterial community with physiochemical analysis is recommended as an effective monitoring tool for the comprehensive management of tidal flats.}, }
@article {pmid30033500, year = {2019}, author = {Clemmons, BA and Voy, BH and Myer, PR}, title = {Altering the Gut Microbiome of Cattle: Considerations of Host-Microbiome Interactions for Persistent Microbiome Manipulation.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {523-536}, pmid = {30033500}, issn = {1432-184X}, mesh = {Animal Feed/analysis/microbiology ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Cattle/metabolism/*microbiology ; *Gastrointestinal Microbiome ; Rumen/metabolism/microbiology ; }, abstract = {The beef cattle industry represents a significant portion of the USA's agricultural sect, with beef cattle accounting for the most red meat consumed in the USA. Feed represents the largest input cost in the beef industry, accounting for approximately 70% of total input cost. Given that, novel methods need to be employed to optimize feed efficiency in cattle to reduce monetary cost as well as environmental cost associated with livestock industries, such as methane production and nitrogen release into the environment. The rumen microbiome contributes to feed efficiency by breaking down low-quality feedstuffs into energy substrates that can subsequently be utilized by the host animal. Attempts to manipulate the rumen microbiome have been met with mixed success, though persistent changes have not yet been achieved beyond changing diet. Recent technological advances have made analyzing host-wide effects of the rumen microbiome possible, as well as provided finer resolution of those effects. This manuscript reviews contributing factors to the rumen microbiome establishment or re-establishment following rumen microbiome perturbation, as well as host-microbiome interactions that may be responsible for possible host specificity of the rumen microbiome. Understanding and accounting for the variety of factors contributing to rumen microbiome establishment or re-establishment in cattle will ultimately lead to identification of biomarkers of feed efficiency that will result in improved selection criteria, as well as aid to determine methods for persistent microbiome manipulation to optimize production phenotypes.}, }
@article {pmid30033172, year = {2018}, author = {Sanz, Y and Romaní-Perez, M and Benítez-Páez, A and Portune, KJ and Brigidi, P and Rampelli, S and Dinan, T and Stanton, C and Delzenne, N and Blachier, F and Neyrinck, AM and Beaumont, M and Olivares, M and Holzer, P and Günther, K and Wolters, M and Ahrens, W and Claus, SP and Campoy, C and Murphy, R and Sadler, C and Fernández, L and Kamp, JV}, title = {Towards microbiome-informed dietary recommendations for promoting metabolic and mental health: Opinion papers of the MyNewGut project.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {37}, number = {6 Pt A}, pages = {2191-2197}, doi = {10.1016/j.clnu.2018.07.007}, pmid = {30033172}, issn = {1532-1983}, mesh = {Animals ; *Diet ; *Gastrointestinal Microbiome ; Humans ; *Mental Health ; *Metabolism ; Mice ; }, abstract = {The gut microbiota coexists in partnership with the human host through adaptations to environmental and physiological changes that help maintain dynamic homeostatic healthy states. Break-down of this delicate balance under sustained exposure to stressors (e.g. unhealthy diets) can, however, contribute to the onset of disease. Diet is a key modifiable environmental factor that modulates the gut microbiota and its metabolic capacities that, in turn, could impact human physiology. On this basis, the diet and the gut microbiota could act as synergistic forces that provide resilience against disease or that speed the progress from health to disease states. Associations between unhealthy dietary patterns, non-communicable diseases and intestinal dysbiosis can be explained by this hypothesis. Translational studies showing that dietary-induced alterations in microbial communities recapitulate some of the pathological features of the original host further support this notion. In this introductory paper by the European project MyNewGut, we briefly summarize the investigations conducted to better understand the role of dietary patterns and food components in metabolic and mental health and the specificities of the microbiome-mediating mechanisms. We also discuss how advances in the understanding of the microbiome's role in dietary health effects can help to provide acceptable scientific grounds on which to base dietary advice for promoting healthy living.}, }
@article {pmid30032189, year = {2018}, author = {Donhauser, J and Frey, B}, title = {Alpine soil microbial ecology in a changing world.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {9}, pages = {}, doi = {10.1093/femsec/fiy099}, pmid = {30032189}, issn = {1574-6941}, mesh = {Arctic Regions ; Biodiversity ; *Climate Change ; Ice Cover ; Permafrost/*chemistry/*microbiology ; *Soil Microbiology ; *Tundra ; }, abstract = {Climate change has a disproportionally large impact on alpine soil ecosystems, leading to pronounced changes in soil microbial diversity and function associated with effects on biogeochemical processes at the local and supraregional scales. However, due to restricted accessibility, high-altitude soils remain largely understudied and a considerable heterogeneity hampers the comparability of different alpine studies. Here, we highlight differences and similarities between alpine and arctic ecosystems, and we discuss the impact of climatic variables and associated vegetation and soil properties on microbial ecology. We consider how microbial alpha-diversity, community structures and function change along altitudinal gradients and with other topographic features such as slope aspect. In addition, we focus on alpine permafrost soils, harboring a surprisingly large unknown microbial diversity and on microbial succession along glacier forefield chronosequences constituting the most thoroughly studied alpine habitat. Finally, highlighting experimental approaches, we present climate change studies showing shifts in microbial community structures and function in response to warming and altered moisture, interestingly with some contradiction. Collectively, despite harsh environmental conditions, many specially adapted microorganisms are able to thrive in alpine environments. Their community structures strongly correlate with climatic, vegetation and soil properties and thus closely mirror the complexity and small-scale heterogeneity of alpine soils.}, }
@article {pmid30031405, year = {2018}, author = {Zhang, AN and Li, LG and Ma, L and Gillings, MR and Tiedje, JM and Zhang, T}, title = {Conserved phylogenetic distribution and limited antibiotic resistance of class 1 integrons revealed by assessing the bacterial genome and plasmid collection.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {130}, pmid = {30031405}, issn = {2049-2618}, mesh = {*Drug Resistance, Bacterial ; Evolution, Molecular ; Gammaproteobacteria/drug effects/*genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Integrons ; Phylogeny ; Plasmids/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Integrons, especially the class 1 integrons, are major contributors to the acquisition and dissemination of antibiotic resistance genes (ARGs). However, comprehensive knowledge of the types, content, and distribution of integrons in bacterial taxa is lacking to evaluate their contribution.<br><br>RESULTS: We have constructed a new integrase database and developed a pipeline that provides comprehensive recovery of class 1 integrons. Previous PCR-based techniques might only detect one fourth of the integron-integrases and integrons recovered in this study. By exploring the class 1 integrons in over 73,000 currently available complete and draft bacterial genomes, the contribution of class 1 integrons in spreading and acquiring ARGs was evaluated. Firstly, the host species of class 1 integrons are highly conserved within (96%) in class Gammaproteobacteria, dominated by four pathogenic species of "ESKAPE." Secondly, more than half of class 1 integrons are embedded in chromosomes with less potential for horizontal gene transfer. Finally, ARGs that have been acquired by these integrons only cover 11% of all the ARG genotypes detected in bacterial genomes.<br><br>CONCLUSIONS: The above observations indicated that there are both biological and ecological limitations to class 1 integrons in acquiring and spreading ARGs across different classes of the domain Bacteria.}, }
@article {pmid30031243, year = {2018}, author = {Paul, W and Marta, C and Tom, VW}, title = {Resolving host-microbe interactions in the gut: the promise of in vitro models to complement in vivo research.}, journal = {Current opinion in microbiology}, volume = {44}, number = {}, pages = {28-33}, doi = {10.1016/j.mib.2018.07.001}, pmid = {30031243}, issn = {1879-0364}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; *Gastrointestinal Microbiome ; *Host Microbial Interactions ; Humans ; Research ; }, abstract = {While animal models remain essential for inferring causality, they exhibit important limitations, which restrict the direct translation of findings into new approaches aimed at steering host-microbe interactions for the improvement of human health. Different in vitro models have therefore been developed which incorporate human cell types and microbiota. By virtue of their intricate designs, these models result in human and microbial read-outs reflective of in vivo gut physiology, and present important alternatives to animal models. However, to allow systematic investigations of the interactions between gut microbiota and different human cell types and body systems, ever more complex cell assemblies are necessary which will culminate in the establishment of personalized in vitro models. Such models will allow the unravelling of human-microbe interdependencies and will open exciting new avenues for microbiome-tailored nutrition and drug development.}, }
@article {pmid30029141, year = {2018}, author = {Cipullo, S and Snapir, B and Tardif, S and Campo, P and Prpich, G and Coulon, F}, title = {Insights into mixed contaminants interactions and its implication for heavy metals and metalloids mobility, bioavailability and risk assessment.}, journal = {The Science of the total environment}, volume = {645}, number = {}, pages = {662-673}, doi = {10.1016/j.scitotenv.2018.07.179}, pmid = {30029141}, issn = {1879-1026}, abstract = {Mobility of heavy metals at contaminated sites is mainly influenced by the soil physicochemical properties and environmental conditions, therefore assessing heavy metals (HMs) and metalloids fractionation can provide insights into their potential risk and the mechanisms that regulate bioavailability. A 12-months mesocosms experiment was setup to investigate the effect of physicochemical factors (pH, moisture, and temperature) and weathering (time) on HMs and metalloids fractionation in three different multi-contaminated soil matrices (low, medium, and high contamination) collected from a soil treatment facility located in the United Kingdom, and two rural contaminated soil samples. The study demonstrates that even though Pb and Zn were found associated with the exchangeable fraction in the soil with the highest contamination (total average Pb 3400 mg/kg, and total average Zn 2100 mg/kg in Soil C), neither the condition applied nor the weathering caused an increase in their mobility. Although it was expected that lower pH (4.5) would favours the dissociation of HMs and metalloids, no significant differences were observed, potentially due to the initial alkaline pH of the genuine-contaminated soil samples. The results show that even though total concentration of Pb, Cu, and Zn exceed the soil standards and guideline values, HMs were predominantly associated with the non-exchangeable fraction, while only 5% were dissolved in the pore water fraction (potentially bioavailable). In addition, the mobility and bioavailability of HMs remained constant over the 12 months monitoring, suggesting that these soils pose negligible risk to the environment.}, }
@article {pmid30029114, year = {2018}, author = {McGillicuddy, E and Morrison, L and Cormican, M and Dockery, P and Morris, D}, title = {Activated charcoal as a capture material for silver nanoparticles in environmental water samples.}, journal = {The Science of the total environment}, volume = {645}, number = {}, pages = {356-362}, doi = {10.1016/j.scitotenv.2018.07.145}, pmid = {30029114}, issn = {1879-1026}, abstract = {Silver nanoparticles (AgNPs), due to their antibacterial activity, have been incorporated into numerous consumer products. Their environmental impact however, is currently unclear. Uncertainties surround the concentration, fate, and effects of AgNPs in aquatic environments. This study examined the suitability of activated charcoal as a capture material for AgNPs from water. Samples of 100 ppb AgNPs were initially generated and exposed to activated charcoal for 24 h to examine the ability of charcoal to capture AgNPs. The decrease in Ag concentration was measured using ICP-MS. Following initial investigations, the surface area of the charcoal was increased firstly with a pestle and mortar and secondly by milling the charcoal using a ball mill. The increased surface area of the milled charcoal increased the capture of the AgNPs from 11.9% to 63.6% for the 100 ppb samples. Further investigations were carried out examining the effect on the capture of AgNP concentration (with concentration ranging from 10 to 100 ppb), particle coating and the effect of exposure time to the activated charcoal. The capture of AgNP increased with decreasing concentration. A hydrochloric acid (HCl) leaching procedure was also developed which successfully removed the captured silver allowing the fraction captured by the charcoal to be quantified with an average of 94.8% recovery. The results show that milled activated charcoal, can successfully capture AgNPs from water samples, and that therefore, activated charcoal may prove to be a cost effective material for the remediation of waters impacted by AgNP or other nano-wastes.}, }
@article {pmid30028282, year = {2018}, author = {Sultanpuram, VR and Mothe, T}, title = {Thalassorhabdus alkalitolerans gen. nov., sp. nov., a novel Bacillaceae member isolated from marine sediment.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {68}, number = {9}, pages = {2969-2976}, doi = {10.1099/ijsem.0.002931}, pmid = {30028282}, issn = {1466-5034}, mesh = {Bacillaceae/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; Cell Wall/chemistry ; DNA, Bacterial/genetics ; Diaminopimelic Acid/chemistry ; Fatty Acids/chemistry ; Geologic Sediments/*microbiology ; India ; Nucleic Acid Hybridization ; Peptidoglycan/chemistry ; Phosphatidylglycerols/analysis ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {A novel Gram-stain-variable, rod-shaped, non-motile and non-endospore-forming bacterium (strain G27[T]) was isolated from near Dhuvaran, Gujarat, India. Based on 16S rRNA gene sequence analysis, strain G27[T] was identified as a member of the class Firmibacteria and was most closely related to Bacillus populi FJAT-45347[T] (94.9 % sequence similarity), Salipaludibacillus aurantiacus S9[T] (94.9 %), Salipaludibacillus neizhouensis KCTC 13187[T] (94.7 %), Alteribacillus iranensis DSM 23995[T] (94.6 %) and other Firmibacteria (<94.6 %). The DNA G+C content of strain G27[T] was 43.4±0.6 mol%. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and five unidentified lipids. The predominant isoprenoid quinone was menaquinone MK-7. Major fatty acids (>5 %) included anteiso-C15:0, iso-C15 : 0, anteiso-C17:0, C16 : 0 and iso-C16 : 0. The results of phylogenetic, chemotaxonomic and biochemical tests allowed the clear differentiation of strain G27[T] from all other members of the family Bacillaceae.It is therefore considered to represent a novel species of a new genus, for which the name Thalassorhabdus alkalitolerans gen. nov., sp. nov., is proposed. The type strain of Thalassorhabdus alkalitolerans is G27[T] (=MCC 3411[T]=CGMCC 1.15772[T]=KCTC 33941[T]).}, }
@article {pmid30025176, year = {2019}, author = {Liang, Z and Shen, Z and Zhang, Y and Ji, D and Li, J and Warren, A and Lin, X}, title = {Morphology and Phylogeny of Four New Vorticella Species (Ciliophora: Peritrichia) from Coastal Waters of Southern China.}, journal = {The Journal of eukaryotic microbiology}, volume = {66}, number = {2}, pages = {267-280}, doi = {10.1111/jeu.12668}, pmid = {30025176}, issn = {1550-7408}, mesh = {China ; DNA, Protozoan/analysis ; Macronucleus/physiology ; Oligohymenophorea/*classification/*cytology ; Saline Waters ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Four new species of Vorticella, V. parachiangi sp. n., V. scapiformis sp. n., V. sphaeroidalis sp. n., and V. paralima sp. n., were isolated from coastal brackish waters of southern China. Their morphology, infraciliature, and silverline system were investigated based on observations of specimens both in vivo and following silver staining. Vorticella parachiangi sp. n. is distinguished by: a J-shaped macronucleus; a single dorsally located contractile vacuole; a two-rowed infundibular polykinetid 3, in which row 1 is shorter than row 2; 21-31 silverlines between peristome and aboral trochal band, 6-11 between aboral trochal band and scopula. Vorticella scapiformis sp. n. is characterized by its conspicuously thin and irregularly edged peristomial lip; a J-shaped macronucleus; a single, ventrally located contractile vacuole; row 1 of the infundibular polykinetid 3 proximally shortened; 18-25 silverlines between peristome and aboral trochal band, 8-12 between aboral trochal band and scopula. Vorticella sphaeroidalis sp. n. can be identified by its small, sub-spherical zooid; a C-shaped macronucleus; a ventrally located contractile vacuole; an aboral trochal band adjacent to the scopula; 16-18 silverlines between persitome and aboral trochal band, two between aboral trochal band and scopula. Vorticella paralima sp. n. can be identified by its ovoidal zooid; a J-shaped macronucleus; a dorsally positioned contractile vacuole; rows 1 and 2 of the infundibular polykinetid 3 proximally shortened; 26-35 silverlines from peristome to aboral trochal band, and 7-13 from aboral trochal band to scopula. The SSU rDNA genes of these four species were sequenced and their phylogeny was analyzed.}, }
@article {pmid30023789, year = {2018}, author = {Mukherjee, I and Ghosh, A and Bhadury, P and De, P}, title = {Leucine-Based Polymer Architecture-Induced Antimicrobial Properties and Bacterial Cell Morphology Switching.}, journal = {ACS omega}, volume = {3}, number = {1}, pages = {769-780}, pmid = {30023789}, issn = {2470-1343}, abstract = {To evaluate the comparative antibacterial activity of leucine-based cationic polymers having linear, hyperbranched, and star architectures containing both hydrophilic and hydrophobic segments against Gram-negative bacterium, Escherichia coli (E. coli), herein we performed zone of inhibition study, minimum inhibitory concentration (MIC) calculation, and bacterial growth experiment. The highest antibacterial activity in terms of the MIC value was found in hyperbranched and star architectures because of the greater extent of cationic and hydrophobic functionality, enhancing cell wall penetration ability compared to that of the linear polymer. The absence of the bacterial regrowth stage in the growth curve exhibited the highest bactericidal capacity of star polymers, when untreated cells (control) already reached to the stationary phase, whereas the bacterial regrowth stage with a delayed lag phase was critically observed for linear and hyperbranched architectures displaying lower bactericidal efficacy. Coagulation of E. coli cells, switching of cell morphology from rod to sphere, and lengthening due to stacking in an antimicrobial polymer-treated environment at the bacterial regrowth stage in liquid media were visualized critically by field emission scanning electron microscopy and confocal fluorescence microscopy instruments in the presence of 4',6-diamidino-2-phenylindole stain.}, }
@article {pmid30022610, year = {2018}, author = {Di Cesare, A and Petrin, S and Fontaneto, D and Losasso, C and Eckert, EM and Tassistro, G and Borello, A and Ricci, A and Wilson, WH and Pruzzo, C and Vezzulli, L}, title = {ddPCR applied on archived Continuous Plankton Recorder samples reveals long-term occurrence of class 1 integrons and a sulphonamide resistance gene in marine plankton communities.}, journal = {Environmental microbiology reports}, volume = {10}, number = {4}, pages = {458-464}, doi = {10.1111/1758-2229.12665}, pmid = {30022610}, issn = {1758-2229}, mesh = {Atlantic Ocean ; Bacteria/*genetics ; Bacterial Proteins/*genetics ; Carrier Proteins/*genetics ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Integrases/*genetics ; North Sea ; Plankton/*genetics ; *Polymerase Chain Reaction ; Seawater/*microbiology ; Time ; }, abstract = {Antibiotic resistance is a rising threat for human health. Although in clinical settings and terrestrial environments the rise of antibiotic resistant bacteria is well documented, their dissemination and spread in the marine environment, covering almost two-thirds of the Earth's surface, is still poorly understood. In this study, the presence and abundance of sulphonamide resistance gene (sul2) and class 1 integron-integrase gene (intI1), used as markers for the occurrence and spread of antibiotic resistance genes since the beginning of the antibiotic era, were investigated. Twenty-nine archived formalin-fixed samples, collected by the Continuous Plankton Recorder (CPR) survey in the Atlantic Ocean and North Sea from 1970 to 2011, were analysed using Droplet Digital PCR (ddPCR) applied for the first time on CPR samples. The two marker genes were present in a large fraction of the samples (48% for sul2 and 76% for intI1). In contrast, results from Real-Time PCR performed on the same samples greatly underestimate their occurrence (21% for sul2 and 52% for intI1). Overall, besides providing successful use of ddPCR for the molecular analysis of CPR samples, this study reveals long-term occurrence and spread of sul2 gene and class 1 integrons in the plankton-associated bacterial communities in the ocean.}, }
@article {pmid30022245, year = {2018}, author = {Kopejtka, K and Tomasch, J and Bunk, B and Spröer, C and Wagner-Döbler, I and Koblížek, M}, title = {The complete genome sequence of Rhodobaca barguzinensis alga05 (DSM 19920) documents its adaptation for life in soda lakes.}, journal = {Extremophiles : life under extreme conditions}, volume = {22}, number = {6}, pages = {839-849}, pmid = {30022245}, issn = {1433-4909}, support = {Algatech Plus (LO1416)//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; Transregio 51 "Roseobacter"//Deutsche Forschungsgemeinschaft/ ; 57155424//Deutscher Akademischer Austauschdienst/ ; P501/12/G055//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; }, mesh = {Adaptation, Physiological ; *Genome, Bacterial ; Lakes/*microbiology ; Molecular Sequence Annotation ; Rhodobacteraceae/*genetics/physiology ; }, abstract = {Soda lakes, with their high salinity and high pH, pose a very challenging environment for life. Microorganisms living in these harsh conditions have had to adapt their physiology and gene inventory. Therefore, we analyzed the complete genome of the haloalkaliphilic photoheterotrophic bacterium Rhodobaca barguzinensis strain alga05. It consists of a 3,899,419 bp circular chromosome with 3624 predicted coding sequences. In contrast to most of Rhodobacterales, this strain lacks any extrachromosomal elements. To identify the genes responsible for adaptation to high pH, we compared the gene inventory in the alga05 genome with genomes of 17 reference strains belonging to order Rhodobacterales. We found that all haloalkaliphilic strains contain the mrpB gene coding for the B subunit of the MRP Na[+]/H[+] antiporter, while this gene is absent in all non-alkaliphilic strains, which indicates its importance for adaptation to high pH. Further analysis showed that alga05 requires organic carbon sources for growth, but it also contains genes encoding the ethylmalonyl-CoA pathway for CO2 fixation. Remarkable is the genetic potential to utilize organophosphorus compounds as a source of phosphorus. In summary, its genetic inventory indicates a large flexibility of the alga05 metabolism, which is advantageous in rapidly changing environmental conditions in soda lakes.}, }
@article {pmid30021874, year = {2018}, author = {Glassman, SI and Martiny, JBH}, title = {Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units.}, journal = {mSphere}, volume = {3}, number = {4}, pages = {}, pmid = {30021874}, issn = {2379-5042}, mesh = {Bacteria/*classification/*genetics ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; *Environmental Microbiology ; Fungi/*classification/*genetics ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Recent discussion focuses on the best method for delineating microbial taxa, based on either exact sequence variants (ESVs) or traditional operational taxonomic units (OTUs) of marker gene sequences. We sought to test if the binning approach (ESVs versus 97% OTUs) affected the ecological conclusions of a large field study. The data set included sequences targeting all bacteria (16S rRNA) and fungi (internal transcribed spacer [ITS]), across multiple environments diverging markedly in abiotic conditions, over three collection times. Despite quantitative differences in microbial richness, we found that all α and β diversity metrics were highly positively correlated (r > 0.90) between samples analyzed with both approaches. Moreover, the community composition of the dominant taxa did not vary between approaches. Consequently, statistical inferences were nearly indistinguishable. Furthermore, ESVs only moderately increased the genetic resolution of fungal and bacterial diversity (1.3 and 2.1 times OTU richness, respectively). We conclude that for broadscale (e.g., all bacteria or all fungi) α and β diversity analyses, ESV or OTU methods will often reveal similar ecological results. Thus, while there are good reasons to employ ESVs, we need not question the validity of results based on OTUs.IMPORTANCE Microbial ecologists have made exceptional improvements in our understanding of microbiomes in the last decade due to breakthroughs in sequencing technologies. These advances have wide-ranging implications for fields ranging from agriculture to human health. Due to limitations in databases, the majority of microbial ecology studies use a binning approach to approximate taxonomy based on DNA sequence similarity. There remains extensive debate on the best way to bin and approximate this taxonomy. Here we examine two popular approaches using a large field-based data set examining both bacteria and fungi and conclude that there are not major differences in the ecological outcomes. Thus, it appears that standard microbial community analyses are not overly sensitive to the particulars of binning approaches.}, }
@article {pmid30019110, year = {2019}, author = {Broman, E and Li, L and Fridlund, J and Svensson, F and Legrand, C and Dopson, M}, title = {Spring and Late Summer Phytoplankton Biomass Impact on the Coastal Sediment Microbial Community Structure.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {288-303}, pmid = {30019110}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biomass ; Cyanobacteria/classification/genetics/*growth &amp; development/isolation &amp; purification ; Diatoms/classification/genetics/*growth &amp; development/isolation &amp; purification ; Eutrophication ; Geologic Sediments/chemistry/*microbiology ; Nitrates/analysis/metabolism ; Nitrites/analysis/metabolism ; Phylogeny ; Phytoplankton/classification/genetics/*growth &amp; development/isolation &amp; purification ; Seasons ; Seawater/chemistry/microbiology ; }, abstract = {Two annual Baltic Sea phytoplankton blooms occur in spring and summer. The bloom intensity is determined by nutrient concentrations in the water, while the period depends on weather conditions. During the course of the bloom, dead cells sink to the sediment where their degradation consumes oxygen to create hypoxic zones (< 2 mg/L dissolved oxygen). These zones prevent the establishment of benthic communities and may result in fish mortality. The aim of the study was to determine how the spring and autumn sediment chemistry and microbial community composition changed due to degradation of diatom or cyanobacterial biomass, respectively. Results from incubation of sediment cores showed some typical anaerobic microbial processes after biomass addition such as a decrease in NO2[-] + NO3[-] in the sediment surface (0-1 cm) and iron in the underlying layer (1-2 cm). In addition, an increase in NO2[-] + NO3[-] was observed in the overlying benthic water in all amended and control incubations. The combination of NO2[-] + NO3[-] diffusion plus nitrification could not account for this increase. Based on 16S rRNA gene sequences, the addition of cyanobacterial biomass during autumn caused a large increase in ferrous iron-oxidizing archaea while diatom biomass amendment during spring caused minor changes in the microbial community. Considering that OTUs sharing lineages with acidophilic microorganisms had a high relative abundance during autumn, it was suggested that specific niches developed in sediment microenvironments. These findings highlight the importance of nitrogen cycling and early microbial community changes in the sediment due to sinking phytoplankton before potential hypoxia occurs.}, }
@article {pmid30018864, year = {2018}, author = {Lydon, KA and Lipp, EK}, title = {Taxonomic annotation errors incorrectly assign the family Pseudoalteromonadaceae to the order Vibrionales in Greengenes: implications for microbial community assessments.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5248}, pmid = {30018864}, issn = {2167-8359}, abstract = {Next-generation sequencing has provided powerful tools to conduct microbial ecology studies. Analysis of community composition relies on annotated databases of curated sequences to provide taxonomic assignments; however, these databases occasionally have errors with implications for downstream analyses. Systemic taxonomic errors were discovered in Greengenes database (v13_5 and 13_8) related to orders Vibrionales and Alteromonadales. These orders have family level annotations that were erroneous at least one taxonomic level, e.g., 100% of sequences assigned to the Pseudoalteromonadaceae family were placed improperly in Vibrionales (rather than Alteromonadales) and >20% of these sequences were indeed Vibrio spp. but were improperly assigned to the Pseudoalteromonadaceae family (rather than to Vibrionaceae). Use of this database is common; we identified 68 peer-reviewed papers since 2013 that likely included erroneous annotations specifically associated with Vibrionales and Pseudoalteromonadaceae, with 20 explicitly stating the incorrect taxonomy. Erroneous assignments using these specific versions of Greengenes can lead to incorrect conclusions, especially in marine systems where these taxa are commonly encountered as conditionally rare organisms and potential pathogens.}, }
@article {pmid30018368, year = {2018}, author = {Mendes, LW and Mendes, R and Raaijmakers, JM and Tsai, SM}, title = {Breeding for soil-borne pathogen resistance impacts active rhizosphere microbiome of common bean.}, journal = {The ISME journal}, volume = {12}, number = {12}, pages = {3038-3042}, pmid = {30018368}, issn = {1751-7370}, mesh = {Bacteria/*growth &amp; development ; Disease Resistance/*genetics ; Fusarium/*immunology ; *Microbiota ; Phaseolus/genetics/*immunology/microbiology ; Plant Breeding ; Plant Roots/genetics/immunology/microbiology ; Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Over the past century, plant breeding programs have substantially improved plant growth and health, but have not yet considered the potential effects on the plant microbiome. Here, we conducted metatranscriptome analysis to determine if and how breeding for resistance of common bean against the root pathogen Fusarium oxysporum (Fox) affected gene expression in the rhizobacterial community. Our data revealed that the microbiome of the Fox-resistant cultivar presented a significantly higher expression of genes associated with nutrient metabolism, motility, chemotaxis, and the biosynthesis of the antifungal compounds phenazine and colicin V. Network analysis further revealed a more complex community for Fox-resistant cultivar and indicated Paenibacillus as a keystone genus in the rhizosphere microbiome. We suggest that resistance breeding in common bean has unintentionally co-selected for plant traits that strengthen the rhizosphere microbiome network structure and enrich for specific beneficial bacterial genera that express antifungal traits involved in plant protection against infections by root pathogens.}, }
@article {pmid30014981, year = {2018}, author = {De Paepe, J and Lindeboom, REF and Vanoppen, M and De Paepe, K and Demey, D and Coessens, W and Lamaze, B and Verliefde, ARD and Clauwaert, P and Vlaeminck, SE}, title = {Refinery and concentration of nutrients from urine with electrodialysis enabled by upstream precipitation and nitrification.}, journal = {Water research}, volume = {144}, number = {}, pages = {76-86}, doi = {10.1016/j.watres.2018.07.016}, pmid = {30014981}, issn = {1879-2448}, mesh = {Biofilms ; Biofouling ; Biological Oxygen Demand Analysis ; Bioreactors/microbiology ; Chemical Precipitation ; Dialysis/*methods ; Humans ; Microbiota/genetics ; Nitrates/chemistry ; Nitrification ; Nitrogen/*isolation &amp; purification ; Oxidation-Reduction ; Phosphates/isolation &amp; purification ; Phosphorus/chemistry/isolation &amp; purification ; RNA, Ribosomal, 16S ; Urine/*chemistry ; Waste Disposal, Fluid/instrumentation/*methods ; }, abstract = {Human urine is a valuable resource for nutrient recovery, given its high levels of nitrogen, phosphorus and potassium, but the compositional complexity of urine presents a challenge for an energy-efficient concentration and refinery of nutrients. In this study, a pilot installation combining precipitation, nitrification and electrodialysis (ED), designed for one person equivalent (1.2 Lurine d[-1]), was continuously operated for ∼7 months. First, NaOH addition yielded calcium and magnesium precipitation, preventing scaling in ED. Second, a moving bed biofilm reactor oxidized organics, preventing downstream biofouling, and yielded complete nitrification on diluted urine (20-40%, i.e. dilution factors 5 and 2.5) at an average loading rate of 215 mg N L[-1] d[-1]. Batch tests demonstrated the halotolerance of the nitrifying community, with nitrification rates not affected up to an electrical conductivity of 40 mS cm[-1] and gradually decreasing, yet ongoing, activity up to 96 mS cm[-1] at 18% of the maximum rate. Next-generation 16S rRNA gene amplicon sequencing revealed that switching from a synthetic influent to real urine induced a profound shift in microbial community and that the AOB community was dominated by halophilic species closely related to Nitrosomonas aestuarii and Nitrosomonas marina. Third, nitrate, phosphate and potassium in the filtered (0.1 μm) bioreactor effluent were concentrated by factors 4.3, 2.6 and 4.6, respectively, with ED. Doubling the urine concentration from 20% to 40% further increased the ED recovery efficiency by ∼10%. Batch experiments at pH 6, 7 and 8 indicated a more efficient phosphate transport to the concentrate at pH 7. The newly proposed three-stage strategy opens up opportunities for energy- and chemical-efficient nutrient recovery from urine. Precipitation and nitrification enabled the long-term continuous operation of ED on fresh urine requiring minimal maintenance, which has, to the best of our knowledge, never been achieved before.}, }
@article {pmid30014593, year = {2018}, author = {Våge, S and Bratbak, G and Egge, J and Heldal, M and Larsen, A and Norland, S and Lund Paulsen, M and Pree, B and Sandaa, RA and Skjoldal, EF and Tsagaraki, TM and Øvreås, L and Thingstad, TF}, title = {Simple models combining competition, defence and resource availability have broad implications in pelagic microbial food webs.}, journal = {Ecology letters}, volume = {21}, number = {9}, pages = {1440-1452}, doi = {10.1111/ele.13122}, pmid = {30014593}, issn = {1461-0248}, mesh = {Biodiversity ; *Ecosystem ; *Food Chain ; }, abstract = {In food webs, interactions between competition and defence control the partitioning of limiting resources. As a result, simple models of these interactions contain links between biogeochemistry, diversity, food web structure and ecosystem function. Working at hierarchical levels, these mechanisms also produce self-similarity and therefore suggest how complexity can be generated from repeated application of simple underlying principles. Reviewing theoretical and experimental literature relevant to the marine photic zone, we argue that there is a wide spectrum of phenomena, including single cell activity of prokaryotes, microbial biodiversity at different levels of resolution, ecosystem functioning, regional biogeochemical features and evolution at different timescales; that all can be understood as variations over a common principle, summarised in what has been termed the 'Killing-the-Winner' (KtW) motif. Considering food webs as assemblages of such motifs may thus allow for a more integrated approach to aquatic microbial ecology.}, }
@article {pmid30013541, year = {2018}, author = {Aguinaga, OE and McMahon, A and White, KN and Dean, AP and Pittman, JK}, title = {Microbial Community Shifts in Response to Acid Mine Drainage Pollution Within a Natural Wetland Ecosystem.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1445}, pmid = {30013541}, issn = {1664-302X}, abstract = {Natural wetlands are known to play an important role in pollutant remediation, such as remediating acid mine drainage (AMD) from abandoned mine sites. However, many aspects of the microbiological mechanisms underlying AMD remediation within wetlands are poorly understood, including the role and composition of associated microbial communities. We have utilized an AMD-polluted river-wetland system to perform rRNA sequence analysis of microbial communities that play a role in biogeochemical activities that are linked to water quality improvement. Next-generation sequencing of bacterial 16S rRNA gene amplicons from river and wetland sediment samples identified variation in bacterial community structure and diversity on the basis of dissolved and particulate metal concentrations, sediment metal concentrations and other water chemistry parameters (pH and conductivity), and wetland plant presence. Metabolic reconstruction analysis allowed prediction of relative abundance of microbial metabolic pathways and revealed differences between samples that cluster on the basis of the severity of AMD pollution. Global metabolic activity was predicted to be significantly higher in unpolluted and wetland sediments in contrast to polluted river sediments, indicating a metabolic stress response to AMD pollution. This is one of the first studies to explore microbial community structure dynamics within a natural wetland exposed to AMD and our findings indicate that wetland ecosystems play critical roles in maintaining diversity and metabolic structure of sediment microbial communities subject to high levels of acidity and metal pollution. Moreover, these microbial communities are predicted to be important for the remediation action of the wetland.}, }
@article {pmid30013236, year = {2018}, author = {Emerson, JB and Roux, S and Brum, JR and Bolduc, B and Woodcroft, BJ and Jang, HB and Singleton, CM and Solden, LM and Naas, AE and Boyd, JA and Hodgkins, SB and Wilson, RM and Trubl, G and Li, C and Frolking, S and Pope, PB and Wrighton, KC and Crill, PM and Chanton, JP and Saleska, SR and Tyson, GW and Rich, VI and Sullivan, MB}, title = {Host-linked soil viral ecology along a permafrost thaw gradient.}, journal = {Nature microbiology}, volume = {3}, number = {8}, pages = {870-880}, pmid = {30013236}, issn = {2058-5276}, mesh = {Bacteria/virology ; Carbon/*metabolism ; Carbon Cycle ; Climate Change ; Ecosystem ; Gene Expression Profiling/*methods ; Genome, Viral ; Glycoside Hydrolases/genetics ; Host Specificity ; Permafrost/*virology ; Phylogeny ; Soil Microbiology ; Sweden ; Viral Proteins/genetics ; Viruses/*classification/genetics/metabolism ; }, abstract = {Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood[1-7]. The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans[8-10], remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling.}, }
@article {pmid30009332, year = {2019}, author = {Bag, S and Ghosh, TS and Banerjee, S and Mehta, O and Verma, J and Dayal, M and Desigamani, A and Kumar, P and Saha, B and Kedia, S and Ahuja, V and Ramamurthy, T and Das, B}, title = {Molecular Insights into Antimicrobial Resistance Traits of Commensal Human Gut Microbiota.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {546-557}, pmid = {30009332}, issn = {1432-184X}, support = {BT/MB/THSTI/HMC-SFC/2011//Department of Biotechnology , Ministry of Science and Technology/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics/isolation &amp; purification ; DNA Transposable Elements/genetics ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects/*genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*genetics ; Genome, Bacterial ; Genotype ; Humans ; Interspersed Repetitive Sequences/genetics ; Metagenome/genetics ; Microbial Sensitivity Tests ; *Phenotype ; *Symbiosis ; Transformation, Genetic/genetics ; Vibrio cholerae/genetics ; Whole Genome Sequencing ; }, abstract = {Antimicrobial resistance (AMR) among bacterial species that resides in complex ecosystems is a natural phenomenon. Indiscriminate use of antimicrobials in healthcare, livestock, and agriculture provides an evolutionary advantage to the resistant variants to dominate the ecosystem. Ascendency of resistant variants threatens the efficacy of most, if not all, of the antimicrobial drugs commonly used to prevent and/or cure microbial infections. Resistant phenotype is very common in enteric bacteria. The most common mechanisms of AMR are enzymatic modifications to the antimicrobials or their target molecules. In enteric bacteria, most of the resistance traits are acquired by horizontal gene transfer from closely or distantly related bacterial population. AMR traits are generally linked with mobile genetic elements (MGEs) and could rapidly disseminate to the bacterial species through horizontal gene transfer (HGT) from a pool of resistance genes. Although prevalence of AMR genes among pathogenic bacteria is widely studied in the interest of infectious disease management, the resistance profile and the genetic traits that encode resistance to the commensal microbiota residing in the gut of healthy humans are not well-studied. In the present study, we have characterized AMR phenotypes and genotypes of five dominant commensal enteric bacteria isolated from the gut of healthy Indians. Our study revealed that like pathogenic bacteria, enteric commensals are also multidrug-resistant. The genes encoding antibiotic resistance are physically linked with MGEs and could disseminate vertically to the progeny and laterally to the distantly related microbial species. Consequently, the AMR genes present in the chromosome of commensal gut bacteria could be a potential source of resistance functions for other enteric pathogens.}, }
@article {pmid30007724, year = {2018}, author = {Lukša, J and Vepštaitė-Monstavičė, I and Yurchenko, V and Serva, S and Servienė, E}, title = {High content analysis of sea buckthorn, black chokeberry, red and white currants microbiota - A pilot study.}, journal = {Food research international (Ottawa, Ont.)}, volume = {111}, number = {}, pages = {597-606}, doi = {10.1016/j.foodres.2018.05.060}, pmid = {30007724}, issn = {1873-7145}, mesh = {Bacteria/classification/genetics ; Biodiversity ; DNA, Bacterial/isolation &amp; purification ; DNA, Fungal/isolation &amp; purification ; Food Industry ; Food Quality ; Fruit/*microbiology ; Fungi/classification/genetics ; Hippophae/*microbiology ; Humans ; Lithuania ; Microbiota/genetics ; Photinia/*microbiology ; Pilot Projects ; Ribes/*microbiology ; }, abstract = {The high potential of sea buckthorn, black chokeberry, red and white currants in healthy food industry boosted interest in the plant cultivation. The present study is the first work providing comprehensive information on microbial populations of these berries. Next Generation Sequencing allowed identification of eukaryotic and prokaryotic microorganisms prevalent on specific berries, including uncultivable microorganisms. Our study revealed the broad diversity of berries-associated bacterial and fungal microorganisms. Analysis of representative microbial OTUs showed a clear separation among inhabitants of sea buckthorn, black chokeberry and both currants, indicating plant-defined differences in the composition of the bacterial and fungal microbiota. Among the microorganisms distributed on tested berries, we documented potentially beneficial fungi and bacteria along with potential phytopathogens or those harmful for humans. Thus, plant microbiota appears to be highly relevant for the evaluation of the microbiota impact on food quality and human health.}, }
@article {pmid30007669, year = {2018}, author = {Zheng, X and Liu, F and Li, K and Shi, X and Ni, Y and Li, B and Zhuge, B}, title = {Evaluating the microbial ecology and metabolite profile in Kazak artisanal cheeses from Xinjiang, China.}, journal = {Food research international (Ottawa, Ont.)}, volume = {111}, number = {}, pages = {130-136}, doi = {10.1016/j.foodres.2018.05.019}, pmid = {30007669}, issn = {1873-7145}, mesh = {Cheese/*microbiology ; China ; Food Microbiology/*methods ; *Microbiota ; }, abstract = {Kazak artisanal cheese is one of the famous fermented food in Uighur Autonomy Region of Xinjiang, China. However, the microbial ecology in Kazak artisanal cheeses across different regions is unclear. In this study, we determined the microbial community composition through amplicon sequencing and measured the flavor profile of 10 cheese samples from different regions of Xinjiang. The associations between microbial communities, flavors and environmental factors were examined by redundancy analysis and Monte Carlo permutation test. Cheeses from different regions had different microbial communities, which was mainly reflected in the relative abundance of Lactobacillus, Streptococcus, Issatchenkia, Debaryomyces and Kluyveromyces. In addition, Pichia and Torulaspora were also the key microbial groups, according to the high relative abundance and large co-occurrence incidence in the correlation network. Using the microbe-metabolites correlation analysis, the major flavor-producing taxa were identified as Kluyveromyces, Anoxybacillus, Torulaspora, Lactobacillus, Streptococcus and Dipodascus. Environmental factors accounted for the majority of the microbial community variations, 88.54% for bacteria and 75.71% for fungi. Compared to physico-chemical factors (temperature, moisture, and pH), geographical factors (longitude, latitude and elevation) had a stronger effect on microbial communities in cheese samples from different regions of Xinjiang.}, }
@article {pmid30006398, year = {2018}, author = {Kougias, PG and Campanaro, S and Treu, L and Tsapekos, P and Armani, A and Angelidaki, I}, title = {Spatial Distribution and Diverse Metabolic Functions of Lignocellulose-Degrading Uncultured Bacteria as Revealed by Genome-Centric Metagenomics.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {18}, pages = {}, pmid = {30006398}, issn = {1098-5336}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodiversity ; Bioreactors/microbiology ; *Genome, Bacterial ; Lignin/*metabolism ; Manure/microbiology ; Metagenomics ; Phylogeny ; Swine ; }, abstract = {The mechanisms by which specific anaerobic microorganisms remain firmly attached to lignocellulosic material, allowing them to efficiently decompose organic matter, have yet to be elucidated. To circumvent this issue, microbiomes collected from anaerobic digesters treating pig manure and meadow grass were fractionated to separate the planktonic microbes from those adhered to lignocellulosic substrate. Assembly of shotgun reads, followed by a binning process, recovered 151 population genomes, 80 out of which were completely new and were not previously deposited in any database. Genome coverage allowed the identification of microbial spatial distribution in the engineered ecosystem. Moreover, a composite bioinformatic analysis using multiple databases for functional annotation revealed that uncultured members of the Bacteroidetes and Firmicutes follow diverse metabolic strategies for polysaccharide degradation. The structure of cellulosome in Firmicutes species can differ depending on the number and functional roles of carbohydrate-binding modules. In contrast, members of the Bacteroidetes are able to adhere to and degrade lignocellulose due to the presence of multiple carbohydrate-binding family 6 modules in beta-xylosidase and endoglucanase proteins or S-layer homology modules in unknown proteins. This study combines the concept of variability in spatial distribution with genome-centric metagenomics, allowing a functional and taxonomical exploration of the biogas microbiome.IMPORTANCE This work contributes new knowledge about lignocellulose degradation in engineered ecosystems. Specifically, the combination of the spatial distribution of uncultured microbes with genome-centric metagenomics provides novel insights into the metabolic properties of planktonic and firmly attached to plant biomass bacteria. Moreover, the knowledge obtained in this study enabled us to understand the diverse metabolic strategies for polysaccharide degradation in different species of Bacteroidetes and Clostridiales Even though structural elements of cellulosome were restricted to Clostridiales species, our study identified a putative mechanism in Bacteroidetes species for biomass decomposition, which is based on a gene cluster responsible for cellulose degradation, disaccharide cleavage to glucose, and transport to cytoplasm.}, }
@article {pmid30006234, year = {2018}, author = {Aliyu, H and Lebre, P and Blom, J and Cowan, D and De Maayer, P}, title = {Corrigendum to "Phylogenomic re-assessment of the thermophilic genus Geobacillus" [Syst. Appl. Microbiol. 39 (2016) 527-533].}, journal = {Systematic and applied microbiology}, volume = {41}, number = {5}, pages = {529-530}, doi = {10.1016/j.syapm.2018.07.001}, pmid = {30006234}, issn = {1618-0984}, }
@article {pmid30005805, year = {2018}, author = {Driscoll, CB and Meyer, KA and Šulčius, S and Brown, NM and Dick, GJ and Cao, H and Gasiūnas, G and Timinskas, A and Yin, Y and Landry, ZC and Otten, TG and Davis, TW and Watson, SB and Dreher, TW}, title = {A closely-related clade of globally distributed bloom-forming cyanobacteria within the Nostocales.}, journal = {Harmful algae}, volume = {77}, number = {}, pages = {93-107}, doi = {10.1016/j.hal.2018.05.009}, pmid = {30005805}, issn = {1878-1470}, mesh = {Bacterial Proteins/analysis ; Cyanobacteria/*classification/genetics ; *Genome, Bacterial ; Harmful Algal Bloom ; Phylogeny ; }, abstract = {In order to better understand the relationships among current Nostocales cyanobacterial blooms, eight genomes were sequenced from cultured isolates or from environmental metagenomes of recent planktonic Nostocales blooms. Phylogenomic analysis of publicly available sequences placed the new genomes among a group of 15 genomes from four continents in a distinct ADA clade (Anabaena/Dolichospermum/Aphanizomenon) within the Nostocales. This clade contains four species-level groups, two of which include members with both Anabaena-like and Aphanizomenon flos-aquae-like morphology. The genomes contain many repetitive genetic elements and a sizable pangenome, in which ABC-type transporters are highly represented. Alongside common core genes for photosynthesis, the differentiation of N2-fixing heterocysts, and the uptake and incorporation of the major nutrients P, N and S, we identified several gene pathways in the pangenome that may contribute to niche partitioning. Genes for problematic secondary metabolites-cyanotoxins and taste-and-odor compounds-were sporadically present, as were other polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters. By contrast, genes predicted to encode the ribosomally generated bacteriocin peptides were found in all genomes.}, }
@article {pmid30004677, year = {2018}, author = {Yu, Y and Han, P and Zhou, LJ and Li, Z and Wagner, M and Men, Y}, title = {Ammonia Monooxygenase-Mediated Cometabolic Biotransformation and Hydroxylamine-Mediated Abiotic Transformation of Micropollutants in an AOB/NOB Coculture.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {16}, pages = {9196-9205}, doi = {10.1021/acs.est.8b02801}, pmid = {30004677}, issn = {1520-5851}, mesh = {*Ammonia ; Bioreactors ; Biotransformation ; Coculture Techniques ; Hydroxylamine ; Hydroxylamines ; *Nitrites ; Oxidation-Reduction ; Oxidoreductases ; }, abstract = {Biotransformation of various micropollutants (MPs) has been found to be positively correlated with nitrification in activated sludge communities. To further elucidate the roles played by ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), we investigated the biotransformation capabilities of an NOB pure culture (Nitrobacter sp.) and an AOB (Nitrosomonas europaea)/NOB (Nitrobacter sp.) coculture for 15 MPs, whose biotransformation was reported previously to be associated with nitrification. The NOB pure culture did not biotransform any investigated MP, whereas the AOB/NOB coculture was capable of biotransforming six MPs (i.e., asulam, bezafibrate, fenhexamid, furosemide, indomethacin, and rufinamide). Transformation products (TPs) were identified, and tentative structures were proposed. Inhibition studies with octyne, an ammonia monooxygenase (AMO) inhibitor, suggested that AMO was the responsible enzyme for MP transformation that occurred cometabolically. For the first time, hydroxylamine, a key intermediate of all aerobic ammonia oxidizers, was found to react with several MPs at concentrations typically occurring in AOB batch cultures. All of these MPs were also biotransformed by the AOB/NOB coculture. Moreover, the same asulam TPs were detected in both biotransformation and hydroxylamine-treated abiotic transformation experiments, whereas rufinamide TPs formed from biological transformation were not detected during hydroxylamine-mediated abiotic transformation, which was consistent with the inability of rufinamide abiotic transformation by hydroxylamine. Thus, in addition to cometabolism likely carried out by AMO, an abiotic transformation route indirectly mediated by AMO might also contribute to MP biotransformation by AOB.}, }
@article {pmid30003276, year = {2019}, author = {Miranda, V and Rothen, C and Yela, N and Aranda-Rickert, A and Barros, J and Calcagno, J and Fracchia, S}, title = {Subterranean Desert Rodents (Genus Ctenomys) Create Soil Patches Enriched in Root Endophytic Fungal Propagules.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {451-459}, pmid = {30003276}, issn = {1432-184X}, support = {PICT 0546//Consejo Nacional de Innovaci&#xf3;n, Ciencia y Tecnolog&#xed;a/ ; }, mesh = {Animals ; Argentina ; *Desert Climate ; Ecosystem ; Endophytes/*growth &amp; development ; Environment ; Fungi/*growth &amp; development ; Mycorrhizae/growth &amp; development ; Plant Roots/*microbiology ; Rodentia/*physiology ; Soil/*chemistry ; Soil Microbiology ; Symbiosis ; }, abstract = {Subterranean rodents are considered major soil engineers, as they can locally modify soil properties by their burrowing activities. In this study, the effect of a subterranean rodent of the genus Ctenomys on soil properties and root endophytic fungal propagules in a shrub desert of northwest Argentina was examined. Our main goal was to include among root endophytic fungi not only arbuscular mycorrhiza but also the dark septate endophytes. We compared the abundance of fungal propagules as well as several microbiological and physicochemical parameters between soils from burrows and those from the surrounding landscape. Our results show that food haulage, the deposition of excretions, and soil mixing by rodents' burrowing promote soil patchiness by (1) the enrichment in both types of root endophytic fungal propagules; (2) the increase in organic matter and nutrients; and (3) changes in soil edaphic properties including moisture, field capacity, and texture. These patches may play a critical role as a source of soil heterogeneity in desert ecosystems, where burrows constructed in interpatches of bare soil can act, once abandoned, as "islands of fertility," promoting the establishment of plants in an otherwise hostile environment.}, }
@article {pmid30003158, year = {2018}, author = {Samanta, B and Bhadury, P}, title = {Study of diatom assemblages in Sundarbans mangrove water based on light microscopy and rbcL gene sequencing.}, journal = {Heliyon}, volume = {4}, number = {6}, pages = {e00663}, pmid = {30003158}, issn = {2405-8440}, abstract = {Sundarbans, the world's largest mangrove deltaic region, is one of the most productive ecosystems in tropical and subtropical latitudes and also serve as a nursery ground for rich coastal fisheries. In this study, we highlighted diatom assemblages from the Indian part of Sundarbans Biosphere Reserve (SBR) area for the first time based on light microscopy and rbcL gene sequencing and phylogeny. In total, 15 diatom species (11 centric forms and 4 pennate forms) were documented using light microscopy, and 3 major clades of diatoms were detected in rbcL phylogeny. Out of 15 diatom species, 7 were the first record from Sundarbans mangrove water. One of the species, Thalassiosira ferelineata Hasle and Fryxell, was reported for the first time in an Asian mangrove ecosystem based on light microscopy. Our study suggests the importance of establishing cultures and their polyphasic taxonomy are the future necessity to create an authenticated diatom database from mangrove water, which is still overlooked globally.}, }
@article {pmid30002454, year = {2018}, author = {Phoma, S and Vikram, S and Jansson, JK and Ansorge, IJ and Cowan, DA and Van de Peer, Y and Makhalanyane, TP}, title = {Agulhas Current properties shape microbial community diversity and potential functionality.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10542}, pmid = {30002454}, issn = {2045-2322}, mesh = {Bacteria/*genetics/isolation &amp; purification/metabolism ; *Biodiversity ; DNA, Bacterial/isolation &amp; purification ; Indian Ocean ; Microbiota/*physiology ; Nitrogen Cycle ; Oceanography ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; Sulfur/metabolism ; *Water Movements ; }, abstract = {Understanding the impact of oceanographic features on marine microbial ecosystems remains a major ecological endeavour. Here we assess microbial diversity, community structure and functional capacity along the Agulhas Current system and the Subtropical Front in the South Indian Ocean (SIO). Samples collected from the epipelagic, oxygen minimum and bathypelagic zones were analysed by 16S rRNA gene amplicon and metagenomic sequencing. In contrast to previous studies, we found high taxonomic richness in surface and deep water samples, but generally low richness for OMZ communities. Beta-diversity analysis revealed significant dissimilarity between the three water depths. Most microbial communities were dominated by marine Gammaproteobacteria, with strikingly low levels of picocyanobacteria. Community composition was strongly influenced by specific environmental factors including depth, salinity, and the availability of both oxygen and light. Carbon, nitrogen and sulfur cycling capacity in the SIO was linked to several autotrophic and copiotrophic Alphaproteobacteria and Gammaproteobacteria. Taken together, our data suggest that the environmental conditions in the Agulhas Current system, particularly depth-related parameters, substantially influence microbial community structure. In addition, the capacity for biogeochemical cycling of nitrogen and sulfur is linked primarily to the dominant Gammaproteobacteria taxa, whereas ecologically rare taxa drive carbon cycling.}, }
@article {pmid30002323, year = {2018}, author = {Barrett, HL and Gomez-Arango, LF and Wilkinson, SA and McIntyre, HD and Callaway, LK and Morrison, M and Dekker Nitert, M}, title = {A Vegetarian Diet Is a Major Determinant of Gut Microbiota Composition in Early Pregnancy.}, journal = {Nutrients}, volume = {10}, number = {7}, pages = {}, pmid = {30002323}, issn = {2072-6643}, mesh = {Adult ; *Diet, Vegetarian ; Digestion ; Female ; Fermentation ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Gestational Age ; Humans ; *Maternal Nutritional Physiological Phenomena ; Nutritional Status ; Nutritive Value ; Obesity/diagnosis/diet therapy/*microbiology/physiopathology ; Pregnancy ; Preliminary Data ; Probiotics/therapeutic use ; Queensland ; }, abstract = {The composition of the gut microbiota can be influenced by dietary composition. In pregnancy, the maternal gut microbiome has associations with maternal and infant metabolic status. There is little known regarding the impact of a vegetarian diet in pregnancy on maternal gut microbiota. This study explored the gut microbiota profile in women who were vegetarian or omnivorous in early gestation. Women were selected from participants in the Study of PRobiotics IN Gestational diabetes (SPRING) randomised controlled trial. Nine women identified as vegetarians were matched to omnivorous women in a 1:2 ratio. Microbiota analyses were performed using 16S rRNA gene amplicon sequencing and analysed using the Quantitative Insights Into Microbial Ecology (QIIME) and Calypso software tools. There was no difference in alpha diversity, but beta diversity was slightly reduced in vegetarians. There were differences seen in the relative abundance of several genera in those on a vegetarian diet, specifically a reduction in Collinsella, Holdemania, and increases in the relative abundances of Roseburia and Lachnospiraceae. In this sub-analysis of gut microbiota from women in early pregnancy, a vegetarian as compared to omnivorous diet, was associated with a different gut microbiome, with features suggesting alterations in fermentation end products from a mixed acid fermentation towards more acetate/butyrate.}, }
@article {pmid30001854, year = {2018}, author = {Berry, D and Loy, A}, title = {Stable-Isotope Probing of Human and Animal Microbiome Function.}, journal = {Trends in microbiology}, volume = {26}, number = {12}, pages = {999-1007}, pmid = {30001854}, issn = {1878-4380}, support = {I 2320/FWF_/Austrian Science Fund FWF/Austria ; P 26127/FWF_/Austrian Science Fund FWF/Austria ; P 27831/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Bacterial Physiological Phenomena ; DNA/chemistry ; Gastrointestinal Microbiome/*physiology ; Host Microbial Interactions/*physiology ; Humans ; Isotope Labeling/*methods ; *Isotopes ; Metagenome ; Metagenomics/methods ; Molecular Probes ; RNA/chemistry ; Spectrum Analysis, Raman/methods ; }, abstract = {Humans and animals host diverse communities of microorganisms important to their physiology and health. Despite extensive sequencing-based characterization of host-associated microbiomes, there remains a dramatic lack of understanding of microbial functions. Stable-isotope probing (SIP) is a powerful strategy to elucidate the ecophysiology of microorganisms in complex host-associated microbiotas. Here, we suggest that SIP methodologies should be more frequently exploited as part of a holistic functional microbiomics approach. We provide examples of how SIP has been used to study host-associated microbes in vivo and ex vivo. We highlight recent developments in SIP technologies and discuss future directions that will facilitate deeper insights into the function of human and animal microbiomes.}, }
@article {pmid29997457, year = {2018}, author = {Majeed, M and Nagabhushanam, K and Arumugam, S and Majeed, S and Ali, F}, title = {Bacillus coagulans MTCC 5856 for the management of major depression with irritable bowel syndrome: a randomised, double-blind, placebo controlled, multi-centre, pilot clinical study.}, journal = {Food &amp; nutrition research}, volume = {62}, number = {}, pages = {}, pmid = {29997457}, issn = {1654-661X}, abstract = {BACKGROUND: The modification of microbial ecology in human gut by supplementing probiotics may be an alternative strategy to ameliorate or prevent depression.<br><br>OBJECTIVE: The current study was conducted to assess the safety and efficacy of the probiotic strain Bacillus coagulans MTCC 5856 for major depressive disorder (MDD) in IBS patients.<br><br>METHOD: Patients (n = 40) diagnosed for MDD with IBS were randomized (1:1) to receive placebo or B. coagulans MTCC 5856 at a daily dose of 2 &#xd7; 109 cfu (2 billion spores) and were maintained to the end of double-blind treatment (90 days). Changes from baseline in clinical symptoms of MDD and IBS were evaluated through questionnaires.<br><br>RESULTS: Significant change (p = 0.01) in favour of the B. coagulans MTCC 5856 was observed for the primary efficacy measure Hamilton Rating Scale for Depression (HAM-D), Montgomery-Asberg Depression Rating Scale (MADRS), Center for Epidemiological Studies Depression Scale (CES-D) and Irritable bowel syndrome quality of life questionnaire (IBS-QOL). Secondary efficacy measures i.e. Clinical Global Impression-Improvement rating Scale (CGI-I), Clinical Global Impression Severity rating Scale (CGI-S), Gastrointestinal Discomfort Questionnaire (GI-DQ) and Modified Epworth Sleepiness Scale (mESS) also showed significant results (p = 0.01) in B. coagulans MTCC 5856 group compared to placebo group except dementia total reaction scoring. Serum myeloperoxidase, an inflammatory biomarker was also significantly reduced (p < 0.01) when compared with the baseline and end of the study. All the safety parameters remained well within the normal clinical range and had no clinically significant difference between the screening and at the end of the study.<br><br>CONCLUSION: B. coagulans MTCC 5856 showed robust efficacy for the treatment of patients experiencing IBS symptoms with major depressive disorder. The improvement in depression and IBS symptoms was statistically significant and clinically meaningful. These findings support B. coagulans MTCC 5856 as an important new treatment option for major depressive disorder in IBS patients.}, }
@article {pmid29995395, year = {2018}, author = {Du, Q and Mu, Q and Cheng, T and Li, N and Wang, X}, title = {Real-Time Imaging Revealed That Exoelectrogens from Wastewater Are Selected at the Center of a Gradient Electric Field.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {15}, pages = {8939-8946}, doi = {10.1021/acs.est.8b01468}, pmid = {29995395}, issn = {1520-5851}, mesh = {*Bioelectric Energy Sources ; Biofilms ; Electricity ; Electrodes ; *Geobacter ; Wastewater ; }, abstract = {Exoelectrogens acclimated from the environment are the key to energy recovery from waste in bioelectrochemical systems. However, it is still unknown how these bacteria are selectively enriched on the electrode. Here we confirmed for the first time that the electric field (EF) intensity selects exoelectrogens from wastewater using an integrated electrovisual system with a gradient EF. Under the operating conditions (I = 3 × 10[-3]A), the EF intensity on the working electrode ranged from 6.00 V/cm at the center to 1.08 V/cm at the edge. A thick biofilm (88.9 μm) with spherical pink aggregates was observed at the center, while the color became gray at the edge (33.8 μm). The coverage of the biofilm also increased linearly with EF intensity from 0.42 at the edge (12 mm to the center) to 0.78 at the center. The biofilm at the center contained 76% Geobacter, which was 25% higher than that at the edge (60%). Geobacter anodireducens was the main species induced by the EF (50% at the center vs 24% at the edge). These results improve our fundamental knowledge of exoelectrogen acclimation and mixed electroactive biofilm formation, which has broader implications for energy recovery from waste and general understanding of microbial ecology.}, }
@article {pmid29992097, year = {2018}, author = {Gil-Pulido, B and Tarpey, E and Almeida, EL and Finnegan, W and Zhan, X and Dobson, ADW and O'Leary, N}, title = {Evaluation of dairy processing wastewater biotreatment in an IASBR system: Aeration rate impacts on performance and microbial ecology.}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {19}, number = {}, pages = {e00263}, pmid = {29992097}, issn = {2215-017X}, abstract = {Dairy processing generates large volumes of wastewater that require extensive nutrient remediation prior to discharge. Significant commercial opportunities exist therefore for cost-effective biotechnologies capable of achieving this requirement. In this study the authors evaluated the use of intermittently aerated sequencing batch reactors, (IASBRs), as a single-tank biotreatment system for co-removal of COD, nitrogen and phosphorus from synthetic dairy processing wastewater. Variation of the IASBR aeration rates, (0.8, 0.6 and 0.4 L/min), had significant impacts on the respective nutrient removal efficiencies and underlying microbial diversity profiles. Aeration at 0.6 L/min was most effective and resulted in >90% co-removal of orthophosphate and ammonium. 16S rRNA based pyrosequencing of biomass DNA samples revealed the family Comamonadaceae was notably enriched (>80% relative abundance) under these conditions. In silico predictive metabolic modelling also identified Comamonadaceae as the major contributor of several known genes for nitrogen and phosphorus assimilation (nirK, nosZ, norB, ppK, ppX and phbC).}, }
@article {pmid29991589, year = {2018}, author = {Kitzinger, K and Koch, H and Lücker, S and Sedlacek, CJ and Herbold, C and Schwarz, J and Daebeler, A and Mueller, AJ and Lukumbuzya, M and Romano, S and Leisch, N and Karst, SM and Kirkegaard, R and Albertsen, M and Nielsen, PH and Wagner, M and Daims, H}, title = {Characterization of the First "Candidatus Nitrotoga" Isolate Reveals Metabolic Versatility and Separate Evolution of Widespread Nitrite-Oxidizing Bacteria.}, journal = {mBio}, volume = {9}, number = {4}, pages = {}, pmid = {29991589}, issn = {2150-7511}, support = {P 25231/FWF_/Austrian Science Fund FWF/Austria ; P 27319/FWF_/Austrian Science Fund FWF/Austria ; P 30570/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Evolution, Molecular ; Gallionellaceae/growth &amp; development/isolation &amp; purification/*metabolism ; *Genome, Bacterial ; Kinetics ; Metabolic Networks and Pathways/genetics ; Nitrates/*metabolism ; Nitrites/*metabolism ; Oxidation-Reduction ; Sewage/*microbiology ; Temperature ; }, abstract = {Nitrification is a key process of the biogeochemical nitrogen cycle and of biological wastewater treatment. The second step, nitrite oxidation to nitrate, is catalyzed by phylogenetically diverse, chemolithoautotrophic nitrite-oxidizing bacteria (NOB). Uncultured NOB from the genus "Candidatus Nitrotoga" are widespread in natural and engineered ecosystems. Knowledge about their biology is sparse, because no genomic information and no pure "Ca Nitrotoga" culture was available. Here we obtained the first "Ca Nitrotoga" isolate from activated sludge. This organism, "Candidatus Nitrotoga fabula," prefers higher temperatures (>20°C; optimum, 24 to 28°C) than previous "Ca Nitrotoga" enrichments, which were described as cold-adapted NOB. "Ca Nitrotoga fabula" also showed an unusually high tolerance to nitrite (activity at 30 mM NO2[-]) and nitrate (up to 25 mM NO3[-]). Nitrite oxidation followed Michaelis-Menten kinetics, with an apparent Km (Km(app)) of ~89 µM nitrite and a Vmax of ~28 µmol of nitrite per mg of protein per h. Key metabolic pathways of "Ca Nitrotoga fabula" were reconstructed from the closed genome. "Ca Nitrotoga fabula" possesses a new type of periplasmic nitrite oxidoreductase belonging to a lineage of mostly uncharacterized proteins. This novel enzyme indicates (i) separate evolution of nitrite oxidation in "Ca Nitrotoga" and other NOB, (ii) the possible existence of phylogenetically diverse, unrecognized NOB, and (iii) together with new metagenomic data, the potential existence of nitrite-oxidizing archaea. For carbon fixation, "Ca Nitrotoga fabula" uses the Calvin-Benson-Bassham cycle. It also carries genes encoding complete pathways for hydrogen and sulfite oxidation, suggesting that alternative energy metabolisms enable "Ca Nitrotoga fabula" to survive nitrite depletion and colonize new niches.IMPORTANCE Nitrite-oxidizing bacteria (NOB) are major players in the biogeochemical nitrogen cycle and critical for wastewater treatment. However, most NOB remain uncultured, and their biology is poorly understood. Here, we obtained the first isolate from the environmentally widespread NOB genus "Candidatus Nitrotoga" and performed a detailed physiological and genomic characterization of this organism ("Candidatus Nitrotoga fabula"). Differences between key phenotypic properties of "Ca Nitrotoga fabula" and those of previously enriched "Ca Nitrotoga" members reveal an unexpectedly broad range of physiological adaptations in this genus. Moreover, genes encoding components of energy metabolisms outside nitrification suggest that "Ca Nitrotoga" are ecologically more flexible than previously anticipated. The identification of a novel nitrite-oxidizing enzyme in "Ca Nitrotoga fabula" expands our picture of the evolutionary history of nitrification and might lead to discoveries of novel nitrite oxidizers. Altogether, this study provides urgently needed insights into the biology of understudied but environmentally and biotechnologically important microorganisms.}, }
@article {pmid29990812, year = {2018}, author = {Ajmi, K and Vismara, E and Manai, I and Haddad, M and Hamdi, M and Bouallagui, H}, title = {Polyvinyl acetate processing wastewater treatment using combined Fenton's reagent and fungal consortium: Application of central composite design for conditions optimization.}, journal = {Journal of hazardous materials}, volume = {358}, number = {}, pages = {243-255}, doi = {10.1016/j.jhazmat.2018.06.050}, pmid = {29990812}, issn = {1873-3336}, mesh = {Aspergillus/growth &amp; development ; Biodegradation, Environmental ; Chaetomium/growth &amp; development ; Fungi/*growth &amp; development ; Hydrogen Peroxide/*chemistry ; Industrial Waste/analysis ; Iron/*chemistry ; Microbial Consortia ; Polyvinyls/*analysis ; Rhizopus/growth &amp; development ; Wastewater/*chemistry ; Water Pollutants, Chemical/*analysis ; Water Purification/*methods ; }, abstract = {The Fenton reaction as an oxidative degradation process was used for industrial chemical wastewater (ICW) pretreatment. The biodegradation of pretreated ICW was performed, in aqueous environment under aerobic condition, by a defined fungal consortium. The central composite design (CCD) was used to study the effect of nitrogen and phosphorus addition and the concentration of the pollution on the removal of polyvinyl alcohol (PVA) and organic compounds. The interaction between parameters was modeled using the response surface methodology (RSM). Results of optimization showed COD, PVA and color removal yields of 97.8%, 98.5% and 99.75%, respectively with a supplementof 1.4 gL[-1] of (NH4)2SO4, 1.2 gL[-1] of KH2PO4 and 75% of concentrated ICW. Enzymatic analysis proved that laccase and lignin peroxidase were involved in the biodegradation with 45 UIL[-1] and 450 UIL[-1], respectively. Furthermore, the analysis of metabolic products using Fourier transforms infrared spectroscopy (FTIR) and nuclear magnetic resonance ([1]HNMR) showed clearly the mineralization of organic compounds and the formation of formic acid and ethanol. Therefore, the effective treatment of ICW was achieved by developing an integrated chemical and biological process which met the requirement for a safety effluent respectful for environment without risks for public health.}, }
@article {pmid29989429, year = {2018}, author = {Ronholm, J and Goordial, J and Sapers, HM and Izawa, MRM and Applin, DM and Pontefract, A and Omelon, CR and Lamarche-Gagnon, G and Cloutis, EA and Whyte, LG}, title = {Characterization of Microbial Communities Hosted in Quartzofeldspathic and Serpentinite Lithologies in Jeffrey Mine, Canada.}, journal = {Astrobiology}, volume = {18}, number = {8}, pages = {1008-1022}, doi = {10.1089/ast.2017.1685}, pmid = {29989429}, issn = {1557-8070}, mesh = {Aluminum Silicates/*chemistry ; Canada ; Heterotrophic Processes ; Magnesium Silicates/*chemistry ; *Microbiota ; Minerals/chemistry ; *Mining ; Phylogeny ; Potassium Compounds/*chemistry ; Quartz/*chemistry ; Spectrophotometry, Infrared ; Spectrum Analysis, Raman ; X-Ray Diffraction ; }, abstract = {The microbial ecology and activity of serpentine deposits and associated hydrated minerals are largely unknown. Previous research has largely focused on microbial communities in active serpentinizing systems, whereas relatively little research has demonstrated the ability of serpentine deposits to host microbial communities after the cessation of serpentinization. Given the potential role of serpentinization reactions fueling primitive microbial metabolisms on early Earth and the identification of serpentine deposits on Mars, knowledge of these geobiological relationships and potential for serpentine to host extant microbial communities and preserve biosignatures is increasingly important for planetary exploration seeking signs of life. The selection of habitable sites most likely to yield putative biosignatures is crucial to mission success. In this study, we aimed to characterize, on the basis of both metabolic activity and taxonomic composition, the microbial communities hosted in two naturally co-occurring and mineralogically distinct substrates within the serpentine-rich Jeffrey Mine pit-igneous quartzofeldspathic intrusives and serpentinite. Detection of heterotrophic activity in both lithologies at 24°C, and in serpentinite at -5°C, demonstrated that each substrate had the ability to host a viable microbial community, at Mars-relevant temperatures. Targeted amplicon sequencing subsequently showed the presence of bacterial, fungal, and photosynthetic microbial communities in both substrates. Here, we have demonstrated the presence of a viable lithic microbial community within two rock types in the Jeffrey Mine and provided evidence that lithologies associated with serpentine deposits and proximal hydrated minerals have the ability to support diverse prokaryotic and eukaryotic microbial colonization.}, }
@article {pmid29987529, year = {2019}, author = {King, WL and Jenkins, C and Go, J and Siboni, N and Seymour, JR and Labbate, M}, title = {Characterisation of the Pacific Oyster Microbiome During a Summer Mortality Event.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {502-512}, pmid = {29987529}, issn = {1432-184X}, mesh = {Animal Diseases/*microbiology/*mortality ; Animals ; Australia ; Bacteria/classification/genetics/isolation &amp; purification ; Crassostrea/*microbiology ; DNA Viruses/pathogenicity ; DNA, Bacterial ; Disease Outbreaks ; *Microbiota/genetics ; Ostreidae/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Seasons ; Vibrio/classification/genetics/isolation &amp; purification/pathogenicity ; }, abstract = {The Pacific oyster, Crassostrea gigas, is a key commercial species that is cultivated globally. In recent years, disease outbreaks have heavily impacted C. gigas stocks worldwide, with many losses incurred during summer. A number of infectious agents have been associated with these summer mortality events, including viruses (particularly Ostreid herpesvirus 1, OsHV-1) and bacteria; however, cases where no known aetiological agent can be identified are common. In this study, we examined the microbiome of disease-affected and disease-unaffected C. gigas during a 2013-2014 summer mortality event in Port Stephens (Australia) where known oyster pathogens including OsHV-1 were not detected. The adductor muscle microbiomes of 70 C. gigas samples across 12 study sites in the Port Stephens estuary were characterised using 16S rRNA (V1-V3 region) amplicon sequencing, with the aim of comparing the influence of spatial location and disease state on the oyster microbiome. Spatial location was found to be a significant determinant of the disease-affected oyster microbiome. Furthermore, microbiome comparisons between disease states identified a significant increase in rare operational taxonomic units (OTUs) belonging to Vibrio harveyi and an unidentified member of the Vibrio genus in the disease-affected microbiome. This is indicative of a potential role of Vibrio species in oyster disease and supportive of previous culture-based examination of this mortality event.}, }
@article {pmid29986719, year = {2018}, author = {Mohr, T and Aliyu, H and Küchlin, R and Polliack, S and Zwick, M and Neumann, A and Cowan, D and de Maayer, P}, title = {CO-dependent hydrogen production by the facultative anaerobe Parageobacillus thermoglucosidasius.}, journal = {Microbial cell factories}, volume = {17}, number = {1}, pages = {108}, pmid = {29986719}, issn = {1475-2859}, support = {031B0180//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 109137//National Research Foundation of South Africa/ ; }, mesh = {Aldehyde Oxidoreductases/genetics/metabolism ; Anaerobiosis ; Bacillus/genetics/*metabolism ; Bacterial Proteins/genetics ; Base Composition ; Carbon Monoxide/*metabolism ; Hydrogen/*metabolism ; Hydrogenase/genetics/metabolism ; Iron-Sulfur Proteins/genetics/metabolism ; Multienzyme Complexes/genetics/metabolism ; }, abstract = {BACKGROUND: The overreliance on dwindling fossil fuel reserves and the negative climatic effects of using such fuels are driving the development of new clean energy sources. One such alternative source is hydrogen (H2), which can be generated from renewable sources. Parageobacillus thermoglucosidasius is a facultative anaerobic thermophilic bacterium which is frequently isolated from high temperature environments including hot springs and compost.<br><br>RESULTS: Comparative genomics performed in the present study showed that P. thermoglucosidasius encodes two evolutionary distinct H2-uptake [Ni-Fe]-hydrogenases and one H2-evolving hydrogenases. In addition, genes encoding an anaerobic CO dehydrogenase (CODH) are co-localized with genes encoding a putative H2-evolving hydrogenase. The co-localized of CODH and uptake hydrogenase form an enzyme complex that might potentially be involved in catalyzing the water-gas shift reaction (CO + H2O &#x2192; CO2 + H2) in P. thermoglucosidasius. Cultivation of P. thermoglucosidasius DSM 2542[T] with an initial gas atmosphere of 50% CO and 50% air showed it to be capable of growth at elevated CO concentrations (50%). Furthermore, GC analyses showed that it was capable of producing hydrogen at an equimolar conversion with a final yield of 1.08 H2/CO.<br><br>CONCLUSIONS: This study highlights the potential of the facultative anaerobic P. thermoglucosidasius DSM 2542[T] for developing new strategies for the biohydrogen production.}, }
@article {pmid29986237, year = {2018}, author = {Zhang, Q and Vlaeminck, SE and DeBarbadillo, C and Su, C and Al-Omari, A and Wett, B and Pümpel, T and Shaw, A and Chandran, K and Murthy, S and De Clippeleir, H}, title = {Supernatant organics from anaerobic digestion after thermal hydrolysis cause direct and/or diffusional activity loss for nitritation and anammox.}, journal = {Water research}, volume = {143}, number = {}, pages = {270-281}, doi = {10.1016/j.watres.2018.06.037}, pmid = {29986237}, issn = {1879-2448}, mesh = {Ammonium Compounds/metabolism ; Anaerobiosis ; Autotrophic Processes ; Bacteria/*metabolism ; Bioreactors/*microbiology ; Diffusion ; Hydrolysis ; Models, Theoretical ; Nitrites/*metabolism ; Nitrogen/metabolism ; Sewage/chemistry ; Waste Disposal, Fluid/instrumentation/*methods ; }, abstract = {Treatment of sewage sludge with a thermal hydrolysis process (THP) followed by anaerobic digestion (AD) enables to boost biogas production and minimize residual sludge volumes. However, the reject water can cause inhibition to aerobic and anoxic ammonium-oxidizing bacteria (AerAOB &amp; AnAOB), the two key microbial groups involved in the deammonification process. Firstly, a detailed investigation elucidated the impact of different organic fractions present in THP-AD return liquor on AerAOB and AnAOB activity. For AnAOB, soluble compounds linked to THP conditions and AD performance caused the main inhibition. Direct inhibition by dissolved organics was also observed for AerAOB, but could be overcome by treating the filtrate with extended aerobic or anaerobic incubation or with activated carbon. AerAOB additionally suffered from particulate and colloidal organics limiting the diffusion of substrates. This was resolved by improving the dewatering process through an optimized flocculant polymer dose and/or addition of coagulant polymer to better capture the large colloidal fraction, especially in case of unstable AD performance. Secondly, a new inhibition model for AerAOB included diffusion-limiting compounds based on the porter-equation, and achieved the best fit with the experimental data, highlighting that AerAOB were highly sensitive to large colloids. Overall, this paper for the first time provides separate identification of organic fractions within THP-AD filtrate causing differential types of inhibition. Moreover, it highlights the combined effect of the performance of THP, AD and dewatering on the downstream autotrophic nitrogen removal kinetics.}, }
@article {pmid29985435, year = {2018}, author = {Mori, G and Rampelli, S and Orena, BS and Rengucci, C and De Maio, G and Barbieri, G and Passardi, A and Casadei Gardini, A and Frassineti, GL and Gaiarsa, S and Albertini, AM and Ranzani, GN and Calistri, D and Pasca, MR}, title = {Shifts of Faecal Microbiota During Sporadic Colorectal Carcinogenesis.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10329}, pmid = {29985435}, issn = {2045-2322}, mesh = {Adult ; Aged ; Bacteria/genetics/isolation &amp; purification ; Case-Control Studies ; Colonic Polyps/pathology ; Colorectal Neoplasms/*pathology ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Hyperplasia ; Male ; Middle Aged ; Neoplasm Staging ; Principal Component Analysis ; RNA, Ribosomal, 16S/chemistry/isolation &amp; purification/metabolism ; }, abstract = {Gut microbiota has been implicated in the etiopathogenesis of colorectal cancer. The development of colorectal cancer is a multistep process by which healthy epithelium slowly develops into preneoplastic lesions, which in turn progress into malignant carcinomas over time. In particular, sporadic colorectal cancers can arise from adenomas (about 85% of cases) or serrated polyps through the "adenoma-carcinoma" or the "serrated polyp-carcinoma" sequences, respectively. In this study, we performed 16 S rRNA gene sequencing of bacterial DNA extracted from faecal samples to compare the microbiota of healthy subjects and patients with different preneoplastic and neoplastic lesions. We identified putative microbial biomarkers associated with stage-specific progression of colorectal cancer. In particular, bacteria belonging to the Firmicutes and Actinobacteria phyla, as well as members of the Lachnospiraceae family, proved to be specific of the faecal microbiota of patients with preneoplastic lesions, including adenomas and hyperplastic polyps. On the other hand, two families of the Proteobacteria phylum, Alcaligeneaceae and Enterobacteriaceae, with Sutterella and Escherichia/Shigella being the most representative genera, appeared to be associated with malignancy. These findings, once confirmed on larger cohorts of patients, can represent an important step towards the development of more effective diagnostic strategies.}, }
@article {pmid29984314, year = {2018}, author = {Danczak, RE and Johnston, MD and Kenah, C and Slattery, M and Wilkins, MJ}, title = {Microbial Community Cohesion Mediates Community Turnover in Unperturbed Aquifers.}, journal = {mSystems}, volume = {3}, number = {4}, pages = {}, pmid = {29984314}, issn = {2379-5077}, abstract = {Microbial ecological processes are frequently studied in the presence of perturbations rather than in undisturbed environments, despite the relatively stable conditions dominating many microbial habitats. To examine processes influencing microbial community structuring in the absence of strong external perturbations, three unperturbed aquifers in Ohio (Greene, Licking, and Athens) were sampled over 2 years and analyzed using geochemical measurements, 16S rRNA gene sequencing, and ecological modeling. Redox conditions ranging from highly reducing to more oxidizing distinguished aquifer geochemistry across the three locations. Distinct microbial communities were present in each aquifer, and overall community structure was related to geochemistry, although community composition was more similar between the Athens and Licking locations. The ecological processes acting upon microbial assemblages within aquifers were varied; geochemical changes affected the Athens location, while time or some unknown factor affected Greene County. Stochastic processes, however, dominated the Licking aquifer, suggesting a decoupling between environmental fluctuations and community development. Although physicochemical differences might be expected to drive variable selection, dispersal limitation (inability to mix) explained differences between Athens and Licking. Finally, community complexity as measured by "cohesion" indicated that less-interconnected communities experienced higher turnover and were more likely to be affected by stochastic processes. Conversely, more-interconnected communities experienced lower turnover and susceptibility to homogenizing selection. Based upon these data, we support the hypothesis that unperturbed environments house dynamic microbial communities due to external and internal forces. IMPORTANCE Many microbial ecology studies have examined community structuring processes in dynamic or perturbed situations, while stable environments have been investigated to a lesser extent. Researchers have predicted that environmental communities never truly reach a steady state but rather exist in states of constant flux due to internal, rather than external, dynamics. The research presented here utilized a combined null model approach to examine the deterministic and stochastic processes responsible for observed community differences in unperturbed, groundwater ecosystems. Additionally, internal dynamics were investigated by relating a recently published measure of community complexity (cohesion) to ecological structuring processes. The data presented here suggest that communities that are more cohesive, and therefore more complex, are more likely affected by homogenizing selection, while less-complex communities are more susceptible to dispersal. By understanding the relationship between internal dynamics and community structuring processes, insight about microbial population development in natural systems can be obtained.}, }
@article {pmid29978357, year = {2019}, author = {Kearns, PJ and Bulseco-McKim, AN and Hoyt, H and Angell, JH and Bowen, JL}, title = {Nutrient Enrichment Alters Salt Marsh Fungal Communities and Promotes Putative Fungal Denitrifiers.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {358-369}, pmid = {29978357}, issn = {1432-184X}, support = {1350491//National Science Foundation (US)/ ; 1353140//National Science Foundation (US)/ ; DBI-1359241//National Science Foundation (US)/ ; OCE0924287//National Science Foundation (US)/ ; OCE0923689//National Science Foundation (US)/ ; DEB0213767//National Science Foundation (US)/ ; DEB1354494//National Science Foundation (US)/ ; OCE1353140//National Science Foundation (US)/ ; OCE 1673630//National Science Foundation (US)/ ; OCE0423565//National Science Foundation (US)/ ; OCE1058747//National Science Foundation (US)/ ; }, mesh = {Carbon/metabolism ; Denitrification ; Ecosystem ; Fungi/classification/genetics/isolation &amp; purification/*metabolism ; Geologic Sediments/chemistry/*microbiology ; Nitrates/metabolism ; Nutrients/chemistry/metabolism ; }, abstract = {Enrichment of ecosystems with excess nutrients is occurring at an alarming rate and has fundamentally altered ecosystems worldwide. Salt marshes, which lie at the land-sea interface, are highly effective at removing anthropogenic nutrients through the action of macrophytes and through microbial processes in coastal sediments. The response of salt marsh bacteria to excess nitrogen has been documented; however, the role of fungi and their response to excess nitrogen in salt marsh sediments is not fully understood. Here, we document the response of salt marsh fungal communities to long-term excess nitrate in four distinct marsh habitats within a northern temperate marsh complex. We show that salt marsh fungal communities varied as a function of salt marsh habitat, with both fungal abundance and diversity increasing with carbon quantity. Nutrient enrichment altered fungal communities in all habitats through an increase in fungal abundance and the proliferation of putative fungal denitrifiers. Nutrient enrichment also altered marsh carbon quality in low marsh surface sediments where fungal response to nutrient enrichment was most dramatic, suggesting nutrient enrichment can alter organic matter quality in coastal sediments. Our results indicate that fungi, in addition to bacteria, likely play an important role in anaerobic decomposition of salt marsh sediment organic matter.}, }
@article {pmid29978356, year = {2019}, author = {Ferrándiz, MJ and Cercenado, MI and Domenech, M and Tirado-Vélez, JM and Escolano-Martínez, MS and Yuste, J and García, E and de la Campa, AG and Martín-Galiano, AJ}, title = {An Uncharacterized Member of the Gls24 Protein Superfamily Is a Putative Sensor of Essential Amino Acid Availability in Streptococcus pneumoniae.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {471-487}, pmid = {29978356}, issn = {1432-184X}, support = {BIO2014-55462-R//Ministerio de Econom&#xed;a y Competitividad/ ; SAF2012-39444-C02//Ministerio de Econom&#xed;a y Competitividad/ ; }, mesh = {Amino Acids, Essential/*metabolism ; Animals ; Bacterial Proteins/genetics/*metabolism ; Culture Media/metabolism ; Gene Expression Regulation, Bacterial ; Humans ; Mice ; Mice, Inbred BALB C ; Multigene Family ; Pneumococcal Infections/*microbiology ; Sequence Deletion ; Streptococcus pneumoniae/genetics/growth &amp; development/*metabolism ; }, abstract = {Proteins belonging to the Gls24 superfamily are involved in survival of pathogenic Gram-positive cocci under oligotrophic conditions and other types of stress, by a still unknown molecular mechanism. In Firmicutes, this superfamily includes three different valine-rich orthologal families (Gls24A, B, C) with different potential interactive partners. Whereas the Streptococcus pneumoniae Δgls24A deletion mutant experienced a general long growth delay, the Δgls24B mutant grew as the parental strain in the semisynthetic AGCH medium but failed to grow in the complex Todd-Hewitt medium. Bovine seroalbumin (BSA) was the component responsible for this phenotype. The effect of BSA on growth was concentration-dependent and was maintained when the protein was proteolyzed but not when heat-denatured, suggesting that BSA dependence was related to oligopeptide supplementation. Global transcriptional analyses of the knockout mutant revealed catabolic derepression and induction of chaperone and oligopeptide transport genes. This mutant also showed increased sensibility to cadmium and high temperature. The Δgls24B mutant behaved as a poor colonizer in the nasopharynx of mice and showed 20-fold competence impairment. Experimental data suggest that Gls24B plays a central role as a sensor of amino acid availability and its connection to sugar catabolism. This metabolic rewiring can be compensated in vitro, at the expenses of external oligopeptide supplementation, but reduce important bacteria skills prior to efficiently address systemic virulence traits. This is an example of how metabolic factors conserved in enterococci, streptococci, and staphylococci can be essential for survival in poor oligopeptide environments prior to infection progression.}, }
@article {pmid29974320, year = {2018}, author = {Makita, H}, title = {Iron-oxidizing bacteria in marine environments: recent progresses and future directions.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {34}, number = {8}, pages = {110}, pmid = {29974320}, issn = {1573-0972}, support = {JP 26820389//JSPS KAKENHI/ ; JP 18K04595//JSPS KAKENHI/ ; }, mesh = {Bacteria/*classification/*metabolism ; Biodiversity ; Corrosion ; Hydrogen-Ion Concentration ; Iron/*metabolism ; Marine Biology ; Oxidation-Reduction ; Oxygen/metabolism ; *Phylogeny ; Phylogeography ; Proteobacteria/classification/cytology/metabolism ; Seawater/*microbiology ; }, abstract = {Iron-oxidizing bacteria (FeOB) refers to a group of bacteria with the ability to exchange and accumulate divalent iron dissolved in water as trivalent iron inside and outside the bacterial cell. Most FeOB belong the largest bacterial phylum, Proteobacteria. Within this phylum, FeOB with varying physiology with regards to their response to oxygen (obligate aerobes, facultative and obligate anaerobes) and pH optimum for proliferation (neutrophiles, moderate and extreme acidophiles) can be found. Although FeOB have been reported from a wide variety of environments, most of them have not been isolated and their biochemical characteristics remain largely unknown. This is especially true for those living in the marine realm, where the properties of FeOB was not known until the isolation of the Zetaproteobacteria Mariprofundus ferrooxydans, first reported in 2007. Since the proposal of Zetaproteobacteria by Emerson et al., the detection and isolation of those microorganisms from the marine environment has greatly escalated. Furthermore, FeOB have also recently been reported from works on ocean drilling and metal corrosion. This review aims to summarize the current state of phylogenetic and physiological diversity in marine FeOB, the significance of their roles in their environments (on both global and local scales), as well as their growing importance and applications in the industry.}, }
@article {pmid29974184, year = {2019}, author = {Pierangelini, M and Glaser, K and Mikhailyuk, T and Karsten, U and Holzinger, A}, title = {Light and Dehydration but Not Temperature Drive Photosynthetic Adaptations of Basal Streptophytes (Hormidiella, Streptosarcina and Streptofilum) Living in Terrestrial Habitats.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {380-393}, pmid = {29974184}, issn = {1432-184X}, support = {GL 909/1-1//Deutsche Forschungsgemeinschaft (DE) Priority Program 1991 "Taxon-omics"/ ; I 1951-B16//Austrian Science Fund/ ; KA899/16//Deutsche Forschungsgemeinschaft/ ; I 1951/FWF_/Austrian Science Fund FWF/Austria ; Ref. No. 06-1000014-6216//Alexander von Humboldt-Stiftung/ ; }, mesh = {Adaptation, Physiological/radiation effects ; Ecosystem ; *Photosynthesis ; Streptophyta/*physiology/*radiation effects ; Temperature ; Ultraviolet Rays ; Water/*metabolism ; }, abstract = {Streptophyte algae are the ancestors of land plants, and several classes contain taxa that are adapted to an aero-terrestrial lifestyle. In this study, four basal terrestrial streptophytes from the class Klebsormidiophyceae, including Hormidiella parvula; two species of the newly described genus Streptosarcina (S. costaricana and S. arenaria); and the newly described Streptofilum capillatum were investigated for their responses to radiation, desiccation and temperature stress conditions. All the strains showed low-light adaptation (Ik < 70 μmol photons m[-2] s[-1]) but differed in photoprotective capacities (such as non-photochemical quenching). Acclimation to enhanced photon fluence rates (160 μmol photons m[-2] s[-1]) increased photosynthetic performance in H. parvula and S. costaricana but not in S. arenaria, showing that low-light adaptation is a constitutive trait for S. arenaria. This lower-light adaptation of S. arenaria was coupled with a higher desiccation tolerance, providing further evidence that dehydration is a selective force shaping species occurrence in low light. For protection against ultraviolet radiation, all species synthesised and accumulated different amounts of mycosporine-like amino acids (MAAs). Biochemically, MAAs synthesised by Hormidiella and Streptosarcina were similar to MAAs from closely related Klebsormidium spp. but differed in retention time and spectral characteristics in S. capillatum. Unlike the different radiation and dehydration tolerances, Hormidiella, Streptosarcina and Streptofilum displayed preferences for similar thermal conditions. These species showed a temperature dependence of photosynthesis similar to respiration, contrasting with Klebsormidium spp. and highlighting an interspecific diversity in thermal requirements, which could regulate species distributions under temperature changes.}, }
@article {pmid29973712, year = {2018}, author = {Das, B and Ghosh, TS and Kedia, S and Rampal, R and Saxena, S and Bag, S and Mitra, R and Dayal, M and Mehta, O and Surendranath, A and Travis, SPL and Tripathi, P and Nair, GB and Ahuja, V}, title = {Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10104}, pmid = {29973712}, issn = {2045-2322}, support = {BT/MB/THSTI/HMC-SFC/2011//Department of Biotechnology, Ministry of Science and Technology (DBT)/International ; INT/UK/P-116/14//Department of Science and Technology, Ministry of Science and Technology (DST)/International ; }, mesh = {Actinobacteria/isolation &amp; purification ; Adolescent ; Adult ; *Altitude ; Bacteroidetes/isolation &amp; purification ; Diet ; Female ; Firmicutes/isolation &amp; purification ; *Gastrointestinal Microbiome ; Humans ; India ; Male ; Middle Aged ; Proteobacteria/isolation &amp; purification ; Rural Population ; Urban Population ; }, abstract = {The diversity and basic functional attributes of the gut microbiome of healthy Indians is not well understood. This study investigated the gut microbiome of three Indian communities: individuals residing in rural and urban (n = 49) sea level Ballabhgarh areas and in rural high altitude areas of Leh, Ladakh in North India (n = 35). Our study revealed that the gut microbiome of Indian communities is dominated by Firmicutes followed by Bacteroidetes, Actinobateria and Proteobacteria. Although, 54 core bacterial genera were detected across the three distinct communities, the gut bacterial composition displayed specific signatures and was observed to be influenced by the topographical location and dietary intake of the individuals. The gut microbiome of individuals living in Leh was observed to be significantly similar with a high representation of Bacteroidetes and low abundance of Proteobacteria. In contrast, the gut microbiome of individuals living in Ballabhgarh areas harbored higher number of Firmicutes and Proteobacteria and is enriched with microbial xenobiotic degradation pathways. The rural community residing in sea level Ballabhgarh areas has unique microbiome characterized not only by a higher diversity, but also a higher degree of interindividual homogeneity.}, }
@article {pmid29967922, year = {2019}, author = {Nesvorna, M and Bittner, V and Hubert, J}, title = {The Mite Tyrophagus putrescentiae Hosts Population-Specific Microbiomes That Respond Weakly to Starvation.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {488-501}, pmid = {29967922}, issn = {1432-184X}, support = {GA15-09038S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; }, mesh = {Acaridae/*microbiology/*physiology ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Feeding Behavior ; Host Specificity ; *Microbiota ; }, abstract = {The effect of short-term nutrient deprivation was studied in five populations of the mite Tyrophagus putrescentiae with different microbiomes. The fresh weight, nutrient status, respiration, and population growth of the mites were observed for the five mite population-scale samples. The starvation caused the larvae and nymphs to be eliminated, resulting in a significant increase in the fresh weight of starved adult specimens. Three populations were negatively influenced by starvation, and the starved specimens were characterized by a decrease in nutrient status, respiration, and population growth. One population was not influenced or was slightly influenced by starvation, which had no effect on population growth or nutrient contents but caused a significant decrease in respiration. One population was positively influenced by starvation; the population growth increased in starved specimens, and starvation had no effect on respiration. Although starvation altered the bacterial profiles of the microbiomes, these differences were much smaller than those between the populations. The bacterial profiles of Staphylococcus, Bacillus, Kocuria, Brevibacterium, and unidentified Micrococcaceae and Enterobacteriaceae increased in starved specimens, whereas those of Bartonella and Solitalea-like genera were reduced in the starved mite populations. The profiles of the intracellular symbiont Cardinium decreased in the starved specimens, and the Wolbachia profile changes were dependent on the mite population. In mite populations, when the symbionts were rare, their profiles varied stochastically. Correlations between changes in the profiles of the bacterial taxa and mite fitness parameters, including nutrient status (lipids, proteins, saccharides, and glycogen contents), mite population growth, and respiration, were observed. Although the microbiomes were resistant to the perturbations caused by nutrition deficiency, the responses of the mites differed in terms of their population growth, respiration, and nutrient status.}, }
@article {pmid29966083, year = {2018}, author = {Palermo, A and Forsberg, EM and Warth, B and Aisporna, AE and Billings, E and Kuang, E and Benton, HP and Berry, D and Siuzdak, G}, title = {Fluorinated Gold Nanoparticles for Nanostructure Imaging Mass Spectrometry.}, journal = {ACS nano}, volume = {12}, number = {7}, pages = {6938-6948}, pmid = {29966083}, issn = {1936-086X}, support = {R35 GM130385/GM/NIGMS NIH HHS/United States ; P01 DA026146/DA/NIDA NIH HHS/United States ; R01 GM114368/GM/NIGMS NIH HHS/United States ; P30 MH062261/MH/NIMH NIH HHS/United States ; }, mesh = {Amino Acids/analysis/metabolism ; Animals ; Bacteroides fragilis/cytology/isolation &amp; purification ; Bile Acids and Salts/analysis/metabolism ; Carbohydrates/analysis ; Colon/chemistry/metabolism ; Gold/*chemistry/metabolism ; *Halogenation ; Lipids/analysis ; *Mass Spectrometry ; Mice ; Mice, Inbred C57BL ; Nanostructures/*chemistry ; Nucleotides/analysis/metabolism ; Optical Imaging ; Sulfur/analysis/metabolism ; }, abstract = {Nanostructure imaging mass spectrometry (NIMS) with fluorinated gold nanoparticles (f-AuNPs) is a nanoparticle assisted laser desorption/ionization approach that requires low laser energy and has demonstrated high sensitivity. Here we describe NIMS with f-AuNPs for the comprehensive analysis of metabolites in biological tissues. F-AuNPs assist in desorption/ionization by laser-induced release of the fluorocarbon chains with minimal background noise. Since the energy barrier required to release the fluorocarbons from the AuNPs is minimal, the energy of the laser is maintained in the low μJ/pulse range, thus limiting metabolite in-source fragmentation. Electron microscopy analysis of tissue samples after f-AuNP NIMS shows a distinct "raising" of the surface as compared to matrix assisted laser desorption ionization ablation, indicative of a gentle desorption mechanism aiding in the generation of intact molecular ions. Moreover, the use of perfluorohexane to distribute the f-AuNPs on the tissue creates a hydrophobic environment minimizing metabolite solubilization and spatial dislocation. The transfer of the energy from the incident laser to the analytes through the release of the fluorocarbon chains similarly enhances the desorption/ionization of metabolites of different chemical nature, resulting in heterogeneous metabolome coverage. We performed the approach in a comparative study of the colon of mice exposed to three different diets. F-AuNP NIMS allows the direct detection of carbohydrates, lipids, bile acids, sulfur metabolites, amino acids, nucleotide precursors as well as other small molecules of varied biological origins. Ultimately, the diversified molecular coverage obtained provides a broad picture of a tissue's metabolic organization.}, }
@article {pmid29965364, year = {2017}, author = {Zhou, HY and Han, ML and Qiu, TL and Gao, M and Sun, XB and Wang, XM}, title = {[Ammonia Removal Rate and Microbial Community Structures in Different Biofilters for Treating Aquaculture Wastewater].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {38}, number = {6}, pages = {2444-2452}, doi = {10.13227/j.hjkx.201610142}, pmid = {29965364}, issn = {0250-3301}, mesh = {Ammonia/*isolation &amp; purification ; *Aquaculture ; Bacteria/*classification ; Biofilms ; Bioreactors/*microbiology ; Filtration ; Wastewater/*chemistry ; }, abstract = {Three MBBRs and three curtain type trickling filters (CTFs) with different carriers were operated in lab-scale simulated RASs. The characteristics of biofilms, ammonia removal rates and microbial communities in six reactors were compared with each other. Compared with the biofilms of MBBRs, the biofilms of CTFs were heavier and grew faster. The weight of biofilms on CTFs with carbon fiber carriers was the maximum (45.97 g·m[-2]), and the ammonia nitrogen removal efficiency (86.76%) of this CTFs was higher than the other filters or reactors (61.96%~78.76%). In addition, the concentration of the accumulated nitrite in the carbon fiber CTFs was the lowest in all the six reactors. The microbial communities of biofilms in the six biofilters were evaluated by the high-throughput Illumina-MiSeq sequencing technology. The results showed that the microbial (bacteria and eukaryote) community in biofilms of CTFs was different from that in biofilms of MBBRs. At both bacteria and micro-eukaryote level, the species richness and biological diversity of biofilms in the trickling filters were higher than those in the MBBRs. On the contrary, the Simpson index of bacterial community in biofilms of MBBRs was higher than that in the trickling filters. In all the six biofilters, Nitrospira and Nakamurella were the dominated bacterial genera. Saprospiraceae was more abundant in CTFs than in MBBRs, but Comamonadaceae was enriched in the MBBRs. At the micro-eukaryote genus level, Rhabditida norank genus was more abundant in CTFs, while Chlorophyceae norank genus was more abundant in the MBBRs. The results provide useful information about microbial ecology that can be used for the application of CTFs in RAS.}, }
@article {pmid29963907, year = {2018}, author = {Kiewra, D and Szymanowski, M and Zalewska, G and Dobracka, B and Dobracki, W and Klakočar, J and Czułowska, A and Plewa-Tutaj, K}, title = {Seroprevalence of Borrelia burgdorferi in forest workers from inspectorates with different forest types in Lower Silesia, SW Poland: preliminary study.}, journal = {International journal of environmental health research}, volume = {28}, number = {5}, pages = {502-510}, doi = {10.1080/09603123.2018.1489954}, pmid = {29963907}, issn = {1369-1619}, mesh = {Adult ; Aged ; Antibodies, Bacterial/blood ; Borrelia burgdorferi/immunology/isolation &amp; purification ; Ecosystem ; Enzyme-Linked Immunosorbent Assay ; Female ; *Forestry ; Forests ; Humans ; Lyme Disease/diagnosis/*epidemiology ; Male ; Middle Aged ; Occupational Diseases/epidemiology/microbiology ; Occupational Exposure/*analysis ; Poland ; Seroepidemiologic Studies ; Workforce ; }, abstract = {To estimate the Lyme borreliosis (LB) risk for forest workers, totally 646 blood samples were tested for IgG and IgM anti-Borrelia burgdorferi s.l. (anti-B.b.) antibody occurrence using ELISA tests confirmed with western blot. To clarify the varied LB risk, additionally, the data from the Forest Data Bank determining the detailed forest habitat type in particular forest inspectorates were used. The occurrence of the anti-B.b. antibody was confirmed in 22% (8.7% IgM, 17.8% IgG) of forest workers. Analysis of the influence of the habitat type (forest types) indicated the significant positive impact of the occurrence of the deciduous and mixed-deciduous forests on the seroprevalence of anti-B.b. IgG level among forestry workers. However, the share of forest type cannot be the only factor taken into account when assessing risk.}, }
@article {pmid29963641, year = {2018}, author = {Tsukayama, P and Boolchandani, M and Patel, S and Pehrsson, EC and Gibson, MK and Chiou, KL and Jolly, CJ and Rogers, J and Phillips-Conroy, JE and Dantas, G}, title = {Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes.}, journal = {mSystems}, volume = {3}, number = {3}, pages = {}, pmid = {29963641}, issn = {2379-5077}, support = {DP2 DK098089/DK/NIDDK NIH HHS/United States ; R01 GM099538/GM/NIGMS NIH HHS/United States ; }, abstract = {Environmental microbes have harbored the capacity for antibiotic production for millions of years, spanning the evolution of humans and other vertebrates. However, the industrial-scale use of antibiotics in clinical and agricultural practice over the past century has led to a substantial increase in exposure of these agents to human and environmental microbiota. This perturbation is predicted to alter the ecology of microbial communities and to promote the evolution and transfer of antibiotic resistance (AR) genes. We studied wild and captive baboon populations to understand the effects of exposure to humans and human activities (e.g., antibiotic therapy) on the composition of the primate fecal microbiota and the antibiotic-resistant genes that it collectively harbors (the "resistome"). Using a culture-independent metagenomic approach, we identified functional antibiotic resistance genes in the gut microbiota of wild and captive baboon groups and saw marked variation in microbiota architecture and resistomes across habitats and lifeways. Our results support the view that antibiotic resistance is an ancient feature of gut microbial communities and that sharing habitats with humans may have important effects on the structure and function of the primate microbiota. IMPORTANCE Antibiotic exposure results in acute and persistent shifts in the composition and function of microbial communities associated with vertebrate hosts. However, little is known about the state of these communities in the era before the widespread introduction of antibiotics into clinical and agricultural practice. We characterized the fecal microbiota and antibiotic resistomes of wild and captive baboon populations to understand the effect of human exposure and to understand how the primate microbiota may have been altered during the antibiotic era. We used culture-independent and bioinformatics methods to identify functional resistance genes in the guts of wild and captive baboons and show that exposure to humans is associated with changes in microbiota composition and resistome expansion compared to wild baboon groups. Our results suggest that captivity and lifestyle changes associated with human contact can lead to marked changes in the ecology of primate gut communities.}, }
@article {pmid29963639, year = {2018}, author = {Nieves-Ramírez, ME and Partida-Rodríguez, O and Laforest-Lapointe, I and Reynolds, LA and Brown, EM and Valdez-Salazar, A and Morán-Silva, P and Rojas-Velázquez, L and Morien, E and Parfrey, LW and Jin, M and Walter, J and Torres, J and Arrieta, MC and Ximénez-García, C and Finlay, BB}, title = {Asymptomatic Intestinal Colonization with Protist Blastocystis Is Strongly Associated with Distinct Microbiome Ecological Patterns.}, journal = {mSystems}, volume = {3}, number = {3}, pages = {}, pmid = {29963639}, issn = {2379-5077}, abstract = {Blastocystis is the most prevalent protist of the human intestine, colonizing approximately 20% of the North American population and up to 100% in some nonindustrialized settings. Blastocystis is associated with gastrointestinal and systemic disease but can also be an asymptomatic colonizer in large populations. While recent findings in humans have shown bacterial microbiota changes associated with this protist, it is unknown whether these occur due to the presence of Blastocystis or as a result of inflammation. To explore this, we evaluated the fecal bacterial and eukaryotic microbiota in 156 asymptomatic adult subjects from a rural population in Xoxocotla, Mexico. Colonization with Blastocystis was strongly associated with an increase in bacterial alpha diversity and broad changes in beta diversity and with more discrete changes to the microbial eukaryome. More than 230 operational taxonomic units (OTUs), including those of dominant species Prevotella copri and Ruminococcus bromii, were differentially abundant in Blastocystis-colonized individuals. Large functional changes accompanied these observations, with differential abundances of 202 (out of 266) predicted metabolic pathways (PICRUSt), as well as lower fecal concentrations of acetate, butyrate, and propionate in colonized individuals. Fecal calprotectin was markedly decreased in association with Blastocystis colonization, suggesting that this ecological shift induces subclinical immune consequences to the asymptomatic host. This work is the first to show a direct association between the presence of Blastocystis and shifts in the gut bacterial and eukaryotic microbiome in the absence of gastrointestinal disease or inflammation. These results prompt further investigation of the role Blastocystis and other eukaryotes play within the human microbiome. IMPORTANCE Given the results of our study and other reports of the effects of the most common human gut protist on the diversity and composition of the bacterial microbiome, Blastocystis and, possibly, other gut protists should be studied as ecosystem engineers that drive community diversity and composition.}, }
@article {pmid29960932, year = {2018}, author = {Proia, L and Anzil, A and Borrego, C and Farrè, M and Llorca, M and Sanchis, J and Bogaerts, P and Balcázar, JL and Servais, P}, title = {Occurrence and persistence of carbapenemases genes in hospital and wastewater treatment plants and propagation in the receiving river.}, journal = {Journal of hazardous materials}, volume = {358}, number = {}, pages = {33-43}, doi = {10.1016/j.jhazmat.2018.06.058}, pmid = {29960932}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*genetics ; Belgium ; Drug Resistance, Bacterial ; *Genes, Bacterial ; *Hospitals ; Rivers/chemistry/*microbiology ; Wastewater/chemistry/*microbiology ; *Water Purification ; beta-Lactamases/*genetics ; }, abstract = {This study aims to investigate the prevalence of clinically relevant carbapenemases genes (blaKPC, blaNDM and blaOXA-48) in water samples collected over one-year period from hospital (H), raw and treated wastewater of two wastewater treatment plants (WWTPs) as well as along the Zenne River (Belgium). The genes were quantified in both particle-attached (PAB) and free-living (FLB) bacteria. Our results showed that absolute abundances were the highest in H waters. Although absolute abundances were significantly reduced in WWTP effluents, the relative abundance (normalized per 16S rRNA) was never lowered through wastewater treatment. Particularly, for the PAB the relative abundances were significantly higher in the effluents respect to the influents of both WWTPs for all the genes. The absolute abundances along the Zenne River increased from upstream to downstream, peaking after the release of WWTPs effluents, in both fractions. Our results demonstrated that blaKPC, blaNDM and blaOXA-48 are widely distributed in the Zenne as a consequence of chronic discharge from WWTPs. To conclude, the levels of carbapenemases genes are significantly lower than other genes conferring resistance to more widely used antibiotics (analyzed in previous studies carried out at the same sites), but could raise up to the levels of high prevalent resistance genes.}, }
@article {pmid29959406, year = {2018}, author = {Kearns, PJ and Shade, A}, title = {Trait-based patterns of microbial dynamics in dormancy potential and heterotrophic strategy: case studies of resource-based and post-press succession.}, journal = {The ISME journal}, volume = {12}, number = {11}, pages = {2575-2581}, pmid = {29959406}, issn = {1751-7370}, mesh = {*Heterotrophic Processes/genetics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Understanding the relationship between microbial community structure and function is a major challenge in microbial ecology. Recent work has shown that community weighted mean 16S rRNA gene copies, as a proxy for heterotrophic growth strategy, is a microbial community trait that decreases predictably over successional trajectories that are underpinned by changes in resource availability. However, it has been challenging to identify other microbial traits that are predictive of community functions and have consistent patterns with succession. Trait-based patterns of secondary succession (e.g., after a disturbance) are less often considered, and these responses may be underpinned by abiotic drivers other than changes in resources. In this perspectives piece, we present hypotheses about microbial traits important for microbial succession in resource-based and post-press disturbance scenarios, as synthesized from previous works and extended within this work. Using four case studies, we compare two traits, heterotrophic strategy and dormancy potential, and two different types of succession, resource-based (endogenous heterotrophic) and post-press. There were decreases in weighted ribosomal operon counts and in dormancy genes over resource-based succession. Both traits also were lower in post-press succession as compared to reference conditions, but increased with time from disturbance. Thus, dormancy potential may be an additional trait that changes predictably with succession. Finally, considering changes in microbial community traits over post-press succession is as important as over resource-based succession. These patterns need to be interpreted carefully and reference and recovering samples can be collected to improve interpretation of changes in community traits over post-press succession.}, }
@article {pmid29958172, year = {2018}, author = {Li, H and Zhou, L and Lin, H and Xu, X and Jia, R and Xia, S}, title = {Dynamic response of biofilm microbial ecology to para-chloronitrobenzene biodegradation in a hydrogen-based, denitrifying and sulfate-reducing membrane biofilm reactor.}, journal = {The Science of the total environment}, volume = {643}, number = {}, pages = {842-849}, doi = {10.1016/j.scitotenv.2018.06.245}, pmid = {29958172}, issn = {1879-1026}, mesh = {*Biofilms ; Bioreactors/*microbiology ; Hydrogen ; Nitrobenzenes/*metabolism ; Sulfates ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The dynamic response of biofilm microbial ecology to para-chloronitrobenzene (p-CNB) biodegradation was systematically evaluated according to the composition and loading of electron acceptors and H2 availability (controlled by H2 pressure) in a hydrogen-based, denitrifying and sulfate-reducing membrane biofilm reactor (MBfR). To accomplish this, a laboratory-scale MBfR was set up and operated with different influent p-CNB concentrations (0, 2, and 5 mg p-CNB/L) and H2 pressures (0.04 and 0.05 MPa). Polymerase chain reaction-denaturing gel electrophoresis (PCR-DGGE) and cloning were then applied to investigate the bacterial diversity response of biofilm during p-CNB biodegradation. The results showed that denitrification and sulfate reduction largely controlled the total demand for H2. Additionally, the DGGE fingerprint demonstrated that the addition of p-CNB, which acted as an electron acceptor, was a critical factor in the dynamics of the MBfR biofilm microbial ecology. The presence of p-CNB also had a more advantageous effect on the biofilm microbial community. Additionally, clone library analysis showed that Proteobacteria (especially beta- and gamma-) comprised the majority of the microbial biofilm response to p-CNB biodegradation, and that Pseudomonas sp. (Gammaproteobacteria) played a significant role in the biotransformation of p-CNB to aniline.}, }
@article {pmid29957118, year = {2018}, author = {Moravej, H and Moravej, Z and Yazdanparast, M and Heiat, M and Mirhosseini, A and Moosazadeh Moghaddam, M and Mirnejad, R}, title = {Antimicrobial Peptides: Features, Action, and Their Resistance Mechanisms in Bacteria.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {24}, number = {6}, pages = {747-767}, doi = {10.1089/mdr.2017.0392}, pmid = {29957118}, issn = {1931-8448}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Antimicrobial Cationic Peptides/*pharmacology/*therapeutic use ; Bacteria/*drug effects ; Biofilms/drug effects ; Drug Resistance, Bacterial/*drug effects ; Humans ; Immunity, Innate/drug effects ; }, abstract = {In recent years, because of increased resistance to conventional antimicrobials, many researchers have started to study the synthesis of new antibiotics to control the disease-causing effects of infectious pathogens. Antimicrobial peptides (AMPs) are among the newest antibiotics; these peptides are integral compounds in all kinds of organisms and play a significant role in microbial ecology, and critically contribute to the innate immunity of organisms by destroying invading microorganisms. Moreover, AMPs may encourage cells to produce chemokines, stimulate angiogenesis, accelerate wound healing, and influence programmed cell death in multicellular organisms. Bacteria differ in their inherent susceptibility and resistance mechanisms to these peptides when responding to the antimicrobial effects of AMPs. Generally, the development of AMP resistance mechanisms is driven by direct competition between bacterial species, and host and pathogen interactions. Several studies have shown diverse mechanisms of bacterial resistance to AMPs, for example, some bacteria produce proteases and trapping proteins; some modify cell surface charge, change membrane fluidity, and activate efflux pumps; and some species make use of biofilms and exopolymers, and develop sensing systems by selective gene expression. A closer understanding of bacterial resistance mechanisms may help in developing novel therapeutic approaches for the treatment of infections caused by pathogenic organisms that are successful in developing extensive resistance to AMPs. Based on these observations, this review discusses the properties of AMPs, their targeting mechanisms, and bacterial resistance mechanisms against AMPs.}, }
@article {pmid29954432, year = {2018}, author = {Faust, K and Bauchinger, F and Laroche, B and de Buyl, S and Lahti, L and Washburne, AD and Gonze, D and Widder, S}, title = {Signatures of ecological processes in microbial community time series.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {120}, pmid = {29954432}, issn = {2049-2618}, support = {V 585/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacterial Load/*methods ; Biodiversity ; *Computer Simulation ; Ecology ; *Ecosystem ; Ecotype ; Gastrointestinal Microbiome/*physiology ; Humans ; *Models, Biological ; *Time and Motion Studies ; }, abstract = {BACKGROUND: Growth rates, interactions between community members, stochasticity, and immigration are important drivers of microbial community dynamics. In sequencing data analysis, such as network construction and community model parameterization, we make implicit assumptions about the nature of these drivers and thereby restrict model outcome. Despite apparent risk of methodological bias, the validity of the assumptions is rarely tested, as comprehensive procedures are lacking. Here, we propose a classification scheme to determine the processes that gave rise to the observed time series and to enable better model selection.<br><br>RESULTS: We implemented a three-step classification scheme in R that first determines whether dependence between successive time steps (temporal structure) is present in the time series and then assesses with a recently developed neutrality test whether interactions between species are required for the dynamics. If the first and second tests confirm the presence of temporal structure and interactions, then parameters for interaction models are estimated. To quantify the importance of temporal structure, we compute the noise-type profile of the community, which ranges from black in case of strong dependency to white in the absence of any dependency. We applied this scheme to simulated time series generated with the Dirichlet-multinomial (DM) distribution, Hubbell's neutral model, the generalized Lotka-Volterra model and its discrete variant (the Ricker model), and a self-organized instability model, as well as to human stool microbiota time series. The noise-type profiles for all but DM data clearly indicated distinctive structures. The neutrality test correctly classified all but DM and neutral time series as non-neutral. The procedure reliably identified time series for which interaction inference was suitable. Both tests were required, as we demonstrated that all structured time series, including those generated with the neutral model, achieved a moderate to high goodness of fit to the Ricker model.<br><br>CONCLUSIONS: We present a fast and robust scheme to classify community structure and to assess the prevalence of interactions directly from microbial time series data. The procedure not only serves to determine ecological drivers of microbial dynamics, but also to guide selection of appropriate community models for prediction and follow-up analysis.}, }
@article {pmid29951743, year = {2019}, author = {Xiao, F and Bi, Y and Li, X and Huang, J and Yu, Y and Xie, Z and Fang, T and Cao, X and He, Z and Juneau, P and Yan, Q}, title = {The Impact of Anthropogenic Disturbance on Bacterioplankton Communities During the Construction of Donghu Tunnel (Wuhan, China).}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {277-287}, pmid = {29951743}, issn = {1432-184X}, support = {31672262//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; China ; Geologic Sediments/microbiology/parasitology ; Lakes/*microbiology/parasitology ; Phylogeny ; Plankton/classification/genetics/*isolation &amp; purification ; Zooplankton/classification/genetics/isolation &amp; purification ; }, abstract = {Bacterioplankton are both primary producers and primary consumers in aquatic ecosystems, which were commonly investigated to reflect environmental changes, evaluate primary productivity, and assess biogeochemical cycles. However, there is relatively less understanding of their responses to anthropogenic disturbances such as constructions of dams/tunnels/roads that may significantly affect the aquatic ecosystem. To fill such gap, this study focused on the bacterioplankton communities' diversity and turnover during a tunnel construction across an urban lake (Lake Donghu, Wuhan, China), and five batches of samples were collected within 2 months according to the tunnel construction progress. Results indicated that both resources and predator factors contributed significant to the variations of bacterioplankton communities, but the closed area and open areas showed different diversity patterns due to the impacts of tunnel construction. Briefly, the phytoplankton, TN, and TP in water were still significantly correlated with the bacterioplankton composition and diversity like that in normal conditions. Additionally, the organic matter, TN, and NH4-N in sediments also showed clear effects on the bacterioplankton. However, the predator effects on the bacterioplankton in the closed-off construction area mainly derived from large zooplankton (i.e., cladocerans), while small zooplankton such as protozoa and rotifers are only responsible for weak predator effects on the bacterioplankton in the open areas. Further analysis about the ecological driving forces indicated that the bacterioplankton communities' turnover during the tunnel construction was mainly governed by the homogeneous selection due to similar environments within the closed area or the open areas at two different stages. This finding suggests that bacterioplankton communities can quickly adapt to the environmental modifications resulting from tunnel construction activities. This study can also give references to enhance our understanding on bacterioplankton communities' response to ecological and environmental changes due to intensification of construction and urbanization in and around lake ecosystems.}, }
@article {pmid29951048, year = {2018}, author = {Zinke, LA and Reese, BK and McManus, J and Wheat, CG and Orcutt, BN and Amend, JP}, title = {Sediment Microbial Communities Influenced by Cool Hydrothermal Fluid Migration.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1249}, pmid = {29951048}, issn = {1664-302X}, abstract = {Cool hydrothermal systems (CHSs) are prevalent across the seafloor and discharge fluid volumes that rival oceanic input from rivers, yet the microbial ecology of these systems are poorly constrained. The Dorado Outcrop on the ridge flank of the Cocos Plate in the northeastern tropical Pacific Ocean is the first confirmed CHS, discharging minimally altered <15°C fluid from the shallow lithosphere through diffuse venting and seepage. In this paper, we characterize the resident sediment microbial communities influenced by cool hydrothermal advection, which is evident from nitrate and oxygen concentrations. 16S rRNA gene sequencing revealed that Thaumarchaea, Proteobacteria, and Planctomycetes were the most abundant phyla in all sediments across the system regardless of influence from seepage. Members of the Thaumarchaeota (Marine Group I), Alphaproteobacteria (Rhodospirillales), Nitrospirae, Nitrospina, Acidobacteria, and Gemmatimonadetes were enriched in the sediments influenced by CHS advection. Of the various geochemical parameters investigated, nitrate concentrations correlated best with microbial community structure, indicating structuring based on seepage of nitrate-rich fluids. A comparison of microbial communities from hydrothermal sediments, seafloor basalts, and local seawater at Dorado Outcrop showed differences that highlight the distinct niche space in CHS. Sediment microbial communities from Dorado Outcrop differ from those at previously characterized, warmer CHS sediment, but are similar to deep-sea sediment habitats with surficial ferromanganese nodules, such as the Clarion Clipperton Zone. We conclude that cool hydrothermal venting at seafloor outcrops can alter the local sedimentary oxidation-reduction pathways, which in turn influences the microbial communities within the fluid discharge affected sediment.}, }
@article {pmid29950696, year = {2018}, author = {Petersen, JM and Kemper, A and Gruber-Vodicka, H and Cardini, U and van der Geest, M and Kleiner, M and Bulgheresi, S and Mußmann, M and Herbold, C and Seah, BKB and Antony, CP and Liu, D and Belitz, A and Weber, M}, title = {Author Correction: Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation.}, journal = {Nature microbiology}, volume = {3}, number = {8}, pages = {961}, doi = {10.1038/s41564-018-0196-5}, pmid = {29950696}, issn = {2058-5276}, abstract = {In this Article, the completeness and number of contigs for draft genomes from two individuals of Laxus oneistus are incorrect in the main text, although the correct information is included in Table 1. The original and corrected versions of the relevant sentence are shown in the correction notice.}, }
@article {pmid29950677, year = {2018}, author = {Candry, P and Van Daele, T and Denis, K and Amerlinck, Y and Andersen, SJ and Ganigué, R and Arends, JBA and Nopens, I and Rabaey, K}, title = {A novel high-throughput method for kinetic characterisation of anaerobic bioproduction strains, applied to Clostridium kluyveri.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {9724}, pmid = {29950677}, issn = {2045-2322}, mesh = {Acetic Acid/metabolism ; Anaerobiosis/physiology ; Anti-Infective Agents/pharmacology ; Butyric Acid/metabolism ; Caproates/metabolism ; Clostridium kluyveri/drug effects/*metabolism ; Ethanol/metabolism ; Kinetics ; }, abstract = {Hexanoic acid (HA), also called caproic acid, can be used as an antimicrobial agent and as a precursor to various chemicals, such as fuels, solvents and fragrances. HA can be produced from ethanol and acetate by the mesophilic anaerobic bacterium Clostridium kluyveri, via two successive elongation steps over butyrate. A high-throughput anaerobic growth curve technique was coupled to a data analysis framework to assess growth kinetics for a range of substrate and product concentrations. Using this method, growth rates and several kinetic parameters were determined for C. kluyveri. A maximum growth rate (µmax) of 0.24 ± 0.01 h[-1] was found, with a half-saturation index for acetic acid (KS,AA) of 3.8 ± 0.9 mM. Inhibition by butyric acid occurred at of 124.7 ± 5.7 mM (KI,BA), while the final product, HA, linearly inhibited growth with complete inhibition above 91.3 ± 10.8 mM (KHA of 10.9*10[-3] ± 1.3*10[-3] mM[-1]) at pH = 7, indicating that the hexanoate anion also exerts toxicity. These parameters were used to create a dynamic mass-balance model for bioproduction of HA. By coupling data collection and analysis to this modelling framework, we have produced a powerful tool to assess the kinetics of anaerobic micro-organisms, demonstrated here with C. kluyveri, in order further explore the potential of micro-organisms for chemicals production.}, }
@article {pmid29950381, year = {2018}, author = {Jenior, ML and Leslie, JL and Young, VB and Schloss, PD}, title = {Clostridium difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization.}, journal = {mSphere}, volume = {3}, number = {3}, pages = {}, pmid = {29950381}, issn = {2379-5042}, support = {UL1 TR000433/TR/NCATS NIH HHS/United States ; T32 GM008353/GM/NIGMS NIH HHS/United States ; R01 GM099514/GM/NIGMS NIH HHS/United States ; T32 GM145304/GM/NIGMS NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*administration &amp; dosage/adverse effects ; Cecum/*chemistry/*microbiology ; Clostridioides difficile/*growth &amp; development ; Clostridium Infections/*microbiology ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; Metabolomics ; Metagenomics ; Mice ; }, abstract = {Susceptibility to Clostridium difficile infection (CDI) is primarily associated with previous exposure to antibiotics, which compromise the structure and function of the gut bacterial community. Specific antibiotic classes correlate more strongly with recurrent or persistent C. difficile infection. As such, we utilized a mouse model of infection to explore the effect of distinct antibiotic classes on the impact that infection has on community-level transcription and metabolic signatures shortly following pathogen colonization and how those changes may associate with persistence of C. difficile Untargeted metabolomic analysis revealed that C. difficile infection had significantly larger impacts on the metabolic environment across cefoperazone- and streptomycin-pretreated mice, which became persistently colonized compared to clindamycin-pretreated mice, where infection quickly became undetectable. Through metagenome-enabled metatranscriptomics, we observed that transcripts for genes associated with carbon and energy acquisition were greatly reduced in infected animals, suggesting that those niches were instead occupied by C. difficile Furthermore, the largest changes in transcription were seen in the least abundant species, indicating that C. difficile may "attack the loser" in gut environments where sustained infection occurs more readily. Overall, our results suggest that C. difficile is able to restructure the nutrient-niche landscape in the gut to promote persistent infection.IMPORTANCEClostridium difficile has become the most common single cause of hospital-acquired infection over the last decade in the United States. Colonization resistance to the nosocomial pathogen is primarily provided by the gut microbiota, which is also involved in clearing the infection as the community recovers from perturbation. As distinct antibiotics are associated with different risk levels for CDI, we utilized a mouse model of infection with 3 separate antibiotic pretreatment regimens to generate alternative gut microbiomes that each allowed for C. difficile colonization but varied in clearance rate. To assess community-level dynamics, we implemented an integrative multi-omics approach that revealed that infection significantly changed many aspects of the gut community. The degree to which the community changed was inversely correlated with clearance during the first 6 days of infection, suggesting that C. difficile differentially modifies the gut environment to promote persistence. This is the first time that metagenome-enabled metatranscriptomics have been employed to study the behavior of a host-associated microbiota in response to an infection. Our results allow for a previously unseen understanding of the ecology associated with C. difficile infection and provide the groundwork for identification of context-specific probiotic therapies.}, }
@article {pmid29948019, year = {2019}, author = {Lin, L and Liu, W and Zhang, M and Lin, X and Zhang, Y and Tian, Y}, title = {Different Height Forms of Spartina alterniflora Might Select Their Own Rhizospheric Bacterial Communities in Southern Coast of China.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {124-135}, pmid = {29948019}, issn = {1432-184X}, support = {20720150097//the Fundamental Research Funds for the Central Universities/ ; }, mesh = {Bacteria/classification/*genetics/*metabolism ; Biodiversity ; China ; DNA, Bacterial/genetics ; Denitrification ; Ecosystem ; Genes, Bacterial/genetics ; Host Microbial Interactions/*physiology ; Microbiota ; Nitrification ; Nitrogen Cycle ; Phylogeny ; Plant Development ; Plant Shoots/growth &amp; development ; Poaceae/*growth &amp; development/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; Wetlands ; }, abstract = {In the southernmost part of coast of China, two height forms of Spartina alterniflora, tall and short, have invaded Leizhou Peninsula within the last decade. However, the effect of different height forms of Spartina alterniflora on plant-microbe interaction has not been clarified. Here, the community structures of rhizosphere bacteria and the abundance of N- and S-cycling functional genes associated with selected S. alterniflora were investigated in the field and a common garden. The community structure of tall-form S. alterniflora was distinct from short-form S. alterniflora at OTU level in the field, even after transplantation into a common garden. The abundance of bacterial amoA, nirS, and nosZ in tall S. alterniflora was significantly greater than those in short S. alterniflora in the field; however, this difference disappeared in a 1-year common garden experiment. These results suggested that compared with the tall-form S. alterniflora, the rhizosphere of short-form S. alterniflora harbored fewer nitrification-denitrification related microorganisms, which might benefit from conserving N in an N limited habitat. Together, our results suggested that tall- and short-form S. alterniflora can host their specific rhizosphere microbial communities and had different strategies of N usage via selecting the composition of rhizosphere bacterial assemblages, which in turn might determine the growth and invasiveness of S. alterniflora in its introduced range.}, }
@article {pmid29948018, year = {2019}, author = {Kamutando, CN and Vikram, S and Kamgan-Nkuekam, G and Makhalanyane, TP and Greve, M and Le Roux, JJ and Richardson, DM and Cowan, DA and Valverde, A}, title = {The Functional Potential of the Rhizospheric Microbiome of an Invasive Tree Species, Acacia dealbata.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {191-200}, pmid = {29948018}, issn = {1432-184X}, support = {CPRR14071676470//National Research Foundation of South Africa (NRF)/ ; }, mesh = {Acacia/growth &amp; development/*microbiology ; Bacteria/classification/genetics ; Bacterial Proteins/genetics ; Bradyrhizobium/genetics/metabolism ; Carbohydrate Metabolism ; DNA, Bacterial/genetics ; Genes, Bacterial/genetics ; *Introduced Species ; Metagenome ; Microbial Interactions/physiology ; Microbiota/genetics/*physiology ; Nitrogen/metabolism ; Nitrogen Fixation/genetics ; Phylogeny ; Plant Development ; Rhizobium/genetics/physiology ; *Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; South Africa ; Vitamins/metabolism ; }, abstract = {Plant-microbe interactions mediate both the invasiveness of introduced plant species and the impacts that they have in invaded ecosystems. Although the phylogenetic composition of the rhizospheric microbiome of Acacia dealbata (an invasive Australian tree species) has been investigated, little is known about the functional potential of the constituents of these altered microbial communities. We used shotgun DNA sequencing to better understand the link between bacterial community composition and functional capacity in the rhizospheric microbiomes associated with invasive A. dealbata populations in South Africa. Our analysis showed that several genes associated with plant growth-promoting (PGP) traits were significantly overrepresented in the rhizospheric metagenomes compared to neighbouring bulk soils collected away from A. dealbata stands. The majority of these genes are involved in the metabolism of nitrogen, carbohydrates and vitamins, and in various membrane transport systems. Overrepresented genes were linked to a limited number of bacterial taxa, mostly Bradyrhizobium species, the preferred N-fixing rhizobial symbiont of Australian acacias. Overall, these findings suggest that A. dealbata enriches rhizosphere soils with potentially beneficial microbial taxa, and that members of the genus Bradyrhizobium may play an integral role in mediating PGP processes that may influence the success of this invader when colonizing novel environments.}, }
@article {pmid29948017, year = {2019}, author = {Mason, CJ and Campbell, AM and Scully, ED and Hoover, K}, title = {Bacterial and Fungal Midgut Community Dynamics and Transfer Between Mother and Brood in the Asian Longhorned Beetle (Anoplophora glabripennis), an Invasive Xylophage.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {230-242}, pmid = {29948017}, issn = {1432-184X}, support = {2015-67013-23287//National Institute of Food and Agriculture/ ; }, mesh = {Acer/microbiology ; Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Coleoptera/*microbiology ; Eggs/microbiology ; Female ; Fungi/*classification/genetics/isolation &amp; purification ; Fusarium/classification ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Larva/microbiology ; Life Cycle Stages ; *Mothers ; Oviposition ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Microbial symbionts play pivotal roles in the ecology and physiology of insects feeding in woody plants. Both eukaryotic and bacterial members occur in these systems where they facilitate digestive and nutrient provisioning. The larval gut of the Asian longhorned beetle (Anoplophora glabripennis) is associated with a microbial consortium that fulfills these metabolic roles. While members of the community vary in presence and abundance among individuals from different hosts, A. glabripennis is consistently associated with a fungus in the Fusarium solani species complex (FSSC). We used amplicon sequencing, taxon-specific PCR, culturing, and imaging to determine how bacterial and fungal communities differ between life stages and possible modes of symbiont transfer. The bacterial and fungal communities of adult guts were more diverse than those from larvae and eggs. The communities of larvae and eggs were more similar to those from oviposition sites than from adult female guts. FSSC isolates were not detected in the reproductive tissues of adult females, but were consistently detected on egg surfaces after oviposition and in frass. These results demonstrate that frass can serve as a vehicle of transmission of a subset for the beetle gut microbiota. Vertically transmitted symbionts are often beneficial to their host, warranting subsequent functional studies.}, }
@article {pmid29948016, year = {2018}, author = {Maki, J}, title = {Introduction.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {1}, doi = {10.1007/s00248-018-1216-y}, pmid = {29948016}, issn = {1432-184X}, mesh = {Biographies as Topic ; Ecology ; History, 20th Century ; Humans ; Ireland ; *Microbiology ; Research Personnel/history ; }, }
@article {pmid29948015, year = {2019}, author = {Väisänen, M and Gavazov, K and Krab, EJ and Dorrepaal, E}, title = {The Legacy Effects of Winter Climate on Microbial Functioning After Snowmelt in a Subarctic Tundra.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {186-190}, pmid = {29948015}, issn = {1432-184X}, mesh = {Bacteria/enzymology/metabolism ; Carbon/metabolism ; Carbon Dioxide/metabolism ; Cell Respiration ; *Climate Change ; Ecology ; Environmental Monitoring ; Enzyme Activation ; Fungi/enzymology/metabolism ; Microbiota/*physiology ; Monophenol Monooxygenase/metabolism ; *Seasons ; *Snow ; Soil/chemistry ; *Soil Microbiology ; Temperature ; *Tundra ; beta-Glucosidase/metabolism ; }, abstract = {Warming-induced increases in microbial CO2 release in northern tundra may positively feedback to climate change. However, shifts in microbial extracellular enzyme activities (EEAs) may alter the impacts of warming over the longer term. We investigated the in situ effects of 3 years of winter warming in combination with the in vitro effects of a rapid warming (6 days) on microbial CO2 release and EEAs in a subarctic tundra heath after snowmelt in spring. Winter warming did not change microbial CO2 release at ambient (10 °C) or at rapidly increased temperatures, i.e., a warm spell (18 °C) but induced changes (P < 0.1) in the Q10 of microbial respiration and an oxidative EEA. Thus, although warmer winters may induce legacy effects in microbial temperature acclimation, we found no evidence for changes in potential carbon mineralization after spring thaw.}, }
@article {pmid29947838, year = {2018}, author = {Melo-Nascimento, AODS and Treumann, C and Neves, C and Andrade, E and Andrade, AC and Edwards, R and Dinsdale, E and Bruce, T}, title = {Functional characterization of ligninolytic Klebsiella spp. strains associated with soil and freshwater.}, journal = {Archives of microbiology}, volume = {200}, number = {8}, pages = {1267-1278}, doi = {10.1007/s00203-018-1532-0}, pmid = {29947838}, issn = {1432-072X}, support = {JCB0064/2013//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado da Bahia/ ; 23038.009420/201271//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; JCB0064/2013//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado da Bahia (BR)/ ; 13330800//National Science Foundation/ ; }, mesh = {Biodegradation, Environmental ; Brazil ; Fresh Water/microbiology ; Klebsiella/classification/*enzymology/genetics/*metabolism ; Lignin/*metabolism ; Oxidoreductases/genetics ; Peroxidases/*genetics ; Soil Microbiology ; }, abstract = {Overcoming recalcitrance of lignin has motivated bioprospecting of high-yielding enzymes from environmental ligninolytic microorganisms associated with lignocellulose degrading-systems. Here, we performed isolation of 21 ligninolytic strains belonging to the genus Klebsiella spp., driven by the presence of lignin in the media. The fastest-growing strains (FP10-5.23, FP10-5.22 and P3TM1) reached the stationary phase in approximately 24 h, in the media containing lignin as the main carbon source. The strains showed biochemical evidence of ligninolytic potential in liquid- and solid media-converting dyes, which the molecular structures are similar to lignin fragments. In liquid medium, higher levels of dye decolorization was observed for P3TM.1 in the presence of methylene blue, reaching 98% decolorization in 48 h. The highest index values (1.25) were found for isolates P3TM.1 and FP10-5.23, in the presence of toluidine blue. The genomic analysis revealed the presence of more than 20 genes associated with known prokaryotic lignin-degrading systems. Identification of peroxidases (lignin peroxidase-LiP, dye-decolorizing peroxidase-DyP, manganese peroxidase-MnP) and auxiliary activities (AA2, AA3, AA6 and AA10 families) among the genetic repertoire suggest the ability to produce extracellular enzymes able to attack phenolic and non-phenolic lignin structures. Our results suggest that the Klebsiella spp. associated with fresh water and soil may play important role in the cycling of recalcitrant molecules in the Caatinga (desert-like Brazilian biome), and represent a potential source of lignin-degrading enzymes with biotechnological applications.}, }
@article {pmid29946784, year = {2019}, author = {Sakoda, S and Aisu, K and Imagami, H and Matsuda, Y}, title = {Comparison of Actinomycete Community Composition on the Surface and Inside of Japanese Black Pine (Pinus thunbergii) Tree Roots Colonized by the Ectomycorrhizal Fungus Cenococcum geophilum.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {370-379}, pmid = {29946784}, issn = {1432-184X}, mesh = {Actinobacteria/classification/genetics/*isolation &amp; purification/physiology ; Ascomycota/classification/genetics/*isolation &amp; purification/physiology ; Biodiversity ; Mycorrhizae/classification/genetics/*isolation &amp; purification/physiology ; Phylogeny ; Pinus/growth &amp; development/*microbiology ; Plant Roots/growth &amp; development/microbiology ; Soil Microbiology ; Symbiosis ; Trees/growth &amp; development/microbiology ; }, abstract = {Various bacteria are associated with ectomycorrhizal roots, which are symbiotic complexes formed between plant roots and fungi. Among these associated bacteria, actinomycetes have received attention for their ubiquity and diverse roles in forest ecosystems. Here, to examine the association of actinomycetes with ectomycorrhizal root tips, we compared the bacterial and actinomycete communities on the surface and inside of root tips of coastal Japanese black pine (Pinus thunbergii) colonized by the fungus Cenococcum geophilum. Next-generation sequences of 16S rDNA of bacteria communities using the Ion Torrent Personal Genome Machine showed that the number of bacterial classes in the surface of C. geophilum ECM roots was significantly higher than that in non-ECM roots. The bacterial community structure of surface, inside, and non-ECM roots was significantly discriminated each other. For an isolation method, a total of 762 and 335 actinomycete isolates were obtained from the surface and inside of the roots, respectively. In addition, the isolation ratio of actinomycetes in these root tips varied depending on the age of the tree and the season. Identification of the isolates based on partial 16S rDNA sequencing revealed that the isolates belonged to nine genera of the order Actinomycetales. On the surface of the roots, most of the isolates belonged to genus Streptomyces (90.4%); inside of the roots, most of the isolates belonged to genus Actinoallomurus (40.0%), which is a relatively new taxon. Our results suggest that actinomycetes as well as bacteria are ubiquitously associated with C. geophilum ectomycorrhizal roots of P. thunbergii, although their communities can vary either surface or inside of individual root tips.}, }
@article {pmid29946053, year = {2018}, author = {MeGraw, VE and Brown, AR and Boothman, C and Goodacre, R and Morris, K and Sigee, D and Anderson, L and Lloyd, JR}, title = {A Novel Adaptation Mechanism Underpinning Algal Colonization of a Nuclear Fuel Storage Pond.}, journal = {mBio}, volume = {9}, number = {3}, pages = {}, pmid = {29946053}, issn = {2150-7511}, support = {BB/F017472/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Cesium Radioisotopes/*analysis/metabolism ; Chlorophyta/*growth &amp; development/metabolism ; Cyanobacteria/growth &amp; development/isolation &amp; purification/metabolism ; Ecosystem ; Nuclear Energy ; Ponds/analysis/*microbiology ; Strontium Radioisotopes/*analysis/metabolism ; United Kingdom ; Water Pollutants, Radioactive/*analysis/metabolism ; Xanthophylls/metabolism ; }, abstract = {Geochemical analyses alongside molecular techniques were used to characterize the microbial ecology and biogeochemistry of an outdoor spent nuclear fuel storage pond at Sellafield, United Kingdom, that is susceptible to seasonal algal blooms that cause plant downtime. 18S rRNA gene profiling of the filtered biomass samples showed the increasing dominance of a species closely related to the alga Haematococcus pluvialis, alongside 16S rRNA genes affiliated with a diversity of freshwater bacteria, including Proteobacteria and Cyanobacteria High retention of [137]Cs and [90]Sr on pond water filters coincided with high levels of microbial biomass in the pond, suggesting that microbial colonization may have an important control on radionuclide fate in the pond. To interpret the unexpected dominance of Haematococcus species during bloom events in this extreme environment, the physiological response of H. pluvialis to environmentally relevant ionizing radiation doses was assessed. Irradiated laboratory cultures produced significant quantities of the antioxidant astaxanthin, consistent with pigmentation observed in pond samples. Fourier transform infrared (FT-IR) spectroscopy suggested that radiation did not have a widespread impact on the metabolic fingerprint of H. pluvialis in laboratory experiments, despite the 80-Gy dose. This study suggests that the production of astaxanthin-rich encysted cells may be related to the preservation of the Haematococcus phenotype, potentially allowing it to survive oxidative stress arising from radiation doses associated with the spent nuclear fuel. The oligotrophic and radiologically extreme conditions in this environment do not prevent extensive colonization by microbial communities, which play a defining role in controlling the biogeochemical fate of major radioactive species present.IMPORTANCE Spent nuclear fuel is stored underwater in large ponds prior to processing and disposal. Such environments are intensively radioactive but can be colonized by microorganisms. Colonization of such inhospitable radioactive ponds is surprising, and the survival mechanisms that microbes use is of fundamental interest. It is also important to study these unusual ecosystems, as microbes growing in the pond waters may accumulate radionuclides present in the waters (for bioremediation applications), while high cell loads can hamper management of the ponds due to poor visibility. In this study, an outdoor pond at the U.K. Sellafield facility was colonized by a seasonal bloom of microorganisms, able to accumulate high levels of [137]Cs and [90]Sr and dominated by the alga Haematococcus This organism is not normally associated with deep water bodies, but it can adapt to radioactive environments via the production of the pigment astaxanthin, which protects the cells from radiation damage.}, }
@article {pmid29945195, year = {2018}, author = {Liu, X and Wu, Y and Wilson, FP and Yu, K and Lintner, C and Cupples, AM and Mattes, TE}, title = {Integrated methodological approach reveals microbial diversity and functions in aerobic groundwater microcosms adapted to vinyl chloride.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {9}, pages = {}, doi = {10.1093/femsec/fiy124}, pmid = {29945195}, issn = {1574-6941}, mesh = {Bacteria, Aerobic/genetics/*metabolism ; *Biodegradation, Environmental ; Carbon/metabolism ; Carbon-Sulfur Lyases/genetics ; Epoxide Hydrolases/metabolism ; Epoxy Compounds/*metabolism ; Ethylenes/metabolism ; Glutathione Transferase/metabolism ; Groundwater/*microbiology ; Humans ; Metagenome ; Metagenomics ; Oxygenases/genetics ; Plasmids/genetics ; Vinyl Chloride/*metabolism ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Vinyl chloride (VC), a known human carcinogen, is often formed in groundwater (GW) by incomplete reductive dechlorination of chlorinated ethenes. An integrated microbial ecology approach involving bacterial enrichments and isolations, carbon stable-isotope probing (SIP) and metagenome and genome sequencing was applied to ethene-fed GW microcosms that rapidly transitioned to aerobic growth on VC. Actinobacteria, Proteobacteria and Bacteroidetes dominated the microbial communities in ethene- and VC-grown cultures. SIP with 13C2-VC demonstrated that Nocardioides spp. significantly participated in carbon uptake from VC (52.1%-75.7% enriched in heavy fractions). Sediminibacterium, Pedobacter and Pseudomonas spp. also incorporated 13C from VC into genomic DNA. Ethene- and VC-assimilating Nocardioides sp. strain XL1 was isolated. Sequencing revealed a large (∼300 kbp) plasmid harboring genes encoding alkene monooxygenase and epoxyalkane: coenzyme M transferase, enzymes known to participate in aerobic VC and ethene biodegradation. The plasmid was 100% identical to pNOCA01 found in VC-assimilating Nocardioides sp. strain JS614. Metagenomic analysis of enrichment cultures indicated other bacteria implicated in carbon uptake from VC possessed the genetic potential to detoxify epoxides via epoxide hydrolase or glutathione S-transferase (Pseudomonas) and/or metabolize VC epoxide breakdown products and downstream VC metabolites. This study provides new functional insights into aerobic VC metabolism within a GW microbial community.}, }
@article {pmid29944836, year = {2018}, author = {Guo, X and Stedtfeld, RD and Hedman, H and Eisenberg, JNS and Trueba, G and Yin, D and Tiedje, JM and Zhang, L}, title = {Antibiotic Resistome Associated with Small-Scale Poultry Production in Rural Ecuador.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {15}, pages = {8165-8172}, doi = {10.1021/acs.est.8b01667}, pmid = {29944836}, issn = {1520-5851}, mesh = {Animals ; *Anti-Bacterial Agents ; Chickens ; Ecuador ; Genes, Bacterial ; Humans ; *Poultry ; RNA, Ribosomal, 16S ; Rural Population ; }, abstract = {Small-scale poultry farming is common in rural communities across the developing world. To examine the extent to which small-scale poultry farming serves as a reservoir for resistance determinants, the resistome of fecal samples was compared between production chickens that received antibiotics and free-ranging household chickens that received no antibiotics from a rural village in northern Ecuador. A qPCR array was used to quantify antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) using 248 primer pairs; and the microbiome structure was analyzed via 16S rRNA gene sequencing. A large number of ARGs (148) and MGEs (29) were detected. The ARG richness in production chickens was significantly higher than that of household chickens with an average of 15 more genes detected (p < 0.01). Moreover, ARGs and MGEs were much more abundant in production chickens than in household chickens (up to a 157-fold difference). Production chicken samples had significantly lower taxonomic diversity and were more abundant in Gammaproteobacteria, Betaproteobacteria, and Flavobacteria. The high abundance and diversity of ARGs and MGEs found in small-scale poultry farming was comparable to the levels previously found in large scale animal production, suggesting that these chickens could act as a local reservoir for spreading ARGs into rural communities.}, }
@article {pmid29941858, year = {2018}, author = {Pimenoff, VN and Houldcroft, CJ and Rifkin, RF and Underdown, S}, title = {The Role of aDNA in Understanding the Coevolutionary Patterns of Human Sexually Transmitted Infections.}, journal = {Genes}, volume = {9}, number = {7}, pages = {}, pmid = {29941858}, issn = {2073-4425}, abstract = {Analysis of pathogen genome data sequenced from clinical and historical samples has made it possible to perform phylogenetic analyses of sexually transmitted infections on a global scale, and to estimate the diversity, distribution, and coevolutionary host relationships of these pathogens, providing insights into pathogen emergence and disease prevention. Deep-sequenced pathogen genomes from clinical studies and ancient samples yield estimates of within-host and between-host evolutionary rates and provide data on changes in pathogen genomic stability and evolutionary responses. Here we examine three groups of pathogens transmitted mainly through sexual contact between modern humans to provide insight into ancient human behavior and history with their pathogens. Exploring ancient pathogen genomic divergence and the ancient viral-host parallel evolutionary histories will help us to reconstruct the origin of present-day geographical distribution and diversity of clinical pathogen infections, and will hopefully allow us to foresee possible environmentally induced pathogen evolutionary responses. Lastly, we emphasize that ancient pathogen DNA research should be combined with modern clinical pathogen data, and be equitable and provide advantages for all researchers worldwide, e.g., through shared data.}, }
@article {pmid29937879, year = {2017}, author = {Nabee, Z and Jeewon, R and Pugo-Gunsam, P}, title = {Oral dysbacteriosis in type 2 diabetes and its role in the progression to cardiovascular disease.}, journal = {African health sciences}, volume = {17}, number = {4}, pages = {1082-1091}, pmid = {29937879}, issn = {1729-0503}, mesh = {Adult ; Aged ; Buffers ; Cardiovascular Diseases/*microbiology ; Case-Control Studies ; DMF Index ; Dental Caries/*microbiology ; Diabetes Mellitus, Type 2/diagnosis/*microbiology ; Disease Progression ; Dysbiosis ; Female ; Humans ; Hydrogen-Ion Concentration ; Lactobacillus/*isolation &amp; purification ; Male ; Middle Aged ; Oral Health ; Saliva/*microbiology ; Streptococcus mutans/*isolation &amp; purification ; }, abstract = {BACKGROUND: Salivary changes and proliferation of specific bacterial communities are known to result in oral disease which may adversely impact on systemic conditions like diabetes and cardiovascular diseases.<br><br>OBJECTIVES: This study reports on the changes in oral ecology of healthy and diseased adults and the possible role in disease causation.<br><br>METHODS: The study comprised 150 participants divided into control (healthy), diabetic and cardiac groups. After dental examination for (Decayed Missing Filled Teeth (DMFT) and Oral Rating Index (ORI), stimulated saliva was sampled to determine flow rate and buffering capacity. Salivary microbial load of Streptococcus mutans and Lactobacilli were subsequently quantified.<br><br>RESULTS: DMFT, ORI, buffering capacity and flow rate were inferior for both diabetic and cardiac patients, who had higher bacterial counts (p<0.05). Long standing diabetics harboured a higher load of Streptococcus mutans. The microbial load of Streptococcus mutans in cardiac patients was double that of diabetics.<br><br>CONCLUSION: Disruption in the salivary environment and changes in microbial ecology with increased load of cariogenic bacteria were found in diabetic and cardiac patients. This study brings forward new evidence of a markedly higher load of Streptococcus mutans in cardiac patients which may underlie the progression of diabetes to cardiovascular disease in this population.}, }
@article {pmid29934850, year = {2018}, author = {Kostina, EV and Sinyakov, AN and Ryabinin, VA}, title = {A many probes-one spot hybridization oligonucleotide microarray.}, journal = {Analytical and bioanalytical chemistry}, volume = {410}, number = {23}, pages = {5817-5823}, doi = {10.1007/s00216-018-1190-8}, pmid = {29934850}, issn = {1618-2650}, mesh = {Base Sequence ; DNA, Viral/*analysis/genetics ; Equipment Design ; Immobilized Nucleic Acids/chemistry/genetics ; *Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis/*instrumentation ; Oligonucleotide Probes/chemistry/genetics ; Orthopoxvirus/chemistry/*genetics ; Poxviridae Infections/virology ; }, abstract = {A variant of the hybridization oligonucleotide microarray, utilizing the principle of many probes-one spot (MPOS-microarrays), is proposed. A case study based on Orthopoxviruses (Variola, Monkeypox, and Ectromelia viruses) demonstrates a considerable increase in the fluorescence signal (up to 100-fold) when several oligonucleotide probes are printed to one spot. Moreover, the specificity of detection also increases (almost 1000-fold), allowing the use of probes that individually lack such high specificity. The optimal probes have a Tm of 32-37 °C and length of 13-15 bases. We suggest that the high specificity and sensitivity of the MPOS-microarray is a result of cooperativity of DNA binding with all probes immobilized in the spot. This variant of DNA detection can be useful for designing biosensors, tools for point-of-care (POC) diagnostics, microbial ecology, analysis of clustered regularly interspaced short palindromic repeats (CRISPR), and others. Graphical abstract ᅟ.}, }
@article {pmid29931762, year = {2019}, author = {Quercia, S and Freccero, F and Castagnetti, C and Soverini, M and Turroni, S and Biagi, E and Rampelli, S and Lanci, A and Mariella, J and Chinellato, E and Brigidi, P and Candela, M}, title = {Early colonisation and temporal dynamics of the gut microbial ecosystem in Standardbred foals.}, journal = {Equine veterinary journal}, volume = {51}, number = {2}, pages = {231-237}, doi = {10.1111/evj.12983}, pmid = {29931762}, issn = {2042-3306}, mesh = {Animals ; Animals, Newborn ; Bacteria/classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Energy Metabolism/physiology ; *Gastrointestinal Microbiome ; Homeostasis/physiology ; Horses/*microbiology/physiology ; Male ; }, abstract = {BACKGROUND: Even if horses strictly depend on the gut microbiota for energy homeostasis, only a few molecular studies have focused on its characterisation and none on the perinatal gut microbial colonisation process.<br><br>OBJECTIVES: To explore the perinatal colonisation process of the foal gut microbial ecosystem and the temporal dynamics of the ecosystem assembly during the first days of life.<br><br>STUDY DESIGN: Longitudinal study.<br><br>METHODS: Thirteen Standardbred mare-foal pairs were included in the study. For each pair, at delivery we collected the mare amniotic fluid, faeces and colostrum, and the foal meconium. Milk samples and faeces of both mare and foal were also taken longitudinally, until day 10 post-partum. Samples were analysed by means of next-generation sequencing of the 16S rRNA gene on Illumina MiSeq.<br><br>RESULTS: Our findings suggest that microbial components derived from the mare symbiont communities establishes in the foal gut since fetal life. After birth, an external transmission route of mare microorganisms takes place. This involves a rapid and dynamic process of assembling the mature foal gut microbiome, in which the founder microbial species are derived from both the milk and the gut microbial ecosystems of the mare.<br><br>MAIN LIMITATIONS: The inability to discriminate between live and dead cells, the possible presence of contaminating bacteria in low biomass samples (e.g. meconium and amniotic fluid), the limits of the phylogenetic assignment down to species level, and the presence of unassigned operational taxonomic units.<br><br>CONCLUSIONS: Our data highlight the importance of mare microbiomes as a key factor for the establishment of the gut microbial ecosystem of the foal.}, }
@article {pmid29931623, year = {2019}, author = {Arai, H and Hirano, T and Akizuki, N and Abe, A and Nakai, M and Kunimi, Y and Inoue, MN}, title = {Multiple Infection and Reproductive Manipulations of Wolbachia in Homona magnanima (Lepidoptera: Tortricidae).}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {257-266}, pmid = {29931623}, issn = {1432-184X}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Bacterial Physiological Phenomena ; Cytoplasm ; DNA, Bacterial/analysis ; Female ; Larva/microbiology ; Male ; Moths/drug effects/*genetics/*microbiology ; Phenotype ; Pupa/microbiology ; Reproduction/*physiology ; Sex Ratio ; Symbiosis ; *Wolbachia/classification/genetics/physiology ; }, abstract = {Endosymbiotic bacterium Wolbachia interacts with host in either a mutualistic or parasitic manner. Wolbachia is frequently identified in various arthropod species, and to date, Wolbachia infections have been detected in different insects. Here, we found a triple Wolbachia infection in Homona magnanima, a serious tea pest, and investigated the effects of three infecting Wolbachia strains (wHm-a, -b, and -c) on the host. Starting with the triple-infected host line (W[abc]), which was collected in western Tokyo in 1999 and maintained in laboratory, we established an uninfected line (W[-]) and three singly infected lines (W[a], W[b], and W[c]) using antibiotics. Mating experiments with the host lines revealed that only wHm-b induced cytoplasmic incompatibility (CI) in H. magnanima, with the intensities of CI different between the W[b] and W[abc] lines. Regarding mutualistic effects, wHm-c shortened larval development time and increased pupal weight in both the W[c] and W[abc] lines to the same extent, whereas no distinct phenotype was observed in lines singly infected with wHm-a. Based on quantitative PCR analysis, Wolbachia density in the W[a] line was higher than in the other host lines (p < 0.01, n = 10). Wolbachia density in the W[b] line was also higher than in the W[c] and W[abc] lines, while no difference was observed between the W[c] and W[abc] lines. These results indicate that the difference in the CI intensity between a single or multiple infection may be attributed to the difference in wHm-b density. However, no correlation was observed between mutualistic effects and Wolbachia density.}, }
@article {pmid29930350, year = {2018}, author = {Dini-Andreote, F and van Elsas, JD and Olff, H and Salles, JF}, title = {Dispersal-competition tradeoff in microbiomes in the quest for land colonization.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {9451}, pmid = {29930350}, issn = {2045-2322}, mesh = {*Biological Evolution ; *Metagenome ; *Microbiota ; Seawater/microbiology ; *Soil Microbiology ; }, abstract = {Ancestor microbes started colonizing inland habitats approximately 2.7 to 3.5 billion years ago. With some exceptions, the key physiological adaptations of microbiomes associated with marine-to-land transitions have remained elusive. This is essentially caused by the lack of suitable systems that depict changes in microbiomes across sufficiently large time scales. Here, we investigate the adaptive routes taken by microbiomes along a contemporary gradient of land formation. Using functional trait-based metagenomics, we show that a switch from a microbial 'dispersal' to a 'competition' response modus best characterizes the microbial trait changes during this eco-evolutionary trajectory. The 'dispersal' modus prevails in microbiomes at the boundary sites between land and sea. It encompasses traits conferring cell chemosensory and motile behaviors, thus allowing the local microbes to exploit short-lived nutritional patches in high-diffusion microhabitats. A systematic transition towards the 'competition' modus occurs progressively as the soil matures, which is likely due to forces of viscosity or strain that favor traits for competition and chemical defense. Concomitantly, progressive increases in the abundances of genes encoding antibiotic resistance and complex organic substrate degradation were found. Our findings constitute a novel perspective on the ecology and evolution of microbiome traits, tracking back one of the most seminal transitions in the evolutionary history of life.}, }
@article {pmid29928771, year = {2018}, author = {Cristea, A and Baricz, A and Leopold, N and Floare, CG and Borodi, G and Kacso, I and Tripon, S and Bulzu, PA and Andrei, A&#x218; and Cadar, O and Levei, EA and Banciu, HL}, title = {Polyhydroxybutyrate production by an extremely halotolerant Halomonas elongata strain isolated from the hypersaline meromictic Fără Fund Lake (Transylvanian Basin, Romania).}, journal = {Journal of applied microbiology}, volume = {125}, number = {5}, pages = {1343-1357}, doi = {10.1111/jam.14029}, pmid = {29928771}, issn = {1365-2672}, support = {PN-II-ID-PCE-2011-3-0546//Romanian National Authority for Scientific Research, CNCS-UEFISCDI/ ; PN-II-ID-PCE-2011-3-0765//Romanian National Authority for Scientific Research, CNCS-UEFISCDI/ ; PN-III-P4-ID-PCE-2016-0303//Romanian National Authority for Scientific Research, CNCS-UEFISCDI/ ; Core Program, PN18-03 02 01//Ministry of Research and Innovation, MCI/ ; 31773.3//Babes-Bolyai University/ ; }, mesh = {Biopolymers/biosynthesis ; Halomonas/genetics/isolation &amp; purification/*metabolism ; Lakes/*microbiology ; Phylogeny ; Polyhydroxyalkanoates/*biosynthesis/chemistry ; RNA, Ribosomal, 16S/genetics ; Romania ; Sodium Chloride/metabolism ; }, abstract = {AIM: This study aimed at unprecedented physical and chemical evaluation of the 'green plastics' polyhydroxyalkanoates (PHAs), in an extremely halotolerant Halomonas elongata strain 2FF under high-salt concentration.<br><br>METHODS AND RESULTS: The investigated bacterial strain was isolated from the surface water of the hypersaline F&#x103;r&#x103; Fund Lake. The 16S rRNA gene sequence phylogeny and phenotypic analysis indicated that the isolate belonged to H. elongata. PHA inclusions were observed by Sudan Black B, Nile Red staining, and transmission electron microscopy during growth at high salinity (10%, w/v, NaCl) on 1% (w/v) d-glucose. The produced polymer was quantitatively and qualitatively assessed using crotonic acid assay, elemental analysis, Fourier transform infrared and Raman spectroscopies. Additionally, X-ray powder diffraction, [1] H-NMR spectroscopy, and differential scanning calorimetry were applied. The investigations showed that the intracellular polymer was polyhydroxybutyrate (PHB) of which the strain produced up to 40 wt% of total cell dry weight after 48&#xa0;h. The analysis of phaC gene from the isolated H. elongata strain indicated that the encoded PHA synthase belongs to Class I PHA synthase family.<br><br>CONCLUSIONS: Overall, our investigations pointed out that the halotolerant H.&#xa0;elongata strain 2FF was capable to produce significant amounts of PHB from&#xa0;d-glucose, and PHAs from various carbon substrates at high-salt concentrations.<br><br>The tested strain showed the ability for significant production of natural, biodegradable polymers under nutrient limitation and hypersaline conditions suggesting its potentiality for further metabolic and molecular investigations towards enhanced biopolymer production. Additionally, this study reports on the unprecedented use of Raman and XPRD techniques to investigate PHAs of an extremely halotolerant bacterium, thus expanding the repertoire of physical methods to study green plastics derived from extremophilic microorganisms.}, }
@article {pmid29927545, year = {2018}, author = {Bäumel, S and Tytgat, HLP and Nemec, B and Schmidt, R and Chia, LW and Smidt, H}, title = {Fifty Percent Human - how art brings us in touch with our microbial cohabitants.}, journal = {Microbial biotechnology}, volume = {11}, number = {4}, pages = {571-574}, pmid = {29927545}, issn = {1751-7915}, mesh = {*Art ; Creativity ; Ecosystem ; Humans ; *Microbiota ; Philosophy ; }, abstract = {The Human Microbiome, as well as the exploration of the microorganisms inhabiting the human body, are not only integral to the field of microbiology but represent an intrinsic part of all human beings. Consequently, along with scientists, artists have been inspired by the microbiome: transforming it in to tangible artefacts in order to critically question, reflect on and break down the barrier between humans and their microcohabitants. By artistic means, artists help us to understand how microbial research topics are inevitably affected by societal influences, including (health) politics, economics and the arts. Fifty Percent Human is a multidisciplinary artistic research project that aims to reshape our understanding of the human body and its environment as well as to explore possibilities for conscious coexistence in order to bridge the gap between science and society.}, }
@article {pmid29926340, year = {2018}, author = {Řezanka, T and Palyzová, A and Sigler, K}, title = {Isolation and identification of siderophores produced by cyanobacteria.}, journal = {Folia microbiologica}, volume = {63}, number = {5}, pages = {569-579}, pmid = {29926340}, issn = {1874-9356}, support = {LO1509//Ministry of Education, Youth and Sports of the Czech Republic/ ; }, mesh = {Chromatography, High Pressure Liquid ; Cyanobacteria/*metabolism ; Iron/metabolism ; Molecular Structure ; Photochemical Processes ; Seawater/microbiology ; Siderophores/*chemistry/*isolation &amp; purification/metabolism ; Tandem Mass Spectrometry ; }, abstract = {Cyanobacteria are one of the most successful and oldest forms of life that are present on Earth. They are prokaryotic photoautotrophic microorganisms that colonize so diverse environments as soil, seawater, and freshwater, but also stones, plants, or extreme habitats such as snow and ice as well as hot springs. This diversity in the type of environment they live in requires a successful adaptation to completely different conditions. For this reason, cyanobacteria form a wide range of different secondary metabolites. In particular, the cyanobacteria living in both freshwater and sea produce many metabolites that have biological activity. In this review, we focus on metabolites called siderophores, which are low molecular weight chemical compounds specifically binding iron ions. They have a relatively low molecular weight and are produced by bacteria and also by fungi. The main role of siderophores is to obtain iron from the environment and to create a soluble complex available to microbial cells. Siderophores play an important role in microbial ecology; for example, in agriculture they support the growth of many plants and increase their production by increasing the availability of Fe in plants. The aim of this review is to demonstrate the modern use of physico-chemical methods for the detection of siderophores in cyanobacteria and the use of these methods for the detection and characterization of the siderophore-producing microorganisms. Using high-performance liquid chromatography-mass spectrometry (LC-MS), it is possible not only to discover new chemical structures but also to identify potential interactions between microorganisms. Based on tandem mass spectrometry (MS/MS) analyses, previous siderophore knowledge can be used to interpret MS/MS data to examine both known and new siderophores.}, }
@article {pmid29926147, year = {2019}, author = {Schaub, I and Baum, C and Schumann, R and Karsten, U}, title = {Effects of an Early Successional Biological Soil Crust from a Temperate Coastal Sand Dune (NE Germany) on Soil Elemental Stoichiometry and Phosphatase Activity.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {217-229}, pmid = {29926147}, issn = {1432-184X}, support = {SAS-2015-IOW-LWC//Leibniz-Gemeinschaft/ ; }, mesh = {Baltic States ; Biomass ; Carbon ; Chlorophyll A ; Geologic Sediments/chemistry ; Germany ; Microbiota ; Nitrogen ; Phosphoric Monoester Hydrolases/*metabolism ; Phosphorus ; Seasons ; Silicon Dioxide/*analysis ; Soil/*chemistry ; *Soil Microbiology ; Water ; }, abstract = {Early successional biological soil crusts (BSCs), a consortium of bacteria, cyanobacteria, and other microalgae, are one of the first settlement stages on temperate coastal sand dunes. In this study, we investigated the algal biomass (Chlorophyll a (Chl a)), algal (Calgal) and microbial carbon (Cmic), elemental stoichiometry (C:N:P), and acid and alkaline phosphatase activity (AcidPA and AlkPA) of two algae-dominated BSCs from a coastal white dune (northeast Germany, on the southwestern Baltic Sea) which differed in the exposure to wind forces. The dune sediment (DS) was generally low in total carbon (TC), nitrogen (TN), and phosphorus (TP). These elements, together with the soil organic matter (SOM) accumulated in the BSC layer and in the sediment underneath (crust sediment CS), leading to initial soil development. The more disturbed BSC (BSC1) exhibited lower algal and microbial biomass and lower Calgal/Cmic ratios than the undisturbed BSC (BSC2). The BSC1 accumulated more organic carbon (OC) than BSC2. However, the OC in the BSC2 was more effectively incorporated into Cmic than in the BSC1, as indicated by lower OC:Cmic ratios. The AcidPA (1.1-1.3 μmol g[-1] DM h[-1] or 147-178 μg g[-1] DM h[-1]) and AlkPA (2.7-5.5 μmol g[-1] DM h[-1] or 372-764 μg g[-1] DM h[-1]) were low in both BSCs. The PA, together with the elemental stoichiometry, indicated no P limitation of both BSCs but rather water limitation followed by N limitation for the algae community and a carbon limitation for the microbial community. Our results explain the observed distribution of early successional and more developed BSCs on the sand dune.}, }
@article {pmid29925614, year = {2018}, author = {Brothers, CJ and Van Der Pol, WJ and Morrow, CD and Hakim, JA and Koo, H and McClintock, JB}, title = {Ocean warming alters predicted microbiome functionality in a common sea urchin.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1881}, pages = {}, pmid = {29925614}, issn = {1471-2954}, support = {P30 AI027767/AI/NIAID NIH HHS/United States ; P30 AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR001417/TR/NCATS NIH HHS/United States ; }, mesh = {Animals ; *Climate Change ; Hot Temperature/*adverse effects ; Lytechinus/*microbiology ; *Microbiota ; Oceans and Seas ; Random Allocation ; Seawater/*analysis ; }, abstract = {The microbiome of sea urchins plays a role in maintaining digestive health and innate immunity. Here, we investigated the effects of long-term (90 day) exposure to elevated seawater temperatures on the microbiome of the common, subtropical sea urchin Lytechinus variegatus The community composition and diversity of microbes varied according to the type of sample collected from the sea urchin (seawater, feed, intestines, coelomic fluid, digested pellet and faeces), with the lowest microbial diversity (predominately the order Campylobacterales) located in the intestinal tissue. Sea urchins exposed to near-future seawater temperatures maintained the community structure and diversity of microbes associated with their tissues. However, marginal, non-significant shifts in microbial community structure with elevated temperature resulted in significant changes in predicted metagenomic functions such as membrane transport and amino acid and carbohydrate metabolism. The predicted changes in key metabolic categories suggest that near-future climate-induced increases in seawater temperature could shift microbial community function and impact sea urchin digestive and immune physiology.}, }
@article {pmid29923792, year = {2018}, author = {Obase, K and Douhan, GW and Matsuda, Y and Smith, ME}, title = {Isolation source matters: sclerotia and ectomycorrhizal roots provide different views of genetic diversity in Cenococcum geophilum.}, journal = {Mycologia}, volume = {110}, number = {3}, pages = {473-481}, doi = {10.1080/00275514.2018.1463130}, pmid = {29923792}, issn = {1557-2536}, mesh = {Ascomycota/*genetics ; DNA, Fungal/genetics ; Forests ; Fungal Proteins/genetics ; *Genetic Variation ; Genotype ; Glyceraldehyde-3-Phosphate Dehydrogenases/genetics ; Microsatellite Repeats/genetics ; Mycorrhizae/*genetics ; Plant Roots/*microbiology ; Soil Microbiology ; }, abstract = {Cenococcum geophilum forms sclerotia and ectomycorrhizas with host plants in forest soils. We demonstrated the differences in genetic diversity of C. geophilum between cultured isolates from sclerotia and those from ectomycorrhizal roots in the same 73 soil samples based on glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene sequences and newly developed microsatellite markers. Based on GAPDH sequences, 759 cultured isolates (553 from sclerotia and 206 from ectomycorrhizas) were classified into 107 "genotypes" with sequence variation of up to 8.6%. The total number of GAPDH genotypes per soil sample ranged from 1 to 9, but genotypes that were shared between sclerotia and ectomycorrhizas were uncommon (0-3 per soil sample). More than 50% of GAPDH genotypes were unique to one source in most soil samples. Unique GAPDH genotypes were detected from either scleotia or ectomycorrhizal roots in most of the soil samples. Multilocus analysis using nine microsatellite markers provided additional resolution to differentiate fungal individuals and supported the results of GAPDH genotyping. The results indicated that sampling both sclerotia and ectomycorrhizal roots maximizes the detection of diversity at the soil core scale. On the other hand, when all isolates were viewed together, 82 GAPDH genotypes were unique to sclerotia whereas only 6 GAPDH genotypes were unique to ectomycorrhizas. Rarefaction analysis indicated that GAPDH genotypic diversity is significantly higher in sclerotia than ectomycorrhizal roots and the diversity within sclerotia is nearly the same as that of both sclerotia and ectomycorrhizas together. These findings suggest that sampling sclerotia alone is likely to detect the majority of GAPDH genotypes in Cenococcum at the regional scale. When deciding whether to sample sclerotia, ectomycorrhizas, or both types of tissues from Cenococcum, it is critical to consider the spatial scale and also the main questions and hypotheses of the study.}, }
@article {pmid29923399, year = {2018}, author = {Pikaar, I and Matassa, S and Bodirsky, BL and Weindl, I and Humpenöder, F and Rabaey, K and Boon, N and Bruschi, M and Yuan, Z and van Zanten, H and Herrero, M and Verstraete, W and Popp, A}, title = {Decoupling Livestock from Land Use through Industrial Feed Production Pathways.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {13}, pages = {7351-7359}, doi = {10.1021/acs.est.8b00216}, pmid = {29923399}, issn = {1520-5851}, mesh = {Agriculture ; Animal Feed ; Animals ; *Greenhouse Gases ; Industry ; *Livestock ; }, abstract = {One of the main challenges for the 21st century is to balance the increasing demand for high-quality proteins while mitigating environmental impacts. In particular, cropland-based production of protein-rich animal feed for livestock rearing results in large-scale agricultural land-expansion, nitrogen pollution, and greenhouse gas emissions. Here we propose and analyze the long-term potential of alternative animal feed supply routes based on industrial production of microbial proteins (MP). Our analysis reveals that by 2050, MP can replace, depending on socio-economic development and MP production pathways, between 10-19% of conventional crop-based animal feed protein demand. As a result, global cropland area, global nitrogen losses from croplands and agricultural greenhouse gas emissions can be decreased by 6% (0-13%), 8% (-3-8%), and 7% (-6-9%), respectively. Interestingly, the technology to industrially produce MP at competitive costs is directly accessible for implementation and has the potential to cause a major structural change in the agro-food system.}, }
@article {pmid29922904, year = {2019}, author = {Ghiloufi, W and Seo, J and Kim, J and Chaieb, M and Kang, H}, title = {Effects of Biological Soil Crusts on Enzyme Activities and Microbial Community in Soils of an Arid Ecosystem.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {201-216}, pmid = {29922904}, issn = {1432-184X}, support = {2016R1D1A1A02937049//National Research Foundation of Korea/ ; 20110030040//National Research Foundation of Korea/ ; 2016R1D1A1A02937049//National Research Foundation of Korea/ ; 2017096A001719BB01//Korea Forest Service/ ; }, mesh = {Bacteria/enzymology/metabolism ; Biodiversity ; Carbon/metabolism ; Carbon Cycle ; Cyanobacteria/growth &amp; development/metabolism ; *Desert Climate ; *Ecosystem ; Environmental Monitoring ; *Enzyme Activation ; Fungi/enzymology/metabolism ; Hydrogen-Ion Concentration ; Hydrolases/metabolism ; Lichens/growth &amp; development/metabolism ; *Microbiota ; Monophenol Monooxygenase ; Nitrogen/metabolism ; Soil/*chemistry ; *Soil Microbiology ; Tunisia ; Water ; }, abstract = {Arid ecosystems constitute 41% of land's surface and play an important role in global carbon cycle. In particular, biological soil crusts (BSC) are known to be a hotspot of carbon fixation as well as mineralization in arid ecosystems. However, little information is available on carbon decomposition and microbes in BSC and key controlling variables for microbial activities in arid ecosystems. The current study, carried out in South Mediterranean arid ecosystem, aimed to evaluate the effects of intact and removed cyanobacteria/lichen crusts on soil properties, soil enzyme activities, and microbial abundances (bacteria and fungi). We compared five different treatments (bare soil, soil with intact cyanobacteria, soil with cyanobacteria removed, soil with intact lichens, and soil with lichens removed) in four different soil layers (0-5, 5-10, 10-15, and 15-20 cm). Regardless of soil treatments, activities of hydrolases and water content increased with increasing soil depth. The presence of lichens increased significantly hydrolase activities, which appeared to be associated with greater organic matter, nitrogen, and water contents. However, phenol oxidase was mainly controlled by pH and oxygen availability. Neither fungal nor bacterial abundance exhibited a significant correlation with enzyme activities suggesting that soil enzyme activities are mainly controlled by edaphic and environmental conditions rather than source microbes. Interestingly, the presence of lichens reduced the abundance of bacteria of which mechanism is still to be investigated.}, }
@article {pmid29920927, year = {2019}, author = {Lee, JR and Magruder, M and Zhang, L and Westblade, LF and Satlin, MJ and Robertson, A and Edusei, E and Crawford, C and Ling, L and Taur, Y and Schluter, J and Lubetzky, M and Dadhania, D and Pamer, E and Suthanthiran, M}, title = {Gut microbiota dysbiosis and diarrhea in kidney transplant recipients.}, journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons}, volume = {19}, number = {2}, pages = {488-500}, pmid = {29920927}, issn = {1600-6143}, support = {K23 AI124464/AI/NIAID NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; R37 AI051652/AI/NIAID NIH HHS/United States ; //Chinese American Medical Society/International ; }, mesh = {Adult ; Bacteria/genetics/*growth &amp; development/isolation &amp; purification ; Case-Control Studies ; Cohort Studies ; Diarrhea/*etiology/pathology ; Dysbiosis/*etiology/pathology ; Feces/microbiology ; Female ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Glomerular Filtration Rate ; Graft Rejection/*etiology/pathology ; Graft Survival ; Humans ; Kidney Failure, Chronic/*surgery ; Kidney Function Tests ; Kidney Transplantation/*adverse effects ; Male ; Middle Aged ; Postoperative Complications ; Prognosis ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; }, abstract = {Posttransplant diarrhea is associated with kidney allograft failure and death, but its etiology remains unknown in the majority of cases. Because altered gut microbial ecology is a potential basis for diarrhea, we investigated whether posttransplant diarrhea is associated with gut dysbiosis. We enrolled 71 kidney allograft recipients for serial fecal specimen collections in the first 3 months of transplantation and profiled the gut microbiota using 16S ribosomal RNA (rRNA) gene V4-V5 deep sequencing. The Shannon diversity index was significantly lower in 28 diarrheal fecal specimens from 25 recipients with posttransplant diarrhea than in 112 fecal specimens from 46 recipients without posttransplant diarrhea. We found a lower relative abundance of 13 commensal genera (Benjamini-Hochberg adjusted P ≤ .15) in the diarrheal fecal specimens including the same 4 genera identified in our prior study. The 28 diarrheal fecal specimens were also evaluated by a multiplexed polymerase chain reaction (PCR) assay for 22 bacterial, viral, and protozoan gastrointestinal pathogens, and 26 specimens were negative for infectious etiologies. Using PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) to predict metagenomic functions, we found that diarrheal fecal specimens had a lower abundance of metabolic genes. Our findings suggest that posttransplant diarrhea is not associated with common infectious diarrheal pathogens but with a gut dysbiosis.}, }
@article {pmid29920462, year = {2018}, author = {Ferguson, RMW and Coulon, F and Villa, R}, title = {Understanding microbial ecology can help improve biogas production in AD.}, journal = {The Science of the total environment}, volume = {642}, number = {}, pages = {754-763}, doi = {10.1016/j.scitotenv.2018.06.007}, pmid = {29920462}, issn = {1879-1026}, mesh = {Anaerobiosis ; Archaea ; *Biofuels ; *Bioreactors ; Ecology ; Methane ; }, abstract = {454-Pyrosequencing and lipid fingerprinting were used to link anaerobic digestion (AD) process parameters (pH, alkalinity, volatile fatty acids (VFAs), biogas production and methane content) with the reactor microbial community structure and composition. AD microbial communities underwent stress conditions after changes in organic loading rate and digestion substrates. 454-Pyrosequencing analysis showed that, irrespectively of the substrate digested, methane content and pH were always significantly, and positively, correlated with community evenness. In AD, microbial communities with more even distributions of diversity are able to use parallel metabolic pathways and have greater functional stability; hence, they are capable of adapting and responding to disturbances. In all reactors, a decrease in methane content to <30% was always correlated with a 50% increase of Firmicutes sequences (particularly in operational taxonomic units (OTUs) related to Ruminococcaceae and Veillonellaceae). Whereas digesters producing higher methane content (above 60%), contained a high number of sequences related to Synergistetes and unidentified bacterial OTUs. Finally, lipid fingerprinting demonstrated that, under stress, the decrease in archaeal biomass was higher than the bacterial one, and that archaeal Phospholipid etherlipids (PLEL) levels were correlated to reactor performances. These results demonstrate that, across a number of parameters such as lipids, alpha and beta diversity, and OTUs, knowledge of the microbial community structure can be used to predict, monitor, or optimise AD performance.}, }
@article {pmid29916010, year = {2019}, author = {Wentzel, LCP and Inforsato, FJ and Montoya, QV and Rossin, BG and Nascimento, NR and Rodrigues, A and Sette, LD}, title = {Fungi from Admiralty Bay (King George Island, Antarctica) Soils and Marine Sediments.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {12-24}, pmid = {29916010}, issn = {1432-184X}, support = {2013/19486-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2016/07957-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 304103/2013-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 305341/2015-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Antarctic Regions ; Ascomycota/classification/isolation &amp; purification ; Basidiomycota/classification/isolation &amp; purification ; Bays ; Biodiversity ; Cold Temperature ; Extremophiles ; Fungi/*classification/enzymology/genetics/*isolation &amp; purification ; Geologic Sediments/*microbiology ; Islands ; Lipase/metabolism ; Peptide Hydrolases/metabolism ; Phylogeny ; Seawater/*microbiology ; *Soil Microbiology ; Species Specificity ; }, abstract = {Extreme environments such as the Antarctic can lead to the discovery of new microbial taxa, as well as to new microbial-derived natural products. Considering that little is known yet about the diversity and the genetic resources present in these habitats, the main objective of this study was to evaluate the fungal communities from extreme environments collected at Aldmiralty Bay (Antarctica). A total of 891 and 226 isolates was obtained from soil and marine sediment samples, respectively. The most abundant isolates from soil samples were representatives of the genera Leucosporidium, Pseudogymnoascus, and a non-identified Ascomycota NIA6. Metschnikowia sp. was the most abundant taxon from marine samples, followed by isolates from the genera Penicillium and Pseudogymnoascus. Many of the genera were exclusive in marine sediment or terrestrial samples. However, representatives of eight genera were found in both types of samples. Data from non-metric multidimensional scaling showed that each sampling site is unique in their physical-chemical composition and fungal community. Biotechnological potential in relation to enzymatic production at low/moderate temperatures was also investigated. Ligninolytic enzymes were produced by few isolates from root-associated soil. Among the fungi isolated from marine sediments, 16 yeasts and nine fungi showed lipase activity and three yeasts and six filamentous fungi protease activity. The present study permitted increasing our knowledge on the diversity of fungi that inhabit the Antarctic, finding genera that have never been reported in this environment before and discovering putative new species of fungi.}, }
@article {pmid29915106, year = {2018}, author = {Bryce, C and Franz-Wachtel, M and Nalpas, NC and Miot, J and Benzerara, K and Byrne, JM and Kleindienst, S and Macek, B and Kappler, A}, title = {Proteome Response of a Metabolically Flexible Anoxygenic Phototroph to Fe(II) Oxidation.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {16}, pages = {}, pmid = {29915106}, issn = {1098-5336}, mesh = {Acetates/pharmacology ; Anaerobiosis ; Biochemical Phenomena ; Ferrous Compounds/metabolism/*pharmacology ; Hydrogen/pharmacology ; Iron/metabolism/pharmacology ; *Oxidation-Reduction ; Phototrophic Processes ; *Proteome ; Rhodopseudomonas/*drug effects/growth &amp; development/metabolism ; }, abstract = {The oxidation of Fe(II) by anoxygenic photosynthetic bacteria was likely a key contributor to Earth's biosphere prior to the evolution of oxygenic photosynthesis and is still found in a diverse range of modern environments. All known phototrophic Fe(II) oxidizers can utilize a wide range of substrates, thus making them very metabolically flexible. However, the underlying adaptations required to oxidize Fe(II), a potential stressor, are not completely understood. We used a combination of quantitative proteomics and cryogenic transmission electron microscopy (cryo-TEM) to compare cells of Rhodopseudomonas palustris TIE-1 grown photoautotrophically with Fe(II) or H2 and photoheterotrophically with acetate. We observed unique proteome profiles for each condition, with differences primarily driven by carbon source. However, these differences were not related to carbon fixation but to growth and light harvesting processes, such as pigment synthesis. Cryo-TEM showed stunted development of photosynthetic membranes in photoautotrophic cultures. Growth on Fe(II) was characterized by a response typical of iron homeostasis, which included an increased abundance of proteins required for metal efflux (particularly copper) and decreased abundance of iron import proteins, including siderophore receptors, with no evidence of further stressors, such as oxidative damage. This study suggests that the main challenge facing anoxygenic phototrophic Fe(II) oxidizers comes from growth limitations imposed by autotrophy, and, once this challenge is overcome, iron stress can be mitigated using iron management mechanisms common to diverse bacteria (e.g., by control of iron influx and efflux).IMPORTANCE The cycling of iron between redox states leads to the precipitation and dissolution of minerals, which can in turn impact other major biogeochemical cycles, such as those of carbon, nitrogen, phosphorus and sulfur. Anoxygenic phototrophs are one of the few drivers of Fe(II) oxidation in anoxic environments and are thought to contribute significantly to iron cycling in both modern and ancient environments. These organisms thrive at high Fe(II) concentrations, yet the adaptations required to tolerate the stresses associated with this are unclear. Despite the general consensus that high Fe(II) concentrations pose numerous stresses on these organisms, our study of the large-scale proteome response of a model anoxygenic phototroph to Fe(II) oxidation demonstrates that common iron homeostasis strategies are adequate to manage this. The bulk of the proteome response is not driven by adaptations to Fe(II) stress but to adaptations required to utilize an inorganic carbon source. Such a global overview of the adaptation of these organisms to Fe(II) oxidation provides valuable insights into the physiology of these biogeochemically important organisms and suggests that Fe(II) oxidation may not pose as many challenges to anoxygenic phototrophs as previously thought.}, }
@article {pmid29915105, year = {2018}, author = {Rosenfeld, CE and James, BR and Santelli, CM}, title = {Persistent Bacterial and Fungal Community Shifts Exhibited in Selenium-Contaminated Reclaimed Mine Soils.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {16}, pages = {}, pmid = {29915105}, issn = {1098-5336}, mesh = {Bacteria/*classification ; Biodegradation, Environmental ; DNA, Bacterial/genetics ; Fungi/*classification ; High-Throughput Nucleotide Sequencing ; Idaho ; *Microbiota ; Mining ; *Mycobiome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Selenium/*analysis ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/analysis ; }, abstract = {Mining and other industrial activities worldwide have resulted in Se-enriched surface soils, which pose risks to human and environmental health. Although not well studied, microbial activity can alter Se bioavailability and distribution, even in oxic environments. We used high-throughput sequencing to profile bacterial and fungal communities inhabiting mine soils in southeastern Idaho, comparing mined and unmined locations within two reclaimed phosphate mine areas containing various Se concentrations. The goal was to determine whether microbial communities differed in (i) different mines, (ii) mined areas compared to unmined areas, and (iii) various soil Se concentrations. Though reclamation occurred 20 to 30 years ago, microbial community structures in mined soils were significantly altered compared to unmined soils, suggesting persistent mining-related impacts on soil processes. Additionally, operational taxonomic unit with a 97% sequence similarity cutoff (OTU0.03) richness and diversity were significantly diminished with increasing Se, though not with other geochemical parameters, suggesting that Se contamination shapes communities in favor of Se-tolerant microorganisms. Two bacterial phyla, Actinobacteria and Gemmatimonadetes, were enriched in high-Se soils, while for fungi, Ascomycota dominated all soils regardless of Se concentration. Combining diversity analyses and taxonomic patterns enables us to move toward connecting physiological function of microbial groups to Se biogeochemical cycling in oxic soil environments.IMPORTANCE Selenium contamination in natural environments is of great concern globally, and microbial processes are known to mediate Se transformations. Such transformations alter Se mobility, bioavailability, and toxicity, which can amplify or mitigate Se pollution. To date, nearly all studies investigating Se-microbe interactions have used culture-based approaches with anaerobic bacteria despite growing knowledge that (i) aerobic Se transformations can occur, (ii) such transformations can be mediated by microorganisms other than bacteria, and (iii) microbial community dynamics, rather than individual organismal activities, are important for metal(loid) cycling in natural environments. We examined bacterial and fungal communities in Se-contaminated reclaimed mine soils and found significant declines in diversity at high Se concentrations. Additionally, we identified specific taxonomic groups that tolerate excess Se and may be useful for bioremediation purposes. These patterns were similar across mines of different ages, suggesting that microbial community impacts may persist long after physicochemical parameters indicate complete site recovery.}, }
@article {pmid29913582, year = {2018}, author = {Zhang, S and Sheng, B and Lin, W and Meng, F}, title = {Day/night temperature differences (DNTD) trigger changes in nutrient removal and functional bacteria in membrane bioreactors.}, journal = {The Science of the total environment}, volume = {636}, number = {}, pages = {1202-1210}, doi = {10.1016/j.scitotenv.2018.04.373}, pmid = {29913582}, issn = {1879-1026}, mesh = {Bioreactors/*microbiology ; *Membranes, Artificial ; Microbiota ; Temperature ; Waste Disposal, Fluid/*methods ; Wastewater ; }, abstract = {Temperature is a well-known environmental stress that influences both microbial metabolism and community structure in the biological wastewater treatment systems. In this study, responses of biological performance and sludge microbiota to the long-term day/night temperature differences (DNTD) were investigated in membrane bioreactors (MBRs). The results showed that the functional bacteria could sustained their ecological functions at low DNTD (20/30 °C), resulting in relatively stable performance with respect to nutrient removal. However, when the activated sludge was subjected to a high DNTD (17/33 °C), the effluent concentrations of COD, TN and TP were significantly higher in MBR-B than that in MBR-A. In addition, more severe membrane fouling occurred under the perturbation of high DNTD as revealed by the transmembrane pressure (TMP) profile, which was mainly attributed to the accumulation of extracellular polymeric substances (EPS). The results of 16S rRNA gene sequencing showed that DNTD showed negligible effect on the bacterial community structures. Nonetheless, the functional bacteria responded differently to DNTD, which were in accordance with the bioreactor performances. Specifically, Nitrospina (NOB) and Tetrasphaera (PAOs) appeared to be sensitive to both low and high DNTD. In contrast, a low DNTD showed marginal effects on the denitrifiers, while a high DNTD significantly decreased their abundances. More strikingly, filamentous bulking bacteria were found to be well-adapted to DNTD, indicating their tolerance to the daily temperature fluctuation. This study will advance our knowledge regarding the response of microbial ecology of activated sludge to daily temperature variations in full-scale MBRs.}, }
@article {pmid29912320, year = {2018}, author = {Kumar, V and Thakur, V and Ambika,  and Kumar, S and Singh, D}, title = {Bioplastic reservoir of diverse bacterial communities revealed along altitude gradient of Pangi-Chamba trans-Himalayan region.}, journal = {FEMS microbiology letters}, volume = {365}, number = {14}, pages = {}, doi = {10.1093/femsle/fny144}, pmid = {29912320}, issn = {1574-6968}, mesh = {Acyltransferases/genetics ; Adaptation, Physiological ; *Altitude ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics ; *Biodiversity ; Environmental Microbiology ; Gene Transfer, Horizontal ; India ; Phylogeny ; Polyhydroxyalkanoates/analysis/*biosynthesis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Himalaya hosts a unique environment for microbial ecology. The present study aimed to explore the bioplastic producing bacterial communities along altitude gradient of Pangi-Chamba trans-Himalayan region. A total of 411 bacteria were isolated and 70 characterized at the molecular level for potential polyhydroxyalkanoates (PHA) producers. The most abundant phylum for PHA synthesis was Proteobacteria (73%), followed by Actinobacteria (11%), Firmicutes (10%) and Bacteroidetes (6%). However, at the genus level, Pseudomonas and Janthinobacterium were dominantly reported. Also, the ability to synthesize PHA was reported for the first time for few genera such as Collimonas, Pseudarthrobacter and Paenarthrobacter. Phylogenetic analysis of partial 16S rDNA and phaC genes revealed conservation in phaC and possibility of horizontal gene transfer among distant taxa. Furthermore, GC-MS also confirmed the ability of potential bacterial isolates to synthesize PHA. In fact, we found that PHA-positive bacteria are dominant in the high altitude of Himalaya, suggesting the vital role of PHA in bacterial adaptation and survival. Together, these findings had revealed the rich bacterial diversity and genetic machinery for PHA synthesis which does have potential for further utilization in the commercial applications.}, }
@article {pmid29910792, year = {2018}, author = {Daniel, R and Simon, M and Wemheuer, B}, title = {Editorial: Molecular Ecology and Genetic Diversity of the Roseobacter Clade.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1185}, pmid = {29910792}, issn = {1664-302X}, }
@article {pmid29909752, year = {2020}, author = {Subramaniam, A and Van Der Pol, WJ and Ptacek, T and Lobashevsky, E and Neely, C and Biggio, JR and Lefkowitz, EJ and Morrow, CD and Edwards, RK}, title = {Midtrimester microbial DNA variations in maternal serum of women who experience spontaneous preterm birth.}, journal = {The journal of maternal-fetal &amp; neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians}, volume = {33}, number = {3}, pages = {359-367}, pmid = {29909752}, issn = {1476-4954}, support = {P30 AI027767/AI/NIAID NIH HHS/United States ; P30 AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR001417/TR/NCATS NIH HHS/United States ; UL1 TR003096/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; DNA, Bacterial/*blood ; Female ; Humans ; *Microbiota ; Pregnancy ; Pregnancy Trimester, Second ; Premature Birth/blood/*microbiology ; Retrospective Studies ; Young Adult ; }, abstract = {Objectives: To evaluate if midtrimester maternal serum contains microbial DNA and whether it differs between women with spontaneous preterm birth (SPTB) and those delivering at term.Study design: In this retrospective case-control study, we identified 20 healthy nulliparas with SPTB at 24-33 weeks of a nonanomalous singleton in 2014. Each case was matched by race/ethnicity to a control delivering at 39-40 weeks. Serum samples, collected at 15-20 weeks and stored at -80 C, were thawed and DNA extracted. PCR with primers targeting the 16S rDNA V4 region were used to prepare an amplicon library, sequenced using Illumina MiSeq, and analyzed using quantitative insight into microbial ecology (QIIME). Taxonomy was assigned using Ribosomal Database program (RDP) Classifier (threshold 0.8) against a modified Greengenes database. Differences in number of observed species, microbial alpha-diversity and beta-diversity, and taxa level analyses were undertaken.Results: All 40 samples were included. Women with SPTB had more unique observed species (p = .046) and higher mean alpha-diversity by Shannon index (but not Chao1 or Simpson) (p = .024). Microbial composition was different between groups by Bray-Curtis clustering (p = .03) but not by weighted (p = .13) or unweighted Unifrac (p = .11). Numerous taxa in the Firmicutes, Proteobacteria, and Actinobacteria phyla differed between groups (p < .05).Conclusions: SPTB is associated with distinct microbial DNA changes detected in midtrimester maternal serum.}, }
@article {pmid29905870, year = {2018}, author = {Rodriguez-R, LM and Gunturu, S and Harvey, WT and Rosselló-Mora, R and Tiedje, JM and Cole, JR and Konstantinidis, KT}, title = {The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level.}, journal = {Nucleic acids research}, volume = {46}, number = {W1}, pages = {W282-W288}, pmid = {29905870}, issn = {1362-4962}, mesh = {Classification ; Genetic Variation/genetics ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; *Genomics ; *Internet ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; *Software ; }, abstract = {The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of prokaryotic species and communities but it offers limited resolution at the species and finer levels, and cannot represent the whole-genome diversity and fluidity. To overcome these limitations, we introduced the Microbial Genomes Atlas (MiGA), a webserver that allows the classification of an unknown query genomic sequence, complete or partial, against all taxonomically classified taxa with available genome sequences, as well as comparisons to other related genomes including uncultivated ones, based on the genome-aggregate Average Nucleotide and Amino Acid Identity (ANI/AAI) concepts. MiGA integrates best practices in sequence quality trimming and assembly and allows input to be raw reads or assemblies from isolate genomes, single-cell sequences, and metagenome-assembled genomes (MAGs). Further, MiGA can take as input hundreds of closely related genomes of the same or closely related species (a so-called 'Clade Project') to assess their gene content diversity and evolutionary relationships, and calculate important clade properties such as the pangenome and core gene sets. Therefore, MiGA is expected to facilitate a range of genome-based taxonomic and diversity studies, and quality assessment across environmental and clinical settings. MiGA is available at http://microbial-genomes.org/.}, }
@article {pmid29905791, year = {2018}, author = {Merlino, G and Barozzi, A and Michoud, G and Ngugi, DK and Daffonchio, D}, title = {Microbial ecology of deep-sea hypersaline anoxic basins.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {7}, pages = {}, doi = {10.1093/femsec/fiy085}, pmid = {29905791}, issn = {1574-6941}, mesh = {Anaerobiosis ; Bacteria/*growth &amp; development/*metabolism ; Black Sea ; Ecosystem ; Extremophiles/*physiology ; Gulf of Mexico ; Indian Ocean ; Mediterranean Sea ; Salinity ; Seawater/*microbiology ; Sodium Chloride/analysis ; }, abstract = {Deep hypersaline anoxic basins (DHABs) are unique water bodies occurring within fractures at the bottom of the sea, where the dissolution of anciently buried evaporites created dense anoxic brines that are separated by a chemocline/pycnocline from the overlying oxygenated deep-seawater column. DHABs have been described in the Gulf of Mexico, the Mediterranean Sea, the Black Sea and the Red Sea. They are characterized by prolonged historical separation of the brines from the upper water column due to lack of mixing and by extreme conditions of salinity, anoxia, and relatively high hydrostatic pressure and temperatures. Due to these combined selection factors, unique microbial assemblages thrive in these polyextreme ecosystems. The topological localization of the different taxa in the brine-seawater transition zone coupled with the metabolic interactions and niche adaptations determine the metabolic functioning and biogeochemistry of DHABs. In particular, inherent metabolic strategies accompanied by genetic adaptations have provided insights on how prokaryotic communities can adapt to salt-saturated conditions. Here, we review the current knowledge of the diversity, genomics, metabolisms and ecology of prokaryotes in DHABs.}, }
@article {pmid29904373, year = {2018}, author = {Le Moine Bauer, S and Stensland, A and Daae, FL and Sandaa, RA and Thorseth, IH and Steen, IH and Dahle, H}, title = {Water Masses and Depth Structure Prokaryotic and T4-Like Viral Communities Around Hydrothermal Systems of the Nordic Seas.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1002}, pmid = {29904373}, issn = {1664-302X}, abstract = {The oceanographic features of the Nordic Seas, situated between Iceland and Svalbard, have been extensively studied over the last decades. As well, the Nordic Seas hydrothermal systems situated on the Arctic Mid-Ocean Ridge System have received an increasing interest. However, there is very little knowledge on the microbial communities inhabiting the water column of the Nordic Seas, and nothing is known about the influence of the different water masses and hydrothermal plumes on the microbial community structures. In this study, we aimed at characterizing the impact of hydrothermal plumes on prokaryotic and T4-like viral communities around the island of Jan Mayen. To this end, we used 16S rRNA-gene and g23-gene profiling as well as flow cytometry counts to examine prokaryotic and viral communities in 27 samples obtained from different water masses in this area. While Thaumarchaeota and Marine group II Archaea dominated the waters deeper than 500 m, members of Flavobacteria generally dominated the shallower waters. Furthermore, extensive chemical and physical characteristics of all samples were obtained, including temperature measurements and concentrations of major ions and gases. The effect of these physiochemical variables on the communities was measured by using constrained and unconstrained multivariate analyzes, Mantel tests, network analyzes, phylogenetic analyzes, taxonomic analyzes and temperature-salinity (Θ-S) plots. Our results suggest that hydrothermal activity has little effect on pelagic microbial communities in hydrothermal plumes of the Nordic Seas. However, we provide evidences that observed differences in prokaryotic community structure can largely be attributed to which water mass each sample was taken from. In contrast, depth was the major factor structuring the T4-like viral communities. Our results also show that it is crucial to include water masses when studying the influence of hydrothermal plumes on microbial communities, as it could prevent to falsely associate a change in community structure with the presence of a plume.}, }
@article {pmid29904372, year = {2018}, author = {Guo, X and Zhou, X and Hale, L and Yuan, M and Feng, J and Ning, D and Shi, Z and Qin, Y and Liu, F and Wu, L and He, Z and Van Nostrand, JD and Liu, X and Luo, Y and Tiedje, JM and Zhou, J}, title = {Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {954}, pmid = {29904372}, issn = {1664-302X}, abstract = {Clipping, removal of aboveground plant biomass, is an important issue in grassland ecology. However, few studies have focused on the effect of clipping on belowground microbial communities. Using integrated metagenomic technologies, we examined the taxonomic and functional responses of soil microbial communities to annual clipping (2010-2014) in a grassland ecosystem of the Great Plains of North America. Our results indicated that clipping significantly (P < 0.05) increased root and microbial respiration rates. Annual temporal variation within the microbial communities was much greater than the significant changes introduced by clipping, but cumulative effects of clipping were still observed in the long-term scale. The abundances of some bacterial and fungal lineages including Actinobacteria and Bacteroidetes were significantly (P < 0.05) changed by clipping. Clipping significantly (P < 0.05) increased the abundances of labile carbon (C) degrading genes. More importantly, the abundances of recalcitrant C degrading genes were consistently and significantly (P < 0.05) increased by clipping in the last 2 years, which could accelerate recalcitrant C degradation and weaken long-term soil carbon stability. Furthermore, genes involved in nutrient-cycling processes including nitrogen cycling and phosphorus utilization were also significantly increased by clipping. The shifts of microbial communities were significantly correlated with soil respiration and plant productivity. Intriguingly, clipping effects on microbial function may be highly regulated by precipitation at the interannual scale. Altogether, our results illustrated the potential of soil microbial communities for increased soil organic matter decomposition under clipping land-use practices.}, }
@article {pmid29902436, year = {2018}, author = {Makki, K and Deehan, EC and Walter, J and Bäckhed, F}, title = {The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease.}, journal = {Cell host &amp; microbe}, volume = {23}, number = {6}, pages = {705-715}, doi = {10.1016/j.chom.2018.05.012}, pmid = {29902436}, issn = {1934-6069}, support = {615362/ERC_/European Research Council/International ; }, mesh = {Bacteria/growth &amp; development/metabolism ; Diabetes Mellitus, Type 2 ; Diet ; Dietary Fiber/*metabolism ; Ecology ; Fatty Acids, Volatile/metabolism ; Food Chain ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/metabolism/microbiology ; Humans ; Microbiota ; Obesity ; }, abstract = {Food is a primordial need for our survival and well-being. However, diet is not only essential to maintain human growth, reproduction, and health, but it also modulates and supports the symbiotic microbial communities that colonize the digestive tract-the gut microbiota. Type, quality, and origin of our food shape our gut microbes and affect their composition and function, impacting host-microbe interactions. In this review, we will focus on dietary fibers, which interact directly with gut microbes and lead to the production of key metabolites such as short-chain fatty acids, and discuss how dietary fiber impacts gut microbial ecology, host physiology, and health. Hippocrates' notion "Let food be thy medicine and medicine be thy food" remains highly relevant millennia later, but requires consideration of how diet can be used for modulation of gut microbial ecology to promote health.}, }
@article {pmid29902263, year = {2018}, author = {Bednarz, VN and Naumann, MS and Cardini, U and van Hoytema, N and Rix, L and Al-Rshaidat, MMD and Wild, C}, title = {Contrasting seasonal responses in dinitrogen fixation between shallow and deep-water colonies of the model coral Stylophora pistillata in the northern Red Sea.}, journal = {PloS one}, volume = {13}, number = {6}, pages = {e0199022}, pmid = {29902263}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/*metabolism ; Indian Ocean ; *Nitrogen Fixation ; Photosynthesis ; *Seasons ; }, abstract = {Tropical corals are often associated with dinitrogen (N2)-fixing bacteria (diazotrophs), and seasonal changes in key environmental parameters, such as dissolved inorganic nitrogen (DIN) availability and seawater temperature, are known to affect N2 fixation in coral-microbial holobionts. Despite, then, such potential for seasonal and depth-related changes in N2 fixation in reef corals, such variation has not yet been investigated. Therefore, this study quantified seasonal (winter vs. summer) N2 fixation rates associated with the reef-building coral Stylophora pistillata collected from depths of 5, 10 and 20 m in the northern Gulf of Aqaba (Red Sea). Findings revealed that corals from all depths exhibited the highest N2 fixation rates during the oligotrophic summer season, when up to 11% of their photo-metabolic nitrogen demand (CPND) could be met by N2 fixation. While N2 fixation remained seasonally stable for deep corals (20 m), it significantly decreased for the shallow corals (5 and 10 m) during the DIN-enriched winter season, accounting for less than 2% of the corals' CPND. This contrasting seasonal response in N2 fixation across corals of different depths could be driven by 1) release rates of coral-derived organic matter, 2) the community composition of the associated diazotrophs, and/or 3) nutrient acquisition by the Symbiodinium community.}, }
@article {pmid29899600, year = {2018}, author = {Saha, M and Goecke, F and Bhadury, P}, title = {Minireview: algal natural compounds and extracts as antifoulants.}, journal = {Journal of applied phycology}, volume = {30}, number = {3}, pages = {1859-1874}, pmid = {29899600}, issn = {0921-8971}, abstract = {Marine biofouling is a paramount phenomenon in the marine environment and causes serious problems to maritime industries worldwide. Marine algae are known to produce a wide variety of chemical compounds with antibacterial, antifungal, antialgal, and anti-macrofouling properties, inhibiting the settlement and growth of other marine fouling organisms. Significant investigations and progress have been made in this field in the last two decades and several antifouling extracts and compounds have been isolated from micro- and macroalgae. In this minireview, we have summarized and evaluated antifouling compounds isolated and identified from macroalgae and microalgae between January 2010 and June 2016. Future directions for their commercialization through metabolic engineering and industrial scale up have been discussed. Upon comparing biogeographical regions, investigations from Southeast Asian waters were found to be rather scarce. Thus, we have also discussed the need to conduct more chemical ecology based research in relatively less explored areas with high algal biodiversity like Southeast Asia.}, }
@article {pmid29899517, year = {2018}, author = {Carrión, VJ and Cordovez, V and Tyc, O and Etalo, DW and de Bruijn, I and de Jager, VCL and Medema, MH and Eberl, L and Raaijmakers, JM}, title = {Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils.}, journal = {The ISME journal}, volume = {12}, number = {9}, pages = {2307-2321}, pmid = {29899517}, issn = {1751-7370}, mesh = {Antibiosis ; Burkholderiaceae/classification/genetics/isolation &amp; purification/*metabolism ; Carbon-Sulfur Lyases/genetics ; Ecosystem ; Fungi/physiology ; Iron-Sulfur Proteins/genetics ; Microbial Consortia ; Oxidoreductases/genetics ; Phylogeny ; Plant Diseases/*microbiology ; Soil ; *Soil Microbiology ; Sulfur/*metabolism ; }, abstract = {Disease-suppressive soils are ecosystems in which plants suffer less from root infections due to the activities of specific microbial consortia. The characteristics of soils suppressive to specific fungal root pathogens are comparable to those of adaptive immunity in animals, as reported by Raaijmakers and Mazzola (Science 352:1392-3, 2016), but the mechanisms and microbial species involved in the soil suppressiveness are largely unknown. Previous taxonomic and metatranscriptome analyses of a soil suppressive to the fungal root pathogen Rhizoctonia solani revealed that members of the Burkholderiaceae family were more abundant and more active in suppressive than in non-suppressive soils. Here, isolation, phylogeny, and soil bioassays revealed a significant disease-suppressive activity for representative isolates of Burkholderia pyrrocinia, Paraburkholderia caledonica, P. graminis, P. hospita, and P. terricola. In vitro antifungal activity was only observed for P. graminis. Comparative genomics and metabolite profiling further showed that the antifungal activity of P. graminis PHS1 was associated with the production of sulfurous volatile compounds encoded by genes not found in the other four genera. Site-directed mutagenesis of two of these genes, encoding a dimethyl sulfoxide reductase and a cysteine desulfurase, resulted in a loss of antifungal activity both in vitro and in situ. These results indicate that specific members of the Burkholderiaceae family contribute to soil suppressiveness via the production of sulfurous volatile compounds.}, }
@article {pmid29897884, year = {2018}, author = {Platzer, A and Polzin, J and Rembart, K and Han, PP and Rauer, D and Nussbaumer, T}, title = {BioSankey: Visualization of Microbial Communities Over Time.}, journal = {Journal of integrative bioinformatics}, volume = {15}, number = {4}, pages = {}, pmid = {29897884}, issn = {1613-4516}, mesh = {*Computer Graphics ; Databases, Factual ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; *Microbiota ; *Software ; }, abstract = {Metagenomics provides quantitative measurements for microbial species over time. To obtain a global overview of an experiment and to explore the full potential of a given dataset, intuitive and interactive visualization tools are needed. Therefore, we established BioSankey to visualize microbial species in microbiome studies over time as a Sankey diagram. These diagrams are embedded into a project-specific webpage which depends only on JavaScript and Google API to allow searches of interesting species without requiring a web server or connection to a database. BioSankey is a valuable tool to visualize different data elements from single or dual RNA-seq datasets and additionally enables a straightforward exchange of results among collaboration partners.}, }
@article {pmid29896162, year = {2018}, author = {Haq, IU and Zwahlen, RD and Yang, P and van Elsas, JD}, title = {The Response of Paraburkholderia terrae Strains to Two Soil Fungi and the Potential Role of Oxalate.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {989}, pmid = {29896162}, issn = {1664-302X}, abstract = {Fungal-associated Paraburkholderia terrae strains in soil have been extensively studied, but their sensing strategies to locate fungi in soil have remained largely elusive. In this study, we investigated the behavior of five mycosphere-isolated P. terrae strains [including the type-3 secretion system negative mutant BS001-ΔsctD and the type strain DSM 17804[T]] with respect to their fungal-sensing strategies. The putative role of oxalic acid as a signaling molecule in the chemotaxis toward soil fungi, as well as a potential carbon source, was assessed. First, all P. terrae strains, including the type strain, were found to sense, and show a chemotactic response toward, the different levels of oxalic acid (0.1, 0.5, and 0.8%) applied at a distance. The chemotactic responses were faster and stronger at lower concentrations (0.1%) than at higher ones. We then tested the chemotactic responses of all strains toward exudates of the soil fungi Lyophyllum sp. strain Karsten and Trichoderma asperellum 302 used in different dilutions (undiluted, 1:10, 1:100 diluted) versus the control. All P. terrae strains showed significant directed chemotactic behavior toward the exudate source, with full-strength exudates inciting the strongest responses. In a separate experiment, strain BS001 was shown to be able to grow on oxalate-amended (0.1 and 0.5%) mineral medium M9. Chemical analyses of the fungal secretomes using proton nuclear magnetic resonance ([1]H NMR), next to high-performance liquid chromatography (HPLC), indeed revealed the presence of oxalic acid (next to glycerol, acetic acid, formic acid, and fumaric acid) in the supernatants of both fungi. In addition, citric acid was found in the Lyophyllum sp. strain Karsten exudates. Given the fact that, next to oxalic acid, the other compounds can also serve as C and energy sources for P. terrae, the two fungi clearly offer ecological benefits to this bacterium. The oxalic acid released by the two fungi may have primarily acted as a signaling molecule, and, as a "second option," a carbon source for P. terrae strains like BS001.}, }
@article {pmid29893876, year = {2018}, author = {Algya, KM and Cross, TL and Leuck, KN and Kastner, ME and Baba, T and Lye, L and de Godoy, MRC and Swanson, KS}, title = {Apparent total-tract macronutrient digestibility, serum chemistry, urinalysis, and fecal characteristics, metabolites and microbiota of adult dogs fed extruded, mildly cooked, and raw diets1.}, journal = {Journal of animal science}, volume = {96}, number = {9}, pages = {3670-3683}, pmid = {29893876}, issn = {1525-3163}, mesh = {Ammonia/metabolism ; *Animal Feed ; Animal Nutritional Physiological Phenomena ; Animals ; *Cooking ; Diet/veterinary ; *Digestion ; *Dogs/physiology ; Feces/chemistry ; *Gastrointestinal Tract/metabolism ; Male ; Microbiota ; Nutrients ; *Raw Foods ; Urinalysis ; }, abstract = {Despite their popularity, little research has been performed on lightly cooked and raw diet formats for pets. Therefore, the objective of this study was to determine the apparent total-tract macronutrient digestibility (ATTD); fecal characteristics, metabolites, and microbiota; serum chemistry metabolites; urinalysis; and voluntary physical activity levels of adult dogs fed commercial diets differing in processing type. The diets included: 1) extruded dry kibble (EXT) diet; 2) high-moisture roasted refrigerated (RR) diet; 3) high-moisture grain-free roasted refrigerated (GFRR) diet; and 4) raw (RAW) diet. Eight dogs (mean age = 3.6; mean BW = 13.0 kg) were used in a replicated 4 × 4 Latin square design. Each period consisted of 28 d, with a 14-d adaptation phase followed by a 7-d phase for measuring voluntary physical activity, 1-d adaptation phase to metabolic cages, 5-d phase for fecal and urine collection, and 1 d for blood collection. Except for microbiota, all data were analyzed statistically by mixed models using SAS. Microbiota data were analyzed using Quantitative Insights Into Microbial Ecology (QIIME) and Statistical Analyses of Metagenomic Profiles (STAMP) software. Many differences in digestibility were observed, including greater (P < 0.05) ATTD of CP and fat in dogs fed GFRR and RR than dogs fed EXT. Dogs fed RAW had the lowest fecal pH and DM %, but fecal scores were not affected. Dogs fed RR had higher (P < 0.05) fecal indole and total phenol and indole concentrations than dogs fed the other diets. Dogs fed RAW had a higher (P < 0.05) fecal ammonia concentration than dogs fed the other diets. Fecal microbial diversity was altered by diet, with dogs fed GFRR and RAW having reduced species richness than dogs fed EXT. Dogs fed RR, GFRR, or RAW had lower (P < 0.05) Actinobacteria and higher (P < 0.05) Fusobacteria than dogs fed EXT. Dogs fed RAW or GFRR had higher (P < 0.05) Proteobacteria than dogs fed EXT or RR. Dogs fed RAW had higher (P < 0.05) Bacteroidetes and lower (P < 0.05) Firmicutes than dogs fed EXT. Serum triglycerides were within reference ranges, but greater (P < 0.05) in dogs fed EXT than dogs fed GFRR and RAW. All diets were well tolerated and dogs remained healthy throughout the study. In conclusion, the lightly cooked and raw diets tested were highly palatable, highly digestible, reduced blood triglycerides, maintained fecal quality and serum chemistry, and modified the fecal microbial community of healthy adult dogs.}, }
@article {pmid29892374, year = {2018}, author = {Harrison, JP and Boardman, C and O'Callaghan, K and Delort, AM and Song, J}, title = {Biodegradability standards for carrier bags and plastic films in aquatic environments: a critical review.}, journal = {Royal Society open science}, volume = {5}, number = {5}, pages = {171792}, pmid = {29892374}, issn = {2054-5703}, abstract = {Plastic litter is encountered in aquatic ecosystems across the globe, including polar environments and the deep sea. To mitigate the adverse societal and ecological impacts of this waste, there has been debate on whether 'biodegradable' materials should be granted exemptions from plastic bag bans and levies. However, great care must be exercised when attempting to define this term, due to the broad and complex range of physical and chemical conditions encountered within natural ecosystems. Here, we review existing international industry standards and regional test methods for evaluating the biodegradability of plastics within aquatic environments (wastewater, unmanaged freshwater and marine habitats). We argue that current standards and test methods are insufficient in their ability to realistically predict the biodegradability of carrier bags in these environments, due to several shortcomings in experimental procedures and a paucity of information in the scientific literature. Moreover, existing biodegradability standards and test methods for aquatic environments do not involve toxicity testing or account for the potentially adverse ecological impacts of carrier bags, plastic additives, polymer degradation products or small (microscopic) plastic particles that can arise via fragmentation. Successfully addressing these knowledge gaps is a key requirement for developing new biodegradability standard(s) for lightweight carrier bags.}, }
@article {pmid29892072, year = {2018}, author = {Krause, SMB and Meima-Franke, M and Veraart, AJ and Ren, G and Ho, A and Bodelier, PLE}, title = {Environmental legacy contributes to the resilience of methane consumption in a laboratory microcosm system.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8862}, pmid = {29892072}, issn = {2045-2322}, mesh = {Bacteria, Aerobic/*growth &amp; development/*metabolism ; Biodiversity ; Biomass ; Climate Change ; Droughts ; Methane/*metabolism ; *Microbiota ; Soil ; *Soil Microbiology ; Water ; *Water Microbiology ; }, abstract = {The increase of extreme drought and precipitation events due to climate change will alter microbial processes. Perturbation experiments demonstrated that microbes are sensitive to environmental alterations. However, only little is known on the legacy effects in microbial systems. Here, we designed a laboratory microcosm experiment using aerobic methane-consuming communities as a model system to test basic principles of microbial resilience and the role of changes in biomass and the presence of non-methanotrophic microbes in this process. We focused on enrichments from soil, sediment, and water reflecting communities with different legacy with respect to exposure to drought. Recovery rates, a recently proposed early warning indicator of a critical transition, were utilized as a measure to detect resilience loss of methane consumption during a series of dry/wet cycle perturbations. We observed a slowed recovery of enrichments originating from water samples, which suggests that the community's legacy with a perturbation is a contributing factor for the resilience of microbial functioning.}, }
@article {pmid29891000, year = {2018}, author = {Lammel, DR and Barth, G and Ovaskainen, O and Cruz, LM and Zanatta, JA and Ryo, M and de Souza, EM and Pedrosa, FO}, title = {Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {106}, pmid = {29891000}, issn = {2049-2618}, support = {1273253/284601/273253//Academy of Finland/International ; 223257//Norges Forskningsr&#xe5;d/International ; }, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Base Sequence ; Brazil ; Ecological and Environmental Phenomena/*physiology ; Greenhouse Gases/analysis ; High-Throughput Nucleotide Sequencing ; Hydrogen-Ion Concentration ; Proton-Motive Force/*physiology ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {BACKGROUND: pH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to "spillover effects" on other chemical parameters (e.g., availability of Al, Fe, Mn, Zn, and Cu) and plant growth, but these indirect effects on the microbial communities are rarely investigated. Usually, pH also co-varies with some confounding factors, such as land use, soil management (e.g., tillage and chemical inputs), plant cover, and/or edapho-climatic conditions. So, a more comprehensive analysis of the direct and indirect effects of pH brings a better understanding of the mechanisms driving prokaryotic (archaeal and bacterial) community structures.<br><br>RESULTS: We evaluated an agricultural soil pH gradient (from 4 to 6, the typical range for tropical farms), in a liming gradient with confounding factors minimized, investigating relationships between prokaryotic communities (16S rRNA) and physical-chemical parameters (indirect effects). Correlations, hierarchical modeling of species communities (HMSC), and random forest (RF) modeling indicated that both direct and indirect effects of the pH gradient affected the prokaryotic communities. Some OTUs were more affected by the pH changes (e.g., some Actinobacteria), while others were more affected by the indirect pH effects (e.g., some Proteobacteria). HMSC detected a phylogenetic signal related to the effects. Both HMSC and RF indicated that the main indirect effect was the pH changes on the availability of some elements (e.g., Al, Fe, and Cu), and secondarily, effects on plant growth and nutrient cycling also affected the OTUs. Additionally, we found that some of the OTUs that responded to pH also correlated with CO2, CH4, and N2O greenhouse gas fluxes.<br><br>CONCLUSIONS: Our results indicate that there are two distinct pH-related mechanisms driving prokaryotic community structures, the direct effect and "spillover effects" of pH (indirect effects). Moreover, the indirect effects are highly relevant for some OTUs and consequently for the community structure; therefore, it is a mechanism that should be further investigated in microbial ecology.}, }
@article {pmid29888841, year = {2018}, author = {Alster, CJ and Weller, ZD and von Fischer, JC}, title = {A meta-analysis of temperature sensitivity as a microbial trait.}, journal = {Global change biology}, volume = {24}, number = {9}, pages = {4211-4224}, doi = {10.1111/gcb.14342}, pmid = {29888841}, issn = {1365-2486}, mesh = {*Bacterial Physiological Phenomena ; Fungi/*physiology ; Hot Temperature/*adverse effects ; Models, Biological ; Temperature ; }, abstract = {Traits-based approaches in microbial ecology provide a valuable way to abstract organismal interaction with the environment and to generate hypotheses about community function. Using macromolecular rate theory (MMRT), we recently identified that temperature sensitivity can be characterized as a distinct microbial trait. As temperature is fundamental in controlling biological reactions, variation in temperature sensitivity across communities, organisms, and processes has the potential to vastly improve understanding of microbial response to climate change. These microbial temperature sensitivity traits include the heat capacity (ΔCP‡), temperature optimum (Topt), and point of maximum temperature sensitivity (TSmax), each of which provide unique insights about organismal response to changes in temperature. In this meta-analysis, we analyzed the distribution of these temperature sensitivity traits from bacteria, fungi, and mixed communities across a variety of biological systems (e.g., soils, oceans, foods, wastewater treatment plants) in order to identify commonalities in temperature responses across these diverse organisms and reaction rates. Our analysis of temperature sensitivity traits from over 350 temperature response curves reveals a wide distribution of temperature sensitivity traits, with Topt and TSmax well within biological relevant temperatures. We find that traits vary significantly depending on organism type, microbial diversity, source environment, and biological process, with higher temperature sensitivity found in fungi than bacteria and in less diverse systems. Carbon dioxide production was found to be less temperature sensitive than denitrification, suggesting that changes in temperature will have a potentially larger impact on nitrogen-related processes. As climate changes, these results have important implications for basic understanding of the temperature sensitivity of biological reactions and for ecological understanding of species' trait distributions, as well as for improved treatment of temperature sensitivity in models.}, }
@article {pmid29887367, year = {2018}, author = {Acosta, N and De Vrieze, J and Sandoval, V and Sinche, D and Wierinck, I and Rabaey, K}, title = {Cocoa residues as viable biomass for renewable energy production through anaerobic digestion.}, journal = {Bioresource technology}, volume = {265}, number = {}, pages = {568-572}, doi = {10.1016/j.biortech.2018.05.100}, pmid = {29887367}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Biofuels ; Biological Oxygen Demand Analysis ; Biomass ; Bioreactors ; Methane/*biosynthesis ; *Renewable Energy ; }, abstract = {The aim of this work was to evaluate the bioenergy potential of cocoa residue via anaerobic digestion. Batch and fed-batch lab-scale reactors were operated under low and high solids conditions. In the batch tests, 59 ± 4% of Chemical Oxygen Demand (COD) was recovered as methane. This corresponded with an average methane yield of 174 (wet) and 193 (dry) L kg[-1] volatile solids fed, whereas a series of fed-batch reactors produced 70 ± 24 (wet) and 107 ± 39 (dry) L CH4 kg[-1] volatile solids fed during stable conditions. A case study was developed for canton Balao (Ecuador) based on our experimental data, operational estimates and available cocoa waste in the area. Annually, 8341 MWh could be produced, meeting 88% of the current electricity demand in Balao. This case study proves the potential for cocoa waste as a source of renewable energy in rural areas.}, }
@article {pmid29886983, year = {2018}, author = {Xu, G and Zhong, X and Al, MA and Warren, A and Xu, H}, title = {Identifying bioindicators across trait-taxon space for assessing water quality in marine environments.}, journal = {Marine pollution bulletin}, volume = {131}, number = {Pt A}, pages = {565-571}, doi = {10.1016/j.marpolbul.2018.04.044}, pmid = {29886983}, issn = {1879-3363}, mesh = {Biological Oxygen Demand Analysis ; China ; Ciliophora ; *Environmental Biomarkers ; Environmental Monitoring/*methods ; Seasons ; *Seawater ; Water Pollution ; *Water Quality ; }, abstract = {The response units of protozoan communities, based on a community-weighted mean (CWM) dataset across trait-taxon space, were investigated in order to determine their utility as bioindicators of marine water quality. From a total of 17 functional categories of seven biological traits, three functional response units (FRUs) were identified at correlation levels of >0.75. FRUs 1 and 3 generally dominated the communities in more polluted areas during warm seasons, while FRU2 appeared to prefer less polluted waters and dominated the communities in spring and winter. Correlation analysis demonstrated that the CWM values of FRUs 1 and 3 were significantly positively correlated to the concentrations of chemical oxygen demand (COD), whereas those of FRU2 were negatively correlated to COD. Across taxon-function space, 16 species were identified as potential bioindicators of water quality. These results suggest that redundancy analysis across trait-taxon space is a useful tool for identifying indicators of environmental quality.}, }
@article {pmid29884244, year = {2018}, author = {Liu, X and Li, M and Castelle, CJ and Probst, AJ and Zhou, Z and Pan, J and Liu, Y and Banfield, JF and Gu, JD}, title = {Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {102}, pmid = {29884244}, issn = {2049-2618}, support = {41506163//National Natural Science Foundation of China/International ; 31622002//National Natural Science Foundation of China/International ; 3160010182//National Natural Science Foundation of China/International ; }, mesh = {Archaea/*classification/genetics/*metabolism ; Ecosystem ; *Evolution, Molecular ; Genome, Archaeal/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: As a recently discovered member of the DPANN superphylum, Woesearchaeota account for a wide diversity of 16S rRNA gene sequences, but their ecology, evolution, and metabolism remain largely unknown.<br><br>RESULTS: Here, we assembled 133 global clone libraries/studies and 19 publicly available genomes to profile these patterns for Woesearchaeota. Phylogenetic analysis shows a high diversity with 26 proposed subgroups for this recently discovered archaeal phylum, which are widely distributed in different biotopes but primarily in inland anoxic environments. Ecological patterns analysis and ancestor state reconstruction for specific subgroups reveal that oxic status of the environments is the key factor driving the distribution and evolutionary diversity of Woesearchaeota. A selective distribution to different biotopes and an adaptive colonization from anoxic to oxic environments can be proposed and supported by evidence of the presence of ferredoxin-dependent pathways in the genomes only from anoxic biotopes but not from oxic biotopes. Metabolic reconstructions support an anaerobic heterotrophic lifestyle with conspicuous metabolic deficiencies, suggesting the requirement for metabolic complementarity with other microbes. Both lineage abundance distribution and co-occurrence network analyses across diverse biotopes confirmed metabolic complementation and revealed a potential syntrophic relationship between Woesearchaeota and methanogens, which is supported by metabolic modeling. If correct, Woesearchaeota may impact methanogenesis in inland ecosystems.<br><br>CONCLUSIONS: The findings provide an ecological and evolutionary framework for Woesearchaeota at a global scale and indicate their potential ecological roles, especially in methanogenesis.}, }
@article {pmid29882155, year = {2019}, author = {Mikhailov, IS and Zakharova, YR and Bukin, YS and Galachyants, YP and Petrova, DP and Sakirko, MV and Likhoshway, YV}, title = {Co-occurrence Networks Among Bacteria and Microbial Eukaryotes of Lake Baikal During a Spring Phytoplankton Bloom.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {96-109}, pmid = {29882155}, issn = {1432-184X}, support = {0345-2016-0005//Federal Agency of Scientific Organizations of Russia/ ; 0345-2016-0001//Federal Agency of Scientific Organizations of Russia/ ; }, mesh = {Bacteria/*classification/genetics ; Bacterial Physiological Phenomena ; Cluster Analysis ; Ecosystem ; Eukaryota/*classification/physiology ; Fresh Water ; Lakes/*microbiology ; *Microbiota ; Phylogeny ; Phytoplankton/*growth &amp; development ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Seasons ; }, abstract = {The pelagic zone of Lake Baikal is an ecological niche where phytoplankton bloom causes increasing microbial abundance in spring which plays a key role in carbon turnover in the freshwater lake. Co-occurrence patterns revealed among different microbes can be applied to predict interactions between the microbes and environmental conditions in the ecosystem. We used 454 pyrosequencing of 16S rRNA and 18S rRNA genes to study bacterial and microbial eukaryotic communities and their co-occurrence patterns at the pelagic zone of Lake Baikal during a spring phytoplankton bloom. We found that microbes within one domain mostly correlated positively with each other and are highly interconnected. The highly connected taxa in co-occurrence networks were operational taxonomic units (OTUs) of Actinobacteria, Bacteroidetes, Alphaproteobacteria, and autotrophic and unclassified Eukaryota which might be analogous to microbial keystone taxa. Constrained correspondence analysis revealed the relationships of bacterial and microbial eukaryotic communities with geographical location.}, }
@article {pmid29882154, year = {2019}, author = {Kerfahi, D and Tripathi, BM and Dong, K and Kim, M and Kim, H and Ferry Slik, JW and Go, R and Adams, JM}, title = {From the High Arctic to the Equator: Do Soil Metagenomes Differ According to Our Expectations?.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {168-185}, pmid = {29882154}, issn = {1432-184X}, support = {0409-20140091//Korea Polar Research Institute/ ; NRF-0409-20150076//National Research Foundation of Korea/ ; }, mesh = {Arctic Regions ; Bacteria/genetics/metabolism ; Biodiversity ; Biota/*genetics/*physiology ; Brunei ; Canada ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; DNA Barcoding, Taxonomic ; Ecosystem ; Eukaryota/genetics/metabolism ; Greenland ; Hydrogen-Ion Concentration ; Malaysia ; Metabolic Networks and Pathways/genetics ; Metagenome/*genetics/*physiology ; Metagenomics/methods ; Microbiota/genetics/physiology ; Rainforest ; Secondary Metabolism/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; Stress, Physiological ; Svalbard ; }, abstract = {Comparing the functional gene composition of soils at opposite extremes of environmental gradients may allow testing of hypotheses about community and ecosystem function. Here, we were interested in comparing how tropical microbial ecosystems differ from those of polar climates. We sampled several sites in the equatorial rainforest of Malaysia and Brunei, and the high Arctic of Svalbard, Canada, and Greenland, comparing the composition and the functional attributes of soil biota between the two extremes of latitude, using shotgun metagenomic Illumina HiSeq2000 sequencing. Based upon "classical" views of how tropical and higher latitude ecosystems differ, we made a series of predictions as to how various gene function categories would differ in relative abundance between tropical and polar environments. Results showed that in some respects our predictions were correct: the polar samples had higher relative abundance of dormancy related genes, and lower relative abundance of genes associated with respiration, and with metabolism of aromatic compounds. The network complexity of the Arctic was also lower than the tropics. However, in various other respects, the pattern was not as predicted; there were no differences in relative abundance of stress response genes or in genes associated with secondary metabolism. Conversely, CRISPR genes, phage-related genes, and virulence disease and defense genes, were unexpectedly more abundant in the Arctic, suggesting more intense biotic interaction. Also, eukaryote diversity and bacterial diversity were higher in the Arctic of Svalbard compared to tropical Brunei, which is consistent with what may expected from amplicon studies in terms of the higher pH of the Svalbard soil. Our results in some respects confirm expectations of how tropical versus polar nature may differ, and in other respects challenge them.}, }
@article {pmid29880912, year = {2018}, author = {Mo, Y and Zhang, W and Yang, J and Lin, Y and Yu, Z and Lin, S}, title = {Biogeographic patterns of abundant and rare bacterioplankton in three subtropical bays resulting from selective and neutral processes.}, journal = {The ISME journal}, volume = {12}, number = {9}, pages = {2198-2210}, pmid = {29880912}, issn = {1751-7370}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Bays ; China ; High-Throughput Nucleotide Sequencing ; Microbiota ; Phylogeography ; Plankton/*classification/genetics/isolation &amp; purification ; *Water Microbiology ; }, abstract = {Unraveling the relative importance of ecological processes regulating microbial community structure is a central goal in microbial ecology. Here, we used high-throughput sequencing to examine the relative contribution of selective and neutral processes in the assembly of abundant and rare subcommunities from three subtropical bays of China. We found that abundant and rare bacterial taxa were distinctly different in diversity, despite the similar biogeographic patterns and strong distance-decay relationships, but the dispersal of rare bacterial taxa was more limited than that of abundant taxa. Furthermore, the environmental (selective processes) and spatial (neutral processes) factors seemed to govern the assembly and biogeography of abundant and rare bacterial subcommunities, although both factors explained only a small fraction of variation within the rare subcommunity. More importantly, variation partitioning (based on adjusted R[2] in redundancy analysis) showed that spatial factors exhibited a slightly greater influence on both abundant and rare subcommunities compared to environmental selection; however, the abundant subcommunity had a much stronger response to spatial factors (17.3% of pure variance was explained) than that shown by the rare bacteria (3.5%). These results demonstrate that environmental selection and neutral processes explained the similar biogeographic patterns of abundant and rare subcommunities, but a large proportion of unexplained variation in the rare taxa (91.1%) implies that more complex assembly mechanisms may exist to shape the rare bacterial assemblages in the three subtropical bays.}, }
@article {pmid29878056, year = {2018}, author = {Martinez-Vernon, AS and Farrell, F and Soyer, OS}, title = {MetQy-an R package to query metabolic functions of genes and genomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {23}, pages = {4134-4137}, pmid = {29878056}, issn = {1367-4811}, support = {BB/K003240/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M017982/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Computational Biology ; Genome ; Genomics ; Metabolic Networks and Pathways/*genetics ; *Metagenomics ; *Software ; }, abstract = {SUMMARY: With the rapid accumulation of sequencing data from genomic and metagenomic studies, there is an acute need for better tools that facilitate their analyses against biological functions. To this end, we developed MetQy, an open-source R package designed for query-based analysis of functional units in [meta]genomes and/or sets of genes using the The Kyoto Encyclopedia of Genes and Genomes (KEGG). Furthermore, MetQy contains visualization and analysis tools and facilitates KEGG's flat file manipulation. Thus, MetQy enables better understanding of metabolic capabilities of known genomes or user-specified [meta]genomes by using the available information and can help guide studies in microbial ecology, metabolic engineering and synthetic biology.<br><br>The MetQy R package is freely available and can be downloaded from our group's website (http://osslab.lifesci.warwick.ac.uk) or GitHub (https://github.com/OSS-Lab/MetQy).}, }
@article {pmid29876609, year = {2019}, author = {Weiss, H and Hertzberg, VS and Dupont, C and Espinoza, JL and Levy, S and Nelson, K and Norris, S and , }, title = {The Airplane Cabin Microbiome.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {87-95}, pmid = {29876609}, issn = {1432-184X}, support = {2001-041-1//The Boeing Company/ ; }, mesh = {*Air Microbiology ; Air Pollution, Indoor/analysis ; Air Travel ; *Aircraft ; Bacteria/*classification/genetics ; Biodiversity ; Communicable Diseases/microbiology/transmission ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Respiratory Tract Infections/microbiology ; }, abstract = {Serving over three billion passengers annually, air travel serves as a conduit for infectious disease spread, including emerging infections and pandemics. Over two dozen cases of in-flight transmissions have been documented. To understand these risks, a characterization of the airplane cabin microbiome is necessary. Our study team collected 229 environmental samples on ten transcontinental US flights with subsequent 16S rRNA sequencing. We found that bacterial communities were largely derived from human skin and oral commensals, as well as environmental generalist bacteria. We identified clear signatures for air versus touch surface microbiome, but not for individual types of touch surfaces. We also found large flight-to-flight beta diversity variations with no distinguishing signatures of individual flights, rather a high between-flight diversity for all touch surfaces and particularly for air samples. There was no systematic pattern of microbial community change from pre- to post-flight. Our findings are similar to those of other recent studies of the microbiome of built environments. In summary, the airplane cabin microbiome has immense airplane to airplane variability. The vast majority of airplane-associated microbes are human commensals or non-pathogenic, and the results provide a baseline for non-crisis-level airplane microbiome conditions.}, }
@article {pmid29876608, year = {2019}, author = {Suffert, F and Delestre, G and Gélisse, S}, title = {Sexual Reproduction in the Fungal Foliar Pathogen Zymoseptoria tritici Is Driven by Antagonistic Density Dependence Mechanisms.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {110-123}, pmid = {29876608}, issn = {1432-184X}, support = {634179//Horizon 2020 Framework Programme (EMPHASIS)/ ; }, mesh = {Ascomycota/*genetics/growth &amp; development/*pathogenicity ; Evolution, Molecular ; Genetic Fitness ; Host-Pathogen Interactions/*genetics ; Plant Diseases/*microbiology ; *Reproduction ; Spores, Fungal/genetics/growth &amp; development ; Triticum/microbiology ; Virulence ; }, abstract = {This study provides empirical evidence for antagonistic density dependence mechanisms driving sexual reproduction in the wheat fungal pathogen Zymoseptoria tritici. Biparental crosses with 12 increasing inoculum concentrations, in controlled conditions, showed that sexual reproduction in Z. tritici was impacted by an Allee effect due to mate limitation and a competition with asexual multiplication for resource allocation. The highest number of ascospores discharged was reached at intermediate inoculum concentrations (from 5 × 10[4] conidia mL[-1] to 10[6] conidia mL[-1]). Consistent with these results for controlled co-inoculation, we found that the intensity of sexual reproduction varied with both cropping period and the vertical position of the host tissues in the field, with a maximum between 25 and 35 cm above the ground. An optimal lesion density (disease severity of 30 to 45%) maximizing offspring (ascospores) number was established, and its eco-evolutionary consequences are considered here. Two ecological mechanisms may be involved: competition for resources between the two modes of reproduction (decrease in the host resources available for sexual reproduction due to their prior use in asexual multiplication), and competitive disequilibrium between the two parental isolates, due to differential interaction dynamics with the host, for example, leading to an imbalance between mating types. A conceptual model based on these results suggests that sexual reproduction plays a key role in the evolution of pathogenicity traits, including virulence and aggressiveness. Ecological knowledge about the determinants of sexual reproduction in Z. tritici may, therefore, open up new perspectives for the management of other fungal foliar pathogens with dual modes of reproduction.}, }
@article {pmid29875749, year = {2018}, author = {Rapp, JZ and Fernández-Méndez, M and Bienhold, C and Boetius, A}, title = {Effects of Ice-Algal Aggregate Export on the Connectivity of Bacterial Communities in the Central Arctic Ocean.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1035}, pmid = {29875749}, issn = {1664-302X}, support = {294757/ERC_/European Research Council/International ; }, abstract = {In summer 2012, Arctic sea ice declined to a record minimum and, as a consequence of the melting, large amounts of aggregated ice-algae sank to the seafloor at more than 4,000 m depth. In this study, we assessed the composition, turnover and connectivity of bacterial and microbial eukaryotic communities across Arctic habitats from sea ice, algal aggregates and surface waters to the seafloor. Eukaryotic communities were dominated by diatoms, dinoflagellates and other alveolates in all samples, and showed highest richness and diversity in sea-ice habitats (∼400-500 OTUs). Flavobacteriia and Gammaproteobacteria were the predominant bacterial classes across all investigated Arctic habitats. Bacterial community richness and diversity peaked in deep-sea samples (∼1,700 OTUs). Algal aggregate-associated bacterial communities were mainly recruited from the sea-ice community, and were transported to the seafloor with the sinking ice algae. The algal deposits at the seafloor had a unique community structure, with some shared sequences with both the original sea-ice community (22% OTU overlap), as well as with the deep-sea sediment community (17% OTU overlap). We conclude that ice-algal aggregate export does not only affect carbon export from the surface to the seafloor, but may change microbial community composition in central Arctic habitats with potential effects for benthic ecosystem functioning in the future.}, }
@article {pmid29875400, year = {2018}, author = {Harrison, CA and Laubitz, D and Ohland, CL and Midura-Kiela, MT and Patil, K and Besselsen, DG and Jamwal, DR and Jobin, C and Ghishan, FK and Kiela, PR}, title = {Microbial dysbiosis associated with impaired intestinal Na[+]/H[+] exchange accelerates and exacerbates colitis in ex-germ free mice.}, journal = {Mucosal immunology}, volume = {11}, number = {5}, pages = {1329-1341}, pmid = {29875400}, issn = {1935-3456}, support = {R01 DK041274/DK/NIDDK NIH HHS/United States ; R01 DK073338/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteroidaceae/immunology ; Colitis/*metabolism ; Dysbiosis/immunology/*metabolism/microbiology ; Epithelial Cells/immunology/metabolism/microbiology ; Female ; Firmicutes/immunology ; Gastrointestinal Microbiome/*immunology ; Germ-Free Life ; Hydrogen-Ion Concentration ; Immunity/immunology ; Inflammation/immunology/metabolism/microbiology ; Inflammatory Bowel Diseases/immunology/metabolism/microbiology ; Interleukin-10/metabolism ; Intestinal Mucosa/immunology/metabolism/microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Sodium-Hydrogen Exchanger 3/metabolism ; Sodium-Hydrogen Exchangers/*metabolism ; }, abstract = {Intestinal epithelial Na[+]/H[+] exchange facilitated by the apical NHE3 (Slc9a3) is a highly regulated process inhibited by intestinal pathogens and in inflammatory bowel diseases. NHE3[-/-] mice develop spontaneous, bacterially mediated colitis, and IBD-like dysbiosis. Disruption of epithelial Na[+]/H[+] exchange in IBD may thus represent a host response contributing to the altered gut microbial ecology, and may play a pivotal role in modulating the severity of inflammation in a microbiome-dependent manner. To test whether microbiome fostered in an NHE3-deficient environment is able to drive mucosal immune responses affecting the onset or severity of colitis, we performed a series of cohousing experiments and fecal microbiome transplants into germ-free Rag-deficient or IL-10[-/-] mice. We determined that in the settings where the microbiome of NHE3-deficient mice was stably engrafted in the recipient host, it was able accelerate the onset and amplify severity of experimental colitis. NHE3-deficiency was characterized by the reduction in pH-sensitive butyrate-producing Firmicutes families Lachnospiraceae and Ruminococcaceae (Clostridia clusters IV and XIVa), with an expansion of inflammation-associated Bacteroidaceae. We conclude that the microbiome fostered by impaired epithelial Na[+]/H[+] exchange enhances the onset and severity of colitis through disruption of the gut microbial ecology.}, }
@article {pmid29868846, year = {2019}, author = {Sankaran, K and Holmes, SP}, title = {Latent variable modeling for the microbiome.}, journal = {Biostatistics (Oxford, England)}, volume = {20}, number = {4}, pages = {599-614}, pmid = {29868846}, issn = {1468-4357}, support = {R01 AI112401/AI/NIAID NIH HHS/United States ; T32 GM096982/GM/NIGMS NIH HHS/United States ; }, mesh = {Biostatistics/*methods ; Humans ; *Microbiota ; *Models, Statistical ; }, abstract = {The human microbiome is a complex ecological system, and describing its structure and function under different environmental conditions is important from both basic scientific and medical perspectives. Viewed through a biostatistical lens, many microbiome analysis goals can be formulated as latent variable modeling problems. However, although probabilistic latent variable models are a cornerstone of modern unsupervised learning, they are rarely applied in the context of microbiome data analysis, in spite of the evolutionary, temporal, and count structure that could be directly incorporated through such models. We explore the application of probabilistic latent variable models to microbiome data, with a focus on Latent Dirichlet allocation, Non-negative matrix factorization, and Dynamic Unigram models. To develop guidelines for when different methods are appropriate, we perform a simulation study. We further illustrate and compare these techniques using the data of Dethlefsen and Relman (2011, Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proceedings of the National Academy of Sciences108, 4554-4561), a study on the effects of antibiotics on bacterial community composition. Code and data for all simulations and case studies are available publicly.}, }
@article {pmid29867972, year = {2018}, author = {Malik, S and Awasthi, A}, title = {Transcriptional Control of Th9 Cells: Role of Foxo1 in Interleukin-9 Induction.}, journal = {Frontiers in immunology}, volume = {9}, number = {}, pages = {995}, pmid = {29867972}, issn = {1664-3224}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Cell Differentiation ; Clinical Trials as Topic ; Forkhead Box Protein O1/*genetics ; Gene Expression Regulation ; Humans ; Interleukin-9/*genetics ; Mice ; Signal Transduction ; T-Lymphocytes, Helper-Inducer/*immunology ; T-Lymphocytes, Regulatory/immunology ; Th17 Cells/immunology ; Th2 Cells/immunology ; *Transcription, Genetic ; }, abstract = {Interleukin (IL) 9-producing helper T (Th) 9 cells play a major role in contributing immunity against extracellular pathogens. In addition, the role of Th9 cells was demonstrated in the pathogenesis of allergic, skin, and intestinal inflammation. The functions of Th9 cells were further extended in antitumor immune response, as Th9 cells were suggested to be potent antitumor Th cells. Given the pleotropic functions of IL-9 in various pathophysiological conditions, it is essential to understand the differentiation and stability of Th9 cells and other IL-9-producing T cells. In addition to Th9 cells, Th2 and Th17 cells as well as induced Foxp3[+] regulatory T cells (iTregs) cells also produce IL-9, but how IL-9 production is regulated in these cell types is not yet clearly defined. Although Th2, Th9 and Th17 cells as well as iTregs develop in the presence of distinct differentiating factors, yet they all express IL-9 together with their own lineage specific cytokines. Here, in this review, we summarize the current understanding of signaling pathways that lead to the promotion of differentiation of Th9 cells and IL-9 induction in Th2 and Th17 cells, as well as in iTregs. We further discuss the transcriptional regulation of Th9 cells in context of Foxo1, as an essential transcription factor required for the development and functions of Th9 and other IL-9-producing T cells.}, }
@article {pmid29867840, year = {2018}, author = {Hücker, SM and Vanderhaeghen, S and Abellan-Schneyder, I and Scherer, S and Neuhaus, K}, title = {The Novel Anaerobiosis-Responsive Overlapping Gene ano Is Overlapping Antisense to the Annotated Gene ECs2385 of Escherichia coli O157:H7 Sakai.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {931}, pmid = {29867840}, issn = {1664-302X}, abstract = {Current notion presumes that only one protein is encoded at a given bacterial genetic locus. However, transcription and translation of an overlapping open reading frame (ORF) of 186 bp length were discovered by RNAseq and RIBOseq experiments. This ORF is almost completely embedded in the annotated L,D-transpeptidase gene ECs2385 of Escherichia coli O157:H7 Sakai in the antisense reading frame -3. The ORF is transcribed as part of a bicistronic mRNA, which includes the annotated upstream gene ECs2384, encoding a murein lipoprotein. The transcriptional start site of the operon resides 38 bp upstream of the ECs2384 start codon and is driven by a predicted σ[70] promoter, which is constitutively active under different growth conditions. The bicistronic operon contains a ρ-independent terminator just upstream of the novel gene, significantly decreasing its transcription. The novel gene can be stably expressed as an EGFP-fusion protein and a translationally arrested mutant of ano, unable to produce the protein, shows a growth advantage in competitive growth experiments compared to the wild type under anaerobiosis. Therefore, the novel antisense overlapping gene is named ano (anaerobiosis responsive overlapping gene). A phylostratigraphic analysis indicates that ano originated very recently de novo by overprinting after the Escherichia/Shigella clade separated from other enterobacteria. Therefore, ano is one of the very rare cases of overlapping genes known in the genus Escherichia.}, }
@article {pmid29867833, year = {2018}, author = {Woo, HL and Hazen, TC}, title = {Enrichment of Bacteria From Eastern Mediterranean Sea Involved in Lignin Degradation via the Phenylacetyl-CoA Pathway.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {922}, pmid = {29867833}, issn = {1664-302X}, abstract = {The degradation of allochthonous terrestrial organic matter, such as recalcitrant lignin and hemicellulose from plants, occurs in the ocean. We hypothesize that bacteria instead of white-rot fungi, the model organisms of aerobic lignin degradation within terrestrial environments, are responsible for lignin degradation in the ocean due to the ocean's oligotrophy and hypersalinity. Warm oxic seawater from the Eastern Mediterranean Sea was enriched on lignin in laboratory microcosms. Lignin mineralization rates by the lignin-adapted consortia improved after two sequential incubations. Shotgun metagenomic sequencing detected a higher abundance of aromatic compound degradation genes in response to lignin, particularly phenylacetyl-CoA, which may be an effective strategy for marine microbes in fluctuating oxygen concentrations. 16S rRNA gene amplicon sequencing detected a higher abundance of Gammaproteobacteria and Alphaproteobacteria bacteria such as taxonomic families Idiomarinaceae, Alcanivoraceae, and Alteromonadaceae in response to lignin. Meanwhile, fungal Ascomycetes and Basidiomycetes remained at very low abundance. Our findings demonstrate the significant potential of bacteria and microbes utilizing the phenylacetyl-CoA pathway to contribute to lignin degradation in the Eastern Mediterranean where environmental conditions are unfavorable for fungi. Exploring the diversity of bacterial lignin degraders may provide important enzymes for lignin conversion in industry. Enzymes may be key in breaking down high molecular weight lignin and enabling industry to use it as a low-cost and sustainable feedstock for biofuels or other higher-value products.}, }
@article {pmid29867788, year = {2018}, author = {Pratama, AA and Chaib De Mares, M and van Elsas, JD}, title = {Evolutionary History of Bacteriophages in the Genus Paraburkholderia.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {835}, pmid = {29867788}, issn = {1664-302X}, abstract = {The genus Paraburkholderia encompasses mostly environmental isolates with diverse predicted lifestyles. Genome analyses have shown that bacteriophages form a considerable portion of some Paraburkholderia genomes. Here, we analyzed the evolutionary history of prophages across all Paraburkholderia spp. Specifically, we investigated to what extent the presence of prophages and their distribution affect the diversity/diversification of Paraburkholderia spp., as well as to what extent phages coevolved with their respective hosts. Particular attention was given to the presence of CRISPR-Cas arrays as a reflection of past interactions with phages. We thus analyzed 36 genomes of Paraburkholderia spp., including those of 11 new strains, next to those of three Burkholderia species. Most genomes were found to contain at least one full prophage sequence. The highest number was found in Paraburkholderia sp. strain MF2-27; the nine prophages found amount to up to 4% of its genome. Among all prophages, potential moron genes (e.g., DNA adenine methylase) were found that might be advantageous for host cell fitness. Co-phylogenetic analyses indicated the existence of complex evolutionary scenarios between the different Paraburkholderia hosts and their prophages, including short-term co-speciation, duplication, host-switching and phage loss events. Analysis of the CRISPR-Cas systems showed a record of diverse, potentially recent, phage infections. We conclude that, overall, different phages have interacted in diverse ways with their Paraburkholderia hosts over evolutionary time.}, }
@article {pmid29860637, year = {2019}, author = {Torres, PJ and Thompson, J and McLean, JS and Kelley, ST and Edlund, A}, title = {Discovery of a Novel Periodontal Disease-Associated Bacterium.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {267-276}, pmid = {29860637}, issn = {1432-184X}, support = {R00 DE024543/DE/NIDCR NIH HHS/United States ; U26IHS300292/NH/NIH HHS/United States ; }, mesh = {Alaska Natives ; Bacteroidetes/*classification/genetics/*isolation &amp; purification/*pathogenicity ; California ; Dental Plaque/microbiology ; Genes, Bacterial/genetics ; Genome, Bacterial/genetics ; Humans ; Indians, North American ; Metagenomics ; Microbiota ; Multigene Family ; Periodontal Diseases/*microbiology ; Periodontitis/microbiology ; *Phylogeny ; Sequence Analysis, DNA ; Virulence Factors/genetics ; }, abstract = {One of the world's most common infectious disease, periodontitis (PD), derives from largely uncharacterized communities of oral bacteria growing as biofilms (a.k.a. plaque) on teeth and gum surfaces in periodontal pockets. Bacteria associated with periodontal disease trigger inflammatory responses in immune cells, which in later stages of the disease cause loss of both soft and hard tissue structures supporting teeth. Thus far, only a handful of bacteria have been characterized as infectious agents of PD. Although deep sequencing technologies, such as whole community shotgun sequencing have the potential to capture a detailed picture of highly complex bacterial communities in any given environment, we still lack major reference genomes for the oral microbiome associated with PD and other diseases. In recent work, by using a combination of supervised machine learning and genome assembly, we identified a genome from a novel member of the Bacteroidetes phylum in periodontal samples. Here, by applying a comparative metagenomics read-classification approach, including 272 metagenomes from various human body sites, and our previously assembled draft genome of the uncultivated Candidatus Bacteroides periocalifornicus (CBP) bacterium, we show CBP's ubiquitous distribution in dental plaque, as well as its strong association with the well-known pathogenic "red complex" that resides in deep periodontal pockets.}, }
@article {pmid29860594, year = {2018}, author = {Vieira, A and Ribera-Guardia, A and Marques, R and Barreto Crespo, MT and Oehmen, A and Carvalho, G}, title = {The link between the microbial ecology, gene expression, and biokinetics of denitrifying polyphosphate-accumulating systems under different electron acceptor combinations.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {15}, pages = {6725-6737}, doi = {10.1007/s00253-018-9077-3}, pmid = {29860594}, issn = {1432-0614}, support = {PTDC/AAC-AMB/120581/2010//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/97640/2013//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; Water JPI project 196//H2020 Environment/ ; COST Action ES1202//Horizon 2020/ ; UID/Multi/04378/2013//Portuguese Government/ ; POCI-01- 0145-FEDER-007728//European Regional Development Fund/ ; LISBOA-01-0145-FEDER-007344//European Regional Development Fund/ ; BES-2012-052753//Secretar&#xed;a de Estado de Investigaci&#xf3;n, Desarrollo e Innovaci&#xf3;n/ ; }, mesh = {Bacteria/classification/*drug effects ; Bioreactors ; Denitrification ; Electrons ; Gene Expression/*drug effects ; Microbiota/drug effects ; Nitrates/chemistry/*pharmacology ; Nitrites/chemistry/*pharmacology ; Nitrous Oxide/chemistry/metabolism/*pharmacology ; Phylogeny ; Polyphosphates/metabolism ; }, abstract = {The emission of the greenhouse gas nitrous oxide (N2O) can occur during biological nutrient removal. Denitrifying enhanced biological phosphorus removal (d-EBPR) systems are an efficient means of removing phosphate and nitrogen, performed by denitrifying polyphosphate-accumulating organisms (d-PAOs). The aim of this work was to study the effect of various combinations of electron acceptors, nitrate (NO3[-]), nitrite (NO2[-]), and N2O, on the denitrification pathway of a d-EBPR system. Batch tests were performed with different electron acceptor combinations, to explore the denitrification pathway. Reverse transcriptase-qPCR (RT-qPCR) and high-throughput sequencing, combined with chemical analysis, were used to study gene expression, microbial diversity, and denitrification kinetics. The potential for N2O production was greater than the potential for its reduction in most tests. A strong correlation was observed between the N2O reduction rate and the relative gene expression of nitrous oxide reductase per nitrite reductase (nosZ/(nirS + nirK)), suggesting that the expression of denitrifying marker genes is a strong predictor of the N2O reduction rate. The d-EBPR community maintained a core population with low variations throughout the study. Furthermore, phylogenetic analyses of the studied marker genes revealed that the organisms actively involved in denitrification were closely related to Thauera sp., Candidatus Accumulibacter phosphatis, and Candidatus Competibacter denitrificans. Moreover, Competibacter-related OTUs seem to be important contributors to the N2O reduction capacity of the system, likely scavenging the N2O produced by other organisms. Overall, this study contributes to a better understanding of the microbial biochemistry and the genetics involving biological denitrification removal, important to minimize N2O emissions in wastewater treatment plants.}, }
@article {pmid29858666, year = {2018}, author = {Magill, DJ and McGrath, JW and O'Flaherty, V and Quinn, JP and Kulakov, LA}, title = {Insights into the structural dynamics of the bacteriophage T7 DNA polymerase and its complexes.}, journal = {Journal of molecular modeling}, volume = {24}, number = {7}, pages = {144}, pmid = {29858666}, issn = {0948-5023}, support = {14/IA/2371//Science Foundation Ireland/Ireland ; }, mesh = {Bacteriophage T7/*enzymology ; Binding Sites ; Cluster Analysis ; DNA/chemistry/metabolism ; DNA-Directed DNA Polymerase/*chemistry/metabolism ; Hydrogen/chemistry ; Hydrogen-Ion Concentration ; *Molecular Dynamics Simulation ; Protein Binding ; Protein Conformation ; Structure-Activity Relationship ; Viral Proteins/chemistry ; }, abstract = {The T7 DNA polymerase is dependent on the host protein thioredoxin (trx) for its processivity and fidelity. Using all-atom molecular dynamics, we demonstrate the specific interactions between trx and the T7 polymerase, and show that trx docking to its binding domain on the polymerase results in a significant level of stability and exposes a series of basic residues within the domain that interact with the phosphodiester backbone of the DNA template. We also characterize the nature of interactions between the T7 DNA polymerase and its DNA template. We show that the trx-binding domain acts as an intrinsic clamp, constraining the DNA via a two-step hinge motion, and characterize the interactions necessary for this to occur. Together, these insights provide a significantly improved understanding of the interactions responsible for highly processive DNA replication by T7 polymerase.}, }
@article {pmid29858646, year = {2019}, author = {McGee, KM and Eaton, WD and Shokralla, S and Hajibabaei, M}, title = {Determinants of Soil Bacterial and Fungal Community Composition Toward Carbon-Use Efficiency Across Primary and Secondary Forests in a Costa Rican Conservation Area.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {148-167}, pmid = {29858646}, issn = {1432-184X}, support = {1262907//Directorate for Biological Sciences/ ; }, mesh = {Bacteria/*classification/genetics ; Biodiversity ; Biomass ; Carbon/*metabolism ; Costa Rica ; Ecosystem ; *Forests ; Fungi/*classification/genetics ; *Microbiota ; Multivariate Analysis ; Mycobiome ; Mycorrhizae ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Tropical secondary forests currently represent over half of the world's remaining tropical forests and are critical candidates for maintaining global biodiversity and enhancing potential carbon-use efficiency (CUE) and, thus, carbon sequestration. However, these ecosystems can exhibit multiple successional pathways, which have hindered our understanding of the soil microbial drivers that facilitate improved CUE. To begin to address this, we examined soil % C; % N; C:N ratio; soil microbial biomass C (Cmic); NO3[-]; NH4[+]; pH; % moisture; % sand, silt, and clay; and elevation, along with soil bacterial and fungal community composition, and determined which soil abiotic properties structure the soil Cmic and the soil bacterial and fungal communities across a primary forest, 33-year-old secondary forest, and 22-year-old young secondary in the Northern Zone of Costa Rica. We provide evidence that soil microbial communities were mostly distinct across the habitat types and that these habitats appear to have affected the soil ectomycorrhizal fungi and the soil microbial groups associated with the degradation of complex carbon compounds. We found that soil Cmic levels increased along the management gradient from young, to old secondary, to primary forest. In addition, the changes in soil Cmic and soil fungal community structure were significantly related to levels of soil NO3[-]. Our analyses showed that even after 33 years of natural forest regrowth, the clearing of tropical forests can have persistent effects on soil microbial communities and that it may take a longer time than we realized for secondary forests to develop carbon-utilization efficiencies similar to that of a primary forest. Our results also indicated that forms of inorganic N may be an important factor in structuring soil Cmic and the soil microbial communities, leading to improved CUE in regenerating secondary forests. This study is the first in the region to highlight some of the factors which appear to be structuring the soil Cmic and soil microbial communities such that they are more conducive for enhanced CUE in secondary forests.}, }
@article {pmid29858645, year = {2019}, author = {Gao, CH and Zhang, M and Wu, Y and Huang, Q and Cai, P}, title = {Divergent Influence to a Pathogen Invader by Resident Bacteria with Different Social Interactions.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {76-86}, pmid = {29858645}, issn = {1432-184X}, support = {2016YFD0800206//National Key R&amp;D Program of China/ ; 41522106//National Natural Science Foundation of China/ ; }, mesh = {Bacillus subtilis/pathogenicity/physiology ; Bacteria/*pathogenicity ; *Bacterial Physiological Phenomena ; Coculture Techniques ; Culture Media/chemistry ; Foodborne Diseases/*microbiology ; Gene Expression Regulation, Bacterial ; Genes, Bacterial/genetics ; Glycerol/metabolism ; Manganese/metabolism ; *Microbial Interactions ; Pseudomonas putida/pathogenicity/physiology ; Vibrio parahaemolyticus/genetics/growth &amp; development/metabolism/pathogenicity ; }, abstract = {Bacterial social interaction is a potential influencing factor in determining the fate of invading pathogens in diverse environments. In this study, interactions between two representative resident species (Bacillus subtilis and Pseudomonas putida) and a leading food-borne disease causative pathogen (Vibrio parahaemolyticus) were examined. An antagonistic effect toward V. parahaemolyticus was observed for B. subtilis but not for P. putida. However, the relative richness of the pathogen remained rather high in B. subtilis co-cultures and was, unexpectedly, not sensitive to the initial inoculation ratios. Furthermore, two approaches were found to be efficient at modulating the relative richness of the pathogen. (1) The addition of trace glycerol and manganese to Luria-Bertani medium (LBGM) reduced the richness of V. parahaemolyticus in the co-culture with B. subtilis and in contrast, increased its richness in the co-culture with P. putida, although it did not affect the growth of V. parahaemolyticus by its own. (2) The relative richness of V. parahaemolyticus on semisolid medium decreased significantly as a function of an agar gradient, ranging from 0 to 2%. Furthermore, we explored the molecular basis of bacterial interaction through transcriptomic analysis. In summary, we investigated the interactions between a pathogen invader and two resident bacteria species, showing that the different influences on a pathogen by different types of interactions can be modulated by chemicals and medium fluidity.}, }
@article {pmid29858203, year = {2018}, author = {Almeida, C and Silva Pereira, C and Gonzalez-Menendez, V and Bills, G and Pascual, J and Sánchez-Hidalgo, M and Kehraus, S and Genilloud, O}, title = {Unveiling Concealed Functions of Endosymbiotic Bacteria Harbored in the Ascomycete Stachylidium bicolor.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {15}, pages = {}, pmid = {29858203}, issn = {1098-5336}, mesh = {Ascomycota/chemistry/growth &amp; development/*physiology ; Burkholderia/genetics/isolation &amp; purification/*physiology ; Mycelium/chemistry/physiology ; Peptides, Cyclic/metabolism ; Sphingomonas/genetics/isolation &amp; purification/*physiology ; Spores, Fungal/growth &amp; development/physiology ; *Symbiosis ; }, abstract = {Among the plethora of unusual secondary metabolites isolated from Stachylidium bicolor are the tetrapeptidic endolides A and B. Both tetrapeptides contain 3-(3-furyl)-alanine residues, previously proposed to originate from bacterial metabolism. Inspired by this observation, we aimed to identify the presence of endosymbiotic bacteria in S. bicolor and to discover the true producer of the endolides. The endobacterium Burkholderia contaminans was initially detected by 16S rRNA gene amplicon sequencing from the fungal metagenome and was subsequently isolated. It was confirmed that the tetrapeptides were produced by the axenic B. contaminans only when in latency. Fungal colonies unable to produce conidia and the tetrapeptides were isolated and confirmed to be free of B. contaminans A second endosymbiont identified as related to Sphingomonas leidyi was also isolated. In situ imaging of the mycelium supported an endosymbiotic relationship between S. bicolor and the two endobacteria. Besides the technical novelty, our in situ analyses revealed that the two endobacteria are compartmentalized in defined fungal cells, prevailing mostly in latency when in symbiosis. Within the emerging field of intracellular bacterial symbioses, fungi are the least studied eukaryotic hosts. Our study further supports the Fungi as a valuable model for understanding endobacterial symbioses in eukaryotes.IMPORTANCE The discovery of two bacterial endosymbionts harbored in Stachylidium bicolor mycelium, Burkholderia contaminans and Sphingomonas leidyi, is described here. Production of tetrapeptides inside the mycelium is ensured by B. contaminans, and fungal sporulation is influenced by the endosymbionts. Here, we illustrate the bacterial endosymbiotic origin of secondary metabolites in an Ascomycota host.}, }
@article {pmid29857194, year = {2018}, author = {Egert, M and Weis, S and Schnell, S}, title = {RNA-based stable isotope probing (RNA-SIP) to unravel intestinal host-microbe interactions.}, journal = {Methods (San Diego, Calif.)}, volume = {149}, number = {}, pages = {25-30}, doi = {10.1016/j.ymeth.2018.05.022}, pmid = {29857194}, issn = {1095-9130}, mesh = {Gastrointestinal Microbiome/*physiology ; Host Microbial Interactions/*physiology ; Humans ; Isotope Labeling/instrumentation/*methods ; Microbiota/*physiology ; RNA Probes/analysis/*metabolism ; Ultracentrifugation/methods ; }, abstract = {The RNA-SIP technology, introduced into molecular microbial ecology in 2002, is an elegant technique to link the structure and function of complex microbial communities, i.e. to identify microbial key-players involved in distinct degradation and assimilation processes under in-situ conditions. Due to its dependence of microbial RNA, this technique is particularly suited for environments with high numbers of very active, i.e. significantly RNA-expressing, bacteria. So far, it was mainly used in environmental studies using microbiotas from soil or water habitats. Here we outline and summarize our application of RNA-SIP for the identification of bacteria involved in the degradation and assimilation of prebiotic carbohydrates in intestinal samples of human and animal origin. Following an isotope label from a prebiotic substrate into the RNA of distinct bacterial taxa will help to better understand the functionality of these medically and economically important nutrients in an intestinal environment.}, }
@article {pmid29856843, year = {2018}, author = {Roley, SS and Duncan, DS and Liang, D and Garoutte, A and Jackson, RD and Tiedje, JM and Robertson, GP}, title = {Associative nitrogen fixation (ANF) in switchgrass (Panicum virgatum) across a nitrogen input gradient.}, journal = {PloS one}, volume = {13}, number = {6}, pages = {e0197320}, pmid = {29856843}, issn = {1932-6203}, mesh = {Carbon/metabolism ; *Ecosystem ; Fertilizers ; Michigan ; Nitrogen/*metabolism ; Nitrogen Fixation/*physiology ; Panicum/*physiology ; Rhizosphere ; Soil Microbiology ; Wisconsin ; }, abstract = {Associative N fixation (ANF), the process by which dinitrogen gas is converted to ammonia by bacteria in casual association with plants, has not been well-studied in temperate ecosystems. We examined the ANF potential of switchgrass (Panicum virgatum L.), a North American prairie grass whose productivity is often unresponsive to N fertilizer addition, via separate short-term 15N2 incubations of rhizosphere soils and excised roots four times during the growing season. Measurements occurred along N fertilization gradients at two sites with contrasting soil fertility (Wisconsin, USA Mollisols and Michigan, USA Alfisols). In general, we found that ANF potentials declined with long-term N addition, corresponding with increased soil N availability. Although we hypothesized that ANF potential would track plant N demand through the growing season, the highest root fixation rates occurred after plants senesced, suggesting that root diazotrophs exploit carbon (C) released during senescence, as C is translocated from aboveground tissues to roots for wintertime storage. Measured ANF potentials, coupled with mass balance calculations, suggest that ANF appears to be an important source of N to unfertilized switchgrass, and, by extension, to temperate grasslands in general.}, }
@article {pmid29854953, year = {2018}, author = {Cardona, C and Lax, S and Larsen, P and Stephens, B and Hampton-Marcell, J and Edwardson, CF and Henry, C and Van Bonn, B and Gilbert, JA}, title = {Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics.}, journal = {mSystems}, volume = {3}, number = {3}, pages = {}, pmid = {29854953}, issn = {2379-5077}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; T32 EB009412/EB/NIBIB NIH HHS/United States ; }, abstract = {Host-associated microbial dynamics are influenced by dietary and immune factors, but how exogenous microbial exposure shapes host-microbe dynamics remains poorly characterized. To investigate this phenomenon, we characterized the skin, rectum, and respiratory tract-associated microbiota in four aquarium-housed dolphins daily over a period of 6 weeks, including administration of a probiotic during weeks 4 to 6. The environmental bacterial sources were also characterized, including the animals' human handlers, the aquarium air and water, and the dolphins' food supply. Continuous microbial exposure occurred between all sites, yet each environment maintained a characteristic microbiota, suggesting that the majority of exposure events do not result in colonization. Small changes in water physicochemistry had a significant but weak correlation with change in dolphin-associated bacterial richness but had no influence on phylogenetic diversity. Food and air microbiota were the richest and had the largest conditional influence on other microbiota in the absence of probiotics, but during probiotic administration, food alone had the largest influence on the stability of the dolphin microbiota. Our results suggest that respiratory tract and gastrointestinal epithelium interactions with air- and food-associated microbes had the biggest influence on host-microbiota dynamics, while other interactions, such as skin transmission, played only a minor role. Finally, direct oral stimulation with a foreign exogenous microbial source can have a profound effect on microbial stability. IMPORTANCE These results provide valuable insights into the ecological influence of exogenous microbial exposure, as well as laying the foundation for improving aquarium management practices. By comparing data for dolphins from aquaria that use natural versus artificial seawater, we demonstrate the potential influence of aquarium water disinfection procedures on dolphin microbial dynamics.}, }
@article {pmid29854043, year = {2017}, author = {Hakkaart, XDV and Pronk, JT and van Maris, AJA}, title = {A Simulator-Assisted Workshop for Teaching Chemostat Cultivation in Academic Classes on Microbial Physiology.}, journal = {Journal of microbiology &amp; biology education}, volume = {18}, number = {3}, pages = {}, pmid = {29854043}, issn = {1935-7877}, abstract = {Understanding microbial growth and metabolism is a key learning objective of microbiology and biotechnology courses, essential for understanding microbial ecology, microbial biotechnology and medical microbiology. Chemostat cultivation, a key research tool in microbial physiology that enables quantitative analysis of growth and metabolism under tightly defined conditions, provides a powerful platform to teach key features of microbial growth and metabolism. Substrate-limited chemostat cultivation can be mathematically described by four equations. These encompass mass balances for biomass and substrate, an empirical relation that describes distribution of consumed substrate over growth and maintenance energy requirements (Pirt equation), and a Monod-type equation that describes the relation between substrate concentration and substrate-consumption rate. The authors felt that the abstract nature of these mathematical equations and a lack of visualization contributed to a suboptimal operative understanding of quantitative microbial physiology among students who followed their Microbial Physiology B.Sc. courses. The studio-classroom workshop presented here was developed to improve student understanding of quantitative physiology by a set of question-guided simulations. Simulations are run on Chemostatus, a specially developed MATLAB-based program, which visualizes key parameters of simulated chemostat cultures as they proceed from dynamic growth conditions to steady state. In practice, the workshop stimulated active discussion between students and with their teachers. Moreover, its introduction coincided with increased average exam scores for questions on quantitative microbial physiology. The workshop can be easily implemented in formal microbial physiology courses or used by individuals seeking to test and improve their understanding of quantitative microbial physiology and/or chemostat cultivation.}, }
@article {pmid29850933, year = {2019}, author = {Gołębiewski, M and Tarasek, A and Sikora, M and Deja-Sikora, E and Tretyn, A and Niklińska, M}, title = {Rapid Microbial Community Changes During Initial Stages of Pine Litter Decomposition.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {56-75}, pmid = {29850933}, issn = {1432-184X}, support = {UMO-2012/05/NZ8/001362//Narodowe Centrum Nauki/ ; DS758//Uniwersytet Jagiello&#x144;ski w Krakowie/ ; DS759//Uniwersytet Jagiello&#x144;ski w Krakowie/ ; DSC//Uniwersytet Jagiello&#x144;ski w Krakowie/ ; }, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics/metabolism ; *Biodiversity ; DNA/isolation &amp; purification ; DNA, Ribosomal/genetics ; *Decompression ; Ecosystem ; Eukaryota/classification/genetics ; Fungi/classification/genetics ; Metagenomics ; *Microbiota/genetics/physiology ; Pinus/*microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; *Soil Microbiology ; Trees/microbiology ; }, abstract = {Plant litter decomposition is a process enabling biogeochemical cycles closing in ecosystems, and decomposition in forests constitutes the largest part of this process taking place in terrestrial biomes. Microbial communities during litter decomposition were studied mainly with low-throughput techniques not allowing detailed insight, particularly into coniferous litter, as it is more difficult to obtain high quality DNA required for analyses. Motivated by these problems, we analyzed archaeal, bacterial, and eukaryotic communities at three decomposition stages: fresh, 3- and 8-month-old litter by 16/18S rDNA pyrosequencing, aiming at detailed insight into early stages of pine litter decomposition. Archaea were absent from our libraries. Bacterial and eukaryotic diversity was greatest in 8-month-old litter and the same applied to bacterial and fungal rDNA content. Community structure was different at various stages of decomposition, and phyllospheric organisms (bacteria: Acetobacteraceae and Pseudomonadaceae members, fungi: Lophodermium, Phoma) were replaced by communities with metabolic capabilities adapted to the particular stage of decomposition. Sphingomonadaceae and Xanthomonadaceae and fungal genera Sistotrema, Ceuthospora, and Athelia were characteristic for 3-month-old samples, while 8-month-old ones were characterized by Bradyrhizobiaceae and nematodes (Plectus). We suggest that bacterial and eukaryotic decomposer communities change at different stages of pine litter decomposition in a way similar to that in broadleaf litter. Interactions between bacteria and eukaryotes appear to be one of the key drivers of microbial community structure.}, }
@article {pmid29850857, year = {2018}, author = {Alfano, M and Ferrarese, R and Locatelli, I and Ventimiglia, E and Ippolito, S and Gallina, P and Cesana, D and Canducci, F and Pagliardini, L and Viganò, P and Clementi, M and Nebuloni, M and Montorsi, F and Salonia, A}, title = {Testicular microbiome in azoospermic men-first evidence of the impact of an altered microenvironment.}, journal = {Human reproduction (Oxford, England)}, volume = {33}, number = {7}, pages = {1212-1217}, pmid = {29850857}, issn = {1460-2350}, mesh = {Azoospermia/*complications/microbiology/pathology ; Cross-Sectional Studies ; Dysbiosis/*complications/microbiology/pathology ; Humans ; Male ; *Microbiota ; Spermatogenesis/physiology ; Testis/*microbiology/pathology ; }, abstract = {STUDY QUESTION: Given the relevant role of the extracellular microenvironment in regulating tissue homeostasis, is testicular bacterial microbiome (BM) associated with germ cell aplasia in idiopathic non-obstructive azoospermia (iNOA)?<br><br>SUMMARY ANSWER: A steady increase of dysbiosis was observed among testis with normal spermatogenesis vs. iNOA with positive sperm retrieval and iNOA with complete germ cell aplasia.<br><br>WHAT IS KNOWN ALREADY: Tissue-associated BM has been reported to be a biologically important extracellular microenvironment component for numerous body habitats, but not yet for the human testis.<br><br>STUDY DESIGN, SIZE, DURATION: Cross-sectional study, investigating tissue-associated BM in the testis of (i) five men with iNOA and negative sperm retrieval at microdissection testicular sperm extraction (microTESE); (ii) five men with iNOA and positive sperm retrieval at microTESE; and (iii) five normozoospermic men upon orchiectomy. Every testicular specimen was histologically classified and analyzed in terms of bacterial community.<br><br>Massive ultra-deep pyrosequencing was applied to investigate testis microbiome. Metagenome was analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Tissue-associated bacterial load was quantified by digital droplet PCR.<br><br>Normozoospermic men showed small amounts of bacteria in the testis, with Actinobacteria, Bacteroidetes, Firmicutes Proteobacteria as the dominating phyla; iNOA individuals had increased amounts of bacterial DNA (P = 0.02), associated with decreased taxa richness due to the lack of Bacteroidetes and Proteobacteria (P = 2 &#xd7; 10-5). Specimens with negative sperm retrieval at microTESE depicted complete germ cell aplasia and a further decrease in terms of Firmicutes and Clostridia (P < 0.05), a complete lack of Peptoniphilus asaccharolyticus, but increased amount of Actinobacteria.<br><br>The limited number of specimens analyzed in this preliminary study deserves external validation. The paraneoplastic microenvironment could have an impact on the residential bacterial flora.<br><br>Human testicular microenvironment is not microbiologically sterile, containing low amounts of Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. A dysbiotic bacterial community was associated with iNOA and complete germ cell aplasia. Novel findings on testicular BM could support future translational therapies of male-factor infertility.<br><br>This work was supported by URI-Urological Research Institute free funds. Authors declared no conflict of interest.<br><br>TRIAL REGISTRATION NUMBER: N/A.}, }
@article {pmid29849169, year = {2018}, author = {Dong, X and Greening, C and Brüls, T and Conrad, R and Guo, K and Blaskowski, S and Kaschani, F and Kaiser, M and Laban, NA and Meckenstock, RU}, title = {Fermentative Spirochaetes mediate necromass recycling in anoxic hydrocarbon-contaminated habitats.}, journal = {The ISME journal}, volume = {12}, number = {8}, pages = {2039-2050}, pmid = {29849169}, issn = {1751-7370}, mesh = {Bacterial Proteins/genetics/metabolism ; Deltaproteobacteria/genetics/metabolism ; Ecosystem ; Fermentation ; Groundwater/analysis/microbiology ; Hydrocarbons/*metabolism ; Oxidation-Reduction ; Proteome ; Proteomics ; Spirochaetales/genetics/isolation &amp; purification/*metabolism ; Sulfates/metabolism ; }, abstract = {Spirochaetes are frequently detected in anoxic hydrocarbon- and organohalide-polluted groundwater, but their role in such ecosystems has remained unclear. To address this, we studied a sulfate-reducing, naphthalene-degrading enrichment culture, mainly comprising the sulfate reducer Desulfobacterium N47 and the rod-shaped Spirochete Rectinema cohabitans HM. Genome sequencing and proteome analysis suggested that the Spirochete is an obligate fermenter that catabolizes proteins and carbohydrates, resulting in acetate, ethanol, and molecular hydrogen (H2) production. Physiological experiments inferred that hydrogen is an important link between the two bacteria in the enrichment culture, with H2 derived from fermentation by R. cohabitans used as reductant for sulfate reduction by Desulfobacterium N47. Differential proteomics and physiological experiments showed that R. cohabitans utilizes biomass (proteins and carbohydrates) released from dead cells of Desulfobacterium N47. Further comparative and community genome analyses indicated that other Rectinema phylotypes are widespread in contaminated environments and may perform a hydrogenogenic fermentative lifestyle similar to R. cohabitans. Together, these findings indicate that environmental Spirochaetes scavenge detrital biomass and in turn drive necromass recycling at anoxic hydrocarbon-contaminated sites and potentially other habitats.}, }
@article {pmid29848762, year = {2018}, author = {Garcia, SL and Buck, M and Hamilton, JJ and Wurzbacher, C and Grossart, HP and McMahon, KD and Eiler, A}, title = {Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.}, journal = {mSphere}, volume = {3}, number = {3}, pages = {}, pmid = {29848762}, issn = {2379-5042}, mesh = {Bacteria/*metabolism ; Fresh Water/*microbiology ; *Metabolism ; *Microbial Consortia ; Microbial Interactions ; }, abstract = {Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members.}, }
@article {pmid29844191, year = {2018}, author = {Kleiner, M and Dong, X and Hinzke, T and Wippler, J and Thorson, E and Mayer, B and Strous, M}, title = {Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {24}, pages = {E5576-E5584}, pmid = {29844191}, issn = {1091-6490}, mesh = {Animals ; Carbon/*metabolism ; Carbon Isotopes/metabolism ; Environmental Microbiology ; Isotope Labeling/methods ; Metabolic Networks and Pathways/*physiology ; Microbiota/*physiology ; Proteome/*metabolism ; Proteomics/*methods ; Software ; Symbiosis/physiology ; }, abstract = {Measurements of stable carbon isotope ratios (δ[13]C) are widely used in biology to address questions regarding food sources and metabolic pathways used by organisms. The analysis of these so-called stable isotope fingerprints (SIFs) for microbes involved in biogeochemical cycling and microbiota of plants and animals has led to major discoveries in environmental microbiology. Currently, obtaining SIFs for microbial communities is challenging as the available methods either only provide low taxonomic resolution, such as the use of lipid biomarkers, or are limited in throughput, such as nanoscale secondary ion MS imaging of single cells. Here we present "direct protein-SIF" and the Calis-p software package (https://sourceforge.net/projects/calis-p/), which enable high-throughput measurements of accurate δ[13]C values for individual species within a microbial community. We benchmark the method using 20 pure culture microorganisms and show that the method reproducibly provides SIF values consistent with gold-standard bulk measurements performed with an isotope ratio mass spectrometer. Using mock community samples, we demonstrate that SIF values can also be obtained for individual species within a microbial community. Finally, a case study of an obligate bacteria-animal symbiosis shows that direct protein-SIF confirms previous physiological hypotheses and can provide unexpected insights into the symbionts' metabolism. This confirms the usefulness of this approach to accurately determine δ[13]C values for different species in microbial community samples.}, }
@article {pmid29809120, year = {2018}, author = {Kim, SH and Kim, JG and Jung, MY and Kim, SJ and Gwak, JH and Yu, WJ and Roh, SW and Kim, YH and Rhee, SK}, title = {Ketobacter alkanivorans gen. nov., sp. nov., an n-alkane-degrading bacterium isolated from seawater.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {68}, number = {7}, pages = {2258-2264}, doi = {10.1099/ijsem.0.002823}, pmid = {29809120}, issn = {1466-5034}, mesh = {Alcanivoraceae/*classification/genetics/isolation &amp; purification ; Alkanes/*metabolism ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Seawater/*microbiology ; Sequence Analysis, DNA ; Ubiquinone/chemistry ; }, abstract = {Strain GI5[T] was isolated from a surface seawater sample collected from Garorim Bay (West Sea, Republic of Korea). The isolated strain was aerobic, Gram-stain-negative, rod-shaped, motile by means of a polar flagellum, negative for catalase and weakly positive for oxidase. The optimum growth pH, salinity and temperature were determined to be pH 7.5-8.0, 3 % NaCl (w/v) and 25 °C, respectively; the growth ranges were pH 6.0-9.0, 1-7 % NaCl (w/v) and 18-40 °C. The results of phylogenetic analysis of 16S rRNA gene sequences indicated that GI5[T] clustered within the family Alcanivoracaceae, and most closely with Alcanivorax dieseloleiB-5[T] and Alcanivorax marinusR8-12[T] (91.9 % and 91.6 % similarity, respectively). The major cellular fatty acids in GI5[T] were C18 : 1ω7c/C18 : 1ω6c (44.45 %), C16 : 1ω6c/C16 : 1ω7c (14.17 %) and C16 : 0 (10.19 %); this profile was distinct from those of the closely related species. The major respiratory quinone of GI5[T] was Q-8. The main polar lipids were phosphatidylethanolamine and phosphatidylglycerol. Two putative alkane hydroxylase (alkB) genes were identified in GI5[T]. The G+C content of the genomic DNA of GI5[T] was determined to be 51.2 mol%. On the basis of the results of phenotypic, chemotaxonomic and phylogenetic studies, strain GI5[T] represents a novel species of a novel genus of the family Alcanivoracaceae, for which we propose the name Ketobacter alkanivorans gen. nov., sp. nov.; the type strain is GI5[T] (=KCTC 52659[T]=JCM 31835[T]).}, }
@article {pmid29808411, year = {2019}, author = {Kumar, A and Ng, DHP and Wu, Y and Cao, B}, title = {Microbial Community Composition and Putative Biogeochemical Functions in the Sediment and Water of Tropical Granite Quarry Lakes.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {1-11}, pmid = {29808411}, issn = {1432-184X}, support = {L2NICCFP1-2013-3//Singapore Ministry of National Development and National Research Foundation/ ; }, mesh = {Archaea/classification/genetics/physiology ; Bacteria/classification/genetics ; Bacterial Physiological Phenomena ; Biodiversity ; Geologic Sediments/*chemistry/*microbiology ; Lakes/*microbiology ; Microbiota/genetics/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Silicon Dioxide/*chemistry ; Singapore ; Water/*chemistry ; *Water Microbiology ; }, abstract = {Re-naturalized quarry lakes are important ecosystems, which support complex communities of flora and fauna. Microorganisms associated with sediment and water form the lowest trophic level in these ecosystems and drive biogeochemical cycles. A direct comparison of microbial taxa in water and sediment microbial communities is lacking, which limits our understanding of the dominant functions that are carried out by the water and sediment microbial communities in quarry lakes. In this study, using the 16S rDNA amplicon sequencing approach, we compared microbial communities in the water and sediment in two re-naturalized quarry lakes in Singapore and elucidated putative functions of the sediment and water microbial communities in driving major biogeochemical processes. The richness and diversity of microbial communities in sediments of the quarry lakes were higher than those in the water. The composition of the microbial communities in the sediments from the two quarries was highly similar to one another, while those in the water differed greatly. Although the microbial communities of the sediment and water samples shared some common members, a large number of microbial taxa (at the phylum and genus levels) were prevalent either in sediment or water alone. Our results provide valuable insights into the prevalent biogeochemical processes carried out by water and sediment microbial communities in tropical granite quarry lakes, highlighting distinct microbial processes in water and sediment that contribute to the natural purification of the resident water.}, }
@article {pmid29806601, year = {2018}, author = {Lekshmi, N and Joseph, I and Ramamurthy, T and Thomas, S}, title = {Changing facades of Vibrio cholerae: An enigma in the epidemiology of cholera.}, journal = {The Indian journal of medical research}, volume = {147}, number = {2}, pages = {133-141}, pmid = {29806601}, issn = {0971-5916}, mesh = {Anti-Bacterial Agents/therapeutic use ; Biofilms/drug effects ; Cholera/*epidemiology/genetics/microbiology/*therapy ; Disease Outbreaks ; Humans ; Vibrio cholerae O1/*pathogenicity ; }, abstract = {Cholera, caused by the Gram-negative bacterium Vibrio cholerae, has ravaged humanity from time immemorial. Although the disease can be treated using antibiotics along with administration of oral rehydration salts and controlled by good sanitation, cholera is known to have produced mayhems in ancient times when little was known about the pathogen. By the 21[st] century, ample information about the pathogen, its epidemiology, genetics, treatment and control strategies was revealed. However, there is still fear of cholera outbreaks in developing countries, especially in the wake of natural calamities. Studies have proved that the bacterium is mutating and evolving, out-competing all our efforts to treat the disease with previously used antibiotics and control with existing vaccines. In this review, the major scientific insights of cholera research are discussed. Considering the important role of biofilm formation in the V. cholerae life cycle, the vast availability of next-generation sequencing data of the pathogen and multi-omic approach, the review thrusts on the identification of suitable biofilm-inhibiting targets and the discovery of anti-biofilm drugs from nature to control the disease.}, }
@article {pmid29804046, year = {2018}, author = {Bae, HS and Huang, L and White, JR and Wang, J and DeLaune, RD and Ogram, A}, title = {Response of microbial populations regulating nutrient biogeochemical cycles to oiling of coastal saltmarshes from the Deepwater Horizon oil spill.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {241}, number = {}, pages = {136-147}, doi = {10.1016/j.envpol.2018.05.033}, pmid = {29804046}, issn = {1873-6424}, mesh = {Bacteria/classification/genetics ; Geologic Sediments/chemistry/microbiology ; Gulf of Mexico ; Louisiana ; Petroleum Pollution/*analysis ; RNA, Ribosomal, 16S/chemistry ; *Water Microbiology ; Water Pollutants, Chemical/*analysis ; Water Quality ; *Wetlands ; }, abstract = {Microbial communities play vital roles in the biogeochemistry of nutrients in coastal saltmarshes, ultimately controlling water quality, nutrient cycling, and detoxification. We determined the structure of microbial populations inhabiting coastal saltmarsh sediments from northern Barataria Bay, Louisiana, USA to gain insight into impacts on the biogeochemical cycles affected by Macondo oil from the 2010 Deepwater Horizon well blowout two years after the accident. Quantitative PCR directed toward specific functional genes revealed that oiled marshes were greatly diminished in the population sizes of diazotrophs, denitrifiers, nitrate-reducers to ammonia, methanogens, sulfate-reducers and anaerobic aromatic degraders, and harbored elevated numbers of alkane-degraders. Illumina 16S rRNA gene sequencing indicated that oiling greatly changed the structure of the microbial communities, including significant decreases in diversity. Oil-driven changes were also demonstrated in the structure of two functional populations, denitrifying and sulfate reducing prokaryotes, using nirS and dsrB as biomarkers, respectively. Collectively, the results from 16S rRNA and functional genes indicated that oiling not only markedly altered the microbial community structures, but also the sizes and structures of populations involved in (or regulating) a number of important nutrient biogeochemical cycles in the saltmarshes. Alterations such as these are associated with potential deterioration of ecological services, and further studies are necessary to assess the trajectory of recovery of microbial-mediated ecosystem functions over time in oiled saltmarsh sediment.}, }
@article {pmid29802797, year = {2018}, author = {Liang, J and Xia, J and Shi, Z and Jiang, L and Ma, S and Lu, X and Mauritz, M and Natali, SM and Pegoraro, E and Penton, CR and Plaza, C and Salmon, VG and Celis, G and Cole, JR and Konstantinidis, KT and Tiedje, JM and Zhou, J and Schuur, EAG and Luo, Y}, title = {Biotic responses buffer warming-induced soil organic carbon loss in Arctic tundra.}, journal = {Global change biology}, volume = {24}, number = {10}, pages = {4946-4959}, doi = {10.1111/gcb.14325}, pmid = {29802797}, issn = {1365-2486}, support = {DE SC00114085//US Department of Energy, Terrestrial Ecosystem Sciences/International ; DE-SC0004601//Biological Systems Research on the Role of Microbial Communities in Carbon Cycling Program/International ; DE-SC0010715//Biological Systems Research on the Role of Microbial Communities in Carbon Cycling Program/International ; EF 1137293//US National Science Foundation (NSF)/International ; OIA-1301789//US National Science Foundation (NSF)/International ; 654132//European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie/International ; }, mesh = {Alaska ; Carbon/*analysis/metabolism ; *Climate Change ; Models, Theoretical ; Permafrost/chemistry/microbiology ; Photosynthesis ; Plants/metabolism ; Soil/*chemistry ; Soil Microbiology ; *Tundra ; }, abstract = {Climate warming can result in both abiotic (e.g., permafrost thaw) and biotic (e.g., microbial functional genes) changes in Arctic tundra. Recent research has incorporated dynamic permafrost thaw in Earth system models (ESMs) and indicates that Arctic tundra could be a significant future carbon (C) source due to the enhanced decomposition of thawed deep soil C. However, warming-induced biotic changes may influence biologically related parameters and the consequent projections in ESMs. How model parameters associated with biotic responses will change under warming and to what extent these changes affect projected C budgets have not been carefully examined. In this study, we synthesized six data sets over 5 years from a soil warming experiment at the Eight Mile Lake, Alaska, into the Terrestrial ECOsystem (TECO) model with a probabilistic inversion approach. The TECO model used multiple soil layers to track dynamics of thawed soil under different treatments. Our results show that warming increased light use efficiency of vegetation photosynthesis but decreased baseline (i.e., environment-corrected) turnover rates of SOC in both the fast and slow pools in comparison with those under control. Moreover, the parameter changes generally amplified over time, suggesting processes of gradual physiological acclimation and functional gene shifts of both plants and microbes. The TECO model predicted that field warming from 2009 to 2013 resulted in cumulative C losses of 224 or 87 g/m[2] , respectively, without or with changes in those parameters. Thus, warming-induced parameter changes reduced predicted soil C loss by 61%. Our study suggests that it is critical to incorporate biotic changes in ESMs to improve the model performance in predicting C dynamics in permafrost regions.}, }
@article {pmid29802607, year = {2018}, author = {Masood, N and Halimoon, N and Aris, AZ and Zakaria, MP and Vaezzadeh, V and Magam, SM and Mustafa, S and Ali, MM and Keshavarzifard, M and Alkhadher, SAA and Bong, CW and Alsalahi, MA}, title = {Seasonal variability of anthropogenic indices of PAHs in sediment from the Kuala Selangor River, west coast Peninsular Malaysia.}, journal = {Environmental geochemistry and health}, volume = {40}, number = {6}, pages = {2551-2572}, pmid = {29802607}, issn = {1573-2983}, support = {6379005//Ministry of Higher Education, Malaysia (MY), HICoE-MOHE Grant IOES-2014/ ; }, mesh = {*Environmental Monitoring ; Estuaries ; Gas Chromatography-Mass Spectrometry ; Geologic Sediments/*analysis ; Malaysia ; Petroleum Pollution/*analysis ; Polycyclic Aromatic Hydrocarbons/*analysis ; *Rivers ; Seasons ; Water Pollutants, Chemical/*analysis ; Water Pollution, Chemical/analysis ; }, abstract = {Rapid increase in industrialization and urbanization in the west coast of Peninsular Malaysia has led to the intense release of petroleum and products of petroleum into the environment. Surface sediment samples were collected from the Selangor River in the west coast of Peninsular Malaysia during four climatic seasons and analyzed for PAHs and biomarkers (hopanes). Sediments were soxhlet extracted and further purified and fractionated through first and second step column chromatography. A gas chromatography-mass spectrometry (GC-MS) was used for analysis of PAHs and hopanes fractions. The average concentrations of total PAHs ranged from 219.7 to 672.3 ng g[-1] dw. The highest concentrations of PAHs were detected at 964.7 ng g[-1] dw in station S5 in the mouth of the Selangor River during the wet inter-monsoonal season. Both pyrogenic and petrogenic PAHs were detected in the sediments with a predominance of the former. The composition of hopanes was homogeneous showing that petroleum hydrocarbons share an identical source in the study area. Diagnostic ratios of hopanes indicated that some of the sediment samples carry the crankcase oil signature.}, }
@article {pmid29802478, year = {2018}, author = {Roussel, C and Sivignon, A and de Vallée, A and Garrait, G and Denis, S and Tsilia, V and Ballet, N and Vandekerckove, P and Van de Wiele, T and Barnich, N and Blanquet-Diot, S}, title = {Anti-infectious properties of the probiotic Saccharomyces cerevisiae CNCM I-3856 on enterotoxigenic E. coli (ETEC) strain H10407.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {14}, pages = {6175-6189}, doi = {10.1007/s00253-018-9053-y}, pmid = {29802478}, issn = {1432-0614}, mesh = {Animals ; Antibiosis/*physiology ; Caco-2 Cells ; Enterotoxigenic Escherichia coli/*physiology ; Escherichia coli Infections/*microbiology ; Humans ; Mice ; *Probiotics ; Saccharomyces cerevisiae/*physiology ; }, abstract = {Enterotoxigenic Escherichia coli (ETEC) are major food-borne pathogens responsible for traveler's diarrhea. The production of adhesins and the secretion of enterotoxins constitute the major virulence traits of the bacteria. Treatments are mainly symptomatic and can involve antibiotherapy. However, given the rise of antibiotic resistance worldwide, there is an urgent need for the development of new preventive strategies for the control of ETEC infections. Among them, a promising approach is the use of probiotics. The aim of this study was to investigate, using complementary in vitro and in vivo approaches, the inhibitory potential of the yeast Saccharomyces cerevisiae CNCM I-3856 against the human ETEC reference strain H10407. In conventional culture media, S. cerevisiae significantly reduced ETEC growth and toxin production. The yeast also inhibited bacterial adhesion to mucin-agar and intestinal Caco-2/TC7 cells in a dose-dependent manner. Lastly, pre-treatment with S. cerevisiae inhibited interleukin-8 production by ETEC-infected intestinal cells. In streptomycin-treated mice, the probiotic yeast decreased bacterial colonization, mainly in the ileum, the main site of ETEC pathogenesis. For the first time, this study shows that the probiotic yeast S. cerevisiae CNCM I-3856 can exert an anti-infectious activity against a human ETEC strain through a multi-targeted approach, including inhibition of bacterial growth and toxin production, reduction of bacterial adhesion to mucins and intestinal epithelial cells, and suppression of ETEC-induced inflammation. Interestingly, the highest activity was obtained with a prophylactic treatment. Further studies will aim to assess the effect of the yeast on ETEC survival and virulence under human simulated digestive conditions.}, }
@article {pmid29802242, year = {2018}, author = {Wilhelmson, AS and Lantero Rodriguez, M and Stubelius, A and Fogelstrand, P and Johansson, I and Buechler, MB and Lianoglou, S and Kapoor, VN and Johansson, ME and Fagman, JB and Duhlin, A and Tripathi, P and Camponeschi, A and Porse, BT and Rolink, AG and Nissbrandt, H and Turley, SJ and Carlsten, H and Mårtensson, IL and Karlsson, MCI and Tivesten, &#xc5;}, title = {Testosterone is an endogenous regulator of BAFF and splenic B cell number.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2067}, pmid = {29802242}, issn = {2041-1723}, mesh = {Adrenergic alpha-Agonists/pharmacology ; Animals ; Autoimmune Diseases/immunology/*metabolism ; B-Cell Activating Factor/blood/*immunology/*metabolism ; B-Cell Activation Factor Receptor/antagonists &amp; inhibitors/metabolism ; B-Lymphocytes/drug effects/*immunology/metabolism ; Castration ; Humans ; Male ; Mice ; Mice, Knockout ; Models, Animal ; Norepinephrine/metabolism ; Oxidopamine/pharmacology ; Receptors, Androgen/genetics/metabolism ; Spleen/cytology/drug effects/immunology ; Testosterone/blood/deficiency/immunology/*metabolism ; }, abstract = {Testosterone deficiency in men is associated with increased risk for autoimmunity and increased B cell numbers through unknown mechanisms. Here we show that testosterone regulates the cytokine BAFF, an essential survival factor for B cells. Male mice lacking the androgen receptor have increased splenic B cell numbers, serum BAFF levels and splenic Baff mRNA. Testosterone deficiency by castration causes expansion of BAFF-producing fibroblastic reticular cells (FRCs) in spleen, which may be coupled to lower splenic noradrenaline levels in castrated males, as an α-adrenergic agonist decreases splenic FRC number in vitro. Antibody-mediated blockade of the BAFF receptor or treatment with the neurotoxin 6-hydroxydopamine revert the increased splenic B cell numbers induced by castration. Among healthy men, serum BAFF levels are higher in men with low testosterone. Our study uncovers a previously unrecognized regulation of BAFF by testosterone and raises important questions about BAFF in testosterone-mediated protection against autoimmunity.}, }
@article {pmid29802195, year = {2018}, author = {Mertens, J and Aliyu, H and Cowan, DA}, title = {LEA Proteins and the Evolution of the WHy Domain.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {15}, pages = {}, pmid = {29802195}, issn = {1098-5336}, mesh = {Bacteria/chemistry/classification/genetics/*metabolism ; Bacterial Proteins/*chemistry/genetics/metabolism ; *Evolution, Molecular ; Phylogeny ; Plant Proteins/chemistry/genetics/*metabolism ; Plants/chemistry/classification/genetics/*metabolism ; Protein Domains ; }, abstract = {The late embryogenesis abundant (LEA) family is composed of a diverse collection of multidomain and multifunctional proteins found in all three domains of the tree of life, but they are particularly common in plants. Most members of the family are known to play an important role in abiotic stress response and stress tolerance in plants but are also part of the plant hypersensitive response to pathogen infection. The mechanistic basis for LEA protein functionality is still poorly understood. The group of LEA 2 proteins harbor one or more copies of a unique domain, the water stress and hypersensitive response (WHy) domain. This domain sequence has recently been identified as a unique open reading frame (ORF) in some bacterial genomes (mostly in the phylum Firmicutes), and the recombinant bacterial WHy protein has been shown to exhibit a stress tolerance phenotype in Escherichia coli and an in vitro protein denaturation protective function. Multidomain phylogenetic analyses suggest that the WHy protein gene sequence may have ancestral origins in the domain Archaea, with subsequent acquisition in Bacteria and eukaryotes via endosymbiont or horizontal gene transfer mechanisms. Here, we review the structure, function, and nomenclature of LEA proteins, with a focus on the WHy domain as an integral component of the LEA constructs and as an independent protein.}, }
@article {pmid29796758, year = {2019}, author = {Pessi, IS and Pushkareva, E and Lara, Y and Borderie, F and Wilmotte, A and Elster, J}, title = {Marked Succession of Cyanobacterial Communities Following Glacier Retreat in the High Arctic.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {136-147}, pmid = {29796758}, issn = {1432-184X}, support = {LM2010009//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; RVO67985939//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; CRCH1011-1513911//Fonds De La Recherche Scientifique - FNRS/ ; FRFC2457009//Fonds De La Recherche Scientifique - FNRS/ ; }, mesh = {Arctic Regions ; Biodiversity ; Cyanobacteria/*classification/genetics ; DNA, Bacterial ; Genotype ; High-Throughput Nucleotide Sequencing ; Ice Cover/*microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Svalbard ; }, abstract = {Cyanobacteria are important colonizers of recently deglaciated proglacial soil but an in-depth investigation of cyanobacterial succession following glacier retreat has not yet been carried out. Here, we report on the successional trajectories of cyanobacterial communities in biological soil crusts (BSCs) along a 100-year deglaciation gradient in three glacier forefields in central Svalbard, High Arctic. Distance from the glacier terminus was used as a proxy for soil age (years since deglaciation), and cyanobacterial abundance and community composition were evaluated by epifluorescence microscopy and pyrosequencing of partial 16S rRNA gene sequences, respectively. Succession was characterized by a decrease in phylotype richness and a marked shift in community structure, resulting in a clear separation between early (10-20 years since deglaciation), mid (30-50 years), and late (80-100 years) communities. Changes in cyanobacterial community structure were mainly connected with soil age and associated shifts in soil chemical composition (mainly moisture, SOC, SMN, K, and Na concentrations). Phylotypes associated with early communities were related either to potentially novel lineages (< 97.5% similar to sequences currently available in GenBank) or lineages predominantly restricted to polar and alpine biotopes, suggesting that the initial colonization of proglacial soil is accomplished by cyanobacteria transported from nearby glacial environments. Late communities, on the other hand, included more widely distributed genotypes, which appear to establish only after the microenvironment has been modified by the pioneering taxa.}, }
@article {pmid29795328, year = {2018}, author = {Knight, R and Vrbanac, A and Taylor, BC and Aksenov, A and Callewaert, C and Debelius, J and Gonzalez, A and Kosciolek, T and McCall, LI and McDonald, D and Melnik, AV and Morton, JT and Navas, J and Quinn, RA and Sanders, JG and Swafford, AD and Thompson, LR and Tripathi, A and Xu, ZZ and Zaneveld, JR and Zhu, Q and Caporaso, JG and Dorrestein, PC}, title = {Best practices for analysing microbiomes.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {7}, pages = {410-422}, doi = {10.1038/s41579-018-0029-9}, pmid = {29795328}, issn = {1740-1534}, mesh = {Animals ; Bacteria/*genetics ; Environmental Microbiology ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Reproducibility of Results ; }, abstract = {Complex microbial communities shape the dynamics of various environments, ranging from the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies and data analysis have provided drastic improvements in microbiome analyses, for example, in taxonomic resolution, false discovery rate control and other properties, over earlier methods. In this Review, we discuss the best practices for performing a microbiome study, including experimental design, choice of molecular analysis technology, methods for data analysis and the integration of multiple omics data sets. We focus on recent findings that suggest that operational taxonomic unit-based analyses should be replaced with new methods that are based on exact sequence variants, methods for integrating metagenomic and metabolomic data, and issues surrounding compositional data analysis, where advances have been particularly rapid. We note that although some of these approaches are new, it is important to keep sight of the classic issues that arise during experimental design and relate to research reproducibility. We describe how keeping these issues in mind allows researchers to obtain more insight from their microbiome data sets.}, }
@article {pmid29789680, year = {2018}, author = {Banerjee, S and Schlaeppi, K and van der Heijden, MGA}, title = {Keystone taxa as drivers of microbiome structure and functioning.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {9}, pages = {567-576}, doi = {10.1038/s41579-018-0024-1}, pmid = {29789680}, issn = {1740-1534}, mesh = {Animals ; Bacteria/classification/isolation &amp; purification/metabolism ; *Environmental Microbiology ; Humans ; *Microbiota ; }, abstract = {Microorganisms have a pivotal role in the functioning of ecosystems. Recent studies have shown that microbial communities harbour keystone taxa, which drive community composition and function irrespective of their abundance. In this Opinion article, we propose a definition of keystone taxa in microbial ecology and summarize over 200 microbial keystone taxa that have been identified in soil, plant and marine ecosystems, as well as in the human microbiome. We explore the importance of keystone taxa and keystone guilds for microbiome structure and functioning and discuss the factors that determine their distribution and activities.}, }
@article {pmid29788358, year = {2018}, author = {Waldschmitt, N and Metwaly, A and Fischer, S and Haller, D}, title = {Microbial Signatures as a Predictive Tool in IBD-Pearls and Pitfalls.}, journal = {Inflammatory bowel diseases}, volume = {24}, number = {6}, pages = {1123-1132}, doi = {10.1093/ibd/izy059}, pmid = {29788358}, issn = {1536-4844}, mesh = {Animals ; *Disease Models, Animal ; Dysbiosis/*complications/diagnosis ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*etiology/*microbiology ; Mice ; }, abstract = {Studies of microbial signatures have improved our understanding of the role of dysbiosis in gut microbiota for the pathogenesis of inflammatory bowel disease (IBD). New technological advances such as next-generation sequencing facilitate investigations on large patient cohorts, but require methodological considerations regarding study design, sample processing, data analysis, and integration. Here, we summarize recent study approaches in microbial ecology with respect to IBD research and discuss crucial process steps for the production and integration of adequate data sets.}, }
@article {pmid29787679, year = {2018}, author = {Bader, M and Dunkel, A and Wenning, M and Kohler, B and Medard, G and Del Castillo, E and Gholami, A and Kuster, B and Scherer, S and Hofmann, T}, title = {Dynamic Proteome Alteration and Functional Modulation of Human Saliva Induced by Dietary Chemosensory Stimuli.}, journal = {Journal of agricultural and food chemistry}, volume = {66}, number = {22}, pages = {5621-5634}, doi = {10.1021/acs.jafc.8b02092}, pmid = {29787679}, issn = {1520-5118}, mesh = {Adult ; Aspartame/metabolism ; Catechols/metabolism ; Citric Acid/metabolism ; Electrophoresis, Polyacrylamide Gel ; Fatty Alcohols/metabolism ; Female ; Humans ; Male ; Muramidase/analysis/metabolism ; Peroxidase/metabolism ; Proteome/*chemistry/metabolism ; Saliva/chemistry/*metabolism ; Sodium Glutamate/metabolism ; Tandem Mass Spectrometry ; Taste ; Young Adult ; }, abstract = {Saliva flow measurements and SDS-PAGE separation of human whole saliva freshly collected after oral stimulation with citric acid (sour), aspartame (sweet), iso-α-acids (bitter), mono sodium l-glutamate (umami), NaCl (salty), 6-gingerol (pungent), hydroxy-α-sanshool (tingling), and hydroxy-β-sanshool (numbing), followed by tryptic digestion, nano-HPLC-MS/MS, and label-free protein quantitation demonstrated a stimulus- and time-dependent influence of the dietary chemosensates on salivation and the salivary proteome composition. Gene ontology enrichment analysis showed evidence for stimulus-induced alterations of the saliva proteome to boot an efficient molecular defense network of the oral cavity, e.g., 6-gingerol increased salivary lactoperoxidase activity, catalyzing the oxidation of thiocyanate to produce the antimicrobial and antifungal hypothiocyanate, from 0.37 ± 0.02 to 0.91 ± 0.05 mU/mL 45 s after stimulation. In comparison, oral citric acid stimulation induced an increase of myeloperoxidase activity, catalyzing the chloride oxidation to generate antimicrobial hypochloride in saliva, from 0.24 ± 0.04 to 0.70 ± 0.1 mU/mL as well as an increase of salivary levels of lysozyme, exhibiting antimicrobial activity on Gram-positive bacteria, from 6.0-10 to 100-150 μg/mL. Finally, microbial growth experiments clearly demonstrated for the first time that the increase of the salivary lysozyme abundance upon oral citric acid stimulation translates into an enhanced biological function, that is an almost complete growth inhibition of the two lysozyme-sensitive Gram-positive bacteria tested.}, }
@article {pmid29787677, year = {2018}, author = {Seuntjens, D and Van Tendeloo, M and Chatzigiannidou, I and Carvajal-Arroyo, JM and Vandendriessche, S and Vlaeminck, SE and Boon, N}, title = {Synergistic Exposure of Return-Sludge to Anaerobic Starvation, Sulfide, and Free Ammonia to Suppress Nitrite Oxidizing Bacteria.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {15}, pages = {8725-8732}, doi = {10.1021/acs.est.7b06591}, pmid = {29787677}, issn = {1520-5851}, mesh = {Ammonia ; Anaerobiosis ; Bacteria ; Bioreactors ; *Nitrites ; Oxidation-Reduction ; *Sewage ; Sulfides ; }, abstract = {A key step toward energy-positive sewage treatment is the development of mainstream partial nitritation/anammox, a nitrogen removal technology where aerobic ammonium-oxidizing bacteria (AerAOB) are desired, while nitrite-oxidizing bacteria (NOB) are not. To suppress NOB, a novel return-sludge treatment was investigated. Single and combined effects of sulfide (0-600 mg S L[-1]), anaerobic starvation (0-8 days), and a free ammonia (FA) shock (30 mg FA-N L[-1] for 1 h) were tested for immediate effects and long-term recovery. AerAOB and NOB were inhibited immediately and proportionally by sulfide, with AerAOB better coping with the inhibition, while the short FA shock and anaerobic starvation had minor effects. Combinatory effects inhibited AerAOB and NOB more strongly. A combined treatment of sulfide (150 mg S L[-1]), 2 days of anaerobic starvation, and FA shock (30 mg FA-N L[-1]) inhibited AerAOB 14% more strongly compared to sulfide addition alone, while the AerAOB/NOB activity ratio remained constant. Despite no positive change being observed in the immediate-stress response, AerAOB recovered much faster than NOB, with a nitrite accumulation ratio (effluent nitrite on nitrite + nitrate) peak of 50% after 12 days. Studying long-term recovery is therefore crucial for design of an optimal NOB-suppression treatment, while applying combined stressors regularly may lead toward practical implementation.}, }
@article {pmid29785352, year = {2018}, author = {Gajigan, AP and Yñiguez, AT and Villanoy, CL and San Diego-McGlone, ML and Jacinto, GS and Conaco, C}, title = {Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4781}, pmid = {29785352}, issn = {2167-8359}, abstract = {Microbes are central to the structuring and functioning of marine ecosystems. Given the remarkable diversity of the ocean microbiome, uncovering marine microbial taxa remains a fundamental challenge in microbial ecology. However, there has been little effort, thus far, to describe the diversity of marine microorganisms in the region of high marine biodiversity around the Philippines. Here, we present data on the taxonomic diversity of bacteria and archaea in Benham Rise, Philippines, Western Pacific Ocean, using 16S V4 rRNA gene sequencing. The major bacterial and archaeal phyla identified in the Benham Rise are Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Marinimicrobia, Thaumarchaeota and, Euryarchaeota. The upper mesopelagic layer exhibited greater microbial diversity and richness compared to surface waters. Vertical zonation of the microbial community is evident and may be attributed to physical stratification of the water column acting as a dispersal barrier. Canonical Correspondence Analysis (CCA) recapitulated previously known associations of taxa and physicochemical parameters in the environment, such as the association of oligotrophic clades with low nutrient surface water and deep water clades that have the capacity to oxidize ammonia or nitrite at the upper mesopelagic layer. These findings provide foundational information on the diversity of marine microbes in Philippine waters. Further studies are warranted to gain a more comprehensive picture of microbial diversity within the region.}, }
@article {pmid29784985, year = {2018}, author = {Chalermwatanachai, T and Vilchez-Vargas, R and Holtappels, G and Lacoere, T and Jáuregui, R and Kerckhof, FM and Pieper, DH and Van de Wiele, T and Vaneechoutte, M and Van Zele, T and Bachert, C}, title = {Chronic rhinosinusitis with nasal polyps is characterized by dysbacteriosis of the nasal microbiota.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {7926}, pmid = {29784985}, issn = {2045-2322}, mesh = {Adult ; Asthma/physiopathology ; Bacteria/*isolation &amp; purification ; Bacterial Infections/*microbiology ; Case-Control Studies ; Chronic Disease ; Dysbiosis/*microbiology ; Female ; Humans ; Inflammation/etiology ; Male ; Middle Aged ; Nasal Polyps/*microbiology ; Nose/*microbiology ; Rhinitis/*microbiology ; Sinusitis/*microbiology ; }, abstract = {Chronic rhinosinusitis with nasal polyp (CRSwNP) patients are often characterized by asthma comorbidity and a type-2 inflammation of the sinonasal mucosa. The mucosal microbiota has been suggested to be implicated in the persistence of inflammation, but associations have not been well defined. To compare the bacterial communities of healthy subjects with CRSwNP patients, we collected nasal swabs from 17 healthy subjects, 21 CRSwNP patients without asthma (CRSwNP-A), and 20 CRSwNP patients with co-morbid asthma (CRSwNP+A). We analysed the microbiota using high-throughput sequencing of the bacterial 16S rRNA. Bacterial communities were different between the three groups. Haemophilus influenzae was significantly enriched in CRSwNP patients, Propionibacterium acnes in the healthy group; Staphylococcus aureus was abundant in the CRSwNP-A group, even though present in 57% of patients. Escherichia coli was found in high amounts in CRSwNP+A patients. Nasal tissues of CRSwNP+A patients expressed significantly higher concentrations of IgE, SE-IgE, and IL-5 compared to those of CRSwNP-A patients. Co-cultivation demonstrated that P. acnes growth was inhibited by H. influenzae, E. coli and S. aureus. The nasal microbiota of healthy subjects are different from those of CRSwNP-A and CRSwNP+A patients. However, the most abundant species in healthy status could not inhibit those in CRSwNP disease.}, }
@article {pmid29783165, year = {2018}, author = {Miller, HC and Morgan, MJ and Walsh, T and Wylie, JT and Kaksonen, AH and Puzon, GJ}, title = {Preferential feeding in Naegleria fowleri; intracellular bacteria isolated from amoebae in operational drinking water distribution systems.}, journal = {Water research}, volume = {141}, number = {}, pages = {126-134}, doi = {10.1016/j.watres.2018.05.004}, pmid = {29783165}, issn = {1879-2448}, mesh = {Biofilms ; Deinococcus/genetics/*isolation &amp; purification/physiology ; Drinking Water/*microbiology ; Environmental Monitoring ; Naegleria fowleri/isolation &amp; purification/*microbiology ; RNA, Ribosomal, 16S ; Water Pollutants/isolation &amp; purification ; }, abstract = {The amoeba Naegleria fowleri is the causative agent of the highly fatal disease, primary amoebic meningoencephalitis, and estimated to cause 16 deaths per year in the United States alone. Colonisation of drinking water distribution systems (DWDSs) by the N. fowleri is a significant public health issue. Understanding the factors which enable this pathogen to colonise and thrive in DWDSs is critical for proper management. The microbial ecology within DWDSs may influence the ability of N. fowleri to colonise DWDSs by facilitating the availability of an appropriate food source. Using biofilm samples obtained from operational DWDSs, 16S rRNA amplicon metabarcoding was combined with genus-specific PCR and Sanger sequencing of intracellular associated bacteria from isolated amoeba and their parental biofilms to identify Meiothermus chliarophilus as a potential food source for N. fowleri. Meiothermus was confirmed as a food source for N. fowleri following successful serial culturing of axenic N. fowleri with M. chliarophilus or M. ruber as the sole food source. The ability to identify environmental and ecological conditions favourable to N. fowleri colonisation, including the detection of appropriate food sources such as Meiothermus, could provide water utilities with a predictive tool for managing N. fowleri colonisation within the DWDS.}, }
@article {pmid29782923, year = {2019}, author = {Wong, SH and Kwong, TNY and Wu, CY and Yu, J}, title = {Clinical applications of gut microbiota in cancer biology.}, journal = {Seminars in cancer biology}, volume = {55}, number = {}, pages = {28-36}, doi = {10.1016/j.semcancer.2018.05.003}, pmid = {29782923}, issn = {1096-3650}, mesh = {Computational Biology ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenomics ; Neoplasms/diagnosis/*genetics/microbiology/therapy ; }, abstract = {The involvement of microorganisms in cancer has been increasing recognized. Collectively, microorganisms have been estimated to account for ∼20% of all cancers worldwide. Recent advances in metagenomics and bioinformatics have provided new insights on the microbial ecology in different tumors, pinpointing the roles of microorganisms in cancer formation, development and response to treatments. Furthermore, studies have emphasized the importance of host-microbial and inter-microbial interactions in the cancer microbiota. These studies have not only revolutionized our understanding of cancer biology, but also opened up new opportunities for cancer prevention, diagnosis, prognostication and treatment. This review article aims to summarize the microbiota in various cancers and their treatments, and explore clinical applications for such relevance.}, }
@article {pmid29780377, year = {2018}, author = {Egerton, S and Culloty, S and Whooley, J and Stanton, C and Ross, RP}, title = {The Gut Microbiota of Marine Fish.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {873}, pmid = {29780377}, issn = {1664-302X}, abstract = {The body of work relating to the gut microbiota of fish is dwarfed by that on humans and mammals. However, it is a field that has had historical interest and has grown significantly along with the expansion of the aquaculture industry and developments in microbiome research. Research is now moving quickly in this field. Much recent focus has been on nutritional manipulation and modification of the gut microbiota to meet the needs of fish farming, while trying to maintain host health and welfare. However, the diversity amongst fish means that baseline data from wild fish and a clear understanding of the role that specific gut microbiota play is still lacking. We review here the factors shaping marine fish gut microbiota and highlight gaps in the research.}, }
@article {pmid29779128, year = {2019}, author = {Kurina, IV and Li, H}, title = {Why Do Testate Amoeba Optima Related to Water Table Depth Vary?.}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {37-55}, pmid = {29779128}, issn = {1432-184X}, support = {16-34-60057//Russian Foundation for Basic Research/ ; }, mesh = {Amoeba/*classification/*physiology ; *Ecology ; Ecosystem ; Environmental Monitoring ; Groundwater/*chemistry/*parasitology ; Hydrogen-Ion Concentration ; Siberia ; Water/chemistry ; Water Microbiology ; }, abstract = {This study focusses on the ecology of testate amoeba species in peatlands of the southern taiga of Western Siberia. To estimate the influence of the trophic state of mires on species optima related to water table depth, a separate study of three calibration datasets including ombrotrophic, minerotrophic and the combined habitats was conducted. In the datasets obtained separately from ombrotrophic and minerotrophic mires, the water table depth was the main factor affecting testate amoeba assemblages. However, the trophic state (specifically pH and ash content) was more important factor in the combined dataset, including all of the studied mires. For 36 testate amoeba species, which were found in the ombrotrophic and minerotrophic mire habitats, their species optima, obtained separately in ombrotrophic and minerotrophic datasets, differed significantly from each other. Some of these species preferred minerotrophic conditions, while others preferred ombrotrophic ones. For all species, the trophic state of the mires affected the values of the species optima related to water table depth, as revealed in the form of a threshold effect. In extreme conditions, the species were more sensitive to the trophic status than to the water table depth, and their optimum related to water table depth was distorted. Variation of the optimum was observed in those species that inhabited both ombrotrophic and minerotrophic mires due to the fact that mires with a different trophic status were included in the training sets. The optima did not vary for species inhabiting only ombrotrophic or only minerotrophic mires.}, }
@article {pmid29776729, year = {2018}, author = {Farhat, A and Manai, I and Gtari, M and Bouallagui, H}, title = {Effect of enhancing nutrient balance in anaerobic digester feedstock by co-substrate addition on the microbial diversity and energy production from municipal sewage sludge.}, journal = {Journal of bioscience and bioengineering}, volume = {126}, number = {4}, pages = {497-506}, doi = {10.1016/j.jbiosc.2018.04.014}, pmid = {29776729}, issn = {1347-4421}, mesh = {Anaerobiosis ; Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Biodegradation, Environmental ; *Biodiversity ; Biofuels/*analysis ; Bioreactors/microbiology ; Methane/biosynthesis ; Sewage/*microbiology ; Wastewater/chemistry/microbiology ; }, abstract = {Enhancement of methane production during anaerobic digestion of waste activated sludge (WAS) could improve the energy self sufficiency of the municipal wastewater treatment plants (WWTPs). Therefore, mixing WAS with organic wastes improved process performance and stability. In this work, the anaerobic co-digestion of WAS combined with the olive processing wastewater (OPW) was investigated and associated with the energetic benefits and microbial populations shifts. The bio-methane potential (BMP) of various WAS and OPW mixtures corresponding to increased phenols concentrations were tested. The anaerobic digestion of better proportions (90%/10% and 80%/20%) was performed in anaerobic sequencing batch reactors (ASBRs). The biodegradation of phenols at concentrations up to 0.76 g/L was confirmed by Sephadex gel filtration showing that ASBR, which is suspended growth reactor, can handle much higher concentration of toxic compounds. Microbial analysis showed that phenols induced significantly the archaea community dynamic, which showed highly richness and diversity in the well performed reactor. The dominant bacteria and archaea phylotypes were affiliated to Proteobacteria and Methanosarcinales, respectively. Therefore, OPW addition increased total energy production from 24.6 kWh/ton to 64.7 kWh/ton, which would provide 0.43 M€/year net benefits only from the electric power. In addition it brings a payback time on investment of 2 years for WWTPs modification, which was considered interesting.}, }
@article {pmid29774016, year = {2018}, author = {Cheaib, B and Le Boulch, M and Mercier, PL and Derome, N}, title = {Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {869}, pmid = {29774016}, issn = {1664-302X}, abstract = {Adaptation of microbial communities to anthropogenic stressors can lead to reductions in microbial diversity and disequilibrium of ecosystem services. Such adaptation can change the molecular signatures of communities with differences in taxonomic and functional composition. Understanding the relationship between taxonomic and functional variation remains a critical issue in microbial ecology. Here, we assessed the taxonomic and functional diversity of a lake metacommunity system along a polymetallic pollution gradient caused by 60 years of chronic exposure to acid mine drainage (AMD). Our results highlight three adaptive signatures. First, a signature of taxon-function decoupling was detected in the microbial communities of moderately and highly polluted lakes. Second, parallel shifts in taxonomic composition occurred between polluted and unpolluted lakes. Third, variation in the abundance of functional modules suggested a gradual deterioration of ecosystem services (i.e., photosynthesis) and secondary metabolism in highly polluted lakes. Overall, changes in the abundance of taxa, function, and more importantly the polymetallic resistance genes such as copA, copB, czcA, cadR, cCusA, were correlated with trace metal content (mainly Cadmium) and acidity. Our findings highlight the impact of polymetallic pollution gradient at the lowest trophic levels.}, }
@article {pmid29774012, year = {2018}, author = {Schultz-Johansen, M and Bech, PK and Hennessy, RC and Glaring, MA and Barbeyron, T and Czjzek, M and Stougaard, P}, title = {A Novel Enzyme Portfolio for Red Algal Polysaccharide Degradation in the Marine Bacterium Paraglaciecola hydrolytica S66[T] Encoded in a Sizeable Polysaccharide Utilization Locus.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {839}, pmid = {29774012}, issn = {1664-302X}, abstract = {Marine microbes are a rich source of enzymes for the degradation of diverse polysaccharides. Paraglaciecola hydrolytica S66[T] is a marine bacterium capable of hydrolyzing polysaccharides found in the cell wall of red macroalgae. In this study, we applied an approach combining genomic mining with functional analysis to uncover the potential of this bacterium to produce enzymes for the hydrolysis of complex marine polysaccharides. A special feature of P. hydrolytica S66[T] is the presence of a large genomic region harboring an array of carbohydrate-active enzymes (CAZymes) notably agarases and carrageenases. Based on a first functional characterization combined with a comparative sequence analysis, we confirmed the enzymatic activities of several enzymes required for red algal polysaccharide degradation by the bacterium. In particular, we report for the first time, the discovery of novel enzyme activities targeting furcellaran, a hybrid carrageenan containing both β-carrageenan and κ/β-carrageenan motifs. Some of these enzymes represent a new subfamily within the CAZy classification. From the combined analyses, we propose models for the complete degradation of agar and κ/β-type carrageenan by P. hydrolytica S66[T]. The novel enzymes described here may find value in new bio-based industries and advance our understanding of the mechanisms responsible for recycling of red algal polysaccharides in marine ecosystems.}, }
@article {pmid29772177, year = {2018}, author = {Alloul, A and Ganigué, R and Spiller, M and Meerburg, F and Cagnetta, C and Rabaey, K and Vlaeminck, SE}, title = {Capture-Ferment-Upgrade: A Three-Step Approach for the Valorization of Sewage Organics as Commodities.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {12}, pages = {6729-6742}, doi = {10.1021/acs.est.7b05712}, pmid = {29772177}, issn = {1520-5851}, mesh = {Biological Oxygen Demand Analysis ; Bioreactors ; Fatty Acids, Volatile ; Fermentation ; Hydrolysis ; *Polyhydroxyalkanoates ; *Sewage ; }, abstract = {This critical review outlines a roadmap for the conversion of chemical oxygen demand (COD) contained in sewage to commodities based on three-steps: capture COD as sludge, ferment it to volatile fatty acids (VFA), and upgrade VFA to products. The article analyzes the state-of-the-art of this three-step approach and discusses the bottlenecks and challenges. The potential of this approach is illustrated for the European Union's 28 member states (EU-28) through Monte Carlo simulations. High-rate contact stabilization captures the highest amount of COD (66-86 g COD person equivalent[-1] day[-1] in 60% of the iterations). Combined with thermal hydrolysis, this would lead to a VFA-yield of 23-44 g COD person equivalent[-1] day[-1]. Upgrading VFA generated by the EU-28 would allow, in 60% of the simulations, for a yearly production of 0.2-2.0 megatonnes of esters, 0.7-1.4 megatonnes of polyhydroxyalkanoates or 0.6-2.2 megatonnes of microbial protein substituting, respectively, 20-273%, 70-140% or 21-72% of their global counterparts (i.e., petrochemical-based esters, bioplastics or fishmeal). From these flows, we conclude that sewage has a strong potential as biorefinery feedstock, although research is needed to enhance capture, fermentation and upgrading efficiencies. These developments need to be supported by economic/environmental analyses and policies that incentivize a more sustainable management of our resources.}, }
@article {pmid29771325, year = {2018}, author = {Armada, E and Leite, MFA and Medina, A and Azcón, R and Kuramae, EE}, title = {Native bacteria promote plant growth under drought stress condition without impacting the rhizomicrobiome.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {7}, pages = {}, doi = {10.1093/femsec/fiy092}, pmid = {29771325}, issn = {1574-6941}, mesh = {Asteraceae/*growth &amp; development/microbiology ; Bacillus thuringiensis/*metabolism ; Biomass ; Droughts ; Ecosystem ; Fungi/*metabolism ; Lavandula/growth &amp; development/*microbiology ; Mycorrhizae/*growth &amp; development ; Plant Development/physiology ; Plant Roots/*growth &amp; development/microbiology ; Plants/microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Rhizosphere ; Soil ; Soil Microbiology ; Thymus Plant/*growth &amp; development/microbiology ; }, abstract = {Inoculation of plants with beneficial plant growth-promoting bacteria (PGPB) emerges a valuable strategy for ecosystem recovery. However, drought conditions might compromise plant-microbe interactions especially in semiarid regions. This study highlights the effect of native PGPB after 1 year inoculation on autochthonous shrubs growth and rhizosphere microbial community composition and activity under drought stress conditions. We inoculated three plant species of semiarid Mediterranean zones, Thymus vulgaris, Santolina chamaecyparissus and Lavandula dentata with a Bacillus thuringiensis strain IAM 12077 and evaluated the impact on plant biomass, plant nutrient contents, arbuscular mycorrhiza fungi (AMF) colonization, soil rhizosphere microbial activity and both the bacterial and fungal communities. Inoculation with strain IAM 12077 improved the ability of all three plants species to uptake nutrients from the soil, promoted L. dentata shoot growth (>65.8%), and doubled the AMF root colonization of S. chamaecyparissus. Inoculation did not change the rhizosphere microbial community. Moreover, changes in rhizosphere microbial activity were mainly plant species-specific and strongly associated with plant nutrients. In conclusion, the strain IAM 12077 induced positive effects on plant growth and nutrient acquisition with no impact on the rhizosphere microbiome, indicating a rhizosphere microbial community resilient to native bacteria inoculation.}, }
@article {pmid29769378, year = {2018}, author = {Warren, FJ and Fukuma, NM and Mikkelsen, D and Flanagan, BM and Williams, BA and Lisle, AT and Ó Cuív, P and Morrison, M and Gidley, MJ}, title = {Food Starch Structure Impacts Gut Microbiome Composition.}, journal = {mSphere}, volume = {3}, number = {3}, pages = {}, pmid = {29769378}, issn = {2379-5042}, mesh = {Animals ; Fermentation ; *Food Analysis ; Gastrointestinal Microbiome/*drug effects ; Models, Biological ; Starch/*administration &amp; dosage/*metabolism ; Swine ; }, abstract = {Starch is a major source of energy in the human diet and is consumed in diverse forms. Resistant starch (RS) escapes small intestinal digestion and is fermented in the colon by the resident microbiota, with beneficial impacts on colonic function and host health, but the impacts of the micro- and nanoscale structure of different physical forms of food starch on the broader microbial community have not been described previously. Here, we use a porcine in vitro fermentation model to establish that starch structure dramatically impacts microbiome composition, including the key amylolytic species, and markedly alters both digestion kinetics and fermentation outcomes. We show that three characteristic food forms of starch that survive digestion in the small intestine each give rise to substantial and distinct changes in the microbiome and in fermentation products. Our results highlight the complexity of starch fermentation processes and indicate that not all forms of RS in foods are degraded or fermented in the same way. This work points the way for the design of RS with tailored degradation by defined microbial communities, informed by an understanding of how substrate structure influences the gut microbiome, to improve nutritive value and/or health benefits.IMPORTANCE Dietary starch is a major component in the human diet. A proportion of the starch in our diet escapes digestion in the small intestine and is fermented in the colon. In this study, we use a model of the colon, seeded with porcine feces, in which we investigate the fermentation of a variety of starches with structures typical of those found in foods. We show that the microbial community changes over time in our model colon are highly dependent on the structure of the substrate and how accessible the starch is to colonic microbes. These findings have important implications for how we classify starches reaching the colon and for the design of foods with improved nutritional properties.}, }
@article {pmid29769279, year = {2018}, author = {Granchelli, AM and Adler, FR and Keogh, RH and Kartsonaki, C and Cox, DR and Liou, TG}, title = {Microbial Interactions in the Cystic Fibrosis Airway.}, journal = {Journal of clinical microbiology}, volume = {56}, number = {8}, pages = {}, pmid = {29769279}, issn = {1098-660X}, support = {R01 HL125520/HL/NHLBI NIH HHS/United States ; T32 HL105321/HL/NHLBI NIH HHS/United States ; U54 CA209978/CA/NCI NIH HHS/United States ; MR/M014827/1//Medical Research Council/United Kingdom ; }, mesh = {Adolescent ; Bacteria/classification/growth &amp; development/isolation &amp; purification ; Child ; Cystic Fibrosis/*microbiology ; Female ; Fungi/classification/growth &amp; development/isolation &amp; purification ; Humans ; Longitudinal Studies ; Male ; *Microbial Interactions ; *Microbiota ; Respiratory Tract Infections/*microbiology ; Sputum/microbiology ; Young Adult ; }, abstract = {Interactions in the airway ecology of cystic fibrosis may alter organism persistence and clinical outcomes. Better understanding of such interactions could guide clinical decisions. We used generalized estimating equations to fit logistic regression models to longitudinal 2-year patient cohorts in the Cystic Fibrosis Foundation Patient Registry, 2003 to 2011, in order to study associations between the airway organisms present in each calendar year and their presence in the subsequent year. Models were adjusted for clinical characteristics and multiple observations per patient. Adjusted models were tested for sensitivity to cystic fibrosis-specific treatments. The study included 28,042 patients aged 6 years and older from 257 accredited U.S. care centers and affiliates. These patients had produced sputum specimens for at least two consecutive years that were cultured for methicillin-sensitive Staphylococcus aureus, methicillin-resistant S. aureus, Pseudomonas aeruginosa, Burkholderia cepacia complex, Stenotrophomonas maltophilia, Achromobacter xylosoxidans, and Candida and Aspergillus species. We analyzed 99.8% of 538,458 sputum cultures from the patients during the study period. Methicillin-sensitive S. aureus was negatively associated with subsequent Paeruginosa. Paeruginosa was negatively associated with subsequent B. cepacia complex, Axylosoxidans, and Smaltophilia. Bcepacia complex was negatively associated with the future presence of all bacteria studied, as well as with that of Aspergillus species. Paeruginosa, B. cepacia complex, and S. maltophilia were each reciprocally and positively associated with Aspergillus species. Independently of patient characteristics, the organisms studied interact and alter the outcomes of treatment decisions, sometimes in unexpected ways. By inhibiting P. aeruginosa, methicillin-sensitive S. aureus may delay lung disease progression. Paeruginosa and B. cepacia complex may inhibit other organisms by decreasing airway biodiversity, potentially worsening lung disease.}, }
@article {pmid29767159, year = {2017}, author = {Luo, D and Gao, Y and Lu, Y and Qu, M and Xiong, X and Xu, L and Zhao, X and Pan, K and Ouyang, K}, title = {Niacin alters the ruminal microbial composition of cattle under high-concentrate condition.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {3}, number = {2}, pages = {180-185}, pmid = {29767159}, issn = {2405-6383}, abstract = {To understand the effects of niacin on the ruminal microbial ecology of cattle under high-concentrate diet condition, Illumina MiSeq sequencing technology was used. Three cattle with rumen cannula were used in a 3 × 3 Latin-square design trial. Three diets were fed to these cattle during 3 periods for 3 days, respectively: high-forage diet (HF; forage-to-concentrate ratio = 80:20), high-concentrate diet (HC; forage-to-concentrate ratio = 20:80), and HC supplemented with 800 mg/kg niacin (HCN). Ruminal pH was measured before feeding and every 2 h after initiating feeding. Ruminal fluid was sampled at the end of each period for microbial DNA extraction. Overall, our findings revealed that subacute ruminal acidosis (SARA) was induced and the α-diversity of ruminal bacterial community decreased in the cattle of HC group. Adding niacin in HC could relieve the symptoms of SARA in the cattle but the ruminal pH value and the Shannon index of ruminal bacterial community of HCN group were still lower than those of HF group. Whatever the diet was, the ruminal bacterial community of cattle was dominated by Bacteroidetes, Firmicutes and Proteobacteria. High-concentrate diet significantly increased the abundance of Prevotella, and decreased the abundance of Paraprevotella, Sporobacter, Ruminococcus and Treponema than HF. Compared with HC, HCN had a trend to decrease the percentage of Prevotella, and to increase the abundance of Succiniclasticum, Acetivibrio and Treponema. Increasing concentrate ratio could decrease ruminal pH value, and change the ruminal microbial composition. Adding niacin in HC could increase the ruminal pH value, alter the ruminal microbial composition.}, }
@article {pmid29766224, year = {2019}, author = {García-Bonilla, E and Brandão, PFB and Pérez, T and Junca, H}, title = {Stable and Enriched Cenarchaeum symbiosum and Uncultured Betaproteobacteria HF1 in the Microbiome of the Mediterranean Sponge Haliclona fulva (Demospongiae: Haplosclerida).}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {25-36}, pmid = {29766224}, issn = {1432-184X}, support = {Doctoral Grant (Convocatoria 528-2011)//Colciencias-Colfuturo/ ; Projects (2012-2014 and 2015-2017//EcosNord-Colciencias/ ; }, mesh = {Animals ; Archaea/*classification/genetics/isolation &amp; purification/physiology ; Bacteria ; Betaproteobacteria/*classification/genetics/isolation &amp; purification/physiology ; DNA, Archaeal/analysis ; DNA, Bacterial/analysis ; France ; Haliclona/*microbiology ; Mediterranean Sea ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; Water Microbiology ; }, abstract = {Sponges harbor characteristic microbiomes derived from symbiotic relationships shaping their lifestyle and survival. Haliclona fulva is encrusting marine sponge species dwelling in coralligenous accretions or semidark caves of the Mediterranean Sea and the near Atlantic Ocean. In this work, we characterized the abundance and core microbial community composition found in specimens of H. fulva by means of electron microscopy and 16S amplicon Illumina sequencing. We provide evidence of its low microbial abundance (LMA) nature. We found that the H. fulva core microbiome is dominated by sequences belonging to the orders Nitrosomonadales and Cenarchaeales. Seventy percent of the reads assigned to these phylotypes grouped in a very small number of high-frequency operational taxonomic units, representing niche-specific species Cenarchaeum symbiosum and uncultured Betaproteobacteria HF1, a new eubacterial ribotype variant found in H. fulva. The microbial composition of H. fulva is quite distinct from those reported in sponge species of the same Haliclona genus. We also detected evidence of an excretion/capturing loop between these abundant microorganisms and planktonic microbes by analyzing shifts in seawater planktonic microbial content exposed to healthy sponge specimens maintained in aquaria. Our results suggest that horizontal transmission is very likely the main mechanism for symbionts' acquisition by H. fulva. So far, this is the first shallow water sponge species harboring such a specific and predominant assemblage composed of these eubacterial and archaeal ribotypes. Our data suggests that this symbiotic relationship is very stable over time, indicating that the identified core microbial symbionts may play key roles in the holobiont functioning.}, }
@article {pmid29763867, year = {2018}, author = {Brehony, C and Cullinan, J and Cormican, M and Morris, D}, title = {Shiga toxigenic Escherichia coli incidence is related to small area variation in cattle density in a region in Ireland.}, journal = {The Science of the total environment}, volume = {637-638}, number = {}, pages = {865-870}, doi = {10.1016/j.scitotenv.2018.05.038}, pmid = {29763867}, issn = {1879-1026}, mesh = {Animals ; Cattle ; *Environmental Monitoring ; Humans ; Incidence ; Ireland ; Shiga-Toxigenic Escherichia coli/*growth &amp; development/isolation &amp; purification ; Small-Area Analysis ; }, abstract = {Shiga toxigenic Escherichia coli (STEC) are pathogenic E. coli that cause infectious diarrhoea. In some cases infection may be complicated by renal failure and death. The incidence of human infection with STEC in Ireland is the highest in Europe. The objective of the study was to examine the spatial incidence of human STEC infection in a region of Ireland with significantly higher rates of STEC incidence than the national average and to identify possible risk factors of STEC incidence at area level. Anonymised laboratory records (n = 379) from 2009 to 2015 were obtained from laboratories serving three counties in the West of Ireland. Data included location and sample date. Population and electoral division (ED) data were obtained from the Irish 2011 Census of Population. STEC incidence was calculated for each ED (n = 498) and used to map hotspots/coldspots using the Getis-Ord Gi* spatial statistic and significant spatial clustering using the Anselin's Local Moran's I statistic. Multivariable regression analysis was used to consider the importance of a number of potential predictors of STEC incidence. Incidence rates for the seven-year period ranged from 0 to 10.9 cases per 1000. A number of areas with significant local clustering of STEC incidence as well as variation in the spatial distribution of the two main serogroups associated with disease in the region i.e. O26 and O157 were identified. Cattle density was found to be a statistically significant predictor of STEC in the region. GIS analysis of routine data indicates that cattle density is associated STEC infection in this high incidence region. This finding points to the importance of agricultural practices for human health and the importance of a "one-health" approach to public policy in relation to agriculture, health and environment.}, }
@article {pmid29762668, year = {2018}, author = {Almeida, A and Mitchell, AL and Tarkowska, A and Finn, RD}, title = {Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments.}, journal = {GigaScience}, volume = {7}, number = {5}, pages = {}, pmid = {29762668}, issn = {2047-217X}, mesh = {Bacteria/*classification/*genetics ; Biodiversity ; Databases, Genetic ; *Environmental Microbiology ; Gastrointestinal Microbiome/genetics ; Humans ; Microbiota/*genetics ; Oceans and Seas ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/*genetics ; Soil ; }, abstract = {BACKGROUND: Taxonomic profiling of ribosomal RNA (rRNA) sequences has been the accepted norm for inferring the composition of complex microbial ecosystems. Quantitative Insights Into Microbial Ecology (QIIME) and mothur have been the most widely used taxonomic analysis tools for this purpose, with MAPseq and QIIME 2 being two recently released alternatives. However, no independent and direct comparison between these four main tools has been performed. Here, we compared the default classifiers of MAPseq, mothur, QIIME, and QIIME 2 using synthetic simulated datasets comprised of some of the most abundant genera found in the human gut, ocean, and soil environments. We evaluate their accuracy when paired with both different reference databases and variable sub-regions of the 16S rRNA gene.<br><br>FINDINGS: We show that QIIME 2 provided the best recall and F-scores at genus and family levels, together with the lowest distance estimates between the observed and simulated samples. However, MAPseq showed the highest precision, with miscall rates consistently <2%. Notably, QIIME 2 was the most computationally expensive tool, with CPU time and memory usage almost 2 and 30 times higher than MAPseq, respectively. Using the SILVA database generally yielded a higher recall than using Greengenes, while assignment results of different 16S rRNA variable sub-regions varied up to 40% between samples analysed with the same pipeline.<br><br>CONCLUSIONS: Our results support the use of either QIIME 2 or MAPseq for optimal 16S rRNA gene profiling, and we suggest that the choice between the two should be based on the level of recall, precision, and/or computational performance required.}, }
@article {pmid29760683, year = {2018}, author = {Angel, R and Nepel, M and Panhölzl, C and Schmidt, H and Herbold, CW and Eichorst, SA and Woebken, D}, title = {Evaluation of Primers Targeting the Diazotroph Functional Gene and Development of NifMAP - A Bioinformatics Pipeline for Analyzing nifH Amplicon Data.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {703}, pmid = {29760683}, issn = {1664-302X}, support = {P 25700/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Diazotrophic microorganisms introduce biologically available nitrogen (N) to the global N cycle through the activity of the nitrogenase enzyme. The genetically conserved dinitrogenase reductase (nifH) gene is phylogenetically distributed across four clusters (I-IV) and is widely used as a marker gene for N2 fixation, permitting investigators to study the genetic diversity of diazotrophs in nature and target potential participants in N2 fixation. To date there have been limited, standardized pipelines for analyzing the nifH functional gene, which is in stark contrast to the 16S rRNA gene. Here we present a bioinformatics pipeline for processing nifH amplicon datasets - NifMAP ("NifH MiSeq Illumina Amplicon Analysis Pipeline"), which as a novel aspect uses Hidden-Markov Models to filter out homologous genes to nifH. By using this pipeline, we evaluated the broadly inclusive primer pairs (Ueda19F-R6, IGK3-DVV, and F2-R6) that target the nifH gene. To evaluate any systematic biases, the nifH gene was amplified with the aforementioned primer pairs in a diverse collection of environmental samples (soils, rhizosphere and roots samples, biological soil crusts and estuarine samples), in addition to a nifH mock community consisting of six phylogenetically diverse members. We noted that all primer pairs co-amplified nifH homologs to varying degrees; up to 90% of the amplicons were nifH homologs with IGK3-DVV in some samples (rhizosphere and roots from tall oat-grass). In regards to specificity, we observed some degree of bias across the primer pairs. For example, primer pair F2-R6 discriminated against cyanobacteria (amongst others), yet captured many sequences from subclusters IIIE and IIIL-N. These aforementioned subclusters were largely missing by the primer pair IGK3-DVV, which also tended to discriminate against Alphaproteobacteria, but amplified sequences within clusters IIIC (affiliated with Clostridia) and clusters IVB and IVC. Primer pair Ueda19F-R6 exhibited the least bias and successfully captured diazotrophs in cluster I and subclusters IIIE, IIIL, IIIM, and IIIN, but tended to discriminate against Firmicutes and subcluster IIIC. Taken together, our newly established bioinformatics pipeline, NifMAP, along with our systematic evaluations of nifH primer pairs permit more robust, high-throughput investigations of diazotrophs in diverse environments.}, }
@article {pmid29759899, year = {2018}, author = {Belgini, DRB and Siqueira, VM and Oliveira, DM and Fonseca, SG and Piccin-Santos, V and Dias, RS and Quartaroli, L and Souza, RS and Torres, APR and Sousa, MP and Silva, CM and Silva, CC and De Paula, SO and Oliveira, VM}, title = {Integrated diversity analysis of the microbial community in a reverse osmosis system from a Brazilian oil refinery.}, journal = {Systematic and applied microbiology}, volume = {41}, number = {5}, pages = {473-486}, doi = {10.1016/j.syapm.2018.03.007}, pmid = {29759899}, issn = {1618-0984}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; *Biodiversity ; Biofilms/growth &amp; development ; Brazil ; Fungi/*classification/genetics/isolation &amp; purification/physiology ; Metagenomics ; *Microbial Consortia ; *Oil and Gas Industry ; Osmosis ; Wastewater/*microbiology ; Water Purification/*methods ; }, abstract = {Oil refineries are known for the large volume of water used in their processes, as well as the amount of wastewater generated at the end of the production chain. Due to strict environmental regulations, the recycling of water has now become a viable alternative for refineries. Among the many methods available to treat wastewater for reuse, the use of membranes in reverse osmosis systems stands out due to several economic and environmental benefits. However, these systems are vulnerable to contamination and deposition of microorganisms, mainly because of the feedwater quality. In this study, the microbial diversity of feedwater and reverse osmosis membranes was investigated using a combination of culture-dependent and culture-independent methods in order to characterize the microorganisms colonizing and deteriorating the membranes. In total, 37 bacterial isolates, 17 filamentous fungi and approximately 400 clones were obtained and analyzed. Among the bacterial genera identified, the most represented were Sphingobium, Acidovorax, Microbacterium, Rhizobium and Shinella. The results revealed genera that acted as candidate key players in initial biofilm formation in membrane systems, and provided important information concerning the microbial ecology of oligotrophic aquatic systems.}, }
@article {pmid29758429, year = {2018}, author = {Najar, IN and Sherpa, MT and Das, S and Das, S and Thakur, N}, title = {Microbial ecology of two hot springs of Sikkim: Predominate population and geochemistry.}, journal = {The Science of the total environment}, volume = {637-638}, number = {}, pages = {730-745}, doi = {10.1016/j.scitotenv.2018.05.037}, pmid = {29758429}, issn = {1879-1026}, mesh = {Archaea ; Biodiversity ; *Ecology ; Hot Springs/*microbiology ; India ; Phylogeny ; RNA, Ribosomal, 16S ; Sikkim ; }, abstract = {Northeastern regions of India are known for their floral and faunal biodiversity. Especially the state of Sikkim lies in the eastern Himalayan ecological hotspot region. The state harbors many sulfur rich hot springs which have therapeutic and spiritual values. However, these hot springs are yet to be explored for their microbial ecology. The development of neo generation techniques such as metagenomics has provided an opportunity for inclusive study of microbial community of different environment. The present study describes the microbial diversity in two hot springs of Sikkim that is Polok and Borong with the assist of culture dependent and culture independent approaches. The culture independent techniques used in this study were next generation sequencing (NGS) and Phospholipid Fatty Acid Analysis (PLFA). Having relatively distinct geochemistry both the hot springs are thermophilic environments with the temperature range of 50-77 °C and pH range of 5-8. Metagenomic data revealed the dominance of bacteria over archaea. The most abundant phyla were Proteobacteria and Bacteroidetes although other phyla were also present such as Acidobacteria, Nitrospirae, Firmicutes, Proteobacteria, Parcubacteria and Spirochaetes. The PLFA studies have shown the abundance of Gram Positive bacteria followed by Gram negative bacteria. The culture dependent technique was correlative with PLFA studies. Most abundant bacteria as isolated and identified were Gram-positive genus Geobacillus and Anoxybacillus. The genus Geobacillus has been reported for the first time in North-Eastern states of India. The Geobacillus species obtained from the concerned hot springs were Geobacillus toebii, Geobacillus lituanicus, Geobacillus Kaustophillus and the Anoxybacillus species includes Anoxybacillus gonensis and Anoxybacillus Caldiproteolyticus. The distribution of major genera and their statistical correlation analyses with the geochemistry of the springs predicted that the temperature, pH, alkalinity, Ca[2+], Mg[2+], Cl[2+], and sulfur were main environmental variables influencing the microbial community composition and diversity. Also the piper diagram suggested that the water of both the hot springs are Ca-HCO[3-] type and can be predicted as shallow fresh ground waters. This study has provided an insight into the ecological interaction of the diverse microbial communities and associated physicochemical parameters, which will help in determining the future studies on different biogeochemical pathways in these hot springs.}, }
@article {pmid29757994, year = {2018}, author = {Ibrahim, B and Arkhipova, K and Andeweg, AC and Posada-Céspedes, S and Enault, F and Gruber, A and Koonin, EV and Kupczok, A and Lemey, P and McHardy, AC and McMahon, DP and Pickett, BE and Robertson, DL and Scheuermann, RH and Zhernakova, A and Zwart, MP and Schönhuth, A and Dutilh, BE and Marz, M}, title = {Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.}, journal = {Viruses}, volume = {10}, number = {5}, pages = {}, pmid = {29757994}, issn = {1999-4915}, support = {MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Computational Biology ; Congresses as Topic ; DNA Viruses ; Ecology ; Genomics ; Humans ; Societies, Scientific ; Software ; *Virology ; }, abstract = {The Second Annual Meeting of the European Virus Bioinformatics Center (EVBC), held in Utrecht, Netherlands, focused on computational approaches in virology, with topics including (but not limited to) virus discovery, diagnostics, (meta-)genomics, modeling, epidemiology, molecular structure, evolution, and viral ecology. The goals of the Second Annual Meeting were threefold: (i) to bring together virologists and bioinformaticians from across the academic, industrial, professional, and training sectors to share best practice; (ii) to provide a meaningful and interactive scientific environment to promote discussion and collaboration between students, postdoctoral fellows, and both new and established investigators; (iii) to inspire and suggest new research directions and questions. Approximately 120 researchers from around the world attended the Second Annual Meeting of the EVBC this year, including 15 renowned international speakers. This report presents an overview of new developments and novel research findings that emerged during the meeting.}, }
@article {pmid29755700, year = {2018}, author = {Sharma, P and Maherchandani, S and Shringi, BN and Kashyap, SK and Sundar, KSG}, title = {Temporal variations in patterns of Escherichia coli strain diversity and antimicrobial resistance in the migrant Egyptian vulture.}, journal = {Infection ecology &amp; epidemiology}, volume = {8}, number = {1}, pages = {1450590}, pmid = {29755700}, issn = {2000-8686}, abstract = {Aims: Multiple antimicrobial resistance in Escherichia coli of wild vertebrates is a global concern with scarce assessments on the subject from developing countries that have high human-wild species interactions. We studied the ecology of E. coli in a wintering population of Egyptian Vultures in India to understand temporal changes in both E. coli strains and patterns of antimicrobial resistance. Methods and Results: We ribotyped E. coli strains and assessed antimicrobial resistance from wintering vultures at a highly synanthropic carcass dump in north-west India. Both E. coli occurence (90.32%) and resistance to multiple antimicrobials (71.43%) were very high. Clear temporal patterns were apparent. Diversity of strains changed and homogenized at the end of the Vultures' wintering period, while the resistance pattern showed significantly difference inter-annually, as well as between arrival and departing individuals within a wintering cycle. Significance of study: The carcass dump environment altered both E. coli strains and multiple antimicrobial resistance in migratory Egyptian Vultures within a season. Long-distance migratory species could therefore disseminate resistant E. coli strains across broad geographical scales rendering regional mitigation strategies to control multiple antimicrobial resistance in bacteria ineffective.}, }
@article {pmid29755434, year = {2018}, author = {Pérez-Cataluña, A and Collado, L and Salgado, O and Lefiñanco, V and Figueras, MJ}, title = {A Polyphasic and Taxogenomic Evaluation Uncovers Arcobacter cryaerophilus as a Species Complex That Embraces Four Genomovars.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {805}, pmid = {29755434}, issn = {1664-302X}, abstract = {The species Arcobacter cryaerophilus is found in many food products of animal origin and is the dominating species in wastewater. In addition, it is associated with cases of farm animal and human infectious diseases,. The species embraces two subgroups i.e., 1A (LMG 24291[T] = LMG 9904[T]) and 1B (LMG 10829) that can be differentiated by their 16S rRNA-RFLP pattern. However, some authors, on the basis of the shared intermediate levels of DNA-DNA hybridization, have suggested abandoning the subgroup classification. This contradiction indicates that the taxonomy of this species is not yet resolved. The objective of the present study was to perform a taxonomic evaluation of the diversity of A. cryaerophilus. Genomic information was used along with a Multilocus Phylogenetic Analysis (MLPA) and phenotypic characterization on a group of 52 temporally and geographically dispersed strains, coming from different types of samples and hosts from nine countries. The MLPA analysis showed that those strains formed four clusters (I-IV). Values of Average Nucleotide Identity (ANI) and in silico DNA-DNA Hybridization (isDDH) obtained between 13 genomes representing strains of the four clusters were below the proposed cut-offs of 96 and 70%, respectively, confirming that each of the clusters represented a different genomic species. However, none of the evaluated phenotypic tests enabled their unequivocal differentiation into species. Therefore, the genomic delimited clusters should be considered genomovars of the species A. cryaerophilus. These genomovars could have different clinical importance, since only the cluster I included strains isolated from human specimens. The discovery of at least one stable distinctive phenotypic character would be needed to define each cluster or genomovar as a different species. Until then, we propose naming them "A. cryaerophilus gv. pseudocryaerophilus" (Cluster I = LMG 10229[T]), "A. cryaerophilus gv. crypticus" (Cluster II = LMG 9065[T]), "A. cryaerophilus gv. cryaerophilus" (Cluster III = LMG 24291[T]) and "A. cryaerophilus gv. occultus" (Cluster IV = LMG 29976[T]).}, }
@article {pmid29752058, year = {2018}, author = {Deng, D and Weidhaas, JL and Lin, LS}, title = {Corrigendum to " Kinetics and microbial ecology of batch sulfidogenic bioreactors for co-treatment of municipal wastewater and acid mine drainage" [J. Hazard. Mater. (2016) 10.1016/j.jhazmat.2015.11.041].}, journal = {Journal of hazardous materials}, volume = {353}, number = {}, pages = {552}, doi = {10.1016/j.jhazmat.2018.04.046}, pmid = {29752058}, issn = {1873-3336}, }
@article {pmid29747113, year = {2018}, author = {Rousk, J and Rousk, K}, title = {Responses of microbial tolerance to heavy metals along a century-old metal ore pollution gradient in a subarctic birch forest.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {240}, number = {}, pages = {297-305}, doi = {10.1016/j.envpol.2018.04.087}, pmid = {29747113}, issn = {1873-6424}, mesh = {Bacteria ; Betula ; Betulaceae ; Biomass ; Drug Tolerance ; Ecosystem ; *Environmental Monitoring ; Environmental Pollution ; *Forests ; Metals, Heavy/analysis/*toxicity ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/analysis/*toxicity ; }, abstract = {Heavy metals are some of the most persistent and potent anthropogenic environmental contaminants. Although heavy metals may compromise microbial communities and soil fertility, it is challenging to causally link microbial responses to heavy metals due to various confounding factors, including correlated soil physicochemistry or nutrient availability. A solution is to investigate whether tolerance to the pollutant has been induced, called Pollution Induced Community Tolerance (PICT). In this study, we investigated soil microbial responses to a century-old gradient of metal ore pollution in an otherwise pristine subarctic birch forest generated by a railway source of iron ore transportation. To do this, we determined microbial biomass, growth, and respiration rates, and bacterial tolerance to Zn and Cu in replicated distance transects (1 m-4 km) perpendicular to the railway. Microbial biomass, growth and respiration rates were stable across the pollution gradient. The microbial community structure could be distinguished between sampled distances, but most of the variation was explained by soil pH differences, and it did not align with distance from the railroad pollution source. Bacterial tolerance to Zn and Cu started from background levels at 4 km distance from the pollution source, and remained at background levels for Cu throughout the gradient. Yet, bacterial tolerance to Zn increased 10-fold 100 m from the railway source. Our results show that the microbial community structure, size and performance remained unaffected by the metal ore exposure, suggesting no impact on ecosystem functioning.}, }
@article {pmid29745026, year = {2018}, author = {De Vrieze, J and Boon, N and Verstraete, W}, title = {Taking the technical microbiome into the next decade.}, journal = {Environmental microbiology}, volume = {20}, number = {6}, pages = {1991-2000}, doi = {10.1111/1462-2920.14269}, pmid = {29745026}, issn = {1462-2920}, support = {//Research Foundation Flanders (FWO-Vlaanderen)/International ; }, mesh = {Agriculture ; *Biological Evolution ; Environmental Microbiology ; Microbiota/*genetics ; Sanitation ; }, abstract = {The 'microbiome' has become a buzzword. Multiple new technologies allow to gather information about microbial communities as they evolve under stable and variable environmental conditions. The challenge of the next decade will be to develop strategies to compose and manage microbiomes. Here, key aspects are considered that will be of crucial importance for future microbial technological developments. First, the need to deal not only with genotypes but also particularly with phenotypes is addressed. Microbial technologies are often highly dependent on specific core organisms to obtain the desired process outcome. Hence, it is essential to combine omics data with phenotypic information to invoke and control specific phenotypes in the microbiome. Second, the development and application of synthetic microbiomes is evaluated. The central importance of the core species is a no-brainer, but the implementation of proper satellite species is an important route to explore. Overall, for the next decade, microbiome research should no longer almost exclusively focus on its capacity to degrade and dissipate but rather on its remarkable capability to capture disordered components and upgrade them into high-value microbial products. These products can become valuable commodities in the cyclic economy, as reflected in the case of 'reversed sanitation', which is introduced here.}, }
@article {pmid29744532, year = {2018}, author = {Peng, C and Wang, H and Jiang, Y and Yang, J and Lai, H and Wei, X}, title = {Exploring the Abundance and Diversity of Bacterial Communities and Quantifying Antibiotic-Related Genes Along an Elevational Gradient in Taibai Mountain, China.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {1053-1062}, pmid = {29744532}, issn = {1432-184X}, support = {2012BAD14B11//National Sci-Tech Support Plan of China/ ; 2016KTZDNY03-03-02//Shaanxi Science &amp; Technology Co-ordination &amp; Innovation Project/ ; 2452017313//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Actinobacteria/genetics ; Anti-Bacterial Agents/*metabolism ; Bacteria/*classification/*genetics/*metabolism ; *Biodiversity ; China ; DNA, Bacterial ; Drug Discovery ; Forests ; Gene Dosage ; Genes, Bacterial/genetics ; Microbiota/*genetics ; Nitrogen ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Thus far, no studies have investigated the soil microbial diversity over an elevational gradient in Taibai Mountain, the central massif of the Qinling Mountain Range. Here, we used Illumina sequencing and quantitative PCR of the 16S rRNA gene to assess the diversity and abundance of bacterial communities along an elevational gradient in representative vegetation soils in Taibai Mountain. We identified the soil, climate, and vegetation factors driving the variations in soil bacterial community structure by Pearson correlation and redundancy analysis. We also evaluated the potential for antibiotic discovery by quantitative PCR of the PKS-I, PKS-II, and NRPS genes from Actinobacteria. The results showed that soil bacterial alpha diversity increased first and then decreased with an elevational rise in both the northern and southern slopes of Taibai Mountain. The bacterial abundance was significantly correlated with soil organic matter and nitrate nitrogen. The average relative abundance of Actinobacteria in Taibai Mountain was markedly higher than those in other mountain forest soils. The absolute abundance of PKS and NPRS gene was significantly higher in the tested soils compared with the gene copy numbers reported in tropical urban soils. Taibai Mountain is rich in actinomycete resources and has great potential for antibiotic excavation.}, }
@article {pmid29744531, year = {2018}, author = {Gioacchini, G and Ciani, E and Pessina, A and Cecchini, C and Silvi, S and Rodiles, A and Merrifield, DL and Olivotto, I and Carnevali, O}, title = {Correction to: Effects of Lactogen 13, a New Probiotic Preparation, on Gut Microbiota and Endocrine Signals Controlling Growth and Appetite of Oreochromis niloticus Juveniles.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {1075}, doi = {10.1007/s00248-018-1194-0}, pmid = {29744531}, issn = {1432-184X}, abstract = {The original version of this article unfortunately contained mistakes in Authors First name/Family name order. Please refer to this paper as Gioacchini et al. and not as Giorgia et al.}, }
@article {pmid29743637, year = {2018}, author = {Ghasemian, E and Inic-Kanada, A and Collingro, A and Tagini, F and Stein, E and Alchalabi, H and Schuerer, N and Keše, D and Babiker, BE and Borel, N and Greub, G and Barisani-Asenbauer, T}, title = {Detection of Chlamydiaceae and Chlamydia-like organisms on the ocular surface of children and adults from a trachoma-endemic region.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {7432}, pmid = {29743637}, issn = {2045-2322}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; Chlamydia trachomatis/*isolation &amp; purification/*physiology ; Chlamydiaceae/*isolation &amp; purification/*physiology ; DNA, Bacterial/analysis ; *Endemic Diseases ; Eye/*microbiology ; Female ; Humans ; Infant ; Male ; Middle Aged ; Phylogeny ; Trachoma/*epidemiology/microbiology ; Young Adult ; }, abstract = {Trachoma, the leading infectious cause of blindness, is caused by Chlamydia trachomatis (Ct), a bacterium of the phylum Chlamydiae. Recent investigations revealed the existence of additional families within the phylum Chlamydiae, also termed Chlamydia-like organisms (CLOs). In this study, the frequency of Ct and CLOs was examined in the eyes of healthy Sudanese (control) participants and those with trachoma (case). We tested 96 children (54 cases and 42 controls) and 93 adults (51 cases and 42 controls) using broad-range Chlamydiae and Ct-specific (omcB) real-time PCR. Samples positive by broad-range Chlamydiae testing were subjected to DNA sequencing. Overall Chlamydiae prevalence was 36%. Sequences corresponded to unclassified and classified Chlamydiae. Ct infection rate was significantly higher in children (31.5%) compared to adults (0%) with trachoma (p < 0.0001). In general, 21.5% of adults and 4.2% of children tested positive for CLOs (p = 0.0003). Our findings are consistent with previous investigations describing the central role of Ct in trachoma among children. This is the first study examining human eyes for the presence of CLOs. We found an age-dependent distribution of CLO DNA in human eyes with significantly higher positivity in adults. Further studies are needed to understand the impact of CLOs in trachoma pathogenicity and/or protection.}, }
@article {pmid29743566, year = {2018}, author = {Willemsen, A and Carrasco, JL and Elena, SF and Zwart, MP}, title = {Going, going, gone: predicting the fate of genomic insertions in plant RNA viruses.}, journal = {Heredity}, volume = {121}, number = {5}, pages = {499-509}, pmid = {29743566}, issn = {1365-2540}, mesh = {DNA Transposable Elements/*genetics ; Gene Transfer, Horizontal ; *Genome, Viral ; Mutagenesis ; Potyvirus/*genetics ; RNA Viruses/*genetics ; Recombination, Genetic ; Sequence Deletion ; }, abstract = {Horizontal gene transfer is common among viruses, while they also have highly compact genomes and tend to lose artificial genomic insertions rapidly. Understanding the stability of genomic insertions in viral genomes is therefore relevant for explaining and predicting their evolutionary patterns. Here, we revisit a large body of experimental research on a plant RNA virus, tobacco etch potyvirus (TEV), to identify the patterns underlying the stability of a range of homologous and heterologous insertions in the viral genome. We obtained a wide range of estimates for the recombination rate-the rate at which deletions removing the insertion occur-and these appeared to be independent of the type of insertion and its location. Of the factors we considered, recombination rate was the best predictor of insertion stability, although we could not identify the specific sequence characteristics that would help predict insertion instability. We also considered experimentally the possibility that functional insertions lead to higher mutational robustness through increased redundancy. However, our observations suggest that both functional and non-functional increases in genome size decreased the mutational robustness. Our results therefore demonstrate the importance of recombination rates for predicting the long-term stability and evolution of viral RNA genomes and suggest that there are unexpected drawbacks to increases in genome size for mutational robustness.}, }
@article {pmid29740008, year = {2018}, author = {Defoirdt, T and Mai Anh, NT and De Schryver, P}, title = {Virulence-inhibitory activity of the degradation product 3-hydroxybutyrate explains the protective effect of poly-β-hydroxybutyrate against the major aquaculture pathogen Vibrio campbellii.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {7245}, pmid = {29740008}, issn = {2045-2322}, mesh = {3-Hydroxybutyric Acid/chemistry/*pharmacology ; Animals ; Antidotes/chemistry/*pharmacology ; Artemia/drug effects/microbiology ; Enzyme Inhibitors/chemistry/*pharmacology ; Hemolysin Proteins/antagonists &amp; inhibitors/toxicity ; Hydrogen-Ion Concentration ; Hydrolysis ; Hydroxybutyrates/chemistry/*pharmacology ; Intestines/drug effects/microbiology ; Larva/drug effects/microbiology ; Peptide Hydrolases/toxicity ; Phospholipases/antagonists &amp; inhibitors/toxicity ; Polyesters/chemistry/*pharmacology ; Vibrio/*drug effects/growth &amp; development/metabolism/pathogenicity ; Virulence Factors/*antagonists &amp; inhibitors/toxicity ; }, abstract = {The bacterial storage compound poly-β-hydroxybutyrate, a polymer of the short-chain fatty acid 3-hydroxybutyrate, has been reported to protect various aquatic animals from bacterial disease. In order to obtain a better mechanistic insight, we aimed to (1) investigate whether 3-hydroxybutyrate is released from poly-β-hydroxybutyrate within sterile brine shrimp larvae, (2) determine the impact of 3-hydroxybutyrate on the virulence of Vibrio campbellii to brine shrimp larvae and on its cell density in the shrimp, and (3) determine the impact of this compound on virulence factor production in the pathogen. We detected 3-hydroxybutyrate in poly-β-hydroxybutyrate-fed brine shrimp, resulting in 24 mM 3-hydroxybutyrate in the intestinal tract of shrimp reared in the presence of 1000 mg l[-1] poly-β-hydroxybutyrate. We further demonstrate that this concentration of 3-hydroxybutyrate does not affect the growth of V. campbellii, whereas it decreases the production of different virulence factors, including hemolysin, phospholipase and protease activities, and swimming motility. We hypothesize that by affecting all these virulence factors at once, 3-hydroxybutyrate (and thus also poly-β-hydroxybutyrate) can exert a significant impact on the virulence of V. campbellii. This hypothesis was confirmed in a challenge test showing that 3-hydroxybutyrate protected gnotobiotic brine shrimp from pathogenic V. campbellii, without affecting the number of host-associated vibrios.}, }
@article {pmid29738975, year = {2018}, author = {Theuerl, S and Klang, J and Heiermann, M and De Vrieze, J}, title = {Marker microbiome clusters are determined by operational parameters and specific key taxa combinations in anaerobic digestion.}, journal = {Bioresource technology}, volume = {263}, number = {}, pages = {128-135}, doi = {10.1016/j.biortech.2018.04.111}, pmid = {29738975}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Biofuels ; *Bioreactors ; *Microbiota ; Sewage ; }, abstract = {In this study, microbiomes of 36 full-scale anaerobic digesters originated from 22 different biogas plants were compared by terminal restriction fragment length polymorphism (TRFLP) analysis. Regarding the differences in microbial community composition, a weighting of the environmental parameters could be derived from higher to lower importance as follows: (i) temperature, (ii) TAN and NH3 concentrations and conductivity, and (iii) the chemical composition of the supplied feedstocks. Biotic interactions between specific bacterial and archaeal community arrangements were revealed, whereby members of the phyla Bacteroidetes and Cloacimonetes combined with the archaeal genus Methanothrix dominated the conversion of homogeneous feedstocks, such as waste water sludge or industrial waste. As most of the detected TRFs were only found in a certain number of anaerobic digestion plants, each plant develops its unique microbiome. The putative rare species, the specialists, are potentially hidden drivers of microbiome functioning as they provide necessary traits under, e.g., process-inconvenient conditions.}, }
@article {pmid29738306, year = {2018}, author = {Svenningsen, NB and Martínez-García, E and Nicolaisen, MH and de Lorenzo, V and Nybroe, O}, title = {The biofilm matrix polysaccharides cellulose and alginate both protect Pseudomonas putida mt-2 against reactive oxygen species generated under matric stress and copper exposure.}, journal = {Microbiology (Reading, England)}, volume = {164}, number = {6}, pages = {883-888}, doi = {10.1099/mic.0.000667}, pmid = {29738306}, issn = {1465-2080}, mesh = {Adaptation, Physiological ; Alginates/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biofilms ; Cellulose/genetics/*metabolism ; Copper/*metabolism/toxicity ; Desiccation ; Extracellular Polymeric Substance Matrix/*chemistry/genetics ; Gene Deletion ; Gene Expression Regulation, Bacterial/drug effects ; Promoter Regions, Genetic ; Pseudomonas putida/genetics/growth &amp; development/metabolism/*physiology ; Reactive Oxygen Species/*metabolism ; Stress, Physiological/drug effects/*physiology ; }, abstract = {In natural environments most bacteria live in biofilms embedded in complex matrices of extracellular polymeric substances (EPS). This lifestyle is known to increase protection against environmental stress. Pseudomonas putida mt-2 harbours genes for the production of at least four different EPS polysaccharides, including alginate and cellulose. Little is known about the functional properties of cellulose, while alginate attenuates the accumulation of reactive oxygen species (ROS) caused by matric stress. By using mutants that are deficient in either alginate or cellulose production we show that even cellulose attenuates the accumulation of matric stress-induced ROS for cells in biofilms. Further, both cellulose and alginate attenuate ROS generated through exposure to copper. Interestingly, the two EPS polysaccharides protect cells in both liquid culture and in biofilms against ROS caused by matric stress, indicating that cellulose and alginate do not need to be produced as an integral part of the biofilm lifestyle to provide tolerance towards environmental stressors.}, }
@article {pmid29738088, year = {2018}, author = {Faure, D and Simon, JC and Heulin, T}, title = {Holobiont: a conceptual framework to explore the eco-evolutionary and functional implications of host-microbiota interactions in all ecosystems.}, journal = {The New phytologist}, volume = {218}, number = {4}, pages = {1321-1324}, doi = {10.1111/nph.15199}, pmid = {29738088}, issn = {1469-8137}, mesh = {*Biological Evolution ; *Ecosystem ; Genomics ; *Host Microbial Interactions/genetics ; Metagenome ; Research Personnel ; }, }
@article {pmid29737382, year = {2018}, author = {Delafont, V and Rodier, MH and Maisonneuve, E and Cateau, E}, title = {Vermamoeba vermiformis: a Free-Living Amoeba of Interest.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {991-1001}, pmid = {29737382}, issn = {1432-184X}, mesh = {Hartmannella/*microbiology/*physiology/virology ; Hospitals ; *Public Health ; RNA, Protozoan ; RNA, Ribosomal, 18S ; Sequence Analysis, RNA ; Water Supply ; }, abstract = {Free-living amoebae are protists that are widely distributed in the environment including water, soil, and air. Although the amoebae of the genus Acanthamoeba are still the most studied, other species, such as Vermamoeba vermiformis (formerly Hartmannella vermiformis), are the subject of increased interest. Found in natural or man-made aquatic environments, V. vermiformis can support the multiplication of other microorganisms and is able to harbor and potentially protect pathogenic bacteria or viruses. This feature is to be noted because of the presence of this thermotolerant amoeba in hospital water networks. As a consequence, this protist could be implicated in health concerns and be indirectly responsible for healthcare-related infections. This review highlights, among others, the consequences of V. vermiformis relationships with other microorganisms and shows that this free-living amoeba species is therefore of interest for public health.}, }
@article {pmid29736898, year = {2018}, author = {Arias-Jayo, N and Abecia, L and Alonso-Sáez, L and Ramirez-Garcia, A and Rodriguez, A and Pardo, MA}, title = {High-Fat Diet Consumption Induces Microbiota Dysbiosis and Intestinal Inflammation in Zebrafish.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {1089-1101}, pmid = {29736898}, issn = {1432-184X}, mesh = {Animals ; Anti-Infective Agents/metabolism ; Bacteria/classification/drug effects/genetics ; Diet, High-Fat/*adverse effects ; Disease Models, Animal ; Dysbiosis/*chemically induced ; Gastrointestinal Microbiome/*drug effects/genetics ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Goblet Cells/metabolism ; Immune System ; *Inflammation ; Intestines/*microbiology/pathology ; Mucins/metabolism ; RNA, Ribosomal, 16S/genetics ; Zebrafish/immunology/microbiology ; }, abstract = {Energy-dense foods and overnutrition represent major starting points altering lipid metabolism, systemic inflammation and gut microbiota. The aim of this work was to investigate the effects of a high-fat diet (HFD) over a period of 25 days on intestinal microbiota and inflammation in zebrafish. Microbial composition of HFD-fed animals was analysed and compared to controls by 16S rRNA sequencing and quantitative PCR. The expression level on several genes related to inflammation was tested. Furthermore, microscopic assessment of the intestine was performed in both conditions. The consumption of the HFD resulted in microbial dysbiosis, characterised by an increase in the relative abundance of the phylum Bacteroidetes. Moreover, an emerging intestinal inflammation via NF-κβ activation was confirmed by the overexpression of several genes related to signalling receptors, antimicrobial metabolism and the inflammatory cascade. The intestinal barrier was also damaged, with an increase of goblet cell mucin production. This is the first study performed in zebrafish which suggests that the consumption of a diet enriched with 10% fat changes the intestinal microbial community composition, which was correlated with low-grade inflammation.}, }
@article {pmid29736335, year = {2018}, author = {Stewart, CJ and Auchtung, TA and Ajami, NJ and Velasquez, K and Smith, DP and De La Garza, R and Salas, R and Petrosino, JF}, title = {Effects of tobacco smoke and electronic cigarette vapor exposure on the oral and gut microbiota in humans: a pilot study.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4693}, pmid = {29736335}, issn = {2167-8359}, support = {I01 CX000994/CX/CSRD VA/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; }, abstract = {BACKGROUND: The use of electronic cigarettes (ECs) has increased drastically over the past five years, primarily as an alternative to smoking tobacco cigarettes. However, the adverse effects of acute and long-term use of ECs on the microbiota have not been explored. In this pilot study, we sought to determine if ECs or tobacco smoking alter the oral and gut microbiota in comparison to non-smoking controls.<br><br>METHODS: We examined a human cohort consisting of 30 individuals: 10 EC users, 10 tobacco smokers, and 10 controls. We collected cross-sectional fecal, buccal swabs, and saliva samples from each participant. All samples underwent V4 16S rRNA gene sequencing.<br><br>RESULTS: Tobacco smoking had a significant effect on the bacterial profiles in all sample types when compared to controls, and in feces and buccal swabs when compared to EC users. The most significant associations were found in the gut, with an increased relative abundance of Prevotella (P = 0.006) and decreased Bacteroides (P = 0.036) in tobacco smokers. The Shannon diversity was also significantly reduced (P = 0.009) in fecal samples collected from tobacco smokers compared to controls. No significant difference was found in the alpha diversity, beta-diversity or taxonomic relative abundances between EC users and controls.<br><br>DISCUSSION: From a microbial ecology perspective, the current pilot data demonstrate that the use of ECs may represent a safer alternative compared to tobacco smoking. However, validation in larger cohorts and greater understanding of the short and long-term impact of EC use on microbiota composition and function is warranted.}, }
@article {pmid29735671, year = {2018}, author = {Bjerg, JT and Boschker, HTS and Larsen, S and Berry, D and Schmid, M and Millo, D and Tataru, P and Meysman, FJR and Wagner, M and Nielsen, LP and Schramm, A}, title = {Long-distance electron transport in individual, living cable bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {22}, pages = {5786-5791}, pmid = {29735671}, issn = {1091-6490}, support = {291650/ERC_/European Research Council/International ; 294343/ERC_/European Research Council/International ; }, mesh = {Bacteria/*chemistry/*metabolism ; Cytochromes/metabolism ; Electron Transport/*physiology ; Geologic Sediments/microbiology ; Oxidation-Reduction ; Oxygen/metabolism ; Spectrum Analysis, Raman ; Sulfides/metabolism ; }, abstract = {Electron transport within living cells is essential for energy conservation in all respiring and photosynthetic organisms. While a few bacteria transport electrons over micrometer distances to their surroundings, filaments of cable bacteria are hypothesized to conduct electric currents over centimeter distances. We used resonance Raman microscopy to analyze cytochrome redox states in living cable bacteria. Cable-bacteria filaments were placed in microscope chambers with sulfide as electron source and oxygen as electron sink at opposite ends. Along individual filaments a gradient in cytochrome redox potential was detected, which immediately broke down upon removal of oxygen or laser cutting of the filaments. Without access to oxygen, a rapid shift toward more reduced cytochromes was observed, as electrons were no longer drained from the filament but accumulated in the cellular cytochromes. These results provide direct evidence for long-distance electron transport in living multicellular bacteria.}, }
@article {pmid29735061, year = {2018}, author = {Martins, MCF and Freitas, R and Deuvaux, JC and Eller, MR and Nero, LA and Carvalho, AF}, title = {Bacterial diversity of artisanal cheese from the Amazonian region of Brazil during the dry and rainy seasons.}, journal = {Food research international (Ottawa, Ont.)}, volume = {108}, number = {}, pages = {295-300}, doi = {10.1016/j.foodres.2018.03.060}, pmid = {29735061}, issn = {1873-7145}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Brazil ; Cheese/*microbiology ; Colony Count, Microbial ; Food Microbiology/methods ; *Rain ; Rainforest ; Ribotyping ; *Seasons ; }, abstract = {The microbiota from artisanal cheeses produced in the Amazonian region is evaluated. Samples of artisanal cheeses were obtained from markets in Conceição do Araguaia and Redenção (Pará, Brazil) over rainy and dry seasons, and their biodiversity was assessed by culture-dependent and culture-independent methods. Mean counts of lactic acid bacteria (LAB) in cheeses ranged from 7.32 to 8.84 log CFU/g, for both seasons. Members of genera Lactobacillus, Lactococcus, Weissella, Enterococcus, Pediococcus, and Leuconostoc were predominant. The amplification of the 16S rRNA V6-V9 region, followed by a temporal temperature-gradient gel electrophoresis (TTGE) and sequencing of the TTGE bands revealed important differences in the microbial composition variability between samples from the two seasons and among cheese samples analyzed. TTGE showed the presence of microorganisms that are frequently found in cheese, such as L. lactis subsp. lactis, as well as other non-usual species, such as Macrococcus caseolyticus and Corynebacterium variabile. Moreover, TTGE analysis revealed the presence of microorganisms that have been isolated from other types of foods (Paralactobacillus selangorenses) along with some not usually found in foods, such as Exiguobacterium acetylicum, plus the presence of pathogenic microorganisms (Granulicatella elegans and Aerococcus sanguinicola). The present molecular approaches combined with culture-dependent methods provided a more detailed description of the microbial ecology of traditional cheeses from the Amazonian region in northern Brazil.}, }
@article {pmid29734762, year = {2018}, author = {Semedo-Aguiar, AP and Pereira-Leal, JB and Leite, RB}, title = {Microbial Diversity and Toxin Risk in Tropical Freshwater Reservoirs of Cape Verde.}, journal = {Toxins}, volume = {10}, number = {5}, pages = {}, pmid = {29734762}, issn = {2072-6651}, mesh = {Bacteria/genetics/isolation &amp; purification ; Bacterial Toxins/genetics ; Biodiversity ; Cabo Verde ; DNA, Bacterial/genetics ; Fresh Water/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; }, abstract = {The Cape Verde islands are part of the African Sahelian arid belt that possesses an erratic rain pattern prompting the need for water reservoirs, which are now critical for the country’s sustainability. Worldwide, freshwater cyanobacterial blooms are increasing in frequency due to global climate change and the eutrophication of water bodies, particularly in reservoirs. To date, there have been no risk assessments of cyanobacterial toxin production in these man-made structures. We evaluated this potential risk using 16S rRNA gene amplicon sequencing and full metagenome sequencing in freshwater reservoirs of Cape Verde. Our analysis revealed the presence of several potentially toxic cyanobacterial genera in all sampled reservoirs. Faveta potentially toxic and bloom-forming Microcystis sp., dominated our samples, while a Cryptomonas green algae and Gammaproteobacteria dominated Saquinho and Poil&amp;atilde;o reservoirs. We reconstructed and assembled the Microcystis genome, extracted from the metagenome of bulk DNA from Faveta water. Phylogenetic analysis of Microcystis cf. aeruginosa CV01’s genome revealed its close relationship with other Microcystis genomes, as well as clustering with other continental African strains, suggesting geographical coherency. In addition, it revealed several clusters of known toxin-producing genes. This survey reinforces the need to better understand the country’s microbial ecology as a whole of water reservoirs on the rise.}, }
@article {pmid29728707, year = {2018}, author = {Li, B and Li, Z and Sun, X and Wang, Q and Xiao, E and Sun, W}, title = {DNA-SIP Reveals the Diversity of Chemolithoautotrophic Bacteria Inhabiting Three Different Soil Types in Typical Karst Rocky Desertification Ecosystems in Southwest China.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {976-990}, pmid = {29728707}, issn = {1432-184X}, support = {41771301, 41420104007//the National Natural Science Foundation of China/ ; 2016GDASRC-0103//the High-Level Leading Talent Introduction Program of GDAS/ ; 2018GDASCX-0601 and 2017GDASCX-0106//1000 Youth Talents Program, the GDAS' Special Project of Science and Technology Development/ ; 2016B070701015//the Science and Technology Planning Project of Guangdong Province/ ; }, mesh = {Bacteria/*classification/growth &amp; development ; *Chemoautotrophic Growth ; China ; DNA, Bacterial/analysis ; *Desert Climate ; Ecosystem ; *Microbiota ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Autotrophs that inhabit soils receive less attention than their counterparts in other ecosystems, such as deep-sea and subsurface sediments, due to the low abundance of autotrophs in soils with high organic contents. However, the karst rocky desertification region is a unique ecosystem that may have a low level of organic compounds. Therefore, we propose that karst rocky desertification ecosystems may harbor diverse autotrophic microbial communities. In this study, DNA-SIP was employed to identify the chemolithoautotrophic bacteria inhabiting three soil types (i.e., grass, forest, and agriculture) of the karst rocky desertification ecosystems. The results indicated that potential chemolithoautotrophic population was observed in each soil type, even at different time points after amending [13]C-NaHCO3, confirming our hypothesis that diverse autotrophs contribute to the carbon cycle in karst soils. Bacteria, such as Ralstonia, Ochrobactrum, Brevibacterium, Acinetobacter, and Corynebacterium, demonstrated their potential to assimilate inorganic carbon and reduce nitrate or thiosulfate as electron acceptors. Putative mixotrophs were identified by DNA-SIP as well, suggesting the metabolic versatility of soil microbiota. A co-occurrence network further indicated that autotrophs and heterotrophs may form associated communities to sustain the ecosystem function. Our current study revealed the metabolic diversity of autotrophic bacteria in soil habitats and demonstrated the potentially important role of chemoautotrophs in karst rocky desertification ecosystems.}, }
@article {pmid29727966, year = {2018}, author = {Pershina, EV and Ivanova, EA and Korvigo, IO and Chirak, EL and Sergaliev, NH and Abakumov, EV and Provorov, NA and Andronov, EE}, title = {Investigation of the core microbiome in main soil types from the East European plain.}, journal = {The Science of the total environment}, volume = {631-632}, number = {}, pages = {1421-1430}, doi = {10.1016/j.scitotenv.2018.03.136}, pmid = {29727966}, issn = {1879-1026}, mesh = {Bacteria/genetics ; *Environmental Monitoring ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Russia ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The main goal of modern microbial ecology is to determine the key factors influencing the global diversity of microorganisms. Because of their complexity, soil communities are largely underexplored in this context. We studied soil genesis (combination of various soil-forming processes, specific to a particular soil type) that is driven by microbial activity. To investigate the interrelation between soil type and microbial diversity, we analyzed six soil types that are common in Russia, the Crimea, and Kazakhstan using 16S rDNA pyrosequencing. Soils of different types varied in the taxonomic composition of microbial communities. Their core microbiomes comprised 47 taxa within the orders Solirubrobacteriales and Hyphomicrobiaceae and the Gaiellaceae family. Two species from Bradyrhizobiaceae and Solirubrobactriaceae were present in all samples, whereas most other taxa were soil-type specific. Multiple resampling analysis revealed that two random soil samples from the same soil type shared more taxa than two samples from different types. The differences in community composition were mostly affected by the variation in pH values and exchangeable potassium content. The results show that data on the soil microbiome could be used for soil identification and clarification of their taxonomic position.}, }
@article {pmid29727935, year = {2018}, author = {Suleiman, AKA and Lourenço, KS and Pitombo, LM and Mendes, LW and Roesch, LFW and Pijl, A and Carmo, JB and Cantarella, H and Kuramae, EE}, title = {Recycling organic residues in agriculture impacts soil-borne microbial community structure, function and N2O emissions.}, journal = {The Science of the total environment}, volume = {631-632}, number = {}, pages = {1089-1099}, doi = {10.1016/j.scitotenv.2018.03.116}, pmid = {29727935}, issn = {1879-1026}, mesh = {Agriculture/*methods ; Fertilizers ; Nitrous Oxide/*analysis ; Recycling/*methods ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Recycling residues is a sustainable alternative to improve soil structure and increase the stock of nutrients. However, information about the magnitude and duration of disturbances caused by crop and industrial wastes on soil microbial community structure and function is still scarce. The objective of this study was to investigate how added residues from industry and crops together with nitrogen (N) fertiliser affect the microbial community structure and function, and nitrous oxide (N2O) emissions. The experimental sugarcane field had the following treatments: (I) control with nitrogen, phosphorus, and potassium (NPK), (II) sugarcane straw with NPK, (III) vinasse (by-product of ethanol industry) with NP, and (IV) vinasse plus sugarcane straw with NP. Soil samples were collected on days 1, 3, 6, 11, 24 and 46 of the experiment for DNA extraction and metagenome sequencing. N2O emissions were also measured. Treatments with straw and vinasse residues induced changes in soil microbial composition and potential functions. The change in the microbial community was highest in the treatments with straw addition with functions related to decomposition of different ranges of C-compounds overrepresented while in vinasse treatment, the functions related to spore-producing microorganisms were overrepresented. Furthermore, all additional residues increased microorganisms related to the nitrogen metabolism and vinasse with straw had a synergetic effect on the highest N2O emissions. The results highlight the importance of residues and fertiliser management in sustainable agriculture.}, }
@article {pmid29723706, year = {2018}, author = {Franciosa, I and Alessandria, V and Dolci, P and Rantsiou, K and Cocolin, L}, title = {Sausage fermentation and starter cultures in the era of molecular biology methods.}, journal = {International journal of food microbiology}, volume = {279}, number = {}, pages = {26-32}, doi = {10.1016/j.ijfoodmicro.2018.04.038}, pmid = {29723706}, issn = {1879-3460}, mesh = {Animals ; Bioreactors ; Europe ; Fermentation/*physiology ; Food Microbiology/*methods ; High-Throughput Nucleotide Sequencing ; Lactobacillales/classification/genetics/*metabolism ; Meat/*microbiology ; Meat Products/*microbiology ; }, abstract = {Fermented sausages have a long tradition originating from Europe and they constitute a significant part of the Mediterranean diet. This kind of products has a specific microbiota that is typical of the region or area where they are produced. Therefore, in order to protect the traditional aspect of these products, it is essential to understand the microbial ecology during fermentation by studying the dynamic changes that occur and to select autochthonous starter cultures that can be used in the production. In this paper we summarize the state of the art concerning the selection and use of starter cultures and ecology aspects of naturally fermented sausages. We pay particular attention to the application of bacteriocinogenic strains as they could provide an additional tool in the prevention of foodborne pathogens as well as enhancing the competitiveness of the starter organisms. Microbial ecology of fermented sausages has been determined by traditional microbiological methods, but the introduction in food microbiology of new molecular techniques complements the studies carried out so far and allows scientists to overcome the limitations of traditional methods. Next Generation Sequencing (NGS) techniques represent a change in the way microbiologists address ecology and diversity in foods. Indeed the application of metataxonomics and metagenomics will permit a detailed understanding of microbial ecology. A thorough knowledge of the mechanisms behind the biological processes will enhance meat fermentation control and modulation to obtain products with desired organoleptic properties.}, }
@article {pmid29722798, year = {2018}, author = {Li, H and Li, T and Qu, J}, title = {Stochastic processes govern bacterial communities from the blood of pikas and from their arthropod vectors.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {6}, pages = {}, doi = {10.1093/femsec/fiy082}, pmid = {29722798}, issn = {1574-6941}, mesh = {Animals ; Arthropod Vectors/*microbiology ; Bacteria/*classification/genetics/*isolation &amp; purification ; Bacterial Infections/microbiology/*transmission ; Gastrointestinal Microbiome/*physiology ; High-Throughput Nucleotide Sequencing ; Humans ; Lagomorpha/blood/*microbiology ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Siphonaptera/*microbiology ; Stochastic Processes ; }, abstract = {Vector-borne microbes influence pathogen transmission and blood microbiomes, thereby affecting the emergence of infectious diseases. Thus, understanding the relationship between host and vector microbiomes is of importance. In this study, we investigated the bacterial community composition, diversity and assembly of the flea (Rhadinopsylla dahurica vicina), torsalo (Hypoderma curzonial), and the blood and gut of their shared pika host, Ochotona curzoniae. Bartonella, Sphingomonas and Bradyrhizobium were enriched in blood, while Wolbachia and Fusobacterium were more abundant in fleas and torsaloes. Most of potential pathogenic microbes (belonging to Fusobacterium, Rickettsia, Kingella, Porphyromonas, Bartonella and Mycoplasma) were present in the blood of pikas and their vectors. Blood communities were more similar to those from fleas than other sample types and were independent of host factors or geographical sites. Notably, blood microbes originate mainly from fleas rather than gut or torsaloes. Interestingly, the community assembly of blood, fleas or torsaloes was primarily governed by stochastic processes, while the gut microbiome was determined by deterministic processes. Ecological drift plays a dominant role in the assembly of blood and flea microbiomes. These results reflect the difficulty for predicting and regulating the microbial ecology of fleas for the prevention of potential microbiome-associated diseases.}, }
@article {pmid29722774, year = {2018}, author = {Etalo, DW and Jeon, JS and Raaijmakers, JM}, title = {Modulation of plant chemistry by beneficial root microbiota.}, journal = {Natural product reports}, volume = {35}, number = {5}, pages = {398-409}, doi = {10.1039/c7np00057j}, pmid = {29722774}, issn = {1460-4752}, mesh = {Crops, Agricultural/chemistry/microbiology ; Endophytes/physiology ; Plant Development ; Plant Roots/*microbiology ; Plants/*chemistry/microbiology ; }, abstract = {Covering: 1981-2017Plants are colonized by an astounding number of microorganisms that can reach cell densities much greater than the number of plant cells. Various plant-associated microorganisms can have profound beneficial effects on plant growth, development, physiology and tolerance to (a)biotic stress. In return, plants release metabolites into their direct surroundings, thereby feeding the microbial community and influencing their composition, gene expression and the production of secondary metabolites. Similarly, microbes living on and in plant tissue may induce known and yet unknown biosynthetic pathways in plants leading to diverse alterations in the plant metabolome. Here, we provide an overview of the impact of beneficial microbiota on plant chemistry, with an emphasis on bacteria living on or inside root tissues. We will also provide new perspectives on deciphering the yet untapped potential of microbe-mediated alteration of plant chemistry as an alternative platform to discover new pathways, genes and enzymes involved the biosynthesis of high value natural plant products.}, }
@article {pmid29721834, year = {2018}, author = {Jung, MY and Kim, SJ and Kim, JG and Hong, H and Gwak, JH and Park, SJ and Kim, YH and Rhee, SK}, title = {Comparative genomic analysis of Geosporobacter ferrireducens and its versatility of anaerobic energy metabolism.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {56}, number = {5}, pages = {365-371}, pmid = {29721834}, issn = {1976-3794}, mesh = {Adenosine Triphosphatases ; Amino Acid Sequence ; Bacteria, Anaerobic/genetics/metabolism ; Bacterial Proteins/classification/genetics ; Bacterial Typing Techniques ; Base Sequence ; Clostridiaceae/classification/enzymology/*genetics/*metabolism ; DNA, Bacterial/genetics ; Energy Metabolism/*genetics/*physiology ; Fermentation ; Firmicutes/classification/genetics ; Genes, Bacterial/genetics ; Genes, rRNA/genetics ; Genome, Bacterial/*genetics ; *Genomics ; Iron/metabolism ; Phylogeny ; Sequence Alignment ; Sugars/metabolism ; }, abstract = {Members of the family Clostridiaceae within phylum Firmicutes are ubiquitous in various iron-reducing environments. However, genomic data on iron-reducing bacteria of the family Clostridiaceae, particularly regarding their environmental distribution, are limited. Here, we report the analysis and comparison of the genomic properties of Geosporobacter ferrireducens IRF9, a strict anaerobe that ferments sugars and degrades toluene under iron-reducing conditions, with those of the closely related species, Geosporobacter subterraneus DSM 17957. Putative alkyl succinate synthase-encoding genes were observed in the genome of strain IRF9 instead of the typical benzyl succinate synthase-encoding genes. Canonical genes associated with iron reduction were not observed in either genome. The genomes of strains IRF9 and DMS 17957 harbored genes for acetogenesis, that encode two types of Rnf complexes mediating the translocation of H[+] and Na[+] ions, respectively. Strain IRF9 harbored two different types of ATPases (Na[+]-dependent F-type ATPase and H[+]-dependent V-type ATPase), which enable full exploitation of ion gradients. The versatile energy conservation potential of strain IRF9 promotes its survival in various environmental conditions.}, }
@article {pmid29721301, year = {2018}, author = {Caballero Ortiz, S and Trienens, M and Pfohl, K and Karlovsky, P and Holighaus, G and Rohlfs, M}, title = {Phenotypic responses to microbial volatiles render a mold fungus more susceptible to insect damage.}, journal = {Ecology and evolution}, volume = {8}, number = {8}, pages = {4328-4339}, pmid = {29721301}, issn = {2045-7758}, abstract = {In decomposer systems, fungi show diverse phenotypic responses to volatile organic compounds of microbial origin (volatiles). The mechanisms underlying such responses and their consequences for the performance and ecological success of fungi in a multitrophic community context have rarely been tested explicitly. We used a laboratory-based approach in which we investigated a tripartite yeast-mold-insect model decomposer system to understand the possible influence of yeast-borne volatiles on the ability of a chemically defended mold fungus to resist insect damage. The volatile-exposed mold phenotype (1) did not exhibit protein kinase A-dependent morphological differentiation, (2) was more susceptible to insect foraging activity, and (3) had reduced insecticidal properties. Additionally, the volatile-exposed phenotype was strongly impaired in secondary metabolite formation and unable to activate "chemical defense" genes upon insect damage. These results suggest that volatiles can be ecologically important factors that affect the chemical-based combative abilities of fungi against insect antagonists and, consequently, the structure and dynamics of decomposer communities.}, }
@article {pmid29720684, year = {2018}, author = {Ramond, JB and Woodborne, S and Hall, G and Seely, M and Cowan, DA}, title = {Namib Desert primary productivity is driven by cryptic microbial community N-fixation.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6921}, pmid = {29720684}, issn = {2045-2322}, mesh = {Africa, Southern ; Biodiversity ; Carbon ; *Desert Climate ; Ecosystem ; *Microbiota ; *Nitrogen Fixation ; Plants ; Soil Microbiology ; }, abstract = {Carbon exchange in drylands is typically low, but during significant rainfall events (wet anomalies) drylands act as a C sink. During these anomalies the limitation on C uptake switches from water to nitrogen. In the Namib Desert of southern Africa, the N inventory in soil organic matter available for mineralisation is insufficient to support the observed increase in primary productivity. The C4 grasses that flourish after rainfall events are not capable of N fixation, and so there is no clear mechanism for adequate N fixation in dryland ecosystems to support rapid C uptake. Here we demonstrate that N fixation by photoautotrophic hypolithic communities forms the basis for the N budget for plant productivity events in the Namib Desert. Stable N isotope (δ[15]N) values of Namib Desert hypolithic biomass, and surface and subsurface soils were measured over 3 years across dune and gravel plain biotopes. Hypoliths showed significantly higher biomass and lower δ[15]N values than soil organic matter. The δ[15]N values of hypoliths approach the theoretical values for nitrogen fixation. Our results are strongly indicative that hypolithic communities are the foundation of productivity after rain events in the Namib Desert and are likely to play similar roles in other arid environments.}, }
@article {pmid29720448, year = {2018}, author = {Fadlallah, J and El Kafsi, H and Sterlin, D and Juste, C and Parizot, C and Dorgham, K and Autaa, G and Gouas, D and Almeida, M and Lepage, P and Pons, N and Le Chatelier, E and Levenez, F and Kennedy, S and Galleron, N and de Barros, JP and Malphettes, M and Galicier, L and Boutboul, D and Mathian, A and Miyara, M and Oksenhendler, E and Amoura, Z and Doré, J and Fieschi, C and Ehrlich, SD and Larsen, M and Gorochov, G}, title = {Microbial ecology perturbation in human IgA deficiency.}, journal = {Science translational medicine}, volume = {10}, number = {439}, pages = {}, doi = {10.1126/scitranslmed.aan1217}, pmid = {29720448}, issn = {1946-6242}, mesh = {Humans ; IgA Deficiency/*immunology/*microbiology ; Immunoglobulin A/metabolism ; Immunoglobulin M/metabolism ; Microbiota/physiology ; }, abstract = {Paradoxically, loss of immunoglobulin A (IgA), one of the most abundant antibodies, does not irrevocably lead to severe infections in humans but rather is associated with relatively mild respiratory infections, atopy, and autoimmunity. IgA might therefore also play covert roles, not uniquely associated with control of pathogens. We show that human IgA deficiency is not associated with massive quantitative perturbations of gut microbial ecology. Metagenomic analysis highlights an expected pathobiont expansion but a less expected depletion in some typically beneficial symbionts. Gut colonization by species usually present in the oropharynx is also reminiscent of spatial microbiota disorganization. IgM only partially rescues IgA deficiency because not all typical IgA targets are efficiently bound by IgM in the intestinal lumen. Together, IgA appears to play a nonredundant role at the forefront of the immune/microbial interface, away from the intestinal barrier, ranging from pathobiont control and regulation of systemic inflammation to preservation of commensal diversity and community networks.}, }
@article {pmid29718292, year = {2018}, author = {Piffaretti, JC and Schink, B and Semenza, JC}, title = {Editorial to the thematic issue climate change and microbiology.}, journal = {FEMS microbiology letters}, volume = {365}, number = {10}, pages = {}, doi = {10.1093/femsle/fny080}, pmid = {29718292}, issn = {1574-6968}, mesh = {Animals ; *Climate Change ; Ecosystem ; Humans ; *Microbiology ; }, }
@article {pmid29718180, year = {2018}, author = {Schmidt, R and Durling, MB and de Jager, V and Menezes, RC and Nordkvist, E and Svatoš, A and Dubey, M and Lauterbach, L and Dickschat, JS and Karlsson, M and Garbeva, P}, title = {Deciphering the genome and secondary metabolome of the plant pathogen Fusarium culmorum.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {6}, pages = {}, doi = {10.1093/femsec/fiy078}, pmid = {29718180}, issn = {1574-6941}, mesh = {Alkyl and Aryl Transferases/*genetics ; Cyclohexenes/metabolism ; Edible Grain/microbiology ; Fusarium/*genetics/*metabolism ; Genome, Fungal/*genetics ; Geologic Sediments/microbiology ; Hordeum/microbiology ; Metabolome/*physiology ; Mycotoxins/biosynthesis ; Plant Diseases/microbiology ; Sesquiterpenes/metabolism ; Soil Microbiology ; Trichothecenes/metabolism ; Triticum/microbiology ; Virulence ; }, abstract = {Fusarium culmorum is one of the most important fungal plant pathogens that causes diseases on a wide diversity of cereal and non-cereal crops. We report herein for the first time the genome sequence of F. culmorum strain PV and its associated secondary metabolome that plays a role in the interaction with other microorganisms and contributes to its pathogenicity on plants. The genome revealed the presence of two terpene synthases, trichodiene and longiborneol synthase, which generate an array of volatile terpenes. Furthermore, we identified two gene clusters, deoxynivalenol and zearalenone, which encode for the production of mycotoxins. Linking the production of mycotoxins with in vitro bioassays, we found high virulence of F. culmorum PV on maize, barley and wheat. By using ultra-performance liquid chromatography-mass spectrometry, we confirmed several compounds important for the behaviour and lifestyle of F. culmorum. This research sets the basis for future studies in microbe-plant interactions.}, }
@article {pmid29717331, year = {2018}, author = {Houles, A and Vincent, B and David, M and Ducousso, M and Galiana, A and Juillot, F and Hannibal, L and Carriconde, F and Fritsch, E and Jourand, P}, title = {Ectomycorrhizal Communities Associated with the Legume Acacia spirorbis Growing on Contrasted Edaphic Constraints in New Caledonia.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {964-975}, pmid = {29717331}, issn = {1432-184X}, support = {N&#xb0; 2013/1434//CIFRE/ ; ANR-12-ADAP-0017 ADASPIR//Agence Nationale pour la Recherche (FR)/ ; }, mesh = {Acacia/growth &amp; development/*microbiology ; Basidiomycota/classification/*physiology ; Mycorrhizae/classification/*physiology ; New Caledonia ; Soil/*chemistry ; *Soil Microbiology ; Symbiosis ; }, abstract = {This study aims to characterize the ectomycorrhizal (ECM) communities associated with Acacia spirorbis, a legume tree widely spread in New Caledonia that spontaneously grows on contrasted edaphic constraints, i.e. calcareous, ferralitic and volcano-sedimentary soils. Soil geochemical parameters and diversity of ECM communities were assessed in 12 sites representative of the three mains categories of soils. The ectomycorrhizal status of Acacia spirorbis was confirmed in all studied soils, with a fungal community dominated at 92% by Basidiomycota, mostly represented by/tomentella-thelephora (27.6%), /boletus (15.8%), /sebacina (10.5%), /russula-lactarius (10.5%) and /pisolithus-scleroderma (7.9%) lineages. The diversity and the proportion of the ECM lineages were similar for the ferralitic and volcano-sedimentary soils but significantly different for the calcareous soils. These differences in the distribution of the ECM communities were statistically correlated with pH, Ca, P and Al in the calcareous soils and with Co in the ferralitic soils. Altogether, these data suggest a high capacity of A. spirorbis to form ECM symbioses with a large spectrum of fungi regardless the soil categories with contrasted edaphic parameters.}, }
@article {pmid29715602, year = {2018}, author = {Ioannidis, AG and Kerckhof, FM and Riahi Drif, Y and Vanderroost, M and Boon, N and Ragaert, P and De Meulenaer, B and Devlieghere, F}, title = {Characterization of spoilage markers in modified atmosphere packaged iceberg lettuce.}, journal = {International journal of food microbiology}, volume = {279}, number = {}, pages = {1-13}, doi = {10.1016/j.ijfoodmicro.2018.04.034}, pmid = {29715602}, issn = {1879-3460}, mesh = {Anaerobiosis/physiology ; Colony Count, Microbial ; Food Microbiology/*methods ; Food Packaging/*methods ; Food Preservation/*methods ; Lactococcus/classification/genetics/isolation &amp; purification ; Lactuca/*microbiology ; Leuconostoc/classification/genetics/isolation &amp; purification ; Odorants/analysis ; Oxygen ; Pseudomonas/classification/genetics/isolation &amp; purification ; Volatile Organic Compounds/*analysis ; }, abstract = {Fresh cut iceberg lettuce spoilage was studied considering the microbial and biochemical activity, the formation of volatile organic compounds (VOC) and consumer acceptability. Lettuce was packaged under three different packaging conditions and stored at 4 °C for 10 days: anaerobic packaging (ANAER), equilibrium modified atmosphere packaging with 3% O2 (EMAP) and perforated packages (AIR). Results indicated a clear distinction between packaging conditions. EMAP and AIR resulted in a short shelf life (≤5.6 days) which was limited due to browning, leading to consumer rejection as assessed via the Weibull hazard analysis method, while no off-odors were detected. Culture- independent 16 s rRNA gene amplicon sequencing revealed Pseudomonas spp. as the dominating species. In contrast, under ANAER conditions, lactic acid bacteria dominated with genera of Leuconostoc spp. and Lactococcus spp. proliferating, while also oligotypes of Pseudomonas spp. were found. Spoilage under ANAER occurred after 6.6 days and it was related to strong fermentative-like off-odors that were present by the end of storage. As revealed by selective ion flow tube mass spectrometry (SIFT-MS), these odors were associated with several VOCs such as: ethanol, 3-methyl-1-butanol, 2,3-butanediol, (Z)-3-hexen-1-ol, hexanal, acetic acid, ethyl acetate and dimethyl sulfide. Panelists rejected the iceberg lettuce due to the formation of off-odors while the overall appearance remained good throughout the study. Hence a sensor based technology incorporated in the packaging, detecting VOCs and in particular ethanol as dominant compound, could serve as a spoilage indicator for ANAER packed lettuce, which proved to have the longest shelf life.}, }
@article {pmid29715551, year = {2018}, author = {Kalil, AC and Sandkovsky, U and Florescu, DF}, title = {Severe infections in critically ill solid organ transplant recipients.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {24}, number = {12}, pages = {1257-1263}, doi = {10.1016/j.cmi.2018.04.022}, pmid = {29715551}, issn = {1469-0691}, mesh = {Anti-Infective Agents/adverse effects/therapeutic use ; Bacterial Infections/diagnosis/*etiology/microbiology/mortality ; Critical Illness ; Cross Infection/diagnosis/drug therapy/etiology/microbiology ; Humans ; Immunocompromised Host ; Intensive Care Units/statistics &amp; numerical data ; Mycoses/diagnosis/drug therapy/etiology ; Opportunistic Infections/diagnosis/drug therapy/*etiology ; Organ Transplantation/*adverse effects ; *Transplant Recipients ; Virus Diseases/diagnosis/drug therapy/etiology ; }, abstract = {BACKGROUND: Severe infections are among the most common causes of death in immunocompromised patients admitted to the intensive care unit. The epidemiology, diagnosis and treatment of these infections has evolved in the last decade.<br><br>AIMS: We aim to provide a comprehensive review of these severe infections in this population.<br><br>SOURCES: Review of the literature pertaining to severe infections in critically ill solid organ transplant recipients. PubMed and Embase databases were searched for documents published since database inception until November 2017.<br><br>CONTENT: The epidemiology of severe infections has changed in the immunocompromised patients. This population is presenting to the intensive care unit with specific transplantation procedure-related infections, device-associated infections, a multitude of opportunistic viral infections, an increasing number of nosocomial infections and bacterial diseases with a more limited therapeutic armamentarium. Both molecular diagnostics and imaging techniques have had substantial progress in the last decade, which will, we hope, translate into faster and more precise diagnoses, as well as more optimal empirical treatment de-escalation.<br><br>IMPLICATIONS: The key clinical elements to improve the outcome of critically ill solid organ transplant recipients depend on the knowledge of geographic epidemiology, specific surgical procedures, net state of immunosuppression, hospital microbial ecology, aggressive diagnostic strategy and search for source control, rapid initiation of antimicrobials and minimization of iatrogenic immunosuppression.}, }
@article {pmid29713791, year = {2018}, author = {Castellano-Hinojosa, A and Armato, C and Pozo, C and González-Martínez, A and González-López, J}, title = {New concepts in anaerobic digestion processes: recent advances and biological aspects.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {12}, pages = {5065-5076}, doi = {10.1007/s00253-018-9039-9}, pmid = {29713791}, issn = {1432-0614}, mesh = {Anaerobiosis ; Archaea/metabolism ; Bacteria/metabolism ; Biofuels ; Biomass ; *Bioreactors ; Industrial Microbiology/*trends ; Refuse Disposal/*methods ; }, abstract = {Waste treatment and the simultaneous production of energy have gained great interest in the world. In the last decades, scientific efforts have focused largely on improving and developing sustainable bioprocess solutions for energy recovery from challenging waste. Anaerobic digestion (AD) has been developed as a low-cost organic waste treatment technology with a simple setup and relatively limited investment and operating costs. Different technologies such as one-stage and two-stage AD have been developed. The viability and performance of these technologies have been extensively reported, showing the supremacy of two-stage AD in terms of overall energy recovery from biomass under different substrates, temperatures, and pH conditions. However, a comprehensive review of the advantages and disadvantages of these technologies is still lacking. Since microbial ecology is critical to developing successful AD, many studies have shown the structure and dynamics of archaeal and bacterial communities in this type of system. However, the role of Eukarya groups remains largely unknown to date. In this review, we provide a comprehensive review of the role, abundance, dynamics, and structure of archaeal, bacterial, and eukaryal communities during the AD process. The information provided could help researchers to select the adequate operational parameters to obtain the best performance and biogas production results.}, }
@article {pmid29712884, year = {2018}, author = {Lezutekong, JN and Nikhanj, A and Oudit, GY}, title = {Imbalance of gut microbiome and intestinal epithelial barrier dysfunction in cardiovascular disease.}, journal = {Clinical science (London, England : 1979)}, volume = {132}, number = {8}, pages = {901-904}, doi = {10.1042/CS20180172}, pmid = {29712884}, issn = {1470-8736}, support = {855332//CIHR/Canada ; }, mesh = {*Cardiovascular Diseases ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; *Hypertension ; Intestines ; }, abstract = {The main function of the intestinal barrier is to regulate the absorption of nutrients, electrolytes, and water from the lumen into circulation and to prevent the entry of pathogenic microorganisms and toxic luminal substances. To maintain this function, an ideal microbiota balance is required and gut microbiota are critical for the intestinal epithelial barrier dysfunction and for the maintenance of physiological homeostasis. There is a demonstrable link between dysbiosis and intestinal dysfunction and diseases such as diabetes, obesity, and cardiovascular disease. However, links amongst gut pathology, microbial ecology, and blood pressure remain elusive. In a recent issue of Clinical Science (vol. 132, issue 6, 701-718), Kim et al. demonstrate a crucial link between gut microbiota and bacterial metabolites such as butyrate, gut leakiness, and hypertension.}, }
@article {pmid29709671, year = {2018}, author = {Ghebre, MA and Pang, PH and Diver, S and Desai, D and Bafadhel, M and Haldar, K and Kebadze, T and Cohen, S and Newbold, P and Rapley, L and Woods, J and Rugman, P and Pavord, ID and Johnston, SL and Barer, M and May, RD and Brightling, CE}, title = {Biological exacerbation clusters demonstrate asthma and chronic obstructive pulmonary disease overlap with distinct mediator and microbiome profiles.}, journal = {The Journal of allergy and clinical immunology}, volume = {141}, number = {6}, pages = {2027-2036.e12}, pmid = {29709671}, issn = {1097-6825}, support = {G1000758/MRC_/Medical Research Council/United Kingdom ; PDF-2013-06-052/DH_/Department of Health/United Kingdom ; G0801980/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; G0601369/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Asthma/*immunology/metabolism/*microbiology ; Female ; Humans ; Inflammation/immunology/metabolism/microbiology ; Male ; Microbiota ; Prospective Studies ; Pulmonary Disease, Chronic Obstructive/*immunology/metabolism/*microbiology ; Sputum/immunology/metabolism/microbiology ; }, abstract = {BACKGROUND: Exacerbations of asthma and chronic obstructive pulmonary disease (COPD) are heterogeneous.<br><br>OBJECTIVE: We sought to investigate the sputum cellular, mediator, and microbiome profiles of both asthma and COPD exacerbations.<br><br>METHODS: Patients with severe asthma or moderate-to-severe COPD were recruited prospectively to a single center. Sputum mediators were available in 32 asthmatic patients and 73 patients with COPD assessed at exacerbation. Biologic clusters were determined by using factor and cluster analyses on a panel of sputum mediators. Patterns of clinical parameters, sputum mediators, and microbiome communities were assessed across the identified clusters.<br><br>RESULTS: The asthmatic patients and patients with COPD had different clinical characteristics and inflammatory profiles but similar microbial ecology. Three exacerbation biologic clusters were identified. Cluster 1 was COPD predominant, with 27 patients with COPD and 7 asthmatic patients exhibiting increased blood and sputum neutrophil counts, proinflammatory mediators (IL-1&#x3b2;, IL-6, IL-6 receptor, TNF-&#x3b1;, TNF receptors 1 and 2, and vascular endothelial growth factor), and proportions of the bacterial phylum Proteobacteria. Cluster 2 had 10 asthmatic patients and 17 patients with COPD with increased blood and sputum eosinophil counts, type 2 mediators (IL-5, IL-13, CCL13, CCL17, and CCL26), and proportions of the bacterial phylum Bacteroidetes. Cluster 3 had 15 asthmatic patients and 29 patients with COPD with increased type 1 mediators (CXCL10, CXCL11, and IFN-&#x3b3;) and proportions of the phyla Actinobacteria and Firmicutes.<br><br>CONCLUSIONS: A biologic clustering approach revealed 3 subgroups of asthma and COPD exacerbations, each with different percentages of patients with overlapping asthma and COPD. The sputum mediator and microbiome profiles were distinct between clusters.}, }
@article {pmid29708639, year = {2018}, author = {Otte, JM and Harter, J and Laufer, K and Blackwell, N and Straub, D and Kappler, A and Kleindienst, S}, title = {The distribution of active iron-cycling bacteria in marine and freshwater sediments is decoupled from geochemical gradients.}, journal = {Environmental microbiology}, volume = {20}, number = {7}, pages = {2483-2499}, doi = {10.1111/1462-2920.14260}, pmid = {29708639}, issn = {1462-2920}, mesh = {Bacteria/classification/*metabolism ; Denmark ; Fresh Water/microbiology ; Geologic Sediments/*microbiology ; Germany ; Iron/*metabolism ; Lakes/microbiology ; Nitrates/metabolism ; Oxidation-Reduction ; RNA, Bacterial ; RNA, Ribosomal, 16S ; Seawater/microbiology ; *Soil Microbiology ; *Water Microbiology ; }, abstract = {Microaerophilic, phototrophic and nitrate-reducing Fe(II)-oxidizers co-exist in coastal marine and littoral freshwater sediments. However, the in situ abundance, distribution and diversity of metabolically active Fe(II)-oxidizers remained largely unexplored. Here, we characterized the microbial community composition at the oxic-anoxic interface of littoral freshwater (Lake Constance, Germany) and coastal marine sediments (Kalø Vig and Norsminde Fjord, Denmark) using DNA-/RNA-based next-generation 16S rRNA (gene) amplicon sequencing. All three physiological groups of neutrophilic Fe(II)-oxidizing bacteria were found to be active in marine and freshwater sediments, revealing up to 0.2% anoxygenic photoferrotrophs (e.g., Rhodopseudomonas, Rhodobacter, Chlorobium), 0.1% microaerophilic Fe(II)-oxidizers (e.g., Mariprofundus, Hyphomonas, Gallionella) and 0.3% nitrate-reducing Fe(II)-oxidizers (e.g., Thiobacillus, Pseudomonas, Denitromonas, Hoeflea). Active Fe(III)-reducing bacteria (e.g., Shewanella, Geobacter) were most abundant (up to 2.8%) in marine sediments and co-occurred with cable bacteria (up to 4.5%). Geochemical profiles of Fe(III), Fe(II), O2 , light, nitrate and total organic carbon revealed a redox stratification of the sediments and explained 75%-85% of the vertical distribution of microbial taxa, while active Fe-cycling bacteria were found to be decoupled from geochemical gradients. We suggest that metabolic flexibility, microniches in the sediments, or interrelationships with cable bacteria might explain the distribution patterns of active Fe-cycling bacteria.}, }
@article {pmid29706324, year = {2018}, author = {Kharchoufi, S and Parafati, L and Licciardello, F and Muratore, G and Hamdi, M and Cirvilleri, G and Restuccia, C}, title = {Edible coatings incorporating pomegranate peel extract and biocontrol yeast to reduce Penicillium digitatum postharvest decay of oranges.}, journal = {Food microbiology}, volume = {74}, number = {}, pages = {107-112}, doi = {10.1016/j.fm.2018.03.011}, pmid = {29706324}, issn = {1095-9998}, mesh = {Antibiosis ; Antifungal Agents/metabolism/pharmacology ; Biological Control Agents/*pharmacology ; Chitosan/pharmacology ; Citrus sinensis/*microbiology ; Disk Diffusion Antimicrobial Tests ; Food Microbiology ; Food Preservation/*methods ; Fruit/microbiology ; Galactans/pharmacology ; Lythraceae/*chemistry ; Mannans/pharmacology ; Methanol/pharmacology ; Penicillium/*drug effects/*growth &amp; development ; Pichia/chemistry ; Plant Diseases/microbiology/*prevention &amp; control ; Plant Extracts/*pharmacology ; Plant Gums/pharmacology ; Yeasts/*metabolism ; }, abstract = {This study investigated the potential use of two edible coatings, chitosan (CH) and locust bean gum (LBG), which incorporated chemically characterized water pomegranate peel extract (WPPE) or methanol pomegranate peel extract (MPPE) and the biocontrol agent (BCA) Wickerhamomyces anomalus, to control the growth of Penicillium digitatum and to reduce the postharvest decay of oranges. CH and LBG including pomegranate peel extracts (PPEs) at different concentrations were tested in vitro against P. digitatum to determine their antifungal efficacy; at the same time, the tolerance of viable cells of W. anomalus to increasing concentrations of WPPE and MPPE extracts was assessed. The potential application of selected bioactive coatings was evaluated in vivo on oranges, which had been artificially inoculated with P. digitatum, causal agent of green mold decay. CH incorporating MPPE or WPPE at all concentrations was able to inhibit in vitro P. digitatum, while LBG was active only at the highest MPPE or WPPE concentrations. W. anomalus BS91 was slightly inhibited only by MPPE-modified coatings, while no inhibition was observed by WPPE, which was therefore selected for the in vivo trials on oranges artificially inoculated with P. digitatum. The experimental results proved that the addition of 0.361 g dry WPPE/mL, both to CH and LBG coatings, significantly reduced disease incidence (DI) by 49 and 28% respectively, with respect to the relative controls. Besides the combination CH or LBG + WPPE, the addition of W. anomalus cells to coatings strengthened the antifungal effect with respect to the relative controls, as demonstrated by the significant reduction of DI (up to 95 and 75% respectively). The findings of the study contribute to the valorization of a value-added industrial byproduct and provide a significant advancement in the development of new food protectant formulations, which benefit from the synergistic effect between biocontrol agents and natural bioactive compounds.}, }
@article {pmid29705905, year = {2018}, author = {McGee, CF and Storey, S and Clipson, N and Doyle, E}, title = {Concentration-dependent responses of soil bacterial, fungal and nitrifying communities to silver nano and micron particles.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {19}, pages = {18693-18704}, pmid = {29705905}, issn = {1614-7499}, mesh = {Agriculture ; Bacteria/*drug effects ; Fungi/*drug effects ; Metal Nanoparticles/*analysis/toxicity ; Oxidation-Reduction ; Silver/*analysis/toxicity ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/*analysis/toxicity ; }, abstract = {The growing use of silver nanoparticles (AgNPs) is likely to result in increased environmental contamination. Although AgNPs have been reported to affect microbial communities in a range of ecosystems, there is still a lack of information concerning the effect of low concentrations of AgNPs on soil microbial community structures and functional groups involved in biogeochemical cycling. In this study, the concentration-dependent effects of AgNPs and silver micron particles (AgMPs) on bacterial and fungal community structures in an agricultural pastureland soil were examined in a microcosm-based experiment using enzyme analysis, molecular fingerprinting, qPCR and amplicon sequencing. Soil enzyme processes were impacted by Ag contamination, with soil dehydrogenase activity reduced by 1 mg kg[-1] of AgNPs and AgMPs. Soil urease activity was less susceptible, but was inhibited by ≥ 10 mg kg[-1] AgNPs. The significant (P ≤ 0.001) decrease in copy numbers of the amoA gene by 10 mg kg[-1] AgNPs indicated that archaea ammonia oxidisers may be more sensitive to AgNP contamination than bacteria. Amplicon sequencing revealed the bacterial phyla Acidobacteria and Verrucomicrobia to be highly sensitive to AgNP contamination. A broad reduction in the relative abundance of Acidobacterial genera was observed, with the exception of the genus Geothrix which increased in response to AgNP and AgMP amendment. Broad tolerance to Ag was observed among the Bacteriodetes, with higher relative abundance of most genera observed in the presence of AgNPs and AgMPs. The proteobacterial genus Dyella was highly tolerant to AgNPs and AgMPs and relative abundance of this genus increased with Ag concentration. Soil fungal community structure responded to both AgNPs and AgMPs, but the nanoparticle had an impact at a lower concentration. This study demonstrates that pastureland soil microbial communities are highly sensitive to AgNP amendment and key functional processes may be disrupted by relatively low levels of contamination.}, }
@article {pmid29705820, year = {2018}, author = {Sándor, AD and Földvári, M and Krawczyk, AI and Sprong, H and Corduneanu, A and Barti, L and Görföl, T and Estók, P and Kováts, D and Szekeres, S and László, Z and Hornok, S and Földvári, G}, title = {Eco-epidemiology of Novel Bartonella Genotypes from Parasitic Flies of Insectivorous Bats.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {1076-1088}, pmid = {29705820}, issn = {1432-184X}, support = {PN-II-RU-TE-2014-4-1389//PN/ ; In the light of evolution: theories and solutions" (GINOP-2.3.2-15-2016-00057)//GINOP/ ; }, mesh = {Animals ; Bartonella/classification/*genetics ; Bartonella Infections/epidemiology/microbiology/*veterinary ; Caves ; *Chiroptera/microbiology/parasitology ; Diptera/*microbiology ; Female ; *Genotype ; Hungary/epidemiology ; Male ; Polymerase Chain Reaction/veterinary ; Romania/epidemiology ; Sequence Analysis, DNA/veterinary ; }, abstract = {Bats are important zoonotic reservoirs for many pathogens worldwide. Although their highly specialized ectoparasites, bat flies (Diptera: Hippoboscoidea), can transmit Bartonella bacteria including human pathogens, their eco-epidemiology is unexplored. Here, we analyzed the prevalence and diversity of Bartonella strains sampled from 10 bat fly species from 14 European bat species. We found high prevalence of Bartonella spp. in most bat fly species with wide geographical distribution. Bat species explained most of the variance in Bartonella distribution with the highest prevalence of infected flies recorded in species living in dense groups exclusively in caves. Bat gender but not bat fly gender was also an important factor with the more mobile male bats giving more opportunity for the ectoparasites to access several host individuals. We detected high diversity of Bartonella strains (18 sequences, 7 genotypes, in 9 bat fly species) comparable with tropical assemblages of bat-bat fly association. Most genotypes are novel (15 out of 18 recorded strains have a similarity of 92-99%, with three sequences having 100% similarity to Bartonella spp. sequences deposited in GenBank) with currently unknown pathogenicity; however, 4 of these sequences are similar (up to 92% sequence similarity) to Bartonella spp. with known zoonotic potential. The high prevalence and diversity of Bartonella spp. suggests a long shared evolution of these bacteria with bat flies and bats providing excellent study targets for the eco-epidemiology of host-vector-pathogen cycles.}, }
@article {pmid29704757, year = {2018}, author = {Campanaro, S and Treu, L and Kougias, PG and Luo, G and Angelidaki, I}, title = {Metagenomic binning reveals the functional roles of core abundant microorganisms in twelve full-scale biogas plants.}, journal = {Water research}, volume = {140}, number = {}, pages = {123-134}, doi = {10.1016/j.watres.2018.04.043}, pmid = {29704757}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Biofuels ; Bioreactors/*microbiology ; Manure ; *Metagenome ; Metagenomics/methods ; Microbiota/*physiology ; Sewage/microbiology ; Waste Disposal, Fluid ; Wastewater ; }, abstract = {The aim of this work was to elucidate the microbial ecology in twelve mesophilic and thermophilic full-scale biogas plants using a genome-centric metagenomic approach. In this study both biogas plants treating manure and those treating sludge from waste water treatment plants were considered. The identification of 132 Metagenome-Assembled Genomes (MAGs) and analysis of their abundance profile in different samples allowed the identification of the most abundant core members of the anaerobic digestion microbiome. Canonical correspondence analysis was used to determine the influence of biotic and environmental factors on MAGs abundance and to investigate the methanogenic performance of the biogas plants. Prediction of the functional properties of MAGs was obtained analyzing their KEGG pathways and their carbohydrate active domains. Network analysis allowed investigation of species-species associations and shed light on syntrophic interactions between members belonging to the anaerobic digestion dark matter (phylum Fermentibacteria). By stratifying and comparing different levels of information, it was predicted that some MAGs have a crucial role in the manure-supplemented thermophilic biogas plants and it was highlighted the importance of the glycine cleavage system in complementing the "truncated" Wood-Ljungdahl pathway.}, }
@article {pmid29702317, year = {2018}, author = {Cardinali, F and Milanović, V and Osimani, A and Aquilanti, L and Taccari, M and Garofalo, C and Polverigiani, S and Clementi, F and Franciosi, E and Tuohy, K and Mercuri, ML and Altissimi, MS and Haouet, MN}, title = {Microbial dynamics of model Fabriano-like fermented sausages as affected by starter cultures, nitrates and nitrites.}, journal = {International journal of food microbiology}, volume = {278}, number = {}, pages = {61-72}, doi = {10.1016/j.ijfoodmicro.2018.04.032}, pmid = {29702317}, issn = {1879-3460}, mesh = {Animals ; Bioreactors ; Colony Count, Microbial ; Enterobacteriaceae/*metabolism ; Fermentation ; Fermented Foods/microbiology ; Italy ; Lactobacillus/*metabolism ; Meat Products/*microbiology ; Nitrates/*metabolism ; Nitrites/*metabolism ; Nitrogen Oxides ; Pediococcus pentosaceus/*metabolism ; Pseudomonas/*metabolism ; Serratia liquefaciens/*metabolism ; Staphylococcus/*metabolism ; Swine ; }, abstract = {The present study promotes the valorization of Fabriano-like fermented sausages, which are central-Italy salami with an origin that dates to the early 17th century, for the possible future selection of autochthonous starter cultures to be used with respect to local traditions. To the best of the authors' knowledge, this study represents the first attempt to define the microbial dynamics in Fabriano-like fermented sausage and the effect of nitrates/nitrites and starter cultures on its natural bacterial biota. Culture and RNA-based techniques (RT-PCR-DGGE and Illumina sequencing) were used to assess the microbial ecology of model Fabriano-like fermented sausages together with the impact of starter cultures and different nitrate and nitrite concentrations. The meat batter was used to produce two batches of fermented sausages that were prepared as follows: i) without commercial starters or ii) with the use of starter cultures composed of Pediococcus pentosaceus and Staphylococcus xylosus. Each batch was further divided into three different batches with the addition of 0/0 mg kg[-1] nitrate/nitrite, 75/60 mg kg[-1] nitrate/nitrite and 150/125 mg kg[-1] nitrate/nitrite to the first, second and third batch, respectively. The samples, which were produced in triplicate, were analyzed on the day of production and after 7, 21, and 42 days of ripening. Enterobacteriaceae counts were always higher in model Fabriano-like sausages produced without the use of starter cultures at all of the sampling times irrespective of the tested nitrate/nitrite concentrations. Lactobacilli counts were positively influenced by the starters, although this influence was not evident over time; moreover, the effect of nitrates and nitrites on the counts of lactobacilli differed over time. As a general trend, coagulase-negative cocci counts were apparently not influenced by the tested nitrate/nitrite concentrations. Regarding the effect of nitrates/nitrites on the microbial diversity revealed by RT-PCR-DGGE, the higher the concentration, the lower the presence of some genera/species such as Pseudomonas spp., Serratia liquefaciens and Staphylococcus spp. However, Illumina sequencing detected Pseudomonas spp. as a minority species after 7, 21 and 42 days of ripening irrespective of the nitrate/nitrite concentration. The presence of Staphylococcus species was highlighted by both RT-PCR-DGGE and Illumina sequencing at all of the stages of ripening, although its presence was massively detected in fermented sausages produced without the use of nitrates/nitrites at the end of ripening. Overall, the data collected clearly highlighted the dominance of Lactobacillus sakei in all of the fermented sausages during ripening (from day 7 to day 42) and irrespective of the nitrate/nitrite concentration and added starter cultures. Moreover, Pediococcus spp. was principally detected in model Fabriano-like fermented sausage with added starter cultures irrespective of the nitrate/nitrite concentration.}, }
@article {pmid29700966, year = {2018}, author = {Mansour, I and Heppell, CM and Ryo, M and Rillig, MC}, title = {Application of the microbial community coalescence concept to riverine networks.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {93}, number = {4}, pages = {1832-1845}, doi = {10.1111/brv.12422}, pmid = {29700966}, issn = {1469-185X}, mesh = {Bacteria/*classification ; Biological Evolution ; *Ecosystem ; Models, Biological ; Rivers/*microbiology ; }, abstract = {Flows of water, soil, litter, and anthropogenic materials in and around rivers lead to the mixing of their resident microbial communities and subsequently to a resultant community distinct from its precursors. Consideration of these events through a new conceptual lens, namely, community coalescence, could provide a means of integrating physical, environmental, and ecological mechanisms to predict microbial community assembly patterns better in these habitats. Here, we review field studies of microbial communities in riverine habitats where environmental mixing regularly occurs, interpret some of these studies within the community coalescence framework and posit novel hypotheses and insights that may be gained in riverine microbial ecology through the application of this concept. Particularly in the face of a changing climate and rivers under increasing anthropogenic pressures, knowledge about the factors governing microbial community assembly is essential to forecast and/or respond to changes in ecosystem function. Additionally, there is the potential for microbial ecology studies in rivers to become a driver of theory development: riverine systems are ideal for coalescence studies because regular and predictable environmental mixing occurs. Data appropriate for testing community coalescence theory could be collected with minimal alteration to existing study designs.}, }
@article {pmid29700144, year = {2018}, author = {Orata, FD and Kits, KD and Stein, LY}, title = {Complete Genome Sequence of Methylomonas denitrificans Strain FJG1, an Obligate Aerobic Methanotroph That Can Couple Methane Oxidation with Denitrification.}, journal = {Genome announcements}, volume = {6}, number = {17}, pages = {}, pmid = {29700144}, issn = {2169-8287}, abstract = {Methylomonas denitrificans strain FJG1 is a member of the gammaproteobacterial methanotrophs. The sequenced genome of FJG1 reveals the presence of genes that encode methane, methanol, formaldehyde, and formate oxidation. It also contains genes that encode enzymes for nitrate reduction to nitrous oxide, consistent with the ability of FJG1 to couple denitrification with methane oxidation.}, }
@article {pmid29696012, year = {2018}, author = {Graw, MF and D'Angelo, G and Borchers, M and Thurber, AR and Johnson, JE and Zhang, C and Liu, H and Colwell, FS}, title = {Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {729}, pmid = {29696012}, issn = {1664-302X}, abstract = {The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea (SCS) experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin's history. Deep subsurface microbial communities were recently sampled by the International Ocean Discovery Program (IODP) at three locations in the SCS with sedimentation rates of 5, 12, and 20 cm per thousand years. Here, we used Illumina sequencing of the 16S ribosomal RNA gene to characterize deep subsurface microbial communities from distinct sediment types at these sites. Communities across all sites were dominated by several poorly characterized taxa implicated in organic matter degradation, including Atribacteria, Dehalococcoidia, and Aerophobetes. Sulfate-reducing bacteria comprised only 4% of the community across sulfate-bearing sediments from multiple cores and did not change in abundance in sediments from the methanogenic zone at the site with the lowest sedimentation rate. Microbial communities were significantly structured by sediment age and the availability of sulfate as an electron acceptor in pore waters. However, microbial communities demonstrated no partitioning based on the sediment type they inhabited. These results indicate that microbial communities in the SCS are structured by the availability of electron donors and acceptors rather than sedimentological characteristics.}, }
@article {pmid29696004, year = {2018}, author = {Pjevac, P and Meier, DV and Markert, S and Hentschker, C and Schweder, T and Becher, D and Gruber-Vodicka, HR and Richter, M and Bach, W and Amann, R and Meyerdierks, A}, title = {Metaproteogenomic Profiling of Microbial Communities Colonizing Actively Venting Hydrothermal Chimneys.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {680}, pmid = {29696004}, issn = {1664-302X}, abstract = {At hydrothermal vent sites, chimneys consisting of sulfides, sulfates, and oxides are formed upon contact of reduced hydrothermal fluids with oxygenated seawater. The walls and surfaces of these chimneys are an important habitat for vent-associated microorganisms. We used community proteogenomics to investigate and compare the composition, metabolic potential and relative in situ protein abundance of microbial communities colonizing two actively venting hydrothermal chimneys from the Manus Basin back-arc spreading center (Papua New Guinea). We identified overlaps in the in situ functional profiles of both chimneys, despite differences in microbial community composition and venting regime. Carbon fixation on both chimneys seems to have been primarily mediated through the reverse tricarboxylic acid cycle and fueled by sulfur-oxidation, while the abundant metabolic potential for hydrogen oxidation and carbon fixation via the Calvin-Benson-Bassham cycle was hardly utilized. Notably, the highly diverse microbial community colonizing the analyzed black smoker chimney had a highly redundant metabolic potential. In contrast, the considerably less diverse community colonizing the diffusely venting chimney displayed a higher metabolic versatility. An increased diversity on the phylogenetic level is thus not directly linked to an increased metabolic diversity in microbial communities that colonize hydrothermal chimneys.}, }
@article {pmid29694942, year = {2018}, author = {Pierra, M and Golozar, M and Zhang, X and Prévoteau, A and De Volder, M and Reynaerts, D and Rabaey, K}, title = {Growth and current production of mixed culture anodic biofilms remain unaffected by sub-microscale surface roughness.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {122}, number = {}, pages = {213-220}, doi = {10.1016/j.bioelechem.2018.04.002}, pmid = {29694942}, issn = {1878-562X}, mesh = {Bioelectric Energy Sources/*microbiology ; Biofilms/*growth &amp; development ; Electricity ; Electrodes ; Equipment Design ; Geobacter/*physiology ; Surface Properties ; }, abstract = {Bioelectrochemical systems couple electricity demand/supply to the metabolic redox reactions of microorganisms. Generally, electrodes act not only as electron acceptors/donors, but also as physical support for an electroactive biofilm. The microorganism-electrode interface can be modified by changing the chemical and/or topographical features of the electrode surface. Thus far, studies have reported conflicting results on the impact of the electrode surface roughness on the growth and current production of biofilms. Here, the surface roughness of the glassy carbon electrodes was successfully modified at the sub-microscale using micro electrodischarge machining, while preserving the surface chemistry of the parent glassy carbon. All microbial electrodes showed similar startup time, maximum current density, charge transport ability across the biofilm and biomass production. Interestingly, an increase in the average surface cavity depth was observed for the biofilm top layer as a function of the electrode surface roughness (from 7 μm to 16 μm for a surface roughness of 5 nm to 682 nm, respectively). These results indicated that the surface roughness at a sub-microscale does not significantly impact the attachment or current production of mixed culture anodic biofilms on glassy carbon. Likely earlier observations were associated with changes in surface chemistry, rather than surface topography.}, }
@article {pmid29692763, year = {2018}, author = {Lourenço, KS and Cassman, NA and Pijl, AS and van Veen, JA and Cantarella, H and Kuramae, EE}, title = {Nitrosospira sp. Govern Nitrous Oxide Emissions in a Tropical Soil Amended With Residues of Bioenergy Crop.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {674}, pmid = {29692763}, issn = {1664-302X}, abstract = {Organic vinasse, a residue produced during bioethanol production, increases nitrous oxide (N2O) emissions when applied with inorganic nitrogen (N) fertilizer in soil. The present study investigated the role of the ammonia-oxidizing bacteria (AOB) community on the N2O emissions in soils amended with organic vinasse (CV: concentrated and V: non-concentrated) plus inorganic N fertilizer. Soil samples and N2O emissions were evaluated at 11, 19, and 45 days after fertilizer application, and the bacterial and archaea gene (amoA) encoding the ammonia monooxygenase enzyme, bacterial denitrifier (nirK, nirS, and nosZ) genes and total bacteria were quantified by real time PCR. We also employed a deep amoA amplicon sequencing approach to evaluate the effect of treatment on the community structure and diversity of the soil AOB community. Both vinasse types applied with inorganic N application increased the total N2O emissions and the abundance of AOB. Nitrosospira sp. was the dominant AOB in the soil and was correlated with N2O emissions. However, the diversity and the community structure of AOB did not change with vinasse and inorganic N fertilizer amendment. The results highlight the importance of residues and fertilizer management in sustainable agriculture and can be used as a reference and an input tool to determine good management practices for organic fertilization.}, }
@article {pmid29691611, year = {2018}, author = {Saleem, F and Mustafa, A and Kori, JA and Hussain, MS and Kamran Azim, M}, title = {Metagenomic Characterization of Bacterial Communities in Drinking Water Supply System of a Mega City.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {899-910}, pmid = {29691611}, issn = {1432-184X}, mesh = {Bacteria/*genetics ; Cities ; Drinking Water/*microbiology ; *Metagenome ; Pakistan ; }, abstract = {Supplying safe water to consumers is vital for protection of public health. With population of > 15 million, Karachi is the main economical hub of Pakistan. Lake Keenjhar serves as the main source of fresh water while Hub dam is the secondary water reservoir for Karachi. In this study, bacterial community of the drinking water supply system (DWSS) of Karachi was studied from source to tap using metagenomics approach. For this purpose, we collected 41 water samples from different areas of the city (n = 38) and water reservoirs (n = 3). 16S rDNA metagenomic sequencing of water samples revealed that 88% sequences were associated with Proteobacteria (52%), Planctomycetes (15%), Becteroidetes (12%), and Verrucomicrobia (6%). On the class level, α-proteobacteria (6-56%) were found to be the most abundant followed by β- (8-41%) and γ-proteobacteria (6-52%). On the genus level, substantial diversity was observed among the samples. Bacterial communities in water from Hub dam was found to be distantly related while among the residential towns, Lyari was highly distant from the others. Twenty-four bacterial genera were found to be exclusively present in residential area samples in comparison to the source waters which is suggestive of their resistance against treatment procedures and/or contamination. Metagenomic analysis revealed abundance of Pseudomonas, Legionella, Neisseria, Acinetobacter, Bosea, and Microcystis genera in residential areas water samples. The present metagenomic analysis of DWSS of Karachi has allowed the evaluation of bacterial communities in source water and the water being supplied to the city. Moreover, measurement of heavy metals in water samples from Karachi revealed arsenic concentration according to WHO standards which is in contrast of recent study which reported extensive arsenic contamination in aquifers in the Indus valley plain. To the best of our knowledge, this is the first metagenomic study of DWSS of Karachi.}, }
@article {pmid29691482, year = {2018}, author = {Johnson, KV and Foster, KR}, title = {Why does the microbiome affect behaviour?.}, journal = {Nature reviews. Microbiology}, volume = {16}, number = {10}, pages = {647-655}, doi = {10.1038/s41579-018-0014-3}, pmid = {29691482}, issn = {1740-1534}, mesh = {Animals ; *Behavior, Animal ; Biological Evolution ; Communicable Diseases/microbiology/parasitology/physiopathology ; Gastrointestinal Microbiome ; Humans ; *Mammals/microbiology/parasitology/physiology ; *Microbiota ; Selection, Genetic ; }, abstract = {Growing evidence indicates that the mammalian microbiome can affect behaviour, and several symbionts even produce neurotransmitters. One common explanation for these observations is that symbionts have evolved to manipulate host behaviour for their benefit. Here, we evaluate the manipulation hypothesis by applying evolutionary theory to recent work on the gut-brain axis. Although the theory predicts manipulation by symbionts under certain conditions, these appear rarely satisfied by the genetically diverse communities of the mammalian microbiome. Specifically, any symbiont investing its resources to manipulate host behaviour is expected to be outcompeted within the microbiome by strains that do not manipulate and redirect their resources into growth and survival. Moreover, current data provide no clear evidence for manipulation. Instead, we show how behavioural effects can readily arise as a by-product of natural selection on microorganisms to grow within the host and natural selection on hosts to depend upon their symbionts. We argue that understanding why the microbiome influences behaviour requires a focus on microbial ecology and local effects within the host.}, }
@article {pmid29690931, year = {2018}, author = {De Rudder, C and Calatayud Arroyo, M and Lebeer, S and Van de Wiele, T}, title = {Modelling upper respiratory tract diseases: getting grips on host-microbe interactions in chronic rhinosinusitis using in vitro technologies.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {75}, pmid = {29690931}, issn = {2049-2618}, support = {118499 / 12R2717N LV//Fonds Wetenschappelijk Onderzoek/International ; 150052//Agentschap voor Innovatie door Wetenschap en Technologie/International ; 150052//Agentschap voor Innovatie door Wetenschap en Technologie/International ; }, mesh = {Cellular Microenvironment ; Chronic Disease ; *Host-Pathogen Interactions ; Humans ; *Microbiota ; *Models, Biological ; Respiratory Mucosa/immunology/metabolism ; Respiratory Tract Diseases/*etiology/*pathology ; Rhinitis/etiology/pathology ; Sinusitis/etiology/pathology ; }, abstract = {Chronic rhinosinusitis (CRS) is a chronic inflammation of the mucosa of the nose and paranasal sinuses affecting approximately 11% of the adult population in Europe. Inadequate immune responses, as well as a dysbiosis of the sinonasal microbiota, have been put forward as aetiological factors of the disease. However, despite the prevalence of this disease, there is no consensus on the aetiology and mechanisms of pathogenesis of CRS. Further research requires in vitro models mimicking the healthy and diseased host environment along with the sinonasal microbiota. This review aims to provide an overview of CRS model systems and proposes in vitro modelling strategies to conduct mechanistic research in an ecological framework on the sinonasal microbiota and its interactions with the host in health and CRS.}, }
@article {pmid29688499, year = {2018}, author = {Choe, YH and Kim, M and Woo, J and Lee, MJ and Lee, JI and Lee, EJ and Lee, YK}, title = {Comparing rock-inhabiting microbial communities in different rock types from a high arctic polar desert.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {6}, pages = {}, doi = {10.1093/femsec/fiy070}, pmid = {29688499}, issn = {1574-6941}, mesh = {Antarctic Regions ; Arctic Regions ; Bacteria/*classification/genetics/*isolation &amp; purification ; Fungi/*classification/genetics/*isolation &amp; purification ; Geologic Sediments/*microbiology ; Microbiota ; Norway ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 28S/genetics ; Soil Microbiology ; Svalbard ; }, abstract = {Although rocks are habitable places for microbes in extreme environments, microbial diversity in these lithic environments is still poorly understood. The diversity and abundance of rock-inhabiting microbial communities in different types of rock in Svalbard, Norwegian High Arctic were examined using NGS sequencing of bacterial 16S rRNA genes and fungal 28S rRNA genes. Compositions of both bacterial and fungal communities varied across different rock types: sandstone, limestone, basalt, granite and travertine. Bacterial communities were dominated by Actinobacteria, Proteobacteria, Chloroflexi, Bacteroidetes and Acidobacteria. Fungal communities consisted of Eurotiomycetes, Lecanoromycetes, Dothideomycetes and Leotiomycetes. Both bacterial and fungal community compositions were significantly correlated with the geochemical characteristics of rocks. Bacterial communities were considerably correlated with the rock elements such as Mg and Ca. Fungal communities were considerably correlated with Fe. Interestingly, many dominant bacterial and fungal operational taxonomic units in the investigated rocks from the study area were closely affiliated to those found in other cold regions such as Alpine area, Arctic and Antarctica, suggesting that environmental constraints such as cold temperature may lead to convergence in microbial community composition. These results confirm that rocks in cold environments act as reservoirs of diverse bacteria and fungi, which may improve our understanding of lithic microbial ecology in the cold desert.}, }
@article {pmid29688462, year = {2018}, author = {Nekrutenko, A and Team, G and Goecks, J and Taylor, J and Blankenberg, D}, title = {Biology Needs Evolutionary Software Tools: Let's Build Them Right.}, journal = {Molecular biology and evolution}, volume = {35}, number = {6}, pages = {1372-1375}, pmid = {29688462}, issn = {1537-1719}, support = {R01 AI134384/AI/NIAID NIH HHS/United States ; U41 HG006620/HG/NHGRI NIH HHS/United States ; }, mesh = {*Biological Evolution ; *Computational Biology ; Software/*standards ; }, abstract = {Research in population genetics and evolutionary biology has always provided a computational backbone for life sciences as a whole. Today evolutionary and population biology reasoning are essential for interpretation of large complex datasets that are characteristic of all domains of today's life sciences ranging from cancer biology to microbial ecology. This situation makes algorithms and software tools developed by our community more important than ever before. This means that we, developers of software tool for molecular evolutionary analyses, now have a shared responsibility to make these tools accessible using modern technological developments as well as provide adequate documentation and training.}, }
@article {pmid29688343, year = {2018}, author = {Tobin, TC and Shade, A}, title = {A town on fire! Integrating 16S rRNA gene amplicon analyses into an undergraduate microbiology lecture class.}, journal = {FEMS microbiology letters}, volume = {365}, number = {10}, pages = {}, pmid = {29688343}, issn = {1574-6968}, support = {R25 GM115335/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Bacteria/classification/*genetics/isolation &amp; purification ; Computational Biology/*education ; Female ; Humans ; Male ; Metagenomics ; Microbiology/*education ; Microbiota ; Phylogeny ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; Soil Microbiology ; Students ; Teaching ; Young Adult ; }, abstract = {Microbiology increasingly relies upon bioinformatics to understand complex microbial interactions. Nevertheless, biology undergraduates often lack the basic quantitative and computer-based skills required for bioinformatics analyses. To address these issues, the course module 'A Town on Fire! 16S rRNA Gene Amplicon Analysis of Microbial Communities Overlying the Centralia, PA Mine Fire' was developed for an undergraduate microbiology lecture course. In this module, microbiology students used Quantitative Insights into Microbial Ecology to perform taxonomic, phylogenetic and statistical analyses on bacterial communities from three hot mine fire-impacted surface soils using 16S rRNA gene amplicon sequences. Pre- and post-module assessment data for each of 2 years were compiled, and indirect assessment indicated that students' confidence regarding their ability to perform bioinformatics analyses, as well as their ability to interpret bioinformatics data both increased, as did their enthusiasm for bioinformatics. Direct assessment demonstrated that students' understanding of topics that they actually used in the module, such as the statistical analyses that underlie bioinformatics investigations and the ability to infer phylogenetic relationships, improved during the module, but that their underlying understanding of techniques that they did not directly perform, such as sequencing and library construction, did not.}, }
@article {pmid29688331, year = {2018}, author = {Ridley, CM and Voordouw, G}, title = {Aerobic microbial taxa dominate deep subsurface cores from the Alberta oil sands.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {6}, pages = {}, doi = {10.1093/femsec/fiy073}, pmid = {29688331}, issn = {1574-6941}, mesh = {Alberta ; Bacteria, Aerobic/*classification/genetics/*isolation &amp; purification ; *Biodegradation, Environmental ; Fungi/classification/genetics/isolation &amp; purification ; Hydrocarbons/*metabolism ; Microbiota/genetics ; Oil and Gas Fields/*microbiology ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {Little is known about the microbial ecology of the subsurface oil sands in Northern Alberta, Canada. Biodegradation of low molecular weight hydrocarbons by indigenous microbes has enriched high molecular weight hydrocarbons, resulting in highly viscous bitumen. This extreme subsurface environment is further characterized by low nutrient availability and limited access to water, thus resulting in low microbial biomass. Improved DNA isolation protocols and increasingly sensitive sequencing methods have allowed an in-depth investigation of the microbial ecology of this unique subsurface environmental niche. Community analysis was performed on core samples (n = 62) that were retrieved from two adjacent sites located in the Athabasca Oil Sands at depths from 220 to 320 m below the surface. Microbial communities were dominated by aerobic taxa, including Pseudomonas and Acinetobacter. Only one core sample microbial community was dominated by anaerobic taxa, including the methanogen Methanoculleus, as well as Desulfomicrobium and Thauera. Although the temperature of the bitumen-containing subsurface is low (8°C), two core samples had high fractions of the potentially thermophilic taxon, Thermus. Predominance of aerobic taxa in the subsurface suggests the potential for in situ aerobic hydrocarbon degradation; however, more studies are required to determine the functional role of these taxa within this unique environment.}, }
@article {pmid29687572, year = {2018}, author = {Compte-Port, S and Borrego, CM and Moussard, H and Jeanbille, M and Restrepo-Ortiz, CX and de Diego, A and Rodriguez-Iruretagoiena, A and Gredilla, A and Fdez-Ortiz de Vallejuelo, S and Galand, PE and Kalenitchenko, D and Rols, JL and Pokrovsky, OS and Gonzalez, AG and Camarero, L and Muñiz, S and Navarro-Navarro, E and Auguet, JC}, title = {Metal contaminations impact archaeal community composition, abundance and function in remote alpine lakes.}, journal = {Environmental microbiology}, volume = {20}, number = {7}, pages = {2422-2437}, doi = {10.1111/1462-2920.14252}, pmid = {29687572}, issn = {1462-2920}, mesh = {Archaea/*drug effects/genetics ; Carbon Cycle ; DNA, Archaeal ; Ecosystem ; Geologic Sediments/microbiology ; Lakes/*microbiology ; Metals/*toxicity ; Phylogeny ; RNA, Ribosomal, 16S ; *Water Microbiology ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Using the 16S rRNA and mcrA genes, we investigated the composition, abundance and activity of sediment archaeal communities within 18 high-mountain lakes under contrasted metal levels from different origins (bedrock erosion, past-mining activities and atmospheric depositions). Bathyarchaeota, Euryarchaeota and Woesearchaeota were the major phyla found at the meta-community scale, representing 48%, 18.3% and 15.2% of the archaeal community respectively. Metals were equally important as physicochemical variables in explaining the assemblage of archaeal communities and their abundance. Methanogenesis appeared as a process of central importance in the carbon cycle within sediments of alpine lakes as indicated by the absolute abundance of methanogen 16S rRNA and mcrA gene transcripts (10[5] to 10[9] copies g[-1]). We showed that methanogen abundance and activity were significantly reduced with increasing concentrations of Pb and Cd, two indicators of airborne metal contaminations. Considering the ecological importance of methanogenesis in sediment habitats, these metal contaminations may have system wide implications even in remote area such as alpine lakes. Overall, this work was pioneer in integrating the effect of long-range atmospheric depositions on archaeal communities and indicated that metal contamination might significantly compromise the contribution of Archaea to the carbon cycling of the mountain lake sediments.}, }
@article {pmid29687224, year = {2018}, author = {Moitinho, MA and Bononi, L and Souza, DT and Melo, IS and Taketani, RG}, title = {Bacterial Succession Decreases Network Complexity During Plant Material Decomposition in Mangroves.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {954-963}, pmid = {29687224}, issn = {1432-184X}, support = {2013/23470-2//FAPESP S&#xe3;o Paulo Research Foundation/ ; 2013/25505-8//FAPESP S&#xe3;o Paulo Research Foundation/ ; 142309/2016-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2013/03158-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {Avicennia/*microbiology ; Bacteria/classification/*growth &amp; development ; Brazil ; Combretaceae/*microbiology ; *Microbiota ; Plant Leaves/*microbiology ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Rhizophoraceae/*microbiology ; Sequence Analysis, RNA ; }, abstract = {In this study, 16S rRNA gene amplicon sequencing was used to assess bacterial diversity and dynamics throughout different stages of leaves decomposition of three plant species (Rhizophora mangle, Laguncularia racemosa, and Avicennia schaueriana) in three distinct mangroves of São Paulo state, Brazil. The experiments were conducted in microcosms. Phylogenetic diversity (Faiths' PD) index showed differences between samples and suggested that some treatments like R. mangle increased their bacterial diversity through time. Principal coordinate analysis revealed that community's profile varied based on mangroves, followed by plant species and time. A clear succession patterns was observed in this study, i.e., some microorganisms with low abundance in the initial phases gradually became dominant (e.g., Alphaproteobacteria), whereas microbes that were initially predominant became low (e.g., Gammaproteobacteria). Co-occurrence analyses were performed for all times of plant degradation aiming to better understand the relationships between bacterial populations. The c-score index was done to test the randomness of the community assemblage during the stages of decomposition. For all degradation time points, the values of the observed c-score were higher than the values of the simulated c-score. This result indicated that during plant decomposition, the bacterial communities presented less co-occurrence than expected by chance and that these communities were not randomly assembled but instead they are driven by species interactions. Network analyses results showed that in the conditions presented in this experiment, the initial stages of leaf decomposition formed more connected and complex networks than the later stages. These results suggest that resource competition was a determinant in these specific mangroves during plant degradation, mainly in the initial periods.}, }
@article {pmid29687145, year = {2018}, author = {Wu, RN and Meng, H and Wang, YF and Gu, JD}, title = {Effects of reforestation on ammonia-oxidizing microbial community composition and abundance in subtropical acidic forest soils.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {12}, pages = {5309-5322}, doi = {10.1007/s00253-018-8873-0}, pmid = {29687145}, issn = {1432-0614}, support = {31470562//National Natural Science Foundation of China/ ; }, mesh = {Ammonia/*metabolism ; Archaea/classification/*physiology ; Bacteria/classification ; *Bacterial Physiological Phenomena ; *Biodiversity ; *Environmental Restoration and Remediation ; *Forests ; Nitrification ; Oxidation-Reduction ; Population Density ; Seasons ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Forest ecosystems have great ecological values in mitigation of climate change and protection of biodiversity of flora and fauna; re-forestry is commonly used to enhance the sequestration of atmospheric CO2 into forest storage biomass. Therefore, seasonal and spatial dynamics of the major microbial players in nitrification, ammonia-oxidizing archaea (AOA) and bacteria (AOB), in acidic soils of young and matured revegetated forests were investigated to elucidate the changes of microbial communities during forest restoration, and compared to delineate the patterns of community shifts under the influences of environmental factors. AOA were more abundant than AOB in both young and matured revegetated forest soils in both summer and winter seasons. In summer, however, the abundance of amoA-AOA decreased remarkably (p < 0.01), ranging from 1.90 (± 0.07) × 10[8] copies per gram dry soil in matured forest to 5.04 (± 0.43) × 10[8] copies per gram dry soil in young forest, and amoA-AOB was below detection limits to obtain any meaningful values. Moreover, exchangeable Al[3+] and organic matter were found to regulate the physiologically functional nitrifiers, especially AOA abundance in acidic forest soils. AOB community in winter showed stronger correlation with the restoration status of revegetated forests and AOA community dominated by Nitrosotalea devanaterra, in contrast, was more sensitive to the seasonal and spatial variations of environmental factors. These results enrich the current knowledge of nitrification during re-forestry and provide valuable information to developmental status of revegetated forests for management through microbial analysis.}, }
@article {pmid29685602, year = {2018}, author = {Zhang, D and Clauwaert, P and Luther, A and López Barreiro, D and Prins, W and Wim Brilman, DWF and Ronsse, F}, title = {Sub- and supercritical water oxidation of anaerobic fermentation sludge for carbon and nitrogen recovery in a regenerative life support system.}, journal = {Waste management (New York, N.Y.)}, volume = {77}, number = {}, pages = {268-275}, doi = {10.1016/j.wasman.2018.04.008}, pmid = {29685602}, issn = {1879-2456}, mesh = {Bioreactors ; Carbon ; *Fermentation ; Humans ; *Nitrogen ; *Sewage ; Waste Disposal, Fluid ; Water ; }, abstract = {Sub- and supercritical water oxidation was applied to recover carbon as CO2, while maintaining nitrogen as NH4[+] or NO3[-], from sludge obtained from an anaerobic fermenter running on a model waste composed of plant residues and human fecal matter. The objective was to fully convert carbon in the organic waste to CO2 while maintaining nutrients (specifically N) in the liquid effluent. In regenerative life support systems, CO2 and nutrients could then be further used in plant production; thus creating a closed carbon and nutrient cycle. The effect of the operational parameters in water oxidation on carbon recovery (C-to-CO2) and nitrogen conversion (to NH4[+], NO3[-]) was investigated. A batch micro-autoclave reactor was used, at pressures ranging between 110 and 300 bar and at temperatures of 300-500 °C using hydrogen peroxide as oxidizer. Residence times of 1, 5 and 10 min were tested. Oxidation efficiency increased as temperature increased, with marginal improvements beyond the critical temperature of water. Prolonging the residence time improved only slightly the carbon oxidation efficiency. Adequate oxygen supply, i.e., exceeding the stoichiometrically required amount, resulted in high carbon conversion efficiencies (>85%) and an odorless, clear liquid effluent. However, the corresponding oxidizer use efficiency was low, up to 50.2% of the supplied oxygen was recovered as O2 in the effluent gas and did not take part in the oxidation. Volatile fatty acids (VFAs) were found as the major soluble organic compounds remaining in the effluent liquid. Nitrogen recovery was high at 1 min residence time (>94.5%) and decreased for longer residence times (down to 36.4% at 10 min). Nitrogen in the liquid effluent was mostly in the form of ammonium.}, }
@article {pmid29685277, year = {2018}, author = {McAllister, TA and Dunière, L and Drouin, P and Xu, S and Wang, Y and Munns, K and Zaheer, R}, title = {Silage review: Using molecular approaches to define the microbial ecology of silage.}, journal = {Journal of dairy science}, volume = {101}, number = {5}, pages = {4060-4074}, doi = {10.3168/jds.2017-13704}, pmid = {29685277}, issn = {1525-3198}, mesh = {Animal Feed/*microbiology ; Bacteria/classification/*genetics/isolation &amp; purification ; Fermentation ; Food Contamination/analysis ; Fungi/classification/*genetics/isolation &amp; purification ; Metagenomics ; Molecular Biology/*methods ; Silage/analysis/*microbiology ; }, abstract = {Ensiling of forages was recognized as a microbial-driven process as early as the late 1800s, when it was associated with the production of "sweet" or "sour" silage. Classical microbiological plating techniques defined the epiphytic microbial populations associated with fresh forage, the pivotal role of lactic acid-producing bacteria in the ensiling process, and the contribution of clostridia, bacilli, yeast, and molds to the spoilage of silage. Many of these classical studies focused on the enumeration and characterization of a limited number of microbial species that could be readily isolated on selective media. Evidence suggested that many of the members of these microbial populations were viable but unculturable, resulting in classical studies underestimating the true microbial diversity associated with ensiling. Polymerase chain reaction-based techniques, including length heterogeneity PCR, terminal RFLP, denaturing gradient gel electrophoresis, and automated ribosomal intergenic spacer analysis, were the first molecular methods used to study silage microbial communities. Further advancements in whole comparative genomic, metagenomic, and metatranscriptomic sequencing have or are in the process of superseding these methods, enabling microbial communities during ensiling to be defined with a degree of detail that is impossible using classical microbiology. These methods have identified new microbial species in silage, as well as characterized shifts in microbial communities with forage type and composition, ensiling method, and in response to aerobic exposure. Strain- and species-specific primers have been used to track the persistence and contribution of silage inoculants to the ensiling process and the role of specific species of yeast and fungi in silage spoilage. Sampling and the methods used to isolate genetic materials for further molecular analysis can have a profound effect on results. Primer selection for PCR amplification and the presence of inhibitors can also lead to biases in the interpretation of sequence data. Bioinformatic analyses are reliant on the integrity and presence of sequence data within established databases and can be subject to low taxonomic resolution. Despite these limitations, advancements in molecular biology are poised to revolutionize our current understanding of the microbial ecology of silage.}, }
@article {pmid29682877, year = {2018}, author = {Bååth, E}, title = {Temperature sensitivity of soil microbial activity modeled by the square root equation as a unifying model to differentiate between direct temperature effects and microbial community adaptation.}, journal = {Global change biology}, volume = {24}, number = {7}, pages = {2850-2861}, doi = {10.1111/gcb.14285}, pmid = {29682877}, issn = {1365-2486}, mesh = {Adaptation, Physiological ; Climate Change ; *Ecosystem ; *Microbiota ; *Models, Biological ; Soil ; *Soil Microbiology ; *Temperature ; }, abstract = {Numerous models have been used to express the temperature sensitivity of microbial growth and activity in soil making it difficult to compare results from different habitats. Q10 still is one of the most common ways to express temperature relationships. However, Q10 is not constant with temperature and will differ depending on the temperature interval used for the calculation. The use of the square root (Ratkowsky) relationship between microbial activity (A) and temperature below optimum temperature, √A = a × (T-Tmin), is proposed as a simple and adequate model that allow for one descriptor, Tmin (a theoretical minimum temperature for growth and activity), to estimate correct Q10-values over the entire in situ temperature interval. The square root model can adequately describe both microbial growth and respiration, allowing for an easy determination of Tmin . Q10 for any temperature interval can then be calculated by Q10 = [(T + 10 - Tmin)/(T-Tmin)][2] , where T is the lowest temperature in the Q10 comparison. Tmin also describes the temperature adaptation of the microbial community. An envelope of Tmin covering most natural soil habitats varying between -15°C (cold habitats like Antarctica/Arctic) to 0°C (tropical habitats like rain forests and deserts) is suggested, with an 0.3°C increase in Tmin per 1°C increase in mean annual temperature. It is shown that the main difference between common temperature relationships used in global models is differences in the assumed temperature adaptation of the soil microbial community. The use of the square root equation will allow for one descriptor, Tmin , determining the temperature response of soil microorganisms, and at the same time allow for comparing temperature sensitivity of microbial activity between habitats, including future projections.}, }
@article {pmid29682861, year = {2018}, author = {Alvarez, G and Shahzad, T and Andanson, L and Bahn, M and Wallenstein, MD and Fontaine, S}, title = {Catalytic power of enzymes decreases with temperature: New insights for understanding soil C cycling and microbial ecology under warming.}, journal = {Global change biology}, volume = {24}, number = {9}, pages = {4238-4250}, doi = {10.1111/gcb.14281}, pmid = {29682861}, issn = {1365-2486}, mesh = {Bacteria/enzymology ; *Carbon Cycle ; Catalysis ; Enzymes/*chemistry ; Fungi/enzymology ; *Global Warming ; Hot Temperature/*adverse effects ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Most current models of soil C dynamics predict that climate warming will accelerate soil C mineralization, resulting in a long-term CO2 release and positive feedback to global warming. However, ecosystem warming experiments show that CO2 loss from warmed soils declines to control levels within a few years. Here, we explore the temperature dependence of enzymatic conversion of polymerized soil organic C (SOC) into assimilable compounds, which is presumed the rate-limiting step of SOC mineralization. Combining literature review, modelling and enzyme assays, we studied the effect of temperature on activity of enzymes considering their thermal inactivation and catalytic activity. We defined the catalytic power of enzymes (Epower) as the cumulative amount of degraded substrate by one unit of enzyme until its complete inactivation. We show a universal pattern of enzyme's thermodynamic properties: activation energy of catalytic activity (EAcat) < activation energy of thermal inactivation (EAinact). By investing in stable enzymes (high EAinact) having high catalytic activity (low EAcat), microorganisms may maximize the Epower of their enzymes. The counterpart of such EAs' hierarchical pattern is the higher relative temperature sensitivity of enzyme inactivation than catalysis, resulting in a reduction in Epower under warming. Our findings could explain the decrease with temperature in soil enzyme pools, microbial biomass (MB) and carbon use efficiency (CUE) reported in some warming experiments and studies monitoring the seasonal variation in soil enzymes. They also suggest that a decrease in soil enzyme pools due to their faster inactivation under warming contributes to the observed attenuation of warming effect on soil C mineralization. This testable theory predicts that the ultimate response of SOC degradation to warming can be positive or negative depending on the relative temperature response of Epower and microbial production of enzymes.}, }
@article {pmid29682571, year = {2018}, author = {Sobhonslidsuk, A and Chanprasertyothin, S and Pongrujikorn, T and Kaewduang, P and Promson, K and Petraksa, S and Ongphiphadhanakul, B}, title = {The Association of Gut Microbiota with Nonalcoholic Steatohepatitis in Thais.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {9340316}, pmid = {29682571}, issn = {2314-6141}, mesh = {Adult ; Bacteria/genetics ; Bacteroidetes/genetics ; Body Mass Index ; Case-Control Studies ; Feces/microbiology ; Female ; Firmicutes/genetics ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; Middle Aged ; Non-alcoholic Fatty Liver Disease/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVES: Nonalcoholic steatohepatitis (NASH) can progress to advanced fibrosis; the link between intestinal bacterial overgrowth and NASH has been proposed. Gut microbiota may promote inflammation and provoke disease progression. We evaluated gut microbiota pattern in NASH and its influencing factors.<br><br>METHODS: A case-controlled study with sixteen NASH and eight control subjects was done. We performed DNA extraction from stool samples and bacterial 16S rRNA sequencing using MiSeq&#x2122;. The sequences were clustered into operational taxonomic units using Quantitative Insights Into Microbial Ecology software. We calculated relative abundances, determined alpha diversity, obtained beta diversity by principal coordinate analysis, and conducted the partial least-squares regression model.<br><br>RESULTS: The relative abundance of Bacteroidetes tended to be higher in NASH group. The Bacteroidetes/Firmicutes (B/F) ratio was significantly elevated in NASH patients. The pattern of gut microbiota in NASH was clearly separated from that of control subjects. Factors influencing the separation of NASH from control subjects were age, diabetes, body mass index, Bacteroidetes phylum, metformin, Actinobacteria, Verrucomicrobia, Thermotogae, and Caldithrix and Bacteroidetes/Firmicutes ratio.<br><br>CONCLUSIONS: Bacteroidetes phylum (Bacteroides and Prevotella genus) is abundant in NASH subjects, who exhibited an elevated B/F ratio. NASH patients showed a specific pattern of gut microbiota independent of diabetes or metformin use.}, }
@article {pmid29681893, year = {2018}, author = {Benevenuto, J and Teixeira-Silva, NS and Kuramae, EE and Croll, D and Monteiro-Vitorello, CB}, title = {Comparative Genomics of Smut Pathogens: Insights From Orphans and Positively Selected Genes Into Host Specialization.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {660}, pmid = {29681893}, issn = {1664-302X}, abstract = {Host specialization is a key evolutionary process for the diversification and emergence of new pathogens. However, the molecular determinants of host range are poorly understood. Smut fungi are biotrophic pathogens that have distinct and narrow host ranges based on largely unknown genetic determinants. Hence, we aimed to expand comparative genomics analyses of smut fungi by including more species infecting different hosts and to define orphans and positively selected genes to gain further insights into the genetics basis of host specialization. We analyzed nine lineages of smut fungi isolated from eight crop and non-crop hosts: maize, barley, sugarcane, wheat, oats, Zizania latifolia (Manchurian rice), Echinochloa colona (a wild grass), and Persicaria sp. (a wild dicot plant). We assembled two new genomes: Ustilago hordei (strain Uhor01) isolated from oats and U. tritici (strain CBS 119.19) isolated from wheat. The smut genomes were of small sizes, ranging from 18.38 to 24.63 Mb. U. hordei species experienced genome expansions due to the proliferation of transposable elements and the amount of these elements varied among the two strains. Phylogenetic analysis confirmed that Ustilago is not a monophyletic genus and, furthermore, detected misclassification of the U. tritici specimen. The comparison between smut pathogens of crop and non-crop hosts did not reveal distinct signatures, suggesting that host domestication did not play a dominant role in shaping the evolution of smuts. We found that host specialization in smut fungi likely has a complex genetic basis: different functional categories were enriched in orphans and lineage-specific selected genes. The diversification and gain/loss of effector genes are probably the most important determinants of host specificity.}, }
@article {pmid29681892, year = {2018}, author = {Behringer, G and Ochsenkühn, MA and Fei, C and Fanning, J and Koester, JA and Amin, SA}, title = {Bacterial Communities of Diatoms Display Strong Conservation Across Strains and Time.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {659}, pmid = {29681892}, issn = {1664-302X}, abstract = {Interactions between phytoplankton and bacteria play important roles in shaping the microenvironment surrounding these organisms and in turn influence global biogeochemical cycles. This microenvironment, known as the phycosphere, is presumed to shape the bacterial diversity around phytoplankton and thus stimulate a diverse array of interactions between both groups. Although many studies have attempted to characterize bacterial communities that associate and interact with phytoplankton, bias in bacterial cultivation and consistency and persistence of bacterial communities across phytoplankton isolates likely impede the understanding of these microbial associations. Here, we isolate four strains of the diatom Asterionellopsis glacialis and three strains of the diatom Nitzschia longissima and show through metabarcoding of the bacterial 16S rDNA gene that though each species possesses a unique bacterial community, the bacterial composition across strains from the same species are highly conserved at the genus level. Cultivation of all seven strains in the laboratory for longer than 1 year resulted in only small changes to the bacterial composition, suggesting that despite strong pressures from laboratory culturing conditions associations between these diatoms and their bacterial communities are robust. Specific operational taxonomic units (OTUs) belonging to the Roseobacter-clade appear to be conserved across all strains and time, suggesting their importance to diatoms. In addition, we isolate a range of cultivable bacteria from one of these cultures, A. glacialis strain A3, including several strains of Shimia marina and Nautella sp. that appear closely related to OTUs conserved across all strains and times. Coculturing of A3 with some of its cultivable bacteria as well as other diatom-associated bacteria shows a wide range of responses that include enhancing diatom growth. Cumulatively, these findings suggest that phytoplankton possess unique microbiomes that are consistent across strains and temporal scales.}, }
@article {pmid29679120, year = {2018}, author = {Young, EB and Sielicki, J and Grothjan, JJ}, title = {Regulation of Hydrolytic Enzyme Activity in Aquatic Microbial Communities Hosted by Carnivorous Pitcher Plants.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {885-898}, pmid = {29679120}, issn = {1432-184X}, mesh = {Animals ; Bacteria/*enzymology ; Bacterial Proteins/*metabolism ; *Food Chain ; Insecta/*physiology ; Sarraceniaceae/*microbiology ; Wisconsin ; }, abstract = {Carnivorous pitcher plants Sarracenia purpurea host diverse eukaryotic and bacterial communities which aid in insect prey digestion, but little is known about the functional processes mediated by the microbial communities. This study aimed to connect pitcher community diversity with functional nutrient transformation processes, identifying bacterial taxa, and measuring regulation of hydrolytic enzyme activity in response to prey and alternative nutrient sources. Genetic analysis identified diverse bacterial taxa known to produce hydrolytic enzyme activities. Chitinase, protease, and phosphatase activities were measured using fluorometric assays. Enzyme activity in field pitchers was positively correlated with bacterial abundance, and activity was suppressed by antibiotics suggesting predominantly bacterial sources of chitinase and protease activity. Fungi, algae, and rotifers observed could also contribute enzyme activity, but fresh insect prey released minimal chitinase activity. Activity of chitinase and proteases was upregulated in response to insect additions, and phosphatase activity was suppressed by phosphate additions. Particulate organic P in prey was broken down, appearing as increasing dissolved organic and inorganic P pools within 14 days. Chitinase and protease were not significantly suppressed by availability of dissolved organic substrates, though organic C and N stimulated bacterial growth, resulting in elevated enzyme activity. This comprehensive field and experimental study show that pitcher plant microbial communities dynamically regulate hydrolytic enzyme activity, to digest prey nutrients to simpler forms, mediating biogeochemical nutrient transformations and release of nutrients for microbial and host plant uptake.}, }
@article {pmid29679119, year = {2018}, author = {Zeng, J and Xu, T and Cao, L and Tong, C and Zhang, X and Luo, D and Han, S and Pang, P and Fu, W and Yan, J and Liu, X and Zhu, Y}, title = {The Role of Iron Competition in the Antagonistic Action of the Rice Endophyte Streptomyces sporocinereus OsiSh-2 Against the Pathogen Magnaporthe oryzae.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {1021-1029}, pmid = {29679119}, issn = {1432-184X}, support = {31672093//National Natural Science Foundation of China/ ; }, mesh = {Disease Resistance ; Dose-Response Relationship, Drug ; Endophytes/*physiology ; Iron/*metabolism ; Magnaporthe/*metabolism ; Oryza/*microbiology ; Plant Diseases/*microbiology ; Siderophores/*metabolism ; Streptomyces/*metabolism ; }, abstract = {Rice blast caused by Magnaporthe oryzae severely impacts global rice yield stability. The rice endophyte Streptomyces sporocinereus OsiSh-2, with strong antagonistic activity towards M. oryzae, has been reported in our previous study. To decipher the model of the antagonistic action of OsiSh-2 towards M. oryzae, we compared the iron-capturing abilities of these two strains. The cultivation of OsiSh-2 and a M. oryzae strain under iron-rich and iron-starved conditions showed that M. oryzae depended more on iron supplementation for growth and development than did OsiSh-2. Genomic analysis of the S. sporocinereus and M. oryzae species strains revealed that they might possess different iron acquisition strategies. The actinobacterium OsiSh-2 is likely to favor siderophore utilization compared to the fungus M. oryzae. In addition, protein annotations found that OsiSh-2 contains the highest number of the siderophore biosynthetic gene clusters among the 13 endophytic actinomycete strains and 13 antifungal actinomycete strains that we compared, indicating the prominent siderophore production potential of OsiSh-2. Additionally, we verified that OsiSh-2 could excrete considerably more siderophores than Guy11 under iron-restricted conditions and displayed greater Fe[3+]-reducing activity during iron-supplemental conditions. Measurements of the iron mobilization between the antagonistic OsiSh-2 and Guy11 showed that the iron concentration is higher around OsiSh-2 than around Guy11. In addition, adding iron near OsiSh-2 could decrease the antagonism of OsiSh-2 towards Guy11. Our study revealed that the antagonistic capacity displayed by OsiSh-2 towards M. oryzae was related to the competition for iron. The highly efficient iron acquisition system of OsiSh-2 may offer valuable insight for the biocontrol of rice blast.}, }
@article {pmid29678912, year = {2018}, author = {Jesser, KJ and Noble, RT}, title = {Vibrio Ecology in the Neuse River Estuary, North Carolina, Characterized by Next-Generation Amplicon Sequencing of the Gene Encoding Heat Shock Protein 60 (hsp60).}, journal = {Applied and environmental microbiology}, volume = {84}, number = {13}, pages = {}, pmid = {29678912}, issn = {1098-5336}, mesh = {Chaperonin 60/*genetics ; *Ecology ; Environmental Microbiology ; Fresh Water ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Indans ; North Carolina ; Public Health ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Salinity ; Seasons ; Temperature ; Vibrio/*genetics/growth &amp; development/*physiology ; Vibrio cholerae/genetics ; Vibrio parahaemolyticus/genetics ; Vibrio vulnificus/genetics ; Water Microbiology ; }, abstract = {Of marine eubacteria, the genus Vibrio is intriguing because member species are relevant to both marine ecology and human health. Many studies have touted the relationships of Vibrio to environmental factors, especially temperature and salinity, to predict total Vibrio abundance but lacked the taxonomic resolution to identify the relationships among species and the key drivers of Vibrio dynamics. To improve next-generation sequencing (NGS) surveys of Vibrio, we have conducted both 16S small subunit rRNA and heat shock protein 60 (hsp60) amplicon sequencing of water samples collected at two well-studied locations in the Neuse River Estuary, NC. Samples were collected between May and December 2016 with enhanced sampling efforts in response to two named storms. Using hsp60 sequences, 21 Vibrio species were identified, including the potential human pathogens V. cholerae, V. parahaemolyticus, and V. vulnificus Changes in the Vibrio community mirrored seasonal and storm-related changes in the water column, especially in response to an influx of nutrient-rich freshwater to the estuary after Hurricane Matthew, which initiated dramatic changes in the overall Vibrio community. Individual species dynamics were wide ranging, indicating that individual Vibrio taxa have unique ecologies and that total Vibrio abundance predictors are insufficient for risk assessments of potentially pathogenic species. Positive relationships between Vibrio, dinoflagellates, and Cyanobacteria were identified, as were intraspecies associations, which further illuminated the interactions of cooccurring Vibrio taxa along environmental gradients.IMPORTANCE The objectives of this research were to utilize a novel approach to improve sequence-based surveys of Vibrio communities and to demonstrate the usefulness of this approach by presenting an analysis of Vibrio dynamics in the context of environmental conditions, with a particular focus on species that cause disease in humans and on storm effects. The methods presented here enabled the analysis of Vibrio dynamics with excellent taxonomic resolution and could be incorporated into future ecological studies and risk prediction strategies for potentially pathogenic species. Next-generation sequencing of hsp60 and other innovative sequence-based approaches are valuable tools and show great promise for studying Vibrio ecology and associated public health risks.}, }
@article {pmid29676790, year = {2018}, author = {Annenkova, NV and Ahrén, D and Logares, R and Kremp, A and Rengefors, K}, title = {Delineating closely related dinoflagellate lineages using phylotranscriptomics.}, journal = {Journal of phycology}, volume = {54}, number = {4}, pages = {571-576}, doi = {10.1111/jpy.12748}, pmid = {29676790}, issn = {1529-8817}, mesh = {Dinoflagellida/*classification/genetics ; *Phylogeny ; RNA, Algal/analysis ; RNA, Protozoan/analysis ; RNA, Ribosomal/analysis ; *Transcriptome ; }, abstract = {Recently radiated dinoflagellates Apocalathium aciculiferum (collected in Lake Erken, Sweden), Apocalathium malmogiense (Baltic Sea) and Apocalathium aff. malmogiense (Highway Lake, Antarctica) represent a lineage with an unresolved phylogeny. We determined their phylogenetic relationships using phylotranscriptomics based on 792 amino acid sequences. Our results showed that A. aciculiferum diverged from the other two closely related lineages, consistent with their different morphologies in cell size, relative cell length and presence of spines. We hypothesized that A. aff. malmogiense and A. malmogiense, which inhabit different hemispheres, are evolutionarily more closely related because they diverged from a marine common ancestor, adapting to a wide salinity range, while A. aciculiferum colonized a freshwater habitat, by acquiring adaptations to this environment, in particular, salinity intolerance. We show that phylotranscriptomics can resolve the phylogeny of recently diverged protists. This has broad relevance, given that many phytoplankton species are morphologically very similar, and single genes sometimes lack the information to determine species' relationships.}, }
@article {pmid29675704, year = {2018}, author = {Saucedo-Carabez, JR and Ploetz, RC and Konkol, JL and Carrillo, D and Gazis, R}, title = {Partnerships Between Ambrosia Beetles and Fungi: Lineage-Specific Promiscuity Among Vectors of the Laurel Wilt Pathogen, Raffaelea lauricola.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {925-940}, pmid = {29675704}, issn = {1432-184X}, mesh = {Animals ; Female ; Florida ; Ophiostomatales/*physiology ; Persea/*microbiology ; Plant Diseases/*microbiology ; *Symbiosis ; Weevils/classification/*microbiology ; }, abstract = {Nutritional mutualisms that ambrosia beetles have with fungi are poorly understood. Although these interactions were initially thought to be specific associations with a primary symbiont, there is increasing evidence that some of these fungi are associated with, and move among, multiple beetle partners. We examined culturable fungi recovered from mycangia of ambrosia beetles associated with trees of Persea humilis (silk bay, one site) and P. americana (avocado, six commercial orchards) that were affected by laurel wilt, an invasive disease caused by a symbiont, Raffaelea lauricola, of an Asian ambrosia beetle, Xyleborus glabratus. Fungi were isolated from 20 adult females of X. glabratus from silk bay and 70 each of Xyleborus affinis, Xyleborus bispinatus, Xyleborus volvulus, Xyleborinus saxesenii, and Xylosandrus crassiusculus from avocado. With partial sequences of ribosomal (LSU and SSU) and nuclear (β-tubulin) genes, one to several operational taxonomic units (OTUs) of fungi were identified in assayed individuals. Distinct populations of fungi were recovered from each of the examined beetle species. Raffaelea lauricola was present in all beetles except X. saxesenii and X. crassiusculus, and Raffaelea spp. predominated in Xyleborus spp. Raffaelea arxii, R. subalba, and R. subfusca were present in more than a single species of Xyleborus, and R. arxii was the most abundant symbiont in both X. affinis and X. volvulus. Raffaelea aguacate was detected for the first time in an ambrosia beetle (X. bispinatus). Yeasts (Ascomycota, Saccharomycotina) were found consistently in the mycangia of the examined beetles, and distinct, putatively co-adapted populations of these fungi were associated with each beetle species. Greater understandings are needed for how mycangia in ambrosia beetles interact with fungi, including yeasts which play currently underresearched roles in these insects.}, }
@article {pmid29675703, year = {2018}, author = {Hernando-Morales, V and Varela, MM and Needham, DM and Cram, J and Fuhrman, JA and Teira, E}, title = {Vertical and Seasonal Patterns Control Bacterioplankton Communities at Two Horizontally Coherent Coastal Upwelling Sites off Galicia (NW Spain).}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {866-884}, pmid = {29675703}, issn = {1432-184X}, support = {CTM2008-03790/MAR//Secretar&#xed;a de Estado de Investigaci&#xf3;n, Desarrollo e Innovaci&#xf3;n/ ; BES-2009-028186//Secretar&#xed;a de Estado de Investigaci&#xf3;n, Desarrollo e Innovaci&#xf3;n/ ; }, mesh = {Atlantic Ocean ; *Bacterial Physiological Phenomena ; *Climate Change ; Microbiota ; Phytoplankton/*physiology ; Seasons ; Spain ; *Water Movements ; }, abstract = {Analysis of seasonal patterns of marine bacterial community structure along horizontal and vertical spatial scales can help to predict long-term responses to climate change. Several recent studies have shown predictable seasonal reoccurrence of bacterial assemblages. However, only a few have assessed temporal variability over both horizontal and vertical spatial scales. Here, we simultaneously studied the bacterial community structure at two different locations and depths in shelf waters of a coastal upwelling system during an annual cycle. The most noticeable biogeographic patterns observed were seasonality, horizontal homogeneity, and spatial synchrony in bacterial diversity and community structure related with regional upwelling-downwelling dynamics. Water column mixing eventually disrupted bacterial community structure vertical heterogeneity. Our results are consistent with previous temporal studies of marine bacterioplankton in other temperate regions and also suggest a marked influence of regional factors on the bacterial communities inhabiting this coastal upwelling system. Bacterial-mediated carbon fluxes in this productive region appear to be mainly controlled by community structure dynamics in surface waters, and local environmental factors at the base of the euphotic zone.}, }
@article {pmid29674547, year = {2018}, author = {de Siqueira, KA and Liotti, RG and Mendes, TAO and Soares, MA}, title = {Draft Genome Sequences of Pseudomonas sp. Strain 382 and Pantoea coffeiphila 342, Endophytic Bacteria Isolated from Brazilian Guarana [Paullinia cupana (Mart.) Ducke].}, journal = {Genome announcements}, volume = {6}, number = {16}, pages = {}, pmid = {29674547}, issn = {2169-8287}, abstract = {Pseudomonas sp. strain 382 and Pantoea coffeiphila 342 are two endophytic bacterial strains isolated from Paullinia cupana (guarana) seeds. Their draft genome sizes were 5.96 and 6.38 Mbp, with 315 and 266 scaffolds and 52% and 62% GC content, respectively.}, }
@article {pmid29673992, year = {2018}, author = {Mai, DT and Stuckey, DC and Oh, S}, title = {Effect of ciprofloxacin on methane production and anaerobic microbial community.}, journal = {Bioresource technology}, volume = {261}, number = {}, pages = {240-248}, doi = {10.1016/j.biortech.2018.04.009}, pmid = {29673992}, issn = {1873-2976}, mesh = {Anaerobiosis ; Bacteria ; *Bioreactors ; Ciprofloxacin/*metabolism ; Fatty Acids, Volatile ; Methane/*metabolism ; Sewage ; }, abstract = {This study investigated the effects and fate of CIP on anaerobic sludge over a wide range of concentrations (0.05-50 mg/L), and 0.5-50 mg/L significantly inhibited organic removal and methanogenic activity, increased volatile fatty acids accumulation and low molecular weight soluble microbial products (SMPs), including p-cresol and nitrogen-containing compounds. Although microbial communities exposed to CIP did not differ significantly from the control in species diversity indices, Syntrophobacter and Methanothrix associated with acetogenesis and acetoclastic methanogenesis, respectively, were underrepresented in the CIP-exposed communities. Our study advances understanding of how environmentally relevant concentrations of CIP disrupts anaerobic digestion, which has important implications for anaerobic engineered systems treating CIP-bearing waste streams.}, }
@article {pmid29673788, year = {2018}, author = {Kiersztyn, B and Kauppinen, ES and Kaliński, T and Chróst, R and Siuda, W}, title = {Quantitative description of respiration processes in meso-eutrophic and eutrophic freshwater environments.}, journal = {Journal of microbiological methods}, volume = {149}, number = {}, pages = {1-8}, doi = {10.1016/j.mimet.2018.04.010}, pmid = {29673788}, issn = {1872-8359}, mesh = {Bacteria/*metabolism ; Bacteriological Techniques/*methods ; Carbon/metabolism ; Lakes/*chemistry/microbiology ; *Oxygen Consumption ; Water Microbiology ; }, abstract = {We propose a modification of measurement methodology allowing the overall respiration rate (VResp) close to the in situ conditions; size of the labile, respirable organic matter pool (OMResp); and its turnover time (Tt) to be calculated. In addition to the respiration of dissolved substrates by free-living bacteria, the respiration of attached bacteria and other planktonic organisms is also taken into account. In case study we evaluated the modified, quantitative description of respiration processes in surface waters of lakes of different trophic status: mezzo-eutrophic and eutrophic. In both types of studied environments, VResp oscillated between 1.0 μmol C l[-1] h[-1] and 3.0 μmol C l[-1] h[-1], and the size of the OMResp pool varied from 39.3 μM C to 828.7 μM C. Despite of higher OMResp concentrations in eutrophic lakes, we found a lower susceptibility of OM to respiration processes in eutrophic than in meso-eutrophic lakes but similar VResp in both types of lakes. We conclude that the proposed method allows a fast quantitative description of labile organic matter utilization by aerobic aquatic microorganisms.}, }
@article {pmid29673081, year = {2018}, author = {Botnen, SS and Davey, ML and Halvorsen, R and Kauserud, H}, title = {Sequence clustering threshold has little effect on the recovery of microbial community structure.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.12894}, pmid = {29673081}, issn = {1755-0998}, abstract = {Analysis of microbial community structure by multivariate ordination methods, using data obtained by high-throughput sequencing of amplified markers (i.e., DNA metabarcoding), often requires clustering of DNA sequences into operational taxonomic units (OTUs). Parameters for the clustering procedure tend not to be justified but are set by tradition rather than being based on explicit knowledge. In this study, we explore the extent to which ordination results are affected by variation in parameter settings for the clustering procedure. Amplicon sequence data from nine microbial community studies, representing different sampling designs, spatial scales and ecosystems, were subjected to clustering into OTUs at seven different similarity thresholds (clustering thresholds) ranging from 87% to 99% sequence similarity. The 63 data sets thus obtained were subjected to parallel DCA and GNMDS ordinations. The resulting community structures were highly similar across all clustering thresholds. We explain this pattern by the existence of strong ecological structuring gradients and phylogenetically diverse sets of abundant OTUs that are highly stable across clustering thresholds. Removing low-abundance, rare OTUs had negligible effects on community patterns. Our results indicate that microbial data sets with a clear gradient structure are highly robust to choice of sequence clustering threshold.}, }
@article {pmid29672704, year = {2018}, author = {Probst, AJ and Banfield, JF}, title = {Homologous Recombination and Transposon Propagation Shape the Population Structure of an Organism from the Deep Subsurface with Minimal Metabolism.}, journal = {Genome biology and evolution}, volume = {10}, number = {4}, pages = {1115-1119}, pmid = {29672704}, issn = {1759-6653}, mesh = {Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; DNA Transposable Elements/*genetics ; Genetics, Population ; Genome, Archaeal/*genetics ; Homologous Recombination/*genetics ; Metagenomics ; }, abstract = {DPANN archaea are primarily known based on genomes from metagenomes and single cells. We reconstructed a complete population genome for Candidatus "Forterrea," a Diapherotrite with a predicted symbiotic lifestyle probably centered around nucleotide metabolism and RuBisCO. Genome-wide analysis of sequence variation provided insights into the processes that shape its population structure in the deep subsurface. The genome contains many transposons, yet reconstruction of a complete genome from a short-read insert data set was possible because most occurred only in some individuals. Accuracy of the final reconstruction could be verified because the genome displays the pattern of cumulative GC skew known for some archaea but more typically associated with bacteria. Sequence variation is highly localized, and most pronounced around transposons and relatively close to the origin of replication. Patterns of variation are best explained by homologous recombination, a process previously not described for DPANN archaea.}, }
@article {pmid29672211, year = {2018}, author = {Olivares, M and Benítez-Páez, A and de Palma, G and Capilla, A and Nova, E and Castillejo, G and Varea, V and Marcos, A and Garrote, JA and Polanco, I and Donat, E and Ribes-Koninckx, C and Calvo, C and Ortigosa, L and Palau, F and Sanz, Y}, title = {Increased prevalence of pathogenic bacteria in the gut microbiota of infants at risk of developing celiac disease: The PROFICEL study.}, journal = {Gut microbes}, volume = {9}, number = {6}, pages = {551-558}, pmid = {29672211}, issn = {1949-0984}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Celiac Disease/genetics/*microbiology ; Clostridium/isolation &amp; purification ; Enterotoxigenic Escherichia coli/isolation &amp; purification ; Feces/microbiology/virology ; Feeding Behavior ; *Gastrointestinal Microbiome/genetics ; *Genetic Predisposition to Disease ; Genotype ; HLA-DQ Antigens/genetics ; Humans ; Infant, Newborn ; Risk ; Spain ; }, abstract = {Celiac disease (CD) is an immune-mediated enteropathy involving genetic and environmental factors, whose interaction influences disease risk. The intestinal microbiota, including viruses and bacteria, could play a role in the pathological process leading to gluten intolerance. In this study, we investigated the prevalence of pathogens in the intestinal microbiota of infants at familial risk of developing CD. We included 127 full-term newborns with at least one first-degree relative with CD. Infants were classified according to milk-feeding practice (breastfeeding or formula feeding) and HLA-DQ genotype (low, intermediate or high genetic risk). The prevalence of pathogenic bacteria and viruses was assessed in the faeces of the infants at 7 days, 1 month and 4 months of age. The prevalence of Clostridium perfringens was higher in formula-fed infants than in breast-fed over the study period, and that of C. difficile at 4 months. Among breastfed infants, a higher prevalence of enterotoxigenic E. coli (ETEC) was found in infants with the highest genetic risk compared either to those with a low or intermediate risk. Among formula-fed infants, a higher prevalence of ETEC was also found in infants with a high genetic risk compared to those of intermediate risk. Our results show that specific factors, such as formula feeding and the HLA-DQ2 genotype, previously linked to a higher risk of developing CD, influence the presence of pathogenic bacteria differently in the intestinal microbiota in early life. Further studies are warranted to establish whether these associations are related to CD onset later in life.}, }
@article {pmid29672134, year = {2018}, author = {Mogul, R and Barding, GA and Lalla, S and Lee, S and Madrid, S and Baki, R and Ahmed, M and Brasali, H and Cepeda, I and Gornick, T and Gunadi, S and Hearn, N and Jain, C and Kim, EJ and Nguyen, T and Nguyen, VB and Oei, A and Perkins, N and Rodriguez, J and Rodriguez, V and Savla, G and Schmitz, M and Tedjakesuma, N and Walker, J}, title = {Metabolism and Biodegradation of Spacecraft Cleaning Reagents by Strains of Spacecraft-Associated Acinetobacter.}, journal = {Astrobiology}, volume = {18}, number = {12}, pages = {1517-1527}, pmid = {29672134}, issn = {1557-8070}, mesh = {2-Propanol/metabolism ; Acinetobacter/drug effects/*enzymology ; Alcohol Dehydrogenase/*metabolism ; Bacterial Proteins/*metabolism ; *Biodegradation, Environmental ; Detergents/metabolism ; Equipment Contamination/prevention &amp; control ; Ethanol/metabolism ; Hydrogen Peroxide/pharmacology ; Microbial Viability/drug effects ; *Spacecraft ; }, abstract = {Spacecraft assembly facilities are oligotrophic and low-humidity environments, which are routinely cleaned using alcohol wipes for benchtops and spacecraft materials, and alkaline detergents for floors. Despite these cleaning protocols, spacecraft assembly facilities possess a persistent, diverse, dynamic, and low abundant core microbiome, where the Acinetobacter are among the dominant members of the community. In this report, we show that several spacecraft-associated Acinetobacter metabolize or biodegrade the spacecraft cleaning reagents of ethanol (ethyl alcohol), 2-propanol (isopropyl alcohol), and Kleenol 30 (floor detergent) under ultraminimal conditions. Using cultivation and stable isotope labeling studies, we show that ethanol is a sole carbon source when cultivating in 0.2 × M9 minimal medium containing 26 μM Fe(NH4)2(SO4)2. Although cultures expectedly did not grow solely on 2-propanol, cultivations on mixtures of ethanol and 2-propanol exhibited enhanced plate counts at mole ratios of ≤0.50. In support, enzymology experiments on cellular extracts were consistent with oxidation of ethanol and 2-propanol by a membrane-bound alcohol dehydrogenase. In the presence of Kleenol 30, untargeted metabolite profiling on ultraminimal cultures of Acinetobacter radioresistens 50v1 indicated (1) biodegradation of Kleenol 30 into products including ethylene glycols, (2) the potential metabolism of decanoate (formed during incubation of Kleenol 30 in 0.2 × M9), and (3) decreases in the abundances of several hydroxy- and ketoacids in the extracellular metabolome. In ultraminimal medium (when using ethanol as a sole carbon source), A. radioresistens 50v1 also exhibits a remarkable survival against hydrogen peroxide (∼1.5-log loss, ∼10[8] colony forming units (cfu)/mL, 10 mM H2O2), indicating a considerable tolerance toward oxidative stress under nutrient-restricted conditions. Together, these results suggest that the spacecraft cleaning reagents may (1) serve as nutrient sources under oligotrophic conditions and (2) sustain extremotolerances against the oxidative stresses associated with low-humidity environments. In perspective, this study provides a plausible biochemical rationale to the observed microbial ecology dynamics of spacecraft-associated environments.}, }
@article {pmid29671884, year = {2018}, author = {Al-Jubury, A and Lu, C and Kania, PW and von Gersdorff Jørgensen, L and Liu, Y and de Bruijn, I and Raaijmakers, J and Buchmann, K}, title = {Impact of Pseudomonas H6 surfactant on all external life cycle stages of the fish parasitic ciliate Ichthyophthirius multifiliis.}, journal = {Journal of fish diseases}, volume = {41}, number = {7}, pages = {1147-1152}, doi = {10.1111/jfd.12810}, pmid = {29671884}, issn = {1365-2761}, mesh = {Animals ; Antiprotozoal Agents/*pharmacology ; Ciliophora Infections/drug therapy/parasitology/*virology ; Dose-Response Relationship, Drug ; Fish Diseases/*drug therapy/parasitology ; Hymenostomatida/*drug effects ; In Vitro Techniques ; Oncorhynchus mykiss ; Pseudomonas/*chemistry ; Surface-Active Agents/*pharmacology ; }, abstract = {A bacterial biosurfactant isolated from Pseudomonas (strain H6) has previously been shown to have a lethal effect on the oomycete Saprolegnia diclina infecting fish eggs. The present work demonstrates that the same biosurfactant has a strong in vitro antiparasitic effect on the fish pathogenic ciliate Ichthyophthirius multifiliis. Three life cycle stages (the infective theront stage, the tomont and the tomocyst containing tomites) were all susceptible to the surfactant. Theronts were the most sensitive showing 100% mortality in as low concentrations as 10 and 13 μg/ml within 30 min. Tomonts were the most resistant but were killed in concentrations of 100 μg/ml. Tomocysts, which generally are considered resistant to chemical and medical treatment, due to the surrounding protective cyst wall, were also sensitive. The surfactant, in concentrations of 10 and 13 μg/ml, penetrated the cyst wall and killed the enclosed tomites within 60 min. Rainbow trout fingerlings exposed to the biosurfactant showed no adverse immediate or late signs following several hours incubation in concentrations effective for killing the parasite. This bacterial surfactant may be further developed for application as an antiparasitic control agent in aquaculture.}, }
@article {pmid29670584, year = {2018}, author = {Siegel-Hertz, K and Edel-Hermann, V and Chapelle, E and Terrat, S and Raaijmakers, JM and Steinberg, C}, title = {Comparative Microbiome Analysis of a Fusarium Wilt Suppressive Soil and a Fusarium Wilt Conducive Soil From the Châteaurenard Region.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {568}, pmid = {29670584}, issn = {1664-302X}, abstract = {Disease-suppressive soils are soils in which specific soil-borne plant pathogens cause only limited disease although the pathogen and susceptible host plants are both present. Suppressiveness is in most cases of microbial origin. We conducted a comparative metabarcoding analysis of the taxonomic diversity of fungal and bacterial communities from suppressive and non-suppressive (conducive) soils as regards Fusarium wilts sampled from the Châteaurenard region (France). Bioassays based on Fusarium wilt of flax confirmed that disease incidence was significantly lower in the suppressive soil than in the conducive soil. Furthermore, we succeeded in partly transferring Fusarium wilt-suppressiveness to the conducive soil by mixing 10% (w/w) of the suppressive soil into the conducive soil. Fungal diversity differed significantly between the suppressive and conducive soils. Among dominant fungal operational taxonomic units (OTUs) affiliated to known genera, 17 OTUs were detected exclusively in the suppressive soil. These OTUs were assigned to the Acremonium, Chaetomium, Cladosporium, Clonostachys, Fusarium, Ceratobasidium, Mortierella, Penicillium, Scytalidium, and Verticillium genera. Additionally, the relative abundance of specific members of the bacterial community was significantly higher in the suppressive and mixed soils than in the conducive soil. OTUs found more abundant in Fusarium wilt-suppressive soils were affiliated to the bacterial genera Adhaeribacter, Massilia, Microvirga, Rhizobium, Rhizobacter, Arthrobacter, Amycolatopsis, Rubrobacter, Paenibacillus, Stenotrophomonas, and Geobacter. Several of the fungal and bacterial genera detected exclusively or more abundantly in the Fusarium wilt-suppressive soil included genera known for their activity against F. oxysporum. Overall, this study supports the potential role of known fungal and bacterial genera in Fusarium wilt suppressive soils from Châteaurenard and pinpoints new bacterial and fungal genera for their putative role in Fusarium wilt suppressiveness.}, }
@article {pmid29669070, year = {2018}, author = {Kerr, BJ and Trabue, SL and van Weelden, MB and Andersen, DS and Pepple, LM}, title = {Impact of narasin on manure composition, microbial ecology, and gas emissions from finishing pigs fed either a corn-soybean meal or a corn-soybean meal-dried distillers grains with solubles diets.}, journal = {Journal of animal science}, volume = {96}, number = {4}, pages = {1317-1329}, pmid = {29669070}, issn = {1525-3163}, mesh = {Animal Feed/*analysis ; Animals ; Diet/veterinary ; Dietary Fiber/analysis ; Dietary Supplements/*analysis ; Eating ; Edible Grain ; Feces/chemistry ; Female ; Gastrointestinal Microbiome/drug effects ; Manure/*analysis/microbiology ; Methane/*metabolism ; Pyrans/*pharmacology ; Random Allocation ; Glycine max ; Swine/microbiology/*physiology ; Zea mays ; }, abstract = {An experiment was conducted to determine the effect of feeding finishing pigs a corn-soybean (CSBM) diet or a CSBM diet supplemented with 30% dried distillers grains with solubles (DDGS), in combination with or without a growth-promoting ionophore (0 or 30 mg narasin/kg of diet), has on manure composition, microbial ecology, and gas emissions. Two separate groups of 24 gilts (initial BW = 145.1 kg, SD = 7.8 kg) were allotted to individual metabolism crates that allowed for total but separate collection of feces and urine during the 48-d collection period. After each of the twice-daily feedings, feces and urine from each crate was collected and added to its assigned enclosed manure storage tank. Each tank contained an individual fan system that pulled a constant stream of air over the manure surface for 2 wk prior to air (day 52) and manure sampling (day 53). After manure sampling, the manure in the tanks was dumped and the tanks cleaned for the second group of pigs. Except for total manure Ca and P output as a percent of intake and for manure methane product rate and biochemical methane potential (P ≤ 0.08), there were no interactions between diet composition and narasin supplementation. Narasin supplementation resulted in increased manure C (P = 0.05), increased manure DM, C, S, Ca, and phosphorus as a percent of animal intake (P ≤ 0.07), and increased manure volatile solids and foaming capacity (P ≤ 0.09). No effect of narasin supplementation was noted on manure VFA concentrations or any of the gas emission parameters measured (P ≥ 0.29). In contrast, feeding finishing pigs a diet containing DDGS dramatically affected manure composition as indicated by increased concentration of DM, C, ammonia, N, and total and volatile solids (P = 0.01), increased manure DM, N, and C as a percent of animal intake (P = 0.01), increased manure total VFA and phenols (P ≤ 0.05), decreased gas emissions of ammonia and volatile sulfur compounds (VSC; P = 0.01), increased emissions of phenols and indoles (P ≤ 0.06), decreased methane production rate (P = 0.01), and slight differences in microbial ecology (R ≤ 0.47). In conclusion, feeding a diet which contains an elevated level of indigestible fiber (i.e., DDGS) resulted in more fiber in the manure which therefore dramatically affected manure composition, gas emissions, and microbial ecology, while narasin supplementation to the diet did not exhibit a significant effect on any of these parameters in the resultant swine manure.}, }
@article {pmid29666882, year = {2018}, author = {Ortmann, AC and Brannock, PM and Wang, L and Halanych, KM}, title = {River Flow Impacts Bacterial and Archaeal Community Structure in Surface Sediments in the Northern Gulf of Mexico.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {941-953}, pmid = {29666882}, issn = {1432-184X}, mesh = {Archaea/genetics/*isolation &amp; purification ; Bacteria/genetics/*isolation &amp; purification ; DNA, Archaeal/analysis ; DNA, Bacterial/analysis ; Geologic Sediments/*chemistry/*microbiology ; Gulf of Mexico ; *Microbiota ; RNA, Ribosomal, 16S/analysis ; Rivers ; Sequence Analysis, DNA ; *Water Movements ; }, abstract = {Meiobenthic community structure in the northern Gulf of Mexico has been shown to be driven by geographical differences due to inshore-offshore gradients and location relative to river discharge. Samples collected along three transects spanning Mobile Bay, Alabama, showed significant differences in meiobenthic communities east of the bay compared to those sampled from the west. In contrast, analysis of bacterial and archaeal communities from the same sediment samples shows that the inshore-offshore gradient has minimal impact on their community structure. Significant differences in community structure were observed for Bacteria and Archaea between the east and west samples, but there was no difference in richness or diversity. Grouped by sediment type, higher richness was observed in silty samples compared to sandy samples. Significant differences were also observed among sediment types for community structure with bacteria communities in silty samples having more anaerobic sulfate reducers compared to aerobic heterotrophs, which had higher abundances in sandy sediments. This is likely due to increased organic matter in the silty sediments from the overlying river leading to low oxygen habitats. Most archaeal sequences represented poorly characterized high-level taxa, limiting interpretation of their distributions. Overlap between groups based on transect and sediment characteristics made determining which factor is more important in structuring bacterial and archaeal communities difficult. However, both factors are driven by discharge from the Mobile River. Although inshore-offshore gradients do not affect Bacteria or Archaea to the same extent as the meiobenthic communities, all three groups are strongly affected by sediment characteristics.}, }
@article {pmid29666290, year = {2018}, author = {Williams, SH and Che, X and Garcia, JA and Klena, JD and Lee, B and Muller, D and Ulrich, W and Corrigan, RM and Nichol, S and Jain, K and Lipkin, WI}, title = {Viral Diversity of House Mice in New York City.}, journal = {mBio}, volume = {9}, number = {2}, pages = {}, pmid = {29666290}, issn = {2150-7511}, support = {U19 AI109761/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Disease Reservoirs/*virology ; Feces/*virology ; High-Throughput Nucleotide Sequencing ; Mice ; New York City ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Viruses/*classification/*isolation &amp; purification ; }, abstract = {The microbiome of wild Mus musculus (house mouse), a globally distributed invasive pest that resides in close contact with humans in urban centers, is largely unexplored. Here, we report analysis of the fecal virome of house mice in residential buildings in New York City, NY. Mice were collected at seven sites in Manhattan, Queens, Brooklyn, and the Bronx over a period of 1 year. Unbiased high-throughput sequencing of feces revealed 36 viruses from 18 families and 21 genera, including at least 6 novel viruses and 3 novel genera. A representative screen of 15 viruses by PCR confirmed the presence of 13 of these viruses in liver. We identified an uneven distribution of diversity, with several viruses being associated with specific locations. Higher mouse weight was associated with an increase in the number of viruses detected per mouse, after adjusting for site, sex, and length. We found neither genetic footprints to known human viral pathogens nor antibodies to lymphocytic choriomeningitis virus.IMPORTANCE Mice carry a wide range of infectious agents with zoonotic potential. Their proximity to humans in the built environment is therefore a concern for public health. Laboratory mice are also the most common experimental model for investigating the pathobiology of infectious diseases. In this survey of mice trapped in multiple locations within New York City over a period of 1 year, we found a diverse collection of viruses that includes some previously not associated with house mice and others that appear to be novel. Although we found no known human pathogens, our findings provide insights into viral ecology and may yield models that have utility for clinical microbiology.}, }
@article {pmid29663040, year = {2018}, author = {Glukhova, LB and Frank, YA and Danilova, EV and Avakyan, MR and Banks, D and Tuovinen, OH and Karnachuk, OV}, title = {Isolation, Characterization, and Metal Response of Novel, Acid-Tolerant Penicillium spp. from Extremely Metal-Rich Waters at a Mining Site in Transbaikal (Siberia, Russia).}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {911-924}, pmid = {29663040}, issn = {1432-184X}, support = {16-04-01619//Russian Fund for Basic Research/ ; }, mesh = {Arsenic/*metabolism ; Fungal Proteins/analysis ; Metals, Heavy/*metabolism ; Penicillium/classification/genetics/*metabolism ; Phylogeny ; Siberia ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The role of fungi in metal cycling in acidic environments has been little explored to date. In this study, two acid-tolerant and metal-resistant Penicillium isolates, strains ShG4B and ShG4C, were isolated from a mine site in the Transbaikal area of Siberia (Russia). Waters at the mine site were characterized by extremely high metal concentrations: up to 18 g l[-1] Fe and > 2 g l[-1] each of Cu, Zn, Al, and As. Both isolates were identified as Penicillium spp. by phylogenetic analyses and they grew well in Czapek medium acidified to pH 2.5. Resistance to Cu, Cd, Ni, Co, and arsenate was in the range of 1-10 g l[-1]. Further experiments with Penicillium strain ShG4C demonstrated that growth in Cu-containing media was accompanied by the precipitation of Cu-oxalate (moolooite) and the formation of extracellular vesicles enriched in Cu on the mycelia. Vesicles were greatly reduced in size in Cd-containing media and were not formed in the presence of Ni or Co. Cd-oxalate was detected as a crystalline solid phase in Cd-exposed mycelia. Hydrated Ni-sulfate (retgersite) and Co-sulfate (bieberite) were detected in mycelia grown in the presence of Ni and Co, respectively. The results demonstrated that acid-tolerant and metal-resistant Penicillium constitute a component in extremophilic microbiomes, contributing to organic matter breakdown and formation of secondary solid phases at pH ranges found in acid rock drainage.}, }
@article {pmid29663039, year = {2018}, author = {Birnbaum, C and Bissett, A and Teste, FP and Laliberté, E}, title = {Symbiotic N2-Fixer Community Composition, but Not Diversity, Shifts in Nodules of a Single Host Legume Across a 2-Million-Year Dune Chronosequence.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {1009-1020}, pmid = {29663039}, issn = {1432-184X}, support = {DE120100352//Australian Research Council/ ; DP130100016//Australian Research Council/ ; }, mesh = {Acacia/metabolism/*microbiology ; Environment ; Microbiota ; *Nitrogen Fixation ; Oxidoreductases/analysis ; Plant Proteins/analysis ; Root Nodules, Plant/metabolism/*microbiology ; Soil/*chemistry ; *Soil Microbiology ; Symbiosis ; Western Australia ; }, abstract = {Long-term soil age gradients are useful model systems to study how changes in nutrient limitation shape communities of plant root mutualists because they represent strong natural gradients of nutrient availability, particularly of nitrogen (N) and phosphorus (P). Here, we investigated changes in the dinitrogen (N2)-fixing bacterial community composition and diversity in nodules of a single host legume (Acacia rostellifera) across the Jurien Bay chronosequence, a retrogressive 2 million-year-old sequence of coastal dunes representing an exceptionally strong natural soil fertility gradient. We collected nodules from plants grown in soils from five chronosequence stages ranging from very young (10s of years; associated with strong N limitation for plant growth) to very old (> 2,000,000 years; associated with strong P limitation), and sequenced the nifH gene in root nodules to determine the composition and diversity of N2-fixing bacterial symbionts. A total of 335 unique nifH gene operational taxonomic units (OTUs) were identified. Community composition of N2-fixing bacteria within nodules, but not diversity, changed with increasing soil age. These changes were attributed to pedogenesis-driven shifts in edaphic conditions, specifically pH, exchangeable manganese, resin-extractable phosphate, nitrate and nitrification rate. A large number of common N2-fixing bacteria genera (e.g. Bradyrhizobium, Ensifer, Mesorhizobium and Rhizobium) belonging to the Rhizobiaceae family (α-proteobacteria) comprised 70% of all raw sequences and were present in all nodules. However, the oldest soils, which show some of the lowest soil P availability ever recorded, harboured the largest proportion of unclassified OTUs, suggesting a unique set of N2-fixing bacteria adapted to extreme P limitation. Our results show that N2-fixing bacterial composition varies strongly during long-term ecosystem development, even within the same host, and therefore rhizobia show strong edaphic preferences.}, }
@article {pmid29662223, year = {2018}, author = {Ratzke, C and Denk, J and Gore, J}, title = {Ecological suicide in microbes.}, journal = {Nature ecology &amp; evolution}, volume = {2}, number = {5}, pages = {867-872}, pmid = {29662223}, issn = {2397-334X}, support = {R01 GM102311/GM/NIGMS NIH HHS/United States ; }, mesh = {*Environment ; Hydrogen-Ion Concentration ; Microbial Interactions ; Paenibacillus/*physiology ; Population Dynamics ; }, abstract = {The growth and survival of organisms often depend on interactions between them. In many cases, these interactions are positive and caused by a cooperative modification of the environment. Examples are the cooperative breakdown of complex nutrients in microbes or the construction of elaborate architectures in social insects, in which the individual profits from the collective actions of her peers. However, organisms can similarly display negative interactions by changing the environment in ways that are detrimental for them, for example by resource depletion or the production of toxic byproducts. Here we find an extreme type of negative interactions, in which Paenibacillus sp. bacteria modify the environmental pH to such a degree that it leads to a rapid extinction of the whole population, a phenomenon that we call ecological suicide. Modification of the pH is more pronounced at higher population densities, and thus ecological suicide is more likely to occur with increasing bacterial density. Correspondingly, promoting bacterial growth can drive populations extinct whereas inhibiting bacterial growth by the addition of harmful substances-such as antibiotics-can rescue them. Moreover, ecological suicide can cause oscillatory dynamics, even in single-species populations. We found ecological suicide in a wide variety of microbes, suggesting that it could have an important role in microbial ecology and evolution.}, }
@article {pmid29662088, year = {2018}, author = {Han, GG and Lee, JY and Jin, GD and Park, J and Choi, YH and Kang, SK and Chae, BJ and Kim, EB and Choi, YJ}, title = {Tracing of the fecal microbiota of commercial pigs at five growth stages from birth to shipment.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6012}, pmid = {29662088}, issn = {2045-2322}, mesh = {Animal Husbandry ; Animals ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Male ; Microbial Interactions ; Swine/*growth &amp; development/*microbiology ; }, abstract = {The intestinal microbiota affect various physiological traits of host animals such as brain development, obesity, age, and the immune system. In the swine industry, understanding the relationship between intestinal microbiota and growth stage is essential because growth stage is directly related to the feeding system of pigs, thus we studied the intestinal microbiota of 32 healthy pigs across five sows at 10, 21, 63, 93, and 147 d of ages. The intestinal microbiota were altered with growth of pigs and were separated into three distinct clusters. The relative abundance of several phyla and genera were significantly different between growth stages. We observed co-occurrence pattern of the intestinal microbiota at each growth stage. In addition, we predicted the functions of the intestinal microbiota and confirmed that several KEGG pathways were significantly different between growth stages. We also explored the relationship between the intestinal microbiota and innate factors such as the maternal effect and gender. When pigs were young, innate factors affected on construction of intestinal microbiota, however this tendency was disappeared with growth. Our findings broaden the understanding of microbial ecology, and the results will be used as a reference for investigating host-microbe interactions in the swine industry.}, }
@article {pmid29661568, year = {2018}, author = {Lima, FR and Ferreira, AJ and Menezes, CG and Miranda, VFO and Dourado, MN and Araújo, WL}, title = {Cultivated bacterial diversity associated with the carnivorous plant Utricularia breviscapa (Lentibulariaceae) from floodplains in Brazil.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {49}, number = {4}, pages = {714-722}, pmid = {29661568}, issn = {1678-4405}, mesh = {Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; *Biodiversity ; Brazil ; Floods ; Magnoliopsida/*microbiology ; Phylogeny ; }, abstract = {Carnivorous plant species, such as Utricularia spp., capture and digest prey. This digestion can occur through the secretion of plant digestive enzymes and/or by bacterial digestive enzymes. To comprehend the physiological mechanisms of carnivorous plants, it is essential to understand the microbial diversity related to these plants. Therefore, in the present study, we isolated and classified bacteria from different organs of Utricularia breviscapa (stolons and utricles) and from different geographic locations (São Paulo and Mato Grosso). We were able to build the first bacterium collection for U. breviscapa and study the diversity of cultivable bacteria. The results show that U. breviscapa bacterial diversity varied according to the geographic isolation site (São Paulo and Mato Grosso) but not the analyzed organs (utricle and stolon). We reported that six genera were common to both sample sites (São Paulo and Mato Grosso). These genera have previously been reported to be beneficial to plants, as well as related to the bioremediation process, showing that these isolates present great biotechnological and agricultural potential. This is the first report of an Acidobacteria isolated from U. breviscapa. The role of these bacteria inside the plant must be further investigated in order to understand their population dynamics within the host.}, }
@article {pmid29657970, year = {2018}, author = {Rodriguez-R, LM and Gunturu, S and Tiedje, JM and Cole, JR and Konstantinidis, KT}, title = {Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity.}, journal = {mSystems}, volume = {3}, number = {3}, pages = {}, pmid = {29657970}, issn = {2379-5077}, abstract = {Estimations of microbial community diversity based on metagenomic data sets are affected, often to an unknown degree, by biases derived from insufficient coverage and reference database-dependent estimations of diversity. For instance, the completeness of reference databases cannot be generally estimated since it depends on the extant diversity sampled to date, which, with the exception of a few habitats such as the human gut, remains severely undersampled. Further, estimation of the degree of coverage of a microbial community by a metagenomic data set is prohibitively time-consuming for large data sets, and coverage values may not be directly comparable between data sets obtained with different sequencing technologies. Here, we extend Nonpareil, a database-independent tool for the estimation of coverage in metagenomic data sets, to a high-performance computing implementation that scales up to hundreds of cores and includes, in addition, a k-mer-based estimation as sensitive as the original alignment-based version but about three hundred times as fast. Further, we propose a metric of sequence diversity (Nd) derived directly from Nonpareil curves that correlates well with alpha diversity assessed by traditional metrics. We use this metric in different experiments demonstrating the correlation with the Shannon index estimated on 16S rRNA gene profiles and show that Nd additionally reveals seasonal patterns in marine samples that are not captured by the Shannon index and more precise rankings of the magnitude of diversity of microbial communities in different habitats. Therefore, the new version of Nonpareil, called Nonpareil 3, advances the toolbox for metagenomic analyses of microbiomes. IMPORTANCE Estimation of the coverage provided by a metagenomic data set, i.e., what fraction of the microbial community was sampled by DNA sequencing, represents an essential first step of every culture-independent genomic study that aims to robustly assess the sequence diversity present in a sample. However, estimation of coverage remains elusive because of several technical limitations associated with high computational requirements and limiting statistical approaches to quantify diversity. Here we described Nonpareil 3, a new bioinformatics algorithm that circumvents several of these limitations and thus can facilitate culture-independent studies in clinical or environmental settings, independent of the sequencing platform employed. In addition, we present a new metric of sequence diversity based on rarefied coverage and demonstrate its use in communities from diverse ecosystems.}, }
@article {pmid29656514, year = {2018}, author = {Johnson, DB and Beddows, PA and Flynn, TM and Osburn, MR}, title = {Microbial diversity and biomarker analysis of modern freshwater microbialites from Laguna Bacalar, Mexico.}, journal = {Geobiology}, volume = {16}, number = {3}, pages = {319-337}, doi = {10.1111/gbi.12283}, pmid = {29656514}, issn = {1472-4669}, mesh = {Bacteria/chemistry/*classification/cytology ; *Biodiversity ; Biomarkers/*analysis ; Fresh Water/*microbiology ; Geologic Sediments/*microbiology ; High-Throughput Nucleotide Sequencing ; Lipids/*analysis ; Mexico ; Microscopy ; }, abstract = {Laguna Bacalar is a sulfate-rich freshwater lake on the Yucatan Peninsula that hosts large microbialites. High sulfate concentrations distinguish Laguna Bacalar from other freshwater microbialite sites such as Pavilion Lake and Alchichica, Mexico, as well as from other aqueous features on the Yucatan Peninsula. While cyanobacterial populations have been described here previously, this study offers a more complete characterization of the microbial populations and corresponding biogeochemical cycling using a three-pronged geobiological approach of microscopy, high-throughput DNA sequencing, and lipid biomarker analyses. We identify and compare diverse microbial communities of Alphaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria that vary with location along a bank-to-bank transect across the lake, within microbialites, and within a neighboring mangrove root agglomeration. In particular, sulfate-reducing bacteria are extremely common and diverse, constituting 7%-19% of phylogenetic diversity within the microbialites, and are hypothesized to significantly influence carbonate precipitation. In contrast, Cyanobacteria account for less than 1% of phylogenetic diversity. The distribution of lipid biomarkers reflects these changes in microbial ecology, providing meaningful biosignatures for the microbes in this system. Polysaturated short-chain fatty acids characteristic of cyanobacteria account for <3% of total abundance in Laguna Bacalar microbialites. By contrast, even short-chain and monounsaturated short-chain fatty acids attributable to both Cyanobacteria and many other organisms including types of Alphaproteobacteria and Gammaproteobacteria constitute 43%-69% and 17%-25%, respectively, of total abundance in microbialites. While cyanobacteria are the largest and most visible microbes within these microbialites and dominate the mangrove root agglomeration, it is clear that their smaller, metabolically diverse associates are responsible for significant biogeochemical cycling in this microbialite system.}, }
@article {pmid29655918, year = {2018}, author = {Dini-Andreote, F and Raaijmakers, JM}, title = {Embracing Community Ecology in Plant Microbiome Research.}, journal = {Trends in plant science}, volume = {23}, number = {6}, pages = {467-469}, doi = {10.1016/j.tplants.2018.03.013}, pmid = {29655918}, issn = {1878-4372}, mesh = {*Biodiversity ; Ecology/methods ; *Microbiota ; Plants/*microbiology ; }, abstract = {Community assembly is mediated by selection, dispersal, drift, and speciation. Environmental selection is mostly used to date to explain patterns in plant microbiome assembly, whereas the influence of the other processes remains largely elusive. Recent studies highlight that adopting community ecology concepts provides a mechanistic framework for plant microbiome research.}, }
@article {pmid29655065, year = {2018}, author = {Xie, Y and Floehr, T and Zhang, X and Xiao, H and Yang, J and Xia, P and Burton, GA and Hollert, H}, title = {In situ microbiota distinguished primary anthropogenic stressor in freshwater sediments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {239}, number = {}, pages = {189-197}, doi = {10.1016/j.envpol.2018.03.099}, pmid = {29655065}, issn = {1873-6424}, mesh = {Acetobacteraceae/genetics/*isolation &amp; purification ; China ; DNA Barcoding, Taxonomic ; Ecotoxicology ; Environmental Monitoring/*methods ; *Geologic Sediments/chemistry/microbiology/parasitology ; Microbiota/genetics ; Oxytricha/genetics/*isolation &amp; purification ; Polycyclic Aromatic Hydrocarbons/*analysis ; Receptors, Aryl Hydrocarbon/*metabolism ; *Rivers/chemistry/microbiology/parasitology ; Water Pollutants, Chemical/*analysis ; }, abstract = {Conventional assessment and evaluation of sediment quality are based on laboratory-based ecotoxicological and chemical measurements with lack of concern for ecological relevance. Microbiotas in sediment are responsive to pollutants and can be used as alternative ecological indicators of sediment pollutants; however, the linkage between the microbial ecology and ecotoxicological endpoints in response to sediment contamination has been poorly evaluated. Here, in situ microbiotas from the Three Gorges Reservoir (TGR) area of the Yangtze River were characterized by DNA metabarcoding approaches, and then, changes of in situ microbiotas were compared with the ecotoxicological endpoint, aryl hydrocarbon receptor (AhR) mediated activity, and level of polycyclic aromatic hydrocarbons (PAHs) in sediments. PAHs and organic pollutant mixtures mediating AhR activity had different effects on the structures of microbiotas. Specifically, Shannon indices of protistan communities were negatively correlated with the levels of AhR mediated activity and PAHs. The sediment AhR activity was positively correlated with the relative abundance of prokaryotic Acetobacteraceae, but had a negative correlation with protistan Oxytrichidae. Furthermore, a quantitative classification model was built to predict the level of AhR activity based on the relative abundances of Acetobacteraceae and Oxytrichidae. These results suggested that in situ Protista communities could provide a useful tool for monitoring and assessing ecological stressors. The observed responses of microbial community provided supplementary evidence to support that the AhR-active pollutants, such as PAHs, were the primary stressors of the aquatic community in TGR area.}, }
@article {pmid29654180, year = {2018}, author = {Wuyts, S and Van Beeck, W and Oerlemans, EFM and Wittouck, S and Claes, IJJ and De Boeck, I and Weckx, S and Lievens, B and De Vuyst, L and Lebeer, S}, title = {Carrot Juice Fermentations as Man-Made Microbial Ecosystems Dominated by Lactic Acid Bacteria.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {12}, pages = {}, pmid = {29654180}, issn = {1098-5336}, mesh = {Antibiosis ; Biodiversity ; Colony Count, Microbial ; Daucus carota/*microbiology ; Enterobacteriaceae/classification ; *Fermentation ; Food Microbiology ; Fruit and Vegetable Juices/*microbiology ; Lactobacillales/*classification/isolation &amp; purification ; Leuconostoc/genetics/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Spontaneous vegetable fermentations, with their rich flavors and postulated health benefits, are regaining popularity. However, their microbiology is still poorly understood, therefore raising concerns about food safety. In addition, such spontaneous fermentations form interesting cases of man-made microbial ecosystems. Here, samples from 38 carrot juice fermentations were collected through a citizen science initiative, in addition to three laboratory fermentations. Culturing showed that Enterobacteriaceae were outcompeted by lactic acid bacteria (LAB) between 3 and 13 days of fermentation. Metabolite-target analysis showed that lactic acid and mannitol were highly produced, as well as the biogenic amine cadaverine. High-throughput 16S rRNA gene sequencing revealed that mainly species of Leuconostoc and Lactobacillus (as identified by 8 and 20 amplicon sequence variants [ASVs], respectively) mediated the fermentations in subsequent order. The analyses at the DNA level still detected a high number of Enterobacteriaceae, but their relative abundance was low when RNA-based sequencing was performed to detect presumptive metabolically active bacterial cells. In addition, this method greatly reduced host read contamination. Phylogenetic placement indicated a high LAB diversity, with ASVs from nine different phylogenetic groups of the Lactobacillus genus complex. However, fermentation experiments with isolates showed that only strains belonging to the most prevalent phylogenetic groups preserved the fermentation dynamics. The carrot juice fermentation thus forms a robust man-made microbial ecosystem suitable for studies on LAB diversity and niche specificity.IMPORTANCE The usage of fermented food products by professional chefs is steadily growing worldwide. Meanwhile, this interest has also increased at the household level. However, many of these artisanal food products remain understudied. Here, an extensive microbial analysis was performed of spontaneous fermented carrot juices which are used as nonalcoholic alternatives for wine in a Belgian Michelin star restaurant. Samples were collected through an active citizen science approach with 38 participants, in addition to three laboratory fermentations. Identification of the main microbial players revealed that mainly species of Leuconostoc and Lactobacillus mediated the fermentations in subsequent order. In addition, a high diversity of lactic acid bacteria was found; however, fermentation experiments with isolates showed that only strains belonging to the most prevalent lactic acid bacteria preserved the fermentation dynamics. Finally, this study showed that the usage of RNA-based 16S rRNA amplicon sequencing greatly reduces host read contamination.}, }
@article {pmid29651504, year = {2019}, author = {Krieg, T and Madjarov, J and Rosa, LFM and Enzmann, F and Harnisch, F and Holtmann, D and Rabaey, K}, title = {Reactors for Microbial Electrobiotechnology.}, journal = {Advances in biochemical engineering/biotechnology}, volume = {167}, number = {}, pages = {231-271}, doi = {10.1007/10_2017_40}, pmid = {29651504}, issn = {0724-6145}, mesh = {*Bacteria/metabolism ; Bioengineering ; *Bioreactors ; Biotechnology/instrumentation ; Electromagnetic Phenomena ; }, abstract = {From the first electromicrobial experiment to a sophisticated microbial electrochemical process - it all takes place in a reactor. Whereas the reactor design and materials used strongly influence the obtained results, there are no common platforms for MES reactors. This is a critical convention gap, as cross-comparison and benchmarking among MES as well as MES vs. conventional biotechnological processes is needed. Only knowledge driven engineering of MES reactors will pave the way to application and commercialization. In this chapter we first assess the requirements on reactors to be used for bioelectrochemical systems as well as potential losses caused by the reactor design. Subsequently, we compile the main types and designs of reactors used for MES so far, starting from simple H-cells to stirred tank reactors. We conclude with a discussion on the weaknesses and strengths of the existing types of reactors for bioelectrochemical systems that are scored on design criteria and draw conclusions for the future engineering of MES reactors.}, }
@article {pmid29651035, year = {2018}, author = {Zaheer, R and Noyes, N and Ortega Polo, R and Cook, SR and Marinier, E and Van Domselaar, G and Belk, KE and Morley, PS and McAllister, TA}, title = {Impact of sequencing depth on the characterization of the microbiome and resistome.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {5890}, pmid = {29651035}, issn = {2045-2322}, support = {T32 OD012201/OD/NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Archaea/classification/drug effects/*genetics/isolation &amp; purification ; Archaeal Proteins/genetics/metabolism ; Bacteria/classification/drug effects/*genetics/isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; Cattle ; Drug Resistance/*genetics ; Feces/microbiology ; Fungal Proteins/genetics/metabolism ; Fungi/classification/drug effects/*genetics/isolation &amp; purification ; Gastrointestinal Microbiome/drug effects/*genetics ; Gene Expression ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Phylogeny ; Viral Proteins/genetics/metabolism ; Viruses/classification/drug effects/*genetics/isolation &amp; purification ; }, abstract = {Developments in high-throughput next generation sequencing (NGS) technology have rapidly advanced the understanding of overall microbial ecology as well as occurrence and diversity of specific genes within diverse environments. In the present study, we compared the ability of varying sequencing depths to generate meaningful information about the taxonomic structure and prevalence of antimicrobial resistance genes (ARGs) in the bovine fecal microbial community. Metagenomic sequencing was conducted on eight composite fecal samples originating from four beef cattle feedlots. Metagenomic DNA was sequenced to various depths, D1, D0.5 and D0.25, with average sample read counts of 117, 59 and 26 million, respectively. A comparative analysis of the relative abundance of reads aligning to different phyla and antimicrobial classes indicated that the relative proportions of read assignments remained fairly constant regardless of depth. However, the number of reads being assigned to ARGs as well as to microbial taxa increased significantly with increasing depth. We found a depth of D0.5 was suitable to describe the microbiome and resistome of cattle fecal samples. This study helps define a balance between cost and required sequencing depth to acquire meaningful results.}, }
@article {pmid29650581, year = {2018}, author = {de Siqueira, KA and Mello, IS and Pietro-Souza, W and Mendes, TAO and Soares, MA}, title = {Draft Genome Sequence of the Mercury-Resistant Strain Acinetobacter baumannii I43.}, journal = {Genome announcements}, volume = {6}, number = {15}, pages = {}, pmid = {29650581}, issn = {2169-8287}, abstract = {Here, we report the draft genome sequence of the Acinetobacter baumannii strain I43, which is highly resistant to mercury. The Illumina-based sequence analysis revealed a genome of approximately 4,520,353 bp composed of 4,091 coding sequences.}, }
@article {pmid29644407, year = {2018}, author = {Ye, F and Ma, MH and Op den Camp, HJM and Chatzinotas, A and Li, L and Lv, MQ and Wu, SJ and Wang, Y}, title = {Different Recovery Processes of Soil Ammonia Oxidizers from Flooding Disturbance.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {1041-1052}, pmid = {29644407}, issn = {1432-184X}, support = {41303053//the National Natural Science Foundation of China/ ; 41571497//the National Natural Science Foundation of China/ ; 41301540//the National Natural Science Foundation of China/ ; }, mesh = {Ammonia/*metabolism ; Archaea/classification/*metabolism ; Bacteria/classification/*metabolism ; China ; *Floods ; Genes, Archaeal ; Genes, Bacterial ; *Microbiota ; Oxidation-Reduction ; *Soil Microbiology ; }, abstract = {Understanding how microorganisms respond to environmental disturbance is one of the key focuses in microbial ecology. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are responsible for ammonia oxidation which is a crucial step in the nitrogen cycle. Although the physiology, distribution, and activity of AOA and AOB in soil have been extensively investigated, their recovery from a natural disturbance remains largely unknown. To assess the recovery capacities, including resistance and resilience, of AOA and AOB, soil samples were taken from a reservoir riparian zone which experienced periodically water flooding. The samples were classified into three groups (flooding, recovery, and control) for a high-throughput sequencing and quantitative PCR analysis. We used a relative quantitative index of both the resistance (RS) and resilience (RL) to assess the variation of gene abundance, alpha-diversity, and community composition. The AOA generally demonstrated a better recovery capability after the flooding disturbance compared to AOB. In particular, AOA were more resilient after the flooding disturbance. Taxa within the AOA and AOB showed different RS and RL values, with the most abundant taxa showing in general the highest RS indices. Soil NH4[+] and Fe[2+]/Fe[3+] were the main variables controlling the key taxa of AOA and AOB and probably influenced the resistance and resilience properties of AOA and AOB communities. The distinct mechanisms of AOA and AOB in maintaining community stability against the flooding disturbance might be linked to the different life-history strategies: the AOA community was more likely to represent r-strategists in contrast to the AOB community following a K-life strategy. Our results indicated that the AOA may play a vital role in ammonia oxidation in a fluctuating habitat and contribute to the stability of riparian ecosystem.}, }
@article {pmid29636742, year = {2018}, author = {Dewanckele, L and Vlaeminck, B and Hernandez-Sanabria, E and Ruiz-González, A and Debruyne, S and Jeyanathan, J and Fievez, V}, title = {Rumen Biohydrogenation and Microbial Community Changes Upon Early Life Supplementation of 22:6n-3 Enriched Microalgae to Goats.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {573}, pmid = {29636742}, issn = {1664-302X}, abstract = {Dietary supplementation of docosahexaenoic acid (DHA)-enriched products inhibits the final step of biohydrogenation in the adult rumen, resulting in the accumulation of 18:1 isomers, particularly of trans(t)-11 18:1. Occasionally, a shift toward the formation of t10 intermediates at the expense of t11 intermediates can be triggered. However, whether similar impact would occur when supplementing DHA-enriched products during pregnancy or early life remains unknown. Therefore, the current in vivo study aimed to investigate the effect of a nutritional intervention with DHA in the early life of goat kids on rumen biohydrogenation and microbial community. Delivery of DHA was achieved by supplementing DHA-enriched microalgae (DHA Gold) either to the maternal diet during pregnancy (prenatal) or to the diet of the young offspring (postnatal). At the age of 12 weeks, rumen fluid was sampled for analysis of long-chain fatty acids and microbial community based on bacterial 16S rRNA amplicon sequencing. Postnatal supplementation with DHA-enriched microalgae inhibited the final biohydrogenation step, as observed in adult animals. This resulted particularly in increased ruminal proportions of t11 18:1 rather than a shift to t10 intermediates, suggesting that both young and adult goats might be less prone to dietary induced shifts toward the formation of t10 intermediates, in comparison with cows. Although Butyrivibrio species have been identified as the most important biohydrogenating bacteria, this genus was more abundant when complete biohydrogenation, i.e. 18:0 formation, was inhibited. Blautia abundance was positively correlated with 18:0 accumulation, whereas Lactobacillus spp. Dialister spp. and Bifidobacterium spp. were more abundant in situations with greater t10 accumulation. Extensive comparisons made between current results and literature data indicate that current associations between biohydrogenation intermediates and rumen bacteria in young goats align with former observations in adult ruminants.}, }
@article {pmid29635439, year = {2018}, author = {Lim, ML and Brooks, MD and Boothe, MA and Krzmarzick, MJ}, title = {Novel bacterial diversity is enriched with chloroperoxidase-reacted organic matter under anaerobic conditions.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {5}, pages = {}, doi = {10.1093/femsec/fiy050}, pmid = {29635439}, issn = {1574-6941}, mesh = {Anaerobiosis ; Bacteria/classification/*enzymology/genetics/*isolation &amp; purification ; Biodegradation, Environmental ; Biodiversity ; Chloride Peroxidase/genetics/*metabolism ; Hydrogen Peroxide/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Fungal chloroperoxidases (CPOs) are one class of enzymes that produce natural organochlorides in soils. The microbial degradation of these organochlorides is not well known, though has implications for bioremediation, microbial ecology and natural chlorine and carbon cycling. In this study, Illumina-based 16S rRNA gene sequencing and real-time quantitative PCR (qPCR) was used to characterize the bacterial community enriched from an amendment of organic matter reacted with CPO under conditions conducive towards chlorination (CPO-OM). In total, 17 bacterial groups were enriched in triplicate microcosms inoculated with creek sediment and amended with CPO-OM. These bacterial groups were neither enriched with amendments of non-reacted organic matter extract, with or without oxidative stress induced by H2O2, nor with amendments of organic matter reacted with CPO under non-chlorinating conditions. Of these, only two represented genera with known organohalide respiring bacteria-Dehalogenimonas and Dehalobacter. The genus Acetobacterium was also found to be enriched but the other 14 groups of enriched bacteria do not currently have any close phylogenetically related isolates. This study highlights a gap in the current understanding of the microbiology involved in natural organochloride turnover and suggests that CPO-OM could be used for isolating and culturing strains from novel bacteria genera.}, }
@article {pmid29631430, year = {2018}, author = {Srivastava, A and Seo, SH and Ko, SR and Ahn, CY and Oh, HM}, title = {Bioflocculation in natural and engineered systems: current perspectives.}, journal = {Critical reviews in biotechnology}, volume = {38}, number = {8}, pages = {1176-1194}, doi = {10.1080/07388551.2018.1451984}, pmid = {29631430}, issn = {1549-7801}, mesh = {*Environmental Microbiology ; Flocculation ; *Industrial Microbiology ; Wastewater/microbiology ; }, abstract = {Microorganisms have the tendency to accumulate at interfaces through the release of extracellular polymeric substances to form aggregates such as films or flocs. This physical association leads to different modes of interactions among cells and the subsequent development of functionally and metabolically diverse consortia. Aggregation of cells in aqueous suspensions often results in the formation of flocs, which are hotspots of enhanced microbial processes. This has important implications for the dynamics of organic and inorganic matter in varied ecosystems. These microbial flocs are not only important components in nutrient turnover, decomposition, and sinking flux but also facilitate contaminant removal and treatment of wastewater and biomass harvesting. Greater insight into the multitude of interactions between microorganisms in flocs would be useful to enhance the efficiency of bioflocculation processes. This review covers the fundamental aspects and outlines the role of bioflocculation in controlled industrial processes and in nature.}, }
@article {pmid29630846, year = {2018}, author = {Perera, M and Al-Hebshi, NN and Perera, I and Ipe, D and Ulett, GC and Speicher, DJ and Chen, T and Johnson, NW}, title = {Inflammatory Bacteriome and Oral Squamous Cell Carcinoma.}, journal = {Journal of dental research}, volume = {97}, number = {6}, pages = {725-732}, doi = {10.1177/0022034518767118}, pmid = {29630846}, issn = {1544-0591}, mesh = {Carcinoma, Squamous Cell/etiology/*microbiology ; Case-Control Studies ; DNA, Bacterial/genetics ; Dysbiosis/complications/microbiology ; Humans ; Inflammation/microbiology ; Male ; *Microbiota/genetics ; Middle Aged ; Mouth Neoplasms/etiology/*microbiology ; Polyps/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Results from microbiome studies on oral cancer have been inconsistent, probably because they focused on compositional analysis, which does not account for functional redundancy among oral bacteria. Based on functional prediction, a recent study revealed enrichment of inflammatory bacterial attributes in oral squamous cell carcinoma (OSCC). Given the high relevance of this finding to carcinogenesis, we aimed here to corroborate them in a case-control study involving 25 OSCC cases and 27 fibroepithelial polyp (FEP) controls from Sri Lanka. DNA extracted from fresh biopsies was sequenced for the V1 to V3 region with Illumina's 2 × 300-bp chemistry. High-quality nonchimeric merged reads were classified to the species level with a prioritized BLASTN-based algorithm. Downstream compositional analysis was performed with QIIME (Quantitative Insights into Microbial Ecology) and linear discriminant analysis effect size, while PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was utilized for bacteriome functional prediction. The OSCC tissues tended to have lower species richness and diversity. Genera Capnocytophaga, Pseudomonas, and Atopobium were overrepresented in OSCC, while Lautropia, Staphylococcus, and Propionibacterium were the most abundant in FEP. At the species level, Campylobacter concisus, Prevotella salivae, Prevotella loeschii, and Fusobacterium oral taxon 204 were enriched in OSCC, while Streptococcus mitis, Streptococcus oral taxon 070, Lautropia mirabilis, and Rothia dentocariosa among others were more abundant in FEP. Functionally, proinflammatory bacterial attributes, including lipopolysaccharide biosynthesis and peptidases, were enriched in the OSCC tissues. Thus, while the results in terms of species composition significantly differed from the original study, they were consistent at the functional level, substantiating evidence for the inflammatory nature of the bacteriome associated with OSCC.}, }
@article {pmid29629421, year = {2018}, author = {Pessotti, RC and Hansen, BL and Traxler, MF}, title = {In Search of Model Ecological Systems for Understanding Specialized Metabolism.}, journal = {mSystems}, volume = {3}, number = {2}, pages = {}, pmid = {29629421}, issn = {2379-5077}, abstract = {Microbes occupy diverse habitats, forming interconnected, dynamic communities. Elucidating the principles of microbial community function is a grand challenge for microbiology, and it will entail experiments that engage microbiomes across multiple levels of complexity. For example, community-level hypotheses often require testing at the mechanistic and/or genetic levels, while mechanistic relationships require community-level evaluation to understand their importance in context. In this Perspective, we articulate the need for model microbiome systems that enable experimentation in both community and reductionist frameworks, with an emphasis on understanding the role of specialized metabolites in microbial communities. We consider essential criteria for developing such model microbiome systems and discuss potential future models that address the ecology of specialized metabolism.}, }
@article {pmid29629416, year = {2018}, author = {Lieberman, TD}, title = {Seven Billion Microcosms: Evolution within Human Microbiomes.}, journal = {mSystems}, volume = {3}, number = {2}, pages = {}, pmid = {29629416}, issn = {2379-5077}, abstract = {Rational microbiome-based therapies may one day treat a wide range of diseases and promote wellness. Yet, we are still limited in our abilities to employ such therapies and to predict which bacterial strains have the potential to stably colonize a person. The Lieberman laboratory is working to close this knowledge gap and to develop an understanding of how individual species and strains behave in the human microbiome, including with regard to their niche ranges, survival strategies, and the degree to which they adapt to individual people. We employ system-level approaches, with a particular emphasis on using de novo mutations and evolutionary inference to reconstruct the history of bacterial lineages within individuals.}, }
@article {pmid29629414, year = {2018}, author = {Wolfe, BE}, title = {Using Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path Ahead.}, journal = {mSystems}, volume = {3}, number = {2}, pages = {}, pmid = {29629414}, issn = {2379-5077}, abstract = {As troves of microbiome sequencing data provide improved resolution of patterns of microbial diversity, new approaches are needed to understand what controls these patterns. Many microbial ecologists are using cultivated model microbial communities to address this challenge. These systems provide opportunities to identify drivers of microbiome assembly, but key challenges and limitations need to be carefully considered in their development, implementation, and interpretation. How well do model microbial communities mimic in vitro communities in terms of taxonomic diversity, trophic levels, intraspecific diversity, and the abiotic environment? What are the best ways to manipulate and measure inputs and outputs in model community experiments? In this perspective, I briefly address some of these challenges on the basis of our experience developing fermented food model communities. Future work integrating genetic and molecular approaches with cultivated model microbial communities will allow microbial ecology to develop a more mechanistic understanding of microbiome diversity.}, }
@article {pmid29629411, year = {2018}, author = {Shade, A}, title = {Understanding Microbiome Stability in a Changing World.}, journal = {mSystems}, volume = {3}, number = {2}, pages = {}, pmid = {29629411}, issn = {2379-5077}, abstract = {Microbiomes underpin biogeochemical processes, sustain the bases of food webs, and recycle carbon and nutrients. Thus, microbes are frontline players in determining ecosystem responses to environmental change. My research team and I investigate the causes and consequences of microbiome stability. Our primary objective is to understand the responses of complex microbiomes to stressors associated with environmental change. This work is important because Earth is changing rapidly and drastically, and these changes are expected to have serious consequences for ecosystems, their inhabiting organisms, and their microbiomes. Therefore, we aim to understand the repercussions of alterations to microbiome structure and functions and to use this information to predict the responses of microbiomes to stressors. This research is critical to prepare for, respond to, and potentially moderate environmental change. We anticipate that the results of our research will contribute toward these goals and will broadly inform management or manipulation of microbiomes toward desired functions.}, }
@article {pmid29625988, year = {2018}, author = {Vandeweyer, D and Wynants, E and Crauwels, S and Verreth, C and Viaene, N and Claes, J and Lievens, B and Van Campenhout, L}, title = {Microbial Dynamics during Industrial Rearing, Processing, and Storage of Tropical House Crickets (Gryllodes sigillatus) for Human Consumption.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {12}, pages = {}, pmid = {29625988}, issn = {1098-5336}, mesh = {Animals ; Bacteria/genetics/*isolation &amp; purification ; Colony Count, Microbial ; Europe ; Food Handling ; *Food Microbiology ; *Food Storage ; Gryllidae/*microbiology ; High-Throughput Nucleotide Sequencing ; Spores, Bacterial ; Tropical Climate ; }, abstract = {In this study, the microbiota during industrial rearing, processing, and storage of the edible tropical house cricket, Gryllodessigillatus, was investigated. To this end, we analyzed samples from the cricket feed, obtained before feeding as well as from the cages, and from the crickets during rearing, after harvest, and after processing into frozen, oven-dried, and smoked and oven-dried (smoked/dried) end products. Although the feed contained lower microbial numbers than the crickets, both were dominated by the same species-level operational taxonomic units, as determined by Illumina MiSeq sequencing. They corresponded, among others, to members of Porphyromonadaceae, Fusobacterium, Parabacteroides, and Erwinia The harvested crickets contained high microbial numbers, but none of the investigated food pathogens Salmonella spp., Listeria monocytogenes, Bacillus cereus, or coagulase-positive staphylococci. However, some possible mycotoxin-producing fungi were isolated from the crickets. A postharvest heat treatment, shortly boiling the crickets, reduced microbial numbers, but an endospore load of 2.4 log CFU/g remained. After processing, an increase in microbial counts was observed for the dried and smoked/dried crickets. Additionally, in the smoked/dried crickets, a high abundance of a Bacillus sp. was observed. Considering the possible occurrence of food-pathogenic species from this genus, it is advised to apply a heat treatment which is sufficient to eliminate spores. Nevertheless, the microbial numbers remained constant over a 6-month storage period, whether frozen (frozen end product) or at ambient temperature (oven-dried and smoked/dried end products).IMPORTANCE The need for sustainable protein sources has led to the emergence of a new food sector, producing and processing edible insects into foods. However, insight into the microbial quality of this new food and into the microbial dynamics during rearing, processing, and storage of edible insects is still limited. Samples monitored for their microbiota were obtained in this study from an industrial rearing and processing cycle. The results lead first to the identification of process steps which are critical for microbial food safety. Second, they can be used in the construction of a Hazard Analysis and Critical Control Points (HACCP) plan and of a Novel Food dossier, which is required in Europe for edible insects. Finally, they confirm the shelf-life period which was determined by the rearer.}, }
@article {pmid29625975, year = {2018}, author = {Lu, YJ and Sasaki, T and Kuwahara-Arai, K and Uehara, Y and Hiramatsu, K}, title = {Development of a New Application for Comprehensive Viability Analysis Based on Microbiome Analysis by Next-Generation Sequencing: Insights into Staphylococcal Carriage in Human Nasal Cavities.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {11}, pages = {}, pmid = {29625975}, issn = {1098-5336}, mesh = {Adult ; Aged ; Aged, 80 and over ; Carrier State/*microbiology ; Female ; Healthy Volunteers ; *High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Microbial Viability ; *Microbiota ; Middle Aged ; Nasal Cavity/*microbiology ; RNA, Ribosomal, 16S/genetics ; Staphylococcal Infections/microbiology ; Staphylococcus/*genetics/isolation &amp; purification ; Staphylococcus aureus/genetics/isolation &amp; purification ; Staphylococcus epidermidis/genetics/isolation &amp; purification ; Young Adult ; }, abstract = {The nasal carriage rate of Staphylococcus aureus in human is 25 to 30%, and S. aureus sporadically causes severe infections. However, the mechanisms underlying staphylococcal carriage remain largely unknown. In the present study, we constructed an rpoB-based microbiome method for staphylococcal species discrimination. Based on a microbiome scheme targeting viable cell DNA using propidium monoazide (PMA) dye (PMA microbiome method), we also developed a new method to allow the comprehensive viability analysis of any bacterial taxon. To clarify the ecological distribution of staphylococci in the nasal microbiota, we applied these methods in 46 nasal specimens from healthy adults. PMA microbiome results showed that Staphylococcaceae and Corynebacteriaceae were the most predominant viable taxa (average relative abundance: 0.435262 and 0.375195, respectively), and Staphylococcus epidermidis exhibited the highest viability in the nasal microbiota. Staphylococcus aureus detection rates from nasal specimens by rpoB-based conventional and PMA microbiome methods were 84.8% (39 of 46) and 69.5% (32 of 46), respectively, which substantially exceeded the values obtained by a culture method using identical specimens (36.9%). Our results suggest that Staphylococcaceae species, especially S. epidermidis, adapted most successfully to human nasal cavity. High detection of S. aureus DNA by microbiome methods suggests that almost all healthy adults are consistently exposed to S. aureus in everyday life. Furthermore, the large difference in S. aureus detection rates between culture and microbiome methods suggests that S. aureus cells frequently exist in a viable but nonculturable state in nasal cavities. Our method and findings will contribute to a better understanding of the mechanisms underlying carriage of indigenous bacteria.IMPORTANCE Metagenomic analyses, such as 16S rRNA microbiome methods, have provided new insights in various research fields. However, conventional 16S rRNA microbiome methods do not permit taxonomic analysis of only the viable bacteria in a sample and have poor resolving power below the genus level. Our new schemes allowed for viable cell-specific analysis and species discrimination, and nasal microbiome data using these methods provided some interesting findings regarding staphylococcal nasal carriage. According to our comprehensive viability analysis, the high viability of Staphylococcus species, especially Staphylococcus epidermidis, in human nasal carriage suggests that this taxon has adapted most successfully to human nasal tissue. Also, a higher detection rate of S. aureus DNA by microbiome methods (84.8%) than by a culture method (36.9%) suggests that almost all healthy adults are consistently exposed to Staphylococcus aureus in the medium and long term. Our findings will contribute to a better understanding of the mechanisms underlying the carriage of indigenous bacteria.}, }
@article {pmid29623358, year = {2018}, author = {Knutie, SA and Gotanda, KM}, title = {A Non-invasive Method to Collect Fecal Samples from Wild Birds for Microbiome Studies.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {851-855}, pmid = {29623358}, issn = {1432-184X}, support = {5599-6643//British Ecological Society/ ; }, mesh = {Animals ; Animals, Wild/microbiology ; Birds/*microbiology ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Microbiological Techniques/economics/instrumentation/*methods ; }, abstract = {Over the past few decades, studies have demonstrated that the gut microbiota strongly influences the physiology, behavior, and fitness of its host. Such studies have been conducted primarily in humans and model organisms under controlled laboratory conditions. More recently, researchers have realized the importance of placing host-associated microbiota studies into a more ecological context; however, few non-destructive methods have been established to collect fecal samples from wild birds. Here, we present an inexpensive and easy-to-use kit for the non-invasive collection of feces from small birds. The portability of the collection kit makes this method amenable to field studies, especially those in remote areas. The main components of the collection kit include a flat-bottomed paper bag, a large modified weigh boat (tray), vinyl-coated hardware cloth fencing (grate), a clothespin, and a 10% bleach solution (to sterilize the tray and grate). In the paper bag, a sterile tray is placed under a small grate, which prevents the birds from contacting the feces and reduces the risk of contamination. After capture, the bird is placed in the bag for 3-5 min until it defecates. After the bird is removed from the bag, the tray is extracted and the fecal sample is moved to a collection tube and frozen or preserved. We believe that our method is an affordable and easy option for researchers studying the gut microbiota of wild birds.}, }
@article {pmid29619022, year = {2018}, author = {Joyce, A and Ijaz, UZ and Nzeteu, C and Vaughan, A and Shirran, SL and Botting, CH and Quince, C and O'Flaherty, V and Abram, F}, title = {Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {540}, pmid = {29619022}, issn = {1664-302X}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Harvesting valuable bioproducts from various renewable feedstocks is necessary for the critical development of a sustainable bioeconomy. Anaerobic digestion is a well-established technology for the conversion of wastewater and solid feedstocks to energy with the additional potential for production of process intermediates of high market values (e.g., carboxylates). In recent years, first-generation biofuels typically derived from food crops have been widely utilized as a renewable source of energy. The environmental and socioeconomic limitations of such strategy, however, have led to the development of second-generation biofuels utilizing, amongst other feedstocks, lignocellulosic biomass. In this context, the anaerobic digestion of perennial grass holds great promise for the conversion of sustainable renewable feedstock to energy and other process intermediates. The advancement of this technology however, and its implementation for industrial applications, relies on a greater understanding of the microbiome underpinning the process. To this end, microbial communities recovered from replicated anaerobic bioreactors digesting grass were analyzed. The bioreactors leachates were not buffered and acidic pH (between 5.5 and 6.3) prevailed at the time of sampling as a result of microbial activities. Community composition and transcriptionally active taxa were examined using 16S rRNA sequencing and microbial functions were investigated using metaproteomics. Bioreactor fraction, i.e., grass or leachate, was found to be the main discriminator of community analysis across the three molecular level of investigation (DNA, RNA, and proteins). Six taxa, namely Bacteroidia, Betaproteobacteria, Clostridia, Gammaproteobacteria, Methanomicrobia, and Negativicutes accounted for the large majority of the three datasets. The initial stages of grass hydrolysis were carried out by Bacteroidia, Gammaproteobacteria, and Negativicutes in the grass biofilms, in addition to Clostridia in the bioreactor leachates. Numerous glycolytic enzymes and carbohydrate transporters were detected throughout the bioreactors in addition to proteins involved in butanol and lactate production. Finally, evidence of the prevalence of stressful conditions within the bioreactors and particularly impacting Clostridia was observed in the metaproteomes. Taken together, this study highlights the functional importance of Clostridia during the anaerobic digestion of grass and thus research avenues allowing members of this taxon to thrive should be explored.}, }
@article {pmid29617997, year = {2018}, author = {Ramió-Pujol, S and Ganigué, R and Bañeras, L and Colprim, J}, title = {Effect of ethanol and butanol on autotrophic growth of model homoacetogens.}, journal = {FEMS microbiology letters}, volume = {365}, number = {10}, pages = {}, doi = {10.1093/femsle/fny084}, pmid = {29617997}, issn = {1574-6968}, mesh = {Autotrophic Processes ; Butanols/analysis/*metabolism ; Carbon Monoxide/analysis/metabolism ; Clostridium/*growth &amp; development/*metabolism ; Ethanol/analysis/*metabolism ; Fermentation ; Gases/analysis/metabolism ; }, abstract = {Research efforts aimed at increasing ethanol and butanol productivity from syngas are currently gaining attention. For most model carboxydotrophic bacteria, production rates, yields and maximum product titres have been studied in detail, but little is known on alcohol toxicity in these bacteria. The aim of this work was to investigate the inhibitory effects of ethanol and butanol on the growth of Clostridium ljungdahlii PETC, C. carboxidivorans P7, and 'Butyribacterium methylotrophicum DSM3468'. Experiments to determine inhibitory effects due to product accumulation were carried out using a synthetic mixture of CO:CO2:H2 as a substrate. These conditions were chosen to mimic gaseous effluents of biomass and waste gasification plants. Inhibition effects were recorded as changes in growth parameters. No significant inhibition was observed for ethanol at concentrations below 15 g/L. The three species exhibited higher sensitivity to butanol. Half inhibition constants for butanol could be estimated for P7 (IC50 = 4.12 g/L), DSM3468 (IC50 = 1.79 g/L), and PETC (IC50 = 9.75 g/L). In conclusion, at least for the tested strains, alcohol toxicity is not an immediate handicap for increasing alcohol production of the tested homoacetogenic strains.}, }
@article {pmid29616281, year = {2018}, author = {Gioacchini, G and Ciani, E and Pessina, A and Cecchini, C and Silvi, S and Rodiles, A and Merrifield, DL and Olivotto, I and Carnevali, O}, title = {Effects of Lactogen 13, a New Probiotic Preparation, on Gut Microbiota and Endocrine Signals Controlling Growth and Appetite of Oreochromis niloticus Juveniles.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {1063-1074}, pmid = {29616281}, issn = {1432-184X}, support = {2201//Ministero dello Sviluppo Economico/International ; }, mesh = {Animal Feed/analysis ; Animals ; *Appetite/drug effects ; Aquaculture ; Cichlids/*growth &amp; development/physiology ; Diet/veterinary ; Endocrine System/*drug effects/physiology ; *Gastrointestinal Microbiome/drug effects ; Lacticaseibacillus rhamnosus/*chemistry ; *Muscle Development/drug effects ; Probiotics/*pharmacology ; Signal Transduction/drug effects/physiology ; }, abstract = {In the present study, Nile tilapia Oreochromis niloticus was used as experimental model to study the molecular effects of a new probiotic preparation, Lactogen 13 (Lactobacillus rhamnosus IMC 501® encapsulated with vegetable fat matrices by spray chilling and further indicated as probiotic microgranules), on growth and appetite during larval development. Probiotic microgranules were administered for 30 days to tilapia larvae starting from first feeding. Molecular analysis using high-throughput sequencing revealed that the probiotic could populate the gastrointestinal tract and modulate the microbial communities by significantly increasing the proportion of Lactobacillus as well as reducing the proportion of potential pathogens such as members of the Family Microbacteriaceae, Legionellaceae, and Weeksellaceae. Morphometric analysis evidenced that body weight and total length significantly increased after probiotic treatment. This increase coincided with the modulation of genes belonging to the insulin-like growth factors (igfs) system and genes involved on myogenesis, such as myogenin, and myogenic differentiation (myod). Alongside the improvement of growth, an increase of feed intake was evidenced at 40 days post-fertilization (dpf) in treated larvae. Gene codifying for signals belonging to the most prominent systems involved in appetite regulation, such as neuropeptide y (npy), agouti-related protein (agrp), leptin, and ghrelin were significantly modulated. These results support the hypothesis that gastrointestinal (GI) microbiota changes due to probiotic administration modulate growth and appetite control, activating the endocrine system of tilapia larvae.}, }
@article {pmid29616009, year = {2018}, author = {Nagy, K and Ábrahám, &#xc1; and Keymer, JE and Galajda, P}, title = {Application of Microfluidics in Experimental Ecology: The Importance of Being Spatial.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {496}, pmid = {29616009}, issn = {1664-302X}, abstract = {Microfluidics is an emerging technology that is used more and more in biology experiments. Its capabilities of creating precisely controlled conditions in cellular dimensions make it ideal to explore cell-cell and cell-environment interactions. Thus, a wide spectrum of problems in microbial ecology can be studied using engineered microbial habitats. Moreover, artificial microfluidic ecosystems can serve as model systems to test ecology theories and principles that apply on a higher level in the hierarchy of biological organization. In this mini review we aim to demonstrate the versatility of microfluidics and the diversity of its applications that help the advance of microbiology, and in more general, experimental ecology.}, }
@article {pmid29615850, year = {2018}, author = {Agustí, A and García-Pardo, MP and López-Almela, I and Campillo, I and Maes, M and Romaní-Pérez, M and Sanz, Y}, title = {Interplay Between the Gut-Brain Axis, Obesity and Cognitive Function.}, journal = {Frontiers in neuroscience}, volume = {12}, number = {}, pages = {155}, pmid = {29615850}, issn = {1662-4548}, abstract = {Obesity continues to be one of the major public health problems due to its high prevalence and co-morbidities. Common co-morbidities not only include cardiometabolic disorders but also mood and cognitive disorders. Obese subjects often show deficits in memory, learning and executive functions compared to normal weight subjects. Epidemiological studies also indicate that obesity is associated with a higher risk of developing depression and anxiety, and vice versa. These associations between pathologies that presumably have different etiologies suggest shared pathological mechanisms. Gut microbiota is a mediating factor between the environmental pressures (e.g., diet, lifestyle) and host physiology, and its alteration could partly explain the cross-link between those pathologies. Westernized dietary patterns are known to be a major cause of the obesity epidemic, which also promotes a dysbiotic drift in the gut microbiota; this, in turn, seems to contribute to obesity-related complications. Experimental studies in animal models and, to a lesser extent, in humans suggest that the obesity-associated microbiota may contribute to the endocrine, neurochemical and inflammatory alterations underlying obesity and its comorbidities. These include dysregulation of the HPA-axis with overproduction of glucocorticoids, alterations in levels of neuroactive metabolites (e.g., neurotransmitters, short-chain fatty acids) and activation of a pro-inflammatory milieu that can cause neuro-inflammation. This review updates current knowledge about the role and mode of action of the gut microbiota in the cross-link between energy metabolism, mood and cognitive function.}, }
@article {pmid29610310, year = {2018}, author = {Friedman, ES and Bittinger, K and Esipova, TV and Hou, L and Chau, L and Jiang, J and Mesaros, C and Lund, PJ and Liang, X and FitzGerald, GA and Goulian, M and Lee, D and Garcia, BA and Blair, IA and Vinogradov, SA and Wu, GD}, title = {Microbes vs. chemistry in the origin of the anaerobic gut lumen.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {16}, pages = {4170-4175}, pmid = {29610310}, issn = {1091-6490}, support = {R01 EB018464/EB/NIBIB NIH HHS/United States ; R24 NS092986/NS/NINDS NIH HHS/United States ; P30 DK050306/DK/NIDDK NIH HHS/United States ; T32 CA009140/CA/NCI NIH HHS/United States ; P30 ES013508/ES/NIEHS NIH HHS/United States ; P42 ES023720/ES/NIEHS NIH HHS/United States ; R01 GM080279/GM/NIGMS NIH HHS/United States ; R01 AI118891/AI/NIAID NIH HHS/United States ; R01 GM103591/GM/NIGMS NIH HHS/United States ; }, mesh = {*Anaerobiosis ; Animals ; Bacteria, Anaerobic/isolation &amp; purification/*metabolism ; Computer Systems ; Gastric Mucosa/metabolism ; Gastrointestinal Contents/chemistry ; *Gastrointestinal Microbiome ; Germ-Free Life ; Intestinal Mucosa/*metabolism ; Lipids/chemistry ; Luminescent Measurements ; Metalloporphyrins/analysis ; Mice ; Mice, Inbred C57BL ; Oxidation-Reduction ; Oxygen/analysis/*metabolism ; Oxygen Consumption ; Proteins/chemistry ; }, abstract = {The succession from aerobic and facultative anaerobic bacteria to obligate anaerobes in the infant gut along with the differences between the compositions of the mucosally adherent vs. luminal microbiota suggests that the gut microbes consume oxygen, which diffuses into the lumen from the intestinal tissue, maintaining the lumen in a deeply anaerobic state. Remarkably, measurements of luminal oxygen levels show nearly identical pO2 (partial pressure of oxygen) profiles in conventional and germ-free mice, pointing to the existence of oxygen consumption mechanisms other than microbial respiration. In vitro experiments confirmed that the luminal contents of germ-free mice are able to chemically consume oxygen (e.g., via lipid oxidation reactions), although at rates significantly lower than those observed in the case of conventionally housed mice. For conventional mice, we also show that the taxonomic composition of the gut microbiota adherent to the gut mucosa and in the lumen throughout the length of the gut correlates with oxygen levels. At the same time, an increase in the biomass of the gut microbiota provides an explanation for the reduction of luminal oxygen in the distal vs. proximal gut. These results demonstrate how oxygen from the mammalian host is used by the gut microbiota, while both the microbes and the oxidative chemical reactions regulate luminal oxygen levels, shaping the composition of the microbial community throughout different regions of the gut.}, }
@article {pmid29609653, year = {2018}, author = {De Vrieze, J and Pinto, AJ and Sloan, WT and Ijaz, UZ}, title = {The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {63}, pmid = {29609653}, issn = {2049-2618}, support = {NE/L011956/1//Natural Environment Research Council/International ; EP/M016811/1//Engineering and Physical Sciences Research Council/International ; }, mesh = {*Anaerobiosis ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Biodiversity ; Metagenomics/methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Amplicon sequencing methods targeting the 16S rRNA gene have been used extensively to investigate microbial community composition and dynamics in anaerobic digestion. These methods successfully characterize amplicons but do not distinguish micro-organisms that are actually responsible for the process. In this research, the archaeal and bacterial community of 48 full-scale anaerobic digestion plants were evaluated on DNA (total community) and RNA (active community) level via 16S rRNA (gene) amplicon sequencing.<br><br>RESULTS: A significantly higher diversity on DNA compared with the RNA level was observed for archaea, but not for bacteria. Beta diversity analysis showed a significant difference in community composition between the DNA and RNA of both bacteria and archaea. This related with 25.5 and 42.3% of total OTUs for bacteria and archaea, respectively, that showed a significant difference in their DNA and RNA profiles. Similar operational parameters affected the bacterial and archaeal community, yet the differentiating effect between DNA and RNA was much stronger for archaea. Co-occurrence networks and functional prediction profiling confirmed the clear differentiation between DNA and RNA profiles.<br><br>CONCLUSIONS: In conclusion, a clear difference in active (RNA) and total (DNA) community profiles was observed, implying the need for a combined approach to estimate community stability in anaerobic digestion.}, }
@article {pmid29607983, year = {2018}, author = {Katsimichas, T and Ohtani, T and Motooka, D and Tsukamoto, Y and Kioka, H and Nakamoto, K and Konishi, S and Chimura, M and Sengoku, K and Miyawaki, H and Sakaguchi, T and Okumura, R and Theofilis, K and Iida, T and Takeda, K and Nakamura, S and Sakata, Y}, title = {Non-Ischemic Heart Failure With Reduced Ejection Fraction Is Associated With Altered Intestinal Microbiota.}, journal = {Circulation journal : official journal of the Japanese Circulation Society}, volume = {82}, number = {6}, pages = {1640-1650}, doi = {10.1253/circj.CJ-17-1285}, pmid = {29607983}, issn = {1347-4820}, mesh = {Bacteroidetes/isolation &amp; purification ; Case-Control Studies ; Classification ; DNA, Bacterial/isolation &amp; purification ; Gastrointestinal Microbiome/genetics/*physiology ; Heart Failure/*microbiology/physiopathology ; Humans ; RNA, Ribosomal, 16S/analysis ; Streptococcus/isolation &amp; purification ; *Stroke Volume ; Veillonella/isolation &amp; purification ; }, abstract = {BACKGROUND: Research suggests that heart failure with reduced ejection fraction (HFrEF) is a state of systemic inflammation that may be triggered by microbial products passing into the bloodstream through a compromised intestinal barrier. However, whether the intestinal microbiota exhibits dysbiosis in HFrEF patients is largely unknown.<br><br>Twenty eight non-ischemic HFrEF patients and 19 healthy controls were assessed by 16S rRNA analysis of bacterial DNA extracted from stool samples. After processing of sequencing data, bacteria were taxonomically classified, diversity indices were used to examine microbial ecology, and relative abundances of common core genera were compared between groups. Furthermore, we predicted gene carriage for bacterial metabolic pathways and inferred microbial interaction networks on multiple taxonomic levels.Bacterial communities of both groups were dominated by the Firmicutes and Bacteroidetes phyla. The most abundant genus in both groups wasBacteroides. Although &#x3b1; diversity did not differ between groups, ordination by &#x3b2; diversity metrics revealed a separation of the groups across components of variation.StreptococcusandVeillonellawere enriched in the common core microbiota of patients, whileSMB53was depleted. Gene families in amino acid, carbohydrate, vitamin, and xenobiotic metabolism showed significant differences between groups. Interaction networks revealed a higher degree of correlations between bacteria in patients.<br><br>CONCLUSIONS: Non-ischemic HFrEF patients exhibited multidimensional differences in intestinal microbial communities compared with healthy subjects.}, }
@article {pmid29595416, year = {2018}, author = {Pavan, ME and Pavan, EE and Glaeser, SP and Etchebehere, C and Kämpfer, P and Pettinari, MJ and López, NI}, title = {Proposal for a new classification of a deep branching bacterial phylogenetic lineage: transfer of Coprothermobacter proteolyticus and Coprothermobacter platensis to Coprothermobacteraceae fam. nov., within Coprothermobacterales ord. nov., Coprothermobacteria classis nov. and Coprothermobacterota phyl. nov. and emended description of the family Thermodesulfobiaceae.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {68}, number = {5}, pages = {1627-1632}, doi = {10.1099/ijsem.0.002720}, pmid = {29595416}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Firmicutes/*classification ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The genus Coprothermobacter (initially named Thermobacteroides) is currently placed within the phylum Firmicutes. Early 16S rRNA gene based phylogenetic studies pointed out the great differences between Coprothermobacter and other members of the Firmicutes, revealing that it constitutes a new deep branching lineage. Over the years, several studies based on 16S rRNA gene and whole genome sequences have indicated that Coprothermobacter is very distant phylogenetically to all other bacteria, supporting its placement in a distinct deeply rooted novel phylum. In view of this, we propose its allocation to the new family Coprothermobacteraceae within the novel order Coprothermobacterales, the new class Coprothermobacteria, and the new phylum Coprothermobacterota, and an emended description of the family Thermodesulfobiaceae.}, }
@article {pmid29594431, year = {2018}, author = {Tall, S and Meyling, NV}, title = {Probiotics for Plants? Growth Promotion by the Entomopathogenic Fungus Beauveria bassiana Depends on Nutrient Availability.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {1002-1008}, pmid = {29594431}, issn = {1432-184X}, support = {331125//FP7 People: Marie-Curie Actions/ ; }, mesh = {Beauveria/*physiology ; Nutrients/metabolism ; Pest Control, Biological ; Probiotics/*analysis ; Zea mays/*growth &amp; development/metabolism/microbiology ; }, abstract = {Cultivation of crops requires nutrient supplements which are costly and impact the environment. Furthermore, global demands for increased crop production call for sustainable solutions to increase yield and utilize resources such as nutrients more effectively. Some entomopathogenic fungi are able to promote plant growth, but studies over such effects have been conducted under optimal conditions where nutrients are abundantly available. We studied the effects of Beauveria bassiana (strain GHA) seed treatment on the growth of maize (Zea mays) at high and low nutrient conditions during 6 weeks in greenhouse. As expected, B. bassiana seed treatment increased plant growth, but only at high nutrient conditions. In contrast, the seed treatment did not benefit plant growth at low nutrient conditions where the fungus potentially constituted a sink and tended to reduce plant growth. The occurrence of endophytic B. bassiana in experimental plant tissues was evaluated by PCR after 6 weeks, but B. bassiana was not documented in any of the above-ground plant tissues indicating that the fungus-plant interaction was independent of endophytic establishment. Our results suggest that B. bassiana seed treatment could be used as a growth promoter of maize when nutrients are abundantly available, while the fungus does not provide any growth benefits when nutrients are scarce.}, }
@article {pmid29594071, year = {2018}, author = {Ji, S and Jiang, T and Yan, H and Guo, C and Liu, J and Su, H and Alugongo, GM and Shi, H and Wang, Y and Cao, Z and Li, S}, title = {Ecological Restoration of Antibiotic-Disturbed Gastrointestinal Microbiota in Foregut and Hindgut of Cows.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {79}, pmid = {29594071}, issn = {2235-2988}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/genetics/*isolation &amp; purification ; Cattle ; Female ; Gastrointestinal Microbiome/*drug effects ; Lactation ; Rectum/*microbiology ; Rumen/*microbiology ; }, abstract = {Antibiotically disturbed gastrointestinal microbiota needs a long period time to be restored to normal, which may cause a series of problems to the host. The understanding of restoration of the biased microbiota by antibiotics remains largely unknown. Here, we investigated the microbiota shift in foregut (rumen) and hindgut (rectum) of lactating cows after antibiotics exposure as well as after antibiotics withdrawal with (Microbiota transplantation, MT group) or without (Control, CON group) microbiota transplantation. We were able to demonstrate that microbiota in both foregut and hindgut significantly changed after 3 or 14 days of antibiotics exposure, and the changes persisted over long period of time (>18 days) after withdrawing the antibiotics. We further observed a faster restoration of microbiota in both foregut and hindgut of MT group than CON group, microbiota in foregut was mainly benefited from microbiota transplantation by restoring the alpha-diversity as well as within-group similarity, while microbiota in hindgut was primarily benefited from microbiota transplantation by reestablishing the co-occurrence network (nodes number, edges number, density, modularity as well as closeness centrality). These results together expanded our understanding of restoration of the biased microbiota by antibiotics, and may also be instructive to deal with the delayed microbiota restoration at least in cows.}, }
@article {pmid29593687, year = {2018}, author = {Wein, T and Dagan, T and Fraune, S and Bosch, TCG and Reusch, TBH and Hülter, NF}, title = {Carrying Capacity and Colonization Dynamics of Curvibacter in the Hydra Host Habitat.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {443}, pmid = {29593687}, issn = {1664-302X}, support = {281357/ERC_/European Research Council/International ; }, abstract = {Most eukaryotic species are colonized by a microbial community - the microbiota - that is acquired during early life stages and is critical to host development and health. Much research has focused on the microbiota biodiversity during the host life, however, empirical data on the basic ecological principles that govern microbiota assembly is lacking. Here we quantify the contribution of colonizer order, arrival time and colonization history to microbiota assembly on a host. We established the freshwater polyp Hydra vulgaris and its dominant colonizer Curvibacter as a model system that enables the visualization and quantification of colonizer population size at the single cell resolution, in vivo, in real time. We estimate the carrying capacity of a single Hydra polyp as 2 × 10[5]Curvibacter cells, which is robust among individuals and time. Colonization experiments reveal a clear priority effect of first colonizers that depends on arrival time and colonization history. First arriving colonizers achieve a numerical advantage over secondary colonizers within a short time lag of 24 h. Furthermore, colonizers primed for the Hydra habitat achieve a numerical advantage in the absence of a time lag. These results follow the theoretical expectations for any bacterial habitat with a finite carrying capacity. Thus, Hydra colonization and succession processes are largely determined by the habitat occupancy over time and Curvibacter colonization history. Our experiments provide empirical data on the basic steps of host-associated microbiota establishment - the colonization stage. The presented approach supplies a framework for studying habitat characteristics and colonization dynamics within the host-microbe setting.}, }
@article {pmid29593685, year = {2018}, author = {Pushkarev, A and Hevroni, G and Roitman, S and Shim, JG and Choi, A and Jung, KH and Béjà, O}, title = {The Use of a Chimeric Rhodopsin Vector for the Detection of New Proteorhodopsins Based on Color.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {439}, pmid = {29593685}, issn = {1664-302X}, abstract = {Student microbial ecology laboratory courses are often conducted as condensed courses in which theory and wet lab work are combined in a very intensive short time period. In last decades, the study of marine microbial ecology is increasingly reliant on molecular-based methods, and as a result many of the research projects conducted in such courses require sequencing that is often not available on site and may take more time than a typical course allows. In this work, we describe a protocol combining molecular and functional methods for analyzing proteorhodopsins (PRs), with visible results in only 4-5 days that do not rely on sequencing. PRs were discovered in oceanic surface waters two decades ago, and have since been observed in different marine environments and diverse taxa, including the abundant alphaproteobacterial SAR11 group. PR subgroups are currently known to absorb green and blue light, and their distribution was previously explained by prevailing light conditions - green pigments at the surface and blue pigments in deeper waters, as blue light travels deeper in the water column. To detect PR in environmental samples, we created a chimeric plasmid suitable for direct expression of PRs using PCR amplification and functional analysis in Escherichia coli cells. Using this assay, we discovered several exceptional cases of PRs whose phenotypes differed from those predicted based on sequence only, including a previously undescribed yellow-light absorbing PRs. We applied this assay in two 10-days marine microbiology courses and found it to greatly enhance students' laboratory experience, enabling them to gain rapid visual feedback and colorful reward for their work. Furthermore we expect this assay to promote the use of functional assays for the discovery of new rhodopsin variants.}, }
@article {pmid29582105, year = {2018}, author = {Bani, A and Borruso, L and Fornasier, F and Pioli, S and Wellstein, C and Brusetti, L}, title = {Microbial Decomposer Dynamics: Diversity and Functionality Investigated through a Transplantation Experiment in Boreal Forests.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {1030-1040}, pmid = {29582105}, issn = {1432-184X}, support = {I52I14000410005//Libera Universit&#xe0; di Bolzano/ ; }, mesh = {Bacteria/*metabolism ; Carbon/*analysis ; Fagus/growth &amp; development ; *Forests ; Italy ; *Microbiota ; Nitrogen/*analysis ; Plant Leaves/*chemistry ; Quercus/growth &amp; development ; Rhododendron/growth &amp; development ; *Soil Microbiology ; }, abstract = {Litter decomposition is the main source of mineral nitrogen (N) in terrestrial ecosystem and a key step in carbon (C) cycle. Microbial community is the main decomposer, and its specialization on specific litter is considered at the basis of higher decomposition rate in its natural environment than in other forests. However, there are contrasting evidences on how the microbial community responds to a new litter input and if the mass loss is higher in natural environment. We selected leaf litter from three different plant species across three sites of different altitudinal ranges: oak (Quercus petraea (Matt.) Liebl., 530 m a.s.l), beech (Fagus sylvatica L., 1000 m a.s.l.), rhododendron (Rhododendron ferrugineum L., 1530 m a.s.l.). A complete transplantation experiment was set up within the native site and the other two altitudinal sites. Microbial community structure was analyzed via amplified ribosomal intergenic spacer analysis (ARISA) fingerprinting. Functionality was investigated by potential enzyme activities. Chemical composition of litter was recorded. Mass loss showed no faster decomposition rate on native site. Similarly, no influence of site was found on microbial structure, while there was a strong temporal variation. Potential enzymatic activities were not affected by the same temporal pattern with a general increase of activities during autumn. Our results suggested that no specialization in microbial community is present due to the lack of influence of the site in structure and in the mass loss dynamics. Finally, different temporal patterns in microbial community and potential enzymatic activities suggest the presence of functional redundancy within decomposers.}, }
@article {pmid29580477, year = {2018}, author = {Wedel, C and Wunsch, A and Wenning, M and Dettling, A and Kayser, KH and Lehner, WD and Hinrichs, J}, title = {Thermal treatment of skim milk concentrates in a novel shear-heating device: Reduction of thermophilic spores and physical properties.}, journal = {Food research international (Ottawa, Ont.)}, volume = {107}, number = {}, pages = {19-26}, doi = {10.1016/j.foodres.2018.02.005}, pmid = {29580477}, issn = {1873-7145}, mesh = {Animals ; Anoxybacillus/*growth &amp; development ; Color ; Equipment Design ; Food Handling/*instrumentation/methods ; Food Microbiology/*instrumentation/methods ; Heating/*instrumentation ; Hot Temperature ; Maillard Reaction ; Microbial Viability ; Milk/*microbiology ; Particle Size ; Powders ; Spores, Bacterial/*growth &amp; development ; }, abstract = {Endospores of thermophilic bacilli are a major concern for producers of dairy powders. In this study, we heat treated 10 different spore suspensions at 110 °C in skim milk and skim milk concentrate (36% dry matter) of the species Geobacillus stearothermophilus (10 min) and Anoxybacillus flavithermus (5 min) in a new shear-heating device. The highest log reduction in skim milk concentrate was 3.5. The death behavior of the spores was strain dependent. Particle formation and Maillard reaction were observed. By increasing the shear-rate up to 1500 s[-1] the particle size was reduced for both heating times (D90 reduction: 57.4 and 77.0%, respectively). The particle size was lessened by a reduction of dry matter of 27%, compared to 36%. This work emphasizes, that heat treatment of concentrated dairy products represents a technological option to reduce thermophilic spores in skim milk concentrate and powders produced thereof.}, }
@article {pmid29579103, year = {2018}, author = {Geldenhuys, M and Mortlock, M and Weyer, J and Bezuidt, O and Seamark, ECJ and Kearney, T and Gleasner, C and Erkkila, TH and Cui, H and Markotter, W}, title = {A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0194527}, pmid = {29579103}, issn = {1932-6203}, mesh = {Adenoviridae/genetics/pathogenicity ; Animals ; Chiroptera/physiology/*virology ; Computational Biology ; Coronavirus/genetics/pathogenicity ; Coronavirus Infections/veterinary/*virology ; Gastrointestinal Tract/physiology/virology ; Genetic Variation ; Genome, Viral/*genetics ; Herpesviridae/genetics/pathogenicity ; High-Throughput Nucleotide Sequencing ; Humans ; Mammals/*virology ; Metagenomics/methods ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; South Africa ; Zoonoses/*virology ; }, abstract = {Species within the Neoromicia bat genus are abundant and widely distributed in Africa. It is common for these insectivorous bats to roost in anthropogenic structures in urban regions. Additionally, Neoromicia capensis have previously been identified as potential hosts for Middle East respiratory syndrome (MERS)-related coronaviruses. This study aimed to ascertain the gastrointestinal virome of these bats, as viruses excreted in fecal material or which may be replicating in rectal or intestinal tissues have the greatest opportunities of coming into contact with other hosts. Samples were collected in five regions of South Africa over eight years. Initial virome composition was determined by viral metagenomic sequencing by pooling samples and enriching for viral particles. Libraries were sequenced on the Illumina MiSeq and NextSeq500 platforms, producing a combined 37 million reads. Bioinformatics analysis of the high throughput sequencing data detected the full genome of a novel species of the Circoviridae family, and also identified sequence data from the Adenoviridae, Coronaviridae, Herpesviridae, Parvoviridae, Papillomaviridae, Phenuiviridae, and Picornaviridae families. Metagenomic sequencing data was insufficient to determine the viral diversity of certain families due to the fragmented coverage of genomes and lack of suitable sequencing depth, as some viruses were detected from the analysis of reads-data only. Follow up conventional PCR assays targeting conserved gene regions for the Adenoviridae, Coronaviridae, and Herpesviridae families were used to confirm metagenomic data and generate additional sequences to determine genetic diversity. The complete coding genome of a MERS-related coronavirus was recovered with additional amplicon sequencing on the MiSeq platform. The new genome shared 97.2% overall nucleotide identity to a previous Neoromicia-associated MERS-related virus, also from South Africa. Conventional PCR analysis detected diverse adenovirus and herpesvirus sequences that were widespread throughout Neoromicia populations in South Africa. Furthermore, similar adenovirus sequences were detected within these populations throughout several years. With the exception of the coronaviruses, the study represents the first report of sequence data from several viral families within a Southern African insectivorous bat genus; highlighting the need for continued investigations in this regard.}, }
@article {pmid29577673, year = {2018}, author = {Ghosh, D and Bhadury, P and Routh, J}, title = {Coping with arsenic stress: Adaptations of arsenite-oxidizing bacterial membrane lipids to increasing arsenic levels.}, journal = {MicrobiologyOpen}, volume = {7}, number = {5}, pages = {e00594}, pmid = {29577673}, issn = {2045-8827}, mesh = {Adaptation, Physiological ; Arsenites/*metabolism/*toxicity ; Bacteria/classification/*drug effects/growth &amp; development/isolation &amp; purification ; Groundwater/*microbiology ; Membrane Lipids/*metabolism ; Oxidation-Reduction ; Phospholipids/metabolism ; }, abstract = {Elevated levels of arsenic (As) in aquifers of South East Asia have caused diverse health problems affecting millions of people who drink As-rich groundwater and consume various contaminated agriculture products. The biogeochemical cycling and mobilization/immobilization of As from its mineral-bound phase is controlled by pH, oxic/anoxic conditions, and different microbial processes. The increased As flux generated from ongoing biogeochemical processes in the subsurface in turn affects the in situ microbial communities. This study analyzes how the indigenous arsenite-oxidizing bacteria combat As stress by various biophysical alterations and self-adaptation mechanisms. Fifteen arsenite-oxidizing bacterial strains were isolated and identified using a polyphasic approach. The bacterial strains isolated from these aquifers belong predominantly to arsenite-oxidizing bacterial groups. Of these, the membrane-bound phospholipid fatty acids (PLFA) were characterized in seven selected bacterial isolates grown at different concentrations of As(III) in the medium. One of the significant findings of this study is how the increase in external stress can induce alteration of membrane PLFAs. The change in fatty acid saturation and alteration of their steric conformation suggests alteration of membrane fluidity due to change in As-related stress. However, different bacterial groups can have different degrees of alteration that can affect sustainability in As-rich aquifers of the Bengal Delta Plain.}, }
@article {pmid29577643, year = {2018}, author = {Hussain, M and Akutse, KS and Lin, Y and Chen, S and Huang, W and Zhang, J and Idrees, A and Qiu, D and Wang, L}, title = {Susceptibilities of Candidatus Liberibacter asiaticus-infected and noninfected Diaphorina citri to entomopathogenic fungi and their detoxification enzyme activities under different temperatures.}, journal = {MicrobiologyOpen}, volume = {7}, number = {6}, pages = {e00607}, pmid = {29577643}, issn = {2045-8827}, mesh = {Animals ; Citrus/microbiology ; Cytochrome P-450 Enzyme System/metabolism ; Esterases/metabolism ; Glutathione Transferase/metabolism ; Hemiptera/*enzymology/*microbiology/physiology ; Insect Proteins/*metabolism ; Insect Vectors/*microbiology/physiology ; Plant Diseases/microbiology ; Rhizobiaceae/pathogenicity/*physiology ; Temperature ; Virulence ; }, abstract = {Some entomopathogenic fungi species, Isaria fumosorosea, and Hirsutella citriformis were found to be efficient against the Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Liviidae). However, the susceptibility to these fungi increases when the psyllid infected with Candidatus Liberibacter asiaticus (Las), which is transmitted by D. citri and causes citrus greening disease. In this study, we examined the Las-infected and Las-uninfected D. citri susceptibility to entomopathogenic fungi at different temperature regimes (5-40°C). When D. citri adults exposed to cold temperature (5°C), they showed less susceptibility to entomopathogenic fungi as compared with control (27°C). Irrespective of infection with Las, a significantly positive correlation was observed between temperature and percentage mortality caused by different isolates of I. fumosorosea, 3A Ifr, 5F Ifr, PS Ifr, and H. citriformis isolates, HC3D and 2H. In contrast, a significantly negative correlation was found between temperature and percentage mortality for 3A Ifr for both Las-infected and Las-uninfected psyllids. Detoxification enzymes, Glutathione S-transferase levels in D. citri showed a negative correlation, whereas cytochrome P450 and general esterase levels were not correlated with changes in temperature. These findings revealed that detoxification enzymes and general esterase levels are not correlated with altered susceptibility to entomopathogenic fungi at the different temperature regimes. Conclusively, temperature fluctuations tested appear to be a significant factor impacting the management strategies of D. citri using entomopathogenic fungi.}, }
@article {pmid29577296, year = {2018}, author = {Slomka, V and Herrero, ER and Boon, N and Bernaerts, K and Trivedi, HM and Daep, C and Quirynen, M and Teughels, W}, title = {Oral prebiotics and the influence of environmental conditions in vitro.}, journal = {Journal of periodontology}, volume = {89}, number = {6}, pages = {708-717}, doi = {10.1002/JPER.17-0437}, pmid = {29577296}, issn = {1943-3670}, mesh = {Bacteria ; *Microbiota ; Prebiotics ; *Probiotics ; }, abstract = {BACKGROUND: Only recently the concept of prebiotics has been introduced in oral health. Few potential oral prebiotics have already been identified in dual species competition assays, showing a stimulatory effect on beneficial bacteria and by this suppressing the outgrowth of pathogenic species. This study aimed to validate the effect of previously identified potential prebiotic substrates on multispecies cultures by shifting the biofilm composition towards a more beneficial species dominated microbiota.<br><br>METHODS: A chemostat culture containing 14 model oral bacterial species was used to grow biofilms for 24&#xa0;hours which subsequently were treated with prebiotic solutions three times a day for 3 consecutive days. Further the influence of environmental factors such as pH, nutrient availability, oxygen concentration and prebiotic dose on the efficacy of the prebiotic substances was investigated.<br><br>RESULTS: Three potential prebiotic substrates N-acetyl-D-mannosamine, succinic acid and Met-Pro were able to bring the beneficial proportion to&#xa0;>&#xa0;95%. While the pH of the prebiotic solution did not have an influence on the prebiotic effect, the interplay of nutrient availability, oxygen concentration and prebiotic treatment resulted in significant changes of the microbial composition identifying N-acetyl-D-mannosamine as the most promising oral prebiotic substrate. Showing a clear dose dependent effect, concentrations of N-acetyl-D-mannosamine of 1.0 and 1.5&#xa0;M resulted in a biofilm composition of 97% beneficial species.<br><br>CONCLUSION: Introducing the prebiotic concept in oral health might reveal a valid approach for treatment and prevention of oral diseases and promote oral health.}, }
@article {pmid29577086, year = {2018}, author = {Minich, JJ and Zhu, Q and Janssen, S and Hendrickson, R and Amir, A and Vetter, R and Hyde, J and Doty, MM and Stillwell, K and Benardini, J and Kim, JH and Allen, EE and Venkateswaran, K and Knight, R}, title = {KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples.}, journal = {mSystems}, volume = {3}, number = {3}, pages = {}, pmid = {29577086}, issn = {2379-5077}, abstract = {Microbiome analyses of low-biomass samples are challenging because of contamination and inefficiencies, leading many investigators to employ low-throughput methods with minimal controls. We developed a new automated protocol, KatharoSeq (from the Greek katharos [clean]), that outperforms single-tube extractions while processing at least five times as fast. KatharoSeq incorporates positive and negative controls to reveal the whole bacterial community from inputs of as few as 50 cells and correctly identifies 90.6% (standard error, 0.013%) of the reads from 500 cells. To demonstrate the broad utility of KatharoSeq, we performed 16S rRNA amplicon and shotgun metagenome analyses of the Jet Propulsion Laboratory spacecraft assembly facility (SAF; n = 192, 96), 52 rooms of a neonatal intensive care unit (NICU; n = 388, 337), and an endangered-abalone-rearing facility (n = 192, 123), obtaining spatially resolved, unique microbiomes reproducible across hundreds of samples. The SAF, our primary focus, contains 32 sOTUs (sub-OTUs, defined as exact sequence matches) and their inferred variants identified by the deblur algorithm, with four (Acinetobacter lwoffii, Paracoccus marcusii, Mycobacterium sp., and Novosphingobium) being present in >75% of the samples. According to microbial spatial topography, the most abundant cleanroom contaminant, A. lwoffii, is related to human foot traffic exposure. In the NICU, we have been able to discriminate environmental exposure related to patient infectious disease, and in the abalone facility, we show that microbial communities reflect the marine environment rather than human input. Consequently, we demonstrate the feasibility and utility of large-scale, low-biomass metagenomic analyses using the KatharoSeq protocol. IMPORTANCE Various indoor, outdoor, and host-associated environments contain small quantities of microbial biomass and represent a niche that is often understudied because of technical constraints. Many studies that attempt to evaluate these low-biomass microbiome samples are riddled with erroneous results that are typically false positive signals obtained during the sampling process. We have investigated various low-biomass kits and methods to determine the limit of detection of these pipelines. Here we present KatharoSeq, a high-throughput protocol combining laboratory and bioinformatic methods that can differentiate a true positive signal in samples with as few as 50 to 500 cells. We demonstrate the application of this method in three unique low-biomass environments, including a SAF, a hospital NICU, and an abalone-rearing facility.}, }
@article {pmid29574496, year = {2018}, author = {Courty, PE and Buée, M and Tech, JJT and Brulé, D and Colin, Y and Leveau, JHJ and Uroz, S}, title = {Impact of soil pedogenesis on the diversity and composition of fungal communities across the California soil chronosequence of Mendocino.}, journal = {Mycorrhiza}, volume = {28}, number = {4}, pages = {343-356}, doi = {10.1007/s00572-018-0829-9}, pmid = {29574496}, issn = {1432-1890}, mesh = {California ; DNA, Fungal/analysis ; Fungi/*classification ; *Microbiota ; Mycorrhizae/classification/isolation &amp; purification ; Sequence Analysis, DNA ; Soil/*classification ; *Soil Microbiology ; }, abstract = {Understanding how soil pedogenesis affects microbial communities and their in situ activities according to ecosystem functioning is a central issue in soil microbial ecology, as soils represent essential nutrient reservoirs and habitats for the biosphere. To address this question, soil chronosequences developed from a single, shared mineralogical parent material and having the same climate conditions are particularly useful, as they isolate the factor of time from other factors controlling the character of soils. In our study, we considered a natural succession of uplifted marine terraces in Mendocino, CA, ranging from highly fertile in the younger terrace (about 100,000 years old) to infertile in the older terraces (about 300,000 years old). Using ITS amplicon pyrosequencing, we analysed and compared the diversity and composition of the soil fungal communities across the first terraces (T1 to T3), with a specific focus in the forested terraces (T2 and T3) on soil samples collected below trees of the same species (Pinus muricata) and of the same age. While diversity and richness indices were highest in the grassland (youngest) terrace (T1), they were higher in the older forested terrace (T3) compared to the younger forested terrace (T2). Interestingly, the most abundant ectomycorrhizal (ECM) taxa that we found within these fungal communities showed high homology with ITS Sanger sequences obtained previously directly from ECM root tips from trees in the same study site, revealing a relative conservation of ECM diversity over time. Altogether, our results provide new information about the diversity and composition of the fungal communities as well as on the dominant ECM species in the soil chronosequence of Mendocino in relation to soil age and ecosystem development.}, }
@article {pmid29573631, year = {2018}, author = {Subirats, J and Timoner, X and Sànchez-Melsió, A and Balcázar, JL and Acuña, V and Sabater, S and Borrego, CM}, title = {Emerging contaminants and nutrients synergistically affect the spread of class 1 integron-integrase (intI1) and sul1 genes within stable streambed bacterial communities.}, journal = {Water research}, volume = {138}, number = {}, pages = {77-85}, doi = {10.1016/j.watres.2018.03.025}, pmid = {29573631}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; Bacteria/genetics ; Bacterial Proteins/*genetics ; Ciprofloxacin ; Diclofenac ; Drug Resistance, Microbial/*genetics ; Erythromycin ; *Genes, Bacterial ; Integrases/*genetics ; Parabens ; Rivers/*microbiology ; Sulfamethoxazole ; Wastewater ; *Water Pollutants ; }, abstract = {Wastewater effluents increase the nutrient load of receiving streams while introducing a myriad of anthropogenic chemical pollutants that challenge the resident aquatic (micro)biota. Disentangling the effects of both kind of stressors and their potential interaction on the dissemination of antibiotic resistance genes in bacterial communities requires highly controlled manipulative experiments. In this work, we investigated the effects of a combined regime of nutrients (at low, medium and high concentrations) and a mixture of emerging contaminants (ciprofloxacin, erythromycin, sulfamethoxazole, diclofenac, and methylparaben) on the bacterial composition, abundance and antibiotic resistance profile of biofilms grown in artificial streams. In particular, we investigated the effect of this combined stress on genes encoding resistance to ciprofloxacin (qnrS), erythromycin (ermB), sulfamethoxazole (sul1 and sul2) as well as the class 1 integron-integrase gene (intI1). Only genes conferring resistance to sulfonamides (sul1 and sul2) and intI1 gene were detected in all treatments during the study period. Besides, bacterial communities exposed to emerging contaminants showed higher copy numbers of sul1 and intI1 genes than those not exposed, whereas nutrient amendments did not affect their abundance. However, bacterial communities exposed to both emerging contaminants and a high nutrient concentration (1, 25 and 1 mg L[-1] of phosphate, nitrate and ammonium, respectively) showed the highest increase on the abundance of sul1 and intI1 genes thus suggesting a factors synergistic effect of both stressors. Since none of the treatments caused a significant change on the composition of bacterial communities, the enrichment of sul1 and intI1 genes within the community was caused by their dissemination under the combined pressure exerted by nutrients and emerging contaminants. To the best of our knowledge, this is the first study demonstrating the contribution of nutrients on the maintenance and spread of antibiotic resistance genes in streambed biofilms under controlled conditions. Our results also highlight that nutrients could enhance the effect of emerging contaminants on the dissemination of antibiotic resistance.}, }
@article {pmid29573318, year = {2018}, author = {Fuentes, L and Braga, L and Castelló, E and Etchebehere, C}, title = {Work scheme to isolate the different micro-organisms found in hydrogen-producing reactors: a study of effectiveness by pyrosequencing analysis.}, journal = {Journal of applied microbiology}, volume = {125}, number = {1}, pages = {96-110}, doi = {10.1111/jam.13763}, pmid = {29573318}, issn = {1365-2672}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Bioreactors/*microbiology ; Cheese/microbiology ; Coculture Techniques ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/standards ; *Hydrogen ; Microbial Interactions ; RNA, Ribosomal, 16S/genetics ; Whey/microbiology ; *Workflow ; }, abstract = {AIM: The aim of this research was to create a work scheme for the isolation of the different micro-organisms commonly found in hydrogen-producing reactors and to test its effectiveness.<br><br>METHODS AND RESULTS: Methods were selected to isolate anaerobic spore-forming fermenters, anaerobic fermenters that do not form spores, facultative aerobic fermenters and lactic acid bacteria. The methods were tested in two samples taken from a hydrogen-producing reactor fed with cheese whey. 16S rRNA gene sequences from isolates were compared with pyrosequencing analysis from the same samples. The isolates represented more than 88% of the abundance detected by pyrosequencing. Organisms from the genera Clostridium, Rahnella, Megasphaera, Lactobacillus, Propionibacterium, Bifidobacterium, Chryseobacterium and Acetobacter were isolated. Hydrogen-producing capacity was confirmed for the Clostridium, Rahnella and Megasphaera isolates. Coculture experiments indicate that Megasphaera prevented the total inhibition of Clostridium by Lactobacillus.<br><br>CONCLUSION: The work scheme proposed was effective to isolate most of the micro-organisms detected by pyrosequencing analysis. Physiological studies suggested a key role of Megasphaera.<br><br>We showed the high culturability of the microbial communities from hydrogen-producing bioreactors. The isolates can be used to perform physiological studies to understand the H2 -producing process.}, }
@article {pmid29571392, year = {2018}, author = {Lim, JH and Lee, CW and Bong, CW and Affendi, YA and Hii, YS and Kudo, I}, title = {Distributions of particulate and dissolved phosphorus in aquatic habitats of Peninsular Malaysia.}, journal = {Marine pollution bulletin}, volume = {128}, number = {}, pages = {415-427}, doi = {10.1016/j.marpolbul.2018.01.037}, pmid = {29571392}, issn = {1879-3363}, mesh = {Alkaline Phosphatase/analysis ; Aquaculture ; Ecosystem ; Environmental Monitoring/*methods ; *Estuaries ; Lakes/*chemistry ; Malaysia ; Phosphorus/*analysis ; Salinity ; Seawater/*chemistry ; Solubility ; Temperature ; }, abstract = {Particulate phosphorus was the dominant phosphorus species and accounted for 72 ± 5% of total phosphorus in coastal habitats, 63 ± 4% in estuaries, 58 ± 6% in lakes and 80 ± 7% in aquaculture farms whereas dissolved inorganic phosphorus (DIP) and dissolved organic phosphorus (DOP) were minor components. Correlation analyses (DIP vs Chl a; R[2] = 0.407, df = 31, p < 0.001) suggested phosphorus limiting conditions in lakes, which was corroborated with the highest alkaline phosphatase activity (APA) that fluctuated from 0.38 to 41.14 nmol L[-1] min[-1]. In contrast, APA was elevated in coastal habitats and estuaries only when DIP concentration decreased below 0.9 μM. Moreover size-fractionation experiment showed that the highest APA was detected in the 0.2-2 μm pico-size fraction. Our results suggested that the main APA in coastal habitats and estuaries was from phototrophic pico-eukaryotes and heterotrophic bacteria, and regulated largely by DIP availability.}, }
@article {pmid29571087, year = {2018}, author = {Seuntjens, D and Han, M and Kerckhof, FM and Boon, N and Al-Omari, A and Takacs, I and Meerburg, F and De Mulder, C and Wett, B and Bott, C and Murthy, S and Carvajal Arroyo, JM and De Clippeleir, H and Vlaeminck, SE}, title = {Pinpointing wastewater and process parameters controlling the AOB to NOB activity ratio in sewage treatment plants.}, journal = {Water research}, volume = {138}, number = {}, pages = {37-46}, doi = {10.1016/j.watres.2017.11.044}, pmid = {29571087}, issn = {1879-2448}, mesh = {Ammonia/metabolism ; Bacteria/metabolism ; Bioreactors/microbiology ; Carbon/metabolism ; Nitrification ; Nitrites/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Waste Disposal, Fluid/*methods ; Wastewater/microbiology ; }, abstract = {Even though nitrification/denitrification is a robust technology to remove nitrogen from sewage, economic incentives drive its future replacement by shortcut nitrogen removal processes. The latter necessitates high potential activity ratios of ammonia oxidizing to nitrite oxidizing bacteria (rAOB/rNOB). The goal of this study was to identify which wastewater and process parameters can govern this in reality. Two sewage treatment plants (STP) were chosen based on their inverse rAOB/rNOB values (at 20 °C): 0.6 for Blue Plains (BP, Washington DC, US) and 1.6 for Nieuwveer (NV, Breda, NL). Disproportional and dissimilar relationships between AOB or NOB relative abundances and respective activities pointed towards differences in community and growth/activity limiting parameters. The AOB communities showed to be particularly different. Temperature had no discriminatory effect on the nitrifiers' activities, with similar Arrhenius temperature dependences (ΘAOB = 1.10, ΘNOB = 1.06-1.07). To uncouple the temperature effect from potential limitations like inorganic carbon, phosphorus and nitrogen, an add-on mechanistic methodology based on kinetic modelling was developed. Results suggest that BP's AOB activity was limited by the concentration of inorganic carbon (not by residual N and P), while NOB experienced less limitation from this. For NV, the sludge-specific nitrogen loading rate seemed to be the most prevalent factor limiting AOB and NOB activities. Altogether, this study shows that bottom-up mechanistic modelling can identify parameters that influence the nitrification performance. Increasing inorganic carbon in BP could invert its rAOB/rNOB value, facilitating its transition to shortcut nitrogen removal.}, }
@article {pmid29569048, year = {2018}, author = {LeBrun, ES and King, RS and Back, JA and Kang, S}, title = {A Metagenome-Based Investigation of Gene Relationships for Non-Substrate-Associated Microbial Phosphorus Cycling in the Water Column of Streams and Rivers.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {856-865}, pmid = {29569048}, issn = {1432-184X}, mesh = {Archaea/genetics/*metabolism ; Arkansas ; Bacteria/genetics/*metabolism ; Genes, Archaeal/genetics ; Genes, Bacterial ; *Metagenome ; *Metagenomics ; Oklahoma ; Phosphorus/*metabolism ; Rivers/*microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Phosphorus (P) is a nutrient of primary importance in all living systems, and it is especially important in streams and rivers which are sensitive to anthropogenic P inputs and eutrophication. Microbes are accepted as the primary mineralizers and solubilizers of P improving bioavailability for organisms at all trophic levels. Here, we use a genomics approach with metagenome sequencing of 24 temperate streams and rivers representing a total P (TP) gradient to identify relationships between functional genes, functional gene groupings, P, and organisms within the P biogeochemical cycle. Combining information from network analyses, functional groupings, and system P levels, we have constructed a System Relational Overview of Gene Groupings (SROGG) which is a cohesive system level representation of P cycle gene and nutrient relationships. Using SROGG analysis in concert with other statistical approaches, we found that the compositional makeup of P cycle genes is strongly correlated to environmental P whereas absolute abundance of P genes shows no significant correlation to environmental P. We also found orthophosphate (PO4[3-]) to be the dominant factor correlating with system P cycle gene composition with little evidence of a strong organic phosphorous correlation present even in more oligotrophic streams.}, }
@article {pmid29564487, year = {2018}, author = {Pulikkan, J and Maji, A and Dhakan, DB and Saxena, R and Mohan, B and Anto, MM and Agarwal, N and Grace, T and Sharma, VK}, title = {Gut Microbial Dysbiosis in Indian Children with Autism Spectrum Disorders.}, journal = {Microbial ecology}, volume = {76}, number = {4}, pages = {1102-1114}, pmid = {29564487}, issn = {1432-184X}, mesh = {Adolescent ; Autism Spectrum Disorder/*microbiology ; Bacteria/classification/isolation &amp; purification ; Biomarkers/analysis ; Child ; Child, Preschool ; DNA, Bacterial/analysis ; Dysbiosis/*epidemiology/microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; India/epidemiology ; Male ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, RNA ; }, abstract = {Autism spectrum disorder (ASD) is a term associated with a group of neurodevelopmental disorders. The etiology of ASD is not yet completely understood; however, a disorder in the gut-brain axis is emerging as a prominent factor leading to autism. To identify the taxonomic composition and markers associated with ASD, we compared the fecal microbiota of 30 ASD children diagnosed using Childhood Autism Rating Scale (CARS) score, DSM-5 approved AIIMS-modified INCLEN Diagnostic Tool for Autism Spectrum Disorder (INDT-ASD), and Indian Scale for Assessment of Autism (ISAA) tool, with family-matched 24 healthy children from Indian population using next-generation sequencing (NGS) of 16S rRNA gene amplicon. Our study showed prominent dysbiosis in the gut microbiome of ASD children, with higher relative abundances of families Lactobacillaceae, Bifidobacteraceae, and Veillonellaceae, whereas the gut microbiome of healthy children was dominated by the family Prevotellaceae. Comparative meta-analysis with a publicly available dataset from the US population consisting of 20 ASD and 20 healthy control samples from children of similar age, revealed a significantly high abundance of genus Lactobacillus in ASD children from both the populations. The results reveal the microbial dysbiosis and an association of selected Lactobacillus species with the gut microbiome of ASD children.}, }
@article {pmid29563897, year = {2018}, author = {Meisner, A and Jacquiod, S and Snoek, BL and Ten Hooven, FC and van der Putten, WH}, title = {Drought Legacy Effects on the Composition of Soil Fungal and Prokaryote Communities.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {294}, pmid = {29563897}, issn = {1664-302X}, abstract = {It is increasingly acknowledged that climate change is influencing terrestrial ecosystems by increased drought and rainfall intensities. Soil microbes are key drivers of many processes in terrestrial systems and rely on water in soil pores to fulfill their life cycles and functions. However, little is known on how drought and rainfall fluctuations, which affect the composition and structure of microbial communities, persist once original moisture conditions have been restored. Here, we study how simulated short-term drying and re-wetting events shape the community composition of soil fungi and prokaryotes. In a mesocosm experiment, soil was exposed to an extreme drought, then re-wetted to optimal moisture (50% WHC, water holding capacity) or to saturation level (100% WHC). Composition, community structure and diversity of microbes were measured by sequencing ITS and 16S rRNA gene amplicons 3 weeks after original moisture content had been restored. Drying and extreme re-wetting decreased richness of microbial communities, but not evenness. Abundance changes were observed in only 8% of prokaryote OTUs, and 25% of fungal OTUs, whereas all other OTUs did not differ between drying and re-wetting treatments. Two specific legacy response groups (LRGs) were observed for both prokaryotes and fungi. OTUs belonging to the first LRG decreased in relative abundance in soil with a history of drought, whereas OTUs that increased in soil with a history of drought formed a second LRG. These microbial responses were spread among different phyla. Drought appeared to be more important for the microbial community composition than the following extreme re-wetting. 16S profiles were correlated with both inorganic N concentration and basal respiration and ITS profiles correlated with fungal biomass. We conclude that a drying and/or an extreme re-wetting history can persist in soil microbial communities via specific response groups composed of members with broad phylogenetic origins, with possible functional consequences on soil processes and plant species. As a large fraction of OTUs responding to drying and re-wetting belonged to the rare biosphere, our results suggest that low abundant microbial species are potentially important for ecosystem responses to extreme weather events.}, }
@article {pmid29561792, year = {2018}, author = {Maciejewska, M and Całusińska, M and Cornet, L and Adam, D and Pessi, IS and Malchair, S and Delfosse, P and Baurain, D and Barton, HA and Carnol, M and Rigali, S}, title = {High-Throughput Sequencing Analysis of the Actinobacterial Spatial Diversity in Moonmilk Deposits.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {7}, number = {2}, pages = {}, pmid = {29561792}, issn = {2079-6382}, abstract = {Moonmilk are cave carbonate deposits that host a rich microbiome, including antibiotic-producing Actinobacteria, making these speleothems appealing for bioprospecting. Here, we investigated the taxonomic profile of the actinobacterial community of three moonmilk deposits of the cave "Grotte des Collemboles" via high-throughput sequencing of 16S rRNA amplicons. Actinobacteria was the most common phylum after Proteobacteria, ranging from 9% to 23% of the total bacterial population. Next to actinobacterial operational taxonomic units (OTUs) attributed to uncultured organisms at the genus level (~44%), we identified 47 actinobacterial genera with Rhodoccocus (4 OTUs, 17%) and Pseudonocardia (9 OTUs, ~16%) as the most abundant in terms of the absolute number of sequences. Streptomycetes presented the highest diversity (19 OTUs, 3%), with most of the OTUs unlinked to the culturable Streptomyces strains that were previously isolated from the same deposits. Furthermore, 43% of the OTUs were shared between the three studied collection points, while 34% were exclusive to one deposit, indicating that distinct speleothems host their own population, despite their nearby localization. This important spatial diversity suggests that prospecting within different moonmilk deposits should result in the isolation of unique and novel Actinobacteria. These speleothems also host a wide range of non-streptomycetes antibiotic-producing genera, and should therefore be subjected to methodologies for isolating rare Actinobacteria.}, }
@article {pmid29560729, year = {2018}, author = {Cordeiro, RA and Weslley Caracas Cedro, E and Raquel Colares Andrade, A and Serpa, R and José de Jesus Evangelista, A and Sales de Oliveira, J and Santos Pereira, V and Pereira Alencar, L and Bruna Leite Mendes, P and Cibelle Soares Farias, B and Maria Maciel Melo, V and Pires de Camargo, Z and de Souza Collares Maia Castelo-Branco, D and Sâmia Nogueira Brilhante, R and Júlio Costa Sidrim, J and Fábio Gadelha Rocha, M}, title = {Inhibitory effect of a lipopeptide biosurfactant produced by Bacillus subtilis on planktonic and sessile cells of Trichosporon spp.}, journal = {Biofouling}, volume = {34}, number = {3}, pages = {309-319}, doi = {10.1080/08927014.2018.1437617}, pmid = {29560729}, issn = {1029-2454}, mesh = {Antifungal Agents/metabolism/*pharmacology ; Bacillus subtilis/*metabolism ; Biofilms/growth &amp; development ; Cell Adhesion/*drug effects ; Lipopeptides/biosynthesis/*pharmacology ; Plankton/drug effects/metabolism/physiology ; Surface-Active Agents/pharmacology ; Trichosporon/*drug effects/metabolism/physiology ; }, abstract = {The present study aimed to investigate the inhibitory effect of a bacterial biosurfactant (TIM96) on clinical strains of Trichosporon. Additionally, the effect of TIM96 on the ergosterol content, cell membrane integrity, and the hydrophobicity of planktonic cells was assessed. The inhibitory activity of TIM96 against Trichosporon biofilms was evaluated by analyzing metabolic activity, biomass and morphology. MIC values ranged from 78.125 to 312.5 μg ml[-1] for TIM96; time-kill curves revealed that the decline in the number of fungal cells started after incubation for 6 h with TIM96 at both MIC and 2×MIC. The biosurfactant reduced the cellular ergosterol content and altered the membrane permeability and the surface hydrophobicity of planktonic cells. Incubation at 10×MIC TIM96 reduced cell adhesion by up to 96.89%, thus interfering with biofilm formation. This concentration also caused up to a 99.2% reduction in the metabolic activity of mature biofilms. The results indicate potential perspectives for the development of new antifungal strategies.}, }
@article {pmid29556538, year = {2018}, author = {Laforest-Lapointe, I and Arrieta, MC}, title = {Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies.}, journal = {mSystems}, volume = {3}, number = {2}, pages = {}, pmid = {29556538}, issn = {2379-5077}, abstract = {Human-associated microbial communities include prokaryotic and eukaryotic organisms across high-level clades of the tree of life. While advances in high-throughput sequencing technology allow for the study of diverse lineages, the vast majority of studies are limited to bacteria, and very little is known on how eukaryote microbes fit in the overall microbial ecology of the human gut. As recent studies consider eukaryotes in their surveys, it is becoming increasingly clear that eukaryotes play important ecological roles in the microbiome as well as in host health. In this perspective, we discuss new evidence on eukaryotes as fundamental species of the human gut and emphasize that future microbiome studies should characterize the multitrophic interactions between microeukaryotes, other microorganisms, and the host.}, }
@article {pmid29556533, year = {2018}, author = {Hug, LA and Co, R}, title = {It Takes a Village: Microbial Communities Thrive through Interactions and Metabolic Handoffs.}, journal = {mSystems}, volume = {3}, number = {2}, pages = {}, pmid = {29556533}, issn = {2379-5077}, abstract = {An enduring theme in microbial ecology is the interdependence of microbial community members. Interactions between community members include provision of cofactors, establishment of redox gradients, and turnover of key nutrients to drive biogeochemical cycles. Pathways canonically conducted by isolated organisms in laboratory cultures are instead collective products of diverse and interchangeable microbes in the environment. Current sequence-based methods provide unprecedented access to uncultivated microorganisms, allowing prediction of previously cryptic roles in biogeochemical cycles and interactions within communities. A renewed focus on cultivation-based methods is required to test predictions derived from environmental sequence data sets and to address the exponential increase in genes lacking predicted functions. Characterization of enriched microbial consortia to annotate hypothetical proteins and identify previously unknown microbial functions can fundamentally change our understanding of biogeochemical cycles. As we gain understanding of microbial processes and interactions, our capacity to harness microbial activities to address anthropogenic impacts increases.}, }
@article {pmid29556373, year = {2018}, author = {Hornung, B and Martins Dos Santos, VAP and Smidt, H and Schaap, PJ}, title = {Studying microbial functionality within the gut ecosystem by systems biology.}, journal = {Genes &amp; nutrition}, volume = {13}, number = {}, pages = {5}, pmid = {29556373}, issn = {1555-8932}, abstract = {Humans are not autonomous entities. We are all living in a complex environment, interacting not only with our peers, but as true holobionts; we are also very much in interaction with our coexisting microbial ecosystems living on and especially within us, in the intestine. Intestinal microorganisms, often collectively referred to as intestinal microbiota, contribute significantly to our daily energy uptake by breaking down complex carbohydrates into simple sugars, which are fermented to short-chain fatty acids and subsequently absorbed by human cells. They also have an impact on our immune system, by suppressing or enhancing the growth of malevolent and beneficial microbes. Our lifestyle can have a large influence on this ecosystem. What and how much we consume can tip the ecological balance in the intestine. A "western diet" containing mainly processed food will have a different effect on our health than a balanced diet fortified with pre- and probiotics. In recent years, new technologies have emerged, which made a more detailed understanding of microbial communities and ecosystems feasible. This includes progress in the sequencing of PCR-amplified phylogenetic marker genes as well as the collective microbial metagenome and metatranscriptome, allowing us to determine with an increasing level of detail, which microbial species are in the microbiota, understand what these microorganisms do and how they respond to changes in lifestyle and diet. These new technologies also include the use of synthetic and in vitro systems, which allow us to study the impact of substrates and addition of specific microbes to microbial communities at a high level of detail, and enable us to gather quantitative data for modelling purposes. Here, we will review the current state of microbiome research, summarizing the computational methodologies in this area and highlighting possible outcomes for personalized nutrition and medicine.}, }
@article {pmid29556222, year = {2018}, author = {Losasso, C and Eckert, EM and Mastrorilli, E and Villiger, J and Mancin, M and Patuzzi, I and Di Cesare, A and Cibin, V and Barrucci, F and Pernthaler, J and Corno, G and Ricci, A}, title = {Assessing the Influence of Vegan, Vegetarian and Omnivore Oriented Westernized Dietary Styles on Human Gut Microbiota: A Cross Sectional Study.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {317}, pmid = {29556222}, issn = {1664-302X}, abstract = {Diet and lifestyle have a strong influence on gut microbiota, which in turn has important implications on a variety of health-related aspects. Despite great advances in the field, it remains unclear to which extent the composition of the gut microbiota is modulated by the intake of animal derived products, compared to a vegetable based diet. Here the specific impact of vegan, vegetarian, and omnivore feeding type on the composition of gut microbiota of 101 adults was investigated among groups homogeneous for variables known to have a role in modulating gut microbial composition such as age, anthropometric variables, ethnicity, and geographic area. The results displayed a picture where the three different dietetic profiles could be well distinguished on the basis of participant's dietetic regimen. Regarding the gut microbiota; vegetarians had a significantly greater richness compared to omnivorous. Moreover, counts of Bacteroidetes related operational taxonomic units (OTUs) were greater in vegans and vegetarians compared to omnivores. Interestingly considering the whole bacterial community composition the three cohorts were unexpectedly similar, which is probably due to their common intake in terms of nutrients rather than food, e.g., high fat content and reduced protein and carbohydrate intake. This finding suggests that fundamental nutritional choices such as vegan, vegetarian, or omnivore do influence the microbiota but do not allow to infer conclusions on gut microbial composition, and suggested the possibility for a preferential impact of other variables, probably related to the general life style on shaping human gut microbial community in spite of dietary influence. Consequently, research were individuals are categorized on the basis of their claimed feeding types is of limited use for scientific studies, since it appears to be oversimplified.}, }
@article {pmid29554765, year = {2018}, author = {Rodríguez-Caballero, G and Caravaca, F and Roldán, A}, title = {The unspecificity of the relationships between the invasive Pennisetum setaceum and mycorrhizal fungi may provide advantages during its establishment at semiarid Mediterranean sites.}, journal = {The Science of the total environment}, volume = {630}, number = {}, pages = {1464-1471}, doi = {10.1016/j.scitotenv.2018.02.321}, pmid = {29554765}, issn = {1879-1026}, mesh = {*Introduced Species ; Mediterranean Region ; Mycorrhizae/*physiology ; Pennisetum/microbiology/*physiology ; Plant Roots/microbiology ; Soil ; Soil Microbiology ; Symbiosis ; }, abstract = {The involvement of mutualistic plant-fungal interactions in invasion processes, especially in some climatic regions including semiarid areas, has not been sufficiently investigated. We compared the arbuscular mycorrhizal fungi (AMF) communities hosted by the invasive plant Pennisetum setaceum with those from the co-occurring native Hyparrhenia hirta at five Mediterranean semiarid locations with different edaphic characteristics. Illumina technology was used to investigate the AMF communities in the roots. The subsequent multivariate analysis showed that native and non-native host plants shared a similar AMF community, whereas the invaded locations differed in AMF communities harbored in the plant roots. The indicator species analysis revealed the absence of indicator virtual taxa for the fungal communities of the roots of native or invasive plants. In contrast, different numbers of indicator species were recorded in different sampling locations. According to the canonical correspondence analysis, the variability in the AMF communities between sampling sites was related to changes in soil total carbon, electrical conductivity, respiration, and protease and urease activities. These findings reveal the unspecificity of P. setaceum in relation to its association with the AMF community encountered in the invaded locations, which could have facilitated its successful establishment and spread.}, }
@article {pmid29552001, year = {2018}, author = {Handley, JA and Park, SH and Kim, SA and Ricke, SC}, title = {Microbiome Profiles of Commercial Broilers Through Evisceration and Immersion Chilling During Poultry Slaughter and the Identification of Potential Indicator Microorganisms.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {345}, pmid = {29552001}, issn = {1664-302X}, abstract = {Commercial poultry abattoirs were evaluated to determine the efficacy of the multi-hurdle antimicrobial strategy employed to reduce the microbial load present on incoming broilers from the farm. As next generation sequencing (NGS) has been recently employed to characterize the poultry production system, this study utilized 16S High throughput sequencing (HTS) and quantitative plating data to profile the microbiota of chicken carcasses and determine the efficacy of the multi-hurdle antimicrobial system. Aerobic plate count (APC) and Enterobacteriaceae (EB) microbial counts were quantified from whole bird carcass rinsates (WBCR). The remaining rinsates underwent microbiome analysis using 16S rRNA gene fragments on an Illumina MiSeq and were analyzed by Quantitative Insights into Microbial Ecology (QIIME). The key stages of processing were determined to be at rehang, pre-chill, and post-chill as per the Salmonella Reduction Regulation (75 Fed. Reg. 27288-27294). The APC microbial data from rehang, pre-chill, and post-chill were mean log 4.63 CFU/mL, 3.21 CFU/mL, and 0.89 CFU/mL and EB counts were mean log 2.99 CFU/mL, 1.95 CFU/mL, and 0.35 CFU/mL. NGS of WBCR identified 222 Operational Taxonomic Units' (OTU's) of which only 23 OTU's or 10% of the population was recovered post-chill. Microbiome data suggested a high relative abundance of Pseudomonas at post-chill. Additionally, Pseudomonas, Enterobacteriaceae, and Weeksellaceae Chryseobacterium have been identified as potential indicator organisms having been isolated from all processing abattoirs and sampling locations. This study provides insight into the microbiota of commercial broilers during poultry processing.}, }
@article {pmid29551616, year = {2018}, author = {Xia, Y and Wen, X and Zhang, B and Yang, Y}, title = {Diversity and assembly patterns of activated sludge microbial communities: A review.}, journal = {Biotechnology advances}, volume = {36}, number = {4}, pages = {1038-1047}, doi = {10.1016/j.biotechadv.2018.03.005}, pmid = {29551616}, issn = {1873-1899}, mesh = {Bacteria/classification/genetics ; Bioreactors/microbiology ; *Microbiota ; Sewage/*microbiology ; Water Purification ; }, abstract = {Understanding diversity and assembly patterns of microbial communities in activated sludge (AS) is pivotal for addressing fundamental ecological questions and wastewater treatment engineering. Recent applications of molecular methods especially high-throughput sequencing (HTS) have led to the explosion of information about AS community diversity, including the identification of uncultured taxa, and characterization of low-abundance but environmentally important populations such as antibiotic resistant bacteria and pathogens. Those progresses have facilitated the leverage of ecological theories in describing AS community assembly. The lognormal species abundance curve has been applied to estimate AS microbial richness. Taxa-area and taxa-time relationships (TAR and TTR) have been observed for AS microbial communities. Core AS microbial communities have been identified. Meanwhile, the roles of both deterministic and stochastic processes in shaping AS community structures have been examined. Nonetheless, it remains challenging to define tempo-spatial scales for reliable identification of community turnover, and find tight links between AS microbial structure and wastewater treatment plant (WWTP) functions. To solve those issues, we expect that future research will focus on identifying active functional populations in AS using omics- methods integrated with stable-isotope probing (SIP) with the development of bioinformatics tools. Developing mathematic models to understand AS community structures and utilize information on AS community to predict the performance of WWTPs will also be vital for advancing knowledge of AS microbial ecology and environmental engineering.}, }
@article {pmid29550356, year = {2018}, author = {Jia, X and Dini-Andreote, F and Falcão Salles, J}, title = {Community Assembly Processes of the Microbial Rare Biosphere.}, journal = {Trends in microbiology}, volume = {26}, number = {9}, pages = {738-747}, doi = {10.1016/j.tim.2018.02.011}, pmid = {29550356}, issn = {1878-4380}, mesh = {Biodiversity ; Ecology ; *Ecosystem ; Genes, rRNA/genetics ; Genetic Variation ; *Microbiota/genetics ; *Phylogeny ; }, abstract = {Our planet teems with microorganisms that often present a skewed abundance distribution in a local community, with relatively few dominant species coexisting alongside a high number of rare species. Recent studies have demonstrated that these rare taxa serve as limitless reservoirs of genetic diversity, and perform disproportionate types of functions despite their low abundances. However, relatively little is known about the mechanisms controlling rarity and the processes promoting the development of the rare biosphere. Here, we propose the use of multivariate cut-offs to estimate rare species and phylogenetic null models applied to predefined rare taxa to disentangle the relative influences of ecoevolutionary processes mediating the assembly of the rare biosphere. Importantly, the identification of the factors controlling rare species assemblages is critical for understanding the types of rarity, how the rare biosphere is established, and how rare microorganisms fluctuate over spatiotemporal scales, thus enabling prospective predictions of ecosystem responses.}, }
@article {pmid29549385, year = {2018}, author = {Receveur, JP and Pechal, JL and Benbow, ME and Donato, G and Rainey, T and Wallace, JR}, title = {Changes in Larval Mosquito Microbiota Reveal Non-target Effects of Insecticide Treatments in Hurricane-Created Habitats.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {719-728}, pmid = {29549385}, issn = {1432-184X}, support = {6032305751//Hunterdon County Vector Control Program (HCVCP) black fly grant/ ; }, mesh = {Aedes/*drug effects/growth &amp; development/microbiology ; Animals ; Bacteria/classification/drug effects/genetics/*isolation &amp; purification ; Cyclonic Storms ; Insecticides/*pharmacology ; Larva/drug effects/growth &amp; development/*microbiology ; Microbiota/*drug effects ; Mosquito Control ; }, abstract = {Ephemeral aquatic habitats and their associated microbial communities (microbiomes) play important roles in the growth and development of numerous aquatic insects, including mosquitoes (Diptera). Biological control agents, such as Bacillus thuringiensis israelensis (Bti) or insect growth regulators (e.g., methoprene), are commonly used to control mosquitoes in these habitats. However, it is unknown how commonly used control compounds affect the mosquito internal microbiome and potentially alter their life history traits. The objectives of this study were threefold: characterize the internal microbiota of Aedes larvae (Culicidae) in ephemeral forested mosquito habitat using high-throughput amplicon based sequencing, assess how mosquito control treatments affect the internal microbial communities of larval mosquitoes, and determine if changes to the microbiome resulted from direct or indirect treatment effects. The larval microbiome varied in community composition and diversity with development stage and treatment, suggesting potential effects of control compounds on insect microbial ecology. While microbial community differences due to Bti treatment were a result of indirect effects on larval development, methoprene had significant impacts on bacterial and algal taxa that could not be explained by indirect treatment effects. These results provide new information on the interactions between pesticide treatments and insect microbial communities.}, }
@article {pmid29549384, year = {2018}, author = {Li, JL and Salam, N and Wang, PD and Chen, LX and Jiao, JY and Li, X and Xian, WD and Han, MX and Fang, BZ and Mou, XZ and Li, WJ}, title = {Discordance Between Resident and Active Bacterioplankton in Free-Living and Particle-Associated Communities in Estuary Ecosystem.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {637-647}, pmid = {29549384}, issn = {1432-184X}, support = {31528001//National Natural Science Foundation of China/ ; 2016A030312003//Natural Science Foundation of Guangdong Province/ ; }, mesh = {Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; *Biodiversity ; Estuaries ; Phylogeny ; Rivers/*microbiology ; Seawater/*microbiology ; }, abstract = {Bacterioplankton are the major driving force for biogeochemical cycles in estuarine ecosystems, but the communities that mediate these processes are largely unexplored. We sampled in the Pearl River Estuary (PRE) to examine potential differences in the taxonomic composition of resident (DNA-based) and active (RNA-based) bacterioplankton communities in free-living and particle-associated fractions. MiSeq sequencing data showed that the overall bacterial diversity in particle-associated fractions was higher than in free-living communities. Further in-depth analyses of the sequences revealed a positive correlation between resident and active bacterioplankton communities for the particle-associated fraction but not in the free-living fraction. However, a large overlapping of OTUs between free-living and particle-associated communities in PRE suggested that the two fractions may be actively exchanged. We also observed that the positive correlation between resident and active communities is more prominent among the abundant OTUs (relative abundance > 0.2%). Further, the results from the present study indicated that low-abundance bacterioplankton make an important contribution towards the metabolic activity in PRE.}, }
@article {pmid29549338, year = {2018}, author = {Duvernoy, MC and Mora, T and Ardré, M and Croquette, V and Bensimon, D and Quilliet, C and Ghigo, JM and Balland, M and Beloin, C and Lecuyer, S and Desprat, N}, title = {Asymmetric adhesion of rod-shaped bacteria controls microcolony morphogenesis.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {1120}, pmid = {29549338}, issn = {2041-1723}, mesh = {Bacterial Adhesion/*physiology ; Biofilms/growth &amp; development ; Cell Wall/*physiology ; Escherichia coli/*growth &amp; development/physiology ; Microscopy, Atomic Force ; Pseudomonas aeruginosa/*growth &amp; development/physiology ; Spatio-Temporal Analysis ; *Stress, Mechanical ; Time-Lapse Imaging ; }, abstract = {Surface colonization underpins microbial ecology on terrestrial environments. Although factors that mediate bacteria-substrate adhesion have been extensively studied, their spatiotemporal dynamics during the establishment of microcolonies remains largely unexplored. Here, we use laser ablation and force microscopy to monitor single-cell adhesion during the course of microcolony formation. We find that adhesion forces of the rod-shaped bacteria Escherichia coli and Pseudomonas aeruginosa are polar. This asymmetry induces mechanical tension, and drives daughter cell rearrangements, which eventually determine the shape of the microcolonies. Informed by experimental data, we develop a quantitative model of microcolony morphogenesis that enables the prediction of bacterial adhesion strength from simple time-lapse measurements. Our results demonstrate how patterns of surface colonization derive from the spatial distribution of adhesive factors on the cell envelope.}, }
@article {pmid29546438, year = {2018}, author = {Rua, CPJ and de Oliveira, LS and Froes, A and Tschoeke, DA and Soares, AC and Leomil, L and Gregoracci, GB and Coutinho, R and Hajdu, E and Thompson, CC and Berlinck, RGS and Thompson, FL}, title = {Microbial and Functional Biodiversity Patterns in Sponges that Accumulate Bromopyrrole Alkaloids Suggest Horizontal Gene Transfer of Halogenase Genes.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {825-838}, pmid = {29546438}, issn = {1432-184X}, support = {CNE E-26/110.735/2013//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; CIMAR 1986/2014//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; BIOTA/BIOprospecTA grant 2013/50228-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2014/17616- 7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {Alkaloids/*metabolism ; Animals ; Bacteria/*enzymology/genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/*genetics/metabolism ; *Biodiversity ; Bromine/metabolism ; Gene Transfer, Horizontal ; Hydrolases/*genetics/metabolism ; Phylogeny ; Porifera/chemistry/*microbiology ; Secondary Metabolism ; }, abstract = {Marine sponge holobionts harbor complex microbial communities whose members may be the true producers of secondary metabolites accumulated by sponges. Bromopyrrole alkaloids constitute a typical class of secondary metabolites isolated from sponges that very often display biological activities. Bromine incorporation into secondary metabolites can be catalyzed by either halogenases or haloperoxidases. The diversity of the metagenomes of sponge holobiont species containing bromopyrrole alkaloids (Agelas spp. and Tedania brasiliensis) as well as holobionts devoid of bromopyrrole alkaloids spanning in a vast biogeographic region (approx. Seven thousand km) was studied. The origin and specificity of the detected halogenases was also investigated. The holobionts Agelas spp. and T. brasiliensis did not share microbial halogenases, suggesting a species-specific pattern. Bacteria of diverse phylogenetic origins encoding halogenase genes were found to be more abundant in bromopyrrole-containing sponges. The sponge holobionts (e.g., Agelas spp.) with the greatest number of sequences related to clustered, interspaced, short, palindromic repeats (CRISPRs) exhibited the fewest phage halogenases, suggesting a possible mechanism of protection from phage infection by the sponge host. This study highlights the potential of phages to transport halogenases horizontally across host sponges, particularly in more permissive holobiont hosts, such as Tedania spp.}, }
@article {pmid29545304, year = {2018}, author = {Karavina, C and Ibaba, JD and Gubba, A}, title = {Genome Sequence of a Tomato-Infecting Tomato Mosaic Virus Isolate from Zimbabwe.}, journal = {Genome announcements}, volume = {6}, number = {11}, pages = {}, pmid = {29545304}, issn = {2169-8287}, abstract = {A tomato-infecting tomato mosaic virus (ToMV) isolate was detected in Zimbabwe using lateral flow kits and double-antibody sandwich enzyme-linked immunosorbent assay. Next-generation sequencing and de novo assembly were subsequently performed to determine its genome sequence. The ToMV genome of the Zimbabwe isolate is the second to be reported in Africa.}, }
@article {pmid29542127, year = {2018}, author = {Kharchoufi, S and Gomez, J and Lasanta, C and Castro, R and Sainz, F and Hamdi, M}, title = {Benchmarking laboratory-scale pomegranate vinegar against commercial wine vinegars: antioxidant activity and chemical composition.}, journal = {Journal of the science of food and agriculture}, volume = {98}, number = {12}, pages = {4749-4758}, doi = {10.1002/jsfa.9011}, pmid = {29542127}, issn = {1097-0010}, mesh = {Acetic Acid/*analysis ; Alcohols/chemistry ; Antioxidants/*chemistry ; Benchmarking ; Fruit/chemistry ; Humans ; Lythraceae/*chemistry ; Phenols/chemistry ; Taste ; Wine/*analysis/economics ; }, abstract = {BACKGROUND: There is growing interest in the beneficial health effects of certain fruits, such as pomegranate, and their by-products, like vinegar. Vinegars contain antioxidant compounds such as polyphenols, which can scavenge free radicals in the body. In this study, the antioxidant properties (2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid and 2,2-diphenyl-1-picrylhydrazyl scavenging capacities) and global polyphenolic composition of a new functional product, namely a pomegranate vinegar produced in the laboratory from the Gabsi variety, were evaluated and compared with those of commercial wine vinegars (Sherry and Rioja red wine Spanish vinegars). The evolution of the polyphenolic and volatile compositions during production of the pomegranate vinegar was also studied.<br><br>RESULTS: The results indicate that pomegranate contained a relatively stable total phenolic content that is suitable for the elaboration of vinegar and that this product had an antioxidant capacity comparable to, or even better than, that observed for aged wine vinegars. Regarding the volatiles profile, a high proportion of esters (close to 50%), in relation to alcohols and fatty acids, was observed for pomegranate vinegar, and this is consistent with the high red fruits character identified by sensory analysis.<br><br>CONCLUSION: Pomegranate vinegar produced in the laboratory has an antioxidant activity and a global phenolic content similar to those of red wine vinegars and higher than most of the white wine vinegars studied. The pomegranate vinegar retained the red fruit sensory character of pomegranate fruit. &#xa9; 2018 Society of Chemical Industry.}, }
@article {pmid29537363, year = {2018}, author = {Lee, HJ and Whang, KS}, title = {Streptomyces fuscigenes sp. nov., isolated from bamboo (Sasa borealis) litter.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {68}, number = {5}, pages = {1541-1545}, doi = {10.1099/ijsem.0.002706}, pmid = {29537363}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Diaminopimelic Acid/chemistry ; Fatty Acids/chemistry ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sasa/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; Streptomyces/*classification/genetics/isolation &amp; purification ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {Three actinomycetes strains, designated JBL-5, JBL-14 and JBL-20[T], were isolated from bamboo (Sasa borealis) litter in Damyang, Republic of Korea. Morphological, chemotaxonomic and phylogenetic analyses demonstrated that the three strains belong to the genus Streptomyces. Microscopic observation revealed that the three strains produced Spirales spore chains with smooth surfaces. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that these strains showed the highest sequence similarity to Streptomyces gelaticus NRRL B-2928[T] (97.8 %), Streptomyces pulveraceus LMG 20322[T] (97.7 %), Streptomyces intermedius NBRC 13049[T] (97.7 %), Streptomyces althioticus NRRL B-3981[T] (97.7 %) and Streptomyces matensis NBRC 12889[T] (97.7 %). The DNA-DNA hybridization values between strains JBL-5, JBL-14 and JBL-20[T] were 91.2-92.4 %, and the values between the three strains and their close phylogenetic relatives were also below 70 %. The predominant menaquinones were MK-9 (H4) and MK-9 (H6). The cell wall contained ll-diaminopimelic acid and the whole-cell sugars were arabinose and xylose. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositolmannoside, two unidentified aminolipids, three unidentified aminophospholipids, one unidentified glycolipid and one unidentified lipid. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C14 : 0, C18 : 1ω7c and iso-C16 : 0. The DNA G+C contents were 71.8-72.4 mol%. On the basis of phylogenetic analyses and physiological and biochemical characterization, strains JBL-5, JBL-14 and JBL-20[T] are considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces fuscigenes sp. nov. is proposed. The type strain is JBL-20[T] (=KACC 18269[T]=NBRC 110629[T]).}, }
@article {pmid29536423, year = {2018}, author = {Kennedy, RC and Fling, RR and Robeson, MS and Saxton, AM and Schneider, LG and Darcy, JL and Bemis, DA and Zhao, L and Chen, J}, title = {Temporal dynamics of gut microbiota in triclocarban-exposed weaned rats.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {15}, pages = {14743-14751}, pmid = {29536423}, issn = {1614-7499}, support = {1R21ES017475-01A1//National Institute of Environmental Health Sciences/ ; }, mesh = {Animals ; Anti-Infective Agents/*toxicity ; Carbanilides/*toxicity ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Lactation ; Rats ; Rats, Sprague-Dawley ; Water Pollutants, Chemical/*toxicity ; Weaning ; }, abstract = {Widely used as an antimicrobial in antibacterial bar soaps, triclocarban (3,4,4'-trichlorocarbanilide; TCC) is effective against Gram-positive bacteria but shows little efficacy against Gram-negative strains, potentially altering the composition of indigenous microflora within and on the human body. To date, the consequence of continuous or previous nonprescription antimicrobial exposure from compounds in personal care products on commensal microflora is still elusive. Previous research has shown that TCC exposure during gestation and lactation induced dysbiosis of gut microbial communities among exposed dams and neonates. However, the impact of antimicrobial exposure specifically after discontinuation of the use of TCC on the gut microbiota has not been investigated. In this study, weaned Sprague Dawley rats (postnatal day, PND 22) were provided ad lib access to TCC-supplemented diet (0.2% w/w or 0.5% w/w) for 4 weeks (phase I) followed by a 4-week washout period (phase II) to determine gut microflora changes both during continuous exposure to TCC and to determine the potential rebound following TCC withdrawal. Fecal samples were collected at baseline (PND 22) prior to TCC exposure and throughout phase I and phase II. The V4 region of 16S rDNA was sequenced from extracted total fecal DNA with the MiSeq platform. Exposure to both 0.2% w/w and 0.5% w/w TCC was sufficient to alter diversity of microbiota during phase I of treatment. This effect was further prolonged into phase II, even when TCC exposure was discontinued. Collectively, these data highlight the impact of both continuous and prior TCC exposure on gut microbial ecology and shed light onto the potential long-term health risk of daily nonprescription antimicrobial personal care product use.}, }
@article {pmid29536132, year = {2018}, author = {Kim, S and Kang, J and Megonigal, JP and Kang, H and Seo, J and Ding, W}, title = {Impacts of Phragmites australis Invasion on Soil Enzyme Activities and Microbial Abundance of Tidal Marshes.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {782-790}, pmid = {29536132}, issn = {1432-184X}, support = {86457858//National Research Foundation of Korea/ ; }, mesh = {Bacteria/classification/*enzymology/genetics/*isolation &amp; purification ; Bacterial Proteins/*analysis/metabolism ; Fungal Proteins/*analysis/metabolism ; Fungi/classification/*enzymology/isolation &amp; purification ; Introduced Species ; Laccase/analysis/metabolism ; Monophenol Monooxygenase/analysis/metabolism ; Poaceae/*growth &amp; development ; Soil/*chemistry ; *Soil Microbiology ; Wetlands ; beta-Glucosidase/analysis/metabolism ; }, abstract = {The rapid expansion of Phragmites australis in brackish marshes of the East Coast of the USA has drawn much attention, because it may change vegetation diversity and ecosystem functions. In particular, higher primary production of Phragmites than that of other native species such as Spartina patens and Schoenoplectus americanus has been noted, suggesting possible changes in carbon storage potential in salt marshes. To better understand the long-term effect of the invasion of Phragmites on carbon storage, however, information on decomposition rates of soil organic matter is essential. To address this issue, we compared microbial enzyme activities and microbial functional gene abundances (fungi, laccase, denitrifier, and methanogens) in three depths of soils with three different plants in a brackish marsh in Maryland, USA. Laccase and phenol oxidase activities were measured to assess the decomposition potential of recalcitrant carbon while β-glucosidase activity was determined as proxy for cellulose decomposition rate. Microbial activities near the surface (0-15 cm) were the highest in Spartina-community sites followed by Phragmites- and Schoenoplectus-community sites. A comparison of stable isotopic signatures (δ13C and δ15N) of soils and plant leaves suggests that deep organic carbon in the soils mainly originated from Spartina, and only the surface soils may have been influenced by Phragmites litter. In contrast, fungal, laccase, and denitrifier abundances determined by real-time qPCR exhibited no discernible patterns among the surface soils of the three vegetation types. However, the abundance of methanogens was higher in the deep Phragmites-community soil. Therefore, Phragmites invasion will accelerate CH4 emission by greater CH4 production in deep soils with abundant methanogens, although enzymatic mechanisms revealed the potential for larger C accumulation by Phragmites invasion in salt marshes in the east coast of the USA.}, }
@article {pmid29536131, year = {2018}, author = {Jani, K and Dhotre, D and Bandal, J and Shouche, Y and Suryavanshi, M and Rale, V and Sharma, A}, title = {World's Largest Mass Bathing Event Influences the Bacterial Communities of Godavari, a Holy River of India.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {706-718}, pmid = {29536131}, issn = {1432-184X}, support = {BT/PR/0054/NDB/52/94/2007//Department of Biotechnology , Ministry of Science and Technology/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Baths ; *Biodiversity ; Humans ; India ; Phylogeny ; Public Health ; Rivers/chemistry/*microbiology ; Water Quality ; }, abstract = {Kumbh Mela is one of the largest religious mass gathering events (MGE) involving bathing in rivers. The exponential rise in the number of devotees, from around 0.4 million in 1903 to 120 million in 2013, bathing in small specified sites can have a dramatic impact on the river ecosystem. Here, we present the spatiotemporal profiling of bacterial communities in Godavari River, Nashik, India, comprising five sites during the Kumbh Mela, held in 2015. Assessment of environmental parameters indicated deterioration of water quality. Targeted amplicon sequencing demonstrates approximately 37.5% loss in microbial diversity because of anthropogenic activity during MGE. A significant decrease in phyla viz. Actinobacteria, Chloroflexi, Proteobacteria, and Bacteroidetes was observed, while we noted substantial increase in prevalence of the phylum Firmicutes (94.6%) during MGE. qPCR estimations suggested nearly 130-fold increase in bacterial load during the event. Bayesian mixing model accounted the source of enormous incorporation of bacterial load of human origin. Further, metagenomic imputations depicted increase in virulence and antibiotic resistance genes during the MGE. These observations suggest the striking impact of the mass bathing on river ecosystem. The subsequent increase in infectious diseases and drug-resistant microbes pose a critical public health concern.}, }
@article {pmid29535703, year = {2018}, author = {Liu, K and Ding, X and Tang, X and Wang, J and Li, W and Yan, Q and Liu, Z}, title = {Macro and Microelements Drive Diversity and Composition of Prokaryotic and Fungal Communities in Hypersaline Sediments and Saline-Alkaline Soils.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {352}, pmid = {29535703}, issn = {1664-302X}, abstract = {Understanding the effects of environmental factors on microbial communities is critical for microbial ecology, but it remains challenging. In this study, we examined the diversity (alpha diversity) and community compositions (beta diversity) of prokaryotes and fungi in hypersaline sediments and salinized soils from northern China. Environmental variables were highly correlated, but they differed significantly between the sediments and saline soils. The compositions of prokaryotic and fungal communities in the hypersaline sediments were different from those in adjacent saline-alkaline soils, indicating a habitat-specific microbial distribution pattern. The macroelements (S, P, K, Mg, and Fe) and Ca were, respectively, correlated closely with the alpha diversity of prokaryotes and fungi, while the macronutrients (e.g., Na, S, P, and Ca) were correlated with the prokaryotic and fungal beta-diversity (P ≤ 0.05). And, the nine microelements (e.g., Al, Ba, Co, Hg, and Mn) and micronutrients (Ba, Cd, and Sr) individually shaped the alpha diversity of prokaryotes and fungi, while the six microelements (e.g., As, Ba, Cr, and Ge) and only the trace elements (Cr and Cu), respectively, influenced the beta diversity of prokaryotes and fungi (P < 0.05). Variation-partitioning analysis (VPA) showed that environmental variables jointly explained 55.49% and 32.27% of the total variation for the prokaryotic and fungal communities, respectively. Together, our findings demonstrate that the diversity and community composition of the prokaryotes and fungi were driven by different macro and microelements in saline habitats, and that geochemical elements could more widely regulate the diversity and community composition of prokaryotes than these of fungi.}, }
@article {pmid29535687, year = {2018}, author = {Jiménez, DJ and Chaib De Mares, M and Salles, JF}, title = {Temporal Expression Dynamics of Plant Biomass-Degrading Enzymes by a Synthetic Bacterial Consortium Growing on Sugarcane Bagasse.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {299}, pmid = {29535687}, issn = {1664-302X}, abstract = {Plant biomass (PB) is an important source of sugars useful for biofuel production, whose degradation efficiency depends on synergistic and dynamic interactions of different enzymes. Here, using a metatranscriptomics-based approach, we explored the expression of PB-degrading enzymes in a five-species synthetic bacterial consortium during cultivation on sugarcane bagasse as a unique carbon source. By analyzing the temporal expression dynamics of a selection of enzymes we revealed the functional role of each consortium member and disentangled the potential interactions between them. Based on normalized expression values and the taxonomic affiliation of all the transcripts within thirty carbohydrate-active enzyme (CAZy) families, we observed a successional profile. For instance, endo-glucanases/-xylanases (e.g., GH8, GH10, and GH16) were significantly expressed at 12 h, whereas exo-glucanases (e.g., GH6 and GH48) and α-arabinosidases/β-xylosidases (e.g., GH43) were highly expressed at 48 h. Indeed, a significant peak of extracellular β-xylosidase activity was observed at this stage. Moreover, we observed a higher expression of several CAZy families at 12-48 h, suggesting easy access to the main plant polysaccharides. Based on this evidence, we predicted that the highest level of collaboration between strains takes place at the initial stages of growth. Here, Paenibacillus, Brevundimonas, and Chryseobacterium were the most important contributors, whereas Stenotrophomonas was highly active at the end of the culture (96-192 h) without contributing to a large extent to the expression of lignocellulolytic enzymes. Our results contribute to the understanding of enzymatic and ecological mechanisms within PB-degrading microbial consortia, yielding new perspectives to improve the PB saccharification processes.}, }
@article {pmid29532871, year = {2018}, author = {Li, X and Li, H and Hu, Q and Lin, J and Zhang, Q and Li, Y and Li, J and Chen, T and Zhang, Q and Qiu, Y}, title = {Detection of epitopes in systemic lupus erythematosus using peptide microarray.}, journal = {Molecular medicine reports}, volume = {17}, number = {5}, pages = {6533-6541}, pmid = {29532871}, issn = {1791-3004}, mesh = {Adult ; Autoantibodies/*immunology ; Autoantigens/*immunology ; Epitopes/*immunology ; Female ; Humans ; Lupus Erythematosus, Systemic/*diagnosis/*immunology ; Male ; *Protein Array Analysis ; }, abstract = {Systemic lupus erythematosus (SLE) is a common autoimmune disease, which features the secretion of antibodies directed against autoantigens in vivo. In the present study, a peptide microarray was developed to detect the epitopes recognized by autoantibodies in patients with SLE for an effective method of diagnosis. SLE‑associated epitopes in 14 autoantigens were predicted using the antigenic epitope prediction software DNA star. Peptides were synthesized based on the predicted antigenic epitopes and immobilized on a slide surface and developed into a peptide microarray. Using this peptide microarray the autoantibodies in 120 patients with SLE and 110 healthy subjects were detected. A total of 73 potential antigenic epitopes in 14 autoantigens were predicted and screened. The peptide microarray based on the 73 epitopes was used to detect the autoantibodies in patients with SLE. A total of 14 epitopes with potential diagnostic values were screened out. The sensitivity and specificity of the 14 epitopes for the diagnosis of SLE were 71.6 and 85.8%, respectively. An optimal set of epitopes for SLE diagnosis was obtained. As individual patients had a specific autoantibody spectrum it was possible to detect autoantibodies in SLE and perform the diagnosis of SLE using the peptide microarray.}, }
@article {pmid29526022, year = {2018}, author = {Tasin, M and Larsson Herrera, S and Knight, AL and Barros-Parada, W and Fuentes Contreras, E and Pertot, I}, title = {Volatiles of Grape Inoculated with Microorganisms: Modulation of Grapevine Moth Oviposition and Field Attraction.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {751-761}, pmid = {29526022}, issn = {1432-184X}, support = {934//Svenska Forskningsr&#xe5;det Formas/ ; }, mesh = {Agricultural Inoculants/physiology ; Animals ; Bacteria ; Female ; Fruit/chemistry/microbiology/parasitology ; Fungi/physiology ; Gas Chromatography-Mass Spectrometry ; Male ; Moths/*physiology ; Odorants/analysis ; Oviposition ; Vitis/chemistry/*microbiology/*parasitology ; Volatile Organic Compounds/*chemistry ; }, abstract = {Semiochemicals released by plant-microbe associations are used by herbivorous insects to access and evaluate food resources and oviposition sites. Adult insects may utilize microbial-derived nutrients to prolong their lifespan, promote egg development, and offer a high nutritional substrate to their offspring. Here, we examined the behavioral role of semiochemicals from grape-microbe interactions on oviposition and field attraction of the grapevine moth Lobesia botrana (Denis &amp; Schiffermüller). The volatile constituents released by grape inoculated with yeasts (Hanseniaspora uvarum (Niehaus), Metschnikowia pulcherrima (Pitt.) M.W. Miller, Pichia anomala, Saccharomyces cerevisiae Meyen ex E.C. Hansen, and Zygosaccharomyces rouxii (Boutroux) Yarrow), sour rot bacteria (Acetobacter aceti (Pasteur) Beijerinck and Gluconobacter oxydans (Henneberg) De Ley), and a fungal pathogen (Botrytis cinerea Pers.) all endemic of the vineyard were sampled by solid-phase microextraction and analyzed by gas-chromatography coupled with mass spectrometry. Ethanol, 3-methyl-1-butanol, and ethyl acetate were the most common volatiles released from all microbe-inoculated grapes. In addition, acetic acid was released at a substantial amount following bacteria inoculation and in a three-way inoculation with yeasts and the fungus. 2-phenylethanol, a compound reported to attract tortricid moths when used in combination with acetic acid, was found at a relatively low level in all microbial combinations as well as in the control grape. While grapes inoculated with a consortium of yeasts stimulated oviposition in comparison with uninoculated berries, the phytopathogenic fungus deterred egg-laying. Nonetheless, the highest preference to lay eggs was measured when the yeasts were co-inoculated with the fungus. The lowest preference was obtained when grapes were inoculated with sour rot bacteria and their binary co-inoculation with yeasts and the fungus. Interestingly, oviposition on berries simultaneously inoculated with all the three microbial groups was unaffected. Lures loaded with either acetic acid or 2-phenylethanol were not attractive when placed in traps as single component in vineyards, but a binary blend attracted both sexes of grapevine moth in significant numbers. Further addition of the three most common volatiles released by infected berries (ethanol, 3-methyl-1-butanol, and ethyl acetate) did not significantly increase moth catch with this binary blend. The ecological implications of the grape-microorganism and grapevine moth interaction as well as the possibility to develop a pest monitoring system based on microbial volatiles are discussed.}, }
@article {pmid29524912, year = {2018}, author = {Vandekerckhove, TGL and Kobayashi, K and Janda, J and Van Nevel, S and Vlaeminck, SE}, title = {Sulfur-based denitrification treating regeneration water from ion exchange at high performance and low cost.}, journal = {Bioresource technology}, volume = {257}, number = {}, pages = {266-273}, doi = {10.1016/j.biortech.2018.02.047}, pmid = {29524912}, issn = {1873-2976}, mesh = {Autotrophic Processes ; *Bioreactors ; *Denitrification ; Ion Exchange ; Nitrates ; Regeneration ; *Sulfur ; Water ; Water Purification ; }, abstract = {Autotrophic denitrification with sulfur is an underexplored alternative to heterotrophic denitrification to remove nitrate from wastewater poor in organics. The application on ion exchange regeneration water (19.4-32.1 mS cm[-1]) is novel. Three fixed bed reactors were tested at 15 °C for >4 months, inoculated with activated sludge from sewage treatment. All were fast in start-up (<10 days) with high performance (94 ± 2% removal efficiency). pH control with NaOH rendered higher nitrate removal rates than limestone addition to the bed (211 ± 13 vs. 102 ± 13 mg N L[-1] d[-1]), related to higher pH (6.64 vs. 6.24) and sulfur surface area. Bacterial communities were strongly enriched in Sulfurimonas (63-67%) and Thiobacillus (24-26%). In an economic comparison, sulfur-based denitrification (€5.3 kg[-1] N) was 15% cheaper than methanol-based denitrification (€6.22 kg[-1] N) and both treatments were opex dominated (85.9 vs. 86.5%). Overall, the technological and economic feasibility should boost further implementation of sulfurotrophic denitrification.}, }
@article {pmid29524281, year = {2018}, author = {Chen, MY and Parfrey, LW}, title = {Incubation with macroalgae induces large shifts in water column microbiota, but minor changes to the epibiota of co-occurring macroalgae.}, journal = {Molecular ecology}, volume = {27}, number = {8}, pages = {1966-1979}, doi = {10.1111/mec.14548}, pmid = {29524281}, issn = {1365-294X}, mesh = {Biofilms/growth &amp; development ; Host Specificity/*genetics ; Microbiota/*genetics ; Phaeophyceae/genetics/microbiology ; Rhodophyta/genetics/microbiology ; Seaweed/genetics/*microbiology ; *Water Microbiology ; }, abstract = {Macroalgae variably promote and deter microbial growth through release of organic carbon and antimicrobial compounds into the water column. Consequently, macroalgae influence the microbial composition of the surrounding water column and biofilms on nearby surfaces. Here, we use manipulative experiments to test the hypotheses that (i) Nereocystis luetkeana and Mastocarpus sp. macroalgae alter the water column microbiota in species-specific manner, that (ii) neighbouring macroalgae alter the bacterial communities on the surface (epibiota) of actively growing Nereocystis luetkeana meristem fragments (NMFs), and that (iii) neighbours alter NMF growth rate. We also assess the impact of laboratory incubation on macroalgal epibiota by comparing each species to wild counterparts. We find strong differences between the Nereocystis and Mastocarpus epibiota that are maintained in the laboratory. Nereocystis and Mastocarpus alter water column bacterial community composition and richness in a species specific manner, but cause only small compositional shifts on NMF surfaces that do not differ by species, and do not change richness. Co-incubation with macroalgae results in significant change in abundance of fivefold more genera in the water column compared to NMF surfaces, although the direction (i.e., enrichment or reduction) of shift is generally consistent between the water and NMF surfaces. Finally, NMFs grew during the experiment, but growth did not depend on the presence or identity of neighbouring macroalgae. Thus, macroalgae exhibit a strong and species-specific influence on the water column microbiota, but a much weaker influence on the epibiota of neighbouring macroalgae. Overall, these results support the idea that macroalgae surfaces are highly selective and demonstrate that modulations of macroalgal microbiota operate within an overarching paradigm of host species specificity.}, }
@article {pmid29520453, year = {2018}, author = {Ludvigsen, J and Amdam, GV and Rudi, K and L'Abée-Lund, TM}, title = {Detection and Characterization of Streptomycin Resistance (strA-strB) in a Honeybee Gut Symbiont (Snodgrassella alvi) and the Associated Risk of Antibiotic Resistance Transfer.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {588-591}, pmid = {29520453}, issn = {1432-184X}, mesh = {Animals ; Bees/*microbiology/physiology ; DNA Transposable Elements ; *Drug Resistance, Bacterial ; Female ; Gastrointestinal Tract/microbiology ; Male ; Neisseriaceae/*drug effects/genetics/*isolation &amp; purification/physiology ; Streptomycin/*pharmacology ; Symbiosis ; }, abstract = {Use of antibiotics in medicine and farming contributes to increasing numbers of antibiotic-resistant bacteria in diverse environments. The ability of antibiotic resistance genes (ARG) to transfer between bacteria genera contributes to this spread. It is difficult to directly link antibiotic exposure to the spread of ARG in a natural environment where environmental settings and study populations cannot be fully controlled. We used managed honeybees in environments with contrasting streptomycin exposure (USA: high exposure, Norway: low exposure) and mapped the prevalence and spread of transferrable streptomycin resistance genes. We found a high prevalence of strA-strB genes in the USA compared to Norway with 17/90 and 1/90 positive samples, respectively (p < 0.00007). We identified strA-strB genes on a transferrable transposon Tn5393 in the honeybee gut symbiont Snodgrassella alvi. Such transfer of resistance genes increases the risk of the spread to new environments as honeybees are moved to new pollination sites.}, }
@article {pmid29520452, year = {2018}, author = {Gao, D and Tao, Y and Fu, Y and Liang, H}, title = {Egalitarianism in Biofilms.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {49-51}, pmid = {29520452}, issn = {1432-184X}, support = {21177033//National Natural Science Foundation of China/ ; }, mesh = {Bacteria ; Biofilms/*growth &amp; development ; Biofouling ; Bioreactors ; Ecology ; Membranes, Artificial ; Microbiota/*physiology ; Sewage/*microbiology ; Waste Disposal, Fluid ; Wastewater/microbiology ; Water Purification/instrumentation/methods ; }, abstract = {Microbial biofilms are multicellular communities of sessile microorganisms encased by the hydrated polymeric matrix. They have significant influences on both aquatic/terrestrial ecosystem and anthropogenic activities. Taking advantage of the governing features of selective stress (Tan and Ng in Water Res 42:1122-1132, 2008; Wei in Water Res 45:863-871, 2011; Dereli in Water Res 59C:11-22, 2014), the evenness of microbial communities in a membrane-centered mesocosm was successfully manipulated. By measuring the biofilm growing rates under different evenness levels of communities, an evenly distributed community favors the formation of biofilms was observed. This finding is not only a new evidence linking biofilm diversity to its functionality but also a clear suggestion on controlling a biofilm-based process via a simple and smart way.}, }
@article {pmid29520451, year = {2018}, author = {Marchello, AE and Dos Santos, AC and Lombardi, AT and de Souza, CWO and Montanhim, GC}, title = {Physiological and Ecological Aspects of Chlorella sorokiniana (Trebouxiophyceae) Under Photoautotrophic and Mixotrophic Conditions.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {791-800}, pmid = {29520451}, issn = {1432-184X}, support = {2014/15894-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 302175/2015-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Autotrophic Processes/radiation effects ; Biomass ; Chlorella/growth &amp; development/*metabolism/*radiation effects ; Chlorophyll/metabolism ; Chlorophyll A ; Glucose/metabolism ; Heterotrophic Processes/radiation effects ; Light ; Microalgae/growth &amp; development/metabolism/radiation effects ; Nitrogen/metabolism ; Photosynthesis/radiation effects ; }, abstract = {Mixotrophy is a metabolic strategy in which an organism is autotrophic and heterotrophic simultaneously. Considering that the aquatic environment provides several organic sources of carbon, it is probably common for microalgae to perform mixotrophy and not only photoautotrophy, but little is known about microalgae mixotrophy. The present work aimed at investigating the growth, photosynthetic activity, morphology, and biochemical composition of the microalga Chlorella sorokiniana in mixotrophic and photo-mixotrophic conditions, comparing it with photoautotrophy. The results showed pH changes after glucose addition, reaching pH 11.62 in mixotrophic and 10.47 in sequential photo-mixotrophic cultures, which limited the microalgal growth. Highest biomass was obtained in the mixotrophic culture in comparison with the sequential photo-mixotrophic one. Rapid light saturation curves showed that α (photosynthetic efficiency, 1.69) and relative electron transport rate (rETR; 565.61) were higher in the mixotrophic cultures, whereas the highest Ik (irradiance saturation, 386.68) was obtained in the photoautotrophic ones. In the sequential photo-mixotrophic cultures, photosynthetic activity varied during glucose consumption, decreasing the maximum quantum yield Fv/Fm after glucose addition, indicating change in metabolism, from photoautotrophy to mixotrophy by the microalga. The results showed that the mixotrophic cultures had higher production of chlorophyll a (6.26 mg mL[-1]), cell density (6.62 × 10[7] cell mL[-1]), and lipids (0.06 pg μm[-3]). Sequential photo-mixotrophic cultures showed the highest biovolume (360.5 μm[3] cell[-1]) and total carbohydrates (0.026 pg μm[-3]). The protein concentration was 3.2 and 2.4 times higher in photoautotrophy and photo-mixotrophic growth, respectively, than in mixotrophy, but lipids were three times higher under mixotrophy. The biochemical changes we observed indicate that the microalga's plasticity in face of new environmental characteristics, such as the presence of organic carbon, can change the flow of energy through natural ecosystems.}, }
@article {pmid29520450, year = {2018}, author = {Ordoñez, OF and Rasuk, MC and Soria, MN and Contreras, M and Farías, ME}, title = {Haloarchaea from the Andean Puna: Biological Role in the Energy Metabolism of Arsenic.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {695-705}, pmid = {29520450}, issn = {1432-184X}, support = {PICT 730//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICT V 3825//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; }, mesh = {Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Archaeal Proteins/genetics/metabolism ; Arsenate Reductases/genetics/metabolism ; Arsenates/metabolism ; Arsenic/*metabolism ; Biofilms ; Chemoautotrophic Growth ; Energy Metabolism ; Lakes/*microbiology ; Phylogeny ; South America ; }, abstract = {Biofilms, microbial mats, and microbialites dwell under highly limiting conditions (high salinity, extreme aridity, pH, and elevated arsenic concentration) in the Andean Puna. Only recent pioneering studies have described the microbial diversity of different Altiplano lakes and revealed their unexpectedly diverse microbial communities. Arsenic metabolism is proposed to be an ancient mechanism to obtain energy by microorganisms. Members of Bacteria and Archaea are able to exploit arsenic as a bioenergetic substrate in either anaerobic arsenate respiration or chemolithotrophic growth on arsenite. Only six aioAB sequences coding for arsenite oxidase and three arrA sequences coding for arsenate reductase from haloarchaea were previously deposited in the NCBI database. However, no experimental data on their expression and function has been reported. Recently, our working group revealed the prevalence of haloarchaea in a red biofilm from Diamante Lake and microbial mat from Tebenquiche Lake using a metagenomics approach. Also, a surprisingly high abundance of genes used for anaerobic arsenate respiration (arr) and arsenite oxidation (aio) was detected in the Diamante's metagenome. In order to study in depth the role of arsenic in these haloarchaeal communities, in this work, we obtained 18 haloarchaea belonging to the Halorubrum genus, tolerant to arsenic. Furthermore, the identification and expression analysis of genes involved in obtaining energy from arsenic compounds (aio and arr) showed that aio and arr partial genes were detected in 11 isolates, and their expression was verified in two selected strains. Better growth of two isolates was obtained in presence of arsenic compared to control. Moreover, one of the isolates was able to oxidize As[III]. The confirmation of the oxidation of arsenic and the transcriptional expression of these genes by RT-PCR strongly support the hypothesis that the arsenic can be used in bioenergetics processes by the microorganisms flourishing in these environments.}, }
@article {pmid29520256, year = {2018}, author = {Andreote, APD and Dini-Andreote, F and Rigonato, J and Machineski, GS and Souza, BCE and Barbiero, L and Rezende-Filho, AT and Fiore, MF}, title = {Contrasting the Genetic Patterns of Microbial Communities in Soda Lakes with and without Cyanobacterial Bloom.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {244}, pmid = {29520256}, issn = {1664-302X}, abstract = {Soda lakes have high levels of sodium carbonates and are characterized by salinity and elevated pH. These ecosystems are found across Africa, Europe, Asia, Australia, North, Central, and South America. Particularly in Brazil, the Pantanal region has a series of hundreds of shallow soda lakes (ca. 600) potentially colonized by a diverse haloalkaliphilic microbial community. Biological information of these systems is still elusive, in particular data on the description of the main taxa involved in the biogeochemical cycling of life-important elements. Here, we used metagenomic sequencing to contrast the composition and functional patterns of the microbial communities of two distinct soda lakes from the sub-region Nhecolândia, state of Mato Grosso do Sul, Brazil. These two lakes differ by permanent cyanobacterial blooms (Salina Verde, green-water lake) and by no record of cyanobacterial blooms (Salina Preta, black-water lake). The dominant bacterial species in the Salina Verde bloom was Anabaenopsis elenkinii. This cyanobacterium altered local abiotic parameters such as pH, turbidity, and dissolved oxygen and consequently the overall structure of the microbial community. In Salina Preta, the microbial community had a more structured taxonomic profile. Therefore, the distribution of metabolic functions in Salina Preta community encompassed a large number of taxa, whereas, in Salina Verde, the functional potential was restrained across a specific set of taxa. Distinct signatures in the abundance of genes associated with the cycling of carbon, nitrogen, and sulfur were found. Interestingly, genes linked to arsenic resistance metabolism were present at higher abundance in Salina Verde and they were associated with the cyanobacterial bloom. Collectively, this study advances fundamental knowledge on the composition and genetic potential of microbial communities inhabiting tropical soda lakes.}, }
@article {pmid29519634, year = {2018}, author = {Doyle, LE and Marsili, E}, title = {Weak electricigens: A new avenue for bioelectrochemical research.}, journal = {Bioresource technology}, volume = {258}, number = {}, pages = {354-364}, doi = {10.1016/j.biortech.2018.02.073}, pmid = {29519634}, issn = {1873-2976}, mesh = {Bioelectric Energy Sources ; *Biofilms ; Cell Respiration ; *Electrochemistry ; Electrodes ; Electron Transport ; Research ; }, abstract = {Electroactivity appears to be a phylogenetically diverse trait independent of cell wall classification, with both Gram-negative and Gram-positive electricigens reported. While numerous electricigens have been observed, the majority of research focuses on a select group of highly electroactive species. Under favorable conditions, many microorganisms can be considered electroactive, either through their own mechanisms or exogenously-added mediators, producing a weak current. Such microbes should not be dismissed based on their modest electroactivity. Rather, they may be key to understanding what drives extracellular electron transfer in response to transient limitations of electron acceptor or donor, with implications for the study of pathogens and industrial bioprocesses. Due to their low electroactivity, such populations are difficult to grow in bioelectrochemical systems and characterise with electrochemistry. Here, a critical review of recent research on weak electricigens is provided, with a focus on the methodology and the overall relevance to microbial ecology and bioelectrochemical systems.}, }
@article {pmid29518982, year = {2018}, author = {Sibanda, S and Kwenda, S and Tanui, CK and Shyntum, DY and Coutinho, TA and Moleleki, LN}, title = {Transcriptome Profiling Reveals the EanI/R Quorum Sensing Regulon in Pantoea Ananatis LMG 2665[T].}, journal = {Genes}, volume = {9}, number = {3}, pages = {}, pmid = {29518982}, issn = {2073-4425}, abstract = {Pantoea ananatis LMG 2665[T] synthesizes and utilizes acyl homoserine lactones (AHLs) for signalling. The complete set of genes regulated by the EanI/R quorum sensing (QS) system in this strain is still not fully known. In this study, RNA-sequencing (RNA-seq) was used to identify the EanI/R regulon in LMG 2665[T]. Pairwise comparisons of LMG 2665[T] in the absence of AHLs (Optical density (OD)600 = 0.2) and in the presence of AHLs (OD600 = 0.5) were performed. Additionally, pairwise comparisons of LMG 2665[T] and its QS mutant at OD600 = 0.5 were undertaken. In total, 608 genes were differentially expressed between LMG 2665[T] at OD600 = 0.5 versus the same strain at OD600 = 0.2 and 701 genes were differentially expressed between LMG 2665[T] versus its QS mutant at OD600 = 0.5. A total of 196 genes were commonly differentially expressed between the two approaches. These constituted approximately 4.5% of the whole transcriptome under the experimental conditions used in this study. The RNA-seq data was validated by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR). Genes found to be regulated by EanI/R QS were those coding for redox sensing, metabolism, flagella formation, flagella dependent motility, cell adhesion, biofilm formation, regulators, transport, chemotaxis, methyl accepting proteins, membrane proteins, cell wall synthesis, stress response and a large number of hypothetical proteins. The results of this study give insight into the genes that are regulated by the EanI/R system in LMG 2665[T]. Functional characterization of the QS regulated genes in LMG 2665[T] could assist in the formulation of control strategies for this plant pathogen.}, }
@article {pmid29518106, year = {2018}, author = {Plouchart, D and Milferstedt, K and Guizard, G and Latrille, E and Hamelin, J}, title = {Multiplexed chemostat system for quantification of biodiversity and ecosystem functioning in anaerobic digestion.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0193748}, pmid = {29518106}, issn = {1932-6203}, mesh = {*Anaerobiosis ; Automation, Laboratory/instrumentation ; Bacteria/genetics/*metabolism ; Biodiversity ; *Biofuels/analysis/microbiology ; *Bioreactors ; Ecological Parameter Monitoring/*instrumentation ; *Ecosystem ; Equipment Design ; Euryarchaeota/genetics/*metabolism ; Linear Models ; Pressure ; Temperature ; Time Factors ; }, abstract = {Continuous cultures in chemostats have proven their value in microbiology, microbial ecology, systems biology and bioprocess engineering, among others. In these systems, microbial growth and ecosystem performance can be quantified under stable and defined environmental conditions. This is essential when linking microbial diversity to ecosystem function. Here, a new system to test this link in anaerobic, methanogenic microbial communities is introduced. Rigorously replicated experiments or a suitable experimental design typically require operating several chemostats in parallel. However, this is labor intensive, especially when measuring biogas production. Commercial solutions for multiplying reactors performing continuous anaerobic digestion exist but are expensive and use comparably large reactor volumes, requiring the preparation of substantial amounts of media. Here, a flexible system of Lab-scale Automated and Multiplexed Anaerobic Chemostat system (LAMACs) with a working volume of 200 mL is introduced. Sterile feeding, biomass wasting and pressure monitoring are automated. One module containing six reactors fits the typical dimensions of a lab bench. Thanks to automation, time required for reactor operation and maintenance are reduced compared to traditional lab-scale systems. Several modules can be used together, and so far the parallel operation of 30 reactors was demonstrated. The chemostats are autoclavable. Parameters like reactor volume, flow rates and operating temperature can be freely set. The robustness of the system was tested in a two-month long experiment in which three inocula in four replicates, i.e., twelve continuous digesters were monitored. Statistically significant differences in the biogas production between inocula were observed. In anaerobic digestion, biogas production and consequently pressure development in a closed environment is a proxy for ecosystem performance. The precision of the pressure measurement is thus crucial. The measured maximum and minimum rates of gas production could be determined at the same precision. The LAMACs is a tool that enables us to put in practice the often-demanded need for replication and rigorous testing in microbial ecology as well as bioprocess engineering.}, }
@article {pmid29516514, year = {2018}, author = {Herrero, ER and Boon, N and Bernaerts, K and Slomka, V and Verspecht, T and Quirynen, M and Teughels, W}, title = {Clinical concentrations of peroxidases cause dysbiosis in in vitro oral biofilms.}, journal = {Journal of periodontal research}, volume = {53}, number = {3}, pages = {457-466}, doi = {10.1111/jre.12534}, pmid = {29516514}, issn = {1600-0765}, mesh = {Bacteria/classification/*drug effects/metabolism ; Biofilms/*drug effects ; Bioreactors ; Catalase/analysis ; Dysbiosis/*ethnology ; Erythrocytes/metabolism ; Gingival Crevicular Fluid/chemistry/enzymology ; Gingivitis/complications/microbiology ; Horseradish Peroxidase/analysis ; Humans ; Hydrogen Peroxide/metabolism ; Lactoperoxidase/metabolism/pharmacology ; Microbiota ; Periodontitis/complications/microbiology ; Peroxidase/metabolism/pharmacology ; Peroxidases/*metabolism/*pharmacology ; Saliva/chemistry/enzymology ; }, abstract = {BACKGROUND AND OBJECTIVE: Little is known about the initiation of dysbiosis in oral biofilms, a topic of prime importance for understanding the etiology of, and preventing, periodontitis. The aim of this study was to evaluate the effect of different concentrations of crevicular and salivary peroxidase and catalase on dysbiosis in multispecies biofilms in vitro.<br><br>MATERIAL AND METHODS: The spotting technique was used to identify the effect of different concentrations of myeloperoxidase, lactoperoxidase, erythrocyte catalase, and horseradish peroxidase in salivary and crevicular fluid on the inhibitory effect of commensals on pathobiont growth. Vitality-quantitative real-time PCR was performed to quantify the dysbiotic effect of the peroxidases (adjusted to concentrations found in periodontal health, gingivitis, and periodontitis) on multispecies microbial communities.<br><br>RESULTS: Agar plate and multispecies ecology experiments showed that production of hydrogen peroxide (H2 O2) by commensal bacteria decreases pathobiont growth and colonization. Peroxidases at concentrations found in crevicular fluid and saliva neutralized this inhibitory effect. In multispecies communities, myeloperoxidase, at the crevicular fluid concentrations found in periodontitis, resulted in a 1-3 Log increase in pathobionts when compared with the crevicular fluid concentrations found in periodontal health. The effect of salivary lactoperoxidase and salivary myeloperoxidase concentrations was, in general, similar to the effect of crevicular myeloperoxidase concentrations.<br><br>CONCLUSIONS: Commensal species suppress pathobionts by producing H2 O2 . Catalase and peroxidases, at clinically relevant concentrations, can neutralize this effect and thereby can contribute to dysbiosis by allowing the outgrowth of pathobionts.}, }
@article {pmid29515121, year = {2018}, author = {Stegen, JC and Johnson, T and Fredrickson, JK and Wilkins, MJ and Konopka, AE and Nelson, WC and Arntzen, EV and Chrisler, WB and Chu, RK and Fansler, SJ and Graham, EB and Kennedy, DW and Resch, CT and Tfaily, M and Zachara, J}, title = {Publisher Correction: Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {1034}, doi = {10.1038/s41467-018-03572-7}, pmid = {29515121}, issn = {2041-1723}, abstract = {The original version of this Article contained an error in Fig. 6e, in which the text in the legend was omitted. This has been corrected in both the PDF and HTML versions of the article.}, }
@article {pmid29511840, year = {2018}, author = {Gadhave, KR and Devlin, PF and Ebertz, A and Ross, A and Gange, AC}, title = {Soil Inoculation with Bacillus spp. Modifies Root Endophytic Bacterial Diversity, Evenness, and Community Composition in a Context-Specific Manner.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {741-750}, pmid = {29511840}, issn = {1432-184X}, mesh = {Agricultural Inoculants/classification/physiology ; Bacillus/classification/*physiology ; Bacteria/classification/genetics/isolation &amp; purification ; *Biodiversity ; Brassica/growth &amp; development/*microbiology ; Endophytes/classification/genetics/*isolation &amp; purification ; Phylogeny ; Plant Roots/growth &amp; development/*microbiology ; *Soil Microbiology ; Species Specificity ; }, abstract = {The use of microbial inoculants containing plant growth-promoting rhizobacteria as a promoter of plant fitness and health is becoming increasingly popular in agriculture. However, whether and how these bacteria affect indigenous bacterial communities in field conditions is sparsely explored. We studied the effects of seed inoculation and field soil application of ubiquitous soil bacteria, B. cereus, B. subtilis, and B. amyloliquefaciens, on the diversity, evenness, and richness of endophytic bacterial communities in sprouting broccoli roots using high-throughput metagenome sequencing. The multiple operational taxonomic units (OTUs) assigned to different bacterial taxa clearly showed changes in ecological measures and relative abundances of certain taxa between control and treatment groups. The Bacillus inocula, themselves, failed to flourish as endophytes; however, the effects they extended on the endophytic bacterial community were both generic as well as species specific. In each case, Pseudomonadales, Rhizobiales, Xanthomonadales, and Burkholderiales were the most abundant orders in the endosphere. B. amyloliquefaciens drastically reduced the most abundant genus, Pseudomonas, while increasing the relative abundance of a range of minor taxa. The Shannon-Weiner diversity and Buzas and Gibson's evenness indices showed that the diversity and evenness were increased in both B. amyloliquefaciens and mixed treated plants. The UniFrac measurement of beta diversity showed that all treatments affected the specific composition of the endophytic bacterial community, with an apparent interspecies competition in the mixed treatment. Taken together, Bacillus species influenced the diversity, evenness, and composition of the endophytic bacterial community. However, these effects varied between different Bacillus spp. in a context-specific manner.}, }
@article {pmid29507896, year = {2018}, author = {Stagaman, K and Cepon-Robins, TJ and Liebert, MA and Gildner, TE and Urlacher, SS and Madimenos, FC and Guillemin, K and Snodgrass, JJ and Sugiyama, LS and Bohannan, BJM}, title = {Market Integration Predicts Human Gut Microbiome Attributes across a Gradient of Economic Development.}, journal = {mSystems}, volume = {3}, number = {1}, pages = {}, pmid = {29507896}, issn = {2379-5077}, support = {P50 GM098911/GM/NIGMS NIH HHS/United States ; T32 GM007413/GM/NIGMS NIH HHS/United States ; }, abstract = {Economic development is marked by dramatic increases in the incidence of microbiome-associated diseases, such as autoimmune diseases and metabolic syndromes, but the lifestyle changes that drive alterations in the human microbiome are not known. We measured market integration as a proxy for economically related lifestyle attributes, such as ownership of specific market goods that index degree of market integration and components of traditional and nontraditional (more modern) house structure and infrastructure, and profiled the fecal microbiomes of 213 participants from a contiguous, indigenous Ecuadorian population. Despite relatively modest differences in lifestyle across the population, greater economic development correlated with significantly lower within-host diversity, higher between-host dissimilarity, and a decrease in the relative abundance of the bacterium Prevotella. These microbiome shifts were most strongly associated with more modern housing, followed by reduced ownership of traditional subsistence lifestyle-associated items. IMPORTANCE Previous research has reported differences in the gut microbiome between populations residing in wealthy versus poorer countries, leading to the assertion that lifestyle changes associated with economic development promote changes in the gut microbiome that promote the proliferation of microbiome-associated diseases. However, a direct relationship between economic development and the gut microbiome has not previously been shown. We surveyed the gut microbiomes of a single indigenous population undergoing economic development and found significant associations between features of the gut microbiome and lifestyle changes associated with economic development. These findings suggest that even the earliest stages of economic development can drive changes in the gut microbiome, which may provide a warning sign for the development of microbiome-associated diseases.}, }
@article {pmid29505618, year = {2018}, author = {Douam, F and Fusil, F and Enguehard, M and Dib, L and Nadalin, F and Schwaller, L and Hrebikova, G and Mancip, J and Mailly, L and Montserret, R and Ding, Q and Maisse, C and Carlot, E and Xu, K and Verhoeyen, E and Baumert, TF and Ploss, A and Carbone, A and Cosset, FL and Lavillette, D}, title = {A protein coevolution method uncovers critical features of the Hepatitis C Virus fusion mechanism.}, journal = {PLoS pathogens}, volume = {14}, number = {3}, pages = {e1006908}, pmid = {29505618}, issn = {1553-7374}, support = {R01 AI079031/AI/NIAID NIH HHS/United States ; R01 AI079031/NH/NIH HHS/United States ; }, mesh = {Animals ; Carcinoma, Hepatocellular/metabolism/pathology/virology ; *Evolution, Molecular ; Hepacivirus/*physiology ; Hepatitis C/metabolism/pathology/virology ; Humans ; Liver Neoplasms/metabolism/pathology/virology ; Mice ; Mice, Inbred C57BL ; Protein Binding ; Tumor Cells, Cultured ; Viral Envelope Proteins/chemistry/genetics/*metabolism ; *Virus Internalization ; Virus Replication ; }, abstract = {Amino-acid coevolution can be referred to mutational compensatory patterns preserving the function of a protein. Viral envelope glycoproteins, which mediate entry of enveloped viruses into their host cells, are shaped by coevolution signals that confer to viruses the plasticity to evade neutralizing antibodies without altering viral entry mechanisms. The functions and structures of the two envelope glycoproteins of the Hepatitis C Virus (HCV), E1 and E2, are poorly described. Especially, how these two proteins mediate the HCV fusion process between the viral and the cell membrane remains elusive. Here, as a proof of concept, we aimed to take advantage of an original coevolution method recently developed to shed light on the HCV fusion mechanism. When first applied to the well-characterized Dengue Virus (DENV) envelope glycoproteins, coevolution analysis was able to predict important structural features and rearrangements of these viral protein complexes. When applied to HCV E1E2, computational coevolution analysis predicted that E1 and E2 refold interdependently during fusion through rearrangements of the E2 Back Layer (BL). Consistently, a soluble BL-derived polypeptide inhibited HCV infection of hepatoma cell lines, primary human hepatocytes and humanized liver mice. We showed that this polypeptide specifically inhibited HCV fusogenic rearrangements, hence supporting the critical role of this domain during HCV fusion. By combining coevolution analysis and in vitro assays, we also uncovered functionally-significant coevolving signals between E1 and E2 BL/Stem regions that govern HCV fusion, demonstrating the accuracy of our coevolution predictions. Altogether, our work shed light on important structural features of the HCV fusion mechanism and contributes to advance our functional understanding of this process. This study also provides an important proof of concept that coevolution can be employed to explore viral protein mediated-processes, and can guide the development of innovative translational strategies against challenging human-tropic viruses.}, }
@article {pmid29505255, year = {2018}, author = {Pepper, IL and Brooks, JP and Gerba, CP}, title = {Antibiotic Resistant Bacteria in Municipal Wastes: Is There Reason for Concern?.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {7}, pages = {3949-3959}, doi = {10.1021/acs.est.7b04360}, pmid = {29505255}, issn = {1520-5851}, mesh = {Animals ; *Anti-Bacterial Agents ; Bacteria ; Drug Resistance, Microbial ; *Genes, Bacterial ; Humans ; Manure ; }, abstract = {Recently, there has been increased concern about the presence of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARG), in treated domestic wastewaters, animal manures and municipal biosolids. The concern is whether these additional sources of ARB contribute to antibiotic resistance levels in the environment, that is, "environmental antibiotic resistance." ARB and ARG occur naturally in soil and water, and it remains unclear whether the introduction of ARB in liquid and solid municipal and animal wastes via land application have any significant impact on the background levels of antibiotic resistance in the environment, and whether they affect human exposure to ARB. In this current review, we examine and re-evaluate the incidence of ARB and ARG resulting from land application activities, and offer a new perspective on the threat of antibiotic resistance to public health via exposure from nonclinical environmental sources. Based on inputs of ARBs and ARGs from land application, their fate in soil due to soil microbial ecology principles, and background indigenous levels of ARBs and ARGs already present in soil, we conclude that while antibiotic resistance levels in soil are increased temporally by land application of wastes, their persistence is not guaranteed and is in fact variable, and often contradictory based on application site. Furthermore, the application of wastes may not produce the most direct impact of ARGs and ARB on public health. Further investigation is still warranted in agriculture and public health, including continued scrutiny of antibiotic use in both sectors.}, }
@article {pmid29504072, year = {2018}, author = {Steele, RE and Nasser, NA and Patterson, RT and Gregory, BRB and Roe, HM and Reinhardt, EG}, title = {An Assessment of Sub-Meter Scale Spatial Variability of Arcellinida (Testate Lobose Amoebae) Assemblages in a Temperate Lake: Implications for Limnological Studies.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {680-694}, pmid = {29504072}, issn = {1432-184X}, mesh = {Amoeba/classification/genetics/*isolation &amp; purification ; Biodiversity ; Canada ; Environmental Monitoring ; Geologic Sediments/chemistry/parasitology ; Iron/analysis ; Lakes/chemistry/*parasitology ; Phylogeny ; }, abstract = {Arcellinida (testate lobose amoebae), a group of benthic protists, were examined from 46 sediment-water interface samples collected from oligotrophic Oromocto Lake, New Brunswick, Canada. To assess (1) assemblage homogeneity at a sub-meter spatial scale and (2) the necessity for collecting samples from multiple stations during intra-lake surveys; multiple samples were collected from three stations (quadrats 1, 2, and 3) across the north basin of Oromocto Lake, with quadrat 1 (n = 16) being the furthest to the west, quadrat 2 (n = 15) situated closer to the center of the basin, and quadrat 3 (n = 15) positioned 300 m south of the mouth of Dead Brook, an inlet stream. Results from cluster analysis and non-metric multidimensional scaling (NMDS) analysis identified two major Arcellinida assemblages, A1 and A2, the latter containing two sub-assemblages (A2a and A2b). Redundancy analysis and variance partitioning results indicated that seven statistically significant environmental variables (K, S, Sb, Ti, Zn, Fe, and Mn) explained 41.5% of the total variation in the Arcellinida distribution. Iron, Ti and K, indicators of detrital runoff, had the greatest influence on assemblage variance. The results of this study reveal that closely spaced samples (~ 10 cm) in an open-water setting are comprised of homogenous arcellinidan assemblages, indicating that replicate sampling is not required. The results, however, must be tempered with respect to the various water properties and physical characteristics that comprise individual lakes as collection of several samples may likely be necessary when sampling multiple sites of a lake basin characterized by varying water depths (e.g., littoral zone vs. open water), or lakes impacted by geogenic or anthropogenic stressors (e.g., eutrophication, or industrial contamination).}, }
@article {pmid29503478, year = {2017}, author = {Crous, PW and Wingfield, MJ and Burgess, TI and Carnegie, AJ and Hardy, GESJ and Smith, D and Summerell, BA and Cano-Lira, JF and Guarro, J and Houbraken, J and Lombard, L and Martín, MP and Sandoval-Denis, M and Alexandrova, AV and Barnes, CW and Baseia, IG and Bezerra, JDP and Guarnaccia, V and May, TW and Hernández-Restrepo, M and Stchigel, AM and Miller, AN and Ordoñez, ME and Abreu, VP and Accioly, T and Agnello, C and Agustin Colmán, A and Albuquerque, CC and Alfredo, DS and Alvarado, P and Araújo-Magalhães, GR and Arauzo, S and Atkinson, T and Barili, A and Barreto, RW and Bezerra, JL and Cabral, TS and Camello Rodríguez, F and Cruz, RHSF and Daniëls, PP and da Silva, BDB and de Almeida, DAC and de Carvalho Júnior, AA and Decock, CA and Delgat, L and Denman, S and Dimitrov, RA and Edwards, J and Fedosova, AG and Ferreira, RJ and Firmino, AL and Flores, JA and García, D and Gené, J and Giraldo, A and Góis, JS and Gomes, AAM and Gonçalves, CM and Gouliamova, DE and Groenewald, M and Guéorguiev, BV and Guevara-Suarez, M and Gusmão, LFP and Hosaka, K and Hubka, V and Huhndorf, SM and Jadan, M and Jurjević, &#x17d; and Kraak, B and Kučera, V and Kumar, TKA and Kušan, I and Lacerda, SR and Lamlertthon, S and Lisboa, WS and Loizides, M and Luangsa-Ard, JJ and Lysková, P and Mac Cormack, WP and Macedo, DM and Machado, AR and Malysheva, EF and Marinho, P and Matočec, N and Meijer, M and Mešić, A and Mongkolsamrit, S and Moreira, KA and Morozova, OV and Nair, KU and Nakamura, N and Noisripoom, W and Olariaga, I and Oliveira, RJV and Paiva, LM and Pawar, P and Pereira, OL and Peterson, SW and Prieto, M and Rodríguez-Andrade, E and Rojo De Blas, C and Roy, M and Santos, ES and Sharma, R and Silva, GA and Souza-Motta, CM and Takeuchi-Kaneko, Y and Tanaka, C and Thakur, A and Smith, MT and Tkalčec, Z and Valenzuela-Lopez, N and van der Kleij, P and Verbeken, A and Viana, MG and Wang, XW and Groenewald, JZ}, title = {Fungal Planet description sheets: 625-715.}, journal = {Persoonia}, volume = {39}, number = {}, pages = {270-467}, pmid = {29503478}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Antarctica: Cadophora antarctica from soil. Australia: Alfaria dandenongensis on Cyperaceae, Amphosoma persooniae on Persoonia sp., Anungitea nullicana on Eucalyptus sp., Bagadiella eucalypti on Eucalyptus globulus, Castanediella eucalyptigena on Eucalyptus sp., Cercospora dianellicola on Dianella sp., Cladoriella kinglakensis on Eucalyptus regnans, Cladoriella xanthorrhoeae (incl. Cladoriellaceae fam. nov. and Cladoriellales ord. nov.) on Xanthorrhoea sp., Cochlearomyces eucalypti (incl. Cochlearomyces gen. nov. and Cochlearomycetaceae fam. nov.) on Eucalyptus obliqua, Codinaea lambertiae on Lambertia formosa, Diaporthe obtusifoliae on Acacia obtusifolia, Didymella acaciae on Acacia melanoxylon, Dothidea eucalypti on Eucalyptus dalrympleana, Fitzroyomyces cyperi (incl. Fitzroyomyces gen. nov.) on Cyperaceae, Murramarangomyces corymbiae (incl. Murramarangomyces gen. nov., Murramarangomycetaceae fam. nov. and Murramarangomycetales ord. nov.) on Corymbia maculata, Neoanungitea eucalypti (incl. Neoanungitea gen. nov.) on Eucalyptus obliqua, Neoconiothyrium persooniae (incl. Neoconiothyrium gen. nov.) on Persoonia laurina subsp. laurina, Neocrinula lambertiae (incl. Neocrinulaceae fam. nov.) on Lambertia sp., Ochroconis podocarpi on Podocarpus grayae, Paraphysalospora eucalypti (incl. Paraphysalospora gen. nov.) on Eucalyptus sieberi, Pararamichloridium livistonae (incl. Pararamichloridium gen. nov., Pararamichloridiaceae fam. nov. and Pararamichloridiales ord. nov.) on Livistona sp., Pestalotiopsis dianellae on Dianella sp., Phaeosphaeria gahniae on Gahnia aspera, Phlogicylindrium tereticornis on Eucalyptus tereticornis, Pleopassalora acaciae on Acacia obliquinervia, Pseudodactylaria xanthorrhoeae (incl. Pseudodactylaria gen. nov., Pseudodactylariaceae fam. nov. and Pseudodactylariales ord. nov.) on Xanthorrhoea sp., Pseudosporidesmium lambertiae (incl. Pseudosporidesmiaceae fam. nov.) on Lambertia formosa, Saccharata acaciae on Acacia sp., Saccharata epacridis on Epacris sp., Saccharata hakeigena on Hakea sericea, Seiridium persooniae on Persoonia sp., Semifissispora tooloomensis on Eucalyptus dunnii, Stagonospora lomandrae on Lomandra longifolia, Stagonospora victoriana on Poaceae, Subramaniomyces podocarpi on Podocarpus elatus, Sympoventuria melaleucae on Melaleuca sp., Sympoventuria regnans on Eucalyptus regnans, Trichomerium eucalypti on Eucalyptus tereticornis, Vermiculariopsiella eucalypticola on Eucalyptus dalrympleana, Verrucoconiothyrium acaciae on Acacia falciformis, Xenopassalora petrophiles (incl. Xenopassalora gen. nov.) on Petrophile sp., Zasmidium dasypogonis on Dasypogon sp., Zasmidium gahniicola on Gahnia sieberiana.Brazil: Achaetomium lippiae on Lippia gracilis, Cyathus isometricus on decaying wood, Geastrum caririense on soil, Lycoperdon demoulinii (incl. Lycoperdon subg. Arenicola) on soil, Megatomentella cristata (incl. Megatomentella gen. nov.) on unidentified plant, Mutinus verrucosus on soil, Paraopeba schefflerae (incl. Paraopeba gen. nov.) on Schefflera morototoni, Phyllosticta catimbauensis on Mandevilla catimbauensis, Pseudocercospora angularis on Prunus persica, Pseudophialophora sorghi on Sorghum bicolor, Spumula piptadeniae on Piptadenia paniculata.Bulgaria: Yarrowia parophonii from gut of Parophonus hirsutulus. Croatia: Pyrenopeziza velebitica on Lonicera borbasiana.Cyprus: Peziza halophila on coastal dunes. Czech Republic: Aspergillus contaminans from human fingernail. Ecuador: Cuphophyllus yacurensis on forest soil, Ganoderma podocarpense on fallen tree trunk. England: Pilidium anglicum (incl. Chaetomellales ord. nov.) on Eucalyptus sp. France: Planamyces parisiensis (incl. Planamyces gen. nov.) on wood inside a house. French Guiana: Lactifluus ceraceus on soil. Germany: Talaromyces musae on Musa sp. India: Hyalocladosporiella cannae on Canna indica, Nothophoma raii from soil. Italy: Setophaeosphaeria citri on Citrus reticulata, Yuccamyces citri on Citrus limon.Japan: Glutinomyces brunneus (incl. Glutinomyces gen. nov.) from roots of Quercus sp. Netherlands (all from soil): Collariella hilkhuijsenii, Fusarium petersiae, Gamsia kooimaniorum, Paracremonium binnewijzendii, Phaeoisaria annesophieae, Plectosphaerella niemeijerarum, Striaticonidium deklijnearum, Talaromyces annesophieae, Umbelopsis wiegerinckiae, Vandijckella johannae (incl. Vandijckella gen. nov. and Vandijckellaceae fam. nov.), Verhulstia trisororum (incl. Verhulstia gen. nov.). New Zealand: Lasiosphaeria similisorbina on decorticated wood. Papua New Guinea: Pseudosubramaniomyces gen. nov. (based on Pseudosubramaniomyces fusisaprophyticus comb. nov.). Slovakia: Hemileucoglossum pusillum on soil. South Africa: Tygervalleyomyces podocarpi (incl. Tygervalleyomyces gen. nov.) on Podocarpus falcatus.Spain: Coniella heterospora from herbivorous dung, Hymenochaete macrochloae on Macrochloa tenacissima, Ramaria cistophila on shrubland of Cistus ladanifer.Thailand: Polycephalomyces phaothaiensis on Coleoptera larvae, buried in soil. Uruguay: Penicillium uruguayense from soil. Vietnam: Entoloma nigrovelutinum on forest soil, Volvariella morozovae on wood of unknown tree. Morphological and culture characteristics along with DNA barcodes are provided.}, }
@article {pmid29502133, year = {2018}, author = {Wang, C and Liu, S and Zhang, Y and Liu, B and He, F and Xu, D and Zhou, Q and Wu, Z}, title = {Bacterial Communities and Their Predicted Functions Explain the Sediment Nitrogen Changes Along with Submerged Macrophyte Restoration.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {625-636}, pmid = {29502133}, issn = {1432-184X}, support = {2017ZX07602-002-004//Ministry of Science and Technology of the People's Republic of China/ ; 2016ACA169//Hubei Provincial Science and Technology Department (CN)/ ; }, mesh = {Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; China ; Ecosystem ; Geologic Sediments/analysis/*microbiology ; Lakes/analysis/*microbiology ; Magnoliopsida/*growth &amp; development ; Nitrogen/analysis/*metabolism ; Phylogeny ; }, abstract = {Submerged vegetation biomass fluctuation usually occurs during the preliminary stage of vegetation restoration in shallow lakes, which impacts the final status and duration for achieving a macrophyte-dominant state. This study uncovered the sediment N characteristics and the sediment bacterial community and their predicted functions during the preliminary stage of vegetation recovery in the West Lake, a typical subtropical degenerated shallow lake in China. Results showed increased amounts of sediment TN and NH4-N, reaching 3425.76 and 345.5 mg kg[-1], respectively, when the vegetation biomass decreased from its maximum to its minimum. The maximum concentration of sediment NH4-N reached 508.60 mg kg[-1] with the decline in vegetation, which might restrict further growth of the submerged macrophytes. The bacterial community structure during the high macrophyte biomass (HMB) period was distinct from that observed during the low macrophyte biomass (LMB) period. Specific taxa such as the phyla Chloroflexi and Acidobacteria and the genus Anaerolineaceae that are related to organic carbon degradation were significantly higher during the LMB period. Potential denitrifiers, such as Lactococcus and Bacillus genera decreased during the LMB period. Accumulation of sediment ammonia could be attributed to the enhanced production by assimilatory nitrate reduction, organic N degradation, and/or the decreased consumption by nitrification. Our findings highlight that the unstable preliminary stage of vegetation restoration brings drastic fluctuation of sediment N loading, of which NH4-N accumulation caused by bacterial communities prevents further growth of the submerged macrophytes. Therefore, extra management measures for the vegetation recovery areas should be taken to avoid excess NH4-N accumulation in sediments.}, }
@article {pmid29502003, year = {2018}, author = {Vignaroli, C and Pasquaroli, S and Citterio, B and Di Cesare, A and Mangiaterra, G and Fattorini, D and Biavasco, F}, title = {Antibiotic and heavy metal resistance in enterococci from coastal marine sediment.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {237}, number = {}, pages = {406-413}, doi = {10.1016/j.envpol.2018.02.073}, pmid = {29502003}, issn = {1873-6424}, mesh = {Adaptation, Physiological/*physiology ; Anti-Bacterial Agents/*analysis/toxicity ; Drug Resistance, Bacterial/*genetics ; Enterococcus/*physiology ; Erythromycin ; Estuaries ; Geologic Sediments/microbiology ; Metals, Heavy/*analysis/toxicity ; Microbial Sensitivity Tests ; Rivers ; Water Pollutants, Chemical/*analysis/toxicity ; }, abstract = {Sediment samples from three coastal sites - two beach resorts (Beach 1 and Beach 2 sites) and an area lying between an oil refinery and a river estuary (Estuarine site) - were analyzed for antibiotic- and heavy metal (HM)-resistant enterococci. A total of 123 enterococci, 36 E. faecium, 34 E. casseliflavus, 33 E. hirae, 5 E. faecalis, 3 E. durans, 3 E. gallinarum, and 9 Enterococcus spp, were recovered. Strains resistant to erythromycin, tetracycline and quinupristin/dalfopristin (Q/D) were recovered from all sites, whereas multidrug-resistant isolates were recovered only from "Beach 2" (14%) and "Estuarine" (3.7%). As regards HM resistance, the strains showed a high frequency (68%) of cadmium and/or copper resistance and uniform susceptibility to mercury. The prevalence of cadmium-resistant strains was significantly higher among erythromycin-resistant than among erythromycin-susceptible strains. A significant association between cadmium or copper resistance and Q/D resistance was also observed at "Estuarine" site. The levels of the two HMs in sediment from all sites were fairly low, ranging from 0.070 to 0.126 μg/g, for cadmium and from 1.00 to 7.64 μg/g for copper. Mercury was always undetectable. These findings are consistent with reports that low HM concentrations may contribute to co-selection of antibiotic-resistant bacterial strains, including enterococci.}, }
@article {pmid29501479, year = {2018}, author = {Daims, H and Wagner, M}, title = {Nitrospira.}, journal = {Trends in microbiology}, volume = {26}, number = {5}, pages = {462-463}, doi = {10.1016/j.tim.2018.02.001}, pmid = {29501479}, issn = {1878-4380}, mesh = {Ammonia/metabolism ; Archaea/metabolism ; Bacteria/classification/*metabolism ; Ecosystem ; Environmental Microbiology ; Formates/metabolism ; Nitrates/metabolism ; *Nitrification ; Nitrites/metabolism ; Oxidation-Reduction ; Oxygen ; }, abstract = {In this infographic, the key metabolic functions of Nitrospira and the role that these bacteria play in nitrification and other processes in the environment is shown. Nitrospira plays pivotal roles in nitrification as an aerobic chemolithoautotrophic nitrite-oxidizing bacterium. These bacteria often occur in close association with ammonia-oxidizing bacteria or archaea that convert ammonia to nitrite, which is further oxidized to nitrate by Nitrospira. However, in 'reciprocal feeding' interactions, Nitrospira can also provide ammonia oxidizers with ammonia released from urea or cyanate, which is further nitrified as described above. Recently discovered Nitrospira members even catalyze both nitrification steps alone and are therefore called complete ammonia oxidizers or 'comammox' organisms. Some strains of Nitrospira utilize alternative substrates, such as H2 and formate, using oxygen or nitrate as terminal electron acceptor, and can exploit these energy sources concurrently with aerobic nitrite oxidation. This metabolic versatility enables Nitrospira to colonize a broad range of habitats and to sustain shifts in environmental conditions such as changing oxygen concentrations.}, }
@article {pmid29500493, year = {2018}, author = {Gomes, T and Pereira, JA and Benhadi, J and Lino-Neto, T and Baptista, P}, title = {Endophytic and Epiphytic Phyllosphere Fungal Communities Are Shaped by Different Environmental Factors in a Mediterranean Ecosystem.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {668-679}, pmid = {29500493}, issn = {1432-184X}, support = {EXCL/AGR-PRO/0591/2012//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/98127/2013//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {Biodiversity ; Climate Change ; Ecosystem ; Endophytes/classification/genetics/*isolation &amp; purification ; Fungi/classification/genetics/*isolation &amp; purification ; Mediterranean Region ; Olea/*microbiology ; Seasons ; Trees/microbiology ; }, abstract = {The diversity and factors influencing fungal assemblages in phyllosphere of Mediterranean tree species have been barely studied, especially when endophytic and epiphytic communities are simultaneously considered. In this work, the endophytic and epiphytic fungal communities from olive tree phyllosphere were studied. This tree species is natural from the Mediterranean region and adapted to grow under adverse climatic conditions. The main objectives were to determine whether there are differences between both fungal communities and to examine whether different abiotic (climate-related) and biotic (plant organs) factors play a pivotal role in structuring these communities. Both communities differed in size and composition, with epiphytic community being richer and more abundant, displaying also a dominance of melanized fungi. Season was the major driver of community composition, especially of epiphytes. Other drivers shaping epiphytes were wind speed and temperature, while plant organ, rainfall, and temperature were the major drivers for endophytic composition. In contrast, canopy orientation caused slight variations in community composition of fungi, but with distinct effects in spring and autumn seasons. In conclusion, epiphytic and endophytic communities are not driven by the same factors. Several sources of variation undergo complex interactions to form and maintain phyllosphere fungal community in Mediterranean climates. Climatic parameters have influence on these fungal communities, suggesting that they are likely to be affected by climate changes in a near future.}, }
@article {pmid29500492, year = {2018}, author = {Holmes, DE and Orelana, R and Giloteaux, L and Wang, LY and Shrestha, P and Williams, K and Lovley, DR and Rotaru, AE}, title = {Potential for Methanosarcina to Contribute to Uranium Reduction during Acetate-Promoted Groundwater Bioremediation.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {660-667}, pmid = {29500492}, issn = {1432-184X}, support = {DE-SC0004080//the Office of Science (BER), US Department of Energy/ ; DE-SC0004814//the Office of Science (BER), US Department of Energy/ ; DE-FC02-02ER63446.AER//Novo Nordisk Foundation, Innovationsfonden/ ; }, mesh = {Acetates/*metabolism ; Biodegradation, Environmental ; Geobacter/growth &amp; development/metabolism ; Groundwater/chemistry/*microbiology ; Methane/analysis ; Methanosarcina/genetics/growth &amp; development/*metabolism ; Oxidation-Reduction ; Uranium/analysis/*metabolism ; Water Pollutants, Chemical/analysis/*metabolism ; }, abstract = {Previous studies of acetate-promoted bioremediation of uranium-contaminated aquifers focused on Geobacter because no other microorganisms that can couple the oxidation of acetate with U(VI) reduction had been detected in situ. Monitoring the levels of methyl CoM reductase subunit A (mcrA) transcripts during an acetate-injection field experiment demonstrated that acetoclastic methanogens from the genus Methanosarcina were enriched after 40 days of acetate amendment. The increased abundance of Methanosarcina corresponded with an accumulation of methane in the groundwater. In order to determine whether Methanosarcina species could be participating in U(VI) reduction in the subsurface, cell suspensions of Methanosarcina barkeri were incubated in the presence of U(VI) with acetate provided as the electron donor. U(VI) was reduced by metabolically active M. barkeri cells; however, no U(VI) reduction was observed in inactive controls. These results demonstrate that Methanosarcina species could play an important role in the long-term bioremediation of uranium-contaminated aquifers after depletion of Fe(III) oxides limits the growth of Geobacter species. The results also suggest that Methanosarcina have the potential to influence uranium geochemistry in a diversity of anaerobic sedimentary environments.}, }
@article {pmid29500265, year = {2018}, author = {Rivière, A and Selak, M and Geirnaert, A and Van den Abbeele, P and De Vuyst, L}, title = {Complementary Mechanisms for Degradation of Inulin-Type Fructans and Arabinoxylan Oligosaccharides among Bifidobacterial Strains Suggest Bacterial Cooperation.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {9}, pages = {}, pmid = {29500265}, issn = {1098-5336}, mesh = {Bifidobacterium/*metabolism ; Biodegradation, Environmental ; Colon/microbiology ; Humans ; Inulin/*metabolism ; *Microbial Interactions ; Oligosaccharides/metabolism ; Xylans/*metabolism ; }, abstract = {Inulin-type fructans (ITF) and arabinoxylan oligosaccharides (AXOS) are broken down to different extents by various bifidobacterial strains present in the human colon. To date, phenotypic heterogeneity in the consumption of these complex oligosaccharides at the strain level remains poorly studied. To examine mechanistic variations in ITF and AXOS constituent preferences present in one individual, ITF and AXOS consumption by bifidobacterial strains isolated from the simulator of the human intestinal microbial ecosystem (SHIME) after inoculation with feces from one healthy individual was investigated. Among the 18 strains identified, four species-independent clusters displaying different ITF and AXOS degradation mechanisms and preferences were found. Bifidobacterium bifidum B46 showed limited growth on all substrates, whereas B. longum B24 and B. longum B18 could grow better on short-chain-length fractions of fructooligosaccharides (FOS) than on fructose. B. longum B24 could cleave arabinose substituents of AXOS extracellularly, without using the AXOS-derived xylose backbones, whereas B. longum B18 was able to consume oligosaccharides (up to xylotetraose) preferentially and consumed AXOS to a limited extent. B. adolescentis B72 degraded all fractions of FOS simultaneously, partially degraded inulin, and could use xylose backbones longer than xylotetraose extracellularly. The strain-specific degradation mechanisms were suggested to be complementary and indicated resource partitioning. Specialization in the degradation of complex carbohydrates by bifidobacteria present on the individual level could have in vivo implications for the successful implementation of ITF and AXOS, aiming at bifidogenic and/or butyrogenic effects. Finally, this work shows the importance of taking microbial strain-level differences into account in gut microbiota research.IMPORTANCE It is well known that bifidobacteria degrade undigestible complex polysaccharides, such as ITF and AXOS, in the human colon. However, this process has never been studied for strains coexisting in the same individual. To examine strain-dependent mechanistic variations in ITF and AXOS constituent preferences present in one individual, ITF and AXOS consumption by bifidobacterial strains isolated from the SHIME after inoculation with feces from one healthy individual was investigated. Among the 18 bifidobacterial strains identified, four species-independent clusters displaying different ITF and AXOS degradation mechanisms and preferences were found, indicating that such strains can coexist in the human colon. Such specialization in the degradation of complex carbohydrates by bifidobacteria present on the individual level could have in vivo implications for the successful implementation of ITF and AXOS, aiming at bifidogenic and/or butyrogenic effects.}, }
@article {pmid29498741, year = {2018}, author = {Valeriani, F and Crognale, S and Protano, C and Gianfranceschi, G and Orsini, M and Vitali, M and Spica, VR}, title = {Metagenomic analysis of bacterial community in a travertine depositing hot spring.}, journal = {The new microbiologica}, volume = {41}, number = {2}, pages = {126-135}, pmid = {29498741}, issn = {1121-7138}, mesh = {Bacteria/*genetics/isolation &amp; purification ; Biodiversity ; Computational Biology ; DNA, Bacterial/genetics ; Hot Springs/*microbiology ; Metagenomics/*methods ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; }, abstract = {Several factors influence bacteria biodiversity in hot springs. The impact of biotic and abiotic pathways on travertine deposition plays a key role in microbial ecology and in the final composition of the waterborne microbiota. The metabolism of some bacterial groups such as photoautotrophs or lithoautotrophs influences water chemistry, favoring carbonate precipitation processes. The role of microbial mats in mineral precipitation processes is not fully clarified. For the first time, a comprehensive metagenomic analysis has been undertaken in the historical Bullicame hot spring. Bacterial biodiversity was characterized and biomineralization activities were assigned to different genera. A higher biodiversity in mat samples compared to water samples was observed: Shannon index of 3.34 and 0.86, respectively. Based on the functional assignment of each Operational Taxonomic Unit, the bacteria involved in biologically- induced mineralization are prevalent in mat and released in the water. According to the principle that each geothermal water specimen has distinctive physic-chemical characteristics, our results suggest new interacting bio-actions within these ecosystems. The saturation index and the chemical composition, as the high concentration of sulfur species and HCO3, can be linked to create a selective environment where pioneer communities are able to live and shape the ecosystem.}, }
@article {pmid29497766, year = {2018}, author = {Zhang, Y and Zhang, M and Tang, L and Che, R and Chen, H and Blumfield, T and Boyd, S and Nouansyvong, M and Xu, Z}, title = {Long-Term Harvest Residue Retention Could Decrease Soil Bacterial Diversities Probably Due to Favouring Oligotrophic Lineages.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {771-781}, pmid = {29497766}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; Carbon/analysis/metabolism ; Nitrogen/analysis/metabolism ; Phylogeny ; Queensland ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Harvest residues contain large stores of carbon (C) and nitrogen (N) in forest plantations. Decomposing residues can release labile C and N into soil and thus provide substrates for soil bacterial communities. Previous studies showed that residue retention could increase soil C and N pools and activate bacterial communities in the short term (≤ 10 years). The current study examined the effects of a long-term (19-year) harvest residue retention on soil total and water and hot water extractable C and N pools, as well as bacterial communities via Illumina MiSeq sequencing. The experiment was established in a randomised complete block design with four replications, southeast Queensland of Australia, including no (R0), single (R1, 51 to 74 t ha[-1] dry matter) and double quantities (R2, 140 t ha[-1] dry matter) of residues retained. Generally, no significant differences existed in total C and N, as well as C and N pools extracted by water and hot water among the three treatments, probably due to negligible amounts of labile C and N released from harvest residues. Soil δ[15]N significantly decreased from R0 to R1 to R2, probably due to reduced N leaching with residue retention (P < 0.001). Residue retention increased the relative abundances of Actinobacteria (P = 0.016) and Spartobacteria (P < 0.001), whereas decreased Betaproteobacteria (P = 0.050). This favour for the oligotrophic groups probably caused the decrease in the bacterial diversity as revealed by Shannon index (P = 0.025). Hence, our study suggests that residue retention is not an appropriate management practice in the long term.}, }
@article {pmid29493143, year = {2017}, author = {Zhang, AH and Lei, FJ and Fu, JF and Zhou, RJ and Zhang, LX}, title = {[Influence of exogenous ginsenosides on new forest soil microbial communities].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {42}, number = {24}, pages = {4756-4761}, doi = {10.19540/j.cnki.cjcmm.2017.0213}, pmid = {29493143}, issn = {1001-5302}, mesh = {*Forests ; Ginsenosides/*pharmacology ; Microbiota/*drug effects ; Panax/*chemistry ; Soil ; *Soil Microbiology ; }, abstract = {Ginsenosides are the main active ingredient and allelochemicals of Panax ginseng, and they play an important role in ginseng growth and in ecological adaptation. To study the influence of ginsenosides on soil microbial communities, the method of given exogenous total ginsenosides of different concentrations were used to study the influence of ginsenosides on new forest soil microbial community, evaluate the change of metabolic activity of microbial community and investigate the ecological effect of ginsenosides on soil microbial community. Results showed that, exogenous total ginsenosides promoted metabolic activity of microbial community in new forest soil at different concentrations compared with the control after 10 d and 40 d treatment. After 10 d,except for the Evenness index, all of the other indices indicated that the functional diversity of the soil microbial community in the new forest firstly increased then decreased with increase of the total ginsenosides concentration. The Substrate richness for 0.01 g•L[-1] soil treatment was significantly different from that of the control. After 20 d, 30 d and 40 d, except for the Evenness index, all of the other indices indicated that the functional diversity of the soil microbial community in the new forest increased with total ginsenosides. These results suggested that ginsenosids can change soil microbial community and microbial metabolic activity, which alter soil microbial ecology and accordingly affect the growth of ginseng with accumulation of ginsenosides in the soil.}, }
@article {pmid29492895, year = {2018}, author = {Rampelli, S and Turroni, S}, title = {From Whole-Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1746}, number = {}, pages = {181-185}, doi = {10.1007/978-1-4939-7683-6_14}, pmid = {29492895}, issn = {1940-6029}, mesh = {Computational Biology ; DNA, Viral/*analysis/genetics ; *Genome, Viral ; Metagenomics/*methods ; *Software ; Viruses/*classification/*genetics ; Whole Genome Sequencing/*methods ; }, abstract = {ViromeScan is an innovative metagenomic analysis tool that allows the viral community characterization in terms of taxonomy from raw data of metagenomics sequencing. It efficiently denoises samples from reads of other microorganisms. Users can adopt the same shotgun metagenomic sequencing data to fully characterize complex microbial ecosystems, including bacteria and viruses. Here we apply ViromeScan pipeline to some examples, thus illustrating the processes computed from raw data to the final output.}, }
@article {pmid29492666, year = {2018}, author = {Cid, FP and Maruyama, F and Murase, K and Graether, SP and Larama, G and Bravo, LA and Jorquera, MA}, title = {Draft genome sequences of bacteria isolated from the Deschampsia antarctica phyllosphere.}, journal = {Extremophiles : life under extreme conditions}, volume = {22}, number = {3}, pages = {537-552}, pmid = {29492666}, issn = {1433-4909}, support = {1160302//Fondo de Fomento al Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; }, mesh = {*Acclimatization ; Bacterial Outer Membrane Proteins/genetics ; *Cold Temperature ; *Genome, Bacterial ; *Microbiota ; Molecular Sequence Annotation ; Poaceae/*microbiology ; Pseudomonas/genetics/isolation &amp; purification/metabolism ; }, abstract = {Genome analyses are being used to characterize plant growth-promoting (PGP) bacteria living in different plant compartiments. In this context, we have recently isolated bacteria from the phyllosphere of an Antarctic plant (Deschampsia antarctica) showing ice recrystallization inhibition (IRI), an activity related to the presence of antifreeze proteins (AFPs). In this study, the draft genomes of six phyllospheric bacteria showing IRI activity were sequenced and annotated according to their functional gene categories. Genome sizes ranged from 5.6 to 6.3 Mbp, and based on sequence analysis of the 16S rRNA genes, five strains were identified as Pseudomonas and one as Janthinobacterium. Interestingly, most strains showed genes associated with PGP traits, such as nutrient uptake (ammonia assimilation, nitrogen fixing, phosphatases, and organic acid production), bioactive metabolites (indole acetic acid and 1-aminocyclopropane-1-carboxylate deaminase), and antimicrobial compounds (hydrogen cyanide and pyoverdine). In relation with IRI activity, a search of putative AFPs using current bioinformatic tools was also carried out. Despite that genes associated with reported AFPs were not found in these genomes, genes connected to ice-nucleation proteins (InaA) were found in all Pseudomonas strains, but not in the Janthinobacterium strain.}, }
@article {pmid29492595, year = {2018}, author = {Lenaers, M and Reyns, W and Czech, J and Carleer, R and Basak, I and Deferme, W and Krupinska, P and Yildiz, T and Saro, S and Remans, T and Vangronsveld, J and De Laender, F and Rineau, F}, title = {Links Between Heathland Fungal Biomass Mineralization, Melanization, and Hydrophobicity.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {762-770}, pmid = {29492595}, issn = {1432-184X}, support = {08M03VGRJ//METHUZALEM/ ; }, mesh = {Biomass ; Ecosystem ; Fungi/*growth &amp; development/metabolism ; Hydrophobic and Hydrophilic Interactions ; Melanins/*analysis ; Plants/chemistry/metabolism ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Comprehending the decomposition process is crucial for our understanding of the mechanisms of carbon (C) sequestration in soils. The decomposition of plant biomass has been extensively studied. It revealed that extrinsic biomass properties that restrict its access to decomposers influence decomposition more than intrinsic ones that are only related to its chemical structure. Fungal biomass has been much less investigated, even though it contributes to a large extent to soil organic matter, and is characterized by specific biochemical properties. In this study, we investigated the extent to which decomposition of heathland fungal biomass was affected by its hydrophobicity (extrinsic property) and melanin content (intrinsic property). We hypothesized that, as for plant biomass, hydrophobicity would have a greater impact on decomposition than melanin content. Mineralization was determined as the mineralization of soil organic carbon (SOC) into CO2 by headspace GC/MS after inoculation by a heathland soil microbial community. Results show that decomposition was not affected by hydrophobicity, but was negatively correlated with melanin content. We argue that it may indicate that either melanin content is both an intrinsic and extrinsic property, or that some soil decomposers evolved the ability to use surfactants to access to hydrophobic biomass. In the latter case, biomass hydrophobicity should not be considered as a crucial extrinsic factor. We also explored the ecology of decomposition, melanin content, and hydrophobicity, among heathland soil fungal guilds. Ascomycete black yeasts had the highest melanin content, and hyaline Basidiomycete yeasts the lowest. Hydrophobicity was an all-or-nothing trait, with most isolates being hydrophobic.}, }
@article {pmid29492594, year = {2018}, author = {Schorn, S and Cypionka, H}, title = {A Crispy Diet: Grazers of Achromatium oxaliferum in Lake Stechlin Sediments.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {584-587}, pmid = {29492594}, issn = {1432-184X}, mesh = {Amoeba/physiology ; Animals ; Ciliophora/physiology ; Geologic Sediments/*microbiology/parasitology ; Gram-Negative Aerobic Bacteria/classification/genetics/*growth &amp; development/isolation &amp; purification ; Lakes/*microbiology/parasitology ; Oligochaeta/physiology ; }, abstract = {Achromatium is the largest freshwater bacterium known to date and easily recognised by conspicuous calcite bodies filling the cell volume. Members of this genus are highly abundant in diverse aquatic sediments and may account for up to 90% of the bacterial biovolume in the oxic-anoxic interfaces. The high abundance implies that Achromatium is either rapidly growing or hardly prone to predation. As Achromatium is still uncultivated and does not appear to grow fast, one could assume that the cells might escape predation by their unusual shape and composition. However, we observed various members of the meiofauna grazing or parasitizing on Achromatium. By microphotography, we documented amoebae, ciliates, oligochetes and plathelminthes having Achromatium cells ingested. Some Achromatium cells harboured structures resembling sporangia of parasitic fungi (chytrids) that could be stained with the chitin-specific dye Calcofluor White. Many Achromatia carried prokaryotic epibionts in the slime layer surrounding the cells. Their regular distribution over the cell might indicate that they are commensalistic rather than harming their hosts. In conclusion, we report on various interactions of Achromatium with the sediment community and show that although Achromatium cells are a crispy diet, full of calcite bodies, predators do not spare them.}, }
@article {pmid29492330, year = {2017}, author = {Lang, JM and Coil, DA and Neches, RY and Brown, WE and Cavalier, D and Severance, M and Hampton-Marcell, JT and Gilbert, JA and Eisen, JA}, title = {A microbial survey of the International Space Station (ISS).}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e4029}, pmid = {29492330}, issn = {2167-8359}, abstract = {BACKGROUND: Modern advances in sequencing technology have enabled the census of microbial members of many natural ecosystems. Recently, attention is increasingly being paid to the microbial residents of human-made, built ecosystems, both private (homes) and public (subways, office buildings, and hospitals). Here, we report results of the characterization of the microbial ecology of a singular built environment, the International Space Station (ISS). This ISS sampling involved the collection and microbial analysis (via 16S rDNA PCR) of 15 surfaces sampled by swabs onboard the ISS. This sampling was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS). Learning more about the microbial inhabitants of the "buildings" in which we travel through space will take on increasing importance, as plans for human exploration continue, with the possibility of colonization of other planets and moons.<br><br>RESULTS: Sterile swabs were used to sample 15 surfaces onboard the ISS. The sites sampled were designed to be analogous to samples collected for (1) the Wildlife of Our Homes project and (2) a study of cell phones and shoes that were concurrently being collected for another component of Project MERCCURI. Sequencing of the 16S rDNA genes amplified from DNA extracted from each swab was used to produce a census of the microbes present on each surface sampled. We compared the microbes found on the ISS swabs to those from both homes on Earth and data from the Human Microbiome Project.<br><br>CONCLUSIONS: While significantly different from homes on Earth and the Human Microbiome Project samples analyzed here, the microbial community composition on the ISS was more similar to home surfaces than to the human microbiome samples. The ISS surfaces are species-rich with 1,036-4,294 operational taxonomic units (OTUs per sample). There was no discernible biogeography of microbes on the 15 ISS surfaces, although this may be a reflection of the small sample size we were able to obtain.}, }
@article {pmid29491857, year = {2018}, author = {Borgo, F and Garbossa, S and Riva, A and Severgnini, M and Luigiano, C and Benetti, A and Pontiroli, AE and Morace, G and Borghi, E}, title = {Body Mass Index and Sex Affect Diverse Microbial Niches within the Gut.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {213}, pmid = {29491857}, issn = {1664-302X}, abstract = {Gut microbiota is considered a separate organ with endocrine capabilities, actively contributing to tissue homeostasis. It consists of at least two separate microbial populations, the lumen-associated (LAM) and the mucosa-associated microbiota (MAM). In the present study, we compared LAM and MAM, by collecting stools and sigmoid brush samples of forty adults without large-bowel symptoms, and through a 16S rRNA gene next-generation sequencing (NGS) approach. MAM sample analysis revealed enrichment in aerotolerant Proteobacteria, probably selected by a gradient of oxygen that decreases from tissue to lumen, and in Streptococcus and Clostridium spp., highly fermenting bacteria. On the other hand, LAM microbiota showed an increased abundance in Bacteroides, Prevotella, and Oscillospira, genera able to digest and to degrade biopolymers in the large intestine. Predicted metagenomic analysis showed LAM to be enriched in genes encoding enzymes mostly involved in energy extraction from carbohydrates and lipids, whereas MAM in amino acid and vitamin metabolism. Moreover, LAM and MAM communities seemed to be influenced by different host factors, such as diet and sex. LAM is affected by body mass index (BMI) status. Indeed, BMI negatively correlates with Faecalibacterium prausnitzii and Flavonifractor plautii abundance, putative biomarkers of healthy status. In contrast, MAM microbial population showed a significant grouping according to sex. Female MAM was enriched in Actinobacteria (with an increased trend of the genus Bifidobacterium), and a significant depletion in Veillonellaceae. Interestingly, we found the species Gemmiger formicilis to be associated with male and Bifidobacterium adolescentis, with female MAM samples. In conclusion, our results suggest that gut harbors microbial niches that differ in both composition and host factor susceptibility, and their richness and diversity may be overlooked evaluating only fecal samples.}, }
@article {pmid29491853, year = {2018}, author = {Daebeler, A and Herbold, CW and Vierheilig, J and Sedlacek, CJ and Pjevac, P and Albertsen, M and Kirkegaard, RH and de la Torre, JR and Daims, H and Wagner, M}, title = {Cultivation and Genomic Analysis of "Candidatus Nitrosocaldus islandicus," an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {193}, pmid = {29491853}, issn = {1664-302X}, support = {294343/ERC_/European Research Council/International ; P 25231/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota are the only known aerobic ammonia oxidizers in geothermal environments. Although molecular data indicate the presence of phylogenetically diverse AOA from the Nitrosocaldus clade, group 1.1b and group 1.1a Thaumarchaeota in terrestrial high-temperature habitats, only one enrichment culture of an AOA thriving above 50°C has been reported and functionally analyzed. In this study, we physiologically and genomically characterized a newly discovered thaumarchaeon from the deep-branching Nitrosocaldaceae family of which we have obtained a high (∼85%) enrichment from biofilm of an Icelandic hot spring (73°C). This AOA, which we provisionally refer to as "Candidatus Nitrosocaldus islandicus," is an obligately thermophilic, aerobic chemolithoautotrophic ammonia oxidizer, which stoichiometrically converts ammonia to nitrite at temperatures between 50 and 70°C. "Ca. N. islandicus" encodes the expected repertoire of enzymes proposed to be required for archaeal ammonia oxidation, but unexpectedly lacks a nirK gene and also possesses no identifiable other enzyme for nitric oxide (NO) generation. Nevertheless, ammonia oxidation by this AOA appears to be NO-dependent as "Ca. N. islandicus" is, like all other tested AOA, inhibited by the addition of an NO scavenger. Furthermore, comparative genomics revealed that "Ca. N. islandicus" has the potential for aromatic amino acid fermentation as its genome encodes an indolepyruvate oxidoreductase (iorAB) as well as a type 3b hydrogenase, which are not present in any other sequenced AOA. A further surprising genomic feature of this thermophilic ammonia oxidizer is the absence of DNA polymerase D genes - one of the predominant replicative DNA polymerases in all other ammonia-oxidizing Thaumarchaeota. Collectively, our findings suggest that metabolic versatility and DNA replication might differ substantially between obligately thermophilic and other AOA.}, }
@article {pmid29488974, year = {2018}, author = {Thwaites, BJ and van den Akker, B and Reeve, PJ and Short, MD and Dinesh, N and Alvarez-Gaitan, JP and Stuetz, R}, title = {Ecology and performance of aerobic granular sludge treating high-saline municipal wastewater.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {77}, number = {3-4}, pages = {1107-1114}, doi = {10.2166/wst.2017.626}, pmid = {29488974}, issn = {0273-1223}, mesh = {Aerobiosis ; Anaerobiosis ; Archaea/classification/metabolism ; Bacteria/classification/metabolism ; Nitrogen/metabolism ; Salinity ; Waste Disposal, Fluid/*methods ; Wastewater ; }, abstract = {The successful development of aerobic granular sludge (AGS) for secondary wastewater treatment has been linked to a dedicated anaerobic feeding phase, which enables key microbes such as poly-phosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms to gain a competitive advantage over floc-forming organisms. The application of AGS to treat high-saline sewage and its subsequent impacts on microbial ecology, however, are less well understood. In this study, the impacts of high-saline sewage on AGS development, performance and ecology were investigated using molecular microbiology methods. Two feeding strategies were compared at pilot scale: a full (100%) anaerobic feed; and a partial (33%) anaerobic feed. The results were compared to a neighbouring full-scale conventional activated sludge (CAS) system (100% aerobic). We observed that AGS developed under decreased anaerobic contact showed a comparable formation, stability and nitrogen removal performance to the 100% anaerobically fed system. Analysis of the microbial ecology showed that the altered anaerobic contact had minimal effect on the abundances of the functional nitrifying and denitrifying bacteria and Archaea; however, there were notable ecological differences when comparing different sized granules. In contrast to previous work, a large enrichment in PAOs in AGS was not observed in high-saline wastewater, which coincided with poor observed phosphate removal performance. Instead, AGS exhibited a substantial enrichment in sulfide-oxidising bacteria, which was complemented by elemental analysis that identified the presence of elemental sulfur precipitation. The potential role for these organisms in AGS treating high-saline wastewater is discussed.}, }
@article {pmid29483968, year = {2018}, author = {Ramaloko, WT and Koen, N and Polliack, S and Aliyu, H and Lebre, PH and Mohr, T and Oswald, F and Zwick, M and Zeigler, DR and Neumann, A and Syldatk, C and Cowan, DA and De Maayer, P}, title = {High Quality Draft Genomes of the Type Strains Geobacillus thermocatenulatus DSM 730[T], G. uzenensis DSM 23175[T] And Parageobacillus galactosidasius DSM 18751[T].}, journal = {Journal of genomics}, volume = {6}, number = {}, pages = {20-23}, pmid = {29483968}, issn = {1839-9940}, abstract = {The thermophilic 'Geobacilli' are important sources of thermostable enzymes and other biotechnologically relevant macromolecules. The present work reports the high quality draft genome sequences of previously unsequenced type strains of Geobacillus uzenensis (DSM 23175[T]), G. thermocatenulatus (DSM 730[T]) and Parageobacillus galactosidasius (DSM 18751[T]). Phylogenomic analyses revealed that DSM 18751[T] and DSM 23175[T] represent later heterotypic synonyms of P. toebii and G. subterraneus, respectively, while DSM 730[T] represents the type strain for the species G. thermocatenulatus. These genome sequences will contribute towards a deeper understanding of the ecological and biological diversity and the biotechnological exploitation of the 'geobacilli'.}, }
@article {pmid29483941, year = {2018}, author = {Cassman, NA and Lourenço, KS and do Carmo, JB and Cantarella, H and Kuramae, EE}, title = {Genome-resolved metagenomics of sugarcane vinasse bacteria.}, journal = {Biotechnology for biofuels}, volume = {11}, number = {}, pages = {48}, pmid = {29483941}, issn = {1754-6834}, abstract = {BACKGROUND: The production of 1 L of ethanol from sugarcane generates up to 12 L of vinasse, which is a liquid waste containing an as-yet uncharacterized microbial assemblage. Most vinasse is destined for use as a fertilizer on the sugarcane fields because of the high organic and K content; however, increased N2O emissions have been observed when vinasse is co-applied with inorganic N fertilizers. Here we aimed to characterize the microbial assemblage of vinasse to determine the gene potential of vinasse microbes for contributing to negative environmental effects during fertirrigation and/or to the obstruction of bioethanol fermentation.<br><br>RESULTS: We measured chemical characteristics and extracted total DNA from six vinasse batches taken over 1.5&#xa0;years from a bioethanol and sugar mill in Sao Paulo State. The vinasse microbial assemblage was characterized by low alpha diversity with 5-15 species across the six vinasses. The core genus was Lactobacillus. The top six represented bacterial genera across the samples were Lactobacillus, Megasphaera and Mitsuokella (Phylum Firmicutes, 35-97% of sample reads); Arcobacter and Alcaligenes (Phylum Proteobacteria, 0-40%); Dysgonomonas (Phylum Bacteroidetes, 0-53%); and Bifidobacterium (Phylum Actinobacteria, 0-18%). Potential genes for denitrification but not nitrification were identified in the vinasse metagenomes, with putative nirK and nosZ genes the most represented. Binning resulted in 38 large bins with between 36.0 and 99.3% completeness, and five small mobile element bins. Of the large bins, 53% could be classified at the phylum level as Firmicutes, 15% as Proteobacteria, 13% as unknown phyla, 13% as Bacteroidetes and 6% as Actinobacteria. The large bins spanned a range of potential denitrifiers; moreover, the genetic repertoires of all the large bins included the presence of genes involved in acetate, CO2, ethanol, H2O2, and lactose metabolism; for many of the large bins, genes related to the metabolism of mannitol, xylose, butyric acid, cellulose, sucrose, "3-hydroxy" fatty acids and antibiotic resistance were present&#xa0;based on the annotations. In total, 21 vinasse bacterial draft genomes were submitted to the genome repository.<br><br>CONCLUSIONS: Identification of the gene repertoires of vinasse bacteria and assemblages supported the idea that organic carbon and nitrogen present in vinasse together with microbiological variation of vinasse might lead to varying patterns of N2O emissions during fertirrigation. Furthermore, we uncovered draft genomes of novel strains of known bioethanol contaminants, as well as draft genomes unknown at the phylum level. This study will aid efforts to improve bioethanol production efficiency and sugarcane agriculture sustainability.}, }
@article {pmid29483898, year = {2018}, author = {Wood, JL and Tang, C and Franks, AE}, title = {Competitive Traits Are More Important than Stress-Tolerance Traits in a Cadmium-Contaminated Rhizosphere: A Role for Trait Theory in Microbial Ecology.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {121}, pmid = {29483898}, issn = {1664-302X}, abstract = {Understanding how biotic and abiotic factors govern the assembly of rhizosphere-microbial communities is a long-standing goal in microbial ecology. In phytoremediation research, where plants are used to remediate heavy metal-contaminated soils, a deeper understanding of rhizosphere-microbial ecology is needed to fully exploit the potential of microbial-assisted phytoremediation. This study investigated whether Grime's competitor/stress-tolerator/ruderal (CSR) theory could be used to describe the impact of cadmium (Cd) and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw.) Schwantes, on the assembly of soil-bacterial communities using Illumina 16S rRNA profiling and the predictive metagenomic-profiling program, PICRUSt. Using predictions based on CSR theory, we hypothesized that Cd and the presence of a rhizosphere would affect community assembly. We predicted that the additional resource availability in the rhizosphere would enrich for competitive life strategists, while the presence of Cd would select for stress-tolerators. Traits identified as competitive followed CSR predictions, discriminating between rhizosphere and bulk-soil communities whilst stress-tolerance traits increased with Cd dose, but only in bulk-soil communities. These findings suggest that a bacterium's competitive attributes are critical to its ability to occupy and proliferate in a Cd-contaminated rhizosphere. Ruderal traits, which relate to community re-colonization potential, were synergistically decreased by the presence of the rhizosphere and Cd dose. Taken together this microcosm study suggests that the CSR theory is broadly applicable to microbial communities. Further work toward developing a simplified and robust strategy for microbial CSR classification will provide an ecologically meaningful framework to interpret community-level changes across a range of biomes.}, }
@article {pmid29482646, year = {2018}, author = {Louca, S and Doebeli, M and Parfrey, LW}, title = {Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {41}, pmid = {29482646}, issn = {2049-2618}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Base Sequence/genetics ; Gene Dosage/*genetics ; Genome, Bacterial/genetics ; Humans ; Metagenomics/methods ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {The 16S ribosomal RNA gene is the most widely used marker gene in microbial ecology. Counts of 16S sequence variants, often in PCR amplicons, are used to estimate proportions of bacterial and archaeal taxa in microbial communities. Because different organisms contain different 16S gene copy numbers (GCNs), sequence variant counts are biased towards clades with greater GCNs. Several tools have recently been developed for predicting GCNs using phylogenetic methods and based on sequenced genomes, in order to correct for these biases. However, the accuracy of those predictions has not been independently assessed. Here, we systematically evaluate the predictability of 16S GCNs across bacterial and archaeal clades, based on ∼ 6,800 public sequenced genomes and using several phylogenetic methods. Further, we assess the accuracy of GCNs predicted by three recently published tools (PICRUSt, CopyRighter, and PAPRICA) over a wide range of taxa and for 635 microbial communities from varied environments. We find that regardless of the phylogenetic method tested, 16S GCNs could only be accurately predicted for a limited fraction of taxa, namely taxa with closely to moderately related representatives (≲15% divergence in the 16S rRNA gene). Consistent with this observation, we find that all considered tools exhibit low predictive accuracy when evaluated against completely sequenced genomes, in some cases explaining less than 10% of the variance. Substantial disagreement was also observed between tools (R[2]<0.5) for the majority of tested microbial communities. The nearest sequenced taxon index (NSTI) of microbial communities, i.e., the average distance to a sequenced genome, was a strong predictor for the agreement between GCN prediction tools on non-animal-associated samples, but only a moderate predictor for animal-associated samples. We recommend against correcting for 16S GCNs in microbiome surveys by default, unless OTUs are sufficiently closely related to sequenced genomes or unless a need for true OTU proportions warrants the additional noise introduced, so that community profiles remain interpretable and comparable between studies.}, }
@article {pmid29477793, year = {2018}, author = {Ganigué, R and Jiang, G and Liu, Y and Sharma, K and Wang, YC and Gonzalez, J and Nguyen, T and Yuan, Z}, title = {Improved sulfide mitigation in sewers through on-line control of ferrous salt dosing.}, journal = {Water research}, volume = {135}, number = {}, pages = {302-310}, doi = {10.1016/j.watres.2018.02.022}, pmid = {29477793}, issn = {1879-2448}, mesh = {*Algorithms ; Australia ; Equipment Design ; Ferrous Compounds/*chemistry ; Hydrogen-Ion Concentration ; Oxidation-Reduction ; Reproducibility of Results ; Sewage/*chemistry ; Sulfides/*chemistry ; }, abstract = {Water utilities worldwide spend annually billions of dollars to control sulfide-induced corrosion in sewers. Iron salts chemically oxidize and/or precipitate dissolved sulfide in sewage and are especially used in medium- and large-size sewers. Iron salt dosing rates are defined ad hoc, ignoring variation in sewage flows and sulfide levels. This often results in iron overdosing or poor sulfide control. Online dosing control can adjust the chemical dosing rates to current (and future) state of the sewer system, allowing high-precision, stable and cost-effective sulfide control. In this paper, we report a novel and robust online control strategy for the dosing of ferrous salt in sewers. The control considers the fluctuation of sewage flow, pH, sulfide levels and also the perturbation from rainfall. Sulfide production in the pipe is predicted using auto-regressive models (AR) based on current flow measurements, which in turn can be used to determine the dose of ferrous salt required for cost-effective sulfide control. Following comprehensive model-based assesment, the control was successfully validated and its effectiveness demonstrated in a 3-week field trial. The online control algorithm controlled sulfide below the target level (0.5 mg S/L) while reducing chemical dosing up to 30%.}, }
@article {pmid29476344, year = {2018}, author = {Skelton, J and Jusino, MA and Li, Y and Bateman, C and Thai, PH and Wu, C and Lindner, DL and Hulcr, J}, title = {Detecting Symbioses in Complex Communities: the Fungal Symbionts of Bark and Ambrosia Beetles Within Asian Pines.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {839-850}, pmid = {29476344}, issn = {1432-184X}, support = {12-CA-11420004-042//U.S. Forest Service/ ; 14-8130-0377-CA//USDA Farm Bill Agreement/ ; DEB 1556283//Division of Environmental Biology/ ; }, mesh = {Animals ; Biodiversity ; China ; Coleoptera/classification/*microbiology/physiology ; Fungi/classification/genetics/*isolation &amp; purification/physiology ; Host Specificity ; Phylogeny ; Pinus/*parasitology ; *Symbiosis ; Vietnam ; }, abstract = {Separating symbioses from incidental associations is a major obstacle in symbiosis research. In this survey of fungi associated with Asian bark and ambrosia beetles, we used quantitative culture and DNA barcode identification to characterize fungal communities associated with co-infesting beetle species in pines (Pinus) of China and Vietnam. To quantitatively discern likely symbioses from coincidental associations, we used multivariate analysis and multilevel pattern analysis (a type of indicator species analysis). Nearly half of the variation in fungal community composition in beetle galleries and on beetle bodies was explained by beetle species. We inferred a spectrum of ecological strategies among beetle-associated fungi: from generalist multispecies associates to highly specialized single-host symbionts that were consistently dominant within the mycangia of their hosts. Statistically significant fungal associates of ambrosia beetles were typically only found with one beetle species. In contrast, bark beetle-associated fungi were often associated with multiple beetle species. Ambrosia beetles and their galleries were frequently colonized by low-prevalence ambrosia fungi, suggesting that facultative ambrosial associations are commonplace, and ecological mechanisms such as specialization and competition may be important in these dynamic associations. The approach used here could effectively delimit symbiotic interactions in any system where symbioses are obscured by frequent incidental associations. It has multiple advantages including (1) powerful statistical tests for non-random associations among potential symbionts, (2) simultaneous evaluation of multiple co-occurring host and symbiont associations, and (3) identifying symbionts that are significantly associated with multiple host species.}, }
@article {pmid29476343, year = {2018}, author = {Stritzler, M and Soto, G and Ayub, N}, title = {Plant Growth-Promoting Genes can Switch to be Virulence Factors via Horizontal Gene Transfer.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {579-583}, pmid = {29476343}, issn = {1432-184X}, support = {PICT-2014-3659//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; }, mesh = {Bacterial Proteins/*genetics/metabolism ; *Gene Transfer, Horizontal ; Medicago sativa/growth &amp; development/*microbiology ; Pectobacterium carotovorum/*genetics/metabolism ; Phylogeny ; Plant Diseases/*microbiology ; Pseudomonas fluorescens/*genetics/metabolism ; Virulence Factors/*genetics/metabolism ; }, abstract = {There are increasing evidences that horizontal gene transfer (HGT) is a critical mechanism of bacterial evolution, while its complete impact remains unclear. A main constraint of HGT effects on microbial evolution seems to be the conservation of the function of the horizontally transferred genes. From this perspective, inflexible nomenclature and functionality criteria have been established for some mobile genetic elements such as pathogenic and symbiotic islands. Adhesion is a universal prerequisite for both beneficial and pathogenic plant-microbe interactions, and thus, adhesion systems (e.g., the Lap cluster) are candidates to have a dual function depending on the genomic background. In this study, we showed that the virulent factor Lap of the phytopathogen Erwinia carotovora SCRI1043, which is located within a genomic island, was acquired by HGT and probably derived from Pseudomonas. The transformation of the phytopathogen Erwinia pyrifoliae Ep1/96 with the beneficial factor Lap from the plant growth-promoting bacterium Pseudomonas fluorescens Pf-5 significantly increased its natural virulence, experimentally recapitulating the beneficial-to-virulence functional switch of the Lap cluster via HGT. To our knowledge, this is the first report of a functional switch of an individual gene or a cluster of genes mediated by HGT.}, }
@article {pmid29476143, year = {2018}, author = {Hausmann, B and Pelikan, C and Herbold, CW and Köstlbacher, S and Albertsen, M and Eichorst, SA and Glavina Del Rio, T and Huemer, M and Nielsen, PH and Rattei, T and Stingl, U and Tringe, SG and Trojan, D and Wentrup, C and Woebken, D and Pester, M and Loy, A}, title = {Peatland Acidobacteria with a dissimilatory sulfur metabolism.}, journal = {The ISME journal}, volume = {12}, number = {7}, pages = {1729-1742}, pmid = {29476143}, issn = {1751-7370}, support = {I 1628/FWF_/Austrian Science Fund FWF/Austria ; P 23117/FWF_/Austrian Science Fund FWF/Austria ; P 25111/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Acidobacteria/genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Oxidation-Reduction ; Soil/chemistry ; Soil Microbiology ; Sulfates/metabolism ; Sulfites/metabolism ; Sulfur/*metabolism ; Wetlands ; }, abstract = {Sulfur-cycling microorganisms impact organic matter decomposition in wetlands and consequently greenhouse gas emissions from these globally relevant environments. However, their identities and physiological properties are largely unknown. By applying a functional metagenomics approach to an acidic peatland, we recovered draft genomes of seven novel Acidobacteria species with the potential for dissimilatory sulfite (dsrAB, dsrC, dsrD, dsrN, dsrT, dsrMKJOP) or sulfate respiration (sat, aprBA, qmoABC plus dsr genes). Surprisingly, the genomes also encoded DsrL, which so far was only found in sulfur-oxidizing microorganisms. Metatranscriptome analysis demonstrated expression of acidobacterial sulfur-metabolism genes in native peat soil and their upregulation in diverse anoxic microcosms. This indicated an active sulfate respiration pathway, which, however, might also operate in reverse for dissimilatory sulfur oxidation or disproportionation as proposed for the sulfur-oxidizing Desulfurivibrio alkaliphilus. Acidobacteria that only harbored genes for sulfite reduction additionally encoded enzymes that liberate sulfite from organosulfonates, which suggested organic sulfur compounds as complementary energy sources. Further metabolic potentials included polysaccharide hydrolysis and sugar utilization, aerobic respiration, several fermentative capabilities, and hydrogen oxidation. Our findings extend both, the known physiological and genetic properties of Acidobacteria and the known taxonomic diversity of microorganisms with a DsrAB-based sulfur metabolism, and highlight new fundamental niches for facultative anaerobic Acidobacteria in wetlands based on exploitation of inorganic and organic sulfur molecules for energy conservation.}, }
@article {pmid29473070, year = {2018}, author = {Casanova-Martí, &#xc0; and Serrano, J and Portune, KJ and Sanz, Y and Blay, MT and Terra, X and Ardévol, A and Pinent, M}, title = {Grape seed proanthocyanidins influence gut microbiota and enteroendocrine secretions in female rats.}, journal = {Food &amp; function}, volume = {9}, number = {3}, pages = {1672-1682}, doi = {10.1039/c7fo02028g}, pmid = {29473070}, issn = {2042-650X}, mesh = {Adiposity/drug effects ; Animals ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Butyrates/metabolism ; Female ; Gallic Acid/metabolism ; Gastrointestinal Microbiome/*drug effects ; Glucagon-Like Peptide 1/*metabolism ; Grape Seed Extract/*administration &amp; dosage ; Humans ; Metabolic Syndrome/*drug therapy/metabolism/*microbiology ; Proanthocyanidins/*administration &amp; dosage ; Rats ; Rats, Wistar ; }, abstract = {Grape seed proanthocyanidin extract (GSPE) modulates several parameters involved in metabolic syndrome. GSPE is a mixture of compounds, some which are rapidly absorbed, while others remain in the lumen where they might have effects that are translated to the whole organism. Our aim was to decipher if the 8-day treatment of GSPE, previously shown to reduce food intake, induces changes in the microbiota and enterohormone secretion. The ratio of Firmicutes : Bacteroidetes was lower in the microbiota of GSPE-treated rats compared to controls, and differences in several taxonomic families and genera were observed. Such modulation led to a reduction in cecal butyrate content. GSPE also increased plasma glucagon-like-peptide-1 (GLP-1). Gallic acid did not induce major changes in the microbiota profile nor in GLP-1 secretion. Correlations between several microbiota taxa and plasma triacylglycerol, adiposity, and enterohormones were observed. Modulation of microbiota may be one of the mechanism by which GSPE impacts metabolic health.}, }
@article {pmid29472898, year = {2018}, author = {Dhami, NK and Mukherjee, A and Watkin, ELJ}, title = {Microbial Diversity and Mineralogical-Mechanical Properties of Calcitic Cave Speleothems in Natural and in Vitro Biomineralization Conditions.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {40}, pmid = {29472898}, issn = {1664-302X}, abstract = {Natural mineral formations are a window into important processes leading to carbon storage and mineralized carbonate structures formed through abiotic and biotic processes. In the current study, we made an attempt to undertake a comprehensive approach to characterize the mineralogical, mechanical, and microbial properties of different kinds of speleothems from karstic caves; with an aim to understand the bio-geo-chemical processes in speleothem structures and their impact on nanomechanical properties. We also investigated the biomineralization abilities of speleothem surface associated microbial communities in vitro. Mineralogical profiling using techniques such as X-ray powder Diffraction (XRD) and Tescan Integrated Mineral Analyzer (TIMA) demonstrated that calcite was the dominant mineral in the majority of speleothems with Energy Dispersive X-ray Analysis (EDS) indicating a few variations in the elemental components. Differing proportions of polymorphs of calcium carbonate such as aragonite and vaterite were also recorded. Significant variations in trace metal content were recorded through Inductively Coupled Plasma Mass Spectrometer (ICP-MS). Scanning Electron Microscopy (SEM) analysis revealed differences in morphological features of the crystals which varied from triangular prismatic shapes to etched spiky forms. Microbial imprints and associations were seen in a few sections. Analysis of the associated microbial diversity showed significant differences between various speleothems at Phylum level; although Proteobacteria and Actinobacteria were found to be the predominant groups. Genus level microbial associations showed a relationship with the geochemistry, mineralogical composition, and metal content of the speleothems. The assessment of nanomechanical properties measured by Nanoindentation revealed that the speleothems with a dominance of calcite were stronger than the speleothems with mixed calcium carbonate polymorphs and silica content. The in vitro metabolic activity of the microbial communities associated with the surfaces of the speleothems resulted in calcium carbonate crystal precipitation. Firmicutes and Proteobacteria dominated these populations, in contrast to the populations seen in natural systems. The precipitation of calcium carbonate crystals in vitro indicated that microbial metabolic activity may also play an important role in the synthesis and dissociation of biominerals in the natural environment. Our study provides novel evidence of the close relationship between mineralogy, microbial ecology, geochemistry, and nanomechanical properties of natural formations.}, }
@article {pmid29472453, year = {2018}, author = {Xiao, J and Yu, F and Zhu, W and Xu, C and Zhang, K and Luo, Y and Tiedje, JM and Zhou, J and Cheng, L}, title = {Comment on "The whole-soil carbon flux in response to warming".}, journal = {Science (New York, N.Y.)}, volume = {359}, number = {6378}, pages = {}, doi = {10.1126/science.aao0218}, pmid = {29472453}, issn = {1095-9203}, abstract = {In a compelling study, Hicks Pries et al (Reports, 31 March 2017, p. 1420) showed that 4°C warming enhanced soil CO2 production in the 1-meter soil profile, with all soil depths displaying similar temperature sensitivity (Q10). We argue that some caveats can be identified in their experimental approach and analysis, and that these critically undermine their conclusions and hence their claim that the strength of feedback between the whole-soil carbon and climate has been underestimated in terrestrial models.}, }
@article {pmid29471872, year = {2018}, author = {Van Goethem, MW and Pierneef, R and Bezuidt, OKI and Van De Peer, Y and Cowan, DA and Makhalanyane, TP}, title = {A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {40}, pmid = {29471872}, issn = {2049-2618}, support = {93074//National Research Foundation of South Africa/International ; 97891//National Research Foundation of South Africa/International ; 99320//National Research Foundation of South Africa/International ; 110717//National Research Foundation/International ; }, mesh = {Antarctic Regions ; Anti-Bacterial Agents/*metabolism ; Bacteria/*classification/*drug effects ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/genetics ; Membrane Transport Proteins/genetics ; Metagenomics/methods ; Soil Microbiology ; }, abstract = {BACKGROUND: Soil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacterial resistance elements in edaphic systems have originated primarily from human-impacted environments, with relatively little information from remote and pristine environments, where the resistome may comprise the ancestral gene diversity.<br><br>METHODS: We used shotgun metagenomics to assess antibiotic resistance gene (ARG) distribution in 17 pristine and remote Antarctic surface soils within the undisturbed Mackay Glacier region. We also interrogated the phylogenetic placement of ARGs compared to environmental ARG sequences and tested for the presence of horizontal gene transfer elements flanking ARGs.<br><br>RESULTS: In total, 177 naturally occurring ARGs were identified, most of which encoded single or multi-drug efflux pumps. Resistance mechanisms for the inactivation of aminoglycosides, chloramphenicol and &#x3b2;-lactam antibiotics were also common. Gram-negative bacteria harboured most ARGs (71%), with fewer genes from Gram-positive Actinobacteria and Bacilli (Firmicutes) (9%), reflecting the taxonomic composition of the soils. Strikingly, the abundance of ARGs per sample had a strong, negative correlation with species richness (r&#x2009;=&#x2009;-&#x2009;0.49, P&#x2009;<&#x2009;0.05). This result, coupled with a lack of mobile genetic elements flanking ARGs, suggests that these genes are ancient acquisitions of horizontal transfer events.<br><br>CONCLUSIONS: ARGs in these remote and uncontaminated soils most likely represent functional efficient historical genes that have since been vertically inherited over generations. The historical ARGs in these pristine environments carry a strong phylogenetic signal and form a monophyletic group relative to ARGs from other similar environments.}, }
@article {pmid29471481, year = {2018}, author = {Deveau, A and Bonito, G and Uehling, J and Paoletti, M and Becker, M and Bindschedler, S and Hacquard, S and Hervé, V and Labbé, J and Lastovetsky, OA and Mieszkin, S and Millet, LJ and Vajna, B and Junier, P and Bonfante, P and Krom, BP and Olsson, S and van Elsas, JD and Wick, LY}, title = {Bacterial-fungal interactions: ecology, mechanisms and challenges.}, journal = {FEMS microbiology reviews}, volume = {42}, number = {3}, pages = {335-352}, doi = {10.1093/femsre/fuy008}, pmid = {29471481}, issn = {1574-6976}, mesh = {Animals ; *Bacterial Physiological Phenomena ; Ecology ; Fungi/*physiology ; Microbial Interactions/*physiology ; }, abstract = {Fungi and bacteria are found living together in a wide variety of environments. Their interactions are significant drivers of many ecosystem functions and are important for the health of plants and animals. A large number of fungal and bacterial families engage in complex interactions that lead to critical behavioural shifts of the microorganisms ranging from mutualism to antagonism. The importance of bacterial-fungal interactions (BFI) in environmental science, medicine and biotechnology has led to the emergence of a dynamic and multidisciplinary research field that combines highly diverse approaches including molecular biology, genomics, geochemistry, chemical and microbial ecology, biophysics and ecological modelling. In this review, we discuss recent advances that underscore the roles of BFI across relevant habitats and ecosystems. A particular focus is placed on the understanding of BFI within complex microbial communities and in regard of the metaorganism concept. We also discuss recent discoveries that clarify the (molecular) mechanisms involved in bacterial-fungal relationships, and the contribution of new technologies to decipher generic principles of BFI in terms of physical associations and molecular dialogues. Finally, we discuss future directions for research in order to stimulate synergy within the BFI research area and to resolve outstanding questions.}, }
@article {pmid29470608, year = {2018}, author = {Cleary, DFR and Polónia, ARM and de Voogd, NJ}, title = {Bacterial Communities Inhabiting the Sponge Biemna fortis, Sediment and Water in Marine Lakes and the Open Sea.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {610-624}, pmid = {29470608}, issn = {1432-184X}, support = {ALW Grant No. 825.12.007//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NL)/ ; PTDC/AAC-AMB/115304/2009//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia (PT)/ ; UID/AMB/50017//CESAM/ ; SFRH/BPD/117563/2016//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {Animals ; Archaea ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Coral Reefs ; Ecosystem ; Geologic Sediments/*microbiology ; Indonesia ; Lakes/*microbiology ; Phylogeny ; Porifera/*microbiology ; Seawater/*microbiology ; }, abstract = {Marine lakes are small bodies of landlocked seawater that are isolated from the open sea and have been shown to house numerous rare and unique taxa. The environmental conditions of the lakes are also characterised by lower pH and salinity and higher temperatures than generally found in the open sea. In the present study, we used a 16S rRNA gene barcoded pyrosequencing approach and a predictive metagenomic approach (PICRUSt) to examine bacterial composition and function in three distinct biotopes (sediment, water and the sponge species Biemna fortis) in three habitats (two marine lakes and the open sea) of the Berau reef system, Indonesia. Both biotope and habitat were significant predictors of higher taxon abundance and compositional variation. Most of the variation in operational taxonomic unit (OTU) composition was related to the biotope (42% for biotope alone versus 9% for habitat alone and 15% combined). Most OTUs were also restricted to a single biotope (1047 for B. fortis, 6120 for sediment and 471 for water). Only 98 OTUs were shared across all three biotopes. Bacterial communities from B. fortis, sediment and water samples were, however, also distinct in marine lake and open sea habitats. This was evident in the abundance of higher bacterial taxa. For example, the phylum Cyanobacteria was significantly more abundant in samples from marine lakes than from the open sea. This difference was most pronounced in the sponge B. fortis. In line with the compositional differences, there were pronounced differences in predicted relative gene count abundance among biotopes and habitats. Of particular interest was the predicted enrichment in B. fortis from the marine lakes for pathways including DNA replication and repair and the glutathione metabolism. This may facilitate adaptation of host and microbes to life in 'stressful' low pH, low salinity and/or high temperature environments such as those encountered in marine lakes.}, }
@article {pmid29468690, year = {2018}, author = {Mommer, L and Cotton, TEA and Raaijmakers, JM and Termorshuizen, AJ and van Ruijven, J and Hendriks, M and van Rijssel, SQ and van de Mortel, JE and van der Paauw, JW and Schijlen, EGWM and Smit-Tiekstra, AE and Berendse, F and de Kroon, H and Dumbrell, AJ}, title = {Lost in diversity: the interactions between soil-borne fungi, biodiversity and plant productivity.}, journal = {The New phytologist}, volume = {218}, number = {2}, pages = {542-553}, pmid = {29468690}, issn = {1469-8137}, mesh = {*Biodiversity ; Biomass ; Fungi/pathogenicity/*physiology ; Host-Pathogen Interactions ; Models, Biological ; *Plant Development ; Plant Roots/genetics/microbiology ; Plants/*microbiology ; *Soil Microbiology ; Species Specificity ; }, abstract = {There is consensus that plant species richness enhances plant productivity within natural grasslands, but the underlying drivers remain debated. Recently, differential accumulation of soil-borne fungal pathogens across the plant diversity gradient has been proposed as a cause of this pattern. However, the below-ground environment has generally been treated as a 'black box' in biodiversity experiments, leaving these fungi unidentified. Using next generation sequencing and pathogenicity assays, we analysed the community composition of root-associated fungi from a biodiversity experiment to examine if evidence exists for host specificity and negative density dependence in the interplay between soil-borne fungi, plant diversity and productivity. Plant species were colonised by distinct (pathogenic) fungal communities and isolated fungal species showed negative, species-specific effects on plant growth. Moreover, 57% of the pathogenic fungal operational taxonomic units (OTUs) recorded in plant monocultures were not detected in eight plant species plots, suggesting a loss of pathogenic OTUs with plant diversity. Our work provides strong evidence for host specificity and negative density-dependent effects of root-associated fungi on plant species in grasslands. Our work substantiates the hypothesis that fungal root pathogens are an important driver of biodiversity-ecosystem functioning relationships.}, }
@article {pmid29467508, year = {2018}, author = {Pang, XN and Han, BZ and Huang, XN and Zhang, X and Hou, LF and Cao, M and Gao, LJ and Hu, GH and Chen, JY}, title = {Effect of the environment microbiota on the flavour of light-flavour Baijiu during spontaneous fermentation.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {3396}, pmid = {29467508}, issn = {2045-2322}, mesh = {Alcoholic Beverages/*microbiology ; Fermentation/*physiology ; Flavoring Agents/*metabolism ; Food Microbiology/methods ; Lactobacillus/physiology ; Microbiota/*physiology ; Taste/physiology ; Volatile Organic Compounds/metabolism ; }, abstract = {Light-flavour Baijiu is a type of Chinese liquor with a pure and mild flavour produced by traditional spontaneous solid-state fermentation. The flavour of this liquor has been found to vary in the different periods of annual production. To explore the factors affecting flavour, the microbiota of the surrounding environment, starter and fermentation process in different periods were investigated. Results showed that the ester content and acidity of light-flavour Baijiu were significantly lower when annual production was resumed after a summer break. HCA plot of volatile flavour profile and bacterial PCoA results indicated that the differences occurred at later stages, mainly due to different structures of Lactobacillus. Correlation analysis by O2PLS indicated that Lactobacillus positively correlated with esters. Species-level analysis showed that the lack of L. acetotolerans on the surface of the jar might cause a lag in fermentation and lower ester content. Thereafter, L. acetotolerans was revived during fermentation and enriched on the surface of the jar, which promoted ester formation. As important sources of L. acetotolerans, the air and fermentation jars played a critical role during fermentation. Therefore, this systematic study on environmental microbial ecology is valuable for quality control and to explore environmental microbiota functions during spontaneous fermentation.}, }
@article {pmid29467397, year = {2018}, author = {Anantharaman, K and Hausmann, B and Jungbluth, SP and Kantor, RS and Lavy, A and Warren, LA and Rappé, MS and Pester, M and Loy, A and Thomas, BC and Banfield, JF}, title = {Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle.}, journal = {The ISME journal}, volume = {12}, number = {7}, pages = {1715-1728}, pmid = {29467397}, issn = {1751-7370}, support = {I 2320/FWF_/Austrian Science Fund FWF/Austria ; P 25111/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; *Biodiversity ; Hydrogensulfite Reductase/genetics/metabolism ; Metagenome ; Oxidation-Reduction ; Phylogeny ; Sulfur/*metabolism ; }, abstract = {A critical step in the biogeochemical cycle of sulfur on Earth is microbial sulfate reduction, yet organisms from relatively few lineages have been implicated in this process. Previous studies using functional marker genes have detected abundant, novel dissimilatory sulfite reductases (DsrAB) that could confer the capacity for microbial sulfite/sulfate reduction but were not affiliated with known organisms. Thus, the identity of a significant fraction of sulfate/sulfite-reducing microbes has remained elusive. Here we report the discovery of the capacity for sulfate/sulfite reduction in the genomes of organisms from 13 bacterial and archaeal phyla, thereby more than doubling the number of microbial phyla associated with this process. Eight of the 13 newly identified groups are candidate phyla that lack isolated representatives, a finding only possible given genomes from metagenomes. Organisms from Verrucomicrobia and two candidate phyla, Candidatus Rokubacteria and Candidatus Hydrothermarchaeota, contain some of the earliest evolved dsrAB genes. The capacity for sulfite reduction has been laterally transferred in multiple events within some phyla, and a key gene potentially capable of modulating sulfur metabolism in associated cells has been acquired by putatively symbiotic bacteria. We conclude that current functional predictions based on phylogeny significantly underestimate the extent of sulfate/sulfite reduction across Earth's ecosystems. Understanding the prevalence of this capacity is integral to interpreting the carbon cycle because sulfate reduction is often coupled to turnover of buried organic carbon. Our findings expand the diversity of microbial groups associated with sulfur transformations in the environment and motivate revision of biogeochemical process models based on microbial community composition.}, }
@article {pmid29463895, year = {2018}, author = {Grujcic, V and Nuy, JK and Salcher, MM and Shabarova, T and Kasalicky, V and Boenigk, J and Jensen, M and Simek, K}, title = {Cryptophyta as major bacterivores in freshwater summer plankton.}, journal = {The ISME journal}, volume = {12}, number = {7}, pages = {1668-1681}, pmid = {29463895}, issn = {1751-7370}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Cryptophyta/*microbiology ; Food Chain ; Fresh Water/microbiology/*parasitology ; Heterotrophic Processes ; In Situ Hybridization, Fluorescence ; Phylogeny ; Plankton/*microbiology ; Seasons ; }, abstract = {Small bacterivorous eukaryotes play a cardinal role in aquatic food webs and their taxonomic classification is currently a hot topic in aquatic microbial ecology. Despite increasing interest in their diversity, core questions regarding predator-prey specificity remain largely unanswered, e.g., which heterotrophic nanoflagellates (HNFs) are the main bacterivores in freshwaters and which prokaryotes support the growth of small HNFs. To answer these questions, we fed natural communities of HNFs from Římov reservoir (Czech Republic) with five different bacterial strains of the ubiquitous betaproteobacterial genera Polynucleobacter and Limnohabitans. We combined amplicon sequencing and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) targeting eukaryotic 18 S rRNA genes to track specific responses of the natural HNF community to prey amendments. While amplicon sequencing provided valuable qualitative data and a basis for designing specific probes, the number of reads was insufficient to accurately quantify certain eukaryotic groups. We also applied a double-hybridization technique that allows simultaneous phylogenetic identification of both predator and prey. Our results show that community composition of HNFs is strongly dependent upon prey type. Surprisingly, Cryptophyta were the most abundant bacterivores, although this phylum has been so far assumed to be mainly autotrophic. Moreover, the growth of a small lineage of Cryptophyta (CRY1 clade) was strongly stimulated by one Limnohabitans strain in our experiment. Thus, our study is the first report that colorless Cryptophyta are major bacterivores in summer plankton samples and can play a key role in the carbon transfer from prokaryotes to higher trophic levels.}, }
@article {pmid29463893, year = {2018}, author = {Ortiz-Álvarez, R and Fierer, N and de Los Ríos, A and Casamayor, EO and Barberán, A}, title = {Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession.}, journal = {The ISME journal}, volume = {12}, number = {7}, pages = {1658-1667}, pmid = {29463893}, issn = {1751-7370}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Ecosystem ; Humans ; Intestines/*microbiology ; *Microbiota ; Plants/*microbiology ; *Soil Microbiology ; rRNA Operon ; }, abstract = {Ecologists have long studied primary succession, the changes that occur in biological communities after initial colonization of an environment. Most of this work has focused on succession in plant communities, laying the conceptual foundation for much of what we currently know about community assembly patterns over time. Because of their prevalence and importance in ecosystems, an increasing number of studies have focused on microbial community dynamics during succession. Here, we conducted a meta-analysis of bacterial primary succession patterns across a range of distinct habitats, including the infant gut, plant surfaces, soil chronosequences, and aquatic environments, to determine whether consistent changes in bacterial diversity, community composition, and functional traits are evident over the course of succession. Although these distinct habitats harbor unique bacterial communities, we were able to identify patterns in community assembly that were shared across habitat types. We found an increase in taxonomic and functional diversity with time while the taxonomic composition and functional profiles of communities became less variable (lower beta diversity) in late successional stages. In addition, we found consistent decreases in the rRNA operon copy number and in the high-efficient phosphate assimilation process (Pst system) suggesting that reductions in resource availability during succession select for taxa adapted to low-resource conditions. Together, these results highlight that, like many plant communities, microbial communities also exhibit predictable patterns during primary succession.}, }
@article {pmid29463661, year = {2018}, author = {He, Z and Zhang, P and Wu, L and Rocha, AM and Tu, Q and Shi, Z and Wu, B and Qin, Y and Wang, J and Yan, Q and Curtis, D and Ning, D and Van Nostrand, JD and Wu, L and Yang, Y and Elias, DA and Watson, DB and Adams, MWW and Fields, MW and Alm, EJ and Hazen, TC and Adams, PD and Arkin, AP and Zhou, J}, title = {Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.}, journal = {mBio}, volume = {9}, number = {1}, pages = {}, pmid = {29463661}, issn = {2150-7511}, mesh = {Biota/*drug effects ; *Ecosystem ; *Environmental Pollution ; Groundwater/*chemistry/*microbiology ; Hydrogen-Ion Concentration ; Metagenome/drug effects ; Nitrates/analysis ; Tennessee ; Uranium/analysis ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Contamination from anthropogenic activities has significantly impacted Earth's biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly (P < 0.05) as uranium or nitrate increased, and their changes could be used to successfully predict uranium and nitrate contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning.IMPORTANCE Disentangling the relationships between biodiversity and ecosystem functioning is an important but poorly understood topic in ecology. Predicting ecosystem functioning on the basis of biodiversity is even more difficult, particularly with microbial biomarkers. As an exploratory effort, this study used key microbial functional genes as biomarkers to provide predictive understanding of environmental contamination and ecosystem functioning. The results indicated that the overall functional gene richness/diversity decreased as uranium increased in groundwater, while specific key microbial guilds increased significantly as uranium or nitrate increased. These key microbial functional genes could be used to successfully predict environmental contamination and ecosystem functioning. This study represents a significant advance in using functional gene markers to predict the spatial distribution of environmental contaminants and ecosystem functioning toward predictive microbial ecology, which is an ultimate goal of microbial ecology.}, }
@article {pmid29460206, year = {2018}, author = {Chia, LW and Hornung, BVH and Aalvink, S and Schaap, PJ and de Vos, WM and Knol, J and Belzer, C}, title = {Deciphering the trophic interaction between Akkermansia muciniphila and the butyrogenic gut commensal Anaerostipes caccae using a metatranscriptomic approach.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {6}, pages = {859-873}, pmid = {29460206}, issn = {1572-9699}, support = {024.002.002//SIAM Gravitation Grant/ ; KB-17-003.02-023//IP/OP program Systems Biology/ ; }, mesh = {Butyrates/metabolism ; Gastrointestinal Microbiome/genetics/physiology ; Intestinal Mucosa/*metabolism ; Microbiota/genetics ; Mucins/metabolism ; Transcriptome/genetics ; Verrucomicrobia/*metabolism ; }, abstract = {Host glycans are paramount in regulating the symbiotic relationship between humans and their gut bacteria. The constant flux of host-secreted mucin at the mucosal layer creates a steady niche for bacterial colonization. Mucin degradation by keystone species subsequently shapes the microbial community. This study investigated the transcriptional response during mucin-driven trophic interaction between the specialised mucin-degrader Akkermansia muciniphila and a butyrogenic gut commensal Anaerostipes caccae. A. muciniphila monocultures and co-cultures with non-mucolytic A. caccae from the Lachnospiraceae family were grown anaerobically in minimal media supplemented with mucin. We analysed for growth, metabolites (HPLC analysis), microbial composition (quantitative reverse transcription PCR), and transcriptional response (RNA-seq). Mucin degradation by A. muciniphila supported the growth of A. caccae and concomitant butyrate production predominantly via the acetyl-CoA pathway. Differential expression analysis (DESeq 2) showed the presence of A. caccae induced changes in the A. muciniphila transcriptional response with increased expression of mucin degradation genes and reduced expression of ribosomal genes. Two putative operons that encode for uncharacterised proteins and an efflux system, and several two-component systems were also differentially regulated. This indicated A. muciniphila changed its transcriptional regulation in response to A. caccae. This study provides insight to understand the mucin-driven microbial ecology using metatranscriptomics. Our findings show that the expression of mucolytic enzymes by A. muciniphila increases upon the presence of a community member. This could indicate its role as a keystone species that supports the microbial community in the mucosal environment by increasing the availability of mucin sugars.}, }
@article {pmid29459309, year = {2018}, author = {Agrawal, S and Seuntjens, D and Cocker, P and Lackner, S and Vlaeminck, SE}, title = {Success of mainstream partial nitritation/anammox demands integration of engineering, microbiome and modeling insights.}, journal = {Current opinion in biotechnology}, volume = {50}, number = {}, pages = {214-221}, doi = {10.1016/j.copbio.2018.01.013}, pmid = {29459309}, issn = {1879-0429}, mesh = {Ammonia/*metabolism ; Anaerobiosis ; *Metabolic Engineering ; *Microbiota ; *Models, Theoretical ; *Nitrification ; Oxidation-Reduction ; }, abstract = {Twenty years ago, mainstream partial nitritation/anammox (PN/A) was conceptually proposed as pivotal for a more sustainable treatment of municipal wastewater. Its economic potential spurred research, yet practice awaits a comprehensive recipe for microbial resource management. Implementing mainstream PN/A requires transferable and operable ways to steer microbial competition as to meet discharge requirements on a year-round basis at satisfactory conversion rates. In essence, the competition for nitrogen, organic carbon and oxygen is grouped into 'ON/OFF' (suppression/promotion) and 'IN/OUT' (wash-out/retention and seeding) strategies, selecting for desirable conversions and microbes. Some insights need mechanistic understanding, while empirical observations suffice elsewhere. The provided methodological R&amp;D framework integrates insights in engineering, microbiome and modeling. Such synergism should catalyze the implementation of energy-positive sewage treatment.}, }
@article {pmid29459210, year = {2018}, author = {Araujo, ASF and Mendes, LW and Bezerra, WM and Nunes, LAPL and Lyra, MDCCP and Figueiredo, MDVB and Melo, VMM}, title = {Archaea diversity in vegetation gradients from the Brazilian Cerrado.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {49}, number = {3}, pages = {522-528}, pmid = {29459210}, issn = {1678-4405}, mesh = {Archaea/classification/genetics/growth &amp; development/*isolation &amp; purification ; Biodiversity ; Brazil ; Phylogeny ; Plant Development ; Plants/classification/*microbiology ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {We used 16S rRNA sequencing to assess the archaeal communities across a gradient of Cerrado. The archaeal communities differed across the gradient. Crenarcheota was the most abundant phyla, with Nitrosphaerales and NRPJ as the predominant classes. Euryachaeota was also found across the Cerrado gradient, including the classes Metanocellales and Methanomassiliicoccaceae.}, }
@article {pmid29458671, year = {2018}, author = {Pascual, J and Foesel, BU and Geppert, A and Huber, KJ and Boedeker, C and Luckner, M and Wanner, G and Overmann, J}, title = {Roseisolibacter agri gen. nov., sp. nov., a novel slow-growing member of the under-represented phylum Gemmatimonadetes.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {68}, number = {4}, pages = {1028-1036}, doi = {10.1099/ijsem.0.002619}, pmid = {29458671}, issn = {1466-5034}, mesh = {Agriculture ; Bacteria/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Electron Transport Complex IV/genetics ; Fatty Acids/chemistry ; Namibia ; Phospholipids/chemistry ; *Phylogeny ; Pigmentation ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {A novel slow-growing bacterium, designated strain AW1220[T], was isolated from agricultural floodplain soil sampled at Mashare (Kavango region, Namibia) by using a high-throughput cultivation approach. Strain AW1220[T] was characterized as a Gram-negative, non-motile, rod-shaped bacterium. Occasionally, some cells attained an unusual length of up to 35 µm. The strain showed positive responses for catalase and cytochrome-c oxidase and divided by binary fission and/or budding. The strain had an aerobic chemoorganoheterotrophic metabolism and was also able to grow under micro-oxic conditions. Colonies were small and pink pigmented. Strain AW1220[T] was found to be a mesophilic, neutrophilic and non-halophilic bacterium. Cells accumulated polyphosphate intracellularly and mainly utilized complex protein substrates for growth. 16S rRNA gene sequence comparisons revealed that strain AW1220[T] belonged to the class Gemmatimonadetes (=group 1). Its closest relatives were found to be Gemmatimonas aurantiaca T-27[T] (90.9 % gene sequence similarity), Gemmatimonas phototrophica AP64[T] (90.8 %) and Longimicrobiumterrae CB-286315[T] (84.2 %). The genomic G+C content was 73.3 mol%. The major fatty acids were iso-C15 : 0, C16 : 1ω7c and/or iso-C15 : 0 2-OH, iso-C17 : 1ω9c, iso-C15 : 0 3-OH and C16 : 0. The predominant respiratory quinone was MK-9, albeit minor amounts of MK-8 and MK-10 are also present. The polar lipids comprised major amounts of phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and one unidentified phosphoglycolipid. On the basis of its polyphasic characterization, strain AW1220[T] represents a novel genus and species of the class Gemmatimonadetes for which the name Roseisolibacter agri gen. nov., sp. nov. is proposed, with the type strain AW1220[T] (=DSM 104292[T]=LMG 29977[T]).}, }
@article {pmid29458413, year = {2018}, author = {Olivares, M and Walker, AW and Capilla, A and Benítez-Páez, A and Palau, F and Parkhill, J and Castillejo, G and Sanz, Y}, title = {Gut microbiota trajectory in early life may predict development of celiac disease.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {36}, pmid = {29458413}, issn = {2049-2618}, support = {Grant 098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bifidobacterium/genetics/*isolation &amp; purification ; Case-Control Studies ; Celiac Disease/*microbiology ; Child, Preschool ; Enterococcus/genetics/*isolation &amp; purification ; Feces/microbiology ; Female ; Firmicutes/genetics/*isolation &amp; purification ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Infant, Newborn ; Male ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: To investigate whether alterations in the developing intestinal microbiota and immune markers precede celiac disease (CD) onset in infants at familial risk of developing the disease.<br><br>METHODS: A nested case-control study was carried out as part of a larger prospective cohort study, which included healthy full-term newborns (>&#x2009;200) with at least one first relative with biopsy-verified CD. The present study includes cases of CD (n&#x2009;=&#x2009;10) and the best-matched controls (n&#x2009;=&#x2009;10) who did not develop the disease after 5-year follow-up. Fecal microbiota, assessed by high-throughput 16S rRNA gene amplicon sequencing, and immune parameters were profiled at 4 and 6&#xa0;months of age and related to CD onset.<br><br>RESULTS: The microbiota of infants who remained healthy showed an increase in bacterial diversity over time, characterized by increases in Firmicutes families, but not those who developed CD. Infants who subsequently developed CD showed a significant reduction in sIgA levels over time, while those who remained healthy showed increases in TNF-&#x3b1; correlated to Bifidobacterium spp. An increased relative abundance of Bifidobacterium longum was associated with control children while increased proportions of Bifidobacterium breve and Enterococcus spp. were associated with CD development.<br><br>CONCLUSION: The findings suggest that alterations in the early trajectory of gut microbiota in infants at CD risk could influence the immune maturation process and predispose to CD, although larger population studies are warranted to confirm this hypothesis.}, }
@article {pmid29457691, year = {2018}, author = {Gougoulias, C and Meade, A and Shaw, LJ}, title = {Apportioning bacterial carbon source utilization in soil using [14] C isotope analysis of FISH-targeted bacterial populations sorted by fluorescence activated cell sorting (FACS): [14] C-FISH-FACS.}, journal = {Environmental microbiology reports}, volume = {10}, number = {3}, pages = {245-254}, doi = {10.1111/1758-2229.12631}, pmid = {29457691}, issn = {1758-2229}, support = {BB/F000251/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Biomass ; Carbon/*metabolism ; Carbon Radioisotopes ; Cell Separation/*methods ; Flow Cytometry/*methods ; In Situ Hybridization, Fluorescence/*methods ; Pseudomonas/*metabolism ; *Rhizosphere ; Salicylic Acid/metabolism ; *Soil Microbiology ; }, abstract = {An unresolved need in microbial ecology is methodology to enable quantitative analysis of in situ microbial substrate carbon use at the population level. Here, we evaluated if a novel combination of radiocarbon-labelled substrate tracing, fluorescence in situ hybridisation (FISH) and fluorescence-activated cell sorting (FACS) to sort the FISH-targeted population for quantification of incorporated radioactivity ([14] C-FISH-FACS) can address this need. Our test scenario used FISH probe PSE1284 targeting Pseudomonas spp. (and some Burkholderia spp.) and salicylic acid added to rhizosphere soil. We examined salicylic acid-[14] C fate (mineralized, cell-incorporated, extractable and non-extractable) and mass balance (0-24 h) and show that the PSE1284 population captured ∼ 50% of the Nycodenz extracted biomass [14] C. Analysis of the taxonomic distribution of the salicylic acid biodegradation trait suggested that PSE1284 population success was not due to conservation of this trait but due to competitiveness for the added carbon. Adding 50KBq of [14] C sample[-1] enabled detection of [14] C in the sorted population at ∼ 60-600 times background; a sensitivity which demonstrates potential extension to analysis of rarer/less active populations. Given its sensitivity and compatibility with obtaining a C mass balance, [14] C-FISH-FACS allows quantitative dissection of C flow within the microbial biomass that has hitherto not been achieved.}, }
@article {pmid29455238, year = {2018}, author = {Gill, K and Kang, R and Sathiananthamoorthy, S and Khasriya, R and Malone-Lee, J}, title = {A blinded observational cohort study of the microbiological ecology associated with pyuria and overactive bladder symptoms.}, journal = {International urogynecology journal}, volume = {29}, number = {10}, pages = {1493-1500}, pmid = {29455238}, issn = {1433-3023}, mesh = {Aged ; Biomarkers/urine ; Cohort Studies ; Colony Count, Microbial/methods ; Female ; Humans ; Microbiota ; Middle Aged ; Pyuria/*microbiology ; Single-Blind Method ; Urinalysis/methods ; Urinary Bladder, Overactive/*microbiology ; Urothelium/*microbiology ; }, abstract = {INTRODUCTION AND HYPOTHESIS: This study sought to characterise the microbial ecology of the lower urinary tract in patients with symptoms of overactive bladder (OAB) using culture of the urinary urothelial cell sediment. The pathological significance of the microbiome was assessed through its relationship with known urothelial inflammatory markers and patient reported symptoms.<br><br>METHODS: Adult female patients with OAB symptoms and asymptomatic controls were assessed at 12 study visits scheduled every 4&#xa0;weeks. At each visit, all participants provided a clean-catch midstream urine (MSU) that was analysed to count white and uroepithelial cells, submitted to standard culture and spun urothelial-cell-sediment culture. Symptoms were assessed using validated questionnaires.<br><br>RESULTS: This analysis shows that OAB patients differ consistently from controls, demonstrating differences in bacterial ecology (t&#x2009;-4.57, p&#x2009;0.0001), in the microscopic pyuria count (t&#x2009;-6.37, p&#x2009;0.0001) and presence of infected urothelial cells (t&#x2009;-4.21, p&#x2009;0.0001). The primary outcome measure of bacterial growth [colony-forming units (CFU) ml[-1]] was higher in OAB patients than in controls throughout the 12&#xa0;months. Data showed a correlation between symptoms and pyuria, with notable urgency correlating with pyuria and epithelial cell shedding. The routine urine cultures (with a threshold of reporting a positive result as 10[5]&#xa0;CFU/ml) were unable to distinguish OAB patients from controls. However, sediment cultures differed significantly, and there was a correlated increased immune response amongst OAB patients.<br><br>CONCLUSIONS: This study supports the need to re-examine the OAB phenotype given this association with microbial colonisation.}, }
@article {pmid29453266, year = {2018}, author = {Pratte, ZA and Besson, M and Hollman, RD and Stewart, FJ}, title = {The Gills of Reef Fish Support a Distinct Microbiome Influenced by Host-Specific Factors.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {9}, pages = {}, pmid = {29453266}, issn = {1098-5336}, mesh = {Animals ; Bacteria/classification/*isolation &amp; purification ; Coral Reefs ; Fishes/*microbiology ; Gills/*microbiology ; *Microbiota ; Polynesia ; }, abstract = {Teleost fish represent the most diverse of the vertebrate groups and play important roles in food webs, as ecosystem engineers, and as vectors for microorganisms. However, the microbial ecology of fishes remains underexplored for most host taxa and for certain niches on the fish body. This is particularly true for the gills, the key sites of respiration and waste exchange in fishes. Here we provide a comprehensive analysis of the gill microbiome. We focus on ecologically diverse taxa from coral reefs around Moorea, sampling the gills and intestines of adults and juveniles representing 15 families. The gill microbiome composition differed significantly from that of the gut for both adults and juveniles, with fish-associated niches having lower alpha diversity values and higher beta diversity values than those for seawater, sediment, and alga-associated microbiomes. Of ∼45,000 operational taxonomic units (OTUs) detected across all samples, 11% and 13% were detected only in the gill and the intestine, respectively. OTUs most enriched in the gill included members of the gammaproteobacterial genus Shewanella and the family Endozoicimonaceae In adult fish, both gill and intestinal microbiomes varied significantly among host species grouped by diet category. Gill and intestinal microbiomes from the same individual were more similar to one another than to gill and intestinal microbiomes from different individuals. These results demonstrate that distinct body sites are jointly influenced by host-specific organizing factors operating at the level of the host individual. The results also identify taxonomic signatures unique to the gill and the intestine, confirming fish-associated niches as distinct reservoirs of marine microbial diversity.IMPORTANCE Fish breathe and excrete waste through their gills. The gills are also potential sites of pathogen invasion and colonization by other microbes. However, we know little about the microbial communities that live on the gill and the factors shaping their diversity. Focusing on ecologically distinct types of coral reef fish, we provide a comprehensive analysis of the fish gill microbiome. By comparison to microbiomes of the gut and the surrounding environment, we identify microbes unique to the gill niche. These microbes may be targets for further studies to determine the contribution of the microbiome to waste exchange or host immunity. We also show that despite exhibiting a unique taxonomic signature, the gill microbiome is influenced by factors that also influence the gut microbiome. These factors include the specific identity of the host individual. These results suggest basic principles describing how association with fishes structures the composition of microbial communities.}, }
@article {pmid29453264, year = {2018}, author = {Li, B and Wu, WM and Watson, DB and Cardenas, E and Chao, Y and Phillips, DH and Mehlhorn, T and Lowe, K and Kelly, SD and Li, P and Tao, H and Tiedje, JM and Criddle, CS and Zhang, T}, title = {Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in a Uranium-Contaminated Site after Bioreduction Followed by Reoxidation.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {9}, pages = {}, pmid = {29453264}, issn = {1098-5336}, mesh = {*Bacterial Physiological Phenomena ; Biodegradation, Environmental ; Groundwater/chemistry ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Nitrates/chemistry ; Oxidation-Reduction ; Tennessee ; Uranium/*adverse effects ; }, abstract = {A site in Oak Ridge, TN, USA, has sediments that contain >3% iron oxides and is contaminated with uranium (U). The U(VI) was bioreduced to U(IV) and immobilized in situ through intermittent injections of ethanol. It then was allowed to reoxidize via the invasion of low-pH (3.6 to 4.0), high-nitrate (up to 200 mM) groundwater back into the reduced zone for 1,383 days. To examine the biogeochemical response, high-throughput sequencing and network analysis were applied to characterize bacterial population shifts, as well as cooccurrence and coexclusion patterns among microbial communities. A paired t test indicated no significant changes of α-diversity for the bioactive wells. However, both nonmetric multidimensional scaling and analysis of similarity confirmed a significant distinction in the overall composition of the bacterial communities between the bioreduced and the reoxidized sediments. The top 20 major genera accounted for >70% of the cumulative contribution to the dissimilarity in the bacterial communities before and after the groundwater invasion. Castellaniella had the largest dissimilarity contribution (17.7%). For the bioactive wells, the abundance of the U(VI)-reducing genera Geothrix, Desulfovibrio, Ferribacterium, and Geobacter decreased significantly, whereas the denitrifying Acidovorax abundance increased significantly after groundwater invasion. Additionally, seven genera, i.e., Castellaniella, Ignavibacterium, Simplicispira, Rhizomicrobium, Acidobacteria Gp1, Acidobacteria Gp14, and Acidobacteria Gp23, were significant indicators of bioactive wells in the reoxidation stage. Canonical correspondence analysis indicated that nitrate, manganese, and pH affected mostly the U(VI)-reducing genera and indicator genera. Cooccurrence patterns among microbial taxa suggested the presence of taxa sharing similar ecological niches or mutualism/commensalism/synergism interactions.IMPORTANCE High-throughput sequencing technology in combination with a network analysis approach were used to investigate the stabilization of uranium and the corresponding dynamics of bacterial communities under field conditions with regard to the heterogeneity and complexity of the subsurface over the long term. The study also examined diversity and microbial community composition shift, the common genera, and indicator genera before and after long-term contaminated-groundwater invasion and the relationship between the target functional community structure and environmental factors. Additionally, deciphering cooccurrence and coexclusion patterns among microbial taxa and environmental parameters could help predict potential biotic interactions (cooperation/competition), shared physiologies, or habitat affinities, thus, improving our understanding of ecological niches occupied by certain specific species. These findings offer new insights into compositions of and associations among bacterial communities and serve as a foundation for future bioreduction implementation and monitoring efforts applied to uranium-contaminated sites.}, }
@article {pmid29453256, year = {2018}, author = {Adesioye, FA and Makhalanyane, TP and Vikram, S and Sewell, BT and Schubert, WD and Cowan, DA}, title = {Structural Characterization and Directed Evolution of a Novel Acetyl Xylan Esterase Reveals Thermostability Determinants of the Carbohydrate Esterase 7 Family.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {8}, pages = {}, pmid = {29453256}, issn = {1098-5336}, mesh = {Acetylesterase/chemistry/*genetics/metabolism ; Africa, Southern ; Amino Acid Sequence ; Bacteria/enzymology/*genetics ; Bacterial Proteins/chemistry/*genetics/metabolism ; Desert Climate ; Metagenome/*genetics ; Sequence Alignment ; }, abstract = {A hot desert hypolith metagenomic DNA sequence data set was screened in silico for genes annotated as acetyl xylan esterases (AcXEs). One of the genes identified encoded an ∼36-kDa protein (Axe1NaM1). The synthesized gene was cloned and expressed, and the resulting protein was purified. NaM1 was optimally active at pH 8.5 and 30°C and functionally stable at salt concentrations of up to 5 M. The specific activity and catalytic efficiency were 488.9 U mg[-1] and 3.26 × 10[6] M[-1] s[-1], respectively. The crystal structure of wild-type NaM1 was solved at a resolution of 2.03 Å, and a comparison with the structures and models of more thermostable carbohydrate esterase 7 (CE7) family enzymes and variants of NaM1 from a directed evolution experiment suggests that reduced side-chain volume of protein core residues is relevant to the thermal stability of NaM1. Surprisingly, a single point mutation (N96S) not only resulted in a simultaneous improvement in thermal stability and catalytic efficiency but also increased the acyl moiety substrate range of NaM1.IMPORTANCE AcXEs belong to nine carbohydrate esterase families (CE1 to CE7, CE12, and CE16), of which CE7 enzymes possess a unique and narrow specificity for acetylated substrates. All structurally characterized members of this family are moderately to highly thermostable. The crystal structure of a novel, mesophilic CE7 AcXE (Axe1NaM1), from a soil metagenome, provides a basis for comparisons with thermostable CE7 enzymes. Using error-prone PCR and site-directed mutagenesis, we enhanced both the stability and activity of the mesophilic AcXE. With comparative structural analyses, we have also identified possible thermal stability determinants. These are valuable for understanding the thermal stability of enzymes within this family and as a guide for future protein engineering of CE7 and other α/β hydrolase enzymes.}, }
@article {pmid29453252, year = {2018}, author = {Romano, S}, title = {Ecology and Biotechnological Potential of Bacteria Belonging to the Genus Pseudovibrio.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {8}, pages = {}, pmid = {29453252}, issn = {1098-5336}, mesh = {Animals ; Anthozoa/microbiology ; Biotechnology ; Environment ; Porifera/microbiology ; Rhodobacteraceae/growth &amp; development/metabolism/*physiology ; *Symbiosis ; }, abstract = {Members of the genus Pseudovibrio have been isolated worldwide from a great variety of marine sources as both free-living and host-associated bacteria. So far, the available data depict a group of alphaproteobacteria characterized by a versatile metabolism, which allows them to use a variety of substrates to meet their carbon, nitrogen, sulfur, and phosphorous requirements. Additionally, Pseudovibrio-related bacteria have been shown to proliferate under extreme oligotrophic conditions, tolerate high heavy-metal concentrations, and metabolize potentially toxic compounds. Considering this versatility, it is not surprising that they have been detected from temperate to tropical regions and are often the most abundant isolates obtained from marine invertebrates. Such an association is particularly recurrent with marine sponges and corals, animals that play a key role in benthic marine systems. The data so far available indicate that these bacteria are mainly beneficial to the host, and besides being involved in major nutrient cycles, they could provide the host with both vitamins/cofactors and protection from potential pathogens via the synthesis of antimicrobial secondary metabolites. In fact, the biosynthetic abilities of Pseudovibrio spp. have been emerging in recent years, and both genomic and analytic studies have underlined how these organisms promise novel natural products of biotechnological value.}, }
@article {pmid29453174, year = {2018}, author = {Proia, L and Anzil, A and Subirats, J and Borrego, C and Farrè, M and Llorca, M and Balcázar, JL and Servais, P}, title = {Antibiotic resistance along an urban river impacted by treated wastewaters.}, journal = {The Science of the total environment}, volume = {628-629}, number = {}, pages = {453-466}, doi = {10.1016/j.scitotenv.2018.02.083}, pmid = {29453174}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Belgium ; Drug Resistance, Microbial/*genetics ; *Environmental Monitoring ; Escherichia coli ; Genes, Bacterial ; Rivers/*microbiology ; Wastewater/*microbiology ; }, abstract = {Urban rivers are impacted ecosystems which may play an important role as reservoirs for antibiotic-resistant (AR) bacteria. The main objective of this study was to describe the prevalence of antibiotic resistance along a sewage-polluted urban river. Seven sites along the Zenne River (Belgium) were selected to study the prevalence of AR Escherichia coli and freshwater bacteria over a 1-year period. Culture-dependent methods were used to estimate E. coli and heterotrophic bacteria resistant to amoxicillin, sulfamethoxazole, nalidixic acid and tetracycline. The concentrations of these four antibiotics have been quantified in the studied river. The antibiotic resistance genes (ARGs), sul1, sul2, tetW, tetO, blaTEM and qnrS were also quantified in both particle-attached (PAB) and free-living (FLB) bacteria. Our results showed an effect of treated wastewaters release on the spread of antibiotic resistance along the river. Although an increase in the abundance of both AR E. coli and resistant heterotrophic bacteria was observed from upstream to downstream sites, the differences were only significant for AR E. coli. A significant positive regression was also found between AR E. coli and resistant heterotrophic bacteria. The concentration of ARGs increased from upstream to downstream sites for both particle-attached (PAB) and free-living bacteria (FLB). Particularly, a significant increase in the abundance of four among six ARGs analyzed was observed after crossing urban area. Although concentrations of tetracycline significantly correlated with tetracycline resistance genes, the antibiotic levels were likely too low to explain this correlation. The analysis of ARGs in different fractions revealed a significantly higher abundance in PAB compared to FLB for tetO and sul2 genes. This study demonstrated that urban activities may increase the spread of antibiotic resistance even in an already impacted river.}, }
@article {pmid29449565, year = {2018}, author = {Bates, KA and Clare, FC and O'Hanlon, S and Bosch, J and Brookes, L and Hopkins, K and McLaughlin, EJ and Daniel, O and Garner, TWJ and Fisher, MC and Harrison, XA}, title = {Amphibian chytridiomycosis outbreak dynamics are linked with host skin bacterial community structure.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {693}, pmid = {29449565}, issn = {2041-1723}, mesh = {Animals ; Antibiosis/*physiology ; Anura/*microbiology ; Bacteria/*classification/isolation &amp; purification ; Bacterial Physiological Phenomena ; Chytridiomycota/genetics/*pathogenicity ; Microbiota/genetics ; Mycoses/microbiology/*prevention &amp; control/*veterinary ; Skin/*microbiology ; }, abstract = {Host-associated microbes are vital for combatting infections and maintaining health. In amphibians, certain skin-associated bacteria inhibit the fungal pathogen Batrachochytrium dendrobatidis (Bd), yet our understanding of host microbial ecology and its role in disease outbreaks is limited. We sampled skin-associated bacteria and Bd from Pyrenean midwife toad populations exhibiting enzootic or epizootic disease dynamics. We demonstrate that bacterial communities differ between life stages with few shared taxa, indicative of restructuring at metamorphosis. We detected a significant effect of infection history on metamorph skin microbiota, with reduced bacterial diversity in epizootic populations and differences in community structure and predicted function. Genome sequencing of Bd isolates supports a single introduction to the Pyrenees and reveals no association between pathogen genetics and epidemiological trends. Our findings provide an ecologically relevant insight into the microbial ecology of amphibian skin and highlight the relative importance of host microbiota and pathogen genetics in predicting disease outcome.}, }
@article {pmid29445826, year = {2018}, author = {Cabal, A and Jun, SR and Jenjaroenpun, P and Wanchai, V and Nookaew, I and Wongsurawat, T and Burgess, MJ and Kothari, A and Wassenaar, TM and Ussery, DW}, title = {Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {801-813}, pmid = {29445826}, issn = {1432-184X}, support = {P20 GM121293/GM/NIGMS NIH HHS/United States ; UL1 TR000039/TR/NCATS NIH HHS/United States ; UL1TR000039/NH/NIH HHS/United States ; P20GM121293/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics ; Bacterial Toxins/metabolism ; Clostridioides difficile/chemistry/classification/*genetics/*isolation &amp; purification ; Clostridium Infections/microbiology ; Gene Dosage ; *Genome, Bacterial ; Humans ; Molecular Sequence Data ; Multilocus Sequence Typing ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {Infections due to Clostridioides difficile (previously known as Clostridium difficile) are a major problem in hospitals, where cases can be caused by community-acquired strains as well as by nosocomial spread. Whole genome sequences from clinical samples contain a lot of information but that needs to be analyzed and compared in such a way that the outcome is useful for clinicians or epidemiologists. Here, we compare 663 public available complete genome sequences of C. difficile using average amino acid identity (AAI) scores. This analysis revealed that most of these genomes (640, 96.5%) clearly belong to the same species, while the remaining 23 genomes produce four distinct clusters within the Clostridioides genus. The main C. difficile cluster can be further divided into sub-clusters, depending on the chosen cutoff. We demonstrate that MLST, either based on partial or full gene-length, results in biased estimates of genetic differences and does not capture the true degree of similarity or differences of complete genomes. Presence of genes coding for C. difficile toxins A and B (ToxA/B), as well as the binary C. difficile toxin (CDT), was deduced from their unique PfamA domain architectures. Out of the 663 C. difficile genomes, 535 (80.7%) contained at least one copy of ToxA or ToxB, while these genes were missing from 128 genomes. Although some clusters were enriched for toxin presence, these genes are variably present in a given genetic background. The CDT genes were found in 191 genomes, which were restricted to a few clusters only, and only one cluster lacked the toxin A/B genes consistently. A total of 310 genomes contained ToxA/B without CDT (47%). Further, published metagenomic data from stools were used to assess the presence of C. difficile sequences in blinded cases of C. difficile infection (CDI) and controls, to test if metagenomic analysis is sensitive enough to detect the pathogen, and to establish strain relationships between cases from the same hospital. We conclude that metagenomics can contribute to the identification of CDI and can assist in characterization of the most probable causative strain in CDI patients.}, }
@article {pmid29445143, year = {2018}, author = {Obrador, B and von Schiller, D and Marcé, R and Gómez-Gener, L and Koschorreck, M and Borrego, C and Catalán, N}, title = {Dry habitats sustain high CO2 emissions from temporary ponds across seasons.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {3015}, pmid = {29445143}, issn = {2045-2322}, abstract = {Despite the increasing understanding of the magnitude and drivers of carbon gas emissions from inland waters, the relevance of water fluctuation and associated drying on their dynamics is rarely addressed. Here, we quantified CO2 and CH4 fluxes from a set of temporary ponds across seasons. The ponds were in all occasion net CO2 emitters irrespective of the presence or absence of water. While the CO2 fluxes were in the upper range of emissions for freshwater lentic systems, CH4 fluxes were mostly undetectable. Dry habitats substantially contributed to these emissions and were always a source of CO2, whereas inundated habitats acted either as a source or a sink of atmospheric CO2 along the year. Higher concentrations of coloured and humic organic matter in water and sediment were linked to higher CO2 emissions. Composition of the sediment microbial community was related both to dissolved organic matter concentration and composition, but we did not find a direct link with CO2 fluxes. The presence of methanogenic archaea in most ponds suggested the potential for episodic CH4 production and emission. Our results highlight the need for spatially and temporally inclusive approaches that consider the dry phases and habitats to characterize carbon cycling in temporary systems.}, }
@article {pmid29442157, year = {2018}, author = {Zhou, J and Song, X and Zhang, CY and Chen, GF and Lao, YM and Jin, H and Cai, ZH}, title = {Distribution Patterns of Microbial Community Structure Along a 7000-Mile Latitudinal Transect from the Mediterranean Sea Across the Atlantic Ocean to the Brazilian Coastal Sea.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {592-609}, pmid = {29442157}, issn = {1432-184X}, support = {KQJSCX20160226190419, JCYJ20170412171959157, and JCYJ20150529164918736//Shenzhen Science and Technology Innovation Committee/ ; 41476092//NSFC/ ; A201603D05//Marine Fishery Science and Technology &amp; Industry Development of Guangdong Province/ ; HIT.NSRIF.201702//HIT Scientific Research Innovation Fund/ ; }, mesh = {Archaea/classification/genetics/growth &amp; development/*isolation &amp; purification ; Atlantic Ocean ; Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; *Biodiversity ; Brazil ; Mediterranean Sea ; Phylogeny ; Seawater/chemistry/*microbiology ; }, abstract = {A central goal in marine microecology is to understand the ecological factors shaping spatiotemporal microbial patterns and the underlying processes. We hypothesized that abiotic and/or biotic interactions are probably more important for explaining the distribution patterns of marine bacterioplankton than environmental filtering. In this study, surface seawater samples were collected about 7000 miles from the Mediterranean Sea, transecting the North Atlantic Ocean, to the Brazilian marginal sea. In bacterial biosphere, SAR11, SAR86, Rhodobacteraceae, and Rhodospiriaceae were predominant in the Mediterranean Sea; Prochlorococcus was more frequent in Atlantic Ocean; whereas in the Brazilian coastal sea, the main bacterial members were Synechococcus and SAR11. With respect to archaea, Euryarchaeota were predominant in the Atlantic Ocean and Thaumarchaeota in the Mediterranean Sea. With respect to the eukaryotes, Syndiniales, Spumellaria, Cryomonadida, and Chlorodendrales were predominant in the open ocean, while diatoms and microzooplankton were dominant in the coastal sea. Distinct clusters of prokaryotes and eukaryotes displayed clear spatial heterogeneity. Among the environmental parameters measured, temperature and salinity were key factors controlling bacterial and archaeal community structure, respectively, whereas N/P/Si contributed to eukaryotic variation. The relative contribution of environmental parameters to the microbial distribution pattern was 45.2%. Interaction analysis showed that Gammaproteobacteria, Alphaproteobacteria, and Flavobacteriia were the keystone taxa within the positive-correlation network, while Thermoplasmata was the main contributor in the negative-correlation network. Our study demonstrated that microbial communities are co-governed by environmental filtering and biotic interactions, which are the main deterministic driving factors modulating the spatiotemporal patterns of marine plankton synergistically at the regional or global levels.}, }
@article {pmid29441664, year = {2018}, author = {Souffreau, C and Busschaert, P and Denis, C and Van Wichelen, J and Lievens, B and Vyverman, W and De Meester, L}, title = {A comparative hierarchical analysis of bacterioplankton and biofilm metacommunity structure in an interconnected pond system.}, journal = {Environmental microbiology}, volume = {20}, number = {3}, pages = {1271-1282}, doi = {10.1111/1462-2920.14073}, pmid = {29441664}, issn = {1462-2920}, mesh = {Aquatic Organisms/growth &amp; development ; Bacteria/*growth &amp; development ; *Biodiversity ; Biofilms/*growth &amp; development ; Ecosystem ; Lakes/*microbiology ; Plankton/*growth &amp; development/microbiology ; Ponds/*microbiology ; }, abstract = {It is unknown whether bacterioplankton and biofilm communities are structured by the same ecological processes, and whether they influence each other through continuous dispersal (known as mass effects). Using a hierarchical sampling approach we compared the relative importance of ecological processes structuring the dominant fraction (relative abundance ≥0.1%) of bacterioplankton and biofilm communities from three microhabitats (open water, Nuphar and Phragmites sites) at within- and among-pond scale in a set of 14 interconnected shallow ponds. Our results demonstrate that while bacterioplankton and biofilm communities are highly distinct, a similar hierarchy of ecological processes is acting on them. For both community types, most variation in community composition was determined by pond identity and environmental variables, with no effect of space. The highest β-diversity within each community type was observed among ponds, while microhabitat type (Nuphar, Phragmites, open water) significantly influenced biofilm communities but not bacterioplankton. Mass effects among bacterioplankton and biofilm communities were not detected, as suggested by the absence of within-site covariation of biofilm and bacterioplankton communities. Both biofilm and plankton communities were thus highly structured by environmental factors (i.e., species sorting), with among-lake variation being more important than within-lake variation, whereas dispersal limitation and mass effects were not observed.}, }
@article {pmid29441043, year = {2018}, author = {Zupančič, J and Raghupathi, PK and Houf, K and Burmølle, M and Sørensen, SJ and Gunde-Cimerman, N}, title = {Synergistic Interactions in Microbial Biofilms Facilitate the Establishment of Opportunistic Pathogenic Fungi in Household Dishwashers.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {21}, pmid = {29441043}, issn = {1664-302X}, abstract = {Biofilms formed on rubber seals in dishwashers harbor diverse microbiota. In this study, we focussed on the microbial composition of bacteria and fungi, isolated from a defined area of one square centimeter of rubber from four domestic dishwashers and assessed their abilities to in vitro multispecies biofilm formation. A total of 80 isolates (64 bacterial and 16 fungal) were analyzed. Multiple combinations of bacterial isolates from each dishwasher were screened for synergistic interactions. 32 out of 140 tested (23%) four-species bacterial combinations displayed consistent synergism leading to an overall increase in biomass, in all experimental trails. Bacterial isolates from two of the four dishwashers generated a high number of synergistically interacting four-species consortia. Network based correlation analyses also showed higher co-occurrence patterns observed between bacterial members in the same two dishwasher samples, indicating cooperative effects. Furthermore, two synergistic four-species bacterial consortia were tested for their abilities to incorporate an opportunistic fungal pathogen, Exophiala dermatitidis and their establishment as biofilms on sterile ethylene propylene diene monomer M-class (EPDM) rubber and polypropylene (PP) surfaces. When the bacterial consortia included E. dermatitidis, the overall cell numbers of both bacteria and fungi increased and a substantial increase in biofilm biomass was observed. These results indicate a novel phenomenon of cross kingdom synergy in biofilm formation and these observations could have potential implications for human health.}, }
@article {pmid29440745, year = {2018}, author = {Cruz, H and Luckman, P and Seviour, T and Verstraete, W and Laycock, B and Pikaar, I}, title = {Rapid removal of ammonium from domestic wastewater using polymer hydrogels.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2912}, pmid = {29440745}, issn = {2045-2322}, abstract = {To date, technologies to recover ammonium from domestic wastewater from the mainstream have not found widespread application. This is largely due to the low ammonium concentrations in these wastewater streams. This paper reports on the use of polymer hydrogels for rapid sorption of ammonium from domestic wastewater coupled with efficient regeneration by mild acid washing. The sorption capacity of the hydrogel was 8.8-32.2 mg NH4-N/g, which corresponds to removal efficiencies ranging from 68% to 80% NH4-N, increasing proportionally with the initial ammonium concentration. It was, however, unaffected by changes in pH, as the sorption capacity remained constant from pH 5.0-8.0. Importantly, effective regeneration of the hydrogels under mildly acidic conditions (i.e. pH 4.0) was demonstrated with minimal loss in sorption performance following multiple sorption/desorption cycles. Overall, this study highlights the potential of low-cost polymer hydrogels for achieving mainstream ammonium recovery from domestic wastewater.}, }
@article {pmid29435598, year = {2018}, author = {Purushotham, N and Jones, E and Monk, J and Ridgway, H}, title = {Community Structure of Endophytic Actinobacteria in a New Zealand Native Medicinal Plant Pseudowintera colorata (Horopito) and Their Influence on Plant Growth.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {729-740}, pmid = {29435598}, issn = {1432-184X}, mesh = {Actinobacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Endophytes/classification/genetics/*isolation &amp; purification ; New Zealand ; Phylogeny ; Plant Leaves/growth &amp; development/microbiology ; Plant Roots/growth &amp; development/microbiology ; Plants, Medicinal/growth &amp; development/*microbiology ; Pseudowintera/growth &amp; development/*microbiology ; }, abstract = {The role of plant endophytic Actinobacteria remains poorly understood with no reports of these communities in New Zealand native plants. This first investigation of endophytic Actinobacteria in New Zealand targeted the culturally significant medicinal shrub Pseudowintera colorata (horopito) as a model plant. Community analysis in plant tissues collected from ten geographically distinct sites showed that tissue type had the strongest influence on diversity and richness of endophytic Actinobacteria. More denaturing gradient gel electrophoresis (DGGE) bands were obtained from stems (n = 18) compared to roots (n = 13). Sequencing analysis of the major bands (n = 20) identified them as uncultured bacteria, Streptomyces sp. and Angustibacter peucedani. Using two Actinobacteria-specific media, nine isolates were recovered from surface-sterilised P. colorata tissues. This was approximately 12% of the total taxa and correlated well with culturable numbers in international studies. In vitro analysis of the functionality of these strains showed that Streptomyces sp. PRY2RB2 inhibited all the tested phytopathogenic fungi (n = 4), Streptomyces sp. UKCW/B and Nocardia sp. TP1BA1B solubilised phosphate and produced siderophores. The functionality of the phosphate solubilising strains (n = 2) in vivo was investigated by inoculation of P. colorata seedlings. After 4 months, the mean shoot height of seedlings treated with Nocardia sp. TP1BA1B was 1.65× longer, had higher shoot dry weight (1.6×) and number of internodes (1.67×) compared to control. This study identified for the first time a key group of endophytic Actinobacteria that are likely to be important in the ecology of New Zealand flora.}, }
@article {pmid29433444, year = {2018}, author = {Hücker, SM and Vanderhaeghen, S and Abellan-Schneyder, I and Wecko, R and Simon, S and Scherer, S and Neuhaus, K}, title = {A novel short L-arginine responsive protein-coding gene (laoB) antiparallel overlapping to a CadC-like transcriptional regulator in Escherichia coli O157:H7 Sakai originated by overprinting.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {21}, pmid = {29433444}, issn = {1471-2148}, support = {SCHE316/3-1,2,3//Deutsche Forschungsgemeinschaft/International ; KE740/13-1,2,3//Deutsche Forschungsgemeinschaft/International ; }, mesh = {Arginine/*metabolism ; Base Sequence ; Escherichia coli O157/*genetics/growth &amp; development/*metabolism ; Escherichia coli Proteins/genetics/*metabolism ; Genes, Bacterial ; *Genes, Overlapping ; Green Fluorescent Proteins/metabolism ; Mutation/genetics ; Open Reading Frames/*genetics ; Phylogeny ; Promoter Regions, Genetic ; Protein Biosynthesis ; Recombinant Fusion Proteins/metabolism ; Trans-Activators/*metabolism ; *Transcription, Genetic ; Transcriptome/genetics ; }, abstract = {BACKGROUND: Due to the DNA triplet code, it is possible that the sequences of two or more protein-coding genes overlap to a large degree. However, such non-trivial overlaps are usually excluded by genome annotation pipelines and, thus, only a few overlapping gene pairs have been described in bacteria. In contrast, transcriptome and translatome sequencing reveals many signals originated from the antisense strand of annotated genes, of which we analyzed an example gene pair in more detail.<br><br>RESULTS: A small open reading frame of Escherichia coli O157:H7 strain Sakai (EHEC), designated laoB (L-arginine responsive overlapping gene), is embedded in reading frame -2 in the antisense strand of ECs5115, encoding a CadC-like transcriptional regulator. This overlapping gene shows evidence of transcription and translation in Luria-Bertani (LB) and brain-heart infusion (BHI) medium based on RNA sequencing (RNAseq) and ribosomal-footprint sequencing (RIBOseq). The transcriptional start site is 289 base pairs (bp) upstream of the start codon and transcription termination is 155&#xa0;bp downstream of the stop codon. Overexpression of LaoB fused to an enhanced green fluorescent protein (EGFP) reporter was possible. The sequence upstream of the transcriptional start site displayed strong promoter activity under different conditions, whereas promoter activity was significantly decreased in the presence of L-arginine. A strand-specific translationally arrested mutant of laoB provided a significant growth advantage in competitive growth experiments in the presence of L-arginine compared to the wild type, which returned to wild type level after complementation of laoB in trans. A phylostratigraphic analysis indicated that the novel gene is restricted to the Escherichia/Shigella clade and might have originated recently by overprinting leading to the expression of part of the antisense strand of ECs5115.<br><br>CONCLUSIONS: Here, we present evidence of a novel small protein-coding gene laoB encoded in the antisense frame -2 of the annotated gene ECs5115. Clearly, laoB is evolutionarily young and it originated in the Escherichia/Shigella clade by overprinting, a process which may cause the de novo evolution of bacterial genes like laoB.}, }
@article {pmid29432683, year = {2018}, author = {De Vrieze, J and De Waele, M and Boeckx, P and Boon, N}, title = {Isotope Fractionation in Biogas Allows Direct Microbial Community Stability Monitoring in Anaerobic Digestion.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {11}, pages = {6704-6713}, doi = {10.1021/acs.est.8b00723}, pmid = {29432683}, issn = {1520-5851}, mesh = {Anaerobiosis ; *Biofuels ; Bioreactors ; Isotopes ; Methane ; *Microbiota ; }, abstract = {Process monitoring of anaerobic digestion is typically based on operational parameters, such as pH and volatile fatty acid concentration, that are lagging on actual microbial community performance. In this study, [13]C isotope fractionation in CH4 and CO2 in the biogas was used to monitor process stability of anaerobic digestion in response to salt stress. A gradual and pulsed increase in salt concentration resulted in a decrease in methane production. No clear shift in δ[13]CH4 was observed in response to the gradual increase in salt concentration, and δ[13]CO2 of the biogas showed only a clear shift after process failure, compared with the control. In contrast, both δ[13]CH4 and δ[13]CO2 in the biogas changed in response to the pulsed increase in salt concentration. This change preceded the decrease in methane production. A significantly different bacterial and archaeal community profile was observed between the DNA and RNA level, which was also reflected in a different relation with the δ[13]CH4 and δ[13]CO2 values. This shows that isotope fractionation in the biogas can predict process stability in anaerobic digestion, as it directly reflects shifts in the total and active microbial community, yet, due to its temporal character, further validation is needed.}, }
@article {pmid29430070, year = {2017}, author = {Ren, B and Bacallado, S and Favaro, S and Holmes, S and Trippa, L}, title = {Bayesian Nonparametric Ordination for the Analysis of Microbial Communities.}, journal = {Journal of the American Statistical Association}, volume = {112}, number = {520}, pages = {1430-1442}, pmid = {29430070}, issn = {0162-1459}, support = {R01 AI112401/AI/NIAID NIH HHS/United States ; DMS-1042785//National Science Foundation/International ; }, abstract = {Human microbiome studies use sequencing technologies to measure the abundance of bacterial species or Operational Taxonomic Units (OTUs) in samples of biological material. Typically the data are organized in contingency tables with OTU counts across heterogeneous biological samples. In the microbial ecology community, ordination methods are frequently used to investigate latent factors or clusters that capture and describe variations of OTU counts across biological samples. It remains important to evaluate how uncertainty in estimates of each biological sample's microbial distribution propagates to ordination analyses, including visualization of clusters and projections of biological samples on low dimensional spaces. We propose a Bayesian analysis for dependent distributions to endow frequently used ordinations with estimates of uncertainty. A Bayesian nonparametric prior for dependent normalized random measures is constructed, which is marginally equivalent to the normalized generalized Gamma process, a well-known prior for nonparametric analyses. In our prior, the dependence and similarity between microbial distributions is represented by latent factors that concentrate in a low dimensional space. We use a shrinkage prior to tune the dimensionality of the latent factors. The resulting posterior samples of model parameters can be used to evaluate uncertainty in analyses routinely applied in microbiome studies. Specifically, by combining them with multivariate data analysis techniques we can visualize credible regions in ecological ordination plots. The characteristics of the proposed model are illustrated through a simulation study and applications in two microbiome datasets.}, }
@article {pmid29429010, year = {2018}, author = {Wei, S and Cui, H and Zhu, Y and Lu, Z and Pang, S and Zhang, S and Dong, H and Su, X}, title = {Shifts of methanogenic communities in response to permafrost thaw results in rising methane emissions and soil property changes.}, journal = {Extremophiles : life under extreme conditions}, volume = {22}, number = {3}, pages = {447-459}, pmid = {29429010}, issn = {1433-4909}, mesh = {Archaeal Proteins/genetics/metabolism ; *Greenhouse Effect ; Methane/*metabolism ; Methanomicrobiales/growth &amp; development/*metabolism ; Methanosarcinales/growth &amp; development/*metabolism ; Microbiota ; Permafrost/*microbiology ; }, abstract = {Permafrost thaw can bring negative consequences in terms of ecosystems, resulting in permafrost collapse, waterlogging, thermokarst lake development, and species composition changes. Little is known about how permafrost thaw influences microbial community shifts and their activities. Here, we show that the dominant archaeal community shifts from Methanomicrobiales to Methanosarcinales in response to the permafrost thaw, and the increase in methane emission is found to be associated with the methanogenic archaea, which rapidly bloom with nearly tenfold increase in total number. The mcrA gene clone libraries analyses indicate that Methanocellales/Rice Cluster I was predominant both in the original permafrost and in the thawed permafrost. However, only species belonging to Methanosarcinales showed higher transcriptional activities in the thawed permafrost, indicating a shift of methanogens from hydrogenotrophic to partly acetoclastic methane-generating metabolic processes. In addition, data also show the soil texture and features change as a result of microbial reproduction and activity induced by this permafrost thaw. Those data indicate that microbial ecology under warming permafrost has potential impacts on ecosystem and methane emissions.}, }
@article {pmid29428982, year = {2018}, author = {de Los Santos-Villalobos, S and Kremer, JM and Parra-Cota, FI and Hayano-Kanashiro, AC and García-Ortega, LF and Gunturu, SK and Tiedje, JM and He, SY and Peña-Cabriales, JJ}, title = {Draft genome of the fungicidal biological control agent Burkholderia anthina strain XXVI.}, journal = {Archives of microbiology}, volume = {200}, number = {5}, pages = {803-810}, doi = {10.1007/s00203-018-1490-6}, pmid = {29428982}, issn = {1432-072X}, support = {DOE Office of Science BER DE-FC02-07ER64494//DOE Great Lakes Bioenergy Research Center/ ; GBMF3037//Gordon and Betty Moore Foundation/ ; }, mesh = {Antibiosis ; Base Sequence ; Biological Control Agents ; Biosynthetic Pathways ; Burkholderia/*genetics/isolation &amp; purification ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; Whole Genome Sequencing ; }, abstract = {Burkholderia anthina XXVI is a rhizosphere bacterium isolated from a mango orchard in Mexico. This strain has a significant biological control activity against the causal agent of mango anthracnose, Colletotrichum gloeosporioides, likely through the production of siderophores and other secondary metabolites. Here, we present a draft genome sequence of B. anthina XXVI (approximately 7.7 Mb; and G + C content of 67.0%), with the aim of gaining insight into the genomic basis of antifungal modes of action, ecological success as a biological control agent, and full biosynthetic potential.}, }
@article {pmid29428864, year = {2018}, author = {Yang, J and Li, G and Qian, Y and Yang, Y and Zhang, F}, title = {Microbial functional gene patterns related to soil greenhouse gas emissions in oil contaminated areas.}, journal = {The Science of the total environment}, volume = {628-629}, number = {}, pages = {94-102}, doi = {10.1016/j.scitotenv.2018.02.007}, pmid = {29428864}, issn = {1879-1026}, mesh = {Carbon Dioxide/analysis ; China ; *Genes, Microbial ; Greenhouse Gases/analysis/*metabolism ; Methane/analysis ; Nitrogen/analysis ; Nitrous Oxide/analysis ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Linking microbial community structure to physiology and ecological processes is a critical focus of microbial ecology. To understand the microbial functional gene patterns related to soil greenhouse gas [carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O)] emissions under oil contamination, we used functional gene array (GeoChip 5.0) analysis and network methods to investigate the feedback responses of soil microbial functional gene patterns and identify keystone genes in Shengli Oilfield, China. The microbial functional gene number, relative abundance and diversity involved in carbon degradation and nitrogen cycling decreased consistently with the reduced CO2 and N2O flux in oil contaminated soils, whereas the gene number and relative abundance of methane-production related genes increased with contamination. Functional molecular ecological networks were built based on random matrix theory, where network structures and properties showed significantly variation between oil contaminated and uncontaminated soils (P<0.05). Network nodes, connectivity and complexity all reduced under oil contamination. The sensitive and the highest connective genes in the network were identified as keystone genes, based on Mann-Whitney U tests and network analysis. Our findings improved the understanding of the microbe-mediated mechanisms affecting soil greenhouse gas emissions.}, }
@article {pmid29428753, year = {2018}, author = {Kairenius, P and Leskinen, H and Toivonen, V and Muetzel, S and Ahvenjärvi, S and Vanhatalo, A and Huhtanen, P and Wallace, RJ and Shingfield, KJ}, title = {Effect of dietary fish oil supplements alone or in combination with sunflower and linseed oil on ruminal lipid metabolism and bacterial populations in lactating cows.}, journal = {Journal of dairy science}, volume = {101}, number = {4}, pages = {3021-3035}, doi = {10.3168/jds.2017-13776}, pmid = {29428753}, issn = {1525-3198}, mesh = {Animal Feed/analysis ; Animal Nutritional Physiological Phenomena/drug effects ; Animals ; Cattle/*metabolism/*microbiology ; Diet/veterinary ; Dietary Supplements/analysis ; Fatty Acids/analysis ; Female ; Fish Oils/administration &amp; dosage/*metabolism ; Gastrointestinal Microbiome/*drug effects ; Lactation ; Linseed Oil/administration &amp; dosage/*metabolism ; *Lipid Metabolism/drug effects ; Omasum/metabolism ; Rumen/drug effects/metabolism/microbiology ; Sunflower Oil/administration &amp; dosage/*metabolism ; }, abstract = {Fish oil (FO) alters ruminal biohydrogenation causing trans fatty acid (FA) intermediates to accumulate, but the effects of 18-carbon polyunsaturated FA supply on ruminal long-chain FA metabolism and microbial communities in cattle fed FO are not well established. Four cows fitted with rumen cannula were used in a 4 × 4 Latin square with 21-d experimental periods to evaluate the effects of FO alone or in combination with plant oils high in 18:2n-6 or 18:3n-3 on rumen microbial ecology and flow of FA at the omasum. Treatments comprised a basal grass silage-based diet containing no additional oil (control) or supplements of FO (200 g/d) or FO (200 g/d) plus 500 g/d of sunflower oil (SFO) or linseed oil (LFO). Flow of FA was determined using the omasal sampling technique. The relative abundance of key biohydrogenating bacteria was assessed by quantitative PCR on 16S rRNA genes in omasal digesta. Fish oil-supplemented treatments increased the amounts of trans-18:1, trans-18:2, and 20- to 22-carbon polyunsaturated FA escaping the rumen. Relative to the control, oil supplements had no effect on the amount of 18:0 leaving the rumen, but LFO decreased the flow of 18:0 at the omasum compared with SFO. Both SFO and LFO increased trans-18:1 relative to FO, whereas LFO resulted in the highest trans-18:2 and 20- to 22-carbon FA flow. Supplements of FO plus plant oils shifted biohydrogenation toward trans-10 18:1 formation. Compared with FO alone, the ruminal metabolism of 22:6n-3 in the rumen of lactating cows is more extensive on diets containing higher amounts of 18-carbon polyunsaturated FA. However, the biohydrogenation of 22:5n-3 was less extensive in LFO than SFO, but showed no difference between FO and diets containing plant oils. Ruminal outflow of 20:5n-3 was not altered when plant oils were added to FO. Alterations in the amount of intermediates at the omasum or ruminal biohydrogenation pathways were not accompanied by major changes in analyzed bacterial populations. In conclusion, dietary supplements of FO alone or in combination with plant oils increase the amount of biohydrogenation intermediates containing 1 or more trans double bonds escaping the rumen, which may have implications for host metabolism and the nutritional quality of ruminant foods.}, }
@article {pmid29427426, year = {2018}, author = {Kim, MS and Bae, JW and Park, EJ}, title = {Geographic and Host-Associated Variations in Bacterial Communities on the Floret Surfaces of Field-Grown Broccoli.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {8}, pages = {}, pmid = {29427426}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Brassica/*microbiology ; Flowers/microbiology ; Geography ; *Microbiota ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Republic of Korea ; }, abstract = {Fresh vegetables harbor diverse bacterial populations on their surfaces. However, information on this microbiota is limited to a few types of fresh vegetables, and little is known about how it varies with geography and host condition. Here, we analyzed bacterial communities on the floret surfaces of 66 field-grown broccoli collected from 22 farms in four farming regions of Jeju Island, South Korea, using 454 pyrosequencing of 16S rRNA amplicons, and we determined their relationships to farming region and host-associated factors. Geographic variations in bacterial community composition and diversity were observed among farming regions, which partly reflected their relative humidity and insolation. The most abundant phyla were Proteobacteria, followed by Actinobacteria, Firmicutes, and Bacteroidetes; core operational taxonomic units (OTUs) assigned to Pseudomonas, Acinetobacter, Oxalobacteraceae, Comamonadaceae, and Enterobacteriaceae contributed to the community differences. Bacterial community composition differed between immature and mature samples, with mature samples harboring higher bacterial diversity. In comparison with communities on other types of fresh vegetables and fruits, bacterial communities on broccoli florets were unique but more similar to those of ground vegetables than to those of tree fruits/vegetables. This study presents novel data on the variability of floret-associated bacterial populations of field-grown broccoli relative to environmental and host-associated factors.IMPORTANCE Fresh vegetables harbor diverse and complex bacterial populations on their surfaces. These indigenous bacteria may play a role in human and crop health; however, the diversity and variability of bacterial communities on fresh vegetables require further study. A popular crop of leafy vegetables, broccoli, is of great agricultural and industrial importance. This study provides a detailed description of the bacterial community composition and diversity on the surfaces of broccoli florets. The variability of bacterial communities is associated with the geographic location of farming sites and is affected by host growth and health. The bacterial communities specific to broccoli were identified and showed greater similarity to those found on ground vegetables than to those found on tree fruits/vegetables. This study presents novel data on the impact of environmental and host-associated conditions on the variability of floret-associated bacterial populations present on field-grown broccoli.}, }
@article {pmid29427300, year = {2018}, author = {McKenney, EA and Koelle, K and Dunn, RR and Yoder, AD}, title = {The ecosystem services of animal microbiomes.}, journal = {Molecular ecology}, volume = {27}, number = {8}, pages = {2164-2172}, doi = {10.1111/mec.14532}, pmid = {29427300}, issn = {1365-294X}, support = {S10 OD018164/OD/NIH HHS/United States ; }, mesh = {*Biological Evolution ; Ecology ; *Ecosystem ; Host Microbial Interactions/*genetics ; Microbiota/*genetics ; }, abstract = {Microbiologists often evaluate microbial community dynamics by formulating functional hypotheses based on ecological processes. Indeed, many of the methods and terms currently used to describe animal microbiomes derive from ecology and evolutionary biology. As our understanding of the composition and functional dynamics of "the microbiome" grows, we increasingly refer to the host as an ecosystem within which microbial processes play out. Even so, an ecosystem service framework that extends to the context of the host has thus far been lacking. Here, we argue that ecosystem services are a useful framework with which to consider the value of microbes to their hosts. We discuss those "microbiome services" in the specific context of the mammalian gut, providing a context from which to develop new hypotheses and to evaluate microbial functions in future studies and novel systems.}, }
@article {pmid29426121, year = {2018}, author = {Flandroy, L and Poutahidis, T and Berg, G and Clarke, G and Dao, MC and Decaestecker, E and Furman, E and Haahtela, T and Massart, S and Plovier, H and Sanz, Y and Rook, G}, title = {The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems.}, journal = {The Science of the total environment}, volume = {627}, number = {}, pages = {1018-1038}, doi = {10.1016/j.scitotenv.2018.01.288}, pmid = {29426121}, issn = {1879-1026}, support = {P 29285/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; *Ecosystem ; *Environmental Microbiology ; Environmental Monitoring ; *Human Activities ; Humans ; Life Style ; Microbiota ; Plants ; }, abstract = {Plants, animals and humans, are colonized by microorganisms (microbiota) and transiently exposed to countless others. The microbiota affects the development and function of essentially all organ systems, and contributes to adaptation and evolution, while protecting against pathogenic microorganisms and toxins. Genetics and lifestyle factors, including diet, antibiotics and other drugs, and exposure to the natural environment, affect the composition of the microbiota, which influences host health through modulation of interrelated physiological systems. These include immune system development and regulation, metabolic and endocrine pathways, brain function and epigenetic modification of the genome. Importantly, parental microbiotas have transgenerational impacts on the health of progeny. Humans, animals and plants share similar relationships with microbes. Research paradigms from humans and other mammals, amphibians, insects, planktonic crustaceans and plants demonstrate the influence of environmental microbial ecosystems on the microbiota and health of organisms, and indicate links between environmental and internal microbial diversity and good health. Therefore, overlapping compositions, and interconnected roles of microbes in human, animal and plant health should be considered within the broader context of terrestrial and aquatic microbial ecosystems that are challenged by the human lifestyle and by agricultural and industrial activities. Here, we propose research priorities and organizational, educational and administrative measures that will help to identify safe microbe-associated health-promoting modalities and practices. In the spirit of an expanding version of "One health" that includes environmental health and its relation to human cultures and habits (EcoHealth), we urge that the lifestyle-microbiota-human health nexus be taken into account in societal decision making.}, }
@article {pmid29423975, year = {2018}, author = {Götz, F and Longnecker, K and Kido Soule, MC and Becker, KW and McNichol, J and Kujawinski, EB and Sievert, SM}, title = {Targeted metabolomics reveals proline as a major osmolyte in the chemolithoautotroph Sulfurimonas denitrificans.}, journal = {MicrobiologyOpen}, volume = {7}, number = {4}, pages = {e00586}, pmid = {29423975}, issn = {2045-8827}, mesh = {Chemoautotrophic Growth ; Chromatography, Liquid ; Ecosystem ; Epsilonproteobacteria/chemistry/genetics/*metabolism ; Metabolomics ; Oxidation-Reduction ; Proline/analysis/*metabolism ; Tandem Mass Spectrometry ; }, abstract = {Chemoautotrophic bacteria belonging to the genus Sulfurimonas in the class Campylobacteria are widespread in many marine environments characterized by redox interfaces, yet little is known about their physiological adaptations to different environmental conditions. Here, we used liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) in a targeted metabolomics approach to study the adaptations of Sulfurimonas denitrificans to varying salt concentrations that are found in its natural habitat of tidal mudflats. Proline was identified as one of the most abundant internal metabolites and its concentration showed a strong positive correlation with ionic strength, suggesting that it acts as an important osmolyte in S. denitrificans. 2,3-dihydroxypropane-1-sulfonate was also positively correlated with ionic strength, indicating it might play a previously unrecognized role in osmoregulation. Furthermore, the detection of metabolites from the reductive tricarboxylic acid cycle at high internal concentrations reinforces the importance of this pathway for carbon fixation in Campylobacteria and as a hub for biosynthesis. As the first report of metabolomic data for an campylobacterial chemolithoautotroph, this study provides data that will be useful to understand the adaptations of Campylobacteria to their natural habitat at redox interfaces.}, }
@article {pmid29423345, year = {2018}, author = {Delmont, TO and Eren, AM}, title = {Linking pangenomes and metagenomes: the Prochlorococcus metapangenome.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4320}, pmid = {29423345}, issn = {2167-8359}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; }, abstract = {Pangenomes offer detailed characterizations of core and accessory genes found in a set of closely related microbial genomes, generally by clustering genes based on sequence homology. In comparison, metagenomes facilitate highly resolved investigations of the relative distribution of microbial genomes and individual genes across environments through read recruitment analyses. Combining these complementary approaches can yield unique insights into the functional basis of microbial niche partitioning and fitness, however, advanced software solutions are lacking. Here we present an integrated analysis and visualization strategy that provides an interactive and reproducible framework to generate pangenomes and to study them in conjunction with metagenomes. To investigate its utility, we applied this strategy to a Prochlorococcus pangenome in the context of a large-scale marine metagenomic survey. The resulting Prochlorococcus metapangenome revealed remarkable differential abundance patterns between very closely related isolates that belonged to the same phylogenetic cluster and that differed by only a small number of gene clusters in the pangenome. While the relationships between these genomes based on gene clusters correlated with their environmental distribution patterns, phylogenetic analyses using marker genes or concatenated single-copy core genes did not recapitulate these patterns. The metapangenome also revealed a small set of core genes that mostly occurred in hypervariable genomic islands of the Prochlorococcus populations, which systematically lacked read recruitment from surface ocean metagenomes. Notably, these core gene clusters were all linked to sugar metabolism, suggesting potential benefits to Prochlorococcus from a high sequence diversity of sugar metabolism genes. The rapidly growing number of microbial genomes and increasing availability of environmental metagenomes provide new opportunities to investigate the functioning and the ecology of microbial populations, and metapangenomes can provide unique insights for any taxon and biome for which genomic and sufficiently deep metagenomic data are available.}, }
@article {pmid29422537, year = {2018}, author = {Stegen, JC and Johnson, T and Fredrickson, JK and Wilkins, MJ and Konopka, AE and Nelson, WC and Arntzen, EV and Chrisler, WB and Chu, RK and Fansler, SJ and Graham, EB and Kennedy, DW and Resch, CT and Tfaily, M and Zachara, J}, title = {Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {585}, pmid = {29422537}, issn = {2041-1723}, mesh = {Carbon/*metabolism ; Ecosystem ; Fresh Water/chemistry/microbiology ; *Groundwater/chemistry/microbiology ; *Rivers/chemistry/microbiology ; *Water Cycle ; *Water Microbiology ; }, abstract = {The hyporheic corridor (HC) encompasses the river-groundwater continuum, where the mixing of groundwater (GW) with river water (RW) in the HC can stimulate biogeochemical activity. Here we propose a novel thermodynamic mechanism underlying this phenomenon and reveal broader impacts on dissolved organic carbon (DOC) and microbial ecology. We show that thermodynamically favorable DOC accumulates in GW despite lower DOC concentration, and that RW contains thermodynamically less-favorable DOC, but at higher concentrations. This indicates that GW DOC is protected from microbial oxidation by low total energy within the DOC pool, whereas RW DOC is protected by lower thermodynamic favorability of carbon species. We propose that GW-RW mixing overcomes these protections and stimulates respiration. Mixing models coupled with geophysical and molecular analyses further reveal tipping points in spatiotemporal dynamics of DOC and indicate important hydrology-biochemistry-microbial feedbacks. Previously unrecognized thermodynamic mechanisms regulated by GW-RW mixing may therefore strongly influence biogeochemical and microbial dynamics in riverine ecosystems.}, }
@article {pmid29421081, year = {2018}, author = {Guo, XP and Lu, DP and Niu, ZS and Feng, JN and Chen, YR and Tou, FY and Liu, M and Yang, Y}, title = {Bacterial community structure in response to environmental impacts in the intertidal sediments along the Yangtze Estuary, China.}, journal = {Marine pollution bulletin}, volume = {126}, number = {}, pages = {141-149}, doi = {10.1016/j.marpolbul.2017.11.003}, pmid = {29421081}, issn = {1879-3363}, mesh = {Bacteria/classification ; China ; *Ecosystem ; *Estuaries ; Geologic Sediments/*microbiology ; *Microbial Consortia ; Nitrogen ; Rivers/microbiology ; Salinity ; }, abstract = {This study was designed to investigate the characteristics of bacterial communities in intertidal sediments along the Yangtze Estuary and their responses to environmental factors. The results showed that bacterial abundance was significantly correlated with salinity, SO4[2-] and total organic carbon, while bacterial diversity was significantly correlated with SO4[2-] and total nitrogen. At different taxonomic levels, both the dominant taxa and their abundances varied among the eight samples, with Proteobacteria being the most dominant phylum in general. Cluster analysis revealed that the bacterial community structure was influenced by river runoff and sewerage discharge. Moreover, SO4[2-], salinity and total phosphorus were the vital environmental factors that influenced the bacterial community structure. Quantitative PCR and sequencing of sulphate-reducing bacteria indicated that the sulphate reduction process occurs frequently in intertidal sediments. These findings are important to understand the microbial ecology and biogeochemical cycles in estuarine environments.}, }
@article {pmid29419886, year = {2018}, author = {Mejdandžić, M and Bosak, S and Nakov, T and Ruck, E and Orlić, S and Gligora Udovič, M and Peharec Štefanić, P and Špoljarić, I and Mršić, G and Ljubešić, Z}, title = {Morphological diversity and phylogeny of the diatom genus Entomoneis (Bacillariophyta) in marine plankton: six new species from the Adriatic Sea.}, journal = {Journal of phycology}, volume = {54}, number = {2}, pages = {275-298}, doi = {10.1111/jpy.12622}, pmid = {29419886}, issn = {1529-8817}, mesh = {Algal Proteins/analysis ; Croatia ; DNA, Algal/analysis ; DNA, Ribosomal/analysis ; Diatoms/*classification/*cytology/genetics/ultrastructure ; Mediterranean Sea ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Phylogeny ; }, abstract = {The diatom genus Entomoneis is known from the benthos and plankton of marine, brackish, and freshwaters. Entomoneis includes diatoms with a bilobate keel elevated above the valve surface, a sigmoid canal raphe, and numerous girdle bands. Owing mostly to the scarcity of molecular data for a diverse set of species, the phylogeny of Entomoneis has not been investigated in depth. The few previous studies that included Entomoneis were focused on broader questions and the available data were from a small number of either unidentified Entomoneis or well-known species (e.g., E. paludosa). Since the first description of new species combining both molecular and morphological characters (E. tenera), we have continued to cultivate and investigate Entomoneis in the plankton of the Adriatic Sea. Combined multigene phylogeny (SSU rDNA sequences, rbcL, and psbC genes) and morphological observations (LM, SEM and TEM) revealed six new Entomoneis species supported by phylogenetic and morphological data: E. pusilla, E. gracilis, E. vilicicii, E. infula, E. adriatica, and E. umbratica. The most important morphological features for species delineation were cell shape, the degree and mode of torsion, valve apices, the appearance and structure of the transition between keel and valve body, the ultrastructure and the shape of the girdle bands, and the arrangement and density of perforations along the valve and valvocopulae. Our results highlight the underappreciated diversity of Entomoneis and call for a more in-depth morphological and molecular investigation of this genus especially in planktonic habitats.}, }
@article {pmid29417188, year = {2018}, author = {Zeng, T and Zhang, S and Gao, X and Wang, G and Lens, PNL and Xie, S}, title = {Assessment of Bacterial Community Composition of Anaerobic Granular Sludge in Response to Short-Term Uranium Exposure.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {648-659}, pmid = {29417188}, issn = {1432-184X}, support = {51408293//National Natural Science Foundation of China/ ; 11475080//National Natural Science Foundation of China/ ; 2013XQD10//Scientific Research Staring Foundation for Doctoral Program in University of South China/ ; 201608430243//Foundation of China Scholarship Council/ ; }, mesh = {Anaerobiosis ; Bacteria/classification/*drug effects/genetics/growth &amp; development ; Biodiversity ; Euryarchaeota/classification/drug effects/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Sewage/*microbiology ; Uranium/*pharmacology ; }, abstract = {The effect of 10-50 μM uranium (U(VI)) on the bacterial community of anaerobic granular sludge was investigated by 24-h exposure tests, after which the bacterial community was analyzed by high-throughput sequencing. The specific U(VI) reducing activity of the anaerobic granular sludge ranged between 3.1 to 19.7 μM U(VI) g[-1](VSS) h[-1], independently of the initial U(VI) concentration. Alpha diversity revealed that microbial richness and diversity was the highest for anaerobic granular sludge upon 10 μM uranium exposure. Compared with the original biomass, the phylum of Euryarchaeota was significantly affected, whereas the Bacteroidetes, Firmicutes, and Synergistetes phyla were only slightly affected. However, the abundance of Chloroflexi and Proteobacteria phyla clearly increased after 24 h uranium exposure. Based on the genus level analysis, significant differences appeared in the bacterial abundance after uranium exposure. The proportions of Pseudomonas, Acinetobacter, Parabacteroides, Brevundimonas, Sulfurovum, and Trichococcus increased significantly, while the abundance of Paludibacter and Erysipelotrichaceae incertae sedis decreased dramatically. This study shows a dynamic diversification of the bacterial composition as a response to a short time (24 h) U(VI) exposure (10-50 μM).}, }
@article {pmid29417187, year = {2018}, author = {Pérez, J and Martínez, A and Descals, E and Pozo, J}, title = {Responses of Aquatic Hyphomycetes to Temperature and Nutrient Availability: a Cross-transplantation Experiment.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {328-339}, pmid = {29417187}, issn = {1432-184X}, support = {CGL2010-22129-C04-01//Ministry of Science and Innovation of the Spanish Government/ ; CGL2011-23984//Ministry of Science and Innovation of the Spanish Government/ ; IT-422-07//Eusko Jaurlaritza/ ; IT-302-10//Eusko Jaurlaritza/ ; }, mesh = {Atlantic Ocean ; Biodiversity ; Canada ; Ecosystem ; Environmental Microbiology ; Microbiota ; Mitosporic Fungi/classification/*physiology ; Mycobiome ; Nitrogen ; *Nutrients ; Plant Leaves/microbiology ; Rivers/chemistry/*microbiology ; *Temperature ; }, abstract = {Aquatic hyphomycetes represent a large component of the microbial assemblage that decomposes submerged leaf-litter in fluvial ecosystems. The structure and activity of these fungal decomposers depend on environmental factors. Fungal communities may adapt to local habitat conditions; however, little is known about how fungal communities respond to abrupt changes in factors such as nutrient availability and temperature. To respond to this question, we carried out a cross-transplantation experiment, which assessed the decomposer activity and structure of this microbial community on decaying leaves transplanted from a cold and oligotrophic stream (S1) to a warmer and nitrogen-richer one (S2) and vice versa. Results were compared to those from untransplanted leaves decomposing either at S1 or at S2. In terms of days, untransplanted leaves were decomposed at a similar rate in both streams; the change to warmer and nitrogen-richer waters (S1 ➔ S2) significantly enhanced the decomposition process while the reciprocal transplantation (S2 ➔ S1) did not alter decomposition rate. However, when standardizing the temperature effects by using degree-days, microbial decomposers under colder conditions were more efficient in terms of accumulated heat, independent of the initial or final incubation site. Regarding community structure, taxa richness and diversity of aquatic hyphomycetes appear to be favoured under warmer and richer conditions, increasing after transplantation to S2 but with little effect on the predominant taxa. However, the reciprocal transplantation (S2 ➔ S1) yielded a clear decline of the dominant taxa at S2 (Lunulospora curvula) in favour of the local dominant ones. Thus, effects of environmental changes on activity and community structure can be highly variable and not always clearly linked or reciprocal. Therefore, results from simplified experimental designs (e.g. artificial assemblages under laboratory conditions) must be taken with caution. Additional field studies and manipulative experimentation dealing with natural communities are required when trying to extend individual results to complex scenarios such as those projected by global change.}, }
@article {pmid29416530, year = {2018}, author = {Baksi, KD and Kuntal, BK and Mande, SS}, title = {'TIME': A Web Application for Obtaining Insights into Microbial Ecology Using Longitudinal Microbiome Data.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {36}, pmid = {29416530}, issn = {1664-302X}, abstract = {Realization of the importance of microbiome studies, coupled with the decreasing sequencing cost, has led to the exponential growth of microbiome data. A number of these microbiome studies have focused on understanding changes in the microbial community over time. Such longitudinal microbiome studies have the potential to offer unique insights pertaining to the microbial social networks as well as their responses to perturbations. In this communication, we introduce a web based framework called 'TIME' (Temporal Insights into Microbial Ecology'), developed specifically to obtain meaningful insights from microbiome time series data. The TIME web-server is designed to accept a wide range of popular formats as input with options to preprocess and filter the data. Multiple samples, defined by a series of longitudinal time points along with their metadata information, can be compared in order to interactively visualize the temporal variations. In addition to standard microbiome data analytics, the web server implements popular time series analysis methods like Dynamic time warping, Granger causality and Dickey Fuller test to generate interactive layouts for facilitating easy biological inferences. Apart from this, a new metric for comparing metagenomic time series data has been introduced to effectively visualize the similarities/differences in the trends of the resident microbial groups. Augmenting the visualizations with the stationarity information pertaining to the microbial groups is utilized to predict the microbial competition as well as community structure. Additionally, the 'causality graph analysis' module incorporated in TIME allows predicting taxa that might have a higher influence on community structure in different conditions. TIME also allows users to easily identify potential taxonomic markers from a longitudinal microbiome analysis. We illustrate the utility of the web-server features on a few published time series microbiome data and demonstrate the ease with which it can be used to perform complex analysis.}, }
@article {pmid29413866, year = {2018}, author = {Vilar-Sanz, A and Pous, N and Puig, S and Balaguer, MD and Colprim, J and Bañeras, L}, title = {Denitrifying nirK-containing alphaproteobacteria exhibit different electrode driven nitrite reduction capacities.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {121}, number = {}, pages = {74-83}, doi = {10.1016/j.bioelechem.2018.01.007}, pmid = {29413866}, issn = {1878-562X}, mesh = {Bioelectric Energy Sources/microbiology ; Electrochemical Techniques/*instrumentation ; Electrodes ; Equipment Design ; Hydrogen/*metabolism ; Nitrate Reductase/*metabolism ; Nitrites/*metabolism ; Oxidation-Reduction ; Rhizobiaceae/*enzymology/*metabolism ; }, }
@article {pmid29412464, year = {2018}, author = {Lee, ES and Song, EJ and Lee, SY and Park, SL and Kim, D and Kim, D and Kim, JH and Lim, SI and Nam, YD}, title = {Effects of bentonite Bgp35b-p on the gut microbiota of mice fed a high-fat diet.}, journal = {Journal of the science of food and agriculture}, volume = {98}, number = {11}, pages = {4369-4373}, doi = {10.1002/jsfa.8934}, pmid = {29412464}, issn = {1097-0010}, mesh = {Animals ; Bacteria/classification/drug effects/genetics/*isolation &amp; purification ; Bentonite/*administration &amp; dosage ; Diet, High-Fat/adverse effects ; Dysbiosis/drug therapy/metabolism/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/metabolism/microbiology ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Obesity/*drug therapy/metabolism/*microbiology ; Republic of Korea ; }, abstract = {BACKGROUND: Bentonite is a natural clay mineral with health-promoting effects due to its high adsorption abilities with high cation-exchange capacity. Previously, we found an anti-obesity effect for Bgp35b-p bentonite produced in South Korea, where its high adsorbent ability of dietary lipids possibly partially removed the lipidic environment in the gut (unpublished). It is hypothesized that Bgp35b-p affects the intestinal microbial community, and thus the microbial changes were investigated via next-generation sequencing targeting the bacterial 16S rRNA gene and bioinformatics using QIIME (Quantitative Insights Into Microbial Ecology) were performed on feces of C57BL/6 male mice fed a high-fat diet (HFD) with the Bgp35b-p.<br><br>RESULTS: The HFD caused microbial dysbiosis, characterized by a decrease in the relative abundance of Bacteroidetes and an increase in abundance of Firmicutes and Proteobacteria. It was found that HFD&#x2009;+&#x2009;Bgp35b-p led to significant changes in the microbial compositions of family-level bacteria known as short-chain fatty-acid-producing bacteria. The relative abundance of Ruminococcaceae was significantly increased, and the abundances of Clostridiaceae and Lachnospiraceae were decreased by HFD&#x2009;+&#x2009;Bgp35b-p, shifting close to that in mice fed a normal diet.<br><br>CONCLUSION: Bgp35b-p induced compositional changes in intestinal microbiota, which can be considered as a prebiotic effect, thus suggesting that bentonite may be a potential prebiotic functional supplement. &#xa9; 2018 Society of Chemical Industry.}, }
@article {pmid29410661, year = {2018}, author = {Mann, E and Wetzels, SU and Wagner, M and Zebeli, Q and Schmitz-Esser, S}, title = {Metatranscriptome Sequencing Reveals Insights into the Gene Expression and Functional Potential of Rumen Wall Bacteria.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {43}, pmid = {29410661}, issn = {1664-302X}, abstract = {Microbiota of the rumen wall constitute an important niche of rumen microbial ecology and their composition has been elucidated in different ruminants during the last years. However, the knowledge about the function of rumen wall microbes is still limited. Rumen wall biopsies were taken from three fistulated dairy cows under a standard forage-based diet and after 4 weeks of high concentrate feeding inducing a subacute rumen acidosis (SARA). Extracted RNA was used for metatranscriptome sequencing using Illumina HiSeq sequencing technology. The gene expression of the rumen wall microbial community was analyzed by mapping 35 million sequences against the Kyoto Encyclopedia for Genes and Genomes (KEGG) database and determining differentially expressed genes. A total of 1,607 functional features were assigned with high expression of genes involved in central metabolism, galactose, starch and sucrose metabolism. The glycogen phosphorylase (EC:2.4.1.1) which degrades (1->4)-alpha-D-glucans was among the highest expressed genes being transcribed by 115 bacterial genera. Energy metabolism genes were also highly expressed, including the pyruvate orthophosphate dikinase (EC:2.7.9.1) involved in pyruvate metabolism, which was covered by 177 genera. Nitrogen metabolism genes, in particular glutamate dehydrogenase (EC:1.4.1.4), glutamine synthetase (EC:6.3.1.2) and glutamate synthase (EC:1.4.1.13, EC:1.4.1.14) were also found to be highly expressed and prove rumen wall microbiota to be actively involved in providing host-relevant metabolites for exchange across the rumen wall. In addition, we found all four urease subunits (EC:3.5.1.5) transcribed by members of the genera Flavobacterium, Corynebacterium, Helicobacter, Clostridium, and Bacillus, and the dissimilatory sulfate reductase (EC 1.8.99.5) dsrABC, which is responsible for the reduction of sulfite to sulfide. We also provide in situ evidence for cellulose and cellobiose degradation, a key step in fiber-rich feed digestion, as well as oxidative stress response and oxygen scavenging at the rumen wall. Archaea, mainly Methanocaldococcus and Methanobrevibacter, were found to be metabolically active with a high number of transcripts matching to methane and carbohydrate metabolism. These findings enhance our understanding of the metabolic function of the bovine rumen wall microbiota.}, }
@article {pmid29407695, year = {2018}, author = {Jones, ZL and Mikkelson, KM and Nygren, S and Sedlak, DL and Sharp, JO}, title = {Establishment and convergence of photosynthetic microbial biomats in shallow unit process open-water wetlands.}, journal = {Water research}, volume = {133}, number = {}, pages = {132-141}, doi = {10.1016/j.watres.2018.01.021}, pmid = {29407695}, issn = {1879-2448}, mesh = {Bacteria/genetics/metabolism ; California ; Denitrification ; Diatoms/genetics/metabolism ; Microbiota ; Nitrates/metabolism ; Photosynthesis ; Phylogeny ; Rivers ; Waste Disposal, Fluid/*methods ; Wastewater ; Water Pollutants, Chemical/metabolism ; *Wetlands ; }, abstract = {The widespread adoption of engineered wetlands designed for water treatment is hindered by uncertainties in system reliability, resilience and management associated with coupled biological and physical processes. To better understand how shallow unit process open-water wetlands self-colonize and evolve, we analyzed the composition of the microbial community in benthic biomats from system establishment through approximately 3 years of operation. Our analysis was conducted across three parallel demonstration-scale (7500 m[2]) cells located within the Prado Constructed Wetlands in Southern California. They received water from the Santa Ana River (5.9 ± 0.2 mg/L NO3-N), a water body where the flow is dominated by municipal wastewater effluent from May to November. Phylogenetic inquiry and microscopy confirmed that diatoms and an associated aerobic bacterial community facilitated early colonization. After approximately nine months of operation, coinciding with late summer, an anaerobic community emerged with the capability for nitrate attenuation. Varying the hydraulic residence time (HRT) from 1 to 4 days the subsequent year resulted in modest ecological changes across the three parallel cells that were most evident in the outlet regions of the cells. The community that established at this time was comparatively stable for the remaining years of operation and converged with one that had previously formed approximately 550 km (350 miles) away in a pilot-scale (400 m[2]) wetland in Northern California. That system received denitrified (20.7 ± 0.7 mg/L NO3-N), secondary treated municipal wastewater for 5 years of operation. Establishment of a core microbiome between the two systems revealed a strong overlap of both aerobic and anaerobic taxa with approximately 50% of the analyzed bacterial sequences shared between the two sites. Additionally the same species of diatom, Stauirsa construens var. venter, was prolific in both systems as the putative dominant primary producer. Our results indicate that despite differences in scale, geographic location and source waters, the shallow open-water wetland design can select for a rapid convergence of microbial structure and functionality associated with the self-colonizing benthic biomat. This resulting biomat matures over the first growing season with operational parameters such as HRT further exerting a modest selective bias on community succession.}, }
@article {pmid29407610, year = {2018}, author = {Abdullah Al, M and Gao, Y and Xu, G and Wang, Z and Warren, A and Xu, H}, title = {Trophic-functional patterns of biofilm-dwelling ciliates at different water depths in coastal waters of the Yellow Sea, northern China.}, journal = {European journal of protistology}, volume = {63}, number = {}, pages = {34-43}, doi = {10.1016/j.ejop.2018.01.003}, pmid = {29407610}, issn = {1618-0429}, mesh = {*Biodiversity ; *Biofilms ; China ; Ciliophora/*physiology ; Ecosystem ; Environmental Monitoring ; Oceans and Seas ; Population Density ; Seawater/*parasitology ; }, abstract = {Vertical variations in trophic-functional patterns of biofilm-dwelling ciliates were studied in coastal waters of the Yellow Sea, northern China. A total of 50 species were identified and assigned to four trophic-functional groups (TFgrs): algivores (A), bacterivorous (B), non-selective (N) and raptors (R). The trophic-functional structures of the ciliate communities showed significant variability among different water depths: (1) with increasing water depth, relative species numbers and relative abundances of groups A and R decreased sharply whereas those of groups B and N increased gradually; (2) in terms of the frequency of occurrences, group A dominated at depths of 1-3.5 m whereas group B dominated at 5 m, while in terms of the probability density function of the trophic-functional spectrum, group A was the highest contributor at 1 m and group B was highest at the other three depths; (3) distance-based redundancy analyses revealed significant differences in trophic-functional patterns among the four depths, except between 2 and 3.5 m (P > 0.05); and (4) the trophic-functional trait diversity increased from 1 to 3.5 m and decreased sharply at 5 m. Our results suggest that the biofilm-dwelling ciliates maintain a stable trophic-functional pattern and high biodiversity at depths of 1-3.5 m.}, }
@article {pmid29407405, year = {2018}, author = {Holt, S and Mukherjee, V and Lievens, B and Verstrepen, KJ and Thevelein, JM}, title = {Bioflavoring by non-conventional yeasts in sequential beer fermentations.}, journal = {Food microbiology}, volume = {72}, number = {}, pages = {55-66}, doi = {10.1016/j.fm.2017.11.008}, pmid = {29407405}, issn = {1095-9998}, mesh = {Beer/analysis/*microbiology ; Esters/analysis/metabolism ; Fermentation ; Flavoring Agents/chemistry/*metabolism ; Humans ; Odorants/analysis ; Saccharomyces cerevisiae/metabolism ; Taste ; Yeasts/classification/genetics/isolation &amp; purification/*metabolism ; }, abstract = {Non-conventional yeast species have great capacity for producing diverse flavor profiles in production of alcoholic beverages, but their potential for beer brewing, in particular in consecutive fermentations with Saccharomyces cerevisiae, has only poorly been explored. We have screened 17 non-conventional yeast species for production of an appealing profile of flavor esters and phenolics in the first phase of alcoholic fermentation, followed by inoculation with S. cerevisiae to complete the fermentation. For measurement of phenolic compounds and their precursors we developed an improved and highly sensitive methodology. The results show that non-conventional yeast species possess promising potential for enhancement of desirable flavors in beer production. Notable examples are increasing isoamyl acetate (fruity, banana flavor) by application of P. kluyverii, augmenting ethyl phenolic compounds (spicy notes) with Brettanomyces species and enhancing 4-vinyl guaiacol (clove-like aroma) with T. delbrueckii. All Pichia strains also produced high levels of ethyl acetate (solvent-like flavor). This might be selectively counteracted by selection of an appropriate S. cerevisiae strain for the second fermentation phase, which lowers total ester profile. Hence, optimization of the process conditions and/or proper strain selection in sequentially inoculated fermentations are required to unlock the full potential for aroma improvement by the non-conventional yeast species.}, }
@article {pmid29403461, year = {2018}, author = {Bartelme, RP and Oyserman, BO and Blom, JE and Sepulveda-Villet, OJ and Newton, RJ}, title = {Stripping Away the Soil: Plant Growth Promoting Microbiology Opportunities in Aquaponics.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {8}, pmid = {29403461}, issn = {1664-302X}, abstract = {As the processes facilitated by plant growth promoting microorganisms (PGPMs) become better characterized, it is evident that PGPMs may be critical for successful sustainable agricultural practices. Microbes enrich plant growth through various mechanisms, such as enhancing resistance to disease and drought, producing beneficial molecules, and supplying nutrients and trace metals to the plant rhizosphere. Previous studies of PGPMs have focused primarily on soil-based crops. In contrast, aquaponics is a water-based agricultural system, in which production relies upon internal nutrient recycling to co-cultivate plants with fish. This arrangement has management benefits compared to soil-based agriculture, as system components may be designed to directly harness microbial processes that make nutrients bioavailable to plants in downstream components. However, aquaponic systems also present unique management challenges. Microbes may compete with plants for certain micronutrients, such as iron, which makes exogenous supplementation necessary, adding production cost and process complexity, and limiting profitability and system sustainability. Research on PGPMs in aquaponic systems currently lags behind traditional agricultural systems, however, it is clear that certain parallels in nutrient use and plant-microbe interactions are retained from soil-based agricultural systems.}, }
@article {pmid29397428, year = {2018}, author = {Cortes-Tolalpa, L and Norder, J and van Elsas, JD and Falcao Salles, J}, title = {Halotolerant microbial consortia able to degrade highly recalcitrant plant biomass substrate.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {6}, pages = {2913-2927}, pmid = {29397428}, issn = {1432-0614}, mesh = {Bacteria/classification/isolation &amp; purification/*metabolism ; *Biomass ; Fungi/classification/isolation &amp; purification/*metabolism ; Hydrolysis ; Lignin/*metabolism ; *Microbial Consortia ; Salinity ; Soil Microbiology ; Triticum/*metabolism ; }, abstract = {The microbial degradation of plant-derived compounds under salinity stress remains largely underexplored. The pretreatment of lignocellulose material, which is often needed to improve the production of lignocellulose monomers, leads to high salt levels, generating a saline environment that raises technical considerations that influence subsequent downstream processes. Here, we constructed halotolerant lignocellulose degrading microbial consortia by enriching a salt marsh soil microbiome on a recalcitrant carbon and energy source, i.e., wheat straw. The consortia were obtained after six cycles of growth on fresh substrate (adaptation phase), which was followed by four cycles on pre-digested (highly-recalcitrant) substrate (stabilization phase). The data indicated that typical salt-tolerant bacteria made up a large part of the selected consortia. These were "trained" to progressively perform better on fresh substrate, but a shift was observed when highly recalcitrant substrate was used. The most dominant bacteria in the consortia were Joostella marina, Flavobacterium beibuense, Algoriphagus ratkowskyi, Pseudomonas putida, and Halomonas meridiana. Interestingly, fungi were sparsely present and negatively affected by the change in the substrate composition. Sarocladium strictum was the single fungal strain recovered at the end of the adaptation phase, whereas it was deselected by the presence of recalcitrant substrate. Consortia selected in the latter substrate presented higher cellulose and lignin degradation than consortia selected on fresh substrate, indicating a specialization in transforming the recalcitrant regions of the substrate. Moreover, our results indicate that bacteria have a prime role in the degradation of recalcitrant lignocellulose under saline conditions, as compared to fungi. The final consortia constitute an interesting source of lignocellulolytic haloenzymes that can be used to increase the efficiency of the degradation process, while decreasing the associated costs.}, }
@article {pmid29397399, year = {2018}, author = {Rothman, JA and Carroll, MJ and Meikle, WG and Anderson, KE and McFrederick, QS}, title = {Longitudinal Effects of Supplemental Forage on the Honey Bee (Apis mellifera) Microbiota and Inter- and Intra-Colony Variability.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {814-824}, pmid = {29397399}, issn = {1432-184X}, support = {15-POLL14-McFrederick/Meikle/Carroll//Almond Board of California/ ; NNX15AP99A//National Aeronautics and Space Administration/ ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bees/*microbiology/physiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Phylogeny ; Pollination ; Symbiosis ; }, abstract = {Honey bees (Apis mellifera) provide vital pollination services for a variety of agricultural crops around the world and are known to host a consistent core bacterial microbiome. This symbiotic microbial community is essential to many facets of bee health, including likely nutrient acquisition, disease prevention and optimal physiological function. Being that the bee microbiome is likely involved in the digestion of nutrients, we either provided or excluded honey bee colonies from supplemental floral forage before being used for almond pollination. We then used 16S rRNA gene sequencing to examine the effects of forage treatment on the bees' microbial gut communities over four months. In agreement with previous studies, we found that the honey bee gut microbiota is quite stable over time. Similarly, we compared the gut communities of bees from separate colonies and sisters sampled from within the same hive over four months. Surprisingly, we found that the gut microbial communities of individual sisters from the same colony can exhibit as much variation as bees from different colonies. Supplemental floral forage had a subtle effect on the composition of the microbiome during the month of March only, with strains of Gilliamella apicola, Lactobacillus, and Bartonella being less proportionally abundant in bees exposed to forage in the winter. Collectively, our findings show that there is unexpected longitudinal variation within the gut microbial communities of sister honey bees and that supplemental floral forage can subtly alter the microbiome of managed honey bees.}, }
@article {pmid29396546, year = {2018}, author = {Gonzalez-Martinez, A and Sihvonen, M and Muñoz-Palazon, B and Rodriguez-Sanchez, A and Mikola, A and Vahala, R}, title = {Microbial ecology of full-scale wastewater treatment systems in the Polar Arctic Circle: Archaea, Bacteria and Fungi.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2208}, pmid = {29396546}, issn = {2045-2322}, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Arctic Regions ; Bacteria/classification/genetics/*isolation &amp; purification ; Bioreactors/*microbiology ; *Biota ; Finland ; Fungi/classification/genetics/*isolation &amp; purification ; Metagenomics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sewage/microbiology ; Wastewater/*microbiology ; Water Purification ; }, abstract = {Seven full-scale biological wastewater treatment systems located in the Polar Arctic Circle region in Finland were investigated to determine their Archaea, Bacteria and Fungi community structure, and their relationship with the operational conditions of the bioreactors by the means of quantitative PCR, massive parallel sequencing and multivariate redundancy analysis. The results showed dominance of Archaea and Bacteria members in the bioreactors. The activated sludge systems showed strong selection of Bacteria but not for Archaea and Fungi, as suggested by diversity analyses. Core OTUs in influent and bioreactors were classified as Methanobrevibacter, Methanosarcina, Terrestrial Group Thaumarchaeota and unclassified Euryarchaeota member for Archaea; Trichococcus, Leptotrichiaceae and Comamonadaceae family, and Methylorosula for Bacteria and Trichosporonaceae family for Fungi. All influents shared core OTUs in all domains, but in bioreactors this did not occur for Bacteria. Oligotype structure of core OTUs showed several ubiquitous Fungi oligotypes as dominant in sewage and bioreactors. Multivariate redundancy analyses showed that the majority of core OTUs were related to organic matter and nutrients removal. Also, there was evidence of competition among Archaea and Fungi core OTUs, while all Bacteria OTUs were positively correlated among them. The results obtained highlighted interesting features of extremely cold temperature bioreactors.}, }
@article {pmid29394879, year = {2018}, author = {Herrero, ER and Fernandes, S and Verspecht, T and Ugarte-Berzal, E and Boon, N and Proost, P and Bernaerts, K and Quirynen, M and Teughels, W}, title = {Dysbiotic Biofilms Deregulate the Periodontal Inflammatory Response.}, journal = {Journal of dental research}, volume = {97}, number = {5}, pages = {547-555}, doi = {10.1177/0022034517752675}, pmid = {29394879}, issn = {1544-0591}, mesh = {*Biofilms ; Dysbiosis/immunology/microbiology/*physiopathology ; Enzyme-Linked Immunosorbent Assay ; Fibroblasts/metabolism/microbiology ; Humans ; Interleukin-1beta/metabolism ; Interleukin-6/metabolism ; Interleukin-8/metabolism ; Male ; Matrix Metalloproteinase 8/metabolism ; Periodontitis/*microbiology/physiopathology ; Polymerase Chain Reaction ; Transcriptome ; Tumor Necrosis Factor-alpha/metabolism ; }, abstract = {Periodontal diseases originate from a dysbiosis within the oral microbiota, which is associated with a deregulation of the host immune response. Although little is known about the initiation of dysbiosis, it has been shown that H2O2 production is one of the main mechanisms by which some commensal bacteria suppress the outgrowth of pathobionts. Current models emphasize the critical nature of complex microbial biofilms that form unique microbial ecologies and of their change during transition from health (homeostatic) to disease (dysbiotic). However, very little is known on how this alters their virulence and host responses. The objective of this study was to determine differences in virulence gene expression by pathobionts and the inflammatory host response in homeostatic and dysbiotic biofilms originating from the same ecology. Quantitative polymerase chain reaction was performed to quantify the pathobiont outgrowth. Expression analysis of bacterial virulence and cellular inflammatory genes together with cytokine enzyme-linked immunosorbent assays were used to detect differences in bacterial virulence and to analyze potential differences in inflammatory response. An increase in pathobionts in induced dysbiotic biofilms was observed compared to homeostatic biofilms. The main virulence genes of all pathobionts were upregulated in dysbiotic biofilms. Exposure of these dysbiotic biofilms to epithelial and fibroblast cultures increased the expression of interleukin (IL)-6, IL-1β, tumor necrosis factor-α, and matrix metalloprotease 8, but especially the chemokine CXCL8 (IL-8). Conversely, homeostatic and beneficial biofilms had a minor immune response at the messenger RNA and protein level. Overall, induced dysbiotic biofilms enriched in pathobionts and virulence factors significantly increased the inflammatory response compared to homeostatic and commensal biofilms.}, }
@article {pmid29393559, year = {2018}, author = {Michalik, A and Schulz, F and Michalik, K and Wascher, F and Horn, M and Szklarzewicz, T}, title = {Coexistence of novel gammaproteobacterial and Arsenophonus symbionts in the scale insect Greenisca brachypodii (Hemiptera, Coccomorpha: Eriococcidae).}, journal = {Environmental microbiology}, volume = {20}, number = {3}, pages = {1148-1157}, doi = {10.1111/1462-2920.14057}, pmid = {29393559}, issn = {1462-2920}, mesh = {Animals ; Enterobacteriaceae/*classification/*genetics/growth &amp; development ; Hemiptera/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Symbiosis/genetics/*physiology ; }, abstract = {Scale insects are commonly associated with obligate, intracellular microorganisms which play important roles in complementing their hosts with essential nutrients. Here we characterized the symbiotic system of Greenisca brachypodii, a member of the family Eriococcidae. Histological and ultrastructural analyses have indicated that G. brachypodii is stably associated with coccoid and rod-shaped bacteria. Phylogenetic analyses have revealed that the coccoid bacteria represent a sister group to the secondary symbiont of the mealybug Melanococcus albizziae, whereas the rod-shaped symbionts are close relatives of Arsenophonus symbionts in insects - to our knowledge, this is the first report of the presence of Arsenophonus bacterium in scale insects. As a comparison of 16S and 23S rRNA genes sequences of the G. brachypodii coccoid symbiont with other gammaprotebacterial sequences showed only low similarity (∼90%), we propose the name 'Candidatus Kotejella greeniscae' for its tentative classification. Both symbionts are transovarially transmitted from one generation to the next. The infection takes place in the neck region of the ovariole. The bacteria migrate between follicular cells, as well as through the cytoplasm of those cells to the perivitelline space, where they form a characteristic 'symbiont ball'. Our findings provide evidence for a polyphyletic origin of symbionts of Eriococcidae.}, }
@article {pmid29392382, year = {2018}, author = {Puentes-Téllez, PE and Falcao Salles, J}, title = {Construction of Effective Minimal Active Microbial Consortia for Lignocellulose Degradation.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {419-429}, pmid = {29392382}, issn = {1432-184X}, support = {729004006//FAPESP-NWO/ ; }, mesh = {Bacteria/*classification/enzymology/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Biodiversity ; Cellulose/metabolism ; DNA, Bacterial/analysis ; Enzyme Assays ; Lignin/*metabolism ; Microbial Consortia/*physiology ; Multivariate Analysis ; Paenibacillus/metabolism ; Phylogeny ; Polysaccharides/metabolism ; Soil Microbiology ; Stenotrophomonas maltophilia/metabolism ; }, abstract = {Enriched microbial communities, obtained from environmental samples through selective processes, can effectively contribute to lignocellulose degradation. Unfortunately, fully controlled industrial degradation processes are difficult to reach given the intrinsically dynamic nature and complexity of the microbial communities, composed of a large number of culturable and unculturable species. The use of less complex but equally effective microbial consortia could improve their applications by allowing for more controlled industrial processes. Here, we combined ecological theory and enrichment principles to develop an effective lignocellulose-degrading minimal active microbial Consortia (MAMC). Following an enrichment of soil bacteria capable of degrading lignocellulose material from sugarcane origin, we applied a reductive-screening approach based on molecular phenotyping, identification, and metabolic characterization to obtain a selection of 18 lignocellulose-degrading strains representing four metabolic functional groups. We then generated 65 compositional replicates of MAMC containing five species each, which vary in the number of functional groups, metabolic potential, and degradation capacity. The characterization of the MAMC according to their degradation capacities and functional diversity measurements revealed that functional diversity positively correlated with the degradation of the most complex lignocellulosic fraction (lignin), indicating the importance of metabolic complementarity, whereas cellulose and hemicellulose degradation were either negatively or not affected by functional diversity. The screening method described here successfully led to the selection of effective MAMC, whose degradation potential reached up 96.5% of the degradation rates when all 18 species were present. A total of seven assembled synthetic communities were identified as the most effective MAMC. A consortium containing Stenotrophomonas maltophilia, Paenibacillus sp., Microbacterium sp., Chryseobacterium taiwanense, and Brevundimonas sp. was found to be the most effective degrading synthetic community.}, }
@article {pmid29391815, year = {2018}, author = {Rajpara, N and Nair, M and Chowdhury, G and Mukhopadhyay, AK and Ramamurthy, T and Niyogi, SK and Bhardwaj, AK}, title = {Molecular analysis of multidrug resistance in clinical isolates of Shigella spp. from 2001-2010 in Kolkata, India: role of integrons, plasmids, and topoisomerase mutations.}, journal = {Infection and drug resistance}, volume = {11}, number = {}, pages = {87-102}, pmid = {29391815}, issn = {1178-6973}, abstract = {To understand the genetic basis of high drug resistance in Shigella, 95 clinical isolates of Shigella spp. (2001-2010) were obtained from the Infectious Diseases Hospital, Kolkata, India. Ninety-three isolates were resistant to three or more antibiotics. Resistance to nalidixic acid, trimethoprim, streptomycin, and co-trimoxazole was most common in this population. Dendrogram analysis showed that S. sonnei strains were more clonally related when compared to the other Shigella species. The role of mobile genetic elements and chromosome-borne resistance factors was analyzed in detail. Integron analysis indicated the preponderance of class 2 and atypical class 1 integrons in that population. Typical class 1 integron was present in only one S. sonnei isolate and harbored trimethoprim resistance-encoding gene dfrV, while atypical class 1 integrons harbored dfrA1-aadA or blaOXA-aadA gene cassettes responsible for resistance to trimethoprim, aminoglycosides, and β-lactams. Class 2 integrons harbored either dfrA1-sat-aadA or dfrA1-sat gene cassettes. Most importantly, a novel gene cassette array InsE-InsO-dfrA1-sat was found in class 2 integron of S. sonnei NK4846. Many of the resistance traits for antibiotics such as trimethoprim, co-trimoxazole, kanamycin, ampicillin, and tetracycline were transferred from parent Shigella isolates to recipient Escherichia coli during conjugation, establishing the role of plasmids in horizontal transfer of resistance genes. Multiple mutations such as S80→I, S83→L, and D87→G/N/Y in quinolone resistance determining regions of topoisomerases from the representative quinolone-resistant isolates could explain the spectrum of minimal inhibitory concentration values for various quinolones. To the best of our knowledge, this is the first comprehensive report that describes the contribution of mobile (plasmids, integrons, and quinolone resistance genes named qnr) and innate genetic elements (mutations in topoisomerases) in determining the resistance phenotype of all the four species of Shigella over a span of ten years.}, }
@article {pmid29389073, year = {2018}, author = {Bakker, MG}, title = {A fungal mock community control for amplicon sequencing experiments.}, journal = {Molecular ecology resources}, volume = {18}, number = {3}, pages = {541-556}, doi = {10.1111/1755-0998.12760}, pmid = {29389073}, issn = {1755-0998}, mesh = {*Biodiversity ; Classification/methods ; DNA Barcoding, Taxonomic ; DNA, Intergenic/chemistry ; Fungi/classification/*genetics/growth &amp; development ; Gene Dosage ; Gene Library ; *Genetic Variation ; Polymerase Chain Reaction ; RNA, Ribosomal/chemistry ; }, abstract = {Microbial ecology has been profoundly advanced by the ability to profile complex microbial communities by sequencing of marker genes amplified from environmental samples. However, inclusion of appropriate controls is vital to revealing the limitations and biases of this technique. "Mock community" samples, in which the composition and relative abundances of community members are known, are particularly valuable for guiding library preparation and data processing decisions. I generated a set of three mock communities using 19 different fungal taxa and demonstrate their utility by contrasting amplicon sequencing data obtained for the same communities under modifications to PCR conditions during library preparation. Increasing the number of PCR cycles elevated rates of chimera formation, and of errors in the final data set. Extension time during PCR had little impact on chimera formation, error rate or observed community structure. Polymerase fidelity impacted error rates significantly. Despite a high error rate, a master mix optimized to minimize amplification bias yielded profiles that were most similar to the true community structure. Bias against particular taxa differed among ITS1 vs. ITS2 loci. Preclustering nearly identical reads substantially reduced error rates, but did not improve similarity to the expected community structure. Inaccuracies in amplicon sequence-based estimates of fungal community structure were associated with amplification bias and size selection processes, as well as variable culling rates among reads from different taxa. In some cases, the numerically dominant taxon was completely absent from final data sets, highlighting the need for further methodological improvements to avoid biased observations of community profiles.}, }
@article {pmid29388541, year = {2018}, author = {Cho, GY and Lee, JC and Whang, KS}, title = {Erratum: Aliifodinibius salicampi sp. nov., a moderately halophilic bacterium isolated from a grey saltern.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {68}, number = {2}, pages = {692}, doi = {10.1099/ijsem.0.002572}, pmid = {29388541}, issn = {1466-5034}, }
@article {pmid29387519, year = {2018}, author = {Martinez, DA and Loening, UE and Graham, MC}, title = {Impacts of glyphosate-based herbicides on disease resistance and health of crops: a review.}, journal = {Environmental sciences Europe}, volume = {30}, number = {1}, pages = {2}, pmid = {29387519}, issn = {2190-4707}, abstract = {Based on experimental data from laboratory and field, numerous authors have raised concern that exposure to glyphosate-based herbicides (GBHs) may pre-dispose crops to damage by microbial pathogens. In this review, we distinguish and evaluate two principal pathways by which GBHs may affect the susceptibility of crops to disease: pathway 1-via disruptions to rhizosphere microbial ecology, and pathway 2-via restriction of nutrients to crops. We conclude that GBHs have the potential to undermine crop health in a number of ways, including: (i) impairment of the innate physiological defences of glyphosate-sensitive (GS) cultivars by interruption of the shikimic acid pathway; (ii) impairment of physiological disease defences has also been shown to occur in some glyphosate-resistant (GR) cultivars, despite their engineered resistance to glyphosate's primary mode of action; (iii) interference with rhizosphere microbial ecology (in particular, GBHs have the potential to enhance the population and/or virulence of some phytopathogenic microbial species in the crop rhizosphere); and finally, (iv) the as yet incompletely elucidated reduction in the uptake and utilisation of nutrient metals by crops. Future progress will best be achieved when growers, regulators and industry collaborate to develop products, practices and policies that minimise the use of herbicides as far as possible and maximise their effectiveness when used, while facilitating optimised food production and security.}, }
@article {pmid29382947, year = {2018}, author = {Veraart, AJ and Garbeva, P and van Beersum, F and Ho, A and Hordijk, CA and Meima-Franke, M and Zweers, AJ and Bodelier, PLE}, title = {Living apart together-bacterial volatiles influence methanotrophic growth and activity.}, journal = {The ISME journal}, volume = {12}, number = {4}, pages = {1163-1166}, pmid = {29382947}, issn = {1751-7370}, mesh = {Heterotrophic Processes ; Methane/*metabolism ; Methylococcaceae/growth &amp; development/metabolism ; Methylocystaceae/growth &amp; development/metabolism ; Pseudomonas/metabolism ; Volatile Organic Compounds/metabolism ; }, abstract = {Volatile organic compounds play an important role in microbial interactions. However, little is known about how volatile-mediated interactions modulate biogeochemical processes. In this study, we show the effect of volatile-mediated interaction on growth and functioning of aerobic methane-oxidizing bacteria, grown in co-culture with five different heterotrophs. Both growth and methane oxidation of Methylobacter luteus were stimulated by interaction with specific heterotrophs. In Methylocystis parvus, we observed significant growth promotion, while methane oxidation was inhibited. Volatolomics of the interaction of each of the methanotrophs with Pseudomonas mandelii, revealed presence of a complex blend of volatiles, including dimethylsulfide, dimethyldisulfide, and bicyclic sesquiterpenes. Although the ecological role of the detected compounds remains to be elucidated, our results provide unprecedented insights into interspecific relations and associated volatiles for stimulating methanotroph functioning, which is of substantial environmental and biotechnological significance.}, }
@article {pmid29380642, year = {2018}, author = {Zhou, Y and Ni, X and Wen, B and Duan, L and Sun, H and Yang, M and Zou, F and Lin, Y and Liu, Q and Zeng, Y and Fu, X and Pan, K and Jing, B and Wang, P and Zeng, D}, title = {Appropriate dose of Lactobacillus buchneri supplement improves intestinal microbiota and prevents diarrhoea in weaning Rex rabbits.}, journal = {Beneficial microbes}, volume = {9}, number = {3}, pages = {401-416}, doi = {10.3920/BM2017.0055}, pmid = {29380642}, issn = {1876-2891}, mesh = {Animals ; Cytokines/analysis ; Denaturing Gradient Gel Electrophoresis ; Diarrhea/pathology/prevention &amp; control/*veterinary ; Enzyme-Linked Immunosorbent Assay ; *Gastrointestinal Microbiome ; Intestines/pathology ; Lactobacillus/*growth &amp; development ; Polymerase Chain Reaction ; Probiotics/*administration &amp; dosage ; Rabbits ; Treatment Outcome ; *Weaning ; }, abstract = {This study examined the effects on intestinal microbiota and diarrhoea of Lactobacillus buchneri supplementation to the diet of weaning Rex rabbits. To this end, rabbits were treated with L. buchneri at two different doses (LC: 10[4] cfu/g diet and HC: 10[5] cfu/g diet) for 4 weeks. PCR-DGGE was used to determine the diversity of the intestinal microbiota, while real-time PCR permitted the detection of individual bacterial species. ELISA and real-time PCR allowed the identification of numerous cytokines in the intestinal tissues. Zonula occludens-1, polymeric immunoglobulin receptor and immunoglobulin A genes were examined to evaluate intestinal barriers. Results showed that the biodiversity of the intestinal microbiota of weaning Rex rabbits improved in the whole tract of the treated groups. The abundance of most detected bacterial species was highly increased in the duodenum, jejunum and ileum after L. buchneri administration. The species abundance in the HC group was more increased than in the LC group when compared to the control. Although the abundance of Enterobacteriaceae exhibited a different pattern, Escherichia coli was inhibited in all treatment groups. Toll-like receptor (TLR)2 and TLR4 genes were down-regulated in all intestinal tissues as the microbiota changed. In the LC group, the secretion of the inflammatory cytokine tumour necrosis factor-α was reduced, the gene expression of the anti-inflammatory cytokine interleukin (IL)-4 was up-regulated and the expression of intestinal-barrier-related genes was enhanced. Conversely, IL-4 expression was increased and the expression of other tested genes did not change in the HC group. The beneficial effects of LC were greater than those of HC or the control in terms of improving the daily weight gain and survival rate of weaning Rex rabbits and reducing their diarrhoea rate. Therefore, 10[4] cfu/g L. buchneri treatment improved the microbiota of weaning Rex rabbits and prevented diarrhoea in these animals.}, }
@article {pmid29380029, year = {2018}, author = {Sirisena, KA and Ramirez, S and Steele, A and Glamoclija, M}, title = {Microbial Diversity of Hypersaline Sediments from Lake Lucero Playa in White Sands National Monument, New Mexico, USA.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {404-418}, pmid = {29380029}, issn = {1432-184X}, support = {NASA-ASTEP NNX14AT28G//National Aeronautics and Space Administration/ ; }, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biodiversity ; Cluster Analysis ; DNA, Archaeal ; DNA, Bacterial ; Eukaryota/classification/genetics ; *Extreme Environments ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; *Microbiota/genetics ; New Mexico ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Salinity ; *Water Microbiology ; }, abstract = {Lake Lucero is a gypsum-rich, hypersaline, ephemeral playa located on the southern part of the Alkali Flat at the White Sands National Monument (WSNM), New Mexico, USA. This modern playa setting provides a dynamic extreme environment that changes from a freshwater lake to a hypersaline dry desert during the year. We investigated the microbial diversity (bacteria, archaea, and microbial eukaryotes) of the Lake Lucero sediments using 16S- and 18S-based amplicon sequencing approach and explored the diversity patterns in different geochemical microenvironments. Our results indicated that similar microbial communities, in particular bacterial communities colonized, were remarkably consistent across our depth profiles. Therefore, these communities show a first-order relevance on the environmental conditions (moisture content, oxygen content, and mineral composition). We found that Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Gemmatimonadetes were the major bacterial phyla, while Cyanobacteria were present in relatively low abundances and appeared only at the surface. Genus level assessment reflected that Truepera, Delftia, and Pseudomonas were the predominant bacterial genera across all samples. Euryarchaeota was the major archaeal phylum in all the samples, while Candidatus Halobonum and Candidatus Nitrososphaera were the main genera. Diatoms were the dominant eukaryotic group in surface samples and Fungi, Ciliophora, Metazoa, and Nematodes were the other major groups. As expected, metabolic inference indicated that aerobic microbial communities were near surface colonizers, with anaerobic communities dominating with increasing depth. We demonstrated that these microbial communities could be used to characterize unique geochemical microenvironments enabling us to extrapolate these results into other terrestrial and possibly extraterrestrial environments with comparable geochemical characteristics.}, }
@article {pmid29380028, year = {2018}, author = {Hede, N and Khandeparker, L}, title = {Influence of Darkness and Aging on Marine and Freshwater Biofilm Microbial Communities Using Microcosm Experiments.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {314-327}, pmid = {29380028}, issn = {1432-184X}, support = {GAP 2429//Ballast Water Management Program, India (Ministry of Shipping and DG shipping)/ ; PSC 0105//CSIR funded Ocean Finder Program/ ; }, mesh = {Alphaproteobacteria/genetics/physiology ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; Biodiversity ; *Biofilms ; Chlorophyll A/analysis ; Colony Count, Microbial ; DNA, Bacterial/genetics ; *Darkness ; Fresh Water/*microbiology ; Gammaproteobacteria/classification/genetics/physiology ; Gene Dosage ; Genes, Bacterial/genetics ; India ; Microbiota/genetics/*physiology ; Phylogeny ; Proteobacteria/classification/genetics/physiology ; RNA, Ribosomal, 16S/genetics ; Salinity ; Seawater/*microbiology ; Temperature ; }, abstract = {Ballast tank biofilms pose an additional risk of microbial invasion if sloughed off during ballasting operations, yet their significance and invasion biology is poorly understood. In this study, biofilms developed in marine and freshwater locations were exposed to prolonged darkness and aging by mimicking ballast water conditions in the laboratory. Upon prolonged darkness, the decay of phytoplankton, as indicated by the decrease in chlorophyll a in marine biofilms, led to remineralization and enhanced bacterial and protist populations. However, the same trend was not observed in the case of freshwater biofilms wherein the microbial parameters (i.e., bacteria, protists) and chlorophyll a decreased drastically. The bacterial community structure in such conditions was evaluated by real-time quantitative PCR (qPCR), and results showed that the biofilm bacterial communities changed significantly over a period of time. α-Proteobacteria was the most stable taxonomic group in the marine biofilms under dark conditions. However, β-proteobacteria dominated the freshwater biofilms and seemed to play an important role in organic matter remineralization. γ-Proteobacteria, which includes most of the pathogenic genera, were affected significantly and decreased in both the types of biofilms. This study revealed that marine biofilm communities were able to adapt better to the dark conditions while freshwater biofilm communities collapsed. Adaptation of tolerant bacterial communities, regeneration of nutrients via cell lysis, and presence of grazers appeared to be key factors for survival upon prolonged darkness. However, the fate of biofilm communities upon discharge in the new environment and their invasion potential is an important topic for future investigation.}, }
@article {pmid29380027, year = {2018}, author = {Ferguson, JA and Northfield, TD and Lach, L}, title = {Honey Bee (Apis mellifera) Pollen Foraging Reflects Benefits Dependent on Individual Infection Status.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {482-491}, pmid = {29380027}, issn = {1432-184X}, support = {DE130100709//Australian Research Council/ ; }, mesh = {Animal Feed ; Animals ; Bees/*microbiology ; Behavior, Animal/*physiology ; Host Microbial Interactions/physiology ; Nosema/pathogenicity/*physiology ; *Pollen ; Survival Rate ; }, abstract = {Parasites often modify host foraging behavior, for example, by spurring changes to nutrient intake ratios or triggering self-medication. The gut parasite, Nosema ceranae, increases energy needs of the European or Western honey bee (Apis mellifera), but little is known about how infection affects foraging behavior. We used a combination of experiments and observations of caged and free-flying individual bees and hives to determine how N. ceranae affects honey bee foraging behavior. In an experiment with caged bees, we found that infected bees with access to a high-quality pollen were more likely to survive than infected bees with access to a lower quality pollen or no pollen. Non-infected bees showed no difference in survival with pollen quality. We then tested free-flying bees in an arena of artificial flowers and found that pollen foraging bees chose pollen commensurate with their infection status; twice as many infected bees selected the higher quality pollen than the lower quality pollen, while healthy bees showed no preference between pollen types. However, healthy and infected bees visited sucrose and pollen flowers in the same proportions. Among hive-level observations, we found no significant correlations between N. ceranae infection intensity in the hive and the proportion of bees returning with pollen. Our results indicate that N. ceranae-infected bees benefit from increased pollen quality and will selectively forage for higher quality while foraging for pollen, but infection status does not lead to increased pollen foraging at either the individual or hive levels.}, }
@article {pmid29379208, year = {2018}, author = {Probst, AJ and Ladd, B and Jarett, JK and Geller-McGrath, DE and Sieber, CMK and Emerson, JB and Anantharaman, K and Thomas, BC and Malmstrom, RR and Stieglmeier, M and Klingl, A and Woyke, T and Ryan, MC and Banfield, JF}, title = {Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface.}, journal = {Nature microbiology}, volume = {3}, number = {3}, pages = {328-336}, pmid = {29379208}, issn = {2058-5276}, mesh = {Archaea/*classification/growth &amp; development ; Autotrophic Processes ; Bacteria/*classification/growth &amp; development ; Carbon Cycle ; Geologic Sediments/*microbiology ; Groundwater/*microbiology ; Metagenomics ; Phylogeny ; *Symbiosis ; }, abstract = {An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome-resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus "Altiarchaeum sp." and phylogenetically deep-branching nanoarchaea dominate the deepest groundwater. A nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. "Altiarchaeum". Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface.}, }
@article {pmid29377716, year = {2018}, author = {Cockell, CS and Biller, B and Bryce, C and Cousins, C and Direito, S and Forgan, D and Fox-Powell, M and Harrison, J and Landenmark, H and Nixon, S and Payler, SJ and Rice, K and Samuels, T and Schwendner, P and Stevens, A and Nicholson, N and Wadsworth, J}, title = {The UK Centre for Astrobiology: A Virtual Astrobiology Centre. Accomplishments and Lessons Learned, 2011-2016.}, journal = {Astrobiology}, volume = {18}, number = {2}, pages = {224-243}, pmid = {29377716}, issn = {1557-8070}, mesh = {*Earth, Planet ; Education/history/methods/*organization &amp; administration ; Education, Distance ; Exobiology/*education/history/methods/organization &amp; administration ; *Extraterrestrial Environment ; History, 21st Century ; United Kingdom ; }, abstract = {The UK Centre for Astrobiology (UKCA) was set up in 2011 as a virtual center to contribute to astrobiology research, education, and outreach. After 5 years, we describe this center and its work in each of these areas. Its research has focused on studying life in extreme environments, the limits of life on Earth, and implications for habitability elsewhere. Among its research infrastructure projects, UKCA has assembled an underground astrobiology laboratory that has hosted a deep subsurface planetary analog program, and it has developed new flow-through systems to study extraterrestrial aqueous environments. UKCA has used this research backdrop to develop education programs in astrobiology, including a massive open online course in astrobiology that has attracted over 120,000 students, a teacher training program, and an initiative to take astrobiology into prisons. In this paper, we review these activities and others with a particular focus on providing lessons to others who may consider setting up an astrobiology center, institute, or science facility. We discuss experience in integrating astrobiology research into teaching and education activities. Key Words: Astrobiology-Centre-Education-Subsurface-Analog research. Astrobiology 18, 224-243.}, }
@article {pmid29376168, year = {2018}, author = {Strickman, RJ and Mitchell, CPJ}, title = {Mercury methylation in stormwater retention ponds at different stages in the management lifecycle.}, journal = {Environmental science. Processes &amp; impacts}, volume = {20}, number = {4}, pages = {595-606}, doi = {10.1039/c7em00486a}, pmid = {29376168}, issn = {2050-7895}, mesh = {Environmental Monitoring/*methods ; Geologic Sediments/chemistry ; Mercury/*analysis ; Methylation ; Methylmercury Compounds/*analysis ; Ponds/*chemistry ; Rain/chemistry ; Water Pollutants, Chemical/*analysis ; *Wetlands ; }, abstract = {Stormwater retention ponds effectively manage erosion, flooding, and pollutant loadings, but are also sources of methylmercury (MeHg), a bioaccumulative neurotoxin which is produced by anaerobic aquatic microorganisms. Stormwater retention ponds have a 10-15 year working life, after which they are dredged and reflooded. In this study, we related MeHg biogeochemistry to the different stages of the management lifecycle. In a new, a dredged, and a mature stormwater retention pond, we measured MeHg and inorganic mercury (IHg) concentrations, and the potential for MeHg formation (Kmeth), during the early summer, peak summer, and fall of 2013. In our study sites, MeHg concentrations appear to be driven by mercury (Hg) methylation, indicated by significant correlations between Kmeth values and MeHg concentrations and the percent of Hg present as MeHg. Relationships between Hg variables and ancillary biogeochemistry suggest that Hg methylation is carried out by sulfate reducing bacteria, but that the process is modulated by the supply of IHg substrate, sediment total and labile organic carbon, and possibly competition with nitrate reducers. Wetlands at different points in the management lifecycle differ in terms of their MeHg biogeochemistry. The organic matter-poor new wetland had low MeHg production (mean Kmeth 0.014 per day) and sediment concentrations (mean 0.015 ng g-1), while the mature wetland both produced and accumulated MeHg about five times more actively. Methylmercury production capacity was only temporarily reduced in the reflooded sediments of the dredged wetland, which experienced rapid increases in Kmeth values from low (mean 0.015 per day) immediately after dredging, to values similar to those in the mature wetland after five months. This pattern may have been related to recolonization of the sediments with mercury methylators or increased microbial activities in response to the addition of fresh organic matter. Additional studies should focus on the applicability of these patterns to stormwater retention ponds in other areas, and particularly investigate the effects of stormwater pond dredging on their microbial ecology and MeHg biogeochemistry.}, }
@article {pmid29375790, year = {2018}, author = {Reese, AT and Lulow, K and David, LA and Wright, JP}, title = {Plant community and soil conditions individually affect soil microbial community assembly in experimental mesocosms.}, journal = {Ecology and evolution}, volume = {8}, number = {2}, pages = {1196-1205}, pmid = {29375790}, issn = {2045-7758}, abstract = {Soils harbor large, diverse microbial communities critical for local and global ecosystem functioning that are controlled by multiple and poorly understood processes. In particular, while there is observational evidence of relationships between both biotic and abiotic conditions and microbial composition and diversity, there have been few experimental tests to determine the relative importance of these two sets of factors at local scales. Here, we report the results of a fully factorial experiment manipulating soil conditions and plant cover on old-field mesocosms across a latitudinal gradient. The largest contributor to beta diversity was site-to-site variation, but, having corrected for that, we observed significant effects of both plant and soil treatments on microbial composition. Separate phyla were associated with each treatment type, and no interactions between soil and plant treatment were observed. Individual soil characteristics and biotic parameters were also associated with overall beta-diversity patterns and phyla abundance. In contrast, soil microbial diversity was only associated with site and not experimental treatment. Overall, plant community treatment explained more variation than soil treatment, a result not previously appreciated because it is difficult to dissociate plant community composition and soil conditions in observational studies across gradients. This work highlights the need for more nuanced, multifactorial experiments in microbial ecology and in particular indicates a greater focus on relationships between plant composition and microbial composition during community assembly.}, }
@article {pmid29374376, year = {2018}, author = {Song, M and Cheng, Z and Luo, C and Jiang, L and Zhang, D and Yin, H and Zhang, G}, title = {Rhizospheric effects on the microbial community of e-waste-contaminated soils using phospholipid fatty acid and isoprenoid glycerol dialkyl glycerol tetraether analyses.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {10}, pages = {9904-9914}, pmid = {29374376}, issn = {1614-7499}, support = {U1501234//National Natural Science Foundation of China/ ; 41673111//National Natural Science Foundation of China/ ; 2015M582430//China Postdoctoral Science Foundation/ ; 201707020034//the Scienfitic and Technological Planning Project of Guangzhou/ ; }, mesh = {Biodegradation, Environmental ; Biomass ; Colocasia/microbiology ; Electronic Waste/*analysis ; Environmental Monitoring/*methods ; Fatty Acids/analysis ; Glyceryl Ethers/analysis ; Metals, Heavy/*analysis ; Phospholipids/analysis ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/*analysis ; Terpenes/analysis ; }, abstract = {We performed the study of rhizospheric effects on soil microbial community structure, including bacteria, fungi, actinomycete, and archaea, at an electronic waste (e-waste) recycling site by analyzing the phospholipid fatty acid (PLFA) and isoprenoid glycerol dialkyl glycerol tetraether (GDGT) contents. By comparing PLFA and isoprenoid GDGT profiles of rhizospheric and surrounding bulk soils of 11 crop species, we observed distinct microbial community structures. The total PLFA concentration was significantly higher in rhizospheric soils than in non-rhizospheric soils, whereas no obvious difference was found in the total isoprenoid GDGT concentrations. The microbial community structure was also different, with higher ratios of fungal-to-bacterial PLFAs (F/B) and lower relative abundance of Gram-positive bacteria in rhizospheric soils. The extent of rhizospheric effects varied among plant species, and Colocasia esculenta L. had the greatest positive effects on the total microbial biomass. Dissolved organic carbon and pH were the main environmental factors affecting the microbial community represented by PLFAs, while the archaeal community was influenced by copper and zinc in all soils. These results offer a comprehensive view of rhizospheric effects on microbes in heavy metal and persistent organic pollutant co-contaminated soil, and provide fundamental knowledge regarding microbial ecology in e-waste-contaminated soils.}, }
@article {pmid29374268, year = {2018}, author = {Mallon, CA and Le Roux, X and van Doorn, GS and Dini-Andreote, F and Poly, F and Salles, JF}, title = {The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader's niche.}, journal = {The ISME journal}, volume = {12}, number = {3}, pages = {728-741}, pmid = {29374268}, issn = {1751-7370}, support = {309555/ERC_/European Research Council/International ; }, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Ecosystem ; *Microbiota ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Although many environments like soils are constantly subjected to invasion by alien microbes, invaders usually fail to succeed, succumbing to the robust diversity often found in nature. So far, only successful invasions have been explored, and it remains unknown to what extent an unsuccessful invasion can impact resident communities. Here we hypothesized that unsuccessful invasions can cause impacts to soil functioning by decreasing the diversity and niche breadth of resident bacterial communities, which could cause shifts to community composition and niche structure-an effect that is likely exacerbated when diversity is compromised. To examine this question, diversity gradients of soil microbial communities were subjected to invasion by the frequent, yet oft-unsuccessful soil invader, Escherichia coli, and evaluated for changes to diversity, bacterial community composition, niche breadth, and niche structure. Contrary to expectations, diversity and niche breadth increased across treatments upon invasion. Community composition and niche structure were also altered, with shifts of niche structure revealing an escape by the resident community away from the invader's resources. Importantly, the extent of the escape varied in response to the community's diversity, where less diverse communities experienced larger shifts. Thus, although transient and unsuccessful, the invader competed for resources with resident species and caused tangible impacts that modified both the diversity and functioning of resident communities, which can likely generate a legacy effect that influences future invasion attempts.}, }
@article {pmid29372281, year = {2018}, author = {Zhao, J and Yao, Y and Li, D and Xu, H and Wu, J and Wen, A and Xie, M and Ni, Q and Zhang, M and Peng, G and Xu, H}, title = {Characterization of the Gut Microbiota in Six Geographical Populations of Chinese Rhesus Macaques (Macaca mulatta), Implying an Adaptation to High-Altitude Environment.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {565-577}, pmid = {29372281}, issn = {1432-184X}, support = {No. 31370407//National Natural Science Foundation of China/ ; }, mesh = {*Acclimatization ; *Altitude ; Animals ; Bacteria/*classification/genetics ; Biodiversity ; China ; Cluster Analysis ; DNA, Bacterial/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Geography ; Macaca mulatta/*microbiology ; Multivariate Analysis ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tibet ; }, abstract = {Knowledge about the impact of different geographical environments on rhesus macaque gut microbiota is limited. In this study, we compared the characteristics of gut microbiota in six different Chinese rhesus macaque populations, including Hainan, Nanning, Guizhou, Xichang, Jianchuan and Tibet. Through the composition analysis of operational taxonomic units (OTUs), we found that there were significant differences in the abundance of core overlapping OTUs in the six Chinese groups. Specifically, the Tibet population exhibited the highest gut microbial diversity and the most unique OTUs. Statistically significant differences in the composition of gut microbiota among the six groups at phylum and family level were evident. Specifically, Tibet had higher abundances of Firmicutes and lower abundances of Bacteroidetes than the other geographical groups, and the higher abundance of Firmicutes in the Tibetan group was mainly caused by a significant increase in the family Ruminococcaceae and Christensenellaceae. Phylogenetic investigation of communities by reconstruction of unobserved state analysis showed that the enrichment ratio for environmental information processing and organismal systems was the highest in the Tibet population. Additionally, our results suggested that in the adaptation process of rhesus macaques to different geographical environments, the abundance of the core common flora of the intestinal microbes had undergone varying degree of change and produced new and unique flora, both of which helped to reshape the gut microbiota of rhesus macaques. In particular, this change was more obvious for animals in the high-altitude environments.}, }
@article {pmid29371357, year = {2018}, author = {Hausmann, B and Pjevac, P and Schreck, K and Herbold, CW and Daims, H and Wagner, M and Loy, A}, title = {Draft Genome Sequence of Telmatospirillum siberiense 26-4b1, an Acidotolerant Peatland Alphaproteobacterium Potentially Involved in Sulfur Cycling.}, journal = {Genome announcements}, volume = {6}, number = {4}, pages = {}, pmid = {29371357}, issn = {2169-8287}, support = {294343/ERC_/European Research Council/International ; P 23117/FWF_/Austrian Science Fund FWF/Austria ; P 25111/FWF_/Austrian Science Fund FWF/Austria ; P 27319/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {The facultative anaerobic chemoorganoheterotrophic alphaproteobacterium Telmatospirillum siberiense 26-4b1 was isolated from a Siberian peatland. We report here a 6.20-Mbp near-complete high-quality draft genome sequence of T. siberiense that reveals expected and novel metabolic potential for the genus Telmatospirillum, including genes for sulfur oxidation.}, }
@article {pmid29368058, year = {2018}, author = {Bestová, H and Munoz, F and Svoboda, P and Škaloud, P and Violle, C}, title = {Ecological and biogeographical drivers of freshwater green algae biodiversity: from local communities to large-scale species pools of desmids.}, journal = {Oecologia}, volume = {186}, number = {4}, pages = {1017-1030}, pmid = {29368058}, issn = {1432-1939}, support = {B Bio 599912/2012//Univerzita Karlova (CZ) Science Foundation/International ; ERC-StG-2014-639706-CONSTRAINTS//European Research Council/International ; }, mesh = {Biodiversity ; *Chlorophyta ; *Desmidiales ; Europe ; Fresh Water ; }, abstract = {Dispersal limitation, niche-based processes as well as historical legacies shape microbial biodiversity, but their respective influences remain unknown for many groups of microbes. We analysed metacommunity structure and functional trait variation in 148 communities of desmids, freshwater green algae, distributed throughout Europe. We delineated biogeographic modules for both taxa and sites using bipartite network analysis given that the taxa of a module co-occurred more often than expected by chance in sites of the same module. The network analysis distinguished two main acidic and neutral habitats, reflecting environmental filtering, and within each habitat separated species pools with distinct geographic locations, representing a plausible influence of historical biogeography. The geographic differentiation was consistent with a hypothesis of glacial refugia on Atlantic coast. Distance decay in community composition in addition to environmental influence further suggested a role of dispersal limitation. Next, we quantified the variation in cell volume and surface-to-volume of taxa within and among communities, to examine morphological and physiological adaptations of desmids in varying environments. Communities from continental climate contained larger desmids. Conversely, we found a functional convergence of smaller, fast-growing, desmids in oceanic regions. Overall, our findings suggest that niche-based processes, dispersal limitation, and historical legacy together drive the distribution and structure of desmid communities. Combining trait- and network-based analyses can resolve long-lasting questions in microbial ecology and biogeography, and could be successfully used in macrobial ecology too.}, }
@article {pmid29363966, year = {2018}, author = {Van den Abbeele, P and Taminiau, B and Pinheiro, I and Duysburgh, C and Jacobs, H and Pijls, L and Marzorati, M}, title = {Arabinoxylo-Oligosaccharides and Inulin Impact Inter-Individual Variation on Microbial Metabolism and Composition, Which Immunomodulates Human Cells.}, journal = {Journal of agricultural and food chemistry}, volume = {66}, number = {5}, pages = {1121-1130}, doi = {10.1021/acs.jafc.7b04611}, pmid = {29363966}, issn = {1520-5118}, mesh = {Acetates/metabolism ; Butyrates/metabolism ; Caco-2 Cells ; Feces/microbiology ; Fermentation ; Gastrointestinal Microbiome/*drug effects/immunology/physiology ; Humans ; Hydrogen-Ion Concentration ; Immunomodulation/*drug effects ; Inulin/*pharmacology ; Oligosaccharides/*pharmacology ; Propionates/metabolism ; Xylans/*pharmacology ; }, abstract = {Fecal batch fermentations coupled to cocultures of epithelial cells and macrophages were used to compare how arabinoxylo-oligosaccharides (AXOS) and inulin modulate gut microbial activity and composition of three different human donors and subsequently the epithelial permeability and immune response. Both inulin and AXOS decreased the pH during incubation (-1.5 pH units), leading to increased productions of acetate, propionate, and butyrate. Differences in terms of metabolites production could be linked to specific microbial alterations at genus level upon inulin/AXOS supplementation (i.e., Bifidobacterium, Bacteroides, Prevotella and unclassified Erysipelotrichaceae), as shown by 16S-targeted Illumina sequencing. Both products stimulated gut barrier and immune function with increases in TEER, NF-KB, IL-10, and IL-6. Ingredients with different structures selectively modulate the microbiota of a specific donor leading to differential changes at metabolic level. The extent of this effect is donor specific and is linked to a final specific modulation of the host's immune system.}, }
@article {pmid29363272, year = {2018}, author = {Mulders, RJ and de Git, KCG and Schéle, E and Dickson, SL and Sanz, Y and Adan, RAH}, title = {Microbiota in obesity: interactions with enteroendocrine, immune and central nervous systems.}, journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity}, volume = {19}, number = {4}, pages = {435-451}, doi = {10.1111/obr.12661}, pmid = {29363272}, issn = {1467-789X}, mesh = {Diet, High-Fat/*adverse effects ; Dysbiosis/etiology/immunology/*physiopathology ; Energy Intake ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/*immunology ; Gene Expression ; Humans ; Hypothalamus/*physiopathology ; Inflammation/etiology/*microbiology/physiopathology ; Microglia/metabolism ; Obesity/complications/*microbiology/physiopathology ; Prebiotics/administration &amp; dosage ; Probiotics/administration &amp; dosage ; Vagus Nerve/metabolism ; }, abstract = {Western diets, with high consumption of simple sugars and saturated fats, contribute to the rise in the prevalence of obesity. It now seems clear that high-fat diets cause obesity, at least in part, by modifying the composition and function of the microorganisms that colonize in the gastrointestinal tract, the microbiota. The exact pathways by which intestinal microbiota contribute to obesity remain largely unknown. High-fat diet-induced alterations in intestinal microbiota have been suggested to increase energy extraction, intestinal permeability and systemic inflammation while decreasing the capability to generate obesity-suppressing short-chain fatty acids. Moreover, by increasing systemic inflammation, microglial activation and affecting vagal nerve activity, 'obese microbiota' indirectly influence hypothalamic gene expression and promote overeating. Because the potential of intestinal microbiota to induce obesity has been recognized, multiple ways to modify its composition and function are being investigated to provide novel preventive and therapeutic strategies against diet-induced obesity.}, }
@article {pmid29359994, year = {2018}, author = {Zhou, CB and Fang, JY}, title = {The regulation of host cellular and gut microbial metabolism in the development and prevention of colorectal cancer.}, journal = {Critical reviews in microbiology}, volume = {44}, number = {4}, pages = {436-454}, doi = {10.1080/1040841X.2018.1425671}, pmid = {29359994}, issn = {1549-7828}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Colorectal Neoplasms/metabolism/*microbiology/prevention &amp; control ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/microbiology ; }, abstract = {Metabolism regulation is crucial in colorectal cancer (CRC) and has emerged as a remarkable field currently. The cellular metabolism of glucose, amino acids and lipids in CRC are all reprogrammed. Each of them changes tumour microenvironment, modulates bacterial composition and activity, and eventually promotes CRC development. Metabolites such as short chain fatty acids, secondary bile acids, N-nitroso compounds, hydrogen sulphide, polyphenols and toxins like fragilysin, FadA, cytolethal distending toxin and colibactin play a dual role in CRC. The relationship of gut microbe-metabolite is essential in remodelling intestinal microbial ecology composition and metabolic activity. It regulates the metabolism of colonic epithelial cells and changes the tumour microenvironment in CRC. Microbial metabolism manipulation has been considered to be potentially preventive in CRC, but more large-scale clinical trials are required before their application in clinical practice in the near future.}, }
@article {pmid29359687, year = {2017}, author = {Kostrzewska-Szlakowska, I and Kiersztyn, B}, title = {Microbial Biomass and Enzymatic Activity of the Surface Microlayer and Subsurface Water in Two Dystrophic Lakes.}, journal = {Polish journal of microbiology}, volume = {66}, number = {1}, pages = {75-84}, doi = {10.5604/17331331.1234995}, pmid = {29359687}, issn = {1733-1331}, mesh = {Bacteria/*enzymology ; *Biomass ; Eutrophication ; Humic Substances ; Lakes/*chemistry/*microbiology ; Time Factors ; *Water Microbiology ; }, abstract = {Nutrient and organic matter concentration, microbial biomass and activities were studied at the surface microlayers (SML) and subsurface waters (SSW) in two small forest lakes of different water colour. The SML in polyhumic lake is more enriched with dissolved inorganic nitrogen (0.141 mg l-1) than that of oligohumic lake (0.124 mg l-1), the former also contains higher levels of total nitrogen (2.66 mg l-1). Higher activities of lipase (Vmax 2290 nmol l-1 h-1 in oligo- and 6098 in polyhumic) and glucosidase (Vmax 41 nmol l-1 h-1 in oligo- and 49 in polyhumic) were in the SMLs in both lakes. Phosphatase activity was higher in the oligohumic SML than in SSW (Vmax 632 vs. 339 nmol l-1 h-1) while in polyhumic lake was higher in SSW (Vmax 2258 nmol l-1 h-1 vs. 1908 nmol l-1 h-1). Aminopeptidase activity in the SSW in both lakes was higher than in SMLs (Vmax 2117 in oligo- and 1213 nmol l-1 h-1 in polyhumic). It seems that solar radiation does inhibit neuston microbial community as a whole because secondary production and the share of active bacteria in total bacteria number were higher in SSW. However, in the oligohumic lake the abundance of bacteria in the SML was always higher than in the SSW (4.07 vs. 2.69 × 106 cells ml-1) while in the polyhumic lake was roughly equal (4.48 vs. 4.33 × 106 cells ml-1) in both layers. Results may also suggest that surface communities are not supplemented by immigration from bulk communities. The SML of humic lakes may act as important sinks for allochthonous nutrient resources and may then generate considerable energy pools for microbial food webs.}, }
@article {pmid29359197, year = {2018}, author = {Shaffer, M and Lozupone, C}, title = {Prevalence and Source of Fecal and Oral Bacteria on Infant, Child, and Adult Hands.}, journal = {mSystems}, volume = {3}, number = {1}, pages = {}, pmid = {29359197}, issn = {2379-5077}, support = {T15 LM007079/LM/NLM NIH HHS/United States ; }, abstract = {Modern hygienic practices are applied to avoid exposure to pathogens that spread via fecal-oral transmission. Despite this, the gastrointestinal tract is quickly colonized by fecal microbes. The hands are an important vector for the transmission of microbes, but the frequency at which fecal and oral microbes exist on hands and the source of those microbes have not been extensively described. Using data from a previous study that characterized the fecal, oral, and skin microbiota from 73 families, we found a significant incidence of fecal and oral microbes on hands. Of palms, 48.9% had fecal signal and 67.2% had oral signal. Fecal, oral, and forehead microbes were tracked to family members and an individual's own palms far more often than to unrelated individuals and showed relationships with age, gender, and parental status. For instance, oral microbes that were specifically sourced to the same individual (oneself) were most common on infant palms; mothers had more infant-child-sourced and oral-sourced microbes on their palms than nonparents. Fecal microbes on palms more often sourced to members of the family than unrelated individuals, but more often to other members of the family than oneself. This study supports that the hands are an important vector for the transfer of fecal and oral microbes within families. IMPORTANCE Bacteria live all around us, and we are constantly exposed to them during our everyday lives. Modern standards of hygiene aim to limit exposure to fecal bacteria, and yet bacteria rapidly colonize the gut in early life and following antibacterial treatment. Exposures to fecal and oral microbes provide risk of disease, but are also necessary since commensal microbes play important roles in health. This work establishes that bacteria of both fecal and oral origins are commonly found on hands. It also establishes that the uniqueness of fecal and oral bacterial communities across people can allow for determination of the likely individual from whom the fecal and oral bacteria came. These techniques allow for understanding the hands as a vector for microbial transmission within families and across populations, which has important implications for public health.}, }
@article {pmid29359193, year = {2018}, author = {Liu, Z and Cichocki, N and Bonk, F and Günther, S and Schattenberg, F and Harms, H and Centler, F and Müller, S}, title = {Ecological Stability Properties of Microbial Communities Assessed by Flow Cytometry.}, journal = {mSphere}, volume = {3}, number = {1}, pages = {}, pmid = {29359193}, issn = {2379-5042}, abstract = {Natural microbial communities affect human life in countless ways, ranging from global biogeochemical cycles to the treatment of wastewater and health via the human microbiome. In order to probe, monitor, and eventually control these communities, fast detection and evaluation methods are required. In order to facilitate rapid community analysis and monitor a community's dynamic behavior with high resolution, we here apply community flow cytometry, which provides single-cell-based high-dimensional data characterizing communities with high acuity over time. To interpret time series data, we draw inspiration from macroecology, in which a rich set of concepts has been developed for describing population dynamics. We focus on the stability paradigm as a promising candidate to interpret such data in an intuitive and actionable way and present a rapid workflow to monitor stability properties of complex microbial ecosystems. Based on single-cell data, we compute the stability properties resistance, resilience, displacement speed, and elasticity. For resilience, we also introduce a method which can be implemented for continuous online community monitoring. The proposed workflow was tested in a long-term continuous reactor experiment employing both an artificial and a complex microbial community, which were exposed to identical short-term disturbances. The computed stability properties uncovered the superior stability of the complex community and demonstrated the global applicability of the protocol to any microbiome. The workflow is able to support high temporal sample densities below bacterial generation times. This may provide new opportunities to unravel unknown ecological paradigms of natural microbial communities, with applications to environmental, biotechnological, and health-related microbiomes. IMPORTANCE Microbial communities drive many processes which affect human well-being directly, as in the human microbiome, or indirectly, as in natural environments or in biotechnological applications. Due to their complexity, their dynamics over time is difficult to monitor, and current sequence-based approaches are limited with respect to the temporal resolution. However, in order to eventually control microbial community dynamics, monitoring schemes of high temporal resolution are required. Flow cytometry provides single-cell-based data in the required temporal resolution, and we here use such data to compute stability properties as easy to interpret univariate indicators of microbial community dynamics. Such monitoring tools will allow for a fast, continuous, and cost-effective screening of stability states of microbiomes. Applicable to various environments, including bioreactors, surface water, and the human body, it will contribute to the development of control schemes to manipulate microbial community structures and performances.}, }
@article {pmid29358736, year = {2018}, author = {Schulz-Bohm, K and Gerards, S and Hundscheid, M and Melenhorst, J and de Boer, W and Garbeva, P}, title = {Calling from distance: attraction of soil bacteria by plant root volatiles.}, journal = {The ISME journal}, volume = {12}, number = {5}, pages = {1252-1262}, pmid = {29358736}, issn = {1751-7370}, mesh = {Animals ; *Bacterial Physiological Phenomena ; Carex Plant/metabolism/microbiology ; Diffusion ; Fusarium/physiology ; *Host Microbial Interactions ; Plant Roots/*metabolism/microbiology ; *Soil Microbiology ; Volatile Organic Compounds/*metabolism ; }, abstract = {Plants release a wide set of secondary metabolites including volatile organic compounds (VOCs). Many of those compounds are considered to function as defense against herbivory, pests, and pathogens. However, little knowledge exists about the role of belowground plant VOCs for attracting beneficial soil microorganisms. We developed an olfactometer system to test the attraction of soil bacteria by VOCs emitted by Carex arenaria roots. Moreover, we tested whether infection of C. arenaria with the fungal pathogen Fusarium culmorum modifies the VOCs profile and bacterial attraction. The results revealed that migration of distant bacteria in soil towards roots can be stimulated by plant VOCs. Upon fungal infection, the blend of root VOCs changed and specific bacteria with antifungal properties were attracted. Tests with various pure VOCs indicated that those compounds can diffuse over long distance but with different diffusion abilities. Overall, this work highlights the importance of plant VOCs in belowground long-distance plant-microbe interactions.}, }
@article {pmid29358405, year = {2018}, author = {Fitzpatrick, CR and Copeland, J and Wang, PW and Guttman, DS and Kotanen, PM and Johnson, MTJ}, title = {Assembly and ecological function of the root microbiome across angiosperm plant species.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {6}, pages = {E1157-E1165}, pmid = {29358405}, issn = {1091-6490}, mesh = {Bacteria/*genetics ; Droughts ; *Ecology ; Magnoliopsida/*microbiology ; *Microbiota ; Phylogeny ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S ; *Rhizosphere ; Soil Microbiology ; Symbiosis/*genetics ; }, abstract = {Across plants and animals, host-associated microbial communities play fundamental roles in host nutrition, development, and immunity. The factors that shape host-microbiome interactions are poorly understood, yet essential for understanding the evolution and ecology of these symbioses. Plant roots assemble two distinct microbial compartments from surrounding soil: the rhizosphere (microbes surrounding roots) and the endosphere (microbes within roots). Root-associated microbes were key for the evolution of land plants and underlie fundamental ecosystem processes. However, it is largely unknown how plant evolution has shaped root microbial communities, and in turn, how these microbes affect plant ecology, such as the ability to mitigate biotic and abiotic stressors. Here we show that variation among 30 angiosperm species, which have diverged for up to 140 million years, affects root bacterial diversity and composition. Greater similarity in root microbiomes between hosts leads to negative effects on plant performance through soil feedback, with specific microbial taxa in the endosphere and rhizosphere potentially affecting competitive interactions among plant species. Drought also shifts the composition of root microbiomes, most notably by increasing the relative abundance of the Actinobacteria. However, this drought response varies across host plant species, and host-specific changes in the relative abundance of endosphere Streptomyces are associated with host drought tolerance. Our results emphasize the causes of variation in root microbiomes and their ecological importance for plant performance in response to biotic and abiotic stressors.}, }
@article {pmid29356320, year = {2018}, author = {Corno, G and Callieri, C}, title = {Deconvolution models for a better understanding of natural microbial communities enumerated by flow-cytometry.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {93}, number = {2}, pages = {180-181}, doi = {10.1002/cyto.a.23330}, pmid = {29356320}, issn = {1552-4930}, mesh = {*Bacteria ; *Flow Cytometry ; }, }
@article {pmid29355470, year = {2018}, author = {Featherstone, JD and Fontana, M and Wolff, M}, title = {Novel Anticaries and Remineralization Agents: Future Research Needs.}, journal = {Journal of dental research}, volume = {97}, number = {2}, pages = {125-127}, pmid = {29355470}, issn = {1544-0591}, mesh = {Biofilms/drug effects ; Biomimetic Materials/pharmacology ; Cariostatic Agents/*pharmacology ; Clinical Trials as Topic ; Congresses as Topic ; Dental Caries/*prevention &amp; control ; *Dental Research ; Fluorides, Topical/*pharmacology ; Forecasting ; Humans ; Pit and Fissure Sealants/*pharmacology ; Tooth Remineralization/*methods ; }, }
@article {pmid29355418, year = {2018}, author = {Zhan, L}, title = {Rebalancing the Caries Microbiome Dysbiosis: Targeted Treatment and Sugar Alcohols.}, journal = {Advances in dental research}, volume = {29}, number = {1}, pages = {110-116}, pmid = {29355418}, issn = {1544-0737}, support = {U54 DE019285/DE/NIDCR NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Cariostatic Agents/*pharmacology ; Dental Caries/*microbiology/*prevention &amp; control ; Dysbiosis/*prevention &amp; control ; Erythritol/pharmacology ; Humans ; Microbiota/*drug effects ; Sugar Alcohols/*pharmacology ; Sweetening Agents/*pharmacology ; Virulence ; Xylitol/pharmacology ; }, abstract = {Dental caries is a disease that results from microbiome dysbiosis with the involvement of multiple cariogenic species, including mutans streptococci (MS), lactobacilli, Scardovia wiggsiae, and several Actinomyces species that have the cariogenic traits of acid production and acid tolerance. Sugar consumption also plays an important role interacting with microbiome dysbiosis, determining the fate of caries development. In addition, the MS transmission that encompasses multiple sources can have long-term impacts on the oral microbiome and caries development in children. Intervention in MS transmission in early childhood may promote effective long-term caries prevention. Anticaries regimens aimed against the above mechanisms will be important for successful caries management. Xylitol and erythritol may serve as good components of anticaries regimens as oral microbiome modifiers, sugar substitutes, and agents to prevent MS transmission in early childhood with both oral and systemic benefits. Further studies are needed to elucidate the mechanism of the anticaries effects of xylitol and erythritol with consideration of their impacts on the microbiome and bacterial virulence, in addition to cariogenic bacteria levels as well as their benefits for overall health. On the other hand, the anticaries agent C16G2, specifically targeting Streptococcus mutans, the most common cariogenic bacterial species, has shown good safety for short-term oral topical use and promising effects in reducing S. mutans in vitro and in vivo with the promotion of oral commensal bacteria. Future study on its anticaries effect will need to include its long-term impact on the oral microbiome and effects on other important cariogenic bacteria.}, }
@article {pmid29355408, year = {2018}, author = {Burne, RA}, title = {Getting to Know "The Known Unknowns": Heterogeneity in the Oral Microbiome.}, journal = {Advances in dental research}, volume = {29}, number = {1}, pages = {66-70}, pmid = {29355408}, issn = {1544-0737}, support = {R01 DE013239/DE/NIDCR NIH HHS/United States ; R01 DE025832/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacterial Physiological Phenomena ; Dental Caries/*microbiology/*prevention &amp; control ; Dysbiosis/physiopathology ; Humans ; Metabolomics ; Microbiota/*physiology ; Mouth/*microbiology ; *Oral Health ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; Symbiosis/physiology ; }, abstract = {Technological advances in DNA sequencing have provided unprecedented insights into the composition of the oral microbiome in health and disease, and RNA-sequencing and metabolomics-related technologies are beginning to yield information on the activities of these organisms. Importantly, progress in this area has brought the scientific community closer to an understanding of what constitutes a health-associated microbiome and is supporting the notion that the microbiota in healthy sites assumes an active role in promoting health and suppressing the acquisition, persistence, and activities of overt and opportunistic pathogens. It is also becoming clear that a significant impediment to developing a conclusive body of evidence that defines a healthy microbiome and the mechanisms by which beneficial bacteria promote health is that an inherent characteristic of the most abundant members of the oral flora, those that potentially play the greatest roles in health and disease, is intraspecies genomic diversity. In particular, individual isolates of abundant commensal and pathogenic streptococci show tremendous variability in gene content, and this variability manifests in tremendous phenotypic heterogeneity. Analysis of the consequences of this diversity has been complicated by the exquisite sensitivity these bacteria have evolved to environmental inputs, inducing rapid and substantial fluctuations in behaviors, and often only within subpopulations of the organisms. Thus, the conditions under which the oral microbiota is studied can produce widely different results within and between species. Fortunately, continually diminishing costs and ongoing refinements in sequencing and metabolomics are making it practical to study the oral microbiome at a level that will create a sufficiently robust understanding of the functions of individual organisms and reveal the complex interrelationships of these microbes ("the known unknowns") in a way that researchers will be able to engage in the rational design of reliable and economical risk assessments and preventive therapies.}, }
@article {pmid29355407, year = {2018}, author = {Fontana, M and Wolff, M and Featherstone, JD}, title = {Introduction to ICNARA 3.}, journal = {Advances in dental research}, volume = {29}, number = {1}, pages = {3}, doi = {10.1177/0022034517746372}, pmid = {29355407}, issn = {1544-0737}, mesh = {California ; Congresses as Topic ; Dental Caries/*prevention &amp; control ; *Dental Research ; Diffusion of Innovation ; Humans ; Tooth Remineralization/*methods ; }, }
@article {pmid29354879, year = {2018}, author = {Cerqueira, T and Barroso, C and Froufe, H and Egas, C and Bettencourt, R}, title = {Metagenomic Signatures of Microbial Communities in Deep-Sea Hydrothermal Sediments of Azores Vent Fields.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {387-403}, pmid = {29354879}, issn = {1432-184X}, support = {M3.1.2/F/052/2011//Dire&#xe7;&#xe3;o Regional da Ci&#xea;ncia e Tecnologia/ ; UID/MAR/04292/2013 granted to MARE//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {Archaea/classification/genetics/metabolism ; Autotrophic Processes ; Azores ; Bacteria/classification/genetics/metabolism ; Biodiversity ; Carbon/metabolism ; Carbon Cycle ; Chemoautotrophic Growth/physiology ; Citric Acid Cycle ; Epsilonproteobacteria/metabolism ; Geologic Sediments/*microbiology ; Hydrothermal Vents/*microbiology ; Metagenome/physiology ; *Metagenomics ; Methane/metabolism ; Microbiota/*physiology ; Nitrogen/metabolism ; Oxidation-Reduction ; Photosynthesis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sulfur/metabolism ; }, abstract = {The organisms inhabiting the deep-seafloor are known to play a crucial role in global biogeochemical cycles. Chemolithoautotrophic prokaryotes, which produce biomass from single carbon molecules, constitute the primary source of nutrition for the higher organisms, being critical for the sustainability of food webs and overall life in the deep-sea hydrothermal ecosystems. The present study investigates the metabolic profiles of chemolithoautotrophs inhabiting the sediments of Menez Gwen and Rainbow deep-sea vent fields, in the Mid-Atlantic Ridge. Differences in the microbial community structure might be reflecting the distinct depth, geology, and distance from vent of the studied sediments. A metagenomic sequencing approach was conducted to characterize the microbiome of the deep-sea hydrothermal sediments and the relevant metabolic pathways used by microbes. Both Menez Gwen and Rainbow metagenomes contained a significant number of genes involved in carbon fixation, revealing the largely autotrophic communities thriving in both sites. Carbon fixation at Menez Gwen site was predicted to occur mainly via the reductive tricarboxylic acid cycle, likely reflecting the dominance of sulfur-oxidizing Epsilonproteobacteria at this site, while different autotrophic pathways were identified at Rainbow site, in particular the Calvin-Benson-Bassham cycle. Chemolithotrophy appeared to be primarily driven by the oxidation of reduced sulfur compounds, whether through the SOX-dependent pathway at Menez Gwen site or through reverse sulfate reduction at Rainbow site. Other energy-yielding processes, such as methane, nitrite, or ammonia oxidation, were also detected but presumably contributing less to chemolithoautotrophy. This work furthers our knowledge of the microbial ecology of deep-sea hydrothermal sediments and represents an important repository of novel genes with potential biotechnological interest.}, }
@article {pmid29354109, year = {2017}, author = {Abarca, JG and Zuniga, I and Ortiz-Morales, G and Lugo, A and Viquez-Cervilla, M and Rodriguez-Hernandez, N and Vázquez-Sánchez, F and Murillo-Cruz, C and Torres-Rivera, EA and Pinto-Tomás, AA and Godoy-Vitorino, F}, title = {Characterization of the Skin Microbiota of the Cane Toad Rhinella cf. marina in Puerto Rico and Costa Rica.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2624}, pmid = {29354109}, issn = {1664-302X}, support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; }, abstract = {Rhinella marina is a toad native to South America that has been introduced in the Antilles, likely carrying high loads of microorganisms, potentially impacting local community diversity. The amphibian skin is involved in pathogen defense and its microbiota has been relatively well studied, however, research focusing on the cane toad microbiota is lacking. We hypothesize that the skin microbial communities will differ between toads inhabiting different geographical regions in Central America and the Caribbean. To test our hypothesis, we compared the microbiota of three populations of R. cf. marina toads, two from Costa Rican (native) and one Puerto Rican (exotic) locations. In Costa Rica, we collected 11 toads, 7 in Sarapiquí and 4 from Turrialba while in Puerto Rico, 10 animals were collected in Santa Ana. Separate swab samples were collected from the dorsal and ventral sites resulting in 42 samples. We found significant differences in the structure of the microbial communities between Puerto Rico and Costa Rica. We detected as much as 35 different phyla; however, communities were dominated by Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Alpha diversity and richness were significantly higher in toads from Puerto Rico and betadiversity revealed significant differences between the microbiota samples from the two countries. At the genus level, we found in Santa Ana, Puerto Rico, a high dominance of Kokuria, Niabella, and Rhodobacteraceae, while in Costa Rica we found Halomonas and Pseudomonas in Sarapiquí, and Acinetobacter and Citrobacter in Turrialba. This is the first report of Niabella associated with the amphibian skin. The core microbiome represented 128 Operational Taxonomic Units (OTUs) mainly from five genera shared among all samples, which may represent the symbiotic Rhinella's skin. These results provide insights into the habitat-induced microbial changes facing this amphibian species. The differences in the microbial diversity in Puerto Rican toads compared to those in Costa Rica provide additional evidence of the geographically induced patterns in the amphibian skin microbiome, and highlight the importance of discussing the microbial tradeoffs in the colonization of new ecosystems.}, }
@article {pmid29350561, year = {2018}, author = {De Filippis, F and Parente, E and Ercolini, D}, title = {Recent Past, Present, and Future of the Food Microbiome.}, journal = {Annual review of food science and technology}, volume = {9}, number = {}, pages = {589-608}, doi = {10.1146/annurev-food-030117-012312}, pmid = {29350561}, issn = {1941-1413}, mesh = {Computational Biology ; Fermentation ; *Food Microbiology ; Food Safety ; Food Technology/*methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics ; Microbiota/*genetics ; }, abstract = {Sequencing technologies have deeply changed our approach to the study of food microbial communities. This review describes recent exploitations of high-throughput sequencing applications to improve our knowledge of food microbial consortia. In the past 10 years, target amplicon sequencing has become routinely used in many food microbiology laboratories, providing a detailed picture of food-associated microbiota. Metagenomics and metatranscriptomics approaches are still underexploited in food microbial ecology, despite their potential to uncover the functionality of complex communities. In a near future, sequencing technologies will surely advance our understanding of how to effectively use the invaluable microbial resources to improve food quality and safety.}, }
@article {pmid29350293, year = {2018}, author = {Larrea-Murrell, JA and Rojas-Badia, MM and García-Soto, I and Romeu-Alvarez, B and Bacchetti, T and Gillis, A and Boltes-Espinola, AK and Heydrich-Perez, M and Lugo-Moya, D and Mahillon, J}, title = {Diversity and enzymatic potentialities of Bacillus sp. strains isolated from a polluted freshwater ecosystem in Cuba.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {34}, number = {2}, pages = {28}, pmid = {29350293}, issn = {1573-0972}, mesh = {Bacillus/*classification/*enzymology/genetics/*isolation &amp; purification ; Bacterial Proteins/genetics ; Bacterial Toxins/analysis ; *Biodiversity ; Cuba ; DNA Gyrase/genetics ; DNA, Bacterial/analysis/genetics ; *Ecosystem ; Electrophoresis, Gel, Pulsed-Field/methods ; Enzyme Assays ; Fresh Water/*microbiology ; Genes, Bacterial/genetics ; Genotype ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers/microbiology ; Species Specificity ; Virulence/genetics ; *Water Microbiology ; Water Pollution ; }, abstract = {Genotypic and phenotypic characterization of Bacillus spp. from polluted freshwater has been poorly addressed. The objective of this research was to determine the diversity and enzymatic potentialities of Bacillus spp. strains isolated from the Almendares River. Bacilli strains from a polluted river were characterized by considering the production of extracellular enzymes using API ZYM. 14 strains were selected and identified using 16S rRNA, gyrB and aroE genes. Genotypic diversity of the Bacillus spp. strains was evaluated using pulsed field gel electrophoresis. Furthermore, the presence of genetic determinants of potential virulence toxins of the Bacillus cereus group and proteinaceous crystal inclusions of Bacillus thuringiensis was determined. 10 strains were identified as B. thuringiensis, two as Bacillus megaterium, one as Bacillus pumilus and one as Bacillus subtilis. Most strains produced proteases, amylases, phosphatases, esterases, aminopeptidases and glucanases, which reflect the abundance of biopolymeric matter in Almendares River. Comparison of the typing results revealed a spatio-temporal distribution among B. thuringiensis strains along the river. The results of the present study highlight the genotypic and phenotypic diversity of Bacillus spp. strains from a polluted river, which contributes to the knowledge of genetic diversity of Bacilli from tropical polluted freshwater ecosystems.}, }
@article {pmid29346885, year = {2017}, author = {Tikhonov, M}, title = {Theoretical microbial ecology without species.}, journal = {Physical review. E}, volume = {96}, number = {3-1}, pages = {032410}, doi = {10.1103/PhysRevE.96.032410}, pmid = {29346885}, issn = {2470-0053}, mesh = {Bacteria ; *Ecosystem ; *Models, Biological ; }, abstract = {Ecosystems are commonly conceptualized as networks of interacting species. However, partitioning natural diversity of organisms into discrete units is notoriously problematic and mounting experimental evidence raises the intriguing question whether this perspective is appropriate for the microbial world. Here an alternative formalism is proposed that does not require postulating the existence of species as fundamental ecological variables and provides a naturally hierarchical description of community dynamics. This formalism allows approaching the species problem from the opposite direction. While the classical models treat a world of imperfectly clustered organism types as a perturbation around well-clustered species, the presented approach allows gradually adding structure to a fully disordered background. The relevance of this theoretical construct for describing highly diverse natural ecosystems is discussed.}, }
@article {pmid29345091, year = {2018}, author = {Birgander, J and Olsson, PA and Rousk, J}, title = {The responses of microbial temperature relationships to seasonal change and winter warming in a temperate grassland.}, journal = {Global change biology}, volume = {24}, number = {8}, pages = {3357-3367}, doi = {10.1111/gcb.14060}, pmid = {29345091}, issn = {1365-2486}, mesh = {Bacteria/growth &amp; development/metabolism ; *Climate Change ; Fungi/growth &amp; development/metabolism ; *Grassland ; Hot Temperature ; Seasons ; *Soil Microbiology ; Sweden ; *Temperature ; }, abstract = {Microorganisms dominate the decomposition of organic matter and their activities are strongly influenced by temperature. As the carbon (C) flux from soil to the atmosphere due to microbial activity is substantial, understanding temperature relationships of microbial processes is critical. It has been shown that microbial temperature relationships in soil correlate with the climate, and microorganisms in field experiments become more warm-tolerant in response to chronic warming. It is also known that microbial temperature relationships reflect the seasons in aquatic ecosystems, but to date this has not been investigated in soil. Although climate change predictions suggest that temperatures will be mostly affected during winter in temperate ecosystems, no assessments exist of the responses of microbial temperature relationships to winter warming. We investigated the responses of the temperature relationships of bacterial growth, fungal growth, and respiration in a temperate grassland to seasonal change, and to 2 years' winter warming. The warming treatments increased winter soil temperatures by 5-6°C, corresponding to 3°C warming of the mean annual temperature. Microbial temperature relationships and temperature sensitivities (Q10) could be accurately established, but did not respond to winter warming or to seasonal temperature change, despite significant shifts in the microbial community structure. The lack of response to winter warming that we demonstrate, and the strong response to chronic warming treatments previously shown, together suggest that it is the peak annual soil temperature that influences the microbial temperature relationships, and that temperatures during colder seasons will have little impact. Thus, mean annual temperatures are poor predictors for microbial temperature relationships. Instead, the intensity of summer heat-spells in temperate systems is likely to shape the microbial temperature relationships that govern the soil-atmosphere C exchange.}, }
@article {pmid29340714, year = {2018}, author = {Keshri, J and Pradeep Ram, AS and Nana, PA and Sime-Ngando, T}, title = {Taxonomical Resolution and Distribution of Bacterioplankton Along the Vertical Gradient Reveals Pronounced Spatiotemporal Patterns in Contrasted Temperate Freshwater Lakes.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {372-386}, pmid = {29340714}, issn = {1432-184X}, mesh = {Actinobacteria/classification/genetics ; Bacteria/*classification/genetics ; Bacteriophages ; Bacteroidetes/classification/genetics ; Biodiversity ; Ecosystem ; France ; Lakes/chemistry/*microbiology ; Microbiota/genetics ; *Phylogeny ; Plankton/*classification/genetics ; Proteobacteria/classification/genetics ; RNA, Ribosomal, 16S/genetics ; Seasons ; Temperature ; *Water Microbiology ; }, abstract = {We examined the relationship between viruses and co-occurring bacterial communities across spatiotemporal scale in two contrasting freshwater lakes, namely meromictic Lake Pavin and dimictic Lake Aydat (Central France). Next-generation sequencing of 16S rRNA genes suggested distinct patterns in bacterioplankton community composition (BCC) between the lakes over depths and seasons. BCC were generally dominated by members of Actinobacteria, Proteobacteria, and Bacteroidetes covering about 95% of all sequences. Oxygen depletion at the bottom waters in Aydat and existence of permanent anoxia in the monimolimnion of Pavin resulted in the occurrence and dominance of lesser known members of lake communities such as Methylotenera, Methylobacter, Gallionella, Sulfurimonas, and Syntrophus in Pavin and Methylotenera and Sulfuritalea in Aydat. Differences in BCC appeared strongly related to dissolved oxygen concentration, temperature, viral infection, and virus-to-bacteria ratio. UniFrac analysis indicated a clear distinction in BCC when the percentage of viral infected bacterial cells and virus-to-bacteria ratio exceeded a threshold level of 10% and 5, respectively, suggesting a link between viruses and their potential bacterial host communities. Our study revealed that in both the lakes, the prevailing environmental factors across time and space structured and influenced the adaptation of bacterial communities to specific ecological niches.}, }
@article {pmid29340028, year = {2017}, author = {Guerrero-Preston, R and White, JR and Godoy-Vitorino, F and Rodríguez-Hilario, A and Navarro, K and González, H and Michailidi, C and Jedlicka, A and Canapp, S and Bondy, J and Dziedzic, A and Mora-Lagos, B and Rivera-Alvarez, G and Ili-Gangas, C and Brebi-Mieville, P and Westra, W and Koch, W and Kang, H and Marchionni, L and Kim, Y and Sidransky, D}, title = {High-resolution microbiome profiling uncovers Fusobacterium nucleatum, Lactobacillus gasseri/johnsonii, and Lactobacillus vaginalis associated to oral and oropharyngeal cancer in saliva from HPV positive and HPV negative patients treated with surgery and chemo-radiation.}, journal = {Oncotarget}, volume = {8}, number = {67}, pages = {110931-110948}, pmid = {29340028}, issn = {1949-2553}, support = {RC2 DE020957/DE/NIDCR NIH HHS/United States ; P50 DE019032/DE/NIDCR NIH HHS/United States ; R01 CA121113/CA/NCI NIH HHS/United States ; K01 CA164092/CA/NCI NIH HHS/United States ; U01 CA084986/CA/NCI NIH HHS/United States ; P20 GM103475/GM/NIGMS NIH HHS/United States ; }, abstract = {Microbiome studies show altered microbiota in head and neck squamous cell carcinoma (HNSCC), both in terms of taxonomic composition and metabolic capacity. These studies utilized a traditional bioinformatics methodology, which allows for accurate taxonomic assignment down to the genus level, but cannot accurately resolve species level membership. We applied Resphera Insight, a high-resolution methodology for 16S rRNA taxonomic assignment that is able to provide species-level context in its assignments of 16S rRNA next generation sequencing (NGS) data. Resphera Insight applied to saliva samples from HNSCC patients and healthy controls led to the discovery that a subset of HNSCC saliva samples is significantly enriched with commensal species from the vaginal flora, including Lactobacillus gasseri/johnsonii (710x higher in saliva) and Lactobacillus vaginalis (52x higher in saliva). These species were not observed in normal saliva from Johns Hopkins patients, nor in 16S rRNA NGS saliva samples from the Human Microbiome Project (HMP). Interestingly, both species were only observed in saliva from Human Papilloma Virus (HPV) positive and HPV negative oropharyngeal cancer patients. We confirmed the representation of both species in HMP data obtained from mid-vagina (n=128) and vaginal introitus (n=121) samples. Resphera Insight also led to the discovery that Fusobacterium nucleatum, an oral cavity flora commensal bacterium linked to colon cancer, is enriched (600x higher) in saliva from a subset of HNSCC patients with advanced tumors stages. Together, these high-resolution analyses on 583 samples suggest a possible role for bacterial species in the therapeutic outcome of HPV positive and HPV negative HNSCC patients.}, }
@article {pmid29339425, year = {2018}, author = {Yan, Q and Lopes, LD and Shaffer, BT and Kidarsa, TA and Vining, O and Philmus, B and Song, C and Stockwell, VO and Raaijmakers, JM and McPhail, KL and Andreote, FD and Chang, JH and Loper, JE}, title = {Secondary Metabolism and Interspecific Competition Affect Accumulation of Spontaneous Mutants in the GacS-GacA Regulatory System in Pseudomonas protegens.}, journal = {mBio}, volume = {9}, number = {1}, pages = {}, pmid = {29339425}, issn = {2150-7511}, mesh = {Bacillus subtilis/*growth &amp; development ; Bacterial Proteins/*genetics ; Energy Metabolism ; Microbial Interactions ; *Mutation ; Phenols/metabolism ; Pseudomonas/*genetics/*growth &amp; development/metabolism ; Pyrroles/metabolism ; *Secondary Metabolism ; Transcription Factors/*genetics ; }, abstract = {Secondary metabolites are synthesized by many microorganisms and provide a fitness benefit in the presence of competitors and predators. Secondary metabolism also can be costly, as it shunts energy and intermediates from primary metabolism. In Pseudomonas spp., secondary metabolism is controlled by the GacS-GacA global regulatory system. Intriguingly, spontaneous mutations in gacS or gacA (Gac[-] mutants) are commonly observed in laboratory cultures. Here we investigated the role of secondary metabolism in the accumulation of Gac[-] mutants in Pseudomonas protegens strain Pf-5. Our results showed that secondary metabolism, specifically biosynthesis of the antimicrobial compound pyoluteorin, contributes significantly to the accumulation of Gac[-] mutants. Pyoluteorin biosynthesis, which poses a metabolic burden on the producer cells, but not pyoluteorin itself, leads to the accumulation of the spontaneous mutants. Interspecific competition also influenced the accumulation of the Gac[-] mutants: a reduced proportion of Gac[-] mutants accumulated when P. protegens Pf-5 was cocultured with Bacillus subtilis than in pure cultures of strain Pf-5. Overall, our study associated a fitness trade-off with secondary metabolism, with metabolic costs versus competitive benefits of production influencing the evolution of P. protegens, assessed by the accumulation of Gac[-] mutants.IMPORTANCE Many microorganisms produce antibiotics, which contribute to ecologic fitness in natural environments where microbes constantly compete for resources with other organisms. However, biosynthesis of antibiotics is costly due to the metabolic burdens of the antibiotic-producing microorganism. Our results provide an example of the fitness trade-off associated with antibiotic production. Under noncompetitive conditions, antibiotic biosynthesis led to accumulation of spontaneous mutants lacking a master regulator of antibiotic production. However, relatively few of these spontaneous mutants accumulated when a competitor was present. Results from this work provide information on the evolution of antibiotic biosynthesis and provide a framework for their discovery and regulation.}, }
@article {pmid29338309, year = {2018}, author = {Vanlancker, E and Vanhoecke, B and Sieprath, T and Bourgeois, J and Beterams, A and De Moerloose, B and De Vos, WH and Van de Wiele, T}, title = {Oral microbiota reduce wound healing capacity of epithelial monolayers, irrespective of the presence of 5-fluorouracil.}, journal = {Experimental biology and medicine (Maywood, N.J.)}, volume = {243}, number = {4}, pages = {350-360}, pmid = {29338309}, issn = {1535-3699}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Antineoplastic Agents/administration &amp; dosage/*adverse effects ; Bacterial Load ; Cell Culture Techniques ; Child ; Child, Preschool ; Female ; Fluorouracil/administration &amp; dosage/*adverse effects ; Humans ; Infant ; Infant, Newborn ; Male ; *Microbiota ; Middle Aged ; Models, Biological ; Mouth/*microbiology ; Mucositis/*pathology ; *Wound Healing ; Young Adult ; }, abstract = {Oral mucositis is still one of the most painful side effects of chemotherapeutic treatment and a mounting body of evidence suggests a key role for the oral microbiome in mucositis development. However, the underlying mechanisms remain elusive. In this work, we have investigated the interactions between the host, the microbiome, and chemotherapeutic treatments in more detail. The effect of 5-fluorouracil, commonly inducing mucositis, was assessed on a co-culture model that consists of an epithelial cell layer and a biofilm derived from oral microbiota from different types of samples (saliva, buccal swabs and tongue swabs) and donors (healthy individuals and patients suffering from mucositis). After 24 h co-incubation, all oral microbial samples were found to reduce wound healing capacity with 26 ± 15% as compared with untreated condition. Compared with saliva and tongue samples, buccal samples were characterized by lower bacterial cell counts and hence higher wound healing capacity. For samples from healthy individuals, an inverse correlation was observed between bacterial cell counts and wound healing capacity, whereas for patients suffering from mucositis no correlation was observed. Moreover, patient-derived samples had a less diverse microbial community and higher abundances of pathogenic genera. No major impact of 5-fluorouracil on wound healing capacity or the composition of the microbiome was seen at physiologically relevant concentrations in the mouth. In conclusion, bacterial cell count is inversely correlated with wound healing capacity, which emphasizes the importance of oral hygiene during oral wound healing in healthy individuals. However, future research on extra measures besides oral hygiene is needed to assure a good wound healing during mucositis, as for patients the bacterial composition seems also crucial. The direct effect of 5-fluorouracil on both the microbiome and wound healing is minimal, pointing to the importance of the host and its immune system in chemotherapy-induced microbial shifts. Impact statement Chemotherapy-induced oral mucositis has a major impact on the quality of life of patients. The additional costs and treatment time associated with this pathology are significant. Although the pathology of the disease is well understood, the role and importance of oral microbiota currently are less clear. In this study, we focused on the effect of oral microbiota on wound healing, the final phase of oral mucositis, during 5-FU exposure. We show that the bacterial load and composition have a major impact on the healing process in contrast to 5-FU which only marginally slows down healing. This emphasizes the importance of good oral health care during oral mucositis to minimize bacterial load around the oral lesions. However, since we show that also the composition of the oral microbiome plays a role in wound recovery, the identification of specific pathogenic species or their metabolites might be worthwhile to allow proper treatment.}, }
@article {pmid29335919, year = {2018}, author = {van der Meij, A and Willemse, J and Schneijderberg, MA and Geurts, R and Raaijmakers, JM and van Wezel, GP}, title = {Inter- and intracellular colonization of Arabidopsis roots by endophytic actinobacteria and the impact of plant hormones on their antimicrobial activity.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {5}, pages = {679-690}, pmid = {29335919}, issn = {1572-9699}, support = {14218//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 14221//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, mesh = {Actinobacteria/classification/growth &amp; development/*physiology ; Anti-Infective Agents/metabolism/*pharmacology ; Arabidopsis/metabolism/*microbiology ; Bacteria/drug effects ; DNA, Bacterial/genetics ; Endophytes/classification/growth &amp; development/isolation &amp; purification/*metabolism ; Microbial Sensitivity Tests ; Plant Growth Regulators/*physiology ; Plant Roots/metabolism/*microbiology ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Streptomyces/classification/growth &amp; development/metabolism ; Symbiosis/physiology ; }, abstract = {Many actinobacteria live in close association with eukaryotes such as fungi, insects, animals and plants. Plant-associated actinobacteria display (endo)symbiotic, saprophytic or pathogenic life styles, and can make up a substantial part of the endophytic community. Here, we characterised endophytic actinobacteria isolated from root tissue of Arabidopsis thaliana (Arabidopsis) plants grown in soil from a natural ecosystem. Many of these actinobacteria belong to the family of Streptomycetaceae with Streptomyces olivochromogenes and Streptomyces clavifer as well represented species. When seeds of Arabidopsis were inoculated with spores of Streptomyces strain coa1, which shows high similarity to S. olivochromogenes, roots were colonised intercellularly and, unexpectedly, also intracellularly. Subsequent exposure of endophytic isolates to plant hormones typically found in root and shoot tissues of Arabidopsis led to altered antibiotic production against Escherichia coli and Bacillus subtilis. Taken together, our work reveals remarkable colonization patterns of endophytic streptomycetes with specific traits that may allow a competitive advantage inside root tissue.}, }
@article {pmid29335664, year = {2018}, author = {Snoeck, D and Wang, J and Bentz, DP and De Belie, N}, title = {Applying a biodeposition layer to increase the bond of a repair mortar on a mortar substrate.}, journal = {Cement &amp; concrete composites}, volume = {86}, number = {}, pages = {30-39}, pmid = {29335664}, issn = {0958-9465}, support = {9999-NIST/ImNIST/Intramural NIST DOC/United States ; }, abstract = {One of the major concerns in infrastructure repair is a sufficient bond between the substrate and the repair material, especially for the long-term performance and durability of the repaired structure. In this study, the bond of the repair material on the mortar substrate is promoted via the biodeposition of a calcium carbonate layer by a ureolytic bacterium. X-ray diffraction and scanning electron microscopy were used to examine the interfaces between the repair material and the substrate, as well as the polymorph of the deposited calcium carbonate. The approximately 50 μm thick biodeposition film on the mortar surface mostly consisted of calcite and vaterite. Both the repair material and the substrate tended to show a good adherence to that layer. The bond, as assessed by slant shear specimen testing, was improved by the presence of the biodeposition layer. A further increase was found when engineering the substrate surface using a structured pattern layer of biodeposition.}, }
@article {pmid29335636, year = {2018}, author = {Berg, G and Raaijmakers, JM}, title = {Saving seed microbiomes.}, journal = {The ISME journal}, volume = {12}, number = {5}, pages = {1167-1170}, pmid = {29335636}, issn = {1751-7370}, mesh = {Domestication ; Genotype ; *Microbiota ; Plants/genetics ; Seeds/*microbiology ; Stress, Physiological ; }, abstract = {Plant seeds are home to diverse microbial communities whose composition is determined by plant genotype, environment, and management practices. Plant domestication is now recognized as an important driver of plant-associated microbial diversity. To what extent and how domestication affects seed microbiomes is less well studied. Here we propose a 'back-to-the-future' approach to harness seed microbiomes of wild relatives of crop cultivars to save and re-instate missing beneficial seed microbes for improved plant tolerance to biotic and abiotic stress.}, }
@article {pmid29335635, year = {2018}, author = {Şimşek, E and Kim, M}, title = {The emergence of metabolic heterogeneity and diverse growth responses in isogenic bacterial cells.}, journal = {The ISME journal}, volume = {12}, number = {5}, pages = {1199-1209}, pmid = {29335635}, issn = {1751-7370}, mesh = {Escherichia coli/*growth &amp; development/*metabolism ; Nutrients ; Phenotype ; }, abstract = {Microorganisms adapt to frequent environmental changes through population diversification. Previous studies demonstrated phenotypic diversity in a clonal population and its important effects on microbial ecology. However, the dynamic changes of phenotypic composition have rarely been characterized. Also, cellular variations and environmental factors responsible for phenotypic diversity remain poorly understood. Here, we studied phenotypic diversity driven by metabolic heterogeneity. We characterized metabolic activities and growth kinetics of starved Escherichia coli cells subject to nutrient upshift at single-cell resolution. We observed three subpopulations with distinct metabolic activities and growth phenotypes. One subpopulation was metabolically active and immediately grew upon nutrient upshift. One subpopulation was metabolically inactive and non-viable. The other subpopulation was metabolically partially active, and did not grow upon nutrient upshift. The ratio of these subpopulations changed dynamically during starvation. A long-term observation of cells with partial metabolic activities indicated that their metabolism was later spontaneously restored, leading to growth recovery. Further investigations showed that oxidative stress can induce the emergence of a subpopulation with partial metabolic activities. Our findings reveal the emergence of metabolic heterogeneity and associated dynamic changes in phenotypic composition. In addition, the results shed new light on microbial dormancy, which has important implications in microbial ecology and biomedicine.}, }
@article {pmid29335555, year = {2018}, author = {Abu-Ali, GS and Mehta, RS and Lloyd-Price, J and Mallick, H and Branck, T and Ivey, KL and Drew, DA and DuLong, C and Rimm, E and Izard, J and Chan, AT and Huttenhower, C}, title = {Metatranscriptome of human faecal microbial communities in a cohort of adult men.}, journal = {Nature microbiology}, volume = {3}, number = {3}, pages = {356-366}, pmid = {29335555}, issn = {2058-5276}, support = {U54 DK102557/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 CA202704/CA/NCI NIH HHS/United States ; U01 CA152904/CA/NCI NIH HHS/United States ; L30 CA209764/CA/NCI NIH HHS/United States ; K24 DK098311/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; UM1 CA167552/CA/NCI NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Feces/*microbiology ; Follow-Up Studies ; Gastrointestinal Microbiome ; *Gene Expression Profiling ; Gene Regulatory Networks ; Humans ; Longitudinal Studies ; Male ; *Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; Prospective Studies ; }, abstract = {The gut microbiome is intimately related to human health, but it is not yet known which functional activities are driven by specific microorganisms' ecological configurations or transcription. We report a large-scale investigation of 372 human faecal metatranscriptomes and 929 metagenomes from a subset of 308 men in the Health Professionals Follow-Up Study. We identified a metatranscriptomic 'core' universally transcribed over time and across participants, often by different microorganisms. In contrast to the housekeeping functions enriched in this core, a 'variable' metatranscriptome included specialized pathways that were differentially expressed both across participants and among microorganisms. Finally, longitudinal metagenomic profiles allowed ecological interaction network reconstruction, which remained stable over the six-month timespan, as did strain tracking within and between participants. These results provide an initial characterization of human faecal microbial ecology into core, subject-specific, microorganism-specific and temporally variable transcription, and they differentiate metagenomically versus metatranscriptomically informative aspects of the human faecal microbiome.}, }
@article {pmid29333583, year = {2018}, author = {Vecchi, M and Newton, ILG and Cesari, M and Rebecchi, L and Guidetti, R}, title = {The Microbial Community of Tardigrades: Environmental Influence and Species Specificity of Microbiome Structure and Composition.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {467-481}, pmid = {29333583}, issn = {1432-184X}, support = {PdR 2013 B1/01//Piano Nazionale Ricerche in Antartide (PNRA) - Ministero dell'Istruzione dell'Universit&#xe0; e della Ricerca (MIUR), Italy/ ; }, mesh = {Animals ; Bacteria/*classification/genetics ; Bacterial Physiological Phenomena ; Bacteroidetes/classification/genetics ; Biodiversity ; DNA, Bacterial/genetics ; Host Microbial Interactions ; Microbiota/genetics/*physiology ; *Phylogeny ; Proteobacteria/classification/genetics ; RNA, Ribosomal, 16S/genetics ; Rickettsiales/classification/genetics ; Species Specificity ; *Symbiosis ; Tardigrada/*microbiology ; }, abstract = {Symbiotic associations of metazoans with bacteria strongly influence animal biology since bacteria are ubiquitous and virtually no animal is completely free from them. Tardigrades are micrometazoans famous for their ability to undergo ametabolic states (cryptobiosis) but very little information is available on potential microbial associations. We characterized the microbiomes of six limnoterrestrial tardigrade species belonging to several phylogenetic lines in tandem with the microbiomes of their respective substrates. The experimental design enabled us to determine the effects of both the environment and the host genetic background on the tardigrade microbiome; we were able to define the microbial community of the same species sampled from different environments, and the communities of different species from the same environment. Our 16S rRNA gene amplicon approach indicated that the tardigrade microbiome is species-specific and well differentiated from the environment. Tardigrade species showed a much lower microbial diversity compared to their substrates, with only one significant exception. Forty-nine common OTUs (operational taxonomic units) were classified into six bacterial phyla, while four common OTUs were unclassified and probably represent novel bacterial taxa. Specifically, the tardigrade microbiome appears dominated by Proteobacteria and Bacteroidetes. Some OTUs were shared between different species from geographically distant samples, suggesting the associated bacteria may be widespread. Putative endosymbionts of tardigrades from the order Rickettsiales were identified. Our results indicated that like all other animals, tardigrades have their own microbiota that is different among species, and its assembly is determined by host genotype and environmental influences.}, }
@article {pmid29332150, year = {2018}, author = {Tomás, G and Martín-Gálvez, D and Ruiz-Castellano, C and Ruiz-Rodríguez, M and Peralta-Sánchez, JM and Martín-Vivaldi, M and Soler, JJ}, title = {Ectoparasite Activity During Incubation Increases Microbial Growth on Avian Eggs.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {555-564}, pmid = {29332150}, issn = {1432-184X}, support = {CGL2013-48193-C3-1-P//Spanish Ministerio de Econom&#xed;a y Competitividad and FEDER/ ; CGL2013-48193-C3-2-P//Spanish Ministerio de Econom&#xed;a y Competitividad and FEDER/ ; }, mesh = {Animal Experimentation ; Animals ; Bacteria/classification/*growth &amp; development/pathogenicity ; Bacterial Load ; Biodiversity ; Biological Evolution ; Bird Diseases/microbiology/mortality/parasitology ; Birds/classification/*microbiology ; Colony Count, Microbial ; Diptera/microbiology ; Ecology ; Egg Shell/microbiology ; Environmental Microbiology ; Feces/microbiology ; Host-Parasite Interactions/*physiology ; Microbiota ; Nesting Behavior ; Ovum/*microbiology ; Species Specificity ; }, abstract = {While direct detrimental effects of parasites on hosts are relatively well documented, other more subtle but potentially important effects of parasitism are yet unexplored. Biological activity of ectoparasites, apart from skin injuries and blood-feeding, often results in blood remains, or parasite faeces that accumulate and modify the host environment. In this way, ectoparasite activities and remains may increase nutrient availability that may favour colonization and growth of microorganisms including potential pathogens. Here, by the experimental addition of hematophagous flies (Carnus hemapterus, a common ectoparasite of birds) to nests of spotless starlings Sturnus unicolor during incubation, we explore this possible side effect of parasitism which has rarely, if ever, been investigated. Results show that faeces and blood remains from parasitic flies on spotless starling eggshells at the end of incubation were more abundant in experimental than in control nests. Moreover, eggshell bacterial loads of different groups of cultivable bacteria including potential pathogens, as well as species richness of bacteria in terms of Operational Taxonomic Units (OTUs), were also higher in experimental nests. Finally, we also found evidence of a link between eggshell bacterial loads and increased embryo mortality, which provides indirect support for a bacterial-mediated negative effect of ectoparasitism on host offspring. Trans-shell bacterial infection might be one of the main causes of embryo death and, consequently, this hitherto unnoticed indirect effect of ectoparasitism might be widespread in nature and could affect our understanding of ecology and evolution of host-parasite interactions.}, }
@article {pmid29330649, year = {2018}, author = {Smith, SL and Johnson, DB}, title = {Growth of Leptospirillum ferriphilum in sulfur medium in co-culture with Acidithiobacillus caldus.}, journal = {Extremophiles : life under extreme conditions}, volume = {22}, number = {2}, pages = {327-333}, pmid = {29330649}, issn = {1433-4909}, support = {NE/M010899/1//Natural Environment Research Council/ ; }, mesh = {Iron/metabolism ; Microbiological Techniques/*methods ; Oxidation-Reduction ; Proteobacteria/growth &amp; development/*metabolism ; Sulfur/*metabolism ; Thermotolerance ; }, abstract = {Leptospirillum ferriphilum and Acidithiobacillus caldus are both thermotolerant acidophilic bacteria that frequently co-exist in natural and man-made environments, such as biomining sites. Both are aerobic chemolithotrophs; L. ferriphilum is known only to use ferrous iron as electron donor, while A. caldus can use zero-valent and reduced sulfur, and also hydrogen, as electron donors. It has recently been demonstrated that A. caldus reduces ferric iron to ferrous when grown aerobically on sulfur. Experiments were carried out which demonstrated that this allowed L. ferriphilum to be sustained for protracted periods in media containing very little soluble iron, implying that dynamic cycling of iron occurred in aerobic mixed cultures of these two bacteria. In contrast, numbers of viable L. ferriphilum rapidly declined in mixed cultures that did not contain sulfur. Data also indicated that growth of A. caldus was partially inhibited in the presence of L. ferriphilum. This was shown to be due to greater sensitivity of the sulfur-oxidizer to ferric than to ferrous iron, and to highly positive redox potentials, which are characteristic of cultures containing Leptospirillum spp. The implications of these results in the microbial ecology of extremely acidic environments and in commercial bioprocessing applications are discussed.}, }
@article {pmid29330647, year = {2018}, author = {Brambilla, S and Frare, R and Soto, G and Jozefkowicz, C and Ayub, N}, title = {Absence of the Nitrous Oxide Reductase Gene Cluster in Commercial Alfalfa Inoculants Is Probably Due to the Extensive Loss of Genes During Rhizobial Domestication.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {299-302}, pmid = {29330647}, issn = {1432-184X}, support = {PICT-2014-3659//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; }, mesh = {Bacteria/*genetics/metabolism ; Denitrification/genetics ; Evolution, Molecular ; Genome Size ; Medicago sativa/*microbiology ; *Multigene Family ; Nitrates/metabolism ; Nitrites/metabolism ; Nitrogen Fixation ; Nitrous Oxide/metabolism ; Oxidoreductases/*genetics ; Rhizobium/*genetics ; Symbiosis ; }, abstract = {As other legume crops, alfalfa cultivation increases the emission of the greenhouse gas nitrous oxide (N2O). Since legume-symbiotic nitrogen-fixing bacteria play a crucial role in this emission, it is important to understand the possible impacts of rhizobial domestication on the evolution of denitrification genes. In comparison with the genomes of non-commercial strains, those of commercial alfalfa inoculants exhibit low total genome size, low number of ORFs and high numbers of both frameshifted genes and pseudogenes, suggesting a dramatic loss of genes during bacterial domestication. Genomic analysis focused on denitrification genes revealed that commercial strains have perfectly conserved the nitrate (NAP), nitrite (NIR) and nitric (NOR) reductase clusters related to the production of N2O from nitrate but completely lost the nitrous oxide (NOS) reductase cluster (nosRZDFYLX genes) associated with the reduction of N2O to gas nitrogen. Based on these results, we propose future screenings for alfalfa-nodulating isolates containing both nitrogen fixation and N2O reductase genes for environmental sustainability of alfalfa production.}, }
@article {pmid29330187, year = {2018}, author = {Bergin, C and Wentrup, C and Brewig, N and Blazejak, A and Erséus, C and Giere, O and Schmid, M and De Wit, P and Dubilier, N}, title = {Acquisition of a Novel Sulfur-Oxidizing Symbiont in the Gutless Marine Worm Inanidrilus exumae.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {7}, pages = {}, pmid = {29330187}, issn = {1098-5336}, mesh = {Animals ; Chromatiaceae/classification/genetics/*physiology ; Genes, Bacterial ; In Situ Hybridization, Fluorescence ; Oligochaeta/*microbiology ; Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, RNA ; *Symbiosis ; }, abstract = {Gutless phallodrilines are marine annelid worms without a mouth or gut, which live in an obligate association with multiple bacterial endosymbionts that supply them with nutrition. In this study, we discovered an unusual symbiont community in the gutless phallodriline Inanidrilus exumae that differs markedly from the microbiomes of all 22 of the other host species examined. Comparative 16S rRNA gene sequence analysis and fluorescence in situ hybridization revealed that I. exumae harbors cooccurring gamma-, alpha-, and deltaproteobacterial symbionts, while all other known host species harbor gamma- and either alpha- or deltaproteobacterial symbionts. Surprisingly, the primary chemoautotrophic sulfur oxidizer "Candidatus Thiosymbion" that occurs in all other gutless phallodriline hosts does not appear to be present in I. exumae Instead, I. exumae harbors a bacterial endosymbiont that resembles "Ca Thiosymbion" morphologically and metabolically but originates from a novel lineage within the class Gammaproteobacteria This endosymbiont, named Gamma 4 symbiont here, had a 16S rRNA gene sequence that differed by at least 7% from those of other free-living and symbiotic bacteria and by 10% from that of "Ca Thiosymbion." Sulfur globules in the Gamma 4 symbiont cells, as well as the presence of genes characteristic for autotrophy (cbbL) and sulfur oxidation (aprA), indicate that this symbiont is a chemoautotrophic sulfur oxidizer. Our results suggest that a novel lineage of free-living bacteria was able to establish a stable and specific association with I. exumae and appears to have displaced the "Ca Thiosymbion" symbionts originally associated with these hosts.IMPORTANCE All 22 gutless marine phallodriline species examined to date live in a highly specific association with endosymbiotic, chemoautotrophic sulfur oxidizers called "Ca Thiosymbion." These symbionts evolved from a single common ancestor and represent the ancestral trait for this host group. They are transmitted vertically and assumed to be in transition to becoming obligate endosymbionts. It is therefore surprising that despite this ancient, evolutionary relationship between phallodriline hosts and "Ca Thiosymbion," these symbionts are apparently no longer present in Inanidrilus exumae They appear to have been displaced by a novel lineage of sulfur-oxidizing bacteria only very distantly related to "Ca Thiosymbion." Thus, this study highlights the remarkable plasticity of both animals and bacteria in establishing beneficial associations: the phallodriline hosts were able to acquire and maintain symbionts from two very different lineages of bacteria, while sulfur-oxidizing bacteria from two very distantly related lineages were able to independently establish symbiotic relationships with phallodriline hosts.}, }
@article {pmid29330184, year = {2018}, author = {Raghupathi, PK and Zupančič, J and Brejnrod, AD and Jacquiod, S and Houf, K and Burmølle, M and Gunde-Cimerman, N and Sørensen, SJ}, title = {Microbial Diversity and Putative Opportunistic Pathogens in Dishwasher Biofilm Communities.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {5}, pages = {}, pmid = {29330184}, issn = {1098-5336}, mesh = {Bacteria/growth &amp; development/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Biofilms/*growth &amp; development ; Fungi/growth &amp; development/isolation &amp; purification/*physiology ; *Household Articles ; Microbiota/*physiology ; }, abstract = {Extreme habitats are not only limited to natural environments, but also exist in manmade systems, for instance, household appliances such as dishwashers. Limiting factors, such as high temperatures, high and low pHs, high NaCl concentrations, presence of detergents, and shear force from water during washing cycles, define microbial survival in this extreme system. Fungal and bacterial diversity in biofilms isolated from rubber seals of 24 different household dishwashers was investigated using next-generation sequencing. Bacterial genera such as Pseudomonas, Escherichia, and Acinetobacter, known to include opportunistic pathogens, were represented in most samples. The most frequently encountered fungal genera in these samples belonged to Candida, Cryptococcus, and Rhodotorula, also known to include opportunistic pathogenic representatives. This study showed how specific conditions of the dishwashers impact the abundance of microbial groups and investigated the interkingdom and intrakingdom interactions that shape these biofilms. The age, usage frequency, and hardness of incoming tap water of dishwashers had significant impact on bacterial and fungal community compositions. Representatives of Candida spp. were found at the highest prevalence (100%) in all dishwashers and are assumed to be one of the first colonizers in recently purchased dishwashers. Pairwise correlations in tested microbiomes showed that certain bacterial groups cooccur, as did the fungal groups. In mixed bacterial-fungal biofilms, early adhesion, contact, and interactions were vital in the process of biofilm formation, where mixed complexes of bacteria and fungi could provide a preliminary biogenic structure for the establishment of these biofilms.IMPORTANCE Worldwide demand for household appliances, such as dishwashers and washing machines, is increasing, as is the number of immunocompromised individuals. The harsh conditions in household dishwashers should prevent the growth of most microorganisms. However, our research shows that persisting polyextremotolerant groups of microorganisms in household appliances are well established under these unfavorable conditions and supported by the biofilm mode of growth. The significance of our research is in identifying the microbial composition of biofilms formed on dishwasher rubber seals, how diverse abiotic conditions affect microbiota, and which key microbial members were represented in early colonization and contamination of dishwashers, as these appliances can present a source of domestic cross-contamination that leads to broader medical impacts.}, }
@article {pmid29327410, year = {2018}, author = {Eichorst, SA and Trojan, D and Roux, S and Herbold, C and Rattei, T and Woebken, D}, title = {Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments.}, journal = {Environmental microbiology}, volume = {20}, number = {3}, pages = {1041-1063}, pmid = {29327410}, issn = {1462-2920}, mesh = {Acidobacteria/*genetics/metabolism ; Bacteriophages/*genetics ; Carbohydrate Metabolism/genetics ; DNA Transposable Elements/*genetics ; DNA, Bacterial/*genetics ; Genome, Bacterial/*genetics ; Genomics ; Nitrification/genetics ; Nitrogen Fixation/genetics ; Oxygen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Members of the phylum Acidobacteria are abundant and ubiquitous across soils. We performed a large-scale comparative genome analysis spanning subdivisions 1, 3, 4, 6, 8 and 23 (n = 24) with the goal to identify features to help explain their prevalence in soils and understand their ecophysiology. Our analysis revealed that bacteriophage integration events along with transposable and mobile elements influenced the structure and plasticity of these genomes. Low- and high-affinity respiratory oxygen reductases were detected in multiple genomes, suggesting the capacity for growing across different oxygen gradients. Among many genomes, the capacity to use a diverse collection of carbohydrates, as well as inorganic and organic nitrogen sources (such as via extracellular peptidases), was detected - both advantageous traits in environments with fluctuating nutrient environments. We also identified multiple soil acidobacteria with the potential to scavenge atmospheric concentrations of H2 , now encompassing mesophilic soil strains within the subdivision 1 and 3, in addition to a previously identified thermophilic strain in subdivision 4. This large-scale acidobacteria genome analysis reveal traits that provide genomic, physiological and metabolic versatility, presumably allowing flexibility and versatility in the challenging and fluctuating soil environment.}, }
@article {pmid29327073, year = {2018}, author = {Choix, FJ and López-Cisneros, CG and Méndez-Acosta, HO}, title = {Azospirillum brasilense Increases CO2 Fixation on Microalgae Scenedesmus obliquus, Chlorella vulgaris, and Chlamydomonas reinhardtii Cultured on High CO2 Concentrations.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {430-442}, pmid = {29327073}, issn = {1432-184X}, support = {247006//Project SENER-CONACyT/ ; 2517//Programa Catedr&#xe1;s CONACyT/ ; }, mesh = {Azospirillum brasilense/growth &amp; development/*metabolism ; Biomass ; *Carbon Cycle ; Carbon Dioxide/*metabolism ; Cell Count ; Cells, Immobilized ; Chlamydomonas reinhardtii/growth &amp; development/*metabolism ; Chlorella vulgaris/growth &amp; development/*metabolism ; Culture Media ; Indoleacetic Acids/metabolism ; Microalgae/growth &amp; development/*metabolism ; Microbial Interactions/physiology ; Plant Growth Regulators/metabolism ; Scenedesmus/*metabolism ; Symbiosis ; Tryptophan/metabolism ; }, abstract = {Mutualism interactions of microalgae with other microorganisms are widely used in several biotechnological processes since symbiotic interaction improves biotechnological capabilities of the microorganisms involved. The interaction of the bacterium Azospirillum brasilense was assessed with three microalgae genus, Scenedesmus, Chlorella, and Chlamydomonas, during CO2 fixation under high CO2 concentrations. The results in this study have demonstrated that A. brasilense maintained a mutualistic interaction with the three microalgae assessed, supported by the metabolic exchange of indole-3-acetic acid (IAA) and tryptophan (Trp), respectively. Besides, CO2 fixation increased, as well as growth and cell compound accumulation, mainly carbohydrates, in each microalgae evaluated, interacting with the bacterium. Overall, these results propose the mutualism interaction of A. brasilense with microalgae for improving biotechnological processes based on microalgae as CO2 capture and their bio-refinery capacity.}, }
@article {pmid29327072, year = {2018}, author = {Wolfson, SJ and Porter, AW and Campbell, JK and Young, LY}, title = {Naproxen Is Transformed Via Acetogenesis and Syntrophic Acetate Oxidation by a Methanogenic Wastewater Consortium.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {362-371}, pmid = {29327072}, issn = {1432-184X}, support = {0903675//National Science Foundation/ ; NJ07212//National Institute of Food and Agriculture/ ; }, mesh = {*Acetic Acid ; Anaerobiosis ; Archaea/classification/genetics/metabolism ; Bacteria/classification/genetics/metabolism ; Biodegradation, Environmental ; DNA, Bacterial ; Demethylation ; Methane/metabolism ; Microbial Consortia/genetics/*physiology ; Naproxen/analogs &amp; derivatives/*metabolism ; Oxidation-Reduction ; Sewage/microbiology ; Time Factors ; Vanillic Acid ; Wastewater/*microbiology ; }, abstract = {Over-the-counter pharmaceutical compounds can serve as microbial substrates in wastewater treatment processes as well as in the environment. The metabolic pathways and intermediates produced during their degradation, however, are poorly understood. In this study, we investigate an anaerobic wastewater community that metabolizes naproxen via demethylation. Enriched cultures, established from anaerobic digester inocula receiving naproxen as the sole carbon source, transformed naproxen to 6-O-desmethylnaproxen (DMN) within 22 days. Continual enrichment and culture transfer resulted in consistent demethylation of naproxen with no loss of DMN observed. Methane was generated at 0.83 mmol per 1 mmol transformed naproxen. In addition to naproxen, the consortium readily demethylated syringic acid and vanillic acid. DNA analysis revealed a community of acetogenic bacteria and syntrophic acetate oxidizing archaea. Combined with the biotransformation data, this suggests the enriched consortium performs aromatic O-demethylation through a syntrophic relationship between specific acetogens, acetate oxidizers, and methanogens. The proposed model of carbon transfer through the anaerobic food web highlights the significance of linked community interactions in the anaerobic transformation of aromatic O-methyl compounds such as naproxen.}, }
@article {pmid29326681, year = {2017}, author = {Chaib De Mares, M and Sipkema, D and Huang, S and Bunk, B and Overmann, J and van Elsas, JD}, title = {Host Specificity for Bacterial, Archaeal and Fungal Communities Determined for High- and Low-Microbial Abundance Sponge Species in Two Genera.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2560}, pmid = {29326681}, issn = {1664-302X}, abstract = {Sponges are engaged in intimate symbioses with a diversity of microorganisms from all three domains of life, namely Bacteria, Archaea and Eukarya. Sponges have been well studied and categorized for their bacterial communities, some displaying a high microbial abundance (HMA), while others show low microbial abundance (LMA). However, the associated Archaea and Eukarya have remained relatively understudied. We assessed the bacterial, archaeal and eukaryotic diversities in the LMA sponge species Dysidea avara and Dysidea etheria by deep amplicon sequencing, and compared the results to those in the HMA sponges Aplysina aerophoba and Aplysina cauliformis. D. avara and A. aerophoba are sympatric in the Mediterranean Sea, while D. etheria and A. cauliformis are sympatric in the Caribbean Sea. The bacterial communities followed a host-specific pattern, with host species identity explaining most of the variation among samples. We identified OTUs shared by the Aplysina species that support a more ancient association of these microbes, before the split of the two species studied here. These shared OTUs are suitable targets for future studies of the microbial traits that mediate interactions with their hosts. Even though the archaeal communities were not as rich as the bacterial ones, we found a remarkable diversification and specificity of OTUs of the family Cenarchaeaceae and the genus Nitrosopumilus in all four sponge species studied. Similarly, the differences in fungal communities were driven by sponge identity. The structures of the communities of small eukaryotes such as dinophytes and ciliophores (alveolates), and stramenopiles, could not be explained by either sponge host, sponge genus or geographic location. Our analyses suggest that the host specificity that was previously described for sponge bacterial communities also extends to the archaeal and fungal communities, but not to other microbial eukaryotes.}, }
@article {pmid29326674, year = {2017}, author = {Gómez Expósito, R and de Bruijn, I and Postma, J and Raaijmakers, JM}, title = {Current Insights into the Role of Rhizosphere Bacteria in Disease Suppressive Soils.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2529}, pmid = {29326674}, issn = {1664-302X}, abstract = {Disease suppressive soils offer effective protection to plants against infection by soil-borne pathogens, including fungi, oomycetes, bacteria, and nematodes. The specific disease suppression that operates in these soils is, in most cases, microbial in origin. Therefore, suppressive soils are considered as a rich resource for the discovery of beneficial microorganisms with novel antimicrobial and other plant protective traits. To date, several microbial genera have been proposed as key players in disease suppressiveness of soils, but the complexity of the microbial interactions as well as the underlying mechanisms and microbial traits remain elusive for most disease suppressive soils. Recent developments in next generation sequencing and other 'omics' technologies have provided new insights into the microbial ecology of disease suppressive soils and the identification of microbial consortia and traits involved in disease suppressiveness. Here, we review the results of recent 'omics'-based studies on the microbial basis of disease suppressive soils, with specific emphasis on the role of rhizosphere bacteria in this intriguing microbiological phenomenon.}, }
@article {pmid29325123, year = {2018}, author = {Tomasch, J and Wang, H and Hall, ATK and Patzelt, D and Preusse, M and Petersen, J and Brinkmann, H and Bunk, B and Bhuju, S and Jarek, M and Geffers, R and Lang, AS and Wagner-Döbler, I}, title = {Packaging of Dinoroseobacter shibae DNA into Gene Transfer Agent Particles Is Not Random.}, journal = {Genome biology and evolution}, volume = {10}, number = {1}, pages = {359-369}, pmid = {29325123}, issn = {1759-6653}, mesh = {Bacterial Proteins/genetics ; Base Composition ; DNA, Bacterial/*genetics ; *Gene Transfer, Horizontal ; Multigene Family ; Oceans and Seas ; Rhodobacteraceae/*genetics ; }, abstract = {Gene transfer agents (GTAs) are phage-like particles which contain a fragment of genomic DNA of the bacterial or archaeal producer and deliver this to a recipient cell. GTA gene clusters are present in the genomes of almost all marine Rhodobacteraceae (Roseobacters) and might be important contributors to horizontal gene transfer in the world's oceans. For all organisms studied so far, no obvious evidence of sequence specificity or other nonrandom process responsible for packaging genomic DNA into GTAs has been found. Here, we show that knock-out of an autoinducer synthase gene of Dinoroseobacter shibae resulted in overproduction and release of functional GTA particles (DsGTA). Next-generation sequencing of the 4.2-kb DNA fragments isolated from DsGTAs revealed that packaging was not random. DNA from low-GC conjugative plasmids but not from high-GC chromids was excluded from packaging. Seven chromosomal regions were strongly overrepresented in DNA isolated from DsGTA. These packaging peaks lacked identifiable conserved sequence motifs that might represent recognition sites for the GTA terminase complex. Low-GC regions of the chromosome, including the origin and terminus of replication, were underrepresented in DNA isolated from DsGTAs. DNA methylation reduced packaging frequency while the level of gene expression had no influence. Chromosomal regions found to be over- and underrepresented in DsGTA-DNA were regularly spaced. We propose that a "headful" type of packaging is initiated at the sites of coverage peaks and, after linearization of the chromosomal DNA, proceeds in both directions from the initiation site. GC-content, DNA-modifications, and chromatin structure might influence at which sides GTA packaging can be initiated.}, }
@article {pmid29324387, year = {2018}, author = {Feng, H and Tang, C and Wang, Q and Liang, Y and Shen, D and Guo, K and He, Q and Jayaprada, T and Zhou, Y and Chen, T and Ying, X and Wang, M}, title = {A novel photoactive and three-dimensional stainless steel anode dramatically enhances the current density of bioelectrochemical systems.}, journal = {Chemosphere}, volume = {196}, number = {}, pages = {476-481}, doi = {10.1016/j.chemosphere.2017.12.166}, pmid = {29324387}, issn = {1879-1298}, mesh = {Bioelectric Energy Sources/*standards ; Biofilms ; Electricity ; Electrodes/*standards ; Ferric Compounds/pharmacology ; Light ; *Stainless Steel ; }, abstract = {This study reports a high-performance 3D stainless-steel photoanode (3D SS photoanode) for bioelectrochemical systems (BESs). The 3D SS photoanode consists of 3D carbon-coated SS felt bioactive side and a flat α-Fe2O3-coated SS plate photoactive side. Without light illumination, the electrode reached a current density of 26.2 ± 1.9 A m[-2], which was already one of the highest current densities reported thus far. Under illumination, the current density of the electrode was further increased to 46.5 ± 2.9 A m[-2]. The mechanism of the photo-enhanced current production can be attributed to the reduced charge-transfer resistance between electrode surface and the biofilm with illumination. It was also found that long-term light illumination can enhance the biofilm formation on the 3D SS photoanode. These findings demonstrate that using the synergistic effect of photocatalysis and microbial electrocatalysis is an efficient way to boost the current production of the existing high-performance 3D anodes for BESs.}, }
@article {pmid29324293, year = {2018}, author = {Rittmann, BE}, title = {Biofilms, active substrata, and me.}, journal = {Water research}, volume = {132}, number = {}, pages = {135-145}, doi = {10.1016/j.watres.2017.12.043}, pmid = {29324293}, issn = {1879-2448}, mesh = {*Biofilms ; Electrodes ; Hydrogen/metabolism ; Oxidation-Reduction ; Water Pollutants/metabolism ; *Water Purification ; }, abstract = {Having worked with biofilms since the 1970s, I know that they are ubiquitous in nature, of great value in water technology, and scientifically fascinating. Biofilms are naturally able to remove BOD, transform N, generate methane, and biodegrade micropollutants. What I also discovered is that biofilms can do a lot more for us in terms of providing environmental services if we give them a bit of help. Here, I explore how we can use active substrata to enable our biofilm partners to provide particularly challenging environmental services. In particular, I delve into three examples in which an active substratum makes it possible for a biofilm to accomplish a task that otherwise seems impossible. The first example is the delivery of hydrogen gas (H2) as an electron donor to drive the reduction and detoxification of the rising number of oxidized contaminant: e.g., perchlorate, selenate, chromate, chlorinated solvents, and more. The active substratum is a gas-transfer membrane that delivers H2 directly to the biofilm in a membrane biofilm reactor (MBfR), which makes it possible to deliver a low-solubility gaseous substrate with 100% efficiency. The second example is the biofilm anode of a microbial electrochemical cell (MxC). Here, the anode is the electron acceptor for anode-respiring bacteria, which "liberate" electrons from organic compounds and send them ultimately to a cathode, where we can harvest valuable products or services. The anode's potential is a sensitive tool for managing the microbial ecology and reaction kinetics of the biofilm anode. The third example is intimately coupled photobiocatalysis (ICPB), in which we use photocatalysis to enable the biodegradation of intrinsically recalcitrant organic pollutants. Photocatalysis transforms the recalcitrant organics just enough so that the products are rapidly biodegradable substrates for bacteria in a nearby biofilm. The macroporous substratum, which houses the photocatalyst on its exterior, actively provides donor substrate and protects the biofilm from UV light and free radicals in its interior. These three well-developed topics illustrate how and why an active substratum expands the scope of what biofilms can do to enhance water sustainability.}, }
@article {pmid29323701, year = {2018}, author = {Schnyder, E and Bodelier, PLE and Hartmann, M and Henneberger, R and Niklaus, PA}, title = {Positive diversity-functioning relationships in model communities of methanotrophic bacteria.}, journal = {Ecology}, volume = {99}, number = {3}, pages = {714-723}, doi = {10.1002/ecy.2138}, pmid = {29323701}, issn = {0012-9658}, mesh = {Bacteria/classification ; Biodiversity ; *Methane ; Phylogeny ; *Soil Microbiology ; }, abstract = {Biodiversity enhances ecosystem functions such as biomass production and nutrient cycling. Although the majority of the terrestrial biodiversity is hidden in soils, very little is known about the importance of the diversity of microbial communities for soil functioning. Here, we tested effects of biodiversity on the functioning of methanotrophs, a specialized group of soil bacteria that plays a key role in mediating greenhouse gas emissions from soils. Using pure strains of methanotrophic bacteria, we assembled artificial communities of different diversity levels, with which we inoculated sterile soil microcosms. To assess the functioning of these communities, we measured methane oxidation by gas chromatography throughout the experiment and determined changes in community composition and community size at several time points by quantitative PCR and sequencing. We demonstrate that microbial diversity had a positive overyielding effect on methane oxidation, in particular at the beginning of the experiment. This higher assimilation of CH4 at high diversity translated into increased growth and significantly larger communities towards the end of the study. The overyielding of mixtures with respect to CH4 consumption and community size were positively correlated. The temporal CH4 consumption profiles of strain monocultures differed, raising the possibility that temporal complementarity of component strains drove the observed community-level strain richness effects; however, the community niche metric we derived from the temporal activity profiles did not explain the observed strain richness effect. The strain richness effect also was unrelated to both the phylogenetic and functional trait diversity of mixed communities. Overall, our results suggest that positive biodiversity-ecosystem-function relationships show similar patterns across different scales and may be widespread in nature. Additionally, biodiversity is probably also important in natural methanotrophic communities for the ecosystem function methane oxidation. Therefore, maintaining soil conditions that support a high diversity of methanotrophs may help to reduce the emission of the greenhouse gas methane.}, }
@article {pmid29322230, year = {2018}, author = {Yang, P and Oliveira da Rocha Calixto, R and van Elsas, JD}, title = {Migration of Paraburkholderia terrae BS001 Along Old Fungal Hyphae in Soil at Various pH Levels.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {443-452}, pmid = {29322230}, issn = {1432-184X}, mesh = {Agaricales/growth &amp; development ; Burkholderiaceae/*physiology ; Hydrogen-Ion Concentration ; *Hyphae/growth &amp; development ; *Locomotion ; Microbial Interactions/physiology ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {The movement of bacterial cells along with fungal hyphae in soil (the mycosphere) has been reported in several previous studies. However, how local soil conditions affect bacterial migration direction in the mycosphere has not been extensively studied. Here, we investigated the influence of two soil parameters, pH and soil moisture content, on the migration, and survival, of Paraburkholderia terrae BS001 in the mycosphere of Lyophyllum sp. strain Karsten in microcosms containing a loamy sand soil. The data showed that bacterial movement along the hyphal networks took place in both the "forward" and the "backward" directions. Low soil pH strongly restricted bacterial survival, as well as dispersal in both directions, in the mycosphere. The backward movement was weakly correlated with the amount of fungal tissue formed in the old mycelial network. The initial soil moisture content, set at 12 versus 17% (corresponding to 42 and 60% of the soil water holding capacity), also significantly affected the bacterial dispersal along the fungal hyphae. Overall, the presence of fungal hyphae was found to increase the soil pH (under conditions of acidity), which possibly exerted protective effects on the bacterial cells. Finally, we provide a refined model that describes the bacterial migration patterns with fungal hyphae based on the new findings in this study.}, }
@article {pmid29321765, year = {2017}, author = {Krauze, P and Kämpf, H and Horn, F and Liu, Q and Voropaev, A and Wagner, D and Alawi, M}, title = {Microbiological and Geochemical Survey of CO2-Dominated Mofette and Mineral Waters of the Cheb Basin, Czech Republic.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2446}, pmid = {29321765}, issn = {1664-302X}, abstract = {The Cheb Basin (NW Bohemia, Czech Republic) is a shallow, neogene intracontinental basin. It is a non-volcanic region which features frequent earthquake swarms and large-scale diffuse degassing of mantle-derived CO2 at the surface that occurs in the form of CO2-rich mineral springs and wet and dry mofettes. So far, the influence of CO2 degassing onto the microbial communities has been studied for soil environments, but not for aquatic systems. We hypothesized, that deep-trenching CO2 conduits interconnect the subsurface with the surface. This admixture of deep thermal fluids should be reflected in geochemical parameters and in the microbial community compositions. In the present study four mineral water springs and two wet mofettes were investigated through an interdisciplinary survey. The waters were acidic and differed in terms of organic carbon and anion/cation concentrations. Element geochemical and isotope analyses of fluid components were used to verify the origin of the fluids. Prokaryotic communities were characterized through quantitative PCR and Illumina 16S rRNA gene sequencing. Putative chemolithotrophic, anaerobic and microaerophilic organisms connected to sulfur (e.g., Sulfuricurvum, Sulfurimonas) and iron (e.g., Gallionella, Sideroxydans) cycling shaped the core community. Additionally, CO2-influenced waters form an ecosystem containing many taxa that are usually found in marine or terrestrial subsurface ecosystems. Multivariate statistics highlighted the influence of environmental parameters such as pH, Fe[2+] concentration and conductivity on species distribution. The hydrochemical and microbiological survey introduces a new perspective on mofettes. Our results support that mofettes are either analogs or rather windows into the deep biosphere and furthermore enable access to deeply buried paleo-sediments.}, }
@article {pmid29321640, year = {2018}, author = {Ehsani, E and Hernandez-Sanabria, E and Kerckhof, FM and Props, R and Vilchez-Vargas, R and Vital, M and Pieper, DH and Boon, N}, title = {Initial evenness determines diversity and cell density dynamics in synthetic microbial ecosystems.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {340}, pmid = {29321640}, issn = {2045-2322}, mesh = {*Biodiversity ; *Ecosystem ; Metagenome ; Metagenomics/methods ; *Microbiota ; Models, Theoretical ; Phenotype ; }, abstract = {The effect of initial evenness on the temporal trajectory of synthetic communities in comprehensive, low-volume microcosm studies remains unknown. We used flow cytometric fingerprinting and 16S rRNA gene amplicon sequencing to assess the impact of time on community structure in one hundred synthetic ecosystems of fixed richness but varying initial evenness. Both methodologies uncovered a similar reduction in diversity within synthetic communities of medium and high initial evenness classes. However, the results of amplicon sequencing showed that there were no significant differences between and within the communities in all evenness groups at the end of the experiment. Nevertheless, initial evenness significantly impacted the cell density of the community after five medium transfers. Highly even communities retained the highest cell densities at the end of the experiment. The relative abundances of individual species could be associated to particular evenness groups, suggesting that their presence was dependent on the initial evenness of the synthetic community. Our results reveal that using synthetic communities for testing ecological hypotheses requires prior assessment of initial evenness, as it impacts temporal dynamics.}, }
@article {pmid29319784, year = {2018}, author = {Molinaro, F and Tyc, O and Beekwilder, J and Cankar, K and Bertea, CM and Negre, M and Garbeva, P}, title = {The effect of isabelin, a sesquiterpene lactone from Ambrosia artemisiifolia on soil microorganisms and human pathogens.}, journal = {FEMS microbiology letters}, volume = {365}, number = {4}, pages = {}, doi = {10.1093/femsle/fny001}, pmid = {29319784}, issn = {1574-6968}, mesh = {Ambrosia/*chemistry ; Anti-Infective Agents/*pharmacology ; Bacteria/*drug effects ; Bacterial Infections/microbiology ; Fungi/*drug effects ; Humans ; Lactones/*pharmacology ; Mycoses/microbiology ; Plant Extracts/*pharmacology ; Sesquiterpenes, Germacrane/*pharmacology ; Soil Microbiology ; }, abstract = {Ambrosia artemisiifolia L. (common ragweed) is an invasive weed, which is well known for the strong allergenic effect of its pollen as well as for its invasiveness and impact in crop fields (e.g. causing yield losses). This species produces a broad range of sesquiterpenoids. In recent years, new bioactive molecules have been discovered in this plant, e.g. isabelin, a sesquiterpene dilactone. The bioactivity of isabelin has been already demonstrated on allergy-related receptors and its inhibitory effect on seeds of various plant species. Isabelin was tested for potential antimicrobial effects by using a selection of soil-borne bacteria and fungi and three human pathogens as model organisms. For the majority of microorganisms tested, no antimicrobial activity of isabelin was observed. However, isabelin revealed strong antimicrobial activity against the Gram-positive soil bacterium Paenibacillus sp. and against the Gram-positive, multidrug-resistant Staphylococcus aureus. The observed inhibitory activity of isabelin can enlighten the importance to study similar compounds for their effect on human pathogens and on soil and rhizosphere microorganisms.}, }
@article {pmid29319530, year = {2017}, author = {Kiersztyn, B and Siuda, W and Chróst, R}, title = {Coomassie Blue G250 for Visualization of Active Bacteria from Lake Environment and Culture.}, journal = {Polish journal of microbiology}, volume = {66}, number = {3}, pages = {365-373}, doi = {10.5604/01.3001.0010.4867}, pmid = {29319530}, issn = {1733-1331}, mesh = {Aquatic Organisms/metabolism ; Bacterial Proteins/*metabolism ; Escherichia coli/classification/*metabolism ; Fluorescent Dyes/chemistry ; Lakes/*microbiology ; Leucyl Aminopeptidase/*metabolism ; Microscopy, Fluorescence ; RNA, Ribosomal, 16S/genetics ; Rosaniline Dyes/*chemistry ; Staining and Labeling/*methods ; }, abstract = {Bacteria play a fundamental role in the cycling of nutrients in aquatic environments. A precise distinction between active and inactive bacteria is crucial for the description of this process. We have evaluated the usefulness of Coomassie Blue G250 for fluorescent staining of protein containing potentially highly active bacteria. We found that the G250 solution has excitation and emission properties appropriate for direct epifluorescence microscopy observations. It enables fast and effective fluorescent visualization of living, protein-rich bacteria, both in freshwater environment and culture. Our results revealed that the number of G250-stained bacteria from eutrophic lake was positively correlated with other standard bacterial activity markers, like number of bacteria containing 16S rRNA, bacterial secondary production or maximal potential leucine-aminopeptidase activity. In case of the E. coli culture, the percentage of bacteria visualized with G250 was similar to that of bacteria which accumulated tetracycline. Compared to other common methods utilizing fluorogenic substances for bacteria staining, the approach we evaluated is inexpensive and less hazardous (for example mutagenic) to the environment and researchers. It can be regarded as an additional or alternative method for protein rich, active bacteria staining.}, }
@article {pmid29318631, year = {2018}, author = {Fazlollahi, M and Chun, Y and Grishin, A and Wood, RA and Burks, AW and Dawson, P and Jones, SM and Leung, DYM and Sampson, HA and Sicherer, SH and Bunyavanich, S}, title = {Early-life gut microbiome and egg allergy.}, journal = {Allergy}, volume = {73}, number = {7}, pages = {1515-1524}, pmid = {29318631}, issn = {1398-9995}, support = {U01 AI066560/AI/NIAID NIH HHS/United States ; UL1 TR000039/TR/NCATS NIH HHS/United States ; UL1 RR025005/RR/NCRR NIH HHS/United States ; UM1 AI130781/AI/NIAID NIH HHS/United States ; S10 OD018522/OD/NIH HHS/United States ; U19 AI066738/AI/NIAID NIH HHS/United States ; UL1 TR000067/TR/NCATS NIH HHS/United States ; U01 AI181962/AI/NIAID NIH HHS/United States ; R01 AI118833/AI/NIAID NIH HHS/United States ; UL1 TR000154/TR/NCATS NIH HHS/United States ; K08 AI093538/AI/NIAID NIH HHS/United States ; }, mesh = {Age Factors ; Case-Control Studies ; Egg Hypersensitivity/*etiology ; Female ; *Gastrointestinal Microbiome/immunology ; Humans ; Immunization ; Immunoglobulin E/immunology ; Infant ; Male ; Metagenome ; Metagenomics ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Gut microbiota may play a role in egg allergy. We sought to examine the association between early-life gut microbiota and egg allergy.<br><br>METHODS: We studied 141 children with egg allergy and controls from the multicenter Consortium of Food Allergy Research study. At enrollment (age 3 to 16&#xa0;months), fecal samples were collected, and clinical evaluation, egg-specific IgE measurement, and egg skin prick test were performed. Gut microbiome was profiled by 16S rRNA sequencing. Analyses for the primary outcome of egg allergy at enrollment, and the secondary outcomes of egg sensitization at enrollment and resolution of egg allergy by age 8&#xa0;years, were performed using Quantitative Insights into Microbial Ecology, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, and Statistical Analysis of Metagenomic Profiles.<br><br>RESULTS: Compared to controls, increased alpha diversity and distinct taxa (PERMANOVA P&#xa0;=&#xa0;5.0&#xa0;&#xd7;&#xa0;10[-4]) characterized the early-life gut microbiome of children with egg allergy. Genera from the Lachnospiraceae, Streptococcaceae, and Leuconostocaceae families were differentially abundant in children with egg allergy. Predicted metagenome functional analyses showed differential purine metabolism by the gut microbiota of egg-allergic subjects (Kruskal-Wallis Padj &#xa0;=&#xa0;0.021). Greater gut microbiome diversity and genera from Lachnospiraceae and Ruminococcaceae were associated with egg sensitization (PERMANOVA P&#xa0;=&#xa0;5.0&#xa0;&#xd7;&#xa0;10[-4]). Among those with egg allergy, there was no association between early-life gut microbiota and egg allergy resolution by age 8&#xa0;years.<br><br>CONCLUSION: The distinct early-life gut microbiota in egg-allergic and egg-sensitized children identified by our study may point to targets for preventive or therapeutic intervention.}, }
@article {pmid29318328, year = {2018}, author = {Xu, H and Zhao, D and Huang, R and Cao, X and Zeng, J and Yu, Z and Hooker, KV and Hambright, KD and Wu, QL}, title = {Contrasting Network Features between Free-Living and Particle-Attached Bacterial Communities in Taihu Lake.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {303-313}, pmid = {29318328}, issn = {1432-184X}, support = {41571108//National Natural Science Foundation of China/ ; 41671078//National Natural Science Foundation of China/ ; BK20151614//Natural Science Foundation of Jiangsu Province, China/ ; 2015BAD13B01//National Key Technology R&amp;D Program/ ; 1650686//US National Science Foundation Graduate Research Fellowship/ ; }, mesh = {*Bacteria/classification/metabolism ; *Bacterial Physiological Phenomena ; Biodiversity ; Cluster Analysis ; DNA, Bacterial/analysis ; Ecosystem ; Environment ; Lakes/*microbiology ; *Microbial Interactions ; Microbiota/*physiology ; Phylogeny ; Species Specificity ; }, abstract = {Free-living (FL) and particle-attached (PA) bacterial communities play critical roles in nutrient cycles, metabolite production, and as a food source in aquatic systems, and while their community composition, diversity, and functions have been well studied, we know little about their community interactions, co-occurrence patterns, and niche occupancy. In the present study, 13 sites in Taihu Lake were selected to study the differences of co-occurrence patterns and niches occupied between the FL and PA bacterial communities using correlation-based network analysis. The results show that both FL and PA bacterial community networks were non-random and significant differences of the network indexes (average path length, clustering coefficient, modularity) were found between the two groups. Furthermore, the PA bacterial community network consisted of more correlations between fewer OTUs, as well as higher average degree, making it more complex. The results of observed (O) to random (R) ratios of intra- or inter-phyla connections indicate more relationships such as cross-feeding, syntrophic, mutualistic, or competitive relationships in the PA bacterial community network. We also found that four OTUs (OTU00074, OTU00755, OTU00079, and OTU00454), which all had important influences on the nutrients cyclings, played different roles in the two networks as connectors or module hubs. Analysis of the relationships between the module eigengenes and environmental variables demonstrated that bacterial groups of the two networks favored quite different environmental conditions. These findings further confirmed the different ecological functions and niches occupied by the FL and PA bacterial communities in the aquatic ecosystem.}, }
@article {pmid29317508, year = {2018}, author = {Inamine, H and Ellner, SP and Newell, PD and Luo, Y and Buchon, N and Douglas, AE}, title = {Spatiotemporally Heterogeneous Population Dynamics of Gut Bacteria Inferred from Fecal Time Series Data.}, journal = {mBio}, volume = {9}, number = {1}, pages = {}, pmid = {29317508}, issn = {2150-7511}, support = {F32 GM099374/GM/NIGMS NIH HHS/United States ; P30 DK020541/DK/NIDDK NIH HHS/United States ; R01 GM095372/GM/NIGMS NIH HHS/United States ; }, mesh = {Acetobacter/*growth &amp; development ; Animals ; Drosophila melanogaster/*microbiology ; Feces/*microbiology ; Gastrointestinal Tract/microbiology ; Models, Theoretical ; Population Dynamics ; Spatio-Temporal Analysis ; }, abstract = {A priority in gut microbiome research is to develop methods to investigate ecological processes shaping microbial populations in the host from readily accessible data, such as fecal samples. Here, we demonstrate that these processes can be inferred from the proportion of ingested microorganisms that is egested and their egestion time distribution, by using general mathematical models that link within-host processes to statistics from fecal time series. We apply this framework to Drosophila melanogaster and its gut bacterium Acetobacter tropicalis Specifically, we investigate changes in their interactions following ingestion of a food bolus containing bacteria in a set of treatments varying the following key parameters: the density of exogenous bacteria ingested by the flies (low/high) and the association status of the host (axenic or monoassociated with A. tropicalis). At 5 h post-ingestion, ~35% of the intact bacterial cells have transited through the gut with the food bolus and ~10% are retained in a viable and culturable state, leaving ~55% that have likely been lysed in the gut. Our models imply that lysis and retention occur over a short spatial range within the gut when the bacteria are ingested from a low density, but more broadly in the host gut when ingested from a high density, by both gnotobiotic and axenic hosts. Our study illustrates how time series data complement the analysis of static abundance patterns to infer ecological processes as bacteria traverse the host. Our approach can be extended to investigate how different bacterial species interact within the host to understand the processes shaping microbial community assembly.IMPORTANCE A major challenge to our understanding of the gut microbiome in animals is that it is profoundly difficult to investigate the fate of ingested microbial cells as they travel through the gut. Here, we created mathematical tools to analyze microbial dynamics in the gut from the temporal pattern of their abundance in fecal samples, i.e., without direct observation of the dynamics, and validated them with Drosophila fruit flies. Our analyses revealed that over 5 h after ingestion, most bacteria have likely died in the host or have been egested as intact cells, while some living cells have been retained in the host. Bacterial lysis or retention occurred across a larger area of the gut when flies ingest bacteria from high densities than when flies ingest bacteria from low densities. Our mathematical tools can be applied to other systems, including the dynamics of gut microbial populations and communities in humans.}, }
@article {pmid29314490, year = {2018}, author = {Shi, Y and Zhao, X and Zhao, J and Zhang, H and Zhai, Q and Narbad, A and Chen, W}, title = {A mixture of Lactobacillus species isolated from traditional fermented foods promote recovery from antibiotic-induced intestinal disruption in mice.}, journal = {Journal of applied microbiology}, volume = {124}, number = {3}, pages = {842-854}, doi = {10.1111/jam.13687}, pmid = {29314490}, issn = {1365-2672}, support = {BBS/OS/NW/000006/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/administration &amp; dosage/*adverse effects/pharmacology ; Brassica/*microbiology ; Cecum/immunology/microbiology ; Colon/immunology/microbiology ; Cytokines/genetics/immunology ; Fermented Foods/*microbiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Ileum/immunology/microbiology ; Intestinal Diseases/*drug therapy/etiology/immunology/microbiology ; Intestinal Mucosa/metabolism ; Intestines/microbiology ; Lactobacillus/genetics/isolation &amp; purification/*physiology ; Male ; Mice ; Mice, Inbred C57BL ; Probiotics/*administration &amp; dosage ; Tumor Necrosis Factor-alpha/genetics/immunology ; }, abstract = {AIMS: This study evaluated the antibiotic-induced changes in microbial ecology, intestinal dysbiosis and low-grade inflammation; and the combined effect of four different Lactobacillus species on recovery of microbiota composition and improvement of gut barrier function in mice.<br><br>METHODS AND RESULTS: Administration of the antibiotic ampicillin for 2&#xa0;weeks decreased microbial community diversity, induced caecum tumefaction and increased gut permeability in mice. Application of a probiotic cocktail of four Lactobacillus species (JUP-Y4) modulated the microbiota community structure and promoted the abundance of potentially beneficial bacteria such as Akkermansia. Ampicillin administration led to a decline in Bacteroidetes from 46&#xb7;6&#xa0;&#xb1;&#xa0;3&#xb7;91% to 0&#xb7;264&#xa0;&#xb1;&#xa0;0&#xb7;0362%; the addition of JUP-Y4 restored this to 41&#xb7;4&#xa0;&#xb1;&#xa0;2&#xb7;87%. This probiotic supplementation was more effective than natural restoration, where the levels of Bacteroidetes were only restored to 29&#xb7;3&#xa0;&#xb1;&#xa0;2&#xb7;07%. Interestingly, JUP-Y4 treatment was more effective in the restoration of microbiota in faecal samples than in caecal samples. JUP-Y4 also significantly reduced the levels of d-lactate and endotoxin (lipopolysaccharide, LPS) in the serum of mice, and increased the expression of tight-junction proteins while reducing the production of inflammatory cytokines (TNF-&#x3b1;, IL-6, MCP-1, IFN-&#x3b3; and IL-1&#x3b2;) in the ileum and the colon of antibiotic-treated mice.<br><br>CONCLUSIONS: JUP-Y4 not only promoted recovery from antibiotic-induced gut dysbiosis, but also enhanced the function of the gut barrier, reduced inflammation and lowered levels of circulating endotoxin in mice.<br><br>Consumption of a mixture of Lactobacillus species may encourage faster recovery from antibiotic-induced gut dysbiosis and gut microbiota-related immune disturbance.}, }
@article {pmid29314434, year = {2018}, author = {House, GL and Bever, JD}, title = {Disturbance reduces the differentiation of mycorrhizal fungal communities in grasslands along a precipitation gradient.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {28}, number = {3}, pages = {736-748}, doi = {10.1002/eap.1681}, pmid = {29314434}, issn = {1051-0761}, mesh = {*Grassland ; Midwestern United States ; *Mycobiome ; *Mycorrhizae ; Poaceae ; *Rain ; Soil Microbiology ; }, abstract = {Given that mycorrhizal fungi play key roles in shaping plant communities, greater attention should be focused on factors that determine the composition of mycorrhizal fungal communities and their sensitivity to anthropogenic disturbance. We investigate changes in arbuscular mycorrhizal (AM) fungal community composition across a precipitation gradient in North American grasslands as well as changes occurring with varying degrees of site disturbance that have resulted in invasive plant establishment. We find strong differentiation of AM fungal communities in undisturbed remnant grasslands across the precipitation gradient, whereas communities in disturbed grasslands were more homogeneous. These changes in community differentiation with disturbance are consistent with more stringent environmental filtering of AM fungal communities in undisturbed sites that may also be promoted by more rigid functional constraints imposed on AM fungi by the native plant communities in these areas. The AM fungal communities in eastern grasslands were particularly sensitive to anthropogenic disturbance, with disturbed sites having low numbers of AM fungal operational taxonomic units (OTUs) commonly found in undisturbed sites, and also the proliferation of AM fungal OTUs in disturbed sites. This proliferation of AM fungi in eastern disturbed sites coincided with increased soil phosphorus availability and is consistent with evidence suggesting the fungi represented by these OTUs would provide reduced benefits to native plants. The differentiation of AM fungal communities along the precipitation gradient in undisturbed grasslands but not in disturbed sites is consistent with AM fungi aiding plant adaptation to climate, and suggests they may be especially important targets for conservation and restoration in order to help maintain or re-establish diverse grassland plant communities.}, }
@article {pmid29313064, year = {2018}, author = {de Sousa, KCM and do Amaral, RB and Herrera, HM and Santos, FM and Macedo, GC and de Andrade Pinto, PCE and Barros-Battesti, DM and Machado, RZ and André, MR}, title = {Genetic Diversity of Bartonella spp. in Wild Mammals and Ectoparasites in Brazilian Pantanal.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {544-554}, pmid = {29313064}, issn = {1432-184X}, support = {2015/14896-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 473575/2014-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Animal Diseases/*microbiology ; Animals ; Animals, Wild/microbiology ; Bacterial Proteins/genetics ; Bartonella/*classification/*genetics/pathogenicity ; Bartonella Infections/epidemiology/microbiology/*veterinary ; Brazil/epidemiology ; Cytoskeletal Proteins/genetics ; DNA, Bacterial/genetics ; Disease Vectors ; Genes, Bacterial/genetics ; *Genetic Variation ; Genotype ; Mammals/*microbiology ; North America/epidemiology ; Phylogeny ; Rodentia/microbiology ; Siphonaptera/microbiology ; *Wetlands ; }, abstract = {The present work aimed to investigate the genetic diversity of Bartonella in mammals and ectoparasites in Pantanal wetland, Brazil. For this purpose, 31 Nasua nasua, 78 Cerdocyon thous, 7 Leopardus pardalis, 110 wild rodents, 30 marsupials, and 42 dogs were sampled. DNA samples were submitted to a quantitative real-time PCR assay (qPCR). Positive samples in qPCR were submitted to conventional PCR assays targeting other five protein-coding genes. Thirty-five wild rodents and three Polygenis (P.) bohlsi bohlsi flea pools showed positive results in qPCR for Bartonella spp. Thirty-seven out of 38 positive samples in qPCR were also positive in cPCR assays based on ftsZ gene, nine in nuoG-cPCR, and six in gltA-cPCR. Concatenated phylogenetic analyses showed that two main genotypes circulate in rodents and ectoparasites in the studied region. While one of them was closely related to Bartonella spp. previously detected in Cricetidae rodents from North America and Brazil, the other one was related to Bartonella alsatica, Bartonella pachyuromydis, Bartonella birtlesii, Bartonella acomydis, Bartonella silvatica, and Bartonella callosciuri. These results showed that at least two Bartonella genotypes circulate among wild rodents. Additionally, the present study suggests that Polygenis (P.) bohlsi bohlsi fleas could act as possible Bartonella vectors among rodents in Pantanal wetland, Brazil.}, }
@article {pmid29312501, year = {2017}, author = {Lian, Y and Li, Z and Fan, Y and Huang, Q and Chen, J and Liu, W and Xiao, C and Xu, H}, title = {The lncRNA-HOXA-AS2/EZH2/LSD1 oncogene complex promotes cell proliferation in pancreatic cancer.}, journal = {American journal of translational research}, volume = {9}, number = {12}, pages = {5496-5506}, pmid = {29312501}, issn = {1943-8141}, abstract = {Emerging evidence have indicated that long non-coding RNAs (lncRNAs) play crucial roles in cancer development and progression. Previous studies have suggested that lncRNA-HOXA cluster antisense RNA 2 (HOXA-AS2) is involved in tumorigenesis of several cancers. However, little is known about the alteration and biological functions of HOXA-AS2 in pancreatic cancer (PC). The purpose of this study is to identify the role of HOXA-AS2 in PC. Here, we provided evidence that lncRNA HOXA-AS2 was up-regulated in PC tissues. In addition, Loss-of-function experiments revealed that HOXA-AS2 knockdown effectively suppressed proliferation by blocking the cell cycle transition and caused apoptosis of PC cells in vitro and in vivo. Mechanistically, we found that HOXA-AS2 directly interacted with enhancer of zeste homolog 2 (EZH2) and lysine specific demethylase 1 (LSD1), which promoted PC cell growth ability. Collectively, our findings demonstrated that lncRNA-HOXA-AS2/EZH2/LSD1 complex may function as an oncogene in PC cell proliferation, and also provides a potential therapy target for PC.}, }
@article {pmid29312256, year = {2017}, author = {Chen, Z and Zheng, W and Yang, L and Boughner, LA and Tian, Y and Zheng, T and Xu, H}, title = {Lytic and Chemotactic Features of the Plaque-Forming Bacterium KD531 on Phaeodactylum tricornutum.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2581}, pmid = {29312256}, issn = {1664-302X}, abstract = {Phaeodactylum tricornutum is a dominant bloom forming species and potential biofuel feedstock. To control P. tricornutum bloom or to release lipids from P. tricornutum, we previously screened and identified the lytic bacterium Labrenzia sp. KD531 toward P. tricornutum. In the present study, we evaluated the lytic activity of Labrenzia sp. KD531 on microalgae and investigated its lytic mechanism. The results indicated that the lytic activity of KD531 was temperature- and pH-dependent, but light-independent. In addition to P. tricornutum, KD531 also showed lytic activity against other algal species, especially green algae. A quantitative analysis of algal cellular protein, carbohydrate and lipid content together with measurements of dry weight after exposure to bacteria-infected algal lysate indicated that the bacterium KD531 influenced the algal biomass by disrupting the algal cells. Both chemotactic analysis and microscopic observations of subsamples from different regions of formed plaques showed that KD531 could move toward and then directly contact algal cells. Direct contact between P. tricornutum and KD531 cells was essential for the lytic process.}, }
@article {pmid29312221, year = {2017}, author = {Sapers, HM and Ronholm, J and Raymond-Bouchard, I and Comrey, R and Osinski, GR and Whyte, LG}, title = {Biological Characterization of Microenvironments in a Hypersaline Cold Spring Mars Analog.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2527}, pmid = {29312221}, issn = {1664-302X}, abstract = {While many habitable niches on Earth are characterized by permanently cold conditions, little is known about the spatial structure of seasonal communities and the importance of substrate-cell associations in terrestrial cyroenvironments. Here we use the 16S rRNA gene as a marker for genetic diversity to compare two visually distinct but spatially integrated surface microbial mats on Axel Heiberg Island, Canadian high arctic, proximal to a perennial saline spring. This is the first study to describe the bacterial diversity in microbial mats on Axel Heiberg Island. The hypersaline springs on Axel Heiberg represent a unique analog to putative subsurface aquifers on Mars. The Martian subsurface represents the longest-lived potentially habitable environment on Mars and a better understanding of the microbial communities on Earth that thrive in analog conditions will help direct future life detection missions. The microbial mats sampled on Axel Heiberg are only visible during the summer months in seasonal flood plains formed by melt water and run-off from the proximal spring. Targeted-amplicon sequencing revealed that not only does the bacterial composition of the two mat communities differ substantially from the sediment community of the proximal cold spring, but that the mat communities are distinct from any other microbial community in proximity to the Arctic springs studied to date. All samples are dominated by Gammaproteobacteria: Thiotichales is dominant within the spring samples while Alteromonadales comprises a significant component of the mat communities. The two mat samples differ in their Thiotichales:Alteromonadales ratio and contribution of Bacteroidetes to overall diversity. The red mats have a greater proportion of Alteromonadales and Bacteroidetes reads. The distinct bacterial composition of the mat bacterial communities suggests that the spring communities are not sourced from the surface, and that seasonal melt events create ephemerally habitable niches with distinct microbial communities in the Canadian high arctic. The finding that these surficial complex microbial communities exist in close proximity to perennial springs demonstrates the existence of a transiently habitable niche in an important Mars analog site.}, }
@article {pmid29312218, year = {2017}, author = {Waidele, L and Korb, J and Voolstra, CR and Künzel, S and Dedeine, F and Staubach, F}, title = {Differential Ecological Specificity of Protist and Bacterial Microbiomes across a Set of Termite Species.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2518}, pmid = {29312218}, issn = {1664-302X}, abstract = {The gut microbiome of lower termites comprises protists and bacteria that help these insects to digest cellulose and to thrive on wood. The composition of the termite gut microbiome correlates with phylogenetic distance of the animal host and host ecology (diet) in termites collected from their natural environment. However, carryover of transient microbes from host collection sites are an experimental concern and might contribute to the ecological imprints on the termite gut microbiome. Here, we set out to test whether an ecological imprint on the termite gut microbiome remains, when focusing on the persistent microbiome. Therefore, we kept five termite species under strictly controlled dietary conditions and subsequently profiled their protist and bacterial gut microbial communities using 18S and 16S rRNA gene amplicon sequencing. The species differed in their ecology; while three of the investigated species were wood-dwellers that feed on the piece of wood they live in and never leave except for the mating flight, the other two species were foragers that regularly leave their nests to forage for food. Despite these prominent ecological differences, protist microbiome structure aligned with phylogenetic relatedness of termite host species. Conversely, bacterial communities seemed more flexible, suggesting that microbiome structure aligned more strongly with the foraging and wood-dwelling ecologies. Interestingly, protist and bacterial community alpha-diversity correlated, suggesting either putative interactions between protists and bacteria, or that both types of microbes in the termite gut follow shared structuring principles. Taken together, our results add to the notion that bacterial communities are more variable over evolutionary time than protist communities and might react more flexibly to changes in host ecology.}, }
@article {pmid29312205, year = {2017}, author = {Karimi, E and Ramos, M and Gonçalves, JMS and Xavier, JR and Reis, MP and Costa, R}, title = {Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2499}, pmid = {29312205}, issn = {1664-302X}, abstract = {Current knowledge of sponge microbiome functioning derives mostly from comparative analyses with bacterioplankton communities. We employed a metagenomics-centered approach to unveil the distinct features of the Spongia officinalis endosymbiotic consortium in the context of its two primary environmental vicinities. Microbial metagenomic DNA samples (n = 10) from sponges, seawater, and sediments were subjected to Hiseq Illumina sequencing (c. 15 million 100 bp reads per sample). Totals of 10,272 InterPro (IPR) predicted protein entries and 784 rRNA gene operational taxonomic units (OTUs, 97% cut-off) were uncovered from all metagenomes. Despite the large divergence in microbial community assembly between the surveyed biotopes, the S. officinalis symbiotic community shared slightly greater similarity (p < 0.05), in terms of both taxonomy and function, to sediment than to seawater communities. The vast majority of the dominant S. officinalis symbionts (i.e., OTUs), representing several, so-far uncultivable lineages in diverse bacterial phyla, displayed higher residual abundances in sediments than in seawater. CRISPR-Cas proteins and restriction endonucleases presented much higher frequencies (accompanied by lower viral abundances) in sponges than in the environment. However, several genomic features sharply enriched in the sponge specimens, including eukaryotic-like repeat motifs (ankyrins, tetratricopeptides, WD-40, and leucine-rich repeats), and genes encoding for plasmids, sulfatases, polyketide synthases, type IV secretion proteins, and terpene/terpenoid synthases presented, to varying degrees, higher frequencies in sediments than in seawater. In contrast, much higher abundances of motility and chemotaxis genes were found in sediments and seawater than in sponges. Higher cell and surface densities, sponge cell shedding and particle uptake, and putative chemical signaling processes favoring symbiont persistence in particulate matrices all may act as mechanisms underlying the observed degrees of taxonomic connectivity and functional convergence between sponges and sediments. The reduced frequency of motility and chemotaxis genes in the sponge microbiome reinforces the notion of a prevalent mutualistic mode of living inside the host. This study highlights the S. officinalis "endosymbiome" as a distinct consortium of uncultured prokaryotes displaying a likely "sit-and-wait" strategy to nutrient foraging coupled to sophisticated anti-viral defenses, unique natural product biosynthesis, nutrient utilization and detoxification capacities, and both microbe-microbe and host-microbe gene transfer amenability.}, }
@article {pmid29312193, year = {2017}, author = {Schulz-Bohm, K and Martín-Sánchez, L and Garbeva, P}, title = {Microbial Volatiles: Small Molecules with an Important Role in Intra- and Inter-Kingdom Interactions.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2484}, pmid = {29312193}, issn = {1664-302X}, abstract = {During the last decades, research on the function of volatile organic compounds focused primarily on the interactions between plants and insects. However, microorganisms can also release a plethora of volatiles and it appears that microbial volatile organic compounds (mVOCs) can play an important role in intra- and inter-kingdom interactions. So far, most studies are focused on aboveground volatile-mediated interactions and much less information is available about the function of volatiles belowground. This minireview summarizes the current knowledge on the biological functions of mVOCs with the focus on mVOCs-mediated interactions belowground. We pinpointed mVOCs involved in microbe-microbe and microbe-plant interactions, and highlighted the ecological importance of microbial terpenes as a largely underexplored group of mVOCs. We indicated challenges in studying belowground mVOCs-mediated interactions and opportunities for further studies and practical applications.}, }
@article {pmid29657581, year = {2017}, author = {Williams, MR and Stedtfeld, RD and Waseem, H and Stedtfeld, T and Upham, B and Khalife, W and Etchebarne, B and Hughes, M and Tiedje, JM and Hashsham, SA}, title = {Implications of direct amplification for measuring antimicrobial resistance using point-of-care devices.}, journal = {Analytical methods : advancing methods and applications}, volume = {9}, number = {8}, pages = {1229-1241}, pmid = {29657581}, issn = {1759-9660}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, abstract = {Antimicrobial resistance (AMR) is recognized as a global threat to human health. Rapid detection and characterization of AMR is a critical component of most antibiotic stewardship programs. Methods based on amplification of nucleic acids for detection of AMR are generally faster than culture-based approaches but they still require several hours to more than a day due to the need for transporting the sample to a centralized laboratory, processing of sample, and sometimes DNA purification and concentration. Nucleic acids-based point-of-care (POC) devices are capable of rapidly diagnosing antibiotic-resistant infections which may help in making timely and correct treatment decisions. However, for most POC platforms, sample processing for nucleic acids extraction and purification is also generally required prior to amplification. Direct amplification, an emerging possibility for a number of polymerases, has the potential to eliminate these steps without significantly impacting diagnostic performance. This review summarizes direct amplification methods and their implication for rapid measurement of AMR. Future research directions that may further strengthen the possibility of integrating direct amplification methods with POC devices are also summarized.}, }
@article {pmid30602074, year = {2016}, author = {Nemchenko, UM and Rakova, EB and Savelkaieva, MV and Serdiuk, LV and Ivanova, EI and Shabanova, NM and Bukharova, EV}, title = {[The complex evaluation of condition of intestinal and nasopharyngeal microbiocenosis in alumni of children's home].}, journal = {Klinicheskaia laboratornaia diagnostika}, volume = {61}, number = {8}, pages = {508-512}, pmid = {30602074}, issn = {0869-2084}, mesh = {Bifidobacterium/isolation &amp; purification/pathogenicity ; Candida/isolation &amp; purification/pathogenicity ; Child, Orphaned ; Child, Preschool ; Escherichia coli/isolation &amp; purification/pathogenicity ; Feces/*microbiology ; Female ; Humans ; Infant ; Infections/epidemiology/*microbiology/virology ; Intestines/*microbiology/virology ; Male ; Nasopharynx/*microbiology/virology ; Staphylococcus aureus/isolation &amp; purification/pathogenicity ; Streptococcus pneumoniae/isolation &amp; purification/pathogenicity ; Streptococcus pyogenes/isolation &amp; purification/pathogenicity ; }, abstract = {The examination of nasopharyngeal and intestinal microbiocenoses was implemented in orphan children aged 1-3 years residing in children;s home of Cheremkhovo of the Irkutskaia oblast. All children had compromised anamnesis: prematurity, hypotrophy, chicken pox, frequent acute respiratory viral infections, intestinal infections, atopic dermatitis. The study was carried out to comprehensively evaluate conditions of intestinal and nasopharyngeal biotops in children residing in closed children’s institution - children’s home. The microbiological analysis of qualitative and quantitative composition of content of intestine and nasopharynx was implemented according standard techniques. The analysis established in 81.2±6.90% of examined children deficiency of Bifidobacterium flora, decreasing of level of population density of bifidobacteria up to 6.9±1.53% lg KOE/g, in 31.2±8.1% - deficiency of normal colibacillus, in 78.1±7.3% - increased level of opportunistic flora. The analysis also established high rate of isolation of Escherichia coli with decreased enzyme activity and in 28.1±7.9% - Escherichia coli with hemolytic activity. The enterococci were permanent participants of nasopharyngeal and intestinal biotop (58.6±8.7%). From opportunistic flora, in nasopharynx were registered pathogenic streptococci - S.pyogenes, S.pneumonia and also pathogenic fungi Candida andpoly-resistant strains S. aureus. The study results demonstrated characteristics of microbial ecology of intestinal and nasopharyngeal biotops of orphan children in conditions of children institution of closed type where the circulation of pathogenic and opportunistic microorganisms occurs intensively, including strains with high medicinal resistance. All this determines necessity to attribute alumni of children’s homes to risk group of infectious pathology and requires constant micro-ecological monitoring for timely correction of microbiocenoses.}, }
@article {pmid29737112, year = {2016}, author = {Li, HL and Ma, B and Zhang, XL and Zhang, QQ and Guo, XH and Fan, P and Gong, J}, title = {[Diversity of culturable endophytic fungi of common reed (Phragmites australis) in coastal wetland.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {27}, number = {7}, pages = {2066-2074}, doi = {10.13287/j.1001-9332.201607.014}, pmid = {29737112}, issn = {1001-9332}, mesh = {Ascomycota/*classification/isolation &amp; purification ; China ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; Fungi ; *Phylogeny ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Plant Stems/microbiology ; Poaceae/*microbiology ; Salinity ; Soil ; *Wetlands ; }, abstract = {Endophytic fungi play an important ecological role in promoting growth and alleviating environmental stress of host plants. In this study, we investigated the diversity and community composition of endophytic fungi isolated from the common reed in wetlands of the Yellow River Delta. A total of 318 endophytic fungal isolates were obtained from 1350 tissue (leaf, stem, and root) fragments and from three tidal zones with different soil salinity levels. rDNA ITS regions of these isolates were PCR amplified, sequenced, and phylogenetically analyzed. All the sequences were divided into 12 operational taxonomic units (OTUs) at the 98% similarity threshold. Ascomycota was found to be the most abundant flora at the level of the phylum and distributed in all tissues and sites. There were generally richer OTUs in roots than in leaves and stems, and leaves and stems shared the same OTU numbers. All the OTUs retrieved from leaves appeared in roots. The supra tide (low salinity zone) had the most OTUs among the three sampling sites, followed by high tide. Furthermore, the roots had the highest richness and diversity, whereas the leaves had the lowest; supra tide held the highest richness, and the middle tide had the highest diversity. Although unique OTUs could be found in different tissues and tidal zones of different salinity, the communities of culturable endophytic fungi were not substantially different among tissues or tidal zones (ANOSIM, P>0.05). Alternaria sp. was the shared dominant taxa among all samples.}, }
@article {pmid29732830, year = {2016}, author = {Zhang, CJ and He, JZ and Shen, JP}, title = {[Global change field manipulative experiments and their applications in soil microbial ecology.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {27}, number = {5}, pages = {1663-1673}, doi = {10.13287/j.1001-9332.201605.010}, pmid = {29732830}, issn = {1001-9332}, mesh = {Carbon Cycle ; Carbon Dioxide ; *Climate Change ; Ecosystem ; Nitrogen Cycle ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {In recent decades, global climate change is one of the main concerns around the world. Land use change and the high demand for fossil fuel have caused severe consequences of climate change, such as elevated greenhouse gases, warming, and altering precipitation pattern. These combined factors have substantial impacts on ecosystem processes, especially carbon and nitrogen cycles in terrestrial ecosystems. Since the 1970s, a series of field manipulative experiments had been set up to stimulate the influences of monofactorial and/or multifactorial climate changes, improving our understanding of ecosystem response and feedback to global change. In this review, we summarized the development history of global change experiments, and discussed the main issues of using field manipulative experiments in simulating global change. The application of multifactorial experiments, such as CO2 enrichment, warming, precipitation and nitrogen deposition, were highlighted in the research of soil microbial ecology. Moreover, the response and feedback of soil biota as well as the biogeochemical processes that they mediated were further addressed. We also proposed the prospects of their application in global change research to explore the impact of global change on terrestrial ecosystems.}, }
@article {pmid29431321, year = {2016}, author = {Fedichkina, TP and Solenova, LG and Zykova, IE and German, SV and Modestova, AV and Kislitsyn, VA and Rakhmanin, YA and Bobrovnitsky, IP}, title = {[Socio-economic aspects of epidemiology of helicobateriosis].}, journal = {Gigiena i sanitariia}, volume = {95}, number = {9}, pages = {861-864}, pmid = {29431321}, issn = {0016-9900}, mesh = {Conservation of Water Resources/methods/statistics &amp; numerical data ; *Helicobacter Infections/economics/epidemiology/etiology/prevention &amp; control ; Helicobacter pylori/isolation &amp; purification ; Humans ; Mass Screening/*economics ; Moscow/epidemiology ; Needs Assessment ; *Public Health/methods/standards ; Socioeconomic Factors ; Time ; Water Microbiology/*standards ; *Water Supply/methods/standards ; }, abstract = {There are considered special social and economic aspects of the epidemiology of Helicobacter pylori. These aspects acquired the particular importance for the last time due to the fact that the provision of the people with pure water has been becoming the focus of the attention of geopolitical and socio-economic interests in a number of countries. The availability ofpure drinking water serves a marker of the socio-economic state of the territory and the population living there. In Russia where different climatic conditions are deposited by considerable regional differences in the conditions of communal services caused both by various level of the socio-economic development of the territory, the supplementation with pure drinking water serves as the social determinant of the ecological conditions of the population’s life. This particularly has impact on the unfeasible technical state of the water distribution systems, microorganism ecology of which can substantially affect public health. The performed by authors a specialized screening ofpresented at the official web site of the joint-stock company «Mosvodokanal» current data concerning the quality of drinking water consumed by 2500 Moscovites, tested for the Helicobacter pylori infection revealed no deviations from the sanitary standards in the water received by the consumers. Along with that, the comparison of the map documents of the distribution of the Helicobacter pylori infection in Moscow with the distribution of citizens’ complaints of the decline of the quality of tap water has revealed a territorial fastening of the high values of the population infection rate of n^ylori and the urban sites with the greatest number of complaints. In the microbial ecology of water-distribution systems there are tightly aligned problems of their epidemiological safety, technical state and economic damage caused by corrosion as a result of microbiotic activity. In contrast to acute bacterial and viral infections which are deemed of the greatest importance when assessing the sanitary condition of water sources and water-distribution systems, the consequences of infection with H. pylori may not be manifestedfor a long time but some years later they may be manifested as serious chronic diseases (from gastritis to adenocarcinoma of the stomach and a wide range of extraintestinal pathologies), which causes great social and economic losses. Thus, the socio-economic aspect of the epidemiology of helicobacteriosis includes at least two components: the technic - the maintenance of the feasible technic and sanitary state of the water distribution systems and the medico-social - expenditures for screening and treatment of infected patients. In total they are an inseparable part of the prevention of socially-important diseases in the public health system.}, }
@article {pmid30011671, year = {2014}, author = {Bianchi, F and Rossi, EA and Sakamoto, IK and Adorno, MAT and Van de Wiele, T and Sivieri, K}, title = {Beneficial effects of fermented vegetal beverages on human gastrointestinal microbial ecosystem in a simulator.}, journal = {Food research international (Ottawa, Ont.)}, volume = {64}, number = {}, pages = {43-52}, doi = {10.1016/j.foodres.2014.05.072}, pmid = {30011671}, issn = {1873-7145}, abstract = {The aim of this study was to evaluate the effects of four beverage formulations (prebiotic - fructooligosaccharide, probiotic - Lactobacillus casei Lc-01, synbiotic - fructooligosaccharide and L. casei Lc-01 and placebo) based on aqueous extracts of soy and quinoa, towards the human intestinal microbiota using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®), a dynamic model of the human gut. To monitor the effects on microbial community composition, plate counts on specific growth media and a PCR-DGGE analysis were performed on samples from all colon compartments - ascending, transverse and descending. To verify the effects on microbial metabolism, we analyzed the ammonium and short chain fatty acids (SCFAs) concentrations. The synbiotic beverage showed the best microbiological results in the ascending colon compartment, stimulating the growth of Lactobacillus spp. and Bifidobacterium spp., and reducing Clostridium spp., Bacteroides spp., enterobacteria and Enterococcus spp. populations in this compartment. A larger reduction (p<0.05) of ammonia ions in the ascending colon was observed during the synbiotic beverage treatment. No statistical difference was observed in SCFA production among the treatments and the basal period. Plate count and DGGE analysis showed the survival of L. casei Lc-01 in the colon. DGGE analysis also showed higher richness and diversity of the Lactobacillus spp. community during the treatment with synbiotic beverage, with higher accentuation in the ascending colon.}, }
@article {pmid29312154, year = {2017}, author = {Etchebarne, BE and Li, Z and Stedtfeld, RD and Nicholas, MC and Williams, MR and Johnson, TA and Stedtfeld, TM and Kostic, T and Khalife, WT and Tiedje, JM and Hashsham, SA and Hughes, MJ}, title = {Evaluation of Nucleic Acid Isothermal Amplification Methods for Human Clinical Microbial Infection Detection.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2211}, pmid = {29312154}, issn = {1664-302X}, abstract = {Battling infection is a major healthcare objective. Untreated infections can rapidly evolve toward the condition of sepsis in which the body begins to fail and resuscitation becomes critical and tenuous. Identification of infection followed by rapid antimicrobial treatment are primary goals of medical care, but precise identification of offending organisms by current methods is slow and broad spectrum empirical therapy is employed to cover most potential pathogens. Current methods for identification of bacterial pathogens in a clinical setting typically require days of time, or a 4- to 8-h growth phase followed by DNA extraction, purification and PCR-based amplification. We demonstrate rapid (70-120 min) genetic diagnostics methods utilizing loop-mediated isothermal amplification (LAMP) to test for 15 common infection pathogen targets, called the Infection Diagnosis Panel (In-Dx). The method utilizes filtration to rapidly concentrate bacteria in sample matrices with lower bacterial loads and direct LAMP amplification without DNA purification from clinical blood, urine, wound, sputum and stool samples. The In-Dx panel was tested using two methods of detection: (1) real-time thermocycler fluorescent detection of LAMP amplification and (2) visual discrimination of color change in the presence of Eriochrome Black T (EBT) dye following amplification. In total, 239 duplicate samples were collected (31 blood, 122 urine, 73 mucocutaneous wound/swab, 11 sputum and two stool) from 229 prospectively enrolled hospital patients with suspected clinical infection and analyzed both at the hospital and by In-Dx. Sensitivity (Se) of the In-Dx panel targets pathogens from urine samples by In-Dx was 91.1% and specificity (Sp) was 97.3%, with a positive predictive value (PPV) of 53.7% and a negative predictive value (NPV) of 99.7% as compared to clinical microbial detection methods. Sensitivity of detection of the In-Dx panel from mucocutaneous swab samples was 65.5% with a Sp of 99.3%, and a PPV of 84% and NPV of 98% as compared to clinical microbial detection methods. Results indicate the LAMP-based In-Dx panel allows rapid and precise diagnosis of clinical infections by targeted pathogens across multiple culture types for point-of-care utilization.}, }
@article {pmid29312153, year = {2017}, author = {Hinchliffe, G and Bollard-Breen, B and Cowan, DA and Doshi, A and Gillman, LN and Maggs-Kolling, G and de Los Rios, A and Pointing, SB}, title = {Advanced Photogrammetry to Assess Lichen Colonization in the Hyper-Arid Namib Desert.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2083}, pmid = {29312153}, issn = {1664-302X}, abstract = {The hyper-arid central region of the Namib Desert is characterized by quartz desert pavement terrain that is devoid of vascular plant covers. In this extreme habitat the only discernible surface covers are epilithic lichens that colonize exposed surfaces of quartz rocks. These lichens are highly susceptible to disturbance and so field surveys have been limited due to concerns about disturbing this unusual desert feature. Here we present findings that illustrate how non-destructive surveys based upon advanced photogrammetry techniques can yield meaningful and novel scientific data on these lichens. We combined 'structure from motion analysis,' computer vision and GIS to create 3-dimensional point clouds from two-dimensional imagery. The data were robust in its application to estimating absolute lichen cover. An orange Stellarangia spp. assemblage had coverage of 22.8% of available substrate, whilst for a black Xanthoparmelia spp. assemblage coverage was markedly lower at 0.6% of available substrate. Hyperspectral signatures for both lichens were distinct in the near-infra red range indicating that Xanthoparmelia spp. was likely under relatively more moisture stress than Stellarangia spp. at the time of sampling, and we postulate that albedo effects may have contributed to this in the black lichen. Further transformation of the data revealed a colonization preference for west-facing quartz surfaces and this coincides with prevailing winds for marine fog that is the major source of moisture in this system. Furthermore, a three-dimensional 'fly through' of the lichen habitat was created to illustrate how the application of computer vision in microbiology has further potential as a research and education tool. We discuss how advanced photogrammetry could be applied in astrobiology using autonomous rovers to add quantitative ecological data for visible surface colonization on the surface of Mars.}, }
@article {pmid29311639, year = {2018}, author = {Segobola, J and Adriaenssens, E and Tsekoa, T and Rashamuse, K and Cowan, D}, title = {Exploring Viral Diversity in a Unique South African Soil Habitat.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {111}, pmid = {29311639}, issn = {2045-2322}, mesh = {Bacteriophages/classification/genetics ; *Biodiversity ; Computational Biology/methods ; Genome, Viral ; Metagenome ; Metagenomics/methods ; Phylogeny ; *Soil Microbiology ; South Africa ; Viruses/*classification/genetics/ultrastructure ; }, abstract = {The Kogelberg Biosphere Reserve in the Cape Floral Kingdom in South Africa is known for its unique plant biodiversity. The potential presence of unique microbial and viral biodiversity associated with this unique plant biodiversity led us to explore the fynbos soil using metaviromic techniques. In this study, metaviromes of a soil community from the Kogelberg Biosphere Reserve has been characterised in detail for the first time. Metaviromic DNA was recovered from soil and sequenced by Next Generation Sequencing. The MetaVir, MG-RAST and VIROME bioinformatics pipelines were used to analyse taxonomic composition, phylogenetic and functional assessments of the sequences. Taxonomic composition revealed members of the order Caudovirales, in particular the family Siphoviridae, as prevalent in the soil samples and other compared viromes. Functional analysis and other metaviromes showed a relatively high frequency of phage-related and structural proteins. Phylogenetic analysis of PolB, PolB2, terL and T7gp17 genes indicated that many viral sequences are closely related to the order Caudovirales, while the remainder were distinct from known isolates. The use of single virome which only includes double stranded DNA viruses limits this study. Novel phage sequences were detected, presenting an opportunity for future studies aimed at targeting novel genetic resources for applied biotechnology.}, }
@article {pmid29307025, year = {2018}, author = {Li, T and Hu, Y and Zhang, B and Yang, X}, title = {Role of Fungi in the Formation of Patinas on Feilaifeng Limestone, China.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {352-361}, pmid = {29307025}, issn = {1432-184X}, support = {21643018//National Natural Science Foundation of China/ ; 2015013//protection of cultural relics by the Cultural Relics Bureau of Zhejiang province/ ; }, mesh = {Animals ; Calcium Carbonate/chemistry/*metabolism ; Calcium Oxalate ; China ; Construction Materials ; Crystallization ; Fungi/classification/genetics/isolation &amp; purification/*metabolism ; Microscopy, Electron, Scanning ; *Soil Microbiology ; X-Ray Diffraction ; }, abstract = {Feilaifeng is a cultural heritage site that contains unique Buddhist statues which date back to the Five Dynasties period (907 AD-960 AD). The site was inscribed on world heritage list by UNESCO in 2011. Various patinas, which may be caused by fungi, have covered the surface of the limestone and have severely diminished the esthetic value of the statues and altered the limestone structure. Culture-dependent method was used to isolate and identify the fungi. After incubation on modified B4 medium, the calcifying fungi were identified by optical microscopy and scanning electron microscopy combined with X-ray energy-dispersive analysis. Aspergillus, Penicillium, and Colletotrichum were observed as the biomineralizing fungi. X-ray diffraction showed that the patina consisted of calcite (CaCO3), but the crystals synthesized by the identified fungi were whewellite (CaC2O4·H2O) for Aspergillus and Penicillium, and vaterite (CaCO3) for Colletotrichum. In addition, the metabolites of Colletotrichum suppressed the transformation of vaterite to calcite, but Mg[2+] could inhibit the function of the metabolites. The different crystal form between the patina and the products of fungi may suggest two different pathways of patina formation and provide important reference data for studies of the mechanisms of biomineralization, cleaning of the patina, and protection of the Feilaifeng statues.}, }
@article {pmid29306554, year = {2018}, author = {Pratama, AA and van Elsas, JD}, title = {The 'Neglected' Soil Virome - Potential Role and Impact.}, journal = {Trends in microbiology}, volume = {26}, number = {8}, pages = {649-662}, doi = {10.1016/j.tim.2017.12.004}, pmid = {29306554}, issn = {1878-4380}, mesh = {Aquatic Organisms/*classification/genetics/*isolation &amp; purification ; Bacteriophages/*classification/genetics/*isolation &amp; purification ; Ecosystem ; Soil ; *Soil Microbiology ; *Water Microbiology ; }, abstract = {Bacteriophages are among the most abundant and diverse biological units in the biosphere. They have contributed to our understanding of the central dogma of biology and have been instrumental in the evolutionary success of bacterial pathogens. In contrast to our current understanding of marine viral communities, the soil virome and its function in terrestrial ecosystems has remained relatively understudied. Here, we examine, in a comparative fashion, the knowledge gathered from studies performed in soil versus marine settings. We address the information with respect to the abundance, diversity, ecological significance, and effects of, in particular, bacteriophages on their host's evolutionary trajectories. We also identify the main challenges that soil virology faces and the studies that are required to accompany the current developments in marine settings.}, }
@article {pmid29306132, year = {2018}, author = {Ye, J and Liang, J and Wang, L and Markou, G and Jia, Q}, title = {Operation optimization of a photo-sequencing batch reactor for wastewater treatment: Study on influencing factors and impact on symbiotic microbial ecology.}, journal = {Bioresource technology}, volume = {252}, number = {}, pages = {7-13}, doi = {10.1016/j.biortech.2017.12.086}, pmid = {29306132}, issn = {1873-2976}, mesh = {Bacteria ; Bioreactors ; Microalgae ; *Waste Disposal, Fluid ; *Wastewater ; }, abstract = {Wastewater treatment technology with better energy efficiency and recyclability is in urgent demand. Photo-Sequencing batch reactor (SBR), which introduces microalgae into conventional SBR, is considered to have more potential for resource recycling. In this study, a photo-SBR was evaluated through the manipulation of several key operational parameters, i.e., aeration strength, light supply intensity and time per cycle, and solid retention time (SRT). The algal-bacterial symbiotic system had the potential of removing COD, NH4[+]-N and TN with limited aeration, representing the advantage of energy-saving by low aeration requirement. Maintaining appropriate proportion of microalgae in the symbiotic system is critical for good system performance. Introducing microalgae into conventional SBR has obvious impact on the original microbial ecology. When the concentration of microalgae is too high (>4.60 mg Chl/L), the inhibition on certain phyla of bacteria, e.g., Bacteroidetes and Actinobacteria, would become prominent and not conducive to the stable operation.}, }
@article {pmid29305629, year = {2018}, author = {Solon, AJ and Vimercati, L and Darcy, JL and Arán, P and Porazinska, D and Dorador, C and Farías, ME and Schmidt, SK}, title = {Microbial Communities of High-Elevation Fumaroles, Penitentes, and Dry Tephra "Soils" of the Puna de Atacama Volcanic Zone.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {340-351}, pmid = {29305629}, issn = {1432-184X}, support = {DEB-1258160//National Science Foundation/ ; FA9550-14-1-0006//Air Force Office of Scientific Research/ ; }, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; Biodiversity ; Chile ; Cluster Analysis ; Computational Biology ; Cyanobacteria/classification ; Desert Climate ; Exobiology ; *Extreme Environments ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil ; *Soil Microbiology ; Temperature ; }, abstract = {The aim of this study was to understand the spatial distribution of microbial communities (18S and 16S rRNA genes) across one of the harshest terrestrial landscapes on Earth. We carried out Illumina sequencing using samples from two expeditions to the high slopes (up to 6050 m.a.s.l.) of Volcán Socompa and Llullaillaco to describe the microbial communities associated with the extremely dry tephra compared to areas that receive water from fumaroles and ice fields made up of nieves penitentes. There were strong spatial patterns relative to these landscape features with the most diverse (alpha diversity) communities being associated with fumaroles. Penitentes did not significantly increase alpha diversity compared to dry tephra at the same elevation (5825 m.a.s.l.) on Volcán Socompa, but the structure of the 18S community (beta diversity) was significantly affected by the presence of penitentes on both Socompa and Llullaillaco. In addition, the 18S community was significantly different in tephra wetted by penitentes versus dry tephra sites across many elevations on Llullaillaco. Traditional phototrophs (algae and cyanobacteria) were abundant in wetter tephra associated with fumaroles, and algae (but not cyanobacteria) were common in tephra associated with penitentes. Dry tephra had neither algae nor cyanobacteria but did host potential phototrophs in the Rhodospirillales on Volcán Llullaillaco, but not on Socompa. These results provide new insights into the distribution of microbes across one of the most extreme terrestrial environments on Earth and provide the first ever glimpse of life associated with nieves penitentes, spire-shaped ice structures that are widespread across the mostly unexplored high-elevation Andean Central Volcanic Zone.}, }
@article {pmid29305503, year = {2018}, author = {Weidhaas, J and Anderson, A and Jamal, R}, title = {Elucidating Waterborne Pathogen Presence and Aiding Source Apportionment in an Impaired Stream.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {6}, pages = {}, pmid = {29305503}, issn = {1098-5336}, mesh = {Bacteria/genetics/*isolation &amp; purification ; Conservation of Water Resources ; Environmental Monitoring/*methods ; Feces/microbiology/parasitology/virology ; Lobosea/genetics/*isolation &amp; purification ; Rivers/*microbiology/*parasitology/virology ; Sewage/*analysis ; Viruses/genetics/*isolation &amp; purification ; West Virginia ; }, abstract = {Fecal indicator bacteria (FIB) are the basis for water quality regulations and are considered proxies for waterborne pathogens when conducting human health risk assessments. The direct detection of pathogens in water and simultaneous identification of the source of fecal contamination are possible with microarrays, circumventing the drawbacks to FIB approaches. A multigene target microarray was used to assess the prevalence of waterborne pathogens in a fecally impaired mixed-use watershed. The results indicate that fecal coliforms have improved substantially in the watershed since its listing as a 303(d) impaired stream in 2002 and are now near United States recreational water criterion standards. However, waterborne pathogens are still prevalent in the watershed, as viruses (bocavirus, hepatitis E and A viruses, norovirus, and enterovirus G), bacteria (Campylobacter spp., Clostridium spp., enterohemorrhagic and enterotoxigenic Escherichia coli, uropathogenic E. coli, Enterococcus faecalis, Helicobacter spp., Salmonella spp., and Vibrio spp.), and eukaryotes (Acanthamoeba spp., Entamoeba histolytica, and Naegleria fowleri) were detected. A comparison of the stream microbial ecology with that of sewage, cattle, and swine fecal samples revealed that human sources of fecal contamination dominate in the watershed. The methodology presented is applicable to a wide range of impaired streams for the identification of human health risk due to waterborne pathogens and for the identification of areas for remediation efforts.IMPORTANCE The direct detection of waterborne pathogens in water overcomes many of the limitations of the fecal indicator paradigm. Furthermore, the identification of the source of fecal impairment aids in identifying areas for remediation efforts. Multitarget gene microarrays are shown to simultaneously identify waterborne pathogens and aid in determining the sources of impairment, enabling further focused investigations. This study shows the use of this methodology in a historically impaired watershed in which total maximum daily load reductions have been successfully implemented to reduce risk. The results suggest that while the fecal indicators have been reduced more than 96% and are nearing recreational water criterion levels, pathogens are still detectable in the watershed. Microbial source tracking results show that additional remediation efforts are needed to reduce the impact of human sewage in the watershed.}, }
@article {pmid29305502, year = {2018}, author = {Rodriguez-R, LM and Castro, JC and Kyrpides, NC and Cole, JR and Tiedje, JM and Konstantinidis, KT}, title = {How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity?.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {6}, pages = {}, pmid = {29305502}, issn = {1098-5336}, mesh = {Bacteria/*classification/genetics ; *Genome, Bacterial ; *Microbiota ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, RNA/*methods ; }, abstract = {The most common practice in studying and cataloguing prokaryotic diversity involves the grouping of sequences into operational taxonomic units (OTUs) at the 97% 16S rRNA gene sequence identity level, often using partial gene sequences, such as PCR-generated amplicons. Due to the high sequence conservation of rRNA genes, organisms belonging to closely related yet distinct species may be grouped under the same OTU. However, it remains unclear how much diversity has been underestimated by this practice. To address this question, we compared the OTUs of genomes defined at the 97% or 98.5% 16S rRNA gene identity level against OTUs of the same genomes defined at the 95% whole-genome average nucleotide identity (ANI), which is a much more accurate proxy for species. Our results show that OTUs resulting from a 98.5% 16S rRNA gene identity cutoff are more accurate than 97% compared to 95% ANI (90.5% versus 89.9% accuracy) but indistinguishable from any other threshold in the 98.29 to 98.78% range. Even with the more stringent thresholds, however, the 16S rRNA gene-based approach commonly underestimates the number of OTUs by ∼12%, on average, compared to the ANI-based approach (∼14% underestimation when using the 97% identity threshold). More importantly, the degree of underestimation can become 50% or more for certain taxa, such as the genera Pseudomonas, Burkholderia, Escherichia, Campylobacter, and Citrobacter These results provide a quantitative view of the degree of underestimation of extant prokaryotic diversity by 16S rRNA gene-defined OTUs and suggest that genomic resolution is often necessary.IMPORTANCE Species diversity is one of the most fundamental pieces of information for community ecology and conservational biology. Therefore, employing accurate proxies for what a species or the unit of diversity is are cornerstones for a large set of microbial ecology and diversity studies. The most common proxies currently used rely on the clustering of 16S rRNA gene sequences at some threshold of nucleotide identity, typically 97% or 98.5%. Here, we explore how well this strategy reflects the more accurate whole-genome-based proxies and determine the frequency with which the high conservation of 16S rRNA sequences masks substantial species-level diversity.}, }
@article {pmid29304850, year = {2018}, author = {Liu, YF and Galzerani, DD and Mbadinga, SM and Zaramela, LS and Gu, JD and Mu, BZ and Zengler, K}, title = {Metabolic capability and in situ activity of microorganisms in an oil reservoir.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {5}, pmid = {29304850}, issn = {2049-2618}, support = {41530318//National Natural Science Foundation of China/International ; 41373070//National Natural Science Foundation of China/International ; 41373070//National Natural Science Foundation of China/International ; 41161160560//NSFC/RGC Joint Research Fund/International ; 201011/2014-0//CNPq under the Brazilian Scientific Mobility Program, Ci&#xea;ncias sem Fronteiras/International ; DE-SC0012586//Biological and Environmental Research (US)/International ; }, mesh = {Acinetobacter/classification/genetics/isolation &amp; purification ; Archaea/*classification/genetics/isolation &amp; purification ; Archaeoglobus/classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Bacterial Proteins/genetics ; China ; Gene Expression Profiling/*methods ; Metabolic Networks and Pathways ; Metagenomics/*methods ; Methanosarcinales/classification/genetics/isolation &amp; purification ; Oil and Gas Fields/*microbiology ; Phylogeny ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; }, abstract = {BACKGROUND: Microorganisms have long been associated with oxic and anoxic degradation of hydrocarbons in oil reservoirs and oil production facilities. While we can readily determine the abundance of microorganisms in the reservoir and study their activity in the laboratory, it has been challenging to resolve what microbes are actively participating in crude oil degradation in situ and to gain insight into what metabolic pathways they deploy.<br><br>RESULTS: Here, we describe the metabolic potential and in situ activity of microbial communities obtained from the Jiangsu Oil Reservoir (China) by an integrated metagenomics and metatranscriptomics approach. Almost complete genome sequences obtained by differential binning highlight the distinct capability of different community members to degrade hydrocarbons under oxic or anoxic condition. Transcriptomic data delineate active members of the community and give insights that Acinetobacter species completely oxidize alkanes into carbon dioxide with the involvement of oxygen, and Archaeoglobus species mainly ferment alkanes to generate acetate which could be consumed by Methanosaeta species. Furthermore, nutritional requirements based on amino acid and vitamin auxotrophies suggest a complex network of interactions and dependencies among active community members that go beyond classical syntrophic exchanges; this network defines community composition and microbial ecology in oil reservoirs undergoing secondary recovery.<br><br>CONCLUSION: Our data expand current knowledge of the metabolic potential and role in hydrocarbon metabolism of individual members of thermophilic microbial communities from an oil reservoir. The study also reveals potential metabolic exchanges based on vitamin and amino acid auxotrophies indicating the presence of complex network of interactions between microbial taxa within the community.}, }
@article {pmid29299771, year = {2018}, author = {Poli, A and Romano, I and Mastascusa, V and Buono, L and Orlando, P and Nicolaus, B and Leone, L and Hong, KW and Chan, KG and Goh, KM and Pascual, J}, title = {Vibrio coralliirubri sp. nov., a new species isolated from mucus of red coral (Corallium rubrum) collected at Procida island, Italy.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {7}, pages = {1105-1115}, doi = {10.1007/s10482-017-1013-5}, pmid = {29299771}, issn = {1572-9699}, support = {Supporto tecnico gestionale in vista della Convenzione CITES sul Corallo Rosso mediterraneo e criteri di distinzione da altre specie di Corallo//the Italian Ministry of Environment Territory and Sea/ ; A-000001-50001//University of Malaya via High Impact Research Grants/ ; H-50001-A000027//the University of Malaya via High Impact Research Grants/ ; 09H98//Universiti Teknologi Malaysia GUP/ ; }, mesh = {Animals ; Anthozoa/*microbiology ; Bacterial Proteins/genetics ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Fatty Acids/chemistry/metabolism ; Italy ; Mucus/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Vibrio/classification/genetics/*isolation &amp; purification/metabolism ; }, abstract = {Strain Corallo1[T] was isolated from mucus of red coral (Corallium rubrum) at Punta Pizzaco (Procida island, Naples, Italy). It was characterised as a Gram-stain negative, motile, rod-shaped bacterium. Strain Corallo1[T] was found to show positive responses for cytochrome-c oxidase, catalase, reduction of nitrate and nitrite, β-galactosidase activity and hydrolysis of starch, xylan, peptone, Tween 40, Tween 80 and casein. Strain Corallo1[T] was found to be mesophilic, neutrophilic to alkalophilic and slightly halophilic. According to analysis of the almost-complete 16S rRNA gene, strain Corallo1[T] is closely related to Vibrio celticus (100% sequence similarity), Vibrio gigantis (100%), Vibrio crassostreae (99.7%), Vibrio artabrorum (99.7%) and Vibrio pomeroyi (99.6%). MLSA of five housekeeping genes (atpA, pyrH, recA, rpoA and rpoD) was performed to refine the phylogenetic relationships of strain Corallo1[T]. A draft genome sequence of strain Corallo1[T] was obtained. The DNA G+C content of this strain was determined to be 44.5 mol %. The major cellular fatty acids of strain Corallo1[T] are C16:1, n-C16:0 and C18:1, and the major isoprenoid ubiquinone is Q8. ANI indexes, in silico estimations of DDH values and wet lab DDH values demonstrated that strain Corallo1[T] represents an independent genomospecies. Based on a polyphasic taxonomic characterisation, strain Corallo1[T] is concluded to represent a novel species of the genus Vibrio, for which the name Vibrio coralliirubri sp. nov. is proposed. The type strain is Corallo1[T] (= DSM 27495[T] = CIP 110630[T]).}, }
@article {pmid29299617, year = {2018}, author = {Deignan, LK and Pawlik, JR and Erwin, PM}, title = {Agelas Wasting Syndrome Alters Prokaryotic Symbiont Communities of the Caribbean Brown Tube Sponge, Agelas tubulata.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {459-466}, pmid = {29299617}, issn = {1432-184X}, support = {OCE-0095724//National Science Foundation/ ; OCE-0550468//National Science Foundation/ ; OCE-1029515//National Science Foundation/ ; OCE-1558580//National Science Foundation/ ; OCE-1558580//National Science Foundation/ ; }, mesh = {Agelas/*microbiology ; Animal Diseases/*microbiology ; Animals ; Archaea/classification/physiology ; Bacteria/classification ; Bacterial Physiological Phenomena ; Cachexia ; Caribbean Region ; Chloroflexi/physiology ; *Dysbiosis ; Florida ; Gammaproteobacteria/physiology ; Microbiota ; Phylogeny ; Porifera/microbiology ; Prokaryotic Cells/*physiology ; Proteobacteria/physiology ; Seawater/microbiology ; *Symbiosis ; Wasting Syndrome/epidemiology/*microbiology ; }, abstract = {The brown tube sponge Agelas tubulata (cf. Agelas conifera) is an abundant and long-lived sponge on Caribbean reefs. Recently, a disease-like condition, Agelas wasting syndrome (AWS), was described from A. tubulata in the Florida Keys, where prevalence of the syndrome increased from 7 to 35% of the sponge population between 2010 and 2015. In this study, we characterized the prokaryotic symbiont community of A. tubulata for the first time from individuals collected within the same monitoring plots where AWS was described. We also sampled tissue from A. tubulata exhibiting symptoms of AWS to determine its effect on the diversity and structure of prokaryotic symbiont communities. Bacteria from the phyla Chloroflexi and Proteobacteria, particularly the class Gammaproteobacteria, dominated the sponge microbiome in tissue samples of both healthy sponges and those exhibiting AWS. Prokaryotic community structure differed significantly between the diseased and healthy sponge samples, with greater variability among communities in diseased samples compared to healthy samples. These differences in prokaryotic community structure included a shift in relative abundance of the dominant, ammonia-oxidizing (Thaumarchaeota) symbionts present in diseased and healthy sponge samples. Further research is required to determine the functional consequences of this shift in microbial community structure and the causal relationship of dysbiosis and sponge disease in A. tubulata.}, }
@article {pmid29298729, year = {2018}, author = {Marasco, R and Rolli, E and Fusi, M and Michoud, G and Daffonchio, D}, title = {Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {3}, pmid = {29298729}, issn = {2049-2618}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Microbiota ; Phylogeny ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/*genetics ; Rhizosphere ; Sequence Analysis, DNA/*methods ; Soil Microbiology ; Vitis/*microbiology ; }, abstract = {BACKGROUND: The plant compartments of Vitis vinifera, including the rhizosphere, rhizoplane, root endosphere, phyllosphere and carposphere, provide unique niches that drive specific bacterial microbiome associations. The majority of phyllosphere endophytes originate from the soil and migrate up to the aerial compartments through the root endosphere. Thus, the soil and root endosphere partially define the aerial endosphere in the leaves and berries, contributing to the terroir of the fruit. However, V. vinifera cultivars are invariably grafted onto the rootstocks of other Vitis species and hybrids. It has been hypothesized that the plant species determines the microbiome of the root endosphere and, as a consequence, the aerial endosphere. In this work, we test the first part of this hypothesis. We investigate whether different rootstocks influence the bacteria selected from the surrounding soil, affecting the bacterial diversity and potential functionality of the rhizosphere and root endosphere.<br><br>METHODS: Bacterial microbiomes from both the root tissues and the rhizosphere of Barbera cultivars, both ungrafted and grafted on four different rootstocks, cultivated in the same soil from the same vineyard, were characterized by 16S rRNA high-throughput sequencing. To assess the influence of the root genotype on the bacterial communities' recruitment in the root system, (i) the phylogenetic diversity coupled with the predicted functional profiles and (ii) the co-occurrence bacterial networks were determined. Cultivation-dependent approaches were used to reveal the plant-growth promoting (PGP) potential associated with the grafted and ungrafted root systems.<br><br>RESULTS: Richness, diversity and bacterial community networking in the root compartments were significantly influenced by the rootstocks. Complementary to a shared bacterial microbiome, different subsets of soil bacteria, including those endowed with PGP traits, were selected by the root system compartments of different rootstocks. The interaction between the root compartments and the rootstock exerted a unique selective pressure that enhanced niche differentiation, but rootstock-specific bacterial communities were still recruited with conserved PGP traits.<br><br>CONCLUSION: While the rootstock significantly influences the taxonomy, structure and network properties of the bacterial community in grapevine roots, a homeostatic effect on the distribution of the predicted and potential functional PGP traits was found.}, }
@article {pmid29298101, year = {2018}, author = {Korpela, K}, title = {Diet, Microbiota, and Metabolic Health: Trade-Off Between Saccharolytic and Proteolytic Fermentation.}, journal = {Annual review of food science and technology}, volume = {9}, number = {}, pages = {65-84}, doi = {10.1146/annurev-food-030117-012830}, pmid = {29298101}, issn = {1941-1413}, mesh = {Colon/*metabolism ; *Diet ; Dietary Carbohydrates/*metabolism ; *Fermentation ; *Gastrointestinal Microbiome ; Humans ; *Proteolysis ; }, abstract = {The intestinal microbiota have emerged as a central regulator of host metabolism and immune function, mediating the effects of diet on host health. However, the large diversity and individuality of the gut microbiota have made it difficult to draw conclusions about microbiota responses to dietary interventions. In the light of recent research, certain general patterns are emerging, revealing how the ecology of the gut microbiota profoundly depends on the quality and quantity of dietary carbohydrates and proteins. In this review, I provide an overview of the dependence of microbial ecology in the human colon on diet and how the effects of diet on host health depend partially on the microbiota. Understanding how the individual-specific microbiota respond to short- and long-term dietary changes and how they influence host energy homeostasis will enable targeted interventions to achieve specific outcomes, such as weight loss in obesity or weight gain in malnutrition.}, }
@article {pmid29297591, year = {2018}, author = {Op De Beeck, M and Troein, C and Peterson, C and Persson, P and Tunlid, A}, title = {Fenton reaction facilitates organic nitrogen acquisition by an ectomycorrhizal fungus.}, journal = {The New phytologist}, volume = {218}, number = {1}, pages = {335-343}, pmid = {29297591}, issn = {1469-8137}, mesh = {Agaricales/*metabolism ; Aspartic Acid/metabolism ; Fungal Proteins/metabolism ; Hydrogen Peroxide/*metabolism ; Hydroxyl Radical/metabolism ; Iron/*metabolism ; Models, Biological ; Mycorrhizae/*metabolism ; Nitrogen/*metabolism ; Organic Chemicals/*metabolism ; Oxidation-Reduction ; Proteolysis ; }, abstract = {Boreal trees rely on their ectomycorrhizal fungal symbionts to acquire growth-limiting nutrients, such as nitrogen (N), which mainly occurs as proteins complexed in soil organic matter (SOM). The mechanisms for liberating this N are unclear as ectomycorrhizal fungi have lost many genes encoding lignocellulose-degrading enzymes present in their saprotrophic ancestors. We hypothesized that hydroxyl radicals ([˙] OH), produced by the ectomycorrhizal fungus Paxillus involutus during growth on SOM, are involved in liberating organic N. Paxillus involutus was grown for 7 d on N-containing or N-free substrates that represent major organic compounds of SOM. [˙] OH production, ammonium assimilation, and proteolytic activity were measured daily. [˙] OH production was strongly induced when P. involutus switched from ammonium to protein as the main N source. Extracellular proteolytic activity was initiated shortly after the oxidation. Oxidized protein substrates induced higher proteolytic activity than unmodified proteins. Dynamic modeling predicted that [˙] OH production occurs in a burst, regulated mainly by ammonium and ferric iron concentrations. We propose that the production of [˙] OH and extracellular proteolytic enzymes are regulated by similar nutritional signals. Oxidation works in concert with proteolysis, improving N liberation from proteins in SOM. Organic N mining by ectomycorrhizal fungi has, until now, only been attributed to proteolysis.}, }
@article {pmid29295915, year = {2018}, author = {McLaren, MR and Callahan, BJ}, title = {In Nature, There Is Only Diversity.}, journal = {mBio}, volume = {9}, number = {1}, pages = {}, pmid = {29295915}, issn = {2150-7511}, mesh = {*Metagenomics ; *RNA, Ribosomal, 16S ; }, abstract = {Microbial ecology has been transformed by the advent of high-throughput marker gene and metagenomic sequencing methods. These tools provide expansive descriptions of microbial communities, but the descriptions are framed in terms of molecular objects, such as 97% ribosomal operational taxonomic units (OTUs), rather than biological objects, such as species. A recent study by A. B. Chase and colleagues (mBio 8:e01809-17, 2017, https://doi.org/10.1128/mBio.01809-17) explores the so-called microdiversity within the Curtobacterium OTU, the most abundant OTU in a leaf litter community. Perhaps unsurprisingly, they find that some important ecologic traits, such as drought response, are coherent within the OTU, but that others vary significantly. Here we discuss their findings in relation to the more general issue of how molecular tools can be effectively used to study microbial ecology. We specifically note the need for investigators to choose the right molecular methods for their biological problem, as nature does not respect the limitations and conventions associated with our methods.}, }
@article {pmid29293959, year = {2018}, author = {Liang, Z and Siegert, M and Fang, W and Sun, Y and Jiang, F and Lu, H and Chen, GH and Wang, S}, title = {Blackening and odorization of urban rivers: a bio-geochemical process.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {3}, pages = {}, doi = {10.1093/femsec/fix180}, pmid = {29293959}, issn = {1574-6941}, mesh = {Bacteria/genetics/isolation &amp; purification/*metabolism ; Color ; Environmental Monitoring ; Iron/analysis/metabolism ; Odorants/analysis ; Rivers/*chemistry/microbiology ; Sulfur/analysis/metabolism ; Urbanization ; }, abstract = {Urban rivers constitute a major part of urban drainage systems, and play critical roles in connecting other surface waters in urban areas. Black-odorous urban rivers are widely found in developing countries experiencing rapid urbanization, and the mismatch between urbanization and sewage treatment is thought to be the reason. The phenomena of blackening and odorization are likely complex bio-geochemical processes of which the microbial interactions with the environment are not fully understood. Here, we provide an overview of the major chemical compounds, such as iron and sulfur, and their bio-geochemical conversions during blackening and odorization of urban rivers. Scenarios explaining the formation of black-odorous urban rivers are proposed. Finally, we point out knowledge gaps in mechanisms and microbial ecology that need to be addressed to better understand the development of black-odorous urban rivers.}, }
@article {pmid29292833, year = {2018}, author = {Schvartzman, MS and Corso, M and Fataftah, N and Scheepers, M and Nouet, C and Bosman, B and Carnol, M and Motte, P and Verbruggen, N and Hanikenne, M}, title = {Adaptation to high zinc depends on distinct mechanisms in metallicolous populations of Arabidopsis halleri.}, journal = {The New phytologist}, volume = {218}, number = {1}, pages = {269-282}, doi = {10.1111/nph.14949}, pmid = {29292833}, issn = {1469-8137}, mesh = {Adaptation, Physiological/*drug effects/genetics ; Arabidopsis/drug effects/genetics/*physiology ; Chlorophyll/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Plant/drug effects ; Geography ; Homeostasis ; Iron/metabolism ; Models, Biological ; Phenotype ; Plant Roots/drug effects/metabolism ; Plant Shoots/drug effects/metabolism ; Principal Component Analysis ; Transcriptome/drug effects/genetics ; Zinc/*toxicity ; }, abstract = {Zinc (Zn) hyperaccumulation and hypertolerance are highly variable traits in Arabidopsis halleri. Metallicolous populations have evolved from nearby nonmetallicolous populations in multiple independent adaptation events. To determine whether these events resulted in similar or divergent adaptive strategies to high soil Zn concentrations, we compared two A. halleri metallicolous populations from distant genetic units in Europe (Poland (PL22) and Italy (I16)). The ionomic (Inductively Coupled Plasma Atomic Emission Spectroscopy (ICP-AES)) and transcriptomic (RNA sequencing (RNA-Seq)) responses to growth at 5 and 150 μM Zn were analyzed in root and shoot tissues to examine the contribution of the geographic origin and treatment to variation among populations. These analyses were enabled by the generation of a reference A. halleri transcriptome assembly. The genetic unit accounted for the largest variation in the gene expression profile, whereas the two populations had contrasting Zn accumulation phenotypes and shared little common response to the Zn treatment. The PL22 population displayed an iron deficiency response at high Zn in roots and shoots, which may account for higher Zn accumulation. By contrast, I16, originating from a highly Zn-contaminated soil, strongly responded to control conditions. Our data suggest that distinct mechanisms support adaptation to high Zn in soils among A. halleri metallicolous populations.}, }
@article {pmid29290035, year = {2018}, author = {Angelella, G and Nalam, V and Nachappa, P and White, J and Kaplan, I}, title = {Endosymbionts Differentially Alter Exploratory Probing Behavior of a Nonpersistent Plant Virus Vector.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {453-458}, pmid = {29290035}, issn = {1432-184X}, support = {107483//U.S. Department of Agriculture - National Institute of Food and Agriculture (US) Predoctoral Fellowship/ ; 2014-67013-21576//U.S. Department of Agriculture - National Institute of Food and Agriculture (US)/ ; }, mesh = {Animals ; Aphids/*microbiology/physiology ; Bacteriophages ; Enterobacteriaceae/physiology/*virology ; Host-Pathogen Interactions ; Insect Vectors/physiology/*virology ; Medicago sativa/virology ; Plant Diseases/virology ; Plant Viruses/pathogenicity/*physiology ; Potyvirus/pathogenicity/physiology ; Robinia/virology ; *Symbiosis ; }, abstract = {Insect endosymbionts (hereafter, symbionts) can modify plant virus epidemiology by changing the physiology or behavior of vectors, but their role in nonpersistent virus pathosystems remains uninvestigated. Unlike propagative and circulative viruses, nonpersistent plant virus transmission occurs via transient contamination of mouthparts, making direct interaction between symbiont and virus unlikely. Nonpersistent virus transmission occurs during exploratory intracellular punctures with styletiform mouthparts when vectors assess potential host-plant quality prior to phloem feeding. Therefore, we used an electrical penetration graph (EPG) to evaluate plant probing of the cowpea aphid, Aphis craccivora Koch, an important vector of cucurbit viruses, in the presence and absence of two facultative, intracellular symbionts. We tested four isolines of A. craccivora: two isolines were from a clone from black locust (Robinia pseudoacacia L.), one infected with Arsenophonus sp. and one cured, and two derived from a clone from alfalfa (Medicago sativa L.), one infected with Hamiltonella defensa and one cured. We quantified exploratory intracellular punctures, indicated by a waveform potential drop recorded by the EPG, initiation speed and frequency within the initial 15 min on healthy and watermelon mosaic virus-infected pumpkins. Symbiont associations differentially modified exploratory intracellular puncture frequency by aphids, with H. defensa-infected aphids exhibiting depressed probing, and Arsenophonus-infected aphids an increased frequency of probing. Further, there was greater overall aphid probing on virus-infected plants, suggesting that viruses manipulate their vectors to enhance acquisition-transmission rates, independent of symbiont infection. These results suggest facultative symbionts differentially affect plant-host exploration behaviors and potentially nonpersistent virus transmission by vectors.}, }
@article {pmid29286182, year = {2018}, author = {Lian, Y and Xiao, C and Yan, C and Chen, D and Huang, Q and Fan, Y and Li, Z and Xu, H}, title = {Knockdown of pseudogene derived from lncRNA DUXAP10 inhibits cell proliferation, migration, invasion, and promotes apoptosis in pancreatic cancer.}, journal = {Journal of cellular biochemistry}, volume = {119}, number = {4}, pages = {3671-3682}, doi = {10.1002/jcb.26578}, pmid = {29286182}, issn = {1097-4644}, mesh = {Animals ; Apoptosis/genetics/physiology ; Cell Cycle/genetics/physiology ; Cell Line, Tumor ; Cell Proliferation/genetics/physiology ; Cell Survival/genetics/physiology ; Computational Biology ; Flow Cytometry ; Gene Expression Regulation, Neoplastic/genetics/physiology ; Humans ; Immunoprecipitation ; Mice ; Mice, Inbred BALB C ; Mice, Nude ; Pancreatic Neoplasms/genetics/*metabolism ; RNA, Long Noncoding/*genetics/physiology ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Current evidence suggests that pseudogene derived lncRNAs may be important players in human cancer progression. Our previous study showed that DUXAP10 could promote cell proliferation in colorectal cancer. However, the clinical significance and potential role of DUXAP10 in human pancreatic cancer (PC) has not been uncovered. In this study, we found that DUXAP10 was overexpressed in PC tissues compared with normal tissues. DUXAP10 expression was significantly higher in patients with an advanced TNM stage and positive lymph node metastasis. Bioinformatic analysis showed that cell cycle progression was increased in patients with high DUXAP10 expression. In vitro and in vivo assays of DUXAP10 alterations revealed a complex integrated phenotype affecting cell growth, apoptosis, migration, and invasion. Mechanistic studies revealed that DUXAP10 has a crucial role in G2/M arrest. We further showed that DUXAP10 regulated PC cell proliferation through interact with RNA-binding protein EZH2 and LSD1. Overall, our findings indicates that DUXAP10 is an oncogenic lncRNA that promotes PC proliferation and metastasis.}, }
@article {pmid29285550, year = {2018}, author = {Kellner, K and Kardish, MR and Seal, JN and Linksvayer, TA and Mueller, UG}, title = {Symbiont-Mediated Host-Parasite Dynamics in a Fungus-Gardening Ant.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {530-543}, pmid = {29285550}, issn = {1432-184X}, support = {DEB-0919519//Division of Environmental Biology/ ; DEB-1354629//Division of Environmental Biology/ ; IOS-1552822//Division of Integrative Organismal Systems/ ; }, mesh = {Animal Diseases/microbiology ; Animals ; Ants/*microbiology ; *Biological Coevolution ; Disease Resistance/physiology ; Ecology ; Fungi/classification/genetics/isolation &amp; purification/*pathogenicity ; *Gardening ; Genotype ; Host-Pathogen Interactions/*physiology ; Hypocreales/classification/genetics/isolation &amp; purification/pathogenicity ; *Symbiosis ; }, abstract = {Group-living can promote the evolution of adaptive strategies to prevent and control disease. Fungus-gardening ants must cope with two sets of pathogens, those that afflict the ants themselves and those of their symbiotic fungal gardens. While much research has demonstrated the impact of specialized fungal pathogens that infect ant fungus gardens, most of these studies focused on the so-called higher attine ants, which are thought to coevolve diffusely with two clades of leucocoprinaceous fungi. Relatively few studies have addressed disease ecology of lower Attini, which are thought to occasionally recruit (domesticate) novel leucocoprinaceous fungi from free-living populations; coevolution between lower-attine ants and their fungi is therefore likely weaker (or even absent) than in the higher Attini, which generally have many derived modifications. Toward understanding the disease ecology of lower-attine ants, this study (a) describes the diversity in the microfungal genus Escovopsis that naturally infect fungus gardens of the lower-attine ant Mycocepurus smithii and (b) experimentally determines the relative contributions of Escovopsis strain (a possible garden disease), M. smithii ant genotype, and fungal cultivar lineage to disease susceptibility and colony fitness. In controlled in-vivo infection laboratory experiments, we demonstrate that the susceptibility to Escovopsis infection was an outcome of ant-cultivar-Escovopsis interaction, rather than solely due to ant genotype or fungal cultivar lineage. The role of complex ant-cultivar-Escovopsis interactions suggests that switching M. smithii farmers onto novel fungus types might be a strategy to generate novel ant-fungus combinations resistant to most, but perhaps not all, Escovopsis strains circulating in a local population of this and other lower-attine ants.}, }
@article {pmid29285238, year = {2017}, author = {Al-Qahtani, AA and Al-Anazi, MR and Nazir, N and Ghai, R and Abdo, AA and Sanai, FM and Al-Hamoudi, WK and Alswat, KA and Al-Ashgar, HI and Khan, MQ and Albenmousa, A and Cruz, DD and Bohol, MFF and Al-Ahdal, MN}, title = {Hepatitis B virus (HBV) X gene mutations and their association with liver disease progression in HBV-infected patients.}, journal = {Oncotarget}, volume = {8}, number = {62}, pages = {105115-105125}, pmid = {29285238}, issn = {1949-2553}, abstract = {Hepatitis B virus (HBV) is one of the most widespread human pathogens causing chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma (HCC). This study investigated the clinical impact of single and combinational mutations in HBx gene on the pathogenesis of HCC during progressive stages of liver disease. The patients were categorized into inactive HBV carriers, active carriers, cirrhosis and HCC groups based on disease severity. Male sex, age > 50 years, and high serum alanine aminotransferase level were associated with risk of progressive liver disease. I127T, V131I, and F132Y/I/R mutations showed a significant increasing trend associated with the disease progression to HCC. H94Y and K130M mutations were also significantly associated with severe liver disease. One double mutation (K130M+V131I) and two triple mutations (I127T+K130M+V131L and K130M+V131I+F132Y) were observed, with significant rising prevalence through progressive clinical phases of liver disease to HCC. Several single and combinational mutations in HBx correlating with severity and progressive clinical phases of HBV infection were identified. The mutational combinations may have a synergistic effect in accelerating the progression to HCC. These specific patterns of HBx mutations can be useful in predicting the clinical outcome of HBV-infected patients and may serve as early markers of high risk of developing HCC.}, }
@article {pmid29282519, year = {2018}, author = {Engel, K and Sauer, J and Jünemann, S and Winkler, A and Wibberg, D and Kalinowski, J and Tauch, A and Caspers, BA}, title = {Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {518-529}, pmid = {29282519}, issn = {1432-184X}, support = {88137//Volkswagen Foundation/ ; }, mesh = {Animals ; Bacteria/*classification/genetics ; Bacterial Load ; Biodiversity ; DNA, Bacterial/genetics ; Finches/*microbiology ; *Host Specificity ; *Microbiota/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Skin/*microbiology ; }, abstract = {An animals' body is densely populated with bacteria. Although a large number of investigations on physiological microbial colonisation have emerged in recent years, our understanding of the composition, ecology and function of the microbiota remains incomplete. Here, we investigated whether songbirds have an individual-specific skin microbiome that is similar across different body regions. We collected skin microbe samples from three different bird species (Taeniopygia gutatta, Lonchura striata domestica and Stagonopleura gutatta) at two body locations (neck region, preen gland area). To characterise the skin microbes and compare the bacterial composition, we used high-throughput 16S rRNA amplicon sequencing. This method proved suitable for identifying the skin microbiome of birds, even though the bacterial load on the skin appeared to be relatively low. We found that across all species, the two evaluated skin areas of each individual harboured very similar microbial communities, indicative of an individual-specific skin microbiome. Despite experiencing the same environmental conditions and consuming the same diet, significant differences in the skin microbe composition were identified among the three species. The bird species differed both quantitatively and qualitatively regarding the observed bacterial taxa. Although each species harboured its own unique set of skin microbes, we identified a core skin microbiome among the studied species. As microbes are known to influence the host's body odour, our findings of an individual-specific skin microbiome might suggest that the skin microbiome in birds is involved in the odour production and could encode information on the host's genotype.}, }
@article {pmid29276775, year = {2018}, author = {Van Dyke, TE and Diaz, PI and Moutsopoulos, N and Alekseyenko, AV and Ioannidou, E}, title = {Task Force on Design and Analysis in Oral Health Research: Host-Microbiome Interactions in Dysbiosis.}, journal = {JDR clinical and translational research}, volume = {3}, number = {1}, pages = {6-9}, pmid = {29276775}, issn = {2380-0844}, support = {R21 AR067459/AR/NIAMS NIH HHS/United States ; R01 DE025383/DE/NIDCR NIH HHS/United States ; R01 DE025020/DE/NIDCR NIH HHS/United States ; R34 DE027410/DE/NIDCR NIH HHS/United States ; R21 DE023967/DE/NIDCR NIH HHS/United States ; R01 DE021578/DE/NIDCR NIH HHS/United States ; }, abstract = {Knowledge Transfer Statement: This article discusses the proceedings of the conference organized by the Task Force on Design and Analysis in Oral Health Research on the new advances in host-microbiome interactions, analytical methods, and their implication in inflammatory periodontal disease management.}, }
@article {pmid29274070, year = {2018}, author = {Sullam, KE and Pichon, S and Schaer, TMM and Ebert, D}, title = {The Combined Effect of Temperature and Host Clonal Line on the Microbiota of a Planktonic Crustacean.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {506-517}, pmid = {29274070}, issn = {1432-184X}, support = {ERC-2010-AdG 268596-MicrobiotaEvolution//European Research Council/International ; 310030B_166677//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {Animals ; Bacteria/classification/genetics ; Bacterial Physiological Phenomena ; Biodiversity ; DNA, Bacterial/genetics ; Daphnia/*microbiology ; Ecology ; *Environmental Microbiology ; Genotype ; Host Microbial Interactions/*physiology ; Host Specificity ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Temperature ; Thermotolerance ; }, abstract = {Host-associated microbiota vary across host individuals and environmental conditions, but the relative importance of their genetic background versus their environment is difficult to disentangle. We sought to experimentally determine the factors shaping the microbiota of the planktonic Crustacean, Daphnia magna. We used clonal lines from a wide geographic distribution, which had been kept under standardized conditions for over 75 generations. Replicate populations were kept for three generations at 20 and 28 °C. The interaction of the host clonal line and environment (i.e., temperature) influenced microbiota community characteristics, including structure, the relative abundance of common microbial species, and the microbial richness and phylogenetic diversity. We did not find any correlation between host-associated microbiota and the geographic origin of the clones or their temperature tolerance. Our results highlight the prominent effects that host clonal lineage and its interaction with the environment has on host-associated microbiota composition.}, }
@article {pmid29273717, year = {2017}, author = {Albanese, D and Donati, C}, title = {Strain profiling and epidemiology of bacterial species from metagenomic sequencing.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {2260}, pmid = {29273717}, issn = {2041-1723}, mesh = {Bacteria/*genetics ; Bifidobacterium longum/genetics ; *Computational Biology ; Databases, Genetic ; Enterococcus faecalis/genetics ; Escherichia coli/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; Neisseria meningitidis/genetics ; Polymorphism, Single Nucleotide ; Propionibacterium acnes/genetics ; Staphylococcus aureus/genetics ; Staphylococcus epidermidis/genetics ; Streptococcus pneumoniae/genetics ; }, abstract = {Microbial communities are often composed by complex mixtures of multiple strains of the same species, characterized by a wide genomic and phenotypic variability. Computational methods able to identify, quantify and classify the different strains present in a sample are essential to fully exploit the potential of metagenomic sequencing in microbial ecology, with applications that range from the epidemiology of infectious diseases to the characterization of the dynamics of microbial colonization. Here we present a computational approach that uses the available genomic data to reconstruct complex strain profiles from metagenomic sequencing, quantifying the abundances of the different strains and cataloging them according to the population structure of the species. We validate the method on synthetic data sets and apply it to the characterization of the strain distribution of several important bacterial species in real samples, showing how its application provides novel insights on the structure and complexity of the microbiota.}, }
@article {pmid29273710, year = {2017}, author = {Goyal, S and Rampal, R and Kedia, S and Mahajan, S and Bopanna, S and Yadav, DP and Jain, S and Singh, AK and Wari, MN and Makharia, G and Awasthi, A and Ahuja, V}, title = {Urinary potassium is a potential biomarker of disease activity in Ulcerative colitis and displays in vitro immunotolerant role.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {18068}, pmid = {29273710}, issn = {2045-2322}, mesh = {Adult ; Biomarkers/urine ; Colitis, Ulcerative/diagnosis/*urine ; Feces/chemistry ; Female ; Humans ; Immune Tolerance/*physiology ; Leukocyte L1 Antigen Complex/analysis ; Male ; Middle Aged ; Potassium/*urine ; Prospective Studies ; Severity of Illness Index ; }, abstract = {We evaluated the in-vitro effect of potassium on CD4[+] T cells and the role of urinary potassium as a potential biomarker of disease activity in patients with ulcerative colitis (UC). This prospective observational cohort study included healthy controls (n = 18) and UC patients [n = 30, median age: 40 (IQR: 28-46) years, 17 males)] with active disease(assessed by Mayo score) from September 2015-May 2016. Twenty-four hours urinary potassium along with fecal calprotectin (FCP) were estimated in UC patients (at baseline and follow-up after 3-6 months) and controls. In healthy volunteers, we also assessed the effect of potassium on CD4[+] T cells differentiated in the presence of Th17 polarizing condition. UC patients had significantly higher FCP (368.2 ± 443.04 vs 12.44 ± 27.51, p < 0.001) and significantly lower urinary potassium (26.6 ± 16.9 vs 46.89 ± 35.91, p = 0.01) levels than controls. At follow-up, a significant increase in urinary potassium among patients who had clinical response [n = 22, 21.4 (14.4-39.7) to 36.5 (20.5-61.6), p = 0.04] and remission [n = 12, 18.7 (9.1-34.3) to 36.5 (23.4-70.5), p = 0.05] was accompanied with a parallel decline in FCP. On in-vitro analysis, potassium under Th17 polarizing conditions significantly inhibited IL-17 and interferon-[Formula: see text] expression while favoring the induction of FoxP3[+] T cells. Therefore, urinary potassium levels are inversely associated with disease activity in UC with in-vitro data supporting an immune-tolerant role of potassium.}, }
@article {pmid29273268, year = {2018}, author = {Meerbergen, K and Willems, KA and Dewil, R and Van Impe, J and Appels, L and Lievens, B}, title = {Isolation and screening of bacterial isolates from wastewater treatment plants to decolorize azo dyes.}, journal = {Journal of bioscience and bioengineering}, volume = {125}, number = {4}, pages = {448-456}, doi = {10.1016/j.jbiosc.2017.11.008}, pmid = {29273268}, issn = {1347-4421}, mesh = {Azo Compounds/isolation &amp; purification/*metabolism/pharmacology ; Bacteria/drug effects/*isolation &amp; purification/*metabolism ; Biodegradation, Environmental/drug effects ; *Color ; Hydrogen-Ion Concentration ; Sewage/chemistry/microbiology ; Sodium Chloride/pharmacology ; Temperature ; *Textile Industry ; Textiles/analysis ; Wastewater/*chemistry/*microbiology ; }, abstract = {The discharge of dye-contaminated wastewater into natural waterways presents a substantial risk to human and environmental health, therefore necessitating the treatment and removal of toxic dyes from colored wastewaters before their release into the ecosystem. The aim of this study was to isolate and characterize bacterial strains capable of decolorizing and/or degrading azo dyes commonly applied in textile production (monoazo dye Reactive Orange 16 and diazo dye Reactive Green 19) from activated sludge systems used in the treatment of (textile) wastewater. Following a prescreening of 125 isolates for their decolorization potential five strains were retained for further evaluation of decolorization rate and effects of physicochemical parameters using a microtiter plate method. Of those five strains, one strain belonging to the genus Acinetobacter (ST16.16/164) and another belonging to Klebsiella (ST16.16/034) outperformed the other tested strains. Both strains exhibited strong decolorization ability (>80%) within a wide temperature range (20 °C-40 °C) and retained good decolorization activity at temperatures as low as 10 °C (especially strain ST16.16/034). Among the different pH values tested (pH 4, 7 and 10), highest dye removal for both strains occurred at pH 7, with decolorization efficiency remaining relatively high under alkaline conditions (pH 10), and neither isolates decolorization efficiency was negatively impacted by high salt or high dye concentration. Furthermore, both strains displayed the highest rate of decolorization and were able to completely (ST16.16/034) or partly (ST16.16/164) degrade the azo dyes. Altogether, our results support the use of these bacteria in the treatment of industrial wastewaters containing azo dyes.}, }
@article {pmid29272844, year = {2018}, author = {Huerta Lwanga, E and Thapa, B and Yang, X and Gertsen, H and Salánki, T and Geissen, V and Garbeva, P}, title = {Decay of low-density polyethylene by bacteria extracted from earthworm's guts: A potential for soil restoration.}, journal = {The Science of the total environment}, volume = {624}, number = {}, pages = {753-757}, doi = {10.1016/j.scitotenv.2017.12.144}, pmid = {29272844}, issn = {1879-1026}, mesh = {Animals ; Bacteria/*metabolism ; *Biodegradation, Environmental ; Oligochaeta/*microbiology ; Plastics/metabolism ; Polyethylene/*metabolism ; Soil ; Soil Pollutants/*metabolism ; }, abstract = {Low-density polyethylene (LDPE) is the most abundant source of microplastic pollution worldwide. A recent study found that LDPE decay was increased and the size of the plastic was decreased after passing through the gut of the earthworm Lumbricus terrestris (Oligochaeta). Here, we investigated the involvement of earthworm gut bacteria in the microplastic decay. The bacteria isolated from the earthworm's gut were Gram-positive, belonging to phylum Actinobacteria and Firmicutes. These bacteria were used in a short-term microcosm experiment performed with gamma-sterilized soil with or without LDPE microplastics (MP). We observed that the LDPE-MP particle size was significantly reduced in the presence of bacteria. In addition, the volatile profiles of the treatments were compared and clear differences were detected. Several volatile compounds such as octadecane, eicosane, docosane and tricosane were measured only in the treatments containing both bacteria and LDPE-MP, indicating that these long-chain alkanes are byproducts of bacterial LDPE-MP decay.}, }
@article {pmid29272841, year = {2018}, author = {Kassotaki, E and Pijuan, M and Joss, A and Borrego, CM and Rodriguez-Roda, I and Buttiglieri, G}, title = {Unraveling the potential of a combined nitritation-anammox biomass towards the biodegradation of pharmaceutically active compounds.}, journal = {The Science of the total environment}, volume = {624}, number = {}, pages = {722-731}, doi = {10.1016/j.scitotenv.2017.12.116}, pmid = {29272841}, issn = {1879-1026}, mesh = {Ammonium Compounds ; Anaerobiosis ; Bacteria, Anaerobic/*metabolism ; *Biodegradation, Environmental ; Biomass ; Bioreactors ; Nitrification ; Nitrogen ; Oxidation-Reduction ; Pharmaceutical Preparations/*metabolism ; }, abstract = {In the past few years, anaerobic ammonium oxidation-based processes have attracted a lot of attention for their implementation at the mainstream line of wastewater treatment plants, due to the possibility of leading to energy autarky if combined with anaerobic digestion. However, little is known about the potential degradation of micropollutants by the microbial groups responsible of these processes and the few results available are inconclusive. This study aimed to assess the degradation capability of biomass withdrawn from a combined nitritation/anaerobic ammonium oxidation (combined N/A) pilot plant towards five pharmaceutically active compounds (ibuprofen, sulfamethoxazole, metoprolol, venlafaxine and carbamazepine). Batch experiments were performed under different conditions by selectively activating or inhibiting different microbial groups: i) regular combined N/A operation, ii) aerobic (optimal for nitrifying bacteria), iii) aerobic with allylthiourea (an inhibitor of ammonia monooxygenase, enzyme of ammonia oxidizing bacteria), iv) anoxic (optimal for anaerobic ammonium oxidizing bacteria), v) aerobic with acetate (optimal for heterotrophic bacteria) and vi) anoxic with acetate (optimal for heterotrophic denitrifying bacteria). Ibuprofen was the most biodegradable compound being significantly degraded (49-100%) under any condition except heterotrophic denitrification. Sulfamethoxazole, exhibited the highest removal (70%) under optimal conditions for nitrifying bacteria but in the rest of the experiments anoxic conditions were found to be slightly more favorable (up to 58%). For metoprolol the highest performance was obtained under anoxic conditions favoring anammox bacteria (62%). Finally, carbamazepine and venlafaxine were hardly removed (≤10% in the majority of cases). Taken together, these results suggest the specificity of different microbial groups that in combination with alternating operational parameters can lead to enhanced removal of some micropollutants.}, }
@article {pmid29270662, year = {2018}, author = {Menezes, L and Alvarez, TM and Persinoti, GF and Franco, JP and Squina, F and Moreira, EA and Alvaredo Paixão, DA and Costa-Leonardo, AM and da Silva, VX and Clerici, MTPS and Arab, A}, title = {Food Storage by the Savanna Termite Cornitermes cumulans (Syntermitinae): a Strategy to Improve Hemicellulose Digestibility?.}, journal = {Microbial ecology}, volume = {76}, number = {2}, pages = {492-505}, pmid = {29270662}, issn = {1432-184X}, support = {2015/21497-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 00878-12//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; 00878-12//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; }, mesh = {Animals ; Bacteria/classification/genetics/metabolism ; Behavior, Animal ; DNA, Bacterial/genetics ; Enzyme Assays ; Feces/microbiology ; *Food Storage ; Fungi/classification/genetics ; Gastrointestinal Microbiome ; Gastrointestinal Tract/enzymology/microbiology ; Genes, rRNA/genetics ; Isoptera/*microbiology ; Lignin/metabolism ; Microbiota/*physiology ; Nesting Behavior ; Phylogeny ; Polysaccharides/*metabolism ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; Sequence Analysis, DNA ; }, abstract = {It has been suggested that food storage inside the nest may offer termites with a nutritional provision during low resource availability. Additionally, feces employed as construction material provide an excellent environment for colonization by microorganisms and, together with the storage of plant material inside the nest, could thus provide some advantage to the termites in terms of lignocellulose decomposition. Here, we conducted for the first time a comprehensive study of the microbial communities associated to a termite exhibiting food storage behavior using Illumina sequencing of the 16S and (ITS2) regions of rRNA genes, together with enzymatic assays and data collected in the field. Cornitermes cumulans (Syntermitinae) stored grass litter in nodules made from feces and saliva located in the nest core. The amount of nodules increased with nest size and isolation, and interestingly, the soluble fraction of extracts from nodules showed a higher activity against hemicellulosic substrates compared to termite guts. Actinobacteria and Sordariales dominated microbial communities of food nodules and nest walls, whereas Spirochetes and Pleosporales dominated gut samples of C. cumulans. Within Syntermitinae, however, gut bacterial assemblages were dissimilar. On the other hand, there is a remarkable convergence of the bacterial community structure of Termitidae nests. Our results suggest that the role of nodules could be related to food storage; however, the higher xylanolytic activity in the nodules and their associated microbiota could also provide C. cumulans with an external source of predigested polysaccharides, which might be advantageous in comparison with litter-feeding termites that do not display food storage behavior.}, }
@article {pmid29270661, year = {2018}, author = {Stabili, L and Gravili, C and Pizzolante, G and Lezzi, M and Tredici, SM and De Stefano, M and Boero, F and Alifano, P}, title = {Aglaophenia octodonta (Cnidaria, Hydrozoa) and the Associated Microbial Community: a Cooperative Alliance?.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {258-271}, pmid = {29270661}, issn = {1432-184X}, mesh = {Ampicillin/pharmacology ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/metabolism ; Biodiversity ; Dinoflagellida/drug effects/genetics/isolation &amp; purification/physiology ; Host Microbial Interactions/*physiology ; Hydrogen Peroxide ; Hydrozoa/classification/cytology/drug effects/*microbiology ; Italy ; Microalgae/classification/drug effects/genetics/isolation &amp; purification ; Microbiota/drug effects/genetics/*physiology ; Oligohymenophorea/classification/genetics/isolation &amp; purification/physiology ; Oxygen ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Seawater ; Symbiosis ; Vibrio/drug effects/genetics/isolation &amp; purification/physiology ; }, abstract = {Recently, genetic approaches have revealed a surprising bacterial world as well as a growing knowledge of the enormous distribution of animal-bacterial interactions. In the present study, the diversity of the microorganisms associated to the hydroid Aglaophenia octodonta was studied with epifluorescence, optical, and scanning electron microscopy. Small subunit ribosomal RNA gene sequencing with "universal" and taxon-specific primers allowed the assignment of the microalgae to Symbiodinium and the peritrich ciliates to Pseudovorticella, while the luminous vibrios were identified as Vibrio jasicida of the Harvey clade. To understand the possible relationships among Vibrio jasicida, Symbiodinium, A. octodonta, and Pseudovorticella, specific treatments were conducted in microcosm experiments, with the antibiotic ampicillin and other substances that interfere with bacterial and hydroid metabolism. Treatment of A. octodonta with ampicillin resulted in a decrease of bacterial luminescence followed by Pseudovorticella detachment and Symbiodinium expulsion and suggesting that these microorganisms form a "consortium" with beneficial metabolic interdependence. This hypothesis was reinforced by the evidence that low concentrations of hydrogen peroxide, which stimulate the bacterial oxidative metabolism and luminescence by releasing oxygen, were able to counteract the detrimental effect of ampicillin on the stability of the studied A. octodonta association. A model is proposed in which microalgae that release oxygen during photosynthesis are useful to luminous bacteria for their metabolism and for establishing/maintaining symbiosis leading to a close alliance and mutual benefit of the system A. octodonta-Vibrio jasicida-Pseudovorticella sp.-Symbiodinium sp.}, }
@article {pmid29270249, year = {2017}, author = {Pratama, AA and Haq, IU and Nazir, R and Chaib De Mares, M and van Elsas, JD}, title = {Draft genome sequences of three fungal-interactive Paraburkholderia terrae strains, BS007, BS110 and BS437.}, journal = {Standards in genomic sciences}, volume = {12}, number = {}, pages = {81}, pmid = {29270249}, issn = {1944-3277}, abstract = {Here, we report the draft genome sequences of three fungal-interactive 10.1601/nm.27008 strains, denoted BS110, BS007 and BS437. Phylogenetic analyses showed that the three strains belong to clade II of the genus 10.1601/nm.1619, which was recently renamed 10.1601/nm.26956. This novel genus primarily contains environmental species, encompassing non-pathogenic plant- as well as fungal-interactive species. The genome of strain BS007 consists of 11,025,273 bp, whereas those of strains BS110 and BS437 have 11,178,081 and 11,303,071 bp, respectively. Analyses of the three annotated genomes revealed the presence of (1) a large suite of substrate capture systems, and (2) a suite of genetic systems required for adaptation to microenvironments in soil and the mycosphere. Thus, genes encoding traits that potentially confer fungal interactivity were found, such as type 4 pili, type 1, 2, 3, 4 and 6 secretion systems, and biofilm formation (PGA, alginate and pel) and glycerol uptake systems. Furthermore, the three genomes also revealed the presence of a highly conserved five-gene cluster that had previously been shown to be upregulated upon contact with fungal hyphae. Moreover, a considerable number of prophage-like and CRISPR spacer sequences was found, next to genetic systems responsible for secondary metabolite production. Overall, the three 10.1601/nm.27008 strains possess the genetic repertoire necessary for adaptation to diverse soil niches, including those influenced by soil fungi.}, }
@article {pmid29270167, year = {2017}, author = {Chiu, L and Bazin, T and Truchetet, ME and Schaeverbeke, T and Delhaes, L and Pradeu, T}, title = {Protective Microbiota: From Localized to Long-Reaching Co-Immunity.}, journal = {Frontiers in immunology}, volume = {8}, number = {}, pages = {1678}, pmid = {29270167}, issn = {1664-3224}, abstract = {Resident microbiota do not just shape host immunity, they can also contribute to host protection against pathogens and infectious diseases. Previous reviews of the protective roles of the microbiota have focused exclusively on colonization resistance localized within a microenvironment. This review shows that the protection against pathogens also involves the mitigation of pathogenic impact without eliminating the pathogens (i.e., "disease tolerance") and the containment of microorganisms to prevent pathogenic spread. Protective microorganisms can have an impact beyond their niche, interfering with the entry, establishment, growth, and spread of pathogenic microorganisms. More fundamentally, we propose a series of conceptual clarifications in support of the idea of a "co-immunity," where an organism is protected by both its own immune system and components of its microbiota.}, }
@article {pmid29268781, year = {2017}, author = {Carda-Diéguez, M and Ghai, R and Rodríguez-Valera, F and Amaro, C}, title = {Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {162}, pmid = {29268781}, issn = {2049-2618}, support = {BES-2012-052361//Secretar&#xed;a de Estado de Investigaci&#xf3;n, Desarrollo e Innovaci&#xf3;n/International ; AGL2014-58933-P (cofunded with FEDER funds)//Secretar&#xed;a de Estado de Investigaci&#xf3;n, Desarrollo e Innovaci&#xf3;n/International ; 17-04828S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/International ; CGL2016-76273-P [AEI/FEDER, EU]//AEI/FEDER/EU/International ; CGL2015-71523-REDC (Acciones de dinamizaci&#xf3;n "REDES DE EXCELENCIA" CONSOLIDER)//Direcci&#xf3;n General de Investigaci&#xf3;n Cient&#xed;fica y T&#xe9;cnica/International ; Prometeo II/2014/012 "AQUAMET"//Generalitat Valenciana/International ; }, mesh = {Anguilla/anatomy &amp; histology/*microbiology ; Animals ; Animals, Wild/microbiology ; Bacteria/genetics/isolation &amp; purification/*pathogenicity ; DNA, Bacterial ; Evolution, Molecular ; Genomic Islands ; Genomics ; Humans ; Metagenomics ; Microbiota/*genetics ; Mucus/*microbiology ; Skin/*microbiology ; Vibrio/genetics/isolation &amp; purification/pathogenicity ; *Water Microbiology ; }, abstract = {BACKGROUND: Fish skin mucosal surfaces (SMS) are quite similar in composition and function to some mammalian MS and, in consequence, could constitute an adequate niche for the evolution of mucosal aquatic pathogens in natural environments. We aimed to test this hypothesis by searching for metagenomic and genomic evidences in the SMS-microbiome of a model fish species (Anguilla Anguilla or eel), from different ecosystems (four natural environments of different water salinity and one eel farm) as well as the water microbiome (W-microbiome) surrounding the host.<br><br>RESULTS: Remarkably, potentially pathogenic Vibrio monopolized wild eel SMS-microbiome from natural ecosystems, Vibrio anguillarum/Vibrio vulnificus and Vibrio cholerae/Vibrio metoecus being the most abundant ones in SMS from estuary and lake, respectively. Functions encoded in the SMS-microbiome differed significantly from those in the W-microbiome and allowed us to predict that successful mucus colonizers should have specific genes for (i) attachment (mainly by forming biofilms), (ii) bacterial competence and communication, and (iii) resistance to mucosal innate immunity, predators (amoeba), and heavy metals/drugs. In addition, we found several mobile genetic elements (mainly integrative conjugative elements) as well as a series of evidences suggesting that bacteria exchange DNA in SMS. Further, we isolated and sequenced a V. metoecus strain from SMS. This isolate shares pathogenicity islands with V. cholerae O1 from intestinal infections that are absent in the rest of sequenced V. metoecus strains, all of them from water and extra-intestinal infections.<br><br>CONCLUSIONS: We have obtained metagenomic and genomic evidence in favor of the hypothesis on the role of fish mucosal surfaces as a specialized habitat selecting microbes capable of colonizing and persisting on other comparable mucosal surfaces, e.g., the human intestine.}, }
@article {pmid29268780, year = {2017}, author = {Ren, T and Boutin, S and Humphries, MM and Dantzer, B and Gorrell, JC and Coltman, DW and McAdam, AG and Wu, M}, title = {Seasonal, spatial, and maternal effects on gut microbiome in wild red squirrels.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {163}, pmid = {29268780}, issn = {2049-2618}, mesh = {Animals ; Animals, Wild/microbiology ; Ecosystem ; Environment ; *Gastrointestinal Microbiome ; Maternal Inheritance ; RNA, Ribosomal, 16S ; Sciuridae/*microbiology ; *Seasons ; Spatio-Temporal Analysis ; }, abstract = {BACKGROUND: Our understanding of gut microbiota has been limited primarily to findings from human and laboratory animals, but what shapes the gut microbiota in nature remains largely unknown. To fill this gap, we conducted a comprehensive study of gut microbiota of a well-studied North American red squirrel (Tamiasciurus hudsonicus) population. Red squirrels are territorial, solitary, and live in a highly seasonal environment and therefore represent a very attractive system to study factors that drive the temporal and spatial dynamics of gut microbiota.<br><br>RESULT: For the first time, this study revealed significant spatial patterns of gut microbiota within a host population, suggesting limited dispersal could play a role in shaping and maintaining the structure of gut microbial communities. We also found a remarkable seasonal rhythm in red squirrel's gut microbial composition manifested by a tradeoff between relative abundance of two genera Oscillospira and Corpococcus and clearly associated with seasonal variation in diet availability. Our results show that in nature, environmental factors exert a much stronger influence on gut microbiota than host-associated factors including age and sex. Despite strong environmental effects, we found clear evidence of individuality and maternal effects, but host genetics did not seem to be a significant driver of the gut microbial communities in red squirrels.<br><br>CONCLUSION: Taken together, the results of this study emphasize the importance of external ecological factors rather than host attributes in driving temporal and spatial patterns of gut microbiota in natural environment.}, }
@article {pmid29268225, year = {2018}, author = {Oberholster, T and Vikram, S and Cowan, D and Valverde, A}, title = {Key microbial taxa in the rhizosphere of sorghum and sunflower grown in crop rotation.}, journal = {The Science of the total environment}, volume = {624}, number = {}, pages = {530-539}, doi = {10.1016/j.scitotenv.2017.12.170}, pmid = {29268225}, issn = {1879-1026}, mesh = {Crop Production ; Helianthus/*microbiology ; Plant Roots/microbiology ; RNA, Ribosomal, 16S ; *Rhizosphere ; *Soil Microbiology ; Sorghum/*microbiology ; }, abstract = {Microbes are key determinants of plant health and productivity. Previous studies have characterized the rhizosphere microbiomes of numerous plant species, but little information is available on how rhizosphere microbial communities change over time under crop rotation systems. Here, we document microbial communities in the rhizosphere of sorghum and sunflower (at seedling, flowering and senescence stages) grown in crop rotation in four different soils under field conditions. A comprehensive 16S rRNA-based amplicon sequencing survey revealed that the differences in alpha-diversity between rhizosphere and bulk soils changed over time. Sorghum rhizosphere soil microbial diversity at flowering and senescence were more diverse than bulk soils, whereas the microbial diversity of sunflower rhizosphere soils at flowering were less diverse with respect to bulk soils. Sampling time was also important in explaining the variation in microbial community composition in soils grown with both crops. Temporal changes observed in the rhizosphere microbiome were both plant-driven and due to seasonal changes in the bulk soil biota. Several individual taxa were relatively more abundant in the rhizosphere and/or found to be important in maintaining rhizosphere microbial networks. Interestingly, some of these taxa showed similar patterns at different sampling times, suggesting that the same organisms may play the same functional/structural role at different plant growth stages and in different crops. Overall, we have identified prominent microbial taxa that might be used to develop microbiome-based strategies for improving the yield and productivity of sorghum and sunflower.}, }
@article {pmid29266796, year = {2018}, author = {Buysschaert, B and Kerckhof, FM and Vandamme, P and De Baets, B and Boon, N}, title = {Flow cytometric fingerprinting for microbial strain discrimination and physiological characterization.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {93}, number = {2}, pages = {201-212}, doi = {10.1002/cyto.a.23302}, pmid = {29266796}, issn = {1552-4930}, mesh = {DNA Fingerprinting/*methods ; Flow Cytometry/*methods ; Lactobacillus/*genetics ; Microbiota/*genetics ; }, abstract = {The analysis of microbial populations is fundamental, not only for developing a deeper understanding of microbial communities but also for their engineering in biotechnological applications. Many methods have been developed to study their characteristics and over the last few decades, molecular analysis tools, such as DNA sequencing, have been used with considerable success to identify the composition of microbial populations. Recently, flow cytometric fingerprinting is emerging as a promising and powerful method to analyze bacterial populations. So far, these methods have primarily been used to observe shifts in the composition of microbial communities of natural samples. In this article, we apply a flow cytometric fingerprinting method to discriminate among 29 Lactobacillus strains. Our results indicate that it is possible to discriminate among 27 Lactobacillus strains by staining with SYBR green I and that the discriminatory power can be increased by combined SYBR green I and propidium iodide staining. Furthermore, we illustrate the impact of physiological changes on the fingerprinting method by demonstrating how flow cytometric fingerprinting is able to discriminate the different growth phases of a microbial culture. The sensitivity of the method is assessed by its ability to detect changes in the relative abundance of a mix of polystyrene beads down to 1.2%. When a mix of bacteria was used, the sensitivity was as between 1.2% and 5%. The presented data demonstrate that flow cytometric fingerprinting is a sensitive and reproducible technique with the potential to be applied as a method for the dereplication of bacterial isolates. © 2017 International Society for Advancement of Cytometry.}, }
@article {pmid29257089, year = {2017}, author = {Poff, KE and Stever, H and Reil, JB and Seabourn, P and Ching, AJ and Aoki, S and Logan, M and Michalski, JR and Santamaria, J and Adams, JW and Eiben, JA and Yew, JY and Ewing, CP and Magnacca, KN and Bennett, GM}, title = {The Native Hawaiian Insect Microbiome Initiative: A Critical Perspective for Hawaiian Insect Evolution.}, journal = {Insects}, volume = {8}, number = {4}, pages = {}, pmid = {29257089}, issn = {2075-4450}, abstract = {Insects associate with a diversity of microbes that can shape host ecology and diversity by providing essential biological and adaptive services. For most insect groups, the evolutionary implications of host-microbe interactions remain poorly understood. Geographically discrete areas with high biodiversity offer powerful, simplified model systems to better understand insect-microbe interactions. Hawaii boasts a diverse endemic insect fauna (~6000 species) characterized by spectacular adaptive radiations. Despite this, little is known about the role of bacteria in shaping this diversity. To address this knowledge gap, we inaugurate the Native Hawaiian Insect Microbiome Initiative (NHIMI). The NHIMI is an effort intended to develop a framework for informing evolutionary and biological studies in Hawaii. To initiate this effort, we have sequenced the bacterial microbiomes of thirteen species representing iconic, endemic Hawaiian insect groups. Our results show that native Hawaiian insects associate with a diversity of bacteria that exhibit a wide phylogenetic breadth. Several groups show predictable associations with obligate microbes that permit diet specialization. Others exhibit unique ecological transitions that are correlated with shifts in their microbiomes (e.g., transition to carrion feeding from plant-feeding in Nysius wekiuicola). Finally, some groups, such as the Hawaiian Drosophila, have relatively diverse microbiomes with a conserved core of bacterial taxa across multiple species and islands.}, }
@article {pmid29255936, year = {2018}, author = {Soares, ARA and Kritzberg, ES and Custelcean, I and Berggren, M}, title = {Bacterioplankton Responses to Increased Organic Carbon and Nutrient Loading in a Boreal Estuary-Separate and Interactive Effects on Growth and Respiration.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {144-155}, pmid = {29255936}, issn = {1432-184X}, support = {2015-05450//Swedish Research Council/ ; 239-2014-698//Formas/ ; }, mesh = {Bacteria/*growth &amp; development/*metabolism ; Carbon/chemistry/*metabolism ; Ecosystem ; Environmental Monitoring ; *Estuaries ; Fresh Water/chemistry ; Heterotrophic Processes ; Nutrients/chemistry/*metabolism ; Phosphorus/metabolism ; Plankton/growth &amp; development/metabolism ; Rivers/chemistry ; Salinity ; Seasons ; Seawater/*microbiology ; Sweden ; }, abstract = {Increases in the terrestrial export of dissolved organic carbon (C) to rivers may be associated with additional loading of organic nitrogen (N) and phosphorus (P) to the coastal zone. However, little is known about how these resources interact in the regulation of heterotrophic bacterioplankton metabolism in boreal coastal ecosystems. Here, we measured changes in bacterioplankton production (BP) and respiration (BR) in response to full-factorial (C, N, and P) enrichment experiments at two sites within the Öre estuary, northern Sweden. The BR was stimulated by single C additions and further enhanced by combined additions of C and other nutrients. Single addition of N or P had no effect on BR rates. In contrast, BP was primarily limited by P at the site close to the river mouth and did not respond to C or N additions. However, at the site further away from the near the river mouth, BP was slightly stimulated by single additions of C. Possibly, the natural inflow of riverine bioavailable dissolved organic carbon induced local P limitation of BP near the river mouth, which was then exhausted and resulted in C-limited BP further away from the river mouth. We observed positive interactions between all elements on all responses except for BP at the site close to the river mouth, where P showed an independent effect. In light of predicted increases in terrestrial P and C deliveries, we expect future increases in BP and increases of BR of terrestrially delivered C substrates at the Öre estuary and similar areas.}, }
@article {pmid29250734, year = {2018}, author = {Martín-Vivaldi, M and Soler, JJ and Martínez-García, &#xc1; and Arco, L and Juárez-García-Pelayo, N and Ruiz-Rodríguez, M and Martínez-Bueno, M}, title = {Acquisition of Uropygial Gland Microbiome by Hoopoe Nestlings.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {285-297}, pmid = {29250734}, issn = {1432-184X}, support = {CGL2009-14006//Ministerio de Ciencia e Innovaci&#xf3;n/ ; CGL2010-19233-C03-01//Ministerio de Ciencia e Innovaci&#xf3;n/ ; CGL2010-19233-C03-03//Ministerio de Ciencia e Innovaci&#xf3;n/ ; CGL2013-48193-C3-1-P//Ministerio de Ciencia e Innovaci&#xf3;n/ ; CGL2013-48193-C3-2-P//Ministerio de Ciencia e Innovaci&#xf3;n/ ; P09-RNM-4557//Agencia de Innovaci&#xf3;n y Desarrollo de Andaluc&#xed;a/ ; Predoctoral grant P09-RNM-4557//Agencia de Innovaci&#xf3;n y Desarrollo de Andaluc&#xed;a/ ; }, mesh = {Animals ; Bacteria/*classification/genetics ; Bacterial Load ; Bacterial Physiological Phenomena ; Biodiversity ; Biological Coevolution ; Birds/*microbiology/physiology ; DNA, Bacterial/genetics ; Exocrine Glands/*microbiology ; Female ; Microbiota/*physiology ; Molecular Typing ; Nesting Behavior/*physiology ; Phylogeny ; Spain ; Symbiosis ; }, abstract = {Mutualistic symbioses between animals and bacteria depend on acquisition of appropriate symbionts while avoiding exploitation by non-beneficial microbes. The mode of acquisition of symbionts would determine, not only the probability of encountering but also evolutionary outcomes of mutualistic counterparts. The microbiome inhabiting the uropygial gland of the European hoopoe (Upupa epops) includes a variety of bacterial strains, some of them providing antimicrobial benefits. Here, the mode of acquisition and stability of this microbiome is analyzed by means of Automated rRNA Intergenic Spacer Analysis and two different experiments. The first experiment impeded mothers' access to their glands, thus avoiding direct transmission of microorganisms from female to offspring secretions. The second experiment explored the stability of the microbiomes by inoculating glands with secretions from alien nests. The first experiment provoked a reduction in similarity of microbiomes of mother and nestlings. Interestingly, some bacterial strains were more often detected when females had not access to their glands, suggesting antagonistic effects among bacteria from different sources. The second experiment caused an increase in richness of the microbiome of receivers in terms of prevalence of Operational Taxonomic Units (OTUs) that reduced differences in microbiomes of donors and receivers. That occurred because OTUs that were present in donors but not in receivers incorporated to the microbiome of the latter, which provoked that cross-inoculated nestlings got similar final microbiomes that included the most prevalent OTUs. The results are therefore consistent with a central role of vertical transmission in bacterial acquisition by nestling hoopoes and support the idea that the typical composition of the hoopoe gland microbiome is reached by the incorporation of some bacteria during the nestling period. This scenario suggests the existence of a coevolved core microbiome composed by a mix of specialized vertically transmitted strains and facultative symbionts able to coexist with them. The implications of this mixed mode of transmission for the evolution of the mutualism are discussed.}, }
@article {pmid29250049, year = {2017}, author = {Leizeaga, A and Estrany, M and Forn, I and Sebastián, M}, title = {Using Click-Chemistry for Visualizing in Situ Changes of Translational Activity in Planktonic Marine Bacteria.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2360}, pmid = {29250049}, issn = {1664-302X}, abstract = {A major challenge in microbial ecology is linking diversity and function to determine which microbes are actively contributing to processes occurring in situ. Bioorthogonal non-canonical amino acid tagging (BONCAT) is a promising technique for detecting and quantifying translationally active bacteria in the environment. This technique consists of incubating a bacterial sample with an analog of methionine and using click-chemistry to identify the cells that have incorporated the substrate. Here, we established an optimized protocol for the visualization of protein-synthesizing cells in oligotrophic waters that can be coupled with taxonomic identification using Catalyzed Reporter Deposition Fluorescent in Situ Hybridization. We also evaluated the use of this technique to track shifts in translational activity by comparing it with leucine incorporation, and used it to monitor temporal changes in both cultures and natural samples. Finally, we determined the optimal concentration and incubation time for substrate incorporation during BONCAT incubations at an oligotrophic site. Our results demonstrate that BONCAT is a fast and powerful semi-quantitative approach to explore the physiological status of marine bacteria.}, }
@article {pmid29247239, year = {2017}, author = {Zamanzadeh, M and Hagen, LH and Svensson, K and Linjordet, R and Horn, SJ}, title = {Biogas production from food waste via co-digestion and digestion- effects on performance and microbial ecology.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {17664}, pmid = {29247239}, issn = {2045-2322}, mesh = {Animals ; Cattle ; Chloroflexi/*physiology ; Fatty Acids/chemistry/metabolism ; Firmicutes/*physiology ; Food ; Food Microbiology ; Gram-Negative Anaerobic Straight, Curved, and Helical Rods/*physiology ; Hot Temperature ; Manure ; *Medical Waste Disposal ; Methane/chemistry/metabolism ; Methanobacteriaceae/*physiology ; RNA, Ribosomal, 16S/*analysis ; *Waste Management ; }, abstract = {In this work, performance and microbial structure of a digestion (food waste-only) and a co-digestion process (mixture of cow manure and food waste) were studied at mesophilic (37 °C) and thermophilic (55 °C) temperatures. The highest methane yield (480 mL/g VS) was observed in the mesophilic digester (MDi) fed with food waste alone. The mesophilic co-digestion of food waste and manure (McoDi) yielded 26% more methane than the sum of individual digestions of manure and food waste. The main volatile fatty acid (VFA) in the mesophilic systems was acetate, averaging 93 and 172 mg/L for McoDi and MDi, respectively. Acetate (2150 mg/L) and propionate (833 mg/L) were the main VFAs in the thermophilic digester (TDi), while propionate (163 mg/L) was the major VFA in the thermophilic co-digester (TcoDi). The dominant bacteria in MDi was Chloroflexi (54%), while Firmicutes was dominant in McoDi (60%). For the mesophilic reactors, the dominant archaea was Methanosaeta in MDi, while Methanobacterium and Methanosaeta had similar abundance in McoDi. In the thermophilic systems, the dominant bacteria were Thermotogae, Firmicutes and Synergistetes in both digesters, however, the relative abundance of these phyla were different. For archaea, the genus Methanothermobacter were entirely dominant in both TDi and TcoDi.}, }
@article {pmid29242394, year = {2018}, author = {Santos, AMC and Doria, MS and Meirinhos-Soares, L and Almeida, AJ and Menezes, JC}, title = {A QRM Discussion of Microbial Contamination of Non-sterile Drug Products, Using FDA and EMA Warning Letters Recorded between 2008 and 2016.}, journal = {PDA journal of pharmaceutical science and technology}, volume = {72}, number = {1}, pages = {62-72}, doi = {10.5731/pdajpst.2016.007252}, pmid = {29242394}, issn = {1948-2124}, mesh = {*Drug Contamination ; Europe ; Government Agencies ; Humans ; Quality Control ; Risk Management ; Sterilization ; United States ; United States Food and Drug Administration ; }, abstract = {Microbial quality control of non-sterile drug products has been a concern to regulatory agencies and the pharmaceutical industry since the 1960s. Despite being an old challenge to companies, microbial contamination still affects a high number of manufacturers of non-sterile products. Consequences go well beyond the obvious direct costs related to batch rejections or product recalls, as human lives and a company's reputation are significantly impacted if such events occur. To better manage risk and establish effective mitigation strategies, it is necessary to understand the microbial hazards involved in non-sterile drug products manufacturing, be able to evaluate their potential impact on final product quality, and apply mitigation actions. Herein we discuss the most likely root causes involved in microbial contaminations referenced in warning letters issued by US health authorities and non-compliance reports issued by European health authorities over a period of several years. The quality risk management tools proposed were applied to the data gathered from those databases, and a generic risk ranking was provided based on a panel of non-sterile drug product manufacturers that was assembled and given the opportunity to perform the risk assessments. That panel identified gaps and defined potential mitigation actions, based on their own experience of potential risks expected for their processes. Major findings clearly indicate that the manufacturers affected by the warning letters should focus their attention on process improvements and microbial control strategies, especially those related to microbial analysis and raw material quality control. Additionally, the WLs considered frequently referred to failures in quality-related issues, which indicates that the quality commitment should be reinforced at most companies to avoid microbiological contaminations.LAY ABSTRACT: Microbial contamination of drug products affects the quality of non-sterile drug products produced by numerous manufacturers, representing a major risk to patients. It is necessary to understand the microbial hazards involved in the manufacturing process and evaluate their impact on final product quality so that effective prevention strategies can be implemented. A risk-based classification of most likely root causes for microbial contamination found in the warning letters issued by the US Food and Drug Administration and the European Medicines Agency is proposed. To validate the likely root causes extracted from the warning letters, a subject matter expert panel made of several manufacturers was formed and consulted. A quality risk management approach to assess microbiological contamination of non-sterile drug products is proposed for the identification of microbial hazards involved in the manufacturing process. To enable ranking of microbial contamination risks, quality risk management metrics related to criticality and overall risk were applied. The results showed that manufacturers of non-sterile drug products should improve their microbial control strategy, with special attention to quality controls of raw materials, primary containers, and closures. Besides that, they should invest in a more robust quality system and culture. As a start, manufacturers may consider investigating their specific microbiological risks, adressing their sites' own microbial ecology, type of manufacturing processes, and dosage form characteristics, as these may lead to increased contamination risks. Authorities should allow and enforce innovative, more comprehensive, and more effective approaches to in-process contamination monitoring and controls.}, }
@article {pmid29238751, year = {2017}, author = {Laforest-Lapointe, I and Messier, C and Kembel, SW}, title = {Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity.}, journal = {mSystems}, volume = {2}, number = {6}, pages = {}, pmid = {29238751}, issn = {2379-5077}, abstract = {Tree leaf-associated microbiota have been studied in natural ecosystems but less so in urban settings, where anthropogenic pressures on trees could impact microbial communities and modify their interaction with their hosts. Additionally, trees act as vectors spreading bacterial cells in the air in urban environments due to the density of microbial cells on aerial plant surfaces. Characterizing tree leaf bacterial communities along an urban gradient is thus key to understand the impact of anthropogenic pressures on urban tree-bacterium interactions and on the overall urban microbiome. In this study, we aimed (i) to characterize phyllosphere bacterial communities of seven tree species in urban environments and (ii) to describe the changes in tree phyllosphere bacterial community structure and diversity along a gradient of increasing urban intensity and at two degrees of tree isolation. Our results indicate that, as anthropogenic pressures increase, urban leaf bacterial communities show a reduction in the abundance of the dominant class in the natural plant microbiome, the Alphaproteobacteria. Our work in the urban environment here reveals that the structures of leaf bacterial communities differ along the gradient of urban intensity. The diversity of phyllosphere microbial communities increases at higher urban intensity, also displaying a greater number and variety of associated indicator taxa than the low and medium urban gradient sites. In conclusion, we find that urban environments influence tree bacterial community composition, and our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes. IMPORTANCE In natural forests, tree leaf surfaces host diverse bacterial communities whose structure and composition are primarily driven by host species identity. Tree leaf bacterial diversity has also been shown to influence tree community productivity, a key function of terrestrial ecosystems. However, most urban microbiome studies have focused on the built environment, improving our understanding of indoor microbial communities but leaving much to be understood, especially in the nonbuilt microbiome. Here, we provide the first multiple-species comparison of tree phyllosphere bacterial structures and diversity along a gradient of urban intensity. We demonstrate that urban trees possess characteristic bacterial communities that differ from those seen with trees in nonurban environments, with microbial community structure on trees influenced by host species identity but also by the gradient of urban intensity and by the degree of isolation from other trees. Our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes.}, }
@article {pmid29237993, year = {2018}, author = {Inaba, T and Hori, T and Sato, Y and Aoyagi, T and Hanajima, D and Ogata, A and Habe, H}, title = {Eukaryotic Microbiomes of Membrane-Attached Biofilms in Membrane Bioreactors Analyzed by High-Throughput Sequencing and Microscopic Observations.}, journal = {Microbes and environments}, volume = {33}, number = {1}, pages = {98-101}, pmid = {29237993}, issn = {1347-4405}, mesh = {Bacteria ; *Biofilms ; Biofouling ; Bioreactors/*microbiology ; *Eukaryota ; High-Throughput Nucleotide Sequencing ; *Microbiota ; RNA, Ribosomal, 18S ; Waste Disposal, Fluid/methods ; Wastewater/microbiology ; }, abstract = {Limited information is currently available on the contribution of eukaryotes to the reactor performance of membrane bioreactors (MBRs). Using high-throughput Illumina sequencing of 18S rRNA genes and microscopic observations, we investigated eukaryotic microbiomes in membrane-attached biofilms in MBRs treating piggery wastewater. Protozoa preying on bacteria were frequently detected under stable conditions when membrane clogging was suppressed. However, the eukaryotes preying upon protozoa became predominant in biofilms when membrane fouling rapidly progressed. We herein demonstrated that a comprehensive investigation of eukaryotic microbiomes using high-throughput sequencing contributes to a better understanding of the microbial ecology involved in wastewater treatment.}, }
@article {pmid29235707, year = {2018}, author = {Brewer, TE and Fierer, N}, title = {Tales from the tomb: the microbial ecology of exposed rock surfaces.}, journal = {Environmental microbiology}, volume = {20}, number = {3}, pages = {958-970}, doi = {10.1111/1462-2920.14024}, pmid = {29235707}, issn = {1462-2920}, mesh = {Bacteria/*classification/genetics ; Biodiversity ; *Calcium Carbonate ; *Metagenomics ; *Microbiota ; *Silicon Dioxide ; }, abstract = {Although a broad diversity of eukaryotic and bacterial taxa reside on rock surfaces where they can influence the weathering of rocks and minerals, these communities and their contributions to mineral weathering remain poorly resolved. To build a more comprehensive understanding of the diversity, ecology and potential functional attributes of microbial communities living on rock, we sampled 149 tombstones across three continents and analysed their bacterial and eukaryotic communities via marker gene and shotgun metagenomic sequencing. We found that geographic location and climate were important factors structuring the composition of these communities. Moreover, the tombstone-associated microbial communities varied as a function of rock type, with granite and limestone tombstones from the same cemeteries harbouring taxonomically distinct microbial communities. The granite and limestone-associated communities also had distinct functional attributes, with granite-associated bacteria having more genes linked to acid tolerance and chemotaxis, while bacteria on limestone were more likely to be lichen associated and have genes involved in photosynthesis and radiation resistance. Together these results indicate that rock-dwelling microbes exhibit adaptations to survive the stresses of the rock surface, differ based on location, climate and rock type, and seem pre-disposed to different ecological strategies (symbiotic versus free-living lifestyles) depending on the rock type.}, }
@article {pmid29234312, year = {2017}, author = {Flynn, TM and Koval, JC and Greenwald, SM and Owens, SM and Kemner, KM and Antonopoulos, DA}, title = {Parallelized, Aerobic, Single Carbon-Source Enrichments from Different Natural Environments Contain Divergent Microbial Communities.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2321}, pmid = {29234312}, issn = {1664-302X}, abstract = {Microbial communities that inhabit environments such as soil can contain thousands of distinct taxa, yet little is known about how this diversity is maintained in response to environmental perturbations such as changes in the availability of carbon. By utilizing aerobic substrate arrays to examine the effect of carbon amendment on microbial communities taken from six distinct environments (soil from a temperate prairie and forest, tropical forest soil, subalpine forest soil, and surface water and soil from a palustrine emergent wetland), we examined how carbon amendment and inoculum source shape the composition of the community in each enrichment. Dilute subsamples from each environment were used to inoculate 96-well microtiter plates containing triplicate wells amended with one of 31 carbon sources from six different classes of organic compounds (phenols, polymers, carbohydrates, carboxylic acids, amines, amino acids). After incubating each well aerobically in the dark for 72 h, we analyzed the composition of the microbial communities on the substrate arrays as well as the initial inocula by sequencing 16S rRNA gene amplicons using the Illumina MiSeq platform. Comparisons of alpha and beta diversity in these systems showed that, while the composition of the communities that grow to inhabit the wells in each substrate array diverges sharply from that of the original community in the inoculum, these enrichment communities are still strongly affected by the inoculum source. We found most enrichments were dominated by one or several OTUs most closely related to aerobes or facultative anaerobes from the Proteobacteria (e.g., Pseudomonas, Burkholderia, and Ralstonia) or Bacteroidetes (e.g., Chryseobacterium). Comparisons within each substrate array based on the class of carbon source further show that the communities inhabiting wells amended with a carbohydrate differ significantly from those enriched with a phenolic compound. Selection therefore seems to play a role in shaping the communities in the substrate arrays, although some stochasticity is also seen whereby several replicate wells within a single substrate array display strongly divergent community compositions. Overall, the use of highly parallel substrate arrays offers a promising path forward to study the response of microbial communities to perturbations in a changing environment.}, }
@article {pmid29234309, year = {2017}, author = {Becraft, ED and Woyke, T and Jarett, J and Ivanova, N and Godoy-Vitorino, F and Poulton, N and Brown, JM and Brown, J and Lau, MCY and Onstott, T and Eisen, JA and Moser, D and Stepanauskas, R}, title = {Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2264}, pmid = {29234309}, issn = {1664-302X}, abstract = {Recent advances in single-cell genomic and metagenomic techniques have facilitated the discovery of numerous previously unknown, deep branches of the tree of life that lack cultured representatives. Many of these candidate phyla are composed of microorganisms with minimalistic, streamlined genomes lacking some core metabolic pathways, which may contribute to their resistance to growth in pure culture. Here we analyzed single-cell genomes and metagenome bins to show that the "Candidate phylum Rokubacteria," formerly known as SPAM, represents an interesting exception, by having large genomes (6-8 Mbps), high GC content (66-71%), and the potential for a versatile, mixotrophic metabolism. We also observed an unusually high genomic heterogeneity among individual Rokubacteria cells in the studied samples. These features may have contributed to the limited recovery of sequences of this candidate phylum in prior cultivation and metagenomic studies. Our analyses suggest that Rokubacteria are distributed globally in diverse terrestrial ecosystems, including soils, the rhizosphere, volcanic mud, oil wells, aquifers, and the deep subsurface, with no reports from marine environments to date.}, }
@article {pmid29230650, year = {2018}, author = {Sun, H and Wu, Y and Bing, H and Zhou, J and Li, N}, title = {Available forms of nutrients and heavy metals control the distribution of microbial phospholipid fatty acids in sediments of the Three Gorges Reservoir, China.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {6}, pages = {5740-5751}, pmid = {29230650}, issn = {1614-7499}, mesh = {China ; Environmental Monitoring/*methods ; Fatty Acids/*analysis ; Geologic Sediments/*microbiology ; Humans ; Metals, Heavy/*analysis ; Phospholipids/*analysis ; Rivers/chemistry/microbiology ; Water Pollutants, Chemical/*analysis ; }, abstract = {The construction of the Three Gorges Reservoir (TGR) as well as the development of local industry and agriculture not only had tremendous impacts on the environment but also affected human health. Although water, soil, and air in the TGR have been well studied for environmental risk assessment, very little information is available on benthic sediments and microorganisms. In this study, sedimentary samples were collected along the main stream of the TGR to examine microbial phospholipid fatty acids (PLFA) and relevant variables (e.g., nutrients and heavy metals) after the full operation of the TGR. The results showed that there were prominent trends (increase or decrease) of sedimentary PLFAs and properties from downstream to upstream. Bacteria-specific PLFA decreased toward the dam, while fungi-specific PLFA did not show any significant trend. The PLFA ratio of fungi to bacteria (F/B) increased along the mainstream. The total PLFA concentration, which represents the microbial biomass, decreased significantly toward the dam. Upstream and downstream sampling points were clearly distinguished by PLFA ordination in the redundancy analysis (RDA). That finding showed microbial PLFAs to have an obvious distribution pattern (increase or decrease) in the TGR. The PLFA distribution was markedly controlled by nutrients and heavy metals, but nutrients were more important. Moreover, among nutrients, Bio-P, NH4[+]-N, NO3[-]-N, and DOC were more important than TP, TN, TOC, and pH in controlling PLFA distribution. For heavy metals, Tl, V, Mo, and Ni were more important than Zn, Cu, Cd, and Pb. These findings suggested that Tl, V, Mo, and Ni should not be ignored to guard against their pollution in the TGR, and we should pay attention to them and make them our first priority. This study highlighted that the construction of the TGR changed riverine environments and altered microbial communities in sediments by affecting sedimentary properties. It is a reminder that the microbial ecology of sediment as an indicator should be considered in assessing the eco-risk of the TGR.}, }
@article {pmid29230649, year = {2018}, author = {Ghosh, A and Bhadury, P}, title = {Investigating monsoon and post-monsoon variabilities of bacterioplankton communities in a mangrove ecosystem.}, journal = {Environmental science and pollution research international}, volume = {25}, number = {6}, pages = {5722-5739}, doi = {10.1007/s11356-017-0852-y}, pmid = {29230649}, issn = {1614-7499}, mesh = {Aquatic Organisms/isolation &amp; purification ; Base Sequence ; Biota/genetics ; Environmental Monitoring/*methods ; Fresh Water/microbiology ; Geologic Sediments/microbiology ; India ; Phylogeny ; Plankton/*isolation &amp; purification ; Proteobacteria/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Seasons ; *Wetlands ; }, abstract = {In mangrove environments, bacterioplankton communities constitute an important component of aquatic biota and play a major role in ecosystem processes. Variability of bacterioplankton communities from Sundarbans mangrove, located in the Indian subcontinent in South Asia and sits on the apex of Bay of Bengal, was investigated over monsoon and post-monsoon seasons. The study was undertaken in two stations in Sundarbans using 16S rRNA clone library and Illumina MiSeq approaches with focus on the functionally important members that participate in coastal biogeochemical cycling. Out of 544 sequenced clones, Proteobacteria dominated the study area (373 sequences) with persistence of two major classes, namely, Gammaproteobacteria and Alphaproteobacteria across both monsoon and post-monsoon seasons in both stations. Several sequences belonging to Sphingomonadales, Chromatiales, Alteromonadales, Oceanospirillales, and Bacteroidetes were encountered that are known to play important roles in coastal carbon cycling. Some sequences showed identity with published uncultured Planctomycetes and Chloroflexi highlighting their role in nitrogen cycling. The detection of two novel clades highlighted the existence of indigenous group of bacterioplankton that may play important roles in this ecosystem. The eubacterial V3-V4 region from environmental DNA extracted from the above two stations, followed by sequencing in Illumina MiSeq system, was also targeted in the study. A congruency between the clone library and Illumina approaches was observed. Strong variability in bacterioplankton community structure was encountered at a seasonal scale in link with precipitation. Drastic increase in sediment associated bacteria such as members of Firmicutes and Desulfovibrio was found in monsoon hinting possible resuspension of sediment-dwelling bacteria into the overlying water column. Principal component analysis (PCA) revealed dissolved ammonium and dissolved nitrate to account for maximum variation observed in the bacterioplankton community structure. Overall, the study showed that a strong interplay exists between environmental parameters and observed variability in bacterioplankton communities as a result of precipitation which can ultimately influence processes and rates linked to coastal biogeochemical cycles.}, }
@article {pmid29230200, year = {2017}, author = {Kreft, JU and Plugge, CM and Prats, C and Leveau, JHJ and Zhang, W and Hellweger, FL}, title = {From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2299}, pmid = {29230200}, issn = {1664-302X}, support = {NC/K000683/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; }, abstract = {Models are important tools in microbial ecology. They can be used to advance understanding by helping to interpret observations and test hypotheses, and to predict the effects of ecosystem management actions or a different climate. Over the past decades, biological knowledge and ecosystem observations have advanced to the molecular and in particular gene level. However, microbial ecology models have changed less and a current challenge is to make them utilize the knowledge and observations at the genetic level. We review published models that explicitly consider genes and make predictions at the population or ecosystem level. The models can be grouped into three general approaches, i.e., metabolic flux, gene-centric and agent-based. We describe and contrast these approaches by applying them to a hypothetical ecosystem and discuss their strengths and weaknesses. An important distinguishing feature is how variation between individual cells (individuality) is handled. In microbial ecosystems, individual heterogeneity is generated by a number of mechanisms including stochastic interactions of molecules (e.g., gene expression), stochastic and deterministic cell division asymmetry, small-scale environmental heterogeneity, and differential transport in a heterogeneous environment. This heterogeneity can then be amplified and transferred to other cell properties by several mechanisms, including nutrient uptake, metabolism and growth, cell cycle asynchronicity and the effects of age and damage. For example, stochastic gene expression may lead to heterogeneity in nutrient uptake enzyme levels, which in turn results in heterogeneity in intracellular nutrient levels. Individuality can have important ecological consequences, including division of labor, bet hedging, aging and sub-optimality. Understanding the importance of individuality and the mechanism(s) underlying it for the specific microbial system and question investigated is essential for selecting the optimal modeling strategy.}, }
@article {pmid29228191, year = {2018}, author = {Escudié, F and Auer, L and Bernard, M and Mariadassou, M and Cauquil, L and Vidal, K and Maman, S and Hernandez-Raquet, G and Combes, S and Pascal, G}, title = {FROGS: Find, Rapidly, OTUs with Galaxy Solution.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {8}, pages = {1287-1294}, doi = {10.1093/bioinformatics/btx791}, pmid = {29228191}, issn = {1367-4811}, mesh = {Bacteria/genetics ; Cluster Analysis ; Metagenomics/*methods ; *Software ; }, abstract = {MOTIVATION: Metagenomics leads to major advances in microbial ecology and biologists need user friendly tools to analyze their data on their own.<br><br>RESULTS: This Galaxy-supported pipeline, called FROGS, is designed to analyze large sets of amplicon sequences and produce abundance tables of Operational Taxonomic Units (OTUs) and their taxonomic affiliation. The clustering uses Swarm. The chimera removal uses VSEARCH, combined with original cross-sample validation. The taxonomic affiliation returns an innovative multi-affiliation output to highlight databases conflicts and uncertainties. Statistical results and numerous graphical illustrations are produced along the way to monitor the pipeline. FROGS was tested for the detection and quantification of OTUs on real and in silico datasets and proved to be rapid, robust and highly sensitive. It compares favorably with the widespread mothur, UPARSE and QIIME.<br><br>Source code and instructions for installation: https://github.com/geraldinepascal/FROGS.git. A companion website: http://frogs.toulouse.inra.fr.<br><br>CONTACT: geraldine.pascal@inra.fr.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid29225380, year = {2017}, author = {Mezgebe, B and Sorial, GA and Sahle-Demessie, E and Hassan, AA and Lu, J}, title = {Performance of Anaerobic Biotrickling Filter and its Microbial Diversity for the Removal of Stripped Disinfection Byproducts.}, journal = {Water, air, and soil pollution}, volume = {228}, number = {}, pages = {1-437}, pmid = {29225380}, issn = {0049-6979}, support = {EPA999999/ImEPA/Intramural EPA/United States ; EPA999999/ImEPA/Intramural EPA/United States ; }, abstract = {The objective of this research was to evaluate the biodegradation of chloroform by using biotrickling filter (BTF) and determining the dominant bacteria responsible for the degradation. The research was conducted in three phases under anaerobic condition, namely, in the presence of co-metabolite (Phase I), in the presence of co-metabolite and surfactant (Phase II) and in the presence of surfactant but no co-metabolite (Phase III). The results showed that the presence of ethanol as a co-metabolite provided 49% removal efficiency. The equivalent elimination capacity (EC) was 0.13 g/(m[3].hr). The addition of Tomadol 25 - 7 as a surfactant in the nutrient solution increased the removal efficiency of chloroform to 64% with corresponding EC of 0.17 g/(m[3].hr). This research also investigated the overall microbial ecology of the BTF utilizing culture-independent gene sequencing alignment of the 16S rRNA allowing identification of isolated species. Taxonomical composition revealed the abundance of deltaproteobacteria and deltaproteobacteria with species level of 97%. A. oryzae (formally dechlorosoma suillum), A. restrica and Geobacter spp. together with other similar groups were the most valuable bacteria for the degradation of chloroform.}, }
@article {pmid29224879, year = {2018}, author = {Bayat, AR and Tapio, I and Vilkki, J and Shingfield, KJ and Leskinen, H}, title = {Plant oil supplements reduce methane emissions and improve milk fatty acid composition in dairy cows fed grass silage-based diets without affecting milk yield.}, journal = {Journal of dairy science}, volume = {101}, number = {2}, pages = {1136-1151}, doi = {10.3168/jds.2017-13545}, pmid = {29224879}, issn = {1525-3198}, mesh = {Ammonia/metabolism ; Animal Feed/analysis ; Animals ; Cattle/*metabolism ; Diet/veterinary ; Dietary Fiber/metabolism ; Dietary Supplements/*analysis ; Digestion ; Energy Intake ; Fatty Acids/chemistry/*metabolism ; Female ; Fermentation ; Lactation ; Linseed Oil/*metabolism ; Methane/*biosynthesis ; Milk/chemistry/metabolism ; Poaceae/metabolism ; Rapeseed Oil/*metabolism ; Rumen/metabolism ; Safflower Oil/*metabolism ; Silage/*analysis ; }, abstract = {Four lipid supplements varying in chain length or degree of unsaturation were examined for their effects on milk yield and composition, ruminal CH4 emissions, rumen fermentation, nutrient utilization, and microbial ecology in lactating dairy cows. Five Nordic Red cows fitted with rumen cannulas were used in a 5 × 5 Latin square with five 28-d periods. Treatments comprised total mixed rations based on grass silage with a forage-to-concentrate ratio of 60:40 supplemented with no lipid (CO) or 50 g/kg of diet dry matter (DM) of myristic acid (MA), rapeseed oil (RO), safflower oil (SO), or linseed oil (LO). Feeding MA resulted in the lowest DM intake, and feeding RO reduced DM intake compared with CO. Feeding MA reduced the yields of milk, milk constituents, and energy-corrected milk. Plant oils did not influence yields of milk and milk constituents, but reduced milk protein content compared with CO. Treatments had no effect on rumen fermentation characteristics, other than an increase in ammonia-N concentration due to feeding MA, RO, and SO compared with CO. Lipid supplements reduced daily ruminal CH4 emission; however, the response was to some extent a result of lower feed intake. Lipids modified microbial community structure without affecting total counts of bacteria, archaea, and ciliate protozoa. Dietary treatments had no effect on the apparent total tract digestibility of organic matter, fiber, and gross energy. Treatments did not affect either energy secreted in milk as a proportion of energy intake or efficiency of dietary N utilization. All lipids lowered de novo fatty acid synthesis in the mammary gland. Plant oils increased proportions of milk fat 18:0, cis 18:1, trans and monounsaturated fatty acids, and decreased saturated fatty acids compared with CO and MA. Both SO and LO increased the proportion of total polyunsaturated fatty acids, total conjugated linolenic acid, and cis-9,trans-11 conjugated linoleic acid. Feeding MA clearly increased the Δ[9] desaturation of fatty acids. Our results provide compelling evidence that plant oils supplemented to a grass silage-based diet reduce ruminal CH4 emission and milk saturated fatty acids, and increase the proportion of unsaturated fatty acids and total conjugated linoleic acid while not interfering with digestibility, rumen fermentation, rumen microbial quantities, or milk production.}, }
@article {pmid29222576, year = {2018}, author = {McGee, CF}, title = {Microbial ecology of the Agaricus bisporus mushroom cropping process.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {3}, pages = {1075-1083}, pmid = {29222576}, issn = {1432-0614}, mesh = {Agaricus/*growth &amp; development ; Bacteria/*metabolism ; Bacterial Physiological Phenomena ; *Composting ; Microbial Consortia/*physiology ; Mycelium/growth &amp; development ; Nitrogen/metabolism ; *Soil Microbiology ; Triticum/microbiology ; }, abstract = {Agaricus bisporus is the most widely cultivated mushroom species in the world. Cultivation is commenced by inoculating beds of semi-pasteurised composted organic substrate with a pure spawn of A. bisporus. The A. bisporus mycelium subsequently colonises the composted substrate by degrading the organic material to release nutrients. A layer of peat, often called "casing soil", is laid upon the surface of the composted substrate to induce the development of the mushroom crop and maintain compost environmental conditions. Extensive research has been conducted investigating the biochemistry and genetics of A. bisporus throughout the cultivation process; however, little is currently known about the wider microbial ecology that co-inhabits the composted substrate and casing layers. The compost and casing microbial communities are known to play important roles in the mushroom production process. Microbial species present in the compost and casing are known for (1) being an important source of nitrogen for the A. bisporus mycelium, (2) releasing sugar residues through the degradation of the wheat straw in the composted substrate, (3) playing a critical role in inducing development of the A. bisporus fruiting bodies and (4) acting as pathogens by parasitising the mushroom mycelium/crop. Despite a long history of research into the mushroom cropping process, an extensive review of the microbial communities present in the compost and casing has not as of yet been undertaken. The aim of this review is to provide a comprehensive summary of the literature investigating the compost and casing microbial communities throughout cultivation of the A. bisporus mushroom crop.}, }
@article {pmid29222101, year = {2018}, author = {Deng, J and Auchtung, JM and Konstantinidis, KT and Caro-Quintero, A and Brettar, I and Höfle, M and Tiedje, JM}, title = {Divergence in Gene Regulation Contributes to Sympatric Speciation of Shewanella baltica Strains.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {4}, pages = {}, pmid = {29222101}, issn = {1098-5336}, mesh = {*Gene Expression Regulation ; *Genetic Speciation ; Genome, Bacterial/*genetics ; Multilocus Sequence Typing ; Nucleic Acid Hybridization ; Shewanella/*genetics ; Sympatry ; }, abstract = {Niche partitioning and sequence evolution drive genomic and phenotypic divergence, which ultimately leads to bacterial diversification. This study investigated the genomic composition of two Shewanella baltica clades previously identified through multilocus sequencing typing and recovered from the redox transition zone in the central Baltic Sea. Comparative genomic analysis revealed significantly higher interclade than intraclade genomic dissimilarity and that a subset of genes present in clade A were associated with potential adaptation to respiration of sulfur compounds present in the redox transition zone. The transcriptomic divergence between two representative strains of clades A and D, OS185 and OS195, was also characterized and revealed marked regulatory differences. We found that both the transcriptional divergence of shared genes and expression of strain-specific genes led to differences in regulatory patterns between strains that correlate with environmental redox niches. For instance, under anoxic conditions of respiratory nitrate ammonification, OS185-the strain isolated from a nitrate-rich environment-upregulated nearly twice the number of shared genes upregulated by OS195-the strain isolated from an H2S-containing anoxic environment. Conversely, OS195 showed stronger induction of strain-specific genes, especially those associated with sulfur compound respiration, under thiosulfate-reducing conditions. A positive association between the level of transcriptional divergence and the level of sequence divergence for shared genes was also noted. Our results provide further support for the hypothesis that genomic changes impacting transcriptional regulation play an important role in the diversification of ecologically distinct populations.IMPORTANCE This study examined potential mechanisms through which co-occurring Shewanella baltica strains diversified to form ecologically distinct populations. At the time of isolation, the strains studied composed the major fraction of culturable nitrate-reducing communities in the Baltica Sea. Analysis of genomic content of 13 S. baltica strains from two clades representing different ecotypes demonstrated that one clade specifically possesses a number of genes that could favor successful adaptation to respire sulfur compounds in the portion of the water column from which these strains were isolated. In addition, transcriptional profiling of fully sequenced strains representative of these two clades, OS185 and OS195, under oxygen-, nitrate-, and thiosulfate-respiring conditions demonstrated that the strains exhibit relatively similar transcriptional responses during aerobic growth but more-distinct transcriptional responses under nitrate- and thiosulfate-respiring conditions. Results from this study provide insights into how genomic and gene regulatory diversification together impacted the redox specialization of the S. baltica strains.}, }
@article {pmid29220785, year = {2018}, author = {Lekunberri, I and Balcázar, JL and Borrego, CM}, title = {Metagenomic exploration reveals a marked change in the river resistome and mobilome after treated wastewater discharges.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {234}, number = {}, pages = {538-542}, doi = {10.1016/j.envpol.2017.12.001}, pmid = {29220785}, issn = {1873-6424}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/*drug effects/*genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial ; Drug Resistance, Microbial/genetics ; Humans ; Metagenomics ; Rivers/*microbiology ; Wastewater/*chemistry/microbiology ; }, abstract = {Mobile genetic elements (MGEs) are key agents in the spread of antibiotic resistance genes (ARGs) across environments. Here we used metagenomics to compare the river resistome (collection of all ARGs) and mobilome (e.g., integrases, transposases, integron integrases and insertion sequence common region "ISCR" elements) between samples collected upstream (n = 6) and downstream (n = 6) of an urban wastewater treatment plant (UWWTP). In comparison to upstream metagenomes, downstream metagenomes showed a drastic increase in the abundance of ARGs, as well as markers of MGEs, particularly integron integrases and ISCR elements. These changes were accompanied by a concomitant prevalence of 16S rRNA gene signatures of bacteria affiliated to families encompassing well-known human and animal pathogens. Our results confirm that chronic discharges of treated wastewater severely impact the river resistome affecting not only the abundance and diversity of ARGs but also their potential spread by enriching the river mobilome in a wide variety of MGEs.}, }
@article {pmid29218373, year = {2018}, author = {Pepori, AL and Bettini, PP and Comparini, C and Sarrocco, S and Bonini, A and Frascella, A and Ghelardini, L and Scala, A and Vannacci, G and Santini, A}, title = {Correction to: Geosmithia-Ophiostoma: a New Fungus-Fungus Association.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {298}, doi = {10.1007/s00248-017-1121-9}, pmid = {29218373}, issn = {1432-184X}, abstract = {The article Geosmithia-Ophiostoma: a New Fungus-Fungus Association, written by Alessia L. Pepori, Priscilla P. Bettini, Cecilia Comparini, Sabrina Sarrocco, Anna Bonini, Arcangela Frascella, Luisa Ghelardini, &amp; Aniello Scala, Giovanni Vannacci, Alberto Santini.}, }
@article {pmid29218372, year = {2018}, author = {Schlatter, DC and Yin, C and Burke, I and Hulbert, S and Paulitz, T}, title = {Location, Root Proximity, and Glyphosate-Use History Modulate the Effects of Glyphosate on Fungal Community Networks of Wheat.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {240-257}, pmid = {29218372}, issn = {1432-184X}, support = {2011-68002-30191//USDA NIFA/ ; }, mesh = {Agriculture ; Biodiversity ; *Community Networks ; DNA, Fungal/analysis ; Fungi/classification/drug effects/genetics ; Glycine/adverse effects/*analogs &amp; derivatives ; Herbicides/*adverse effects ; Mycobiome/*drug effects/genetics ; Plant Roots/*microbiology ; Rhizosphere ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; Triticum/*microbiology ; Washington ; Glyphosate ; }, abstract = {Glyphosate is the most-used herbicide worldwide and an essential tool for weed control in no-till cropping systems. However, concerns have been raised regarding the long-term effects of glyphosate on soil microbial communities. We examined the impact of repeated glyphosate application on bulk and rhizosphere soil fungal communities of wheat grown in four soils representative of the dryland wheat production region of Eastern Washington, USA. Further, using soils from paired fields, we contrasted the response of fungal communities that had a long history of glyphosate exposure and those that had no known exposure. Soil fungal communities were characterized after three cycles of wheat growth in the greenhouse followed by termination with glyphosate or manual clipping of plants. We found that cropping system, location, year, and root proximity were the primary drivers of fungal community compositions, and that glyphosate had only small impacts on fungal community composition or diversity. However, the taxa that responded to glyphosate applications differed between rhizosphere and bulk soil and between cropping systems. Further, a greater number of fungal OTUs responded to glyphosate in soils with a long history of glyphosate use. Finally, fungal co-occurrence patterns, but not co-occurrence network characteristics, differed substantially between glyphosate-treated and non-treated communities. Results suggest that most fungi influenced by glyphosate are saprophytes that likely feed on dying roots.}, }
@article {pmid29217934, year = {2017}, author = {Onuoha, SC}, title = {The Prevalence of Antibiotic Resistant Diarrhogenic Bacterial Species in Surface Waters, South Eastern Nigeria.}, journal = {Ethiopian journal of health sciences}, volume = {27}, number = {4}, pages = {319-330}, pmid = {29217934}, issn = {2413-7170}, mesh = {*Anti-Bacterial Agents/therapeutic use ; *Bacteria ; Diarrhea/etiology/*microbiology ; *Drug Resistance, Bacterial ; Enterobacter ; Escherichia coli ; Humans ; Klebsiella ; Microbial Sensitivity Tests ; Nigeria ; Prevalence ; Pseudomonas ; Rivers/*microbiology ; Salmonella ; Shigella ; *Water Microbiology ; }, abstract = {BACKGROUND: This study assessed the bacteriological qualities of surface waters in Afikpo, between April and September 2016.<br><br>METHODS: Surface water samples were collected from three streams for bacteriological analysis. Bacteria species were isolated using standard microbiological and biochemical techniques. Antibiotic susceptibility study was carried out using Kirby Bauer disc diffusion method.<br><br>RESULTS: The result of the mean heterotrophic bacteria count from the streams showed that Okpu stream had 209.5CFU/100 mL, Ohino Ngodo 162.5 CFU/100mL, and Ngwogo stream 162.0 CFU/100mL respectively. Out of the twenty-six (26) isolates obtained, E. coli and Staphylococcus species had the highest percentage occurrence (23.1%) respectively. Klebsiella, Shigella and Enterobacter sp had (11.5%) each, Pseudomonas spp (7.7%), while Salmonella and Streptococcus sp had the least percentage occurrence of (3.8%). The antibiotic susceptibility studies showed that large proportions of isolates were resistant to sulphamethaxoid (SUL), cephalothin (CEP), tetracycline (TET), penicillin G (PEN), oxytetracycline (OXY), cefotaxime (CEF), nalidixic acid (NAL) and cefuroxime sodium (CXM). The most effective antibiotic was azithromycin followed by imipenem.<br><br>CONCLUSION: The presence of these multi-drug resistant strains in water samples could facilitate transmission of antibiotic resistance. This emphasizes the need for proper treatment of water in the study area.}, }
@article {pmid29217396, year = {2018}, author = {Sutherland, WJ and Butchart, SHM and Connor, B and Culshaw, C and Dicks, LV and Dinsdale, J and Doran, H and Entwistle, AC and Fleishman, E and Gibbons, DW and Jiang, Z and Keim, B and Roux, XL and Lickorish, FA and Markillie, P and Monk, KA and Mortimer, D and Pearce-Higgins, JW and Peck, LS and Pretty, J and Seymour, CL and Spalding, MD and Tonneijck, FH and Gleave, RA}, title = {A 2018 Horizon Scan of Emerging Issues for Global Conservation and Biological Diversity.}, journal = {Trends in ecology &amp; evolution}, volume = {33}, number = {1}, pages = {47-58}, doi = {10.1016/j.tree.2017.11.006}, pmid = {29217396}, issn = {1872-8383}, mesh = {*Biodiversity ; *Conservation of Natural Resources ; *Ecosystem ; }, abstract = {This is our ninth annual horizon scan to identify emerging issues that we believe could affect global biological diversity, natural capital and ecosystem services, and conservation efforts. Our diverse and international team, with expertise in horizon scanning, science communication, as well as conservation science, practice, and policy, reviewed 117 potential issues. We identified the 15 that may have the greatest positive or negative effects but are not yet well recognised by the global conservation community. Themes among these topics include new mechanisms driving the emergence and geographic expansion of diseases, innovative biotechnologies, reassessments of global change, and the development of strategic infrastructure to facilitate global economic priorities.}, }
@article {pmid29216487, year = {2018}, author = {Eckert, EM and Di Cesare, A and Kettner, MT and Arias-Andres, M and Fontaneto, D and Grossart, HP and Corno, G}, title = {Microplastics increase impact of treated wastewater on freshwater microbial community.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {234}, number = {}, pages = {495-502}, doi = {10.1016/j.envpol.2017.11.070}, pmid = {29216487}, issn = {1873-6424}, mesh = {Bacteria/classification/*drug effects/genetics/isolation &amp; purification ; *Biodiversity ; Ecosystem ; Environmental Monitoring/methods ; Lakes/chemistry/*microbiology ; Plastics/analysis/*pharmacology ; Wastewater/chemistry ; Water Pollutants, Chemical/analysis/*pharmacology ; }, abstract = {Plastic pollution is a major global concern with several million microplastic particles entering every day freshwater ecosystems via wastewater discharge. Microplastic particles stimulate biofilm formation (plastisphere) throughout the water column and have the potential to affect microbial community structure if they accumulate in pelagic waters, especially enhancing the proliferation of biohazardous bacteria. To test this scenario, we simulated the inflow of treated wastewater into a temperate lake using a continuous culture system with a gradient of concentration of microplastic particles. We followed the effect of microplastics on the microbial community structure and on the occurrence of integrase 1 (int1), a marker associated with mobile genetic elements known as a proxy for anthropogenic effects on the spread of antimicrobial resistance genes. The abundance of int1 increased in the plastisphere with increasing microplastic particle concentration, but not in the water surrounding the microplastic particles. Likewise, the microbial community on microplastic was more similar to the original wastewater community with increasing microplastic concentrations. Our results show that microplastic particles indeed promote persistence of typical indicators of microbial anthropogenic pollution in natural waters, and substantiate that their removal from treated wastewater should be prioritised.}, }
@article {pmid29212730, year = {2017}, author = {Perofsky, AC and Lewis, RJ and Abondano, LA and Di Fiore, A and Meyers, LA}, title = {Hierarchical social networks shape gut microbial composition in wild Verreaux's sifaka.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1868}, pages = {}, pmid = {29212730}, issn = {1471-2954}, support = {U01 GM087719/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Female ; *Gastrointestinal Microbiome ; Grooming ; Madagascar ; Male ; RNA, Ribosomal, 16S/genetics ; *Social Behavior ; Strepsirhini/*microbiology/*physiology ; }, abstract = {In wild primates, social behaviour influences exposure to environmentally acquired and directly transmitted microorganisms. Prior studies indicate that gut microbiota reflect pairwise social interactions among chimpanzee and baboon hosts. Here, we demonstrate that higher-order social network structure-beyond just pairwise interactions-drives gut bacterial composition in wild lemurs, which live in smaller and more cohesive groups than previously studied anthropoid species. Using 16S rRNA gene sequencing and social network analysis of grooming contacts, we estimate the relative impacts of hierarchical (i.e. multilevel) social structure, individual demographic traits, diet, scent-marking, and habitat overlap on bacteria acquisition in a wild population of Verreaux's sifaka (Propithecus verreauxi) consisting of seven social groups. We show that social group membership is clearly reflected in the microbiomes of individual sifaka, and that social groups with denser grooming networks have more homogeneous gut microbial compositions. Within social groups, adults, more gregarious individuals, and individuals that scent-mark frequently harbour the greatest microbial diversity. Thus, the community structure of wild lemurs governs symbiotic relationships by constraining transmission between hosts and partitioning environmental exposure to microorganisms. This social cultivation of mutualistic gut flora may be an evolutionary benefit of tight-knit group living.}, }
@article {pmid29211803, year = {2017}, author = {Šket, R and Treichel, N and Kublik, S and Debevec, T and Eiken, O and Mekjavić, I and Schloter, M and Vital, M and Chandler, J and Tiedje, JM and Murovec, B and Prevoršek, Z and Likar, M and Stres, B}, title = {Hypoxia and inactivity related physiological changes precede or take place in absence of significant rearrangements in bacterial community structure: The PlanHab randomized trial pilot study.}, journal = {PloS one}, volume = {12}, number = {12}, pages = {e0188556}, pmid = {29211803}, issn = {1932-6203}, mesh = {Bacteria/*classification/genetics ; *Bacterial Physiological Phenomena ; Chromatography, High Pressure Liquid ; Cross-Over Studies ; Exercise ; Feces/chemistry ; Healthy Volunteers ; Humans ; Hypoxia/*metabolism ; Male ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {We explored the assembly of intestinal microbiota in healthy male participants during the randomized crossover design of run-in (5 day) and experimental phases (21-day normoxic bed rest (NBR), hypoxic bed rest (HBR) and hypoxic ambulation (HAmb) in a strictly controlled laboratory environment, with balanced fluid and dietary intakes, controlled circadian rhythm, microbial ambiental burden and 24/7 medical surveillance. The fraction of inspired O2 (FiO2) and partial pressure of inspired O2 (PiO2) were 0.209 and 133.1 ± 0.3 mmHg for NBR and 0.141 ± 0.004 and 90.0 ± 0.4 mmHg for both hypoxic variants (HBR and HAmb; ~4000 m simulated altitude), respectively. A number of parameters linked to intestinal environment such as defecation frequency, intestinal electrical conductivity (IEC), sterol and polyphenol content and diversity, indole, aromaticity and spectral characteristics of dissolved organic matter (DOM) were measured (64 variables). The structure and diversity of bacterial microbial community was assessed using 16S rRNA amplicon sequencing. Inactivity negatively affected frequency of defecation and in combination with hypoxia increased IEC (p < 0.05). In contrast, sterol and polyphenol diversity and content, various characteristics of DOM and aromatic compounds, the structure and diversity of bacterial microbial community were not significantly affected over time. A new in-house PlanHab database was established to integrate all measured variables on host physiology, diet, experiment, immune and metabolic markers (n = 231). The observed progressive decrease in defecation frequency and concomitant increase in IEC suggested that the transition from healthy physiological state towards the developed symptoms of low magnitude obesity-related syndromes was dose dependent on the extent of time spent in inactivity and preceded or took place in absence of significant rearrangements in bacterial microbial community. Species B. thetaiotamicron, B. fragilis, B. dorei and other Bacteroides with reported relevance for dysbiotic medical conditions were significantly enriched in HBR, characterized with most severe inflammation symptoms, indicating a shift towards host mucin degradation and proinflammatory immune crosstalk.}, }
@article {pmid29208946, year = {2018}, author = {Mehrshad, M and Rodriguez-Valera, F and Amoozegar, MA and López-García, P and Ghai, R}, title = {The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling.}, journal = {The ISME journal}, volume = {12}, number = {3}, pages = {655-668}, pmid = {29208946}, issn = {1751-7370}, support = {322669/ERC_/European Research Council/International ; }, mesh = {Chloroflexi/classification/genetics/*isolation &amp; purification/*metabolism ; Genomics ; Metagenome ; Metagenomics ; Microbiota ; Oceans and Seas ; Phylogeny ; Seawater/*microbiology ; Sulfur/*metabolism ; }, abstract = {The dark ocean microbiota represents the unknown majority in the global ocean waters. The SAR202 cluster belonging to the phylum Chloroflexi was the first microbial lineage discovered to specifically inhabit the aphotic realm, where they are abundant and globally distributed. The absence of SAR202 cultured representatives is a significant bottleneck towards understanding their metabolic capacities and role in the marine environment. In this work, we use a combination of metagenome-assembled genomes from deep-sea datasets and publicly available single-cell genomes to construct a genomic perspective of SAR202 phylogeny, metabolism and biogeography. Our results suggest that SAR202 cluster members are medium sized, free-living cells with a heterotrophic lifestyle, broadly divided into two distinct clades. We present the first evidence of vertical stratification of these microbes along the meso- and bathypelagic ocean layers. Remarkably, two distinct species of SAR202 cluster are highly abundant in nearly all deep bathypelagic metagenomic datasets available so far. SAR202 members metabolize multiple organosulfur compounds, many appear to be sulfite-oxidizers and are predicted to play a major role in sulfur turnover in the dark water column. This concomitantly suggests an unsuspected availability of these nutrient sources to allow for the high abundance of these microbes in the deep sea.}, }
@article {pmid29208740, year = {2017}, author = {Mikkelson, KM and Brouillard, BM and Bokman, CM and Sharp, JO}, title = {Ecosystem Resilience and Limitations Revealed by Soil Bacterial Community Dynamics in a Bark Beetle-Impacted Forest.}, journal = {mBio}, volume = {8}, number = {6}, pages = {}, pmid = {29208740}, issn = {2150-7511}, mesh = {Ammonium Compounds/analysis ; Animals ; Bacteria/*classification/genetics ; Biodiversity ; Carbon/analysis ; Coleoptera/*physiology ; Colorado ; DNA, Bacterial/genetics ; *Ecosystem ; *Forests ; Microbial Consortia ; Plant Bark/*parasitology ; Plant Diseases/parasitology/statistics &amp; numerical data ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Forested ecosystems throughout the world are experiencing increases in the incidence and magnitude of insect-induced tree mortality with large ecologic ramifications. Interestingly, correlations between water quality and the extent of tree mortality in Colorado montane ecosystems suggest compensatory effects from adjacent live vegetation that mute responses in less severely impacted forests. To this end, we investigated whether the composition of the soil bacterial community and associated functionality beneath beetle-killed lodgepole pine was influenced by the extent of surrounding tree mortality. The most pronounced changes were observed in the potentially active bacterial community, where alpha diversity increased in concert with surrounding tree mortality until mortality exceeded a tipping point of ~30 to 40%, after which diversity stabilized and decreased. Community structure also clustered in association with the extent of surrounding tree mortality with compositional trends best explained by differences in NH4[+] concentrations and C/N ratios. C/N ratios, which were lower in soils under beetle-killed trees, further correlated with the relative abundance of putative nitrifiers and exoenzyme activity. Collectively, the response of soil microorganisms that drive heterotrophic respiration and decay supports observations of broader macroscale threshold effects on water quality in heavily infested forests and could be utilized as a predictive mechanism during analogous ecosystem disruptions.IMPORTANCE Forests around the world are succumbing to insect infestation with repercussions for local soil biogeochemistry and downstream water quality and quantity. This study utilized microbial community dynamics to address why we are observing watershed scale biogeochemical impacts from forest mortality in some impacted areas but not others. Through a unique "tree-centric" approach, we were able to delineate plots with various tree mortality levels within the same watershed to see if surviving surrounding vegetation altered microbial and biogeochemical responses. Our results suggest that forests with lower overall tree mortality levels are able to maintain "normal" ecosystem function, as the bacterial community appears resistant to tree death. However, surrounding tree mortality influences this mitigating effect with various linear and threshold responses whereupon the bacterial community and its function are altered. Our study lends insight into how microscale responses propagate upward into larger-scale observations, which may be useful for future predictions during analogous disruptions.}, }
@article {pmid29207350, year = {2018}, author = {Garbisu, C and Garaiyurrebaso, O and Lanzén, A and Álvarez-Rodríguez, I and Arana, L and Blanco, F and Smalla, K and Grohmann, E and Alkorta, I}, title = {Mobile genetic elements and antibiotic resistance in mine soil amended with organic wastes.}, journal = {The Science of the total environment}, volume = {621}, number = {}, pages = {725-733}, doi = {10.1016/j.scitotenv.2017.11.221}, pmid = {29207350}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Codon, Nonsense ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/genetics ; *Integrons ; *Mining ; *Plasmids ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Metal resistance has been associated with antibiotic resistance due to co- or cross-resistance mechanisms. Here, metal contaminated mine soil treated with organic wastes was screened for the presence of mobile genetic elements (MGEs). The occurrence of conjugative IncP-1 and mobilizable IncQ plasmids, as well as of class 1 integrons, was confirmed by PCR and Southern blot hybridization, suggesting that bacteria from these soils have gene-mobilizing capacity with implications for the dissemination of resistance factors. Moreover, exogenous isolation of MGEs from the soil bacterial community was attempted under antibiotic selection pressure by using Escherichia coli as recipient. Seventeen putative transconjugants were identified based on increased antibiotic resistance. Metabolic traits and metal resistance of putative transconjugants were investigated, and whole genome sequencing was carried out for two of them. Most putative transconjugants displayed a multi-resistant phenotype for a broad spectrum of antibiotics. They also displayed changes regarding the ability to metabolise different carbon sources, RNA: DNA ratio, growth rate and biofilm formation. Genome sequencing of putative transconjugants failed to detect genes acquired by horizontal gene transfer, but instead revealed a number of nonsense mutations, including in ubiH, whose inactivation was linked to the observed resistance to aminoglycosides. Our results confirm that mine soils contain MGEs encoding antibiotic resistance. Moreover, they point out the role of spontaneous mutations in achieving low-level antibiotic resistance in a short time, which was associated with a trade-off in the capability to metabolise specific carbon sources.}, }
@article {pmid29207308, year = {2018}, author = {Oyserman, BO and Medema, MH and Raaijmakers, JM}, title = {Road MAPs to engineer host microbiomes.}, journal = {Current opinion in microbiology}, volume = {43}, number = {}, pages = {46-54}, doi = {10.1016/j.mib.2017.11.023}, pmid = {29207308}, issn = {1879-0364}, mesh = {Animals ; Genetic Engineering/*methods ; Host Microbial Interactions/*genetics ; Humans ; Microbial Consortia/*genetics ; Microbiota/genetics ; Phenotype ; Probiotics ; }, abstract = {Microbiomes contribute directly or indirectly to host health and fitness. Thus far, investigations into these emergent traits, referred to here as microbiome-associated phenotypes (MAPs), have been primarily qualitative and taxonomy-driven rather than quantitative and trait-based. We present the MAPs-first approach, a theoretical and experimental roadmap that involves quantitative profiling of MAPs across genetically variable hosts and subsequent identification of the underlying mechanisms. We outline strategies for developing 'modular microbiomes'-synthetic microbial consortia that are engineered in concert with the host genotype to confer different but mutually compatible MAPs to a single host or host population. By integrating host and microbial traits, these strategies will facilitate targeted engineering of microbiomes to the benefit of agriculture, human/animal health and biotechnology.}, }
@article {pmid29207271, year = {2017}, author = {Rillig, MC and Mansour, I}, title = {Microbial Ecology: Community Coalescence Stirs Things Up.}, journal = {Current biology : CB}, volume = {27}, number = {23}, pages = {R1280-R1282}, doi = {10.1016/j.cub.2017.10.027}, pmid = {29207271}, issn = {1879-0445}, mesh = {Chemoautotrophic Growth ; *Euryarchaeota ; Methane ; *Microbiota ; }, abstract = {When methane-producing microbial communities are mixed experimentally, the resulting community is dominated by the community with the greatest resource-use efficiency. These results suggest a degree of community cohesion, or the maintenance of that initial community in the mix.}, }
@article {pmid29206925, year = {2018}, author = {de Bruijn, I and Liu, Y and Wiegertjes, GF and Raaijmakers, JM}, title = {Exploring fish microbial communities to mitigate emerging diseases in aquaculture.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {1}, pages = {}, doi = {10.1093/femsec/fix161}, pmid = {29206925}, issn = {1574-6941}, mesh = {Animal Feed ; Animals ; Aquaculture/*methods ; Bacteria/*classification/*isolation &amp; purification ; Fish Diseases/microbiology ; Fishes/*microbiology ; Humans ; *Microbial Consortia ; Seafood/*microbiology ; Shellfish/*microbiology ; }, abstract = {Aquaculture is the fastest growing animal food sector worldwide and expected to further increase to feed the growing human population. However, existing and (re-)emerging diseases are hampering fish and shellfish cultivation and yield. For many diseases, vaccination protocols are not in place and the excessive use of antibiotics and other chemicals is of substantial concern. A more sustainable disease control strategy to protect fish and shellfish from (re-)emerging diseases could be achieved by introduction or augmentation of beneficial microbes. To establish and maintain a 'healthy' fish microbiome, a fundamental understanding of the diversity and temporal-spatial dynamics of fish-associated microbial communities and their impact on growth and health of their aquatic hosts is required. This review describes insights in the diversity and functions of the fish bacterial communities elucidated with next-generation sequencing and discusses the potential of the microbes to mitigate (re-)emerging diseases in aquaculture.}, }
@article {pmid29204781, year = {2018}, author = {Veach, AM and Stokes, CE and Knoepp, J and Jumpponen, A and Baird, R}, title = {Fungal Communities and Functional Guilds Shift Along an Elevational Gradient in the Southern Appalachian Mountains.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {156-168}, pmid = {29204781}, issn = {1432-184X}, support = {DEB0218001//National Science Foundation/ ; DEB0823293//National Science Foundation/ ; }, mesh = {Biodiversity ; DNA, Fungal/analysis ; Ecosystem ; Forests ; Fungi/classification/physiology ; Hydrogen-Ion Concentration ; Mortierella/physiology ; Mycobiome/*physiology ; Mycorrhizae/*chemistry ; Nitrogen ; North Carolina ; Plants ; Soil/*chemistry ; *Soil Microbiology ; Temperature ; }, abstract = {Nitrogen deposition alters forest ecosystems particularly in high elevation, montane habitats where nitrogen deposition is greatest and continues to increase. We collected soils across an elevational (788-1940 m) gradient, encompassing both abiotic (soil chemistry) and biotic (vegetation community) gradients, at eight locations in the southern Appalachian Mountains of southwestern North Carolina and eastern Tennessee. We measured soil chemistry (total N, C, extractable PO4, soil pH, cation exchange capacity [ECEC], percent base saturation [% BS]) and dissected soil fungal communities using ITS2 metabarcode Illumina MiSeq sequencing. Total soil N, C, PO4, % BS, and pH increased with elevation and plateaued at approximately 1400 m, whereas ECEC linearly increased and C/N decreased with elevation. Fungal communities differed among locations and were correlated with all chemical variables, except PO4, whereas OTU richness increased with total N. Several ecological guilds (i.e., ectomycorrhizae, saprotrophs, plant pathogens) differed in abundance among locations; specifically, saprotroph abundance, primarily attributable to genus Mortierella, was positively correlated with elevation. Ectomycorrhizae declined with total N and soil pH and increased with total C and PO4 where plant pathogens increased with total N and decreased with total C. Our results demonstrate significant turnover in taxonomic and functional fungal groups across elevational gradients which facilitate future predictions on forest ecosystem change in the southern Appalachians as nitrogen deposition rates increase and regional temperature and precipitation regimes shift.}, }
@article {pmid29202841, year = {2017}, author = {Xu, J and Verbrugghe, A and Lourenço, M and Cools, A and Liu, DJX and Van de Wiele, T and Marzorati, M and Eeckhaut, V and Van Immerseel, F and Vanhaecke, L and Campos, M and Hesta, M}, title = {The response of canine faecal microbiota to increased dietary protein is influenced by body condition.}, journal = {BMC veterinary research}, volume = {13}, number = {1}, pages = {374}, pmid = {29202841}, issn = {1746-6148}, support = {20101061//China Scholarship Council/ ; }, mesh = {Animals ; Case-Control Studies ; DNA, Bacterial/genetics ; Dietary Proteins/*pharmacology ; Dog Diseases/metabolism/*microbiology/physiopathology ; Dogs/*metabolism/physiology ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Male ; Obesity/metabolism/microbiology/physiopathology/*veterinary ; Polymerase Chain Reaction/veterinary ; }, abstract = {BACKGROUND: High protein diets shift the faecal microbiota into a more unfavourable composition in obese humans. In lean dogs, higher protein consumption is accompanied with increased production of putrefactive fermentation products, whereas obese dogs have a different gut microbiota compared to lean dogs. Still, the impact of high dietary protein on gut microbiota in obese dogs remains unclear. The aim of this study was to investigate faecal microbial changes in lean and obese dogs in response to two different levels of dietary protein. Six healthy lean and six obese Beagles were fed a high protein diet (HP) and a low protein diet (LP) for 28 days each in a crossover design. Denaturing gradient gel electrophoresis and quantitative PCR were performed on faecal samples for microbial profiling. Plasma acylcarnitine and fermentation metabolites were measured.<br><br>RESULTS: Dogs fed HP had higher concentrations of protein fermentation metabolites including faecal ammonia, isovalerate, isobutyrate, phenol, indole, serum indoxyl sulphate and plasma 3-OH isovalerylcarnitine compared to dogs fed LP, whereas no changes in faecal concentrations of acetate and butyrate were observed. The abundances of clostridial clusters IV and XIVa, covering the majority of butyrate-producing bacteria, and of the butyrate kinase gene, one of the terminal genes of the butyrate synthesis pathway were higher in dogs on HP compared to LP. Significant interactions between diet and body condition were found for the abundance of Firmicutes, Lactobacillus and clostridial cluster I. The similarity coefficient of faecal microbiota between the two diets was smaller in obese dogs than in lean dogs.<br><br>CONCLUSIONS: High protein diet increased the abundance and activity of butyrate-producing bacteria in Beagles independent of the body condition. In addition, increasing dietary protein content had a greater overall impact on faecal microbiota in obese compared to lean dogs.}, }
@article {pmid29197773, year = {2018}, author = {De Cocker, P and Bessiere, Y and Hernandez-Raquet, G and Dubos, S and Mozo, I and Gaval, G and Caligaris, M and Barillon, B and Vlaeminck, SE and Sperandio, M}, title = {Enrichment and adaptation yield high anammox conversion rates under low temperatures.}, journal = {Bioresource technology}, volume = {250}, number = {}, pages = {505-512}, doi = {10.1016/j.biortech.2017.11.079}, pmid = {29197773}, issn = {1873-2976}, mesh = {Ammonium Compounds ; *Bioreactors ; Nitrogen ; Oxidation-Reduction ; Temperature ; }, abstract = {This study compared two anammox sequencing batch reactors (SBR) for one year. SBRconstantT was kept at 30 °C while temperature in SBRloweringT was decreased step-wise from 30 °C to 20 °C and 15 °C followed by over 140 days at 12.5 °C and 10 °C. High retention of anammox bacteria (AnAOB) and minimization of competition with AnAOB were key. 5-L anoxic reactors with the same inoculum were fed synthetic influent containing 25.9 mg NH4[+]-N/L and 34.1 mg NO2[-]-N/L (no COD). Specific ammonium removal rates continuously increased in SBRconstantT, reaching 785 mg NH4[+]-N/gVSS/d, and were maintained in SBRloweringT, reaching 82.2 and 91.8 mg NH4[+]-N/gVSS/d at 12.5 and 10 °C respectively. AnAOB enrichment (increasing hzsA and 16S rDNA gene concentrations) and adaptation (shift from Ca. Brocadia to Ca. Kuenenia in SBRloweringT) contributed to these high rates. Rapidly settling granules developed, with average diameters of 1.2 (SBRconstantT) and 1.6 mm (SBRloweringT). Results reinforce the potential of anammox for mainstream applications.}, }
@article {pmid29196844, year = {2018}, author = {Fonseca, EDS and Peixoto, RS and Rosado, AS and Balieiro, FC and Tiedje, JM and Rachid, CTCDC}, title = {Correction to: The Microbiome of Eucalyptus Roots under Different Management Conditions and Its Potential for Biological Nitrogen Fixation.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {192}, doi = {10.1007/s00248-017-1122-8}, pmid = {29196844}, issn = {1432-184X}, abstract = {The original version of this article unfortunately contained mistakes in the first author's name and the running page headers.}, }
@article {pmid29196843, year = {2018}, author = {Munir, S and He, P and Wu, Y and He, P and Khan, S and Huang, M and Cui, W and He, P and He, Y}, title = {Huanglongbing Control: Perhaps the End of the Beginning.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {192-204}, pmid = {29196843}, issn = {1432-184X}, support = {201003029//Ministry of Agriculture of the People's Republic of China/ ; 2008CC024//Natural Science Foundation of Yunnan Province/ ; 31560503//National Natural Science Foundation of China/ ; 2009EB060//THE R&amp;D FOUNDATION OF YUNNAN PROVINCE/ ; }, mesh = {Americas ; Anti-Infective Agents/*pharmacology/*therapeutic use ; Biological Control Agents/pharmacology/therapeutic use ; Brassinosteroids/pharmacology ; Citrus/*microbiology ; Host-Pathogen Interactions ; Hyperthermia, Induced/methods ; Plant Diseases/microbiology/*prevention &amp; control ; Plant Leaves/microbiology ; Rhizobiaceae/classification/*drug effects/pathogenicity ; Volatile Organic Compounds/pharmacology ; }, abstract = {Huanglongbing (HLB) is one of the most destructive citrus plant diseases worldwide. It is associated with the fastidious phloem-limited α-proteobacteria 'Candidatus Liberibacter asiaticus', 'Ca. Liberibacter africanus' and 'Ca. Liberibacter americanus'. In recent years, HLB-associated Liberibacters have extended to North and South America. The causal agents of HLB have been putatively identified, and their transmission pathways and worldwide population structure have been extensively studied. However, very little is known about the epidemiologic relationships of Ca. L. asiaticus, which has limited the scope of HLB research and especially the development of control strategies. HLB-affected plants produce damaged fruits and die within several years. To control the disease, scientists have developed new compounds and screened existing compounds for their antibiotic and antimicrobial activities against the disease. These compounds, however, have very little or even no effect on the disease. The aim of the present review was to compile and compare different methods of HLB disease control with newly developed integrative strategies. In light of recent studies, we also describe how to control the vectors of this disease and the biological control of other citrus plant pathogens. This work could steer the attention of scientists towards integrative control strategies.}, }
@article {pmid29196000, year = {2017}, author = {Liu, MK and Tang, YM and Guo, XJ and Zhao, K and Tian, XH and Liu, Y and Yao, WC and Deng, B and Ren, DQ and Zhang, XP}, title = {Deep sequencing reveals high bacterial diversity and phylogenetic novelty in pit mud from Luzhou Laojiao cellars for Chinese strong-flavor Baijiu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {102}, number = {}, pages = {68-76}, doi = {10.1016/j.foodres.2017.09.075}, pmid = {29196000}, issn = {1873-7145}, mesh = {Alcoholic Beverages/*microbiology ; Bacteria/classification/*genetics/growth &amp; development/isolation &amp; purification ; China ; DNA, Bacterial/classification/*genetics/isolation &amp; purification ; *Fermentation ; Food Microbiology/*methods ; Genotype ; *High-Throughput Nucleotide Sequencing ; Phenotype ; *Phylogeny ; Ribotyping/*methods ; *Soil Microbiology ; }, abstract = {The pit mud (PM) in fermentation cellar is a complex ecosystem that hosts diverse microbial communities that contribute to the production of Chinese strong-flavor Baijiu (CSFB). However, the microbial ecology of PM, particularly the extent of their phylogenetic novelty remains poorly understood. Here we conducted Illumina MiSeq sequencing to explore the diversity and novelty patterns of PM bacterial communities from Luzhou Laojiao cellars in use for 40 and 400years. High diversity indices were found in the PM with 16 phyla and 105 genera. Interestingly, the compositions of dominant genera of the PM were significantly different than that reported previously for PM sampled from other geographic sites, suggesting greater microbial diversity of PM. The dominant genus of Caproiciproducens, a caproic acid-producing bacterium, is the first reported for Chinese Baijiu production. Our results demonstrate that the PM hosts a large number of novel taxa, with 26% of the total OTUs (operational taxonomic units) distant to cultured counterparts. The class Clostridia within Firmicutes presented the highest proportion of novel OTUs. Most novel OTUs were initially isolated from diverse environments, the most abundant of which came from Chinese Baijiu brewing ecosystems, highlighting the huge culturing gap within the PM, but at the same time suggesting the importance of these OTUs in CSFB production. The data presented in this study significantly increases the number of bacteria known to be associated with CSFB production and should help guide the future exploration of microbial resources for biotechnological applications.}, }
@article {pmid29195186, year = {2018}, author = {Vignola, M and Werner, D and Wade, MJ and Meynet, P and Davenport, RJ}, title = {Medium shapes the microbial community of water filters with implications for effluent quality.}, journal = {Water research}, volume = {129}, number = {}, pages = {499-508}, doi = {10.1016/j.watres.2017.09.042}, pmid = {29195186}, issn = {1879-2448}, mesh = {Bacteria/genetics ; Drinking Water/chemistry/microbiology ; Filtration/instrumentation/*methods ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; Water Purification/instrumentation/*methods ; *Water Quality ; }, abstract = {Little is known about the forces that determine the assembly of diverse bacterial communities inhabiting drinking water treatment filters and how this affects drinking water quality. Two contrasting ecological theories can help to understand how natural microbial communities assemble; niche theory and neutral theory, where environmental deterministic factors or stochastic factors predominate respectively. This study investigates the development of the microbial community on two common contrasting filter materials (quartz sand and granular activated carbon-GAC), to elucidate the main factors governing their assembly, through the evaluation of environmental (i.e. filter medium type) and stochastic forces (random deaths, births and immigration). Laboratory-scale filter columns were used to mimic a rapid gravity filter; the microbiome of the filter materials, and of the filter influent and effluent, was characterised using next generation 16S rRNA gene amplicon sequencing and flow-cytometry. Chemical parameters (i.e. dissolved organic carbon, trihalomethanes formation) were also monitored to assess the final effluent quality. The filter communities seemed to be strongly assembled by selection rather than neutral processes, with only 28% of those OTUs shared with the source water detected on the filter medium following predictions using a neutral community model. GAC hosted a phylogenetically more diverse community than sand. The two filter media communities seeded the effluent water, triggering differences in both water quality and community composition of the effluents. Overall, GAC proved to be better than sand in controlling microbial growth, by promoting higher bacterial decay rates and hosting less bacterial cells, and showed better performance for putative pathogen control by leaking less Legionella cells into the effluent water.}, }
@article {pmid29195004, year = {2018}, author = {Yi, Y and Frenzel, E and Spoelder, J and Elzenga, JTM and van Elsas, JD and Kuipers, OP}, title = {Optimized fluorescent proteins for the rhizosphere-associated bacterium Bacillus mycoides with endophytic and biocontrol agent potential.}, journal = {Environmental microbiology reports}, volume = {10}, number = {1}, pages = {57-74}, doi = {10.1111/1758-2229.12607}, pmid = {29195004}, issn = {1758-2229}, mesh = {Bacillus/*chemistry/genetics/metabolism ; Biosensing Techniques/methods ; Endophytes/chemistry/genetics/metabolism ; Green Fluorescent Proteins/*analysis/genetics ; Hydrogen-Ion Concentration ; Luminescent Proteins/*analysis/genetics ; Mannose/metabolism ; Plant Roots/microbiology ; Promoter Regions, Genetic/genetics ; Recombinant Fusion Proteins/analysis/chemistry ; *Rhizosphere ; Red Fluorescent Protein ; }, abstract = {Tracking of fluorescent protein (FP)-labelled rhizobacteria is a key prerequisite to gain insights into plant-bacteria interaction mechanisms. However, the performance of FPs mostly has to be optimized for the bacterial host and for the environment of intended application. We report on the construction of mutational libraries of the superfolder green fluorescent protein sfGFP and the red fluorescent protein mKate2 in the bacterium B. mycoides, which next to its potential as plant-biocontrol agent occasionally enters an endophytic lifestyle. By fluorescence-activated cell sorting and comparison of signal intensities at the colony and single-cell level, the variants sfGFP(SPS6) and mKate (KPS12) with significantly increased brightness were isolated. Their high applicability for plant-bacteria interaction studies was shown by confocal laser scanning microscopy tracking of FP-tagged B. mycoides strains after inoculation to Chinese cabbage plants in a hydroponic system. During the process of colonization, strain EC18 rapidly attached to plant roots and formed a multicellular matrix, especially at the branching regions of the root hair, which probably constitute entrance sites to establish an endophytic lifestyle. The universal applicability of the novels FPs was proven by expression from a weak promoter, dual-labelling of B. mycoides, and by excellent expression and detectability in additional soil- and rhizosphere-associated Bacillus species.}, }
@article {pmid29192628, year = {2017}, author = {Anukam, KC and Agbakoba, NR}, title = {A comparative study of the oral microbiome compositions of healthy postmenopausal, premenopausal, and prepubertal Nigerian females, using 16s rrna metagenomics methods.}, journal = {Nigerian journal of clinical practice}, volume = {20}, number = {10}, pages = {1250-1258}, doi = {10.4103/njcp.njcp_32_17}, pmid = {29192628}, issn = {1119-3077}, mesh = {Adolescent ; Adult ; Aged ; Bacteria/classification/*genetics ; Child ; Female ; Humans ; Metagenomics/*methods ; *Microbiota ; Middle Aged ; Mouth/*microbiology ; Pilot Projects ; *Postmenopause ; *Premenopause ; RNA, Ribosomal, 16S/*genetics ; Young Adult ; }, abstract = {INTRODUCTION: There is a paucity of information on the oral microbiome compositions of Nigerians, mostly due to lack of appropriate molecular techniques. In this pilot study, we sought to determine and characterize the oral bacterial compositions of "healthy" females.<br><br>MATERIALS AND METHODS: Oral samples were collected from three randomly selected females aged 56, 28, and 8 years. DNA was extracted and 16S rRNA V4 region was amplified using custom-barcoded primers before sequencing with Illumina MiSeq platform. Quantitative Insights into Microbial Ecology pipeline was used for 16S rRNA recognition. Distribution of taxonomic categories at different levels of resolution was done using the ribosomal RNA similarities to entries in the REFseq protein database. Diversity score was calculated based on the inverse Simpson's index.<br><br>RESULTS: The inverse Simpson's diversity index for the postmenopausal, premenopausal, and prepubertal was 7.74, 6.95, and 7.42 respectively. A total of 12 phyla, 70 genera, and 85 species were detected. Firmicutes followed by Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria dominated the oral microbiome of the subjects. Streptococcus thermophilus (33.19%) was the most abundance species in subject 1, while subject 2 was highly predominated by Haemophilus parainfluenzae (80.65%), and subject 3 was predominated by Haemophilus influenzae (23.05%).<br><br>CONCLUSION: The study has revealed that bacteria with varying diversities colonized the subjects and it highlighted the importance of metagenomics in deciphering the oral bacterial compositions from females of different age groups. More studies are needed using metagenomics approach, to appreciate these bacterial organisms that are associated with health and disease in our environment.}, }
@article {pmid29192335, year = {2018}, author = {Salmaso, N and Albanese, D and Capelli, C and Boscaini, A and Pindo, M and Donati, C}, title = {Diversity and Cyclical Seasonal Transitions in the Bacterial Community in a Large and Deep Perialpine Lake.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {125-143}, pmid = {29192335}, issn = {1432-184X}, support = {Ph.D. fellowship//FIRS&gt;T/ ; }, mesh = {Bacteria/*classification/genetics/growth &amp; development ; *Biodiversity ; Cyanobacteria/classification/growth &amp; development ; DNA, Bacterial/genetics ; Ecosystem ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Lakes/*microbiology ; *Microbiota ; *Phylogeny ; Phytoplankton/classification/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; *Seasons ; Temperature ; *Water Microbiology ; Water Quality ; }, abstract = {High-throughput sequencing (HTS) was used to analyze the seasonal variations in the bacterioplankton community composition (BCC) in the euphotic layer of a large and deep lake south of the Alps (Lake Garda). The BCC was analyzed throughout two annual cycles by monthly samplings using the amplification and sequencing of the V3-V4 hypervariable region of the 16S rRNA gene by the MiSeq Illumina platform. The dominant and most diverse bacterioplankton phyla were among the more frequently reported in freshwater ecosystems, including the Proteobacteria, Cyanobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, and Planctomycetes. As a distinctive feature, the development of the BCC showed a cyclical temporal pattern in the two analyzed years and throughout the euphotic layer. The recurring temporal development was controlled by the strong seasonality in water temperature and thermal stratification, and by cyclical temporal changes in nutrients and, possibly, by the remarkable annual cyclical development of cyanobacteria and eukaryotic phytoplankton hosting bacterioplankton that characterizes Lake Garda. Further downstream analyses of operational taxonomic units associated to cyanobacteria allowed confirming the presence of the most abundant taxa previously identified by microscopy and/or phylogenetic analyses, as well as the presence of other small Synechococcales/Chroococcales and rare Nostocales never identified so far in the deep lakes south of the Alps. The implications of the high diversity and strong seasonality are relevant, opening perspectives for the definition of common and discriminating patterns characterizing the temporal and spatial distribution in the BCC, and for the application of the new sequencing technologies in the monitoring of water quality in large and deep lakes.}, }
@article {pmid29191399, year = {2018}, author = {Nai, C and Meyer, V}, title = {From Axenic to Mixed Cultures: Technological Advances Accelerating a Paradigm Shift in Microbiology.}, journal = {Trends in microbiology}, volume = {26}, number = {6}, pages = {538-554}, doi = {10.1016/j.tim.2017.11.004}, pmid = {29191399}, issn = {1878-4380}, mesh = {*Axenic Culture ; Bacteria/*growth &amp; development ; Coculture Techniques/instrumentation/trends ; Fungi/*growth &amp; development ; Metabolomics ; Microbiological Techniques/instrumentation/*trends ; Secondary Metabolism ; Symbiosis ; }, abstract = {Since the onset of microbiology in the late 19th century, scientists have been growing microorganisms almost exclusively as pure cultures, resulting in a limited and biased view of the microbial world. Only a paradigm shift in cultivation techniques - from axenic to mixed cultures - can allow a full comprehension of the (chemical) communication of microorganisms, with profound consequences for natural product discovery, microbial ecology, symbiosis, and pathogenesis, to name a few areas. Three main technical advances during the last decade are fueling the realization of this revolution in microbiology: microfluidics, next-generation 3D-bioprinting, and single-cell metabolomics. These technological advances can be implemented for large-scale, systematic cocultivation studies involving three or more microorganisms. In this review, we present recent trends in microbiology tools and discuss how these can be employed to decode the chemical language that microorganisms use to communicate.}, }
@article {pmid29189901, year = {2018}, author = {Masoudi, A and Koprowski, JL and Bhattarai, UR and Wang, D}, title = {Elevational distribution and morphological attributes of the entomopathogenic fungi from forests of the Qinling Mountains in China.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {3}, pages = {1483-1499}, pmid = {29189901}, issn = {1432-0614}, support = {31670659//NSFC grant/ ; 201404403-09//Special Fund for Forest Scientific Research in the Public Welfare/ ; 2014KTCL02-14//Shaanxi Provincial Science and technology Innovation Project/ ; }, mesh = {Animals ; Beauveria/*classification/genetics/isolation &amp; purification ; Biological Control Agents/isolation &amp; purification ; China ; Climate ; DNA, Fungal/genetics ; DNA, Intergenic/genetics ; *Forests ; Genetic Variation ; Insecta/microbiology ; Larva/microbiology ; Metarhizium/*classification/genetics/isolation &amp; purification ; Pest Control, Biological ; Phylogeny ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Entomopathogenic fungi are considered to be a safe microbiological pesticide alternative to chemical control. Efforts are underway to understand precisely their taxonomy and natural distribution through mycological and biodiversity studies based on molecular markers. Here, we present descriptions of the diversity of the entomopathogenic fungi in the genera Metarhizium and Beauveria found along the elevational gradients of the Qinling subtropical and temperate forests of Shaanxi province in China, using morphological aspects and molecular markers. Molecular characterization using the Mz_IGS3 intergenic region revealed that Metarhizium isolates phylogenetically clustered in the PARB clade with four different distinguishable species, but the 5'-TEF gene allowed only ambiguous delimitation of Metarhizium species. Beauveria isolates were characterized by sequence analyses of the translation elongation factor 1-α and the Bloc region. The richness of Metarhizium species decreased with increasing elevation, with Metarhizium robertsii s.l. being the most abundant species along the elevational gradient. Our bioassay suggests that certain species of Metarhizium are significantly pathogenic to the insect model Tenebrio molitor at both the adult and larvae stages and could potentially serve as a control of insect pests of forests.}, }
@article {pmid29188459, year = {2017}, author = {Grote, M}, title = {Petri dish versus Winogradsky column: a longue durée perspective on purity and diversity in microbiology, 1880s-1980s.}, journal = {History and philosophy of the life sciences}, volume = {40}, number = {1}, pages = {11}, doi = {10.1007/s40656-017-0175-9}, pmid = {29188459}, issn = {0391-9714}, mesh = {*Historiography ; History, 19th Century ; History, 20th Century ; Microbiological Techniques/*history ; Microbiology/*history ; }, abstract = {Microbial diversity has become a leitmotiv of contemporary microbiology, as epitomized in the concept of the microbiome, with significant consequences for the classification of microbes. In this paper, I contrast microbiology's current diversity ideal with its influential predecessor in the twentieth century, that of purity, as epitomized in Robert Koch's bacteriological culture methods. Purity and diversity, the two polar opposites with regard to making sense of the microbial world, have been operationalized in microbiological practice by tools such as the "clean" Petri dish versus the "dirty" Winogradsky column, the latter a container that mimics, in the laboratory, the natural environment that teems with diverse microbial life. By tracing the impact of the practices and concepts of purity and diversity on microbial classification through a history of techniques, tools, and manuals, I show the shifts in these concepts over the last century. Juxtaposing the dominant purity ideal with the more restricted, but continuously articulated, diversity ideal in microbial ecology not only provides a fresh perspective on microbial classification that goes beyond its intellectual history, but also contextualizes the present focus on diversity. By covering the period of a century, this paper outlines a revised longue durée historiography that takes its inspiration from artifacts, such as Petri dish and the Winogradsky column, and thereby simple, but influential technologies that often remain invisible. This enables the problem of historical continuity in modern science to be addressed and the accelerationist narratives of its development to be countered.}, }
@article {pmid29188341, year = {2018}, author = {Yadav, M and Verma, MK and Chauhan, NS}, title = {A review of metabolic potential of human gut microbiome in human nutrition.}, journal = {Archives of microbiology}, volume = {200}, number = {2}, pages = {203-217}, doi = {10.1007/s00203-017-1459-x}, pmid = {29188341}, issn = {1432-072X}, mesh = {Bacteria/*metabolism ; Carbohydrate Metabolism/physiology ; *Diet ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*metabolism/*microbiology ; Humans ; Symbiosis ; }, abstract = {The human gut contains a plethora of microbes, providing a platform for metabolic interaction between the host and microbiota. Metabolites produced by the gut microbiota act as a link between gut microbiota and its host. These metabolites act as messengers having the capacity to alter the gut microbiota. Recent advances in the characterization of the gut microbiota and its symbiotic relationship with the host have provided a platform to decode metabolic interactions. The human gut microbiota, a crucial component for dietary metabolism, is shaped by the genetic, epigenetic and dietary factors. The metabolic potential of gut microbiota explains its significance in host health and diseases. The knowledge of interactions between microbiota and host metabolism, as well as modification of microbial ecology, is really beneficial to have effective therapeutic treatments for many diet-related diseases in near future. This review cumulates the information to map the role of human gut microbiota in dietary component metabolism, the role of gut microbes derived metabolites in human health and host-microbe metabolic interactions in health and diseases.}, }
@article {pmid29188302, year = {2018}, author = {McKenney, EA and Maslanka, M and Rodrigo, A and Yoder, AD}, title = {Bamboo Specialists from Two Mammalian Orders (Primates, Carnivora) Share a High Number of Low-Abundance Gut Microbes.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {272-284}, pmid = {29188302}, issn = {1432-184X}, support = {S10 OD018164/OD/NIH HHS/United States ; 1455848//National Science Foundation/ ; }, mesh = {Ailuridae/microbiology ; Animal Feed ; Animals ; Bacteria/*classification/genetics ; *Bambusa ; Biodiversity ; DNA, Bacterial/genetics ; *Diet ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Herbivory ; Host Microbial Interactions/*physiology ; Phylogeny ; Primates/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Ursidae/microbiology ; }, abstract = {Bamboo specialization is one of the most extreme examples of convergent herbivory, yet it is unclear how this specific high-fiber diet might selectively shape the composition of the gut microbiome compared to host phylogeny. To address these questions, we used deep sequencing to investigate the nature and comparative impact of phylogenetic and dietary selection for specific gut microbial membership in three bamboo specialists-the bamboo lemur (Hapalemur griseus, Primates: Lemuridae), giant panda (Ailuropoda melanoleuca, Carnivora: Ursidae), and red panda (Ailurus fulgens, Carnivora: Musteloideadae), as well as two phylogenetic controls-the ringtail lemur (Lemur catta) and the Asian black bear (Ursus thibetanus). We detected significantly higher Shannon diversity in the bamboo lemur (10.029) compared to both the giant panda (8.256; p = 0.0001936) and the red panda (6.484; p = 0.0000029). We also detected significantly enriched bacterial taxa that distinguished each species. Our results complement previous work in finding that phylogeny predominantly governs high-level microbiome community structure. However, we also find that 48 low-abundance OTUs are shared among bamboo specialists, compared to only 8 OTUs shared by the bamboo lemur and its sister species, the ringtail lemur (Lemur catta, a generalist). Our results suggest that deep sequencing is necessary to detect low-abundance bacterial OTUs, which may be specifically adapted to a high-fiber diet. These findings provide a more comprehensive framework for understanding the evolution and ecology of the microbiome as well as the host.}, }
@article {pmid29188301, year = {2018}, author = {Schmid, CAO and Schröder, P and Armbruster, M and Schloter, M}, title = {Organic Amendments in a Long-term Field Trial-Consequences for the Bulk Soil Bacterial Community as Revealed by Network Analysis.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {226-239}, pmid = {29188301}, issn = {1432-184X}, mesh = {Agriculture/methods ; Bacteria/classification/genetics/*metabolism ; *Biodiversity ; DNA, Bacterial/genetics ; *Fertilizers ; Germany ; Manure ; Microbial Interactions ; Microbiota/*physiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {This study intended to elucidate the long-term effects of organic soil amendments on bacterial co-occurrence in bulk soil with and without addition of mineral fertiliser. Previous research mostly neglected the bacterial co-occurrence structure and focussed mainly on the parameters species diversity and abundance changes of species. Here we present a systematic comparison of two frequently used soil amendments, manure and straw, with regard to their impact on bacterial co-occurrence in a long-term field trial in Speyer, Germany. The approach involved 16S amplicon sequencing in combination with a bacterial network analysis, comparing the different fertiliser regimes. The results show an increase of bacterial diversity as well as an accumulation of bacteria of the order Bacillales in plots fertilised with manure compared to a control treatment. In the straw-amended plots neither an increase in diversity was found nor were indicative species detectable. Furthermore, network analysis revealed a clear impact of mineral fertiliser addition on bacterial co-occurrence structure. Most importantly, both organic amendments increased network complexity irrespective of mineral fertilisation regime. At the same time, the effects of manure and straw exhibited differences that might be explained by differences in their nutritional/chemical contents. It is concluded that bacterial interactions are a crucial parameter for the assessment of amendment effects regarding soil health and sustainability.}, }
@article {pmid29186623, year = {2017}, author = {Hoffman, DJ and Reynolds, RM and Hardy, DB}, title = {Developmental origins of health and disease: current knowledge and potential mechanisms.}, journal = {Nutrition reviews}, volume = {75}, number = {12}, pages = {951-970}, doi = {10.1093/nutrit/nux053}, pmid = {29186623}, issn = {1753-4887}, mesh = {Animals ; Body Composition ; Databases, Factual ; Diet ; Dyslipidemias/*epidemiology/etiology ; Female ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Glucocorticoids/administration &amp; dosage/adverse effects ; Humans ; Infant ; *Infant Nutritional Physiological Phenomena ; Malnutrition/complications/*epidemiology ; *Maternal Nutritional Physiological Phenomena ; Metabolic Diseases/*epidemiology/etiology ; Models, Animal ; Nutritional Status ; Obesity/*epidemiology ; Observational Studies as Topic ; Prevalence ; Randomized Controlled Trials as Topic ; Socioeconomic Factors ; }, abstract = {Epidemiologic and clinical research has provided a large body of evidence supporting the developmental origins of health and disease (DOHaD), but there has been a relative dearth of mechanistic studies in humans due to the complexity of working with large, longitudinal cohorts. Nonetheless, animal models of undernutrition have provided substantial evidence for the potential epigenetic, metabolic, and endocrine mechanisms behind DOHaD. Furthermore, recent research has explored the interaction between the environment and the gastrointestinal system by investigating how the gut microbial ecology may impact the capacity for nutrient processing and absorption in a manner that may limit growth. This review presents a summary of current research that supports the concept of DOHaD, as well as potential mechanisms and interactions that explain how nutrition in utero and during early childhood influences lifelong health.}, }
@article {pmid29185915, year = {2018}, author = {Do, TT and Tamames, J and Stedtfeld, RD and Guo, X and Murphy, S and Tiedje, JM and Walsh, F}, title = {Antibiotic Resistance Gene Detection in the Microbiome Context.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {24}, number = {5}, pages = {542-546}, doi = {10.1089/mdr.2017.0199}, pmid = {29185915}, issn = {1931-8448}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Bacteria/drug effects/*genetics ; Drug Resistance, Microbial/*genetics ; Feces/microbiology ; Gene Transfer, Horizontal/genetics ; Genes, Bacterial/*genetics ; Humans ; Microbiota/drug effects/*genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Within the past decade, microbiologists have moved from detecting single antibiotic resistance genes (ARGs) to detecting all known resistance genes within a sample due to advances in next generation sequencing. This has provided a wealth of data on the variation and relative abundances of ARGs present in a total bacterial population. However, to use these data in terms of therapy or risk to patients, they must be analyzed in the context of the background microbiome. Using a quantitative PCR ARG chip and 16S rRNA amplicon sequencing, we have sought to identify the ARGs and bacteria present in a fecal sample of a healthy adult using genomic tools. Of the 42 ARGs detected, 12 fitted into the ResCon1 category of ARGs: cfxA, cphA, bacA, sul3, aadE, blaTEM, aphA1, aphA3, aph(2')-Id, aacA/aphd, catA1, and vanC. Therefore, we describe these 12 genes as the core resistome of this person's fecal microbiome and the remaining 30 ARGs as descriptors of the microbial population within the fecal microbiome. The dominant phyla and genera agree with those previously detected in the greatest abundances in fecal samples of healthy humans. The majority of the ARGs detected were associated with the presence of specific bacterial taxa, which were confirmed using microbiome analysis. We acknowledge the limitations of the data in the context of the limited sample set. However, the principle of combining qPCR and microbiome analysis was shown to be helpful to identify the association of the ARGs with specific taxa.}, }
@article {pmid29185498, year = {2017}, author = {Cheng, HY and Hou, YN and Zhang, X and Yang, ZN and Xu, T and Wang, AJ}, title = {Activating electrochemical catalytic activity of bio-palladium by hybridizing with carbon nanotube as "e[-] Bridge".}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {16588}, pmid = {29185498}, issn = {2045-2322}, abstract = {Nano metal catalysts produced by bacteria has received increasing attention owing to its environmental friendly synthesis route. However, the formed metal nanoparticles are associated with poorly conductive cells and challenged to be electrochemically applied. In this study, Palladium (Pd) nanoparticles were synthesized by Shewanella oneidensis MR-1. We demonstrated the limitation of palladized cells (Pd-cells) serving as electro-catalysts can be relieved by hybridizing with the conductive carbon nanotubes (Pd-cells-CNTs hybrid). Compared to the Pd-cells, the electrochemical active surface area of Pd in Pd-cells-CNTs10 (the ratio of Pd/CNTs is 1/10 w/w) were dramatically increased by 68 times to 20.44 m[2]·g[-1]. A considerable enhancement of electrocatalytic activity was further confirmed for Pd-cells-CNTs10 as indicated by a 5-fold increase of steady state current density for nitrobenzene reduction at -0.55 V vs Ag/AgCl. These results indicate that the biogenetic palladium could has been an efficient electro-catalyst but just limited due to lacking an electron transport path (e [-] Bridge). This finding may also be helpful to guide the way to electrochemically use other biogenetic metal nano-materials.}, }
@article {pmid29184976, year = {2018}, author = {Kerfahi, D and Tripathi, BM and Slik, JWF and Sukri, RS and Jaafar, S and Adams, JM}, title = {Distinctive Soil Archaeal Communities in Different Variants of Tropical Equatorial Forest.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {215-225}, pmid = {29184976}, issn = {1432-184X}, support = {NRF-0409-20150076//National Research Foundation of Korea/ ; }, mesh = {Archaea/*classification/genetics/isolation &amp; purification ; *Biodiversity ; Brunei ; DNA, Archaeal/genetics ; Hydrogen-Ion Concentration ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Rainforest ; Soil/*chemistry ; *Soil Microbiology ; Trees/microbiology ; Tropical Climate ; }, abstract = {Little is known of how soil archaeal community composition and diversity differ between local variants of tropical rainforests. We hypothesized that (1) as with plants, animals, fungi, and bacteria, the soil archaeal community would differ between different variants of tropical forest; (2) that spatially rarer forest variants would have a less diverse archaeal community than common ones; (3) that a history of forest disturbance would decrease archaeal alpha- and beta-diversity; and (4) that archaeal distributions within the forest would be governed more by deterministic than stochastic factors. We sampled soil across several different forest types within Brunei, Northwest Borneo. Soil DNA was extracted, and the 16S rRNA gene of archaea was sequenced using Illumina MiSeq. We found that (1) as hypothesized, there are distinct archaeal communities for each forest type, and community composition significantly correlates with soil parameters including pH, organic matter, and available phosphorous. (2) As hypothesized, the "rare" white sand forest variants kerangas and inland heath had lower archaeal diversity. A nestedness analysis showed that archaeal community in inland heath and kerangas was mainly a less diverse subset of that in dipterocarp forests. However, primary dipterocarp forest had the lowest beta-diversity among the other tropical forest types. (3) Also, as predicted, forest disturbance resulted in lower archaeal alpha-diversity-but increased beta-diversity in contrast with our predictions. (4) Contrary to our predictions, the BetaNTI of the various primary forest types indicated community assembly was mainly stochastic. The possible effects of these habitat and disturbance-related effects on N cycling should be investigated.}, }
@article {pmid29184540, year = {2017}, author = {Walter, JM and Coutinho, FH and Dutilh, BE and Swings, J and Thompson, FL and Thompson, CC}, title = {Ecogenomics and Taxonomy of Cyanobacteria Phylum.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2132}, pmid = {29184540}, issn = {1664-302X}, abstract = {Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats, although only a few studies have analyzed the association of phylogenomic clades to specific environmental niches. In this study, we adopted an ecogenomics strategy with the aim to delineate ecological niche preferences of Cyanobacteria and integrate them to the genomic taxonomy of these bacteria. First, an appropriate phylogenomic framework was established using a set of genomic taxonomy signatures (including a tree based on conserved gene sequences, genome-to-genome distance, and average amino acid identity) to analyse ninety-nine publicly available cyanobacterial genomes. Next, the relative abundances of these genomes were determined throughout diverse global marine and freshwater ecosystems, using metagenomic data sets. The whole-genome-based taxonomy of the ninety-nine genomes allowed us to identify 57 (of which 28 are new genera) and 87 (of which 32 are new species) different cyanobacterial genera and species, respectively. The ecogenomic analysis allowed the distinction of three major ecological groups of Cyanobacteria (named as i. Low Temperature; ii. Low Temperature Copiotroph; and iii. High Temperature Oligotroph) that were coherently linked to the genomic taxonomy. This work establishes a new taxonomic framework for Cyanobacteria in the light of genomic taxonomy and ecogenomic approaches.}, }
@article {pmid29184093, year = {2017}, author = {Stearns, JC and Simioni, J and Gunn, E and McDonald, H and Holloway, AC and Thabane, L and Mousseau, A and Schertzer, JD and Ratcliffe, EM and Rossi, L and Surette, MG and Morrison, KM and Hutton, EK}, title = {Intrapartum antibiotics for GBS prophylaxis alter colonization patterns in the early infant gut microbiome of low risk infants.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {16527}, pmid = {29184093}, issn = {2045-2322}, support = {MSH-136665//CIHR/Canada ; }, mesh = {Adult ; Anti-Bacterial Agents/*administration &amp; dosage ; *Antibiotic Prophylaxis ; Bifidobacterium/drug effects ; Delivery, Obstetric ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infant ; Infant, Newborn ; Male ; *Maternal Exposure ; Metagenome ; Metagenomics ; Pregnancy ; Streptococcal Infections/*microbiology/*prevention &amp; control ; Streptococcus agalactiae/*drug effects/physiology ; }, abstract = {Early life microbial colonization and succession is critically important to healthy development with impacts on metabolic and immunologic processes throughout life. A longitudinal prospective cohort was recruited from midwifery practices to include infants born at full term gestation to women with uncomplicated pregnancies. Here we compare bacterial community succession in infants born vaginally, with no exposure to antibiotics (n = 53), with infants who were exposed to intrapartum antibiotic prophylaxis (IAP) for Group B Streptococcus (GBS; n = 14), and infants born by C-section (n = 7). Molecular profiles of the 16 S rRNA genes indicate that there is a delay in the expansion of Bifidobacterium, which was the dominate infant gut colonizer, over the first 12 weeks and a persistence of Escherichia when IAP for GBS exposure is present during vaginal labour. Longer duration of IAP exposure increased the magnitude of the effect on Bifidobacterium populations, suggesting a longer delay in microbial community maturation. As with prior studies, we found altered gut colonisation following C-section that included a notable lack of Bacteroidetes. This study found that exposure of infants to IAP for GBS during vaginal birth affected aspects of gut microbial ecology that, although dramatic at early time points, disappeared by 12 weeks of age in most infants.}, }
@article {pmid29184020, year = {2017}, author = {Luo, E and Aylward, FO and Mende, DR and DeLong, EF}, title = {Bacteriophage Distributions and Temporal Variability in the Ocean's Interior.}, journal = {mBio}, volume = {8}, number = {6}, pages = {}, pmid = {29184020}, issn = {2150-7511}, mesh = {Bacteriophages/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; DNA, Viral/analysis/genetics ; Genotype ; Lysogeny ; Metagenomics ; *Oceans and Seas ; Seawater/*virology ; Spatio-Temporal Analysis ; }, abstract = {Bacteriophages are numerically the most abundant DNA-containing entities in the oligotrophic ocean, yet how specific phage populations vary over time and space remains to be fully explored. Here, we conducted a metagenomic time-series survey of double-stranded DNA phages throughout the water column in the North Pacific Subtropical Gyre, encompassing 1.5 years from depths of 25 to 1,000 m. Viral gene sequences were identified in assembled metagenomic samples, yielding an estimated 172,385 different viral gene families. Viral marker gene distributions suggested that lysogeny was more prevalent at mesopelagic depths than in surface waters, consistent with prior prophage induction studies using mitomycin C. A total of 129 ALOHA viral genomes and genome fragments from 20 to 108 kbp were selected for further study, which represented the most abundant phages in the water column. Phage genotypes displayed discrete population structures. Most phages persisted throughout the time-series and displayed a strong depth structure that mirrored the stratified depth distributions of co-occurring bacterial taxa in the water column. Mesopelagic phages were distinct from surface water phages with respect to diversity, gene content, putative life histories, and temporal persistence, reflecting depth-dependent differences in host genomic architectures and phage reproductive strategies. The spatiotemporal distributions of the most abundant open-ocean bacteriophages that we report here provide new insight into viral temporal persistence, life history, and virus-host-environment interactions throughout the open-ocean water column.IMPORTANCE The North Pacific Subtropical Gyre represents one of the largest biomes on the planet, where microbial communities are central mediators of ecosystem dynamics and global biogeochemical cycles. Critical members of these communities are the viruses of marine bacteria, which can alter microbial metabolism and significantly influence their survival and productivity. To better understand these viral assemblages, we conducted genomic analyses of planktonic viruses over a seasonal cycle to ocean depths of 1,000 m. We identified 172,385 different viral gene families and 129 unique virus genotypes in this open-ocean setting. The spatiotemporal distributions of the most abundant open-ocean viruses that we report here provide new insights into viral temporal variability, life history, and virus-host-environment interactions throughout the water column.}, }
@article {pmid29182421, year = {2018}, author = {McKenney, EA and O'Connell, TM and Rodrigo, A and Yoder, AD}, title = {Feeding strategy shapes gut metagenomic enrichment and functional specialization in captive lemurs.}, journal = {Gut microbes}, volume = {9}, number = {3}, pages = {202-217}, pmid = {29182421}, issn = {1949-0984}, support = {S10 OD018164/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/metabolism ; Biodiversity ; *Diet ; Feces/chemistry/microbiology ; Feeding Methods/veterinary ; Fermentation ; Fruit/chemistry/metabolism ; Gastrointestinal Tract/*microbiology/physiology ; Lemur/metabolism/*microbiology ; Metabolic Networks and Pathways ; *Metagenome ; Microbiota/genetics/*physiology ; Plant Leaves/chemistry/metabolism ; Species Specificity ; Strepsirhini/metabolism/microbiology ; }, abstract = {Many studies have demonstrated the effects of host diet on gut microbial membership, metagenomics, and fermentation individually; but few have attempted to interpret the relationship among these biological phenomena with respect to host features (e.g. gut morphology). We quantitatively compare the fecal microbial communities, metabolic pathways, and fermentation products associated with the nutritional intake of frugivorous (fruit-eating) and folivorous (leaf-eating) lemurs. Our results provide a uniquely multidimensional and comparative perspective on the adaptive dynamics between host and microbiome. Shotgun metagenomic sequencing revealed significant differential taxonomic and metabolic pathway enrichment, tailored to digest and detoxify different diets. Frugivorous metagenomes feature pathways to degrade simple carbohydrates and host-derived glycosaminoglycans, while folivorous metagenomes are equipped to break down phytic acid and other phytochemical compounds in an anaerobic environment. We used nuclear magnetic resonance based metabolic profiling of fecal samples to link metabolic pathways to fermentation products, confirming that the dissimilar substrates provided in each diet select for specific microbial functions. Fecal samples from frugivorous lemurs contained significantly different profiles of short chain fatty acids, alcohol fermentation products, amino acids, glucose, and glycerol compared to folivorous lemurs. We present the relationships between these datasets as an integrated visual framework, which we refer to as microbial geometry. We use microbial geometry to compare empirical gut microbial profiles across different feeding strategies, and suggest additional utility as a tool for hypothesis-generation.}, }
@article {pmid29180368, year = {2018}, author = {Reumer, M and Harnisz, M and Lee, HJ and Reim, A and Grunert, O and Putkinen, A and Fritze, H and Bodelier, PLE and Ho, A}, title = {Impact of Peat Mining and Restoration on Methane Turnover Potential and Methane-Cycling Microorganisms in a Northern Bog.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {3}, pages = {}, pmid = {29180368}, issn = {1098-5336}, mesh = {Bacterial Proteins/genetics/metabolism ; Carbon/metabolism ; Ecosystem ; Euryarchaeota/genetics/metabolism ; Methane/*metabolism ; Microbiota/genetics/*physiology ; *Mining ; Nitrogen Fixation ; Oxidation-Reduction ; Oxygenases ; Phylogeny ; *Soil ; *Soil Microbiology ; Sphagnopsida/metabolism ; Wetlands ; }, abstract = {Ombrotrophic peatlands are a recognized global carbon reservoir. Without restoration and peat regrowth, harvested peatlands are dramatically altered, impairing their carbon sink function, with consequences for methane turnover. Previous studies determined the impact of commercial mining on the physicochemical properties of peat and the effects on methane turnover. However, the response of the underlying microbial communities catalyzing methane production and oxidation have so far received little attention. We hypothesize that with the return of Sphagnum spp. postharvest, methane turnover potential and the corresponding microbial communities will converge in a natural and restored peatland. To address our hypothesis, we determined the potential methane production and oxidation rates in natural (as a reference), actively mined, abandoned, and restored peatlands over two consecutive years. In all sites, the methanogenic and methanotrophic population sizes were enumerated using quantitative PCR (qPCR) assays targeting the mcrA and pmoA genes, respectively. Shifts in the community composition were determined using Illumina MiSeq sequencing of the mcrA gene and a pmoA-based terminal restriction fragment length polymorphism (t-RFLP) analysis, complemented by cloning and sequence analysis of the mmoX gene. Peat mining adversely affected methane turnover potential, but the rates recovered in the restored site. The recovery in potential activity was reflected in the methanogenic and methanotrophic abundances. However, the microbial community composition was altered, being more pronounced for the methanotrophs. Overall, we observed a lag between the recovery of the methanogenic/methanotrophic activity and the return of the corresponding microbial communities, suggesting that a longer duration (>15 years) is needed to reverse mining-induced effects on the methane-cycling microbial communities.IMPORTANCE Ombrotrophic peatlands are a crucial carbon sink, but this environment is also a source of methane, an important greenhouse gas. Methane emission in peatlands is regulated by methane production and oxidation catalyzed by methanogens and methanotrophs, respectively. Methane-cycling microbial communities have been documented in natural peatlands. However, less is known of their response to peat mining and of the recovery of the community after restoration. Mining exerts an adverse impact on potential methane production and oxidation rates and on methanogenic and methanotrophic population abundances. Peat mining also induced a shift in the methane-cycling microbial community composition. Nevertheless, with the return of Sphagnum spp. in the restored site after 15 years, methanogenic and methanotrophic activity and population abundance recovered well. The recovery, however, was not fully reflected in the community composition, suggesting that >15 years are needed to reverse mining-induced effects.}, }
@article {pmid29180365, year = {2018}, author = {Walworth, NG and Fu, FX and Lee, MD and Cai, X and Saito, MA and Webb, EA and Hutchins, DA}, title = {Nutrient-Colimited Trichodesmium as a Nitrogen Source or Sink in a Future Ocean.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {3}, pages = {}, pmid = {29180365}, issn = {1098-5336}, mesh = {Adaptation, Biological ; Carbon Dioxide/*metabolism ; Methylamines/*metabolism ; Nitrogen/*metabolism ; Nitrogen Cycle ; Nitrogen Fixation ; Nutrients/metabolism ; Oceans and Seas ; Seawater/*chemistry/microbiology ; Trichodesmium/*metabolism ; }, abstract = {Nitrogen-fixing (N2) cyanobacteria provide bioavailable nitrogen to vast ocean regions but are in turn limited by iron (Fe) and/or phosphorus (P), which may force them to employ alternative nitrogen acquisition strategies. The adaptive responses of nitrogen fixers to global-change drivers under nutrient-limited conditions could profoundly alter the current ocean nitrogen and carbon cycles. Here, we show that the globally important N2 fixer Trichodesmium fundamentally shifts nitrogen metabolism toward organic-nitrogen scavenging following long-term high-CO2 adaptation under iron and/or phosphorus (co)limitation. Global shifts in transcripts and proteins under high-CO2/Fe-limited and/or P-limited conditions include decreases in the N2-fixing nitrogenase enzyme, coupled with major increases in enzymes that oxidize trimethylamine (TMA). TMA is an abundant, biogeochemically important organic nitrogen compound that supports rapid Trichodesmium growth while inhibiting N2 fixation. In a future high-CO2 ocean, this whole-cell energetic reallocation toward organic nitrogen scavenging and away from N2 fixation may reduce new-nitrogen inputs by Trichodesmium while simultaneously depleting the scarce fixed-nitrogen supplies of nitrogen-limited open-ocean ecosystems.IMPORTANCETrichodesmium is among the most biogeochemically significant microorganisms in the ocean, since it supplies up to 50% of the new nitrogen supporting open-ocean food webs. We used Trichodesmium cultures adapted to high-CO2 conditions for 7 years, followed by additional exposure to iron and/or phosphorus (co)limitation. We show that "future ocean" conditions of high CO2 and concurrent nutrient limitation(s) fundamentally shift nitrogen metabolism away from nitrogen fixation and instead toward upregulation of organic nitrogen-scavenging pathways. We show that the responses of Trichodesmium to projected future ocean conditions include decreases in the nitrogen-fixing nitrogenase enzymes coupled with major increases in enzymes that oxidize the abundant organic nitrogen source trimethylamine (TMA). Such a shift toward organic nitrogen uptake and away from nitrogen fixation may substantially reduce new-nitrogen inputs by Trichodesmium to the rest of the microbial community in the future high-CO2 ocean, with potential global implications for ocean carbon and nitrogen cycling.}, }
@article {pmid29179109, year = {2018}, author = {Welz, PJ and Ramond, JB and Braun, L and Vikram, S and Le Roes-Hill, M}, title = {Bacterial nitrogen fixation in sand bioreactors treating winery wastewater with a high carbon to nitrogen ratio.}, journal = {Journal of environmental management}, volume = {207}, number = {}, pages = {192-202}, doi = {10.1016/j.jenvman.2017.11.015}, pmid = {29179109}, issn = {1095-8630}, mesh = {*Bioreactors ; Carbon ; Nitrogen ; *Nitrogen Fixation ; Waste Disposal, Fluid ; *Wastewater ; }, abstract = {Heterotrophic bacteria proliferate in organic-rich environments and systems containing sufficient essential nutrients. Nitrogen, phosphorus and potassium are the nutrients required in the highest concentrations. The ratio of carbon to nitrogen is an important consideration for wastewater bioremediation because insufficient nitrogen may result in decreased treatment efficiency. It has been shown that during the treatment of effluent from the pulp and paper industry, bacterial nitrogen fixation can supplement the nitrogen requirements of suspended growth systems. This study was conducted using physicochemical analyses and culture-dependent and -independent techniques to ascertain whether nitrogen-fixing bacteria were selected in biological sand filters used to treat synthetic winery wastewater with a high carbon to nitrogen ratio (193:1). The systems performed well, with the influent COD of 1351 mg/L being reduced by 84-89%. It was shown that the nitrogen fixing bacterial population was influenced by the presence of synthetic winery effluent in the surface layers of the biological sand filters, but not in the deeper layers. It was hypothesised that this was due to the greater availability of atmospheric nitrogen at the surface. The numbers of culture-able nitrogen-fixing bacteria, including presumptive Azotobacter spp. exhibited 1-2 log increases at the surface. The results of this study confirm that nitrogen fixation is an important mechanism to be considered during treatment of high carbon to nitrogen wastewater. If biological treatment systems can be operated to stimulate this phenomenon, it may obviate the need for nitrogen addition.}, }
@article {pmid29177812, year = {2018}, author = {Marozava, S and Mouttaki, H and Müller, H and Laban, NA and Probst, AJ and Meckenstock, RU}, title = {Anaerobic degradation of 1-methylnaphthalene by a member of the Thermoanaerobacteraceae contained in an iron-reducing enrichment culture.}, journal = {Biodegradation}, volume = {29}, number = {1}, pages = {23-39}, pmid = {29177812}, issn = {1572-9729}, mesh = {Adenosine Triphosphate/biosynthesis ; Anaerobiosis ; Biodegradation, Environmental ; Carbon/pharmacology ; Deltaproteobacteria/growth &amp; development/*metabolism ; Iron/*metabolism ; Likelihood Functions ; Metabolome ; Naphthalenes/*metabolism ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/metabolism ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; }, abstract = {An anaerobic culture (1MN) was enriched with 1-methylnaphthalene as sole source of carbon and electrons and Fe(OH)3 as electron acceptor. 1-Naphthoic acid was produced as a metabolite during growth with 1-methylnaphthalene while 2-naphthoic acid was detected with naphthalene and 2-methylnaphthalene. This indicates that the degradation pathway of 1-methylnaphthalene might differ from naphthalene and 2-methylnaphthalene degradation in sulfate reducers. Terminal restriction fragment length polymorphism and pyrosequencing revealed that the culture is mainly composed of two bacteria related to uncultured Gram-positive Thermoanaerobacteraceae and uncultured gram-negative Desulfobulbaceae. Stable isotope probing showed that a [13]C-carbon label from [13]C10-naphthalene as growth substrate was mostly incorporated by the Thermoanaerobacteraceae. The presence of putative genes involved in naphthalene degradation in the genome of this organism was confirmed via assembly-based metagenomics and supports that it is the naphthalene-degrading bacterium in the culture. Thermoanaerobacteraceae have previously been detected in oil sludge under thermophilic conditions, but have not been shown to degrade hydrocarbons so far. The second member of the community belongs to the Desulfobulbaceae and has high sequence similarity to uncultured bacteria from contaminated sites including recently proposed groundwater cable bacteria. We suggest that the gram-positive Thermoanaerobacteraceae degrade polycyclic aromatic hydrocarbons while the Desulfobacterales are mainly responsible for Fe(III) reduction.}, }
@article {pmid29177753, year = {2018}, author = {Lee, JH and Lee, BJ}, title = {Microbial Reduction of Fe(III) and SO4[2-] and Associated Microbial Communities in the Alluvial Aquifer Groundwater and Sediments.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {182-191}, pmid = {29177753}, issn = {1432-184X}, support = {14-3211//Korea Institute of Geoscience and Mineral Resources/ ; 14-3211//Korea Institute of Geoscience and Mineral Resources/ ; PJ012263//Rural Development Administration/ ; }, mesh = {Bacteria/classification/genetics/metabolism ; Biodiversity ; Carbon/chemistry ; Ferric Compounds/*metabolism ; Fresh Water/chemistry/microbiology ; Geologic Sediments/*microbiology ; Groundwater/chemistry/*microbiology ; Microbiota/genetics/*physiology ; *Oxidation-Reduction ; Phylogeny ; Republic of Korea ; Rivers/chemistry/microbiology ; Sequence Analysis, DNA ; Sulfates/*metabolism ; *Water Microbiology ; }, abstract = {Agricultural demands continuously increased use of groundwater, causing drawdown of water table and need of artificial recharge using adjacent stream waters. River water intrusion into groundwater can alter the geochemical and microbiological characteristics in the aquifer and subsurface. In an effort to investigate the subsurface biogeochemical activities before operation of artificial recharge at the test site, established at the bank of Nakdong River, Changwon, South Korea, organic carbon transported from river water to groundwater was mimicked and the effect on the indigenous microbial communities was investigated with the microcosm incubations of the groundwater and subsurface sediments. Laboratory incubations indicated microbial reduction of Fe(III) and sulfate. Next-generation Illumina MiSeq sequences of V4 region of 16S rRNA gene provided that the shifts of microbial taxa to Fe(III)-reducing and/or sulfate-reducing microorganisms such as Geobacter, Albidiferax, Desulfocapsa, Desulfuromonas, and Desulfovibrio were in good correlation with the sequential flourishment of microbial reduction of Fe(III) and sulfate as the incubations progressed. This suggests the potential role of dissolved organic carbons migrated with the river water into groundwater in the managed aquifer recharge system on the indigenous microbial community composition and following alterations of subsurface biogeochemistry and microbial metabolic activities.}, }
@article {pmid29177752, year = {2018}, author = {Renault, D and Déniel, F and Vallance, J and Bruez, E and Godon, JJ and Rey, P}, title = {Bacterial Shifts in Nutrient Solutions Flowing Through Biofilters Used in Tomato Soilless Culture.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {169-181}, pmid = {29177752}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/metabolism/pathogenicity ; *Bacterial Physiological Phenomena ; Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Filtration ; Fusarium/pathogenicity ; Solanum lycopersicum/*microbiology ; Microbiota/*physiology ; Nutrients/*chemistry ; Pythium/pathogenicity ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {In soilless culture, slow filtration is used to eliminate plant pathogenic microorganisms from nutrient solutions. The present study focused on the characterization and the potential functions of microbial communities colonizing the nutrient solutions recycled on slow filters during a whole cultivation season of 7 months in a tomato growing system. Bacterial microflora colonizing the solutions before and after they flew through the columns were studied. Two filters were amended with Pseudomonas putida (P-filter) or Bacillus cereus strains (B-filter), and a third filter was a control (C-filter). Biological activation of filter unit through bacterial amendment enhanced very significantly filter efficacy against plant potential pathogens Pythium spp. and Fusarium oxysporum. However, numerous bacteria (10[3]-10[4] CFU/mL) were detected in the effluent solutions. The community-level physiological profiling indicated a temporal shift of bacterial microflora, and the metabolism of nutrient solutions originally oriented towards carbohydrates progressively shifted towards degradation of amino acids and carboxylic acids over the 7-month period of experiment. Single-strand conformation polymorphism fingerprinting profiles showed that a shift between bacterial communities colonizing influent and effluent solutions of slow filters occurred. In comparison with influent, 16S rDNA sequencing revealed that phylotype diversity was low in the effluent of P- and C-filters, but no reduction was observed in the effluent of the B-filter. Suppressive potential of solutions filtered on a natural filter (C-filter), where the proportion of Proteobacteria (α- and β-) increased, whereas the proportion of uncultured candidate phyla rose in P- and B-filters, is discussed.}, }
@article {pmid29176587, year = {2017}, author = {Borrelli, L and Coretti, L and Dipineto, L and Bovera, F and Menna, F and Chiariotti, L and Nizza, A and Lembo, F and Fioretti, A}, title = {Insect-based diet, a promising nutritional source, modulates gut microbiota composition and SCFAs production in laying hens.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {16269}, pmid = {29176587}, issn = {2045-2322}, mesh = {Animal Feed ; Animals ; Chickens ; Diet ; Fatty Acids, Volatile/metabolism ; Female ; Gastrointestinal Microbiome/*physiology ; *Insecta ; }, abstract = {Insects could be potential nutritional sources both for humans and animals. Among these, Hermetia illucens, with good amount of chitin and proteins, represents a suitable diet replacement for laying hens. Little is known about insect diet effects on the microbial ecology of the gastrointestinal tract and bacterial metabolites production. In this study we investigated the effect of H. illucens larvae meal administration on cecal microbiota and short chain fatty acids (SCFAs) production in laying hens. 16S rDNA sequencing showed strong differences between cecal microbiota of soybean (SD) and insect diet (ID) groups both in type and relative abundance (unweighted and weighted beta diversity) of microbial species. In particular, Bacteroides plebeius, Elusimicrobium minutum, Alkaliphilus transvaalensis, Christensenella minuta, Vallitalea guaymasensis and Flavonifractor plautii represented the principal contributors of changes in gut microbiota composition of ID group (FDR p-values < 0.05). Of these, F. plautii, C. minuta and A. transvaalensis have the potential to degrade the chitin's insect meal and correlated with the observed high levels of gut SCFAs produced in ID group. These microorganisms may thus connect the chitin degradation with high SCFAs production. Our results suggest H. illucens as a potential prebiotic by well feeding gut microbiota.}, }
@article {pmid29173645, year = {2018}, author = {Quijada, NM and De Filippis, F and Sanz, JJ and García-Fernández, MDC and Rodríguez-Lázaro, D and Ercolini, D and Hernández, M}, title = {Different Lactobacillus populations dominate in "Chorizo de León" manufacturing performed in different production plants.}, journal = {Food microbiology}, volume = {70}, number = {}, pages = {94-102}, doi = {10.1016/j.fm.2017.09.009}, pmid = {29173645}, issn = {1095-9998}, mesh = {Animals ; DNA, Bacterial/genetics ; Fermentation ; Food Microbiology ; Lactobacillus/classification/genetics/*isolation &amp; purification/metabolism ; Meat Products/*microbiology ; RNA, Ribosomal, 16S/genetics ; Spain ; Staphylococcus/classification/genetics/*isolation &amp; purification/metabolism ; Swine ; }, abstract = {"Chorizo de Léon" is a high-value Spanish dry fermented sausage traditionally manufactured without the use of starter cultures, owing to the activity of a house-specific autochthonous microbiota that naturally contaminates the meat from the environment, the equipment and the raw materials. Lactic acid bacteria (particularly Lactobacillus) and coagulase-negative cocci (mainly Staphylococcus) have been reported as the most important bacterial groups regarding the organoleptic and safety properties of the dry fermented sausages. In this study, samples from raw minced meat to final products were taken from five different producers and the microbial diversity was investigated by high-throughput sequencing of 16S rRNA gene amplicons. The diverse microbial composition observed during the first stages of "Chorizo de Léon" evolved during ripening to a microbiota mainly composed by Lactobacillus in the final product. Oligotyping performed on 16S rRNA gene sequences of Lactobacillus and Staphylococcus populations revealed sub-genus level diversity within the different manufacturers, likely responsible of the characteristic organoleptic properties of the products from different companies.}, }
@article {pmid29173642, year = {2018}, author = {Rouger, A and Moriceau, N and Prévost, H and Remenant, B and Zagorec, M}, title = {Diversity of bacterial communities in French chicken cuts stored under modified atmosphere packaging.}, journal = {Food microbiology}, volume = {70}, number = {}, pages = {7-16}, doi = {10.1016/j.fm.2017.08.013}, pmid = {29173642}, issn = {1095-9998}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Chickens ; Food Microbiology ; Food Packaging ; France ; Meat/*microbiology ; }, abstract = {Poultry meat, the second most consumed meat in France, is commercialized mainly as portions of chicken cuts with various quality labels, stored under various modified atmosphere packaging (MAP), with shelf-life ranging from 9 to 17 days. We used 16S rDNA pyrosequencing to describe microbiota of chicken legs. Ten samples representing a wide diversity of labels and MAP available on the market were collected from local supermarkets and stored at 4 °C. Microbiota were collected, total DNA was extracted, and V1-V3 fragment of 16S rRNA genes were amplified and sequenced. For data analysis several pipelines were compared. The Qiime pipeline was chosen to cluster reads and we used a database previously developed for a meat and fish microbial ecology study. Variability between samples was observed and a listing of bacteria present on chicken meat was established. The structure of the bacterial communities were compared with traditional cultural methods and validated with quantitative real time PCR. Brochothrix thermosphacta, Pseudomonas sp., and Carnobacterium sp. were dominant and the nature of the gas used for packaging influenced the relative abundance of each suggesting a MAP gas composition dependent competition between these species. We also noticed that slaughterhouse environment may influence the nature of the contaminants.}, }
@article {pmid29173632, year = {2018}, author = {Kuuliala, L and Al Hage, Y and Ioannidis, AG and Sader, M and Kerckhof, FM and Vanderroost, M and Boon, N and De Baets, B and De Meulenaer, B and Ragaert, P and Devlieghere, F}, title = {Microbiological, chemical and sensory spoilage analysis of raw Atlantic cod (Gadus morhua) stored under modified atmospheres.}, journal = {Food microbiology}, volume = {70}, number = {}, pages = {232-244}, doi = {10.1016/j.fm.2017.10.011}, pmid = {29173632}, issn = {1095-9998}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Food Packaging/*methods ; Food Storage ; Gadus morhua/*microbiology ; Humans ; Meat/analysis/*microbiology ; Seafood/analysis/*microbiology ; Taste ; Volatile Organic Compounds/analysis/metabolism ; }, abstract = {During fish spoilage, microbial metabolism leads to the production of volatile organic compounds (VOCs), characteristic off-odors and eventual consumer rejection. The aim of the present study was to contribute to the development of intelligent packaging technologies by identifying and quantifying VOCs that indicate spoilage of raw Atlantic cod (Gadus morhua) under atmospheres (%v/v CO2/O2/N2) 60/40/0, 60/5/35 and air. Spoilage was examined by microbiological, chemical and sensory analyses over storage time at 4 or 8 °C. Selected-ion flow-tube mass spectrometry (SIFT-MS) was used for quantifying selected VOCs and amplicon sequencing of the 16S rRNA gene was used for the characterization of the cod microbiota. OTUs classified within the Photobacterium genus increased in relative abundance over time under all storage conditions, suggesting that Photobacterium contributed to spoilage and VOC production. The onset of exponential VOC concentration increase and sensory rejection occurred at high total plate counts (7-7.5 log). Monitoring of early spoilage thus calls for sensitivity for low VOC concentrations.}, }
@article {pmid29173626, year = {2018}, author = {Wynants, E and Crauwels, S and Verreth, C and Gianotten, N and Lievens, B and Claes, J and Van Campenhout, L}, title = {Microbial dynamics during production of lesser mealworms (Alphitobius diaperinus) for human consumption at industrial scale.}, journal = {Food microbiology}, volume = {70}, number = {}, pages = {181-191}, doi = {10.1016/j.fm.2017.09.012}, pmid = {29173626}, issn = {1095-9998}, mesh = {Animal Feed/analysis ; Animals ; Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; *Biodiversity ; Food Contamination/*analysis ; Food Safety ; Humans ; Tenebrio/chemistry/metabolism/*microbiology ; }, abstract = {In this study, the microbial dynamics during an industrial production cyle of lesser mealworms (Alphitobius diaperinus), sold for human consumption, were characterised. The microbial numbers as well as the microbial diversity were generally higher for the substrate, existing of remaining feed, faeces and exuviae, than for the larvae. Most of the species-level operational taxonomic units, identified using Illumina MiSeq sequencing, that were present in the feed were also detected in the larvae and vice versa. However, bacterial diversity decreased in the larvae during rearing. These results suggested that the feed is an important determinant of the insect bacterial community, but that some bacterial species show a competitive advantage inside the insect gut and become dominant. A blanching treatment of the larvae after harvest reduced most microbial counts, but the number of aerobic endospores remained at 4.0 log cfu/g. Whereas food pathogens Salmonella spp., Listeria monocytogenes, Bacillus cereus or coagulase-positive staphylococci were not detected in our study, fungal isolates corresponding to the genera Aspergillus and Fusarium were recovered. Therefore, it cannot be excluded that mycotoxins were present. The results of this study contribute to a better understanding of the microbial dynamics and food safety aspects during the production of edible insects.}, }
@article {pmid29169016, year = {2017}, author = {}, title = {Principles of Systems Biology, No. 23.}, journal = {Cell systems}, volume = {5}, number = {5}, pages = {428-430}, doi = {10.1016/j.cels.2017.11.008}, pmid = {29169016}, issn = {2405-4712}, abstract = {This month: protein engineering (Mootha, Chica), synthetic biology (Khalil, You, Ting Lu, Timothy K. Lu), microbial ecology and evolution (Desai), side-stepping antibiotic resistance (Chandrasekaran), and mapping microbiomes (Borisy).}, }
@article {pmid29167922, year = {2018}, author = {Keller, AH and Kleinsteuber, S and Vogt, C}, title = {Correction to: Anaerobic Benzene Mineralization by Nitrate-Reducing and Sulfate-Reducing Microbial Consortia Enriched From the Same Site: Comparison of Community Composition and Degradation Characteristics.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {954}, doi = {10.1007/s00248-017-1111-y}, pmid = {29167922}, issn = {1432-184X}, abstract = {The original version of this article unfortunately contained mistakes in Table 1. The two data sets were accidentally missing in the table. The original article has been corrected.}, }
@article {pmid29167267, year = {2017}, author = {Bag, S and Ghosh, TS and Das, B}, title = {Complete Genome Sequence of Collinsella aerofaciens Isolated from the Gut of a Healthy Indian Subject.}, journal = {Genome announcements}, volume = {5}, number = {47}, pages = {}, pmid = {29167267}, issn = {2169-8287}, abstract = {Collinsella aerofaciens, a rod-shaped nonmotile obligate anaerobe, is the most abundant actinobacterium in the gastrointestinal tract of healthy humans. An altered abundance of C. aerofaciens may be linked with several health disorders, including irritable bowel syndrome. In the present study, we report the complete genome sequence of C. aerofaciens strain indica.}, }
@article {pmid29163419, year = {2017}, author = {Cabello-Yeves, PJ and Ghai, R and Mehrshad, M and Picazo, A and Camacho, A and Rodriguez-Valera, F}, title = {Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2131}, pmid = {29163419}, issn = {1664-302X}, abstract = {The phylum Verrucomicrobia contains freshwater representatives which remain poorly studied at the genomic, taxonomic, and ecological levels. In this work we present eighteen new reconstructed verrucomicrobial genomes from two freshwater reservoirs located close to each other (Tous and Amadorio, Spain). These metagenome-assembled genomes (MAGs) display a remarkable taxonomic diversity inside the phylum and comprise wide ranges of estimated genome sizes (from 1.8 to 6 Mb). Among all Verrucomicrobia studied we found some of the smallest genomes of the Spartobacteria and Opitutae classes described so far. Some of the Opitutae family MAGs were small, cosmopolitan, with a general heterotrophic metabolism with preference for carbohydrates, and capable of xylan, chitin, or cellulose degradation. Besides, we assembled large copiotroph genomes, which contain a higher number of transporters, polysaccharide degrading pathways and in general more strategies for the uptake of nutrients and carbohydrate-based metabolic pathways in comparison with the representatives with the smaller genomes. The diverse genomes revealed interesting features like green-light absorbing rhodopsins and a complete set of genes involved in nitrogen fixation. The large diversity in genome sizes and physiological properties emphasize the diversity of this clade in freshwaters enlarging even further the already broad eco-physiological range of these microbes.}, }
@article {pmid29163388, year = {2017}, author = {Becraft, ED and Dodsworth, JA and Murugapiran, SK and Thomas, SC and Ohlsson, JI and Stepanauskas, R and Hedlund, BP and Swingley, WD}, title = {Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2082}, pmid = {29163388}, issn = {1664-302X}, abstract = {Recent progress based on single-cell genomics and metagenomic investigations of archaea in a variety of extreme environments has led to significant advances in our understanding of the diversity, evolution, and metabolic potential of archaea, yet the vast majority of archaeal diversity remains undersampled. In this work, we coordinated single-cell genomics with metagenomics in order to construct a near-complete genome from a deeply branching uncultivated archaeal lineage sampled from Great Boiling Spring (GBS) in the U.S. Great Basin, Nevada. This taxon is distantly related (distinct families) to an archaeal genome, designated "Novel Archaeal Group 1" (NAG1), which was extracted from a metagenome recovered from an acidic iron spring in Yellowstone National Park (YNP). We compared the metabolic predictions of the NAG1 lineage to better understand how these archaea could inhabit such chemically distinct environments. Similar to the NAG1 population previously studied in YNP, the NAG1 population from GBS is predicted to utilize proteins as a primary carbon source, ferment simple carbon sources, and use oxygen as a terminal electron acceptor under oxic conditions. However, GBS NAG1 populations contained distinct genes involved in central carbon metabolism and electron transfer, including nitrite reductase, which could confer the ability to reduce nitrite under anaerobic conditions. Despite inhabiting chemically distinct environments with large variations in pH, GBS NAG1 populations shared many core genomic and metabolic features with the archaeon identified from YNP, yet were able to carve out a distinct niche at GBS.}, }
@article {pmid29159493, year = {2018}, author = {Lyra, ML and Bletz, MC and Haddad, CFB and Vences, M}, title = {The Intestinal Microbiota of Tadpoles Differs from Those of Syntopic Aquatic Invertebrates.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {121-124}, pmid = {29159493}, issn = {1432-184X}, support = {#2013/50741-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 88881.062205/2014-01//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {Animals ; Bacteria/*classification/genetics ; DNA, Bacterial/genetics ; Gastrointestinal Microbiome/genetics/*physiology ; Gastrointestinal Tract/*microbiology ; Gastropoda/microbiology ; Genes, Bacterial/genetics ; Host Microbial Interactions ; Insecta/microbiology ; Invertebrates/*microbiology ; Larva/*microbiology ; *Phylogeny ; Ponds ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Bacterial communities associated to eukaryotes play important roles in the physiology, development, and health of their hosts. Here, we examine the intestinal microbiota in tadpoles and aquatic invertebrates (insects and gastropods) to better understand the degree of specialization in the tadpole microbiotas. Samples were collected at the same time in one pond, and the V4 region of the bacterial 16S rRNA gene was sequenced with Illumina amplicon sequencing. We found that bacterial richness and diversity were highest in two studied snail individuals, intermediate in tadpoles, and lowest in the four groups of aquatic insects. All groups had substantial numbers of exclusive bacterial operational taxonomic units (OTUs) in their guts, but also shared a high proportion of OTUs, probably corresponding to transient environmental bacteria. Significant differences were found for all pairwise comparisons of tadpoles and snails with the major groups of insects, but not among insect groups or between snails and tadpoles. The similarity between tadpoles and snails may be related to similar feeding mode as both snails and tadpoles scratch biofilms and algae from surfaces; however, this requires confirmation due to low sample sizes. Overall, the gut microbiota differences found among syntopic aquatic animals are likely shaped by both food preferences and host identity.}, }
@article {pmid29158969, year = {2017}, author = {Vanlancker, E and Vanhoecke, B and Stringer, A and Van de Wiele, T}, title = {5-Fluorouracil and irinotecan (SN-38) have limited impact on colon microbial functionality and composition in vitro.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e4017}, pmid = {29158969}, issn = {2167-8359}, abstract = {Gastrointestinal mucositis is a debilitating side effect of chemotherapy treatment, with currently no treatment available. As changes in microbial composition have been reported upon chemotherapy treatment in vivo, it is thought that gut microbiota dysbiosis contribute to the mucositis etiology. Yet it is not known whether chemotherapeutics directly cause microbial dysbiosis, thereby increasing mucositis risk, or whether the chemotherapeutic subjected host environment disturbs the microbiome thereby aggravating the disease. To address this question, we used the M-SHIME[®], an in vitro mucosal simulator of the human intestinal microbial ecosystem, as an experimental setup that excludes the host factor. The direct impact of two chemotherapeutics, 5-fluorouracil (5-FU) and SN-38 (active metabolite of irinotecan), on the luminal and mucosal gut microbiota from several human donors was investigated through monitoring fermentation activity and next generation sequencing. At a dose of 10 µM in the mucosal environment, 5-FU impacted the functionality and composition of the colon microbiota to a minor extent. Similarly, a daily dose of 10 µM SN-38 in the luminal environment did not cause significant changes in the functionality or microbiome composition. As our mucosal model does not include a host-compartment, our findings strongly indicate that a putative microbial contribution to mucositis is initially triggered by an altered host environment upon chemotherapy.}, }
@article {pmid29155834, year = {2017}, author = {Kalan, L and Zhou, M and Labbie, M and Willing, B}, title = {Measuring the microbiome of chronic wounds with use of a topical antimicrobial dressing - A feasibility study.}, journal = {PloS one}, volume = {12}, number = {11}, pages = {e0187728}, pmid = {29155834}, issn = {1932-6203}, mesh = {Adult ; Aged ; Anti-Bacterial Agents/therapeutic use ; Anti-Infective Agents/*therapeutic use ; Bandages/*microbiology ; Biofilms/drug effects/growth &amp; development ; Debridement ; Feasibility Studies ; Female ; Humans ; Male ; Microbiota/drug effects/*genetics ; Middle Aged ; Oxides/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Silver Compounds/therapeutic use ; Wound Healing/*drug effects/genetics ; }, abstract = {BACKGROUND: Polymicrobial communities colonize all wounds, and biofilms are hypothesized to be a key link to the chronic state and stalled healing. Molecular methods offer greater insight when studying microbial ecology in chronic wounds, as only a small fraction of wound bacteria are cultured by currently available methods and studies have shown little agreement between culture and molecular based approaches. Some interventions, like dressings with oxidized silver, are reported to help the stalled wounds move to a normal healing trajectory but the underlying mechanisms are difficult to measure. One hypothesis is that the use of topical antimicrobial dressings targets the wound microbiome and reduces bioburden.<br><br>OBJECTIVES: Our objective was to determine if culture-independent molecular methods could be used to identify the microbial composition in chronic wounds, and measure the microbiome over time when a topical antimicrobial dressing is used to reduce bioburden.<br><br>METHODS: Patients with chronic wounds defined as >6 weeks in duration and not taking systemic antibiotics were recruited to participate. A wound contact layer containing silver oxynitrate was applied immediately after routine sharp debridement material was collected and swabs of the wound bed taken. Next-generation sequencing of the bacterial 16S rRNA gene in each specimen was used to measure the microbiome.<br><br>RESULTS: Distinct bacterial communities were observed between swab and debridement samples, highlighting spatial differences and the importance of sampling consistency. The microbial communities appeared to be similar between different diabetes statuses, but different among the three wound categories included.<br><br>CONCLUSIONS: Culture-independent methods can be applied to measure the microbiome of chronic wounds even when a topical antimicrobial dressing is applied to the wound.}, }
@article {pmid29154097, year = {2018}, author = {Qian, X and Gu, J and Sun, W and Wang, XJ and Su, JQ and Stedfeld, R}, title = {Diversity, abundance, and persistence of antibiotic resistance genes in various types of animal manure following industrial composting.}, journal = {Journal of hazardous materials}, volume = {344}, number = {}, pages = {716-722}, doi = {10.1016/j.jhazmat.2017.11.020}, pmid = {29154097}, issn = {1873-3336}, mesh = {Animals ; Cattle ; Chickens ; *Composting ; DNA Transposable Elements/genetics ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; Industrial Waste ; Manure/*analysis ; Metals, Heavy/analysis ; Nitrogen/analysis ; Swine ; }, abstract = {Aerobic composting is used widely for animal manure recycling, and it may reduce the amount of antibiotic resistance genes (ARGs) that enter the environment. We sampled three types of animal (bovine, chicken, and pig) manure and the corresponding composts from 12 large-scale farms, and tested multiple ARGs and mobile genetic elements (MGEs) by high-throughput qPCR. A total of 109 ARGs were detected in the manure and compost samples, thereby demonstrating that both are important ARG reservoirs. The diversity and abundance of ARGs were significantly higher in chicken and pig manure than bovine manure, but industrial composting was more efficient at reducing the ARGs in chicken manure than pig and bovine manure. Composting universally reduced some ARGs, but inconsistently influenced other ARGs from different types of animal manures. Network analysis detected the widespread co-occurrence of ARGs and MGEs. floR, ermF, catB3, aac(6')-lb(akaaacA4), and aadA were identified as suitable indicator genes for estimating the total abundance of ARGs. Our results suggest that different animal species had significant effects on the diversity, abundance, and persistence of ARGs, where the abundance of transposons, heavy metal concentration, total nitrogen level, and the dosage and duration of exposure to antibiotics may explain these differences.}, }
@article {pmid29153320, year = {2017}, author = {Dudek, NK and Sun, CL and Burstein, D and Kantor, RS and Aliaga Goltsman, DS and Bik, EM and Thomas, BC and Banfield, JF and Relman, DA}, title = {Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome.}, journal = {Current biology : CB}, volume = {27}, number = {24}, pages = {3752-3762.e6}, doi = {10.1016/j.cub.2017.10.040}, pmid = {29153320}, issn = {1879-0445}, mesh = {Animals ; Archaea/*classification ; Bacteria/*classification ; Bottle-Nosed Dolphin/*microbiology ; Female ; *Genome, Archaeal ; *Genome, Bacterial ; Male ; *Metagenome ; Metagenomics ; *Microbiota ; Mouth/microbiology ; }, abstract = {The vast majority of bacterial diversity lies within phylum-level lineages called "candidate phyla," which lack isolated representatives and are poorly understood. These bacteria are surprisingly abundant in the oral cavity of marine mammals. We employed a genome-resolved metagenomic approach to recover and characterize genomes and functional potential from microbes in the oral gingival sulcus of two bottlenose dolphins (Tursiops truncatus). We detected organisms from 24 known bacterial phyla and one archaeal phylum. We also recovered genomes from two deep-branching, previously uncharacterized phylum-level lineages (here named "Candidatus Delphibacteria" and "Candidatus Fertabacteria"). The Delphibacteria lineage is found in both managed and wild dolphins; its metabolic profile suggests a capacity for denitrification and a possible role in dolphin health. We uncovered a rich diversity of predicted Cas9 proteins, including the two longest predicted Cas9 proteins to date. Notably, we identified the first type II CRISPR-Cas systems encoded by members of the Candidate Phyla Radiation. Using their spacer sequences, we subsequently identified and assembled a complete Saccharibacteria phage genome. These findings underscore the immense microbial diversity and functional potential that await discovery in previously unexplored environments.}, }
@article {pmid29151852, year = {2017}, author = {Rifkin, RF and Potgieter, M and Ramond, JB and Cowan, DA}, title = {Ancient oncogenesis, infection and human evolution.}, journal = {Evolutionary applications}, volume = {10}, number = {10}, pages = {949-964}, pmid = {29151852}, issn = {1752-4571}, abstract = {The recent discovery that malignant neoplastic lesions date back nearly 2 million years ago not only highlights the antiquity of cancer in the human lineage, but also provides remarkable insight into ancestral hominin disease pathology. Using these Early Pleistocene examples as a point of departure, we emphasize the prominent role of viral and bacterial pathogens in oncogenesis and evaluate the impact of pathogens on human evolutionary processes in Africa. In the Shakespearean vernacular "what's past is prologue," we highlight the significance of novel information derived from ancient pathogenic DNA. In particular, and given the temporal depth of human occupation in sub-Saharan Africa, it is emphasized that the region is ideally positioned to play a strategic role in the discovery of ancient pathogenic drivers of not only human mortality, but also human evolution. Ancient African pathogen genome data can provide novel revelations concerning human-pathogen coevolutionary processes, and such knowledge is essential for forecasting the ways in which emerging zoonotic and increasingly transmissible diseases might influence human demography and longevity in the future.}, }
@article {pmid29150733, year = {2018}, author = {Baumann, JH and Davies, SW and Aichelman, HE and Castillo, KD}, title = {Correction to: Coral Symbiodinium Community Composition Across the Belize Mesoamerican Barrier Reef System is Influenced by Host Species and Thermal Variability.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {916}, doi = {10.1007/s00248-017-1112-x}, pmid = {29150733}, issn = {1432-184X}, abstract = {The authors regret that acknowledgment for Dr. Adrian Marchetti was omitted from the manuscript. The correct acknowledgment is written below.}, }
@article {pmid29148895, year = {2018}, author = {Lambrecht, E and Van Meervenne, E and Boon, N and Van de Wiele, T and Wattiau, P and Herman, L and Heyndrickx, M and Van Coillie, E}, title = {Characterization of Cefotaxime- and Ciprofloxacin-Resistant Commensal Escherichia coli Originating from Belgian Farm Animals Indicates High Antibiotic Resistance Transfer Rates.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {24}, number = {6}, pages = {707-717}, doi = {10.1089/mdr.2017.0226}, pmid = {29148895}, issn = {1931-8448}, mesh = {Animals ; Animals, Domestic/*microbiology ; Anti-Bacterial Agents/*pharmacology ; Belgium ; Cefotaxime/*pharmacology ; Ciprofloxacin/*pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/genetics ; Escherichia coli Proteins/*drug effects/*genetics ; Integrons/genetics ; Microbial Sensitivity Tests/methods ; Phylogeny ; Plasmids/genetics ; }, abstract = {Food-producing animals represent one of the sources of antibiotic resistant commensal bacteria. There is an increasing awareness that these bacteria might have the potential to transfer their resistance genes to other (pathogenic) bacteria. In this study, 50 commensal Escherichia coli strains originating from food-producing animals and resistant to the "highest priority, critically important antibiotics" cefotaxime and/or ciprofloxacin, were selected for further characterization. For each strain (i) an antibiogram, (ii) the phylogenetic group, (iii) plasmid replicon type, (iv) presence and identification of integrons, and (v) antibiotic resistance transfer ratios were determined. Forty-five of these strains were resistant to 5 or more antibiotics, and 6 strains were resistant to 10 or more antibiotics. Resistance was most common to ampicillin (100%), sulfamethoxazole, ciprofloxacin (82%), trimethoprim, tetracycline (74%), cefotaxime, (70%) and ceftazidime (62%). Phylogenetic groups A (62%) and B1 (26%) were most common, followed by C (8%) and E (4%). In 43 strains, more than 1 replicon type was detected, with FII (88%), FIB (70%), and I1 (48%) being the most encountered types. Forty strains, positive for integrons, all harbored a class I integron and seven of them contained an additional class II integron. No class III integrons were detected. The antibiotic resistance transfer was assessed by liquid mating experiments. The transfer ratio, expressed as the number of transconjugants per recipient, was between 10[-5] and 10[0] for cefotaxime resistance and between 10[-7] and 10[-1] for ciprofloxacin resistance. The results of the current study prove that commensal E. coli in food-production animals can be a source of multiple resistance genes and that these bacteria can easily spread their ciprofloxacin and cefotaxime resistance.}, }
@article {pmid29147973, year = {2018}, author = {Schlemper, TR and van Veen, JA and Kuramae, EE}, title = {Co-Variation of Bacterial and Fungal Communities in Different Sorghum Cultivars and Growth Stages is Soil Dependent.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {205-214}, pmid = {29147973}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; DNA, Fungal/genetics/isolation &amp; purification ; Fungi/classification/genetics ; Genotype ; *Microbiota/genetics ; *Mycobiome/genetics ; Netherlands ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Rhizosphere ; Soil/*chemistry ; *Soil Microbiology ; Sorghum/classification/*growth &amp; development/*microbiology ; }, abstract = {Rhizosphere microbial community composition can be influenced by different biotic and abiotic factors. We investigated the composition and co-variation of rhizosphere bacterial and fungal communities from two sorghum genotypes (BRS330 and SRN-39) in three different plant growth stages (emergence of the second leaf, (day10), vegetative to reproductive differentiation point (day 35), and at the last visible emerged leaf (day 50)) in two different soil types, Clue field (CF) and Vredepeel (VD). We observed that either bacterial or fungal community had its composition stronger influenced by soil followed by plant growth stage and cultivar. However, the influence of plant growth stage was higher on fungal community composition than on the bacterial community composition. Furthermore, we showed that sorghum rhizosphere bacterial and fungal communities can affect each other's composition and structure. The decrease in relative abundance of the fungus genus Gibberella over plant growth stages was followed by decrease of the bacterial families Oxalobacteracea and Sphingobacteriacea. Although cultivar effect was not the major responsible for bacterial and fungal community composition, cultivar SRN-39 showed to promote a stronger co-variance between bacterial and fungal communities.}, }
@article {pmid29146862, year = {2017}, author = {Bag, S and Ghosh, TS and Das, B}, title = {Complete Genome Sequence of Faecalibacterium prausnitzii Isolated from the Gut of a Healthy Indian Adult.}, journal = {Genome announcements}, volume = {5}, number = {46}, pages = {}, pmid = {29146862}, issn = {2169-8287}, abstract = {Faecalibacterium prausnitzii is the most abundant (~4%) member of the phylum Firmicutes found in the colon of healthy humans. It is a strict anaerobe and plays an important role in intestinal homeostasis. Here, we report the complete genome sequence of F. prausnitzii strain Indica.}, }
@article {pmid29145139, year = {2018}, author = {Xu, Z and Ben, Y and Chen, Z and Jiang, A and Shen, J and Han, X}, title = {Application and microbial ecology of psychrotrophs in domestic wastewater treatment at low temperature.}, journal = {Chemosphere}, volume = {191}, number = {}, pages = {946-953}, doi = {10.1016/j.chemosphere.2017.10.121}, pmid = {29145139}, issn = {1879-1298}, mesh = {Bacteria/growth &amp; development/isolation &amp; purification/*metabolism ; Bacterial Adhesion ; *Biodegradation, Environmental ; Bioreactors/microbiology ; Climate ; *Cold Temperature ; Ecology ; Polyurethanes ; Seasons ; Waste Disposal, Fluid/methods ; Wastewater/*microbiology ; Water Purification/methods ; }, abstract = {The feasibility of a bunch of screened psychrotrophs being applied to low-temperature wastewater treatment was investigated. The screened psychrophillic strains are capable of growth at a broad temperature-range from 0 to 40 °C and exhibit a preferable TTC-dehydrogenase activity at low temperature (4-10 °C). Along the sharply fluctuant temperatures (25-4-25 °C), the screened psychrotrophs (compared with the indigenous mesophiles) demonstrate less fluctuations of COD removal and more rapid recovery after temperature shocks. COD removal of approximate 80% was recorded by single psychrotrophs (while only 10% by single mesophiles) at low temperature (4 °C). Soft polyurethane foam showed better performance for psychrotrophs immobilization, with the optimal filling rate of 30% (v/v) in the bioreactor. The observation shows that the immobilized psychrotrophs demonstrated a relatively high performance on both conventional and emerging organic contaminants removals at low temperature. In order to check the feasibility of the screened psychrotrophs in treating actual domestic wastewater, a pilot-scale ICABR bioreactor was operated firstly at low temperature (4 °C) and then at seasonal varying temperatures (0-30 °C) for one year, the influent COD of 150-600 mg L[-1] was efficiently reduced to 40 ± 18 mg L[-1] under the conditions of an overall hydraulic retention time of 10 h. Furthermore, psychrotrophs performed stably as the predominant bacteria family during the whole operation. This study provides evidence that microbial intensification with psychrotrophs was a feasible strategy to improve the efficiency of conventional wastewater treatment process at low temperature.}, }
@article {pmid29143494, year = {2018}, author = {van der Plas, F and Ratcliffe, S and Ruiz-Benito, P and Scherer-Lorenzen, M and Verheyen, K and Wirth, C and Zavala, MA and Ampoorter, E and Baeten, L and Barbaro, L and Bastias, CC and Bauhus, J and Benavides, R and Benneter, A and Bonal, D and Bouriaud, O and Bruelheide, H and Bussotti, F and Carnol, M and Castagneyrol, B and Charbonnier, Y and Cornelissen, JHC and Dahlgren, J and Checko, E and Coppi, A and Dawud, SM and Deconchat, M and De Smedt, P and De Wandeler, H and Domisch, T and Finér, L and Fotelli, M and Gessler, A and Granier, A and Grossiord, C and Guyot, V and Haase, J and Hättenschwiler, S and Jactel, H and Jaroszewicz, B and Joly, FX and Jucker, T and Kambach, S and Kaendler, G and Kattge, J and Koricheva, J and Kunstler, G and Lehtonen, A and Liebergesell, M and Manning, P and Milligan, H and Müller, S and Muys, B and Nguyen, D and Nock, C and Ohse, B and Paquette, A and Peñuelas, J and Pollastrini, M and Radoglou, K and Raulund-Rasmussen, K and Roger, F and Seidl, R and Selvi, F and Stenlid, J and Valladares, F and van Keer, J and Vesterdal, L and Fischer, M and Gamfeldt, L and Allan, E}, title = {Continental mapping of forest ecosystem functions reveals a high but unrealised potential for forest multifunctionality.}, journal = {Ecology letters}, volume = {21}, number = {1}, pages = {31-42}, doi = {10.1111/ele.12868}, pmid = {29143494}, issn = {1461-0248}, mesh = {*Biodiversity ; Climate ; *Ecosystem ; Europe ; *Forests ; Humans ; }, abstract = {Humans require multiple services from ecosystems, but it is largely unknown whether trade-offs between ecosystem functions prevent the realisation of high ecosystem multifunctionality across spatial scales. Here, we combined a comprehensive dataset (28 ecosystem functions measured on 209 forest plots) with a forest inventory dataset (105,316 plots) to extrapolate and map relationships between various ecosystem multifunctionality measures across Europe. These multifunctionality measures reflected different management objectives, related to timber production, climate regulation and biodiversity conservation/recreation. We found that trade-offs among them were rare across Europe, at both local and continental scales. This suggests a high potential for 'win-win' forest management strategies, where overall multifunctionality is maximised. However, across sites, multifunctionality was on average 45.8-49.8% below maximum levels and not necessarily highest in protected areas. Therefore, using one of the most comprehensive assessments so far, our study suggests a high but largely unrealised potential for management to promote multifunctional forests.}, }
@article {pmid29140991, year = {2017}, author = {Schwager, E and Mallick, H and Ventz, S and Huttenhower, C}, title = {A Bayesian method for detecting pairwise associations in compositional data.}, journal = {PLoS computational biology}, volume = {13}, number = {11}, pages = {e1005852}, pmid = {29140991}, issn = {1553-7358}, support = {R01 HG005220/HG/NHGRI NIH HHS/United States ; T32 GM074897/GM/NIGMS NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; }, mesh = {Algorithms ; *Bayes Theorem ; Computational Biology/*methods ; *Computer Simulation ; Ecology ; Humans ; Markov Chains ; Microbiota ; *Models, Biological ; Proteobacteria ; }, abstract = {Compositional data consist of vectors of proportions normalized to a constant sum from a basis of unobserved counts. The sum constraint makes inference on correlations between unconstrained features challenging due to the information loss from normalization. However, such correlations are of long-standing interest in fields including ecology. We propose a novel Bayesian framework (BAnOCC: Bayesian Analysis of Compositional Covariance) to estimate a sparse precision matrix through a LASSO prior. The resulting posterior, generated by MCMC sampling, allows uncertainty quantification of any function of the precision matrix, including the correlation matrix. We also use a first-order Taylor expansion to approximate the transformation from the unobserved counts to the composition in order to investigate what characteristics of the unobserved counts can make the correlations more or less difficult to infer. On simulated datasets, we show that BAnOCC infers the true network as well as previous methods while offering the advantage of posterior inference. Larger and more realistic simulated datasets further showed that BAnOCC performs well as measured by type I and type II error rates. Finally, we apply BAnOCC to a microbial ecology dataset from the Human Microbiome Project, which in addition to reproducing established ecological results revealed unique, competition-based roles for Proteobacteria in multiple distinct habitats.}, }
@article {pmid29140977, year = {2017}, author = {Nuñez, I and Matute, T and Herrera, R and Keymer, J and Marzullo, T and Rudge, T and Federici, F}, title = {Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering.}, journal = {PloS one}, volume = {12}, number = {11}, pages = {e0187163}, pmid = {29140977}, issn = {1932-6203}, support = {BB/L014130/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R44 MH093334/MH/NIMH NIH HHS/United States ; }, mesh = {Biology/*education ; Biomedical Engineering/*methods ; Biomedical Research ; Cell Line ; Equipment Design ; Equipment and Supplies/economics ; Escherichia coli/growth &amp; development ; Optical Imaging/*instrumentation ; }, abstract = {The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates. We developed a set of genetic components (e.g. promoters, coding sequences, terminators) and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, we screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins. We found CyOFP1, mBeRFP and sfGFP to be the most compatible set for 3-channel fluorescent imaging. We developed open source Python code to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information. To demonstrate the potential application of this integral system, we tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology. We also assessed its potential use in a high school environment to teach biology, hardware design, optics, and programming. Together, these results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for education, scientific research and bioengineering. All the resources developed here are available under open source licenses.}, }
@article {pmid29139087, year = {2018}, author = {de Villiers, D and Potgieter, M and Ambele, MA and Adam, L and Durandt, C and Pepper, MS}, title = {The Role of Reactive Oxygen Species in Adipogenic Differentiation.}, journal = {Advances in experimental medicine and biology}, volume = {1083}, number = {}, pages = {125-144}, doi = {10.1007/5584_2017_119}, pmid = {29139087}, issn = {0065-2598}, mesh = {Adipocytes/*cytology ; *Adipogenesis ; Antioxidants/metabolism ; *Cell Differentiation ; Humans ; Mesenchymal Stem Cells/*cytology ; Obesity/physiopathology ; Reactive Oxygen Species/*metabolism ; }, abstract = {Interest in reactive oxygen species and adipocyte differentiation/adipose tissue function is steadily increasing. This is due in part to a search for alternative avenues for combating obesity, which results from the excess accumulation of adipose tissue. Obesity is a major risk factor for complex disorders such as cancer, type 2 diabetes, and cardiovascular diseases. The ability of mesenchymal stromal/stem cells (MSCs) to differentiate into adipocytes is often used as a model for studying adipogenesis in vitro. A key focus is the effect of both intra- and extracellular reactive oxygen species (ROS) on adipogenesis. The consensus from the majority of studies is that ROS, irrespective of the source, promote adipogenesis.The effect of ROS on adipogenesis is suppressed by antioxidants or ROS scavengers. Reactive oxygen species are generated during the process of adipocyte differentiation as well as by other cell metabolic processes. Despite many studies in this field, it is still not possible to state with certainty whether ROS measured during adipocyte differentiation are a cause or consequence of this process. In addition, it is still unclear what the exact sources are of the ROS that initiate and/or drive adipogenic differentiation in MSCs in vivo. This review provides an overview of our understanding of the role of ROS in adipocyte differentiation as well as how certain ROS scavengers and antioxidants might affect this process.}, }
@article {pmid29135971, year = {2018}, author = {Aleklett, K and Kiers, ET and Ohlsson, P and Shimizu, TS and Caldas, VE and Hammer, EC}, title = {Build your own soil: exploring microfluidics to create microbial habitat structures.}, journal = {The ISME journal}, volume = {12}, number = {2}, pages = {312-319}, pmid = {29135971}, issn = {1751-7370}, support = {335542/ERC_/European Research Council/International ; }, mesh = {Biodiversity ; Computer Simulation ; Dimethylpolysiloxanes/chemistry ; *Ecosystem ; Electrochemical Techniques ; *Imaging, Three-Dimensional ; *Lab-On-A-Chip Devices ; *Microbiota ; Microfluidics/*methods ; Optics and Photonics ; Soil ; *Soil Microbiology ; }, abstract = {Soil is likely the most complex ecosystem on earth. Despite the global importance and extraordinary diversity of soils, they have been notoriously challenging to study. We show how pioneering microfluidic techniques provide new ways of studying soil microbial ecology by allowing simulation and manipulation of chemical conditions and physical structures at the microscale in soil model habitats.}, }
@article {pmid29134738, year = {2018}, author = {Xiao, X and Liang, Y and Zhou, S and Zhuang, S and Sun, B}, title = {Fungal community reveals less dispersal limitation and potentially more connected network than that of bacteria in bamboo forest soils.}, journal = {Molecular ecology}, volume = {27}, number = {2}, pages = {550-563}, doi = {10.1111/mec.14428}, pmid = {29134738}, issn = {1365-294X}, mesh = {Biodiversity ; Carbon/metabolism ; China ; Forests ; Fungi/*growth &amp; development ; Microbiota/*genetics ; Plants/genetics/microbiology ; Sasa/genetics/*microbiology ; *Soil Microbiology ; }, abstract = {A central aim of this microbial ecology research was to investigate the mechanisms shaping the assembly of soil microbial communities. Despite the importance of bacterial and fungal mediation of carbon cycling in forest ecosystems, knowledge concerning their distribution patterns and underlying mechanisms remains insufficient. Here, soils were sampled from six bamboo forests across the main planting area of Moso bamboo in southern China. The bacterial and fungal diversities were assessed by sequencing 16S rRNA and ITS gene amplicons, respectively, with an Illumina MiSeq. Based on structural equation modelling, dispersal limitation had strongest impact on bacterial beta diversity, while the mean annual precipitation had a smaller impact by directly or indirectly mediating the soil organic carbon density. However, only the mean annual temperature and precipitation played direct roles in fungal beta diversity. Moreover, the co-occurrence network analyses revealed a possibly much higher network connectivity in the fungal network than in the bacteria. With less dispersal limitation, stronger environmental selection and a potentially more connected network, the fungal community had more important roles in the soil carbon metabolisms in bamboo forests. Fungal beta diversity and the clustering coefficient explained approximately 14.4% and 6.1% of the variation in the carbon metabolic profiles among sites, respectively, but that of bacteria only explained approximately 1.7% and 1.8%, respectively. This study explored soil microbial spatial patterns along with the underlying mechanisms of dispersal limitation, selection and connectivity of ecological networks, thus providing novel insights into the study of the distinct functional traits of different microbial taxa.}, }
@article {pmid29134587, year = {2018}, author = {Vandenheuvel, D and Rombouts, S and Adriaenssens, EM}, title = {Purification of Bacteriophages Using Anion-Exchange Chromatography.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1681}, number = {}, pages = {59-69}, doi = {10.1007/978-1-4939-7343-9_5}, pmid = {29134587}, issn = {1940-6029}, mesh = {Anions ; Bacteriophages/*isolation &amp; purification ; Chromatography, Ion Exchange/*methods ; Ethanolamines/chemistry ; }, abstract = {In bacteriophage research and therapy, most applications ask for highly purified phage suspensions. The standard technique for this is ultracentrifugation using cesium chloride gradients. This technique is cumbersome, elaborate and expensive. Moreover, it is unsuitable for the purification of large quantities of phage suspensions.The protocol described here, uses anion-exchange chromatography to bind phages to a stationary phase. This is done using an FLPC system, combined with Convective Interaction Media (CIM[®]) monoliths. Afterward, the column is washed to remove impurities from the CIM[®] disk. By using a buffer solution with a high ionic strength, the phages are subsequently eluted from the column and collected. In this way phages can be efficiently purified and concentrated.This protocol can be used to determine the optimal buffers, stationary phase chemistry and elution conditions, as well as the maximal capacity and recovery of the columns.}, }
@article {pmid29134235, year = {2018}, author = {Ma, ZS}, title = {Correction to: The P/N (Positive-to-Negative Links) Ratio in Complex Networks-A Promising In Silico Biomarker for Detecting Changes Occurring in the Human Microbiome.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {1074}, doi = {10.1007/s00248-017-1107-7}, pmid = {29134235}, issn = {1432-184X}, abstract = {The original version of this article unfortunately contained a missing image. The flowchart was not captured in PDF version. The original article was corrected.}, }
@article {pmid29133866, year = {2017}, author = {Das, A and Pereira, V and Saxena, S and Ghosh, TS and Anbumani, D and Bag, S and Das, B and Nair, GB and Abraham, P and Mande, SS}, title = {Gastric microbiome of Indian patients with Helicobacter pylori infection, and their interaction networks.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15438}, pmid = {29133866}, issn = {2045-2322}, mesh = {Adult ; Aged ; Aged, 80 and over ; DNA, Bacterial/isolation &amp; purification ; Female ; Gastric Mucosa/*microbiology ; Gastrointestinal Microbiome/*physiology ; Halomonas/isolation &amp; purification/physiology ; Helicobacter Infections/*microbiology ; Helicobacter pylori/isolation &amp; purification/physiology ; Humans ; India ; Lactobacillus/isolation &amp; purification/physiology ; Male ; *Microbial Interactions ; Middle Aged ; Prevotella/isolation &amp; purification/physiology ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {The gastric microbiome is suspected to have a role in the causation of diseases by Helicobacter pylori. Reports on their relative abundance vis-à-vis H. pylori are available from various ethnic and geographic groups, but little is known about their interaction patterns. Endoscopic mucosal biopsy samples from the gastric antrum and corpus of 39 patients with suspected H. pylori infection were collected and microbiomes were analyzed by 16S rDNA profiling. Four groups of samples were identified, which harbored Helicobacter as well as a diverse group of bacteria including Lactobacillus, Halomonas and Prevotella. There was a negative association between the microbiome diversity and Helicobacter abundance. Network analyses showed that Helicobacter had negative interactions with members of the gastric microbiome, while other microbes interacted positively with each other, showing a higher tendency towards intra-cluster co-occurrence/co-operation. Cross-geographic comparisons suggested the presence of region-specific microbial abundance profiles. We report the microbial diversity, abundance variation and interaction patterns of the gastric microbiota of Indian patients with H. pylori infection and present a comparison of the same with the gastric microbial ecology in samples from different geographic regions. Such microbial abundance profiles and microbial interactions can help in understanding the pathophysiology of gastric ailments and can thus help in development of new strategies to curb it.}, }
@article {pmid29132819, year = {2018}, author = {Defoirdt, T}, title = {Quorum-Sensing Systems as Targets for Antivirulence Therapy.}, journal = {Trends in microbiology}, volume = {26}, number = {4}, pages = {313-328}, doi = {10.1016/j.tim.2017.10.005}, pmid = {29132819}, issn = {1878-4380}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/*drug effects/pathogenicity ; Bacterial Infections/drug therapy/prevention &amp; control ; Bacterial Physiological Phenomena/*drug effects ; Drug Resistance, Bacterial/drug effects ; Humans ; Plants ; Pseudomonas/drug effects/metabolism/pathogenicity ; Quorum Sensing/*drug effects/physiology ; Vibrio/drug effects/metabolism/pathogenicity ; Virulence/drug effects ; Virulence Factors ; Xanthomonas/drug effects/metabolism/pathogenicity ; }, abstract = {The development of novel therapies to control diseases caused by antibiotic-resistant pathogens is one of the major challenges we are currently facing. Many important plant, animal, and human pathogens regulate virulence by quorum sensing, bacterial cell-to-cell communication with small signal molecules. Consequently, a significant research effort is being undertaken to identify and use quorum-sensing-interfering agents in order to control diseases caused by these pathogens. In this review, an overview of our current knowledge of quorum-sensing systems of Gram-negative model pathogens is presented as well as the link with virulence of these pathogens, and recent advances and challenges in the development of quorum-sensing-interfering therapies are discussed.}, }
@article {pmid29131365, year = {2017}, author = {Mörkl, S and Lackner, S and Müller, W and Gorkiewicz, G and Kashofer, K and Oberascher, A and Painold, A and Holl, A and Holzer, P and Meinitzer, A and Mangge, H and Holasek, S}, title = {Gut microbiota and body composition in anorexia nervosa inpatients in comparison to athletes, overweight, obese, and normal weight controls.}, journal = {The International journal of eating disorders}, volume = {50}, number = {12}, pages = {1421-1431}, doi = {10.1002/eat.22801}, pmid = {29131365}, issn = {1098-108X}, mesh = {Adolescent ; Adult ; Anorexia Nervosa/*microbiology ; Athletes/*statistics &amp; numerical data ; Body Composition/*physiology ; Body Weight ; Cross-Sectional Studies ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Obesity/*microbiology ; Overweight/*microbiology ; Young Adult ; }, abstract = {OBJECTIVES: Anorexia nervosa (AN) is a heterogeneous eating disorder associated with alterations of body structure and the gut microbiome. We aimed to investigate the gut microbiota composition of a large female cohort including different BMI groups and activity levels along with body composition parameters.<br><br>METHOD: 106 female participants were included in this cross-sectional study: AN patients (n&#xa0;=&#xa0;18), athletes (n&#xa0;=&#xa0;20), normal weight (n&#xa0;=&#xa0;26), overweight (n&#xa0;=&#xa0;22), and obese women (n&#xa0;=&#xa0;20). DNA was extracted from stool samples and subjected to 16S rRNA gene analysis. The software Quantitative Insights Into Microbial Ecology (QIIME) was used to analyze data. Additionally, we performed anthropometric assessments, ultrasound measurements of subcutaneous adipose tissue thickness, bioimpedance analysis, administered depression inventories, and ascertained laboratory parameters and dietary intakes.<br><br>RESULTS: Alpha diversity was particularly lower in AN patients and obese participants compared to other groups, while athletes showed highest alpha diversity. Several categories significantly associated with community structure were identified: body fat parameters, serum lipids, CRP, depression scales and smoking. Comparative analysis revealed Coriobacteriaceae as the only enriched phylotype in AN compared to other entities (LDA score >3.5).<br><br>DISCUSSION: This study provides further evidence of intestinal dysbiosis in AN and sheds light on characteristics of the gut microbiome in different BMI and physical activity groups. These insights point to new modulation possibilities of the gut microbiota which could improve the standard therapy of AN.}, }
@article {pmid29130763, year = {2017}, author = {Bouvier, M and Miszczycha, SD and Guillarme, X and Tadla, C and Collinet, L and Sergentet, DT}, title = {Comparative Evaluation of a Novel Phage Protein Ligand Assay and Immunomagnetic Separation Method To Isolate the Seven Top Serogroups of Escherichia coli (O157, O26, O103, O145, O111, O45, and O121) in Foods at Risk.}, journal = {Journal of food protection}, volume = {80}, number = {12}, pages = {1973-1979}, doi = {10.4315/0362-028X.JFP-16-479}, pmid = {29130763}, issn = {1944-9097}, mesh = {Bacteriophages ; Food Microbiology ; Humans ; *Immunomagnetic Separation/methods ; Meat/microbiology ; Serogroup ; *Shiga-Toxigenic Escherichia coli/isolation &amp; purification ; }, abstract = {The presence of Shiga toxin-producing Escherichia coli (STEC) in food is a major concern for food safety authorities and industries. Methods for detecting these pathogenic bacteria are crucial. Enrichment of foods for STEC identification has been optimized, but selective concentration of bacteria before isolation still needs to be improved. In the present study, we tested the performance of the VIDAS ESPT detection method against that of the immunomagnetic separation (IMS) method. A preenrichment inoculation was performed to provide a realistic scenario of the contamination that occurs in foods, and the methods were then compared. Results obtained were then confirmed in naturally contaminated foods. Preenrichment inoculation assays revealed that the novel concentration method using phage recombinant proteins or the selective capture of the target top seven STEC serogroups is as specific and sensitive as IMS. Subsequent evaluation of naturally contaminated samples confirmed that the novel concentration method and IMS are equivalent in performance under the conditions tested.}, }
@article {pmid29129942, year = {2017}, author = {Eisenhauer, N and Antunes, PM and Bennett, AE and Birkhofer, K and Bissett, A and Bowker, MA and Caruso, T and Chen, B and Coleman, DC and de Boer, W and de Ruiter, P and DeLuca, TH and Frati, F and Griffiths, BS and Hart, MM and Hättenschwiler, S and Haimi, J and Heethoff, M and Kaneko, N and Kelly, LC and Leinaas, HP and Lindo, Z and Macdonald, C and Rillig, MC and Ruess, L and Scheu, S and Schmidt, O and Seastedt, TR and van Straalen, NM and Tiunov, AV and Zimmer, M and Powell, JR}, title = {Priorities for research in soil ecology.}, journal = {Pedobiologia}, volume = {63}, number = {}, pages = {1-7}, pmid = {29129942}, issn = {0031-4056}, support = {677232/ERC_/European Research Council/International ; }, abstract = {The ecological interactions that occur in and with soil are of consequence in many ecosystems on the planet. These interactions provide numerous essential ecosystem services, and the sustainable management of soils has attracted increasing scientific and public attention. Although soil ecology emerged as an independent field of research many decades ago, and we have gained important insights into the functioning of soils, there still are fundamental aspects that need to be better understood to ensure that the ecosystem services that soils provide are not lost and that soils can be used in a sustainable way. In this perspectives paper, we highlight some of the major knowledge gaps that should be prioritized in soil ecological research. These research priorities were compiled based on an online survey of 32 editors of Pedobiologia - Journal of Soil Ecology. These editors work at universities and research centers in Europe, North America, Asia, and Australia.The questions were categorized into four themes: (1) soil biodiversity and biogeography, (2) interactions and the functioning of ecosystems, (3) global change and soil management, and (4) new directions. The respondents identified priorities that may be achievable in the near future, as well as several that are currently achievable but remain open. While some of the identified barriers to progress were technological in nature, many respondents cited a need for substantial leadership and goodwill among members of the soil ecology research community, including the need for multi-institutional partnerships, and had substantial concerns regarding the loss of taxonomic expertise.}, }
@article {pmid29129876, year = {2017}, author = {Hillman, ET and Lu, H and Yao, T and Nakatsu, CH}, title = {Microbial Ecology along the Gastrointestinal Tract.}, journal = {Microbes and environments}, volume = {32}, number = {4}, pages = {300-313}, pmid = {29129876}, issn = {1347-4405}, mesh = {Animals ; Archaea/*classification ; Bacteria/*classification ; Biodiversity ; Diet ; Food ; Fungi/*classification ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology ; Humans ; Mice ; Models, Animal ; Rats ; Swine ; Viruses/*classification ; }, abstract = {The ecosystem of the human gastrointestinal (GI) tract traverses a number of environmental, chemical, and physical conditions because it runs from the oral cavity to the anus. These differences in conditions along with food or other ingested substrates affect the composition and density of the microbiota as well as their functional roles by selecting those that are the most suitable for that environment. Previous studies have mostly focused on Bacteria, with the number of studies conducted on Archaea, Eukarya, and Viruses being limited despite their important roles in this ecosystem. Furthermore, due to the challenges associated with collecting samples directly from the inside of humans, many studies are still exploratory, with a primary focus on the composition of microbiomes. Thus, mechanistic studies to investigate functions are conducted using animal models. However, differences in physiology and microbiomes need to be clarified in order to aid in the translation of animal model findings into the context of humans. This review will highlight Bacteria, Archaea, Fungi, and Viruses, discuss differences along the GI tract of healthy humans, and perform comparisons with three common animal models: rats, mice, and pigs.}, }
@article {pmid29128951, year = {2018}, author = {Sutcliffe, B and Chariton, AA and Harford, AJ and Hose, GC and Stephenson, S and Greenfield, P and Midgley, DJ and Paulsen, IT}, title = {Insights from the Genomes of Microbes Thriving in Uranium-Enriched Sediments.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {970-984}, pmid = {29128951}, issn = {1432-184X}, mesh = {Bacteria/classification/enzymology/*genetics ; Bacterial Proteins/genetics ; Carbohydrate Metabolism ; DNA, Bacterial/genetics ; Drug Tolerance ; Ecology ; Genes, Bacterial/genetics ; *Genomics ; Geobacter/classification/genetics ; Geologic Sediments/*microbiology ; *Metagenome ; Molecular Sequence Annotation ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Uranium/*metabolism ; }, abstract = {Elevated uranium dose (4 g kg[-1]) causes a shift in billabong sediment communities that result in the enrichment of five bacterial species. These taxa include Geobacter, Geothrix and Dyella species, as well as a novel-potentially predatory-Bacteroidetes species, and a new member of class Anaerolineae (Chloroflexi). Additionally, a population of methanogenic Methanocella species was also identified. Genomic reconstruction and metabolic examination of these taxa reveal a host of divergent life strategies and putative niche partitioning. Resistance-nodulation-division heavy metal efflux (RND-HME) transporters are implicated as potential uranium tolerance strategies among the bacterial taxa. Potential interactions, uranium tolerance and ecologically relevant catabolism are presented in a conceptual model of life in this environment.}, }
@article {pmid29128765, year = {2018}, author = {Santos, IC and Martin, MS and Reyes, ML and Carlton, DD and Stigler-Granados, P and Valerio, MA and Whitworth, KW and Hildenbrand, ZL and Schug, KA}, title = {Exploring the links between groundwater quality and bacterial communities near oil and gas extraction activities.}, journal = {The Science of the total environment}, volume = {618}, number = {}, pages = {165-173}, doi = {10.1016/j.scitotenv.2017.10.264}, pmid = {29128765}, issn = {1879-1026}, support = {T42 OH008421/OH/NIOSH CDC HHS/United States ; }, mesh = {*Bacteria ; Groundwater/*chemistry/microbiology ; Hydrocarbons ; *Oil and Gas Fields ; Oil and Gas Industry ; Organic Chemicals ; Texas ; *Water Microbiology ; *Water Quality ; }, abstract = {Bacterial communities in groundwater are very important as they maintain a balanced biogeochemical environment. When subjected to stressful environments, for example, due to anthropogenic contamination, bacterial communities and their dynamics change. Studying the responses of the groundwater microbiome in the face of environmental changes can add to our growing knowledge of microbial ecology, which can be utilized for the development of novel bioremediation strategies. High-throughput and simpler techniques that allow the real-time study of different microbiomes and their dynamics are necessary, especially when examining larger data sets. Matrix-assisted laser desorption-ionization (MALDI) time-of-flight mass spectrometry (TOF-MS) is a workhorse for the high-throughput identification of bacteria. In this work, groundwater samples were collected from a rural area in southern Texas, where agricultural activities and unconventional oil and gas development are the most prevalent anthropogenic activities. Bacterial communities were assessed using MALDI-TOF MS, with bacterial diversity and abundance being analyzed with the contexts of numerous organic and inorganic groundwater constituents. Mainly denitrifying and heterotrophic bacteria from the Phylum Proteobacteria were isolated. These microorganisms are able to either transform nitrate into gaseous forms of nitrogen or degrade organic compounds such as hydrocarbons. Overall, the bacterial communities varied significantly with respect to the compositional differences that were observed from the collected groundwater samples. Collectively, these data provide a baseline measurement of bacterial diversity in groundwater located near anthropogenic surface and subsurface activities.}, }
@article {pmid29127500, year = {2018}, author = {Schmidt, CS and Lovecká, P and Mrnka, L and Vychodilová, A and Strejček, M and Fenclová, M and Demnerová, K}, title = {Distinct Communities of Poplar Endophytes on an Unpolluted and a Risk Element-Polluted Site and Their Plant Growth-Promoting Potential In Vitro.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {955-969}, pmid = {29127500}, issn = {1432-184X}, mesh = {Antioxidants/metabolism ; Bacteria/classification/drug effects/isolation &amp; purification/metabolism ; Biodegradation, Environmental ; Biodiversity ; Biomass ; Carbon-Carbon Lyases/metabolism ; Czech Republic ; Drug Tolerance ; Endophytes/*classification/*drug effects/isolation &amp; purification/metabolism ; Environmental Pollutants/*toxicity ; Fungi/classification/drug effects/isolation &amp; purification/metabolism ; In Vitro Techniques ; Microbiota/*drug effects/physiology ; Phosphates/metabolism ; Phylogeny ; *Plant Development ; Plant Growth Regulators/metabolism ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Populus/*microbiology ; Siderophores/metabolism ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Numerous studies demonstrated that endophytic microbes can promote plant growth and increase plant stress resistance. We aimed at isolating poplar endophytes able to increase their hosts' fitness both in nutrient-limited and polluted environments. To achieve this goal, endophytic bacteria and fungi were isolated from roots and leaves of hybrid poplars (Populus nigra × P. maximowiczii clone Max-4) on an unpolluted and a risk element-polluted site in the Czech Republic and subsequently screened by a number of in vitro tests. Bacterial communities at the unpolluted site were dominated by Gammaproteobacteria with Pseudomonas sp. as the prominent member of the class, followed by Bacilli with prevailing Bacillus sp., whereas Alphaproteobacteria, mostly Rhizobium sp., prevailed at the polluted site. The fungal endophytic community was dominated by Ascomycetes and highly distinct on both sites. Dothideomycetes, mostly Cladosporium, prevailed at the non-polluted site while unclassified Sordariomycetous fungi dominated at the polluted site. Species diversity of endophytes was higher at the unpolluted site. Many tested endophytic strains solubilized phosphate and produced siderophores, phytohormones, and antioxidants. Some strains also exhibited ACC-deaminase activity. Selected bacteria showed high tolerance and the ability to accumulate risk elements, making them promising candidates for use in inocula promoting biomass production and phytoremediation. Graphical Abstract ᅟ.}, }
@article {pmid29126642, year = {2018}, author = {O'Flaherty, E and Borrego, CM and Balcázar, JL and Cummins, E}, title = {Human exposure assessment to antibiotic-resistant Escherichia coli through drinking water.}, journal = {The Science of the total environment}, volume = {616-617}, number = {}, pages = {1356-1364}, doi = {10.1016/j.scitotenv.2017.10.180}, pmid = {29126642}, issn = {1879-1026}, mesh = {Dietary Exposure/*statistics &amp; numerical data ; Drinking Water/*microbiology ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/*physiology ; Europe ; Humans ; Water Microbiology ; Water Purification ; Water Supply ; }, abstract = {Antibiotic-resistant bacteria (ARB) are a potential threat to human health through drinking water with strong evidence of ARB presence in post treated tap water around the world. This study examines potential human exposure to antibiotic-resistant (AR) Escherichia coli (E. coli) through drinking water, the effect of different drinking water treatments on AR E. coli and the concentration of AR E. coli required in the source water for the EU Drinking Water Directive (DWD) (Council Directive 98/83/EC, 0CFU/100ml of E. coli in drinking water) to be exceeded. A number of scenarios were evaluated to examine different water treatment combinations and to reflect site specific conditions at a study site in Europe. A literature search was carried out to collate data on the effect of environmental conditions on AR E. coli, the effect of different water treatments on AR E. coli and typical human consumption levels of tap water. A human exposure assessment model was developed with probability distributions used to characterise uncertainty and variability in the input data. Overall results show the mean adult human exposure to AR E. coli from tap water consumption ranged between 3.44×10[-7] and 2.95×10[-1]cfu/day for the scenarios tested and varied depending on the water treatments used. The level of AR E. coli required in the source water pre-treatment to exceed the DWD varied between 1 and 5logcfu/ml, depending on the water treatments used. This can be used to set possible monitoring criteria in pre-treated water for potential ARB exposure in drinking water.}, }
@article {pmid29125596, year = {2018}, author = {Wu, W and Lu, HP and Sastri, A and Yeh, YC and Gong, GC and Chou, WC and Hsieh, CH}, title = {Contrasting the relative importance of species sorting and dispersal limitation in shaping marine bacterial versus protist communities.}, journal = {The ISME journal}, volume = {12}, number = {2}, pages = {485-494}, pmid = {29125596}, issn = {1751-7370}, mesh = {Bacteria/genetics/*isolation &amp; purification ; DNA, Ribosomal/chemistry ; Ecosystem ; Eukaryota/genetics/isolation &amp; purification ; Seawater/*microbiology ; }, abstract = {A central challenge in microbial ecology is to understand the underlying mechanisms driving community assembly, particularly in the continuum of species sorting and dispersal limitation. However, little is known about the relative importance of species sorting and dispersal limitation in shaping marine microbial communities; especially, how they are related to organism types/traits and water depth. Here, we used variation partitioning and null model analysis to compare mechanisms driving bacterial and protist metacommunity dynamics at the basin scale in the East China Sea, based on MiSeq paired-end sequencing of 16S ribosomal DNA (rDNA) and 18S rDNA, respectively, in surface, deep chlorophyll maximum and bottom layers. Our analyses indicated that protist communities were governed more strongly by species sorting relative to dispersal limitation than were bacterial communities; this pattern was consistent across the three-depth layers, albeit to different degrees. Furthermore, we detected that bacteria exhibited wider habitat niche breadths than protists, whereas, passive dispersal abilities were not appreciably different between them. Our findings support the 'size-plasticity' hypothesis: smaller organisms (bacteria) are less environment filtered than larger organisms (protists), as smaller organisms are more likely to be plastic in metabolic abilities and have greater environmental tolerance.}, }
@article {pmid29124857, year = {2017}, author = {Wang, T and Tian, Z and Bengtson, P and Tunlid, A and Persson, P}, title = {Mineral surface-reactive metabolites secreted during fungal decomposition contribute to the formation of soil organic matter.}, journal = {Environmental microbiology}, volume = {19}, number = {12}, pages = {5117-5129}, doi = {10.1111/1462-2920.13990}, pmid = {29124857}, issn = {1462-2920}, mesh = {Basidiomycota/*metabolism ; Biomass ; Carbon Cycle/physiology ; Ecosystem ; Iron Compounds/*metabolism ; Minerals/*metabolism ; Mycorrhizae/metabolism ; Soil/*chemistry ; *Soil Microbiology ; Surface-Active Agents/*metabolism ; Taiga ; }, abstract = {Soil organic matter (SOM) constitutes the largest terrestrial C pool. An emerging, untested, view is that oxidation and depolymerization of SOM by microorganisms promote the formation of SOM-mineral associations that is critical for SOM stabilization. To test this hypothesis, we performed laboratory-scale experiments involving one ectomycorrhizal and one saprotrophic fungus that represent the two major functional groups of microbial decomposers in the boreal forest soils. Fungal decomposition enhanced the retention of SOM on goethite, partly because of oxidative modifications of organic matter (OM) by the fungi. Moreover, both fungi secreted substantial amounts (> 10% new biomass C) of aromatic metabolites that also contributed to an enhanced mineral retention of OM. Our study demonstrates that soil fungi can form mineral-stabilized SOM not only by oxidative conversion of the SOM but also by synthesizing mineral surface-reactive metabolites. Metabolites produced by fungal decomposers can play a yet overlooked role in the formation and stabilization of SOM.}, }
@article {pmid29124312, year = {2018}, author = {Keller, AH and Kleinsteuber, S and Vogt, C}, title = {Anaerobic Benzene Mineralization by Nitrate-Reducing and Sulfate-Reducing Microbial Consortia Enriched From the Same Site: Comparison of Community Composition and Degradation Characteristics.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {941-953}, pmid = {29124312}, issn = {1432-184X}, mesh = {Anaerobiosis ; Azoarcus/metabolism ; Bacteria/classification/genetics/*metabolism ; Benzene/*metabolism ; Betaproteobacteria/metabolism ; Biodegradation, Environmental ; DNA, Bacterial/genetics ; Groundwater/microbiology ; Isotope Labeling ; Microbial Consortia/genetics/*physiology ; Nitrates/*metabolism ; Oxidation-Reduction ; Peptococcaceae/metabolism ; RNA, Ribosomal, 16S/metabolism ; Rhodocyclaceae/metabolism ; Sulfates/*metabolism ; }, abstract = {Benzene mineralization under nitrate-reducing conditions was successfully established in an on-site reactor continuously fed with nitrate and sulfidic, benzene-containing groundwater extracted from a contaminated aquifer. Filling material from the reactor columns was used to set up anoxic enrichment cultures in mineral medium with benzene as electron donor and sole organic carbon source and nitrate as electron acceptor. Benzene degradation characteristics and community composition under nitrate-reducing conditions were monitored and compared to those of a well-investigated benzene-mineralizing consortium enriched from the same column system under sulfate-reducing conditions. The nitrate-reducing cultures degraded benzene at a rate of 10.1 ± 1.7 μM d[-1], accompanied by simultaneous reduction of nitrate to nitrite. The previously studied sulfate-reducing culture degraded benzene at similar rates. Carbon and hydrogen stable isotope enrichment factors determined for nitrate-dependent benzene degradation differed significantly from those of the sulfate-reducing culture (Λ[H/C nitrate] = 12 ± 3 compared to Λ[H/C sulfate] = 28 ± 3), indicating different benzene activation mechanisms under the two conditions. The nitrate-reducing community was mainly composed of Betaproteobacteria, Ignavibacteria, and Anaerolineae. Azoarcus and a phylotype related to clone Dok59 (Rhodocyclaceae) were the dominant genera, indicating an involvement in nitrate-dependent benzene degradation. The primary benzene degrader of the sulfate-reducing consortium, a phylotype belonging to the Peptococcaceae, was absent in the nitrate-reducing consortium.}, }
@article {pmid29124311, year = {2018}, author = {Zeng, J and Shen, JP and Wang, JT and Hu, HW and Zhang, CJ and Bai, R and Zhang, LM and He, JZ}, title = {Impacts of Projected Climate Warming and Wetting on Soil Microbial Communities in Alpine Grassland Ecosystems of the Tibetan Plateau.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {1009-1023}, pmid = {29124311}, issn = {1432-184X}, support = {41230857//National Science Foundation of China/ ; 2013CB956300//Ministry of Science and Technology of the People's Republic of China/ ; }, mesh = {Ammonia/metabolism ; Bacteria/classification/genetics/metabolism ; Bacterial Proteins/genetics ; Biodiversity ; *Climate Change ; DNA, Bacterial/genetics ; Denitrification/genetics ; Environmental Monitoring ; Enzyme Activation ; Enzyme Assays ; Genes, Bacterial/genetics ; *Grassland ; Microbiota/*genetics/*physiology ; Nitrification/genetics ; Nitrogen/metabolism ; Nitrogen Cycle ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; Temperature ; Tibet ; }, abstract = {Climate change is projected to have impacts on precipitation and temperature regimes in drylands of high elevation regions, with especially large effects in the Qinghai-Tibetan Plateau. However, there was limited information about how the projected climate change will impact on the soil microbial community and their activity in the region. Here, we present results from a study conducted across 72 soil samples from 24 different sites along a temperature and precipitation gradient (substituted by aridity index ranging from 0.079 to 0.89) of the Plateau, to assess how changes in aridity affect the abundance, community composition, and diversity of bacteria, ammonia-oxidizers, and denitrifers (nirK/S and nosZ genes-containing communities) as well as nitrogen (N) turnover enzyme activities. We found V-shaped or inverted V-shaped relationships between the aridity index (AI) and soil microbial parameters (gene abundance, community structures, microbial diversity, and N turnover enzyme activities) with a threshold at AI = 0.27. The increasing or decreasing rates of the microbial parameters were higher in areas with AI < 0.27 (alpine steppes) than in mesic areas with 0.27 < AI < 0.89 (alpine meadow and swamp meadow). The results indicated that the projected warming and wetting have a strong impact on soil microbial communities in the alpine steppes.}, }
@article {pmid29124310, year = {2018}, author = {Gomes, PP and Ferreira, V and Tonin, AM and Medeiros, AO and Júnior, JFG}, title = {Combined Effects of Dissolved Nutrients and Oxygen on Plant Litter Decomposition and Associated Fungal Communities.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {854-862}, pmid = {29124310}, issn = {1432-184X}, mesh = {Biomass ; Brazil ; Ecosystem ; Euphorbiaceae/microbiology ; Fungi/*drug effects ; Mycobiome/*drug effects ; Nitrogen ; Nutrients/*pharmacology ; Oxygen/*pharmacology ; Phosphorus ; Plant Leaves/microbiology ; Rivers/microbiology ; Spores, Fungal/growth &amp; development ; *Water Microbiology ; }, abstract = {Aquatic ecosystems worldwide have been substantially altered by human activities, which often induce changes in multiple factors that can interact to produce complex effects. Here, we evaluated the combined effects of dissolved nutrients (nitrogen [N] and phosphorus [P]; three levels: concentration found in oligotrophic streams in the Cerrado biome, 10× and 100× enriched) and oxygen (O2; three levels: hypoxic [4% O2], depleted [55% O2], and saturated [96% O2]) on plant litter decomposition and associated fungal decomposers in laboratory microcosms simulating stream conditions under distinct scenarios of water quality deterioration. Senescent leaves of Maprounea guianensis were incubated for 10 days in an oligotrophic Cerrado stream to allow microbial colonization and subsequently incubated in microcosms for 21 days. Leaves lost 1.1-3.0% of their initial mass after 21 days, and this was not affected either by nutrients or oxygen levels. When considering simultaneous changes in nutrients and oxygen concentrations, simulating increased human pressure, fungal biomass accumulation, and sporulation rates were generally inhibited. Aquatic hyphomycete community structure was also affected by changes in nutrients and oxygen availability, with stronger effects found in hypoxic treatments than in depleted or saturated oxygen treatments. This study showed that the effects of simultaneous changes in the availability of dissolved nutrients and oxygen in aquatic environments can influence the activity and composition of fungal communities, although these effects were not translated into changes in litter decomposition rates.}, }
@article {pmid29124129, year = {2017}, author = {Schmidt, V and Gomez-Chiarri, M and Roy, C and Smith, K and Amaral-Zettler, L}, title = {Subtle Microbiome Manipulation Using Probiotics Reduces Antibiotic-Associated Mortality in Fish.}, journal = {mSystems}, volume = {2}, number = {6}, pages = {}, pmid = {29124129}, issn = {2379-5077}, abstract = {Prophylactic antibiotics in the aquaculture and ornamental fish industry are intended to prevent the negative impacts of disease outbreaks. Research in mice and humans suggests that antibiotics may disturb microbiome communities and decrease microbiome-mediated disease resistance, also known as "colonization resistance." If antibiotics impact fish as they do mice and humans, prophylactic administrations on aquaculture farms may increase downstream disease susceptibility in target hosts, despite short-term pathogen control benefits. We tested the effects of antibiotics on mortality after a pathogen challenge in the Poecilia sphenops black molly and subsequently tested if probiotic inoculations could reverse any antibiotic-induced losses of disease resistance. We found that antibiotic treatment significantly increased fish mortality. We further found that our two candidate probiotic bacterial species, Phaeobacter inhibens S4Sm and Bacillus pumilus RI06-95Sm, were able to colonize black molly microbiomes and reverse the negative impacts of antibiotics. Despite the positive impact on survival, probiotic treatment did not influence overall microbiome community structure or diversity. Our results suggest that subtle manipulations of microbiome composition can have dramatic impacts on host phenotype. The results of this study have implications for how antibiotic-treated microbiomes can be restored and suggest that small-scale additions may be as effective as wholesale transplants. IMPORTANCE Prophylactic antibiotics are widespread in the aquaculture industry and are used where vaccination is impossible or overly expensive. If antibiotics impact fish as they do mice and humans, prophylactic administrations in aquaculture and ornamental fish farms may increase downstream disease susceptibility in target hosts, despite short-term pathogen control benefits. Recent research has suggested that their use exacerbates bacterial outbreaks by creating sterile, nutrient-rich environments for invading pathogens to colonize and could help to explain rising economic costs of bacterial outbreaks in aquaculture. Our findings suggest a long-term cost of prophylactic antibiotic use and demonstrate a probiotic-based solution that does not rely on full microbiome community transplantation.}, }
@article {pmid29121419, year = {2018}, author = {Averill, C and Waring, B}, title = {Nitrogen limitation of decomposition and decay: How can it occur?.}, journal = {Global change biology}, volume = {24}, number = {4}, pages = {1417-1427}, doi = {10.1111/gcb.13980}, pmid = {29121419}, issn = {1365-2486}, mesh = {Biodegradation, Environmental ; Biomass ; Carbon/chemistry ; *Ecosystem ; Models, Theoretical ; Nitrogen/*chemistry ; Plant Leaves/chemistry ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {The availability of nitrogen (N) is a critical control on the cycling and storage of soil carbon (C). Yet, there are conflicting conceptual models to explain how N availability influences the decomposition of organic matter by soil microbial communities. Several lines of evidence suggest that N availability limits decomposition; the earliest stages of leaf litter decay are associated with a net import of N from the soil environment, and both observations and models show that high N organic matter decomposes more rapidly. In direct contrast to these findings, experimental additions of inorganic N to soils broadly show a suppression of microbial activity, which is inconsistent with N limitation of decomposition. Resolving this apparent contradiction is critical to representing nutrient dynamics in predictive ecosystem models under a multitude of global change factors that alter soil N availability. Here, we propose a new conceptual framework, the Carbon, Acidity, and Mineral Protection hypothesis, to understand the effects of N availability on soil C cycling and storage and explore the predictions of this framework with a mathematical model. Our model simulations demonstrate that N addition can have opposing effects on separate soil C pools (particulate and mineral-protected carbon) because they are differentially affected by microbial biomass growth. Moreover, changes in N availability are frequently linked to shifts in soil pH or osmotic stress, which can independently affect microbial biomass dynamics and mask N stimulation of microbial activity. Thus, the net effect of N addition on soil C is dependent upon interactions among microbial physiology, soil mineralogy, and soil acidity. We believe that our synthesis provides a broadly applicable conceptual framework to understand and predict the effect of changes in soil N availability on ecosystem C cycling under global change.}, }
@article {pmid29119317, year = {2018}, author = {Woodhams, DC and LaBumbard, BC and Barnhart, KL and Becker, MH and Bletz, MC and Escobar, LA and Flechas, SV and Forman, ME and Iannetta, AA and Joyce, MD and Rabemananjara, F and Gratwicke, B and Vences, M and Minbiole, KPC}, title = {Prodigiosin, Violacein, and Volatile Organic Compounds Produced by Widespread Cutaneous Bacteria of Amphibians Can Inhibit Two Batrachochytrium Fungal Pathogens.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {1049-1062}, pmid = {29119317}, issn = {1432-184X}, support = {DEB-1136662//Division of Environmental Biology/ ; }, mesh = {Animals ; Antifungal Agents/pharmacology ; Anura/microbiology ; Bacteria/classification/isolation &amp; purification/*metabolism ; Biological Control Agents/antagonists &amp; inhibitors ; Chytridiomycota/*drug effects/growth &amp; development/pathogenicity ; Indoles/*antagonists &amp; inhibitors/chemistry/*metabolism ; Microbial Sensitivity Tests ; Panama ; Phylogeny ; Prodigiosin/*antagonists &amp; inhibitors/chemistry/*metabolism ; Serratia/classification/isolation &amp; purification/metabolism ; Skin/microbiology ; Switzerland ; Symbiosis ; United States ; Volatile Organic Compounds/*antagonists &amp; inhibitors/chemistry/*metabolism ; }, abstract = {Symbiotic bacteria can produce secondary metabolites and volatile compounds that contribute to amphibian skin defense. Some of these symbionts have been used as probiotics to treat or prevent the emerging disease chytridiomycosis. We examined 20 amphibian cutaneous bacteria for the production of prodigiosin or violacein, brightly colored defense compounds that pigment the bacteria and have characteristic spectroscopic properties making them readily detectable, and evaluated the antifungal activity of these compounds. We detected violacein from all six isolates of Janthinobacterium lividum on frogs from the USA, Switzerland, and on captive frogs originally from Panama. We detected prodigiosin from five isolates of Serratia plymuthica or S. marcescens, but not from four isolates of S. fonticola or S. liquefaciens. All J. lividum isolates produced violacein when visibly purple, while prodigiosin was only detected on visibly red Serratia isolates. When applied to cultures of chytrid fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), prodigiosin caused significant growth inhibition, with minimal inhibitory concentrations (MIC) of 10 and 50 μM, respectively. Violacein showed a MIC of 15 μM against both fungi and was slightly more active against Bsal than Bd at lower concentrations. Although neither violacein nor prodigiosin showed aerosol activity and is not considered a volatile organic compound (VOC), J. lividum and several Serratia isolates did produce antifungal VOCs. White Serratia isolates with undetectable prodigiosin levels could still inhibit Bd growth indicating additional antifungal compounds in their chemical arsenals. Similarly, J. lividum can produce antifungal compounds such as indole-3-carboxaldehyde in addition to violacein, and isolates are not always purple, or turn purple under certain growth conditions. When Serratia isolates were grown in the presence of cell-free supernatant (CFS) from the fungi, CFS from Bd inhibited growth of the prodigiosin-producing isolates, perhaps indicative of an evolutionary arms race; Bsal CFS did not inhibit bacterial growth. In contrast, growth of one J. lividum isolate was facilitated by CFS from both fungi. Isolates that grow and continue to produce antifungal compounds in the presence of pathogens may represent promising probiotics for amphibians infected or at risk of chytridiomycosis. In a global analysis, 89% of tested Serratia isolates and 82% of J. lividum isolates were capable of inhibiting Bd and these have been reported from anurans and caudates from five continents, indicating their widespread distribution and potential for host benefit.}, }
@article {pmid29119316, year = {2018}, author = {Grigorescu, AS and Renoz, F and Sabri, A and Foray, V and Hance, T and Thonart, P}, title = {Accessing the Hidden Microbial Diversity of Aphids: an Illustration of How Culture-Dependent Methods Can Be Used to Decipher the Insect Microbiota.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {1035-1048}, pmid = {29119316}, issn = {1432-184X}, support = {Grant FRFC 6886819//Fonds De La Recherche Scientifique - FNRS/ ; }, mesh = {Animals ; Aphids/*microbiology ; Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; *Biodiversity ; Culture Techniques/*methods ; DNA/isolation &amp; purification ; Fungi/classification/genetics/growth &amp; development/*isolation &amp; purification ; Genes, Bacterial/genetics ; Genes, Fungal/genetics ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics/*physiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Serratia/classification/isolation &amp; purification/physiology ; Symbiosis ; }, abstract = {Microorganism communities that live inside insects can play critical roles in host development, nutrition, immunity, physiology, and behavior. Over the past decade, high-throughput sequencing reveals the extraordinary microbial diversity associated with various insect species and provides information independent of our ability to culture these microbes. However, their cultivation in the laboratory remains crucial for a deep understanding of their physiology and the roles they play in host insects. Aphids are insects that received specific attention because of their ability to form symbiotic associations with a wide range of endosymbionts that are considered as the core microbiome of these sap-feeding insects. But, if the functional diversity of obligate and facultative endosymbionts has been extensively studied in aphids, the diversity of gut symbionts and other associated microorganisms received limited consideration. Herein, we present a culture-dependent method that allowed us to successfully isolate microorganisms from several aphid species. The isolated microorganisms were assigned to 24 bacterial genera from the Actinobacteria, Firmicutes, and Proteobacteria phyla and three fungal genera from the Ascomycota and Basidiomycota phyla. In our study, we succeeded in isolating already described bacteria found associated to aphids (e.g., the facultative symbiont Serratia symbiotica), as well as microorganisms that have never been described in aphids before. By unraveling a microbial community that so far has been ignored, our study expands our current knowledge on the microbial diversity associated with aphids and illustrates how fast and simple culture-dependent approaches can be applied to insects in order to capture their diverse microbiota members.}, }
@article {pmid29119315, year = {2018}, author = {DeLong, JP and Al-Ameeli, Z and Lyon, S and Van Etten, JL and Dunigan, DD}, title = {Size-dependent Catalysis of Chlorovirus Population Growth by A Messy Feeding Predator.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {847-853}, pmid = {29119315}, issn = {1432-184X}, mesh = {Animals ; Catalysis ; Chlorella/virology ; Ciliophora/*physiology ; DNA Viruses ; Food Chain ; Host-Pathogen Interactions/*physiology ; Paramecium/*virology ; Phycodnaviridae/growth &amp; development/*physiology ; Population Dynamics ; *Predatory Behavior ; *Symbiosis ; }, abstract = {Many chloroviruses replicate in endosymbiotic zoochlorellae that are protected from infection by their symbiotic host. To reach the high virus concentrations that often occur in natural systems, a mechanism is needed to release zoochlorellae from their hosts. We demonstrate that the ciliate predator Didinium nasutum foraging on zoochlorellae-bearing Paramecium bursaria can release live zoochlorellae from the ruptured prey cell that can then be infected by chloroviruses. The catalysis process is very effective, yielding roughly 95% of the theoretical infectious virus yield as determined by sonication of P. bursaria. Chlorovirus activation is more effective with smaller Didinia, as larger Didinia typically consume entire P. bursaria cells without rupturing them, precluding the release of zoochlorellae. We also show that the timing of Chlorovirus growth is tightly linked to the predator-prey cycle between Didinium and Paramecium, with the most rapid increase in chloroviruses temporally linked to the peak foraging rate of Didinium, supporting the idea that predator-prey cycles can drive cycles of Chlorovirus abundance.}, }
@article {pmid29118781, year = {2017}, author = {Wilschut, RA and Silva, JCP and Garbeva, P and van der Putten, WH}, title = {Belowground Plant-Herbivore Interactions Vary among Climate-Driven Range-Expanding Plant Species with Different Degrees of Novel Chemistry.}, journal = {Frontiers in plant science}, volume = {8}, number = {}, pages = {1861}, pmid = {29118781}, issn = {1664-462X}, abstract = {An increasing number of studies report plant range expansions to higher latitudes and altitudes in response to global warming. However, consequences for interactions with other species in the novel ranges are poorly understood. Here, we examine how range-expanding plant species interact with root-feeding nematodes from the new range. Root-feeding nematodes are ubiquitous belowground herbivores that may impact the structure and composition of natural vegetation. Because of their ecological novelty, we hypothesized that range-expanding plant species will be less suitable hosts for root-feeding nematodes than native congeneric plant species. In greenhouse and lab trials we compared nematode preference and performance of two root-feeding nematode species between range-expanding plant species and their congeneric natives. In order to understand differences in nematode preferences, we compared root volatile profiles of all range-expanders and congeneric natives. Nematode preferences and performances differed substantially among the pairs of range-expanders and natives. The range-expander that had the most unique volatile profile compared to its related native was unattractive and a poor host for nematodes. Other range-expanding plant species that differed less in root chemistry from native congeners, also differed less in nematode attraction and performance. We conclude that the three climate-driven range-expanding plant species studied varied considerably in their chemical novelty compared to their congeneric natives, and therefore affected native root-feeding nematodes in species-specific ways. Our data suggest that through variation in chemical novelty, range-expanding plant species may vary in their impacts on belowground herbivores in the new range.}, }
@article {pmid29118751, year = {2017}, author = {Van Goethem, MW and Makhalanyane, TP and Cowan, DA and Valverde, A}, title = {Cyanobacteria and Alphaproteobacteria May Facilitate Cooperative Interactions in Niche Communities.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2099}, pmid = {29118751}, issn = {1664-302X}, abstract = {Hypoliths, microbial assemblages found below translucent rocks, provide important ecosystem services in deserts. While several studies have assessed microbial diversity of hot desert hypoliths and whether these communities are metabolically active, the interactions among taxa remain unclear. Here, we assessed the structure, diversity, and co-occurrence patterns of hypolithic communities from the hyperarid Namib Desert by comparing total (DNA) and potentially active (RNA) communities. The potentially active and total hypolithic communities differed in their composition and diversity, with significantly higher levels of Cyanobacteria and Alphaproteobacteria in potentially active hypoliths. Several phyla known to be abundant in total hypolithic communities were metabolically inactive, indicating that some hypolithic taxa may be dormant or dead. The potentially active hypolith network was highly modular in structure with almost exclusively positive co-occurrences (>95% of the total) between taxa. Members of the Cyanobacteria and Alphaproteobacteria were identified as potential keystone taxa, and exhibited numerous positive co-occurrences with other microbes, suggesting that these groups might have important roles in maintaining network topological structure despite their low abundance.}, }
@article {pmid29118739, year = {2017}, author = {Kleyer, H and Tecon, R and Or, D}, title = {Resolving Species Level Changes in a Representative Soil Bacterial Community Using Microfluidic Quantitative PCR.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2017}, pmid = {29118739}, issn = {1664-302X}, abstract = {Rapid advances in genome sequencing technologies enable determination of relative bacterial abundances and community composition, yet, changes at the species level remain difficult to detect despite importance for certain ecological inferences. We present a method for extraction and direct quantification of species composition of a predefined multispecies bacterial community using microfluidic-based quantitative real-time PCR (qPCR). We employ a nested PCR approach based on universal 16S rRNA gene pre-amplification followed by detection and quantification of absolute abundance of bacterial species using microfluidic array of parallel singleplex qPCR reactions. Present microfluidic qPCR supports 2,304 simultaneous reactions on a single chip, while automatic distribution of samples and reactants minimizes pipetting errors and technical variations. The utility of the method is illustrated using a synthetic soil bacterial community grown in two contrasting environments - sand microcosms and batch cultures. The protocol entails extraction of total nucleic acid, preparation of genomic DNA, and steps for qPCR assessment of bacterial community composition. This method provides specific and sensitive quantification of bacterial species requiring only 2 ng of community DNA. Optimized extraction protocol and preamplification step allow for rapid, quantitative, and simultaneous detection of candidate species with high throughput. The proposed method offers a simple and accurate alternative to present sequencing methods especially when absolute values of species abundance are required. Quantification of changes at the species level contributes to the mechanistic understanding of the roles of particular species in a bacterial community functioning.}, }
@article {pmid29116347, year = {2018}, author = {Cadena, S and García-Maldonado, JQ and López-Lozano, NE and Cervantes, FJ}, title = {Methanogenic and Sulfate-Reducing Activities in a Hypersaline Microbial Mat and Associated Microbial Diversity.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {930-940}, pmid = {29116347}, issn = {1432-184X}, support = {1289//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; }, mesh = {Bacteria/classification/genetics/*metabolism ; Biodiversity ; *Chemoautotrophic Growth ; Hydrogen Sulfide/metabolism ; Methane/*metabolism ; Methylamines/metabolism ; Mexico ; Microbiota/genetics/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Sulfates/*metabolism ; }, abstract = {Methanogenesis and sulfate reduction are important microbial processes in hypersaline environments. However, key aspects determining substrate competition between these microbial processes have not been well documented. We evaluated competitive and non-competitive substrates for stimulation of both processes through microcosm experiments of hypersaline microbial mat samples from Guerrero Negro, Baja California Sur, Mexico, and we assessed the effect of these substrates on the microbial community composition. Methylotrophic methanogenesis evidenced by sequences belonging to methanogens of the family Methanosarcinaceae was found as the dominant methanogenic pathway in the studied hypersaline microbial mat. Nevertheless, our results showed that incubations supplemented with acetate and lactate, performed in absence of sulfate, also produced methane after 40 days of incubation, apparently driven by hydrogenotrophic methanogens affiliated to the family Methanomicrobiaceae. Sulfate reduction was mainly stimulated by addition of acetate and lactate; however, after 40 days of incubation, an increase of the H2S concentrations in microcosms amended with trimethylamine and methanol was also observed, suggesting that these substrates are putatively used for sulfate reduction. Moreover, 16S rRNA gene sequencing analysis showed remarkable differences in the microbial community composition among experimental treatments. In the analyzed sample amended with acetate, sulfate-reducing bacteria (SRB) belonging to the family Desulfobacteraceae were dominant, while members of Desulfohalobiaceae, Desulfomicrobiaceae, and Desulfovibrionaceae were found in the incubation with lactate. Additionally, we detected an unexpected high abundance of unclassified Hydrogenedentes (near 25%) in almost all the experimental treatments. This study contributes to better understand methanogenic and sulfate-reducing activities, which play an important role in the functioning of hypersaline environments.}, }
@article {pmid29115058, year = {2018}, author = {Randle-Boggis, RJ and Ashton, PD and Helgason, T}, title = {Increasing flooding frequency alters soil microbial communities and functions under laboratory conditions.}, journal = {MicrobiologyOpen}, volume = {7}, number = {1}, pages = {}, pmid = {29115058}, issn = {2045-8827}, mesh = {Archaea/*classification/*growth &amp; development ; Bacteria/*classification/*growth &amp; development ; *Biota ; *Floods ; Metabolic Networks and Pathways/genetics ; Metabolism ; Models, Theoretical ; *Soil Microbiology ; }, abstract = {The impacts of increased flooding frequency on soil microbial communities and potential functions, in line with predicted environmental changes, were investigated in a laboratory-controlled environment. More frequent flooding events altered microbial community composition and significantly increased the resolved species alpha-diversity (Shannon index). The Bacteria:Archaea ratio was greater at the end of the experiment than at the start, more-so after only one flood. Significant changes in taxa and functional gene abundances were identified and quantified. These include genes related to the reduction and oxidation of substances associated with anoxia, for example, those involved in nitrogen and sulfur cycling. No significant changes were observed in the methanogenesis pathway, another function associated with anoxia and which contributes to the emission of greenhouse gases.}, }
@article {pmid29114246, year = {2017}, author = {Soverini, M and Turroni, S and Biagi, E and Quercia, S and Brigidi, P and Candela, M and Rampelli, S}, title = {Variation of Carbohydrate-Active Enzyme Patterns in the Gut Microbiota of Italian Healthy Subjects and Type 2 Diabetes Patients.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2079}, pmid = {29114246}, issn = {1664-302X}, abstract = {The human gut microbiota (GM) has been associated, to date, with various complex functions, essentials for the host health. Among these, it is certainly worth noting the degradation of the so-called microbiota-accessible carbohydrates (MACs), which the GM breaks down through specific enzymes, referred to as carbohydrate-active enzymes (CAZymes). This degradation constitutes the first step in the production of short-chain fatty acids (SCFAs), key microbial small molecules having multiple health-promoting effects for the host organism. The decline in MAC dietary intake in urban Western populations forced the shrinkage of CAZyme repertoire in the GM, as shown by the literature comparing the microbiome layout between Western urban citizens and traditional rural populations. Even if this reduction in GM functional complexity has been associated with the onset of the so-called "diseases of civilization," only few information regarding the CAZyme variation within Western populations has been provided to date, and its connections with diet and health are still unexplored. In this scenario, here we explore the GM-encoded CAZyme repertoire across two Italian adult cohorts, including healthy lean subjects consuming a Mediterranean diet and obese patients affected by type 2 diabetes, consuming a high-fat diet. In order to impute the CAZyme panel, a pipeline consisting of publicly available software - QIIME, FragGeneScan and HMMER - was specifically implemented. Our study highlighted the existence of robust clusters of bacterial species sharing a common MAC degradation profile in the Italian GM, allowing the stratification of the individual GM into different steady states according to the carbohydrate degradation profile, with possible connections with diet and health.}, }
@article {pmid29113091, year = {2017}, author = {Wemheuer, B and Wemheuer, F and Meier, D and Billerbeck, S and Giebel, HA and Simon, M and Scherber, C and Daniel, R}, title = {Linking Compositional and Functional Predictions to Decipher the Biogeochemical Significance in DFAA Turnover of Abundant Bacterioplankton Lineages in the North Sea.}, journal = {Microorganisms}, volume = {5}, number = {4}, pages = {}, pmid = {29113091}, issn = {2076-2607}, abstract = {Deciphering the ecological traits of abundant marine bacteria is a major challenge in marine microbial ecology. In the current study, we linked compositional and functional predictions to elucidate such traits for abundant bacterioplankton lineages in the North Sea. For this purpose, we investigated entire and active bacterioplankton composition along a transect ranging from the German Bight to the northern North Sea by pyrotag sequencing of bacterial 16S rRNA genes and transcripts. Functional profiles were inferred from 16S rRNA data using Tax4Fun. Bacterioplankton communities were dominated by well-known marine lineages including clusters/genera that are affiliated with the Roseobacter group and the Flavobacteria. Variations in community composition and function were significantly explained by measured environmental and microbial properties. Turnover of dissolved free amino acids (DFAA) showed the strongest correlation to community composition and function. We applied multinomial models, which enabled us to identify bacterial lineages involved in DFAA turnover. For instance, the genus Planktomarina was more abundant at higher DFAA turnover rates, suggesting its vital role in amino acid degradation. Functional predictions further indicated that Planktomarina is involved in leucine and isoleucine degradation. Overall, our results provide novel insights into the biogeochemical significance of abundant bacterioplankton lineages in the North Sea.}, }
@article {pmid29112388, year = {2017}, author = {Christiaens, MER and Gildemyn, S and Matassa, S and Ysebaert, T and De Vrieze, J and Rabaey, K}, title = {Electrochemical Ammonia Recovery from Source-Separated Urine for Microbial Protein Production.}, journal = {Environmental science &amp; technology}, volume = {51}, number = {22}, pages = {13143-13150}, doi = {10.1021/acs.est.7b02819}, pmid = {29112388}, issn = {1520-5851}, mesh = {*Ammonia ; Ammonium Compounds ; *Bacterial Proteins ; Electrodes ; Electrolysis ; *Nitrogen ; Urine ; }, abstract = {Conventional plant and meat protein production have low nitrogen usage efficiencies and high energy needs. Microbial protein (MP) is an alternative that offers higher nitrogen conversion efficiencies with low energy needs if nitrogen is recovered from a concentrated waste source such as source-separated urine. An electrochemical cell (EC) was optimized for ammonia recovery as NH3/H2 gas mixtures usable for MP production. Undiluted hydrolyzed urine was fed to the caustic-generating cathode compartment for ammonia stripping with redirection to the anode compartment for additional ammonium extraction. Using synthetic urine at 48 A m[-2] the nitrogen removal efficiency reached 91.6 ± 2.1%. Tests with real urine at 20 A m[-2], achieved 87.1 ± 6.0% and 68.4 ± 14.6% requiring 5.8 and 13.9 kWh kg N[-1] recovered, via absorption in acid or MP medium, respectively. Energy savings through accompanying electrolytic H2 and O2 production were accounted for. Subsequently, MP was grown in fed-batch on MP medium with conventional NH4[+] or urine-derived NH3 yielding 3.74 ± 1.79 and 4.44 ± 1.59 g CDW L[-1], respectively. Dissolution of gaseous NH3 in MP medium maintained neutral pH in the MP reactor preventing caustic addition and thus salt accumulation. Urine-nitrogen could thus be valorized as MP via electrochemical ammonia recovery.}, }
@article {pmid29110088, year = {2018}, author = {Botha, J and Mizrachi, E and Myburg, AA and Cowan, DA}, title = {Carbohydrate active enzyme domains from extreme thermophiles: components of a modular toolbox for lignocellulose degradation.}, journal = {Extremophiles : life under extreme conditions}, volume = {22}, number = {1}, pages = {1-12}, pmid = {29110088}, issn = {1433-4909}, mesh = {Bacteria/enzymology ; *Catalytic Domain ; Extreme Heat ; Hydrolases/*chemistry/metabolism ; Lignin/*metabolism ; Lyases/*chemistry/metabolism ; Plants/enzymology ; *Thermotolerance ; }, abstract = {Lignocellulosic biomass is a promising feedstock for the manufacture of biodegradable and renewable bioproducts. However, the complex lignocellulosic polymeric structure of woody tissue is difficult to access without extensive industrial pre-treatment. Enzyme processing of partly depolymerised biomass is an established technology, and there is evidence that high temperature (extremely thermophilic) lignocellulose degrading enzymes [carbohydrate active enzymes (CAZymes)] may enhance processing efficiency. However, wild-type thermophilic CAZymes will not necessarily be functionally optimal under industrial pre-treatment conditions. With recent advances in synthetic biology, it is now potentially possible to build CAZyme constructs from individual protein domains, tailored to the conditions of specific industrial processes. In this review, we identify a 'toolbox' of thermostable CAZyme domains from extremely thermophilic organisms and highlight recent advances in CAZyme engineering which will allow for the rational design of CAZymes tailored to specific aspects of lignocellulose digestion.}, }
@article {pmid29110066, year = {2018}, author = {Jones, AC and Hambright, KD and Caron, DA}, title = {Ecological Patterns Among Bacteria and Microbial Eukaryotes Derived from Network Analyses in a Low-Salinity Lake.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {917-929}, pmid = {29110066}, issn = {1432-184X}, support = {grant F-61-R//Oklahoma Department of Wildlife Conservation through the Sport Fish Restoration Program/ ; }, mesh = {Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; Biodiversity ; Cluster Analysis ; *Ecology ; Ecosystem ; Eukaryota/classification/genetics/*physiology ; Genes, rRNA/genetics ; Harmful Algal Bloom ; Lakes/chemistry/*microbiology ; *Microbial Interactions ; Microbiota/genetics/physiology ; Oklahoma ; Phylogeny ; Rain ; Salinity ; Seasons ; Texas ; *Water Microbiology ; }, abstract = {Microbial communities are comprised of complex assemblages of highly interactive taxa. We employed network analyses to identify and describe microbial interactions and co-occurrence patterns between microbial eukaryotes and bacteria at two locations within a low salinity (0.5-3.5 ppt) lake over an annual cycle. We previously documented that the microbial diversity and community composition within Lake Texoma, southwest USA, were significantly affected by both seasonal forces and a site-specific bloom of the harmful alga, Prymnesium parvum. We used network analyses to answer ecological questions involving both the bacterial and microbial eukaryotic datasets and to infer ecological relationships within the microbial communities. Patterns of connectivity at both locations reflected the seasonality of the lake including a large rain disturbance in May, while a comparison of the communities between locations revealed a localized response to the algal bloom. A network built from shared nodes (microbial operational taxonomic units and environmental variables) and correlations identified conserved associations at both locations within the lake. Using network analyses, we were able to detect disturbance events, characterize the ecological extent of a harmful algal bloom, and infer ecological relationships not apparent from diversity statistics alone.}, }
@article {pmid29110065, year = {2018}, author = {Li, J and Chen, D and Yu, B and He, J and Zheng, P and Mao, X and Yu, J and Luo, J and Tian, G and Huang, Z and Luo, Y}, title = {Fungi in Gastrointestinal Tracts of Human and Mice: from Community to Functions.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {821-829}, pmid = {29110065}, issn = {1432-184X}, support = {31301987//National Natural Science Foundation of China/ ; 3167131062//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Ascomycota/physiology ; Basidiomycota/physiology ; Biodiversity ; Candida/pathogenicity/physiology ; Chytridiomycota/physiology ; Diet ; Dysbiosis/microbiology ; Food ; Fungi/classification/*pathogenicity/*physiology ; Gastrointestinal Microbiome/immunology/*physiology ; Gastrointestinal Tract/immunology/*microbiology ; *Host-Pathogen Interactions/immunology/physiology ; Humans ; Inflammatory Bowel Diseases/immunology/microbiology ; Intestinal Mucosa/microbiology ; Lectins, C-Type/metabolism ; Mice ; Mycobiome/*physiology ; Mycoses ; Symbiosis ; Toll-Like Receptor 2/metabolism ; Toll-Like Receptor 4/metabolism ; }, abstract = {Fungi are often ignored in studies on gut microbes because of their low level of presence (making up only 0.1% of the total microorganisms) in the gastrointestinal tract (GIT) of monogastric animals. Recent studies using novel technologies such as next generation sequencing have expanded our understanding on the importance of intestinal fungi in humans and animals. Here, we provide a comprehensive review on the fungal community, the so-called mycobiome, and their functions from recent studies in humans and mice. In the GIT of humans, fungi belonging to the phyla Ascomycota, Basidiomycota and Chytridiomycota are predominant. The murine intestines harbor a more diverse assemblage of fungi. Diet is one of the major factors influencing colonization of fungi in the GIT. Presence of the genus Candida is positively associated with dietary carbohydrates, but are negatively correlated with dietary amino acids, proteins, and fatty acids. However, the relationship between diet and the fungal community (and functions), as well as the underlying mechanisms remains unclear. Dysbiosis of intestinal fungi can cause invasive infections and inflammatory bowel diseases (IBD). However, it is not clear whether dysbiosis of the mycobiome is a cause, or a result of IBD. Compared to non-inflamed intestinal mucosa, the abundance and diversity of fungi is significantly increased in the inflamed mucosa. The commonly observed commensal fungal species Candida albicans might contribute to occurrence and development of IBD. Limited studies show that Candida albicans might interact with immune cells of the host intestines through the pathways associated with Dectin-1, Toll-like receptor 2 (TLR2), and TLR4. This review is expected to provide new thoughts for future studies on intestinal fungi and for new therapies to fungal infections in the GIT of human and animals.}, }
@article {pmid29110064, year = {2018}, author = {Baraniya, D and Nannipieri, P and Kublik, S and Vestergaard, G and Schloter, M and Schöler, A}, title = {The Impact of the Diurnal Cycle on the Microbial Transcriptome in the Rhizosphere of Barley.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {830-833}, pmid = {29110064}, issn = {1432-184X}, mesh = {Amino Acids/metabolism ; Bacteria/classification/genetics/metabolism ; Carbohydrate Metabolism ; Circadian Rhythm/*physiology ; Hordeum/*microbiology ; Microbiota/*physiology ; Plant Roots/microbiology ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; *Transcriptome ; }, abstract = {While root exudation follows diurnal rhythms, little is known about the consequences for the microbiome of the rhizosphere. In this study, we used a metatranscriptomic approach to analyze the active microbial communities, before and after sunrise, in the rhizosphere of barley. We detected increased activities of many prokaryotic microbial taxa and functions at the pre-dawn stage, compared to post-dawn. Actinomycetales, Planctomycetales, Rhizobiales, and Burkholderiales were the most abundant and therefore the most active orders in the barley rhizosphere. The latter two, as well as Xanthomonadales, Sphingomonadales, and Caulobacterales showed a significantly higher abundance in pre-dawn samples compared to post-dawn samples. These changes in taxonomy coincide with functional changes as genes involved in both carbohydrate and amino acid metabolism were more abundant in pre-dawn samples compared to post-dawn samples. This study significantly enhances our present knowledge on how rhizospheric microbiota perceives and responds to changes in the soil during dark and light periods.}, }
@article {pmid29109478, year = {2018}, author = {Kolinko, S and Wu, YW and Tachea, F and Denzel, E and Hiras, J and Gabriel, R and Bäcker, N and Chan, LJG and Eichorst, SA and Frey, D and Chen, Q and Azadi, P and Adams, PD and Pray, TR and Tanjore, D and Petzold, CJ and Gladden, JM and Simmons, BA and Singer, SW}, title = {A bacterial pioneer produces cellulase complexes that persist through community succession.}, journal = {Nature microbiology}, volume = {3}, number = {1}, pages = {99-107}, pmid = {29109478}, issn = {2058-5276}, support = {S10 OD018530/OD/NIH HHS/United States ; }, mesh = {Bacteria/*classification/*enzymology/metabolism ; Bacterial Proteins/analysis/isolation &amp; purification ; Biological Evolution ; Cellulase/*analysis/isolation &amp; purification ; Cellulose/*metabolism ; Composting ; Genome, Bacterial/genetics ; Glycoside Hydrolases/analysis/isolation &amp; purification ; Glycosylation ; Heterotrophic Processes ; Metagenomics ; Microbial Consortia/*physiology ; Models, Biological ; Multienzyme Complexes/*analysis/isolation &amp; purification ; *Phylogeny ; Soil Microbiology ; }, abstract = {Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, 'Candidatus Reconcilibacillus cellulovorans', possessed a gene cluster containing multidomain glycoside hydrolases (GHs). Purification of the soluble cellulase activity from a 300litre cultivation of this consortium revealed that ~70% of the activity arose from the 'Ca. Reconcilibacillus cellulovorans' multidomain GHs assembled into cellulase complexes through glycosylation. These remarkably stable complexes have supramolecular structures for enzymatic cellulose hydrolysis that are distinct from cellulosomes. The persistence of these complexes during cultivation indicates that they may be active through multiple cultivations of this consortium and act as public goods that sustain the community. The provision of extracellular GHs as public goods may influence microbial community dynamics in native biomass-deconstructing communities relevant to agriculture, human health and biotechnology.}, }
@article {pmid29107553, year = {2017}, author = {Sierocinski, P and Milferstedt, K and Bayer, F and Großkopf, T and Alston, M and Bastkowski, S and Swarbreck, D and Hobbs, PJ and Soyer, OS and Hamelin, J and Buckling, A}, title = {A Single Community Dominates Structure and Function of a Mixture of Multiple Methanogenic Communities.}, journal = {Current biology : CB}, volume = {27}, number = {21}, pages = {3390-3395.e4}, doi = {10.1016/j.cub.2017.09.056}, pmid = {29107553}, issn = {1879-0445}, support = {BB/K003240/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anaerobiosis/*physiology ; Bacteria/classification/genetics/*metabolism ; Chemoautotrophic Growth/physiology ; Methane/*biosynthesis ; Microbial Consortia/*physiology ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; Silage/microbiology ; }, abstract = {The ecology of microbes frequently involves the mixing of entire communities (community coalescence), for example, flooding events, host excretion, and soil tillage [1, 2], yet the consequences of this process for community structure and function are poorly understood [3-7]. Recent theory suggests that a community, due to coevolution between constituent species, may act as a partially cohesive unit [8-11], resulting in one community dominating after community coalescence. This dominant community is predicted to be the one that uses resources most efficiently when grown in isolation [11]. We experimentally tested these predictions using methanogenic communities, for which efficient resource use, quantified by methane production, requires coevolved cross-feeding interactions between species [12]. After propagation in laboratory-scale anaerobic digesters, community composition (determined from 16S rRNA sequencing) and methane production of mixtures of communities closely resembled that of the single most productive community grown in isolation. Analysis of each community's contribution toward the final mixture suggests that certain combinations of taxa within a community might be co-selected as a result of coevolved interactions. As a corollary of these findings, we also show that methane production increased with the number of inoculated communities. These findings are relevant to the understanding of the ecological dynamics of natural microbial communities, as well as demonstrating a simple method of predictably enhancing microbial community function in biotechnology, health, and agriculture [13].}, }
@article {pmid29105293, year = {2018}, author = {Diaz-Trujillo, C and Chong, P and Stergiopoulos, I and Cordovez, V and Guzman, M and De Wit, PJGM and Meijer, HJG and Scalliet, G and Sierotzki, H and Lilia Peralta, E and Arango Isaza, RE and Kema, GHJ}, title = {A new mechanism for reduced sensitivity to demethylation-inhibitor fungicides in the fungal banana black Sigatoka pathogen Pseudocercospora fijiensis.}, journal = {Molecular plant pathology}, volume = {19}, number = {6}, pages = {1491-1503}, pmid = {29105293}, issn = {1364-3703}, mesh = {Ascomycota/drug effects/*pathogenicity ; Fungicides, Industrial/pharmacology ; Genotype ; Musa/*microbiology ; Plant Diseases/microbiology ; Promoter Regions, Genetic/drug effects/genetics ; }, abstract = {The Dothideomycete Pseudocercospora fijiensis, previously Mycosphaerella fijiensis, is the causal agent of black Sigatoka, one of the most destructive diseases of bananas and plantains. Disease management depends on fungicide applications, with a major contribution from sterol demethylation-inhibitors (DMIs). The continued use of DMIs places considerable selection pressure on natural P. fijiensis populations, enabling the selection of novel genotypes with reduced sensitivity. The hitherto explanatory mechanism for this reduced sensitivity was the presence of non-synonymous point mutations in the target gene Pfcyp51, encoding the sterol 14α-demethylase enzyme. Here, we demonstrate a second mechanism involved in DMI sensitivity of P. fijiensis. We identified a 19-bp element in the wild-type (wt) Pfcyp51 promoter that concatenates in strains with reduced DMI sensitivity. A polymerase chain reaction (PCR) assay identified up to six Pfcyp51 promoter repeats in four field populations of P. fijiensis in Costa Rica. We used transformation experiments to swap the wt promoter of a sensitive field isolate with a promoter from a strain with reduced DMI sensitivity that comprised multiple insertions. Comparative in vivo phenotyping showed a functional and proportional up-regulation of Pfcyp51, which consequently decreased DMI sensitivity. Our data demonstrate that point mutations in the Pfcyp51 coding domain, as well as promoter inserts, contribute to the reduced DMI sensitivity of P. fijiensis. These results provide new insights into the importance of the appropriate use of DMIs and the need for the discovery of new molecules for black Sigatoka management.}, }
@article {pmid29104938, year = {2017}, author = {Hubalek, V and Buck, M and Tan, B and Foght, J and Wendeberg, A and Berry, D and Bertilsson, S and Eiler, A}, title = {Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions.}, journal = {mSystems}, volume = {2}, number = {5}, pages = {}, pmid = {29104938}, issn = {2379-5077}, abstract = {Syntrophy among Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH4 and CO2. Particularly during aliphatic and aromatic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance. Using micromanipulation combined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methanogenic conditions. Metabolic reconstruction revealed that only a small fraction of genes in the metagenome-assembled genomes encode the capacity for fermentation of alkanes facilitated by energy conservation linked to H2 metabolism. Instead, the presence of inferred lifestyles based on scavenging anabolic products and intermediate fermentation products derived from detrital biomass was a common feature. Additionally, inferred auxotrophy for vitamins and amino acids suggests that the hydrocarbon-degrading microbial assemblages are structured and maintained by multiple interactions beyond the canonical H2-producing and syntrophic alkane degrader-methanogen partnership. Compared to previous work, our report points to a higher order of complexity in microbial consortia engaged in anaerobic hydrocarbon transformation. IMPORTANCE Microbial interactions between Archaea and Bacteria mediate many important chemical transformations in the biosphere from degrading abundant polymers to synthesis of toxic compounds. Two of the most pressing issues in microbial interactions are how consortia are established and how we can modulate these microbial communities to express desirable functions. Here, we propose that public goods (i.e., metabolites of high energy demand in biosynthesis) facilitate energy conservation for life under energy-limited conditions and determine the assembly and function of the consortia. Our report suggests that an understanding of public good dynamics could result in new ways to improve microbial pollutant degradation in anaerobic systems.}, }
@article {pmid29104565, year = {2017}, author = {Perry, EK and Digby, A and Taylor, MW}, title = {The Low-Diversity Fecal Microbiota of the Critically Endangered Kākāpō Is Robust to Anthropogenic Dietary and Geographic Influences.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2033}, pmid = {29104565}, issn = {1664-302X}, abstract = {The critically endangered kākāpō, an herbivorous parrot endemic to New Zealand, is subject to intensive management to increase its population size. Key aspects of the management program include supplementary feeding and translocation of kākāpō between different predator-free islands to optimize the genetic composition of the breeding populations. While these practices have helped boost the kākāpō population, their impact on the kākāpō fecal microbiota is uncertain. Previous studies have found that the kākāpō possesses a low-diversity fecal microbiota, typically dominated by Escherichia/Shigella spp. However, the question of whether the low diversity of the kākāpō fecal microbiota is an inadvertent consequence of human interventions has yet to be investigated. To that end, we used high-throughput Illumina sequencing of 16S rRNA gene amplicons obtained from fecal material of 63 kākāpō representing different diets, islands, and ages. Remarkably, neither supplementary feeding nor geographic location were associated with significant differences in the overall fecal microbial community structures of adult kākāpō, suggesting that the kākāpō's low-diversity fecal microbiota is both inherent to this species and robust to these external influences.}, }
@article {pmid29101383, year = {2017}, author = {Koh, HW and Hur, M and Kang, MS and Ku, YB and Ghai, R and Park, SJ}, title = {Physiological and genomic insights into the lifestyle of arsenite-oxidizing Herminiimonas arsenitoxidans.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15007}, pmid = {29101383}, issn = {2045-2322}, mesh = {Bacterial Typing Techniques ; DNA, Bacterial/*genetics ; Oxalobacteraceae/genetics/*physiology ; *Phylogeny ; *RNA, Ribosomal, 16S ; }, abstract = {Arsenic, a representative toxic metalloid, is responsible for serious global health problems. Most organisms possess arsenic resistance strategies to mitigate this toxicity. Here, we reported a microorganism, strain AS8, from heavy metal/metalloid-contaminated soil that is able to oxidize arsenite, and investigated its physiological and genomic traits. Its cells were rod-shaped and Gram-negative, and formed small beige-pigmented colonies. 16S rRNA-based phylogenetic analysis indicated that the strain belongs to the genus Herminiimonas and is closely related to Herminiimonas glaciei UMB49[T] (98.7% of 16S rRNA gene sequence similarity), Herminiimonas arsenicoxydans ULPAs1[T] (98.4%), and Herminiimonas saxobsidens NS11[T] (98.4%). Under chemolithoheterotrophic conditions, the strain utilized some organic acids and amino acids as carbon and/or nitrogen sources but not electron sources. Further, the strain grew as a sulfur oxidizer in a complex medium (trypticase soy agar). Unexpectedly, most carbohydrates failed to support its growth as sole carbon sources. Genome sequencing supported these observations, and very few ABC transporters capable of oligo/monosaccharide uptake were identified in the AS8 genome. The genome harbored genes required for the colonization, flagella biosynthesis, urea degradation, and heavy metal and antibiotic resistance. Based on these polyphasic and genomic analyses, we propose that the strain AS8 be named Herminiimonas arsenitoxidans.}, }
@article {pmid29098760, year = {2017}, author = {Herbold, CW and Lehtovirta-Morley, LE and Jung, MY and Jehmlich, N and Hausmann, B and Han, P and Loy, A and Pester, M and Sayavedra-Soto, LA and Rhee, SK and Prosser, JI and Nicol, GW and Wagner, M and Gubry-Rangin, C}, title = {Ammonia-oxidising archaea living at low pH: Insights from comparative genomics.}, journal = {Environmental microbiology}, volume = {19}, number = {12}, pages = {4939-4952}, pmid = {29098760}, issn = {1462-2920}, support = {294343/ERC_/European Research Council/International ; P 23117/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Ammonia/*metabolism ; Base Sequence ; Biological Evolution ; DNA, Archaeal/genetics ; Euryarchaeota/*genetics/*metabolism ; Gene Transfer, Horizontal ; Genome, Archaeal/*genetics ; Genomics ; Nitrification/*physiology ; Oxidation-Reduction ; Phylogeny ; Proteomics ; Sequence Analysis, DNA ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus (Ca. N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca. Nitrosotalea strains, extracted an almost complete Ca. Nitrosotalea metagenome-assembled genome from an acidic fen, and performed comparative genomics of the four Ca. Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four Ca. Nitrosotalea strains represent separate species within the genus. The four Ca. Nitrosotalea genomes contained a core set of 103 orthologous gene families absent from all other ammonia-oxidizing archaea and, for most of these gene families, expression could be demonstrated in laboratory culture or the environment via proteomic or metatranscriptomic analyses respectively. Phylogenetic analyses indicated that four of these core gene families were acquired by the Ca. Nitrosotalea common ancestor via horizontal gene transfer from acidophilic representatives of Euryarchaeota. We hypothesize that gene exchange with these acidophiles contributed to the competitive success of the Ca. Nitrosotalea lineage in acidic environments.}, }
@article {pmid29098358, year = {2018}, author = {Baumann, JH and Davies, SW and Aichelman, HE and Castillo, KD}, title = {Coral Symbiodinium Community Composition Across the Belize Mesoamerican Barrier Reef System is Influenced by Host Species and Thermal Variability.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {903-915}, pmid = {29098358}, issn = {1432-184X}, support = {15802-1//Rufford Foundation/ ; OCE 1459522//Division of Ocean Sciences/ ; }, mesh = {Animals ; Anthozoa/genetics/*parasitology ; Belize ; DNA/analysis ; Dinoflagellida/*classification/genetics/*physiology ; Environmental Monitoring ; Genetic Variation ; *Host Specificity ; Hot Temperature ; Oceans and Seas ; Phylogeny ; Symbiosis/physiology ; Temperature ; Thermotolerance ; }, abstract = {Reef-building corals maintain a symbiotic relationship with dinoflagellate algae of the genus Symbiodinium, and this symbiosis is vital for the survival of the coral holobiont. Symbiodinium community composition within the coral host has been shown to influence a coral's ability to resist and recover from stress. A multitude of stressors including ocean warming, ocean acidification, and eutrophication have been linked to global scale decline in coral health and cover in recent decades. Three distinct thermal regimes (highTP, modTP, and lowTP) following an inshore-offshore gradient of declining average temperatures and thermal variation were identified on the Belize Mesoamerican Barrier Reef System (MBRS). Quantitative metabarcoding of the ITS-2 locus was employed to investigate differences and similarities in Symbiodinium genetic diversity of the Caribbean corals Siderastrea siderea, S. radians, and Pseudodiploria strigosa between the three thermal regimes. A total of ten Symbiodinium lineages were identified across the three coral host species. S. siderea was associated with distinct Symbiodinium communities; however, Symbiodinium communities of its congener, S. radians and P. strigosa, were more similar to one another. Thermal regime played a role in defining Symbiodinium communities in S. siderea but not S. radians or P. strigosa. Against expectations, Symbiodinium trenchii, a symbiont known to confer thermal tolerance, was dominant only in S. siderea at one sampled offshore site and was rare inshore, suggesting that coral thermal tolerance in more thermally variable inshore habitats is achieved through alternative mechanisms. Overall, thermal parameters alone were likely not the only primary drivers of Symbiodinium community composition, suggesting that environmental variables unrelated to temperature (i.e., light availability or nutrients) may play key roles in structuring coral-algal communities in Belize and that the relative importance of these environmental variables may vary by coral host species.}, }
@article {pmid29098357, year = {2018}, author = {Kulakova, NV and Sakirko, MV and Adelshin, RV and Khanaev, IV and Nebesnykh, IA and Pérez, T}, title = {Brown Rot Syndrome and Changes in the Bacterial Сommunity of the Baikal Sponge Lubomirskia baicalensis.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {1024-1034}, pmid = {29098357}, issn = {1432-184X}, support = {16-54-150007//Russian Foundation for Basic Research/ ; 216483//The French Centre National de la Recherche Scientifique/ ; 0345-2016-0002//Russian State Project/ ; 0345-2016-0008//Russian State Project/ ; }, mesh = {Animal Diseases/epidemiology/*microbiology ; Animals ; Bacteria/*classification/genetics ; Biodiversity ; Cyanobacteria ; Host Specificity ; Lakes/chemistry/microbiology ; *Microbial Consortia ; Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Russia ; }, abstract = {Mass mortality events have led to a collapse of the sponge fauna of Lake Baikal. We describe a new Brown Rot Syndrome affecting the endemic species Lubomirskia baicalensis. The main symptoms are the appearance of brown patches at the sponge surface, necrosis, and cyanobacterial fouling. 16S rRNA gene sequencing was used to characterize the bacterial community of healthy versus diseased sponges, in order to identify putative pathogens. The relative abundance of 89 eubacterial OTUs out of 340 detected has significantly changed between healthy and diseased groups. This can be explained by the depletion of host-specific prokaryotes and by the appearance and proliferation of disease-specific OTUs. In diseased sponges, the most represented OTUs belong to the families Oscillatoriaceae, Cytophagaceae, Flavobacteriaceae, Chitinophagaceae, Sphingobacteriaceae, Burkholderiaceae, Rhodobacteraceae, Comamonadaceae, Oxalobacteraceae, and Xanthomonadaceae. Although these families may contain pathogenic agents, the primary causes of changes in the sponge bacterial community and their relationship with Brown Rot Syndrome remain unclear. A better understanding of this ecological crisis will thus require a more integrative approach.}, }
@article {pmid29089611, year = {2017}, author = {Kumar, P and Bag, S and Ghosh, TS and Dey, P and Dayal, M and Saha, B and Verma, J and Pant, A and Saxena, S and Desigamani, A and Rana, P and Kumar, D and Sharma, NC and Hanpude, P and Maiti, TK and Mukhopadhyay, AK and Bhadra, RK and Nair, GB and Ramamurthy, T and Das, B}, title = {Molecular Insights into Antimicrobial Resistance Traits of Multidrug Resistant Enteric Pathogens isolated from India.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {14468}, pmid = {29089611}, issn = {2045-2322}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Bacterial Infections/drug therapy ; Drug Resistance, Bacterial/*drug effects ; Drug Resistance, Multiple/*genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Gastrointestinal Microbiome/drug effects/*genetics ; Gram-Negative Bacteria/drug effects ; Humans ; India ; Microbial Sensitivity Tests ; Phenotype ; Whole Genome Sequencing ; }, abstract = {Emergence of antimicrobial resistant Gram-negative bacteria has created a serious global health crisis and threatens the effectiveness of most, if not all, antibiotics commonly used to prevent and treat bacterial infections. There is a dearth of detailed studies on the prevalence of antimicrobial resistance (AMR) patterns in India. Here, we have isolated and examined AMR patterns of 654 enteric pathogens and investigated complete genome sequences of isolates from six representative genera, which in aggregate encode resistance against 22 antibiotics representing nine distinct drug classes. This study revealed that ~97% isolates are resistant against ≥2 antibiotics, ~24% isolates are resistant against ≥10 antibiotics and ~3% isolates are resistant against ≥15 antibiotics. Analyses of whole genome sequences of six extensive drug resistant enteric pathogens revealed presence of multiple mobile genetic elements, which are physically linked with resistance traits. These elements are therefore appearing to be responsible for disseminating drug resistance among bacteria through horizontal gene transfer. The present study provides insights into the linkages between the resistance patterns to certain antibiotics and their usage in India. The findings would be useful to understand the genetics of resistance traits and severity of and difficulty in tackling AMR enteric pathogens.}, }
@article {pmid29089428, year = {2017}, author = {Allen, RC and Pfrunder-Cardozo, KR and Meinel, D and Egli, A and Hall, AR}, title = {Associations among Antibiotic and Phage Resistance Phenotypes in Natural and Clinical Escherichia coli Isolates.}, journal = {mBio}, volume = {8}, number = {5}, pages = {}, pmid = {29089428}, issn = {2150-7511}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Coliphages/*physiology ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/*drug effects/genetics/pathogenicity/*virology ; Escherichia coli Infections/*microbiology ; Evolution, Molecular ; Genome, Bacterial/drug effects ; Humans ; Phage Therapy ; Phenotype ; Plasmids ; Receptors, Virus/metabolism ; }, abstract = {The spread of antibiotic resistance is driving interest in new approaches to control bacterial pathogens. This includes applying multiple antibiotics strategically, using bacteriophages against antibiotic-resistant bacteria, and combining both types of antibacterial agents. All these approaches rely on or are impacted by associations among resistance phenotypes (where bacteria resistant to one antibacterial agent are also relatively susceptible or resistant to others). Experiments with laboratory strains have shown strong associations between some resistance phenotypes, but we lack a quantitative understanding of associations among antibiotic and phage resistance phenotypes in natural and clinical populations. To address this, we measured resistance to various antibiotics and bacteriophages for 94 natural and clinical Escherichia coli isolates. We found several positive associations between resistance phenotypes across isolates. Associations were on average stronger for antibacterial agents of the same type (antibiotic-antibiotic or phage-phage) than different types (antibiotic-phage). Plasmid profiles and genetic knockouts suggested that such associations can result from both colocalization of resistance genes and pleiotropic effects of individual resistance mechanisms, including one case of antibiotic-phage cross-resistance. Antibiotic resistance was predicted by core genome phylogeny and plasmid profile, but phage resistance was predicted only by core genome phylogeny. Finally, we used observed associations to predict genes involved in a previously uncharacterized phage resistance mechanism, which we verified using experimental evolution. Our data suggest that susceptibility to phages and antibiotics are evolving largely independently, and unlike in experiments with lab strains, negative associations between antibiotic resistance phenotypes in nature are rare. This is relevant for treatment scenarios where bacteria encounter multiple antibacterial agents.IMPORTANCE Rising antibiotic resistance is making it harder to treat bacterial infections. Whether resistance to a given antibiotic spreads or declines is influenced by whether it is associated with altered susceptibility to other antibiotics or other stressors that bacteria encounter in nature, such as bacteriophages (viruses that infect bacteria). We used natural and clinical isolates of Escherichia coli, an abundant species and key pathogen, to characterize associations among resistance phenotypes to various antibiotics and bacteriophages. We found associations between some resistance phenotypes, and in contrast to past work with laboratory strains, they were exclusively positive. Analysis of bacterial genome sequences and horizontally transferred genetic elements (plasmids) helped to explain this, as well as our finding that there was no overall association between antibiotic resistance and bacteriophage resistance profiles across isolates. This improves our understanding of resistance evolution in nature, potentially informing new rational therapies that combine different antibacterials, including bacteriophages.}, }
@article {pmid29089134, year = {2018}, author = {Zhang, J and Ding, X and Guan, R and Zhu, C and Xu, C and Zhu, B and Zhang, H and Xiong, Z and Xue, Y and Tu, J and Lu, Z}, title = {Evaluation of different 16S rRNA gene V regions for exploring bacterial diversity in a eutrophic freshwater lake.}, journal = {The Science of the total environment}, volume = {618}, number = {}, pages = {1254-1267}, doi = {10.1016/j.scitotenv.2017.09.228}, pmid = {29089134}, issn = {1879-1026}, mesh = {Bacteria/classification/*genetics ; China ; *Environmental Monitoring ; *Eutrophication ; Genes, Bacterial ; Genetic Variation ; Lakes/*microbiology ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {Massive partial sequencing of 16S rRNA genes has become the predominant tool used for studying microbial ecology. However, determining which hypervariable regions and primer sets should be used for screening microbial communities requires extensive investigation if controversial results are to be avoided. Here, the performances of different variable regions of the 16S rRNA gene on bacterial diversity studies were evaluated in silico with respect to the SILVA non-redundant reference database (SILVA SSU Ref 123NR), and subsequently verified using samples from Lake Taihu in China, a eutrophic lake. We found that the bacterial community composition results were strongly impacted by the different V regions. The results show that V1-V2 and V1-V3 regions were the most reliable regions in the full-length 16S rRNA sequences, while most V3 to V6 regions (including V3, V4, V3-V4, V5, V4-V5, V6, V3-V6, V4-V6, and V5-V6) were more closely aligned with the SILVA SSU Ref 123NR database. Overall, V4 was the most prominent V region for achieving good domain specificity, higher coverage and a broader spectrum in the Bacteria domain, as confirmed by the validation experiments. S-D-Bact-0564-a-S-15/S-D-Bact-0785-b-A-18 is, therefore, a promising primer set for surveying bacterial diversity in eutrophic lakes.}, }
@article {pmid29087435, year = {2018}, author = {Piccolo, BD and Wankhade, UD and Chintapalli, SV and Bhattacharyya, S and Chunqiao, L and Shankar, K}, title = {Dynamic assessment of microbial ecology (DAME): a web app for interactive analysis and visualization of microbial sequencing data.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {6}, pages = {1050-1052}, pmid = {29087435}, issn = {1367-4811}, support = {UL1 TR001449/TR/NCATS NIH HHS/United States ; }, mesh = {*Data Interpretation, Statistical ; *Ecosystem ; Microbiological Techniques ; Microbiology ; Programming Languages ; Sequence Analysis ; *Software ; }, abstract = {SUMMARY: Dynamic assessment of microbial ecology (DAME) is a Shiny-based web application for interactive analysis and visualization of microbial sequencing data. DAME provides researchers not familiar with R programming the ability to access the most current R functions utilized for ecology and gene sequencing data analyses. Currently, DAME supports group comparisons of several ecological estimates of α-diversity and β-diversity, along with differential abundance analysis of individual taxa. Using the Shiny framework, the user has complete control of all aspects of the data analysis, including sample/experimental group selection and filtering, estimate selection, statistical methods and visualization parameters. Furthermore, graphical and tabular outputs are supported by R packages using D3.js and are fully interactive.<br><br>DAME was implemented in R but can be modified by Hypertext Markup Language (HTML), Cascading Style Sheets (CSS), and JavaScript. It is freely available on the web at https://acnc-shinyapps.shinyapps.io/DAME/. Local installation and source code are available through Github (https://github.com/bdpiccolo/ACNC-DAME). Any system with R can launch DAME locally provided the shiny package is installed.<br><br>CONTACT: bdpiccolo@uams.edu.}, }
@article {pmid29087370, year = {2017}, author = {Hallam, SJ and Torres-Beltrán, M and Hawley, AK}, title = {Monitoring microbial responses to ocean deoxygenation in a model oxygen minimum zone.}, journal = {Scientific data}, volume = {4}, number = {}, pages = {170158}, pmid = {29087370}, issn = {2052-4463}, mesh = {Climate Change ; *Ecosystem ; *Microbiota ; *Models, Biological ; Oxygen ; }, abstract = {Today in Scientific Data, two compendia of geochemical and multi-omic sequence information (DNA, RNA, protein) generated over almost a decade of time series monitoring in a seasonally anoxic coastal marine setting are presented to the scientific community. These data descriptors introduce a model ecosystem for the study of microbial responses to ocean deoxygenation, a phenotype that is currently expanding due to climate change. Public access to this time series information is intended to promote scientific collaborations and the generation of new hypotheses relevant to microbial ecology, biogeochemistry and global change issues.}, }
@article {pmid29085573, year = {2017}, author = {Herath, D and Jayasundara, D and Ackland, D and Saeed, I and Tang, SL and Halgamuge, S}, title = {Assessing Species Diversity Using Metavirome Data: Methods and Challenges.}, journal = {Computational and structural biotechnology journal}, volume = {15}, number = {}, pages = {447-455}, pmid = {29085573}, issn = {2001-0370}, abstract = {Assessing biodiversity is an important step in the study of microbial ecology associated with a given environment. Multiple indices have been used to quantify species diversity, which is a key biodiversity measure. Measuring species diversity of viruses in different environments remains a challenge relative to measuring the diversity of other microbial communities. Metagenomics has played an important role in elucidating viral diversity by conducting metavirome studies; however, metavirome data are of high complexity requiring robust data preprocessing and analysis methods. In this review, existing bioinformatics methods for measuring species diversity using metavirome data are categorised broadly as either sequence similarity-dependent methods or sequence similarity-independent methods. The former includes a comparison of DNA fragments or assemblies generated in the experiment against reference databases for quantifying species diversity, whereas estimates from the latter are independent of the knowledge of existing sequence data. Current methods and tools are discussed in detail, including their applications and limitations. Drawbacks of the state-of-the-art method are demonstrated through results from a simulation. In addition, alternative approaches are proposed to overcome the challenges in estimating species diversity measures using metavirome data.}, }
@article {pmid29085354, year = {2017}, author = {Águila-Arcos, S and Álvarez-Rodríguez, I and Garaiyurrebaso, O and Garbisu, C and Grohmann, E and Alkorta, I}, title = {Biofilm-Forming Clinical Staphylococcus Isolates Harbor Horizontal Transfer and Antibiotic Resistance Genes.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2018}, pmid = {29085354}, issn = {1664-302X}, abstract = {Infections caused by staphylococci represent a medical concern, especially when related to biofilms located in implanted medical devices, such as prostheses and catheters. Unfortunately, their frequent resistance to high doses of antibiotics makes the treatment of these infections a difficult task. Moreover, biofilms represent a hot spot for horizontal gene transfer (HGT) by bacterial conjugation. In this work, 25 biofilm-forming clinical staphylococcal isolates were studied. We found that Staphylococcus epidermidis isolates showed a higher biofilm-forming capacity than Staphylococcus aureus isolates. Additionally, horizontal transfer and relaxase genes of two common staphylococcal plasmids, pSK41 and pT181, were detected in all isolates. In terms of antibiotic resistance genes, aac6-aph2a, ermC, and tetK genes, which confer resistance to gentamicin, erythromycin, and tetracycline, respectively, were the most prevalent. The horizontal transfer and antibiotic resistance genes harbored on these staphylococcal clinical strains isolated from biofilms located in implanted medical devices points to the potential risk of the development and dissemination of multiresistant bacteria.}, }
@article {pmid29085345, year = {2017}, author = {Schiessl, KT and Janssen, EM and Kraemer, SM and McNeill, K and Ackermann, M}, title = {Magnitude and Mechanism of Siderophore-Mediated Competition at Low Iron Solubility in the Pseudomonas aeruginosa Pyochelin System.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1964}, pmid = {29085345}, issn = {1664-302X}, abstract = {A central question in microbial ecology is whether microbial interactions are predominantly cooperative or competitive. The secretion of siderophores, microbial iron chelators, is a model system for cooperative interactions. However, siderophores have also been shown to mediate competition by sequestering available iron and making it unavailable to competitors. The details of how siderophores mediate competition are not well understood, especially considering the complex distribution of iron phases in the environment. One pertinent question is whether sequestering iron through siderophores can indeed be effective in natural conditions; many natural environments are characterized by large pools of precipitated iron, and it is conceivable that any soluble iron that is sequestered by siderophores is replenished by the dissolution of these precipitated iron sources. Our goal here was to address this issue, and investigate the magnitude and mechanism of siderophore-mediated competition in the presence of precipitated iron. We combined experimental work with thermodynamic modeling, using Pseudomonas aeruginosa as a model system and ferrihydrite precipitates as the iron source with low solubility. Our experiments show that competitive growth inhibition by the siderophore pyochelin is indeed efficient, and that inhibition of a competitor can even have a stronger growth-promoting effect than solubilization of precipitated iron. Based on the results of our thermodynamic models we conclude that the observed inhibition of a competitor is effective because sequestered iron is only very slowly replenished by the dissolution of precipitated iron. Our research highlights the importance of competitive benefits mediated by siderophores, and underlines that the dynamics of siderophore production and uptake in environmental communities could be a signature of competitive, not just cooperative, dynamics.}, }
@article {pmid29085343, year = {2017}, author = {Besmer, MD and Sigrist, JA and Props, R and Buysschaert, B and Mao, G and Boon, N and Hammes, F}, title = {Laboratory-Scale Simulation and Real-Time Tracking of a Microbial Contamination Event and Subsequent Shock-Chlorination in Drinking Water.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1900}, pmid = {29085343}, issn = {1664-302X}, abstract = {Rapid contamination of drinking water in distribution and storage systems can occur due to pressure drop, backflow, cross-connections, accidents, and bio-terrorism. Small volumes of a concentrated contaminant (e.g., wastewater) can contaminate large volumes of water in a very short time with potentially severe negative health impacts. The technical limitations of conventional, cultivation-based microbial detection methods neither allow for timely detection of such contaminations, nor for the real-time monitoring of subsequent emergency remediation measures (e.g., shock-chlorination). Here we applied a newly developed continuous, ultra high-frequency flow cytometry approach to track a rapid pollution event and subsequent disinfection of drinking water in an 80-min laboratory scale simulation. We quantified total (TCC) and intact (ICC) cell concentrations as well as flow cytometric fingerprints in parallel in real-time with two different staining methods. The ingress of wastewater was detectable almost immediately (i.e., after 0.6% volume change), significantly changing TCC, ICC, and the flow cytometric fingerprint. Shock chlorination was rapid and detected in real time, causing membrane damage in the vast majority of bacteria (i.e., drop of ICC from more than 380 cells μl[-1] to less than 30 cells μl[-1] within 4 min). Both of these effects as well as the final wash-in of fresh tap water followed calculated predictions well. Detailed and highly quantitative tracking of microbial dynamics at very short time scales and for different characteristics (e.g., concentration, membrane integrity) is feasible. This opens up multiple possibilities for targeted investigation of a myriad of bacterial short-term dynamics (e.g., disinfection, growth, detachment, operational changes) both in laboratory-scale research and full-scale system investigations in practice.}, }
@article {pmid29084513, year = {2017}, author = {Svenningsen, NB and Damgaard, M and Rasmussen, M and Pérez-Pantoja, D and Nybroe, O and Nicolaisen, MH}, title = {Cupriavidus pinatubonensis AEO106 deals with copper-induced oxidative stress before engaging in biodegradation of the herbicide 4-chloro-2-methylphenoxyacetic acid.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {211}, pmid = {29084513}, issn = {1471-2180}, mesh = {2-Methyl-4-chlorophenoxyacetic Acid/*metabolism ; Biodegradation, Environmental/*drug effects ; Copper/*toxicity ; Cupriavidus/*drug effects/enzymology/genetics/metabolism ; Flow Cytometry ; Gene Expression Regulation, Bacterial/drug effects ; Genes, Bacterial/genetics ; Herbicides/*metabolism ; *Oxidative Stress ; Reactive Oxygen Species/metabolism ; Real-Time Polymerase Chain Reaction ; *Soil Microbiology ; Soil Pollutants/metabolism/toxicity ; }, abstract = {BACKGROUND: Microbial degradation of phenoxy acid (PA) herbicides in agricultural soils is important to minimize herbicide leaching to groundwater reservoirs. Degradation may, however, be hampered by exposure of the degrader bacteria to toxic metals as copper (Cu) in the soil environment. Exposure to Cu leads to accumulation of intracellular reactive oxygen species (ROS) in some bacteria, but it is not known how Cu-derived ROS and an ensuing oxidative stress affect the degradation of PA herbicides. Based on the previously proposed paradigm that bacteria deal with environmental stress before they engage in biodegradation, we studied how the degradation of the PA herbicide 2-methyl-4-chlorophenoxyacetic acid (MCPA) by the model PA degrader Cupriavidus pinatubonensis AEO106 was affected by Cu exposure.<br><br>RESULTS: Exposure of C. pinatubonensis in batch culture to sublethal concentrations of Cu increased accumulation of ROS measured by the oxidant sensing probe 2,7-dichlorodihydrofluorescein diacetate and flow cytometry, and resulted in upregulation of a gene encoding a protein belong to the Ohr/OsmC protein family. The ohr/osmC gene was also highly induced by H2O2 exposure suggesting that it is involved in the oxidative stress response in C. pinatubonensis. The increased ROS accumulation and increased expression of the oxidative stress defense coincided with a delay in the catabolic performance, since both expression of the catabolic tfdA gene and MCPA mineralization were delayed compared to unexposed control cells.<br><br>CONCLUSIONS: The current study suggests that Cu-induced ROS accumulation in C. pinatubonensis activates a stress response involving the product of the ohr/osmC gene. Further, the stress response is launched before induction of the catabolic tfdA gene and mineralization occurs.}, }
@article {pmid29083891, year = {2017}, author = {Defoirdt, T and Vlaeminck, SE and Sun, X and Boon, N and Clauwaert, P}, title = {Ureolytic Activity and Its Regulation in Vibrio campbellii and Vibrio harveyi in Relation to Nitrogen Recovery from Human Urine.}, journal = {Environmental science &amp; technology}, volume = {51}, number = {22}, pages = {13335-13343}, doi = {10.1021/acs.est.7b03829}, pmid = {29083891}, issn = {1520-5851}, mesh = {Humans ; Hydrolysis ; *Nitrogen ; *Urea ; Urease ; *Vibrio ; }, abstract = {Human urine contains a high concentration of nitrogen and is therefore an interesting source for nutrient recovery. Ureolysis is a key requirement in many processes aiming at nitrogen recovery from urine. Although ureolytic activity is widespread in terrestrial and aquatic environments, very little is known about the urease activity and regulation in specific bacteria other than human pathogens. Given the relatively high salt concentration of urine, marine bacteria would be particularly well suited for biotechnological applications involving nitrogen recovery from urine, and therefore, in this study, we investigated ureolytic activity and its regulation in marine vibrios. Thirteen out of 14 strains showed ureolytic activity. The urease activity was induced by urea, since complete and very rapid hydrolysis, up to 4 g L[-1] h[-1] of urea, was observed in synthetic human urine when the bacteria were pretreated with 10 g L[-1] urea, whereas slow hydrolysis occurred when they were pretreated with 1 g L[-1] urea (14-35% hydrolysis after 2 days). There was no correlation between biofilm formation and motility on one hand, and ureolysis on the other hand, and biofilm and motility inhibitors did not affect ureolysis. Together, our data demonstrate for the first time the potential of marine vibrios as fast urea hydrolyzers for biotechnological applications aiming at nutrient recovery from human urine.}, }
@article {pmid29081767, year = {2017}, author = {Kumar, M and van Elsas, JD and Nissinen, R}, title = {Strong Regionality and Dominance of Anaerobic Bacterial Taxa Characterize Diazotrophic Bacterial Communities of the Arcto-Alpine Plant Species Oxyria digyna and Saxifraga oppositifolia.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1972}, pmid = {29081767}, issn = {1664-302X}, abstract = {Arctic and alpine biomes are most often strongly nitrogen-limited, and hence biological nitrogen fixation is a strong driver of these ecosystems. Both biomes are characterized by low temperatures and short growing seasons, but they differ in seasonality of solar radiation and in soil water balance due to underlying permafrost in the Arctic. Arcto-alpine plant species are well-adapted to the low temperatures that prevail in their habitats, and plant growth is mainly limited by the availability of nutrients, in particular nitrogen, due to slow mineralization. Nitrogen fixing bacteria are likely important for plant growth in these habitats, but very little is known of these bacteria or forces shaping their communities. In this study, we characterized the potential nitrogen fixing bacterial (PNFB) communities associated with two arcto-alpine pioneer plant species, Oxyria digyna (mountain sorrel) and Saxifraga oppositifolia (blue saxifrage), in three climate regions. Both of these plants readily colonize low nutrient mineral soils. Our goal was to investigate how climate (region) and, on the other hand, host plant and plant species shape these communities. To our knowledge, this is the first comprehensive study describing PNFB communities associated with pioneer plants in different arcto-alpine biomes. Replicate samples were taken from two arctic regions, Kilpisjärvi and Ny-Ålesund, and one alpine region, Mayrhofen. In these, the PNFB communities in the bulk and rhizosphere soils and the plant endospheres were characterized by nifH-targeted PCR and massive parallel sequencing. The data revealed strong effects of climatic region on the dominating nitrogen fixers. Specifically, nifH sequences related to Geobacter (δ-Proteobacteria) were present in high relative abundances in the nitrogen-fixing communities in the Mayrhofen and Kilpisjärvi regions, while members of the Clostridiales prevailed in the Kilpisjärvi and Ny-Ålesund regions. The bulk and rhizosphere soil as well as the endosphere communities in the Mayrhofen region were all characterized by high relative abundances of nifH sequences related to Geobacter. In contrast, the endosphere and soil (bulk or rhizosphere soil) communities in the High Arctic were highly divergent: endosphere communities in the arctic regions were shaped by Clostridium spp., while nifH sequences representing δ-Proteobacteria, β-Proteobacteria, Cyanobacteria (in Ny-Ålesund), and Verrucomicrobia (in Kilpisjärvi) dominated the soil communities. Interestingly, the major PNFB genera identified in this study have been previously identified as members of conserved core microbiomes in the endospheres and seeds of these plants by 16S rRNA gene based analyses combined with bacterial isolation, suggesting a very tight interaction between diazotrophic bacteria and these arctic pioneer plants. Overall, anaerobic bacterial taxa dominated the PNFB communities of the endospheres and rhizospheres of the two plant species in all study sites. This could indicate anoxic conditions in and around plant roots at the time of sampling (early growth season), created by melting snow and underlying permafrost.}, }
@article {pmid29080910, year = {2018}, author = {Russo, CD and Weller, DW and Nelson, KE and Chivers, SJ and Torralba, M and Grimes, DJ}, title = {Bacterial Species Identified on the Skin of Bottlenose Dolphins Off Southern California via Next Generation Sequencing Techniques.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {303-309}, pmid = {29080910}, issn = {1432-184X}, support = {M10AF20151//Bureau of Ocean Energy Management/ ; Scientific Research Permit No. 774-1714//National Marine Fisheries Service/ ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Bottle-Nosed Dolphin/*microbiology ; California ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Skin/*microbiology ; }, abstract = {The dermis of cetaceans is in constant contact with microbial species. Although the skin of the bottlenose dolphin provides adequate defense against most disease-causing microbes, it also provides an environment for microbial community development. Microbial community uniqueness and richness associated with bottlenose dolphin skin is a function of varying habitats and changing environmental conditions. The current study uses ribosomal DNA as a marker to identify bacteria found on the skin of coastal and offshore bottlenose dolphins off of Southern California. The unique microbial communities recovered from these dolphins suggest a greater microbial diversity on the skin of offshore ecotype bottlenose dolphins, while microbial populations associated with the coastal ecotype include species that are more closely related to each other and that suggest exposure to communities that are likely to be associated with terrestrial runoff.}, }
@article {pmid29080101, year = {2018}, author = {Schwarz, A and Adetutu, EM and Juhasz, AL and Aburto-Medina, A and Ball, AS and Shahsavari, E}, title = {Microbial Degradation of Phenanthrene in Pristine and Contaminated Sandy Soils.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {888-902}, pmid = {29080101}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/metabolism ; Biodegradation, Environmental ; Biodiversity ; Biphenyl Compounds/*metabolism ; Carbamates/*metabolism ; Fungi/classification/genetics/metabolism ; Genes, rRNA/genetics ; Isotope Labeling/methods ; Microbiota/genetics/*physiology ; Niacinamide/*analogs &amp; derivatives/metabolism ; Phenanthrenes/*metabolism ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/metabolism ; Pyrazoles/*metabolism ; Soil ; *Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {Phenanthrene mineralisation studies in both pristine and contaminated sandy soils were undertaken through detailed assessment of the activity and diversity of the microbial community. Stable isotope probing (SIP) was used to assess and identify active [13]C-labelled phenanthrene degraders. Baseline profiling indicated that there was little difference in fungal diversity but a significant difference in bacterial diversity dependent on contamination history. Identification of dominant fungal and bacterial species highlighted the presence of organisms capable of degrading various petroleum-based compounds together with other anthropogenic compounds, regardless of contamination history. Community response following a simulated contamination event ([14]C-phenanthrene) showed that the microbial community in deep pristine and shallow contaminated soils adapted most to the presence of phenanthrene. The similarity in microbial community structure of well-adapted soils demonstrated that a highly adaptable fungal community in these soils enabled a rapid response to the introduction of a contaminant. Ten fungal and 15 bacterial species were identified as active degraders of phenanthrene. The fungal degraders were dominated by the phylum Basidiomycota including the genus Crypotococcus, Cladosporium and Tremellales. Bacterial degraders included the genera Alcanivorax, Marinobacter and Enterococcus. There was little synergy between dominant baseline microbes, predicted degraders and those that were determined to be actually degrading the contaminant. Overall, assessment of baseline microbial community in contaminated soils provides useful information; however, additional laboratory assessment of the microbial community's ability to degrade pollutants allows for better prediction of the bioremediation potential of a soil.}, }
@article {pmid29079629, year = {2018}, author = {Cheng, X and Redanz, S and Cullin, N and Zhou, X and Xu, X and Joshi, V and Koley, D and Merritt, J and Kreth, J}, title = {Plasticity of the Pyruvate Node Modulates Hydrogen Peroxide Production and Acid Tolerance in Multiple Oral Streptococci.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {2}, pages = {}, pmid = {29079629}, issn = {1098-5336}, support = {R01 DE018893/DE/NIDCR NIH HHS/United States ; R01 DE021726/DE/NIDCR NIH HHS/United States ; R01 DE022083/DE/NIDCR NIH HHS/United States ; }, mesh = {Acids/*pharmacology ; Bacterial Proteins/metabolism ; Biofilms ; Dental Caries/microbiology ; Dental Plaque/*microbiology ; Humans ; Hydrogen Peroxide/analysis/*metabolism ; Hydrogen-Ion Concentration ; Mouth/microbiology ; Pyruvic Acid/*metabolism ; Streptococcus/*drug effects/*metabolism ; Streptococcus gordonii/metabolism ; Streptococcus mutans/metabolism ; Streptococcus sanguis/metabolism ; Stress, Physiological/drug effects ; }, abstract = {Commensal Streptococcus sanguinis and Streptococcus gordonii are pioneer oral biofilm colonizers. Characteristic for both is the SpxB-dependent production of H2O2, which is crucial for inhibiting competing biofilm members, especially the cariogenic species Streptococcus mutans H2O2 production is strongly affected by environmental conditions, but few mechanisms are known. Dental plaque pH is one of the key parameters dictating dental plaque ecology and ultimately oral health status. Therefore, the objective of the current study was to characterize the effects of environmental pH on H2O2 production by S. sanguinis and S. gordoniiS. sanguinis H2O2 production was not found to be affected by moderate changes in environmental pH, whereas S. gordonii H2O2 production declined markedly in response to lower pH. Further investigation into the pyruvate node, the central metabolic switch modulating H2O2 or lactic acid production, revealed increased lactic acid levels for S. gordonii at pH 6. The bias for lactic acid production at pH 6 resulted in concomitant improvement in the survival of S. gordonii at low pH and seems to constitute part of the acid tolerance response of S. gordonii Differential responses to pH similarly affect other oral streptococcal species, suggesting that the observed results are part of a larger phenomenon linking environmental pH, central metabolism, and the capacity to produce antagonistic amounts of H2O2IMPORTANCE Oral biofilms are subject to frequent and dramatic changes in pH. S. sanguinis and S. gordonii can compete with caries- and periodontitis-associated pathogens by generating H2O2 Therefore, it is crucial to understand how S. sanguinis and S. gordonii adapt to low pH and maintain their competitiveness under acid stress. The present study provides evidence that certain oral bacteria respond to environmental pH changes by tuning their metabolic output in favor of lactic acid production, to increase their acid survival, while others maintain their H2O2 production at a constant level. The differential control of H2O2 production provides important insights into the role of environmental conditions for growth competition of the oral flora.}, }
@article {pmid29077733, year = {2017}, author = {Ghodsalavi, B and Svenningsen, NB and Hao, X and Olsson, S and Nicolaisen, MH and Al-Soud, WA and Sørensen, SJ and Nybroe, O}, title = {A novel baiting microcosm approach used to identify the bacterial community associated with Penicillium bilaii hyphae in soil.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0187116}, pmid = {29077733}, issn = {1932-6203}, mesh = {*Genes, Fungal ; Penicillium/genetics/*isolation &amp; purification ; *Soil Microbiology ; }, abstract = {It is important to identify and recover bacteria associating with fungi under natural soil conditions to enable eco-physiological studies, and to facilitate the use of bacterial-fungal consortia in environmental biotechnology. We have developed a novel type of baiting microcosm, where fungal hyphae interact with bacteria under close-to-natural soil conditions; an advantage compared to model systems that determine fungal influences on bacterial communities in laboratory media. In the current approach, the hyphae are placed on a solid support, which enables the recovery of hyphae with associated bacteria in contrast to model systems that compare bulk soil and mycosphere soil. We used the baiting microcosm approach to determine, for the first time, the composition of the bacterial community associating in the soil with hyphae of the phosphate-solubilizer, Penicillium bilaii. By applying a cultivation-independent 16S rRNA gene-targeted amplicon sequencing approach, we found a hypha-associated bacterial community with low diversity compared to the bulk soil community and exhibiting massive dominance of Burkholderia OTUs. Burkholderia is known be abundant in soil environments affected by fungi, but the discovery of this massive dominance among bacteria firmly associating with hyphae in soil is novel and made possible by the current bait approach.}, }
@article {pmid29075322, year = {2017}, author = {Zhou, H and Liu, B and Wang, Q and Sun, J and Xie, G and Ren, N and Ren, ZJ and Xing, D}, title = {Pulse electromagnetic fields enhance extracellular electron transfer in magnetic bioelectrochemical systems.}, journal = {Biotechnology for biofuels}, volume = {10}, number = {}, pages = {238}, pmid = {29075322}, issn = {1754-6834}, abstract = {BACKGROUND: Microbial extracellular electron transfer (EET) is essential in driving the microbial interspecies interaction and redox reactions in bioelectrochemical systems (BESs). Magnetite (Fe3O4) and magnetic fields (MFs) were recently reported to promote microbial EET, but the mechanisms of MFs stimulation of EET and current generation in BESs are not known. This study investigates the behavior of current generation and EET in a state-of-the-art pulse electromagnetic field (PEMF)-assisted magnetic BES (PEMF-MBES), which was equipped with magnetic carbon particle (Fe3O4@N-mC)-coated electrodes. Illumina Miseq sequencing of 16S rRNA gene amplicons was also conducted to reveal the changes of microbial communities and interactions on the anode in response to magnetic field.<br><br>RESULTS: PEMF had significant influences on current generation. When reactors were operated in microbial fuel cell (MFC) mode with pulse electromagnetic field (PEMF-MMFCs), power densities increased by 25.3-36.0% compared with no PEMF control MFCs (PEMF-OFF-MMFCs). More interestingly, when PEMF was removed, the power density dropped by 25.7%, while when PEMF was reintroduced, the value was restored to the previous level. Illumina sequencing of 16S rRNA gene amplicon and principal component analysis (PCA) based on operational taxonomic units (OTUs) indicate that PEMFs led to the shifts in microbial community and changes in species evenness that decreased biofilm microbial diversity. Geobacter spp. were found dominant in all anode biofilms, but the relative abundance in PEMF-MMFCs (86.1-90.0%) was higher than in PEMF-OFF-MMFCs (82.5-82.7%), indicating that the magnetic field enriched Geobacter on the anode. The current generation of Geobacter-inoculated microbial electrolysis cells (MECs) presented the same change regularity, the accordingly increase or decrease corresponding with switch of PEMF, which confirmed the reversible stimulation of PEMFs on microbial electron transfer.<br><br>CONCLUSION: The pulse electromagnetic field (PEMF) showed significant influence on sta&#xfeff;te-of-the-art pulse&#xa0;magnetic bioelectrochemical systems (PEMF-MBES) in terms of current generation and microbial ecology. EET was instantaneously and reversibly enhanced in MBESs inoculated with either mixed-culture or Geobacter. PEMF notably decreased bacterial and archaeal diversities of the anode biofilms in MMFCs via changing species evenness rather than species richness, and facilitated specific enrichment of exoelectrogenic bacteria (Geobacter) on the anode surface. This study demonstrates a new magnetic approach for understanding and facilitating microbial electrochemical activities.}, }
@article {pmid29073232, year = {2017}, author = {Tanaka, SE and Aikawa, T and Takeuchi-Kaneko, Y and Fukuda, K and Kanzaki, N}, title = {Artificial induction of third-stage dispersal juveniles of Bursaphelenchus xylophilus using newly established inbred lines.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0187127}, pmid = {29073232}, issn = {1932-6203}, mesh = {Animals ; Life Cycle Stages ; Nematoda/*growth &amp; development ; Pinus/parasitology ; }, abstract = {The pine wood nematode, Bursaphelenchus xylophilus, is the causal agent of pine wilt disease. This nematode has two developmental forms in its life cycle; i.e., the propagative and dispersal forms. The former is the form that builds up its population inside the host pine. The latter is specialized for transport by the vector. This form is separated into two dispersal stages (third and fourth); the third-stage dispersal juvenile (JIII) is specialized for survival under unfavorable conditions, whereas the fourth-stage juvenile (JIV), which is induced by a chemical signal from the carrier Monochamus beetle, is transported to new host pines and invades them. Because of its importance in the disease cycle, molecular and chemical aspects of the JIV have been investigated, while the mechanism of JIII induction has not been sufficiently investigated. In an effort to clarify the JIII induction process, we established inbred lines of B. xylophilus and compared their biological features. We found that the total number of nematodes (propagation proportion) was negatively correlated with the JIII emergence proportion, likely because nematode development was arrested at JIII; i.e., they could not develop to adults via the reproductive stage. In addition, JIII induction seemed to be regulated by a small number of genes because the JIII induction proportion varied among inbred lines despite the high homozygosity of the parental line. We also demonstrated that JIII can be artificially induced by the nematode's secreted substances. This is the first report of artificial induction of JIII in B. xylophilus. The dauer (dispersal) juvenile of the model organism Caenorhabditis elegans corresponds functionally to JIII of B. xylophilus, and this stage is known to be induced by a chemical signal referred to as daumone, derived from the nematodes' secretion. The artificial induction of JIII suggests the presence of daumone-like material in B. xylophilus.}, }
@article {pmid29073107, year = {2017}, author = {Mark Welch, JL and Hasegawa, Y and McNulty, NP and Gordon, JI and Borisy, GG}, title = {Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {43}, pages = {E9105-E9114}, pmid = {29073107}, issn = {1091-6490}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; R01 DK030292/DK/NIDDK NIH HHS/United States ; R01 DK070977/DK/NIDDK NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Colon/*diagnostic imaging/*microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; In Situ Hybridization, Fluorescence ; Intestinal Mucosa/microbiology ; Male ; Mice, Inbred C57BL ; }, abstract = {Knowledge of the spatial organization of the gut microbiota is important for understanding the physical and molecular interactions among its members. These interactions are thought to influence microbial succession, community stability, syntrophic relationships, and resiliency in the face of perturbations. The complexity and dynamism of the gut microbiota pose considerable challenges for quantitative analysis of its spatial organization. Here, we illustrate an approach for addressing this challenge, using (i) a model, defined 15-member consortium of phylogenetically diverse, sequenced human gut bacterial strains introduced into adult gnotobiotic mice fed a polysaccharide-rich diet, and (ii) in situ hybridization and spectral imaging analysis methods that allow simultaneous detection of multiple bacterial strains at multiple spatial scales. Differences in the binding affinities of strains for substrates such as mucus or food particles, combined with more rapid replication in a preferred microhabitat, could, in principle, lead to localized clonally expanded aggregates composed of one or a few taxa. However, our results reveal a colonic community that is mixed at micrometer scales, with distinct spatial distributions of some taxa relative to one another, notably at the border between the mucosa and the lumen. Our data suggest that lumen and mucosa in the proximal colon should be conceptualized not as stratified compartments but as components of an incompletely mixed bioreactor. Employing the experimental approaches described should allow direct tests of whether and how specified host and microbial factors influence the nature and functional contributions of "microscale" mixing to the dynamic operations of the microbiota in health and disease.}, }
@article {pmid29073089, year = {2017}, author = {Probst, AJ and Hu, P and Sun, CL and Dubinsky, EA and Sieber, CMK and Banfield, JF and Andersen, GL}, title = {Reply to Delmont and Eren: Strain variants and population structure during the Deepwater Horizon oil spill.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {43}, pages = {E8950-E8952}, pmid = {29073089}, issn = {1091-6490}, mesh = {Environmental Monitoring ; Gulf of Mexico ; Petroleum/*analysis ; *Petroleum Pollution ; Water Pollutants, Chemical/analysis ; }, }
@article {pmid29071368, year = {2018}, author = {Theron-De Bruin, N and Dreyer, LL and Ueckermann, EA and Wingfield, MJ and Roets, F}, title = {Birds Mediate a Fungus-Mite Mutualism.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {863-874}, pmid = {29071368}, issn = {1432-184X}, support = {na//Department of Science and Technology/National Research Foundation Centre of Excellence in Tree Health Biotechnology/ ; }, mesh = {Animals ; Arthropod Vectors/*microbiology ; Birds/*microbiology ; DNA, Fungal/analysis ; Fungi/isolation &amp; purification/*physiology ; Mites/*microbiology ; Proteaceae/microbiology ; South Africa ; Spores, Fungal ; Symbiosis/*physiology ; Trees/microbiology ; }, abstract = {Mutualisms between ophiostomatoid fungi and arthropods have been well documented. These fungi commonly aid arthropod nutrition and, in turn, are transported to new niches by these arthropods. The inflorescences of Protea trees provide a niche for a unique assemblage of ophiostomatoid fungi. Here, mites feed on Sporothrix fungi and vector the spores to new niches. Protea-pollinating beetles transport the spore-carrying mites between Protea trees. However, many Protea species are primarily pollinated by birds that potentially play a central role in the Protea-Sporothrix-mite system. To investigate the role of birds in the movement of mites and/or fungal spores, mites were collected from Protea inflorescences and cape sugarbirds, screened for Sporothrix fungal spores and tested for their ability to feed and reproduce on the fungal associates. Two mite species where abundant in both Protea inflorescences and on cape sugarbirds and regularly carried Sporothrix fungal spores. One of these mite species readily fed and reproduced on its transported fungal partner. For dispersal, this mite (a Glycyphagus sp.) attached to a larger mite species (Proctolaelaps vandenbergi) which, in turn, were carried by the birds to new inflorescences. The results of this study provide compelling evidence for a new mite-fungus mutualism, new mite-mite commensalisms and the first evidence of birds transporting mites with Sporothrix fungal spores to colonise new Protea trees.}, }
@article {pmid29071172, year = {2017}, author = {Roopnarain, A and Mukhuba, M and Adeleke, R and Moeletsi, M}, title = {Biases during DNA extraction affect bacterial and archaeal community profile of anaerobic digestion samples.}, journal = {3 Biotech}, volume = {7}, number = {6}, pages = {375}, pmid = {29071172}, issn = {2190-572X}, abstract = {The anaerobic digestion (AD) of organic waste for biogas production has received much attention in recent years due to the increasing need for renewable energy and environmentally friendly waste management systems. Identification of the microbial community involved in AD aids in better understanding and optimising of the process. The choice of DNA extraction method is an integral step in any molecular biodiversity study. In the present study, potential biases introduced by DNA extraction methods were examined by comparing quality, quantity and representability of DNA extracted from AD samples using various extraction methods. In spite of the non-kit based method (cetyltrimethylammonium bromide) yielding the largest quantity of DNA (approximately 44 µg DNA per gram dry weight), the extracted DNA contained PCR inhibitors. Furthermore, the quantity of extracted DNA was not proportional to species diversity. Diversity, determined using denaturing gradient gel electrophoresis (DGGE), was strongly linked to the type of extraction method used. The spin-column filter-based kit that incorporated mechanical and chemical lysis (Macherey-Nagel kit) gave the best results in terms of bacterial and archaeal diversity (Shannon-Wiener indices: average 2.5 and 2.6, respectively). Furthermore, this kit was the most effective at lysing hard-to-lyse bacterial and archaeal cells. The choice of DNA extraction method significantly influences the reliability and comparability of results obtained during AD microbial ecology investigations. Moreover, the careful selection of the DNA extraction method is of particular importance when analysing AD samples since these samples are rich in PCR inhibitors and hard-to-lyse cells such as archaea and gram-positive bacteria.}, }
@article {pmid29069382, year = {2018}, author = {Bengtsson-Palme, J and Kristiansson, E and Larsson, DGJ}, title = {Environmental factors influencing the development and spread of antibiotic resistance.}, journal = {FEMS microbiology reviews}, volume = {42}, number = {1}, pages = {}, pmid = {29069382}, issn = {1574-6976}, mesh = {Bacterial Physiological Phenomena/*genetics ; Drug Resistance, Microbial/*genetics ; *Environment ; *Evolution, Molecular ; }, abstract = {Antibiotic resistance and its wider implications present us with a growing healthcare crisis. Recent research points to the environment as an important component for the transmission of resistant bacteria and in the emergence of resistant pathogens. However, a deeper understanding of the evolutionary and ecological processes that lead to clinical appearance of resistance genes is still lacking, as is knowledge of environmental dispersal barriers. This calls for better models of how resistance genes evolve, are mobilized, transferred and disseminated in the environment. Here, we attempt to define the ecological and evolutionary environmental factors that contribute to resistance development and transmission. Although mobilization of resistance genes likely occurs continuously, the great majority of such genetic events do not lead to the establishment of novel resistance factors in bacterial populations, unless there is a selection pressure for maintaining them or their fitness costs are negligible. To enable preventative measures it is therefore critical to investigate under what conditions and to what extent environmental selection for resistance takes place. In addition, understanding dispersal barriers is not only key to evaluate risks, but also to prevent resistant pathogens, as well as novel resistance genes, from reaching humans.}, }
@article {pmid29067002, year = {2017}, author = {Cortes-Tolalpa, L and Salles, JF and van Elsas, JD}, title = {Bacterial Synergism in Lignocellulose Biomass Degradation - Complementary Roles of Degraders As Influenced by Complexity of the Carbon Source.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1628}, pmid = {29067002}, issn = {1664-302X}, abstract = {Lignocellulosic biomass (LCB) is an attractive source of carbon for the production of sugars and other chemicals. Due to its inherent complexity and heterogeneity, efficient biodegradation requires the actions of different types of hydrolytic enzymes. In nature, complex microbial communities that work efficiently and often synergistically accomplish degradation. Studying such synergisms in LCB degradation is fundamental for the establishment of an optimal biological degradation process. Here, we examine the wheat straw degradation potential of synthetic microbial consortia composed of bacteria and fungi. Growth of, and enzyme secretion by, monocultures of degrader strains were studied in aerobic cultures using wheat straw as the sole carbon and energy source. To investigate synergism, co-cultures were constructed from selected strains and their performance was tested in comparison with the respective monocultures. In monoculture, each organism - with a typical enzymatic profile - was found to mainly consume the cellulose part of the substrate. One strain, Flavobacterium ginsengisoli so9, displayed an extremely high degradation capacity, as measured by its secreted enzymes. Among 13 different co-cultures, five presented synergisms. These included four bacterial bicultures and one bacterial-fungal triculture. The highest level of synergism was found in a Citrobacter freundii/Sphingobacterium multivorum biculture, which revealed an 18.2-fold increase of the produced biomass. As compared to both monocultures, this bacterial pair showed significantly increased enzymatic activities, in particular of cellobiohydrolases, mannosidases, and xylosidases. Moreover, the synergism was unique to growth on wheat straw, as it was completely absent in glucose-grown bicultures. Spent supernatants of either of the two partners were found to stimulate the growth on wheat straw of the counterpart organism, in a directional manner. Thus, the basis of the LCB-specific synergism might lie in the specific release of compounds or agents by S. multivorum w15 that promote the activity of C. freundii so4 and vice versa.}, }
@article {pmid29066578, year = {2017}, author = {Hayase, E and Hashimoto, D and Nakamura, K and Noizat, C and Ogasawara, R and Takahashi, S and Ohigashi, H and Yokoi, Y and Sugimoto, R and Matsuoka, S and Ara, T and Yokoyama, E and Yamakawa, T and Ebata, K and Kondo, T and Hiramine, R and Aizawa, T and Ogura, Y and Hayashi, T and Mori, H and Kurokawa, K and Tomizuka, K and Ayabe, T and Teshima, T}, title = {R-Spondin1 expands Paneth cells and prevents dysbiosis induced by graft-versus-host disease.}, journal = {The Journal of experimental medicine}, volume = {214}, number = {12}, pages = {3507-3518}, pmid = {29066578}, issn = {1540-9538}, mesh = {Administration, Oral ; Animals ; Bacteria/metabolism ; Cell Differentiation/drug effects ; Cytoprotection/drug effects ; Dysbiosis/*etiology/pathology/*prevention &amp; control ; Female ; Graft vs Host Disease/*complications/pathology ; Humans ; Intestines/pathology ; Mice, Inbred C57BL ; Paneth Cells/drug effects/metabolism/*pathology ; Recombinant Proteins/administration &amp; dosage/pharmacology/therapeutic use ; Stem Cell Transplantation ; Stem Cells/drug effects/metabolism ; Thrombospondins/*pharmacology/*therapeutic use ; alpha-Defensins/metabolism ; }, abstract = {The intestinal microbial ecosystem is actively regulated by Paneth cell-derived antimicrobial peptides such as α-defensins. Various disorders, including graft-versus-host disease (GVHD), disrupt Paneth cell functions, resulting in unfavorably altered intestinal microbiota (dysbiosis), which further accelerates the underlying diseases. Current strategies to restore the gut ecosystem are bacteriotherapy such as fecal microbiota transplantation and probiotics, and no physiological approach has been developed so far. In this study, we demonstrate a novel approach to restore gut microbial ecology by Wnt agonist R-Spondin1 (R-Spo1) or recombinant α-defensin in mice. R-Spo1 stimulates intestinal stem cells to differentiate to Paneth cells and enhances luminal secretion of α-defensins. Administration of R-Spo1 or recombinant α-defensin prevents GVHD-mediated dysbiosis, thus representing a novel and physiological approach at modifying the gut ecosystem to restore intestinal homeostasis and host-microbiota cross talk toward therapeutic benefits.}, }
@article {pmid29066255, year = {2018}, author = {Gonzalez, OA and Kirakodu, S and Novak, MJ and Stromberg, AJ and Orraca, L and Gonzalez-Martinez, J and Burgos, A and Ebersole, JL}, title = {Comparative analysis of microbial sensing molecules in mucosal tissues with aging.}, journal = {Immunobiology}, volume = {223}, number = {3}, pages = {279-287}, pmid = {29066255}, issn = {1878-3279}, support = {UL1 TR000117/TR/NCATS NIH HHS/United States ; P20 RR020145/RR/NCRR NIH HHS/United States ; P40 RR003640/RR/NCRR NIH HHS/United States ; P20 GM103538/GM/NIGMS NIH HHS/United States ; P40 OD012217/OD/NIH HHS/United States ; P30 GM110788/GM/NIGMS NIH HHS/United States ; P20 GM103436/GM/NIGMS NIH HHS/United States ; }, mesh = {Aging/*immunology ; Animals ; Gingiva/immunology ; Gingivitis/*immunology ; Homeostasis ; Host-Pathogen Interactions ; Humans ; Macaca mulatta ; Microarray Analysis ; Models, Animal ; Mouth Mucosa/*immunology ; Pathogen-Associated Molecular Pattern Molecules/immunology ; Periodontitis/*immunology ; Receptors, Pattern Recognition/genetics/*metabolism ; Transcriptome ; }, abstract = {Host-bacterial interactions at mucosal surfaces require recognition of the bacteria by host cells enabling targeted responses to maintain tissue homeostasis. It is now well recognized that an array of host-derived pattern recognition receptors (PRRs), both cell-bound and soluble, are critical to innate immune engagement of microbes via microbial-associated molecular patterns (MAMP). This report describes the use of a nonhuman primate model to evaluate changes in the expression of these sensing molecules related to aging in healthy gingival tissues. Macaca mulatta aged 3-24 years were evaluated clinically and gingival tissues obtained, RNA isolated and microarray analysis conducted for gene expression of the sensing pattern recognition receptors (PRRs). The results demonstrated increased expression of various PRRs in healthy aging gingiva including extracellular (CD14, CD209, CLEC4E, TLR4), intracellular (NAIP, IFIH1, DAI) and soluble (PTX4, SAA1) PRRs. Selected PRRs were also correlated with both bleeding on probing (BOP) and pocket depth (PD) in the animals. These findings suggest that aged animals express altered levels of various PRRs that could affect the ability of the tissues to interact effectively with the juxtaposed microbial ecology, presumably contributing to an enhanced risk of periodontitis even in clinically healthy oral mucosal tissues with aging.}, }
@article {pmid29064247, year = {2017}, author = {Watts, MP and Gan, HM and Peng, LY and Lê Cao, KA and Moreau, JW}, title = {In Situ Stimulation of Thiocyanate Biodegradation through Phosphate Amendment in Gold Mine Tailings Water.}, journal = {Environmental science &amp; technology}, volume = {51}, number = {22}, pages = {13353-13362}, doi = {10.1021/acs.est.7b04152}, pmid = {29064247}, issn = {1520-5851}, mesh = {*Biodegradation, Environmental ; *Gold ; Mining ; Phosphates ; *Thiocyanates ; }, abstract = {Thiocyanate (SCN[-]) is a contaminant requiring remediation in gold mine tailings and wastewaters globally. Seepage of SCN[-]-contaminated waters into aquifers can occur from unlined or structurally compromised mine tailings storage facilities. A wide variety of microorganisms are known to be capable of biodegrading SCN[-]; however, little is known regarding the potential of native microbes for in situ SCN[-] biodegradation, a remediation option that is less costly than engineered approaches. Here we experimentally characterize the principal biogeochemical barrier to SCN[-] biodegradation for an autotrophic microbial consortium enriched from mine tailings, to arrive at an environmentally realistic assessment of in situ SCN[-] biodegradation potential. Upon amendment with phosphate, the consortium completely degraded up to ∼10 mM SCN[-] to ammonium and sulfate, with some evidence of nitrification of the ammonium to nitrate. Although similarly enriched in known SCN[-]-degrading strains of thiobacilli, this consortium differed in its source (mine tailings) and metabolism (autotrophy) from those of previous studies. Our results provide a proof of concept that phosphate limitation may be the principal barrier to in situ SCN[-] biodegradation in mine tailing waters and also yield new insights into the microbial ecology of in situ SCN[-] bioremediation involving autotrophic sulfur-oxidizing bacteria.}, }
@article {pmid29063148, year = {2018}, author = {Marcos, MS and Barboza, AD and Keijzer, RM and Laanbroek, HJ}, title = {Tide as Steering Factor in Structuring Archaeal and Bacterial Ammonia-Oxidizing Communities in Mangrove Forest Soils Dominated by Avicennia germinans and Rhizophora mangle.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {997-1008}, pmid = {29063148}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*metabolism ; Avicennia/*microbiology ; Bacteria/classification/genetics/*metabolism ; Florida ; Genes, Archaeal/genetics ; Genes, Bacterial/genetics ; Metagenomics ; Microbiota/*physiology ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizophoraceae/*microbiology ; Soil/chemistry ; *Soil Microbiology ; *Wetlands ; }, abstract = {Mangrove species are adapted to grow at specific zones in a tidal gradient. Here we tested the hypothesis that the archaeal and bacterial ammonia-oxidizing microbial communities differ in soils dominated by the mangrove species Avicennia germinans and Rhizophora mangle. Two of the sampling locations were tidal locations, while the other location was impounded. Differences in the community compositions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were analyzed by denaturing gradient gel electrophoresis (DGGE) of amoA genes and by MiSeq 16S rRNA gene-sequencing. The abundances of AOA and AOB were established by quantitative PCR of amoA genes. In addition, we analyzed the total microbial community composition based on 16S rRNA genes and explored the influence of soil physicochemical properties underneath Avicennia germinans and Rhizophora mangle on microbial communities. AOA were always more abundant than AOB, but the effect of mangrove species on total numbers of ammonia oxidizers was location-specific. The microbial communities including the ammonia oxidizers in soils associated with A. germinans and R. mangle differed only at the tidal locations. In conclusion, potential site-specific effects of mangrove species on soil microbial communities including those of the AOA and AOB are apparently overruled by the absence or presence of tide.}, }
@article {pmid29063147, year = {2018}, author = {Roguet, A and Therial, C and Catherine, A and Bressy, A and Varrault, G and Bouhdamane, L and Tran, V and Lemaire, BJ and Vincon-Leite, B and Saad, M and Moulin, L and Lucas, FS}, title = {Importance of Local and Regional Scales in Shaping Mycobacterial Abundance in Freshwater Lakes.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {834-846}, pmid = {29063147}, issn = {1432-184X}, support = {ANR-10-CEPL-010//Agence Nationale de la Recherche (ANR)/ ; }, mesh = {Bacterial Load ; Bacterial Proton-Translocating ATPases/genetics ; *Biodiversity ; DNA, Bacterial/genetics ; *Ecosystem ; Environmental Monitoring ; Geologic Sediments/microbiology ; Lakes/chemistry/*microbiology ; *Mycobacterium/classification/genetics ; Nontuberculous Mycobacteria/classification/genetics ; Paris ; Real-Time Polymerase Chain Reaction ; Rivers/microbiology ; Seasons ; *Water Microbiology ; }, abstract = {Biogeographical studies considering the entire bacterial community may underestimate mechanisms of bacterial assemblages at lower taxonomic levels. In this context, the study aimed to identify factors affecting the spatial and temporal dynamic of the Mycobacterium, a genus widespread in aquatic ecosystems. Nontuberculous mycobacteria (NTM) density variations were quantified in the water column of freshwater lakes at the regional scale (annual monitoring of 49 lakes in the Paris area) and at the local scale (2-year monthly monitoring in Créteil Lake) by real-time quantitative PCR targeting the atpE gene. At the regional scale, mycobacteria densities in water samples ranged from 6.7 × 10[3] to 1.9 × 10[8] genome units per liter. Density variations were primarily explained by water pH, labile iron, and dispersal processes through the connection of the lakes to a river. In Créteil Lake, no spatial variation of mycobacterial densities was noticed over the 2-year monthly survey, except after large rainfall events. Indeed, storm sewer effluents locally and temporarily increased NTM densities in the water column. The temporal dynamic of the NTM densities in Créteil Lake was associated with suspended solid concentrations. No clear seasonal variation was noticed despite a shift in NTM densities observed over the 2012-2013 winter. Temporal NTM densities fluctuations were well predicted by the neutral community model, suggesting a random balance between loss and gain of mycobacterial taxa within Créteil Lake. This study highlights the importance of considering multiple spatial scales for understanding the spatio-temporal dynamic of bacterial populations in natural environments.}, }
@article {pmid29062312, year = {2017}, author = {Garbisu, C and Garaiyurrebaso, O and Epelde, L and Grohmann, E and Alkorta, I}, title = {Plasmid-Mediated Bioaugmentation for the Bioremediation of Contaminated Soils.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1966}, pmid = {29062312}, issn = {1664-302X}, abstract = {Bioaugmentation, or the inoculation of microorganisms (e.g., bacteria harboring the required catabolic genes) into soil to enhance the rate of contaminant degradation, has great potential for the bioremediation of soils contaminated with organic compounds. Regrettably, cell bioaugmentation frequently turns into an unsuccessful initiative, owing to the rapid decrease of bacterial viability and abundance after inoculation, as well as the limited dispersal of the inoculated bacteria in the soil matrix. Genes that encode the degradation of organic compounds are often located on plasmids and, consequently, they can be spread by horizontal gene transfer into well-established, ecologically competitive, indigenous bacterial populations. Plasmid-mediated bioaugmentation aims to stimulate the spread of contaminant degradation genes among indigenous soil bacteria by the introduction of plasmids, located in donor cells, harboring such genes. But the acquisition of plasmids by recipient cells can affect the host's fitness, a crucial aspect for the success of plasmid-mediated bioaugmentation. Besides, environmental factors (e.g., soil moisture, temperature, organic matter content) can play important roles for the transfer efficiency of catabolic plasmids, the expression of horizontally acquired genes and, finally, the contaminant degradation activity. For plasmid-mediated bioaugmentation to be reproducible, much more research is needed for a better selection of donor bacterial strains and accompanying plasmids, together with an in-depth understanding of indigenous soil bacterial populations and the environmental conditions that affect plasmid acquisition and the expression and functioning of the catabolic genes of interest.}, }
@article {pmid29059507, year = {2017}, author = {Beaudry, FEG and Iwanicki, TW and Mariluz, BRZ and Darnet, S and Brinkmann, H and Schneider, P and Taylor, JS}, title = {The non-visual opsins: eighteen in the ancestor of vertebrates, astonishing increase in ray-finned fish, and loss in amniotes.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {328}, number = {7}, pages = {685-696}, doi = {10.1002/jez.b.22773}, pmid = {29059507}, issn = {1552-5015}, mesh = {Animals ; *Biological Evolution ; Fishes/*genetics ; Gene Expression Regulation/physiology ; Opsins/genetics/*metabolism ; }, abstract = {Non-visual opsins were discovered in the early 1990s. These genes play roles in circadian rhythm in mammals, seasonal reproduction in birds, light avoidance in amphibian larvae, and neural development in fish. However, the interpretation of such studies and the success of future work are compromised by the fact that non-visual opsin repertoires have not been properly characterized in any of these lineages. Here, we show that non-visual opsins from tetrapods and ray-finned fish are distributed among 18 monophyletic subfamilies. An amphibian sequence occurs in every subfamily, whereas mammalian orthologs occur in only seven. Species in the major ray-finned fish lineages, Holostei, Osteoglossomorpha, Otomorpha, Protacanthopterygii, and Neoteleostei, have large numbers of non-visual opsins (22-32 genes) as a result of gene duplication events including, but not limited to, the teleost genome duplication (TGD). In contrast to visual opsins, where lineage-specific duplication is common, the ray-finned fish non-visual opsin repertoire appears to have stabilized shortly after the TGD event and consequently even distantly related species have repertoires of similar size and composition. Most non-visual opsins have been named without the benefit of a phylogenetic perspective and, accordingly, major revisions are proposed.}, }
@article {pmid29057500, year = {2018}, author = {Wang, L and Wu, D and Yan, T and Wang, L}, title = {The impact of rumen cannulation on the microbial community of goat rumens as measured using 16S rRNA high-throughput sequencing.}, journal = {Journal of animal physiology and animal nutrition}, volume = {102}, number = {1}, pages = {175-183}, doi = {10.1111/jpn.12676}, pmid = {29057500}, issn = {1439-0396}, mesh = {Animals ; Bacteria/classification/*genetics/isolation &amp; purification ; Catheterization ; Goats/*microbiology/physiology ; *High-Throughput Nucleotide Sequencing ; Male ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; Rumen/*microbiology ; }, abstract = {The main objective of this study was to determine the impact of rumen cannulation on the microbial community of goat rumens using 16S rRNA high-throughput sequencing. Twelve Boer crossbred goats were used in the experiment: six goats were surgically fitted with rumen cannula, and the other six were used as controls. All goats were fed the same diet for 20 days, after which their rumen digesta were sampled once per week for three consecutive weeks. Total microbial DNA was extracted from the collected rumen fluid and was used as a template to amplify the V4 hypervariable region of the 16S rRNA gene. High-throughput sequencing was performed using an Illumina MiSeq platform, and the sequences were analyzed primarily using the Quantitative Insights into Microbial Ecology pipeline software. The results showed that the Chao 1 index, the observed species index and the Shannon-Wiener index were not significantly different (p > 0.05) between the two groups. Bacteroidetes, Firmicutes, Tenericutes were the predominant phylum in both groups, and their relative abundance was 60.63%, 29.48%, 2.24% (n = 6, CT group) and 61.17%, 26.92%, 1.66% (n = 6, RC group) respectively. At the phylum level, the relative abundance of Proteobacteria was significantly higher (p < 0.001) in the microbial communities of RC goats, and Planctomycetes and Chloroflexi were significantly lower (p = 0.02). The abundances of other phyla were not significantly different between treatments. A total of 19 lower-level taxa also exhibited significant differences (p < 0.05) in relative abundance between the groups. In addition, there were 18 genera shared within the control group, 26 shared within the rumen-cannulated group, and 16 shared by both groups. Prevotella was the most abundant shared genus, although its abundance was not significantly different (p > 0.05) between the groups. In conclusion, although the most abundant microbes kept stable, rumen cannulation had the potential to significantly change rumen microbial communities in goats.}, }
@article {pmid29056457, year = {2017}, author = {Singh, PK and Bartalomej, S and Hartmann, R and Jeckel, H and Vidakovic, L and Nadell, CD and Drescher, K}, title = {Vibrio cholerae Combines Individual and Collective Sensing to Trigger Biofilm Dispersal.}, journal = {Current biology : CB}, volume = {27}, number = {21}, pages = {3359-3366.e7}, pmid = {29056457}, issn = {1879-0445}, mesh = {Bacterial Proteins/metabolism ; Biofilms/*growth &amp; development ; Biological Transport/physiology ; Gene Expression Regulation, Bacterial ; Quorum Sensing/*physiology ; Sigma Factor/metabolism ; Starvation/*metabolism ; Vibrio cholerae/*growth &amp; development/physiology ; }, abstract = {Bacteria can generate benefits for themselves and their kin by living in multicellular, matrix-enclosed communities, termed biofilms, which are fundamental to microbial ecology and the impact bacteria have on the environment, infections, and industry [1-6]. The advantages of the biofilm mode of life include increased stress resistance and access to concentrated nutrient sources [3, 7, 8]. However, there are also costs associated with biofilm growth, including the metabolic burden of biofilm matrix production, increased resource competition, and limited mobility inside the community [9-11]. The decision-making strategies used by bacteria to weigh the costs between remaining in a biofilm or actively dispersing are largely unclear, even though the dispersal transition is a central aspect of the biofilm life cycle and critical for infection transmission [12-14]. Using a combination of genetic and novel single-cell imaging approaches, we show that Vibrio cholerae integrates dual sensory inputs to control the dispersal response: cells use the general stress response, which can be induced via starvation, and they also integrate information about the local cell density and molecular transport conditions in the environment via the quorum sensing apparatus. By combining information from individual (stress response) and collective (quorum sensing) avenues of sensory input, biofilm-dwelling bacteria can make robust decisions to disperse from large biofilms under distress, while preventing premature dispersal when biofilm populations are small. These insights into triggers and regulators of biofilm dispersal are a key step toward actively inducing biofilm dispersal for technological and medical applications, and for environmental control of biofilms.}, }
@article {pmid29054869, year = {2018}, author = {Kevorkian, R and Bird, JT and Shumaker, A and Lloyd, KG}, title = {Estimating Population Turnover Rates by Relative Quantification Methods Reveals Microbial Dynamics in Marine Sediment.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {1}, pages = {}, pmid = {29054869}, issn = {1098-5336}, mesh = {Archaea/*physiology ; Bacterial Physiological Phenomena ; Geologic Sediments/*microbiology ; North Carolina ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Real-Time Polymerase Chain Reaction/*methods ; Seawater/*microbiology ; }, abstract = {The difficulty involved in quantifying biogeochemically significant microbes in marine sediments limits our ability to assess interspecific interactions, population turnover times, and niches of uncultured taxa. We incubated surface sediments from Cape Lookout Bight, North Carolina, USA, anoxically at 21°C for 122 days. Sulfate decreased until day 68, after which methane increased, with hydrogen concentrations consistent with the predicted values of an electron donor exerting thermodynamic control. We measured turnover times using two relative quantification methods, quantitative PCR (qPCR) and the product of 16S gene read abundance and total cell abundance (FRAxC, which stands for "fraction of read abundance times cells"), to estimate the population turnover rates of uncultured clades. Most 16S rRNA reads were from deeply branching uncultured groups, and ∼98% of 16S rRNA genes did not abruptly shift in relative abundance when sulfate reduction gave way to methanogenesis. Uncultured Methanomicrobiales and Methanosarcinales increased at the onset of methanogenesis with population turnover times estimated from qPCR at 9.7 ± 3.9 and 12.6 ± 4.1 days, respectively. These were consistent with FRAxC turnover times of 9.4 ± 5.8 and 9.2 ± 3.5 days, respectively. Uncultured Syntrophaceae, which are possibly fermentative syntrophs of methanogens, and uncultured Kazan-3A-21 archaea also increased at the onset of methanogenesis, with FRAxC turnover times of 14.7 ± 6.9 and 10.6 ± 3.6 days. Kazan-3A-21 may therefore either perform methanogenesis or form a fermentative syntrophy with methanogens. Three genera of sulfate-reducing bacteria, Desulfovibrio, Desulfobacter, and Desulfobacterium, increased in the first 19 days before declining rapidly during sulfate reduction. We conclude that population turnover times on the order of days can be measured robustly in organic-rich marine sediment, and the transition from sulfate-reducing to methanogenic conditions stimulates growth only in a few clades directly involved in methanogenesis, rather than in the whole microbial community.IMPORTANCE Many microbes cannot be isolated in pure culture to determine their preferential growth conditions and predict their response to changing environmental conditions. We created a microcosm of marine sediments that allowed us to simulate a diagenetic profile using a temporal analog for depth. This allowed for the observation of the microbial community population dynamics caused by the natural shift from sulfate reduction to methanogenesis. Our research provides evidence for the population dynamics of uncultured microbes as well as the application of a novel method of turnover rate analysis for individual taxa within a mixed incubation, FRAxC, which stands for "fraction of read abundance times cells," which was verified by quantitative PCR. This allows for the calculation of population turnover times for microbes in a natural setting and the identification of uncultured clades involved in geochemical processes.}, }
@article {pmid29054674, year = {2018}, author = {Jurburg, SD and Natal-da-Luz, T and Raimundo, J and Morais, PV and Sousa, JP and van Elsas, JD and Salles, JF}, title = {Bacterial communities in soil become sensitive to drought under intensive grazing.}, journal = {The Science of the total environment}, volume = {618}, number = {}, pages = {1638-1646}, doi = {10.1016/j.scitotenv.2017.10.012}, pmid = {29054674}, issn = {1879-1026}, mesh = {Bacteria/classification ; Biota ; Climate Change ; *Droughts ; Ecosystem ; *Environmental Monitoring ; *Herbivory ; Phylogeny ; Soil ; *Soil Microbiology ; }, abstract = {Increasing climatic and anthropogenic pressures on soil ecosystems are expected to create a global patchwork of disturbance scenarios. Some regions will be strongly impacted by climate change, others by agricultural intensification, and others by both. Soil microbial communities are integral components of terrestrial ecosystems, but their responses to multiple perturbations are poorly understood. Here, we exposed soils from sustainably- or intensively-managed grasslands in an agro-silvo-pastoral oak woodland to month-long intensified drought and flood simulation treatments in a controlled mesocosm setting. We monitored the response of the bacterial communities at the end of one month as well as during the following month of recovery. The communities in sustainably-managed plots under all precipitation regimes were richer and more diverse than those in intensively-managed plots, and contained a lower proportion of rapidly-growing taxa. Soils from both land managements exhibited changes in bacterial community composition in response to flooding, but only intensively-managed soils were affected by drought. The ecologies of bacteria favored by both drought and flood point to both opportunism and stress tolerance as key traits shaping the community following disturbance. Finally, the response of several taxa (i.e. Chloracidobacteria RB41, Janthinobacterium sp.) to precipitation depended on land management, suggesting that the community itself affected individual disturbance responses. Our findings provide an in-depth view of the complexity of soil bacterial community responses to climatic and anthropogenic pressures in time, and highlight the potential of these stressors to have multiplicative effects on the soil biota.}, }
@article {pmid29054663, year = {2018}, author = {Martin, MS and Santos, IC and Carlton, DD and Stigler-Granados, P and Hildenbrand, ZL and Schug, KA}, title = {Characterization of bacterial diversity in contaminated groundwater using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.}, journal = {The Science of the total environment}, volume = {622-623}, number = {}, pages = {1562-1571}, doi = {10.1016/j.scitotenv.2017.10.027}, pmid = {29054663}, issn = {1879-1026}, mesh = {Bacteria/*classification ; DNA, Bacterial/genetics ; Drinking Water ; Groundwater/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {Groundwater is a major source for drinking water in the United States, and therefore, its quality and quantity is of extreme importance. One major concern that has emerged is the possible contamination of groundwater due to the unconventional oil and gas extraction activities. As such, the impacts of exogenous contaminants on microbial ecology is an area to be explored to understand what are the chemical and physical conditions that allow the proliferation of pathogenic bacteria and to find alternatives for water treatment by identifying organic-degrading bacteria. In this work, we assess the interplay between groundwater quality and the microbiome in contaminated groundwaters rich in hydrocarbon gases, volatile organic and inorganic compounds, and various metals. Opportunistic pathogenic bacteria, such as Aeromonas hydrophila, Bacillus cereus, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia, were identified, increasing the risk for consumption of and exposure to these contaminated groundwaters. Additionally, antimicrobial tests revealed that many of the identified bacteria were resistant to different antibiotics. The MALDI-TOF MS results were successfully confirmed with 16S rRNA gene sequencing, proving the accuracy of this high-throughput method. Collectively, these data provide a seminal understanding of the microbial populations in contaminated groundwater overlying anthropogenic activities like unconventional oil and gas development.}, }
@article {pmid29054301, year = {2017}, author = {Aguilar-Trigueros, CA and Rillig, MC and Ballhausen, MB}, title = {Environmental Filtering Is a Relic. A Response to Cadotte and Tucker.}, journal = {Trends in ecology &amp; evolution}, volume = {32}, number = {12}, pages = {882-884}, pmid = {29054301}, issn = {1872-8383}, support = {694368/ERC_/European Research Council/International ; }, mesh = {*Ecology ; *Ecosystem ; }, }
@article {pmid29051237, year = {2017}, author = {Bag, S and Ghosh, TS and Das, B}, title = {Whole-Genome Sequence of a Megasphaera elsdenii Strain Isolated from the Gut of a Healthy Indian Adult Subject.}, journal = {Genome announcements}, volume = {5}, number = {42}, pages = {}, pmid = {29051237}, issn = {2169-8287}, abstract = {Megasphaera elsdenii has been previously reported in the gut of ruminating animals. Its role as an animal probiotic is being investigated, specifically from the perspective of enhancing animal productivity. Herein, we report the draft genome sequence of M. elsdenii strain indica isolated from the stool sample of a healthy Indian subject.}, }
@article {pmid29046936, year = {2018}, author = {Nakamura, N and Tanaka, E and Tanaka, C and Takeuchi-Kaneko, Y}, title = {Localization of helotialean fungi on ectomycorrhizae of Castanopsis cuspidata visualized by in situ hybridization.}, journal = {Mycorrhiza}, volume = {28}, number = {1}, pages = {17-28}, pmid = {29046936}, issn = {1432-1890}, support = {KAKENHI Grant Number 24380081//Japan Society for the Promotion of Science/ ; }, mesh = {Ascomycota/classification/*physiology ; Fagaceae/*microbiology ; In Situ Hybridization ; Mycorrhizae/classification/*physiology ; Plant Roots/microbiology ; Trees/microbiology ; }, abstract = {Non-ectomycorrhizal fungi that associate with typical ectomycorrhizae often remain hidden, and their localization inside ectomycorrhizal (ECM) roots has remained uncharacterized. In this study, the fungal community associated with the ectomycorrhizae of Castanopsis cuspidata was investigated using a culture-dependent isolation technique. Additionally, the species composition and localization were determined using molecular techniques. The results of the isolation and identification of fungal species revealed the predominance of a few species belonging to the order Helotiales. Furthermore, the fungal community structures were significantly different depending on the taxa of the ectomycorrhiza-forming fungi. A taxon-specific probe was developed to analyze the localization of one dominant Hyaloscyphaceae (Helotiales) species in ECM tissues by in situ hybridization. Hybridization signals were detected on the surface of the fungal mantle and around the ECM fungal cells within the mantle. Hyphal penetration into ECM hyphal cells of fungal mantles was also observed. Signals were not detected in the Hartig net or plant tissues inside the mantle in healthy ectomycorrhizae. These findings suggest that the analyzed species interact not only with host plant as root endophyte but also directly with the ECM fungi.}, }
@article {pmid29041965, year = {2017}, author = {Noyes, NR and Weinroth, ME and Parker, JK and Dean, CJ and Lakin, SM and Raymond, RA and Rovira, P and Doster, E and Abdo, Z and Martin, JN and Jones, KL and Ruiz, J and Boucher, CA and Belk, KE and Morley, PS}, title = {Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {142}, pmid = {29041965}, issn = {2049-2618}, support = {T32 OD012201/OD/NIH HHS/United States ; }, mesh = {Drug Resistance, Microbial/*genetics ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Virulence/genetics ; Whole Genome Sequencing/methods ; }, abstract = {BACKGROUND: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias.<br><br>RESULTS: The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistance gene haplotypes that were used to discriminate between sample origins.<br><br>CONCLUSIONS: These results demonstrate that the rare resistome-virulome contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance. Access to the rare resistome-virulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of microbiome-resistome dynamics.}, }
@article {pmid29039187, year = {2017}, author = {Liu, S and Han, P and Hink, L and Prosser, JI and Wagner, M and Brüggemann, N}, title = {Abiotic Conversion of Extracellular NH2OH Contributes to N2O Emission during Ammonia Oxidation.}, journal = {Environmental science &amp; technology}, volume = {51}, number = {22}, pages = {13122-13132}, doi = {10.1021/acs.est.7b02360}, pmid = {29039187}, issn = {1520-5851}, mesh = {*Ammonia ; Archaea ; Nitrification ; *Nitrosomonas europaea ; Nitrous Oxide ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; }, abstract = {Abiotic processes involving the reactive ammonia-oxidation intermediates nitric oxide (NO) or hydroxylamine (NH2OH) for N2O production have been indicated recently. The latter process would require the availability of substantial amounts of free NH2OH for chemical reactions during ammonia (NH3) oxidation, but little is known about extracellular NH2OH formation by the different clades of ammonia-oxidizing microbes. Here we determined extracellular NH2OH concentrations in culture media of several ammonia-oxidizing bacteria (AOB) and archaea (AOA), as well as one complete ammonia oxidizer (comammox) enrichment (Ca. Nitrospira inopinata) during incubation under standard cultivation conditions. NH2OH was measurable in the incubation media of Nitrosomonas europaea, Nitrosospira multiformis, Nitrososphaera gargensis, and Ca. Nitrosotenuis uzonensis, but not in media of the other tested AOB and AOA. NH2OH was also formed by the comammox enrichment during NH3 oxidation. This enrichment exhibited the largest NH2OH:final product ratio (1.92%), followed by N. multiformis (0.56%) and N. gargensis (0.46%). The maximum proportions of NH4[+] converted to N2O via extracellular NH2OH during incubation, estimated on the basis of NH2OH abiotic conversion rates, were 0.12%, 0.08%, and 0.14% for AOB, AOA, and Ca. Nitrospira inopinata, respectively, and were consistent with published NH4[+]:N2O conversion ratios for AOB and AOA.}, }
@article {pmid29038747, year = {2017}, author = {Tilstra, A and Wijgerde, T and Dini-Andreote, F and Eriksson, BK and Salles, JF and Pen, I and Osinga, R and Wild, C}, title = {Light induced intraspecific variability in response to thermal stress in the hard coral Stylophora pistillata.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3802}, pmid = {29038747}, issn = {2167-8359}, abstract = {Recent research suggests that prior exposure of several months to elevated irradiance induces enhanced thermal tolerance in scleractinian corals. While this tolerance has been reported at the species level, individual coral colonies may react differently due to individual variability in thermal tolerance. As thermal anomalies are predicted to become common in the upcoming future, intraspecific variation may be key to the survival of coral populations. In order to study light-history based thermal stress responses on individual colonies, we developed a preliminary microcosm experiment where three randomly chosen, aquacultured colonies of the model coral Stylophora pistillata were exposed to two irradiance treatments (200 and 400 μmol photons m[-2] s[-1]) for 31 days, followed by artificially induced heat stress (∼33.4 °C). We found different responses to occur at both the intraspecific and the intracolonial levels, as indicated by either equal, less severe, delayed, and/or even non-necrotic responses of corals previously exposed to the irradiance of 400 compared to 200 μmol photons m[-2] s[-1]. In addition, all individual colonies revealed light-enhanced calcification. Finally, elevated irradiance resulted in a lower chlorophyll a concentration in one colony compared to the control treatment, and the same colony displayed more rapid bleaching compared to the other ones. Taken together, this study highlights the potential importance of intra-individual variability in physiological responses of scleractinian corals and provides recommendations for improving methodological designs for future studies.}, }
@article {pmid29037090, year = {2018}, author = {Cych, P and Kiewra, D and Szczepańska, A}, title = {Prevention and the state of knowledge of tick-borne diseases among orienteers in Poland.}, journal = {Infectious diseases (London, England)}, volume = {50}, number = {3}, pages = {236-238}, doi = {10.1080/23744235.2017.1388538}, pmid = {29037090}, issn = {2374-4243}, mesh = {Encephalitis Viruses, Tick-Borne ; *Encephalitis, Tick-Borne ; Humans ; Poland ; *Tick-Borne Diseases ; Ticks ; }, }
@article {pmid29036210, year = {2017}, author = {Williams, MR and Stedtfeld, RD and Engle, C and Salach, P and Fakher, U and Stedtfeld, T and Dreelin, E and Stevenson, RJ and Latimore, J and Hashsham, SA}, title = {Isothermal amplification of environmental DNA (eDNA) for direct field-based monitoring and laboratory confirmation of Dreissena sp.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0186462}, pmid = {29036210}, issn = {1932-6203}, mesh = {Animals ; DNA/*genetics ; Dreissena/*genetics ; *Environment ; Environmental Monitoring/*methods ; Introduced Species ; *Laboratories ; Nucleic Acid Amplification Techniques/*methods ; Pilot Projects ; Time Factors ; Water ; }, abstract = {Loop-mediated isothermal amplification (LAMP) of aquatic invasive species environmental DNA (AIS eDNA) was used for rapid, sensitive, and specific detection of Dreissena sp. relevant to the Great Lakes (USA) basin. The method was validated for two uses including i) direct amplification of eDNA using a hand filtration system and ii) confirmation of the results after DNA extraction using a conventional thermal cycler run at isothermal temperatures. Direct amplification eliminated the need for DNA extraction and purification and allowed detection of target invasive species in grab or concentrated surface water samples, containing both free DNA as well as larger cells and particulates, such as veligers, eggs, or seeds. The direct amplification method validation was conducted using Dreissena polymorpha and Dreissena bugensis and uses up to 1 L grab water samples for high target abundance (e.g., greater than 10 veligers (larval mussels) per L for Dreissena sp.) or 20 L samples concentrated through 35 μm nylon screens for low target abundance, at less than 10 veligers per liter water. Surface water concentrate samples were collected over a period of three years, mostly from inland lakes in Michigan with the help of a network of volunteers. Field samples collected from 318 surface water locations included i) filtered concentrate for direct amplification validation and ii) 1 L grab water sample for eDNA extraction and confirmation. Though the extraction-based protocol was more sensitive (resulting in more positive detections than direct amplification), direct amplification could be used for rapid screening, allowing for quicker action times. For samples collected between May and August, results of eDNA direct amplification were consistent with known presence/absence of selected invasive species. A cross-platform smartphone application was also developed to disseminate the analyzed results to volunteers. Field tests of the direct amplification protocol using a portable device (Gene-Z) showed the method could be used in the field to obtain results within one hr (from sample to result). Overall, the direct amplification has the potential to simplify the eDNA-based monitoring of multiple aquatic invasive species. Additional studies are warranted to establish quantitative correlation between eDNA copy number, veliger, biomass or organismal abundance in the field.}, }
@article {pmid29033923, year = {2017}, author = {El Hage, R and Hernandez-Sanabria, E and Van de Wiele, T}, title = {Emerging Trends in "Smart Probiotics": Functional Consideration for the Development of Novel Health and Industrial Applications.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1889}, pmid = {29033923}, issn = {1664-302X}, abstract = {The link between gut microbiota and human health is well-recognized and described. This ultimate impact on the host has contributed to explain the mutual dependence between humans and their gut bacteria. Gut microbiota can be manipulated through passive or active strategies. The former includes diet, lifestyle, and environment, while the latter comprise antibiotics, pre- and probiotics. Historically, conventional probiotic strategies included a phylogenetically limited diversity of bacteria and some yeast strains. However, biotherapeutic strategies evolved in the last years with the advent of fecal microbiota transplant (FMT), successfully applied for treating CDI, IBD, and other diseases. Despite the positive outcomes, long-term effects resulting from the uncharacterized nature of FMT are not sufficiently studied. Thus, developing strategies to simulate the FMT, using characterized gut colonizers with identified phylogenetic diversity, may be a promising alternative. As the definition of probiotics states that the microorganism should have beneficial effects on the host, several bacterial species with proven efficacy have been considered next generation probiotics. Non-conventional candidate strains include Akkermansia muciniphila, Faecalibacterium prausnitzii, Bacteroides fragilis, and members of the Clostridia clusters IV, XIVa, and XVIII. However, viable intestinal delivery is one of the current challenges, due to their stringent survival conditions. In this review, we will cover current perspectives on the development and assessment of next generation probiotics and the approaches that industry and stakeholders must consider for a successful outcome.}, }
@article {pmid29032640, year = {2017}, author = {Kim, BR and Shin, J and Guevarra, R and Lee, JH and Kim, DW and Seol, KH and Lee, JH and Kim, HB and Isaacson, R}, title = {Deciphering Diversity Indices for a Better Understanding of Microbial Communities.}, journal = {Journal of microbiology and biotechnology}, volume = {27}, number = {12}, pages = {2089-2093}, doi = {10.4014/jmb.1709.09027}, pmid = {29032640}, issn = {1738-8872}, mesh = {Bacteria/*classification/genetics ; *Biodiversity ; DNA, Bacterial/genetics ; Genetic Variation ; *Microbial Consortia ; Microbiota/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The past decades have been a golden era during which great tasks were accomplished in the field of microbiology, including food microbiology. In the past, culture-dependent methods have been the primary choice to investigate bacterial diversity. However, using cultureindependent high-throughput sequencing of 16S rRNA genes has greatly facilitated studies exploring the microbial compositions and dynamics associated with health and diseases. These culture-independent DNA-based studies generate large-scale data sets that describe the microbial composition of a certain niche. Consequently, understanding microbial diversity becomes of greater importance when investigating the composition, function, and dynamics of the microbiota associated with health and diseases. Even though there is no general agreement on which diversity index is the best to use, diversity indices have been used to compare the diversity among samples and between treatments with controls. Tools such as the Shannon- Weaver index and Simpson index can be used to describe population diversity in samples. The purpose of this review is to explain the principles of diversity indices, such as Shannon- Weaver and Simpson, to aid general microbiologists in better understanding bacterial communities. In this review, important questions concerning microbial diversity are addressed. Information from this review should facilitate evidence-based strategies to explore microbial communities.}, }
@article {pmid29032430, year = {2018}, author = {Iwaoka, C and Imada, S and Taniguchi, T and Du, S and Yamanaka, N and Tateno, R}, title = {The Impacts of Soil Fertility and Salinity on Soil Nitrogen Dynamics Mediated by the Soil Microbial Community Beneath the Halophytic Shrub Tamarisk.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {985-996}, pmid = {29032430}, issn = {1432-184X}, support = {15H05113//Japan Society for the Promotion of Science/ ; 4141114003//Japan Society for the Promotion of Science/ ; 24-4309//Japan Society for the Promotion of Science London/ ; 41171419//National Natural Science Foundation of China/ ; }, mesh = {Archaea/classification/genetics/metabolism ; Bacteria/classification/genetics/metabolism ; China ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Ecosystem ; Islands ; Microbiota/genetics/*physiology ; Nitrogen/metabolism ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Salt-Tolerant Plants/*microbiology ; Soil/*chemistry ; *Soil Microbiology ; Tamaricaceae/*microbiology ; }, abstract = {Nitrogen (N) is one of the most common limiting nutrients for primary production in terrestrial ecosystems. Soil microbes transform organic N into inorganic N, which is available to plants, but soil microbe activity in drylands is sometimes critically suppressed by environmental factors, such as low soil substrate availability or high salinity. Tamarisk (Tamarix spp.) is a halophytic shrub species that is widely distributed in the drylands of China; it produces litter enriched in nutrients and salts that are thought to increase soil fertility and salinity under its crown. To elucidate the effects of tamarisks on the soil microbial community, and thus N dynamics, by creating "islands of fertility" and "islands of salinity," we collected soil samples from under tamarisk crowns and adjacent barren areas at three habitats in the summer and fall. We analyzed soil physicochemical properties, inorganic N dynamics, and prokaryotic community abundance and composition. In soils sampled beneath tamarisks, the N mineralization rate was significantly higher, and the prokaryotic community structure was significantly different, from soils sampled in barren areas, irrespective of site and season. Tamarisks provided suitable nutrient conditions for one of the important decomposers in the area, Verrucomicrobia, by creating "islands of fertility," but provided unsuitable salinity conditions for other important decomposers, Flavobacteria, Gammaproteobacteria, and Deltaproteobacteria, by mitigating salt accumulation. However, the quantity of these decomposers tended to be higher beneath tamarisks, because they were relatively unaffected by the small salinity gradient created by the tamarisks, which may explain the higher N mineralization rate beneath tamarisks.}, }
@article {pmid29032328, year = {2018}, author = {Grobbler, C and Virdis, B and Nouwens, A and Harnisch, F and Rabaey, K and Bond, PL}, title = {Effect of the anode potential on the physiology and proteome of Shewanella oneidensis MR-1.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {119}, number = {}, pages = {172-179}, doi = {10.1016/j.bioelechem.2017.10.001}, pmid = {29032328}, issn = {1878-562X}, mesh = {Bacterial Proteins/metabolism ; Biofilms/growth &amp; development ; Cell Membrane/metabolism ; Electrochemistry ; Electrodes ; Electron Transport ; *Proteomics ; Shewanella/cytology/*metabolism/physiology ; }, abstract = {Shewanella species respire using iron and manganese oxides as well as electrodes as solid terminal electron acceptors. Shewanella oneidenis MR-1 exploits mediated as well as direct extracellular electron transfer (EET) modes to transfer electrons at different formal potentials. These different EET modes at different potentials may utilise alternate electron transfer pathways. Therefore, we investigated how different anode potentials, providing different maximum microbial energy gains impacted S. oneidensis microbial physiology. Using quantitative proteomics, comparative analysis of the cellular variations to different anode potentials was performed. A label-free proteomic mass spectrometric analysis method, SWATH-MS, was used to gather quantitative information to determine physiological changes of Shewanella oneidensis MR-1 grown at different anodic potentials. S. oneidensis was cultured and grown in electrochemical cells at the set anode potentials of +0.71V, +0.21V &amp; -0.19V versus SHE reference electrode, while the current production was monitored. At maximum current, electrodes were removed and whole-cell proteins extracted. Subsequent SWATH-MS analysis revealed information on 740 identified proteins across the three electrode potentials. For the first time, we show the abundance of S. oneidensis electron transfer proteins differs with electrode potential.}, }
@article {pmid29031631, year = {2017}, author = {Kanitkar, YH and Stedtfeld, RD and Hatzinger, PB and Hashsham, SA and Cupples, AM}, title = {Most probable number with visual based LAMP for the quantification of reductive dehalogenase genes in groundwater samples.}, journal = {Journal of microbiological methods}, volume = {143}, number = {}, pages = {44-49}, doi = {10.1016/j.mimet.2017.10.003}, pmid = {29031631}, issn = {1872-8359}, mesh = {Chloroflexi/*enzymology/genetics ; False Positive Reactions ; *Gene Dosage ; Groundwater/*microbiology ; Hydrolases/*analysis/genetics ; Nucleic Acid Amplification Techniques/*methods ; }, abstract = {The remediation of chlorinated solvent contaminated sites frequently involves bioaugmentation with mixed cultures containing Dehalococcoides mccartyi. Their activity is then examined by quantifying reductive dehalogenase (RDase) genes. Recently, we described a rapid, low cost approach, based on loop mediated isothermal amplification (LAMP), which allowed for the visual detection of RDase genes from groundwater. In that study, samples were concentrated (without DNA extraction), incubated in a water bath (avoiding the use of a thermal cycler) and amplification was visualized by the addition of SYBR green (post incubation). Despite having a detection limit less than the threshold recommended for effective remediation, the application of the assay was limited because of the semi-quantitative nature of the data. Moreover, the assay was prone to false positives due to the aerosolization of amplicons. In this study, deoxyuridine triphosphate (dUTP) and uracil DNA glycosylase (UNG) were incorporated into the assay to reduce the probability of false positives. Optimization experiments revealed a UNG concentration of 0.2units per reaction was adequate for degrading trace levels of AUGC based contamination (~1.4×10[4] gene copies/reaction) without significant changes to the detection limit (~100 gene copies/reaction). Additionally, the optimized assay was used with the most probable number (MPN) method to quantify RDase genes (vcrA and tceA) in multiple groundwater samples from a chlorinated solvent contaminated site. Using this approach, gene concentrations were significantly correlated to concentrations obtained using traditional methods (qPCR and DNA templates). Although the assay underestimated RDase genes concentrations, a strong correlation (R[2]=0.78 and 0.94) was observed between the two data sets. The regression equations obtained will be valuable to determine gene copies in groundwater using the newly developed, low cost and time saving method.}, }
@article {pmid29029865, year = {2018}, author = {Skarżyńska, E and Kiersztyn, B and Wilczyńska, P and Jakimiuk, A and Lisowska-Myjak, B}, title = {Total proteolytic activity and concentration of alpha-1 antitrypsin in meconium for assessment of the protease/antiprotease balance.}, journal = {European journal of obstetrics, gynecology, and reproductive biology}, volume = {223}, number = {}, pages = {133-138}, doi = {10.1016/j.ejogrb.2017.10.006}, pmid = {29029865}, issn = {1872-7654}, mesh = {Adult ; Female ; Humans ; Infant, Newborn ; Meconium/*chemistry/*enzymology ; Peptide Hydrolases/*analysis ; Protease Inhibitors/*analysis ; Trypsin Inhibitors/analysis ; alpha 1-Antitrypsin/*analysis ; }, abstract = {BACKGROUND: During intrauterine life, various proteolytic enzymes and their main inhibitor, alpha-1 antitrypsin, accumulate naturally in meconium. A protease/antiprotease balance is required to maintain the biological stability of the environment in which the fetus develops.<br><br>METHODS: The pool of active proteases was determined using the EnzChek Protease Assay Kit. The concentration of alpha-1 antitrypsin in meconium was measured by enzyme-linked immunosorbent assay. Serial portions of meconium (n=80) were collected from healthy full-term neonates (n=19).<br><br>RESULTS: Mean concentrations of active proteases and alpha-1 antitrypsin were 1.55 [standard deviation (SD) 1.3]mgg[-1] (range 0.15-6.17) and 3.72 (SD 1.78)mgg[-1] (range 0.76-8.55), respectively, with significant correlation (Rs=0.32, p=0.004). A significant increase in the concentration of active proteases was found between the first and last meconium portions (p<0.05). The proteases in the last meconium portions had a higher reaction velocity and affinity for the substrate than the proteases in the first meconium portions. The active protease:alpha-1 antitrypsin ratio was <0.5 in all first meconium portions, but was higher in the last meconium portions.<br><br>CONCLUSIONS: Strong correlation between the concentrations of active proteases and alpha-1 antitrypsin in meconium may indicate their mutual interaction in the intrauterine environment. Alpha-1 antitrypsin maintains the protease/antiprotease balance during fetal development.}, }
@article {pmid29028000, year = {2018}, author = {Mendes, LW and Raaijmakers, JM and de Hollander, M and Mendes, R and Tsai, SM}, title = {Influence of resistance breeding in common bean on rhizosphere microbiome composition and function.}, journal = {The ISME journal}, volume = {12}, number = {1}, pages = {212-224}, pmid = {29028000}, issn = {1751-7370}, mesh = {Bacteria/genetics/isolation &amp; purification ; Disease Resistance ; Fusarium/physiology ; Metagenome ; *Microbiota ; Phaseolus/*microbiology ; Plant Breeding ; Plant Diseases/microbiology ; Plant Roots/*microbiology ; *Rhizosphere ; Soil/chemistry ; Soil Microbiology ; }, abstract = {The rhizosphere microbiome has a key role in plant growth and health, providing a first line of defense against root infections by soil-borne pathogens. Here, we investigated the composition and metabolic potential of the rhizobacterial community of different common bean (Phaseolus vulgaris) cultivars with variable levels of resistance to the fungal root pathogen Fusarium oxysporum (Fox). For the different bean cultivars grown in two soils with contrasting physicochemical properties and microbial diversity, rhizobacterial abundance was positively correlated with Fox resistance. Pseudomonadaceae, bacillaceae, solibacteraceae and cytophagaceae were more abundant in the rhizosphere of the Fox-resistant cultivar. Network analyses showed a modular topology of the rhizosphere microbiome of the Fox-resistant cultivar, suggesting a more complex and highly connected bacterial community than in the rhizosphere of the Fox-susceptible cultivar. Metagenome analyses further revealed that specific functional traits such as protein secretion systems and biosynthesis genes of antifungal phenazines and rhamnolipids were more abundant in the rhizobacterial community of the Fox-resistant cultivar. Our findings suggest that breeding for Fox resistance in common bean may have co-selected for other unknown plant traits that support a higher abundance of specific beneficial bacterial families in the rhizosphere with functional traits that reinforce the first line of defense.}, }
@article {pmid29027374, year = {2018}, author = {Props, R and Schmidt, ML and Heyse, J and Vanderploeg, HA and Boon, N and Denef, VJ}, title = {Flow cytometric monitoring of bacterioplankton phenotypic diversity predicts high population-specific feeding rates by invasive dreissenid mussels.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {521-534}, doi = {10.1111/1462-2920.13953}, pmid = {29027374}, issn = {1462-2920}, mesh = {Animals ; Bacteria/*classification/genetics ; *Biodiversity ; Bivalvia/*physiology ; Ecosystem ; *Flow Cytometry ; *Introduced Species ; Lakes/microbiology ; Phenotype ; Plankton/*classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Species invasion is an important disturbance to ecosystems worldwide, yet knowledge about the impacts of invasive species on bacterial communities remains sparse. Using a novel approach, we simultaneously detected phenotypic and derived taxonomic change in a natural bacterioplankton community when subjected to feeding pressure by quagga mussels, a widespread aquatic invasive species. We detected a significant decrease in diversity within 1 h of feeding and a total diversity loss of 11.6 ± 4.1% after 3 h. This loss of microbial diversity was caused by the selective removal of high nucleic acid populations (29 ± 5% after 3 h). We were able to track the community diversity at high temporal resolution by calculating phenotypic diversity estimates from flow cytometry (FCM) data of minute amounts of sample. Through parallel FCM and 16S rRNA gene amplicon sequencing analysis of environments spanning a broad diversity range, we showed that the two approaches resulted in highly correlated diversity measures and captured the same seasonal and lake-specific patterns in community composition. Based on our results, we predict that selective feeding by invasive dreissenid mussels directly impacts the microbial component of the carbon cycle, as it may drive bacterioplankton communities toward less diverse and potentially less productive states.}, }
@article {pmid29027362, year = {2017}, author = {Wöhlbrand, L and Feenders, C and Nachbaur, J and Freund, H and Engelen, B and Wilkes, H and Brumsack, HJ and Rabus, R}, title = {Impact of Extraction Methods on the Detectable Protein Complement of Metaproteomic Analyses of Marine Sediments.}, journal = {Proteomics}, volume = {17}, number = {22}, pages = {}, doi = {10.1002/pmic.201700241}, pmid = {29027362}, issn = {1615-9861}, mesh = {Geologic Sediments/*analysis ; Oceans and Seas ; Phenol/chemistry ; Proteins/*isolation &amp; purification/metabolism ; Proteome/*analysis/isolation &amp; purification ; Proteomics/*methods ; Urea/chemistry ; }, abstract = {Metaproteomic analysis targets proteins, the catalytic entities in the habitat, thereby providing direct insights into the metabolic activity of the community studied. A major challenge still remaining for metaproteomics is the effective and comprehensive extraction of proteins from environmental samples, due to their high complexity with respect to organismic diversity and abundance range. Moreover, in certain habitats, the inherent matrix may interfere with protein extraction. In recent years, several studies reported different protein extraction methods for soils known for their complex geochemistry, but only three analyzed marine sediments that generally comprise different though similarly complex geochemistry. In this study, the impact of four different extraction methods was investigated for coastal North Sea and deep sea Pacific Ocean sediments. The extraction methods comprised (i) phenol, (ii) SDS, (iii) a mixture of SDS and phenol, and (iv) urea and thiourea. Prior to extraction, a cell and protein standard (CPS) was added to the sediment samples to trace recovery of proteins from different subcellular locations as well as dissolved BSA. While each extraction method detected distinct peptide complements, SDS-phenol extraction generally achieved highest protein yield and most comprehensive CPS protein identification. Application of two different methods was shown to further improve proteome coverage.}, }
@article {pmid29027346, year = {2018}, author = {Angel, R and Panhölzl, C and Gabriel, R and Herbold, C and Wanek, W and Richter, A and Eichorst, SA and Woebken, D}, title = {Application of stable-isotope labelling techniques for the detection of active diazotrophs.}, journal = {Environmental microbiology}, volume = {20}, number = {1}, pages = {44-61}, pmid = {29027346}, issn = {1462-2920}, support = {636928/ERC_/European Research Council/International ; P 25700/FWF_/Austrian Science Fund FWF/Austria ; P 26392/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; Isotope Labeling/*methods ; Nitrogen Fixation/genetics/*physiology ; Nitrogen Isotopes/*analysis/chemistry ; Soil Microbiology ; Spectrum Analysis, Raman/methods ; }, abstract = {Investigating active participants in the fixation of dinitrogen gas is vital as N is often a limiting factor for primary production. Biological nitrogen fixation is performed by a diverse guild of bacteria and archaea (diazotrophs), which can be free-living or symbionts. Free-living diazotrophs are widely distributed in the environment, yet our knowledge about their identity and ecophysiology is still limited. A major challenge in investigating this guild is inferring activity from genetic data as this process is highly regulated. To address this challenge, we evaluated and improved several [15] N-based methods for detecting N2 fixation activity (with a focus on soil samples) and studying active diazotrophs. We compared the acetylene reduction assay and the [15] N2 tracer method and demonstrated that the latter is more sensitive in samples with low activity. Additionally, tracing [15] N into microbial RNA provides much higher sensitivity compared to bulk soil analysis. Active soil diazotrophs were identified with a [15] N-RNA-SIP approach optimized for environmental samples and benchmarked to [15] N-DNA-SIP. Lastly, we investigated the feasibility of using SIP-Raman microspectroscopy for detecting [15] N-labelled cells. Taken together, these tools allow identifying and investigating active free-living diazotrophs in a highly sensitive manner in diverse environments, from bulk to the single-cell level.}, }
@article {pmid29026984, year = {2018}, author = {Röhl, O and Graupner, N and Peršoh, D and Kemler, M and Mittelbach, M and Boenigk, J and Begerow, D}, title = {Flooding Duration Affects the Structure of Terrestrial and Aquatic Microbial Eukaryotic Communities.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {875-887}, pmid = {29026984}, issn = {1432-184X}, support = {Pr-2013-0036//Stiftung Mercator Schweiz (CH)/ ; }, mesh = {Ammonium Compounds ; Biodiversity ; Chlorides ; Climate Change ; DNA/analysis ; Ecosystem ; Eukaryota/*classification/genetics ; *Floods ; Genes, rRNA/genetics ; *Microbiota ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; *Water Microbiology ; }, abstract = {The increasing number and duration of inundations is reported to be a consequence of climate change and may severely compromise non-adapted macroorganisms. The effect of flooding events on terrestrial and aquatic microbial communities is, however, less well understood. They may respond to the changed abiotic properties of their native habitat, and the native community may change due to the introduction of alien species. We designed an experiment to investigate the effect of five different flooding durations on the terrestrial and aquatic communities of eukaryotic microorganism, using the AquaFlow mesocosms. With amplicon sequencing of the small subunit (SSU) and internal transcribed spacer (ITS) rRNA gene regions, we analyzed community compositions directly before and after flooding. Subsequently, they were monitored for another 28 days, to determine the sustainability of community changes. Our results revealed a temporary increase in similarity between terrestrial and aquatic communities according to OTU composition (operational taxonomic unit, serves as a proxy for species). Increased similarity was mainly caused by the transmission of OTUs from water to soil. A minority of these were able to persist in soil until the end of the experiment. By contrast, the vast majority of soil OTUs was not transmitted to water. Flooding duration affected the community structure (abundance) more than composition (occurrence). Terrestrial communities responded immediately to flooding and the flooding duration influenced the community changes. Independent from flooding duration, all terrestrial communities recovered largely after flooding, indicating a remarkable resilience to the applied disturbances. Aquatic communities responded immediately to the applied inundations too. At the end of the experiment, they grouped according to the applied flooding duration and the amount of ammonium and chloride that leached from the soil. This indicates a sustained long-term response of the aquatic communities to flooding events.}, }
@article {pmid29025929, year = {2017}, author = {Bag, S and Ghosh, TS and Das, B}, title = {Whole-Genome Sequence of Bifidobacterium longum Strain Indica, Isolated from the Gut of a Healthy Indian Adult.}, journal = {Genome announcements}, volume = {5}, number = {41}, pages = {}, pmid = {29025929}, issn = {2169-8287}, abstract = {Bifidobacterium longum, a Gram-positive rod-shaped anaerobic bacterium, inhabits the human gastrointestinal tract and contributes significantly to oligosaccharide production, amino acid metabolism, and protection against intestinal inflammation. Here, we report the whole-genome sequence of B. longum, which was isolated from the gastrointestinal tract of a healthy Indian adult.}, }
@article {pmid29022063, year = {2018}, author = {Shiau, YJ and Cai, Y and Lin, YT and Jia, Z and Chiu, CY}, title = {Community Structure of Active Aerobic Methanotrophs in Red Mangrove (Kandelia obovata) Soils Under Different Frequency of Tides.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {761-770}, pmid = {29022063}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*metabolism ; DNA, Bacterial/genetics ; Genes, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Isotopes ; Methane/*metabolism ; Methylococcaceae/genetics ; Microbiota/*genetics ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizophoraceae/*microbiology ; Soil ; *Soil Microbiology ; Taiwan ; }, abstract = {Methanotrophs are important microbial communities in coastal ecosystems. They reduce CH4 emission in situ, which is influenced by soil conditions. This study aimed to understand the differences in active aerobic methanotrophic communities in mangrove forest soils experiencing different inundation frequency, i.e., in soils from tidal mangroves, distributed at lower elevations, and from dwarf mangroves, distributed at higher elevations. Labeling of pmoA gene of active methanotrophs using DNA-based stable isotope probing (DNA-SIP) revealed that methanotrophic activity was higher in the dwarf mangrove soils than in the tidal mangrove soils, possibly because of the more aerobic soil conditions. Methanotrophs affiliated with the cluster deep-sea-5 belonging to type Ib methanotrophs were the most dominant methanotrophs in the fresh mangrove soils, whereas type II methanotrophs also appeared in the fresh dwarf mangrove soils. Furthermore, Methylobacter and Methylosarcina were the most important active methanotrophs in the dwarf mangrove soils, whereas Methylomonas and Methylosarcina were more active in the tidal mangrove soils. High-throughput sequencing of the 16S ribosomal RNA (rRNA) gene also confirmed similar differences in methanotrophic communities at the different locations. However, several unclassified methanotrophic bacteria were found by 16S rRNA MiSeq sequencing in both fresh and incubated mangrove soils, implying that methanotrophic communities in mangrove forests may significantly differ from the methanotrophic communities documented in previous studies. Overall, this study showed the feasibility of [13]CH4 DNA-SIP to study the active methanotrophic communities in mangrove forest soils and revealed differences in the methanotrophic community structure between coastal mangrove forests experiencing different tide frequencies.}, }
@article {pmid29021788, year = {2017}, author = {Williams, MR and Stedtfeld, RD and Tiedje, JM and Hashsham, SA}, title = {MicroRNAs-Based Inter-Domain Communication between the Host and Members of the Gut Microbiome.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1896}, pmid = {29021788}, issn = {1664-302X}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, abstract = {The gut microbiome is an important modulator of host gene expression, impacting important functions such as the innate immune response. Recent evidence suggests that the inter-domain communication between the gut microbiome and host may in part occur via microRNAs (small, non-coding RNA molecules) which are often differentially expressed in the presence of bacteria and can even be released and taken up by bacteria. The role of microRNAs in microbiome-host communication in intestinal diseases is not fully understood, particularly in diseases impacted by exposure to environmental toxicants. Here, we review the present knowledge in the areas of microbiome and microRNA expression-based communication, microbiome and intestinal disease relationships, and microRNA expression responses to intestinal diseases. We also examine potential links between host microRNA-microbiota communication and exposure to environmental toxicants by reviewing connections between (i) toxicants and microRNA expression, (ii) toxicants and gut diseases, and (iii) toxicants and the gut microbiome. Future multidisciplinary research in this area is needed to uncover these interactions with the potential to impact how gut-microbiome associated diseases [e.g., inflammatory bowel disease (IBD) and many others] are managed.}, }
@article {pmid29021219, year = {2017}, author = {Zhou, J and Ning, D}, title = {Stochastic Community Assembly: Does It Matter in Microbial Ecology?.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {81}, number = {4}, pages = {}, pmid = {29021219}, issn = {1098-5557}, mesh = {Animals ; Ecology/*statistics &amp; numerical data ; Humans ; *Microbial Consortia ; Models, Theoretical ; Multivariate Analysis ; *Stochastic Processes ; }, abstract = {Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research.}, }
@article {pmid29020773, year = {2017}, author = {Lin, HW and Couvreur, K and Donose, BC and Rabaey, K and Yuan, Z and Pikaar, I}, title = {Electrochemical Production of Magnetite Nanoparticles for Sulfide Control in Sewers.}, journal = {Environmental science &amp; technology}, volume = {51}, number = {21}, pages = {12229-12234}, doi = {10.1021/acs.est.7b01748}, pmid = {29020773}, issn = {1520-5851}, mesh = {Ferrosoferric Oxide ; Iron ; *Magnetite Nanoparticles ; *Sewage ; *Sulfides ; }, abstract = {Recently, naturally occurring magnetite (Fe3O4) has emerged as a new material for sulfide control in sewers. However, unrefined magnetite could have high heavy metal contents (e.g., Cr, Zn, Ni, Sn, etc.) and the capacity to remove dissolved sulfide is reasonably limited due to relatively large particle sizes. To overcome the drawbacks of unrefined magnetite we used an electrochemical system with mild steel as sacrificial electrodes to in-situ generate high strength solutions of plate-like magnetite nanoparticles (MNP). MNP with a size range between 120 and 160 nm were electrochemically generated at 9.35 ± 0.28 g Fe3O4-Fe/L, resulting in a Coulombic efficiency (CE) for iron oxidation of 93.5 ± 2.8%. The produced MNP were found to effectively reduce sulfide levels in sewage from 12.7 ± 0.3 to 0.2 ± 0.0 mg S/L at a sulfide-to-MNP ratio of 0.26 g S/g Fe3O4-Fe. Subsequently, MNP were continuously generated with polarity switching at stable cell voltage for 31 days at 4.53 ± 0.35 g Fe3O4-Fe/L with a CE for iron oxidation of 92.4 ± 7.2%. The continuously produced MNP reduced sulfide at similar levels to around 0.2 mg S/L at a ratio of 0.28 g S/g Fe3O4-Fe.}, }
@article {pmid29020640, year = {2017}, author = {Viggi, CC and Matturro, B and Frascadore, E and Insogna, S and Mezzi, A and Kaciulis, S and Sherry, A and Mejeha, OK and Head, IM and Vaiopoulou, E and Rabaey, K and Rossetti, S and Aulenta, F}, title = {Bridging spatially segregated redox zones with a microbial electrochemical snorkel triggers biogeochemical cycles in oil-contaminated River Tyne (UK) sediments.}, journal = {Water research}, volume = {127}, number = {}, pages = {11-21}, doi = {10.1016/j.watres.2017.10.002}, pmid = {29020640}, issn = {1879-2448}, mesh = {*Biodegradation, Environmental ; Geologic Sediments/*chemistry/microbiology ; Hydrocarbons ; Oxidation-Reduction ; Petroleum/*metabolism ; *Petroleum Pollution ; Rivers/*chemistry/microbiology ; United Kingdom ; }, abstract = {Marine sediments represent an important sink for a number of anthropogenic organic contaminants, including petroleum hydrocarbons following an accidental oil spill. Degradation of these compounds largely depends on the activity of sedimentary microbial communities linked to biogeochemical cycles, in which abundant elements such as iron and sulfur are shuttled between their oxidized and reduced forms. Here we show that introduction of a small electrically conductive graphite rod ("the electrochemical snorkel") into an oil-contaminated River Tyne (UK) sediment, so as to create an electrochemical connection between the anoxic contaminated sediment and the oxygenated overlying water, has a large impact on the rate of metabolic reactions taking place in the bulk sediment. The electrochemical snorkel accelerated sulfate reduction processes driven by organic contaminant oxidation and suppressed competitive methane-producing reactions. The application of a comprehensive suite of chemical, spectroscopic, biomolecular and thermodynamic analyses suggested that the snorkel served as a scavenger of toxic sulfide via a redox interaction with the iron cycle. Taken as a whole, the results of this work highlight a new strategy for controlling biological processes, such as bioremediation, through the manipulation of the electron flows in contaminated sediments.}, }
@article {pmid29018917, year = {2018}, author = {Machado, L and Tomkins, N and Magnusson, M and Midgley, DJ and de Nys, R and Rosewarne, CP}, title = {In Vitro Response of Rumen Microbiota to the Antimethanogenic Red Macroalga Asparagopsis taxiformis.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {811-818}, doi = {10.1007/s00248-017-1086-8}, pmid = {29018917}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/drug effects/metabolism ; DNA, Bacterial/genetics ; Fermentation ; Halogenation ; Hydrogen/metabolism ; In Vitro Techniques ; Livestock/microbiology ; Methane/*analogs &amp; derivatives/metabolism ; Methanobacteriales/drug effects/metabolism ; Methanomicrobiales/drug effects/metabolism ; Microbiota/*drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; Rhodophyta/*metabolism ; Rumen/*microbiology ; Seaweed/*metabolism ; Trihalomethanes/pharmacology ; }, abstract = {The red macroalga Asparagopsis taxiformis has been shown to significantly decrease methane production by rumen microbial communities. This has been attributed to the bioaccumulation of halogenated methane analogues produced as algal secondary metabolites. The objective of this study was to evaluate the impact of A. taxiformis supplementation on the relative abundance of methanogens and microbial community structure during in vitro batch fermentation. Addition of A. taxiformis (2% organic matter) or the halogenated methane analogue bromoform (5 μM) reduced methane production by over 99% compared to a basal substrate-only control. Quantitative PCR confirmed that the decrease in methane production was correlated with a decrease in the relative abundance of methanogens. High-throughput 16S ribosomal RNA gene amplicon sequencing showed that both treatments reduced the abundance of the three main orders of methanogens present in ruminants (Methanobacteriales, Methanomassiliicoccales and Methanomicrobiales). Shifts in bacterial community structure due to the addition of A. taxiformis and 5 μM bromoform were similar and concomitant with increases in hydrogen concentration in the headspace of the fermenters. With high potency and broad-spectrum activity against rumen methanogens, A. taxiformis represents a promising natural strategy for reducing enteric methane emissions from ruminant livestock.}, }
@article {pmid29018902, year = {2018}, author = {Ma, ZS}, title = {The P/N (Positive-to-Negative Links) Ratio in Complex Networks-A Promising In Silico Biomarker for Detecting Changes Occurring in the Human Microbiome.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {1063-1073}, pmid = {29018902}, issn = {1432-184X}, mesh = {Biodiversity ; *Biomarkers ; Computer Simulation ; Female ; Gastrointestinal Microbiome ; Humans ; Lung/microbiology ; Microbial Interactions/*physiology ; Microbiota/*physiology ; Mouth/microbiology ; Skin/microbiology ; Vagina/microbiology ; }, abstract = {Relatively little progress in the methodology for differentiating between the healthy and diseased microbiomes, beyond comparing microbial community diversities with traditional species richness or Shannon index, has been made. Network analysis has increasingly been called for the task, but most currently available microbiome datasets only allows for the construction of simple species correlation networks (SCNs). The main results from SCN analysis are a series of network properties such as network degree and modularity, but the metrics for these network properties often produce inconsistent evidence. We propose a simple new network property, the P/N ratio, defined as the ratio of positive links to the number of negative links in the microbial SCN. We postulate that the P/N ratio should reflect the balance between facilitative and inhibitive interactions among microbial species, possibly one of the most important changes occurring in diseased microbiome. We tested our hypothesis with five datasets representing five major human microbiome sites and discovered that the P/N ratio exhibits contrasting differences between healthy and diseased microbiomes and may be harnessed as an in silico biomarker for detecting disease-associated changes in the human microbiome, and may play an important role in personalized diagnosis of the human microbiome-associated diseases.}, }
@article {pmid28993853, year = {2018}, author = {Lee, SH and Kim, JH and Chung, CW and Kim, DY and Rhee, YH}, title = {Analysis of Medium-Chain-Length Polyhydroxyalkanoate-Producing Bacteria in Activated Sludge Samples Enriched by Aerobic Periodic Feeding.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {720-728}, pmid = {28993853}, issn = {1432-184X}, support = {2013-1080-02//Korea National Research Foundation Grant/ ; KGM2131622//A grant from the KRIBB Research Initiative Program/ ; }, mesh = {Aerobiosis ; Bacteria/enzymology/genetics/*metabolism ; Biodiversity ; Bioreactors/microbiology ; Carbon/metabolism ; Cell Culture Techniques ; Culture Media/chemistry ; DNA, Bacterial/genetics ; Fatty Acids/metabolism ; Microbiota ; Polyhydroxyalkanoates/*biosynthesis ; Pseudomonas/classification/enzymology/genetics/metabolism ; Pseudomonas aeruginosa/enzymology/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Temperature ; }, abstract = {Analysis of mixed microbial populations responsible for the production of medium-chain-length polyhydroxyalkanoates (MCL-PHAs) under periodic substrate feeding in a sequencing batch reactor (SBR) was conducted. Regardless of activated sludge samples and the different MCL alkanoic acids used as the sole external carbon substrate, denaturing gradient gel electrophoresis analysis indicated that Pseudomonas aeruginosa was the dominant bacterium enriched during the SBR process. Several P. aeruginosa strains were isolated from the enriched activated sludge samples. The isolates were subdivided into two groups, one that produced only MCL-PHAs and another that produced both MCL- and short-chain-length PHAs. The SBR periodic feeding experiments with five representative MCL-PHA-producing Pseudomonas species revealed that P. aeruginosa has an advantage over other species that enables it to become dominant in the bacterial community.}, }
@article {pmid28993764, year = {2017}, author = {Jurburg, SD and Nunes, I and Brejnrod, A and Jacquiod, S and Priemé, A and Sørensen, SJ and Van Elsas, JD and Salles, JF}, title = {Legacy Effects on the Recovery of Soil Bacterial Communities from Extreme Temperature Perturbation.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1832}, pmid = {28993764}, issn = {1664-302X}, abstract = {The type and frequency of disturbances experienced by soil microbiomes is expected to increase given predicted global climate change scenarios and intensified anthropogenic pressures on ecosystems. While the direct effect of multiple disturbances to soil microbes has been explored in terms of function, their effect on the recovery of microbial community composition remains unclear. Here, we used soil microcosm experiments and multiple model disturbances to explore their short-term effect on the recovery of soil microbiota after identical or novel stresses. Soil microcosms were exposed to a heat shock to create an initial effect. Upon initial community recovery (25 days after stress), they were subjected to a second stress, either a heat or a cold shock, and they were monitored for additional 25 days. To carefully verify the bacterial response to the disturbances, we monitored changes in community composition throughout the experiment using 16S rRNA gene transcript amplicon sequencing. The application of a heat shock to soils with or without the initial heat shock resulted in similar successional dynamics, but these dynamics were faster in soils with a prior heat shock. The application of a cold shock had negligible effects on previously undisturbed soils but, in combination with an initial heat shock, caused the largest shift in the community composition. Our findings show that compounded perturbation affects bacterial community recovery by altering community structure and thus, the community's response during succession. By altering dominance patterns, disturbance legacy affects the microbiome's ability to recover from further perturbation within the 25 days studied. Our results highlight the need to consider the soil's disturbance history in the development of soil management practices in order to maintain the system's resilience.}, }
@article {pmid28993609, year = {2017}, author = {Malik, S and Sadhu, S and Elesela, S and Pandey, RP and Chawla, AS and Sharma, D and Panda, L and Rathore, D and Ghosh, B and Ahuja, V and Awasthi, A}, title = {Transcription factor Foxo1 is essential for IL-9 induction in T helper cells.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {815}, pmid = {28993609}, issn = {2041-1723}, support = {//Wellcome Trust/United Kingdom ; //Wellcome Trust-DBT India Alliance/India ; }, abstract = {Interleukin 9 (IL-9)-producing helper T (Th9) cells have a crucial function in allergic inflammation, autoimmunity, immunity to extracellular pathogens and anti-tumor immune responses. In addition to Th9, Th2, Th17 and Foxp3[+] regulatory T (Treg) cells produce IL-9. A transcription factor that is critical for IL-9 induction in Th2, Th9 and Th17 cells has not been identified. Here we show that the forkhead family transcription factor Foxo1 is required for IL-9 induction in Th9 and Th17 cells. We further show that inhibition of AKT enhances IL-9 induction in Th9 cells while it reciprocally regulates IL-9 and IL-17 in Th17 cells via Foxo1. Mechanistically, Foxo1 binds and transactivates IL-9 and IRF4 promoters in Th9, Th17 and iTreg cells. Furthermore, loss of Foxo1 attenuates IL-9 in mouse and human Th9 and Th17 cells, and ameliorates allergic inflammation in asthma. Our findings thus identify that Foxo1 is essential for IL-9 induction in Th9 and Th17 cells.The transcription factor Foxo1 can control regulatory T cell and Th1 function. Here the authors show that Foxo1 is also critical for IL-9 production by Th9 cells and other IL-9-producing cells.}, }
@article {pmid28992459, year = {2017}, author = {Peng, L and Carvajal-Arroyo, JM and Seuntjens, D and Prat, D and Colica, G and Pintucci, C and Vlaeminck, SE}, title = {Smart operation of nitritation/denitritation virtually abolishes nitrous oxide emission during treatment of co-digested pig slurry centrate.}, journal = {Water research}, volume = {127}, number = {}, pages = {1-10}, doi = {10.1016/j.watres.2017.09.049}, pmid = {28992459}, issn = {1879-2448}, mesh = {Ammonium Compounds/chemistry ; Animals ; Bioreactors ; Carbon/analysis ; Environmental Pollutants/*analysis/metabolism ; Nitrates/analysis ; Nitrites/*chemistry ; Nitrogen/chemistry/metabolism ; Nitrous Oxide/*analysis/metabolism ; Oxygen/analysis ; *Swine ; Waste Management/methods ; Wastewater/*chemistry ; }, abstract = {The implementation of nitritation/denitritation (Nit/DNit) as alternative to nitrification/denitrification (N/DN) is driven by operational cost savings, e.g. 1.0-1.8 EUR/ton slurry treated. However, as for any biological nitrogen removal process, Nit/DNit can emit the potent greenhouse gas nitrous oxide (N2O). Challenges remain in understanding formation mechanisms and in mitigating the emissions, particularly at a low ratio of organic carbon consumption to nitrogen removal (CODrem/Nrem). In this study, the centrate (centrifuge supernatant) from anaerobic co-digestion of pig slurry was treated in a sequencing batch reactor. The process removed approximately 100% of ammonium a satisfactory nitrogen loading rate (0.4 g N/L/d), with minimum nitrite and nitrate in the effluent. Substantial N2O emission (around 17% of the ammonium nitrogen loading) was observed at the baseline operational condition (dissolved oxygen, DO, levels averaged at 0.85 mg O2/L; CODrem/Nrem of 2.8) with ∼68% of the total emission contributed by nitritation. Emissions increased with higher nitrite accumulation and lower organic carbon to nitrogen ratio. Yet, higher DO levels (∼2.2 mg O2/L) lowered the aerobic N2O emission and weakened the dependency on nitrite concentration, suggesting a shift in N2O production pathway. The most effective N2O mitigation strategy combined intermittent patterns of aeration, anoxic feeding and anoxic carbon dosage, decreasing emission by over 99% (down to ∼0.12% of the ammonium nitrogen loading). Without anaerobic digestion, mitigated Nit/DNit decreases the operational carbon footprint with about 80% compared to N/DN. With anaerobic digestion included, about 4 times more carbon is sequestered. In conclusion, the low CODrem/Nrem feature of Nit/DNit no longer offsets its environmental sustainability provided the process is smartly operated.}, }
@article {pmid28986712, year = {2018}, author = {Allen, JL and Ten-Hage, L and Leflaive, J}, title = {Regulation of Fatty Acid Production and Release in Benthic Algae: Could Parallel Allelopathy Be Explained with Plant Defence Theories?.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {609-621}, pmid = {28986712}, issn = {1432-184X}, mesh = {*Allelopathy ; Biomass ; Carbon/metabolism ; Chlorophyta/growth &amp; development/metabolism ; Culture Media ; Diatoms/drug effects/growth &amp; development ; Fatty Acids/*metabolism/*pharmacology ; Light ; Linoleic Acid/metabolism/pharmacology ; Microalgae/growth &amp; development/*metabolism ; Oligohymenophorea/growth &amp; development/metabolism ; Palmitic Acid/metabolism ; Pheromones/*metabolism ; Plants/*metabolism ; Secondary Metabolism ; Stearic Acids/metabolism ; alpha-Linolenic Acid/metabolism/pharmacology ; }, abstract = {Many organisms produce chemical compounds, generally referred as secondary metabolites, to defend against predators and competitors (allelopathic compounds). Several hypotheses have been proposed to explain the interaction between environmental factors and secondary metabolites production. However, microalgae commonly use simple metabolites having a role in primary metabolism as allelopathic compounds. The aim of this study was to determine whether classical theories of plant chemical defences could be applied to microalgae producing allelochemicals derived from the primary metabolism. Our study was designed to investigate how growth phase, algal population density, nutrient limitation and carbon assimilation affect the production and release of allelopathic free fatty acids (FFAs) among other FFAs. The model species used was Uronema confervicolum, a benthic filamentous green alga that produces two allelopathic FFAs (linoleic and α-linolenic acids) inhibiting diatom growth. FFAs have been quantified in algal biomass and in culture medium. Our results were analysed according to two classical plant defence theories: the growth-differentiation balance hypothesis (GDBH) and the optimal defence theory (ODT), based on the metabolic capacities for defence production and on the need for defence, respectively. While a higher production of allelopathic compounds under increased light conditions supports the use of GDBH with this microalga, the observation of a negative feedback mechanism mostly supports ODT. Therefore, both theories were insufficient to explain all the observed effects of environmental factors on the production of these allelochemicals. This highlights the needs of new theories and models to better describe chemical interactions of microalgae.}, }
@article {pmid28986657, year = {2018}, author = {Chaudhary, DR and Kim, J and Kang, H}, title = {Influences of Different Halophyte Vegetation on Soil Microbial Community at Temperate Salt Marsh.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {729-738}, pmid = {28986657}, issn = {1432-184X}, support = {20110030040; 2015K2A2A2002194; 2016R1D1A1A02937049//Korean Ministry of Science, ICT and Future Planning (MSIP) and National Research Foundation of Korea; Korean Ministry of Education/ ; }, mesh = {Adaptation, Biological ; Archaea/enzymology/genetics/metabolism ; Bacteria/enzymology/genetics/metabolism ; Bacterial Proteins/genetics ; Chenopodiaceae/genetics/microbiology ; Cyperaceae/genetics/microbiology ; Denitrification/genetics ; Enzyme Activation ; Enzymes/genetics/metabolism ; Fatty Acids/analysis ; Fungal Proteins/genetics ; Fungi/enzymology/genetics/metabolism ; Gene Dosage ; Methane/metabolism ; Microbiota/*physiology ; Phospholipids/analysis ; Poaceae/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Salt-Tolerant Plants/genetics/*metabolism/*microbiology ; Soil/chemistry ; *Soil Microbiology ; Sulfites/metabolism ; *Wetlands ; }, abstract = {Salt marshes are transitional zone between terrestrial and aquatic ecosystems, occupied mainly by halophytic vegetation which provides numerous ecological services to coastal ecosystem. Halophyte-associated microbial community plays an important role in the adaptation of plants to adverse condition and also affected habitat characteristics. To explore the relationship between halophytes and soil microbial community, we studied the soil enzyme activities, soil microbial community structure, and functional gene abundance in halophytes- (Carex scabrifolia, Phragmites australis, and Suaeda japonica) covered and un-vegetated (mud flat) soils at Suncheon Bay, South Korea. Higher concentrations of total, Gram-positive, Gram-negative, total bacterial, and actinomycetes PLFAs (phospholipid fatty acids) were observed in the soil underneath the halophytes compared with mud flat soil and were highest in Carex soil. Halophyte-covered soils had different microbial community composition due to higher abundance of Gram-negative bacteria than mud flat soil. Similar to PLFA concentrations, the increased activities of β-glucosidase, cellulase, phosphatase, and sulfatase enzymes were observed under halophyte soil compared to mud flat soil and Carex exhibited highest activities. The abundance of archaeal 16S rRNA, fungal ITS, and denitrifying genes (nirK, nirS, and nosZ) were not influenced by the halophytes. Abundance bacterial 16S rRNA and dissimilatory (bi)sulfite (dsrA) genes were highest in Carex-covered soil. The abundance of functional genes involved in methane cycle (mcrA and pmoA) was not affected by the halophytes. However, the ratios of mcrA/pmoA and mcrA/dsrA increased in halophyte-covered soils which indicate higher methanogenesis activities. The finding of the study also suggests that halophytes had increased the microbial and enzyme activities, and played a pivotal role in shaping microbial community structure.}, }
@article {pmid28985400, year = {2017}, author = {Sanders, JG and Lukasik, P and Frederickson, ME and Russell, JA and Koga, R and Knight, R and Pierce, NE}, title = {Dramatic Differences in Gut Bacterial Densities Correlate with Diet and Habitat in Rainforest Ants.}, journal = {Integrative and comparative biology}, volume = {57}, number = {4}, pages = {705-722}, doi = {10.1093/icb/icx088}, pmid = {28985400}, issn = {1557-7023}, mesh = {Animals ; Ants/*microbiology ; *Bacterial Physiological Phenomena ; *Diet ; *Ecosystem ; *Gastrointestinal Microbiome ; Microscopy, Fluorescence ; Peru ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Rainforest ; Real-Time Polymerase Chain Reaction ; }, abstract = {Abundance is a key parameter in microbial ecology, and important to estimates of potential metabolite flux, impacts of dispersal, and sensitivity of samples to technical biases such as laboratory contamination. However, modern amplicon-based sequencing techniques by themselves typically provide no information about the absolute abundance of microbes. Here, we use fluorescence microscopy and quantitative polymerase chain reaction as independent estimates of microbial abundance to test the hypothesis that microbial symbionts have enabled ants to dominate tropical rainforest canopies by facilitating herbivorous diets, and compare these methods to microbial diversity profiles from 16S rRNA amplicon sequencing. Through a systematic survey of ants from a lowland tropical forest, we show that the density of gut microbiota varies across several orders of magnitude among ant lineages, with median individuals from many genera only marginally above detection limits. Supporting the hypothesis that microbial symbiosis is important to dominance in the canopy, we find that the abundance of gut bacteria is positively correlated with stable isotope proxies of herbivory among canopy-dwelling ants, but not among ground-dwelling ants. Notably, these broad findings are much more evident in the quantitative data than in the 16S rRNA sequencing data. Our results provide quantitative context to the potential role of bacteria in facilitating the ants' dominance of the tropical rainforest canopy, and have broad implications for the interpretation of sequence-based surveys of microbial diversity.}, }
@article {pmid28983932, year = {2017}, author = {Harrison, E and Brockhurst, MA}, title = {Ecological and Evolutionary Benefits of Temperate Phage: What Does or Doesn't Kill You Makes You Stronger.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {39}, number = {12}, pages = {}, doi = {10.1002/bies.201700112}, pmid = {28983932}, issn = {1521-1878}, support = {311490/ERC_/European Research Council/International ; }, mesh = {Bacteria/genetics/growth &amp; development/*virology ; Bacteriophages/*genetics/growth &amp; development ; *Biological Coevolution ; Chromosomes, Bacterial/chemistry ; Ecosystem ; Gene Transfer, Horizontal ; Genetic Variation ; Mutagenesis, Insertional ; Symbiosis/*genetics ; }, abstract = {Infection by a temperate phage can lead to death of the bacterial cell, but sometimes these phages integrate into the bacterial chromosome, offering the potential for a more long-lasting relationship to be established. Here we define three major ecological and evolutionary benefits of temperate phage for bacteria: as agents of horizontal gene transfer (HGT), as sources of genetic variation for evolutionary innovation, and as weapons of bacterial competition. We suggest that a coevolutionary perspective is required to understand the roles of temperate phages in bacterial populations.}, }
@article {pmid28975425, year = {2018}, author = {Chignell, JF and Park, S and Lacerda, CMR and De Long, SK and Reardon, KF}, title = {Label-Free Proteomics of a Defined, Binary Co-culture Reveals Diversity of Competitive Responses Between Members of a Model Soil Microbial System.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {701-719}, pmid = {28975425}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/metabolism ; Antibiosis ; Bacillus/growth &amp; development/metabolism ; Bacterial Proteins ; Bacterial Toxins/metabolism ; Biofilms ; *Coculture Techniques ; Culture Media/chemistry ; Iron/metabolism ; Magnesium/metabolism ; Microbial Interactions/*physiology ; *Models, Biological ; Proteome ; *Proteomics ; Pseudomonas putida/growth &amp; development/metabolism ; Rhizosphere ; Secondary Metabolism ; Soil ; *Soil Microbiology ; Virulence Factors/metabolism ; Zinc/metabolism ; }, abstract = {Interactions among members of microbial consortia drive the complex dynamics in soil, gut, and biotechnology microbiomes. Proteomic analysis of defined co-cultures of well-characterized species provides valuable information about microbial interactions. We used a label-free approach to quantify the responses to co-culture of two model bacterial species relevant to soil and rhizosphere ecology, Bacillus atrophaeus and Pseudomonas putida. Experiments determined the ratio of species in co-culture that would result in the greatest number of high-confidence protein identifications for both species. The 281 and 256 proteins with significant shifts in abundance for B. atrophaeus and P. putida, respectively, indicated responses to co-culture in overall metabolism, cell motility, and response to antagonistic compounds. Proteins associated with a virulent phenotype during surface-associated growth were significantly more abundant for P. putida in co-culture. Co-culture on agar plates triggered a filamentous phenotype in P. putida and avoidance of P. putida by B. atrophaeus colonies, corroborating antagonistic interactions between these species. Additional experiments showing increased relative abundance of P. putida under conditions of iron or zinc limitation and increased relative abundance of B. atrophaeus under magnesium limitation were consistent with patterns of changes in abundance of metal-binding proteins during co-culture. These results provide details on the nature of interactions between two species with antagonistic capabilities. Significant challenges remaining for the development of proteomics as a tool in microbial ecology include accurate quantification of low-abundance peptides, especially from rare species present at low relative abundance in a consortium.}, }
@article {pmid28974945, year = {2017}, author = {Beaton, ED and Stuart, M and Stroes-Gascoyne, S and King-Sharp, KJ and Gurban, I and Festarini, A and Chen, HQ}, title = {Spatial Autocorrelation, Source Water and the Distribution of Total and Viable Microbial Abundances within a Crystalline Formation to a Depth of 800 m.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1731}, pmid = {28974945}, issn = {1664-302X}, abstract = {Proposed radioactive waste repositories require long residence times within deep geological settings for which we have little knowledge of local or regional subsurface dynamics that could affect the transport of hazardous species over the period of radioactive decay. Given the role of microbial processes on element speciation and transport, knowledge and understanding of local microbial ecology within geological formations being considered as host formations can aid predictions for long term safety. In this relatively unexplored environment, sampling opportunities are few and opportunistic. We combined the data collected for geochemistry and microbial abundances from multiple sampling opportunities from within a proposed host formation and performed multivariate mixing and mass balance (M3) modeling, spatial analysis and generalized linear modeling to address whether recharge can explain how subsurface communities assemble within fracture water obtained from multiple saturated fractures accessed by boreholes drilled into the crystalline formation underlying the Chalk River Laboratories site (Deep River, ON, Canada). We found that three possible source waters, each of meteoric origin, explained 97% of the samples, these are: modern recharge, recharge from the period of the Laurentide ice sheet retreat (ca. ∼12000 years before present) and a putative saline source assigned as Champlain Sea (also ca. 12000 years before present). The distributed microbial abundances and geochemistry provide a conceptual model of two distinct regions within the subsurface associated with bicarbonate - used as a proxy for modern recharge - and manganese; these regions occur at depths relevant to a proposed repository within the formation. At the scale of sampling, the associated spatial autocorrelation means that abundances linked with geochemistry were not unambiguously discerned, although fine scale Moran's eigenvector map (MEM) coefficients were correlated with the abundance data and suggest the action of localized processes possibly associated with the manganese and sulfate content of the fracture water.}, }
@article {pmid28974615, year = {2017}, author = {Cabello, FC and Tomova, A and Ivanova, L and Godfrey, HP}, title = {Aquaculture and mcr Colistin Resistance Determinants.}, journal = {mBio}, volume = {8}, number = {5}, pages = {}, pmid = {28974615}, issn = {2150-7511}, mesh = {Aquaculture ; *Colistin ; *Drug Resistance, Bacterial ; Escherichia coli ; }, }
@article {pmid28974259, year = {2017}, author = {Schwendner, P and Mahnert, A and Koskinen, K and Moissl-Eichinger, C and Barczyk, S and Wirth, R and Berg, G and Rettberg, P}, title = {Preparing for the crewed Mars journey: microbiota dynamics in the confined Mars500 habitat during simulated Mars flight and landing.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {129}, pmid = {28974259}, issn = {2049-2618}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; *Confined Spaces ; *Ecological Systems, Closed ; High-Throughput Nucleotide Sequencing ; Humans ; *Mars ; *Microbiota/genetics/physiology ; RNA, Ribosomal, 16S ; *Space Flight ; *Space Simulation ; *Spacecraft ; }, abstract = {BACKGROUND: The Mars500 project was conceived as the first full duration simulation of a crewed return flight to Mars. For 520 days, six crew members lived confined in a specifically designed spacecraft mock-up. The herein described "MIcrobial ecology of Confined Habitats and humAn health" (MICHA) experiment was implemented to acquire comprehensive microbiota data from this unique, confined manned habitat, to retrieve important information on the occurring microbiota dynamics, the microbial load and diversity in the air and on various surfaces. In total, 360 samples from 20 (9 air, 11 surface) locations were taken at 18 time-points and processed by extensive cultivation, PhyloChip and next generation sequencing (NGS) of 16S rRNA gene amplicons.<br><br>RESULTS: Cultivation assays revealed a Staphylococcus and Bacillus-dominated microbial community on various surfaces, with an average microbial load that did not exceed the allowed limits for ISS in-flight requirements indicating adequate maintenance of the facility. Areas with high human activity were identified as hotspots for microbial accumulation. Despite substantial fluctuation with respect to microbial diversity and abundance throughout the experiment, the location within the facility and the confinement duration were identified as factors significantly shaping the microbial diversity and composition, with the crew representing the main source for microbial dispersal. Opportunistic pathogens, stress-tolerant or potentially mobile element-bearing microorganisms were predicted to be prevalent throughout the confinement, while the overall microbial diversity dropped significantly over time.<br><br>CONCLUSIONS: Our findings clearly indicate that under confined conditions, the community structure remains a highly dynamic system which adapts to the prevailing habitat and micro-conditions. Since a sterile environment is not achievable, these dynamics need to be monitored to avoid spreading of highly resistant or potentially pathogenic microorganisms and a potentially harmful decrease of microbial diversity. If necessary, countermeasures are required, to maintain a healthy, diverse balance of beneficial, neutral and opportunistic pathogenic microorganisms. Our results serve as an important data collection for (i) future risk estimations of crewed space flight, (ii) an optimized design and planning of a spacecraft mission and (iii) for the selection of appropriate microbial monitoring approaches and potential countermeasures, to ensure a microbiologically safe space-flight environment.}, }
@article {pmid28971238, year = {2018}, author = {Rodrigues, EM and Morais, DK and Pylro, VS and Redmile-Gordon, M and de Oliveira, JA and Roesch, LFW and Cesar, DE and Tótola, MR}, title = {Aliphatic Hydrocarbon Enhances Phenanthrene Degradation by Autochthonous Prokaryotic Communities from a Pristine Seawater.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {688-700}, pmid = {28971238}, issn = {1432-184X}, support = {405544/2012-0//CNPq/ ; }, mesh = {Alkanes ; Alphaproteobacteria/drug effects/metabolism ; Bacteria/classification/*drug effects/genetics/*metabolism ; Biodegradation, Environmental ; Biodiversity ; Brazil ; DNA, Bacterial/genetics ; Ecosystem ; Gammaproteobacteria/drug effects/metabolism ; High-Throughput Nucleotide Sequencing ; Hydrocarbons/*adverse effects ; Islands ; Metagenomics ; Microbial Consortia/*drug effects/genetics/*physiology ; Petroleum Pollution/adverse effects ; Phenanthrenes/*metabolism ; Polycyclic Aromatic Hydrocarbons/pharmacology ; Pyrenes ; RNA, Ribosomal, 16S/metabolism ; Seawater/*microbiology ; Water Pollutants ; }, abstract = {The microbial diversity and functioning around oceanic islands is poorly described, despite its importance for ecosystem homeostasis. Here, we aimed to verify the occurrence of microbe-driven phenanthrene co-oxidation in the seawater surrounding the Trindade Island (Brazil). We also used Next-Generation Sequencing to evaluate the effects of aliphatic and polycyclic aromatic hydrocarbons (PAHs) on these microbial community assemblies. Microcosms containing seawater from the island enriched with either labelled (9-[14]C) or non-labelled phenanthrene together with hexadecane, weathered oil, fluoranthene or pyrene, and combinations of these compounds were incubated. Biodegradation of phenanthrene-9-[14]C was negatively affected in the presence of weathered oil and PAHs but increased in the presence of hexadecane. PAH contamination caused shifts in the seawater microbial community-from a highly diverse one dominated by Alphaproteobacteria to less diverse communities dominated by Gammaproteobacteria. Furthermore, the combination of PAHs exerted a compounded negative influence on the microbial community, reducing its diversity and thus functional capacity of the ecosystem. These results advance our understanding of bacterial community dynamics in response to contrasting qualities of hydrocarbon contamination. This understanding is fundamental in the application and monitoring of bioremediation strategies if accidents involving oil spillages occur near Trindade Island and similar ecosystems.}, }
@article {pmid28971068, year = {2017}, author = {Benítez-Páez, A and Gómez Del Pulgar, EM and Sanz, Y}, title = {The Glycolytic Versatility of Bacteroides uniformis CECT 7771 and Its Genome Response to Oligo and Polysaccharides.}, journal = {Frontiers in cellular and infection microbiology}, volume = {7}, number = {}, pages = {383}, pmid = {28971068}, issn = {2235-2988}, mesh = {Animals ; Bacteroides/genetics/*metabolism ; Cohort Studies ; Dietary Fiber/metabolism ; Gastrointestinal Microbiome/genetics/*physiology ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Genome, Bacterial/*physiology ; Glycolysis/genetics/*physiology ; Humans ; Infant ; Obesity/microbiology ; Polysaccharides/*metabolism ; Prospective Studies ; Symbiosis/physiology ; }, abstract = {Bacteroides spp. are dominant components of the phylum Bacteroidetes in the gut microbiota and prosper in glycan enriched environments. However, knowledge of the machinery of specific species isolated from humans (like Bacteroides uniformis) contributing to the utilization of dietary and endogenous sources of glycans and their byproducts is limited. We have used the cutting-edge nanopore-based technology to sequence the genome of B. uniformis CECT 7771, a human symbiont with a proven pre-clinical efficacy on metabolic and immune dysfunctions in obesity animal models. We have also used massive sequencing approaches to distinguish the genome expression patterns in response to carbon sources of different complexity during growth. At genome-wide level, our analyses globally demonstrate that B. uniformis strains exhibit an expanded glycolytic capability when compared with other Bacteroides species. Moreover, by studying the growth and whole-genome expression of B. uniformis CECT 7771 in response to different carbon sources, we detected a differential growth fitness and expression patterns across the genome depending on the carbon source of the culture media. The dietary fibers used exerted different effects on B. uniformis CECT 7771 activating different molecular pathways and, therefore, allowing the production of different metabolite types with potential impact on gut health. The genome and transcriptome analysis of B. uniformis CECT 7771, in response to different carbon sources, shows its high versatility to utilize both dietary and endogenous glycans along with the production of potentially beneficial end products for both the bacterium and the host, pointing to a mechanistic basis of a mutualistic relationship.}, }
@article {pmid28970223, year = {2017}, author = {Xiao, C and Lu, ZM and Zhang, XJ and Wang, ST and Ao, L and Shen, CH and Shi, JS and Xu, ZH}, title = {Bio-Heat Is a Key Environmental Driver Shaping the Microbial Community of Medium-Temperature Daqu.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {23}, pages = {}, pmid = {28970223}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodiversity ; China ; Edible Grain/microbiology ; *Microbiota ; Temperature ; Wine/analysis/*microbiology ; }, abstract = {"Daqu" is a saccharifying and fermenting agent commonly used in the traditional solid-state fermentation industry (e.g., baijiu and vinegar). The patterns of microbial community succession and flavor formation are highly similar among batches, yet the mechanisms promoting temporal succession in the Daqu microbial ecology remain unclear. Here, we first correlated temporal profiles of microbial community succession with environmental variables (temperature, moisture, and titratable acidity) in medium temperature Daqu (MT-Daqu) throughout fermentation. Temperature dynamics significantly correlated (P < 0.05) with the quick succession of MT-Daqu microbiota in the first 12 d of fermentation, while the community structure was relatively stable after 12 d. Then, we explored the effect of temperature on the MT-Daqu community assembly. In the first 4 d of fermentation, the rapid propagation of most bacterial taxa and several fungal taxa, including Candida, Wickerhamomyces, and unclassified Dipodascaceae and Saccharomycetales species, significantly increased MT-Daqu temperature to 55°C. Subsequently, sustained bio-heat generated by microbial metabolism (53 to 56°C) within MT-Daqu inhibited the growth of most microbes from day 4 to day 12, while thermotolerant taxa, including Bacillus, unclassified Streptophyta, Weissella, Thermoactinomyces, Thermoascus, and Thermomyces survived or kept on growing. Furthermore, temperature as a major driving force on the shaping of MT-Daqu microbiota was validated. Lowering the fermentation temperature by placing the MT-Daqu in a 37°C incubator resulted in decreased relative abundances of thermotolerant taxa, including Bacillus, Thermoactinomyces, and Thermoascus, in the MT-Daqu microbiota. This study revealed that bio-heat functioned as a primary endogenous driver promoting the formation of functional MT-Daqu microbiota.IMPORTANCE Humans have mastered the Daqu preparation technique of cultivating functional microbiota on starchy grains over thousands of years, and it is well known that the metabolic activity of these microbes is key to the flavor production of Chinese baijiu. The pattern of microbial community succession and flavor formation remains highly similar between batches, yet mechanistic insight into these patterns and into microbial population fidelity to specific environmental conditions remains unclear. Our study revealed that bio-heat was generated within Daqu bricks in the first 4 d of fermentation, concomitant with rapid microbial propagation and metabolism. The sustained bio-heat may then function as a major endogenous driving force promoting the formation of the MT-Daqu microbiota from day 4 to day 12. The bio-heat-driven growth of thermotolerant microorganisms might contribute to the formation of flavor metabolites. This study provides useful information for the temperature-based modulation of microbiota function during the fermentation of Daqu.}, }
@article {pmid28968189, year = {2018}, author = {Vázquez-Baeza, Y and Callewaert, C and Debelius, J and Hyde, E and Marotz, C and Morton, JT and Swafford, A and Vrbanac, A and Dorrestein, PC and Knight, R}, title = {Impacts of the Human Gut Microbiome on Therapeutics.}, journal = {Annual review of pharmacology and toxicology}, volume = {58}, number = {}, pages = {253-270}, doi = {10.1146/annurev-pharmtox-042017-031849}, pmid = {28968189}, issn = {1545-4304}, mesh = {Animals ; Anti-Inflammatory Agents, Non-Steroidal/pharmacology/therapeutic use ; Antineoplastic Agents/pharmacology/therapeutic use ; Cardiac Glycosides/pharmacology/therapeutic use ; Gastrointestinal Microbiome/*drug effects/*physiology ; Humans ; Microbiota/*drug effects/*physiology ; Signal Transduction/drug effects ; }, abstract = {The human microbiome contains a vast source of genetic and biochemical variation, and its impacts on therapeutic responses are just beginning to be understood. This expanded understanding is especially important because the human microbiome differs far more among different people than does the human genome, and it is also dramatically easier to change. Here, we describe some of the major factors driving differences in the human microbiome among individuals and populations. We then describe some of the many ways in which gut microbes modify the action of specific chemotherapeutic agents, including nonsteroidal anti-inflammatory drugs and cardiac glycosides, and outline the potential of fecal microbiota transplant as a therapeutic. Intriguingly, microbes also alter how hosts respond to therapeutic agents through various pathways acting at distal sites. Finally, we discuss some of the computational and practical issues surrounding use of the microbiome to stratify individuals for drug response, and we envision a future where the microbiome will be modified to increase everyone's potential to benefit from therapy.}, }
@article {pmid28966922, year = {2017}, author = {Gionco, B and Tavares, ER and de Oliveira, AG and Yamada-Ogatta, SF and do Carmo, AO and Pereira, UP and Chideroli, RT and Simionato, AS and Navarro, MOP and Chryssafidis, AL and Andrade, G}, title = {New Insights about Antibiotic Production by Pseudomonas aeruginosa: A Gene Expression Analysis.}, journal = {Frontiers in chemistry}, volume = {5}, number = {}, pages = {66}, pmid = {28966922}, issn = {2296-2646}, abstract = {The bacterial resistance for antibiotics is one of the most important problems in public health and only a small number of new products are in development. Antagonistic microorganisms from soil are a promising source of new candidate molecules. Products of secondary metabolism confer adaptive advantages for their producer, in the competition for nutrients in the microbial community. The biosynthesis process of compounds with antibiotic activity is the key to optimize their production and the transcriptomic study of microorganisms is of great benefit for the discovery of these metabolic pathways. Pseudomonas aeruginosa LV strain growing in the presence of copper chloride produces a bioactive organometallic compound, which has a potent antimicrobial activity against various microorganisms. The objective of this study was to verify overexpressed genes and evaluate their relation to the organometallic biosynthesis in this microorganism. P. aeruginosa LV strain was cultured in presence and absence of copper chloride. Two methods were used for transcriptomic analysis, genome reference-guided assembly and de novo assembly. The genome referenced analysis identified nine upregulated genes when bacteria were exposed to copper chloride, while the De Novo Assembly identified 12 upregulated genes. Nineteen genes can be related to an increased microbial metabolism for the extrusion process of exceeding intracellular copper. Two important genes are related to the biosynthesis of phenazine and tetrapyrroles compounds, which can be involved in the bioremediation of intracellular copper and we suggesting that may involve in the biosynthesis of the organometallic compound. Additional studies are being carried out to further prove the function of the described genes and relate them to the biosynthetic pathway of the organometallic compound.}, }
@article {pmid28963577, year = {2018}, author = {Fiałkowska, E and Pajdak-Stós, A}, title = {Temperature-Dependence of Predator-Prey Dynamics in Interactions Between the Predatory Fungus Lecophagus sp. and Its Prey L. inermis Rotifers.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {400-406}, pmid = {28963577}, issn = {1432-184X}, support = {GEKON1/O3/214361/8/2014//National Center for Research and Development/ ; DS/WBiNoS/INoS/757//Uniwersytet Jagiello&#x144;ski w Krakowie/ ; }, mesh = {Animals ; Ascomycota/growth &amp; development/*physiology ; Ecosystem ; Feeding Behavior ; Mycelium/growth &amp; development/physiology ; Rotifera/*physiology ; Spores, Fungal/growth &amp; development/physiology ; Temperature ; Wastewater/chemistry/microbiology/parasitology ; Water Wells ; }, abstract = {Temperature is considered an important factor that influences the bottom-up and top-down control in water habitats. We examined the influence of temperature on specific predatory-prey dynamics in the following two-level trophic system: the predatory fungus Lecophagus sp. and its prey Lecane inermis rotifers, both of which originated from activated sludge obtained from a wastewater treatment plant (WWTP). The experiments investigating the ability of conidia to trap rotifers and the growth of fungal mycelium were performed in a temperature range that is similar to that in WWTPs in temperate climate. At 20 °C, 80% of the conidia trapped the prey during the first 24 h, whereas at 8 °C, no conidium was successful. The mycelium growth rate was the highest at 20 °C (r = 1.44) during the first 48 h but decreased during the following 24 h (r = 0.98), suggesting the quickest use of resources. At a medium temperature of 15 °C, the tendency was opposite, and the r value was lower during the first 48 h. At 8 °C, the growth rate was very low and remained at the same level even though numerous active rotifers were potentially available for the fungus. The temperature also influences the production of new conidia; on the 7th day, new conidia were observed in 96% of the wells at 20 °C, but no new conidia were observed at 8°C. These results show that the prey (rotifers)-predator (Lecophagus) dynamics in WWTPs is temperature-dependent, and a temperature of 8 °C is a strongly limiting factor for the fungus. Moderate temperatures ensure the most stable coexistence of the fungus and its prey, whereas the highest temperature can promote the prevalence of the predator.}, }
@article {pmid28963574, year = {2018}, author = {Olapade, OA}, title = {Community Composition and Diversity of Coastal Bacterioplankton Assemblages in Lakes Michigan, Erie, and Huron.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {598-608}, pmid = {28963574}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics ; Biodiversity ; DNA, Bacterial/genetics ; Fresh Water/chemistry/microbiology ; In Situ Hybridization, Fluorescence/methods ; Lakes/chemistry/*microbiology ; Michigan ; *Microbiota/genetics ; *Phylogeny ; Plankton/*classification/genetics ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; }, abstract = {The Laurentian Great Lakes, including Lakes Superior, Michigan, Huron, Erie, and Ontario, located in the eastern part of North America are considered the largest of freshwater lakes in the world; however, very little is known about the diversity and distribution of indigenous microbial assemblages within these vast bodies of freshwater systems. Therefore, to delineate the microbial structure and community composition in these aquatic environments, combinations of high-throughput sequencing and fluorescent in situ hybridization (FISH) approaches were utilized to quantitatively characterize the occurrence, diversity, and distribution of bacterioplankton assemblages in six different sites located along the coastal regions of Lakes Michigan, Huron, and Erie. Phylogenetic examination showed a diverse bacterial community belonging to 11 different taxonomic groups. Pyrosequencing results revealed that the majority of the sequences were clustered into four main groups, i.e., Proteobacteria, Bacteriodetes, Actinobacteria, and Cyanobacteria, while fluorescent in situ hybridization also showed the numerical dominance of members of the Gammaproteobacteria and the Cytophaga-Flavobacterium in the six lake sites examined. Overall, the assemblages were shown to be quite diverse in distribution among the lake sites examined, comprising mostly of various heterotrophic populations, with the exception of the Lake Erie-Sandusky Bay site with more than 50% domination by autotrophic Cyanobacteria. This indicates that combinations of factors including water chemistry and various anthropogenic disturbances as well as the lake morphometric characteristics are probably influencing the community structure and diversity of the bacterial assemblages within the systems.}, }
@article {pmid28961970, year = {2017}, author = {Nielsen, TK and Rasmussen, M and Demanèche, S and Cecillon, S and Vogel, TM and Hansen, LH}, title = {Evolution of Sphingomonad Gene Clusters Related to Pesticide Catabolism Revealed by Genome Sequence and Mobilomics of Sphingobium herbicidovorans MH.}, journal = {Genome biology and evolution}, volume = {9}, number = {9}, pages = {2477-2490}, pmid = {28961970}, issn = {1759-6653}, mesh = {2-Methyl-4-chlorophenoxyacetic Acid/*metabolism ; Bacterial Proteins/genetics ; Biodegradation, Environmental ; *Evolution, Molecular ; Genes, Bacterial ; Herbicides/*metabolism ; *Interspersed Repetitive Sequences ; *Multigene Family ; Oxygenases/genetics ; Sphingomonadaceae/*genetics ; }, abstract = {Bacterial degraders of chlorophenoxy herbicides have been isolated from various ecosystems, including pristine environments. Among these degraders, the sphingomonads constitute a prominent group that displays versatile xenobiotic-degradation capabilities. Four separate sequencing strategies were required to provide the complete sequence of the complex and plastic genome of the canonical chlorophenoxy herbicide-degrading Sphingobium herbicidovorans MH. The genome has an intricate organization of the chlorophenoxy-herbicide catabolic genes sdpA, rdpA, and cadABCD that encode the (R)- and (S)-enantiomer-specific 2,4-dichlorophenoxypropionate dioxygenases and four subunits of a Rieske non-heme iron oxygenase involved in 2-methyl-chlorophenoxyacetic acid degradation, respectively. Several major genomic rearrangements are proposed to help understand the evolution and mobility of these important genes and their genetic context. Single-strain mobilomic sequence analysis uncovered plasmids and insertion sequence-associated circular intermediates in this environmentally important bacterium and enabled the description of evolutionary models for pesticide degradation in strain MH and related organisms. The mobilome presented a complex mosaic of mobile genetic elements including four plasmids and several circular intermediate DNA molecules of insertion-sequence elements and transposons that are central to the evolution of xenobiotics degradation. Furthermore, two individual chromosomally integrated prophages were shown to excise and form free circular DNA molecules. This approach holds great potential for improving the understanding of genome plasticity, evolution, and microbial ecology.}, }
@article {pmid28961933, year = {2017}, author = {Tecon, R and Or, D}, title = {Biophysical processes supporting the diversity of microbial life in soil.}, journal = {FEMS microbiology reviews}, volume = {41}, number = {5}, pages = {599-623}, pmid = {28961933}, issn = {1574-6976}, mesh = {*Biodiversity ; *Biophysical Phenomena ; Ecosystem ; Microbiota/*physiology ; *Soil Microbiology ; }, abstract = {Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms. This review explores key drivers for microbial life in soils under different climates and land-use practices at scales ranging from soil pores to landscapes. We delineate special features of soil as a microbial habitat (focusing on bacteria) and the consequences for microbial communities. This review covers recent modeling advances that link soil physical processes with microbial life (termed biophysical processes). Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly dynamic soil aqueous phase. The narrow hydrological windows of wetting and aqueous phase connectedness are crucial for resource distribution and longer range transport of microorganisms. Feedbacks between microbial activity and their immediate environment are responsible for emergence and stabilization of soil structure-the scaffolding for soil ecological functioning. We synthesize insights from historical and contemporary studies to provide an outlook for the challenges and opportunities for developing a quantitative ecological framework to delineate and predict the microbial component of soil functioning.}, }
@article {pmid28961781, year = {2017}, author = {Alkorta, I and Epelde, L and Garbisu, C}, title = {Environmental parameters altered by climate change affect the activity of soil microorganisms involved in bioremediation.}, journal = {FEMS microbiology letters}, volume = {364}, number = {19}, pages = {}, doi = {10.1093/femsle/fnx200}, pmid = {28961781}, issn = {1574-6968}, mesh = {Bacteria/*metabolism ; Biodegradation, Environmental ; *Climate Change ; Plant Development ; Plants/metabolism ; *Soil Microbiology ; Soil Pollutants/metabolism ; }, abstract = {Bioremediation, based on the use of microorganisms to break down pollutants, can be very effective at reducing soil pollution. But the climate change we are now experiencing is bound to have an impact on bioremediation performance, since the activity and degrading abilities of soil microorganisms are dependent on a series of environmental parameters that are themselves being altered by climate change, such as soil temperature, moisture, amount of root exudates, etc. Many climate-induced effects on soil microorganisms occur indirectly through changes in plant growth and physiology derived from increased atmospheric CO2 concentrations and temperatures, the alteration of precipitation patterns, etc., with a concomitant effect on rhizoremediation performance (i.e. the plant-assisted microbial degradation of pollutants in the rhizosphere). But these effects are extremely complex and mediated by processes such as acclimation and adaptation. Besides, soil microorganisms form complex networks of interactions with a myriad of organisms from many taxonomic groups that will also be affected by climate change, further complicating data interpretation.}, }
@article {pmid28959736, year = {2017}, author = {Stressmann, FA and Couve-Deacon, E and Chainier, D and Chauhan, A and Wessel, A and Durand-Fontanier, S and Escande, MC and Kriegel, I and Francois, B and Ploy, MC and Beloin, C and Ghigo, JM}, title = {Comparative Analysis of Bacterial Community Composition and Structure in Clinically Symptomatic and Asymptomatic Central Venous Catheters.}, journal = {mSphere}, volume = {2}, number = {5}, pages = {}, pmid = {28959736}, issn = {2379-5042}, abstract = {Totally implanted venous access ports (TIVAPs) are commonly used catheters for the management of acute or chronic pathologies. Although these devices improve health care, repeated use of this type of device for venous access over long periods of time is also associated with risk of colonization and infection by pathogenic bacteria, often originating from skin. However, although the skin microbiota is composed of both pathogenic and nonpathogenic bacteria, the extent and the consequences of TIVAP colonization by nonpathogenic bacteria have rarely been studied. Here, we used culture-dependent and 16S rRNA gene-based culture-independent approaches to identify differences in bacterial colonization of TIVAPs obtained from two French hospitals. To explore the relationships between nonpathogenic organisms colonizing TIVAPs and the potential risk of infection, we analyzed the bacterial community parameters between TIVAPs suspected (symptomatic) or not (asymptomatic) of infection. Although we did not find a particular species assemblage or community marker to distinguish infection risk on an individual sample level, we identified differences in bacterial community composition, diversity, and structure between clinically symptomatic and asymptomatic TIVAPs that could be explored further. This study therefore provides a new view of bacterial communities and colonization patterns in intravascular TIVAPs and suggests that microbial ecology approaches could improve our understanding of device-associated infections and could be a prognostic tool to monitor the evolution of bacterial communities in implants and their potential susceptibility to infections. IMPORTANCE Totally implanted venous access ports (TIVAPs) are commonly used implants for the management of acute or chronic pathologies. Although their use improves the patient's health care and quality of life, they are associated with a risk of infection and subsequent clinical complications, often leading to implant removal. While all TIVAPs appear to be colonized, only a fraction become infected, and the relationship between nonpathogenic organisms colonizing TIVAPs and the potential risk of infection is unknown. We explored bacteria present on TIVAPs implanted in patients with or without signs of TIVAP infection and identified differences in phylum composition and community structure. Our data suggest that the microbial ecology of intravascular devices could be predictive of TIVAP infection status and that ultimately a microbial ecological signature could be identified as a tool to predict TIVAP infection susceptibility and improve clinical management.}, }
@article {pmid28959245, year = {2017}, author = {De Maayer, P and Aliyu, H and Vikram, S and Blom, J and Duffy, B and Cowan, DA and Smits, THM and Venter, SN and Coutinho, TA}, title = {Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1755}, pmid = {28959245}, issn = {1664-302X}, abstract = {Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart's wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes, has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis. While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range.}, }
@article {pmid28957586, year = {2017}, author = {Soares, M and Kritzberg, ES and Rousk, J}, title = {Labile carbon 'primes' fungal use of nitrogen from submerged leaf litter.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {9}, pages = {}, doi = {10.1093/femsec/fix110}, pmid = {28957586}, issn = {1574-6941}, mesh = {Bacteria/growth &amp; development/*metabolism ; Carbon/*metabolism ; Fresh Water ; Fungi/growth &amp; development/*metabolism ; Nitrogen/*metabolism ; Photosynthesis ; Plant Leaves/*microbiology ; Plants/metabolism/microbiology ; }, abstract = {Microbial decomposers colonising submerged leaf litter are in close spatial proximity with periphytic algae and can use carbon (C) exudates released during photosynthesis. We investigated whether labile C delivered as algal exudates could affect the microbial colonisation and decomposition of leaf litter. Using microcosms, we submerged leaf litter in pond water and monitored fungal and bacterial growth over time and tested the effect of algal photosynthetic exudates by comparing microcosms in light and dark. In order to experimentally assign the effect of algal products to labile C delivery and test for a C driven mechanism, we ran a parallel experiment with microcosms in the dark where we mimicked the delivery of algal labile C by continuously adding glucose. Labile C delivered as algal exudates or glucose resulted in a dominance of fungal decomposers over bacteria, and stimulated the acquisition of more N-rich OM fractions from litter during periods of active fungal growth. Our results highlight that labile C stimulates fungal decomposers and increases N removal from leaf litter. Since fungal necromass is more resistant to degradation than bacterial, we expect that a fungal-dominated litter degradation might contribute to more protected C pools.}, }
@article {pmid28956349, year = {2017}, author = {Nguyen, NL and Yu, WJ and Yang, HY and Kim, JG and Jung, MY and Park, SJ and Roh, SW and Rhee, SK}, title = {A novel methanotroph in the genus Methylomonas that contains a distinct clade of soluble methane monooxygenase.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {55}, number = {10}, pages = {775-782}, pmid = {28956349}, issn = {1976-3794}, mesh = {Alcohol Oxidoreductases/genetics ; Bacterial Typing Techniques ; Base Sequence ; Carbon/metabolism ; DNA, Bacterial/genetics ; Fresh Water/microbiology ; Genes, Bacterial/genetics ; Methane/metabolism ; Methylococcaceae/classification ; Methylomonas/classification/*enzymology/*genetics/isolation &amp; purification ; Nitrogen ; Nitrogen Fixation ; Oxygenases/classification/*genetics/*metabolism ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; Water Microbiology ; }, abstract = {Aerobic methane oxidation is a key process in the global carbon cycle that acts as a major sink of methane. In this study, we describe a novel methanotroph designated EMGL16-1 that was isolated from a freshwater lake using the floating filter culture technique. Based on a phylogenetic analysis of 16S rRNA gene sequences, the isolate was found to be closely related to the genus Methylomonas in the family Methylococcaceae of the class Gammaproteobacteria with 94.2-97.4% 16S rRNA gene similarity to Methylomonas type strains. Comparison of chemotaxonomic and physiological properties further suggested that strain EMGL16-1 was taxonomically distinct from other species in the genus Methylomonas. The isolate was versatile in utilizing nitrogen sources such as molecular nitrogen, nitrate, nitrite, urea, and ammonium. The genes coding for subunit of the particulate form methane monooxygenase (pmoA), soluble methane monooxygenase (mmoX), and methanol dehydrogenase (mxaF) were detected in strain EMGL16-1. Phylogenetic analysis of mmoX indicated that mmoX of strain EMGL16-1 is distinct from those of other strains in the genus Methylomonas. This isolate probably represents a novel species in the genus. Our study provides new insights into the diversity of species in the genus Methylomonas and their environmental adaptations.}, }
@article {pmid28956100, year = {2018}, author = {Guivier, E and Martin, JF and Pech, N and Ungaro, A and Chappaz, R and Gilles, A}, title = {Microbiota Diversity Within and Between the Tissues of Two Wild Interbreeding Species.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {799-810}, doi = {10.1007/s00248-017-1077-9}, pmid = {28956100}, issn = {1432-184X}, support = {FACIES//&#xc9;lectricit&#xe9; de France/ ; }, mesh = {Animals ; Bacteria/*classification/genetics ; *Biodiversity ; Cyprinidae/*microbiology ; DNA, Bacterial ; Female ; France ; Gastrointestinal Microbiome ; Gills/microbiology ; Host Microbial Interactions/genetics/physiology ; Host Specificity ; Hybridization, Genetic ; Male ; Microbiota/genetics/*physiology ; Mucous Membrane/microbiology ; *Phylogeny ; Skin/microbiology ; }, abstract = {Understanding the role of microbiota as reproductive barriers or sources of adaptive novelty in the fundamental biological phenomenon of speciation is an exciting new challenge necessitating exploration of microbiota variation in wild interbreeding species. We focused on two interbreeding cyprinid species, Chondrostoma nasus and Parachondrostoma toxostoma, which have geographic distributions characterized by a mosaic of hybrid zones. We described microbiota diversity and composition in the three main teleost mucosal tissues, the skin, gills and gut, in the parental parapatric populations. We found that tissue type was the principal determinant of bacterial community composition. In particular, there was strong microbiota differentiation between external and internal tissues, with secondary discrimination between the two species. These findings suggest that specific environmental and genetic filters associated with each species have shaped the bacterial communities, potentially reflecting deterministic assemblages of bacteria. We defined the core microbiota common to both Chondrostoma species for each tissue, highlighting the occurrence of microbe-host genome interactions at this critical level for studies of the functional consequences of hybridization. Further investigations will explore to what extend these specific tissue-associated microbiota signatures could be profoundly altered in hybrids, with functional consequences for post-mating reproductive isolation in relation to environmental constraints.}, }
@article {pmid28954508, year = {2017}, author = {Yuan, H and Sun, S and Abu-Reesh, IM and Badgley, BD and He, Z}, title = {Unravelling and Reconstructing the Nexus of Salinity, Electricity, and Microbial Ecology for Bioelectrochemical Desalination.}, journal = {Environmental science &amp; technology}, volume = {51}, number = {21}, pages = {12672-12682}, doi = {10.1021/acs.est.7b03763}, pmid = {28954508}, issn = {1520-5851}, mesh = {Bayes Theorem ; *Bioelectric Energy Sources ; Electricity ; Electrodes ; Salinity ; *Water Purification ; }, abstract = {Microbial desalination cells (MDCs) are an emerging concept for simultaneous water/wastewater treatment and energy recovery. The key to developing MDCs is to understand fundamental problems, such as the effects of salinity on system performance and the role of microbial community and functional dynamics. Herein, a tubular MDC was operated under a wide range of salt concentrations (0.05-4 M), and the salinity effects were comprehensively examined. The MDC generated higher current with higher salt concentrations in the desalination chamber. When fed with 4 M NaCl, the MDC achieve a current density of 300 A m[-3] (anode volume), which was one of the highest among bioelectrochemical system studies. Community analysis and electrochemical measurements suggested that electrochemically active bacteria Pseudomonas and Acinetobacter transferred electrons extracellularly via electron shuttles, and the consequent ion migration led to high anode salinities and conductivity that favored their dominance. Predictive functional dynamics and Bayesian networks implied that the taxa putatively not capable of extracellular electron transfer (e.g., Bacteroidales and Clostridiales) might indirectly contribute to bioelectrochemical desalination. By integrating the Bayesian network with logistic regression, current production was successfully predicted from taxonomic data. This study has demonstrated uncompromised system performance under high salinity and thus has highlighted the potential of MDCs as an energy-efficient technology to address water-energy challenges. The statistical modeling approach developed in this study represents a significant step toward understating microbial communities and predicting system performance in engineered biological systems.}, }
@article {pmid28954249, year = {2018}, author = {Bensidhom, G and Ben Hassen-Trabelsi, A and Alper, K and Sghairoun, M and Zaafouri, K and Trabelsi, I}, title = {Pyrolysis of Date palm waste in a fixed-bed reactor: Characterization of pyrolytic products.}, journal = {Bioresource technology}, volume = {247}, number = {}, pages = {363-369}, doi = {10.1016/j.biortech.2017.09.066}, pmid = {28954249}, issn = {1873-2976}, mesh = {*Biofuels ; Hot Temperature ; *Phoeniceae ; Plant Oils ; Polyphenols ; Waste Products ; }, abstract = {The pyrolysis of several Tunisian Date Palm Wastes (DPW): Date Palm Rachis (DPR), Date Palm Leaflets (DPL), Empty Fruit Bunches (EFB) and Date Palm Glaich (DPG) was run using a fixed-bed reactor, from room temperature to 500°C, with 15°C/min as heating rate and -5°C as condensation temperature, in order to produce bio-oil, biochar and syngas. In these conditions, the bio-oil yield ranges from 17.03wt% for DPL to 25.99wt% for EFB. For the biochar, the highest yield (36.66wt%) was obtained for DPL and the lowest one (31.66wt%) was obtained from DPG while the syngas production varies from 39.10wt% for DPR to 46.31wt% DPL. The raw material and pyrolysis products have been characterized using elemental analysis thermogravimetric analysis (TGA), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM). The syngas composition has been characterized using gas analyzer.}, }
@article {pmid28951994, year = {2018}, author = {Marić Pfannkuchen, D and Godrijan, J and Smodlaka Tanković, M and Baričević, A and Kužat, N and Djakovac, T and Pustijanac, E and Jahn, R and Pfannkuchen, M}, title = {The Ecology of One Cosmopolitan, One Newly Introduced and One Occasionally Advected Species from the Genus Skeletonema in a Highly Structured Ecosystem, the Northern Adriatic.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {674-687}, pmid = {28951994}, issn = {1432-184X}, support = {UIP-2014-09-6563//Hrvatska Zaklada za Znanost/ ; DE-TAF-4090//European Union/ ; DE-TAF-4112//European Union/ ; }, mesh = {Biota ; China ; DNA/analysis/genetics ; DNA, Ribosomal/genetics ; Diatoms/*classification/cytology/genetics/isolation &amp; purification ; *Ecology ; *Ecosystem ; Fresh Water/microbiology ; Genes, rRNA/genetics ; Genetic Markers/genetics ; Geographic Mapping ; India ; Japan ; *Marine Biology ; Microscopy, Electron ; Nutrients ; Oman ; *Phylogeny ; Phytoplankton/classification ; Salinity ; Seasons ; Seawater/chemistry ; Species Specificity ; Yemen ; }, abstract = {The diatom genus Skeletonema is globally distributed and often an important constituent of the phytoplankton community. In the marine phytoplankton of the northern Adriatic Sea, we found three species of the genus Skeletonema: Skeletonema menzelii, Skeletonema marinoi and Skeletonema grevillei. Making use of the steep ecological gradients that characterise the northern Adriatic, along which we could observe those species, we report here on the ecological circumstances under which those species thrive and how their respective populations are globally connected. This is the first detailed ecological study for the species S. grevillei. This study is also the first report for S. grevillei for the Adriatic Sea and Mediterranean together with additional electron microscopic details on fresh in situ samples for this species. S. marinoi appears to clearly prefer strong freshwater influence and high nutrient concentrations delivered by low salinity waters. It can outcompete other diatom species and dominate microphytoplankton blooms. S. grevillei on the other hand appears to thrive in high nutrient concentrations triggered by water column mixing. It also appears to prefer higher salinity waters and coastal embayments. Genetic analysis of S. grevillei demonstrated a peculiar dissimilarity with isolates from coastal waters off Yemen, India, Oman and China. However, a closely related sequence was isolated from coastal waters off Japan. These results indicate that S. grevillei is an introduced species, possibly transported by ballast waters. S. menzelii is a sporadic visitor in the northern Adriatic, advected from rather oligotrophic middle Adriatic waters and never dominates the phytoplankton community in the northern Adriatic.}, }
@article {pmid28951889, year = {2017}, author = {Daniel, SG and Ball, CL and Besselsen, DG and Doetschman, T and Hurwitz, BL}, title = {Functional Changes in the Gut Microbiome Contribute to Transforming Growth Factor β-Deficient Colon Cancer.}, journal = {mSystems}, volume = {2}, number = {5}, pages = {}, pmid = {28951889}, issn = {2379-5077}, support = {P30 CA023074/CA/NCI NIH HHS/United States ; R01 AI067903/AI/NIAID NIH HHS/United States ; U01 CA084291/CA/NCI NIH HHS/United States ; R01 HD026471/HD/NICHD NIH HHS/United States ; T32 CA009213/CA/NCI NIH HHS/United States ; }, abstract = {Colorectal cancer (CRC) is one of the most treatable cancers, with a 5-year survival rate of ~64%, yet over 50,000 deaths occur yearly in the United States. In 15% of cases, deficiency in mismatch repair leads to null mutations in transforming growth factor β (TGF-β) type II receptor, yet genotype alone is not responsible for tumorigenesis. Previous work in mice shows that disruptions in TGF-β signaling combined with Helicobacter hepaticus cause tumorigenesis, indicating a synergistic effect between genotype and microbial environment. Here, we examine functional shifts in the gut microbiome in CRC using integrated -omics approaches to untangle the role of host genotype, inflammation, and microbial ecology. We profile the gut microbiome of 40 mice with/without deficiency in TGF-β signaling from a Smad3 (mothers against decapentaplegic homolog-3) knockout and with/without inoculation with H. hepaticus. Clear functional differences in the microbiome tied to specific bacterial species emerge from four pathways related to human colon cancer: lipopolysaccharide (LPS) production, polyamine synthesis, butyrate metabolism, and oxidative phosphorylation (OXPHOS). Specifically, an increase in Mucispirillum schaedleri drives LPS production, which is associated with an inflammatory response. We observe a commensurate decrease in butyrate production from Lachnospiraceae bacterium A4, which could promote tumor formation. H. hepaticus causes an increase in OXPHOS that may increase DNA-damaging free radicals. Finally, multiple bacterial species increase polyamines that are associated with colon cancer, implicating not just diet but also the microbiome in polyamine levels. These insights into cross talk between the microbiome, host genotype, and inflammation could promote the development of diagnostics and therapies for CRC. IMPORTANCE Most research on the gut microbiome in colon cancer focuses on taxonomic changes at the genus level using 16S rRNA gene sequencing. Here, we develop a new methodology to integrate DNA and RNA data sets to examine functional shifts at the species level that are important to tumor development. We uncover several metabolic pathways in the microbiome that, when perturbed by host genetics and H. hepaticus inoculation, contribute to colon cancer. The work presented here lays a foundation for improved bioinformatics methodologies to closely examine the cross talk between specific organisms and the host, important for the development of diagnostics and pre/probiotic treatment.}, }
@article {pmid28950279, year = {2017}, author = {Nagpal, R and Yadav, H}, title = {Bacterial Translocation from the Gut to the Distant Organs: An Overview.}, journal = {Annals of nutrition &amp; metabolism}, volume = {71 Suppl 1}, number = {}, pages = {11-16}, doi = {10.1159/000479918}, pmid = {28950279}, issn = {1421-9697}, mesh = {Bacterial Translocation/*physiology ; Gastrointestinal Tract/microbiology/*physiology ; Humans ; }, abstract = {BACKGROUND: The intestinal epithelial layer is the chief barricade between the luminal contents and the host. A healthy homeostatic intestinal barrier is pivotal for maintaining gastrointestinal health, which impacts the overall health as it safeguards the gut-blood axis and checks gut microbes including potential pathogens from entering into the circulation.<br><br>SUMMARY: Under healthy milieus, the intestinal barrier is generally very dynamic and effective, with luminal side being heavily infested with a wide variety of gut microbes while the basolateral side remains virtually sterile. However, certain conditions such as abnormal exposure to toxins, drugs, pathogens etc. or a state of hyper-inflammation due to disease conditions may weaken or destabilize the integrity of gut epithelia. A perturbed gut integrity and permeability ("leaky gut") may lead to microbial (bacterial) translocation, and the eventual leakage of bacteria or their metabolites into the circulation can make the host susceptible to various types of diseases via inducing chronic or acute inflammatory response. Key Message: Given a close association with gut integrity, bacterial translocation and inflammatory responses have recently emerged as a clinically important research field and have unveiled novel aspects of gut microbial ecology and various gastrointestinal, metabolic, and lifestyle diseases. This review aims to describe the significance of a healthy gut barrier integrity and permeability, as well as the factors and consequences associated with a compromised gut barrier, while discussing briefly the dietary approaches including probiotics and prebiotics that could ameliorate gut health by restoring gut environment and barrier integrity, thereby preventing bacterial translocation.}, }
@article {pmid28949865, year = {2017}, author = {Decostere, B and Coppens, J and Vervaeren, H and Vlaeminck, SE and Gelder, L and Boon, N and Nopens, I and Hulle, SWHV}, title = {Kinetic exploration of intracellular nitrate storage in marine microalgae.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances &amp; environmental engineering}, volume = {52}, number = {14}, pages = {1303-1311}, doi = {10.1080/10934529.2017.1364921}, pmid = {28949865}, issn = {1532-4117}, mesh = {Diatoms/growth &amp; development/*metabolism ; Kinetics ; Microalgae/growth &amp; development/*metabolism ; *Models, Biological ; Nitrates/*metabolism ; Species Specificity ; Wastewater/chemistry ; Water Pollutants, Chemical/*analysis ; }, abstract = {In this study, a recently developed model accounting for intracellular nitrate storage kinetics was thoroughly studied to understand and compare the storage capacity of Phaeodactylum tricornutum and Amphora coffeaeformis. In the first stage the identifiability of the biokinetic parameters was examined. Next, the kinetic model was calibrated for both microalgal species based on experimental observations during batch growth experiments. Two kinetic parameters were calibrated, namely the maximum specific growth rate [Formula: see text] and the nitrate storage rate ([Formula: see text]). A significant difference was observed for the nitrate storage rate between both species. For P. tricornutum, the nitrate storage rate was much higher ([Formula: see text] = 0.036 m[3] g[-1] DW d[-1]) compared to A. coffeaeformis ([Formula: see text] = 0.0004 m[3] g[-1] DW d[-1]). This suggests that P. tricornutum has a more efficient nitrate uptake ability and intracellular nitrate storage capacity and also indicates the need for determination of [Formula: see text] in order to quantify nitrate storage.}, }
@article {pmid28948217, year = {2017}, author = {Shevchenko, V and Mager, T and Kovalev, K and Polovinkin, V and Alekseev, A and Juettner, J and Chizhov, I and Bamann, C and Vavourakis, C and Ghai, R and Gushchin, I and Borshchevskiy, V and Rogachev, A and Melnikov, I and Popov, A and Balandin, T and Rodriguez-Valera, F and Manstein, DJ and Bueldt, G and Bamberg, E and Gordeliy, V}, title = {Inward H[+] pump xenorhodopsin: Mechanism and alternative optogenetic approach.}, journal = {Science advances}, volume = {3}, number = {9}, pages = {e1603187}, pmid = {28948217}, issn = {2375-2548}, mesh = {Archaea/metabolism ; Binding Sites ; Cell Line ; Chromatography, High Pressure Liquid ; Escherichia coli/metabolism ; Humans ; Hydrogen-Ion Concentration ; Light ; Liposomes ; Models, Molecular ; *Optogenetics/methods ; Protein Binding ; Protein Conformation ; Proton Pumps/*metabolism ; Protons ; Retina/metabolism ; Rhodopsin/chemistry/*metabolism ; Spectrum Analysis ; }, abstract = {Generation of an electrochemical proton gradient is the first step of cell bioenergetics. In prokaryotes, the gradient is created by outward membrane protein proton pumps. Inward plasma membrane native proton pumps are yet unknown. We describe comprehensive functional studies of the representatives of the yet noncharacterized xenorhodopsins from Nanohaloarchaea family of microbial rhodopsins. They are inward proton pumps as we demonstrate in model membrane systems, Escherichia coli cells, human embryonic kidney cells, neuroblastoma cells, and rat hippocampal neuronal cells. We also solved the structure of a xenorhodopsin from the nanohalosarchaeon Nanosalina (NsXeR) and suggest a mechanism of inward proton pumping. We demonstrate that the NsXeR is a powerful pump, which is able to elicit action potentials in rat hippocampal neuronal cells up to their maximal intrinsic firing frequency. Hence, inwardly directed proton pumps are suitable for light-induced remote control of neurons, and they are an alternative to the well-known cation-selective channelrhodopsins.}, }
@article {pmid28948010, year = {2017}, author = {Brinkman, EP and Raaijmakers, CE and de Boer, W and van der Putten, WH}, title = {Changing soil legacies to direct restoration of plant communities.}, journal = {AoB PLANTS}, volume = {9}, number = {5}, pages = {plx038}, pmid = {28948010}, issn = {2041-2851}, abstract = {It is increasingly acknowledged that soil biota may influence interactions among plant species; however, little is known about how to change historical influences of previous land management on soil biota, the so-called 'biotic soil legacy effect'. We used a two-phase plant community-soil feedback approach to study how plant species typical to original (i.e. undisturbed) and degraded fen meadows may influence effects of the soil community on Carex species that are dominant in fen meadows. In phase 1, soil from original, degraded, successfully and unsuccessfully restored fen meadows was conditioned by growing plants typical to original or to degraded fen meadows. In phase 2, interactions between Carex and neighbouring plant species were studied to quantify plant community-soil feedback effects in different neighbour plant mixtures. Soil conditioning with plants typical to original fen meadows resulted in significantly more Carex biomass than with plants typical to degraded fen meadows. These effects were strongest when the soil originated from unsuccessfully restored fen meadows. However, biomass of plants typical of degraded fen meadows was also higher in soil conditioned by typical fen meadow plants. We conclude that soil legacy effects of plants from degraded fen meadows can be altered by growing typical fen meadow plant species in that soil, as this enhances priority effects that favour growth of other typical fen meadow plants. As also plant species from degraded fen meadows benefitted from soil conditioning, further studies are needed to reveal if plant species can be chosen that change negative soil legacy effects for rare and endangered fen meadow plant species, but not for plant species that are typical to degraded fen meadows.}, }
@article {pmid28945542, year = {2017}, author = {Lee, JC and Whang, KS}, title = {Salirhabdus salicampi sp. nov., a halotolerant bacterium isolated from a saltern.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {67}, number = {11}, pages = {4578-4583}, doi = {10.1099/ijsem.0.002334}, pmid = {28945542}, issn = {1466-5034}, mesh = {Bacillaceae/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Diaminopimelic Acid/chemistry ; Fatty Acids/chemistry ; Peptidoglycan/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Salinity ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {A Gram-stain-positive, halotolerant bacterium, designated strain BH128[T], was isolated from soil of a saltern located at Bigeum Island in south-west Korea. Cells were aerobic, motile, spore-forming rods and grew at 15-53 °C (optimum, 35 °C), at pH 5.5-9.0 (optimum, pH 7.0) and at salinities of 0-16 % (w/v) NaCl (optimum, 8 % NaCl). The predominant isoprenoid quinone was menaquinone-7 (MK-7), and the cell-wall peptidoglycan type was A1γ, with meso-diaminopimelic acid as the diagnostic diamino acid. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 and anteiso-C17 : 0. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and four unknown phospholipids. The DNA G+C content was 36.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BH128[T] belonged to the genus Salirhabdus and showed highest similarity to Salirhabduseuzebyi CVS-14[T] (95.8 %). On the basis of the phylogenetic, phenotypic and chemotaxonomic analyses in this study, strain BH128[T] is considered to represent a novel species of the genus Salirhabdus, for which the name Salirhabdussalicampi sp. nov. is proposed. The type strain is BH128[T] (=KACC 18690[T]=NBRC 111874[T]).}, }
@article {pmid28945537, year = {2017}, author = {Huber, KJ and Geppert, AM and Groß, U and Luckner, M and Wanner, G and Cooper, P and Abakah, J and Janssen, I and Overmann, J}, title = {Aridibacter nitratireducens sp. nov., a member of the family Blastocatellaceae, class Blastocatellia, isolated from an African soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {67}, number = {11}, pages = {4487-4493}, doi = {10.1099/ijsem.0.002318}, pmid = {28945537}, issn = {1466-5034}, mesh = {Acidobacteria/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Ghana ; Nucleic Acid Hybridization ; *Phylogeny ; Pigmentation ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {Members of the class Blastocatellia are frequently found in soils with a neutral and (slightly) basic pH where they constitute an important fraction of the microbial community. A novel representative of the class Blastocatellia was isolated from a Ghanaian soil and was characterized in detail. Cells of strain A24_SHP_-5_238[T] were non-motile rods that divided by binary fission and formed orange to salmon-coloured colonies on agar plates. Strain A24_SHP_-5_238[T] tolerated pH values of pH 6.0-9.0 (best growth at pH 7.0-8.5) and temperature values of 8-45 °C (best growth at 33-40 °C). It grew chemo-organoheterotrophically on several sugars, a few amino acids, organic acids and different complex protein substrates. In addition, strain A24_SHP_-5_238[T] was able to use nitrate as an alternative electron acceptor in the absence of oxygen. Major fatty acids of A24_SHP_-5_238[T] were iso-C15 : 0, summed feature 1 (C13 : 0 3-OH/iso-C15 : 1 H), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), anteiso-C17 : 0 and anteiso-C15 : 0. The major quinone was MK-8, and the DNA G+C content was 53.5 mol%. The closest described phylogenetic relatives were Aridibacter famidurans A22_HD_4H[T] and Aridibacter kavangonensis Ac_23_E3[T] with a 16S rRNA gene sequence identity of 97.6 and 97.2 %, respectively. The DNA-DNA hybridization values (<28.5 %) confirmed that A24_SHP_-5_238[T] represents a novel species within the genus Aridibacter. Based on its morphological, physiological and molecular characteristics, we propose the novel species Aridibacter nitratireducens sp. nov. (type strain A24_SHP_-5_238[T] = DSM 102177[T] = CECT 9235[T]).}, }
@article {pmid28945499, year = {2018}, author = {Baek, K and Ji, S and Choi, Y}, title = {Complex Intratissue Microbiota Forms Biofilms in Periodontal Lesions.}, journal = {Journal of dental research}, volume = {97}, number = {2}, pages = {192-200}, pmid = {28945499}, issn = {1544-0591}, mesh = {Adult ; Biofilms/*classification ; Chronic Periodontitis/*microbiology ; DNA, Bacterial/analysis ; Dental Plaque/*microbiology ; Female ; Humans ; Male ; Microbiota/*physiology ; Microscopy, Atomic Force ; Periodontal Index ; RNA, Ribosomal, 16S/analysis ; Republic of Korea ; }, abstract = {Periodontitis is caused by dysbiotic subgingival bacterial communities that may lead to increased bacterial invasion into gingival tissues. Although shifts in community structures associated with transition from health to periodontitis have been well characterized, the nature of bacteria present within the gingival tissue of periodontal lesions is not known. To characterize microbiota within tissues of periodontal lesions and compare them with plaque microbiota, gingival tissues and subgingival plaques were obtained from 7 patients with chronic periodontitis. A sequencing analysis of the 16S rRNA gene revealed that species richness and diversity were not significantly different between the 2 groups. However, intersubject variability of intratissue communities was smaller than that of plaque communities. In addition, when compared with the plaque communities, intratissue communities were characterized by decreased abundance of Firmicutes and increased abundance of Fusobacteria and Chloroflexi. In particular, Fusobacterium nucleatum and Porphyromonas gingivalis were highly enriched within the tissue, composing 15% to 40% of the total bacteria. Furthermore, biofilms, as visualized by alcian blue staining and atomic force microscopy, were observed within the tissue where the degradation of connective tissue fibers was prominent. In conclusion, very complex bacterial communities exist in the form of biofilms within the gingival tissue of periodontal lesions, which potentially serve as a reservoir for persistent infection. This novel finding may prompt new research on therapeutic strategies to treat periodontitis.}, }
@article {pmid28944402, year = {2017}, author = {Ying, X and Guo, K and Chen, W and Gu, Y and Shen, D and Zhou, Y and Liang, Y and Wang, Y and Wang, M and Feng, H}, title = {The impact of electron donors and anode potentials on the anode-respiring bacteria community.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {21}, pages = {7997-8005}, doi = {10.1007/s00253-017-8518-8}, pmid = {28944402}, issn = {1432-0614}, support = {51478431//National Natural Science Foundation of China/ ; LQ17E080002//Science and Technology Planning Project from the Science and Technology Department in Zhejiang Province/ ; GJ201623003//the Innovative and Entrepreneurial Training Plan of National College Students/ ; 2016R408030//the Xinmiao Talent Project in Zhejiang province/ ; 2016R408028//the Xinmiao Talent Project in Zhejiang province/ ; }, mesh = {Acetates/metabolism ; Bacteria/*classification/*growth &amp; development ; *Bioelectric Energy Sources ; Biofilms/*growth &amp; development ; *Biota ; Culture Media/chemistry ; Electricity ; Electrochemical Techniques ; Electrodes/*microbiology ; Electron Transport ; Oxidation-Reduction ; Sucrose/metabolism ; }, abstract = {Both anode potentials and substrates can affect the process of biofilm formation in bioelectrochemical systems, but it is unclear who primarily determine the anode-respiring bacteria (ARB) community structure and composition. To address this issue, we divided microbial electrolysis cells (MECs) into groups, feeding them with different substrates and culturing them at various potentials. Non-turnover cyclic voltammetry indicated that the extracellular electron transfer components were uniform when feeding acetate, because the same oxidation peaks occurred at - 0.36 ± 0.01 and - 0.17 ± 0.01 V (vs. Ag/AgCl). Illumina MiSeq sequencing revealed that the dominating ARB was Geobacter, which did not change with different potentials. When the MECs were cultured with sucrose and mixed substrates, oxidation peak P3 (- 0.29 ± 0.015 V) occurred at potentials of - 0.29 and 0.01 V. This may be because of the appearance of Unclassified_AKYG597. In addition, oxidation peak P4 (- 0.99 ± 0.01 V) occurred at high and low potentials (0.61 and - 0.45 V, respectively), and the maximum current densities were far below those of the middle potentials. Illumina MiSeq sequencing showed that fermentation microorganisms (Lactococcus and Sphaerochaeta) dominated the biofilms. Consequently, substrate primarily determined the dominating ARB, and Geobacter invariably dominated the acetate-fed biofilms with potentials changed. Conversely, different potentials mainly affected fermentable substrate-fed biofilms, with dominating ARB turning into Unclassified_AKYG59.}, }
@article {pmid28942559, year = {2018}, author = {Belevich, TA and Ilyash, LV and Milyutina, IA and Logacheva, MD and Goryunov, DV and Troitsky, AV}, title = {Photosynthetic Picoeukaryotes in the Land-Fast Ice of the White Sea, Russia.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {582-597}, pmid = {28942559}, issn = {1432-184X}, support = {16-05-00502//Russian Foundation for Basic Research/ ; 14-50-00029//Russian Science Foundation/ ; }, mesh = {Arctic Regions ; Biodiversity ; Biomass ; Chlorophyll/analysis ; Chlorophyta/classification/genetics/physiology ; DNA/analysis/isolation &amp; purification ; Eukaryota/*classification/genetics/isolation &amp; purification/*physiology ; Haptophyta/classification/genetics/physiology ; High-Throughput Nucleotide Sequencing ; Ice Cover/chemistry/*parasitology ; *Photosynthesis ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; Russia ; Seasons ; Seawater/parasitology ; Stramenopiles/classification/genetics/isolation &amp; purification/physiology ; Temperature ; }, abstract = {The White Sea is a unique marine environment combining features of temperate and Arctic seas. The composition and abundance of photosynthetic picoeukaryotes (PPEs) were investigated in the land-fast ice of the White Sea, Russia, in March 2013 and 2014. High-throughput tag sequencing (Illumina MiSeq system) of the V4 region of the 18S rRNA gene was used to reveal the diversity of PPE ice community. The integrated PPE abundance varied from 11 × 10[6] cells/m[2] to 364 × 10[6] cells/m[2]; the integrated biomass ranged from 0.02 to 0.26 mg С/m[2]. The composition of sea-ice PPEs was represented by 16 algae genera belonging to eight classes and three super-groups. Chlorophyta, especially Mamiellophyceae, dominated among ice PPEs. The detailed analysis revealed the latent diversity of Micromonas and Mantоniella. Micromonas clade E2 revealed in the subarctic White Sea ice indicates that the area of distribution of this species is wider than previously thought. We suppose there exists a new Micromonas clade F. Micromonas clade C and Minutocellulus polymorphus were first discovered in the ice and extend the modern concept of sympagic communities' diversity generally and highlights the importance of further targeting subarctic sea ice for microbial study.}, }
@article {pmid28939987, year = {2018}, author = {Kobiałka, M and Michalik, A and Walczak, M and Szklarzewicz, T}, title = {Dual "Bacterial-Fungal" Symbiosis in Deltocephalinae Leafhoppers (Insecta, Hemiptera, Cicadomorpha: Cicadellidae).}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {771-782}, pmid = {28939987}, issn = {1432-184X}, support = {2015/17/N/NZ8/01573//Narodowe Centrum Nauki/ ; }, mesh = {Abdomen/microbiology ; Animals ; Ascomycota/physiology ; Bacteria/*classification/genetics ; *Bacterial Physiological Phenomena ; Bacteroidetes/physiology ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; Female ; Fungi/*classification/genetics/*physiology ; Hemiptera/*microbiology ; *Microbiota ; *Phylogeny ; RNA, Ribosomal/genetics ; *Symbiosis ; }, abstract = {The symbiotic systems (types of symbionts, their distribution in the host insect body, and their transovarial transmission between generations) of four Deltocephalinae leafhoppers: Fieberiella septentrionalis, Graphocraerus ventralis, Orientus ishidae, and Cicadula quadrinotata have been examined by means of histological, ultrastructural, and molecular techniques. In all four species, two types of symbionts are present: bacterium Sulcia (phylum Bacteroidetes) and yeast-like symbionts closely related to the entomopathogenic fungi (phylum Ascomycota, class Sordariomycetes). Sulcia bacteria are always harbored in giant bacteriocytes, which are grouped into large organs termed "bacteriomes." In F. septentrionalis, G. ventralis, and O. ishidae, numerous yeast-like microorganisms are localized in cells of the fat body, whereas in C. quadrinotata, they occupy the cells of midgut epithelium in large number. Additionally, in C. quadrinotata, a small amount of yeast-like microorganisms occurs intracellularly in the fat body cells and, extracellularly, in the hemolymph. Sulcia bacteria in F. septentrionalis, G. ventralis, O. ishidae, and C. quadrinotata, and the yeast-like symbionts residing in the fat body of F. septentrionalis, G. ventralis, and O. ishidae are transovarially transmitted; i.e., they infect the ovarioles which constitute the ovaries.}, }
@article {pmid28939599, year = {2017}, author = {Jochum, LM and Chen, X and Lever, MA and Loy, A and Jørgensen, BB and Schramm, A and Kjeldsen, KU}, title = {Depth Distribution and Assembly of Sulfate-Reducing Microbial Communities in Marine Sediments of Aarhus Bay.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {23}, pages = {}, pmid = {28939599}, issn = {1098-5336}, support = {294200/ERC_/European Research Council/International ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Bays/microbiology ; DNA, Bacterial/genetics ; Denmark ; Geologic Sediments/*microbiology ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sulfates/*metabolism ; }, abstract = {Most sulfate-reducing microorganisms (SRMs) present in subsurface marine sediments belong to uncultured groups only distantly related to known SRMs, and it remains unclear how changing geochemical zones and sediment depth influence their community structure. We mapped the community composition and abundance of SRMs by amplicon sequencing and quantifying the dsrB gene, which encodes dissimilatory sulfite reductase subunit beta, in sediment samples covering different vertical geochemical zones ranging from the surface sediment to the deep sulfate-depleted subsurface at four locations in Aarhus Bay, Denmark. SRMs were present in all geochemical zones, including sulfate-depleted methanogenic sediment. The biggest shift in SRM community composition and abundance occurred across the transition from bioturbated surface sediments to nonbioturbated sediments below, where redox fluctuations and the input of fresh organic matter due to macrofaunal activity are absent. SRM abundance correlated with sulfate reduction rates determined for the same sediments. Sulfate availability showed a weaker correlation with SRM abundances and no significant correlation with the composition of the SRM community. The overall SRM species diversity decreased with depth, yet we identified a subset of highly abundant community members that persists across all vertical geochemical zones of all stations. We conclude that subsurface SRM communities assemble by the persistence of members of the surface community and that the transition from the bioturbated surface sediment to the unmixed sediment below is a main site of assembly of the subsurface SRM community.IMPORTANCE Sulfate-reducing microorganisms (SRMs) are key players in the marine carbon and sulfur cycles, especially in coastal sediments, yet little is understood about the environmental factors controlling their depth distribution. Our results suggest that macrofaunal activity is a key driver of SRM abundance and community structure in marine sediments and that a small subset of SRM species of high relative abundance in the subsurface SRM community persists from the sulfate-rich surface sediment to sulfate-depleted methanogenic subsurface sediment. More generally, we conclude that SRM communities inhabiting the subsurface seabed assemble by the selective survival of members of the surface community.}, }
@article {pmid28938908, year = {2017}, author = {Lesaulnier, CC and Herbold, CW and Pelikan, C and Berry, D and Gérard, C and Le Coz, X and Gagnot, S and Niggemann, J and Dittmar, T and Singer, GA and Loy, A}, title = {Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {126}, pmid = {28938908}, issn = {2049-2618}, support = {P 25111/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/classification/*isolation &amp; purification ; Betaproteobacteria/classification/isolation &amp; purification ; Biodiversity ; *Drinking Water/chemistry/microbiology ; Europe ; Mass Spectrometry ; *Microbiota/genetics ; Mineral Waters/analysis/*microbiology ; Organic Chemicals/*analysis/chemistry ; RNA, Ribosomal, 16S ; *Water Microbiology ; }, abstract = {BACKGROUND: Non-carbonated natural mineral waters contain microorganisms that regularly grow after bottling despite low concentrations of dissolved organic matter (DOM). Yet, the compositions of bottled water microbiota and organic substrates that fuel microbial activity, and how both change after bottling, are still largely unknown.<br><br>RESULTS: We performed a multifaceted analysis of microbiota and DOM diversity in 12 natural mineral waters from six European countries. 16S rRNA gene-based analyses showed that less than 10 species-level operational taxonomic units (OTUs) dominated the bacterial communities in the water phase and associated with the bottle wall after a short phase of post-bottling growth. Members of the betaproteobacterial genera Curvibacter, Aquabacterium, and Polaromonas (Comamonadaceae) grew in most waters and represent ubiquitous, mesophilic, heterotrophic aerobes in bottled waters. Ultrahigh-resolution mass spectrometry of DOM in bottled waters and their corresponding source waters identified thousands of molecular formulae characteristic of mostly refractory, soil-derived DOM.<br><br>CONCLUSIONS: The bottle environment, including source water physicochemistry, selected for growth of a similar low-diversity microbiota across various bottled waters. Relative abundance changes of hundreds of multi-carbon molecules were related to growth of less than ten abundant OTUs. We thus speculate that individual bacteria cope with oligotrophic conditions by simultaneously consuming diverse DOM molecules.}, }
@article {pmid28938903, year = {2017}, author = {O'Hara, NB and Reed, HJ and Afshinnekoo, E and Harvin, D and Caplan, N and Rosen, G and Frye, B and Woloszynek, S and Ounit, R and Levy, S and Butler, E and Mason, CE}, title = {Metagenomic characterization of ambulances across the USA.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {125}, pmid = {28938903}, issn = {2049-2618}, support = {R01 AI125416/AI/NIAID NIH HHS/United States ; }, mesh = {*Ambulances ; Bacteria/classification/genetics/*isolation &amp; purification/pathogenicity ; Cross Infection/microbiology ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Hospitals ; Humans ; *Metagenome ; *Metagenomics ; *Microbial Consortia/genetics ; *Microbiota/genetics ; United States ; }, abstract = {BACKGROUND: Microbial communities in our built environments have great influence on human health and disease. A variety of built environments have been characterized using a metagenomics-based approach, including some healthcare settings. However, there has been no study to date that has used this approach in pre-hospital settings, such as ambulances, an important first point-of-contact between patients and hospitals.<br><br>RESULTS: We sequenced 398 samples from 137 ambulances across the USA using shotgun sequencing. We analyzed these data to explore the microbial ecology of ambulances including characterizing microbial community composition, nosocomial pathogens, patterns of diversity, presence of functional pathways and antimicrobial resistance, and potential spatial and environmental factors that may contribute to community composition. We found that the top 10 most abundant species are either common built environment microbes, microbes associated with the human microbiome (e.g., skin), or are species associated with nosocomial infections. We also found widespread evidence of antimicrobial resistance markers (hits ~&#x2009;90% samples). We identified six factors that may influence the microbial ecology of ambulances including ambulance surfaces, geographical-related factors (including region, longitude, and latitude), and weather-related factors (including temperature and precipitation).<br><br>CONCLUSIONS: While the vast majority of microbial species classified were beneficial, we also found widespread evidence of species associated with nosocomial infections and antimicrobial resistance markers. This study indicates that metagenomics may be useful to characterize the microbial ecology of pre-hospital ambulance settings and that more rigorous testing and cleaning of ambulances may be warranted.}, }
@article {pmid28936223, year = {2017}, author = {Cerri, M and Sapkota, R and Coppi, A and Ferri, V and Foggi, B and Gigante, D and Lastrucci, L and Selvaggi, R and Venanzoni, R and Nicolaisen, M and Ferranti, F and Reale, L}, title = {Oomycete Communities Associated with Reed Die-Back Syndrome.}, journal = {Frontiers in plant science}, volume = {8}, number = {}, pages = {1550}, pmid = {28936223}, issn = {1664-462X}, abstract = {Phragmites australis (Cav.) Trin. ex Steud. die-back is a widely-studied phenomenon that was first discovered in northern Europe and that, until recently, was almost unknown in the Mediterranean basin. It has been described as a complex syndrome affecting reed populations leading to their retreat and decline, with significant impacts on valuable ecosystem services. Among the factors that cause the decline, soil-living microorganisms can be crucial. The aims of this study were to analyze the diversity of oomycetes communities associated with reed stands, and to understand whether they could play a key role in the decline. Variations in the structure of oomycetes communities were studied by metabarcoding of the internal transcribed spacer (ITS) 1 region of ribosomal DNA, from the sediments of five Italian freshwater ecosystems. They were chosen to cover a large variability in terms of surface area, water depth, microclimate, and presence of documented reed retreat. From 96 samples collected from reed roots, rhizosphere, and bulk soil, we assembled 207661 ITS1 reads into 523 OTUs. We demonstrated that oomycete communities were structured by several factors, among which the most important was die-back occurrence. Our study also indicates that Pythiogeton spp. could be potentially involved in the development of die-back. The role of heavy metals in the soil was also explored, and cadmium concentration was shown to affect oomycetes distribution. This study represents a significant step forward for the characterization of microbial communities associated with reed die-back syndrome and helps to gain knowledge of the complexity of these important wet ecosystems.}, }
@article {pmid28936204, year = {2017}, author = {Stedtfeld, RD and Chai, B and Crawford, RB and Stedtfeld, TM and Williams, MR and Xiangwen, S and Kuwahara, T and Cole, JR and Kaminski, NE and Tiedje, JM and Hashsham, SA}, title = {Modulatory Influence of Segmented Filamentous Bacteria on Transcriptomic Response of Gnotobiotic Mice Exposed to TCDD.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1708}, pmid = {28936204}, issn = {1664-302X}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, abstract = {Environmental toxicants such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), an aryl hydrocarbon receptor (AhR), are known to induce host toxicity and structural shifts in the gut microbiota. Key bacterial populations with similar or opposing functional responses to AhR ligand exposure may potentially help regulate expression of genes associated with immune dysfunction. To examine this question and the mechanisms for AhR ligand-induced bacterial shifts, C57BL/6 gnotobiotic mice were colonized with and without segmented filamentous bacteria (SFB) - an immune activator. Mice were also colonized with polysaccharide A producing Bacteroides fragilis - an immune suppressor to serve as a commensal background. Following colonization, mice were administered TCDD (30 μg/kg) every 4 days for 28 days by oral gavage. Quantified with the nCounter[®] mouse immunology panel, opposing responses in ileal gene expression (e.g., genes associated with T-cell differentiation via the class II major histocompatibility complex) as a result of TCDD dosing and SFB colonization were observed. Genes that responded to TCDD in the presence of SFB did not show a significant response in the absence of SFB, and vice versa. Regulatory T-cells examined in the mesenteric lymph-nodes, spleen, and blood were also less impacted by TCDD in mice colonized with SFB. TCDD-induced shifts in abundance of SFB and B. fragilis compared with previous studies in mice with a traditional gut microbiome. With regard to the mouse model colonized with individual populations, results indicate that TCDD-induced host response was significantly modulated by the presence of SFB in the gut microbiome, providing insight into therapeutic potential between AhR ligands and key commensals.}, }
@article {pmid28934589, year = {2017}, author = {Fan, W and Ren, H and Cao, Y and Wang, Y and Huo, G}, title = {Low dietary protein and high carbohydrate infant formula affects the microbial ecology of the large intestine in neonatal rats.}, journal = {Canadian journal of microbiology}, volume = {63}, number = {12}, pages = {951-960}, doi = {10.1139/cjm-2017-0242}, pmid = {28934589}, issn = {1480-3275}, mesh = {Animals ; Animals, Newborn ; Bacteria/classification ; Bacterial Physiological Phenomena ; Diet ; Dietary Carbohydrates/*metabolism ; Dietary Proteins/metabolism ; Female ; Gastrointestinal Contents/chemistry/microbiology ; Gastrointestinal Microbiome/*physiology ; Gene Expression Regulation ; Humans ; Infant Formula/*chemistry ; Infant, Newborn ; Intestine, Large/*microbiology ; Male ; Milk, Human/chemistry ; Random Allocation ; Rats ; Rats, Sprague-Dawley ; }, abstract = {The aim of this study was to investigate the effects of a low dietary protein and high carbohydrate infant formula on the large intestine of neonatal rats. A total of 24 neonatal Sprague-Dawley rats (14-days-old) were randomly assigned to the low protein, high carbohydrate infant formula-fed group (I group) and a human breast milk-fed group (H group). After 7 days, we selected 6 rats at random from each group to study. No significantly different microbial colonization patterns were observed in the 2 groups at the phylum level. At the family level, Enterobacteriaceae and Bacteroidaceae were the dominant bacteria in I and H rats. While Bacteroides was the most abundant bacteria at the genus level, no significant difference was observed between the 2 groups. Methanoic acid, acetate, and butyrate increased in concentration in the I group compared with the H group. Protease activities, ammonia, and indole in the large intestine were lower in I rats than H rats. A significant increase in the expression of GADPH and decrease in the expression of aquaporin 8, aminopeptidase A, cathepsin F precursor, and ubiquitin carboxyl-terminal hydrolase FAF-Y were observed in I rats compared with H rats. These results suggest that a low protein diet could modulate the microbial ecology in the large intestine of neonatal rats.}, }
@article {pmid28932895, year = {2018}, author = {He, J and Tu, Q and Ge, Y and Qin, Y and Cui, B and Hu, X and Wang, Y and Deng, Y and Wang, K and Van Nostrand, JD and Li, J and Zhou, J and Li, Y and Zhou, X}, title = {Taxonomic and Functional Analyses of the Supragingival Microbiome from Caries-Affected and Caries-Free Hosts.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {543-554}, pmid = {28932895}, issn = {1432-184X}, mesh = {Adult ; Bacteria/*classification/genetics/*isolation &amp; purification ; Dental Caries/*microbiology ; Dental Plaque/*microbiology ; Female ; Gingiva/*microbiology ; Humans ; Male ; *Microbiota ; Middle Aged ; }, abstract = {Caries is one of the most prevalent and costly infectious diseases affecting humans of all ages. It is initiated by cariogenic supragingival dental plaques forming on saliva-coated tooth surfaces, yet the etiology remains elusive. To determine which microbial populations may predispose a patient to caries, we report here an in-depth and comprehensive view of the microbial community associated with supragingival dental plaque collected from the healthy teeth of caries patients and healthy adults. We found that microbial communities from caries patients had a higher evenness and inter-individual variations but simpler ecological networks compared to healthy controls despite the overall taxonomic structure being similar. Genera including Selenomonas, Treponema, Atopobium, and Bergeriella were distributed differently between the caries and healthy groups with disturbed co-occurrence patterns. In addition, caries and healthy subjects carried different Treponema, Atopobium, and Prevotella species. Moreover, distinct populations of 13 function genes involved in organic acid synthesis, glycan biosynthesis, complex carbohydrate degradation, amino acid synthesis and metabolism, purine and pyrimidine metabolism, isoprenoid biosynthesis, lipid metabolism, and co-factor biosynthesis were present in each of the healthy and caries groups. Our results suggested that the fundamental differences in dental plaque ecology partially explained the patients' susceptibility to caries, and could be used for caries risk prediction in the future.}, }
@article {pmid28929212, year = {2018}, author = {Parmar, K and Dafale, N and Pal, R and Tikariha, H and Purohit, H}, title = {An Insight into Phage Diversity at Environmental Habitats using Comparative Metagenomics Approach.}, journal = {Current microbiology}, volume = {75}, number = {2}, pages = {132-141}, pmid = {28929212}, issn = {1432-0991}, mesh = {Bacteriophages/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; *Ecosystem ; Metagenomics ; *Water Microbiology ; }, abstract = {Bacteriophages play significant role in driving microbial diversity; however, little is known about the diversity of phages in different ecosystems. A dynamic predator-prey mechanism called "kill the winner" suggests the elimination of most active bacterial populations through phages. Thus, interaction between phage and host has an effect on the composition of microbial communities in ecosystems. In this study, secondary phage metagenome data from aquatic habitats: wastewater treatment plant (WWTP), fresh, marine, and hot water spring habitat were analyzed using MG-RAST and STAMP tools to explore the diversity of the viruses. Differential relative abundance of phage families-Siphoviridae (34%) and Myoviridae (26%) in WWTP, Myoviridae (30%) and Podoviridae (23%) in fresh water, and Myoviridae (41%) and Podoviridae (8%) in marine-was found to be a discriminating factor among four habitats while Rudiviridae (9%), Globuloviridae (8%), and Lipothrixviridae (1%) were exclusively observed in hot water spring. Subsequently, at genera level, Bpp-1-like virus, Chlorovirus, and T4-like virus were found abundant in WWTP, fresh, and marine habitat, respectively. PCA analysis revealed completely disparate composition of phage in hot water spring from other three ecosystems. Similar analysis of relative abundance of functional features corroborated observations from taxa analysis. Functional features corresponding to phage packaging machinery, replication, integration and excision, and gene transfer discriminated among four habitats. The comparative metagenomics approach exhibited genetically distinct phage communities among four habitats. Results revealed that selective distribution of phage communities would help in understanding the role of phages in food chains, nutrient cycling, and microbial ecology. Study of specific phages would also help in controlling environmental pathogens including MDR bacterial populations using phage therapy approach by selective mining and isolation of phages against specific pathogens persisting in a given environment.}, }
@article {pmid28929202, year = {2018}, author = {Gainza, O and Ramírez, C and Ramos, AS and Romero, J}, title = {Intestinal Microbiota of White Shrimp Penaeus vannamei Under Intensive Cultivation Conditions in Ecuador.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {562-568}, pmid = {28929202}, issn = {1432-184X}, support = {1140734//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; 1171129//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; }, mesh = {Animals ; Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Ecuador ; Fisheries ; *Gastrointestinal Microbiome/genetics ; Penaeidae/*microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The goal of the study was to characterize the intestinal tract bacterial microbiota composition of Penaeus vannamei in intensive commercial ponds in Ecuador, comparing two shrimp-farming phases: nursery and harvest. Bacterial microbiota was examined by sequencing amplicons V2-V3 of the 16S rRNA using Ion Torrent technology. Archaea sequences were detected in both phases. Sequence analyses revealed quantitative and qualitative differences between the nursery phase and the harvest phase in shrimp intestinal microbiota composition. The main differences were observed at the phylum level during the nursery phase, and the prevailing phyla were CKC4 (37.3%), Proteobacteria (29.8%), Actinobacteria (11.6%), and Firmicutes (10.1%). In the harvest phase, the prevailing phyla were Proteobacteria (28.4%), Chloroflexi (19.9%), and Actinobacteria (15.1%). At the genus level, microbiota from the nursery phase showed greater relative abundances of CKC4 uncultured bacterium (37%) and Escherichia-Shigella (18%). On the contrary, in the microbiota of harvested shrimp, the prevailing genera were uncultured Caldilinea (19%) and Alphaproteobacteria with no other assigned rate (10%). The analysis of similarity ANOSIM test (beta diversity) indicated significant differences between the shrimp microbiota for these two farming phases. Similarly, alfa-diversity analysis (Chao1) indicated that the microbiota at harvest was far more diverse than the microbiota during the nursery phase, which showed a homogeneous composition. These results suggest that shrimp microbiota diversify their composition during intensive farming. The present work offers the most detailed description of the microbiota of P. vannamei under commercial production conditions to date.}, }
@article {pmid28928718, year = {2017}, author = {Hugerth, LW and Andersson, AF}, title = {Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1561}, pmid = {28928718}, issn = {1664-302X}, abstract = {Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.}, }
@article {pmid28928457, year = {2017}, author = {Kip, N and Jansen, S and Leite, MFA and de Hollander, M and Afanasyev, M and Kuramae, EE and Veen, JAV}, title = {Methanogens predominate in natural corrosion protective layers on metal sheet piles.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11899}, pmid = {28928457}, issn = {2045-2322}, abstract = {Microorganisms are able to cause, but also to inhibit or protect against corrosion. Corrosion inhibition by microbial processes may be due to the formation of mineral deposition layers on metal objects. Such deposition layers have been found in archaeological studies on ancient metal objects, buried in soil, which were hardly corroded. Recent field investigations showed that natural mineral deposition layers can be found on sheet piles in soil. We investigated the microbial communities of these deposition layers and the adjacent soil. Our data, from five different sampling sites, all show striking differences between microbial communities of the deposition layer versus the adjacent soil over the depth profile. Bacterial species dominated in top soil while archaeal sequences increased in abundance with depth. All mineral deposition layers from the steel surface were dominated by Euryarchaeota, of which almost all sequences were phylogenetically related with the Methanobacteria genus. The mineral layer consisted of carbonate precipitates. Based on 16S rDNA gene sequencing data we hypothesize that the methanogens directly extract electrons from the metal surface, thereby, initially inducing mild corrosion, but simultaneously, inducing carbonate precipitation. This, will cause encrustation of the archaea, which drastically slow down their activity and create a natural protective layer against further corrosion.}, }
@article {pmid28927524, year = {2017}, author = {Mahaye, N and Thwala, M and Cowan, DA and Musee, N}, title = {Genotoxicity of metal based engineered nanoparticles in aquatic organisms: A review.}, journal = {Mutation research. Reviews in mutation research}, volume = {773}, number = {}, pages = {134-160}, doi = {10.1016/j.mrrev.2017.05.004}, pmid = {28927524}, issn = {1388-2139}, mesh = {Animals ; Aquatic Organisms/*drug effects ; Chromosome Aberrations/drug effects ; Comet Assay ; DNA Damage/*drug effects ; Metal Nanoparticles/chemistry/*toxicity ; Micronucleus Tests ; }, abstract = {Engineered nanoparticles (ENPs) are an emerging class of environmental contaminants, but are generally found in very low concentrations and are therefore likely to exert sub-lethal effects on aquatic organisms. In this review, we: (i) highlight key mechanisms of metal-based ENP-induced genotoxicity, (ii) identify key nanoparticle and environmental factors which influence the observed genotoxic effects, and (iii) highlight the challenges involved in interpreting reported data and provide recommendations on how these challenges might be addressed. We review the application of eight different genotoxicity assays, where the Comet Assay is generally preferred due to its capacity to detect low levels of DNA damage. Most ENPs have been shown to cause genotoxic responses; e.g., DNA or/and chromosomal fragmentation, or DNA strand breakage, but at unrealistic high concentrations. The genotoxicity of the ENPs was dependent on the inherent physico-chemical properties (e.g. size, coating, surface chemistry, e.tc.), and the presence of co-pollutants. To enhance the value of published genotoxicity data, the role of environmental processes; e.g., dissolution, aggregation and agglomeration, and adsorption of ENPs when released in aquatic systems, should be included, and assay protocols must be standardized. Such data could be used to model ENP genotoxicity processes in open environmental systems.}, }
@article {pmid28925074, year = {2017}, author = {Ratcliffe, S and Wirth, C and Jucker, T and van der Plas, F and Scherer-Lorenzen, M and Verheyen, K and Allan, E and Benavides, R and Bruelheide, H and Ohse, B and Paquette, A and Ampoorter, E and Bastias, CC and Bauhus, J and Bonal, D and Bouriaud, O and Bussotti, F and Carnol, M and Castagneyrol, B and Chećko, E and Dawud, SM and Wandeler, H and Domisch, T and Finér, L and Fischer, M and Fotelli, M and Gessler, A and Granier, A and Grossiord, C and Guyot, V and Haase, J and Hättenschwiler, S and Jactel, H and Jaroszewicz, B and Joly, FX and Kambach, S and Kolb, S and Koricheva, J and Liebersgesell, M and Milligan, H and Müller, S and Muys, B and Nguyen, D and Nock, C and Pollastrini, M and Purschke, O and Radoglou, K and Raulund-Rasmussen, K and Roger, F and Ruiz-Benito, P and Seidl, R and Selvi, F and Seiferling, I and Stenlid, J and Valladares, F and Vesterdal, L and Baeten, L}, title = {Biodiversity and ecosystem functioning relations in European forests depend on environmental context.}, journal = {Ecology letters}, volume = {20}, number = {11}, pages = {1414-1426}, doi = {10.1111/ele.12849}, pmid = {28925074}, issn = {1461-0248}, mesh = {*Biodiversity ; Climate Change ; *Ecosystem ; Europe ; *Forests ; }, abstract = {The importance of biodiversity in supporting ecosystem functioning is generally well accepted. However, most evidence comes from small-scale studies, and scaling-up patterns of biodiversity-ecosystem functioning (B-EF) remains challenging, in part because the importance of environmental factors in shaping B-EF relations is poorly understood. Using a forest research platform in which 26 ecosystem functions were measured along gradients of tree species richness in six regions across Europe, we investigated the extent and the potential drivers of context dependency of B-EF relations. Despite considerable variation in species richness effects across the continent, we found a tendency for stronger B-EF relations in drier climates as well as in areas with longer growing seasons and more functionally diverse tree species. The importance of water availability in driving context dependency suggests that as water limitation increases under climate change, biodiversity may become even more important to support high levels of functioning in European forests.}, }
@article {pmid28924451, year = {2017}, author = {Mukherjee, V and Radecka, D and Aerts, G and Verstrepen, KJ and Lievens, B and Thevelein, JM}, title = {Phenotypic landscape of non-conventional yeast species for different stress tolerance traits desirable in bioethanol fermentation.}, journal = {Biotechnology for biofuels}, volume = {10}, number = {}, pages = {216}, pmid = {28924451}, issn = {1754-6834}, abstract = {BACKGROUND: Non-conventional yeasts present a huge, yet barely exploited, resource of yeast biodiversity for industrial applications. This presents a great opportunity to explore alternative ethanol-fermenting yeasts that are more adapted to some of the stress factors present in the harsh environmental conditions in second-generation (2G) bioethanol fermentation. Extremely tolerant yeast species are interesting candidates to investigate the underlying tolerance mechanisms and to identify genes that when transferred to existing industrial strains could help to design more stress-tolerant cell factories. For this purpose, we performed a high-throughput phenotypic evaluation of a large collection of non-conventional yeast species to identify the tolerance limits of the different yeast species for desirable stress tolerance traits in 2G bioethanol production. Next, 12 multi-tolerant strains were selected and used in fermentations under different stressful conditions. Five strains out of which, showing desirable fermentation characteristics, were then evaluated in small-scale, semi-anaerobic fermentations with lignocellulose hydrolysates.<br><br>RESULTS: Our results revealed the phenotypic landscape of many non-conventional yeast species which have not been previously characterized for tolerance to stress conditions relevant for bioethanol production. This has identified for each stress condition evaluated several extremely tolerant non-Saccharomyces yeasts. It also revealed multi-tolerance in several yeast species, which makes those species good candidates to investigate the molecular basis of a robust general stress tolerance. The results showed that some non-conventional yeast species have similar or even better fermentation efficiency compared to S. cerevisiae in the presence of certain stressful conditions.<br><br>CONCLUSION: Prior to this study, our knowledge on extreme stress-tolerant phenotypes in non-conventional yeasts was limited to only few species. Our work has now revealed in a systematic way the potential of non-Saccharomyces species to emerge either as alternative host species or as a source of valuable genetic information for construction of more robust industrial S. serevisiae bioethanol production yeasts. Striking examples include yeast species like Pichia kudriavzevii and Wickerhamomyces anomalus that show very high tolerance to diverse stress factors. This large-scale phenotypic analysis has yielded a detailed database useful as a resource for future studies to understand and benefit from the molecular mechanisms underlying the extreme phenotypes of non-conventional yeast species.}, }
@article {pmid28921475, year = {2017}, author = {Zhang, S and Liu, X and Jiang, Q and Shen, G and Ding, W}, title = {Legacy effects of continuous chloropicrin-fumigation for 3-years on soil microbial community composition and metabolic activity.}, journal = {AMB Express}, volume = {7}, number = {1}, pages = {178}, pmid = {28921475}, issn = {2191-0855}, abstract = {Chloropicrin is widely used to control ginger wilt in China, which have an enormous impact on soil microbial diversity. However, little is known on the possible legacy effects on soil microbial community composition with continuous fumigation over different years. In this report, we used high throughput Illumina sequencing and Biolog ECO microplates to determine the bacterial community and microbial metabolic activity in ginger harvest fields of non-fumigation (NF), chloropicrin-fumigation for 1 year (F_1) and continuous chloropicrin-fumigation for 3 years (F_3). The results showed that microbial richness and diversity in F_3 were the lowest, while the metabolic activity had no significant difference. With the increase of fumigation years, the incidence of bacterial wilt was decreased, the relative abundance of Actinobacteria and Saccharibacteria were gradually increased. Using LEfSe analyses, we found that Saccharibacteria was the most prominent biomarker in F_3. Eight genera associated with antibiotic production in F_3 were screened out, of which seven belonged to Actinobacteria, and one belonged to Bacteroidetes. The study indicated that with the increase of fumigation years, soil antibacterial capacity may be increased (possible reason for reduced the incidence of bacterial wilt), and Saccharibacteria played a potential role in evaluating the biological effects of continuous fumigation.}, }
@article {pmid28921462, year = {2018}, author = {Agusti, A and Moya-Pérez, A and Campillo, I and Montserrat-de la Paz, S and Cerrudo, V and Perez-Villalba, A and Sanz, Y}, title = {Bifidobacterium pseudocatenulatum CECT 7765 Ameliorates Neuroendocrine Alterations Associated with an Exaggerated Stress Response and Anhedonia in Obese Mice.}, journal = {Molecular neurobiology}, volume = {55}, number = {6}, pages = {5337-5352}, pmid = {28921462}, issn = {1559-1182}, support = {AGL2014-52101-P//the Spanish Ministry of Economy and Competitiveness (MINECO)/ ; PTA//MINECO/ ; }, mesh = {Adiposity ; *Anhedonia ; Animals ; Anxiety/blood/metabolism/microbiology ; Behavior, Animal ; Bifidobacterium/*physiology ; Catecholamines/metabolism ; Corticosterone/metabolism ; Depression/blood/metabolism/microbiology ; Feces ; Leptin/blood/metabolism ; Male ; Mice, Inbred C57BL ; Mice, Obese ; Motor Activity ; Neurosecretory Systems/*metabolism ; Receptors, Glucocorticoid/metabolism ; Receptors, Leptin/metabolism ; Serotonin/metabolism ; *Stress, Physiological ; Toll-Like Receptor 2/metabolism ; Weight Gain ; }, abstract = {Obesity, besides being a problem of metabolic dysfunction, constitutes a risk factor for psychological disorders. Experimental models of diet-induced obesity have revealed that obese animals are prone to anxious and depressive-like behaviors. The present study aimed to evaluate whether Bifidobacterium pseudocatenulatum CECT 7765 could reverse the neurobehavioral consequences of obesity in a high-fat diet (HFD) fed mouse model via regulation of the gut-brain axis. Adult male wild-type C57BL-6 mice were fed a standard diet or HFD, supplemented with either placebo or the bifidobacterial strain for 13 weeks. Behavioral tests were performed, and immune and neuroendocrine parameters were analyzed including leptin and corticosterone and their receptors, Toll-like receptor 2 (TLR2) and neurotransmitters. We found that obese mice showed anhedonia (p < 0.050) indicative of a depressive-like behavior and an exaggerated hypothalamic-pituitary axis (HPA)-mediated stress response to acute physical (p < 0.001) and social stress (p < 0.050), but these alterations were ameliorated by B. pseudocatenulatum CECT 7765 (p < 0.050). These behavioral effects were parallel to reductions of the obesity-associated hyperleptinemia (p < 0.001) and restoration of leptin signaling (p < 0.050), along with fat mass loss (p < 0.010). B. pseudocatenulatum CECT 7765 administration also led to restoration of the obesity-induced reductions in adrenaline in the hypothalamus (p < 0.010), involved in the hypothalamic control of energy balance. Furthermore, the bifidobacterial strain reduced the obesity-induced upregulation of TLR2 protein or gene expression in the intestine (p < 0.010) and the hippocampus (p < 0.050) and restored the alterations of 5-HT levels in the hippocampus (p < 0.050), which could contribute to attenuating the obesity-associated depressive-like behavior (p < 0.050). In summary, the results indicate that B. pseudocatenulatum CECT 7765 could play a role in depressive behavior comorbid with obesity via regulation of endocrine and immune mediators of the gut-brain axis.}, }
@article {pmid28921080, year = {2018}, author = {Hyder, R and Piri, T and Hantula, J and Nuorteva, H and Vainio, EJ}, title = {Erratum to: Distribution of Viruses Inhabiting Heterobasidion annosum in a Pine-Dominated Forest Plot in Southern Finland.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {631}, doi = {10.1007/s00248-017-1067-y}, pmid = {28921080}, issn = {1432-184X}, }
@article {pmid28920836, year = {2017}, author = {Lee, JC and Whang, KS}, title = {Mycobacterium aquiterrae sp. nov., a rapidly growing bacterium isolated from groundwater.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {67}, number = {10}, pages = {4104-4110}, doi = {10.1099/ijsem.0.002261}, pmid = {28920836}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Genes, Bacterial ; Groundwater/*microbiology ; Multilocus Sequence Typing ; Mycobacterium/*classification/genetics/isolation &amp; purification ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {A strain representing a rapidly growing, Gram-stain-positive, aerobic, rod-shaped, non-motile, non-sporulating and non-pigmented species of the genus Mycobacterium, designated strain S-I-6[T], was isolated from groundwater at Daejeon in Korea. The strain grew at temperatures between 10 and 37 °C (optimal growth at 25 °C), between pH 4.0 and 9.0 (optimal growth at pH 7.0) and at salinities of 0-5 % (w/v) NaCl, growing optimally with 2 % (w/v) NaCl. Phylogenetic analyses based on multilocus sequence analysis of the 16S rRNAgene, hsp65, rpoB and the 16S-23S internal transcribed spacer indicated that strain S-I-6[T] belonged to the rapidly growing mycobacteria, being most closely related to Mycobacterium sphagni. On the basis of polyphasic taxonomic analysis, the bacterial strain was distinguished from its phylogenetic neighbours by chemotaxonomic properties and other biochemical characteristics. DNA-DNA relatedness among strain S-I-6[T] and the closest phylogenetic neighbour strongly support the proposal that this strain represents a novel species within the genus Mycobacterium, for which the name Mycobacterium aquiterrae sp. nov. is proposed. The type strain is S-I-6[T] (=KACC 17600[T]=NBRC 109805[T]=NCAIM B 02535[T]).}, }
@article {pmid28920165, year = {2018}, author = {Keshri, J and Pradeep Ram, AS and Sime-Ngando, T}, title = {Distinctive Patterns in the Taxonomical Resolution of Bacterioplankton in the Sediment and Pore Waters of Contrasted Freshwater Lakes.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {662-673}, pmid = {28920165}, issn = {1432-184X}, mesh = {Adaptation, Biological ; Aquatic Organisms ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Carbon/metabolism ; DNA, Bacterial/genetics ; Ecosystem ; France ; Fresh Water/chemistry/*microbiology ; Geologic Sediments/*microbiology ; High-Throughput Nucleotide Sequencing ; Lakes/chemistry/*microbiology ; Microbiota ; *Phylogeny ; Plankton/*classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; Sulfur/metabolism ; Viruses/classification ; *Water Microbiology ; }, abstract = {Bacteria assemblages in lake sediments play a key role in various biogeochemical processes, yet their association with interstitial pore waters has been scarcely investigated. In this study, we utilized Illumina next-generation amplicon sequencing of the 16S rRNA gene to characterize the seasonal bacterial communities in the sediments and pore waters of three contrasted temperate freshwater lakes, namely Pavin, Aydat, and Grangent (French Massif Central). Despite occupying seemingly similar habitats, bacterial communities differed substantially between sediments and pore waters at all seasons with low sharing of operational taxonomic units (OTUs, 6.7 to 20.3%) between them. Sediment-associated bacteria were more rich and diverse than pore water bacteria, indicating a high heterogeneity in the sediment microhabitat. The changes in both sediment and pore water bacterial communities were lake and season specific. The bacterial community showed distinct differences between the lakes, with larger presence of strict anaerobes such as Syntrophus, Syntrophorhabdus, and Sulfuricurvum in the pore water and sediments of Pavin responsible for carbon and sulfur cycling. In both Aydat and Grangent, the hgcI_clade dominated throughout the study period in the pore waters. The higher representation of lesser-known transient members of lake communities such as Methylotenera in the pore waters of Aydat, and Clostridium and Sulfuricurvum in the pore and sediments of Grangent, respectively, were observed during the period of temporary anoxia in summer caused by lake stratification. Our study revealed that in the investigated lakes, the prevailing environmental factors across time and space structured and influenced the adaptation of bacterial communities to specific ecological niches.}, }
@article {pmid28920144, year = {2018}, author = {Malafaia, CB and Jardelino, ACS and Silva, AG and de Souza, EB and Macedo, AJ and Correia, MTDS and Silva, MV}, title = {Effects of Caatinga Plant Extracts in Planktonic Growth and Biofilm Formation in Ralstonia solanacearum.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {555-561}, pmid = {28920144}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/*pharmacology ; Biofilms/*drug effects/growth &amp; development ; Biological Control Agents/pharmacology ; Brazil ; Microbial Sensitivity Tests ; Plant Diseases/microbiology/prevention &amp; control ; Plant Extracts/*pharmacology ; Plants, Medicinal ; Ralstonia solanacearum/*drug effects/physiology ; Tracheophyta/*chemistry ; }, abstract = {This study describes the first antibiofilm and antibacterial screening for plants from Caatinga against Ralstonia solanacearum, a causal agent of bacterial wilt that presents serious difficulties in control. There were prepared 22 aqueous extracts of plants collected in the Vale do Catimbau-PE, Brazil. The potential antibacterial activity was evaluated by absorbance in OD600 and the antibiofilm activity through the crystal violet method, both of them performed in microplate against isolates of R. solanacearum biofilm formers. The results of the screening showed that Jacaranda rugosa presented antimicrobial activity higher than 90%, while Harpochilus neesianus and Myroxylon peruiferum presented antibiofilm activity higher than 50% for all tested isolates. However, Croton heliotropiifolius showed both the activities, being thus very promising for application in the control of this phytopathogen. The search for viable alternatives to the development of new bioactive compounds safe for the environment, humans, and animals from an adverse and scarce environment such as the Caatinga and encouraged us to find plants that produce effective metabolites against phytopathogenic microorganisms. This in vitro screening is important to guide the development of new products in addition to guide research studies of bioactive compounds.}, }
@article {pmid28919887, year = {2017}, author = {Ferrari, E and Walter, MC and Huptas, C and Scherer, S and Müller-Herbst, S}, title = {Complete Circular Genome Sequence and Temperature Independent Adaptation to Anaerobiosis of Listeria weihenstephanensis DSM 24698.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1672}, pmid = {28919887}, issn = {1664-302X}, abstract = {The aim of this study was to analyze the adaptation of the environmental Listeria weihenstephanensis DSM 24698 to anaerobiosis. The complete circular genome sequence of this species is reported and the adaptation of L. weihenstephanensis DSM 24698 to oxygen availability was investigated by global transcriptional analyses via RNAseq at 18 and 34°C. A list of operons was created based on the transcriptional data. Forty-two genes were upregulated anaerobically and 62 genes were downregulated anaerobically. The oxygen dependent gene expression of selected genes was further validated via qPCR. Many of the differentially regulated genes encode metabolic enzymes indicating broad metabolic adaptations with respect to oxygen availability. Genes showing the strongest oxygen-dependent adaption encoded nitrate (narGHJI) and nitrite (nirBD) reductases. Together with the observation that nitrate supported anaerobic growth, these data indicate that L. weihenstephanensis DSM 24698 performs anaerobic nitrate respiration. The wide overlap between the oxygen-dependent transcriptional regulation at 18 and 34°C suggest that temperature does not play a key role in the oxygen-dependent transcriptional regulation of L. weihenstephanensis DSM 24698.}, }
@article {pmid28916990, year = {2017}, author = {Sun, H and Yu, P and Li, Q and Ren, H and Liu, B and Ye, L and Zhang, XX}, title = {Transformation of anaerobic granules into aerobic granules and the succession of bacterial community.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {20}, pages = {7703-7713}, doi = {10.1007/s00253-017-8491-2}, pmid = {28916990}, issn = {1432-0614}, support = {BK20160657//Natural Science Foundation of Jiangsu Province/ ; 51608256//National Natural Science Foundation of China/ ; 51378252//National Natural Science Foundation of China/ ; SBK2015010297//Science Foundation for Distinguished Young Scholars of Jiangsu Province of China/ ; 2014BAC08B04//National Key Technology Support Program of China/ ; }, mesh = {Aerobiosis ; Anaerobiosis ; Bacteria, Aerobic/*classification/*growth &amp; development ; Bacteria, Anaerobic/*classification/*growth &amp; development ; Bioreactors/microbiology ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Nitrogen/analysis ; Organic Chemicals/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; Water/chemistry ; *Water Purification ; }, abstract = {In this study, we demonstrated that anaerobic granular sludge could be successfully transformed into aerobic granular sludge in a continuous up-flow reactor in 45 days. An aerobic microbial community successfully developed in the granules and high organic matter and nitrogen removal performance was achieved. Under an ammonia nitrogen loading rate of 0.8 kg N/(m[3] day), ammonia nitrogen and the total nitrogen removal efficiency of the reactor reached up to 100 and 93%, respectively. An obvious bacterial community shift in granular sludge was observed during the transformation process. By comparing with the bacterial community in aerobic granules cultivated from floccular activated sludge, some bacteria (affiliated with Comamonadaceae, Xanthomonadaceae, Rhodocyclaceae, Moraxellaceae, and Nitrosomonadaceae) playing significant roles in maintaining the structures and functions of aerobic granules were identified. After the transformation, the granules could be clearly separated into the inner core and outer shell. 16S rRNA gene sequencing results indicated many bacterial species present in both the inner core and outer shell; however, their abundance differed significantly. Overall, this study confirms the feasibility of transforming anaerobic granules into aerobic granules and provides novel approaches and insights to understand the microbial ecology in granular sludge.}, }
@article {pmid28913903, year = {2017}, author = {Krzyściak, P and Chmielarczyk, A and Pobiega, M and Romaniszyn, D and Wójkowska-Mach, J}, title = {Acinetobacter baumannii isolated from hospital-acquired infection: biofilm production and drug susceptibility.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {125}, number = {11}, pages = {1017-1026}, doi = {10.1111/apm.12739}, pmid = {28913903}, issn = {1600-0463}, mesh = {Acinetobacter Infections/drug therapy/*microbiology ; Acinetobacter baumannii/*drug effects/growth &amp; development/isolation &amp; purification ; Aged ; Aminoglycosides/pharmacology ; Anti-Bacterial Agents/*pharmacology ; Biofilms/*drug effects/growth &amp; development ; Cephalosporins/pharmacology ; Cross Infection/drug therapy/*microbiology ; Culture Media/chemistry ; Drug Resistance, Multiple, Bacterial/physiology ; Female ; Fluoroquinolones/pharmacology ; Humans ; Intensive Care Units ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Plankton/*drug effects/growth &amp; development/isolation &amp; purification ; Trimethoprim, Sulfamethoxazole Drug Combination/pharmacology ; }, abstract = {Acinetobacter baumannii cause opportunistic nosocomial infections and is often multidrug resistant. It has ability to form biofilm. The possession of drug resistance mechanism and ability of biofilm formation seems to be the different way to enhancement of viability in stressful environment. In this study, we evaluate relation between these two factors. The biofilm formation was investigated in M63 medium with casein in microtiter plates, and the drug susceptibility was performed by disk diffusion methods. We found that 80-98% strains formed a biofilm. Strains showing sensitivity to amikacin and tobramycin from ICU produced more biofilm than strains showing resistance to these antibiotics. Ceftazidime-sensitive strains formed a smaller biofilm than resistant. The logistic regression shows association between drug resistance and strains originating from ICU. In case of ceftazidime, strong biofilm formation and descending from ICU reduced the likelihood of drug sensitivity. For other drugs such as aminoglycosides, fluoroquinolones, trimethoprim/sulfamethoxazole, and tetracycline, we found opposite relation (but it was not statistically significance). However, generally it seems that strong biofilm producers from ICUs are often more susceptible to antibiotics. This situation can be explained by the fact that bacteria protected in biofilm do not need mechanisms responsible for resistance of planktonic cells.}, }
@article {pmid28912310, year = {2017}, author = {Bag, S and Ghosh, TS and Das, B}, title = {Draft Genome Sequence of Prevotella copri Isolated from the Gut of a Healthy Indian Adult.}, journal = {Genome announcements}, volume = {5}, number = {37}, pages = {}, pmid = {28912310}, issn = {2169-8287}, abstract = {Prevotella copri, a Gram-negative anaerobic rod-shaped bacterium, is frequently associated with the human gastrointestinal tract and influences host physiology, immunity, and metabolic pathways. In the present study, we report the draft genome sequence of P. copri isolated from the gut of a healthy Indian adult.}, }
@article {pmid28910352, year = {2017}, author = {Zieliński, B and Plichta, A and Misztal, K and Spurek, P and Brzychczy-Włoch, M and Ochońska, D}, title = {Deep learning approach to bacterial colony classification.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184554}, pmid = {28910352}, issn = {1932-6203}, mesh = {Bacteria/*classification ; Databases, Factual ; Machine Learning ; *Neural Networks, Computer ; Support Vector Machine ; }, abstract = {In microbiology it is diagnostically useful to recognize various genera and species of bacteria. It can be achieved using computer-aided methods, which make the recognition processes more automatic and thus significantly reduce the time necessary for the classification. Moreover, in case of diagnostic uncertainty (the misleading similarity in shape or structure of bacterial cells), such methods can minimize the risk of incorrect recognition. In this article, we apply the state of the art method for texture analysis to classify genera and species of bacteria. This method uses deep Convolutional Neural Networks to obtain image descriptors, which are then encoded and classified with Support Vector Machine or Random Forest. To evaluate this approach and to make it comparable with other approaches, we provide a new dataset of images. DIBaS dataset (Digital Image of Bacterial Species) contains 660 images with 33 different genera and species of bacteria.}, }
@article {pmid28905697, year = {2017}, author = {Pascual, J and García-López, M and González, I and Genilloud, O}, title = {Luteolibacter gellanilyticus sp. nov., a gellan-gum-degrading bacterium of the phylum Verrucomicrobia isolated from miniaturized diffusion chambers.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {67}, number = {10}, pages = {3951-3959}, doi = {10.1099/ijsem.0.002227}, pmid = {28905697}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; *Forests ; Phospholipids/chemistry ; *Phylogeny ; Polysaccharides, Bacterial/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Spain ; Verrucomicrobia/*classification/genetics/isolation &amp; purification ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {A novel chemo-organoheterotrophic bacterium, strain CB-286403[T], was isolated from a Mediterranean forest soil, collected at Sierra de Tejeda, Almijara and Alhama Natural Park, Spain, by using the Diffusion Sandwich System, a device with 384 miniature diffusion chambers. The 16S rRNA gene sequence analyses identified the isolate as a member of the genus Luteolibacter where the type strains Luteolibacterpohnpeiensis A4T-83[T] (GenBank acc. no. AB331895), Luteolibacteryonseiensis EBTL01[T] (JQ319003), Luteolibacterluojiensis DR4-30[T] (JN630810) and Luteolibacteralgae A5J-41-2[T] (AB331893) were the closest relatives with similarities of 97.0, 96.3, 96.3 and 94.5 %, respectively. The novel isolate was characterized as a Gram-stain-negative, non-motile, short-rod-shaped bacterium. The strain showed a positive response for catalase and cytochrome-c oxidase, divided by binary fission and/or budding, and exhibited an aerobic metabolism. Strain CB-286403[T] showed a mesophilic and neutrophilic growth range and showed a nutritional preference for simple sugars and complex protein substrates. Major fatty acids included iso-C14 : 0, C16 : 0, C16 : 1ω7c/iso-C15 : 0 2-OH and anteiso-C15 : 0. The predominant respiratory quinone was MK-9. Polar lipids comprised major amounts of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol and minor amounts of three unidentified lipids, a glycolipid, a phospholipid and a phosphoglycolipid. Based on a polyphasic taxonomic characterization, strain CB-286403[T] represents a novel species of the genus Luteolibacter, for which the name Luteolibacter gellanilyticus sp. nov. is proposed. The type strain is CB-286403[T] (=DSM 28998[T]=CECT 8659[T]).}, }
@article {pmid28905200, year = {2018}, author = {Kostric, M and Milger, K and Krauss-Etschmann, S and Engel, M and Vestergaard, G and Schloter, M and Schöler, A}, title = {Development of a Stable Lung Microbiome in Healthy Neonatal Mice.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {529-542}, pmid = {28905200}, issn = {1432-184X}, mesh = {Animals ; Animals, Newborn/microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Lung/*microbiology ; Mice ; Mice, Inbred BALB C ; *Microbiota ; }, abstract = {The lower respiratory tract has been previously considered sterile in a healthy state, but advances in culture-independent techniques for microbial identification and characterization have revealed that the lung harbors a diverse microbiome. Although research on the lung microbiome is increasing and important questions were already addressed, longitudinal studies aiming to describe developmental stages of the microbial communities from the early neonatal period to adulthood are lacking. Thus, little is known about the early-life development of the lung microbiome and the impact of external factors during these stages. In this study, we applied a barcoding approach based on high-throughput sequencing of 16S ribosomal RNA gene amplicon libraries to determine age-dependent differences in the bacterial fraction of the murine lung microbiome and to assess potential influences of differing "environmental microbiomes" (simulated by the application of used litter material to the cages). We could clearly show that the diversity of the bacterial community harbored in the murine lung increases with age. Interestingly, bacteria belonging to the genera Delftia and Rhodococcus formed an age-independent core microbiome. The addition of the used litter material influenced the lung microbiota of young mice but did not significantly alter the community composition of adult animals. Our findings elucidate the dynamic nature of the early-life lung microbiota and its stabilization with age. Further, this study indicates that even slight environmental changes modulate the bacterial community composition of the lung microbiome in early life, whereas the lung microbes of adults demonstrate higher resilience towards environmental variations.}, }
@article {pmid28904999, year = {2017}, author = {de Muinck, EJ and Lundin, KEA and Trosvik, P}, title = {Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota.}, journal = {mSystems}, volume = {2}, number = {5}, pages = {}, pmid = {28904999}, issn = {2379-5077}, abstract = {The gastrointestinal (GI) microbiome is a densely populated ecosystem where dynamics are determined by interactions between microbial community members, as well as host factors. The spatial organization of this system is thought to be important in human health, yet this aspect of our resident microbiome is still poorly understood. In this study, we report significant spatial structure of the GI microbiota, and we identify general categories of spatial patterning in the distribution of microbial taxa along a healthy human GI tract. We further estimate the biotic interaction structure in the GI microbiota, both through time series and cooccurrence modeling of microbial community data derived from a large number of sequentially collected fecal samples. Comparison of these two approaches showed that species pairs involved in significant negative interactions had strong positive contemporaneous correlations and vice versa, while for species pairs without significant interactions, contemporaneous correlations were distributed around zero. We observed similar patterns when comparing these models to the spatial correlations between taxa identified in the adherent microbiota. This suggests that colocalization of microbial taxon pairs, and thus the spatial organization of the GI microbiota, is driven, at least in part, by direct or indirect biotic interactions. Thus, our study can provide a basis for an ecological interpretation of the biogeography of the human gut. IMPORTANCE The human gut microbiome is the subject of intense study due to its importance in health and disease. The majority of these studies have been based on the analysis of feces. However, little is known about how the microbial composition in fecal samples relates to the spatial distribution of microbial taxa along the gastrointestinal tract. By characterizing the microbial content both in intestinal tissue samples and in fecal samples obtained daily, we provide a conceptual framework for how the spatial structure relates to biotic interactions on the community level. We further describe general categories of spatial distribution patterns and identify taxa conforming to these categories. To our knowledge, this is the first study combining spatial and temporal analyses of the human gut microbiome. This type of analysis can be used for identifying candidate probiotics and designing strategies for clinical intervention.}, }
@article {pmid28904372, year = {2017}, author = {Geirnaert, A and Calatayud, M and Grootaert, C and Laukens, D and Devriese, S and Smagghe, G and De Vos, M and Boon, N and Van de Wiele, T}, title = {Butyrate-producing bacteria supplemented in vitro to Crohn's disease patient microbiota increased butyrate production and enhanced intestinal epithelial barrier integrity.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11450}, pmid = {28904372}, issn = {2045-2322}, mesh = {Bacteria/*metabolism ; Butyrates/*metabolism ; Cell Line, Tumor ; Crohn Disease/drug therapy/*etiology ; Dietary Supplements ; Fatty Acids/biosynthesis/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/metabolism/*microbiology/pathology ; Permeability ; Probiotics ; }, abstract = {The management of the dysbiosed gut microbiota in inflammatory bowel diseases (IBD) is gaining more attention as a novel target to control this disease. Probiotic treatment with butyrate-producing bacteria has therapeutic potential since these bacteria are depleted in IBD patients and butyrate has beneficial effects on epithelial barrier function and overall gut health. However, studies assessing the effect of probiotic supplementation on microbe-microbe and host-microbe interactions are rare. In this study, butyrate-producing bacteria (three mono-species and one multispecies mix) were supplemented to the fecal microbial communities of ten Crohn's disease (CD) patients in an in vitro system simulating the mucus- and lumen-associated microbiota. Effects of supplementation in short-chain fatty acid levels, bacterial colonization of mucus environment and intestinal epithelial barrier function were evaluated. Treatment with F. prausnitzii and the mix of six butyrate-producers significantly increased the butyrate production by 5-11 mol%, and colonization capacity in mucus- and lumen-associated CD microbiota. Treatments with B. pullicaecorum 25-3[T] and the mix of six butyrate-producers improved epithelial barrier integrity in vitro. This study provides proof-of-concept data for the therapeutic potential of butyrate-producing bacteria in CD and supports the future preclinical development of a probiotic product containing butyrate-producing species.}, }
@article {pmid28904370, year = {2017}, author = {Mir, BA and Myburg, AA and Mizrachi, E and Cowan, DA}, title = {In planta expression of hyperthermophilic enzymes as a strategy for accelerated lignocellulosic digestion.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11462}, pmid = {28904370}, issn = {2045-2322}, mesh = {Arabidopsis/enzymology/genetics ; Biomass ; Enzymes/*genetics/*metabolism ; *Gene Expression ; Genetic Engineering ; *Hot Temperature ; Hydrogen-Ion Concentration ; Hydrolysis ; Lignin/*metabolism ; Phenotype ; Plant Proteins/genetics ; Plants/*enzymology/*genetics ; Plants, Genetically Modified ; Plasmids/genetics ; }, abstract = {Conversion of lignocellulosic biomass to biofuels and biomaterials suffers from high production costs associated with biomass pretreatment and enzymatic hydrolysis. In-planta expression of lignocellulose-digesting enzymes is a promising approach to reduce these cost elements. However, this approach faces a number of challenges, including auto-hydrolysis of developing cell walls, plant growth and yield penalties, low expression levels and the limited stability of expressed enzymes at the high temperatures generally used for biomass processing to release fermentable sugars. To overcome these challenges we expressed codon-optimized recombinant hyperthermophilic endoglucanase (EG) and xylanase (Xyn) genes in A. thaliana. Transgenic Arabidopsis lines expressing EG and Xyn enzymes at high levels without any obvious plant growth or yield penalties were selected for further analysis. The highest enzyme activities were observed in the dry stems of transgenic lines, indicating that the enzymes were not degraded during stem senescence and storage. Biomass from transgenic lines exhibited improved saccharification efficiency relative to WT control plants. We conclude that the expression of hyperthermophilic enzymes in plants is a promising approach for combining pretreatment and enzymatic hydrolysis processes in lignocellulosic digestion. This study provides a valid foundation for further studies involving in planta co-expression of core and accessory lignocellulose-digesting enzymes.}, }
@article {pmid28904265, year = {2017}, author = {Tanaka, S and Yamamoto, K and Hamajima, C and Takahashi, F and Yamada, K and Furuya, K and Uyeno, Y}, title = {Changes in Gut Microbial Ecology and Immunological Responses of Mice Fed the Insoluble Fraction of Brassica rapa L. that was Fermented or Not.}, journal = {Microbes and environments}, volume = {32}, number = {3}, pages = {268-274}, pmid = {28904265}, issn = {1347-4405}, mesh = {Animals ; *Brassica rapa ; Diet ; Dietary Fiber/*administration &amp; dosage ; Faecalibacterium/isolation &amp; purification ; Fatty Acids, Volatile ; *Fermentation ; Gastrointestinal Tract/*microbiology ; Male ; Mice ; Mice, Inbred C57BL ; }, abstract = {We aimed to investigate the effects of feeding fermented Brassica rapa L. on ecological and immunological changes in the mouse gut using in vitro cultivation tests and in vivo experiments in normal mice. In the preliminary in vitro study, two B. rapa L. products from different fermentation periods (one d [SF] or six months [LF]) were evaluated along with non-fermented vegetables (NF). Among the components of each product, the insoluble fraction resulted in the most prominent change such as a relative increase in butyrate production during a cultivation inoculated with mouse cecum contents. Based on this result, the boiled water-insoluble fractions of B. rapa L. (SF, LF, and NF samples) were selected as test materials for the subsequent in vivo experiment. Male C57BL/6J mice were divided into four groups and fed either a control diet (CON) or control diet plus one of the insoluble fractions for two weeks. The NF and LF groups had higher relative populations of Faecalibacterium prausnitzii than the CON group. Therefore, colonic butyrate concentrations were higher in the NF and LF groups than in the CON group. The oral administration of B. rapa L. extract induced immune regulatory effects, even when mice were fed NF and SF, but not LF, as assessed by an increase in regulatory T cell numbers. Our results indicate that feeding a purified insoluble fraction from B. rapa L. affects enteric short-chain fatty acid production and immunological responses in the mouse gut in a similar manner, regardless of the fermentation status.}, }
@article {pmid28903954, year = {2017}, author = {Beaumont, M and Portune, KJ and Steuer, N and Lan, A and Cerrudo, V and Audebert, M and Dumont, F and Mancano, G and Khodorova, N and Andriamihaja, M and Airinei, G and Tomé, D and Benamouzig, R and Davila, AM and Claus, SP and Sanz, Y and Blachier, F}, title = {Quantity and source of dietary protein influence metabolite production by gut microbiota and rectal mucosa gene expression: a randomized, parallel, double-blind trial in overweight humans.}, journal = {The American journal of clinical nutrition}, volume = {106}, number = {4}, pages = {1005-1019}, doi = {10.3945/ajcn.117.158816}, pmid = {28903954}, issn = {1938-3207}, mesh = {Adult ; Amino Acids/metabolism ; Bacteria/genetics/*metabolism ; Caseins/pharmacology ; DNA, Bacterial/analysis ; *Diet, Carbohydrate-Restricted ; Dietary Proteins/administration &amp; dosage/metabolism/*pharmacology ; Double-Blind Method ; Feces ; Female ; *Gastrointestinal Microbiome ; Homeostasis ; Humans ; Intestinal Mucosa/*metabolism/microbiology ; Intestine, Large/*metabolism/microbiology ; Male ; Obesity/diet therapy ; RNA, Ribosomal, 16S ; Rectum/metabolism/microbiology ; Soybean Proteins/pharmacology ; *Transcriptome ; }, abstract = {Background: Although high-protein diets (HPDs) are frequently consumed for body-weight control, little is known about the consequences for gut microbiota composition and metabolic activity and for large intestine mucosal homeostasis. Moreover, the effects of HPDs according to the source of protein need to be considered in this context.Objective: The objective of this study was to evaluate the effects of the quantity and source of dietary protein on microbiota composition, bacterial metabolite production, and consequences for the large intestinal mucosa in humans.Design: A randomized, double-blind, parallel-design trial was conducted in 38 overweight individuals who received a 3-wk isocaloric supplementation with casein, soy protein, or maltodextrin as a control. Fecal and rectal biopsy-associated microbiota composition was analyzed by 16S ribosomal DNA sequencing. Fecal, urinary, and plasma metabolomes were assessed by [1]H-nuclear magnetic resonance. Mucosal transcriptome in rectal biopsies was determined with the use of microarrays.Results: HPDs did not alter the microbiota composition, but induced a shift in bacterial metabolism toward amino acid degradation with different metabolite profiles according to the protein source. Correlation analysis identified new potential bacterial taxa involved in amino acid degradation. Fecal water cytotoxicity was not modified by HPDs, but was associated with a specific microbiota and bacterial metabolite profile. Casein and soy protein HPDs did not induce inflammation, but differentially modified the expression of genes playing key roles in homeostatic processes in rectal mucosa, such as cell cycle or cell death.Conclusions: This human intervention study shows that the quantity and source of dietary proteins act as regulators of gut microbiota metabolite production and host gene expression in the rectal mucosa, raising new questions on the impact of HPDs on the large intestine mucosa homeostasis. This trial was registered at clinicaltrials.gov as NCT02351297.}, }
@article {pmid28902868, year = {2017}, author = {Hücker, SM and Ardern, Z and Goldberg, T and Schafferhans, A and Bernhofer, M and Vestergaard, G and Nelson, CW and Schloter, M and Rost, B and Scherer, S and Neuhaus, K}, title = {Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184119}, pmid = {28902868}, issn = {1932-6203}, mesh = {Conserved Sequence ; DNA, Bacterial/genetics ; DNA, Intergenic/*genetics ; Escherichia coli O157/*genetics ; *Genes, Bacterial ; Genetic Association Studies ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Open Reading Frames/genetics ; RNA, Bacterial/genetics ; Transcriptome ; }, abstract = {In the past, short protein-coding genes were often disregarded by genome annotation pipelines. Transcriptome sequencing (RNAseq) signals outside of annotated genes have usually been interpreted to indicate either ncRNA or pervasive transcription. Therefore, in addition to the transcriptome, the translatome (RIBOseq) of the enteric pathogen Escherichia coli O157:H7 strain Sakai was determined at two optimal growth conditions and a severe stress condition combining low temperature and high osmotic pressure. All intergenic open reading frames potentially encoding a protein of ≥ 30 amino acids were investigated with regard to coverage by transcription and translation signals and their translatability expressed by the ribosomal coverage value. This led to discovery of 465 unique, putative novel genes not yet annotated in this E. coli strain, which are evenly distributed over both DNA strands of the genome. For 255 of the novel genes, annotated homologs in other bacteria were found, and a machine-learning algorithm, trained on small protein-coding E. coli genes, predicted that 89% of these translated open reading frames represent bona fide genes. The remaining 210 putative novel genes without annotated homologs were compared to the 255 novel genes with homologs and to 250 short annotated genes of this E. coli strain. All three groups turned out to be similar with respect to their translatability distribution, fractions of differentially regulated genes, secondary structure composition, and the distribution of evolutionary constraint, suggesting that both novel groups represent legitimate genes. However, the machine-learning algorithm only recognized a small fraction of the 210 genes without annotated homologs. It is possible that these genes represent a novel group of genes, which have unusual features dissimilar to the genes of the machine-learning algorithm training set.}, }
@article {pmid28900024, year = {2017}, author = {Thrash, JC and Seitz, KW and Baker, BJ and Temperton, B and Gillies, LE and Rabalais, NN and Henrissat, B and Mason, OU}, title = {Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico "Dead Zone".}, journal = {mBio}, volume = {8}, number = {5}, pages = {}, pmid = {28900024}, issn = {2150-7511}, mesh = {Anaerobiosis ; Bacteria/classification/*genetics/isolation &amp; purification/*metabolism ; Carbon/metabolism ; Eukaryota ; Euryarchaeota/classification/genetics/isolation &amp; purification/*metabolism ; Eutrophication ; Gulf of Mexico ; Metagenomics/methods ; Nitrates/metabolism ; Oxygen/metabolism ; Plankton/*metabolism ; Seawater/*microbiology ; }, abstract = {Marine regions that have seasonal to long-term low dissolved oxygen (DO) concentrations, sometimes called "dead zones," are increasing in number and severity around the globe with deleterious effects on ecology and economics. One of the largest of these coastal dead zones occurs on the continental shelf of the northern Gulf of Mexico (nGOM), which results from eutrophication-enhanced bacterioplankton respiration and strong seasonal stratification. Previous research in this dead zone revealed the presence of multiple cosmopolitan bacterioplankton lineages that have eluded cultivation, and thus their metabolic roles in this ecosystem remain unknown. We used a coupled shotgun metagenomic and metatranscriptomic approach to determine the metabolic potential of Marine Group II Euryarchaeota, SAR406, and SAR202. We recovered multiple high-quality, nearly complete genomes from all three groups as well as candidate phyla usually associated with anoxic environments-Parcubacteria (OD1) and Peregrinibacteria Two additional groups with putative assignments to ACD39 and PAUC34f supplement the metabolic contributions by uncultivated taxa. Our results indicate active metabolism in all groups, including prevalent aerobic respiration, with concurrent expression of genes for nitrate reduction in SAR406 and SAR202, and dissimilatory nitrite reduction to ammonia and sulfur reduction by SAR406. We also report a variety of active heterotrophic carbon processing mechanisms, including degradation of complex carbohydrate compounds by SAR406, SAR202, ACD39, and PAUC34f. Together, these data help constrain the metabolic contributions from uncultivated groups in the nGOM during periods of low DO and suggest roles for these organisms in the breakdown of complex organic matter.IMPORTANCE Dead zones receive their name primarily from the reduction of eukaryotic macrobiota (demersal fish, shrimp, etc.) that are also key coastal fisheries. Excess nutrients contributed from anthropogenic activity such as fertilizer runoff result in algal blooms and therefore ample new carbon for aerobic microbial metabolism. Combined with strong stratification, microbial respiration reduces oxygen in shelf bottom waters to levels unfit for many animals (termed hypoxia). The nGOM shelf remains one of the largest eutrophication-driven hypoxic zones in the world, yet despite its potential as a model study system, the microbial metabolisms underlying and resulting from this phenomenon-many of which occur in bacterioplankton from poorly understood lineages-have received only preliminary study. Our work details the metabolic potential and gene expression activity for uncultivated lineages across several low DO sites in the nGOM, improving our understanding of the active biogeochemical cycling mediated by these "microbial dark matter" taxa during hypoxia.}, }
@article {pmid28894891, year = {2018}, author = {Mookherjee, A and Bera, P and Mitra, A and Maiti, MK}, title = {Characterization and Synergistic Effect of Antifungal Volatile Organic Compounds Emitted by the Geotrichum candidum PF005, an Endophytic Fungus from the Eggplant.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {647-661}, pmid = {28894891}, issn = {1432-184X}, support = {IIT/SRIC/BT/GRT/2014//SGIRG-SRIC, IIT-Kharagpur/ ; F. No. 4-25/2013-TS-1//Food Security Project, IIT-Kharagpur/ ; }, mesh = {Antifungal Agents/chemistry/*pharmacology ; Carbon/metabolism ; Culture Media/chemistry ; DNA, Fungal/genetics ; Endophytes/genetics/growth &amp; development/isolation &amp; purification/*metabolism ; Genotype ; Geotrichum/genetics/growth &amp; development/isolation &amp; purification/*metabolism ; Microbial Sensitivity Tests ; Mycelium/drug effects/growth &amp; development ; Plant Diseases/microbiology/prevention &amp; control ; RNA, Ribosomal, 18S/genetics ; Rhizoctonia/drug effects/growth &amp; development/pathogenicity ; Solanum melongena/*microbiology ; Volatile Organic Compounds/chemistry/*pharmacology ; }, abstract = {Plant-associated endophytes are recognized as sources of novel bioactive molecules having diverse applications. In this study, an endophytic yeast-like fungal strain was isolated from the fruit of eggplant (Solanum melongena) and identified as Geotrichum candidum through phenotypic and genotypic characterizations. This endophytic G. candidum isolate PF005 was found to emit fruity scented volatiles. The compositional profiling of volatile organic compounds (VOCs) revealed the presence of 3-methyl-1-butanol, ethyl 3-methylbutanoate, 2-phenylethanol, isopentyl acetate, naphthalene, and isobutyl acetate in significant proportion when analyzed on a time-course basis. The VOCs from G. candidum exhibited significant mycelial growth inhibition (54%) of phytopathogen Rhizoctonia solani, besides having mild antifungal activity against a few other fungi. The source of carbon as a nutrient was found to be an important factor for the enhanced biosynthesis of antifungal VOCs. The antifungal activity against phytopathogen R. solani was improved up to 91% by feeding the G. candidum with selective precursors of alcohol and ester volatiles. Furthermore, the antifungal activity of VOCs was enhanced synergistically up to 92% upon the exogenous addition of naphthalene (1.0 mg/plate). This is the first report of G. candidum as an endophyte emitting antifungal VOCs, wherein 2-penylethanol, isopentyl acetate, and naphthalene were identified as important contributors to its antifungal activity. Possible utilization of G. candidum PF005 as a mycofumigant has been discussed based upon its antifungal activity and the qualified presumption of safety status.}, }
@article {pmid28894881, year = {2018}, author = {Hale, VL and Tan, CL and Niu, K and Yang, Y and Knight, R and Zhang, Q and Cui, D and Amato, KR}, title = {Erratum to: Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {528}, doi = {10.1007/s00248-017-1070-3}, pmid = {28894881}, issn = {1432-184X}, }
@article {pmid28894651, year = {2017}, author = {Moller, AG and Liang, C}, title = {MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3788}, pmid = {28894651}, issn = {2167-8359}, abstract = {Clustered regularly interspaced short palindromic repeat (CRISPR) systems are the adaptive immune systems of bacteria and archaea against viral infection. While CRISPRs have been exploited as a tool for genetic engineering, their spacer sequences can also provide valuable insights into microbial ecology by linking environmental viruses to their microbial hosts. Despite this importance, metagenomic CRISPR detection remains a major challenge. Here we present a reference-guided CRISPR spacer detection tool (Metagenomic CRISPR Reference-Aided Search Tool-MetaCRAST) that constrains searches based on user-specified direct repeats (DRs). These DRs could be expected from assembly or taxonomic profiles of metagenomes. We compared the performance of MetaCRAST to those of two existing metagenomic CRISPR detection tools-Crass and MinCED-using both real and simulated acid mine drainage (AMD) and enhanced biological phosphorus removal (EBPR) metagenomes. Our evaluation shows MetaCRAST improves CRISPR spacer detection in real metagenomes compared to the de novo CRISPR detection methods Crass and MinCED. Evaluation on simulated metagenomes show it performs better than de novo tools for Illumina metagenomes and comparably for 454 metagenomes. It also has comparable performance dependence on read length and community composition, run time, and accuracy to these tools. MetaCRAST is implemented in Perl, parallelizable through the Many Core Engine (MCE), and takes metagenomic sequence reads and direct repeat queries (FASTA or FASTQ) as input. It is freely available for download at https://github.com/molleraj/MetaCRAST.}, }
@article {pmid28894646, year = {2017}, author = {Dangerfield, CR and Nadkarni, NM and Brazelton, WJ}, title = {Canopy soil bacterial communities altered by severing host tree limbs.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3773}, pmid = {28894646}, issn = {2167-8359}, abstract = {Trees of temperate rainforests host a large biomass of epiphytic plants, which are associated with soils formed in the forest canopy. Falling of epiphytic material results in the transfer of carbon and nutrients from the canopy to the forest floor. This study provides the first characterization of bacterial communities in canopy soils enabled by high-depth environmental sequencing of 16S rRNA genes. Canopy soil included many of the same major taxonomic groups of Bacteria that are also found in ground soil, but canopy bacterial communities were lower in diversity and contained different operational taxonomic units. A field experiment was conducted with epiphytic material from six Acer macrophyllum trees in Olympic National Park, Washington, USA to document changes in the bacterial communities of soils associated with epiphytic material that falls to the forest floor. Bacterial diversity and composition of canopy soil was highly similar, but not identical, to adjacent ground soil two years after transfer to the forest floor, indicating that canopy bacteria are almost, but not completely, replaced by ground soil bacteria. Furthermore, soil associated with epiphytic material on branches that were severed from the host tree and suspended in the canopy contained altered bacterial communities that were distinct from those in canopy material moved to the forest floor. Therefore, the unique nature of canopy soil bacteria is determined in part by the host tree and not only by the physical environmental conditions associated with the canopy. Connection to the living tree appears to be a key feature of the canopy habitat. These results represent an initial survey of bacterial diversity of the canopy and provide a foundation upon which future studies can more fully investigate the ecological and evolutionary dynamics of these communities.}, }
@article {pmid28892231, year = {2017}, author = {Cheng, X and Etalo, DW and van de Mortel, JE and Dekkers, E and Nguyen, L and Medema, MH and Raaijmakers, JM}, title = {Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens.}, journal = {Environmental microbiology}, volume = {19}, number = {11}, pages = {4638-4656}, doi = {10.1111/1462-2920.13927}, pmid = {28892231}, issn = {1462-2920}, mesh = {Amino Acyl-tRNA Synthetases/genetics ; Arabidopsis/*growth &amp; development/*microbiology ; Arabidopsis Proteins/genetics ; Genome-Wide Association Study ; Immunity, Innate ; Plant Development/*genetics ; Plant Diseases/*microbiology ; Plant Roots/*growth &amp; development/microbiology ; Pseudomonas fluorescens/*genetics ; Pseudomonas syringae/genetics/*pathogenicity ; }, abstract = {Pseudomonas fluorescens strain SS101 (Pf.SS101) promotes growth of Arabidopsis thaliana, enhances greening and lateral root formation, and induces systemic resistance (ISR) against the bacterial pathogen Pseudomonas syringae pv. tomato (Pst). Here, targeted and untargeted approaches were adopted to identify bacterial determinants and underlying mechanisms involved in plant growth promotion and ISR by Pf.SS101. Based on targeted analyses, no evidence was found for volatiles, lipopeptides and siderophores in plant growth promotion by Pf.SS101. Untargeted, genome-wide analyses of 7488 random transposon mutants of Pf.SS101 led to the identification of 21 mutants defective in both plant growth promotion and ISR. Many of these mutants, however, were auxotrophic and impaired in root colonization. Genetic analysis of three mutants followed by site-directed mutagenesis, genetic complementation and plant bioassays revealed the involvement of the phosphogluconate dehydratase gene edd, the response regulator gene colR and the adenylsulfate reductase gene cysH in both plant growth promotion and ISR. Subsequent comparative plant transcriptomics analyses strongly suggest that modulation of sulfur assimilation, auxin biosynthesis and transport, steroid biosynthesis and carbohydrate metabolism in Arabidopsis are key mechanisms linked to growth promotion and ISR by Pf.SS101.}, }
@article {pmid28890994, year = {2018}, author = {Liu, D and Nishida, M and Takahashi, T and Asakawa, S}, title = {Transcription of mcrA Gene Decreases Upon Prolonged Non-flooding Period in a Methanogenic Archaeal Community of a Paddy-Upland Rotational Field Soil.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {751-760}, pmid = {28890994}, issn = {1432-184X}, support = {143218//The Environmental Research Projects from the Sumitomo Foundation/ ; eDNA-07-101-1//The Soil e-DNA Project from the Ministry of Agriculture, Forestry, and Fisheries of Japan/ ; }, mesh = {Amino Acid Sequence ; Archaea/*genetics ; Chemoautotrophic Growth/*genetics ; DNA, Archaeal/genetics ; Gene Dosage ; Genes, Archaeal/genetics ; Methane/metabolism ; Microbiota/*genetics ; Oryza/microbiology ; Oxidoreductases/*genetics ; Soil ; *Soil Microbiology ; Glycine max/microbiology ; Transcriptome ; }, abstract = {Methanogenic archaea survive under aerated soil conditions in paddy fields, and their community is stable under these conditions. Changes in the abundance and composition of an active community of methanogenic archaea were assessed by analyzing mcrA gene (encoding α subunit of methyl-coenzyme M reductase) and transcripts during a prolonged drained period in a paddy-upland rotational field. Paddy rice (Oryza sativa L.) was planted in the flooded field and rotated with soybean (Glycine max [L.] Merr.) under upland soil conditions. Soil samples were collected from the rotational plot in the first year, with paddy rice, and in the two successive years, with soybean, at six time points, before seeding, during cultivation, and after harvest as well as from a consecutive paddy (control) plot. By the time that soybean was grown in the second year, the methanogenic archaeal community in the rotational plot maintained high mcrA transcript levels, comparable with those of the control plot community, but the levels drastically decreased by over three orders of magnitude after 2 years of upland conversion. The composition of active methanogenic archaeal communities that survived upland conversion in the rotational plot was similar to that of the active community in the control plot. These results revealed that mcrA gene transcription of methanogenic archaeal community in the rotational field was affected by a prolonged non-flooding period, longer than 1 year, indicating that unknown mechanisms maintain the stability of methanogenic archaeal community in paddy fields last up to 1 year after the onset of drainage.}, }
@article {pmid28887494, year = {2017}, author = {Walker, A and Pfitzner, B and Harir, M and Schaubeck, M and Calasan, J and Heinzmann, SS and Turaev, D and Rattei, T and Endesfelder, D and Castell, WZ and Haller, D and Schmid, M and Hartmann, A and Schmitt-Kopplin, P}, title = {Sulfonolipids as novel metabolite markers of Alistipes and Odoribacter affected by high-fat diets.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11047}, pmid = {28887494}, issn = {2045-2322}, mesh = {Animals ; Bacteroidetes/*chemistry/*metabolism ; Cecum/*microbiology ; Chromatography, Liquid ; *Diet, High-Fat ; Gastrointestinal Microbiome/*drug effects ; Lipids/*analysis ; Mass Spectrometry ; Mice ; }, abstract = {The gut microbiota generates a huge pool of unknown metabolites, and their identification and characterization is a key challenge in metabolomics. However, there are still gaps on the studies of gut microbiota and their chemical structures. In this investigation, an unusual class of bacterial sulfonolipids (SLs) is detected in mouse cecum, which was originally found in environmental microbes. We have performed a detailed molecular level characterization of this class of lipids by combining high-resolution mass spectrometry and liquid chromatography analysis. Eighteen SLs that differ in their capnoid and fatty acid chain compositions were identified. The SL called "sulfobacin B" was isolated, characterized, and was significantly increased in mice fed with high-fat diets. To reveal bacterial producers of SLs, metagenome analysis was acquired and only two bacterial genera, i.e., Alistipes and Odoribacter, were revealed to be responsible for their production. This knowledge enables explaining a part of the molecular complexity introduced by microbes to the mammalian gastrointestinal tract and can be used as chemotaxonomic evidence in gut microbiota.}, }
@article {pmid28884952, year = {2017}, author = {Li, Q and Wu, T and Liu, R and Zhang, M and Wang, R}, title = {Soluble Dietary Fiber Reduces Trimethylamine Metabolism via Gut Microbiota and Co-Regulates Host AMPK Pathways.}, journal = {Molecular nutrition &amp; food research}, volume = {61}, number = {12}, pages = {}, doi = {10.1002/mnfr.201700473}, pmid = {28884952}, issn = {1613-4133}, mesh = {AMP-Activated Protein Kinases/*metabolism ; Animals ; Cholesterol/blood ; Diet ; Dietary Fiber/*pharmacology ; Energy Intake/drug effects ; Fatty Acids, Volatile/metabolism ; Fermented Foods ; Gastrointestinal Microbiome/*drug effects/physiology ; Intestinal Mucosa/metabolism ; Lipids/blood ; Metagenome ; Methylamines/blood/*metabolism ; Mice, Inbred C57BL ; Red Meat ; Solubility ; }, abstract = {SCOPE: Evidence from animal experiments and clinical medicine suggests that high dietary fiber intake, followed by gut microbiota-mediated fermentation, decreases trimethylamine (TMA) metabolism, the mechanism of which, however, remains unclear. The objective of this analysis was to evaluate, using mice fed with red meat, the effects of soluble dietary fiber (SDF) intervention on TMA metabolism.<br><br>METHODS AND RESULTS: Low- or high-dose soluble dietary fiber (SDF) from natural wheat bran (LN and HN, low- and high-dose natural SDF), fermented wheat bran (LF and HF, low- and high-dose fermented SDF), and steam-exploded wheat bran (LE and HE, low- and high-dose exploded SDF groups) were used to examine whether SDF interventions in mice fed with red meat can alter TMA and trimethylamine N-oxide (TMAO) metabolism by gut microbial communities in a diet-specific manner. Results demonstrated that SDF-diets could reduce TMA and trimethylamine N-oxide (TMAO) metabolism by 40.6 and 62.6%, respectively. DF feeding, particularly fermented SDF, reshaped gut microbial ecology and promoted the growth of certain beneficial microflora species. SDF-diet decreased energy intake, weight gain, intestinal pH values, and serum lipid and cholesterol levels. SDF-diet also enhanced the production of short chain fatty acids with activation of the intestinal epithelial adenosine monophosphate-activated protein kinase (AMPK).<br><br>CONCLUSION: These findings suggest a central mechanism via which SDF-diet may control TMA metabolism by gut microflora and co-regulate the AMPK pathways of the host.}, }
@article {pmid28883811, year = {2017}, author = {Medina, D and Walke, JB and Gajewski, Z and Becker, MH and Swartwout, MC and Belden, LK}, title = {Culture Media and Individual Hosts Affect the Recovery of Culturable Bacterial Diversity from Amphibian Skin.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1574}, pmid = {28883811}, issn = {1664-302X}, abstract = {One current challenge in microbial ecology is elucidating the functional roles of the large diversity of free-living and host-associated bacteria identified by culture-independent molecular methods. Importantly, the characterization of this immense bacterial diversity will likely require merging data from culture-independent approaches with work on bacterial isolates in culture. Amphibian skin bacterial communities have become a recent focus of work in host-associated microbial systems due to the potential role of these skin bacteria in host defense against the pathogenic fungus Batrachochytrium dendrobatidis (Bd), which is associated with global amphibian population declines and extinctions. As there is evidence that some skin bacteria may inhibit growth of Bd and prevent infection in some cases, there is interest in using these bacteria as probiotic therapy for conservation of at-risk amphibians. In this study, we used skin swabs from American toads (Anaxyrus americanus) to: (1) assess the diversity and community structure of culturable amphibian skin bacteria grown on high and low nutrient culture media, (2) determine which culture media recover the highest proportion of the total skin bacterial community of individual toads relative to culture-independent data, and (3) assess whether the plated communities from the distinct media types vary in their ability to inhibit Bd growth in in-vitro assays. Overall, we found that culture media with low nutrient concentrations facilitated the growth of more diverse bacterial taxa and grew distinct communities relative to media with higher nutrient concentrations. Use of low nutrient media also resulted in culturing proportionally more of the bacterial diversity on individual toads relative to the overall community defined using culture-independent methods. However, while there were differences in diversity among media types, the variation among individual hosts was greater than variation among media types, suggesting that swabbing more individuals in a population is the best way to maximize culture collections, regardless of media type. Lastly, the function of the plated communities against Bd did not vary across culture media type or between high and low nutrient media. These results inform current efforts for developing a probiotic-based approach for amphibian conservation and help to ensure that culture collections are capturing the majority of the important diversity in these systems.}, }
@article {pmid28881263, year = {2017}, author = {Vandeweyer, D and Crauwels, S and Lievens, B and Van Campenhout, L}, title = {Metagenetic analysis of the bacterial communities of edible insects from diverse production cycles at industrial rearing companies.}, journal = {International journal of food microbiology}, volume = {261}, number = {}, pages = {11-18}, doi = {10.1016/j.ijfoodmicro.2017.08.018}, pmid = {28881263}, issn = {1879-3460}, mesh = {Animals ; Bacteria/classification/*genetics/*isolation &amp; purification ; Food Contamination/analysis ; Food Safety ; Gryllidae/*microbiology ; Humans ; Larva/microbiology ; Metagenomics ; Tenebrio/*microbiology ; }, abstract = {Despite the continuing development of new insect-derived food products, microbial research on edible insects and insect-based foods is still very limited. The goal of this study was to increase the knowledge on the microbial quality of edible insects by comparing the bacterial community composition of mealworms (Tenebrio molitor) and crickets (Acheta domesticus and Gryllodes sigillatus) from several production cycles and rearing companies. Remarkable differences in the bacterial community composition were found between different mealworm rearing companies and mealworm production cycles from the same company. In comparison with mealworms, the bacterial community composition of the investigated crickets was more similar among different companies, and was highly similar between both cricket species investigated. Mealworm communities were dominated by Spiroplasma and Erwinia species, while crickets were abundantly colonised by (Para)bacteroides species. With respect to food safety, only a few operational taxonomic units could be associated with potential human pathogens such as Cronobacter or spoilage bacteria such as Pseudomonas. In summary, our results implicate that at least for cricket rearing, production cycles of constant and good quality in terms of bacterial composition can be obtained by different rearing companies. For mealworms however, more variation in terms of microbial quality occurs between companies.}, }
@article {pmid28878756, year = {2017}, author = {Ofaim, S and Ofek-Lalzar, M and Sela, N and Jinag, J and Kashi, Y and Minz, D and Freilich, S}, title = {Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1606}, pmid = {28878756}, issn = {1664-302X}, abstract = {Advances in metagenomics enable high resolution description of complex bacterial communities in their natural environments. Consequently, conceptual approaches for community level functional analysis are in high need. Here, we introduce a framework for a metagenomics-based analysis of community functions. Environment-specific gene catalogs, derived from metagenomes, are processed into metabolic-network representation. By applying established ecological conventions, network-edges (metabolic functions) are assigned with taxonomic annotations according to the dominance level of specific groups. Once a function-taxonomy link is established, prediction of the impact of dominant taxa on the overall community performances is assessed by simulating removal or addition of edges (taxa associated functions). This approach is demonstrated on metagenomic data describing the microbial communities from the root environment of two crop plants - wheat and cucumber. Predictions for environment-dependent effects revealed differences between treatments (root vs. soil), corresponding to documented observations. Metabolism of specific plant exudates (e.g., organic acids, flavonoids) was linked with distinct taxonomic groups in simulated root, but not soil, environments. These dependencies point to the impact of these metabolite families as determinants of community structure. Simulations of the activity of pairwise combinations of taxonomic groups (order level) predicted the possible production of complementary metabolites. Complementation profiles allow formulating a possible metabolic role for observed co-occurrence patterns. For example, production of tryptophan-associated metabolites through complementary interactions is unique to the tryptophan-deficient cucumber root environment. Our approach enables formulation of testable predictions for species contribution to community activity and exploration of the functional outcome of structural shifts in complex bacterial communities. Understanding community-level metabolism is an essential step toward the manipulation and optimization of microbial function. Here, we introduce an analysis framework addressing three key challenges of such data: producing quantified links between taxonomy and function; contextualizing discrete functions into communal networks; and simulating environmental impact on community performances. New technologies will soon provide a high-coverage description of biotic and a-biotic aspects of complex microbial communities such as these found in gut and soil. This framework was designed to allow the integration of high-throughput metabolomic and metagenomic data toward tackling the intricate associations between community structure, community function, and metabolic inputs.}, }
@article {pmid28878747, year = {2017}, author = {Sannasiddappa, TH and Lund, PA and Clarke, SR}, title = {In Vitro Antibacterial Activity of Unconjugated and Conjugated Bile Salts on Staphylococcus aureus.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1581}, pmid = {28878747}, issn = {1664-302X}, abstract = {Bile salts are potent antimicrobial agents and are an important component of innate defenses in the intestine, giving protection against invasive organisms. They play an important role in determining microbial ecology of the intestine and alterations in their levels can lead to increased colonization by pathogens. We have previously demonstrated survival of the opportunistic pathogen Staphylococcus aureus in the human colonic model. Thus investigating the interaction between S. aureus and bile salts is an important factor in understanding its ability to colonize in the host intestine. Harnessing bile salts may also give a new avenue to explore in the development of therapeutic strategies to control drug resistant bacteria. Despite this importance, the antibacterial activity of bile salts on S. aureus is poorly understood. In this study, we investigated the antibacterial effects of the major unconjugated and conjugated bile salts on S. aureus. Several concentration-dependent antibacterial mechanisms were found. Unconjugated bile salts at their minimum inhibitory concentration (cholic and deoxycholic acid at 20 and 1 mM, respectively) killed S. aureus, and this was associated with increased membrane disruption and leakage of cellular contents. Unconjugated bile salts (cholic and deoxycholic acid at 8 and 0.4 mM, respectively) and conjugated bile salts (glycocholic and taurocholic acid at 20 mM) at their sub inhibitory concentrations were still able to inhibit growth through disruption of the proton motive force and increased membrane permeability. We also demonstrated that unconjugated bile salts possess more potent antibacterial action on S. aureus than conjugated bile salts.}, }
@article {pmid28878171, year = {2017}, author = {Zagorec, M and Champomier-Vergès, MC}, title = {Lactobacillus sakei: A Starter for Sausage Fermentation, a Protective Culture for Meat Products.}, journal = {Microorganisms}, volume = {5}, number = {3}, pages = {}, pmid = {28878171}, issn = {2076-2607}, abstract = {Among lactic acid bacteria of meat products, Lactobacillus sakei is certainly the most studied species due to its role in the fermentation of sausage and its prevalence during cold storage of raw meat products. Consequently, the physiology of this bacterium regarding functions involved in growth, survival, and metabolism during meat storage and processing are well known. This species exhibits a wide genomic diversity that can be observed when studying different strains and on which probably rely its multiple facets in meat products: starter, spoiler, or protective culture. The emerging exploration of the microbial ecology of meat products also revealed the multiplicity of bacterial interactions L. sakei has to face and their various consequences on microbial quality and safety at the end of storage.}, }
@article {pmid28875307, year = {2018}, author = {Dias, ACF and Cotta, SR and Andreote, FD and van Elsas, JD}, title = {The parA Region of Broad-Host-Range PromA Plasmids Is a Carrier of Mobile Genes.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {479-486}, pmid = {28875307}, issn = {1432-184X}, support = {2015/01290-8//FAPESP/ ; 443815/2014-3//CNPq/ ; }, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Ecosystem ; *Gene Transfer, Horizontal ; Plasmids/*genetics/metabolism ; Polymerase Chain Reaction/*methods ; Soil/chemistry ; Species Specificity ; }, abstract = {The ecological competences in microbiomes are driven by the adaptive capabilities present within microbiome members. Horizontal gene transfer (HGT) promoted by plasmids provides a rapid adaptive strategy to microbiomes, an interesting feature considering the constantly changing conditions in most environments. This study examined the parA locus, found in the highly promiscuous PromA class of plasmids, as the insertion site for incoming genes. A novel PCR system was designed that enabled examining insertions into this locus. Microbiomes of mangrove sediments, salt marsh, mycosphere, and bulk soil revealed habitat-specific sets of insertions in this plasmid region. Furthermore, such habitats could be differentiated based on patterns of parA-inserted genes, and the genes carried by these plasmids. Thus, a suite of dioxygenase-related genes and transposase elements were found in oil-affected mangroves, whereas genes involved in nitrogen and carbon cycling were detected in salt marsh and soils. All genes detected could be associated with capabilities of members of the microbiome to adapt to and survive in each habitat. The methodology developed in this work was effective, sensitive, and practical, allowing detection of mobilized genes between microorganisms.}, }
@article {pmid28875273, year = {2018}, author = {Gallart, M and Adair, KL and Love, J and Meason, DF and Clinton, PW and Xue, J and Turnbull, MH}, title = {Host Genotype and Nitrogen Form Shape the Root Microbiome of Pinus radiata.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {419-433}, pmid = {28875273}, issn = {1432-184X}, support = {No C04X1306//New Zealand Ministry of Business, Innovation and Employment/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Fungi/classification/genetics/*isolation &amp; purification/metabolism ; Genotype ; *Microbiota ; Nitrogen/*analysis/metabolism ; Pinus/*genetics/metabolism/microbiology ; Plant Roots/genetics/metabolism/*microbiology ; *Soil Microbiology ; }, abstract = {A central challenge in community ecology is understanding the role that phenotypic variation among genotypes plays in structuring host-associated communities. While recent studies have investigated the relationship between plant genotype and the composition of soil microbial communities, the effect of genotype-by-environment interactions on the plant microbiome remains unclear. In this study, we assessed the influence of tree genetics (G), nitrogen (N) form and genotype-by-environment interaction (G x N) on the composition of the root microbiome. Rhizosphere communities (bacteria and fungi) and root-associated fungi (including ectomycorrhizal and saprotrophic guilds) were characterised in two genotypes of Pinus radiata with contrasting physiological responses to exogenous organic or inorganic N supply. Genotype-specific responses to N form influenced the composition of the root microbiome. Specifically, (1) diversity and composition of rhizosphere bacterial and root-associated fungal communities differed between genotypes that had distinct responses to N form, (2) shifts in the relative abundance of individual taxa were driven by the main effects of N form or host genotype and (3) the root microbiome of the P. radiata genotype with the most divergent growth responses to organic and inorganic N was most sensitive to differences in N form. Our results show that intraspecific variation in tree response to N form has significant consequences for the root microbiome of P. radiata, demonstrating the importance of genotype-by-environment interactions in shaping host-associated communities.}, }
@article {pmid28875260, year = {2018}, author = {Pepori, AL and Bettini, PP and Comparini, C and Sarrocco, S and Bonini, A and Frascella, A and Ghelardini, L and Scala, A and Vannacci, G and Santini, A}, title = {Geosmithia-Ophiostoma: a New Fungus-Fungus Association.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {632-646}, pmid = {28875260}, issn = {1432-184X}, support = {2009RZ94KA_003//MIUR/ ; }, mesh = {Animals ; Ascomycota/genetics/growth &amp; development/physiology ; Biological Control Agents ; Coleoptera/microbiology ; DNA, Fungal/genetics ; Fungal Proteins/genetics ; Gene Transfer, Horizontal ; Genes, Fungal/genetics ; Hyphae ; Hypocreales/genetics/growth &amp; development/*physiology ; Microbial Interactions/genetics/*physiology ; Ophiostoma/genetics/growth &amp; development/pathogenicity/*physiology ; Plant Diseases/microbiology ; Ulmus/*microbiology ; }, abstract = {In Europe as in North America, elms are devastated by Dutch elm disease (DED), caused by the alien ascomycete Ophiostoma novo-ulmi. Pathogen dispersal and transmission are ensured by local species of bark beetles, which established a novel association with the fungus. Elm bark beetles also transport the Geosmithia fungi genus that is found in scolytids' galleries colonized by O. novo-ulmi. Widespread horizontal gene transfer between O. novo-ulmi and Geosmithia was recently observed. In order to define the relation between these two fungi in the DED pathosystem, O. novo-ulmi and Geosmithia species from elm, including a GFP-tagged strain, were grown in dual culture and mycelial interactions were observed by light and fluorescence microscopy. Growth and sporulation of O. novo-ulmi in the absence or presence of Geosmithia were compared. The impact of Geosmithia on DED severity was tested in vivo by co-inoculating Geosmithia and O. novo-ulmi in elms. A close and stable relation was observed between the two fungi, which may be classified as mycoparasitism by Geosmithia on O. novo-ulmi. These results prove the existence of a new component in the complex of organisms involved in DED, which might be capable of reducing the disease impact.}, }
@article {pmid28875073, year = {2017}, author = {Godoy-Vitorino, F and Ruiz-Diaz, CP and Rivera-Seda, A and Ramírez-Lugo, JS and Toledo-Hernández, C}, title = {The microbial biosphere of the coral Acropora cervicornis in Northeastern Puerto Rico.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3717}, pmid = {28875073}, issn = {2167-8359}, support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: Coral reefs are the most biodiverse ecosystems in the marine realm, and they not only contribute a plethora of ecosystem services to other marine organisms, but they also are beneficial to humankind via, for instance, their role as nurseries for commercially important fish species. Corals are considered holobionts (host + symbionts) since they are composed not only of coral polyps, but also algae, other microbial eukaryotes and prokaryotes. In recent years, Caribbean reef corals, including the once-common scleractinian coral Acropora cervicornis, have suffered unprecedented mortality due to climate change-related stressors. Unfortunately, our basic knowledge of the molecular ecophysiology of reef corals, particularly with respect to their complex bacterial microbiota, is currently too poor to project how climate change will affect this species. For instance, we do not know how light influences microbial communities of A. cervicornis, arguably the most endangered of all Caribbean coral species. To this end, we characterized the microbiota of A. cervicornis inhabiting water depths with different light regimes.<br><br>METHODS: Six A. cervicornis fragments from different individuals were collected at two different depths (three at 1.5 m and three at 11 m) from a reef 3.2 km off the northeastern coast of Puerto Rico. We characterized the microbial communities by sequencing the 16S rRNA gene region V4 with the Illumina platform.<br><br>RESULTS: A total of 173,137 good-quality sequences were binned into 803 OTUs with a 97% similarity. We uncovered eight bacterial phyla at both depths with a dominance of 725 Rickettsiales OTUs (Proteobacteria). A fewer number (38) of low dominance OTUs varied by depth and taxa enriched in shallow water corals included Proteobacteria (e.g. Rhodobacteraceae and Serratia) and Firmicutes (Streptococcus). Those enriched in deeper water corals featured different Proteobacterial taxa (Campylobacterales and Bradyrhizobium) and Firmicutes (Lactobacillus).<br><br>DISCUSSION: Our results confirm that the microbiota of A. cervicornis inhabiting the northeastern region of Puerto Rico is dominated by a Rickettsiales-like bacterium and that there are significant changes in less dominant taxa at different water depths. These changes in less dominant taxa may potentially impact the coral's physiology, particularly with respect to its ability to respond to future increases in temperature and CO2.}, }
@article {pmid28870194, year = {2017}, author = {Pinheiro, I and Robinson, L and Verhelst, A and Marzorati, M and Winkens, B and den Abbeele, PV and Possemiers, S}, title = {A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial.}, journal = {BMC complementary and alternative medicine}, volume = {17}, number = {1}, pages = {441}, pmid = {28870194}, issn = {1472-6882}, mesh = {Adolescent ; Adult ; Aged ; Biological Therapy ; Constipation/*microbiology/physiopathology/*therapy ; Defecation ; Double-Blind Method ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; Pilot Projects ; Saccharomyces cerevisiae/*metabolism ; Young Adult ; }, abstract = {BACKGROUND: Constipation and symptoms of gastrointestinal discomfort such as bloating are common among otherwise healthy individuals, but with significant impact on quality of life. Despite the recognized contribution of the gut microbiome to this pathology, little is known about which group(s) of microorganism(s) are playing a role. A previous study performed in vitro suggests that EpiCor® fermentate has prebiotic-like properties, being able to favorably modulate the composition of the gut microbiome. Therefore, the aim of this study was to investigate the effects of EpiCor fermentate in a population with symptoms of gastrointestinal discomfort and reduced bowel movements and to evaluate its effect at the level of the gut microbiome.<br><br>METHODS: This pilot study was performed according to a randomized, double-blind, placebo-controlled parallel design. Eighty subjects with symptoms of gastrointestinal discomfort and constipation were allocated to one of two trial arms (placebo or EpiCor fermentate). Randomization was done in a stratified manner according to symptom severity, resulting in two subgroups of patients: severe and moderate. Daily records of gastrointestinal symptoms were assessed on a 5-point scale, and also stool frequency and consistency were documented during a 2-week run-in and a 6-week intervention phases. Averages over two-week intervals were calculated. Constipation-associated quality of life and general perceived stress were assessed at baseline and after 3 and 6&#xa0;weeks of intervention. Fecal samples were also collected at these same time points.<br><br>RESULTS: EpiCor fermentate led to a significant improvement of symptoms such as bloating/distension (p&#xa0;=&#xa0;0.033 and p&#xa0;=&#xa0;0.024 after 2 and 4&#xa0;weeks of intervention, respectively), feeling of fullness (p&#xa0;=&#xa0;0.004 and p&#xa0;=&#xa0;0.023 after 2 and 4&#xa0;weeks of intervention, respectively) and general daily scores (p&#xa0;=&#xa0;0.046 after 2&#xa0;weeks of intervention) in the moderate subgroup. A significant improvement in stool consistency was observed for the total population (p&#xa0;=&#xa0;0.023 after 2&#xa0;weeks of intervention) as well as for the severe subgroup (p&#xa0;=&#xa0;0.046 after 2&#xa0;weeks of intervention), and a nearly significant increase in stool frequency was detected for the total cohort (p&#xa0;=&#xa0;0.083 and p&#xa0;=&#xa0;0.090 after 2 and 4&#xa0;weeks of intervention, respectively). These effects were accompanied by an improvement in constipation-associated quality of life and general perceived stress, particularly in the moderate subgroup. Members of the families Bacteroidaceae and Prevotellaceae, two groups of bacteria that have been previously reported to be deficient in constipated patients, were found to increase with EpiCor fermentate in the severe subgroup. In the moderate subgroup, a significant increase in Akkermansia muciniphila was observed.<br><br>CONCLUSIONS: Despite the relatively low dose administered (500&#xa0;mg/day), particularly when comparing to the high recommended doses for prebiotic fibers, EpiCor fermentate was able to modulate the composition of the gut microbiome, resulting in improvement of constipation-associated symptoms. Conversely, the reported increase in bowel movements may have altered the gut microbial community by increasing those groups of bacteria that are better adapted to a faster gastrointestinal transit time.<br><br>TRIAL REGISTRATION: NCT03051399 at ClinicalTrials.gov. Retrospectively registered. Registration date: 13 February 2017.}, }
@article {pmid28868756, year = {2017}, author = {Timmis, K and de Lorenzo, V and Verstraete, W and Ramos, JL and Danchin, A and Brüssow, H and Singh, BK and Timmis, JK}, title = {The contribution of microbial biotechnology to economic growth and employment creation.}, journal = {Microbial biotechnology}, volume = {10}, number = {5}, pages = {1137-1144}, pmid = {28868756}, issn = {1751-7915}, mesh = {Biotechnology/economics/education ; Economic Development ; Employment/*economics ; Humans ; Industrial Microbiology/*economics/education ; Workforce ; }, abstract = {Our communication discusses the profound impact of bio-based economies - in particular microbial biotechnologies - on SDG 8: Promote sustained, inclusive and sustainable economic growth, full and productive employment and decent work for all. A bio-based economy provides significant potential for improving labour supply, education and investment, and thereby for substantially increasing the demographic dividend. This, in turn, improves the sustainable development of economies.}, }
@article {pmid28868049, year = {2017}, author = {Naughton, LM and Romano, S and O'Gara, F and Dobson, ADW}, title = {Identification of Secondary Metabolite Gene Clusters in the Pseudovibrio Genus Reveals Encouraging Biosynthetic Potential toward the Production of Novel Bioactive Compounds.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1494}, pmid = {28868049}, issn = {1664-302X}, abstract = {Increased incidences of antimicrobial resistance and the emergence of pan-resistant 'superbugs' have provoked an extreme sense of urgency amongst researchers focusing on the discovery of potentially novel antimicrobial compounds. A strategic shift in focus from the terrestrial to the marine environment has resulted in the discovery of a wide variety of structurally and functionally diverse bioactive compounds from numerous marine sources, including sponges. Bacteria found in close association with sponges and other marine invertebrates have recently gained much attention as potential sources of many of these novel bioactive compounds. Members of the genus Pseudovibrio are one such group of organisms. In this study, we interrogate the genomes of 21 Pseudovibrio strains isolated from a variety of marine sources, for the presence, diversity and distribution of biosynthetic gene clusters (BGCs). We expand on results obtained from antiSMASH analysis to demonstrate the similarity between the Pseudovibrio-related BGCs and those characterized in other bacteria and corroborate our findings with phylogenetic analysis. We assess how domain organization of the most abundant type of BGCs present among the isolates (Non-ribosomal peptide synthetases and Polyketide synthases) may influence the diversity of compounds produced by these organisms and highlight for the first time the potential for novel compound production from this genus of bacteria, using a genome guided approach.}, }
@article {pmid28866755, year = {2018}, author = {Kosiba, J and Krztoń, W and Wilk-Woźniak, E}, title = {Effect of Microcystins on Proto- and Metazooplankton Is More Evident in Artificial Than in Natural Waterbodies.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {293-302}, pmid = {28866755}, issn = {1432-184X}, mesh = {Animals ; Biomass ; Cyanobacteria/genetics/growth &amp; development/*metabolism ; Ecosystem ; Harmful Algal Bloom ; Lakes/*chemistry/microbiology/parasitology ; Microcystins/*analysis/metabolism ; Zooplankton/classification/drug effects/genetics/*growth &amp; development ; }, abstract = {The increasing proliferation of cyanobacterial blooms prolongs the impact of cyanobacteria on aquatic fauna, potentially altering trophic relationships. We hypothesized that any effect of dissolved microcystins (toxins produced by cyanobacteria) on plankton assemblages would be more evident in artificial reservoirs and ponds than in natural ones. The concentrations of dissolved microcystins in the waters we studied ranged widely from 0.07 to 0.81 μg/L. We showed that the artificial ponds were subjected to more frequent and longer-lasting harmful algal blooms. The plankton occurring in them were exposed to significantly higher concentrations of dissolved microcystins than those in natural oxbow lakes. Using a general linear model (GLM) regression, our study identified a significant relationship between dissolved microcystins and both the density and biomass of particular zooplankton groups (ciliates, rotifers, cladocerans, copepods). The density, biomass, and richness of the animal plankton were significantly lower in the artificial ponds than in the natural oxbow lakes. The impact of microcystins and the length of time that they remained in the water caused structural homogenization of the plankton.}, }
@article {pmid28865967, year = {2017}, author = {West, CE and Dzidic, M and Prescott, SL and Jenmalm, MC}, title = {Bugging allergy; role of pre-, pro- and synbiotics in allergy prevention.}, journal = {Allergology international : official journal of the Japanese Society of Allergology}, volume = {66}, number = {4}, pages = {529-538}, doi = {10.1016/j.alit.2017.08.001}, pmid = {28865967}, issn = {1440-1592}, mesh = {Animals ; Clinical Studies as Topic ; Humans ; Hypersensitivity/*immunology/*prevention &amp; control/therapy ; Immune Tolerance ; Immunity ; Immunomodulation ; Microbiota/immunology ; Outcome Assessment, Health Care ; Prebiotics/*administration &amp; dosage ; Probiotics/*administration &amp; dosage ; Synbiotics/*administration &amp; dosage ; }, abstract = {Large-scale biodiversity loss and complex changes in social behaviors are altering human microbial ecology. This is increasingly implicated in the global rise in inflammatory diseases, most notably the "allergy epidemic" in very early life. Colonization of human ecological niches, particularly the gastrointestinal tract, is critical for normal local and systemic immune development and regulation. Disturbances in composition, diversity and timing of microbial colonization have been associated with increased allergy risk, indicating the importance of strategies to restore a dysbiotic gut microbiota in the primary prevention of allergic diseases, including the administration of probiotics, prebiotics and synbiotics. Here, we summarize and discuss findings of randomized clinical trials that have examined the effects of these microbiome-related strategies on short and long-term allergy preventative effects - including new guidelines from the World Allergy Organization which now recommend probiotics and prebiotics for allergy prevention under certain conditions. The relatively low quality evidence, limited comparative studies and large heterogeneity between studies, have collectively hampered recommendations on specific probiotic strains, specific timing and specific conditions for the most effective preventive management. At the same time the risk of using available products is low. While further research is needed before specific practice guidelines on supplement probiotics and prebiotics, it is equally important that the underlying dietary and lifestyle factors of dysbiosis are addressed at both the individual and societal levels.}, }
@article {pmid28865669, year = {2017}, author = {Rahman, A and Meerburg, FA and Jimenez, J and Ravadagundhi, S and Wett, B and Bott, C and Al-Omari, A and Riffat, R and Murthy, S and De Clippeleir, H}, title = {Reply for comment on "Bioflocculation management through high-rate contact-stabilization: A promising technology to recover organic carbon from low-strength wastewater by Rahman, A., Meerburg, F. A., Ravadagundhi, S., Wett, B., Jimenez, J., Bott, C., Al-Omari, A., Riffat, R., Murthy, S. and De Clippeleir, H. [Water Research 104 (2016) 485-496]".}, journal = {Water research}, volume = {126}, number = {}, pages = {527-529}, doi = {10.1016/j.watres.2017.08.014}, pmid = {28865669}, issn = {1879-2448}, mesh = {*Carbon ; Sewage ; Waste Disposal, Fluid ; *Wastewater ; }, }
@article {pmid28865007, year = {2018}, author = {Nuskern, L and Ježić, M and Liber, Z and Mlinarec, J and Ćurković-Perica, M}, title = {Cryphonectria hypovirus 1-Induced Epigenetic Changes in Infected Phytopathogenic Fungus Cryphonectria parasitica.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {790-798}, pmid = {28865007}, issn = {1432-184X}, support = {5381//Hrvatska Zaklada za Znanost/ ; IZ73Z0_152525/1//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (CH)/ ; }, mesh = {Ascomycota/*genetics/growth &amp; development/pathogenicity/*virology ; DNA Methylation ; DNA, Fungal/analysis ; *Epigenesis, Genetic ; Epigenomics ; Fungal Viruses/*genetics/*physiology ; Genes, Fungal/genetics ; Genome, Viral ; Host-Pathogen Interactions/*genetics/physiology ; Pest Control, Biological ; Plant Diseases/microbiology ; Virulence Factors/genetics ; }, abstract = {Biotic stress caused by virus infections induces epigenetic changes in infected plants and animals, but this is the first report on methylation pattern changes in a fungus after mycovirus infection. As a model pathosystem for mycovirus-host interactions, we used Cryphonectria hypovirus 1 (CHV1) and its host fungus Cryphonectria parasitica, in which deregulation of methylation cycle enzymes upon virus infection was observed previously. Six CHV1 strains of different subtypes were transferred into three different C. parasitica isolates in order to assess the effect of different CHV1 strains and/or subtypes on global cytosine methylation level in infected fungus, using methylation-sensitive amplification polymorphism (MSAP). Infection with CHV1 affected the methylation pattern of the C. parasitica genome; it increased the number and diversity of methylated, hemi-methylated, and total MSAP markers found in infected fungal isolates compared to virus-free controls. The increase in methylation levels correlated well with the CHV1-induced reduction of fungal growth in vitro, indicating that C. parasitica genome methylation upon CHV1 infection, rather than being the defensive mechanism of the fungus, is more likely to be the virulence determinant of the virus. Furthermore, the severity of CHV1 effect on methylation levels of infected C. parasitica isolates depended mostly on individual CHV1 strains and on the combination of host and virus genomes, rather than on the virus subtype. These novel findings broaden our knowledge about CHV1 strains which could potentially be used in human-aided biocontrol of chestnut blight, a disease caused by C. parasitica in chestnut forest ecosystems and orchards.}, }
@article {pmid28862999, year = {2017}, author = {Romaní-Pérez, M and Agusti, A and Sanz, Y}, title = {Innovation in microbiome-based strategies for promoting metabolic health.}, journal = {Current opinion in clinical nutrition and metabolic care}, volume = {20}, number = {6}, pages = {484-491}, doi = {10.1097/MCO.0000000000000419}, pmid = {28862999}, issn = {1473-6519}, mesh = {Animals ; Bacteroides ; *Diet ; Disease Management ; Disease Models, Animal ; Eubacterium ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Humans ; Membrane Proteins/metabolism ; Obesity/therapy ; *Probiotics ; }, abstract = {PURPOSE OF REVIEW: Update on the development of microbiome-based interventions and dietary supplements to combat obesity and related comorbidities, which are leading causes of global mortality.<br><br>RECENT FINDINGS: The role of intestinal dysbiosis, partly resulting from unhealthy diets, in the development of obesity and metabolic disorders, is well documented by recent translational research. Human experimental trials with whole-faecal transplants are ongoing, and their results will be crucial as proof of concept that interventions intended to modulate the microbiome composition and function could be alternatives for the management of obesity and related comorbidities. Potential next-generation probiotic bacteria (Akkermansia, Bacteroides spp., Eubacterium halli) and microbiota-derived molecules (e.g. membrane proteins, short-chain fatty acids) are being evaluated in preclinical and clinical trials to promote the development of innovative dietary supplements. The fact that live or inactivated bacteria and their products can regulate pathways that increase energy expenditure, and reduce energy intake, and absorption and systemic inflammation make them attractive research targets from a nutritional and clinical perspective.<br><br>SUMMARY: Understanding which are the beneficial bacteria and their bioactive products is helping us to envisage innovative microbiome-based dietary interventions to tackle obesity. Advances will likely result from future refinements of these strategies according to the individual's microbiome configuration and its particular response to interventions, thereby progressing towards personalized nutrition.}, }
@article {pmid28862473, year = {2018}, author = {Burges, A and Alkorta, I and Epelde, L and Garbisu, C}, title = {From phytoremediation of soil contaminants to phytomanagement of ecosystem services in metal contaminated sites.}, journal = {International journal of phytoremediation}, volume = {20}, number = {4}, pages = {384-397}, doi = {10.1080/15226514.2017.1365340}, pmid = {28862473}, issn = {1549-7879}, mesh = {Biodegradation, Environmental ; Ecosystem ; Metals ; *Soil ; Soil Pollutants/*analysis ; }, abstract = {Since the emergence of phytoremediation, much research has focused on its development for (i) the removal of metals from soil and/or (ii) the reduction of metal bioavailability, mobility, and ecotoxicity in soil. Here, we review the lights and shades of the two main strategies (i.e., phytoextraction and phytostabilization) currently used for the phytoremediation of metal contaminated soils, irrespective of the level of such contamination. Both strategies face limitations to become successful at commercial scale and, then, often generate skepticism regarding their usefulness. Recent innovative approaches and paradigms are gradually establishing these phytoremediation strategies as suitable options for the management of metal contaminated soils. The combination of these phytotechnologies with a sustainable and profitable site use (a strategy called phytomanagement) grants value to the many benefits that can be obtained during the phytoremediation of metal contaminated sites, such as, for instance, the restoration of important ecosystem services, e.g. nutrient cycling, carbon storage, water flow regulation, erosion control, water purification, fertility maintenance, etc.}, }
@article {pmid28861598, year = {2018}, author = {Jorquera, MA and Gabler, S and Inostroza, NG and Acuña, JJ and Campos, MA and Menezes-Blackburn, D and Greiner, R}, title = {Screening and Characterization of Phytases from Bacteria Isolated from Chilean Hydrothermal Environments.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {387-399}, pmid = {28861598}, issn = {1432-184X}, support = {code PCCI 1-2011//CONICYT/ ; code USA2013-0010//CONICYT/ ; 1120505//FONDECYT/ ; 1160302//FONDECYT/ ; 3140620//FONDECYT/ ; 11160112//FONDECYT/ ; }, mesh = {6-Phytase/*chemistry/genetics/*metabolism ; Bacteria/classification/*enzymology/genetics/isolation &amp; purification ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Enzyme Stability ; Hydrogen-Ion Concentration ; Hydrothermal Vents/*microbiology ; Kinetics ; Temperature ; }, abstract = {Phytases are enzymes involved in organic phosphorus cycling in nature and widely used as feed additives in animal diets. Thermal tolerance is a desired property of phytases. The objectives of this study were to screen and characterize bacterial phytases from Chilean hydrothermal environments. In this study, 60% (30 of 63) of screened thermophilic (60 °C) isolates showed phytase activity in crude protein extracts. The characterization of phytase from two selected isolates (9B and 15C) revealed that both isolates produce phytases with a pH optimum at 5.0. The temperature optimum for phytate dephosphorylation was determined to be 60 and 50 °C for the phytases from the isolates 9B and 15C, respectively. Interestingly, the phytase from the isolate 15C showed a residual activity of 46% after incubation at 90 °C for 20 min. The stepwise dephosphorylation of phytate by protein extracts of the isolates 9B and 15C was verified by HLPC analysis. Finally, the isolates 9B and 15C were identified by partial sequencing of the 16S rRNA gene as members of the genera Bacillus and Geobacillus, respectively.}, }
@article {pmid28861526, year = {2017}, author = {Hamilton, JJ and Garcia, SL and Brown, BS and Oyserman, BO and Moya-Flores, F and Bertilsson, S and Malmstrom, RR and Forest, KT and McMahon, KD}, title = {Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI.}, journal = {mSystems}, volume = {2}, number = {4}, pages = {}, pmid = {28861526}, issn = {2379-5077}, abstract = {An explosion in the number of available genome sequences obtained through metagenomics and single-cell genomics has enabled a new view of the diversity of microbial life, yet we know surprisingly little about how microbes interact with each other or their environment. In fact, the majority of microbial species remain uncultivated, while our perception of their ecological niches is based on reconstruction of their metabolic potential. In this work, we demonstrate how the "seed set framework," which computes the set of compounds that an organism must acquire from its environment (E. Borenstein, M. Kupiec, M. W. Feldman, and E. Ruppin, Proc Natl Acad Sci U S A 105:14482-14487, 2008, https://doi.org/10.1073/pnas.0806162105), enables computational analysis of metabolic reconstructions while providing new insights into a microbe's metabolic capabilities, such as nutrient use and auxotrophies. We apply this framework to members of the ubiquitous freshwater actinobacterial lineage acI, confirming and extending previous experimental and genomic observations implying that acI bacteria are heterotrophs reliant on peptides and saccharides. We also present the first metatranscriptomic study of the acI lineage, revealing high expression of transport proteins and the light-harvesting protein actinorhodopsin. Putative transport proteins complement predictions of nutrients and essential metabolites while providing additional support of the hypothesis that members of the acI are photoheterotrophs. IMPORTANCE The metabolic activity of uncultivated microorganisms contributes to numerous ecosystem processes, ranging from nutrient cycling in the environment to influencing human health and disease. Advances in sequencing technology have enabled the assembly of genomes for these microorganisms, but our ability to generate reference genomes far outstrips our ability to analyze them. Common approaches to analyzing microbial metabolism require reconstructing the entirety of an organism's metabolic pathways or performing targeted searches for genes involved in a specific process. This paper presents a third approach, in which draft metabolic reconstructions are used to identify compounds through which an organism may interact with its environment. These compounds can then guide more-intensive metabolic reconstruction efforts and can also provide new hypotheses about the specific contributions that microbes make to ecosystem-scale metabolic processes.}, }
@article {pmid28861064, year = {2017}, author = {Durán, P and Jorquera, M and Viscardi, S and Carrion, VJ and Mora, ML and Pozo, MJ}, title = {Screening and Characterization of Potentially Suppressive Soils against Gaeumannomyces graminis under Extensive Wheat Cropping by Chilean Indigenous Communities.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1552}, pmid = {28861064}, issn = {1664-302X}, abstract = {Wheat production around the world is severely compromised by the occurrence of "take-all" disease, which is caused by the soil-borne pathogen Gaeumannomyces graminis var. tritici (Ggt). In this context, suppressive soils are those environments in which plants comparatively suffer less soil-borne pathogen diseases than expected, owing to native soil microorganism activities. In southern Chile, where 85% of the national cereal production takes place, several studies have suggested the existence of suppressive soils under extensive wheat cropping. Thus, this study aimed to screen Ggt-suppressive soil occurrence in 16 locations managed by indigenous "Mapuche" communities, using extensive wheat cropping for more than 10 years. Ggt growth inhibition in vitro screenings allowed the identification of nine putative suppressive soils. Six of these soils, including Andisols and Ultisols, were confirmed to be suppressive, since they reduced take-all disease in wheat plants growing under greenhouse conditions. Suppressiveness was lost upon soil sterilization, and recovered by adding 1% of the natural soil, hence confirming that suppressiveness was closely associated to the soil microbiome community composition. Our results demonstrate that long-term extensive wheat cropping, established by small Mapuche communities, can generate suppressive soils that can be used as effective microorganism sources for take-all disease biocontrol. Accordingly, suppressive soil identification and characterization are key steps for the development of environmentally-friendly and efficient biotechnological applications for soil-borne disease control.}, }
@article {pmid28861063, year = {2017}, author = {Terrisse, F and Cravo-Laureau, C and Noël, C and Cagnon, C and Dumbrell, AJ and McGenity, TJ and Duran, R}, title = {Variation of Oxygenation Conditions on a Hydrocarbonoclastic Microbial Community Reveals Alcanivorax and Cycloclasticus Ecotypes.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1549}, pmid = {28861063}, issn = {1664-302X}, abstract = {Deciphering the ecology of marine obligate hydrocarbonoclastic bacteria (MOHCB) is of crucial importance for understanding their success in occupying distinct niches in hydrocarbon-contaminated marine environments after oil spills. In marine coastal sediments, MOHCB are particularly subjected to extreme fluctuating conditions due to redox oscillations several times a day as a result of mechanical (tide, waves and currents) and biological (bioturbation) reworking of the sediment. The adaptation of MOHCB to the redox oscillations was investigated by an experimental ecology approach, subjecting a hydrocarbon-degrading microbial community to contrasting oxygenation regimes including permanent anoxic conditions, anoxic/oxic oscillations and permanent oxic conditions. The most ubiquitous MOHCB, Alcanivorax and Cycloclasticus, showed different behaviors, especially under anoxic/oxic oscillation conditions, which were more favorable for Alcanivorax than for Cycloclasticus. The micro-diversity of 16S rRNA gene transcripts from these genera revealed specific ecotypes for different oxygenation conditions and their dynamics. It is likely that such ecotypes allow the colonization of distinct ecological niches that may explain the success of Alcanivorax and Cycloclasticus in hydrocarbon-contaminated coastal sediments during oil-spills.}, }
@article {pmid28856796, year = {2017}, author = {Stüeken, EE and Buick, R and Anderson, RE and Baross, JA and Planavsky, NJ and Lyons, TW}, title = {Environmental niches and metabolic diversity in Neoarchean lakes.}, journal = {Geobiology}, volume = {15}, number = {6}, pages = {767-783}, doi = {10.1111/gbi.12251}, pmid = {28856796}, issn = {1472-4669}, mesh = {*Biological Evolution ; Cyanobacteria/*metabolism ; Ecosystem ; Geologic Sediments/*chemistry ; Lakes/*chemistry ; Paleontology ; Western Australia ; }, abstract = {The diversification of macro-organisms over the last 500 million years often coincided with the development of new environmental niches. Microbial diversification over the last 4 billion years likely followed similar patterns. However, linkages between environmental settings and microbial ecology have so far not been described from the ancient rock record. In this study, we investigated carbon, nitrogen, and molybdenum isotopes, and iron speciation in five non-marine stratigraphic units of the Neoarchean Fortescue Group, Western Australia, that are similar in age (2.78-2.72 Ga) but differ in their hydro-geologic setting. Our data suggest that the felsic-dominated and hydrologically open lakes of the Bellary and Hardey formations were probably dominated by methanogenesis (δ[13] Corg = -38.7 ± 4.2‰) and biologic N2 fixation (δ[15] Nbulk =-0.6 ± 1.0‰), whereas the Mt. Roe, Tumbiana and Kylena Formations, with more mafic siliciclastic sediments, preserve evidence of methanotrophy (δ[13] Corg as low as -57.4‰, δ[13] Ccarb as low as -9.2‰) and NH3 loss under alkaline conditions. Evidence of oxygenic photosynthesis is recorded only in the closed evaporitic Tumbiana lakes marked by abundant stromatolites, limited evidence of Fe and S cycling, fractionated Mo isotopes (δ[98/95] Mo = +0.4 ± 0.4‰), and the widest range in δ[13] Corg (-57‰ to -15‰), suggesting oxidative processes and multiple carbon fixation pathways. Methanotrophy in the three mafic settings was probably coupled to a combination of oxidants, including O2 and SO4[2-] . Overall, our results may indicate that early microbial evolution on the Precambrian Earth was in part influenced by geological parameters. We speculate that expanding habitats, such as those linked to continental growth, may have been an important factor in the evolution of life.}, }
@article {pmid28856421, year = {2018}, author = {Guterres, A and de Oliveira, RC and Fernandes, J and Maia, RM and Teixeira, BR and Oliveira, FCG and Bonvicino, CR and D'Andrea, PS and Schrago, CG and de Lemos, ERS}, title = {Co-circulation of Araraquara and Juquitiba Hantavirus in Brazilian Cerrado.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {783-789}, pmid = {28856421}, issn = {1432-184X}, support = {407664/2012-2 APQ//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Animals ; Brazil ; Coinfection/genetics/*virology ; Communicable Diseases/virology ; Disease Reservoirs/*veterinary/virology ; Ecosystem ; Genome, Viral ; Orthohantavirus/*classification/genetics/isolation &amp; purification/pathogenicity ; Hantavirus Infections/epidemiology/*transmission ; Humans ; *Phylogeny ; Recombination, Genetic ; Rodent Diseases/epidemiology/virology ; Sequence Analysis, DNA ; Sigmodontinae/*virology ; Species Specificity ; }, abstract = {Hantavirus cardiopulmonary syndrome is an emerging serious disease in the Americas, transmitted from wild rodents to humans through inhalation of aerosol containing virus. Herein, we characterized two distinct hantaviruses circulating in rodent species form Central Plateau, Midwestern region of Brazil in the Cerrado (savanna-like) biome, an area characterized by small trees and grasses adapted to climates with long dry periods. In this study, we identified the co-circulation of the Araraquara virus and a possible new lineage of the Juquitiba virus (JUQV) in Oligoryzomys nigripes. The implications of co-circulation are still unknown, but it can be the key for increasing viral diversity or emergence of new species through spillover or host switching events leading to co-infection and consequently recombination or reassortment between different virus species. Phylogenetic analyses based on the complete S segment indicated that, alongside with Oligoryzomys mattogrossae rodents, O. nigripes species could also have a whole as JUQV reservoir in the Cerrado biome. Although these rodents' species are common in the Cerrado biome, they are not abundant demonstrating how complex and different hantavirus enzootic cycles can be in this particular biome.}, }
@article {pmid28856162, year = {2017}, author = {Ben Hassen Trabelsi, A and Ghrib, A and Zaafouri, K and Friaa, A and Ouerghi, A and Naoui, S and Belayouni, H}, title = {Hydrogen-Rich Syngas Production from Gasification and Pyrolysis of Solar Dried Sewage Sludge: Experimental and Modeling Investigations.}, journal = {BioMed research international}, volume = {2017}, number = {}, pages = {7831470}, pmid = {28856162}, issn = {2314-6141}, mesh = {Biofuels ; Gases/chemistry ; Humans ; Hydrogen/chemistry ; Refuse Disposal/*methods ; Sewage/*chemistry ; Solar Energy ; Waste Management/*methods ; }, abstract = {Solar dried sewage sludge (SS) conversion by pyrolysis and gasification processes has been performed, separately, using two laboratory-scale reactors, a fixed-bed pyrolyzer and a downdraft gasifier, to produce mainly hydrogen-rich syngas. Prior to SS conversion, solar drying has been conducted in order to reduce moisture content (up to 10%). SS characterization reveals that these biosolids could be appropriate materials for gaseous products production. The released gases from SS pyrolysis and gasification present relatively high heating values (up to 9.96 MJ/kg for pyrolysis and 8.02 9.96 MJ/kg for gasification) due to their high contents of H2 (up to 11 and 7 wt%, resp.) and CH4 (up to 17 and 5 wt%, resp.). The yields of combustible gases (H2 and CH4) show further increase with pyrolysis. Stoichiometric models of both pyrolysis and gasification reactions were determined based on the global biomass formula, CαHβOγNδSε, in order to assist in the products yields optimization.}, }
@article {pmid28852308, year = {2017}, author = {Cenit, MC and Sanz, Y and Codoñer-Franch, P}, title = {Influence of gut microbiota on neuropsychiatric disorders.}, journal = {World journal of gastroenterology}, volume = {23}, number = {30}, pages = {5486-5498}, pmid = {28852308}, issn = {2219-2840}, mesh = {Animals ; Brain/growth &amp; development/*physiopathology ; DNA Methylation ; Disease Models, Animal ; Epigenesis, Genetic ; Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/*physiology ; Humans ; Hypothalamo-Hypophyseal System/physiopathology ; Neurodegenerative Diseases/*etiology/prevention &amp; control ; Neurodevelopmental Disorders/*etiology/prevention &amp; control ; Pituitary-Adrenal System/physiopathology ; Stress, Psychological/*complications/physiopathology ; }, abstract = {The last decade has witnessed a growing appreciation of the fundamental role played by an early assembly of a diverse and balanced gut microbiota and its subsequent maintenance for future health of the host. Gut microbiota is currently viewed as a key regulator of a fluent bidirectional dialogue between the gut and the brain (gut-brain axis). A number of preclinical studies have suggested that the microbiota and its genome (microbiome) may play a key role in neurodevelopmental and neurodegenerative disorders. Furthermore, alterations in the gut microbiota composition in humans have also been linked to a variety of neuropsychiatric conditions, including depression, autism and Parkinson's disease. However, it is not yet clear whether these changes in the microbiome are causally related to such diseases or are secondary effects thereof. In this respect, recent studies in animals have indicated that gut microbiota transplantation can transfer a behavioral phenotype, suggesting that the gut microbiota may be a modifiable factor modulating the development or pathogenesis of neuropsychiatric conditions. Further studies are warranted to establish whether or not the findings of preclinical animal experiments can be generalized to humans. Moreover, although different communication routes between the microbiota and brain have been identified, further studies must elucidate all the underlying mechanisms involved. Such research is expected to contribute to the design of strategies to modulate the gut microbiota and its functions with a view to improving mental health, and thus provide opportunities to improve the management of psychiatric diseases. Here, we review the evidence supporting a role of the gut microbiota in neuropsychiatric disorders and the state of the art regarding the mechanisms underlying its contribution to mental illness and health. We also consider the stages of life where the gut microbiota is more susceptible to the effects of environmental stressors, and the possible microbiota-targeted intervention strategies that could improve health status and prevent psychiatric disorders in the near future.}, }
@article {pmid28851370, year = {2017}, author = {Tangedal, S and Aanerud, M and Grønseth, R and Drengenes, C and Wiker, HG and Bakke, PS and Eagan, TM}, title = {Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patients.}, journal = {Respiratory research}, volume = {18}, number = {1}, pages = {164}, pmid = {28851370}, issn = {1465-993X}, mesh = {Adult ; Aged ; Female ; Follow-Up Studies ; Humans ; Male ; Microbiota/*physiology ; Middle Aged ; Norway/epidemiology ; Pulmonary Disease, Chronic Obstructive/diagnosis/*epidemiology/*microbiology ; Sputum/*microbiology ; }, abstract = {BACKGROUND: Induced and spontaneous sputum are used to evaluate the airways microbiota. Whether the sputum types can be used interchangeably in microbiota research is unknown. Our aim was to compare microbiota in induced and spontaneous sputum from COPD patients sampled during the same consultation.<br><br>METHODS: COPD patients from Bergen, Norway, were followed between 2006/2010, examined during the stable state and exacerbations. 30 patients delivered 36 sample pairs. DNA was extracted by enzymatic and mechanical lysis methods. The V3-V4 region of the 16S rRNA gene was PCR-amplified and prepared for paired-end sequencing. Illumina Miseq System was used for sequencing, and Quantitative Insights Into Microbial Ecology (QIIME) and Stata were used for bioinformatics and statistical analyses.<br><br>RESULTS: Approximately 4 million sequences were sorted into 1004 different OTUs and further assigned to 106 different taxa. Pair-wise comparison of both taxonomic composition and beta-diversity revealed significant differences in one or both parameters in 1/3 of sample pairs. Alpha-diversity did not differ. Comparing abundances for each taxa identified, showed statistically significant differences between the mean abundances in induced versus spontaneous samples for 15 taxa when disease state was considered. This included potential pathogens like Haemophilus and Moraxella.<br><br>CONCLUSION: When studying microbiota in sputum samples one should take into consideration how samples are collected and avoid the usage of both induced and spontaneous sputum in the same study.}, }
@article {pmid28848583, year = {2017}, author = {Iffis, B and St-Arnaud, M and Hijri, M}, title = {Petroleum Contamination and Plant Identity Influence Soil and Root Microbial Communities While AMF Spores Retrieved from the Same Plants Possess Markedly Different Communities.}, journal = {Frontiers in plant science}, volume = {8}, number = {}, pages = {1381}, pmid = {28848583}, issn = {1664-462X}, abstract = {Phytoremediation is a promising in situ green technology based on the use of plants to cleanup soils from organic and inorganic pollutants. Microbes, particularly bacteria and fungi, that closely interact with plant roots play key roles in phytoremediation processes. In polluted soils, the root-associated microbes contribute to alleviation of plant stress, improve nutrient uptake and may either degrade or sequester a large range of soil pollutants. Therefore, improving the efficiency of phytoremediation requires a thorough knowledge of the microbial diversity living in the rhizosphere and in close association with plant roots in both the surface and the endosphere. This study aims to assess fungal ITS and bacterial 16S rRNA gene diversity using high-throughput sequencing in rhizospheric soils and roots of three plant species (Solidago canadensis, Populus balsamifera, and Lycopus europaeus) growing spontaneously in three petroleum hydrocarbon polluted sedimentation basins. Microbial community structures of rhizospheric soils and roots were compared with those of microbes associated with arbuscular mycorrhizal fungal (AMF) spores to determine the links between the root and rhizosphere communities and those associated with AMF. Our results showed a difference in OTU richness and community structure composition between soils and roots for both bacteria and fungi. We found that petroleum hydrocarbon pollutant (PHP) concentrations have a significant effect on fungal and bacterial community structures in both soils and roots, whereas plant species identity showed a significant effect only on the roots for bacteria and fungi. Our results also showed that the community composition of bacteria and fungi in soil and roots varied from those associated with AMF spores harvested from the same plants. This let us to speculate that in petroleum hydrocarbon contaminated soils, AMF may release chemical compounds by which they recruit beneficial microbes to tolerate or degrade the PHPs present in the soil.}, }
@article {pmid28848535, year = {2017}, author = {Zhang, Z and Li, D and Refaey, MM and Xu, W}, title = {High Spatial and Temporal Variations of Microbial Community along the Southern Catfish Gastrointestinal Tract: Insights into Dynamic Food Digestion.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1531}, pmid = {28848535}, issn = {1664-302X}, abstract = {The fish intestinal microbiota is affected by dietary shifts or diet-related seasonal fluctuations making it highly variable and dynamic. It assists with the digestion and absorption of food that is a common, yet dynamic process. However, fundamental dynamics of microbial ecology associated with food digestion in intestine and stomach are poorly understood in fish. We selected the southern catfish, Silurus meridionalis, as the targeted species, owing to its foraging behavior with a large meal that can assure clear periodic rhythms in food digestion, to study spatial variations of the microbial community along the gastrointestinal (GI) tract. We further evaluated temporal microbial dynamics by collecting GI tract samples at time intervals 03, 12, and 24h after feeding. High-throughput sequencing results showed higher microbial diversity in the stomach than in the intestine and distinguishable community structures between stomach and intestine. Firmicutes were dominated by both Clostridium and unclassified Clostridiaceae, which was the most abundant taxon in the stomach, whereas Fusobacteria were dominated by Cetobacterium, which prevailed in the intestine. Firmicutes was significantly increased and Fusobacteria was decreased after feeding. Furthermore, inter-stomach microbial variability was greater than inter-intestine microbial variability. These results demonstrate that GI microbial assemblies are specific per anatomical site and are highly dynamic during food digestion, indicating that digestive status and/or sampling time are factors potentially influencing the microbial compositions. Furthermore, the finding of high spatial and temporal variations of the microbial community along the GI tract suggests limitations of single sampling regime to study food-derived microbial ecology.}, }
@article {pmid28848519, year = {2017}, author = {Hiraoka, S and Miyahara, M and Fujii, K and Machiyama, A and Iwasaki, W}, title = {Seasonal Analysis of Microbial Communities in Precipitation in the Greater Tokyo Area, Japan.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1506}, pmid = {28848519}, issn = {1664-302X}, abstract = {The presence of microbes in the atmosphere and their transport over long distances across the Earth's surface was recently shown. Precipitation is likely a major path by which aerial microbes fall to the ground surface, affecting its microbial ecosystems and introducing pathogenic microbes. Understanding microbial communities in precipitation is of multidisciplinary interest from the perspectives of microbial ecology and public health; however, community-wide and seasonal analyses have not been conducted. Here, we carried out 16S rRNA amplicon sequencing of 30 precipitation samples that were aseptically collected over 1 year in the Greater Tokyo Area, Japan. The precipitation microbial communities were dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria and were overall consistent with those previously reported in atmospheric aerosols and cloud water. Seasonal variations in composition were observed; specifically, Proteobacteria abundance significantly decreased from summer to winter. Notably, estimated ordinary habitats of precipitation microbes were dominated by animal-associated, soil-related, and marine-related environments, and reasonably consistent with estimated air mass backward trajectories. To our knowledge, this is the first amplicon-sequencing study investigating precipitation microbial communities involving sampling over the duration of a year.}, }
@article {pmid28847001, year = {2017}, author = {Kits, KD and Sedlacek, CJ and Lebedeva, EV and Han, P and Bulaev, A and Pjevac, P and Daebeler, A and Romano, S and Albertsen, M and Stein, LY and Daims, H and Wagner, M}, title = {Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle.}, journal = {Nature}, volume = {549}, number = {7671}, pages = {269-272}, pmid = {28847001}, issn = {1476-4687}, support = {294343/ERC_/European Research Council/International ; P 25231/FWF_/Austrian Science Fund FWF/Austria ; P 27319/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Ammonia/*metabolism ; Archaea/metabolism ; Bacteria/genetics/growth &amp; development/isolation &amp; purification/*metabolism ; *Ecosystem ; Hot Springs/microbiology ; Kinetics ; Nitrates/metabolism ; *Nitrification ; Nitrites/metabolism ; Oxidation-Reduction ; Soil Microbiology ; }, abstract = {Nitrification, the oxidation of ammonia (NH3) via nitrite (NO2[-]) to nitrate (NO3[-]), is a key process of the biogeochemical nitrogen cycle. For decades, ammonia and nitrite oxidation were thought to be separately catalysed by ammonia-oxidizing bacteria (AOB) and archaea (AOA), and by nitrite-oxidizing bacteria (NOB). The recent discovery of complete ammonia oxidizers (comammox) in the NOB genus Nitrospira, which alone convert ammonia to nitrate, raised questions about the ecological niches in which comammox Nitrospira successfully compete with canonical nitrifiers. Here we isolate a pure culture of a comammox bacterium, Nitrospira inopinata, and show that it is adapted to slow growth in oligotrophic and dynamic habitats on the basis of a high affinity for ammonia, low maximum rate of ammonia oxidation, high growth yield compared to canonical nitrifiers, and genomic potential for alternative metabolisms. The nitrification kinetics of four AOA from soil and hot springs were determined for comparison. Their surprisingly poor substrate affinities and lower growth yields reveal that, in contrast to earlier assumptions, AOA are not necessarily the most competitive ammonia oxidizers present in strongly oligotrophic environments and that N. inopinata has the highest substrate affinity of all analysed ammonia oxidizer isolates except the marine AOA Nitrosopumilus maritimus SCM1 (ref. 3). These results suggest a role for comammox organisms in nitrification under oligotrophic and dynamic conditions.}, }
@article {pmid28844839, year = {2017}, author = {Varjani, SJ and Gnansounou, E}, title = {Microbial dynamics in petroleum oilfields and their relationship with physiological properties of petroleum oil reservoirs.}, journal = {Bioresource technology}, volume = {245}, number = {Pt A}, pages = {1258-1265}, doi = {10.1016/j.biortech.2017.08.028}, pmid = {28844839}, issn = {1873-2976}, mesh = {Ecosystem ; *Euryarchaeota ; Nitrates ; Oil and Gas Fields ; *Petroleum ; }, abstract = {Petroleum is produced by thermal decay of buried organic material over millions of years. Petroleum oilfield ecosystems represent resource of reduced carbon which favours microbial growth. Therefore, it is obvious that many microorganisms have adapted to harsh environmental conditions of these ecosystems specifically temperature, oxygen availability and pressure. Knowledge of microorganisms present in ecosystems of petroleum oil reservoirs; their physiological and biological properties help in successful exploration of petroleum. Understanding microbiology of petroleum oilfield(s) can be used to enhance oil recovery, as microorganisms in oil reservoirs produce various metabolites viz. gases, acids, solvents, biopolymers and biosurfactants. The aim of this review is to discuss characteristics of petroleum oil reservoirs. This review also provides an updated literature on microbial ecology of these extreme ecosystems including microbial origin as well as various types of microorganisms such as methanogens; iron, nitrate and sulphate reducing bacteria, and fermentative microbes present in petroleum oilfield ecosystems.}, }
@article {pmid28843369, year = {2018}, author = {Lu, ZM and Wang, ZM and Zhang, XJ and Mao, J and Shi, JS and Xu, ZH}, title = {Microbial ecology of cereal vinegar fermentation: insights for driving the ecosystem function.}, journal = {Current opinion in biotechnology}, volume = {49}, number = {}, pages = {88-93}, doi = {10.1016/j.copbio.2017.07.006}, pmid = {28843369}, issn = {1879-0429}, mesh = {Acetic Acid/*metabolism ; *Ecosystem ; Edible Grain/*metabolism ; *Fermentation ; *Microbiota ; }, abstract = {Over thousands of years, humans have mastered the natural vinegar fermentation technique of cultivating functional microbiota on different raw materials. Functional microbial communities that form reproducibly on non-autoclaved raw materials through repeated batch acetic acid fermentation underpin the flavour development of traditional cereal vinegars. However, how to modulate rationally and optimise the metabolic function of these naturally engineered acidic ecosystems remains unclear. Exploring two key minorities in a vinegar ecosystem, including microbial functions (e.g., flavour and aroma synthesis) and microbial strains, is a crucial step for the vinegar industry to modulate the metabolic function of vinegar microbiota, to monitor the fermentation process, and to maintain the flavour quality of final product.}, }
@article {pmid28842282, year = {2017}, author = {Lekunberri, I and Balcázar, JL and Borrego, CM}, title = {Detection and quantification of the plasmid-mediated mcr-1 gene conferring colistin resistance in wastewater.}, journal = {International journal of antimicrobial agents}, volume = {50}, number = {6}, pages = {734-736}, doi = {10.1016/j.ijantimicag.2017.08.018}, pmid = {28842282}, issn = {1872-7913}, mesh = {Anti-Bacterial Agents/*pharmacology ; Colistin/*pharmacology ; *Drug Resistance, Bacterial ; *Genes, Bacterial ; Plasmids/*analysis ; Real-Time Polymerase Chain Reaction/methods ; Spain ; Wastewater/*microbiology ; Water Purification ; }, abstract = {There is a global concern about the increasing resistance of bacterial pathogens to colistin, an antibiotic of last resort for the treatment of multidrug-resistant Gram-negative bacterial infections (e.g. carbapenemase-producing Enterobacteriaceae). In this study, an increasing prevalence of colistin resistance in raw and treated wastewater was demonstrated using a new developed SYBR Green-based real-time PCR assay for specific detection and quantification of the plasmid-mediated mcr-1 gene. Raw and treated wastewater samples were collected from a wastewater treatment plant in Girona (Spain) at two different time periods (November 2011-January 2012 and December 2016-February 2017). In both periods, the absolute abundance of the mcr-1 gene was significantly higher (P <0.05) in raw sewage samples, suggesting that conventional wastewater treatment reduces colistin-resistant bacteria. Moreover, the analysis revealed an increase from 1-2 orders of magnitude in the absolute abundance of mcr-1 between the studied periods (winter 2011 versus winter 2016, P <0.05), suggesting that colistin resistance has increased over time. This study gives evidence of the growing spread of mcr-1 and provides a real-time PCR assay for its rapid detection and quantification.}, }
@article {pmid28840974, year = {2017}, author = {Timmis, K and de Vos, WM and Ramos, JL and Vlaeminck, SE and Prieto, A and Danchin, A and Verstraete, W and de Lorenzo, V and Lee, SY and Brüssow, H and Timmis, JK and Singh, BK}, title = {The contribution of microbial biotechnology to sustainable development goals.}, journal = {Microbial biotechnology}, volume = {10}, number = {5}, pages = {984-987}, pmid = {28840974}, issn = {1751-7915}, mesh = {Bacteria/genetics/*metabolism ; *Biotechnology/methods ; *Conservation of Natural Resources/methods ; Humans ; }, abstract = {The signature and almost unique characteristic of microbial technology is the exceptional diversity of applications it can address, and the exceptional range of human activities and needs to which it is and can be applied. Precisely because sustainability goals have very diverse and complex components and requirements, microbial technology has the ability to contribute substantively on many levels in many arenas to global efforts to achieve sustainability. Indeed, microbial technology could be viewed as a unifying element in our progress towards sustainability.}, }
@article {pmid28840330, year = {2018}, author = {Rho, H and Hsieh, M and Kandel, SL and Cantillo, J and Doty, SL and Kim, SH}, title = {Do Endophytes Promote Growth of Host Plants Under Stress? A Meta-Analysis on Plant Stress Mitigation by Endophytes.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {407-418}, pmid = {28840330}, issn = {1432-184X}, support = {2012-68002-19824//National Institute of Food and Agriculture (US)/ ; }, mesh = {Bacteria/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Biomass ; Endophytes/genetics/isolation &amp; purification/*physiology ; Fungi/genetics/isolation &amp; purification/*physiology ; *Plant Development ; *Plant Physiological Phenomena ; Plants/*microbiology ; Stress, Physiological ; }, abstract = {Endophytes are microbial symbionts living inside plants and have been extensively researched in recent decades for their functions associated with plant responses to environmental stress. We conducted a meta-analysis of endophyte effects on host plants' growth and fitness in response to three abiotic stress factors: drought, nitrogen deficiency, and excessive salinity. Ninety-four endophyte strains and 42 host plant species from the literature were evaluated in the analysis. Endophytes increased biomass accumulation of host plants under all three stress conditions. The stress mitigation effects by endophytes were similar among different plant taxa or functional groups with few exceptions; eudicots and C4 species gained more biomass than monocots and C3 species with endophytes, respectively, under drought conditions. Our analysis supports the effectiveness of endophytes in mitigating drought, nitrogen deficiency, and salinity stress in a wide range of host species with little evidence of plant-endophyte specificity.}, }
@article {pmid28838619, year = {2018}, author = {Carvalho, G and Pedras, I and Karst, SM and Oliveira, CSS and Duque, AF and Nielsen, PH and Reis, MAM}, title = {Functional redundancy ensures performance robustness in 3-stage PHA-producing mixed cultures under variable feed operation.}, journal = {New biotechnology}, volume = {40}, number = {Pt B}, pages = {207-217}, doi = {10.1016/j.nbt.2017.08.007}, pmid = {28838619}, issn = {1876-4347}, mesh = {Azoarcus/metabolism ; Bacillaceae/metabolism ; *Cheese ; Fermentation ; *Molasses ; Paenibacillus/metabolism ; Paracoccus/metabolism ; Polyhydroxyalkanoates/*biosynthesis ; Saccharum/chemistry/*metabolism ; Thauera/metabolism ; Whey/chemistry/*metabolism ; }, abstract = {Polyhydroxyalkanoates (PHA) are biopolymers that can be produced by mixed microbial cultures using wastes or industrial by-products, which represent an economical and environmental advantage over pure culture processes. The use of alternate feedstocks enables using seasonal by-products, providing that the process is resilient to transient conditions. The mixed microbial communities of a 3-stage PHA producing system fed initially with molasses and then cheese whey were investigated through amplicon sequencing of the 16S rRNA gene. The transition in feedstock resulted in an adaptation of the acidogenic community, where Actinobacteria dominated with sugarcane molasses (up to 93% of the operational taxonomic units) and Firmicutes, with cheese whey (up to 97%). The resulting fermentation products profile also changed, with a higher fraction of HV precursors obtained with molasses than cheese whey (7.1±0.5 and 1.7±0.7 gCOD/L, respectively). As for the PHA storing culture, the genera Azoarcus, Thauera and Paracoccus were enriched with fermented molasses (average 89% of Bacteria). Later, fermented cheese whey fostered a higher diversity, including some less characterised PHA-storers such as the genera Paenibacillus and Lysinibacillus. Although the microbial community structure was significantly affected by the feedstock shift, the acidogenic and PHA storing performance of the 3-stage system was very similar once a pseudo steady state was attained, showing that a reliable level of functional redundancy was attained in both mixed cultures.}, }
@article {pmid28831604, year = {2018}, author = {Mendes, LW and Tsai, SM}, title = {Distinct taxonomic and functional composition of soil microbiomes along the gradient forest-restinga-mangrove in southeastern Brazil.}, journal = {Antonie van Leeuwenhoek}, volume = {111}, number = {1}, pages = {101-114}, doi = {10.1007/s10482-017-0931-6}, pmid = {28831604}, issn = {1572-9699}, support = {2007/01859-4//FAPESP/ ; }, mesh = {Biodiversity ; Brazil ; *Forests ; Geography ; *Metagenome ; *Metagenomics/methods ; *Soil Microbiology ; *Wetlands ; }, abstract = {Soil microorganisms play crucial roles in ecosystem functioning, and the central goal in microbial ecology studies is to elucidate which factors shape community structure. A better understanding of the relationship between microbial diversity, functions and environmental parameters would increase our ability to set conservation priorities. Here, the bacterial and archaeal community structure in Atlantic Forest, restinga and mangrove soils was described and compared based on shotgun metagenomics. We hypothesized that each distinct site would harbor a distinct taxonomic and functional soil community, which is influenced by environmental parameters. Our data showed that the microbiome is shaped by soil properties, with pH, base saturation, boron and iron content significantly correlated to overall community structure. When data of specific phyla were correlated to specific soil properties, we demonstrated that parameters such as boron, copper, sulfur, potassium and aluminum presented significant correlation with the most number of bacterial groups. Mangrove soil was the most distinct site and presented the highest taxonomic and functional diversity in comparison with forest and restinga soils. From the total 34 microbial phyla identified, 14 were overrepresented in mangrove soils, including several archaeal groups. Mangrove soils hosted a high abundance of sequences related to replication, survival and adaptation; forest soils included high numbers of sequences related to the metabolism of nutrients and other composts; while restinga soils included abundant genes related to the metabolism of carbohydrates. Overall, our finds show that the microbial community structure and functional potential were clearly different across the environmental gradient, followed by functional adaptation and both were related to the soil properties.}, }
@article {pmid28831124, year = {2017}, author = {Pratama, AA and van Elsas, JD}, title = {A novel inducible prophage from the mycosphere inhabitant Paraburkholderia terrae BS437.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {9156}, pmid = {28831124}, issn = {2045-2322}, mesh = {Burkholderiaceae/drug effects/genetics/*virology ; Genome, Bacterial ; *Genome, Viral ; Mitomycin/pharmacology ; Prophages/genetics/*growth &amp; development ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; Soil Microbiology ; Virus Activation ; }, abstract = {Bacteriophages constitute key gene transfer agents in many bacteria. Specifically, they may confer gene mobility to Paraburkholderia spp. that dwells in soil and the mycosphere. In this study, we first screened mycosphere and bulk soils for phages able to produce plaques, however found these to be below detection. Then, prophage identification methods were applied to the genome sequences of the mycosphere-derived Paraburkholderia terrae strains BS001, BS007, BS110 and BS437, next to P. phytofirmans strains BS455, BIFAS53, J1U5 and PsJN. These analyses revealed all bacterial genomes to contain considerable amounts [up to 13.3%] of prophage-like sequences. One sequence predicted to encode a complete phage was found in the genome of P. terrae BS437. Using the inducing agent mitomycin C, we produced high-titered phage suspensions. These indeed encompassed the progeny of the identified prophage (denoted ɸ437), as evidenced using phage major capsid gene molecular detection. We obtained the full sequence of phage ɸ437, which, remarkably, had undergone a reshuffling of two large gene blocks. One predicted moron gene was found, and it is currently analyzed to understand the extent of its ecological significance for the host.}, }
@article {pmid28830094, year = {2017}, author = {Dzialo, MC and Park, R and Steensels, J and Lievens, B and Verstrepen, KJ}, title = {Physiology, ecology and industrial applications of aroma formation in yeast.}, journal = {FEMS microbiology reviews}, volume = {41}, number = {Supp_1}, pages = {S95-S128}, pmid = {28830094}, issn = {1574-6976}, mesh = {Acetaldehyde/chemistry ; Acetic Acid/chemistry ; Amino Acids/metabolism ; Animals ; Carbon Dioxide/chemistry ; Ethanol/*metabolism ; Fermentation/*physiology ; Industrial Microbiology/*methods ; Insecta/metabolism/physiology ; Odorants/*analysis ; Saccharomyces cerevisiae/genetics/*metabolism ; Sulfur Compounds/chemistry ; }, abstract = {Yeast cells are often employed in industrial fermentation processes for their ability to efficiently convert relatively high concentrations of sugars into ethanol and carbon dioxide. Additionally, fermenting yeast cells produce a wide range of other compounds, including various higher alcohols, carbonyl compounds, phenolic compounds, fatty acid derivatives and sulfur compounds. Interestingly, many of these secondary metabolites are volatile and have pungent aromas that are often vital for product quality. In this review, we summarize the different biochemical pathways underlying aroma production in yeast as well as the relevance of these compounds for industrial applications and the factors that influence their production during fermentation. Additionally, we discuss the different physiological and ecological roles of aroma-active metabolites, including recent findings that point at their role as signaling molecules and attractants for insect vectors.}, }
@article {pmid28830071, year = {2017}, author = {Schlemper, TR and Leite, MFA and Lucheta, AR and Shimels, M and Bouwmeester, HJ and van Veen, JA and Kuramae, EE}, title = {Rhizobacterial community structure differences among sorghum cultivars in different growth stages and soils.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {8}, pages = {}, doi = {10.1093/femsec/fix096}, pmid = {28830071}, issn = {1574-6941}, mesh = {Acidobacteria/classification/*isolation &amp; purification ; Burkholderiaceae/classification/*isolation &amp; purification ; Comamonadaceae/classification/*isolation &amp; purification ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Microbiota ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; Sorghum/*microbiology ; }, abstract = {Plant genotype selects the rhizosphere microbiome. The success of plant-microbe interactions is dependent on factors that directly or indirectly influence the plant rhizosphere microbial composition. We investigated the rhizosphere bacterial community composition of seven different sorghum cultivars in two different soil types (abandoned (CF) and agricultural (VD)). The rhizosphere bacterial community was evaluated at four different plant growth stages: emergence of the second (day 10) and third leaves (day 20), the transition between the vegetative and reproductive stages (day 35), and the emergence of the last visible leaf (day 50). At early stages (days 10 and 20), the sorghum rhizosphere bacterial community composition was mainly driven by soil type, whereas at late stages (days 35 and 50), the bacterial community composition was also affected by the sorghum genotype. Although this effect of sorghum genotype was small, different sorghum cultivars assembled significantly different bacterial community compositions. In CF soil, the striga-resistant cultivar had significantly higher relative abundances of Acidobacteria GP1, Burkholderia, Cupriavidus (Burkholderiaceae), Acidovorax and Albidiferax (Comamonadaceae) than the other six cultivars. This study is the first to simultaneously investigate the contributions of plant genotype, plant growth stage and soil type in shaping sorghum rhizosphere bacterial community composition.}, }
@article {pmid28828261, year = {2017}, author = {Walsh, K and Haggerty, JM and Doane, MP and Hansen, JJ and Morris, MM and Moreira, APB and de Oliveira, L and Leomil, L and Garcia, GD and Thompson, F and Dinsdale, EA}, title = {Aura-biomes are present in the water layer above coral reef benthic macro-organisms.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3666}, pmid = {28828261}, issn = {2167-8359}, abstract = {As coral reef habitats decline worldwide, some reefs are transitioning from coral- to algal-dominated benthos with the exact cause for this shift remaining elusive. Increases in the abundance of microbes in the water column has been correlated with an increase in coral disease and reduction in coral cover. Here we investigated how multiple reef organisms influence microbial communities in the surrounding water column. Our study consisted of a field assessment of microbial communities above replicate patches dominated by a single macro-organism. Metagenomes were constructed from 20 L of water above distinct macro-organisms, including (1) the coral Mussismilia braziliensis, (2) fleshy macroalgae (Stypopodium, Dictota and Canistrocarpus), (3) turf algae, and (4) the zoanthid Palythoa caribaeorum and were compared to the water microbes collected 3 m above the reef. Microbial genera and functional potential were annotated using MG-RAST and showed that the dominant benthic macro-organisms influence the taxa and functions of microbes in the water column surrounding them, developing a specific "aura-biome". The coral aura-biome reflected the open water column, and was associated with Synechococcus and functions suggesting oligotrophic growth, while the fleshy macroalgae aura-biome was associated with Ruegeria, Pseudomonas, and microbial functions suggesting low oxygen conditions. The turf algae aura-biome was associated with Vibrio, Flavobacterium, and functions suggesting pathogenic activity, while zoanthids were associated with Alteromonas and functions suggesting a stressful environment. Because each benthic organism has a distinct aura-biome, a change in benthic cover will change the microbial community of the water, which may lead to either the stimulation or suppression of the recruitment of benthic organisms.}, }
@article {pmid28827675, year = {2017}, author = {Bukowska, A and Kaliński, T and Koper, M and Kostrzewska-Szlakowska, I and Kwiatowski, J and Mazur-Marzec, H and Jasser, I}, title = {Predicting blooms of toxic cyanobacteria in eutrophic lakes with diverse cyanobacterial communities.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8342}, pmid = {28827675}, issn = {2045-2322}, mesh = {Bacterial Proteins/*metabolism ; Bacterial Toxins/*metabolism ; Cyanobacteria/*classification/genetics/pathogenicity ; DNA, Bacterial/genetics ; Gene Expression Regulation, Bacterial ; *Harmful Algal Bloom ; Lakes/*microbiology ; Microcystins/genetics/metabolism ; Microcystis/*classification/genetics/pathogenicity ; Phylogeny ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA ; }, abstract = {We investigated possibility of predicting whether blooms, if they occur, would be formed of microcystin-producing cyanobacteria. DGGE analysis of 16S-ITS and mcyA genes revealed that only Planktothrix and Microcystis possessed mcy-genes and Planktothrix was the main microcystin producer. qPCR analysis revealed that the proportion of cells with mcy-genes in Planktothrix populations was almost 100%. Microcystin concentration correlated with the number of potentially toxic and total Planktothrix cells and the proportion of Planktothrix within all cyanobacteria, but not with the proportion of cells with mcy-genes in total Planktothrix. The share of Microcystis cells with mcy-genes was low and variable in time. Neither the number of mcy-possessing cells, nor the proportion of these cells in total Microcystis, correlated with the concentration of microcystins. This suggests that it is possible to predict whether the bloom in the Masurian Lakes will be toxic based on Planktothrix occurrence. Two species of toxin producing Planktothrix, P. agardhii and P. rubescens, were identified by phylogenetic analysis of 16S-ITS. Based on morphological and ecological features, the toxic Planktothrix was identified as P. agardhii. However, the very high proportion of cells with mcy-genes suggests P. rubescens. Our study reveals the need of universal primers for mcyA genes from environment.}, }
@article {pmid28826938, year = {2017}, author = {Tanaka, M and Nakayama, J}, title = {Development of the gut microbiota in infancy and its impact on health in later life.}, journal = {Allergology international : official journal of the Japanese Society of Allergology}, volume = {66}, number = {4}, pages = {515-522}, doi = {10.1016/j.alit.2017.07.010}, pmid = {28826938}, issn = {1440-1592}, mesh = {Age Factors ; Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Biodiversity ; Delivery, Obstetric/methods ; Disease Susceptibility ; Food ; *Gastrointestinal Microbiome ; *Health Status ; Host-Pathogen Interactions/immunology ; Humans ; Hypersensitivity/etiology ; Immune System/cytology/immunology/metabolism ; Infant ; Infant, Newborn ; Microbiota ; Milk, Human ; }, abstract = {Gut microbial ecology and function are dynamic in infancy, but are stabilized in childhood. The 'new friends' have a great impact on the development of the digestive tract and host immune system. In the first year of life, especially, the gut microbiota dramatically changes through interactions with the developing immune system in the gut. The process of establishing the gut microbiota is affected by various environmental factors, with the potential to be a main determinant of life-long health. In this review, we summarize recent findings regarding gut microbiota establishment, including the importance of various factors related to the development of the immune system and allergic diseases later in life.}, }
@article {pmid28826768, year = {2017}, author = {Papizadeh, M and Rohani, M and Nahrevanian, H and Javadi, A and Pourshafie, MR}, title = {Probiotic characters of Bifidobacterium and Lactobacillus are a result of the ongoing gene acquisition and genome minimization evolutionary trends.}, journal = {Microbial pathogenesis}, volume = {111}, number = {}, pages = {118-131}, doi = {10.1016/j.micpath.2017.08.021}, pmid = {28826768}, issn = {1096-1208}, mesh = {Animals ; Bifidobacterium/classification/*genetics ; Ecology ; Evolution, Molecular ; Gastrointestinal Tract/microbiology ; *Genome, Bacterial ; *Genomics ; Humans ; Lactobacillus/classification/*genetics ; Phylogeny ; *Probiotics ; Species Specificity ; }, abstract = {Bifidobacterium and Lactobacillus are the main probiotic genera. Collectively, these two genera harbor over 200 species among which are many strains have been introduced as probiotics. These health-promoting microbes confer health benefits upon the host and so used in food productions and as supplements. Considering the economic importance of probiotics, the biochemistry, genomics, phylogeny and physiology of such genera have been exhaustively studied. According to the genomic data, the probiotic capabilities are strain specific which may be a result of the niche-specialization of the genomes of these bacteria to certain ecological niches like gastrointestinal tract of a diverse range of animals. These microbes have a wide distribution but the culture-based studies and either genomics data suggest selective affinity of some Lactobacillus and either Bifidobacterium species to certain ecological niches. An ongoing genome degradation, which is thought to be a result of passage through an evolutionary bottleneck, is the major trend in the evolution of lactobacilli. Further, evolutionary events resulted into two categories of lactobacilli: habitat generalists and habitat specialists. In place, the main trend in the evolution of bifidobacteria tend to be the gene acquisition. However, probiotic features are the results of a co-evolutionary relationship between these bacteria and their hosts and the aforementioned evolutionary tends have driven the evolution of these probiotic genera.}, }
@article {pmid28826586, year = {2018}, author = {Lucas, SK and Yang, R and Dunitz, JM and Boyer, HC and Hunter, RC}, title = {16S rRNA gene sequencing reveals site-specific signatures of the upper and lower airways of cystic fibrosis patients.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {17}, number = {2}, pages = {204-212}, pmid = {28826586}, issn = {1873-5010}, support = {R00 HL114862/HL/NHLBI NIH HHS/United States ; T90 DE022732/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Bacterial Load ; Chronic Disease ; Cohort Studies ; Cystic Fibrosis/complications/*microbiology ; Endoscopy ; Gram-Negative Bacteria/*isolation &amp; purification ; Gram-Positive Bacteria/*isolation &amp; purification ; Humans ; Lung/*microbiology ; Microbiota ; Middle Aged ; Paranasal Sinuses/*microbiology ; RNA, Bacterial ; RNA, Ribosomal, 16S ; Sinusitis/*microbiology ; Sputum/microbiology ; Young Adult ; }, abstract = {BACKGROUND: Metastasis of upper airway microbiota may have significant implications in the development of chronic lung disease. Here, we compare bacterial communities of matched sinus and lung mucus samples from cystic fibrosis (CF) subjects undergoing endoscopic surgery for treatment of chronic sinusitis.<br><br>METHODS: Mucus from one maxillary sinus and expectorated sputum were collected from twelve patients. 16S rRNA gene sequencing was then performed on sample pairs to compare the structure and function of CF airway microbiota.<br><br>RESULTS: Bacterial diversity was comparable between airway sites, though sinuses harbored a higher prevalence of dominant microorganisms. Ordination analyses revealed that samples clustered more consistently by airway niche rather than by individual. Finally, predicted metagenomes suggested that anaerobiosis was enriched in the lung.<br><br>CONCLUSIONS: Our findings indicate that while the lung may be seeded by individual sinus pathogens, airway microenvironments harbor distinct bacterial communities that should be considered in selecting antimicrobial therapies.}, }
@article {pmid28825127, year = {2018}, author = {Yu, DT and Han, LL and Zhang, LM and He, JZ}, title = {Diversity and Distribution Characteristics of Viruses in Soils of a Marine-Terrestrial Ecotone in East China.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {375-386}, pmid = {28825127}, issn = {1432-184X}, support = {41571248//the National Science Foundation of China/ ; 41230857//the National Science Foundation of China/ ; }, mesh = {*Biodiversity ; China ; DNA Viruses/classification/genetics/*isolation &amp; purification ; Ecosystem ; Phylogeny ; Salinity ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {A substantial gap remains in our understanding of the abundance, diversity, and ecology of viruses in soil although some advances have been achieved in recent years. In this study, four soil samples according to the salinity gradient from shore to inland in East China have been characterized. Results showed that spherical virus particles represented the largest viral component in all of the four samples. The viromes had remarkably different taxonomic compositions, and most of the sequences were derived from single-stranded DNA viruses, especially from families Microviridae and Circoviridae. Compared with viromes from other aquatic and sediment samples, the community compositions of our four soil viromes resembled each other, meanwhile coastal sample virome closely congregated with sediment and hypersaline viromes, and high salinity paddy soil sample virome was similar with surface sediment virome. Phylogenetic analysis of functional genes showed that four viromes have high diversity of the subfamily Gokushovirinae in family Microviridae and most of Circoviridae replicase protein sequences grouped within the CRESS-DNA viruses. This work provided an initial outline of the viral communities in marine-terrestrial ecotone and will improve our understanding of the ecological functions of soil viruses.}, }
@article {pmid28824606, year = {2017}, author = {Pjevac, P and Schauberger, C and Poghosyan, L and Herbold, CW and van Kessel, MAHJ and Daebeler, A and Steinberger, M and Jetten, MSM and Lücker, S and Wagner, M and Daims, H}, title = {AmoA-Targeted Polymerase Chain Reaction Primers for the Specific Detection and Quantification of Comammox Nitrospira in the Environment.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1508}, pmid = {28824606}, issn = {1664-302X}, support = {294343/ERC_/European Research Council/International ; 339880/ERC_/European Research Council/International ; P 25231/FWF_/Austrian Science Fund FWF/Austria ; P 27319/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be catalyzed by the concerted activity of ammonia- and nitrite-oxidizing microorganisms. Only recently, complete ammonia oxidizers ("comammox"), which oxidize ammonia to nitrate on their own, were identified in the bacterial genus Nitrospira, previously assumed to contain only canonical nitrite oxidizers. Nitrospira are widespread in nature, but for assessments of the distribution and functional importance of comammox Nitrospira in ecosystems, cultivation-independent tools to distinguish comammox from strictly nitrite-oxidizing Nitrospira are required. Here we developed new PCR primer sets that specifically target the amoA genes coding for subunit A of the distinct ammonia monooxygenase of comammox Nitrospira. While existing primers capture only a fraction of the known comammox amoA diversity, the new primer sets cover as much as 95% of the comammox amoA clade A and 92% of the clade B sequences in a reference database containing 326 comammox amoA genes with sequence information at the primer binding sites. Application of the primers to 13 samples from engineered systems (a groundwater well, drinking water treatment and wastewater treatment plants) and other habitats (rice paddy and forest soils, rice rhizosphere, brackish lake sediment and freshwater biofilm) detected comammox Nitrospira in all samples and revealed a considerable diversity of comammox in most habitats. Excellent primer specificity for comammox amoA was achieved by avoiding the use of highly degenerate primer preparations and by using equimolar mixtures of oligonucleotides that match existing comammox amoA genes. Quantitative PCR with these equimolar primer mixtures was highly sensitive and specific, and enabled the efficient quantification of clade A and clade B comammox amoA gene copy numbers in environmental samples. The measured relative abundances of comammox Nitrospira, compared to canonical ammonia oxidizers, were highly variable across environments. The new comammox amoA-targeted primers enable more encompassing future studies of nitrifying microorganisms in diverse habitats. For example, they may be used to monitor the population dynamics of uncultured comammox organisms under changing environmental conditions and in response to altered treatments in engineered and agricultural ecosystems.}, }
@article {pmid28824589, year = {2017}, author = {Dong, X and Kleiner, M and Sharp, CE and Thorson, E and Li, C and Liu, D and Strous, M}, title = {Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1461}, pmid = {28824589}, issn = {1664-302X}, abstract = {Microbial community profiling by barcoded 16S rRNA gene amplicon sequencing currently has many applications in microbial ecology. The low costs of the parallel sequencing of multiplexed samples, combined with the relative ease of data processing and interpretation (compared to shotgun metagenomes) have made this an entry-level approach. Here we present the MetaAmp pipeline for processing of SSU rRNA gene and other non-coding or protein-coding amplicon sequencing data by investigators that are inexperienced with bioinformatics procedures. It accepts single-end or paired-end sequences in fasta or fastq format from various sequencing platforms. It includes read quality control, and merging of forward and reverse reads of paired-end reads. It makes use of UPARSE, Mothur, and the SILVA database for clustering, removal of chimeric reads, taxonomic classification, and generation of diversity metrics. The pipeline has been validated with a mock community of known composition. MetaAmp provides a convenient web interface as well as command line interface. It is freely available at: http://ebg.ucalgary.ca/metaamp. Since its launch 2 years ago, MetaAmp has been used >2,800 times, by many users worldwide.}, }
@article {pmid28824378, year = {2017}, author = {El Aidy, S and Ramsteijn, AS and Dini-Andreote, F and van Eijk, R and Houwing, DJ and Salles, JF and Olivier, JDA}, title = {Serotonin Transporter Genotype Modulates the Gut Microbiota Composition in Young Rats, an Effect Augmented by Early Life Stress.}, journal = {Frontiers in cellular neuroscience}, volume = {11}, number = {}, pages = {222}, pmid = {28824378}, issn = {1662-5102}, abstract = {The neurotransmitter serotonin (5-HT) plays a vital regulatory role in both the brain and gut. 5-HT is crucial for regulating mood in the brain as well as gastrointestinal motility and secretion peripherally. Alterations in 5-HT transmission have been linked to pathological symptoms in both intestinal and psychiatric disorders and selective 5-HT transporter (5-HTT) inhibitors, affecting the 5-HT system by blocking the 5-HT transporter (5-HTT) have been successfully used to treat CNS- and intestinal disorders. Humans that carry the short allele of the 5-HTT-linked polymorphic region (5-HTTLPR) are more vulnerable to adverse environmental stressors, in particular early life stress. Although, early life stress has been shown to alter the composition of the gut microbiota, it is not known whether a lower 5-HTT expression is also associated with an altered microbiome composition. To investigate this, male and female wild type (5-HTT[+/+]), heterozygous (5-HTT[+/-]), and knockout (5-HTT[-/-]) 5-HT transporter rats were maternally separated for 6 h a day from postnatal day 2 till 15. On postnatal day 21, fecal samples were collected and the impact of 5-HTT genotype and maternal separation (MS) on the microbiome was analyzed using high-throughput sequencing of the bacterial 16S rRNA gene. MS showed a shift in the ratio between the two main bacterial phyla characterized by a decrease in Bacteroidetes and an increase in Firmicutes. Interestingly, the 5-HTT genotype caused a greater microbal dysbiosis (microbial imbalance) compared with MS. A significant difference in microbiota composition was found segregating 5-HTT[-/-] apart from 5-HTT[+/-] and 5-HTT[+/+] rats. Moreover, exposure of rats with 5-HTT diminished expression to MS swayed the balance of their microbiota away from homeostasis to 'inflammatory' type microbiota characterized by higher abundance of members of the gut microbiome including Desulfovibrio, Mucispirillum, and Fusobacterium, all of which are previously reported to be associated with a state of intestinal inflammation, including inflammation associated with MS and brain disorders like multiple depressive disorders. Overall, our data show for the first time that altered expression of 5-HTT induces disruptions in male and female rat gut microbes and these 5-HTT genotype-related disruptions are augmented when combined with early life stress.}, }
@article {pmid28823476, year = {2017}, author = {Jünemann, S and Kleinbölting, N and Jaenicke, S and Henke, C and Hassa, J and Nelkner, J and Stolze, Y and Albaum, SP and Schlüter, A and Goesmann, A and Sczyrba, A and Stoye, J}, title = {Bioinformatics for NGS-based metagenomics and the application to biogas research.}, journal = {Journal of biotechnology}, volume = {261}, number = {}, pages = {10-23}, doi = {10.1016/j.jbiotec.2017.08.012}, pmid = {28823476}, issn = {1873-4863}, mesh = {Anaerobiosis ; Biofuels/*microbiology ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome/*genetics ; Metagenomics/*methods ; }, abstract = {Metagenomics has proven to be one of the most important research fields for microbial ecology during the last decade. Starting from 16S rRNA marker gene analysis for the characterization of community compositions to whole metagenome shotgun sequencing which additionally allows for functional analysis, metagenomics has been applied in a wide spectrum of research areas. The cost reduction paired with the increase in the amount of data due to the advent of next-generation sequencing led to a rapidly growing demand for bioinformatic software in metagenomics. By now, a large number of tools that can be used to analyze metagenomic datasets has been developed. The Bielefeld-Gießen center for microbial bioinformatics as part of the German Network for Bioinformatics Infrastructure bundles and imparts expert knowledge in the analysis of metagenomic datasets, especially in research on microbial communities involved in anaerobic digestion residing in biogas reactors. In this review, we give an overview of the field of metagenomics, introduce into important bioinformatic tools and possible workflows, accompanied by application examples of biogas surveys successfully conducted at the Center for Biotechnology of Bielefeld University.}, }
@article {pmid28823015, year = {2017}, author = {Lim, JH and Lee, CW}, title = {Effects of eutrophication on diatom abundance, biovolume and diversity in tropical coastal waters.}, journal = {Environmental monitoring and assessment}, volume = {189}, number = {9}, pages = {432}, pmid = {28823015}, issn = {1573-2959}, mesh = {Biomass ; *Diatoms/genetics/growth &amp; development ; Environmental Monitoring ; *Eutrophication ; Malaysia ; Tropical Climate ; }, abstract = {Diatom abundance, biovolume and diversity were measured over a 2-year period along the Straits of Malacca at two stations with upper (Klang) and lower (Port Dickson) states of eutrophication. Diatom abundance, which ranged from 0.2 × 10[4] to 21.7 × 10[4] cells L[-1] at Klang and 0.9 × 10[3]- 41.3 × 10[3] cells L[-1] at Port Dickson, was influenced partly by nutrient concentrations. At Klang, the diatoms were generally smaller and less diverse (H' = 0.77 ± 0.48) and predominated by Skeletonema spp. (60 ± 32% of total diatom biomass). In contrast, diatoms were larger and more diverse (H' = 1.40 ± 0.67) at Port Dickson. Chaetoceros spp. were the most abundant diatoms at Port Dickson but attributed only 48 ± 30% of total diatom biomass. Comparison of both Klang and Port Dickson showed that their diatom community structure differed and that eutrophication reduced diatom diversity at Klang. We also observed how Si(OH)4 affected the abundance of Skeletonema spp. which in turn influenced the temporal variation of diatom community at Klang. Our results highlighted how eutrophication affects diatom diversity and community structure.}, }
@article {pmid28822208, year = {2017}, author = {Kiewra, D and Rydzanicz, K and Czułowska, A}, title = {Professor Elżbieta Lonc, D. Sc. (1951–2017) – pro memoriam.}, journal = {Annals of parasitology}, volume = {63}, number = {2}, pages = {143-146}, doi = {10.17420/ap6302.99}, pmid = {28822208}, issn = {2299-0631}, mesh = {History, 20th Century ; History, 21st Century ; *Microbiology/history ; *Parasitology/history ; Poland ; }, }
@article {pmid28821552, year = {2017}, author = {Chiriac, CM and Szekeres, E and Rudi, K and Baricz, A and Hegedus, A and Dragoş, N and Coman, C}, title = {Differences in Temperature and Water Chemistry Shape Distinct Diversity Patterns in Thermophilic Microbial Communities.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {21}, pages = {}, pmid = {28821552}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; Hot Springs/chemistry/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Temperature ; Water/chemistry ; }, abstract = {This report describes the biodiversity and ecology of microbial mats developed in thermal gradients (20 to 65°C) in the surroundings of three drillings (Chiraleu [CH], Ciocaia [CI], and Mihai Bravu [MB]) tapping a hyperthermal aquifer in Romania. Using a metabarcoding approach, 16S rRNA genes were sequenced from both DNA and RNA transcripts (cDNA) and compared. The relationships between the microbial diversity and the physicochemical factors were explored. Additionally, the cDNA data were used for in silico functionality predictions, bringing new insights into the functional potential and dynamics of these communities. The results showed that each hot spring determined the formation of distinct microbial communities. In the CH mats (40 to 53°C), the abundance of Cyanobacteria decreased with temperature, opposite to those of Chloroflexi and ProteobacteriaEctothiorhodospira, Oscillatoria, and methanogenic archaea dominated the CI communities (20 to 65°C), while the MB microbial mats (53 to 65°C) were mainly composed of Chloroflexi, Hydrogenophilus, Thermi, and Aquificae Alpha-diversity was negatively correlated with the increase in water temperature, while beta-diversity was shaped in each hot spring by the unique combination of physicochemical parameters, regardless of the type of nucleic acid analyzed (DNA versus cDNA). The rank correlation analysis revealed a unique model that associated environmental data with community composition, consisting in the combined effect of Na[+], K[+], HCO3[-], and PO4[3-] concentrations, together with temperature and electrical conductivity. These factors seem to determine the grouping of samples according to location, rather than with the similarities in thermal regimes, showing that other parameters beside temperature are significant drivers of biodiversity.IMPORTANCE Hot spring microbial mats represent a remarkable manifestation of life on Earth and have been intensively studied for decades. Moreover, as hot spring areas are isolated and have a limited exchange of organisms, nutrients, and energy with the surrounding environments, hot spring microbial communities can be used in model studies to elucidate the colonizing potential within extreme settings. Thus, they are of great importance in evolutionary biology, microbial ecology, and exobiology. In spite of all the efforts that have been made, the current understanding of the influence of temperature and water chemistry on the microbial community composition, diversity, and abundance in microbial mats is limited. In this study, the composition and diversity of microbial communities developed in thermal gradients in the vicinity of three hot springs from Romania were investigated, each having particular physicochemical characteristics. Our results expose new factors that could determine the formation of these ecosystems, expanding the current knowledge in this regard.}, }
@article {pmid28821301, year = {2017}, author = {Casero, D and Gill, K and Sridharan, V and Koturbash, I and Nelson, G and Hauer-Jensen, M and Boerma, M and Braun, J and Cheema, AK}, title = {Space-type radiation induces multimodal responses in the mouse gut microbiome and metabolome.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {105}, pmid = {28821301}, issn = {2049-2618}, support = {P01 DK046763/DK/NIDDK NIH HHS/United States ; P20 GM109005/GM/NIGMS NIH HHS/United States ; P30 CA051008/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Carbohydrate Metabolism/radiation effects ; Gastrointestinal Microbiome/genetics/physiology/*radiation effects ; Humans ; Linear Energy Transfer ; Lipopolysaccharides/biosynthesis/radiation effects ; Metabolic Networks and Pathways/radiation effects ; Metabolome/genetics/physiology/*radiation effects ; Metagenome/*radiation effects ; Mice ; Obesity ; *Radiation, Ionizing ; }, abstract = {BACKGROUND: Space travel is associated with continuous low dose rate exposure to high linear energy transfer (LET) radiation. Pathophysiological manifestations after low dose radiation exposure are strongly influenced by non-cytocidal radiation effects, including changes in the microbiome and host gene expression. Although the importance of the gut microbiome in the maintenance of human health is well established, little is known about the role of radiation in altering the microbiome during deep-space travel.<br><br>RESULTS: Using a mouse model for exposure to high LET radiation, we observed substantial changes in the composition and functional potential of the gut microbiome. These were accompanied by changes in the abundance of multiple metabolites, which were related to the enzymatic activity of the predicted metagenome by means of metabolic network modeling. There was a complex dynamic in microbial and metabolic composition at different radiation doses, suggestive of transient, dose-dependent interactions between microbial ecology and signals from the host's cellular damage repair processes. The observed radiation-induced changes in microbiota diversity and composition were analyzed at the functional level. A constitutive change in activity was found for several pathways dominated by microbiome-specific enzymatic reactions like carbohydrate digestion and absorption and lipopolysaccharide biosynthesis, while the activity in other radiation-responsive pathways like phosphatidylinositol signaling could be linked to dose-dependent changes in the abundance of specific taxa.<br><br>CONCLUSIONS: The implication of microbiome-mediated pathophysiology after low dose ionizing radiation may be an unappreciated biologic hazard of space travel and deserves experimental validation. This study provides a conceptual and analytical basis of further investigations to increase our understanding of the chronic effects of space radiation on human health, and points to potential new targets for intervention in adverse radiation effects.}, }
@article {pmid28818949, year = {2017}, author = {Böck, D and Medeiros, JM and Tsao, HF and Penz, T and Weiss, GL and Aistleitner, K and Horn, M and Pilhofer, M}, title = {In situ architecture, function, and evolution of a contractile injection system.}, journal = {Science (New York, N.Y.)}, volume = {357}, number = {6352}, pages = {713-717}, pmid = {28818949}, issn = {1095-9203}, support = {I 1628/FWF_/Austrian Science Fund FWF/Austria ; /ERC_/European Research Council/International ; }, mesh = {Amoeba/*microbiology ; Bacteriophages/chemistry/ultrastructure ; Bacteroidetes/*physiology ; Cryoelectron Microscopy ; Electron Microscope Tomography ; Multigene Family ; Phagosomes/chemistry/ultrastructure ; Phylogeny ; Protein Conformation ; Symbiosis ; Type VI Secretion Systems/*chemistry/classification/genetics/ultrastructure ; }, abstract = {Contractile injection systems mediate bacterial cell-cell interactions by a bacteriophage tail-like structure. In contrast to extracellular systems, the type 6 secretion system (T6SS) is defined by intracellular localization and attachment to the cytoplasmic membrane. Here we used cryo-focused ion beam milling, electron cryotomography, and functional assays to study a T6SS in Amoebophilus asiaticus The in situ architecture revealed three modules, including a contractile sheath-tube, a baseplate, and an anchor. All modules showed conformational changes upon firing. Lateral baseplate interactions coordinated T6SSs in hexagonal arrays. The system mediated interactions with host membranes and may participate in phagosome escape. Evolutionary sequence analyses predicted that T6SSs are more widespread than previously thought. Our insights form the basis for understanding T6SS key concepts and exploring T6SS diversity.}, }
@article {pmid28817594, year = {2017}, author = {van Gils, S and Tamburini, G and Marini, L and Biere, A and van Agtmaal, M and Tyc, O and Kos, M and Kleijn, D and van der Putten, WH}, title = {Soil pathogen-aphid interactions under differences in soil organic matter and mineral fertilizer.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0179695}, pmid = {28817594}, issn = {1932-6203}, mesh = {Analysis of Variance ; Animals ; *Aphids ; Biomass ; Carbon/analysis ; *Fertilizers ; *Minerals/chemistry ; Nitrogen/analysis ; *Organic Chemicals ; Plant Diseases/microbiology/parasitology ; Plants ; Soil/*chemistry ; Triticum ; }, abstract = {There is increasing evidence showing that microbes can influence plant-insect interactions. In addition, various studies have shown that aboveground pathogens can alter the interactions between plants and insects. However, little is known about the role of soil-borne pathogens in plant-insect interactions. It is also not known how environmental conditions, that steer the performance of soil-borne pathogens, might influence these microbe-plant-insect interactions. Here, we studied effects of the soil-borne pathogen Rhizoctonia solani on aphids (Sitobion avenae) using wheat (Triticum aestivum) as a host. In a greenhouse experiment, we tested how different levels of soil organic matter (SOM) and fertilizer addition influence the interactions between plants and aphids. To examine the influence of the existing soil microbiome on the pathogen effects, we used both unsterilized field soil and sterilized field soil. In unsterilized soil with low SOM content, R. solani addition had a negative effect on aphid biomass, whereas it enhanced aphid biomass in soil with high SOM content. In sterilized soil, however, aphid biomass was enhanced by R. solani addition and by high SOM content. Plant biomass was enhanced by fertilizer addition, but only when SOM content was low, or in the absence of R. solani. We conclude that belowground pathogens influence aphid performance and that the effect of soil pathogens on aphids can be more positive in the absence of a soil microbiome. This implies that experiments studying the effect of pathogens under sterile conditions might not represent realistic interactions. Moreover, pathogen-plant-aphid interactions can be more positive for aphids under high SOM conditions. We recommend that soil conditions should be taken into account in the study of microbe-plant-insect interactions.}, }
@article {pmid28816440, year = {2017}, author = {Bergmann, M and Wirzberger, V and Krumpen, T and Lorenz, C and Primpke, S and Tekman, MB and Gerdts, G}, title = {High Quantities of Microplastic in Arctic Deep-Sea Sediments from the HAUSGARTEN Observatory.}, journal = {Environmental science &amp; technology}, volume = {51}, number = {19}, pages = {11000-11010}, doi = {10.1021/acs.est.7b03331}, pmid = {28816440}, issn = {1520-5851}, mesh = {Arctic Regions ; Chlorophyll/*chemistry ; Chlorophyll A ; Ecosystem ; Environmental Monitoring/*methods ; Geologic Sediments/*analysis/chemistry ; Ice Cover ; Plastics/*analysis/chemistry ; Polyethylene/analysis/*chemistry ; Polymers ; Water Pollutants, Chemical/*analysis ; }, abstract = {Although mounting evidence suggests the ubiquity of microplastic in aquatic ecosystems worldwide, our knowledge of its distribution in remote environments such as Polar Regions and the deep sea is scarce. Here, we analyzed nine sediment samples taken at the HAUSGARTEN observatory in the Arctic at 2340-5570 m depth. Density separation by MicroPlastic Sediment Separator and treatment with Fenton's reagent enabled analysis via Attenuated Total Reflection FTIR and μFTIR spectroscopy. Our analyses indicate the wide spread of high numbers of microplastics (42-6595 microplastics kg[-1]). The northernmost stations harbored the highest quantities, indicating sea ice as a possible transport vehicle. A positive correlation between microplastic abundance and chlorophyll a content suggests vertical export via incorporation in sinking (ice-) algal aggregates. Overall, 18 different polymers were detected. Chlorinated polyethylene accounted for the largest proportion (38%), followed by polyamide (22%) and polypropylene (16%). Almost 80% of the microplastics were ≤25 μm. The microplastic quantities are among the highest recorded from benthic sediments. This corroborates the deep sea as a major sink for microplastics and the presence of accumulation areas in this remote part of the world, fed by plastics transported to the North via the Thermohaline Circulation.}, }
@article {pmid28812645, year = {2017}, author = {Kirchman, DL}, title = {Marine microbial ecology: Life after volcanic destruction.}, journal = {Nature ecology &amp; evolution}, volume = {1}, number = {6}, pages = {157}, doi = {10.1038/s41559-017-0157}, pmid = {28812645}, issn = {2397-334X}, }
@article {pmid28812142, year = {2017}, author = {Stedtfeld, RD and Brett Sallach, J and Crawford, RB and Stedtfeld, TM and Williams, MR and Waseem, H and Johnston, CT and Li, H and Teppen, BJ and Kaminski, NE and Boyd, SA and Tiedje, JM and Hashsham, SA}, title = {TCDD administered on activated carbon eliminates bioavailability and subsequent shifts to a key murine gut commensal.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {19}, pages = {7409-7415}, pmid = {28812142}, issn = {1432-0614}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; P42ES004911/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Biological Availability ; Charcoal/*administration &amp; dosage/pharmacokinetics ; Corn Oil/administration &amp; dosage/pharmacokinetics ; Female ; Gastrointestinal Microbiome/*drug effects ; Ileum/microbiology ; Lactobacillaceae/metabolism ; Mice ; Polychlorinated Dibenzodioxins/*administration &amp; dosage/pharmacokinetics/toxicity ; RNA, Ribosomal, 16S/genetics ; Transcriptome ; }, abstract = {Activated carbon (AC) is an increasingly attractive remediation alternative for the sequestration of dioxins at contaminated sites globally. However, the potential for AC to reduce the bioavailability of dioxins in mammals and the residing gut microbiota has received less attention. This question was partially answered in a recent study examining 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-induced hallmark toxic responses in mice administered with TCDD sequestered by AC or freely available in corn oil by oral gavage. Results from that study support the use of AC to significantly reduce the bioavailability of TCDD to the host. Herein, we examined the bioavailability of TCDD sequestered to AC on a key murine gut commensal and the influence of AC on the community structure of the gut microbiota. The analysis included qPCR to quantify the expression of segmented filamentous bacteria (SFB) in the mouse ileum, which has responded to TCDD-induced host toxicity in previous studies and community structure via sequencing the 16S ribosomal RNA (rRNA) gene. The expression of SFB 16S rRNA gene and functional genes significantly increased with TCDD administered with corn oil vehicle. Such a response was absent when TCDD was sequestered by AC. In addition, AC appeared to have a minimal influence on murine gut community structure and diversity, affecting only the relative abundance of Lactobacillaceae and two other groups. Results of this study further support the remedial use of AC for eliminating bioavailability of TCDD to host and subsequent influence on the gut microbiome.}, }
@article {pmid28811633, year = {2017}, author = {Kwambana-Adams, B and Hanson, B and Worwui, A and Agbla, S and Foster-Nyarko, E and Ceesay, F and Ebruke, C and Egere, U and Zhou, Y and Ndukum, M and Sodergren, E and Barer, M and Adegbola, R and Weinstock, G and Antonio, M}, title = {Rapid replacement by non-vaccine pneumococcal serotypes may mitigate the impact of the pneumococcal conjugate vaccine on nasopharyngeal bacterial ecology.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8127}, pmid = {28811633}, issn = {2045-2322}, support = {G0801980/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacteria/classification/genetics ; Humans ; Infant ; Infant, Newborn ; Longitudinal Studies ; Microbiota/drug effects/genetics/physiology ; Nasopharynx/drug effects/*immunology/microbiology ; Phylogeny ; Pneumococcal Infections/drug therapy/*immunology/microbiology ; Pneumococcal Vaccines/administration &amp; dosage/*immunology ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Serogroup ; Streptococcus pneumoniae/classification/genetics/*immunology ; Vaccines, Conjugate/administration &amp; dosage/immunology ; }, abstract = {There is growing concern that interventions that alter microbial ecology can adversely affect health. We characterised the impact of the seven-valent pneumococcal conjugate vaccine (PCV7) on pneumococcal carriage and the bacterial component of the nasopharyngeal microbiome during infancy. Newborns were recruited into three groups as follows: Group1 (n = 33) was the control group and comprised infants who received PCV7 after 6 months and came from unvaccinated communities. Group 2 (n = 30) came from unvaccinated communities and Group 3 (n = 39) came from vaccinated communities. Both group 2 and 3 received PCV7 at 2, 3 and 4 months. Culture and 16 S rRNA gene sequencing were performed on nasopharyngeal specimens collected at regular intervals from infants. Nasopharyngeal carriage of PCV7 serotypes in Group 1 was significantly higher than in Group 2 and 3 (p < 0.01). However, pneumococcal carriage remained comparable due to an expansion of non-vaccine serotypes in Groups 2 and 3. Determination of phylogenetic dis(similarities) showed that the bacterial community structures were comparable across groups. A mixed effects model showed no difference in community richness (p = 0.15) and Shannon α-diversity (p = 0.48) across the groups. Immediate replacement of pneumococcal vaccine serotypes with non-vaccine serotypes may mitigate the impact of PCV7 on nasopharyngeal bacterial community structure and ecology.}, }
@article {pmid28811339, year = {2017}, author = {Sasson, G and Kruger Ben-Shabat, S and Seroussi, E and Doron-Faigenboim, A and Shterzer, N and Yaacoby, S and Berg Miller, ME and White, BA and Halperin, E and Mizrahi, I}, title = {Heritable Bovine Rumen Bacteria Are Phylogenetically Related and Correlated with the Cow's Capacity To Harvest Energy from Its Feed.}, journal = {mBio}, volume = {8}, number = {4}, pages = {}, pmid = {28811339}, issn = {2150-7511}, mesh = {Animal Feed ; Animals ; Bacteria/*genetics ; Biomass ; Cattle ; *Energy Metabolism ; Female ; Gastrointestinal Microbiome/*genetics ; Metagenome ; Methane/metabolism ; Phylogeny ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Ruminants sustain a long-lasting obligatory relationship with their rumen microbiome dating back 50 million years. In this unique host-microbiome relationship, the host's ability to digest its feed is completely dependent on its coevolved microbiome. This extraordinary alliance raises questions regarding the dependent relationship between ruminants' genetics and physiology and the rumen microbiome structure, composition, and metabolism. To elucidate this relationship, we examined the association of host genetics with the phylogenetic and functional composition of the rumen microbiome. We accomplished this by studying a population of 78 Holstein-Friesian dairy cows, using a combination of rumen microbiota data and other phenotypes from each animal with genotypic data from a subset of 47 animals. We identified 22 operational taxonomic units (OTUs) whose abundances were associated with rumen metabolic traits and host physiological traits and which showed measurable heritability. The abundance patterns of these microbes can explain high proportions of variance in rumen metabolism and many of the host physiological attributes such as its energy-harvesting efficiency. Interestingly, these OTUs shared higher phylogenetic similarity between themselves than expected by chance, suggesting occupation of a specific ecological niche within the rumen ecosystem. The findings presented here suggest that ruminant genetics and physiology are correlated with microbiome structure and that host genetics may shape the microbiome landscape by enriching for phylogenetically related taxa that may occupy a unique niche.IMPORTANCE Dairy cows are an essential nutritional source for the world's population; as such, they are extensively farmed throughout our planet and subsequently impact our environment. The microbial communities that reside in the upper digestive tract of these animals in a compartment named the rumen degrade and ferment the plant biomass that the animal ingests. Our recent efforts, as well as those of others, have shown that this microbial community's composition and functionality are tightly linked to the cow's capacity to harvest energy from its feed, as well as to other physiological traits. In this study, we identified microbial groups that are heritable and also linked to the cow's production parameters. This finding could potentially allow us to apply selection programs on specific rumen microbial components that are linked to the animal's physiology and beneficial to production. Hence, it is a steppingstone toward microbiome manipulation for increasing food availability while lowering environmental impacts such as methane emission.}, }
@article {pmid28810907, year = {2017}, author = {Emerson, JB and Adams, RI and Román, CMB and Brooks, B and Coil, DA and Dahlhausen, K and Ganz, HH and Hartmann, EM and Hsu, T and Justice, NB and Paulino-Lima, IG and Luongo, JC and Lymperopoulou, DS and Gomez-Silvan, C and Rothschild-Mancinelli, B and Balk, M and Huttenhower, C and Nocker, A and Vaishampayan, P and Rothschild, LJ}, title = {Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {86}, pmid = {28810907}, issn = {2049-2618}, mesh = {Bacteria/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; Biomass ; *Ecosystem ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/methods ; Microbial Consortia ; *Microbial Viability ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms. In this review, we describe a number of techniques, from microscopy- to molecular-based, that have been used to test for viability (live/dead determination) and/or activity in various contexts, including newer techniques that are compatible with or complementary to downstream nucleic acid sequencing. We describe the compatibility of these viability assessments with high-throughput quantification techniques, including flow cytometry and quantitative PCR (qPCR). Although bacterial viability-linked community characterizations are now feasible in many environments and thus are the focus of this critical review, further methods development is needed for complex environmental samples and to more fully capture the diversity of microbes (e.g., eukaryotic microbes and viruses) and metabolic states (e.g., spores) of microbes in natural environments.}, }
@article {pmid28810737, year = {2018}, author = {Cohen, LJ and Han, S and Huang, YH and Brady, SF}, title = {Identification of the Colicin V Bacteriocin Gene Cluster by Functional Screening of a Human Microbiome Metagenomic Library.}, journal = {ACS infectious diseases}, volume = {4}, number = {1}, pages = {27-32}, pmid = {28810737}, issn = {2373-8227}, support = {K08 DK109287/DK/NIDDK NIH HHS/United States ; T32 GM007739/GM/NIGMS NIH HHS/United States ; U01 GM110714/GM/NIGMS NIH HHS/United States ; }, mesh = {Colicins/*genetics ; Gene Library ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; *Multigene Family ; Sequence Analysis, DNA ; }, abstract = {The forces that shape human microbial ecology are complex. It is likely that human microbiota, similarly to other microbiomes, use antibiotics as one way to establish an ecological niche. In this study, we use functional metagenomics to identify human microbial gene clusters that encode for antibiotic functions. Screening of a metagenomic library prepared from a healthy patient stool sample led to the identification of a family of clones with inserts that are 99% identical to a region of a virulence plasmid found in avian pathogenic Escherichia coli. Characterization of the metagenomic DNA sequence identified a colicin V biosynthetic cluster as being responsible for the observed antibiotic effect of the metagenomic clone against E. coli. This study presents a scalable method to recover antibiotic gene clusters from humans using functional metagenomics and highlights a strategy to study bacteriocins in the human microbiome which can provide a resource for therapeutic discovery.}, }
@article {pmid28808742, year = {2017}, author = {Wu, RN and Meng, H and Wang, YF and Lan, W and Gu, JD}, title = {A More Comprehensive Community of Ammonia-Oxidizing Archaea (AOA) Revealed by Genomic DNA and RNA Analyses of amoA Gene in Subtropical Acidic Forest Soils.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {910-922}, pmid = {28808742}, issn = {1432-184X}, mesh = {Ammonia/metabolism ; Archaea/classification/*physiology ; Archaeal Proteins/*analysis ; China ; Cunninghamia/growth &amp; development ; *Forestry ; Forests ; *Microbiota ; Oxidation-Reduction ; Phylogeny ; *Soil Microbiology ; }, abstract = {Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the main nitrifiers which are well studied in natural environments, and AOA frequently outnumber AOB by orders especially in acidic conditions, making AOA the most promising ammonia oxidizers. The phylogeny of AOA revealed in related studies, however, often varied and hardly reach a consensus on functional phylotypes. The objective of this study was to compare ammonia-oxidizing communities by amoA gene and transcript based on both genomic DNA and RNA in extremely acidic forest soils (pH <4.5). Our results support the numerical and functional dominance of AOA over AOB in acidic soils as bacterial amoA gene and transcript were both under detection limits and archaeal amoA, in contrast, were abundant and responded to the fluctuations of environmental factors. Organic matter from tree residues was proposed as the main source of microbial available nitrogen, and the potential co-precipitation of dissolved organic matter (DOM) with soluble Al[3+] species in acidic soil matrix may further restrict the amount of nitrogen sources required by AOB besides NH3/NH4[+] equilibrium. Although AOA were better adapted to oligotrophic environments, they were susceptible to the toxicity of exchangeable Al[3+]. Phylotypes affiliated to Nitrososphaera, Nitrososphaera sister group, and Nitrosotalea were detected by amoA gene and transcript. Nitrosotalea devantaerra and Nitrososphaera sister group were the major AOA. Compared to the genomic DNA data, higher relative abundances of Nitrososphaera and Nitrososphaera sister group were recognized in amoA transcript inferred AOA communities, where Nitrosotalea relative abundance was found lower, implying the functional activities of Nitrososphaera sister group and Nitrososphaera were easily underestimated and Nitrosotalea did not attribute proportionally to nitrification in extremely acidic soils. Further comparison of the different AOA community compositions and relative abundance of each phylotypes revealed by amoA genes and transcripts make it possible to identify the functional AOA species and assess their ecological role in extremely acidic soils.}, }
@article {pmid28805354, year = {2018}, author = {Koch, C and Korth, B and Harnisch, F}, title = {Microbial ecology-based engineering of Microbial Electrochemical Technologies.}, journal = {Microbial biotechnology}, volume = {11}, number = {1}, pages = {22-38}, pmid = {28805354}, issn = {1751-7915}, mesh = {Bioreactors/*microbiology ; Electricity ; Electrochemical Techniques/*methods/trends ; *Metabolism ; *Microbial Consortia ; Microbiological Techniques/*methods/trends ; }, abstract = {Microbial ecology is devoted to the understanding of dynamics, activity and interaction of microorganisms in natural and technical ecosystems. Bioelectrochemical systems represent important technical ecosystems, where microbial ecology is of highest importance for their function. However, whereas aspects of, for example, materials and reactor engineering are commonly perceived as highly relevant, the study and engineering of microbial ecology are significantly underrepresented in bioelectrochemical systems. This shortfall may be assigned to a deficit on knowledge and power of these methods as well as the prerequisites for their thorough application. This article discusses not only the importance of microbial ecology for microbial electrochemical technologies but also shows which information can be derived for a knowledge-driven engineering. Instead of providing a comprehensive list of techniques from which it is hard to judge the applicability and value of information for a respective one, this review illustrates the suitability of selected techniques on a case study. Thereby, best practice for different research questions is provided and a set of key questions for experimental design, data acquisition and analysis is suggested.}, }
@article {pmid28803409, year = {2018}, author = {Vezzulli, L and Stagnaro, L and Grande, C and Tassistro, G and Canesi, L and Pruzzo, C}, title = {Comparative 16SrDNA Gene-Based Microbiota Profiles of the Pacific Oyster (Crassostrea gigas) and the Mediterranean Mussel (Mytilus galloprovincialis) from a Shellfish Farm (Ligurian Sea, Italy).}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {495-504}, pmid = {28803409}, issn = {1432-184X}, support = {678589//Horizon 2020 Framework Programme/ ; }, mesh = {Animals ; Aquaculture ; Bacteria/classification/genetics/*isolation &amp; purification ; Crassostrea/growth &amp; development/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/*genetics ; Gastrointestinal Tract/microbiology ; Hemolymph/microbiology ; Italy ; *Microbiota ; Mytilus/growth &amp; development/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Shellfish/analysis/*microbiology ; }, abstract = {The pacific oyster Crassostrea gigas and the Mediterranean mussel Mytilus galloprovincialis are two widely farmed bivalve species which show contrasting behaviour in relation to microbial diseases, with C. gigas being more susceptible and M. galloprovincialis being generally resistant. In a recent study, we showed that different susceptibility to infection exhibited by these two bivalve species may depend on their different capability to kill invading pathogens (e.g., Vibrio spp.) through the action of haemolymph components. Specific microbial-host interactions may also impact bivalve microbiome structure and further influence susceptibility/resistance to microbial diseases. To further investigate this concept, a comparative study of haemolymph and digestive gland 16SrDNA gene-based bacterial microbiota profiles in C. gigas and M. galloprovincialis co-cultivated at the same aquaculture site was carried out using pyrosequencing. Bacterial communities associated with bivalve tissues (hemolymph and digestive gland) were significantly different from those of seawater, and were dominated by relatively few genera such as Vibrio and Pseudoalteromonas. In general, Vibrio accounted for a larger fraction of the microbiota in C. gigas (on average 1.7-fold in the haemolymph) compared to M. galloprovincialis, suggesting that C. gigas may provide better conditions for survival for these bacteria, including potential pathogenic species such as V. aestuarianus. Vibrios appeared to be important members of C. gigas and M. galloprovincialis microbiota and might play a contrasting role in health and disease of bivalve species. Accordingly, microbiome analyses performed on bivalve specimens subjected to commercial depuration highlighted the ineffectiveness of such practice in removing Vibrio species from bivalve tissues.}, }
@article {pmid28803054, year = {2017}, author = {Meerbergen, K and Crauwels, S and Willems, KA and Dewil, R and Van Impe, J and Appels, L and Lievens, B}, title = {Decolorization of reactive azo dyes using a sequential chemical and activated sludge treatment.}, journal = {Journal of bioscience and bioengineering}, volume = {124}, number = {6}, pages = {668-673}, doi = {10.1016/j.jbiosc.2017.07.005}, pmid = {28803054}, issn = {1347-4421}, mesh = {Azo Compounds/*chemistry/*metabolism ; *Color ; Hydrogen Peroxide/chemistry ; Iron/chemistry ; Naphthalenesulfonates/chemistry/metabolism ; Oxidation-Reduction ; Sewage/*chemistry/*microbiology ; Textiles ; Wastewater/chemistry ; }, abstract = {Textile wastewater contains high concentrations of organic substances derived from diverse dyes and auxiliary chemicals, some of which are non-biodegradable and/or toxic. Therefore, it is essential that textile wastewater is treated and that these substances are removed before being discharged into the environment. A combination of advanced oxidation processes (AOPs) to obtain partial dye degradation followed by a biological treatment has been suggested as a promising method for cost-effective decolorization of wastewater. The aim of this study was to develop and evaluate a combined method of partial Fenton's oxidation and biological treatment using activated sludge for decolorization of azo dyes, which represent an important group of recalcitrant, toxic textile dyes. Using Reactive Violet 5 (RV5) as a model dye, color removal was significantly higher when the combined Fenton treatment/activated sludge method was used, as opposed to separate application of these treatments. More specifically, pretreatment with Fenton's reagent removed 52.9, 83.9 and 91.3 % of color from a 500 mg l[-1] RV5 aqueous solution within 60 min when H2O2 concentrations of 1.0, 1.5, and 2.0 mM were used, respectively. Subsequent biological treatment was found to significantly enhance the chemical treatment, with microbial decolorization removing 70.2 % of the remaining RV5 concentration, on average. Molecular analysis of the microbial community within the activated sludge revealed that exposure to RV5 shifted the community composition from diverse towards a highly-specialized community harboring taxa with azo dye degrading activity, including Trichosporon, Aspergillus and Clostridium species.}, }
@article {pmid28801990, year = {2017}, author = {Sharma, D and Mal, G and Kannan, A and Bhar, R and Sharma, R and Singh, B}, title = {Degradation of euptox A by tannase-producing rumen bacteria from migratory goats.}, journal = {Journal of applied microbiology}, volume = {123}, number = {5}, pages = {1194-1202}, doi = {10.1111/jam.13563}, pmid = {28801990}, issn = {1365-2672}, mesh = {Ageratina/chemistry/metabolism/*toxicity ; Animal Migration ; Animals ; Carboxylic Ester Hydrolases/genetics/*metabolism ; Goats/metabolism/microbiology ; Klebsiella/enzymology/genetics/isolation &amp; purification/*metabolism ; Rumen/*microbiology ; Sesquiterpenes/analysis/*metabolism/toxicity ; }, abstract = {AIMS: The gut microbiota capable of degrading plant biomass and antinutritional phytometabolites are of immense importance. This study reports isolation and characterization of tannase-producing rumen bacteria that could also degrade euptox A (9-oxo-10,11-dehydroageraphorone) present in Eupatorium adenophorum (Spreng).<br><br>METHODS AND RESULTS: Migratory Gaddi goats were selected as source of inoculums for isolating rumen bacteria with ability to produce tannase which catalyses degradation of hydrolysable tannins (HTs). Three rumen bacterial isolates producing tannase were studied, and identified as Klebsiella variicola strain PLP G-17 LC, K. variicola strain PLP S-18 and Klebsiella pneumoniae strain PLP G-17 SC. The isolates exhibited optimal tannase activity at 40&#xb0;C, and pH 6&#xb7;0. The bacteria could also degrade euptox A, a potent hepatotoxin in E. adenophorum Spreng, a widely distributed noxious weed.<br><br>CONCLUSIONS: The rumen bacteria could degrade antinutritional HTs and euptox A. Culture-independent metagenomic interventions are envisioned to completely decipher the rumen microbial ecology and exploit its genetic and metabolic potential.<br><br>The bacteria producing tannase which catalyses degradation of HTs, and concurrently degrading euptox A, may have potential as microbial feed additives to increase utilization of plant biomass containing antinutritional phytometabolites.}, }
@article {pmid28801232, year = {2017}, author = {Mamantopoulos, M and Ronchi, F and Van Hauwermeiren, F and Vieira-Silva, S and Yilmaz, B and Martens, L and Saeys, Y and Drexler, SK and Yazdi, AS and Raes, J and Lamkanfi, M and McCoy, KD and Wullaert, A}, title = {Nlrp6- and ASC-Dependent Inflammasomes Do Not Shape the Commensal Gut Microbiota Composition.}, journal = {Immunity}, volume = {47}, number = {2}, pages = {339-348.e4}, doi = {10.1016/j.immuni.2017.07.011}, pmid = {28801232}, issn = {1097-4180}, support = {281600/ERC_/European Research Council/International ; 281785/ERC_/European Research Council/International ; 683144/ERC_/European Research Council/International ; }, mesh = {Animals ; Apoptosis Regulatory Proteins/*metabolism ; Bacteria/*genetics ; CARD Signaling Adaptor Proteins ; Cells, Cultured ; Colitis/chemically induced/*immunology/microbiology ; Dysbiosis/*immunology/microbiology ; Female ; Gastrointestinal Microbiome/*immunology ; Genetic Background ; Immunity, Innate ; Inflammasomes/*metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Microbiota ; RNA, Ribosomal, 16S/analysis ; Receptors, Cell Surface/genetics/*metabolism ; Sodium Dodecyl Sulfate ; }, abstract = {The gut microbiota regulate susceptibility to multiple human diseases. The Nlrp6-ASC inflammasome is widely regarded as a hallmark host innate immune axis that shapes the gut microbiota composition. This notion stems from studies reporting dysbiosis in mice lacking these inflammasome components when compared with non-littermate wild-type animals. Here, we describe microbial analyses in inflammasome-deficient mice while minimizing non-genetic confounders using littermate-controlled Nlrp6-deficient mice and ex-germ-free littermate-controlled ASC-deficient mice that were all allowed to shape their gut microbiota naturally after birth. Careful microbial phylogenetic analyses of these cohorts failed to reveal regulation of the gut microbiota composition by the Nlrp6- and ASC-dependent inflammasomes. Our results obtained in two geographically separated animal facilities dismiss a generalizable impact of Nlrp6- and ASC-dependent inflammasomes on the composition of the commensal gut microbiota and highlight the necessity for littermate-controlled experimental design in assessing the influence of host immunity on gut microbial ecology.}, }
@article {pmid28800851, year = {2017}, author = {Justo, A and Miettinen, O and Floudas, D and Ortiz-Santana, B and Sjökvist, E and Lindner, D and Nakasone, K and Niemelä, T and Larsson, KH and Ryvarden, L and Hibbett, DS}, title = {A revised family-level classification of the Polyporales (Basidiomycota).}, journal = {Fungal biology}, volume = {121}, number = {9}, pages = {798-824}, doi = {10.1016/j.funbio.2017.05.010}, pmid = {28800851}, issn = {1878-6146}, mesh = {Bayes Theorem ; DNA, Fungal/chemistry/isolation &amp; purification ; Fungal Proteins/chemistry/*genetics ; *Genome, Fungal/genetics ; Likelihood Functions ; *Phylogeny ; Polymerase Chain Reaction ; Polyporales/*classification/enzymology/genetics ; RNA Polymerase II/genetics ; Sequence Alignment ; }, abstract = {Polyporales is strongly supported as a clade of Agaricomycetes, but the lack of a consensus higher-level classification within the group is a barrier to further taxonomic revision. We amplified nrLSU, nrITS, and rpb1 genes across the Polyporales, with a special focus on the latter. We combined the new sequences with molecular data generated during the PolyPEET project and performed Maximum Likelihood and Bayesian phylogenetic analyses. Analyses of our final 3-gene dataset (292 Polyporales taxa) provide a phylogenetic overview of the order that we translate here into a formal family-level classification. Eighteen clades are assigned a family name, including three families described as new (Cerrenaceae fam. nov., Gelatoporiaceae fam. nov., Panaceae fam. nov.) and fifteen others (Dacryobolaceae, Fomitopsidaceae, Grifolaceae, Hyphodermataceae, Incrustoporiaceae, Irpicaceae, Ischnodermataceae, Laetiporaceae, Meripilaceae, Meruliaceae, Phanerochaetaceae, Podoscyphaceae, Polyporaceae, Sparassidaceae, Steccherinaceae). Three clades are given informal names (/hypochnicium,/climacocystis and/fibroporia + amyloporia). Four taxa (Candelabrochete africana, Mycoleptodonoides vassiljevae, Auriporia aurea, and Tyromyces merulinus) cannot be assigned to a family within the Polyporales. The classification proposed here provides a framework for further taxonomic revision and will facilitate communication among applied and basic scientists. A survey of morphological, anatomical, physiological, and genetic traits confirms the plasticity of characters previously emphasized in taxonomy of Polyporales.}, }
@article {pmid28800687, year = {2017}, author = {Šulčius, S and Montvydienė, D and Mazur-Marzec, H and Kasperovičienė, J and Rulevičius, R and Cibulskaitė, &#x17d;}, title = {The profound effect of harmful cyanobacterial blooms: From food-web and management perspectives.}, journal = {The Science of the total environment}, volume = {609}, number = {}, pages = {1443-1450}, doi = {10.1016/j.scitotenv.2017.07.253}, pmid = {28800687}, issn = {1879-1026}, mesh = {*Conservation of Natural Resources ; Cyanobacteria/*growth &amp; development ; Environmental Monitoring ; *Eutrophication ; *Food Chain ; }, abstract = {Sustainable and effective water management plans must have a reliable risk assessment strategies for harmful cyanobacterial blooms (HABs) that would enable timely decisions to be made, thus avoiding the trespassing of ecological thresholds, leading to the collapse of ecosystem structure and function. Such strategies are usually based on cyanobacterial biomass and/or on the monitoring of known toxins, which may, however, in many cases, under- or over-represent the actual toxicity of the HAB. Therefore, in this study, by the application of growth-inhibition assays using different bacteria, algae, zooplankton and fish species, we assessed the toxicological potential of two cyanobacterial blooms that differed in total cyanobacterial biomass, species composition and cyanopeptide profiles. We demonstrated that neither cyanobacterial community composition nor its relative abundance, nor indeed concentrations of known toxins reflected the potential risk of HAB based on growth-inhibition assays. We discuss our findings in the context of food-web dynamics and ecosystem management, and suggest that toxicological tests should constitute a key element in the routine monitoring of water bodies so as to prevent under-/over-estimation of potential HAB risk for both ecosystem and public health.}, }
@article {pmid28796186, year = {2017}, author = {Santos, IC and Martin, MS and Carlton, DD and Amorim, CL and Castro, PML and Hildenbrand, ZL and Schug, KA}, title = {MALDI-TOF MS for the Identification of Cultivable Organic-Degrading Bacteria in Contaminated Groundwater near Unconventional Natural Gas Extraction Sites.}, journal = {Microorganisms}, volume = {5}, number = {3}, pages = {}, pmid = {28796186}, issn = {2076-2607}, abstract = {Groundwater quality and quantity is of extreme importance as it is a source of drinking water in the United States. One major concern has emerged due to the possible contamination of groundwater from unconventional oil and natural gas extraction activities. Recent studies have been performed to understand if these activities are causing groundwater contamination, particularly with respect to exogenous hydrocarbons and volatile organic compounds. The impact of contaminants on microbial ecology is an area to be explored as alternatives for water treatment are necessary. In this work, we identified cultivable organic-degrading bacteria in groundwater in close proximity to unconventional natural gas extraction. Pseudomonas stutzeri and Acinetobacter haemolyticus were identified using matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry (MALDI-TOF MS), which proved to be a simple, fast, and reliable method. Additionally, the potential use of the identified bacteria in water and/or wastewater bioremediation was studied by determining the ability of these microorganisms to degrade toluene and chloroform. In fact, these bacteria can be potentially applied for in situ bioremediation of contaminated water and wastewater treatment, as they were able to degrade both compounds.}, }
@article {pmid28792642, year = {2017}, author = {Subirats, J and Triadó-Margarit, X and Mandaric, L and Acuña, V and Balcázar, JL and Sabater, S and Borrego, CM}, title = {Wastewater pollution differently affects the antibiotic resistance gene pool and biofilm bacterial communities across streambed compartments.}, journal = {Molecular ecology}, volume = {26}, number = {20}, pages = {5567-5581}, doi = {10.1111/mec.14288}, pmid = {28792642}, issn = {1365-294X}, mesh = {Bacteria/*classification/genetics ; *Biofilms ; Drug Resistance, Microbial/*genetics ; *Gene Pool ; *Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Rivers/chemistry/microbiology ; Sequence Analysis, DNA ; Spain ; *Wastewater ; Water Microbiology ; Water Pollution ; }, abstract = {Wastewater discharges introduce antibiotic residues and antibiotic-resistant bacteria (ARB) into surface waters. Both inputs directly affect the streambed resistome, either by exerting a selective pressure that favour the proliferation of resistant phenotypes or by enriching the resident communities with wastewater-associated ARB. Here, we investigated the impact of raw and treated urban wastewater discharges on epilithic (growing on rocks) and epipsammic (growing on sandy substrata) streambed biofilms. The effects were assessed by comparing control and impact sites (i) on the composition of bacterial communities; (ii) on the abundance of twelve antibiotic resistance genes (ARGs) encoding resistance to β-lactams, fluoroquinolones, sulphonamides, tetracyclines, macrolides and vancomycin, as well as the class 1 integron-integrase gene (intI1); (iii) on the occurrence of wastewater-associated bacteria, including putative pathogens, and their potential linkage to target ARGs. We measured more pronounced effects of raw sewage than treated wastewater at the three studied levels. This effect was especially noticeable in epilithic biofilms, which showed a higher contribution of wastewater-associated bacteria and ARB than in epipsammic biofilms. Comparison of correlation coefficients obtained between the relative abundance of both target ARGs and operational taxonomic units classified as either potential pathogens or nonpathogens yielded significant higher correlations between the former category and genes intI1, sul1, sul2 and ermB. Altogether, these results indicate that wastewater-associated micro-organisms, including potential pathogens, contribute to maintain the streambed resistome and that epilithic biofilms appear as sensitive biosensors of the effect of wastewater pollution in surface waters.}, }
@article {pmid28791467, year = {2018}, author = {Shen, Z and Penton, CR and Lv, N and Xue, C and Yuan, X and Ruan, Y and Li, R and Shen, Q}, title = {Banana Fusarium Wilt Disease Incidence Is Influenced by Shifts of Soil Microbial Communities Under Different Monoculture Spans.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {739-750}, pmid = {28791467}, issn = {1432-184X}, support = {2015CB150500//National Key Basic Research Program of China/ ; KJQN201746//Fundamental Research Funds for the Central Universities/ ; 31601836, 31572212, 31372142//National Natural Science Foundation of China/ ; 2016YFD0800605 and 2016YFE0101100//National key research and development program/ ; 2016B020202006//Science and Technology Planning Project of Guangdong Province/ ; 2016M590469//China Postdoctoral Science Foundation/ ; }, mesh = {Ascomycota/pathogenicity ; Bacteria/classification/drug effects/genetics ; Biodiversity ; Biological Control Agents/adverse effects ; Crops, Agricultural ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; Fungi/classification/drug effects/genetics ; Fusarium/*pathogenicity ; Incidence ; Microbial Interactions/physiology ; Microbiota/drug effects/*physiology ; Musa/*microbiology ; Phylogeny ; Plant Diseases/*microbiology ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The continuous cropping of banana in the same field may result in a serious soil-borne Fusarium wilt disease and a severe yield decline, a phenomenon known as soil sickness. Although soil microorganisms play key roles in maintaining soil health, the alternations of soil microbial community and relationship between these changes and soil sickness under banana monoculture are still unclear. Bacterial and fungal communities in the soil samples collected from banana fields with different monoculture spans were profiled by sequencing of the 16S rRNA genes and internal transcribed spacer using the MiSeq platform to explore the relationship between banana monoculture and Fusarium wilt disease in the present study. The results showed that successive cropping of banana was significantly correlated with the Fusarium wilt disease incidence. Fungal communities responded more obviously and quickly to banana consecutive monoculture than bacterial community. Moreover, a higher fungal richness significantly correlated to a higher banana Fusarium wilt disease incidence but a lower yield. Banana fungal pathogenic genus of Fusarium and Phyllosticta were closely associated with banana yield depletion and disease aggravation. Potential biocontrol agents, such as Funneliformis, Mortierella, Flavobacterium, and Acidobacteria subgroups, exhibited a significant correlation to lower disease occurrence. Further networks analysis revealed that the number of functionally interrelated modules decreased, the composition shifted from bacteria- to fungi-dominated among these modules, and more resources-competitive interactions within networks were observed after banana long-term monoculture. Our results also showed that bacterial and fungal communities were mainly driven by soil organic matter. Overall, the findings indicated that the bacterial and fungal community structures altered significantly after banana long-term monoculture, and the fungal richness, abundance of Fusarium, interactions between and within bacteria and fungi in ecological networks, and soil organic matter were associated with banana soil-borne Fusarium wilt disease.}, }
@article {pmid28791465, year = {2018}, author = {Veresoglou, SD and Wang, D and Andrade-Linares, DR and Hempel, S and Rillig, MC}, title = {Fungal Decision to Exploit or Explore Depends on Growth Rate.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {289-292}, pmid = {28791465}, issn = {1432-184X}, mesh = {Fungal Proteins/genetics/metabolism ; Fungi/chemistry/genetics/*growth &amp; development/metabolism ; Kinetics ; }, }
@article {pmid28790201, year = {2017}, author = {Lowery, NV and McNally, L and Ratcliff, WC and Brown, SP}, title = {Division of Labor, Bet Hedging, and the Evolution of Mixed Biofilm Investment Strategies.}, journal = {mBio}, volume = {8}, number = {4}, pages = {}, pmid = {28790201}, issn = {2150-7511}, support = {//Wellcome Trust/United Kingdom ; WT095831//Wellcome Trust/United Kingdom ; }, mesh = {Adaptation, Physiological ; Bacteria/*genetics/growth &amp; development/metabolism ; *Bacterial Physiological Phenomena/genetics ; *Biofilms ; *Biological Evolution ; Environment ; *Genetic Fitness ; Models, Biological ; Phenotype ; }, abstract = {Bacterial cells, like many other organisms, face a tradeoff between longevity and fecundity. Planktonic cells are fast growing and fragile, while biofilm cells are often slower growing but stress resistant. Here we ask why bacterial lineages invest simultaneously in both fast- and slow-growing types. We develop a population dynamic model of lineage expansion across a patchy environment and find that mixed investment is favored across a broad range of environmental conditions, even when transmission is entirely via biofilm cells. This mixed strategy is favored because of a division of labor where exponentially dividing planktonic cells can act as an engine for the production of future biofilm cells, which grow more slowly. We use experimental evolution to test our predictions and show that phenotypic heterogeneity is persistent even under selection for purely planktonic or purely biofilm transmission. Furthermore, simulations suggest that maintenance of a biofilm subpopulation serves as a cost-effective hedge against environmental uncertainty, which is also consistent with our experimental findings.IMPORTANCE Cell types specialized for survival have been observed and described within clonal bacterial populations for decades, but why are these specialists continually produced under benign conditions when such investment comes at a high reproductive cost? Conversely, when survival becomes an imperative, does it ever benefit the population to maintain a pool of rapidly growing but vulnerable planktonic cells? Using a combination of mathematical modeling, simulations, and experiments, we find that mixed investment strategies are favored over a broad range of environmental conditions and rely on a division of labor between cell types, where reproductive specialists amplify survival specialists, which can be transmitted through the environment with a limited mortality rate. We also show that survival specialists benefit rapidly growing populations by serving as a hedge against unpredictable changes in the environment. These results help to clarify the general evolutionary and ecological forces that can generate and maintain diverse subtypes within clonal bacterial populations.}, }
@article {pmid28786973, year = {2017}, author = {Ridenhour, BJ and Brooker, SL and Williams, JE and Van Leuven, JT and Miller, AW and Dearing, MD and Remien, CH}, title = {Modeling time-series data from microbial communities.}, journal = {The ISME journal}, volume = {11}, number = {11}, pages = {2526-2537}, pmid = {28786973}, issn = {1751-7370}, support = {P20 GM104420/GM/NIGMS NIH HHS/United States ; P30 GM103324/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Arvicolinae/*microbiology/physiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Feeding Behavior ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Kinetics ; Models, Biological ; Phylogeny ; Plants/parasitology ; }, abstract = {As sequencing technologies have advanced, the amount of information regarding the composition of bacterial communities from various environments (for example, skin or soil) has grown exponentially. To date, most work has focused on cataloging taxa present in samples and determining whether the distribution of taxa shifts with exogenous covariates. However, important questions regarding how taxa interact with each other and their environment remain open thus preventing in-depth ecological understanding of microbiomes. Time-series data from 16S rDNA amplicon sequencing are becoming more common within microbial ecology, but methods to infer ecological interactions from these longitudinal data are limited. We address this gap by presenting a method of analysis using Poisson regression fit with an elastic-net penalty that (1) takes advantage of the fact that the data are time series; (2) constrains estimates to allow for the possibility of many more interactions than data; and (3) is scalable enough to handle data consisting of thousands of taxa. We test the method on gut microbiome data from white-throated woodrats (Neotoma albigula) that were fed varying amounts of the plant secondary compound oxalate over a period of 22 days to estimate interactions between OTUs and their environment.}, }
@article {pmid28785816, year = {2018}, author = {Schmidt, PA and Schmitt, I and Otte, J and Bandow, C and Römbke, J and Bálint, M and Rolshausen, G}, title = {Season-Long Experimental Drought Alters Fungal Community Composition but Not Diversity in a Grassland Soil.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {468-478}, pmid = {28785816}, issn = {1432-184X}, mesh = {Biodiversity ; Droughts ; Ecosystem ; Fungi/classification/genetics/*isolation &amp; purification ; Grassland ; Mycobiome ; Phylogeny ; Seasons ; Soil/chemistry ; *Soil Microbiology ; Water/analysis ; }, abstract = {Using terrestrial model ecosystems (TMEs), we investigated how reduced moisture conditions impact soil fungal communities from a temperate grassland over the course of an entire season. Starting at about 65% of the soil's maximum water holding capacity (WHCmax), TME soils were adjusted to three moisture levels for 15 weeks: 70% WHCmax, approximating starting conditions, 50% WHCmax, and 30% WHCmax, representing reduced moisture conditions. Diversity and abundances of soil fungi at the start and at the end of the experiment were characterized using Illumina meta-barcoding. Community diversity at the end of the experiment did not differ between experimental moisture levels and was comparable to diversity measures from the field. However, fungal communities did change compositionally in both abundances and presence/absence of species. Analyzing class-level and individual contributions of fungi to these changes revealed that only a minor portion reacted significantly, indicating that most compositional change was likely driven by many consistent small-scale shifts in presence/absences or abundances. Together, our results show that prolonged reduction in soil moisture conditions will trigger compositional changes in soil fungal communities but not necessarily change overall diversity. We highlight the cumulative contribution of minor but consistent changes among community members, as opposed to significant responses of individual species. We also detected a strong general experimental effect on soil fungi that are moved from the field to experimental TMEs, suggesting the importance of acclimatization effects in these communities under laboratory conditions.}, }
@article {pmid28785722, year = {2017}, author = {The Scientific World Journal, }, title = {Retracted: Microbial Ecology of Anaerobic Digesters: The Key Players of Anaerobiosis.}, journal = {TheScientificWorldJournal}, volume = {2017}, number = {}, pages = {3852369}, pmid = {28785722}, issn = {1537-744X}, abstract = {[This retracts the article DOI: 10.1155/2014/183752.].}, }
@article {pmid28785271, year = {2017}, author = {Cordovez, V and Mommer, L and Moisan, K and Lucas-Barbosa, D and Pierik, R and Mumm, R and Carrion, VJ and Raaijmakers, JM}, title = {Plant Phenotypic and Transcriptional Changes Induced by Volatiles from the Fungal Root Pathogen Rhizoctonia solani.}, journal = {Frontiers in plant science}, volume = {8}, number = {}, pages = {1262}, pmid = {28785271}, issn = {1664-462X}, abstract = {Beneficial soil microorganisms can affect plant growth and resistance by the production of volatile organic compounds (VOCs). Yet, little is known on how VOCs from soil-borne plant pathogens affect plant growth and resistance. Here we show that VOCs released from mycelium and sclerotia of the fungal root pathogen Rhizoctonia solani enhance growth and accelerate development of Arabidopsis thaliana. Seedlings briefly exposed to the fungal VOCs showed similar phenotypes, suggesting that enhanced biomass and accelerated development are primed already at early developmental stages. Fungal VOCs did not affect plant resistance to infection by the VOC-producing pathogen itself but reduced aboveground resistance to the herbivore Mamestra brassicae. Transcriptomics of A. thaliana revealed that genes involved in auxin signaling were up-regulated, whereas ethylene and jasmonic acid signaling pathways were down-regulated by fungal VOCs. Mutants disrupted in these pathways showed similar VOC-mediated growth responses as the wild-type A. thaliana, suggesting that other yet unknown pathways play a more prominent role. We postulate that R. solani uses VOCs to predispose plants for infection from a distance by altering root architecture and enhancing root biomass. Alternatively, plants may use enhanced root growth upon fungal VOC perception to sacrifice part of the root biomass and accelerate development and reproduction to survive infection.}, }
@article {pmid28785257, year = {2017}, author = {Muziasari, WI and Pitkänen, LK and Sørum, H and Stedtfeld, RD and Tiedje, JM and Virta, M}, title = {Corrigendum: The Resistome of Farmed Fish Feces Contributes to the Enrichment of Antibiotic Resistance Genes in Sediments below Baltic Sea Fish Farms.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1491}, doi = {10.3389/fmicb.2017.01491}, pmid = {28785257}, issn = {1664-302X}, abstract = {[This corrects the article on p. 2137 in vol. 7, PMID: 28111573.].}, }
@article {pmid28783713, year = {2017}, author = {Siddharth, J and Chakrabarti, A and Pannérec, A and Karaz, S and Morin-Rivron, D and Masoodi, M and Feige, JN and Parkinson, SJ}, title = {Aging and sarcopenia associate with specific interactions between gut microbes, serum biomarkers and host physiology in rats.}, journal = {Aging}, volume = {9}, number = {7}, pages = {1698-1720}, pmid = {28783713}, issn = {1945-4589}, mesh = {Aging/*physiology ; Animals ; Bacteria/classification ; Biomarkers/blood ; *Gastrointestinal Microbiome/physiology ; Genome, Bacterial ; Genomics ; Host-Pathogen Interactions ; Rats ; *Sarcopenia ; }, abstract = {The microbiome has been demonstrated to play an integral role in the maintenance of many aspects of health that are also associated with aging. In order to identify areas of potential exploration and intervention, we simultaneously characterized age-related alterations in gut microbiome, muscle physiology and serum proteomic and lipidomic profiles in aged rats to define an integrated signature of the aging phenotype. We demonstrate that aging skews the composition of the gut microbiome, in particular by altering the Sutterella to Barneseilla ratio, and alters the metabolic potential of intestinal bacteria. Age-related changes of the gut microbiome were associated with the physiological decline of musculoskeletal function, and with molecular markers of nutrient processing/availability, and inflammatory/immune status in aged versus adult rats. Altogether, our study highlights that aging leads to a complex interplay between the microbiome and host physiology, and provides candidate microbial species to target physical and metabolic decline during aging by modulating gut microbial ecology.}, }
@article {pmid28782508, year = {2017}, author = {Hegazy, AN and West, NR and Stubbington, MJT and Wendt, E and Suijker, KIM and Datsi, A and This, S and Danne, C and Campion, S and Duncan, SH and Owens, BMJ and Uhlig, HH and McMichael, A and ,  and Bergthaler, A and Teichmann, SA and Keshav, S and Powrie, F}, title = {Circulating and Tissue-Resident CD4[+] T Cells With Reactivity to Intestinal Microbiota Are Abundant in Healthy Individuals and Function Is Altered During Inflammation.}, journal = {Gastroenterology}, volume = {153}, number = {5}, pages = {1320-1337.e16}, pmid = {28782508}, issn = {1528-0012}, support = {UM1 AI100645/AI/NIAID NIH HHS/United States ; G0200231/MRC_/Medical Research Council/United Kingdom ; 260507/ERC_/European Research Council/International ; /WT_/Wellcome Trust/United Kingdom ; MC_UU_00008/7/MRC_/Medical Research Council/United Kingdom ; MC_UU_12010/7/MRC_/Medical Research Council/United Kingdom ; NIHR-RP-R3-12-026/DH_/Department of Health/United Kingdom ; }, mesh = {Bacteria/classification/*immunology ; CD4 Lymphocyte Count ; CD4-Positive T-Lymphocytes/*immunology/microbiology ; Case-Control Studies ; Cell Line ; Colitis, Ulcerative/blood/diagnosis/*immunology ; Crohn Disease/blood/diagnosis/*immunology ; Gastrointestinal Microbiome/*immunology ; Host-Pathogen Interactions ; Humans ; Immunity, Mucosal ; Immunologic Memory ; Interleukin-17/immunology ; Intestines/*immunology/microbiology ; Phenotype ; Receptors, Antigen, T-Cell, alpha-beta/immunology ; Th17 Cells/immunology/microbiology ; }, abstract = {BACKGROUND &amp; AIMS: Interactions between commensal microbes and the immune system are tightly regulated and maintain intestinal homeostasis, but little is known about these interactions in humans. We investigated responses of human CD4[+] T cells to the intestinal microbiota. We measured the abundance of T cells in circulation and intestinal tissues that respond to intestinal microbes and determined their clonal diversity. We also assessed their functional phenotypes and effects on intestinal resident cell populations, and studied alterations in microbe-reactive T cells in patients with chronic intestinal inflammation.<br><br>METHODS: We collected samples of peripheral blood mononuclear cells and intestinal tissues from healthy individuals (controls, n&#xa0;= 13-30) and patients with inflammatory bowel diseases (n&#xa0;= 119; 59 with ulcerative colitis and 60 with Crohn's disease). We used 2 independent assays (CD154 detection and carboxy-fluorescein succinimidyl ester dilution assays) and 9 intestinal bacterial species (Escherichia coli, Lactobacillus acidophilus, Bifidobacterium animalis subsp lactis, Faecalibacterium prausnitzii, Bacteroides vulgatus, Roseburia intestinalis, Ruminococcus obeum, Salmonella typhimurium, and Clostridium difficile) to quantify, expand, and characterize microbe-reactive CD4[+] T&#xa0;cells. We sequenced T-cell receptor V&#x3b2; genes in expanded microbe-reactive T-cell lines to determine their clonal diversity. We examined the effects of microbe-reactive CD4[+] T&#xa0;cells on intestinal stromal and epithelial cell lines. Cytokines, chemokines, and gene expression patterns were measured by flow cytometry and quantitative polymerase chain reaction.<br><br>RESULTS: Circulating and gut-resident CD4[+] T cells from controls responded to bacteria at frequencies of 40-4000 per million for each bacterial species tested. Microbiota-reactive CD4[+] T cells were mainly of a memory phenotype, present in peripheral blood mononuclear cells and intestinal tissue, and had a diverse T-cell receptor V&#x3b2;&#xa0;repertoire. These cells were functionally heterogeneous, produced barrier-protective cytokines, and stimulated intestinal stromal and epithelial cells via interleukin 17A, interferon gamma, and tumor necrosis factor. In patients with inflammatory bowel diseases, microbiota-reactive CD4[+] T cells were reduced in the blood compared with intestine; T-cell responses that we detected had an increased frequency of interleukin 17A production compared with responses of T cells from blood or intestinal tissues of controls.<br><br>CONCLUSIONS: In an analysis of peripheral blood mononuclear cells and intestinal tissues from patients with inflammatory bowel diseases vs controls, we found that reactivity to intestinal bacteria is a normal property of the human CD4[+] T-cell repertoire, and does not necessarily indicate disrupted interactions between immune cells and the commensal microbiota. T-cell responses to commensals might support intestinal homeostasis, by producing barrier-protective cytokines and providing a large pool of T cells that react to pathogens.}, }
@article {pmid28779297, year = {2018}, author = {Hyder, R and Piri, T and Hantula, J and Nuorteva, H and Vainio, EJ}, title = {Distribution of Viruses Inhabiting Heterobasidion annosum in a Pine-Dominated Forest Plot in Southern Finland.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {622-630}, pmid = {28779297}, issn = {1432-184X}, support = {251193, 258520//Suomen Akatemia/ ; }, mesh = {Basidiomycota/isolation &amp; purification/pathogenicity/*virology ; *Biodiversity ; Coinfection/virology ; Finland ; *Forests ; Fungal Viruses/classification/genetics/isolation &amp; purification/*physiology ; Genes, Viral/genetics ; Genetic Variation ; Genome, Viral ; Pinus/*microbiology ; Plant Diseases/*microbiology/prevention &amp; control ; RNA Viruses/classification/genetics/isolation &amp; purification/*physiology ; RNA, Viral/genetics/isolation &amp; purification ; Sequence Analysis ; Virus Physiological Phenomena ; }, abstract = {We investigated the diversity and spatial distribution of viruses infecting strains of the root rot fungus Heterobasidion annosum collected from pine stumps at a heavily infected forest site. Four different partitiviruses were detected in 14 H. annosum isolates at the study site, constituting approximately 29% of all Heterobasidion isolates investigated (N = 48). Two of the viruses detected were new partitiviruses designated here as Heterobasidion partitivirus 16 (HetPV16) and HetPV20, and two were previously known partitiviruses: HetPV7 and HetPV13. The two new partitiviruses found, HetPV16-an1 and HetPV20-an1, shared ~70% RdRp nucleotide sequence identity with the alphapartitivirus Rosellinia necatrix partitivirus 2, and less than 40% identity with known viruses of Heterobasidion spp. HetPV7-an1 was closely similar to HetPV7-pa1 isolated earlier from Heterobasidion parviporum, supporting the view of conspecific virus pools in different Heterobasidion species. Three fungal isolates were found to be co-infected with two different partitivirus strains (HetPV7-an1 and HetPV13-an2 or HetPV16-an1 and HetPV20-an1). Different isolates representing each host clone had variable virus compositions, and virus strains occurring in more than one host clone showed minor sequence variations between clones.}, }
@article {pmid28779296, year = {2018}, author = {Lavergne, C and Hugoni, M and Hubas, C and Debroas, D and Dupuy, C and Agogué, H}, title = {Diel Rhythm Does Not Shape the Vertical Distribution of Bacterial and Archaeal 16S rRNA Transcript Diversity in Intertidal Sediments: a Mesocosm Study.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {364-374}, pmid = {28779296}, issn = {1432-184X}, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Ecosystem ; Geologic Sediments/*chemistry/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {In intertidal sediments, circadian oscillations (i.e., tidal and diel rhythms) and/or depth may affect prokaryotic activity. However, it is difficult to distinguish the effect of each single force on active community changes in these natural and complex intertidal ecosystems. Therefore, we developed a tidal mesocosm to control the tidal rhythm and test whether diel fluctuation or sediment depth influence active prokaryotes in the top 10 cm of sediment. Day- and nighttime emersions were compared as they are expected to display contrasting conditions through microphytobenthic activity in five different sediment layers. A multiple factor analysis revealed that bacterial and archaeal 16S ribosomal RNA (rRNA) transcript diversity assessed by pyrosequencing was similar between day and night emersions. Potentially active benthic Bacteria were highly diverse and influenced by chlorophyll a and phosphate concentrations. While in oxic and suboxic sediments, Thaumarchaeota Marine Group I (MGI) was the most active archaeal phylum, suggesting the importance of the nitrogen cycle in muddy sediments, in anoxic sediments, the mysterious archaeal C3 group dominated the community. This work highlighted that active prokaryotes organize themselves vertically within sediments independently of diel fluctuations suggesting adaptation to physicochemical-specific conditions associated with sediment depth.}, }
@article {pmid28779295, year = {2018}, author = {Tin, HS and Palaniveloo, K and Anilik, J and Vickneswaran, M and Tashiro, Y and Vairappan, CS and Sakai, K}, title = {Impact of Land-use Change on Vertical Soil Bacterial Communities in Sabah.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {459-467}, pmid = {28779295}, issn = {1432-184X}, mesh = {Agriculture ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Ecosystem ; Forests ; Malaysia ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Decline in forest productivity due to forest conversion is defining the Bornean landscape. Responses of bacterial communities due to land-use changes are vital and could define our understanding of ecosystem functions. This study reports the changes in bacterial community structure in organic soil (0-5 cm; O-Horizon) and organic-mineral soil (5-15 cm; A-Horizon) across Maliau Basin Conservation Area old growth forest (MBOG), Fragment E logged forest (FELF) located in Kalabakan Forest Reserve to Benta Wawasan oil palm plantation (BWOP) using two-step PCR amplicon analysis of bacteria DNA on Illumina Miseq next generation sequencing. A total of 30 soil samples yielded 893,752-OTU reads at ≥97% similarity from 5,446,512 good quality sequences. Soil from BWOP plantation showed highest unshared OTUs for organic (49.2%) and organic-mineral (50.9%) soil. MBOG soil showed a drop in unshared OTUs between organic (48.6%) and organic-mineral (33.9%). At phylum level, Proteobacteria dominated MBOG but shifted to Actinobacteria in logged and plantation soil. Present findings also indicated that only FELF exhibited change in bacterial communities along the soil depth, moving from the organic to the organic-mineral layer. Both layers of BWOP plantation soils deviated from other forests' soil in β-diversity analysis. To our knowledge, this is the first report on transitions of bacterial community structures with different soil horizons in the tropical rainforest including Borneo, Sabah. Borneo tropical soils form a large reservoir for soil bacteria and future exploration is needed for fully understanding the diversity structure and their bacterial functional properties.}, }
@article {pmid28779294, year = {2018}, author = {Sousa, NMF and Veresoglou, SD and Oehl, F and Rillig, MC and Maia, LC}, title = {Predictors of Arbuscular Mycorrhizal Fungal Communities in the Brazilian Tropical Dry Forest.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {447-458}, pmid = {28779294}, issn = {1432-184X}, support = {1374510//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; 206415/2014-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; }, mesh = {Altitude ; Biodiversity ; Brazil ; Ecosystem ; Forests ; Fungi/classification/genetics/*isolation &amp; purification ; Mycobiome ; Mycorrhizae/classification/genetics/*isolation &amp; purification ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) are symbiotic fungi with a broad distribution, and many taxa have physiological and ecological adaptations to specific environments, including semiarid ecosystems. Our aim was to address regional distribution patterns of AMF communities in such semiarid environments based on spore morphological techniques. We assessed AMF spores at the bottom and top of inselbergs distributed throughout the tropical dry forest in the Northeast region of Brazil. Across 10 replicate inselbergs and the surrounding area, spanning a range of altitude between 140 and 2000 m, we scored the AMF soil diversity and properties in 52 plots. We fitted parsimonious ordination analyses and variance partitioning models to determine the environmental factors which explained the variation in AMF community, based on morphological spore analysis. The diversity of AMF was similar at the bottom and top of inselbergs; however, we detected high variation in abundance and richness across sites. We formulated a parsimonious richness model that used physical soil factors as predictors. The AMF community structure could be best explained through the variables coarse and total sand, iron, organic matter, potassium, silt, and sodium which together accounted for 17.8% of total variance. Several AMF species were indicators of either deficiency or high values of specific soil properties. We demonstrated that habitat isolation of the inselbergs compared with surrounding areas did not trigger differences in AMF communities in semiarid regions of Brazil. At the regional scale, soil predictors across sites drove the distribution of symbiotic mycorrhizal fungi.}, }
@article {pmid28779293, year = {2018}, author = {García-Mena, J and Murugesan, S and Pérez-Muñoz, AA and García-Espitia, M and Maya, O and Jacinto-Montiel, M and Monsalvo-Ponce, G and Piña-Escobedo, A and Domínguez-Malfavón, L and Gómez-Ramírez, M and Cervantes-Gonzáles, E and Núñez-Cardona, MT}, title = {Erratum to: Airborne bacterial diversity from the low atmosphere of Greater Mexico City.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {819}, doi = {10.1007/s00248-017-1046-3}, pmid = {28779293}, issn = {1432-184X}, }
@article {pmid28778896, year = {2017}, author = {Justice, NB and Sczesnak, A and Hazen, TC and Arkin, AP}, title = {Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {20}, pages = {}, pmid = {28778896}, issn = {1098-5336}, support = {F32 GM113547/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Environmental Microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Nitrates/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A central goal of microbial ecology is to identify and quantify the forces that lead to observed population distributions and dynamics. However, these forces, which include environmental selection, dispersal, and organism interactions, are often difficult to assess in natural environments. Here, we present a method that links microbial community structures with selective and stochastic forces through highly replicated subsampling and enrichment of a single environmental inoculum. Specifically, groundwater from a well-studied natural aquifer was serially diluted and inoculated into nearly 1,000 aerobic and anaerobic nitrate-reducing cultures, and the final community structures were evaluated with 16S rRNA gene amplicon sequencing. We analyzed the frequency and abundance of individual operational taxonomic units (OTUs) to understand how probabilistic immigration, relative fitness differences, environmental factors, and organismal interactions contributed to divergent distributions of community structures. We further used a most probable number (MPN) method to estimate the natural condition-dependent cultivable abundance of each of the nearly 400 OTU cultivated in our study and infer the relative fitness of each. Additionally, we infer condition-specific organism interactions and discuss how this high-replicate culturing approach is essential in dissecting the interplay between overlapping ecological forces and taxon-specific attributes that underpin microbial community assembly.IMPORTANCE Through highly replicated culturing, in which inocula are subsampled from a single environmental sample, we empirically determine how selective forces, interspecific interactions, relative fitness, and probabilistic dispersal shape bacterial communities. These methods offer a novel approach to untangle not only interspecific interactions but also taxon-specific fitness differences that manifest across different cultivation conditions and lead to the selection and enrichment of specific organisms. Additionally, we provide a method for estimating the number of cultivable units of each OTU in the original sample through the MPN approach.}, }
@article {pmid28777379, year = {2017}, author = {Handley, KM and Piceno, YM and Hu, P and Tom, LM and Mason, OU and Andersen, GL and Jansson, JK and Gilbert, JA}, title = {Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill.}, journal = {The ISME journal}, volume = {11}, number = {11}, pages = {2569-2583}, pmid = {28777379}, issn = {1751-7370}, mesh = {Alkanes/analysis/metabolism ; Bacteria/*classification/genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Geologic Sediments/analysis/*microbiology ; Gulf of Mexico ; Petroleum/metabolism ; Petroleum Pollution/analysis ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/analysis/metabolism ; Seawater/analysis/*microbiology ; Water Pollutants, Chemical/analysis/*metabolism ; }, abstract = {The release of 700 million liters of oil into the Gulf of Mexico over a few months in 2010 produced dramatic changes in the microbial ecology of the water and sediment. Here, we reconstructed the genomes of 57 widespread uncultivated bacteria from post-spill deep-sea sediments, and recovered their gene expression pattern across the seafloor. These genomes comprised a common collection of bacteria that were enriched in heavily affected sediments around the wellhead. Although rare in distal sediments, some members were still detectable at sites up to 60 km away. Many of these genomes exhibited phylogenetic clustering indicative of common trait selection by the environment, and within half we identified 264 genes associated with hydrocarbon degradation. Alkane degradation ability was near ubiquitous among candidate hydrocarbon degraders, whereas just three harbored elaborate gene inventories for the degradation of alkanes and aromatic and polycyclic aromatic hydrocarbons (PAHs). Differential gene expression profiles revealed a spill-promoted microbial sulfur cycle alongside gene upregulation associated with PAH degradation. Gene expression associated with alkane degradation was widespread, although active alkane degrader identities changed along the pollution gradient. Analyses suggest that a broad metabolic capacity to respond to oil inputs exists across a large array of usually rare indigenous deep-sea bacteria.}, }
@article {pmid28776044, year = {2017}, author = {Ransom-Jones, E and McCarthy, AJ and Haldenby, S and Doonan, J and McDonald, JE}, title = {Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity.}, journal = {mSphere}, volume = {2}, number = {4}, pages = {}, pmid = {28776044}, issn = {2379-5042}, support = {G0900753/MRC_/Medical Research Council/United Kingdom ; MR/K002279/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {The microbial conversion of lignocellulosic biomass for biofuel production represents a renewable alternative to fossil fuels. However, the discovery of new microbial enzymes with high activity is critical for improving biomass conversion processes. While attempts to identify superior lignocellulose-degrading enzymes have focused predominantly on the animal gut, biomass-degrading communities in landfill sites represent an unexplored resource of hydrolytic enzymes for biomass conversion. Here, to address the paucity of information on biomass-degrading microbial diversity beyond the gastrointestinal tract, cellulose (cotton) "baits" were incubated in landfill leachate microcosms to enrich the landfill cellulolytic microbial community for taxonomic and functional characterization. Metagenome and 16S rRNA gene amplicon sequencing demonstrated the dominance of Firmicutes, Bacteroidetes, Spirochaetes, and Fibrobacteres in the landfill cellulolytic community. Functional metagenome analysis revealed 8,371 carbohydrate active enzymes (CAZymes) belonging to 244 CAZyme families. In addition to observing biomass-degrading enzymes of anaerobic bacterial "cellulosome" systems of members of the Firmicutes, we report the first detection of the Fibrobacter cellulase system and the Bacteroidetes polysaccharide utilization locus (PUL) in landfill sites. These data provide evidence for the presence of multiple mechanisms of biomass degradation in the landfill microbiome and highlight the extraordinary functional diversity of landfill microorganisms as a rich source of biomass-degrading enzymes of potential biotechnological significance. IMPORTANCE The microbial conversion of lignocellulosic biomass for biofuel production represents a renewable alternative to fossil fuels. However, the discovery of new microbial enzymes with high activity is critical for improving biomass conversion processes. While attempts to identify superior lignocellulose-degrading enzymes have focused predominantly on the animal gut, biomass-degrading communities in landfill sites represent an unexplored resource of hydrolytic enzymes for biomass conversion. Here, we identified Firmicutes, Spirochaetes, and Fibrobacteres as key phyla in the landfill cellulolytic community, detecting 8,371 carbohydrate active enzymes (CAZymes) that represent at least three of the recognized strategies for cellulose decomposition. These data highlight substantial hydrolytic enzyme diversity in landfill sites as a source of new enzymes for biomass conversion.}, }
@article {pmid28772023, year = {2018}, author = {Dyksma, S and Pjevac, P and Ovanesov, K and Mussmann, M}, title = {Evidence for H2 consumption by uncultured Desulfobacterales in coastal sediments.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {450-461}, doi = {10.1111/1462-2920.13880}, pmid = {28772023}, issn = {1462-2920}, mesh = {Deltaproteobacteria/genetics/isolation &amp; purification/*metabolism ; Geologic Sediments/*microbiology ; Hydrogen/*metabolism ; Metagenomics ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Sulfates/metabolism ; }, abstract = {Molecular hydrogen (H2) is the key intermediate in the anaerobic degradation of organic matter. Its removal by H2 -oxidizing microorganisms is essential to keep anaerobic degradation energetically favourable. Sulfate-reducing microorganisms (SRM) are known as the main H2 scavengers in anoxic marine sediments. Although the community of marine SRM has been extensively studied, those consuming H2 in situ are completely unknown. We combined metagenomics, PCR-based clone libraries, single-amplified genomes (SAGs) and metatranscriptomics to identify potentially H2 -consuming SRM in anoxic coastal sediments. The vast majority of SRM-related H2 ase sequences were assigned to group 1b and 1c [NiFe]-H2 ases of the deltaproteobacterial order Desulfobacterales. Surprisingly, the same sequence types were similarly highly expressed in spring and summer, suggesting that these are stable and integral members of the H2 -consuming community. Notably, one sequence cluster from the SRM group 1 consistently accounted for around half of all [NiFe]-H2 ase transcripts. Using SAGs, we could link this cluster with the 16S rRNA genes of the uncultured Sva0081-group of the family Desulfobacteraceae. Sequencing of 16S rRNA gene amplicons and H2 ase gene libraries suggested consistently high in situ abundance of the Sva0081 group also in other marine sediments. Together with other Desulfobacterales these likely are important H2 -scavengers in marine sediments.}, }
@article {pmid28771931, year = {2017}, author = {Verstraete, W and De Vrieze, J}, title = {Microbial technology with major potentials for the urgent environmental needs of the next decades.}, journal = {Microbial biotechnology}, volume = {10}, number = {5}, pages = {988-994}, pmid = {28771931}, issn = {1751-7915}, mesh = {Archaea/genetics/*metabolism ; Biodegradation, Environmental ; Climate Change ; Environment ; Industrial Microbiology/methods/*trends ; Methane/metabolism ; Nitrogen Cycle ; }, abstract = {Several needs in the context of the water-energy-food nexus will become more prominent in the next decades. It is crucial to delineate these challenges and to find opportunities for innovative microbial technologies in the framework of sustainability and climate change. Here, we focus on four key issues, that is the imbalance in the nitrogen cycle, the diffuse emission of methane, the necessity for carbon capture and the deterioration of freshwater reserves. We suggest a set of microbial technologies to deal with each of these issues, such as (i) the production of microbial protein as food and feed, (ii) the control of methanogenic archaea and better use of methanotrophic consortia, (iii) the avoidance of nitrification and (iv) the upgrading of CO2 to microbial bioproducts. The central message is that instead of using crude methods to exploit microorganisms for degradations, the potentials of the microbiomes should be used to create processes and products that fit the demands of the cyclic market economy.}, }
@article {pmid28771569, year = {2017}, author = {Lin, Y and Xu, S and Zeng, D and Ni, X and Zhou, M and Zeng, Y and Wang, H and Zhou, Y and Zhu, H and Pan, K and Li, G}, title = {Disruption in the cecal microbiota of chickens challenged with Clostridium perfringens and other factors was alleviated by Bacillus licheniformis supplementation.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0182426}, pmid = {28771569}, issn = {1932-6203}, mesh = {Animals ; Bacillus licheniformis/*physiology ; Cecum/*microbiology ; Chickens ; Clostridium Infections/microbiology/*veterinary ; Clostridium perfringens/*pathogenicity ; *Dietary Supplements ; Microbiota/*physiology ; Phylogeny ; Poultry Diseases/microbiology/*therapy ; }, abstract = {Clostridium perfringens can induce necrotic enteritis of chickens, which causes large economic losses every year. Bacillus licheniformis, a probiotic, can inhibit the growth of pathogenic bacteria such as Clostridium perfringens, thereby improving the health status of chickens. However, from a microbial ecology perspective, the mechanisms by which alterations to the gut microbiota improve health remain unknown. In this study, we used Illumina MiSeq sequencing to investigate the cecal microbiota of a negative control group (NC), a C. perfringens and Eimeria challenge group with fishmeal supplementation (PC), a group supplemented with fishmeal and infected with coccidia (FC), and group PC with B. licheniformis supplementation (BL). We found that the health status of C. perfringens-challenged chickens was compromised, and that B. licheniformis improved the growth of the chickens challenged with pathogens. Microbial diversity analysis and taxonomic profiling of groups NC, PC, and FC revealed a disturbed cecal microflora of the birds with C. perfringens. We also characterized the microbiota of the chickens in the BL group using several methods. Principal coordinate analysis demonstrated that, compared with group PC, the bacterial community structure of group BL was more similar to that of group NC. Linear discriminant analysis with effect size revealed less differentially represented bacterial taxa between groups BL and NC than between groups PC and NC. In addition, groups BL and NC appeared to have similar overrepresented microbial taxa (such as Bacteroides, Helicobacter, Megamonas, and Akkermansia) compared with group PC. Finally, a phylogenetic investigation of communities by reconstruction of unobserved states analysis indicated that large differences existed between group PC and groups NC and BL. In conclusion, pre-treatment with B. licheniformis reduced the disturbance of the cecal microbiome induced by challenge with C. perfringens and other factors in broiler chickens.}, }
@article {pmid28769920, year = {2017}, author = {Sidhu, C and Vikram, S and Pinnaka, AK}, title = {Unraveling the Microbial Interactions and Metabolic Potentials in Pre- and Post-treated Sludge from a Wastewater Treatment Plant Using Metagenomic Studies.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1382}, pmid = {28769920}, issn = {1664-302X}, abstract = {Sewage waste represents an ecosystem of complex and interactive microbial consortia which proliferate with different kinetics according to their individual genetic as well as metabolic potential. We performed metagenomic shotgun sequencing on Ion-Torrent platform, to explore the microbial community structure, their biological interactions and associated functional capacity of pre-treated/raw sludge (RS) and post-treated/dried sludge (DS) of wastewater treatment plant. Bacterial phylotypes belonging to Epsilonproteobacteria (∼45.80%) dominated the RS with relatively few Archaea (∼1.94%) whereas DS has the dominance of beta- (30.23%) and delta- (13.38%) classes of Proteobacteria with relatively greater abundance of Archaea (∼7.18%). In particular, Epsilonproteobacteria appears as a primary energy source in RS and sulfur-reducing bacteria with methanogens seems to be in the potential syntrophic association in DS. These interactions could be ultimately responsible for carrying out amino-acid degradation, aromatic compound degradation and degradation of propionate and butyrate in DS. Our data also reveal the presence of key genes in the sludge microbial community responsible for degradation of polycyclic aromatic hydrocarbons. Potential pathogenic microbes and genes for the virulence factors were found to be relatively abundant in RS which clearly reflect the necessity of treatment of RS. After treatment, potential pathogens load was reduced, indicating the sludge hygienisation in DS. Additionally, the interactions found in this study would reveal the biological and environmental cooperation among microbial communities for domestic wastewater treatment.}, }
@article {pmid28768551, year = {2017}, author = {Gao, P and Ma, C and Sun, Z and Wang, L and Huang, S and Su, X and Xu, J and Zhang, H}, title = {Feed-additive probiotics accelerate yet antibiotics delay intestinal microbiota maturation in broiler chicken.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {91}, pmid = {28768551}, issn = {2049-2618}, mesh = {Animal Feed/*microbiology ; Animals ; Anti-Bacterial Agents/administration &amp; dosage/*pharmacology ; Chickens/*microbiology ; Drug Resistance, Bacterial ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; High-Throughput Nucleotide Sequencing ; Intestines/microbiology ; Lactobacillus/growth &amp; development/isolation &amp; purification/physiology ; Metagenome ; Probiotics/*administration &amp; dosage ; }, abstract = {BACKGROUND: Reducing antibiotics overuse in animal agriculture is one key in combat against the spread of antibiotic resistance. Probiotics are a potential replacement of antibiotics in animal feed; however, it is not clear whether and how probiotics and antibiotics differ in impact on physiology and microbial ecology of host animals.<br><br>RESULTS: Host phenotype and fecal microbiota of broilers with either antibiotics or probiotics as feed additive were simultaneously sampled at four time points from birth to slaughter and then compared. Probiotic feeding resulted in a lower feed conversion ratio (FCR) and induced the highest level of immunity response, suggesting greater economic benefits in broiler farming. Probiotic use but not antibiotic use recapitulated the characteristics of age-dependent development of gut microbiota in the control group. The maturation of intestinal microbiota was greatly accelerated by probiotic feeding, yet significantly retarded and eventually delayed by antibiotic feeding. LP-8 stimulated the growth of many intestinal Lactobacillus spp. and led to an altered bacterial correlation network where Lactobacillus spp. are negatively correlated with 14 genera and positively linked with none, yet from the start antibiotic feeding featured a less-organized network where such inter-genera interactions were fewer and weaker. Consistently, microbiota-encoded functions as revealed by metagenome sequencing were highly distinct between the two groups. Thus, "intestinal microbiota maturation index" was proposed to quantitatively compare impact of feed additives on animal microecology.<br><br>CONCLUSIONS: Our results reveal a tremendous potential of probiotics as antibiotics' substitute in poultry farming.}, }
@article {pmid28765980, year = {2018}, author = {Wu, SH and Huang, BH and Huang, CL and Li, G and Liao, PC}, title = {The Aboveground Vegetation Type and Underground Soil Property Mediate the Divergence of Soil Microbiomes and the Biological Interactions.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {434-446}, pmid = {28765980}, issn = {1432-184X}, support = {MOST 105-2628-B-003-001-MY3//Ministry of Science and Technology, Taiwan/ ; 105-2628-B-003-002-MY3//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Ecosystem ; Forests ; *Microbiota ; Poaceae/classification/*growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil/*chemistry ; *Soil Microbiology ; Trees/classification/*growth &amp; development ; }, abstract = {The composition of the soil microbiome is influenced by environmental (abiotic) variables and biological interactions (biotic factors). To determine whether the aboveground vegetation and soil physicochemical properties were the main determinant of beta-diversity and biological interaction of soil microbial community, we sampled soils from the temperate coniferous forest and grassland. Clustering of operational taxonomic units was conducted using 16S rRNA gene. We found that the microbial composition of the rhizospheres, in which root exudates influence the microbial environment, show lower alpha-diversity than that of nonroot soils. The nonsignificant rhizosphere effect suggested other undetermined factors or stochastic processes accounted for microbial diversity in the rhizosphere. More significant microbe-microbe interactions were observed in forest and rhizosphere soils relative to the grassland soils. The elevated number of positive correlations for relative abundances in forest soil implied beneficial associations being common among bacteria, in particular within the rhizosphere environment. The particular soil properties generated by root exudates also alter the physicochemical properties of soil such as K and pH value, and might in turn favor the adoption of teamwork-cooperation strategies for microbe-microbe interactions, represented as large clusters of positive associations among bacterial taxa. Specific biological interactions differentiated the microbiomes within forest soils. Thus, the environmental selection pressure of aboveground vegetation accounts for differences between soil microbiomes while biotic factors are responsible for fine-scale differences of the microbial community in forest soils.}, }
@article {pmid28765630, year = {2017}, author = {Zhang, X and Guo, K and Shen, D and Feng, H and Wang, M and Zhou, Y and Jia, Y and Liang, Y and Zhou, M}, title = {Carbon black as an alternative cathode material for electrical energy recovery and transfer in a microbial battery.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6981}, pmid = {28765630}, issn = {2045-2322}, abstract = {Rather than the conventional concept of viewing conductive carbon black (CB) to be chemically inert in microbial electrochemical cells (MECs), here we confirmed the redox activity of CB for its feasibility as an electron sink in the microbial battery (MB). Acting as the cathode of a MB, the solid-state CB electrode showed the highest electron capacity equivalent of 18.58 ± 0.46 C/g for the unsintered one and the lowest capacity of 2.29 ± 0.48 C/g for the one sintered under 100% N2 atmosphere. The capacity vibrations of CBs were strongly in coincidence with the abundances of C=O moiety caused by different pretreatments and it implied one plausible mechanism based on CB's surface functionality for its electron capturing. Once subjected to electron saturation, CB could be completely regenerated by different strategies in terms of electrochemical discharging or donating electrons to biologically-catalyzed nitrate reduction. Surface characterization also revealed that CB's regeneration fully depended on the reversible shift of C=O moiety, further confirming the functionality-based mechanism for CB's feasibility as the role of MB's cathode. Moreover, resilience tests demonstrated that CB cathode was robust for the multi-cycles charging-discharging operations. These results imply that CB is a promising alternative material for the solid-state cathode in MBs.}, }
@article {pmid28761776, year = {2017}, author = {Geyer, KM and Takacs-Vesbach, CD and Gooseff, MN and Barrett, JE}, title = {Primary productivity as a control over soil microbial diversity along environmental gradients in a polar desert ecosystem.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3377}, pmid = {28761776}, issn = {2167-8359}, abstract = {Primary production is the fundamental source of energy to foodwebs and ecosystems, and is thus an important constraint on soil communities. This coupling is particularly evident in polar terrestrial ecosystems where biological diversity and activity is tightly constrained by edaphic gradients of productivity (e.g., soil moisture, organic carbon availability) and geochemical severity (e.g., pH, electrical conductivity). In the McMurdo Dry Valleys of Antarctica, environmental gradients determine numerous properties of soil communities and yet relatively few estimates of gross or net primary productivity (GPP, NPP) exist for this region. Here we describe a survey utilizing pulse amplitude modulation (PAM) fluorometry to estimate rates of GPP across a broad environmental gradient along with belowground microbial diversity and decomposition. PAM estimates of GPP ranged from an average of 0.27 μmol O2/m[2]/s in the most arid soils to an average of 6.97 μmol O2/m[2]/s in the most productive soils, the latter equivalent to 217 g C/m[2]/y in annual NPP assuming a 60 day growing season. A diversity index of four carbon-acquiring enzyme activities also increased with soil productivity, suggesting that the diversity of organic substrates in mesic environments may be an additional driver of microbial diversity. Overall, soil productivity was a stronger predictor of microbial diversity and enzymatic activity than any estimate of geochemical severity. These results highlight the fundamental role of environmental gradients to control community diversity and the dynamics of ecosystem-scale carbon pools in arid systems.}, }
@article {pmid28759322, year = {2017}, author = {McGee, CF and Byrne, H and Irvine, A and Wilson, J}, title = {Diversity and dynamics of the DNA- and cDNA-derived compost fungal communities throughout the commercial cultivation process for Agaricus bisporus.}, journal = {Mycologia}, volume = {109}, number = {3}, pages = {475-484}, doi = {10.1080/00275514.2017.1349498}, pmid = {28759322}, issn = {0027-5514}, mesh = {Agaricus/*growth &amp; development ; *Biota ; Cluster Analysis ; *Composting ; DNA, Complementary/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Fungi/*classification/*genetics ; *Genetic Variation ; Phylogeny ; RNA, Ribosomal, 5.8S/genetics ; Sequence Analysis, DNA ; }, abstract = {Commercial cultivation of the button mushroom Agaricus bisporus is performed through the inoculation of a semipasteurized composted material. Pasteurization of the compost material prior to inoculation results in a substrate with a fungal community that becomes dominated by A. bisporus. However, little is known about the composition and activity in the wider fungal community beyond the presence of A. bisporus in compost throughout the mushroom cropping process. In this study, the fungal cropping compost community was characterized by sequencing nuc rDNA ITS1-5.8S-ITS2 amplified from extractable DNA and RNA. The fungal community generated from DNA extracts identified a diverse community containing 211 unique species, although only 51 were identified from cDNA. Agaricus bisporus was found to dominate in the DNA-derived fungal community for the duration of the cropping process. However, analysis of cDNA extracts found A. bisporus to dominate only up to the first crop flush, after which activity decreased sharply and a much broader fungal community became active. This study has highlighted the diverse fungal community that is present in mushroom compost during cropping.}, }
@article {pmid28758626, year = {2017}, author = {Cho, GY and Lee, JC and Whang, KS}, title = {Aliifodinibius salicampi sp. nov., a moderately halophilic bacterium isolated from a grey saltern.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {67}, number = {8}, pages = {2598-2603}, doi = {10.1099/ijsem.0.001981}, pmid = {28758626}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Geologic Sediments/*microbiology ; Gram-Negative Bacteria/*classification/genetics/isolation &amp; purification ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Salinity ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry ; *Water Microbiology ; }, abstract = {Three strains of a Gram-stain-negative, moderately halophilic bacterium, designated strain KHM44T, KHM29 and HHM4, were isolated from the sediment of a grey saltern located on Sinui island at Shinan, Korea. The isolates were aerobic, non-motile rods and grew at 15-50 °C (optimum, 37 °C), at pH 6.0-9.0 (optimum, pH 8.0) and at salinities of 3-25 % (w/v) NaCl (optimum, 10 % NaCl). The predominant isoprenoid quinone was menaquinone-7 (MK-7), and the major fatty acids were iso-C15 : 0, C16 : 1ω7c and/or iso-C15 : 0 2-OH, iso-C17 : 1ω9c and anteiso-C15 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and glycolipid. The DNA G+C contents were 48.5-48.7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains KHM44T, KHM29 and HHM4 belonged to the genus Aliifodinibius in the family Balneolaceae, with sequence similarities of 95.1-97.2 % to members of this genus. Levels of DNA-DNA relatedness between strain KHM44T and the type strains of the other species of the genus Aliifodinibius ranged from 35.4 to 48.0 %. On the basis of polyphasic analysis from this study, strains KHM44T, KHM29 and HHM4 are considered to represent a novel species of the genus Aliifodinibius, for which the name Aliifodinibius salicampi sp. nov. is proposed. The type strain is KHM44T (=KACC 19060T=NBRC 112531T).}, }
@article {pmid28758303, year = {2017}, author = {Ebersole, JL and Dawson, D and Emecen-Huja, P and Nagarajan, R and Howard, K and Grady, ME and Thompson, K and Peyyala, R and Al-Attar, A and Lethbridge, K and Kirakodu, S and Gonzalez, OA}, title = {The periodontal war: microbes and immunity.}, journal = {Periodontology 2000}, volume = {75}, number = {1}, pages = {52-115}, doi = {10.1111/prd.12222}, pmid = {28758303}, issn = {1600-0757}, mesh = {Biofilms ; Host-Pathogen Interactions/*immunology ; Humans ; Microbiota/immunology ; Mouth/*microbiology ; Periodontitis/*immunology/*microbiology ; }, abstract = {Maintenance of periodontal health or transition to a periodontal lesion reflects the continuous and ongoing battle between the vast microbial ecology in the oral cavity and the array of resident and emigrating inflammatory/immune cells in the periodontium. This war clearly signifies many 'battlefronts' representing the interface of the mucosal-surface cells with the dynamic biofilms composed of commensal and potential pathogenic species, as well as more recent knowledge demonstrating active invasion of cells and tissues of the periodontium leading to skirmishes in connective tissue, the locality of bone and even in the local vasculature. Research in the discipline has uncovered a concerted effort of the microbiome, using an array of survival strategies, to interact with other bacteria and host cells. These strategies aid in colonization by 'ambushing, infiltrating and outflanking' host cells and molecules, responding to local environmental changes (including booby traps for host biomolecules), communicating within and between genera and species that provide MASINT (Measurement and Signature Intelligence) to enhance sustained survival, sabotage the host inflammatory and immune responses and by potentially adopting a 'Fabian strategy' with a war of attrition and resulting disease manifestations. Additionally, much has been learned regarding the ever-increasing complexity of the host-response armamentarium at both cellular and molecular levels that is addressed in this review. Knowledge regarding how these systems fully interact requires both new laboratory and clinical tools, as well as sophisticated modeling of the networks that help maintain homeostasis and are dysregulated in disease. Finally, the triggers resulting in a 'coup de main' by the microbiome (exacerbation of disease) and the characteristics of susceptible hosts that can result in 'pyrrhic victories' with collateral damage to host tissues, the hallmark of periodontitis, remains unclear. While much has been learned, substantial gaps in our understanding of the 'parameters of this war' remain elusive toward fulfilling the Sun Tzu adage: 'If you know the enemy and know yourself, you need not fear the result of a hundred battles.'}, }
@article {pmid28756344, year = {2017}, author = {De Swaef, E and Demeestere, K and Boon, N and Van den Broeck, W and Haesebrouck, F and Decostere, A}, title = {Development of a reliable experimental set-up for Dover sole larvae Solea solea L. and exploring the possibility of implementing this housing system in a gnotobiotic model.}, journal = {Research in veterinary science}, volume = {115}, number = {}, pages = {418-424}, doi = {10.1016/j.rvsc.2017.07.025}, pmid = {28756344}, issn = {1532-2661}, mesh = {Animals ; Aquaculture/*methods ; Flatfishes/*growth &amp; development/physiology ; *Germ-Free Life ; *Housing, Animal ; Larva/growth &amp; development ; Ovum ; }, abstract = {Due to the increasing importance of the aquaculture sector, diversification in the number of cultured species imposes itself. Dover sole Solea solea L. is put forward as an important new aquaculture candidate due to its high market value and high flesh quality. However, as for many other fish species, sole production is hampered by amongst others high susceptibility to diseases and larval mortality, rendering the need for more research in this area. In this respect, in first instance, a housing system for Dover sole larvae was pinpointed by keeping the animals individually in 24-well plates for 26days with good survival rates and initiating metamorphosis. This ensures a standardised and reliable experimental set-up in which the possible death of one larva has no effect on the other larvae, rendering experiments adopting such a system more reproducible. In addition to proving valuable in many other applications, this multi well system constitutes a firm basis to enable the gnotobiotic rearing of larvae, which hitherto is non-existing for Dover sole. In this respect, secondly, a large number of disinfection protocols were tested, making use of widely employed disinfectants as hydrogen peroxide, glutaraldehyde and/or ozone whether or not combined with a mixture of antimicrobial agents for 24h. Although none of the tested protocols was sufficient to reproducibly generate a gnotobiotic model, the combination of glutaraldehyde and hydrogen peroxide resulted in hatchable, bacteria-free eggs in some cases.}, }
@article {pmid28755810, year = {2017}, author = {Guo, XP and Niu, ZS and Lu, DP and Feng, JN and Chen, YR and Tou, FY and Liu, M and Yang, Y}, title = {Bacterial community structure in the intertidal biofilm along the Yangtze Estuary, China.}, journal = {Marine pollution bulletin}, volume = {124}, number = {1}, pages = {314-320}, doi = {10.1016/j.marpolbul.2017.07.051}, pmid = {28755810}, issn = {1879-3363}, mesh = {Bacteria/classification/*genetics/growth &amp; development ; *Biodiversity ; *Biofilms ; China ; Ecology ; *Estuaries ; High-Throughput Nucleotide Sequencing ; Hydrogen-Ion Concentration ; Microbial Consortia/*genetics ; Oxygen ; Proteobacteria/classification/genetics/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sequence Analysis, DNA ; }, abstract = {In this study, the 16S rRNA-based Illumina MiSeq sequencing was used to investigate the bacterial community structure and composition of intertidal biofilm taken along the Yangtze Estuary. The results showed that 680,721 valid sequences of seven samples were assigned to 147,239 operational taxonomic units, which belonged to 49 phyla, 246 family and 314 genera. Compared to other studies on water and sediments in the study area, biofilms showed highest index of bacterial diversity and abundances. At different taxonomic levels, both dominant taxa and their abundances varied among the seven samples, with Proteobacteria as the dominant phylum in general. Principal component analysis and cluster analysis revealed that bacterial communities at WSK differed from those at other sampling sites. Salinity, dissolved oxygen, pH and nutrients were the vital environmental factors to influence the bacterial community structure of biofilms. These results may provide a new insight into the microbial ecology in estuarine environments.}, }
@article {pmid28755027, year = {2018}, author = {Pagliaccia, D and Urak, RZ and Wong, F and Douhan, LI and Greer, CA and Vidalakis, G and Douhan, GW}, title = {Genetic Structure of the Rice Blast Pathogen (Magnaporthe oryzae) over a Decade in North Central California Rice Fields.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {310-317}, pmid = {28755027}, issn = {1432-184X}, support = {SA7279, AMD 2//USDA-NIFA/UC Division of Ag. And Nat'l Resources (UCANR)/ ; }, mesh = {California ; Genetic Variation ; Genotype ; Magnaporthe/classification/*genetics/*isolation &amp; purification/physiology ; Oryza/growth &amp; development/*microbiology ; Phylogeny ; Plant Diseases/*microbiology ; }, abstract = {Rice blast, caused by the ascomycete Magnaporthe oryzae, is one of the most destructive rice diseases worldwide. Even though the disease has been present in California since 1996, there is no data for the pathogen population biology in the state. Using amplified fragment length polymorphisms and mating-type markers, the M. oryzae population diversity was investigated using isolates collected when the disease was first established in California and isolates collected a decade later. While in the 1990 samples, a single multilocus genotype (MLG) was identified (MLG1), over a decade later, we found 14 additional MLGs in the 2000 isolates. Some of these MLGs were found to infect the only rice blast-resistant cultivar (M-208) available for commercial production in California. The same samples also had a significant decrease of MLG1. MLG1 was found infecting the resistant rice cultivar M-208 on one occasion whereas MLG7 was the most common genotype infecting the M-208. MLG7 was identified in the 2000 samples, and it was not present in the M. oryzae population a decade earlier. Our results demonstrate a significant increase in genotypic diversity over time with no evidence of sexual reproduction and suggest a recent introduction of new virulent race(s) of the pathogen. In addition, our data could provide information regarding the durability of the Pi-z resistance gene of the M-208. This information will be critical to plant breeders in developing strategies for deployment of other rice blast resistance genes/cultivars in the future.}, }
@article {pmid28754286, year = {2017}, author = {Harish, A and Kurland, CG}, title = {Mitochondria are not captive bacteria.}, journal = {Journal of theoretical biology}, volume = {434}, number = {}, pages = {88-98}, doi = {10.1016/j.jtbi.2017.07.011}, pmid = {28754286}, issn = {1095-8541}, mesh = {Biological Coevolution ; *Biological Evolution ; Mitochondria/chemistry/*genetics ; *Phylogeny ; *Proteome ; Symbiosis ; }, abstract = {Lynn Sagan's conjecture (1967) that three of the fundamental organelles observed in eukaryote cells, specifically mitochondria, plastids and flagella were once free-living primitive (prokaryotic) cells was accepted after considerable opposition. Even though the idea was swiftly refuted for the specific case of origins of flagella in eukaryotes, the symbiosis model in general was accepted for decades as a realistic hypothesis to describe the endosymbiotic origins of eukaryotes. However, a systematic analysis of the origins of the mitochondrial proteome based on empirical genome evolution models now indicates that 97% of modern mitochondrial protein domains as well their homologues in bacteria and archaea were present in the universal common ancestor (UCA) of the modern tree of life (ToL). These protein domains are universal modular building blocks of modern genes and genomes, each of which is identified by a unique tertiary structure and a specific biochemical function as well as a characteristic sequence profile. Further, phylogeny reconstructed from genome-scale evolution models reveals that Eukaryotes and Akaryotes (archaea and bacteria) descend independently from UCA. That is to say, Eukaryotes and Akaryotes are both primordial lineages that evolved in parallel. Finally, there is no indication of massive inter-lineage exchange of coding sequences during the descent of the two lineages. Accordingly, we suggest that the evolution of the mitochondrial proteome was autogenic (endogenic) and not endosymbiotic (exogenic).}, }
@article {pmid28752953, year = {2017}, author = {Guerrero, LD and Vikram, S and Makhalanyane, TP and Cowan, DA}, title = {Evidence of microbial rhodopsins in Antarctic Dry Valley edaphic systems.}, journal = {Environmental microbiology}, volume = {19}, number = {9}, pages = {3755-3767}, doi = {10.1111/1462-2920.13877}, pmid = {28752953}, issn = {1462-2920}, mesh = {Antarctic Regions ; Bacteroidetes/genetics/*metabolism ; Ecosystem ; Fresh Water/microbiology ; Genome, Bacterial/genetics ; Metagenomics/methods ; Proteobacteria/genetics/*metabolism ; Rhodopsins, Microbial/genetics/*metabolism ; Seawater/microbiology ; }, abstract = {Microorganisms able to synthesize rhodopsins have the capacity to translocate ions through their membranes, using solar energy to generate a proton motive force. Rhodopsins are the most abundant phototrophic proteins in oceanic surface waters and are key constituents in marine bacterial ecology. However, it remains unclear how rhodopsins are used in most microorganisms. Despite their abundance in marine and fresh-water systems, the presence of functional rhodopsin systems in edaphic habitats has never been reported. Here, we show the presence of several new putative H[+] , Na[+] and Cl[+] pumping rhodopsins identified by metagenomic analysis of Antarctic desert hypolithic communities. Reconstruction of two Proteobacteria genomes harboring xanthorhodopsin-like proteins and one Bacteroidetes genome with a Na-pumping-like rhodopsin indicated that these bacteria were aerobic heterotrophs possessing the apparent capacity for the functional expression of rhodopsins. The existence of these protein systems in hypolithic bacteria expands the known role of rhodopsins to include terrestrial environments and suggests a possible predominant function as heterotrophic energy supply proteins, a feasible microbial adaptation to the harsh conditions prevalent in Antarctic edaphic systems.}, }
@article {pmid28751883, year = {2017}, author = {Borbón-García, A and Reyes, A and Vives-Flórez, M and Caballero, S}, title = {Captivity Shapes the Gut Microbiota of Andean Bears: Insights into Health Surveillance.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1316}, pmid = {28751883}, issn = {1664-302X}, abstract = {The Andean bear is an endemic species of the tropical Andes who has an almost exclusively plant-based diet. Since herbivorous mammals do not carry enzymes for fiber degradation, the establishment of symbiosis with cellulolytic microorganisms in their gastrointestinal (GI) tract is necessary to help them fulfill their nutritional needs. Furthermore, as described for other mammals, a stable, diverse, and balanced gut microbial composition is an indicator of a healthy status of the host; under disturbances this balance can be lost, leading to potential diseases of the host. The goal of this study was to describe the gut microbiota of wild and captive Andean bears and determine how habitat status influences the composition and diversity of the gut symbiotic community. Fecal samples from wild (n = 28) and captive (n = 8) Andean bears were collected in "Reserva Pantano de Martos" and "Fundación Bioandina", Colombia. Composition and diversity analyses were performed using amplicons from the V4 region of the 16S rDNA gene sequenced using the Ion PGM platform. PICRUSt algorithm was applied to predict the gene content of the gut microbiome of wild and captive Andean bears. A total of 5,411 and 838 OTUs were identified for wild and captive bears, respectively. Captive bears contained a lower number of bacterial phyla (n = 7) compared to wild individuals (n = 9). Proteobacteria (59.03%) and Firmicutes (14.03%) were the phyla that contributed the most to differences between wild and captive bears (overall dissimilarity = 87.72%). At family level, Enterobacteriaceae drove the main differences between the two groups (13.7%). PICRUSt metagenomics predictions suggested a similar pattern of relative abundance of gene families associated with the metabolism of carbohydrates across samples in wild individuals, despite the taxonomic differences of their gut microbiota. Captivity alters the availability and diversity of food resources, which likely reduces microbiota richness and diversity compared to wild individuals. Further considerations should be taken into account for nutritional schemes improving ex-situ conservation and its potential as a surveillance tool of endangered populations of wild Andean bears.}, }
@article {pmid28748040, year = {2017}, author = {Janus, MM and Volgenant, CMC and Brandt, BW and Buijs, MJ and Keijser, BJF and Crielaard, W and Zaura, E and Krom, BP}, title = {Effect of erythritol on microbial ecology of in vitro gingivitis biofilms.}, journal = {Journal of oral microbiology}, volume = {9}, number = {1}, pages = {1337477}, pmid = {28748040}, issn = {2000-2297}, abstract = {Gingivitis is one of the most common oral infections in humans. While sugar alcohols such as erythritol are suggested to have caries-preventive properties, it may also have beneficial effects in prevention of gingivitis by preventing maturation of oral biofilms. The aim of this study was to assess the effect of erythritol on the microbial ecology and the gingivitis phenotype of oral microcosms. Biofilms were inoculated with stimulated saliva from 20 healthy donors and grown in a gingivitis model in the continuous presence of 0 (control group), 5, and 10% erythritol. After 9 days of growth, biofilm formation, protease activity (gingivitis phenotype), and microbial profile analyses were performed. Biofilm growth was significantly reduced in the presence of erythritol, and this effect was dose dependent. Protease activity and the Shannon diversity index of the microbial profiles of the biofilms were significantly lower when erythritol was present. Microbial profile analysis revealed that presence of erythritol induced a compositional shift from periodontitis- and gingivitis-related taxa toward early colonizers. The results of this study suggest that erythritol suppresses maturation of the biofilms toward unhealthy composition. The gingivitis phenotype was suppressed and biofilm formation was reduced in the presence of erythritol. Therefore, it is concluded that erythritol may contribute to a healthy oral ecosystem in vitro.}, }
@article {pmid28747705, year = {2017}, author = {Kamutando, CN and Vikram, S and Kamgan-Nkuekam, G and Makhalanyane, TP and Greve, M and Roux, JJL and Richardson, DM and Cowan, D and Valverde, A}, title = {Soil nutritional status and biogeography influence rhizosphere microbial communities associated with the invasive tree Acacia dealbata.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6472}, pmid = {28747705}, issn = {2045-2322}, mesh = {Acacia/*growth &amp; development ; Bacteria/*classification/genetics/isolation &amp; purification ; Bacterial Proteins/genetics ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; Fungal Proteins/genetics ; Fungi/*classification/genetics/isolation &amp; purification ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Fungal ; High-Throughput Nucleotide Sequencing/*methods ; Introduced Species ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Sequence Analysis, DNA/*methods ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {Invasiveness and the impacts of introduced plants are known to be mediated by plant-microbe interactions. Yet, the microbial communities associated with invasive plants are generally poorly understood. Here we report on the first comprehensive investigation of the bacterial and fungal communities inhabiting the rhizosphere and the surrounding bulk soil of a widespread invasive tree, Acacia dealbata. Amplicon sequencing data indicated that rhizospheric microbial communities differed significantly in structure and composition from those of the bulk soil. Two bacterial (Alphaproteobacteria and Gammaproteobacteria) and two fungal (Pezizomycetes and Agaricomycetes) classes were enriched in the rhizosphere compared with bulk soils. Changes in nutritional status, possibly induced by A. dealbata, primarily shaped rhizosphere soil communities. Despite a high degree of geographic variability in the diversity and composition of microbial communities, invasive A. dealbata populations shared a core of bacterial and fungal taxa, some of which are known to be involved in N and P cycling, while others are regarded as plant pathogens. Shotgun metagenomic analysis also showed that several functional genes related to plant growth promotion were overrepresented in the rhizospheres of A. dealbata. Overall, results suggest that rhizosphere microbes may contribute to the widespread success of this invader in novel environments.}, }
@article {pmid28745865, year = {2017}, author = {Prévoteau, A and Rabaey, K}, title = {Electroactive Biofilms for Sensing: Reflections and Perspectives.}, journal = {ACS sensors}, volume = {2}, number = {8}, pages = {1072-1085}, doi = {10.1021/acssensors.7b00418}, pmid = {28745865}, issn = {2379-3694}, abstract = {Microbial electrochemistry has from the onset been recognized for its sensing potential due to the microbial ability to enhance signals through metabolic cascades, its relative selectivity toward substrates, and the higher stability conferred by the microbial ability to self-replicate. The greatest challenge has been to achieve stable and efficient transduction between a microorganism and an electrode surface. Over the past decades, a new kind of microbial architecture has been observed to spontaneously develop on polarized electrodes: the electroactive biofilm (EAB). The EAB conducts electrons over long distances and performs quasi-reversible electron transfer on conventional electrode surfaces. It also possesses self-regenerative properties. In only a few years, EABs have inspired considerable research interest for use as biosensors for environmental or bioprocess monitoring. Multiple challenges still need to be overcome before implementation at larger scale of this new kind of biosensors can be realized. This perspective first introduces the specific characteristics of the EAB with respect to other electrochemical biosensors. It summarizes the sensing applications currently proposed for EABs, stresses their limitations, and suggests strategies toward potential solutions. Conceptual prospects to engineer EABs for sensing purposes are also discussed.}, }
@article {pmid28744555, year = {2017}, author = {Sultanpuram, VR and Mothe, T and Chintalapati, S and Chintalapati, VR}, title = {Bacillus catenulatus sp. nov., an alkalitolerant bacterium isolated from a soda lake.}, journal = {Archives of microbiology}, volume = {199}, number = {10}, pages = {1391-1397}, doi = {10.1007/s00203-017-1413-y}, pmid = {28744555}, issn = {1432-072X}, mesh = {*Bacillus/classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition/genetics ; Cell Wall/chemistry ; DNA, Bacterial/genetics ; Diaminopimelic Acid/analysis ; Fatty Acids/analysis ; India ; Lakes/*microbiology ; Nucleic Acid Hybridization ; Peptidoglycan/chemistry ; Phosphatidylethanolamines/analysis ; Phospholipids/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sodium Chloride/analysis ; Spores, Bacterial/physiology ; }, abstract = {Two novel (18C[T] and 6C) Gram-stain-positive, rod shaped, motile and endospore-forming bacterial strains were isolated from Lonar soda lake, India. Based on 16S rRNA gene sequence analysis, strains 18C[T] and 6C were identified as belonging to the class Firmibacteria, and were most closely related to Bacillus cohnii KCTC 3572[T] (99.3 and 99.9%, respectively), Bacillus zhanjiangensis KCTC 13713[T] (97.4 and 98.0%, respectively), Bacillus halmapalus LMG 17950[T] (97.0 and 97.6%, respectively) and other members in the genus Bacillus (<97.0%). However, the DNA-DNA relatedness between 18C[T] and 6C and B. cohnii KCTC 3572[T] (49.6 ± 0.9 and 51.6 ± 0.7, respectively), B. zhanjiangensis KCTC 13713[T] (42.9 ± 0.8 and 47.1 ± 0.3, respectively) and B. halmapalus LMG 17950[T] (39.9 ± 0.8 and 40.8 ± 0.3, respectively) indicated that the novel strains were distantly related to these strains. Further, the high 16S rRNA gene sequence similarity (100%) and DNA-DNA relatedness (90 ± 5%) suggested that strains 18C[T] and 6C were members of a genomospecies. The strains grew optimally at a pH of 7.5 with 2-3% (w/v) NaCl and temperature of 37 °C. Strains 18C[T] and 6C were catalase and oxidase negative. The cell wall of strain 18C[T] contained meso-diaminopimelic acid as the diagnostic diamino acid, which was in contrast with its nearest neighbour B. cohnii KCTC 3572[T], which contained ornithine and aspartic acid. Polar lipids include diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), an unknown phospholipid (PL) and three unknown lipids (L1-3). The predominant isoprenoid quinone was MK-7. iso-C15:0 (32.5%) was the predominant fatty acid and significant proportions of anteiso-C15:0 (19.5%), C16:0 (11.5%), iso-C17:0 (9.5%) and anteiso-C17:0 (6.3%) were also detected. The DNA G + C content of strains 18C[T] and 6C were 39.3 and 39.2 mol%, respectively. The results of molecular, biochemical and chemotaxonomic tests showed a clear differentiation of strains 18C[T] and 6C from all other members of the genus Bacillus, for which the name Bacillus catenulatus sp. nov. is proposed. The type strain is 18C[T] (=KCTC 33781[T] = CGMCC 1.15475[T]).}, }
@article {pmid28744257, year = {2017}, author = {Pan, D and Nolan, J and Williams, KH and Robbins, MJ and Weber, KA}, title = {Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1199}, pmid = {28744257}, issn = {1664-302X}, abstract = {Viruses are the most abundant biological entity on Earth and their interactions with microbial communities are recognized to influence microbial ecology and impact biogeochemical cycling in various ecosystems. While the factors that control the distribution of viruses in surface aquatic environments are well-characterized, the abundance and distribution of continental subsurface viruses with respect to microbial abundance and biogeochemical parameters have not yet been established. In order to begin to understand the factors governing virus distribution in subsurface environments, we assessed microbial cell and virus abundance in groundwater concurrent with groundwater chemistry in a uranium impacted alluvial aquifer adjoining the Colorado River near Rifle, CO. Virus abundance ranged from 8.0 × 10[4] to 1.0 × 10[6] mL[-1] and exceeded cell abundance in all samples (cell abundance ranged from 5.8 × 10[4] to 6.1 × 10[5] mL[-1]). The virus to microbial cell ratio ranged from 1.1 to 8.1 and averaged 3.0 ± 1.6 with virus abundance most strongly correlated to cell abundance (Spearman's ρ = 0.73, p < 0.001). Both viruses and cells were positively correlated to dissolved organic carbon (DOC) with cells having a slightly stronger correlation (Spearman's ρ = 0.46, p < 0.05 and ρ = 0.54, p < 0.05; respectively). Groundwater uranium was also strongly correlated with DOC and virus and cell abundance (Spearman's ρ = 0.62, p < 0.05; ρ = 0.46, p < 0.05; and ρ = 0.50, p < 0.05; respectively). Together the data indicate that microbial cell and virus abundance are correlated to the geochemical conditions in the aquifer. As such local geochemical conditions likely control microbial host cell abundance which in turn controls viral abundance. Given the potential impacts of viral-mediated cell lysis such as liberation of labile organic matter from lysed cells and changes in microbial community structure, viral interactions with the microbiota should be considered in an effort to understand subsurface biogeochemical cycling and contaminant mobility.}, }
@article {pmid28742878, year = {2017}, author = {Lin, G and Sun, F and Wang, C and Zhang, L and Zhang, X}, title = {Assessment of the effect of Enteromorpha prolifera on bacterial community structures in aquaculture environment.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0179792}, pmid = {28742878}, issn = {1932-6203}, mesh = {Actinomycetales/classification/genetics/isolation &amp; purification ; *Aquaculture ; Bacteria/classification/*genetics/*isolation &amp; purification ; China ; *Eutrophication ; Microbiota ; Phylogeny ; Ponds/microbiology ; Rhodobacteraceae/classification/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Ulva/*growth &amp; development/isolation &amp; purification ; *Water Microbiology ; }, abstract = {In recent years, Enteromorpha prolifera blooms had serious impacts on costal environments and fisheries in China. Nevertheless, the effects of E. prolifera on microbial ecology remain unknown. In this study, for the first time, an Illumina sequencing analysis was used to investigate bacterial communities in source water, aquaculture ponds with E. prolifera, and an aquaculture pond in which E. prolifera -free. Principal coordinate and phylogenic analyses revealed obvious differences among the bacterial communities in the pond water with and without E. prolifera. Abundant bacterial taxa in the E. prolifera-containing pond were generally absent from the pond without E. prolifera. Interestingly, pond water with E. prolifera was dominated by Actinomycetales (> 50%), as well as by anaerobic bacteria in the underlying sediment (Desulfobacterales and Desulfuromonadales (> 20%). Pond water in which E. prolifera-free was dominated by Rhodobacterales (58.19%), as well as aerobic and facultative anaerobic bacteria in the sediment. In addition, the ecological functions of other dominant bacteria, such as Candidatus Aquiluna, Microcella spp., and Marivita spp., should be studied in depth. Overall, massive growth of E. prolifera will have serious effects on bacterial communities, and, thus, it will have an important impact on the environment. The novel findings in this study will be valuable for understanding green tides.}, }
@article {pmid28742846, year = {2017}, author = {Pietro-Souza, W and Mello, IS and Vendruscullo, SJ and Silva, GFD and Cunha, CND and White, JF and Soares, MA}, title = {Endophytic fungal communities of Polygonum acuminatum and Aeschynomene fluminensis are influenced by soil mercury contamination.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0182017}, pmid = {28742846}, issn = {1932-6203}, mesh = {Endophytes/*drug effects ; Fabaceae/*microbiology ; Mercury/*adverse effects ; Plant Roots/drug effects/microbiology ; Polygonum/*microbiology ; *Soil Microbiology ; }, abstract = {The endophytic fungal communities of Polygonum acuminatum and Aeschynomene fluminensis were examined with respect to soil mercury (Hg) contamination. Plants were collected in places with and without Hg+2 for isolation and identification of their endophytic root fungi. We evaluated frequency of colonization, number of isolates and richness, indices of diversity and similarity, functional traits (hydrolytic enzymes, siderophores, indoleacetic acid, antibiosis and metal tolerance) and growth promotion of Aeschynomene fluminensis inoculated with endophytic fungi on soil with mercury. The frequency of colonization, structure and community function, as well as the abundant distribution of taxa of endophytic fungi were influenced by mercury contamination, with higher endophytic fungi in hosts in soil with mercury. The presence or absence of mercury in the soil changes the profile of the functional characteristics of the endophytic fungal community. On the other hand, tolerance of lineages to multiple metals is not associated with contamination. A. fluminensis depends on its endophytic fungi, since plants free of endophytic fungi grew less than expected due to mercury toxicity. In contrast plants containing certain endophytic fungi showed good growth in soil containing mercury, even exceeding growth of plants cultivated in soil without mercury. The data obtained confirm the hypothesis that soil contamination by mercury alters community structure of root endophytic fungi in terms of composition, abundance and species richness. The inoculation of A. fluminensis with certain strains of stress tolerant endophytic fungi contribute to colonization and establishment of the host and may be used in processes that aim to improve phytoremediation of soils with toxic concentrations of mercury.}, }
@article {pmid28741266, year = {2018}, author = {Mucha, J and Peay, KG and Smith, DP and Reich, PB and Stefański, A and Hobbie, SE}, title = {Effect of Simulated Climate Warming on the Ectomycorrhizal Fungal Community of Boreal and Temperate Host Species Growing Near Their Shared Ecotonal Range Limits.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {348-363}, pmid = {28741266}, issn = {1432-184X}, support = {grant no. DE-FG02-07ER64456//US Department of Energy Program on Ecological Research/ ; project no. 2011/01/D/NZ9/02871//the National Science Centre, Poland/ ; }, mesh = {Betula/growth &amp; development/*microbiology ; Biodiversity ; Climate Change ; Ecosystem ; Forests ; Fungi/classification/genetics/growth &amp; development/*isolation &amp; purification ; Host Specificity ; Minnesota ; Mycorrhizae/classification/genetics/growth &amp; development/*isolation &amp; purification ; Phylogeny ; Picea/growth &amp; development/*microbiology ; Pinus/growth &amp; development/*microbiology ; Plant Roots/growth &amp; development/microbiology ; Soil Microbiology ; Temperature ; }, abstract = {Ectomycorrhizal (ECM) fungi can influence the establishment and performance of host species by increasing nutrient and water absorption. Therefore, understanding the response of ECM fungi to expected changes in the global climate is crucial for predicting potential changes in the composition and productivity of forests. While anthropogenic activity has, and will continue to, cause global temperature increases, few studies have investigated how increases in temperature will affect the community composition of ectomycorrhizal fungi. The effects of global warming are expected to be particularly strong at biome boundaries and in the northern latitudes. In the present study, we analyzed the effects of experimental manipulations of temperature and canopy structure (open vs. closed) on ectomycorrhizal fungi identified from roots of host seedlings through 454 pyrosequencing. The ecotonal boundary site selected for the study was between the southern boreal and temperate forests in northern Minnesota, USA, which is the southern limit range for Picea glauca and Betula papyrifera and the northern one for Pinus strobus and Quercus rubra. Manipulations that increased air and soil temperature by 1.7 and 3.4 °C above ambient temperatures, respectively, did not change ECM richness but did alter the composition of the ECM community in a manner dependent on host and canopy structure. The prediction that colonization of boreal tree species with ECM symbionts characteristic of temperate species would occur was not substantiated. Overall, only a small proportion of the ECM community appears to be strongly sensitive to warming.}, }
@article {pmid28740492, year = {2017}, author = {Laforest-Lapointe, I and Arrieta, MC}, title = {Patterns of Early-Life Gut Microbial Colonization during Human Immune Development: An Ecological Perspective.}, journal = {Frontiers in immunology}, volume = {8}, number = {}, pages = {788}, pmid = {28740492}, issn = {1664-3224}, abstract = {Alterations in gut microbial colonization during early life have been reported in infants that later developed asthma, allergies, type 1 diabetes, as well as in inflammatory bowel disease patients, previous to disease flares. Mechanistic studies in animal models have established that microbial alterations influence disease pathogenesis via changes in immune system maturation. Strong evidence points to the presence of a window of opportunity in early life, during which changes in gut microbial colonization can result in immune dysregulation that predisposes susceptible hosts to disease. Although the ecological patterns of microbial succession in the first year of life have been partly defined in specific human cohorts, the taxonomic and functional features, and diversity thresholds that characterize these microbial alterations are, for the most part, unknown. In this review, we summarize the most important links between the temporal mosaics of gut microbial colonization and the age-dependent immune functions that rely on them. We also highlight the importance of applying ecology theory to design studies that explore the interactions between this complex ecosystem and the host immune system. Focusing research efforts on understanding the importance of temporally structured patterns of diversity, keystone groups, and inter-kingdom microbial interactions for ecosystem functions has great potential to enable the development of biologically sound interventions aimed at maintaining and/or improving immune system development and preventing disease.}, }
@article {pmid28736793, year = {2018}, author = {Vogt, JC and Abed, RMM and Albach, DC and Palinska, KA}, title = {Bacterial and Archaeal Diversity in Hypersaline Cyanobacterial Mats Along a Transect in the Intertidal Flats of the Sultanate of Oman.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {331-347}, pmid = {28736793}, issn = {1432-184X}, support = {[project PA 842/9-1]//Deutsche Forschungsgemeinschaft (DE)/ ; }, mesh = {Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; Cyanobacteria/genetics/*growth &amp; development/metabolism ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Ecosystem ; Geologic Sediments/analysis/*microbiology ; Oman ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; Seawater/analysis/microbiology ; Sodium Chloride/analysis/metabolism ; }, abstract = {Hypersaline intertidal zones are highly dynamic ecosystems that are exposed to multiple extreme environmental conditions including rapidly and frequently changing parameters (water, nutrients, temperature) as well as highly elevated salinity levels often caused by high temperatures and evaporation rates. Microbial mats in most extreme settings, as found at the coastline of the subtropical-arid Arabian Peninsula, have been relatively less studied compared to their counterparts around the world. We report, here, for the first time on the diversity of the bacterial and archaeal communities of marine microbial mats along an intertidal transect in a wide salt flat with strongly increased salinity employing Illumina MiSeq technology for amplicon sequencing of 16S rRNA gene fragments. Microbial communities were dominated by typical halotolerant to halophilic microorganisms, with clear shifts in community composition, richness, and diversity along the transect. Highly adapted specialists (e.g., Euhalothece, Salinibacter, Nanohaloarchaeota) were mainly found at the most extreme, upper tidal sites and less specialized organisms with wide tolerance ranges (e.g., Lyngbya, Rhodovibrio, Salisaeta, Halobacteria) in intermediate sites of the transect. The dominating taxa in the lower tidal sites were typical members of well-stabilized mats (e.g., Coleofasciculus, Anaerolineaceae, Thaumarchaeota). Up to 40% of the archaeal sequences per sample represented so far unknown phyla. In conclusion, the bacterial richness and diversity increased from upper towards lower tidal sites in line with increasing mat stabilization and functional diversity, opposed to that of cyanobacteria only and archaea, which showed their highest richness and diversity in upper tidal samples.}, }
@article {pmid28735426, year = {2018}, author = {Hale, VL and Tan, CL and Niu, K and Yang, Y and Knight, R and Zhang, Q and Cui, D and Amato, KR}, title = {Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {515-527}, pmid = {28735426}, issn = {1432-184X}, mesh = {Animal Feed/analysis ; Animals ; Animals, Wild/metabolism/microbiology ; Animals, Zoo/metabolism/microbiology ; Bacteria/*classification/genetics/isolation &amp; purification ; China ; Colobinae/metabolism/*microbiology ; Diet/veterinary ; *Gastrointestinal Microbiome ; *Host Specificity ; *Phylogeny ; Species Specificity ; }, abstract = {Both diet and host phylogeny shape the gut microbial community, and separating out the effects of these variables can be challenging. In this study, high-throughput sequencing was used to evaluate the impact of diet and phylogeny on the gut microbiota of nine colobine monkey species (N = 64 individuals). Colobines are leaf-eating monkeys that fare poorly in captivity-often exhibiting gastrointestinal (GI) problems. This study included eight Asian colobines (Rhinopithecus brelichi, Rhinopithecus roxellana, Rhinopithecus bieti, Pygathrix nemaeus, Nasalis larvatus, Trachypithecus francoisi, Trachypithecus auratus, and Trachypithecus vetulus) and one African colobine (Colobus guereza). Monkeys were housed at five different captive institutes: Panxi Wildlife Rescue Center (Guizhou, China), Beijing Zoo, Beijing Zoo Breeding Center, Singapore Zoo, and Singapore Zoo Primate Conservation Breeding Center. Captive diets varied widely between institutions, but within an institution, all colobine monkey species were fed nearly identical or identical diets. In addition, four monkey species were present at multiple captive institutes. This allowed us to parse the effects of diet and phylogeny in these captive colobines. Gut microbial communities clustered weakly by host species and strongly by diet, and overall, colobine phylogenetic relationships were not reflected in gut microbiota analyses. Core microbiota analyses also identified several key taxa-including microbes within the Ruminococcaceae and Lachnospiraceae families-that were shared by over 90% of the monkeys in this study. Microbial species within these families include many butyrate producers that are important for GI health. These results highlight the importance of diet in captive colobines.}, }
@article {pmid28735425, year = {2018}, author = {Strano, CP and Malacrinò, A and Campolo, O and Palmeri, V}, title = {Influence of Host Plant on Thaumetopoea pityocampa Gut Bacterial Community.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {487-494}, pmid = {28735425}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Feeding Behavior ; *Gastrointestinal Microbiome ; Larva/microbiology/physiology ; Moths/*microbiology/physiology ; Pinus/classification/*parasitology ; Species Specificity ; }, abstract = {Microbial communities associated to the gut of insects are attracting an increasing interest, mainly because of their role in influencing several host life-traits. The characterization of the gut microbial community is pivotal for understanding insect ecology and, thus, to develop novel pest management strategies. The pine processionary moth, Thaumetopoea pytiocampa (Denis &amp; Schiff.) (Lepidoptera: Thaumetopoeidae), is a severe defoliator of pine forests, able to feed on several pine species. In this work, we performed a metabarcoding analysis to investigate, for the first time, the diversity of the gut bacterial community of pine processionary larvae associated with three different host pine species (Pinus halepensis, Pinus nigra subsp. laricio, and Pinus pinaster). We found that the gut microbial community of T. pityocampa larvae collected on P. halapensis was different from that associated with larvae collected from P. nigra and P. pinaster. Moreover, the high presence of bacteria belonging to the genera Modestobacter, Delftia, and unidentified Methylobacteriaceae retrieved in larvae feeding on P. halapensis suggested that specific interactions can occur. Our results provide the evidence that different host plant differently impact on the microbiota diversity of T. pityocampa larvae, contributing to the general knowledge of this pest with information that could be useful in shaping the next generation of pest control strategies.}, }
@article {pmid28735323, year = {2017}, author = {Brzychczy-Włoch, M and Ochońska, D and Piotrowska, A and Bulanda, M}, title = {Gas Gangrene of Different Origin Associated with Clostridium perfringens Type A in Three Patients Simultaneously Hospitalized in a Single Department of Orthopedics and Traumatology in Poland.}, journal = {Polish journal of microbiology}, volume = {65}, number = {4}, pages = {399-406}, doi = {10.5604/17331331.1227665}, pmid = {28735323}, issn = {1733-1331}, mesh = {Aged ; Aged, 80 and over ; Clostridium perfringens/*genetics/*isolation &amp; purification ; Fatal Outcome ; Female ; Gas Gangrene/epidemiology/*microbiology/*pathology ; Genotype ; Hospital Units/organization &amp; administration ; Humans ; Infection Control/organization &amp; administration ; Male ; Middle Aged ; Poland/epidemiology ; }, abstract = {The objective of the study was to perform a comparative analysis of phenotypic and genetic similarity, determination of resistance profiles, detection of toxin-encoding genes and molecular typing of Clostridium perfringens isolates originating from patients with gas gangrene. The study encompassed three patients with a clinical and microbiological diagnosis of gas gangrene who were hospitalized in one of the hospitals of the Kujawsko-Pomorskie province in the same period of time between 8[th] April 2015 and 20[th] April 2015. The three C. perfringens isolates studied had identical biochemical profiles. Two isolates had identical resistance patterns, while the third presented a different profile. Using the multiplex PCR method, all isolates showed the presence of cpa gene encoding α-toxin; furthermore, the presence of the cpb2 gene encoding β2-toxin was confirmed in two isolates. Genotyping with the use of pulsed field gel electrophoresis (PFGE) indicated that the isolates originating from the three studied patients represent three genetically different restrictive patterns which corresponded to three different clones - clone A, clone B and clone C. As a result of the study, it is possible to conclude that the studied patients simultaneously hospitalized in a single Department of Orthopedics and Traumatology developed three different endogenous infections.}, }
@article {pmid28733590, year = {2017}, author = {Andrei, A&#x15e; and Baricz, A and Robeson, MS and Păuşan, MR and Tămaş, T and Chiriac, C and Szekeres, E and Barbu-Tudoran, L and Levei, EA and Coman, C and Podar, M and Banciu, HL}, title = {Hypersaline sapropels act as hotspots for microbial dark matter.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6150}, pmid = {28733590}, issn = {2045-2322}, mesh = {Archaea/*classification/genetics/isolation &amp; purification ; Bacteroidetes/genetics/isolation &amp; purification ; Benzopyrans/*analysis ; Chloroflexi/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/*genetics ; Geologic Sediments/*microbiology ; Humic Substances/*analysis ; Lakes/microbiology ; Phylogeny ; Proteobacteria/genetics/isolation &amp; purification ; Romania ; Sequence Analysis, DNA ; }, abstract = {Present-day terrestrial analogue sites are crucial ground truth proxies for studying life in geochemical conditions close to those assumed to be present on early Earth or inferred to exist on other celestial bodies (e.g. Mars, Europa). Although hypersaline sapropels are border-of-life habitats with moderate occurrence, their microbiological and physicochemical characterization lags behind. Here, we study the diversity of life under low water activity by describing the prokaryotic communities from two disparate hypersaline sapropels (Transylvanian Basin, Romania) in relation to geochemical milieu and pore water chemistry, while inferring their role in carbon cycling by matching taxa to known taxon-specific biogeochemical functions. The polyphasic approach combined deep coverage SSU rRNA gene amplicon sequencing and bioinformatics with RT-qPCR and physicochemical investigations. We found that sapropels developed an analogous elemental milieu and harbored prokaryotes affiliated with fifty-nine phyla, among which the most abundant were Proteobacteria, Bacteroidetes and Chloroflexi. Containing thirty-two candidate divisions and possibly undocumented prokaryotic lineages, the hypersaline sapropels were found to accommodate one of the most diverse and novel ecosystems reported to date and may contribute to completing the phylogenetic branching of the tree of life.}, }
@article {pmid28731707, year = {2017}, author = {Song, Y and Bian, Y and Wang, F and Xu, M and Ni, N and Yang, X and Gu, C and Jiang, X}, title = {Dynamic Effects of Biochar on the Bacterial Community Structure in Soil Contaminated with Polycyclic Aromatic Hydrocarbons.}, journal = {Journal of agricultural and food chemistry}, volume = {65}, number = {32}, pages = {6789-6796}, doi = {10.1021/acs.jafc.7b02887}, pmid = {28731707}, issn = {1520-5118}, mesh = {Adsorption ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Charcoal/*chemistry ; Polycyclic Aromatic Hydrocarbons/*chemistry ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/*chemistry ; Triticum/chemistry ; }, abstract = {Amending soil with biochar is an effective soil remediation strategy for organic contaminants. This study investigated the dynamic effects of wheat straw biochar on the bacterial community structure during remediation by high-throughput sequencing. The wheat straw biochar amended into the soil significantly reduced the bioavailability and toxicity of polycyclic aromatic hydrocarbons (PAHs). Biochar amendment helped to maintain the bacterial diversity in the PAH-contaminated soil. The relationship between the immobilization of PAHs and the soil bacterial diversity fit a quadratic model. Before week 12 of the incubation, the incubation time was the main factor contributing to the changes in the soil bacterial community structure. However, biochar greatly affected the bacterial community structure after 12 weeks of amendment, and the effects were dependent upon the biochar type. Amendment with biochar mainly facilitated the growth of rare bacterial genera (relative abundance of 0.01-1%) in the studied soil. Therefore, the application of wheat straw biochar into PAH-contaminated soil can reduce the environmental risks of PAHs and benefit the soil microbial ecology.}, }
@article {pmid28731477, year = {2017}, author = {Herren, CM and McMahon, KD}, title = {Cohesion: a method for quantifying the connectivity of microbial communities.}, journal = {The ISME journal}, volume = {11}, number = {11}, pages = {2426-2438}, pmid = {28731477}, issn = {1751-7370}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Classification/*methods ; Ecology ; Lakes/*microbiology ; Phytoplankton/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The ability to predict microbial community dynamics lags behind the quantity of data available in these systems. Most predictive models use only environmental parameters, although a long history of ecological literature suggests that community complexity should also be an informative parameter. Thus, we hypothesize that incorporating information about a community's complexity might improve predictive power in microbial models. Here, we present a new metric, called community 'cohesion,' that quantifies the degree of connectivity of a microbial community. We analyze six long-term (10+ years) microbial data sets using the cohesion metrics and validate our approach using data sets where absolute abundances of taxa are available. As a case study of our metrics' utility, we show that community cohesion is a strong predictor of Bray-Curtis dissimilarity (R[2]=0.47) between phytoplankton communities in Lake Mendota, WI, USA. Our cohesion metrics outperform a model built using all available environmental data collected during a long-term sampling program. The result that cohesion corresponds strongly to Bray-Curtis dissimilarity is consistent across the six long-term time series, including five phytoplankton data sets and one bacterial 16S rRNA gene sequencing data set. We explain here the calculation of our cohesion metrics and their potential uses in microbial ecology.}, }
@article {pmid28730722, year = {2017}, author = {Doyle, CJ and O'Toole, PW and Cotter, PD}, title = {Metagenome-based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments.}, journal = {Environmental microbiology}, volume = {19}, number = {11}, pages = {4382-4391}, doi = {10.1111/1462-2920.13859}, pmid = {28730722}, issn = {1462-2920}, mesh = {Bacteria/classification/*genetics ; Environment ; Food Contamination/*analysis ; Food Handling ; Food Microbiology/*methods ; Food Safety/*methods ; Foodborne Diseases/microbiology/*prevention &amp; control ; Humans ; Metagenome/genetics ; Metagenomics/*methods ; }, abstract = {Metagenomic-based analyses have the potential to revolutionize our understanding of the microbiology of food production and processing environments. By adopting such approaches, it will be possible to more accurately determine sources of microbial contamination, identify critical control points for such contaminants, and select practices that optimize quality and safety. This mini-review will discuss the merits of adopting metagenostic-based approaches, highlight novel insights that they have provided to date and consider how they could be further implemented.}, }
@article {pmid28730353, year = {2018}, author = {Vieira, FR and Pecchia, JA}, title = {An Exploration into the Bacterial Community under Different Pasteurization Conditions during Substrate Preparation (Composting-Phase II) for Agaricus bisporus Cultivation.}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {318-330}, pmid = {28730353}, issn = {1432-184X}, support = {005707/2012-05//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {Agaricus/*growth &amp; development/metabolism ; Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Biodiversity ; Composting ; Culture Media/*chemistry/metabolism ; DNA, Bacterial/genetics ; Hot Temperature ; Pasteurization/instrumentation/*methods ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {Substrate preparation (i.e., composting) for Agaricus bisporus cultivation is the most critical point of mushroom production. Among many factors involved in the composting process, the microbial ecology of the system is the underlying drive of composting and can be influenced by composting management techniques. Pasteurization temperature at the beginning of phase II, in theory, may influence the bacterial community and subsequently the "selectivity" and nutrition of the final substrate. Therefore, this hypothesis was tested by simulation in bioreactors under different pasteurization conditions (57 °C/6 h, 60 °C/2 h, and 68 °C/2 h), simulating conditions adopted by many producers. Bacterial diversity, based on 16S ribosomal RNA obtained by high-throughput sequencing and classified in operational taxonomic units (OTUs), was greater than previously reported using culture-dependent methods. Alpha diversity estimators show a lower diversity of OTUs under a high-temperature pasteurization condition. Bacillales order shows a relatively higher OTU abundance under a high-pasteurization temperature, which also was related to high ammonia emission measurements. On the other hand, beta diversity analysis showed no significantly changes in the bacterial community structure under different conditions. Agaricus bisporus mycelium growth during a standard spawn run period was significantly slower in the compost pasteurized at high temperature. Since the bacterial community structure was not greatly affected by different pasteurization conditions but by-products left (e.g., ammonia) at the end of compost conditioning varied, further studies need to be conducted to determine the functional role of the microbial communities found during substrate preparation for Agaricus bisporus cultivation.}, }
@article {pmid28729534, year = {2017}, author = {Jacobs, CB and Maksov, AB and Muckley, ES and Collins, L and Mahjouri-Samani, M and Ievlev, A and Rouleau, CM and Moon, JW and Graham, DE and Sumpter, BG and Ivanov, IN}, title = {UV-activated ZnO films on a flexible substrate for room temperature O2 and H2O sensing.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6053}, pmid = {28729534}, issn = {2045-2322}, abstract = {We demonstrate that UV-light activation of polycrystalline ZnO films on flexible polyimide (Kapton) substrates can be used to detect and differentiate between environmental changes in oxygen and water vapor. The in-plane resistive and impedance properties of ZnO films, fabricated from bacteria-derived ZnS nanoparticles, exhibit unique resistive and capacitive responses to changes in O2 and H2O. We propose that the distinctive responses to O2 and H2O adsorption on ZnO could be utilized to statistically discriminate between the two analytes. Molecular dynamic simulations (MD) of O2 and H2O adsorption energy on ZnO surfaces were performed using the large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) with a reactive force-field (ReaxFF). These simulations suggest that the adsorption mechanisms differ for O2 and H2O adsorption on ZnO, and are governed by the surface termination and the extent of surface hydroxylation. Electrical response measurements, using DC resistance, AC impedance spectroscopy, and Kelvin Probe Force Microscopy (KPFM), demonstrate differences in response to O2 and H2O, confirming that different adsorption mechanisms are involved. Statistical and machine learning approaches were applied to demonstrate that by integrating the electrical and kinetic responses the flexible ZnO sensor can be used for detection and discrimination between O2 and H2O at low temperature.}, }
@article {pmid28729273, year = {2017}, author = {Schultz, J and de Souza, YAP and Mansur, MCPPR and Vermelho, AB and da Mota, FF and Rosado, AS}, title = {Draft Genome Sequence of Microbacterium sp. Strain LEMMJ01, Isolated from Antarctic Ornithogenic Soil.}, journal = {Genome announcements}, volume = {5}, number = {29}, pages = {}, pmid = {28729273}, issn = {2169-8287}, abstract = {We report here the 3,637,012-bp draft genome sequence of Microbacterium sp. strain LEMMJ01, isolated from ornithogenic soil from King George Island, Antarctica. The total number of genes presented in the draft genome sequence was 3,553, and the total number of coding sequences was 3,497. In addition, genes related to the production of terpene and carotenoids were revealed.}, }
@article {pmid28728121, year = {2017}, author = {Wang, F and van Halem, D and Liu, G and Lekkerkerker-Teunissen, K and van der Hoek, JP}, title = {Effect of residual H2O2 from advanced oxidation processes on subsequent biological water treatment: A laboratory batch study.}, journal = {Chemosphere}, volume = {185}, number = {}, pages = {637-646}, doi = {10.1016/j.chemosphere.2017.07.073}, pmid = {28728121}, issn = {1879-1298}, mesh = {Bacteria, Anaerobic ; Biodegradation, Environmental ; Hydrogen Peroxide/*chemistry ; Oxidation-Reduction ; Ultraviolet Rays ; Water ; Water Pollutants, Chemical/*analysis ; Water Purification/*methods ; }, abstract = {H2O2 residuals from advanced oxidation processes (AOPs) may have critical impacts on the microbial ecology and performance of subsequent biological treatment processes, but little is known. The objective of this study was to evaluate how H2O2 residuals influence sand systems with an emphasis on dissolved organic carbon (DOC) removal, microbial activity change and bacterial community evolution. The results from laboratory batch studies showed that 0.25 mg/L H2O2 lowered DOC removal by 10% while higher H2O2 concentrations at 3 and 5 mg/L promoted DOC removal by 8% and 28%. A H2O2 dosage of 0.25 mg/L did not impact microbial activity (as measured by ATP) while high H2O2 dosages, 1, 3 and 5 mg/L, resulted in reduced microbial activity of 23%, 37% and 37% respectively. Therefore, DOC removal was promoted by the increase of H2O2 dosage while microbial activity was reduced. The pyrosequencing results illustrated that bacterial communities were dominated by Proteobacteria. The presence of H2O2 showed clear influence on the diversity and composition of bacterial communities, which became more diverse under 0.25 mg/L H2O2 but conversely less diverse when the dosage increased to 5 mg/L H2O2. Anaerobic bacteria were found to be most sensitive to H2O2 as their growth in batch reactors was limited by both 0.25 and 5 mg/L H2O2 (17-88% reduction). In conclusion, special attention should be given to effects of AOPs residuals on microbial ecology before introducing AOPs as a pre-treatment to biological (sand) processes. Additionally, the guideline on the maximum allowable H2O2 concentration should be properly evaluated.}, }
@article {pmid28725945, year = {2018}, author = {Lee, S and Jo, SD and Son, K and An, I and Jeong, J and Wang, SJ and Kim, Y and Jheong, W and Oem, JK}, title = {Genetic Characteristics of Coronaviruses from Korean Bats in 2016.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {174-182}, pmid = {28725945}, issn = {1432-184X}, mesh = {Animals ; China ; Chiroptera/*virology ; Coronavirus/classification/genetics/*isolation &amp; purification ; Coronavirus Infections/*veterinary/virology ; Genetic Variation ; Genome, Viral ; Hong Kong ; Humans ; Phylogeny ; Republic of Korea ; }, abstract = {Bats have increasingly been recognized as the natural reservoir of severe acute respiratory syndrome (SARS), coronavirus, and other coronaviruses found in mammals. However, little research has been conducted on bat coronaviruses in South Korea. In this study, bat samples (332 oral swabs, 245 fecal samples, 38 urine samples, and 57 bat carcasses) were collected at 33 natural bat habitat sites in South Korea. RT-PCR and sequencing were performed for specific coronavirus genes to identify the bat coronaviruses in different bat samples. Coronaviruses were detected in 2.7% (18/672) of the samples: 13 oral swabs from one species of the family Rhinolophidae, and four fecal samples and one carcass (intestine) from three species of the family Vespertiliodae. To determine the genetic relationships of the 18 sequences obtained in this study and previously known coronaviruses, the nucleotide sequences of a 392-nt region of the RNA-dependent RNA polymerase (RdRp) gene were analyzed phylogenetically. Thirteen sequences belonging to SARS-like betacoronaviruses showed the highest nucleotide identity (97.1-99.7%) with Bat-CoV-JTMC15 reported in China. The other five sequences were most similar to MERS-like betacoronaviruses. Four nucleotide sequences displayed the highest identity (94.1-95.1%) with Bat-CoV-HKU5 from Hong Kong. The one sequence from a carcass showed the highest nucleotide identity (99%) with Bat-CoV-SC2013 from China. These results suggest that careful surveillance of coronaviruses from bats should be continued, because animal and human infections may result from the genetic variants present in bat coronavirus reservoirs.}, }
@article {pmid28725944, year = {2018}, author = {Bataille, A and Lee-Cruz, L and Tripathi, B and Waldman, B}, title = {Skin Bacterial Community Reorganization Following Metamorphosis of the Fire-Bellied Toad (Bombina orientalis).}, journal = {Microbial ecology}, volume = {75}, number = {2}, pages = {505-514}, pmid = {28725944}, issn = {1432-184X}, support = {2014-063422//National Research Foundation of Korea/ ; 2015R1D1A1A01057282//National Research Foundation of Korea/ ; 2010-0002767//Ministry of Science, ICT and Future Planning/ ; 2012R1A1A2044449//Ministry of Science, ICT and Future Planning/ ; }, mesh = {Animals ; Anura/*growth &amp; development/*microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Chytridiomycota/classification/genetics/isolation &amp; purification ; Metamorphosis, Biological ; *Microbiota ; Mycoses/microbiology/veterinary ; Phylogeny ; Skin/*microbiology ; }, abstract = {In organisms with complex life histories, dramatic changes in microbial community structure may occur with host development and immune system maturation. Amphibian host susceptibility to diseases such as chytridiomycosis may be affected by the reorganization of skin microbial community structure that occurs during metamorphosis. We tracked changes in the bacterial communities inhabiting skin of Korean fire-bellied toads (Bombina orientalis) that we infected as tadpoles with different strains of Batrachochytrium dendrobatidis (Bd), the pathogenic fungus that causes chytridiomycosis. We found that B. orientalis undergoes a major change in skin bacterial community composition between 5 and 15 days following metamorphosis. Richness indices and phylogenetic diversity measures began to diverge earlier, between aquatic and terrestrial stages. Our results further reveal differences in skin bacterial community composition among infection groups, suggesting that the effect of Bd infection on skin microbiome composition may differ by Bd strain. Additional studies are needed to further investigate the structural and temporal dynamics of microbiome shifts during metamorphosis in wild and captive amphibian populations. Analyses of the ontogeny of microbiome shifts may contribute to an understanding of why amphibians vary in their susceptibility to chytridiomycosis.}, }
@article {pmid28725664, year = {2017}, author = {Rekadwad, BN and Khobragade, CN}, title = {Morphotypes and pigment profiles of halophilic bacteria: Practical data useful for novelty, taxonomic categorization and for describing novel species or new taxa.}, journal = {Data in brief}, volume = {13}, number = {}, pages = {609-619}, pmid = {28725664}, issn = {2352-3409}, abstract = {Halophilic bacteria were isolated from oil spill samples collected from West-coast of Goa. Bacteria were isolated from oil studded soil, salt marsh and offshore samples (A, A7, CSM, CB and CM) collected along the West coastline in Goa (India) i.e. Arambol beach, Calanguate beach, Candolim beach and Colva beach on Zobell Marine agar, R2A agar, Mannitol salt agar and Blood agar at temperature 22 to 24 °C. Isolates showed growth in the presence of hydrocarbons (1% phenanthrene and 2% bitumen). Diverse profiles of pigments were observed on different nutrient medium. Color of pigments produced on agar media recorded as per standard color chart. All isolates showed different growth pattern. Isolate no 11 (GOACSMMS-11) showed three different morphological features/growth patterns on Zobell Marine Agar and R2A medium in the presence of hydrocarbons. Results obtained yield new information which gives a clear idea about morphological features and pigmented profiles of hydrocarbon resistant morphotypes in the presence different media compositions. The presented datasets will be useful for studies on bacterial species showing high sequence similarity. Hence, generated data serves as a benchmark for to distinguish between genetically similar bacteria and for further research in phenotype based microbial diversity, microbial ecology of microorganisms and microbial systematics and taxonomy in addition to genotype data.}, }
@article {pmid28724405, year = {2017}, author = {Adriaenssens, EM and Kramer, R and Van Goethem, MW and Makhalanyane, TP and Hogg, I and Cowan, DA}, title = {Environmental drivers of viral community composition in Antarctic soils identified by viromics.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {83}, pmid = {28724405}, issn = {2049-2618}, mesh = {Antarctic Regions ; Bacteriophages/classification/*genetics/isolation &amp; purification ; Ecosystem ; *Environment ; Genome, Viral ; Phylogeny ; RNA, Ribosomal, 16S ; *Soil Microbiology ; Viruses/classification/*genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: The Antarctic continent is considered the coldest and driest place on earth with simple ecosystems, devoid of higher plants. Soils in the ice-free regions of Antarctica are known to harbor a wide range of microorganisms from primary producers to grazers, yet their ecology and particularly the role of viruses is poorly understood. In this study, we examined the virus community structures of 14 soil samples from the Mackay Glacier region.<br><br>METHODS: Viral communities were extracted from soil and the dsDNA was extracted, amplified using single-primer amplification, and sequenced using the Ion Torrent Proton platform. Metadata on soil physico-chemistry was collected from all sites. Both read and contig datasets were analyzed with reference-independent and reference-dependent methods to assess viral community structures and the influence of environmental parameters on their distribution.<br><br>RESULTS: We observed a high heterogeneity in virus signatures, independent of geographical proximity. Tailed bacteriophages were dominant in all samples, but the incidences of the affiliated families Siphoviridae and Myoviridae were inversely correlated, suggesting direct competition for hosts. Viruses of the families Phycodnaviridae and Mimiviridae were present at significant levels in high-diversity soil samples and were found to co-occur, implying little competition between them. Combinations of soil factors, including pH, calcium content, and site altitude, were found to be the main drivers of viral community structure.<br><br>CONCLUSIONS: The pattern of viral community structure with higher levels of diversity at lower altitude and pH, and co-occurring viral families, suggests that these cold desert soil viruses interact with each other, the host, and the environment in an intricate manner, playing a potentially crucial role in maintaining host diversity and functioning of the microbial ecosystem in the extreme environments of Antarctic soil.}, }
@article {pmid28721506, year = {2018}, author = {Walczyńska, A and Sobczyk, M and Fiałkowska, E and Pajdak-Stós, A and Fyda, J and Wiąckowski, K}, title = {Interaction Between a Bacterivorous Ciliate Aspidisca cicada and a Rotifer Lecane inermis: Doozers and Fraggles in Aquatic Flocs.}, journal = {Microbial ecology}, volume = {75}, number = {3}, pages = {569-581}, pmid = {28721506}, issn = {1432-184X}, support = {GEKON1/O3/214361/8/2014//Narodowe Centrum Bada&#x144; i Rozwoju/ ; }, mesh = {Ammonia/analysis/metabolism ; Animals ; Batch Cell Culture Techniques ; Biological Oxygen Demand Analysis ; Cell Proliferation ; Flocculation ; Hypotrichida/*growth &amp; development/*physiology ; Nitrates/analysis ; Phosphorus/analysis ; Rotifera/*physiology ; Sewage/*microbiology ; Waste Disposal, Fluid ; Wastewater/parasitology ; Water Purification ; }, abstract = {Activated sludge is a semi-natural habitat composed of macroaggregates made by flocculating bacteria and inhabited by numerous protozoans and metazoans, creating a complicated interactome. The activated sludge resembles the biological formation of naturally occurring floc habitats, such as "marine snow." So far, these two types of habitat have been analyzed separately, despite their similarities. We examined the effect of a bacterivorous ciliate, Aspidisca cicada, on the quality of the macroaggregate ecosystem by estimating (i) the floc characteristics, (ii) the proliferation of other bacterivores (rotifers), and (iii) the chemical processes. We found that A. cicada (i) positively affected floc quality by creating flocs of larger size; (ii) promoted the population growth of the rotifer Lecane inermis, an important biological agent in activated sludge systems; and (iii) increased the efficiency of ammonia removal while at the same time improving the oxygen conditions. The effect of A. cicada was detectable long after its disappearance from the system. We therefore claim that A. cicada is a very specialized scavenger of flocs with a key role in floc ecosystem functioning. These results may be relevant to the ecology of any natural and engineered aggregates.}, }
@article {pmid28721505, year = {2018}, author = {Park, BS and Li, Z and Kang, YH and Shin, HH and Joo, JH and Han, MS}, title = {Distinct Bloom Dynamics of Toxic and Non-toxic Microcystis (Cyanobacteria) Subpopulations in Hoedong Reservoir (Korea).}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {163-173}, pmid = {28721505}, issn = {1432-184X}, support = {Mid-career Researcher Program (2015R1A2A2A01008115)//National Research Foundation of Korea/ ; }, mesh = {Bacterial Toxins/metabolism ; Cyanobacteria Toxins ; Ecosystem ; Eutrophication ; Lakes/chemistry/*microbiology ; Marine Toxins/metabolism ; Microcystins/metabolism ; Microcystis/classification/genetics/*growth &amp; development/metabolism ; Phylogeny ; Republic of Korea ; Seasons ; Temperature ; }, abstract = {Despite the importance of understanding the bloom mechanisms that influence cyanobacterial toxin production, the dynamics of toxic Microcystis subpopulations are largely unknown. Here, we quantified both toxic and entire (i.e., toxic and non-toxic) Microcystis populations based on the microcystin synthetase E (mcyE) and 16S ribosomal RNA genes. Samples were collected from pelagic water and sediments twice per week from October to December 2011, and we investigated the effects of physicochemical factors (pH, water temperature, dissolved oxygen, nutrients, etc.) and biological factors (ciliates and zooplankton) on the abundance of toxic and non-toxic Microcystis. During the study period, Microcystis blooms were composed of toxic and non-toxic subpopulations. Resting stage Microcystis in sediment may be closely linked to Microcystis populations in pelagic water and may contribute to the toxic subpopulation composition in surface Microcystis blooms. In pelagic water, the toxic and entire Microcystis population had a significant positive correlation with the pH and water temperature (p < 0.05). However, their responses to changes in environmental factors were thought to be distinct. The ratio of the toxic to non-toxic Microcystis subpopulations was significantly (p < 0.05) enhanced by a lower pH and water temperature and an increase in protozoan grazers, reflecting environmental stresses. These results suggest that the toxic and non-toxic subpopulations of Microcystis have distinct tolerance levels against these stressors. The intracellular microcystin (MC) concentration was positively associated with the abundance of the mcyE-positive Microcystis. By comparison, the MC concentration in pelagic water body (extracellular) increased when Microcystis was lysed due to environmental stresses.}, }
@article {pmid28721504, year = {2018}, author = {LeBrun, ES and King, RS and Back, JA and Kang, S}, title = {Microbial Community Structure and Function Decoupling Across a Phosphorus Gradient in Streams.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {64-73}, pmid = {28721504}, issn = {1432-184X}, mesh = {Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Biodiversity ; Ecosystem ; Metagenome ; *Microbiota ; Phosphorus/*analysis/metabolism ; Phylogeny ; Rivers/chemistry/*microbiology ; }, abstract = {Phosphorus (P) is a key biological element with important and unique biogeochemical cycling in natural ecosystems. Anthropogenic phosphorus inputs have been shown to greatly affect natural ecosystems, and this has been shown to be especially true of freshwater systems. While the importance of microbial communities in the P cycle is widely accepted, the role, composition, and relationship to P of these communities in freshwater systems still hold many secrets. Here, we investigated combined bacterial and archaeal communities utilizing 16S ribosomal RNA (rRNA) gene sequencing and computationally predicted functional metagenomes (PFMs) in 25 streams representing a strong P gradient. We discovered that 16S rRNA community structure and PFMs demonstrate a degree of decoupling between structure and function in the system. While we found that total phosphorus (TP) was correlated to the structure and functional capability of bacterial and archaeal communities in the system, turbidity had a stronger, but largely independent, correlation. At TP levels of approximately 55 μg/L, we see sharp differences in the abundance of numerous ecologically important taxa related to vegetation, agriculture, sediment, and other ecosystem inhabitants.}, }
@article {pmid28721503, year = {2018}, author = {Junger, PC and Amado, AM and Paranhos, R and Cabral, AS and Jacques, SMS and Farjalla, VF}, title = {Salinity Drives the Virioplankton Abundance but Not Production in Tropical Coastal Lagoons.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {52-63}, pmid = {28721503}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Ecosystem ; Plankton/classification/genetics/growth &amp; development/*isolation &amp; purification ; Salinity ; Seawater/*chemistry/microbiology/*virology ; Viruses/classification/genetics/growth &amp; development/*isolation &amp; purification ; }, abstract = {Viruses are the most abundant components of microbial food webs and play important ecological and biogeochemical roles in aquatic ecosystems. Virioplankton is regulated by several environmental factors, such as salinity, turbidity, and humic substances. However, most of the studies aimed to investigate virioplankton regulation were conducted in temperate systems combining a limited range of environmental variables. In this study, virus abundance and production were determined and their relation to bacterial and limnological variables was assessed in 20 neighboring shallow tropical coastal lagoons that present wide environmental gradients of turbidity (2.32-571 NTU), water color (1.82-92.49 m[-1]), dissolved organic carbon (0.71-16.7 mM), salinity (0.13-332.1‰), and chlorophyll-a (0.28 to 134.5 μg L[-1]). Virus abundance varied from 0.37 × 10[8] to 117 × 10[8] virus-like-particle (VLP) mL[-1], with the highest values observed in highly salty aquatic systems. Salinity and heterotrophic bacterial abundance were the main variables positively driving viral abundances in these lagoons. We suggest that, with increased salinity, there is a decrease in the protozoan control on bacterial populations and lower bacterial diversity (higher encounter rates with virus specific hosts), both factors positively affecting virus abundance. Virus production varied from 0.68 × 10[7] to 56.5 × 10[7] VLP mL[-1] h[-1] and was regulated by bacterial production and total phosphorus, but it was not directly affected by salinity. The uncoupling between virus abundance and virus production supports that the hypothesis that the lack of grazing pressure on viral and bacterial populations is an important mechanism causing virus abundance to escalate with increasing salt concentrations.}, }
@article {pmid28721502, year = {2018}, author = {Bunesova, V and Lacroix, C and Schwab, C}, title = {Mucin Cross-Feeding of Infant Bifidobacteria and Eubacterium hallii.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {228-238}, pmid = {28721502}, issn = {1432-184X}, support = {13.151//SCIEX (CA)/ ; }, mesh = {Adult ; Animals ; Bifidobacterium/growth &amp; development/isolation &amp; purification/*metabolism ; Breast Feeding ; Eubacterium/growth &amp; development/isolation &amp; purification/*metabolism ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Female ; Fermentation ; Gastrointestinal Microbiome ; Humans ; Infant ; Intestines/microbiology ; Male ; Mucins/*metabolism ; }, abstract = {Mucus production is initiated before birth and provides mucin glycans to the infant gut microbiota. Bifidobacteria are the major bacterial group in the feces of vaginally delivered and breast milk-fed infants. Among the bifidobacteria, only Bifidobacterium bifidum is able to degrade mucin and to release monosaccharides which can be used by other gut microbes colonizing the infant gut. Eubacterium hallii is an early occurring commensal that produces butyrate and propionate from fermentation metabolites but that cannot degrade complex oligo- and polysaccharides. We aimed to demonstrate that mucin cross-feeding initiated by B. bifidum enables growth and metabolite formation of E. hallii leading to short-chain fatty acid (SCFA) formation. Growth and metabolite formation of co-cultures of B. bifidum, of Bifidobacterium breve or Bifidobacterium infantis, which use mucin-derived hexoses and fucose, and of E. hallii were determined. Growth of E. hallii in the presence of lactose and mucin monosaccharides was tested. In co-culture fermentations, the presence of B. bifidum enabled growth of the other strains. B. bifidum/B. infantis co-cultures yielded acetate, formate, and lactate while co-cultures of B. bifidum and E. hallii formed acetate, formate, and butyrate. In three-strain co-cultures, B. bifidum, E. hallii, and B. breve or B. infantis produced up to 16 mM acetate, 5 mM formate, and 4 mM butyrate. The formation of propionate (approximately 1 mM) indicated cross-feeding on fucose. Lactose, galactose, and GlcNAc were identified as substrates of E. hallii. This study shows that trophic interactions of bifidobacteria and E. hallii lead to the formation of acetate, butyrate, propionate, and formate, potentially contributing to intestinal SCFA formation with potential benefits for the host and for microbial colonization of the infant gut. The ratios of SCFA formed differed depending on the microbial species involved in mucin cross-feeding.}, }
@article {pmid28721252, year = {2016}, author = {Lim, CP and Mai, PNQ and Roizman Sade, D and Lam, YC and Cohen, Y}, title = {Biofilm development of an opportunistic model bacterium analysed at high spatiotemporal resolution in the framework of a precise flow cell.}, journal = {NPJ biofilms and microbiomes}, volume = {2}, number = {}, pages = {16023}, pmid = {28721252}, issn = {2055-5008}, abstract = {Life of bacteria is governed by the physical dimensions of life in microscales, which is dominated by fast diffusion and flow at low Reynolds numbers. Microbial biofilms are structurally and functionally heterogeneous and their development is suggested to be interactively related to their microenvironments. In this study, we were guided by the challenging requirements of precise tools and engineered procedures to achieve reproducible experiments at high spatial and temporal resolutions. Here, we developed a robust precise engineering approach allowing for the quantification of real-time, high-content imaging of biofilm behaviour under well-controlled flow conditions. Through the merging of engineering and microbial ecology, we present a rigorous methodology to quantify biofilm development at resolutions of single micrometre and single minute, using a newly developed flow cell. We designed and fabricated a high-precision flow cell to create defined and reproducible flow conditions. We applied high-content confocal laser scanning microscopy and developed image quantification using a model biofilm of a defined opportunistic strain, Pseudomonas putida OUS82. We observed complex patterns in the early events of biofilm formation, which were followed by total dispersal. These patterns were closely related to the flow conditions. These biofilm behavioural phenomena were found to be highly reproducible, despite the heterogeneous nature of biofilm.}, }
@article {pmid28721250, year = {2016}, author = {Van den Abbeele, P and Marzorati, M and Derde, M and De Weirdt, R and Joan, V and Possemiers, S and Van de Wiele, T}, title = {Arabinoxylans, inulin and Lactobacillus reuteri 1063 repress the adherent-invasive Escherichia coli from mucus in a mucosa-comprising gut model.}, journal = {NPJ biofilms and microbiomes}, volume = {2}, number = {}, pages = {16016}, pmid = {28721250}, issn = {2055-5008}, abstract = {The microbiota that colonises the intestinal mucus may particularly affect human health given its proximity to the epithelium. For instance, the presence of the adherent-invasive Escherichia coli (AIEC) in this mucosal microbiota has been correlated with Crohn's disease. Using short-term screening assays and a novel long-term dynamic gut model, which comprises a simulated mucosal environment (M-SHIME), we investigated how (potential) pro- and prebiotics may repress colonisation of AIEC from mucus. Despite that during the short-term screening assays, some of the investigated Lactobacillus strains adhered strongly to mucins, none of them competed with AIEC for mucin-adhesion. In contrast, AIEC survival and growth during co-culture batch incubations was decreased by Lactobacillus rhamnosus GG and L. reuteri 1063, which correlated with (undissociated) lactic acid and reuterin levels. Regarding the prebiotics, long-chain arabinoxylans (LC-AX) lowered the initial mucin-adhesion of AIEC, while both inulin (IN) and galacto-oligosaccharides (GOS) limited AIEC survival and growth during batch incubations. L. reuteri 1063, LC-AX and IN were thus retained for a long-term study with the M-SHIME. All treatments repressed AIEC from mucus without affecting AIEC numbers in the luminal content. As a possible explanation, L. reuteri 1063 treatment increased lactobacilli levels in mucus, while LC-AX and IN additionally increased mucosal bifidobacteria levels, thus leading to antimicrobial effects against AIEC in mucus. Overall, this study shows that pro- and prebiotics can beneficially modulate the in vitro mucosal microbiota, thus limiting occurrence of opportunistic pathogens among those mucosal microbes which may directly interact with the host given their proximity to the epithelium.}, }
@article {pmid28717834, year = {2018}, author = {Aagesen, AM and Phuvasate, S and Su, YC and Häse, CC}, title = {Characterizing the Adherence Profiles of Virulent Vibrio parahaemolyticus Isolates.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {152-162}, pmid = {28717834}, issn = {1432-184X}, support = {2011-68003-30005//National Institute of Food and Agriculture/ ; 2011-68003-30005//National Research Initiative Food Safety and Epidemiology Program (32.0A)/ ; }, mesh = {Animals ; *Bacterial Adhesion ; Biofilms ; Humans ; Ostreidae/growth &amp; development/*microbiology ; Shellfish/*microbiology ; Vibrio parahaemolyticus/classification/genetics/isolation &amp; purification/*physiology ; }, abstract = {The human pathogen Vibrio parahaemolyticus is a leading cause of seafood-borne illness in the USA, and infections with V. parahaemolyticus typically result from eating raw or undercooked oysters. V. parahaemolyticus has been shown to be highly resistant to oyster depuration, suggesting that the bacterium possesses specific mechanisms or factors for colonizing oysters and persisting during depuration. In this study, we characterized eight different V. parahaemolyticus strains for differences in resistance to oyster depuration, biofilm formation, and motility. While each strain exhibited distinct phenotypes in the various assays, we determined that biofilm formation on abiotic surfaces, such as glass or plastic, does not directly correlate with bacterial retention in oysters during depuration. However, we did observe that the motility phenotype of a strain appeared to be a better indicator for persistence in the oyster. Further studies examining the molecular mechanisms underlying the observed colonization differences by these and other V. parahaemolyticus strains may provide beneficial insights into what critical factors are required for proficient colonization of the Pacific oyster.}, }
@article {pmid28715758, year = {2017}, author = {Turolla, A and Sabatino, R and Fontaneto, D and Eckert, EM and Colinas, N and Corno, G and Citterio, B and Biavasco, F and Antonelli, M and Mauro, A and Mangiaterra, G and Di Cesare, A}, title = {Defence strategies and antibiotic resistance gene abundance in enterococci under stress by exposure to low doses of peracetic acid.}, journal = {Chemosphere}, volume = {185}, number = {}, pages = {480-488}, doi = {10.1016/j.chemosphere.2017.07.032}, pmid = {28715758}, issn = {1879-1298}, mesh = {Bacteria/*drug effects ; Disinfectants/pharmacology ; Disinfection/methods ; Dose-Response Relationship, Drug ; Drug Resistance, Microbial/*genetics ; Enterococcus/*drug effects ; Peracetic Acid/*pharmacology ; *Stress, Physiological ; Water Microbiology ; Water Purification/methods ; }, abstract = {Peracetic acid (PAA) is an organic compound used efficiently as disinfectant in wastewater treatments. Yet, at low doses it may cause selection; thus, the effect of low doses of PAA on Enterococcus faecium as a proxy of human-related microbial waste was evaluated. Bacteria were treated with increasing doses of PAA (from 0 to 25 mg L[-1] min) and incubated in regrowth experiments under non-growing, limiting conditions and under growing, favorable conditions. The changes in bacterial abundance, in bacterial phenotype (number and composition of small cell clusters), and in the abundance of an antibiotic resistance gene (ARG) was evaluated. The experiment demonstrated that the selected doses of PAA efficiently removed enterococci, and induced a long-lasting effect after PAA inactivation. The relative abundance of small clusters increased during the experiment when compared with that of the inoculum. Moreover, under growing favorable conditions the relative abundance of small clusters decreased and the number of cells per cluster increased with increasing PAA doses. A strong stability of the measured ARG was found, not showing any effect during the whole experiment. The results demonstrated the feasibility of low doses of PAA to inactivate bacteria. However, the stress induced by PAA disinfection promoted a bacterial adaptation, even if potentially without affecting the abundance of the ARG.}, }
@article {pmid28715138, year = {2018}, author = {Yuan, MM and Zhang, J and Xue, K and Wu, L and Deng, Y and Deng, J and Hale, L and Zhou, X and He, Z and Yang, Y and Van Nostrand, JD and Schuur, EAG and Konstantinidis, KT and Penton, CR and Cole, JR and Tiedje, JM and Luo, Y and Zhou, J}, title = {Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil.}, journal = {Global change biology}, volume = {24}, number = {1}, pages = {297-307}, doi = {10.1111/gcb.13820}, pmid = {28715138}, issn = {1365-2486}, mesh = {Alaska ; Carbon/analysis ; Climate Change ; Fungi/metabolism ; Permafrost/*chemistry/*microbiology ; *Soil Microbiology ; Temperature ; *Tundra ; }, abstract = {Permafrost soil in high latitude tundra is one of the largest terrestrial carbon (C) stocks and is highly sensitive to climate warming. Understanding microbial responses to warming-induced environmental changes is critical to evaluating their influences on soil biogeochemical cycles. In this study, a functional gene array (i.e., geochip 4.2) was used to analyze the functional capacities of soil microbial communities collected from a naturally degrading permafrost region in Central Alaska. Varied thaw history was reported to be the main driver of soil and plant differences across a gradient of minimally, moderately, and extensively thawed sites. Compared with the minimally thawed site, the number of detected functional gene probes across the 15-65 cm depth profile at the moderately and extensively thawed sites decreased by 25% and 5%, while the community functional gene β-diversity increased by 34% and 45%, respectively, revealing decreased functional gene richness but increased community heterogeneity along the thaw progression. Particularly, the moderately thawed site contained microbial communities with the highest abundances of many genes involved in prokaryotic C degradation, ammonification, and nitrification processes, but lower abundances of fungal C decomposition and anaerobic-related genes. Significant correlations were observed between functional gene abundance and vascular plant primary productivity, suggesting that plant growth and species composition could be co-evolving traits together with microbial community composition. Altogether, this study reveals the complex responses of microbial functional potentials to thaw-related soil and plant changes and provides information on potential microbially mediated biogeochemical cycles in tundra ecosystems.}, }
@article {pmid28714057, year = {2018}, author = {He, X and Chaganti, SR and Heath, DD}, title = {Population-Specific Responses to Interspecific Competition in the Gut Microbiota of Two Atlantic Salmon (Salmo salar) Populations.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {140-151}, pmid = {28714057}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; DNA, Bacterial/genetics ; *Gastrointestinal Microbiome ; Intestines/*microbiology ; Ontario ; RNA, Ribosomal, 16S/genetics ; Salmo salar/classification/*microbiology ; }, abstract = {The gut microbial community in vertebrates plays a role in nutrient digestion and absorption, development of intestine and immune systems, resistance to infection, regulation of bone mass and even host behavior and can thus impact host fitness. Atlantic salmon (Salmo salar) reintroduction efforts into Lake Ontario, Canada, have been unsuccessful, likely due to competition with non-native salmonids. In this study, we explored interspecific competition effects on the gut microbiota of two Atlantic salmon populations (LaHave and Sebago) resulting from four non-native salmonids. After 10 months of rearing in semi-natural stream tanks under six interspecific competition treatments, we characterized the gut microbiota of 178 Atlantic salmon by parallel sequencing the 16S rRNA gene. We found 3978 bacterial OTUs across all samples. Microbiota alpha diversity and abundance of 27 OTUs significantly differed between the two populations. Interspecific competition reduced relative abundance of potential beneficial bacteria (six genera of lactic acid bacteria) as well as 13 OTUs, but only in the LaHave population, indicating population-specific competition effects. The pattern of gut microbiota response to interspecific competition may reflect local adaptation of the host-microbiota interactions and can be used to select candidate populations for improved species reintroduction success.}, }
@article {pmid28712045, year = {2018}, author = {Francioli, D and Schulz, E and Buscot, F and Reitz, T}, title = {Dynamics of Soil Bacterial Communities Over a Vegetation Season Relate to Both Soil Nutrient Status and Plant Growth Phenology.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {216-227}, pmid = {28712045}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biomass ; Microbiota ; *Plant Development ; Plants/classification/*microbiology ; Seasons ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Soil microorganisms regulate element cycling and plant nutrition, mediate co-existence of neighbors, and stabilize plant communities. Many of these effects are dependent upon environmental conditions and, in particular, on nutrient quality and availability in soils. In this context, we set up a pot experiment in order to examine the combined effects of soil nutrient availability and microbial communities on plant-soil interactions and to investigate assemblage rules for soil bacterial communities under changed nutrient conditions. Four gamma-sterilized soils, strongly differing in their nutrient contents, were obtained from different fertilization treatments of a centenary field experiment and used to grow communities of grassland plants. The sterilized soils were either self- or cross-inoculated with microbial consortia from the same four soils. Molecular fingerprinting analyses were carried out at several time points in order to identify drivers and underlying processes of microbial community assemblage. We observed that the bacterial communities that developed in the inoculated sterilized soils differed from those in the original soils, displaying dynamic shifts over time. These shifts were illustrated by the appearance of numerous OTUs that had not been detected in the original soils. The community patterns observed in the inoculated treatments suggested that bacterial community assembly was determined by both niche-mediated and stochastic-neutral processes, whereby the relative impacts of these processes changed over the course of the vegetation season. Moreover, our experimental approach allowed us not only to evaluate the effects of soil nutrients on plant performance but also to recognize a negative effect of the microbial community present in the soil that had not been fertilized for more than 100 years on plant biomass. Our findings demonstrate that soil inoculation-based approaches are valid for investigating plant-soil-microbe interactions and for examining rules that shape soil microbial community assemblages under variable ecological conditions.}, }
@article {pmid28709972, year = {2017}, author = {Sari, T and Wade, MJ}, title = {Generalised approach to modelling a three-tiered microbial food-web.}, journal = {Mathematical biosciences}, volume = {291}, number = {}, pages = {21-37}, pmid = {28709972}, issn = {1879-3134}, support = {BB/K003240/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria, Anaerobic/*metabolism ; *Food Chain ; Kinetics ; *Models, Biological ; }, abstract = {The complexity of the anaerobic digestion process has motivated the development of complex models, such as the widely used Anaerobic Digestion Model No. 1. However, this complexity makes it intractable to identify the stability profile coupled to the asymptotic behaviour of existing steady-states as a function of conventional chemostat operating parameters (substrate inflow concentration and dilution rate). In a previous study this model was simplified and reduced to its very backbone to describe a three-tiered chlorophenol mineralising food-web, with its stability analysed numerically using consensus values for the various biological parameters of the Monod growth functions. Steady-states where all organisms exist were always stable and non-oscillatory. Here we investigate a generalised form of this three-tiered food-web, whose kinetics do not rely on the specific kinetics of Monod form. The results are valid for a large class of growth kinetics as long as they keep the signs of their derivatives. We examine the existence and stability of the identified steady-states and find that, without a maintenance term, the stability of the system may be characterised analytically. These findings permit a better understanding of the operating region of the bifurcation diagram where all organisms exist, and its dependence on the biological parameters of the model. For the previously studied Monod kinetics, we identify four interesting cases that show this dependence of the operating diagram with respect to the biological parameters. When maintenance is included, it is necessary to perform numerical analysis. In both cases we verify the discovery of two important phenomena; i) the washout steady-state is always stable, and ii) a switch in dominance between two organisms competing for hydrogen results in the system becoming unstable and a loss in viability. We show that our approach results in the discovery of an unstable operating region in its positive steady-state, where all three organisms exist, a fact that has not been reported in a previous numerical study. This type of analysis can be used to determine critical behaviour in microbial communities in response to changing operating conditions.}, }
@article {pmid28709884, year = {2017}, author = {Yuan, Y and Bolan, N and Prévoteau, A and Vithanage, M and Biswas, JK and Ok, YS and Wang, H}, title = {Applications of biochar in redox-mediated reactions.}, journal = {Bioresource technology}, volume = {246}, number = {}, pages = {271-281}, doi = {10.1016/j.biortech.2017.06.154}, pmid = {28709884}, issn = {1873-2976}, mesh = {Biomass ; *Charcoal ; Graphite ; Oxidation-Reduction ; }, abstract = {Biochar is chemically more reduced and reactive than the original feedstock biomass. Graphite regions, functional groups, and redox-active metals in biochar contribute to its redox characteristics. While the functional groups such as phenolic species in biochar are the main electron donating moieties (i.e., reducers), the quinones and polycondensed aromatic functional groups are the components accepting electrons (oxidants). The redox capacity of biochar depends on feedstock properties and pyrolysis conditions. This paper aims to review and summarize the various synthesis techniques for biochars and the methods for probing their redox characteristics. We review the abiotic and microbial applications of biochars as electron donors, electron acceptors, or electron shuttles for pollutant degradation, metal(loid)s (im)mobilization, nutrient transformation, and discuss the underlying mechanisms. Furthermore, knowledge gaps that exist in the exploration and differentiation of the electron transfer mechanisms involving biochars are also identified.}, }
@article {pmid28709370, year = {2017}, author = {Auguet, O and Pijuan, M and Borrego, CM and Rodriguez-Mozaz, S and Triadó-Margarit, X and Giustina, SVD and Gutierrez, O}, title = {Sewers as potential reservoirs of antibiotic resistance.}, journal = {The Science of the total environment}, volume = {605-606}, number = {}, pages = {1047-1054}, doi = {10.1016/j.scitotenv.2017.06.153}, pmid = {28709370}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Biofilms ; Drug Resistance, Bacterial/*genetics ; *Genes, Bacterial ; Integrons ; *Sanitation ; Spain ; Wastewater/*microbiology ; }, abstract = {Wastewater transport along sewers favors the colonization of inner pipe surfaces by wastewater-derived microorganisms that grow forming biofilms. These biofilms are composed of rich and diverse microbial communities that are continuously exposed to antibiotic residues and antibiotic resistant bacteria (ARB) from urban wastewater. Sewer biofilms thus appear as an optimal habitat for the dispersal and accumulation of antibiotic resistance genes (ARGs). In this study, the concentration of antibiotics, integron (intI1) and antibiotic resistance genes (qnrS, sul1, sul2, blaTEM, blaKPC, ermB, tetM and tetW), and potential bacterial pathogens were analyzed in wastewater and biofilm samples collected at the inlet and outlet sections of a pressurized sewer pipe. The most abundant ARGs detected in both wastewater and biofilm samples were sul1 and sul2 with roughly 1 resistance gene for each 10 copies of 16s RNA gene. Significant differences in the relative abundance of gene intI1 and genes conferring resistance to fluoroquinolones (qnrS), sulfonamides (sul1 and sul2) and betalactams (blaTEM) were only measured between inlet and outlet biofilm samples. Composition of bacterial communities also showed spatial differences in biofilms and a higher prevalence of Operational Taxonomic Units (OTUs) with high sequence identity (>98%) to well-known human pathogens was observed in biofilms collected at the inlet pipe section. Our study highlights the role of sewer biofilms as source and sink of ARB and ARGs and supports the idea that community composition rather than antibiotic concentration is the main factor driving the diversity of the sewage resistome.}, }
@article {pmid28709076, year = {2017}, author = {Dasgupta, S and Wu, S and Goel, R}, title = {Coupling autotrophic denitrification with partial nitritation-anammox (PNA) for efficient total inorganic nitrogen removal.}, journal = {Bioresource technology}, volume = {243}, number = {}, pages = {700-707}, doi = {10.1016/j.biortech.2017.06.130}, pmid = {28709076}, issn = {1873-2976}, mesh = {Autotrophic Processes ; Bacteria/genetics ; Bioreactors ; *Denitrification ; Nitrogen ; *RNA, Ribosomal, 16S ; }, abstract = {The performance of and the microbial ecology in an integrated lab scale set up comprising of a PN/A bioreactor and an elemental sulfur-supported packed bed autotrophic denitrification (ESSAD) are reported. The PN/A reactor exhibited an average removal rate of 0.56±0.103kgNm[-3]d[-1], whereas the ESSAD reactor removed an average of 0.0018kg NO3[-]-Nm[-3]d[-1]. The combined average removal rate was 0.6kgNm[-3]d[-1], yielding an overall total inorganic nitrogen efficiency of 97%. Based on 16S rRNA gene clone libraries from the ESSAD reactor, the extracted Operational Taxonomic Units (OTUs) formed a clade with Thiobacillus denitrificans sp. indicating a common ancestral relationship. High throughput amplicon sequencing targeting V3 region of 16S rRNA gene for the biofilm in the ESSAD also revealed an abundance of the Thiobacillus genus. Additionally, 16s rRNA amplicon sequencing of the genomic DNA from the PN/A reactor reflected a dominance of the Planctomycetes phylum.}, }
@article {pmid28708058, year = {2017}, author = {Si, OJ and Yang, HY and Hwang, CY and Kim, SJ and Choi, SB and Kim, JG and Jung, MY and Kim, SG and Roh, SW and Rhee, SK}, title = {Kiloniella antarctica sp. nov., isolated from a polynya of Amundsen Sea in Western Antarctic Sea.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {67}, number = {7}, pages = {2397-2402}, doi = {10.1099/ijsem.0.001968}, pmid = {28708058}, issn = {1466-5034}, mesh = {Alphaproteobacteria/*classification/genetics/isolation &amp; purification ; Antarctic Regions ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {A taxonomic study was conducted on strain soj2014T, which was isolated from the surface water of a polynya in the Antarctic Sea. Comparative 16S rRNA gene sequence analysis showed that strain soj2014T belongs to the family Kiloniellaceae and is closely related to Kiloniella spongiae MEBiC09566T, 'Kiloniella litopenaei' P1-1T and Kiloniella laminariae LD81T (98.0 %, 97.8 % and 96.2 % 16S rRNA gene sequence similarity, respectively). The DNA-DNA hybridization values between strain soj2014T and closely related strains were below 28.6 %. The G+C content of the genomic DNA of strain soj2014T was 45.5 mol%. The predominant cellular fatty acids were summed feature 8 (composed of C18 : 1ω6c/C18 : 1ω7c, 57.0 %) and summed feature 3 (composed of C16 : 1ω6c/C16 : 1ω7c, 23.5 %). Strain soj2014T was Gram-stain-negative, slightly curved, spiral-shaped, and motile with a single polar flagellum. The strain grew at 0-30 °C (optimum, 25 °C), in 1.5-5.1 % (w/v) NaCl (optimum, 2.1-2.4 %) and at pH 5.5-9.5 (optimum, 7.5-8.0). It also had differential carbohydrate utilization traits and enzyme activities compared with closely related strains. Based on these phylogenetic, phenotypic and chemotaxonomic analyses, strain soj2014T represents a distinct species, separable from the reference strains, and is, therefore, proposed as a novel species, Kiloniella antarctica sp. nov. The type strain is soj2014T (=KCTC 42186T=JCM 30386T).}, }
@article {pmid28707145, year = {2018}, author = {Laanbroek, HJ and Veenhuizen, PTM and Keijzer, RM and Hefting, MM}, title = {Numerical Relationships Between Archaeal and Bacterial amoA Genes Vary by Icelandic Andosol Classes.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {204-215}, pmid = {28707145}, issn = {1432-184X}, mesh = {Ammonia/metabolism ; Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Proteins/*genetics ; Biodiversity ; Iceland ; Oxidation-Reduction ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {Bacterial amoA genes had not been detectable by qPCR in freshly sampled Icelandic Andosols thus far. Hence, a new primer set yielding shorter gene fragments has been designed to verify the absence of ammonia-oxidizing bacteria in different Icelandic Andosol classes. At the same time, a new primer set was also constructed for archaeal amoA genes that should improve the quality of PCR products. Although a large part of the soil samples were found to be amoA-negative, bacterial amoA genes were detectable with new as well as old primer sets. The same results were obtained for the archaeal amoA genes. The relative distribution of archaeal and bacterial amoA genes varied between Andosol classes. Archaeal amoA genes were significantly more abundant in Brown than in Histic Andosols, while the opposite was observed for bacterial amoA genes. The numbers of archaeal and bacterial amoA genes in Gleyic Andosols were not significantly different from those in Histic and Brown Andosols. The numbers of bacterial amoA genes, but not the numbers of archaeal amoA genes, correlated significantly and positively with potential ammonia oxidation activities. The presence of the bacterial nitrification inhibitor allylthiourea inhibited the potential ammonia oxidation activities during the first 12 h of incubation. Hence, it was concluded that ammonia-oxidizing bacteria profited most from the conditions during the measurements of potential ammonia oxidation activities.}, }
@article {pmid28706508, year = {2017}, author = {Maciejewska, M and Adam, D and Naômé, A and Martinet, L and Tenconi, E and Całusińska, M and Delfosse, P and Hanikenne, M and Baurain, D and Compère, P and Carnol, M and Barton, HA and Rigali, S}, title = {Assessment of the Potential Role of Streptomyces in Cave Moonmilk Formation.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1181}, pmid = {28706508}, issn = {1664-302X}, abstract = {Moonmilk is a karstic speleothem mainly composed of fine calcium carbonate crystals (CaCO3) with different textures ranging from pasty to hard, in which the contribution of biotic rock-building processes is presumed to involve indigenous microorganisms. The real microbial input in the genesis of moonmilk is difficult to assess leading to controversial hypotheses explaining the origins and the mechanisms (biotic vs. abiotic) involved. In this work, we undertook a comprehensive approach in order to assess the potential role of filamentous bacteria, particularly a collection of moonmilk-originating Streptomyces, in the genesis of this speleothem. Scanning electron microscopy (SEM) confirmed that indigenous filamentous bacteria could indeed participate in moonmilk development by serving as nucleation sites for CaCO3 deposition. The metabolic activities involved in CaCO3 transformation were furthermore assessed in vitro among the collection of moonmilk Streptomyces, which revealed that peptides/amino acids ammonification, and to a lesser extend ureolysis, could be privileged metabolic pathways participating in carbonate precipitation by increasing the pH of the bacterial environment. Additionally, in silico search for the genes involved in biomineralization processes including ureolysis, dissimilatory nitrate reduction to ammonia, active calcium ion transport, and reversible hydration of CO2 allowed to identify genetic predispositions for carbonate precipitation in Streptomyces. Finally, their biomineralization abilities were confirmed by environmental SEM, which allowed to visualize the formation of abundant mineral deposits under laboratory conditions. Overall, our study provides novel evidences that filamentous Actinobacteria could be key protagonists in the genesis of moonmilk through a wide spectrum of biomineralization processes.}, }
@article {pmid28706260, year = {2017}, author = {Lewis, MC and Merrifield, CA and Berger, B and Cloarec, O and Duncker, S and Mercenier, A and Nicholson, JK and Holmes, E and Bailey, M}, title = {Early intervention with Bifidobacterium lactis NCC2818 modulates the host-microbe interface independent of the sustained changes induced by the neonatal environment.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5310}, pmid = {28706260}, issn = {2045-2322}, mesh = {Animals ; Animals, Newborn ; Bifidobacterium animalis/*growth &amp; development ; Early Intervention, Educational ; *Environmental Exposure ; *Gastrointestinal Microbiome ; Immunity, Mucosal ; Metabolic Diseases/prevention &amp; control ; Probiotics/*administration &amp; dosage ; Swine ; Swine Diseases/prevention &amp; control ; Systemic Inflammatory Response Syndrome/prevention &amp; control ; }, abstract = {Inflammatory and metabolic diseases can originate during early-life and have been correlated with shifts in intestinal microbial ecology. Here we demonstrate that minor environmental fluctuations during the early neonatal period had sustained effects on the developing porcine microbiota and host-microbe interface. These inter-replicate effects appear to originate during the first day of life, and are likely to reflect very early microbiota acquisition from the environment. We statistically link early systemic inflammation with later local increases in inflammatory cytokine (IL-17) production, which could have important enteric health implications. Immunity, intestinal barrier function, host metabolism and host-microbiota co-metabolism were further modified by Bifidobacterium lactis NCC2818 supplementation, although composition of the in situ microbiota remained unchanged. Finally, our robust model identified novel, strong correlations between urinary metabolites (eg malonate, phenylacetylglycine, alanine) and mucosal immunoglobulin (IgM) and cytokine (IL-10, IL-4) production, thus providing the possibility of the development of urinary 'dipstick' tests to assess non-accessible mucosal immune development and identify early precursors (biomarkers) of disease. These results have important implications for infants exposed to neonatal factors including caesarean delivery, antibiotic therapy and delayed discharge from hospital environments, which may predispose to the development of inflammatory and metabolic diseases in later life.}, }
@article {pmid28705228, year = {2017}, author = {Vandegrift, R and Bateman, AC and Siemens, KN and Nguyen, M and Wilson, HE and Green, JL and Van Den Wymelenberg, KG and Hickey, RJ}, title = {Cleanliness in context: reconciling hygiene with a modern microbial perspective.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {76}, pmid = {28705228}, issn = {2049-2618}, mesh = {Hand Disinfection ; Hand Hygiene ; Humans ; *Hygiene Hypothesis ; Infections/microbiology/transmission/virology ; Microbial Interactions ; *Microbiota ; Skin/*microbiology ; Symbiosis ; }, abstract = {The concept of hygiene is rooted in the relationship between cleanliness and the maintenance of good health. Since the widespread acceptance of the germ theory of disease, hygiene has become increasingly conflated with sterilization. In reviewing studies across the hygiene literature (most often hand hygiene), we found that nearly all studies of hand hygiene utilize bulk reduction in bacterial load as a proxy for reduced transmission of pathogenic organisms. This treatment of hygiene may be insufficient in light of recent microbial ecology research, which has demonstrated that humans have intimate and evolutionarily significant relationships with a diverse assemblage of microorganisms (our microbiota). The human skin is home to a diverse and specific community of microorganisms, which include members that exist across the ecological spectrum from pathogen through commensal to mutualist. Most evidence suggests that the skin microbiota is likely of direct benefit to the host and only rarely exhibits pathogenicity. This complex ecological context suggests that the conception of hygiene as a unilateral reduction or removal of microbes has outlived its usefulness. As such, we suggest the explicit definition of hygiene as "those actions and practices that reduce the spread or transmission of pathogenic microorganisms, and thus reduce the incidence of disease."}, }
@article {pmid28703111, year = {2017}, author = {Borycka-Kiciak, K and Strus, M and Pietrzak, P and Wawiernia, K and Mikołajczyk, D and Gałęcka, M and Heczko, P and Tarnowski, W}, title = {Clinical and microbiological aspects of the use of Lactobacillus rhamnosus PL1 strains in proctological patients with symptoms of chronic proctitis.}, journal = {Polski przeglad chirurgiczny}, volume = {89}, number = {3}, pages = {16-22}, pmid = {28703111}, issn = {2299-2847}, mesh = {Anti-Bacterial Agents/administration &amp; dosage ; Chronic Disease ; Colony Count, Microbial ; Feces/*microbiology ; Female ; Gastrointestinal Tract/microbiology ; Humans ; *Lacticaseibacillus rhamnosus ; Male ; Probiotics/*administration &amp; dosage ; Proctitis/*drug therapy/*microbiology ; Treatment Outcome ; }, abstract = {UNLABELLED: Recurrent proctitis and the symptoms associated therewith pose significant clinical problem in proctological patients. The objective of this study was to assess the impact of the probiotic Lactobacillus rhamnosus PL1 strain on the clinical presentation and composition of intestinal microbiota in patients with symptoms of proctitis in the course of hemorrhoidal disease and diverticulosis. Material consisted of 24 patients in whom no complete clinical improvement could be obtained after the treatment of the underlying disease. Subject to the assessment was the presence and the intensity of clinical symptoms as well as qualitative and quantitative changes in the composition of bacterial flora detected in the stool before, during and after a 9-week supplementation with the probiotic Lactobacillus rhamnosus PL1 strain.<br><br>RESULTS: In the entire study group, the intensity of pain after 12 weeks was significantly lower (p=0,.011) compared to baseline; the intensity of flatulence and abdominal discomfort was reduced significantly as early as after 3 weeks, with the difference reaching a highly significant level after 12 weeks (pP<0,.0001). No significant difference was observed in the frequency of the reported episodes of diarrhea, constipation, as well as itching and burning in the anal region. As early as after 3 weeks of supplementation with the probiotic L. rhamnosus PL1 strain, significant qualitative and quantitative changes were observed in the composition of intestinal microbiota; the changes differed depending on the underlying disease. An increase in the total counts of the bacteria of Lactobacillus genus, particularly L. rhamnosus PL1 strain was observed regardless of the underlying disease.<br><br>CONCLUSION: Tthe probiotic Lactobacillus rhamnosus PL1 strain appears to be useful in restoring appropriate ratios of bacterial populations in patients presenting with symptoms of proctitis in the course of the treatment of certain diseases of the lower gastrointestinal tract.}, }
@article {pmid28702708, year = {2018}, author = {Chiriac, CM and Baricz, A and Szekeres, E and Rudi, K and Dragoș, N and Coman, C}, title = {Microbial Composition and Diversity Patterns in Deep Hyperthermal Aquifers from the Western Plain of Romania.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {38-51}, pmid = {28702708}, issn = {1432-184X}, support = {3499/20.05.2015//EEA Grants/ ; POSDRU/187/1.5/S/155383//POSDRU/ ; POSDRU/187/1.5/S/155383//POSDRU/ ; }, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Ecosystem ; Groundwater/chemistry/*microbiology ; Hot Temperature ; Phylogeny ; Romania ; }, abstract = {A limited number of studies have investigated the biodiversity in deep continental hyperthermal aquifers and its influencing factors. Here, we present the first description of microbial communities inhabiting the Pannonian and Triassic hyperthermal aquifers from the Western Plain of Romania, the first one being considered a deposit of "fossilized waters," while the latter is embedded in the hydrological cycle due to natural refilling. The 11 investigated drillings have an open interval between 952 and 3432 m below the surface, with collected water temperatures ranging between 47 and 104 °C, these being the first microbial communities characterized in deep continental water deposits with outflow temperatures exceeding 80 °C. The abundances of bacterial 16S rRNA genes varied from approximately 10[5]-10[6] mL[-1] in the Pannonian to about 10[2]-10[4] mL[-1] in the Triassic aquifer. A 16S rRNA gene metabarcoding analysis revealed distinct microbial communities in the two water deposits, especially in the rare taxa composition. The Pannonian aquifer was dominated by the bacterial genera Hydrogenophilus and Thermodesulfobacterium, together with archaeal methanogens from the Methanosaeta and Methanothermobacter groups. Firmicutes was prevalent in the Triassic deposit with a large number of OTUs affiliated to Thermoanaerobacteriaceae, Thermacetogenium, and Desulfotomaculum. Species richness, evenness, and phylogenetic diversity increased alongside with the abundance of mesophiles, their presence in the Triassic aquifer being most probably caused by the refilling with large quantities of meteoric water in the Carpathian Mountains. Altogether, our results show that the particular physico-cheminal characteristics of each aquifer, together with the water refilling possibilities, seem to determine the microbial community structure.}, }
@article {pmid28702707, year = {2018}, author = {Dastogeer, KMG and Li, H and Sivasithamparam, K and Jones, MGK and Wylie, SJ}, title = {Host Specificity of Endophytic Mycobiota of Wild Nicotiana Plants from Arid Regions of Northern Australia.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {74-87}, pmid = {28702707}, issn = {1432-184X}, support = {the Research Training Scholarship//Australian Government and Murdoch University/ ; }, mesh = {Australia ; Desert Climate ; Endophytes/classification/genetics/isolation &amp; purification/*physiology ; Fungi/classification/genetics/isolation &amp; purification/*physiology ; *Host Specificity ; *Mycobiome ; Phylogeny ; Soil/chemistry ; Symbiosis ; Nicotiana/*microbiology ; }, abstract = {In arid regions of northern Australia, plants survive under water deficit, high temperatures, intense solar radiation and nutrient-impoverished soils. They employ various morpho-physiological and biochemical adaptations including interaction with microbial symbionts. We evaluated identity, host and tissue association with geographical distribution of fungal endophytes isolated from above- and below-ground tissues of plants of three indigenous Australian Nicotiana species. Isolation frequency and α-diversity were significantly higher for root endophyte assemblages than those of stem and leaf tissues. We recorded no differences in endophyte species richness or diversity as a function of sampling location, but did detect differences among different host genotypes and plant tissues. There was a significant pattern of community similarity associated with host genotypes but no consistent pattern of fungal community structuring associated with sampling location and tissue type, regardless of the community similarity measurements used.}, }
@article {pmid28702706, year = {2018}, author = {Espínola, F and Dionisi, HM and Borglin, S and Brislawn, CJ and Jansson, JK and Mac Cormack, WP and Carroll, J and Sjöling, S and Lozada, M}, title = {Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {123-139}, pmid = {28702706}, issn = {1432-184X}, support = {CSP proposal ID 328//Joint Genome Institute/ ; ANPCyT PICT2008 N&#xba; 0468//National Agency for the Promotion of Science and Technology of Argentina/ ; 112-200801-01736//CONICET/ ; UBA 20020100100378//Secretaria de Ciencia y Tecnica, Universidad de Buenos Aires/ ; grant No. 228107//Research Council of Norway/ ; DE-AC05-76RL01830//Laboratory Directed Research and Development Program at PNNL/ ; }, mesh = {Anaerobiosis ; Bacteria/classification/*genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Cold Climate ; DNA, Bacterial/genetics ; Geologic Sediments/*microbiology ; Hydrocarbons/*metabolism ; Metagenomics ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon's index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.}, }
@article {pmid28702705, year = {2018}, author = {Duplouy, A and Brattström, O}, title = {Wolbachia in the Genus Bicyclus: a Forgotten Player.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {255-263}, pmid = {28702705}, issn = {1432-184X}, support = {266021//Suomen Akatemia/ ; }, mesh = {Animals ; Biological Evolution ; Butterflies/growth &amp; development/*microbiology/physiology ; Phylogeny ; Symbiosis ; Wolbachia/classification/genetics/*isolation &amp; purification/physiology ; }, abstract = {Bicyclus butterflies are key species for studies of wing pattern development, phenotypic plasticity, speciation and the genetics of Lepidoptera. One of the key endosymbionts in butterflies, the alpha-Proteobacterium Wolbachia pipientis, is affecting many of these biological processes; however, Bicyclus butterflies have not been investigated systematically as hosts to Wolbachia. In this study, we screen for Wolbachia infection in several Bicyclus species from natural populations across Africa as well as two laboratory populations. Out of the 24 species tested, 19 were found to be infected, and no double infection was found, but both A- and B-supergroup strains colonise this butterfly group. We also show that many of the Wolbachia strains identified in Bicyclus butterflies belong to the ST19 clonal complex. We discuss the importance of our results in regard to routinely screening for Wolbachia when using Bicyclus butterflies as the study organism of research in eco-evolutionary biology.}, }
@article {pmid28702085, year = {2017}, author = {Khor, WC and Andersen, S and Vervaeren, H and Rabaey, K}, title = {Electricity-assisted production of caproic acid from grass.}, journal = {Biotechnology for biofuels}, volume = {10}, number = {}, pages = {180}, pmid = {28702085}, issn = {1754-6834}, abstract = {BACKGROUND: Medium chain carboxylic acids, such as caproic acid, are conventionally produced from food materials. Caproic acid can be produced through fermentation by the reverse β-oxidation of lactic acid, generated from low value lignocellulosic biomass. In situ extraction of caproic acid can be achieved by membrane electrolysis coupled to the fermentation process, allowing recovery by phase separation.<br><br>RESULTS: Grass was fermented to lactic acid in a leach-bed-type reactor, which was then further converted to caproic acid in a secondary fermenter. The lactic acid concentration was 9.36&#xa0;&#xb1;&#xa0;0.95&#xa0;g&#xa0;L[-1] over a 33-day semi-continuous operation, and converted to caproic acid at pH 5.5-6.2, with a concentration of 4.09&#xa0;&#xb1;&#xa0;0.54&#xa0;g&#xa0;L[-1] during stable production. The caproic acid product stream was extracted in its anionic form, concentrated and converted to caproic acid by membrane electrolysis, resulting in a&#xa0;>70&#xa0;wt% purity solution. In a parallel test exploring the upper limits of production rate through cell retention, we achieved the highest reported caproic acid production rate to date from a lignocellulosic biomass (grass, via a coupled process), at 0.99&#xa0;&#xb1;&#xa0;0.02&#xa0;g L[-1]&#xa0;h[-1]. The fermenting microbiome (mainly consisting of Clostridium IV and Lactobacillus) was capable of producing a maximum caproic acid concentration of 10.92&#xa0;&#xb1;&#xa0;0.62&#xa0;g&#xa0;L[-1] at pH 5.5, at the border of maximum solubility of protonated caproic acid.<br><br>CONCLUSIONS: Grass can be utilized as a substrate to produce caproic acid. The biological intermediary steps were enhanced by separating the steps to focus on the lactic acid intermediary. Notably, the pipeline was almost completely powered through electrical inputs, and thus could potentially be driven from sustainable energy without need for chemical input.Graphical abstractMicrobial and electrochemical production of lactic acid, caproic acid and decane from grass.}, }
@article {pmid28699015, year = {2018}, author = {Coelho, FJRC and Cleary, DFR and Gomes, NCM and Pólonia, ARM and Huang, YM and Liu, LL and de Voogd, NJ}, title = {Sponge Prokaryote Communities in Taiwanese Coral Reef and Shallow Hydrothermal Vent Ecosystems.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {239-254}, pmid = {28699015}, issn = {1432-184X}, support = {UID/AMB/50017 - POCI-01-0145- FEDER-007638//CESAM/ ; PTDC/AAC-AMB/115304/2009//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia (PT)/ ; PTDC/BIA-MIC/6473/2014 - POCI-01- 0145-FEDER-016531//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; NSC 102-2815-C-346-010-B)//Ministry of Science and Technology, Taiwan/ ; SFRH/BPD/92366/2013//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Coral Reefs ; Ecosystem ; Hydrothermal Vents/*microbiology ; Phylogeny ; Porifera/classification/*microbiology ; Taiwan ; }, abstract = {Previously, it was believed that the prokaryote communities of typical 'low-microbial abundance' (LMA) or 'non-symbiont harboring' sponges were merely subsets of the prokaryote plankton community. Recent research has, however, shown that these sponges are dominated by particular clades of Proteobacteria or Cyanobacteria. Here, we expand on this research and assess the composition and putative functional profiles of prokaryotic communities from LMA sponges collected in two ecosystems (coral reef and hydrothermal vent) from vicinal islands of Taiwan with distinct physicochemical conditions. Six sponge species identified as Acanthella cavernosa (Bubarida), Echinodictyum asperum, Ptilocaulis spiculifer (Axinellida), Jaspis splendens (Tetractinellida), Stylissa carteri (Scopalinida) and Suberites sp. (Suberitida) were sampled in coral reefs in the Penghu archipelago. One sponge species provisionally identified as Hymeniacidon novo spec. (Suberitida) was sampled in hydrothermal vent habitat. Each sponge was dominated by a limited set of operational taxonomic units which were similar to sequences from organisms previously obtained from other LMA sponges. There was a distinct bacterial community between sponges collected in coral reef and in hydrothermal vents. The putative functional profile revealed that the prokaryote community from sponges collected in hydrothermal vents was significantly enriched for pathways related to DNA replication and repair.}, }
@article {pmid28698878, year = {2017}, author = {Rebolledo, C and Cuevas, A and Zambrano, T and Acuña, JJ and Jorquera, MA and Saavedra, K and Martínez, C and Lanas, F and Serón, P and Salazar, LA and Saavedra, N}, title = {Bacterial Community Profile of the Gut Microbiota Differs between Hypercholesterolemic Subjects and Controls.}, journal = {BioMed research international}, volume = {2017}, number = {}, pages = {8127814}, pmid = {28698878}, issn = {2314-6141}, mesh = {Aged ; Female ; *Gastrointestinal Microbiome ; Humans ; Hypercholesterolemia/blood/*microbiology ; Male ; Middle Aged ; }, abstract = {The role of gut microbiota in the development of metabolic illnesses has been abundantly demonstrated. Recent studies suggest that gut microbiota alterations may also be related to the development of hypercholesterolemia. Therefore, we aimed to assess differences in the gut bacterial community profiles between hypercholesterolemic subjects and controls. Thirty cases diagnosed with hypercholesterolemia and 27 normocholesterolemic controls were included. A fasting whole blood sample was obtained to determine the lipid profile. In parallel, stool samples were collected and total DNA was isolated to assess the bacterial community profiles by denaturing gradient gel electrophoresis (DGGE). In addition, the Richness, Shannon-Weaver, and Simpson indexes were used to evaluate the richness and diversity of bacterial communities. As expected, serum concentrations of total cholesterol, triglycerides, and LDL-cholesterol were significantly higher in the cases compared with controls. Moreover, DGGE analysis showed a lower richness and diversity of bacterial communities in hypercholesterolemic subjects. In conclusion, our results showed differences in the profiles of bacterial communities between hypercholesterolemic subjects and controls, suggesting a possible role of the gut microbiota in the development of hypercholesterolemia.}, }
@article {pmid28693809, year = {2017}, author = {Vaezzadeh, V and Zakaria, MP and Bong, CW}, title = {Aliphatic hydrocarbons and triterpane biomarkers in mangrove oyster (Crassostrea belcheri) from the west coast of Peninsular Malaysia.}, journal = {Marine pollution bulletin}, volume = {124}, number = {1}, pages = {33-42}, doi = {10.1016/j.marpolbul.2017.07.008}, pmid = {28693809}, issn = {1879-3363}, mesh = {Alkanes/*metabolism ; Animals ; Biomarkers/metabolism ; Crassostrea/*metabolism ; Malaysia ; Petroleum Pollution/*analysis ; Triterpenes/*metabolism ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The Straits of Malacca is one of the world's busiest shipping routes where frequent oil spills occur. Rapid development in the west coast of Peninsular Malaysia is the other major source of petroleum pollution in this narrow waterway. In order to identify occurrence and origin of hydrocarbons in the Straits, mangrove oysters (Crassostrea belcheri) were collected from five sampling locations and analysed for n-alkanes and biomarkers. Soxhlet apparatus and two step column chromatography were used for extraction, purification and fractionation of the oysters. Petroleum origin n-alkanes were detected in majority of the sampling locations which is indicative of anthropogenic activities in this region. Using source and maturity diagnostic ratios for hopanes revealed used crankcase oil as the main source of petroleum hydrocarbons in oysters from all sampling locations except for the Pulau Merambong where signature of South East Asia crude oil (SEACO) was detected.}, }
@article {pmid28693474, year = {2017}, author = {van der Walt, AJ and van Goethem, MW and Ramond, JB and Makhalanyane, TP and Reva, O and Cowan, DA}, title = {Assembling metagenomes, one community at a time.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {521}, pmid = {28693474}, issn = {1471-2164}, mesh = {Benchmarking ; Databases, Genetic ; Environment ; Metagenomics/*methods ; }, abstract = {BACKGROUND: Metagenomics allows unprecedented access to uncultured environmental microorganisms. The analysis of metagenomic sequences facilitates gene prediction and annotation, and enables the assembly of draft genomes, including uncultured members of a community. However, while several platforms have been developed for this critical step, there is currently no clear framework for the assembly of metagenomic sequence data.<br><br>RESULTS: To assist with selection of an appropriate metagenome assembler we evaluated the capabilities of nine prominent assembly tools on nine publicly-available environmental metagenomes, as well as three simulated datasets. Overall, we found that SPAdes provided the largest contigs and highest N50 values across 6 of the 9 environmental datasets, followed by MEGAHIT and metaSPAdes. MEGAHIT emerged as a computationally inexpensive alternative to SPAdes, assembling the most complex dataset using less than 500 GB of RAM and within 10 hours.<br><br>CONCLUSIONS: We found that assembler choice ultimately depends on the scientific question, the available resources and the bioinformatic competence of the researcher. We provide a concise workflow for the selection of the best assembly tool.}, }
@article {pmid28690591, year = {2017}, author = {Wilkinson, TJ and Cowan, AA and Vallin, HE and Onime, LA and Oyama, LB and Cameron, SJ and Gonot, C and Moorby, JM and Waddams, K and Theobald, VJ and Leemans, D and Bowra, S and Nixey, C and Huws, SA}, title = {Characterization of the Microbiome along the Gastrointestinal Tract of Growing Turkeys.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1089}, pmid = {28690591}, issn = {1664-302X}, support = {BB/H009582/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {The turkey microbiome is largely understudied, despite its relationship with bird health and growth, and the prevalence of human pathogens such as Campylobacter spp. In this study we investigated the microbiome within the small intestine (SI), caeca (C), large intestine (LI), and cloaca (CL) of turkeys at 6, 10, and 16 weeks of age. Eight turkeys were dissected within each age category and the contents of the SI, C, LI, and CL were harvested. 16S rDNA based QPCR was performed on all samples and samples for the four locations within three birds/age group were sequenced using ion torrent-based sequencing of the 16S rDNA. Sequencing data showed on a genus level, an abundance of Lactobacillus, Streptococcus, and Clostridium XI (38.2, 28.1, and 13.0% respectively) irrespective of location and age. The caeca exhibited the greatest microbiome diversity throughout the development of the turkey. PICRUSt data predicted an array of bacterial function, with most differences being apparent in the caeca of the turkeys as they matured. QPCR revealed that the caeca within 10 week old birds, contained the most Campylobacter spp. Understanding the microbial ecology of the turkey gastrointestinal tract is essential in terms of understanding production efficiency and in order to develop novel strategies for targeting Campylobacter spp.}, }
@article {pmid28690156, year = {2017}, author = {De Vrieze, J and Christiaens, MER and Verstraete, W}, title = {The microbiome as engineering tool: Manufacturing and trading between microorganisms.}, journal = {New biotechnology}, volume = {39}, number = {Pt B}, pages = {206-214}, doi = {10.1016/j.nbt.2017.07.001}, pmid = {28690156}, issn = {1876-4347}, mesh = {Bacteria/*metabolism ; Biotechnology/*methods ; *Microbiota ; Synthetic Biology ; Waste Products ; }, abstract = {The integration of microbial technologies within the framework of the water-energy nexus has been taking place for over a century, but these mixed microbial communities are considered hard to deal with 'black boxes'. Process steering is mainly based on avoiding process failure by monitoring conventional parameters, e.g., pH and temperature, which often leads to operation far below the intrinsic potential. Mixed microbial communities do not reflect a randomised individual mix, but an interacting microbiological entity. Advance monitoring to obtain effective engineering of the microbiome is achievable, and even crucial to obtain the desired performance and products. This can be achieved via a top-down or bottom-up approach. The top-down strategy is reflected in the microbial resource management concept that considers the microbial community as a well-structured network. This network can be monitored by means of molecular techniques that will allow the development of accurate and quick decision tools. In contrast, the bottom-up approach makes use of synthetic cultures that can be composed starting from defined axenic cultures, based on the requirements of the process under consideration. The success of both approaches depends on real-time monitoring and control. Of particular importance is the necessity to identify and characterise the key players in the process. These key players not only relate with the establishment of functional conversions, but also with the interaction between partner bacteria. This emphasises the importance of molecular (screening) techniques to obtain structural and functional insights, minimise energy input, and maximise product output by means of integrated microbiome processes.}, }
@article {pmid28686570, year = {2017}, author = {Mendes, LW and Braga, LPP and Navarrete, AA and Souza, DG and Silva, GGZ and Tsai, SM}, title = {Using Metagenomics to Connect Microbial Community Biodiversity and Functions.}, journal = {Current issues in molecular biology}, volume = {24}, number = {}, pages = {103-118}, doi = {10.21775/cimb.024.103}, pmid = {28686570}, issn = {1467-3045}, mesh = {Bacteria/classification/*genetics/*metabolism ; *Biodiversity ; *Ecosystem ; Metagenomics/*methods ; Phylogeny ; *Soil Microbiology ; }, abstract = {Microbes constitute about a third of the Earth's biomass and are composed by an enormous genetic diversity. In a majority of environments the microbial communities play crucial roles for the ecosystem functioning, where a drastic biodiversity alteration or loss could lead to negative effects on the environment and sustainability. A central goal in microbiome studies is to elucidate the relation between microbial diversity to functions. A better understanding of the relation diversity-function would increase the ability to manipulate that diversity to improve plant and animal health and also setting conservation priorities. The recent advances in genomic methodologies in microbial ecology have provide means to assess highly complex communities in detail, making possible the link between diversity and the functions performed by the microbes. In this work we first explore some advances in bioinformatics tools to connect the microbial community biodiversity to their potential metabolism and after present some examples of how this information can be useful for a better understanding of the microbial role in the environment.}, }
@article {pmid28686423, year = {2017}, author = {Avellan, A and Schwab, F and Masion, A and Chaurand, P and Borschneck, D and Vidal, V and Rose, J and Santaella, C and Levard, C}, title = {Nanoparticle Uptake in Plants: Gold Nanomaterial Localized in Roots of Arabidopsis thaliana by X-ray Computed Nanotomography and Hyperspectral Imaging.}, journal = {Environmental science &amp; technology}, volume = {51}, number = {15}, pages = {8682-8691}, doi = {10.1021/acs.est.7b01133}, pmid = {28686423}, issn = {1520-5851}, mesh = {Arabidopsis/*chemistry ; *Gold ; *Nanoparticles ; Plant Roots ; X-Rays ; }, abstract = {Terrestrial plants can internalize and translocate nanoparticles (NPs). However, direct evidence for the processes driving the NP uptake and distribution in plants is scarce at the cellular level. Here, NP-root interactions were investigated after 10 days of exposure of Arabidopsis thaliana to 10 mg·L[-1] of negatively or positively charged gold NPs (∼12 nm) in gels. Two complementary imaging tools were used: X-ray computed nanotomography (nano-CT) and enhanced dark-field microscopy combined with hyperspectral imaging (DF-HSI). The use of these emerging techniques improved our ability to detect and visualize NP in plant tissue: by spectral confirmation via DF-HSI, and in three dimensions via nano-CT. The resulting imaging provides direct evidence that detaching border-like cells (i.e., sheets of border cells detaching from the root) and associated mucilage can accumulate and trap NPs irrespective of particle charge. On the contrary, border cells on the root cap behaved in a charge-specific fashion: positively charged NPs induced a higher mucilage production and adsorbed to it, which prevented translocation into the root tissue. Negatively charged NPs did not adsorb to the mucilage and were able to translocate into the apoplast. These observations provide direct mechanistic insight into NP-plant interactions, and reveal the important function of border cells and mucilage in interactions of plants with charged NPs.}, }
@article {pmid28681143, year = {2018}, author = {van de Water, JAJM and Voolstra, CR and Rottier, C and Cocito, S and Peirano, A and Allemand, D and Ferrier-Pagès, C}, title = {Seasonal Stability in the Microbiomes of Temperate Gorgonians and the Red Coral Corallium rubrum Across the Mediterranean Sea.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {274-288}, pmid = {28681143}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; High-Throughput Nucleotide Sequencing ; Mediterranean Sea ; *Microbiota ; Phylogeny ; Seasons ; Seawater ; Symbiosis ; }, abstract = {Populations of key benthic habitat-forming octocoral species have declined significantly in the Mediterranean Sea due to mass mortality events caused by microbial disease outbreaks linked to high summer seawater temperatures. Recently, we showed that the microbial communities of these octocorals are relatively structured; however, our knowledge on the seasonal dynamics of these microbiomes is still limited. To investigate their seasonal stability, we collected four soft gorgonian species (Eunicella singularis, Eunicella cavolini, Eunicella verrucosa and Leptogorgia sarmentosa) and the precious red coral (Corallium rubrum) from two coastal locations with different terrestrial impact levels in the Mediterranean Sea, and used next-generation amplicon sequencing of the 16S rRNA gene. The microbiomes of all soft gorgonian species were dominated by the same 'core microbiome' bacteria belonging to the Endozoicomonas and the Cellvibrionales clade BD1-7, whereas the red coral microbiome was primarily composed of 'core' Spirochaetes, Oceanospirillales ME2 and Parcubacteria. The associations with these bacterial taxa were relatively consistent over time at each location for each octocoral species. However, differences in microbiome composition and seasonal dynamics were observed between locations and could primarily be attributed to locally variant bacteria. Overall, our data provide further evidence of the intricate symbiotic relationships that exist between Mediterranean octocorals and their associated microbes, which are ancient and highly conserved over both space and time, and suggest regulation of the microbiome composition by the host, depending on local conditions.}, }
@article {pmid28680968, year = {2017}, author = {Linz, AM and Crary, BC and Shade, A and Owens, S and Gilbert, JA and Knight, R and McMahon, KD}, title = {Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes.}, journal = {mSphere}, volume = {2}, number = {3}, pages = {}, pmid = {28680968}, issn = {2379-5042}, abstract = {Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multiyear time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. The sites that we studied encompassed a range of water column mixing frequencies, which we hypothesized would be associated with trends in alpha and beta diversity. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likely reflected the environmental conditions of each lake type sampled, including Actinobacteria in polymictic lakes (i.e., lakes with multiple mixing events per year), Methylophilales in dimictic lakes (lakes with two mixing events per year, usually in spring and fall), and "Candidatus Omnitrophica" in meromictic lakes (lakes with no recorded mixing events). The community present during each year at each site was also surprisingly unique. Despite unexpected interannual variability in community composition, we detected a core community of taxa found in all lakes and layers, including Actinobacteria tribe acI-B2 and Betaprotobacteria lineage PnecC. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term multisite observations, as analyzing only a single year of data or one lake would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here. IMPORTANCE Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community composition varies by year, a finding which likely applies to other ecosystems and has implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource for anyone seeking to answer their own microbial ecology questions using a multiyear time series.}, }
@article {pmid28680419, year = {2017}, author = {Cabello-Yeves, PJ and Haro-Moreno, JM and Martin-Cuadrado, AB and Ghai, R and Picazo, A and Camacho, A and Rodriguez-Valera, F}, title = {Novel Synechococcus Genomes Reconstructed from Freshwater Reservoirs.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1151}, pmid = {28680419}, issn = {1664-302X}, abstract = {Freshwater picocyanobacteria including Synechococcus remain poorly studied at the genomic level, compared to their marine representatives. Here, using a metagenomic assembly approach we discovered two novel Synechococcus sp. genomes from two freshwater reservoirs Tous and Lake Lanier, both sharing 96% average nucleotide identity and displaying high abundance levels in these two lakes located at similar altitudes and temperate latitudes. These new genomes have the smallest estimated size (2.2 Mb) and average intergenic spacer length (20 bp) of any previously sequenced freshwater Synechococcus, which may contribute to their success in oligotrophic freshwater systems. Fluorescent in situ hybridization confirmed that Synechococcus sp. Tous comprises small cells (0.987 ± 0.139 μm length, 0.723 ± 0.119 μm width) that amount to 90% of the picocyanobacteria in Tous. They appear together in a phylogenomic tree with Synechococcus sp. RCC307 strain, the main representative of sub-cluster 5.3 that has itself one of the smallest marine Synechococcus genomes. We detected a type II phycobilisome (PBS) gene cluster in both genomes, which suggests that they belong to a phycoerythrin-rich pink low-light ecotype. The decrease of acidic proteins and the higher content of basic transporters and membrane proteins in the novel Synechococcus genomes, compared to marine representatives, support their freshwater specialization. A sulfate Cys transporter which is absent in marine but has been identified in many freshwater cyanobacteria was also detected in Synechococcus sp. Tous. The RuBisCo subunits from this microbe are phylogenetically close to the freshwater amoeba Paulinella chromatophora symbiont, hinting to a freshwater origin of the carboxysome operon of this protist. The novel genomes enlarge the known diversity of freshwater Synechococcus and improve the overall knowledge of the relationships among members of this genus at large.}, }
@article {pmid28680053, year = {2017}, author = {Cheng, G and Sun, M and Lu, J and Ge, X and Zhang, H and Xu, X and Lou, L and Lin, Q}, title = {Role of biochar in biodegradation of nonylphenol in sediment: Increasing microbial activity versus decreasing bioavailability.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4726}, pmid = {28680053}, issn = {2045-2322}, mesh = {Bacteria/drug effects ; Biodegradation, Environmental ; Biological Availability ; Charcoal/*chemistry ; Geologic Sediments/chemistry/*microbiology ; Oryza/chemistry ; Phenols/*chemistry/toxicity ; Soil Pollutants/chemistry ; }, abstract = {The observed strong sorption of hydrophobic organic contaminants (HOCs) to biochar presents potential implications for HOCs bioavailability and bioaccessibility in sediments, while biochar could impact sediment microbial ecology. However, the comprehensive study on the effects of biochar on HOC biodegradation coupled with bioavailability and microbial ecology are rarely documented. In this paper, the effects of biochar on the biodegradation of nonylphenol (NP) were investigated using 3 different NP concentrations (20, 50 and 500 mg/Kg) in sediments amended with different percentage of rice straw biochar (RC). Results showed that the influence of RC on NP biodegradation varied with different NP concentrations. At low NP concentrations, RC suppressed NP biodegradation by reducing NP bioavailability, while at high NP concentrations, moderate RC addition promoted biodegradation by reducing toxicity of NP to microbes. The effects of NP on microbial community structures were significant (P < 0.01), but those of RC were not significant (P > 0.05). The RC affected microorganisms through altering NP toxicity, microbial quantity and activity, but not microbial community structures. This study indicated that there could be an optimal biochar percentage in biochar-sediment systems at different HOC concentrations, which strengthened HOC biodegradation process and accelerated biodegradation rate, forming adsorption-biodegradation coupled bioremediation.}, }
@article {pmid28679746, year = {2017}, author = {Lyons, NA and Kolter, R}, title = {Bacillus subtilis Protects Public Goods by Extending Kin Discrimination to Closely Related Species.}, journal = {mBio}, volume = {8}, number = {4}, pages = {}, pmid = {28679746}, issn = {2150-7511}, support = {R01 GM058213/GM/NIGMS NIH HHS/United States ; }, mesh = {*Antibiosis ; Bacillus/physiology ; Bacillus subtilis/*genetics/*physiology ; Bacterial Proteins/metabolism ; Biofilms ; Biological Evolution ; Biota ; Gene Expression Regulation, Bacterial ; Microbial Interactions ; Phenotype ; Phylogeny ; }, abstract = {Kin discrimination systems are found in numerous communal contexts like multicellularity and are theorized to prevent exploitation of cooperative behaviors. The kin discrimination system in Bacillus subtilis differs from most other such systems because it excludes nonkin cells rather than including kin cells. Because nonkin are the target of the system, B. subtilis can potentially distinguish degrees of nonkin relatedness, not just kin versus nonkin. We examined this by testing a large strain collection of diverse Bacillus species against B. subtilis in different multicellular contexts. The effects of kin discrimination extend to nearby species, as the other subtilis clade species were treated with the same antagonism as nonkin. Species in the less-related pumilus clade started to display varied phenotypes but were mostly still discriminated against, while cereus clade members and beyond were no longer subject to kin discrimination. Seeking a reason why other species are perceived as antagonistic nonkin, we tested the ability of B. subtilis to steal communally produced surfactant from these species. We found that the species treated as nonkin were the only ones that made a surfactant that B. subtilis could utilize and that nonkin antagonism prevented such stealing when the two strains were mixed. The nonkin exclusion kin discrimination method thus allows effective protection of the cooperative behaviors prevalent in multicellularity while still permitting interactions with more distant species that are not a threat.IMPORTANCE Multicellular systems like bacterial biofilms and swarms rely on cooperative behaviors that could be undermined by exploitative invaders. Discriminating kin from nonkin is one way to help guard against such exploitation but has thus far been examined only intraspecifically, so the phylogenetic range of this important trait is unknown. We tested whether Bacillus subtilis treats other species as nonkin by testing a single strain against a diverse collection of Bacillus isolates. We found that the species in the same clade were treated as nonkin, which then lessened in more distant relatives. Further experiments showed that these nonkin species produced a cooperative good that could be stolen by B. subtilis and that treating each other as nonkin largely prevented this exploitation. These results impact our understanding of interspecies interactions, as bacterial populations can interact only after they have diverged enough to no longer be a threat to their cooperative existences.}, }
@article {pmid28678006, year = {2017}, author = {Redhu, NS and Bakthavatchalu, V and Conaway, EA and Shouval, DS and Tsou, A and Goettel, JA and Biswas, A and Wang, C and Field, M and Muller, W and Bleich, A and Li, N and Gerber, GK and Bry, L and Fox, JG and Snapper, SB and Horwitz, BH}, title = {Macrophage dysfunction initiates colitis during weaning of infant mice lacking the interleukin-10 receptor.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, pmid = {28678006}, issn = {2050-084X}, support = {T32 OD010978/OD/NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 AI100114/AI/NIAID NIH HHS/United States ; P30 ES002109/ES/NIEHS NIH HHS/United States ; 201411MFE-339308-254788//CIHR/Canada ; R01 OD011141/OD/NIH HHS/United States ; }, mesh = {Animals ; Animals, Newborn ; Colitis/*pathology ; Interleukin-10/*metabolism ; Macrophages/*immunology ; Mice ; Mice, Knockout ; Receptors, Interleukin-10/*deficiency ; *Weaning ; }, abstract = {Infants with defects in the interleukin 10 receptor (IL10R) develop very early onset inflammatory bowel disease. Whether IL10R regulates lamina propria macrophage function during infant development in mice and whether macrophage-intrinsic IL10R signaling is required to prevent colitis in infancy is unknown. Here we show that although signs of colitis are absent in IL10R-deficient mice during the first two weeks of life, intestinal inflammation and macrophage dysfunction begin during the third week of life, concomitant with weaning and accompanying diversification of the intestinal microbiota. However, IL10R did not directly regulate the microbial ecology during infant development. Interestingly, macrophage depletion with clodronate inhibited the development of colitis, while the absence of IL10R specifically on macrophages sensitized infant mice to the development of colitis. These results indicate that IL10R-mediated regulation of macrophage function during the early postnatal period is indispensable for preventing the development of murine colitis.}, }
@article {pmid28677326, year = {2017}, author = {Jacob, JH and Hussein, EI and Shakhatreh, MAK and Cornelison, CT}, title = {Microbial community analysis of the hypersaline water of the Dead Sea using high-throughput amplicon sequencing.}, journal = {MicrobiologyOpen}, volume = {6}, number = {5}, pages = {}, pmid = {28677326}, issn = {2045-8827}, mesh = {Bacteria/classification/genetics ; Biodiversity ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; *Salinity ; Seawater/*chemistry/*microbiology ; *Water Microbiology ; }, abstract = {Amplicon sequencing using next-generation technology (bTEFAP[®]) has been utilized in describing the diversity of Dead Sea microbiota. The investigated area is a well-known salt lake in the western part of Jordan found in the lowest geographical location in the world (more than 420 m below sea level) and characterized by extreme salinity (approximately, 34%) in addition to other extreme conditions (low pH, unique ionic composition different from sea water). DNA was extracted from Dead Sea water. A total of 314,310 small subunit RNA (SSU rRNA) sequences were parsed, and 288,452 sequences were then clustered. For alpha diversity analysis, sample was rarefied to 3,000 sequences. The Shannon-Wiener index curve plot reached a plateau at approximately 3,000 sequences indicating that sequencing depth was sufficient to capture the full scope of microbial diversity. Archaea was found to be dominating the sequences (52%), whereas Bacteria constitute 45% of the sequences. Altogether, prokaryotic sequences (which constitute 97% of all sequences) were found to predominate. The findings expand on previous studies by using high-throughput amplicon sequencing to describe the microbial community in an environment which in recent years has been shown to hide some interesting diversity.}, }
@article {pmid28677256, year = {2018}, author = {Nakato, V and Mahuku, G and Coutinho, T}, title = {Xanthomonas campestris pv. musacearum: a major constraint to banana, plantain and enset production in central and east Africa over the past decade.}, journal = {Molecular plant pathology}, volume = {19}, number = {3}, pages = {525-536}, pmid = {28677256}, issn = {1364-3703}, mesh = {Africa, Central ; Africa, Eastern ; Musa/*microbiology ; Plantago/*microbiology ; Xanthomonas campestris/*genetics/*pathogenicity ; }, abstract = {TAXONOMY: Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadaceae; Genus Xanthomonas; currently classified as X. campestris pv. musacearum (Xcm). However, fatty acid methyl ester analysis and genetic and genomic evidence suggest that this pathogen is X. vasicola and resides in a separate pathovar.<br><br>ISOLATION AND DETECTION: Xcm can be isolated on yeast extract peptone glucose agar (YPGA), cellobiose cephalexin agar and yeast extract tryptone sucrose agar (YTSA) complemented with 5-fluorouracil, cephalexin and cycloheximide to confer semi-selectivity. Xcm can also be identified using direct antigen coating enzyme-linked immunosorbent assay (DAC-ELISA), species-specific polymerase chain reaction (PCR) using GspDm primers and lateral flow devices that detect latent infections.<br><br>HOST RANGE: Causes Xanthomonas wilt on plants belonging to the Musaceae, primarily banana (Musa acuminata), plantain (M. acuminata &#xd7; balbisiana) and enset (Ensete ventricosum).<br><br>DIVERSITY: There is a high level of genetic homogeneity within Xcm, although genome sequencing has revealed two major sublineages.<br><br>SYMPTOMS: Yellowing and wilting of leaves, premature fruit ripening and dry rot, bacterial exudate from cut stems.<br><br>DISTRIBUTION: Xcm has only been found in African countries, namely Burundi, Ethiopia, Democratic Republic of the Congo, Kenya, Rwanda, Tanzania and Uganda.<br><br>ECOLOGY AND EPIDEMIOLOGY: Xcm is transmitted by insects, bats, birds and farming implements. Long-distance dispersal of the pathogen is by the transportation of latently infected plants into new areas.<br><br>MANAGEMENT: The management of Xcm has relied on cultural practices that keep the pathogen population at tolerable levels. Biotechnology programmes have been successful in producing resistant banana plants. However, the deployment of such genetic material has not as yet been achieved in farmers' fields, and the sustainability of transgenic resistance remains to be addressed.}, }
@article {pmid28675677, year = {2017}, author = {Birgander, J and Rousk, J and Olsson, PA}, title = {Warmer winters increase the rhizosphere carbon flow to mycorrhizal fungi more than to other microorganisms in a temperate grassland.}, journal = {Global change biology}, volume = {23}, number = {12}, pages = {5372-5382}, doi = {10.1111/gcb.13803}, pmid = {28675677}, issn = {1365-2486}, mesh = {Atmosphere/chemistry ; Carbon/*metabolism ; Carbon Cycle ; *Climate Change ; Fungi/metabolism ; *Grassland ; Mycorrhizae/*metabolism/physiology ; Plants/metabolism/microbiology ; *Rhizosphere ; Seasons ; Soil Microbiology ; }, abstract = {A decisive set of steps in the terrestrial carbon (C) cycle is the fixation of atmospheric C by plants and the subsequent C-transfer to rhizosphere microorganisms. With climate change winters are expected to become milder in temperate ecosystems. Although the rate and pathways of rhizosphere C input to soil could be impacted by milder winters, the responses remain unknown. To address this knowledge-gap, a winter-warming experiment was established in a seminatural temperate grassland to follow the C flow from atmosphere, via the plants, to different groups of soil microorganisms. In situ [13] CO2 pulse labelling was used to track C into signature fatty acids of microorganisms. The winter warming did not result in any changes in biomass of any of the groups of microorganisms. However, the C flow from plants to arbuscular mycorrhizal (AM) fungi, increased substantially by winter warming. Saprotrophic fungi also received large amounts of plant-derived C-indicating a higher importance for the turnover of rhizosphere C than biomass estimates would suggest-still, this C flow was unaffected by winter warming. AM fungi was the only microbial group positively affected by winter warming-the group with the closest connection to plants. Winter warming resulted in higher plant productivity earlier in the season, and this aboveground change likely induced plant nutrient limitation in warmed plots, thus stimulating the plant dependence on, and C allocation to, belowground nutrient acquisition. The preferential C allocation to AM fungi was at the expense of C flow to other microbial groups, which were unaffected by warming. Our findings imply that warmer winters may shift rhizosphere C-fluxes to become more AM fungal-dominated. Surprisingly, the stimulated rhizosphere C flow was matched by increased microbial turnover, leading to no accumulation of soil microbial biomass.}, }
@article {pmid28674774, year = {2018}, author = {Fujimoto, M and Lovett, B and Angoshtari, R and Nirenberg, P and Loch, TP and Scribner, KT and Marsh, TL}, title = {Antagonistic Interactions and Biofilm Forming Capabilities Among Bacterial Strains Isolated from the Egg Surfaces of Lake Sturgeon (Acipenser fulvescens).}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {22-37}, pmid = {28674774}, issn = {1432-184X}, mesh = {Animals ; *Antibiosis ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; *Biofilms ; Fishes/*microbiology ; Lakes/microbiology ; Ovum/*microbiology ; Phylogeny ; }, abstract = {Characterization of interactions within a host-associated microbiome can help elucidate the mechanisms of microbial community formation on hosts and can be used to identify potential probiotics that protect hosts from pathogens. Microbes employ various modes of antagonism when interacting with other members of the community. The formation of biofilm by some strains can be a defense against antimicrobial compounds produced by other taxa. We characterized the magnitude of antagonistic interactions and biofilm formation of 25 phylogenetically diverse taxa that are representative of isolates obtained from egg surfaces of the threatened fish species lake sturgeon (Acipenser fulvescens) at two ecologically relevant temperature regimes. Eight isolates exhibited aggression to at least one other isolate. Pseudomonas sp. C22 was found to be the most aggressive strain, while Flavobacterium spp. were found to be one of the least aggressive and the most susceptible genera. Temperature affected the prevalence and intensity of antagonism. The aggressive strains identified also inhibited growth of known fish pathogens. Biofilm formations were observed for nine isolates and were dependent on temperature and growth medium. The most aggressive of the isolates disrupted biofilm formation of two well-characterized isolates but enhanced biofilm formation of a fish pathogen. Our results revealed the complex nature of interactions among members of an egg associated microbial community yet underscored the potential of specific microbial populations as host probiotics.}, }
@article {pmid28670307, year = {2017}, author = {Ben Said, S and Or, D}, title = {Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1125}, pmid = {28670307}, issn = {1664-302X}, support = {320499/ERC_/European Research Council/International ; }, abstract = {The metabolic diversity present in microbial communities enables cooperation toward accomplishing more complex tasks than possible by a single organism. Members of a consortium communicate by exchanging metabolites or signals that allow them to coordinate their activity through division of labor. In contrast with monocultures, evidence suggests that microbial consortia self-organize to form spatial patterns, such as observed in biofilms or in soil aggregates, that enable them to respond to gradient, to improve resource interception and to exchange metabolites more effectively. Current biotechnological applications of microorganisms remain rudimentary, often relying on genetically engineered monocultures (e.g., pharmaceuticals) or mixed-cultures of partially known composition (e.g., wastewater treatment), yet the vast potential of "microbial ecological power" observed in most natural environments, remains largely underused. In line with the Unified Microbiome Initiative (UMI) which aims to "discover and advance tools to understand and harness the capabilities of Earth's microbial ecosystems," we propose in this concept paper to capitalize on ecological insights into the spatial and modular design of interlinked microbial consortia that would overcome limitations of natural systems and attempt to optimize the functionality of the members and the performance of the engineered consortium. The topology of the spatial connections linking the various members and the regulated fluxes of media between those modules, while representing a major engineering challenge, would allow the microbial species to interact. The modularity of such spatially linked microbial consortia (SLMC) could facilitate the design of scalable bioprocesses that can be incorporated as parts of a larger biochemical network. By reducing the need for a compatible growth environment for all species simultaneously, SLMC will dramatically expand the range of possible combinations of microorganisms and their potential applications. We briefly review existing tools to engineer such assemblies and optimize potential benefits resulting from the collective activity of their members. Prospective microbial consortia and proposed spatial configurations will be illustrated and preliminary calculations highlighting the advantages of SLMC over co-cultures will be presented, followed by a discussion of challenges and opportunities for moving forward with some designs.}, }
@article {pmid28670304, year = {2017}, author = {Shen, J and Liu, Z and Yu, Z and Zhu, W}, title = {Monensin and Nisin Affect Rumen Fermentation and Microbiota Differently In Vitro.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1111}, pmid = {28670304}, issn = {1664-302X}, abstract = {Nisin, a bacteriocin, is a potential alternative to antibiotics to modulate rumen fermentation. However, little is known about its impacts on rumen microbes. This study evaluated the effects of nisin (1 and 5 μM) on in vitro rumen fermentation characteristics, microbiota, and select groups of rumen microbes in comparison with monensin (5 μM), one of the most commonly used ionophores in ruminants. Nisin had greater effects than monensin in inhibiting methane production and decreasing acetate/propionate ratio. Unlike monensin, nisin had no adverse effect on dry matter digestibility. Real-time PCR analysis showed that both monensin and nisin reduced the populations of total bacteria, fungi, and methanogens, while the population of protozoa was reduced only by monensin. Principal component analysis of bacterial 16S rRNA gene amplicons showed a clear separation between the microbiota shaped by monensin and by nisin. Comparative analysis also revealed a significant difference in relative abundance of some bacteria in different taxa between monensin and nisin. The different effects of monensin and nisin on microbial populations and bacterial communities are probably responsible for the discrepancy in their effects on rumen fermentation. Nisin may have advantages over monensin in modulating ruminal microbial ecology and reducing ruminant methane production without adversely affecting feed digestion, and thus it may be used as a potential alternative to monensin fed to ruminants.}, }
@article {pmid28669592, year = {2018}, author = {Koch, C and Müller, S}, title = {Personalized microbiome dynamics - Cytometric fingerprints for routine diagnostics.}, journal = {Molecular aspects of medicine}, volume = {59}, number = {}, pages = {123-134}, doi = {10.1016/j.mam.2017.06.005}, pmid = {28669592}, issn = {1872-9452}, mesh = {Flow Cytometry/*methods ; Humans ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; Single-Cell Analysis/*methods ; }, abstract = {Microbiomes convoy human life in countless ways. They are an essential part of the human body and interact with its host in countless ways. Currently, extensive microbiome analyses assessing the microbiomes' composition and functions based on sequencing information are still far away from being routine analyses due to the complexity of applied techniques and data analysis, their time demand as well as high costs. With the growing demand for on-time community assessment and monitoring of its dynamic behavior with high resolution, alternative high-throughput methods such as microbial community flow cytometry come into focus. Our flow cytometric approach provides single-cell based high-dimensional data by using only three parameters but for every cell in a system which is enough to characterize whole communities' attributes with high acuity over time. To interpret such complex cytometric time-series data, novel concepts are required. We provide a workflow which is applicable for easy-to-use handling and measurement of microbiomes. Drawing inspiration from macro-ecology, in which a rich set of concepts has been developed for describing population dynamics, we interpret huge sets of community single cell data in an intuitive and actionable way using a series of bioinformatics tools which we either developed or adapted from sequence based evaluation approaches for the interpretation of single cell data. The developed evaluation pipeline tests for e.g. ecological measures such as community assembly, functioning, and evolution. We also addressed the meta-community-concept which is a well acknowledged idea in macro-ecology on how interconnected communities perform. The last concept discusses stability which is a metrics of paramount importance. A fast quantification of stability properties may not only detect disturbances and their impact on the organisms but also allow for on-time microbiome treatment. The workflow's immanent ability to support high temporal sample densities below bacterial generation times provides new insight into the ecology of microbiomes and may also provide access to community control for microbiome based health management. The future developments will facilitate cytometric fingerprinting for human routine diagnostics to be as simple and meaningful as a blood count today.}, }
@article {pmid28669057, year = {2018}, author = {Sun, W and Krumins, V and Dong, Y and Gao, P and Ma, C and Hu, M and Li, B and Xia, B and He, Z and Xiong, S}, title = {A Combination of Stable Isotope Probing, Illumina Sequencing, and Co-occurrence Network to Investigate Thermophilic Acetate- and Lactate-Utilizing Bacteria.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {113-122}, pmid = {28669057}, issn = {1432-184X}, support = {LY12C01003//Natural Science Foundation of Zhejiang Province/ ; }, mesh = {Acetates/*metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Carbon Isotopes/analysis/metabolism ; Lactic Acid/*metabolism ; Methane/metabolism ; Microbiota ; Oxidation-Reduction ; Sequence Analysis, DNA ; Temperature ; }, abstract = {Anaerobic digestion is a complicated microbiological process that involves a wide diversity of microorganisms. Acetate is one of the most important intermediates, and interactions between acetate-oxidizing bacteria and archaea could play an important role in the formation of methane in anoxic environments. Anaerobic digestion at thermophilic temperatures is known to increase methane production, but the effects on the microbial community are largely unknown. In the current study, stable isotope probing was used to characterize acetate- and lactate-oxidizing bacteria in thermophilic anaerobic digestion. In microcosms fed [13]C-acetate, bacteria related to members of Clostridium, Hydrogenophaga, Fervidobacterium, Spirochaeta, Limnohabitans, and Rhodococcus demonstrated elevated abundances of [13]C-DNA fractions, suggesting their activities in acetate oxidation. In the treatments fed [13]C-lactate, Anaeromyxobacter, Desulfobulbus, Syntrophus, Cystobacterineae, and Azospira were found to be the potential thermophilic lactate utilizers. PICRUSt predicted that enzymes related to nitrate and nitrite reduction would be enriched in [13]C-DNA fractions, suggesting that the acetate and lactate oxidation may be coupled with nitrate and/or nitrite reduction. Co-occurrence network analysis indicated bacterial taxa not enriched in [13]C-DNA fractions that may also play a critical role in thermophilic anaerobic digestion.}, }
@article {pmid28667427, year = {2018}, author = {Xia, X and Liu, H and Choi, D and Noh, JH}, title = {Variation of Synechococcus Pigment Genetic Diversity Along Two Turbidity Gradients in the China Seas.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {10-21}, pmid = {28667427}, issn = {1432-184X}, support = {661912//General Research Fund by Hong Kong Research Grants Council/ ; 2015CB954003//the National Key Scientific Research Projects of China/ ; 41330961//Natural Science Foundation of China/ ; }, mesh = {Bacterial Proteins/*genetics/metabolism ; *Genetic Variation ; Oceans and Seas ; Operon ; Phylogeny ; Pigments, Biological/genetics/*metabolism ; Seawater/*chemistry/*microbiology ; Synechococcus/classification/*genetics/isolation &amp; purification/metabolism ; }, abstract = {Synechococcus are important and widely distributed picocyanobacteria that encompass a high pigment diversity. In this study, we developed a primer set (peBF/peAR) for amplifying the cpeBA operon sequence from Synechococcus genomic DNA to study Synechococcus pigment diversity along two turbidity gradients in the China seas. Our data revealed that all previously reported pigment types occurred in the South (SCS) and East (ECS) China Seas. In addition, a novel pigment genetic type (type 3f), represented by the high phycourobilin Synechococcus sp. strain KORDI-100 (Exc495:545 = 2.35), was detected. This pigment genetic type differs from the 3c/3d types not only for a very high PUB/PEB ratio but also for a different intergenic spacer sequence and gene organization of the phycobilisome. Synechococcus of different pigment types exhibited clear niche differentiation. Type 2 dominated in the coastal waters, whereas type 3c/3d and 3f were predominant in oceanic waters of the SCS in summer. In the ECS, however, type 3a was the major pigment type throughout the transect. We suggest that in marine environment, various pigment types often co-occur but with one type dominant and PUB/PEB ratio is related to geographic distribution of Synechococcus pigment types. The two marginal seas of China have markedly different Synechococcus pigment compositions.}, }
@article {pmid28667104, year = {2017}, author = {Vázquez-Campos, X and Kinsela, AS and Bligh, MW and Harrison, JJ and Payne, TE and Waite, TD}, title = {Response of Microbial Community Function to Fluctuating Geochemical Conditions within a Legacy Radioactive Waste Trench Environment.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {17}, pages = {}, pmid = {28667104}, issn = {1098-5336}, mesh = {Australia ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Environment ; Geologic Sediments/analysis/microbiology ; Groundwater/*microbiology ; Metagenomics ; Phylogeny ; Radioactive Waste/*analysis ; Water Microbiology ; }, abstract = {During the 1960s, small quantities of radioactive materials were codisposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in 3-meter-deep, unlined trenches. Chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess the impact of changing water levels upon the microbial ecology and contaminant mobility. Collectively, results demonstrated that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the potentially important role that the taxonomically diverse microbial community played in this transition. In particular, aerobes dominated in the first day, followed by an increase of facultative anaerobes/denitrifiers at day 4. Toward the mid-end of the sampling period, the functional and taxonomic profiles depicted an anaerobic community distinguished by a higher representation of dissimilatory sulfate reduction and methanogenesis pathways. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs.IMPORTANCE The role of chemical and microbiological factors in mediating the biogeochemistry of groundwaters from trenches used to dispose of radioactive materials during the 1960s is examined in this study. Specifically, chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess how changing water levels influence microbial ecology and contaminant mobility. Results demonstrate that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the important role that the taxonomically diverse microbial community played in this transition. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs.}, }
@article {pmid28666129, year = {2017}, author = {Ceuppens, S and De Coninck, D and Bottledoorn, N and Van Nieuwerburgh, F and Uyttendaele, M}, title = {Microbial community profiling of fresh basil and pitfalls in taxonomic assignment of enterobacterial pathogenic species based upon 16S rRNA amplicon sequencing.}, journal = {International journal of food microbiology}, volume = {257}, number = {}, pages = {148-156}, doi = {10.1016/j.ijfoodmicro.2017.06.016}, pmid = {28666129}, issn = {1879-3460}, mesh = {Algorithms ; Computational Biology ; Databases, Factual ; Foodborne Diseases/microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Molecular Typing ; Ocimum basilicum/*microbiology ; RNA, Ribosomal, 16S/*genetics ; Real-Time Polymerase Chain Reaction ; Salmonella enterica/classification/*genetics/*isolation &amp; purification ; }, abstract = {Application of 16S rRNA (gene) amplicon sequencing on food samples is increasingly applied for assessing microbial diversity but may as unintended advantage also enable simultaneous detection of any human pathogens without a priori definition. In the present study high-throughput next-generation sequencing (NGS) of the V1-V2-V3 regions of the 16S rRNA gene was applied to identify the bacteria present on fresh basil leaves. However, results were strongly impacted by variations in the bioinformatics analysis pipelines (MEGAN, SILVAngs, QIIME and MG-RAST), including the database choice (Greengenes, RDP and M5RNA) and the annotation algorithm (best hit, representative hit and lowest common ancestor). The use of pipelines with default parameters will lead to discrepancies. The estimate of microbial diversity of fresh basil using 16S rRNA (gene) amplicon sequencing is thus indicative but subject to biases. Salmonella enterica was detected at low frequencies, between 0.1% and 0.4% of bacterial sequences, corresponding with 37 to 166 reads. However, this result was dependent upon the pipeline used: Salmonella was detected by MEGAN, SILVAngs and MG-RAST, but not by QIIME. Confirmation of Salmonella sequences by real-time PCR was unsuccessful. It was shown that taxonomic resolution obtained from the short (500bp) sequence reads of the 16S rRNA gene containing the hypervariable regions V1-V3 cannot allow distinction of Salmonella with closely related enterobacterial species. In conclusion 16S amplicon sequencing, getting the status of standard method in microbial ecology studies of foods, needs expertise on both bioinformatics and microbiology for analysis of results. It is a powerful tool to estimate bacterial diversity but amenable to biases. Limitations concerning taxonomic resolution for some bacterial species or its inability to detect sub-dominant (pathogenic) species should be acknowledged in order to avoid overinterpretation of results.}, }
@article {pmid28665262, year = {2017}, author = {Sultanpuram, VR and Mothe, T and Chintalapati, S and Chintalapati, VR}, title = {Nesterenkonia cremea sp. nov., a bacterium isolated from a soda lake.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {67}, number = {6}, pages = {1861-1866}, doi = {10.1099/ijsem.0.001876}, pmid = {28665262}, issn = {1466-5034}, mesh = {*Alkalies ; Bacterial Typing Techniques ; Base Composition ; Cell Wall/chemistry ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; India ; Lakes/*microbiology ; Micrococcaceae/*classification/genetics/isolation &amp; purification ; Nucleic Acid Hybridization ; Peptidoglycan/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vitamin K 2/chemistry ; }, abstract = {A Gram-stain-positive, aerobic, non-motile, rod-shaped, non-endospore-forming bacterial strain, 10CT, was isolated from Lonar soda lake in India. Based on the 16S rRNA gene sequence analysis, this strain was identified as belonging to the genus Nesterenkonia and was most closely related to the type strains of Nesterenkonia lacusekhoensis (99.1 %, sequence similarity), Nesterenkonia aethiopica (96.9 %), Nesterenkonia flava (96.9 %) and related of the genus Nesterenkonia (<96.6 %, sequence similarity). However, the DNA-DNA relatedness of strain 10CT with N. lacusekhoensis KCTC 19283T was only 34.6±0.9. The DNA G+C content of strain 10CT was 68.6 mol%. Strain 10CT was an aerobic microbe with optimal growth at 37 °C, pH 7.5-8.0 and 5-6 % (w/v) NaCl. The cell-wall peptidoglycan of strain 10CT was of the type A4α (l-Lys-l-Glu). The major polar lipids present were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine. The major isoprenoid quinones were MK-7, MK-8 and MK-9. Major fatty acids of strain 10CT were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The results of phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strain 10CT, which represents a novel member of the genus Nesterenkonia for which the name Nesterenkonia cremea sp. nov. is proposed. The type strain is 10CT (=LMG 29100T=KCTC 39636T=CGMCC 1.15388T).}, }
@article {pmid28664731, year = {2017}, author = {Beerens, K and De Winter, K and Van de Walle, D and Grootaert, C and Kamiloglu, S and Miclotte, L and Van de Wiele, T and Van Camp, J and Dewettinck, K and Desmet, T}, title = {Biocatalytic Synthesis of the Rare Sugar Kojibiose: Process Scale-Up and Application Testing.}, journal = {Journal of agricultural and food chemistry}, volume = {65}, number = {29}, pages = {6030-6041}, doi = {10.1021/acs.jafc.7b02258}, pmid = {28664731}, issn = {1520-5118}, mesh = {Bifidobacterium adolescentis/genetics/*metabolism ; Biocatalysis ; Caco-2 Cells ; Disaccharides/*metabolism ; Fatty Acids, Volatile/metabolism ; Fermentation ; Gastrointestinal Microbiome ; Glucose/metabolism ; Humans ; Industrial Microbiology ; Intestinal Mucosa/metabolism ; Intestines/microbiology ; Sucrose/metabolism ; }, abstract = {Cost-efficient (bio)chemical production processes are essential to evaluate the commercial and industrial applications of promising carbohydrates and also are essential to ensure economically viable production processes. Here, the synthesis of the naturally occurring disaccharide kojibiose (2-O-α-d-glucopyranosyl-d-glucopyranoside) was evaluated using different Bifidobacterium adolescentis sucrose phosphorylase variants. Variant L341I_Q345S was found to efficiently synthesize kojibiose while remaining fully active after 1 week of incubation at 55 °C. Process optimization allowed kojibiose production at the kilogram scale, and simple but efficient downstream processing, using a yeast treatment and crystallization, resulted in more than 3 kg of highly pure crystalline kojibiose (99.8%). These amounts allowed a deeper characterization of its potential in food applications. It was found to have possible beneficial health effects, including delayed glucose release and potential to trigger SCFA production. Finally, we compared the bulk functionality of highly pure kojibiose to that of sucrose, hereby mapping its potential as a new sweetener in confectionery products.}, }
@article {pmid28663443, year = {2017}, author = {Robertson, GP and Hamilton, SK and Barham, BL and Dale, BE and Izaurralde, RC and Jackson, RD and Landis, DA and Swinton, SM and Thelen, KD and Tiedje, JM}, title = {Cellulosic biofuel contributions to a sustainable energy future: Choices and outcomes.}, journal = {Science (New York, N.Y.)}, volume = {356}, number = {6345}, pages = {}, doi = {10.1126/science.aal2324}, pmid = {28663443}, issn = {1095-9203}, mesh = {*Biofuels ; Climate ; *Conservation of Natural Resources ; Crops, Agricultural/growth &amp; development/*metabolism ; Fertilizers ; Lignin/*metabolism ; Nitrogen ; Plants/microbiology ; }, abstract = {Cellulosic crops are projected to provide a large fraction of transportation energy needs by mid-century. However, the anticipated land requirements are substantial, which creates a potential for environmental harm if trade-offs are not sufficiently well understood to create appropriately prescriptive policy. Recent empirical findings show that cellulosic bioenergy concerns related to climate mitigation, biodiversity, reactive nitrogen loss, and crop water use can be addressed with appropriate crop, placement, and management choices. In particular, growing native perennial species on marginal lands not currently farmed provides substantial potential for climate mitigation and other benefits.}, }
@article {pmid28662395, year = {2017}, author = {Lin, Q and De Vrieze, J and Li, C and Li, J and Li, J and Yao, M and Hedenec, P and Li, H and Li, T and Rui, J and Frouz, J and Li, X}, title = {Temperature regulates deterministic processes and the succession of microbial interactions in anaerobic digestion process.}, journal = {Water research}, volume = {123}, number = {}, pages = {134-143}, doi = {10.1016/j.watres.2017.06.051}, pmid = {28662395}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Bioreactors ; Methane ; *Microbial Interactions ; *Temperature ; }, abstract = {Temperature plays crucial roles in microbial interactions that affect the stability and performance of anaerobic digestion. In this study, the microbial interactions and their succession in the anaerobic digestion process were investigated at three levels, represented by (1) present and (2) active micro-organisms, and (3) gene expressions under a temperature gradient from 25 to 55 °C. Network topological features indicated a global variation in microbial interactions at different temperatures. The variations of microbial interactions in terms of network modularity and deterministic processes based on topological features, corresponded well with the variations of methane productions, but not with temperatures. A common successional pattern of microbial interactions was observed at different temperatures, which showed that both deterministic processes and network modularity increased over time during the digestion process. It was concluded that the increase in temperature-mediated network modularity and deterministic processes on shaping the microbial interactions improved the stability and efficiency of anaerobic digestion process.}, }
@article {pmid28662197, year = {2017}, author = {Alexeev, EE and He, X and Slupsky, CM and Lönnerdal, B}, title = {Effects of iron supplementation on growth, gut microbiota, metabolomics and cognitive development of rat pups.}, journal = {PloS one}, volume = {12}, number = {6}, pages = {e0179713}, pmid = {28662197}, issn = {1932-6203}, mesh = {Animals ; *Animals, Newborn ; *Cognition ; Dose-Response Relationship, Drug ; Female ; *Growth ; Intestines/*microbiology ; *Metabolomics ; Microbiota ; Pregnancy ; Rats ; Rats, Sprague-Dawley ; }, abstract = {BACKGROUND: Iron deficiency is common during infancy and therefore iron supplementation is recommended. Recent reports suggest that iron supplementation in already iron replete infants may adversely affect growth, cognitive development, and morbidity.<br><br>METHODS: Normal and growth restricted rat pups were given iron daily (30 or 150 &#x3bc;g/d) from birth to postnatal day (PD) 20, and followed to PD56. At PD20, hematology, tissue iron, and the hepatic metabolome were measured. The plasma metabolome and colonic microbial ecology were assessed at PD20 and PD56. T-maze (PD35) and passive avoidance (PD40) tests were used to evaluate cognitive development.<br><br>RESULTS: Iron supplementation increased iron status in a dose-dependent manner in both groups, but no significant effect of iron on growth was observed. Passive avoidance was significantly lower only in normal rats given high iron compared with controls. In plasma and liver of normal and growth-restricted rats, excess iron increased 3-hydroxybutyrate and decreased several amino acids, urea and myo-inositol. While a profound difference in gut microbiota of normal and growth-restricted rats was observed, with iron supplementation differences in the abundance of strict anaerobes were observed.<br><br>CONCLUSION: Excess iron adversely affects cognitive development, which may be a consequence of altered metabolism and/or shifts in gut microbiota.}, }
@article {pmid28660691, year = {2017}, author = {Sambles, C and Moore, K and Lux, TM and Jones, K and Littlejohn, GR and Gouveia, JD and Aves, SJ and Studholme, DJ and Lee, R and Love, J}, title = {Metagenomic analysis of the complex microbial consortium associated with cultures of the oil-rich alga Botryococcus braunii.}, journal = {MicrobiologyOpen}, volume = {6}, number = {4}, pages = {}, pmid = {28660691}, issn = {2045-8827}, support = {BB/K003240/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; WT097835MF/WT_/Wellcome Trust/United Kingdom ; BB/K003240/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/M008924/1/MRC_/Medical Research Council/United Kingdom ; WT101650MA/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*classification/genetics/growth &amp; development/*isolation &amp; purification ; Chlorophyta/*growth &amp; development ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Metagenomics ; *Microbial Consortia ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Microalgae are widely viewed as a promising and sustainable source of renewable chemicals and biofuels. Botryococcus braunii synthesizes and secretes significant amounts of long-chain (C30 -C40) hydrocarbons that can be subsequently converted into gasoline, diesel, and aviation fuel. B. braunii cultures are not axenic and the effects of co-cultured microorganisms on B. braunii growth and hydrocarbon yield are important, but sometimes contradictory. To understand the composition of the B. braunii microbial consortium, we used high throughput Illumina sequencing of metagenomic DNA to profile the microbiota within a well established, stable B. braunii culture and characterized the demographic changes in the microcosm following modification to the culture conditions. DNA sequences attributed to B. braunii were present in equal quantities in all treatments, whereas sequences assigned to the associated microbial community were dramatically altered. Bacterial species least affected by treatments, and more robustly associated with the algal cells, included members of Rhizobiales, comprising Bradyrhizobium and Methylobacterium, and representatives of Dyadobacter, Achromobacter and Asticcacaulis. The presence of bacterial species identified by metagenomics was confirmed by additional 16S rDNA analysis of bacterial isolates. Our study demonstrates the advantages of high throughput sequencing and robust metagenomic analyses to define microcosms and further our understanding of microbial ecology.}, }
@article {pmid28660292, year = {2018}, author = {Abreu-Yanes, E and Martin-Alonso, A and Martin-Carrillo, N and Livia, KG and Marrero-Gagliardi, A and Valladares, B and Feliu, C and Foronda, P}, title = {Bartonella in Rodents and Ectoparasites in the Canary Islands, Spain: New Insights into Host-Vector-Pathogen Relationships.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {264-273}, pmid = {28660292}, issn = {1432-184X}, support = {2016_21//Fundaci&#xf3;n CajaCanarias/ ; }, mesh = {Animals ; Bacterial Proteins/genetics ; Bartonella/classification/genetics/*isolation &amp; purification/physiology ; Bartonella Infections/*microbiology/transmission ; Disease Reservoirs/*microbiology ; Disease Vectors ; Host Specificity ; Host-Pathogen Interactions ; Humans ; Islands ; Mice ; Phylogeny ; Rats ; Rodentia/classification/*microbiology ; Siphonaptera/microbiology ; Spain ; Zoonoses/microbiology ; }, abstract = {Bartonella genus is comprised of several species of zoonotic relevance and rodents are reservoirs for some of these Bartonella species. As there were no data about the range of Bartonella species circulating among rodents in the Canary Islands, our main aim was to overcome this lack of knowledge by targeting both the citrate synthase (gltA) and the RNA polymerase beta subunit (rpoB) genes. A total of 181 small mammals and 154 ectoparasites were obtained in three of the Canary Islands, namely Tenerife, La Palma, and Lanzarote. The overall prevalence of Bartonella DNA in rodents was 18.8%, whereas the prevalence in ectoparasites was 13.6%. Bartonella sequences closely related to the zoonotic species Bartonella elizabethae, Bartonella tribocorum, and Bartonella rochalimae were identified in rodents, whereas two different gltA haplotypes similar to B. elizabethae were also detected in fleas. Furthermore, Bartonella queenslandensis DNA was also identified in rodents. A strong host specificity was observed, since B. elizabethae DNA was only found in Mus musculus domesticus, whereas gltA and rpoB sequences closely related to the rest of Bartonella species were only identified in Rattus rattus, which is probably due to the host specificity of the arthropod species that act as vectors in these islands. Our results indicate that humans may contract Bartonella infection by contact with rodents in the Canary Islands.}, }
@article {pmid28659879, year = {2017}, author = {Olins, HC and Rogers, DR and Preston, C and Ussler, W and Pargett, D and Jensen, S and Roman, B and Birch, JM and Scholin, CA and Haroon, MF and Girguis, PR}, title = {Co-registered Geochemistry and Metatranscriptomics Reveal Unexpected Distributions of Microbial Activity within a Hydrothermal Vent Field.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1042}, pmid = {28659879}, issn = {1664-302X}, abstract = {Despite years of research into microbial activity at diffuse flow hydrothermal vents, the extent of microbial niche diversity in these settings is not known. To better understand the relationship between microbial activity and the associated physical and geochemical conditions, we obtained co-registered metatranscriptomic and geochemical data from a variety of different fluid regimes within the ASHES vent field on the Juan de Fuca Ridge. Microbial activity in the majority of the cool and warm fluids sampled was dominated by a population of Gammaproteobacteria (likely sulfur oxidizers) that appear to thrive in a variety of chemically distinct fluids. Only the warmest, most hydrothermally-influenced flows were dominated by active populations of canonically vent-endemic Epsilonproteobacteria. These data suggest that the Gammaproteobacteria collected during this study may be generalists, capable of thriving over a broader range of geochemical conditions than the Epsilonproteobacteria. Notably, the apparent metabolic activity of the Gammaproteobacteria-particularly carbon fixation-in the seawater found between discrete fluid flows (the intra-field water) suggests that this area within the Axial caldera is a highly productive, and previously overlooked, habitat. By extension, our findings suggest that analogous, diffuse flow fields may be similarly productive and thus constitute a very important and underappreciated aspect of deep-sea biogeochemical cycling that is occurring at the global scale.}, }
@article {pmid28658633, year = {2017}, author = {Matar, GK and Bagchi, S and Zhang, K and Oerther, DB and Saikaly, PE}, title = {Membrane biofilm communities in full-scale membrane bioreactors are not randomly assembled and consist of a core microbiome.}, journal = {Water research}, volume = {123}, number = {}, pages = {124-133}, doi = {10.1016/j.watres.2017.06.052}, pmid = {28658633}, issn = {1879-2448}, mesh = {*Biofilms ; *Bioreactors ; Microbiota ; RNA, Ribosomal, 16S ; Washington ; *Waste Disposal, Fluid ; }, abstract = {Finding efficient biofouling control strategies requires a better understanding of the microbial ecology of membrane biofilm communities in membrane bioreactors (MBRs). Studies that characterized the membrane biofilm communities in lab-and pilot-scale MBRs are numerous, yet similar studies in full-scale MBRs are limited. Also, most of these studies have characterized the mature biofilm communities with very few studies addressing early biofilm communities. In this study, five full-scale MBRs located in Seattle (Washington, U.S.A.) were selected to address two questions concerning membrane biofilm communities (early and mature): (i) Is the assembly of biofilm communities (early and mature) the result of random immigration of species from the source community (i.e. activated sludge)? and (ii) Is there a core membrane biofilm community in full-scale MBRs? Membrane biofilm (early and mature) and activated sludge (AS) samples were collected from the five MBRs, and 16S rRNA gene sequencing was applied to investigate the bacterial communities of AS and membrane biofilms (early and mature). Alpha and beta diversity measures revealed clear differences in the bacterial community structure between the AS and biofilm (early and mature) samples in the five full-scale MBRs. These differences were mainly due to the presence of large number of unique but rare operational taxonomic units (∼13% of total reads in each MBR) in each sample. In contrast, a high percentage (∼87% of total reads in each MBR) of sequence reads was shared between AS and biofilm samples in each MBR, and these shared sequence reads mainly belong to the dominant taxa in these samples. Despite the large fraction of shared sequence reads between AS and biofilm samples, simulated biofilm communities from random sampling of the respective AS community revealed that biofilm communities differed significantly from the random assemblages (P < 0.001 for each MBR), indicating that the biofilm communities (early and mature) are unlikely to represent a random sample of the AS community. In addition to the presence of unique operational taxonomic units in each biofilm sample (early or mature), comparative analysis of operational taxonomic units and genera revealed the presence of a core biofilm community in the five full-scale MBRs. These findings provided insight into the membrane biofilm communities in full-scale MBRs. More comparative studies are needed in the future to elucidate the factors shaping the core and unique biofilm communities in full-scale MBRs.}, }
@article {pmid28658154, year = {2017}, author = {Ashton, JJ and Colquhoun, CM and Cleary, DW and Coelho, T and Haggarty, R and Mulder, I and Batra, A and Afzal, NA and Beattie, RM and Scott, KP and Ennis, S}, title = {16S sequencing and functional analysis of the fecal microbiome during treatment of newly diagnosed pediatric inflammatory bowel disease.}, journal = {Medicine}, volume = {96}, number = {26}, pages = {e7347}, pmid = {28658154}, issn = {1536-5964}, mesh = {Adolescent ; Biodiversity ; Child ; Fatty Acids, Volatile/analysis ; Feces/chemistry/*microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Inflammatory Bowel Diseases/genetics/metabolism/*microbiology/*therapy ; Longitudinal Studies ; Male ; Prospective Studies ; RNA, Bacterial/*analysis ; RNA, Ribosomal, 16S/*analysis ; Sequence Analysis, RNA ; Siblings ; Treatment Outcome ; }, abstract = {The human microbiome is of considerable interest to pediatric inflammatory bowel disease (PIBD) researchers with 1 potential mechanism for disease development being aberrant immune handling of the intestinal bacteria. This study analyses the fecal microbiome through treatment in newly diagnosed PIBD patients and compares to cohabiting siblings where possible. Patients were recruited on clinical suspicion of PIBD before diagnosis. Treatment-naïve fecal samples were collected, with further samples at 2 and 6 weeks into treatment. Samples underwent 16S ribosomal ribonucleic acid (RNA) gene sequencing and short-chain fatty acids (SCFAs) analysis, results were analyzed using quantitative-insights-into-microbial-ecology. Six PIBD patients were included in the cohort: 4 Crohn disease (CD), 1 ulcerative colitis (UC), 1 inflammatory bowel disease (IBD) unclassified, and median age 12.6 (range 10-15.1 years); 3 patients had an unaffected healthy sibling recruited. Microbial diversity (observed species/Chao1/Shannon diversity) was reduced in treatment-naïve patients compared to siblings and patients in remission. Principal coordinate analysis using Bray-Curtis dissimilarity and UniFrac revealed microbial shifts in CD over the treatment course. In treatment-naïve PIBD, there was reduction in functional ability for amino acid metabolism and carbohydrate handling compared to controls (P = .038) and patients in remission (P = .027). Metabolic function returned to normal after remission was achieved. SCFA revealed consistent detection of lactate in treatment-naïve samples. This study adds in-depth 16S rRNA sequencing analysis on a small longitudinal cohort to the literature and includes sibling controls and patients with UC/IBD unclassified. It highlights the initial dysbiosis, reduced diversity, altered functional potential, and subsequent shifts in bacteria from diagnosis over time to remission.}, }
@article {pmid28657886, year = {2017}, author = {Porter, NT and Martens, EC}, title = {The Critical Roles of Polysaccharides in Gut Microbial Ecology and Physiology.}, journal = {Annual review of microbiology}, volume = {71}, number = {}, pages = {349-369}, doi = {10.1146/annurev-micro-102215-095316}, pmid = {28657886}, issn = {1545-3251}, mesh = {Bacteria/*growth &amp; development/*metabolism ; *Gastrointestinal Microbiome ; Humans ; Metabolic Networks and Pathways ; *Microbiota ; Polysaccharides/*metabolism ; *Symbiosis ; }, abstract = {The human intestine harbors a dense microbial ecosystem (microbiota) that is different between individuals, dynamic over time, and critical for aspects of health and disease. Dietary polysaccharides directly shape the microbiota because of a gap in human digestive physiology, which is equipped to assimilate only proteins, lipids, simple sugars, and starch, leaving nonstarch polysaccharides as major nutrients reaching the microbiota. A mutualistic role of gut microbes is to digest dietary complex carbohydrates, liberating host-absorbable energy via fermentation products. Emerging data indicate that polysaccharides play extensive roles in host-gut microbiota symbiosis beyond dietary polysaccharide digestion, including microbial interactions with endogenous host glycans and the importance of microbial polysaccharides. In this review, we consider multiple mechanisms through which polysaccharides mediate aspects of host-microbe symbiosis in the gut, including some affecting health. As host and microbial metabolic pathways are intimately connected with diet, we highlight the potential to manipulate this system for health.}, }
@article {pmid28654195, year = {2017}, author = {Adserias-Garriga, J and Quijada, NM and Hernandez, M and Rodríguez Lázaro, D and Steadman, D and Garcia-Gil, LJ}, title = {Dynamics of the oral microbiota as a tool to estimate time since death.}, journal = {Molecular oral microbiology}, volume = {32}, number = {6}, pages = {511-516}, doi = {10.1111/omi.12191}, pmid = {28654195}, issn = {2041-1014}, mesh = {Adult ; Aged, 80 and over ; Bacteria/*classification/genetics ; Biodiversity ; *Cadaver ; DNA, Bacterial/analysis ; Decompression ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Microbiota/genetics ; Mouth/*microbiology ; Postmortem Changes ; RNA, Ribosomal, 16S/genetics ; Sex Factors ; }, abstract = {The oral cavity harbors one of the most diverse microbiomes in the human body. It has been shown to be the second most complex in the body after the gastrointestinal tract. Upon death, the indigenous microorganisms lead to the decomposition of the carcass. Therefore, the oral cavity and gastrointestinal tract microbiomes play a key role in human decomposition. The aim of the present study is to monitor the microbiome of decaying bodies on a daily basis and to identify signature bacterial taxa, that can improve postmortem interval estimation. Three individuals (one male and two female) donated to the University of Tennessee Forensic Anthropology Center for the W.M. Bass Donated Skeletal Collection were studied. Oral swab samples were taken daily throughout the different stages of cadaveric putrefaction. DNA was extracted and analyzed by next-generation sequencing techniques. The three cadavers showed similar overall successional changes during the decomposition process. Firmicutes and Actinobacteria are the predominant phyla in the fresh stage. The presence of Tenericutes corresponds to bloat stage. Firmicutes is the predominant phylum in advanced decay, but the Firmicutes community is a different one from the predominant Firmicutes of the fresh stage. This study depicts the thanatomicrobiome successional changes in the oral cavity, and highlights its potential use in forensic cases as a quantitative and objective approach to estimate postmortem interval, from an ecological rationale.}, }
@article {pmid28653084, year = {2017}, author = {Sultanpuram, VR and Mothe, T and Chintalapati, S and Chintalapati, VR}, title = {Bacillus alcaliphilum sp. nov., a bacterium isolated from a soda lake.}, journal = {Archives of microbiology}, volume = {199}, number = {9}, pages = {1303-1309}, doi = {10.1007/s00203-017-1403-0}, pmid = {28653084}, issn = {1432-072X}, support = {SB/FT/LS-115/2012//Science and Engineering Research Board/ ; SB/FT/LS-320/2012//Science and Engineering Research Board/ ; }, mesh = {*Bacillus/classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition/genetics ; Cell Wall/metabolism ; DNA, Bacterial/genetics ; Diaminopimelic Acid/analysis ; Fatty Acids/analysis ; India ; Lakes/*microbiology ; Nucleic Acid Hybridization ; Peptidoglycan/chemistry ; Phosphatidylethanolamines/analysis ; Phospholipids/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sodium Chloride/analysis ; Spores, Bacterial/physiology ; }, abstract = {Two novel (14B[T] and 7B) Gram-stain-positive, rod-shaped, motile and endospore-forming bacterial strains were isolated from Lonar soda lake, India. Based on 16S rRNA gene sequence analysis, the strains 14B[T] and 7B were identified as belonging to the class Firmibacteria and were most closely related to Bacillus halodurans LMG 7121[T] (99.7 and 99.8%, respectively), Bacillus okuhidensis LMG 22468[T] (99.1 and 99.2%, respectively) and other members in the genus Bacillus (<97.0%). However, the DNA-DNA relatedness studies indicated that the strains 14B[T] and 7B were distantly related to B. halodurans LMG 7121[T] (49.1 ± 0.6 and 45.7 ± 0.6, respectively) and B. okuhidensis LMG 22468[T] (40.9 ± 0.9 and 42.1 ± 0.5, respectively). The high 16S rRNA gene sequence similarity (99.9%) and DNA-DNA relatedness (88 ± 9) indicated that strains 14B[T] and 7B were members of a single species. The strains grew optimally at a pH of 9.0-9.5 with 2-5% (w/v) NaCl and temperature of 37 °C. Strains 14B[T] and 7B were catalase positive and oxydase negative. The cell wall of strain 14B[T] contained meso-diaminopimelic acid as the diagnostic diamino acid. Polar lipids include diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), an unknown aminophospholipid (APL1) and three unknown lipids (L1-3). The predominant isoprenoid quinone is MK-7. anteiso-C15:0 (30.8%) was the predominant fatty acid, and significant proportions of iso-C15:0 (24.9%), iso-C16:0 (17.9%) and anteiso-C17:0 (12.3%) were also detected in strains 14B[T] and 7B. The DNA G+C content of strains 14B[T] and 7B was 41.6 and 41.3 mol%, respectively. The results of molecular, physiological and biochemical tests allowed a clear differentiation of strains 14B[T] and 7B from all other members of the genus Bacillus, for which the name Bacillus alcaliphilum sp. nov. is proposed. The type strain is 14B[T] (=KCTC 33777[T] = CGMCC 1.15474[T]).}, }
@article {pmid28652975, year = {2017}, author = {Vikram, S and Govender, N and Kabwe, MH and Bezuidt, O and Makhalanyane, TP}, title = {Draft genome sequence of Massilia sp. KIM isolated from South African grassland biome soils.}, journal = {Genomics data}, volume = {13}, number = {}, pages = {24-26}, pmid = {28652975}, issn = {2213-5960}, abstract = {Massilia sp. are aerobic, Gram-negative, rod-shaped bacteria that are found in air, water, and soils. Here we describe the draft genome sequence of Massilia sp. KIM, isolated from the South African grassland soils. The total length of the genome was estimated at 5.73 Mb, comprised of 17 contigs. The draft genome has been deposited in the DDBJ/EMBL/GenBank under the accession MVAD10000000 and is available for download at: https://www.ncbi.nlm.nih.gov/nuccore/MVAD00000000. Additionally, the raw short reads are available in the NCBI SRA database under the accession number: SRR5469241.}, }
@article {pmid28652974, year = {2017}, author = {Kabwe, MH and Govender, N and Vikram, S and Bezuidt, OM and Makhalanyane, TP}, title = {The draft genome sequence of Hymenobacter sp. CRA2 isolated from Nama Karoo shrub land soils from South Africa.}, journal = {Genomics data}, volume = {13}, number = {}, pages = {21-23}, pmid = {28652974}, issn = {2213-5960}, abstract = {Here we report the draft genome sequence of Hymenobacter sp. CRA2 isolated from the Nama Karoo shrub land soils of the Northern Cape, South Africa. This genome is approximately 5.88 Mb long and the assembly comprised 45 contigs. The draft genome sequence has been deposited in DDBJ/EMBL/GenBank under the accession number NZ_MVBC00000000 and is available for download at: https://www.ncbi.nlm.nih.gov/nuccore/NZ_MVBC00000000.1.}, }
@article {pmid28649274, year = {2017}, author = {Lai, B and Yu, S and Bernhardt, PV and Rabaey, K and Virdis, B and Krömer, JO}, title = {Erratum to: Anoxic metabolism and biochemical production in Pseudomonas putida F1 driven by a bioelectrochemical system.}, journal = {Biotechnology for biofuels}, volume = {10}, number = {}, pages = {155}, pmid = {28649274}, issn = {1754-6834}, abstract = {[This corrects the article DOI: 10.1186/s13068-016-0452-y.].}, }
@article {pmid28648868, year = {2017}, author = {Luongo, D and Treppiccione, L and Sorrentino, A and Ferrocino, I and Turroni, S and Gatti, M and Di Cagno, R and Sanz, Y and Rossi, M}, title = {Immune-modulating effects in mouse dendritic cells of lactobacilli and bifidobacteria isolated from individuals following omnivorous, vegetarian and vegan diets.}, journal = {Cytokine}, volume = {97}, number = {}, pages = {141-148}, doi = {10.1016/j.cyto.2017.06.007}, pmid = {28648868}, issn = {1096-0023}, mesh = {Animals ; B7-1 Antigen/genetics ; B7-2 Antigen/genetics ; Bifidobacterium/*immunology/isolation &amp; purification ; Cytokines/genetics ; Dendritic Cells/*immunology/microbiology ; *Diet ; *Diet, Vegan ; Down-Regulation ; Feces/microbiology ; Gastrointestinal Microbiome/*immunology ; Humans ; *Immunomodulation ; Interleukin-10/genetics ; Interleukin-12/genetics ; Lactobacillus/*immunology/isolation &amp; purification ; Mice ; Tumor Necrosis Factor-alpha/genetics ; Up-Regulation ; Vegetarians ; }, abstract = {Lactobacilli and bifidobacteria play a primary role in modulation of gut immunity. By considering that microbiota composition depends on various factors, including diet, we asked whether functional differences could characterize faecal populations of lactobacilli and bifidobacteria isolated from individuals with different dietary habits. 155 healthy volunteers who followed omnivorous, ovo-lacto-vegetarian or vegan diets were recruited at four Italian centres (Turin, Parma, Bologna and Bari). Faecal samples were collected; lactobacilli and bifidobacteria were isolated on selective media and their immunomodulatory activity was tested in mouse dendritic cells (DCs). Pre-incubation with lactobacilli increased LPS-induced expression of the maturation markers CD80 and CD86, whereas pre-incubation with bifidobacteria decreased such expression. Analysis of the cytokine profile indicated that strains of both genera induced down-regulation of IL-12 and up-regulation of IL-10, whereas expression of TNF-α was not modulated. Notably, analysis of anti-inflammatory potential (IL-10/IL-12 ratio) showed that lactobacilli evoked a greater anti-inflammatory effect than did bifidobacteria in the omnivorous group (P<0.05). We also found significantly reduced anti-inflammatory potential in the bacterial strains isolated from Bari's volunteers in comparison with those from the cognate groups from the other centres. In conclusion, lactobacilli and bifidobacteria showed a genus-specific ability of modulating in vitro innate immunity associated with a specific dietary habit. Furthermore, the geographical area had a significant impact on the anti-inflammatory potential of some components of faecal microbiota.}, }
@article {pmid28648723, year = {2017}, author = {Biancalana, F and Kopprio, GA and Lara, RJ and Alonso, C}, title = {A protocol for the simultaneous identification of chitin-containing particles and their associated bacteria.}, journal = {Systematic and applied microbiology}, volume = {40}, number = {5}, pages = {314-320}, doi = {10.1016/j.syapm.2017.05.004}, pmid = {28648723}, issn = {1618-0984}, mesh = {Bacteria/*classification/metabolism ; Chitin/*analysis ; Diatoms/*classification ; Dinoflagellida/*classification ; Fluorescein-5-isothiocyanate/analogs &amp; derivatives/chemistry ; Fungi/*classification ; In Situ Hybridization, Fluorescence/*methods ; Staining and Labeling/methods ; Wheat Germ Agglutinins/chemistry ; }, abstract = {Chitin is the second most abundant polymer on Earth, playing a crucial role in the biogeochemical cycles. A core issue for studying its processing in aquatic systems is the identification and enumeration of chitin-containing particles and organisms, ideally in a manner that can be directly linked to bulk chitin quantification. The aim of this study was the development of such a technique. We successfully combined the methodology of bulk chitin determination using wheat germ agglutinin (FITC-WGA) for staining chitin-containing particles and organisms along with CARD-FISH staining of either chitin-containing eukaryotic cells or bacteria associated with them. Environmental chitin staining was successfully applied to natural water samples. Fungal hyphae, diatoms, and dinoflagellates, sestonic aggregates and chitin-containing structures derived from metazoa were observed. Also, hybridized bacteria attached to chitinaceous debris were clearly visualized. Finally, as proof of principle, cultured yeast cells were simultaneously-targeted by FITC-WGA and the EUK516 probe without exhibiting any interference between both stains. The presented approach appears as a powerful tool to evaluate the contribution of different size classes and organisms to chitin production and consumption, opening the possibility for application of single-cell approaches targeting the ecophysiology of chitin transformations in aquatic systems.}, }
@article {pmid28648267, year = {2017}, author = {Jiménez, DJ and Dini-Andreote, F and DeAngelis, KM and Singer, SW and Salles, JF and van Elsas, JD}, title = {Ecological Insights into the Dynamics of Plant Biomass-Degrading Microbial Consortia.}, journal = {Trends in microbiology}, volume = {25}, number = {10}, pages = {788-796}, doi = {10.1016/j.tim.2017.05.012}, pmid = {28648267}, issn = {1878-4380}, mesh = {Biofuels/microbiology ; Biomass ; Ecology/methods ; Microbial Consortia/*physiology ; Plants/*microbiology ; Soil Microbiology ; }, abstract = {Plant biomass (PB) is an important resource for biofuel production. However, the frequent lack of efficiency of PB saccharification is still an industrial bottleneck. The use of enzyme cocktails produced from PB-degrading microbial consortia (PB-dmc) is a promising approach to optimize this process. Nevertheless, the proper use and manipulation of PB-dmc depends on a sound understanding of the ecological processes and mechanisms that exist in these communities. This Opinion article provides an overview of arguments as to how spatiotemporal nutritional fluxes influence the successional dynamics and ecological interactions (synergism versus competition) between populations in PB-dmc. The themes of niche occupancy, 'sugar cheaters', minimal effective consortium, and the Black Queen Hypothesis are raised as key subjects that foster our appraisal of such systems. Here we provide a conceptual framework that describes the critical topics underpinning the ecological basis of PB-dmc, giving a solid foundation upon which further prospective experimentation can be developed.}, }
@article {pmid28647755, year = {2018}, author = {Scola, V and Ramond, JB and Frossard, A and Zablocki, O and Adriaenssens, EM and Johnson, RM and Seely, M and Cowan, DA}, title = {Namib Desert Soil Microbial Community Diversity, Assembly, and Function Along a Natural Xeric Gradient.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {193-203}, pmid = {28647755}, issn = {1432-184X}, support = {N00113-95565//National Research Foundation of South Africa/ ; }, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Biodiversity ; Desert Climate ; *Microbiota ; Namibia ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The hyperarid Namib desert is a coastal desert in southwestern Africa and one of the oldest and driest deserts on the planet. It is characterized by a west/east increasing precipitation gradient and by regular coastal fog events (extending up to 75 km inland) that can also provide soil moisture. In this study, we evaluated the role of this natural aridity and xeric gradient on edaphic microbial community structure and function in the Namib desert. A total of 80 individual soil samples were collected at 10-km intervals along a 190-km transect from the fog-dominated western coastal region to the eastern desert boundary. Seventeen physicochemical parameters were measured for each soil sample. Soil parameters reflected the three a priori defined climatic/xeric zones along the transect ("fog," "low rain," and "high rain"). Microbial community structures were characterized by terminal restriction fragment length polymorphism fingerprinting and shotgun metaviromics, and their functional capacities were determined by extracellular enzyme activity assays. Both microbial community structures and activities differed significantly between the three xeric zones. The deep sequencing of surface soil metavirome libraries also showed shifts in viral composition along the xeric transect. While bacterial community assembly was influenced by soil chemistry and stochasticity along the transect, variations in community "function" were apparently tuned by xeric stress.}, }
@article {pmid28646410, year = {2018}, author = {Hajek, AE and Harris, DC and Bittner, TD}, title = {Symbiont Spillover from Invasive to Native Woodwasps.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {7-9}, pmid = {28646410}, issn = {1432-184X}, support = {12-CA-11420004-043//USDA Forest Service/ ; 2009-02182//USDA NIFA AFRI/ ; }, mesh = {Animals ; Basidiomycota/classification/genetics/isolation &amp; purification/*physiology ; Female ; Host-Pathogen Interactions ; Male ; North America ; Phylogeny ; Pinus/parasitology ; *Symbiosis ; Trees/parasitology ; Wasps/*microbiology/physiology ; }, abstract = {Hosts and their associated microbes are being increasingly introduced around the world, which can lead to novel host/microbe associations via new sympatries. Woodwasps (Hymenoptera: Siricidae) are able to utilize wood for its nutrients due to obligate mutualistic associations with white rot fungi in the genus Amylostereum and when invasive woodwasps are introduced to new areas, their symbionts accompany them. There is increasing evidence that woodwasp-fungus associations previously believed to be highly specific are actually flexible. We show that in North America, both Urocerus albicornis and Urocerus cressoni, which develop in trees in the Pinaceae, usually use Amylostereum chailletii but sometimes carry an Amylostereum areolatum strain putatively introduced to North America by the invasive woodwasp Sirex noctilio. Symbiont spillover from invasive to native hosts is a source of new host/introduced symbiont associations that could result in changes in microbes and host fitness with the potential to impact communities.}, }
@article {pmid28645232, year = {2017}, author = {Hacquard, S and Spaepen, S and Garrido-Oter, R and Schulze-Lefert, P}, title = {Interplay Between Innate Immunity and the Plant Microbiota.}, journal = {Annual review of phytopathology}, volume = {55}, number = {}, pages = {565-589}, doi = {10.1146/annurev-phyto-080516-035623}, pmid = {28645232}, issn = {1545-2107}, mesh = {*Microbiota ; Plant Diseases/immunology/microbiology ; *Plant Immunity ; Plants/*immunology/*microbiology ; Receptors, Pattern Recognition/*immunology ; Symbiosis ; }, abstract = {The innate immune system of plants recognizes microbial pathogens and terminates their growth. However, recent findings suggest that at least one layer of this system is also engaged in cooperative plant-microbe interactions and influences host colonization by beneficial microbial communities. This immune layer involves sensing of microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) that initiate quantitative immune responses to control host-microbial load, whereas diversification of MAMPs and PRRs emerges as a mechanism that locally sculpts microbial assemblages in plant populations. This suggests a more complex microbial management role of the innate immune system for controlled accommodation of beneficial microbes and in pathogen elimination. The finding that similar molecular strategies are deployed by symbionts and pathogens to dampen immune responses is consistent with this hypothesis but implies different selective pressures on the immune system due to contrasting outcomes on plant fitness. The reciprocal interplay between microbiota and the immune system likely plays a critical role in shaping beneficial plant-microbiota combinations and maintaining microbial homeostasis.}, }
@article {pmid28645197, year = {2017}, author = {Di Sante, L and Morroni, G and Brenciani, A and Vignaroli, C and Antonelli, A and D'Andrea, MM and Di Cesare, A and Giovanetti, E and Varaldo, PE and Rossolini, GM and Biavasco, F}, title = {pHTβ-promoted mobilization of non-conjugative resistance plasmids from Enterococcus faecium to Enterococcus faecalis.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {72}, number = {9}, pages = {2447-2453}, doi = {10.1093/jac/dkx197}, pmid = {28645197}, issn = {1460-2091}, mesh = {Anti-Bacterial Agents/*pharmacology ; Blotting, Southern ; *Conjugation, Genetic ; DNA, Bacterial/genetics ; *Drug Resistance, Multiple, Bacterial ; Enterococcus faecalis/drug effects/*genetics ; Enterococcus faecium/drug effects/*genetics ; Erythromycin/pharmacology ; Genes, Bacterial/drug effects ; Humans ; Plasmids/*drug effects ; Polymerase Chain Reaction ; *Recombination, Genetic ; Tetracycline Resistance/genetics ; }, abstract = {OBJECTIVES: To analyse the recombination events associated with conjugal mobilization of two multiresistance plasmids, pRUM17i48 and pLAG (formerly named pDO1-like), from Enterococcus faecium 17i48 to Enterococcus faecalis JH2-2.<br><br>METHODS: The plasmids from two E. faecalis transconjugants (JH-4T, tetracycline resistant, and JH-8E, erythromycin resistant) and from the E. faecium donor (also carrying a pHT&#x3b2;-like conjugative plasmid, named pHT&#x3b2;17i48) were investigated by several methods, including PCR mapping and sequencing, S1-PFGE followed by Southern blotting and hybridization, and WGS.<br><br>RESULTS: Two locations of repApHT&#x3b2; were detected in both transconjugants, one on a &#x223c;50&#x2009;kb plasmid (as in the donor) and the other on plasmids of larger sizes. In JH-4T, WGS disclosed an 88.6&#x2009;kb plasmid resulting from the recombination of pHT&#x3b2;17i48 (&#x223c;50&#x2009;kb) and a new plasmid, named pLAG (35.3&#x2009;kb), carrying the tet(M), tet(L), lsa(E), lnu(B), spw and aadE resistance genes. In JH-8E, a 75&#x2009;kb plasmid resulting from the recombination of pHT&#x3b2;17i48 and pRUM17i48 was observed. In both cases, the cointegrates were apparently derived from replicative transposition of an IS1216 present in each of the multiresistance plasmids into pHT&#x3b2;17i48. The cointegrates could resolve to yield the multiresistance plasmids and a pHT&#x3b2;17i48 derivative carrying an IS1216 (unlike the pHT&#x3b2;17i48 of the donor).<br><br>CONCLUSIONS: Our results completed the characterization of the multiresistance plasmids carried by the E. faecium 17i48, confirming the role of pHT plasmids in the mobilization of non-conjugative antibiotic resistance elements among enterococci. Results also revealed that mobilization to E. faecalis was associated with the generation of cointegrate plasmids promoted by IS1216-mediated transposition.}, }
@article {pmid28644444, year = {2017}, author = {Momper, L and Jungbluth, SP and Lee, MD and Amend, JP}, title = {Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community.}, journal = {The ISME journal}, volume = {11}, number = {10}, pages = {2319-2333}, pmid = {28644444}, issn = {1751-7370}, mesh = {Acetyl Coenzyme A/metabolism ; Autotrophic Processes ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Carbon/*metabolism ; Carbon Cycle ; Geologic Sediments/analysis/*microbiology ; Metabolic Networks and Pathways ; Metagenome ; Metagenomics ; Mining ; Phylogeny ; }, abstract = {The terrestrial deep subsurface is a huge repository of microbial biomass, but in relation to its size and physical heterogeneity, few sites have been investigated in detail. Here, we applied a culture-independent metagenomic approach to characterize the microbial community composition in deep (1500 meters below surface) terrestrial fluids. Samples were collected from a former gold mine in Lead, South Dakota, USA, now Sanford Underground Research Facility (SURF). We reconstructed 74 genomes from metagenomes (MAGs), enabling the identification of common metabolic pathways. Sulfate and nitrate/nitrite reduction were the most common putative energy metabolisms. Complete pathways for autotrophic carbon fixation were found in more than half of the MAGs, with the reductive acetyl-CoA pathway by far the most common. Nearly 40% (29 of 74) of the recovered MAGs belong to bacterial phyla without any cultivated members-microbial dark matter. Three of our MAGs constitute two novel phyla previously only identified in 16 S rRNA gene surveys. The uniqueness of this data set-its physical depth in the terrestrial subsurface, the relative abundance and completeness of microbial dark matter genomes and the overall diversity of this physically deep, dark, community-make it an invaluable addition to our knowledge of deep subsurface microbial ecology.}, }
@article {pmid28644443, year = {2017}, author = {Collingro, A and Köstlbacher, S and Mussmann, M and Stepanauskas, R and Hallam, SJ and Horn, M}, title = {Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae.}, journal = {The ISME journal}, volume = {11}, number = {10}, pages = {2334-2344}, pmid = {28644443}, issn = {1751-7370}, support = {281633/ERC_/European Research Council/International ; I 291/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Chlamydia/classification/*cytology/*genetics/pathogenicity ; Chlamydia Infections/*microbiology ; Flagella/genetics/metabolism ; *Genome, Bacterial ; Genomics ; Humans ; Seawater/*microbiology ; Virulence ; }, abstract = {Chlamydiae are obligate intracellular bacteria comprising important human pathogens and symbionts of protists. Molecular evidence indicates a tremendous diversity of chlamydiae particularly in marine environments, yet our current knowledge is based mainly on terrestrial representatives. Here we provide first insights into the biology of marine chlamydiae representing three divergent clades. Our analysis of single-cell amplified genomes revealed hallmarks of the chlamydial lifestyle, supporting the ancient origin of their characteristic developmental cycle and major virulence mechanisms. Surprisingly, these chlamydial genomes encode a complete flagellar apparatus, a previously unreported feature. We show that flagella are an ancient trait that was subject to differential gene loss among extant chlamydiae. Together with a chemotaxis system, these marine chlamydiae are likely motile, with flagella potentially playing a role during host cell infection. This study broadens our view on chlamydial biology and indicates a largely underestimated potential to adapt to different hosts and environments.}, }
@article {pmid28642992, year = {2018}, author = {Tomova, A and Ivanova, L and Buschmann, AH and Godfrey, HP and Cabello, FC}, title = {Plasmid-Mediated Quinolone Resistance (PMQR) Genes and Class 1 Integrons in Quinolone-Resistant Marine Bacteria and Clinical Isolates of Escherichia coli from an Aquacultural Area.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {104-112}, pmid = {28642992}, issn = {1432-184X}, support = {FB001//Lenfest Ocean Program/Pew Charitable Trusts/ ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Aquaculture ; *Drug Resistance, Bacterial ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/genetics/metabolism ; Fishes/growth &amp; development/microbiology ; Gene Transfer, Horizontal ; Humans ; *Integrons ; Microbial Sensitivity Tests ; Plasmids/*genetics/metabolism ; Quinolones/*pharmacology ; Seawater/*microbiology ; Uropathogenic Escherichia coli/classification/*drug effects/genetics/isolation &amp; purification ; }, abstract = {Antimicrobial usage in aquaculture selects for antimicrobial-resistant microorganisms in the marine environment. The relevance of this selection to terrestrial animal and human health is unclear. Quinolone-resistance genes qnrA, qnrB, and qnrS were chromosomally located in four randomly chosen quinolone-resistant marine bacteria isolated from an aquacultural area with heavy quinolone usage. In quinolone-resistant uropathogenic clinical isolates of Escherichia coli from a coastal area bordering the same aquacultural region, qnrA was chromosomally located in two E. coli isolates, while qnrB and qnrS were located in small molecular weight plasmids in two other E. coli isolates. Three quinolone-resistant marine bacteria and three quinolone-resistant E. coli contained class 1 integrons but without physical association with PMQR genes. In both marine bacteria and uropathogenic E. coli, class 1 integrons had similar co-linear structures, identical gene cassettes, and similarities in their flanking regions. In a Marinobacter sp. marine isolate and in one E. coli clinical isolate, sequences immediately upstream of the qnrS gene were homologous to comparable sequences of numerous plasmid-located qnrS genes while downstream sequences were different. The observed commonality of quinolone resistance genes and integrons suggests that aquacultural use of antimicrobials might facilitate horizontal gene transfer between bacteria in diverse ecological locations.}, }
@article {pmid28642991, year = {2018}, author = {Haruna, E and Zin, NM and Kerfahi, D and Adams, JM}, title = {Extensive Overlap of Tropical Rainforest Bacterial Endophytes between Soil, Plant Parts, and Plant Species.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {88-103}, pmid = {28642991}, issn = {1432-184X}, support = {GUP-2015-042//Universiti Kebangsaan Malaysia/ ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; Endophytes/classification/genetics/*isolation &amp; purification ; Phylogeny ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Plant Stems/microbiology ; Plants/classification/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rainforest ; Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The extent to which distinct bacterial endophyte communities occur between different plant organs and species is poorly known and has implications for bioprospecting efforts. Using the V3 region of the bacterial 16S ribosomal RNA (rRNA) gene, we investigated the diversity patterns of bacterial endophyte communities of three rainforest plant species, comparing leaf, stem, and root endophytes plus rhizosphere soil community. There was extensive overlap in bacterial communities between plant organs, between replicate plants of the same species, between plant species, and between plant organ and rhizosphere soil, with no consistent clustering by compartment or host plant species. The non-metric multidimensional scaling (NMDS) analysis highlighted an extensively overlapping bacterial community structure, and the β-nearest taxon index (βNTI) analysis revealed dominance of stochastic processes in community assembly, suggesting that bacterial endophyte operational taxonomic units (OTUs) were randomly distributed among plant species and organs and rhizosphere soil. Percentage turnover of OTUs within pairs of samples was similar both for plant individuals of the same species and of different species at around 80-90%. Our results suggest that sampling extra individuals, extra plant organs, extra species, or use of rhizosphere soil, might be about equally effective for obtaining new OTUs for culture. These observations suggest that the plant endophyte community may be much more diverse, but less predictable, than would be expected from culturing efforts alone.}, }
@article {pmid28642737, year = {2017}, author = {Damsté, JSS and Rijpstra, WIC and Dedysh, SN and Foesel, BU and Villanueva, L}, title = {Pheno- and Genotyping of Hopanoid Production in Acidobacteria.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {968}, pmid = {28642737}, issn = {1664-302X}, abstract = {Hopanoids are pentacyclic triterpenoid lipids synthesized by different bacterial groups. Methylated hopanoids were believed to be exclusively synthesized by cyanobacteria and aerobic methanotrophs until the genes encoding for the methylation at the C-2 and C-3 position (hpnP and hpnR) were found to be widespread in the bacterial domain, invalidating their use as specific biomarkers. These genes have been detected in the genome of the Acidobacterium "Ca. Koribacter versatilis," but our knowledge of the synthesis of hopanoids and the presence of genes of their biosynthetic pathway in other member of the Acidobacteria is limited. We analyzed 38 different strains of seven Acidobacteria subdivisions (SDs 1, 3, 4, 6, 8, 10, and 23) for the presence of C30 hopenes and C30+ bacteriohopane polyols (BHPs) using the Rohmer reaction. BHPs and/or C30 hopenes were detected in all strains of SD1 and SD3 but not in SD4 (excepting Chloracidobacterium thermophilum), 6, 8, 10, and 23. This is in good agreement with the presence of genes required for hopanoid biosynthesis in the 31 available whole genomes of cultivated Acidobacteria. All genomes encode the enzymes involved in the non-mevalonate pathway ultimately leading to farnesyl diphosphate but only SD1 and 3 Acidobacteria and C. thermophilum encode all three enzymes required for the synthesis of squalene, its cyclization (shc), and addition and modification of the extended side chain (hpnG, hpnH, hpnI, hpnJ, hpnO). In almost all strains, only tetrafunctionalized BHPs were detected; three strains contained variable relative abundances (up to 45%) of pentafunctionalized BHPs. Only "Ca. K. versatilis" contained methylated hopanoids (i.e., 2,3-dimethyl bishomohopanol), although in low (<10%) amounts. These genes are not present in any other Acidobacterium, consistent with the absence of methylated BHPs in the other examined strains. These data are in agreement with the scattered occurrence of methylated BHPs in other bacterial phyla such as the Alpha-, Beta-, and Gammaproteobacteria and the Cyanobacteria, limiting their biomarker potential. Metagenomes of Acidobacteria were also examined for the presence of genes required for hopanoid biosynthesis. The complete pathway for BHP biosynthesis was evident in SD2 Acidobacteria and a group phylogenetically related to SD1 and SD3, in line with the limited occurrence of BHPs in acidobacterial cultures.}, }
@article {pmid28639032, year = {2018}, author = {Tomei Torres, FA}, title = {Case Study: Microbial Ecology and Forensics of Chinese Drywall-Elemental Sulfur Disproportionation as Primary Generator of Hydrogen Sulfide.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {37-48}, pmid = {28639032}, issn = {1432-184X}, mesh = {Bacteria/*metabolism ; Biofouling ; Calcium Sulfate ; China ; Construction Materials/*analysis ; Copper ; Corrosion ; *Ecology ; Hydrogen Sulfide/*metabolism ; Hydrogen-Ion Concentration ; Oxidation-Reduction ; Sulfates/metabolism ; Sulfides/metabolism ; Sulfur/*chemistry ; Sulfur Dioxide/chemistry ; Thiosulfates/chemistry ; }, abstract = {Drywall manufactured in China released foul odors attributed to volatile sulfur compounds. These included hydrogen sulfide, methyl mercaptan, and sulfur dioxide. Given that calcium sulfate is the main component of drywall, one would suspect bacterial reduction of sulfate to sulfide as the primary culprit. However, when the forensics, i.e., the microbial and chemical signatures left in the drywall, are studied, the evidence suggests that, rather than dissimilatory sulfate reduction, disproportionation of elemental sulfur to hydrogen sulfide and sulfate was actually the primary cause of the malodors. Forensic evidence suggests that the transformation of elemental sulfur went through several abiological and microbial stages: (1) partial volatilization of elemental sulfur during the manufacture of plaster of Paris, (2) partial abiotic disproportionation of elemental sulfur to sulfide and thiosulfate during the manufacture of drywall, (3) microbial disproportionation of elemental sulfur to sulfide and sulfate resulting in neutralization of all alkalinity, and acidification below pH 4, (4) acidophilic microbial disproportionation of elemental sulfur to sulfide and sulfuric acid, and (5) hydrogen sulfide volatilization, coating of copper fixtures resulting in corrosion, and oxidation to sulfur dioxide.}, }
@article {pmid28638806, year = {2017}, author = {Hernandez-Sanabria, E and Slomka, V and Herrero, ER and Kerckhof, FM and Zaidel, L and Teughels, W and Boon, N}, title = {In vitro Increased Respiratory Activity of Selected Oral Bacteria May Explain Competitive and Collaborative Interactions in the Oral Microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {7}, number = {}, pages = {235}, pmid = {28638806}, issn = {2235-2988}, mesh = {Bacteria/classification/growth &amp; development/*metabolism/pathogenicity ; Bacterial Physiological Phenomena ; Biofilms/growth &amp; development ; Carbon/metabolism ; Ecosystem ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions ; Microbial Interactions/*physiology ; Microbiota/genetics/*physiology ; Mouth/*microbiology ; Multivariate Analysis ; Nitrogen/metabolism ; Peptides/metabolism ; Phenotype ; Symbiosis ; }, abstract = {Understanding the driving forces behind the shifts in the ecological balance of the oral microbiota will become essential for the future management and treatment of periodontitis. As the use of competitive approaches for modulating bacterial outgrowth is unexplored in the oral ecosystem, our study aimed to investigate both the associations among groups of functional compounds and the impact of individual substrates on selected members of the oral microbiome. We employed the Phenotype Microarray high-throughput technology to analyse the microbial cellular phenotypes of 15 oral bacteria. Multivariate statistical analysis was used to detect respiratory activity triggers and to assess similar metabolic activities. Carbon and nitrogen were relevant for the respiration of health-associated bacteria, explaining competitive interactions when grown in biofilms. Carbon, nitrogen, and peptides tended to decrease the respiratory activity of all pathobionts, but not significantly. None of the evaluated compounds significantly increased activity of pathobionts at both 24 and 48 h. Additionally, metabolite requirements of pathobionts were dissimilar, suggesting that collective modulation of their respiratory activity may be challenging. Flow cytometry indicated that the metabolic activity detected in the Biolog plates may not be a direct result of the number of bacterial cells. In addition, damage to the cell membrane may not influence overall respiratory activity. Our methodology confirmed previously reported competitive and collaborative interactions among bacterial groups, which could be used either as marker of health status or as targets for modulation of the oral environment.}, }
@article {pmid28637853, year = {2017}, author = {Schilder, J and van Hardenbroek, M and Bodelier, P and Kirilova, EP and Leuenberger, M and Lotter, AF and Heiri, O}, title = {Trophic state changes can affect the importance of methane-derived carbon in aquatic food webs.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1857}, pages = {}, pmid = {28637853}, issn = {1471-2954}, support = {239858/ERC_/European Research Council/International ; }, mesh = {Animals ; Carbon/*chemistry ; Carbon Isotopes/analysis ; Chironomidae ; Daphnia ; Eutrophication ; *Food Chain ; Lakes ; Methane/*chemistry ; Netherlands ; }, abstract = {Methane-derived carbon, incorporated by methane-oxidizing bacteria, has been identified as a significant source of carbon in food webs of many lakes. By measuring the stable carbon isotopic composition (δ[13]C values) of particulate organic matter, Chironomidae and Daphnia spp. and their resting eggs (ephippia), we show that methane-derived carbon presently plays a relevant role in the food web of hypertrophic Lake De Waay, The Netherlands. Sediment geochemistry, diatom analyses and δ[13]C measurements of chironomid and Daphnia remains in the lake sediments indicate that oligotrophication and re-eutrophication of the lake during the twentieth century had a strong impact on in-lake oxygen availability. This, in turn, influenced the relevance of methane-derived carbon in the diet of aquatic invertebrates. Our results show that, contrary to expectations, methane-derived relative to photosynthetically produced organic carbon became more relevant for at least some invertebrates during periods with higher nutrient availability for algal growth, indicating a proportionally higher use of methane-derived carbon in the lake's food web during peak eutrophication phases. Contributions of methane-derived carbon to the diet of the investigated invertebrates are estimated to have ranged from 0-11% during the phase with the lowest nutrient availability to 13-20% during the peak eutrophication phase.}, }
@article {pmid28637301, year = {2017}, author = {Münch, PC and Stecher, B and McHardy, AC}, title = {EDEN: evolutionary dynamics within environments.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {20}, pages = {3292-3295}, pmid = {28637301}, issn = {1367-4811}, mesh = {Bacteria/genetics ; *Biological Evolution ; Metagenomics/*methods ; Phenotype ; *Phylogeny ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {SUMMARY: Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data. EDEN is the first software for the rapid detection of protein families and regions under positive selection, as well as their associated biological processes, from meta- and pangenome data. It provides an interactive result visualization for detailed comparative analyses.<br><br>EDEN is available as a Docker installation under the GPL 3.0 license, allowing its use on common operating systems, at http://www.github.com/hzi-bifo/eden.<br><br>CONTACT: alice.mchardy@helmholtz-hzi.de.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid28636321, year = {2017}, author = {Guo, J and Gao, SH and Lu, J and Bond, PL and Verstraete, W and Yuan, Z}, title = {Copper Oxide Nanoparticles Induce Lysogenic Bacteriophage and Metal-Resistance Genes in Pseudomonas aeruginosa PAO1.}, journal = {ACS applied materials &amp; interfaces}, volume = {9}, number = {27}, pages = {22298-22307}, doi = {10.1021/acsami.7b06433}, pmid = {28636321}, issn = {1944-8252}, mesh = {Bacteriophages ; Copper ; *Metal Nanoparticles ; Pseudomonas aeruginosa ; }, abstract = {The intensive use of metal-based nanoparticles results in their continuous release into the environment, leading to potential risks for human health and microbial ecosystems. Although previous studies have indicated that nanoparticles may be toxic to microorganisms, there is a scarcity of data available to assess the underlying molecular mechanisms of inhibitory and biocidal effects of nanoparticles on microorganisms. This study used physiological experiments, microscopy, live/dead staining, and the genome-wide RNA sequencing to investigate the multiple responses of Pseudomonas aeruginosa to the exposure of copper oxide nanoparticles (CuO NPs). The results for the first time show that CuO NPs induce lysogenic bacteriophage, which might render defective within a bacterial host. The presence of CuO NPs causes nitrite accumulation and great increases in N2O emissions. Respiration is likely inhibited as denitrification activity is depleted in terms of decreased transcript levels of most denitrification genes. Meanwhile, CuO NPs exposure significantly up-regulated gene expression for those coding for copper resistance, resistance-nodulation-division, P-type ATPase efflux, and cation diffusion facilitator transporters. Our findings offer insights into the interaction between environmental bacteria and CuO NPs at the transcriptional level and, thus, improve our understanding of potential risks of nanoparticles on microbial ecosystems and public health.}, }
@article {pmid28634640, year = {2018}, author = {Fonseca, EDS and Peixoto, RS and Rosado, AS and Balieiro, FC and Tiedje, JM and Rachid, CTCDC}, title = {The Microbiome of Eucalyptus Roots under Different Management Conditions and Its Potential for Biological Nitrogen Fixation.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {183-191}, pmid = {28634640}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; DNA, Bacterial/genetics ; Endophytes/classification/genetics/isolation &amp; purification/*metabolism ; Eucalyptus/*microbiology ; *Microbiota ; *Nitrogen Fixation ; Phylogeny ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {Eucalyptus plantations offer a cost-effective and renewable source of raw material. There is substantial interest in improving forestry production, especially through sustainable strategies such as the use of plant growth-promoting bacteria. However, little is known about Eucalyptus microbiology. In this study, the endophytic bacterial community was assessed in Eucalyptus urograndis roots using culture-dependent and culture-independent techniques with plants grown under different conditions. Three phyla accounted for approximately 95% of the community, with Actinobacteria corresponding to approximately 59%. This contrasts with previous studies in which Actinobacteria accounted for only 5 to 10%. Our data also revealed a high diversity of bacteria, with 359 different genera but a high level of dominance. Six genera, Mycobacterium, Bradyrhizobium, Streptomyces, Bacillus, Actinospica, and Burkholderia, accounted for more than 50% of the classified sequences. We observed a significant influence of the treatments on some genera, causing changes in the bacterial community structure. The obtained data also suggest that Eucalyptus may benefit from biological nitrogen fixation, with many abundant genera being closely related to nitrogen-fixing bacteria. Using N-depleted media, we also cultured 95 bacterial isolates, of which 24 tested positive for the nifH gene and were able to maintain growth without any N source in the medium.}, }
@article {pmid28634639, year = {2018}, author = {Erler, S and Lewkowski, O and Poehlein, A and Forsgren, E}, title = {The Curious Case of Achromobacter eurydice, a Gram-Variable Pleomorphic Bacterium Associated with European Foulbrood Disease in Honeybees.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {1-6}, pmid = {28634639}, issn = {1432-184X}, support = {ER 786/1-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Achromobacter/classification/genetics/isolation &amp; purification/*physiology ; Animals ; Bees/growth &amp; development/*microbiology ; Europe ; Larva/growth &amp; development/microbiology ; }, abstract = {Honeybees are prone to parasite and pathogen infestations/infections due to their social colony life. Bacterial pathogens in particular lead to destructive infections of the brood. European foulbrood is caused by the bacterium Melissococcus plutonius in combination with several other Gram-positive bacteria (Achromobacter eurydice, Bacillus pumilus, Brevibacillus laterosporus, Enterococcus faecalis, Paenibacillus alvei, Paenibacillus dendritiformis) involved as secondary invaders following the initial infection. More than a century ago, A. eurydice was discovered to be associated with European foulbrood and morphologically and biochemically characterized. However, since the 1950s-1960s, only a few studies are known covering the biological relevance of this bacterium. Here, we review the biology, ecology, morphology, and biochemistry and discuss the still unclear systematic classification of A. eurydice.}, }
@article {pmid28634638, year = {2017}, author = {Xu, S and Lu, W and Mustafa, MF and Caicedo, LM and Guo, H and Fu, X and Wang, H}, title = {Co-existence of Anaerobic Ammonium Oxidation Bacteria and Denitrifying Anaerobic Methane Oxidation Bacteria in Sewage Sludge: Community Diversity and Seasonal Dynamics.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {832-840}, pmid = {28634638}, issn = {1432-184X}, mesh = {Ammonium Compounds/*metabolism ; Anaerobiosis ; *Bacteria/classification/metabolism ; Beijing ; China ; *Denitrification ; Methane/*metabolism ; Microbiota ; Oxidation-Reduction ; Seasons ; Sewage/*microbiology ; }, abstract = {Anaerobic ammonium oxidation (ANAMMOX) and denitrifying anaerobic methane oxidation (DAMO) have been recently discovered as relevant processes in the carbon and nitrogen cycles of wastewater treatment plants. In this study, the seasonal dynamics of ANAMMOX and DAMO bacterial community structures and their abundance in sewage sludge collected from wastewater treatment plants were analysed. Results indicated that ANAMMOX and DAMO bacteria co-existed in sewage sludge in different seasons and their abundance was positively correlated (P < 0.05). The high abundance of ANAMMOX and DAMO bacteria in autumn and winter indicated that these seasons were the preferred time to favour the growth of ANAMMOX and DAMO bacteria. The community structure of ANNAMOX and DAMO bacteria could also shift with seasonal changes. The "Candidatus Brocadia" genus of ANAMMOX bacteria was mainly recovered in spring and summer, and an unknown cluster was primarily detected in autumn and winter. Similar patterns of seasonal variation in the community structure of DAMO bacteria were also observed. Group B was the dominant in spring and summer, whereas in autumn and winter, group A and group B presented almost the same proportion. The redundancy analysis revealed that pH and nitrate were the most significant factors affecting community structures of these two groups (P < 0.01). This study reported the diversity of ANAMMOX and DAMO in wastewater treatment plants that may be the basis for new nitrogen removal technologies.}, }
@article {pmid28633067, year = {2017}, author = {Batlle-Vilanova, P and Ganigué, R and Ramió-Pujol, S and Bañeras, L and Jiménez, G and Hidalgo, M and Balaguer, MD and Colprim, J and Puig, S}, title = {Microbial electrosynthesis of butyrate from carbon dioxide: Production and extraction.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {117}, number = {}, pages = {57-64}, doi = {10.1016/j.bioelechem.2017.06.004}, pmid = {28633067}, issn = {1878-562X}, mesh = {Bioreactors/*microbiology ; Butyric Acid/*isolation &amp; purification/*metabolism ; Carbon Dioxide/*metabolism ; Electrochemistry ; Electrodes ; Electron Transport ; }, abstract = {To date acetate is the main product of microbial electrosynthesis (MES) from carbon dioxide (CO2). In this work a tubular bioelectrochemical system was used to carry out MES and enhance butyrate production over the other organic products. Batch tests were performed at a fixed cathode potential of -0.8V vs SHE. The reproducibility of the results according to previous experiments was validated in a preliminary test. According to the literature butyrate production could take place by chain elongation reactions at low pH and high hydrogen partial pressure (pH2). During the experiment, CO2 supply was limited to build up pH2 and trigger the production of compounds with a higher degree of reduction. In test 1 butyrate became the predominant end-product, with a concentration of 59.7mMC versus 20.3mMC of acetate, but limitation on CO2 supply resulted in low product titers. CO2 limitation was relaxed in test 2 to increase the bioelectrochemical activity but increase pH2 and promote the production of butyrate, what resulted in the production of 87.5mMC of butyrate and 34.7mMC of acetate. The consumption of ethanol, and the presence of other products in the biocathode (i.e. caproate) suggested that butyrate production took place through chain elongation reactions, likely driven by Megasphaera sueciensis (>39% relative abundance). Extraction and concentration of butyrate was performed by liquid membrane extraction. A concentration phase with 252.4mMC of butyrate was obtained, increasing also butyrate/acetate ratio to 16.4. The results are promising for further research on expanding the product portfolio of MES.}, }
@article {pmid28632115, year = {2017}, author = {Pascual, J and Foesel, BU and Geppert, A and Huber, KJ and Overmann, J}, title = {Flaviaesturariibacter luteus sp. nov., isolated from an agricultural floodplain soil, and emended description of the genus Flaviaesturariibacter.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {67}, number = {6}, pages = {1727-1734}, doi = {10.1099/ijsem.0.001854}, pmid = {28632115}, issn = {1466-5034}, mesh = {Agriculture ; Bacterial Typing Techniques ; Bacteroidetes/*classification/genetics/isolation &amp; purification ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Namibia ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {A novel slow-growing bacterial strain designated as AW305T was isolated from an agricultural floodplain soil located in Mashare, Kavango region, Namibia. Cells stained Gram-negative, were non-motile, non-spore-forming, coccoid to rod-shaped and did not form a capsule. Colonies were yellow-pigmented, but flexirubin-type pigments were not detected. AW305T had an aerobic chemo-organoheterotrophic metabolism, using a narrow spectrum of carbon sources for growth, with preference for complex protein substrates, organic acids and amino acids. AW305T was able to grow at 15-40 °C, pH 5.3-8.3 and in the presence of up to 0.25 % (w/v) NaCl. 16S rRNA gene sequence comparison showed that AW305T belonged to the genus Flaviaesturariibacter (family Chitinophagaceae). Its closest relatives were Flaviaesturariibacter amylovorans GCR0105T (97.0 %), Flavisolibacter ginsengiterrae Gsoil 492T (93.6 %) and Flavisolibacter ginsengisoli Gsoil 643T (93.2 %). DNA-DNA hybridization experiments corroborated that AW305T represents an independent genomospecies. The genomic DNA G+C content was 57.6 mol%. Major fatty acids were iso-C15 : 1 G, iso-C15 : 0, C16 : 1ω5c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The predominant respiratory quinone was MK-7, albeit minor amounts of MK-6 were also detected. The polar lipids comprised major amounts of phosphatidylethanolamine and minor amounts of two unidentified lipids, an unidentified phospholipid, an unidentified glycolipid and an unidentified aminoglycophospholipid. On the basis of the polyphasic characterization, strain AW305T represents a novel species of the genus Flaviaesturariibacter for which the name Flaviaesturariibacter luteus sp. nov. is proposed, with the type strain AW305T (=DSM 100282T=LMG 29416T).}, }
@article {pmid28631411, year = {2017}, author = {Pascual, J and von Hoermann, C and Rottler-Hoermann, AM and Nevo, O and Geppert, A and Sikorski, J and Huber, KJ and Steiger, S and Ayasse, M and Overmann, J}, title = {Function of bacterial community dynamics in the formation of cadaveric semiochemicals during in situ carcass decomposition.}, journal = {Environmental microbiology}, volume = {19}, number = {8}, pages = {3310-3322}, doi = {10.1111/1462-2920.13828}, pmid = {28631411}, issn = {1462-2920}, mesh = {Animals ; Autolysis/*metabolism ; Bacteria/classification/*metabolism ; *Cadaver ; Gas Chromatography-Mass Spectrometry ; Humans ; Insecta/*metabolism ; Necrosis/*metabolism ; Pheromones ; RNA, Ribosomal, 16S/genetics ; Sus scrofa/metabolism ; Swine/metabolism ; Volatile Organic Compounds/metabolism ; }, abstract = {The decomposition of dead mammalian tissue involves a complex temporal succession of epinecrotic bacteria. Microbial activity may release different cadaveric volatile organic compounds which in turn attract other key players of carcass decomposition such as scavenger insects. To elucidate the dynamics and potential functions of epinecrotic bacteria on carcasses, we monitored bacterial communities developing on still-born piglets incubated in different forest ecosystems by combining high-throughput Illumina 16S rRNA sequencing with gas chromatography-mass spectrometry of volatiles. Our results show that the community structure of epinecrotic bacteria and the types of cadaveric volatile compounds released over the time course of decomposition are driven by deterministic rather than stochastic processes. Individual cadaveric volatile organic compounds were correlated with specific taxa during the first stages of decomposition which are dominated by bacteria. Through best-fitting multiple linear regression models, the synthesis of acetic acid, indole and phenol could be linked to the activity of Enterobacteriaceae, Tissierellaceae and Xanthomonadaceae, respectively. These conclusions are also commensurate with the metabolism described for the dominant taxa identified for these families. The predictable nature of in situ synthesis of cadaveric volatile organic compounds by epinecrotic bacteria provides a new basis for future chemical ecology and forensic studies.}, }
@article {pmid28631214, year = {2017}, author = {Barnhart, K and Forman, ME and Umile, TP and Kueneman, J and McKenzie, V and Salinas, I and Minbiole, KPC and Woodhams, DC}, title = {Identification of Bufadienolides from the Boreal Toad, Anaxyrus boreas, Active Against a Fungal Pathogen.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {990-1000}, pmid = {28631214}, issn = {1432-184X}, mesh = {Animals ; Antifungal Agents/*pharmacology ; Bufanolides/isolation &amp; purification/*pharmacology ; Bufonidae/*metabolism/*microbiology ; Chytridiomycota/*drug effects ; }, abstract = {Amphibian granular glands provide a wide range of compounds on the skin that defend against pathogens and predators. We identified three bufadienolides-the steroid-like compounds arenobufagin, gamabufotalin, and telocinobufagin-from the boreal toad, Anaxyrus boreas, through liquid chromatography mass spectrometry (LC/MS). Compounds were detected both after inducing skin gland secretions and in constitutive mucosal rinses from toads. We described the antimicrobial properties of each bufadienolide against Batrachochytrium dendrobatidis (Bd), an amphibian fungal pathogen linked with boreal toad population declines. All three bufadienolides were found to inhibit Bd growth at similar levels. The maximum Bd inhibition produced by arenobufagin, gamabufotalin, and telocinobufagin were approximately 50%, in contrast to the complete Bd inhibition shown by antimicrobial skin peptides produced by some amphibian species. In addition, skin mucus samples significantly reduced Bd viability, and bufadienolides were detected in 15 of 62 samples. Bufadienolides also appeared to enhance growth of the anti-Bd bacterium Janthinobacterium lividum, and thus may be involved in regulation of the skin microbiome. Here, we localized skin bacteria within the mucus layer and granular glands of toads with fluorescent in situ hybridization. Overall, our results suggest that bufadienolides can function in antifungal defense on amphibian skin and their production is a potentially convergent trait similar to antimicrobial peptide defenses found on the skin of other species. Further studies investigating bufadienolide expression across toad populations, their regulation, and interactions with other components of the skin mucosome will contribute to understanding the complexities of amphibian immune defense.}, }
@article {pmid28629505, year = {2017}, author = {Lee, HJ and Whang, KS}, title = {Micromonospora fulva sp. nov., isolated from forest soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {67}, number = {6}, pages = {1746-1751}, doi = {10.1099/ijsem.0.001858}, pmid = {28629505}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Diaminopimelic Acid/chemistry ; Fatty Acids/chemistry ; *Forests ; Micromonospora/*classification/genetics/isolation &amp; purification ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; Pigmentation ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; *Soil Microbiology ; Ubiquinone/chemistry ; Vitamin K 2/chemistry ; }, abstract = {A novel actinobacterium, designated strain UDF-1T, was isolated from forest soil in Chungnam, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain UDF-1T formed a branched brownish-orange substrate mycelium with spherical or oval spores. No aerial mycelium was formed. Comparative 16S rRNA gene sequence analysis indicated that strain UDF-1T belongs to the genus Micromonospora, showing the highest sequence similarity to Micromonospora palomenae NEAU-CX1T (99.2 % 16S rRNA gene sequence similarity), 'Micromonospora maoerensis' NEAU-MES19 (99.0 %), Micromonospora endolithica DSM 44398T (98.8 %) and Micromonospora matsumotoense IMSNU 22003T (98.8 %). The predominant menaquinones of strain UDF-1T were MK-10 (H4) and MK-10 (H6). The cell wall contained meso-diaminopimelic acid and the whole-cell sugars were arabinose and xylose. The major polar lipids were phosphatidylinositol, diphosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0 and iso-C15 : 0. The genomic DNA G+C content was 73.1 mol%. DNA-DNA relatedness between strain UDF-1T and closely related type strains in the genus Micromonospora was below 30 %. On the basis of the polyphasic analysis conducted in this study, strain UDF-1T represents a novel species of the genus Micromonospora, for which the name Micromonospora fulva sp. nov. is proposed. The type strain is UDF-1T (=KACC 18696T=NBRC 111826T).}, }
@article {pmid28626612, year = {2017}, author = {DeBruyn, JM and Hauther, KA}, title = {Postmortem succession of gut microbial communities in deceased human subjects.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3437}, pmid = {28626612}, issn = {2167-8359}, abstract = {The human microbiome has demonstrated an importance for the health and functioning in living individuals. However, the fate of the microbiome after death is less understood. In addition to a better understanding of microbe-mediated decomposition processes, postmortem succession of human-associated microbial communities has been suggested as a possible forensic tool for estimating time since death, or postmortem interval (PMI). The objective of our study was to document postmortem changes in human gut bacterial communities. Gut microflora were repeatedly sampled from the caeca of cadavers as they decayed under natural environmental conditions. 16S rRNA gene amplicon sequencing revealed that over time, bacterial richness significantly increased (rs = 0.449) while diversity decreased (rs = - 0.701). The composition of gut bacterial communities changed in a similar manner over time towards a common decay community. OTUs belonging to Bacteroidales (Bacteroides, Parabacteroides) significantly declined while Clostridiales (Clostridium, Anaerosphaera) and the fly-associated Gammaproteobacteria Ignatzschineria and Wohlfahrtiimonas increased. Our examination of human caeca microflora in decomposing cadavers adds to the growing literature on postmortem microbial communities, which will ultimately contribute to a better understanding of decomposition processes.}, }
@article {pmid28625991, year = {2017}, author = {De Filippis, F and Laiola, M and Blaiotta, G and Ercolini, D}, title = {Different Amplicon Targets for Sequencing-Based Studies of Fungal Diversity.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {17}, pages = {}, pmid = {28625991}, issn = {1098-5336}, mesh = {Biodiversity ; DNA Primers/genetics ; DNA, Fungal/genetics ; DNA, Intergenic/genetics ; Fungi/classification/*genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/*methods ; Mycological Typing Techniques/*methods ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Target-gene amplicon sequencing is the most exploited high-throughput sequencing application in microbial ecology. The targets are taxonomically relevant genes, with 16S rRNA being the gold standard for bacteria. As for fungi, the most commonly used target is the internal transcribed spacer (ITS). However, the uneven ITS length among species may promote preferential amplification and sequencing and incorrect estimation of their abundance. Therefore, the use of different targets is desirable. We evaluated the use of three different target amplicons for the characterization of fungal diversity. After an in silico primer evaluation, we compared three amplicons (the ITS1-ITS2 region [ITS1-2], 18S ribosomal small subunit RNA, and the D1/D2 domain of the 26S ribosomal large subunit RNA), using biological samples and a mock community of common fungal species. All three targets allowed for accurate identification of the species present. Nevertheless, high heterogeneity in ITS1-2 length was found, and this caused an overestimation of the abundance of species with a shorter ITS, while both 18S and 26S amplicons allowed for more reliable quantification. We demonstrated that ITS1-2 amplicon sequencing, although widely used, may lead to an incorrect evaluation of fungal communities, and efforts should be made to promote the use of different targets in sequencing-based microbial ecology studies.IMPORTANCE Amplicon-sequencing approaches for fungi may rely on different targets affecting the diversity and abundance of the fungal species. An increasing number of studies will address fungal diversity by high-throughput amplicon sequencing. The description of the communities must be accurate and reliable in order to draw useful insights and to address both ecological and biological questions. By analyzing a mock community and several biological samples, we demonstrate that using different amplicon targets may change the results of fungal microbiota analysis, and we highlight how a careful choice of the target is fundamental for a thorough description of the fungal communities.}, }
@article {pmid28624904, year = {2017}, author = {Coelho-Souza, SA and Jenkins, SR and Casarin, A and Baeta-Neves, MH and Salgado, LT and Guimaraes, JRD and Coutinho, R}, title = {The Effect of Light on Bacterial Activity in a Seaweed Holobiont.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {868-876}, pmid = {28624904}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Autotrophic Processes ; *Bacterial Physiological Phenomena/drug effects ; *Biofilms/drug effects/growth &amp; development/radiation effects ; Brazil ; Circadian Rhythm ; *Light ; Sargassum/microbiology ; Seasons ; }, abstract = {Holobionts are characterized by the relationship between host and their associated organisms such as the biofilm associated with macroalgae. Considering that light is essential to macroalgae survival, the aim of this study was to verify the effect of light on the heterotrophic activity in biofilms of the brown macroalgae Sargassum furcatum during its growth cycle. Measurements of heterotrophic activity were done under natural light levels at different times during a daily cycle and under an artificial extinction of natural light during the afternoon. We also measured Sargassum primary production under these light levels in the afternoon. Both measurements were done with and without photosynthesis inhibitor and antibiotics. Biofilm composition was mainly represented by bacteria but diatoms, cyanobacteria, and other organisms were also common. When a peak of diatom genera was recorded, the heterotrophic activity of the biofilm was higher. Heterotrophic activity was usually highest during the afternoon and the presence of a photosynthesis inhibitor caused an average reduction of 17% but there was no relationship with Sargassum primary production. These results indicate that autotrophic production in the biofilm was reduced by the inhibitor with consequences on bacterial activity. Heterotrophic activity was mainly bacterial and the antibiotics chloramphenicol and penicillin were more effective than streptomycin. We suggest primary producers in the biofilm are more important to increase bacterial activity than the macroalgae itself because of coherence of the peaks of heterotrophic and autotrophic activity in biofilm during the afternoon and the effects of autotrophic inhibitors on heterotrophic activity.}, }
@article {pmid28624358, year = {2017}, author = {Xu, G and Yang, EJ and Xu, H}, title = {Environmental drivers of heterogeneity in the trophic-functional structure of protozoan communities during an annual cycle in a coastal ecosystem.}, journal = {Marine pollution bulletin}, volume = {121}, number = {1-2}, pages = {400-403}, doi = {10.1016/j.marpolbul.2017.06.012}, pmid = {28624358}, issn = {1879-3363}, mesh = {*Ciliophora ; *Ecosystem ; Environment ; Environmental Monitoring ; Food Chain ; Population Dynamics ; *Water Quality ; }, abstract = {Trophic-functional groupings are an important biological trait to summarize community structure in functional space. The heterogeneity of the tropic-functional pattern of protozoan communities and its environmental drivers were studied in coastal waters of the Yellow Sea during a 1-year cycle. Samples were collected using the glass slide method at four stations within a water pollution gradient. A second-stage matrix-based analysis was used to summarize spatial variation in the annual pattern of the functional structure. A clustering analysis revealed significant variability in the trophic-functional pattern among the four stations during the 1-year cycle. The heterogeneity in the trophic-functional pattern of the communities was significantly related to changes in environmental variables, particularly ammonium-nitrogen and nitrates, alone or in combination with dissolved oxygen. These results suggest that the heterogeneity in annual patterns of protozoan trophic-functional structure may reflect water quality status in coastal ecosystems.}, }
@article {pmid28623391, year = {2017}, author = {Piché-Choquette, S and Khdhiri, M and Constant, P}, title = {Survey of High-Affinity H2-Oxidizing Bacteria in Soil Reveals Their Vast Diversity Yet Underrepresentation in Genomic Databases.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {771-775}, pmid = {28623391}, issn = {1432-184X}, mesh = {Bacteria/*classification/*genetics/isolation &amp; purification ; *Databases, Genetic ; Genes, Bacterial ; *Microbiota ; Oxidation-Reduction ; Phylogeny ; *Soil Microbiology ; }, abstract = {While high-affinity H2-oxidizing bacteria (HA-HOB) serve as the main sink of atmospheric H2, the ecology of this specialist functional group is rather unknown due to its recent discovery. The main purpose of our study is to provide the first extensive survey of HA-HOB in farmland, larch, and poplar soils exposed to 0.5 and 10,000 ppmv H2. Using qPCR and qRT-PCR assays along with PCR amplicon high-throughput sequencing of hhyL gene encoding for the large subunit of high-affinity [NiFe]-hydrogenases (HAH), we found that hhyL gene expression ratio explained better variation in measured H2 oxidation rates than HA-HOB species richness. Carbon, nitrogen, pH, and bacterial species richness appeared as the most important drivers of HA-HOB community structure. Our study also highlights the need to cultivate HA-HOB due to the huge gap in current genomic databases.}, }
@article {pmid28621836, year = {2017}, author = {Qu, W and Yuan, X and Zhao, J and Zhang, Y and Hu, J and Wang, J and Li, J}, title = {Dietary advanced glycation end products modify gut microbial composition and partially increase colon permeability in rats.}, journal = {Molecular nutrition &amp; food research}, volume = {61}, number = {10}, pages = {}, doi = {10.1002/mnfr.201700118}, pmid = {28621836}, issn = {1613-4133}, mesh = {Ammonia/metabolism ; Animals ; Bacteroidetes/drug effects/isolation &amp; purification ; Colon/*drug effects/metabolism/microbiology ; Cyanobacteria/drug effects/isolation &amp; purification ; DNA, Bacterial/genetics ; *Diet ; Fatty Acids, Volatile/metabolism ; Fermentation ; Firmicutes/drug effects/isolation &amp; purification ; Gastrointestinal Microbiome/*drug effects ; Glycation End Products, Advanced/*pharmacology ; Male ; Occludin/genetics/metabolism ; Permeability ; Proteobacteria/drug effects/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; Sequence Analysis, DNA ; Verrucomicrobia/drug effects/isolation &amp; purification ; Zonula Occludens-1 Protein/genetics/metabolism ; }, abstract = {SCOPE: The adverse impacts of dietary advanced glycation end products (AGEs) on health are currently of interest. These compounds are inevitably formed during thermal food processing and make foods less digestible because of protein cross-linking. This study examined not only whether dietary AGEs alter cecal microbiota and their metabolites but also their effects on colon permeability.<br><br>METHODS AND RESULTS: Sprague-Dawley rats were exposed to a high-AGEs diet (AGEs content was increased by heating food at 125&#xb0;C/3&#xa0;h) for 6, 12, or 18 weeks. Cecal microbiota was analyzed by 16S rDNA gene sequencing. Colon permeability was assessed through histopathology, immunohistochemistry and endotoxin testing. Microbial metabolites (e.g. ammonia and short-chain fatty acids (SCFAs)) were also measured. AGEs treatment reduced the diversity and richness of the microbiota, especially saccharolytic bacteria such as Ruminococcaceae and Alloprevotella, which can produce SCFAs, whereas some putatively harmful bacteria (Desulfovibrio and Bacteroides) were increased. Protein fermentation was enhanced, supported by elevated ammonia and branched-chain fatty acid levels (p&#xa0;<&#xa0;0.05). Additionally, the colonocytes structure changed and the expression of tight junction proteins in colon were decreased.<br><br>CONCLUSION: Dietary AGEs detrimentally modulate gut microbial ecology and may partially increase colon permeability, which can adversely impact host health.}, }
@article {pmid28620785, year = {2017}, author = {Liang, J and Bai, Y and Qu, J}, title = {Microbial Interspecies Interactions Affect Arsenic Fate in the Presence of Mn[II].}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {788-794}, pmid = {28620785}, issn = {1432-184X}, mesh = {Adsorption ; Arsenic/*chemistry ; Arthrobacter/genetics/*metabolism ; Manganese/*chemistry ; Oxidation-Reduction ; Sphingomonadaceae/genetics/*metabolism ; Water Pollutants, Chemical/*chemistry ; }, abstract = {Biotransformation of arsenic (As) plays an important role in its environmental fate. However, the impact of direct microbial interspecies interactions on valence state and migration of As is rarely reported and cognized. Here, by co-cultivating two aerobic As[V]-reducing bacteria (Arthrobacter sp. QXT-31 and Sphingopyxis sp. QXT-31) in a culture medium containing initial As[V] (10 μM) and bivalent manganese (Mn[II], 175 μM), we demonstrated how the interactions between strains affect valence state and partition of As. The results showed that both the strains first reduced As[V] to As[III] via a detoxification mechanism during aerobic growth, with participation of As[V]-reducing gene arsC; the expression of a Mn[II]-oxidizing gene of Arthrobacter sp. QXT-31 was then triggered in the presence of Sphingopyxis sp. QXT-31, and emerging Mn[II]-oxidizing activity oxidized 90% of Mn[II] to Mn oxides; the formed Mn oxides oxidized As[III] to As[V] and adsorbed As[V]; Mn[II]-oxidizing activity decreased significantly in the later stage, resulting to desorption of As[V] from Mn oxides and subsequent bioreduction in aqueous phase. Considering the universality of the two bacterial genera and the interspecies interactions, our study hints at the pervasive impact of direct microbial interspecies interactions on the environmental fate of As in an aquatic ecosystem containing Mn.}, }
@article {pmid28620784, year = {2017}, author = {Eom, HJ and Park, W}, title = {Inhibitory Effect of Taurine on Biofilm Formation During Alkane Degradation in Acinetobacter oleivorans DR1.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {821-831}, pmid = {28620784}, issn = {1432-184X}, mesh = {Acinetobacter/*drug effects/*physiology ; Alkanes/*metabolism ; Antioxidants/*pharmacology ; Biodegradation, Environmental ; Biofilms/*drug effects ; Hydrophobic and Hydrophilic Interactions ; Quorum Sensing ; Taurine/*pharmacology ; }, abstract = {Taurine, 2-aminoethanesulfonate, is known to function as an antioxidant or membrane stabilizer in eukaryotic cells, but its role in bacteria has been poorly characterized. Biofilm formation of Acinetobacter oleivorans DR1 was significantly reduced by taurine only during alkane degradation, suggesting that taurine affects alkane-induced cell surface. Structurally similar compounds harboring an amine group such as hypotaurine or ethylenediamine have a similar effect, which was not observed with sulfonate-containing chemicals such as ethanesulfonic acid, hexanesulfonic acid. Our biochemical assays and physiological tests demonstrate that taurine reduced cell surface hydrophobicity, which resulted in interruption of the interactions between cells and oily substrate surfaces, such that cells utilized alkanes less effectively. Interestingly, taurine-mediated reduction of quorum sensing (QS) signal production and QS-control sapA gene expression indicated that membrane permeability of quorum signals was also interfered by taurine. Composition and biomass of extracellular polymeric saccharides were changed in taurine-amended conditions. Taken together, our data provide evidence that amine-containing taurine can inhibit biofilm formation of DR1 cells during alkane degradation by (i) changing cell surface charge and (ii) reducing membrane hydrophobicity and QS sensing.}, }
@article {pmid28618173, year = {2017}, author = {De Paepe, K and Kerckhof, FM and Verspreet, J and Courtin, CM and Van de Wiele, T}, title = {Inter-individual differences determine the outcome of wheat bran colonization by the human gut microbiome.}, journal = {Environmental microbiology}, volume = {19}, number = {8}, pages = {3251-3267}, doi = {10.1111/1462-2920.13819}, pmid = {28618173}, issn = {1462-2920}, mesh = {Bacteroides/growth &amp; development/*metabolism ; Bifidobacterium/growth &amp; development/*metabolism ; Butyrates/metabolism ; Clostridium/growth &amp; development/*metabolism ; Diet ; Dietary Fiber/*metabolism/microbiology ; Feces/microbiology ; Fermentation ; Gastrointestinal Microbiome/*physiology ; Humans ; Inulin/*metabolism ; Prevotella/growth &amp; development/*metabolism ; Propionates/metabolism ; }, abstract = {Gut microbiota research reveals a vital role for the luminal and mucosal gut microbiota in human health. Fewer studies, however, have characterized the microbiome associated with undigested, insoluble dietary particles in the gut. These particles can act as a food source for bacteria and offer a physical platform to which they can attach. In this study, the microbiome colonizing wheat bran particles was analyzed. In a batch experiment, wheat bran particles were separately incubated with the faecal microbiota derived from 10 donors and washed after 48 h to remove loosely attached bacteria. The response of the luminal community to wheat bran and inulin, acting as a well-characterized control, was largely donor-dependent, both functionally, and with respect to the microbiome composition. Depending on the donor, wheat bran and inulin fermentation yielded proportionally higher propionate or butyrate production. Clostridium cluster XIVa and, depending on the donor, Prevotella, Roseburia, Megamonas, Bifidobacterium and Bacteroides species were enriched on the wheat bran particles. These genera include species with the documented ability to serve as primary degraders of wheat bran components and other species depending on cross-feeding to obtain their energy. Both functional groups were present in all donors, despite the large inter-individual differences.}, }
@article {pmid28614760, year = {2017}, author = {Nasri, E and Subirats, J and Sànchez-Melsió, A and Mansour, HB and Borrego, CM and Balcázar, JL}, title = {Abundance of carbapenemase genes (blaKPC, blaNDM and blaOXA-48) in wastewater effluents from Tunisian hospitals.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {229}, number = {}, pages = {371-374}, doi = {10.1016/j.envpol.2017.05.095}, pmid = {28614760}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents ; Bacterial Proteins/*genetics ; Carbapenems ; Drug Resistance, Bacterial/*genetics ; Enterobacteriaceae ; Hospitals ; Humans ; Tunisia ; Wastewater/*chemistry/microbiology ; beta-Lactamases/*genetics ; }, abstract = {Carbapenems are β-lactam antibiotics with a broad spectrum of activity and are usually considered the last resort for the treatment of severe infections caused by multidrug-resistant pathogens. The clinically most significant carbapenemases are KPC, NDM, and OXA-48-like enzymes, whose genes have been increasingly reported worldwide in members of the family Enterobacteriaceae. In this study, we quantified the abundance of these genes in wastewater effluents from different Tunisian hospitals. The blaNDM and blaOXA-48-like genes were detected at similar concentrations in all hospital wastewater effluents. In contrast, the blaKPC gene was detected at lower concentration than other genes and it was only detected in three of the seven effluents analyzed. To the best of our knowledge, this study quantified for the first time the abundance of blaKPC, blaNDM, and blaOXA-48-like genes in wastewater effluents from Tunisian hospitals, highlighting the widespread distribution of these carbapenemase genes.}, }
@article {pmid28614743, year = {2017}, author = {Liu, M and Wang, S and Nobu, MK and Bocher, BTW and Kaley, SA and Liu, WT}, title = {Impacts of biostimulation and bioaugmentation on the performance and microbial ecology in methanogenic reactors treating purified terephthalic acid wastewater.}, journal = {Water research}, volume = {122}, number = {}, pages = {308-316}, doi = {10.1016/j.watres.2017.06.008}, pmid = {28614743}, issn = {1879-2448}, mesh = {Anaerobiosis ; Bioreactors ; Phthalic Acids/*chemistry ; RNA, Ribosomal, 16S ; Sewage ; *Waste Disposal, Fluid ; Wastewater ; Water Microbiology ; }, abstract = {Up-flow anaerobic sludge blanket (UASB) processes treating purified terephthalic acid (PTA) wastewater often face challenges associated with biomass loss. As excessive biomass loss could lead to deterioration of PTA removal, biostimulation and bioaugmentation were often practiced without understanding the microbial impact in UASB. Three laboratory-scale UASB reactors were operated with synthetic PTA wastewater as the feed, with two added with co-substrate (glucose or molasses) on Day 170 for 90 days, and one with external granules on Day 118. Throughout the operation, treatment performance was measured together with the analysis of microbial communities of biomass samples using 16S rRNA-based gene Illumina sequencing. Glucose amendment destabilized both terephthalic acid and para-toluic acid removal, while molasses amendment improved para-toluic acid removal. Both substrate addition generally led to decreases in the abundances of syntrophs and methanogens and increases in carbohydrate-fermenting bacteria in the granular sludge. Regarding bioaugmentation, paper mill granule addition led to a temporary crash of terephthalic acid removal for 42 days, and deterioration of para-toluic acid removal throughout the operation. Syntrophs and methanogens were observed to colonize on the paper mill granules after three months, meanwhile growth of methanogens were stimulated on the PTA granules added initially. Overall, proper level of molasses amendment and external granule inoculation could be promising strategies to make up for biomass loss during the operation of PTA-degrading UASB.}, }
@article {pmid28611749, year = {2017}, author = {Troussellier, M and Escalas, A and Bouvier, T and Mouillot, D}, title = {Sustaining Rare Marine Microorganisms: Macroorganisms As Repositories and Dispersal Agents of Microbial Diversity.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {947}, pmid = {28611749}, issn = {1664-302X}, abstract = {Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. Surprisingly, few studies have considered the effect of macroorganism-microbe interactions on the ecology and distribution dynamics of rare microbial taxa. In this review, we synthesize several lines of evidence that these relationships cannot be neglected any longer. First, we provide empirical support that the microbiota of macroorganisms represents a significant part of marine bacterial biodiversity and that host-microbe interactions benefit to certain microbial populations which are part of the rare biosphere (i.e., opportunistic copiotrophic organisms). Second, we reveal the major role that macroorganisms may have on the dispersal and the geographic distribution of microbes. Third, we introduce an innovative and integrated view of the interactions between microbes and macroorganisms, namely sustaining the rares, which suggests that macroorganisms favor the maintenance of marine microbial diversity and are involved in the regulation of its richness and dynamics. Finally, we show how this hypothesis complements existing theories in microbial ecology and offers new perspectives about the importance of macroorganisms for the microbial biosphere, particularly the rare members.}, }
@article {pmid28611430, year = {2017}, author = {Tsao, HF and Scheikl, U and Volland, JM and Köhsler, M and Bright, M and Walochnik, J and Horn, M}, title = {'Candidatus Cochliophilus cryoturris' (Coxiellaceae), a symbiont of the testate amoeba Cochliopodium minus.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3394}, pmid = {28611430}, issn = {2045-2322}, support = {I 1628/FWF_/Austrian Science Fund FWF/Austria ; P 24565/FWF_/Austrian Science Fund FWF/Austria ; TRP 209/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Amebiasis/*microbiology ; Amoebida/*classification/isolation &amp; purification ; Coxiellaceae/*physiology ; *Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S ; *Symbiosis ; }, abstract = {Free-living amoebae are well known for their role in controlling microbial community composition through grazing, but some groups, namely Acanthamoeba species, also frequently serve as hosts for bacterial symbionts. Here we report the first identification of a bacterial symbiont in the testate amoeba Cochliopodium. The amoeba was isolated from a cooling tower water sample and identified as C. minus. Fluorescence in situ hybridization and transmission electron microscopy revealed intracellular symbionts located in vacuoles. 16S rRNA-based phylogenetic analysis identified the endosymbiont as member of a monophyletic group within the family Coxiellaceae (Gammaprotebacteria; Legionellales), only moderately related to known amoeba symbionts. We propose to tentatively classify these bacteria as 'Candidatus Cochliophilus cryoturris'. Our findings add both, a novel group of amoeba and a novel group of symbionts, to the growing list of bacteria-amoeba relationships.}, }
@article {pmid28611409, year = {2017}, author = {Harter, J and El-Hadidi, M and Huson, DH and Kappler, A and Behrens, S}, title = {Soil biochar amendment affects the diversity of nosZ transcripts: Implications for N2O formation.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3338}, pmid = {28611409}, issn = {2045-2322}, abstract = {Microbial nitrogen transformation processes such as denitrification represent major sources of the potent greenhouse gas nitrous oxide (N2O). Soil biochar amendment has been shown to significantly decrease N2O emissions in various soils. However, the effect of biochar on the structure and function of microbial communities that actively perform nitrogen redox transformations has not been studied in detail yet. To analyse the community composition of actively denitrifying and N2O-reducing microbial communities, we collected RNA samples at different time points from a soil microcosm experiment conducted under denitrifying conditions and performed Illumina amplicon sequencing targeting nirK, typical nosZ and atypical nosZ mRNA transcripts. Within 10 days, biochar significantly increased the diversity of nirK and typical nosZ transcripts and resulted in taxonomic shifts among the typical nosZ-expressing microbial community. Furthermore, biochar addition led to a significant increase in transcript production among microbial species that are specialized on direct N2O reduction from the environment. Our results point towards a potential coupling of biochar-induced N2O emission reduction and an increase in microbial N2O reduction activity among specific groups of typical and atypical N2O reducers. However, experiments with other soils and biochars will be required to verify the transferability of these findings to other soil-biochar systems.}, }
@article {pmid28608318, year = {2017}, author = {López-Lozano, NE and Pereira E Silva, MC and Poly, F and Guillaumaud, N and van Elsas, JD and Salles, JF}, title = {Denitrifying bacterial communities display different temporal fluctuation patterns across Dutch agricultural soils.}, journal = {Antonie van Leeuwenhoek}, volume = {110}, number = {11}, pages = {1453-1465}, doi = {10.1007/s10482-017-0898-3}, pmid = {28608318}, issn = {1572-9699}, mesh = {Agriculture ; Bacteria/*enzymology ; Denitrification/*physiology ; Genes, Bacterial/genetics ; Netherlands ; Nitrite Reductases/genetics/*metabolism ; Real-Time Polymerase Chain Reaction ; Regression Analysis ; Soil/*chemistry ; *Soil Microbiology ; Spatio-Temporal Analysis ; }, abstract = {Considering the great agronomic and environmental importance of denitrification, the aim of the present study was to study the temporal and spatial factors controlling the abundance and activity of denitrifying bacterial communities in a range of eight agricultural soils over 2 years. Abundance was quantified by qPCR of the nirS, nirK and nosZ genes, and the potential denitrification enzyme activity (DEA) was estimated. Our data showed a significant temporal variation considerably high for the abundance of nirK-harboring communities, followed by nosZ and nirS communities. Regarding soil parameters, the abundances of nosZ, nirS and nirK were mostly influenced by organic material, pH, and slightly by NO3[-], respectively. Soil texture was the most important factor regulating DEA, which could not be explained by the abundance of denitrifiers. Analyses of general patterns across lands to understand the soil functioning is not an easy task because the multiple factors influencing processes such as denitrification can skew the data. Careful analysis of atypical sites are necessary to classify the soils according to trait similarity and in this way reach a better predictability of the denitrifiers dynamics.}, }
@article {pmid28607347, year = {2017}, author = {Tang, FHM and Maggi, F}, title = {Living microorganisms change the information (Shannon) content of a geophysical system.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3320}, pmid = {28607347}, issn = {2045-2322}, mesh = {Bacteria/growth &amp; development/*metabolism ; Biomass ; Colony Count, Microbial ; *Ecosystem ; *Entropy ; }, abstract = {The detection of microbial colonization in geophysical systems is becoming of interest in various disciplines of Earth and planetary sciences, including microbial ecology, biogeochemistry, geomicrobiology, and astrobiology. Microorganisms are often observed to colonize mineral surfaces, modify the reactivity of minerals either through the attachment of their own biomass or the glueing of mineral particles with their mucilaginous metabolites, and alter both the physical and chemical components of a geophysical system. Here, we hypothesise that microorganisms engineer their habitat, causing a substantial change to the information content embedded in geophysical measures (e.g., particle size and space-filling capacity). After proving this hypothesis, we introduce and test a systematic method that exploits this change in information content to detect microbial colonization in geophysical systems. Effectiveness and robustness of this method are tested using a mineral sediment suspension as a model geophysical system; tests are carried out against 105 experiments conducted with different suspension types (i.e., pure mineral and microbially-colonized) subject to different abiotic conditions, including various nutrient and mineral concentrations, and different background entropy production rates. Results reveal that this method can systematically detect microbial colonization with less than 10% error in geophysical systems with low-entropy background production rate.}, }
@article {pmid28605506, year = {2017}, author = {Benítez-Páez, A and Sanz, Y}, title = {Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer.}, journal = {GigaScience}, volume = {6}, number = {7}, pages = {1-12}, pmid = {28605506}, issn = {2047-217X}, mesh = {Genetic Loci ; *Genome, Bacterial ; *Microbiota ; *Nanopores ; Operon ; Sequence Analysis, DNA/*instrumentation/methods ; }, abstract = {The miniaturized and portable DNA sequencer MinION™ has demonstrated great potential in different analyses such as genome-wide sequencing, pathogen outbreak detection and surveillance, human genome variability, and microbial diversity. In this study, we tested the ability of the MinION™ platform to perform long amplicon sequencing in order to design new approaches to study microbial diversity using a multi-locus approach. After compiling a robust database by parsing and extracting the rrn bacterial region from more than 67000 complete or draft bacterial genomes, we demonstrated that the data obtained during sequencing of the long amplicon in the MinION™ device using R9 and R9.4 chemistries were sufficient to study 2 mock microbial communities in a multiplex manner and to almost completely reconstruct the microbial diversity contained in the HM782D and D6305 mock communities. Although nanopore-based sequencing produces reads with lower per-base accuracy compared with other platforms, we presented a novel approach consisting of multi-locus and long amplicon sequencing using the MinION™ MkIb DNA sequencer and R9 and R9.4 chemistries that help to overcome the main disadvantage of this portable sequencing platform. Furthermore, the nanopore sequencing library, constructed with the last releases of pore chemistry (R9.4) and sequencing kit (SQK-LSK108), permitted the retrieval of the higher level of 1D read accuracy sufficient to characterize the microbial species present in each mock community analysed. Improvements in nanopore chemistry, such as minimizing base-calling errors and new library protocols able to produce rapid 1D libraries, will provide more reliable information in the near future. Such data will be useful for more comprehensive and faster specific detection of microbial species and strains in complex ecosystems.}, }
@article {pmid28602521, year = {2017}, author = {Gresse, R and Chaucheyras-Durand, F and Fleury, MA and Van de Wiele, T and Forano, E and Blanquet-Diot, S}, title = {Gut Microbiota Dysbiosis in Postweaning Piglets: Understanding the Keys to Health.}, journal = {Trends in microbiology}, volume = {25}, number = {10}, pages = {851-873}, doi = {10.1016/j.tim.2017.05.004}, pmid = {28602521}, issn = {1878-4380}, mesh = {Animals ; Diet/methods ; Dysbiosis/*microbiology/*physiopathology ; Gastrointestinal Microbiome/*physiology ; Intestines/microbiology/physiology ; Microbiota/physiology ; Probiotics/administration &amp; dosage ; Swine/*microbiology/*physiology ; Weaning ; }, abstract = {Weaning is a critical event in the pig's life cycle, frequently associated with severe enteric infections and overuse of antibiotics; this raises serious economic and public health concerns. In this review, we explain why gut microbiota dysbiosis, induced by abrupt changes in the diet and environment of piglets, emerges as a leading cause of post-weaning diarrhea, even if the exact underlying mechanisms remain unclear. Then, we focus on nonantimicrobial alternatives, such as zinc oxide, essential oils, and prebiotics or probiotics, which are currently evaluated to restore intestinal balance and allow a better management of the crucial weaning transition. Finally, we discuss how in vitro models of the piglet gut could be advantageously used as a complement to ex vivo and in vivo studies for the development and testing of new feed additives.}, }
@article {pmid28601973, year = {2017}, author = {Dwidar, M and Im, H and Seo, JK and Mitchell, RJ}, title = {Attack-Phase Bdellovibrio bacteriovorus Responses to Extracellular Nutrients Are Analogous to Those Seen During Late Intraperiplasmic Growth.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {937-946}, pmid = {28601973}, issn = {1432-184X}, mesh = {Bacterial Proteins/*genetics/metabolism ; Bdellovibrio bacteriovorus/*genetics/metabolism ; Gene Expression Profiling ; Peptide Hydrolases/*genetics/metabolism ; }, abstract = {Bdellovibrio bacteriovorus is a predatory bacterium which lives by invading the periplasm of gram-negative bacteria and consuming them from within. This predator was thought to be dependent upon prey for nutrients since it lacks genes encoding for critical enzymes involved in amino acid biosynthesis. This study, however, found that planktonic attack-phase predators are not just dependent upon prey for nutrients, but rather, they respond to nutrients in the surrounding medium and, subsequently, synthesize and secrete proteases in a nutrient-dependent manner. The major secreted proteases were identified through mass spectrometry analyses. Subsequent RT-qPCR analyses found that the nutrient-induced proteases are similar to those expressed within the prey periplasm during the late intraperiplasmic growth phase. Furthermore, RNA sequencing found that incubating the planktonic attack-phase cells in a nutritious environment for a short period of time (4 h) changes its gene expression pattern to a status that is akin to the late intraperiplasmic phase, with more than 94% of the genes previously identified as being late intraperiplasmic-specific also being induced by nutrient broth in this study. This strong correlation between the gene expression patterns hints that the availability of hydrolyzed prey cell components to the predator is likely the stimulus controlling the expression of late intraperiplasmic B. bacteriovorus genes during predation.}, }
@article {pmid28600590, year = {2017}, author = {Schneider, S and Tajrin, T and Lundström, JO and Hendriksen, NB and Melin, P and Sundh, I}, title = {Do Multi-year Applications of Bacillus thuringiensis subsp. israelensis for Control of Mosquito Larvae Affect the Abundance of B. cereus Group Populations in Riparian Wetland Soils?.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {901-909}, pmid = {28600590}, issn = {1432-184X}, mesh = {Animals ; Bacillus cereus/*physiology ; Bacillus thuringiensis/*physiology ; Culicidae/growth &amp; development ; Larva ; *Mosquito Control ; *Pest Control, Biological ; Seasons ; *Soil Microbiology ; Sweden ; Wetlands ; }, abstract = {Bacillus thuringiensis subsp. israelensis (Bti) is a soil-borne bacterium affiliated to the Bacillus cereus group (Bcg) and has been used in biocontrol products against nematoceran larvae for several decades. However, knowledge is limited on whether long-term Bti application can affect the structure of indigenous communities of Bcg and the overall abundance of Bti. Using species- and group-specific quantitative PCR assays, we measured the Bcg- and Bti-abundances in riparian wetlands in the River Dalälven floodplains of central Sweden. On five occasions during one vegetative season, soil samples were collected in alder swamps and wet meadows which had been treated with Bti for mosquito larvae control during the preceding 11 years, as well as in untreated control sites and well-drained forests in the same area. The average abundance of Bcg in alder swamps was around three times higher than in wet meadows. Across all sites and habitats, the Bti treatments had no effect on the Bcg-abundance, whereas the Bti-abundance was significantly higher in the treated than in the control sites. However, for individual sampling sites, abundances of Bti and Bcg were not correlated with the number of Bti applications, indicating that added Bti possibly influenced the total population of Bti in the short term but had only a limited effect in the longer term. The findings of this study increase the understanding of the ecology of Bti applications for mosquito control, which can facilitate environmental risk assessment in connection with approval of microbiological control agents.}, }
@article {pmid28600313, year = {2017}, author = {Jones, DS and Lapakko, KA and Wenz, ZJ and Olson, MC and Roepke, EW and Sadowsky, MJ and Novak, PJ and Bailey, JV}, title = {Novel Microbial Assemblages Dominate Weathered Sulfide-Bearing Rock from Copper-Nickel Deposits in the Duluth Complex, Minnesota, USA.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {16}, pages = {}, pmid = {28600313}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Copper/*metabolism ; Geologic Sediments/chemistry/*microbiology ; Industrial Waste/analysis ; Iron/metabolism ; Mining ; Minnesota ; Nickel/*metabolism ; Phylogeny ; Sulfides/*metabolism ; }, abstract = {The Duluth Complex in northeastern Minnesota hosts economically significant deposits of copper, nickel, and platinum group elements (PGEs). The primary sulfide mineralogy of these deposits includes the minerals pyrrhotite, chalcopyrite, pentlandite, and cubanite, and weathering experiments show that most sulfide-bearing rock from the Duluth Complex generates moderately acidic leachate (pH 4 to 6). Microorganisms are important catalysts for metal sulfide oxidation and could influence the quality of water from mines in the Duluth Complex. Nevertheless, compared with that of extremely acidic environments, much less is known about the microbial ecology of moderately acidic sulfide-bearing mine waste, and so existing information may have little relevance to those microorganisms catalyzing oxidation reactions in the Duluth Complex. Here, we characterized the microbial communities in decade-long weathering experiments (kinetic tests) conducted on crushed rock and tailings from the Duluth Complex. Analyses of 16S rRNA genes and transcripts showed that differences among microbial communities correspond to pH, rock type, and experimental treatment. Moreover, microbial communities from the weathered Duluth Complex rock were dominated by taxa that are not typically associated with acidic mine waste. The most abundant operational taxonomic units (OTUs) were from the genera Meiothermus and Sulfuriferula, as well as from diverse clades of uncultivated Chloroflexi, Acidobacteria, and Betaproteobacteria Specific taxa, including putative sulfur-oxidizing Sulfuriferula spp., appeared to be primarily associated with Duluth Complex rock, but not pyrite-bearing rocks subjected to the same experimental treatment. We discuss the implications of these results for the microbial ecology of moderately acidic mine waste with low sulfide content, as well as for kinetic testing of mine waste.IMPORTANCE Economic sulfide mineral deposits in the Duluth Complex may represent the largest undeveloped source of copper and nickel on Earth. Microorganisms are important catalysts for sulfide mineral oxidation, and research on extreme acidophiles has improved our ability to manage and remediate mine wastes. We found that the microbial assemblages associated with weathered rock from the Duluth Complex are dominated by organisms not widely associated with mine waste or mining-impacted environments, and we describe geochemical and experimental influences on community composition. This report will be a useful foundation for understanding the microbial biogeochemistry of moderately acidic mine waste from these and similar deposits.}, }
@article {pmid28598217, year = {2018}, author = {Saum, L and Jiménez, MB and Crowley, D}, title = {Influence of biochar and compost on phytoremediation of oil-contaminated soil.}, journal = {International journal of phytoremediation}, volume = {20}, number = {1}, pages = {54-60}, doi = {10.1080/15226514.2017.1337063}, pmid = {28598217}, issn = {1549-7879}, mesh = {Bacteria ; *Biodegradation, Environmental ; *Charcoal ; *Composting ; Petroleum ; Soil Microbiology ; *Soil Pollutants ; }, abstract = {The use of pyrolyzed carbon, biochar, as a soil amendment is of potential interest for improving phytoremediation of soil that has been contaminated by petroleum hydrocarbons. To examine this question, the research reported here compared the effects of biochar, plants (mesquite tree seedlings), compost and combinations of these treatments on the rate of biodegradation of oil in a contaminated soil and the population size of oil-degrading bacteria. The presence of mesquite plants significantly enhanced oil degradation in all treatments except when biochar was used as the sole amendment without compost. The greatest extent of oil degradation was achieved in soil planted with mesquite and amended with compost (44% of the light hydrocarbon fraction). Most probable number assays showed that biochar generally reduced the population size of the oil-degrading community. The results of this study suggest that biochar addition to petroleum-contaminated soils does not improve the rate of bioremediation. In contrast, the use of plants and compost additions to soil are confirmed as important bioremediation technologies.}, }
@article {pmid28597955, year = {2017}, author = {Vannette, RL and Fukami, T}, title = {Dispersal enhances beta diversity in nectar microbes.}, journal = {Ecology letters}, volume = {20}, number = {7}, pages = {901-910}, doi = {10.1111/ele.12787}, pmid = {28597955}, issn = {1461-0248}, mesh = {Animals ; Bacteria ; *Flowers ; *Plant Nectar ; Plants ; Yeasts ; }, abstract = {Dispersal is considered a key driver of beta diversity, the variation in species composition among local communities, but empirical tests remain limited. We manipulated dispersal of nectar-inhabiting bacteria and yeasts via flower-visiting animals to examine how dispersal influenced microbial beta diversity among flowers. Contrary to the prevailing view that dispersal lowers beta diversity, we found beta diversity was highest when dispersal was least limited. Our analysis suggested that this unexpected pattern might have resulted from stronger priority effects under increased dispersal. Dispersal is highly stochastic, generating variability in species arrival history and consequently the potential for community divergence via priority effects, in these and likely many other microbial, plant, and animal communities. Yet most previous experiments eliminated this possibility. We suggest that the positive effects of dispersal on beta diversity, like the one we report here, may have been greatly underappreciated.}, }
@article {pmid28593195, year = {2017}, author = {Denef, VJ and Carrick, HJ and Cavaletto, J and Chiang, E and Johengen, TH and Vanderploeg, HA}, title = {Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder.}, journal = {mSphere}, volume = {2}, number = {3}, pages = {}, pmid = {28593195}, issn = {2379-5042}, abstract = {One approach to improve forecasts of how global change will affect ecosystem processes is to better understand how anthropogenic disturbances alter bacterial assemblages that drive biogeochemical cycles. Species invasions are important contributors to global change, but their impacts on bacterial community ecology are rarely investigated. Here, we studied direct impacts of invasive dreissenid mussels (IDMs), one of many invasive filter feeders, on freshwater lake bacterioplankton. We demonstrated that direct effects of IDMs reduced bacterial abundance and altered assemblage composition by preferentially removing larger and particle-associated bacteria. While this increased the relative abundances of many free-living bacterial taxa, some were susceptible to filter feeding, in line with efficient removal of phytoplankton cells of <2 μm. This selective removal of particle-associated and larger bacteria by IDMs altered inferred bacterial functional group representation, defined by carbon and energy source utilization. Specifically, we inferred an increased relative abundance of chemoorganoheterotrophs predicted to be capable of rhodopsin-dependent energy generation. In contrast to the few previous studies that have focused on the longer-term combined direct and indirect effects of IDMs on bacterioplankton, our study showed that IDMs act directly as a biological disturbance to which freshwater bacterial assemblages are sensitive. The negative impacts on particle-associated bacteria, which have been shown to be more active than free-living bacteria, and the inferred shifts in functional group representation raise the possibility that IDMs may directly alter bacterially mediated ecosystem functions. IMPORTANCE Freshwater bacteria play fundamental roles in global elemental cycling and are an intrinsic part of local food webs. Human activities are altering freshwater environments, and much has been learned regarding the sensitivity of bacterial assemblages to a variety of these disturbances. Yet, relatively few studies have focused on how species invasion, which is one of the most important aspects of anthropogenic global change, affects freshwater bacterial assemblages. This study focuses on the impact of invasive dreissenid mussels (IDMs), a globally distributed group of invasive species with large impacts on freshwater phyto- and zooplankton assemblages. We show that IDMs have direct effects on lake bacterioplankton abundance, taxonomic composition, and inferred bacterial functional group representation.}, }
@article {pmid28592860, year = {2017}, author = {Yang, P and Zhang, M and van Elsas, JD}, title = {Role of flagella and type four pili in the co-migration of Burkholderia terrae BS001 with fungal hyphae through soil.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2997}, pmid = {28592860}, issn = {2045-2322}, mesh = {Agaricales/*growth &amp; development ; *Bacterial Adhesion ; Burkholderia/*cytology/*physiology ; Fimbriae, Bacterial/metabolism ; Flagella/metabolism ; Hyphae/growth &amp; development ; Locomotion ; Microbial Interactions ; Microscopy, Electron ; *Soil Microbiology ; Trichoderma/*growth &amp; development ; }, abstract = {Burkholderia terrae BS001 has previously been found to be able to disperse along with growing fungal hyphae in soil, with the type-3 secretion system having a supportive role in this movement. In this study, we focus on the role of two motility- and adherence-associated appendages, i.e. type-4 pili (T4P) and flagella. Electron microcopy and motility testing revealed that strain BS001 produces polar flagella and can swim on semi-solid R2A agar. Flagellum- and T4P-negative mutants were then constructed to examine the ecological roles of the respective systems. Both in liquid media and on swimming agar, the mutant strains showed similar fitness to the wild-type strain in mixed culture. The flagellar mutant had completely lost its flagella, as well as its swimming capacity. It also lost its co-migration ability with two soil-exploring fungi, Lyophyllum sp. strain Karsten and Trichoderma asperellum 302, in soil microcosms. In contrast, the T4P mutant showed reduced surface twitching motility, whereas its co-migration ability in competition with the wild-type strain was slightly reduced. We conclude that the co-migration of strain BS001 with fungal hyphae through soil is dependent on the presence of functional flagella conferring swimming motility, with the T4P system having a minor effect.}, }
@article {pmid28589226, year = {2017}, author = {Ausec, L and Berini, F and Casciello, C and Cretoiu, MS and van Elsas, JD and Marinelli, F and Mandic-Mulec, I}, title = {The first acidobacterial laccase-like multicopper oxidase revealed by metagenomics shows high salt and thermo-tolerance.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {15}, pages = {6261-6276}, doi = {10.1007/s00253-017-8345-y}, pmid = {28589226}, issn = {1432-0614}, mesh = {Acidobacteria/*enzymology/*genetics/metabolism ; Bacterial Proteins/genetics ; Cloning, Molecular ; Escherichia coli/genetics ; Gene Expression ; Genomic Library ; Hydrogen-Ion Concentration ; Laccase/*genetics/*metabolism ; Metagenome ; Metagenomics ; Oxidoreductases/*genetics/isolation &amp; purification/*metabolism ; Salt Tolerance ; *Soil Microbiology ; Substrate Specificity ; Temperature ; }, abstract = {Metagenomics is a powerful tool that allows identifying enzymes with novel properties from the unculturable component of microbiomes. However, thus far only a limited number of laccase or laccase -like enzymes identified through metagenomics has been subsequently biochemically characterized. This work describes the successful bio-mining of bacterial laccase-like enzymes in an acidic bog soil metagenome and the characterization of the first acidobacterial laccase-like multicopper oxidase (LMCO). LMCOs have hitherto been mostly studied in fungi and some have already found applications in diverse industries. However, improved LMCOs are in high demand. Using molecular screening of a small metagenomic library (13,500 clones), a gene encoding a three-domain LMCO (LacM) was detected, showing the highest similarity to putative copper oxidases of Candidatus Solibacter (Acidobacteria). The encoded protein was expressed in Escherichia coli, purified by affinity chromatography and biochemically characterized. LacM oxidized a variety of phenolic substrates, including two standard laccase substrates (2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS), k cat/k M = 8.45 s[-1] mM[-1]; 2,6-dimethoxyphenol (2,6-DMP), k cat/k M = 6.42 s[-1] mM[-1]), next to L-3,4-dihydroxyphenylalanine (L-DOPA), vanillic acid, syringaldazine, pyrogallol, and pyrocatechol. With respect to the latter two lignin building blocks, LacM showed the highest catalytic activity (k cat/k M = 173.6 s[-1] mM[-1]) for pyrogallol, with ca. 20% activity preserved even at pH 8.0. The enzyme was thermostable and heat-activated in the interval 40-60 °C, with an optimal activity on ABTS at 50 °C. It was rather stable at high salt concentration (e.g., 34% activity preserved at 500 mM NaCl) and in the presence of organic solvents. Remarkably, LacM decolored azo and triphenylmethane dyes, also in the absence of redox mediators.}, }
@article {pmid28589212, year = {2017}, author = {Fernandez-Leborans, G and Román, S and Martin, D}, title = {Erratum to: A New Deep-Sea Suctorian-Nematode Epibiosis (Loricophrya-Tricoma) from the Blanes Submarine Canyon (NW Mediterranean).}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {1009}, doi = {10.1007/s00248-017-1005-z}, pmid = {28589212}, issn = {1432-184X}, }
@article {pmid28588643, year = {2017}, author = {Maruthamuthu, M and van Elsas, JD}, title = {Molecular cloning, expression, and characterization of four novel thermo-alkaliphilic enzymes retrieved from a metagenomic library.}, journal = {Biotechnology for biofuels}, volume = {10}, number = {}, pages = {142}, pmid = {28588643}, issn = {1754-6834}, abstract = {BACKGROUND: Enzyme discovery is a promising approach to aid in the deconstruction of recalcitrant plant biomass in an industrial process. Novel enzymes can be readily discovered by applying metagenomics on whole microbiomes. Our goal was to select, examine, and characterize eight novel glycoside hydrolases that were previously detected in metagenomic libraries, to serve biotechnological applications with high performance.<br><br>RESULTS: Here, eight glycosyl hydrolase family candidate genes were selected from metagenomes of wheat straw-degrading microbial consortia using molecular cloning and subsequent gene expression studies in Escherichia coli. Four of the eight enzymes had significant activities on either pNP-&#x3b2;-d-galactopyranoside, pNP-&#x3b2;-d-xylopyranoside, pNP-&#x3b1;-l-arabinopyranoside or pNP-&#x3b1;-d-glucopyranoside. These proteins, denoted as proteins 1, 2, 5 and 6, were his-tag purified and their nature and activities further characterized using molecular and activity screens with the pNP-labeled substrates. Proteins 1 and 2 showed high homologies with (1) a &#x3b2;-galactosidase (74%) and (2) a &#x3b2;-xylosidase (84%), whereas the remaining two (5 and 6) were homologous with proteins reported as a diguanylate cyclase and an aquaporin, respectively. The &#x3b2;-galactosidase- and &#x3b2;-xylosidase-like proteins 1 and 2 were confirmed as being responsible for previously found thermo-alkaliphilic glycosidase activities of extracts of E. coli carrying the respective source fosmids. Remarkably, the &#x3b2;-xylosidase-like protein 2 showed activities with both pNP-Xyl and pNP-Ara in the temperature range 40-50&#xa0;&#xb0;C and pH range 8.0-10.0. Moreover, proteins 5 and 6 showed thermotolerant &#x3b1;-glucosidase activity at pH 10.0. In silico structure prediction of protein 5 revealed the presence of a potential "GGDEF" catalytic site, encoding &#x3b1;-glucosidase activity, whereas that of protein 6 showed a "GDSL" site, encoding a 'new family' &#x3b1;-glucosidase activity.<br><br>CONCLUSION: Using a rational screening approach, we identified and characterized four thermo-alkaliphilic glycosyl hydrolases that have the potential to serve as constituents of enzyme cocktails that produce sugars from lignocellulosic plant remains.}, }
@article {pmid28588144, year = {2017}, author = {Cremer, J and Arnoldini, M and Hwa, T}, title = {Effect of water flow and chemical environment on microbiota growth and composition in the human colon.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {25}, pages = {6438-6443}, pmid = {28588144}, issn = {1091-6490}, support = {R01 GM095903/GM/NIGMS NIH HHS/United States ; R01 GM109069/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*growth &amp; development ; Bacterial Physiological Phenomena ; Biological Phenomena ; Colon/*microbiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Microbiota/*physiology ; }, abstract = {The human gut harbors a dynamic microbial community whose composition bears great importance for the health of the host. Here, we investigate how colonic physiology impacts bacterial growth, which ultimately dictates microbiota composition. Combining measurements of bacterial physiology with analysis of published data on human physiology into a quantitative, comprehensive modeling framework, we show how water flow in the colon, in concert with other physiological factors, determine the abundances of the major bacterial phyla. Mechanistically, our model shows that local pH values in the lumen, which differentially affect the growth of different bacteria, drive changes in microbiota composition. It identifies key factors influencing the delicate regulation of colonic pH, including epithelial water absorption, nutrient inflow, and luminal buffering capacity, and generates testable predictions on their effects. Our findings show that a predictive and mechanistic understanding of microbial ecology in the gut is possible. Such predictive understanding is needed for the rational design of intervention strategies to actively control the microbiota.}, }
@article {pmid28586691, year = {2017}, author = {Keeling, PJ and Campo, JD}, title = {Marine Protists Are Not Just Big Bacteria.}, journal = {Current biology : CB}, volume = {27}, number = {11}, pages = {R541-R549}, doi = {10.1016/j.cub.2017.03.075}, pmid = {28586691}, issn = {1879-0445}, mesh = {Aquatic Organisms/classification/*physiology ; *Biodiversity ; Biological Evolution ; Eukaryota/*physiology ; Genomics/*methods ; Marine Biology/methods ; Phylogeny ; Seawater/*microbiology ; Transcriptome ; }, abstract = {The study of marine microbial ecology has been completely transformed by molecular and genomic data: after centuries of relative neglect, genomics has revealed the surprising extent of microbial diversity and how microbial processes transform ocean and global ecosystems. But the revolution is not complete: major gaps in our understanding remain, and one obvious example is that microbial eukaryotes, or protists, are still largely neglected. Here we examine various ways in which protists might be better integrated into models of marine microbial ecology, what challenges this will present, and why understanding the limitations of our tools is a significant concern. In part this is a technical challenge - eukaryotic genomes are more difficult to characterize - but eukaryotic adaptations are also more dependent on morphology and behaviour than they are on the metabolic diversity that typifies bacteria, and these cannot be inferred from genomic data as readily as metabolism can be. We therefore cannot simply follow in the methodological footsteps of bacterial ecology and hope for similar success. Understanding microbial eukaryotes will require different approaches, including greater emphasis on taxonomically and trophically diverse model systems. Molecular sequencing will continue to play a role, and advances in environmental sequence tag studies and single-cell methods for genomic and transcriptomics offer particular promise.}, }
@article {pmid28585939, year = {2017}, author = {Pérez-Jaramillo, JE and Carrión, VJ and Bosse, M and Ferrão, LFV and de Hollander, M and Garcia, AAF and Ramírez, CA and Mendes, R and Raaijmakers, JM}, title = {Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits.}, journal = {The ISME journal}, volume = {11}, number = {10}, pages = {2244-2257}, pmid = {28585939}, issn = {1751-7370}, mesh = {Genetic Variation ; Humans ; *Microbiota ; Phaseolus/*microbiology ; Plant Roots/microbiology ; Rhizosphere ; }, abstract = {Plant domestication was a pivotal accomplishment in human history, but also led to a reduction in genetic diversity of crop species compared to their wild ancestors. How this reduced genetic diversity affected plant-microbe interactions belowground is largely unknown. Here, we investigated the genetic relatedness, root phenotypic traits and rhizobacterial community composition of modern and wild accessions of common bean (Phaseolus vulgaris) grown in agricultural soil from the highlands of Colombia, one of the centers of common bean diversification. Diversity Array Technology-based genotyping and phenotyping of local common bean accessions showed significant genetic and root architectural differences between wild and modern accessions, with a higher specific root length for the wild accessions. Canonical Correspondence Analysis indicated that the divergence in rhizobacterial community composition between wild and modern bean accessions is associated with differences in specific root length. Along the bean genotypic trajectory, going from wild to modern, we observed a gradual decrease in relative abundance of Bacteroidetes, mainly Chitinophagaceae and Cytophagaceae, and an increase in relative abundance of Actinobacteria and Proteobacteria, in particular Nocardioidaceae and Rhizobiaceae, respectively. Collectively, these results establish a link between common bean domestication, specific root morphological traits and rhizobacterial community assembly.}, }
@article {pmid28585935, year = {2017}, author = {Hannula, SE and Morriën, E and de Hollander, M and van der Putten, WH and van Veen, JA and de Boer, W}, title = {Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture.}, journal = {The ISME journal}, volume = {11}, number = {10}, pages = {2294-2304}, pmid = {28585935}, issn = {1751-7370}, mesh = {Agriculture ; Bacteria/classification/genetics/isolation &amp; purification ; Biomass ; Carbon/metabolism ; Ecosystem ; Fungi/classification/genetics/*isolation &amp; purification ; Mycorrhizae/classification/genetics/isolation &amp; purification ; Netherlands ; Plant Roots/microbiology ; Plants/microbiology ; Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Activities of rhizosphere microbes are key to the functioning of terrestrial ecosystems. It is commonly believed that bacteria are the major consumers of root exudates and that the role of fungi in the rhizosphere is mostly limited to plant-associated taxa, such as mycorrhizal fungi, pathogens and endophytes, whereas less is known about the role of saprotrophs. In order to test the hypothesis that the role of saprotrophic fungi in rhizosphere processes increases with increased time after abandonment from agriculture, we determined the composition of fungi that are active in the rhizosphere along a chronosequence of ex-arable fields in the Netherlands. Intact soil cores were collected from nine fields that represent three stages of land abandonment and pulse labeled with [13]CO2. The fungal contribution to metabolization of plant-derived carbon was evaluated using phospholipid analysis combined with stable isotope probing (SIP), whereas fungal diversity was analyzed using DNA-SIP combined with 454-sequencing. We show that in recently abandoned fields most of the root-derived [13]C was taken up by bacteria but that in long-term abandoned fields most of the root-derived [13]C was found in fungal biomass. Furthermore, the composition of the active functional fungal community changed from one composed of fast-growing and pathogenic fungal species to one consisting of beneficial and slower-growing fungal species, which may have essential consequences for the carbon flow through the soil food web and consequently nutrient cycling and plant succession.}, }
@article {pmid28585934, year = {2017}, author = {Oswald, K and Graf, JS and Littmann, S and Tienken, D and Brand, A and Wehrli, B and Albertsen, M and Daims, H and Wagner, M and Kuypers, MM and Schubert, CJ and Milucka, J}, title = {Crenothrix are major methane consumers in stratified lakes.}, journal = {The ISME journal}, volume = {11}, number = {9}, pages = {2124-2140}, pmid = {28585934}, issn = {1751-7370}, mesh = {Bacterial Proteins/genetics/metabolism ; Gammaproteobacteria/classification/genetics/isolation &amp; purification/*metabolism ; Lakes/chemistry/*microbiology ; Methane/analysis/*metabolism ; Oxidation-Reduction ; Oxygenases/genetics/metabolism ; }, abstract = {Methane-oxidizing bacteria represent a major biological sink for methane and are thus Earth's natural protection against this potent greenhouse gas. Here we show that in two stratified freshwater lakes a substantial part of upward-diffusing methane was oxidized by filamentous gamma-proteobacteria related to Crenothrix polyspora. These filamentous bacteria have been known as contaminants of drinking water supplies since 1870, but their role in the environmental methane removal has remained unclear. While oxidizing methane, these organisms were assigned an 'unusual' methane monooxygenase (MMO), which was only distantly related to 'classical' MMO of gamma-proteobacterial methanotrophs. We now correct this assignment and show that Crenothrix encode a typical gamma-proteobacterial PmoA. Stable isotope labeling in combination swith single-cell imaging mass spectrometry revealed methane-dependent growth of the lacustrine Crenothrix with oxygen as well as under oxygen-deficient conditions. Crenothrix genomes encoded pathways for the respiration of oxygen as well as for the reduction of nitrate to N2O. The observed abundance and planktonic growth of Crenothrix suggest that these methanotrophs can act as a relevant biological sink for methane in stratified lakes and should be considered in the context of environmental removal of methane.}, }
@article {pmid28578235, year = {2017}, author = {Lin, HW and Lu, Y and Ganigué, R and Sharma, KR and Rabaey, K and Yuan, Z and Pikaar, I}, title = {Simultaneous use of caustic and oxygen for efficient sulfide control in sewers.}, journal = {The Science of the total environment}, volume = {601-602}, number = {}, pages = {776-783}, doi = {10.1016/j.scitotenv.2017.05.225}, pmid = {28578235}, issn = {1879-1026}, abstract = {Periodic caustic shock-loading is a commonly used method for sulfide control in sewers. Caustic shock-loading relies on the elevation of the sewage pH to ≥10.5 for several hours, thereby removing sewer pipe biofilms as well as deactivating SRB activity in the remaining biofilm. Although a widely used method, SRB activity is often not completely inhibited, and as such sulfide is still being generated. Here, we propose and experimentally demonstrate an innovative approach which combines caustic with oxygen, another commonly used method, as a dosing strategy for overcoming the drawbacks of caustic shock-loading. Six laboratory-scale rising main reactors were subjected to three dosing schemes over a period of three months, namely (i) simultaneous caustic and oxygen addition, (ii) caustic addition and (iii) no chemical addition. Our results showed that the combination of caustic and oxygen achieved efficient sulfide control, leading to a prolonged biofilm recovery period in between caustic shocks. In addition, methane emissions were reduced to a negligible level compared to caustic treatment only. To translate the findings to real-life application, the key parameters obtained during the long-term lab-scale experiments were subjected to extensive simulation studies using the SeweX model under a wide range of conditions commonly found in sewers. Overall, this study highlights the potential of periodic shock-loading and intermittent oxygen injection as combined dosing strategy for efficient sulfide control in sewers.}, }
@article {pmid28577167, year = {2017}, author = {Honeker, LK and Neilson, JW and Root, RA and Gil-Loaiza, J and Chorover, J and Maier, RM}, title = {Bacterial Rhizoplane Colonization Patterns of Buchloe dactyloides Growing in Metalliferous Mine Tailings Reflect Plant Status and Biogeochemical Conditions.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {853-867}, pmid = {28577167}, issn = {1432-184X}, support = {P42 ES004940/ES/NIEHS NIH HHS/United States ; R01 ES017079/ES/NIEHS NIH HHS/United States ; }, mesh = {Arizona ; *Bacterial Physiological Phenomena ; DNA, Bacterial/genetics ; In Situ Hybridization, Fluorescence ; Mining ; Poaceae/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; Soil Pollutants/*analysis ; }, abstract = {Plant establishment during phytostabilization of legacy mine tailings in semiarid regions is challenging due to low pH, low organic carbon, low nutrients, and high toxic metal(loid) concentrations. Plant-associated bacterial communities are particularly important under these harsh conditions because of their beneficial services to plants. We hypothesize that bacterial colonization profiles on rhizoplane surfaces reflect deterministic processes that are governed by plant health and the root environment. The aim of this study was to identify associations between bacterial colonization patterns on buffalo grass (Buchloe dactyloides) rhizoplanes and both plant status (leaf chlorophyll and plant cover) and substrate biogeochemistry (pH, electrical conductivity, total organic carbon, total nitrogen, and rhizosphere microbial community). Buffalo grass plants from mesocosm- and field-scale phytostabilization trials conducted with tailings from the Iron King Mine and Humboldt Smelter Superfund Site in Dewey-Humboldt, Arizona, were analyzed. These tailings are extremely acidic and have arsenic and lead concentrations of 2-4 g kg[-1] substrate. Bacterial communities on rhizoplanes and in rhizosphere-associated substrate were characterized using fluorescence in situ hybridization and 16S rRNA gene amplicon sequencing, respectively. The results indicated that the metabolic status of rhizoplane bacterial colonizers is significantly related to plant health. Principal component analysis revealed that root-surface Alphaproteobacteria relative abundance was associated most strongly with substrate pH and Gammaproteobacteria relative abundance associated strongly with substrate pH and plant cover. These factors also affected the phylogenetic profiles of the associated rhizosphere communities. In summary, rhizoplane bacterial colonization patterns are plant specific and influenced by plant status and rhizosphere biogeochemical conditions.}, }
@article {pmid28576763, year = {2017}, author = {Gill, AS and Lee, A and McGuire, KL}, title = {Phylogenetic and Functional Diversity of Total (DNA) and Expressed (RNA) Bacterial Communities in Urban Green Infrastructure Bioswale Soils.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {16}, pages = {}, pmid = {28576763}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Biodiversity ; DNA, Bacterial/genetics ; Hydrocarbons/metabolism ; New York City ; *Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Urban Renewal ; }, abstract = {New York City (NYC) is pioneering green infrastructure with the use of bioswales and other engineered soil-based habitats to provide stormwater infiltration and other ecosystem functions. In addition to avoiding the environmental and financial costs of expanding traditional built infrastructure, green infrastructure is thought to generate cobenefits in the form of diverse ecological processes performed by its plant and microbial communities. Yet, although plant communities in these habitats are closely managed, we lack basic knowledge about how engineered ecosystems impact the distribution and functioning of soil bacteria. We sequenced amplicons of the 16S ribosomal subunit, as well as seven genes associated with functional pathways, generated from both total (DNA-based) and expressed (RNA) soil communities in the Bronx, NYC, NY, in order to test whether bioswale soils host characteristic bacterial communities with evidence for enriched microbial functioning, compared to nonengineered soils in park lawns and tree pits. Bioswales had distinct, phylogenetically diverse bacterial communities, including taxa associated with nutrient cycling and metabolism of hydrocarbons and other pollutants. Bioswale soils also had a significantly greater diversity of genes involved in several functional pathways, including carbon fixation (cbbL-R [cbbL gene, red-like subunit] and apsA), nitrogen cycling (noxZ and amoA), and contaminant degradation (bphA); conversely, no functional genes were significantly more abundant in nonengineered soils. These results provide preliminary evidence that urban land management can shape the diversity and activity of soil communities, with positive consequences for genetic resources underlying valuable ecological functions, including biogeochemical cycling and degradation of common urban pollutants.IMPORTANCE Management of urban soil biodiversity by favoring taxa associated with decontamination or other microbial metabolic processes is a powerful prospect, but it first requires an understanding of how engineered soil habitats shape patterns of microbial diversity. This research adds to our understanding of urban microbial biogeography by providing data on soil bacteria in bioswales, which had relatively diverse and compositionally distinct communities compared to park and tree pit soils. Bioswales also contained comparatively diverse pools of genes related to carbon sequestration, nitrogen cycling, and contaminant degradation, suggesting that engineered soils may serve as effective reservoirs of functional microbial biodiversity. We also examined both total (DNA-based) and expressed (RNA) communities, revealing that total bacterial communities (the exclusive targets in the vast majority of soil studies) were poor predictors of expressed community diversity, pointing to the value of quantifying RNA, especially when ecological functioning is considered.}, }
@article {pmid28576374, year = {2017}, author = {Ramezani, M and Hosseini, SM and Ferrocino, I and Amoozegar, MA and Cocolin, L}, title = {Molecular investigation of bacterial communities during the manufacturing and ripening of semi-hard Iranian Liqvan cheese.}, journal = {Food microbiology}, volume = {66}, number = {}, pages = {64-71}, doi = {10.1016/j.fm.2017.03.019}, pmid = {28576374}, issn = {1095-9998}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Biodiversity ; Cheese/*microbiology ; Denaturing Gradient Gel Electrophoresis ; Food Handling ; Food Microbiology ; Iran ; Milk/*microbiology ; Sheep ; }, abstract = {Liqvan (or Lighvan) is a traditional Iranian cheese from the East Azerbaijan province of Iran, which is made of raw ewe's milk without the addition of a starter. The grazing pastures, environmental conditions and the ancient regional production methods allocate a distinctive microbial ecology to this type of cheese, and these factors are consequently associated with the quality of the product. In this study, the microbiota of the milk, curd and cheese has been investigated using culture independent approaches. Denaturing gradient gel electrophoresis (DGGE) of the bacteria, 16S rRNA based high-throughput sequencing and enumeration of the live bacterial community by means of quantitative PCR (qPCR) have been used for this purpose. The results showed that the main bacterial population in the milk belonged to both microbial contaminants and lactic acid bacteria (LAB). However, both of these populations were totally replaced by LAB during ripening. The present survey contributes by describing the microbiota of this ancient cheese in more detail during fermentation and ripening.}, }
@article {pmid28574490, year = {2017}, author = {Singer, E and Wagner, M and Woyke, T}, title = {Capturing the genetic makeup of the active microbiome in situ.}, journal = {The ISME journal}, volume = {11}, number = {9}, pages = {1949-1963}, pmid = {28574490}, issn = {1751-7370}, support = {294343/ERC_/European Research Council/International ; }, mesh = {Bacteria/classification/*genetics/growth &amp; development/*isolation &amp; purification ; Ecosystem ; *Environmental Microbiology ; *Genetic Techniques ; *Microbiota ; }, abstract = {More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.}, }
@article {pmid28572798, year = {2017}, author = {He, M and Cai, L and Zhang, C and Jiao, N and Zhang, R}, title = {Phylogenetic Diversity of T4-Type Phages in Sediments from the Subtropical Pearl River Estuary.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {897}, pmid = {28572798}, issn = {1664-302X}, abstract = {Viruses are an abundant and active component of marine sediments and play a significant role in microbial ecology and biogeochemical cycling at local and global scales. To obtain a better understanding of the ecological characteristics of the viriobenthos, the abundance and morphology of viruses and the diversity and community structure of T4-type phages were systematically investigated in the surface sediments of the subtropical Pearl River Estuary (PRE). Viral abundances ranged from 4.49 × 10[8] to 11.7 × 10[8] viruses/g and prokaryotic abundances ranged from 2.63 × 10[8] to 9.55 × 10[8] cells/g, and both decreased from freshwater to saltwater. Diverse viral morphotypes, including tailed, spherical, filamentous, and rod-shaped viruses, were observed using transmission electron microscopy. Analysis of the major capsid gene (g23) indicated that the sediment T4-type phages were highly diverse and, similar to the trend in viral abundances, their diversity decreased as the salinity increased. Phylogenetic analysis suggested that most of the g23 operational taxonomic units were affiliated with marine, paddy soil, and lake groups. The T4-type phage communities in freshwater and saltwater sediments showed obvious differences, which were related to changes in the Pearl River discharge. The results of this study demonstrated both allochthonous and autochthonous sources of the viral community in the PRE sediments and the movement of certain T4-type viral groups between the freshwater and saline water biomes.}, }
@article {pmid28571852, year = {2017}, author = {Fernandez-Bayo, JD and Toniato, J and Simmons, BA and Simmons, CW}, title = {Structure and activity of thermophilic methanogenic microbial communities exposed to quaternary ammonium sanitizer.}, journal = {Journal of environmental sciences (China)}, volume = {56}, number = {}, pages = {164-168}, doi = {10.1016/j.jes.2016.10.005}, pmid = {28571852}, issn = {1001-0742}, mesh = {Ammonium Compounds ; Bioreactors/microbiology ; Methane ; Quaternary Ammonium Compounds/*toxicity ; Waste Disposal, Fluid/*methods ; *Water Microbiology ; }, abstract = {Food processing facilities often use antimicrobial quaternary ammonium compound (QAC) sanitizers to maintain cleanliness. These QACs can end up in wastewaters used as feedstock for anaerobic digestion. The aim of this study was to measure the effect of QAC contamination on biogas production and structure of microbial communities in thermophilic digester sludge. Methane production and biogas quality data were analyzed in batch anaerobic digesters containing QAC at 0, 15, 50, 100 and 150mg/L. Increasing sanitizer concentration in the bioreactors negatively impacted methane production rate and biogas quality. Microbial community composition data was obtained through 16S rRNA gene sequencing from the QAC-contaminated sludges. Sequencing data showed no significant restructuring of the bacterial communities. However, significant restructuring was observed within the archaeal communities as QAC concentration increased. Further studies to confirm these effects on a larger scale and with a longer retention time are necessary.}, }
@article {pmid28571487, year = {2017}, author = {Garcia, SS and Blackledge, MS and Michalek, S and Su, L and Ptacek, T and Eipers, P and Morrow, C and Lefkowitz, EJ and Melander, C and Wu, H}, title = {Targeting of Streptococcus mutans Biofilms by a Novel Small Molecule Prevents Dental Caries and Preserves the Oral Microbiome.}, journal = {Journal of dental research}, volume = {96}, number = {7}, pages = {807-814}, pmid = {28571487}, issn = {1544-0591}, support = {P30 AI027767/AI/NIAID NIH HHS/United States ; R01 DE019452/DE/NIDCR NIH HHS/United States ; F31 DE024041/DE/NIDCR NIH HHS/United States ; UL1 TR000165/TR/NCATS NIH HHS/United States ; P30 AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR001417/TR/NCATS NIH HHS/United States ; R01 DE022350/DE/NIDCR NIH HHS/United States ; T90 DE022736/DE/NIDCR NIH HHS/United States ; }, mesh = {Animals ; Biofilms/*drug effects ; Dental Caries/*prevention &amp; control ; Dental Enamel/drug effects ; Imidazoles/*pharmacology ; Microbiota/*drug effects ; Microscopy, Confocal ; Polymerase Chain Reaction ; Rats ; Streptococcus gordonii/drug effects ; Streptococcus mutans/*drug effects ; Streptococcus sanguis/drug effects ; }, abstract = {Dental caries is a costly and prevalent disease characterized by the demineralization of the tooth's enamel. Disease outcome is influenced by host factors, dietary intake, cariogenic bacteria, and other microbes. The cariogenic bacterial species Streptococcus mutans metabolizes sucrose to initiate biofilm formation on the tooth surface and consequently produces lactic acid to degrade the tooth's enamel. Persistence of S. mutans biofilms in the oral cavity can lead to tooth decay. To date, no anticaries therapies that specifically target S. mutans biofilms but do not disturb the overall oral microbiome are available. We screened a library of 2-aminoimidazole antibiofilm compounds with a biofilm dispersion assay and identified a small molecule that specifically targets S. mutans biofilms. At 5 µM, the small molecule annotated 3F1 dispersed 50% of the established S. mutans biofilm but did not disperse biofilms formed by the commensal species Streptococcus sanguinis or Streptococcus gordonii. 3F1 dispersed S. mutans biofilms independently of biofilm-related factors such as antigen I/II and glucosyltransferases. 3F1 treatment effectively prevented dental caries by controlling S. mutans in a rat caries model without perturbing the oral microbiota. Our study demonstrates that selective targeting of S. mutans biofilms by 3F1 was able to effectively reduce dental caries in vivo without affecting the overall oral microbiota shaped by the intake of dietary sugars, suggesting that the pathogenic biofilm-specific treatment is a viable strategy for disease prevention.}, }
@article {pmid28567446, year = {2017}, author = {Holman, DB and Brunelle, BW and Trachsel, J and Allen, HK}, title = {Meta-analysis To Define a Core Microbiota in the Swine Gut.}, journal = {mSystems}, volume = {2}, number = {3}, pages = {}, pmid = {28567446}, issn = {2379-5077}, abstract = {The swine gut microbiota encompasses a large and diverse population of bacteria that play a significant role in pig health. As such, a number of recent studies have utilized high-throughput sequencing of the 16S rRNA gene to characterize the composition and structure of the swine gut microbiota, often in response to dietary feed additives. It is important to determine which factors shape the composition of the gut microbiota among multiple studies and if certain bacteria are always present in the gut microbiota of swine, independently of study variables such as country of origin and experimental design. Therefore, we performed a meta-analysis using 20 publically available data sets from high-throughput 16S rRNA gene sequence studies of the swine gut microbiota. Next to the "study" itself, the gastrointestinal (GI) tract section that was sampled had the greatest effect on the composition and structure of the swine gut microbiota (P = 0.0001). Technical variation among studies, particularly the 16S rRNA gene hypervariable region sequenced, also significantly affected the composition of the swine gut microbiota (P = 0.0001). Despite this, numerous commonalities were discovered. Among fecal samples, the genera Prevotella, Clostridium, Alloprevotella, and Ruminococcus and the RC9 gut group were found in 99% of all fecal samples. Additionally, Clostridium, Blautia, Lactobacillus, Prevotella, Ruminococcus, Roseburia, the RC9 gut group, and Subdoligranulum were shared by >90% of all GI samples, suggesting a so-called "core" microbiota for commercial swine worldwide. IMPORTANCE The results of this meta-analysis demonstrate that "study" and GI sample location are the most significant factors in shaping the swine gut microbiota. However, in comparisons of results from different studies, some biological factors may be obscured by technical variation among studies. Nonetheless, there are some bacterial taxa that appear to form a core microbiota within the swine GI tract regardless of country of origin, diet, age, or breed. Thus, these results provide the framework for future studies to manipulate the swine gut microbiota for potential health benefits.}, }
@article {pmid28567035, year = {2017}, author = {Berry, D and Gutierrez, T}, title = {Evaluating the Detection of Hydrocarbon-Degrading Bacteria in 16S rRNA Gene Sequencing Surveys.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {896}, pmid = {28567035}, issn = {1664-302X}, abstract = {Hydrocarbonoclastic bacteria (HCB) play a key role in the biodegradation of oil hydrocarbons in marine and other environments. A small number of taxa have been identified as obligate HCB, notably the Gammaproteobacterial genera Alcanivorax, Cycloclasticus, Marinobacter, Neptumonas, Oleiphilus, Oleispira, and Thalassolituus, as well as the Alphaproteobacterial genus Thalassospira. Detection of HCB in amplicon-based sequencing surveys relies on high coverage by PCR primers and accurate taxonomic classification. In this study, we performed a phylogenetic analysis to identify 16S rRNA gene sequence regions that represent the breadth of sequence diversity within these taxa. Using validated sequences, we evaluated 449 universal 16S rRNA gene-targeted bacterial PCR primer pairs for their coverage of these taxa. The results of this analysis provide a practical framework for selection of suitable primer sets for optimal detection of HCB in sequencing surveys.}, }
@article {pmid28562180, year = {2018}, author = {Gutleben, J and Chaib De Mares, M and van Elsas, JD and Smidt, H and Overmann, J and Sipkema, D}, title = {The multi-omics promise in context: from sequence to microbial isolate.}, journal = {Critical reviews in microbiology}, volume = {44}, number = {2}, pages = {212-229}, doi = {10.1080/1040841X.2017.1332003}, pmid = {28562180}, issn = {1549-7828}, mesh = {Metabolomics/*methods ; Metagenomics/*methods ; Microbiological Techniques/*methods ; *Microbiota ; Proteomics/*methods ; }, abstract = {The numbers and diversity of microbes in ecosystems within and around us is unmatched, yet most of these microorganisms remain recalcitrant to in vitro cultivation. Various high-throughput molecular techniques, collectively termed multi-omics, provide insights into the genomic structure and metabolic potential as well as activity of complex microbial communities. Nonetheless, pure or defined cultures are needed to (1) decipher microbial physiology and thus test multi-omics-based ecological hypotheses, (2) curate and improve database annotations and (3) realize novel applications in biotechnology. Cultivation thus provides context. In turn, we here argue that multi-omics information awaits integration into the development of novel cultivation strategies. This can build the foundation for a new era of omics information-guided microbial cultivation technology and reduce the inherent trial-and-error search space. This review discusses how information that can be extracted from multi-omics data can be applied for the cultivation of hitherto uncultured microorganisms. Furthermore, we summarize groundbreaking studies that successfully translated information derived from multi-omics into specific media formulations, screening techniques and selective enrichments in order to obtain novel targeted microbial isolates. By integrating these examples, we conclude with a proposed workflow to facilitate future omics-aided cultivation strategies that are inspired by the microbial complexity of the environment.}, }
@article {pmid28560606, year = {2018}, author = {de Souza, TAF and de Andrade, LA and Freitas, H and da Silva Sandim, A}, title = {Biological Invasion Influences the Outcome of Plant-Soil Feedback in the Invasive Plant Species from the Brazilian Semi-arid.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {102-112}, pmid = {28560606}, issn = {1432-184X}, mesh = {Apocynaceae/growth &amp; development ; Biodiversity ; Biomass ; Brazil ; Fabaceae/growth &amp; development ; Forests ; Glomeromycota/physiology ; *Introduced Species ; Mycorrhizae/classification/growth &amp; development/*physiology ; Phosphorus/metabolism ; *Plant Development ; Plant Roots/microbiology ; Plants/*microbiology ; Prosopis/growth &amp; development ; Seasons ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Plant-soil feedback is recognized as the mutual interaction between plants and soil microorganisms, but its role on the biological invasion of the Brazilian tropical seasonal dry forest by invasive plants still remains unclear. Here, we analyzed and compared the arbuscular mycorrhizal fungi (AMF) communities and soil characteristics from the root zone of invasive and native plants, and tested how these AMF communities affect the development of four invasive plant species (Cryptostegia madagascariensis, Parkinsonia aculeata, Prosopis juliflora, and Sesbania virgata). Our field sampling revealed that AMF diversity and frequency of the Order Diversisporales were positively correlated with the root zone of the native plants, whereas AMF dominance and frequency of the Order Glomerales were positively correlated with the root zone of invasive plants. We grew the invasive plants in soil inoculated with AMF species from the root zone of invasive (I changed) and native (I unaltered) plant species. We also performed a third treatment with sterilized soil inoculum (control). We examined the effects of these three AMF inoculums on plant dry biomass, root colonization, plant phosphorous concentration, and plant responsiveness to mycorrhizas. We found that I unaltered and I changed promoted the growth of all invasive plants and led to a higher plant dry biomass, mycorrhizal colonization, and P uptake than control, but I changed showed better results on these variables than I unaltered. For plant responsiveness to mycorrhizas and fungal inoculum effect on plant P concentration, we found positive feedback between changed-AMF community (I changed) and three of the studied invasive plants: C. madagascariensis, P. aculeata, and S. virgata.}, }
@article {pmid28559161, year = {2017}, author = {Rocchi, S and Valot, B and Reboux, G and Millon, L}, title = {DNA metabarcoding to assess indoor fungal communities: Electrostatic dust collectors and Illumina sequencing.}, journal = {Journal of microbiological methods}, volume = {139}, number = {}, pages = {107-112}, doi = {10.1016/j.mimet.2017.05.014}, pmid = {28559161}, issn = {1872-8359}, mesh = {*Air Microbiology ; *Air Pollution, Indoor ; DNA Barcoding, Taxonomic/*methods ; DNA Primers ; DNA, Fungal/genetics ; *Dust ; Environmental Monitoring/methods ; France ; Fungi/*classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/instrumentation/methods ; Microbial Consortia/genetics ; Real-Time Polymerase Chain Reaction ; *Static Electricity ; }, abstract = {DNA metabarcoding is increasingly being used to characterize the microbiological composition of both the indoor and outdoor environments of dwellings. Our study aimed to evaluate metabarcoding and bioinformatic analysis resulting from calibrated samples and samples collected by an electrostatic dust collector (EDC) in dwellings with no moisture problems. Thus, the fungal communities of 14 dwellings (eastern France, Franche-Comté region) were analyzed by Illumina MiSeq technology after amplification of the ITS2 region. Using the standard samples of 11 species of yeasts and molds allowed us to validate the Operational taxonomic units (OTU) assignment. These calibrated samples also showed a low amplification bias, a low rate of sequencing errors and the semi-quantitative nature of the technique. Only one species from the calibrated samples (Lichtheimia corymbifera) was less amplified probably due to the presence of two mismatches in its3 primer. EDC analysis identified 3594OTU with 75% of reads corresponding to 30 genera. The main genera are those usually found by culture techniques (Penicillium, Aspergillus and Cladosporium), but findings also indicate others less commonly isolated in culture such as Epicoccum, the fourth detected genus in our study. The type of heating systems was correlated with fungal diversity. We found less diversity in the dwellings with wood heating and larger quantities of Epicoccum nigrum verified by qPCR. DNA metabarcoding analysis applied to EDC seems promising. However, we think that it must be used along with qPCR, to obtain a more global view of microbial ecology and relative quantification of species of interest within communities.}, }
@article {pmid28558432, year = {2017}, author = {Mbareche, H and Brisebois, E and Veillette, M and Duchaine, C}, title = {Bioaerosol sampling and detection methods based on molecular approaches: No pain no gain.}, journal = {The Science of the total environment}, volume = {599-600}, number = {}, pages = {2095-2104}, doi = {10.1016/j.scitotenv.2017.05.076}, pmid = {28558432}, issn = {1879-1026}, mesh = {Aerosols/*analysis ; *Air Microbiology ; Environmental Monitoring/*methods ; }, abstract = {Bioaerosols are among the less studied particles in the environment. The lack of standardization in sampling procedures, difficulties related to the effect of sampling processes on the integrity of microorganisms, and challenges associated with the application of environmental microbiology analyses and molecular and culture methods frighten many young scientists. Every microorganism has its own particularities and acts differently when aerosolized in various conditions. Because the air is an extremely biologically diluted environment, it is necessary to concentrate its content before any analysis is performed. Challenges faced when applying molecular methods to air samples reveal the need for a better standardization of approaches for cell and nucleic acid recovery, the choice of genetic markers, and interpretation of data. This paper presents a few of the limits and difficulties tackled when molecular methods are applied to bioaerosols, suggests some improvements by specifying the critical stages that should be considered when studying the microbial ecology of bioaerosols, and provides thoughtful insights on how to overcome the challenges encountered.}, }
@article {pmid28557379, year = {2017}, author = {Tyc, O and de Jager, VCL and van den Berg, M and Gerards, S and Janssens, TKS and Zaagman, N and Kai, M and Svatos, A and Zweers, H and Hordijk, C and Besselink, H and de Boer, W and Garbeva, P}, title = {Exploring bacterial interspecific interactions for discovery of novel antimicrobial compounds.}, journal = {Microbial biotechnology}, volume = {10}, number = {4}, pages = {910-925}, pmid = {28557379}, issn = {1751-7915}, mesh = {Anti-Bacterial Agents/*isolation &amp; purification/*metabolism ; *Antibiosis ; Biological Products/*isolation &amp; purification/*metabolism ; Burkholderia/growth &amp; development/*physiology ; Gene Expression Profiling ; Humans ; Metabolomics ; Paenibacillus/growth &amp; development/*physiology ; Secondary Metabolism ; Volatile Organic Compounds/analysis ; }, abstract = {Recent studies indicated that the production of secondary metabolites by soil bacteria can be triggered by interspecific interactions. However, little is known to date about interspecific interactions between Gram-positive and Gram-negative bacteria. In this study, we aimed to understand how the interspecific interaction between the Gram-positive Paenibacillus sp. AD87 and the Gram-negative Burkholderia sp. AD24 affects the fitness, gene expression and the production of soluble and volatile secondary metabolites of both bacteria. To obtain better insight into this interaction, transcriptome and metabolome analyses were performed. Our results revealed that the interaction between the two bacteria affected their fitness, gene expression and the production of secondary metabolites. During interaction, the growth of Paenibacillus was not affected, whereas the growth of Burkholderia was inhibited at 48 and 72 h. Transcriptome analysis revealed that the interaction between Burkholderia and Paenibacillus caused significant transcriptional changes in both bacteria as compared to the monocultures. The metabolomic analysis revealed that the interaction increased the production of specific volatile and soluble antimicrobial compounds such as 2,5-bis(1-methylethyl)-pyrazine and an unknown Pederin-like compound. The pyrazine volatile compound produced by Paenibacillus was subjected to bioassays and showed strong inhibitory activity against Burkholderia and a range of plant and human pathogens. Moreover, strong additive antimicrobial effects were observed when soluble extracts from the interacting bacteria were combined with the pure 2,5-bis(1-methylethyl)-pyrazine. The results obtained in this study highlight the importance to explore bacterial interspecific interactions to discover novel secondary metabolites and to perform simultaneously metabolomics of both, soluble and volatile compounds.}, }
@article {pmid28555058, year = {2017}, author = {Munir, A and Waseem, H and Williams, MR and Stedtfeld, RD and Gulari, E and Tiedje, JM and Hashsham, SA}, title = {Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB.}, journal = {Microarrays (Basel, Switzerland)}, volume = {6}, number = {2}, pages = {}, pmid = {28555058}, issn = {2076-3905}, abstract = {Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface and its complementary strand present in the sample are of interest. To achieve optimal sensitivity with minimum sample size and rapid hybridization, ability to predict the kinetics of hybridization based on the thermodynamic characteristics of the probe is crucial. In this study, a computer aided numerical model for the design and optimization of a flow-through biochip was developed using a finite element technique packaged software tool (FEMLAB; package included in COMSOL Multiphysics) to simulate the transport of DNA through a microfluidic chamber to the reaction surface. The model accounts for fluid flow, convection and diffusion in the channel and on the reaction surface. Concentration, association rate constant, dissociation rate constant, recirculation flow rate, and temperature were key parameters affecting the rate of hybridization. The model predicted the kinetic profile and signal intensities of eighteen 20-mer probes targeting vancomycin resistance genes (VRGs). Predicted signal intensities and hybridization kinetics strongly correlated with experimental data in the biochip (R[2] = 0.8131).}, }
@article {pmid28553266, year = {2017}, author = {Morgan, HH and du Toit, M and Setati, ME}, title = {The Grapevine and Wine Microbiome: Insights from High-Throughput Amplicon Sequencing.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {820}, pmid = {28553266}, issn = {1664-302X}, abstract = {From the time when microbial activity in wine fermentation was first demonstrated, the microbial ecology of the vineyard, grape, and wine has been extensively investigated using culture-based methods. However, the last 2 decades have been characterized by an important change in the approaches used for microbial examination, due to the introduction of DNA-based community fingerprinting methods such as DGGE, SSCP, T-RFLP, and ARISA. These approaches allowed for the exploration of microbial community structures without the need to cultivate, and have been extensively applied to decipher the microbial populations associated with the grapevine as well as the microbial dynamics throughout grape berry ripening and wine fermentation. These techniques are well-established for the rapid more sensitive profiling of microbial communities; however, they often do not provide direct taxonomic information and possess limited ability to detect the presence of rare taxa and taxa with low abundance. Consequently, the past 5 years have seen an upsurge in the application of high-throughput sequencing methods for the in-depth assessment of the grapevine and wine microbiome. Although a relatively new approach in wine sciences, these methods reveal a considerably greater diversity than previously reported, and identified several species that had not yet been reported. The aim of the current review is to highlight the contribution of high-throughput next generation sequencing and metagenomics approaches to vineyard microbial ecology especially unraveling the influence of vineyard management practices on microbial diversity.}, }
@article {pmid28551539, year = {2017}, author = {Lekunberri, I and Villagrasa, M and Balcázar, JL and Borrego, CM}, title = {Contribution of bacteriophage and plasmid DNA to the mobilization of antibiotic resistance genes in a river receiving treated wastewater discharges.}, journal = {The Science of the total environment}, volume = {601-602}, number = {}, pages = {206-209}, doi = {10.1016/j.scitotenv.2017.05.174}, pmid = {28551539}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/analysis ; Bacteriophages/genetics ; DNA, Viral/*analysis ; Drug Resistance, Microbial/*genetics ; Environmental Monitoring ; *Genes, Bacterial ; Plasmids/*analysis ; Rivers/*microbiology ; Spain ; *Wastewater/microbiology/virology ; Water Pollutants, Chemical/analysis ; }, abstract = {In this study, we quantified eleven antibiotic compounds and nine antibiotic resistance genes (ARGs) in water samples collected upstream and downstream of the discharge point from a municipal wastewater treatment plant (WWTP) into the Ter River. Antibiotics were analyzed by liquid chromatography coupled to mass spectrometry, whereas the concentration of ARGs in bacterial, phage and plasmid DNA fractions was determined by real-time PCR to explore their contribution to environmental antibiotic resistance. WWTP discharges resulted in higher concentrations of antibiotic residues as well as ARGs in water samples collected downstream the impact point. Specifically, genes conferring resistance to macrolides (ermB), fluoroquinolones (qnrS) and tetracyclines (tetW) showed significant differences (p<0.05) between upstream and downstream sites in the three DNA fractions (i.e. bacteria, plasmids and phages). Interestingly, genes conferring resistance to β-lactams (blaTEM, blaNDM and blaKPC) and glycopeptides (vanA) only showed significant differences (p<0.05) between upstream and downstream sites in phage and plasmid DNA but not in the bacterial DNA fraction. Our results show for the first time the extent to which phages and plasmids contribute to the mobilization of ARGs in an aquatic environment exposed to chronic antibiotic pollution via WWTP discharges. Accordingly, these mobile genetic elements should be included in further studies to get a global view of the spread of antibiotic resistance.}, }
@article {pmid28550943, year = {2017}, author = {Stanley, CE and van der Heijden, MGA}, title = {Microbiome-on-a-Chip: New Frontiers in Plant-Microbiota Research.}, journal = {Trends in microbiology}, volume = {25}, number = {8}, pages = {610-613}, doi = {10.1016/j.tim.2017.05.001}, pmid = {28550943}, issn = {1878-4380}, mesh = {Ecosystem ; *Lab-On-A-Chip Devices ; *Microbiota ; Plants/*microbiology ; Research ; *Soil Microbiology ; Symbiosis ; }, abstract = {An enigmatic concoction of interactions between microbes and hosts takes place below ground, yet the function(s) of the individual components in this complex playground are far from understood. This Forum article highlights how microfluidic - or 'Microbiome-on-a-Chip' - technology could help to shed light on such relationships, opening new frontiers in plant-microbiota research.}, }
@article {pmid28550339, year = {2017}, author = {Santamaria, O and Lledó, S and Rodrigo, S and Poblaciones, MJ}, title = {Effect of Fungal Endophytes on Biomass Yield, Nutritive Value and Accumulation of Minerals in Ornithopus compressus.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {841-852}, pmid = {28550339}, issn = {1432-184X}, mesh = {Animal Feed/analysis ; *Biomass ; Endophytes/*physiology ; Fungi/*physiology ; Lotus/*metabolism/*microbiology ; Minerals/metabolism ; *Nutritive Value ; }, abstract = {Yellow serradella (Ornithopus compressus), a valuable pasture species in Mediterranean areas, presents a high diversity of endophytic mycoflora. In the present work, the hypothesis of a significant effect of fungal endophytic species on the parameters of forage production, nutritive value and mineral status of herbage was tested. O. compressus plants were inoculated with each of seven endophytes (four in 2012/2013 and three in 2013/2014). After inoculation, two experiments (under greenhouse and field conditions) were established. Results evidenced a certain influence of several endophytes on herbage yield, nutritive value and mineral status of O. compressus forage. Byssochlamys spectabilis increased herbage biomass yield by around 42% in the field experiment. Stemphylium sp. improved the nutritive value of forage either by increasing crude protein, digestibility and the concentration of essential minerals (such as B, Mo, P or S) or by reducing the concentration of toxic elements such as Al or Pb. In conclusion, the results presented here provide evidence that plant inoculation with endophytes could be a suitable strategy to increase forage yield and its nutritive value or to deal with potential nutrient deficiencies or potential mineral toxicity in forage.}, }
@article {pmid28545863, year = {2017}, author = {Williams, AK and Bacosa, HP and Quigg, A}, title = {The impact of dissolved inorganic nitrogen and phosphorous on responses of microbial plankton to the Texas City "Y" oil spill in Galveston Bay, Texas (USA).}, journal = {Marine pollution bulletin}, volume = {121}, number = {1-2}, pages = {32-44}, doi = {10.1016/j.marpolbul.2017.05.033}, pmid = {28545863}, issn = {1879-3363}, mesh = {Bays ; Gulf of Mexico ; *Nitrogen ; *Petroleum Pollution ; *Phosphorus ; Plankton/*growth &amp; development ; Polycyclic Aromatic Hydrocarbons ; Population Dynamics ; Texas ; }, abstract = {Ongoing bioremediation research seeks to promote naturally occurring microbial polycyclic aromatic hydrocarbon (PAH) degradation during and after oil spill events. However, complex relationships among functionally different microbial groups, nutrients and PAHs remain unconstrained. We conducted a surface water survey and corresponding nutrient amendment bioassays following the Texas City "Y" oil spill in Galveston Bay, Texas. Resident microbial groups, defined as either heterotrophic or autotrophic were enumerated by flow cytometry. Heterotrophic abundance was increased by oil regardless of nutrient concentrations. Contrastingly, autotrophic abundance was inhibited by oil, but this reaction was less severe when nutrient concentrations were higher. Several PAH compounds were reduced in nutrient amended treatments relative to controls suggesting nutrient enhanced microbial PAH processing. These findings provide a first-look at nutrient limitation during microbial oil processing in Galveston Bay, an important step in understanding if nutrient additions would be a useful bioremediation strategy in this and other estuarine systems.}, }
@article {pmid28544612, year = {2017}, author = {Hoque, E and Fritscher, J}, title = {Ecology, adaptation, and function of methane-sulfidic spring water biofilm microorganisms, including a strain of anaerobic fungus Mucor hiemalis.}, journal = {MicrobiologyOpen}, volume = {6}, number = {4}, pages = {}, pmid = {28544612}, issn = {2045-8827}, mesh = {Anaerobiosis ; Archaea/classification/growth &amp; development/*isolation &amp; purification ; Bacteria/classification/growth &amp; development/*isolation &amp; purification ; Biofilms/growth &amp; development ; *Biota ; Ciliophora/classification/growth &amp; development/*isolation &amp; purification ; Fungi/classification/growth &amp; development/*isolation &amp; purification ; Germany ; Methane/analysis ; Natural Springs/chemistry/*microbiology ; Sulfides/analysis ; Temperature ; }, abstract = {Ecological aspects, adaptation, and some functions of a special biofilm and its unique key anaerobic fungus Mucor hiemalis strain EH11 isolated from a pristine spring (Künzing, Bavaria, Germany) are described. The spring's pure nature is characterized by, for example, bubbling methane, marine-salinity, mild hydrothermal (~19.1°C), sulfidic, and reductive-anoxic (Eh : -241 to -253 mV, O2 : ≤ 0.1 mg/L) conditions. It is geoecologically located at the border zone between Bavarian Forest (crystalline rocky mountains) and the moor-like Danube River valley, where geological displacements bring the spring's water from the deeper layers of former marine sources up to the surface. In the spring's outflow, a special biofilm with selective microorganisms consisting of archaea, bacteria, protozoa (ciliate), and fungus was found. Typical sulfidic-spring bryophyta and macrozoobenthos were missing, but many halo- and anaerotolerant diatoms and ciliate Vorticella microstoma beside EH11 were identified. Phase contrast and scanning electron microscopy revealed the existence of a stabilizing matrix in the biofilm formed by the sessile fungal hyphae and the exopolysaccharide substance (EPS) structures, which harbors other microorganisms. In response to ecological adaptation pressure caused by methane bubbles, EH11 developed an atypical spring-like hyphal morphology, similar to the spiral stalk of ciliate V. microstoma, to rise up with methane bubbles. For the first time, it was also demonstrated that under strict anaerobic conditions EH11 changes its asexual reproduction process by forming pseudosporangia via hyphal cell divisions as well as switching its metabolism to chemoautotrophic bacteria-like anaerobic life using acetate as an e-donor and ferrihydrite as an e-acceptor, all without fermentation. EH11 can be suggested to be useful for the microbial community in the Künzing biofilm not only due to its physical stabilization of the biofilm's matrix but also due to its ecological functions in element recycling as well as a remover of toxic metals.}, }
@article {pmid28540488, year = {2017}, author = {Maritz, JM and Rogers, KH and Rock, TM and Liu, N and Joseph, S and Land, KM and Carlton, JM}, title = {An 18S rRNA Workflow for Characterizing Protists in Sewage, with a Focus on Zoonotic Trichomonads.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {923-936}, pmid = {28540488}, issn = {1432-184X}, mesh = {Blastocystis hominis/genetics ; Cryptosporidium parvum/genetics ; Giardia lamblia/genetics ; High-Throughput Nucleotide Sequencing/*methods ; RNA, Protozoan/*analysis ; RNA, Ribosomal, 18S/*analysis ; Sewage/*parasitology ; Toxoplasma/genetics ; Trichomonadida/*genetics ; Workflow ; }, abstract = {Microbial eukaryotes (protists) are important components of terrestrial and aquatic environments, as well as animal and human microbiomes. Their relationships with metazoa range from mutualistic to parasitic and zoonotic (i.e., transmissible between humans and animals). Despite their ecological importance, our knowledge of protists in urban environments lags behind that of bacteria, largely due to a lack of experimentally validated high-throughput protocols that produce accurate estimates of protist diversity while minimizing non-protist DNA representation. We optimized protocols for detecting zoonotic protists in raw sewage samples, with a focus on trichomonad taxa. First, we investigated the utility of two commonly used variable regions of the 18S rRNA marker gene, V4 and V9, by amplifying and Sanger sequencing 23 different eukaryotic species, including 16 protist species such as Cryptosporidium parvum, Giardia intestinalis, Toxoplasma gondii, and species of trichomonad. Next, we optimized wet-lab methods for sample processing and Illumina sequencing of both regions from raw sewage collected from a private apartment building in New York City. Our results show that both regions are effective at identifying several zoonotic protists that may be present in sewage. A combination of small extractions (1 mL volumes) performed on the same day as sample collection, and the incorporation of a vertebrate blocking primer, is ideal to detect protist taxa of interest and combat the effects of metazoan DNA. We expect that the robust, standardized methods presented in our workflow will be applicable to investigations of protists in other environmental samples, and will help facilitate large-scale investigations of protistan diversity.}, }
@article {pmid28540487, year = {2017}, author = {Tomassone, L and Ceballos, LA and Ragagli, C and Martello, E and De Sousa, R and Stella, MC and Mannelli, A}, title = {Importance of Common Wall Lizards in the Transmission Dynamics of Tick-Borne Pathogens in the Northern Apennine Mountains, Italy.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {961-968}, pmid = {28540487}, issn = {1432-184X}, mesh = {Animals ; Borrelia burgdorferi Group/*isolation &amp; purification ; Disease Reservoirs/microbiology ; Female ; Italy/epidemiology ; Ixodes/growth &amp; development/microbiology ; Ixodidae/growth &amp; development/*microbiology ; Larva/growth &amp; development/microbiology ; Lizards/*microbiology ; Male ; Nymph/growth &amp; development/microbiology ; Rickettsia/*isolation &amp; purification ; Tick Infestations/epidemiology/parasitology/*veterinary ; Tick-Borne Diseases/*transmission ; }, abstract = {During the investigations on ticks and tick-borne pathogens (TBP) range expansion in the Northern Apennines, we captured 107 Podarcis muralis lizards. Sixty-eight animals were infested by immature Ixodes ricinus, Haemaphysalis sulcata and H. punctata. Borrelia burgdorferi s.l. was detected in 3.7% of I. ricinus larvae and 8.0% of nymphs. Together with the species-specific B. lusitaniae, we identified B. garinii, B. afzelii and B. valaisiana. Rickettsia spp. (18.1% larvae, 12.0% nymphs), namely R. monacensis, R. helvetica and R. hoogstraalii, were also found in I. ricinus. R. hoogstraalii was detected in H. sulcata nymphs as well, while the two H. punctata did not harbour any bacteria. One out of 16 lizard tail tissues was positive to R. helvetica. Our results support the hypothesis that lizards are involved in the epidemiological cycles of TBP. The heterogeneity of B. burgdorferi genospecies mirrors previous findings in questing ticks in the area, and their finding in attached I. ricinus larvae suggests that lizards may contribute to the maintenance of different genospecies. The rickettsiae are new findings in the study area, and R. helvetica infection in a tail tissue indicates a systemic infection. R. hoogstraalii is reported for the first time in I. ricinus ticks. Lizards seem to favour the bacterial exchange among different tick species, with possible public health consequences.}, }
@article {pmid28540040, year = {2017}, author = {Pinzon, EH and Sierra, DA and Suarez, MO and Orduz, S and Florez, AM}, title = {DNA secondary structure formation by DNA shuffling of the conserved domains of the Cry protein of Bacillus thuringiensis.}, journal = {BMC biophysics}, volume = {10}, number = {}, pages = {4}, pmid = {28540040}, issn = {2046-1682}, abstract = {BACKGROUND: The Cry toxins, or δ-endotoxins, are a diverse group of proteins produced by Bacillus thuringiensis. While DNA secondary structures are biologically relevant, it is unknown if such structures are formed in regions encoding conserved domains of Cry toxins under shuffling conditions. We analyzed 5 holotypes that encode Cry toxins and that grouped into 4 clusters according to their phylogenetic closeness. The mean number of DNA secondary structures that formed and the mean Gibbs free energy [Formula: see text] were determined by an in silico analysis using different experimental DNA shuffling scenarios. In terms of spontaneity, shuffling efficiency was directly proportional to the formation of secondary structures but inversely proportional to ∆G.<br><br>RESULTS: The results showed a shared thermodynamic pattern for each cluster and relationships among sequences that are phylogenetically close at the protein level. The regions of the cry11Aa, Ba and Bb genes that encode domain I showed more spontaneity and thus a greater tendency to form secondary structures (<&#x2206;G). In the region of domain III; this tendency was lower (>&#x2206;G) in the cry11Ba and Bb genes. Proteins that are phylogenetically closer to Cry11Ba and Cry11Bb, such as Cry2Aa and Cry18Aa, maintained the same thermodynamic pattern. More distant proteins, such as Cry1Aa, Cry1Ab, Cry30Aa and Cry30Ca, featured different thermodynamic patterns in their DNA.<br><br>CONCLUSION: These results suggest the presence of thermodynamic variations associated to the formation of secondary structures and an evolutionary relationship with regions that encode highly conserved domains in Cry proteins. The findings of this study may have a role in the in silico design of cry gene assembly by DNA shuffling techniques.}, }
@article {pmid28539820, year = {2017}, author = {Mauricio, MD and Serna, E and Fernández-Murga, ML and Portero, J and Aldasoro, M and Valles, SL and Sanz, Y and Vila, JM}, title = {Bifidobacterium pseudocatenulatum CECT 7765 supplementation restores altered vascular function in an experimental model of obese mice.}, journal = {International journal of medical sciences}, volume = {14}, number = {5}, pages = {444-451}, pmid = {28539820}, issn = {1449-1907}, mesh = {Animals ; Bifidobacterium pseudocatenulatum/*chemistry ; Diet, High-Fat/adverse effects ; Dietary Supplements ; Gene Expression Regulation/drug effects ; Humans ; Mice ; Mice, Obese ; Nitric Oxide/metabolism ; Nitric Oxide Synthase Type III/*genetics ; Nitroprusside/administration &amp; dosage ; Obesity/*diet therapy/genetics/pathology ; Probiotics/*administration &amp; dosage/chemistry ; Vascular Remodeling/drug effects ; }, abstract = {Aims.Bifidobacterium pseudocatenulatum CECT 7765 improves metabolic and immunological altered functions in high fat fed mice, however little is known about the effects of potential probiotics on vascular reactivity. The aim of the present study was to investigate the effects of a potential probiotic strain, Bifidobacterium pseudocatenulatum CECT 7765, on vascular response in obese mice. Methods. Aorta samples were obtained from mice, which were divided into three groups: a control group, receiving a standard diet; an obese group, receiving a high-fat diet; and an obese group receiving high-fat diet and a daily dose of B. pseudocatenulatum CECT 7765 by oral gavage. Aortic rings were suspended in organ baths for isometric recording of tension. mRNA expression of eNOS was evaluated by real-time polymerase chain reaction. Results. Contractions induced by KCl, noradrenaline and thromboxane analogue were 33%, 30% and 45% lower respectively in aortic rings from obese mice. Bifidobacteria administration reversed this effect. eNOS inhibition increased the response to noradrenaline in the three groups with a significant lower magnitude in aortic rings from obese mice receiving bifidobacteria supplement. Acetylcholine caused a greater vasodilation in aorta from obese group (46±3% for control and 69±4% for obese group; p<0.05) and bifidobacteria reversed it (57±5%). Response to sodium nitroprusside was displaced 2.9 times to the left in a parallel manner in obese group. Relaxation to sodium nitroprusside remained unchanged in the bifidobacteria fed group. There was about five-fold decreased mRNA expression of eNOS in aortic segments from the group receiving bifidobacteria. Conclusion.Bifidobacterium pseudocatenulatum CECT 7765 restores the obesity-induced altered vascular function mainly by reducing nitric oxide release.}, }
@article {pmid28536858, year = {2017}, author = {Williams, MR and Stedtfeld, RD and Stedtfeld, TM and Tiedje, JM and Hashsham, SA}, title = {Quantification of microRNAs directly from body fluids using a base-stacking isothermal amplification method in a point-of-care device.}, journal = {Biomedical microdevices}, volume = {19}, number = {3}, pages = {45}, pmid = {28536858}, issn = {1572-8781}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Blood Chemical Analysis ; Body Fluids/*chemistry ; Feces/chemistry ; Limit of Detection ; Mice ; MicroRNAs/*antagonists &amp; inhibitors/blood/chemistry/*genetics ; Nucleic Acid Amplification Techniques/*instrumentation ; *Point-of-Care Systems ; }, abstract = {MicroRNAs have been proposed to be a class of biomarkers of disease as expression levels are significantly altered in various tissues and body fluids when compared to healthy controls. As such, the detection and quantification of microRNAs is imperative. While many methods have been established for quantification of microRNAs, they typically rely on time consuming handling such as RNA extraction, purification, or ligation. Here we describe a novel method for quantification of microRNAs using direct amplification in body fluids without upstream sample preparation. Tested with a point-of-care device (termed Gene-Z), the presence of microRNA promotes base-stacking hybridization, and subsequent amplification between two universal strands. The base-stacking approach, which was achieved in <60 min, provided a sensitivity of 1.4 fmol per reaction. Tested in various percentages of whole blood, plasma, and faeces, precision (coefficient of variation = 2.6%) was maintained and comparable to amplification in pristine samples. Overall, the developed method represents a significant step towards rapid, one-step detection of microRNAs.}, }
@article {pmid28536564, year = {2017}, author = {Alvarenga, DO and Fiore, MF and Varani, AM}, title = {A Metagenomic Approach to Cyanobacterial Genomics.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {809}, pmid = {28536564}, issn = {1664-302X}, abstract = {Cyanobacteria, or oxyphotobacteria, are primary producers that establish ecological interactions with a wide variety of organisms. Although their associations with eukaryotes have received most attention, interactions with bacterial and archaeal symbionts have also been occurring for billions of years. Due to these associations, obtaining axenic cultures of cyanobacteria is usually difficult, and most isolation efforts result in unicyanobacterial cultures containing a number of associated microbes, hence composing a microbial consortium. With rising numbers of cyanobacterial blooms due to climate change, demand for genomic evaluations of these microorganisms is increasing. However, standard genomic techniques call for the sequencing of axenic cultures, an approach that not only adds months or even years for culture purification, but also appears to be impossible for some cyanobacteria, which is reflected in the relatively low number of publicly available genomic sequences of this phylum. Under the framework of metagenomics, on the other hand, cumbersome techniques for achieving axenic growth can be circumvented and individual genomes can be successfully obtained from microbial consortia. This review focuses on approaches for the genomic and metagenomic assessment of non-axenic cyanobacterial cultures that bypass requirements for axenity. These methods enable researchers to achieve faster and less costly genomic characterizations of cyanobacterial strains and raise additional information about their associated microorganisms. While non-axenic cultures may have been previously frowned upon in cyanobacteriology, latest advancements in metagenomics have provided new possibilities for in vitro studies of oxyphotobacteria, renewing the value of microbial consortia as a reliable and functional resource for the rapid assessment of bloom-forming cyanobacteria.}, }
@article {pmid28534616, year = {2017}, author = {Pikaar, I and Matassa, S and Rabaey, K and Bodirsky, BL and Popp, A and Herrero, M and Verstraete, W}, title = {Microbes and the Next Nitrogen Revolution.}, journal = {Environmental science &amp; technology}, volume = {51}, number = {13}, pages = {7297-7303}, doi = {10.1021/acs.est.7b00916}, pmid = {28534616}, issn = {1520-5851}, mesh = {*Agriculture ; Animal Feed ; Animals ; *Bacteria ; *Bioreactors ; Crops, Agricultural ; Environmental Pollution ; *Food Supply ; Humans ; *Nitrogen ; }, abstract = {The Haber Bosch process is among the greatest inventions of the 20th century. It provided agriculture with reactive nitrogen and ultimately mankind with nourishment for a population of 7 billion people. However, the present agricultural practice of growing crops for animal production and human food constitutes a major threat to the sustainability of the planet in terms of reactive nitrogen pollution. In view of the shortage of directly feasible and cost-effective measures to avoid these planetary nitrogen burdens and the necessity to remediate this problem, we foresee the absolute need for and expect a revolution in the use of microbes as a source of protein. Bypassing land-based agriculture through direct use of Haber Bosch produced nitrogen for reactor-based production of microbial protein can be an inspiring concept for the production of high quality animal feed and even straightforward supply of proteinaceous products for human food, without significant nitrogen losses to the environment and without the need for genetic engineering to safeguard feed and food supply for the generations to come.}, }
@article {pmid28534089, year = {2017}, author = {Hubert, J and Erban, T and Kopecky, J and Sopko, B and Nesvorna, M and Lichovnikova, M and Schicht, S and Strube, C and Sparagano, O}, title = {Comparison of Microbiomes between Red Poultry Mite Populations (Dermanyssus gallinae): Predominance of Bartonella-like Bacteria.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {947-960}, pmid = {28534089}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bartonella/classification/genetics/isolation &amp; purification ; Czech Republic ; DNA Barcoding, Taxonomic ; *Microbiota ; Mites/growth &amp; development/*microbiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {Blood feeding red poultry mites (RPM) serve as vectors of pathogenic bacteria and viruses among vertebrate hosts including wild birds, poultry hens, mammals, and humans. The microbiome of RPM has not yet been studied by high-throughput sequencing. RPM eggs, larvae, and engorged adult/nymph samples obtained in four poultry houses in Czechia were used for microbiome analyses by Illumina amplicon sequencing of the 16S ribosomal RNA (rRNA) gene V4 region. A laboratory RPM population was used as positive control for transcriptome analysis by pyrosequencing with identification of sequences originating from bacteria. The samples of engorged adult/nymph stages had 100-fold more copies of 16S rRNA gene copies than the samples of eggs and larvae. The microbiome composition showed differences among the four poultry houses and among observed developmental stadia. In the adults' microbiome 10 OTUs comprised 90 to 99% of all sequences. Bartonella-like bacteria covered between 30 and 70% of sequences in RPM microbiome and 25% bacterial sequences in transcriptome. The phylogenetic analyses of 16S rRNA gene sequences revealed two distinct groups of Bartonella-like bacteria forming sister groups: (i) symbionts of ants; (ii) Bartonella genus. Cardinium, Wolbachia, and Rickettsiella sp. were found in the microbiomes of all tested stadia, while Spiroplasma eriocheiris and Wolbachia were identified in the laboratory RPM transcriptome. The microbiomes from eggs, larvae, and engorged adults/nymphs differed. Bartonella-like symbionts were found in all stadia and sampling sites. Bartonella-like bacteria was the most diversified group within the RPM microbiome. The presence of identified putative pathogenic bacteria is relevant with respect to human and animal health issues while the identification of symbiontic bacteria can lead to new control methods targeting them to destabilize the arthropod host.}, }
@article {pmid28528399, year = {2017}, author = {Castillo, JD and Vivanco, JM and Manter, DK}, title = {Bacterial Microbiome and Nematode Occurrence in Different Potato Agricultural Soils.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {888-900}, pmid = {28528399}, issn = {1432-184X}, mesh = {*Agriculture ; Animal Distribution ; Animals ; *Bacteria/classification/genetics ; Colorado ; *Microbiota ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Soil/*parasitology ; *Soil Microbiology ; Solanum tuberosum/growth &amp; development ; Tylenchoidea/*physiology ; }, abstract = {Pratylenchus neglectus and Meloidogyne chitwoodi are the main plant-parasitic nematodes in potato crops of the San Luis Valley, Colorado. Bacterial microbiome (16S rRNA copies per gram of soil) and nematode communities (nematodes per 200 g of soil) from five different potato farms were analyzed to determine negative and positive correlations between any bacterial genus and P. neglectus and M. chitwoodi. Farms showed differences in bacterial communities, percentage of bacterivorous and fungivorous nematodes, and numbers of P. neglectus and M. chitwoodi. The farm with the lowest population of P. neglectus and M. chitwoodi had higher abundances of the bacterial genera Bacillus spp., Arthrobacter spp., and Lysobacter spp., and the soil nematode community was composed of more than 30% of fungivorous nematodes. In contrast, the farm with higher numbers of P. neglectus and M. chitwoodi had a lower abundance of the abovementioned bacterial genera, higher abundance of Burkholderia spp., and less than 25% of fungivorous nematodes. The α-Proteobacteria Rhodoplanes, Phenylobacterium, and Kaistobacter positively correlated with M. chitwoodi, and the Bacteroidia and γ-Proteobacteria positively correlated with P. neglectus. Our results, based largely on co-occurrence analyses, suggest that the abundance of Bacillus spp., Arthrobacter spp., and Lysobacter spp. in Colorado potato soils is negatively correlated with P. neglectus and M. chitwoodi abundance. Further studies will isolate and identify bacterial strains of these genera, and evaluate their nematode-antagonistic activity.}, }
@article {pmid28527390, year = {2017}, author = {Samhan, FA and Stedtfeld, TM and Waseem, H and Williams, MR and Stedtfeld, RD and Hashsham, SA}, title = {On-filter direct amplification of Legionella pneumophila for rapid assessment of its abundance and viability.}, journal = {Water research}, volume = {121}, number = {}, pages = {162-170}, pmid = {28527390}, issn = {1879-2448}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, mesh = {DNA Primers ; Legionella ; Legionella pneumophila/*genetics ; *Nucleic Acid Amplification Techniques ; RNA, Ribosomal, 16S ; *Real-Time Polymerase Chain Reaction ; Sensitivity and Specificity ; *Water Microbiology ; }, abstract = {Guidelines and regulations to control Legionella pneumophila in cooling water systems of large buildings are evolving due to the increasing number of outbreaks. Rapid, on-site, simple, and sensitive quantification methods that are also able to assess viability may be extremely useful in monitoring and control. Culture-based methods for measuring L. pneumophila may take 4-10 days and qPCR-based methods are also slow, requiring at least a day from sample to result, albeit mainly due to the need for sample transport to a centralized laboratory. This study reports a rapid isothermal amplification method for L. pneumophila concentration and detection with live/dead differentiation under field conditions. Using an on-filter direct amplification (i.e., amplification of cells without DNA extraction and purification) approach with propidium monoazide (PMA), and a real time isothermal amplification platform (Gene-Z), L. pneumophila could be detected in 1-2 h at ∼1 cfu/100 ml of tap water. Signature sequences from 16S rRNA and cadA genes were used as genetic markers for L. pneumophila and loop-mediated isothermal amplification (LAMP) primers were designed using Primer Explorer V4. Result were also compared with direct amplification of cells spiked into distilled, tap, and cooling water samples as well as extracted DNA by qPCR. This method may be useful to managers of cooling water systems in large buildings for rapid detection of L. pneumophila. The overall approach of on-site sample concentration, on-filter amplification, and live/dead differentiation may be extended to other organisms where analytical sensitivity and speed are equally important.}, }
@article {pmid28526791, year = {2017}, author = {Dorosky, RJ and Yu, JM and Pierson, LS and Pierson, EA}, title = {Pseudomonas chlororaphis Produces Two Distinct R-Tailocins That Contribute to Bacterial Competition in Biofilms and on Roots.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {15}, pages = {}, pmid = {28526791}, issn = {1098-5336}, mesh = {Antibiosis ; Bacterial Proteins/genetics/metabolism ; Bacteriocins/*metabolism ; *Biofilms ; Plant Roots/*microbiology ; Pseudomonas/physiology ; Pseudomonas chlororaphis/genetics/*physiology ; Rhizosphere ; Soil Microbiology ; }, abstract = {R-type tailocins are high-molecular-weight bacteriocins that resemble bacteriophage tails and are encoded within the genomes of many Pseudomonas species. In this study, analysis of the P. chlororaphis 30-84 R-tailocin gene cluster revealed that it contains the structural components to produce two R-tailocins of different ancestral origins. Two distinct R-tailocin populations differing in length were observed in UV-induced lysates of P. chlororaphis 30-84 via transmission electron microscopy. Mutants defective in the production of one or both R-tailocins demonstrated that the killing spectrum of each tailocin is limited to Pseudomonas species. The spectra of pseudomonads killed by the two R-tailocins differed, although a few Pseudomonas species were either killed by or insusceptible to both tailocins. Tailocin release was disrupted by deletion of the holin gene within the tailocin gene cluster, demonstrating that the lysis cassette is required for the release of both R-tailocins. The loss of functional tailocin production reduced the ability of P. chlororaphis 30-84 to compete with an R-tailocin-sensitive strain within biofilms and rhizosphere communities. Our study demonstrates that Pseudomonas species can produce more than one functional R-tailocin particle sharing the same lysis cassette but differing in their killing spectra. This study provides evidence for the role of R-tailocins as determinants of bacterial competition among plant-associated Pseudomonas in biofilms and the rhizosphere.IMPORTANCE Recent studies have identified R-tailocin gene clusters potentially encoding more than one R-tailocin within the genomes of plant-associated Pseudomonas but have not demonstrated that more than one particle is produced or the ecological significance of the production of multiple R-tailocins. This study demonstrates for the first time that Pseudomonas strains can produce two distinct R-tailocins with different killing spectra, both of which contribute to bacterial competition between rhizosphere-associated bacteria. These results provide new insight into the previously uncharacterized role of R-tailocin production by plant-associated Pseudomonas species in bacterial population dynamics within surface-attached biofilms and on roots.}, }
@article {pmid28524866, year = {2017}, author = {Vigneron, A and Alsop, EB and Lomans, BP and Kyrpides, NC and Head, IM and Tsesmetzis, N}, title = {Succession in the petroleum reservoir microbiome through an oil field production lifecycle.}, journal = {The ISME journal}, volume = {11}, number = {9}, pages = {2141-2154}, pmid = {28524866}, issn = {1751-7370}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Ecosystem ; *Microbiota ; Nitrates/metabolism ; North Sea ; Oil and Gas Fields/*microbiology ; Petroleum/metabolism ; Seawater/microbiology ; Sulfides/metabolism ; }, abstract = {Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth's surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron acceptors, donors and exogenous microbes during oil exploration and production. Despite the fundamental and practical significance of this perturbation, there has never been a systematic evaluation of the ecological changes that occur over the production lifetime of an active offshore petroleum production system. Analysis of the entire Halfdan oil field in the North Sea (32 producing wells in production for 1-15 years) using quantitative PCR, multigenic sequencing, comparative metagenomic and genomic bins reconstruction revealed systematic shifts in microbial community composition and metabolic potential, as well as changing ecological strategies in response to anthropogenic perturbation of the oil field ecosystem, related to length of time in production. The microbial communities were initially dominated by slow growing anaerobes such as members of the Thermotogales and Clostridiales adapted to living on hydrocarbons and complex refractory organic matter. However, as seawater and nitrate injection (used for secondary oil production) delivered oxidants, the microbial community composition progressively changed to fast growing opportunists such as members of the Deferribacteres, Delta-, Epsilon- and Gammaproteobacteria, with energetically more favorable metabolism (for example, nitrate reduction, H2S, sulfide and sulfur oxidation). This perturbation has profound consequences for understanding the microbial ecology of the system and is of considerable practical importance as it promotes detrimental processes such as reservoir souring and metal corrosion. These findings provide a new conceptual framework for understanding the petroleum reservoir biosphere and have consequences for developing strategies to manage microbiological problems in the oil industry.}, }
@article {pmid28523377, year = {2017}, author = {Borda-Molina, D and Montaña, JS and Zambrano, MM and Baena, S}, title = {Mining lipolytic enzymes in community DNA from high Andean soils using a targeted approach.}, journal = {Antonie van Leeuwenhoek}, volume = {110}, number = {8}, pages = {1035-1051}, doi = {10.1007/s10482-017-0877-8}, pmid = {28523377}, issn = {1572-9699}, mesh = {Amino Acid Sequence ; Bacteria/enzymology ; DNA ; Lipase/*metabolism ; Phylogeny ; Sequence Alignment ; Soil ; *Soil Microbiology ; Substrate Specificity ; }, abstract = {Microbial enrichments cultures are a useful strategy to speed up the search for enzymes that can be employed in industrial processes. Lipases have gained special attention because they show unique properties such as: broad substrate specificity, enantio- and regio-selectivity and stability in organic solvents. A major goal is to identify novel lipolytic enzymes from microorganisms living in cold extreme environments such as high Andean soils, of relevance to our study being their capability be used in industrial processes. Paramo and glacier soils from the Nevados National Park in Colombia were sampled and microbial communities enriched through a fed-batch fermentation using olive oil as an inductor substrate. After 15 days of enrichment under aerobic conditions, total DNA was extracted. Subsequently, metagenomic libraries were constructed in the cosmid vector pWEB-TNC™. After functional screening, twenty and eighteen lipolytic clones were obtained from Paramo and Glacier soil enrichments, respectively. Based on lipid hydrolysis halo dimensions, the clone (Gla1) from a glacier enrichment was selected. A gene related to lipolytic activity was subcloned to evaluate enzyme properties. Phylogenetic analysis of the identified gene showed that the encoded lipase belongs to the family GDSL from a Ralstonia-like species. Interestingly, the secreted enzyme exhibited stability at high temperature and alkaline conditions, specifically the preferred conditions at 80 °C and pH 9.0. Thus, with the identification of an enzyme with non-expected properties, in this study is shown the potential of extreme cold environments to be explored for new catalytic molecules, using current molecular biology techniques, with applications in industrial processes, which demand stability under harsh conditions.}, }
@article {pmid28523076, year = {2017}, author = {Speda, J and Jonsson, BH and Carlsson, U and Karlsson, M}, title = {Metaproteomics-guided selection of targeted enzymes for bioprospecting of mixed microbial communities.}, journal = {Biotechnology for biofuels}, volume = {10}, number = {}, pages = {128}, pmid = {28523076}, issn = {1754-6834}, abstract = {BACKGROUND: Hitherto, the main goal of metaproteomic analyses has been to characterize the functional role of particular microorganisms in the microbial ecology of various microbial communities. Recently, it has been suggested that metaproteomics could be used for bioprospecting microbial communities to query for the most active enzymes to improve the selection process of industrially relevant enzymes. In the present study, to reduce the complexity of metaproteomic samples for targeted bioprospecting of novel enzymes, a microbial community capable of producing cellulases was maintained on a chemically defined medium in an enzyme suppressed metabolic steady state. From this state, it was possible to specifically and distinctively induce the desired cellulolytic activity. The extracellular fraction of the protein complement of the induced sample could thereby be purified and compared to a non-induced sample of the same community by differential gel electrophoresis to discriminate between constitutively expressed proteins and proteins upregulated in response to the inducing substance.<br><br>RESULTS: Using the applied approach, downstream analysis by mass spectrometry could be limited to only proteins recognized as upregulated in the cellulase-induced sample. Of 39 selected proteins, the majority were found to be linked to the need to degrade, take up, and metabolize cellulose. In addition, 28 (72%) of the proteins were non-cytosolic and 17 (44%) were annotated as carbohydrate-active enzymes. The results demonstrated both the applicability of the proposed approach for identifying extracellular proteins and guiding the selection of proteins toward those specifically upregulated and targeted by the enzyme inducing substance. Further, because identification of interesting proteins was based on the regulation of enzyme expression in response to a need to hydrolyze and utilize a specific substance, other unexpected enzyme activities were able to be identified.<br><br>CONCLUSIONS: The described approach created the conditions necessary to be able to select relevant extracellular enzymes that were extracted from the enzyme-induced microbial community. However, for the purpose of bioprospecting for enzymes to clone, produce, and characterize for practical applications, it was concluded that identification against public databases was not sufficient to identify the correct gene or protein sequence for cloning of the identified novel enzymes.}, }
@article {pmid28522975, year = {2017}, author = {Šket, R and Treichel, N and Debevec, T and Eiken, O and Mekjavic, I and Schloter, M and Vital, M and Chandler, J and Tiedje, JM and Murovec, B and Prevoršek, Z and Stres, B}, title = {Hypoxia and Inactivity Related Physiological Changes (Constipation, Inflammation) Are Not Reflected at the Level of Gut Metabolites and Butyrate Producing Microbial Community: The PlanHab Study.}, journal = {Frontiers in physiology}, volume = {8}, number = {}, pages = {250}, pmid = {28522975}, issn = {1664-042X}, abstract = {We explored the assembly of intestinal microbiota in healthy male participants during the run-in (5 day) and experimental phases [21-day normoxic bed rest (NBR), hypoxic bedrest (HBR)], and hypoxic ambulation (HAmb) in a strictly controlled laboratory environment, balanced fluid, and dietary intakes, controlled circadian rhythm, microbial ambiental burden, and 24/7 medical surveillance. The fraction of inspired O2 (FiO2) and partial pressure of inspired O2 (PiO2) were 0.209 and 133.1 ± 0.3 mmHg for NBR and 0.141 ± 0.004 and 90.0 ± 0.4 mmHg for both hypoxic variants (HBR and HAmb; ~4,000 m simulated altitude), respectively. A number of parameters linked to intestinal transit spanning Bristol Stool Scale, defecation rates, zonulin, α1-antitrypsin, eosinophil derived neurotoxin, bile acids, reducing sugars, short chain fatty acids, total soluble organic carbon, water content, diet composition, and food intake were measured (167 variables). The abundance, structure, and diversity of butyrate producing microbial community were assessed using the two primary bacterial butyrate synthesis pathways, butyryl-CoA: acetate CoA-transferase (but) and butyrate kinase (buk) genes. Inactivity negatively affected fecal consistency and in combination with hypoxia aggravated the state of gut inflammation (p < 0.05). In contrast, gut permeability, various metabolic markers, the structure, diversity, and abundance of butyrate producing microbial community were not significantly affected. Rearrangements in the butyrate producing microbial community structure were explained by experimental setup (13.4%), experimentally structured metabolites (12.8%), and gut metabolite-immunological markers (11.9%), with 61.9% remaining unexplained. Many of the measured parameters were found to be correlated and were hence omitted from further analyses. The observed progressive increase in two immunological intestinal markers suggested that the transition from healthy physiological state toward the developed symptoms of low magnitude obesity-related syndromes was primarily driven by the onset of inactivity (lack of exercise in NBR) that were exacerbated by systemic hypoxia (HBR) and significantly alleviated by exercise, despite hypoxia (HAmb). Butyrate producing community in colon exhibited apparent resilience toward short-term modifications in host exercise or hypoxia. Progressive constipation (decreased intestinal motility) and increased local inflammation marker suggest that changes in microbial colonization and metabolism were taking place at the location of small intestine.}, }
@article {pmid28521336, year = {2017}, author = {van der Meij, A and Worsley, SF and Hutchings, MI and van Wezel, GP}, title = {Chemical ecology of antibiotic production by actinomycetes.}, journal = {FEMS microbiology reviews}, volume = {41}, number = {3}, pages = {392-416}, doi = {10.1093/femsre/fux005}, pmid = {28521336}, issn = {1574-6976}, mesh = {Actinomyces/*metabolism ; Animals ; Anti-Bacterial Agents/*biosynthesis ; Antibiosis/genetics/*physiology ; Biological Products/metabolism ; Coculture Techniques ; Fungi/*metabolism ; Insecta/microbiology ; Multigene Family/genetics ; Plant Roots/metabolism/microbiology ; Plants/metabolism/microbiology ; Streptomyces/*metabolism ; Symbiosis/*physiology ; }, abstract = {Actinomycetes are a diverse family of filamentous bacteria that produce a plethora of natural products relevant for agriculture, biotechnology and medicine, including the majority of the antibiotics we use in the clinic. Rather than as free-living bacteria, many actinomycetes have evolved to live in symbiosis with among others plants, fungi, insects and sponges. As a common theme, these organisms profit from the natural products and enzymes produced by the actinomycetes, for example, for protection against pathogenic microbes, for growth promotion or for the degradation of complex natural polymers such as lignocellulose. At the same time, the actinomycetes benefit from the resources of the hosts they interact with. Evidence is accumulating that these interactions control the expression of biosynthetic gene clusters and have played a major role in the evolution of the high chemical diversity of actinomycete-produced secondary metabolites. Many of the biosynthetic gene clusters for antibiotics are poorly expressed under laboratory conditions, but they are likely expressed in response to host-specific demands. Here, we review the environmental triggers and cues that control natural product formation by actinomycetes and provide pointers as to how these insights may be harnessed for drug discovery.}, }
@article {pmid28518116, year = {2017}, author = {Comstock, WJ and Huh, E and Weekes, R and Watson, C and Xu, T and Dorrestein, PC and Quinn, RA}, title = {The WinCF Model - An Inexpensive and Tractable Microcosm of a Mucus Plugged Bronchiole to Study the Microbiology of Lung Infections.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {123}, pages = {}, doi = {10.3791/55532}, pmid = {28518116}, issn = {1940-087X}, mesh = {Bronchioles/*microbiology ; Cystic Fibrosis/microbiology ; Humans ; Lung/microbiology ; *Models, Biological ; Mucus/microbiology ; Respiratory Tract Infections/*microbiology ; Sputum/microbiology ; }, abstract = {Many chronic airway diseases result in mucus plugging of the airways. Lungs of an individual with cystic fibrosis are an exemplary case where their mucus-plugged bronchioles create a favorable habitat for microbial colonization. Various pathogens thrive in this environment interacting with each other and driving many of the symptoms associated with CF disease. Like any microbial community, the chemical conditions of their habitat have a significant impact on the community structure and dynamics. For example, different microorganisms thrive in differing levels of oxygen or other solute concentrations. This is also true in the CF lung, where oxygen concentrations are believed to drive community physiology and structure. The methods described here are designed to mimic the lung environment and grow pathogens in a manner more similar to that from which they cause disease. Manipulation of the chemical surroundings of these microbes is then used to study how the chemistry of lung infections governs its microbial ecology. The method, called the WinCF system, is based on artificial sputum medium and narrow capillary tubes meant to provide an oxygen gradient similar to that which exists in mucus-plugged bronchioles. Manipulating chemical conditions, such as the media pH of the sputum or antibiotics pressure, allows for visualization of the microbiological differences in those samples using colored indicators, watching for gas or biofilm production, or extracting and sequencing the nucleic acid contents of each sample.}, }
@article {pmid28515083, year = {2017}, author = {Scoma, A and Yakimov, MM and Daffonchio, D and Boon, N}, title = {Self-healing capacity of deep-sea ecosystems affected by petroleum hydrocarbons: Understanding microbial oil degradation at hydrocarbon seeps is key to sustainable bioremediation protocols.}, journal = {EMBO reports}, volume = {18}, number = {6}, pages = {868-872}, pmid = {28515083}, issn = {1469-3178}, mesh = {Biodegradation, Environmental ; *Ecosystem ; Hydrocarbons/*chemistry ; Petroleum ; }, abstract = {A rich microbiota in the deep‐sea oceans has evolved to live off petroleum from natural oil seeps. Understanding their ecology and biology could inform measures for sustainable bioremediation of artificial oil spills. [Image: see text]}, }
@article {pmid28512033, year = {2017}, author = {Moya-Pérez, A and Perez-Villalba, A and Benítez-Páez, A and Campillo, I and Sanz, Y}, title = {Bifidobacterium CECT 7765 modulates early stress-induced immune, neuroendocrine and behavioral alterations in mice.}, journal = {Brain, behavior, and immunity}, volume = {65}, number = {}, pages = {43-56}, doi = {10.1016/j.bbi.2017.05.011}, pmid = {28512033}, issn = {1090-2139}, mesh = {Animals ; Bifidobacterium/metabolism/*physiology ; Central Nervous System/microbiology/physiology ; Cytokines/blood ; Diet, High-Fat ; Dietary Supplements ; Hypothalamo-Hypophyseal System/metabolism ; Inflammation/immunology ; Intestines/microbiology ; Male ; Maternal Deprivation ; Mice ; Mice, Inbred C57BL ; Microbiota/physiology ; Neurosecretory Systems ; Neurotransmitter Agents/metabolism ; Obesity/immunology ; Pituitary-Adrenal System/metabolism ; Probiotics ; RNA, Ribosomal, 16S/genetics ; Stress, Physiological/*drug effects/*physiology ; }, abstract = {Emerging evidence suggests that there is a window of opportunity within the early developmental period, when microbiota-based interventions could play a major role in modulating the gut-brain axis and, thereby, in preventing mood disorders. This study aims at evaluating the effects and mode of action of Bifidobacterium pseudocatenulatum CECT 7765 in a murine model of chronic stress induced by maternal separation (MS). C57Bl/6J male breast-fed pups were divided into four groups, which were subjected or not to MS and supplemented with placebo or B. pseudocatenulatum CECT7765 until postnatal period (P) 21 and followed-up until P41. Behavioral tests were performed and neuroendocrine parameters were analyzed including corticosterone, cytokine/chemokine concentrations and neurotransmitters. Microbiota was also analyzed in stools by 16S rRNA gene sequencing. B. pseudocatenulatum CECT 7765 administration attenuated some aspects of the excessive MS-induced stress response of the hypothalamic-pituitary-adrenal (HPA) axis, particularly corticosterone production at baseline and in response to subsequent acute stress in adulthood. B. pseudocatenulatum CECT 7765 also down-regulated MS-induced intestinal inflammation (reducing interferon gamma [IFN-γ]) and intestinal hypercatecholaminergic activity (reducing dopamine [DA] and adrenaline [A] concentrations) at P21. These effects have a long-term impact on the central nervous system (CNS) of adult mice since MS mice fed B. pseudocatenulatum CECT 7765 showed lower anxiety levels than placebo-fed MS mice, as well as normal neurotransmitter levels in the hypothalamus. The anti-inflammatory effect of B. pseudocatenulatum CECT 7765 seemed to be related to an improvement in glucocorticoid sensitivity in mesenteric lymph node immunocompetent cells at P21. The administration of B. pseudocatenulatum CECT 7765 to MS animals also reversed intestinal dysbiosis affecting the proportions of ten Operational Taxonomic Units (OTUs) at P21, which could partly explain the restoration of immune, neuroendocrine and behavioral alterations caused by stress in early and later life. In summary, we show that B. pseudocatenulatum CECT 7765 is able to beneficially modulate the consequences of chronic stress on the HPA response produced by MS during infancy with long-lasting effects in adulthood, via modulation of the intestinal neurotransmitter and cytokine network with short and long-term consequences in brain biochemistry and behavior.}, }
@article {pmid28511936, year = {2017}, author = {Mapelli, F and Scoma, A and Michoud, G and Aulenta, F and Boon, N and Borin, S and Kalogerakis, N and Daffonchio, D}, title = {Biotechnologies for Marine Oil Spill Cleanup: Indissoluble Ties with Microorganisms.}, journal = {Trends in biotechnology}, volume = {35}, number = {9}, pages = {860-870}, doi = {10.1016/j.tibtech.2017.04.003}, pmid = {28511936}, issn = {1879-3096}, mesh = {Biodegradation, Environmental ; Biotechnology/*methods ; *Petroleum Pollution ; Seawater/*microbiology ; *Water Microbiology ; Water Pollutants, Chemical/*metabolism ; Water Purification/*methods ; }, abstract = {The ubiquitous exploitation of petroleum hydrocarbons (HCs) has been accompanied by accidental spills and chronic pollution in marine ecosystems, including the deep ocean. Physicochemical technologies are available for oil spill cleanup, but HCs must ultimately be mineralized by microorganisms. How environmental factors drive the assembly and activity of HC-degrading microbial communities remains unknown, limiting our capacity to integrate microorganism-based cleanup strategies with current physicochemical remediation technologies. In this review, we summarize recent findings about microbial physiology, metabolism and ecology and describe how microbes can be exploited to create improved biotechnological solutions to clean up marine surface and deep waters, sediments and beaches.}, }
@article {pmid28511559, year = {2017}, author = {Houldcroft, CJ and Ramond, JB and Rifkin, RF and Underdown, SJ}, title = {Migrating microbes: what pathogens can tell us about population movements and human evolution.}, journal = {Annals of human biology}, volume = {44}, number = {5}, pages = {397-407}, doi = {10.1080/03014460.2017.1325515}, pmid = {28511559}, issn = {1464-5033}, mesh = {Africa South of the Sahara ; Animal Distribution ; Animals ; *Archaeology ; *Biological Evolution ; Communicable Diseases/epidemiology ; *Human Migration ; Humans ; }, abstract = {BACKGROUND: The biology of human migration can be observed from the co-evolutionary relationship with infectious diseases. While many pathogens are brief, unpleasant visitors to human bodies, others have the ability to become life-long human passengers. The story of a pathogen's genetic code may, therefore, provide insight into the history of its human host. The evolution and distribution of disease in Africa is of particular interest, because of the deep history of human evolution in Africa, the presence of a variety of non-human primates, and tropical reservoirs of emerging infectious diseases.<br><br>METHODS: This study explores which pathogens leave traces in the archaeological record, and whether there are realistic prospects that these pathogens can be recovered from sub-Saharan African archaeological contexts.<br><br>RESULTS: Three stories are then presented of germs on a journey. The first is the story of HIV's spread on the back of colonialism and the railway networks over the last 150&#x2009;years. The second involves the spread of Schistosoma mansoni, a parasite which shares its history with the trans-Atlantic slave trade and the origins of fresh-water fishing. Finally, we discuss the tantalising hints of hominin migration and interaction found in the genome of human herpes simplex virus 2.<br><br>CONCLUSIONS: Evidence from modern African pathogen genomes can provide data on human behaviour and migration in deep time and contribute to the improvement of human quality-of-life and longevity.}, }
@article {pmid28509909, year = {2017}, author = {Lenski, RE}, title = {Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations.}, journal = {The ISME journal}, volume = {11}, number = {10}, pages = {2181-2194}, pmid = {28509909}, issn = {1751-7370}, mesh = {Acclimatization ; Ecotype ; Escherichia coli/genetics ; *Evolution, Molecular ; *Genome, Bacterial ; Mutation ; Selection, Genetic ; }, abstract = {Evolution is an on-going process, and it can be studied experimentally in organisms with rapid generations. My team has maintained 12 populations of Escherichia coli in a simple laboratory environment for >25 years and 60 000 generations. We have quantified the dynamics of adaptation by natural selection, seen some of the populations diverge into stably coexisting ecotypes, described changes in the bacteria's mutation rate, observed the new ability to exploit a previously untapped carbon source, characterized the dynamics of genome evolution and used parallel evolution to identify the genetic targets of selection. I discuss what the future might hold for this particular experiment, briefly highlight some other microbial evolution experiments and suggest how the fields of experimental evolution and microbial ecology might intersect going forward.}, }
@article {pmid28508926, year = {2017}, author = {Compte-Port, S and Subirats, J and Fillol, M and Sànchez-Melsió, A and Marcé, R and Rivas-Ruiz, P and Rosell-Melé, A and Borrego, CM}, title = {Abundance and Co-Distribution of Widespread Marine Archaeal Lineages in Surface Sediments of Freshwater Water Bodies across the Iberian Peninsula.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {776-787}, pmid = {28508926}, issn = {1432-184X}, mesh = {Aquatic Organisms/classification/genetics/physiology ; Archaea/classification/genetics/*physiology ; DNA, Archaeal/genetics ; Geologic Sediments/*microbiology ; Lakes/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spain ; }, abstract = {Archaea inhabiting marine and freshwater sediments have a relevant role in organic carbon mineralization, affecting carbon fluxes at a global scale. Despite current evidences suggesting that freshwater sediments largely contribute to this process, few large-scale surveys have been addressed to uncover archaeal diversity and abundance in freshwater sedimentary habitats. In this work, we quantified and high-throughput sequenced the archaeal 16S rRNA gene from surficial sediments collected in 21 inland waterbodies across the Iberian Peninsula differing in typology and trophic status. Whereas methanogenic groups were dominant in most of the studied systems, especially in organic-rich sediments, archaea affiliated to widespread marine lineages (the Bathyarchaeota and the Thermoplasmata) were also ubiquitous and particularly abundant in euxinic sediments. In these systems, Bathyarchaeota communities were dominated by subgroups Bathyarchaeota-6 (87.95 ± 12.71%) and Bathyarchaeota-15 (8.17 ± 9.2%) whereas communities of Thermoplasmata were mainly composed of members of the order Thermoplasmatales. Our results also indicate that Archaea accounted for a minor fraction of sedimentary prokaryotes despite remarkable exceptions in reservoirs and some stratified lakes. Copy numbers of archaeal and bathyarchaeotal 16S rRNA genes were significantly different when compared according to system type (i.e., lakes, ponds, and reservoirs), but no differences were obtained when compared according to their trophic status (from oligotrophy to eutrophy). Interestingly, we obtained significant correlations between the abundance of reads (Spearman r = 0.5, p = 0.021) and OTU richness (Spearman r = 0.677, p < 0.001) of Bathyarchaeota and Thermoplasmata across systems, reinforcing the hypothesis of a potential syntrophic interaction between members of both lineages.}, }
@article {pmid28507535, year = {2017}, author = {Connelly, S and Shin, SG and Dillon, RJ and Ijaz, UZ and Quince, C and Sloan, WT and Collins, G}, title = {Bioreactor Scalability: Laboratory-Scale Bioreactor Design Influences Performance, Ecology, and Community Physiology in Expanded Granular Sludge Bed Bioreactors.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {664}, pmid = {28507535}, issn = {1664-302X}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Studies investigating the feasibility of new, or improved, biotechnologies, such as wastewater treatment digesters, inevitably start with laboratory-scale trials. However, it is rarely determined whether laboratory-scale results reflect full-scale performance or microbial ecology. The Expanded Granular Sludge Bed (EGSB) bioreactor, which is a high-rate anaerobic digester configuration, was used as a model to address that knowledge gap in this study. Two laboratory-scale idealizations of the EGSB-a one-dimensional and a three- dimensional scale-down of a full-scale design-were built and operated in triplicate under near-identical conditions to a full-scale EGSB. The laboratory-scale bioreactors were seeded using biomass obtained from the full-scale bioreactor, and, spent water from the distillation of whisky from maize was applied as substrate at both scales. Over 70 days, bioreactor performance, microbial ecology, and microbial community physiology were monitored at various depths in the sludge-beds using 16S rRNA gene sequencing (V4 region), specific methanogenic activity (SMA) assays, and a range of physical and chemical monitoring methods. SMA assays indicated dominance of the hydrogenotrophic pathway at full-scale whilst a more balanced activity profile developed during the laboratory-scale trials. At each scale, Methanobacterium was the dominant methanogenic genus present. Bioreactor performance overall was better at laboratory-scale than full-scale. We observed that bioreactor design at laboratory-scale significantly influenced spatial distribution of microbial community physiology and taxonomy in the bioreactor sludge-bed, with 1-D bioreactor types promoting stratification of each. In the 1-D laboratory bioreactors, increased abundance of Firmicutes was associated with both granule position in the sludge bed and increased activity against acetate and ethanol as substrates. We further observed that stratification in the sludge-bed in 1-D laboratory-scale bioreactors was associated with increased richness in the underlying microbial community at species (OTU) level and improved overall performance.}, }
@article {pmid28506317, year = {2017}, author = {Khanna, S and Vazquez-Baeza, Y and González, A and Weiss, S and Schmidt, B and Muñiz-Pedrogo, DA and Rainey, JF and Kammer, P and Nelson, H and Sadowsky, M and Khoruts, A and Farrugia, SL and Knight, R and Pardi, DS and Kashyap, PC}, title = {Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {55}, pmid = {28506317}, issn = {2049-2618}, support = {K08 DK100638/DK/NIDDK NIH HHS/United States ; P30 DK084567/DK/NIDDK NIH HHS/United States ; R03 DK111850/DK/NIDDK NIH HHS/United States ; UL1 TR000135/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/*classification/genetics ; Clostridioides difficile/physiology ; Clostridium Infections/complications/microbiology/*therapy ; Fecal Microbiota Transplantation/*methods ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*complications/microbiology ; Male ; Middle Aged ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {BACKGROUND: Gut microbiota play a key role in maintaining homeostasis in the human gut. Alterations in the gut microbial ecosystem predispose to Clostridium difficile infection (CDI) and gut inflammatory disorders such as inflammatory bowel disease (IBD). Fecal microbiota transplantation (FMT) from a healthy donor can restore gut microbial diversity and pathogen colonization resistance; consequently, it is now being investigated for its ability to improve inflammatory gut conditions such as IBD. In this study, we investigated changes in gut microbiota following FMT in 38 patients with CDI with or without underlying IBD.<br><br>RESULTS: There was a significant change in gut microbial composition towards the donor microbiota and an overall increase in microbial diversity consistent with previous studies after FMT. FMT was successful in treating CDI using a diverse set of donors, and varying degrees of donor stool engraftment suggesting that donor type and degree of engraftment are not drivers of a successful FMT treatment of CDI. However, patients with underlying IBD experienced an increased number of CDI relapses (during a 24-month follow-up) and a decreased growth of new taxa, as compared to the subjects without IBD. Moreover, the need for IBD therapy did not change following FMT. These results underscore the importance of the existing gut microbial landscape as a decisive factor to successfully treat CDI and potentially for improvement of the underlying pathophysiology in IBD.<br><br>CONCLUSIONS: FMT leads to a significant change in microbial diversity in patients with recurrent CDI and complete resolution of symptoms. Stool donor type (related or unrelated) and degree of engraftment are not the key for successful treatment of CDI by FMT. However, CDI patients with IBD have higher proportion of the original community after FMT and lack of improvement of their IBD symptoms and increased episodes of CDI on long-term follow-up.}, }
@article {pmid28504445, year = {2017}, author = {Rydzanicz, K and Czułowska, A and Manz, C and Jawień, P}, title = {First record of Anopheles daciae (Linton, Nicolescu &amp; Harbach, 2004) in Poland.}, journal = {Journal of vector ecology : journal of the Society for Vector Ecology}, volume = {42}, number = {1}, pages = {196-199}, doi = {10.1111/jvec.12257}, pmid = {28504445}, issn = {1948-7134}, mesh = {Animals ; Anopheles/*genetics/physiology ; Mosquito Vectors/*genetics/physiology ; Poland ; Polymorphism, Restriction Fragment Length/genetics ; }, }
@article {pmid28503167, year = {2017}, author = {Byloos, B and Coninx, I and Van Hoey, O and Cockell, C and Nicholson, N and Ilyin, V and Van Houdt, R and Boon, N and Leys, N}, title = {The Impact of Space Flight on Survival and Interaction of Cupriavidus metallidurans CH34 with Basalt, a Volcanic Moon Analog Rock.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {671}, pmid = {28503167}, issn = {1664-302X}, abstract = {Microbe-mineral interactions have become of interest for space exploration as microorganisms could be used to biomine from extra-terrestrial material and extract elements useful as micronutrients in life support systems. This research aimed to identify the impact of space flight on the long-term survival of Cupriavidus metallidurans CH34 in mineral water and the interaction with basalt, a lunar-type rock in preparation for the ESA spaceflight experiment, BIOROCK. Therefore, C. metallidurans CH34 cells were suspended in mineral water supplemented with or without crushed basalt and send for 3 months on board the Russian FOTON-M4 capsule. Long-term storage had a significant impact on cell physiology and energy status (by flow cytometry analysis, plate count and intracellular ATP measurements) as 60% of cells stored on ground lost their cell membrane potential, only 17% were still active, average ATP levels per cell were significantly lower and cultivability dropped to 1%. The cells stored in the presence of basalt and exposed to space flight conditions during storage however showed less dramatic changes in physiology, with only 16% of the cells lost their cell membrane potential and 24% were still active, leading to a higher cultivability (50%) and indicating a general positive effect of basalt and space flight on survival. Microbe-mineral interactions and biofilm formation was altered by spaceflight as less biofilm was formed on the basalt during flight conditions. Leaching from basalt also changed (measured with ICP-OES), showing that cells release more copper from basalt and the presence of cells also impacted iron and magnesium concentration irrespective of the presence of basalt. The flight conditions thus could counteract some of the detrimental effects observed after the 3 month storage conditions.}, }
@article {pmid28500319, year = {2017}, author = {Chiu, CY and Chan, YL and Tsai, YS and Chen, SA and Wang, CJ and Chen, KF and Chung, IF}, title = {Airway Microbial Diversity is Inversely Associated with Mite-Sensitized Rhinitis and Asthma in Early Childhood.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1820}, pmid = {28500319}, issn = {2045-2322}, mesh = {Allergens/immunology ; Animals ; Asthma/diagnosis/epidemiology/*etiology ; Biodiversity ; Case-Control Studies ; Child, Preschool ; Disease Susceptibility ; Female ; Humans ; Immunization ; Male ; *Microbiota ; Mites/*immunology ; Respiratory Mucosa/*microbiology ; Rhinitis, Allergic/diagnosis/epidemiology/*etiology ; }, abstract = {Microbiota plays an important role in regulating immune responses associated with atopic diseases. We sought to evaluate relationships among airway microbiota, serum IgE levels, allergic sensitization and their relevance to rhinitis and asthma. Microbial characterization was performed using Illumina-based 16S rRNA gene sequencing of 87 throat swabs collected from children with asthma (n = 32) and rhinitis (n = 23), and from healthy controls (n = 32). Data analysis was performed using QIIME (Quantitative Insights Into Microbial Ecology) v1.8. Significantly higher abundance of Proteobacteria was found in children with rhinitis than in the healthy controls (20.1% vs. 16.1%, P = 0.009). Bacterial species richness (Chao1 index) and diversity (Shannon index) were significantly reduced in children with mite sensitization but not in those with food or IgE sensitization. Compared with healthy children without mite sensitization, the mite-sensitized children with rhinitis and asthma showed significantly lower Chao1 and Shannon indices. Moraxella and Leptotrichia species were significantly found in the interaction of mite sensitization with rhinitis and asthma respectively. Airway microbial diversity appears to be inversely associated with sensitization to house dust mites. A modulation between airway dysbiosis and responses to allergens may potentially cause susceptibility to rhinitis and asthma in early childhood.}, }
@article {pmid28499076, year = {2017}, author = {Fu, R and Gong, J}, title = {Single Cell Analysis Linking Ribosomal (r)DNA and rRNA Copy Numbers to Cell Size and Growth Rate Provides Insights into Molecular Protistan Ecology.}, journal = {The Journal of eukaryotic microbiology}, volume = {64}, number = {6}, pages = {885-896}, pmid = {28499076}, issn = {1550-7408}, mesh = {Cell Size ; Ciliophora/*cytology/growth &amp; development/*physiology ; DNA, Ribosomal/*analysis/genetics ; Ecology ; Gene Dosage ; RNA, Ribosomal/*analysis/genetics ; *Single-Cell Analysis ; }, abstract = {Ribosomal (r)RNA and rDNA have been golden molecular markers in microbial ecology. However, it remains poorly understood how ribotype copy number (CN)-based characteristics are linked with diversity, abundance, and activity of protist populations and communities observed at organismal levels. Here, we applied a single-cell approach to quantify ribotype CNs in two ciliate species reared at different temperatures. We found that in actively growing cells, the per-cell rDNA and rRNA CNs scaled with cell volume (CV) to 0.44 and 0.58 powers, respectively. The modeled rDNA and rRNA concentrations thus appear to be much higher in smaller than in larger cells. The observed rRNA:rDNA ratio scaled with CV[0.14] . The maximum growth rate could be well predicted by a combination of per-cell ribotype CN and temperature. Our empirical data and modeling on single-cell ribotype scaling are in agreement with both the metabolic theory of ecology and the growth rate hypothesis, providing a quantitative framework for linking cellular rDNA and rRNA CNs with body size, growth (activity), and biomass stoichiometry. This study also demonstrates that the expression rate of rRNA genes is constrained by cell size, and favors biomass rather than abundance-based interpretation of quantitative ribotype data in population and community ecology of protists.}, }
@article {pmid28495244, year = {2017}, author = {Xue, D and Chen, H and Zhao, X and Xu, S and Hu, L and Xu, T and Jiang, L and Zhan, W}, title = {Rumen prokaryotic communities of ruminants under different feeding paradigms on the Qinghai-Tibetan Plateau.}, journal = {Systematic and applied microbiology}, volume = {40}, number = {4}, pages = {227-236}, doi = {10.1016/j.syapm.2017.03.006}, pmid = {28495244}, issn = {1618-0984}, mesh = {Animals ; Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Base Sequence ; Cattle/microbiology ; Fatty Acids, Volatile/analysis ; *Feeding Behavior ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; Sheep/microbiology ; Tibet ; }, abstract = {Yak and Tibetan sheep are the major indigenous ruminants on the Qinghai-Tibetan Plateau in China. The aim of this work was to study the differences in ruminal fermentation parameters and rumen prokaryotic community composition between hosts and feeding paradigms. The 16S rRNA genes targeting bacteria and archaea were sequenced using the MiSeq platform. The results showed that the prokaryotic community structure between yak and Tibetan sheep was significantly different (P<0.01). A significant difference in structure was also found between groups of yaks barn fed with a total mixed ration (TMR) and those naturally grazing (NG) (P=0.034), as well as for Tibetan sheep of the two groups (P=0.026). The core prokaryotic populations that existed in the rumen mostly dominated the structure. There was an obvious correlation of the prokaryotic community composition at the phylum and genus levels with the host or the feeding pattern. In addition, Tibetan sheep showed significantly higher yields of volatile fatty acids (VFAs) than yak, as did the NG group compared with the TMR group. In conclusion, both the host and feeding pattern may influence rumen microbial ecology system, with host effects being more important than those of the feeding pattern.}, }
@article {pmid28494086, year = {2016}, author = {Fernández-Martínez, MA and Pointing, SB and Pérez-Ortega, S and Arróniz-Crespo, M and Green, TGA and Rozzi, R and Sancho, LG and de Los Ríos, A}, title = {Functional ecology of soil microbial communities along a glacier forefield in Tierra del Fuego (Chile).}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {19}, number = {3}, pages = {161-173}, doi = {10.2436/20.1501.01.274}, pmid = {28494086}, issn = {1139-6709}, mesh = {Carbon/metabolism ; Carbon Cycle ; Chile ; Ecology ; Ice Cover/*microbiology ; Nitrogen/metabolism ; Oligonucleotide Array Sequence Analysis ; *Soil Microbiology ; }, abstract = {A previously established chronosequence from Pia Glacier forefield in Tierra del Fuego (Chile) containing soils of different ages (from bare soils to forest ones) is analyzed. We used this chronosequence as framework to postulate that microbial successional development would be accompanied by changes in functionality. To test this, the GeoChip functional microarray was used to identify diversity of genes involved in microbial carbon and nitrogen metabolism, as well as other genes related to microbial stress response and biotic interactions. Changes in putative functionality generally reflected succession-related taxonomic composition of soil microbiota. Major shifts in carbon fixation and catabolism were observed, as well as major changes in nitrogen metabolism. At initial microbial dominated succession stages, microorganisms could be mainly involved in pathways that help to increase nutrient availability, while more complex microbial transformations such as denitrification and methanogenesis, and later degradation of complex organic substrates, could be more prevalent at vegetated successional states. Shifts in virus populations broadly reflected changes in microbial diversity. Conversely, stress response pathways appeared relatively well conserved for communities along the entire chronosequence. We conclude that nutrient utilization is likely the major driver of microbial succession in these soils. [Int Microbiol 19(3):161-173 (2016)].}, }
@article {pmid28492990, year = {2017}, author = {Schulz, S and Kölbl, A and Ebli, M and Buegger, F and Schloter, M and Fiedler, S}, title = {Field-Scale Pattern of Denitrifying Microorganisms and N2O Emission Rates Indicate a High Potential for Complete Denitrification in an Agriculturally Used Organic Soil.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {765-770}, pmid = {28492990}, issn = {1432-184X}, mesh = {Agriculture ; Bacteria/genetics/*metabolism ; *Denitrification ; *Genes, Bacterial ; Germany ; Nitrous Oxide/*metabolism ; Seasons ; *Soil Microbiology ; }, abstract = {More than 50% of all anthropogenic N2O emissions come from the soil. Drained Histosols that are used for agricultural purposes are particularly potent sources of denitrification due to higher stocks of organic matter and fertiliser application. However, conditions that favour denitrification can vary considerably across a field and change significantly throughout the year. Spatial and temporal denitrifier dynamics were assessed in a drained, intensely managed Histosol by focusing on the genetic nitrite and N2O reduction potential derived from the abundance of nirK, nirS and nosZ genes. These data were correlated with soil properties at two different points in time in 2013. N2O emissions were measured every 2 weeks over three vegetation periods (2012-2014). Very low N2O emission rates were measured throughout the entire period of investigation in accordance with the geostatistical data that revealed an abundance of microbes carrying the N2O reductase gene nosZ. This, along with neutral soil pH values, is indicative of high microbial denitrification potential. While the distribution of the microbial communities was strongly influenced by total organic carbon and nitrogen pools in March, the spatial distribution pattern was not related to the distribution of soil properties in October, when higher nutrient availability was observed. Different nitrite reducer groups prevailed in spring and autumn. While nirS, followed by nosZ and nirK, was most abundant in March, the latter was the dominant nitrite reductase in October.}, }
@article {pmid28492989, year = {2017}, author = {Duguma, D and Hall, MW and Smartt, CT and Neufeld, JD}, title = {Temporal Variations of Microbiota Associated with the Immature Stages of Two Florida Culex Mosquito Vectors.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {979-989}, pmid = {28492989}, issn = {1432-184X}, mesh = {Animals ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Culex/growth &amp; development/*microbiology ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Florida ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Introduced Species ; Larva/growth &amp; development/microbiology ; Mosquito Vectors/growth &amp; development/microbiology ; Pupa/growth &amp; development/microbiology ; RNA, Ribosomal, 16S/genetics ; Seasons ; }, abstract = {Microbiota associated with mosquito vector populations impact several traits of mosquitoes, including survival, reproduction, control, and immunity against pathogens. The influence of seasonal variations and mosquito species on mosquito gut microbiota is poorly understood. We sought to determine whether the mosquito microbiota associated with immature stages of two congeners (Culex coronator and Culex nigripalpus) differ temporally and between the two species. Using high throughput 16S rRNA gene sequence analysis, we characterized bacterial and archaeal communities found in the immature stages of the two Culex mosquito species sampled over three seasons to compare the diversity of bacteria between the two species. Beta diversity analyses of the larval microbiota sequences revealed that the two Culex species differed significantly, both temporally within each species and between the two species. Bacteria in Cx. coronator larvae were dominated by Alphaproteobacteria, mainly associated with Roseoccocus and unidentified species of Rhizobiales, and two unidentified species of Cyanobacteria. In contrast, Cx. nigripalpus was dominated by Thorsellia anophelis (Gammaproteobacteria), Clostridium, an unidentified species of Ruminococcacae (Clostridiales), and additional unidentified species associated with Erysipelotrichaceae (Erysipelotrichales), Bacteroidales, and Mollicutes. Results of our study revealed both seasonal and interspecies differences in bacterial community composition associated with the immature stages of Cx. coronator and Cx. nigripalpus vector populations in Florida. These results have important implications for our understanding of the underlying factors of variations in disease transmission among seasons, susceptibility to various pesticides, and other biotic factors, including the role of the microbiota on the spread of invasive species. In addition, our results suggest close associations of certain bacteria species with each of the two Culex species that will be further targeted for their potential in the development of microbial-based control strategies.}, }
@article {pmid28492988, year = {2017}, author = {Brinkac, L and Voorhies, A and Gomez, A and Nelson, KE}, title = {The Threat of Antimicrobial Resistance on the Human Microbiome.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {1001-1008}, pmid = {28492988}, issn = {1432-184X}, support = {U19 AI110819/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Infective Agents/*pharmacology ; *Drug Resistance, Microbial ; Humans ; Microbiota/*drug effects ; }, abstract = {Ubiquitous in nature, antimicrobial resistance (AMR) has existed long before the golden age of antimicrobials. While antimicrobial agents are beneficial to combat infection, their widespread use contributes to the increase in and emergence of novel resistant microbes in virtually all environmental niches. The human microbiome is an important reservoir of AMR with initial exposure occurring in early life. Once seeded with AMR, commensal organisms may be key contributors to the dissemination of resistance due to the interconnectedness of microbial communities. When acquired by pathogens however, AMR becomes a serious public health threat worldwide. Our ability to combat the threat of emerging resistance relies on accurate AMR detection methods and the development of therapeutics that function despite the presence of antimicrobial resistance.}, }
@article {pmid28492987, year = {2017}, author = {Li, J and Liu, YR and Cui, LJ and Hu, HW and Wang, JT and He, JZ}, title = {Copper Pollution Increases the Resistance of Soil Archaeal Community to Changes in Water Regime.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {877-887}, pmid = {28492987}, issn = {1432-184X}, mesh = {Archaea/drug effects/*physiology ; China ; Copper/*analysis ; High-Throughput Nucleotide Sequencing ; Microbiota/drug effects/physiology ; Polymerase Chain Reaction ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/*analysis ; Water/*analysis ; }, abstract = {Increasing efforts have been devoted to exploring the impact of environmental stresses on soil bacterial communities, but the work on the archaeal community is seldom. Here, we constructed microcosm experiments to investigate the responses of archaeal communities to the subsequent dry-rewetting (DW) disturbance in two contrasting soils (fluvo-aquic and red soil) after 6 years of copper pollution. Ten DW cycles were exerted on the two soils with different copper levels, followed by a 6-week recovery period. In both soils, archaeal diversity (Shannon index) in the high copper-level treatments increased over the incubation period, and archaeal community structure changed remarkably as revealed by the non-metric multidimensional scaling ordinations. In both soils, copper pollution altered the response of dominant operational taxonomic units (OTUs) to the DW disturbance. Throughout the incubation and recovery period, the resistance of archaeal abundance to the DW disturbance was higher in the copper-polluted soils than soils without pollution. Taken together, copper pollution altered the response of soil archaeal diversity and community composition to the DW disturbance and increased the resistance of the archaeal abundance. These findings have important implications for understanding soil microbial responses to ongoing environmental change.}, }
@article {pmid28489329, year = {2017}, author = {Dassen, S and Cortois, R and Martens, H and de Hollander, M and Kowalchuk, GA and van der Putten, WH and De Deyn, GB}, title = {Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity.}, journal = {Molecular ecology}, volume = {26}, number = {15}, pages = {4085-4098}, doi = {10.1111/mec.14175}, pmid = {28489329}, issn = {1365-294X}, mesh = {Archaea/classification ; Bacteria/classification ; *Biodiversity ; *Ecosystem ; Fungi/classification ; Germany ; Mycorrhizae/classification ; Plants/*classification ; *Soil Microbiology ; }, abstract = {Plants are known to influence belowground microbial community structure along their roots, but the impacts of plant species richness and plant functional group (FG) identity on microbial communities in the bulk soil are still not well understood. Here, we used 454-pyrosequencing to analyse the soil microbial community composition in a long-term biodiversity experiment at Jena, Germany. We examined responses of bacteria, fungi, archaea, and protists to plant species richness (communities varying from 1 to 60 sown species) and plant FG identity (grasses, legumes, small herbs, tall herbs) in bulk soil. We hypothesized that plant species richness and FG identity would alter microbial community composition and have a positive impact on microbial species richness. Plant species richness had a marginal positive effect on the richness of fungi, but we observed no such effect on bacteria, archaea and protists. Plant species richness also did not have a large impact on microbial community composition. Rather, abiotic soil properties partially explained the community composition of bacteria, fungi, arbuscular mycorrhizal fungi (AMF), archaea and protists. Plant FG richness did not impact microbial community composition; however, plant FG identity was more effective. Bacterial richness was highest in legume plots and lowest in small herb plots, and AMF and archaeal community composition in legume plant communities was distinct from that in communities composed of other plant FGs. We conclude that soil microbial community composition in bulk soil is influenced more by changes in plant FG composition and abiotic soil properties, than by changes in plant species richness per se.}, }
@article {pmid28489302, year = {2017}, author = {Maruthamuthu, M and Jiménez, DJ and van Elsas, JD}, title = {Characterization of a furan aldehyde-tolerant β-xylosidase/α-arabinosidase obtained through a synthetic metagenomics approach.}, journal = {Journal of applied microbiology}, volume = {123}, number = {1}, pages = {145-158}, doi = {10.1111/jam.13484}, pmid = {28489302}, issn = {1365-2672}, support = {//BE-Basic foundation/ ; }, abstract = {AIMS: The aim of the study was to characterize 10 hemicellulolytic enzymes obtained from a wheat straw-degrading microbial consortium.<br><br>METHODS AND RESULTS: Based on previous metagenomics analyses, 10 glycosyl hydrolases were selected, codon-optimized, synthetized, cloned and expressed in Escherichia coli. Nine of the overexpressed recombinant proteins accumulated in cellular inclusion bodies, whereas one, a 37&#xb7;5-kDa protein encoded by gene xylM1989, was found in the soluble fractions. The resulting protein, denoted XylM1989, showed &#x3b2;-xylosidase and &#x3b1;-arabinosidase activities. It fell in the GH43 family and resembled a Sphingobacterium sp. protein. The XylM1989 showed optimum activity at 20&#xb0;C and pH 8&#xb7;0. Interestingly, it kept approximately 80% of its &#x3b2;-xylosidase activity in the presence of 0&#xb7;5% (w/v) furfural and 0&#xb7;1% (w/v) 5-hydroxymethylfurfural. Additionally, the presence of Ca[2+] , Mg[2+] and Mn[2+] ions increased the enzymatic activity and conferred complete tolerance to 500&#xa0;mmol&#xa0;l[-1] of xylose. Protein XylM1989 is also able to release sugars from complex polysaccharides.<br><br>CONCLUSION: We report the characterization of a novel bifunctional hemicellulolytic enzyme obtained through a targeted synthetic metagenomics approach.<br><br>The properties of XylM1989 turn this protein into a promising enzyme that could be useful for the efficient saccharification of plant biomass.}, }
@article {pmid28488787, year = {2017}, author = {Kinnunen, M and Gülay, A and Albrechtsen, HJ and Dechesne, A and Smets, BF}, title = {Nitrotoga is selected over Nitrospira in newly assembled biofilm communities from a tap water source community at increased nitrite loading.}, journal = {Environmental microbiology}, volume = {19}, number = {7}, pages = {2785-2793}, doi = {10.1111/1462-2920.13792}, pmid = {28488787}, issn = {1462-2920}, mesh = {Biofilms/*growth &amp; development ; Bioreactors/microbiology ; Drinking Water/microbiology ; Gallionellaceae/classification/growth &amp; development/*metabolism ; Nitrites/*metabolism ; Oxidation-Reduction ; Water Microbiology ; }, abstract = {Community assembly is a central topic in microbial ecology: how do assembly processes interact and what is the relative contribution of stochasticity and determinism? Here, we exposed replicate flow-through biofilm systems, fed with nitrite-supplemented tap water, to continuous immigration from a source community, present in the tap water, to determine the extent of selection and neutral processes in newly assembled biofilm communities at both the community and the functional guild (of nitrite-oxidizing bacteria, NOB) levels. The community composition of biofilms assembled under low and high nitrite loading was described after 40 days of complete nitrite removal. The total community assembly, as well as the NOB guild assembly were largely governed by a combination of deterministic and stochastic processes. Furthermore, we observed deterministic enrichment of certain types of NOB in the biofilms. Specifically, elevated nitrite loading selected for a single Nitrotoga representative, while lower nitrite conditions selected for a number of Nitrospira. Therefore, even when focusing on ecologically coherent ensembles, assembly is the result of complex stochastic and deterministic processes that can only be interrogated by observing multiple assemblies under controlled conditions.}, }
@article {pmid28484799, year = {2017}, author = {Sampaio, DS and Almeida, JRB and de Jesus, HE and Rosado, AS and Seldin, L and Jurelevicius, D}, title = {Distribution of Anaerobic Hydrocarbon-Degrading Bacteria in Soils from King George Island, Maritime Antarctica.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {810-820}, pmid = {28484799}, issn = {1432-184X}, mesh = {Antarctic Regions ; Bacteria, Anaerobic/classification/genetics/*isolation &amp; purification ; Biodegradation, Environmental ; Gasoline/analysis ; Hydrocarbons/metabolism ; Islands ; *Microbiota ; *Soil Microbiology ; Soil Pollutants/analysis ; }, abstract = {Anaerobic diesel fuel Arctic (DFA) degradation has already been demonstrated in Antarctic soils. However, studies comparing the distribution of anaerobic bacterial groups and of anaerobic hydrocarbon-degrading bacteria in Antarctic soils containing different concentrations of DFA are scarce. In this study, functional genes were used to study the diversity and distribution of anaerobic hydrocarbon-degrading bacteria (bamA, assA, and bssA) and of sulfate-reducing bacteria (SRB-apsR) in highly, intermediate, and non-DFA-contaminated soils collected during the summers of 2009, 2010, and 2011 from King George Island, Antarctica. Signatures of bamA genes were detected in all soils analyzed, whereas bssA and assA were found in only 4 of 10 soils. The concentration of DFA was the main factor influencing the distribution of bamA-containing bacteria and of SRB in the analyzed soils, as shown by PCR-DGGE results. bamA sequences related to genes previously described in Desulfuromonas, Lautropia, Magnetospirillum, Sulfuritalea, Rhodovolum, Rhodomicrobium, Azoarcus, Geobacter, Ramlibacter, and Gemmatimonas genera were dominant in King George Island soils. Although DFA modulated the distribution of bamA-hosting bacteria, DFA concentration was not related to bamA abundance in the soils studied here. This result suggests that King George Island soils show functional redundancy for aromatic hydrocarbon degradation. The results obtained in this study support the hypothesis that specialized anaerobic hydrocarbon-degrading bacteria have been selected by hydrocarbon concentrations present in King George Island soils.}, }
@article {pmid28484604, year = {2017}, author = {Djurhuus, A and Mikalsen, SO and Giebel, HA and Rogers, AD}, title = {Cutting through the smoke: the diversity of microorganisms in deep-sea hydrothermal plumes.}, journal = {Royal Society open science}, volume = {4}, number = {4}, pages = {160829}, pmid = {28484604}, issn = {2054-5703}, abstract = {There are still notable gaps regarding the detailed distribution of microorganisms between and within insular habitats such as deep-sea hydrothermal vents. This study investigates the community composition of black smoker vent microorganisms in the Southern Hemisphere, and changes thereof along a spatial and chemical gradient ranging from the vent plume to surrounding waters. We sampled two hydrothermal vent fields, one at the South West Indian Ridge (SWIR), the other at the East Scotia Ridge (ESR). Samples were collected across vent fields at varying vertical distances from the origin of the plumes. The microbial data were sequenced on an Illumina MiSeq platform for the 16SrRNA gene. A substantial amount of vent-specific putative chemosynthetic microorganisms were found, particularly in samples from focused hydrothermal venting. Common vent-specific organisms from both vent fields were the genera Arcobacter, Caminibacter and Sulfurimonas from the Epsilonproteobacteria and the SUP05 group from the Gammaproteobacteria. There were no major differences in microbial composition between SWIR and ESR for focused plume samples. However, within the ESR the diffuse flow and focused samples differed significantly in microbial community composition and relative abundance. For Epsilonproteobacteria, we found evidence of niche-specificity to hydrothermal vent environments. This taxon decreased in abundance by three orders of magnitude from the vent orifice to background water. Epsilonproteobacteria distribution followed a distance-decay relationship as vent-effluents mixed with the surrounding seawater. This study demonstrates strong habitat affinity of vent microorganisms on a metre scale with distinct environmental selection.}, }
@article {pmid28484516, year = {2017}, author = {Scoma, A and Tóth, SZ}, title = {On the pathways feeding the H2 production process in nutrient-replete, hypoxic conditions. Commentary on the article "Low oxygen levels contribute to improve photohydrogen production in mixotrophic non-stressed Chlamydomonas cultures", by Jurado-Oller et al., Biotechnology for Biofuels, published September 7, 2015; 8:149.}, journal = {Biotechnology for biofuels}, volume = {10}, number = {}, pages = {116}, pmid = {28484516}, issn = {1754-6834}, abstract = {BACKGROUND: Under low O2 concentration (hypoxia) and low light, Chlamydomonas cells can produce H2 gas in nutrient-replete conditions. This process is hindered by the presence of O2, which inactivates the [FeFe]-hydrogenase enzyme responsible for H2 gas production shifting algal cultures back to normal growth. The main pathways accounting for H2 production in hypoxia are not entirely understood, as much as culture conditions setting the optimal redox state in the chloroplast supporting long-lasting H2 production. The reducing power for H2 production can be provided by photosystem II (PSII) and photofermentative processes during which proteins are degraded via yet unknown pathways. In hetero- or mixotrophic conditions, acetate respiration was proposed to indirectly contribute to H2 evolution, although this pathway has not been described in detail.<br><br>MAIN BODY: Recently, Jurado-Oller et al. (Biotechnol Biofuels 8: 149, 7) proposed that acetate respiration may substantially support H2 production in nutrient-replete hypoxic conditions. Addition of low amounts of O2 enhanced acetate respiration rate, particularly in the light, resulting in improved H2 production. The authors surmised that acetate oxidation through the glyoxylate pathway generates intermediates such as succinate and malate, which would be in turn oxidized in the chloroplast generating FADH2 and NADH. The latter would enter a PSII-independent pathway at the level of the plastoquinone pool, consistent with the light dependence of H2 production. The authors concluded that the water-splitting activity of PSII has a minor role in H2 evolution in nutrient-replete, mixotrophic cultures under hypoxia. However, their results with the PSII inhibitor DCMU also reveal that O2 or acetate additions promoted acetate respiration over the usually dominant PSII-dependent pathway. The more oxidized state experienced by these cultures in combination with the relatively short experimental time prevented acclimation to hypoxia, thus precluding the PSII-dependent pathway from contributing to H2 production.<br><br>CONCLUSIONS: In Chlamydomonas, continuous H2 gas evolution is expected once low O2 partial pressure and optimal reducing conditions are set. Under nutrient-replete conditions, the electrogenic processes involved in H2 photoproduction may rely on various electron transport pathways. Understanding how physiological conditions select for specific metabolic routes is key to achieve economic viability of this renewable energy source.}, }
@article {pmid28484431, year = {2017}, author = {Niño-García, JP and Ruiz-González, C and Del Giorgio, PA}, title = {Exploring the Ecological Coherence between the Spatial and Temporal Patterns of Bacterioplankton in Boreal Lakes.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {636}, pmid = {28484431}, issn = {1664-302X}, abstract = {One of the major contemporary challenges in microbial ecology has been to discriminate the reactive core from the random, unreactive components of bacterial communities. In previous work we used the spatial abundance distributions of bacterioplankton across boreal lakes of Québec to group taxa into four distinct categories that reflect either hydrology-mediated dispersal along the aquatic network or environmental selection mechanisms within lakes. Here, we test whether this categorization derived from the spatial distribution of taxa is maintained over time, by analyzing the temporal dynamics of the operational taxonomic units (OTUs) within those spatially derived categories along an annual cycle in the oligotrophic lake Croche (Québec, Canada), and assessing the coherence in the patterns of abundance, occurrence, and environmental range of these OTUs over space and time. We report that the temporal dynamics of most taxa within a single lake are largely coherent with those derived from their spatial distribution over large spatial scales, suggesting that these properties must be intrinsic of particular taxa. We also identified a set of rare taxa cataloged as having a random occupancy based on their spatial distribution, but which showed clear seasonality and abundance peaks along the year, yet these comprised a very small fraction of the total rare OTUs. We conclude that the presence of most rare bacterioplankton taxa in boreal lakes is random, since both their temporal and spatial dynamics suggest links to passive downstream transport and persistence in freshwater networks, rather than environmental selection.}, }
@article {pmid28478110, year = {2017}, author = {Harish, A and Kurland, CG}, title = {Empirical genome evolution models root the tree of life.}, journal = {Biochimie}, volume = {138}, number = {}, pages = {137-155}, doi = {10.1016/j.biochi.2017.04.014}, pmid = {28478110}, issn = {1638-6183}, mesh = {Archaea/genetics ; Bacteria/genetics ; Bayes Theorem ; Eukaryota/genetics ; *Evolution, Molecular ; *Genome ; *Models, Genetic ; *Phylogeny ; }, abstract = {A reliable phylogenetic reconstruction of the evolutionary history of contemporary species depends on a robust identification of the universal common ancestor (UCA) at the root of the Tree of Life (ToL). That root polarizes the tree so that the evolutionary succession of ancestors to descendants is discernable. In effect, the root determines the branching order and the direction of character evolution. Typically, conventional phylogenetic analyses implement time-reversible models of evolution for which character evolution is un-polarized. Such practices leave the root and the direction of character evolution undefined by the data used to construct such trees. In such cases, rooting relies on theoretic assumptions and/or the use of external data to interpret unrooted trees. The most common rooting method, the outgroup method is clearly inapplicable to the ToL, which has no outgroup. Both here and in the accompanying paper (Harish and Kurland, 2017) we have explored the theoretical and technical issues related to several rooting methods. We demonstrate (1) that Genome-level characters and evolution models are necessary for species phylogeny reconstructions. By the same token, standard practices exploiting sequence-based methods that implement gene-scale substitution models do not root species trees; (2) Modeling evolution of complex genomic characters and processes that are non-reversible and non-stationary is required to reconstruct the polarized evolution of the ToL; (3) Rooting experiments and Bayesian model selection tests overwhelmingly support the earlier finding that akaryotes and eukaryotes are sister clades that descend independently from UCA (Harish and Kurland, 2013); (4) Consistent ancestral state reconstructions from independent genome samplings confirm the previous finding that UCA features three fourths of the unique protein domain-superfamilies encoded by extant genomes.}, }
@article {pmid28477198, year = {2017}, author = {Malik, S and Dardalhon, V and Awasthi, A}, title = {Characterization of Th9 Cells in the Development of EAE and IBD.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1585}, number = {}, pages = {201-216}, doi = {10.1007/978-1-4939-6877-0_16}, pmid = {28477198}, issn = {1940-6029}, mesh = {Animals ; Autoimmunity/genetics/*physiology ; CD4-Positive T-Lymphocytes/metabolism ; Encephalomyelitis, Autoimmune, Experimental/immunology/*metabolism ; Interleukin-2/metabolism ; Interleukin-4/metabolism ; Interleukin-9/metabolism ; Mice ; T-Lymphocyte Subsets/metabolism ; Th1 Cells/metabolism ; Th17 Cells/metabolism ; Transforming Growth Factor alpha/metabolism ; }, abstract = {Encephalitogenic and colitogenic effector T cells have been implicated in the induction of experimental autoimmune encephalomyelitis (EAE) and inflammatory bowel disease (IBD), respectively. Effector functions of Th1 and Th17 cells have been well characterized and described for the induction and development of EAE and IBD; however, the recently identified Th9 cells have also been suggested to play an important role in these autoimmune pathologies. Th9 cells, primarily characterized by their high level of production of IL-9, are not only essential in controlling extracellular pathogens but also contribute to the development of autoimmunity and allergic inflammation. Furthermore, it was also demonstrated that IL-9 promotes Th17 cell-mediated tissue pathology in EAE and it compromises the barrier functions of the gut in IBD. In vivo adoptive transfer of in vitro differentiated Th9 cells induces the development of autoimmune tissue inflammation in EAE and IBD. Here we describe methods for in vitro differentiation of naïve murine CD4+ T cells to generate IL-9-producing Th9 cells and follow their effector functions in EAE and IBD murine models.}, }
@article {pmid28477173, year = {2017}, author = {Majewska, R and de Vijver, BV and Nasrolahi, A and Ehsanpour, M and Afkhami, M and Bolaños, F and Iamunno, F and Santoro, M and De Stefano, M}, title = {Shared Epizoic Taxa and Differences in Diatom Community Structure Between Green Turtles (Chelonia mydas) from Distant Habitats.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {969-978}, pmid = {28477173}, issn = {1432-184X}, mesh = {Animal Shells ; Animals ; *Biota ; Costa Rica ; Diatoms/*physiology ; *Ecosystem ; Iran ; Turtles/*physiology ; }, abstract = {The first reports of diatoms growing on marine mammals date back to the early 1900s. However, only recently has direct evidence been provided for similar associations between diatoms and sea turtles. We present a comparison of diatom communities inhabiting carapaces of green turtles Chelonia mydas sampled at two remote sites located within the Indian (Iran) and Atlantic (Costa Rica) Ocean basins. Diatom observations and counts were carried out using scanning electron microscopy. Techniques involving critical point drying enabled observations of diatoms and other microepibionts still attached to sea turtle carapace and revealed specific aspects of the epizoic community structure. Species-poor, well-developed diatom communities were found on all examined sea turtles. Significant differences between the two host sea turtle populations were observed in terms of diatom abundance and their community structure (including growth form structure). A total of 12 and 22 diatom taxa were found from sea turtles in Iran and Costa Rica, respectively, and eight of these species belonging to Amphora, Chelonicola, Cocconeis, Navicula, Nitzschia and Poulinea genera were observed in samples from both locations. Potential mechanisms of diatom dispersal and the influence of the external environment, sea turtle behaviour, its life stage, and foraging and breeding habitats, as well as epibiotic bacterial flora on epizoic communities, are discussed.}, }
@article {pmid28475713, year = {2017}, author = {Stedtfeld, RD and Stedtfeld, TM and Fader, KA and Williams, MR and Bhaduri, P and Quensen, J and Zacharewski, TR and Tiedje, JM and Hashsham, SA}, title = {TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {5}, pages = {}, pmid = {28475713}, issn = {1574-6941}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/*genetics ; Dysbiosis/*chemically induced ; Enterobacteriaceae/*drug effects/*genetics ; Female ; Gastrointestinal Microbiome/*drug effects ; Interspersed Repetitive Sequences/genetics ; Mice ; Mice, Inbred C57BL ; Polychlorinated Dibenzodioxins/*pharmacology ; Receptors, Aryl Hydrocarbon/antagonists &amp; inhibitors ; }, abstract = {Dysbiosis of the gut microbiome via antibiotics, changes in diet and infection can select for bacterial groups that more frequently harbor antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). However, the impact of environmental toxicants on the reservoir of ARGs in the gut microbiome has received less attention. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a potent aryl hydrocarbon receptor (AhR) agonist with multiple toxic health effects including immune dysfunction. The selective pressure of TCDD on the abundance of ARG and MGE-harboring gut populations was examined using C57BL/6 mice exposed to 0-30 μg/kg TCDD for 28 and 92 days with the latter having a 30-day recovery period. DNA extracted from temporally collected fecal pellets was characterized using a qPCR array with 384 assays targeting ARGs and MGEs. Fourteen genes, typically observed in Enterobacteriaceae, increased significantly within 8 days of initial dosing, persisted throughout the treatment period, and remained induced 30 days post dosing. A qPCR primer set targeting Enterobacteriaceae also showed 10- to 100-fold higher abundance in TCDD-treated groups, which was further verified using metagenomics. Results show a bloom of ARG-harboring bacterial groups in the gut due to a xenobiotic compound that is not a metal, biocide or antimicrobial.}, }
@article {pmid28473826, year = {2017}, author = {Duarte, AC and Holman, DB and Alexander, TW and Durmic, Z and Vercoe, PE and Chaves, AV}, title = {The Type of Forage Substrate Preparation Included as Substrate in a RUSITEC System Affects the Ruminal Microbiota and Fermentation Characteristics.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {704}, pmid = {28473826}, issn = {1664-302X}, abstract = {In vitro fermentation systems such as the rumen simulation technique (RUSITEC) are frequently used to assess dietary manipulations in livestock, thereby limiting the use of live animals. Despite being in use for nearly 40 years, improvements are continually sought in these systems to better reflect and mimic natural processes in ruminants. The aim of this study was to evaluate the effect of forage preparation, i.e., frozen minced (FM) and freeze-dried and ground (FDG), on the ruminal microbiota and on fermentation characteristics when included as a substrate in a RUSITEC system. A completely randomized design experiment was performed over a 15-day period, with 7 days of adaptation and an 8-day experimental period. Fermentation parameters (total gas, CH4, and volatile fatty acid production) were analyzed on a daily basis over the experimental period and the archaeal and bacterial microbiota (liquid-associated microbes [LAM] and solid-associated microbes [SAM] was assessed at 0, 5, 10, and 15 days using high-throughput sequencing of the 16S rRNA gene. Results from this study suggested a tendency (P = 0.09) of FM treatment to increase daily CH4 (mg/d) production by 16.7% when compared with FDG treatment. Of the major volatile fatty acids (acetate, propionate, and butyrate), only butyrate production was greater (P = 0.01) with FM treatment compared with FDG substrate. The archaeal and bacterial diversity and richness did not differ between the forage preparations, although feed particle size of the forage had a significant effect on microbial community structure in the SAM and LAM samples. The Bacteroidetes phylum was more relatively abundant in the FM substrate treatment, while Proteobacteria was enriched in the FDG treatment. At the genus-level, Butyrivibrio, Prevotella, and Roseburia were enriched in the FM substrate treatment and Campylobacter and Lactobacillus in the FDG substrate treatment. Evidence from this study suggests that forage preparation affects CH4 production, butyrate production, and the structure of the rumen microbiota during in vitro fermentation.}, }
@article {pmid28473000, year = {2017}, author = {Lee, STM and Kahn, SA and Delmont, TO and Shaiber, A and Esen, &#xd6;C and Hubert, NA and Morrison, HG and Antonopoulos, DA and Rubin, DT and Eren, AM}, title = {Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {50}, pmid = {28473000}, issn = {2049-2618}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; T32 EB009412/EB/NIBIB NIH HHS/United States ; }, mesh = {Adult ; Bacteria/classification/*growth &amp; development ; Clostridium Infections/microbiology/*therapy ; DNA, Bacterial/genetics ; Fecal Microbiota Transplantation/*methods ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Living Donors ; Male ; Metagenomics/*methods ; Phylogeny ; Sequence Analysis, DNA/methods ; Young Adult ; }, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the recipient gut, and the widely used approaches to study the microbial ecology of FMT experiments fail to provide enough resolution to identify populations that are likely responsible for FMT-derived benefits.<br><br>METHODS: We used shotgun metagenomics together with assembly and binning strategies to reconstruct metagenome-assembled genomes (MAGs) from fecal samples of a single FMT donor. We then used metagenomic mapping to track the occurrence and distribution patterns of donor MAGs in two FMT recipients.<br><br>RESULTS: Our analyses revealed that 22% of the 92 highly complete bacterial MAGs that we identified from the donor successfully colonized and remained abundant in two recipients for at least 8&#xa0;weeks. Most MAGs with a high colonization rate belonged to the order Bacteroidales. The vast majority of those that lacked evidence of colonization belonged to the order Clostridiales, and colonization success was negatively correlated with the number of genes related to sporulation. Our analysis of 151 publicly available gut metagenomes showed that the donor MAGs that colonized both recipients were prevalent, and the ones that colonized neither were rare across the participants of the Human Microbiome Project. Although our dataset showed a link between taxonomy and the colonization ability of a given MAG, we also identified MAGs that belong to the same taxon with different colonization properties, highlighting the importance of an appropriate level of resolution to explore the functional basis of colonization and to identify targets for cultivation, hypothesis generation, and testing in model systems.<br><br>CONCLUSIONS: The analytical strategy adopted in our study can provide genomic insights into bacterial populations that may be critical to the efficacy of FMT due to their success in gut colonization and metabolic properties, and guide cultivation efforts to investigate mechanistic underpinnings of this procedure beyond associations.}, }
@article {pmid28472072, year = {2017}, author = {Olesen, SW and Duvallet, C and Alm, EJ}, title = {dbOTU3: A new implementation of distribution-based OTU calling.}, journal = {PloS one}, volume = {12}, number = {5}, pages = {e0176335}, pmid = {28472072}, issn = {1932-6203}, mesh = {Algorithms ; *Phylogeny ; }, abstract = {Distribution-based operational taxonomic unit-calling (dbOTU) improves on other approaches by incorporating information about the input sequences' distribution across samples. Previous implementations of dbOTU presented challenges for users. Here we introduce and evaluate a new implementation of dbOTU that is faster and more user-friendly. We show that this new implementation has theoretical and practical improvements over previous implementations of dbOTU, making the algorithm more accessible to microbial ecology and biomedical researchers.}, }
@article {pmid28470601, year = {2017}, author = {Kuipers, G and Peschke, M and Ismail, NB and Hjelm, A and Schlegel, S and Vikström, D and Luirink, J and de Gier, JW}, title = {Optimizing E. coli-Based Membrane Protein Production Using Lemo21(DE3) or pReX and GFP-Fusions.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1586}, number = {}, pages = {109-126}, doi = {10.1007/978-1-4939-6887-9_7}, pmid = {28470601}, issn = {1940-6029}, support = {R01 GM081827/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Culture Techniques ; Cloning, Molecular/methods ; Escherichia coli/*genetics ; Gene Expression ; Genetic Vectors/genetics ; Green Fluorescent Proteins/*genetics ; Humans ; Membrane Proteins/*genetics ; Recombinant Fusion Proteins/genetics ; Transformation, Genetic ; }, abstract = {Optimizing the conditions for the production of membrane proteins in E. coli is usually a laborious and time-consuming process. Combining the Lemo21(DE3) strain or the pReX T7-based expression vector with membrane proteins C-terminally fused to Green Fluorescent Protein (GFP) greatly facilitates the optimization of membrane protein production yields. Both Lemo21(DE3) and pReX allow precise regulation of expression intensities of genes encoding membrane proteins, which is critical to identify the optimal production condition for a membrane protein. The use of GFP-fusions allows direct monitoring and visualization of membrane proteins at any stage during the production optimization process.}, }
@article {pmid28469939, year = {2017}, author = {Díaz-Muñoz, SL}, title = {Viral coinfection is shaped by host ecology and virus-virus interactions across diverse microbial taxa and environments.}, journal = {Virus evolution}, volume = {3}, number = {1}, pages = {vex011}, pmid = {28469939}, issn = {2057-1577}, abstract = {Infection of more than one virus in a host, coinfection, is common across taxa and environments. Viral coinfection can enable genetic exchange, alter the dynamics of infections, and change the course of viral evolution. Yet, a systematic test of the factors explaining variation in viral coinfection across different taxa and environments awaits completion. Here I employ three microbial data sets of virus-host interactions covering cross-infectivity, culture coinfection, and single-cell coinfection (total: 6,564 microbial hosts, 13,103 viruses) to provide a broad, comprehensive picture of the ecological and biological factors shaping viral coinfection. I found evidence that ecology and virus-virus interactions are recurrent factors shaping coinfection patterns. Host ecology was a consistent and strong predictor of coinfection across all three data sets: cross-infectivity, culture coinfection, and single-cell coinfection. Host phylogeny or taxonomy was a less consistent predictor, being weak or absent in the cross-infectivity and single-cell coinfection models, yet it was the strongest predictor in the culture coinfection model. Virus-virus interactions strongly affected coinfection. In the largest test of superinfection exclusion to date, prophage sequences reduced culture coinfection by other prophages, with a weaker effect on extrachromosomal virus coinfection. At the single-cell level, prophage sequences eliminated coinfection. Virus-virus interactions also increased culture coinfection with ssDNA-dsDNA coinfections >2× more likely than ssDNA-only coinfections. The presence of CRISPR spacers was associated with a ∼50% reduction in single-cell coinfection in a marine bacteria, despite the absence of exact spacer matches in any active infection. Collectively, these results suggest the environment bacteria inhabit and the interactions among surrounding viruses are two factors consistently shaping viral coinfection patterns. These findings highlight the role of virus-virus interactions in coinfection with implications for phage therapy, microbiome dynamics, and viral infection treatments.}, }
@article {pmid28468277, year = {2017}, author = {Hill, P and Heberlig, GW and Boddy, CN}, title = {Sampling Terrestrial Environments for Bacterial Polyketides.}, journal = {Molecules (Basel, Switzerland)}, volume = {22}, number = {5}, pages = {}, pmid = {28468277}, issn = {1420-3049}, mesh = {Animals ; Anti-Bacterial Agents/*chemistry/isolation &amp; purification ; Drug Discovery ; *Environmental Microbiology ; Genes, Bacterial ; Humans ; Insecta/microbiology ; Molecular Typing ; Polyketides/*chemistry/isolation &amp; purification ; }, abstract = {Bacterial polyketides are highly biologically active molecules that are frequently used as drugs, particularly as antibiotics and anticancer agents, thus the discovery of new polyketides is of major interest. Since the 1980s discovery of polyketides has slowed dramatically due in large part to the repeated rediscovery of known compounds. While recent scientific and technical advances have improved our ability to discover new polyketides, one key area has been under addressed, namely the distribution of polyketide-producing bacteria in the environment. Identifying environments where producing bacteria are abundant and diverse should improve our ability to discover (bioprospect) new polyketides. This review summarizes for the bioprospector the state-of-the-field in terrestrial microbial ecology. It provides insight into the scientific and technical challenges limiting the application of microbial ecology discoveries for bioprospecting and summarizes key developments in the field that will enable more effective bioprospecting. The major recent efforts by researchers to sample new environments for polyketide discovery is also reviewed and key emerging environments such as insect associated bacteria, desert soils, disease suppressive soils, and caves are highlighted. Finally strategies for taking and characterizing terrestrial samples to help maximize discovery efforts are proposed and the inclusion of non-actinomycetal bacteria in any terrestrial discovery strategy is recommended.}, }
@article {pmid28466638, year = {2017}, author = {Bai, L and Cao, C and Wang, C and Xu, H and Zhang, H and Slaveykova, VI and Jiang, H}, title = {Toward Quantitative Understanding of the Bioavailability of Dissolved Organic Matter in Freshwater Lake during Cyanobacteria Blooming.}, journal = {Environmental science &amp; technology}, volume = {51}, number = {11}, pages = {6018-6026}, doi = {10.1021/acs.est.7b00826}, pmid = {28466638}, issn = {1520-5851}, mesh = {Biological Availability ; *Bioreactors ; China ; *Cyanobacteria ; Eutrophication ; Lakes ; *Organic Chemicals ; }, abstract = {Occurrence of cyanobacterial harmful algal blooms (CyanoHAB) can induce considerable patchiness in the concentration and bioavailability of dissolved organic matter (DOM), which could influence biogeochemical processes and fuel microbial metabolism. In the present study, a laboratory 4-stage plug-flow bioreactor was used to successfully separate the CyanoHAB-derived DOM isolated from the eutrophic Lake Taihu (China) into continuum classes of bioavailable compounds. A combination of new state-of-the-art tools borrowed from analytical chemistry and microbial ecology were used to characterize quantitatively the temporary evolution of DOM and to get deeper insights into its bioavailability. The results showed a total 79% dissolved organic carbon loss over time accompanied by depletion of protein-like fluorescent components, especially the relatively hydrophilic ones. However, hydrophilic humic-like fluorescent components exhibited bioresistant behavior. Consistently, ultrahigh resolution mass spectrometry (FTICR-MS) revealed that smaller, less aromatic, more oxygenated, and nitrogen-rich molecules were preferentially consumed by microorganisms with the production of lipid-like species, whereas recalcitrant molecules were primarily composed of carboxylic-rich alicyclic compounds. Moreover, the bioavailability of DOM was negatively correlated with microbial community diversity in the bioreactor. Results from this study provide deeper insights into the fate of DOM and relevant biogeochemical processes in eutrophic lakes.}, }
@article {pmid28466089, year = {2017}, author = {Prado-Irwin, SR and Bird, AK and Zink, AG and Vredenburg, VT}, title = {Intraspecific Variation in the Skin-Associated Microbiome of a Terrestrial Salamander.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {745-756}, pmid = {28466089}, issn = {1432-184X}, support = {R25 GM059298/GM/NIGMS NIH HHS/United States ; R25-GM059298//National Institutes of Health (US)/ ; DGE-1144152//National Science Foundation/ ; IOS - 1258133//National Science Foundation/ ; }, mesh = {Age Factors ; Animals ; Bacteria/classification/*isolation &amp; purification ; California ; Female ; Geography ; Male ; *Microbiota ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sex Factors ; Skin/*microbiology ; Caudata/*microbiology ; }, abstract = {Resident microbial communities living on amphibian skin can have significant effects on host health, yet the basic ecology of the host-microbiome relationship of many amphibian taxa is poorly understood. We characterized intraspecific variation in the skin microbiome of the salamander Ensatina eschscholtzii xanthoptica, a subspecies composed of four genetically distinct populations distributed throughout the San Francisco Bay Area and the Sierra Nevada mountains in California, USA. We found that salamanders from four geographically and genetically isolated populations harbor similar skin microbial communities, which are dominated by a common core set of bacterial taxa. Additionally, within a population, the skin microbiome does not appear to differ significantly between salamanders of different ages or sexes. In all cases, the salamander skin microbiomes were significantly different from those of the surrounding terrestrial environment. These results suggest that the relationship between E. e. xanthoptica salamanders and their resident skin microbiomes is conserved, possibly indicating a stable mutualism between the host and microbiome.}, }
@article {pmid28465424, year = {2017}, author = {Mund, A and Diggle, SP and Harrison, F}, title = {The Fitness of Pseudomonas aeruginosa Quorum Sensing Signal Cheats Is Influenced by the Diffusivity of the Environment.}, journal = {mBio}, volume = {8}, number = {3}, pages = {}, pmid = {28465424}, issn = {2150-7511}, mesh = {Bacterial Proteins/genetics ; Culture Media/chemistry ; Environment ; *Genetic Fitness ; Mutation ; Pseudomonas aeruginosa/*genetics/growth &amp; development/pathogenicity/*physiology ; Quorum Sensing/*genetics ; Virulence ; }, abstract = {Experiments examining the social dynamics of bacterial quorum sensing (QS) have focused on mutants which do not respond to signals and the role of QS-regulated exoproducts as public goods. The potential for QS signal molecules to themselves be social public goods has received much less attention. Here, we analyze how signal-deficient (lasI) mutants of the opportunistic pathogen Pseudomonas aeruginosa interact with wild-type cells in an environment where QS is required for growth. We show that when growth requires a "private" intracellular metabolic mechanism activated by the presence of QS signal, lasI mutants act as social cheats and outcompete signal-producing wild-type bacteria in mixed cultures, because they can exploit the signals produced by wild-type cells. However, reducing the ability of signal molecules to diffuse through the growth medium results in signal molecules becoming less accessible to mutants, leading to reduced cheating. Our results indicate that QS signal molecules can be considered social public goods in a way that has been previously described for other exoproducts but that spatial structuring of populations reduces exploitation by noncooperative signal cheats.IMPORTANCE Bacteria communicate via signaling molecules to regulate the expression of a whole range of genes. This process, termed quorum sensing (QS), moderates bacterial metabolism under many environmental conditions, from soil and water (where QS-regulated genes influence nutrient cycling) to animal hosts (where QS-regulated genes determine pathogen virulence). Understanding the ecology of QS could therefore yield vital clues to how we might modify bacterial behavior for environmental or clinical gains. Here, we demonstrate that QS signals act as shareable public goods. This means that their evolution, and therefore population-level responses to interference with QS, will be constrained by population structure. Further, we show that environmental structure (constraints on signal diffusion) alters the accessibility of QS signals and demonstrates that we need to consider population and environmental structure to help us further our understanding of QS signaling systems.}, }
@article {pmid28464950, year = {2017}, author = {Johnston, D and Earley, B and Cormican, P and Murray, G and Kenny, DA and Waters, SM and McGee, M and Kelly, AK and McCabe, MS}, title = {Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue.}, journal = {BMC veterinary research}, volume = {13}, number = {1}, pages = {118}, pmid = {28464950}, issn = {1746-6148}, mesh = {Animals ; Bacterial Infections/microbiology/veterinary ; Bovine Respiratory Disease Complex/*microbiology ; Cattle/microbiology ; DNA, Bacterial/genetics ; Female ; Fusobacteria/genetics ; Leptotrichia/genetics ; Lung/*microbiology ; Lymph Nodes/*microbiology ; Male ; Mediastinum/microbiology ; Mycoplasma/genetics ; Pasteurellaceae/genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {BACKGROUND: Bovine respiratory disease (BRD) is caused by growth of single or multiple species of pathogenic bacteria in lung tissue following stress and/or viral infection. Next generation sequencing of 16S ribosomal RNA gene PCR amplicons (NGS 16S amplicon analysis) is a powerful culture-independent open reference method that has recently been used to increase understanding of BRD-associated bacteria in the upper respiratory tract of BRD cattle. However, it has not yet been used to examine the microbiome of the bovine lower respiratory tract. The objective of this study was to use NGS 16S amplicon analysis to identify bacteria in post-mortem lung and lymph node tissue samples harvested from fatal BRD cases and clinically healthy animals. Cranial lobe and corresponding mediastinal lymph node post-mortem tissue samples were collected from calves diagnosed as BRD cases by veterinary laboratory pathologists and from clinically healthy calves. NGS 16S amplicon libraries, targeting the V3-V4 region of the bacterial 16S rRNA gene were prepared and sequenced on an Illumina MiSeq. Quantitative insights into microbial ecology (QIIME) was used to determine operational taxonomic units (OTUs) which corresponded to the 16S rRNA gene sequences.<br><br>RESULTS: Leptotrichiaceae, Mycoplasma, Pasteurellaceae, and Fusobacterium were the most abundant OTUs identified in the lungs and lymph nodes of the calves which died from BRD. Leptotrichiaceae, Fusobacterium, Mycoplasma, Trueperella and Bacteroides had greater relative abundances in post-mortem lung samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Leptotrichiaceae, Mycoplasma and Pasteurellaceae showed higher relative abundances in post-mortem lymph node samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Two Leptotrichiaceae sequence contigs were subsequently assembled from bacterial DNA-enriched shotgun sequences.<br><br>CONCLUSIONS: The microbiomes of the cranial lung lobe and mediastinal lymph node from calves which died from BRD and from clinically healthy H-F calves have been characterised. Contigs corresponding to the abundant Leptotrichiaceae OTU were sequenced and found not to be identical to any known bacterial genus. This suggests that we have identified a novel bacterial species associated with BRD.}, }
@article {pmid28461155, year = {2017}, author = {Harish, A and Kurland, CG}, title = {Akaryotes and Eukaryotes are independent descendants of a universal common ancestor.}, journal = {Biochimie}, volume = {138}, number = {}, pages = {168-183}, doi = {10.1016/j.biochi.2017.04.013}, pmid = {28461155}, issn = {1638-6183}, mesh = {Archaea/genetics ; Bacteria/genetics ; Bayes Theorem ; Eukaryota/genetics ; *Evolution, Molecular ; *Genome ; Mitochondria ; *Models, Genetic ; *Phylogeny ; *Proteome ; }, abstract = {We reconstructed a global tree of life (ToL) with non-reversible and non-stationary models of genome evolution that root trees intrinsically. We implemented Bayesian model selection tests and compared the statistical support for four conflicting ToL hypotheses. We show that reconstructions obtained with a Bayesian implementation (Klopfstein et al., 2015) are consistent with reconstructions obtained with an empirical Sankoff parsimony (ESP) implementation (Harish et al., 2013). Both are based on the genome contents of coding sequences for protein domains (superfamilies) from hundreds of genomes. Thus, we conclude that the independent descent of Eukaryotes and Akaryotes (archaea and bacteria) from the universal common ancestor (UCA) is the most probable as well as the most parsimonious hypothesis for the evolutionary origins of extant genomes. Reconstructions of ancestral proteomes by both Bayesian and ESP methods suggest that at least 70% of unique domain-superfamilies known in extant species were present in the UCA. In addition, identification of a vast majority (96%) of the mitochondrial superfamilies in the UCA proteome precludes a symbiotic hypothesis for the origin of eukaryotes. Accordingly, neither the archaeal origin of eukaryotes nor the bacterial origin of mitochondria is supported by the data. The proteomic complexity of the UCA suggests that the evolution of cellular phenotypes in the two primordial lineages, Akaryotes and Eukaryotes, was driven largely by duplication of common superfamilies as well as by loss of unique superfamilies. Finally, innovation of novel superfamilies has played a surprisingly small role in the evolution of Akaryotes and only a marginal role in the evolution of Eukaryotes.}, }
@article {pmid28460328, year = {2017}, author = {Stedtfeld, RD and Stedtfeld, TM and Waseem, H and Fitschen-Brown, M and Guo, X and Chai, B and Williams, MR and Shook, T and Logan, A and Graham, A and Chae, JC and Sul, WJ and VanHouten, J and Cole, JR and Zylstra, GJ and Tiedje, JM and Upham, BL and Hashsham, SA}, title = {Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers.}, journal = {Journal of environmental management}, volume = {198}, number = {Pt 1}, pages = {213-220}, pmid = {28460328}, issn = {1095-8630}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, mesh = {*Drug Resistance, Microbial ; *Environmental Monitoring ; Humans ; Integrases/*genetics ; Integrons ; *RNA, Ribosomal, 16S ; }, abstract = {Antimicrobial resistance genes (ARGs) present in the environment pose a risk to human health due to potential for transfer to human pathogens. Surveillance is an integral part of mitigating environmental dissemination. Quantification of the mobile genetic element class 1 integron-integrase gene (intI1) has been proposed as a surrogate to measuring multiple ARGs. Measurement of such indicator genes can be further simplified by adopting emerging nucleic acids methods such as loop mediated isothermal amplification (LAMP). In this study, LAMP assays were designed and tested for estimating relative abundance of the intI1 gene, which included design of a universal bacteria 16S rRNA gene assay. Following validation of sensitivity and specificity with known bacterial strains, the assays were tested using DNA extracted from river and lake samples. Results showed a significant Pearson correlation (R[2] = 0.8) between the intI1 gene LAMP assay and ARG relative abundance (measured via qPCR). To demonstrate the ruggedness of the LAMP assays, experiments were also run in the hands of relatively "untrained" personnel by volunteer undergraduate students at a local community college using a hand-held real-time DNA analysis device - Gene-Z. Overall, results support use of the intI1 gene as an indicator of ARGs and the LAMP assays exhibit the opportunity for volunteers to monitor environmental samples for anthropogenic pollution outside of a specialized laboratory.}, }
@article {pmid28459967, year = {2017}, author = {Blanchard, LS and Monin, A and Ouertani, H and Touaibia, L and Michel, E and Buret, F and Simonet, P and Morris, CE and Demanèche, S}, title = {Survival and electrotransformation of Pseudomonas syringae strains under simulated cloud-like conditions.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {5}, pages = {}, doi = {10.1093/femsec/fix057}, pmid = {28459967}, issn = {1574-6941}, mesh = {Adaptation, Physiological/*genetics ; Biological Evolution ; DNA, Bacterial/metabolism ; Electric Stimulation ; Electroporation/methods ; Escherichia coli/genetics ; Gene Transfer, Horizontal/*genetics ; Ice ; Lightning ; Pseudomonas syringae/*genetics/growth &amp; development/*metabolism ; Weather ; }, abstract = {To diversify their genetic material, and thereby allow adaptation to environmental disturbances and colonization of new ecological niches, bacteria use various evolutionary processes, including the acquisition of new genetic material by horizontal transfer mechanisms such as conjugation, transduction and transformation. Electrotransformation mediated by lightning-related electrical phenomena may constitute an additional gene-transfer mechanism occurring in nature. The presence in clouds of bacteria such as Pseudomonas syringae capable of forming ice nuclei that lead to precipitation, and that are likely to be involved in triggering lightning, led us to postulate that natural electrotransformation in clouds may contribute to the adaptive potential of these bacteria. Here, we quantify the survival rate of 10 P. syringae strains in liquid and icy media under such electrical pulses and their capacity to acquire exogenous DNA. In comparison to two other bacteria (Pseudomonas sp. N3 and Escherichia coli TOP10), P. syringae CC0094 appears to be best adapted for survival and for genetic electrotransformation under these conditions, which suggests that this bacterium would be able to survive and to get a boost in its adaptive potential while being transported in clouds and falling back to Earth with precipitation from storms.}, }
@article {pmid28459886, year = {2017}, author = {Tress, B and Dorn, ES and Suchodolski, JS and Nisar, T and Ravindran, P and Weber, K and Hartmann, K and Schulz, BS}, title = {Bacterial microbiome of the nose of healthy dogs and dogs with nasal disease.}, journal = {PloS one}, volume = {12}, number = {5}, pages = {e0176736}, pmid = {28459886}, issn = {1932-6203}, mesh = {Animals ; Chronic Disease ; Dog Diseases/*microbiology/pathology ; Dogs ; Female ; Male ; *Microbiota/genetics ; Nose/*microbiology/pathology ; Nose Neoplasms/microbiology/pathology/*veterinary ; RNA, Ribosomal, 16S/genetics ; Rhinitis/microbiology/pathology/*veterinary ; }, abstract = {The role of bacterial communities in canine nasal disease has not been studied so far using next generation sequencing methods. Sequencing of bacterial 16S rRNA genes has revealed that the canine upper respiratory tract harbors a diverse microbial community; however, changes in the composition of nasal bacterial communities in dogs with nasal disease have not been described so far. Aim of the study was to characterize the nasal microbiome of healthy dogs and compare it to that of dogs with histologically confirmed nasal neoplasia and chronic rhinitis. Nasal swabs were collected from healthy dogs (n = 23), dogs with malignant nasal neoplasia (n = 16), and dogs with chronic rhinitis (n = 8). Bacterial DNA was extracted and sequencing of the bacterial 16S rRNA gene was performed. Data were analyzed using Quantitative Insights Into Microbial Ecology (QIIME). A total of 376 Operational Taxonomic Units out of 26 bacterial phyla were detected. In healthy dogs, Moraxella spp. was the most common species, followed by Phyllobacterium spp., Cardiobacteriaceae, and Staphylococcus spp. While Moraxella spp. were significantly decreased in diseased compared to healthy dogs (p = 0.005), Pasteurellaceae were significantly increased (p = 0.001). Analysis of similarities used on the unweighted UniFrac distance metric (p = 0.027) was significantly different when nasal microbial communities of healthy dogs were compared to those of dogs with nasal disease. The study showed that the canine nasal cavity is inhabited by a highly species-rich bacterial community, and suggests significant differences between the nasal microbiome of healthy dogs and dogs with nasal disease.}, }
@article {pmid28453559, year = {2017}, author = {Wen, C and Wu, L and Qin, Y and Van Nostrand, JD and Ning, D and Sun, B and Xue, K and Liu, F and Deng, Y and Liang, Y and Zhou, J}, title = {Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform.}, journal = {PloS one}, volume = {12}, number = {4}, pages = {e0176716}, pmid = {28453559}, issn = {1932-6203}, mesh = {Analysis of Variance ; Biodiversity ; DNA ; High-Throughput Nucleotide Sequencing/*instrumentation ; Microbiota/*genetics ; Polymerase Chain Reaction/*instrumentation ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Soil Microbiology ; }, abstract = {Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered, the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1-3%, p<0.001). Increasing the sequencing depth to 160,000 reads by deep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was observed when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the reproducibility was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used appropriately and with caution. For example, including technical replicates, removing spurious sequences and unrepresentative OTUs, using a clustering method with a high stringency for OTU generation, estimating treatment effects at higher taxonomic levels, and adapting the unique molecular identifier (UMI) and other newly developed methods to lower PCR and sequencing error and to identify true low abundance rare species all can increase reproducibility.}, }
@article {pmid28453251, year = {2017}, author = {Muurinen, J and Stedtfeld, R and Karkman, A and Pärnänen, K and Tiedje, J and Virta, M}, title = {Influence of Manure Application on the Environmental Resistome under Finnish Agricultural Practice with Restricted Antibiotic Use.}, journal = {Environmental science &amp; technology}, volume = {51}, number = {11}, pages = {5989-5999}, doi = {10.1021/acs.est.7b00551}, pmid = {28453251}, issn = {1520-5851}, mesh = {Animals ; *Anti-Bacterial Agents ; Bacteria/genetics ; *Drug Resistance, Microbial ; Finland ; Genes, Bacterial ; *Manure ; Swine ; }, abstract = {The co-occurrence of antibiotic-resistance genes (ARGs) and mobile genetic elements (MGEs) in farm environments can potentially foster the development of antibiotic-resistant pathogens. We studied the resistome of Finnish dairy and swine farms where use of antibiotics is limited to treating bacterial infections and manure is only applied from April to September. The resistome of manure, soil, and tile drainage water from the ditch was investigated from the beginning of the growing season until forage harvest. The relative ARG and MGE abundance was measured using a qPCR array with 363 primer pairs. Manure samples had the highest abundance of ARGs and MGEs, which increased during storage. Immediately following land application, the ARGs abundant in manure were detected in soil, but their abundance decreased over time with many becoming undetectable. This suggests that increases in ARG abundances after fertilizing are temporary and occur annually under agricultural practices that restrict antibiotic use. A few of the ARGs were detected in the ditch water, but most of them were undetected in the manure. Our results document the dissipation and dissemination off farm of ARGs under Finnish limited antibiotic use and suggest that such practices could help reduce the load of antibiotic-resistance genes in the environment.}, }
@article {pmid28451743, year = {2017}, author = {Durand, A and Maillard, F and Foulon, J and Gweon, HS and Valot, B and Chalot, M}, title = {Environmental Metabarcoding Reveals Contrasting Belowground and Aboveground Fungal Communities from Poplar at a Hg Phytomanagement Site.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {795-809}, pmid = {28451743}, issn = {1432-184X}, mesh = {Biodegradation, Environmental ; *DNA Barcoding, Taxonomic ; Ecosystem ; France ; Fungi/*classification/genetics ; Mercury/metabolism ; Microbiota ; Plant Roots/*microbiology ; Populus/*microbiology ; *Soil Microbiology ; }, abstract = {Characterization of microbial communities in stressful conditions at a field level is rather scarce, especially when considering fungal communities from aboveground habitats. We aimed at characterizing fungal communities from different poplar habitats at a Hg-contaminated phytomanagement site by using Illumina-based sequencing, network analysis approach, and direct isolation of Hg-resistant fungal strains. The highest diversity estimated by the Shannon index was found for soil communities, which was negatively affected by soil Hg concentration. Among the significant correlations between soil operational taxonomic units (OTUs) in the co-occurrence network, 80% were negatively correlated revealing dominance of a pattern of mutual exclusion. The fungal communities associated with Populus roots mostly consisted of OTUs from the symbiotic guild, such as members of the Thelephoraceae, thus explaining the lowest diversity found for root communities. Additionally, root communities showed the highest network connectivity index, while rarely detected OTUs from the Glomeromycetes may have a central role in the root network. Unexpectedly high richness and diversity were found for aboveground habitats, compared to the root habitat. The aboveground habitats were dominated by yeasts from the Lalaria, Davidiella, and Bensingtonia genera, not detected in belowground habitats. Leaf and stem habitats were characterized by few dominant OTUs such as those from the Dothideomycete class producing mutual exclusion with other OTUs. Aureobasidium pullulans, one of the dominating OTUs, was further isolated from the leaf habitat, in addition to Nakazawaea populi species, which were found to be Hg resistant. Altogether, these findings will provide an improved point of reference for microbial research on inoculation-based programs of tailings dumps.}, }
@article {pmid28451742, year = {2017}, author = {Rivett, DW and Lilley, AK and Connett, GJ and Carroll, MP and Legg, JP and Bruce, KD}, title = {Contributions of Composition and Interactions to Bacterial Respiration Are Reliant on the Phylogenetic Similarity of the Measured Community.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {757-760}, pmid = {28451742}, issn = {1432-184X}, mesh = {Bacteria/classification ; *Bacterial Physiological Phenomena ; Carbon Dioxide/*metabolism ; Ecotype ; *Microbiota ; Phylogeny ; Pseudomonas aeruginosa/genetics/*physiology ; }, abstract = {Bacterial diversity underpins many ecosystem functions; however, the impact of within-species variation on the relationship between diversity and function remains unclear. Processes involving strain differentiation, such as niche radiation, are often overlooked in studies that focus on phylogenetic variation. This study used bacterial isolates assembled in two comparable microcosm experiments to test how species variation affected ecosystem function. We compared the relationship between diversity and activity (CO2 production) in increasingly diverse multispecies microcosms and with multiple ecotypes of a single species. The bacteria used were isolated from a low-diversity environment and are species of potential clinical significance such as Pseudomonas aeruginosa. All isolates were profiled for single carbon source utilisation. These data showed an increased breadth of resource use in the multiple ecotypes when compared to the mixed-species. The study observed significantly increasing respiration in more complex mixed-species assemblages, which was not observed when ecotypes of a single species were combined. We further demonstrate that the variation observed in the bacterial activity was due to the roles of each of the constituent isolates; between different species, the interactions between the isolates drove the variation in activity, whilst in single species, assemblage variation was due to which isolates were present. We conclude that both between- and within-species variations play different roles in community function, although through different mechanisms, and should be included in models of changing diversity and ecosystem functioning.}, }
@article {pmid28450860, year = {2017}, author = {Harrison, JP and Berry, D}, title = {Vibrational Spectroscopy for Imaging Single Microbial Cells in Complex Biological Samples.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {675}, pmid = {28450860}, issn = {1664-302X}, abstract = {Vibrational spectroscopy is increasingly used for the rapid and non-destructive imaging of environmental and medical samples. Both Raman and Fourier-transform infrared (FT-IR) imaging have been applied to obtain detailed information on the chemical composition of biological materials, ranging from single microbial cells to tissues. Due to its compatibility with methods such as stable isotope labeling for the monitoring of cellular activities, vibrational spectroscopy also holds considerable power as a tool in microbial ecology. Chemical imaging of undisturbed biological systems (such as live cells in their native habitats) presents unique challenges due to the physical and chemical complexity of the samples, potential for spectral interference, and frequent need for real-time measurements. This Mini Review provides a critical synthesis of recent applications of Raman and FT-IR spectroscopy for characterizing complex biological samples, with a focus on developments in single-cell imaging. We also discuss how new spectroscopic methods could be used to overcome current limitations of single-cell analyses. Given the inherent complementarity of Raman and FT-IR spectroscopic methods, we discuss how combining these approaches could enable us to obtain new insights into biological activities either in situ or under conditions that simulate selected properties of the natural environment.}, }
@article {pmid28449738, year = {2017}, author = {Mahon, BM and Brehony, C and McGrath, E and Killeen, J and Cormican, M and Hickey, P and Keane, S and Hanahoe, B and Dolan, A and Morris, D}, title = {Indistinguishable NDM-producing Escherichia coli isolated from recreational waters, sewage, and a clinical specimen in Ireland, 2016 to 2017.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {22}, number = {15}, pages = {}, pmid = {28449738}, issn = {1560-7917}, mesh = {*Bathing Beaches ; Enterobacteriaceae/classification/*enzymology/*isolation &amp; purification ; Feces/microbiology ; Humans ; Ireland ; Sewage/*microbiology ; *Water Microbiology ; Water Pollutants/*isolation &amp; purification ; beta-Lactamases/*metabolism ; }, abstract = {In this study, New Delhi metallo-beta-lactamase (NDM)-producing Enterobacteriaceae were identified in Irish recreational waters and sewage. Indistinguishable NDM-producing Escherichia coli by pulsed-field gel electrophoresis were isolated from sewage, a fresh water stream and a human source. NDM-producing Klebsiella pneumoniae isolated from sewage and seawater in the same area were closely related to each other and to a human isolate. This raises concerns regarding the potential for sewage discharges to contribute to the spread of carbapenemase-producing Enterobacteriaceae.}, }
@article {pmid28448616, year = {2017}, author = {Yarygin, K and Tyakht, A and Larin, A and Kostryukova, E and Kolchenko, S and Bitner, V and Alexeev, D}, title = {Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses.}, journal = {PloS one}, volume = {12}, number = {4}, pages = {e0176154}, pmid = {28448616}, issn = {1932-6203}, mesh = {Algorithms ; Anti-Bacterial Agents/pharmacology ; Gastrointestinal Microbiome/drug effects/*genetics ; *Gene Expression Profiling ; *Metagenomics ; }, abstract = {The gut microbiota is essentially a multifunctional bioreactor within a human being. The exploration of its enormous metabolic potential provides insights into the mechanisms underlying microbial ecology and interactions with the host. The data obtained using "shotgun" metagenomics capture information about the whole spectrum of microbial functions. However, each new study presenting new sequencing data tends to extract only a little of the information concerning the metabolic potential and often omits specific functions. A meta-analysis of the available data with an emphasis on biomedically relevant gene groups can unveil new global trends in the gut microbiota. As a step toward the reuse of metagenomic data, we developed a method for the quantitative profiling of user-defined groups of genes in human gut metagenomes. This method is based on the quick analysis of a gene coverage matrix obtained by pre-mapping the metagenomic reads to a global gut microbial catalogue. The method was applied to profile the abundance of several gene groups related to antibiotic resistance, phages, biosynthesis clusters and carbohydrate degradation in 784 metagenomes from healthy populations worldwide and patients with inflammatory bowel diseases and obesity. We discovered country-wise functional specifics in gut resistome and virome compositions. The most distinct features of the disease microbiota were found for Crohn's disease, followed by ulcerative colitis and obesity. Profiling of the genes belonging to crAssphage showed that its abundance varied across the world populations and was not associated with clinical status. We demonstrated temporal resilience of crAssphage and the influence of the sample preparation protocol on its detected abundance. Our approach offers a convenient method to add value to accumulated "shotgun" metagenomic data by helping researchers state and assess novel biological hypotheses.}, }
@article {pmid28439658, year = {2017}, author = {Lee, JY and Han, GG and Choi, J and Jin, GD and Kang, SK and Chae, BJ and Kim, EB and Choi, YJ}, title = {Pan-Genomic Approaches in Lactobacillus reuteri as a Porcine Probiotic: Investigation of Host Adaptation and Antipathogenic Activity.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {709-721}, pmid = {28439658}, issn = {1432-184X}, support = {914005-04//Strategic Initiative for Microbiomes in Agriculture and Food, Ministry of Agriculture, Food and Rural Affairs, Republic of Korea/ ; 520160476//2016 Research Grant from Kangwon National University/ ; }, mesh = {Animals ; Feces/microbiology ; *Genome, Bacterial ; Genomics/methods ; Limosilactobacillus reuteri/chemistry/*genetics ; Probiotics/*analysis/metabolism ; *Sus scrofa/genetics/metabolism/microbiology ; }, abstract = {After the introduction of a ban on the use of antibiotic growth promoters (AGPs) for livestock, reuterin-producing Lactobacillus reuteri is getting attention as an alternative to AGPs. In this study, we investigated genetic features of L. reuteri associated with host specificity and antipathogenic effect. We isolated 104 L. reuteri strains from porcine feces, and 16 strains, composed of eight strains exhibiting the higher antipathogenic effect (group HS) and eight strains exhibiting the lower effect (group LS), were selected for genomic comparison. We generated draft genomes of the 16 isolates and investigated their pan-genome together with the 26 National Center for Biotechnology Information-registered genomes. L. reuteri genomes organized six clades with multi-locus sequence analysis, and the clade IV includes the 16 isolates. First, we identified six L. reuteri clade IV-specific genes including three hypothetical protein-coding genes. The three annotated genes encode transposases and cell surface proteins, indicating that these genes are the result of adaptation to the host gastrointestinal epithelia and that these host-specific traits were acquired by horizontal gene transfer. We also identified differences between groups HS and LS in the pdu-cbi-cob-hem gene cluster, which is essential for reuterin and cobalamin synthesis, and six genes specific to group HS are revealed. While the strains of group HS possessed all genes of this cluster, LS strains have lost many genes of the cluster. This study provides a deeper understanding of the relationship between probiotic properties and genomic features of L. reuteri.}, }
@article {pmid28439126, year = {2017}, author = {Rodriguez Herrero, E and Boon, N and Pauwels, M and Bernaerts, K and Slomka, V and Quirynen, M and Teughels, W}, title = {Necrotrophic growth of periodontopathogens is a novel virulence factor in oral biofilms.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1107}, pmid = {28439126}, issn = {2045-2322}, mesh = {Bacteria/*growth &amp; development/*metabolism ; Biofilms/*growth &amp; development ; Cell Survival ; Epithelial Cells/microbiology/physiology ; Humans ; Mouth/*microbiology ; Up-Regulation ; Virulence ; Virulence Factors/biosynthesis ; }, abstract = {The oral use of antimicrobial agents embedded in toothpastes and mouth rinses results in an oral microbial massacre with high amounts of dead bacteria in close proximity to few surviving bacteria. It was hypothesized that this provides the surviving pathogenic bacteria a large amount of dead microbial biomass as a nutritional source for growth (necrotrophy). This study demonstrated the necrotrophic growth of periodontal pathogens in the presence of different dead oral species. In addition, the presence of dead bacteria resulted in an outgrowth of several periodontal pathogens in complex multi-species biofilms. Additionally, upon contact with dead oral bacteria, virulence genes of P. intermedia and P. gingivalis were up-regulated (necrovirulence). This resulted in a more pronounced epithelial cytotoxicity (necrotoxicity). These findings indicate that presence of dead bacteria induce necrotrophy, necrovirulence and necrotoxicity in several oral pathogens.}, }
@article {pmid28438356, year = {2017}, author = {Di Cesare, A and Eckert, EM and Rogora, M and Corno, G}, title = {Rainfall increases the abundance of antibiotic resistance genes within a riverine microbial community.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {226}, number = {}, pages = {473-478}, doi = {10.1016/j.envpol.2017.04.036}, pmid = {28438356}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents ; Bacteria/drug effects ; Drug Resistance, Microbial/*genetics ; *Environmental Monitoring ; *Genes, Bacterial ; Humans ; *Rain ; Rivers/*microbiology ; Soil ; }, abstract = {Infections with antibiotic resistant bacteria are among the major threats for human health. Studies elucidating the role of the environment in their spread are still in their infancy, it, however, seems that different environments might function as a long-term reservoir of antibiotic resistance genes (ARGs) that reside within their microbial communities. An increasing number of studies target the presence and the persistence of ARGs in waters and soils that are exposed to human activities; they, however, rarely consider the spatial/temporal variability that predominate in these environments. Here we evaluated the effect of a moderate rain event (4 mm rain h[-1]) on the abundance and distribution of ARGs (tetA, ermB, blaCTXM, sulII, and qnrS), by comparing measurements of gene abundances during the rainfall to the yearly average, in the waters of a large subalpine river. ARG abundances, which all increased during the rain event, were then correlated to several microbiological, physical and chemical variables, in order to establish their potential origin. Increments in ARG abundances during rainfall (total ARGs: 24 fold) was concomitant to an increase in total phosphorous, N-NH4, and microbial aggregates. Our results show a strong influence of a moderate rainfall on the abundances of ARGs, and suggest the catchment as their source. The impact of moderate rainfalls in areas exposed to anthropic activities should then be considered in modelling and management of ARG dynamics.}, }
@article {pmid28437664, year = {2017}, author = {de Boer, W}, title = {Upscaling of fungal-bacterial interactions: from the lab to the field.}, journal = {Current opinion in microbiology}, volume = {37}, number = {}, pages = {35-41}, doi = {10.1016/j.mib.2017.03.007}, pmid = {28437664}, issn = {1879-0364}, mesh = {Bacteria/*growth &amp; development ; *Biota ; Fungi/*growth &amp; development ; *Microbial Interactions ; Plant Diseases/*prevention &amp; control ; Plants/*microbiology ; }, abstract = {Fungal-bacterial interactions (FBI) are an integral component of microbial community networks in terrestrial ecosystems. During the last decade, the attention for FBI has increased tremendously. For a wide variety of FBI, information has become available on the mechanisms and functional responses. Yet, most studies have focused on pairwise interactions under controlled conditions. The question to what extent such studies are relevant to assess the importance of FBI for functioning of natural microbial communities in real ecosystems remains largely unanswered. Here, the information obtained by studying a type of FBI, namely antagonistic interactions between bacteria and plant pathogenic fungi, is discussed for different levels of community complexity. Based on this, general recommendations are given to integrate pairwise and ecosystem FBI studies. This approach could lead to the development of novel strategies to steer terrestrial ecosystem functioning.}, }
@article {pmid28435856, year = {2017}, author = {Kwong, WK and Medina, LA and Koch, H and Sing, KW and Soh, EJY and Ascher, JS and Jaffé, R and Moran, NA}, title = {Dynamic microbiome evolution in social bees.}, journal = {Science advances}, volume = {3}, number = {3}, pages = {e1600513}, pmid = {28435856}, issn = {2375-2548}, support = {R01 GM108477/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bees/*microbiology ; Gastrointestinal Microbiome/*physiology ; Species Specificity ; }, abstract = {The highly social (eusocial) corbiculate bees, comprising the honey bees, bumble bees, and stingless bees, are ubiquitous insect pollinators that fulfill critical roles in ecosystem services and human agriculture. Here, we conduct wide sampling across the phylogeny of these corbiculate bees and reveal a dynamic evolutionary history behind their microbiota, marked by multiple gains and losses of gut associates, the presence of generalist as well as host-specific strains, and patterns of diversification driven, in part, by host ecology (for example, colony size). Across four continents, we found that different host species have distinct gut communities, largely independent of geography or sympatry. Nonetheless, their microbiota has a shared heritage: The emergence of the eusocial corbiculate bees from solitary ancestors appears to coincide with the acquisition of five core gut bacterial lineages, supporting the hypothesis that host sociality facilitates the development and maintenance of specialized microbiomes.}, }
@article {pmid28435195, year = {2017}, author = {Sugiharto, S and Yudiarti, T and Isroli, I and Widiastuti, E and Putra, FD}, title = {Intestinal microbial ecology and hematological parameters of broiler fed cassava waste pulp fermented with Acremonium charticola.}, journal = {Veterinary world}, volume = {10}, number = {3}, pages = {324-330}, pmid = {28435195}, issn = {0972-8988}, abstract = {AIM: The aim of this study was to evaluate the effect of feeding Acremonium charticola-fermented cassava pulp (AC-FCP) on the intestinal microbial ecology and hematological indices of broiler chickens.<br><br>MATERIALS AND METHODS: A total of 240 male Lohman day-old-chicks were randomly allotted to one of the four experimental diets including control diet, control diet + antimicrobials (neomycin; 300 mg/kg diet), diet containing AC-FCP (16 g/100 g diet) or diet containing AC-FCP + antimicrobials. At day 28, the birds from each pen were blood sampled, sacrificed and immediately the internal organs were removed and weighed. Digesta were obtained from the ileum and cecum.<br><br>RESULTS: Birds fed AC-FCP had lower (p<0.05) coliform bacteria count in the ileal digesta than birds fed control diet or control diet + antimicrobials. Butiric acid was higher (p<0.05) in the cecal content of birds fed AC-FCP than in other birds. Propionic acid was also higher in AC-FCP fed birds than in other birds although statistically not significant. The percentages of lymphocytes and heterophils were higher (p<0.05) and tended (p=0.07) to be lower, respectively, in broilers fed control diet than in other birds. The birds provided control diet had lower (p<0.05) heterophils to lymphocytes ratio compared to those receiving AC-FCP or AC-FCP + antimicrobials. Serum total protein and globulin were higher (p<0.01) in birds fed control diet or control diet + antimicrobials compared to AC-FCP or AC-FCP + antimicrobials fed birds. Serum albumin was lower (p<0.01) in AC-FCP birds than that in other birds. There was a tendency (p=0.09) that birds fed AC-FCP diet had lower total serum cholesterol than other birds.<br><br>CONCLUSION: Feeding AC-FCP has potential to improve the intestinal health and protect the birds from acute infections.}, }
@article {pmid28431360, year = {2017}, author = {Doğan-Subaşı, E and Elsner, M and Qiu, S and Cretnik, S and Atashgahi, S and Shouakar-Stash, O and Boon, N and Dejonghe, W and Bastiaens, L}, title = {Contrasting dual (C, Cl) isotope fractionation offers potential to distinguish reductive chloroethene transformation from breakdown by permanganate.}, journal = {The Science of the total environment}, volume = {596-597}, number = {}, pages = {169-177}, doi = {10.1016/j.scitotenv.2017.03.292}, pmid = {28431360}, issn = {1879-1026}, abstract = {cis-1,2-Dichloroethene (cis-DCE) and trichloroethene (TCE) are persistent, toxic and mobile pollutants in groundwater systems. They are both conducive to reductive dehalogenation and to oxidation by permanganate. In this study, the potential of dual element (C, Cl) compound specific isotope analyses (CSIA) for distinguishing between chemical oxidation and anaerobic reductive dechlorination of cis-DCE and TCE was investigated. Well-controlled cis-DCE degradation batch tests gave similar carbon isotope enrichment factors εC (‰), but starkly contrasting dual element isotope slopes Δδ[13]C/Δδ[37]Cl for permanganate oxidation (εC=-26‰±6‰, Δδ[13]C/Δδ[37]Cl≈-125±47) compared to reductive dechlorination (εC=-18‰±4‰, Δδ[13]C/Δδ[37]Cl≈4.5±3.4). The difference can be tracked down to distinctly different chlorine isotope fractionation: an inverse isotope effect during chemical oxidation (εCl=+0.2‰±0.1‰) compared to a large normal isotope effect in reductive dechlorination (εCl=-3.3‰±0.9‰) (p≪0.05). A similar trend was observed for TCE. The dual isotope approach was evaluated in the field before and up to 443days after a pilot scale permanganate injection in the subsurface. Our study indicates, for the first time, the potential of the dual element isotope approach for distinguishing cis-DCE (and TCE) concentration drops caused by dilution, oxidation by permanganate and reductive dechlorination both at laboratory and field scale.}, }
@article {pmid28430940, year = {2017}, author = {Coton, M and Pawtowski, A and Taminiau, B and Burgaud, G and Deniel, F and Coulloumme-Labarthe, L and Fall, A and Daube, G and Coton, E}, title = {Unraveling microbial ecology of industrial-scale Kombucha fermentations by metabarcoding and culture-based methods.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {5}, pages = {}, doi = {10.1093/femsec/fix048}, pmid = {28430940}, issn = {1574-6941}, mesh = {Acetic Acid/metabolism ; Acetobacter/classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Biofilms/growth &amp; development ; Dekkera/classification/genetics/isolation &amp; purification ; Fermentation/*physiology ; Hanseniaspora/classification/genetics/isolation &amp; purification ; Kombucha Tea/*microbiology ; Lactic Acid/metabolism ; Microbiota/*genetics ; Mycological Typing Techniques ; Oenococcus/classification/genetics/isolation &amp; purification ; Saccharomyces cerevisiae/classification/genetics/isolation &amp; purification ; Zygosaccharomyces/classification/genetics/isolation &amp; purification ; }, abstract = {Kombucha, historically an Asian tea-based fermented drink, has recently become trendy in Western countries. Producers claim it bears health-enhancing properties that may come from the tea or metabolites produced by its microbiome. Despite its long history of production, microbial richness and dynamics have not been fully unraveled, especially at an industrial scale. Moreover, the impact of tea type (green or black) on microbial ecology was not studied. Here, we compared microbial communities from industrial-scale black and green tea fermentations, still traditionally carried out by a microbial biofilm, using culture-dependent and metabarcoding approaches. Dominant bacterial species belonged to Acetobacteraceae and to a lesser extent Lactobacteriaceae, while the main identified yeasts corresponded to Dekkera, Hanseniaspora and Zygosaccharomyces during all fermentations. Species richness decreased over the 8-day fermentation. Among acetic acid bacteria, Gluconacetobacter europaeus, Gluconobacter oxydans, G. saccharivorans and Acetobacter peroxydans emerged as dominant species. The main lactic acid bacteria, Oenococcus oeni, was strongly associated with green tea fermentations. Tea type did not influence yeast community, with Dekkera bruxellensis, D. anomala, Zygosaccharomyces bailii and Hanseniaspora valbyensis as most dominant. This study unraveled a distinctive core microbial community which is essential for fermentation control and could lead to Kombucha quality standardization.}, }
@article {pmid28430189, year = {2017}, author = {Cheng, L and Zhang, N and Yuan, M and Xiao, J and Qin, Y and Deng, Y and Tu, Q and Xue, K and Van Nostrand, JD and Wu, L and He, Z and Zhou, X and Leigh, MB and Konstantinidis, KT and Schuur, EA and Luo, Y and Tiedje, JM and Zhou, J}, title = {Warming enhances old organic carbon decomposition through altering functional microbial communities.}, journal = {The ISME journal}, volume = {11}, number = {8}, pages = {1825-1835}, pmid = {28430189}, issn = {1751-7370}, mesh = {Bacteria/classification/genetics ; Carbon/*chemistry ; *Climate Change ; *Hot Temperature ; Metagenomics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Soil organic matter (SOM) stocks contain nearly three times as much carbon (C) as the atmosphere and changes in soil C stocks may have a major impact on future atmospheric carbon dioxide concentrations and climate. Over the past two decades, much research has been devoted to examining the influence of warming on SOM decomposition in topsoil. Most SOM, however, is old and stored in subsoil. The fate of subsoil SOM under future warming remains highly uncertain. Here, by combining a long-term field warming experiment and a meta-analysis study, we showed that warming significantly increased SOM decomposition in subsoil. We also showed that a decade of warming promoted decomposition of subsoil SOM with turnover times of decades to millennia in a tall grass prairie and this effect was largely associated with shifts in the functional gene structure of microbial communities. By coupling stable isotope probing with metagenomics, we found that microbial communities in warmed soils possessed a higher relative abundance of key functional genes involved in the degradation of organic materials with varying recalcitrance than those in control soils. These findings suggest warming may considerably alter the stability of the vast pool of old SOM in subsoil, contributing to the long-term positive feedback between the C cycle and climate.}, }
@article {pmid28428832, year = {2017}, author = {Scharf, ME and Cai, Y and Sun, Y and Sen, R and Raychoudhury, R and Boucias, DG}, title = {A meta-analysis testing eusocial co-option theories in termite gut physiology and symbiosis.}, journal = {Communicative &amp; integrative biology}, volume = {10}, number = {2}, pages = {e1295187}, pmid = {28428832}, issn = {1942-0889}, support = {R01 AI125982/AI/NIAID NIH HHS/United States ; }, abstract = {The termite gut accomplishes key physiologic functions that underlie termite symbiosis and sociality. However, potential candidate functions of the host-symbiont holobiome have not yet been explored across seemingly divergent processes such as digestion, immunity, caste differentiation, and xenobiotic tolerance. This study took a meta-analysis approach for concurrently studying host and symbiont gut metatranscriptome responses of the lower termite Reticulitermes flavipes, which has ancestral characteristics and hosts a diverse mix of eukaryotic and bacterial symbionts. Thirteen treatments were compared from 5 categories (dietary, social, hormonal, immunological, and xenobiotic), revealing 3 main insights. First, each of the 5 tested colonies had distinct magnitudes of transcriptome response, likely as a result of unique symbiont profiles, which highlights the uniqueness of individual termite colonies. Second, after normalization to standardize colony response magnitudes, unique treatment-linked metatranscriptome topologies became apparent. Third, despite colony and topology differences, 4 co-opted master genes emerged that were universally responsive across diverse treatments. These master genes encode host functions related to protein translation and symbiont functions related to protein degradation and pore formation in microbial cell walls. Three of the 4 master genes were from co-evolved protist symbionts, highlighting potentially co-evolved roles for gut symbiota in coordinating functional responses of the collective host-symbiont holobiome. Lastly, for host genes identified, these results provide annotations of recent termite genome sequences. By revealing conserved domain genes, as well as apparent roles for gut symbiota in holobiome regulation, this study provides new insights into co-opted eusocial genes and symbiont roles in termite sociobiology.}, }
@article {pmid28428272, year = {2017}, author = {Lang, M and Berry, D and Passecker, K and Mesteri, I and Bhuju, S and Ebner, F and Sedlyarov, V and Evstatiev, R and Dammann, K and Loy, A and Kuzyk, O and Kovarik, P and Khare, V and Beibel, M and Roma, G and Meisner-Kober, N and Gasche, C}, title = {HuR Small-Molecule Inhibitor Elicits Differential Effects in Adenomatosis Polyposis and Colorectal Carcinogenesis.}, journal = {Cancer research}, volume = {77}, number = {9}, pages = {2424-2438}, pmid = {28428272}, issn = {1538-7445}, support = {P 24121/FWF_/Austrian Science Fund FWF/Austria ; W 1261/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Adenomatous Polyposis Coli/*genetics/microbiology/pathology ; Animals ; Apoptosis/drug effects ; Carcinogenesis/genetics ; Cell Proliferation/drug effects ; Chemokine CCL11/genetics ; Colorectal Neoplasms/*genetics/microbiology/pathology ; ELAV-Like Protein 1/antagonists &amp; inhibitors/*genetics ; Feces/microbiology ; Furans/administration &amp; dosage ; Gastrointestinal Microbiome/drug effects/genetics ; HCT116 Cells ; Humans ; Inflammatory Bowel Diseases/*genetics/microbiology/pathology ; Interleukin-18/genetics ; Mice ; Naphthols/administration &amp; dosage ; RAW 264.7 Cells ; }, abstract = {HuR is an RNA-binding protein implicated in immune homeostasis and various cancers, including colorectal cancer. HuR binding to AU-rich elements within the 3' untranslated region of mRNAs encoding oncogenes, growth factors, and various cytokines leads message stability and translation. In this study, we evaluated HuR as a small-molecule target for preventing colorectal cancer in high-risk groups such as those with familial adenomatosis polyposis (FAP) or inflammatory bowel disease (IBD). In human specimens, levels of cytoplasmic HuR were increased in colonic epithelial cells from patients with IBD, IBD-cancer, FAP-adenoma, and colorectal cancer, but not in patients with IBD-dysplasia. Intraperitoneal injection of the HuR small-molecule inhibitor MS-444 in AOM/DSS mice, a model of IBD and inflammatory colon cancer, augmented DSS-induced weight loss and increased tumor multiplicity, size, and invasiveness. MS-444 treatment also abrogated tumor cell apoptosis and depleted tumor-associated eosinophils, accompanied by a decrease in IL18 and eotaxin-1. In contrast, HuR inhibition in APC[Min] mice, a model of FAP and colon cancer, diminished the number of small intestinal tumors generated. In this setting, fecal microbiota, evaluated by 16S rRNA gene amplicon sequencing, shifted to a state of reduced bacterial diversity, with an increased representation of Prevotella, Akkermansia, and Lachnospiraceae Taken together, our results indicate that HuR activation is an early event in FAP-adenoma but is not present in IBD-dysplasia. Furthermore, our results offer a preclinical proof of concept for HuR inhibition as an effective means of FAP chemoprevention, with caution advised in the setting of IBD. Cancer Res; 77(9); 2424-38. ©2017 AACR.}, }
@article {pmid28421748, year = {2017}, author = {Podduturi, R and Petersen, MA and Mahmud, S and Rahman, MM and Jørgensen, NOG}, title = {Potential Contribution of Fish Feed and Phytoplankton to the Content of Volatile Terpenes in Cultured Pangasius (Pangasianodon hypophthalmus) and Tilapia (Oreochromis niloticus).}, journal = {Journal of agricultural and food chemistry}, volume = {65}, number = {18}, pages = {3730-3736}, doi = {10.1021/acs.jafc.7b00497}, pmid = {28421748}, issn = {1520-5118}, mesh = {Animal Feed/*analysis ; Animals ; Aquaculture ; Bangladesh ; Catfishes/growth &amp; development/*metabolism ; Cichlids/growth &amp; development/*metabolism ; Meat/*analysis ; Phytoplankton/chemistry/*metabolism ; Seafood/*analysis ; Terpenes/chemistry/*metabolism ; Volatilization ; }, abstract = {Geosmin and 2-methylisoborneol are the most recognized off-flavors in freshwater fish, but terpenes may also contribute off-flavor in fish. We identified six monoterpenes, 11 sesquiterpenes, and three terpene-related compounds in pangasius and tilapia from aquaculture farms in Bangladesh. The concentrations of most of the volatiles were below published odor thresholds, except for α-pinene, limonene, β-caryophyllene, α-humulene, and β-ionone in tilapia, and limonene and β-ionone in pangasius. To identify sources of the terpenes, terpene profiles of fish feed and phytoplankton in the ponds were analyzed. In feed and mustard cake (feed ingredient), five monoterpenes and two sesquiterpenes were identified, and five of these compounds were also detected in the fish. In phytoplankton, 11 monoterpenes were found and three also occurred in the fish. The higher number of terpenes common to both fish and feed, than to fish and phytoplankton, suggests that feed was a more abundant source of odor-active terpenes in the fish than phytoplankton.}, }
@article {pmid28419895, year = {2017}, author = {Lin, HW and Kustermans, C and Vaiopoulou, E and Prévoteau, A and Rabaey, K and Yuan, Z and Pikaar, I}, title = {Electrochemical oxidation of iron and alkalinity generation for efficient sulfide control in sewers.}, journal = {Water research}, volume = {118}, number = {}, pages = {114-120}, doi = {10.1016/j.watres.2017.02.069}, pmid = {28419895}, issn = {1879-2448}, mesh = {Electrochemical Techniques ; Hydrogen Sulfide ; Iron ; Oxidation-Reduction ; *Sewage ; *Sulfides ; }, abstract = {The addition of iron salts is one of the most commonly used dosing strategies for sulfide control in sewers. However, iron salts decrease the sewage pH which not only reduces the effectiveness of sulfide precipitation but also enhances the release of residual sulfide to the sewer atmosphere. Equally important, concentrated iron salt solutions are corrosive and their frequent transport, handling, and on-site storage often come with Occupational Health and Safety (OH&amp;S) concerns. Here, we experimentally demonstrated a novel sulfide control approach using electrochemical systems with parallel placed iron electrodes. This enabled combining anodic dissolved iron species release with cathodic hydroxyl anion production, which alleviates all the aforementioned concerns. A long-term experiment was successfully carried out achieving an average sulfide removal efficiency of 95.4 ± 4.4% at low voltage input of 2.90 ± 0.54 V over the course of 8 weeks. This electrochemical method was demonstrated to successfully achieve efficient sulfide control. In addition, it increases the sewage pH, thereby overcoming the drawbacks associated with the pH decrease in the case of conventional iron salt dosing. Ferrous ions were produced at an overall coulombic efficiency (CE) of 98.2 ± 1.2%, whereas oxygen evolution and direct sulfide oxidation were not observed. Short-term experiments showed that increasing either inter-electrode gap or current density increased the cell voltage associated with the increase in the ohmic drop of the system. Overall, this study highlights the practical potential of in-situ generation of dissolved iron species and simultaneous hydroxyl anion generation for efficient sulfide control in sewers.}, }
@article {pmid28419734, year = {2017}, author = {Wasmund, K and Mußmann, M and Loy, A}, title = {The life sulfuric: microbial ecology of sulfur cycling in marine sediments.}, journal = {Environmental microbiology reports}, volume = {9}, number = {4}, pages = {323-344}, pmid = {28419734}, issn = {1758-2229}, support = {P 25111/FWF_/Austrian Science Fund FWF/Austria ; P 29426/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Ecosystem ; Geologic Sediments/chemistry/*microbiology ; Phylogeny ; Seawater/analysis/microbiology ; Sulfur/analysis/*metabolism ; }, abstract = {Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle.}, }
@article {pmid28419666, year = {2017}, author = {Hotaling, S and Hood, E and Hamilton, TL}, title = {Microbial ecology of mountain glacier ecosystems: biodiversity, ecological connections and implications of a warming climate.}, journal = {Environmental microbiology}, volume = {19}, number = {8}, pages = {2935-2948}, doi = {10.1111/1462-2920.13766}, pmid = {28419666}, issn = {1462-2920}, mesh = {Biodiversity ; Ecology ; *Ecosystem ; *Global Warming ; Hot Temperature ; Ice Cover/*microbiology ; Microbiota/*physiology ; Rivers/*microbiology ; *Water Microbiology ; }, abstract = {Glacier ecosystems are teeming with life on, beneath, and to a lesser degree, within their icy masses. This conclusion largely stems from polar research, with less attention paid to mountain glaciers that overlap environmentally and ecologically with their polar counterparts in some ways, but diverge in others. One difference lies in the susceptibility of mountain glaciers to the near-term threat of climate change, as they tend to be much smaller in both area and volume. Moreover, mountain glaciers are typically steeper, more dependent upon basal sliding for movement, and experience higher seasonal precipitation. Here, we provide a modern synthesis of the microbial ecology of mountain glacier ecosystems, and particularly those at low- to mid-latitudes. We focus on five ecological zones: the supraglacial surface, englacial interior, subglacial bedrock-ice interface, proglacial streams and glacier forefields. For each, we discuss the role of microbiota in biogeochemical cycling and outline ecological and hydrological connections among zones, underscoring the interconnected nature of these ecosystems. Collectively, we highlight the need to: better document the biodiversity and functional roles of mountain glacier microbiota; describe the ecological implications of rapid glacial retreat under climate change and resolve the relative contributions of ecological zones to broader ecosystem function.}, }
@article {pmid28416814, year = {2017}, author = {Kowalchuk, GA and Bailey, MJ}, title = {ISMEJ turns 10: tracking rapid progress in microbial ecology.}, journal = {The ISME journal}, volume = {11}, number = {5}, pages = {1059-1060}, doi = {10.1038/ismej.2017.50}, pmid = {28416814}, issn = {1751-7370}, }
@article {pmid28414441, year = {2017}, author = {Yu, P and Mathieu, J and Yang, Y and Alvarez, PJJ}, title = {Suppression of Enteric Bacteria by Bacteriophages: Importance of Phage Polyvalence in the Presence of Soil Bacteria.}, journal = {Environmental science &amp; technology}, volume = {51}, number = {9}, pages = {5270-5278}, doi = {10.1021/acs.est.7b00529}, pmid = {28414441}, issn = {1520-5851}, mesh = {*Bacteriophages ; Coliphages ; *Enterobacteriaceae ; Escherichia coli ; Soil ; }, abstract = {Bacteriophages are widely recognized for their importance in microbial ecology and bacterial control. However, little is known about how phage polyvalence (i.e., broad host range) affects bacterial suppression and interspecies competition in environments harboring enteric pathogens and soil bacteria. Here we compare the efficacy of polyvalent phage PEf1 versus coliphage T4 in suppressing a model enteric bacterium (E. coli K-12) in mixtures with soil bacteria (Pseudomonas putida F1 and Bacillus subtilis 168). Although T4 was more effective than PEf1 in infecting E. coli K-12 in pure cultures, PEf1 was 20-fold more effective in suppressing E. coli under simulated multispecies biofilm conditions because polyvalence enhanced PEf1 propagation in P. putida. In contrast, soil bacteria do not propagate coliphages and hindered T4 diffusion through the biofilm. Similar tests were also conducted under planktonic conditions to discern how interspecies competition contributes to E. coli suppression without the confounding effects of restricted phage diffusion. Significant synergistic suppression was observed by the combined effects of phages plus competing bacteria. T4 was slightly more effective in suppressing E. coli in these planktonic mixed cultures, even though PEf1 reached higher concentrations by reproducing also in P. putida (7.2 ± 0.4 vs 6.0 ± 1.0 log10PFU/mL). Apparently, enhanced suppression by higher PEf1 propagation was offset by P. putida lysis, which decreased stress from interspecies competition relative to incubations with T4. In similar planktonic tests with more competing soil bacteria species, P. putida lysis was less critical in mitigating interspecies competition and PEf1 eliminated E. coli faster than T4 (36 vs 42 h). Overall, this study shows that polyvalent phages can propagate in soil bacteria and significantly enhance suppression of co-occurring enteric species.}, }
@article {pmid28412534, year = {2017}, author = {Vandermaesen, J and Lievens, B and Springael, D}, title = {Isolation and identification of culturable bacteria, capable of heterotrophic growth, from rapid sand filters of drinking water treatment plants.}, journal = {Research in microbiology}, volume = {168}, number = {6}, pages = {594-607}, doi = {10.1016/j.resmic.2017.03.008}, pmid = {28412534}, issn = {1769-7123}, mesh = {Aeromonas/classification/genetics/isolation &amp; purification ; Alphaproteobacteria/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/*growth &amp; development/*isolation &amp; purification ; Betaproteobacteria/classification/genetics/isolation &amp; purification ; Comamonadaceae/classification/genetics/isolation &amp; purification ; Drinking Water/*microbiology ; Gammaproteobacteria/classification/genetics/isolation &amp; purification ; *Heterotrophic Processes ; High-Throughput Nucleotide Sequencing ; Microbial Consortia/genetics/physiology ; RNA, Ribosomal, 16S ; Silicon Dioxide/chemistry ; Water Purification ; }, abstract = {The microbial community in sand filters (SFs) of drinking water treatment plants (DWTPs) likely contributes to SF functionalities, such as organic carbon removal through heterotrophic metabolism. However, the dynamics and functionality of the SF microbiome and microbial communities in oligotrophic freshwater environments in general, are poorly understood. Therefore, the availability of bacterial strains from these oligotrophic environments is of great interest, but such organisms are currently underrepresented in culture collections. Focusing on heterotrophic carbon metabolism, bacteria were isolated from SFs using conventional media and media that contained SF extracts to mimic the SF environment. The majority of isolates belonged to Betaproteobacteria, more specifically to the families Comamonadaceae (genera Acidovorax, Curvibacter, Hydrogenophaga, Simplicispira, Paucibacter, Pelomonas, Piscinibacter and Rhodoferax) and Oxalobacteraceae (Undibacterium). Additionally, members of Alphaproteobacteria (Mesorhizobium), Gammaproteobacteria (Aeromonas and Perlucidibaca) and Actinobacteria (Rhodococcus and Brachybacterium) were isolated. Several of those genera have only rarely been described, but appear typical inhabitants of oligotrophic freshwater environments. In this regard, the Comamonadaceae isolates are of particular interest. Our study shows that bacteria representative of oligotrophic environments can be isolated using simple isolation procedures. The isolates provide a microbial framework for extending our knowledge of the taxonomy, physiology and functionality of oligotrophic freshwater microbiomes and their interactions with possible invaders.}, }
@article {pmid28411302, year = {2017}, author = {Cañavate, JP and Armada, I and Hachero-Cruzado, I}, title = {Common and Species-Specific Effects of Phosphate on Marine Microalgae Fatty Acids Shape Their Function in Phytoplankton Trophic Ecology.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {623-639}, pmid = {28411302}, issn = {1432-184X}, support = {Atlantic Area 670 Transnational Programme//European Union/ ; }, mesh = {Biomarkers/analysis ; Fatty Acids/*metabolism ; Phosphates/*metabolism ; Phytoplankton/*metabolism ; Species Specificity ; }, abstract = {The use of fatty acids (FA) to infer structure of phytoplankton assemblages and as indicators of microalgae nutritional value is acquiring relevance in modern phytoplankton ecology and new advances concerning factors influencing FA variability among microalgae are demanded. In this regard, the relationship between phosphorus and FA remains particularly little studied in marine phytoplankton. In the present study, we focus on phosphate effects on FA from a diversified set of marine microalgae and provide new insights into the applicability of FA in phytoplankton trophic ecology. Phosphate deprivation mainly induced monounsaturated FA production in eight out of nine microalgae and their changes were species-specific, with palmitoleic acid exhibiting extreme variation and discriminating between haptophyte classes. The important phosphate-induced and interspecific variability found for oleic acid was perceived as a concern for the current application of this FA as a trophic position indicator in grazers. Chloroplast C-16 and C-18 polyunsaturated FA were more affected by phosphate than C-20 and C-22 highly unsaturated FA (HUFA). The relative stability of stearidonic acid to phosphate in cryptophytes and haptophytes pinpointed this FA as a suited marker for both microalgae groups. Taken all species together, phosphate deprivation and taxonomy accounted for 20.8 and 50.7% of total FA variation, respectively. HUFA were minimally affected by phosphate indicating their suitability as indicators of phytoplankton trophic value. The asymptotic relationship between HUFA and phosphorus cell content suggested mineral composition (phosphorus) could be more important than HUFA content as attribute of marine microalgae nutritional value at the species level.}, }
@article {pmid28409197, year = {2017}, author = {Blay, ES and Schwabedissen, SG and Magnuson, TS and Aho, KA and Sheridan, PP and Lohse, KA}, title = {Variation in Biological Soil Crust Bacterial Abundance and Diversity as a Function of Climate in Cold Steppe Ecosystems in the Intermountain West, USA.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {691-700}, pmid = {28409197}, issn = {1432-184X}, support = {#NSF EAR 1331872//National Science Foundation/ ; #P20GM103408//National Institute of General Medical Sciences/ ; }, mesh = {Agriculture ; *Climate ; Climate Change ; Cold Temperature ; Environmental Biomarkers ; *Grassland ; Idaho ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, RNA ; *Soil Microbiology ; }, abstract = {Biological soil crust (biocrust) is a composite of mosses, lichens, and bacteria that performs many important soil system functions, including increasing soil stability, protecting against wind erosion, reducing nutrient loss, and mediating carbon and nitrogen fixation cycles. These cold desert and steppe ecosystems are expected to experience directional changes in both climate and disturbance. These include increased temperatures, precipitation phase changes, and increased disturbance from anthropogenic land use. In this study, we assessed how climate and grazing disturbance may affect the abundance and diversity of bacteria in biocrusts in cold steppe ecosystems located in southwestern Idaho, USA. To our knowledge, our study is the first to document how biocrust bacterial composition and diversity change along a cold steppe climatic gradient. Analyses based on 16S small subunit ribosomal RNA gene sequences identified the phylum Actinobacteria as the major bacterial component within study site biocrusts (relative abundance = 36-51%). The abundance of the phyla Actinobacteria and Firmicutes was higher at elevations experiencing cooler, wetter climates, while the abundance of Cyanobacteria, Proteobacteria, and Chloroflexi decreased. The abundance of the phyla Cyanobacteria and Proteobacteria showed no significant evidence of decline in grazed areas. Taken together, results from this study indicate that bacterial communities from rolling biocrusts found in cold steppe ecosystems are affected by climate regime and differ substantially from other cold desert ecosystems, resulting in potential differences in nutrient cycling and ecosystem dynamics.}, }
@article {pmid28409116, year = {2017}, author = {Lakhujani, V and Badapanda, C}, title = {prepare_taxa_charts.py: A Python program to automate generation of publication ready taxonomic pie chart images from QIIME.}, journal = {Genomics data}, volume = {12}, number = {}, pages = {97-101}, pmid = {28409116}, issn = {2213-5960}, abstract = {QIIME (Quantitative Insights Into Microbial Ecology) is one of the most popular open-source bioinformatics suite for performing metagenome, 16S rRNA amplicon and Internal Transcribed Spacer (ITS) data analysis. Although, it is very comprehensive and powerful tool, it lacks a method to provide publication ready taxonomic pie charts. The script plot_taxa_summary.py bundled with QIIME generate a html file and a folder containing taxonomic pie chart and legend as separate images. The images have randomly generated alphanumeric names. Therefore, it is difficult to associate the pie chart with the legend and the corresponding sample identifier. Even if the option to have the legend within the html file is selected while executing plot_taxa_summary.py, it is very tedious to crop a complete image (having both the pie chart and the legend) due to unequal image sizes. It requires a lot of time to manually prepare the pie charts for multiple samples for publication purpose. Moreover, there are chances of error while identifying the pie chart and legend pair due to random alphanumeric names of the images. To bypass all these bottlenecks and make this process efficient, we have developed a python based program, prepare_taxa_charts.py, to automate the renaming, cropping and merging of taxonomic pie chart and corresponding legend image into a single, good quality publication ready image. This program not only augments the functionality of plot_taxa_summary.py but is also very fast in terms of CPU time and user friendly.}, }
@article {pmid28408760, year = {2017}, author = {Schmidt, R and Jager, V and Zühlke, D and Wolff, C and Bernhardt, J and Cankar, K and Beekwilder, J and Ijcken, WV and Sleutels, F and Boer, W and Riedel, K and Garbeva, P}, title = {Fungal volatile compounds induce production of the secondary metabolite Sodorifen in Serratia plymuthica PRI-2C.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {862}, pmid = {28408760}, issn = {2045-2322}, mesh = {Bacterial Proteins/genetics ; Bridged Bicyclo Compounds/*metabolism ; Energy Metabolism/drug effects ; Fungal Proteins/pharmacology ; Fusarium/*chemistry ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial/drug effects ; Metabolome/drug effects ; Octanes/*metabolism ; Secondary Metabolism/drug effects ; Sequence Analysis, DNA/methods ; Serratia/drug effects/genetics/*growth &amp; development/metabolism ; Volatile Organic Compounds/*pharmacology ; }, abstract = {The ability of bacteria and fungi to communicate with each other is a remarkable aspect of the microbial world. It is recognized that volatile organic compounds (VOCs) act as communication signals, however the molecular responses by bacteria to fungal VOCs remain unknown. Here we perform transcriptomics and proteomics analyses of Serratia plymuthica PRI-2C exposed to VOCs emitted by the fungal pathogen Fusarium culmorum. We find that the bacterium responds to fungal VOCs with changes in gene and protein expression related to motility, signal transduction, energy metabolism, cell envelope biogenesis, and secondary metabolite production. Metabolomic analysis of the bacterium exposed to the fungal VOCs, gene cluster comparison, and heterologous co-expression of a terpene synthase and a methyltransferase revealed the production of the unusual terpene sodorifen in response to fungal VOCs. These results strongly suggest that VOCs are not only a metabolic waste but important compounds in the long-distance communication between fungi and bacteria.}, }
@article {pmid28407513, year = {2017}, author = {Queiroga, FR and Marques-Santos, LF and Hégaret, H and Sassi, R and Farias, ND and Santana, LN and da Silva, PM}, title = {Effects of cyanobacteria Synechocystis spp. in the host-parasite model Crassostrea gasar-Perkinsus marinus.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {187}, number = {}, pages = {100-107}, doi = {10.1016/j.aquatox.2017.03.019}, pmid = {28407513}, issn = {1879-1514}, mesh = {Alveolata/drug effects/*growth &amp; development/immunology ; Animals ; Brazil ; Cell Count ; Cell Survival ; Crassostrea/drug effects/immunology/*parasitology ; Flow Cytometry ; Hemocytes/drug effects/immunology ; *Host-Parasite Interactions/drug effects/immunology ; Marine Toxins/toxicity ; *Models, Biological ; Phagocytosis/drug effects/immunology ; Synechocystis/chemistry/*growth &amp; development ; Water Pollutants, Chemical/toxicity ; }, abstract = {Perkinsosis is a disease caused by protozoan parasites from the Perkinsus genus. In Brazil, two species, P. beihaiensis and P. marinus, are frequently found infecting native oysters (Crassostrea gasar and C. rhizophorae) from cultured and wild populations in several states of the Northeast region. The impacts of this disease in bivalves from Brazil, as well as the interactions with environmental factors, are poorly studied. In the present work, we evaluated the in vitro effects of the cyanobacteria Synechocystis spp. on trophozoites of P. marinus and haemocytes of C. gasar. Four cyanobacteria strains isolated from the Northeast Brazilian coast were used as whole cultures (WCs) and extracellular products (ECPs). Trophozoites of P. marinus were exposed for short (4h) and long (48h and 7days, the latter only for ECPs) periods, while haemocytes were exposed for a short period (4h). Cellular and immune parameters, i.e. cell viability, cell count, reactive oxygen species production (ROS) and phagocytosis of inert (latex beads) and biological particles (zymosan and trophozoites of P. marinus) were measured by flow cytometry. The viability of P. marinus trophozoites was improved in response to WCs of Synechocystis spp., which could be a beneficial effect of the cyanobacteria providing nutrients and reducing reactive oxygen species. Long-term exposure of trophozoites to ECPs of cyanobacteria did not modify in vitro cell proliferation nor viability. In contrast, C. gasar haemocytes showed a reduction in cell viability when exposed to WCs, but not to ECPs. However, ROS production was not altered. Haemocyte ability to engulf latex particles was reduced when exposed mainly to ECPs of cyanobacteria; while neither the WCs nor the ECPs modified phagocytosis of the biological particles, zymosan and P. marinus. Our results suggest a negative effect of cyanobacteria from the Synechocystis genus on host immune cells, in contrast to a more beneficial effect on the parasite cell, which could together disrupt the balance of the host-parasite interaction and make oysters more susceptible to P. marinus as well as opportunistic infections.}, }
@article {pmid28406242, year = {2017}, author = {Ehtesham, E and Bengtson, P}, title = {Decoupling of soil carbon and nitrogen turnover partly explains increased net ecosystem production in response to nitrogen fertilization.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {46286}, pmid = {28406242}, issn = {2045-2322}, abstract = {During the last decade there has been an ongoing controversy regarding the extent to which nitrogen fertilization can increase carbon sequestration and net ecosystem production in forest ecosystems. The debate is complicated by the fact that increased nitrogen availability caused by nitrogen deposition has coincided with increasing atmospheric carbon dioxide concentrations. The latter could further stimulate primary production but also result in increased allocation of carbon to root exudates, which could potentially 'prime' the decomposition of soil organic matter. Here we show that increased input of labile carbon to forest soil caused a decoupling of soil carbon and nitrogen cycling, which was manifested as a reduction in respiration of soil organic matter that coincided with a substantial increase in gross nitrogen mineralization. An estimate of the magnitude of the effect demonstrates that the decoupling could potentially result in an increase in net ecosystem production by up to 51 kg C ha[-1] day[-1] in nitrogen fertilized stands during peak summer. Even if the effect is several times lower on an annual basis, the results still suggest that nitrogen fertilization can have a much stronger influence on net ecosystem production than can be expected from a direct stimulation of primary production alone.}, }
@article {pmid28401707, year = {2017}, author = {Mohr, KI and Zindler, T and Wink, J and Wilharm, E and Stadler, M}, title = {Myxobacteria in high moor and fen: An astonishing diversity in a neglected extreme habitat.}, journal = {MicrobiologyOpen}, volume = {6}, number = {4}, pages = {}, pmid = {28401707}, issn = {2045-8827}, mesh = {*Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Ecosystem ; *Environmental Microbiology ; Myxococcales/*classification/genetics/growth &amp; development/*isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Increasing antibiotic resistances of numerous pathogens mean that myxobacteria, well known producers of new antibiotics, are becoming more and more interesting. More than 100 secondary metabolites, most of them with bioactivity, were described from the order Myxococcales. Especially new myxobacterial genera and species turned out to be reliable sources for novel antibiotics and can be isolated from uncommon neglected habitats like, for example, acidic soils. Almost nothing is known about the diversity of myxobacteria in moors, except some information from cultivation studies of the 1970s. Therefore, we evaluated the myxobacterial community composition of acidic high moor and fen both with cultivation-independent 16S rRNA clone bank analysis and with cultivation. Phylogenetic analyses of clone sequences revealed a great potential of undescribed myxobacteria in high moor and fen, whereby all sequences represent unknown taxa and were detected exclusively by cultivation-independent analyses. However, many clones were assigned to sequences from other cultivation-independent studies of eubacterial diversity in acidic habitats. Cultivation revealed different strains exclusively from the genus Corallococcus. Our study shows that the neglected habitat moor is a promising source and of high interest with regard to the cultivation of prospective new bioactive secondary metabolite producing myxobacteria.}, }
@article {pmid28401262, year = {2017}, author = {da Silva, IR and de Souza, FA and da Silva, DKA and Oehl, F and Maia, LC}, title = {Patterns of Arbuscular Mycorrhizal Fungal Distribution on Mainland and Island Sandy Coastal Plain Ecosystems in Brazil.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {654-669}, pmid = {28401262}, issn = {1432-184X}, support = {563.342/2010-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 491.912/2013-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 351.008/2013-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 302.416/2010-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 446.144/2014-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 140.535/2013-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; AMD-0258-2.00/14//Funda&#xe7;&#xe3;o de Amparo &#xe0; Ci&#xea;ncia e Tecnologia do Estado de Pernambuco (BR)/ ; DCR-0039.2.03/13//Funda&#xe7;&#xe3;o de Amparo &#xe0; Ci&#xea;ncia e Tecnologia do Estado de Pernambuco/ ; }, mesh = {Brazil ; Glomeromycota/*physiology ; Islands ; *Microbiota ; *Mycorrhizae ; *Soil Microbiology ; }, abstract = {Although sandy coastal plains are important buffer zones to protect the coast line and maintain biological diversity and ecosystem services, these ecosystems have been endangered by anthropogenic activities. Thus, information on coastal biodiversity and forces shaping coastal biological diversity are extremely important for effective conservation strategies. In this study, we aimed to compare arbuscular mycorrhizal (AM) fungal communities from soil samples collected on the mainland and nearby islands located in Brazilian sandy coastal plain ecosystems (Restingas) to get information about AM fungal biogeography and identify factors shaping these communities. Soil samples were collected in 2013 and 2014 on the beachfront of the tropical sandy coastal plain at six sites (three island and three mainland locations) across the northeast, southeast, and south regions of Brazil. Overall, we recorded 53 AM fungal species from field and trap culture samples. The richness and diversity of AM fungal species did not differ between mainland and island locations, but AM fungal community assemblages were different between mainland and island environments and among most sites sampled. Glomeromycota communities registered from island samples showed higher heterogeneity than communities from mainland samples. Sandy coastal plains harbor diverse AM fungal communities structured by climatic, edaphic, and spatial factors, while the distance from the colonizing source (mainland environments) does not strongly affect the AM fungal communities in Brazilian coastal environments.}, }
@article {pmid28399822, year = {2017}, author = {De Mandal, S and Chatterjee, R and Kumar, NS}, title = {Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {90}, pmid = {28399822}, issn = {1471-2180}, mesh = {Amino Acids/metabolism ; Ammonia/metabolism ; Bacteria/*classification/genetics/*isolation &amp; purification/*metabolism ; Base Sequence ; Biodiversity ; Carbohydrate Metabolism ; Carbon/metabolism ; Carbon Cycle/*physiology ; Caves/*microbiology ; Classification ; DNA, Bacterial ; Ecology ; Ferric Compounds/metabolism ; Geologic Sediments/chemistry/microbiology ; India ; Metabolic Networks and Pathways/physiology ; Metagenome ; Metagenomics ; Nitrates/metabolism ; Nitrification ; Nitrogen/metabolism ; Nitrogen Cycle/*physiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis ; Soil Microbiology ; Survival ; }, abstract = {BACKGROUND: Bacteria present in cave often survive by modifying their metabolic pathway or other mechanism. Understanding these adopted bacteria and their survival strategy inside the cave is an important aspect of microbial ecology. Present study focuses on the bacterial community and geochemistry in five caves of Mizoram, Northeast India. The objective of this study was to explore the taxonomic composition and presumed functional diversity of cave sediment metagenomes using paired end Illumina sequencing using V3 region of 16S rRNA gene and bioinformatics pipeline.<br><br>RESULTS: Actinobacteria, Proteobacteria, Verrucomicrobia and Acidobacteria were the major phyla in all the five cave sediment samples. Among the five caves the highest diversity is found in Lamsialpuk with a Shannon index 12.5 and the lowest in Bukpuk (Shannon index 8.22). In addition, imputed metagenomic approach was used to predict the functional role of microbial community in biogeochemical cycling in the cave environments. Functional module showed high representation of genes involved in Amino Acid Metabolism in (20.9%) and Carbohydrate Metabolism (20.4%) in the KEGG pathways. Genes responsible for carbon degradation, carbon fixation, methane metabolism, nitrification, nitrate reduction and ammonia assimilation were also predicted in the present study.<br><br>CONCLUSION: The cave sediments of the biodiversity hotspot region possessing a oligotrophic environment harbours high phylogenetic diversity dominated by Actinobacteria and Proteobacteria. Among the geochemical factors, ferric oxide was correlated with increased microbial diversity. In-silico analysis detected genes involved in carbon, nitrogen, methane metabolism and complex metabolic pathways responsible for the survival of the bacterial community in nutrient limited cave environments. Present study with Paired end Illumina sequencing along with bioinformatics analysis revealed the essential ecological role of the cave bacterial communities. These results will be useful in documenting the biospeleology of this region and systematic understanding of bacterial communities in natural sediment environments as well.}, }
@article {pmid28395941, year = {2017}, author = {Ricciardi, A and Blackburn, TM and Carlton, JT and Dick, JTA and Hulme, PE and Iacarella, JC and Jeschke, JM and Liebhold, AM and Lockwood, JL and MacIsaac, HJ and Pyšek, P and Richardson, DM and Ruiz, GM and Simberloff, D and Sutherland, WJ and Wardle, DA and Aldridge, DC}, title = {Invasion Science: A Horizon Scan of Emerging Challenges and Opportunities.}, journal = {Trends in ecology &amp; evolution}, volume = {32}, number = {6}, pages = {464-474}, doi = {10.1016/j.tree.2017.03.007}, pmid = {28395941}, issn = {1872-8383}, mesh = {*Ecosystem ; *Introduced Species ; }, abstract = {We identified emerging scientific, technological, and sociopolitical issues likely to affect how biological invasions are studied and managed over the next two decades. Issues were ranked according to their probability of emergence, pervasiveness, potential impact, and novelty. Top-ranked issues include the application of genomic modification tools to control invasions, effects of Arctic globalization on invasion risk in the Northern Hemisphere, commercial use of microbes to facilitate crop production, the emergence of invasive microbial pathogens, and the fate of intercontinental trade agreements. These diverse issues suggest an expanding interdisciplinary role for invasion science in biosecurity and ecosystem management, burgeoning applications of biotechnology in alien species detection and control, and new frontiers in the microbial ecology of invasions.}, }
@article {pmid28389730, year = {2017}, author = {Porrini, MP and Porrini, LP and Garrido, PM and de Melo E Silva Neto, C and Porrini, DP and Muller, F and Nuñez, LA and Alvarez, L and Iriarte, PF and Eguaras, MJ}, title = {Nosema ceranae in South American Native Stingless Bees and Social Wasp.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {761-764}, pmid = {28389730}, issn = {1432-184X}, mesh = {Animals ; Argentina ; Bees/*microbiology ; Brazil ; Nosema/genetics/*physiology ; RNA, Fungal/analysis ; RNA, Ribosomal, 16S/analysis ; Wasps/*microbiology ; }, abstract = {Besides the incipient research effort, the role of parasites as drivers of the reduction affecting pollinator populations is mostly unknown. Given the worldwide extension of the beekeeping practice and the diversity of pathogens affecting Apis mellifera populations, honey bee colonies are a certain source of parasite dispersion to other species. Here, we communicate the detection of the microsporidium Nosema ceranae, a relatively new parasite of honey bees, in stingless bees (Meliponini) and the social wasp Polybia scutellaris (Vespidae) samples from Argentina and Brazil by means of duplex PCR. Beyond the geographic location of the nests, N. ceranae was detected in seven from the eight Meliponini species analyzed, while Nosema apis, another common parasite of A. mellifera, was absent in all samples tested. Further research is necessary to determine if the presence of the parasite is also associated with established infection in host tissues. The obtained information enriches the current knowledge about pathologies that can infect or, at least, be vectored by native wild pollinators from South America.}, }
@article {pmid28389729, year = {2017}, author = {Bhattarai, S and Cassarini, C and Gonzalez-Gil, G and Egger, M and Slomp, CP and Zhang, Y and Esposito, G and Lens, PNL}, title = {Anaerobic Methane-Oxidizing Microbial Community in a Coastal Marine Sediment: Anaerobic Methanotrophy Dominated by ANME-3.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {608-622}, pmid = {28389729}, issn = {1432-184X}, support = {grant agreement FPA no. 2010-0009//Erasmus Mundus Joint Doctorate Program Environmental Technologies for Contaminated Solids, Soils and Sediments/ ; ERC Starting Grant #278364//European Research Council (BE)/ ; NWO Vici grant 865.13.005//Netherlands Organization for Scientific Research/ ; SUREANMetOX-300078//Marie Curie Intra European Fellowship/ ; }, mesh = {Anaerobiosis ; Archaea/classification/*metabolism ; Bacteria, Anaerobic/classification/*metabolism ; Geologic Sediments/*microbiology ; Lakes/microbiology ; Methane/*metabolism ; Netherlands ; Oxidation-Reduction ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, RNA ; }, abstract = {The microbial community inhabiting the shallow sulfate-methane transition zone in coastal sediments from marine Lake Grevelingen (The Netherlands) was characterized, and the ability of the microorganisms to carry out anaerobic oxidation of methane coupled to sulfate reduction was assessed in activity tests. In vitro activity tests of the sediment with methane and sulfate demonstrated sulfide production coupled to the simultaneous consumption of sulfate and methane at approximately equimolar ratios over a period of 150 days. The maximum sulfate reduction rate was 5 μmol sulfate per gram dry weight per day during the incubation period. Diverse archaeal and bacterial clades were retrieved from the sediment with the majority of them clustered with Euryarchaeota, Thaumarcheota, Bacteroidetes, and Proteobacteria. The 16S rRNA gene sequence analysis showed that the sediment from marine Lake Grevelingen contained anaerobic methanotrophic Archaea (ANME) and methanogens as archaeal clades with a role in the methane cycling. ANME at the studied site mainly belong to the ANME-3 clade. This study provides one of the few reports for the presence of ANME-3 in a shallow coastal sediment. Sulfate-reducing bacteria from Desulfobulbus clades were found among the sulfate reducers, however, with very low relative abundance. Desulfobulbus has previously been commonly found associated with ANME, whereas in our study, ANME-3 and Desulfobulbus were not observed simultaneously in clusters, suggesting the possibility of independent AOM by ANME-3.}, }
@article {pmid28389728, year = {2017}, author = {Krashevska, V and Sandmann, D and Marian, F and Maraun, M and Scheu, S}, title = {Leaf Litter Chemistry Drives the Structure and Composition of Soil Testate Amoeba Communities in a Tropical Montane Rainforest of the Ecuadorian Andes.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {681-690}, pmid = {28389728}, issn = {1432-184X}, mesh = {Amoebozoa/*physiology ; *Biota ; Ecuador ; Plant Leaves/*chemistry ; *Rainforest ; Soil/*chemistry ; Trees/chemistry ; }, abstract = {We investigated the role of leaf litter chemistry and richness in affecting testate amoeba communities of tropical rainforest in the Ecuadorian Andes. Litterbags containing leaf litter from four dominating tree species (Clusia sp., Myrcia pubescens, Graffenrieda emarginata, and Cecropia andina) with richness 1, 2, and 4 species were established and exposed in the field for 12 months at 2000 m a.s.l. Chemical elements and compounds of leaf litter were analyzed before exposure. At the end of exposure, microbial biomass and litter mass loss were measured, and living testate amoeba species number, density, biomass, and community composition were determined. In total, 125 testate amoeba species colonized the litter in litterbags. The results suggest that high litter nitrogen and low lignin concentrations are indicators of high litter quality for testate amoebae density and species richness. Their species number and density significantly declined in the order 1 > 4 > 2 leaf litter species and varied with leaf litter chemistry being at a maximum in high-quality single leaf litter species and low in low-quality leaf litter. Further, the addition of litter of high-quality to low-quality litter increased testate amoebae biomass and density; however, the values did not exceed the ones in single high-quality litter treatments. Moreover, the structure of testate amoeba communities varied with litter chemistry, with Fe, Na, lignin, and litter C-to-N ratio being of major importance, and indicating that litter chemistry reflects habitat quality for testate amoebae. Overall, the data show that leaf litter chemistry overrides leaf litter richness in structuring testate amoeba communities.}, }
@article {pmid28389727, year = {2017}, author = {Gaby, JC and Buckley, DH}, title = {The Use of Degenerate Primers in qPCR Analysis of Functional Genes Can Cause Dramatic Quantification Bias as Revealed by Investigation of nifH Primer Performance.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {701-708}, pmid = {28389727}, issn = {1432-184X}, support = {MCB-0447586//National Science Foundation (US)/ ; 2005-35107-15266//National Institute of Food and Agriculture/ ; }, mesh = {Bacteria/*classification ; Bacterial Proteins/*analysis ; DNA Primers/*analysis ; DNA, Bacterial/analysis ; Microbiological Techniques/methods ; Oxidoreductases/*analysis ; Polymerase Chain Reaction/*methods ; *Soil Microbiology ; }, abstract = {The measurement of functional gene abundance in diverse microbial communities often employs quantitative PCR (qPCR) with highly degenerate oligonucleotide primers. While degenerate PCR primers have been demonstrated to cause template-specific bias in PCR applications, the effect of such bias on qPCR has been less well explored. We used a set of diverse, full-length nifH gene standards to test the performance of several universal nifH primer sets in qPCR. We found significant template-specific bias in all but the PolF/PolR primer set. Template-specific bias caused more than 1000-fold mis-estimation of nifH gene copy number for three of the primer sets and one primer set resulted in more than 10,000-fold mis-estimation. Furthermore, such template-specific bias will cause qPCR estimates to vary in response to beta-diversity, thereby causing mis-estimation of changes in gene copy number. A reduction in bias was achieved by increasing the primer concentration. We conclude that degenerate primers should be evaluated across a range of templates, annealing temperatures, and primer concentrations to evaluate the potential for template-specific bias prior to their use in qPCR.}, }
@article {pmid28389726, year = {2017}, author = {Morling, K and Raeke, J and Kamjunke, N and Reemtsma, T and Tittel, J}, title = {Tracing Aquatic Priming Effect During Microbial Decomposition of Terrestrial Dissolved Organic Carbon in Chemostat Experiments.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {534-549}, pmid = {28389726}, issn = {1432-184X}, support = {02WT1290A//German Federal Ministry of Education and Research/ ; }, mesh = {Bacteria/*metabolism ; Germany ; Humic Substances/*analysis ; Mass Spectrometry ; Soil/*chemistry ; Spectroscopy, Fourier Transform Infrared ; Water/*chemistry ; }, abstract = {Microbial decomposition of terrestrial carbon may be enhanced by the addition of easily decomposable compounds, a phenomenon referred to as priming effect. We investigated the microbial decomposition of terrestrial dissolved organic carbon (DOC) in one-stage and two-stage flow-through cultures (chemostats) in the absence and presence of growing phytoplankton as phytoplankton-derived organic matter might facilitate the mineralization of more refractory terrestrial compounds. Peat water and soil leachate were used as terrestrial substrates, and only slight DOC decomposition was observed in the absence of phytoplankton for both substrates. A priming effect was revealed via [14]C data. Priming was more pronounced for the peat water substrate than for the soil leachate. The total DOC concentrations increased for both substrates in the presence of phytoplankton due to exudation and cell lysis. Samples from the soil leachate experiments were analyzed using ultra-high-resolution mass spectrometry (FT-ICR MS). Predominantly, the same saturated, aliphatic molecules with H/C ratios >1.5 were completely decomposed in the absence and in the presence of phytoplankton. The decomposition of more stable molecules differed in their intensity. Oxidized and unsaturated molecules with H/C ratios <1.0 and O/C ratios >0.4 were more strongly decomposed in phytoplankton presence (i.e., under priming). We conclude that an aquatic priming effect is not easily detectable via net concentration changes alone, and that qualitative investigations of the DOC processed by bacterial decomposition are necessary to detect aquatic priming.}, }
@article {pmid28387771, year = {2017}, author = {Bonfante, P and Desirò, A}, title = {Who lives in a fungus? The diversity, origins and functions of fungal endobacteria living in Mucoromycota.}, journal = {The ISME journal}, volume = {11}, number = {8}, pages = {1727-1735}, pmid = {28387771}, issn = {1751-7370}, mesh = {Bacteria/*genetics ; Biological Evolution ; Fungi/*classification/*physiology ; *Symbiosis ; Tenericutes/*genetics/physiology ; }, abstract = {Bacterial interactions with plants and animals have been examined for many years; differently, only with the new millennium the study of bacterial-fungal interactions blossomed, becoming a new field of microbiology with relevance to microbial ecology, human health and biotechnology. Bacteria and fungi interact at different levels and bacterial endosymbionts, which dwell inside fungal cells, provide the most intimate example. Bacterial endosymbionts mostly occur in fungi of the phylum Mucoromycota and include Betaproteobacteria (Burkhoderia-related) and Mollicutes (Mycoplasma-related). Based on phylogenomics and estimations of divergence time, we hypothesized two different scenarios for the origin of these interactions (early vs late bacterial invasion). Sequencing of the genomes of fungal endobacteria revealed a significant reduction in genome size, particularly in endosymbionts of Glomeromycotina, as expected by their uncultivability and host dependency. Similar to endobacteria of insects, the endobacteria of fungi show a range of behaviours from mutualism to antagonism. Emerging results suggest that some benefits given by the endobacteria to their plant-associated fungal host may propagate to the interacting plant, giving rise to a three-level inter-domain interaction.}, }
@article {pmid28386770, year = {2017}, author = {Zitnick-Anderson, KK and Norland, JE and Del Río Mendoza, LE and Fortuna, AM and Nelson, BD}, title = {Probability Models Based on Soil Properties for Predicting Presence-Absence of Pythium in Soybean Roots.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {550-560}, pmid = {28386770}, issn = {1432-184X}, support = {FAR0019230//North Dakota Soybean Council/ ; }, mesh = {Models, Biological ; North Dakota ; Plant Roots/microbiology ; Probability ; Pythium/*physiology ; Soil/*chemistry ; *Soil Microbiology ; Glycine max/*microbiology ; }, abstract = {Associations between soil properties and Pythium groups on soybean roots were investigated in 83 commercial soybean fields in North Dakota. A data set containing 2877 isolates of Pythium which included 26 known spp. and 1 unknown spp. and 13 soil properties from each field were analyzed. A Pearson correlation analysis was performed with all soil properties to observe any significant correlation between properties. Hierarchical clustering, indicator spp., and multi-response permutation procedures were used to identify groups of Pythium. Logistic regression analysis using stepwise selection was employed to calculate probability models for presence of groups based on soil properties. Three major Pythium groups were identified and three soil properties were associated with these groups. Group 1, characterized by P. ultimum, was associated with zinc levels; as zinc increased, the probability of group 1 being present increased (α = 0.05). Pythium group 2, characterized by Pythium kashmirense and an unknown Pythium sp., was associated with cation exchange capacity (CEC) (α < 0.05); as CEC increased, these spp. increased. Group 3, characterized by Pythium heterothallicum and Pythium irregulare, were associated with CEC and calcium carbonate exchange (CCE); as CCE increased and CEC decreased, these spp. increased (α = 0.05). The regression models may have value in predicting pathogenic Pythium spp. in soybean fields in North Dakota and adjacent states.}, }
@article {pmid28386769, year = {2017}, author = {Fromont, C and Riegler, M and Cook, JM}, title = {Relative Abundance and Strain Diversity in the Bacterial Endosymbiont Community of a Sap-Feeding Insect Across Its Native and Introduced Geographic Range.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {722-734}, pmid = {28386769}, issn = {1432-184X}, support = {HSF 12/10//The Hermon Slade Foundation/ ; }, mesh = {Animals ; Australia ; Bacteria/*classification/genetics ; *Bacterial Physiological Phenomena ; Female ; Ficus/growth &amp; development ; Hemiptera/growth &amp; development/*microbiology ; Herbivory ; High-Throughput Nucleotide Sequencing ; Male ; *Microbiota ; New Zealand ; Nymph/growth &amp; development/microbiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; }, abstract = {Most insects are associated with bacterial symbionts. The bacterial diversity and community composition within hosts may play an important role in shaping insect population biology, ecology and evolution. We focussed on the bacterial microbiome of the Australian fig homotomid Mycopsylla fici (Hemiptera: Psylloidea), which can cause defoliation of its only host tree, Ficus macrophylla. This sap-feeding insect is native to mainland Australia and Lord Howe Island (LHI) but also occurs where its host has been planted, notably in New Zealand. By using a high-throughput 16S rDNA amplicon sequencing approach, we compared the bacterial diversity and community composition in individual adult males of four host populations, Sydney, Brisbane, LHI and Auckland. We also compared males, females and nymphs of the Sydney population. The microbiome of M. fici was simple and consisted mostly of the following three maternally inherited endosymbiont species: the primary endosymbiont Carsonella, a secondary (S-) endosymbiont and Wolbachia. However, the relative abundance of their sequence reads varied between host populations, except for similarities between Sydney and Auckland. In addition, insects from Sydney and Auckland had identical bacterial strains supporting the hypothesis that Sydney is the source population for Auckland. In contrast, mainland and LHI populations harboured the same S-endosymbiont, co-diverged Carsonella but different Wolbachia strains. Besides detecting endosymbiont-specific patterns of either co-evolution or horizontal acquisition, our study highlights that relative abundance of maternally inherited endosymbionts should also be taken into account when studying bacterial communities across host populations, as variations in bacterial density may impact host biology and ecology.}, }
@article {pmid28386768, year = {2017}, author = {Segovia, BT and Dias, JD and Cabral, AF and Meira, BR and Lansac-Tôha, FM and Lansac-Tôha, FA and Bini, LM and Velho, LFM}, title = {Common and Rare Taxa of Planktonic Ciliates: Influence of Flood Events and Biogeographic Patterns in Neotropical Floodplains.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {522-533}, pmid = {28386768}, issn = {1432-184X}, mesh = {Animals ; *Biodiversity ; Brazil ; Ciliophora/classification/*physiology ; *Floods ; Geography ; Lakes ; Zooplankton/classification/*physiology ; }, abstract = {After much discussion about the cosmopolitan nature of microbes, the great issue nowadays is to identify at which spatial extent microorganisms may display biogeographic patterns and if temporal variation is important in altering those patterns. Here, planktonic ciliates were sampled from shallow lakes of four Neotropical floodplains, distributed over a spatial extent of ca. 3000 km, during high and low water periods, along with several abiotic and biotic variables potentially affecting the ciliate community. We found that common ciliate species were more associated with environmental gradients and rare species were more related to spatial variables; however, this pattern seemed to change depending on the temporal and spatial scales considered. Environmental gradients were more important in the high waters for both common and rare species. In low waters, common species continued to be mainly driven by environmental conditions, but rare species were more associated with the spatial component, suggesting dispersal limitation likely due to differences in dispersal ability and ecological tolerance of species. We also found that common and rare species were related to different environmental variables, suggesting different ecological niches. At the largest spatial extents, rare species showed clear biogeographic patterns.}, }
@article {pmid28386012, year = {2017}, author = {Schulz, F and Yutin, N and Ivanova, NN and Ortega, DR and Lee, TK and Vierheilig, J and Daims, H and Horn, M and Wagner, M and Jensen, GJ and Kyrpides, NC and Koonin, EV and Woyke, T}, title = {Giant viruses with an expanded complement of translation system components.}, journal = {Science (New York, N.Y.)}, volume = {356}, number = {6333}, pages = {82-85}, doi = {10.1126/science.aal4657}, pmid = {28386012}, issn = {1095-9203}, support = {P 27319/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Amino Acyl-tRNA Synthetases/chemistry/*genetics ; Austria ; *Genome, Viral ; Giant Viruses/*classification/*genetics/isolation &amp; purification ; Metagenomics ; Phylogeny ; Protein Biosynthesis/*genetics ; Wastewater/virology ; }, abstract = {The discovery of giant viruses blurred the sharp division between viruses and cellular life. Giant virus genomes encode proteins considered as signatures of cellular organisms, particularly translation system components, prompting hypotheses that these viruses derived from a fourth domain of cellular life. Here we report the discovery of a group of giant viruses (Klosneuviruses) in metagenomic data. Compared with other giant viruses, the Klosneuviruses encode an expanded translation machinery, including aminoacyl transfer RNA synthetases with specificities for all 20 amino acids. Notwithstanding the prevalence of translation system components, comprehensive phylogenomic analysis of these genes indicates that Klosneuviruses did not evolve from a cellular ancestor but rather are derived from a much smaller virus through extensive gain of host genes.}, }
@article {pmid28385669, year = {2017}, author = {Van Den Hende, S and Rodrigues, A and Hamaekers, H and Sonnenholzner, S and Vervaeren, H and Boon, N}, title = {Microalgal bacterial flocs treating paper mill effluent: A sunlight-based approach for removing carbon, nitrogen, phosphorus, and calcium.}, journal = {New biotechnology}, volume = {39}, number = {Pt A}, pages = {1-10}, doi = {10.1016/j.nbt.2017.03.004}, pmid = {28385669}, issn = {1876-4347}, mesh = {Bacteria/*metabolism ; Batch Cell Culture Techniques ; Biodegradation, Environmental ; Bioreactors/microbiology ; Calcium/isolation &amp; purification ; Calcium Carbonate/chemistry ; Carbon/isolation &amp; purification ; Carbon Cycle ; Carbonic Anhydrases/metabolism ; Chemical Precipitation ; Flocculation ; Hydrogen-Ion Concentration ; Industrial Waste/*analysis ; Microalgae/*metabolism ; Nitrogen/isolation &amp; purification ; *Paper ; Phosphorus/isolation &amp; purification ; *Sunlight ; *Waste Disposal, Fluid ; Water Pollutants, Chemical/*isolation &amp; purification ; Water Purification/*methods ; X-Ray Diffraction ; }, abstract = {Treatment of upflow anaerobic sludge blanket (UASB) effluent from a paper mill in aerated activated sludge reactors involves high aeration costs. Moreover, this calcium-rich effluent leads to problematic scale formation. Therefore, a novel strategy for the aerobic treatment of paper mill UASB effluent in microalgal bacterial floc sequencing batch reactors (MaB-floc SBRs) is proposed, in which oxygen is provided via photosynthesis, and calcium is removed via bio-mineralization. Based on the results of batch experiments in the course of this study, a MaB-floc SBR was operated at an initial neutral pH. This SBR removed 58±21% organic carbon, 27±8% inorganic carbon, 77±5% nitrogen, 73±2% phosphorus, and 27±11% calcium. MaB-flocs contained 10±3% calcium, including biologically-influenced calcite crystals. The removal of calcium and inorganic carbon by MaB-flocs significantly decreased when inhibiting extracellular carbonic anhydrase (CA), an enzyme that catalyses the hydration and dehydration of CO2. This study demonstrates the potential of MaB-floc SBRs for the alternative treatment of calcium-rich paper mill effluent, and highlights the importance of extracellular CA in this treatment process.}, }
@article {pmid28383027, year = {2017}, author = {Jurburg, SD and Nunes, I and Stegen, JC and Le Roux, X and Priemé, A and Sørensen, SJ and Salles, JF}, title = {Autogenic succession and deterministic recovery following disturbance in soil bacterial communities.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {45691}, pmid = {28383027}, issn = {2045-2322}, mesh = {Bacteria/*classification/*radiation effects ; Biota/*radiation effects ; *Environmental Exposure ; *Hot Temperature ; *Soil Microbiology ; }, abstract = {The response of bacterial communities to environmental change may affect local to global nutrient cycles. However the dynamics of these communities following disturbance are poorly understood, given that they are often evaluated over macro-ecological time scales and end-point measurements. In order to understand the successional trajectory of soil bacterial communities following disturbances and the mechanisms controlling these dynamics at a scale relevant for these organisms, we subjected soil microcosms to a heat disturbance and followed the community composition of active bacteria over 50 days. The disturbance imposed a strong selective pressure that persisted for up to 10 days, after which the importance of stochastic processes increased. Three successional stages were detected: a primary response in which surviving taxa increased in abundance; a secondary response phase during which community dynamics slowed down, and a stability phase (after 29 days), during which the community tended towards its original composition. Phylogenetic turnover patterns indicated that the community experienced stronger deterministic selection during recovery. Thus, soil bacterial communities, despite their extreme diversity and functional redundancy, respond to disturbances like many macro-ecological systems and exhibit path-dependent, autogenic dynamics during secondary succession. These results highlight the role of autogenic factors and successional dynamics in microbial recovery.}, }
@article {pmid28382585, year = {2018}, author = {Adler, A and Dücker, E}, title = {When Pasteurian Science Went to Sea: The Birth of Marine Microbiology.}, journal = {Journal of the history of biology}, volume = {51}, number = {1}, pages = {107-133}, pmid = {28382585}, issn = {1573-0387}, mesh = {*Aquatic Organisms ; Expeditions ; History, 19th Century ; History, 20th Century ; Microbiology/*history ; *Oceans and Seas ; }, abstract = {In the late nineteenth century, French naturalists were global leaders in microbial research. Louis Pasteur advanced sterilization techniques and demonstrated that dust particles in the air could contaminate a putrefiable liquid. Pasteur's discoveries prompted a new research program for the naturalists of the Talisman and Travailleur expeditions: to recover uncontaminated water and mud samples from the deep sea. French naturalists Adrien Certes and Paul Regnard both independently conducted experiments to address the question of whether microorganisms inhabited the oceans and whether organic material in the deep sea was subject to decomposition. The experiments of Certes and Regnard have largely been omitted from histories of microbiology and marine science. However, an examination of their work is crucial for understanding the context in which marine microbiology first developed. At the end of the nineteenth century, marine microbiology emerged from the disciplinary melding of terrestrial microbial ecology, experimental physiology, and the then-nascent field of deep-sea biology.}, }
@article {pmid28382027, year = {2017}, author = {Bosmans, L and De Bruijn, I and Gerards, S and Moerkens, R and Van Looveren, L and Wittemans, L and Van Calenberge, B and Paeleman, A and Van Kerckhove, S and De Mot, R and Rozenski, J and Rediers, H and Raaijmakers, JM and Lievens, B}, title = {Potential for Biocontrol of Hairy Root Disease by a Paenibacillus Clade.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {447}, pmid = {28382027}, issn = {1664-302X}, abstract = {Rhizogenic Agrobacterium biovar 1 is the causative agent of hairy root disease (HRD) in the hydroponic cultivation of tomato and cucumber causing significant losses in marketable yield. In order to prevent and control the disease chemical disinfectants such as hydrogen peroxide or hypochlorite are generally applied to sanitize the hydroponic system and/or hydroponic solution. However, effective control of HRD sometimes requires high disinfectant doses that may have phytotoxic effects. Moreover, several of these chemicals may be converted to unwanted by-products with human health hazards. Here we explored the potential of beneficial bacteria as a sustainable means to control HRD. A large collection of diverse bacterial genera was screened for antagonistic activity against rhizogenic Agrobacterium biovar 1 using the agar overlay assay. Out of more than 150 strains tested, only closely related Paenibacillus strains belonging to a particular clade showed antagonistic activity, representing the species P. illinoisensis, P. pabuli, P. taichungensis, P. tundrae, P. tylopili, P. xylanexedens, and P. xylanilyticus. Assessment of the spectrum of activity revealed that some strains were able to inhibit the growth of all 35 rhizogenic agrobacteria strains tested, while others were only active against part of the collection, suggesting a different mode of action. Preliminary characterization of the compounds involved in the antagonistic activity of two closely related Paenibacillus strains, tentatively identified as P. xylanexedens, revealed that they are water-soluble and have low molecular weight. Application of a combination of these strains in greenhouse conditions resulted in a significant reduction of HRD, indicating the great potential of these strains to control HRD.}, }
@article {pmid28379446, year = {2017}, author = {Antwis, RE and Griffiths, SM and Harrison, XA and Aranega-Bou, P and Arce, A and Bettridge, AS and Brailsford, FL and de Menezes, A and Devaynes, A and Forbes, KM and Fry, EL and Goodhead, I and Haskell, E and Heys, C and James, C and Johnston, SR and Lewis, GR and Lewis, Z and Macey, MC and McCarthy, A and McDonald, JE and Mejia-Florez, NL and O'Brien, D and Orland, C and Pautasso, M and Reid, WDK and Robinson, HA and Wilson, K and Sutherland, WJ}, title = {Fifty important research questions in microbial ecology.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {5}, pages = {}, doi = {10.1093/femsec/fix044}, pmid = {28379446}, issn = {1574-6941}, support = {BB/F004311/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/*growth &amp; development ; *Biological Evolution ; *Communicable Diseases ; Ecology ; *Ecosystem ; *Food Safety ; Humans ; *Microbiota ; }, abstract = {Microbial ecology provides insights into the ecological and evolutionary dynamics of microbial communities underpinning every ecosystem on Earth. Microbial communities can now be investigated in unprecedented detail, although there is still a wealth of open questions to be tackled. Here we identify 50 research questions of fundamental importance to the science or application of microbial ecology, with the intention of summarising the field and bringing focus to new research avenues. Questions are categorised into seven themes: host-microbiome interactions; health and infectious diseases; human health and food security; microbial ecology in a changing world; environmental processes; functional diversity; and evolutionary processes. Many questions recognise that microbes provide an extraordinary array of functional diversity that can be harnessed to solve real-world problems. Our limited knowledge of spatial and temporal variation in microbial diversity and function is also reflected, as is the need to integrate micro- and macro-ecological concepts, and knowledge derived from studies with humans and other diverse organisms. Although not exhaustive, the questions presented are intended to stimulate discussion and provide focus for researchers, funders and policy makers, informing the future research agenda in microbial ecology.}, }
@article {pmid28378066, year = {2017}, author = {de Oliveira, DV and Nunes, LS and Barth, AL and Van Der Sand, ST}, title = {Genetic Background of β-Lactamases in Enterobacteriaceae Isolates from Environmental Samples.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {599-607}, pmid = {28378066}, issn = {1432-184X}, support = {Scholarship//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Brazil ; Electrophoresis, Gel, Pulsed-Field ; Enterobacteriaceae/drug effects/*genetics ; *Genetic Background ; Rivers/microbiology ; Sewage/microbiology ; *beta-Lactam Resistance ; beta-Lactamases/*genetics/metabolism ; }, abstract = {The prevalence of β-lactamase-producing Enterobacteriaceae has increased worldwide. Although antibiotic-resistant bacteria are usually associated with hospitals, there are a growing number of reports of resistant bacteria in other environments. Concern about resistant microorganisms outside the hospital setting highlights the need to investigate mechanisms of antibiotic resistance in isolates collected from the environment. The present study evaluated the resistance mechanism to β-lactam antibiotics in 40 isolates from hospital sewage and surface water from the Dilúvio Stream, Porto Alegre City, Southern Brazil. The multiplex PCR technique was used to detect several resistance genes of β-lactamases: extended-spectrum β-lactamases (ESBLs), carbapenemases, and β-lactamase AmpC. After genes, detection amplicons were sequenced to confirm their identification. The clonal relationship was established by DNA macrorestriction using the XbaI enzyme, followed by pulsed-field gel electrophoresis (PFGE). The results indicated that resistance genes were present in 85% of the isolates. The most prevalent genes encoded narrow-spectrum β-lactamase, such as TEM-1 and SHV-1 with 70% of the strains, followed by carbapenemase KPC and GES (45%), ESBL types SHV-5 and CTX-M-8 (27.5%), and AmpC (ACT-1/MIR-1) (2.5%). Twelve isolates contained only one resistance gene, 14 contained two, and eight isolates had three resistance genes. PFGE indicated a clonal relationship among K. pneumoniae isolates. It was not possible to establish a clonal relationship between Enterobacter sp. isolates. The results highlight the potential of these resistance genes to spread in the polluted environment and to present a health risk to communities. This report is the first description of these resistance genes present in environmental samples other than a hospital in the city of Porto Alegre/RS.}, }
@article {pmid28375652, year = {2017}, author = {Knight, R and Callewaert, C and Marotz, C and Hyde, ER and Debelius, JW and McDonald, D and Sogin, ML}, title = {The Microbiome and Human Biology.}, journal = {Annual review of genomics and human genetics}, volume = {18}, number = {}, pages = {65-86}, doi = {10.1146/annurev-genom-083115-022438}, pmid = {28375652}, issn = {1545-293X}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Humans ; *Immune System ; *Metabolome ; *Metagenome ; Microbiota/*genetics ; *Sequence Analysis, DNA ; }, abstract = {Over the past few years, microbiome research has dramatically reshaped our understanding of human biology. New insights range from an enhanced understanding of how microbes mediate digestion and disease processes (e.g., in inflammatory bowel disease) to surprising associations with Parkinson's disease, autism, and depression. In this review, we describe how new generations of sequencing technology, analytical advances coupled to new software capabilities, and the integration of animal model data have led to these new discoveries. We also discuss the prospects for integrating studies of the microbiome, metabolome, and immune system, with the goal of elucidating mechanisms that govern their interactions. This systems-level understanding will change how we think about ourselves as organisms.}, }
@article {pmid28374172, year = {2017}, author = {Damaceno, QS and Souza, JP and Nicoli, JR and Paula, RL and Assis, GB and Figueiredo, HC and Azevedo, V and Martins, FS}, title = {Evaluation of Potential Probiotics Isolated from Human Milk and Colostrum.}, journal = {Probiotics and antimicrobial proteins}, volume = {9}, number = {4}, pages = {371-379}, pmid = {28374172}, issn = {1867-1314}, mesh = {Adult ; Bacterial Load ; Bifidobacterium breve/isolation &amp; purification ; Colostrum/*microbiology ; Female ; Humans ; Lactobacillus gasseri/isolation &amp; purification ; Milk, Human/*microbiology ; *Probiotics ; Staphylococcus epidermidis/isolation &amp; purification ; Streptococcus salivarius/isolation &amp; purification ; Young Adult ; }, abstract = {Several studies have demonstrated a diversity of bacterial species in human milk, even in aseptically collected samples. The present study evaluated potential probiotic bacteria isolated from human milk and associated maternal variables. Milk samples were collected from 47 healthy women and cultured on selective and universal agar media under aerobic and anaerobic conditions. Bacterial isolates were counted and identified by Biotyper Matrix-Assisted Laser Desorption Ionization-Time of Flight mass spectrometry and then tested for probiotic properties. Total bacteria in human milk ranged from 1.5 to 4.0 log10 CFU/mL. The higher bacterial counts were found in colostrum (mean = 3.9 log10 CFU/mL, 95% CI 3.14-4.22, p = 0.00001). The most abundant species was Staphylococcus epidermidis (n = 76). The potential probiotic candidates were Lactobacillus gasseri (n = 4), Bifidobacterium breve (n = 1), and Streptococcus salivarius (n = 4). Despite the small sample size, L. gasseri was isolated only in breast milk from mothers classified into a normal weight range and after a vaginally delivered partum. No potential probiotics showed antagonism against pathogens, but all of them agglutinated different pathogens. Nine bacterial isolates belonging to the species L. gasseri, B. breve, and S. salivarius were selected as potential probiotics. The present study confirms the presence in breast milk of a bacterial microbiota that could be the source of potential probiotic candidates to be used in the formula of simulated maternal milk.}, }
@article {pmid28374061, year = {2017}, author = {Briand, JF and Barani, A and Garnier, C and Réhel, K and Urvois, F and LePoupon, C and Bouchez, A and Debroas, D and Bressy, C}, title = {Spatio-Temporal Variations of Marine Biofilm Communities Colonizing Artificial Substrata Including Antifouling Coatings in Contrasted French Coastal Environments.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {585-598}, pmid = {28374061}, issn = {1432-184X}, mesh = {Atlantic Ocean ; *Bacterial Physiological Phenomena ; Biofilms/*growth &amp; development ; *Biofouling/prevention &amp; control ; Diatoms/*physiology ; Flow Cytometry ; France ; Mediterranean Sea ; Seasons ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Surface colonization in seawater first corresponds to the selection of specific microbial biofilm communities. By coupling flow cytometry, microscopy and high throughput sequencing (HTS, 454 pyrosequencing) with artificial surfaces and environmental analyses, we intend to identify the contribution of biofilm community drivers at two contrasted French sites, one temperate and eutrophic (Lorient, Atlantic coast) and the other at a mesotrophic but highly contaminated bay (Toulon, North-Western Mediterranean Sea). Microbial communities were shaped by high temperatures, salinity and lead at Toulon by but nutrients and DOC at Lorient. Coatings including pyrithione exhibited a significant decrease of their microbial densities except for nanoeukaryotes. Clustering of communities was mainly based on the surface type and secondly the site, whereas seasons appeared of less importance. The in-depth HTS revealed that γ- and α-proteobacteria, but also Bacteroidetes, dominated highly diversified bacterial communities with a relative low β-diversity. Sensitivity to biocides released by the tested antifouling coatings could be noticed at different taxonomic levels: the percentage of Bacteroidetes overall decreased with the presence of pyrithione, whereas the α/γ-proteobacteria ratio decreased at Toulon when increased at Lorient. Small diatom cells (Amphora and Navicula spp.) dominated on all surfaces, whereas site-specific sub-dominant taxa appeared clearly more sensitive to biocides. This overall approach exhibited the critical significance of surface characteristics in biofilm community shaping.}, }
@article {pmid28367917, year = {2017}, author = {Narihiro, T and Kamagata, Y}, title = {Genomics and Metagenomics in Microbial Ecology: Recent Advances and Challenges.}, journal = {Microbes and environments}, volume = {32}, number = {1}, pages = {1-4}, pmid = {28367917}, issn = {1347-4405}, mesh = {Biota ; *Environmental Microbiology ; Genome, Microbial ; *Genomics/trends ; Host Microbial Interactions ; *Metagenomics/trends ; Microbial Interactions ; }, }
@article {pmid28367229, year = {2017}, author = {Sharp, CE and Urschel, S and Dong, X and Brady, AL and Slater, GF and Strous, M}, title = {Robust, high-productivity phototrophic carbon capture at high pH and alkalinity using natural microbial communities.}, journal = {Biotechnology for biofuels}, volume = {10}, number = {}, pages = {84}, pmid = {28367229}, issn = {1754-6834}, abstract = {BACKGROUND: Bioenergy with carbon capture and storage (BECCS) has come to be seen as one of the most viable technologies to provide the negative carbon dioxide emissions needed to constrain global temperatures. In practice, algal biotechnology is the only form of BECCS that could be realized at scale without compromising food production. Current axenic algae cultivation systems lack robustness, are expensive and generally have marginal energy returns.<br><br>RESULTS: Here it is shown that microbial communities sampled from alkaline soda lakes, grown as biofilms at high pH (up to 10) and high alkalinity (up to 0.5&#xa0;kmol&#xa0;m[-3] NaHCO3 and NaCO3) display excellent (>1.0&#xa0;kg&#xa0;m[-3]&#xa0;day[-1]) and robust (>80&#xa0;days) biomass productivity, at low projected overall costs. The most productive biofilms contained >100 different species and were dominated by a cyanobacterium closely related to Phormidium kuetzingianum (>60%).<br><br>CONCLUSION: Frequent harvesting and red light were the key factors that governed the assembly of a stable and productive microbial community.}, }
@article {pmid28367228, year = {2017}, author = {Gildemyn, S and Molitor, B and Usack, JG and Nguyen, M and Rabaey, K and Angenent, LT}, title = {Upgrading syngas fermentation effluent using Clostridium kluyveri in a continuous fermentation.}, journal = {Biotechnology for biofuels}, volume = {10}, number = {}, pages = {83}, pmid = {28367228}, issn = {1754-6834}, abstract = {BACKGROUND: The product of current syngas fermentation systems is an ethanol/acetic acid mixture and the goal is to maximize ethanol recovery. However, ethanol currently has a relatively low market value and its separation from the fermentation broth is energy intensive. We can circumvent these disadvantages of ethanol production by converting the dilute ethanol/acetic acid mixture into products with longer carbon backbones, which are of higher value and are more easily extracted than ethanol. Chain elongation, which is the bioprocess in which ethanol is used to elongate short-chain carboxylic acids to medium-chain carboxylic acids (MCCAs), has been studied with pure cultures and open cultures of microbial consortia (microbiomes) with several different substrates. While upgrading syngas fermentation effluent has been studied with open cultures, to our knowledge, no study exists that has performed this with pure cultures.<br><br>RESULTS: Here, pure cultures of Clostridium kluyveri were used in continuous bioreactors to convert ethanol/acetic acid mixtures into MCCAs. Besides changing the operating conditions in regards to substrate loading rates and composition, the effect of in-line product extraction, pH, and the use of real syngas fermentation effluent on production rates were tested. Increasing the organic loading rates resulted in proportionally higher production rates of n-caproic acid, which were up to 40&#xa0;mM&#xa0;day[-1] (4.64&#xa0;g&#xa0;L[-1]&#xa0;day[-1]) at carbon conversion efficiencies of 90% or higher. The production rates were similar for bioreactors with and without in-line product extraction. Furthermore, a lower ethanol/acetic acid ratio (3:1 instead of 10:1) enabled faster and more efficient n-caproic acid production. In addition, n-caprylic acid production was observed for the first time with C. kluyveri (up to 2.19&#xa0;&#xb1;&#xa0;0.34&#xa0;mM in batch). Finally, the use of real effluent from syngas fermentation, without added yeast extract, but with added defined growth factors, did maintain similar production rates. Throughout the operating period, we observed that the metabolism of C. kluyveri was inhibited at a mildly acidic pH value of 5.5 compared to a pH value of 7.0, while reactor microbiomes perform successfully at mildly acidic conditions.<br><br>CONCLUSIONS: Clostridium kluyveri can be used as a biocatalyst to upgrade syngas fermentation effluent into MCCAs at pH values above 5.5.}, }
@article {pmid28365797, year = {2017}, author = {Wang, J and Jonkers, HM and Boon, N and De Belie, N}, title = {Bacillus sphaericus LMG 22257 is physiologically suitable for self-healing concrete.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {12}, pages = {5101-5114}, doi = {10.1007/s00253-017-8260-2}, pmid = {28365797}, issn = {1432-0614}, mesh = {Alkalies/metabolism ; Bacillus/growth &amp; development/*physiology ; Calcium Carbonate/chemistry/*metabolism ; Construction Materials/*microbiology ; Hydrogen-Ion Concentration ; *Industrial Microbiology ; Oxygen/metabolism ; Spores, Bacterial/growth &amp; development ; Urea/metabolism ; }, abstract = {The suitability of using a spore-forming ureolytic strain, Bacillus sphaericus, was evaluated for self-healing of concrete cracks. The main focus was on alkaline tolerance, calcium tolerance, oxygen dependence, and low-temperature adaptability. Experimental results show that B. sphaericus had a good tolerance. It can grow and germinate in a broad range of alkaline pH. The optimal pH range is 7 ∼ 9. High alkaline conditions (pH 10 ∼ 11) slow down but not stop the growth and germination. Oxygen was strictly needed during bacterial growth and germination, but not an essential factor during bacterial urea decomposition. B. sphaericus also had a good Ca tolerance, especially at a high bacterial concentration of 10[8] cells/mL; no significant influence was observed on bacterial ureolytic activity of the presence of 0.9M Ca[2+]. Furthermore, at a low temperature (10 °C), bacterial spores germinated and revived ureolytic activity with some retardation. However, this retardation can be counteracted by using a higher bacterial concentration and by supplementing yeast extract. It can be concluded that B. sphaericus is a suitable bacterium for application in bacteria-based self-healing concrete.}, }
@article {pmid28364728, year = {2017}, author = {Cabrol, L and Marone, A and Tapia-Venegas, E and Steyer, JP and Ruiz-Filippi, G and Trably, E}, title = {Microbial ecology of fermentative hydrogen producing bioprocesses: useful insights for driving the ecosystem function.}, journal = {FEMS microbiology reviews}, volume = {41}, number = {2}, pages = {158-181}, doi = {10.1093/femsre/fuw043}, pmid = {28364728}, issn = {1574-6976}, mesh = {Biodiversity ; *Biofuels ; *Ecosystem ; Fermentation ; Hydrogen/metabolism ; Microbiota/*physiology ; }, abstract = {One of the most important biotechnological challenges is to develop environment friendly technologies to produce new sources of energy. Microbial production of biohydrogen through dark fermentation, by conversion of residual biomass, is an attractive solution for short-term development of bioH2 producing processes. Efficient biohydrogen production relies on complex mixed communities working in tight interaction. Species composition and functional traits are of crucial importance to maintain the ecosystem service. The analysis of microbial community revealed a wide phylogenetic diversity that contributes in different-and still mostly unclear-ways to hydrogen production. Bridging this gap of knowledge between microbial ecology features and ecosystem functionality is essential to optimize the bioprocess and develop strategies toward a maximization of the efficiency and stability of substrate conversion. The aim of this review is to provide a comprehensive overview of the most up-to-date biodata available and discuss the main microbial community features of biohydrogen engineered ecosystems, with a special emphasis on the crucial role of interactions and the relationships between species composition and ecosystem service. The elucidation of intricate relationships between community structure and ecosystem function would make possible to drive ecosystems toward an improved functionality on the basis of microbial ecology principles.}, }
@article {pmid28364130, year = {2017}, author = {Li, T and Li, H and Gatesoupe, FJ and She, R and Lin, Q and Yan, X and Li, J and Li, X}, title = {Bacterial Signatures of "Red-Operculum" Disease in the Gut of Crucian Carp (Carassius auratus).}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {510-521}, pmid = {28364130}, issn = {1432-184X}, support = {No. 2013CB733502//973 project/ ; Sino BON//China Biodiversity Observation Networks/ ; }, mesh = {Animals ; Bacteria/*classification/genetics ; *Bacterial Physiological Phenomena ; *Carps ; Fish Diseases/*microbiology ; *Gastrointestinal Microbiome ; Goldfish ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA/veterinary ; }, abstract = {Fish gut microbiota play important roles in fish immunity, nutrition, and the adaptation to environmental changes. To date, few studies have focused on the interactions among environmental factors, fish diseases, and gut microbiota compositions. We compared the gut bacterial communities of healthy crucian carps (Carassius auratus) with those of individuals affected by "red-operculum" disease and corresponding water and sediment microbiota in four fish farm ponds. Distinct gut bacterial communities were observed in healthy and diseased fish. The bacterial communities of diseased fish were less diverse and stable than those of healthy individuals. The differences in bacterial community compositions between diseased and healthy fish were explained by the changes in the relative abundances of some specific bacterial OTUs, which belonged to the genera such as Vibrio, Aeromonas, and Shewanella, and they were prevalent in diseased fish, but rare or even absent in environmental samples. Water temperature and ammonia concentration were the two most important environmental factors that impacted gut microbiota in diseased fish. These results highlighted the surge of some potential pathogens as bacterial signatures that were associated with "red-operculum" disease in crucian carps.}, }
@article {pmid28363961, year = {2017}, author = {Khdhiri, M and Piché-Choquette, S and Tremblay, J and Tringe, SG and Constant, P}, title = {The Tale of a Neglected Energy Source: Elevated Hydrogen Exposure Affects both Microbial Diversity and Function in Soil.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {11}, pages = {}, pmid = {28363961}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; *Biodiversity ; Fungi/classification/genetics/*isolation &amp; purification/metabolism ; Hydrogen/*metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The enrichment of H2-oxidizing bacteria (HOB) by H2 generated by nitrogen-fixing nodules has been shown to have a fertilization effect on several different crops. The benefit of HOB is attributed to their production of plant growth-promoting factors, yet their interactions with other members of soil microbial communities have received little attention. Here we report that the energy potential of H2, when supplied to soil, alters ecological niche partitioning of bacteria and fungi, with multifaceted consequences for both generalist and specialist microbial functions. We used dynamic microcosms to expose soil to the typical atmospheric H2 mixing ratio (0.5 ppmv) permeating soils, as well as mixing ratios comparable to those found at the soil-nodule interface (10,000 ppmv). Elevated H2 exposure exerted direct effects on two HOB subpopulations distinguished by their affinity for H2 while enhancing community level carbon substrate utilization potential and lowering CH4 uptake activity in soil. We found that H2 triggered changes in the abundance of microorganisms that were reproducible yet inconsistent across soils at the taxonomic level and even among HOB. Overall, H2 exposure altered microbial process rates at an intensity that depends upon soil abiotic and biotic features. We argue that further examination of direct and indirect effects of H2 on soil microbial communities will lead to a better understanding of the H2 fertilization effect and soil biogeochemical processes.IMPORTANCE An innovative dynamic microcosm chamber system was used to demonstrate that H2 diffusing in soil triggers changes in the distribution of HOB and non-HOB. Although the response was uneven at the taxonomic level, an unexpected coordinated response of microbial functions was observed, including abatement of CH4 oxidation activity and stimulation of carbon turnover. Our work suggests that elevated H2 rewires soil biogeochemical structure through a combination of direct effects on the growth and persistence of HOB and indirect effects on a variety of microbial processes involving HOB and non-HOB.}, }
@article {pmid28361266, year = {2017}, author = {Grange, ZL and Biggs, PJ and Rose, SP and Gartrell, BD and Nelson, NJ and French, NP}, title = {Genomic Epidemiology and Management of Salmonella in Island Ecosystems Used for Takahe Conservation.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {735-744}, pmid = {28361266}, issn = {1432-184X}, mesh = {Animals ; Bird Diseases/*epidemiology/microbiology/transmission ; *Birds ; Conservation of Natural Resources ; Disease Reservoirs/*microbiology ; New Zealand ; Polymorphism, Single Nucleotide ; Prevalence ; Salmonella/classification/*genetics/isolation &amp; purification ; Salmonella Infections, Animal/*epidemiology/microbiology/transmission ; }, abstract = {Translocation and isolation of threatened wildlife in new environments may have unforeseen consequences on pathogen transmission and evolution in host populations. Disease threats associated with intensive conservation management of wildlife remain speculative without gaining an understanding of pathogen dynamics in meta-populations and how location attributes may determine pathogen prevalence. We determined the prevalence and population structure of an opportunistic pathogen, Salmonella, in geographically isolated translocated sub-populations of an endangered New Zealand flightless bird, the takahe (Porphyrio hochstetteri). Out of the nine sub-populations tested, Salmonella was only isolated from takahe living on one private island. The apparent prevalence of Salmonella in takahe on the private island was 32% (95% CI 13-57%), with two serotypes, Salmonella Mississippi and Salmonella houtenae 40:gt-, identified. Epidemiological investigation of reservoirs on the private island and another island occupied by takahe identified environmental and reptile sources of S. Mississippi and S. houtenae 40:gt- on the private island. Single nucleotide polymorphism analysis of core genomes revealed low-level diversity among isolates belonging to the same serotype and little differentiation according to host and environmental source. The pattern observed may be representative of transmission between sympatric hosts and environmental sources, the presence of a common unsampled source, and/or evidence of a recent introduction into the ecosystem. This study highlights how genomic epidemiology can be used to ascertain and understand disease dynamics to inform the management of disease threats in endangered wildlife populations.}, }
@article {pmid28361265, year = {2017}, author = {Liu, C and Jiang, Y and Wang, X and Chen, D and Chen, X and Wang, L and Han, L and Huang, X and Jiang, C}, title = {Diversity, Antimicrobial Activity, and Biosynthetic Potential of Cultivable Actinomycetes Associated with Lichen Symbiosis.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {570-584}, pmid = {28361265}, issn = {1432-184X}, support = {31270001//National Natural Science Foundation of China/ ; 31170023//National Natural Science Foundation of China/ ; 31400022//National Natural Science Foundation of China/ ; 31370069//National Natural Science Foundation of China/ ; 81573327//National Natural Science Foundation of China/ ; 31460005//National Natural Science Foundation of China (CN)/ ; }, mesh = {Actinobacteria/*chemistry/growth &amp; development/isolation &amp; purification/*physiology ; Anti-Infective Agents/metabolism ; *Antibiosis ; *Biodiversity ; Lichens/*physiology ; *Symbiosis ; }, abstract = {Lichens are structured associations of a fungus with a cyanobacteria and/or green algae in a symbiotic relationship, which provide specific habitats for diverse bacterial communities, including actinomycetes. However, few studies have been performed on the phylogenetic relationships and biosynthetic potential of actinomycetes across lichen species. In the present study, a total of 213 actinomycetes strains were isolated from 35 lichen samples (22 lichen genera) collected in Yunnan Province, China. 16S rRNA gene sequence analysis revealed an unexpected level of diversity among these isolates, which were distributed into 38 genera, 19 families, and 9 orders within the Actinobacteria phylum. The detailed taxa of isolates had no clear relationship to the taxonomic affiliations of the associated lichens. To the best of our knowledge, this is the first report to describe the isolation of Actinophytocola, Angustibacter, Herbiconiux, Kibdelosporangium, Kineosporia, Kitasatospora, Nakamurella, Nonomuraea, Labedella, Lechevalieria, Lentzea, Schumannella, and Umezawaea species from lichens. At least 40 isolates (18.78%) are likely to represent novel actinomycetes taxa within 15 genera. In addition, all 213 isolates were tested for antimicrobial activity and screened for genes associated with secondary metabolite production to evaluate their biosynthetic potential. These results demonstrate that the lichens of Yunnan Province represent an extremely rich reservoir for the isolation of a significant diversity of actinomycetes, including novel species, which are potential source for discovering biologically active compounds.}, }
@article {pmid28360899, year = {2017}, author = {Schueller, K and Riva, A and Pfeiffer, S and Berry, D and Somoza, V}, title = {Members of the Oral Microbiota Are Associated with IL-8 Release by Gingival Epithelial Cells in Healthy Individuals.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {416}, pmid = {28360899}, issn = {1664-302X}, support = {P 26127/FWF_/Austrian Science Fund FWF/Austria ; P 27831/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {The triggers for the onset of oral diseases are still poorly understood. The aim of this study was to characterize the oral bacterial community in healthy humans and its association with nutrition, oral hygiene habits, and the release of the inflammatory marker IL-8 from gingival epithelial cells (GECs) with and without stimulation by bacterial endotoxins to identify possible indicator operational taxonomic units (OTUs) associated with inflammatory marker status. GECs from 21 healthy participants (13 females, 8 males) were incubated with or without addition of bacterial lipopolysaccharides (LPSs), and the oral microbiota was profiled using 16S rRNA gene-targeted sequencing. The basal IL-8 release after 6 h was between 9.9 and 98.2 pg/ml, and bacterial communities were characteristic for healthy oral microbiota. The composition of the oral microbiota was associated with basal IL-8 levels, the intake of meat, tea, white wine, sweets and the use of chewing gum, as well as flossing habits, allergies, gender and body mass index. Additionally, eight OTUs were associated with high basal levels of IL-8 and GEC response to LPS, with high basal levels of IL-8, and 1 with low basal levels of IL8. The identification of indicator bacteria in healthy subjects with high levels of IL-8 release is of importance as they may be promising early warning indicators for the possible onset of oral diseases.}, }
@article {pmid28359536, year = {2017}, author = {Zhong, X and Xu, G and Xu, H}, title = {Use of multiple functional traits of protozoa for bioassessment of marine pollution.}, journal = {Marine pollution bulletin}, volume = {119}, number = {2}, pages = {33-38}, doi = {10.1016/j.marpolbul.2017.03.043}, pmid = {28359536}, issn = {1879-3363}, mesh = {Biodiversity ; *Biological Oxygen Demand Analysis ; *Ciliophora ; Ecosystem ; *Environmental Monitoring ; Water Pollutants/*toxicity ; }, abstract = {Ecological parameters based on multiply functional traits have many advantages for monitoring programs by reducing "signal to noise" ratios of observed species data. To identify potential indicators for bioassessment of marine pollution in function space, the functional patterns of protozoan communities and relationships with environmental changes were studied in coastal waters of the Yellow Sea during a 1-year period. The results showed that: (1) the spatial variability in functional trait distributions of the protozoa was significantly associated with changes in environmental variables, especially chemical oxygen demand (COD) and nutrients on spatial scale; (2) the functional traits, especially food resources and feeding type, were significantly correlated with COD and nutrients; and (3) the functional diversity indices were generally related to nutrients or COD. Based on the results, we suggest that the functional traits and diversity indices of protozoan communities may be used as more effective indicators for bioassessment of marine pollution.}, }
@article {pmid28358885, year = {2017}, author = {Harlow, BE and Lawrence, LM and Harris, PA and Aiken, GE and Flythe, MD}, title = {Exogenous lactobacilli mitigate microbial changes associated with grain fermentation (corn, oats, and wheat) by equine fecal microflora ex vivo.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0174059}, pmid = {28358885}, issn = {1932-6203}, mesh = {Animal Nutritional Physiological Phenomena ; Animals ; Avena/chemistry ; Digestion/physiology ; Feces/chemistry/*microbiology ; Fermentation/drug effects ; Gram-Positive Cocci/chemistry/*metabolism ; Horses/microbiology ; Hydrogen-Ion Concentration ; Lactobacillus/chemistry/*metabolism ; Probiotics/chemistry/*metabolism ; Starch/chemistry/metabolism ; Triticum/chemistry ; Zea mays/chemistry ; }, abstract = {Cereal grains are often included in equine diets. When starch intake exceeds foregut digestion starch will reach the hindgut, impacting microbial ecology. Probiotics (e.g., lactobacilli) are reported to mitigate GI dysbioses in other species. This study was conducted to determine the effect of exogenous lactobacilli on pH and the growth of amylolytic and lactate-utilizing bacteria. Feces were collected from 3 mature geldings fed grass hay with access to pasture. Fecal microbes were harvested by differential centrifugation, washed, and re-suspended in anaerobic media containing ground corn, wheat, or oats at 1.6% (w/v) starch and one of five treatments: Control (substrate only), L. acidophilus, L. buchneri, L. reuteri, or an equal mixture of all three (107 cells/mL, final concentration). After 24 h of incubation (37°C, 160 rpm), samples were collected for pH and enumerations of total amylolytics, Group D Gram-positive cocci (GPC; Enterococci, Streptococci), lactobacilli, and lactate-utilizing bacteria. Enumeration data were log transformed prior to ANOVA (SAS, v. 9.3). Lactobacilli inhibited pH decline in corn and wheat fermentations (P < 0.0001). Specifically, addition of either L. reuteri or L. acidophilus was most effective at mitigating pH decline with both corn and wheat fermentation, in which the greatest acidification occurred (P < 0.05). Exogenous lactobacilli decreased amylolytics, while increasing lactate-utilizers in corn and wheat fermentations (P < 0.0001). In oat fermentations, L. acidophilus and L. reuteri inhibited pH decline and increased lactate-utilizers while decreasing amylolytics (P < 0.0001). For all substrates, L. reuteri additions (regardless of viability) had the lowest number of GPC and the highest number of lactobacilli and lactate-utilizers (P < 0.05). There were no additive effects when lactobacilli were mixed. Exogenous lactobacilli decreased the initial (first 8 h) rate of starch catalysis when wheat was the substrate, but did not decrease total (24 h) starch utilization in any case. These results indicate that exogenous lactobacilli can impact the microbial community and pH of cereal grain fermentations by equine fecal microflora ex vivo. Additionally, dead (autoclaved) exogenous lactobacilli had similar effects as live lactobacilli on fermentation. This latter result indicates that the mechanism by which lactobacilli impact other amylolytic bacteria is not simple resource competition.}, }
@article {pmid28358818, year = {2017}, author = {Ossowicki, A and Jafra, S and Garbeva, P}, title = {The antimicrobial volatile power of the rhizospheric isolate Pseudomonas donghuensis P482.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0174362}, pmid = {28358818}, issn = {1932-6203}, mesh = {Agrobacterium/drug effects ; Anti-Infective Agents/chemistry/*pharmacology ; Antifungal Agents/chemistry/pharmacology ; Bacterial Proteins/metabolism ; Fungi/drug effects ; Fusarium/drug effects ; Gas Chromatography-Mass Spectrometry ; Hydrogen Cyanide/metabolism ; Oomycetes/drug effects ; Pseudomonas/*metabolism ; Pseudomonas fluorescens/drug effects ; Pythium/drug effects ; Rhizoctonia/drug effects ; Volatile Organic Compounds/chemistry/*pharmacology ; }, abstract = {Soil and rhizosphere bacteria produce an array of secondary metabolites including a wide range of volatile organic compounds (VOCs). These compounds play an important role in the long-distance interactions and communication between (micro)organisms. Furthermore, bacterial VOCs are involved in plant pathogens inhibition and induction of soil fungistasis and suppressivenes. In the present study, we analysed the volatile blend emitted by the rhizospheric isolate Pseudomonas donghuensis P482 and evaluated the volatile effect on the plant pathogenic fungi and bacteria as well as one oomycete. Moreover, we investigated the role of the GacS/GacA system on VOCs production in P. donghuensis P482. The results obtained demonstrated that VOCs emitted by P. donghuensis P482 have strong antifungal and antioomycete, but not antibacterial activity. The production of certain volatiles such as dimethyl sulfide, S-methyl thioacetate, methyl thiocyanate, dimethyl trisulfide, 1-undecan and HCN is depended on the GacS/GacA two-component regulatory system. Apparently, these compounds play an important role in the pathogens suppression as the gacA mutant entirely lost the ability to inhibit via volatiles the growth of tested plant pathogens.}, }
@article {pmid28351612, year = {2017}, author = {Gildemyn, S and Rozendal, RA and Rabaey, K}, title = {A Gibbs Free Energy-Based Assessment of Microbial Electrocatalysis.}, journal = {Trends in biotechnology}, volume = {35}, number = {5}, pages = {393-406}, doi = {10.1016/j.tibtech.2017.02.005}, pmid = {28351612}, issn = {1879-3096}, mesh = {*Bacterial Physiological Phenomena ; Biodegradation, Environmental ; Bioelectric Energy Sources/*microbiology ; Catalysis ; Computer Simulation ; Electrochemistry/*methods ; Electrodes/*microbiology ; *Energy Transfer ; *Models, Biological ; Models, Chemical ; Thermodynamics ; }, abstract = {The use of microbial catalysts for electrode reactions enables novel bioremediation and bioproduction processes. To understand the electrochemical performance of the electrode reactions, knowledge of their thermodynamics is essential. We elaborate here on the Growth Reference System (GRS), simplifying thermodynamic calculations in the aforementioned context to, for example, demonstrate that cathodic bioprocesses generally suffer from higher overpotentials than do anodic processes. Abiotic hydrogen production cannot be thermodynamically excluded for any of the cathodic microbial electrosynthesis processes described thus far. Predictions for maximum biomass production correlated to electron flow are in line with experimental observations. We include a comprehensive set of thermodynamic and electrochemical data to support calculations relevant to the field of microbial electrocatalysis.}, }
@article {pmid28349162, year = {2017}, author = {Zúñiga, C and Leiva, D and Carú, M and Orlando, J}, title = {Substrates of Peltigera Lichens as a Potential Source of Cyanobionts.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {561-569}, pmid = {28349162}, issn = {1432-184X}, support = {11100381//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; F_02-10//Instituto Ant&#xe1;rtico Chileno/ ; }, mesh = {Cyanobacteria/*genetics ; Lichens/microbiology/*physiology ; Nostoc/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; *Soil Microbiology ; *Symbiosis ; }, abstract = {Photobiont availability is one of the main factors determining the success of the lichenization process. Although multiple sources of photobionts have been proposed, there is no substantial evidence confirming that the substrates on which lichens grow are one of them. In this work, we obtained cyanobacterial 16S ribosomal RNA gene sequences from the substrates underlying 186 terricolous Peltigera cyanolichens from localities in Southern Chile and maritime Antarctica and compared them with the sequences of the cyanobionts of these lichens, in order to determine if cyanobacteria potentially available for lichenization were present in the substrates. A phylogenetic analysis of the sequences showed that Nostoc phylotypes dominated the cyanobacterial communities of the substrates in all sites. Among them, an overlap was observed between the phylotypes of the lichen cyanobionts and those of the cyanobacteria present in their substrates, suggesting that they could be a possible source of lichen photobionts. Also, in most cases, higher Nostoc diversity was observed in the lichens than in the substrates from each site. A better understanding of cyanobacterial diversity in lichen substrates and their relatives in the lichens would bring insights into mycobiont selection and the distribution patterns of lichens, providing a background for hypothesis testing and theory development for future studies of the lichenization process.}, }
@article {pmid28348642, year = {2017}, author = {Negi, V and Lal, R}, title = {Metagenomic Analysis of a Complex Community Present in Pond Sediment.}, journal = {Journal of genomics}, volume = {5}, number = {}, pages = {36-47}, pmid = {28348642}, issn = {1839-9940}, abstract = {The metagenomic profiling of complex communities is gaining immense interest across the scientific community. A complex community present in the pond sediment of a water body located close to a hexachlorocyclohexane (HCH) production site of the Indian Pesticide Limited (IPL) (Chinhat, Lucknow) was selected in an attempt to identify and analyze the unique microbial diversity and functional profile of the site. In this study, we supplement the metagenomic study of pond sediment with a variety of binning approaches along with an in depth functional analysis. Our results improve the understanding of ecology, in terms of community dynamics. The findings are crucial with respect to the mechanisms such as those involving the lin group of genes that are known to be implicated in the HCH degradation pathway or the Type VI secretory system (T6SS) and its effector molecules. Metagenomic studies using the comparative genomics approach involving the isolates from adjacent HCH contaminated soils have contributed significantly towards improving our understanding of unexplored concepts, while simultaneously uncovering the novel mechanisms of microbial ecology.}, }
@article {pmid28348235, year = {2017}, author = {Massalha, H and Korenblum, E and Malitsky, S and Shapiro, OH and Aharoni, A}, title = {Live imaging of root-bacteria interactions in a microfluidics setup.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {17}, pages = {4549-4554}, pmid = {28348235}, issn = {1091-6490}, mesh = {Arabidopsis/*microbiology ; Bacillus subtilis/*physiology ; Microfluidics/*instrumentation/methods ; Microscopy, Confocal/*instrumentation/methods ; Plant Roots/*microbiology/physiology ; Symbiosis ; }, abstract = {Plant roots play a dominant role in shaping the rhizosphere, the environment in which interaction with diverse microorganisms occurs. Tracking the dynamics of root-microbe interactions at high spatial resolution is currently limited because of methodological intricacy. Here, we describe a microfluidics-based approach enabling direct imaging of root-bacteria interactions in real time. The microfluidic device, which we termed tracking root interactions system (TRIS), consists of nine independent chambers that can be monitored in parallel. The principal assay reported here monitors behavior of fluorescently labeled Bacillus subtilis as it colonizes the root of Arabidopsis thaliana within the TRIS device. Our results show a distinct chemotactic behavior of B. subtilis toward a particular root segment, which we identify as the root elongation zone, followed by rapid colonization of that same segment over the first 6 h of root-bacteria interaction. Using dual inoculation experiments, we further show active exclusion of Escherichia coli cells from the root surface after B. subtilis colonization, suggesting a possible protection mechanism against root pathogens. Furthermore, we assembled a double-channel TRIS device that allows simultaneous tracking of two root systems in one chamber and performed real-time monitoring of bacterial preference between WT and mutant root genotypes. Thus, the TRIS microfluidics device provides unique insights into the microscale microbial ecology of the complex root microenvironment and is, therefore, likely to enhance the current rate of discoveries in this momentous field of research.}, }
@article {pmid28346507, year = {2017}, author = {Liehr, M and Mereu, A and Pastor, JJ and Quintela, JC and Staats, S and Rimbach, G and Ipharraguerre, IR}, title = {Olive oil bioactives protect pigs against experimentally-induced chronic inflammation independently of alterations in gut microbiota.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0174239}, pmid = {28346507}, issn = {1932-6203}, mesh = {Animals ; Anti-Inflammatory Agents/chemistry/*therapeutic use ; Caco-2 Cells ; Chronic Disease ; Cytokines/blood ; *Gastrointestinal Microbiome ; Humans ; Inflammation/blood/*prevention &amp; control ; Male ; Mice ; Olive Oil/chemistry/*therapeutic use ; RAW 264.7 Cells ; Swine/blood/*growth &amp; development/microbiology ; }, abstract = {Subclinical chronic inflammation (SCI) is associated with impaired animal growth. Previous work has demonstrated that olive-derived plant bioactives exhibit anti-inflammatory properties that could possibly counteract the growth-depressing effects of SCI. To test this hypothesis and define the underlying mechanism, we conducted a 30-day study in which piglets fed an olive-oil bioactive extract (OBE) and their control counterparts (C+) were injected repeatedly during the last 10 days of the study with increasing doses of Escherichia coli lipopolysaccharides (LPS) to induce SCI. A third group of piglets remained untreated throughout the study and served as a negative control (C-). In C+ pigs, SCI increased the circulating concentration of interleukin 1 beta (p < 0.001) and decreased feed ingestion (p < 0.05) and weight gain (p < 0.05). These responses were not observed in OBE animals. Although intestinal inflammation and colonic microbial ecology was not altered by treatments, OBE enhanced ileal mRNA abundance of tight and adherens junctional proteins (p < 0.05) and plasma recovery of mannitol (p < 0.05) compared with C+ and C-. In line with these findings, OBE improved transepithelial electrical resistance (p < 0.01) in TNF-α-challenged Caco-2/TC-7 cells, and repressed the production of inflammatory cytokines (p < 0.05) in LPS-stimulated macrophages. In summary, this work demonstrates that OBE attenuates the suppressing effect of SCI on animal growth through a mechanism that appears to involve improvements in intestinal integrity unrelated to alterations in gut microbial ecology and function.}, }
@article {pmid28341673, year = {2017}, author = {Staley, C and Kaiser, T and Gidley, ML and Enochs, IC and Jones, PR and Goodwin, KD and Sinigalliano, CD and Sadowsky, MJ and Chun, CL}, title = {Differential Impacts of Land-Based Sources of Pollution on the Microbiota of Southeast Florida Coral Reefs.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {10}, pages = {}, pmid = {28341673}, issn = {1098-5336}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Coral Reefs ; Florida ; Fungi/classification/genetics/*isolation &amp; purification ; *Microbiota ; Seawater/*microbiology ; Wastewater/chemistry/microbiology ; }, abstract = {Coral reefs are dynamic ecosystems known for decades to be endangered due, in large part, to anthropogenic impacts from land-based sources of pollution (LBSP). In this study, we utilized an Illumina-based next-generation sequencing approach to characterize prokaryotic and fungal communities from samples collected off the southeast coast of Florida. Water samples from coastal inlet discharges, oceanic outfalls of municipal wastewater treatment plants, treated wastewater effluent before discharge, open ocean samples, and coral tissue samples (mucus and polyps) were characterized to determine the relationships between microbial communities in these matrices and those in reef water and coral tissues. Significant differences in microbial communities were noted among all sample types but varied between sampling areas. Contamination from outfalls was found to be the greatest potential source of LBSP influencing native microbial community structure among all reef samples, although pollution from inlets was also noted. Notably, reef water and coral tissue communities were found to be more greatly impacted by LBSP at southern reefs, which also experienced the most degradation during the course of the study. The results of this study provide new insights into how microbial communities from LBSP can impact coral reefs in southeast Florida and suggest that wastewater outfalls may have a greater influence on the microbial diversity and structure of these reef communities than do contaminants carried in runoff, although the influences of runoff and coastal inlet discharge on coral reefs are still substantial.IMPORTANCE Coral reefs are known to be endangered due to sewage discharge and to runoff of nutrients, pesticides, and other substances associated with anthropogenic activity. Here, we used next-generation sequencing to characterize the microbial communities of potential contaminant sources in order to determine how environmental discharges of microbiota and their genetic material may influence the microbiomes of coral reef communities and coastal receiving waters. Runoff delivered through inlet discharges impacted coral microbial communities, but impacts from oceanic outfalls carrying treated wastewater were greater. Geographic differences in the degree of impact suggest that coral microbiomes may be influenced by the microbiological quality of treated wastewater.}, }
@article {pmid28341009, year = {2017}, author = {Schellenberg, JJ and Patterson, MH and Hill, JE}, title = {Gardnerella vaginalis diversity and ecology in relation to vaginal symptoms.}, journal = {Research in microbiology}, volume = {168}, number = {9-10}, pages = {837-844}, doi = {10.1016/j.resmic.2017.02.011}, pmid = {28341009}, issn = {1769-7123}, mesh = {Female ; *Gardnerella vaginalis/classification/genetics/pathogenicity ; Gram-Positive Bacterial Infections/*microbiology ; Humans ; RNA, Ribosomal, 16S/genetics ; Vagina/*microbiology ; Vaginosis, Bacterial/*microbiology ; }, abstract = {Gardnerella vaginalis was first described in 1953, and subsequently identified as the causative agent of a cluster of vaginal symptoms currently known as vaginosis. Research has so far failed to confirm whether and by which mechanism G. vaginalis initiates vaginosis, with, consequently, poor diagnostics and treatment outcomes. Recent molecular analyses of protein-coding genes demonstrate that the taxon G. vaginalis consists of at least four distinct species. This development may represent a critical turning point in clarifying ecological interactions and virulence factors contributing to symptoms and/or sequelae of vaginosis.}, }
@article {pmid28340597, year = {2017}, author = {Turroni, S and Rampelli, S and Biagi, E and Consolandi, C and Severgnini, M and Peano, C and Quercia, S and Soverini, M and Carbonero, FG and Bianconi, G and Rettberg, P and Canganella, F and Brigidi, P and Candela, M}, title = {Temporal dynamics of the gut microbiota in people sharing a confined environment, a 520-day ground-based space simulation, MARS500.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {39}, pmid = {28340597}, issn = {2049-2618}, mesh = {*Confined Spaces ; Environment ; *Gastrointestinal Microbiome ; Humans ; Space Flight ; *Space Simulation ; *Systems Analysis ; Time Factors ; }, abstract = {BACKGROUND: The intestinal microbial communities and their temporal dynamics are gaining increasing interest due to the significant implications for human health. Recent studies have shown the dynamic behavior of the gut microbiota in free-living, healthy persons. To date, it is not known whether these dynamics are applicable during prolonged life sharing in a confined and controlled environment.<br><br>RESULTS: The MARS500 project, the longest ground-based space simulation ever, provided us with a unique opportunity to trace the crew microbiota over 520&#xa0;days of isolated confinement, such as that faced by astronauts in real long-term interplanetary space flights, and after returning to regular life, for a total of 2&#xa0;years. According to our data, even under the strictly controlled conditions of an enclosed environment, the human gut microbiota is inherently dynamic, capable of shifting between different steady states, typically with rearrangements of autochthonous members. Notwithstanding a strong individuality in the overall gut microbiota trajectory, some key microbial components showed conserved temporal dynamics, with potential implications for the maintenance of a health-promoting, mutualistic microbiota configuration.<br><br>CONCLUSIONS: Sharing life in a confined habitat does not affect the resilience of the individual gut microbial ecosystem, even in the long term. However, the temporal dynamics of certain microbiota components should be monitored when programming future mission simulations and real space flights, to prevent breakdowns in the metabolic and immunological homeostasis of the crewmembers.}, }
@article {pmid28340433, year = {2017}, author = {Abid, A and Saidane, F and Hamdi, M}, title = {Feasibility of carbon dioxide sequestration by Spongiochloris sp microalgae during petroleum wastewater treatment in airlift bioreactor.}, journal = {Bioresource technology}, volume = {234}, number = {}, pages = {297-302}, doi = {10.1016/j.biortech.2017.03.041}, pmid = {28340433}, issn = {1873-2976}, mesh = {Bioreactors ; Carbon Dioxide/metabolism ; Microalgae/*metabolism ; Petroleum/metabolism ; *Wastewater ; }, abstract = {The aim of this work was to study the ability of using Hydrocabonoclastic native microbial and Spongiochloris sp microalgae in airlift bioreactors couples in order to restore hydrocarbons wastewater and develop the capacity of natural systems to reduce greenhouse effect through maximal control of CO2 gas emission in atmosphere. The kinetic parameters of CO2 gas fixation level and conversion it into biological material by microalgae as the biodegradation process effect in hydrocarbon have been evaluated. The result present that maximum specific growth rate μmax of Spongiochloris sp was (0.87±0.04day[-1]) and the biomass productivity Pmax was attended (1.5±0.3gL[-1]day[-1]) with maximal CO2 biofixation rate RCO2 (2.9205gL[-1]day[-1]). At 30°C and pH (7.6-7.4) the bioreactor showed a good wastewater removal efficiency (99.18%) in total hydrocarbons with COD stabilized within (1.30g/L), this result obtained suggesting that, the bioreactor applied system represented a useful strategy for maximizing CO2 bio-mitigation.}, }
@article {pmid28339946, year = {2017}, author = {Park, SH and Perrotta, A and Hanning, I and Diaz-Sanchez, S and Pendleton, S and Alm, E and Ricke, SC}, title = {Pasture flock chicken cecal microbiome responses to prebiotics and plum fiber feed amendments.}, journal = {Poultry science}, volume = {96}, number = {6}, pages = {1820-1830}, doi = {10.3382/ps/pew441}, pmid = {28339946}, issn = {1525-3171}, mesh = {Animal Feed/analysis ; Animals ; Bacteria/genetics/isolation &amp; purification ; Cecum/microbiology ; Chickens/*microbiology ; Diet/veterinary ; Dietary Fiber/*administration &amp; dosage ; Dietary Supplements ; *Microbiota ; Oligosaccharides/administration &amp; dosage/*pharmacology ; Prebiotics/*administration &amp; dosage ; *Prunus domestica ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {When prebiotics and other fermentation substrates are delivered to animals as feed supplements, the typical goal is to improve weight gain and feed conversion. In this work, we examined pasture flock chicken cecal contents using next generation sequencing (NGS) to identify and understand the composition of the microbiome when prebiotics and fermentation substrates were supplemented. We generated 16S rRNA sequencing data for 120 separate cecal samples from groups of chickens receiving one of 3 prebiotics or fiber feed additives. The data indicated that respective feed additives enrich for specific bacterial community members and modulate the diversity of the microbiome. We applied synthetic learning in microbial ecology (SLiME) analysis to interpret 16S rRNA microbial community data and identify specific bacterial operational taxonomic units (OTU) that are predictive of the particular feed additives used in these experiments. The results suggest that feed can influence microbiome composition in a predictable way, and thus diet may have indirect effects on weight gain and feed conversion through the microbiome.}, }
@article {pmid28337181, year = {2017}, author = {Iskandar, CF and Borges, F and Taminiau, B and Daube, G and Zagorec, M and Remenant, B and Leisner, JJ and Hansen, MA and Sørensen, SJ and Mangavel, C and Cailliez-Grimal, C and Revol-Junelles, AM}, title = {Comparative Genomic Analysis Reveals Ecological Differentiation in the Genus Carnobacterium.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {357}, pmid = {28337181}, issn = {1664-302X}, abstract = {Lactic acid bacteria (LAB) differ in their ability to colonize food and animal-associated habitats: while some species are specialized and colonize a limited number of habitats, other are generalist and are able to colonize multiple animal-linked habitats. In the current study, Carnobacterium was used as a model genus to elucidate the genetic basis of these colonization differences. Analyses of 16S rRNA gene meta-barcoding data showed that C. maltaromaticum followed by C. divergens are the most prevalent species in foods derived from animals (meat, fish, dairy products), and in the gut. According to phylogenetic analyses, these two animal-adapted species belong to one of two deeply branched lineages. The second lineage contains species isolated from habitats where contact with animal is rare. Genome analyses revealed that members of the animal-adapted lineage harbor a larger secretome than members of the other lineage. The predicted cell-surface proteome is highly diversified in C. maltaromaticum and C. divergens with genes involved in adaptation to the animal milieu such as those encoding biopolymer hydrolytic enzymes, a heme uptake system, and biopolymer-binding adhesins. These species also exhibit genes for gut adaptation and respiration. In contrast, Carnobacterium species belonging to the second lineage encode a poorly diversified cell-surface proteome, lack genes for gut adaptation and are unable to respire. These results shed light on the important genomics traits required for adaptation to animal-linked habitats in generalist Carnobacterium.}, }
@article {pmid28334335, year = {2017}, author = {Pangesti, N and Vandenbrande, S and Pineda, A and Dicke, M and Raaijmakers, JM and Van Loon, JJA}, title = {Antagonism between two root-associated beneficial Pseudomonas strains does not affect plant growth promotion and induced resistance against a leaf-chewing herbivore.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {4}, pages = {}, doi = {10.1093/femsec/fix038}, pmid = {28334335}, issn = {1574-6941}, mesh = {Arabidopsis/metabolism ; Arabidopsis Proteins ; Gene Expression Regulation, Plant ; *Herbivory ; Mastication ; Plant Development ; Plant Leaves/metabolism ; Plant Roots/metabolism/*physiology ; Pseudomonas/metabolism/*physiology ; Pseudomonas fluorescens/growth &amp; development ; Rhizosphere ; }, abstract = {Plant growth-promoting microbes residing on the roots may cooperate or compete, thereby affecting their collective benefit to the host plant. Pseudomonas simiae WCS417r (formerly known as P. fluorescens WCS417r) and Pseudomonas fluorescens SS101 are well known for their ability to induce systemic resistance in Arabidopsis. Here, we evaluate how these species interact on the roots of Arabidopsis thaliana Col-0 and how their co-inoculation affects plant defense to the leaf-chewing herbivore Mamestra brassicae and plant growth promotion. WCS417r and SS101, applied individually to root tips or at two different positions along the roots, established similar population densities on Arabidopsis roots. When co-inoculated at the same position on the roots, however, WCS417r established significantly higher population densities than SS101. Both upon single inoculation and co-inoculation, the two pseudomonads induced the same level of induced systemic resistance against the caterpillar M. brassicae and the same increase in plant biomass. These results suggest that combined inoculation of both Pseudomonas strains does not significantly modify the plant's defensive capacity compared to individual inoculation, resulting in a similar effect on performance of the generalist herbivore M. brassicae.}, }
@article {pmid28334256, year = {2017}, author = {Kokocinski, M and Gagala, I and Jasser, I and Karosiene, J and Kasperoviciene, J and Kobos, J and Koreiviene, J and Soininen, J and Szczurowska, A and Woszczyk, M and Mankiewicz-Boczek, J}, title = {Distribution of invasive Cylindrospermopsis raciborskii in the East-Central Europe is driven by climatic and local environmental variables.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {4}, pages = {}, doi = {10.1093/femsec/fix035}, pmid = {28334256}, issn = {1574-6941}, mesh = {Cyanobacteria/physiology ; Cylindrospermopsis/isolation &amp; purification/*physiology ; Environmental Monitoring ; Europe ; Global Warming ; *Introduced Species ; Lakes/microbiology ; Lithuania ; Phytoplankton ; Poland ; Seasons ; Temperature ; *Water Microbiology ; }, abstract = {Mechanisms behind expansion of an invasive cyanobacterium Cylindrospermopsis raciborskii have not been fully resolved, and different hypotheses, such as global warming, are suggested. In the East-Central Europe, it is widely occurring in western part of Poland but only in single locations in the East due to some limiting factors. Therefore, broad-scale phytoplankton survey including 117 randomly selected lakes in Poland and Lithuania was conducted. The results showed that C. raciborskii occurred widely in western part of Poland but was absent from other regions and Lithuania except one lake. The regions in which C. raciborskii was present had higher annual mean air temperature, higher maximum air temperature of the warmest month and higher minimum temperature of the coldest month, demonstrating that average air temperature, and indirectly, the duration of growing season might be more important factor driving C. raciborskii distribution than measured in situ water temperature. In turn, the presence of C. raciborskii in single localities may be more related to physiological adaptations of separated ecotype. Collectively, these results provide novel evidence on the influence of temperature on C. raciborskii distribution in East-European regions but also indicate high ecological plasticity of this species.}, }
@article {pmid28334251, year = {2017}, author = {Eggermont, M and Bossier, P and Pande, GSJ and Delahaut, V and Rayhan, AM and Gupta, N and Islam, SS and Yumo, E and Nevejan, N and Sorgeloos, P and Gomez-Gil, B and Defoirdt, T}, title = {Isolation of Vibrionaceae from wild blue mussel (Mytilus edulis) adults and their impact on blue mussel larviculture.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {4}, pages = {}, doi = {10.1093/femsec/fix039}, pmid = {28334251}, issn = {1574-6941}, mesh = {Animals ; Aquaculture ; Mytilus edulis/*microbiology ; Vibrio ; Vibrionaceae/growth &amp; development/*isolation &amp; purification ; }, abstract = {The blue mussel (Mytilus edulis) is known as a robust bivalve species, although its larviculture appears to be highly susceptible to diseases. In this study, we isolated 17 strains from induced mortality events in healthy wild-caught blue mussel adults and demonstrated that they caused between 17% and 98% mortality in blue mussel larvae in a newly developed, highly controlled immersion challenge test model. Eight of the isolates belong to the Splendidus clade of vibrios, while the other isolates belong to the genus Photobacterium. The genomes of the most virulent Vibrio isolate and the most virulent Photobacterium isolate were sequenced and contained several genes encoding factors that have previously been linked to virulence towards bivalves. In vitro tests confirmed that all 17 isolates were positive for these virulence factors. The sequenced genomes also contained a remarkably high number of multidrug resistance genes. We therefore assessed the sensitivity of all isolates to a broad range of antibiotics and found that there were indeed many strong positive correlations between the sensitivities of the isolates to different antibiotics. Our data provide an ecological insight into mass mortality in blue mussels as they indicate that wild mussels contain a reservoir of pathogenic bacteria.}, }
@article {pmid28334218, year = {2017}, author = {Mysara, M and Vandamme, P and Props, R and Kerckhof, FM and Leys, N and Boon, N and Raes, J and Monsieurs, P}, title = {Reconciliation between operational taxonomic units and species boundaries.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {4}, pages = {}, pmid = {28334218}, issn = {1574-6941}, mesh = {Biological Evolution ; Classification ; Cluster Analysis ; DNA Primers ; *Genetic Variation ; *High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The development of high-throughput sequencing technologies has revolutionised the field of microbial ecology via 16S rRNA gene amplicon sequencing approaches. Clustering those amplicon sequencing reads into operational taxonomic units (OTUs) using a fixed cut-off is a commonly used approach to estimate microbial diversity. A 97% threshold was chosen with the intended purpose that resulting OTUs could be interpreted as a proxy for bacterial species. Our results show that the robustness of such a generalised cut-off is questionable when applied to short amplicons only covering one or two variable regions of the 16S rRNA gene. It will lead to biases in diversity metrics and makes it hard to compare results obtained with amplicons derived with different primer sets. The method introduced within this work takes into account the differential evolutional rates of taxonomic lineages in order to define a dynamic and taxonomic-dependent OTU clustering cut-off score. For a taxonomic family consisting of species showing high evolutionary conservation in the amplified variable regions, the cut-off will be more stringent than 97%. By taking into consideration the amplified variable regions and the taxonomic family when defining this cut-off, such a threshold will lead to more robust results and closer correspondence between OTUs and species. This approach has been implemented in a publicly available software package called DynamiC.}, }
@article {pmid28333314, year = {2017}, author = {Calcuttawala, F and Hariharan, C and Pazhani, GP and Saha, DR and Ramamurthy, T}, title = {Characterization of E-type colicinogenic plasmids from Shigella sonnei.}, journal = {FEMS microbiology letters}, volume = {364}, number = {7}, pages = {}, doi = {10.1093/femsle/fnx060}, pmid = {28333314}, issn = {1574-6968}, mesh = {Colicins/*genetics/pharmacology ; DNA Restriction Enzymes/metabolism ; DNA, Single-Stranded ; Dysentery, Bacillary/microbiology ; Escherichia coli/genetics ; Microscopy, Electron, Transmission ; *Plasmids ; Real-Time Polymerase Chain Reaction ; Shigella sonnei/drug effects/*genetics/ultrastructure ; }, abstract = {Colicinogenic plasmids encode toxic proteins which have antagonistic activity against closely related bacteria. This study describes the molecular characterization of three colicinogenic plasmids designated as pSSE3, pSSE and pSSE2, each with a molecular size of ∼6 kb, identified in clinical isolates of Shigella sonnei. Sequence analysis revealed that pSSE and pSSE2 shared extensive sequence homology with each other and with Escherichia coli E-type colicinogenic plasmids. The plasmid pSSE3 lacked an additional gene imparting immunity to colicin E8, a unique feature not observed in any of the previously reported sequences of colicin E3 plasmids. Incomplete digestion of colicinogenic plasmids by restriction endonucleases, metachromatic staining with acridine orange and presence of single stranded initiation (ssi) region confirmed the coexistence of ssDNA along with dsDNA. Plasmid copy number as determined by real-time PCR was found to be about 20. Transmission electron microscopy revealed DNA impairment in test bacteria after colicin exposure. We hypothesize that S. sonnei has acquired E-group colicin plasmids from its close relative E. coli, with their sequences undergoing subtle changes depending on the cohabitation in the same milieu.}, }
@article {pmid28333045, year = {2017}, author = {Pintucci, C and Carballa, M and Varga, S and Sarli, J and Peng, L and Bousek, J and Pedizzi, C and Ruscalleda, M and Tarragó, E and Prat, D and Colica, G and Picavet, M and Colsen, J and Benito, O and Balaguer, M and Puig, S and Lema, JM and Colprim, J and Fuchs, W and Vlaeminck, SE}, title = {The ManureEcoMine pilot installation: advanced integration of technologies for the management of organics and nutrients in livestock waste.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {75}, number = {5-6}, pages = {1281-1293}, doi = {10.2166/wst.2016.559}, pmid = {28333045}, issn = {0273-1223}, mesh = {Acids/chemistry ; Ammonia/analysis ; Ammonium Compounds/analysis ; Anaerobiosis ; Animals ; Centrifugation ; Chemical Precipitation ; *Livestock ; Manure/*analysis ; Membranes, Artificial ; Nitrogen/analysis ; Organic Chemicals/*analysis ; Permeability ; Phosphorus/analysis ; Pilot Projects ; Struvite/chemistry ; Swine ; Temperature ; Ultrafiltration ; Waste Management/*methods ; Waste Products/*analysis ; }, abstract = {Manure represents an exquisite mining opportunity for nutrient recovery (nitrogen and phosphorus), and for their reuse as renewable fertilisers. The ManureEcoMine proposes an integrated approach of technologies, operated in a pilot-scale installation treating swine manure (83.7%) and Ecofrit[®] (16.3%), a mix of vegetable residues. Thermophilic anaerobic digestion was performed for 150 days, the final organic loading rate was 4.6 kgCOD m[-3] d[-1], with a biogas production rate of 1.4 Nm[3] m[-3] d[-1]. The digester was coupled to an ammonia side-stream stripping column and a scrubbing unit for free ammonia inhibition reduction in the digester, and nitrogen recovery as ammonium sulphate. The stripped digestate was recirculated daily in the digester for 15 days (68% of the digester volume), increasing the gas production rate by 27%. Following a decanter centrifuge, the digestate liquid fraction was treated with an ultrafiltration membrane. The filtrate was fed into a struvite reactor, with a phosphorus recovery efficiency of 83% (as orthophosphate). Acidification of digestate could increment the soluble orthophosphate concentration up to four times, enhancing phosphorus enrichment in the liquid fraction and its recovery via struvite. A synergistic combination of manure processing steps was demonstrated to be technologically feasible to upgrade livestock waste into refined, concentrated fertilisers.}, }
@article {pmid28331950, year = {2017}, author = {Lee, SH and Megonigal, PJ and Kang, H}, title = {How do Elevated CO2 and Nitrogen Addition Affect Functional Microbial Community Involved in Greenhouse Gas Flux in Salt Marsh System.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {670-680}, pmid = {28331950}, issn = {1432-184X}, support = {NRF (2011-0030040)//National Research Foundation of Korea/ ; SGER (2016R1D1A1A02937049)//National Research Foundation of Korea/ ; }, mesh = {Bacteria/*metabolism ; Carbon Dioxide/*metabolism ; Greenhouse Gases/metabolism ; Maryland ; Microbiota ; Nitrogen/*metabolism ; Polymorphism, Restriction Fragment Length ; Real-Time Polymerase Chain Reaction ; Seasons ; *Wetlands ; }, abstract = {Salt marshes are unique ecosystem of which a microbial community is expected to be affected by global climate change. In this study, by using T-RFLP analysis, quantitative PCR, and pyrosequencing, we comprehensively analyzed the microbial community structure responding to elevated CO2 (eCO2) and N addition in a salt marsh ecosystem subjected to CO2 manipulation and N addition for about 3 years. We focused on the genes of microbes relevant to N-cycling (denitrification and nitrification), CH4-flux (methanogens and methanotrophs), and S-cycling (sulfate reduction) considering that they are key functional groups involved in the nutrient cycle of salt marsh system. Overall, this study suggests that (1) eCO2 and N addition affect functional microbial community involved in greenhouse gas flux in salt marsh system. Specifically, the denitrification process may be facilitated, while the methanogenesis may be impeded due to the outcompeting of sulfate reduction by eCO2 and N. This implies that future global change may cause a probable change in GHGs flux and positive feedback to global climate change in salt marsh; (2) the effect of eCO2 and N on functional group seems specific and to contrast with each other, but the effect of single factor would not be compromised but complemented by combination of two factors. (3) The response of functional groups to eCO2 and/or N may be directly or indirectly related to the plant community and its response to eCO2 and/or N. This study provides new insights into our understanding of functional microbial community responses to eCO2 and/or N addition in a C3/C4 plant mixed salt marsh system.}, }
@article {pmid28326437, year = {2017}, author = {Barford, C and Montoya, J and Altabet, M and Mitchell, R}, title = {Steady-State Oxygen Isotope Effects of N2O Production in Paracoccus denitrificans.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {507-509}, pmid = {28326437}, issn = {1432-184X}, support = {NAG 2-843//National Aeronautics and Space Administration/ ; OCE-95-30187//National Science Foundation/ ; DEB-96-33510//National Science Foundation/ ; OCE-95-26356//National Science Foundation/ ; }, mesh = {*Denitrification ; Nitrous Oxide/*metabolism ; Oxygen Isotopes/*analysis ; Paracoccus denitrificans/*metabolism ; }, abstract = {Knowledge of isotopic discrimination, or fractionation, by denitrifying bacteria can benefit agricultural fertilizer management, wastewater treatment, and other applications. However, the complexity of N transformation pathways in the environment and the sensitivity of denitrification to environmental conditions warrant better isotopic distinction between denitrification and other processes, especially for oxygen isotopes. Here, we present a dataset of δ[18]O measurements in continuous culture of Paracoccus denitrificans. The authors hope that it will be useful in further studies of N2O in the environment.}, }
@article {pmid28326074, year = {2017}, author = {Andrei, A&#x15e; and Păuşan, MR and Tămaş, T and Har, N and Barbu-Tudoran, L and Leopold, N and Banciu, HL}, title = {Diversity and Biomineralization Potential of the Epilithic Bacterial Communities Inhabiting the Oldest Public Stone Monument of Cluj-Napoca (Transylvania, Romania).}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {372}, pmid = {28326074}, issn = {1664-302X}, abstract = {In this study, we investigated the biomineralization potential and diversity of the epilithic bacterial communities dwelling on the limestone statue of Saint Donatus, the oldest public monument of Cluj-Napoca city (Transylvania region, NW Romania). Their spatial distribution together with phylogenetic and metabolic diversity, as well as their capacity to precipitate calcium carbonate was evaluated by combining molecular and phenotypic fingerprinting methods with X-ray diffraction, Fourier transform infrared spectroscopy, and scanning electron-microscopy analyses. The results of real-time quantitative PCR, molecular fingerprinting and community-level physiological profiling showed that diverse and abundant bacterial assemblages that differ in relation to their collection site colonized the statue. The cultivation and molecular identification procedures allowed the characterization of 79 bacterial isolates belonging to Proteobacteria (73.4%), Firmicutes (19%), and Actinobacteria (7.6%). Amongst them, the 22 strains identified as being capable of calcium carbonate precipitation were found to belong mostly to Bacillus and Pseudomonas genera. We found that bacteria acted as nucleation sites, inducing the formation of nanoscale aggregates that were shown to be principally composed of vaterite. Furthermore, we expanded the current knowledge on culturable diversity of carbonatogenic bacteria by providing evidence for biogenic vaterite/calcite formation mediated by: Pseudomonas synxantha, P. graminis, Brevibacterium iodinum, Streptomyces albidoflavus, and Stenotrophomonas chelatiphaga. Overall, this study highlights the need to evaluate the carbonatogenetic potential of all the bacterial communities present on stone artwork prior to designing an efficient conservation treatment based on biomineralization.}, }
@article {pmid28325746, year = {2017}, author = {Chassaing, B and Van de Wiele, T and De Bodt, J and Marzorati, M and Gewirtz, AT}, title = {Dietary emulsifiers directly alter human microbiota composition and gene expression ex vivo potentiating intestinal inflammation.}, journal = {Gut}, volume = {66}, number = {8}, pages = {1414-1427}, pmid = {28325746}, issn = {1468-3288}, support = {R01 DK083890/DK/NIDDK NIH HHS/United States ; R01 DK099071/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Carboxymethylcellulose Sodium/*pharmacology ; Diet ; Emulsifying Agents/*pharmacology ; Enteritis/*microbiology ; Female ; Flagellin/metabolism ; Food Additives/pharmacology ; Gastrointestinal Microbiome/*drug effects/*genetics/physiology ; Gene Expression ; Germ-Free Life ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Models, Biological ; Polysorbates/*pharmacology ; }, abstract = {OBJECTIVE: The intestinal microbiota plays a central role in the development of many chronic inflammatory diseases including IBD and metabolic syndrome. Administration of substances that alter microbiota composition, including the synthetic dietary emulsifiers polysorbate 80 (P80) and carboxymethylcellulose (CMC), can promote such inflammatory disorders. However, that inflammation itself impacts microbiota composition has obfuscated defining the extent to which these compounds or other substances act directly upon the microbiota versus acting on host parameters that promote inflammation, which subsequently reshapes the microbiota.<br><br>DESIGN: We examined the direct impact of CMC and P80 on the microbiota using the mucosal simulator of the human intestinal microbial ecosystem (M-SHIME) model that maintains a complex stable human microbiota in the absence of a live host.<br><br>RESULTS: This approach revealed that both P80 and CMC acted directly upon human microbiota to increase its proinflammatory potential, as revealed by increased levels of bioactive flagellin. The CMC-induced increase in flagellin was rapid (1&#x2005;day) and driven by altered microbiota gene expression. In contrast, the P80-induced flagellin increase occurred more slowly and was closely associated with altered species composition. Transfer of both emulsifier-treated M-SHIME microbiotas to germ-free recipient mice recapitulated many of the host and microbial alterations observed in mice directly treated with emulsifiers.<br><br>CONCLUSIONS: These results demonstrate a novel paradigm of deconstructing host-microbiota interactions and indicate that the microbiota can be directly impacted by these commonly used food additives, in a manner that subsequently drives intestinal inflammation.}, }
@article {pmid28317257, year = {2017}, author = {Mueller, P and Granse, D and Nolte, S and Do, HT and Weingartner, M and Hoth, S and Jensen, K}, title = {Top-down control of carbon sequestration: grazing affects microbial structure and function in salt marsh soils.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {27}, number = {5}, pages = {1435-1450}, doi = {10.1002/eap.1534}, pmid = {28317257}, issn = {1051-0761}, mesh = {Animals ; Bacteria/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; *Carbon Sequestration ; Fungi/genetics/isolation &amp; purification/*physiology ; Genes, Bacterial ; Genes, Fungal ; Germany ; *Herbivory ; Livestock ; Sheep ; Soil/*chemistry ; *Soil Microbiology ; Wetlands ; }, abstract = {Tidal wetlands have been increasingly recognized as long-term carbon sinks in recent years. Work on carbon sequestration and decomposition processes in tidal wetlands focused so far mainly on effects of global-change factors such as sea-level rise and increasing temperatures. However, little is known about effects of land use, such as livestock grazing, on organic matter decomposition and ultimately carbon sequestration. The present work aims at understanding the mechanisms by which large herbivores can affect organic matter decomposition in tidal wetlands. This was achieved by studying both direct animal-microbe interactions and indirect animal-plant-microbe interactions in grazed and ungrazed areas of two long-term experimental field sites at the German North Sea coast. We assessed bacterial and fungal gene abundance using quantitative PCR, as well as the activity of microbial exo-enzymes by conducting fluorometric assays. We demonstrate that grazing can have a profound impact on the microbial community structure of tidal wetland soils, by consistently increasing the fungi-to-bacteria ratio by 38-42%, and therefore potentially exerts important control over carbon turnover and sequestration. The observed shift in the microbial community was primarily driven by organic matter source, with higher contributions of recalcitrant autochthonous (terrestrial) vs. easily degradable allochthonous (marine) sources in grazed areas favoring relative fungal abundance. We propose a novel and indirect form of animal-plant-microbe interaction: top-down control of aboveground vegetation structure determines the capacity of allochthonous organic matter trapping during flooding and thus the structure of the microbial community. Furthermore, our data provide the first evidence that grazing slows down microbial exo-enzyme activity and thus decomposition through changes in soil redox chemistry. Activities of enzymes involved in C cycling were reduced by 28-40%, while activities of enzymes involved in N cycling were not consistently affected by grazing. It remains unclear if this is a trampling-driven direct grazing effect, as hypothesized in earlier studies, or if the effect on redox chemistry is plant mediated and thus indirect. This study improves our process-level understanding of how grazing can affect the microbial ecology and biogeochemistry of semi-terrestrial ecosystems that may help explain and predict differences in C turnover and sequestration rates between grazed and ungrazed systems.}, }
@article {pmid28316329, year = {2017}, author = {Lebre, PH and De Maayer, P and Cowan, DA}, title = {Xerotolerant bacteria: surviving through a dry spell.}, journal = {Nature reviews. Microbiology}, volume = {15}, number = {5}, pages = {285-296}, pmid = {28316329}, issn = {1740-1534}, mesh = {Adaptation, Physiological/*physiology ; Bacteria/*metabolism ; *Bacterial Physiological Phenomena ; Cell Membrane/physiology ; Climate Change ; DNA Damage/physiology ; *Desert Climate ; Desiccation ; Oxidative Stress/physiology ; Reactive Oxygen Species/metabolism ; Water/*metabolism ; }, abstract = {Water is vital for many biological processes and is essential for all living organisms. However, numerous macroorganisms and microorganisms have adapted to survive in environments in which water is scarce; such organisms are collectively termed xerotolerant. With increasing global desertification due to climate change and human-driven desertification processes, it is becoming ever more important to understand how xerotolerant organisms cope with a lack of water. In this Review, we discuss the environmental, physiological and molecular adaptations that enable xerotolerant bacteria to survive in environments in which water is scarce and highlight insights from modern 'omics' technologies. Understanding xerotolerance will inform and hopefully aid efforts to regulate and even reverse desertification.}, }
@article {pmid28315161, year = {2017}, author = {Castanho, S and Califano, G and Soares, F and Costa, R and Mata, L and Pousão-Ferreira, P and Ribeiro, L}, title = {The effect of live feeds bathed with the red seaweed Asparagopsis armata on the survival, growth and physiology status of Sparus aurata larvae.}, journal = {Fish physiology and biochemistry}, volume = {43}, number = {4}, pages = {1043-1054}, pmid = {28315161}, issn = {1573-5168}, mesh = {Animal Feed/*microbiology ; Animals ; Anti-Bacterial Agents/chemistry/pharmacology ; Artemia/*microbiology ; Bacteria/drug effects ; Diet/veterinary ; Digestion/drug effects/physiology ; Feeding Behavior/drug effects ; Larva/drug effects/growth &amp; development ; Plant Extracts/chemistry/*pharmacology ; Rhodophyta/*chemistry ; Rotifera/*microbiology ; Sea Bream/*growth &amp; development ; }, abstract = {Larval rearing is affected by a wide range of microorganisms that thrive in larviculture systems. Some seaweed species have metabolites capable of reducing the bacterial load. However, no studies have yet tested whether including seaweed metabolites on larval rearing systems has any effects on the larvae development. This work assessed the development of Sparus aurata larvae fed preys treated with an Asparagopsis armata product. Live prey, Brachionus spp. and Artemia sp., were immersed in a solution containing 0.5% of a commercial extract of A. armata (Ysaline 100, YSA) for 30 min, before being fed to seabream larvae (n = 4 each). In the control, the live feed was immersed in clear water. Larval parameters such as growth, survival, digestive capacity (structural-histology and functional-enzymatic activity), stress level (cortisol content), non-specific immune response (lysozyme activity), anti-bacterial activity (disc-diffusion assay) and microbiota quantification (fish larvae gut and rearing water) were monitored. Fish larvae digestive capacity, stress level and non-specific immune response were not affected by the use of YSA. The number of Vibrionaceae was significantly reduced both in water and larval gut when using YSA. Growth was enhanced for YSA treatment, but higher mortality was also observed, especially until 10 days after hatching (DAH). The mortality peak observed at 8 DAH for both treatments, but higher for YSA, indicates larval higher susceptibility at this development stage, suggesting that lower concentrations of YSA should be used until 10 DAH. The application of YSA after 10 DAH onwards promotes a safer rearing environment.}, }
@article {pmid28314899, year = {2017}, author = {Sneck, ME and Rudgers, JA and Young, CA and Miller, TEX}, title = {Variation in the Prevalence and Transmission of Heritable Symbionts Across Host Populations in Heterogeneous Environments.}, journal = {Microbial ecology}, volume = {74}, number = {3}, pages = {640-653}, pmid = {28314899}, issn = {1432-184X}, support = {1145588//National Science Foundation/ ; }, mesh = {Arkansas ; Elymus/*microbiology/physiology ; Endophytes/*physiology ; Environment ; Midwestern United States ; Southwestern United States ; *Symbiosis ; }, abstract = {Heritable microbes are abundant in nature and influential to their hosts and the communities in which they reside. However, drivers of variability in the prevalence of heritable symbionts and their rates of transmission are poorly resolved, particularly across host populations experiencing variable biotic and abiotic environments. To fill these gaps, we surveyed 25 populations of two native grasses (Elymus virginicus and Elymus canadensis) across the southern Great Plains (USA). Both grass species host heritable endophytic fungi (genus Epichloё) and can hybridize where their ranges overlap. From a subset of hosts, we characterized endophyte genotype using genetic loci that link to bioactive alkaloid production. First, we found mean vertical transmission rates and population-level prevalence were positively correlated, specifically for E. virginicus. However, both endophyte prevalence and transmission varied substantially across populations and did not strongly correlate with abiotic variables, with one exception: endophyte prevalence decreased as drought stress decreased for E. virginicus hosts. Second, we evaluated the potential influence of biotic factors and found that, after accounting for climate, endophyte genotype explained significant variation in symbiont inheritance. We also contrasted populations where host species co-occurred in sympatry vs. allopatry. Sympatry could potentially increase interspecific hybridization, but this variable did not associate with patterns of symbiont prevalence or transmission success. Our results reveal substantial variability in symbiont prevalence and transmission across host populations and identify symbiont genotype, and to a lesser extent, the abiotic environment as sources of this variation.}, }
@article {pmid28314395, year = {2016}, author = {Couto, CR and Jurelevicius, DA and Alvarez, VM and van Elsas, JD and Seldin, L}, title = {Response of the bacterial community in oil-contaminated marine water to the addition of chemical and biological dispersants.}, journal = {Journal of environmental management}, volume = {184}, number = {Pt 3}, pages = {473-479}, doi = {10.1016/j.jenvman.2016.10.039}, pmid = {28314395}, issn = {1095-8630}, mesh = {*Biodegradation, Environmental ; Hydrocarbons/metabolism ; Petroleum/metabolism ; Surface-Active Agents/metabolism ; *Water ; Water Pollution ; }, abstract = {The use of dispersants in different stages of the oil production chain and for the remediation of water and soil is a well established practice. However, the choice for a chemical or biological dispersant is still a controversial subject. Chemical surfactants that persist long in the environment may pose problems of toxicity themselves; therefore, biosurfactants are considered to constitute an environmentally friendly and effective alternative. Nevertheless, the putative effects of such agents on the microbiomes of oil-contaminated and uncontaminated marine environments have not been sufficiently evaluated. Here, we studied the effects of the surfactant Ultrasperse II[®] and the surfactin (biosurfactant) produced by Bacillus sp. H2O-1 on the bacterial communities of marine water. Specifically, we used quantitative PCR and genetic fingerprint analyses to study the abundance and structure of the bacterial communities in marine water collected from two regions with contrasting climatic conditions. The addition of either chemical surfactant or biosurfactant influenced the structure and abundance of total and oil-degrading bacterial communities of oil-contaminated and uncontaminated marine waters. Remarkably, the bacterial communities responded similarly to the addition of oil and/or either the surfactant or the biosurfactant in both set of microcosms. After 30 days of incubation, the addition of surfactin enhanced the oil-degrading bacteria more than the chemical surfactant. However, no increase of hydrocarbon biodegradation values was observed, irrespective of the dispersant used. These data contribute to an increased understanding of the impact of novel dispersants on marine bacteriomes before commercial release into the environment.}, }
@article {pmid28314230, year = {2017}, author = {Pepi, M and Heipieper, HJ and Balestra, C and Borra, M and Biffali, E and Casotti, R}, title = {Toxicity of diatom polyunsaturated aldehydes to marine bacterial isolates reveals their mode of action.}, journal = {Chemosphere}, volume = {177}, number = {}, pages = {258-265}, doi = {10.1016/j.chemosphere.2017.03.031}, pmid = {28314230}, issn = {1879-1298}, mesh = {Aldehydes/*chemistry ; Bacteria/*chemistry ; Diatoms/*chemistry ; Esters/chemistry ; Eutrophication ; Fatty Acids, Unsaturated/*chemistry ; Geography ; Hydrophobic and Hydrophilic Interactions ; Lipids/chemistry ; Mediterranean Sea ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; }, abstract = {Diatoms produce and release polyunsaturated aldehydes (PUAs) during senescence in culture and at the end of blooms in nature and these compounds play different ecological roles, as infochemicals, allelochemicals and pheromones In order to elucidate the toxic effects of PUAs, we isolated six bacterial strains from the Mediterranean Sea during a diatom bloom and tested their tolerance to PUA in terms of growth and cell membrane properties. Based upon 16S rRNA sequencing, these bacteria were assigned to the genera Pseudomonas, Sufflavibacter, Halomonas, Vibrio, Idiomarina, and Labrenzia. Growth of these strains was reduced by 50% (EC50) at PUA concentrations ranging from 600 to 1700 μM of 2E,4E/Z-heptadienal (HEPTA), 400-800 μM of 2E, 4E/Z-octadienal (OCTA), and 70-400 μM of 2E, 4E/Z-decadienal (DECA). Two of these strains, Vibrio sp. and Halomonas, sp. were also investigated for membrane fatty acid composition in terms of adaptive modifications of their degree of saturation (ratio between saturated and unsaturated fatty acids) by GC-FID. A direct correlation between hydrophobicity and PUA toxicity was observed, and these bacteria were also found to react to PUAs by increasing the degree of saturation of their membranes fatty acids. Tested PUAs were 4-fold more toxic than the well-investigated n-alkanols, most probably due to their additional chemical aldehyde toxicity to disrupting proteins by the formation of Schiff's bases, and therefore, they act as very toxic and effective poison, probably accumulating in cytoplasmic membranes because of their high hydrophobicity.}, }
@article {pmid28303666, year = {2017}, author = {Chaudhary, PP and Rulík, M and Blaser, M}, title = {Is the methanogenic community reflecting the methane emissions of river sediments?-comparison of two study sites.}, journal = {MicrobiologyOpen}, volume = {6}, number = {4}, pages = {}, pmid = {28303666}, issn = {2045-8827}, mesh = {Archaea/*classification/genetics/*metabolism ; *Biodiversity ; Czech Republic ; DNA, Archaeal/genetics ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Polymorphism, Restriction Fragment Length ; Real-Time Polymerase Chain Reaction ; Rivers/*microbiology ; }, abstract = {Studies on methanogenesis from freshwater sediments have so far primarily focused on lake sediments. To expand our knowledge on the community composition of methanogenic archaea in river sediments, we studied the abundance and diversity of methanogenic archaea at two localities along a vertical profile (top 50 cm) obtained from sediment samples from Sitka stream (the Czech Republic). In this study, we compare two sites which previously have been shown to have a 10-fold different methane emission. Archaeal and methanogen abundance were analyzed by real-time PCR and T-RFLP. Our results show that the absolute numbers for the methanogenic community (qPCR) are relatively stable along a vertical profile as well as for both study sites. This was also true for the archaeal community and for the three major methanogenic orders in our samples (Methanosarcinales, Methanomicrobiales, and Methanobacteriales). However, the underlying community structure (T-RFLP) reveals different community compositions of the methanogens for both locations as well as for different depth layers and over different sampling times. In general, our data confirm that Methanosarcinales together with Methanomicrobiales are the two dominant methanogenic orders in river sediments, while members of Methanobacteriales contribute a smaller community and Methanocellales are only rarely present in this sediment. Our results show that the previously observed 10-fold difference in methane emission of the two sites could not be explained by molecular methods alone.}, }
@article {pmid28303622, year = {2017}, author = {Omar, A and Zhang, Q and Zou, S and Gong, J}, title = {Morphology and Phylogeny of the Soil Ciliate Metopus yantaiensis n. sp. (Ciliophora, Metopida), with Identification of the Intracellular Bacteria.}, journal = {The Journal of eukaryotic microbiology}, volume = {64}, number = {6}, pages = {792-805}, doi = {10.1111/jeu.12411}, pmid = {28303622}, issn = {1550-7408}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; China ; Ciliophora/*classification/cytology/genetics/*microbiology ; Cluster Analysis ; Cytoplasm/*microbiology ; DNA, Bacterial/chemistry/genetics ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Microscopy ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The morphology and infraciliature of a new ciliate, Metopus yantaiensis n. sp., discovered in coastal soil of northern China, were investigated. It is distinguished from its congeners by a combination of the following features: nuclear apparatus situated in the preoral dome; 18-21 somatic ciliary rows, of which three extend onto the preoral dome (dome kineties); three to five distinctly elongated caudal cilia, and 21-29 adoral polykinetids. The 18S rRNA genes of this new species and two congeners, Metopus contortus and Metopus hasei, were sequenced and phylogenetically analyzed. The new species is more closely related to M. hasei and the clevelandellids than to other congeners; both the genus Metopus and the order Metopida are not monophyletic. In addition, the digestion-resistant bacteria in the cytoplasm of M. yantaiensis were identified, using a 16S rRNA gene clone library, sequencing, and fluorescence in situ hybridization. The detected intracellular bacteria are affiliated with Sphingomonadales, Rhizobiales, Rickettsiales (Alphaproteobacteria), Pseudomonas (Gammaproteobacteria), Rhodocyclales (Betaproteobacteria), Clostridiales (Firmicutes), and Flavobacteriales (Bacteroidetes).}, }
@article {pmid28303313, year = {2017}, author = {Fouilland, E and Trottet, A and Alves-de-Souza, C and Bonnet, D and Bouvier, T and Bouvy, M and Boyer, S and Guillou, L and Hatey, E and Jing, H and Leboulanger, C and Le Floc'h, E and Liu, H and Mas, S and Mostajir, B and Nouguier, J and Pecqueur, D and Rochelle-Newall, E and Roques, C and Salles, C and Tournoud, MG and Vasseur, C and Vidussi, F}, title = {Significant Change in Marine Plankton Structure and Carbon Production After the Addition of River Water in a Mesocosm Experiment.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {289-301}, pmid = {28303313}, issn = {1432-184X}, mesh = {Animals ; Bacteria ; Carbon/*chemistry ; Food Chain ; France ; Fresh Water ; *Plankton ; Rivers/*chemistry ; Rotifera ; Salinity ; }, abstract = {Rivers are known to be major contributors to eutrophication in marine coastal waters, but little is known on the short-term impact of freshwater surges on the structure and functioning of the marine plankton community. The effect of adding river water, reducing the salinity by 15 and 30%, on an autumn plankton community in a Mediterranean coastal lagoon (Thau Lagoon, France) was determined during a 6-day mesocosm experiment. Adding river water brought not only nutrients but also chlorophyceans that did not survive in the brackish mesocosm waters. The addition of water led to initial increases (days 1-2) in bacterial production as well as increases in the abundances of bacterioplankton and picoeukaryotes. After day 3, the increases were more significant for diatoms and dinoflagellates that were already present in the Thau Lagoon water (mainly Pseudo-nitzschia spp. group delicatissima and Prorocentrum triestinum) and other larger organisms (tintinnids, rotifers). At the same time, the abundances of bacterioplankton, cyanobacteria, and picoeukaryote fell, some nutrients (NH4[+], SiO4[3-]) returned to pre-input levels, and the plankton structure moved from a trophic food web based on secondary production to the accumulation of primary producers in the mesocosms with added river water. Our results also show that, after freshwater inputs, there is rapid emergence of plankton species that are potentially harmful to living organisms. This suggests that flash flood events may lead to sanitary issues, other than pathogens, in exploited marine areas.}, }
@article {pmid28303312, year = {2017}, author = {Shirani, S and Hellweger, FL}, title = {Neutral Evolution and Dispersal Limitation Produce Biogeographic Patterns in Microcystis aeruginosa Populations of Lake Systems.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {416-426}, pmid = {28303312}, issn = {1432-184X}, mesh = {*Evolution, Molecular ; *Genetic Drift ; Great Lakes Region ; Lakes/*microbiology ; Microcystis/*genetics ; }, abstract = {Molecular observations reveal substantial biogeographic patterns of cyanobacteria within systems of connected lakes. An important question is the relative role of environmental selection and neutral processes in the biogeography of these systems. Here, we quantify the effect of genetic drift and dispersal limitation by simulating individual cyanobacteria cells using an agent-based model (ABM). In the model, cells grow (divide), die, and migrate between lakes. Each cell has a full genome that is subject to neutral mutation (i.e., the growth rate is independent of the genome). The model is verified by simulating simplified lake systems, for which theoretical solutions are available. Then, it is used to simulate the biogeography of the cyanobacterium Microcystis aeruginosa in a number of real systems, including the Great Lakes, Klamath River, Yahara River, and Chattahoochee River. Model output is analyzed using standard bioinformatics tools (BLAST, MAFFT). The emergent patterns of nucleotide divergence between lakes are dynamic, including gradual increases due to accumulation of mutations and abrupt changes due to population takeovers by migrant cells (coalescence events). The model predicted nucleotide divergence is heterogeneous within systems, and for weakly connected lakes, it can be substantial. For example, Lakes Superior and Michigan are predicted to have an average genomic nucleotide divergence of 8200 bp or 0.14%. The divergence between more strongly connected lakes is much lower. Our results provide a quantitative baseline for future biogeography studies. They show that dispersal limitation can be an important factor in microbe biogeography, which is contrary to the common belief, and could affect how a system responds to environmental change.}, }
@article {pmid28299401, year = {2017}, author = {Paulo, AMS and Aydin, R and Dimitrov, MR and Vreeling, H and Cavaleiro, AJ and García-Encina, PA and Stams, AJM and Plugge, CM}, title = {Sodium lauryl ether sulfate (SLES) degradation by nitrate-reducing bacteria.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {12}, pages = {5163-5173}, pmid = {28299401}, issn = {1432-0614}, support = {323009/ERC_/European Research Council/International ; }, mesh = {Aeromonas/isolation &amp; purification/metabolism ; Biodegradation, Environmental ; Carbon/metabolism ; Comamonadaceae/isolation &amp; purification/metabolism ; Comamonas/isolation &amp; purification/metabolism ; *Denitrification ; Gram-Negative Bacteria/genetics/isolation &amp; purification/*metabolism ; Oxidation-Reduction ; Pseudomonas/isolation &amp; purification/metabolism ; Sewage/microbiology ; Sodium Dodecyl Sulfate/*analogs &amp; derivatives/chemistry/metabolism ; Surface-Active Agents/chemistry/metabolism ; }, abstract = {The surfactant sodium lauryl ether sulfate (SLES) is widely used in the composition of detergents and frequently ends up in wastewater treatment plants (WWTPs). While aerobic SLES degradation is well studied, little is known about the fate of this compound in anoxic environments, such as denitrification tanks of WWTPs, nor about the bacteria involved in the anoxic biodegradation. Here, we used SLES as sole carbon and energy source, at concentrations ranging from 50 to 1000 mg L[-1], to enrich and isolate nitrate-reducing bacteria from activated sludge of a WWTP with the anaerobic-anoxic-oxic (A[2]/O) concept. In the 50 mg L[-1] enrichment, Comamonas (50%), Pseudomonas (24%), and Alicycliphilus (12%) were present at higher relative abundance, while Pseudomonas (53%) became dominant in the 1000 mg L[-1] enrichment. Aeromonas hydrophila strain S7, Pseudomonas stutzeri strain S8, and Pseudomonas nitroreducens strain S11 were isolated from the enriched cultures. Under denitrifying conditions, strains S8 and S11 degraded 500 mg L[-1] SLES in less than 1 day, while strain S7 required more than 6 days. Strains S8 and S11 also showed a remarkable resistance to SLES, being able to grow and reduce nitrate with SLES concentrations up to 40 g L[-1]. Strain S11 turned out to be the best anoxic SLES degrader, degrading up to 41% of 500 mg L[-1]. The comparison between SLES anoxic and oxic degradation by strain S11 revealed differences in SLES cleavage, degradation, and sulfate accumulation; both ester and ether cleavage were probably employed in SLES anoxic degradation by strain S11.}, }
@article {pmid28298910, year = {2017}, author = {Boutin, S and Hagenfeld, D and Zimmermann, H and El Sayed, N and Höpker, T and Greiser, HK and Becher, H and Kim, TS and Dalpke, AH}, title = {Clustering of Subgingival Microbiota Reveals Microbial Disease Ecotypes Associated with Clinical Stages of Periodontitis in a Cross-Sectional Study.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {340}, pmid = {28298910}, issn = {1664-302X}, abstract = {Periodontitis is characterized by chronic inflammation associated with alteration of the oral microbiota. In contrast to previous microbiome studies focusing a priori on comparison between extreme phenotypes, our study analyzed a random sample of 85 people. The aim of this study was to link microbial differences to disease's prevalence and severity. Using next generation sequencing of 16S rRNA amplicons and cluster analysis, we observed that the population can be divided into two major ecotypes: One mainly contained periodontal healthy/mild periodontitis individuals whereas the second ecotype showed a heterogeneous microbial distribution and clustered into three distinct sub-ecotypes. Those sub-ecotypes differed with respect to the frequency of diseased patients and displayed a gradual change in distinct subgingival microbiota that goes along with clinical disease symptoms. In ecotype 2, the subgroup with no clinical signs of disease was linked to an increase of F. nucleatum vincentii but also several other species, while only in "end-stage" dysbiosis classical red complex bacteria gained overweight. Therefore, the microbial disease ecotypes observed in our population can lead to an establishment of an early microbial risk profile for clinically healthy patients.}, }
@article {pmid28296352, year = {2017}, author = {Agrawal, S and Karst, SM and Gilbert, EM and Horn, H and Nielsen, PH and Lackner, S}, title = {The role of inoculum and reactor configuration for microbial community composition and dynamics in mainstream partial nitritation anammox reactors.}, journal = {MicrobiologyOpen}, volume = {6}, number = {4}, pages = {}, pmid = {28296352}, issn = {2045-8827}, mesh = {Ammonium Compounds/*metabolism ; Anaerobiosis ; Bacteria/*classification/*metabolism ; Bioreactors/*microbiology ; *Biota ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Denitrification ; Nitrification ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Temperature ; }, abstract = {Implementation of partial nitritation anammox (PNA) in the mainstream (municipal wastewater treatment) is still under investigation. Microbial community structure and reactor type can influence the performance of PNA reactor; yet, little is known about the role of the community composition of the inoculum and the reactor configuration under mainstream conditions. Therefore, this study investigated the community structure of inocula of different origin and their consecutive community dynamics in four different lab-scale PNA reactors with 16S rRNA gene amplicon sequencing. These reactors were operated for almost 1 year and subjected to realistic seasonal temperature fluctuations as in moderate climate regions, that is, from 20°C in summer to 10°C in winter. The sequencing analysis revealed that the bacterial community in the reactors comprised: (1) a nitrifying community (consisting of anaerobic ammonium-oxidizing bacteria (AnAOB), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB)); (2) different heterotrophic denitrifying bacteria and other putative heterotrophic bacteria (HB). The nitrifying community was the same in all four reactors at the genus level, although the biomasses were of different origin. Community dynamics revealed a stable community in the moving bed biofilm reactors (MBBR) in contrast to the sequencing batch reactors (SBR) at the genus level. Moreover, the reactor design seemed to influence the community dynamics, and reactor operation significantly influenced the overall community composition. The MBBR seems to be the reactor type of choice for mainstream wastewater treatment.}, }
@article {pmid28295810, year = {2017}, author = {Wellenreuther, M and Rosenquist, H and Jaksons, P and Larson, KW}, title = {Local adaptation along an environmental cline in a species with an inversion polymorphism.}, journal = {Journal of evolutionary biology}, volume = {30}, number = {6}, pages = {1068-1077}, doi = {10.1111/jeb.13064}, pmid = {28295810}, issn = {1420-9101}, mesh = {*Adaptation, Physiological ; Animals ; *Chromosome Inversion ; Diptera/*genetics ; *Gene Flow ; North Sea ; *Polymorphism, Genetic ; Population Dynamics ; }, abstract = {Polymorphic inversions are ubiquitous across the animal kingdom and are frequently associated with clines in inversion frequencies across environmental gradients. Such clines are thought to result from selection favouring local adaptation; however, empirical tests are scarce. The seaweed fly Coelopa frigida has an α/β inversion polymorphism, and previous work demonstrated that the α inversion frequency declines from the North Sea to the Baltic Sea and is correlated with changes in tidal range, salinity, algal composition and wrackbed stability. Here, we explicitly test the hypothesis that populations of C. frigida along this cline are locally adapted by conducting a reciprocal transplant experiment of four populations along this cline to quantify survival. We found that survival varied significantly across treatments and detected a significant Location x Substrate interaction, indicating local adaptation. Survival models showed that flies from locations at both extremes had highest survival on their native substrates, demonstrating that local adaptation is present at the extremes of the cline. Survival at the two intermediate locations was, however, not elevated at the native substrates, suggesting that gene flow in intermediate habitats may override selection. Together, our results support the notion that population extremes of species with polymorphic inversions are often locally adapted, even when spatially close, consistent with the growing view that inversions can have direct and strong effects on the fitness of species.}, }
@article {pmid28293696, year = {2017}, author = {Delgado, ML and Singh, P and Funk, JA and Moore, JA and Cannell, EM and Kanesfsky, J and Manning, SD and Scribner, KT}, title = {Intestinal Microbial Community Dynamics of White-Tailed Deer (Odocoileus virginianus) in an Agroecosystem.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {496-506}, pmid = {28293696}, issn = {1432-184X}, mesh = {Animals ; Deer/*microbiology ; Feces/microbiology ; Firmicutes/classification/isolation &amp; purification ; *Gastrointestinal Microbiome ; Proteobacteria/classification/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Seasons ; }, abstract = {The intestinal microbiota has important functions that contribute to host health. The compositional dynamics of microbial communities are affected by many factors, including diet and presence of pathogens. In contrast to humans and domestic mammals, the composition and seasonal dynamics of intestinal microbiota of wildlife species remain comparatively understudied. White-tailed deer (Odocoileus virginianus) is an ecologically and economically important wildlife species that inhabits agricultural ecosystems and is known to be a reservoir of enteric pathogens. Nevertheless, there is a lack of knowledge of white-tailed deer intestinal microbiota diversity and taxonomic composition. This study's first objective was to characterize and compare the intestinal microbiota of 66 fecal samples from white-tailed deer collected during two sampling periods (March and June) using 16S rDNA pyrosequencing. Associations between community diversity and composition and factors including season, sex, host genetic relatedness, and spatial location were quantified. Results revealed that white-tailed deer intestinal microbiota was predominantly comprised of phyla Firmicutes and Proteobacteria, whose relative frequencies varied significantly between sampling periods. The second objective was to examine the associations between the presence of Escherichia coli and Salmonella, and microbiota composition and diversity. Results indicated that relative abundance of some microbial taxa varied when a pathogen was present. This study provides insights into microbial compositional dynamics of a wildlife species inhabiting coupled natural and agricultural landscapes. Data focus attention on the high prevalence of Proteobacteria particularly during the summer and highlight the need for future research regarding the role of white-tailed deer as a natural pathogen reservoir in agroecosystems.}, }
@article {pmid28292322, year = {2017}, author = {Gasc, C and Peyret, P}, title = {Revealing large metagenomic regions through long DNA fragment hybridization capture.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {33}, pmid = {28292322}, issn = {2049-2618}, mesh = {Bacteria/*genetics/isolation &amp; purification ; Base Sequence ; DNA Probes ; High-Throughput Nucleotide Sequencing/methods ; *Metagenome ; Metagenomics/*methods ; *Nucleic Acid Hybridization ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {BACKGROUND: High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the de novo assembly of whole genomes from single organisms or metagenomic samples. However, due to the limited capacity of short-read sequence data to assemble complex or low coverage regions, genomes are typically fragmented, leading to draft genomes with numerous underexplored large genomic regions. Revealing these missing sequences is a major goal to resolve concerns in numerous biological studies.<br><br>METHODS: To overcome these limitations, we developed an innovative target enrichment method for the reconstruction of large unknown genomic regions. Based on a hybridization capture strategy, this approach enables the enrichment of large genomic regions allowing the reconstruction of tens of kilobase pairs flanking a short, targeted DNA sequence.<br><br>RESULTS: Applied to a metagenomic soil sample targeting the linA gene, the biomarker of hexachlorocyclohexane (HCH) degradation, our method permitted the enrichment of the gene and its flanking regions leading to the reconstruction of several contigs and complete plasmids exceeding tens of kilobase pairs surrounding linA. Thus, through gene association and genome reconstruction, we identified microbial species involved in HCH degradation which constitute targets to improve biostimulation treatments.<br><br>CONCLUSIONS: This new hybridization capture strategy makes surveying and deconvoluting complex genomic regions possible through large genomic regions enrichment and allows the efficient exploration of metagenomic diversity. Indeed, this approach enables to assign identity and function to microorganisms in natural environments,&#xa0;one of the ultimate goals of microbial ecology.}, }
@article {pmid28290203, year = {2017}, author = {Eymann, C and Lassek, C and Wegner, U and Bernhardt, J and Fritsch, OA and Fuchs, S and Otto, A and Albrecht, D and Schiefelbein, U and Cernava, T and Aschenbrenner, I and Berg, G and Grube, M and Riedel, K}, title = {Symbiotic Interplay of Fungi, Algae, and Bacteria within the Lung Lichen Lobaria pulmonaria L. Hoffm. as Assessed by State-of-the-Art Metaproteomics.}, journal = {Journal of proteome research}, volume = {16}, number = {6}, pages = {2160-2173}, doi = {10.1021/acs.jproteome.6b00974}, pmid = {28290203}, issn = {1535-3907}, mesh = {*Ascomycota ; Biodiversity ; *Chlorophyta ; *Cyanobacteria ; *Lichens ; Metabolomics ; Microbial Interactions ; Proteomics ; Pulmonaria ; *Symbiosis ; }, abstract = {Lichens are recognized by macroscopic structures formed by a heterotrophic fungus, the mycobiont, which hosts internal autotrophic photosynthetic algal and/or cyanobacterial partners, referred to as the photobiont. We analyzed the structure and functionality of the entire lung lichen Lobaria pulmonaria L. Hoffm. collected from two different sites by state-of-the-art metaproteomics. In addition to the green algae and the ascomycetous fungus, a lichenicolous fungus as well as a complex prokaryotic community (different from the cyanobacteria) was found, the latter dominated by methanotrophic Rhizobiales. Various partner-specific proteins could be assigned to the different lichen symbionts, for example, fungal proteins involved in vesicle transport, algal proteins functioning in photosynthesis, cyanobacterial nitrogenase and GOGAT involved in nitrogen fixation, and bacterial enzymes responsible for methanol/C1-compound metabolism as well as CO-detoxification. Structural and functional information on proteins expressed by the lichen community complemented and extended our recent symbiosis model depicting the functional multiplayer network of single holobiont partners.1 Our new metaproteome analysis strongly supports the hypothesis (i) that interactions within the self-supporting association are multifaceted and (ii) that the strategy of functional diversification within the single lichen partners may support the longevity of L. pulmonaria under certain ecological conditions.}, }
@article {pmid28289903, year = {2017}, author = {Cenit, MC and Nuevo, IC and Codoñer-Franch, P and Dinan, TG and Sanz, Y}, title = {Gut microbiota and attention deficit hyperactivity disorder: new perspectives for a challenging condition.}, journal = {European child &amp; adolescent psychiatry}, volume = {26}, number = {9}, pages = {1081-1092}, pmid = {28289903}, issn = {1435-165X}, mesh = {Attention Deficit Disorder with Hyperactivity/*physiopathology ; Brain/*microbiology/physiopathology ; Gastrointestinal Microbiome/*immunology ; Humans ; }, abstract = {A bidirectional communication between the gut and the brain (gut-brain axis) is well recognized with the gut microbiota viewed as a key regulator of this cross-talk. Currently, a body of preclinical and to a lesser extent epidemiological evidence supports the notion that host-microbe interactions play a key role in brain development and function and in the etiology of neurodevelopmental disorders. Early life events and shifts away from traditional lifestyles are known to impact gut microbiota composition and function and, thereby, may increase the risk of developing neurodevelopmental disorders. Attention deficit hyperactivity disorder (ADHD) is nowadays the most prevalent neurodevelopmental disorder. Despite many years of research its etiology is unclear and its diagnosis and treatment are still challenging. Different factors reported to be associated with the risk of developing ADHD and/or linked to different ADHD manifestations have also been linked to shifts in gut microbiota composition, suggesting a link between the microbiota and the disorder. Evidence from preliminary human studies also suggests that dietary components that modulate gut microbiota may also influence ADHD development or symptoms, although further studies are warranted to confirm this hypothesis. Here, we firstly review the potential mechanisms by which the gut microbiota may regulate the brain-gut axis and influence behavior and neurodevelopmental disorders. Secondly, we discuss the current knowledge about the different factors and dietary components reported to be associated with the risk of developing ADHD or its manifestations and with shifts in gut microbiota composition. Finally, we briefly highlight the need to progress our understanding regarding the role of the gut microbiota in ADHD, since this could open new avenues for early intervention and improved management of the disease.}, }
@article {pmid28289836, year = {2017}, author = {La Ferla, R and Azzaro, M and Michaud, L and Caruso, G and Lo Giudice, A and Paranhos, R and Cabral, AS and Conte, A and Cosenza, A and Maimone, G and Papale, M and Rappazzo, AC and Guglielmin, M}, title = {Prokaryotic Abundance and Activity in Permafrost of the Northern Victoria Land and Upper Victoria Valley (Antarctica).}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {402-415}, pmid = {28289836}, issn = {1432-184X}, mesh = {Antarctic Regions ; Cold Temperature ; Enzymes/analysis ; Permafrost/*microbiology ; *Soil Microbiology ; Water ; }, abstract = {Victoria Land permafrost harbours a potentially large pool of cold-affected microorganisms whose metabolic potential still remains underestimated. Three cores (BC-1, BC-2 and BC-3) drilled at different depths in Boulder Clay (Northern Victoria Land) and one sample (DY) collected from a core in the Dry Valleys (Upper Victoria Valley) were analysed to assess the prokaryotic abundance, viability, physiological profiles and potential metabolic rates. The cores drilled at Boulder Clay were a template of different ecological conditions (different temperature regime, ice content, exchanges with atmosphere and with liquid water) in the same small basin while the Dry Valleys site was very similar to BC-2 conditions but with a complete different geological history and ground ice type. Image analysis was adopted to determine cell abundance, size and shape as well as to quantify the potential viable and respiring cells by live/dead and 5-cyano-2,3-ditolyl-tetrazolium chloride staining, respectively. Subpopulation recognition by apparent nucleic acid contents was obtained by flow cytometry. Moreover, the physiological profiles at community level by Biolog-Ecoplate™ as well as the ectoenzymatic potential rates on proteinaceous (leucine-aminopeptidase) and glucidic (ß-glucosidase) organic matter and on organic phosphates (alkaline-phosphatase) by fluorogenic substrates were tested. The adopted methodological approach gave useful information regarding viability and metabolic performances of microbial community in permafrost. The occurrence of a multifaceted prokaryotic community in the Victoria Land permafrost and a large number of potentially viable and respiring cells (in the order of 10[4]-10[5]) were recognised. Subpopulations with a different apparent DNA content within the different samples were observed. The physiological profiles stressed various potential metabolic pathways among the samples and intense utilisation rates of polymeric carbon compounds and carbohydrates, mainly in deep samples. The measured enzymatic activity rates suggested the potential capability of the microbial community to decompose proteins and polysaccharides. The microbial community seems to be appropriate to contribute to biogeochemical cycling in this extreme environment.}, }
@article {pmid28289787, year = {2017}, author = {Meeboon, N and Leewis, MC and Kaewsuwan, S and Maneerat, S and Leigh, MB}, title = {Changes in bacterial diversity associated with bioremediation of used lubricating oil in tropical soils.}, journal = {Archives of microbiology}, volume = {199}, number = {6}, pages = {839-851}, pmid = {28289787}, issn = {1432-072X}, support = {P20 GM103395/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; *Biodiversity ; Lubricants/analysis/*metabolism ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/analysis/*metabolism ; Tropical Climate ; }, abstract = {Used lubricating oil (ULO) is a widespread contaminant, particularly throughout tropical regions, and may be a candidate for bioremediation. However, little is known about the biodegradation potential or basic microbial ecology of ULO-contaminated soils. This study aims to determine the effects of used ULO on bacterial community structure and diversity. Using a combination of culture-based (agar plate counts) and molecular techniques (16S rRNA gene sequencing and DGGE), we investigated changes in soil bacterial communities from three different ULO-contaminated soils collected from motorcycle mechanical workshops (soil A, B, and C). We further explored the relationship between bacterial community structure, physiochemical soil parameters, and ULO composition in three ULO-contaminated soils. Results indicated that the three investigated soils had different community structures, which may be a result of the different ULO characteristics and physiochemical soil parameters of each site. Soil C had the highest ULO concentration and also the greatest diversity and richness of bacteria, which may be a result of higher nutrient retention, organic matter and cation exchange capacity, as well as freshness of oil compared to the other soils. In soils A and B, Proteobacteria (esp. Gammaproteobacteria) dominated the bacterial community, and in soil C, Actinobacteria and Firmicutes dominated. The genus Enterobacter, a member of the class Gammaproteobacteria, is known to include ULO-degraders, and this genus was the only one found in all three soils, suggesting that it could play a key role in the in situ degradation of ULO-contaminated tropical Thai soils. This study provides insights into our understanding of soil microbial richness, diversity, composition, and structure in tropical ULO-contaminated soils, and may be useful for the development of strategies to improve bioremediation.}, }
@article {pmid28289728, year = {2017}, author = {Westcott, SL and Schloss, PD}, title = {OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units.}, journal = {mSphere}, volume = {2}, number = {2}, pages = {}, pmid = {28289728}, issn = {2379-5042}, support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; }, abstract = {Assignment of 16S rRNA gene sequences to operational taxonomic units (OTUs) is a computational bottleneck in the process of analyzing microbial communities. Although this has been an active area of research, it has been difficult to overcome the time and memory demands while improving the quality of the OTU assignments. Here, we developed a new OTU assignment algorithm that iteratively reassigns sequences to new OTUs to optimize the Matthews correlation coefficient (MCC), a measure of the quality of OTU assignments. To assess the new algorithm, OptiClust, we compared it to 10 other algorithms using 16S rRNA gene sequences from two simulated and four natural communities. Using the OptiClust algorithm, the MCC values averaged 15.2 and 16.5% higher than the OTUs generated when we used the average neighbor and distance-based greedy clustering with VSEARCH, respectively. Furthermore, on average, OptiClust was 94.6 times faster than the average neighbor algorithm and just as fast as distance-based greedy clustering with VSEARCH. An empirical analysis of the efficiency of the algorithms showed that the time and memory required to perform the algorithm scaled quadratically with the number of unique sequences in the data set. The significant improvement in the quality of the OTU assignments over previously existing methods will significantly enhance downstream analysis by limiting the splitting of similar sequences into separate OTUs and merging of dissimilar sequences into the same OTU. The development of the OptiClust algorithm represents a significant advance that is likely to have numerous other applications. IMPORTANCE The analysis of microbial communities from diverse environments using 16S rRNA gene sequencing has expanded our knowledge of the biogeography of microorganisms. An important step in this analysis is the assignment of sequences into taxonomic groups based on their similarity to sequences in a database or based on their similarity to each other, irrespective of a database. In this study, we present a new algorithm for the latter approach. The algorithm, OptiClust, seeks to optimize a metric of assignment quality by shuffling sequences between taxonomic groups. We found that OptiClust produces more robust assignments and does so in a rapid and memory-efficient manner. This advance will allow for a more robust analysis of microbial communities and the factors that shape them.}, }
@article {pmid28289564, year = {2017}, author = {Graham, ED and Heidelberg, JF and Tully, BJ}, title = {BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3035}, pmid = {28289564}, issn = {2167-8359}, abstract = {Metagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is important for interpreting microbial community functions and the impacts these communities have on geochemical cycles. However, with metagenomic studies there is the computational hurdle of 'binning' contigs into phylogenetically related units or putative genomes. Binning methods have been implemented with varying approaches such as k-means clustering, Gaussian mixture models, hierarchical clustering, neural networks, and two-way clustering; however, many of these suffer from biases against low coverage/abundance organisms and closely related taxa/strains. We are introducing a new binning method, BinSanity, that utilizes the clustering algorithm affinity propagation (AP), to cluster assemblies using coverage with compositional based refinement (tetranucleotide frequency and percent GC content) to optimize bins containing multiple source organisms. This separation of composition and coverage based clustering reduces bias for closely related taxa. BinSanity was developed and tested on artificial metagenomes varying in size and complexity. Results indicate that BinSanity has a higher precision, recall, and Adjusted Rand Index compared to five commonly implemented methods. When tested on a previously published environmental metagenome, BinSanity generated high completion and low redundancy bins corresponding with the published metagenome-assembled genomes.}, }
@article {pmid28285593, year = {2017}, author = {Obiegala, A and Król, N and Oltersdorf, C and Nader, J and Pfeffer, M}, title = {The enzootic life-cycle of Borrelia burgdorferi (sensu lato) and tick-borne rickettsiae: an epidemiological study on wild-living small mammals and their ticks from Saxony, Germany.}, journal = {Parasites &amp; vectors}, volume = {10}, number = {1}, pages = {115}, pmid = {28285593}, issn = {1756-3305}, mesh = {Anaplasma phagocytophilum/genetics/isolation &amp; purification ; Animals ; Animals, Wild/*microbiology/parasitology ; Borrelia burgdorferi/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Dermacentor/genetics ; *Disease Reservoirs ; Germany/epidemiology ; Ixodes/genetics/*microbiology ; Lyme Disease/epidemiology/microbiology/*veterinary ; Mammals/*microbiology/parasitology ; Multilocus Sequence Typing ; Rickettsia/genetics/*isolation &amp; purification ; Rickettsia Infections/epidemiology/microbiology/*veterinary ; }, abstract = {BACKGROUND: Borrelia burgdorferi (sensu lato) and rickettsiae of the spotted fever group are zoonotic tick-borne pathogens. While small mammals are confirmed reservoirs for certain Borrelia spp., little is known about the reservoirs for tick-borne rickettsiae. Between 2012 and 2014, ticks were collected from the vegetation and small mammals which were trapped in Saxony, Germany. DNA extracted from ticks and the small mammals' skin was analyzed for the presence of Rickettsia spp. and B. burgdorferi (s.l.) by qPCR targeting the gltA and p41 genes, respectively. Partial sequencing of the rickettsial ompB gene and an MLST of B. burgdorferi (s.l.) were conducted for species determination.<br><br>RESULTS: In total, 673 small mammals belonging to eight species (Apodemus agrarius, n&#x2009;=&#x2009;7; A. flavicollis, n&#x2009;=&#x2009;214; Microtus arvalis, n&#x2009;=&#x2009;8; Microtus agrestis, n&#x2009;=&#x2009;1; Mustela nivalis, n&#x2009;=&#x2009;2; Myodes glareolus, n&#x2009;=&#x2009;435; Sorex araneus, n&#x2009;=&#x2009;5; and Talpa europaea, n&#x2009;=&#x2009;1) were collected and examined. In total, 916 questing ticks belonging to three species (Ixodes ricinus, n&#x2009;=&#x2009;741; Dermacentor reticulatus, n&#x2009;=&#x2009;174; and I. trianguliceps, n&#x2009;=&#x2009;1) were collected. Of these, 474 ticks were further investigated. The prevalence for Rickettsia spp. and B. burgdorferi (s.l.) in the investigated small mammals was 25.3 and 31.2%, respectively. The chance of encountering Rickettsia spp. in M. glareolus was seven times higher for specimens infested with D. reticulatus than for those which were free of D. reticulatus (OR: 7.0; 95% CI: 3.3-14.7; P&#x2009;<&#x2009;0.001). In total, 11.4% of questing I. ricinus and 70.5% of D. reticulatus were positive for Rickettsia spp. DNA of B. burgdorferi (s.l.) was detected only in I. ricinus (5.5%). Sequence analysis revealed 9 R. helvetica, 5 R. raoultii, and 1 R. felis obtained from 15 small mammal samples.<br><br>CONCLUSION: Small mammals may serve as reservoirs for Rickettsia spp. and B. burgdorferi (s.l.). While the prevalence for Rickettsia spp. in M. glareolus is most likely depending on the abundance of attached D. reticulatus, the prevalence for B. burgdorferi (s.l.) in small mammals is independent of tick abundance. Dermacentor reticulatus may be the main vector of certain Rickettsia spp. but not for Borrelia spp.}, }
@article {pmid28283029, year = {2017}, author = {Weil, T and De Filippo, C and Albanese, D and Donati, C and Pindo, M and Pavarini, L and Carotenuto, F and Pasqui, M and Poto, L and Gabrieli, J and Barbante, C and Sattler, B and Cavalieri, D and Miglietta, F}, title = {Legal immigrants: invasion of alien microbial communities during winter occurring desert dust storms.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {32}, pmid = {28283029}, issn = {2049-2618}, mesh = {Africa, Northern ; *Air Microbiology ; Bacteria/classification/genetics/*isolation &amp; purification/pathogenicity ; Biodiversity ; Climate Change ; *Desert Climate ; Dust/*analysis ; Ecosystem ; Global Warming ; Italy ; Metagenomics ; Microbial Consortia ; *Microbiota ; Public Health ; Seasons ; Silicon Dioxide ; *Wind ; }, abstract = {BACKGROUND: A critical aspect regarding the global dispersion of pathogenic microorganisms is associated with atmospheric movement of soil particles. Especially, desert dust storms can transport alien microorganisms over continental scales and can deposit them in sensitive sink habitats. In winter 2014, the largest ever recorded Saharan dust event in Italy was efficiently deposited on the Dolomite Alps and was sealed between dust-free snow. This provided us the unique opportunity to overcome difficulties in separating dust associated from "domestic" microbes and thus, to determine with high precision microorganisms transported exclusively by desert dust.<br><br>RESULTS: Our metagenomic analysis revealed that sandstorms can move not only fractions but rather large parts of entire microbial communities far away from their area of origin and that this microbiota contains several of the most stress-resistant organisms on Earth, including highly destructive fungal and bacterial pathogens. In particular, we provide first evidence that winter-occurring dust depositions can favor a rapid microbial contamination of sensitive sink habitats after snowmelt.<br><br>CONCLUSIONS: Airborne microbial depositions accompanying extreme meteorological events represent a realistic threat for ecosystem and public health. Therefore, monitoring the spread and persistence of storm-travelling alien microbes is a priority while considering future trajectories of climatic anomalies as well as anthropogenically driven changes in land use in the source regions.}, }
@article {pmid28282040, year = {2017}, author = {Ji, P and Rhoads, WJ and Edwards, MA and Pruden, A}, title = {Impact of water heater temperature setting and water use frequency on the building plumbing microbiome.}, journal = {The ISME journal}, volume = {11}, number = {6}, pages = {1318-1330}, pmid = {28282040}, issn = {1751-7370}, mesh = {Bacteria/*classification ; Biofilms ; *Drinking Water ; Hot Temperature ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Sanitary Engineering ; Temperature ; *Water Microbiology ; *Water Supply ; }, abstract = {Hot water plumbing is an important conduit of microbes into the indoor environment and can increase risk of opportunistic pathogens (for example, Legionella pneumophila). We examined the combined effects of water heater temperature (39, 42, 48, 51 and 58 °C), pipe orientation (upward/downward), and water use frequency (21, 3 and 1 flush per week) on the microbial composition at the tap using a pilot-scale pipe rig. 16S rRNA gene amplicon sequencing indicated that bulk water and corresponding biofilm typically had distinct taxonomic compositions (R[2]Adonis=0.246, PAdonis=0.001), yet similar predicted functions based on PICRUSt analysis (R[2]Adonis=0.087, PAdonis=0.001). Although a prior study had identified 51 °C under low water use frequency to enrich Legionella at the tap, here we reveal that 51 °C is also a threshold above which there are marked effects of the combined influences of temperature, pipe orientation, and use frequency on taxonomic and functional composition. A positive association was noted between relative abundances of Legionella and mitochondrial DNA of Vermamoeba, a genus of amoebae that can enhance virulence and facilitate replication of some pathogens. This study takes a step towards intentional control of the plumbing microbiome and highlights the importance of microbial ecology in governing pathogen proliferation.}, }
@article {pmid28281565, year = {2017}, author = {Wang, H and Marshall, CW and Cheng, M and Xu, H and Li, H and Yang, X and Zheng, T}, title = {Changes in land use driven by urbanization impact nitrogen cycling and the microbial community composition in soils.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {44049}, pmid = {28281565}, issn = {2045-2322}, mesh = {China ; *Nitrogen Cycle ; Soil/chemistry ; *Soil Microbiology ; *Urbanization ; }, abstract = {Transition of populations from rural to urban living causes landscape changes and alters the functionality of soil ecosystems. It is unclear how this urbanization disturbs the microbial ecology of soils and how the disruption influences nitrogen cycling. In this study, microbial communities in turfgrass-grown soils from urban and suburban areas around Xiamen City were compared to microbial communities in the soils from rural farmlands. The potential N2O emissions, potential denitrification activity, and abundances of denitrifiers were higher in the rural farmland soils compared with the turfgrass soils. Ammonia oxidizing archaea (AOA) were more abundant than ammonia oxidizing bacteria (AOB) in turfgrass soils. Within turfgrass soils, the potential nitrification activities and AOA abundances were higher in the urban than in the suburban soils. These results indicate a more pivotal role of AOA in nitrification, especially in urban soils. Microbial community composition was distinctly grouped along urbanization categories (urban, suburban, and rural) classified according to the population density, which can in part be attributed to the differences in soil properties. These observed changes could potentially have a broader impact on soil nutrient availability and greenhouse gas emissions.}, }
@article {pmid28280926, year = {2017}, author = {Nandre, VS and Bachate, SP and Salunkhe, RC and Bagade, AV and Shouche, YS and Kodam, KM}, title = {Enhanced Detoxification of Arsenic Under Carbon Starvation: A New Insight into Microbial Arsenic Physiology.}, journal = {Current microbiology}, volume = {74}, number = {5}, pages = {614-622}, pmid = {28280926}, issn = {1432-0991}, mesh = {Arsenic/*metabolism ; Bacteria/classification/genetics/metabolism ; *Biodegradation, Environmental ; Carbon/metabolism ; *Environmental Microbiology ; Genes, Bacterial ; Oxidation-Reduction ; Phylogeny ; Soil Microbiology ; }, abstract = {Nutrient availability in nature influenced the microbial ecology and behavior present in existing environment. In this study, we have focused on isolation of arsenic-oxidizing cultures from arsenic devoid environment and studied effect of carbon starvation on rate of arsenite oxidation. In spite of the absence of arsenic, a total of 40 heterotrophic, aerobic, arsenic-transforming bacterial strains representing 18 different genera were identified. Nineteen bacterial species were isolated from tannery effluent and twenty-one from tannery soil. A strong co-relation between the carbon starvation and arsenic oxidation potential of the isolates obtained from the said niche was observed. Interestingly, low carbon content enhanced the arsenic oxidation ability of the strains across different genera in Proteobacteria obtained. This represents the impact of physiological response of carbon metabolism under metal stress conditions. Enhanced arsenic-oxidizing ability of the strains was validated by the presence of aio gene and RT-PCR, where 0.5- to 26-fold up-regulation of arsenite oxidase gene in different genera was observed. The cultures isolated from tannery environment in this study show predominantly arsenic oxidation ability. This detoxification of arsenic in lack of carbon content can aid in effective in situ arsenic bioremediation.}, }
@article {pmid28279880, year = {2017}, author = {Daghio, M and Aulenta, F and Vaiopoulou, E and Franzetti, A and Arends, JB and Sherry, A and Suárez-Suárez, A and Head, IM and Bestetti, G and Rabaey, K}, title = {Electrobioremediation of oil spills.}, journal = {Water research}, volume = {114}, number = {}, pages = {351-370}, doi = {10.1016/j.watres.2017.02.030}, pmid = {28279880}, issn = {1879-2448}, mesh = {Biodegradation, Environmental ; Electrodes ; Hydrocarbons ; *Petroleum ; *Petroleum Pollution ; }, abstract = {Annually, thousands of oil spills occur across the globe. As a result, petroleum substances and petrochemical compounds are widespread contaminants causing concern due to their toxicity and recalcitrance. Many remediation strategies have been developed using both physicochemical and biological approaches. Biological strategies are most benign, aiming to enhance microbial metabolic activities by supplying limiting inorganic nutrients, electron acceptors or donors, thus stimulating oxidation or reduction of contaminants. A key issue is controlling the supply of electron donors/acceptors. Bioelectrochemical systems (BES) have emerged, in which an electrical current serves as either electron donor or acceptor for oil spill bioremediation. BES are highly controllable and can possibly also serve as biosensors for real time monitoring of the degradation process. Despite being promising, multiple aspects need to be considered to make BES suitable for field applications including system design, electrode materials, operational parameters, mode of action and radius of influence. The microbiological processes, involved in bioelectrochemical contaminant degradation, are currently not fully understood, particularly in relation to electron transfer mechanisms. Especially in sulfate rich environments, the sulfur cycle appears pivotal during hydrocarbon oxidation. This review provides a comprehensive analysis of the research on bioelectrochemical remediation of oil spills and of the key parameters involved in the process.}, }
@article {pmid28278266, year = {2017}, author = {Hanemaaijer, M and Olivier, BG and Röling, WF and Bruggeman, FJ and Teusink, B}, title = {Model-based quantification of metabolic interactions from dynamic microbial-community data.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0173183}, pmid = {28278266}, issn = {1932-6203}, mesh = {Clostridium acetobutylicum/growth &amp; development/*metabolism ; Coculture Techniques ; Hydrogen/*metabolism ; Metabolic Networks and Pathways ; *Models, Theoretical ; Species Specificity ; Wolinella/growth &amp; development/*metabolism ; }, abstract = {An important challenge in microbial ecology is to infer metabolic-exchange fluxes between growing microbial species from community-level data, concerning species abundances and metabolite concentrations. Here we apply a model-based approach to integrate such experimental data and thereby infer metabolic-exchange fluxes. We designed a synthetic anaerobic co-culture of Clostridium acetobutylicum and Wolinella succinogenes that interact via interspecies hydrogen transfer and applied different environmental conditions for which we expected the metabolic-exchange rates to change. We used stoichiometric models of the metabolism of the two microorganisms that represents our current physiological understanding and found that this understanding - the model - is sufficient to infer the identity and magnitude of the metabolic-exchange fluxes and it suggested unexpected interactions. Where the model could not fit all experimental data, it indicates specific requirement for further physiological studies. We show that the nitrogen source influences the rate of interspecies hydrogen transfer in the co-culture. Additionally, the model can predict the intracellular fluxes and optimal metabolic exchange rates, which can point to engineering strategies. This study therefore offers a realistic illustration of the strengths and weaknesses of model-based integration of heterogenous data that makes inference of metabolic-exchange fluxes possible from community-level experimental data.}, }
@article {pmid28276795, year = {2017}, author = {Szczepańska, A and Kiewra, D and Lonc, E}, title = {Influence of the fabric colour for the ticks, Ixodes ricinus and Dermacentor reticulatus attachment.}, journal = {Infectious diseases (London, England)}, volume = {49}, number = {7}, pages = {558-560}, doi = {10.1080/23744235.2017.1293842}, pmid = {28276795}, issn = {2374-4243}, mesh = {Animals ; *Color ; Dermacentor/*physiology ; Female ; Humans ; Ixodes/*physiology ; Male ; Poland/epidemiology ; Textiles/*parasitology ; Tick Bites/epidemiology/prevention &amp; control ; }, }
@article {pmid28276199, year = {2017}, author = {Dai, J}, title = {New insights into a hot environment for early life.}, journal = {Environmental microbiology reports}, volume = {9}, number = {3}, pages = {203-210}, doi = {10.1111/1758-2229.12528}, pmid = {28276199}, issn = {1758-2229}, mesh = {Bacteria/metabolism ; Cell Wall/metabolism ; Cellulose/chemistry ; *Cosmic Radiation ; Disaccharides/*chemical synthesis ; Glucose/*analogs &amp; derivatives/chemical synthesis ; Glucosides/chemistry ; Hot Temperature ; Hydrothermal Vents/*microbiology ; *Microwaves ; *Origin of Life ; Peptidoglycan/chemistry ; }, abstract = {Investigating the physical-chemical setting of early life is a challenging task. In this contribution, the author attempted to introduce a provocative concept from cosmology - cosmic microwave background (CMB), which is the residual thermal radiation from a hot early Universe - to the field. For this purpose, the author revisited a recently deduced biomarker, the 1,6-anhydro bond of sugars in bacteria. In vitro, the 1,6-anhydro bond of sugars reflects and captures residual thermal radiation in thermochemical processes and therefore is somewhat analogous to CMB. In vivo, the formation process of the 1,6-anhydro bond of sugars on the peptidoglycan of prokaryotic cell wall is parallel to in vitro processes, suggesting that the 1,6-anhydro bond is an ideal CMB-like analogue that suggests a hot setting for early life. The CMB-like 1,6-anhydro bond is involved in the life cycle of viruses and the metabolism of eukaryotes, underlying this notion. From a novel perspective, the application of the concept of the CMB to microbial ecology may give new insights into a hot environment, such as hydrothermal vents, supporting early life and providing hypotheses to test in molecular palaeontology.}, }
@article {pmid28273592, year = {2017}, author = {Li, J and Jiang, X and Li, G and Jing, Z and Zhou, L and Ke, Z and Tan, Y}, title = {Distribution of picoplankton in the northeastern South China Sea with special reference to the effects of the Kuroshio intrusion and the associated mesoscale eddies.}, journal = {The Science of the total environment}, volume = {589}, number = {}, pages = {1-10}, doi = {10.1016/j.scitotenv.2017.02.208}, pmid = {28273592}, issn = {1879-1026}, mesh = {Bacteria/isolation &amp; purification ; Biomass ; China ; Phylogeny ; Phytoplankton/*isolation &amp; purification ; Prochlorococcus/isolation &amp; purification ; *Seawater ; Synechococcus/isolation &amp; purification ; *Water Movements ; }, abstract = {We investigated picoplankton distribution patterns and environmental variables along an east-to-west transect in the northeastern South China Sea (SCS) during late winter 2016, giving us the opportunity to examine the impacts of the Kuroshio intrusion and the associated eddies. The results indicated that the subsurface (50-75m) phytoplankton biomass chlorophyll (Chl a) maximum (SCM) disappeared and was replaced by higher Chl a in the middle part of the transect due to the impacts of the Kuroshio intrusion and mesoscale eddies. Both flow cytometry and pyrosequencing data revealed that picoplankton abundance and community structure were significantly influenced by perturbations in complex physical processes. Picoeukaryotes represented most of the total phytoplankton biomass, and their maximum abundance (>10[4]cellsmL[-1]) occurred within cyclonic eddy-affected regions (Stations 11 and 12), whereas the abundance of Prochlorococcus was the lowest in these regions. Prochlorococcus showed a higher abundance in the Kuroshio-affected area, while Synechococcus was mostly distributed at the upper well-lit depths, with its maximum abundance observed in surface waters (0-30m) adjacent to the cyclonic eddy center. Heterotrophic bacteria (HBA) displayed high abundance along the transect, consistent with the total phytoplankton biomass. Phylogenetic analysis revealed 26 bacterial phyla, with major components belonging to Proteobacteria, Cyanobacteria, Actinobacteria, and Bacteroidetes, as well as SAR406. Notably, relatively more Rhodobacterales, Flavobacteriales, Alteromonadales, and Vibrionales that were distributed in surface waters of the cyclonic eddy center were specifically associated with the phytoplankton (mainly picoeukaryotes) bloom. Our study highlights the impacts of the Kuroshio intrusion in regulating the microbial ecology of the northeastern SCS and the potential coupling between phytoplankton and bacteria.}, }
@article {pmid28265694, year = {2017}, author = {Mieczan, T and Tarkowska-Kukuryk, M}, title = {Microbial Communities as Environmental Indicators of Ecological Disturbance in Restored Carbonate Fen-Results of 10 Years of Studies.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {384-401}, pmid = {28265694}, issn = {1432-184X}, mesh = {*Biodiversity ; *Carbonates ; Ecology ; *Food Chain ; *Microbiota ; *Wetlands ; }, abstract = {Interactions between bacteria and protists are essential to the ecosystem ecology of fens. Until now, however, there has been almost no information on how restoration procedures in carbonate fens affect the functioning of microbial food webs. Changes in vegetation patterns resulting from restoration may take years to be observed, whereas microbial processes display effects even after short-term exposure to changes in environmental conditions caused by restoration. Therefore, microbial processes and patterns can be used as sensitive indicators of changes in environmental conditions. The present study attempts to verify the hypothesis that the species richness and abundance of microbial loop components would differ substantially before and after restoration. The effect of restoration processes on the functioning of the food web was investigated for a 10 years in a carbonate-rich fen, before and after restoration. The restoration procedure (particularly the improvement in hydrological conditions) distinctly modified the taxonomic composition and functioning of microbial food webs. This is reflected in the increased abundance and diversity of testate amoeba, i.e. top predators, within the microbial food web and in the pronounced increase in the abundance of bacteria. This study suggests potential use of microbial loop components as bio-indicators and bio-monitoring tools for hydrological status of fens and concentrations of nutrients. Better understanding of what regulates microbial populations and activity in fens and unravelling of these fundamental mechanisms are particularly critical in order to more accurately predict how fens will respond to global change or anthropogenic disturbances.}, }
@article {pmid28265693, year = {2017}, author = {Gruner, A and Mangelsdorf, K and Vieth-Hillebrand, A and Horsfield, B and van der Kraan, GM and Köhler, T and Janka, C and Morris, BEL and Wilkes, H}, title = {Membrane Lipids as Indicators for Viable Bacterial Communities Inhabiting Petroleum Systems.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {373-383}, pmid = {28265693}, issn = {1432-184X}, mesh = {Austria ; Bacteria/*classification ; Membrane Lipids/*analysis ; Oil and Gas Fields/*microbiology ; Petroleum/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbial activity in petroleum reservoirs has been implicated in a suite of detrimental effects including deterioration of petroleum quality, increases in oil sulfur content, biofouling of steel pipelines and other infrastructures, and well plugging. Here, we present a biogeochemical approach, using phospholipid fatty acids (PLFAs), for detecting viable bacteria in petroleum systems. Variations within the bacterial community along water flow paths (producing well, topside facilities, and injection well) can be elucidated in the field using the same technique, as shown here within oil production plants in the Molasse Basin of Upper Austria. The abundance of PLFAs is compared to total cellular numbers, as detected by qPCR of the 16S rDNA gene, to give an overall comparison between the resolutions of both methods in a true field setting. Additionally, the influence of biocide applications on lipid- and DNA-based quantification was investigated. The first oil field, Trattnach, showed significant PLFA abundances and cell numbers within the reservoir and topside facilities. In contrast, the second field (Engenfeld) showed very low PLFA levels overall, likely due to continuous treatment of the topside facilities with a glutaraldehyde-based antimicrobial. In comparison, Trattnach is dosed once per week in a batch fashion. Changes within PLFA compositions across the flow path, throughout the petroleum production plants, point to cellular adaptation within the system and may be linked to shifts in the dominance of certain bacterial types in oil reservoirs versus topside facilities. Overall, PLFA-based monitoring provides a useful tool to assess the abundance and high-level taxonomic diversity of viable microbial populations in oil production wells, topside infrastructure, pipelines, and other related facilities.}, }
@article {pmid28265558, year = {2017}, author = {Andersen, SJ and De Groof, V and Khor, WC and Roume, H and Props, R and Coma, M and Rabaey, K}, title = {A Clostridium Group IV Species Dominates and Suppresses a Mixed Culture Fermentation by Tolerance to Medium Chain Fatty Acids Products.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {5}, number = {}, pages = {8}, pmid = {28265558}, issn = {2296-4185}, abstract = {A microbial community is engaged in a complex economy of cooperation and competition for carbon and energy. In engineered systems such as anaerobic digestion and fermentation, these relationships are exploited for conversion of a broad range of substrates into products, such as biogas, ethanol, and carboxylic acids. Medium chain fatty acids (MCFAs), for example, hexanoic acid, are valuable, energy dense microbial fermentation products, however, MCFA tend to exhibit microbial toxicity to a broad range of microorganisms at low concentrations. Here, we operated continuous mixed population MCFA fermentations on biorefinery thin stillage to investigate the community response associated with the production and toxicity of MCFA. In this study, an uncultured species from the Clostridium group IV (related to Clostridium sp. BS-1) became enriched in two independent reactors that produced hexanoic acid (up to 8.1 g L[-1]), octanoic acid (up to 3.2 g L[-1]), and trace concentrations of decanoic acid. Decanoic acid is reported here for the first time as a possible product of a Clostridium group IV species. Other significant species in the community, Lactobacillus spp. and Acetobacterium sp., generate intermediates in MCFA production, and their collapse in relative abundance resulted in an overall production decrease. A strong correlation was present between the community composition and both the hexanoic acid concentration (p = 0.026) and total volatile fatty acid concentration (p = 0.003). MCFA suppressed species related to Clostridium sp. CPB-6 and Lactobacillus spp. to a greater extent than others. The proportion of the species related to Clostridium sp. BS-1 over Clostridium sp. CPB-6 had a strong correlation with the concentration of octanoic acid (p = 0.003). The dominance of this species and the increase in MCFA resulted in an overall toxic effect on the mixed community, most significantly on the Lactobacillus spp., which resulted in a decrease in total hexanoic acid concentration to 32 ± 2% below the steady-state average. As opposed to the current view of MCFA toxicity broadly leading to production collapse, this study demonstrates that varied tolerance to MCFA within the community can lead to the dominance of some species and the suppression of others, which can result in a decreased productivity of the fermentation.}, }
@article {pmid28261716, year = {2017}, author = {Waseem, H and Williams, MR and Stedtfeld, T and Chai, B and Stedtfeld, RD and Cole, JR and Tiedje, JM and Hashsham, SA}, title = {Virulence factor activity relationships (VFARs): a bioinformatics perspective.}, journal = {Environmental science. Processes &amp; impacts}, volume = {19}, number = {3}, pages = {247-260}, pmid = {28261716}, issn = {2050-7895}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/pathogenicity ; *Computational Biology/methods/trends ; *Databases, Factual ; Disease Outbreaks/prevention &amp; control ; Drug Resistance, Microbial/genetics ; *Models, Theoretical ; Quantitative Structure-Activity Relationship ; Risk Assessment ; Virulence ; *Virulence Factors/genetics/metabolism ; Viruses/classification/genetics/pathogenicity ; Water Microbiology/*standards ; }, abstract = {Virulence factor activity relationships (VFARs) - a concept loosely based on quantitative structure-activity relationships (QSARs) for chemicals was proposed as a predictive tool for ranking risks due to microorganisms relevant to water safety. A rapid increase in sequencing capabilities and bioinformatics tools has significantly increased the potential for VFAR-based analyses. This review summarizes more than 20 bioinformatics databases and tools, developed over the last decade, along with their virulence and antimicrobial resistance prediction capabilities. With the number of bacterial whole genome sequences exceeding 241 000 and metagenomic analysis projects exceeding 13 000 and the ability to add additional genome sequences for few hundred dollars, it is evident that further development of VFARs is not limited by the availability of information at least at the genomic level. However, additional information related to co-occurrence, treatment response, modulation of virulence due to environmental and other factors, and economic impact must be gathered and incorporated in a manner that also addresses the associated uncertainties. Of the bioinformatics tools, a majority are either designed exclusively for virulence/resistance determination or equipped with a dedicated module. The remaining have the potential to be employed for evaluating virulence. This review focusing broadly on omics technologies and tools supports the notion that these tools are now sufficiently developed to allow the application of VFAR approaches combined with additional engineering and economic analyses to rank and prioritize organisms important to a given niche. Knowledge gaps do exist but can be filled with focused experimental and theoretical analyses that were unimaginable a decade ago. Further developments should consider the integration of the measurement of activity, risk, and uncertainty to improve the current capabilities.}, }
@article {pmid28261166, year = {2017}, author = {Califano, G and Castanho, S and Soares, F and Ribeiro, L and Cox, CJ and Mata, L and Costa, R}, title = {Molecular Taxonomic Profiling of Bacterial Communities in a Gilthead Seabream (Sparus aurata) Hatchery.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {204}, pmid = {28261166}, issn = {1664-302X}, abstract = {As wild fish stocks decline worldwide, land-based fish rearing is likely to be of increasing relevance to feeding future human generations. Little is known about the structure and role of microbial communities in fish aquaculture, particularly at larval developmental stages where the fish microbiome develops and host animals are most susceptible to disease. We employed next-generation sequencing (NGS) of 16S rRNA gene reads amplified from total community DNA to reveal the structure of bacterial communities in a gilthead seabream (Sparus aurata) larviculture system. Early- (2 days after hatching) and late-stage (34 days after hatching) fish larvae presented remarkably divergent bacterial consortia, with the genera Pseudoalteromonas, Marinomonas, Acinetobacter, and Acidocella (besides several unclassified Alphaproteobacteria) dominating the former, and Actinobacillus, Streptococcus, Massilia, Paracoccus, and Pseudomonas being prevalent in the latter. A significant reduction in rearing-water bacterial diversity was observed during the larviculture trial, characterized by higher abundance of the Cryomorphaceae family (Bacteroidetes), known to populate microniches with high organic load, in late-stage rearing water in comparison with early-stage rearing-water. Furthermore, we observed the recruitment, into host tissues, of several bacterial phylotypes-including putative pathogens as well as mutualists-that were detected at negligible densities in rearing-water or in the live feed (i.e., rotifers and artemia). These results suggest that, besides host-driven selective forces, both the live feed and the surrounding rearing environment contribute to shaping the microbiome of farmed gilthead sea-bream larvae, and that a differential establishment of host-associated bacteria takes place during larval development.}, }
@article {pmid28255686, year = {2017}, author = {Gökalsın, B and Aksoydan, B and Erman, B and Sesal, NC}, title = {Reducing Virulence and Biofilm of Pseudomonas aeruginosa by Potential Quorum Sensing Inhibitor Carotenoid: Zeaxanthin.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {466-473}, pmid = {28255686}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/*pharmacology ; Biofilms/drug effects ; Pseudomonas aeruginosa/*drug effects/pathogenicity ; Quorum Sensing/*drug effects ; Virulence/*drug effects ; Zeaxanthins/*pharmacology ; }, abstract = {Pseudomonas aeruginosa can regulate its virulence gene expressions by using a signal system called quorum sensing. It is known that inhibition of quorum sensing can block biofilm formation and leave the bacteria defenseless. Therefore, it is necessary to determine natural sources to obtain potential quorum sensing inhibitors. This study aims to investigate an alternative treatment approach by utilizing the carotenoid zeaxanthin to reduce the expressions of P. aeruginosa virulence factors through quorum sensing inhibition. The inhibition potential of zeaxanthin was determined by in silico screening from a library of 638 lichen metabolites. Fluorescent monitor strains were utilized for quorum sensing inhibitor screens, and quantitative reverse-transcriptase PCR assay was performed for evaluating gene expression. Results indicate that zeaxanthin is a better inhibitor than the lichen secondary metabolite evernic acid, which was previously shown to be capable of inhibiting P. aeruginosa quorum sensing systems.}, }
@article {pmid28255685, year = {2017}, author = {Wang, C and Liu, S and Zhang, Y and Liu, B and Zeng, L and He, F and Zhou, Q and Wu, Z}, title = {Effects of Planted Versus Naturally Growing Vallisneria natans on the Sediment Microbial Community in West Lake, China.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {278-288}, pmid = {28255685}, issn = {1432-184X}, mesh = {China ; *Ecosystem ; Environmental Restoration and Remediation ; Geologic Sediments/*microbiology ; Hydrocharitaceae/*growth &amp; development ; Lakes/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sulfur-Reducing Bacteria/*classification ; }, abstract = {Submerged macrophytes play an important role in aquatic ecosystems, which has led to an increase in studies on vegetation recovery in polluted lakes from which submerged macrophytes have disappeared. The comparison of microbial communities in sediment cloned with planted and naturally growing submerged macrophytes is an interesting but rarely studied topic. In this investigation, Maojiabu and Xilihu, two adjacent sublakes of West Lake (Hangzhou, China), were selected as aquatic areas with planted and naturally growing macrophytes, respectively. Sediment samples from sites with/without Vallisneria natans were collected from both sublakes. The results showed that sediment total nitrogen and organic matter were significantly lower in the plant-covered sites than that in the non-plant sites in Maojiabu. Additionally, the sediment microbial community characterized by 16S ribosomal RNA (rRNA) sequencing differed more significantly for Maojiabu than for Xilihu. The relative abundances of microbes involved in C, N, and S elemental cycling were significantly higher in the sediments with plants than in those without. Results from both fatty acid methyl ester analysis and 16S rRNA sequencing indicated that vegetation significantly influenced the sulfate-reducing bacteria (SRB). Thus, the gene copies and composition of SRB were explored further. The relative gene abundance of SRB was 66% higher with natural vegetation colonization but was not influenced by artificial colonization. An increase in dominant SRB members from the families Syntrophobacteraceae and Thermodesulfovibrionaceae contributed to the increase of total SRB. Thus, macrophyte planting influences sediment nutrient levels and microbial community more than natural growth does, whereas the latter is more beneficial to sediment SRB.}, }
@article {pmid28255684, year = {2017}, author = {Plante, CJ}, title = {Defining Disturbance for Microbial Ecology.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {259-263}, pmid = {28255684}, issn = {1432-184X}, mesh = {Animals ; Biomass ; Climate Change ; *Ecology ; *Ecosystem ; *Microbiota ; Plants ; *Terminology as Topic ; }, abstract = {Disturbance can profoundly modify the structure of natural communities. However, microbial ecologists' concept of "disturbance" has often deviated from conventional practice. Definitions (or implicit usage) have frequently included climate change and other forms of chronic environmental stress, which contradict the macrobiologist's notion of disturbance as a discrete event that removes biomass. Physical constraints and disparate biological characteristics were compared to ask whether disturbances fundamentally differ in microbial and macroorganismal communities. A definition of "disturbance" for microbial ecologists is proposed that distinguishes from "stress" and other competing terms, and that is in accord with definitions accepted by plant and animal ecologists.}, }
@article {pmid28253864, year = {2017}, author = {Duniere, L and Xu, S and Long, J and Elekwachi, C and Wang, Y and Turkington, K and Forster, R and McAllister, TA}, title = {Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {50}, pmid = {28253864}, issn = {1471-2180}, mesh = {*Aerobiosis ; Avena/microbiology ; Bacteria/*classification/genetics/metabolism ; Base Sequence ; Biodiversity ; DNA, Bacterial ; DNA, Fungal ; Ecology ; Edible Grain/chemistry/*microbiology ; Fermentation ; Food Analysis ; Fungi/*classification/genetics/metabolism ; High-Throughput Nucleotide Sequencing/methods ; Hordeum/microbiology ; Lactic Acid/analysis ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Silage/*microbiology ; Temperature ; Triticale/microbiology ; }, abstract = {BACKGROUND: Describing the microbial populations present in small grain silage and understanding their changes during ensiling is of interest for improving the nutrient value of these important forage crops. Barley, oat and triticale forages as well as an intercropped mixture of the 3 crops were harvested and ensiled in mini silos for a period of 90 days, followed by 14 days of aerobic exposure. Changes in fermentation characteristics and nutritive value were assessed in terminal silages and bacterial and fungal communities during ensiling and aerobic exposure were described using 16S and 18S rDNA sequencing, respectively.<br><br>RESULTS: All small grain silages exhibited chemical traits that were associated with well ensiled forages, such as low pH value (4.09&#x2009;&#xb1;&#x2009;0.28) and high levels of lactic acid (59.8&#x2009;&#xb1;&#x2009;14.59&#xa0;mg/g DM). The number of microbial core genome operational taxonomic units (OTUs) decreased with time of ensiling. Taxonomic bacterial community profiles were dominated by the Lactobacillales after fermentation, with a notable increase in Bacillales as a result of aerobic exposure. Diversity of the fungal core microbiome was shown to also be reduced during ensiling. Operational taxonomic units assigned to filamentous fungi were found in the core microbiome at ensiling and after aerobic exposure, whereas the Saccharomycetales were the dominate yeast population after 90 days of ensiling and aerobic exposure. Bacterial and fungal orders typically associated with silage spoilage were identified in the core microbiome after aerobic exposure.<br><br>CONCLUSION: Next Generation Sequencing was successfully used to describe bacterial communities and the first record of fungal communities throughout the process of ensiling and utilization. Adequately describing the microbial ecology of silages could lead to improved ensiling practices and the selection of silage inoculants that act synergistically with the natural forage microbiome.}, }
@article {pmid28252943, year = {2017}, author = {Cheyns, K and Waegeneers, N and Van de Wiele, T and Ruttens, A}, title = {Arsenic Release from Foodstuffs upon Food Preparation.}, journal = {Journal of agricultural and food chemistry}, volume = {65}, number = {11}, pages = {2443-2453}, doi = {10.1021/acs.jafc.6b05721}, pmid = {28252943}, issn = {1520-5118}, mesh = {Animals ; Arsenic/*chemistry ; Cooking ; Fishes ; Food Contamination/*analysis ; Oryza/*chemistry ; Seafood/*analysis ; Vegetables/*chemistry ; }, abstract = {In this study the concentration of total arsenic (As) and arsenic species (inorganic As, arsenobetaine, dimethylarsinate, and methylarsonate) was monitored in different foodstuffs (rice, vegetables, algae, fish, crustacean, molluscs) before and after preparation using common kitchen practices. By measuring the water content of the foodstuff and by reporting arsenic concentrations on a dry weight base, we were able to distinguish between As release effects due to food preparation and As decrease due to changes in moisture content upon food preparation. Arsenic species were released to the broth during boiling, steaming, frying, or soaking of the food. Concentrations declined with maxima of 57% for total arsenic, 65% for inorganic As, and 32% for arsenobetaine. On the basis of a combination of our own results and literature data, we conclude that the extent of this release of arsenic species is species specific, with inorganic arsenic species being released most easily, followed by the small organic As species and the large organic As species.}, }
@article {pmid28251783, year = {2017}, author = {Yang, Q and Pande, GSJ and Wang, Z and Lin, B and Rubin, RA and Vora, GJ and Defoirdt, T}, title = {Indole signalling and (micro)algal auxins decrease the virulence of Vibrio campbellii, a major pathogen of aquatic organisms.}, journal = {Environmental microbiology}, volume = {19}, number = {5}, pages = {1987-2004}, doi = {10.1111/1462-2920.13714}, pmid = {28251783}, issn = {1462-2920}, mesh = {Animals ; Aquatic Organisms/genetics/metabolism ; Artemia/embryology/*microbiology ; Bacterial Proteins/*metabolism ; Biofilms/growth &amp; development ; Indoleacetic Acids/*metabolism ; Larva/microbiology ; Quorum Sensing/genetics/physiology ; Sigma Factor/*metabolism ; Vibrio/*genetics/*pathogenicity ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Vibrios belonging to the Harveyi clade are major pathogens of marine vertebrates and invertebrates, causing major losses in wild and cultured organisms. Despite their significant impact, the pathogenicity mechanisms of these bacteria are not yet completely understood. In this study, the impact of indole signalling on the virulence of Vibrio campbellii was investigated. Elevated indole levels significantly decreased motility, biofilm formation, exopolysaccharide production and virulence to crustacean hosts. Indole furthermore inhibited the three-channel quorum sensing system of V. campbellii, a regulatory mechanism that is required for full virulence of the pathogen. Further, indole signalling was found to interact with the stress sigma factor RpoS. Together with the observations that energy-consuming processes (motility and bioluminescence) are downregulated, and microarray-based transcriptomics demonstrating that indole decreases the expression of genes involved in energy and amino acid metabolism, the data suggest that indole is a starvation signal in V. campbellii. Finally, it was found that the auxins indole-3-acetic acid and indole-3-acetamide, which were produced by various (micro)algae sharing the aquatic environment with V. campbellii, have a similar effect as observed for indole. Auxins might, therefore, have a significant impact on the interactions between vibrios, (micro)algae and higher organisms, with major ecological and practical implications.}, }
@article {pmid28251186, year = {2017}, author = {Morton, JT and Toran, L and Edlund, A and Metcalf, JL and Lauber, C and Knight, R}, title = {Uncovering the Horseshoe Effect in Microbial Analyses.}, journal = {mSystems}, volume = {2}, number = {1}, pages = {}, pmid = {28251186}, issn = {2379-5077}, support = {R00 DE024543/DE/NIDCR NIH HHS/United States ; }, abstract = {The horseshoe effect is a phenomenon that has long intrigued ecologists. The effect was commonly thought to be an artifact of dimensionality reduction, and multiple techniques were developed to unravel this phenomenon and simplify interpretation. Here, we provide evidence that horseshoes arise as a consequence of distance metrics that saturate-a familiar concept in other fields but new to microbial ecology. This saturation property loses information about community dissimilarity, simply because it cannot discriminate between samples that do not share any common features. The phenomenon illuminates niche differentiation in microbial communities and indicates species turnover along environmental gradients. Here we propose a rationale for the observed horseshoe effect from multiple dimensionality reduction techniques applied to simulations, soil samples, and samples from postmortem mice. An in-depth understanding of this phenomenon allows targeting of niche differentiation patterns from high-level ordination plots, which can guide conventional statistical tools to pinpoint microbial niches along environmental gradients. IMPORTANCE The horseshoe effect is often considered an artifact of dimensionality reduction. We show that this is not true in the case for microbiome data and that, in fact, horseshoes can help analysts discover microbial niches across environments.}, }
@article {pmid28250895, year = {2017}, author = {Patil, Y and Müller, N and Schink, B and Whitman, WB and Huntemann, M and Clum, A and Pillay, M and Palaniappan, K and Varghese, N and Mikhailova, N and Stamatis, D and Reddy, TBK and Daum, C and Shapiro, N and Ivanova, N and Kyrpides, N and Woyke, T and Junghare, M}, title = {High-quality-draft genome sequence of the fermenting bacterium Anaerobium acetethylicum type strain GluBS11[T] (DSM 29698).}, journal = {Standards in genomic sciences}, volume = {12}, number = {}, pages = {24}, pmid = {28250895}, issn = {1944-3277}, abstract = {Anaerobium acetethylicum strain GluBS11[T] belongs to the family Lachnospiraceae within the order Clostridiales. It is a Gram-positive, non-motile and strictly anaerobic bacterium isolated from biogas slurry that was originally enriched with gluconate as carbon source (Patil, et al., Int J Syst Evol Microbiol 65:3289-3296, 2015). Here we describe the draft genome sequence of strain GluBS11[T] and provide a detailed insight into its physiological and metabolic features. The draft genome sequence generated 4,609,043 bp, distributed among 105 scaffolds assembled using the SPAdes genome assembler method. It comprises in total 4,132 genes, of which 4,008 were predicted to be protein coding genes, 124 RNA genes and 867 pseudogenes. The G + C content was 43.51 mol %. The annotated genome of strain GluBS11[T] contains putative genes coding for the pentose phosphate pathway, the Embden-Meyerhoff-Parnas pathway, the Entner-Doudoroff pathway and the tricarboxylic acid cycle. The genome revealed the presence of most of the necessary genes required for the fermentation of glucose and gluconate to acetate, ethanol, and hydrogen gas. However, a candidate gene for production of formate was not identified.}, }
@article {pmid28246922, year = {2017}, author = {VanMensel, D and Chaganti, SR and Boudens, R and Reid, T and Ciborowski, J and Weisener, C}, title = {Investigating the Microbial Degradation Potential in Oil Sands Fluid Fine Tailings Using Gamma Irradiation: A Metagenomic Perspective.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {362-372}, pmid = {28246922}, issn = {1432-184X}, mesh = {Biodegradation, Environmental ; *Gamma Rays ; *Metagenome ; *Microbial Consortia ; Mining ; Oil and Gas Fields/*microbiology ; Ponds ; }, abstract = {Open-pit mining of the Athabasca oil sands has generated large volumes of waste termed fluid fine tailings (FFT), stored in tailings ponds. Accumulation of toxic organic substances in the tailings ponds is one of the biggest concerns. Gamma irradiation (GI) treatment could accelerate the biodegradation of toxic organic substances. Hence, this research investigates the response of the microbial consortia in GI-treated FFT materials with an emphasis on changes in diversity and organism-related stimuli. FFT materials from aged and fresh ponds were used in the study under aerobic and anaerobic conditions. Variations in the microbial diversity in GI-treated FFT materials were monitored for 52 weeks and significant stimuli (p < 0.05) were observed. Chemoorganotrophic organisms dominated in fresh and aged ponds and showed increased relative abundance resulting from GI treatment. GI-treated anaerobic FFTaged reported stimulus of organisms with biodegradation potential (e.g., Pseudomonas, Enterobacter) and methylotrophic capabilities (e.g., Syntrophus, Smithella). In comparison, GI-treated anaerobic FFTfresh stimulated Desulfuromonas as the principle genus at 52 weeks. Under aerobic conditions, GI-treated FFTaged showed stimulation of organisms capable of sulfur and iron cycling (e.g., Geobacter). However, GI-treated aerobic FFTfresh showed no stimulus at 52 weeks. This research provides an enhanced understanding of oil sands tailings biogeochemistry and the impacts of GI treatment on microorganisms as an effect for targeting toxic organics. The outcomes of this study highlight the potential for this approach to accelerate stabilization and reclamation end points. Graphical Abstract.}, }
@article {pmid28243679, year = {2017}, author = {Miyamoto, T and Koda, K and Kawaguchi, A and Uraki, Y}, title = {Ligninolytic Activity at 0 °C of Fungi on Oak Leaves Under Snow Cover in a Mixed Forest in Japan.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {322-331}, pmid = {28243679}, issn = {1432-184X}, mesh = {Forests ; Fungi/classification/*metabolism ; Japan ; Lignin/*metabolism ; Plant Leaves/*microbiology ; Quercus/*microbiology ; *Snow ; Trees ; }, abstract = {Despite the importance of litter decomposition under snow cover in boreal forests and tundra, very little is known regarding the characteristics and functions of litter-decomposing fungi adapted to the cold climate. We investigated the decomposition of oak leaves in a heavy snowfall forest region of Japan. The rate of litter weight loss reached 26.5% during the snow cover period for 7 months and accounted for 64.6% of the annual loss (41.1%). Although no statistically significant lignin loss was detected, decolourization portions of oak leaf litter, which was attributable to the activities of ligninolytic fungi, were observed during snow cover period. This suggests that fungi involved in litter decomposition can produce extracellular enzymes to degrade lignin that remain active at 0 °C. Fungi were isolated from oak leaves collected from the forest floor under the snow layer. One hundred and sixty-six strains were isolated and classified into 33 operational taxonomic units (OTUs) based on culture characteristics and nuclear rDNA internal transcribed spacer (ITS) region sequences. To test the ability to degrade lignin, the production of extracellular phenoloxidases by isolates was quantified at 0 °C. Ten OTUs (9 Ascomycota and 1 Basidiomycota) of fungi exhibited mycelial growth and ligninolytic activity. These results suggested that some litter-decomposing fungi that had the potential to degrade lignin at 0 °C significantly contribute to litter decomposition under snow cover.}, }
@article {pmid28243606, year = {2017}, author = {Zaafouri, K and Ziadi, M and Ben Hassen-Trabelsi, A and Mekni, S and Aïssi, B and Alaya, M and Bergaoui, L and Hamdi, M}, title = {Optimization of Hydrothermal and Diluted Acid Pretreatments of Tunisian Luffa cylindrica (L.) Fibers for 2G Bioethanol Production through the Cubic Central Composite Experimental Design CCD: Response Surface Methodology.}, journal = {BioMed research international}, volume = {2017}, number = {}, pages = {9524521}, pmid = {28243606}, issn = {2314-6141}, mesh = {*Biofuels ; Biomass ; Biotechnology/*methods ; Distillation ; Ethanol/*metabolism ; Fermentation/drug effects ; Hydrolysis ; Lignin/metabolism ; Luffa/*drug effects ; Regression Analysis ; Spectroscopy, Fourier Transform Infrared ; Sulfuric Acids/*pharmacology ; *Temperature ; Thermogravimetry ; Water/*pharmacology ; }, abstract = {This paper opens up a new issue dealing with Luffa cylindrica (LC) lignocellulosic biomass recovery in order to produce 2G bioethanol. LC fibers are composed of three principal fractions, namely, α-cellulose (45.80% ± 1.3), hemicelluloses (20.76% ± 0.3), and lignins (13.15% ± 0.6). The optimization of LC fibers hydrothermal and diluted acid pretreatments duration and temperature were achieved through the cubic central composite experimental design CCD. The pretreatments optimization was monitored via the determination of reducing sugars. Then, the 2G bioethanol process feasibility was tested by means of three successive steps, namely, LC fibers hydrothermal pretreatment performed at 96°C during 54 minutes, enzymatic saccharification carried out by means of a commercial enzyme AP2, and the alcoholic fermentation fulfilled with Saccharomyces cerevisiae. LC fibers hydrothermal pretreatment liberated 33.55 g/kg of reducing sugars. Enzymatic hydrolysis allowed achieving 59.4 g/kg of reducing sugars. The conversion yield of reducing sugar to ethanol was 88.66%. After the distillation step, concentration of ethanol was 1.58% with a volumetric yield about 70%.}, }
@article {pmid28242419, year = {2017}, author = {Coda, R and Kianjam, M and Pontonio, E and Verni, M and Di Cagno, R and Katina, K and Rizzello, CG and Gobbetti, M}, title = {Sourdough-type propagation of faba bean flour: Dynamics of microbial consortia and biochemical implications.}, journal = {International journal of food microbiology}, volume = {248}, number = {}, pages = {10-21}, doi = {10.1016/j.ijfoodmicro.2017.02.009}, pmid = {28242419}, issn = {1879-3460}, mesh = {Bread/microbiology ; DNA, Bacterial/genetics ; Fermentation ; Flour/*microbiology ; Food Microbiology ; Lactobacillus/classification/genetics/*isolation &amp; purification ; Leuconostoc/classification/genetics/*isolation &amp; purification ; Microbial Consortia/*genetics ; Pediococcus/classification/genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vicia faba/*microbiology ; Weissella/classification/genetics/*isolation &amp; purification ; Yeasts/classification/genetics/*isolation &amp; purification ; }, abstract = {The microbial ecology of faba bean sourdoughs obtained from an Italian (Ita) and a Finnish (Fi) cultivar, belonging respectively to Vicia faba major and V. faba minor groups, was described by 16S rRNA gene pyrosequencing and culture-dependent analysis. The sourdoughs were propagated with traditional backslopping procedure throughout 14days. Higher microbial diversity was found in the sourdough deriving from V. faba minor (Fi), still containing residual hulls after the milling procedure. After 2days of propagation, the microbial profile of Ita sourdough was characterized by the dominance of the genera Pediococcus, Leuconostoc and Weissella, while the genera Lactococcus, Lactobacillus and Escherichia, as well as Enterobacteriaceae were present in Fi sourdoughs. Yeasts were in very low cell density until the second backslopping and were not anymore found after this time by plate count or pyrosequencing analysis. Among the lactic acid bacteria isolates, Pediococcus pentosaceus, Leuconostoc mesenteroides and Weissella koreensis had the highest frequency of occurrence in both the sourdoughs. Lactobacillus sakei was the only lactobacillus isolated from the first to the last propagation day in Fi sourdough. According to microbiological and acidification properties, the maturity of the sourdoughs was reached after 5days. The presence of hulls and the different microbial composition reflected on biochemical characteristics of Fi sourdoughs, including acidification and phenolic compounds. Moreover, proteolysis in Fi sourdough was more intense compared to Ita. The microbial dynamic of the faba bean sourdoughs showed some differences with the most studied cereal sourdoughs.}, }
@article {pmid28238079, year = {2017}, author = {Kanitkar, YH and Stedtfeld, RD and Hatzinger, PB and Hashsham, SA and Cupples, AM}, title = {Development and application of a rapid, user-friendly, and inexpensive method to detect Dehalococcoides sp. reductive dehalogenase genes from groundwater.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {11}, pages = {4827-4835}, doi = {10.1007/s00253-017-8203-y}, pmid = {28238079}, issn = {1432-0614}, mesh = {Benzothiazoles ; Biodegradation, Environmental ; Biomass ; Chloroflexi/enzymology/*genetics ; DNA, Bacterial/genetics ; Diamines ; *Genes, Bacterial ; Groundwater/*microbiology ; Halogenation/genetics ; Limit of Detection ; *Nucleic Acid Amplification Techniques/economics/methods ; Organic Chemicals ; Quinolines ; RNA, Ribosomal, 16S ; Water Microbiology ; Water Pollutants, Chemical ; }, abstract = {TaqMan probe-based quantitative polymerase chain reaction (qPCR) specific to the biomarker reductive dehalogenase (RDase) genes is a widely accepted molecular biological tool (MBT) for determining the abundance of Dehalococcoides sp. in groundwater samples from chlorinated solvent-contaminated sites. However, there are significant costs associated with this MBT. In this study, we describe an approach that requires only low-cost laboratory equipment (a bench top centrifuge and a water bath) and requires less time and resources compared to qPCR. The method involves the concentration of biomass from groundwater, without DNA extraction, and loop-mediated isothermal amplification (LAMP) of the cell templates. The amplification products are detected by a simple visual color change (orange/green). The detection limits of the assay were determined using groundwater from a contaminated site. In addition, the assay was tested with groundwater from three additional contaminated sites. The final approach to detect RDase genes, without DNA extraction or a thermal cycler, was successful to 1.8 × 10[5] gene copies per L for vcrA and 1.3 × 10[5] gene copies per L for tceA. Both values are below the threshold recommended for effective in situ dechlorination.}, }
@article {pmid28238016, year = {2017}, author = {Aboagye, SY and Ampah, KA and Ross, A and Asare, P and Otchere, ID and Fyfe, J and Yeboah-Manu, D}, title = {Seasonal Pattern of Mycobacterium ulcerans, the Causative Agent of Buruli Ulcer, in the Environment in Ghana.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {350-361}, pmid = {28238016}, issn = {1432-184X}, mesh = {Animals ; Bryophyta/microbiology ; Buruli Ulcer/*microbiology ; Ghana ; Humans ; Mycobacterium ulcerans/*isolation &amp; purification ; Rain ; Real-Time Polymerase Chain Reaction ; *Seasons ; Snails/microbiology ; Soil Microbiology ; Water ; }, abstract = {This study aimed to contribute to the understanding of Mycobacterium ulcerans (MU) ecology by analysing both clinical and environmental samples collected from ten communities along two major river basins (Offin and Densu) associated with Buruli ulcer (BU) at different seasons. We collected clinical samples from presumptive BU cases and environmental samples from ten communities. Following DNA extraction, clinical samples were confirmed by IS2404 PCR and environmental samples were confirmed by targeting MU-specific genes, IS2404, IS2606 and the ketoreductase (KR) using real-time PCR. Environmental samples were first analysed for IS2404; after which, IS2404-positive samples were multiplexed for the IS2606 and KR gene. Our findings indicate an overall decline in BU incidence along both river basins, although incidence at Densu outweighs that of Offin. Overall, 1600 environmental samples were screened along Densu (434, 27 %) and Offin (1166, 73 %) and MU was detected in 139 (9 %) of the combined samples. The positivity of MU along the Densu River basin was 89/434 (20.5 %), whilst that of the Offin River basin was 50/1166 (4.3 %). The DNA was detected mainly in snails (5/6, 83 %), moss (8/40, 20 %), soil (55/586, 9 %) and vegetation (55/675, 8 %). The proportion of MU positive samples recorded was higher during the months with higher rainfall levels (126/1175, 11 %) than during the dry season months (13/425, 3 %). This study indicates for the first time that there is a seasonal pattern in the presence of MU in the environment, which may be related to recent rainfall or water in the soil.}, }
@article {pmid28224054, year = {2017}, author = {Zojer, M and Schuster, LN and Schulz, F and Pfundner, A and Horn, M and Rattei, T}, title = {Variant profiling of evolving prokaryotic populations.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e2997}, pmid = {28224054}, issn = {2167-8359}, support = {281633/ERC_/European Research Council/International ; }, abstract = {Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and clinical diagnostics, and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequency alleles or haplotypes. However, false positive variant predictions due to sequencing errors and mapping artifacts of short reads need to be prevented. We therefore created VarCap, a workflow for the reliable prediction of different types of variants even at low frequencies. In order to predict SNPs, InDels and structural variations, we evaluated the sensitivity and accuracy of different software tools using synthetic read data. The results suggested that the best sensitivity could be reached by a union of different tools, however at the price of increased false positives. We identified possible reasons for false predictions and used this knowledge to improve the accuracy by post-filtering the predicted variants according to properties such as frequency, coverage, genomic environment/localization and co-localization with other variants. We observed that best precision was achieved by using an intersection of at least two tools per variant. This resulted in the reliable prediction of variants above a minimum relative abundance of 2%. VarCap is designed for being routinely used within experimental evolution experiments or for clinical diagnostics. The detected variants are reported as frequencies within a VCF file and as a graphical overview of the distribution of the different variant/allele/haplotype frequencies. The source code of VarCap is available at https://github.com/ma2o/VarCap. In order to provide this workflow to a broad community, we implemeted VarCap on a Galaxy webserver, which is accessible at http://galaxy.csb.univie.ac.at.}, }
@article {pmid28223979, year = {2017}, author = {Leite, DC and Leão, P and Garrido, AG and Lins, U and Santos, HF and Pires, DO and Castro, CB and van Elsas, JD and Zilberberg, C and Rosado, AS and Peixoto, RS}, title = {Broadcast Spawning Coral Mussismilia hispida Can Vertically Transfer its Associated Bacterial Core.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {176}, pmid = {28223979}, issn = {1664-302X}, abstract = {The hologenome theory of evolution (HTE), which is under fierce debate, presupposes that parts of the microbiome are transmitted from one generation to the next [vertical transmission (VT)], which may also influence the evolution of the holobiont. Even though bacteria have previously been described in early life stages of corals, these early life stages (larvae) could have been inoculated in the water and not inside the parental colony (through gametes) carrying the parental microbiome. How Symbiodinium is transmitted to offspring is also not clear, as only one study has described this mechanism in spawners. All other studies refer to incubators. To explore the VT hypothesis and the key components being transferred, colonies of the broadcast spawner species Mussismilia hispida were kept in nurseries until spawning. Gamete bundles, larvae and adult corals were analyzed to identify their associated microbiota with respect to composition and location. Symbiodinium and bacteria were detected by sequencing in gametes and coral planula larvae. However, no cells were detected using microscopy at the gamete stage, which could be related to the absence of those cells inside the oocytes/dispersed in the mucus or to a low resolution of our approach. A preliminary survey of Symbiodinium diversity indicated that parental colonies harbored Symbiodinium clades B, C and G, whereas only clade B was found in oocytes and planula larvae [5 days after fertilization (a.f.)]. The core bacterial populations found in the bundles, planula larvae and parental colonies were identified as members of the genera Burkholderia, Pseudomonas, Acinetobacter, Ralstonia, Inquilinus and Bacillus, suggesting that these populations could be vertically transferred through the mucus. The collective data suggest that spawner corals, such as M. hispida, can transmit Symbiodinium cells and the bacterial core to their offspring by a coral gamete (and that this gamete, with its bacterial load, is released into the water), supporting the HTE. However, more data are required to indicate the stability of the transmitted populations to indicate whether the holobiont can be considered a unit of natural selection or a symbiotic assemblage of independently evolving organisms.}, }
@article {pmid28223972, year = {2017}, author = {Wang, Z and Elekwachi, C and Jiao, J and Wang, M and Tang, S and Zhou, C and Tan, Z and Forster, RJ}, title = {Changes in Metabolically Active Bacterial Community during Rumen Development, and Their Alteration by Rhubarb Root Powder Revealed by 16S rRNA Amplicon Sequencing.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {159}, pmid = {28223972}, issn = {1664-302X}, abstract = {The objective of this present study was to explore the initial establishment of metabolically active bacteria and subsequent evolution in four fractions: rumen solid-phase (RS), liquid-phase (RL), protozoa-associated (RP), and epithelium-associated (RE) through early weaning and supplementing rhubarb root powder in 7 different age groups (1, 10, 20, 38, 41, 50, and 60 d) during rumen development. Results of the 16S rRNA sequencing based on RNA isolated from the four fractions revealed that the potentially active bacterial microbiota in four fractions were dominated by the phyla Proteobacteria, Firmicutes, and Bacteroidetes regardless of different ages. An age-dependent increment of Chao 1 richness was observed in the fractions of RL and RE. The principal coordinate analysis (PCoA) indicated that samples in four fractions all clustered based on different age groups, and the structure of the bacterial community in RE was distinct from those in other three fractions. The abundances of Proteobacteria decreased significantly (P < 0.05) with age, while increases in the abundances of Firmicutes and Bacteroidetes were noted. At the genus level, the abundance of the predominant genus Mannheimia in the Proteobacteria phylum decreased significantly (P < 0.05) after 1 d, while the genera Quinella, Prevotella, Fretibacterium, Ruminococcus, Lachnospiraceae NK3A20 group, and Atopobium underwent different manners of increases and dominated the bacterial microbiota across four fractions. Variations of the distributions of some specific bacterial genera across fractions were observed, and supplementation of rhubarb affected the relative abundance of various genera of bacteria.}, }
@article {pmid28223257, year = {2017}, author = {Isaiah, A and Parambeth, JC and Steiner, JM and Lidbury, JA and Suchodolski, JS}, title = {The fecal microbiome of dogs with exocrine pancreatic insufficiency.}, journal = {Anaerobe}, volume = {45}, number = {}, pages = {50-58}, doi = {10.1016/j.anaerobe.2017.02.010}, pmid = {28223257}, issn = {1095-8274}, mesh = {Animals ; Bacteria/*classification/*genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Dog Diseases/drug therapy/*microbiology/pathology ; Dogs ; *Dysbiosis ; *Enzyme Replacement Therapy ; Exocrine Pancreatic Insufficiency/complications/drug therapy/pathology/*veterinary ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Male ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Exocrine pancreatic insufficiency (EPI) in dogs is a syndrome of inadequate synthesis and secretion of pancreatic enzymes. Small intestinal bacterial dysbiosis occurs in dogs with EPI, and is reversed with pancreatic enzyme therapy. However, there are no studies evaluating the fecal microbiome of dogs with EPI. The objective of this study was to evaluate the fecal microbiome of dogs with EPI. Three day pooled fecal samples were collected from healthy dogs (n = 18), untreated (n = 7) dogs with EPI, and dogs with EPI treated with enzyme replacement therapy (n = 19). Extracted DNA from fecal samples was used for Illumina sequencing of the bacterial 16S rRNA gene and analyzed using Quantitative Insights Into Microbial Ecology (QIIME) and PICRUSt was used to predict the functional gene content of the microbiome. Linear discriminant analysis effect size (LEfSe) revealed significant differences in bacterial groups and functional genes between the healthy dogs and dogs with EPI. There was a significant difference in fecal microbial communities when healthy dogs were compared to treated and untreated dogs with EPI (unweighted UniFrac distance, ANOSIM P = 0.001, and 0.001 respectively). Alpha diversity was significantly decreased in untreated and treated EPI dogs when compared to the healthy dogs with respect to Chao1, Observed OTU, and Shannon diversity (P = 0.008, 0.003, and 0.002 respectively). The families Bifidobacteriaceae (P = 0.005), Enterococcaceae (P = 0.018), and Lactobacillaceae (P = 0.001) were significantly increased in the untreated and treated dogs with EPI when compared to healthy dogs. In contrast, Lachnospiraceae (P < 0.001), and Ruminococcaceae (P < 0.01) were significantly decreased in dogs with EPI. Dogs with EPI (before treatment) had significant increases in functional genes associated with secretion system, fatty acid metabolism, and phosphotransferase system. In contrast, healthy dogs had a significant increase in genes related to phenylalanine, tyrosine and tryptophan biosynthesis, transcription machinery and sporulation. In conclusion, this study shows that the fecal microbiome of dogs with EPI (both treated and untreated) is different to that of healthy dogs.}, }
@article {pmid28222236, year = {2017}, author = {Aschenbrenner, IA and Cernava, T and Erlacher, A and Berg, G and Grube, M}, title = {Differential sharing and distinct co-occurrence networks among spatially close bacterial microbiota of bark, mosses and lichens‬‬.}, journal = {Molecular ecology}, volume = {26}, number = {10}, pages = {2826-2838}, doi = {10.1111/mec.14070}, pmid = {28222236}, issn = {1365-294X}, mesh = {Bacteria/*classification ; Bryophyta/*microbiology ; Ecology ; Ecosystem ; Lichens/*microbiology ; *Microbiota ; Plant Bark/*microbiology ; Trees ; }, abstract = {Knowledge of bacterial community host-specificity has increased greatly in recent years. However, the intermicrobiome relationships of unrelated but spatially close organisms remain little understood. Trunks of trees covered by epiphytes represent complex habitats with a mosaic of ecological niches. In this context, we investigated the structure, diversity and interactions of microbiota associated with lichens, mosses and the bare tree bark. Comparative analysis revealed significant differences in the habitat-associated community structures. Corresponding co-occurrence analysis indicated that the lichen microbial network is less complex and less densely interconnected than the moss- and bark-associated networks. Several potential generalists and specialists were identified for the selected habitats. Generalists belonged mainly to Proteobacteria, with Sphingomonas as the most abundant genus. The generalists comprise microorganisms with generally beneficial features, such as nitrogen fixation or other supporting functions, according to a metagenomic analysis. We argue that beneficial strains shared among hosts contribute to ecological stability of the host biocoenoses.}, }
@article {pmid28220442, year = {2017}, author = {Heng, PL and Lim, JH and Lee, CW}, title = {Synechococcus production and grazing loss rates in nearshore tropical waters.}, journal = {Environmental monitoring and assessment}, volume = {189}, number = {3}, pages = {117}, pmid = {28220442}, issn = {1573-2959}, mesh = {*Environmental Monitoring ; Seawater ; Synechococcus/*physiology ; Temperature ; }, abstract = {Temporal variation of Synechococcus, its production (μ) and grazing loss (g) rates were studied for 2 years at nearshore stations, i.e. Port Dickson and Port Klang along the Straits of Malacca. Synechococcus abundance at Port Dickson (0.3-2.3 × 10[5] cell ml[-1]) was always higher than at Port Klang (0.3-7.1 × 10[4] cell ml[-1]) (p < 0.001). μ ranged up to 0.98 day[-1] (0.51 ± 0.29 day[-1]), while g ranged from 0.02 to 0.31 day[-1] (0.15 ± 0.07 day[-1]) at Port Klang. At Port Dickson, μ and g averaged 0.47 ± 0.13 day[-1] (0.29-0.82 day[-1]) and 0.31 ± 0.14 day[-1] (0.13-0.63 day[-1]), respectively. Synechococcus abundance did not correlate with temperature (p > 0.25), but nutrient and light availability were important factors for their distribution. The relationship was modelled as log Synechococcus = 0.37Secchi - 0.01DIN + 4.52 where light availability (as Secchi disc depth) was a more important determinant. From a two-factorial experiment, nutrients were not significant for Synechococcus growth as in situ nutrient concentrations exceeded the threshold for saturated growth. However, light availability was important and elevated Synechococcus growth rates especially at Port Dickson (F = 5.94, p < 0.05). As for grazing loss rates, they were independent of either nutrients or light intensity (p > 0.30). In nearshore tropical waters, an estimated 69 % of Synechococcus production could be grazed.}, }
@article {pmid28220237, year = {2017}, author = {Wenzel, J and Fuentes, L and Cabezas, A and Etchebehere, C}, title = {Microbial fuel cell coupled to biohydrogen reactor: a feasible technology to increase energy yield from cheese whey.}, journal = {Bioprocess and biosystems engineering}, volume = {40}, number = {6}, pages = {807-819}, doi = {10.1007/s00449-017-1746-6}, pmid = {28220237}, issn = {1615-7605}, mesh = {Bioelectric Energy Sources ; *Cheese ; RNA, Ribosomal, 16S ; Whey ; Whey Proteins ; }, abstract = {An important pollutant produced during the cheese making process is cheese whey which is a liquid by-product with high content of organic matter, composed mainly by lactose and proteins. Hydrogen can be produced from cheese whey by dark fermentation but, organic matter is not completely removed producing an effluent rich in volatile fatty acids. Here we demonstrate that this effluent can be further used to produce energy in microbial fuel cells. Moreover, current production was not feasible when using raw cheese whey directly to feed the microbial fuel cell. A maximal power density of 439 mW/m[2] was obtained from the reactor effluent which was 1000 times more than when using raw cheese whey as substrate. 16S rRNA gene amplicon sequencing showed that potential electroactive populations (Geobacter, Pseudomonas and Thauera) were enriched on anodes of MFCs fed with reactor effluent while fermentative populations (Clostridium and Lactobacillus) were predominant on the MFC anode fed directly with raw cheese whey. This result was further demonstrated using culture techniques. A total of 45 strains were isolated belonging to 10 different genera including known electrogenic populations like Geobacter (in MFC with reactor effluent) and known fermentative populations like Lactobacillus (in MFC with cheese whey). Our results show that microbial fuel cells are an attractive technology to gain extra energy from cheese whey as a second stage process during raw cheese whey treatment by dark fermentation process.}, }
@article {pmid28214969, year = {2017}, author = {Herrmann, M and Opitz, S and Harzer, R and Totsche, KU and Küsel, K}, title = {Attached and Suspended Denitrifier Communities in Pristine Limestone Aquifers Harbor High Fractions of Potential Autotrophs Oxidizing Reduced Iron and Sulfur Compounds.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {264-277}, pmid = {28214969}, issn = {1432-184X}, mesh = {Bacteria/*classification ; *Calcium Carbonate ; *Denitrification ; Germany ; Groundwater/*microbiology ; Iron/*metabolism ; Sulfur Compounds/*metabolism ; }, abstract = {Oxygen and nitrate availability as well as the presence of suitable organic or inorganic electron donors are strong drivers of denitrification; however, the factors influencing denitrifier abundance and community composition in pristine aquifers are not well understood. We explored the denitrifier community structure of suspended and attached groundwater microorganisms in two superimposed limestone aquifer assemblages with contrasting oxygen regime in the Hainich Critical Zone Exploratory (Germany). Attached communities were retrieved from freshly crushed parent rock material which had been exposed for colonization in two groundwater wells (12.7 and 48 m depth). Quantitative PCR and amplicon pyrosequencing of nirK and nirS genes encoding copper-containing or cytochrome cd1 heme-type nitrite reductase, respectively, and of bacterial 16S ribosomal RNA genes showed a numerical predominance of nirS-type denitrifiers in both attached and suspended groundwater communities and a dominance of nirS-type denitrifiers closely related to the autotrophic thiosulfate- and hydrogen-oxidizing Sulfuritalea hydrogenivorans and the iron- and sulfide-oxidizing Sideroxydans lithotrophicus ES-1. Potential rates of nitrate reduction in association with exposed crushed rock material were higher with an inorganic electron donor (thiosulfate) compared to an organic electron donor (fumarate/acetate) in the upper aquifer assemblage but similar in the lower, oxic aquifer. Our results have clearly demonstrated that groundwater from pristine limestone aquifers harbors diverse denitrifier communities which appear to selectively attach to rock surfaces and harbor a high potential for nitrate reduction. Our findings suggest that the availability of suitable inorganic versus organic electron donors rather than oxygen availability shapes denitrifier communities and their potential activity in these limestone aquifers.}, }
@article {pmid28214393, year = {2017}, author = {Van Nevel, S and Koetzsch, S and Proctor, CR and Besmer, MD and Prest, EI and Vrouwenvelder, JS and Knezev, A and Boon, N and Hammes, F}, title = {Flow cytometric bacterial cell counts challenge conventional heterotrophic plate counts for routine microbiological drinking water monitoring.}, journal = {Water research}, volume = {113}, number = {}, pages = {191-206}, doi = {10.1016/j.watres.2017.01.065}, pmid = {28214393}, issn = {1879-2448}, mesh = {Bacteria ; Cell Count ; Colony Count, Microbial ; Drinking Water/*microbiology ; Flow Cytometry ; *Water Microbiology ; Water Quality ; Water Supply ; }, abstract = {Drinking water utilities and researchers continue to rely on the century-old heterotrophic plate counts (HPC) method for routine assessment of general microbiological water quality. Bacterial cell counting with flow cytometry (FCM) is one of a number of alternative methods that challenge this status quo and provide an opportunity for improved water quality monitoring. After more than a decade of application in drinking water research, FCM methodology is optimised and established for routine application, supported by a considerable amount of data from multiple full-scale studies. Bacterial cell concentrations obtained by FCM enable quantification of the entire bacterial community instead of the minute fraction of cultivable bacteria detected with HPC (typically < 1% of all bacteria). FCM measurements are reproducible with relative standard deviations below 3% and can be available within 15 min of samples arriving in the laboratory. High throughput sample processing and complete automation are feasible and FCM analysis is arguably less expensive than HPC when measuring more than 15 water samples per day, depending on the laboratory and selected staining procedure(s). Moreover, many studies have shown FCM total (TCC) and intact (ICC) cell concentrations to be reliable and robust process variables, responsive to changes in the bacterial abundance and relevant for characterising and monitoring drinking water treatment and distribution systems. The purpose of this critical review is to initiate a constructive discussion on whether FCM could replace HPC in routine water quality monitoring. We argue that FCM provides a faster, more descriptive and more representative quantification of bacterial abundance in drinking water.}, }
@article {pmid28214040, year = {2018}, author = {Salden, BN and Troost, FJ and Wilms, E and Truchado, P and Vilchez-Vargas, R and Pieper, DH and Jáuregui, R and Marzorati, M and van de Wiele, T and Possemiers, S and Masclee, AA}, title = {Reinforcement of intestinal epithelial barrier by arabinoxylans in overweight and obese subjects: A randomized controlled trial: Arabinoxylans in gut barrier.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {37}, number = {2}, pages = {471-480}, doi = {10.1016/j.clnu.2017.01.024}, pmid = {28214040}, issn = {1532-1983}, mesh = {Adolescent ; Adult ; Aged ; Double-Blind Method ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Intestinal Mucosa/*drug effects/microbiology/*physiology ; Male ; Middle Aged ; Obesity/blood/complications/microbiology ; Overweight/blood/complications/*microbiology ; Permeability ; Xylans/*pharmacology ; Young Adult ; }, abstract = {BACKGROUND &amp; AIMS: Obesity and metabolic diseases are associated with alterations in microbial composition and impaired gut barrier. Previous in vitro and animal studies have shown that arabinoxylans (AX) have the potential to modulate gut microbiota and gut barrier and therefore could have a protective role. Primary aim of the study was to investigate the effect of AX on intestinal permeability. Secondary aims included the effect of AX on gene transcription and protein expression of tight junctions (TJ), intestinal microbiota composition and activity, immune response and metabolic markers in overweight and obese individuals.<br><br>METHODS: In this randomized, double-blind, placebo-controlled trial, 47 overweight subjects were randomly assigned to groups receiving 7.5&#xa0;g/d AX (n&#xa0;=&#xa0;16), 15&#xa0;g/d AX (n&#xa0;=&#xa0;17) or 15&#xa0;g/d placebo (n&#xa0;=&#xa0;14) for 6&#xa0;wks. Intestinal permeability was investigated using a multi-sugar test. Sigmoid colon tissue was obtained from a subgroup (n&#xa0;=&#xa0;26) for analyzing gene transcription and mucosal expression of TJ proteins. Fecal samples were collected to assess microbial composition and activity. Furthermore, the production of cytokines by stimulated peripheral blood mononuclear cells (PBMCs) was examined. Blood was also sampled for measuring metabolic markers.<br><br>RESULTS: No significant changes in gastrointestinal permeability and TJ protein expression were observed after 6&#xa0;wks AX supplementation compared to placebo. However, gene transcription of occludin was upregulated in the 7.5&#xa0;g AX group, and transcription of claudin-3 and claudin-4 were upregulated in the 15&#xa0;g AX group compared to placebo. Furthermore, fecal microbiota diversity was decreased after 6&#xa0;wks 15&#xa0;g AX treatment, but no change in relative abundance of dominant phyla was observed. AX intake significantly decreased fecal pH and increased fecal concentrations of total SCFAs, acetate, propionate and butyrate, compared to placebo. Additionally, a decreased TNF&#x3b1; production by stimulated PBMCs was observed after 15&#xa0;g AX treatment. No changes in metabolic markers were detected.<br><br>CONCLUSIONS: Regular consumption of AX resulted in a more beneficial fermentation profile in overweight and obese individuals. Further studies are required to assess whether such fermentation profile will translate into improved gut barrier function and immune health. The trial has been registered at ClinicalTrials.gov with study ID number NCT01877044.}, }
@article {pmid28213337, year = {2017}, author = {Li, D and Stanford, B and Dickenson, E and Khunjar, WO and Homme, CL and Rosenfeldt, EJ and Sharp, JO}, title = {Effect of advanced oxidation on N-nitrosodimethylamine (NDMA) formation and microbial ecology during pilot-scale biological activated carbon filtration.}, journal = {Water research}, volume = {113}, number = {}, pages = {160-170}, doi = {10.1016/j.watres.2017.02.004}, pmid = {28213337}, issn = {1879-2448}, mesh = {Charcoal ; Dimethylnitrosamine/*chemistry ; Filtration ; Hydrogen Peroxide/*chemistry ; Ozone/chemistry ; Water Pollutants, Chemical/chemistry ; Water Purification ; }, abstract = {Water treatment combining advanced oxidative processes with subsequent exposure to biological activated carbon (BAC) holds promise for the attenuation of recalcitrant pollutants. Here we contrast oxidation and subsequent biofiltration of treated wastewater effluent employing either ozone or UV/H2O2 followed by BAC during pilot-scale implementation. Both treatment trains largely met target water quality goals by facilitating the removal of a suite of trace organics and bulk water parameters. N-nitrosodimethylamine (NDMA) formation was observed in ozone fed BAC columns during biofiltration and to a lesser extent in UV/H2O2 fed columns and was most pronounced at 20 min of empty bed contact time (EBCT) when compared to shorter EBCTs evaluated. While microbial populations were highly similar in the upper reaches, deeper samples revealed a divergence within and between BAC filtration systems where EBCT was identified to be a significant environmental predictor for shifts in microbial populations. The abundance of Nitrospira in the top samples of both columns provides an explanation for the oxidation of nitrite and corresponding increases in nitrate concentrations during BAC transit and support interplay between nitrogen cycling with nitrosamine formation. The results of this study demonstrate that pretreatments using ozone versus UV/H2O2 impart modest differences to the overall BAC microbial population structural and functional attributes, and further highlight the need to evaluate NDMA formation prior to full-scale implementation of BAC in potable reuse applications.}, }
@article {pmid28205388, year = {2017}, author = {Schink, B and Montag, D and Keller, A and Müller, N}, title = {Hydrogen or formate: Alternative key players in methanogenic degradation.}, journal = {Environmental microbiology reports}, volume = {9}, number = {3}, pages = {189-202}, doi = {10.1111/1758-2229.12524}, pmid = {28205388}, issn = {1758-2229}, mesh = {Bicarbonates/*metabolism ; Biofuels/microbiology ; Bioreactors/microbiology ; Chemoautotrophic Growth ; Fermentation ; Formates/*metabolism ; Hydrogen/*metabolism ; Methane/*biosynthesis ; Sewage/microbiology ; Thermococcus/*metabolism ; }, abstract = {Hydrogen and formate are important electron carriers in methanogenic degradation in anoxic environments such as sediments, sewage sludge digestors and biogas reactors. Especially in the terminal steps of methanogenesis, they determine the energy budgets of secondary (syntrophically) fermenting bacteria and their methanogenic partners. The literature provides considerable data on hydrogen pool sizes in such habitats, but little data exist for formate concentrations due to technical difficulties in formate determination at low concentration. Recent evidence from biochemical and molecular biological studies indicates that several secondary fermenters can use both hydrogen and formate for electron release, and may do so even simultaneously. Numerous strictly anaerobic bacteria contain enzymes which equilibrate hydrogen and formate pools to energetically equal values, and recent measurements in sewage digestors and biogas reactors indicate that - beyond occasional fluctuations - the pool sizes of hydrogen and formate are indeed energetically nearly equivalent. Nonetheless, a thermophilic archaeon from a submarine hydrothermal vent, Thermococcus onnurineus, can obtain ATP from the conversion of formate to hydrogen plus bicarbonate at 80°C, indicating that at least in this extreme environment the pools of formate and hydrogen are likely to be sufficiently different to support such an unusual type of energy conservation.}, }
@article {pmid28202080, year = {2017}, author = {Chopyk, J and Chattopadhyay, S and Kulkarni, P and Claye, E and Babik, KR and Reid, MC and Smyth, EM and Hittle, LE and Paulson, JN and Cruz-Cano, R and Pop, M and Buehler, SS and Clark, PI and Sapkota, AR and Mongodin, EF}, title = {Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {22}, pmid = {28202080}, issn = {2049-2618}, support = {P50 CA180523/CA/NCI NIH HHS/United States ; }, mesh = {Black or African American ; Bacteria/genetics/*isolation &amp; purification/pathogenicity ; DNA, Bacterial ; Humans ; Menthol/*analysis ; Microbiota/genetics/*physiology ; Polymerase Chain Reaction ; Pseudomonas/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S ; *Smoking ; Tobacco Products/analysis/*microbiology ; }, abstract = {BACKGROUND: There is a paucity of data regarding the microbial constituents of tobacco products and their impacts on public health. Moreover, there has been no comparative characterization performed on the bacterial microbiota associated with the addition of menthol, an additive that has been used by tobacco manufacturers for nearly a century. To address this knowledge gap, we conducted bacterial community profiling on tobacco from user- and custom-mentholated/non-mentholated cigarette pairs, as well as a commercially-mentholated product. Total genomic DNA was extracted using a multi-step enzymatic and mechanical lysis protocol followed by PCR amplification of the V3-V4 hypervariable regions of the 16S rRNA gene from five cigarette products (18 cigarettes per product for a total of 90 samples): Camel Crush, user-mentholated Camel Crush, Camel Kings, custom-mentholated Camel Kings, and Newport Menthols. Sequencing was performed on the Illumina MiSeq platform and sequences were processed using the Quantitative Insights Into Microbial Ecology (QIIME) software package.<br><br>RESULTS: In all products, Pseudomonas was the most abundant genera and included Pseudomonas oryzihabitans and Pseudomonas putida, regardless of mentholation status. However, further comparative analysis of the five products revealed significant differences in the bacterial compositions across products. Bacterial community richness was higher among non-mentholated products compared to those that were mentholated, particularly those that were custom-mentholated. In addition, mentholation appeared to be correlated with a reduction in potential human bacterial pathogens and an increase in bacterial species resistant to harsh environmental conditions.<br><br>CONCLUSIONS: Taken together, these data provide preliminary evidence that the mentholation of commercially available cigarettes can impact the bacterial community of these products.}, }
@article {pmid28201744, year = {2016}, author = {Dolinšek, J and Goldschmidt, F and Johnson, DR}, title = {Synthetic microbial ecology and the dynamic interplay between microbial genotypes.}, journal = {FEMS microbiology reviews}, volume = {40}, number = {6}, pages = {961-979}, doi = {10.1093/femsre/fuw024}, pmid = {28201744}, issn = {1574-6976}, mesh = {Bacteria ; *Ecology ; *Microbial Interactions ; *Population Dynamics ; *Synthetic Biology ; }, abstract = {Assemblages of microbial genotypes growing together can display surprisingly complex and unexpected dynamics and result in community-level functions and behaviors that are not readily expected from analyzing each genotype in isolation. This complexity has, at least in part, inspired a discipline of synthetic microbial ecology. Synthetic microbial ecology focuses on designing, building and analyzing the dynamic behavior of ‘ecological circuits’ (i.e. a set of interacting microbial genotypes) and understanding how community-level properties emerge as a consequence of those interactions. In this review, we discuss typical objectives of synthetic microbial ecology and the main advantages and rationales of using synthetic microbial assemblages. We then summarize recent findings of current synthetic microbial ecology investigations. In particular, we focus on the causes and consequences of the interplay between different microbial genotypes and illustrate how simple interactions can create complex dynamics and promote unexpected community-level properties. We finally propose that distinguishing between active and passive interactions and accounting for the pervasiveness of competition can improve existing frameworks for designing and predicting the dynamics of microbial assemblages.}, }
@article {pmid28201512, year = {2016}, author = {Duran, R and Cravo-Laureau, C}, title = {Role of environmental factors and microorganisms in determining the fate of polycyclic aromatic hydrocarbons in the marine environment.}, journal = {FEMS microbiology reviews}, volume = {40}, number = {6}, pages = {814-830}, pmid = {28201512}, issn = {1574-6976}, mesh = {*Aquatic Organisms ; *Bacteria ; *Biodegradation, Environmental ; Ecosystem ; *Polycyclic Aromatic Hydrocarbons ; *Water Pollutants, Chemical ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are widespread in marine ecosystems and originate from natural sources and anthropogenic activities. PAHs enter the marine environment in two main ways, corresponding to chronic pollution or acute pollution by oil spills. The global PAH fluxes in marine environments are controlled by the microbial degradation and the biological pump, which plays a role in particle settling and in sequestration through bioaccumulation. Due to their low water solubility and hydrophobic nature, PAHs tightly adhere to sediments leading to accumulation in coastal and deep sediments. Microbial assemblages play an important role in determining the fate of PAHs in water and sediments, supporting the functioning of biogeochemical cycles and the microbial loop. This review summarises the knowledge recently acquired in terms of both chronic and acute PAH pollution. The importance of the microbial ecology in PAH-polluted marine ecosystems is highlighted as well as the importance of gaining further in-depth knowledge of the environmental services provided by microorganisms.}, }
@article {pmid28198425, year = {2017}, author = {Leite, MF and Pan, Y and Bloem, J and Berge, HT and Kuramae, EE}, title = {Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {42634}, pmid = {28198425}, issn = {2045-2322}, mesh = {Bacteria ; Carbon/chemistry/metabolism ; Fungi ; Metagenome ; Metagenomics/methods ; Microbiota ; Nitrogen/*chemistry/*metabolism ; *Soil Microbiology ; }, abstract = {Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake.}, }
@article {pmid28197855, year = {2017}, author = {McGee, CF and Storey, S and Clipson, N and Doyle, E}, title = {Soil microbial community responses to contamination with silver, aluminium oxide and silicon dioxide nanoparticles.}, journal = {Ecotoxicology (London, England)}, volume = {26}, number = {3}, pages = {449-458}, pmid = {28197855}, issn = {1573-3017}, mesh = {Agriculture ; Aluminum Oxide/*toxicity ; Nanoparticles/*toxicity ; Risk Assessment ; Silicon Dioxide/*toxicity ; Silver/*toxicity ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/*toxicity ; }, abstract = {Soil microorganisms are key contributors to nutrient cycling and are essential for the maintenance of healthy soils and sustainable agriculture. Although the antimicrobial effects of a broad range of nanoparticulate substances have been characterised in vitro, little is known about the impact of these compounds on microbial communities in environments such as soil. In this study, the effect of three widely used nanoparticulates (silver, silicon dioxide and aluminium oxide) on bacterial and fungal communities in an agricultural pastureland soil was examined in a microcosm-based experiment using a combination of enzyme analysis, molecular fingerprinting and amplicon sequencing. A relatively low concentration of silver nanoparticles (AgNPs) significantly reduced total soil dehydrogenase and urease activity, while Al2O3 and SiO2 nanoparticles had no effect. Amplicon sequencing revealed substantial shifts in bacterial community composition in soils amended with AgNPs, with significant decreases in the relative abundance of Acidobacteria and Verrucomicrobia and an increase in Proteobacteria. In particular, the relative abundance of the Proteobacterial genus Dyella significantly increased in AgNP amended soil. The effects of Al2O3 and SiO2 NPs on bacterial community composition were less pronounced. AgNPs significantly reduced bacterial and archaeal amoA gene abundance in soil, with the archaea more susceptible than bacteria. AgNPs also significantly impacted soil fungal community structure, while Al2O3 and SiO2 NPs had no effect. Several fungal ribotypes increased in soil amended with AgNPs, compared to control soil. This study highlights the need to consider the effects of individual nanoparticles on soil microbial communities when assessing their environmental impact.}, }
@article {pmid28197647, year = {2017}, author = {Defez, R and Andreozzi, A and Bianco, C}, title = {The Overproduction of Indole-3-Acetic Acid (IAA) in Endophytes Upregulates Nitrogen Fixation in Both Bacterial Cultures and Inoculated Rice Plants.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {441-452}, pmid = {28197647}, issn = {1432-184X}, mesh = {Bacteria/*metabolism ; Endophytes/metabolism ; Indoleacetic Acids/*metabolism ; *Nitrogen Fixation ; Oryza/*microbiology ; Plant Roots/microbiology ; }, abstract = {Endophytic bacteria from roots and leaves of rice plants were isolated and identified in order to select the diazotrophs and improve their nitrogen-fixing abilities. The nitrogen-fixing endophytes were identified by PCR amplification of the nifH gene fragment. For this purpose, two isolates, Enterobacter cloacae RCA25 and Klebsiella variicola RCA26, and two model bacteria (Herbaspirillum seropedicae z67 and Sinorhizobium fredii NGR234) were transformed to increase the biosynthesis of the main plant auxin indole-3-acetic acid (IAA). A significant increase in the production of IAA was observed for all strains. When the expression of nifH gene and the activity of the nitrogenase enzyme were analyzed in liquid cultures, we found that they were positively affected in the IAA-overproducing endophytes as compared to the wild-type ones. Rice plants inoculated with these modified strains showed a significant upregulation of the nitrogenase activity when plants infected with the wild-type strains were used as reference. Similar results were obtained too with common bean plants infected with the S. fredii NGR234 strain. These findings suggest that IAA overproduction improves nitrogen-fixing apparatus of endophytic bacteria both in liquid cultures and in inoculated host plants. The present study highlights new perspectives to enhance nitrogen-fixing ability in non-legume crops. These strains could be used as bioinoculants to improve the growth and the yield of agricultural crops, offering an alternative to the use of chemical nitrogen fertilizers.}, }
@article {pmid28197147, year = {2017}, author = {Doll, EV and Scherer, S and Wenning, M}, title = {Spoilage of Microfiltered and Pasteurized Extended Shelf Life Milk Is Mainly Induced by Psychrotolerant Spore-Forming Bacteria that often Originate from Recontamination.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {135}, pmid = {28197147}, issn = {1664-302X}, abstract = {Premature spoilage and varying product quality due to microbial contamination still constitute major problems in the production of microfiltered and pasteurized extended shelf life (ESL) milk. Spoilage-associated bacteria may enter the product either as part of the raw milk microbiota or as recontaminants in the dairy plant. To identify spoilage-inducing bacteria and their routes of entry, we analyzed end products for their predominant microbiota as well as the prevalence and biodiversity of psychrotolerant spores in bulk tank milk. Process analyses were performed to determine the removal of psychrotolerant spores at each production step. To detect transmission and recontamination events, strain typing was conducted with isolates obtained from all process stages. Microbial counts in 287 ESL milk packages at the end of shelf life were highly diverse ranging from <1 to 7.9 log cfu/mL. In total, 15% of samples were spoiled. High G+C Gram-positive bacteria were the most abundant taxonomic group, but were responsible for only 31% of spoilage. In contrast, psychrotolerant spores were isolated from 55% of spoiled packages. In 90% of samples with pure cultures of Bacillus cereus sensu lato and Paenibacillus spp., counts exceeded 6 log cfu/mL. In bulk tank milk, the concentration of psychrotolerant spores was low, accounting for merely 0.5 ± 0.8 MPN/mL. Paenibacillus amylolyticus/xylanexedens was by far the most dominant species in bulk tank milk (48% of all isolates), but was never detected in ESL milk, pointing to efficient removal during manufacturing. Six large-scale process analyses confirmed a high removal rate for psychrotolerant spores (reduction by nearly 4 log-units). B. cereus sensu lato, on the contrary, was frequently found in spoiled end products, but was rarely detected in bulk tank milk. Due to low counts in bulk tank samples and efficient spore removal during production, we suggest that shelf life is influenced only to a minor extent by raw-milk-associated factors. In contrast, recontamination with spores, particularly from the B. cereus complex, seems to occur. To enhance milk quality throughout the entire shelf life, improved plant sanitation and disinfection that target the elimination of spores are necessary.}, }
@article {pmid28197142, year = {2017}, author = {Menke, S and Gillingham, MA and Wilhelm, K and Sommer, S}, title = {Home-Made Cost Effective Preservation Buffer Is a Better Alternative to Commercial Preservation Methods for Microbiome Research.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {102}, pmid = {28197142}, issn = {1664-302X}, abstract = {The investigation of wildlife gastrointestinal microbiomes by next-generation sequencing approaches is a growing field in microbial ecology and conservation. Such studies often face difficulties in sample preservation if neither freezing facilities nor liquid nitrogen (LQN) are readily available. Thus, in order to prevent microbial community changes because of bacterial growth after sampling, preservation buffers need to be applied to samples. However, the amount of microbial community variation attributable to the different preservation treatments and potentially affecting biological interpretation is hardly known. Here, we sampled feces of 11 sheep (Ovis aries sp.) by using swabs and analyzed the effect of air-drying, an inexpensive self-made nucleic acid preservation buffer (NAP), DNA/RNA Shield™, and RNAlater®, each together with freezing (for 10 days) or storing at room temperature (for 10 days) prior to 16S rRNA gene high-throughput sequencing to determine bacterial communities. Results revealed that the proportions of operational taxonomic units (OTUs) belonging to a bacterial phylum were affected by the preservation treatments, and that alpha diversities [observed OTUs, Shannon index, and phylogenetic diversity (PD)] were lower in all preservation treatments than in samples taken by forensic swabs and immediately frozen which is considered as the favored preservation treatment in the absence of any logistic constraints. Overall, NAP had better preservation qualities than RNAlater® and DNA/RNA Shield™ making this self-made buffer a valuable solution in wildlife microbiome studies.}, }
@article {pmid28197130, year = {2017}, author = {Pisapia, C and Gérard, E and Gérard, M and Lecourt, L and Lang, SQ and Pelletier, B and Payri, CE and Monnin, C and Guentas, L and Postec, A and Quéméneur, M and Erauso, G and Ménez, B}, title = {Mineralizing Filamentous Bacteria from the Prony Bay Hydrothermal Field Give New Insights into the Functioning of Serpentinization-Based Subseafloor Ecosystems.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {57}, pmid = {28197130}, issn = {1664-302X}, abstract = {Despite their potential importance as analogs of primitive microbial metabolisms, the knowledge of the structure and functioning of the deep ecosystems associated with serpentinizing environments is hampered by the lack of accessibility to relevant systems. These hyperalkaline environments are depleted in dissolved inorganic carbon (DIC), making the carbon sources and assimilation pathways in the associated ecosystems highly enigmatic. The Prony Bay Hydrothermal Field (PHF) is an active serpentinization site where, similar to Lost City (Mid-Atlantic Ridge), high-pH fluids rich in H2 and CH4 are discharged from carbonate chimneys at the seafloor, but in a shallower lagoonal environment. This study aimed to characterize the subsurface microbial ecology of this environment by focusing on the earliest stages of chimney construction, dominated by the discharge of hydrothermal fluids of subseafloor origin. By jointly examining the mineralogy and the microbial diversity of the conduits of juvenile edifices at the micrometric scale, we find a central role of uncultivated bacteria belonging to the Firmicutes in the ecology of the PHF. These bacteria, along with members of the phyla Acetothermia and Omnitrophica, are identified as the first chimneys inhabitants before archaeal Methanosarcinales. They are involved in the construction and early consolidation of the carbonate structures via organomineralization processes. Their predominance in the most juvenile and nascent hydrothermal chimneys, and their affiliation with environmental subsurface microorganisms, indicate that they are likely discharged with hydrothermal fluids from the subseafloor. They may thus be representative of endolithic serpentinization-based ecosystems, in an environment where DIC is limited. In contrast, heterotrophic and fermentative microorganisms may consume organic compounds from the abiotic by-products of serpentinization processes and/or from life in the deeper subsurface. We thus propose that the Firmicutes identified at PHF may have a versatile metabolism with the capability to use diverse organic compounds from biological or abiotic origin. From that perspective, this study sheds new light on the structure of deep microbial communities living at the energetic edge in serpentinites and may provide an alternative model of the earliest metabolisms.}, }
@article {pmid28197129, year = {2017}, author = {Nazir, R and Mazurier, S and Yang, P and Lemanceau, P and van Elsas, JD}, title = {The Ecological Role of Type Three Secretion Systems in the Interaction of Bacteria with Fungi in Soil and Related Habitats Is Diverse and Context-Dependent.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {38}, pmid = {28197129}, issn = {1664-302X}, abstract = {Bacteria and fungi constitute important organisms in many ecosystems, in particular terrestrial ones. Both organismal groups contribute significantly to biogeochemical cycling processes. Ecological theory postulates that bacteria capable of receiving benefits from host fungi are likely to evolve efficient association strategies. The purpose of this review is to examine the mechanisms that underpin the bacterial interactions with fungi in soil and other systems, with special focus on the type III secretion system (T3SS). Starting with a brief description of the versatility of the T3SS as an interaction system with diverse eukaryotic hosts, we subsequently examine the recent advances made in our understanding of its contribution to interactions with soil fungi. The analysis used data sets ranging from circumstantial evidence to gene-knockout-based experimental data. The initial finding that the abundance of T3SSs in microbiomes is often enhanced in fungal-affected habitats like the mycosphere and the mycorrhizosphere is now substantiated with in-depth knowledge of the specific systems involved. Different fungal-interactive bacteria, in positive or negative associations with partner fungi, harbor and express T3SSs, with different ecological outcomes. In some particular cases, bacterial T3SSs have been shown to modulate the physiology of its fungal partner, affecting its ecological characteristics and consequently shaping its own habitat. Overall, the analyses of the collective data set revealed that diverse T3SSs have assumed diverse roles in the interactions of bacteria with host fungi, as driven by ecological and evolutionary niche requirements.}, }
@article {pmid28195581, year = {2017}, author = {Sauder, LA and Albertsen, M and Engel, K and Schwarz, J and Nielsen, PH and Wagner, M and Neufeld, JD}, title = {Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system.}, journal = {The ISME journal}, volume = {11}, number = {5}, pages = {1142-1157}, pmid = {28195581}, issn = {1751-7370}, support = {294343/ERC_/European Research Council/International ; }, mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Carbon/metabolism ; Genome, Archaeal ; Nitrification ; Nitrites/metabolism ; Oxidation-Reduction ; Phylogeny ; Wastewater/*microbiology ; }, abstract = {Thaumarchaeota have been detected in several industrial and municipal wastewater treatment plants (WWTPs), despite the fact that ammonia-oxidizing archaea (AOA) are thought to be adapted to low ammonia environments. However, the activity, physiology and metabolism of WWTP-associated AOA remain poorly understood. We report the cultivation and complete genome sequence of Candidatus Nitrosocosmicus exaquare, a novel AOA representative from a municipal WWTP in Guelph, Ontario (Canada). In enrichment culture, Ca. N. exaquare oxidizes ammonia to nitrite stoichiometrically, is mesophilic, and tolerates at least 15 mm of ammonium chloride or sodium nitrite. Microautoradiography (MAR) for enrichment cultures demonstrates that Ca. N. exaquare assimilates bicarbonate in association with ammonia oxidation. However, despite using inorganic carbon, the ammonia-oxidizing activity of Ca. N. exaquare is greatly stimulated in enrichment culture by the addition of organic compounds, especially malate and succinate. Ca. N. exaquare cells are coccoid with a diameter of ~1-2 μm. Phylogenetically, Ca. N. exaquare belongs to the Nitrososphaera sister cluster within the Group I.1b Thaumarchaeota, a lineage which includes most other reported AOA sequences from municipal and industrial WWTPs. The 2.99 Mbp genome of Ca. N. exaquare encodes pathways for ammonia oxidation, bicarbonate fixation, and urea transport and breakdown. In addition, this genome encodes several key genes for dealing with oxidative stress, including peroxidase and catalase. Incubations of WWTP biofilm demonstrate partial inhibition of ammonia-oxidizing activity by 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), suggesting that Ca. N. exaquare-like AOA may contribute to nitrification in situ. However, CARD-FISH-MAR showed no incorporation of bicarbonate by detected Thaumarchaeaota, suggesting that detected AOA may incorporate non-bicarbonate carbon sources or rely on an alternative and yet unknown metabolism.}, }
@article {pmid28194679, year = {2017}, author = {Liu, X and Liu, W and Wang, Q and Wu, L and Luo, Y and Christie, P}, title = {Soil properties and microbial ecology of a paddy field after repeated applications of domestic and industrial sewage sludges.}, journal = {Environmental science and pollution research international}, volume = {24}, number = {9}, pages = {8619-8628}, pmid = {28194679}, issn = {1614-7499}, mesh = {*Fertilizers ; Metals, Heavy/analysis ; Nitrogen/analysis ; Polycyclic Aromatic Hydrocarbons ; *Sewage/chemistry ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The effects of repeated application of two types of sewage sludge, domestic and industrial (petrochemical, PSS) sludges, into paddy fields over a 5-year period on the soil properties and microbial ecology were studied and compared with conventional NPK fertilizer application. Soil organic matter and total nitrogen contents were significantly higher in the two sludge treatments than that in fertilized plots after 5 years. Soil concentrations of potentially toxic metals were low after 5 years of both sludge treatments, but the polycyclic aromatic hydrocarbons (PAHs) showed differences between the two sludge types. Concentrations of high-molecular-weight PAHs were significantly higher (p < 0.05) in the petrochemical sludge treatment than the domestic sludge treatment or the fertilizer control, although the total concentrations of 16 types of PAH in the petrochemical sludge treatment were only slightly higher than in the domestic sludge treatment and the control. The biological toxicity of soil dimethyl sulfoxide extracts from the petrochemical sludge treatment was also significantly higher (p < 0.05) than those from the fertilizer control and the domestic sludge treatment when evaluated using Photobacterium phosphoreum T3. Both types of sewage sludge increased soil microbial activity, but only the petrochemical sludge led to enrichment with specific PAH degraders such as Mycobacterium, Nocardioides, and Sphingomonas.}, }
@article {pmid28188331, year = {2017}, author = {Strobel, G and Ericksen, A and Sears, J and Xie, J and Geary, B and Blatt, B}, title = {Urnula sp., an Endophyte of Dicksonia antarctica, Making a Fragrant Mixture of Biologically Active Volatile Organic Compounds.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {312-321}, pmid = {28188331}, issn = {1432-184X}, mesh = {Antibiosis ; Ascomycota/*chemistry ; Endophytes/*chemistry ; Tracheophyta/*microbiology ; Volatile Organic Compounds/*analysis ; }, abstract = {Urnula sp. was isolated as an endophyte of Dicksonia antarctica and identified primarily on the basis of its ITS sequence and morphological features. The anamorphic state of the fungus appeared as a hyphomyceteous-like fungus as based on its features in culture and scanning electron microscopy examination of its spores. On potato dextrose agar (PDA), the organism makes a characteristic fragrance resembling peach pie with vanilla overtones. A GC/MS analysis done on the volatile organic compounds (VOCs) of this organism, trapped by carbotrap methodology, revealed over 150 compounds with high MS matching quality being noted for 44 of these. Some of the most abundantly produced compounds included 4-decene, tridecane, 2-decene (E), 2-dodecene, (Z,E)-alpha-farnesene, butanoic acid, pentyl ester, and 1-hexanol,2-ethyl. In addition, vanillin, methyl vanillin, and many other fragrant substances were noted including isomenthol, pyrazine derivatives, and 3-decanone. In split plate bioassay tests on potato dextrose agar (PDA), Botrytis cinerea, Ceratocystis ulmi, Pythium ultimum, Fusarium solani, and Rhizoctonia solani were inhibited at levels of 24 to 50% of their normal growth on this medium. Bioreactors supporting fungal growth on 50 g of beet pulp waste, using stainless steel carbotraps, yielded over 180 mg of hydrocarbon-based products collected over 6 weeks of incubation. Similarly, because this organism is making one of the largest sets of VOCs as any fungus examined to date, producing many compounds of commercial interest, it has enormous biotechnical potential. The role of the VOCs in the biology and ecology of this endophyte may be related to the antimicrobial activities that they possess.}, }
@article {pmid28185400, year = {2017}, author = {Larkin, AA and Martiny, AC}, title = {Microdiversity shapes the traits, niche space, and biogeography of microbial taxa.}, journal = {Environmental microbiology reports}, volume = {9}, number = {2}, pages = {55-70}, doi = {10.1111/1758-2229.12523}, pmid = {28185400}, issn = {1758-2229}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Biological Evolution ; *Ecosystem ; Models, Theoretical ; *Phylogeography ; }, abstract = {With rapidly improving sequencing technologies, scientists have recently gained the ability to examine diverse microbial communities at high genomic resolution, revealing that both free-living and host-associated microbes partition their environment at fine phylogenetic scales. This 'microdiversity,' or closely related (> 97% similar 16S rRNA gene) but ecologically and physiologically distinct sub-taxonomic groups, appears to be an intrinsic property of microorganisms. However, the functional implications of microdiversity as well as its effects on microbial biogeography are poorly understood. Here, we present two theoretical models outlining the evolutionary mechanisms that drive the formation of microdiverse 'sub-taxa.' Additionally, we review recent literature and reveal that microdiversity influences a wide range of functional traits across diverse ecosystems and microbes. Moving to higher levels of organization, we use laboratory data from marine, soil, and host-associated bacteria to demonstrate that the aggregated trait-based response of microdiverse sub-taxa modifies the fundamental niche of microbes. The correspondence between microdiversity and niche space represents a critical tool for future studies of microbial ecology. By combining growth experiments on diverse isolates with examinations of environmental abundance patterns, researchers can better quantify the fundamental and realized niches of microbes and improve understanding of microbial biogeography and response to future environmental change.}, }
@article {pmid28177786, year = {2017}, author = {Liu, Y and Zhang, Z and Li, Y and Fei, Y}, title = {Response of microbial communities to roxarsone under different culture conditions.}, journal = {Canadian journal of microbiology}, volume = {63}, number = {8}, pages = {661-670}, doi = {10.1139/cjm-2016-0652}, pmid = {28177786}, issn = {1480-3275}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; *Biodegradation, Environmental ; Chickens ; Fertilizers ; Food Additives/*pharmacology ; Manure ; Roxarsone/*pharmacology ; *Soil Microbiology ; Soil Pollutants/metabolism ; }, abstract = {Roxarsone is a feed additive widely used in the broiler and swine industries that has the potential to contaminate the environment, mainly via the use of poultry manure as fertilizer, which results in release of inorganic arsenic to the soil and water. This study was conducted to investigate roxarsone degradation and the response of the microbial community under different culture conditions using high-throughput sequencing technology. Poultry litter was incubated for 288 h in the presence of roxarsone under light aerobic, dark aerobic, or dark anaerobic conditions. The results showed that roxarsone was completely degraded after 48 h of dark anaerobic incubation, while 79.9% and 94.5% of roxarsone was degraded after 288 h of dark aerobic and light aerobic incubation, respectively. Under dark aerobic conditions with microbial inhibitor sodium azide, roxarsone was rarely degraded during the 288 h of incubation, illustrating that microorganisms play an important role in roxarsone degradation. Microbial community structure was significantly different among various culture conditions. Olivibacter, Sphingobacterium, and Proteiniphilum were the top 3 genera in the control samples. Sphingobacterium and Alishewanella dominated the light aerobic samples, while the dominant microflora of the dark aerobic samples were Acinetobacter spp. Pseudomonas and Advenella were the predominant genera of dark anaerobic samples. This study emphasizes the potential importance of microbes in roxarsone degradation and expands our current understanding of microbial ecology during roxarsone degradation under different environmental conditions.}, }
@article {pmid28176768, year = {2017}, author = {Morriën, E and Hannula, SE and Snoek, LB and Helmsing, NR and Zweers, H and de Hollander, M and Soto, RL and Bouffaud, ML and Buée, M and Dimmers, W and Duyts, H and Geisen, S and Girlanda, M and Griffiths, RI and Jørgensen, HB and Jensen, J and Plassart, P and Redecker, D and Schmelz, RM and Schmidt, O and Thomson, BC and Tisserant, E and Uroz, S and Winding, A and Bailey, MJ and Bonkowski, M and Faber, JH and Martin, F and Lemanceau, P and de Boer, W and van Veen, JA and van der Putten, WH}, title = {Soil networks become more connected and take up more carbon as nature restoration progresses.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {14349}, pmid = {28176768}, issn = {2041-1723}, mesh = {Bacteria/metabolism ; *Biomass ; Biota/*physiology ; Carbon/chemistry ; Environmental Restoration and Remediation ; *Food Chain ; Fungi/metabolism ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid- and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered.}, }
@article {pmid28175972, year = {2017}, author = {Plaizier, JC and Li, S and Danscher, AM and Derakshani, H and Andersen, PH and Khafipour, E}, title = {Changes in Microbiota in Rumen Digesta and Feces Due to a Grain-Based Subacute Ruminal Acidosis (SARA) Challenge.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {485-495}, pmid = {28175972}, issn = {1432-184X}, mesh = {Acidosis/microbiology/*veterinary ; *Animal Feed ; Animals ; Cattle ; Cattle Diseases/*microbiology ; Cross-Over Studies ; Diet ; Feces/microbiology ; Female ; Hydrogen-Ion Concentration ; Lactation ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; }, abstract = {The effects of a grain-based subacute ruminal acidosis (SARA) challenge on bacteria in the rumen and feces of lactating dairy cows were determined. Six lactating, rumen-cannulated Danish Holstein cows were used in a cross-over study with two periods. Periods included two cows on a control diet and two cows on a SARA challenge. The control diet was a total mixed ration containing 45.5% dry matter (DM), 43.8% DM neutral detergent fiber, and 19.6% DM starch. The SARA challenge was conducted by gradually substituting the control diet with pellets containing 50% wheat and 50% barley over 3 days to reach a diet containing 55.6% DM, 31.3% DM neutral detergent fiber, and 31.8% DM starch, which was fed for four more days. Rumen fluid samples were collected at day 7 and 10 of experimental periods. Feces samples were collected on days 8 and 10 of these periods. Extracted DNA from the rumen and feces samples was analyzed to assess their bacterial communities using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. The induction of SARA reduced the richness, diversity, and stability of bacterial communities and resulted in distinctly different microbiota in the rumen and feces. Bacteroidetes and Firmicutes were the most abundant phyla and, combined, they represented 76.9 and 94.4% of the bacterial community in the rumen fluid and the feces, respectively. Only the relative abundance of Firmicutes in the rumen was increased by the SARA challenge. In rumen fluid and feces, the abundances of nine out of the 90 and 25 out of the 89 taxa, respectively, were affected by the challenge. Hence, SARA challenge altered the composition of the bacterial community at the lower taxonomical level in the feces and therefore also likely in the hindgut, as well as in the rumen. However, only reductions in the bacterial richness and diversity in the rumen fluid and feces were in agreement with those of other studies and had a biological basis. Although the composition of the bacterial community of the feces was affected by the SARA challenge, bacterial taxa in the feces that can be used for accurate and non-invasive diagnosis of SARA could not be identified.}, }
@article {pmid28174556, year = {2017}, author = {Kumar, M and Brader, G and Sessitsch, A and Mäki, A and van Elsas, JD and Nissinen, R}, title = {Plants Assemble Species Specific Bacterial Communities from Common Core Taxa in Three Arcto-Alpine Climate Zones.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {12}, pmid = {28174556}, issn = {1664-302X}, abstract = {Evidence for the pivotal role of plant-associated bacteria to plant health and productivity has accumulated rapidly in the last years. However, key questions related to what drives plant bacteriomes remain unanswered, among which is the impact of climate zones on plant-associated microbiota. This is particularly true for wild plants in arcto-alpine biomes. Here, we hypothesized that the bacterial communities associated with pioneer plants in these regions have major roles in plant health support, and this is reflected in the formation of climate and host plant specific endophytic communities. We thus compared the bacteriomes associated with the native perennial plants Oxyria digyna and Saxifraga oppositifolia in three arcto-alpine regions (alpine, low Arctic and high Arctic) with those in the corresponding bulk soils. As expected, the bulk soil bacterial communities in the three regions were significantly different. The relative abundances of Proteobacteria decreased progressively from the alpine to the high-arctic soils, whereas those of Actinobacteria increased. The candidate division AD3 and Acidobacteria abounded in the low Arctic soils. Furthermore, plant species and geographic region were the major determinants of the structures of the endophere communities. The plants in the alpine region had higher relative abundances of Proteobacteria, while plants from the low- and high-arctic regions were dominated by Firmicutes. A highly-conserved shared set of ubiquitous bacterial taxa (core bacteriome) was found to occur in the two plant species. Burkholderiales, Actinomycetales and Rhizobiales were the main taxa in this core, and they were also the main contributors to the differences in the endosphere bacterial community structures across compartments as well as regions. We postulate that the composition of this core is driven by selection by the two plants.}, }
@article {pmid28168354, year = {2017}, author = {Xie, XG and Fu, WQ and Zhang, FM and Shi, XM and Zeng, YT and Li, H and Zhang, W and Dai, CC}, title = {The Endophytic Fungus Phomopsis liquidambari Increases Nodulation and N2 Fixation in Arachis hypogaea by Enhancing Hydrogen Peroxide and Nitric Oxide Signalling.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {427-440}, pmid = {28168354}, issn = {1432-184X}, mesh = {Arachis/*microbiology ; Ascomycota/*physiology ; Endophytes/physiology ; Hydrogen Peroxide/metabolism ; Nitric Oxide/metabolism ; *Nitrogen Fixation ; *Plant Root Nodulation ; Symbiosis ; }, abstract = {The continuous cropping obstacles in monoculture fields are a major production constraint for peanuts. Application of the endophytic fungus Phomopsis liquidambari has increased peanut yields, and nodulation and N2 fixation increases have been considered as important factors for P. liquidambari infection-improved peanut yield. However, the mechanisms involved in this process remain unknown. This work showed that compared with only Bradyrhizobium inoculation, co-inoculation with P. liquidambari significantly elevated endogenous H2O2 and NO levels in peanut roots. Pre-treatment of seedlings with specific scavengers of H2O2 (CAT) and NO (cPTIO) blocked P. liquidambari-induced nodulation and N2 fixation. CAT not only suppressed the P. liquidambari-induced nodulation and N2 fixation, but also suppressed the enhanced H2O2 and NO generation. Nevertheless, the cPTIO did not significantly inhibit the induced H2O2 biosynthesis, implying that H2O2 acted upstream of NO production. These results were confirmed by observations that exogenous H2O2 and sodium nitroprusside (SNP) reversed the inhibition of P. liquidambari-increased nodulation and N2 fixation by the specific scavengers. The transcriptional activities of the symbiosis-related genes SymRK and CCaMK of peanut-Bradyrhizobium interactions also increased significantly in response to P. liquidambari, H2O2 and SNP treatments. The pot experiment further confirmed that the P. liquidambari infection-enhanced H2O2 and NO signalling pathways were significantly related to the increase in peanut nodulation and N2 fixation. This is the first report that endophytic fungus P. liquidambari can increase peanut-Bradyrhizobium interactions via enhanced H2O2/NO-dependent signalling crosstalk, which is conducive to the alleviation of continuous cropping obstacles via an increase in nodulation and N2 fixation.}, }
@article {pmid28168224, year = {2017}, author = {Loy, A and Pfann, C and Steinberger, M and Hanson, B and Herp, S and Brugiroux, S and Gomes Neto, JC and Boekschoten, MV and Schwab, C and Urich, T and Ramer-Tait, AE and Rattei, T and Stecher, B and Berry, D}, title = {Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota.}, journal = {mSystems}, volume = {2}, number = {1}, pages = {}, pmid = {28168224}, issn = {2379-5077}, support = {I 2320/FWF_/Austrian Science Fund FWF/Austria ; P 27831/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals and has been suggested to be a pathobiont, a commensal that plays a role in disease. In order to gain insights into its lifestyle, we analyzed the genome and transcriptome of M. schaedleri ASF 457 and performed physiological experiments to test traits predicted by its genome. Although described as a mucus inhabitant, M. schaedleri has limited capacity for degrading host-derived mucosal glycans and other complex polysaccharides. Additionally, M. schaedleri reduces nitrate and expresses systems for scavenging oxygen and reactive oxygen species in vivo, which may account for its localization close to the mucosal tissue and expansion during inflammation. Also of note, M. schaedleri harbors a type VI secretion system and putative effector proteins and can modify gene expression in mucosal tissue, suggesting intimate interactions with its host and a possible role in inflammation. The M. schaedleri genome has been shaped by extensive horizontal gene transfer, primarily from intestinal Epsilon- and Deltaproteobacteria, indicating that horizontal gene transfer has played a key role in defining its niche in the gut ecosystem. IMPORTANCE Shifts in gut microbiota composition have been associated with intestinal inflammation, but it remains unclear whether inflammation-associated bacteria are commensal or detrimental to their host. Here, we studied the lifestyle of the gut bacterium Mucispirillum schaedleri, which is associated with inflammation in widely used mouse models. We found that M. schaedleri has specialized systems to handle oxidative stress during inflammation. Additionally, it expresses secretion systems and effector proteins and can modify the mucosal gene expression of its host. This suggests that M. schaedleri undergoes intimate interactions with its host and may play a role in inflammation. The insights presented here aid our understanding of how commensal gut bacteria may be involved in altering susceptibility to disease.}, }
@article {pmid28168105, year = {2017}, author = {Dimitrov, MR and Veraart, AJ and de Hollander, M and Smidt, H and van Veen, JA and Kuramae, EE}, title = {Successive DNA extractions improve characterization of soil microbial communities.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e2915}, pmid = {28168105}, issn = {2167-8359}, abstract = {Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1-374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition.}, }
@article {pmid28167944, year = {2017}, author = {Rodríguez-Carrio, J and López, P and Sánchez, B and González, S and Gueimonde, M and Margolles, A and de Los Reyes-Gavilán, CG and Suárez, A}, title = {Intestinal Dysbiosis Is Associated with Altered Short-Chain Fatty Acids and Serum-Free Fatty Acids in Systemic Lupus Erythematosus.}, journal = {Frontiers in immunology}, volume = {8}, number = {}, pages = {23}, pmid = {28167944}, issn = {1664-3224}, abstract = {Metabolic impairments are a frequent hallmark of systemic lupus erythematosus (SLE). Increased serum levels of free fatty acids (FFA) are commonly found in these patients, although the underlying causes remain elusive. Recently, it has been suggested that factors other than inflammation or clinical features may be involved. The gut microbiota is known to influence the host metabolism, the production of short-chain fatty acids (SCFA) playing a potential role. Taking into account that lupus patients exhibit an intestinal dysbiosis, we wondered whether altered FFA levels may be associated with the intestinal microbial composition in lupus patients. To this aim, total and specific serum FFA levels, fecal SCFA levels, and gut microbiota composition were determined in 21 SLE patients and 25 healthy individuals. The Firmicutes to Bacteroidetes (F/B) ratio was strongly associated with serum FFA levels in healthy controls (HC), even after controlling for confounders. However, this association was not found in lupus patients, where a decreased F/B ratio and increased FFA serum levels were noted. An altered production of SCFA was related to the intestinal dysbiosis in lupus, while SCFA levels paralleled those of serum FFA in HC. Although a different serum FFA profile was not found in SLE, specific FFA showed distinct patterns on a principal component analysis. Immunomodulatory omega-3 FFA were positively correlated to the F/B ratio in HC, but not in SLE. Furthermore, divergent associations were observed for pro- and anti-inflammatory FFA with endothelial activation biomarkers in lupus patients. Overall, these findings support a link between the gut microbial ecology and the host metabolism in the pathological framework of SLE. A potential link between intestinal dysbiosis and surrogate markers of endothelial activation in lupus patients is supported, FFA species having a pivotal role.}, }
@article {pmid28167930, year = {2016}, author = {Colangelo-Lillis, J and Wing, BA and Raymond-Bouchard, I and Whyte, LG}, title = {Viral Induced Microbial Mortality in Arctic Hypersaline Spring Sediments.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {2158}, pmid = {28167930}, issn = {1664-302X}, abstract = {Viruses are a primary influence on microbial mortality in the global ocean. The impacts of viruses on their microbial hosts in low-energy environments are poorly explored and are the focus of this study. To investigate the role of viruses in mediating mortality in low-energy environments where contacts between viruses and microbes are infrequent, we conducted a set of in situ time series incubations in the outlet and channel sediments of two cold, hypersaline springs of the Canadian High Arctic. We found microbial and viral populations in dynamic equilibrium, indicating approximately equal birth and death rates for each population. In situ rates of microbial growth were low (0.5-50 × 10[3] cells cm[-3] h[-1]) as were rates of viral decay (0.09-170 × 10[4] virions cm[-3] h[-1]). A large fraction of the springs' viral communities (49-100%) were refractory to decay over the timescales of our experiments. Microcosms amended with lactate or acetate exhibited increased microbial growth rates (up to three-fold) indicating organic carbon as one limiting resource for the microbial communities in these environments. A substantial fraction (15-71%) of the microbial populations contained inducible proviruses that were released- occasionally in multiple pulses- over the eight monitored days following chemical induction. Our findings indicate that viruses in low-energy systems maintain low rates of production and activity, have a small but notable impact on microbial mortality (8-29% attenuation of growth) and that successful viral replication may primarily proceed by non-lethal strategies. In cold, low biomass marine systems of similar character (e.g., subsurface sediments), viruses may be a relatively minor driver of community mortality compared to less energy-limited environments such as the marine water column or surface sediments.}, }
@article {pmid28166218, year = {2017}, author = {Karwacz, K and Miraldi, ER and Pokrovskii, M and Madi, A and Yosef, N and Wortman, I and Chen, X and Watters, A and Carriero, N and Awasthi, A and Regev, A and Bonneau, R and Littman, D and Kuchroo, VK}, title = {Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation.}, journal = {Nature immunology}, volume = {18}, number = {4}, pages = {412-421}, pmid = {28166218}, issn = {1529-2916}, support = {R01 NS030843/NS/NINDS NIH HHS/United States ; P30 CA093373/CA/NCI NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; R01 GM112192/GM/NIGMS NIH HHS/United States ; P01 AI056299/AI/NIAID NIH HHS/United States ; R01 NS045937/NS/NINDS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; P30 CA014051/CA/NCI NIH HHS/United States ; P01 NS076410/NS/NINDS NIH HHS/United States ; P01 AI039671/AI/NIAID NIH HHS/United States ; R01 DK103358/DK/NIDDK NIH HHS/United States ; T32 AI100853/AI/NIAID NIH HHS/United States ; P01 AI073748/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Autoimmune Diseases/genetics/immunology/metabolism ; Autoimmunity ; Basic-Leucine Zipper Transcription Factors/genetics/*metabolism ; Cell Differentiation/genetics/*immunology ; Chromatin/genetics/*metabolism ; Cluster Analysis ; Cytokines/metabolism/pharmacology ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Regulatory Networks ; Interferon Regulatory Factor-1/genetics/*metabolism ; Mice ; Mice, Knockout ; Promoter Regions, Genetic ; T-Lymphocyte Subsets/drug effects/immunology/metabolism ; T-Lymphocytes, Regulatory/cytology/drug effects/*immunology/*metabolism ; Transcription Factors/metabolism ; Transcriptome ; }, abstract = {Type 1 regulatory T cells (Tr1 cells) are induced by interleukin-27 (IL-27) and have critical roles in the control of autoimmunity and resolution of inflammation. We found that the transcription factors IRF1 and BATF were induced early on after treatment with IL-27 and were required for the differentiation and function of Tr1 cells in vitro and in vivo. Epigenetic and transcriptional analyses revealed that both transcription factors influenced chromatin accessibility and expression of the genes required for Tr1 cell function. IRF1 and BATF deficiencies uniquely altered the chromatin landscape, suggesting that these factors serve a pioneering function during Tr1 cell differentiation.}, }
@article {pmid28163780, year = {2017}, author = {Scoma, A and Coma, M and Kerckhof, FM and Boon, N and Rabaey, K}, title = {Efficient molasses fermentation under high salinity by inocula of marine and terrestrial origin.}, journal = {Biotechnology for biofuels}, volume = {10}, number = {}, pages = {23}, pmid = {28163780}, issn = {1754-6834}, abstract = {BACKGROUND: Molasses is a dense and saline by-product of the sugar agroindustry. Its high organic content potentially fuels a myriad of renewable products of industrial interest. However, the biotechnological exploitation of molasses is mainly hampered by the high concentration of salts, an issue that is nowadays tackled through dilution. In the present study, the performance of microbial communities derived from marine sediment was compared to that of communities from a terrestrial environment (anaerobic digester sludge). The aim was to test whether adaptation to salinity represented an advantage for fermenting molasses into renewable chemicals such as volatile fatty acids (VFAs) although high sugar concentrations are uncommon to marine sediment, contrary to anaerobic digesters.<br><br>RESULTS: Terrestrial and marine microbial communities were enriched in consecutive batches at different initial pH values (pHi; either 6 or 7) and molasses dilutions (equivalent to organic loading rates (OLRs) of 1 or 5&#xa0;gCOD&#xa0;L[-1]&#xa0;d[-1]) to determine the best VFA production conditions. Marine communities were supplied with NaCl to maintain their native salinity. Due to molasses inherent salinity, terrestrial communities experienced conditions comparable to brackish or saline waters (20-47&#xa0;mS&#xa0;cm[-1]), while marine conditions resembled brine waters (>47&#xa0;mS&#xa0;cm[-1]). Enrichments at optimal conditions of OLR 5&#xa0;gCOD L[-1]&#xa0;d[-1] and pHi 7 were transferred into packed-bed biofilm reactors operated continuously. The reactors were first operated at 5 gCOD L[-1]&#xa0;d[-1], which was later increased to OLR 10&#xa0;gCOD&#xa0;L[-1]&#xa0;d[-1]. Terrestrial and marine reactors had different gas production and community structures but identical, remarkably high VFA bioconversion yields (above 85%) which were obtained with conductivities up to 90&#xa0;mS&#xa0;cm[-1]. COD-to-VFA conversion rates were comparable to the highest reported in literature while processing other organic leftovers at much lower salinities.<br><br>CONCLUSIONS: Although salinity represents a major driver for microbial community structure, proper acclimation yielded highly efficient systems treating molasses, irrespective of the inoculum origin. Selection of equivalent pathways in communities derived from different environments suggests that culture conditions select for specific functionalities rather than microbial representatives. Mass balances, microbial community composition, and biochemical analysis indicate that biomass turnover rather than methanogenesis represents the main limitation to further increasing VFA production with molasses. This information is relevant to moving towards molasses fermentation to industrial application.}, }
@article {pmid28160057, year = {2017}, author = {Dos-Santos, CM and de Souza, DG and Balsanelli, E and Cruz, LM and de Souza, EM and Baldani, JI and Schwab, S}, title = {A Culture-Independent Approach to Enrich Endophytic Bacterial Cells from Sugarcane Stems for Community Characterization.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {453-465}, pmid = {28160057}, issn = {1432-184X}, mesh = {Bacteria/*classification ; Bacteriological Techniques ; Endophytes/classification ; *Phylogeny ; Saccharum/*microbiology ; }, abstract = {Bacterial endophytes constitute a very diverse community and they confer important benefits which help to improve agricultural yield. Some of these benefits remain underexplored or little understood, mainly due to the bottlenecks associated with the plant feature, a low number of endophytic bacterial cells in relation to the plant, and difficulties in accessing these bacteria using cultivation-independent methods. Enriching endophytic bacterial cells from plant tissues, based on a non-biased, cultivation-independent physical enrichment method, may help to circumvent those problems, especially in the case of sugarcane stems, which have a high degree of interfering factors, such as polysaccharides, phenolic compounds, nucleases, and fibers. In the present study, an enrichment approach for endophytic bacterial cells from sugarcane lower stems is described. The results demonstrate that the enriched bacterial cells are suitable for endophytic community characterization. A community analysis revealed the presence of previously well-described but also novel endophytic bacteria in sugarcane tissues which may exert functions such as plant growth promotion and biological control, with a predominance of the Proteobacterial phylum, but also Actinobacteria, Bacteroidetes, and Firmicutes, among others. In addition, by comparing the present and literature data, it was possible to list the most frequently detected bacterial endophyte genera in sugarcane tissues. The presented enrichment approach paves the way for improved future research toward the assessment of endophytic bacterial community in sugarcane and other biofuel crops.}, }
@article {pmid28160056, year = {2017}, author = {Nuskern, L and Tkalec, M and Ježić, M and Katanić, Z and Krstin, L and Ćurković-Perica, M}, title = {Cryphonectria hypovirus 1-Induced Changes of Stress Enzyme Activity in Transfected Phytopathogenic Fungus Cryphonectria parasitica.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {302-311}, pmid = {28160056}, issn = {1432-184X}, mesh = {Aesculus/microbiology ; Ascomycota/*enzymology/pathogenicity/*virology ; *Oxidative Stress ; Plant Diseases/microbiology ; Proteome ; RNA Viruses/*pathogenicity ; Transcriptome ; }, abstract = {Cryphonectria parasitica is a phytopathogenic fungus introduced from Eastern Asia to North America and to Europe, where it causes chestnut blight, a devastating disease of chestnut trees. The disease can be biologically controlled utilising the mycovirus Cryphonectria hypovirus 1 (CHV1), which changes the physiology of the host, reducing its virulence towards chestnut. We measured fungal growth in vitro and activities of glutathione S-transferase, catalase and superoxide dismutase, enzymes involved in oxidative stress response, to elucidate the effects of CHV1 infection on the host. Six CHV1 strains of different subtypes and three fungal isolates were used in different combinations to better represent natural conditions, where higher genetic diversity of both fungus and virus is expected. The infection with different CHV1 strains decreased in vitro growth rate of infected fungal isolates and increased activity of their stress enzymes in most of the studied fungus/virus combinations, indicating increased oxidative stress following CHV1 infection. All our field CHV1 strains belong to the Italian subtype, but while strain M56-1 had equal or even stronger effect on its fungal host than prototypic strain EP713 of French subtype F1, strain B11 had no effect. Thus, the severity of the observed effects depended on a particular virus strain, fungal isolate, and the combination of the two, rather than solely on the virus subtype. Since previous research showed discordance between accumulation of mRNA and stress-related proteins in CHV1 infected C. parasitica, our results emphasise the importance of enzymes' activity measurements as an invaluable extension of transcriptomic and proteomic analyses.}, }
@article {pmid28159795, year = {2017}, author = {Lipus, D and Vikram, A and Ross, D and Bain, D and Gulliver, D and Hammack, R and Bibby, K}, title = {Predominance and Metabolic Potential of Halanaerobium spp. in Produced Water from Hydraulically Fractured Marcellus Shale Wells.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {8}, pages = {}, pmid = {28159795}, issn = {1098-5336}, mesh = {Biofouling ; Firmicutes/genetics/isolation &amp; purification/*metabolism ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways ; Metagenome ; *Microbial Consortia ; Oil and Gas Fields/*microbiology ; Pennsylvania ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Wastewater/*microbiology ; }, abstract = {Microbial activity in the produced water from hydraulically fractured oil and gas wells may potentially interfere with hydrocarbon production and cause damage to the well and surface infrastructure via corrosion, sulfide release, and fouling. In this study, we surveyed the microbial abundance and community structure of produced water sampled from 42 Marcellus Shale wells in southwestern Pennsylvania (well age ranged from 150 to 1,846 days) to better understand the microbial diversity of produced water. We sequenced the V4 region of the 16S rRNA gene to assess taxonomy and utilized quantitative PCR (qPCR) to evaluate the microbial abundance across all 42 produced water samples. Bacteria of the order Halanaerobiales were found to be the most abundant organisms in the majority of the produced water samples, emphasizing their previously suggested role in hydraulic fracturing-related microbial activity. Statistical analyses identified correlations between well age and biocide formulation and the microbial community, in particular, the relative abundance of Halanaerobiales We further investigated the role of members of the order Halanaerobiales in produced water by reconstructing and annotating a Halanaerobium draft genome (named MDAL1), using shotgun metagenomic sequencing and metagenomic binning. The recovered draft genome was found to be closely related to the species H. congolense, an oil field isolate, and Halanaerobium sp. strain T82-1, also recovered from hydraulic fracturing produced water. Reconstruction of metabolic pathways revealed Halanaerobium sp. strain MDAL1 to have the potential for acid production, thiosulfate reduction, and biofilm formation, suggesting it to have the ability to contribute to corrosion, souring, and biofouling events in the hydraulic fracturing infrastructure.IMPORTANCE There are an estimated 15,000 unconventional gas wells in the Marcellus Shale region, each generating up to 8,000 liters of hypersaline produced water per day throughout its lifetime (K. Gregory, R. Vidic, and D. Dzombak, Elements 7:181-186, 2011, https://doi.org/10.2113/gselements.7.3.181; J. Arthur, B. Bohm, and M. Layne, Gulf Coast Assoc Geol Soc Trans 59:49-59, 2009; https://www.marcellusgas.org/index.php). Microbial activity in produced waters could lead to issues with corrosion, fouling, and souring, potentially interfering with hydraulic fracturing operations. Previous studies have found microorganisms contributing to corrosion, fouling, and souring to be abundant across produced water samples from hydraulically fractured wells; however, these findings were based on a limited number of samples and well sites. In this study, we investigated the microbial community structure in produced water samples from 42 unconventional Marcellus Shale wells, confirming the dominance of the genus Halanaerobium in produced water and its metabolic potential for acid and sulfide production and biofilm formation.}, }
@article {pmid28155666, year = {2016}, author = {Xie, C and Goi, CL and Huson, DH and Little, PF and Williams, RB}, title = {RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys.}, journal = {BMC bioinformatics}, volume = {17}, number = {Suppl 19}, pages = {508}, pmid = {28155666}, issn = {1471-2105}, mesh = {Bacteria/*genetics ; Computational Biology/methods ; DNA, Ribosomal/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Metagenome ; Metagenomics ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA/*methods ; *Software ; *Transcriptome ; }, abstract = {BACKGROUND: Taxonomic profiling of microbial communities is often performed using small subunit ribosomal RNA (SSU) amplicon sequencing (16S or 18S), while environmental shotgun sequencing is often focused on functional analysis. Large shotgun datasets contain a significant number of SSU sequences and these can be exploited to perform an unbiased SSU--based taxonomic analysis.<br><br>RESULTS: Here we present a new program called RiboTagger that identifies and extracts taxonomically informative ribotags located in a specified variable region of the SSU gene in a high-throughput fashion.<br><br>CONCLUSIONS: RiboTagger permits fast recovery of SSU-RNA sequences from shotgun nucleic acid surveys of complex microbial communities. The program targets all three domains of life, exhibits high sensitivity and specificity and is substantially faster than comparable programs.}, }
@article {pmid28154556, year = {2017}, author = {Amado, AM and Roland, F}, title = {Editorial: Microbial Role in the Carbon Cycle in Tropical Inland Aquatic Ecosystems.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {20}, pmid = {28154556}, issn = {1664-302X}, }
@article {pmid28153886, year = {2017}, author = {Wang, G and Barrett, NH and McCarthy, PJ}, title = {Draft Genome Sequence of Deep-Sea Alteromonas sp. Strain V450 Isolated from the Marine Sponge Leiodermatium sp.}, journal = {Genome announcements}, volume = {5}, number = {5}, pages = {}, pmid = {28153886}, issn = {2169-8287}, support = {R21 CA209189/CA/NCI NIH HHS/United States ; }, abstract = {The proteobacterium Alteromonas sp. strain V450 was isolated from the Atlantic deep-sea sponge Leiodermatium sp. Here, we report the draft genome sequence of this strain, with a genome size of approx. 4.39 Mb and a G+C content of 44.01%. The results will aid deep-sea microbial ecology, evolution, and sponge-microbe association studies.}, }
@article {pmid28151030, year = {2017}, author = {Simonin, M and Martins, JM and Le Roux, X and Uzu, G and Calas, A and Richaume, A}, title = {Toxicity of TiO2 nanoparticles on soil nitrification at environmentally relevant concentrations: Lack of classical dose-response relationships.}, journal = {Nanotoxicology}, volume = {11}, number = {2}, pages = {247-255}, doi = {10.1080/17435390.2017.1290845}, pmid = {28151030}, issn = {1743-5404}, mesh = {Ammonia/analysis ; Archaea/drug effects ; Dose-Response Relationship, Drug ; Nanoparticles/chemistry/*toxicity ; Nitrification ; Nitrobacter/drug effects ; Oxidation-Reduction ; Soil/*chemistry ; *Soil Microbiology/standards ; Titanium/chemistry/*toxicity ; }, abstract = {Titanium-dioxide nanoparticles (TiO2-NPs) are increasingly released in agricultural soils through, e.g. biosolids, irrigation or nanoagrochemicals. Soils are submitted to a wide range of concentrations of TiO2-NPs depending on the type of exposure. However, most studies have assessed the effects of unrealistically high concentrations, and the dose-response relationships are not well characterized for soil microbial communities. Here, using soil microcosms, we assessed the impact of TiO2-NPs at concentrations ranging from 0.05 to 500 mg kg[-1 ]dry-soil, on the activity and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizing bacteria (Nitrobacter and Nitrospira). In addition, aggregation and oxidative potential of TiO2-NPs were measured in the spiking suspensions, as they can be important drivers of TiO2-NPs toxicity. After 90 days of exposure, non-classical dose-response relationships were observed for nitrifier abundance or activity, making threshold concentrations impossible to compute. Indeed, AOA abundance was reduced by 40% by TiO2-NPs whatever the concentration, while Nitrospira was never affected. Moreover, AOB and Nitrobacter abundances were decreased mainly at intermediate concentrations nitrification was reduced by 25% at the lowest (0.05 mg kg[-1]) and the highest (100 and 500 mg kg[-1]) TiO2-NPs concentrations. Path analyses indicated that TiO2-NPs affected nitrification through an effect on the specific activity of nitrifiers, in addition to indirect effects on nitrifier abundances. Altogether these results point out the need to include very low concentrations of NPs in soil toxicological studies, and the lack of relevance of classical dose-response tests and ecotoxicological dose metrics (EC50, IC50…) for TiO2-NPs impact on soil microorganisms.}, }
@article {pmid28150014, year = {2017}, author = {Huwyler, C and Heiniger, N and Chomel, BB and Kim, M and Kasten, RW and Koehler, JE}, title = {Dynamics of Co-Infection with Bartonella henselae Genotypes I and II in Naturally Infected Cats: Implications for Feline Vaccine Development.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {474-484}, pmid = {28150014}, issn = {1432-184X}, support = {U54 AI065359/AI/NIAID NIH HHS/United States ; R01 AI103299/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bartonella Infections/*veterinary ; Bartonella henselae/*classification ; Cats/*microbiology ; Coinfection/*microbiology ; Genotype ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bartonella henselae is an emerging bacterial pathogen causing cat-scratch disease and potentially fatal bacillary angiomatosis in humans. Bacteremic cats constitute a large reservoir for human infection. Although feline vaccination is a potential strategy to prevent human infection, selection of appropriate B. henselae strains is critical for successful vaccine development. Two distinct genotypes of B. henselae (type I, type II) have been identified and are known to co-infect the feline host, but very little is known about the interaction of these two genotypes during co-infection in vivo. To study the in vivo dynamics of type I and type II co-infection, we evaluated three kittens that were naturally flea-infected with both B. henselae type I and type II. Fifty individual bloodstream isolates from each of the cats over multiple time points were molecularly typed (by 16S rRNA gene sequencing), to determine the prevalence of the two genotypes over 2 years of persistent infection. We found that both B. henselae genotypes were transmitted simultaneously to each cat via natural flea infestation, resulting in mixed infection with both genotypes. Although the initial infection was predominately type I, after the first 2 months, the isolated genotype shifted to exclusively type II, which then persisted with a relapsing pattern. Understanding the parameters of protection against both genotypes of B. henselae, and the competitive dynamics in vivo between the two genotypes, will be critical in the development of a successful feline vaccine that can ultimately prevent B. henselae transmission to human contacts.}, }
@article {pmid28147296, year = {2017}, author = {Bednařík, A and Blaser, M and Matoušů, A and Hekera, P and Rulík, M}, title = {Effect of weir impoundments on methane dynamics in a river.}, journal = {The Science of the total environment}, volume = {584-585}, number = {}, pages = {164-174}, doi = {10.1016/j.scitotenv.2017.01.163}, pmid = {28147296}, issn = {1879-1026}, abstract = {We measured CH4 concentration, CH4 oxidation in the water column and total CH4 emissions to the atmosphere (diffusion and ebullition) in three weir impoundments and river reaches between them, in order to understand their role in river methane (CH4) dynamics. Sediment samples were also collected to determine CH4 consumption and production potentials together with the contribution of individual methanogenic pathways. The CH4 surface water concentration increased 7.5 times in the 16km long river stretch. Microbial CH4 oxidation in the water column reached values ranging from 51 to 403nmoll[-1]d[-1] and substantially contributed to the CH4 removal from surface water, together with CH4 emissions. The total CH4 emissions to the atmosphere varied between 0.8 and 207.1mmolCH4m[-2]d[-1] with the highest values observed upstream of the weirs (mean 68.5±29.9mmolCH4m[-2]d[-1]). Most of the CH4 was transported through the air-water interface by ebullition upstream of the weirs, while the ebullition accounted for 95.8±2.0% of the total CH4 emissions. Both CH4 production and oxidation potential of sediments were higher upstream of the weirs compared to downstream of the weirs. The contribution of hydrogenotrophic methanogenesis to total CH4 sediment production was 36.7-89.4% and prevailed upstream of the weirs. Our findings indicate that weirs might influence river CH4 dynamics, especially by increased CH4 production and consumption by sediments, followed by increasing CH4 emissions to the atmosphere.}, }
@article {pmid28144700, year = {2017}, author = {Cerqueira, T and Pinho, D and Froufe, H and Santos, RS and Bettencourt, R and Egas, C}, title = {Sediment Microbial Diversity of Three Deep-Sea Hydrothermal Vents Southwest of the Azores.}, journal = {Microbial ecology}, volume = {74}, number = {2}, pages = {332-349}, pmid = {28144700}, issn = {1432-184X}, mesh = {Archaea/*classification ; Atlantic Ocean ; Azores ; Bacteria/*classification ; Eukaryota/*classification ; Geologic Sediments/*microbiology ; Hydrothermal Vents/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Menez Gwen, Lucky Strike and Rainbow are the three most visited and well-known deep-sea hydrothermal vent fields in the Azores region, located in the Mid-Atlantic Ridge. Their distinct geological and ecological features allow them to support a diversity of vent communities, which are largely dependent on Bacteria and Archaea capable of anaerobic or microaerophilic metabolism. These communities play important ecological roles through chemoautotrophy, feeding and in establishing symbiotic associations. However, the occurrence and distribution of these microbes remain poorly understood, especially in deep-sea sediments. In this study, we provide for the first time a comparative survey of the sediment-associated microbial communities from these three neighbouring vent fields. Sediment samples collected in the Menez Gwen, Lucky Strike and Rainbow vent fields showed significant differences in trace-metal concentrations and associated microbiomes. The taxonomic profiles of bacterial, archaeal and eukaryotic representatives were assessed by rRNA gene-tag pyrosequencing, identified anaerobic methanogens and microaerobic Epsilonproteobacteria, particularly at the Menez Gwen site, suggesting sediment communities potentially enriched in sub-seafloor microbes rather than from pelagic microbial taxa. Cosmopolitan OTUs were also detected mostly at Lucky Strike and Rainbow sites and affiliated with the bacterial clades JTB255, Sh765B-TzT-29, Rhodospirillaceae and OCS155 marine group and with the archaeal Marine Group I. Some variations in the community composition along the sediment depth were revealed. Elemental contents and hydrothermal influence are suggested as being reflected in the composition of the microbial assemblages in the sediments of the three vent fields. Altogether, these findings represent valuable information for the understanding of the microbial distribution and potential ecological roles in deep-sea hydrothermal fields.}, }
@article {pmid28144631, year = {2017}, author = {Asnicar, F and Manara, S and Zolfo, M and Truong, DT and Scholz, M and Armanini, F and Ferretti, P and Gorfer, V and Pedrotti, A and Tett, A and Segata, N}, title = {Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling.}, journal = {mSystems}, volume = {2}, number = {1}, pages = {}, pmid = {28144631}, issn = {2379-5077}, abstract = {The gut microbiome becomes shaped in the first days of life and continues to increase its diversity during the first months. Links between the configuration of the infant gut microbiome and infant health are being shown, but a comprehensive strain-level assessment of microbes vertically transmitted from mother to infant is still missing. We collected fecal and breast milk samples from multiple mother-infant pairs during the first year of life and applied shotgun metagenomic sequencing followed by computational strain-level profiling. We observed that several specific strains, including those of Bifidobacterium bifidum, Coprococcus comes, and Ruminococcus bromii, were present in samples from the same mother-infant pair, while being clearly distinct from those carried by other pairs, which is indicative of vertical transmission. We further applied metatranscriptomics to study the in vivo gene expression of vertically transmitted microbes and found that transmitted strains of Bacteroides and Bifidobacterium species were transcriptionally active in the guts of both adult and infant. By combining longitudinal microbiome sampling and newly developed computational tools for strain-level microbiome analysis, we demonstrated that it is possible to track the vertical transmission of microbial strains from mother to infants and to characterize their transcriptional activity. Our work provides the foundation for larger-scale surveys to identify the routes of vertical microbial transmission and its influence on postinfancy microbiome development. IMPORTANCE Early infant exposure is important in the acquisition and ultimate development of a healthy infant microbiome. There is increasing support for the idea that the maternal microbial reservoir is a key route of microbial transmission, and yet much is inferred from the observation of shared species in mother and infant. The presence of common species, per se, does not necessarily equate to vertical transmission, as species exhibit considerable strain heterogeneity. It is therefore imperative to assess whether shared microbes belong to the same genetic variant (i.e., strain) to support the hypothesis of vertical transmission. Here we demonstrate the potential of shotgun metagenomics and strain-level profiling to identify vertical transmission events. Combining these data with metatranscriptomics, we show that it is possible not only to identify and track the fate of microbes in the early infant microbiome but also to investigate the actively transcribing members of the community. These approaches will ultimately provide important insights into the acquisition, development, and community dynamics of the infant microbiome.}, }
@article {pmid28141994, year = {2021}, author = {Godoy-Vitorino, F and Rodriguez-Hilario, A and Alves, AL and Gonçalves, F and Cabrera-Colon, B and Mesquita, CS and Soares-Castro, P and Ferreira, M and Marçalo, A and Vingada, J and Eira, C and Santos, PM}, title = {Corrigendum to "The microbiome of a striped dolphin (Stenella coeruleoalba) stranded in Portugal" [Res Microbiol (2017) 85-93].}, journal = {Research in microbiology}, volume = {172}, number = {1}, pages = {103564}, doi = {10.1016/j.resmic.2017.01.003}, pmid = {28141994}, issn = {1769-7123}, }
@article {pmid28138721, year = {2017}, author = {Kleinteich, J and Golubic, S and Pessi, IS and Velázquez, D and Storme, JY and Darchambeau, F and Borges, AV and Compère, P and Radtke, G and Lee, SJ and Javaux, EJ and Wilmotte, A}, title = {Cyanobacterial Contribution to Travertine Deposition in the Hoyoux River System, Belgium.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {33-53}, pmid = {28138721}, issn = {1432-184X}, mesh = {Belgium ; Carbonates/*analysis ; Cyanobacteria/genetics/*metabolism ; DNA, Ribosomal Spacer/genetics ; Europe ; RNA, Ribosomal, 16S/genetics ; *Rivers ; }, abstract = {Travertine deposition is a landscape-forming process, usually building a series of calcareous barriers differentiating the river flow into a series of cascades and ponds. The process of carbonate precipitation is a complex relationship between biogenic and abiotic causative agents, involving adapted microbial assemblages but also requiring high levels of carbonate saturation, spontaneous degassing of carbon dioxide and slightly alkaline pH. We have analysed calcareous crusts and water chemistry from four sampling sites along the Hoyoux River and its Triffoy tributary (Belgium) in winter, spring, summer and autumn 2014. Different surface textures of travertine deposits correlated with particular microenvironments and were influenced by the local water flow. In all microenvironments, we have identified the cyanobacterium Phormidium incrustatum (Nägeli) Gomont as the organism primarily responsible for carbonate precipitation and travertine fabric by combining morphological analysis with molecular sequencing (16S rRNA gene and ITS, the Internal Transcribed Spacer fragments), targeting both field populations and cultures to exclude opportunistic microorganisms responding favourably to culture conditions. Several closely related cyanobacterial strains were cultured; however, only one proved identical with the sequences obtained from the field population by direct PCR. This strain was the dominant primary producer in the calcareous deposits under study and in similar streams in Europe. The dominance of one organism that had a demonstrated association with carbonate precipitation presented a valuable opportunity to study its function in construction, preservation and fossilisation potential of ambient temperature travertine deposits. These relationships were examined using scanning electron microscopy and Raman microspectroscopy.}, }
@article {pmid28130576, year = {2017}, author = {Chen, J and Gu, JD}, title = {Faunal Burrows Alter the Diversity, Abundance, and Structure of AOA, AOB, Anammox and n-Damo Communities in Coastal Mangrove Sediments.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {140-156}, pmid = {28130576}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Ammonium Compounds/metabolism ; Animals ; Archaea/*classification ; Bacteria/*classification ; *Brachyura ; Geologic Sediments/*microbiology ; Hong Kong ; Oxidation-Reduction ; *Phylogeny ; }, abstract = {In the present work, the diversity, community structures, and abundances of aerobic ammonia-oxidizing archaea (AOA) and bacteria (AOB), anaerobic ammonium-oxidizing (anammox) bacteria, and denitrifying anaerobic methane oxidization (n-damo) bacteria were unraveled in the bioturbated areas of the coastal Mai Po mangrove sediments. Results indicated that the bioturbation by burrowing in mangrove sediments was associated with higher concentration of NH4[+] but lower concentrations of both NO2[-] and NO3[-], and increase in diversity and richness of both AOA and AOB, but relatively lower diversity and richness of n-damo bacteria. The phylotypes of anammox bacterial community were significantly increased while their phylogenetic lineages observed in the less bioturbated areas were also maintained. Infauna also showed a great impact on the composition of n-damo bacterial phylotypes and burrowing activity altered the n-damo community structure profoundly in the sampled areas. The communities of n-damo bacteria in the surrounding bulk sediments showed similar structures to marine n-damo communities, but those on the burrow wall and in the ambient surface layer had a freshwater pattern, which was different from previous findings in Mai Po wetland. On the other hand, the abundances of AOA, AOB, and n-damo bacteria were greatly stimulated on burrow walls while the abundance of anammox bacteria remained unchanged. Infaunal burrows and mangrove roots affected the relative abundance of AOA and AOB. The benthic infauna stimulated the abundances of AOA, AOB, anammox, and n-damo bacteria. Furthermore, NH4[+] and NO2[-] were important environmental factors changing the structure of each group. The communities of anammox and n-damo bacteria in bioturbated areas showed a competitive relationship.}, }
@article {pmid28128467, year = {2017}, author = {Slomka, V and Hernandez-Sanabria, E and Herrero, ER and Zaidel, L and Bernaerts, K and Boon, N and Quirynen, M and Teughels, W}, title = {Nutritional stimulation of commensal oral bacteria suppresses pathogens: the prebiotic concept.}, journal = {Journal of clinical periodontology}, volume = {44}, number = {4}, pages = {344-352}, doi = {10.1111/jcpe.12700}, pmid = {28128467}, issn = {1600-051X}, mesh = {*Bacterial Physiological Phenomena ; Humans ; Mouth/*microbiology ; *Oral Health ; *Prebiotics ; *Symbiosis ; }, abstract = {AIM: To identify potential oral prebiotics that selectively stimulate commensal, albeit beneficial bacteria of the resident oral microbial community while suppressing the growth of pathogenic bacteria.<br><br>MATERIAL AND METHODS: Using Phenotype MicroArrays as a high-throughput method, the change in respiratory activity of 16 oral bacteria in response to 742 nutritional compounds was screened. Most promising prebiotic compounds were selected and applied in single species growth and biofilm formation assays, as well as dual species (beneficial-pathogen) competition assays.<br><br>RESULTS: Increased respiratory activity could not always be related to an increase in growth or biofilm formation. Six compounds were used in dual species competition assays to directly monitor if selective nutritional stimulation of the beneficial bacterium results in the suppression of the pathogenic bacterium. Two compounds, beta-methyl-d-galactoside and N-acetyl-d-mannosamine, could be identified as potential oral prebiotic compounds, triggering selectively beneficial oral bacteria throughout the experiments and shifting dual species biofilm communities towards a beneficial dominating composition at in&#xa0;vitro level.<br><br>CONCLUSION: Our observations support the hypothesis that nutritional stimulation of beneficial bacteria by prebiotics could be used to restore the microbial balance in the oral cavity and by this promote oral health.}, }
@article {pmid28127719, year = {2017}, author = {Ferreira de Araujo, AS and Bezerra, WM and Dos Santos, VM and Nunes, LA and de Lyra, MD and do Vale Barreto Figueiredo, M and Melo, VM}, title = {Fungal diversity in soils across a gradient of preserved Brazilian Cerrado.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {55}, number = {4}, pages = {273-279}, pmid = {28127719}, issn = {1976-3794}, mesh = {*Biodiversity ; Brazil ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fungi/*classification/genetics/*isolation &amp; purification ; Genes, rRNA ; Parks, Recreational ; RNA, Fungal/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The preserved Cerrado from Northeastern Brazil presents different physicochemical properties and plant diversity, which can influence the fungal communities. Therefore, we evaluated the fungal diversity in preserved sites, at Sete Cidades National Park, across a gradient of vegetation that included Campo graminoide, Cerrado stricto sensu, Cerradao, and Floresta decidual. Of all of the operational taxonomic units (OTUs) obtained, the Floresta decidual presented the highest richness. Ascomycota were the most abundant phylum (45%), followed by Basidiomycota (32%). Basal fungi and other phyla accounted for 23% of the total dataset. Agaricomycetes, Eurotiomycetes, Lecanoromycetes, Basidiobolus, Dothideomycetes, and Taphrinomycetes were the most abundant classes of fungi found across the gradient of Cerrado vegetation. In conclusion, our study suggests that the Brazilian Cerrado from Sete Cidades National Park presents a high fungal diversity and includes sources of new fungal species for biotechnological purposes.}, }
@article {pmid28126934, year = {2017}, author = {Jiménez, DJ and Hector, RE and Riley, R and Lipzen, A and Kuo, RC and Amirebrahimi, M and Barry, KW and Grigoriev, IV and van Elsas, JD and Nichols, NN}, title = {Draft Genome Sequence of Coniochaeta ligniaria NRRL 30616, a Lignocellulolytic Fungus for Bioabatement of Inhibitors in Plant Biomass Hydrolysates.}, journal = {Genome announcements}, volume = {5}, number = {4}, pages = {}, pmid = {28126934}, issn = {2169-8287}, abstract = {Here, we report the first draft genome sequence (42.38 Mb containing 13,657 genes) of Coniochaeta ligniaria NRRL 30616, an ascomycete with biotechnological relevance in the bioenergy field given its high potential for bioabatement of toxic furanic compounds in plant biomass hydrolysates and its capacity to degrade lignocellulosic material.}, }
@article {pmid28126050, year = {2017}, author = {Cho, GY and Lee, JC and Whang, KS}, title = {Rhodanobacter rhizosphaerae sp. nov., isolated from soil of ginseng rhizosphere.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {67}, number = {5}, pages = {1387-1392}, doi = {10.1099/ijsem.0.001825}, pmid = {28126050}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Nucleic Acid Hybridization ; Panax/*microbiology ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; Ubiquinone/chemistry ; Xanthomonadaceae/*classification/genetics/isolation &amp; purification ; }, abstract = {A Gram-stain-negative, aerobic, non-motile, non-spore-forming, yellow and rod-shaped bacterium, designated strain CR164T, was isolated from the rhizosphere soil of a ginseng field at Geumsan in Korea. CR164T grew at between 15 and 37 °C (optimal growth at 28 °C), between pH 6.0 and 9.0 (optimal growth at pH 7.0) and at salinities of 0-1.0 % (w/v) NaCl, growing optimally in the absence of NaCl. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that CR164T represents a member of the genus Rhodanobacter, showing the highest sequence similarity to Rhodanobactercaeni MJ01T (98.5 %), Rhodanobacter ginsenosidimutans Gsoil 3054T (98.4 %), Rhodanobacter thiooxydans LCS2T (98.3 %), Rhodanobacter lindaniclasticus RP5557T (98.1 %), Rhodanobacter denitrificans 2APBS1T (98.0 %), Rhodanobacter fulvus Jip2T (97.6 %), Rhodanobacter soli DCY45T (97.3 %) and 'Rhodanobacterxiangquanii' BJQ-6 (97.0 %). The major fatty acids were iso-C17 : 1ω9c (21.8 %), iso-C15 : 0 (12.1 %), iso-C11 : 0 (11.9 %) and iso-C16 : 0 (11.1 %). The predominant ubiquinone was Q-8. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The G+C content of the genomic DNA was 62.3 mol%. DNA-DNA relatedness between CR164T and the type strains of eight other species of the genus ranged from 51 to 9 %. On the basis of the polyphasic analysis, CR164T represents a novel species of the genus Rhodanobacter, for which the name Rhodanobacter rhizosphaerae sp. nov. is proposed. The type strain is CR164T (=KACC 18699T=NBRC 111845T).}, }
@article {pmid28124727, year = {2017}, author = {Amato, KR and Van Belle, S and Di Fiore, A and Estrada, A and Stumpf, R and White, B and Nelson, KE and Knight, R and Leigh, SR}, title = {Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {250-258}, pmid = {28124727}, issn = {1432-184X}, mesh = {Alouatta/*microbiology ; Animals ; Female ; *Gastrointestinal Microbiome ; Male ; *Social Behavior ; }, abstract = {Studies of human and domestic animal models indicate that related individuals and those that spend the most time in physical contact typically have more similar gut microbial communities. However, few studies have examined these factors in wild mammals where complex social dynamics and a variety of interacting environmental factors may impact the patterns observed in controlled systems. Here, we explore the effect of host kinship and time spent in social contact on the gut microbiota of wild, black howler monkeys (Alouatta pigra). Our results indicate that closely related individuals had less similar gut microbial communities than non-related individuals. However, the effect was small. In contrast, as previously reported in baboons and chimpanzees, individuals that spent more time in contact (0 m) and close proximity (0-1 m) had more similar gut microbial communities. This pattern was driven by adult female-adult female dyads, which generally spend more time in social contact than adult male-adult male dyads or adult male-adult female dyads. Relative abundances of individual microbial genera such as Bacteroides, Clostridium, and Streptococcus were also more similar in individuals that spent more time in contact or close proximity. Overall, our data suggest that even in arboreal primates that live in small social groups and spend a relatively low proportion of their time in physical contact, social interactions are associated with variation in gut microbiota composition. Additionally, these results demonstrate that within a given host species, subgroups of individuals may interact with the gut microbiota differently.}, }
@article {pmid28124726, year = {2017}, author = {Hernández-Domínguez, C and Guzmán-Franco, AW}, title = {Species Diversity and Population Dynamics of Entomopathogenic Fungal Species in the Genus Metarhizium-a Spatiotemporal Study.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {194-206}, pmid = {28124726}, issn = {1432-184X}, mesh = {Genetics, Population ; Genotype ; Haplotypes ; Metarhizium/*classification ; Microsatellite Repeats ; *Phylogeny ; Saccharum/microbiology ; Soil Microbiology ; Spatio-Temporal Analysis ; }, abstract = {We studied the species diversity and population genetic structure of isolates of fungi from the entomopathogenic genus Metarhizium that had been isolated from sugarcane crops and surrounding grass. Soil and leaf samples were taken on four sampling occasions over 13 months (October 2014-October 2015). Isolations were made using the Galleria mellonella baiting method and selective media. Phylogenetic placement of isolates was done by sequencing a fragment of the 5' of the elongation factor 1-α gene (EF1-α). Population genetic structure was determined by analysing this sequence information using AMOVA and Haplotype network analyses. Genotypic diversity was studied using microsatellite genotyping. The most abundant species was M. anisopliae s.s. (80 isolates), then M. pingshaense (three isolates), and M. guizhouense (one isolate). More than 50% of the genetic variation was explained by the time the samples were collected regardless of plant host association. Some haplotypes were found on the first sampling date and then not found on subsequent sampling dates, while other haplotypes were found initially, disappeared, but then found again on the last sampling date. To the best of our knowledge, this is the first report of the population genetic structure of M. anisopliae species in time and space. The effect of abiotic factors is discussed.}, }
@article {pmid28123098, year = {2017}, author = {Harrison, JP and Angel, R and Cockell, CS}, title = {Astrobiology as a framework for investigating antibiotic susceptibility: a study of Halomonas hydrothermalis.}, journal = {Journal of the Royal Society, Interface}, volume = {14}, number = {126}, pages = {}, pmid = {28123098}, issn = {1742-5662}, mesh = {Anti-Bacterial Agents/*pharmacology ; Drug Resistance, Bacterial/drug effects/*physiology ; *Ecosystem ; Exobiology ; Halomonas/*physiology ; *Salinity ; }, abstract = {Physical and chemical boundaries for microbial multiplication on Earth are strongly influenced by interactions between environmental extremes. However, little is known about how interactions between multiple stress parameters affect the sensitivity of microorganisms to antibiotics. Here, we assessed how 12 distinct permutations of salinity, availability of an essential nutrient (iron) and atmospheric composition (aerobic or microaerobic) affect the susceptibility of a polyextremotolerant bacterium, Halomonas hydrothermalis, to ampicillin, kanamycin and ofloxacin. While salinity had a significant impact on sensitivity to all three antibiotics (as shown by turbidimetric analyses), the nature of this impact was modified by iron availability and the ambient gas composition, with differing effects observed for each compound. These two parameters were found to be of particular importance when considered in combination and, in the case of ampicillin, had a stronger combined influence on antibiotic tolerance than salinity. Our data show how investigating microbial responses to multiple extremes, which are more representative of natural habitats than single extremes, can improve our understanding of the effects of antimicrobial compounds and suggest how studies of habitability, motivated by the desire to map the limits of life, can be used to systematically assess the effectiveness of antibiotics.}, }
@article {pmid28118386, year = {2017}, author = {Philips, J and Rabaey, K and Lovley, DR and Vargas, M}, title = {Biofilm Formation by Clostridium ljungdahlii Is Induced by Sodium Chloride Stress: Experimental Evaluation and Transcriptome Analysis.}, journal = {PloS one}, volume = {12}, number = {1}, pages = {e0170406}, pmid = {28118386}, issn = {1932-6203}, mesh = {Biofilms/*drug effects/growth &amp; development ; Biomass ; Carbon ; Clostridium/*drug effects/genetics/physiology/ultrastructure ; Culture Media ; Culture Techniques/instrumentation ; Fimbriae, Bacterial ; Flagella ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Glass ; Graphite ; Osmotic Pressure ; RNA, Bacterial/genetics ; RNA, Ribosomal/genetics ; Sodium Chloride/*pharmacology ; Spores, Bacterial ; Stress, Physiological ; }, abstract = {The acetogen Clostridium ljungdahlii is capable of syngas fermentation and microbial electrosynthesis. Biofilm formation could benefit both these applications, but was not yet reported for C. ljungdahlii. Biofilm formation does not occur under standard growth conditions, but attachment or aggregation could be induced by different stresses. The strongest biofilm formation was observed with the addition of sodium chloride. After 3 days of incubation, the biomass volume attached to a plastic surface was 20 times higher with than without the addition of 200 mM NaCl to the medium. The addition of NaCl also resulted in biofilm formation on glass, graphite and glassy carbon, the latter two being often used electrode materials for microbial electrosynthesis. Biofilms were composed of extracellular proteins, polysaccharides, as well as DNA, while pilus-like appendages were observed with, but not without, the addition of NaCl. A transcriptome analysis comparing planktonic (no NaCl) and biofilm (NaCl addition) cells showed that C. ljungdahlii coped with the salt stress by the upregulation of the general stress response, Na+ export and osmoprotectant accumulation. A potential role for poly-N-acetylglucosamines and D-alanine in biofilm formation was found. Flagellar motility was downregulated, while putative type IV pili biosynthesis genes were not expressed. Moreover, the gene expression analysis suggested the involvement of the transcriptional regulators LexA, Spo0A and CcpA in stress response and biofilm formation. This study showed that NaCl addition might be a valuable strategy to induce biofilm formation by C. ljungdahlii, which can improve the efficacy of syngas fermentation and microbial electrosynthesis applications.}, }
@article {pmid28117455, year = {2017}, author = {Kielak, AM and Castellane, TC and Campanharo, JC and Colnago, LA and Costa, OY and Corradi da Silva, ML and van Veen, JA and Lemos, EG and Kuramae, EE}, title = {Characterization of novel Acidobacteria exopolysaccharides with potential industrial and ecological applications.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41193}, pmid = {28117455}, issn = {2045-2322}, mesh = {Acidobacteria/*chemistry ; Biopolymers ; Emulsifying Agents/chemistry/isolation &amp; purification ; Emulsions/chemistry ; Monosaccharides/chemistry ; Polysaccharides, Bacterial/*chemistry/*isolation &amp; purification ; Rheology ; Soil Microbiology ; }, abstract = {Acidobacteria have been described as one of the most abundant and ubiquitous bacterial phyla in soil. However, factors contributing to this ecological success are not well elucidated mainly due to difficulties in bacterial isolation. Acidobacteria may be able to survive for long periods in soil due to protection provided by secreted extracellular polymeric substances that include exopolysaccharides (EPSs). Here we present the first study to characterize EPSs derived from two strains of Acidobacteria from subdivision 1 belonging to Granulicella sp. EPS are unique heteropolysaccharides containing mannose, glucose, galactose and xylose as major components, and are modified with carboxyl and methoxyl functional groups that we characterized by Fourier transform infrared (FTIR) spectroscopy. Both EPS compounds we identified can efficiently emulsify various oils (sunflower seed, diesel, and liquid paraffin) and hydrocarbons (toluene and hexane). Moreover, the emulsions are more thermostable over time than those of commercialized xanthan. Acidobacterial EPS can now be explored as a source of biopolymers that may be attractive and valuable for industrial applications due to their natural origin, sustainability, biodegradability and low toxicity.}, }
@article {pmid28116618, year = {2017}, author = {Ayed, L and Asses, N and Chammem, N and Ben Othman, N and Hamdi, M}, title = {Advanced oxidation process and biological treatments for table olive processing wastewaters: constraints and a novel approach to integrated recycling process: a review.}, journal = {Biodegradation}, volume = {28}, number = {2-3}, pages = {125-138}, doi = {10.1007/s10532-017-9782-0}, pmid = {28116618}, issn = {1572-9729}, mesh = {Biodegradation, Environmental ; Olea/*chemistry ; Oxidation-Reduction ; Recycling/*methods ; Waste Disposal, Fluid/methods ; Wastewater/*chemistry ; }, abstract = {Table olive processing wastewaters constitute a dangerous environmental problem in the Mediterranean countries because of their large volumes, high organic matter and salt concentration. The quantity and the characteristics of wastewaters produced, and thus, their environmental impact, varied depending on the season, varieties, soil and process employed. Several chemicals, biological and combined technologies have proven effective at bringing down organic pollution and toxicity of these effluents. Advanced oxidation processes have recognized as highly efficient treatments for the degradation of organic matter. Nonetheless, complete mineralization is generally expensive without salt removal. Biological processes are the most environmentally compatible and least-expensive treatment methods, but these operations do not always provide satisfactory results. This article surveys the current available technologies and suggests an effective, cheaper alternative for the recycling and the valorization of green table olives wastewaters.}, }
@article {pmid28115400, year = {2017}, author = {Ho, A and Di Lonardo, DP and Bodelier, PL}, title = {Revisiting life strategy concepts in environmental microbial ecology.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {3}, pages = {}, doi = {10.1093/femsec/fix006}, pmid = {28115400}, issn = {1574-6941}, mesh = {Animals ; Bacteria/genetics ; *Ecology ; Environment ; *Environmental Microbiology ; Fungi/genetics ; Phenotype ; Phylogeny ; Plants ; }, abstract = {Microorganisms are physiologically diverse, possessing disparate genomic features and mechanisms for adaptation (functional traits), which reflect on their associated life strategies and determine at least to some extent their prevalence and distribution in the environment. Unlike animals and plants, there is an unprecedented diversity and intractable metabolic versatility among bacteria, making classification or grouping these microorganisms based on their functional traits as has been done in animal and plant ecology challenging. Nevertheless, based on representative pure cultures, microbial traits distinguishing different life strategies had been proposed, and had been the focus of previous reviews. In the environment, however, the vast majority of naturally occurring microorganisms have yet to be isolated, restricting the association of life strategies to broad phylogenetic groups and/or physiological characteristics. Here, we reviewed the literature to determine how microbial life strategy concepts (i.e. copio- and oligotrophic strategists, and competitor-stress tolerator-ruderals framework) are applied in complex microbial communities. Because of the scarcity of direct empirical evidence elucidating the associated life strategies in complex communities, we rely heavily on observational studies determining the response of microorganisms to (a)biotic cues (e.g. resource availability) to infer microbial life strategies. Although our focus is on the life strategies of bacteria, parallels were drawn from the fungal community. Our literature search showed inconsistency in the community response of proposed copiotrophic- and oligotrophic-associated microorganisms (phyla level) to changing environmental conditions. This suggests that tracking microorganisms at finer phylogenetic and taxonomic resolution (e.g. family level or lower) may be more effective to capture changes in community response and/or that edaphic factors exert a stronger effect in community response. We discuss the limitations and provide recommendations for future research applying microbial life strategies in environmental studies.}, }
@article {pmid28115375, year = {2017}, author = {Van den Bossche, L and Hindryckx, P and Devisscher, L and Devriese, S and Van Welden, S and Holvoet, T and Vilchez-Vargas, R and Vital, M and Pieper, DH and Vanden Bussche, J and Vanhaecke, L and Van de Wiele, T and De Vos, M and Laukens, D}, title = {Ursodeoxycholic Acid and Its Taurine- or Glycine-Conjugated Species Reduce Colitogenic Dysbiosis and Equally Suppress Experimental Colitis in Mice.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {7}, pages = {}, pmid = {28115375}, issn = {1098-5336}, mesh = {Animals ; Bacteroides/drug effects ; Colon/microbiology ; Dextran Sulfate/administration &amp; dosage ; Disease Models, Animal ; Dysbiosis/*drug therapy ; Feces/microbiology ; Firmicutes/drug effects ; Gastrointestinal Microbiome/*drug effects ; Humans ; Inflammatory Bowel Diseases/*drug therapy ; Mice ; Taurine/chemistry ; Taurochenodeoxycholic Acid/administration &amp; dosage/*therapeutic use ; Ursodeoxycholic Acid/administration &amp; dosage/*analogs &amp; derivatives/chemistry/*therapeutic use ; }, abstract = {The promising results seen in studies of secondary bile acids in experimental colitis suggest that they may represent an attractive and safe class of drugs for the treatment of inflammatory bowel diseases (IBD). However, the exact mechanism by which bile acid therapy confers protection from colitogenesis is currently unknown. Since the gut microbiota plays a crucial role in the pathogenesis of IBD, and exogenous bile acid administration may affect the community structure of the microbiota, we examined the impact of the secondary bile acid ursodeoxycholic acid (UDCA) and its taurine or glycine conjugates on the fecal microbial community structure during experimental colitis. Daily oral administration of UDCA, tauroursodeoxycholic acid (TUDCA), or glycoursodeoxycholic acid (GUDCA) equally lowered the severity of dextran sodium sulfate-induced colitis in mice, as evidenced by reduced body weight loss, colonic shortening, and expression of inflammatory cytokines. Illumina sequencing demonstrated that bile acid therapy during colitis did not restore fecal bacterial richness and diversity. However, bile acid therapy normalized the colitis-associated increased ratio of Firmicutes to Bacteroidetes Interestingly, administration of bile acids prevented the loss of Clostridium cluster XIVa and increased the abundance of Akkermansia muciniphila, bacterial species known to be particularly decreased in IBD patients. We conclude that UDCA, which is an FDA-approved drug for cholestatic liver disorders, could be an attractive treatment option to reduce dysbiosis and ameliorate inflammation in human IBD.IMPORTANCE Secondary bile acids are emerging as attractive candidates for the treatment of inflammatory bowel disease. Although bile acids may affect the intestinal microbial community structure, which significantly contributes to the course of these inflammatory disorders, the impact of bile acid therapy on the fecal microbiota during colitis has not yet been considered. Here, we studied the alterations in the fecal microbial abundance in colitic mice following the administration of secondary bile acids. Our results show that secondary bile acids reduce the severity of colitis and ameliorate colitis-associated fecal dysbiosis at the phylum level. This study indicates that secondary bile acids might act as a safe and effective drug for inflammatory bowel disease.}, }
@article {pmid28111899, year = {2017}, author = {Buchkowski, RW and Bradford, MA and Grandy, AS and Schmitz, OJ and Wieder, WR}, title = {Applying population and community ecology theory to advance understanding of belowground biogeochemistry.}, journal = {Ecology letters}, volume = {20}, number = {2}, pages = {231-245}, doi = {10.1111/ele.12712}, pmid = {28111899}, issn = {1461-0248}, mesh = {*Biomass ; Biota ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Approaches to quantifying and predicting soil biogeochemical cycles mostly consider microbial biomass and community composition as products of the abiotic environment. Current numerical approaches then primarily emphasise the importance of microbe-environment interactions and physiology as controls on biogeochemical cycles. Decidedly less attention has been paid to understanding control exerted by community dynamics and biotic interactions. Yet a rich literature of theoretical and empirical contributions highlights the importance of considering how variation in microbial population ecology, especially biotic interactions, is related to variation in key biogeochemical processes like soil carbon formation. We demonstrate how a population and community ecology perspective can be used to (1) understand the impact of microbial communities on biogeochemical cycles and (2) reframe current theory and models to include more detailed microbial ecology. Through a series of simulations we illustrate how density dependence and key biotic interactions, such as competition and predation, can determine the degree to which microbes regulate soil biogeochemical cycles. The ecological perspective and model simulations we present lay the foundation for developing empirical research and complementary models that explore the diversity of ecological mechanisms that operate in microbial communities to regulate biogeochemical processes.}, }
@article {pmid28111574, year = {2016}, author = {Turroni, F and Berry, D and Ventura, M}, title = {Editorial: Bifidobacteria and Their Role in the Human Gut Microbiota.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {2148}, pmid = {28111574}, issn = {1664-302X}, }
@article {pmid28111573, year = {2016}, author = {Muziasari, WI and Pitkänen, LK and Sørum, H and Stedtfeld, RD and Tiedje, JM and Virta, M}, title = {The Resistome of Farmed Fish Feces Contributes to the Enrichment of Antibiotic Resistance Genes in Sediments below Baltic Sea Fish Farms.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {2137}, pmid = {28111573}, issn = {1664-302X}, abstract = {Our previous studies showed that particular antibiotic resistance genes (ARGs) were enriched locally in sediments below fish farms in the Northern Baltic Sea, Finland, even when the selection pressure from antibiotics was negligible. We assumed that a constant influx of farmed fish feces could be the plausible source of the ARGs enriched in the farm sediments. In the present study, we analyzed the composition of the antibiotic resistome from the intestinal contents of 20 fish from the Baltic Sea farms. We used a high-throughput method, WaferGen qPCR array with 364 primer sets to detect and quantify ARGs, mobile genetic elements (MGE), and the 16S rRNA gene. Despite a considerably wide selection of qPCR primer sets, only 28 genes were detected in the intestinal contents. The detected genes were ARGs encoding resistance to sulfonamide (sul1), trimethoprim (dfrA1), tetracycline [tet(32), tetM, tetO, tetW], aminoglycoside (aadA1, aadA2), chloramphenicol (catA1), and efflux-pumps resistance genes (emrB, matA, mefA, msrA). The detected genes also included class 1 integron-associated genes (intI1, qacEΔ1) and transposases (tnpA). Importantly, most of the detected genes were the same genes enriched in the farm sediments. This preliminary study suggests that feces from farmed fish contribute to the ARG enrichment in farm sediments despite the lack of contemporaneous antibiotic treatments at the farms. We observed that the intestinal contents of individual farmed fish had their own resistome compositions. Our result also showed that the total relative abundances of transposases and tet genes were significantly correlated (p = 0.001, R[2] = 0.71). In addition, we analyzed the mucosal skin and gill filament resistomes of the farmed fish but only one multidrug-efflux resistance gene (emrB) was detected. To our knowledge, this is the first study reporting the resistome of farmed fish using a culture-independent method. Determining the possible sources of ARGs, especially mobilized ARGs, is essential for controlling the occurrence and spread of ARGs at fish farming facilities and for lowering the risk of ARG spread from the farms to surrounding environments.}, }
@article {pmid28108759, year = {2017}, author = {Aizenberg-Gershtein, Y and Izhaki, I and Halpern, M}, title = {From Microhabitat of Floral Nectar Up to Biogeographic Scale: Novel Insights on Neutral and Niche Bacterial Assemblies.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {128-139}, pmid = {28108759}, issn = {1432-184X}, mesh = {Bacteria/*classification ; *Biodiversity ; Israel ; *Plant Nectar ; Nicotiana/*microbiology ; }, abstract = {Microbial model systems are very useful in addressing macro-ecological questions. Two major theories exist to date, to explain the community structure of organisms: (1) the dispersal (neutral) assembly theory which predicts that community similarity decreases with increasing geographic distance, independent of any environmental variables, and (2) the niche assembly theory which predicts that the communities' compositions are more homogeneous among sites characterized by similar environmental conditions. Our study system offered a unique opportunity to investigate the relative role of environmental conditions and spatial factors in shaping community composition. We explored the bacterial community composition (BCC) of Nicotiana glauca floral nectar using the Illumina MiSeq technique at three spatial scales (plants, site, and region) and two taxonomic levels. Floral nectar samples were collected from 69 N. glauca plants at 11 different sites along a 200-km transect in Israel, along three biogeographic regions. A distance decay of BCC was found among all plants throughout Israel, but such pattern was not found among either sites or biogeographical regions. The BCC was also governed by environmental conditions in all examined scales (from the plant up to the biogeographical region). We also found that taxonomic resolution (89 and 97% sequence identity for clustering operational taxonomic units) affected the results of these BCC analyses. Hence, our study revealed that the BCC in N. glauca floral nectar is shaped by both the environmental conditions and the distance between plants, depending on the sampling scale under examination as well as by taxonomic resolution.}, }
@article {pmid28108758, year = {2017}, author = {Li, X and Zhou, L and Yu, Y and Ni, J and Xu, W and Yan, Q}, title = {Composition of Gut Microbiota in the Gibel Carp (Carassius auratus gibelio) Varies with Host Development.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {239-249}, pmid = {28108758}, issn = {1432-184X}, mesh = {Animals ; Bacteria/*classification ; *Gastrointestinal Microbiome ; Goldfish/growth &amp; development/*microbiology ; Phylogeny ; }, abstract = {To understand how a bacteria-free fish gut ecosystem develops microbiota as the fish ages, we performed a 1-year study on the gut microbiota of hatchling gibel carp (Carassius auratus gibelio). Our results indicate that the gut microbial diversity increases significantly as the fish develop. The gut microbial community composition showed significant shifts corresponding to host age and appeared to shift at two time points despite consistent diet and environmental conditions, suggesting that some features of the gut microbial community may be determined by the host's development. Dietary and environmental changes also seem to cause significant shifts in the fish gut microbial community. This study revealed that the gut microbiota of gibel carp assemble into distinct communities at different times during the host's development and that this process is less affected by the surrounding environment than by the host diet and development. Community phylogenetic analyses based on the net relatedness index further showed that environmental filtering (host selection) deterministically governs the gut microbial community composition. More importantly, the influence of host-associated deterministic filtering tends to weaken significantly over the course of the host's development. However, further studies are needed to assess whether this host development-dependent shift in gut microbiota will still exist under different rearing strategies.}, }
@article {pmid28108123, year = {2017}, author = {Holden, PA}, title = {DEB modeling for nanotoxicology, microbial ecology, and environmental engineering: Comment on: "Physics of metabolic organization" by Marko Jusup et al.}, journal = {Physics of life reviews}, volume = {20}, number = {}, pages = {49-51}, doi = {10.1016/j.plrev.2017.01.013}, pmid = {28108123}, issn = {1873-1457}, mesh = {*Biochemical Phenomena ; Ecology ; Engineering ; *Physics ; }, }
@article {pmid28106010, year = {2017}, author = {Sneppen, K}, title = {Models of life: epigenetics, diversity and cycles.}, journal = {Reports on progress in physics. Physical Society (Great Britain)}, volume = {80}, number = {4}, pages = {042601}, doi = {10.1088/1361-6633/aa5aeb}, pmid = {28106010}, issn = {1361-6633}, mesh = {Animals ; Bacteria/genetics/metabolism ; Bacteriophage lambda/genetics/metabolism ; *Biodiversity ; Biological Evolution ; *Epigenesis, Genetic ; Humans ; *Models, Biological ; Population Dynamics ; }, abstract = {This review emphasizes aspects of biology that can be understood through repeated applications of simple causal rules. The selected topics include perspectives on gene regulation, phage lambda development, epigenetics, microbial ecology, as well as model approaches to diversity and to punctuated equilibrium in evolution. Two outstanding features are repeatedly described. One is the minimal number of rules to sustain specific states of complex systems for a long time. The other is the collapse of such states and the subsequent dynamical cycle of situations that restitute the system to a potentially new metastable state.}, }
@article {pmid28105701, year = {2017}, author = {Hotaling, S and Finn, DS and Joseph Giersch, J and Weisrock, DW and Jacobsen, D}, title = {Climate change and alpine stream biology: progress, challenges, and opportunities for the future.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {92}, number = {4}, pages = {2024-2045}, doi = {10.1111/brv.12319}, pmid = {28105701}, issn = {1469-185X}, mesh = {*Altitude ; Animals ; *Biodiversity ; *Climate Change ; Databases, Factual ; Genomics ; *Rivers ; }, abstract = {In alpine regions worldwide, climate change is dramatically altering ecosystems and affecting biodiversity in many ways. For streams, receding alpine glaciers and snowfields, paired with altered precipitation regimes, are driving shifts in hydrology, species distributions, basal resources, and threatening the very existence of some habitats and biota. Alpine streams harbour substantial species and genetic diversity due to significant habitat insularity and environmental heterogeneity. Climate change is expected to affect alpine stream biodiversity across many levels of biological resolution from micro- to macroscopic organisms and genes to communities. Herein, we describe the current state of alpine stream biology from an organism-focused perspective. We begin by reviewing seven standard and emerging approaches that combine to form the current state of the discipline. We follow with a call for increased synthesis across existing approaches to improve understanding of how these imperiled ecosystems are responding to rapid environmental change. We then take a forward-looking viewpoint on how alpine stream biologists can make better use of existing data sets through temporal comparisons, integrate remote sensing and geographic information system (GIS) technologies, and apply genomic tools to refine knowledge of underlying evolutionary processes. We conclude with comments about the future of biodiversity conservation in alpine streams to confront the daunting challenge of mitigating the effects of rapid environmental change in these sentinel ecosystems.}, }
@article {pmid28105510, year = {2017}, author = {Amin, A and Ahmed, I and Salam, N and Kim, BY and Singh, D and Zhi, XY and Xiao, M and Li, WJ}, title = {Diversity and Distribution of Thermophilic Bacteria in Hot Springs of Pakistan.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {116-127}, pmid = {28105510}, issn = {1432-184X}, mesh = {Chloroflexi/classification/*isolation &amp; purification ; Hot Springs/*microbiology ; Hot Temperature ; Pakistan ; Proteobacteria/classification/*isolation &amp; purification ; Sulfur-Reducing Bacteria/classification/*isolation &amp; purification ; }, abstract = {Chilas and Hunza areas, located in the Main Mantle Thrust and Main Karakoram Thrust of the Himalayas, host a range of geochemically diverse hot springs. This Himalayan geothermal region encompassed hot springs ranging in temperature from 60 to 95 °C, in pH from 6.2 to 9.4, and in mineralogy from bicarbonates (Tato Field), sulfates (Tatta Pani) to mixed type (Murtazaabad). Microbial community structures in these geothermal springs remained largely unexplored to date. In this study, we report a comprehensive, culture-independent survey of microbial communities in nine samples from these geothermal fields by employing a bar-coded pyrosequencing technique. The bacterial phyla Proteobacteria and Chloroflexi were dominant in all samples from Tato Field, Tatta Pani, and Murtazaabad. The community structures however depended on temperature, pH, and physicochemical parameters of the geothermal sites. The Murtazaabad hot springs with relatively higher temperature (90-95 °C) favored the growth of phylum Thermotogae, whereas the Tatta Pani thermal spring site TP-H3-b (60 °C) favored the phylum Proteobacteria. At sites with low silica and high temperature, OTUs belonging to phylum Chloroflexi were dominant. Deep water areas of the Murtazaabad hot springs favored the sulfur-reducing bacteria. About 40% of the total OTUs obtained from these samples were unclassified or uncharacterized, suggesting the presence of many undiscovered and unexplored microbiota. This study has provided novel insights into the nature of ecological interactions among important taxa in these communities, which in turn will help in determining future study courses in these sites.}, }
@article {pmid28105509, year = {2017}, author = {Medina, D and Hughey, MC and Becker, MH and Walke, JB and Umile, TP and Burzynski, EA and Iannetta, A and Minbiole, KPC and Belden, LK}, title = {Variation in Metabolite Profiles of Amphibian Skin Bacterial Communities Across Elevations in the Neotropics.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {227-238}, pmid = {28105509}, issn = {1432-184X}, mesh = {Animals ; Anura/*microbiology ; Bacteria/*metabolism ; Chytridiomycota/pathogenicity ; *Metabolome ; Panama ; RNA, Ribosomal, 16S/genetics ; Skin/*microbiology ; }, abstract = {Both the structure and function of host-associated microbial communities are potentially impacted by environmental conditions, just as the outcomes of many free-living species interactions are context-dependent. Many amphibian populations have declined around the globe due to the fungal skin pathogen, Batrachochytrium dendrobatidis (Bd), but enivronmental conditions may influence disease dynamics. For instance, in Panamá, the most severe Bd outbreaks have occurred at high elevation sites. Some amphibian species harbor bacterial skin communities that can inhibit the growth of Bd, and therefore, there is interest in understanding whether environmental context could also alter these host-associated microbial communities in a way that might ultimately impact Bd dynamics. In a field survey in Panamá, we assessed skin bacterial communities (16S rRNA amplicon sequencing) and metabolite profiles (HPLC-UV/Vis) of Silverstoneia flotator from three high- and three low-elevation populations representing a range of environmental conditions. Across elevations, frogs had similar skin bacterial communities, although one lowland site appeared to differ. Interestingly, we found that bacterial richness decreased from west to east, coinciding with the direction of Bd spread through Panamá. Moreover, metabolite profiles suggested potential functional variation among frog populations and between elevations. While the frogs have similar bacterial community structure, the local environment might shape the metabolite profiles. Ultimately, host-associated community structure and function could be dependent on environmental conditions, which could ultimately influence host disease susceptibility across sites.}, }
@article {pmid28101080, year = {2016}, author = {Lupatini, M and Korthals, GW and de Hollander, M and Janssens, TK and Kuramae, EE}, title = {Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {2064}, pmid = {28101080}, issn = {1664-302X}, abstract = {Organic farming system and sustainable management of soil pathogens aim at reducing the use of agricultural chemicals in order to improve ecosystem health. Despite the essential role of microbial communities in agro-ecosystems, we still have limited understanding of the complex response of microbial diversity and composition to organic and conventional farming systems and to alternative methods for controlling plant pathogens. In this study we assessed the microbial community structure, diversity and richness using 16S rRNA gene next generation sequences and report that conventional and organic farming systems had major influence on soil microbial diversity and community composition while the effects of the soil health treatments (sustainable alternatives for chemical control) in both farming systems were of smaller magnitude. Organically managed system increased taxonomic and phylogenetic richness, diversity and heterogeneity of the soil microbiota when compared with conventional farming system. The composition of microbial communities, but not the diversity nor heterogeneity, were altered by soil health treatments. Soil health treatments exhibited an overrepresentation of specific microbial taxa which are known to be involved in soil suppressiveness to pathogens (plant-parasitic nematodes and soil-borne fungi). Our results provide a comprehensive survey on the response of microbial communities to different agricultural systems and to soil treatments for controlling plant pathogens and give novel insights to improve the sustainability of agro-ecosystems by means of beneficial microorganisms.}, }
@article {pmid28100229, year = {2017}, author = {Lau, JS and Kiss, C and Roberts, E and Horne, K and Korman, TM and Woolley, I}, title = {Surveillance of life-long antibiotics: a review of antibiotic prescribing practices in an Australian Healthcare Network.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {16}, number = {1}, pages = {3}, pmid = {28100229}, issn = {1476-0711}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/*therapeutic use ; Australia ; Bacterial Infections/*drug therapy/immunology/pathology ; Child ; Child, Preschool ; Cross-Sectional Studies ; Delivery of Health Care/trends ; Drug Prescriptions/*statistics &amp; numerical data ; Drug Utilization/*statistics &amp; numerical data ; Female ; Fluoroquinolones/therapeutic use ; Humans ; *Immunocompromised Host ; Macrolides/therapeutic use ; Male ; Middle Aged ; Practice Patterns, Physicians'/*statistics &amp; numerical data ; Retrospective Studies ; }, abstract = {BACKGROUND: The rise of antimicrobial use in the twentieth century has significantly reduced morbidity due to infection, however it has also brought with it the rise of increasing resistance. Some patients are on prolonged, if not "life-long" course of antibiotics. The reasons for this are varied, and include non-infectious indications. We aimed to study the characteristics of this potential source of antibiotic resistance, by exploring the antibiotic dispensing practices and describing the population of patients on long-term antibiotic therapy.<br><br>METHODS: A retrospective cross-sectional study of antibiotic dispensing records was performed at a large university hospital-based healthcare network in Melbourne, Australia. Outpatient prescriptions were extracted from the hospital pharmacy database over a 6&#xa0;month period in 2014. Medical records of these patients were reviewed to determine the indication for prescription, including microbiology, the intended duration, and the prescribing unit. A descriptive analysis was performed on this data.<br><br>RESULTS: 66,127 dispensing episodes were reviewed. 202 patients were found to have been prescribed 1 or more antibiotics with an intended duration of 1&#xa0;year or longer. 69/202 (34%) of these patients were prescribed prolonged antibiotics for primary prophylaxis in the setting of immunosuppression. 43/202 (21%) patients were prescribed long-term suppressive antibiotics for infections of thought incurable (e.g. vascular graft infections), and 34/43 (79%) were prescribed by Infectious Diseases doctors. 66/202 (33%) patients with cystic fibrosis were prescribed prolonged courses of macrolides or fluoroquinolones, by respiratory physicians. There was great heterogeneity noted in indications for prolonged antibiotic courses, as well as antibiotic agents utilised.<br><br>CONCLUSION: Our study found that that continuous antibiotic therapy represented only a small proportion of overall antibiotic prescribing at our health network. Prolonged courses of antibiotics were used mainly to suppress infections thought incurable, but also as primary and secondary prophylaxis and as anti-inflammatory agents. More research is needed to understand the impact of long-term antibiotic consumption on both patients and microbial ecology.}, }
@article {pmid28100022, year = {2017}, author = {Waud, M and Brys, R and Van Landuyt, W and Lievens, B and Jacquemyn, H}, title = {Mycorrhizal specificity does not limit the distribution of an endangered orchid species.}, journal = {Molecular ecology}, volume = {26}, number = {6}, pages = {1687-1701}, doi = {10.1111/mec.14014}, pmid = {28100022}, issn = {1365-294X}, mesh = {Animals ; Belgium ; Endangered Species ; France ; Mycorrhizae/*classification ; Orchidaceae/*microbiology ; Species Specificity ; *Symbiosis ; }, abstract = {What factors determine the distribution of a species is a central question in ecology and conservation biology. In general, the distribution of plant species is assumed to be controlled by dispersal or environmentally controlled recruitment. For plant species which are critically dependent on mycorrhizal symbionts for germination and seedling establishment, specificity in mycorrhizal associations and availability of suitable mycorrhizal fungi can be expected to have a major impact on successful colonization and establishment and thus ultimately on a species distribution. We combined seed germination experiments with soil analyses and fungal assessments using 454 amplicon pyrosequencing to test the relative importance of dispersal limitation, mycorrhizal availability and local growth conditions on the distribution of the orchid species Liparis loeselii, which, despite being widely distributed, is rare and endangered in Europe. We compared local soil conditions, seed germination and mycorrhizal availability in the soil between locations in northern Belgium and France where L. loeselii occurs naturally and locations where conditions appear suitable, but where adults of the species are absent. Our results indicated that mycorrhizal communities associating with L. loeselii varied among sites and plant life cycle stages, but the observed variations did not affect seed germination, which occurred regardless of current L. loeselii presence and was significantly affected by soil moisture content. These results indicate that L. loeselii is a mycorrhizal generalist capable of opportunistically associating with a variety of fungal partners to induce seed germination. They also indicate that availability of fungal associates is not necessarily the determining factor driving the distribution of mycorrhizal plant species.}, }
@article {pmid28100018, year = {2017}, author = {Meyer, KM and Klein, AM and Rodrigues, JL and Nüsslein, K and Tringe, SG and Mirza, BS and Tiedje, JM and Bohannan, BJ}, title = {Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms.}, journal = {Molecular ecology}, volume = {26}, number = {6}, pages = {1547-1556}, doi = {10.1111/mec.14011}, pmid = {28100018}, issn = {1365-294X}, mesh = {*Agriculture ; Animals ; Bacteria ; Cattle ; Methane/*metabolism ; *Rainforest ; Soil ; *Soil Microbiology ; }, abstract = {Land use change is one of the greatest environmental impacts worldwide, especially to tropical forests. The Amazon rainforest has been subject to particularly high rates of land use change, primarily to cattle pasture. A commonly observed response to cattle pasture establishment in the Amazon is the conversion of soil from a methane sink in rainforest, to a methane source in pasture. However, it is not known how the microorganisms that mediate methane flux are altered by land use change. Here, we use the deepest metagenomic sequencing of Amazonian soil to date to investigate differences in methane-cycling microorganisms and their traits across rainforest and cattle pasture soils. We found that methane-cycling microorganisms responded to land use change, with the strongest responses exhibited by methane-consuming, rather than methane-producing, microorganisms. These responses included a reduction in the relative abundance of methanotrophs and a significant decrease in the abundance of genes encoding particulate methane monooxygenase. We also observed compositional changes to methanotroph and methanogen communities as well as changes to methanotroph life history strategies. Our observations suggest that methane-cycling microorganisms are vulnerable to land use change, and this vulnerability may underlie the response of methane flux to land use change in Amazon soils.}, }
@article {pmid28097058, year = {2017}, author = {Moller, AG and Liang, C}, title = {Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e2844}, pmid = {28097058}, issn = {2167-8359}, abstract = {Solar salterns are excellent model ecosystems for studying virus-microbial interactions because of their low microbial diversity, environmental stability, and high viral density. By using the power of CRISPR spacers to link viruses to their prokaryotic hosts, we explored virus-host interactions in geographically diverse salterns. Using taxonomic profiling, we identified hosts such as archaeal Haloquadratum, Halorubrum, and Haloarcula and bacterial Salinibacter, and we found that community composition related to not only salinity but also local environmental dynamics. Characterizing glycerol metabolism genes in these metagenomes suggested Halorubrum and Haloquadratum possess most dihydroxyacetone kinase genes while Salinibacter possesses most glycerol-3-phosphate dehydrogenase genes. Using two different methods, we detected fewer CRISPR spacers in Haloquadratum-dominated compared with Halobacteriaceae-dominated saltern metagenomes. After CRISPR detection, spacers were aligned against haloviral genomes to map virus to host. While most alignments for each saltern metagenome linked viruses to Haloquadratum walsbyi, there were also alignments indicating interactions with the low abundance taxa Haloarcula and Haloferax. Further examination of the dinucleotide and trinucleotide usage differences between paired viruses and their hosts confirmed viruses and hosts had similar nucleotide usage signatures. Detection of cas genes in the salterns supported the possibility of CRISPR activity. Taken together, our studies suggest similar virus-host interactions exist in different solar salterns and that the glycerol metabolism gene dihydroxyacetone kinase is associated with Haloquadratum and Halorubrum.}, }
@article {pmid28094796, year = {2017}, author = {Westhoff, S and van Leeuwe, TM and Qachach, O and Zhang, Z and van Wezel, GP and Rozen, DE}, title = {The evolution of no-cost resistance at sub-MIC concentrations of streptomycin in Streptomyces coelicolor.}, journal = {The ISME journal}, volume = {11}, number = {5}, pages = {1168-1178}, pmid = {28094796}, issn = {1751-7370}, support = {BB/J006009/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Biological Evolution ; Drug Resistance, Bacterial/genetics ; Mutation ; Soil Microbiology ; Streptomyces coelicolor/*drug effects/genetics ; Streptomycin/*pharmacology ; }, abstract = {At the high concentrations used in medicine, antibiotics exert strong selection on bacterial populations for the evolution of resistance. However, these lethal concentrations may not be representative of the concentrations bacteria face in soil, a recognition that has led to questions of the role of antibiotics in soil environments as well as the dynamics of resistance evolution during sublethal challenge. Here we examine the evolution of resistance to sub-minimal inhibitory concentrations (sub-MIC) of streptomycin in the filamentous soil bacterium Streptomyces coelicolor. First, we show that spontaneous resistance to streptomycin causes an average fitness deficit of ~21% in the absence of drugs; however, these costs are eliminated at concentrations as low as 1/10 the MIC of susceptible strains. Using experimental evolution, we next show that resistance to >MIC levels of streptomycin readily evolves when bacteria are exposed to sub-MIC doses for 500 generations. Furthermore, the resistant clones that evolved at sub-MIC streptomycin concentrations carry no fitness cost. Whole-genome analyses reveal that evolved resistant clones fixed some of the same mutations as those isolated at high drug concentrations; however, all evolved clones carry additional mutations and some fixed mutations that either compensate for costly resistance or have no associated fitness costs. Our results broaden the conditions under which resistance can evolve in nature and suggest that rather than low-concentration antibiotics acting as signals, resistance evolves in response to antibiotics used as weapons.}, }
@article {pmid28091706, year = {2017}, author = {Martin, G and Webb, RJ and Chen, C and Plowright, RK and Skerratt, LF}, title = {Microclimates Might Limit Indirect Spillover of the Bat Borne Zoonotic Hendra Virus.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {106-115}, pmid = {28091706}, issn = {1432-184X}, support = {P20 GM103474/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Australia ; Chiroptera/*virology ; *Hendra Virus ; Henipavirus Infections/*transmission/veterinary ; Horses ; Humans ; *Microclimate ; Zoonoses/*virology ; }, abstract = {Infectious diseases are transmitted when susceptible hosts are exposed to pathogen particles that can replicate within them. Among factors that limit transmission, the environment is particularly important for indirectly transmitted parasites. To try and assess a pathogens' ability to be transmitted through the environment and mitigate risk, we need to quantify its decay where transmission occurs in space such as the microclimate harbouring the pathogen. Hendra virus, a Henipavirus from Australian Pteropid bats, spills-over to horses and humans, causing high mortality. While a vaccine is available, its limited uptake has reduced opportunities for adequate risk management to humans, hence the need to develop synergistic preventive measures, like disrupting its transmission pathways. Transmission likely occurs shortly after virus excretion in paddocks; however, no survival estimates to date have used real environmental conditions. Here, we recorded microclimate conditions and fitted models that predict temperatures and potential evaporation, which we used to simulate virus survival with a temperature-survival model and modification based on evaporation. Predicted survival was lower than previously estimated and likely to be even lower according to potential evaporation. Our results indicate that transmission should occur shortly after the virus is excreted, in a relatively direct way. When potential evaporation is low, and survival is more similar to temperature dependent estimates, transmission might be indirect because the virus can wait several hours until contact is made. We recommend restricting horses' access to trees during night time and reducing grass under trees to reduce virus survival.}, }
@article {pmid28091705, year = {2017}, author = {Mukhacheva, TA and Kovalev, SY}, title = {Bacteria of the Family 'Candidatus Midichloriaceae' in Sympatric Zones of Ixodes Ticks: Genetic Evidence for Vertical Transmission.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {185-193}, pmid = {28091705}, issn = {1432-184X}, mesh = {Alphaproteobacteria/*genetics ; Animals ; Estonia ; Genetic Variation ; Ixodes/classification/*microbiology ; *Symbiosis ; Sympatry ; }, abstract = {Ixodes ticks transmit infectious agents and also harbor their own parasites and symbionts. The presumptive endosymbiont of Ixodes ricinus, 'Candidatus Midichloria mitochondrii', has a unique ability to invade mitochondria within tick ovarian cells and is transovarially transmitted with 100% efficiency. A closely related bacterium, provisionally named Montezuma (now 'Candidatus Lariskella arthropodarum'), was isolated from the Ixodes persulcatus ticks and human blood in 2004 as well as from Ixodes pavlovskyi in 2015. These microorganisms belong to the family 'Candidatus Midichloriaceae fam. nov.' and were detected not only in tick salivary glands, but also in animal blood. Nevertheless, the relative importance of vertical and horizontal routes for their transmission or maintenance in natural tick populations remains unclear. We analyzed the prevalence of L. arthropodarum and M. mitochondrii in two sympatric zones, where I. persulcatus/I. ricinus and I. persulcatus/I. pavlovskyi cohabit and produce interspecific hybrids. A specificity of the associations of L. arthropodarum with I. persulcatus (100%) and M. mitochondrii with I. ricinus (96.2%) was observed in the sympatric zone in Estonia, possibly showing poor contribution of the horizontal route to the overall prevalence of endosymbionts. L. arthropodarum was observed probably multiplying in I. pavlovskyi and also subjected to transovarial transmission, but much less efficiently compared to I. persulcatus. We revealed two new genetic variants of the rrl-rrf intergenic spacer of L. arthropodarum isolated from I. pavlovskyi ticks that possibly could indicate an ongoing process of adaptation of the microorganism to a new host species.}, }
@article {pmid28089124, year = {2017}, author = {Kiewra, D and Stefańska-Krzaczek, E and Szymanowski, M and Szczepańska, A}, title = {Local-scale spatio-temporal distribution of questing Ixodes ricinus L. (Acari: Ixodidae)-A case study from a riparian urban forest in Wrocław, SW Poland.}, journal = {Ticks and tick-borne diseases}, volume = {8}, number = {3}, pages = {362-369}, doi = {10.1016/j.ttbdis.2016.12.011}, pmid = {28089124}, issn = {1877-9603}, mesh = {Animals ; *Forests ; *Ixodes ; Larva ; Nymph/microbiology ; Poland/epidemiology ; Spatio-Temporal Analysis ; Urban Renewal ; }, abstract = {This paper presents the distribution of questing Ixodes ricinus ticks in suburban forest intensively visited by people. The local-scale observations conducted during a 4-year study at 99 plots (of 100m[2] each) located throughout the entire area of a riparian urban forest, showed a high variation in the density of ticks from year to year. Although I. ricinus is generally permanent in the study area, spatial distribution of sample plots harbouring I. ricinus is variable, i.e. mainly random for adults and larvae, and random or clustered for nymphs. Among the most common plant species in the herb layer, there were not any species which had a statistically significant and constant impact on the occurrence of any of the development stages of I. ricinus. Also relations between the density of tick development stages and vegetation variables, including cover of the herb layer, total species number, species number of the herb layer, and percentage coverage of particular species, as well as ecological indices for light, soil moisture, reaction, and nutrients, did not show any constant and predictable pattern in subsequent years of the study. Only tree and shrub layers were found as variables positively affecting the density of ticks. Although small, suburban forests can be considered as tick-borne risk areas, it is impossible to determine in details areas of tick-borne risk.}, }
@article {pmid28088532, year = {2017}, author = {Thwaites, BJ and Reeve, P and Dinesh, N and Short, MD and van den Akker, B}, title = {Comparison of an anaerobic feed and split anaerobic-aerobic feed on granular sludge development, performance and ecology.}, journal = {Chemosphere}, volume = {172}, number = {}, pages = {408-417}, doi = {10.1016/j.chemosphere.2016.12.133}, pmid = {28088532}, issn = {1879-1298}, mesh = {Aerobiosis ; Agriculture ; Anaerobiosis ; Biomass ; *Bioreactors ; Equipment Design ; Nitrogen/*chemistry ; RNA, Ribosomal, 16S/chemistry/genetics ; Sewage/*chemistry ; Waste Disposal, Fluid/*methods ; Wastewater ; Water Microbiology ; }, abstract = {The retrofitting of existing wastewater sequencing batch reactors (SBRs) to select for rapid-settling aerobic granular sludge (AGS) over floc-based conventional activated sludge (CAS), could be a viable option to decrease reactor cycle time and increase hydraulic capacity. Successful CAS-to-AGS conversion has previously been shown to be highly dependent on having a dedicated anaerobic feed, which presents additional engineering challenges when retrofitting SBRs. In this study we compared the performance of a split anaerobic-aerobic (An-Aer) feed with that of a traditional dedicated anaerobic feed regarding AGS formation and stability, nitrogen removal performance and microbial ecology. Using pilot trials, we showed that AGS could be established and maintained when using a split An-Aer feed at low organic loading rates analogous to that of a parallel full-scale conventional SBR. Additionally, we showed that AGS start-up time and nitrogen removal performance were comparable under a split An-Aer feed and dedicated anaerobic feed. Microbial ecology characterisations based on whole-of-community 16S rRNA profiles and targeted analysis of functional genes specific for nitrifying and denitrifying microorganisms, showed that the two different feed strategies had only subtle impacts on both the overall community composition and functional ecology. A much greater divergence in microbial ecology was seen when comparing AGS with CAS. Data presented here will be of value to those planning to retrofit existing CAS-based SBRs to operate with AGS and demonstrates the viability of using a more cost-effective split An-Aer feed configuration over a dedicated anaerobic feed.}, }
@article {pmid28088423, year = {2017}, author = {Oh, J and Harper, M and Giallongo, F and Bravo, DM and Wall, EH and Hristov, AN}, title = {Effects of rumen-protected Capsicum oleoresin on productivity and responses to a glucose tolerance test in lactating dairy cows.}, journal = {Journal of dairy science}, volume = {100}, number = {3}, pages = {1888-1901}, doi = {10.3168/jds.2016-11665}, pmid = {28088423}, issn = {1525-3198}, mesh = {Animal Feed ; Animals ; Capsicum ; Cattle ; Diet/veterinary ; Female ; Glucose Tolerance Test ; *Lactation ; Milk/metabolism ; Rumen/*metabolism ; }, abstract = {The objective of this experiment was to investigate the effects of rumen-protected Capsicum oleoresin (RPC) supplementation on feed intake, milk yield and composition, nutrient utilization, fecal microbial ecology, and responses to a glucose tolerance test in lactating dairy cows. Nine multiparous Holstein cows were used in a replicated 3 × 3 Latin square design balanced for residual effects with three 28-d periods. Each period consisted of 14 d for adaptation and 14 d for data collection and sampling. Treatments were 0 (control), 100, and 200 mg of RPC/cow per day. They were mixed with a small portion of the total mixed ration and top-dressed. Glucose tolerance test was conducted once during each experimental period by intravenous administration of glucose at a rate of 0.3 g/kg of body weight. Dry matter intake was not affected by RPC. Milk yield tended to increase for RPC treatments compared to the control. Feed efficiency was linearly increased by RPC supplementation. Concentrations of fat, true protein, and lactose in milk were not affected by RPC. Apparent total-tract digestibility of dry matter, organic matter, and crude protein was linearly increased, and fecal nitrogen excretion was linearly decreased by RPC supplementation. Rumen-protected Capsicum oleoresin did not affect the composition of fecal bacteria. Glucose concentration in serum was not affected by RPC supplementation post glucose challenge. However, compared to the control, RPC decreased serum insulin concentration at 5, 10, and 40 min post glucose challenge. The area under the insulin concentration curve was also decreased 25% by RPC. Concentration of nonesterified fatty acids and β-hydroxybutyrate in serum were not affected by RPC following glucose administration. In this study, RPC tended to increase milk production and increased feed efficiency in dairy cows. In addition, RPC decreased serum insulin concentration during the glucose tolerance test, but glucose concentration was not affected by treatment.}, }
@article {pmid28087803, year = {2017}, author = {Bondoso, J and Godoy-Vitorino, F and Balagué, V and Gasol, JM and Harder, J and Lage, OM}, title = {Epiphytic Planctomycetes communities associated with three main groups of macroalgae.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {3}, pages = {}, pmid = {28087803}, issn = {1574-6941}, support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics ; DNA Primers ; DNA, Ribosomal ; Denaturing Gradient Gel Electrophoresis ; Host Specificity ; Phylogeny ; Planctomycetales/genetics/*physiology ; Portugal ; RNA, Ribosomal, 16S/genetics ; Seaweed/*microbiology ; }, abstract = {Planctomycetes, a unique group of widespread and understudied bacteria, are known to be associated with macroalgae. The temporal dynamics and the host-specific association of planctomycetal communities on Fucus spiralis, Ulva sp. and Chondrus crispus from two locations in the North Coast of Portugal were assessed both by denaturing gradient gel electrophoresis with group-specific primers and 16S rDNA amplicon libraries. The epiphytic planctomycetal communities showed a significant association with the host macroalgal species independently of the geographical location and the season. This pattern was confirmed by clone libraries of winter and summer samples: we obtained 720 16S rRNA gene sequences that represented 44 operational taxonomic units (OTUs) within the phylum Planctomycetes. Most of the OTUs belonged to Blastopirellula, followed by Rhodopirellula, Planctomyces, the Pir4 lineage and the uncultured class OM190 (this last one nearly 30% of the OTUs). Ulva sp. and C. crispus had more diverse planctomycetal communities than F. spiralis. Analysis of beta diversity showed that the planctomycetal microbiome was host specific. We hypothesize that the specific association of Planctomycetes and their macroalgal hosts is likely determined by nutritional molecules provided by the algae and the set of sulfatases inherent to each Planctomycetes species.}, }
@article {pmid28086074, year = {2017}, author = {Behera, P and Venkata Ramana, V and Maharana, B and Joseph, N and Vaishampayan, P and Singh, NK and Shouche, Y and Bhadury, P and Mishra, SR and Raina, V and Suar, M and Pattnaik, AK and Rastogi, G}, title = {Mangrovibacter phragmitis sp. nov., an endophyte isolated from the roots of Phragmites karka.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {67}, number = {5}, pages = {1228-1234}, doi = {10.1099/ijsem.0.001789}, pmid = {28086074}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Endophytes/classification/genetics/isolation &amp; purification ; Enterobacteriaceae/*classification/genetics/isolation &amp; purification ; Fatty Acids/chemistry ; India ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; Plant Roots/*microbiology ; Poaceae/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {A facultatively anaerobic, Gram-stain-negative, rod-shaped, nitrogen-fixing, endophytic bacterial strain designated MP23T was isolated from the roots of Phragmites karka growing in Chilika Lagoon, Odisha, India. Strain MP23T was slightly halophilic, and the optimal NaCl concentration and temperature for growth were 1 % and 30 °C, respectively. On the basis of 16S rRNA gene sequence similarities, strain MP23T was affiliated to the family Enterobacteriaceae and most closely related to Mangrovibacter yixingensis KCTC 42181T and Mangrovibacter plantisponsor DSM 19579T with 99.71 % similarity, followed by Salmonella enterica subsp. salamae DSM 9220T (97.22 %), Cronobacter condimenti LMG 26250T (97.14 %) and Salmonella enterica subsp. diarizonae DSM 14847T (97 %). Sequence analysis of 16S rRNA, hsp60, gyrB and rpoB genes showed that strain MP23T formed a phylogenetic cluster with M. yixingensis KCTC 42181T and M. plantisponsor DSM 19579T indicating that it belongs to the genus Mangrovibacter. The major cellular fatty acids were C16 : 0, C18 : 1ω6c and/or C18 : 1ω7c, C16 : 1ω6c and/or C16 : 1ω7c, C14 : 0, C14 : 0 3-OH and/or iso-C16 : 1 I and C17 : 0 cyclo. Polar lipids of strain MP23T consisted of phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 50.3 mol%. Based on experimental DNA-DNA hybridization values and average nucleotide identity derived from in silico comparison of whole-genome sequences, strain MP23T could be distinguished from its closest neighbours. We therefore conclude that strain MP23T represents a novel species of the genus Mangrovibacter for which the name Mangrovibacter phragmitis sp. nov. is proposed. The type strain is MP23T (=DSM 100250T=KCTC 42580T).}, }
@article {pmid28084599, year = {2017}, author = {Subirats, J and Royo, E and Balcázar, JL and Borrego, CM}, title = {Real-time PCR assays for the detection and quantification of carbapenemase genes (bla KPC, bla NDM, and bla OXA-48) in environmental samples.}, journal = {Environmental science and pollution research international}, volume = {24}, number = {7}, pages = {6710-6714}, pmid = {28084599}, issn = {1614-7499}, mesh = {Bacterial Proteins/*genetics ; Benzothiazoles ; Biofilms ; Diamines ; Environmental Microbiology ; Fluorescent Dyes/chemistry ; Genes, Bacterial ; Limit of Detection ; Organic Chemicals/chemistry ; Quinolines ; *Real-Time Polymerase Chain Reaction ; Wastewater/microbiology ; beta-Lactamases/*genetics ; }, abstract = {In this study, we have developed real-time PCR assays using SYBR Green chemistry to detect all known alleles of bla KPC, bla NDM, and bla OXA-48-like carbapenemase genes in water, sediment, and biofilm samples collected from hospital and wastewater treatment plant (WWTP) effluents and rivers receiving chronic WWTP discharges. The amplification of bla KPC, bla NDM, and bla OXA-48 DNA was linear over 7 log dilutions (R [2] between 0.995 and 0.997) and showing efficiencies ranging from 92.6% to 100.3%. The analytical sensitivity indicated that the reaction for bla KPC, bla NDM, and bla OXA-48-like genes was able to detect 35, 16, and 19 copy numbers per assay, respectively. The three carbapenemase genes were detected in hospital effluents, whereas only the bla KPC and bla NDM genes were detected in biofilm and sediment samples collected from wastewater-impacted rivers. The detection of bla KPC, bla NDM, and bla OXA-48-like genes in different matrices suggests that carbapenem-resistant bacteria occur in both planktonic and benthic habitats thus expanding the range of resistance reservoirs for last-resort antibiotics. We believe that these real-time PCR assays would be a powerful tool for the rapid detection and quantification of bla KPC, bla NDM, and bla OXA-48-like genes in complex environmental samples.}, }
@article {pmid28083638, year = {2017}, author = {Fernandez-Leborans, G and Román, S and Martin, D}, title = {A New Deep-Sea Suctorian-Nematode Epibiosis (Loricophrya-Tricoma) from the Blanes Submarine Canyon (NW Mediterranean).}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {15-21}, pmid = {28083638}, issn = {1432-184X}, mesh = {Animals ; Ciliophora/*classification/isolation &amp; purification ; Mediterranean Sea ; *Nematoda ; }, abstract = {During a pluri-disciplinary study carried out within the frame of the Spanish research project DOS MARES, multicore samples were collected along the Blanes submarine canyon and its adjacent open slope to study the structure and dynamics of the meiofaunal organisms, mainly nematodes. Among the 5808 nematode individuals identified, only 190 of them belonged to the genus Tricoma (Desmoscolecidae), and only two harboured epibiont suctorian ciliates. The three specimens were located near the tail of the basibionts. A careful examination of the ciliates revealed that they were suctorians, which are here described as a new species of Loricophrya, namely L. mediterranea sp. nov. The new species is characterized by having a conical, slightly elongated lorica, narrowing towards posterior end; an anterior end inward curved, surrounding the lorica opening; a body placed near the lorica opening, occupying 1/3 of the lorica length, 4-8 capitate tentacles, and a peripheral, oval to sausage-shaped macronucleus. Our findings represent the first known report of an association with a deep-sea species of Tricoma, and the first record in the Mediterranean Sea, for a species of Loricophrya. The significance of the relationships between suctorian ciliates and their host in extreme environments such as deep-sea submarine canyons is discussed.}, }
@article {pmid28082503, year = {2017}, author = {Zablocki, O and Adriaenssens, EM and Frossard, A and Seely, M and Ramond, JB and Cowan, D}, title = {Metaviromes of Extracellular Soil Viruses along a Namib Desert Aridity Gradient.}, journal = {Genome announcements}, volume = {5}, number = {2}, pages = {}, pmid = {28082503}, issn = {2169-8287}, abstract = {The Namib Desert in southwest Africa is hyperarid and composed of distinct microbial communities affected by a longitudinal aridity gradient. Here, we report four soil metaviromes from the Namib Desert, assessed using deep sequencing of metavirome libraries prepared from DNA extracted from gravel plain surface soils.}, }
@article {pmid28074247, year = {2017}, author = {Tripathi, BM and Moroenyane, I and Sherman, C and Lee, YK and Adams, JM and Steinberger, Y}, title = {Trends in Taxonomic and Functional Composition of Soil Microbiome Along a Precipitation Gradient in Israel.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {168-176}, pmid = {28074247}, issn = {1432-184X}, mesh = {Climate Change ; *Ecosystem ; Israel ; *Microbiota ; Soil ; *Soil Microbiology ; Water ; }, abstract = {The soil microbiome is important for the functioning of terrestrial ecosystems. However, the impacts of climate on taxonomic and functional diversity of soil microbiome are not well understood. A precipitation gradient along regional scale transects may offer a model setting for understanding the effect of climate on the composition and function of the soil microbiome. Here, we compared taxonomic and functional attributes of soil microorganisms in arid, semiarid, Mediterranean, and humid Mediterranean climatic conditions of Israel using shotgun metagenomic sequencing. We hypothesized that there would be a distinct taxonomic and functional soil community for each precipitation zone, with arid environments having lower taxonomic and functional diversity, greater relative abundance of stress response and sporulation-related genes, and lower relative abundance of genes related to nutrient cycling and degradation of complex organic compounds. As hypothesized, our results showed a distinct taxonomic and functional community in each precipitation zone, revealing differences in soil taxonomic and functional selection in the different climates. Although the taxonomic diversity remained similar across all sites, the functional diversity was-as hypothesized-lower in the arid environments, suggesting that functionality is more constrained in "extreme" environments. Also, with increasing aridity, we found a significant increase in genes related to dormancy/sporulation and a decrease in those related to nutrient cycling (genes related to nitrogen, potassium, and sulfur metabolism), respectively. However, relative abundance of genes related to stress response were lower in arid soils. Overall, these results indicate that climatic conditions play an important role in shaping taxonomic and functional attributes of soil microbiome. These findings have important implications for understanding the impacts of climate change (e.g., precipitation change) on structure and function of the soil microbiome.}, }
@article {pmid28074246, year = {2017}, author = {Speth, DR and Lagkouvardos, I and Wang, Y and Qian, PY and Dutilh, BE and Jetten, MSM}, title = {Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {1-5}, pmid = {28074246}, issn = {1432-184X}, support = {232937/ERC_/European Research Council/International ; 339880/ERC_/European Research Council/International ; }, mesh = {Bacteria/*classification/genetics ; *Genome, Bacterial ; Indian Ocean ; Oxidation-Reduction ; *Phylogeny ; Quaternary Ammonium Compounds ; RNA, Ribosomal, 16S/genetics ; Salts ; Seawater/*microbiology ; }, abstract = {Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the possibility of anammox at BSI sites using metagenomic shotgun sequencing of DNA obtained from the BSI above the Discovery Deep brine pool. Analysis of sequencing reads matching the 16S rRNA and hzsA genes confirmed presence of anammox bacteria of the genus Scalindua. Phylogenetic analysis of the 16S rRNA gene indicated that this Scalindua sp. belongs to a distinct group, separate from the anammox bacteria in the seawater column, that contains mostly sequences retrieved from high-salt environments. Using coverage- and composition-based binning, we extracted and assembled the draft genome of the dominant anammox bacterium. Comparative genomic analysis indicated that this Scalindua species uses compatible solutes for osmoadaptation, in contrast to other marine anammox bacteria that likely use a salt-in strategy. We propose the name Candidatus Scalindua rubra for this novel species, alluding to its discovery in the Red Sea.}, }
@article {pmid28074245, year = {2017}, author = {Axelsson, K and Konstanzer, V and Rajarao, GK and Terenius, O and Seriot, L and Nordenhem, H and Nordlander, G and Borg-Karlson, AK}, title = {Antifeedants Produced by Bacteria Associated with the Gut of the Pine Weevil Hylobius abietis.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {177-184}, pmid = {28074245}, issn = {1432-184X}, mesh = {Animals ; Bacteria/*chemistry ; *Feeding Behavior ; Gas Chromatography-Mass Spectrometry ; *Herbivory ; Pinus ; Solid Phase Microextraction ; Volatile Organic Compounds/*chemistry ; Weevils/*microbiology/physiology ; }, abstract = {The pine weevil, Hylobius abietis, is a severe forest pest insect as it feeds on newly planted conifer seedlings. To identify and develop an antifeedant could be one step towards the protection of seedlings from feeding damage by the pine weevil. With the aim to trace the origin of the antifeedants previously found in feces of the pine weevil, we investigated the culturable bacteria associated with the gut and identified the volatiles they produced. Bacterial isolates were identified by 16S ribosomal RNA gene analysis. The volatile emissions of selected bacteria, cultivated on NB media or on the grated phloem of Scots pine twigs dispersed in water, were collected and analyzed by solid-phase microextraction gas chromatography-mass spectrometry. The bacterial isolates released a variety of compounds, among others 2-methoxyphenol, 2-phenylethanol, 3-methyl-1-butanol, 1-octen-3-ol, 3-octanone, dimethyl disulfide, and dimethyl trisulfide. A strong antifeedant effect was observed by 2-phenylethanol, which could thus be a good candidate for use to protect planted conifer seedlings against feeding damage caused by H. abietis.}, }
@article {pmid28071809, year = {2017}, author = {Sun, GX and Van de Wiele, T and Alava, P and Tack, FMG and Du Laing, G}, title = {Bioaccessibility of selenium from cooked rice as determined in a simulator of the human intestinal tract (SHIME).}, journal = {Journal of the science of food and agriculture}, volume = {97}, number = {11}, pages = {3540-3545}, doi = {10.1002/jsfa.8208}, pmid = {28071809}, issn = {1097-0010}, mesh = {China ; Cooking ; Humans ; Intestinal Mucosa/*metabolism ; Intestines/chemistry ; Models, Biological ; Oryza/*chemistry/metabolism ; Selenium/*analysis/metabolism ; }, abstract = {BACKGROUND: As an essential but also potentially toxic element, both overexposure and underexposure to selenium (Se) can significantly affect public health. Rice is a common source of Se, especially in Asia. Not all Se may be released from the rice and become available for absorption into the bloodstream upon digestion in the gastrointestinal tract. Therefore, the bioaccessibility of Se in cooked white (polished) rice was assessed in vitro using the static gastrointestinal simulator SHIME (Simulator of the Human Intestinal Microbial Ecosystem).<br><br>RESULTS: The common cooking procedure in China prior to consumption [i.e. boiling at low rice:water ratios (1:3) until all of the water is absorbed into the rice] did not change total Se levels in the rice. Gastrointestinal digestion of the cooked rice matrix revealed a Se bioaccessibility of 67-76% of total Se. Subsequent microbial activity in the colon reduced the accessibility of Se in the cooked rice to 51-62%.<br><br>CONCLUSION: Not all Se present in cooked white rice should be considered as being bioavailable in the small intestine. A minor part is transferred with the remaining food matrix to the colon, where it is available for the microbial metabolism. &#xa9; 2017 Society of Chemical Industry.}, }
@article {pmid28071697, year = {2017}, author = {Gunnigle, E and Frossard, A and Ramond, JB and Guerrero, L and Seely, M and Cowan, DA}, title = {Diel-scale temporal dynamics recorded for bacterial groups in Namib Desert soil.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {40189}, pmid = {28071697}, issn = {2045-2322}, mesh = {Bacteria/*classification/*genetics ; *Biota ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Desert Climate ; Humidity ; Microbial Interactions ; Namibia ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Temperature ; }, abstract = {Microbes in hot desert soil partake in core ecosystem processes e.g., biogeochemical cycling of carbon. Nevertheless, there is still a fundamental lack of insights regarding short-term (i.e., over a 24-hour [diel] cycle) microbial responses to highly fluctuating microenvironmental parameters like temperature and humidity. To address this, we employed T-RFLP fingerprinting and 454 pyrosequencing of 16S rRNA-derived cDNA to characterize potentially active bacteria in Namib Desert soil over multiple diel cycles. Strikingly, we found that significant shifts in active bacterial groups could occur over a single 24-hour period. For instance, members of the predominant Actinobacteria phyla exhibited a significant reduction in relative activity from morning to night, whereas many Proteobacterial groups displayed an opposite trend. Contrary to our leading hypothesis, environmental parameters could only account for 10.5% of the recorded total variation. Potential biotic associations shown through co-occurrence networks indicated that non-random inter- and intra-phyla associations were 'time-of-day-dependent' which may constitute a key feature of this system. Notably, many cyanobacterial groups were positioned outside and/or between highly interconnected bacterial associations (modules); possibly acting as inter-module 'hubs' orchestrating interactions between important functional consortia. Overall, these results provide empirical evidence that bacterial communities in hot desert soils exhibit complex and diel-dependent inter-community associations.}, }
@article {pmid28070679, year = {2017}, author = {Andrade, AC and Fróes, A and Lopes, F&#xc1;C and Thompson, FL and Krüger, RH and Dinsdale, E and Bruce, T}, title = {Diversity of Microbial Carbohydrate-Active enZYmes (CAZYmes) Associated with Freshwater and Soil Samples from Caatinga Biome.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {89-105}, pmid = {28070679}, issn = {1432-184X}, mesh = {Alphaproteobacteria/enzymology ; Brazil ; Carbohydrates ; Enzymes/*analysis ; Fresh Water/*chemistry ; Glycoside Hydrolases/analysis ; Glycosyltransferases/analysis ; Planctomycetales/enzymology ; Soil/*chemistry ; Soil Microbiology ; Water Microbiology ; }, abstract = {Semi-arid and arid areas occupy about 33% of terrestrial ecosystems. However, little information is available about microbial diversity in the semi-arid Caatinga, which represents a unique biome that extends to about 11% of the Brazilian territory and is home to extraordinary diversity and high endemism level of species. In this study, we characterized the diversity of microbial genes associated with biomass conversion (carbohydrate-active enzymes, or so-called CAZYmes) in soil and freshwater of the Caatinga. Our results showed distinct CAZYme profiles in the soil and freshwater samples. Glycoside hydrolases and glycosyltransferases were the most abundant CAZYme families, with glycoside hydrolases more dominant in soil (∼44%) and glycosyltransferases more abundant in freshwater (∼50%). The abundances of individual glycoside hydrolase, glycosyltransferase, and carbohydrate-binding module subfamilies varied widely between soil and water samples. A predominance of glycoside hydrolases was observed in soil, and a higher contribution of enzymes involved in carbohydrate biosynthesis was observed in freshwater. The main taxa associated with the CAZYme sequences were Planctomycetia (relative abundance in soil, 29%) and Alphaproteobacteria (relative abundance in freshwater, 27%). Approximately 5-7% of CAZYme sequences showed low similarity with sequences deposited in non-redundant databases, suggesting putative homologues. Our findings represent a first attempt to describe specific microbial CAZYme profiles for environmental samples. Characterizing these enzyme groups associated with the conversion of carbohydrates in nature will improve our understanding of the significant roles of enzymes in the carbon cycle. We identified a CAZYme signature that can be used to discriminate between soil and freshwater samples, and this signature may be related to the microbial species adapted to the habitat. The data show the potential ecological roles of the CAZYme repertoire and associated biotechnological applications.}, }
@article {pmid28070678, year = {2017}, author = {Schwartz, MH and Pan, T}, title = {tRNA Misacylation with Methionine in the Mouse Gut Microbiome in Situ.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {10-14}, pmid = {28070678}, issn = {1432-184X}, support = {DP1 GM105386/GM/NIGMS NIH HHS/United States ; T32 GM007183/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteroidetes/metabolism ; Cecum/microbiology ; Firmicutes/metabolism ; *Gastrointestinal Microbiome ; Methionine/*chemistry ; Methionine-tRNA Ligase/metabolism ; Mice/microbiology ; RNA, Transfer/*chemistry ; }, abstract = {Global protein mistranslation with methionine has been shown to be a conserved biological process that affords distinct functional advantages in all three domains of life. In all instances, methionine mistranslation occurs through a regulated process where low-fidelity forms of methionyl-tRNA synthetase are conditionally induced to mischarge non-methionyl-tRNAs with methionine followed by the utilization of the misacylated tRNAs in translation. In mammals, methionine mistranslation contributes to oxidative stress response; in the hyperthermophilic archaeon Aeropyrum pernix, methionine mistranslation produces proteins that are better adapted to low temperature growth; in E. coli, methionine mistranslation increases resistance to antibiotics and chemical stressors. The phenotypic benefits conferred by tRNA mismethionylation suggest that it should be a widespread adaptational mechanism in diverse bacterial lineages, yet this response has only been described in E. coli. Furthermore, previous microbial investigations on this response have been confined to axenic laboratory cultures. It was unknown whether tRNA mismethionylation was relevant in a natural microbial habitat. Here we show that four abundant gut microbiotal genera belonging to the Firmicutes and Bacteroidetes phyla perform constitutive tRNA misacylation with methionine in the mouse cecum in situ. These results reveal the ubiquity of the tRNA mismethionylation process among bacteria and implicate the potential importance of this response for subsistence and adaptation in natural habitats.}, }
@article {pmid28070677, year = {2017}, author = {Cameron, KA and Stibal, M and Olsen, NS and Mikkelsen, AB and Elberling, B and Jacobsen, CS}, title = {Potential Activity of Subglacial Microbiota Transported to Anoxic River Delta Sediments.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {6-9}, pmid = {28070677}, issn = {1432-184X}, mesh = {Geologic Sediments/*microbiology ; Greenland ; Ice Cover/*microbiology ; Methane ; Methanomicrobiales ; Methanosarcinales ; *Microbiota ; Peptococcaceae ; Rivers/*microbiology ; Sulfates ; }, abstract = {The Watson River drains a portion of the SW Greenland ice sheet, transporting microbial communities from subglacial environments to a delta at the head of Søndre Strømfjord. This study investigates the potential activity and community shifts of glacial microbiota deposited and buried under layers of sediments within the river delta. A long-term (12-month) incubation experiment was established using Watson River delta sediment under anaerobic conditions, with and without CO2/H2 enrichment. Within CO2/H2-amended incubations, sulphate depletion and a shift in the microbial community to a 52% predominance of Desulfosporosinus meridiei by day 371 provides evidence for sulphate reduction. We found evidence of methanogenesis in CO2/H2-amended incubations within the first 5 months, with production rates of ~4 pmol g[-1] d[-1], which was likely performed by methanogenic Methanomicrobiales- and Methanosarcinales-related organisms. Later, a reduction in methane was observed to be paired with the depletion of sulphate, and we hypothesise that sulphate reduction out competed hydrogenotrophic methanogenesis. The structure and diversity of the original CO2/H2-amended incubation communities changed dramatically with a major shift in predominant community members and a decline in diversity and cell abundance. These results highlight the need for further investigations into the fate of subglacial microbiota within downstream environments.}, }
@article {pmid28070613, year = {2017}, author = {Pham, VT and Rediers, H and Ghequire, MG and Nguyen, HH and De Mot, R and Vanderleyden, J and Spaepen, S}, title = {The plant growth-promoting effect of the nitrogen-fixing endophyte Pseudomonas stutzeri A15.}, journal = {Archives of microbiology}, volume = {199}, number = {3}, pages = {513-517}, doi = {10.1007/s00203-016-1332-3}, pmid = {28070613}, issn = {1432-072X}, mesh = {Endophytes/physiology ; Mutation ; Nitrogen/pharmacology ; Nitrogen Fixation/drug effects/genetics/*physiology ; Oryza/*microbiology ; Plant Development/drug effects/physiology ; Plant Roots/microbiology ; Pseudomonas stutzeri/*physiology ; }, abstract = {The use of plant growth-promoting rhizobacteria as a sustainable alternative for chemical nitrogen fertilizers has been explored for many economically important crops. For one such strain isolated from rice rhizosphere and endosphere, nitrogen-fixing Pseudomonas stutzeri A15, unequivocal evidence of the plant growth-promoting effect and the potential contribution of biological nitrogen fixation (BNF) is still lacking. In this study, we investigated the effect of P. stutzeri A15 inoculation on the growth of rice seedlings in greenhouse conditions. P. stutzeri A15 induced significant growth promotion compared to uninoculated rice seedlings. Furthermore, inoculation with strain A15 performed significantly better than chemical nitrogen fertilization, clearly pointing to the potential of this bacterium as biofertilizer. To assess the contribution of BNF to the plant growth-promoting effect, rice seedlings were also inoculated with a nitrogen fixation-deficient mutant. Our results suggest that BNF (at best) only partially contributes to the stimulation of plant growth.}, }
@article {pmid28070331, year = {2017}, author = {Oh, JK and Pajarillo, EAB and Chae, JP and Kim, IH and Yang, DS and Kang, DK}, title = {Effects of Bacillus subtilis CSL2 on the composition and functional diversity of the faecal microbiota of broiler chickens challenged with Salmonella Gallinarum.}, journal = {Journal of animal science and biotechnology}, volume = {8}, number = {}, pages = {1}, pmid = {28070331}, issn = {1674-9782}, abstract = {BACKGROUND: The chicken gastrointestinal tract contains a diverse microbiota whose composition and structure play important roles in gut functionality. In this study, microbial shifts resulting from feed supplementation with Bacillus subtilis CSL2 were evaluated in broilers challenged and unchallenged with Salmonella Gallinarum. To analyse bacterial community composition and functionality, 454 GS-FLX pyrosequencing of 16S rRNA gene amplicons was performed.<br><br>RESULTS: The Quantitative Insights into Microbial Ecology (QIIME) pipeline was used to analyse changes in the faecal microbiota over a 24-h period. A total of 718,204 sequences from broiler chickens were recorded and analysed. At the phylum level, Firmicutes, Bacteroidetes, and Proteobacteria were the predominant bacterial taxa. In Salmonella-infected chickens (SC), Bacteroidetes were more highly abundant compared to control (NC) and Bacillus-treated (BT) chickens. At the genus level, in the NC and BT groups, Lactobacillus was present at high abundance, and the abundance of Turicibacter, unclassified Enterobacteriaceae, and Bacteroides increased in SC broilers. Furthermore, taxon-independent analysis showed that the SC and BT groups were compositionally distinct at the end of the 24-h period. Further analysis of functional properties showed that B. subtilis CSL2 administration increased gut-associated energy supply mechanisms (i.e. carbohydrate transport and metabolism) to maintain a stable microbiota and protect gut integrity.<br><br>CONCLUSIONS: This study demonstrated that S. Gallinarum infection and B. subtilis CSL2 supplementation in the diet of broiler chickens influenced the diversity, composition, and functional diversity of the faecal microbiota. Moreover, the findings offer significant insights to understand potential mechanisms of Salmonella infection and the mode of action of probiotics in broiler chickens.}, }
@article {pmid28066872, year = {2017}, author = {Rineau, F and Lmalem, H and Ahren, D and Shah, F and Johansson, T and Coninx, L and Ruytinx, J and Nguyen, H and Grigoriev, I and Kuo, A and Kohler, A and Morin, E and Vangronsveld, J and Martin, F and Colpaert, JV}, title = {Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes.}, journal = {Mycorrhiza}, volume = {27}, number = {4}, pages = {383-396}, pmid = {28066872}, issn = {1432-1890}, mesh = {Fungal Proteins/*genetics ; *Gene Duplication ; *Genome, Fungal ; Genomics ; Mycelium ; Mycorrhizae/*genetics ; }, abstract = {Hydrophobins are small secreted proteins that are present as several gene copies in most fungal genomes. Their properties are now well understood: they are amphiphilic and assemble at hydrophilic/hydrophobic interfaces. However, their physiological functions remain largely unexplored, especially within mycorrhizal fungi. In this study, we identified hydrophobin genes and analysed their distribution in eight mycorrhizal genomes. We then measured their expression levels in three different biological conditions (mycorrhizal tissue vs. free-living mycelium, organic vs. mineral growth medium and aerial vs. submerged growth). Results confirmed that the size of the hydrophobin repertoire increased in the terminal orders of the fungal evolutionary tree. Reconciliation analysis predicted that in 41% of the cases, hydrophobins evolved from duplication events. Whatever the treatment and the fungal species, the pattern of expression of hydrophobins followed a reciprocal function, with one gene much more expressed than others from the same repertoire. These most-expressed hydrophobin genes were also among the most expressed of the whole genome, which suggests that they play a role as structural proteins. The fine-tuning of the expression of hydrophobin genes in each condition appeared complex because it differed considerably between species, in a way that could not be explained by simple ecological traits. Hydrophobin gene regulation in mycorrhizal tissue as compared with free-living mycelium, however, was significantly associated with a calculated high exposure of hydrophilic residues.}, }
@article {pmid28066406, year = {2016}, author = {Rakonjac, J and Das, B and Derda, R}, title = {Editorial: Filamentous Bacteriophage in Bio/Nano/Technology, Bacterial Pathogenesis and Ecology.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {2109}, doi = {10.3389/fmicb.2016.02109}, pmid = {28066406}, issn = {1664-302X}, }
@article {pmid28066376, year = {2016}, author = {Barbato, M and Scoma, A and Mapelli, F and De Smet, R and Banat, IM and Daffonchio, D and Boon, N and Borin, S}, title = {Hydrocarbonoclastic Alcanivorax Isolates Exhibit Different Physiological and Expression Responses to n-dodecane.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {2056}, pmid = {28066376}, issn = {1664-302X}, abstract = {Autochthonous microorganisms inhabiting hydrocarbon polluted marine environments play a fundamental role in natural attenuation and constitute promising resources for bioremediation approaches. Alcanivorax spp. members are ubiquitous in contaminated surface waters and are the first to flourish on a wide range of alkanes after an oil-spill. Following oil contamination, a transient community of different Alcanivorax spp. develop, but whether they use a similar physiological, cellular and transcriptomic response to hydrocarbon substrates is unknown. In order to identify which cellular mechanisms are implicated in alkane degradation, we investigated the response of two isolates belonging to different Alcanivorax species, A. dieselolei KS 293 and A. borkumensis SK2 growing on n-dodecane (C12) or on pyruvate. Both strains were equally able to grow on C12 but they activated different strategies to exploit it as carbon and energy source. The membrane morphology and hydrophobicity of SK2 changed remarkably, from neat and hydrophilic on pyruvate to indented and hydrophobic on C12, while no changes were observed in KS 293. In addition, SK2 accumulated a massive amount of intracellular grains when growing on pyruvate, which might constitute a carbon reservoir. Furthermore, SK2 significantly decreased medium surface tension with respect to KS 293 when growing on C12, as a putative result of higher production of biosurfactants. The transcriptomic responses of the two isolates were also highly different. KS 293 changes were relatively balanced when growing on C12 with respect to pyruvate, giving almost the same amount of upregulated (28%), downregulated (37%) and equally regulated (36%) genes, while SK2 transcription was upregulated for most of the genes (81%) when growing on pyruvate when compared to C12. While both strains, having similar genomic background in genes related to hydrocarbon metabolism, retained the same capability to grow on C12, they nevertheless presented very different physiological, cellular and transcriptomic landscapes.}, }
@article {pmid28066357, year = {2016}, author = {Weisskopf, L and Ryu, CM and Raaijmakers, JM and Garbeva, P}, title = {Editorial: Smelly Fumes: Volatile-Mediated Communication between Bacteria and Other Organisms.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {2031}, pmid = {28066357}, issn = {1664-302X}, }
@article {pmid28065710, year = {2017}, author = {Evans, JK and Buchanan, KL and Griffith, SC and Klasing, KC and Addison, B}, title = {Ecoimmunology and microbial ecology: Contributions to avian behavior, physiology, and life history.}, journal = {Hormones and behavior}, volume = {88}, number = {}, pages = {112-121}, doi = {10.1016/j.yhbeh.2016.12.003}, pmid = {28065710}, issn = {1095-6867}, mesh = {Animals ; *Biological Evolution ; Birds/*microbiology/*physiology ; Breeding ; Ecosystem ; Life Cycle Stages ; Microbiota ; Molting ; Reproduction/*physiology ; }, abstract = {Bacteria have had a fundamental impact on vertebrate evolution not only by affecting the evolution of the immune system, but also generating complex interactions with behavior and physiology. Advances in molecular techniques have started to reveal the intricate ways in which bacteria and vertebrates have coevolved. Here, we focus on birds as an example system for understanding the fundamental impact bacteria have had on the evolution of avian immune defenses, behavior, physiology, reproduction and life histories. The avian egg has multiple characteristics that have evolved to enable effective defense against pathogenic attack. Microbial risk of pathogenic infection is hypothesized to vary with life stage, with early life risk being maximal at either hatching or fledging. For adult birds, microbial infection risk is also proposed to vary with habitat and life stage, with molt inducing a period of increased vulnerability. Bacteria not only play an important role in shaping the immune system as well as trade-offs with other physiological systems, but also for determining digestive efficiency and nutrient uptake. The relevance of avian microbiomes for avian ecology, physiology and behavior is highly topical and will likely impact on our understanding of avian welfare, conservation, captive breeding as well as for our understanding of the nature of host-microbe coevolution.}, }
@article {pmid28064361, year = {2017}, author = {Dunker, S and Althammer, J and Pohnert, G and Wilhelm, C}, title = {A Fateful Meeting of Two Phytoplankton Species-Chemical vs. Cell-Cell-Interactions in Co-Cultures of the Green Algae Oocystis marsonii and the Cyanobacterium Microcystis aeruginosa.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {22-32}, pmid = {28064361}, issn = {1432-184X}, mesh = {*Allelopathy ; Chlorophyta/chemistry/*physiology ; Coculture Techniques ; Microcystis/chemistry/*physiology ; Phytoplankton/chemistry/physiology ; }, abstract = {Massive growth of single species of cyanobacteria is a common phenomenon in many eutrophicated waters worldwide. Allelopathic growth control of phytoplankton species is one suggested mechanism, but still controversially discussed. The fact that the synthesis of biological active compounds requires high energy costs and carbon investment for a single cell in contrast to high dilution rates in natural systems questions the universal validity of allelopathic mechanisms, even more as high concentrations of allelopathic substances are often needed in several experiments to cause biological effects. In this study, it was tested, if growth inhibition is induced by chemical signaling alone or via direct cell-cell interaction. As a test system, we used a co-culture of the green algae Oocystis marsonii (Trebouxiophyceae) with the cyanobacterium Microcystis aeruginosa which is known to strongly reduce the growth of the green algal competitor. In this study, direct co-culturing as well as membrane-separated growth chambers were used to test for chemical and contact-mediated interactions. In the membrane-separated chambers, both species can be co-cultivated and a membrane allows the exchange of metabolites. Growth of O. marsonii was only affected in the direct co-cultivation situation, where direct cell-to-cell contact was possible. During direct co-cultivation, deviating cellular traits, namely cell cycle pattern and large cell-aggregate formation of both species, could be detected. These data strongly support the hypothesis of a direct cell-cell-contact necessary for allelopathic growth control in this model system. Such direct contact would allow targeting allelopathic metabolites directly towards the competitor and thereby minimizing dilution effects.}, }
@article {pmid28064360, year = {2017}, author = {Piovia-Scott, J and Rejmanek, D and Woodhams, DC and Worth, SJ and Kenny, H and McKenzie, V and Lawler, SP and Foley, JE}, title = {Greater Species Richness of Bacterial Skin Symbionts Better Suppresses the Amphibian Fungal Pathogen Batrachochytrium Dendrobatidis.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {217-226}, pmid = {28064360}, issn = {1432-184X}, mesh = {Animals ; Antibiosis ; *Bacteria ; Chytridiomycota/*pathogenicity ; Ranidae/*microbiology ; Skin/*microbiology ; *Symbiosis ; }, abstract = {The symbiotic microbes that grow in and on many organisms can play important roles in protecting their hosts from pathogen infection. While species diversity has been shown to influence community function in many other natural systems, the question of how species diversity of host-associated symbiotic microbes contributes to pathogen resistance is just beginning to be explored. Understanding diversity effects on pathogen resistance could be particularly helpful in combating the fungal pathogen Batrachochytrium dendrobatidis (Bd) which has caused dramatic population declines in many amphibian species and is a major concern for amphibian conservation. Our study investigates the ability of host-associated bacteria to inhibit the proliferation of Bd when grown in experimentally assembled biofilm communities that differ in species number and composition. Six bacterial species isolated from the skin of Cascades frogs (Rana cascadae) were used to assemble bacterial biofilm communities containing 1, 2, 3, or all 6 bacterial species. Biofilm communities were grown with Bd for 7 days following inoculation. More speciose bacterial communities reduced Bd abundance more effectively. This relationship between bacterial species richness and Bd suppression appeared to be driven by dominance effects-the bacterial species that were most effective at inhibiting Bd dominated multi-species communities-and complementarity: multi-species communities inhibited Bd growth more than monocultures of constituent species. These results underscore the notion that pathogen resistance is an emergent property of microbial communities, a consideration that should be taken into account when designing probiotic treatments to reduce the impacts of infectious disease.}, }
@article {pmid28063827, year = {2017}, author = {Thiele, S and Richter, M and Balestra, C and Glöckner, FO and Casotti, R}, title = {Taxonomic and functional diversity of a coastal planktonic bacterial community in a river-influenced marine area.}, journal = {Marine genomics}, volume = {32}, number = {}, pages = {61-69}, doi = {10.1016/j.margen.2016.12.003}, pmid = {28063827}, issn = {1876-7478}, mesh = {Archaea/*classification ; Bacteria/*classification ; Italy ; Mediterranean Sea ; *Microbiota ; Plankton/*classification ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Salinity ; }, abstract = {The Gulf of Naples is a dynamical area with intense exchanges between offshore oligotrophic and coastal eutrophic waters with frequent freshwater inputs. The Sarno River, one of the most polluted rivers in Europe, strongly contributes to the pollution of the area, discharging high amounts of heavy metals and organic wastes from heavily cultivated and industrial areas. This paper reports on the diversity and community structure of the marine residential Bacteria and Archaea of the Gulf of Naples in an area close to the river Sarno plume and investigates their small-scale taxonomic diversity and expression patterns as a proxy of potential metabolic activity using metagenomics and metatranscriptomics. Bacteria and Archaea were mainly represented by marine clades, with only minor contributors from freshwater ones. The community was dominated by Alpha- and Gammaproteobacteria, of which Rhodospirillales, Pelagibacteriales, and Oceanospirilalles were most represented. However, Alteromonadales and Rhodobacterales were the most active, despite their relative lower abundance, suggesting that they are important for overall ecosystem functioning and nutrient cycling. Nitrification and a reversed form of dissimilatory sulfate reduction were the major metabolic processes found in the metatrascriptomes and were mainly associated to Nitrosopumilales and Pelagibacter, respectively. No clear indication of transcripts related to stress induced by heavy metals or organic pollutants was found. In general, despite the high loads of pollutants discharged continuously by the Sarno River, the microbial community did not show marks of stress-induced changes neither structural nor functional, thus suggesting that this river has little or no effect on the planktonic bacterial community of the Gulf of Naples.}, }
@article {pmid28063363, year = {2017}, author = {Puig, S and Ganigué, R and Batlle-Vilanova, P and Balaguer, MD and Bañeras, L and Colprim, J}, title = {Tracking bio-hydrogen-mediated production of commodity chemicals from carbon dioxide and renewable electricity.}, journal = {Bioresource technology}, volume = {228}, number = {}, pages = {201-209}, doi = {10.1016/j.biortech.2016.12.035}, pmid = {28063363}, issn = {1873-2976}, mesh = {*Biofilms ; Bioreactors/*microbiology ; Carbon Dioxide/*metabolism ; Clostridium/metabolism ; *Electricity ; Hydrogenase/metabolism ; Rhodobacter ; }, abstract = {This study reveals that reduction of carbon dioxide (CO2) to commodity chemicals can be functionally compartmentalized in bioelectrochemical systems. In the present example, a syntrophic consortium composed by H2-producers (Rhodobacter sp.) in the biofilm is combined with carboxidotrophic Clostridium species, mainly found in the bulk liquid. The performance of these H2-mediated electricity-driven systems could be tracked by the activity of a biological H2 sensory protein identified at cathode potentials between -0.2V and -0.3V vs SHE. This seems to point out that such signal is not strain specific, but could be detected in any organism containing hydrogenases. Thus, the findings of this work open the door to the development of a biosensor application or soft sensors for monitoring such systems.}, }
@article {pmid28063283, year = {2017}, author = {De Vrieze, J and Christiaens, MER and Walraedt, D and Devooght, A and Ijaz, UZ and Boon, N}, title = {Microbial community redundancy in anaerobic digestion drives process recovery after salinity exposure.}, journal = {Water research}, volume = {111}, number = {}, pages = {109-117}, doi = {10.1016/j.watres.2016.12.042}, pmid = {28063283}, issn = {1879-2448}, mesh = {Anaerobiosis ; Archaea/metabolism ; Bioreactors/*microbiology ; Methane/metabolism ; *Salinity ; Sewage/microbiology ; }, abstract = {Anaerobic digestion of high-salinity wastewaters often results in process inhibition due to the susceptibility of the methanogenic archaea. The ability of the microbial community to deal with increased salinity levels is of high importance to ensure process perseverance or recovery after failure. The exact strategy of the microbial community to ensure process endurance is, however, often unknown. In this study, we investigated how the microbial community is able to recover process performance following a disturbance through the application of high-salinity molasses wastewater. After a stable start-up, methane production quickly decreased from 625 ± 17 to 232 ± 35 mL CH4 L[-1] d[-1] with a simultaneous accumulation in volatile fatty acids up to 20.5 ± 1.4 g COD L[-1], indicating severe process disturbance. A shift in feedstock from molasses wastewater to waste activated sludge resulted in complete process recovery. However, the bacterial and archaeal communities did not return to their original composition as before the disturbance, despite similar process conditions. Microbial community diversity was recovered to similar levels as before disturbance, which indicates that the metabolic potential of the community was maintained. A mild increase in ammonia concentration after process recovery did not influence methane production, indicating a well-balanced microbial community. Hence, given the change in community composition following recovery after salinity disturbance, it can be assumed that microbial community redundancy was the major strategy to ensure the continuation of methane production, without loss of functionality or metabolic flexibility.}, }
@article {pmid28063252, year = {2017}, author = {Shabarova, T and Kasalický, V and Šimek, K and Nedoma, J and Znachor, P and Posch, T and Pernthaler, J and Salcher, MM}, title = {Distribution and ecological preferences of the freshwater lineage LimA (genus Limnohabitans) revealed by a new double hybridization approach.}, journal = {Environmental microbiology}, volume = {19}, number = {3}, pages = {1296-1309}, doi = {10.1111/1462-2920.13663}, pmid = {28063252}, issn = {1462-2920}, mesh = {Comamonadaceae/classification/genetics/*isolation &amp; purification ; Ecology ; In Situ Hybridization, Fluorescence ; Lakes/analysis/*microbiology ; RNA, Ribosomal, 16S/genetics ; Seasons ; }, abstract = {The ecological relevance and factors shaping dynamics of Limnohabitans sp. have been largely studied by fluorescence in situ hybridization with a 16S rRNA probe targeting the R-BT group (lineages LimBCDE), but not lineage LimA. Consequently, ecology and distribution of LimA remained unknown. We developed a double hybridization strategy using a novel 23S rRNA probe specifically targeting LimA and LimE that in combination with the existing R-BT probe can discriminate LimA populations. This technique was applied for more than 1000 samples from 46 freshwater sites including long-term data sets from oligo-mesotrophic Lake Zurich, CH and meso-eutrophic Římov reservoir, CZ. LimA was ubiquitously distributed and highly abundant. Observed ecological preferences of LimA in Lake Zurich were in general similar to already reported for Limnohabitans with highest numbers in surface waters during growing seasons. Three times higher densities of LimA were detected in Římov reservoir, where they were significantly more abundant at the riverine zone especially after flood events that introduced fresh terrestrial DOM (dissolved organic matter). Moreover, statistical analyses of biological and physicochemical parameters obtained from small dynamic water bodies confirmed a correspondence between LimA and allochthonous DOM, in opposite to R-BT that was more related to algal primary production.}, }
@article {pmid28062901, year = {2017}, author = {Cho, H and Kim, M and Tripathi, B and Adams, J}, title = {Changes in Soil Fungal Community Structure with Increasing Disturbance Frequency.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {62-77}, pmid = {28062901}, issn = {1432-184X}, mesh = {Bacteria ; *Biodiversity ; Fungi/*classification ; Soil ; *Soil Microbiology ; }, abstract = {Although disturbance is thought to be important in many ecological processes, responses of fungal communities to soil disturbance have been little studied experimentally. We subjected a soil microcosm to physical disturbance, at a range of frequencies designed to simulate ecological disturbance events. We analyzed the fungal community structure using Illumina HiSeq sequencing of the ITS1 region. Fungal diversity was found to decline with the increasing disturbance frequencies, with no sign of the "humpback" pattern found in many studies of larger sedentary organisms. There is thus no evidence of an effect of release from competition resulting from moderate disturbance-which suggests that competition and niche overlap may not be important in limiting soil fungal diversity. Changing disturbance frequency also led to consistent differences in community composition. There were clear differences in OTU-level composition, with different disturbance treatments each having distinct fungal communities. The functional profile of fungal groups (guilds) was changed by the level of disturbance frequency. These predictable differences in community composition suggest that soil fungi can possess different niches in relation to disturbance frequency, or time since last disturbance. Fungi appear to be most abundant relative to bacteria at intermediate disturbance frequencies, on the time scale we studied here.}, }
@article {pmid28062463, year = {2017}, author = {Chou, WC and Huang, SC and Chiu, CH and Chen, YM}, title = {YMC-2011, a Temperate Phage of Streptococcus salivarius 57.I.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {6}, pages = {}, pmid = {28062463}, issn = {1098-5336}, mesh = {Base Sequence ; DNA, Viral/genetics ; Lysogeny/drug effects/*genetics ; Mitomycin/*pharmacology ; Mouth/microbiology ; Promoter Regions, Genetic/genetics ; Sequence Analysis, DNA ; Streptococcus Phages/classification/*genetics ; Streptococcus salivarius/genetics/isolation &amp; purification/*virology ; Virus Activation/*drug effects ; }, abstract = {Streptococcus salivarius is an abundant isolate of the oral cavity. The genome of S. salivarius 57.I consists of a 2-Mb chromosome and a 40,758-bp circular molecule, designated YMC-2011. Annotation of YMC-2011 revealed 55 open reading frames, most of them associated with phage production, although plaque formation is not observed in S. salivarius 57.I after lytic induction using mitomycin C. Results from Southern hybridization and quantitative real-time PCR confirmed that YMC-2011 exists extrachromosomally, with an estimated copy number of 3 to 4. Phage particles were isolated from the supernatant of mitomycin C-treated S. salivarius 57.I cultures, and transmission electron microscopic examination indicated that YMC-2011 belongs to the Siphoviridae family. Phylogenetic analysis suggests that phage YMC-2011 and the cos-type phages of Streptococcus thermophilus originated from a common ancestor. An extended -10 element (p L) and a σ[70]-like promoter (p R) were mapped 5' to Ssal_phage00013 (encoding a CI-like repressor) and Ssal_phage00014 (encoding a hypothetical protein), respectively, using 5' rapid amplification of cDNA ends, indicating that YMC-2011 transcribes at least two mRNAs in opposite orientations. Studies using promoter-chloramphenicol acetyltransferase reporter gene fusions revealed that p R , but not p L , was sensitive to mitomycin C induction, suggesting that the switch from lysogenic growth to lytic growth was controlled mainly by the activity of these two promoters. In conclusion, a lysogenic state is maintained in S. salivarius 57.I, presumably by the repression of genes encoding proteins for lytic growth.IMPORTANCE The movement of mobile genetic elements such as bacteriophages and the establishment of lysogens may have profound effects on the balance of microbial ecology where lysogenic bacteria reside. The discovery of phage YMC-2011 from Streptococcus salivarius 57.I suggests that YMC-2011 and Streptococcus thermophilus-infecting phages share an ancestor. Although S. salivarius and S. thermophilus are close phylogenetically, S. salivarius is a natural inhabitant of the human mouth, whereas S. thermophilus is commonly found in the mammary mucosa of bovine species. Thus, the identification of YMC-2011 suggests that horizontal gene transfer via phage infection could take place between species from different ecological niches.}, }
@article {pmid28060363, year = {2017}, author = {Mußmann, M and Pjevac, P and Krüger, K and Dyksma, S}, title = {Genomic repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members of microbial communities in marine sediments.}, journal = {The ISME journal}, volume = {11}, number = {5}, pages = {1276-1281}, pmid = {28060363}, issn = {1751-7370}, mesh = {Australia ; Autotrophic Processes ; Gammaproteobacteria/classification/*genetics/isolation &amp; purification/metabolism ; Genome, Bacterial ; Geologic Sediments/*microbiology ; Heterotrophic Processes ; Metagenomics ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {To date, very little is known about the bacterial core community of marine sediments. Here we study the environmental distribution, abundance and ecogenomics of the gammaproteobacterial Woeseiaceae/JTB255 marine benthic group. A meta-analysis of published work shows that the Woeseiaceae/JTB255 are ubiquitous and consistently rank among the most abundant 16S rRNA gene sequences in diverse marine sediments. They account for up to 22% of bacterial amplicons and 6% of total cell counts in European and Australian coastal sediments. The analysis of a single-cell genome, metagenomic bins and the genome of the next cultured relative Woeseia oceani indicated a broad physiological range, including heterotrophy and facultative autotrophy. All tested (meta)genomes encode a truncated denitrification pathway to nitrous oxide. The broad range of energy-yielding metabolisms possibly explains the ubiquity and high abundance of Woeseiaceae/JTB255 in marine sediments, where they carry out diverse, but yet unknown ecological functions.}, }
@article {pmid28059479, year = {2018}, author = {Arends, JBA}, title = {The next step towards usable microbial bioelectrochemical sensors?.}, journal = {Microbial biotechnology}, volume = {11}, number = {1}, pages = {20-21}, pmid = {28059479}, issn = {1751-7915}, mesh = {Biosensing Techniques/*methods/trends ; Electricity ; Electrochemical Techniques/*methods/trends ; Electrodes/microbiology ; Metabolism ; Microbiological Techniques/*methods/trends ; }, }
@article {pmid28058513, year = {2017}, author = {Johnson, RM and Ramond, JB and Gunnigle, E and Seely, M and Cowan, DA}, title = {Namib Desert edaphic bacterial, fungal and archaeal communities assemble through deterministic processes but are influenced by different abiotic parameters.}, journal = {Extremophiles : life under extreme conditions}, volume = {21}, number = {2}, pages = {381-392}, pmid = {28058513}, issn = {1433-4909}, mesh = {Archaea/*growth &amp; development ; Bacteria/*growth &amp; development ; *Desert Climate ; Fungi/*growth &amp; development ; Microbial Consortia/*physiology ; Namibia ; *Soil Microbiology ; }, abstract = {The central Namib Desert is hyperarid, where limited plant growth ensures that biogeochemical processes are largely driven by microbial populations. Recent research has shown that niche partitioning is critically involved in the assembly of Namib Desert edaphic communities. However, these studies have mainly focussed on the Domain Bacteria. Using microbial community fingerprinting, we compared the assembly of the bacterial, fungal and archaeal populations of microbial communities across nine soil niches from four Namib Desert soil habitats (riverbed, dune, gravel plain and salt pan). Permutational multivariate analysis of variance indicated that the nine soil niches presented significantly different physicochemistries (R [2] = 0.8306, P ≤ 0.0001) and that bacterial, fungal and archaeal populations were soil niche specific (R [2] ≥ 0.64, P ≤ 0.001). However, the abiotic drivers of community structure were Domain-specific (P < 0.05), with P, clay and sand fraction, and NH4 influencing bacterial, fungal and archaeal communities, respectively. Soil physicochemistry and soil niche explained over 50% of the variation in community structure, and communities displayed strong non-random patterns of co-occurrence. Taken together, these results demonstrate that in central Namib Desert soil microbial communities, assembly is principally driven by deterministic processes.}, }
@article {pmid28058470, year = {2017}, author = {Essarioui, A and LeBlanc, N and Kistler, HC and Kinkel, LL}, title = {Plant Community Richness Mediates Inhibitory Interactions and Resource Competition between Streptomyces and Fusarium Populations in the Rhizosphere.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {157-167}, pmid = {28058470}, issn = {1432-184X}, mesh = {Andropogon/*microbiology ; Ecosystem ; Fusarium/*physiology ; Lespedeza/*microbiology ; *Rhizosphere ; *Soil Microbiology ; Streptomyces/*physiology ; }, abstract = {Plant community characteristics impact rhizosphere Streptomyces nutrient competition and antagonistic capacities. However, the effects of Streptomyces on, and their responses to, coexisting microorganisms as a function of plant host or plant species richness have received little attention. In this work, we characterized antagonistic activities and nutrient use among Streptomyces and Fusarium from the rhizosphere of Andropogon gerardii (Ag) and Lespedeza capitata (Lc) plants growing in communities of 1 (monoculture) or 16 (polyculture) plant species. Streptomyces from monoculture were more antagonistic against Fusarium than those from polyculture. In contrast, Fusarium isolates from polyculture had greater inhibitory capacities against Streptomyces than isolates from monoculture. Although Fusarium isolates had on average greater niche widths, the collection of Streptomyces isolates in total used a greater diversity of nutrients for growth. Plant richness, but not plant host, influenced the potential for resource competition between the two taxa. Fusarium isolates had greater niche overlap with Streptomyces in monoculture than polyculture, suggesting greater potential for Fusarium to competitively challenge Streptomyces in monoculture plant communities. In contrast, Streptomyces had greater niche overlap with Fusarium in polyculture than monoculture, suggesting that Fusarium experiences greater resource competition with Streptomyces in polyculture than monoculture. These patterns of competitive and inhibitory phenotypes among Streptomyces and Fusarium populations are consistent with selection for Fusarium-antagonistic Streptomyces populations in the presence of strong Fusarium resource competition in plant monocultures. Similarly, these results suggest selection for Streptomyces-inhibitory Fusarium populations in the presence of strong Streptomyces resource competition in more diverse plant communities. Thus, landscape-scale variation in plant species richness may be critical to mediating the coevolutionary dynamics and selective trajectories for inhibitory and nutrient use phenotypes among Streptomyces and Fusarium populations in soil, with significant implications for microbial community functional characteristics.}, }
@article {pmid28058469, year = {2017}, author = {Monggoot, S and Popluechai, S and Gentekaki, E and Pripdeevech, P}, title = {Fungal Endophytes: an Alternative Source for Production of Volatile Compounds from Agarwood Oil of Aquilaria subintegra.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {54-61}, pmid = {28058469}, issn = {1432-184X}, mesh = {Ascomycota/*chemistry ; Colletotrichum/*chemistry ; Endophytes/*chemistry ; Gas Chromatography-Mass Spectrometry ; Plant Oils/*analysis ; Thailand ; Thymelaeaceae/*microbiology ; Volatile Organic Compounds/*analysis ; }, abstract = {Fungal endophytes are microorganisms that are well-known for producing a diverse array of secondary metabolites. Recent studies have uncovered the bioprospecting potential of several plant endophytic fungi. Here, we demonstrate the presence of highly bioactive fungal endophytic species in Aquilaria subintegra, a fragrant wood plant collected from Thailand. Thirty-three fungal endophytic strains were isolated and further identified to genus level based on morphological characteristics. These genera included Colletotrichum, Pestalotiopsis, Fusarium, Russula, Arthrinium, Diaporthe and Cladosporium. All strains were cultured on potato dextrose broth for 30 days prior to partitioning with ethyl acetate. The volatile compounds of all extracts were investigated by gas chromatography-mass spectrometry (GC-MS). Four strains-Arthrinium sp. MFLUCC16-0042, Colletotrichum sp. MFLUCC16-0047, Colletotrichum sp. MFLUCC16-0048 and Diaporthe sp. MFLUCC16-0051-produced a broad spectrum of volatile compounds, including β-agarofuran, α-agarofuran, δ-eudesmol, oxo-agarospirol, and β-dihydro agarofuran. These compounds are especially important, because they greatly resemble those originating from the host-produced agarwood oil. Our findings demonstrate the potential of endophytic fungi to produce bioactive compounds with applications in perfumery and cosmetic industries. Antioxidant activity of all extracts was also evaluated by using 2,2-diphenyl-2-picrylhydrazyl radical scavenging assays. The ethyl acetate extract of Diaporthe sp. MFLUCC16-0051 demonstrated superior antioxidant capacity, which was comparable to that of the gallic acid standard. Our results indicate that the MFLUCC16-0051 strain is a resource of natural antioxidant with potential medicinal applications.}, }
@article {pmid28057476, year = {2017}, author = {Bonnevialle, P}, title = {Operative treatment of early infection after internal fixation of limb fractures (exclusive of severe open fractures).}, journal = {Orthopaedics &amp; traumatology, surgery &amp; research : OTSR}, volume = {103}, number = {1S}, pages = {S67-S73}, doi = {10.1016/j.otsr.2016.06.019}, pmid = {28057476}, issn = {1877-0568}, mesh = {Anti-Bacterial Agents/therapeutic use ; Decision Support Techniques ; Femoral Fractures/surgery ; Fracture Fixation, Internal/*adverse effects/methods ; *Fracture Healing ; Fractures, Bone/*surgery ; Humans ; Humeral Fractures/surgery ; Surgical Wound Infection/drug therapy/microbiology/*surgery ; Wound Closure Techniques ; }, abstract = {Early infection after open reduction and internal fixation (ORIF) of a limb bone is defined as bacteriologically documented, deep and/or superficial surgical-site infection (SSI) diagnosed within 6months after the surgical procedure. This interval is arbitrarily considered sufficient to obtain fracture healing. The treatment of early infection after ORIF should be decided by a multidisciplinary team. The principles are the same as for revision arthroplasty. Superficial SSIs should be differentiated from deep SSIs, based on the results of bacteriological specimens collected using flawless technique. A turning point in the local microbial ecology occurs around the third or fourth week, when a biofilm develops around metallic implants. This biofilm protects the bacteria. The treatment relies on both non-operative and operative measures, which are selected based on the time to occurrence of the infection, condition of the soft tissues, and stage of bone healing. Both the surgical strategy and the antibiotic regimen should be determined during a multidisciplinary discussion. When treating superficial SSIs after ORIF, soft-tissue management is the main challenge. The treatment differs according to whether the hardware is covered or exposed. Defects in the skin and/or fascia can be managed using reliable reconstructive surgery techniques, either immediately or after a brief period of vacuum-assisted closure. In deep SSIs, deciding whether to leave or to remove the hardware is difficult. If the hardware is removed, the fracture site can be stabilised provisionally using either external fixation or a cement rod. Once infection control is achieved, several measures can be taken to stimulate bone healing before the end of the classical 6-month interval. If the hardware was removed, then internal fixation must be performed once the infection is eradicated.}, }
@article {pmid28056822, year = {2017}, author = {O'Connor, C and Philip, RK and Kelleher, J and Powell, J and O'Gorman, A and Slevin, B and Woodford, N and Turton, JF and McGrath, E and Finnegan, C and Power, L and O'Connell, NH and Dunne, CP}, title = {The first occurrence of a CTX-M ESBL-producing Escherichia coli outbreak mediated by mother to neonate transmission in an Irish neonatal intensive care unit.}, journal = {BMC infectious diseases}, volume = {17}, number = {1}, pages = {16}, pmid = {28056822}, issn = {1471-2334}, mesh = {Adult ; Disease Outbreaks ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/*genetics/*isolation &amp; purification ; Escherichia coli Infections/congenital/*diagnosis/microbiology/transmission ; Escherichia coli Proteins/*genetics/metabolism ; Female ; Humans ; Infant, Newborn ; Infection Control ; *Infectious Disease Transmission, Vertical ; Intensive Care Units, Neonatal ; Ireland ; Male ; Molecular Typing ; Mothers ; Pregnancy ; Pregnancy Complications, Infectious/microbiology ; beta-Lactamases/*genetics/metabolism ; }, abstract = {BACKGROUND: Escherichia coli (E. coli) comprise part of the normal vaginal microflora. Transfer from mother to neonate can occur during delivery resulting, sometimes, in neonatal bacterial disease. Here, we aim to report the first outbreak of CTX-M ESBL-producing E. coli with evidence of mother-to-neonate transmission in an Irish neonatal intensive care unit (NICU) followed by patient-to-patient transmission.<br><br>METHODS: Investigation including molecular typing was conducted. Infection was defined by clinical and laboratory criteria and requirement for antimicrobial therapy with or without positive blood cultures. Colonisation was determined by isolation without relevant symptoms or indicators of infection.<br><br>RESULTS: Index case was an 8-day-old baby born at 34&#xa0;weeks gestation who developed ESBL-producing E. coli infections at multiple body sites. Screening confirmed their mother as colonised with ESBL-producing E. coli. Five other neonates, in the NICU simultaneously with the index case, also tested positive. Of these, four were colonised while one neonate developed sepsis, requiring antimicrobial therapy. The second infected neonate's mother was also colonised by ESBL-producing E. coli. Isolates from all eight positive patients (6 neonates, 2 mothers) were compared using pulsed-field gel electrophoresis (PFGE). Two distinct ESBL-producing strains were implicated, with evidence of transmission between mothers and neonates for both strains. All isolates were confirmed as CTX-M ESBL-producers. There were no deaths associated with the outbreak.<br><br>CONCLUSIONS: Resources were directed towards control interventions focused on hand hygiene and antimicrobial stewardship, which ultimately proved successful. Since this incident, all neonates admitted to the NICU have been screened for ESBL-producers and expectant mothers are screened at their first antenatal appointment. To date, there have been no further outbreaks.}, }
@article {pmid28056169, year = {2017}, author = {Maes, S and Zhuang, WQ and Rabaey, K and Alvarez-Cohen, L and Hennebel, T}, title = {Concomitant Leaching and Electrochemical Extraction of Rare Earth Elements from Monazite.}, journal = {Environmental science &amp; technology}, volume = {51}, number = {3}, pages = {1654-1661}, doi = {10.1021/acs.est.6b03675}, pmid = {28056169}, issn = {1520-5851}, mesh = {Citric Acid ; Lanthanum ; Metals, Rare Earth/*isolation &amp; purification ; *Neodymium ; Phosphates ; Recycling ; }, abstract = {Rare earth elements (REEs) have become increasingly important in modern day technologies. Unfortunately, their recycling is currently limited, and the conventional technologies for their extraction and purification are exceedingly energy and chemical intensive. New sustainable technologies for REE extraction from both primary and secondary resources would be extremely beneficial. This research investigated a two-stage recovery strategy focused on the recovery of neodymium (Nd) and lanthanum (La) from monazite ore that combines microbially based leaching (using citric acid and spent fungal supernatant) with electrochemical extraction. Pretreating the phosphate-based monazite rock (via roasting) dramatically increased the microbial REE leaching efficiency. Batch experiments demonstrated the effective and continued leaching of REEs by recycled citric acid, with up to 392 mg of Nd L[-1] and 281 mg of La L[-1] leached during seven consecutive 24 h cycles. Neodymium was further extracted in the catholyte of a three-compartment electrochemical system, with up to 880 mg of Nd L[-1] achieved within 4 days (at 40 A m[-2]). Meanwhile, the radioactive element thorium and counterions phosphate and citrate were separated effectively from the REEs in the anolyte, favoring REE extraction and allowing sustainable reuse of the leaching agent. This study shows a promising technology that is suitable for primary ores and can further be optimized for secondary resources.}, }
@article {pmid28054304, year = {2017}, author = {Han, G and Lee, HJ and Jeong, SE and Jeon, CO and Hyun, S}, title = {Comparative Analysis of Drosophila melanogaster Gut Microbiota with Respect to Host Strain, Sex, and Age.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {207-216}, pmid = {28054304}, issn = {1432-184X}, mesh = {Acetobacter ; Age Factors ; Animals ; Drosophila melanogaster/*microbiology ; Female ; *Gastrointestinal Microbiome ; Male ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Sex Factors ; }, abstract = {Microbiota has a significant impact on the health of the host individual. The complexity of the interactions between mammalian hosts and their microbiota highlights the value of using Drosophila melanogaster as a model organism, because of its relatively simple microbial community and ease of physiological and genetic manipulation. However, highly variable and sometimes inconsistent results regarding the microbiota of D. melanogaster have been reported for host samples collected from different geographical locations; discrepancies that may be because of the inherent physiological conditions of the D. melanogaster host. Here, we conducted a comparative analysis of the gut microbiota of two D. melanogaster laboratory strains, w [1118] and Canton S, with respect to the sex and age of the host, by pyrosequencing of the 16S rRNA gene. In addition to the widespread and abundant commensal bacterial genera Lactobacillus and Acetobacter, we identified Enterococcus and Leuconostoc as major host-strain-specific bacterial genera. The relative proportions of these bacterial genera, and those of the species within each, were found to differ markedly with respect to strain, sex, and age of the host, even though host individuals were reared under the same nutritional conditions. By using various bioinformatic tools, we uncovered several characteristic features of microbiota corresponding to specific categories of the flies: host-sex-bias association of specific bacteria, age-dependent alteration of microbiota across host species and sex, and uniqueness of the microbiota of female w [1118] flies. Our results, thus, help to further our understanding of host-microbe interactions in the D. melanogaster model.}, }
@article {pmid28052139, year = {2017}, author = {Hoshino, T and Inagaki, F}, title = {Application of Stochastic Labeling with Random-Sequence Barcodes for Simultaneous Quantification and Sequencing of Environmental 16S rRNA Genes.}, journal = {PloS one}, volume = {12}, number = {1}, pages = {e0169431}, pmid = {28052139}, issn = {1932-6203}, mesh = {Base Sequence ; *DNA Barcoding, Taxonomic ; *Environment ; Gene Dosage ; High-Throughput Nucleotide Sequencing/*methods ; RNA, Ribosomal, 16S/*genetics ; Stochastic Processes ; }, abstract = {Next-generation sequencing (NGS) is a powerful tool for analyzing environmental DNA and provides the comprehensive molecular view of microbial communities. For obtaining the copy number of particular sequences in the NGS library, however, additional quantitative analysis as quantitative PCR (qPCR) or digital PCR (dPCR) is required. Furthermore, number of sequences in a sequence library does not always reflect the original copy number of a target gene because of biases caused by PCR amplification, making it difficult to convert the proportion of particular sequences in the NGS library to the copy number using the mass of input DNA. To address this issue, we applied stochastic labeling approach with random-tag sequences and developed a NGS-based quantification protocol, which enables simultaneous sequencing and quantification of the targeted DNA. This quantitative sequencing (qSeq) is initiated from single-primer extension (SPE) using a primer with random tag adjacent to the 5' end of target-specific sequence. During SPE, each DNA molecule is stochastically labeled with the random tag. Subsequently, first-round PCR is conducted, specifically targeting the SPE product, followed by second-round PCR to index for NGS. The number of random tags is only determined during the SPE step and is therefore not affected by the two rounds of PCR that may introduce amplification biases. In the case of 16S rRNA genes, after NGS sequencing and taxonomic classification, the absolute number of target phylotypes 16S rRNA gene can be estimated by Poisson statistics by counting random tags incorporated at the end of sequence. To test the feasibility of this approach, the 16S rRNA gene of Sulfolobus tokodaii was subjected to qSeq, which resulted in accurate quantification of 5.0 × 103 to 5.0 × 104 copies of the 16S rRNA gene. Furthermore, qSeq was applied to mock microbial communities and environmental samples, and the results were comparable to those obtained using digital PCR and relative abundance based on a standard sequence library. We demonstrated that the qSeq protocol proposed here is advantageous for providing less-biased absolute copy numbers of each target DNA with NGS sequencing at one time. By this new experiment scheme in microbial ecology, microbial community compositions can be explored in more quantitative manner, thus expanding our knowledge of microbial ecosystems in natural environments.}, }
@article {pmid28051919, year = {2017}, author = {Sadowsky, MJ and Staley, C and Heiner, C and Hall, R and Kelly, CR and Brandt, L and Khoruts, A}, title = {Analysis of gut microbiota - An ever changing landscape.}, journal = {Gut microbes}, volume = {8}, number = {3}, pages = {268-275}, pmid = {28051919}, issn = {1949-0984}, mesh = {Animals ; Clostridium Infections/therapy ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {In the last two decades, the field of metagenomics has greatly expanded due to improvement in sequencing technologies allowing for a more comprehensive characterization of microbial communities. The use of these technologies has led to an unprecedented understanding of human, animal, and environmental microbiomes and have shown that the gut microbiota are comparable to an organ that is intrinsically linked with a variety of diseases. Characterization of microbial communities using next-generation sequencing-by-synthesis approaches have revealed important shifts in microbiota associated with debilitating diseases such as Clostridium difficile infection. But due to limitations in sequence read length, primer biases, and the quality of databases, genus- and species-level classification have been difficult. Third-generation technologies, such as Pacific Biosciences' single molecule, real-time (SMRT) approach, allow for unbiased, more specific identification of species that are likely clinically relevant. Comparison of Illumina next-generation characterization and SMRT sequencing of samples from patients treated for C. difficile infection revealed similarities in community composition at the phylum and family levels, but SMRT sequencing further allowed for species-level characterization - permitting a better understanding of the microbial ecology of this disease. Thus, as sequencing technologies continue to advance, new species-level insights can be gained in the study of complex and clinically-relevant microbial communities.}, }
@article {pmid28046131, year = {2017}, author = {Maes, S and Props, R and Fitts, JP and De Smet, R and Vanhaecke, F and Boon, N and Hennebel, T}, title = {Biological Recovery of Platinum Complexes from Diluted Aqueous Streams by Axenic Cultures.}, journal = {PloS one}, volume = {12}, number = {1}, pages = {e0169093}, pmid = {28046131}, issn = {1932-6203}, mesh = {Antineoplastic Agents/analysis ; *Axenic Culture ; Carboplatin/analysis ; Cisplatin/analysis ; Cupriavidus ; Environmental Monitoring ; Environmental Pollutants/*analysis ; *Environmental Restoration and Remediation ; Flow Cytometry ; Geobacter ; Microbial Viability ; Microscopy, Electron, Transmission ; Platinum/*analysis ; Platinum Compounds/analysis ; Shewanella ; Wastewater ; Water Purification ; }, abstract = {The widespread use of platinum in high-tech and catalytic applications has led to the production of diverse Pt loaded wastewaters. Effective recovery strategies are needed for the treatment of low concentrated waste streams to prevent pollution and to stimulate recovery of this precious resource. The biological recovery of five common environmental Pt-complexes was studied under acidic conditions; the chloro-complexes PtCl42- and PtCl62-, the amine-complex Pt(NH3)4Cl2 and the pharmaceutical complexes cisplatin and carboplatin. Five bacterial species were screened on their platinum recovery potential; the Gram-negative species Shewanella oneidensis MR-1, Cupriavidus metallidurans CH34, Geobacter metallireducens, and Pseudomonas stutzeri, and the Gram-positive species Bacillus toyonensis. Overall, PtCl42- and PtCl62- were completely recovered by all bacterial species while only S. oneidensis and C. metallidurans were able to recover cisplatin quantitatively (99%), all in the presence of H2 as electron donor at pH 2. Carboplatin was only partly recovered (max. 25% at pH 7), whereas no recovery was observed in the case of the Pt-tetraamine complex. Transmission electron microscopy (TEM) revealed the presence of both intra- and extracellular platinum particles. Flow cytometry based microbial viability assessment demonstrated the decrease in number of intact bacterial cells during platinum reduction and indicated C. metallidurans to be the most resistant species. This study showed the effective and complete biological recovery of three common Pt-complexes, and estimated the fate and transport of the Pt-complexes in wastewater treatment plants and the natural environment.}, }
@article {pmid28043001, year = {2017}, author = {Van Nevel, S and Buysschaert, B and De Roy, K and De Gusseme, B and Clement, L and Boon, N}, title = {Flow cytometry for immediate follow-up of drinking water networks after maintenance.}, journal = {Water research}, volume = {111}, number = {}, pages = {66-73}, doi = {10.1016/j.watres.2016.12.040}, pmid = {28043001}, issn = {1879-2448}, mesh = {Drinking Water/*microbiology ; *Flow Cytometry ; Follow-Up Studies ; Water Microbiology ; Water Supply ; }, abstract = {Drinking water networks need maintenance every once in a while, either planned interventions or emergency repairs. When this involves opening of the water pipes, precautionary measures need to be taken to avoid contamination of the drinking water at all time. Drinking water suppliers routinely apply plating for faecal indicator organisms as quality control in such a situation. However, this takes at least 21 h of waiting time, which can be crucial when dealing with major supply pipes. A combination of flow cytometric (FCM) bacterial cell counts with FCM fingerprinting techniques is proposed in this study as a fast and sensitive additional technique. In three full scale situations, major supply pipes with 400-1050 mm diameter were emptied for maintenance, shock-chlorinated and flushed with large amounts of clean drinking water before taking back in operation. FCM measurements of the discharged flushing water revealed fast lowering and stabilizing bacterial concentrations once flushing is initiated. Immediate comparison with clean reference drinking water used for flushing was done, and the moment when both waters had similar bacterial concentrations was considered as the endpoint of the necessary flushing works. This was usually after 2-4 h of flushing. FCM fingerprinting, based on both bacteria and FCM background, was used as additional method to verify how similar flushing and reference samples were and yielded similar results. The FCM approved samples were several hours later approved as well by the drinking water supplier after plating and incubation for total Coliforms and Enterococci. These were used as decisive control to set the pipes back in operation. FCM proved to be a more conservative test than plating, yet it yielded immediate results. Application of these FCM methods can therefore avoid long unnecessary waiting times and large drinking water losses.}, }
@article {pmid28042698, year = {2017}, author = {Tang, T and Mohr, W and Sattin, SR and Rogers, DR and Girguis, PR and Pearson, A}, title = {Geochemically distinct carbon isotope distributions in Allochromatium vinosum DSM 180[T] grown photoautotrophically and photoheterotrophically.}, journal = {Geobiology}, volume = {15}, number = {2}, pages = {324-339}, doi = {10.1111/gbi.12221}, pmid = {28042698}, issn = {1472-4669}, mesh = {Acetates/metabolism ; Amino Acids/analysis ; Carbon Cycle ; Carbon Dioxide/metabolism ; Carbon Isotopes/*analysis ; Chromatiaceae/*chemistry/*growth &amp; development/metabolism ; Fatty Acids/analysis ; Phytol/analysis ; Proteins/analysis ; RNA, Bacterial/analysis ; }, abstract = {Anoxygenic, photosynthetic bacteria are common at redox boundaries. They are of interest in microbial ecology and geosciences through their role in linking the carbon, sulfur, and iron cycles, yet much remains unknown about how their flexible carbon metabolism-permitting either autotrophic or heterotrophic growth-is recorded in the bulk sedimentary and lipid biomarker records. Here, we investigated patterns of carbon isotope fractionation in a model photosynthetic sulfur-oxidizing bacterium, Allochromatium vinosum DSM180[T] . In one treatment, A. vinosum was grown with CO2 as the sole carbon source, while in a second treatment, it was grown on acetate. Different intracellular isotope patterns were observed for fatty acids, phytol, individual amino acids, intact proteins, and total RNA between the two experiments. Photoautotrophic CO2 fixation yielded typical isotopic ordering for the lipid biomarkers: δ[13] C values of phytol > n-alkyl lipids. In contrast, growth on acetate greatly suppressed intracellular isotopic heterogeneity across all molecular classes, except for a marked [13] C-depletion in phytol. This caused isotopic "inversion" in the lipids (δ[13] C values of phytol < n-alkyl lipids). The finding suggests that inverse δ[13] C patterns of n-alkanes and pristane/phytane in the geologic record may be at least in part a signal for photoheterotrophy. In both experimental scenarios, the relative isotope distributions could be predicted from an isotope flux-balance model, demonstrating that microbial carbon metabolisms can be interrogated by combining compound-specific stable isotope analysis with metabolic modeling. Isotopic differences among molecular classes may be a means of fingerprinting microbial carbon metabolism, both in the modern environment and the geologic record.}, }
@article {pmid28040838, year = {2017}, author = {Adriaenssens, EM and Krupovic, M and Knezevic, P and Ackermann, HW and Barylski, J and Brister, JR and Clokie, MR and Duffy, S and Dutilh, BE and Edwards, RA and Enault, F and Jang, HB and Klumpp, J and Kropinski, AM and Lavigne, R and Poranen, MM and Prangishvili, D and Rumnieks, J and Sullivan, MB and Wittmann, J and Oksanen, HM and Gillis, A and Kuhn, JH}, title = {Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee.}, journal = {Archives of virology}, volume = {162}, number = {4}, pages = {1153-1157}, doi = {10.1007/s00705-016-3173-4}, pmid = {28040838}, issn = {1432-8798}, mesh = {Viruses/*classification/genetics ; }, }
@article {pmid28040210, year = {2017}, author = {Burges, A and Epelde, L and Blanco, F and Becerril, JM and Garbisu, C}, title = {Ecosystem services and plant physiological status during endophyte-assisted phytoremediation of metal contaminated soil.}, journal = {The Science of the total environment}, volume = {584-585}, number = {}, pages = {329-338}, doi = {10.1016/j.scitotenv.2016.12.146}, pmid = {28040210}, issn = {1879-1026}, mesh = {Biodegradation, Environmental ; Brassicaceae/*metabolism/microbiology ; Ecosystem ; Endophytes/*physiology ; Metals/*isolation &amp; purification ; Rumex/*metabolism/microbiology ; Soil ; *Soil Microbiology ; Soil Pollutants/*isolation &amp; purification ; }, abstract = {Mining sites shelter a characteristic biodiversity with large potential for the phytoremediation of metal contaminated soils. Endophytic plant growth-promoting bacteria were isolated from two metal-(hyper)accumulator plant species growing in a metal contaminated mine soil. After characterizing their plant growth-promoting traits, consortia of putative endophytes were used to carry out an endophyte-assisted phytoextraction experiment using Noccaea caerulescens and Rumex acetosa (singly and in combination) under controlled conditions. We evaluated the influence of endophyte-inoculated plants on soil physicochemical and microbial properties, as well as plant physiological parameters and metal concentrations. Data interpretation through the grouping of soil properties within a set of ecosystem services was also carried out. When grown together, we observed a 41 and 16% increase in the growth of N. caerulescens and R. acetosa plants, respectively, as well as higher values of Zn phytoextraction and soil microbial biomass and functional diversity. Inoculation of the consortia of putative endophytes did not lead to higher values of plant metal uptake, but it improved the plants' physiological status, by increasing the content of chlorophylls and carotenoids by up to 28 and 36%, respectively, indicating a reduction in the stress level of plants. Endophyte-inoculation also stimulated soil microbial communities: higher values of acid phosphatase activity (related to the phosphate solubilising traits of the endophytes), bacterial and fungal abundance, and structural diversity. The positive effects of plant growth and endophyte inoculation on soil properties were reflected in an enhancement of some ecosystem services (biodiversity, nutrient cycling, water flow regulation, water purification and contamination control).}, }
@article {pmid28038926, year = {2017}, author = {Tyc, O and Song, C and Dickschat, JS and Vos, M and Garbeva, P}, title = {The Ecological Role of Volatile and Soluble Secondary Metabolites Produced by Soil Bacteria.}, journal = {Trends in microbiology}, volume = {25}, number = {4}, pages = {280-292}, doi = {10.1016/j.tim.2016.12.002}, pmid = {28038926}, issn = {1878-4380}, mesh = {Antibiosis/physiology ; Bacteria/*metabolism ; Rhizosphere ; Secondary Metabolism/*physiology ; Soil/*chemistry ; *Soil Microbiology ; Volatile Organic Compounds/*metabolism ; }, abstract = {The rich diversity of secondary metabolites produced by soil bacteria has been appreciated for over a century, and advances in chemical analysis and genome sequencing continue to greatly advance our understanding of this biochemical complexity. However, we are just at the beginning of understanding the physicochemical properties of bacterial metabolites, the factors that govern their production and ecological roles. Interspecific interactions and competitor sensing are among the main biotic factors affecting the production of bacterial secondary metabolites. Many soil bacteria produce both volatile and soluble compounds. In contrast to soluble compounds, volatile organic compounds can diffuse easily through air- and gas-filled pores in the soil and likely play an important role in long-distance microbial interactions. In this review we provide an overview of the most important soluble and volatile classes of secondary metabolites produced by soil bacteria, their ecological roles, and their possible synergistic effects.}, }
@article {pmid28035742, year = {2017}, author = {Pereira, FC and Berry, D}, title = {Microbial nutrient niches in the gut.}, journal = {Environmental microbiology}, volume = {19}, number = {4}, pages = {1366-1378}, pmid = {28035742}, issn = {1462-2920}, support = {P 26127/FWF_/Austrian Science Fund FWF/Austria ; P 27831/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Cellular Microenvironment ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {The composition and function of the mammalian gut microbiota has been the subject of much research in recent years, but the principles underlying the assembly and structure of this complex community remain incompletely understood. Processes that shape the gut microbiota are thought to be mostly niche-driven, with environmental factors such as the composition of available nutrients largely determining whether or not an organism can establish. The concept that the nutrient landscape dictates which organisms can successfully colonize and persist in the gut was first proposed in Rolf Freter's nutrient niche theory. In a situation where nutrients are perfectly mixed and there is balanced microbial growth, Freter postulated that an organism can only survive if it is able to utilize one or a few limiting nutrients more efficiently than its competitors. Recent experimental work indicates, however, that nutrients in the gut vary in space and time. We propose that in such a scenario, Freter's nutrient niche theory must be expanded to account for the co-existence of microorganisms utilizing the same nutrients but in distinct sites or at different times, and that metabolic flexibility and mixed-substrate utilization are common strategies for survival in the face of ever-present nutrient fluctuations.}, }
@article {pmid28034543, year = {2017}, author = {Molineux, CJ and Gange, AC and Newport, DJ}, title = {Using soil microbial inoculations to enhance substrate performance on extensive green roofs.}, journal = {The Science of the total environment}, volume = {580}, number = {}, pages = {846-856}, doi = {10.1016/j.scitotenv.2016.12.031}, pmid = {28034543}, issn = {1879-1026}, mesh = {Agricultural Inoculants ; Architecture ; *Biodiversity ; Conservation of Natural Resources ; Plant Development ; *Plants ; Soil ; *Soil Microbiology ; }, abstract = {Green roofs are increasing in popularity in the urban environment for their contribution to green infrastructure; but their role for biodiversity is not often a design priority. Maximising biodiversity will impact positively on ecosystem services and is therefore fundamental for achieving the greatest benefits from green roofs. Extensive green roofs are lightweight systems generally constructed with a specialised growing medium that tends to be biologically limited and as such can be a harsh habitat for plants to thrive in. Thus, this investigation aimed to enhance the soil functioning with inoculations of soil microbes to increase plant diversity, improve vegetation health/performance and maximise access to soil nutrients. Manipulations included the addition of mycorrhizal fungi and a microbial mixture ('compost tea') to green roof rootzones, composed mainly of crushed brick or crushed concrete. The study revealed that growing media type and depth play a vital role in the microbial ecology of green roofs, with complex relationships between depth and type of substrate and the type of microbial inoculant applied, with no clear pattern being observed. For bait plant measurements (heights, leaf numbers, root/shoot biomass, leaf nutrients), a compost tea may have positive effects on plant performance when grown in substrates of shallower depths (5.5cm), even one year after inoculums are applied. Results from the species richness surveys show that diversity was significantly increased with the application of an AM fungal treatment and that overall, results suggest that brick-based substrate blends are most effective for vegetation performance as are deeper depths (although this varied with time). Microbial inoculations of green roof habitats appeared to be sustainable; they need only be done once for benefits to still been seen in subsequent years where treatments are added independently (not in combination). They seem to be a novel and viable method of enhancing rooftop conditions.}, }
@article {pmid28033847, year = {2017}, author = {Azevedo, AS and Almeida, C and Melo, LF and Azevedo, NF}, title = {Impact of polymicrobial biofilms in catheter-associated urinary tract infections.}, journal = {Critical reviews in microbiology}, volume = {43}, number = {4}, pages = {423-439}, doi = {10.1080/1040841X.2016.1240656}, pmid = {28033847}, issn = {1549-7828}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Biofilms/*growth &amp; development ; Catheter-Related Infections/drug therapy/microbiology/*pathology ; Drug Resistance, Bacterial/*physiology ; Escherichia coli/drug effects ; Escherichia coli Infections/drug therapy/microbiology ; Klebsiella Infections/drug therapy/microbiology ; Klebsiella pneumoniae/drug effects ; Microbial Interactions/*physiology ; Microbiota/*physiology ; Pseudomonas Infections/drug therapy/microbiology ; Pseudomonas aeruginosa/drug effects ; Urinary Tract Infections/drug therapy/microbiology/*pathology ; }, abstract = {Recent reports have demonstrated that most biofilms involved in catheter-associated urinary tract infections are polymicrobial communities, with pathogenic microorganisms (e.g. Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae) and uncommon microorganisms (e.g. Delftia tsuruhatensis, Achromobacter xylosoxidans) frequently co-inhabiting the same urinary catheter. However, little is known about the interactions that occur between different microorganisms and how they impact biofilm formation and infection outcome. This lack of knowledge affects CAUTIs management as uncommon bacteria action can, for instance, influence the rate at which pathogens adhere and grow, as well as affect the overall biofilm resistance to antibiotics. Another relevant aspect is the understanding of factors that drive a single pathogenic bacterium to become prevalent in a polymicrobial community and subsequently cause infection. In this review, a general overview about the IMDs-associated biofilm infections is provided, with an emphasis on the pathophysiology and the microbiome composition of CAUTIs. Based on the available literature, it is clear that more research about the microbiome interaction, mechanisms of biofilm formation and of antimicrobial tolerance of the polymicrobial consortium are required to better understand and treat these infections.}, }
@article {pmid28033417, year = {2016}, author = {Tyc, O and Tomás-Menor, L and Garbeva, P and Barrajón-Catalán, E and Micol, V}, title = {Validation of the AlamarBlue® Assay as a Fast Screening Method to Determine the Antimicrobial Activity of Botanical Extracts.}, journal = {PloS one}, volume = {11}, number = {12}, pages = {e0169090}, pmid = {28033417}, issn = {1932-6203}, mesh = {Anti-Infective Agents/*pharmacology ; Candida albicans/drug effects/growth &amp; development ; Drug Evaluation, Preclinical/*methods ; Escherichia coli/drug effects/growth &amp; development ; Kinetics ; Microbial Sensitivity Tests ; Plant Extracts/*pharmacology ; Staphylococcus aureus/drug effects/growth &amp; development ; Time Factors ; }, abstract = {Plant compounds are a potential source of new antimicrobial molecules against a variety of infections. Plant extracts suppose complex phytochemical libraries that may be used for the first stages of the screening process for antimicrobials. However, their large variability and complexity require fast and inexpensive methods that allow a rapid and adequate screening for antimicrobial activity against a variety of bacteria and fungi. In this study, a multi-well plate assay using the AlamarBlue® fluorescent dye was applied to screen for antimicrobial activity of several botanical extracts and the data were correlated with microbial colony forming units (CFU). This correlation was performed for three pathogenic model microorganisms: Escherichia coli (Gram negative bacteria), Staphylococcus aureus (Gram positive bacteria) and for the yeast-like fungi Candida albicans. A total of ten plant extracts from different Mediterranean plants, including several Cistus and Hibiscus species, were successfully tested. HPLC-DAD-ESI-MS/MS analysis was utilized for the characterization of the extracts in order to establish structure-activity correlations. The results show that extracts enriched in ellagitannins and flavonols are promising antibacterial agents against both Gram positive and Gram negative bacteria. In contrast, phenolic acids, anthocyanidins and flavonols may be related to the observed antifungal activity.}, }
@article {pmid28033374, year = {2016}, author = {Stephen, AS and Millhouse, E and Sherry, L and Aduse-Opoku, J and Culshaw, S and Ramage, G and Bradshaw, DJ and Burnett, GR and Allaker, RP}, title = {In Vitro Effect of Porphyromonas gingivalis Methionine Gamma Lyase on Biofilm Composition and Oral Inflammatory Response.}, journal = {PloS one}, volume = {11}, number = {12}, pages = {e0169157}, pmid = {28033374}, issn = {1932-6203}, mesh = {Adhesins, Bacterial/metabolism ; Biofilms/*growth &amp; development ; Carbon-Sulfur Lyases/deficiency/genetics/*metabolism ; Cell Line ; Cysteine Endopeptidases/metabolism ; Cytokines/metabolism ; Gene Knockout Techniques ; Gingipain Cysteine Endopeptidases ; Humans ; Inflammation/microbiology ; Keratinocytes/metabolism/microbiology ; Mouth/*microbiology ; Porphyromonas gingivalis/*enzymology/*physiology ; Sulfur/chemistry/metabolism ; }, abstract = {Methanethiol (methyl mercaptan) is an important contributor to oral malodour and periodontal tissue destruction. Porphyromonas gingivalis, Prevotella intermedia and Fusobacterium nucleatum are key oral microbial species that produce methanethiol via methionine gamma lyase (mgl) activity. The aim of this study was to compare an mgl knockout strain of P. gingivalis with its wild type using a 10-species biofilm co-culture model with oral keratinocytes and its effect on biofilm composition and inflammatory cytokine production. A P. gingivalis mgl knockout strain was constructed using insertion mutagenesis from wild type W50 with gas chromatographic head space analysis confirming lack of methanethiol production. 10-species biofilms consisting of Streptococcus mitis, Streptococcus oralis, Streptococcus intermedius, Fusobacterium nucleatum ssp polymorphum, Fusobacterium nucleatum ssp vincentii, Veillonella dispar, Actinomyces naeslundii, Prevotella intermedia and Aggregatibacter actinomycetemcomitans with either the wild type or mutant P. gingivalis were grown on Thermanox cover slips and used to stimulate oral keratinocytes (OKF6-TERT2), under anaerobic conditions for 4 and 24 hours. Biofilms were analysed by quantitative PCR with SYBR Green for changes in microbial ecology. Keratinocyte culture supernatants were analysed using a multiplex bead immunoassay for cytokines. Significant population differences were observed between mutant and wild type biofilms; V. dispar proportions increased (p<0.001), whilst A. naeslundii (p<0.01) and Streptococcus spp. (p<0.05) decreased in mutant biofilms. Keratinocytes produced less IL-8, IL-6 and IL-1α when stimulated with the mutant biofilms compared to wild type. Lack of mgl in P. gingivalis has been shown to affect microbial ecology in vitro, giving rise to a markedly different biofilm composition, with a more pro-inflammatory cytokine response from the keratinocytes observed. A possible role for methanethiol in biofilm formation and cytokine response with subsequent effects on oral malodor and periodontitis is suggested.}, }
@article {pmid28032128, year = {2017}, author = {Pappa, O and Beloukas, A and Vantarakis, A and Mavridou, A and Kefala, AM and Galanis, A}, title = {Molecular Characterization and Phylogenetic Analysis of Pseudomonas aeruginosa Isolates Recovered from Greek Aquatic Habitats Implementing the Double-Locus Sequence Typing Scheme.}, journal = {Microbial ecology}, volume = {74}, number = {1}, pages = {78-88}, pmid = {28032128}, issn = {1432-184X}, mesh = {Bacterial Typing Techniques ; *Ecosystem ; Greece ; *Multilocus Sequence Typing ; *Phylogeny ; Pseudomonas aeruginosa/*classification ; *Water Microbiology ; }, abstract = {The recently described double-locus sequence typing (DLST) scheme implemented to deeply characterize the genetic profiles of 52 resistant environmental Pseudomonas aeruginosa isolates deriving from aquatic habitats of Greece. DLST scheme was able not only to assign an already known allelic profile to the majority of the isolates but also to recognize two new ones (ms217-190, ms217-191) with high discriminatory power. A third locus (oprD) was also used for the molecular typing, which has been found to be fundamental for the phylogenetic analysis of environmental isolates given the resulted increased discrimination between the isolates. Additionally, the circulation of acquired resistant mechanisms in the aquatic habitats according to their genetic profiles was proved to be more extent. Hereby, we suggest that the combination of the DLST to oprD typing can discriminate phenotypically and genetically related environmental P. aeruginosa isolates providing reliable phylogenetic analysis at a local level.}, }
@article {pmid28032127, year = {2017}, author = {Boscaro, V and Rossi, A and Vannini, C and Verni, F and Fokin, SI and Petroni, G}, title = {Strengths and Biases of High-Throughput Sequencing Data in the Characterization of Freshwater Ciliate Microbiomes.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {865-875}, pmid = {28032127}, issn = {1432-184X}, mesh = {Biodiversity ; Ciliophora/*classification/*cytology/*genetics/isolation &amp; purification ; DNA, Protozoan/analysis ; Environmental Microbiology ; Fresh Water/*parasitology ; Genes, rRNA ; Geologic Sediments/parasitology ; High-Throughput Nucleotide Sequencing/*methods ; Italy ; Microbiota/*genetics ; *Phylogeny ; Phylogeography ; Sequence Analysis ; }, abstract = {Molecular surveys of eukaryotic microbial communities employing high-throughput sequencing (HTS) techniques are rapidly supplanting traditional morphological approaches due to their larger data output and reduced bench work time. Here, we directly compare morphological and Illumina data obtained from the same samples, in an effort to characterize ciliate faunas from sediments in freshwater environments. We show how in silico processing affects the final outcome of our HTS analysis, providing evidence that quality filtering protocols strongly impact the number of predicted taxa, but not downstream conclusions such as biogeography patterns. We determine the abundance distribution of ciliates, showing that a small fraction of abundant taxa dominates read counts. At the same time, we advance reasons to believe that biases affecting HTS abundances may be significant enough to blur part of the underlying biological picture. We confirmed that the HTS approach detects many more taxa than morphological inspections, and highlight how the difference varies among taxonomic groups. Finally, we hypothesize that the two datasets actually correspond to different conceptions of "diversity," and consequently that neither is entirely superior to the other when investigating environmental protists.}, }
@article {pmid28028549, year = {2016}, author = {Lynch, MD and Neufeld, JD}, title = {SSUnique: Detecting Sequence Novelty in Microbiome Surveys.}, journal = {mSystems}, volume = {1}, number = {6}, pages = {}, pmid = {28028549}, issn = {2379-5077}, abstract = {High-throughput sequencing of small-subunit (SSU) rRNA genes has revolutionized understanding of microbial communities and facilitated investigations into ecological dynamics at unprecedented scales. Such extensive SSU rRNA gene sequence libraries, constructed from DNA extracts of environmental or host-associated samples, often contain a substantial proportion of unclassified sequences, many representing organisms with novel taxonomy (taxonomic "blind spots") and potentially unique ecology. Indeed, these novel taxonomic lineages are associated with so-called microbial "dark matter," which is the genomic potential of these lineages. Unfortunately, characterization beyond "unclassified" is challenging due to relatively short read lengths and large data set sizes. Here we demonstrate how mining of phylogenetically novel sequences from microbial ecosystems can be automated using SSUnique, a software pipeline that filters unclassified and/or rare operational taxonomic units (OTUs) from 16S rRNA gene sequence libraries by screening against consensus structural models for SSU rRNA. Phylogenetic position is inferred against a reference data set, and additional characterization of novel clades is also included, such as targeted probe/primer design and mining of assembled metagenomes for genomic context. We show how SSUnique reproduced a previous analysis of phylogenetic novelty from an Arctic tundra soil and demonstrate the recovery of highly novel clades from data sets associated with both the Earth Microbiome Project (EMP) and Human Microbiome Project (HMP). We anticipate that SSUnique will add to the expanding computational toolbox supporting high-throughput sequencing approaches for the study of microbial ecology and phylogeny. IMPORTANCE Extensive SSU rRNA gene sequence libraries, constructed from DNA extracts of environmental or host-associated samples, often contain many unclassified sequences, many representing organisms with novel taxonomy (taxonomic "blind spots") and potentially unique ecology. This novelty is poorly explored in standard workflows, which narrows the breadth and discovery potential of such studies. Here we present the SSUnique analysis pipeline, which will promote the exploration of unclassified diversity in microbiome research and, importantly, enable the discovery of substantial novel taxonomic lineages through the analysis of a large variety of existing data sets.}, }
@article {pmid28028456, year = {2016}, author = {Sinclair, L and Ijaz, UZ and Jensen, LJ and Coolen, MJL and Gubry-Rangin, C and Chroňáková, A and Oulas, A and Pavloudi, C and Schnetzer, J and Weimann, A and Ijaz, A and Eiler, A and Quince, C and Pafilis, E}, title = {Seqenv: linking sequences to environments through text mining.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e2690}, pmid = {28028456}, issn = {2167-8359}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. Here we introduce a software program, seqenv, to carry out precisely such a task. It automatically performs similarity searches of short sequences against the "nt" nucleotide database provided by NCBI and, out of every hit, extracts-if it is available-the textual metadata field. After collecting all the isolation sources from all the search results, we run a text mining algorithm to identify and parse words that are associated with the Environmental Ontology (EnvO) controlled vocabulary. This, in turn, enables us to determine both in which environments individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples. We present two demonstrative applications of seqenv to a survey of ammonia oxidizing archaea as well as to a plankton paleome dataset from the Black Sea. These demonstrate the ability of the tool to reveal novel patterns in HTS and its utility in the fields of environmental source tracking, paleontology, and studies of microbial biogeography. To install seqenv, go to: https://github.com/xapple/seqenv.}, }
@article {pmid28025668, year = {2017}, author = {Timonen, S and Sinkko, H and Sun, H and Sietiö, OM and Rinta-Kanto, JM and Kiheri, H and Heinonsalo, J}, title = {Ericoid Roots and Mycospheres Govern Plant-Specific Bacterial Communities in Boreal Forest Humus.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {939-953}, pmid = {28025668}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Base Sequence ; Biodiversity ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; Finland ; Forests ; High-Throughput Nucleotide Sequencing/methods ; *Microbial Consortia ; Mycorrhizae/genetics ; Phylogeny ; Pinus/microbiology ; Plant Roots/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; *Taiga ; }, abstract = {In this study, the bacterial populations of roots and mycospheres of the boreal pine forest ericoid plants, heather (Calluna vulgaris), bilberry (Vaccinium myrtillus), and lingonberry (Vaccinium vitis-idaea), were studied by qPCR and next-generation sequencing (NGS). All bacterial communities of mycosphere soils differed from soils uncolonized by mycorrhizal mycelia. Colonization by mycorrhizal hyphae increased the total number of bacterial 16S ribosomal DNA (rDNA) gene copies in the humus but decreased the number of different bacterial operational taxonomic units (OTUs). Nevertheless, ericoid roots and mycospheres supported numerous OTUs not present in uncolonized humus. Bacterial communities in bilberry mycospheres were surprisingly similar to those in pine mycospheres but not to bacterial communities in heather and lingonberry mycospheres. In contrast, bacterial communities of ericoid roots were more similar to each other than to those of pine roots. In all sample types, the relative abundances of bacterial sequences belonging to Alphaproteobacteria and Acidobacteria were higher than the sequences belonging to other classes. Soil samples contained more Actinobacteria, Deltaproteobacteria, Opitutae, and Planctomycetia, whereas Armatimonadia, Betaproteobacteria, Gammaproteobacteria, and Sphingobacteriia were more common to roots. All mycosphere soils and roots harbored bacteria unique to that particular habitat. Our study suggests that the habitation by ericoid plants increases the overall bacterial diversity of boreal forest soils.}, }
@article {pmid28025470, year = {2016}, author = {Takai, K}, title = {Virologists are "Symbionts" in Microbial Ecology.}, journal = {Microbes and environments}, volume = {31}, number = {4}, pages = {367-368}, pmid = {28025470}, issn = {1347-4405}, }
@article {pmid28018655, year = {2016}, author = {Jover, LF and Romberg, J and Weitz, JS}, title = {Inferring phage-bacteria infection networks from time-series data.}, journal = {Royal Society open science}, volume = {3}, number = {11}, pages = {160654}, pmid = {28018655}, issn = {2054-5703}, abstract = {In communities with bacterial viruses (phage) and bacteria, the phage-bacteria infection network establishes which virus types infect which host types. The structure of the infection network is a key element in understanding community dynamics. Yet, this infection network is often difficult to ascertain. Introduced over 60 years ago, the plaque assay remains the gold standard for establishing who infects whom in a community. This culture-based approach does not scale to environmental samples with increased levels of phage and bacterial diversity, much of which is currently unculturable. Here, we propose an alternative method of inferring phage-bacteria infection networks. This method uses time-series data of fluctuating population densities to estimate the complete interaction network without having to test each phage-bacteria pair individually. We use in silico experiments to analyse the factors affecting the quality of network reconstruction and find robust regimes where accurate reconstructions are possible. In addition, we present a multi-experiment approach where time series from different experiments are combined to improve estimates of the infection network. This approach also mitigates against the possibility of evolutionary changes to relevant phenotypes during the time course of measurement.}, }
@article {pmid28012242, year = {2017}, author = {Hochkogler, CM and Lieder, B and Rust, P and Berry, D and Meier, SM and Pignitter, M and Riva, A and Leitinger, A and Bruk, A and Wagner, S and Hans, J and Widder, S and Ley, JP and Krammer, GE and Somoza, V}, title = {A 12-week intervention with nonivamide, a TRPV1 agonist, prevents a dietary-induced body fat gain and increases peripheral serotonin in moderately overweight subjects.}, journal = {Molecular nutrition &amp; food research}, volume = {61}, number = {5}, pages = {}, doi = {10.1002/mnfr.201600731}, pmid = {28012242}, issn = {1613-4133}, mesh = {Adiponectin/blood ; Adiposity/drug effects ; Adult ; Blood Glucose/metabolism ; Body Composition ; Body Mass Index ; Body Weight ; Capsaicin/administration &amp; dosage/*analogs &amp; derivatives ; Cholesterol/blood ; Diet ; Dietary Fats/*adverse effects ; Female ; Gastrointestinal Hormones/blood ; Gastrointestinal Microbiome/drug effects ; Humans ; Insulin/blood ; Leptin/blood ; Male ; Overweight/*drug therapy ; Postprandial Period ; Satiation ; Sensory System Agents/administration &amp; dosage ; Serotonin/*blood ; TRPV Cation Channels/*agonists ; Triglycerides/blood ; Weight Gain/*drug effects ; Young Adult ; }, abstract = {SCOPE: A bolus administration of 0.15 mg nonivamide has previously been demonstrated to reduce energy intake in moderately overweight men. This 12-week intervention investigated whether a daily consumption of nonivamide in a protein-based product formulation promotes a reduction in body weight in healthy overweight subjects and affects outcome measures associated with mechanisms regulating food intake, e.g. plasma concentrations of (an)orexigenic hormones, energy substrates as well as changes in fecal microbiota.<br><br>METHODS AND RESULTS: Nineteen overweight subjects were randomly assigned to either a control (C) or a nonivamide (NV) group. Changes in the body composition and plasma concentrations of satiating hormones were determined at fasting and 15, 30, 60, 90, and 120 min after a glucose load. Participants were instructed to consume 0.15 mg nonivamide per day in 450 mL of a milk shake additionally to their habitual diet. After treatment, a group difference in body fat mass change (-0.61 &#xb1; 0.36% in NV and +1.36 &#xb1; 0.38% in C) and an increase in postprandial plasma serotonin were demonstrated. Plasma metabolome and fecal microbiome read outs were not affected.<br><br>CONCLUSIONS: A daily intake of 0.15 mg nonivamide helps to support to maintain a healthy body composition.}, }
@article {pmid28012222, year = {2017}, author = {Jiao, S and Zhang, Z and Yang, F and Lin, Y and Chen, W and Wei, G}, title = {Temporal dynamics of microbial communities in microcosms in response to pollutants.}, journal = {Molecular ecology}, volume = {26}, number = {3}, pages = {923-936}, doi = {10.1111/mec.13978}, pmid = {28012222}, issn = {1365-294X}, mesh = {Bacteria/*classification ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; *Soil Pollutants ; Time Factors ; }, abstract = {Elucidating the mechanisms underlying microbial succession is a major goal of microbial ecology research. Given the increasing human pressure on the environment and natural resources, responses to the repeated introduction of organic and inorganic pollutants are of particular interest. To investigate the temporal dynamics of microbial communities in response to pollutants, we analysed the microbial community structure in batch microcosms that were inoculated with soil bacteria following exposure to individual or combined pollutants (phenanthrene, n-octadecane, phenanthrene + n-octadecane and phenanthrene + n-octadecane + CdCl2). Subculturing was performed at 10-day intervals, followed by high-throughput sequencing of 16S rRNA genes. The dynamics of microbial communities in response to different pollutants alone and in combination displayed similar patterns during enrichment. Specifically, the repression and induction of microbial taxa were dominant, and the fluctuation was not significant. The rate of appearance for new taxa and the temporal turnover within microbial communities were higher than the rates reported in other studies of microbial communities in air, water and soil samples. In addition, conditionally rare taxa that were specific to the treatments exhibited higher betweenness centrality values in the co-occurrence network, indicating a strong influence on other interactions in the community. These results suggest that the repeated introduction of pollutants could accelerate microbial succession in microcosms, resulting in the rapid re-equilibration of microbial communities.}, }
@article {pmid28011994, year = {2017}, author = {Donner, A and Glaser, K and Borchhardt, N and Karsten, U}, title = {Ecophysiological Response on Dehydration and Temperature in Terrestrial Klebsormidium (Streptophyta) Isolated from Biological Soil Crusts in Central European Grasslands and Forests.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {850-864}, pmid = {28011994}, issn = {1432-184X}, mesh = {*Adaptation, Physiological ; Biodiversity ; Chlorophyll ; Chlorophyll A ; DNA, Ribosomal/genetics ; *Dehydration ; Desiccation ; Ecology ; Ecosystem ; Forests ; Germany ; Grassland ; Photosynthesis ; Phylogeny ; Soil ; Streptophyta/*classification/genetics/growth &amp; development/*physiology ; Stress, Physiological ; *Temperature ; }, abstract = {The green algal genus Klebsormidium (Klebsormidiophyceae, Streptophyta) is a typical member of biological soil crusts (BSCs) worldwide. Ecophysiological studies focused so far on individual strains and thus gave only limited insight on the plasticity of this genus. In the present study, 21 Klebsormidium strains (K. dissectum, K. flaccidum, K. nitens, K. subtile) from temperate BSCs in Central European grassland and forest sites were investigated. Photosynthetic performance under desiccation and temperature stress was measured under identical controlled conditions. Photosynthesis decreased during desiccation within 335-505 min. After controlled rehydration, most isolates recovered, but with large variances between single strains and species. However, all K. dissectum strains had high recovery rates (>69%). All 21 Klebsormidium isolates exhibited the capability to grow under a wide temperature range. Except one strain, all others grew at 8.5 °C and four strains were even able to grow at 6.2 °C. Twenty out of 21 Klebsormidium isolates revealed an optimum growth temperature >17 °C, indicating psychrotrophic features. Growth rates at optimal temperatures varied between strains from 0.26 to 0.77 μ day[-1]. Integrating phylogeny and ecophysiological traits, we found no phylogenetic signal in the traits investigated. However, multivariate statistical analysis indicated an influence of the recovery rate and growth rate. The results demonstrate a high infraspecific and interspecific physiological plasticity, and thus wide ecophysiological ability to cope with strong environmental gradients. This might be the reason why members of the genus Klebsormidium successfully colonize terrestrial habitats worldwide.}, }
@article {pmid28011599, year = {2017}, author = {Garaiyurrebaso, O and Garbisu, C and Blanco, F and Lanzén, A and Martín, I and Epelde, L and Becerril, JM and Jechalke, S and Smalla, K and Grohmann, E and Alkorta, I}, title = {Long-term effects of aided phytostabilisation on microbial communities of metal-contaminated mine soil.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {3}, pages = {}, doi = {10.1093/femsec/fiw252}, pmid = {28011599}, issn = {1574-6941}, mesh = {Biodegradation, Environmental ; Biomass ; Environmental Pollution ; Environmental Restoration and Remediation/*methods ; Manure/microbiology ; Metals/*analysis ; Metals, Heavy/analysis ; *Mining ; Paper ; Plants ; Sewage ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/*analysis ; Time ; }, abstract = {Aided phytostabilisation uses metal-tolerant plants, together with organic or inorganic amendments, to reduce metal bioavailability in soil while improving soil quality. The long-term effects of the following organic amendments were examined as part of an aided phytostabilisation field study in an abandoned Pb/Zn mining area: cow slurry, sheep manure and paper mill sludge mixed with poultry manure. In the mining area, two heavily contaminated vegetated sites, showing different levels of soil metal contamination (LESS and MORE contaminated site), were selected for this study. Five years after amendment application, metal bioavailability (CaCl2 extractability) along with a variety of indicators of soil microbial activity, biomass and diversity were analysed. Paper mill sludge mixed with poultry manure treatment resulted in the highest reduction of Cd, Pb and Zn bioavailability, as well as in stimulation of soil microbial activity and diversity, especially at the LESS contaminated site. In contrast, cow slurry was the least successful treatment. Our results emphasise the importance of the (i) long-term monitoring of soil quality at sites subjected to aided phytostabilisation and (ii) selection of the most efficient amendments and plants in terms of both reduction of metal bioavailability and improvement of soil quality.}, }
@article {pmid28011597, year = {2017}, author = {De Mulder, T and Goossens, K and Peiren, N and Vandaele, L and Haegeman, A and De Tender, C and Ruttink, T and de Wiele, TV and De Campeneere, S}, title = {Exploring the methanogen and bacterial communities of rumen environments: solid adherent, fluid and epimural.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {3}, pages = {}, doi = {10.1093/femsec/fiw251}, pmid = {28011597}, issn = {1574-6941}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Cattle ; *Gastrointestinal Microbiome ; Methane/*metabolism ; Real-Time Polymerase Chain Reaction ; Rumen/anatomy &amp; histology/*microbiology ; }, abstract = {The rumen microbiome occupies a central role in animal health and productivity. A better understanding of the rumen ecosystem is essential to increase productivity or decrease methane production. Samples were collected from the three main rumen environments: the solid-adherent fraction, the liquid fraction and the epithelium. For the liquid and solid fraction, two alternative sample processing protocols were compared, resulting in a total of five sample types: crude solids (S), the eluted solid-adherent fraction (Ad), free-living species in the crude rumen liquid (CRL), strained liquid samples (Lq) and epimural scrapings (Ep). The bacterial and methanogen communities of these sample types were analysed using 16S metabarcoding and qPCR. The results indicate that the liquid and solid-adherent environments are distinguished mainly by the differential abundance of specific taxonomic groups. Cellulolytic bacteria that pioneer biofilm formation, together with secondary colonisers are prevalent in solid-adherent samples, while dominant species in the fluid samples are primarily identified as consumers of soluble nutrients. Also, methanogen species are found to have a preference for either a solid-adherent or free-living occurrence. The epimural environment is characterised by a different microbial profile. Ten bacterial families and two methanogen genera are almost exclusively found in this environment.}, }
@article {pmid28008997, year = {2016}, author = {Harter, J and Guzman-Bustamante, I and Kuehfuss, S and Ruser, R and Well, R and Spott, O and Kappler, A and Behrens, S}, title = {Gas entrapment and microbial N2O reduction reduce N2O emissions from a biochar-amended sandy clay loam soil.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {39574}, pmid = {28008997}, issn = {2045-2322}, mesh = {Aluminum Silicates ; Carbon ; Charcoal/*chemistry ; Clay ; Denitrification ; Electric Conductivity ; Fertilizers ; Gases ; Hydrogen-Ion Concentration ; Nitrification ; Nitrogen/chemistry ; Nitrous Oxide/*analysis ; Polymerase Chain Reaction ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/*chemistry ; }, abstract = {Nitrous oxide (N2O) is a potent greenhouse gas that is produced during microbial nitrogen transformation processes such as nitrification and denitrification. Soils represent the largest sources of N2O emissions with nitrogen fertilizer application being the main driver of rising atmospheric N2O concentrations. Soil biochar amendment has been proposed as a promising tool to mitigate N2O emissions from soils. However, the underlying processes that cause N2O emission suppression in biochar-amended soils are still poorly understood. We set up microcosm experiments with fertilized, wet soil in which we used [15]N tracing techniques and quantitative polymerase chain reaction (qPCR) to investigate the impact of biochar on mineral and gaseous nitrogen dynamics and denitrification-specific functional marker gene abundance and expression. In accordance with previous studies our results showed that biochar addition can lead to a significant decrease in N2O emissions. Furthermore, we determined significantly higher quantities of soil-entrapped N2O and N2 in biochar microcosms and a biochar-induced increase in typical and atypical nosZ transcript copy numbers. Our findings suggest that biochar-induced N2O emission mitigation is based on the entrapment of N2O in water-saturated pores of the soil matrix and concurrent stimulation of microbial N2O reduction resulting in an overall decrease of the N2O/(N2O + N2) ratio.}, }
@article {pmid28007479, year = {2017}, author = {Geudens, N and Nasir, MN and Crowet, JM and Raaijmakers, JM and Fehér, K and Coenye, T and Martins, JC and Lins, L and Sinnaeve, D and Deleu, M}, title = {Membrane Interactions of Natural Cyclic Lipodepsipeptides of the Viscosin Group.}, journal = {Biochimica et biophysica acta. Biomembranes}, volume = {1859}, number = {3}, pages = {331-339}, doi = {10.1016/j.bbamem.2016.12.013}, pmid = {28007479}, issn = {0005-2736}, mesh = {Bacterial Proteins/chemistry/metabolism ; Circular Dichroism ; Gram-Negative Bacteria/drug effects ; Gram-Positive Bacteria/drug effects ; Lipid Bilayers/*chemistry/metabolism ; Lipopeptides/*chemistry/metabolism/pharmacology ; Magnetic Resonance Spectroscopy ; Microbial Sensitivity Tests ; Peptides, Cyclic/*chemistry/metabolism/pharmacology ; Permeability/drug effects ; Pseudomonas/metabolism ; Spectroscopy, Fourier Transform Infrared ; }, abstract = {Many Pseudomonas spp. produce cyclic lipodepsipeptides (CLPs), which, besides their role in biological functions such as motility, biofilm formation and interspecies interactions, are antimicrobial. It has been established that interaction with the cellular membrane is central to the mode of action of CLPs. In this work, we focus on the CLPs of the so-called viscosin group, aiming to assess the impact of the main structural variations observed within this group on both the antimicrobial activity and the interaction with model membranes. The antimicrobial activity of viscosin, viscosinamide A, WLIP and pseudodesmin A were all tested on a broad panel of mainly Gram-positive bacteria. Their capacity to permeabilize or fuse PG/PE/cardiolipin model membrane vesicles is assessed using fluorescent probes. We find that the Glu2/Gln2 structural variation within the viscosin group is the main factor that influences both the membrane permeabilization properties and the minimum inhibitory concentration of bacterial growth, while the configuration of the Leu5 residue has no apparent effect. The CLP-membrane interactions were further evaluated using CD and FT-IR spectroscopy on model membranes consisting of PG/PE/cardiolipin or POPC with or without cholesterol. In contrast to previous studies, we observe no conformational change upon membrane insertion. The CLPs interact both with the polar heads and aliphatic tails of model membrane systems, altering bilayer fluidity, while cholesterol reduces CLP insertion depth.}, }
@article {pmid28004884, year = {2017}, author = {Patil, Y and Junghare, M and Müller, N}, title = {Fermentation of glycerol by Anaerobium acetethylicum and its potential use in biofuel production.}, journal = {Microbial biotechnology}, volume = {10}, number = {1}, pages = {203-217}, pmid = {28004884}, issn = {1751-7915}, mesh = {Acetates/metabolism ; *Biofuels ; Clostridiales/growth &amp; development/*metabolism ; Ethanol/*metabolism ; Fermentation ; Formates/metabolism ; Glycerol/*metabolism ; Hydrogen/metabolism ; Metabolic Networks and Pathways ; Propylene Glycol/metabolism ; }, abstract = {Growth of biodiesel industries resulted in increased coproduction of crude glycerol which is therefore becoming a waste product instead of a valuable 'coproduct'. Glycerol can be used for the production of valuable chemicals, e.g. biofuels, to reduce glycerol waste disposal. In this study, a novel bacterial strain is described which converts glycerol mainly to ethanol and hydrogen with very little amounts of acetate, formate and 1,2-propanediol as coproducts. The bacterium offers certain advantages over previously studied glycerol-fermenting microorganisms. Anaerobium acetethylicum during growth with glycerol produces very little side products and grows in the presence of maximum glycerol concentrations up to 1500 mM and in the complete absence of complex organic supplements such as yeast extract or tryptone. The highest observed growth rate of 0.116 h[-1] is similar to that of other glycerol degraders, and the maximum concentration of ethanol that can be tolerated was found to be about 60 mM (2.8 g l[-1]) and further growth was likely inhibited due to ethanol toxicity. Proteome analysis as well as enzyme assays performed in cell-free extracts demonstrated that glycerol is degraded via glyceraldehyde-3-phosphate, which is further metabolized through the lower part of glycolysis leading to formation of mainly ethanol and hydrogen. In conclusion, fermentation of glycerol to ethanol and hydrogen by this bacterium represents a remarkable option to add value to the biodiesel industries by utilization of surplus glycerol.}, }
@article {pmid28004158, year = {2017}, author = {Wang, Q and Wang, R and He, L and Sheng, X}, title = {Location-Related Differences in Weathering Behaviors and Populations of Culturable Rock-Weathering Bacteria Along a Hillside of a Rock Mountain.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {838-849}, pmid = {28004158}, issn = {1432-184X}, mesh = {Acids/metabolism ; Bacillus/genetics/isolation &amp; purification/metabolism ; Bacteria/*classification/genetics/*isolation &amp; purification/metabolism ; *Bacterial Physiological Phenomena ; Biota/physiology ; China ; Climate ; Colony Count, Microbial ; Culture Media/chemistry ; DNA, Bacterial ; Elements ; Environmental Microbiology ; Genes, Bacterial ; Geological Phenomena ; Geology ; Hydrogen-Ion Concentration ; Minerals/chemistry/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Siderophores/biosynthesis ; Soil/*chemistry ; *Soil Microbiology ; *Weather ; }, abstract = {Bacteria play important roles in rock weathering, elemental cycling, and soil formation. However, little is known about the weathering potential and population of bacteria inhabiting surfaces of rocks. In this study, we isolated bacteria from the top, middle, and bottom rock samples along a hillside of a rock (trachyte) mountain as well as adjacent soils and characterized rock-weathering behaviors and populations of the bacteria. Per gram of rock or surface soil, 10[6]-10[7] colony forming units were obtained and total 192 bacteria were isolated. Laboratory rock dissolution experiments indicated that the proportions of the highly effective Fe (ranging from 67 to 92 %), Al (ranging from 40 to 48 %), and Cu (ranging from 54 to 81 %) solubilizers were significantly higher in the top rock and soil samples, while the proportion of the highly effective Si (56 %) solubilizers was significantly higher in the middle rock samples. Furthermore, 78, 96, and 6 % of bacteria from the top rocks, soils, and middle rocks, respectively, significantly acidified the culture medium (pH < 4.0) in the rock dissolution process. Most rock-weathering bacteria (79 %) from the rocks were different to those from the soils and most of them (species level) have not been previously reported. Furthermore, location-specific rock-weathering bacterial populations were found and Bacillus species were the most (66 %) frequently isolated rock-weathering bacteria in the rocks based on cultivation methods. Notably, the top rocks and soils had the highest and lowest diversity of rock-weathering bacterial populations, respectively. The results suggested location-related differences in element (Si, Al, Fe, and Cu) releasing effectiveness and communities of rock-weathering bacteria along the hillside of the rock mountain.}, }
@article {pmid27999874, year = {2017}, author = {Ambrosini, R and Musitelli, F and Navarra, F and Tagliaferri, I and Gandolfi, I and Bestetti, G and Mayer, C and Minora, U and Azzoni, RS and Diolaiuti, G and Smiraglia, C and Franzetti, A}, title = {Diversity and Assembling Processes of Bacterial Communities in Cryoconite Holes of a Karakoram Glacier.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {827-837}, pmid = {27999874}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; Biota ; DNA, Bacterial ; Ecosystem ; Genes, Bacterial ; High-Throughput Screening Assays/methods ; Hydrogen-Ion Concentration ; Ice Cover/*microbiology ; Lakes/microbiology ; Microbial Consortia ; Pakistan ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Cryoconite holes are small ponds that form on the surface of glaciers that contain a dark debris, the cryoconite, at the bottom and host active ecological communities. Differences in the structure of bacterial communities have been documented among Arctic and mountain glaciers, and among glaciers in different areas of the world. In this study, we investigated the structure of bacterial communities of cryoconite holes of Baltoro Glacier, a large (62 km in length and 524 km[2] of surface) glacier of the Karakoram, by high-throughput sequencing of the V5-V6 hypervariable regions of the 16S rRNA gene. We found that Betaproteobacteria dominated bacterial communities, with large abundance of genera Polaromonas, probably thanks to its highly versatile metabolism, and Limnohabitans, which may have been favoured by the presence of supraglacial lakes in the area where cryoconite holes were sampled. Variation in bacterial communities among different sampling areas of the glacier could be explained by divergent selective processes driven by variation in environmental conditions, particularly pH, which was the only environmental variable that significantly affected the structure of bacterial communities. This variability may be due to both temporal and spatial patterns of variation in environmental conditions.}, }
@article {pmid27999158, year = {2016}, author = {Gibbons, SM and Scholz, M and Hutchison, AL and Dinner, AR and Gilbert, JA and Coleman, ML}, title = {Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System.}, journal = {mBio}, volume = {7}, number = {6}, pages = {}, pmid = {27999158}, issn = {2150-7511}, support = {T32 EB009412/EB/NIBIB NIH HHS/United States ; T32 GM007281/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {*Biodiversity ; *Ecosystem ; Environment ; *Microbial Consortia ; Models, Theoretical ; Ultraviolet Rays/adverse effects ; }, abstract = {UNLABELLED: Diversity is often associated with the functional stability of ecological communities from microbes to macroorganisms. Understanding how diversity responds to environmental perturbations and the consequences of this relationship for ecosystem function are thus central challenges in microbial ecology. Unimodal diversity-disturbance relationships, in which maximum diversity occurs at intermediate levels of disturbance, have been predicted for ecosystems where life history tradeoffs separate organisms along a disturbance gradient. However, empirical support for such peaked relationships in macrosystems is mixed, and few studies have explored these relationships in microbial systems. Here we use complex microbial microcosm communities to systematically determine diversity-disturbance relationships over a range of disturbance regimes. We observed a reproducible switch between community states, which gave rise to transient diversity maxima when community states were forced to mix. Communities showed reduced compositional stability when diversity was highest. To further explore these dynamics, we formulated a simple model that reveals specific regimes under which diversity maxima are stable. Together, our results show how both unimodal and non-unimodal diversity-disturbance relationships can be observed as a system switches between two distinct microbial community states; this process likely occurs across a wide range of spatially and temporally heterogeneous microbial ecosystems.<br><br>IMPORTANCE: The diversity of microbial communities is linked to the functioning and stability of ecosystems. As humanity continues to impact ecosystems worldwide, and as diet and disease perturb our own commensal microbial communities, the ability to predict how microbial diversity will respond to disturbance is of critical importance. Using microbial microcosm experiments, we find that community diversity responds to different disturbance regimes in a reproducible and predictable way. Maximum diversity occurs when two communities, each suited to different environmental conditions, are mixed due to disturbance. This maximum diversity is transient except under specific regimes. Using a simple mathematical model, we show that transient unimodality is likely a common feature of microbial diversity-disturbance relationships in fluctuating environments.}, }
@article {pmid27997838, year = {2016}, author = {Petersen, JM}, title = {Ecology and Fisheries: Dark Carbon on Your Dinner Plate.}, journal = {Current biology : CB}, volume = {26}, number = {24}, pages = {R1277-R1279}, doi = {10.1016/j.cub.2016.11.016}, pmid = {27997838}, issn = {1879-0445}, mesh = {Animals ; Bacteria/metabolism ; Carbon/*metabolism ; Caribbean Region ; *Ecosystem ; *Fisheries/economics ; Palinuridae/*physiology ; Sunlight ; Symbiosis ; }, abstract = {Chemosynthetic primary production by symbiotic microbes powers entire ecosystems in the remote deep sea. New research shows that in shallow waters chemosynthetic symbioses can contribute substantially to a vital economic resource - lobster fisheries in the Caribbean Sea.}, }
@article {pmid27997146, year = {2017}, author = {Bertuccio, AJ and Tilton, RD}, title = {Silver Sink Effect of Humic Acid on Bacterial Surface Colonization in the Presence of Silver Ions and Nanoparticles.}, journal = {Environmental science &amp; technology}, volume = {51}, number = {3}, pages = {1754-1763}, doi = {10.1021/acs.est.6b04957}, pmid = {27997146}, issn = {1520-5851}, mesh = {*Humic Substances ; Ions/pharmacology ; Metal Nanoparticles ; Plankton/drug effects ; Silver/*pharmacology ; }, abstract = {Silver nanoparticles (AgNPs) released from consumer products may enter the environment and possibly harm microbial communities. Prior research showed that surface-adherent AgNPs inhibit bacterial surface colonization, a precursor to biofilm formation, only when planktonic bacterial inoculum concentrations are less than a threshold level (Wirth and co-workers, J. Colloid Interface Sci. 2016 , 467 , 17 - 27). This inoculum effect is due to a decrease in free silver ion concentration associated with sublethal binding to bacteria. Natural organic matter can be an additional silver sink in environmental systems. Using Pseudomonas fluorescens as a model biofilm-forming bacterium, we find significant increases in minimum bactericidal concentrations for AgNP suspensions and Ag[+] in solution when adding humic acid (HA) to bacterial suspensions. When HA is present, planktonic bacteria survive and colonize AgNP-laden glass surfaces at lower bacterial inoculum concentrations than were needed for survival and colonization in its absence. This occurs despite the observed tendency of HA to inhibit colonization on bare glass surfaces when silver is absent. Results are interpreted through equilibrium Ag[+] binding isotherms to HA and suspended bacteria. These results indicate that silver ion sinks may lessen AgNP impacts on natural microbial ecology relative to the disruption observed in pristine laboratory conditions.}, }
@article {pmid27995301, year = {2017}, author = {Hamšíková, Z and Coipan, C and Mahríková, L and Minichová, L and Sprong, H and Kazimírová, M}, title = {Borrelia miyamotoi and Co-Infection with Borrelia afzelii in Ixodes ricinus Ticks and Rodents from Slovakia.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {1000-1008}, pmid = {27995301}, issn = {1432-184X}, mesh = {Animals ; Arvicolinae/microbiology/parasitology ; Bacterial Proteins/genetics ; Borrelia/genetics/*isolation &amp; purification ; Borrelia burgdorferi Group/genetics/*isolation &amp; purification ; *Coinfection ; DNA, Bacterial/chemistry ; Disease Reservoirs/microbiology/veterinary ; Europe ; Female ; Genes, Bacterial ; Insect Vectors/microbiology ; Ixodes/*microbiology ; Lyme Disease/epidemiology/*microbiology/*veterinary ; Male ; Murinae/microbiology/parasitology ; Nymph/microbiology ; Phosphoric Diester Hydrolases/genetics ; Phylogeny ; Prevalence ; Rodent Diseases/epidemiology/microbiology ; Rodentia/*microbiology/parasitology ; Sequence Analysis ; Slovakia/epidemiology ; }, abstract = {Borrelia miyamotoi causes relapsing fever in humans. The occurrence of this spirochete has been reported in Ixodes ricinus and wildlife, but there are still gaps in the knowledge of its eco-epidemiology and public health impact. In the current study, questing I. ricinus (nymphs and adults) and skin biopsies from rodents captured in Slovakia were screened for the presence of B. miyamotoi and Borrelia burgdorferi s.l. DNA. The prevalence of B. miyamotoi and B. burgdorferi s.l. in questing ticks was 1.7 and 16.9%, respectively. B. miyamotoi was detected in Apodemus flavicollis (9.3%) and Myodes glareolus (4.4%). In contrast, B. burgdorferi s.l. was identified in 11.9% of rodents, with the highest prevalence in Microtus arvalis (68.4%) and a lower prevalence in Apodemus spp. (8.4%) and M. glareolus (12.4%). Borrelia afzelii was the prevailing genospecies infecting questing I. ricinus (37.9%) and rodents (72.2%). Co-infections of B. miyamotoi and B. burgdorferi s.l. were found in 24.1 and 9.3% of the questing ticks and rodents, respectively, whereas the proportion of ticks and rodents co-infected with B. miyamotoi and B. afzelii was 6.9 and 7.0%, respectively. The results suggest that B. miyamotoi and B. afzelii share amplifying hosts. The sequences of the B. miyamotoi glpQ gene fragment from our study showed a high degree of identity with sequences of the gene amplified from ticks and human patients in Europe. The results seem to suggest that humans in Slovakia are at risk of contracting tick-borne relapsing fever, and in some cases together with Lyme borreliosis.}, }
@article {pmid27991591, year = {2016}, author = {Dennis, PG and Virdis, B and Vanwonterghem, I and Hassan, A and Hugenholtz, P and Tyson, GW and Rabaey, K}, title = {Anode potential influences the structure and function of anodic electrode and electrolyte-associated microbiomes.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {39114}, pmid = {27991591}, issn = {2045-2322}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Bioelectric Energy Sources/*microbiology ; Biofilms/*growth &amp; development ; Electrodes ; Genes, Archaeal ; Genes, Bacterial ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Three bioelectrochemical systems were operated with set anode potentials of +300 mV, +550 mV and +800 mV vs. Standard Hydrogen Electrode (SHE) to test the hypothesis that anode potential influences microbial diversity and is positively associated with microbial biomass and activity. Bacterial and archaeal diversity was characterized using 16 S rRNA gene amplicon sequencing, and biofilm thickness was measured as a proxy for biomass. Current production and substrate utilization patterns were used as measures of microbial activity and the mid-point potentials of putative terminal oxidases were assessed using cyclic voltammetry. All measurements were performed after 4, 16, 23, 30 and 38 days. Microbial biomass and activity differed significantly between anode potentials and were lower at the highest potential. Anodic electrode and electrolyte associated community composition was also significantly influenced by anode potential. While biofilms at +800 mV were thinner, transferred less charge and oxidized less substrate than those at lower potentials, they were also associated with putative terminal oxidases with higher mid-point potentials and generated more biomass per unit charge. This indicates that microbes at +800 mV were unable to capitalize on the potential for additional energy gain due to a lack of adaptive traits to high potential solid electron acceptors and/or sensitivity to oxidative stress.}, }
@article {pmid27988980, year = {2017}, author = {Xia, W and Nielly-Thibault, L and Charron, G and Landry, CR and Kasimer, D and Anderson, JB and Kohn, LM}, title = {Population genomics reveals structure at the individual, host-tree scale and persistence of genotypic variants of the undomesticated yeast Saccharomyces paradoxus in a natural woodland.}, journal = {Molecular ecology}, volume = {26}, number = {4}, pages = {995-1007}, doi = {10.1111/mec.13954}, pmid = {27988980}, issn = {1365-294X}, mesh = {*Forests ; *Genetics, Population ; Ontario ; Quercus/*microbiology ; Saccharomyces/*genetics ; Trees/microbiology ; }, abstract = {Genetic diversity in experimental, domesticated and wild populations of the related yeasts, Saccharomyces cerevisiae and Saccharomyces paradoxus, has been well described at the global scale. We investigated the population genomics of a local population on a small spatial scale to address two main questions. First, is there genomic variation in a S. paradoxus population at a spatial scale spanning centimetres (microsites) to tens of metres? Second, does the distribution of genomic variants persist over time? Our sample consisted of 42 S. paradoxus strains from 2014 and 43 strains from 2015 collected from the same 72 microsites around four host trees (Quercus rubra and Quercus alba) within 1 km[2] in a mixed hardwood forest in southern Ontario. Six additional S. paradoxus strains recovered from adjacent maple and beech trees in 2015 are also included in the sample. Whole-genome sequencing and genomic SNP analysis revealed five differentiated groups (clades) within the sampled area. The signal of persistence of genotypes in their microsites from 2014 to 2015 was highly significant. Isolates from the same tree tended to be more related than strains from different trees, with limited evidence of dispersal between trees. In growth assays, one genotype had a significantly longer lag phase than the other strains. Our results indicate that different clades coexist at fine spatial scale and that population structure persists over at least a one-year interval in these wild yeasts, suggesting the efficacy of yearly sampling to follow longer term genetic dynamics in future studies.}, }
@article {pmid27986083, year = {2016}, author = {Narayanasamy, S and Jarosz, Y and Muller, EE and Heintz-Buschart, A and Herold, M and Kaysen, A and Laczny, CC and Pinel, N and May, P and Wilmes, P}, title = {IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses.}, journal = {Genome biology}, volume = {17}, number = {1}, pages = {260}, pmid = {27986083}, issn = {1474-760X}, mesh = {Algorithms ; Computational Biology ; Genomics ; Metagenome/*genetics ; Microbiota/*genetics ; *Software ; Transcriptome/*genetics ; Workflow ; }, abstract = {Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data. IMP incorporates robust read preprocessing, iterative co-assembly, analyses of microbial community structure and function, automated binning, as well as genomic signature-based visualizations. The IMP-based data integration strategy enhances data usage, output volume, and output quality as demonstrated using relevant use-cases. Finally, IMP is encapsulated within a user-friendly implementation using Python and Docker. IMP is available at http://r3lab.uni.lu/web/imp/ (MIT license).}, }
@article {pmid27984802, year = {2017}, author = {Demanèche, S and Schauser, L and Dawson, L and Franqueville, L and Simonet, P}, title = {Microbial soil community analyses for forensic science: Application to a blind test.}, journal = {Forensic science international}, volume = {270}, number = {}, pages = {153-158}, doi = {10.1016/j.forsciint.2016.12.004}, pmid = {27984802}, issn = {1872-6283}, mesh = {*DNA, Ribosomal Spacer ; Forensic Sciences ; High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; *RNA, Ribosomal, 16S ; *Soil Microbiology ; }, abstract = {Soil complexity, heterogeneity and transferability make it valuable in forensic investigations to help obtain clues as to the origin of an unknown sample, or to compare samples from a suspect or object with samples collected at a crime scene. In a few countries, soil analysis is used in matters from site verification to estimates of time after death. However, up to date the application or use of soil information in criminal investigations has been limited. In particular, comparing bacterial communities in soil samples could be a useful tool for forensic science. To evaluate the relevance of this approach, a blind test was performed to determine the origin of two questioned samples (one from the mock crime scene and the other from a 50:50 mixture of the crime scene and the alibi site) compared to three control samples (soil samples from the crime scene, from a context site 25m away from the crime scene and from the alibi site which was the suspect's home). Two biological methods were used, Ribosomal Intergenic Spacer Analysis (RISA), and 16S rRNA gene sequencing with Illumina Miseq, to evaluate the discriminating power of soil bacterial communities. Both techniques discriminated well between soils from a single source, but a combination of both techniques was necessary to show that the origin was a mixture of soils. This study illustrates the potential of applying microbial ecology methodologies in soil as an evaluative forensic tool.}, }
@article {pmid27984592, year = {2016}, author = {Raguideau, S and Plancade, S and Pons, N and Leclerc, M and Laroche, B}, title = {Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota.}, journal = {PLoS computational biology}, volume = {12}, number = {12}, pages = {e1005252}, pmid = {27984592}, issn = {1553-7358}, mesh = {Algorithms ; Bacteria/genetics/metabolism ; Carbohydrate Metabolism/genetics/physiology ; Dietary Fiber/metabolism ; Feces/microbiology ; Fermentation ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenomics/*methods ; }, abstract = {Whole Genome Shotgun (WGS) metagenomics is increasingly used to study the structure and functions of complex microbial ecosystems, both from the taxonomic and functional point of view. Gene inventories of otherwise uncultured microbial communities make the direct functional profiling of microbial communities possible. The concept of community aggregated trait has been adapted from environmental and plant functional ecology to the framework of microbial ecology. Community aggregated traits are quantified from WGS data by computing the abundance of relevant marker genes. They can be used to study key processes at the ecosystem level and correlate environmental factors and ecosystem functions. In this paper we propose a novel model based approach to infer combinations of aggregated traits characterizing specific ecosystemic metabolic processes. We formulate a model of these Combined Aggregated Functional Traits (CAFTs) accounting for a hierarchical structure of genes, which are associated on microbial genomes, further linked at the ecosystem level by complex co-occurrences or interactions. The model is completed with constraints specifically designed to exploit available genomic information, in order to favor biologically relevant CAFTs. The CAFTs structure, as well as their intensity in the ecosystem, is obtained by solving a constrained Non-negative Matrix Factorization (NMF) problem. We developed a multicriteria selection procedure for the number of CAFTs. We illustrated our method on the modelling of ecosystemic functional traits of fiber degradation by the human gut microbiota. We used 1408 samples of gene abundances from several high-throughput sequencing projects and found that four CAFTs only were needed to represent the fiber degradation potential. This data reduction highlighted biologically consistent functional patterns while providing a high quality preservation of the original data. Our method is generic and can be applied to other metabolic processes in the gut or in other ecosystems.}, }
@article {pmid27983878, year = {2017}, author = {Roussel, C and Sivignon, A and de Wiele, TV and Blanquet-Diot, S}, title = {Foodborne enterotoxigenic Escherichia coli: from gut pathogenesis to new preventive strategies involving probiotics.}, journal = {Future microbiology}, volume = {12}, number = {}, pages = {73-93}, doi = {10.2217/fmb-2016-0101}, pmid = {27983878}, issn = {1746-0921}, mesh = {Enterotoxigenic Escherichia coli/*isolation &amp; purification ; Escherichia coli Infections/microbiology/prevention &amp; control ; Foodborne Diseases/microbiology/*prevention &amp; control ; Gastrointestinal Diseases/microbiology/prevention &amp; control ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Humans ; Hydrogen-Ion Concentration ; Probiotics/*administration &amp; dosage ; }, abstract = {Enterotoxigenic Escherichia coli (ETEC) are a major cause of traveler's diarrhea and infant mortality in developing countries. Given the rise of antibiotic resistance worldwide, there is an urgent need for the development of new preventive strategies. Among them, a promising approach is the use of probiotics. Although many studies, mostly performed under piglet digestive conditions, have shown the beneficial effects of probiotics on ETEC by interfering with their survival, virulence or adhesion to mucosa, underlying mechanisms remain unclear. This review describes ETEC pathogenesis, its modulation by human gastrointestinal cues as well as novel preventive strategies with a particular emphasis on probiotics. The potential of in vitro models simulating human digestion in elucidating probiotic mode of action will be discussed.}, }
@article {pmid27983719, year = {2017}, author = {Szabó, G and Schulz, F and Toenshoff, ER and Volland, JM and Finkel, OM and Belkin, S and Horn, M}, title = {Convergent patterns in the evolution of mealybug symbioses involving different intrabacterial symbionts.}, journal = {The ISME journal}, volume = {11}, number = {3}, pages = {715-726}, pmid = {27983719}, issn = {1751-7370}, support = {P 22533/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Bacteria/genetics ; Betaproteobacteria/*genetics/physiology ; *Biological Evolution ; Gammaproteobacteria/*genetics/physiology ; Hemiptera/*microbiology ; Symbiosis/*genetics/physiology ; }, abstract = {Mealybugs (Insecta: Hemiptera: Pseudococcidae) maintain obligatory relationships with bacterial symbionts, which provide essential nutrients to their insect hosts. Most pseudococcinae mealybugs harbor a unique symbiosis setup with enlarged betaproteobacterial symbionts ('Candidatus Tremblaya princeps'), which themselves contain gammaproteobacterial symbionts. Here we investigated the symbiosis of the manna mealybug, Trabutina mannipara, using a metagenomic approach. Phylogenetic analyses revealed that the intrabacterial symbiont of T. mannipara represents a novel lineage within the Gammaproteobacteria, for which we propose the tentative name 'Candidatus Trabutinella endobia'. Combining our results with previous data available for the nested symbiosis of the citrus mealybug Planococcus citri, we show that synthesis of essential amino acids and vitamins and translation-related functions partition between the symbiotic partners in a highly similar manner in the two systems, despite the distinct evolutionary origin of the intrabacterial symbionts. Bacterial genes found in both mealybug genomes and complementing missing functions in both symbioses were likely integrated in ancestral mealybugs before T. mannipara and P. citri diversified. The high level of correspondence between the two mealybug systems and their highly intertwined metabolic pathways are unprecedented. Our work contributes to a better understanding of the only known intracellular symbiosis between two bacteria and suggests that the evolution of this unique symbiosis included the replacement of intrabacterial symbionts in ancestral mealybugs.}, }
@article {pmid27975134, year = {2017}, author = {Sclocchi, MC and Kraková, L and Pinzari, F and Colaizzi, P and Bicchieri, M and Šaková, N and Pangallo, D}, title = {Microbial Life and Death in a Foxing Stain: a Suggested Mechanism of Photographic Prints Defacement.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {815-826}, pmid = {27975134}, issn = {1432-184X}, mesh = {Aluminum/metabolism ; Bacteria/cytology/genetics/*isolation &amp; purification/metabolism ; Bacterial Adhesion ; Base Sequence ; Cell Culture Techniques/methods ; Coloring Agents/analysis/*metabolism ; DNA/analysis ; Fungi/cytology/genetics/*isolation &amp; purification/metabolism ; Gelatin/metabolism ; Iron/metabolism ; *Microbial Consortia ; Microbial Viability ; Microscopy, Electron, Scanning/methods ; Phosphates/metabolism ; *Photography ; Potassium Compounds/metabolism ; RNA/analysis ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 28S/genetics ; Silver/metabolism ; Spectrometry, X-Ray Emission/methods ; }, abstract = {The gelatin-silver halide black and white prints represent an enormous photography heritage with a great value. Unaesthetic phenomena, the foxing stains that are caused by microbial growth on surface, have been described in stamps, drawings, books, and tissues but, until now, scarcely for photographic materials. In this study, a combination of various techniques, including culture-dependent and culture-independent approaches (RNA and DNA analysis), scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS) and μ-Raman spectroscopy supported by X-ray fluorescence analysis (XRF), permitted to describe the microbial contamination dynamics of foxing stains present on the surface of two gelatin-silver halide photographs. The investigation provided also information on the effects of microbial activity on the materials' chemistry of the two prints. The action of microbial community resulted locally in either (a) formation of mixed aluminum-iron-potassium phosphate compounds that could be attributed to the hydrolytic activity of bacteria, (b) leaching of barite,}, }
@article {pmid27975077, year = {2016}, author = {Boughner, LA and Singh, P}, title = {Microbial Ecology: Where are we now?.}, journal = {Postdoc journal : a journal of postdoctoral research and postdoctoral affairs}, volume = {4}, number = {11}, pages = {3-17}, pmid = {27975077}, issn = {2328-9791}, support = {U19 AI090872/AI/NIAID NIH HHS/United States ; }, abstract = {Conventional microbiological methods have been readily taken over by newer molecular techniques due to the ease of use, reproducibility, sensitivity and speed of working with nucleic acids. These tools allow high throughput analysis of complex and diverse microbial communities, such as those in soil, freshwater, saltwater, or the microbiota living in collaboration with a host organism (plant, mouse, human, etc). For instance, these methods have been robustly used for characterizing the plant (rhizosphere), animal and human microbiome specifically the complex intestinal microbiota. The human body has been referred to as the Superorganism since microbial genes are more numerous than the number of human genes and are essential to the health of the host. In this review we provide an overview of the Next Generation tools currently available to study microbial ecology, along with their limitations and advantages.}, }
@article {pmid27966037, year = {2017}, author = {Margesin, R and Siles, JA and Cajthaml, T and Öhlinger, B and Kistler, E}, title = {Microbiology Meets Archaeology: Soil Microbial Communities Reveal Different Human Activities at Archaic Monte Iato (Sixth Century BC).}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {925-938}, pmid = {27966037}, issn = {1432-184X}, mesh = {Acetates/metabolism ; *Archaeology ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Bacterial Load ; Biodiversity ; Biomass ; Carboxylic Acids/metabolism ; Cluster Analysis ; DNA, Bacterial ; DNA, Fungal ; Enzyme Assays ; Fatty Acids/metabolism ; Fungi/classification/genetics/metabolism ; Heterotrophic Processes ; History, Ancient ; Human Activities/*history ; Microbial Consortia/genetics/*physiology ; Phospholipids/metabolism ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Microbial ecology has been recognized as useful in archaeological studies. At Archaic Monte Iato in Western Sicily, a native (indigenous) building was discovered. The objective of this study was the first examination of soil microbial communities related to this building. Soil samples were collected from archaeological layers at a ritual deposit (food waste disposal) in the main room and above the fireplace in the annex. Microbial soil characterization included abundance (cellular phospholipid fatty acids (PLFA), viable bacterial counts), activity (physiological profiles, enzyme activities of viable bacteria), diversity, and community structure (bacterial and fungal Illumina amplicon sequencing, identification of viable bacteria). PLFA-derived microbial abundance was lower in soils from the fireplace than in soils from the deposit; the opposite was observed with culturable bacteria. Microbial communities in soils from the fireplace had a higher ability to metabolize carboxylic and acetic acids, while those in soils from the deposit metabolized preferentially carbohydrates. The lower deposit layer was characterized by higher total microbial and bacterial abundance and bacterial richness and by a different carbohydrate metabolization profile compared to the upper deposit layer. Microbial community structures in the fireplace were similar and could be distinguished from those in the two deposit layers, which had different microbial communities. Our data confirmed our hypothesis that human consumption habits left traces on microbiota in the archaeological evidence; therefore, microbiological residues as part of the so-called ecofacts are, like artifacts, key indicators of consumer behavior in the past.}, }
@article {pmid27966036, year = {2017}, author = {Xiong, J and Dai, W and Zhu, J and Liu, K and Dong, C and Qiu, Q}, title = {The Underlying Ecological Processes of Gut Microbiota Among Cohabitating Retarded, Overgrown and Normal Shrimp.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {988-999}, pmid = {27966036}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/enzymology/genetics/isolation &amp; purification ; Biodiversity ; China ; Cluster Analysis ; Crustacea/enzymology/*growth &amp; development/*microbiology ; DNA, Bacterial/genetics ; Digestion ; *Ecology ; Enzyme Assays ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology ; Larva/microbiology ; Microbial Consortia/genetics ; Molecular Sequence Data ; Obesity/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Increasing evidence of tight links among the gut microbiota, obesity, and host health has emerged, but knowledge of the ecological processes that shape the variation in microbial assemblages across growth rates remains elusive. Moreover, inadequately control for differences in factors that profoundly affect the gut microbial community, hampers evaluation of the gut microbiota roles in regulating growth rates. To address this gap, we evaluated the composition and ecological processes of the gut bacterial community in cohabitating retarded, overgrown, and normal shrimps from identically managed ponds. Gut bacterial community structures were distinct (P = 0.0006) among the shrimp categories. Using a structural equation modeling (SEM), we found that changes in the gut bacterial community were positively related to digestive activities, which subsequently affected shrimp growth rate. This association was further supported by intensified interspecies interaction and enriched lineages with high nutrient intake efficiencies in overgrown shrimps. However, the less phylogenetic clustering of gut microbiota in overgrown and retarded subjects may offer empty niches for pathogens invasion, as evidenced by higher abundances of predicted functional pathways involved in disease infection. Given no differences in biotic and abiotic factors among the cohabitating shrimps, we speculated that the distinct gut community assembly could be attributed to random colonization in larval shrimp (e.g., priority effects) and that an altered microbiota could be a causative factor in overgrowth or retardation in shrimp. To our knowledge, this is the first study to provide an integrated overview of the direct roles of gut microbiota in shaping shrimp growth rate and the underlying ecological mechanisms.}, }
@article {pmid27965632, year = {2016}, author = {Hannula, SE and van Veen, JA}, title = {Primer Sets Developed for Functional Genes Reveal Shifts in Functionality of Fungal Community in Soils.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1897}, pmid = {27965632}, issn = {1664-302X}, abstract = {Phylogenetic diversity of soil microbes is a hot topic at the moment. However, the molecular tools for the assessment of functional diversity in the fungal community are less developed than tools based on genes encoding the ribosomal operon. Here 20 sets of primers targeting genes involved mainly in carbon cycling were designed and/or validated and the functioning of soil fungal communities along a chronosequence of land abandonment from agriculture was evaluated using them. We hypothesized that changes in fungal community structure during secondary succession would lead to difference in the types of genes present in soils and that these changes would be directional. We expected an increase in genes involved in degradation of recalcitrant organic matter in time since agriculture. Out of the investigated genes, the richness of the genes related to carbon cycling was significantly higher in fields abandoned for longer time. The composition of six of the genes analyzed revealed significant differences between fields abandoned for shorter and longer time. However, all genes revealed significant variance over the fields studied, and this could be related to other parameters than the time since agriculture such as pH, organic matter, and the amount of available nitrogen. Contrary to our initial hypothesis, the genes significantly different between fields were not related to the decomposition of more recalcitrant matter but rather involved in degradation of cellulose and hemicellulose.}, }
@article {pmid27956491, year = {2017}, author = {Crauwels, S and Van Opstaele, F and Jaskula-Goiris, B and Steensels, J and Verreth, C and Bosmans, L and Paulussen, C and Herrera-Malaver, B and de Jonge, R and De Clippeleer, J and Marchal, K and De Samblanx, G and Willems, KA and Verstrepen, KJ and Aerts, G and Lievens, B}, title = {Fermentation assays reveal differences in sugar and (off-) flavor metabolism across different Brettanomyces bruxellensis strains.}, journal = {FEMS yeast research}, volume = {17}, number = {1}, pages = {}, doi = {10.1093/femsyr/fow105}, pmid = {27956491}, issn = {1567-1364}, mesh = {Adaptation, Biological ; Brettanomyces/classification/genetics/isolation &amp; purification/*metabolism ; *Carbohydrate Metabolism ; Culture Media/chemistry ; *Fermentation ; *Food Microbiology ; Genetic Variation ; Volatile Organic Compounds/*metabolism ; }, abstract = {Brettanomyces (Dekkera) bruxellensis is an ascomycetous yeast of major importance in the food, beverage and biofuel industry. It has been isolated from various man-made ecological niches that are typically characterized by harsh environmental conditions such as wine, beer, soft drink, etc. Recent comparative genomics studies revealed an immense intraspecific diversity, but it is still unclear whether this genetic diversity also leads to systematic differences in fermentation performance and (off-)flavor production, and to what extent strains have evolved to match their ecological niche. Here, we present an evaluation of the fermentation properties of eight genetically diverse B. bruxellensis strains originating from beer, wine and soft drinks. We show that sugar consumption and aroma production during fermentation are determined by both the yeast strain and composition of the medium. Furthermore, our results indicate a strong niche adaptation of B. bruxellensis, most clearly for wine strains. For example, only strains originally isolated from wine were able to thrive well and produce the typical Brettanomyces-related phenolic off-flavors 4-ethylguaiacol and 4-ethylphenol when inoculated in red wine. Sulfite tolerance was found as a key factor explaining the observed differences in fermentation performance and off-flavor production. Sequence analysis of genes related to phenolic off-flavor production, however, revealed only marginal differences between the isolates tested, especially at the amino acid level. Altogether, our study provides novel insights in the Brettanomyces metabolism of flavor production, and is highly relevant for both the wine and beer industry.}, }
@article {pmid27943642, year = {2017}, author = {Ben Hania, W and Joseph, M and Bunk, B and Spröer, C and Klenk, HP and Fardeau, ML and Spring, S}, title = {Characterization of the first cultured representative of a Bacteroidetes clade specialized on the scavenging of cyanobacteria.}, journal = {Environmental microbiology}, volume = {19}, number = {3}, pages = {1134-1148}, doi = {10.1111/1462-2920.13639}, pmid = {27943642}, issn = {1462-2920}, mesh = {Animals ; Bacteroidetes/classification/genetics/growth &amp; development/*isolation &amp; purification ; Base Composition ; Cyanobacteria/genetics/metabolism ; Fatty Acids/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sodium Chloride/metabolism ; }, abstract = {The anaerobic, mesophilic and moderately halophilic strain L21-Spi-D4[T] was recently isolated from the suboxic zone of a hypersaline cyanobacterial mat using protein-rich extracts of Arthrospira (formerly Spirulina) platensis as substrate. Phylogenetic analyses based on 16S rRNA genes indicated an affiliation of the novel strain with the Bacteroidetes clade MgMjR-022, which is widely distributed and abundant in hypersaline microbial mats and heretofore comprised only sequences of uncultured bacteria. Analyses of the complete genome sequence of strain L21-Spi-D4[T] revealed a possible specialization on the degradation of cyanobacterial biomass. Besides genes for enzymes degrading specific cyanobacterial proteins a conspicuous transport complex for the polypeptide cyanophycin could be identified that is homologous to typical polysaccharide utilization loci of Bacteroidetes. A distinct and reproducible co-occurrence pattern of environmental 16S rRNA gene sequences of the MgMjR-022 clade and cyanobacteria in the suboxic zone of hypersaline mats points to a specific dependence of members of this clade on decaying cyanobacteria. Based on a comparative analysis of phenotypic, genomic and ecological characteristics we propose to establish the novel taxa Salinivirga cyanobacteriivorans gen. nov., sp. nov., represented by the type strain L21-Spi-D4[T] , and Salinivirgaceae fam. nov., comprising sequences of the MgMjR-022 clade.}, }
@article {pmid27942767, year = {2017}, author = {Shanmugam, SG and Magbanua, ZV and Williams, MA and Jangid, K and Whitman, WB and Peterson, DG and Kingery, WL}, title = {Erratum to: Bacterial Diversity Patterns Differ in Soils Developing in Sub-tropical and Cool-Temperate Ecosystems.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {570}, doi = {10.1007/s00248-016-0909-3}, pmid = {27942767}, issn = {1432-184X}, }
@article {pmid27942457, year = {2017}, author = {Ghosh, A and Bhadury, P}, title = {Insights into bacterioplankton community structure from Sundarbans mangrove ecoregion using Sanger and Illumina MiSeq sequencing approaches: A comparative analysis.}, journal = {Genomics data}, volume = {11}, number = {}, pages = {39-42}, pmid = {27942457}, issn = {2213-5960}, abstract = {Next generation sequencing using platforms such as Illumina MiSeq provides a deeper insight into the structure and function of bacterioplankton communities in coastal ecosystems compared to traditional molecular techniques such as clone library approach which incorporates Sanger sequencing. In this study, structure of bacterioplankton communities was investigated from two stations of Sundarbans mangrove ecoregion using both Sanger and Illumina MiSeq sequencing approaches. The Illumina MiSeq data is available under the BioProject ID PRJNA35180 and Sanger sequencing data under accession numbers KX014101-KX014140 (Stn1) and KX014372-KX014410 (Stn3). Proteobacteria-, Firmicutes- and Bacteroidetes-like sequences retrieved from both approaches appeared to be abundant in the studied ecosystem. The Illumina MiSeq data (2.1 GB) provided a deeper insight into the structure of bacterioplankton communities and revealed the presence of bacterial phyla such as Actinobacteria, Cyanobacteria, Tenericutes, Verrucomicrobia which were not recovered based on Sanger sequencing. A comparative analysis of bacterioplankton communities from both stations highlighted the presence of genera that appear in both stations and genera that occur exclusively in either station. However, both the Sanger sequencing and Illumina MiSeq data were coherent at broader taxonomic levels. Pseudomonas, Devosia, Hyphomonas and Erythrobacter-like sequences were the abundant bacterial genera found in the studied ecosystem. Both the sequencing methods showed broad coherence although as expected the Illumina MiSeq data helped identify rarer bacterioplankton groups and also showed the presence of unassigned OTUs indicating possible presence of novel bacterioplankton from the studied mangrove ecosystem.}, }
@article {pmid27936088, year = {2016}, author = {Kuroda, K and Nobu, MK and Mei, R and Narihiro, T and Bocher, BT and Yamaguchi, T and Liu, WT}, title = {A Single-Granule-Level Approach Reveals Ecological Heterogeneity in an Upflow Anaerobic Sludge Blanket Reactor.}, journal = {PloS one}, volume = {11}, number = {12}, pages = {e0167788}, pmid = {27936088}, issn = {1932-6203}, mesh = {Anaerobiosis ; Bacteria/genetics/isolation &amp; purification/*metabolism ; Bioreactors/*microbiology ; Fermentation ; Microbial Consortia ; *Microbial Interactions ; Phthalic Acids/chemistry ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Water Purification/*instrumentation ; }, abstract = {Upflow anaerobic sludge blanket (UASB) reactor has served as an effective process to treat industrial wastewater such as purified terephthalic acid (PTA) wastewater. For optimal UASB performance, balanced ecological interactions between syntrophs, methanogens, and fermenters are critical. However, much of the interactions remain unclear because UASB have been studied at a "macro"-level perspective of the reactor ecosystem. In reality, such reactors are composed of a suite of granules, each forming individual micro-ecosystems treating wastewater. Thus, typical approaches may be oversimplifying the complexity of the microbial ecology and granular development. To identify critical microbial interactions at both macro- and micro- level ecosystem ecology, we perform community and network analyses on 300 PTA-degrading granules from a lab-scale UASB reactor and two full-scale reactors. Based on MiSeq-based 16S rRNA gene sequencing of individual granules, different granule-types co-exist in both full-scale reactors regardless of granule size and reactor sampling depth, suggesting that distinct microbial interactions occur in different granules throughout the reactor. In addition, we identify novel networks of syntrophic metabolic interactions in different granules, perhaps caused by distinct thermodynamic conditions. Moreover, unseen methanogenic relationships (e.g. "Candidatus Aminicenantes" and Methanosaeta) are observed in UASB reactors. In total, we discover unexpected microbial interactions in granular micro-ecosystems supporting UASB ecology and treatment through a unique single-granule level approach.}, }
@article {pmid27935617, year = {2016}, author = {Tagg, AS and Harrison, JP and Ju-Nam, Y and Sapp, M and Bradley, EL and Sinclair, CJ and Ojeda, JJ}, title = {Fenton's reagent for the rapid and efficient isolation of microplastics from wastewater.}, journal = {Chemical communications (Cambridge, England)}, volume = {53}, number = {2}, pages = {372-375}, doi = {10.1039/c6cc08798a}, pmid = {27935617}, issn = {1364-548X}, mesh = {Chemical Fractionation/*methods ; Hydrogen Peroxide/*chemistry ; Iron/*chemistry ; Plastics/chemistry/*isolation &amp; purification ; Time Factors ; Wastewater/*chemistry ; Water Pollutants, Chemical/chemistry/*isolation &amp; purification ; }, abstract = {Fenton's reagent was used to isolate microplastics from organic-rich wastewater. The catalytic reaction did not affect microplastic chemistry or size, enabling its use as a pre-treatment method for focal plane array-based micro-FT-IR imaging. Compared with previously described microplastic treatment methods, Fenton's reagent offers a considerable reduction in sample preparation times.}, }
@article {pmid27935589, year = {2017}, author = {Choi, J and Yang, F and Stepanauskas, R and Cardenas, E and Garoutte, A and Williams, R and Flater, J and Tiedje, JM and Hofmockel, KS and Gelder, B and Howe, A}, title = {Strategies to improve reference databases for soil microbiomes.}, journal = {The ISME journal}, volume = {11}, number = {4}, pages = {829-834}, pmid = {27935589}, issn = {1751-7370}, }
@article {pmid27934909, year = {2016}, author = {Yang, Y and Lu, S and Shen, W and Zhao, X and Shen, M and Tan, Y and Li, G and Li, M and Wang, J and Hu, F and Le, S}, title = {Characterization of the first double-stranded RNA bacteriophage infecting Pseudomonas aeruginosa.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {38795}, pmid = {27934909}, issn = {2045-2322}, mesh = {Bacterial Typing Techniques ; Bacteriophages/genetics/*isolation &amp; purification ; China ; Cross Infection/microbiology ; Genome, Viral ; Host Specificity ; Humans ; Medical Waste ; Open Reading Frames ; Phylogeny ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/isolation &amp; purification/*virology ; RNA, Double-Stranded/isolation &amp; purification ; RNA, Viral/isolation &amp; purification ; Sewage/virology ; }, abstract = {Bacteriophages (phages) are widely distributed in the biosphere and play a key role in modulating microbial ecology in the soil, ocean, and humans. Although the role of DNA bacteriophages is well described, the biology of RNA bacteriophages is poorly understood. More than 1900 phage genomes are currently deposited in NCBI, but only 6 dsRNA bacteriophages and 12 ssRNA bacteriophages genome sequences are reported. The 6 dsRNA bacteriophages were isolated from legume samples or lakes with Pseudomonas syringae as the host. Here, we report the first Pseudomonas aeruginosa phage phiYY with a three-segmented dsRNA genome. phiYY was isolated from hospital sewage in China with the clinical P. aeruginosa strain, PAO38, as a host. Moreover, the dsRNA phage phiYY has a broad host range, which infects 99 out of 233 clinical P. aeruginosa strains isolated from four provinces in China. This work presented a detailed characterization of the dsRNA bacteriophage infecting P. aeruginosa.}, }
@article {pmid27933054, year = {2016}, author = {Penton, CR and Yang, C and Wu, L and Wang, Q and Zhang, J and Liu, F and Qin, Y and Deng, Y and Hemme, CL and Zheng, T and Schuur, EA and Tiedje, J and Zhou, J}, title = {NifH-Harboring Bacterial Community Composition across an Alaskan Permafrost Thaw Gradient.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1894}, pmid = {27933054}, issn = {1664-302X}, abstract = {Since nitrogen (N) is often limiting in permafrost soils, we investigated the N2-fixing genetic potential and the inferred taxa harboring those genes by sequencing nifH gene fragments in samples taken along a permafrost thaw gradient in an Alaskan boreal soil. Samples from minimally, moderately and extensively thawed sites were taken to a depth of 79 cm to encompass zones above and below the depth of the water table. NifH reads were translated with frameshift correction and 112,476 sequences were clustered at 5% amino acid dissimilarity resulting in 1,631 OTUs. Sample depth in relation to water table depth was correlated to differences in the NifH sequence classes with those most closely related to group I nifH-harboring Alpha- and Beta-Proteobacteria in higher abundance above water table depth while those related to group III nifH-harboring Delta Proteobacteria more abundant below. The most dominant below water table depth NifH sequences, comprising 1/3 of the total, were distantly related to Verrucomicrobia-Opitutaceae. Overall, these results suggest that permafrost thaw alters the class-level composition of N2-fixing communities in the thawed soil layers and that this distinction corresponds to the depth of the water table. These nifH data were also compared to nifH sequences obtained from a study at an Alaskan taiga site, and to those of other geographically distant, non-permafrost sites. The two Alaska sites were differentiated largely by changes in relative abundances of the same OTUs, whereas the non-Alaska sites were differentiated by the lack of many Alaskan OTUs, and the presence of unique halophilic, sulfate- and iron-reducing taxa in the Alaska sites.}, }
@article {pmid27933046, year = {2016}, author = {Herlemann, DP and Lundin, D and Andersson, AF and Labrenz, M and Jürgens, K}, title = {Phylogenetic Signals of Salinity and Season in Bacterial Community Composition Across the Salinity Gradient of the Baltic Sea.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1883}, pmid = {27933046}, issn = {1664-302X}, abstract = {Understanding the key processes that control bacterial community composition has enabled predictions of bacterial distribution and function within ecosystems. In this study, we used the Baltic Sea as a model system to quantify the phylogenetic signal of salinity and season with respect to bacterioplankton community composition. The abundances of 16S rRNA gene amplicon sequencing reads were analyzed from samples obtained from similar geographic locations in July and February along a brackish to marine salinity gradient in the Baltic Sea. While there was no distinct pattern of bacterial richness at different salinities, the number of bacterial phylotypes in winter was significantly higher than in summer. Bacterial community composition in brackish vs. marine conditions, and in July vs. February was significantly different. Non-metric multidimensional scaling showed that bacterial community composition was primarily separated according to salinity and secondly according to seasonal differences at all taxonomic ranks tested. Similarly, quantitative phylogenetic clustering implicated a phylogenetic signal for both salinity and seasonality. Our results suggest that global patterns of bacterial community composition with respect to salinity and season are the result of phylogenetically clustered ecological preferences with stronger imprints from salinity.}, }
@article {pmid28330122, year = {2016}, author = {Mothe, T and Sultanpuram, VR}, title = {Production, purification and characterization of a thermotolerant alkaline serine protease from a novel species Bacillus caseinilyticus.}, journal = {3 Biotech}, volume = {6}, number = {1}, pages = {53}, pmid = {28330122}, issn = {2190-572X}, abstract = {Alkaline proteases are important enzymes in many industrial applications, especially as additives in laundry detergent industry. Though there are a number of Bacillus species which are reported to be producing proteases, the efficiency of a protease produced by a novel strain has to be studied in comparison to the others. Hence, in this study, an alkaline serine protease produced by a novel species Bacillus caseinilyticus was purified and characterized for its possible usage in detergent industry. Ammonium sulphate, dialysis and DEAE column chromatographic methods were used for purification of the isolated alkaline protease. The molecular weight of the protease was determined by SDS-PAGE and it was found to be 66 kDa. Peptide mass fingerprinting (PMF) was carried out using MALDI-TOF-TOF mass spectrometry and the peptides were found to be similar to that of subtilisin protease. Specific activity of purified protein was found to be 89.2 U/mg. Optimum pH and temperature for enzyme activity were at pH 8 and 60 °C, respectively, showing stability with 10 mM CaCl2. Phenyl methyl sulphonyl fluoride (PMSF) at both 5 and 10 mM concentrations completely inhibited the enzyme activity suggesting its serine nature. EDTA, metal ions Mg[2+] and Ca[2+] increased the enzyme activity. The one factor at a time optimisation of the protease production was carried to identify the important factors that affect its production. After optimisation, the protease was produced at lab scale, purified and characterised. This alkali, thermotolerant serine protease was found to be significantly stable in the presence of various surfactants and H2O2. Also, it was successfully able to remove blood stain when used as an additive along with commercial detergent suggesting its potential application in the laundry detergent industry.}, }
@article {pmid28721237, year = {2015}, author = {De Weirdt, R and Van de Wiele, T}, title = {Micromanagement in the gut: microenvironmental factors govern colon mucosal biofilm structure and functionality.}, journal = {NPJ biofilms and microbiomes}, volume = {1}, number = {}, pages = {15026}, pmid = {28721237}, issn = {2055-5008}, abstract = {The human gut microbiome provides us with functional features that we did not have to evolve ourselves and can be viewed as a structured microbial community that operates like a microbial organ within the human host. A minor but important part of this microbiome is the ability to colonise and thrive within the mucous layer that covers the colon epithelium. These mucosal microbes intimately interact with the intestinal tissue and seem to be important modulators of human health. Embedded in the host-secreted mucous matrix, they form a 'mucosal biofilm' with a distinct composition and functionality. In this review, we provide evidence that six specific (micro)environmental factors near the colon mucosa shape and determine mucosal biofilm formation and stability, that is, (1) mucous rigidity, (2) gradients of fluid shear, (3) radial oxygen gradients, (4) secretions of host defense molecules, (5) the presence of a rich but challenging nutrient platform and (6) the presence of niches at the colon epithelial surface. In addition, it appears that microbes actively participate in shaping their mucosal environment. Current insights into the interaction between mucosal microbes and their environment are rather limited, and many questions regarding the contribution of mucosal biofilm functionality and stability to human health remain to be answered. Yet, given the higher potency of mucosal microbes than their luminal counterparts to interact with the host, new insights can accelerate the development of novel disease-preventive or therapeutic strategies.}, }
@article {pmid28454970, year = {2015}, author = {Fotschki, J and Szyc, AM and Moisés Laparra, J and Wróblewska, B}, title = {Corrigendum to "Mare's and cow's milk: Promote similar metabolic effects and expression of innate markers in Caco-2 cells?" [Food Res. Int. 72 (2015) 184-190].}, journal = {Food research international (Ottawa, Ont.)}, volume = {75}, number = {}, pages = {385}, doi = {10.1016/j.foodres.2015.07.021}, pmid = {28454970}, issn = {1873-7145}, }
@article {pmid28721225, year = {2015}, author = {Verstraete, W}, title = {The technological side of the microbiome.}, journal = {NPJ biofilms and microbiomes}, volume = {1}, number = {}, pages = {15001}, pmid = {28721225}, issn = {2055-5008}, }
@article {pmid28324393, year = {2015}, author = {Agrawal, PK and Agrawal, S and Shrivastava, R}, title = {Modern molecular approaches for analyzing microbial diversity from mushroom compost ecosystem.}, journal = {3 Biotech}, volume = {5}, number = {6}, pages = {853-866}, pmid = {28324393}, issn = {2190-572X}, abstract = {Biosphere is a store house of various microorganisms that may be employed to isolate and exploit microbes for environmental, pharmaceutical, agricultural and industrial applications. There is restricted data regarding the structure and dynamics of microbial communities in several ecosystems because only a little fraction of microbial diversity is accessible by culture methods. Owing to limitations of traditional enrichment methods and pure culture techniques, microbiological studies have offered a narrow portal for investigating microbial flora. The bacterial community represented by the morphological and nutritional criteria failed to provide a natural taxonomic order according to the evolutionary relationship. Genetic diversity among the isolates recovered from mushroom compost has not been widely studied. To understand genetic diversity and community composition of the mushroom compost microflora, different approaches are now followed by taxonomists, to characterize and identify isolates up to species level. Molecular microbial ecology is an emerging discipline of biology under molecular approach which can provide complex community profiles along with useful phylogenetic information. The genomic era has resulted in the development of new molecular tools and techniques for study of culturable microbial diversity including the DNA base ratio (mole% G + C), DNA-DNA hybridization, DNA microarray and reverse sample genome probing. In addition, non-culturable diversity of mushroom compost ecosystem can be characterized by employing various molecular tools which would be discussed in the present review.}, }
@article {pmid28955019, year = {2014}, author = {Kleinsteuber, S}, title = {Special Issue on "Microbial Ecology of Anaerobic Digestion".}, journal = {Bioengineering (Basel, Switzerland)}, volume = {1}, number = {2}, pages = {111-112}, doi = {10.3390/bioengineering1020111}, pmid = {28955019}, issn = {2306-5354}, abstract = {Anaerobic digestion (AD) is an efficient and sustainable way of using organic carbon from residual biomass and organic waste for the production of renewable energy, while simultaneously recycling nutrients and cleaning up waste streams. The process relies on complex microbial communities comprised of diverse functional guilds; these communities have manifold metabolic pathways and interactions. In contrast to the conventional view of an anaerobic digester as a black box, advanced microbiological methods have paved the way for understanding and even controlling complex microbial networks. Nowadays, microbial resource management is crucial for technological progress in AD, and offers new perspectives concerning sustainable waste management, renewable energy production, resource efficiency, and advanced bio-refineries; these perspectives lead to novel applications of AD processes that go beyond biogas as the main product. [...].}, }
@article {pmid28250399, year = {2013}, author = {Matallana-Surget, S and Wattiez, R}, title = {Impact of Solar Radiation on Gene Expression in Bacteria.}, journal = {Proteomes}, volume = {1}, number = {2}, pages = {70-86}, pmid = {28250399}, issn = {2227-7382}, abstract = {Microorganisms often regulate their gene expression at the level of transcription and/or translation in response to solar radiation. In this review, we present the use of both transcriptomics and proteomics to advance knowledge in the field of bacterial response to damaging radiation. Those studies pertain to diverse application areas such as fundamental microbiology, water treatment, microbial ecology and astrobiology. Even though it has been demonstrated that mRNA abundance is not always consistent with the protein regulation, we present here an exhaustive review on how bacteria regulate their gene expression at both transcription and translation levels to enable biomarkers identification and comparison of gene regulation from one bacterial species to another.}, }
@article {pmid28741822, year = {2012}, author = {Rousk, J and Frey, SD and Bååth, E}, title = {Temperature adaptation of bacterial communities in experimentally warmed forest soils.}, journal = {Global change biology}, volume = {18}, number = {10}, pages = {3252-3258}, doi = {10.1111/j.1365-2486.2012.02764.x}, pmid = {28741822}, issn = {1365-2486}, abstract = {A detailed understanding of the influence of temperature on soil microbial activity is critical to predict future atmospheric CO2 concentrations and feedbacks to anthropogenic warming. We investigated soils exposed to 3-4 years of continuous 5 °C-warming in a field experiment in a temperate forest. We found that an index for the temperature adaptation of the microbial community, Tmin for bacterial growth, increased by 0.19 °C per 1 °C rise in temperature, showing a community shift towards one adapted to higher temperature with a higher temperature sensitivity (Q10(5-15 °C) increased by 0.08 units per 1 °C). Using continuously measured temperature data from the field experiment we modelled in situ bacterial growth. Assuming that warming did not affect resource availability, bacterial growth was modelled to become 60% higher in warmed compared to the control plots, with the effect of temperature adaptation of the community only having a small effect on overall bacterial growth (<5%). However, 3 years of warming decreased bacterial growth, most likely due to substrate depletion because of the initially higher growth in warmed plots. When this was factored in, the result was similar rates of modelled in situ bacterial growth in warmed and control plots after 3 years, despite the temperature difference. We conclude that although temperature adaptation for bacterial growth to higher temperatures was detectable, its influence on annual bacterial growth was minor, and overshadowed by the direct temperature effect on growth rates.}, }
@article {pmid28547337, year = {2000}, author = {Broughton, LC and Gross, KL}, title = {Patterns of diversity in plant and soil microbial communities along a productivity gradient in a Michigan old-field.}, journal = {Oecologia}, volume = {125}, number = {3}, pages = {420-427}, doi = {10.1007/s004420000456}, pmid = {28547337}, issn = {1432-1939}, abstract = {The relationship between plant diversity and productivity has received much attention in ecology, but the relationship of these factors to soil microbial communities has been little explored. The carbon resources that support soil microbial communities are primarily derived from plants, so it is likely that the soil microbial community should respond to changes in plant diversity or productivity, particularly if the plant community affects the quality or quantity of available carbon. We investigated the relationship of plant diversity and productivity to the composition of the soil microbial community along a topographic gradient in a mid-successional old-field in southwestern Michigan. Soil moisture, soil inorganic N, and plant biomass increased from the top to the base of the slope, while light at ground level decreased along this same gradient. We characterized the changes in resource levels along this gradient using an index of productivity that incorporated light levels, soil N, soil moisture, and plant biomass. Average plant species richness declined with this productivity index and there were associated compositional changes in the plant community along the gradient. The plant community shifted from predominantly low-growing perennial forbs at low productivities to perennial grasses at higher productivities. Although there was variation in the structure of the soil microbial community [as indicated by fatty acid methyl ester (FAME) profiles], changes in the composition of the soil microbial community were not correlated with plant productivity or diversity. However, microbial activity [as indicated by Biolog average well color development and substrate-induced respiration (SIR)] was positively correlated with plant productivity. The similarity between patterns of plant biomass and soil microbial activity suggests that either plant productivity is driving microbial productivity or that limiting resources for each of these two communities co-vary.}, }
@article {pmid28565406, year = {1999}, author = {Mongold, JA and Bennett, AF and Lenski, RE}, title = {EVOLUTIONARY ADAPTATION TO TEMPERATURE. VII. EXTENSION OF THE UPPER THERMAL LIMIT OF ESCHERICHIA COLI.}, journal = {Evolution; international journal of organic evolution}, volume = {53}, number = {2}, pages = {386-394}, doi = {10.1111/j.1558-5646.1999.tb03774.x}, pmid = {28565406}, issn = {1558-5646}, abstract = {What factors influence the ability of populations to adapt to extreme environments that lie outside their current tolerance limits? We investigated this question by exposing experimental populations of the bacterium Escherichia coli to lethally high temperatures. We asked: (1) whether we could obtain thermotolerant mutants with an extended upper thermal limit by this selective screen; (2) whether the propensity to obtain thermotolerant mutants depended on the prior selective history of the progenitor genotypes; and (3) how the fitness properties of these mutants compared to those of their progenitors within the ancestral thermal niche. Specifically, we subjected 15 independent populations founded from each of six progenitors to 44°C; all of the progenitors had upper thermal limits between about 40°C and 42°C. Two of the progenitors were from populations that had previously adapted to 32°C, two were from populations adapted to 37°C, and two were from populations adapted to 41-42°C. All 90 populations were screened for mutants that could survive and grow at 44°C. We obtained three thermotolerant mutants, all derived from progenitors previously adapted to 41-42°C. In an earlier study, we serendipitously found one other thermotolerant mutant derived from a population that had previously adapted to 32°C. Thus, prior selection at an elevated but nonlethal temperature may predispose organisms to evolve more extreme thermotolerance, but this is not an absolute requirement. It is evidently possible to obtain mutants that tolerate more extreme temperatures, so why did they not become prevalent during prior selection at 41-42°C, near the upper limit of the thermal niche? To address this question, we measured the fitness of the thermotolerant mutants at high temperatures just within the ancestral niche. None of the four thermotolerant mutants had an advantage relative to their progenitor even very near the upper limit of the thermal niche; in fact, all of the mutants showed a noticeable loss of fitness around 41°C. Thus, the genetic adaptations that improve competitive fitness at high but nonlethal temperatures are distinct from those that permit tolerance of otherwise lethal temperatures.}, }
@article {pmid28565201, year = {1999}, author = {Bohannan, BJM and Travisano, M and Lenski, RE}, title = {EPISTATIC INTERACTIONS CAN LOWER THE COST OF RESISTANCE TO MULTIPLE CONSUMERS.}, journal = {Evolution; international journal of organic evolution}, volume = {53}, number = {1}, pages = {292-295}, doi = {10.1111/j.1558-5646.1999.tb05355.x}, pmid = {28565201}, issn = {1558-5646}, abstract = {It is widely assumed that resistance to consumers (e.g., predators or pathogens) comes at a "cost," that is, when the consumer is absent the resistant organisms are less fit than their susceptible counterparts. It is unclear what factors determine this cost. We demonstrate that epistasis between genes that confer resistance to two different consumers can alter the cost of resistance. We used as a model system the bacterium Escherichia coli and two different viruses (bacteriophages), T4 and Λ, that prey upon E. coli. Epistasis tended to reduce the costs of multiple resistance in this system. However, the extent of cost savings and its statistical significance depended on the environment in which fitness was measured, whether the null hypothesis for gene interaction was additive or multiplicative, and subtle differences among mutations that conferred the same resistance phenotype.}, }
@article {pmid28568337, year = {1998}, author = {Turner, PE and Cooper, VS and Lenski, RE}, title = {TRADEOFF BETWEEN HORIZONTAL AND VERTICAL MODES OF TRANSMISSION IN BACTERIAL PLASMIDS.}, journal = {Evolution; international journal of organic evolution}, volume = {52}, number = {2}, pages = {315-329}, doi = {10.1111/j.1558-5646.1998.tb01634.x}, pmid = {28568337}, issn = {1558-5646}, abstract = {It has been hypothesized that there is a fundamental conflict between horizontal (infectious) and vertical (intergenerational) modes of parasite transmission. Activities of a parasite that increase its rate of infectious transmission are presumed to reduce its host's fitness. This reduction in host fitness impedes vertical transmission of the parasite and causes a tradeoff between horizontal and vertical transmission. Given this tradeoff, and assuming no multiple infections (no within-host competition among parasites), a simple model predicts that the density of uninfected hosts in the environment should determine the optimum balance between modes of parasite transmission. When susceptible hosts are abundant, selection should favor increased rates of horizontal transfer, even at the expense of reduced vertical transmission. Conversely, when hosts are rare, selection should favor increased vertical transmission even at the expense of lower horizontal transfer. We tested the tradeoff hypothesis and these evolutionary predictions using conjugative plasmids and the bacteria that they infect. Plasmids were allowed to evolve for 500 generations in environments with different densities of susceptible hosts. The plasmid's rate of horizontal transfer by conjugation increased at the expense of host fitness, indicating a tradeoff between horizontal and vertical transmission. Also, reductions in conjugation rate repeatedly coincided with the loss of a particular plasmid-encoded antibiotic resistance gene. However, susceptible host density had no significant effect on the evolution of horizontal versus vertical modes of plasmid transmission. We consider several possible explanations for the failure to observe such an effect.}, }
@article {pmid28565475, year = {1997}, author = {Elena, SF and Lenski, RE}, title = {LONG-TERM EXPERIMENTAL EVOLUTION IN ESCHERICHIA COLI. VII. MECHANISMS MAINTAINING GENETIC VARIABILITY WITHIN POPULATIONS.}, journal = {Evolution; international journal of organic evolution}, volume = {51}, number = {4}, pages = {1058-1067}, doi = {10.1111/j.1558-5646.1997.tb03953.x}, pmid = {28565475}, issn = {1558-5646}, abstract = {Six replicate populations of the bacterium Escherichia coli were propagated for more than 10,000 generations in a defined environment. We sought to quantify the variation among clones within these populations with respect to their relative fitness, and to evaluate the roles of three distinct population genetic processes in maintaining this variation. On average, a pair of clones from the same population differed from one another in their relative fitness by approximately 4%. This within-population variation was small compared with the average fitness gain relative to the common ancestor, but it was statistically significant. According to one hypothesis, the variation in fitness is transient and reflects the ongoing substitution of beneficial alleles. We used Fisher's fundamental theorem to compare the observed rate of each population's change in mean fitness with the extent of variation for fitness within that population, but we failed to discern any correspondence between these quantities. A second hypothesis supposes that the variation in fitness is maintained by recurrent deleterious mutations that give rise to a mutation-selection balance. To test this hypothesis, we made use of the fact that two of the six replicate populations had evolved mutator phenotypes, which gave them a genomic mutation rate approximately 100-fold higher than that of the other populations. There was a marginally significant correlation between a population's mutation rate and the extent of its within-population variance for fitness, but this correlation was driven by only one population (whereas two of the populations had elevated mutation rates). Under a third hypothesis, this variation is maintained by frequency-dependent selection, whereby genotypes have an advantage when they are rare relative to when they are common. In all six populations, clones were more fit, on average, when they were rare than when they were common, although the magnitude of the advantage when rare was usually small (~1% in five populations and ~5% in the other). These three hypotheses are not mutually exclusive, but frequency-dependent selection appears to be the primary force maintaining the fitness variation within these experimental populations.}, }
@article {pmid28568801, year = {1997}, author = {Bennett, AF and Lenski, RE}, title = {EVOLUTIONARY ADAPTATION TO TEMPERATURE. VI. PHENOTYPIC ACCLIMATION AND ITS EVOLUTION IN ESCHERICHIA COLI.}, journal = {Evolution; international journal of organic evolution}, volume = {51}, number = {1}, pages = {36-44}, doi = {10.1111/j.1558-5646.1997.tb02386.x}, pmid = {28568801}, issn = {1558-5646}, abstract = {Acclimation refers to reversible, nongenetic changes in phenotype that are induced by specific environmental conditions. Acclimation is generally assumed to improve function in the environment that induces it (the beneficial acclimation hypothesis). In this study, we experimentally tested this assumption by measuring relative fitness of the bacterium Escherichia coli acclimated to different thermal environments. The beneficial acclimation hypothesis predicts that bacteria acclimated to the temperature of competition should have greater fitness than do bacteria acclimated to any other temperature. The benefit predicted by the hypothesis was found in only seven of 12 comparisons; in the other comparisons, either no statistically demonstrable benefit was observed or a detrimental effect of acclimation was demonstrated. For example, in a lineage evolutionarily adapted to 37°C, bacteria acclimated to 37°C have a higher fitness at 32°C than do bacteria acclimated to 32°C, a result exactly contrary to prediction; acclimation to 27°C or 40°C prior to competition at those temperatures confers no benefit over 37°C acclimated forms. Consequently, the beneficial acclimation hypothesis must be rejected as a general prediction of the inevitable result of phenotypic adjustments associated with new environments. However, the hypothesis is supported in many instances when the acclimation and competition temperatures coincide with the historical temperature at which the bacterial populations have evolved. For example, when the evolutionary temperature of the population was 37°C, bacteria acclimated to 37°C had superior fitness at 37°C to those acclimated to 32°C; similarly, bacteria evolutionarily adapted to 32°C had a higher fitness during competition at 32°C than they did when acclimated to 37°C. The more surprising results are that when the bacteria are acclimated to their historical evolutionary temperature, they are frequently competitively superior even at other temperatures. For example, bacteria that have evolved at either 20°C or 32°C and are acclimated to their respective evolutionary temperatures have a greater fitness at 37°C than when they are acclimated to 37°C. Thus, acclimation to evolutionary temperature may, as a correlated consequence, enhance performance not only in the evolutionary environment, but also in a variety of other thermal environments.}, }
@article {pmid28307813, year = {1996}, author = {Stadler, B and Müller, T}, title = {Aphid honeydew and its effect on the phyllosphere microflora of Picea abies (L.) Karst.}, journal = {Oecologia}, volume = {108}, number = {4}, pages = {771-776}, pmid = {28307813}, issn = {1432-1939}, abstract = {Aphids of the genus Cinara, feeding on Norway spruce, excrete copious amounts of honeydew, a carbon-rich waste product, which accumulates locally on needles and twigs. We investigated the role of honeydew as a potential source of energy which might promote the growth of micro-organisms in the phyllosphere of conifer trees. To approach this question, we followed the population dynamics of Cinara spp. in a natural forest stand over two seasons. We also studied the amounts of honeydew produced by individual aphids and identified potential parameters which might influence honeydew production. Finally, we determined the growth of micro-organisms on infested and uninfested needles of Norway spruce during the growing season. Confined to Picea abies, the investigated Cinara species only became abundant in midsummer, when needles and shoots were expanding. The populations showed only a single peak in abundance, the timing and magnitude of which may vary from year to year due to weather conditions, changes in plant quality in a yearly cycle or the impact of natural enemies. The amount of honeydew produced by individual aphids was dependent on the developmental stage of the aphid, the nutritional supply of its host plant and on the developmental state of the Norway spruce (e.g. bud burst, end of shoot extension). The presence of honeydew significantly increased the growth of bacteria, yeast and filamentous fungi on the surface of needles and there was a pronounced seasonal trend, with the highest abundance in midsummer correlating with the period of peak aphid abundance. Taken together, these findings indicate that aphids have an influence on microbial ecology in the phyllosphere of trees. The implication of our study, from interactions at the population level to effects and potential consequences for C and N fluxes at the level of forest ecosystems, is discussed.}, }
@article {pmid28568929, year = {1996}, author = {Bennett, AF and Lenski, RE}, title = {EVOLUTIONARY ADAPTATION TO TEMPERATURE. V. ADAPTIVE MECHANISMS AND CORRELATED RESPONSES IN EXPERIMENTAL LINES OF ESCHERICHIA COLI.}, journal = {Evolution; international journal of organic evolution}, volume = {50}, number = {2}, pages = {493-503}, doi = {10.1111/j.1558-5646.1996.tb03862.x}, pmid = {28568929}, issn = {1558-5646}, abstract = {We previously demonstrated temperature-specific genetic adaptation in experimental lines of Escherichia coli. Six initially identical populations were propagated for 2000 generations under each of five regimes: constant 20°C, 32°C, 37°C, and 42°C, and a daily switch between 32°C and 42°C. Glucose was the sole carbon source in all cases. Here, we examine the physiological bases of adaptation to determine whether the same mechanisms evolved among the replicate lines within each thermal regime and across different regimes. Specifically, we investigate whether changes in glucose transport may account for the temperature-specific adaptation. We compared each line's direct response of fitness to glucose with its correlated response to maltose; glucose and maltose enter the cell by different pathways, but their catabolism is identical. Except for lines maintained at the ancestral temperature (37°C), almost all derived lines had significantly different fitnesses (relative to their common ancestor) in glucose and maltose, supporting the hypothesis that adaptation involved changes in glucose transport. An alternative explanation, that maltose transport decayed by genetic drift, appears unlikely for reasons that are discussed. Although most lines showed evidence of temperature-specific adaptation in glucose transport, several different mechanisms may underlie these improvements, as indicated by heterogeneity in correlated responses (across temperatures and substrates) among replicate lines adapted to the same regime. This heterogeneity provides a latent pool of genetic variation for responding to environmental change.}, }
@article {pmid28568880, year = {1996}, author = {Mongold, JA and Bennett, AF and Lenski, RE}, title = {EVOLUTIONARY ADAPTATION TO TEMPERATURE. IV. ADAPTATION OF ESCHERICHIA COLI AT A NICHE BOUNDARY.}, journal = {Evolution; international journal of organic evolution}, volume = {50}, number = {1}, pages = {35-43}, doi = {10.1111/j.1558-5646.1996.tb04470.x}, pmid = {28568880}, issn = {1558-5646}, abstract = {Following an environmental change, the course of a population's adaptive evolution may be influenced by environmental factors, such as the degree of marginality of the new environment relative to the organism's potential range, and by genetic factors, including constraints that may have arisen during its past history. Experimental populations of bacteria were used to address these issues in the context of evolutionary adaptation to the thermal environment. Six replicate lines of Escherichia coli (20°C group), founded from a common ancestor, were propagated for 2000 generations at 20°C, a novel temperature that is very near the lower thermal limit at which it can maintain a stable population size in a daily serial transfer (100-fold dilution) regime. Four additional groups (32/20, 37/20, 42/20, and 32-42/20°C groups) of six lines, each with 2000 generation selection histories at different temperatures (32, 37, 42, and daily alternation of 32 and 42°C), were moved to the same 20°C environment and propagated in parallel to ascertain whether selection histories influence the adaptive response in this novel environment. Adaptation was measured by improvement in fitness relative to the common ancestor in direct competition experiments conducted at 20°C. All five groups showed improvement in relative fitness in this environment; the mean fitness of the 20°C group after 2000 generations increased by about 8%. Selection history had no discernible effect on the rate or final magnitude of the fitness responses of the four groups with different histories after 2000 generations. The correlated fitness responses of the 20°C group were measured across the entire thermal niche. There were significant tradeoffs in fitness at higher temperatures; for example, at 40°C the average fitness of the 20°C group was reduced by almost 20% relative to the common ancestor. We also observed a downward shift of 1-2°C in both the upper and lower thermal niche limits for the 20°C selected group. These observations are contrasted with previous observations of a markedly greater rate of adaptation to growth near the upper thermal limit (42°C) and a lack of trade-off in fitness at lower temperatures for lines adapted to that high temperature. The evolutionary implications of this asymmetry are discussed.}, }
@article {pmid28593661, year = {1995}, author = {Travisano, M and Vasi, F and Lenski, RE}, title = {LONG-TERM EXPERIMENTAL EVOLUTION IN ESCHERICHIA COLI. III. VARIATION AMONG REPLICATE POPULATIONS IN CORRELATED RESPONSES TO NOVEL ENVIRONMENTS.}, journal = {Evolution; international journal of organic evolution}, volume = {49}, number = {1}, pages = {189-200}, doi = {10.1111/j.1558-5646.1995.tb05970.x}, pmid = {28593661}, issn = {1558-5646}, abstract = {Twelve populations of Escherichia coli were founded from a single clone and propagated for 2000 generations in identical glucose-limited environments. During this time, the mean fitnesses of the evolving populations relative to their common ancestor improved greatly, but their fitnesses relative to one another diverged only slightly. Although the populations showed similar fitness increases, they may have done so by different underlying adaptations, or they may have diverged in other respects by random genetic drift. Therefore, we examined the relative fitnesses of independently derived genotypes in two other sugars, maltose and lactose, to determine whether they were homogeneous or heterogeneous in these environments. The genetic variation among the derived lines in fitness on maltose and lactose was more than 100-times greater than their variation in fitness on glucose. Moreover, the glucose-adapted genotypes, on average, showed significant adaptation to lactose, but not to maltose. That pathways for use of maltose and glucose are virtually identical in E. coli, except for their distinct mechanisms of uptake, suggests that the derived genotypes have adapted primarily by improved glucose transport. From consideration of the number of generations of divergence, the mutation rate in E. coli, and the proportion of its genome required for growth on maltose (but not glucose), we hypothesize that pleiotropy involving the selected alleles, rather than random genetic drift of alleles at other loci, was the major cause of the variation among the derived genotypes in fitness on these other sugars.}, }
@article {pmid28568417, year = {1994}, author = {Bell, JA and Friedman, SB}, title = {GENETIC STRUCTURE AND DIVERSITY WITHIN LOCAL POPULATIONS OF BACILLUS MYCOIDES.}, journal = {Evolution; international journal of organic evolution}, volume = {48}, number = {5}, pages = {1698-1714}, doi = {10.1111/j.1558-5646.1994.tb02206.x}, pmid = {28568417}, issn = {1558-5646}, abstract = {Sixty strains of Bacillus mycoides were isolated from each of two sites and characterized by their responses to standard metabolic tests used in bacterial taxonomy, by multilocus enzyme electrophoresis (MLEE), and by restriction-fragment-length polymorphism (RFLP) analysis of Southern blots probed with both a conserved DNA fragment derived from a Salmonella typhimurium ribosomal cistron and with two cosmid probes derived from B. mycoides ATCC strain 6463. Both MLEE and RFLP analyses indicated that the collection contained two genetically distinct sets of strains (I and II); one of these sets was further differentiated genetically by the same analyses (IIA and IIB). Standard taxonomic analysis did not distinguish these sets of strains; biochemical test profiles were similar for all isolates. The genetic distance between groups I and II is as great as that observed for recognized species of bacteria. It is proposed that these groups are sibling species having a common evolutionary descent and that their metabolic phenotype has been conserved, whereas their DNA and protein sequences have diverged. No strong evidence of geographic differentiation between strains from the two sites appeared in either genetic or phenetic characters.}, }
@article {pmid28564463, year = {1994}, author = {Leroi, AM and Lenski, RE and Bennett, AF}, title = {EVOLUTIONARY ADAPTATION TO TEMPERATURE. III. ADAPTATION OF ESCHERICHIA COLI TO A TEMPORALLY VARYING ENVIRONMENT.}, journal = {Evolution; international journal of organic evolution}, volume = {48}, number = {4}, pages = {1222-1229}, doi = {10.1111/j.1558-5646.1994.tb05307.x}, pmid = {28564463}, issn = {1558-5646}, abstract = {Six lines of the bacterium Escherichia coli were propagated for 2,000 generations in a temporally varying environment. The imposed environmental regime consisted of alternating days at 32°C and 42°C, with rapid transitions between them. These derived lines are competitively superior to their ancestor in this variable temperature regime. We also measured changes in the fitness of these lines, relative to their common ancestor, in both the constant (32°C and 42°C) and transition (from 32°C to 42°C and from 42°C to 32°C) components of this temporally varying environment, to determine whether the bacteria had adapted to the particular constant temperatures or the transitions between them, or both. The experimentally evolved lines had significantly improved fitness in each of the constant environmental components (32°C and 42°C). However, the experimental lines had not improved in making the sudden temperature transitions that were a potentially important aspect of the temporally variable environment. In fact, fitness in making at least one of the transitions (between 32°C and 42°C) unexpectedly decreased. This reduced adaptation to the abrupt transitions between these temperatures is probably a pleiotropic effect of mutations that were responsible for the increased fitness at the component temperatures. Among the six experimental lines, significant heterogeneity occurred in their adaptation to the constant and transition components of the variable environment.}, }
@article {pmid28314028, year = {1993}, author = {Wardle, DA and Parkinson, D and Waller, JE}, title = {Interspecific competitive interactions between pairs of fungal species in natural substrates.}, journal = {Oecologia}, volume = {94}, number = {2}, pages = {165-172}, pmid = {28314028}, issn = {1432-1939}, abstract = {The role of interspecific competition in fungal communities in natural substrates is poorly understood because fungi do not form easily definable populations. A new approach to investigating fungal competition, using natural substrates containing a range of known biomass concentrations of each of two species, is described. Relative competitive success of each species is assessed over time in terms of propagule production and substrate colonisation by each species. In an agricultural soil Mucor hiemalis usually out-competed Trichoderma harzianum. After 27 days, the success of both species in the mixtures was independent of the initial biomass concentration of either species, although the success of T. harzianum in these mixtures was substantially inhibited relative to the T. harzianum monocultures. In a forest soil, T. polysporum maintained a competitive advantage over M. hiemalis, and induced M. hiemalis to produce propagules rather than mycelia. Coexistence of both species always occurred in both experiments, and in the forest soil experiment the two-species mixtures all contained a higher total microbial biomass than the monocultures of either species by day 47, suggesting some niche differentiation.}, }
@article {pmid28568084, year = {1993}, author = {Bennett, AF and Lenski, RE}, title = {EVOLUTIONARY ADAPTATION TO TEMPERATURE II. THERMAL NICHES OF EXPERIMENTAL LINES OF ESCHERICHIA COLI.}, journal = {Evolution; international journal of organic evolution}, volume = {47}, number = {1}, pages = {1-12}, doi = {10.1111/j.1558-5646.1993.tb01194.x}, pmid = {28568084}, issn = {1558-5646}, abstract = {Groups of replicated lines of the bacterium Escherichia coli were propagated for 2,000 generations at constant 32, 37, or 42°C, or in an environment that alternated between 32 and 42°C. Here, we examine the performance of each group across a temperature range of 12-44°C measuring the temperatures over which each line can maintain itself in serial dilution culture (the thermal niche). Thermal niche was not affected by selection history: average lower and upper limits remained about 19 and 42°C for all groups. In addition, no significant differences among groups were observed in rate of extinction at more extreme temperatures. Within the thermal niche, we measured the mean fitness of the evolved groups relative to their common ancestor. Increases in mean fitness were temperature specific, with the largest increase for each group occurring near its selected temperature. Thus, the temperature at which mean fitness relative to the ancestor was greatest (the thermal optimum) diverged by about 10°C for the groups selected at constant 32°C versus constant 42°C. Tradeoffs in relative fitness (decrements relative to the ancestor elsewhere within the thermal niche) did not necessarily accompany fitness improvements, although tradeoffs were observed for a few of the lines. We conclude that adaptation in this system was quite temperature specific, but substantial divergence among groups in thermal optima had little effect on the limits of their thermal niches and did not necessarily involve tradeoffs in fitness at other temperatures.}, }
@article {pmid28312602, year = {1992}, author = {Krebs, RA and Barker, JS and Armstrong, TP}, title = {Coexistence of ecologically similar colonising species III. Drosophila aldrichi and D. buzzatii: larval performance on, and adult preference for, three Opuntia cactus species.}, journal = {Oecologia}, volume = {92}, number = {3}, pages = {362-372}, pmid = {28312602}, issn = {1432-1939}, abstract = {Two Drosophila species, D. buzzatti and D. aldrichi, coexist on several species of Opuntia cacti in Australia, primarily on O. tomentosa and O. streptacantha in the northern part of the cactus distribution, and on O. stricta in the south. Thorax length of field-collected adults was less, and the variance in length greater, than that for flies reared on simulated rots in the laboratory, indicating that these species are affected by crowding in nature. A larval performance index, measured on simulated cactus rots at low, moderate and high densities in single-species cultures, and at moderate and high densities in mixed-species cultures, was used to compare the relative intensity of intra- and interspecific competition at the same total larval density per 5 g necrotic cactus. Larval performance of both fly species was greatest on O. streptacantha, intermediate on O. tomentosa, and least on O. stricta in both single-species and mixed-species cultures. On O. stricta, the performances of D. aldrichi and D. buzzatii were not different when in single-species cultures, but that of D. aldrichi decreased significantly in mixed-species cultures. On the other two cactus species, the performances of D. aldrichi and D. buzzattii were not different in mixed-species cultures. The order of preferences by adult females for the cacti differed from that for larval performance, with females of both species prefering O. stricta. Analysis of microbial numbers growing on the cacti showed little difference among cacti at the rot age used for testing adult preference, but later growth was greater on O. tomentosa and O. streptacantha, the cacti that best supported larvae. Differential larval performance on O. stricta may contribute to the rare presence of D. aldrichi in the southern part of the cactus distribution, while the superior quality of O. tomentosa and O. streptacantha (larger rot size and higher microbial concentration) may reduce competition and facilitate cocxistence of the fly species in the north.}, }
@article {pmid28312211, year = {1988}, author = {Holzmann, H- and Haselwandter, K}, title = {Contribution of nitrogen fixation to nitrogen nutrition in an alpine sedge community (Caricetum curvulae).}, journal = {Oecologia}, volume = {76}, number = {2}, pages = {298-302}, pmid = {28312211}, issn = {1432-1939}, abstract = {In situ acetylene reduction assays (ARA) were carried out over two growing seasons at 2550 m in the upper alpine zone of the Tyrolean Central Alps of Austria. For comparative purposes, some Fabaceae species introduced into the upper alpine zone from lower elevation (2000 m) were subjected to ARA. At the end of the growing season the potted plants were transferred to the laboratory where their acetylene reducing activities were measured again. In situ nitrogenase activity is very low. The highest values were found in association with Leucanthemopsis alpina and Veronica bellidioides (150 and 217 nmol ethylene 24 h[-1] per pot respectively). Higher levels of activity were detected in pots transferred to the laboratory (maximum value 750 nmol ethylene 24 h[-1] per pot; assay temperature about 12°C higher than in the field) and in the Fabaceae transferred to the upper alpine zone (14×10[3] nmol ethylene 24 h[-1] per pot of Trifolium badium and T. pallescens). Maximum nitrogen input in the field is in the range of 8 mg m[-2] a[-1]. Therefore, under natural circumstances biological nitrogen fixation contributes only very small amounts of nitrogen to this alpine vegetation system, the process being inhibited by low soil temperatures. Possible alternative sources and patterns of N acquisition are discussed in relation to the overall nitrogen economics of plants of the upper alpine zone.}, }
@article {pmid28312988, year = {1987}, author = {Kinkel, LL and Andrews, JH and Berbee, FM and Nordheim, EV}, title = {Leaves as islands for microbes.}, journal = {Oecologia}, volume = {71}, number = {3}, pages = {405-408}, pmid = {28312988}, issn = {1432-1939}, abstract = {The equilibrium theory of island biogeography provided a framework for describing the colonization of apple leaf 'islands' by filamentous fungi. Surface sterilization of living leaves in situ by hydrogen peroxide allowed the colonization process to be followed from its inception. Numbers of species of filamentous fungi per leaf fluctuated from 6 to 21 during the first 2 weeks of colonization and equilibrated at about 12 by the third week. Turnover occurred in species composition at equilibrium. The equilibrium number of species was not related to leaf area.The presence of an equilibrium condition with turnover on the leaf surfaces is consistent with two key tenets of the theory of island biogeography. However, the apparent back of a species-area relationship is inconsistent with the island model.}, }
@article {pmid27931297, year = {2016}, author = {Brightling, CE}, title = {Chronic obstructive pulmonary disease phenotypes, biomarkers, and prognostic indicators.}, journal = {Allergy and asthma proceedings}, volume = {37}, number = {6}, pages = {432-438}, doi = {10.2500/aap.2016.37.3996}, pmid = {27931297}, issn = {1539-6304}, mesh = {Airway Remodeling ; *Biomarkers ; Emphysema/complications/pathology ; Humans ; Infections/complications/microbiology/pathology/virology ; Inflammation/complications/pathology ; *Phenotype ; Prognosis ; Pulmonary Disease, Chronic Obstructive/*diagnosis/etiology ; }, abstract = {Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease associated with significant morbidity and mortality. Current diagnostic criteria are based on lung function impairment, symptoms, and exacerbation frequency but do not capture the heterogeneity of the disease in terms of the complex pathologic changes that occur within lung, the different airway inflammatory patterns, or the airway microbial ecology. Recognition of the importance of defining the heterogeneity of COPD has led to the identification of important phenotypes with specific biomarkers, treatment responses, and underlying pathophysiologic mechanisms. This review summarized the presentation at the Eastern Allergy Conference 2016, which considered how multidimensional phenotyping provides important clinical insights that enable the clinician to move toward a precision medicine approach for COPD.}, }
@article {pmid27928597, year = {2017}, author = {Santos, SS and Hendriksen, NB and Jakobsen, HH and Winding, A}, title = {Effects of Bacillus cereus Endospores on Free-Living Protist Growth.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {699-709}, pmid = {27928597}, issn = {1432-184X}, mesh = {Animals ; Bacillus cereus/*growth &amp; development ; Colony Count, Microbial ; Eukaryota/*metabolism ; Predatory Behavior ; Spores, Bacterial/*growth &amp; development ; }, abstract = {We studied the predator-prey interactions between heterotrophic protists and endospores of Bacillus cereus group bacteria, in order to gain insight on survival and dispersal of B. cereus endospores in the environment. It has been hypothesised that the spore stage protects against digestion by predating protists. Therefore, experiments were carried out to investigate the impact of B. cereus endospores and vegetative cells, as the only food source, on individual amoeboid, flagellated and ciliated protists. The presence of fluorescent-labelled intracellular bacteria confirmed that B. cereus endospores as well as vegetative cells were ingested by protists and appeared intact in the food vacuoles when observed by epifluorescence microscopy. Furthermore, protist growth and bacterial predation were followed by qPCR. Protists were able to grow on vegetative cells as well as endospores of B. cereus, despite the lower cell division rates observed for some protists when feeding on bacterial endospores. Survival and proliferation of ingested bacteria inside protists cells was also observed. Finally, B. cereus spore germination and growth was observed within all protists with higher abundance in the amoeboid protist after antibiotic treatment of the protist surface. These observations support that protists can act as a potential breeding ground for B. cereus endospores.}, }
@article {pmid27924593, year = {2017}, author = {Lawley, B and Tannock, GW}, title = {Analysis of 16S rRNA Gene Amplicon Sequences Using the QIIME Software Package.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1537}, number = {}, pages = {153-163}, doi = {10.1007/978-1-4939-6685-1_9}, pmid = {27924593}, issn = {1940-6029}, mesh = {Algorithms ; Biodiversity ; *Computational Biology/methods ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; RNA, Ribosomal, 16S/*genetics ; *Software ; Web Browser ; }, abstract = {The study of microbial ecology has undergone a paradigm shift in recent years, with rapid advances in molecular and bioinformatic tools allowing researchers with wide-ranging interests and backgrounds access to community profiling methods. While these advances have undoubtedly led to exciting new understanding of many systems, the array of protocols available and the idiosyncrasies of particular approaches can lead to confusion or, at worst, erroneous interpretation of results. Here, we describe a workflow from raw 16S rRNA gene amplicon sequence data, generated on an Illumina MiSeq instrument, to microbial community taxonomy profiles and basic diversity measures. The workflow can be adapted to input from major sequence platforms and uses freely available open source software that can be implemented on a range of operating systems.}, }
@article {pmid27924403, year = {2017}, author = {Gao, M and Liu, J and Qiao, Y and Zhao, M and Zhang, XH}, title = {Diversity and Abundance of the Denitrifying Microbiota in the Sediment of Eastern China Marginal Seas and the Impact of Environmental Factors.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {602-615}, pmid = {27924403}, issn = {1432-184X}, mesh = {Bacteria/genetics/*metabolism ; Biodiversity ; China ; Denitrification/*genetics ; Geologic Sediments/*microbiology ; Microbiota/*genetics ; Nitrate Reductases/*genetics ; Nitrates/metabolism ; Nitrite Reductases/*genetics ; Nitrites/metabolism ; Nitrogen Cycle/*genetics/physiology ; Oceans and Seas ; Oxidoreductases/genetics ; Phylogeny ; Soil Microbiology ; }, abstract = {Investigating the environmental influence on the community composition and abundance of denitrifiers in marine sediment ecosystem is essential for understanding of the ecosystem-level controls on the biogeochemical process of denitrification. In the present study, nirK-harboring denitrifying communities in different mud deposit zones of eastern China marginal seas (ECMS) were investigated via clone library analysis. The abundance of three functional genes affiliated with denitrification (narG, nirK, nosZ) was assessed by fluorescent quantitative PCR. The nirK-harboring microbiota were dominated by a few operational taxonomic units (OTUs), which were widely distributed in different sites with each site harboring their unique phylotypes. The mean abundance of nirK was significantly higher than that of narG and nosZ genes, and the abundance of narG was higher than that of nosZ. The inconsistent abundance profile of different functional genes along the process of denitrification might indicate that nitrite reduction occurred independently of denitrification in the mud deposit zones of ECMS, and sedimentary denitrification was accomplished by cooperation of different denitrifying species rather than a single species. Such important information would be missed when targeting only a single denitrifying functional gene. Analysis of correlation between abundance ratios and environmental factors revealed that the response of denitrifiers to environmental factors was not invariable in different mud deposit zones. Our results suggested that a comprehensive analysis of different denitrifying functional genes may gain more information about the dynamics of denitrifying microbiota in marine sediments.}, }
@article {pmid27924402, year = {2017}, author = {Liu, C and Li, XH and Chen, YX and Cheng, ZH and Duan, QH and Meng, QH and Tao, XP and Shang, B and Dong, HM}, title = {Age-Related Response of Rumen Microbiota to Mineral Salt and Effects of Their Interactions on Enteric Methane Emissions in Cattle.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {590-601}, pmid = {27924402}, issn = {1432-184X}, mesh = {Ammonia/metabolism ; Animals ; Bacteroides/isolation &amp; purification/metabolism ; Butyrates/metabolism ; Cattle ; Dietary Supplements ; Female ; Fermentation/drug effects ; Firmicutes/isolation &amp; purification/metabolism ; Methane/*metabolism ; Microbiota/*drug effects ; Minerals/*pharmacology ; Prevotella/isolation &amp; purification/metabolism ; Propionates/metabolism ; Rumen/*microbiology ; Salts/*pharmacology ; Trace Elements/*pharmacology ; }, abstract = {Mineral salt bricks are often used in cow raising as compensation for mineral losses to improve milk yield, growth, and metabolic activity. Generally, effects of minerals are partially thought to result from improvement of microbial metabolism, but their influence on the rumen microbiota has rarely been documented to date. In this study, we investigated the response of microbiota to mineral salt in heifer and adult cows and evaluated ruminal fermentation and enteric methane emissions of cows fed mineral salts. Twelve lactating Holstein cows and twelve heifers fed a total mixed ration (TMR) diet were randomly allocated into two groups, respectively: a treatment group comprising half of the adults and heifers that were fed mineral salt and a control group containing the other half fed a diet with no mineral salt supplement. Enteric methane emissions were reduced by 9.6% (P < 0.05) in adults ingesting a mineral salt diet, while concentrations of ruminal ammonia, butyrate, and propionate were increased to a significant extent (P < 0.05). Enteric methane emissions were also reduced in heifers ingesting a mineral salt diet, but not to a significant extent (P > 0.05). Moreover, the concentrations of ammonia and volatile fatty acids (VFAs) were not significantly altered in heifers (P > 0.05). Based on these results, we performed high-throughput sequencing to explore the bacterial and archaeal communities of the rumen samples. Succiniclasticum and Prevotella, two propionate-producing bacteria, were predominant in samples of both adults and heifers. At the phylotype level, mineral salt intake led to a significant shift from Succiniclasticum to Prevotella and Prevotellaceae populations in adults. In contrast, reduced abundance of Succiniclasticum and Prevotella phylotypes was observed, with no marked shift in propionate-producing bacteria in heifers. Methanogenic archaea were not significantly abundant between groups, either in adult cows or heifers. The shift of Succiniclasticum to Prevotella and Prevotellaceae in adults suggests a response of microbiota to mineral salt that contributes to higher propionate production, which competes for hydrogen utilized by methanogens. Our data collectively indicate that a mineral salt diet can alter interactions of bacterial taxa that result in enteric methane reduction, and this effect is also influenced in an age-dependent manner.}, }
@article {pmid27924401, year = {2017}, author = {Suleiman, M and Brandt, FB and Brenzinger, K and Martinson, GO and Braker, G}, title = {Potential N2O Emissions from the Tanks of Bromeliads Suggest an Additional Source of N2O in the Neotropics.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {751-754}, pmid = {27924401}, issn = {1432-184X}, mesh = {Bromeliaceae/genetics/*metabolism ; Denitrification/genetics ; Environment ; Forests ; Nitrites/metabolism ; Nitrogen/metabolism ; Nitrous Oxide/*metabolism ; }, abstract = {We studied the propensity of the tank bromeliad Werauhia gladioliflora to emit the greenhouse gas nitrous oxide (N2O) at current and at increased N deposition levels in the range of predicted future scenarios. Potential production rates and net accumulation of N2O from tank substrate corresponded to N availability. N2O was produced in excess at all N levels due to a low level of N2O reductase activity which agreed well with a low abundance of N2O reducers compared to nitrite reducers. Transcriptional activation, however, indicated that expression of denitrification genes may be enhanced with increasing N supply eventually leading to more efficient N2O turnover with potential for adaptation of denitrifier communities to higher N levels. Our findings indicate that tank bromeliads may constitute a novel source of N2O in Neotropical forest canopies but further studies are required to understand the size and significance of in situ N2O fluxes from tank bromeliads to the environment.}, }
@article {pmid27924400, year = {2017}, author = {Qadri, M and Nalli, Y and Jain, SK and Chaubey, A and Ali, A and Strobel, GA and Vishwakarma, RA and Riyaz-Ul-Hassan, S}, title = {An Insight into the Secondary Metabolism of Muscodor yucatanensis: Small-Molecule Epigenetic Modifiers Induce Expression of Secondary Metabolism-Related Genes and Production of New Metabolites in the Endophyte.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {954-965}, pmid = {27924400}, issn = {1432-184X}, mesh = {Amino Acid Sequence ; Azacitidine/metabolism ; Brefeldin A/metabolism ; DNA, Fungal ; Endophytes/*enzymology/*genetics/metabolism ; *Epigenomics ; Ergosterol/metabolism ; Gene Expression Regulation, Fungal/*genetics ; Genes, Fungal ; Hydroxamic Acids/metabolism ; Peptide Synthases/chemistry/genetics ; Phenotype ; Phylogeny ; Polyketide Synthases/chemistry/genetics ; Polymerase Chain Reaction/methods ; Protein Conformation ; Secondary Metabolism/*genetics ; Sequence Alignment ; Volatile Organic Compounds/analysis/chemistry/metabolism ; Vorinostat ; Xylariales/classification/*enzymology/*genetics/metabolism ; }, abstract = {Muscodor spp. are proficient producers of bioactive volatile organic compounds (VOCs) with many potential applications. However, all members of this genus produce varying amounts and types of VOCs which suggests the involvement of epigenetics as a possible explanation. The members of this genus are poorly explored for the production of soluble compounds (extrolites). In this study, the polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes from an endophyte, Muscodor yucatanensis Ni30, were cloned and sequenced. The PKS genes belonged to reduced, partially reduced, non-reduced, and highly reduced subtypes. Strains over-expressing PKS genes were developed through the use of small-molecule epigenetic modifiers (suberoylanilide hydroxamic acid (SAHA) and 5-azacytidine). The putative epigenetic variants of this organism differed considerably from the wild type in morphological features and cultural characteristics as well as metabolites that were produced. Each variant produced a different set of VOCs distinct from the wild type, and several VOCs including methyl 3-(3,5-di-tert-butyl-4-hydroxyphenyl)hexane-2,4-diol and 2-carboxymethyl-3-n-hexylmaleic appeared in the variant strains, the production of which could be attributed to the activity of otherwise silent PKS genes. The bioactive extrolite brefeldin A was isolated and characterized from the wild type. However, this metabolite was not detected in EV-1, but instead, two other products were isolated and characterized as ergosterol and xylaguaianol C. Hence, M. yucatanensis has the genetic potential to produce several previously undetectable VOCs and organic solvent soluble products. It is also the case that small-molecule epigenetic modifiers can be used to produce stable variant strains of fungi with the potential to produce new molecules. Finally, this work hints to the prospect that the epigenetics of an endophytic microorganism can be influenced by any number of environmental and chemical factors associated with its host plant which may help to explain the enormous chemical diversity of secondary metabolic products found in Muscodor spp.}, }
@article {pmid27923608, year = {2017}, author = {Gildemyn, S and Verbeeck, K and Jansen, R and Rabaey, K}, title = {The type of ion selective membrane determines stability and production levels of microbial electrosynthesis.}, journal = {Bioresource technology}, volume = {224}, number = {}, pages = {358-364}, doi = {10.1016/j.biortech.2016.11.088}, pmid = {27923608}, issn = {1873-2976}, mesh = {Acetates/metabolism ; Bacteria/*metabolism ; Bicarbonates/analysis ; Bioelectric Energy Sources/*microbiology ; Bioreactors ; Electric Conductivity ; *Electricity ; Electrodes ; Hydrogen-Ion Concentration ; Ions ; *Membranes, Artificial ; Oxidation-Reduction ; }, abstract = {Microbial electrosynthesis (MES) can enable electricity-driven bioproduction from CO2. Several membrane types such as anion exchange, cation exchange, and bipolar membranes (AEM/CEM/BPM) can be used to separate the anodic oxidation from the biocathodic reduction. The impact of the membrane type on MES has not yet been studied. Therefore we compared the three membranes for MES of acetic acid. The reactor with AEM enabled in situ recovery of acetic acid. This extraction led to a 32% higher production rate and efficiency compared to the systems that did not include product recovery, as product inhibition was likely occurring. Besides H[+]/OH[-], mainly HCO3[-] contributed to charge balancing. Due to water displacement across the membrane, the product concentration in the AEM reactor (9g/L) did not exceed the concentration in the CEM reactor (10.5g/L). Overall this comparison shows that the membrane type in MES can be critical towards a stable and efficient process.}, }
@article {pmid27919649, year = {2017}, author = {Marí-Almirall, M and Cosgaya, C and Higgins, PG and Van Assche, A and Telli, M and Huys, G and Lievens, B and Seifert, H and Dijkshoorn, L and Roca, I and Vila, J}, title = {MALDI-TOF/MS identification of species from the Acinetobacter baumannii (Ab) group revisited: inclusion of the novel A. seifertii and A. dijkshoorniae species.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {23}, number = {3}, pages = {210.e1-210.e9}, doi = {10.1016/j.cmi.2016.11.020}, pmid = {27919649}, issn = {1469-0691}, mesh = {Acinetobacter/chemistry/*classification/genetics/*isolation &amp; purification ; Acinetobacter Infections/*diagnosis ; Bacteriological Techniques/*methods ; Cluster Analysis ; DNA-Directed RNA Polymerases/genetics ; Humans ; Multilocus Sequence Typing ; Predictive Value of Tests ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; }, abstract = {OBJECTIVES: Rapid identification of Acinetobacter species is critical as members of the A. baumannii (Ab) group differ in antibiotic susceptibility and clinical outcomes. A. baumannii, A. pittii, and A. nosocomialis can be identified by MALDI-TOF/MS, while the novel species A. seifertii and A. dijkshoorniae cannot. Low identification rates for A. nosocomialis also have been reported. We evaluated the use of MALDI-TOF/MS to identify isolates of A. seifertii and A. dijkshoorniae and revisited the identification of A. nosocomialis to update the Bruker taxonomy database.<br><br>METHODS: Species characterization was performed by rpoB-clustering and MLSA. MALDI-TOF/MS spectra were recovered from formic acid/acetonitrile bacterial extracts overlaid with &#x3b1;-cyano-4-hydroxy-cinnamic acid matrix on a MicroflexLT in linear positive mode and 2000-20 000 m/z range mass. Spectra were examined with the ClinProTools v2.2 software. Mean spectra (MSP) were created with the BioTyper software.<br><br>RESULTS: Seventy-eight Acinetobacter isolates representative of the Ab group were used to calculate the average spectra/species and generate pattern recognition models. Species-specific peaks were identified for all species, and MSPs derived from three A.&#xa0;seifertii, two A.&#xa0;dijkshoorniae, and two A.&#xa0;nosocomialis strains were added to the Bruker taxonomy database, allowing successful identification of all isolates using spectra from either bacterial extracts or direct colonies, resulting in a positive predictive value (PPV) of 99.6% (777/780) and 96.8% (302/312), respectively.<br><br>CONCLUSIONS: The use of post-processing data software identified statistically significant species-specific peaks to generate reference signatures for rapid accurate identification of species within the Ab group, providing relevant information for the clinical management of Acinetobacter infections.}, }
@article {pmid27917180, year = {2016}, author = {Cheng, X and Cordovez, V and Etalo, DW and van der Voort, M and Raaijmakers, JM}, title = {Role of the GacS Sensor Kinase in the Regulation of Volatile Production by Plant Growth-Promoting Pseudomonas fluorescens SBW25.}, journal = {Frontiers in plant science}, volume = {7}, number = {}, pages = {1706}, pmid = {27917180}, issn = {1664-462X}, abstract = {In plant-associated Pseudomonas species, the production of several secondary metabolites and exoenzymes is regulated by the GacS/GacA two-component regulatory system (the Gac-system). Here, we investigated if a mutation in the GacS sensor kinase affects the production of volatile organic compounds (VOCs) in P. fluorescens SBW25 (Pf.SBW25) and how this impacts on VOCs-mediated growth promotion and induced systemic resistance of Arabidopsis and tobacco. A total of 205 VOCs were detected by Gas Chromatography Mass Spectrometry for Pf. SBW25 and the gacS-mutant grown on two different media for 3 and 6 days. Discriminant function analysis followed by hierarchical clustering revealed 24 VOCs that were significantly different in their abundance between Pf.SBW25 and the gacS-mutant, which included three acyclic alkenes (3-nonene, 4-undecyne, 1-undecene). These alkenes were significantly reduced by the gacS mutation independently of the growth media and of the incubation time. For Arabidopsis, both Pf.SBW25 and the gacS-mutant enhanced, via VOCs, root and shoot biomass, induced systemic resistance against leaf infections by P. syringae and rhizosphere acidification to the same extent. For tobacco, however, VOCs-mediated effects on shoot and root growth were significantly different between Pf.SBW25 and the gacS-mutant. While Pf.SBW25 inhibited tobacco root growth, the gacS-mutant enhanced root biomass and lateral root formation relative to the non-treated control plants. Collectively these results indicate that the sensor kinase GacS is involved in the regulation of VOCs production in Pf.SBW25, affecting plant growth in a plant species-dependent manner.}, }
@article {pmid27917167, year = {2016}, author = {Balk, M and Keuskamp, JA and Laanbroek, HJ}, title = {Potential for Sulfate Reduction in Mangrove Forest Soils: Comparison between Two Dominant Species of the Americas.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1855}, pmid = {27917167}, issn = {1664-302X}, abstract = {Avicennia and Rhizophora are globally occurring mangrove genera with different traits that place them in different parts of the intertidal zone. It is generally accepted that the oxidizing capacity of Avicennia roots is larger than that of Rhizophora roots, which initiates more reduced conditions in the soil below the latter genus. We hypothesize that the more reduced conditions beneath Rhizophora stands lead to more active sulfate-reducing microbial communities compared to Avicennia stands. To test this hypothesis, we measured sulfate reduction traits in soil samples collected from neighboring Avicennia germinans and Rhizophora mangle stands at three different locations in southern Florida. The traits measured were sulfate reduction rates (SRR) in flow-through reactors containing undisturbed soil layers in the absence and presence of easily degradable carbon compounds, copy numbers of the dsrB gene, which is specific for sulfate-reducing microorganisms, and numbers of sulfate-reducing cells that are able to grow in liquid medium on a mixture of acetate, propionate and lactate as electron donors. At the tidal locations Port of the Islands and South Hutchinson Islands, steady state SRR, dsrB gene copy numbers and numbers of culturable cells were higher at the A. germinans than at the R. mangle stands, although not significantly for the numbers at Port of the Islands. At the non-tidal location North Hutchinson Island, results are mixed with respect to these sulfate reduction traits. At all locations, the fraction of culturable cells were significantly higher at the R. mangle than at the A. germinans stands. The dynamics of the initial SRR implied a more in situ active sulfate-reducing community at the intertidal R. mangle stands. It was concluded that in agreement with our hypothesis R. mangle stands accommodate a more active sulfate-reducing community than A. germinans stands, but only at the tidal locations. The differences between R. mangle and A. germinans stands were absent at the non-tidal, impounded location.}, }
@article {pmid27911440, year = {2017}, author = {Schulz-Bohm, K and Geisen, S and Wubs, ER and Song, C and de Boer, W and Garbeva, P}, title = {The prey's scent - Volatile organic compound mediated interactions between soil bacteria and their protist predators.}, journal = {The ISME journal}, volume = {11}, number = {3}, pages = {817-820}, pmid = {27911440}, issn = {1751-7370}, mesh = {Bacteria/*metabolism ; Eukaryota/*physiology ; Soil Microbiology ; Volatile Organic Compounds/*metabolism ; }, abstract = {Protists are major predators of bacteria in soils. However, it remains unknown how protists sense their prey in this highly complex environment. Here, we investigated whether volatile organic compounds (VOCs) of six phylogenetic distinct soil bacteria affect the performance of three different soil protists and how that relates to direct feeding interactions. We observed that most bacteria affected protist activity by VOCs. However, the response of protists to the VOCs was strongly dependent on both the bacterial and protist interacting partner. Stimulation of protist activity by volatiles and in direct trophic interaction assays often coincided, suggesting that VOCs serve as signals for protists to sense suitable prey. Furthermore, bacterial terpene synthase mutants lost the ability to affect protists, indicating that terpenes represent key components of VOC-mediated communication. Overall, we demonstrate that volatiles are directly involved in protist-bacterial predator-prey interactions.}, }
@article {pmid27910828, year = {2016}, author = {Howlin, RP and Winnard, C and Frapwell, CJ and Webb, JS and Cooper, JJ and Aiken, SS and Stoodley, P}, title = {Biofilm prevention of gram-negative bacterial pathogens involved in periprosthetic infection by antibiotic-loaded calcium sulfate beads in vitro.}, journal = {Biomedical materials (Bristol, England)}, volume = {12}, number = {1}, pages = {015002}, doi = {10.1088/1748-605X/12/1/015002}, pmid = {27910828}, issn = {1748-605X}, mesh = {Acinetobacter baumannii ; Anti-Bacterial Agents/*pharmacology ; *Biofilms ; Calcium Sulfate/*chemistry ; Gram-Negative Bacteria/*drug effects ; Humans ; Klebsiella pneumoniae ; Microbial Sensitivity Tests ; Microscopy, Confocal ; Prosthesis-Related Infections/drug therapy/*prevention &amp; control ; Pseudomonas aeruginosa ; Tobramycin/pharmacology ; Vancomycin/pharmacology ; }, abstract = {Biofilm formation represents a key stage in the pathogenesis of prosthetic infections (PIs). More tolerant to antibiotics than their planktonic counterparts, biofilm bacteria are difficult to eradicate using conventional therapeutic regimes. A common approach in PI management is the adjunctive use of localised antibiotics in addition to systemic administration in an attempt to protect the implant from colonisation by infiltrating bacteria. This study evaluates the antibacterial and antibiofilm efficacy of antibiotic-loaded dissolvable calcium sulphate, previously shown to be effective against key gram-positive pathogens, against gram-negative species important in the establishment of chronic infection in PIs. Synthetic calcium sulfate beads loaded with tobramycin, vancomycin and both antibiotics in combination were assessed for their ability to eradicate planktonic Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae strains. The efficacy of the beads in preventing biofilm formation and eliminating established biofilms over multiple days was evaluated using confocal laser scanning microscopy (CSLM) imaging combined with image analysis and viable cell counts. Beads loaded with antibiotics demonstrated effective eluting concentrations for up to 37 d depending on the bacterial strain. In the presence of repeated bacterial challenges, antibiotic-loaded beads prevented bacterial colonisation and significantly reduce biofilm formation for the duration of the assay (7 d). Complete eradication of established biofilms was more difficult with evidence of biofilm regrowth after 1 week of contact with antibiotic-loaded beads, despite data suggesting a complete kill was achieved at earlier timepoints of 24 h and 72 h in the case of K. pneumoniae and P. aeruginosa. This study provides further evidence that calcium sulfate beads loaded with vancomycin and tobramycin may be a useful adjunctive component to the successful management of PIs.}, }
@article {pmid27909750, year = {2017}, author = {Serafin, CF and Paris, AP and Paula, CR and Simão, RC and Gandra, RF}, title = {Repression of Proteases and Hsp90 Chaperone Expression Induced by an Antiretroviral in Virulent Environmental Strains of Cryptococcus neoformans.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {583-589}, pmid = {27909750}, issn = {1432-184X}, mesh = {Animals ; Anti-Retroviral Agents/*pharmacology ; Columbidae/microbiology ; Cryptococcus neoformans/*metabolism ; Electrophoresis, Polyacrylamide Gel ; HSP90 Heat-Shock Proteins/*biosynthesis ; Peptide Hydrolases/*biosynthesis ; Protease Inhibitors/*metabolism ; Ritonavir/*pharmacology ; }, abstract = {This study evaluated the effect of the antiretroviral ritonavir on protease secretion in different strains of Cryptococcus neoformans isolated from the environment and investigated the expression of heat shock protein (Hsp90), classically described virulence factors in other yeast in the presence of the same antiretroviral. The presence of the enzyme was detected by the formation of a degradation of the halo around the colonies. The results were classified as follows: level 1 (without proteases), level 2 (positive for proteases), and level 3 (strongly positive for proteases). Total protein extract isolated from the cell walls of the 12 strains incubated in the absence and presence of ritonavir (0.3125 mg mL[-1]) were resolved by SDS-PAGE and analyzed by Western blot assays using an antiserum against Hsp90 from Blastocladiella emersonii. All strains tested showed inhibition of proteinase activity in the presence of ritonavir at 0.3125 to 1.25 mg mL[-1]. High levels of Hsp90 were observed in the absence of ritonavir (0.3125 mg mL[-1]), except for the non-virulent control cells. In contrast, in the presence of the antiretroviral, a drastic reduction in the expression of the chaperone was observed. The data suggest that ritonavir, in addition to containing viral replication, could inhibit the expression of virulence factors in opportunistic yeast, as proteases and Hsp90. According to our current knowledge, this is the first time that the inhibition of Hsp90 by an antiretroviral was reported for environmental isolates of C. neoformans.}, }
@article {pmid27909749, year = {2017}, author = {Wang, L and Cheung, MK and Liu, R and Wong, CK and Kwan, HS and Hwang, JS}, title = {Diversity of Total Bacterial Communities and Chemoautotrophic Populations in Sulfur-Rich Sediments of Shallow-Water Hydrothermal Vents off Kueishan Island, Taiwan.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {571-582}, pmid = {27909749}, issn = {1432-184X}, mesh = {Alphaproteobacteria/classification/genetics/*metabolism ; Chemoautotrophic Growth/*physiology ; Epsilonproteobacteria/classification/isolation &amp; purification/*metabolism ; Geologic Sediments/chemistry/*microbiology ; Hydrothermal Vents/*microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sulfur/chemistry ; Taiwan ; }, abstract = {Shallow-water hydrothermal vents (HTVs) are an ecologically important habitat with a geographic origin similar to that of deep-sea HTVs. Studies on shallow-water HTVs have not only facilitated understanding of the influences of vents on local ecosystems but also helped to extend the knowledge on deep-sea vents. In this study, the diversity of bacterial communities in the sediments of shallow-water HTVs off Kueishan Island, Taiwan, was investigated by examining the 16S ribosomal RNA gene as well as key functional genes involved in chemoautotrophic carbon fixation (aclB, cbbL and cbbM). In the vent area, Sulfurovum and Sulfurimonas of Epsilonproteobacteria appeared to dominate the benthic bacterial community. Results of aclB gene analysis also suggested involvement of these bacteria in carbon fixation using the reductive tricarboxylic acid (rTCA) cycle. Analysis of the cbbM gene showed that Alphaproteobacterial members such as the purple non-sulfur bacteria were the major chemoautotrophic bacteria involving in carbon fixation via the Calvin-Benson-Bassham (CBB) cycle. However, they only accounted for <2% of the total bacterial community in the vent area. These findings suggest that the rTCA cycle is the major chemoautotrophic carbon fixation pathway in sediments of the shallow-water HTVs off Kueishan Island.}, }
@article {pmid27909426, year = {2016}, author = {Avena, CV and Parfrey, LW and Leff, JW and Archer, HM and Frick, WF and Langwig, KE and Kilpatrick, AM and Powers, KE and Foster, JT and McKenzie, VJ}, title = {Deconstructing the Bat Skin Microbiome: Influences of the Host and the Environment.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1753}, pmid = {27909426}, issn = {1664-302X}, abstract = {Bats are geographically widespread and play an important role in many ecosystems, but relatively little is known about the ecology of their associated microbial communities and the role microbial taxa play in bat health, development, and evolution. Moreover, few vertebrate animal skin microbiomes have been comprehensively assessed, and thus characterizing the bat skin microbiome will yield valuable insight into the variability of vertebrate skin microbiomes as a whole. The recent emergence of the skin fungal disease white-nose syndrome highlights the potentially important role bat skin microbial communities could play in bat health. Understanding the determinant of bat skin microbial communities could provide insight into important factors allowing individuals to persist with disease. We collected skin swabs from a total of 11 bat species from the eastern United States (n = 45) and Colorado (n = 119), as well as environmental samples (n = 38) from a subset of sites, and used 16S rRNA marker gene sequencing to observe bacterial communities. In addition, we conducted a literature survey to compare the skin microbiome across vertebrate groups, including the bats presented in this study. Host species, region, and site were all significant predictors of the variability across bat skin bacterial communities. Many bacterial taxa were found both on bats and in the environment. However, some bacterial taxa had consistently greater relative abundances on bat skin relative to their environments. Bats shared many of their abundant taxa with other vertebrates, but also hosted unique bacterial lineages such as the class Thermoleophilia (Actinobacteria). A strong effect of site on the bat skin microbiome indicates that the environment very strongly influences what bacteria are present on bat skin. Bat skin microbiomes are largely composed of site-specific microbiota, but there do appear to be important host-specific taxa. How this translates to differences in host-microbial interactions and bat health remains an important knowledge gap, but this work suggests that habitat variability is very important. We identify some bacterial groups that are more consistent on bats despite site differences, and these may be important ones to study in terms of their function as potential core microbiome members.}, }
@article {pmid27904921, year = {2017}, author = {Brígido, C and Glick, BR and Oliveira, S}, title = {Survey of Plant Growth-Promoting Mechanisms in Native Portuguese Chickpea Mesorhizobium Isolates.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {900-915}, pmid = {27904921}, issn = {1432-184X}, mesh = {Acid Phosphatase/metabolism ; Biodegradation, Environmental ; Biodiversity ; Cicer/*growth &amp; development/*microbiology ; Cytokinins/biosynthesis ; DNA, Bacterial/genetics ; Geography ; Indoleacetic Acids/metabolism ; Mesorhizobium/*classification/genetics/*isolation &amp; purification/metabolism ; Metals, Heavy/metabolism ; Nitrogen Fixation ; Phosphates/chemistry ; Phylogeny ; *Plant Development ; Portugal ; RNA, Ribosomal, 16S/genetics ; Rhizobium ; Sequence Analysis, DNA ; Siderophores/biosynthesis ; *Soil Microbiology ; Symbiosis ; Tryptophan/metabolism ; }, abstract = {Rhizobia may possess other plant growth-promoting mechanisms besides nitrogen fixation. These mechanisms and the tolerance to different environmental factors, such as metals, may contribute to the use of rhizobia inocula to establish a successful legume-rhizobia symbiosis. Our goal was to characterize a collection of native Portuguese chickpea Mesorhizobium isolates in terms of plant growth-promoting (PGP) traits and tolerance to different metals as well as to investigate whether these characteristics are related to the biogeography of the isolates. The occurrence of six PGP mechanisms and tolerance to five metals were evaluated in 61 chickpea Mesorhizobium isolates previously obtained from distinct provinces in Portugal and assigned to different species clusters. Chickpea microsymbionts show high diversity in terms of PGP traits as well as in their ability to tolerate different metals. All isolates synthesized indoleacetic acid, 50 isolates produced siderophores, 19 isolates solubilized phosphate, 12 isolates displayed acid phosphatase activity, and 22 exhibited cytokinin activity. Most isolates tolerated Zn or Pb but not Ni, Co, or Cu. Several associations between specific PGP mechanisms and the province of origin and species clusters of the isolates were found. Our data suggests that the isolate's tolerance to metals and ability to solubilize inorganic phosphate and to produce IAA may be responsible for the persistence and distribution of the native Portuguese chickpea Mesorhizobium species. Furthermore, this study revealed several chickpea microsymbionts with potential as PGP rhizobacteria as well as for utilization in phytoremediation strategies.}, }
@article {pmid27904880, year = {2016}, author = {Bik, HM and Maritz, JM and Luong, A and Shin, H and Dominguez-Bello, MG and Carlton, JM}, title = {Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City.}, journal = {mSphere}, volume = {1}, number = {6}, pages = {}, pmid = {27904880}, issn = {2379-5042}, abstract = {In densely populated urban environments, the distribution of microbes and the drivers of microbial community assemblages are not well understood. In sprawling metropolitan habitats, the "urban microbiome" may represent a mix of human-associated and environmental taxa. Here we carried out a baseline study of automated teller machine (ATM) keypads in New York City (NYC). Our goal was to describe the biodiversity and biogeography of both prokaryotic and eukaryotic microbes in an urban setting while assessing the potential source of microbial assemblages on ATM keypads. Microbial swab samples were collected from three boroughs (Manhattan, Queens, and Brooklyn) during June and July 2014, followed by generation of Illumina MiSeq datasets for bacterial (16S rRNA) and eukaryotic (18S rRNA) marker genes. Downstream analysis was carried out in the QIIME pipeline, in conjunction with neighborhood metadata (ethnicity, population, age groups) from the NYC Open Data portal. Neither the 16S nor 18S rRNA datasets showed any clustering patterns related to geography or neighborhood demographics. Bacterial assemblages on ATM keypads were dominated by taxonomic groups known to be associated with human skin communities (Actinobacteria, Bacteroides, Firmicutes, and Proteobacteria), although SourceTracker analysis was unable to identify the source habitat for the majority of taxa. Eukaryotic assemblages were dominated by fungal taxa as well as by a low-diversity protist community containing both free-living and potentially pathogenic taxa (Toxoplasma, Trichomonas). Our results suggest that ATM keypads amalgamate microbial assemblages from different sources, including the human microbiome, eukaryotic food species, and potentially novel extremophilic taxa adapted to air or surfaces in the built environment. DNA obtained from ATM keypads may thus provide a record of both human behavior and environmental sources of microbes. IMPORTANCE Automated teller machine (ATM) keypads represent a specific and unexplored microhabitat for microbial communities. Although the number of built environment and urban microbial ecology studies has expanded greatly in recent years, the majority of research to date has focused on mass transit systems, city soils, and plumbing and ventilation systems in buildings. ATM surfaces, potentially retaining microbial signatures of human inhabitants, including both commensal taxa and pathogens, are interesting from both a biodiversity perspective and a public health perspective. By focusing on ATM keypads in different geographic areas of New York City with distinct population demographics, we aimed to characterize the diversity and distribution of both prokaryotic and eukaryotic microbes, thus making a unique contribution to the growing body of work focused on the "urban microbiome." In New York City, the surface area of urban surfaces in Manhattan far exceeds the geographic area of the island itself. We have only just begun to describe the vast array of microbial taxa that are likely to be present across diverse types of urban habitats.}, }
@article {pmid27904402, year = {2016}, author = {Frece, J and Vrdoljak, M and Filipčić, M and Jelić, M and Čanak, I and Jakopović, &#x17d; and Pleadin, J and Gobin, I and Dragičević, TL and Markov, K}, title = {Microbiological Quality and Variability of Natural Microbiota in Croatian Cheese Maturing in Lambskin Sacks.}, journal = {Food technology and biotechnology}, volume = {54}, number = {2}, pages = {129-134}, pmid = {27904402}, issn = {1330-9862}, abstract = {As in the traditional production of cheese in lambskin sacks raw cow's or sheep's milk is mostly used, the purpose of this study is to see how the production affects the microbiological quality of the cheese. To do that, we tested 39 samples of raw cow's and sheep's milk, curd, ripened cheese (15, 30 and 45 days) and lambskin sacks for native microbial population. Two-thirds of the milk, curd and cheese samples had higher counts of staphylococci and enterobacteria than permitted by regulations. Not a single sample had Salmonella and Listeria monocytogenes, but we did find Escherichia coli in sheep's milk and cheese, and yeast and mould in both types of milk and cheese. Staphylococcus xylosus prevailed in lambskin sacks. Despite the high incidence of S. aureus, even in the final product, staphylococcal enterotoxin was detected in only two sheep's cheese samples. Among the lactic acid bacteria, Lactococcus lactis and Lactobacillus paracasei prevailed in cow's cheese, whereas Leuconostoc mesenteroides and Lactobacillus plantarum prevailed in sheep's cheese. In the lambskin sacks Leuconostoc mesenteroides and Lactobacillus plantarum were predominant. Our findings give an important insight into the fermentation and microbial ecology of the cheese in lambskin sacks.}, }
@article {pmid27903594, year = {2017}, author = {Hoggard, M and Wagner Mackenzie, B and Jain, R and Taylor, MW and Biswas, K and Douglas, RG}, title = {Chronic Rhinosinusitis and the Evolving Understanding of Microbial Ecology in Chronic Inflammatory Mucosal Disease.}, journal = {Clinical microbiology reviews}, volume = {30}, number = {1}, pages = {321-348}, pmid = {27903594}, issn = {1098-6618}, mesh = {Anti-Infective Agents/therapeutic use ; Bacteria/*classification/growth &amp; development/isolation &amp; purification ; Biofilms ; Clinical Trials as Topic ; Fungi/*classification/growth &amp; development/isolation &amp; purification ; Humans ; Rhinitis/drug therapy/*microbiology/virology ; Sinusitis/drug therapy/*microbiology/virology ; Treatment Outcome ; Viruses/classification/growth &amp; development/isolation &amp; purification ; }, abstract = {Chronic rhinosinusitis (CRS) encompasses a heterogeneous group of debilitating chronic inflammatory sinonasal diseases. Despite considerable research, the etiology of CRS remains poorly understood, and debate on potential roles of microbial communities is unresolved. Modern culture-independent (molecular) techniques have vastly improved our understanding of the microbiology of the human body. Recent studies that better capture the full complexity of the microbial communities associated with CRS reintroduce the possible importance of the microbiota either as a direct driver of disease or as being potentially involved in its exacerbation. This review presents a comprehensive discussion of the current understanding of bacterial, fungal, and viral associations with CRS, with a specific focus on the transition to the new perspective offered in recent years by modern technology in microbiological research. Clinical implications of this new perspective, including the role of antimicrobials, are discussed in depth. While principally framed within the context of CRS, this discussion also provides an analogue for reframing our understanding of many similarly complex and poorly understood chronic inflammatory diseases for which roles of microbes have been suggested but specific mechanisms of disease remain unclear. Finally, further technological advancements on the horizon, and current pressing questions for CRS microbiological research, are considered.}, }
@article {pmid27902282, year = {2017}, author = {Dedysh, SN and Kulichevskaya, IS and Huber, KJ and Overmann, J}, title = {Defining the taxonomic status of described subdivision 3 Acidobacteria: proposal of Bryobacteraceae fam. nov.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {67}, number = {2}, pages = {498-501}, doi = {10.1099/ijsem.0.001687}, pmid = {27902282}, issn = {1466-5034}, mesh = {Acidobacteria/*classification ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The phylum Acidobacteria represents one of the highly diverse but poorly characterized phylogenetic groups of the domain Bacteria. The taxonomically described acidobacteria belong to 27 genera and 49 species, which represent subdivisions 1, 3, 4, 6, 8, 10 and 23 of this phylum. However, the corresponding family ranks have been defined only for some of these characterized micro-organisms. Here, we suggest the establishment of a novel family, Bryobacteraceae fam. nov., to accommodate taxonomically described members of subdivision 3 Acidobacteria. This family is characterized by Gram-stain-negative, non-spore-forming and non-motile rods, which divide by binary fission. Members of this family are mildly acidophilic, mesophilic, aerobic and facultatively anaerobic chemoheterotrophs that utilize various sugars and polysaccharides. The major fatty acids are iso-C15 : 0 and C16 : 1ω7c; the cells also contain significant amounts of 13,16-dimethyloctacosanedioic (iso-diabolic) acid. Currently, the family comprises the genera Bryobacter and Paludibaculum.}, }
@article {pmid27902263, year = {2017}, author = {Han, SI and Lee, YR and Kim, JO and Whang, KS}, title = {Terrimonas rhizosphaerae sp. nov., isolated from ginseng rhizosphere soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {67}, number = {2}, pages = {391-395}, doi = {10.1099/ijsem.0.001639}, pmid = {27902263}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Bacteroidetes/*classification/genetics/isolation &amp; purification ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Nucleic Acid Hybridization ; Panax/*microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {The novel isolate belonging to the genus Terrimonas, designated CR94T, was isolated from rhizosphere soil of a ginseng field in Geumsan, Korea. Cells of strain CR94T were strictly aerobic, Gram-stain-negative, non-motile, non-filamentous single rods. Growth was observed at 10-37 °C (optimum 28 °C) and at pH 4.0-10.0 (optimum pH 6.0). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain CR94T belonged to the genus Terrimonas, showing highest sequence similarity to Terrimonas lutea DYT (97.3 %), Terrimonas pekingensis QHT (97.1 %), Terrimonas aquatica RIB1-6T (95.6 %), Terrimonas rubra M-8T (94.7 %) and Terrimonas ferruginea ATCC 13524T (93.8 %). DNA-DNA relatedness values between strain CR94T and T. lutea KACC 13047T, T. pekingensis KACC 18795T, T. ferruginea KACC 11310T and T. aquatica LMG 24825T were 30.5, 28.9, 17.8 and 13.5 %, respectively. The DNA G+C content was 46.5 mol% and the major respiratory quinone was menaquinone-7 (MK-7). The major cellular fatty acids of strain CR94T were iso-C15:1 G and iso-C15 : 0. On the basis of the polyphasic analysis, strain CR94T represents a novel species of the genus Terrimonas, for which the name Terrimonas rhizosphaerae sp. nov. is proposed. The type strain is CR94T (=KACC 17564T=NCAIM B 025317T).}, }
@article {pmid27902258, year = {2017}, author = {Kim, JO and Lee, HJ and Han, SI and Whang, KS}, title = {Marinobacter halotolerans sp. nov., a halophilic bacterium isolated from a saltern crystallizing pond.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {67}, number = {2}, pages = {460-465}, doi = {10.1099/ijsem.0.001653}, pmid = {27902258}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Marinobacter/*classification/genetics/isolation &amp; purification ; Nucleic Acid Hybridization ; *Phylogeny ; Ponds/*microbiology ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Salinity ; Sequence Analysis, DNA ; Ubiquinone/chemistry ; }, abstract = {A Gram-stain-negative, moderately halophilic, motile bacterium, designated strain CP12T, was isolated from a crystallizing pond of a saltern of the Yellow Sea in Korea. Cells of strain CP12T were non-spore-forming rods and produced whitish-yellow colonies. Growth was observed at 10-37 °C (optimum 37 °C), at pH 6.0-9.0 (optimum pH 7.0), and in the presence of 0.5-20 % (w/v) NaCl (optimum 3 %). Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CP12T was closely related to Marinobacter flavimaris SW-145T (98.4 % 16S rRNA gene sequence similarity), Marinobacter algicola DG893T (98.2 %), Marinobacter adhaerens HP15T (98.2 %), Marinobacter salsuginis SD-14BT (97.9 %), Marinobacter salarius R9SW1T (97.6 %) and Marinobacter lipolyticus SM19T (97.1 %). DNA-DNA hybridization studies showed values lower than 18.6 % between strain CP12T and any of these species. The predominant respiratory isoprenoid quinone was ubiquinone-9 and the major cellular fatty acids of strain CP12T were C16 : 0, C12 : 0 3-OH, C12 : 0, Summed feature 3, C16 : 0 10-methyl and C18 : 1ω9c. On the basis of phenotypic properties, and phylogenetic and chemotaxonomic data, it is evident that strain CP12T represents a novel species of the genus Marinobacter, for which the name Marinobacter halotolerans sp. nov. is proposed. The type strain is CP12T (=KACC 18381T=NBRC 110910T).}, }
@article {pmid27900684, year = {2017}, author = {Jameson, E and Taubert, M and Coyotzi, S and Chen, Y and Eyice, &#xd6; and Schäfer, H and Murrell, JC and Neufeld, JD and Dumont, MG}, title = {DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1539}, number = {}, pages = {57-74}, doi = {10.1007/978-1-4939-6691-2_5}, pmid = {27900684}, issn = {1940-6029}, mesh = {*Biomarkers ; DNA/chemistry/genetics ; Gene Expression Profiling/methods ; *High-Throughput Screening Assays ; *Isotope Labeling/methods ; Metagenome ; Metagenomics/methods ; *Microbiota ; *Molecular Probes ; Proteins/chemistry ; Proteomics/methods ; RNA/chemistry/genetics ; }, abstract = {Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of [13]C, [18]O, or [15]N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labeled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labeled populations by targeted gene analysis. Such approaches usually involved fingerprint-based analyses or sequencing of clone libraries containing 16S rRNA genes or functional marker gene amplicons. Although molecular fingerprinting remains a valuable approach for rapid confirmation of isotope labeling, recent advances in sequencing technology mean that it is possible to obtain affordable and comprehensive amplicon profiles, metagenomes, or metatranscriptomes from SIP experiments. Not only can the abundance of microbial groups be inferred from metagenomes, but researchers can bin, assemble, and explore individual genomes to build hypotheses about the metabolic capabilities of labeled microorganisms. Analysis of labeled mRNA is a more recent advance that can provide independent metatranscriptome-based analysis of active microorganisms. The power of metatranscriptomics is that mRNA abundance often correlates closely with the corresponding activity of encoded enzymes, thus providing insight into microbial metabolism at the time of sampling. Together, these advances have improved the sensitivity of SIP methods and allow the use of labeled substrates at ecologically relevant concentrations. Particularly as methods improve and costs continue to drop, we expect that the integration of SIP with multiple omics-based methods will become prevalent components of microbial ecology studies, leading to further breakthroughs in our understanding of novel microbial populations and elucidation of the metabolic function of complex microbial communities. In this chapter we provide protocols for obtaining labeled DNA, RNA, and proteins that can be used for downstream omics-based analyses.}, }
@article {pmid27900461, year = {2017}, author = {Domingues, CD and da Silva, LH and Rangel, LM and de Magalhães, L and de Melo Rocha, A and Lobão, LM and Paiva, R and Roland, F and Sarmento, H}, title = {Microbial Food-Web Drivers in Tropical Reservoirs.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {505-520}, pmid = {27900461}, issn = {1432-184X}, mesh = {Animals ; Bacteria/*metabolism ; Brazil ; Ciliophora/*metabolism ; Cladocera/*metabolism ; Copepoda/*metabolism ; Ecosystem ; Eutrophication ; *Food Chain ; Fresh Water/microbiology ; Nitrogen/metabolism ; Plankton/*metabolism ; Temperature ; Water Microbiology ; }, abstract = {Element cycling in aquatic systems is driven chiefly by planktonic processes, and the structure of the planktonic food web determines the efficiency of carbon transfer through trophic levels. However, few studies have comprehensively evaluated all planktonic food-web components in tropical regions. The aim of this study was to unravel the top-down controls (metazooplankton community structure), bottom-up controls (resource availability), and hydrologic (water residence time) and physical (temperature) variables that affect different components of the microbial food web (MFW) carbon stock in tropical reservoirs, through structural equation models (SEM). We conducted a field study in four deep Brazilian reservoirs (Balbina, Tucuruí, Três Marias, and Funil) with different trophic states (oligo-, meso-, and eutrophic). We found evidence of a high contribution of the MFW (up to 50% of total planktonic carbon), especially in the less-eutrophic reservoirs (Balbina and Tucuruí). Bottom-up and top-down effects assessed through SEM indicated negative interactions between soluble reactive phosphorus and phototrophic picoplankton (PPP), dissolved inorganic nitrogen, and heterotrophic nanoflagellates (HNF). Copepods positively affected ciliates, and cladocerans positively affected heterotrophic bacteria (HB) and PPP. Higher copepod/cladoceran ratios and an indirect positive effect of copepods on HB might strengthen HB-HNF coupling. We also found low values for the degree of uncoupling (D) and a low HNF/HB ratio compared with literature data (mostly from temperate regions). This study demonstrates the importance of evaluating the whole size spectrum (including microbial compartments) of the different planktonic compartments, in order to capture the complex carbon dynamics of tropical aquatic ecosystems.}, }
@article {pmid27900439, year = {2017}, author = {González, O and Ortíz-Castro, R and Díaz-Pérez, C and Díaz-Pérez, AL and Magaña-Dueñas, V and López-Bucio, J and Campos-García, J}, title = {Non-ribosomal Peptide Synthases from Pseudomonas aeruginosa Play a Role in Cyclodipeptide Biosynthesis, Quorum-Sensing Regulation, and Root Development in a Plant Host.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {616-629}, pmid = {27900439}, issn = {1432-184X}, mesh = {Arabidopsis/*microbiology ; Dipeptides/genetics/*metabolism ; Gene Expression Regulation, Bacterial/*genetics ; Indoleacetic Acids/metabolism ; Indoles/metabolism ; Peptide Biosynthesis, Nucleic Acid-Independent/*genetics ; Peptides, Cyclic/genetics/*metabolism ; Piperazines/*metabolism ; Plant Roots/*embryology ; Pseudomonas aeruginosa/enzymology/genetics/*metabolism ; Pyocyanine/metabolism ; Quorum Sensing/genetics/*physiology ; Signal Transduction ; Virulence Factors/metabolism ; }, abstract = {Diverse molecules mediate cross-kingdom communication between bacteria and their eukaryotic partners and determine pathogenic or symbiotic relationships. N-acyl-L-homoserine lactone-dependent quorum-sensing signaling represses the biosynthesis of bacterial cyclodipeptides (CDPs) that act as auxin signal mimics in the host plant Arabidopsis thaliana. In this work, we performed bioinformatics, biochemical, and plant growth analyses to identify non-ribosomal peptide synthase (NRPS) proteins of Pseudomonas aeruginosa, which are involved in CDP synthesis. A reverse genetics strategy allowed the identification of the genes encoding putative multi-modular-NRPS (MM-NRPS). Mutations in these genes affected the synthesis of the CDPs cyclo(L-Pro-L-Val), cyclo(L-Pro-L-Leu), and cyclo(L-Pro-L-Tyr), while showing wild-type-like levels of virulence factors, such as violacein, elastase, and pyocyanin. When analyzing the bioactivity of purified, naturally produced CDPs, it was found that cyclo(L-Pro-L-Tyr) and cyclo(L-Pro-L-Val) were capable of antagonizing quorum-sensing-LasR (QS-LasR)-dependent signaling in a contrasting manner in the cell-free supernatants of the selected NRPS mutants, which showed QS induction. Using a bacteria-plant interaction system, we further show that the pvdJ, ambB, and pchE P. aeruginosa mutants failed to repress primary root growth, but improved root branching in A. thaliana seedlings. These results indicated that the CDP production in P. aeruginosa depended on the functional MM-NRPS, which influences quorum-sensing of bacteria and plays a role in root architecture remodeling.}, }
@article {pmid27897256, year = {2016}, author = {Herrero, ER and Slomka, V and Boon, N and Bernaerts, K and Hernandez-Sanabria, E and Quirynen, M and Teughels, W}, title = {Dysbiosis by neutralizing commensal mediated inhibition of pathobionts.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {38179}, pmid = {27897256}, issn = {2045-2322}, mesh = {Biofilms/*growth &amp; development ; Blood Proteins/metabolism ; Dysbiosis/metabolism/*microbiology ; Gram-Positive Bacteria/*physiology ; Humans ; Hydrogen Peroxide/metabolism ; Microbiota/*physiology ; Periodontium/*metabolism ; Peroxidase/metabolism ; }, abstract = {Dysbiosis in the periodontal microbiota is associated with the development of periodontal diseases. Little is known about the initiation of dysbiosis. It was hypothesized that some commensal bacteria suppress the outgrowth of pathobionts by H2O2 production. However, serum and blood components released due to inflammation can neutralize this suppressive effect, leading to the initiation of dysbiosis. Agar plate, dual-species and multi-species ecology experiments showed that H2O2 production by commensal bacteria decreases pathobiont growth and colonization. Peroxidase and blood components neutralize this inhibitory effect primarily by an exogenous peroxidase activity without stimulating growth and biofilm formation of pathobionts directly. In multi-species environments, neutralization of H2O2 resulted in 2 to 3 log increases in pathobionts, a hallmark for dysbiosis. Our data show that in oral biofilms, commensal species suppress the amounts of pathobionts by H2O2 production. Inflammation can neutralize this effect and thereby initiates dysbiosis by allowing the outgrowth of pathobionts.}, }
@article {pmid27896376, year = {2017}, author = {Jones, MB and Nierman, WC and Shan, Y and Frank, BC and Spoering, A and Ling, L and Peoples, A and Zullo, A and Lewis, K and Nelson, KE}, title = {Reducing the Bottleneck in Discovery of Novel Antibiotics.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {658-667}, pmid = {27896376}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/*pharmacology ; Biological Transport/genetics ; Drug Discovery/*methods ; Drug Resistance, Multiple, Bacterial ; Gene Expression Profiling/*methods ; Microbial Sensitivity Tests ; Sequence Analysis, RNA ; Staphylococcus aureus/*drug effects/genetics ; Streptomyces/*metabolism ; }, abstract = {Most antibiotics were discovered by screening soil actinomycetes, but the efficiency of the discovery platform collapsed in the 1960s. By now, more than 3000 antibiotics have been described and most of the current discovery effort is focused on the rediscovery of known compounds, making the approach impractical. The last marketed broad-spectrum antibiotics discovered were daptomycin, linezolid, and fidaxomicin. The current state of the art in the development of new anti-infectives is a non-existent pipeline in the absence of a discovery platform. This is particularly troubling given the emergence of pan-resistant pathogens. The current practice in dealing with the problem of the background of known compounds is to use chemical dereplication of extracts to assess the relative novelty of a compound it contains. Dereplication typically requires scale-up, extraction, and often fractionation before an accurate mass and structure can be produced by MS analysis in combination with 2D NMR. Here, we describe a transcriptome analysis approach using RNA sequencing (RNASeq) to identify promising novel antimicrobial compounds from microbial extracts. Our pipeline permits identification of antimicrobial compounds that produce distinct transcription profiles using unfractionated cell extracts. This efficient pipeline will eliminate the requirement for purification and structure determination of compounds from extracts and will facilitate high-throughput screen of cell extracts for identification of novel compounds.}, }
@article {pmid27895628, year = {2016}, author = {Morris, MM and Haggerty, JM and Papudeshi, BN and Vega, AA and Edwards, MS and Dinsdale, EA}, title = {Nearshore Pelagic Microbial Community Abundance Affects Recruitment Success of Giant Kelp, Macrocystis pyrifera.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1800}, pmid = {27895628}, issn = {1664-302X}, abstract = {Marine microbes mediate key ecological processes in kelp forest ecosystems and interact with macroalgae. Pelagic and biofilm-associated microbes interact with macroalgal propagules at multiple stages of recruitment, yet these interactions have not been described for Macrocystis pyrifera. Here we investigate the influence of microbes from coastal environments on recruitment of giant kelp, M. pyrifera. Through repeated laboratory experiments, we tested the effects of altered pelagic microbial abundance on the settlement and development of the microscopic propagules of M. pyrifera during recruitment. M. pyrifera zoospores were reared in laboratory microcosms exposed to environmental microbial communities from seawater during the complete haploid stages of the kelp recruitment cycle, including zoospore release, followed by zoospore settlement, to gametophyte germination and development. We altered the microbial abundance states differentially in three independent experiments with repeated trials, where microbes were (a) present or absent in seawater, (b) altered in community composition, and (c) altered in abundance. Within the third experiment, we also tested the effect of nearshore versus offshore microbial communities on the macroalgal propagules. Distinct pelagic microbial communities were collected from two southern California temperate environments reflecting contrasting intensity of human influence, the nearshore Point Loma kelp forest and the offshore Santa Catalina Island kelp forest. The Point Loma kelp forest is a high impacted coastal region adjacent to the populous San Diego Bay; whereas the kelp forest at Catalina Island is a low impacted region of the Channel Islands, 40 km offshore the southern California coast, and is adjacent to a marine protected area. Kelp gametophytes reared with nearshore Point Loma microbes showed lower survival, growth, and deteriorated morphology compared to gametophytes with the offshore Catalina Island microbial community, and these effects were magnified under high microbial abundances. Reducing abundance of Point Loma microbes restored M. pyrifera propagule success. Yet an intermediate microbial abundance was optimal for kelp propagules reared with Catalina Island microbes, suggesting that microbes also have a beneficial influence on kelp. Our study shows that pelagic microbes from nearshore and offshore environments are differentially influencing kelp propagule success, which has significant implications for kelp recruitment and kelp forest ecosystem health.}, }
@article {pmid27894722, year = {2017}, author = {Nuzzo, A and Hosseinkhani, B and Boon, N and Zanaroli, G and Fava, F}, title = {Impact of bio-palladium nanoparticles (bio-Pd NPs) on the activity and structure of a marine microbial community.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {220}, number = {Pt B}, pages = {1068-1078}, doi = {10.1016/j.envpol.2016.11.036}, pmid = {27894722}, issn = {1873-6424}, mesh = {Aliivibrio fischeri/*drug effects ; Catalysis ; Environmental Pollutants/chemistry/metabolism ; Geologic Sediments/*microbiology ; Halogenation ; Metal Nanoparticles/*chemistry ; Palladium/*chemistry/*pharmacology ; Polychlorinated Biphenyls/chemistry/metabolism ; }, abstract = {Biogenic palladium nanoparticles (bio-Pd NPs) represent a promising catalyst for organohalide remediation in water and sediments. However, the available information regarding their possible impact in case of release into the environment, particularly on the environmental microbiota, is limited. In this study the toxicity of bio-Pd NPs on the model marine bacterium V. fischeri was assessed. The impacts of different concentrations of bio-Pd NPs on the respiratory metabolisms (i.e. organohalide respiration, sulfate reduction and methanogenesis) and the structure of a PCB-dechlorinating microbial community enriched form a marine sediment were also investigated in microcosms mimicking the actual sampling site conditions. Bio-Pd NPs had no toxic effect on V. fischeri. In addition, they had no significant effects on PCB-dehalogenating activity, while showing a partial, dose-dependent inhibitory effect on sulfate reduction as well as on methanogenesis. No toxic effects by bio-Pd NPs could be also observed on the total bacterial community structure, as its biodiversity was increased compared to the not exposed community. In addition, resilience of the microbial community to bio-Pd NPs exposure was observed, being the final community organization (Gini coefficient) of samples exposed to bio-Pd NPs similar to that of the not exposed one. Considering all the factors evaluated, bio-Pd NPs could be deemed as non-toxic to the marine microbiota in the conditions tested. This is the first study in which the impact of bio-Pd NPs is extensively evaluated over a microbial community in relevant environmental conditions, providing important information for the assessment of their environmental safety.}, }
@article {pmid27892611, year = {2017}, author = {Callewaert, C and Lambert, J and Van de Wiele, T}, title = {Towards a bacterial treatment for armpit malodour.}, journal = {Experimental dermatology}, volume = {26}, number = {5}, pages = {388-391}, doi = {10.1111/exd.13259}, pmid = {27892611}, issn = {1600-0625}, mesh = {Antiperspirants/pharmacology ; Axilla/*microbiology ; Deodorants/pharmacology ; Humans ; Microbiota/drug effects ; Odorants/*prevention &amp; control ; *Probiotics ; }, abstract = {Axillary malodour is a frustrating condition for many people. It can lead to significant discomforts and various psychological effects. The underarm microbiome plays a major role in axillary malodour formation. Not only the bacteria on the epidermis, but also and especially those living in the sweat glands, sweat pores and hair follicles play a pivotal role in malodour development. To treat underarm malodour, this viewpoint article envisions a bacterial treatment. Replacing the autochthonous malodour-causing microbiome with a non-odour-causing microbiome, through an armpit bacterial transplantation or direct application of probiotics/non-odour-causing bacteria, could resolve the condition. Selective steering of the microbiome with prebiotics, biochemicals or plant extracts can likewise greatly help in improving the underarm odour. Elimination/inhibition of the "bad bugs" and application/stimulation of the "good bugs" will be part of the future treatment for axillary body odour.}, }
@article {pmid27891123, year = {2016}, author = {Pajares, S and Bohannan, BJ and Souza, V}, title = {Editorial: The Role of Microbial Communities in Tropical Ecosystems.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1805}, pmid = {27891123}, issn = {1664-302X}, }
@article {pmid27890586, year = {2017}, author = {Lekunberri, I and Subirats, J and Borrego, CM and Balcázar, JL}, title = {Exploring the contribution of bacteriophages to antibiotic resistance.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {220}, number = {Pt B}, pages = {981-984}, doi = {10.1016/j.envpol.2016.11.059}, pmid = {27890586}, issn = {1873-6424}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics ; Bacteriophages/genetics/*physiology ; Drug Resistance, Microbial/*genetics ; Feces/microbiology/virology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genes, Viral ; Genome, Viral ; Sewage/microbiology/virology ; Water Microbiology ; }, abstract = {Bacteriophages (phages) are the most abundant and diverse biological entities in our planet. They infect susceptible bacterial hosts into which they either multiply or persist. In the latter case, phages can confer new functions to their hosts as a result of gene transfer, thus contributing to their adaptation (short-term) and evolution (long-term). In this regard, the role of phages on the dissemination of antibiotic resistance genes (ARGs) among bacterial hosts in natural environments has not yet been clearly resolved. Here, we carry out a comprehensive analysis of thirty-three viromes from different habitats to investigate whether phages harbor ARGs. Our results demonstrate that while human-associated viromes do not or rarely carry ARGs, viromes from non-human sources (e.g. pig feces, raw sewage, and freshwater and marine environments) contain a large reservoir of ARGs, thus pointing out that phages could play a part on the spread of antibiotic resistance. Given this, the role of phages should not be underestimated and it should be considered when designing strategies to tackle the global crisis of antibiotic resistance.}, }
@article {pmid27889811, year = {2017}, author = {Shanmugam, SG and Magbanua, ZV and Williams, MA and Jangid, K and Whitman, WB and Peterson, DG and Kingery, WL}, title = {Bacterial Diversity Patterns Differ in Soils Developing in Sub-tropical and Cool-Temperate Ecosystems.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {556-569}, pmid = {27889811}, issn = {1432-184X}, mesh = {Bacteria/*classification/*genetics ; Base Sequence ; Biodiversity ; Climate ; DNA, Bacterial/genetics ; *Ecosystem ; Geography ; Georgia ; Michigan ; Microbiota/*genetics ; Plants/classification/microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Microbial diversity patterns have been surveyed in many different soils and ecosystems, but we are unaware of studies comparing similar soils developing from similar parent materials in contrasting climates. In 2008, developmental chronosequences with ages ranging from 105 to 500,000 years across Georgia (GA) and Michigan (MI) were studied to investigate how bacterial community composition and diversity change as a result of local environmental gradients that develop during pedogenesis. Geographic factors were studied between and within locations spanning two scales: (1) regionally between 0.1 and 50 and (2) ∼1700 km apart. The diversity was surveyed using high-throughput pyrosequencing, and variance partitioning was used to describe the effects of spatial, environmental, and spatio-environmental factors on bacterial community composition. At the local scale, variation in bacterial communities was most closely related to environmental factors (rM = 0.59, p = 0.0001). There were differences in bacterial communities between the two locations, indicating spatial biogeography. Estimates of bacterial diversity were much greater in MI (numbers of OTU, ACE, and Chao1) and remained 2-3× greater in MI than GA after removing the effect of soil properties. The large differences in diversity between geographically separated bacterial communities in different climates need further investigation. It is not known if the rare members of the community, which contributed to greater bacterial diversity in GA relative to MI, play an important role in ecosystem function but has been hypothesized to play a role in ecosystem resiliency, resistance, and stability. Further research on the link between bacterial diversity and spatial variability related to climate needs further investigation.}, }
@article {pmid27889387, year = {2017}, author = {Holmes, AJ and Chew, YV and Colakoglu, F and Cliff, JB and Klaassens, E and Read, MN and Solon-Biet, SM and McMahon, AC and Cogger, VC and Ruohonen, K and Raubenheimer, D and Le Couteur, DG and Simpson, SJ}, title = {Diet-Microbiome Interactions in Health Are Controlled by Intestinal Nitrogen Source Constraints.}, journal = {Cell metabolism}, volume = {25}, number = {1}, pages = {140-151}, doi = {10.1016/j.cmet.2016.10.021}, pmid = {27889387}, issn = {1932-7420}, mesh = {Animals ; Bacteria/drug effects/metabolism ; Biodiversity ; Computer Simulation ; *Diet ; Dietary Carbohydrates/pharmacology ; Dietary Proteins/pharmacology ; Energy Metabolism/drug effects ; Food ; *Health ; Intestinal Mucosa/*metabolism ; Intestines/drug effects ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; *Microbiota/drug effects ; Mucins/metabolism ; Nitrogen/*metabolism ; Spectrometry, Mass, Secondary Ion ; }, abstract = {Diet influences health and patterns of disease in populations. How different diets do this and why outcomes of diets vary between individuals are complex and involve interaction with the gut microbiome. A major challenge for predicting health outcomes of the host-microbiome dynamic is reconciling the effects of different aspects of diet (food composition or intake rate) on the system. Here we show that microbial community assembly is fundamentally shaped by a dichotomy in bacterial strategies to access nitrogen in the gut environment. Consequently, the pattern of dietary protein intake constrains the host-microbiome dynamic in ways that are common to a very broad range of diet manipulation strategies. These insights offer a mechanism for the impact of high protein intake on metabolic health and form the basis for a general theory of the impact of different diet strategies on host-microbiome outcomes.}, }
@article {pmid27888456, year = {2016}, author = {Kim, JM and Roh, AS and Choi, SC and Kim, EJ and Choi, MT and Ahn, BK and Kim, SK and Lee, YH and Joa, JH and Kang, SS and Lee, SA and Ahn, JH and Song, J and Weon, HY}, title = {Soil pH and electrical conductivity are key edaphic factors shaping bacterial communities of greenhouse soils in Korea.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {54}, number = {12}, pages = {838-845}, pmid = {27888456}, issn = {1976-3794}, mesh = {Acidobacteria/genetics/isolation &amp; purification/physiology ; Agriculture/methods ; Bacteria/*classification/*isolation &amp; purification ; Crop Production ; Ecosystem ; *Electric Conductivity ; High-Throughput Nucleotide Sequencing ; Hydrogen-Ion Concentration ; Microbial Consortia/*physiology ; Plants ; Proteobacteria/genetics/isolation &amp; purification/physiology ; RNA, Ribosomal, 16S ; Republic of Korea ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Soil microorganisms play an essential role in soil ecosystem processes such as organic matter decomposition, nutrient cycling, and plant nutrient availability. The land use for greenhouse cultivation has been increasing continuously, which involves an intensive input of agricultural materials to enhance productivity; however, relatively little is known about bacterial communities in greenhouse soils. To assess the effects of environmental factors on the soil bacterial diversity and community composition, a total of 187 greenhouse soil samples collected across Korea were subjected to bacterial 16S rRNA gene pyrosequencing analysis. A total of 11,865 operational taxonomic units at a 97% similarity cutoff level were detected from 847,560 sequences. Among nine soil factors evaluated; pH, electrical conductivity (EC), exchangeable cations (Ca[2+], Mg[2+], Na[+], and K[+]), available P2O5, organic matter, and NO3-N, soil pH was most strongly correlated with bacterial richness (polynomial regression, pH: R[2] = 0.1683, P < 0.001) and diversity (pH: R[2] = 0.1765, P < 0.001). Community dissimilarities (Bray-Curtis distance) were positively correlated with Euclidean distance for pH and EC (Mantel test, pH: r = 0.2672, P < 0.001; EC: r = 0.1473, P < 0.001). Among dominant phyla (> 1%), the relative abundances of Proteobacteria, Gemmatimonadetes, Acidobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes were also more strongly correlated with pH and EC values, compared with other soil cation contents, such as Ca[2+], Mg[2+], Na[+], and K[+]. Our results suggest that, despite the heterogeneity of various environmental variables, the bacterial communities of the intensively cultivated greenhouse soils were particularly influenced by soil pH and EC. These findings therefore shed light on the soil microbial ecology of greenhouse cultivation, which should be helpful for devising effective management strategies to enhance soil microbial diversity and improving crop productivity.}, }
@article {pmid27888292, year = {2017}, author = {Saad, SA and Wade, CM}, title = {Seasonal and Spatial Variations of Saltmarsh Benthic Foraminiferal Communities from North Norfolk, England.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {539-555}, pmid = {27888292}, issn = {1432-184X}, mesh = {Biodiversity ; England ; Environment ; Environmental Monitoring ; Foraminifera/*classification/*isolation &amp; purification ; Geologic Sediments/*parasitology ; Seasons ; Seawater/*parasitology ; *Wetlands ; }, abstract = {Time series foraminiferal data were obtained from samples collected from three sites at Brancaster Overy Staithe, Burnham Overy Staithe and Thornham on the North Norfolk coast over a 1-year period. At each collection point, six environmental variables-temperature, chlorophyll, sand, mud, pH and salinity-were also measured. The principle aim of this study was to examine the benthic foraminiferal fauna in regard to the temporal variability of foraminiferal abundance, seasonal trend, dominant species, species diversity and the impact of environmental variables on the foraminiferal communities in the top 1 cm of sediment over a 1-year time series. The foraminiferal assemblages at the three sites were dominated by three species: Haynesina germanica, Ammonia sp. and Elphidium williamsoni. Foraminiferal species showed considerable seasonal and temporal fluctuation throughout the year at the three investigated sites. The foraminiferal assemblage at the three low marsh zones showed a maximum abundance in autumn between September and November and a minimum abundance observed between July and August. There were two separate peaks in the abundance of Ammonia sp. and E. williamsoni, one in spring and another in autumn. In contrast, H. germanica showed a single peak in its abundance in autumn. A generalized additive modelling approach was used to explain the variation in the observed foraminiferal abundance and to estimate the significant impact of each of the environmental variables on living foraminiferal assemblages, with taxa abundance as the dependent variable. When included in the model as predictors, most of the environmental variables contributed little in explaining the observed variation in foraminiferal species abundance. However, the hypotheses for differences amongst sites, salinity and pH were significant and explained most of the variability in species relative abundance.}, }
@article {pmid27888291, year = {2017}, author = {Vezzulli, L and Grande, C and Tassistro, G and Brettar, I and Höfle, MG and Pereira, RP and Mushi, D and Pallavicini, A and Vassallo, P and Pruzzo, C}, title = {Whole-Genome Enrichment Provides Deep Insights into Vibrio cholerae Metagenome from an African River.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {734-738}, pmid = {27888291}, issn = {1432-184X}, mesh = {Base Sequence ; DNA, Bacterial/*genetics ; Genotyping Techniques ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Rivers/*microbiology ; Sequence Analysis, DNA ; Tanzania ; Vibrio cholerae/*genetics/*isolation &amp; purification ; }, abstract = {The detection and typing of Vibrio cholerae in natural aquatic environments encounter major methodological challenges related to the fact that the bacterium is often present in environmental matrices at very low abundance in nonculturable state. This study applied, for the first time to our knowledge, a whole-genome enrichment (WGE) and next-generation sequencing (NGS) approach for direct genotyping and metagenomic analysis of low abundant V. cholerae DNA (<50 genome unit/L) from natural water collected in the Morogoro river (Tanzania). The protocol is based on the use of biotinylated RNA baits for target enrichment of V. cholerae metagenomic DNA via hybridization. An enriched V. cholerae metagenome library was generated and sequenced on an Illumina MiSeq platform. Up to 1.8 × 10[7] bp (4.5× mean read depth) were found to map against V. cholerae reference genome sequences representing an increase of about 2500 times in target DNA coverage compared to theoretical calculations of performance for shotgun metagenomics. Analysis of metagenomic data revealed the presence of several V. cholerae virulence and virulence associated genes in river water including major virulence regions (e.g. CTX prophage and Vibrio pathogenicity island-1) and genetic markers of epidemic strains (e.g. O1-antigen biosynthesis gene cluster) that were not detectable by standard culture and molecular techniques. Overall, besides providing a powerful tool for direct genotyping of V. cholerae in complex environmental matrices, this study provides a 'proof of concept' on the methodological gap that might currently preclude a more comprehensive understanding of toxigenic V. cholerae emergence from natural aquatic environments.}, }
@article {pmid27886631, year = {2017}, author = {Ziller, A and Yadav, RK and Capdevila, M and Reddy, MS and Vallon, L and Marmeisse, R and Atrian, S and Palacios, &#xd2; and Fraissinet-Tachet, L}, title = {Metagenomics analysis reveals a new metallothionein family: Sequence and metal-binding features of new environmental cysteine-rich proteins.}, journal = {Journal of inorganic biochemistry}, volume = {167}, number = {}, pages = {1-11}, doi = {10.1016/j.jinorgbio.2016.11.017}, pmid = {27886631}, issn = {1873-3344}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; *Metagenome ; Metagenomics ; *Metallothionein/chemistry/genetics ; Metals, Heavy/*chemistry ; Molecular Sequence Data ; }, abstract = {Metallothioneins are cysteine-rich proteins, which function as (i) metal carriers in basal cell metabolism and (ii) protective metal chelators in conditions of metal excess. Metallothioneins have been characterized from different eukaryotic model and cultivable species. Presently, they are categorized in 15 families but evolutionary relationships between these metallothionein families remain unresolved. Several cysteine-rich protein encoding genes that conferred Cd-tolerance in Cd-sensitive yeast mutants have previously been isolated from soil eukaryotic metatranscriptomes. They were called CRPs for "cysteine-rich proteins". These proteins, of unknown taxonomic origins, share conserved cysteine motifs and could be considered as metallothioneins. In the present work, we analyzed these CRPs with respect to their amino acid sequence features and their metal-binding abilities towards Cd, Zn and Cu metal ions. Sequence analysis revealed that they share common features with different known metallothionein families, but also exhibit unique specific features. Noticeably, CRPs display two separate cysteine-rich domains which, when expressed separately in yeast, confer Cd-tolerance. The N-terminal domain contains some conserved atypical Cys motifs, such as one CCC and two CXCC ones. Five CRPs were expressed and purified as recombinant proteins and their metal-binding characteristics were studied. All these CRPs chelated Cd(II), Zn(II) and Cu(I), although displaying a better capacity for Zn(II) coordination. All CRPs are able to confer Cd-tolerance, and four of them confer Zn-tolerance in the Zn-sensitive zrc1Δ yeast mutant. We designated these CRPs as environmental metallothioneins belonging to a new formerly undescribed metallothionein family.}, }
@article {pmid27886384, year = {2017}, author = {Aouidi, F and Okba, A and Hamdi, M}, title = {Valorization of functional properties of extract and powder of olive leaves in raw and cooked minced beef meat.}, journal = {Journal of the science of food and agriculture}, volume = {97}, number = {10}, pages = {3195-3203}, doi = {10.1002/jsfa.8164}, pmid = {27886384}, issn = {1097-0010}, mesh = {Animals ; Antioxidants/*chemistry ; Cattle ; Cooking ; Food Additives/*chemistry ; Food Preservation/*methods ; Lipids/chemistry ; Meat/*analysis ; Myoglobin/chemistry ; Olea/*chemistry ; Oxidation-Reduction ; Plant Extracts/*chemistry ; Plant Leaves/chemistry ; }, abstract = {BACKGROUND: Olive leaves (OL), available in huge amounts from pruning, are known to be a useful source of biologically active compounds. This study investigated the potential application of OL as a supplement to minced beef meat in order to develop a functional product. The effect of OL extract or powder (100 and 150 µg phenols g[-1] meat) on the quality and stability of raw and cooked meat during refrigerated storage was examined.<br><br>RESULTS: Microwave drying at 600&#x2009;W gave OL with the highest antioxidant quality (evaluated by TEAC/[phenols] (mg&#x2009;mg[-1]) and DPPH/[phenols] (mg&#x2009;mg[-1])) compared with other methods. OL showed an ability to inhibit (P < 0.05) lipid oxidation (TBARS values (mg MDA kg[-1]) were reduced by 25-65%) and myoglobin oxidation (metmyoglobin production was 43-65% in control samples and 14-35% in treated samples). OL also improved the technological quality of the meat, decreasing (P < 0.05) storage loss (%) and defrosting loss (%) without affecting cooking loss (%) and Napole yield (%). Sensory properties were not modified by the added ingredient at the tested levels (P < 0.05).<br><br>CONCLUSION: OL (extract or powder) may have applications in the development of functional meat products of good technological quality that remain stable during storage. &#xa9; 2016 Society of Chemical Industry.}, }
@article {pmid27883264, year = {2017}, author = {De Weirdt, R and Hernandez-Sanabria, E and Fievez, V and Mees, E and Geirnaert, A and Van Herreweghen, F and Vilchez-Vargas, R and Van den Abbeele, P and Jauregui, R and Pieper, DH and Vlaeminck, B and Van de Wiele, T}, title = {Mucosa-associated biohydrogenating microbes protect the simulated colon microbiome from stress associated with high concentrations of poly-unsaturated fat.}, journal = {Environmental microbiology}, volume = {19}, number = {2}, pages = {722-739}, doi = {10.1111/1462-2920.13622}, pmid = {27883264}, issn = {1462-2920}, mesh = {Adult ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Butyrates/metabolism ; Colon/*microbiology/physiology ; Fatty Acids, Unsaturated/*metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/*microbiology ; Linoleic Acid/metabolism ; Microbiota/drug effects ; Stearic Acids/metabolism ; Young Adult ; }, abstract = {Polyunsaturated fatty acids (PUFAs) may affect colon microbiome homeostasis by exerting (specific) antimicrobial effects and/or interfering with mucosal biofilm formation at the gut mucosal interface. We used standardized batch incubations and the Mucosal-Simulator of the Human Microbial Intestinal Ecosystem (M-SHIME) to show the in vitro luminal and mucosal effects of the main PUFA in the Western diet, linoleic acid (LA). High concentrations of LA were found to decrease butyrate production and Faecalibacterium prausnitzii numbers dependent on LA biohydrogenation to vaccenic acid (VA) and stearic acid (SA). In faecal batch incubations, LA biohydrogenation and butyrate production were positively correlated and SA did not inhibit butyrate production. In the M-SHIME, addition of a mucosal environment stimulated biohydrogenation to SA and protected F. prausnitzii from inhibition by LA. This was probably due to the preference of two biohydrogenating genera Roseburia and Pseudobutyrivibrio for the mucosal niche. Co-culture batch incubations using Roseburia hominis and F. prausnitzii validated these observations. Correlations networks further uncovered the central role of Roseburia and Pseudobutyrivibrio in protecting luminal and mucosal SHIME microbiota from LA-induced stress. Our results confirm how cross-shielding interactions provide resilience to the microbiome and demonstrate the importance of biohydrogenating, mucosal bacteria for recovery from LA stress.}, }
@article {pmid27883008, year = {2016}, author = {Jacquemyn, H and Waud, M and Merckx, VS and Brys, R and Tyteca, D and Hedrén, M and Lievens, B}, title = {Habitat-driven variation in mycorrhizal communities in the terrestrial orchid genus Dactylorhiza.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {37182}, pmid = {27883008}, issn = {2045-2322}, support = {260601/ERC_/European Research Council/International ; }, mesh = {Basidiomycota/*genetics ; DNA, Fungal/genetics ; Ecosystem ; Europe ; Molecular Typing ; Mycological Typing Techniques ; Mycorrhizae/*genetics ; Orchidaceae/*microbiology ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Symbiosis ; }, abstract = {Orchid species are critically dependent on mycorrhizal fungi for completion of their life cycle, particularly during the early stages of their development when nutritional resources are scarce. As such, orchid mycorrhizal fungi play an important role in the population dynamics, abundance, and spatial distribution of orchid species. However, less is known about the ecology and distribution of orchid mycorrhizal fungi. In this study, we used 454 amplicon pyrosequencing to investigate ecological and geographic variation in mycorrhizal associations in fourteen species of the orchid genus Dactylorhiza. More specifically, we tested the hypothesis that variation in orchid mycorrhizal communities resulted primarily from differences in habitat conditions where the species were growing. The results showed that all investigated Dactylorhiza species associated with a large number of fungal OTUs, the majority belonging to the Tulasnellaceae, Ceratobasidiaceae and Sebacinales. Mycorrhizal specificity was low, but significant variation in mycorrhizal community composition was observed between species inhabiting different ecological habitats. Although several fungi had a broad geographic distribution, Species Indicator Analysis revealed some fungi that were characteristic for specific habitats. Overall, these results indicate that orchid mycorrhizal fungi may have a broad geographic distribution, but that their occurrence is bounded by specific habitat conditions.}, }
@article {pmid27882545, year = {2017}, author = {Kurm, V and van der Putten, WH and de Boer, W and Naus-Wiezer, S and Hol, WH}, title = {Low abundant soil bacteria can be metabolically versatile and fast growing.}, journal = {Ecology}, volume = {98}, number = {2}, pages = {555-564}, doi = {10.1002/ecy.1670}, pmid = {27882545}, issn = {0012-9658}, mesh = {Bacteria/*growth &amp; development ; Carbon ; Phylogeny ; Soil ; *Soil Microbiology ; }, abstract = {The abundance of species is assumed to depend on their life history traits, such as growth rate and resource specialization. However, this assumption has not been tested for bacteria. Here we investigate how abundance of soil bacteria relates to slow growth and substrate specialization (oligotrophy) vs. fast growth and substrate generalization (copiotrophy). We collected 47 saprotrophic soil bacterial isolates of differing abundances and measured their growth rate and the ability to use a variety of single carbon sources. Opposite to our expectation, there was no relationship between abundance in soil and the measured growth rate or substrate utilization profile (SUP). However, isolates with lower growth rates used fewer substrates than faster growing ones supporting the assumption that growth rate may relate to substrate specialization. Interestingly, growth rate and SUP were correlated with phylogeny, rather than with abundance in soil. Most markedly, Gammaproteobacteria on average grew significantly faster and were able to use more substrates than other bacterial classes, whereas Alphaproteobacteria were growing relatively slowly and used fewer substrates. This finding suggests that growth and substrate utilization are phylogenetically deeply conserved. We conclude that growth rate and substrate utilization of soil bacteria are not general determinants of their abundance. Future studies on explaining bacterial abundance need to determine how other factors, such as competition, predation and abiotic factors may contribute to rarity or abundance in soil bacteria.}, }
@article {pmid27882076, year = {2016}, author = {Kracke, F and Virdis, B and Bernhardt, PV and Rabaey, K and Krömer, JO}, title = {Redox dependent metabolic shift in Clostridium autoethanogenum by extracellular electron supply.}, journal = {Biotechnology for biofuels}, volume = {9}, number = {}, pages = {249}, pmid = {27882076}, issn = {1754-6834}, abstract = {BACKGROUND: Microbial electrosynthesis is a novel approach that aims at shifting the cellular metabolism towards electron-dense target products by extracellular electron supply. Many organisms including several acetogenic bacteria have been shown to be able to consume electrical current. However, suitable hosts for relevant industrial processes are yet to be discovered, and major knowledge gaps about the underlying fundamental processes still remain.<br><br>RESULTS: In this paper, we present the first report of electron uptake by the Gram-positive, ethanol-producing acetogen, Clostridium&#xa0;autoethanogenum. Under heterotrophic conditions, extracellular electron supply induced a significant metabolic shift away from acetate. In electrically enhanced fermentations on fructose, acetate production was cut by more than half, while production of lactate and 2,3-butanediol increased by 35-fold and threefold, respectively. The use of mediators with different redox potential revealed a direct dependency of the metabolic effect on the redox potential at which electrons are supplied. Only electrons delivered at a redox potential low enough to reduce ferredoxin caused the reported effect.<br><br>CONCLUSIONS: Production in acetogenic organisms is usually challenged by cellular energy limitations if the target product does not lead to a net energy gain as in the case of acetate. The presented results demonstrate a significant shift of carbon fluxes away from acetate towards the products, lactate and 2,3-butanediol, induced by small electricity input (~0.09&#xa0;mol of electrons per mol of substrate). This presents a simple and attractive method to optimize acetogenic fermentations for production of chemicals and fuels using electrochemical techniques. The relationship between metabolic shift and redox potential of electron feed gives an indication of possible electron-transfer mechanisms and helps to prioritize further research efforts.}, }
@article {pmid27881544, year = {2016}, author = {Loscar, ME and Huptas, C and Wenning, M and Sieber, V and Schmid, J}, title = {Draft Genome Sequence of Lysinibacillus xylanilyticus SR-86.}, journal = {Genome announcements}, volume = {4}, number = {6}, pages = {}, pmid = {27881544}, issn = {2169-8287}, abstract = {Lysinibacillus xylanilyticus belongs to the family Bacillaceae and was first described in 2010 with the type strain L. xylanilyticus XDB9. It is able to both degrade xylan and use it as the sole carbon source. Here, we describe the 4.8-Mb genome of the strain L. xylanilyticus SR-86, which was isolated from organic waste.}, }
@article {pmid27881419, year = {2017}, author = {Zhang, W and Zhu, YH and Zhou, D and Wu, Q and Song, D and Dicksved, J and Wang, JF}, title = {Oral Administration of a Select Mixture of Bacillus Probiotics Affects the Gut Microbiota and Goblet Cell Function following Escherichia coli Challenge in Newly Weaned Pigs of Genotype MUC4 That Are Supposed To Be Enterotoxigenic E. coli F4ab/ac Receptor Negative.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {3}, pages = {}, pmid = {27881419}, issn = {1098-5336}, mesh = {Administration, Oral ; Animal Feed/analysis ; Animals ; Bacillus licheniformis/chemistry ; Bacillus subtilis/chemistry ; Diet/veterinary ; Enterotoxigenic Escherichia coli/drug effects ; Escherichia coli Infections/immunology/microbiology/*veterinary ; Female ; Gastrointestinal Microbiome/*drug effects ; Genotype ; Goblet Cells/*drug effects ; Male ; Mucin-4/genetics ; Probiotics/*administration &amp; dosage ; Sus scrofa/genetics ; Swine ; Swine Diseases/*immunology/microbiology ; }, abstract = {UNLABELLED: Structural disruption of the gut microbiota and impaired goblet cell function are collateral etiologic factors in enteric diseases. Low, moderate, or high doses of a Bacillus licheniformis-B. subtilis mixture (BLS mix) were orally administered to piglets of genotype MUC4 that are supposed to be F4-expressing enterotoxigenic Escherichia coli strain (F4[+] ETEC) F4ab/ac receptor negative (i.e., MUC4-resistant piglets) for 1 week before F4[+] ETEC challenge. The luminal contents were collected from the mucosa of the colon on day 8 after F4[+] ETEC challenge. The BLS mix attenuated E. coli-induced expansion of Bacteroides uniformis, Eubacterium eligens, Acetanaerobacterium, and Sporobacter populations. Clostridium and Turicibacter populations increased following F4[+] ETEC challenge in pigs pretreated with low-dose BLS mix. Lactobacillus gasseri and Lactobacillus salivarius populations increased after administration of BLS mix during E. coli infection. The beneficial effects of BLS mix were due in part to the expansion of certain Clostridium, Lactobacillus, and Turicibacter populations, with a corresponding increase in the number of goblet cells in the ileum via upregulated Atoh1 expression, in turn increasing MUC2 production and thus preserving the mucus barrier and enhancing host defenses against enteropathogenic bacteria. However, excessive BLS mix consumption may increase the risk for enteritis, partly through disruption of colonic microbial ecology, characterized by expansion of Proteobacteria and impaired goblet cell function in the ileum. Our findings suggest that oral administration of BLS mix reprograms the gut microbiota and enhances goblet cell function to ameliorate enteritis.<br><br>IMPORTANCE: The present study is important for improving our understanding of the protective role of probiotics against Escherichia coli infection in piglets. Structural disruption of the gut microbiota and impaired goblet cell function are collateral etiologic factors in enteric diseases. In this study, low, moderate, or high doses of a Bacillus licheniformis-B. subtilis mixture (BLS mix) were orally administered to MUC4-resistant piglets for 1 week before the F4-expressing ETEC strain (F4[+] ETEC) challenge. Our findings suggest that oral administration of BLS mix reprograms the gut microbiota and enhances goblet cell function to ameliorate enteritis.}, }
@article {pmid27878347, year = {2017}, author = {Rani, S and Koh, HW and Rhee, SK and Fujitani, H and Park, SJ}, title = {Detection and Diversity of the Nitrite Oxidoreductase Alpha Subunit (nxrA) Gene of Nitrospina in Marine Sediments.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {111-122}, pmid = {27878347}, issn = {1432-184X}, mesh = {Bacteria/*genetics/isolation &amp; purification/*metabolism ; Base Sequence ; DNA, Bacterial/genetics ; Geologic Sediments/*microbiology ; Nitrification/*genetics ; Nitrites/*metabolism ; Oxidation-Reduction ; Oxidoreductases/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Nitrite-oxidizing bacteria (NOB) are chemolithoautotrophs that catalyze the oxidation of nitrite to nitrate, which is the second step of aerobic nitrification. In marine ecosystems, Nitrospina is assumed to be a major contributor to nitrification. To date, two strains of Nitrospina have been isolated from marine environments. Despite their ecological relevance, their ecophysiology and environmental distribution are understudied owing to fastidious cultivation techniques and the lack of a sufficient functional gene marker. To estimate the abundance, diversity, and distribution of Nitrospina in various marine sediments, we used nxrA, which encodes the alpha subunit of nitrite oxidoreductase, as a functional and phylogenetic marker. We observed that Nitrospina diversity in polar sediments was significantly lower than that of non-polar samples. Moreover, nxrA-like sequences revealed an unexpected diversity of Nitrospina, with approximately 41,000 different sequences based on a 95% similarity cutoff from six marine sediments. We detected nxrA gene copy numbers of up to 3.57 × 10[4] per gram of marine sediment sample. The results of this study provide insight into the distribution and diversity of Nitrospina, which is fundamentally important for understanding their contribution to the nitrogen cycle in marine sediments.}, }
@article {pmid27878346, year = {2017}, author = {Deng, Y and Liu, Y and Dumont, M and Conrad, R}, title = {Salinity Affects the Composition of the Aerobic Methanotroph Community in Alkaline Lake Sediments from the Tibetan Plateau.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {101-110}, pmid = {27878346}, issn = {1432-184X}, mesh = {Biodiversity ; DNA, Bacterial/genetics ; Geologic Sediments/*chemistry/*microbiology ; Lakes/*chemistry/*microbiology ; Methane/*metabolism ; Methylobacterium/classification/genetics/isolation &amp; purification ; Methylococcaceae/classification/genetics/isolation &amp; purification ; Methylocystaceae/classification/genetics/isolation &amp; purification ; Oxidoreductases/genetics ; Phylogeny ; Polymorphism, Restriction Fragment Length ; *Salinity ; Sequence Analysis, DNA ; Sodium Chloride/*metabolism ; Tibet ; }, abstract = {Lakes are widely distributed on the Tibetan Plateau, which plays an important role in natural methane emission. Aerobic methanotrophs in lake sediments reduce the amount of methane released into the atmosphere. However, no study to date has analyzed the methanotroph community composition and their driving factors in sediments of these high-altitude lakes (>4000 m). To provide new insights on this aspect, the abundance and composition in the sediments of six high-altitude alkaline lakes (including both freshwater and saline lakes) on the Tibetan Plateau were studied. The quantitative PCR, terminal restriction fragment length polymorphism, and 454-pyrosequencing methods were used to target the pmoA genes. The pmoA gene copies ranged 10[4]-10[6] per gram fresh sediment. Type I methanotrophs predominated in Tibetan lake sediments, with Methylobacter and uncultivated type Ib methanotrophs being dominant in freshwater lakes and Methylomicrobium in saline lakes. Combining the pmoA-pyrosequencing data from Tibetan lakes with other published pmoA-sequencing data from lake sediments of other regions, a significant salinity and alkalinity effect (P = 0.001) was detected, especially salinity, which explained ∼25% of methanotroph community variability. The main effect was Methylomicrobium being dominant (up to 100%) in saline lakes only. In freshwater lakes, however, methanotroph composition was relatively diverse, including Methylobacter, Methylocystis, and uncultured type Ib clusters. This study provides the first methanotroph data for high-altitude lake sediments (>4000 m) and shows that salinity is a driving factor for the community composition of aerobic methanotrophs.}, }
@article {pmid27878079, year = {2016}, author = {Smith, CR and Blair, PL and Boyd, C and Cody, B and Hazel, A and Hedrick, A and Kathuria, H and Khurana, P and Kramer, B and Muterspaw, K and Peck, C and Sells, E and Skinner, J and Tegeler, C and Wolfe, Z}, title = {Microbial community responses to soil tillage and crop rotation in a corn/soybean agroecosystem.}, journal = {Ecology and evolution}, volume = {6}, number = {22}, pages = {8075-8084}, pmid = {27878079}, issn = {2045-7758}, abstract = {The acreage planted in corn and soybean crops is vast, and these crops contribute substantially to the world economy. The agricultural practices employed for farming these crops have major effects on ecosystem health at a worldwide scale. The microbial communities living in agricultural soils significantly contribute to nutrient uptake and cycling and can have both positive and negative impacts on the crops growing with them. In this study, we examined the impact of the crop planted and soil tillage on nutrient levels, microbial communities, and the biochemical pathways present in the soil. We found that farming practice, that is conventional tillage versus no-till, had a much greater impact on nearly everything measured compared to the crop planted. No-till fields tended to have higher nutrient levels and distinct microbial communities. Moreover, no-till fields had more DNA sequences associated with key nitrogen cycle processes, suggesting that the microbial communities were more active in cycling nitrogen. Our results indicate that tilling of agricultural soil may magnify the degree of nutrient waste and runoff by altering nutrient cycles through changes to microbial communities. Currently, a minority of acreage is maintained without tillage despite clear benefits to soil nutrient levels, and a decrease in nutrient runoff-both of which have ecosystem-level effects and both direct and indirect effects on humans and other organisms.}, }
@article {pmid27872949, year = {2017}, author = {Guidolin, AS and Cônsoli, FL}, title = {Symbiont Diversity of Aphis (Toxoptera) citricidus (Hemiptera: Aphididae) as Influenced by Host Plants.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {201-210}, pmid = {27872949}, issn = {1432-184X}, mesh = {Animals ; Aphids/*microbiology ; Biodiversity ; Buchnera/genetics/*isolation &amp; purification ; Enterobacteriaceae/genetics/*isolation &amp; purification ; Proteobacteria/genetics/*isolation &amp; purification ; Symbiosis ; }, abstract = {Aphids are well known for their association with endosymbiont bacteria. Almost all aphids harbor Buchnera aphidicola as an obligate symbiont and several other bacteria as facultative symbionts. Associations of facultative symbionts and aphids are quite variable in terms of diversity and prevalence across aphid species. Facultative symbionts can have a major impact on aphid bioecological traits. A number of factors shape the outcome of the facultative symbiont-aphid association, including aphid clone, bacterial genotype, geography, and host plant association. The effects of host plant on aphid-facultative symbiont associations are the least understood. We performed deep sequencing of the bacterial community associated with field populations of the oligophagous aphid Aphis (Toxoptera) citricidus collected from different host plants. We demonstrate that (i) A. citricidus has low symbiont diversity, (ii) symbiont diversity is affected by host plant, and (iii) host plants affect the relative abundance of the obligate symbiont Buchnera and an unknown genus of Enterobacteriaceae.}, }
@article {pmid27869789, year = {2016}, author = {Brugiroux, S and Beutler, M and Pfann, C and Garzetti, D and Ruscheweyh, HJ and Ring, D and Diehl, M and Herp, S and Lötscher, Y and Hussain, S and Bunk, B and Pukall, R and Huson, DH and Münch, PC and McHardy, AC and McCoy, KD and Macpherson, AJ and Loy, A and Clavel, T and Berry, D and Stecher, B}, title = {Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium.}, journal = {Nature microbiology}, volume = {2}, number = {}, pages = {16215}, doi = {10.1038/nmicrobiol.2016.215}, pmid = {27869789}, issn = {2058-5276}, support = {I 2320/FWF_/Austrian Science Fund FWF/Austria ; P 26127/FWF_/Austrian Science Fund FWF/Austria ; P 27831/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; *Antibiosis ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Mice ; Salmonella Infections, Animal/*prevention &amp; control ; Salmonella typhimurium/*physiology ; }, abstract = {Protection against enteric infections, also termed colonization resistance, results from mutualistic interactions of the host and its indigenous microbes. The gut microbiota of humans and mice is highly diverse and it is therefore challenging to assign specific properties to its individual members. Here, we have used a collection of murine bacterial strains and a modular design approach to create a minimal bacterial community that, once established in germ-free mice, provided colonization resistance against the human enteric pathogen Salmonella enterica serovar Typhimurium (S. Tm). Initially, a community of 12 strains, termed Oligo-Mouse-Microbiota (Oligo-MM[12]), representing members of the major bacterial phyla in the murine gut, was selected. This community was stable over consecutive mouse generations and provided colonization resistance against S. Tm infection, albeit not to the degree of a conventional complex microbiota. Comparative (meta)genome analyses identified functions represented in a conventional microbiome but absent from the Oligo-MM[12]. By genome-informed design, we created an improved version of the Oligo-MM community harbouring three facultative anaerobic bacteria from the mouse intestinal bacterial collection (miBC) that provided conventional-like colonization resistance. In conclusion, we have established a highly versatile experimental system that showed efficacy in an enteric infection model. Thus, in combination with exhaustive bacterial strain collections and systems-based approaches, genome-guided design can be used to generate insights into microbe-microbe and microbe-host interactions for the investigation of ecological and disease-relevant mechanisms in the intestine.}, }
@article {pmid27869357, year = {2017}, author = {Jain, R and Kumar, H and Tawhai, M and Douglas, R}, title = {The impact of endoscopic sinus surgery on paranasal physiology in simulated sinus cavities.}, journal = {International forum of allergy &amp; rhinology}, volume = {7}, number = {3}, pages = {248-255}, doi = {10.1002/alr.21879}, pmid = {27869357}, issn = {2042-6984}, mesh = {Chronic Disease ; Computer Simulation ; *Endoscopy ; Humans ; *Models, Anatomic ; Nasal Sprays ; Paranasal Sinuses/diagnostic imaging/metabolism/*physiology/*surgery ; Rhinitis/diagnostic imaging/drug therapy/physiopathology/surgery ; Sinusitis/diagnostic imaging/drug therapy/physiopathology/surgery ; Tomography, X-Ray Computed ; }, abstract = {BACKGROUND: Surgery improves symptoms for the majority of chronic rhinosinusitis (CRS) patients; however, physiological changes in the sinus cavities remain poorly characterized. Direct measurement of changes in airflow, pressure, temperature, humidity, and intranasal spray distribution following surgery is technically challenging. Accordingly, we have used computational fluid dynamic modeling to quantify how these parameters change postoperatively.<br><br>METHODS: Computed tomography images from a normal control, a patient with CRS preoperatively and postoperatively, and a patient following an endoscopic Lothrop procedure (ELP) were used to create 4 three-dimensional models of the sinus cavities. Changes in physiologic parameters and topical drug distribution were modeled (inhaled air at 16&#xb0;C and 10% humidity) at the maxillary ostium, frontal recess, and sphenoid ostium.<br><br>RESULTS: Large differences were seen between models. Following surgery, the maxillary ostia were found on average to be cooler (by 2.4&#xb0;C), with an increased airflow (0.26 m/second; from 0 m/second), and a 9% reduction in absolute humidity. Sphenoid ostial parameters followed a similar trend. Significant changes in frontal recess physiology were seen following ELP in which the recess was 4.2&#xb0;C cooler, had increased airflow (0.76 m/second) and a 17% reduction in absolute humidity. Topical drug distribution increased with surgery, particularly after ELP.<br><br>CONCLUSION: Surgery changes the geometry and physiology of the paranasal sinuses. These changes are likely to have an impact on wound healing, mucociliary function, and microbial ecology in postoperative cavities. Application of this model to further understand the effects of surgery may help to optimize surgical techniques and improve topical drug delivery.}, }
@article {pmid27868387, year = {2017}, author = {Shulse, CN and Maillot, B and Smith, CR and Church, MJ}, title = {Polymetallic nodules, sediments, and deep waters in the equatorial North Pacific exhibit highly diverse and distinct bacterial, archaeal, and microeukaryotic communities.}, journal = {MicrobiologyOpen}, volume = {6}, number = {2}, pages = {}, pmid = {27868387}, issn = {2045-8827}, mesh = {Aquatic Organisms/classification/genetics ; Archaea/*classification/genetics/isolation &amp; purification ; Cobalt/isolation &amp; purification ; Copper/isolation &amp; purification ; Cryptophyta/*classification/genetics/isolation &amp; purification ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Geologic Sediments/*microbiology/*parasitology ; Manganese/isolation &amp; purification ; Microbiota/*genetics ; Nickel/isolation &amp; purification ; Pacific Ocean ; Proteobacteria/*classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Concentrated seabed deposits of polymetallic nodules, which are rich in economically valuable metals (e.g., copper, nickel, cobalt, manganese), occur over vast areas of the abyssal Pacific Ocean floor. Little is currently known about the diversity of microorganisms inhabiting abyssal habitats. In this study, sediment, nodule, and water column samples were collected from the Clarion-Clipperton Zone of the Eastern North Pacific. The diversities of prokaryote and microeukaryote communities associated with these habitats were examined. Microbial community composition and diversity varied with habitat type, water column depth, and sediment horizon. Thaumarchaeota were relatively enriched in the sediments and nodules compared to the water column, whereas Gammaproteobacteria were the most abundant sequences associated with nodules. Among the Eukaryota, rRNA genes belonging to the Cryptomonadales were relatively most abundant among organisms associated with nodules, whereas rRNA gene sequences deriving from members of the Alveolata were relatively enriched in sediments and the water column. Nine operational taxonomic unit (OTU)s were identified that occur in all nodules in this dataset, as well as all nodules found in a study 3000-9000 km from our site. Microbial communities in the sediments had the highest diversity, followed by nodules, and then by the water column with <1/3 the number of OTUs as in the sediments.}, }
@article {pmid27863329, year = {2017}, author = {Vandeweyer, D and Crauwels, S and Lievens, B and Van Campenhout, L}, title = {Microbial counts of mealworm larvae (Tenebrio molitor) and crickets (Acheta domesticus and Gryllodes sigillatus) from different rearing companies and different production batches.}, journal = {International journal of food microbiology}, volume = {242}, number = {}, pages = {13-18}, doi = {10.1016/j.ijfoodmicro.2016.11.007}, pmid = {27863329}, issn = {1879-3460}, mesh = {Animals ; Europe ; Food Contamination/*analysis ; Food Safety ; Fungi/growth &amp; development/isolation &amp; purification ; Gryllidae/*microbiology ; Humans ; Larva/*microbiology ; Listeria monocytogenes/growth &amp; development/isolation &amp; purification ; Salmonella/growth &amp; development/isolation &amp; purification ; Tenebrio/*microbiology ; }, abstract = {The rising interest in insects for human consumption and the changing regulations in Europe require a profound insight into the food safety of insects reared and sold in Western society. The microbial quality of edible insects has only been studied occasionally. This study aimed at generating an overview of intrinsic parameters (pH, water activity and moisture content) and microbial quality of fresh mealworm larvae and crickets for several rearing companies and for several batches per rearer. In total, 21 batches obtained from 7 rearing companies were subjected to analysis of intrinsic parameters, a range of plate counts and presence-absence tests for Salmonella spp. and Listeria monocytogenes. The microbial counts of the fresh insects were generally high. Different rearing batches from a single rearing company showed differences in microbial counts which could not be explained by variations in intrinsic properties. The largest variations were found in numbers of bacterial endospores, psychrotrophs and fungi. Salmonella spp. and L. monocytogenes were not detected in any of the samples. Altogether, our study shows that large variations were found between batches from individual rearers. As a consequence, no overall differences between rearers could be observed.}, }
@article {pmid27862555, year = {2017}, author = {Vanhove, M and Beale, MA and Rhodes, J and Chanda, D and Lakhi, S and Kwenda, G and Molloy, S and Karunaharan, N and Stone, N and Harrison, TS and Bicanic, T and Fisher, MC}, title = {Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African HIV/AIDS cohort.}, journal = {Molecular ecology}, volume = {26}, number = {7}, pages = {1991-2005}, pmid = {27862555}, issn = {1365-294X}, support = {G1100814/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adaptation, Physiological/*genetics ; Cryptococcus gattii/*genetics ; Cryptococcus neoformans/*genetics ; DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; *Forests ; Genetics, Population ; Genome, Fungal ; Genomics ; Humans ; Meningitis, Cryptococcal/epidemiology/*microbiology ; Models, Biological ; Phylogeny ; Plant Bark/microbiology ; Polymorphism, Single Nucleotide ; Soil Microbiology ; Trees/microbiology ; Zambia ; }, abstract = {Emerging infections caused by fungi have become a widely recognized global phenomenon and are causing an increasing burden of disease. Genomic techniques are providing new insights into the structure of fungal populations, revealing hitherto undescribed fine-scale adaptations to environments and hosts that govern their emergence as infections. Cryptococcal meningitis is a neglected tropical disease that is responsible for a large proportion of AIDS-related deaths across Africa; however, the ecological determinants that underlie a patient's risk of infection remain largely unexplored. Here, we use genome sequencing and ecological genomics to decipher the evolutionary ecology of the aetiological agents of cryptococcal meningitis, Cryptococcus neoformans and Cryptococcus gattii, across the central African country of Zambia. We show that the occurrence of these two pathogens is differentially associated with biotic (macroecological) and abiotic (physical) factors across two key African ecoregions, Central Miombo woodlands and Zambezi Mopane woodlands. We show that speciation of Cryptococcus has resulted in adaptation to occupy different ecological niches, with C. neoformans found to occupy Zambezi Mopane woodlands and C. gattii primarily recovered from Central Miombo woodlands. Genome sequencing shows that C. neoformans causes 95% of human infections in this region, of which over three-quarters belonged to the globalized lineage VNI. We show that VNI infections are largely associated with urbanized populations in Zambia. Conversely, the majority of C. neoformans isolates recovered in the environment belong to the genetically diverse African-endemic lineage VNB, and we show hitherto unmapped levels of genomic diversity within this lineage. Our results reveal the complex evolutionary ecology that underpins the reservoirs of infection for this, and likely other, deadly pathogenic fungi.}, }
@article {pmid27862531, year = {2017}, author = {Kohl, KD and Brun, A and Magallanes, M and Brinkerhoff, J and Laspiur, A and Acosta, JC and Caviedes-Vidal, E and Bordenstein, SR}, title = {Gut microbial ecology of lizards: insights into diversity in the wild, effects of captivity, variation across gut regions and transmission.}, journal = {Molecular ecology}, volume = {26}, number = {4}, pages = {1175-1189}, doi = {10.1111/mec.13921}, pmid = {27862531}, issn = {1365-294X}, mesh = {Animals ; Bacteria/*classification ; Feces ; Gastrointestinal Tract/*microbiology ; Lizards/*microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Animals maintain complex associations with a diverse microbiota living in their guts. Our understanding of the ecology of these associations is extremely limited in reptiles. Here, we report an in-depth study into the microbial ecology of gut communities in three syntopic and viviparous lizard species (two omnivores: Liolaemus parvus and Liolaemus ruibali and an herbivore: Phymaturus williamsi). Using 16S rRNA gene sequencing to inventory various bacterial communities, we elucidate four major findings: (i) closely related lizard species harbour distinct gut bacterial microbiota that remain distinguishable in captivity; a considerable portion of gut bacterial diversity (39.1%) in nature overlap with that found on plant material, (ii) captivity changes bacterial community composition, although host-specific communities are retained, (iii) faecal samples are largely representative of the hindgut bacterial community and thus represent acceptable sources for nondestructive sampling, and (iv) lizards born in captivity and separated from their mothers within 24 h shared 34.3% of their gut bacterial diversity with their mothers, suggestive of maternal or environmental transmission. Each of these findings represents the first time such a topic has been investigated in lizard hosts. Taken together, our findings provide a foundation for comparative analyses of the faecal and gastrointestinal microbiota of reptile hosts.}, }
@article {pmid27859123, year = {2016}, author = {de Carvalho, TS and Jesus, ED and Barlow, J and Gardner, TA and Soares, IC and Tiedje, JM and Moreira, FM}, title = {Land use intensification in the humid tropics increased both alpha and beta diversity of soil bacteria.}, journal = {Ecology}, volume = {97}, number = {10}, pages = {2760-2771}, doi = {10.1002/ecy.1513}, pmid = {27859123}, issn = {0012-9658}, mesh = {Agriculture ; Bacteria/genetics ; *Biodiversity ; *Forests ; RNA, Ribosomal, 16S ; Soil ; *Soil Microbiology ; }, abstract = {Anthropogenic pressures on tropical forests are rapidly intensifying, but our understanding of their implications for biological diversity is still very limited, especially with regard to soil biota, and in particular soil bacterial communities. Here we evaluated bacterial community composition and diversity across a gradient of land use intensity in the eastern Amazon from undisturbed primary forest, through primary forests varyingly disturbed by fire, regenerating secondary forest, pasture, and mechanized agriculture. Soil bacteria were assessed by paired-end Illumina sequencing of 16S rRNA gene fragments (V4 region). The resulting sequences were clustered into operational taxonomic units (OTU) at a 97% similarity threshold. Land use intensification increased the observed bacterial diversity (both OTU richness and community heterogeneity across space) and this effect was strongly associated with changes in soil pH. Moreover, land use intensification and subsequent changes in soil fertility, especially pH, altered the bacterial community composition, with pastures and areas of mechanized agriculture displaying the most contrasting communities in relation to undisturbed primary forest. Together, these results indicate that tropical forest conversion impacts soil bacteria not through loss of diversity, as previously thought, but mainly by imposing marked shifts on bacterial community composition, with unknown yet potentially important implications for ecological functions and services performed by these communities.}, }
@article {pmid27856622, year = {2017}, author = {Grimaldi, R and Cela, D and Swann, JR and Vulevic, J and Gibson, GR and Tzortzis, G and Costabile, A}, title = {In vitro fermentation of B-GOS: impact on faecal bacterial populations and metabolic activity in autistic and non-autistic children.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {2}, pages = {}, pmid = {27856622}, issn = {1574-6941}, mesh = {Anti-Bacterial Agents ; Autistic Disorder/*microbiology ; Bacteroides/metabolism ; Bifidobacterium/growth &amp; development/metabolism ; *Child ; Clostridium/metabolism ; Fatty Acids, Volatile/metabolism ; Feces/*microbiology ; *Fermentation ; Humans ; In Situ Hybridization, Fluorescence ; Lactic Acid ; Lactobacillus/metabolism ; Microbiota ; Oligosaccharides/metabolism ; *Prebiotics ; }, abstract = {Children with autism spectrum disorders (ASD) often suffer gastrointestinal problems consistent with imbalances in the gut microbial population. Treatment with antibiotics or pro/prebiotics has been postulated to regulate microbiota and improve gut symptoms, but there is a lack of evidence for such approaches, especially for prebiotics. This study assessed the influence of a prebiotic galactooligosaccharide (B-GOS) on gut microbial ecology and metabolic function using faecal samples from autistic and non-autistic children in an in vitro gut model system. Bacteriology was analysed using flow cytometry combined with fluorescence in situ hybridization and metabolic activity by HPLC and [1]H-NMR. Consistent with previous studies, the microbiota of children with ASD contained a higher number of Clostridium spp. and a lower number of bifidobacteria compared with non-autistic children. B-GOS administration significantly increased bifidobacterial populations in each compartment of the models, both with autistic and non-autistic-derived samples, and lactobacilli in the final vessel of non-autistic models. In addition, changes in other bacterial population have been seen in particular for Clostridium, Rosburia, Bacteroides, Atopobium, Faecalibacterium prausnitzii, Sutterella spp. and Veillonellaceae. Furthermore, the addition of B-GOS to the models significantly altered short-chain fatty acid production in both groups, and increased ethanol and lactate in autistic children.}, }
@article {pmid27856567, year = {2017}, author = {Hücker, SM and Simon, S and Scherer, S and Neuhaus, K}, title = {Transcriptional and translational regulation by RNA thermometers, riboswitches and the sRNA DsrA in Escherichia coli O157:H7 Sakai under combined cold and osmotic stress adaptation.}, journal = {FEMS microbiology letters}, volume = {364}, number = {2}, pages = {}, doi = {10.1093/femsle/fnw262}, pmid = {27856567}, issn = {1574-6968}, mesh = {Adaptation, Physiological ; *Cold Temperature ; Escherichia coli O157/*genetics ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Nucleic Acid Conformation ; *Osmotic Pressure ; Protein Biosynthesis ; RNA, Bacterial/chemistry/genetics/*metabolism ; RNA, Double-Stranded/chemistry/genetics/metabolism ; *Riboswitch ; Sodium Chloride/metabolism ; Transcription, Genetic ; }, abstract = {The enteric pathogen Escherichia coli O157:H7 Sakai (EHEC) is able to grow at lower temperatures compared to commensal E. coli Growth at environmental conditions displays complex challenges different to those in a host. EHEC was grown at 37°C and at 14°C with 4% NaCl, a combination of cold and osmotic stress as present in the food chain. Comparison of RNAseq and RIBOseq data provided a snap shot of ongoing transcription and translation, differentiating transcriptional and post-transcriptional gene regulation, respectively. Indeed, cold and osmotic stress related genes are simultaneously regulated at both levels, but translational regulation clearly dominates. Special emphasis was given to genes regulated by RNA secondary structures in their 5[']UTRs, such as RNA thermometers and riboswitches, or genes controlled by small RNAs encoded in trans The results reveal large differences in gene expression between short-time shock compared to adaptation in combined cold and osmotic stress. Whereas the majority of cold shock proteins, such as CspA, are translationally downregulated after adaptation, many osmotic stress genes are still significantly upregulated mainly translationally, but several also transcriptionally.}, }
@article {pmid27856278, year = {2017}, author = {Ahmad, F and Stedtfeld, RD and Waseem, H and Williams, MR and Cupples, AM and Tiedje, JM and Hashsham, SA}, title = {Most probable number - loop mediated isothermal amplification (MPN-LAMP) for quantifying waterborne pathogens in &lt;25min.}, journal = {Journal of microbiological methods}, volume = {132}, number = {}, pages = {27-33}, pmid = {27856278}, issn = {1872-8359}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, mesh = {Azides/chemistry ; Colony Count, Microbial ; DNA, Bacterial/*isolation &amp; purification ; Enterococcus faecalis/*isolation &amp; purification ; Escherichia coli/*isolation &amp; purification ; Food Contamination ; Food Microbiology ; Genes, Bacterial ; Microbial Viability ; Microfluidic Analytical Techniques ; Propidium/analogs &amp; derivatives/chemistry ; Real-Time Polymerase Chain Reaction ; Sensitivity and Specificity ; Signal-To-Noise Ratio ; *Water Microbiology ; }, abstract = {We are reporting a most probable number approach integrated to loop mediated isothermal technique (MPN-LAMP) focusing on Gram-negative Escherichia coli and Gram-positive Enterococcus faecalis bacterial cells without nucleic acids extraction. LAMP assays for uidA from E. coli and gelE from E. faecalis were successfully performed directly on cells up to single digit concentration using a commercial real time PCR instrument. Threshold time values of LAMP assays of bacterial cells, heat treated bacterial cells (95°C for 5min), and their purified genomic DNA templates were similar, implying that amplification could be achieved directly from bacterial cells at 63°C. Viability of bacterial cells was confirmed by using propidium monoazide in a LAMP assay with E. faecalis. To check its functionality on a microfluidic platform, MPN-LAMP assays targeting <10CFU of bacteria were also translated onto polymeric microchips and monitored by a low-cost fluorescence imaging system. The overall system provided signal-to-noise (SNR) ratios up to 800, analytical sensitivity of <10CFU, and time to positivity of about 20min. MPN-LAMP assays were performed for cell concentrations in the range of 10[5]CFU to <10CFU. MPN values from LAMP assays confirmed that the amplifications were from <10CFU. The method described here, applicable directly on cells at 63°C, eliminates the requirement of complex nucleic acids extraction steps, facilitating the development of sensitive, rapid, low-cost, and field-deployable systems. This rapid MPN-LAMP approach has the potential to replace conventional MPN method for waterborne pathogens.}, }
@article {pmid27853840, year = {2017}, author = {Lambais, MR and Barrera, SE and Santos, EC and Crowley, DE and Jumpponen, A}, title = {Phyllosphere Metaproteomes of Trees from the Brazilian Atlantic Forest Show High Levels of Functional Redundancy.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {123-134}, pmid = {27853840}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Base Sequence ; Biodiversity ; Brazil ; DNA, Bacterial/*genetics ; Forests ; Microbiota/*genetics ; Phylogeny ; Plant Leaves/*microbiology ; Proteome/*analysis/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Trees/*microbiology ; }, abstract = {The phyllosphere of the Brazilian Atlantic Forest has been estimated to contain several million bacterial species that are associated with approximately 20000 plant species. Despite the high bacterial diversity in the phyllosphere, the function of these microorganisms and the mechanisms driving their community assembly are largely unknown. In this study, we characterized the bacterial communities in the phyllospheres of four tree species of the Atlantic Forest (Mollinedia schottiana, Ocotea dispersa, Ocotea teleiandra, and Tabebuia serratifolia) and their metaproteomes to examine the basic protein functional groups expressed in the phyllosphere. Bacterial community analyses using 16S rRNA gene sequencing confirmed prior observations that plant species harbor distinct bacterial communities and that plants of the same taxon have more similar communities than more distantly related taxa. Using LC-ESI-Q-TOF, we identified 216 nonredundant proteins, based on 3503 peptide mass spectra. Most protein families were shared among the phyllosphere communities, suggesting functional redundancy despite differences in the species compositions of the bacterial communities. Proteins involved in glycolysis and anaerobic carbohydrate metabolism, solute transport, protein metabolism, cell motility, stress and antioxidant responses, nitrogen metabolism, and iron homeostasis were among the most frequently detected. In contrast to prior studies on crop plants and Arabidopsis, a low abundance of OTUs related to Methylobacterium and no proteins associated with the metabolism of one-carbon molecules were detected in the phyllospheres of the tree species studied here. Our data suggest that even though the phyllosphere bacterial communities of different tree species are phylogenetically diverse, their metaproteomes are functionally convergent with respect to traits required for survival on leaf surfaces.}, }
@article {pmid27844108, year = {2017}, author = {Haq, IU and Dini-Andreote, F and van Elsas, JD}, title = {Transcriptional Responses of the Bacterium Burkholderia terrae BS001 to the Fungal Host Lyophyllum sp. Strain Karsten under Soil-Mimicking Conditions.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {236-252}, pmid = {27844108}, issn = {1432-184X}, mesh = {Agaricales/*growth &amp; development/*metabolism ; Burkholderia/*genetics ; Chemotaxis/physiology ; DNA-Directed DNA Polymerase/biosynthesis ; Ethanolamine/metabolism ; Hyphae/growth &amp; development ; Mandelic Acids/metabolism ; Microbial Interactions/*physiology ; Oxidative Stress/physiology ; Sigma Factor/genetics ; Soil ; *Soil Microbiology ; Transcriptome/genetics ; }, abstract = {In this study, the mycosphere isolate Burkholderia terrae BS001 was confronted with the soil fungus Lyophyllum sp. strain Karsten on soil extract agar plates in order to examine its transcriptional responses over time. At the initial stages of the experiment (T1-day 3; T2-day 5), contact between both partner organisms was absent, whereas in the final stage (T3-day 8), the two populations made intimate physical contact. Overall, a strong modulation of the strain BS001 gene expression patterns was found. First, the stationary-phase sigma factor RpoS, and numerous genes under its control, were strongly expressed as a response to the soil extract agar, and this extended over the whole temporal regime. In the system, B. terrae BS001 apparently perceived the presence of the fungal hyphae already at the early experimental stages (T1, T2), by strongly upregulating a suite of chemotaxis and flagellar motility genes. With respect to specific metabolism and energy generation, a picture of differential involvement in different metabolic routes was obtained. Initial (T1, T2) up- or downregulation of ethanolamine and mandelate uptake and utilization pathways was substituted by a strong investment, in the presence of the fungus, in the expression of putative metabolic gene clusters (T3). Specifically at T3, five clustered genes that are potentially involved in energy generation coupled to an oxidative stress response, and two genes encoding short-chain dehydrogenases/oxidoreductases (SDR), were highly upregulated. In contrast, the dnaE2 gene (related to general stress response; encoding error-prone DNA polymerase) was transcriptionally downregulated at this stage. This study revealed that B. terrae BS001, from a stress-induced state, resulting from the soil extract agar milieu, responds positively to fungal hyphae that encroach upon it, in a temporally dynamic manner. The response is characterized by phases in which the modulation of (1) chemotaxis, (2) metabolic activity, and (3) oxidative stress responses are key mechanisms.}, }
@article {pmid27843713, year = {2016}, author = {DeMaere, MZ and Darling, AE}, title = {Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C).}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e2676}, pmid = {27843713}, issn = {2167-8359}, abstract = {BACKGROUND: Chromosome conformation capture, coupled with high throughput DNA sequencing in protocols like Hi-C and 3C-seq, has been proposed as a viable means of generating data to resolve the genomes of microorganisms living in naturally occuring environments. Metagenomic Hi-C and 3C-seq datasets have begun to emerge, but the feasibility of resolving genomes when closely related organisms (strain-level diversity) are present in the sample has not yet been systematically characterised.<br><br>METHODS: We developed a computational simulation pipeline for metagenomic 3C and Hi-C sequencing to evaluate the accuracy of genomic reconstructions at, above, and below an operationally defined species boundary. We simulated datasets and measured accuracy over a wide range of parameters. Five clustering algorithms were evaluated (2 hard, 3 soft) using an adaptation of the extended B-cubed validation measure.<br><br>RESULTS: When all genomes in a sample are below 95% sequence identity, all of the tested clustering algorithms performed well. When sequence data contains genomes above 95% identity (our operational definition of strain-level diversity), a naive soft-clustering extension of the Louvain method achieves the highest performance.<br><br>DISCUSSION: Previously, only hard-clustering algorithms have been applied to metagenomic 3C and Hi-C data, yet none of these perform well when strain-level diversity exists in a metagenomic sample. Our simple extension of the Louvain method performed the best in these scenarios, however, accuracy remained well below the levels observed for samples without strain-level diversity. Strain resolution is also highly dependent on the amount of available 3C sequence data, suggesting that depth of sequencing must be carefully considered during experimental design. Finally, there appears to be great scope to improve the accuracy of strain resolution through further algorithm development.}, }
@article {pmid27843490, year = {2016}, author = {De Vrieze, J and Regueiro, L and Props, R and Vilchez-Vargas, R and Jáuregui, R and Pieper, DH and Lema, JM and Carballa, M}, title = {Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion.}, journal = {Biotechnology for biofuels}, volume = {9}, number = {}, pages = {244}, pmid = {27843490}, issn = {1754-6834}, abstract = {BACKGROUND: The microbial community in anaerobic digestion is mainly monitored by means of DNA-based methods. This may lead to incorrect interpretation of the community parameters, because microbial abundance does not necessarily reflect activity. In this research, the difference between microbial community response on DNA (total community) and RNA (active community) based on the 16S rRNA (gene) with respect to salt concentration and response time was evaluated.<br><br>RESULTS: The application of higher NaCl concentrations resulted in a decrease in methane production. A stronger and faster response to salt concentration was observed on RNA level. This was reflected in terms of microbial community composition and organization, as richness, evenness, and overall diversity were differentially impacted. A higher divergence of community structure was observed on RNA level as well, indicating that total community composition depends on deterministic processes, while the active community is determined by stochastic processes. Methanosaeta was identified as the most abundant methanogen on DNA level, but its relative abundance decreased on RNA level, related to salt perturbation.<br><br>CONCLUSIONS: This research demonstrated the need for RNA-based community screening to obtain reliable information on actual community parameters and to identify key species that determine process stability.}, }
@article {pmid27842516, year = {2016}, author = {De Maayer, P and Cowan, DA}, title = {Comparative genomic analysis of the flagellin glycosylation island of the Gram-positive thermophile Geobacillus.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {913}, pmid = {27842516}, issn = {1471-2164}, mesh = {Biosynthetic Pathways ; Comparative Genomic Hybridization ; Flagellin/*genetics/*metabolism ; Gene Order ; *Genome, Bacterial ; *Genomics/methods ; Geobacillus/classification/*genetics/*metabolism ; Glycosylation ; Phylogeny ; Polysaccharides/biosynthesis ; Quantitative Trait Loci ; Virulence ; }, abstract = {BACKGROUND: Protein glycosylation involves the post-translational attachment of sugar chains to target proteins and has been observed in all three domains of life. Post-translational glycosylation of flagellin, the main structural protein of the flagellum, is a common characteristic among many Gram-negative bacteria and Archaea. Several distinct functions have been ascribed to flagellin glycosylation, including stabilisation and maintenance of the flagellar filament, motility, surface recognition, adhesion, and virulence. However, little is known about this trait among Gram-positive bacteria.<br><br>RESULTS: Using comparative genomic approaches the flagellin glycosylation loci of multiple strains of the Gram-positive thermophilic genus Geobacillus were identified and characterized. Eighteen of thirty-six compared strains of the genus carry these loci, which show evidence of horizontal acquisition. The Geobacillus flagellin glycosylation islands (FGIs) can be clustered into five distinct types, which are predicted to encode highly variable glycans decorated with distinct and heavily modified sugars.<br><br>CONCLUSIONS: Our comparative genomic analyses showed that, while not universal, flagellin glycosylation islands are relatively common among members of the genus Geobacillus and that the encoded flagellin glycans are highly variable. This suggests that flagellin glycosylation plays an important role in the lifestyles of members of this thermophilic genus.}, }
@article {pmid27838765, year = {2017}, author = {Liu, X and Chen, CR and Hughes, JM and Wang, WJ and Lewis, T}, title = {Temporal Changes Rather than Long-Term Repeated Burning Predominately Control the Shift in the Abundance of Soil Denitrifying Community in an Australian Sclerophyll Forest.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {177-187}, pmid = {27838765}, issn = {1432-184X}, mesh = {Australia ; Bacteria/*classification/genetics/*metabolism ; Denitrification ; Fires ; Forests ; Nitrite Reductase (NAD(P)H)/genetics ; Oxidoreductases/genetics ; RNA, Ribosomal, 16S/genetics ; Rain ; Soil/*chemistry ; *Soil Microbiology ; Trees/*microbiology ; }, abstract = {To understand the temporal dynamics of soil bacterial denitrifying community in response to long-term prescribed burning and its resilience and recovery following a fire, a wet sclerophyll forest study site under two treatments (2 yearly burning (2YB) and no burning (NB)) and with 40-year-old burning history was used. Similar temporal patterns in the abundance of total (16S rRNA) and denitrifying (narG, nirK, nirS, nosZ) bacteria between two burning treatments revealed strong temporal influences. The magnitude of burning impacts on the abundance of 16S rRNA and denitrification genes was smaller compared with the impact of sampling time, but significant burning and temporal impacts were recorded for all (P < 0.001)-except for the nirS gene. Impacts of prescribed fire on the abundance of soil denitrifying community could be observed immediately after fire, and this impact diminished over a 24-month period prior to the next prescribed burning event. In conclusion, temporal changes govern the fluctuations of the abundance of soil denitrifying genes over the sampling period and the denitrifying community can recover after fire, suggesting that this community is resilient to the effects of prescribed burning. A combination of biotic and abiotic factors may account for the different temporal dynamics of denitrification gene abundance.}, }
@article {pmid27838764, year = {2017}, author = {Lynn, TM and Ge, T and Yuan, H and Wei, X and Wu, X and Xiao, K and Kumaresan, D and Yu, SS and Wu, J and Whiteley, AS}, title = {Soil Carbon-Fixation Rates and Associated Bacterial Diversity and Abundance in Three Natural Ecosystems.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {645-657}, pmid = {27838764}, issn = {1432-184X}, mesh = {Autotrophic Processes/genetics/*physiology ; Bacteria/enzymology/genetics/*metabolism ; Carbon/metabolism ; Carbon Cycle/*physiology ; Carbon Dioxide/*metabolism ; DNA, Bacterial/genetics ; Forests ; Grassland ; Ribulose-Bisphosphate Carboxylase/metabolism ; Soil/chemistry ; *Soil Microbiology ; Wetlands ; }, abstract = {CO2 assimilation by autotrophic microbes is an important process in soil carbon cycling, and our understanding of the community composition of autotrophs in natural soils and their role in carbon sequestration of these soils is still limited. Here, we investigated the autotrophic C incorporation in soils from three natural ecosystems, i.e., wetland (WL), grassland (GR), and forest (FO) based on the incorporation of labeled C into the microbial biomass. Microbial assimilation of [14]C ([14]C-MBC) differed among the soils from three ecosystems, accounting for 14.2-20.2% of [14]C-labeled soil organic carbon ([14]C-SOC). We observed a positive correlation between the cbbL (ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large-subunit gene) abundance, [14]C-SOC level, and [14]C-MBC concentration confirming the role of autotrophic bacteria in soil carbon sequestration. Distinct cbbL-bearing bacterial communities were present in each soil type; form IA and form IC RubisCO-bearing bacteria were most abundant in WL, followed by GR soils, with sequences from FO soils exclusively derived from the form IC clade. Phylogenetically, the diversity of CO2-fixing autotrophs and CO oxidizers differed significantly with soil type, whereas cbbL-bearing bacterial communities were similar when assessed using coxL. We demonstrate that local edaphic factors such as pH and salinity affect the C-fixation rate as well as cbbL and coxL gene abundance and diversity. Such insights into the effect of soil type on the autotrophic bacterial capacity and subsequent carbon cycling of natural ecosystems will provide information to enhance the sustainable management of these important natural ecosystems.}, }
@article {pmid27838508, year = {2017}, author = {Cheng, X and Liu, J and Li, J and Zhou, X and Wang, L and Liu, J and Xu, X}, title = {Comparative effect of a stannous fluoride toothpaste and a sodium fluoride toothpaste on a multispecies biofilm.}, journal = {Archives of oral biology}, volume = {74}, number = {}, pages = {5-11}, doi = {10.1016/j.archoralbio.2016.10.030}, pmid = {27838508}, issn = {1879-1506}, mesh = {Biofilms/classification/*drug effects ; Drug Screening Assays, Antitumor ; In Situ Hybridization, Fluorescence/methods ; Microbial Viability/drug effects ; Models, Biological ; Porphyromonas gingivalis/drug effects/growth &amp; development ; Real-Time Polymerase Chain Reaction/methods ; Sodium Fluoride/*antagonists &amp; inhibitors ; Species Specificity ; Streptococcus mutans/drug effects/growth &amp; development ; Streptococcus sanguis/drug effects/growth &amp; development ; Time Factors ; Tin Fluorides/*antagonists &amp; inhibitors ; Toothpastes/chemistry/*pharmacology ; }, abstract = {OBJECTIVES: This paper aimed to compare the mode of action of a stannous fluoride-containing toothpaste with a conventional sodium fluoride-containing toothpaste on anti-biofilm properties.<br><br>METHODS: A three-species biofilm model that consists of Streptococcus mutans, Streptococcus sanguinis and Porphyromonas gingivalis was established to compare the anti-biofilm properties of a stannous fluoride-containing toothpaste (CPH), a conventional sodium fluoride-containing toothpaste (CCP) and a negative control (PBS). The 48h biofilms were subjected to two-minute episodes of treatment with test agents twice a day for 5 consecutive days. Crystal violet staining and XTT assays were used to evaluate the biomass and viability of the treated biofilm. Live/dead staining and bacteria/extracellular polysaccharides (EPS) double-staining were used to visualize the biofilm structure and to quantify microbial/extracellular components of the treated biofilms. Species-specific fluorescent in situ hybridization and quantitative polymerase chain reaction (qPCR) were used to analyze microbial composition of the biofilms after treatment.<br><br>RESULTS: The biomass and viability of the biofilms were significantly reduced after CPH toothpaste treatment. The inhibitory effect was further confirmed by the live/dead staining. The EPS amounts of the three-species biofilm were significantly reduced by CCP and CPH treatments, and CPH toothpaste demonstrated significant inhibition on EPS production. More importantly, CPH toothpaste significantly suppressed S. mutans and P. gingvalis, and enriched S. sanguinis in the three-species biofilm. In all experiments CPH had a significantly greater effect than CCP (p<0.05) and CCP had a greater effect than PBS (p<0.05).<br><br>CONCLUSIONS: Stannous fluoride-containing toothpaste not only showed better inhibitory effect against oral microbial biofilm, but was also able to modulate microbial composition within multi-species biofilm compared with conventional sodium fluoride-containing toothpaste.}, }
@article {pmid27838466, year = {2017}, author = {Starke, R and Müller, M and Gaspar, M and Marz, M and Küsel, K and Totsche, KU and von Bergen, M and Jehmlich, N}, title = {Candidate Brocadiales dominates C, N and S cycling in anoxic groundwater of a pristine limestone-fracture aquifer.}, journal = {Journal of proteomics}, volume = {152}, number = {}, pages = {153-160}, doi = {10.1016/j.jprot.2016.11.003}, pmid = {27838466}, issn = {1876-7737}, mesh = {Bacteria/*isolation &amp; purification/metabolism ; Biodiversity ; Calcium Carbonate ; Carbon/*metabolism ; Ecosystem ; Groundwater/*microbiology ; Nitrogen/*metabolism ; Phylogeny ; Planctomycetales/*metabolism ; Sulfur/*metabolism ; }, abstract = {UNLABELLED: Groundwater-associated microorganisms are known to play an important role in the biogeochemical C, N and S cycling. Metaproteomics was applied to characterize the diversity and the activity of microbes to identify key species in major biogeochemical processes in the anoxic groundwater of a pristine karstic aquifer located in Hainich, central Germany. Sampling was achieved by pumping 1000L water from two sites of the upper aquifer assemblage and filtration on 0.3μm glass filters. In total, 3808 protein groups were identified. Interestingly, the two wells (H4/2 and H5/2) differed not only in microbial density but also in the prevalence of different C, N and S cycling pathways. The well H5/2 was dominated by the anaerobic ammonia-oxidizing (anammox) candidate Brocadiales (31%) while other orders such as Burkholderiales (2%) or Nitrospirales (3%) were less abundant. Otherwise, the well H4/2 featured only low biomass and remarkably fewer proteins (391 to 3631 at H5/2). Candidate Brocadiales was affiliated to all major carbon fixation strategies, and to the cycling of N and S implying a major role in biogeochemical processes of groundwater aquifers. The findings of our study support functions which can be linked to the ecosystem services provided by the microbial communities present in aquifers.<br><br>SIGNIFICANCE: Subsurface environments especially the groundwater ecosystems represent a large habitat for microbial activity. Microbes are responsible for energy and nutrient cycling and are massively involved in the planet's sustainability. Microbial diversity is tremendous and the central question in current microbial ecology is "Who eats what, where and when?". In this study, we characterize a natural aquifer inhabiting microbial community to obtain evidence for the phylogenetic diversity and the metabolic activity by protein abundance and we highlight important biogeochemical cycling processes. The aquifer was dominated by Candidatus Brocadiales while other phylotypes such as Burkholderiales, Caulobacterales and Nitrospirales were less abundant. The candidate comprised all major carbon fixation strategies, ammonification, anammox and denitrification as well as assimilatory sulfate reduction. Our findings have broad implications for the understanding of microbial activities in this aquifer and consequently specific functions can be linked to the ecosystem services provided by the microbial communities present in aquifers.}, }
@article {pmid27837253, year = {2017}, author = {Branchiccela, B and Arredondo, D and Higes, M and Invernizzi, C and Martín-Hernández, R and Tomasco, I and Zunino, P and Antúnez, K}, title = {Characterization of Nosema ceranae Genetic Variants from Different Geographic Origins.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {978-987}, pmid = {27837253}, issn = {1432-184X}, mesh = {Animal Diseases/microbiology ; Animals ; Antimicrobial Cationic Peptides/genetics/metabolism ; Bees/genetics/immunology/*microbiology ; DNA, Fungal/chemistry ; Down-Regulation ; Gene Expression Regulation ; Genes, Fungal/genetics ; *Genetic Variation ; Geography ; Insect Proteins/genetics/metabolism ; Microsporidiosis/immunology/veterinary ; Muramidase/metabolism ; Nosema/classification/*genetics/*pathogenicity ; RNA, Fungal/chemistry ; Real-Time Polymerase Chain Reaction/methods ; }, abstract = {In recent years, large-scale colony losses of honey bees (Apis mellifera) have been reported and the infection with the microsporidia Nosema ceranae has been involved. However, the effect of N. ceranae at the colony level and its role in colony losses vary in different geographic areas. This difference may be related to the presence of multiple N. ceranae genetic variants resulting in different biological consequences. In this study, we analyzed the genetic diversity of 75 N. ceranae samples obtained from 13 countries and Hawaii through inter-sequence single repetition (ISSR) and evaluated if two of these genetic variants triggered different immune responses when infecting Apis mellifera iberiensis. The genetic diversity analysis showed that 41% of the samples had the same DNA amplification pattern, including samples from most European countries except Spain, while the remaining samples showed high variability. Infection assays were performed to analyze the infection levels and the immune response of bees infected with N. ceranae from Spain and Uruguay. The infected bees presented similar infection levels, and both isolates downregulated the expression of abaecin, confirming the ability of the microsporidia to depress the immune response. Only N. ceranae from Uruguay downregulated the expression level of imd compared to control bees. On the other hand, both genetic variants triggered different expression levels of lysozyme. As imd and lysozyme play important roles in the response to pathogens, these results could reflect differences in the biological consequences of N. ceranae variants in A. mellifera infection.}, }
@article {pmid27837252, year = {2017}, author = {Cañavate, JP and Armada, I and Hachero-Cruzado, I}, title = {Polar Lipids Analysis of Cultured Phytoplankton Reveals Significant Inter-taxa Changes, Low Influence of Growth Stage, and Usefulness in Chemotaxonomy.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {755-774}, pmid = {27837252}, issn = {1432-184X}, mesh = {Betaine/analysis ; Biodiversity ; Biomass ; Chlorophyta/chemistry/classification ; Classification ; Diatoms/chemistry/classification ; Glycolipids/metabolism ; Lipids/*analysis/*chemistry ; Marine Biology ; Microalgae/chemistry/classification/growth &amp; development ; Phosphatidylcholines/metabolism ; Phosphatidylethanolamines/metabolism ; Phosphatidylglycerols/metabolism ; Phospholipids/analysis ; Phytoplankton/*chemistry/*classification/*growth &amp; development ; Species Specificity ; }, abstract = {The high lipid diversity of microalgae has been used to taxonomically differentiate phytoplankton taxa at the class level. However, important lipids such as phospholipids (PL) and betaine lipids (BL) with potential chemotaxonomy application in phytoplankton ecology have been scarcely studied. The chemotaxonomy value of PL and BL depends on their intraspecific extent of variation as microalgae respond to external changing factors. To determine such effects, lipid class changes occurring at different growth stages in 15 microalgae from ten different classes were analyzed. BL occurred in 14 species and were the less affected lipids by growth stage with diacylglyceryl-hydroxymethyl-N,N,N-trimethyl-b-alanine (DGTA) showing the highest stability. PL were more influenced by growth stage with phosphatidylcholine (PC), phosphatidylglycerol (PG), and phosphatidyletanolamine (PE) declining towards older culture stages in some species. Glycolipids were the more common lipids, and no evident age-related variability pattern could be associated to taxonomic diversity. Selecting BL and PL as descriptor variables optimally distinguished microalgae taxonomic variability at all growth stages. Principal coordinate analysis arranged species through a main tendency from diacylglyceryl-hydroxymethyl-N,N,N-trimethyl-b-alanine (DGCC) containing species (mainly dinoflagellates and haptophytes) to DGTA or PC containing species (mainly cryptophytes). Two diatom classes with similar fatty acid profiles could be distinguished from their respective content in DGTA (Bacillariophyceae) or DGCC (Mediophyceae). In green lineage classes (Trebouxiophyceae, Porphyridophyceae, and Chlorodendrophyceae), PC was a better descriptor than BL. BL and PL explained a higher proportion of microalgae taxonomic variation than did fatty acids and played a complementary role as lipid markers.}, }
@article {pmid27836842, year = {2017}, author = {Hoetzinger, M and Schmidt, J and Jezberová, J and Koll, U and Hahn, MW}, title = {Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {3}, pages = {}, pmid = {27836842}, issn = {1098-5336}, support = {I 482/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Austria ; Burkholderiaceae/*genetics/growth &amp; development ; *Genetic Variation ; *Genome, Bacterial ; *Genomic Islands ; Phylogeny ; Ponds/*microbiology ; }, abstract = {UNLABELLED: Microdiversification of a planktonic freshwater bacterium was studied by comparing 37 Polynucleobacter asymbioticus strains obtained from three geographically separated sites in the Austrian Alps. Genome comparison of nine strains revealed a core genome of 1.8 Mb, representing 81% of the average genome size. Seventy-five percent of the remaining flexible genome is clustered in genomic islands (GIs). Twenty-four genomic positions could be identified where GIs are potentially located. These positions are occupied strain specifically from a set of 28 GI variants, classified according to similarities in their gene content. One variant, present in 62% of the isolates, encodes a pathway for the degradation of aromatic compounds, and another, found in 78% of the strains, contains an operon for nitrate assimilation. Both variants were shown in ecophysiological tests to be functional, thus providing the potential for microniche partitioning. In addition, detected interspecific horizontal exchange of GIs indicates a large gene pool accessible to Polynucleobacter species. In contrast to core genes, GIs are spread more successfully across spatially separated freshwater habitats. The mobility and functional diversity of GIs allow for rapid evolution, which may be a key aspect for the ubiquitous occurrence of Polynucleobacter bacteria.<br><br>IMPORTANCE: Assessing the ecological relevance of bacterial diversity is a key challenge for current microbial ecology. The polyphasic approach which was applied in this study, including targeted isolation of strains, genome analysis, and ecophysiological tests, is crucial for the linkage of genetic and ecological knowledge. Particularly great importance is attached to the high number of closely related strains which were investigated, represented by genome-wide average nucleotide identities (ANI) larger than 97%. The extent of functional diversification found on this narrow phylogenetic scale is compelling. Moreover, the transfer of metabolically relevant genomic islands between more distant members of the Polynucleobacter community provides important insights toward a better understanding of the evolution of these globally abundant freshwater bacteria.}, }
@article {pmid27833995, year = {2017}, author = {Thomas, P and Sekhar, AC}, title = {Cultivation Versus Molecular Analysis of Banana (Musa sp.) Shoot-Tip Tissue Reveals Enormous Diversity of Normally Uncultivable Endophytic Bacteria.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {885-899}, pmid = {27833995}, issn = {1432-184X}, mesh = {Bacteria/*classification/*genetics/isolation &amp; purification ; Biodiversity ; Chloroplasts/genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; DNA, Ribosomal/genetics ; Ecosystem ; Endophytes/*classification/*genetics/isolation &amp; purification ; India ; Metagenome ; Metagenomics/methods ; Microbiota ; Mitochondria/genetics ; Musa/*microbiology ; *Phylogeny ; Plant Shoots/*growth &amp; development/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {The interior of plants constitutes a unique environment for microorganisms with various organisms inhabiting as endophytes. Unlike subterranean plant parts, aboveground parts are relatively less explored for endophytic microbial diversity. We employed a combination of cultivation and molecular approaches to study the endophytic bacterial diversity in banana shoot-tips. Cultivable bacteria from 20 sucker shoot-tips of cv. Grand Naine included 37 strains under 16 genera and three phyla (Proteobacteria, Actinobacteria, Firmicutes). 16S rRNA gene-ribotyping approach on 799f and 1492r PCR-amplicons to avoid plant organelle sequences was ineffective showing limited bacterial diversity. 16S rRNA metagene profiling targeting the V3-V4 hypervariable region after filtering out the chloroplast (74.2 %), mitochondrial (22.9 %), and unknown sequences (1.1 %) revealed enormous bacterial diversity. Proteobacteria formed the predominant phylum (64 %) succeeded by Firmicutes (12.1 %), Actinobacteria (9.5 %), Bacteroidetes (6.4 %), Planctomycetes, Cyanobacteria, and minor shares (<1 %) of 14 phyla including several candidate phyla besides the domain Euryarchaeota (0.2 %). Microbiome analysis of single shoot-tips through 16S rRNA V3 region profiling showed similar taxonomic richness and diversity and was less affected by plant sequence interferences. DNA extraction kit ominously influenced the phylogenetic diversity. The study has revealed vast diversity of normally uncultivable endophytic bacteria prevailing in banana shoot-tips (20 phyla, 46 classes) with about 2.6 % of the deciphered 269 genera and 1.5 % of the 656 observed species from the same source of shoot-tips attained through cultivation. The predominant genera included several agriculturally important bacteria. The study reveals an immense ecosystem of endophytic bacteria in banana shoot tissues endorsing the earlier documentation of intracellular "Cytobacts" and "Peribacts" with possible roles in plant holobiome and hologenome.}, }
@article {pmid27833591, year = {2016}, author = {Vila, T and Nazir, R and Rozental, S and Dos Santos, GM and Calixto, RO and Barreto-Bergter, E and Wick, LY and van Elsas, JD}, title = {The Role of Hydrophobicity and Surface Receptors at Hyphae of Lyophyllum sp. Strain Karsten in the Interaction with Burkholderia terrae BS001 - Implications for Interactions in Soil.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1689}, pmid = {27833591}, issn = {1664-302X}, abstract = {The soil bacterium Burkholderia terrae strain BS001 can interact with varying soil fungi, using mechanisms that range from the utilization of carbon/energy sources such as glycerol to the ability to reach novel territories in soil via co-migration with growing fungal mycelia. Here, we investigate the intrinsic properties of the B. terrae BS001 interaction with the basidiomycetous soil fungus Lyophyllum sp. strain Karsten. In some experiments, the ascomycetous Trichoderma asperellum 302 was also used. The hyphae of Lyophyllum sp. strain Karsten were largely hydrophilic on water-containing media versus hydrophobic when aerial, as evidenced by contact angle analyses (CA). Co-migration of B. terrae strain BS001 cells with the hyphae of the two fungi occurred preferentially along the - presumably hydrophilic - soil-dwelling hyphae, whereas aerial hyphae did not allow efficient migration, due to reduced thickness of their surrounding mucous films. Moreover, the cell numbers over the length of the hyphae in soil showed an uneven distribution, i.e., the CFU numbers increased from minima at the inoculation point to maximal numbers in the middle of the extended hyphae, then decreasing toward the terminal side. Microscopic analyses of the strain BS001 associations with the Lyophyllum sp. strain Karsten hyphae in the microcosms confirmed the presence of B. terrae BS001 cells on the mucous matter that was present at the hyphal surfaces of the fungi used. Cell agglomerates were found to accumulate at defined sites on the hyphal surfaces, which were coined 'fungal-interactive' hot spots. Evidence was further obtained for the contention that receptors for a physical bacterium-fungus interaction occur at the Lyophyllum sp. strain Karsten hyphal surface, in which the specific glycosphingolipid ceramide monohexoside (CMH) plays an important role. Thus, bacterial adherence may be mediated by heterogeneously distributed fungal-specific receptors, implying the CMH moieties. This study sheds light on the physical aspects of the B. terrae BS001 - Lyophyllum sp. strain Karsten interaction, highlighting heterogeneity along the hyphae with respect to hydrophobicity and the presence of potential anchoring sites.}, }
@article {pmid27832305, year = {2017}, author = {Sánchez, O}, title = {Constructed Wetlands Revisited: Microbial Diversity in the -omics Era.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {722-733}, pmid = {27832305}, issn = {1432-184X}, mesh = {Bacteria/*metabolism ; *Biodegradation, Environmental ; Biodiversity ; Waste Disposal, Fluid/*methods ; Wastewater/*microbiology ; Water Purification/*methods ; *Wetlands ; }, abstract = {Constructed wetlands (CWs) constitute an interesting alternative option to conventional systems for wastewater treatment. This technology is based on the utilization of the concerted activity of microorganisms for the removal of contaminants. Consequently, knowledge on the microbial assemblages dwelling CWs and the different environmental factors which can alter their activities is crucial for understanding their performance. In the last decades, the use of molecular techniques to characterize these communities and more recently, application of -omics tools, have broaden our view of microbial diversity and function in wastewater microbiology. In this manuscript, a review of the current knowledge on microbial diversity in CWs is offered, placing particular emphasis on the different molecular studies carried out in this field. The effect of environmental conditions, such as plant species, hydraulic design, water depth, organic carbon, temperature and substrate type on prokaryotic communities has been carefully revised, and the different studies highlight the importance of these factors in carbon, nitrogen and sulfur cycles. Overall, the novel -omics open a new horizon to study the diversity and ecophysiology of microbial assemblages and their interactions in CWs, particularly for those microorganisms belonging to the rare biosphere not detectable with conventional molecular techniques.}, }
@article {pmid27832214, year = {2016}, author = {Schloss, PD}, title = {Application of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking Methods.}, journal = {mSystems}, volume = {1}, number = {2}, pages = {}, pmid = {27832214}, issn = {2379-5077}, abstract = {Assignment of 16S rRNA gene sequences to operational taxonomic units (OTUs) allows microbial ecologists to overcome the inconsistencies and biases within bacterial taxonomy and provides a strategy for clustering similar sequences that do not have representatives in a reference database. I have applied the Matthews correlation coefficient to assess the ability of 15 reference-independent and -dependent clustering algorithms to assign sequences to OTUs. This metric quantifies the ability of an algorithm to reflect the relationships between sequences without the use of a reference and can be applied to any data set or method. The most consistently robust method was the average neighbor algorithm; however, for some data sets, other algorithms matched its performance.}, }
@article {pmid27832154, year = {2016}, author = {Defoirdt, T}, title = {Implications of Ecological Niche Differentiation in Marine Bacteria for Microbial Management in Aquaculture to Prevent Bacterial Disease.}, journal = {PLoS pathogens}, volume = {12}, number = {11}, pages = {e1005843}, pmid = {27832154}, issn = {1553-7374}, mesh = {Animals ; Aquaculture/*methods ; *Bacteria ; Bacterial Infections/*veterinary ; Seafood/*microbiology ; }, }
@article {pmid27825829, year = {2016}, author = {Bouhajja, E and Agathos, SN and George, IF}, title = {Metagenomics: Probing pollutant fate in natural and engineered ecosystems.}, journal = {Biotechnology advances}, volume = {34}, number = {8}, pages = {1413-1426}, doi = {10.1016/j.biotechadv.2016.10.006}, pmid = {27825829}, issn = {1873-1899}, mesh = {*Biodegradation, Environmental ; *Ecosystem ; *Environmental Pollutants/analysis/chemistry/isolation &amp; purification/metabolism ; Metabolic Networks and Pathways/genetics ; Metagenome/*genetics ; *Metagenomics ; Microbial Consortia/*genetics ; }, abstract = {Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field. In this review, we survey the main steps of metagenomics applied to environments contaminated with organic compounds or heavy metals. We emphasize technical solutions proposed to overcome encountered obstacles. We then compare two metagenomic approaches, i.e. library-based targeted metagenomics and direct sequencing of metagenomes. In the former, environmental DNA is cloned inside a host, and then clones of interest are selected based on (i) their expression of biodegradative functions or (ii) sequence homology with probes and primers designed from relevant, already known sequences. The highest score for the discovery of novel genes and degradation pathways has been achieved so far by functional screening of large clone libraries. On the other hand, direct sequencing of metagenomes without a cloning step has been more often applied to polluted environments for characterization of the taxonomic and functional composition of microbial communities and their dynamics. In this case, the analysis has focused on 16S rRNA genes and marker genes of biodegradation. Advances in next generation sequencing and in bioinformatic analysis of sequencing data have opened up new opportunities for assessing the potential of biodegradation by microbes, but annotation of collected genes is still hampered by a limited number of available reference sequences in databases. Although metagenomics is still facing technical and computational challenges, our review of the recent literature highlights its value as an aid to efficiently monitor the clean-up of contaminated environments and develop successful strategies to mitigate the impact of pollutants on ecosystems.}, }
@article {pmid27824274, year = {2017}, author = {Van Herreweghen, F and Van den Abbeele, P and De Mulder, T and De Weirdt, R and Geirnaert, A and Hernandez-Sanabria, E and Vilchez-Vargas, R and Jauregui, R and Pieper, DH and Belzer, C and De Vos, WM and Van de Wiele, T}, title = {In vitro colonisation of the distal colon by Akkermansia muciniphila is largely mucin and pH dependent.}, journal = {Beneficial microbes}, volume = {8}, number = {1}, pages = {81-96}, doi = {10.3920/BM2016.0013}, pmid = {27824274}, issn = {1876-2891}, mesh = {Colon/*microbiology ; Epithelium ; Humans ; Hydrogen-Ion Concentration ; Models, Biological ; Mucins/*metabolism ; *Prebiotics ; Verrucomicrobia/*physiology ; }, abstract = {Host mucin is the main constituent of the mucus layer that covers the gut epithelium of the host, and an important source of glycans for the bacteria colonising the intestine. Akkermansia muciniphila is a mucin-degrading bacterium, abundant in the human gut, that is able to produce acetate and propionate during this degradation process. A. muciniphila has been correlated with human health in previous studies, but a mechanistic explanation is lacking. In this study, the main site of colonisation was characterised alongside additional conditions, such as differences in colon pH, prebiotic supplementation and variable mucin supply. To overcome the limitations of in vivo studies concerning variations in mucin availability and difficult access to proximal regions of the colon, a dynamic in vitro gut model (SHIME) was used. In this model, A. muciniphila was found to colonise the distal colon compartment more abundantly than the proximal colon ((±8 log copies/ml compared to ±4 log copies/ml) and the preference for the distal compartment was found to be pH-dependent. The addition of mucin caused a specific increase of A. muciniphila (±4.5 log increase over two days), far exceeding the response of other bacteria present, together with an increase in propionate. These findings suggest that colonisation and mucin degradation by A. muciniphila is dependent on pH and the concentration of mucin. Our results revealed the preference of A. muciniphila for the distal colon environment due to its higher pH and uncovered the quick and stable response of A. muciniphila to mucin supplementation.}, }
@article {pmid27822618, year = {2017}, author = {Zdanowski, MK and Bogdanowicz, A and Gawor, J and Gromadka, R and Wolicka, D and Grzesiak, J}, title = {Enrichment of Cryoconite Hole Anaerobes: Implications for the Subglacial Microbiome.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {532-538}, pmid = {27822618}, issn = {1432-184X}, mesh = {Actinobacteria/classification/genetics/*isolation &amp; purification ; Anaerobiosis/physiology ; Bacteria, Anaerobic/classification/genetics/isolation &amp; purification ; Bacteroidetes/classification/genetics/*isolation &amp; purification ; Base Sequence ; Ecosystem ; Fresh Water/microbiology ; Geologic Sediments/*microbiology ; High-Throughput Nucleotide Sequencing ; Ice Cover/*microbiology ; Planctomycetales/classification/genetics/*isolation &amp; purification ; Proteobacteria/classification/genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Glaciers have recently been recognized as ecosystems comprised of several distinct habitats: a sunlit and oxygenated glacial surface, glacial ice, and a dark, mostly anoxic glacial bed. Surface meltwaters annually flood the subglacial sediments by means of drainage channels. Glacial surfaces host aquatic microhabitats called cryoconite holes, regarded as "hot spots" of microbial abundance and activity, largely contributing to the meltwaters' bacterial diversity. This study presents an investigation of cryoconite hole anaerobes and discusses their possible impact on subglacial microbial communities, combining 16S rRNA gene fragment amplicon sequencing and the traditional enrichment culture technique. Cryoconite hole sediment harbored bacteria belonging mainly to the Proteobacteria (21%), Bacteroidetes (16%), Actinobacteria (14%), and Planctomycetes (6%) phyla. An 8-week incubation of those sediments in Postgate C medium for sulfate reducers in airtight bottles, emulating subglacial conditions, eliminated a great majority of dominant taxa, leading to enrichment of the Firmicutes (62%), Proteobacteria (14%), and Bacteroidetes (13%), which consisted of anaerobic genera like Clostridium, Psychrosinus, Paludibacter, and Acetobacterium. Enrichment of Pseudomonas spp. also occurred, suggesting it played a role as a dominant oxygen scavenger, providing a possible scenario for anaerobic niche establishment in subglacial habitats. To our knowledge, this is the first paper to provide insight into the diversity of the anaerobic part of the cryoconite hole microbial community and its potential to contribute to matter turnover in anoxic, subglacial sites.}, }
@article {pmid27822556, year = {2016}, author = {Knudsen, BE and Bergmark, L and Munk, P and Lukjancenko, O and Priemé, A and Aarestrup, FM and Pamp, SJ}, title = {Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition.}, journal = {mSystems}, volume = {1}, number = {5}, pages = {}, pmid = {27822556}, issn = {2379-5077}, abstract = {Explorations of complex microbiomes using genomics greatly enhance our understanding about their diversity, biogeography, and function. The isolation of DNA from microbiome specimens is a key prerequisite for such examinations, but challenges remain in obtaining sufficient DNA quantities required for certain sequencing approaches, achieving accurate genomic inference of microbiome composition, and facilitating comparability of findings across specimen types and sequencing projects. These aspects are particularly relevant for the genomics-based global surveillance of infectious agents and antimicrobial resistance from different reservoirs. Here, we compare in a stepwise approach a total of eight commercially available DNA extraction kits and 16 procedures based on these for three specimen types (human feces, pig feces, and hospital sewage). We assess DNA extraction using spike-in controls and different types of beads for bead beating, facilitating cell lysis. We evaluate DNA concentration, purity, and stability and microbial community composition using 16S rRNA gene sequencing and for selected samples using shotgun metagenomic sequencing. Our results suggest that inferred community composition was dependent on inherent specimen properties as well as DNA extraction method. We further show that bead beating or enzymatic treatment can increase the extraction of DNA from Gram-positive bacteria. Final DNA quantities could be increased by isolating DNA from a larger volume of cell lysate than that in standard protocols. Based on this insight, we designed an improved DNA isolation procedure optimized for microbiome genomics that can be used for the three examined specimen types and potentially also for other biological specimens. A standard operating procedure is available from https://dx.doi.org/10.6084/m9.figshare.3475406. IMPORTANCE Sequencing-based analyses of microbiomes may lead to a breakthrough in our understanding of the microbial worlds associated with humans, animals, and the environment. Such insight could further the development of innovative ecosystem management approaches for the protection of our natural resources and the design of more effective and sustainable solutions to prevent and control infectious diseases. Genome sequence information is an organism (pathogen)-independent language that can be used across sectors, space, and time. Harmonized standards, protocols, and workflows for sample processing and analysis can facilitate the generation of such actionable information. In this study, we assessed several procedures for the isolation of DNA for next-generation sequencing. Our study highlights several important aspects to consider in the design and conduct of sequence-based analysis of microbiomes. We provide a standard operating procedure for the isolation of DNA from a range of biological specimens particularly relevant in clinical diagnostics and epidemiology.}, }
@article {pmid27822539, year = {2016}, author = {Herren, CM and Webert, KC and McMahon, KD}, title = {Environmental Disturbances Decrease the Variability of Microbial Populations within Periphyton.}, journal = {mSystems}, volume = {1}, number = {3}, pages = {}, pmid = {27822539}, issn = {2379-5077}, abstract = {A central pursuit of microbial ecology is to accurately model changes in microbial community composition in response to environmental factors. This goal requires a thorough understanding of the drivers of variability in microbial populations. However, most microbial ecology studies focus on the effects of environmental factors on mean population abundances, rather than on population variability. Here, we imposed several experimental disturbances upon periphyton communities and analyzed the variability of populations within disturbed communities compared with those in undisturbed communities. We analyzed both the bacterial and the diatom communities in the periphyton under nine different disturbance regimes, including regimes that contained multiple disturbances. We found several similarities in the responses of the two communities to disturbance; all significant treatment effects showed that populations became less variable as the result of environmental disturbances. Furthermore, multiple disturbances to these communities were often interactive, meaning that the effects of two disturbances could not have been predicted from studying single disturbances in isolation. These results suggest that environmental factors had repeatable effects on populations within microbial communities, thereby creating communities that were more similar as a result of disturbances. These experiments add to the predictive framework of microbial ecology by quantifying variability in microbial populations and by demonstrating that disturbances can place consistent constraints on the abundance of microbial populations. Although models will never be fully predictive due to stochastic forces, these results indicate that environmental stressors may increase the ability of models to capture microbial community dynamics because of their consistent effects on microbial populations. IMPORTANCE There are many reasons why microbial community composition is difficult to model. For example, the high diversity and high rate of change of these communities make it challenging to identify causes of community turnover. Furthermore, the processes that shape community composition can be either deterministic, which cause communities to converge upon similar compositions, or stochastic, which increase variability in community composition. However, modeling microbial community composition is possible only if microbes show repeatable responses to extrinsic forcing. In this study, we hypothesized that environmental stress acts as a deterministic force that shapes microbial community composition. Other studies have investigated if disturbances can alter microbial community composition, but relatively few studies ask about the repeatability of the effects of disturbances. Mechanistic models implicitly assume that communities show consistent responses to stressors; here, we define and quantify microbial variability to test this assumption. Author Video: An author video summary of this article is available.}, }
@article {pmid27822523, year = {2016}, author = {Bryson, S and Li, Z and Pett-Ridge, J and Hettich, RL and Mayali, X and Pan, C and Mueller, RS}, title = {Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton.}, journal = {mSystems}, volume = {1}, number = {2}, pages = {}, pmid = {27822523}, issn = {2379-5077}, abstract = {Heterotrophic marine bacterioplankton are a critical component of the carbon cycle, processing nearly a quarter of annual primary production, yet defining how substrate utilization preferences and resource partitioning structure microbial communities remains a challenge. In this study, proteomic stable isotope probing (proteomic SIP) was used to characterize population-specific assimilation of dissolved free amino acids (DFAAs), a major source of dissolved organic carbon for bacterial secondary production in aquatic environments. Microcosms of seawater collected from Newport, Oregon, and Monterey Bay, California, were incubated with 1 µM [13]C-labeled amino acids for 15 and 32 h. The taxonomic compositions of microcosm metaproteomes were highly similar to those of the sampled natural communities, with Rhodobacteriales, SAR11, and Flavobacteriales representing the dominant taxa. Analysis of [13]C incorporation into protein biomass allowed for quantification of the isotopic enrichment of identified proteins and subsequent determination of differential amino acid assimilation patterns between specific bacterioplankton populations. Proteins associated with Rhodobacterales tended to have a significantly high frequency of [13]C-enriched peptides, opposite the trend for Flavobacteriales and SAR11 proteins. Rhodobacterales proteins associated with amino acid transport and metabolism had an increased frequency of [13]C-enriched spectra at time point 2. Alteromonadales proteins also had a significantly high frequency of [13]C-enriched peptides, particularly within ribosomal proteins, demonstrating their rapid growth during incubations. Overall, proteomic SIP facilitated quantitative comparisons of DFAA assimilation by specific taxa, both between sympatric populations and between protein functional groups within discrete populations, allowing an unprecedented examination of population level metabolic responses to resource acquisition in complex microbial communities. IMPORTANCE An estimated 50 gigatons of carbon is annually fixed within marine systems, of which heterotrophic microbial populations process nearly half. These communities vary in composition and activity across spatial and temporal scales, so understanding how these changes affect global processes requires the delineation of functional roles for individual members. In a step toward ascertaining these roles, we applied proteomic stable isotope probing to quantify the assimilation of organic carbon from DFAAs into microbial protein biomass, since the turnover of DFAAs accounts for a substantial fraction of marine microbial carbon metabolism that is directed into biomass production. We conducted experiments at two coastal North Pacific locations and found taxonomically distinct responses. This approach allowed us to compare amino acid assimilation by specific bacterioplankton populations and characterize their allocation of this substrate among cellular functions.}, }
@article {pmid27822518, year = {2016}, author = {Walters, W and Hyde, ER and Berg-Lyons, D and Ackermann, G and Humphrey, G and Parada, A and Gilbert, JA and Jansson, JK and Caporaso, JG and Fuhrman, JA and Apprill, A and Knight, R}, title = {Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys.}, journal = {mSystems}, volume = {1}, number = {1}, pages = {}, pmid = {27822518}, issn = {2379-5077}, abstract = {Designing primers for PCR-based taxonomic surveys that amplify a broad range of phylotypes in varied community samples is a difficult challenge, and the comparability of data sets amplified with varied primers requires attention. Here, we examined the performance of modified 16S rRNA gene and internal transcribed spacer (ITS) primers for archaea/bacteria and fungi, respectively, with nonaquatic samples. We moved primer bar codes to the 5' end, allowing for a range of different 3' primer pairings, such as the 515f/926r primer pair, which amplifies variable regions 4 and 5 of the 16S rRNA gene. We additionally demonstrated that modifications to the 515f/806r (variable region 4) 16S primer pair, which improves detection of Thaumarchaeota and clade SAR11 in marine samples, do not degrade performance on taxa already amplified effectively by the original primer set. Alterations to the fungal ITS primers did result in differential but overall improved performance compared to the original primers. In both cases, the improved primers should be widely adopted for amplicon studies. IMPORTANCE We continue to uncover a wealth of information connecting microbes in important ways to human and environmental ecology. As our scientific knowledge and technical abilities improve, the tools used for microbiome surveys can be modified to improve the accuracy of our techniques, ensuring that we can continue to identify groundbreaking connections between microbes and the ecosystems they populate, from ice caps to the human body. It is important to confirm that modifications to these tools do not cause new, detrimental biases that would inhibit the field rather than continue to move it forward. We therefore demonstrated that two recently modified primer pairs that target taxonomically discriminatory regions of bacterial and fungal genomic DNA do not introduce new biases when used on a variety of sample types, from soil to human skin. This confirms the utility of these primers for maintaining currently recommended microbiome research techniques as the state of the art.}, }
@article {pmid27818507, year = {2016}, author = {Arendt, D and Musser, JM and Baker, CVH and Bergman, A and Cepko, C and Erwin, DH and Pavlicev, M and Schlosser, G and Widder, S and Laubichler, MD and Wagner, GP}, title = {The origin and evolution of cell types.}, journal = {Nature reviews. Genetics}, volume = {17}, number = {12}, pages = {744-757}, pmid = {27818507}, issn = {1471-0064}, mesh = {Animals ; *Biological Evolution ; *Cell Differentiation ; *Cell Lineage ; Cells/classification/*cytology ; *Gene Regulatory Networks ; Humans ; Phylogeny ; }, abstract = {Cell types are the basic building blocks of multicellular organisms and are extensively diversified in animals. Despite recent advances in characterizing cell types, classification schemes remain ambiguous. We propose an evolutionary definition of a cell type that allows cell types to be delineated and compared within and between species. Key to cell type identity are evolutionary changes in the 'core regulatory complex' (CoRC) of transcription factors, that make emergent sister cell types distinct, enable their independent evolution and regulate cell type-specific traits termed apomeres. We discuss the distinction between developmental and evolutionary lineages, and present a roadmap for future research.}, }
@article {pmid27816988, year = {2017}, author = {Parafati, L and Cirvilleri, G and Restuccia, C and Wisniewski, M}, title = {Potential Role of Exoglucanase Genes (WaEXG1 and WaEXG2) in the Biocontrol Activity of Wickerhamomyces anomalus.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {876-884}, pmid = {27816988}, issn = {1432-184X}, mesh = {Antibiosis/*physiology ; *Biological Control Agents ; Botrytis/drug effects/pathogenicity ; Cell Wall/chemistry ; Cellulases/biosynthesis/classification/*genetics/*pharmacology ; Cellulose 1,4-beta-Cellobiosidase/biosynthesis/genetics/pharmacology ; Culture Media/chemistry ; DNA Primers ; DNA, Fungal/genetics ; Food Microbiology ; Fruit/microbiology ; Gene Expression Regulation, Fungal ; Genes, Essential ; Glucose/metabolism ; Penicillium/drug effects/pathogenicity ; Plant Diseases/microbiology ; RNA, Fungal/analysis ; Real-Time Polymerase Chain Reaction/methods ; Saccharomycetales/*enzymology/*genetics/growth &amp; development/physiology ; Vitis/microbiology ; Yeasts ; }, abstract = {The use of yeasts, including Wickerhamomyces anomalus, as biocontrol agents of fungi responsible for postharvest diseases of fruits and vegetables has been investigated for the past two decades. Among a variety of mechanisms, the production of glucanases coded by the "killer genes" WaEXG1 and WaEXG2 have been reported to play a role in the ability of yeast to inhibit other fungi. The objective of the present study was to determine the expression of these genes by RT-qPCR, utilizing gene-specific primers, when W. anomalus was grown on grape berries and oranges that were either non-inoculated or inoculated with Botrytis cinerea or Penicillium digitatum, or in minimal media supplemented with cell walls of various plant pathogens and different amounts of glucose. Results indicated that WaEXG2 was more responsive than WaEXG1 to the nutritional environment (including the addition of glucose to cell wall-amended media) in vitro and appeared to play a greater role in the cellular metabolism of W. anomalus. WaEXG2 expression also appeared to be more responsive to the presence of cell walls of P. digitatum and B. cinerea than other fungal species, whereas the same level of induction was not seen in vivo when the yeast was grown in wounded/pathogen-inoculated fruits.}, }
@article {pmid27815590, year = {2017}, author = {Zhuang, L and Ma, J and Tang, J and Tang, Z and Zhou, S}, title = {Cysteine-Accelerated Methanogenic Propionate Degradation in Paddy Soil Enrichment.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {916-924}, pmid = {27815590}, issn = {1432-184X}, mesh = {Anaerobiosis ; Archaea/classification/drug effects/genetics/metabolism ; Bacteria/classification/drug effects/genetics/metabolism ; Biodegradation, Environmental/*drug effects ; Cysteine/administration &amp; dosage/*pharmacology ; DNA, Archaeal/analysis/isolation &amp; purification ; DNA, Bacterial/analysis/isolation &amp; purification ; Electron Transport/drug effects ; Formates/metabolism ; Hydrogen/metabolism ; Kinetics ; Methane/analysis/*metabolism ; Methanobacteriaceae/metabolism ; Microbial Consortia/genetics ; Oxidation-Reduction ; Phylogeny ; Propionates/analysis/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {Propionate degradation is a critical step during the conversion of complex organic matter under methanogenic conditions, and it requires a syntrophic cooperation between propionate-oxidizing bacteria and methanogenic archaea. Increasing evidences suggest that interspecies electron transfer for syntrophic metabolism is not limited to the reducing equivalents of hydrogen and formate. This study tested the ability of an electron shuttle to mediate interspecies electron transfer in syntrophic methanogenesis. We found that cysteine supplementation (100, 400, and 800 μM) accelerated CH4 production from propionate in paddy soil enrichments. Of the concentrations tested, 100 μM cysteine was the most effective at enhancing propionate degradation to CH4, and the rates of CH4 production and propionate degradation were increased by 109 and 79%, respectively, compared with the cysteine-free control incubations. We eliminated the possibility that the stimulatory effect of cysteine on methanogenesis was attributable to the function of cysteine as a methanogenic substrate in the presence of propionate. The potential catalytic effect involved cysteine serving as an electron carrier to mediate interspecies electron transfer in syntrophic propionate oxidization. The redox potential of cystine/cysteine, which is dependent on the concentration, might be more suitable to facilitate interspecies electron transfer between syntrophic partners at a concentration of 100 μM. Pelotomaculum, obligately syntrophic, propionate-oxidizing bacteria, and hydrogenotrophic methanogens of the family Methanobacteriaceae are predominant in cysteine-mediated methanogenic propionate degradation. The stimulatory effect of cysteine on syntrophic methanogenesis offers remarkable potential for improving the performance of anaerobic digestion and conceptually broaden strategies for interspecies electron transfer in syntrophic metabolism.}, }
@article {pmid27815589, year = {2017}, author = {Torralba, MG and Franks, JS and Gomez, A and Yooseph, S and Nelson, KE and Grimes, DJ}, title = {Effect of Macondo Prospect 252 Oil on Microbiota Associated with Pelagic Sargassum in the Northern Gulf of Mexico.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {91-100}, pmid = {27815589}, issn = {1432-184X}, mesh = {Actinobacteria/*classification/genetics/isolation &amp; purification ; Bacteroidetes/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Environment ; Environmental Monitoring/*methods ; Firmicutes/*classification/genetics/isolation &amp; purification ; Gulf of Mexico ; Microbiota/genetics ; Oil and Gas Industry ; Petroleum/toxicity ; *Petroleum Pollution ; Proteobacteria/*classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sargassum/growth &amp; development/*microbiology ; Seawater/chemistry/microbiology ; Verrucomicrobia/*classification/genetics/isolation &amp; purification ; }, abstract = {The environmental impact of major oil spills on marine microorganisms has yet to be thoroughly investigated using molecular biology techniques. The Deepwater Horizon (DWH) drilling rig explosion of 2010 affected an approximately 176,000 km[2] surface area of the Gulf of Mexico (GOM) when an estimated 210 million gallons of oil from the Macondo Prospect spilled into the environment. Pelagic Sargassum, a complex of two surface drifting species (Sargassum natans and Sargassum fluitans) of marine brown macroalgae and a critically important habitat in the GOM ecosystem, was suffused by Macondo Prospect 252 oil released during the DWH event. Using 16S rRNA PCR and Roche 454 pyrosequencing, the effect of the oil on the bacterial population associated with pelagic Sargassum and contiguous waters was examined by comparing sequence data generated from samples collected from oiled and non-oiled locations in the northern GOM. Sequence data showed similar microbial composition in Sargassum regardless of exposure to oil primarily dominated by five phyla; Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, and unclassified bacteria. The microbial composition in water samples was significantly less diverse than for Sargassum and consisted primarily of Proteobacteria, Firmicutes, and Bacteroidetes. Due to the evenly distributed abundance of microbial species on oiled and non-oiled pelagic Sargassum, study findings indicate that DWH spilled oil had minimal effect on the composition and diversity of the microbial community associated with Sargassum and contiguous waters. However, higher abundances of Sulfitobacter and one species of Psychrobacter were found in oiled water samples when compared to non-oiled water samples indicating some effect of DHW oil in the microbial composition of seawater. Though there are a number of marine studies using molecular biology approaches, this is the first molecular examination of the impact of the DWH oil spill on bacterial communities associated with pelagic Sargassum and contiguous waters from the GOM.}, }
@article {pmid27814897, year = {2017}, author = {Coats, ER and Brinkman, CK and Lee, S}, title = {Characterizing and contrasting the microbial ecology of laboratory and full-scale EBPR systems cultured on synthetic and real wastewaters.}, journal = {Water research}, volume = {108}, number = {}, pages = {124-136}, pmid = {27814897}, issn = {1879-2448}, support = {P20 GM103408/GM/NIGMS NIH HHS/United States ; }, mesh = {Bioreactors/microbiology ; Glycerol ; *Phosphorus ; Polyphosphates ; Rhodocyclaceae ; Wastewater/*microbiology ; }, abstract = {The anthropogenic discharge of phosphorus (P) into surface waters can induce the proliferation of cyanobacteria and algae, which can negatively impact water quality. Enhanced biological P removal (EBPR) is an engineered process that can be employed to efficiently remove significant quantities of P from wastewater. Within this engineered system, the mixed microbial consortium (MMC) becomes enriched with polyphosphate accumulating organisms (PAOs). To date much knowledge has been developed on PAOs, and the EBPR process is generally well understood; nonetheless, the engineered process remains underutilized. In this study, investigations were conducted using qPCR and Illumina MiSeq to assess the impacts of wastewater (synthetic vs. real) on EBPR microbial ecology. While a strong relationship was demonstrated between EBPR metrics (P:C; influent VFA:P) and excellent P removal across diverse EBPR systems and MMCs, no such correlations existed with the specific MMCs. Moreover, MMCs exhibited distinct clusters based on substrate, and qPCR results based on the putative PAO Accumulibacter did not correlate with BLASTN eubacterial results for either Accumulibacter or Rhodocyclaceae. More critically, PAO-based sequences aligned poorly with Accumulibacter for both eubacterial and PAO primer sets, which strongly suggests that the conventional PAO primers applied in FISH and qPCR analysis do not sufficiently target the putative PAO Accumulibacter. In particular, negligible alignment was observed for PAO amplicons obtained from a MMC performing excellent EBPR on crude glycerol (an atypical substrate). A synthetic wastewater-based MMC exhibited the best observed BLASTN match of the PAO amplicons, raising concerns about the potential relevance in using synthetic substrates in the study of EBPR.}, }
@article {pmid27814552, year = {2016}, author = {Rafraf, ID and Lekunberri, I and Sànchez-Melsió, A and Aouni, M and Borrego, CM and Balcázar, JL}, title = {Abundance of antibiotic resistance genes in five municipal wastewater treatment plants in the Monastir Governorate, Tunisia.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {219}, number = {}, pages = {353-358}, doi = {10.1016/j.envpol.2016.10.062}, pmid = {27814552}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents/*analysis ; Cities ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial/*drug effects ; *Integrons ; Sewage/*chemistry ; Tunisia ; Waste Disposal, Fluid/*methods ; Wastewater/*analysis ; }, abstract = {Antimicrobial resistance is a growing and significant threat to global public health, requiring better understanding of the sources and mechanisms involved in its emergence and spread. We investigated the abundance of antibiotic resistance genes (ARGs) before and after treatment in five wastewater treatment plants (WWTPs) located in different areas of the Monastir Governorate (Tunisia). Three of these WWTPs (Frina, Sahline and Zaouiet) use a conventional activated sludge process as secondary treatment, whereas the WWTP located in Beni Hassen applies an ultraviolet disinfection step after the activated sludge process and the WWTP located in Moknine treats wastewater using naturally aerated lagoons as a secondary treatment process. The abundance of six ARGs (blaCTX-M, blaTEM, qnrA, qnrS, sul I and ermB) and the class 1 integron-integrase gene (intI1) were determined by quantitative PCR. All ARGs and the intI1 gene were detected in the wastewater samples, except the blaCTX-M gene, which was not detected in both influent and effluent samples from Sahline and Beni Hassen WWTPs, and the qnrS gene, which was not detected neither in the WWTP influent in Moknine nor in the WWTP effluent in Beni Hassen. Although the relative concentration of ARGs was generally found to be similar between samples collected before and after the wastewater treatment, the abundance of blaCTX-M, blaTEM, and qnrS genes was higher in the effluent of the Frina WWTP which, unlike other WWTPs, not only receives domestic or industrial sewage but also untreated hospital waste. To the best of our knowledge, this study quantified for the first time the abundance of ARGs in different Tunisian WWTPs, and the results agree with previous studies suggesting that conventional wastewater treatment does not efficiently reduce ARGs. Therefore, these findings could be useful to improve the design or operation of WWTPs.}, }
@article {pmid27811967, year = {2016}, author = {Yang, GL and Hou, SG and Le Baoge, R and Li, ZG and Xu, H and Liu, YP and Du, WT and Liu, YQ}, title = {Differences in Bacterial Diversity and Communities Between Glacial Snow and Glacial Soil on the Chongce Ice Cap, West Kunlun Mountains.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {36548}, pmid = {27811967}, issn = {2045-2322}, mesh = {Bacteria/*genetics ; Biodiversity ; Ecosystem ; Ice Cover/*microbiology ; Snow/*microbiology ; Soil ; }, abstract = {A detailed understanding of microbial ecology in different supraglacial habitats is important due to the unprecedented speed of glacier retreat. Differences in bacterial diversity and community structure between glacial snow and glacial soil on the Chongce Ice Cap were assessed using 454 pyrosequencing. Based on rarefaction curves, Chao1, ACE, and Shannon indices, we found that bacterial diversity in glacial snow was lower than that in glacial soil. Principal coordinate analysis (PCoA) and heatmap analysis indicated that there were major differences in bacterial communities between glacial snow and glacial soil. Most bacteria were different between the two habitats; however, there were some common bacteria shared between glacial snow and glacial soil. Some rare or functional bacterial resources were also present in the Chongce Ice Cap. These findings provide a preliminary understanding of the shifts in bacterial diversity and communities from glacial snow to glacial soil after the melting and inflow of glacial snow into glacial soil.}, }
@article {pmid27810887, year = {2016}, author = {Campanharo, JC and Kielak, AM and Castellane, TCL and Kuramae, EE and Lemos, EGM}, title = {Optimized medium culture for Acidobacteria subdivision 1 strains.}, journal = {FEMS microbiology letters}, volume = {363}, number = {21}, pages = {}, doi = {10.1093/femsle/fnw245}, pmid = {27810887}, issn = {1574-6968}, abstract = {Members of subdivision 1 of the phylum Acidobacteria were grown at different pH values in a new medium formulation named PSYL 5, which includes sucrose as a carbon source and other compounds (such as KH2PO4 and MgSO4.7H2O). Growth rate was nearly constant at pH 5.0 and declined at pH 3-4 and 6-7. However, it was found that effects involving good carbon/nitrogen ratios and pH on the growth of the members of Acidobacteria subdivision 1 were significant, and the strongest effect of these conditions was at pH 5.0. In addition, incubation time of 48, 72, 96 and 120 h was shorter than that described previously for members of Acidobacteria subdivision 1 on solid laboratory media.}, }
@article {pmid27789346, year = {2016}, author = {Diesner, SC and Bergmayr, C and Pfitzner, B and Assmann, V and Krishnamurthy, D and Starkl, P and Endesfelder, D and Rothballer, M and Welzl, G and Rattei, T and Eiwegger, T and Szépfalusi, Z and Fehrenbach, H and Jensen-Jarolim, E and Hartmann, A and Pali-Schöll, I and Untersmayr, E}, title = {A distinct microbiota composition is associated with protection from food allergy in an oral mouse immunization model.}, journal = {Clinical immunology (Orlando, Fla.)}, volume = {173}, number = {}, pages = {10-18}, pmid = {27789346}, issn = {1521-7035}, support = {KLI 284/FWF_/Austrian Science Fund FWF/Austria ; P 21884/FWF_/Austrian Science Fund FWF/Austria ; WKP 39/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Administration, Oral ; Allergens/administration &amp; dosage ; Anaphylaxis/immunology/*microbiology ; Animals ; Anti-Ulcer Agents/pharmacology ; Bacteria/isolation &amp; purification ; Cytokines/immunology ; Disease Models, Animal ; Feces/microbiology ; Female ; Food Hypersensitivity/immunology/*microbiology ; Gastric Acid ; Immunization ; Immunoglobulin A/immunology ; Immunoglobulin E/immunology ; Immunoglobulin G/immunology ; Intestines/anatomy &amp; histology/immunology ; Mice, Inbred BALB C ; *Microbiota ; Ovalbumin/administration &amp; dosage/blood ; Spleen/cytology/immunology ; Stomach/anatomy &amp; histology/immunology ; Sucralfate/pharmacology ; }, abstract = {In our mouse model, gastric acid-suppression is associated with antigen-specific IgE and anaphylaxis development. We repeatedly observed non-responder animals protected from food allergy. Here, we aimed to analyse reasons for this protection. Ten out of 64 mice, subjected to oral ovalbumin (OVA) immunizations under gastric acid-suppression, were non-responders without OVA-specific IgE or IgG1 elevation, indicating protection from allergy. In these non-responders, allergen challenges confirmed reduced antigen uptake and lack of anaphylactic symptoms, while in allergic mice high levels of mouse mast-cell protease-1 and a body temperature reduction, indicative for anaphylaxis, were determined. Upon OVA stimulation, significantly lower IL-4, IL-5, IL-10 and IL-13 levels were detected in non-responders, while IL-22 was significantly higher. Comparison of fecal microbiota revealed differences of bacterial communities on single bacterial Operational-Taxonomic-Unit level between the groups, indicating protection from food allergy being associated with a distinct microbiota composition in a non-responding phenotype in this mouse model.}, }
@article {pmid27807645, year = {2017}, author = {Argiroff, WA and Zak, DR and Lanser, CM and Wiley, MJ}, title = {Microbial Community Functional Potential and Composition Are Shaped by Hydrologic Connectivity in Riverine Floodplain Soils.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {630-644}, pmid = {27807645}, issn = {1432-184X}, mesh = {Base Sequence ; *Floods ; Gene Library ; High-Throughput Nucleotide Sequencing ; *Hydrology ; Metagenome/genetics ; Microbiota/*genetics ; Nitrogen/metabolism ; Rivers/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; *Wetlands ; }, abstract = {Riverine floodplains are ecologically and economically valuable ecosystems that are heavily threatened by anthropogenic stressors. Microbial communities in floodplain soils mediate critical biogeochemical processes, yet we understand little about the relationship between these communities and variation in hydrologic connectivity related to land management or topography. Here, we present metagenomic evidence that differences among microbial communities in three floodplain soils correspond to a long-term gradient of hydrologic connectivity. Specifically, all strictly anaerobic taxa and metabolic pathways were positively associated with increased hydrologic connectivity and flooding frequency. In contrast, most aerobic taxa and all strictly aerobic pathways were negatively related to hydrologic connectivity and flooding frequency. Furthermore, the genetic potential to metabolize organic compounds tended to decrease as hydrologic connectivity increased, which may reflect either the observed concomitant decline of soil organic matter or the parallel increase in both anaerobic taxa and pathways. A decline in soil N, accompanied by an increased genetic potential for oligotrophic N acquisition subsystems, suggests that soil nutrients also shape microbial communities in these soils. We conclude that differences among floodplain soil microbial communities can be conceptualized along a gradient of hydrologic connectivity. Additionally, we show that these differences are likely due to connectivity-related variation in flooding frequency, soil organic matter, and soil N. Our findings are particularly relevant to the restoration and management of microbially mediated biogeochemical processes in riverine floodplain wetlands.}, }
@article {pmid27807430, year = {2016}, author = {Conficoni, D and Losasso, C and Cortini, E and Di Cesare, A and Cibin, V and Giaccone, V and Corno, G and Ricci, A}, title = {Resistance to Biocides in Listeria monocytogenes Collected in Meat-Processing Environments.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1627}, pmid = {27807430}, issn = {1664-302X}, abstract = {The emergence of microorganisms exerting resistance to biocides is a challenge to meat-processing environments. Bacteria can be intrinsically resistant to biocides but resistance can also be acquired by adaptation to their sub-lethal concentrations. Moreover, the presence of biocide resistance determinants, which is closely linked to antibiotic resistance determinants, could lead to co-selection during disinfection practices along the food chain, and select cross-resistant foodborne pathogens. The purpose of this work was to test the resistance of wild strains of Listeria monocytogenes, isolated from pork meat processing plants, toward benzalkonium chloride (BC), used as proxy of quaternary ammonium compounds. Furthermore, the expression of two non-specific efflux pumps genes (lde and mdrL) under biocide exposure was evaluated. L. monocytogenes were isolated from five processing plants located in the Veneto region (northeast of Italy) before and after cleaning and disinfection (C&amp;D) procedures. A total of 45 strains were collected: 36 strains before and nine after the C&amp;D procedures. Collected strains were typed according to MLST and ERIC profiles. Strains sampled in the same site, isolated before, and after the C&amp;D procedures and displaying the same MLST and ERIC profiles were tested for their sensitivity to different concentrations of BC, in a time course assay. The expression of non-specific efflux pumps was evaluated at each time point by qPCR using tufA gene as housekeeping. A differential expression of the two investigated genes was observed: lde was found to be more expressed by the strains isolated before C&amp;D procedures while its expression was dose-dependent in the case of the post C&amp;D procedures strain. On the contrary, the expression of mdrL was inhibited under low biocidal stress (10 ppm BC) and enhanced in the presence of high stress (100 ppm BC). These findings suggests a possible role for C&amp;D procedures to select L. monocytogenes persisters, pointing out the importance of dealing with the identification of risk factors in food plants sanification procedures that might select more tolerant strains.}, }
@article {pmid27664049, year = {2017}, author = {Jensen, S and Fortunato, SA and Hoffmann, F and Hoem, S and Rapp, HT and Øvreås, L and Torsvik, VL}, title = {The Relative Abundance and Transcriptional Activity of Marine Sponge-Associated Microorganisms Emphasizing Groups Involved in Sulfur Cycle.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {668-676}, pmid = {27664049}, issn = {1432-184X}, mesh = {Acidobacteria/genetics/isolation &amp; purification/metabolism ; Alphaproteobacteria/genetics/isolation &amp; purification/metabolism ; Animals ; Biodiversity ; Chloroflexi/genetics/isolation &amp; purification/metabolism ; DNA, Bacterial/genetics ; Deltaproteobacteria/genetics/isolation &amp; purification/metabolism ; Euryarchaeota/genetics/isolation &amp; purification/metabolism ; Gammaproteobacteria/genetics/isolation &amp; purification/metabolism ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sulfur/*metabolism ; }, abstract = {During the last decades, our knowledge about the activity of sponge-associated microorganisms and their contribution to biogeochemical cycling has gradually increased. Functional groups involved in carbon and nitrogen metabolism are well documented, whereas knowledge about microorganisms involved in the sulfur cycle is still limited. Both sulfate reduction and sulfide oxidation has been detected in the cold water sponge Geodia barretti from Korsfjord in Norway, and with specimens from this site, the present study aims to identify extant versus active sponge-associated microbiota with focus on sulfur metabolism. Comparative analysis of small subunit ribosomal RNA (16S rRNA) gene (DNA) and transcript (complementary DNA (cDNA)) libraries revealed profound differences. The transcript library was predominated by Chloroflexi despite their low abundance in the gene library. An opposite result was found for Acidobacteria. Proteobacteria were detected in both libraries with representatives of the Alpha- and Gammaproteobacteria related to clades with presumably thiotrophic bacteria from sponges and other marine invertebrates. Sequences that clustered with sponge-associated Deltaproteobacteria were remotely related to cultivated sulfate-reducing bacteria. The microbes involved in sulfur cycling were identified by the functional gene aprA (adenosine-5'-phosphosulfate reductase) and its transcript. Of the aprA sequences (DNA and cDNA), 87 % affiliated with sulfur-oxidizing bacteria. They clustered with Alphaproteobacteria and with clades of deep-branching Gammaproteobacteria. The remaining sequences clustered with sulfate-reducing Archaea of the phylum Euryarchaeota. These results indicate an active role of yet uncharacterized Bacteria and Archaea in the sponge's sulfur cycle.}, }
@article {pmid27801908, year = {2017}, author = {Ponnudurai, R and Kleiner, M and Sayavedra, L and Petersen, JM and Moche, M and Otto, A and Becher, D and Takeuchi, T and Satoh, N and Dubilier, N and Schweder, T and Markert, S}, title = {Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis.}, journal = {The ISME journal}, volume = {11}, number = {2}, pages = {463-477}, pmid = {27801908}, issn = {1751-7370}, mesh = {Animals ; Biosynthetic Pathways ; Gammaproteobacteria/*physiology ; Gills/microbiology ; Hydrothermal Vents ; Methane/metabolism ; Mytilidae/genetics/*microbiology ; Oxidation-Reduction ; *Proteome ; Species Specificity ; Sulfur/metabolism ; *Symbiosis ; }, abstract = {The hydrothermal vent mussel Bathymodiolus azoricus lives in an intimate symbiosis with two types of chemosynthetic Gammaproteobacteria in its gills: a sulfur oxidizer and a methane oxidizer. Despite numerous investigations over the last decades, the degree of interdependence between the three symbiotic partners, their individual metabolic contributions, as well as the mechanism of carbon transfer from the symbionts to the host are poorly understood. We used a combination of proteomics and genomics to investigate the physiology and metabolism of the individual symbiotic partners. Our study revealed that key metabolic functions are most likely accomplished jointly by B. azoricus and its symbionts: (1) CO2 is pre-concentrated by the host for carbon fixation by the sulfur-oxidizing symbiont, and (2) the host replenishes essential biosynthetic TCA cycle intermediates for the sulfur-oxidizing symbiont. In return (3), the sulfur oxidizer may compensate for the host's putative deficiency in amino acid and cofactor biosynthesis. We also identified numerous 'symbiosis-specific' host proteins by comparing symbiont-containing and symbiont-free host tissues and symbiont fractions. These proteins included a large complement of host digestive enzymes in the gill that are likely involved in symbiont digestion and carbon transfer from the symbionts to the host.}, }
@article {pmid27429202, year = {2016}, author = {Roussel, C and Cordonnier, C and Galia, W and Le Goff, O and Thévenot, J and Chalancon, S and Alric, M and Thevenot-Sergentet, D and Leriche, F and Van de Wiele, T and Livrelli, V and Blanquet-Diot, S}, title = {Increased EHEC survival and virulence gene expression indicate an enhanced pathogenicity upon simulated pediatric gastrointestinal conditions.}, journal = {Pediatric research}, volume = {80}, number = {5}, pages = {734-743}, pmid = {27429202}, issn = {1530-0447}, mesh = {Adhesins, Bacterial/genetics/*metabolism ; Adult ; Child ; Enterohemorrhagic Escherichia coli/*genetics/*growth &amp; development/pathogenicity ; Escherichia coli Infections/*microbiology ; Escherichia coli O157/genetics/growth &amp; development/pathogenicity ; Flow Cytometry ; Gastric Mucosa/metabolism ; Humans ; Intestine, Small/metabolism ; Kinetics ; Models, Biological ; Shiga Toxin/genetics/*metabolism ; Virulence ; Virulence Factors/genetics/*metabolism ; }, abstract = {BACKGROUND: Enterohemorrhagic Escherichia coli (EHEC) are major foodborne pathogens that constitute a serious public health threat, mainly in young children. Shiga toxins (Stx) are the main virulence determinants of EHEC pathogenesis but adhesins like intimin (eae) and Long polar fimbriae (Lpf) also contribute to infection. The TNO GastroIntestinal Model (TIM) was used for a comparative study of EHEC O157:H7 survival and virulence under adult and child digestive conditions.<br><br>METHODS: Survival kinetics in the in vitro digestive tract were determined by plating while bacterial viability was assessed by flow cytometry analysis. Expression of stx, eae, and lpf genes was followed by reverse transcriptase-quantitative PCR (RT-qPCR) and Stx production was measured by ELISA (enzyme-linked immunosorbent assay).<br><br>RESULTS: Upon gastrointestinal passage, a higher amount of viable cells was found in the simulated ileal effluents of children compared to that of adults (with 34 and 6% of viable cells, respectively). Expression levels of virulence genes were up to 125-fold higher in children. Stx was detected only in child ileal effluents.<br><br>CONCLUSION: Differences in digestive physicochemical parameters may partially explain why children are more susceptible to EHEC infection than adults. Such data are essential for a full understanding of EHEC pathogenesis and would help in designing novel therapeutic approaches.}, }
@article {pmid27798598, year = {2016}, author = {Nguyen, DD and Melnik, AV and Koyama, N and Lu, X and Schorn, M and Fang, J and Aguinaldo, K and Lincecum, TL and Ghequire, MG and Carrion, VJ and Cheng, TL and Duggan, BM and Malone, JG and Mauchline, TH and Sanchez, LM and Kilpatrick, AM and Raaijmakers, JM and De Mot, R and Moore, BS and Medema, MH and Dorrestein, PC}, title = {Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides.}, journal = {Nature microbiology}, volume = {2}, number = {}, pages = {16197}, pmid = {27798598}, issn = {2058-5276}, support = {S10 RR029121/RR/NCRR NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; P41 GM103484/GM/NIGMS NIH HHS/United States ; R01 GM097509/GM/NIGMS NIH HHS/United States ; K12 HD055892/HD/NICHD NIH HHS/United States ; }, mesh = {Biosynthetic Pathways ; Lipopeptides/*isolation &amp; purification ; Mass Spectrometry ; *Metabolome ; Peptides, Cyclic/*isolation &amp; purification ; Pseudomonas/*chemistry/genetics ; Triticum/microbiology ; }, abstract = {Pseudomonads are cosmopolitan microorganisms able to produce a wide array of specialized metabolites. These molecules allow Pseudomonas to scavenge nutrients, sense population density and enhance or inhibit growth of competing microorganisms. However, these valuable metabolites are typically characterized one-molecule-one-microbe at a time, instead of being inventoried in large numbers. To index and map the diversity of molecules detected from these organisms, 260 strains of ecologically diverse origins were subjected to mass-spectrometry-based molecular networking. Molecular networking not only enables dereplication of molecules, but also sheds light on their structural relationships. Moreover, it accelerates the discovery of new molecules. Here, by indexing the Pseudomonas specialized metabolome, we report the molecular-networking-based discovery of four molecules and their evolutionary relationships: a poaeamide analogue and a molecular subfamily of cyclic lipopeptides, bananamides 1, 2 and 3. Analysis of their biosynthetic gene cluster shows that it constitutes a distinct evolutionary branch of the Pseudomonas cyclic lipopeptides. Through analysis of an additional 370 extracts of wheat-associated Pseudomonas, we demonstrate how the detailed knowledge from our reference index can be efficiently propagated to annotate complex metabolomic data from other studies, akin to the way in which newly generated genomic information can be compared to data from public databases.}, }
@article {pmid27797708, year = {2016}, author = {Salden, BN and Troost, FJ and de Groot, E and Stevens, YR and Garcés-Rimón, M and Possemiers, S and Winkens, B and Masclee, AA}, title = {Randomized clinical trial on the efficacy of hesperidin 2S on validated cardiovascular biomarkers in healthy overweight individuals.}, journal = {The American journal of clinical nutrition}, volume = {104}, number = {6}, pages = {1523-1533}, doi = {10.3945/ajcn.116.136960}, pmid = {27797708}, issn = {1938-3207}, mesh = {Adult ; Aged ; Biomarkers/*blood ; Blood Pressure/drug effects ; Body Mass Index ; Cardiovascular Diseases/*blood ; Cell Adhesion Molecules/blood ; Dietary Supplements ; Double-Blind Method ; Down-Regulation ; Endothelium, Vascular/drug effects/metabolism ; Female ; Hesperidin/*administration &amp; dosage ; Humans ; Male ; Middle Aged ; Obesity/*blood ; Overweight/*blood ; P-Selectin/blood ; Postprandial Period ; Treatment Outcome ; Vascular Cell Adhesion Molecule-1/genetics/metabolism ; }, abstract = {BACKGROUND: Endothelial dysfunction (ED) is involved in the development of atherosclerosis. Hesperidin, a citrus flavonoid with antioxidant and other biological properties, potentially exerts beneficial effects on endothelial function (EF).<br><br>OBJECTIVE: We investigated the effect of hesperidin 2S supplementation on EF in overweight individuals.<br><br>DESIGN: This was a randomized, double-blind, placebo-controlled study in which 68 individuals were randomly assigned to receive hesperidin 2S (450 mg/d) or a placebo for 6 wk. At baseline and after 6 wk of intervention, flow-mediated dilation (FMD), soluble vascular adhesion molecule-1 (sVCAM-1), soluble intracellular adhesion molecule-1 (sICAM-1), soluble P-selectin (sP-selectin), systolic blood pressure (SBP), and diastolic blood pressure (DBP) were assessed. Acute, reversible ED was induced by intake of a high-fat meal (HFM). A second FMD scan was performed 2 h postprandially, and adhesion molecules were assessed 2 and 4 h postprandially. An additional exploratory analysis was performed in subjects with baseline FMD &#x2265;3%.<br><br>RESULTS: No significant change in fasting or postprandial FMD was observed after 6 wk of hesperidin intake compared with placebo intake. However, there was a trend for a reduction of sVCAM-1, sICAM-1, sP-selectin, SBP, and DBP after 6 wk of hesperidin treatment. In the FMD &#x2265;3% group, hesperidin protected individuals from postprandial ED (P = 0.050) and significantly downregulated sVCAM-1 and sICAM-1 (all P &#x2264; 0.030). The results reported in the current article were not adjusted for multiplicity.<br><br>CONCLUSIONS: Six weeks of consumption of hesperidin 2S did not improve basal or postprandial FMD in our total study population. There was a tendency toward a reduction of adhesion molecules and a decrease in SBP and DBP. Further exploratory analyses revealed that, in subjects with baseline FMD &#x2265;3%, hesperidin 2S improved ED after an HFM and reduced adhesion molecules. These results indicate the cardiovascular health benefits of hesperidin 2S in overweight and obese individuals with a relatively healthy endothelium. This trial was registered at clinicaltrials.gov as NCT02228291.}, }
@article {pmid27796418, year = {2017}, author = {Miyaoka, Y and Hatamoto, M and Yamaguchi, T and Syutsubo, K}, title = {Eukaryotic Community Shift in Response to Organic Loading Rate of an Aerobic Trickling Filter (Down-Flow Hanging Sponge Reactor) Treating Domestic Sewage.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {801-814}, pmid = {27796418}, issn = {1432-184X}, mesh = {*Aerobiosis ; Alveolata/classification ; Animals ; Bacteria/growth &amp; development/metabolism ; Bioreactors/*microbiology/*parasitology ; Cell Count ; Eukaryota/*classification/genetics/growth &amp; development/metabolism ; Porifera ; RNA, Ribosomal, 18S/genetics ; Rhizaria/classification ; Sewage/*microbiology/*parasitology ; Waste Disposal, Fluid ; Water Purification ; Water Quality ; }, abstract = {In this study, changes in eukaryotic community structure and water quality were investigated in an aerobic trickling filter (down-flow hanging sponge, DHS) treating domestic sewage under different organic loading rates (OLRs). The OLR clearly influenced both sponge pore water quality and relative flagellates and ciliates (free-swimming, carnivorous, crawling, and stalked protozoa) abundances in the retained sludge. Immediately after the OLR was increased from 1.05 to 1.97 kg chemical oxygen demand (COD) m[-3] day[-1], COD and NH4[+]-N treatment efficiencies both deteriorated, and relative flagellates and ciliates abundances then increased from 2-8 % to 51-65 % total cells in the middle-bottom part of the DHS reactor. In a continuous operation at a stable OLR (2.01 kg COD m[-3] day[-1]), effluent water quality improved, and relative flagellates and ciliates abundances decreased to 15-46 % total cells in the middle-bottom part of the DHS reactor. This result may indicate that flagellates and ciliates preferentially graze on dispersed bacteria, thus, stabilizing effluent water quality. Additionally, to investigate eukaryotic community structure, clone libraries based on the 18S ribosomal ribonucleic acid (rRNA) gene of the retained sludge were constructed. The predominant group was Nucletmycea phylotypes, representing approximately 29-56 % total clones. Furthermore, a large proportion of the clones had <97 % sequence identity in the NCBI database. This result indicates that phylogenetically unknown eukaryotes were present in the DHS reactor. These results provide insights into eukaryotic community shift in the DHS reactor treating domestic sewage.}, }
@article {pmid27789535, year = {2017}, author = {Mašínová, T and Bahnmann, BD and Větrovský, T and Tomšovský, M and Merunková, K and Baldrian, P}, title = {Drivers of yeast community composition in the litter and soil of a temperate forest.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {2}, pages = {}, doi = {10.1093/femsec/fiw223}, pmid = {27789535}, issn = {1574-6941}, mesh = {*Biodiversity ; Fagus/microbiology ; *Forests ; Fungi/genetics ; Picea/microbiology ; Saccharomyces cerevisiae ; Soil/chemistry ; *Soil Microbiology ; Trees/microbiology ; Yeasts/*classification/genetics/growth &amp; development ; }, abstract = {Fungi represent a group of soil microorganisms fulfilling important ecological functions. Although several studies have shown that yeasts represent a significant proportion of fungal communities, our current knowledge is based mainly on cultivation experiments. In this study, we used amplicon sequencing of environmental DNA to describe the composition of yeast communities in European temperate forest and to identify the potential biotic and abiotic drivers of community assembly. Based on the analysis of ITS2 PCR amplicons, yeasts represented a substantial proportion of fungal communities ranging from 0.4 to 14.3% of fungal sequences in soil and 0.2 to 9.9% in litter. The species richness at individual sites was 28 ± 9 in soil and 31 ± 11 in litter. The basidiomycetous yeasts dominated over ascomycetous ones. In litter, yeast communities differed significantly among beech-, oak- and spruce-dominated stands. Drivers of community assembly are probably more complex in soils and comprise the effects of environmental conditions and vegetation.}, }
@article {pmid27743387, year = {2017}, author = {Emerson, JB and Keady, PB and Clements, N and Morgan, EE and Awerbuch, J and Miller, SL and Fierer, N}, title = {High temporal variability in airborne bacterial diversity and abundance inside single-family residences.}, journal = {Indoor air}, volume = {27}, number = {3}, pages = {576-586}, doi = {10.1111/ina.12347}, pmid = {27743387}, issn = {1600-0668}, mesh = {*Air Microbiology ; Air Pollutants/*analysis ; Air Pollution/*analysis ; Air Pollution, Indoor/analysis ; Analysis of Variance ; Bacteria ; Colorado ; Environmental Monitoring/methods ; Housing ; Humans ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Our homes are microbial habitats, and although the amounts and types of bacteria in indoor air have been shown to vary substantially across residences, temporal variability within homes has rarely been characterized. Here, we sought to quantify the temporal variability in the amounts and types of airborne bacteria in homes, and what factors drive this variability. We collected filter samples of indoor and outdoor air in 15 homes over 1 year (approximately eight time points per home, two per season), and we used culture-independent DNA sequencing approaches to characterize bacterial community composition. Significant differences in indoor air community composition were observed both between homes and within each home over time. Indoor and outdoor air community compositions were not significantly correlated, suggesting that indoor and outdoor air communities are decoupled. Indoor air communities from the same home were often just as different at adjacent time points as they were across larger temporal distances, and temporal variation correlated with changes in environmental conditions, including temperature and relative humidity. Although all homes had highly variable indoor air communities, homes with the most temporally variable communities had more stable, lower average microbial loads than homes with less variable communities.}, }
@article {pmid27660605, year = {2016}, author = {Cipriano, MA and Lupatini, M and Lopes-Santos, L and da Silva, MJ and Roesch, LF and Destéfano, SA and Freitas, SS and Kuramae, EE}, title = {Lettuce and rhizosphere microbiome responses to growth promoting Pseudomonas species under field conditions.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {12}, pages = {}, doi = {10.1093/femsec/fiw197}, pmid = {27660605}, issn = {1574-6941}, mesh = {Base Sequence ; Biomass ; DNA, Bacterial/genetics ; Lactuca/*growth &amp; development/*microbiology ; Microbiota ; Oxidoreductases/genetics ; Phosphates ; Phylogeny ; Plant Development/*physiology ; Pseudomonas/classification/physiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Seedlings/*growth &amp; development/*microbiology ; Sequence Analysis, DNA ; Soil ; Soil Microbiology ; }, abstract = {Plant growth promoting rhizobacteria are well described and recommended for several crops worldwide. However, one of the most common problems in research into them is the difficulty in obtaining reproducible results. Furthermore, few studies have evaluated plant growth promotion and soil microbial community composition resulting from bacterial inoculation under field conditions. Here we evaluated the effect of 54 Pseudomonas strains on lettuce (Lactuca sativa) growth. The 12 most promising strains were phylogenetically and physiologically characterized for plant growth-promoting traits, including phosphate solubilization, hormone production and antagonism to pathogen compounds, and their effect on plant growth under farm field conditions. Additionally, the impact of beneficial strains on the rhizospheric bacterial community was evaluated for inoculated plants. The strains IAC-RBcr4 and IAC-RBru1, with different plant growth promoting traits, improved lettuce plant biomass yields up to 30%. These two strains also impacted rhizosphere bacterial groups including Isosphaera and Pirellula (phylum Planctomycetes) and Acidothermus, Pseudolabrys and Singusphaera (phylum Actinobacteria). This is the first study to demonstrate consistent results for the effects of Pseudomonas strains on lettuce growth promotion for seedlings and plants grown under tropical field conditions.}, }
@article {pmid27793217, year = {2016}, author = {Mika, A and Rumian, N and Loughridge, AB and Fleshner, M}, title = {Exercise and Prebiotics Produce Stress Resistance: Converging Impacts on Stress-Protective and Butyrate-Producing Gut Bacteria.}, journal = {International review of neurobiology}, volume = {131}, number = {}, pages = {165-191}, doi = {10.1016/bs.irn.2016.08.004}, pmid = {27793217}, issn = {2162-5514}, mesh = {Animals ; Bacteria/*drug effects ; Butyrates/*pharmacology ; Exercise/*physiology ; *Gastrointestinal Tract/drug effects/microbiology/physiology ; Humans ; Prebiotics/*administration &amp; dosage ; *Stress, Psychological/microbiology/prevention &amp; control/rehabilitation ; }, abstract = {The gut microbial ecosystem can mediate the negative health impacts of stress on the host. Stressor-induced disruptions in microbial ecology (dysbiosis) can lead to maladaptive health effects, while certain probiotic organisms and their metabolites can protect against these negative impacts. Prebiotic diets and exercise are feasible and cost-effective strategies that can increase stress-protective bacteria and produce resistance against the detrimental behavioral and neurobiological impacts of stress. The goal of this review is to describe research demonstrating that both prebiotic diets and exercise produce adaptations in gut ecology and the brain that arm the organism against inescapable stress-induced learned helplessness. The results of this research support the novel hypothesis that some of the stress-protective effects of prebiotics and exercise are due to increases in stress-protective gut microbial species and their metabolites. In addition, new evidence also suggests that prebiotic diet or exercise interventions are most effective if given early in life (juvenile-adolescence) when both the gut microbial ecosystem and the brain are plastic. Based on our new understanding of the mechanistic convergence of these interventions, it is feasible to propose that in adults, both interventions delivered in combination may elevate their efficacy to promote a stress-resistant phenotype.}, }
@article {pmid27790207, year = {2016}, author = {Deines, P and Bosch, TC}, title = {Transitioning from Microbiome Composition to Microbial Community Interactions: The Potential of the Metaorganism Hydra as an Experimental Model.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1610}, pmid = {27790207}, issn = {1664-302X}, abstract = {Animals are home to complex microbial communities, which are shaped through interactions within the community, interactions with the host, and through environmental factors. The advent of high-throughput sequencing methods has led to novel insights in changing patterns of community composition and structure. However, deciphering the different types of interactions among community members, with their hosts and their interplay with their environment is still a challenge of major proportion. The emerging fields of synthetic microbial ecology and community systems biology have the potential to decrypt these complex relationships. Studying host-associated microbiota across multiple spatial and temporal scales will bridge the gap between individual microorganism studies and large-scale whole community surveys. Here, we discuss the unique potential of Hydra as an emerging experimental model in microbiome research. Through in vivo, in vitro, and in silico approaches the interaction structure of host-associated microbial communities and the effects of the host on the microbiota and its interactions can be disentangled. Research in the model system Hydra can unify disciplines from molecular genetics to ecology, opening up the opportunity to discover fundamental rules that govern microbiome community stability.}, }
@article {pmid27789631, year = {2016}, author = {Schmid, J and Huptas, C and Wenning, M}, title = {Draft Genome Sequence of the Xanthan Producer Xanthomonas campestris LMG 8031.}, journal = {Genome announcements}, volume = {4}, number = {5}, pages = {}, pmid = {27789631}, issn = {2169-8287}, abstract = {Here, we report the draft genome sequence of Xanthomonas campestris LMG 8031, for which nearly no genetic information is available, despite its good xanthan-producing properties. We performed an Illumina-based sequencing approach of LMG 8031. The genome revealed a 5.0-Mb chromosome having 4,434 coding sequences and a G+C content of 65%.}, }
@article {pmid27787408, year = {2017}, author = {Michels, N and Van de Wiele, T and De Henauw, S}, title = {Chronic Psychosocial Stress and Gut Health in Children: Associations With Calprotectin and Fecal Short-Chain Fatty Acids.}, journal = {Psychosomatic medicine}, volume = {79}, number = {8}, pages = {927-935}, doi = {10.1097/PSY.0000000000000413}, pmid = {27787408}, issn = {1534-7796}, mesh = {Adolescent ; Affective Symptoms/*physiopathology ; Child ; Fatty Acids, Volatile/*analysis ; Feces/*chemistry ; Female ; *Gastrointestinal Microbiome ; Hair/chemistry ; Heart Rate/*physiology ; Humans ; Hydrocortisone/metabolism ; Inflammatory Bowel Diseases/*metabolism ; Leukocyte L1 Antigen Complex/*analysis ; Male ; Stress, Psychological/*physiopathology ; }, abstract = {OBJECTIVES: The mechanisms underpinning the association between chronic stress and gut health are poorly understood. We aimed to investigate the relationship between bacterial produced short-chain fatty acids, gut barrier function, and stress measures.<br><br>METHODS: A fecal sample, hair sample, and questionnaire data were collected from 113 Belgian children (8-16 years old). Biological measures of stress included hair cortisol (most proximal 3 cm) and 5-minute heart rate variability (high frequency). Self-report measures of stress included emotional problems and negative events. Fecal calprotectin was determined as a marker of intestinal inflammation and an indirect indicator of gut barrier integrity. Fecal short-chain fatty acids (butyrate, propionate, acetate, valerate, isobutyrate, and isovalerate) were measured with gas chromatography. Linear regression analyses were adjusted for sex, age, socioeconomic status, body mass index, fiber intake, and protein intake.<br><br>RESULTS: Emotional problems were significantly associated with higher butyrate (&#x3b2; = 0.263), valerate (&#x3b2; = 0.230), isovalerate (&#x3b2; = 0.231), and isobutyrate (&#x3b2; = 0.233). Heart rate variability reflecting higher parasympathetic activity was related to lower valerate levels (&#x3b2; = -0.217). Hair cortisol was not associated with the short-chain fatty acids. None of the stress measures and none of the fecal short-chain fatty acids were significantly related to fecal calprotectin.<br><br>CONCLUSIONS: In healthy children, the impact of chronic stress is manifested more obviously in short-chain fatty acids than in intestinal inflammation as measured by levels of calprotectin. Despite the rather counterintuitive associations with butyrate, these results point to the need for further research on gut microbiome composition.}, }
@article {pmid27696597, year = {2016}, author = {Khadempour, L and Burnum-Johnson, KE and Baker, ES and Nicora, CD and Webb-Robertson, BM and White, RA and Monroe, ME and Huang, EL and Smith, RD and Currie, CR}, title = {The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates.}, journal = {Molecular ecology}, volume = {25}, number = {22}, pages = {5795-5805}, pmid = {27696597}, issn = {1365-294X}, support = {R01 ES022190/ES/NIEHS NIH HHS/United States ; U01 CA184783/CA/NCI NIH HHS/United States ; }, mesh = {Agaricales/*enzymology ; Animals ; Ants/*microbiology ; Flowers/metabolism ; Fungal Proteins/*metabolism ; Plant Leaves/metabolism ; Plants/*metabolism ; Proteomics ; Symbiosis ; }, abstract = {Herbivores use symbiotic microbes to help derive energy and nutrients from plant material. Leaf-cutter ants are a paradigmatic example, cultivating their mutualistic fungus Leucoagaricus gongylophorus on plant biomass that workers forage from a diverse collection of plant species. Here, we investigate the metabolic flexibility of the ants' fungal cultivar for utilizing different plant biomass. Using feeding experiments and a novel approach in metaproteomics, we examine the enzymatic response of L. gongylophorus to leaves, flowers, oats or a mixture of all three. Across all treatments, our analysis identified and quantified 1766 different fungal proteins, including 161 putative biomass-degrading enzymes. We found significant differences in the protein profiles in the fungus gardens of subcolonies fed different plant substrates. When provided with leaves or flowers, which contain the majority of their energy as recalcitrant plant polymers, the fungus gardens produced more proteins predicted to break down cellulose: endoglucanase, exoglucanase and β-glucosidase. Further, the complete metaproteomes for the leaves and flowers treatments were very similar, while the mixed substrate treatment closely resembled the treatment with oats alone. This indicates that when provided a mixture of plant substrates, fungus gardens preferentially break down the simpler, more digestible substrates. This flexible, substrate-specific enzymatic response of the fungal cultivar allows leaf-cutter ants to derive energy from a wide range of substrates, which likely contributes to their ability to be dominant generalist herbivores.}, }
@article {pmid27645138, year = {2017}, author = {Sheridan, C and Depuydt, P and De Ro, M and Petit, C and Van Gysegem, E and Delaere, P and Dixon, M and Stasiak, M and Aciksöz, SB and Frossard, E and Paradiso, R and De Pascale, S and Ventorino, V and De Meyer, T and Sas, B and Geelen, D}, title = {Microbial Community Dynamics and Response to Plant Growth-Promoting Microorganisms in the Rhizosphere of Four Common Food Crops Cultivated in Hydroponics.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {378-393}, pmid = {27645138}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics ; Base Sequence ; Biodiversity ; Crops, Agricultural/*growth &amp; development/*microbiology ; DNA, Bacterial ; DNA, Fungal ; Food ; Fungi/classification/genetics ; Hydrogen-Ion Concentration ; *Hydroponics ; Life Cycle Stages ; *Microbial Consortia/genetics ; Phylogeny ; Plant Roots/growth &amp; development/microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Solanum tuberosum/growth &amp; development/microbiology ; Glycine max/growth &amp; development/microbiology ; Triticum/growth &amp; development/microbiology ; Water Microbiology ; }, abstract = {Plant growth promoting microorganisms (PGPMs) of the plant root zone microbiome have received limited attention in hydroponic cultivation systems. In the framework of a project aimed at the development of a biological life support system for manned missions in space, we investigated the effects of PGPMs on four common food crops (durum and bread wheat, potato and soybean) cultivated in recirculating hydroponic systems for a whole life cycle. Each crop was inoculated with a commercial PGPM mixture and the composition of the microbial communities associated with their root rhizosphere, rhizoplane/endosphere and with the recirculating nutrient solution was characterised through 16S- and ITS-targeted Illumina MiSeq sequencing. PGPM addition was shown to induce changes in the composition of these communities, though these changes varied both between crops and over time. Microbial communities of PGPM-treated plants were shown to be more stable over time. Though additional development is required, this study highlights the potential benefits that PGPMs may confer to plants grown in hydroponic systems, particularly when cultivated in extreme environments such as space.}, }
@article {pmid27687789, year = {2017}, author = {Triadó-Margarit, X and Veillette, M and Duchaine, C and Talbot, M and Amato, F and Minguillón, MC and Martins, V and de Miguel, E and Casamayor, EO and Moreno, T}, title = {Bioaerosols in the Barcelona subway system.}, journal = {Indoor air}, volume = {27}, number = {3}, pages = {564-575}, doi = {10.1111/ina.12343}, pmid = {27687789}, issn = {1600-0668}, mesh = {Aerosols/analysis ; *Air Microbiology ; Air Pollutants/*analysis ; Air Pollution, Indoor/*analysis ; Aspergillus fumigatus/isolation &amp; purification ; Bacteria/isolation &amp; purification ; Environmental Monitoring ; Humans ; Influenza A virus/isolation &amp; purification ; Influenza B virus/isolation &amp; purification ; Microbiota ; Particle Size ; Particulate Matter/analysis ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; *Railroads ; Rhinovirus/isolation &amp; purification ; Spain ; }, abstract = {Subway systems worldwide transport more than 100 million people daily; therefore, air quality on station platforms and inside trains is an important urban air pollution issue. We examined the microbiological composition and abundance in space and time of bioaerosols collected in the Barcelona subway system during a cold period. Quantitative PCR was used to quantify total bacteria, Aspergillus fumigatus, influenza A and B, and rhinoviruses. Multitag 454 pyrosequencing of the 16S rRNA gene was used to assess bacterial community composition and biodiversity. The results showed low bioaerosol concentrations regarding the targeted microorganisms, although the bacterial bioburden was rather high (10[4] bacteria/m[3]). Airborne bacterial communities presented a high degree of overlap among the different subway environments sampled (inside trains, platforms, and lobbies) and were dominated by a few widespread taxa, with Methylobacterium being the most abundant genus. Human-related microbiota in sequence dataset and ascribed to potentially pathogenic bacteria were found in low proportion (maximum values below 2% of sequence readings) and evenly detected. Hence, no important biological exposure marker was detected in any of the sampled environments. Overall, we found that commuters are not the main source of bioaerosols in the Barcelona subway system.}, }
@article {pmid27599709, year = {2016}, author = {Koczura, R and Mokracka, J and Taraszewska, A and Łopacinska, N}, title = {Abundance of Class 1 Integron-Integrase and Sulfonamide Resistance Genes in River Water and Sediment Is Affected by Anthropogenic Pressure and Environmental Factors.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {909-916}, pmid = {27599709}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Carrier Proteins/genetics ; DNA Copy Number Variations/genetics ; Enterobacteriaceae/*drug effects/*genetics/isolation &amp; purification ; Gene Frequency/genetics ; Genes, Bacterial ; Geologic Sediments/*microbiology ; Integrases/*genetics ; Integrons/*genetics ; Rivers/*microbiology ; Sewage/*microbiology ; Water Microbiology ; }, abstract = {In this study, we determined the presence of class 1 integron-integrase gene in culturable heterotrophic bacteria isolated from river water and sediment sampled upstream and downstream of a wastewater treatment plant effluent discharge. Moreover, we quantified intI1 and sulfonamide resistance genes (sul1 and sul2) in the water and sediment using qPCR. There was no correlation between the results from water and sediment samples, which suggests integron-containing bacteria are differentially retained in these two environmental compartments. The discharge of treated wastewater significantly increased the frequency of intI1 among culturable bacteria and the gene copy number in river water, and increased the number of sul1 genes in the sediment. We also observed seasonal differences in the frequency of the class 1 integron-integrase gene among culturable heterotrophs as well as intI1 copy number in water, but not in sediment. The results suggest that the abundance of class 1 integrons in aquatic habitat depends on anthropogenic pressure and environmental factors.}, }
@article {pmid27538872, year = {2016}, author = {Zhu, J and Dai, W and Qiu, Q and Dong, C and Zhang, J and Xiong, J}, title = {Contrasting Ecological Processes and Functional Compositions Between Intestinal Bacterial Community in Healthy and Diseased Shrimp.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {975-985}, pmid = {27538872}, issn = {1432-184X}, mesh = {Actinomycetales/classification/genetics/isolation &amp; purification ; Alphaproteobacteria/classification/genetics/isolation &amp; purification ; Animals ; DNA, Bacterial/genetics ; Gammaproteobacteria/classification/genetics/isolation &amp; purification ; Gastrointestinal Microbiome/*physiology ; Homeostasis ; Intestines/*microbiology ; Microbial Interactions/*physiology ; Penaeidae/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Shellfish/*microbiology ; }, abstract = {Intestinal bacterial communities play a pivotal role in promoting host health; therefore, the disruption of intestinal bacterial homeostasis could result in disease. However, the effect of the occurrences of disease on intestinal bacterial community assembly remains unclear. To address this gap, we compared the multifaceted ecological differences in maintaining intestinal bacterial community assembly between healthy and diseased shrimps. The neutral model analysis shows that the relative importance of neutral processes decreases when disease occurs. This pattern is further corroborated by the ecosphere null model, revealing that the bacterial community assembly of diseased samples is dominated by stochastic processes. In addition, the occurrence of shrimp disease reduces the complexity and cooperative activities of species-to-species interactions. The keystone taxa affiliated with Alphaproteobacteria and Actinobacteria in healthy shrimp gut shift to Gammaproteobacteria species in diseased shrimp. Changes in intestinal bacterial communities significantly alter biological functions in shrimp. Within a given metabolic pathway, the pattern of enrichment or decrease between healthy and deceased shrimp is correlated with its functional effects. We propose that stressed shrimp are more prone to invasion by alien strains (evidenced by more stochastic assembly and higher migration rate in diseased shrimp), which, in turn, disrupts the cooperative activity among resident species. These findings greatly aid our understanding of the underlying mechanisms that govern shrimp intestinal community assembly between health statuses.}, }
@article {pmid27418176, year = {2016}, author = {Yang, Y and Cao, X and Lin, H and Wang, J}, title = {Antibiotics and Antibiotic Resistance Genes in Sediment of Honghu Lake and East Dongting Lake, China.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {791-801}, pmid = {27418176}, issn = {1432-184X}, mesh = {Agriculture/methods ; Anti-Bacterial Agents/analysis/*isolation &amp; purification/pharmacology ; Antiporters/genetics ; Bacteria/drug effects/*genetics ; Bacterial Proteins/genetics ; Carrier Proteins/genetics ; China ; Drug Resistance, Bacterial/genetics ; Environmental Monitoring ; Geologic Sediments/chemistry/*microbiology ; Lakes/chemistry/*microbiology ; RNA, Ribosomal, 16S/genetics ; Repressor Proteins/genetics ; Sulfonamides/*analysis/isolation &amp; purification ; Tetracycline Resistance/*genetics ; Tetracyclines/*analysis/isolation &amp; purification ; Water Microbiology ; }, abstract = {Sediment is an ideal medium for the aggregation and dissemination of antibiotics and antibiotic resistance genes (ARGs). The levels of antibiotics and ARGs in Honghu Lake and East Dongting Lake of central China were investigated in this study. The concentrations of eight antibiotics (four sulfonamides and four tetracyclines) in Honghu Lake were in the range 90.00-437.43 μg kg[-1] (dry weight (dw)) with mean value of 278.21 μg kg[-1] dw, which was significantly higher than those in East Dongting Lake (60.02-321.04 μg kg[-1] dw, mean value of 195.70 μg kg[-1] dw). Among the tested three sulfonamide resistance genes (sul) and eight tetracycline resistance genes (tet), sul1, sul2, tetA, tetC, and tetM had 100 % detection frequency in sediment samples of East Dongting Lake, while only sul1, sul2, and tetC were observed in all samples of Honghu Lake. The relative abundance of sul2 was higher than that of sul1 at p < 0.05 level in both lakes. The relative abundance of tet genes in East Dongting Lake was in the following order: tetM > tetB > tetC > tetA. The relative abundance of sul1, sul2, and tetC in East Dongting Lake was significantly higher than those in Honghu Lake. The abundance of background bacteria may play an important role in the horizontal spread of sul2 and tetC genes in Honghu Lake and sul1 in East Dongting Lake, respectively. Redundancy analysis indicated that tetracyclines may play a more important role than sulfonamides in the abundance of sul1, sul2, and tetC gens in Honghu Lake and East Dongting Lake.}, }
@article {pmid27357141, year = {2016}, author = {Arora, P and Wani, ZA and Nalli, Y and Ali, A and Riyaz-Ul-Hassan, S}, title = {Antimicrobial Potential of Thiodiketopiperazine Derivatives Produced by Phoma sp., an Endophyte of Glycyrrhiza glabra Linn.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {802-812}, pmid = {27357141}, issn = {1432-184X}, mesh = {Ampicillin/pharmacology ; Anti-Bacterial Agents/isolation &amp; purification/metabolism/*pharmacology ; Biofilms/drug effects/growth &amp; development ; Ciprofloxacin/pharmacology ; Drug Combinations ; Endophytes/*metabolism ; Glycyrrhiza/*microbiology ; Microbial Sensitivity Tests ; Real-Time Polymerase Chain Reaction ; Saccharomycetales/*metabolism ; Staphylococcus aureus/*growth &amp; development ; Streptococcus pyogenes/*growth &amp; development ; Streptomycin/pharmacology ; Xanthophylls/biosynthesis ; }, abstract = {During the screening of endophytes obtained from Glycyrrhiza glabra Linn., the extract from a fungal culture designated as GG1F1 showed significant antimicrobial activity. The fungus was identified as a species of the genus Phoma and was most closely related to Phoma cucurbitacearum. The chemical investigation of the GG1F1 extract led to the isolation and characterization of two thiodiketopiperazine derivatives. Both the compounds inhibited the growth of several bacterial pathogens especially that of Staphylococcus aureus and Streptococcus pyogenes, with IC50 values of less than 10 μM. The compounds strongly inhibited biofilm formation in both the pathogens. In vitro time kill kinetics showed efficient bactericidal activity of these compounds. The compounds were found to act synergistically with streptomycin while producing varying effects in combination with ciprofloxacin and ampicillin. The compounds inhibited bacterial transcription/translation in vitro, and also inhibited staphyloxanthin production in S. aureus. Although similar in structure, they differed significantly in some of their properties, particularly the effect on the expression of pathogenecity related genes in S. aureus at sub-lethal concentrations. Keeping in view the antimicrobial potential of these compounds, it would be needful to scale up the production of these compounds through fermentation technology and further explore their potential as antibiotics using in vivo models.}, }
@article {pmid27349661, year = {2016}, author = {Vishnuvardhan Reddy, S and Thirumala, M and Farooq, M and Sasikala, C and Venkata Ramana, C}, title = {Marinococcus salis sp., nov., a moderately halophilic bacterium isolated from a salt marsh.}, journal = {Archives of microbiology}, volume = {198}, number = {10}, pages = {1013-1018}, doi = {10.1007/s00203-016-1263-z}, pmid = {27349661}, issn = {1432-072X}, mesh = {Bacillaceae/*classification/genetics/*isolation &amp; purification/metabolism ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Diaminopimelic Acid/analysis ; Fatty Acids/analysis ; India ; Nucleic Acid Hybridization ; Peptidoglycan/chemistry ; Phospholipids/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sodium Chloride/analysis ; Wetlands ; }, abstract = {A novel Gram-stain-positive, coccoid-shaped, facultative anaerobic, motile and halophilic bacterium strain 5M[T] was isolated from Surajbari in India. Based on the 16S rRNA gene sequence analysis, it was identified as belonging to the genus Marinococcus and was most closely related to Marinococcus luteus KCTC 13214[T] (99.3 %, sequence similarity), Marinococcus halotolerans KCTC 19045[T] (99.0 %), Marinococcus halophilus LMG 17439[T] (98.8 %) and Marinococcus tarijensis LMG 26930[T] (98.7 %). However, the DNA-DNA relatedness of strain 5M[T] with M. luteus KCTC 13214[T], M. halotolerans KCTC 19045[T], M. halophilus LMG 17439[T] and M. tarijensis LMG 26930[T] was 42.6 ± 0.8, 48.6 ± 0.8, 40.9 ± 0.8 and 39.8 ± 0.9 %, respectively. Strain 5M[T] grows optimally at 5 % (w/v) NaCl, pH 7.5-8.5 and 37 °C. The cell-wall peptidoglycan of strain 5M[T] contains meso-diaminopimelic acid. Polar lipids of the strain 5M[T] include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and two unknown lipids. The predominant isoprenoid quinone was MK-7. DNA G+C content was 48.9 mol%, and anteiso-C15:0 (40.9 %) was the predominant fatty acid. The results of phylogenetic, biochemical tests and chemotaxonomic allowed a clear differentiation of strain 5M[T] from all of its nearest phylogenetic neighbours, which represents a novel member of the genus Marinococcus, for which the name Marinococcus salis sp., nov., is proposed. The type strain is 5M[T] (=KCTC 33743[T] = LMG 29101[T] = CGMCC 1.15385[T]).}, }
@article {pmid27339258, year = {2016}, author = {Kielak, AM and Cipriano, MA and Kuramae, EE}, title = {Acidobacteria strains from subdivision 1 act as plant growth-promoting bacteria.}, journal = {Archives of microbiology}, volume = {198}, number = {10}, pages = {987-993}, pmid = {27339258}, issn = {1432-072X}, mesh = {Acidobacteria/*metabolism ; Arabidopsis/*growth &amp; development/metabolism/microbiology ; Biomass ; Indoleacetic Acids/*metabolism ; Plant Development ; Plant Roots/*microbiology ; Polysaccharides, Bacterial/*metabolism ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil ; Soil Microbiology ; Symbiosis/physiology ; }, abstract = {Acidobacteria is one of the most abundant phyla in soils and has been detected in rhizosphere mainly based on cultivation-independent approaches such as 16S rRNA gene survey. Although putative interaction of Acidobacteria with plants was suggested, so far no plant-bacterial interactions were shown. Therefore, we performed several in vitro tests to evaluate Acidobacteria-plant interactions and the possible mechanisms involved in such interaction. We observed that Arabidopsis thaliana inoculated with three strains belonging to Acidobacteria subdivision 1 showed increase in biomass of roots and shoots as well as morphological changes in root system. Our results indicate that the plant hormone indole-3-acetic acid production and iron acquisition are plausibly involved in the plant and Acidobacteria interactions. Here, we confirm for the first time that Acidobacteria can actively interact with plants and act as plant growth-promoting bacteria. In addition, we show that Acidobacteria strains produce exopolysaccharide which supports the adhesion of bacteria to the root surfaces.}, }
@article {pmid27220973, year = {2016}, author = {Silaghi, C and Pfeffer, M and Kiefer, D and Kiefer, M and Obiegala, A}, title = {Bartonella, Rodents, Fleas and Ticks: a Molecular Field Study on Host-Vector-Pathogen Associations in Saxony, Eastern Germany.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {965-974}, pmid = {27220973}, issn = {1432-184X}, mesh = {Animals ; Bartonella/classification/genetics/*isolation &amp; purification ; Bartonella Infections/microbiology/*transmission ; DNA, Bacterial/genetics ; DNA, Intergenic/genetics ; Disease Reservoirs/*microbiology ; *Disease Vectors ; Female ; Germany ; Humans ; Ixodidae/*microbiology ; Male ; Rodent Diseases/microbiology ; Rodentia/*microbiology ; Siphonaptera/*microbiology ; }, abstract = {Bartonellae cause zoonotic diseases and are transmitted by arthropods. Rodents are reservoirs for most Bartonella spp. As the knowledge about Bartonella in rodents and their parasitizing ectoparasites is scarce in Germany, this study's objectives were to investigate Bartonella spp. in small mammals and in their ectoparasites. A total of 79 small mammals (seven species) were captured and their ectoparasites collected at seven sites around Leipzig, Saxony, Germany, in 2010 and 2011. Altogether, 79 spleen samples, 135 fleas (five species) and 365 ticks (three species) were investigated for Bartonella spp. by PCR targeting the ITS 16S-23S rRNA region. In total, 52 (65.8 %) small mammals, 73 (54.1 %) fleas and 51 (16.3 %) ticks were positive for Bartonella spp. Most small mammals were positive for uncultured Bartonella sp. (n = 29) followed by Bartonella grahamii (n = 12), Bartonella taylorii (n = 8) and Bartonella sp. N40 (n = 3). Likewise, most fleas were positive for uncultured Bartonella sp. (n = 45) followed by B. grahamii (n = 14), B. taylorii (n = 8), B. sp. N40 (n = 5) and Bartonella elizabethae (n = 2). Most ticks were positive for B. sp. (n = 19) followed by B. grahamii (n = 10), Bartonella chomelii (n = 3), B. taylorii (n = 2) and B. sp. N40 (n = 1). This study's results suggest that rodents and fleas may be reservoirs and vectors, respectively. Zoonotic B. grahamii and B. elizabethae were found in rodents and their fleas. Therefore, humans may contract Bartonella infection by contact to wild rodents. Ticks seem of minor importance in transmitting Bartonella spp. found in fleas and rodents. However, ticks might be vectors of B. chomelii.}, }
@article {pmid27220972, year = {2016}, author = {Heß, S and Gallert, C}, title = {Growth Behavior of E. coli, Enterococcus and Staphylococcus Species in the Presence and Absence of Sub-inhibitory Antibiotic Concentrations: Consequences for Interpretation of Culture-Based Data.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {898-908}, pmid = {27220972}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/*pharmacology ; Ciprofloxacin/pharmacology ; Clindamycin/pharmacology ; Drinking Water/microbiology ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterococcus faecalis/drug effects ; Enterococcus faecium/drug effects ; Erythromycin/analogs &amp; derivatives/pharmacology ; Escherichia coli/classification/*growth &amp; development/isolation &amp; purification ; Methicillin-Resistant Staphylococcus aureus/classification/*growth &amp; development/isolation &amp; purification ; Microbial Sensitivity Tests ; Sewage/microbiology ; Sulfamethoxazole/pharmacology ; Trimethoprim/pharmacology ; Vancomycin-Resistant Enterococci/classification/*growth &amp; development/isolation &amp; purification ; Water Microbiology ; }, abstract = {Culture-based approaches are used to monitor, e.g., drinking water or bathing water quality and to investigate species diversity and antibiotic resistance levels in environmental samples. For health risk assessment, it is important to know whether the growing cultures display the actual abundance of, e.g., clinically relevant antibiotic resistance phenotypes such as vancomycin-resistant Enterococcus faecium/Enterococcus faecalis (VRE) or methicillin-resistant Staphylococcus aureus. In addition, it is important to know whether sub-inhibitory antibiotic concentrations, which are present in surface waters, favor the growth of antibiotic-resistant strains. Therefore, clinically relevant bacteria were isolated from different water sources and the growth behavior of 58 Escherichia coli, 71 Enterococcus, and 120 Staphylococcus isolates, belonging to different species and revealing different antibiotic resistance patterns, was studied with respect to "environmental" antibiotic concentrations. The finding that VRE could only be detected after specific enrichment can be explained by their slow growth compared to non-resistant strains. Interpreting their absence in standardized culture-based methods as nonexistent might be a fallacy. Sub-inhibitory antibiotic concentrations that were detected in sewage and receiving river water did not specifically promote antibiotic-resistant strains. Generally, those antibiotics that influenced cell metabolism directly led to slightly reduced growth rates and less than maximal optical densities after 48 h of incubation.}, }
@article {pmid27216529, year = {2016}, author = {González-Barrio, D and Hagen, F and Tilburg, JJ and Ruiz-Fons, F}, title = {Coxiella burnetii Genotypes in Iberian Wildlife.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {890-897}, pmid = {27216529}, issn = {1432-184X}, mesh = {Animals ; Coxiella burnetii/*genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Deer/*microbiology ; Genetic Variation/genetics ; Genotype ; Humans ; Livestock/*microbiology ; Mice ; Multilocus Sequence Typing ; Q Fever/microbiology/*transmission/*veterinary ; Rabbits ; Rats ; Spain ; Sus scrofa/*microbiology ; }, abstract = {To investigate if Coxiella burnetii, the causative agent of Q fever, genotypes circulating in wildlife are associated with those infecting livestock and humans, multiple-locus variable number tandem-repeat analysis (MLVA-6-marker) was carried out over C. burnetii obtained from red deer (Cervus elaphus), Eurasian wild boar (Sus scrofa), European wild rabbit (Oryctolagus cuniculus), black rat (Rattus rattus), and wood mouse (Apodemus sylvaticus). MLVA typing was performed by using six variable loci in C. burnetii: Ms23, Ms24, Ms27, Ms28, Ms33, and Ms34. The C. burnetii cooperative database from MLVABank 5.0 was employed to compare genotypes found in this study with 344 isolates of diverse origin. Twenty-two genotypes from wildlife and two genotypes from domestic goats were identified. Some MLVA genotypes identified in wildlife or in farmed game clustered with genotypes of human Q fever clinical cases, supporting the idea that humans and wildlife share C. burnetii genotypes. The major part of genotypes identified in coexisting red deer and rabbits clustered according to their host of origin, suggesting host specificity for particular C. burnetii genotypes. These findings provide important insights to understand the epidemiology of C. burnetii at the wildlife-livestock-human interface.}, }
@article {pmid27193154, year = {2016}, author = {Penttinen, R and Kinnula, H and Lipponen, A and Bamford, JK and Sundberg, LR}, title = {High Nutrient Concentration Can Induce Virulence Factor Expression and Cause Higher Virulence in an Environmentally Transmitted Pathogen.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {955-964}, pmid = {27193154}, issn = {1432-184X}, mesh = {Animals ; Chondroitin Lyases/genetics/*metabolism ; Collagenases/genetics/*metabolism ; Environmental Exposure ; Fish Diseases/*microbiology ; Flavobacterium/*pathogenicity ; Food ; Oncorhynchus mykiss/*microbiology ; Real-Time Polymerase Chain Reaction ; Virulence Factors/*metabolism ; Water Microbiology ; }, abstract = {Environmentally transmitted opportunistic pathogens shuttle between two substantially different environments: outside-host and within-host habitats. These environments differ from each other especially with respect to nutrient availability. Consequently, the pathogens are required to regulate their behavior in response to environmental cues in order to survive, but how nutrients control the virulence in opportunistic pathogens is still poorly understood. In this study, we examined how nutrient level in the outside-host environment affects the gene expression of putative virulence factors of the opportunistic fish pathogen Flavobacterium columnare. The impact of environmental nutrient concentration on bacterial virulence was explored by cultivating the bacteria in various nutrient conditions, measuring the gene expression of putative virulence factors with RT-qPCR and, finally, experimentally challenging rainbow trout (Oncorhynchus mykiss) fry with these bacteria. Our results show that increased environmental nutrient concentration can increase the expression of putative virulence genes, chondroitinase (cslA) and collagenase, in the outside-host environment and may lead to more rapid fish mortality. These findings address that the environmental nutrients may act as significant triggers of virulence gene expression and therefore contribute to the interaction between an environmentally transmitted opportunistic pathogen and its host.}, }
@article {pmid27193001, year = {2016}, author = {Abia, AL and Ubomba-Jaswa, E and Momba, MN}, title = {Competitive Survival of Escherichia coli, Vibrio cholerae, Salmonella typhimurium and Shigella dysenteriae in Riverbed Sediments.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {881-889}, pmid = {27193001}, issn = {1432-184X}, mesh = {Escherichia coli/*isolation &amp; purification ; Geologic Sediments/*microbiology ; Rivers/*microbiology ; Salmonella typhimurium/*isolation &amp; purification ; Shigella dysenteriae/*isolation &amp; purification ; Temperature ; Vibrio cholerae/*isolation &amp; purification ; Water Microbiology ; Water Pollution ; }, abstract = {Studies on the survival of bacterial enteric pathogens in riverbed sediments have mostly focused on individual organisms. Reports on the competitive survival of these pathogens in riverbed sediments under the same experimental setup are limited. We investigated the survival of Escherichia coli, Salmonella enterica ser. Typhimurium, Vibrio cholerae and Shigella dysenteriae in riverbed sediments of the Apies River. Experiments were performed in flow chambers containing three sediment types and connected to aquarium pumps immersed in river water to maintain continuous water circulation. Each chamber was inoculated with ~10[7] CFU/mL (final concentration) of each microorganism and kept at 4, 20 and 30 °C. Chambers were sampled on days 0, 1, 2, 7, 14 and 28. At 4 °C, only E. coli and S. typhimurium survived throughout the 28 experimental days. V. cholerae had the shortest survival time at this temperature and was not detected in any of the sediment chambers 24 h after inoculation. S. dysenteriae only survived until day 7. At an increased temperature of 20 °C, only S. dysenteriae was not detected on day 28 of the experiment. At 30 °C, V. cholerae and Salmonella survived longer (28 days) than E. coli (14 days) and S. dysenteriae (4 days). Vibrio cholerae was shown to have the highest T 90 values (32 days) in all sediment types at 20 and 30 °C. We conclude that the sediments of the Apies River present a favourable environment for the survival of indicator and pathogenic bacteria depending on the prevailing temperature.}, }
@article {pmid27147439, year = {2016}, author = {Jakuschkin, B and Fievet, V and Schwaller, L and Fort, T and Robin, C and Vacher, C}, title = {Deciphering the Pathobiome: Intra- and Interkingdom Interactions Involving the Pathogen Erysiphe alphitoides.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {870-880}, pmid = {27147439}, issn = {1432-184X}, mesh = {Ascomycota/*genetics/pathogenicity ; Base Sequence ; DNA, Fungal/genetics ; Disease Resistance/physiology ; Microbial Interactions/*physiology ; Microbiota/physiology ; Plant Diseases/*microbiology ; Plant Leaves/*microbiology ; Quercus/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Plant-inhabiting microorganisms interact directly with each other, forming complex microbial interaction networks. These interactions can either prevent or facilitate the establishment of new microbial species, such as a pathogen infecting the plant. Here, our aim was to identify the most likely interactions between Erysiphe alphitoides, the causal agent of oak powdery mildew, and other foliar microorganisms of pedunculate oak (Quercus robur L.). We combined metabarcoding techniques and a Bayesian method of network inference to decipher these interactions. Our results indicate that infection with E. alphitoides is accompanied by significant changes in the composition of the foliar fungal and bacterial communities. They also highlight 13 fungal operational taxonomic units (OTUs) and 13 bacterial OTUs likely to interact directly with E. alphitoides. Half of these OTUs, including the fungal endophytes Mycosphaerella punctiformis and Monochaetia kansensis, could be antagonists of E. alphitoides according to the inferred microbial network. Further studies will be required to validate these potential interactions experimentally. Overall, we showed that a combination of metabarcoding and network inference, by highlighting potential antagonists of pathogen species, could potentially improve the biological control of plant diseases.}, }
@article {pmid27115499, year = {2016}, author = {Álvarez-Pérez, S and Blanco, JL and Peláez, T and Martínez-Nevado, E and García, ME}, title = {Water Sources in a Zoological Park Harbor Genetically Diverse Strains of Clostridium Perfringens Type A with Decreased Susceptibility to Metronidazole.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {783-790}, pmid = {27115499}, issn = {1432-184X}, mesh = {Animals ; Animals, Zoo ; Anti-Bacterial Agents/*pharmacology ; Bacterial Toxins/genetics ; Clostridium perfringens/classification/*drug effects/isolation &amp; purification ; DNA Fingerprinting ; Drug Resistance, Bacterial/*genetics ; Fresh Water/*microbiology ; Metronidazole/*pharmacology ; Microbial Sensitivity Tests ; Polymerase Chain Reaction ; Spain ; Water Microbiology ; }, abstract = {The presence of Clostridium perfringens in water is generally regarded as an indicator of fecal contamination, and exposure to waterborne spores is considered a possible source of infection for animals. We assessed the presence and genetic diversity of C. perfringens in water sources in a zoological park located in Madrid (Spain). A total of 48 water samples from 24 different sources were analyzed, and recovered isolates were toxinotyped, genotyped by fluorophore-enhanced repetitive polymerase chain reaction (rep-PCR) fingerprinting and tested for antimicrobial susceptibility. C. perfringens was recovered from 43.8 % of water samples and 50 % of water sources analyzed. All isolates (n = 70) were type A and 42.9 % were β2-toxigenic (i.e., cpb2+), but none contained the enterotoxin-encoding gene (cpe). Isolates belonged to 15 rep-PCR genotypes and most genetic diversity (88 %) was distributed among isolates obtained from the same sample. Most isolates displayed intermediate susceptibility (57.1 %; MIC = 16 μg ml[-1]) or resistance (5.7 %; MIC ≥ 32 μg ml[-1]) to metronidazole. No resistance to other antimicrobials was detected, although some isolates showed elevated MICs to erythromycin and/or linezolid. Finally, a marginally significant association between absence of cpb2 and decreased susceptibility to metronidazole (MIC ≥ 16 μg ml[-1]) was detected. In conclusion, our results reveal a high prevalence of C. perfringens type A in the studied water reservoirs, which constitutes a health risk for zoo animals. The elevated MICs to metronidazole observed for genetically diverse isolates is a cause of additional concern, but more work is required to clarify the significance of reduced metronidazole susceptibility in environmental strains.}, }
@article {pmid27079455, year = {2016}, author = {Farkas, A and Crăciunaş, C and Chiriac, C and Szekeres, E and Coman, C and Butiuc-Keul, A}, title = {Exploring the Role of Coliform Bacteria in Class 1 Integron Carriage and Biofilm Formation During Drinking Water Treatment.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {773-782}, pmid = {27079455}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/*pharmacology ; Base Sequence ; Biofilms/*growth &amp; development ; DNA, Bacterial/genetics ; Disinfectants/*pharmacology ; Drinking Water/chemistry/*microbiology ; Drug Resistance, Bacterial/*genetics ; Enterobacteriaceae/*drug effects/*genetics/isolation &amp; purification ; Integrases/genetics ; Membrane Transport Proteins/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Water Microbiology ; Water Purification/*methods ; }, abstract = {This study investigates the role of coliforms in the carriage of class 1 integron and biocide resistance genes in a drinking water treatment plant and explores the relationship between the carriage of such genes and the biofouling abilities of the strain. The high incidence of class 1 integron and biocide resistance genes (33.3 % of the isolates) highlights the inherent risk of genetic contamination posed by coliform populations during drinking water treatment. The association between the presence of intI1 gene and qac gene cassettes, especially qacH, was greater in biofilm cells. In coliforms recovered from biofilms, a higher frequency of class 1 integron elements and higher diversity of genetic patterns occurred, compared to planktonic cells. The coliform isolates under the study proved to mostly carry non-classical class 1 integrons lacking the typical qacEΔ1/sul1 genes or a complete tni module, but bearing the qacH gene. No link was found between the carriage of integron genes and the biofouling degree of the strain, neither in aerobic or in anaerobic conditions. Coliform bacteria isolated from established biofilms rather adhere in oxygen depleted environments, while the colonization ability of planktonic cells is not significantly affected by oxygen availability.}, }
@article {pmid27041371, year = {2016}, author = {Canesi, L and Grande, C and Pezzati, E and Balbi, T and Vezzulli, L and Pruzzo, C}, title = {Killing of Vibrio cholerae and Escherichia coli Strains Carrying D-mannose-sensitive Ligands by Mytilus Hemocytes is Promoted by a Multifunctional Hemolymph Serum Protein.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {759-762}, pmid = {27041371}, issn = {1432-184X}, mesh = {Animals ; Bacterial Adhesion/physiology ; Escherichia coli/*immunology ; Hemocytes/*immunology ; Hemolymph/*immunology ; Mannose/pharmacology ; Mytilus/*immunology/*microbiology ; Opsonin Proteins ; Vibrio cholerae/*immunology ; }, abstract = {In aquatic environments, bivalve mollusks represent an important ecological niche for microorganisms. Persistence of bacteria in bivalve tissues partly depends on their capacity to survive the bactericidal activity of the hemolymph due to both cellular (hemocyes) and soluble serum factors (e.g., enzymes, lectins, opsonins). The extrapallial protein (EP) present in serum of Mytilus galloprovincialis (MgEP) has been recently shown to work as an opsonin promoting D-mannose sensitive (MS) interactions of the bivalve pathogen Vibrio aestuarianus 01/032 strain with the hemocytes. In this study, the role of MgEP in adhesion and killing of other bacteria carrying MS sensitive ligands was investigated. MgEP enhanced adhesion to and killing by hemocytes of Vibrio cholerae ElTor N16961, expressing the MS hemagglutin (MSHA), as well as of Escherichia coli MG1655, carrying type 1 fimbriae. These results further support the recent finding that the multifunctional MgEP also acts as an opsonin involved in mussel defense towards bacteria carrying MS ligands. In addition, these results contribute to elucidate the ecology of bacterial pathogens that can be transmitted to humans via shellfish consumption.}, }
@article {pmid26984253, year = {2016}, author = {Vlčková, K and Gomez, A and Petrželková, KJ and Whittier, CA and Todd, AF and Yeoman, CJ and Nelson, KE and Wilson, BA and Stumpf, RM and Modrý, D and White, BA and Leigh, SR}, title = {Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla).}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {943-954}, pmid = {26984253}, issn = {1432-184X}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Ape Diseases/*drug therapy ; Bacteroidetes/growth &amp; development ; Central African Republic ; Cephalosporins/*pharmacology ; Feces/microbiology ; Firmicutes/growth &amp; development ; Gastrointestinal Microbiome/*drug effects ; Gorilla gorilla/*microbiology ; RNA, Ribosomal, 16S/genetics ; Ruminococcus/growth &amp; development ; }, abstract = {The mammalian gastrointestinal (GI) microbiome, which plays indispensable roles in host nutrition and health, is affected by numerous intrinsic and extrinsic factors. Among them, antibiotic (ATB) treatment is reported to have a significant effect on GI microbiome composition in humans and other animals. However, the impact of ATBs on the GI microbiome of free-ranging or even captive great apes remains poorly characterized. Here, we investigated the effect of cephalosporin treatment (delivered by intramuscular dart injection during a serious respiratory outbreak) on the GI microbiome of a wild habituated group of western lowland gorillas (Gorilla gorilla gorilla) in the Dzanga Sangha Protected Areas, Central African Republic. We examined 36 fecal samples from eight individuals, including samples before and after ATB treatment, and characterized the GI microbiome composition using Illumina-MiSeq sequencing of the bacterial 16S rRNA gene. The GI microbial profiles of samples from the same individuals before and after ATB administration indicate that the ATB treatment impacts GI microbiome stability and the relative abundance of particular bacterial taxa within the colonic ecosystem of wild gorillas. We observed a statistically significant increase in Firmicutes and a decrease in Bacteroidetes levels after ATB treatment. We found disruption of the fibrolytic community linked with a decrease of Ruminoccocus levels as a result of ATB treatment. Nevertheless, the nature of the changes observed after ATB treatment differs among gorillas and thus is dependent on the individual host. This study has important implications for ecology, management, and conservation of wild primates.}, }
@article {pmid26932464, year = {2016}, author = {Winkworth-Lawrence, C and Lange, K}, title = {Antibiotic Resistance Genes in Freshwater Biofilms May Reflect Influences from High-Intensity Agriculture.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {763-772}, pmid = {26932464}, issn = {1432-184X}, mesh = {Agriculture/methods ; Animals ; Animals, Domestic/microbiology ; Anti-Bacterial Agents/*pharmacology ; Antiporters/genetics ; Bacteria/*drug effects/*genetics ; Biofilms/*growth &amp; development ; Databases, Factual ; Drug Resistance, Bacterial/*genetics ; Fresh Water/*microbiology ; Genes, Bacterial/genetics ; Humans ; Interspersed Repetitive Sequences/genetics ; Methyltransferases/genetics ; Microbial Sensitivity Tests ; New Zealand ; Tetracycline Resistance/genetics ; }, abstract = {Antibiotic resistance is a major public health concern with growing evidence of environmental gene reservoirs, especially in freshwater. However, the presence of antibiotic resistance genes in freshwater, in addition to the wide spectrum of land use contaminants like nitrogen and phosphate, that waterways are subjected to is inconclusive. Using molecular analyses, freshwater benthic rock biofilms were screened for genes conferring resistance to antibiotics used in both humans and farmed animals (aacA-aphD to aminoglycosides; mecA to ß-lactams; ermA and ermB to macrolides; tetA, tetB, tetK, and tetM to tetracyclines; vanA and vanB to glycopeptides). We detected widespread low levels of antibiotic resistance genes from 20 waterways across southern New Zealand throughout the year (1.3 % overall detection rate; 480 samples from three rocks per site, 20 sites, eight occasions; July 2010-May 2011). Three of the ten genes, ermB, tetK, and tetM, were detected in 62 of the 4800 individual screens; representatives confirmed using Sanger sequencing. No distinction could be made between human and agricultural land use contamination sources based on gene presence distribution alone. However, land use pressures are suggested by moderate correlations between antibiotic resistance genes and high-intensity farming in winter. The detection of antibiotic resistance genes at several sites not subject to known agricultural pressures suggests human sources of resistance, like waterway contamination resulting from unsatisfactory toilet facilities at recreational sites.}, }
@article {pmid26748500, year = {2016}, author = {Drzewiecka, D}, title = {Significance and Roles of Proteus spp. Bacteria in Natural Environments.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {741-758}, pmid = {26748500}, issn = {1432-184X}, mesh = {Animals ; Environment ; Gastrointestinal Microbiome ; Houseflies/microbiology ; Humans ; Insect Vectors/microbiology ; *Proteus/classification/metabolism/pathogenicity ; Proteus Infections/*microbiology ; Soil Microbiology ; Virulence Factors/metabolism ; Water Microbiology ; Water Pollution ; }, abstract = {Proteus spp. bacteria were first described in 1885 by Gustav Hauser, who had revealed their feature of intensive swarming growth. Currently, the genus is divided into Proteus mirabilis, Proteus vulgaris, Proteus penneri, Proteus hauseri, and three unnamed genomospecies 4, 5, and 6 and consists of 80 O-antigenic serogroups. The bacteria are known to be human opportunistic pathogens, isolated from urine, wounds, and other clinical sources. It is postulated that intestines are a reservoir of these proteolytic organisms. Many wild and domestic animals may be hosts of Proteus spp. bacteria, which are commonly known to play a role of parasites or commensals. However, interesting examples of their symbiotic relationships with higher organisms have also been described. Proteus spp. bacteria present in soil or water habitats are often regarded as indicators of fecal pollution, posing a threat of poisoning when the contaminated water or seafood is consumed. The health risk may also be connected with drug-resistant strains sourcing from intestines. Positive aspects of the bacteria presence in water and soil are connected with exceptional features displayed by autochthonic Proteus spp. strains detected in these environments. These rods acquire various metabolic abilities allowing their adaptation to different environmental conditions, such as high concentrations of heavy metals or toxic substances, which may be exploited as sources of energy and nutrition by the bacteria. The Proteus spp. abilities to tolerate or utilize polluting compounds as well as promote plant growth provide a possibility of employing these microorganisms in bioremediation and environmental protection.}, }
@article {pmid26687342, year = {2016}, author = {Alcalá, L and Alonso, CA and Simón, C and González-Esteban, C and Orós, J and Rezusta, A and Ortega, C and Torres, C}, title = {Wild Birds, Frequent Carriers of Extended-Spectrum β-Lactamase (ESBL) Producing Escherichia coli of CTX-M and SHV-12 Types.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {861-869}, pmid = {26687342}, issn = {1432-184X}, mesh = {Animals ; Animals, Wild/microbiology ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Birds/*microbiology ; Cefotaxime/pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics/isolation &amp; purification ; Escherichia coli Proteins/*genetics ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Spain ; beta-Lactamases/*genetics ; }, abstract = {To get a better insight into the role of birds as reservoirs of extended-spectrum β-lactamase (ESBL) and plasmidic AmpC β-lactamase (pAmpC) Escherichia coli producers, 100 fecal samples belonging to 15 different wild avian species from Northern Spain were analyzed. Cefotaxime-resistant (CTX[R]) E. coli isolates were identified in 16 of the 100 tested birds, which corresponded to 9 animal species (Gyps fulvus-griffon vulture, Larus michahellis-yellow-legged gull, Milvus migrans-black kite, Milvus milvus-red kite, Ciconia ciconia-white stork, Sturnus unicolor-spotless starling, Aquila chrysaetos-golden eagle, Cuculus canorus-common cuckoo, Tyto alba-barn owl). Fifteen isolates harbored ESBL or pAmpC-encoding genes (number of isolates): bla SHV-12 (9), bla CTX-M-1 (3), bla CTX-M-14 (2), and bla CMY-2 (1). The last CTX[R] isolate presented a -42-point-mutation in the chromosomal ampC promoter. Eleven out of 15 ESBL/pAmpC E. coli isolates were multiresistant (most common resistance phenotype: β-lactams-quinolones-tetracycline-sulfamethoxazole/trimethoprim). A plasmid-mediated quinolone resistance determinant (qnrS1) was identified in one E. coli from a barn owl. High genetic diversity was observed among ESBL/pAmpC E. coli isolates, with 12 different sequence types (STs), including several strains of STs frequently detected among human clinical isolates (ST38/D, ST131/B2, ST155/B1, ST10/A). The ST131 isolate belonged to the emergent ciprofloxacin-resistant H30R subclone. This study reveals a high percentage of bird as carriers of ESBL/pAmpC E. coli isolates in Spain, highlighting the elevated rate among storks, kites, and vultures. Wild birds can contribute to the global spread of ESBL/pAmpC-producing E. coli in natural ecosystems.}, }
@article {pmid26566933, year = {2016}, author = {Katyal, I and Chaban, B and Hill, JE}, title = {Comparative Genomics of cpn60-Defined Enterococcus hirae Ecotypes and Relationship of Gene Content Differences to Competitive Fitness.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {917-930}, pmid = {26566933}, issn = {1432-184X}, mesh = {Animals ; Chaperonin 60/*genetics ; *Ecotype ; Enterococcus hirae/classification/*genetics/isolation &amp; purification ; Feces/microbiology ; Genetic Variation ; Genome, Bacterial/*genetics ; Glutamine/metabolism ; Microbial Interactions/*genetics ; Proline/metabolism ; Selenocysteine/metabolism ; Swine/microbiology ; Swine Diseases/microbiology ; }, abstract = {Natural microbial communities undergo selection-driven succession with changes in environmental conditions and available nutrients. In a previous study of the pig faecal Enterococcus community, we demonstrated that cpn60 universal target (UT) sequences could resolve phenotypically and genotypically distinct ecotypes of Enterococcus spp. that emerged over time in the faecal microbiome of growing pigs. In this study, we characterized genomic diversity in the identified Enterococcus hirae ecotypes in order to define further the nature and degree of genome content differences between taxa resolved by cpn60 UT sequences. Genome sequences for six representative isolates (two from each of three ecotypes) were compared. Differences in phosphotransferase systems and amino acid metabolism pathways for glutamine, proline and selenocysteine were observed. Differences in the lac family phosphotransferase system corresponded to lactose utilization phenotypes of the isolates. Competitive fitness of the E. hirae ecotypes was evaluated by in vitro growth competition assays in pig faecal extract medium. Isolates from E. hirae-1 and E. hirae-2 ecotypes were able to out-compete isolates from the E. hirae-3 ecotype, consistent with the relatively low abundance of E. hirae-3 relative to E. hirae-1 and E. hirae-2 previously observed in the pig faecal microbiome, and with observed differences between the ecotypes in gene content related to biosynthetic capacity. Results of this study provide a genomic basis for the definition of ecotypes within E. hirae and confirm the utility of the cpn60 UT sequence for high-resolution profiling of complex microbial communities.}, }
@article {pmid26552396, year = {2016}, author = {Dubert, J and Osorio, CR and Prado, S and Barja, JL}, title = {Persistence of Antibiotic Resistant Vibrio spp. in Shellfish Hatchery Environment.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {851-860}, pmid = {26552396}, issn = {1432-184X}, mesh = {Amoxicillin/pharmacology ; Animals ; Anti-Bacterial Agents/*pharmacology ; Base Sequence ; Bivalvia/*microbiology ; Chloramphenicol/pharmacology ; Chloramphenicol O-Acetyltransferase/genetics ; Chloramphenicol Resistance/*genetics ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Escherichia coli/drug effects/*genetics ; *Fisheries ; Microbial Sensitivity Tests ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Shellfish/*microbiology ; Streptomycin/pharmacology ; Tetracycline/pharmacology ; Vibrio/drug effects/*genetics/isolation &amp; purification ; }, abstract = {The characterization of antibiotic-resistant vibrios isolated from shellfish aquaculture is necessary to elucidate the potential transfer of resistance and to establish effective strategies against vibriosis. With this aim, we analyzed a collection of bacterial isolates obtained from 15 failed hatchery larval cultures that, for the most part, had been treated experimentally with chloramphenicol to prevent vibriosis. Isolates were obtained during a 2-year study from experimental cultures of five different clam species. Among a total of 121 Vibrio isolates studied, 28 were found to be chloramphenicol resistant, suggesting that the shellfish hatchery had been using a sublethal concentration of the antibiotic. Interestingly, chloramphenicol-resistant vibrios showed also resistance to tetracycline and amoxicillin (group A; n = 19) or to streptomycin (group B; n = 9). Chloramphenicol-resistant vibrios were subjected to a PCR amplification and DNA sequencing of the chloramphenicol acetyltransferase genes (cat), and the same approach was followed to study the tetracycline resistance markers (tet). 16S ribosomal RNA (rRNA) gene sequencing revealed that chloramphenicol-resistant vibrios pertained mostly to the Splendidus clade. Conjugation assays demonstrated that various R-plasmids which harbored the cat II/tet(D) genes and cat III gene in groups A and B respectively, were transferred to E. coli and bivalve pathogenic vibrios. Most interestingly, transconjugants exhibited the antibiotic resistance patterns of the donors, despite having been selected only on the basis of chloramphenicol resistance. This is the first report carried out in a bivalve hatchery elucidating the persistence of resistant vibrios, the mechanisms of antibiotic resistance, and the transfer of different R-plasmids.}, }
@article {pmid26530280, year = {2016}, author = {McArthur, JV and Fletcher, DE and Tuckfield, RC and Baker-Austin, C}, title = {Patterns of Multi-Antibiotic-Resistant Escherichia Coli from Streams with No History of Antimicrobial Inputs.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {840-850}, pmid = {26530280}, issn = {1432-184X}, mesh = {Aminoglycosides/pharmacology ; Anti-Bacterial Agents/*pharmacology ; Ciprofloxacin/pharmacology ; Drug Combinations ; Drug Resistance, Multiple, Bacterial/*physiology ; Escherichia coli/*drug effects/isolation &amp; purification ; Fluoroquinolones/pharmacology ; Gatifloxacin ; Geologic Sediments/*microbiology ; Microbial Sensitivity Tests ; Rivers/*microbiology ; Water Microbiology ; beta-Lactam Resistance/genetics ; beta-Lactams/pharmacology ; }, abstract = {A growing body of evidence suggests that contaminated environments may harbor a greater proportion of antibiotic-resistant microorganisms than unpolluted reference sites. Here, we report the screening of 427 Escherichia coli strains isolated from 11 locations on nine streams draining the US Department of Energy's Savannah River Site against a panel of five antibiotics. Streams were chosen to capture a wide range of watersheds from minimally disturbed to highly impacted. Overall, higher levels of resistance were found in waterborne E. coli that also generally exhibited low spatial variability. However, 3 of 11 locations also demonstrated elevated resistance levels in sediments. Two of these occurred in highly disturbed tributaries with no obvious sources of antimicrobials. To further investigate these patterns, we screened a subset of isolates obtained from three streams against 23 antibiotics or antibiotic combinations. A large proportion of these isolates (>40 %) demonstrated resistance to 10 or more antimicrobials, suggesting that environmental multi-antibiotic resistance may be prevalent in this bacterial commensal. Only 4 of 87 viable isolates were tested susceptible to all 23 antibiotics and combinations. Among these multi-antibiotic-resistant isolates, several demonstrated resistance to all structural classes of antimicrobial agents tested, including frontline antibiotics such as gatifloxacin and ciprofloxacin.}, }
@article {pmid27777983, year = {2016}, author = {Hambright, WS and Deng, J and Tiedje, JM and Brettar, I and Rodrigues, JL}, title = {Shewanella baltica Ecotypes Have Wide Transcriptional Variation under the Same Growth Conditions.}, journal = {mSphere}, volume = {1}, number = {5}, pages = {}, pmid = {27777983}, issn = {2379-5042}, abstract = {In bacterial populations, subtle expressional differences may promote ecological specialization through the formation of distinct ecotypes. In a barrier-free habitat, this process most likely precedes population divergence and may predict speciation events. To examine this, we used four sequenced strains of the bacterium Shewanella baltica, OS155, OS185, OS195, and OS223, as models to assess transcriptional variation and ecotype formation within a prokaryotic population. All strains were isolated from different depths throughout a water column of the Baltic Sea, occupying different ecological niches characterized by various abiotic parameters. Although the genome sequences are nearly 100% conserved, when grown in the laboratory under standardized conditions, all strains exhibited different growth rates, suggesting significant expressional variation. Using the Ecotype Simulation algorithm, all strains were considered to be discrete ecotypes when compared to 32 other S. baltica strains isolated from the same water column, suggesting ecological divergence. Next, we employed custom microarray slides containing oligonucleotide probes representing the core genome of OS155, OS185, OS195, and OS223 to detect natural transcriptional variation among strains grown under identical conditions. Significant transcriptional variation was noticed among all four strains. Differentially expressed gene profiles seemed to coincide with the metabolic signatures of the environment at the original isolation depth. Transcriptional pattern variations such as the ones highlighted here may be used as indicators of short-term evolution emerging from the formation of bacterial ecotypes. IMPORTANCE Eukaryotic studies have shown considerable transcriptional variation among individuals from the same population. It has been suggested that natural variation in eukaryotic gene expression may have significant evolutionary consequences and may explain large-scale phenotypic divergence of closely related species, such as humans and chimpanzees (M.-C. King and A. C. Wilson, Science 188:107-116, 1975, http://dx.doi.org/10.1126/science.1090005; M. F. Oleksiak, G. A. Churchill, and D. L. Crawford, Nat Genet 32:261-266, 2002, http://dx.doi.org/10.1038/ng983). However, natural variation in gene expression is much less well understood in prokaryotic organisms. In this study, we used four sequenced strains of the marine bacterium Shewanella baltica to better understand the natural transcriptional divergence of a stratified prokaryotic population. We found substantial low-magnitude expressional variation among the four S. baltica strains cultivated under identical laboratory conditions. Collectively, our results indicate that transcriptional variation is an important factor for ecological speciation.}, }
@article {pmid27696631, year = {2016}, author = {Almeida, A and Alves-Barroco, C and Sauvage, E and Bexiga, R and Albuquerque, P and Tavares, F and Santos-Sanches, I and Glaser, P}, title = {Persistence of a dominant bovine lineage of group B Streptococcus reveals genomic signatures of host adaptation.}, journal = {Environmental microbiology}, volume = {18}, number = {11}, pages = {4216-4229}, doi = {10.1111/1462-2920.13550}, pmid = {27696631}, issn = {1462-2920}, mesh = {Adaptation, Physiological ; Animals ; Anti-Bacterial Agents/pharmacology ; Cattle ; Cattle Diseases/*microbiology ; Europe ; Female ; Genomics ; Male ; Streptococcal Infections/microbiology/*veterinary ; Streptococcus agalactiae/classification/drug effects/genetics/*physiology ; }, abstract = {Group B Streptococcus (GBS) is a host-generalist species, most notably causing disease in humans and cattle. However, the differential adaptation of GBS to its two main hosts, and the risk of animal to human infection remain poorly understood. Despite improvements in control measures across Europe, GBS is still one of the main causative agents of bovine mastitis in Portugal. Here, by whole-genome analysis of 150 bovine GBS isolates we discovered that a single CC61 clone is spreading throughout Portuguese herds since at least the early 1990s, having virtually replaced the previous GBS population. Mutations within an iron/manganese transporter were independently acquired by all of the CC61 isolates, underlining a key adaptive strategy to persist in the bovine host. Lateral transfer of bacteriocin production and antibiotic resistance genes also underscored the contribution of the microbial ecology and genetic pool within the bovine udder environment to the success of this clone. Compared to strains of human origin, GBS evolves twice as fast in bovines and undergoes recurrent pseudogenizations of human-adapted traits. Our work provides new insights into the potentially irreversible adaptation of GBS to the bovine environment.}, }
@article {pmid27093047, year = {2016}, author = {Hemp, J and Lücker, S and Schott, J and Pace, LA and Johnson, JE and Schink, B and Daims, H and Fischer, WW}, title = {Genomics of a phototrophic nitrite oxidizer: insights into the evolution of photosynthesis and nitrification.}, journal = {The ISME journal}, volume = {10}, number = {11}, pages = {2669-2678}, pmid = {27093047}, issn = {1751-7370}, support = {T32 DK007202/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/enzymology/genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Evolution, Molecular ; Genome, Bacterial ; Genomics ; Nitrification ; Nitrite Reductases/genetics/metabolism ; Nitrites/*metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; *Photosynthesis ; Phototrophic Processes ; Phylogeny ; }, abstract = {Oxygenic photosynthesis evolved from anoxygenic ancestors before the rise of oxygen ~2.32 billion years ago; however, little is known about this transition. A high redox potential reaction center is a prerequisite for the evolution of the water-oxidizing complex of photosystem II. Therefore, it is likely that high-potential phototrophy originally evolved to oxidize alternative electron donors that utilized simpler redox chemistry, such as nitrite or Mn. To determine whether nitrite could have had a role in the transition to high-potential phototrophy, we sequenced and analyzed the genome of Thiocapsa KS1, a Gammaproteobacteria capable of anoxygenic phototrophic nitrite oxidation. The genome revealed a high metabolic flexibility, which likely allows Thiocapsa KS1 to colonize a great variety of habitats and to persist under fluctuating environmental conditions. We demonstrate that Thiocapsa KS1 does not utilize a high-potential reaction center for phototrophic nitrite oxidation, which suggests that this type of phototrophic nitrite oxidation did not drive the evolution of high-potential phototrophy. In addition, phylogenetic and biochemical analyses of the nitrite oxidoreductase (NXR) from Thiocapsa KS1 illuminate a complex evolutionary history of nitrite oxidation. Our results indicate that the NXR in Thiocapsa originates from a different nitrate reductase clade than the NXRs in chemolithotrophic nitrite oxidizers, suggesting that multiple evolutionary trajectories led to modern nitrite-oxidizing bacteria.}, }
@article {pmid27022995, year = {2016}, author = {Widder, S and Allen, RJ and Pfeiffer, T and Curtis, TP and Wiuf, C and Sloan, WT and Cordero, OX and Brown, SP and Momeni, B and Shou, W and Kettle, H and Flint, HJ and Haas, AF and Laroche, B and Kreft, JU and Rainey, PB and Freilich, S and Schuster, S and Milferstedt, K and van der Meer, JR and Groβkopf, T and Huisman, J and Free, A and Picioreanu, C and Quince, C and Klapper, I and Labarthe, S and Smets, BF and Wang, H and ,  and Soyer, OS}, title = {Challenges in microbial ecology: building predictive understanding of community function and dynamics.}, journal = {The ISME journal}, volume = {10}, number = {11}, pages = {2557-2568}, pmid = {27022995}, issn = {1751-7370}, support = {BB/K003240/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; NC/K000683/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; }, mesh = {*Air Microbiology ; Animals ; Ecosystem ; Humans ; Models, Theoretical ; Seawater/*microbiology ; *Soil Microbiology ; }, abstract = {The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth's soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and manage the function of these highly complex, dynamically changing communities is limited. Building predictive models that link MC composition to function is a key emerging challenge in microbial ecology. Here, we argue that addressing this challenge requires close coordination of experimental data collection and method development with mathematical model building. We discuss specific examples where model-experiment integration has already resulted in important insights into MC function and structure. We also highlight key research questions that still demand better integration of experiments and models. We argue that such integration is needed to achieve significant progress in our understanding of MC dynamics and function, and we make specific practical suggestions as to how this could be achieved.}, }
@article {pmid27775707, year = {2016}, author = {Petersen, JM and Kemper, A and Gruber-Vodicka, H and Cardini, U and van der Geest, M and Kleiner, M and Bulgheresi, S and Mußmann, M and Herbold, C and Seah, BK and Antony, CP and Liu, D and Belitz, A and Weber, M}, title = {Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation.}, journal = {Nature microbiology}, volume = {2}, number = {1}, pages = {16195}, pmid = {27775707}, issn = {2058-5276}, mesh = {Animals ; Aquatic Organisms/*microbiology ; Bacteria/*enzymology/genetics ; Bivalvia/*microbiology ; Chromadorea/*microbiology ; Gene Expression Profiling ; *Nitrogen Fixation ; Nitrogenase/genetics ; Proteome/analysis ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Chemosynthetic symbioses are partnerships between invertebrate animals and chemosynthetic bacteria. The latter are the primary producers, providing most of the organic carbon needed for the animal host's nutrition. We sequenced genomes of the chemosynthetic symbionts from the lucinid bivalve Loripes lucinalis and the stilbonematid nematode Laxus oneistus. The symbionts of both host species encoded nitrogen fixation genes. This is remarkable as no marine chemosynthetic symbiont was previously known to be capable of nitrogen fixation. We detected nitrogenase expression by the symbionts of lucinid clams at the transcriptomic and proteomic level. Mean stable nitrogen isotope values of Loripes lucinalis were within the range expected for fixed atmospheric nitrogen, further suggesting active nitrogen fixation by the symbionts. The ability to fix nitrogen may be widespread among chemosynthetic symbioses in oligotrophic habitats, where nitrogen availability often limits primary productivity.}, }
@article {pmid27775220, year = {2017}, author = {Bjørnsgaard Aas, A and Davey, ML and Kauserud, H}, title = {ITS all right mama: investigating the formation of chimeric sequences in the ITS2 region by DNA metabarcoding analyses of fungal mock communities of different complexities.}, journal = {Molecular ecology resources}, volume = {17}, number = {4}, pages = {730-741}, doi = {10.1111/1755-0998.12622}, pmid = {27775220}, issn = {1755-0998}, mesh = {Algorithms ; *DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/*genetics ; Fungi/*classification ; Polymerase Chain Reaction ; }, abstract = {The formation of chimeric sequences can create significant methodological bias in PCR-based DNA metabarcoding analyses. During mixed-template amplification of barcoding regions, chimera formation is frequent and well documented. However, profiling of fungal communities typically uses the more variable rDNA region ITS. Due to a larger research community, tools for chimera detection have been developed mainly for the 16S/18S markers. However, these tools are widely applied to the ITS region without verification of their performance. We examined the rate of chimera formation during amplification and 454 sequencing of the ITS2 region from fungal mock communities of different complexities. We evaluated the chimera detecting ability of two common chimera-checking algorithms: perseus and uchime. Large proportions of the chimeras reported were false positives. No false negatives were found in the data set. Verified chimeras accounted for only 0.2% of the total ITS2 reads, which is considerably less than what is typically reported in 16S and 18S metabarcoding analyses. Verified chimeric 'parent sequences' had significantly higher per cent identity to one another than to random members of the mock communities. Community complexity increased the rate of chimera formation. GC content was higher around the verified chimeric break points, potentially facilitating chimera formation through base pair mismatching in the neighbouring regions of high similarity in the chimeric region. We conclude that the hypervariable nature of the ITS region seems to buffer the rate of chimera formation in comparison with other, less variable barcoding regions, due to shorter regions of high sequence similarity.}, }
@article {pmid27173172, year = {2016}, author = {Schievano, A and Pepé Sciarria, T and Vanbroekhoven, K and De Wever, H and Puig, S and Andersen, SJ and Rabaey, K and Pant, D}, title = {Electro-Fermentation - Merging Electrochemistry with Fermentation in Industrial Applications.}, journal = {Trends in biotechnology}, volume = {34}, number = {11}, pages = {866-878}, doi = {10.1016/j.tibtech.2016.04.007}, pmid = {27173172}, issn = {1879-3096}, mesh = {*Bioreactors ; *Electrochemical Techniques ; *Fermentation ; *Industrial Microbiology ; Oxidation-Reduction ; }, abstract = {Electro-fermentation (EF) merges traditional industrial fermentation with electrochemistry. An imposed electrical field influences the fermentation environment and microbial metabolism in either a reductive or oxidative manner. The benefit of this approach is to produce target biochemicals with improved selectivity, increase carbon efficiency, limit the use of additives for redox balance or pH control, enhance microbial growth, or in some cases enhance product recovery. We discuss the principles of electrically driven fermentations and how EF can be used to steer both pure culture and microbiota-based fermentations. An overview is given on which advantages EF may bring to both existing and innovative industrial fermentation processes, and which doors might be opened in waste biomass utilization towards added-value biorefineries.}, }
@article {pmid27770517, year = {2016}, author = {Siddiqui, H and Chen, T and Aliko, A and Mydel, PM and Jonsson, R and Olsen, I}, title = {Microbiological and bioinformatics analysis of primary Sjogren's syndrome patients with normal salivation.}, journal = {Journal of oral microbiology}, volume = {8}, number = {}, pages = {31119}, pmid = {27770517}, issn = {2000-2297}, support = {R37 DE016937/DE/NIDCR NIH HHS/United States ; }, abstract = {BACKGROUND: Reduced salivation is considered a major clinical feature of most but not all cases of primary Sjögren's syndrome (pSS). Reduced saliva flow may lead to changes in the salivary microbiota. These changes have mainly been studied with culture that typically recovers only 65% of the bacteria present.<br><br>OBJECTIVE: This study was to use high throughput sequencing, covering both cultivated and not-yet-cultivated bacteria, to assess the bacterial microbiota of whole saliva in pSS patients with normal salivation.<br><br>METHODS: Bacteria of whole unstimulated saliva from nine pSS patients with normal salivation flow and from nine healthy controls were examined by high throughput sequencing of the hypervariable region V1V2 of 16S rRNA using the 454 GS Junior system. Raw sequence reads were subjected to a species-level, reference-based taxonomy assignment pipeline specially designed for studying the human oral microbial community. Each of the sequence reads was BLASTN-searched against a database consisting of reference sequences representing 1,156 oral and 12,013 non-oral species. Unassigned reads were then screened for high-quality non-chimeras and subjected to de novo species-level operational taxonomy unit (OTU) calling for potential novel species. Downstream analyses, including alpha and beta diversities, were analyzed using the Quantitative Insights into Microbial Ecology (QIIME) pipeline. To reveal significant differences between the microbiota of control saliva and Sj&#xf6;gren's saliva, a statistical method introduced in Metastats www.metastats.cbcb.umd.edu was used.<br><br>RESULTS: Saliva of pSS patients with normal salivation had a significantly higher frequency of Firmicutes compared with controls (p=0.004). Two other major phyla, Synergistetes and Spirochaetes, were significantly depleted in pSS (p=0.001 for both). In addition, we saw a nearly 17% decrease in the number of genera in pSS (25 vs. 30). While Prevotella was almost equally abundant in both groups (25% in pSS and 22% in controls), about a twofold increase in pSS of Streptococcus (28% vs. 17%) and Veillonella (26% vs. 12%) was detected. Prevotella melaninogenica was the major species in controls (13%) while Veillonella atypica and the Veillonella parvula groups dominated in patient samples (14 and 14%). The scarcity in bacterial species in pSS compared with controls was also demonstrated by alpha and beta diversity analyses, as well as read abundance depicted in a phylogenetic tree.<br><br>CONCLUSIONS: While Firmicutes was significantly higher in pSS patients than in controls, Synergistetes and Spirochaetes were significantly lower. The number of bacterial genera and species was also lower. These data showed that microbial dysbiosis is another key characteristic of pSS whole saliva which can occur independent of hyposalivation.}, }
@article {pmid27770349, year = {2016}, author = {Anza, M and Epelde, L and Artetxe, U and Becerril, JM and Garbisu, C}, title = {Control of Cortaderia selloana with a glyphosate-based herbicide led to a short-term stimulation of soil fungal communities.}, journal = {Environmental monitoring and assessment}, volume = {188}, number = {11}, pages = {631}, pmid = {27770349}, issn = {1573-2959}, mesh = {Biomass ; Ecosystem ; Fungi/*drug effects ; Glycine/*analogs &amp; derivatives/pharmacology ; Herbicides/*pharmacology ; Introduced Species ; Nitrogen/analysis ; *Poaceae ; Rhizosphere ; *Soil Microbiology ; Spain ; Glyphosate ; }, abstract = {In the north of Spain, Cortaderia selloana plants have invaded ecosystems of high ecological value. Control of this species is carried out with the application of glyphosate-based formulations. The aim of this work was to determine, under microcosm conditions, the short-term (2 months) effects of the application of a glyphosate-based herbicide (Roundup®) on C. selloana rhizosphere microbial communities. To this purpose, before and after the application of Roundup®, several parameters that provide information on the biomass, activity and diversity of rhizosphere fungal and bacterial communities (enzyme activities, basal and substrate-induced respiration, potentially mineralizable nitrogen, nitrification potential rate, ergosterol content and community-level profiles with Biolog™ plates and ARISA) were determined. We observed a stimulation of some microbial parameters, in particular those related to fungal communities. Further research is needed to determine the long-term consequences of this short-term fungal stimulation for soil functioning.}, }
@article {pmid27770039, year = {2017}, author = {Rostami, N and Shields, RC and Yassin, SA and Hawkins, AR and Bowen, L and Luo, TL and Rickard, AH and Holliday, R and Preshaw, PM and Jakubovics, NS}, title = {A Critical Role for Extracellular DNA in Dental Plaque Formation.}, journal = {Journal of dental research}, volume = {96}, number = {2}, pages = {208-216}, doi = {10.1177/0022034516675849}, pmid = {27770039}, issn = {1544-0591}, support = {DRF-2015-08-077/DH_/Department of Health/United Kingdom ; }, mesh = {Biofilms/growth &amp; development ; DNA, Bacterial/*physiology ; Dental Implants/microbiology ; Dental Plaque/*etiology/microbiology/ultrastructure ; Enterococcus faecalis/genetics/metabolism ; Humans ; Microscopy, Electron, Scanning ; Saliva/metabolism ; }, abstract = {Extracellular DNA (eDNA) has been identified in the matrix of many different monospecies biofilms in vitro, including some of those produced by oral bacteria. In many cases, eDNA stabilizes the structure of monospecies biofilms. Here, the authors aimed to determine whether eDNA is an important component of natural, mixed-species oral biofilms, such as plaque on natural teeth or dental implants. To visualize eDNA in oral biofilms, approaches for fluorescently stained eDNA with either anti-DNA antibodies or an ultrasensitive cell-impermeant dye, YOYO-1, were first developed using Enterococcus faecalis, an organism that has previously been shown to produce extensive eDNA structures within biofilms. Oral biofilms were modelled as in vitro "microcosms" on glass coverslips inoculated with the natural microbial population of human saliva and cultured statically in artificial saliva medium. Using antibodies and YOYO-1, eDNA was found to be distributed throughout microcosm biofilms, and was particularly abundant in the immediate vicinity of cells. Similar arrangements of eDNA were detected in biofilms on crowns and overdenture abutments of dental implants that had been recovered from patients during the restorative phase of treatment, and in subgingival dental plaque of periodontitis patients, indicating that eDNA is a common component of natural oral biofilms. In model oral biofilms, treatment with a DNA-degrading enzyme, NucB from Bacillus licheniformis, strongly inhibited the accumulation of biofilms. The bacterial species diversity was significantly reduced by treatment with NucB and particularly strong reductions were observed in the abundance of anaerobic, proteolytic bacteria such as Peptostreptococcus, Porphyromonas and Prevotella. Preformed biofilms were not significantly reduced by NucB treatment, indicating that eDNA is more important or more exposed during the early stages of biofilm formation. Overall, these data demonstrate that dental plaque eDNA is potentially an important target for oral biofilm control.}, }
@article {pmid27769902, year = {2017}, author = {Garrido-Benavent, I and Pérez-Ortega, S and de Los Ríos, A}, title = {From Alaska to Antarctica: Species boundaries and genetic diversity of Prasiola (Trebouxiophyceae), a foliose chlorophyte associated with the bipolar lichen-forming fungus Mastodia tessellata.}, journal = {Molecular phylogenetics and evolution}, volume = {107}, number = {}, pages = {117-131}, doi = {10.1016/j.ympev.2016.10.013}, pmid = {27769902}, issn = {1095-9513}, mesh = {Alaska ; Antarctic Regions ; Ascomycota/*genetics ; Bayes Theorem ; Chlorophyta/*genetics/*microbiology ; Cluster Analysis ; Genetic Loci ; *Genetic Variation ; Haplotypes/genetics ; Lichens/*microbiology ; Likelihood Functions ; Phylogeny ; Phylogeography ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; }, abstract = {Symbiotic associations between green algae (Chlorophyta) and fungi give rise to morphologically and eco-physiologically distinct entities, or so-called, lichens. In one of the most peculiar of these associations, the partners are species of the macroscopic genus Prasiola (Trebouxiophyceae) and the ascomycete Mastodia tessellata (Verrucariaceae). This is the only known case of a lichen symbiosis involving a foliose green alga. Despite intense research targeted at understanding the biology of this particular association, little is known about the genetic variability of its symbionts. This study focuses on the photobiont partner of this lichen and was designed to explore and compare its genetic diversity along a latitudinal axis from Alaska to Antarctica. Molecular sequence data were generated for three loci: two nuclear markers (nrITS, RPL10A) and one plastid-encoded marker (tufA). The usefulness of the Prasiola nrITS and RPL10A data was examined at the species and intraspecific levels. We used the population assignment tests implemented in BAPS and STRUCTURE and two algorithmic species delimitation procedures (ABGD, GMYC) to generate species boundary discovery hypotheses, which were subsequently tested using Bayes factors. Population genetic differentiation and structure were also assessed through fixation indices, polymorphism statistics and haplotype networks. Based on the results of the species validation method, we propose that at least two species of Prasiola associate with the lichen-forming fungus Mastodia tessellata. Of these, P. borealis is broadly distributed in Alaska, Tierra del Fuego and the Antarctic Peninsula, whereas the second, undescribed, species is restricted to the Antarctic Peninsula. We detected significant phylogeographic substructure in P. borealis, including greater haplotype diversity in the Tierra del Fuego populations. Our findings provide new data that will be useful to unravel the cryptic diversity and phylogeographic patterns of the green alga partners of lichens.}, }
@article {pmid27768826, year = {2016}, author = {Berg, JS and Michellod, D and Pjevac, P and Martinez-Perez, C and Buckner, CR and Hach, PF and Schubert, CJ and Milucka, J and Kuypers, MM}, title = {Intensive cryptic microbial iron cycling in the low iron water column of the meromictic Lake Cadagno.}, journal = {Environmental microbiology}, volume = {18}, number = {12}, pages = {5288-5302}, doi = {10.1111/1462-2920.13587}, pmid = {27768826}, issn = {1462-2920}, mesh = {Bacteria/genetics/isolation &amp; purification/*metabolism ; Carbon/metabolism ; Iron/chemistry/*metabolism ; Lakes/chemistry/*microbiology ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Iron redox reactions play an important role in carbon remineralization, supporting large microbial communities in iron-rich terrestrial and aquatic sediments. Stratified water columns with comparably low iron concentrations are globally widespread, but microbial iron cycling in these systems has largely been ignored. We found evidence for unexpectedly high iron turnover rates in the low (1-2 µmol·l[-1]) iron waters of Lake Cadagno. Light-dependent, biological iron oxidation rates (1.4-13.8 µmol·l[-1] ·d[-1]) were even higher than in ferruginous lakes with well-studied microbial iron cycles. This photoferrotrophic iron oxidation may account for up to 10% of total primary production in the chemocline. Iron oxides could not be detected and were presumably reduced immediately by iron-reducing microorganisms. Sequences of putative iron oxidizers and reducers were retrieved from in situ 16S rRNA gene amplicon libraries and some of these bacteria were identified in our enrichment cultures supplemented with Fe(II) and FeS. Based on our results, we propose a model in which iron is oxidized by photoferrotrophs and microaerophiles, and iron oxides are immediately reduced by heterotrophic iron reducers, resulting in a cryptic iron cycle. We hypothesize that microbial iron cycling may be more prevalent in water column redoxclines, especially those within the photic zone, than previously believed.}, }
@article {pmid27768533, year = {2017}, author = {Wang, S and Pu, Y and Wei, C}, title = {COD and nitrogen removal and microbial communities in a novel waterfall biofilm reactor operated at different COD/TN ratios.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances &amp; environmental engineering}, volume = {52}, number = {2}, pages = {99-105}, doi = {10.1080/10934529.2016.1237115}, pmid = {27768533}, issn = {1532-4117}, mesh = {Biofilms ; Biological Oxygen Demand Analysis ; Bioreactors/*microbiology ; Denitrification ; Humans ; Nitrogen/*chemistry ; Wastewater ; *Water Microbiology ; Water Purification/methods ; }, abstract = {The aim of this study was to characterize the pollutant removal efficiency and the microbial communities that arose in a newly designed waterfall biofilm reactor (WFBR) at different chemical oxygen demand/total nitrogen (COD/TN) ratios. The reactor was operated continuously for 28 days at different COD/TN ratios, and its efficiency was evaluated. Results showed that as the thickness of the biofilm increased, the structure of the biofilm encouraged anaerobic-aerobic, anoxic-anaerobic, and fully anaerobic conditions in one reactor. The COD/TN ratios used had a significant effect on the removal of COD and nitrogen components. At a COD/TN ratio of 14, the ammonium nitrogen removal efficiency reached its highest value (99%), but the COD removal efficiency remained at approximately 90%. High-throughput sequencing revealed that the highest community diversity and richness were seen at a COD/TN ratio of 18, and the major phyla were Proteobacteria (average abundance of 47%), Actinobacteria (24%), and Bacteroidetes (13%). As the COD/TN ratios increased from 7 to 18, the abundance of Proteobacteria gradually increased from 25% to 68%. These results could provide important guidance for the design of new wastewater treatment systems and also enrich our theoretical understanding of microbial ecology.}, }
@article {pmid27762325, year = {2016}, author = {Chen, W and Dai, X and Cao, D and Wang, S and Hu, X and Liu, W and Yang, D}, title = {Performance and microbial ecology of a nitritation sequencing batch reactor treating high-strength ammonia wastewater.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {35693}, pmid = {27762325}, issn = {2045-2322}, mesh = {Ammonia/*metabolism ; Bacteria/*classification/genetics ; Bioreactors/*microbiology ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Nitrification ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Wastewater/*chemistry/*microbiology ; }, abstract = {The partial nitrification (PN) performance and the microbial community variations were evaluated in a sequencing batch reactor (SBR) for 172 days, with the stepwise elevation of ammonium concentration. Free ammonia (FA) and low dissolved oxygen inhibition of nitrite-oxidized bacteria (NOB) were used to achieve nitritation in the SBR. During the 172 days operation, the nitrogen loading rate of the SBR was finally raised to 3.6 kg N/m[3]/d corresponding the influent ammonium of 1500 mg/L, with the ammonium removal efficiency and nitrite accumulation rate were 94.12% and 83.54%, respectively, indicating that the syntrophic inhibition of FA and low dissolved oxygen contributed substantially to the stable nitrite accumulation. The results of the 16S rRNA high-throughput sequencing revealed that Nitrospira, the only nitrite-oxidizing bacteria in the system, were successively inhibited and eliminated, and the SBR reactor was dominated finally by Nitrosomonas, the ammonium-oxidizing bacteria, which had a relative abundance of 83%, indicating that the Nitrosomonas played the primary roles on the establishment and maintaining of nitritation. Followed by Nitrosomonas, Anaerolineae (7.02%) and Saprospira (1.86%) were the other mainly genera in the biomass.}, }
@article {pmid27761636, year = {2017}, author = {Liu, J and Ren, H and Ye, X and Wang, W and Liu, Y and Lou, L and Cheng, D and He, X and Zhou, X and Qiu, S and Fu, L and Hu, B}, title = {Bacterial community radial-spatial distribution in biofilms along pipe wall in chlorinated drinking water distribution system of East China.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {2}, pages = {749-759}, doi = {10.1007/s00253-016-7887-8}, pmid = {27761636}, issn = {1432-0614}, mesh = {Bacteria/classification/genetics/*growth &amp; development ; Bacterial Load ; Biofilms/*growth &amp; development ; Biota ; China ; Chlorine ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Disinfection ; Drinking Water/chemistry ; *Environmental Microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Biofilms in the pipe wall may lead to water quality deterioration and biological instability in drinking water distribution systems (DWDSs). In this study, bacterial community radial-spatial distribution in biofilms along the pipe wall in a chlorinated DWDS of East China was investigated. Three pipes of large diameter (300, 600, and 600 mm) were sampled in this DWDS, including a ductile cast iron pipe (DCIP) with pipe age of 11 years and two gray cast iron pipes (GCIP) with pipe ages of 17 and 19 years, and biofilms in the upper, middle, and lower parts of each pipe wall were collected. Real-time quantitative polymerase chain reaction (qPCR) and culture-based method were used to quantify bacteria. 454 pyrosequencing was used for bacterial community analysis. The results showed that the biofilm density and total solid (TS) and volatile solid (VS) contents increased gradually from the top to the bottom along the pipe wall. Microorganisms were concentrated in the upper and lower parts of the pipe wall, together accounting for more than 80 % of the total biomass in the biofilms. The bacterial communities in biofilms were significantly different in different areas of the pipe wall and had no strong interaction. Compared with the upper and lower parts of the pipe wall, the bacterial community in the middle of the pipe wall was distributed evenly and had the highest diversity. The 16S rRNA genes of various possible pathogens, including Escherichia coli, Staphylococcus epidermidis, Pseudomonas aeruginosa, and Salmonella enterica, were detected in the biofilms, and the abundances of these possible pathogens were highest in the middle of the pipe wall among three areas. The detachment of the biofilms is the main reason for the deterioration of the water quality in DWDSs. The results of this study suggest that the biofilms in the middle of the pipe wall have highly potential risk for drinking water safety, which provides new ideas for the study of the microbial ecology in DWDS.}, }
@article {pmid27760410, year = {2016}, author = {Kjerstadius, H and de Vrieze, J and la Cour Jansen, J and Davidsson, &#xc5;}, title = {Detection of acidification limit in anaerobic membrane bioreactors at ambient temperature.}, journal = {Water research}, volume = {106}, number = {}, pages = {429-438}, doi = {10.1016/j.watres.2016.10.032}, pmid = {27760410}, issn = {1879-2448}, mesh = {Anaerobiosis ; Bacteria, Anaerobic/metabolism ; *Bioreactors ; Methane/metabolism ; Real-Time Polymerase Chain Reaction ; *Temperature ; Wastewater ; }, abstract = {High-volume, low-strength industrial wastewaters constitute a large potential for biogas production, which could be realized by membrane bioreactors operating at the ambient temperature of the wastewater. However, the start-up of low-temperature anaerobic processes using unadapted inoculum can be sensitive to overloading, which results in acidification. This study assessed if a novel acidification limit test can be used to identify stable organic loading rates as well as process over-loading. The test is based on easy-to-apply batch experiments for determination of the hydrolysis rate constant and the specific methanogenic activity of the acetotrophic and hydrogenotrophic pathways. For evaluation, two anaerobic membrane bioreactors, treating synthetic dairy wastewater at an ambient temperature of 24 °C, were used with a slow or a rapid start-up regime, respectively. Tests for hydrolysis rate and methanogenic activity were performed throughout the experiment and were used to calculate acidification limits for each system throughout the start-up. The acidification limit test was able to successfully identify both stable operation of one reactor and process failure of the other reactor as the organic loading rate increased. The reactor failure was caused by over-loading the acetotrophic pathway and coincided with microbial changes observed in real-time PCR and moving window analysis. Overall, the acidification limit tests seem promising as an easy applicable method for estimating what organic loading rate can be utilized, without risking acidification of anaerobic systems.}, }
@article {pmid27757753, year = {2017}, author = {Liu, Y and Zhang, Y and Zhao, Z and Ngo, HH and Guo, W and Zhou, J and Peng, L and Ni, BJ}, title = {A modeling approach to direct interspecies electron transfer process in anaerobic transformation of ethanol to methane.}, journal = {Environmental science and pollution research international}, volume = {24}, number = {1}, pages = {855-863}, pmid = {27757753}, issn = {1614-7499}, mesh = {Anaerobiosis ; Carbon/chemistry ; Electron Transport ; Ethanol/*analysis/metabolism ; Geobacter/*metabolism ; Hydrogen/metabolism ; Methane/*analysis/metabolism ; Methanosarcina/*metabolism ; *Models, Theoretical ; Species Specificity ; }, abstract = {Recent studies have shown that direct interspecies electron transfer (DIET) plays an important part in contributing to methane production from anaerobic digestion. However, so far anaerobic digestion models that have been proposed only consider two pathways for methane production, namely, acetoclastic methanogenesis and hydrogenotrophic methanogenesis, via indirect interspecies hydrogen transfer, which lacks an effective way for incorporating DIET into this paradigm. In this work, a new mathematical model is specifically developed to describe DIET process in anaerobic digestion through introducing extracellular electron transfer as a new pathway for methane production, taking anaerobic transformation of ethanol to methane as an example. The developed model was able to successfully predict experimental data on methane dynamics under different experimental conditions, supporting the validity of the developed model. Modeling predictions clearly demonstrated that DIET plays an important role in contributing to overall methane production (up to 33 %) and conductive material (i.e., carbon cloth) addition would significantly promote DIET through increasing ethanol conversion rate and methane production rate. The model developed in this work will potentially enhance our current understanding on syntrophic metabolism via DIET.}, }
@article {pmid27561962, year = {2016}, author = {Svenningsen, NB and Nicolaisen, MH and Hansen, HC and de Lorenzo, V and Nybroe, O}, title = {Nitrogen regulation of the xyl genes of Pseudomonas putida mt-2 propagates into a significant effect of nitrate on m-xylene mineralization in soil.}, journal = {Microbial biotechnology}, volume = {9}, number = {6}, pages = {814-823}, pmid = {27561962}, issn = {1751-7915}, mesh = {Ammonium Compounds/metabolism ; Biotransformation ; Cation Transport Proteins/biosynthesis/genetics ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Nitrates/*metabolism ; Pseudomonas putida/drug effects/genetics/*metabolism ; Soil/*chemistry ; *Soil Microbiology ; Xylenes/*metabolism ; }, abstract = {The nitrogen species available in the growth medium are key factors determining expression of xyl genes for biodegradation of aromatic compounds by Pseudomonas putida. Nitrogen compounds are frequently amended to promote degradation at polluted sites, but it remains unknown how regulation observed in the test tube is propagated into actual catabolism of, e.g. m-xylene in soil, the natural habitat of this bacterium. To address this issue, we have developed a test-tube-to-soil model system that exposes the end-effects of remediation practices influencing gene expression of P. putida mt-2. We found that NO3[-] compared with NH4[+] had a stimulating effect on xyl gene expression in pure culture as well as in soil, and that this stimulation was translated into increased m-xylene mineralization in soil. Furthermore, expression analysis of the nitrogen-regulated genes amtB and gdhA allowed us to monitor nitrogen sensing status in both experimental systems. Hence, for nitrogen sources, regulatory patterns that emerge in soil reflect those observed in liquid cultures. The current study shows how distinct regulatory traits can lead to discrete environmental consequences; and it underpins that attempts to improve bioremediation by nitrogen amendment should integrate knowledge on their effects on growth and on catabolic gene regulation under natural conditions.}, }
@article {pmid27752719, year = {2017}, author = {Zhang, Y and Simon, SE and Johnson, JA and Allen, MS}, title = {Spatial Microbial Composition Along the Gastrointestinal Tract of Captive Attwater's Prairie Chicken.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {966-977}, pmid = {27752719}, issn = {1432-184X}, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Birds ; Cecum/microbiology ; Cloaca/microbiology ; DNA, Bacterial ; Galliformes/*microbiology ; Gastrointestinal Tract/*microbiology ; Ileum/microbiology ; Intestine, Large/microbiology ; *Microbial Consortia ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Gastrointestinal microbiota is increasingly recognized as an important component of individual health, and therefore, our ability to quantify its diversity accurately is central for exploring different ways to improve health. Non-invasive sampling methods, such as cloaca swabs, are often used to measure gastrointestinal microbiota diversity within an individual. However, few studies have addressed to what degree differences exist in microbial community composition along the gastrointestinal tract, and measures obtained from the cloaca may not actually represent the diversity present elsewhere in the gastrointestinal tract. In this study, we systematically characterized the gastrointestinal microbial community of the critically endangered Attwater's Prairie chicken (Tympanuchus cupido attwateri) by opportunistically sampling four different locations (ileum, cecum, large intestine, and cloaca) along the gastrointestinal tract of eight individuals. Spatial variation of microbial community was observed at different sampling locations within the gastrointestinal tract. The cecum harbored the most diverse and significantly different microbiota from the other locations, while the microbial α- and β-diversities were similar in the ileum, large intestine, and cloaca. The results of this study provide evidence that microbiota diversity can differ depending on sampling location and metric used to quantify diversity. As shown here, non-invasive cloacal sampling strategies may reflect microbiota diversity elsewhere in the gastrointestinal tract, yet caution is warranted when making generalizations in terms of the microbiota diversity correlations when samples are obtained from a single location within the gastrointestinal tract.}, }
@article {pmid27752718, year = {2017}, author = {Abdelfattah, A and Cacciola, SO and Mosca, S and Zappia, R and Schena, L}, title = {Analysis of the Fungal Diversity in Citrus Leaves with Greasy Spot Disease Symptoms.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {739-749}, pmid = {27752718}, issn = {1432-184X}, mesh = {Ascomycota/*classification/genetics/*isolation &amp; purification ; Base Sequence ; Citrus/*microbiology ; DNA Barcoding, Taxonomic ; DNA, Fungal/*genetics ; Italy ; Metagenomics ; Phylogeny ; Plant Diseases/*microbiology ; Plant Leaves/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Citrus greasy spot (CGS) is a disease of citrus with worldwide distribution and recent surveys have revealed a high level of incidence and severity of symptoms of the disease in Sicily, southern Italy. Although Mycosphaerel la citri (anamorph Zasmidium citri-griseum) and other related species are generally considered as causal agents, the etiology of CGS is still unclear. Here, we report the use of an amplicon metagenomic approach to investigate the fungal communities on citrus leaves symptomatic or asymptomatic for CGS from an orchard in Sicily showing typical CGS symptoms. A total of 35,537 high-quality chimeric free reads were obtained and assigned to 176 operational taxonomic units (OTUs), clustered at 99 % similarity threshold. Data revealed a dominating presence of the phylum Ascomycota (92.6 %) over other fungal phyla. No significant difference was observed between symptomatic and asymptomatic leaves according to both alpha and beta diversity analyses. The family Mycosphaerellaceae was the most abundant and was represented by the genera Ramularia, Mycosphaerella, and Septoria with 44.8, 2.4, and 1.7 % of the total detected sequences, respectively. However, none of the species currently reported as causal agents of CGS was detected in the present study. The most abundant sequence type (ST) was associated to Ramularia brunnea, a species originally described to cause leaf spot in a perennial herbaceous plant of the family Asteraceae. Results exclude that CGS symptoms observed in Sicily are caused by Z. citri-griseum and, moreover, they indicate that a considerable part of the fungal diversity in citrus leaves is still unknown.}, }
@article {pmid27661780, year = {2017}, author = {Lescat, M and Launay, A and Ghalayini, M and Magnan, M and Glodt, J and Pintard, C and Dion, S and Denamur, E and Tenaillon, O}, title = {Using long-term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin-treated mouse gut.}, journal = {Molecular ecology}, volume = {26}, number = {7}, pages = {1802-1817}, pmid = {27661780}, issn = {1365-294X}, support = {310944/ERC_/European Research Council/International ; }, mesh = {*Adaptation, Physiological ; Animals ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/*genetics ; *Evolution, Molecular ; Female ; Gastrointestinal Tract/*microbiology ; Genes, Bacterial ; Mice ; Mutation ; Operon ; Streptomycin/*pharmacology ; }, abstract = {Although microbial ecology of the gut is now a major focus of interest, little is known about the molecular determinants of microbial adaptation in the gut. Experimental evolution coupled with whole-genome sequencing can provide insights of the adaptive process. In vitro experiments have revealed some conserved patterns: intermediate convergence, and epistatic interactions between beneficial mutations and mutations in global regulators. To test the relevance of these patterns and to identify the selective pressures acting in vivo, we have performed a long-term adaptation of an E. coli natural isolate, the streptomycin-resistant strain 536, in the digestive tract of streptomycin-treated mice. After a year of evolution, a clone from 15 replicates was sequenced. Consistently with in vitro observations, the identified mutations revealed a strong pattern of convergence at the mutation, gene, operon and functional levels. Yet, the rate of molecular evolution was lower than in in vitro, and no mutations in global regulators were recovered. More specific targets were observed: the dgo operon, involved in the galactonate pathway that improved growth on D-galactonate, and rluD and gidB, implicated in the maturation of the ribosomes, which mutations improved growth only in the presence of streptomycin. As in vitro, the nonrandom associations of mutations within the same pathways suggested a role of epistasis in shaping the adaptive landscape. Overall, we show that 'evolve and sequence' approach coupled with an analysis of convergence, when applied to a natural isolate, can be used to study adaptation in vivo and uncover the specific selective pressures of that environment.}, }
@article {pmid27750077, year = {2017}, author = {Habtom, H and Demanèche, S and Dawson, L and Azulay, C and Matan, O and Robe, P and Gafny, R and Simonet, P and Jurkevitch, E and Pasternak, Z}, title = {Soil characterisation by bacterial community analysis for forensic applications: A quantitative comparison of environmental technologies.}, journal = {Forensic science international. Genetics}, volume = {26}, number = {}, pages = {21-29}, doi = {10.1016/j.fsigen.2016.10.005}, pmid = {27750077}, issn = {1878-0326}, mesh = {DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Forensic Genetics ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Microarray Analysis ; *Microbiota ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {The ubiquity and transferability of soil makes it a resource for the forensic investigator, as it can provide a link between agents and scenes. However, the information contained in soils, such as chemical compounds, physical particles or biological entities, is seldom used in forensic investigations; due mainly to the associated costs, lack of available expertise, and the lack of soil databases. The microbial DNA in soil is relatively easy to access and analyse, having thus the potential to provide a powerful means for discriminating soil samples or linking them to a common origin. We compared the effectiveness and reliability of multiple methods and genes for bacterial characterisation in the differentiation of soil samples: ribosomal intergenic spacer analysis (RISA), terminal restriction fragment length polymorphism (TRFLP) of the rpoB gene, and five methods using the 16S rRNA gene: phylogenetic microarrays, TRFLP, and high throughput sequencing with Roche 454, Illumina MiSeq and IonTorrent PGM platforms. All these methods were also compared to long-chain hydrocarbons (n-alkanes) and fatty alcohol profiling of the same soil samples. RISA, 16S TRFLP and MiSeq performed best, reliably and significantly discriminating between adjacent, similar soil types. As TRFLP employs the same capillary electrophoresis equipment and procedures used to analyse human DNA, it is readily available for use in most forensic laboratories. TRFLP was optimized for forensic usage in five parameters: choice of primer pair, fluorescent tagging, concentrating DNA after digestion, number of PCR amplifications per sample and number of capillary electrophoresis runs per PCR amplification. This study shows that molecular microbial ecology methodologies are robust in discriminating between soil samples, illustrating their potential usage as an evaluative forensic tool.}, }
@article {pmid27747959, year = {2016}, author = {Grossmann, L and Beisser, D and Bock, C and Chatzinotas, A and Jensen, M and Preisfeld, A and Psenner, R and Rahmann, S and Wodniok, S and Boenigk, J}, title = {Trade-off between taxon diversity and functional diversity in European lake ecosystems.}, journal = {Molecular ecology}, volume = {25}, number = {23}, pages = {5876-5888}, doi = {10.1111/mec.13878}, pmid = {27747959}, issn = {1365-294X}, mesh = {*Biodiversity ; Chlorophyta/classification ; Ciliophora/classification ; Diatoms/classification ; *Ecosystem ; Germany ; Italy ; *Lakes ; Romania ; Spain ; Transcriptome ; }, abstract = {Inferring ecosystem functioning and ecosystem services through inspections of the species inventory is a major aspect of ecological field studies. Ecosystem functions are often stable despite considerable species turnover. Using metatranscriptome analyses, we analyse a thus-far unparalleled freshwater data set which comprises 21 mainland European freshwater lakes from the Sierra Nevada (Spain) to the Carpathian Mountains (Romania) and from northern Germany to the Apennines (Italy) and covers an altitudinal range from 38 m above sea level (a.s.l) to 3110 m a.s.l. The dominant taxa were Chlorophyta and streptophytic algae, Ciliophora, Bacillariophyta and Chrysophyta. Metatranscriptomics provided insights into differences in community composition and into functional diversity via the relative share of taxa to the overall read abundance of distinct functional genes on the ecosystem level. The dominant metabolic pathways in terms of the fraction of expressed sequences in the cDNA libraries were affiliated with primary metabolism, specifically oxidative phosphorylation, photosynthesis and the TCA cycle. Our analyses indicate that community composition is a good first proxy for the analysis of ecosystem functions. However, differential gene regulation modifies the relative importance of taxa in distinct pathways. Whereas taxon composition varies considerably between lakes, the relative importance of distinct metabolic pathways is much more stable, indicating that ecosystem functioning is buffered against shifts in community composition through a functional redundancy of taxa.}, }
@article {pmid27744477, year = {2017}, author = {Asemaninejad, A and Thorn, RG and Lindo, Z}, title = {Experimental Climate Change Modifies Degradative Succession in Boreal Peatland Fungal Communities.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {521-531}, pmid = {27744477}, issn = {1432-184X}, mesh = {Ascomycota/*classification/genetics/metabolism ; Biodiversity ; Climate ; *Climate Change ; DNA, Fungal/genetics ; Microbiota/*genetics ; Mortierella/*classification/genetics/growth &amp; development ; Mycorrhizae/*classification/growth &amp; development ; Soil/chemistry ; Soil Microbiology ; Sphagnopsida/*microbiology ; Temperature ; Wetlands ; }, abstract = {Peatlands play an important role in global climate change through sequestration of atmospheric CO2. Climate-driven changes in the structure of fungal communities in boreal peatlands that favor saprotrophic fungi can substantially impact carbon dynamics and nutrient cycling in these crucial ecosystems. In a mesocosm study using a full factorial design, 100 intact peat monoliths, complete with living Sphagnum and above-ground vascular vegetation, were subjected to three climate change variables (increased temperature, reduced water table, and elevated CO2 concentrations). Peat litterbags were placed in mesocosms, and fungal communities in litterbags were monitored over 12 months to assess the impacts of climate change variables on peat-inhabiting fungi. Changes in fungal richness, diversity, and community composition were assessed using Illumina MiSeq sequencing of ribosomal DNA (rDNA). While general fungal richness reduced under warming conditions, Ascomycota exhibited higher diversity under increased temperature treatments over the course of the experiment. Both increased temperature and lowered water table position drove shifts in fungal community composition with a strong positive effect on endophytic and mycorrhizal fungi (including one operational taxonomic unit (OTU) tentatively identified as Barrenia panicia) and different groups of saprotrophs identified as Mortierella, Galerina, and Mycena. These shifts were observed during a predicted degradative succession in the decomposer community as different carbon substrates became available. Since fungi play a central role in peatland communities, increased abundances of saprotrophic fungi under warming conditions, at the expense of reduced fungal richness overall, may increase decomposition rates under future climate scenarios and could potentially aggravate the impacts of climate change.}, }
@article {pmid27744476, year = {2017}, author = {Lu, XM and Chen, C and Zheng, TL}, title = {Metagenomic Insights into Effects of Chemical Pollutants on Microbial Community Composition and Function in Estuarine Sediments Receiving Polluted River Water.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {791-800}, pmid = {27744476}, issn = {1432-184X}, mesh = {Acetolactate Synthase/metabolism ; Aconitate Hydratase/metabolism ; Amino Acids/metabolism ; Bacteria/*classification/enzymology/*genetics/metabolism ; Base Sequence ; Carbon Cycle ; China ; *Estuaries ; Fresh Water ; Geologic Sediments/chemistry/*microbiology ; Ketone Oxidoreductases/metabolism ; Metabolic Networks and Pathways ; Metagenomics/*methods ; Microbial Consortia/drug effects/*genetics ; Nitrobenzenes/adverse effects ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/adverse effects ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Salinity ; Sequence Analysis ; Water Pollutants, Chemical/*analysis/chemistry ; }, abstract = {Pyrosequencing and metagenomic profiling were used to assess the phylogenetic and functional characteristics of microbial communities residing in sediments collected from the estuaries of Rivers Oujiang (OS) and Jiaojiang (JS) in the western region of the East China Sea. Another sediment sample was obtained from near the shore far from estuaries, used for contrast (CS). Characterization of estuary sediment bacterial communities showed that toxic chemicals potentially reduced the natural variability in microbial communities, while they increased the microbial metabolic enzymes and pathways. Polycyclic aromatic hydrocarbons (PAHs) and nitrobenzene were negatively correlated with the bacterial community variation. The dominant class in the sediments was Gammaproteobacteria. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) enzyme profiles, dominant enzymes were found in estuarine sediments, which increased greatly, such as 2-oxoglutarate synthase, acetolactate synthase, inorganic diphosphatase, and aconitate hydratase. In KEGG pathway profiles, most of the pathways were also dominated by specific metabolism in these sediments and showed a marked increase, for instance alanine, aspartate, and glutamate metabolism, carbon fixation pathways in prokaryotes, and aminoacyl-tRNA biosynthesis. The estuarine sediment bacterial diversity varied with the polluted river water inputs. In the estuary receiving river water from the more seriously polluted River Oujiang, the sediment bacterial community function was more severely affected.}, }
@article {pmid27744226, year = {2017}, author = {Williams, DW and Gibson, G}, title = {Individualization of pubic hair bacterial communities and the effects of storage time and temperature.}, journal = {Forensic science international. Genetics}, volume = {26}, number = {}, pages = {12-20}, doi = {10.1016/j.fsigen.2016.09.006}, pmid = {27744226}, issn = {1878-0326}, mesh = {Coitus ; *Cryopreservation ; Female ; Genitalia, Female ; Genitalia, Male ; Hair/*microbiology ; Humans ; Male ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; Specimen Handling/*methods ; *Temperature ; Time Factors ; }, abstract = {A potential application of microbial genetics in forensic science is detection of transfer of the pubic hair microbiome between individuals during sexual intercourse using high-throughput sequencing. In addition to the primary need to show whether the pubic hair microbiome is individualizing, one aspect that must be addressed before using the microbiome in criminal casework involves the impact of storage on the microbiome of samples recovered for forensic testing. To test the effects of short-term storage, pubic hair samples were collected from volunteers and stored at room temperature (∼20°C), refrigerated (4°C), and frozen (-20°C) for 1 week, 2 weeks, 4 weeks, and 6 weeks along with a baseline sample. Individual microbial profiles (R[2]=0.69) and gender (R[2]=0.17) were the greatest sources of variation between samples. Because of this variation, individual and gender could be predicted using Random Forests supervised classification in this sample set with an overall error rate of 2.7%± 5.8% and 1.7%±5.2%, respectively. There was no statistically significant difference attributable to time of sampling or temperature of storage within individuals. Further work on larger sample sets will quantify the temporal consistency of individual profiles and define whether it is plausible to detect transfer between sexual partners. For short-term storage (≤6 weeks), recovery of the microbiome was not affected significantly by either storage time or temperature, suggesting that investigators and crime laboratories can use existing evidence storage methods.}, }
@article {pmid27744152, year = {2017}, author = {McGillicuddy, E and Murray, I and Kavanagh, S and Morrison, L and Fogarty, A and Cormican, M and Dockery, P and Prendergast, M and Rowan, N and Morris, D}, title = {Silver nanoparticles in the environment: Sources, detection and ecotoxicology.}, journal = {The Science of the total environment}, volume = {575}, number = {}, pages = {231-246}, doi = {10.1016/j.scitotenv.2016.10.041}, pmid = {27744152}, issn = {1879-1026}, mesh = {Aquatic Organisms/*drug effects ; *Ecotoxicology ; *Environmental Exposure ; Metal Nanoparticles/*analysis ; Silver/*analysis ; Water Pollutants, Chemical/analysis ; }, abstract = {The environmental impact of silver nanoparticles (AgNP) has become a topic of interest recently, this is due to the fact that AgNPs have been included in numerous consumer products including textiles, medical products, domestic appliances, food containers, cosmetics, paints and nano-functionalised plastics. The production, use and disposal of these AgNP containing products are potential routes for environmental exposure. These concerns have led to a number of studies investigating the release of particles from nano-functionalised products, the detection of the particles in the aquatic environment and the potential environmental toxicology of these AgNPs to aquatic organisms. The overall aim of this review is to examine methods for the capture and detection of AgNPs, potential toxicity and transmission routes in the aquatic environment.}, }
@article {pmid27742997, year = {2017}, author = {Rahim, K and Saleha, S and Zhu, X and Huo, L and Basit, A and Franco, OL}, title = {Bacterial Contribution in Chronicity of Wounds.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {710-721}, pmid = {27742997}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Bacteria/*isolation &amp; purification ; Bacterial Load ; Biofilms/drug effects/*growth &amp; development ; Diabetic Foot/microbiology ; Humans ; Hygiene ; Leg Ulcer/microbiology ; Pressure Ulcer/microbiology ; Surgical Wound Infection/microbiology ; Wound Healing/*physiology ; Wounds and Injuries/*microbiology ; }, abstract = {A wound is damage of a tissue usually caused by laceration of a membrane, generally the skin. Wound healing is accomplished in three stages in healthy individuals, including inflammatory, proliferative, and remodeling stages. Healing of wounds normally starts from the inflammatory phase and ends up in the remodeling phase, but chronic wounds remain in an inflammatory stage and do not show progression due to some specific reasons. Chronic wounds are classified in different categories, such as diabetic foot ulcer (DFU), venous leg ulcers (VLU) and pressure ulcer (PU), surgical site infection (SSI), abscess, or trauma ulcers. Globally, the incidence rate of DFU is 1-4 % and prevalence rate is 5.3-10.5 %. However, colonization of pathogenic bacteria at the wound site is associated with wound chronicity. Most chronic wounds contain more than one bacterial species and produce a synergetic effect that results in previously non-virulent bacterial species becoming virulent and causing damage to the host. While investigating bacterial diversity in chronic wounds, Staphylococcus, Pseudomonas, Peptoniphilus, Enterobacter, Stenotrophomonas, Finegoldia, and Serratia were found most frequently in chronic wounds. Recently, it has been observed that bacteria in chronic wounds develop biofilms that contribute to a delay in healing. In a mature biofilm, bacteria grow slowly due to deficiency of nutrients that results in the resistance of bacteria to antibiotics. The present review reflects the reasons why acute wounds become chronic. Interesting findings include the bacterial load, which forms biofilms and shows high-level resistance toward antibiotics, which is a threat to human health in general and particularly to some patients who have acute wounds.}, }
@article {pmid27741161, year = {2016}, author = {Cenit, MC and Codoñer-Franch, P and Sanz, Y}, title = {Gut Microbiota and Risk of Developing Celiac Disease.}, journal = {Journal of clinical gastroenterology}, volume = {50 Suppl 2, Proceedings from the 8th Probiotics, Prebiotics &amp; New Foods for Microbiota and Human Health meeting held in Rome, Italy on September 13-15, 2015}, number = {}, pages = {S148-S152}, doi = {10.1097/MCG.0000000000000688}, pmid = {27741161}, issn = {1539-2031}, mesh = {Celiac Disease/*microbiology ; Environment ; *Epigenesis, Genetic ; Gastrointestinal Microbiome/*genetics ; Humans ; Infant ; Risk Factors ; }, abstract = {Gut microbiota shapes the development of the mucosal immune system and may provide protection against immune-mediated diseases. Celiac disease (CD) is a chronic inflammatory condition triggered by dietary gluten proteins, recently associated with gut microbiota alterations in cross-sectional studies comparing patients and controls. Whether or not these differences are causally related to the disease has yet to be elucidated, but evaluation of specific bacteria isolated from CD patients in experimental models suggests that they can promote an adverse response to dietary gluten, whereas other commensal bacteria can be protective. Genetic and environmental factors associated with increased CD risk have also been linked to shifts in the gut microbiota composition in infants early in life. Epigenetic mechanisms also seem to play an important role in modulating gut microbiota composition and function and, theoretically, could also influence CD risk. Here, we review the current knowledge on how host genetics, environmental factors, and epigenetic modifications could modulate gut microbiota functionality and how this may influence CD risk. Greater understanding of the role of this triad in CD onset and pathogenesis will be valuable in designing proof-of concept interventions in the gut ecosystem, with a view to improving CD management.}, }
@article {pmid27741154, year = {2016}, author = {Marzorati, M and Van de Wiele, T}, title = {An Advanced In Vitro Technology Platform to Study the Mechanism of Action of Prebiotics and Probiotics in the Gastrointestinal Tract.}, journal = {Journal of clinical gastroenterology}, volume = {50 Suppl 2, Proceedings from the 8th Probiotics, Prebiotics &amp; New Foods for Microbiota and Human Health meeting held in Rome, Italy on September 13-15, 2015}, number = {}, pages = {S124-S125}, doi = {10.1097/MCG.0000000000000711}, pmid = {27741154}, issn = {1539-2031}, mesh = {*Computer Simulation ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology ; Humans ; *Models, Biological ; *Prebiotics ; Probiotics/*pharmacology ; }, abstract = {The gastrointestinal tract (GIT) hosts the most complex microbial community in the human body. Given the extensive metabolic potential which is present in this community, this additional organ is of key importance to maintain a healthy status and several diseases are frequently correlated with an alteration of the composition/functionality of the gut microbiota. Consequently, there is a great interest in identifying potential approaches that could modulate the microbiota and its metabolism to bring about a positive health effect. A classical approach to reach this goal is the use of prebiotics and/or probiotics. How to study the potential effect of new prebiotics/probiotics and how to localize this effect along the full GIT? Human intervention trials are the golden standard to validate functional properties of food products. Yet, most studies on gut microbiota are based on the analysis of fecal samples because they are easily collected in a non-invasive manner. A complementary option is represented by well-designed in vitro simulation technologies. Among all the available systems, the Simulator of Human Intestinal Microbial Ecosystem has already been shown to be a useful model for nutrition studies in terms of analysis of the intestinal microbial community composition and activity. The Simulator of Human Intestinal Microbial Ecosystem is a scientifically validated platform representing the physiology and microbiology of the adult human GIT. Furthermore, recent advances in in vitro modelling also allow to combine the study of bacteria-host interactions, such as mucosal adhesion and interaction with the immune system, thereby further increasing the value of the scientific output.}, }
@article {pmid27736640, year = {2016}, author = {Berry, D}, title = {Making It Stick: A Compelling Case for Precision Microbiome Reconstitution.}, journal = {Cell host &amp; microbe}, volume = {20}, number = {4}, pages = {415-417}, doi = {10.1016/j.chom.2016.09.012}, pmid = {27736640}, issn = {1934-6069}, mesh = {Bacteria ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; }, abstract = {Modification of the intestinal microbiome is an emerging target to improve health and prevent or treat a number of diseases. In this issue of Cell Host &amp; Microbe, Maldonado-Gómez et al. (2016) uncover the basic principles that govern the successful establishment and persistence of an exogenously introduced gut bacterium.}, }
@article {pmid27734626, year = {2016}, author = {Numberger, D and Herlemann, DP and Jürgens, K and Dehnhardt, G and Schulz-Vogt, H}, title = {Comparative analysis of the fecal bacterial community of five harbor seals (Phoca vitulina).}, journal = {MicrobiologyOpen}, volume = {5}, number = {5}, pages = {782-792}, pmid = {27734626}, issn = {2045-8827}, mesh = {Animals ; Bacteroidetes/classification/genetics/isolation &amp; purification ; Feces/*microbiology ; Firmicutes/classification/genetics/isolation &amp; purification ; Fusobacteria/classification/genetics/isolation &amp; purification ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; In Situ Hybridization, Fluorescence ; Male ; Phoca/*microbiology ; Proteobacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The gut microbiota has many beneficial effects on host metabolism and health, and its composition is determined by numerous factors. It is also assumed that there was a co-evolution of mammals and the bacteria inhabiting their gut. Current knowledge of the mammalian gut microbiota mainly derives from studies on humans and terrestrial animals, whereas those on marine mammals are sparse. However, they could provide additional information on influencing factors, such as the role of diet and co-evolution with the host. In this study, we investigated and compared the bacterial diversity in the feces of five male harbor seals (Phoca vitulina). Because this small population included two half-brother pairs, each sharing a common father, it allowed an evaluation of the impact of host relatedness or genetic similarity on the gut microbial community. Fresh feces obtained from the seals by an enema were analyzed by fluorescence in situ hybridization and amplicon sequencing of 16S rRNA genes. The results showed that the bacterial communities in the seals' feces mainly consisted of the phyla Firmicutes (19-43%), Bacteroidetes (22-36%), Fusobacteria (18-32%), and Proteobacteria (5-17%) . Twenty-one bacterial members present in the fecal samples of the five seals contributed an average relative abundance of 93.7 + 8.7% of the total fecal microbial community. Contrary to all expectations based on previous studies a comparison of the fecal community between individual seals showed a higher similarity between unrelated than related individuals.}, }
@article {pmid27734123, year = {2017}, author = {Samuelsen, ED and Badawi, N and Nybroe, O and Sørensen, SR and Aamand, J}, title = {Adhesion to sand and ability to mineralise low pesticide concentrations are required for efficient bioaugmentation of flow-through sand filters.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {1}, pages = {411-421}, doi = {10.1007/s00253-016-7909-6}, pmid = {27734123}, issn = {1432-0614}, mesh = {2-Methyl-4-chlorophenoxyacetic Acid/*metabolism ; *Bacterial Adhesion ; Biotransformation ; Burkholderia/metabolism/*physiology ; Cupriavidus/metabolism/*physiology ; Filtration/methods ; Locomotion ; Pesticides/*metabolism ; Sphingomonas/metabolism/*physiology ; Water Pollutants, Chemical/metabolism ; Water Purification/*methods ; }, abstract = {Pesticide-polluted drinking water may be remediated by inoculating waterworks sand filters with specific degrading bacteria. However, degradation efficiency is often hampered by the poor adhesion behaviour of the introduced bacteria. The phenoxy acid herbicide 4-chloro-2-methyl-phenoxy-acetic acid (MCPA) is a widespread groundwater contaminant. The aim of this study was to investigate whether specific surface characteristics of MCPA-degrading bacteria could be linked to their degrading capabilities in sand filters. Four MCPA degraders with different taxonomic affiliations and original habitats (Sphingomonas sp. PM2, Sphingomonas sp. ERG5, Burkholderia sp. TFD34, Cupriavidus sp. TFD38) were characterised with regard to their motility, cell surface hydrophobicity, biofilm formation, adhesion behaviour and ability to mineralise MCPA. Strains PM2 and ERG5 were non-motile and hydrophobic, whilst strains TFD34 and TFD38 were motile and less hydrophobic. All the strains except ERG5 showed low biofilm formation on polystyrene, although it was significantly higher on glass. PM2 was the most efficient MCPA degrader as it displayed no lag phase and reached >50 % mineralisation at all concentrations (0.0016-25 mg L[-1]). PM2 adhered significantly better to sand than the other strains. No link was found between motility, biofilm formation and the ability to adhere to sand. PM2 completely removed MCPA for 14 days when inoculated in sand columns with a constant inlet of 1 mg L[-1] MCPA. These results demonstrate that besides the ability to degrade the contaminant, surface hydrophobicity and adherence abilities are significant parameters controlling sustained degradation in flow-through sand columns and must be considered when selecting bacteria for bioaugmentation.}, }
@article {pmid27734121, year = {2017}, author = {Van Assche, A and Álvarez-Pérez, S and de Breij, A and De Brabanter, J and Willems, KA and Dijkshoorn, L and Lievens, B}, title = {Phylogenetic signal in phenotypic traits related to carbon source assimilation and chemical sensitivity in Acinetobacter species.}, journal = {Applied microbiology and biotechnology}, volume = {101}, number = {1}, pages = {367-379}, doi = {10.1007/s00253-016-7866-0}, pmid = {27734121}, issn = {1432-0614}, mesh = {Acinetobacter/classification/*genetics/metabolism/*physiology ; *Biological Evolution ; Carbohydrate Metabolism ; Carbon/*metabolism ; Genetic Variation ; *Genotype ; *Phenotype ; *Phylogeny ; }, abstract = {A common belief is that the phylogeny of bacteria may reflect molecular functions and phenotypic characteristics, pointing towards phylogenetic conservatism of traits. Here, we tested this hypothesis for a large set of Acinetobacter strains. Members of the genus Acinetobacter are widespread in nature, demonstrate a high metabolic diversity and are resistant to several environmental stressors. Notably, some species are known to cause opportunistic human infections. A total of 133 strains belonging to 33 species with validly published names, two genomic species and species of an as-yet unknown taxonomic status were analyzed using the GENIII technology of Biolog, which allows high-throughput phenotyping. We estimated the strength and significance of the phylogenetic signal of each trait across phylogenetic reconstructions based on partial RNA polymerase subunit B (rpoB) and core genome sequences. Secondly, we tested whether phylogenetic distance was a good predictor of trait differentiation by Mantel test analysis. And finally, evolutionary model fitting was used to determine if the data for each phenotypic character was consistent with a phylogenetic or an essentially random model of trait distribution. Our data revealed that some key phenotypic traits related to substrate assimilation and chemical sensitivity are linked to the phylogenetic placement of Acinetobacter species. The strongest phylogenetic signals found were for utilization of different carbon sources such as some organic acids, amino acids and sugars, thus suggesting that in the diversification of Acinetobacter carbon source assimilation has had a relevant role. Future work should be aimed to clarify how such traits have shaped the remarkable ability of this bacterial group to dominate in a wide variety of habitats.}, }
@article {pmid27734114, year = {2017}, author = {Kerfahi, D and Tateno, R and Takahashi, K and Cho, H and Kim, H and Adams, JM}, title = {Development of Soil Bacterial Communities in Volcanic Ash Microcosms in a Range of Climates.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {775-790}, pmid = {27734114}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification/metabolism ; Biodiversity ; Carbon/metabolism ; *Climate ; DNA, Bacterial/chemistry/genetics ; Hydrogen-Ion Concentration ; Japan ; *Microbial Consortia ; Nitrogen/metabolism ; Photosynthesis ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; Temperature ; *Volcanic Eruptions ; }, abstract = {There is considerable interest in understanding the processes of microbial development in volcanic ash. We tested the predictions that there would be (1) a distinctive bacterial community associated with soil development on volcanic ash, including groups previously implicated in weathering studies; (2) a slower increase in bacterial abundance and soil C and N accumulation in cooler climates; and (3) a distinct communities developing on the same substrate in different climates. We set up an experiment, taking freshly fallen, sterilized volcanic ash from Sakurajima volcano, Japan. Pots of ash were positioned in multiple locations, with mean annual temperature (MAT) ranging from 18.6 to -3 °C. Within 12 months, bacteria were detectable by qPCR in all pots. By 24 months, bacterial copy numbers had increased by 10-100 times relative to a year before. C and N content approximately doubled between 12 and 24 months. HiSeq and MiSeq sequencing of the 16S rRNA gene revealed a distinctive bacterial community, different from developed vegetated soils in the same areas, for example in containing an abundance of unclassified bacterial groups. Community composition also differed between the ash pots at different sites, while showing no pattern in relation to MAT. Contrary to our predictions, the bacterial abundance did not show any relation to MAT. It also did not correlate to pH or N, and only C was statistically significant. It appears that bacterial community development on volcanic ash can be a rapid process not closely sensitive to temperature, involving distinct communities from developed soils.}, }
@article {pmid27733847, year = {2016}, author = {Shelton, JL and Akob, DM and McIntosh, JC and Fierer, N and Spear, JR and Warwick, PD and McCray, JE}, title = {Environmental Drivers of Differences in Microbial Community Structure in Crude Oil Reservoirs across a Methanogenic Gradient.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1535}, pmid = {27733847}, issn = {1664-302X}, abstract = {Stimulating in situ microbial communities in oil reservoirs to produce natural gas is a potentially viable strategy for recovering additional fossil fuel resources following traditional recovery operations. Little is known about what geochemical parameters drive microbial population dynamics in biodegraded, methanogenic oil reservoirs. We investigated if microbial community structure was significantly impacted by the extent of crude oil biodegradation, extent of biogenic methane production, and formation water chemistry. Twenty-two oil production wells from north central Louisiana, USA, were sampled for analysis of microbial community structure and fluid geochemistry. Archaea were the dominant microbial community in the majority of the wells sampled. Methanogens, including hydrogenotrophic and methylotrophic organisms, were numerically dominant in every well, accounting for, on average, over 98% of the total Archaea present. The dominant Bacteria groups were Pseudomonas, Acinetobacter, Enterobacteriaceae, and Clostridiales, which have also been identified in other microbially-altered oil reservoirs. Comparing microbial community structure to fluid (gas, water, and oil) geochemistry revealed that the relative extent of biodegradation, salinity, and spatial location were the major drivers of microbial diversity. Archaeal relative abundance was independent of the extent of methanogenesis, but closely correlated to the extent of crude oil biodegradation; therefore, microbial community structure is likely not a good sole predictor of methanogenic activity, but may predict the extent of crude oil biodegradation. However, when the shallow, highly biodegraded, low salinity wells were excluded from the statistical analysis, no environmental parameters could explain the differences in microbial community structure. This suggests that the microbial community structure of the 5 shallow, up-dip wells was different than the 17 deeper, down-dip wells. Also, the 17 down-dip wells had statistically similar microbial communities despite significant changes in environmental parameters between oil fields. Together, this implies that no single microbial population is a reliable indicator of a reservoir's ability to degrade crude oil to methane, and that geochemistry may be a more important indicator for selecting a reservoir suitable for microbial enhancement of natural gas generation.}, }
@article {pmid27730366, year = {2017}, author = {Hubert, J and Bicianova, M and Ledvinka, O and Kamler, M and Lester, PJ and Nesvorna, M and Kopecky, J and Erban, T}, title = {Changes in the Bacteriome of Honey Bees Associated with the Parasite Varroa destructor, and Pathogens Nosema and Lotmaria passim.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {685-698}, pmid = {27730366}, issn = {1432-184X}, mesh = {Animals ; Bartonella/classification/genetics/*isolation &amp; purification ; Bees/*microbiology/*parasitology ; Kinetoplastida/*pathogenicity ; Lactobacillus/classification/genetics/*isolation &amp; purification ; Microbiota/genetics ; Mite Infestations/pathology ; Nosema/*pathogenicity ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; Varroidae/*pathogenicity ; }, abstract = {The honey bee, Apis mellifera, is a globally important species that suffers from a variety of pathogens and parasites. These parasites and pathogens may have sublethal effects on their bee hosts via an array of mechanisms, including through a change in symbiotic bacterial taxa. Our aim was to assess the influence of four globally widespread parasites and pathogens on the honey bee bacteriome. We examined the effects of the ectoparasitic mite Varroa destructor, the fungal pathogens Nosema apis and Nosema ceranae, and the trypanosome Lotmaria passim. Varroa was detected by acaricidal treatment, Nosema and L. passim by PCR, and the bacteriome using MiSeq 16S rRNA gene sequencing. Overall, the 1,858,850 obtained sequences formed 86 operational taxonomic units (OTUs) at 3 % dissimilarity. Location, time of year, and degree of infestation by Varroa had significant effects on the composition of the bacteriome of honey bee workers. Based on statistical correlations, we found varroosis more important factor than N. ceranae, N. apis, and L. passim infestation influencing the honey bee bacteriome and contributing to the changes in the composition of the bacterial community in adult bees. At the population level, Varroa appeared to modify 20 OTUs. In the colonies with high Varroa infestation levels (varroosis), the relative abundance of the bacteria Bartonella apis and Lactobacillus apis decreased. In contrast, an increase in relative abundance was observed for several taxa including Lactobacillus helsingborgensis, Lactobacillus mellis, Commensalibacter intestini, and Snodgrassella alvi. The results showed that the "normal" bacterial community is altered by eukaryotic parasites as well as displaying temporal changes and changes associated with the geographical origin of the beehive.}, }
@article {pmid27726901, year = {2016}, author = {Aliyu, H and Lebre, P and Blom, J and Cowan, D and De Maayer, P}, title = {Phylogenomic re-assessment of the thermophilic genus Geobacillus.}, journal = {Systematic and applied microbiology}, volume = {39}, number = {8}, pages = {527-533}, doi = {10.1016/j.syapm.2016.09.004}, pmid = {27726901}, issn = {1618-0984}, mesh = {Base Composition/*genetics ; DNA, Bacterial/*genetics ; Geobacillus/*classification/*genetics ; *Molecular Typing ; Nucleic Acid Hybridization ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Geobacillus is a genus of Gram-positive, aerobic, spore-forming obligate thermophiles. The descriptions and subsequent affiliations of the species in the genus have mostly been based on polyphasic taxonomy rules that include traditional sequence-based methods such as DNA-DNA hybridization and comparison of 16S rRNA gene sequences. Currently, there are fifteen validly described species within the genus. The availability of whole genome sequences has provided an opportunity to validate and/or re-assess these conventional estimates of genome relatedness. We have applied whole genome approaches to estimate the phylogenetic relatedness among the sixty-three Geobacillus strains for which genome sequences are currently publicly available, including the type strains of eleven validly described species. The phylogenomic metrics AAI (Average Amino acid Identity), ANI (Average Nucleotide Identity) and dDDH (digital DNA-DNA hybridization) indicated that the current genus Geobacillus is comprised of sixteen distinct genomospecies, including several potentially novel species. Furthermore, a phylogeny constructed on the basis of the core genes identified from the whole genome analyses indicated that the genus clusters into two monophyletic clades that clearly differ in terms of nucleotide base composition. The G+C content ranges for clade I and II were 48.8-53.1% and 42.1-44.4%, respectively. We therefore suggest that the Geobacillus species currently residing within clade II be considered as a new genus.}, }
@article {pmid27726803, year = {2016}, author = {Berry, ED and Wells, JE}, title = {Reducing Foodborne Pathogen Persistence and Transmission in Animal Production Environments: Challenges and Opportunities.}, journal = {Microbiology spectrum}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/microbiolspec.PFS-0006-2014}, pmid = {27726803}, issn = {2165-0497}, mesh = {Animal Husbandry/*methods ; Animals ; Communicable Disease Control/methods ; Food Handling/*methods ; Food Safety/*methods ; Foodborne Diseases/*prevention &amp; control ; Humans ; Zoonoses/prevention &amp; control ; }, abstract = {Preharvest strategies to reduce zoonotic pathogens in food animals are important components of the farm-to-table food safety continuum. The problem is complex; there are multiple pathogens of concern, multiple animal species under different production and management systems, and a variety of sources of pathogens, including other livestock and domestic animals, wild animals and birds, insects, water, and feed. Preharvest food safety research has identified a number of intervention strategies, including probiotics, direct-fed microbials, competitive exclusion cultures, vaccines, and bacteriophages, in addition to factors that can impact pathogens on-farm, such as seasonality, production systems, diet, and dietary additives. Moreover, this work has revealed both challenges and opportunities for reducing pathogens in food animals. Animals that shed high levels of pathogens and predominant pathogen strains that exhibit long-term persistence appear to play significant roles in maintaining the prevalence of pathogens in animals and their production environment. Continued investigation and advancements in sequencing and other technologies are expected to reveal the mechanisms that result in super-shedding and persistence, in addition to increasing the prospects for selection of pathogen-resistant food animals and understanding of the microbial ecology of the gastrointestinal tract with regard to zoonotic pathogen colonization. It is likely that this continued research will reveal other challenges, which may further indicate potential targets or critical control points for pathogen reduction in livestock. Additional benefits of the preharvest reduction of pathogens in food animals are the reduction of produce, water, and environmental contamination, and thereby lower risk for human illnesses linked to these sources.}, }
@article {pmid27726035, year = {2017}, author = {Valdespino-Castillo, PM and Alcántara-Hernández, RJ and Merino-Ibarra, M and Alcocer, J and Macek, M and Moreno-Guillén, OA and Falcón, LI}, title = {Phylotype Dynamics of Bacterial P Utilization Genes in Microbialites and Bacterioplankton of a Monomictic Endorheic Lake.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {296-309}, pmid = {27726035}, issn = {1432-184X}, mesh = {Alkaline Phosphatase/genetics ; Aquatic Organisms/genetics/metabolism ; Bacteria/enzymology/*genetics/metabolism ; Bacteroidetes/genetics/metabolism ; Base Sequence ; DNA, Bacterial/analysis ; Ecosystem ; Environment ; Gene Expression Regulation, Bacterial ; Genes, Bacterial/*genetics ; Genetic Markers/genetics ; *Genetic Variation ; Lakes/*microbiology ; Mexico ; Oxygen/chemistry ; Phosphorus/chemistry/*metabolism ; Phosphorus Compounds/chemistry/metabolism ; *Phylogeny ; Polymerase Chain Reaction/methods ; Proteobacteria/genetics/metabolism ; RNA, Bacterial/analysis ; Seasons ; Sequence Analysis ; Water/chemistry ; }, abstract = {Microbes can modulate ecosystem function since they harbor a vast genetic potential for biogeochemical cycling. The spatial and temporal dynamics of this genetic diversity should be acknowledged to establish a link between ecosystem function and community structure. In this study, we analyzed the genetic diversity of bacterial phosphorus utilization genes in two microbial assemblages, microbialites and bacterioplankton of Lake Alchichica, a semiclosed (i.e., endorheic) system with marked seasonality that varies in nutrient conditions, temperature, dissolved oxygen, and water column stability. We focused on dissolved organic phosphorus (DOP) utilization gene dynamics during contrasting mixing and stratification periods. Bacterial alkaline phosphatases (phoX and phoD) and alkaline beta-propeller phytases (bpp) were surveyed. DOP utilization genes showed different dynamics evidenced by a marked change within an intra-annual period and a differential circadian pattern of expression. Although Lake Alchichica is a semiclosed system, this dynamic turnover of phylotypes (from lake circulation to stratification) points to a different potential of DOP utilization by the microbial communities within periods. DOP utilization gene dynamics was different among genetic markers and among assemblages (microbialite vs. bacterioplankton). As estimated by the system's P mass balance, P inputs and outputs were similar in magnitude (difference was <10 %). A theoretical estimation of water column P monoesters was used to calculate the potential P fraction that can be remineralized on an annual basis. Overall, bacterial groups including Proteobacteria (Alpha and Gamma) and Bacteroidetes seem to be key participants in DOP utilization responses.}, }
@article {pmid27726034, year = {2017}, author = {Yang, Y and Dai, Y and Li, N and Li, B and Xie, S and Liu, Y}, title = {Temporal and Spatial Dynamics of Sediment Anaerobic Ammonium Oxidation (Anammox) Bacteria in Freshwater Lakes.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {285-295}, pmid = {27726034}, issn = {1432-184X}, mesh = {Ammonium Compounds/*metabolism ; Anaerobiosis ; Bacteria/*classification/genetics/*metabolism ; Bacteria, Anaerobic/classification/genetics/metabolism ; Biodiversity ; China ; DNA, Bacterial ; Fresh Water/chemistry/*microbiology ; Genes, Bacterial ; Geologic Sediments/chemistry/*microbiology ; High-Throughput Nucleotide Sequencing/methods ; Lakes/chemistry/*microbiology ; Multigene Family ; Nitrogen Cycle ; Oxidation-Reduction ; Phylogeny ; Planctomycetales/metabolism ; RNA, Ribosomal, 16S/genetics ; Seasons ; }, abstract = {Anaerobic ammonium-oxidizing (anammox) process can play an important role in freshwater nitrogen cycle. However, the distribution of anammox bacteria in freshwater lake and the associated environmental factors remain essentially unclear. The present study investigated the temporal and spatial dynamics of sediment anammox bacterial populations in eutrotrophic Dianchi Lake and mesotrophic Erhai Lake on the Yunnan Plateau (southwestern China). The remarkable spatial change of anammox bacterial abundance was found in Dianchi Lake, while the relatively slight spatial shift occurred in Erhai Lake. Dianchi Lake had greater anammox bacterial abundance than Erhai Lake. In both Dianchi Lake and Erhai Lake, anammox bacteria were much more abundant in summer than in spring. Anammox bacterial community richness, diversity, and structure in these two freshwater lakes were subjected to temporal and spatial variations. Sediment anammox bacterial communities in Dianchi Lake and Erhai Lake were dominated by Candidatus Brocadia and a novel phylotype followed by Candidatus Kuenenia; however, these two lakes had distinct anammox bacterial community structure. In addition, trophic status determined sediment anammox bacterial community structure.}, }
@article {pmid27726033, year = {2017}, author = {van de Water, JA and Melkonian, R and Voolstra, CR and Junca, H and Beraud, E and Allemand, D and Ferrier-Pagès, C}, title = {Comparative Assessment of Mediterranean Gorgonian-Associated Microbial Communities Reveals Conserved Core and Locally Variant Bacteria.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {466-478}, pmid = {27726033}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/genetics/isolation &amp; purification ; Base Sequence ; Biodiversity ; Classification ; Coral Reefs ; DNA, Bacterial/genetics ; Gene Library ; Mediterranean Sea ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; Seawater/microbiology ; Species Specificity ; Temperature ; }, abstract = {Gorgonians are key habitat-forming species of Mediterranean benthic communities, but their populations have suffered from mass mortality events linked to high summer seawater temperatures and microbial disease. However, our knowledge on the diversity, dynamics and function of gorgonian-associated microbial communities is limited. Here, we analysed the spatial variability of the microbiomes of five sympatric gorgonian species (Eunicella singularis, Eunicella cavolini, Eunicella verrucosa, Leptogorgia sarmentosa and Paramuricea clavata), collected from the Mediterranean Sea over a scale of ∼1100 km, using next-generation amplicon sequencing of the 16S rRNA gene. The microbiomes of all gorgonian species were generally dominated by members of the genus Endozoicomonas, which were at very low abundance in the surrounding seawater. Although the composition of the core microbiome (operational taxonomic units consistently present in a species) was found to be unique for each host species, significant overlap was observed. These spatially consistent associations between gorgonians and their core bacteria suggest intricate symbiotic relationships and regulation of the microbiome composition by the host. At the same time, local variations in microbiome composition were observed. Functional predictive profiling indicated that these differences could be attributed to seawater pollution. Taken together, our data indicate that gorgonian-associated microbiomes are composed of spatially conserved bacteria (core microbiome members) and locally variant members, and that local pollution may influence these local associations, potentially impacting gorgonian health.}, }
@article {pmid27725929, year = {2016}, author = {Roume, H and Arends, JB and Ameril, CP and Patil, SA and Rabaey, K}, title = {Enhanced Product Recovery from Glycerol Fermentation into 3-Carbon Compounds in a Bioelectrochemical System Combined with In Situ Extraction.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {4}, number = {}, pages = {73}, pmid = {27725929}, issn = {2296-4185}, abstract = {Given the large amount of crude glycerol formed as a by-product in the biodiesel industries and the concomitant decrease in its overall market price, there is a need to add extra value to this biorefinery side stream. Upgrading can be achieved by new biotechnologies dealing with recovery and conversion of glycerol present in wastewaters into value-added products, aiming at a zero-waste policy and developing an economically viable process. In microbial bioelectrochemical systems (BESs), the mixed microbial community growing on the cathode can convert glycerol reductively to 1,3-propanediol (1,3-PDO). However, the product yield is rather limited in BESs compared with classic fermentation processes, and the synthesis of side-products, resulting from oxidation of glycerol, such as organic acids, represents a major burden for recovery of 1,3-PDO. Here, we show that the use of an enriched mixed-microbial community of glycerol degraders and in situ extraction of organic acids positively impacts 1,3-PDO yield and allows additional recovery of propionate from glycerol. We report the highest production yield achieved (0.72 mol1,3-PDO mol[-1]glycerol) in electricity-driven 1,3-PDO biosynthesis from raw glycerol, which is very close to the 1,3-PDO yield reported thus far for a mixed-microbial culture-based glycerol fermentation process. We also present a combined approach for 1,3-PDO production and propionate extraction in a single three chamber reactor system, which leads to recovery of additional 3-carbon compounds in BESs. This opens up further opportunities for an economical upgrading of biodiesel refinery side or waste streams.}, }
@article {pmid27725809, year = {2016}, author = {Imam, J and Singh, PK and Shukla, P}, title = {Plant Microbe Interactions in Post Genomic Era: Perspectives and Applications.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1488}, pmid = {27725809}, issn = {1664-302X}, abstract = {Deciphering plant-microbe interactions is a promising aspect to understand the benefits and the pathogenic effect of microbes and crop improvement. The advancement in sequencing technologies and various 'omics' tool has impressively accelerated the research in biological sciences in this area. The recent and ongoing developments provide a unique approach to describing these intricate interactions and test hypotheses. In the present review, we discuss the role of plant-pathogen interaction in crop improvement. The plant innate immunity has always been an important aspect of research and leads to some interesting information like the adaptation of unique immune mechanisms of plants against pathogens. The development of new techniques in the post - genomic era has greatly enhanced our understanding of the regulation of plant defense mechanisms against pathogens. The present review also provides an overview of beneficial plant-microbe interactions with special reference to Agrobacterium tumefaciens-plant interactions where plant derived signal molecules and plant immune responses are important in pathogenicity and transformation efficiency. The construction of various Genome-scale metabolic models of microorganisms and plants presented a better understanding of all metabolic interactions activated during the interactions. This review also lists the emerging repertoire of phytopathogens and its impact on plant disease resistance. Outline of different aspects of plant-pathogen interactions is presented in this review to bridge the gap between plant microbial ecology and their immune responses.}, }
@article {pmid27722870, year = {2016}, author = {Zhao, X and Skurnik, M}, title = {Bacteriophages of Yersinia pestis.}, journal = {Advances in experimental medicine and biology}, volume = {918}, number = {}, pages = {361-375}, doi = {10.1007/978-94-024-0890-4_13}, pmid = {27722870}, issn = {0065-2598}, mesh = {Animals ; *Bacteriophages/classification/genetics/isolation &amp; purification ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Genetic Variation ; Genomic Islands ; Humans ; Prophages/classification/genetics/isolation &amp; purification ; Receptors, Virus/physiology ; Yersinia pestis/*virology ; }, abstract = {Bacteriophage play many varied roles in microbial ecology and evolution. This chapter collates a vast body of knowledge and expertise on Yersinia pestis phages, including the history of their isolation and classical methods for their isolation and identification. The genomic diversity of Y. pestis phage and bacteriophage islands in the Y. pestis genome are also discussed because all phage research represents a branch of genetics. In addition, our knowledge of the receptors that are recognized by Y. pestis phage, advances in phage therapy for Y. pestis infections, the application of phage in the detection of Y. pestis, and clustered regularly interspaced short palindromic repeats (CRISPRs) sequences of Y. pestis from prophage DNA are all reviewed here.}, }
@article {pmid27721808, year = {2016}, author = {Stegen, JC and Hurlbert, AH and Bond-Lamberty, B and Chen, X and Anderson, CG and Chu, RK and Dini-Andreote, F and Fansler, SJ and Hess, NJ and Tfaily, M}, title = {Aligning the Measurement of Microbial Diversity with Macroecological Theory.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1487}, pmid = {27721808}, issn = {1664-302X}, abstract = {The number of microbial operational taxonomic units (OTUs) within a community is akin to species richness within plant/animal ("macrobial") systems. A large literature documents OTU richness patterns, drawing comparisons to macrobial theory. There is, however, an unrecognized fundamental disconnect between OTU richness and macrobial theory: OTU richness is commonly estimated on a per-individual basis, while macrobial richness is estimated per-area. Furthermore, the range or extent of sampled environmental conditions can strongly influence a study's outcomes and conclusions, but this is not commonly addressed when studying OTU richness. Here we (i) propose a new sampling approach that estimates OTU richness per-mass of soil, which results in strong support for species energy theory, (ii) use data reduction to show how support for niche conservatism emerges when sampling across a restricted range of environmental conditions, and (iii) show how additional insights into drivers of OTU richness can be generated by combining different sampling methods while simultaneously considering patterns that emerge by restricting the range of environmental conditions. We propose that a more rigorous connection between microbial ecology and macrobial theory can be facilitated by exploring how changes in OTU richness units and environmental extent influence outcomes of data analysis. While fundamental differences between microbial and macrobial systems persist (e.g., species concepts), we suggest that closer attention to units and scale provide tangible and immediate improvements to our understanding of the processes governing OTU richness and how those processes relate to drivers of macrobial species richness.}, }
@article {pmid27720620, year = {2016}, author = {Klotz, A and Georg, J and Bučinská, L and Watanabe, S and Reimann, V and Januszewski, W and Sobotka, R and Jendrossek, D and Hess, WR and Forchhammer, K}, title = {Awakening of a Dormant Cyanobacterium from Nitrogen Chlorosis Reveals a Genetically Determined Program.}, journal = {Current biology : CB}, volume = {26}, number = {21}, pages = {2862-2872}, doi = {10.1016/j.cub.2016.08.054}, pmid = {27720620}, issn = {1879-0445}, mesh = {*Gene Expression Regulation, Bacterial ; Nitrogen/*metabolism ; RNA, Bacterial/metabolism ; RNA, Untranslated/metabolism ; Synechocystis/genetics/*physiology ; }, abstract = {The molecular and physiological mechanisms involved in the transition of microbial cells from a resting state to the active vegetative state are critically relevant for solving problems in fields ranging from microbial ecology to infection microbiology. Cyanobacteria that cannot fix nitrogen are able to survive prolonged periods of nitrogen starvation as chlorotic cells in a dormant state. When provided with a usable nitrogen source, these cells re-green within 48 hr and return to vegetative growth. Here we investigated the resuscitation of chlorotic Synechocystis sp. PCC 6803 cells at the physiological and molecular levels with the aim of understanding the awakening process of a dormant bacterium. Almost immediately upon nitrate addition, the cells initiated a highly organized resuscitation program. In the first phase, they suppressed any residual photosynthetic activity and activated respiration to gain energy from glycogen catabolism. Concomitantly, they restored the entire translational apparatus, ATP synthesis, and nitrate assimilation. After only 12-16 hr, the cells re-activated the synthesis of the photosynthetic apparatus and prepared for metabolic re-wiring toward photosynthesis. When the cells reached full photosynthetic capacity after ∼48 hr, they resumed cell division and entered the vegetative cell cycle. An analysis of the transcriptional dynamics during the resuscitation process revealed a perfect match to the observed physiological processes, and it suggested that non-coding RNAs play a major regulatory role during the lifestyle switch in awakening cells. This genetically encoded program ensures rapid colonization of habitats in which nitrogen starvation imposes a recurring growth limitation.}, }
@article {pmid27716432, year = {2016}, author = {Harrison, EM and Ludden, C and Brodrick, HJ and Blane, B and Brennan, G and Morris, D and Coll, F and Reuter, S and Brown, NM and Holmes, MA and O'Connell, B and Parkhill, J and Török, ME and Cormican, M and Peacock, SJ}, title = {Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks.}, journal = {Genome medicine}, volume = {8}, number = {1}, pages = {102}, pmid = {27716432}, issn = {1756-994X}, support = {G1001787/MRC_/Medical Research Council/United Kingdom ; 201344/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; G1000803/MRC_/Medical Research Council/United Kingdom ; MR/N029399/1/MRC_/Medical Research Council/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Cross Infection/epidemiology/microbiology/prevention &amp; control/*transmission ; DNA, Bacterial/*genetics ; Female ; Health Facility Environment/organization &amp; administration ; High-Throughput Nucleotide Sequencing ; Humans ; Infection Control ; Long-Term Care ; Male ; Methicillin-Resistant Staphylococcus aureus/*genetics/isolation &amp; purification ; Middle Aged ; Multilocus Sequence Typing ; Prospective Studies ; Staphylococcal Infections/epidemiology/microbiology/prevention &amp; control/*transmission ; United Kingdom/epidemiology ; }, abstract = {BACKGROUND: Long-term care facilities (LTCF) are potential reservoirs for methicillin-resistant Staphylococcus aureus (MRSA), control of which may reduce MRSA transmission and infection elsewhere in the healthcare system. Whole-genome sequencing (WGS) has been used successfully to understand MRSA epidemiology and transmission in hospitals and has the potential to identify transmission between these and LTCF.<br><br>METHODS: Two prospective observational studies of MRSA carriage were conducted in LTCF in England and Ireland. MRSA isolates were whole-genome sequenced and analyzed using established methods. Genomic data were available for MRSA isolated in the local healthcare systems (isolates submitted by hospitals and general practitioners).<br><br>RESULTS: We sequenced a total of 181 MRSA isolates from the two study sites. The majority of MRSA were multilocus sequence type (ST)22. WGS identified one likely transmission event between residents in the English LTCF and three putative transmission events in the Irish LTCF. WGS also identified closely related isolates present in colonized Irish residents and their immediate environment. Based on phylogenetic reconstruction, closely related MRSA clades were identified between the LTCF and their healthcare referral network, together with putative MRSA acquisition by LTCF residents during hospital admission.<br><br>CONCLUSIONS: These data confirm that MRSA is transmitted between residents of LTCF and is both acquired and transmitted to others in referral hospitals and beyond. Our data present compelling evidence for the importance of environmental contamination in MRSA transmission, reinforcing the importance of environmental cleaning. The use of WGS in this study highlights the need to consider infection control in hospitals and community healthcare facilities as a continuum.}, }
@article {pmid27716053, year = {2016}, author = {Peterson, BF and Scharf, ME}, title = {Metatranscriptome analysis reveals bacterial symbiont contributions to lower termite physiology and potential immune functions.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {772}, pmid = {27716053}, issn = {1471-2164}, mesh = {Amidohydrolases/genetics/metabolism ; Animals ; Antibiosis ; Bacteria/*genetics ; Computational Biology/methods ; Fungi/physiology ; Gene Expression Profiling ; Genes, rRNA ; Glutathione Transferase/metabolism ; Isoptera/*immunology/metabolism/*microbiology ; *Metagenome ; *Metagenomics/methods ; Oxidative Stress ; Reactive Oxygen Species/metabolism ; Reproducibility of Results ; *Symbiosis ; *Transcriptome ; }, abstract = {BACKGROUND: Symbioses throughout the animal kingdom are known to extend physiological and ecological capabilities to hosts. Insect-microbe associations are extremely common and are often related to novel niche exploitation, fitness advantages, and even speciation events. These phenomena include expansions in host diet, detoxification of insecticides and toxins, and increased defense against pathogens. However, dissecting the contributions of individual groups of symbionts at the molecular level is often underexplored due to methodological and analytical limitations. Termites are one of the best studied systems for physiological collaborations between host and symbiota; however, most work in lower termites (those with bacterial and protist symbionts) focuses on the eukaryotic members of this symbiotic consortium. Here we present a metatranscriptomic analysis which provides novel insights into bacterial contributions to the holobiont of the eastern subterranean termite, Reticulitermes flavipes, in the presence and absence of a fungal pathogen.<br><br>RESULTS: Using a customized ribodepletion strategy, a metatranscriptome assembly was obtained representing the host termite as well as bacterial and protist symbiota. Sequence data provide new insights into biosynthesis, catabolism, and transport of major organic molecules and ions by the gut consortium, and corroborate previous findings suggesting that bacteria play direct roles in nitrogen fixation, amino acid biosynthesis, and lignocellulose digestion. With regard to fungal pathogen challenge, a total of 563 differentially expressed candidate host and symbiont contigs were identified (162 up- and 401 downregulated; &#x3b1;/FDR&#x2009;=&#x2009;0.05) including an upregulated bacterial amidohydrolase.<br><br>CONCLUSIONS: This study presents the most complete bacterial metatranscriptome from a lower termite and provides a framework on which to build a more complete model of termite-symbiont interactions including, but not limited to, digestion and pathogen defense.}, }
@article {pmid27713962, year = {2016}, author = {Giuliani, C and Marzorati, M and Innocenti, M and Vilchez-Vargas, R and Vital, M and Pieper, DH and Van de Wiele, T and Mulinacci, N}, title = {Dietary supplement based on stilbenes: a focus on gut microbial metabolism by the in vitro simulator M-SHIME®.}, journal = {Food &amp; function}, volume = {7}, number = {11}, pages = {4564-4575}, doi = {10.1039/c6fo00784h}, pmid = {27713962}, issn = {2042-650X}, mesh = {Bacteria ; Colon/metabolism/microbiology ; *Dietary Supplements ; Gastrointestinal Microbiome/*drug effects ; Humans ; Plant Extracts/chemistry/pharmacology ; Stilbenes/chemistry/*pharmacology ; Vitis/chemistry ; }, abstract = {Polyphenols and intestinal microbiota can influence each other, modifying metabolism and gut wellness. Data on this mutual effect need to be improved. Several studies on the biological activities of resveratrol and derivatives have been carried out, but the effects of a continuous administration of stilbenes on gut microbiota have not yet been investigated. This study evaluated the effects of an extract from Vitis vinifera, containing a combination of t-resveratrol and ε-viniferin, on intestinal microbiota, using the advanced gastrointestinal simulator M-SHIME®. A triple M-SHIME® experiment was performed using two concentrations of the extract (i.e. 1 and 2 g L[-1]), simulating a continuous daily intake. The effects were evaluated in terms of microbial functionality (SCFA and NH4[+]) and composition (DGGE and Illumina sequencing), since the microbiological aspect has been less considered so far. The treatment induced changes in microbial functionality and composition. In fact, the levels of SCFA and NH4[+] suffered a strong decrease (i.e. inhibition of the saccharolytic and proteolytic activity), while DGGE and Illumina showed important modifications of the microbiota composition, associated with an imbalance of the colonic microbiota (i.e. increase in the relative abundance of Enterobacteriaceae). HPLC-DAD-TOF-MS analyses demonstrated that the metabolism of t-resveratrol and other stilbenes was inhibited by continuous administration. Our results suggest M-SHIME® as an explorative tool to define the dosage of food supplements, in particular to simulate effective continuous administration in humans.}, }
@article {pmid27713206, year = {2017}, author = {Chen, Y and Ye, L and Zhao, F and Xiao, L and Cheng, S and Zhang, XX}, title = {Bacterial Community Shift during the Startup of a Full-Scale Oxidation Ditch Treating Sewage.}, journal = {Journal of microbiology and biotechnology}, volume = {27}, number = {1}, pages = {141-148}, doi = {10.4014/jmb.1607.07007}, pmid = {27713206}, issn = {1738-8872}, abstract = {The oxidation ditch (OD) is one of the most widely used processes for treating municipal wastewater. However, the microbial communities in the OD systems have not been well characterized, and little information about the shift of bacterial community during the startup process of the OD systems is available. In this study, we investigated the bacterial community changes during the startup period (over 100 days) of a full-scale OD. The results showed that the bacterial community dramatically changed during the startup period. Similar to the activated sludge samples in other studies, Proteobacteria (accounting for 26.3%-48.4%) was the most dominant bacterial phylum in the OD system, but its relative abundance declined nearly 40% during the startup process. It was also found that Planctomycetes proliferated greatly (from 4.79% to 13.5%) and finally replaced Bacteroidetes as the second abundant phylum in the OD system. Specifically, some bacteria affiliated with genus Flavobacterium exhibited remarkable decreasing trends, whereas bacterial species belonging to the OD1 candidate division and Saprospiraceae family were found to increase during the startup process. Despite of the bacterial community shift, the organic matter, nitrogen, and phosphorus in the effluent were always in low concentrations, suggesting the functional redundancy of the bacterial community. Moreover, by comparing with the bacterial community in other municipal wastewater treatment bioreactors, some potentially novel bacterial species were found to be present in the OD system. Collectively, this study improved our understandings of the bacterial community structure and microbial ecology during the startup of a full-scale wastewater treatment bioreactor.}, }
@article {pmid27709807, year = {2017}, author = {De Filippis, F and Parente, E and Ercolini, D}, title = {Metagenomics insights into food fermentations.}, journal = {Microbial biotechnology}, volume = {10}, number = {1}, pages = {91-102}, pmid = {27709807}, issn = {1751-7915}, mesh = {Computational Biology ; *Fermentation ; *Food Microbiology ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; *Microbial Consortia ; }, abstract = {This review describes the recent advances in the study of food microbial ecology, with a focus on food fermentations. High-throughput sequencing (HTS) technologies have been widely applied to the study of food microbial consortia and the different applications of HTS technologies were exploited in order to monitor microbial dynamics in food fermentative processes. Phylobiomics was the most explored application in the past decade. Metagenomics and metatranscriptomics, although still underexploited, promise to uncover the functionality of complex microbial consortia. The new knowledge acquired will help to understand how to make a profitable use of microbial genetic resources and modulate key activities of beneficial microbes in order to ensure process efficiency, product quality and safety.}, }
@article {pmid27709435, year = {2017}, author = {Kokkinos, P and Kozyra, I and Lazic, S and Söderberg, K and Vasickova, P and Bouwknegt, M and Rutjes, S and Willems, K and Moloney, R and de Roda Husman, AM and Kaupke, A and Legaki, E and D'Agostino, M and Cook, N and von Bonsdorff, CH and Rzeżutka, A and Petrovic, T and Maunula, L and Pavlik, I and Vantarakis, A}, title = {Virological Quality of Irrigation Water in Leafy Green Vegetables and Berry Fruits Production Chains.}, journal = {Food and environmental virology}, volume = {9}, number = {1}, pages = {72-78}, pmid = {27709435}, issn = {1867-0342}, mesh = {Agricultural Irrigation ; Europe ; Food Contamination/*analysis ; Fresh Water/chemistry/*virology ; Fruit/growth &amp; development/*virology ; Plant Leaves/growth &amp; development/*virology ; Vegetables/growth &amp; development/*virology ; Viruses/classification/genetics/*isolation &amp; purification ; }, abstract = {This study condenses data acquired during investigations of the virological quality of irrigation water used in production of fresh produce. One hundred and eight samples of irrigation water were collected from five berry fruit farms in Finland (1), the Czech Republic (1), Serbia (2), and Poland (1), and sixty-one samples were collected from three leafy green vegetable farms in Poland, Serbia, and Greece. Samples were analyzed for index viruses of human or animal fecal contamination (human and porcine adenoviruses, and bovine polyoma viruses), and human pathogenic viruses (hepatitis A virus, hepatitis E virus, and noroviruses GI/GII). Both index and pathogenic viruses were found in irrigation water samples from the leafy green vegetables production chain. The data on the presence of index viruses indicated that the highest percentage of fecal contamination was of human origin (28.1 %, 18/64), followed by that of porcine (15.4 %, 6/39) and bovine (5.1 %, 2/39) origins. Hepatitis E virus (5 %, 1/20) and noroviruses GII (14.3 %, 4/28) were also detected. Samples from berry fruit production were also positive for both index and pathogenic viruses. The highest percentage of fecal contamination was of human origin (8.3 %, 9/108), followed by that of porcine, 4.5 % (4/89) and bovine, 1.1 % (1/89) origins. Norovirus GII (3.6 %, 2/56) was also detected. These data demonstrate that irrigation water used in primary production is an important vehicle of viral contamination for fresh produce, and thus is a critical control point which should be integrated into food safety management systems for viruses. The recommendations of Codex Alimentarius, as well as regulations on the use of water of appropriate quality for irrigation purposes, should be followed.}, }
@article {pmid27709247, year = {2017}, author = {Lee, JA and Francis, CA}, title = {Spatiotemporal Characterization of San Francisco Bay Denitrifying Communities: a Comparison of nirK and nirS Diversity and Abundance.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {271-284}, pmid = {27709247}, issn = {1432-184X}, mesh = {Ammonia/metabolism ; Bacteria/*genetics ; Base Sequence ; Bays/microbiology ; *Biodiversity ; Cytochrome c Group ; Cytochromes/genetics ; DNA, Bacterial ; Denitrification/genetics ; Estuaries ; Genes, Bacterial ; Geologic Sediments/chemistry/*microbiology ; Nitrates/metabolism ; Nitrite Reductases/*genetics ; Nitrogen/metabolism ; Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Salinity ; San Francisco ; Seawater/chemistry/*microbiology ; Temperature ; }, abstract = {Denitrifying bacteria play a critical role in the estuarine nitrogen cycle. Through the transformation of nitrate into nitrogen gas, these organisms contribute to the loss of bioavailable (i.e., fixed) nitrogen from low-oxygen environments such as estuary sediments. Denitrifiers have been shown to vary in abundance and diversity across the spatial environmental gradients that characterize estuaries, such as salinity and nitrogen availability; however, little is known about how their communities change in response to temporal changes in those environmental properties. Here, we present a 1-year survey of sediment denitrifier communities along the estuarine salinity gradient of San Francisco Bay. We used quantitative PCR and sequencing of functional genes coding for a key denitrifying enzyme, dissimilatory nitrite reductase, to compare two groups of denitrifiers: those with nirK (encoding copper-dependent nitrite reductase) and those with nirS (encoding the cytochrome-cd 1-dependent variant). We found that nirS was consistently more abundant and more diverse than nirK in all parts of the estuary. The abundances of the two genes were tightly linked across space but differed temporally, with nirK peaking when temperature was low and nirS peaking when nitrate was high. Likewise, the diversity and composition of nirK- versus nirS-type communities differed in their responses to seasonal variations, though both were strongly determined by site. Furthermore, our sequence libraries detected deeply branching clades with no cultured isolates, evidence of enormous diversity within the denitrifiers that remains to be explored.}, }
@article {pmid27709246, year = {2017}, author = {Dos Santos, DF and Istvan, P and Quirino, BF and Kruger, RH}, title = {Functional Metagenomics as a Tool for Identification of New Antibiotic Resistance Genes from Natural Environments.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {479-491}, pmid = {27709246}, issn = {1432-184X}, mesh = {Animals ; Anti-Bacterial Agents/classification/pharmacology ; Bacterial Infections/drug therapy/microbiology ; Base Sequence ; Culture Techniques ; DNA, Bacterial ; Drug Resistance, Bacterial/genetics/physiology ; Drug Resistance, Microbial/*genetics ; *Environment ; Genes, Bacterial/genetics ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; }, abstract = {Antibiotic resistance has become a major concern for human and animal health, as therapeutic alternatives to treat multidrug-resistant microorganisms are rapidly dwindling. The problem is compounded by low investment in antibiotic research and lack of new effective antimicrobial drugs on the market. Exploring environmental antibiotic resistance genes (ARGs) will help us to better understand bacterial resistance mechanisms, which may be the key to identifying new drug targets. Because most environment-associated microorganisms are not yet cultivable, culture-independent techniques are essential to determine which organisms are present in a given environmental sample and allow the assessment and utilization of the genetic wealth they represent. Metagenomics represents a powerful tool to achieve these goals using sequence-based and functional-based approaches. Functional metagenomic approaches are particularly well suited to the identification new ARGs from natural environments because, unlike sequence-based approaches, they do not require previous knowledge of these genes. This review discusses functional metagenomics-based ARG research and describes new possibilities for surveying the resistome in environmental samples.}, }
@article {pmid27708627, year = {2016}, author = {Maciejewska, M and Adam, D and Martinet, L and Naômé, A and Całusińska, M and Delfosse, P and Carnol, M and Barton, HA and Hayette, MP and Smargiasso, N and De Pauw, E and Hanikenne, M and Baurain, D and Rigali, S}, title = {A Phenotypic and Genotypic Analysis of the Antimicrobial Potential of Cultivable Streptomyces Isolated from Cave Moonmilk Deposits.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1455}, pmid = {27708627}, issn = {1664-302X}, abstract = {Moonmilk speleothems of limestone caves host a rich microbiome, among which Actinobacteria represent one of the most abundant phyla. Ancient medical texts reported that moonmilk had therapeutical properties, thereby suggesting that its filamentous endemic actinobacterial population might be a source of natural products useful in human treatment. In this work, a screening approach was undertaken in order to isolate cultivable Actinobacteria from moonmilk of the Grotte des Collemboles in Belgium, to evaluate their taxonomic profile, and to assess their potential in biosynthesis of antimicrobials. Phylogenetic analysis revealed that all 78 isolates were exclusively affiliated to the genus Streptomyces and clustered into 31 distinct phylotypes displaying various pigmentation patterns and morphological features. Phylotype representatives were tested for antibacterial and antifungal activities and their genomes were mined for secondary metabolite biosynthetic genes coding for non-ribosomal peptide synthetases (NRPSs), and polyketide synthases (PKS). The moonmilk Streptomyces collection was found to display strong inhibitory activities against a wide range of reference organisms, as 94, 71, and 94% of the isolates inhibited or impaired the growth of Gram-positive, Gram-negative bacteria, and fungi, respectively. Interestingly, 90% of the cave strains induced strong growth suppression against the multi-drug resistant Rasamsonia argillacea, a causative agent of invasive mycosis in cystic fibrosis and chronic granulomatous diseases. No correlation was observed between the global antimicrobial activity of an individual strain and the number of NRPS and PKS genes predicted in its genome, suggesting that approaches for awakening cryptic metabolites biosynthesis should be applied to isolates with no antimicrobial phenotype. Overall, our work supports the common belief that moonmilk might effectively treat various infectious diseases thanks to the presence of a highly diverse population of prolific antimicrobial producing Streptomyces, and thus may indeed constitute a promising reservoir of potentially novel active natural compounds.}, }
@article {pmid27706829, year = {2017}, author = {Gillings, MR}, title = {Lateral gene transfer, bacterial genome evolution, and the Anthropocene.}, journal = {Annals of the New York Academy of Sciences}, volume = {1389}, number = {1}, pages = {20-36}, doi = {10.1111/nyas.13213}, pmid = {27706829}, issn = {1749-6632}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Anti-Infective Agents ; Bacteria/drug effects/*genetics ; Bacterial Infections/genetics ; *Biological Evolution ; DNA, Bacterial/analysis ; Ecosystem ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Humans ; Phenotype ; }, abstract = {Lateral gene transfer (LGT) has significantly influenced bacterial evolution since the origins of life. It helped bacteria generate flexible, mosaic genomes and enables individual cells to rapidly acquire adaptive phenotypes. In turn, this allowed bacteria to mount strong defenses against human attempts to control their growth. The widespread dissemination of genes conferring resistance to antimicrobial agents has precipitated a crisis for modern medicine. Our actions can promote increased rates of LGT and also provide selective forces to fix such events in bacterial populations. For instance, the use of selective agents induces the bacterial SOS response, which stimulates LGT. We create hotspots for lateral transfer, such as wastewater systems, hospitals, and animal production facilities. Conduits of gene transfer between humans and animals ensure rapid dissemination of recent transfer events, as does modern transport and globalization. As resistance to antibacterial compounds becomes universal, there is likely to be increasing selection pressure for phenotypes with adverse consequences for human welfare, such as enhanced virulence, pathogenicity, and transmission. Improved understanding of the ecology of LGT could help us devise strategies to control this fundamental evolutionary process.}, }
@article {pmid27702488, year = {2016}, author = {Adesioye, FA and Makhalanyane, TP and Biely, P and Cowan, DA}, title = {Phylogeny, classification and metagenomic bioprospecting of microbial acetyl xylan esterases.}, journal = {Enzyme and microbial technology}, volume = {93-94}, number = {}, pages = {79-91}, doi = {10.1016/j.enzmictec.2016.07.001}, pmid = {27702488}, issn = {1879-0909}, mesh = {Acetylesterase/*classification/*genetics/metabolism ; Bioprospecting ; Data Mining ; Databases, Protein ; Extremophiles/enzymology/genetics ; Lignin/chemistry/metabolism ; Metagenomics ; Phylogeny ; Substrate Specificity ; Xylans/chemistry/metabolism ; }, abstract = {Acetyl xylan esterases (AcXEs), also termed xylan deacetylases, are broad specificity Carbohydrate-Active Enzymes (CAZymes) that hydrolyse ester bonds to liberate acetic acid from acetylated hemicellulose (typically polymeric xylan and xylooligosaccharides). They belong to eight families within the Carbohydrate Esterase (CE) class of the CAZy database. AcXE classification is largely based on sequence-dependent phylogenetic relationships, supported in some instances with substrate specificity data. However, some sequence-based predictions of AcXE-encoding gene identity have proved to be functionally incorrect. Such ambiguities can lead to mis-assignment of genes and enzymes during sequence data-mining, reinforcing the necessity for the experimental confirmation of the functional properties of putative AcXE-encoding gene products. Although one-third of all characterized CEs within CAZy families 1-7 and 16 are AcXEs, there is a need to expand the sequence database in order to strengthen the link between AcXE gene sequence and specificity. Currently, most AcXEs are derived from a limited range of (mostly microbial) sources and have been identified via culture-based bioprospecting methods, restricting current knowledge of AcXEs to data from relatively few microbial species. More recently, the successful identification of AcXEs via genome and metagenome mining has emphasised the huge potential of culture-independent bioprospecting strategies. We note, however, that the functional metagenomics approach is still hampered by screening bottlenecks. The most relevant recent reviews of AcXEs have focused primarily on the biochemical and functional properties of these enzymes. In this review, we focus on AcXE phylogeny, classification and the future of metagenomic bioprospecting for novel AcXEs.}, }
@article {pmid27701451, year = {2016}, author = {Vilajeliu-Pons, A and Bañeras, L and Puig, S and Molognoni, D and Vilà-Rovira, A and Hernández-Del Amo, E and Balaguer, MD and Colprim, J}, title = {External Resistances Applied to MFC Affect Core Microbiome and Swine Manure Treatment Efficiencies.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0164044}, pmid = {27701451}, issn = {1932-6203}, mesh = {Animals ; Bioelectric Energy Sources/*microbiology ; Firmicutes/*classification/genetics/isolation &amp; purification ; Gammaproteobacteria/*classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Hydrodynamics ; Manure/*microbiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Swine ; }, abstract = {Microbial fuel cells (MFCs) can be designed to combine water treatment with concomitant electricity production. Animal manure treatment has been poorly explored using MFCs, and its implementation at full-scale primarily relies on the bacterial distribution and activity within the treatment cell. This study reports the bacterial community changes at four positions within the anode of two almost identically operated MFCs fed swine manure. Changes in the microbiome structure are described according to the MFC fluid dynamics and the application of a maximum power point tracking system (MPPT) compared to a fixed resistance system (Ref-MFC). Both external resistance and cell hydrodynamics are thought to heavily influence MFC performance. The microbiome was characterised both quantitatively (qPCR) and qualitatively (454-pyrosequencing) by targeting bacterial 16S rRNA genes. The diversity of the microbial community in the MFC biofilm was reduced and differed from the influent swine manure. The adopted electric condition (MPPT vs fixed resistance) was more relevant than the fluid dynamics in shaping the MFC microbiome. MPPT control positively affected bacterial abundance and promoted the selection of putatively exoelectrogenic bacteria in the MFC core microbiome (Sedimentibacter sp. and gammaproteobacteria). These differences in the microbiome may be responsible for the two-fold increase in power production achieved by the MPPT-MFC compared to the Ref-MFC.}, }
@article {pmid27698620, year = {2016}, author = {Bik, EM}, title = {The Hoops, Hopes, and Hypes of Human Microbiome Research.}, journal = {The Yale journal of biology and medicine}, volume = {89}, number = {3}, pages = {363-373}, pmid = {27698620}, issn = {1551-4056}, mesh = {Autistic Disorder/genetics ; Computational Biology/methods ; Humans ; Inflammatory Bowel Diseases/genetics ; Microbiota/*genetics ; }, abstract = {Recent developments in sequencing methods and bioinformatics analysis tools have greatly enabled the culture-independent analysis of complex microbial communities associated with environmental samples, plants, and animals. This has led to a spectacular increase in the number of studies on both membership and functionalities of these hitherto invisible worlds, in particular those of the human microbiome. The wide variety in available microbiome tools and platforms can be overwhelming, and making sound conclusions from scientific research can be challenging. Here, I will review 1) the methodological and analytic hoops a good microbiome study has to jump through, including DNA extraction and choice of bioinformatics tools, 2) the hopes this field has generated for diseases such as autism and inflammatory bowel diseases, and 3) some of the hypes that it has created, e.g., by confusing correlation and causation, and the recent pseudoscientific commercialization of microbiome research.}, }
@article {pmid27697892, year = {2016}, author = {Li, X and Lu, N and Brady, HR and Packman, AI}, title = {Biomineralization strongly modulates the formation of Proteus mirabilis and Pseudomonas aeruginosa dual-species biofilms.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {12}, pages = {}, doi = {10.1093/femsec/fiw189}, pmid = {27697892}, issn = {1574-6941}, abstract = {Proteus mirabilis and Pseudomonas aeruginosa are common pathogens that often form biofilms together in catheter-associated urinary tract infections (CAUTI). However, the interactions between these two species in biofilms are largely unknown. P. mirabilis induces ureolytic biomineralization that substantially modifies key biofilm properties including morphology, persistence, and recalcitrance to antimicrobial therapy. These processes are well known to complicate CAUTI, but the consequences for colonization and persistence of P. mirabilis in polymicrobial biofilms have not been explored. Here we characterized the role of biomineralization in regulating the development of P. mirabilis and P. aeruginosa dual-species biofilms. Time-series observations revealed that the dominance of P. mirabilis was synchronized with mineral formation in the biofilm. After 24 hours of development, the dual-species biofilm was dominated by P. mirabilis, and the distribution of P. mirabilis biomass was strongly correlated with the mineral fraction of the biofilm. Conversely, dual-species growth without biomineralization yielded strikingly different patterns in the biofilm, with P. aeruginosa dominating the biofilm biomass. These results show that biomineralization is responsible for the increased success of P. mirabilis in the polymicrobial biofilm. Since biofilm biomineralization commonly occurs in diverse clinical, natural and engineered systems, these findings imply that biomineralization could broadly influence the microbial ecology of multispecies biofilms.}, }
@article {pmid27697693, year = {2017}, author = {Koopman, JE and Hoogenkamp, MA and Buijs, MJ and Brandt, BW and Keijser, BJ and Crielaard, W and Ten Cate, JM and Zaura, E}, title = {Changes in the oral ecosystem induced by the use of 8% arginine toothpaste.}, journal = {Archives of oral biology}, volume = {73}, number = {}, pages = {79-87}, doi = {10.1016/j.archoralbio.2016.09.008}, pmid = {27697693}, issn = {1879-1506}, mesh = {Adult ; Arginine/*pharmacology ; Female ; Healthy Volunteers ; Humans ; Hydrogen-Ion Concentration ; Male ; Microbiota/*drug effects ; Mouth/*drug effects/*microbiology ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; Sequence Analysis ; Toothpastes/*pharmacology ; }, abstract = {OBJECTIVE: Bacterial metabolism of arginine in the oral cavity has a pH-raising and thus, potential anti-caries effect. However, the influence of arginine on the oral microbial ecosystem remains largely unresolved.<br><br>DESIGN: In this pilot study, nine healthy individuals used toothpaste containing 8% arginine for eight weeks. Saliva was collected to determine arginolytic potential and sucrose metabolic activity at the Baseline, Week 4, Week 8 and after a two weeks Wash-out period. To follow the effects on microbial ecology, 16S rDNA sequencing on saliva and plaque samples at Baseline and Week 8 and metagenome sequencing on selected saliva samples of the same time-points was performed.<br><br>RESULTS: During the study period, the arginolytic potential of saliva increased, while the sucrose metabolism in saliva decreased. These effects were reversed during the Wash-out period. Although a few operational taxonomic units (OTUs) in plaque changed in abundance during the study period, there was no real shift in the plaque microbiome. In the saliva microbiome there was a significant compositional shift, specifically the genus Veillonella had increased significantly in abundance at Week 8.<br><br>CONCLUSION: Indeed, the presence of arginine in toothpaste affects the arginolytic capacity of saliva and reduces its sucrose metabolic activity. Additionally, it leads to a shift in the salivary microbiome composition towards a healthy ecology from a caries point of view. Therefore, arginine can be regarded as a genuine oral prebiotic.}, }
@article {pmid27697682, year = {2016}, author = {Coats, ER and Watson, BS and Brinkman, CK}, title = {Polyhydroxyalkanoate synthesis by mixed microbial consortia cultured on fermented dairy manure: Effect of aeration on process rates/yields and the associated microbial ecology.}, journal = {Water research}, volume = {106}, number = {}, pages = {26-40}, pmid = {27697682}, issn = {1879-2448}, support = {P20 GM103408/GM/NIGMS NIH HHS/United States ; }, mesh = {Bioreactors ; Fermentation ; Manure ; *Microbial Consortia ; Polyhydroxyalkanoates/*biosynthesis ; }, abstract = {Polyhydroxyalkanoates (PHAs) are biodegradable polymers that can substitute for petroleum-based plastics in a variety of applications. One avenue to commercial PHA production involves coupling waste-based synthesis with the use of mixed microbial consortia (MMC). In this regard, production requires maximizing the enrichment of a MMC capable of feast-famine PHA synthesis, with the metabolic response induced through imposition of aerobic-dynamic feeding (ADF) conditions. However, the concept of PHA production in complex matrices remains unrefined; process operational improvements are needed, along with an enhanced understanding of the MMC. Research presented herein investigated the effect of aeration on feast-famine PHA synthesis, with four independent aeration state systems studied; MMC were fed volatile fatty acid (VFA)-rich fermented dairy manure. Regardless of the aeration state, all MMC exhibited a feast-famine response based on observed carbon cycling. Moreover, there was no statistical difference in PHA synthesis rates, with qPHA ranging from 0.10 to 0.19 CmmolPHA gVSS[-1] min[-1]; VFA uptake rates exhibited similar statistical indifferences. PHA production assessments on the enriched MMC resulted in maximum intracellular concentrations ranging from 22.5 to 90.7% (mgPHA mgVSS[-1]); at maximum concentration, the mean hydroxyvalerate mol content was 73 ± 0.6%. While a typical feast-famine dissolved oxygen (DO) pattern was observed at maximum aeration, less resolution was observed at decreasing aeration rates, suggesting that DO may not be an optimal process monitoring parameter. At lower aeration states, nitrogen cycling patterns, supported by molecular investigations targeting AOBs and NOBs, indicate that NO2 and NO3 sustained feast-famine PHA synthesis. Next-generation sequencing analysis of the respective MMC revealed numerous and diverse genera exhibiting the potential to achieve PHA synthesis, suggesting functional redundancy embedded in the diverse MMC. Ultimately, results demonstrate that aeration can be controlled in waste-based ADF systems to sustain PHA production potential, while enriching for a diverse MMC that exhibits potential functional redundancy. Reduced aeration could also enhance cost competitiveness of waste-based PHA production, with potential further benefits associated with nitrogen treatment.}, }
@article {pmid27695447, year = {2016}, author = {Thøgersen, MS and Delpin, MW and Melchiorsen, J and Kilstrup, M and Månsson, M and Bunk, B and Spröer, C and Overmann, J and Nielsen, KF and Gram, L}, title = {Production of the Bioactive Compounds Violacein and Indolmycin Is Conditional in a maeA Mutant of Pseudoalteromonas luteoviolacea S4054 Lacking the Malic Enzyme.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1461}, pmid = {27695447}, issn = {1664-302X}, abstract = {It has previously been reported that some strains of the marine bacterium Pseudoalteromonas luteoviolacea produce the purple bioactive pigment violacein as well as the antibiotic compound indolmycin, hitherto only found in Streptomyces. The purpose of the present study was to determine the relative role of each of these two compounds as antibacterial compounds in P. luteoviolacea S4054. Using Tn10 transposon mutagenesis, a mutant strain that was significantly reduced in violacein production in mannose-containing substrates was created. Full genome analyses revealed that the vio-biosynthetic gene cluster was not interrupted by the transposon; instead the insertion was located to the maeA gene encoding the malic enzyme. Supernatant of the mutant strain inhibited Vibrio anguillarum and Staphylococcus aureus in well diffusion assays and in MIC assays at the same level as the wild type strain. The mutant strain killed V. anguillarum in co-culture experiments as efficiently as the wild type. Using UHPLC-UV/Vis analyses, we quantified violacein and indolmycin, and the mutant strain only produced 7-10% the amount of violacein compared to the wild type strain. In contrast, the amount of indolmycin produced by the mutant strain was about 300% that of the wild type. Since inhibition of V. anguillarum and S. aureus by the mutant strain was similar to that of the wild type, it is concluded that violacein is not the major antibacterial compound in P. luteoviolacea. We furthermore propose that production of violacein and indolmycin may be metabolically linked and that yet unidentified antibacterial compound(s) may be play a role in the antibacterial activity of P. luteoviolacea.}, }
@article {pmid27693307, year = {2016}, author = {Maldonado-Gómez, MX and Martínez, I and Bottacini, F and O'Callaghan, A and Ventura, M and van Sinderen, D and Hillmann, B and Vangay, P and Knights, D and Hutkins, RW and Walter, J}, title = {Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome.}, journal = {Cell host &amp; microbe}, volume = {20}, number = {4}, pages = {515-526}, doi = {10.1016/j.chom.2016.09.001}, pmid = {27693307}, issn = {1934-6069}, mesh = {Administration, Oral ; Bifidobacterium longum/*growth &amp; development ; *Carrier State ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Probiotics/*administration &amp; dosage ; Time Factors ; }, abstract = {Live bacteria (such as probiotics) have long been used to modulate gut microbiota and human physiology, but their colonization is mostly transient. Conceptual understanding of the ecological principles as they apply to exogenously introduced microbes in gut ecosystems is lacking. We find that, when orally administered to humans, Bifidobacterium longum AH1206 stably persists in the gut of 30% of individuals for at least 6 months without causing gastrointestinal symptoms or impacting the composition of the resident gut microbiota. AH1206 engraftment was associated with low abundance of resident B. longum and underrepresentation of specific carbohydrate utilization genes in the pre-treatment microbiome. Thus, phylogenetic limiting and resource availability are two factors that control the niche opportunity for AH1206 colonization. These findings suggest that bacterial species and functional genes absent in the gut microbiome of individual humans can be reestablished, providing opportunities for precise and personalized microbiome reconstitution.}, }
@article {pmid27690185, year = {2016}, author = {Rubio-Portillo, E and Santos, F and Martínez-García, M and de Los Ríos, A and Ascaso, C and Souza-Egipsy, V and Ramos-Esplá, AA and Anton, J}, title = {Structure and temporal dynamics of the bacterial communities associated to microhabitats of the coral Oculina patagonica.}, journal = {Environmental microbiology}, volume = {18}, number = {12}, pages = {4564-4578}, doi = {10.1111/1462-2920.13548}, pmid = {27690185}, issn = {1462-2920}, mesh = {Animals ; Anthozoa/*microbiology ; Denaturing Gradient Gel Electrophoresis ; Ecosystem ; Mediterranean Sea ; Vibrio/isolation &amp; purification/physiology ; }, abstract = {Corals are known to contain a diverse microbiota that plays a paramount role in the physiology and health of holobiont. However, few studies have addressed the variability of bacterial communities within the coral host. In this study, bacterial community composition from the mucus, tissue and skeleton of the scleractinian coral Oculina patagonica were investigated seasonally at two locations in the Western Mediterranean Sea, to further understand how environmental conditions and the coral microbiome structure are related. We used denaturing gradient gel electrophoresis in combination with next-generation sequencing and electron microscopy to characterize the bacterial community. The bacterial communities were significantly different among coral compartments, and coral tissue displayed the greatest changes related to environmental conditions and coral health status. Species belonging to the Rhodobacteraceae and Vibrionaceae families form part of O. patagonica tissues core microbiome and may play significant roles in the nitrogen cycle. Furthermore, sequences related to the coral pathogens, Vibrio mediterranei and Vibrio coralliilyticus, were detected not only in bleached corals but also in healthy ones, even during cold months. This fact opens a new view onto unveiling the role of pathogens in the development of coral diseases in the future.}, }
@article {pmid27688981, year = {2016}, author = {Burke, CM and Darling, AE}, title = {A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e2492}, pmid = {27688981}, issn = {2167-8359}, abstract = {BACKGROUND: The bacterial 16S rRNA gene has historically been used in defining bacterial taxonomy and phylogeny. However, there are currently no high-throughput methods to sequence full-length 16S rRNA genes present in a sample with precision.<br><br>RESULTS: We describe a method for sequencing near full-length 16S rRNA gene amplicons using the high throughput Illumina MiSeq platform and test it using DNA from human skin swab samples. Proof of principle of the approach is demonstrated, with the generation of 1,604 sequences greater than 1,300 nt from a single Nano MiSeq run, with accuracy estimated to be 100-fold higher than standard Illumina reads. The reads were chimera filtered using information from a single molecule dual tagging scheme that boosts the signal available for chimera detection.<br><br>CONCLUSIONS: This method could be scaled up to generate many thousands of sequences per MiSeq run and could be applied to other sequencing platforms. This has great potential for populating databases with high quality, near full-length 16S rRNA gene sequences from under-represented taxa and environments and facilitates analyses of microbial communities at higher resolution.}, }
@article {pmid27687990, year = {2016}, author = {Buysschaert, B and Byloos, B and Leys, N and Van Houdt, R and Boon, N}, title = {Reevaluating multicolor flow cytometry to assess microbial viability.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {21}, pages = {9037-9051}, doi = {10.1007/s00253-016-7837-5}, pmid = {27687990}, issn = {1432-0614}, mesh = {Bacteriological Techniques/*methods ; Color ; Flow Cytometry/*methods ; *Microbial Viability ; Staining and Labeling/*methods ; }, abstract = {Flow cytometry is a rapid and quantitative method to determine bacterial viability. Although different stains can be used to establish viability, staining protocols are inconsistent and lack a general optimization approach. Very few "true" multicolor protocols, where dyes are combined in one sample, have been developed for microbiological applications. In this mini-review, the discrepancy between protocols for cell-permeant nucleic acid and functional stains are discussed as well as their use as viability dyes. Furthermore, optimization of staining protocols for a specific setup are described. Original data using the red-excitable SYTO dyes SYTO 59 to 64 and SYTO 17, combined with functional stains, for double and triple staining applications is also included. As each dye and dye combination behaves differently within a certain combination of medium matrix, microorganism, and instrument, protocols need to be tuned to obtain reproducible results. Therefore, single, double, and triple stains are reviewed, including the different parameters that influence staining such as stain kinetics, optimal stain concentration, and the effect of the chelator EDTA as membrane permeabilizer. In the last section, we highlight the need to investigate the stability of multicolor assays to ensure correct results as multiwell autoloaders are now commonly used.}, }
@article {pmid27687872, year = {2017}, author = {Malacrinò, A and Schena, L and Campolo, O and Laudani, F and Mosca, S and Giunti, G and Strano, CP and Palmeri, V}, title = {A Metabarcoding Survey on the Fungal Microbiota Associated to the Olive Fruit Fly.}, journal = {Microbial ecology}, volume = {73}, number = {3}, pages = {677-684}, pmid = {27687872}, issn = {1432-184X}, mesh = {Alternaria/*classification/genetics/isolation &amp; purification ; Animals ; Ascomycota/*classification/genetics/isolation &amp; purification ; Base Sequence ; Cladosporium/*classification/genetics/isolation &amp; purification ; Colletotrichum/*classification/genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; DNA, Intergenic/genetics ; High-Throughput Nucleotide Sequencing ; Mycobiome/*genetics ; Olea ; Sequence Analysis, DNA ; Tephritidae/*microbiology ; }, abstract = {The occurrence of interaction between insects and fungi is interesting from an ecological point of view, particularly when these interactions involve insect pests and plant pathogens within an agroecosystem. In this study, we aimed to perform an accurate analysis on the fungal microbiota associated to Bactrocera oleae (Rossi) through a metabarcoding approach based on 454 pyrosequencing. From this analysis, we retrieved 43,549 reads that clustered into 128 operational taxonomic units (OTUs), of which 29 resulted in the "core" associate fungi of B. oleae. This fungal community was mainly represented by sooty mould fungi, such as Cladosporium spp., Alternaria spp. and Aureobasidium spp., by plant pathogens like Colletotrichum spp. and Pseudocercospora spp., along with several other less abundant taxa whose ecology is unclear in most of the cases. Our findings lead to new insights into the microbial ecology of this specific ecological niche, enabling the understanding of a complex network of interactions within the olive agroecosystem.}, }
@article {pmid27687871, year = {2017}, author = {Hujslová, M and Kubátová, A and Bukovská, P and Chudíčková, M and Kolařík, M}, title = {Extremely Acidic Soils are Dominated by Species-Poor and Highly Specific Fungal Communities.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {321-337}, pmid = {27687871}, issn = {1432-184X}, mesh = {Acids ; Ascomycota/classification/isolation &amp; purification ; Base Sequence ; *Biodiversity ; Classification ; Czech Republic ; DNA, Fungal/analysis ; Ecosystem ; Fungi/*classification/genetics/growth &amp; development/*isolation &amp; purification ; Hydrogen-Ion Concentration ; Penicillium/classification/isolation &amp; purification ; *Phylogeny ; Soil/*chemistry ; *Soil Microbiology ; Species Specificity ; }, abstract = {Highly acidic soils (pH < 3) represent an environment which might potentially offer new biotechnologically interesting fungi. Nevertheless, only little data on fungal communities in highly acidic habitats are available. Here, we focused on the diversity of cultivable filamentous microfungi in highly acidic soils (pH < 3) in the Czech Republic. Altogether, 16 soil samples were collected from four sampling sites and were processed by various approaches. In total, 54 fungal taxa were isolated and identified using classical as well as molecular markers. All dominant species were found both as living mycelia and as resistant stages. Numerous recently described or unknown taxa were isolated. The core of the fungal assemblage under study consisted of phylogenetically unrelated and often globally distributed fungi exclusively inhabiting highly acidic habitats like Acidiella bohemica, Acidomyces acidophilus, and unidentified helotialean fungus, as well as taxa known from less acidic and often extreme environments like Acidea extrema, Penicillium simplicissimum s.l., and Penicillium spinulosum. The large number of identified specialized species indicates that highly acidic environments provide suitable conditions for the evolution of specialist species. The occurrence of ubiquitous fungi in highly acidic substrates points to the principal role of competition in the colonization of such environments. The detected taxa did not require low pH to survive, because they can grow in a broad range of pH.}, }
@article {pmid27687784, year = {2017}, author = {Manach, C and Milenkovic, D and Van de Wiele, T and Rodriguez-Mateos, A and de Roos, B and Garcia-Conesa, MT and Landberg, R and Gibney, ER and Heinonen, M and Tomás-Barberán, F and Morand, C}, title = {Addressing the inter-individual variation in response to consumption of plant food bioactives: Towards a better understanding of their role in healthy aging and cardiometabolic risk reduction.}, journal = {Molecular nutrition &amp; food research}, volume = {61}, number = {6}, pages = {}, pmid = {27687784}, issn = {1613-4133}, mesh = {Cardiovascular Diseases/*prevention &amp; control ; Diet ; Diet, Healthy ; Health Behavior ; *Healthy Aging ; Humans ; Metabolic Diseases/*prevention &amp; control ; Phytochemicals/*analysis ; Plants, Edible/*chemistry ; Randomized Controlled Trials as Topic ; Risk Factors ; Risk Reduction Behavior ; }, abstract = {Bioactive compounds in plant-based foods have health properties that contribute to the prevention of age-related chronic diseases, particularly cardiometabolic disorders. Conclusive proof and understanding of these benefits in humans is essential in order to provide effective dietary recommendations but, so far, the evidence obtained from human intervention trials is limited and contradictory. This is partly due to differences between individuals in the absorption, distribution, metabolism and excretion of bioactive compounds, as well as to heterogeneity in their biological response regarding cardiometabolic health outcomes. Identifying the main factors underlying inter-individual differences, as well as developing new and innovative methodologies to account for such variability constitute an overarching goal to ultimately optimize the beneficial health effects of plant food bioactives for each and every one of us. In this respect, this position paper from the COST Action FA1403-POSITIVe examines the main factors likely to affect the individual responses to consumption of plant food bioactives and presents perspectives for assessment and consideration of inter-individual variability.}, }
@article {pmid27682576, year = {2016}, author = {Kamagata, Y and Narihiro, T}, title = {Symbiosis Studies in Microbial Ecology.}, journal = {Microbes and environments}, volume = {31}, number = {3}, pages = {201-203}, pmid = {27682576}, issn = {1347-4405}, }
@article {pmid27681918, year = {2016}, author = {Gutierrez, T and Berry, D and Teske, A and Aitken, MD}, title = {Enrichment of Fusobacteria in Sea Surface Oil Slicks from the Deepwater Horizon Oil Spill.}, journal = {Microorganisms}, volume = {4}, number = {3}, pages = {}, pmid = {27681918}, issn = {2076-2607}, support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; P42 ES005948/ES/NIEHS NIH HHS/United States ; }, abstract = {The Deepwater Horizon (DWH) oil spill led to rapid microbial community shifts in the Gulf of Mexico, including the formation of unprecedented quantities of marine oil snow (MOS) and of a massive subsurface oil plume. The major taxa that bloomed in sea surface oil slicks during the spill included Cycloclasticus, and to a lesser extent Halomonas, Alteromonas, and Pseudoalteromonas-organisms that grow and degrade oil hydrocarbons aerobically. Here, we show that sea surface oil slicks at DWH contained obligate and facultative anaerobic taxa, including members of the obligate anaerobic phylum Fusobacteria that are commonly found in marine sediment environments. Pyrosequencing analysis revealed that Fusobacteria were strongly selected for when sea surface oil slicks were allowed to develop anaerobically. These organisms have been found in oil-contaminated sediments in the Gulf of Mexico, in deep marine oil reservoirs, and other oil-contaminated sites, suggesting they have putative hydrocarbon-degrading qualities. The occurrence and strong selection for Fusobacteria in a lab-based incubation of a sea surface oil slick sample collected during the spill suggests that these organisms may have become enriched in anaerobic zones of suspended particulates, such as MOS. Whilst the formation and rapid sinking of MOS is recognised as an important mechanism by which a proportion of the Macondo oil had been transported to the sea floor, its role in potentially transporting microorganisms, including oil-degraders, from the upper reaches of the water column to the seafloor should be considered. The presence of Fusobacteria on the sea surface-a highly oxygenated environment-is intriguing, and may be explained by the vertical upsurge of oil that provided a carrier to transport these organisms from anaerobic/micro-aerophilic zones in the oil plume or seabed to the upper reaches of the water column. We also propose that the formation of rapidly-sinking MOS may have re-transported these, and other microbial taxa, to the sediment in the Gulf of Mexico.}, }
@article {pmid27681913, year = {2016}, author = {Imhoff, JF}, title = {New Dimensions in Microbial Ecology-Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment.}, journal = {Microorganisms}, volume = {4}, number = {2}, pages = {}, pmid = {27681913}, issn = {2076-2607}, abstract = {During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA) as target for the green sulfur bacteria and of two reaction center proteins (pufLM) for the phototrophic purple bacteria, with genes of adenosine-5'phosphosulfate (APS) reductase (aprA), sulfate thioesterase (soxB) and dissimilatory sulfite reductase (dsrAB) for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA) for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK) for denitrifying bacteria and with genes of methane monooxygenase (pmoA) for methane oxidizing bacteria.}, }
@article {pmid27680878, year = {2016}, author = {Armstrong, A and Valverde, A and Ramond, JB and Makhalanyane, TP and Jansson, JK and Hopkins, DW and Aspray, TJ and Seely, M and Trindade, MI and Cowan, DA}, title = {Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {34434}, pmid = {27680878}, issn = {2045-2322}, abstract = {The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.}, }
@article {pmid27677972, year = {2017}, author = {Asfahl, KL and Schuster, M}, title = {Social interactions in bacterial cell-cell signaling.}, journal = {FEMS microbiology reviews}, volume = {41}, number = {1}, pages = {92-107}, doi = {10.1093/femsre/fuw038}, pmid = {27677972}, issn = {1574-6976}, mesh = {*Bacterial Physiological Phenomena/genetics ; Microbial Interactions/*physiology ; *Signal Transduction ; }, abstract = {Cooperation and conflict in microorganisms is being recognized as an important factor in the organization and function of microbial communities. Many of the cooperative behaviors described in bacteria are governed through a cell-cell signaling process generally termed quorum sensing. Communication and cooperation in diverse microorganisms exhibit predictable trends that behave according to social evolutionary theory, notably that public goods dilemmas produce selective pressures for divergence in social phenotypes including cheating. In this review, we relate the general features of quorum sensing and social adaptation in microorganisms to established evolutionary theory. We then describe physiological and molecular mechanisms that have been shown to stabilize cooperation in microbes, thereby preventing a tragedy of the commons. Continued study of the role of communication and cooperation in microbial ecology and evolution is important to clinical treatment of pathogens, as well as to our fundamental understanding of cooperative selection at all levels of life.}, }
@article {pmid27677894, year = {2017}, author = {Sanchez, E and Bletz, MC and Duntsch, L and Bhuju, S and Geffers, R and Jarek, M and Dohrmann, AB and Tebbe, CC and Steinfartz, S and Vences, M}, title = {Cutaneous Bacterial Communities of a Poisonous Salamander: a Perspective from Life Stages, Body Parts and Environmental Conditions.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {455-465}, pmid = {27677894}, issn = {1432-184X}, mesh = {Alkaloids ; Animal Diseases/prevention &amp; control ; Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Base Sequence ; Biodiversity ; Biological Control Agents ; Classification ; DNA, Bacterial ; Environment ; Germany ; Larva/microbiology ; *Microbiota ; Parotid Gland/microbiology ; *Phylogeny ; Poisons ; Ponds/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis ; Skin/*microbiology ; Caudata/*microbiology ; }, abstract = {Amphibian skin provides a habitat for bacterial communities in its mucus. Understanding the structure and function of this "mucosome" in the European fire salamander (Salamandra salamandra) is critical in the context of novel emerging pathogenic diseases. We compare the cutaneous bacterial communities of this species using amplicon-based sequencing of the 16S rRNA V4 region. Across 290 samples, over 4000 OTUs were identified, four of them consistently present in all samples. Larvae and post-metamorphs exhibited distinct cutaneous microbial communities. In adults, the parotoid gland surface had a community structure different from the head, dorsum, flanks and ventral side. Larvae from streams had higher phylogenetic diversity than those found in ponds. Their bacterial community structure also differed; species of Burkholderiaceae, Comamonadaceae, Methylophilaceae and Sphingomonadaceae were more abundant in pond larvae, possibly related to differences in factors like desiccation and decomposition rate in this environment. The observed differences in the cutaneous bacterial community among stages, body parts and habitats of fire salamanders suggest that both host and external factors shape these microbiota. We hypothesize that the variation in cutaneous bacterial communities might contribute to variation in pathogen susceptibility among individual salamanders.}, }
@article {pmid27677893, year = {2017}, author = {Hernández-Gómez, O and Kimble, SJ and Briggler, JT and Williams, RN}, title = {Characterization of the Cutaneous Bacterial Communities of Two Giant Salamander Subspecies.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {445-454}, pmid = {27677893}, issn = {1432-184X}, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Base Sequence ; Biodiversity ; Classification ; DNA, Bacterial ; Microbiota/*physiology ; Missouri ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Skin/*microbiology ; Caudata/classification/*microbiology ; Wounds and Injuries/microbiology ; }, abstract = {Pathogens currently threaten the existence of many amphibian species. In efforts to combat global declines, researchers have characterized the amphibian cutaneous microbiome as a resource for disease management. Characterization of microbial communities has become useful in studying the links between organismal health and the host microbiome. Hellbender salamanders (Cryptobranchus alleganiensis) provide an ideal system to explore the cutaneous microbiome as this species requires extensive conservation management across its range. In addition, the Ozark hellbender subspecies (Cryptobranchus alleganiensis bishopi) exhibits chronic wounds hypothesized to be caused by bacterial infections, whereas the eastern hellbender (Cryptobranchus alleganiensis alleganiensis) does not. We assessed the cutaneous bacterial microbiome of both subspecies at two locations in the state of Missouri, USA. Through 16S rRNA gene-based amplicon sequencing, we detected more than 1000 distinct operational taxonomic units (OTUs) in the cutaneous and environmental bacterial microbiome. Phylogenetic and abundance-based dissimilarity matrices identified differences in the bacterial communities between the two subspecies, but only the abundance-based dissimilarity matrix identified differences between wounds and healthy skin on Ozark hellbenders. The higher abundance of OTUs on Ozark wounds suggests that commensal bacteria present on the skin and environment may be opportunistically colonizing the wounds. This brief exploration of the hellbender cutaneous bacterial microbiome provides foundational support for future studies seeking to understand the hellbender cutaneous bacterial microbiome and the role of the bacterial microbiota on chronic wounds of Ozark hellbenders.}, }
@article {pmid27677892, year = {2017}, author = {Ishaq, SL and Johnson, SP and Miller, ZJ and Lehnhoff, EA and Olivo, S and Yeoman, CJ and Menalled, FD}, title = {Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {417-434}, pmid = {27677892}, issn = {1432-184X}, mesh = {Agriculture ; Avena ; Bacteria/*classification/genetics ; Base Sequence ; Biodiversity ; Biota ; Classification ; Crops, Agricultural/*microbiology ; DNA, Bacterial/analysis/genetics ; Genes, Bacterial ; Metagenomics ; *Microbial Consortia ; Montana ; Nitrogen Fixation ; *Phylogeny ; Plant Development ; Plant Weeds ; Plants/classification/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Farming practices affect the soil microbial community, which in turn impacts crop growth and crop-weed interactions. This study assessed the modification of soil bacterial community structure by organic or conventional cropping systems, weed species identity [Amaranthus retroflexus L. (redroot pigweed) or Avena fatua L. (wild oat)], and living or sterilized inoculum. Soil from eight paired USDA-certified organic and conventional farms in north-central Montana was used as living or autoclave-sterilized inoculant into steam-pasteurized potting soil, planted with Am. retroflexus or Av. fatua and grown for two consecutive 8-week periods to condition soil nutrients and biota. Subsequently, the V3-V4 regions of the microbial 16S rRNA gene were sequenced by Illumina MiSeq. Treatments clustered significantly, with living or sterilized inoculum being the strongest delineating factor, followed by organic or conventional cropping system, then individual farm. Living inoculum-treated soil had greater species richness and was more diverse than sterile inoculum-treated soil (observed OTUs, Chao, inverse Simpson, Shannon, P < 0.001) and had more discriminant taxa delineating groups (linear discriminant analysis). Living inoculum soil contained more Chloroflexi and Acidobacteria, while the sterile inoculum soil had more Bacteroidetes, Firmicutes, Gemmatimonadetes, and Verrucomicrobia. Organically farmed inoculum-treated soil had greater species richness, more diversity (observed OTUs, Chao, Shannon, P < 0.05), and more discriminant taxa than conventionally farmed inoculum-treated soil. Cyanobacteria were higher in pots growing Am. retroflexus, regardless of inoculum type, for three of the four organic farms. Results highlight the potential of cropping systems and species identity to modify soil bacterial communities, subsequently modifying plant growth and crop-weed competition.}, }
@article {pmid27677790, year = {2016}, author = {Chaguza, C and Andam, CP and Harris, SR and Cornick, JE and Yang, M and Bricio-Moreno, L and Kamng'ona, AW and Parkhill, J and French, N and Heyderman, RS and Kadioglu, A and Everett, DB and Bentley, SD and Hanage, WP}, title = {Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule.}, journal = {mBio}, volume = {7}, number = {5}, pages = {}, pmid = {27677790}, issn = {2150-7511}, support = {//Wellcome Trust/United Kingdom ; R01 AI106786/AI/NIAID NIH HHS/United States ; }, abstract = {UNLABELLED: Streptococcus pneumoniae causes a high burden of invasive pneumococcal disease (IPD) globally, especially in children from resource-poor settings. Like many bacteria, the pneumococcus can import DNA from other strains or even species by transformation and homologous recombination, which has allowed the pneumococcus to evade clinical interventions such as antibiotics and pneumococcal conjugate vaccines (PCVs). Pneumococci are enclosed in a complex polysaccharide capsule that determines the serotype; the capsule varies in size and is associated with properties including carriage prevalence and virulence. We determined and quantified the association between capsule and recombination events using genomic data from a diverse collection of serotypes sampled in Malawi. We determined both the amount of variation introduced by recombination relative to mutation (the relative rate) and how many individual recombination events occur per isolate (the frequency). Using univariate analyses, we found an association between both recombination measures and multiple factors associated with the capsule, including duration and prevalence of carriage. Because many capsular factors are correlated, we used multivariate analysis to correct for collinearity. Capsule size and carriage duration remained positively associated with recombination, although with a reduced P value, and this effect may be mediated through some unassayed additional property associated with larger capsules. This work describes an important impact of serotype on recombination that has been previously overlooked. While the details of how this effect is achieved remain to be determined, it may have important consequences for the serotype-specific response to vaccines and other interventions.<br><br>IMPORTANCE: The capsule determines >90 different pneumococcal serotypes, which vary in capsule size, virulence, duration, and prevalence of carriage. Current serotype-specific vaccines elicit anticapsule antibodies. Pneumococcus can take up exogenous DNA by transformation and insert it into its chromosome by homologous recombination. This mechanism has disseminated drug resistance and generated vaccine escape variants. It is hence crucial to pneumococcal evolutionary response to interventions, but there has been no systematic study quantifying whether serotypes vary in recombination and whether this is associated with serotype-specific properties such as capsule size or carriage duration. Larger capsules could physically inhibit DNA uptake, or given the longer carriage duration for larger capsules, this may promote recombination. We find that recombination varies among capsules and is associated with capsule size, carriage duration, and carriage prevalence and negatively associated with invasiveness. The consequence of this work is that serotypes with different capsules may respond differently to selective pressures like vaccines.}, }
@article {pmid27677789, year = {2016}, author = {Xue, K and Yuan, MM and Xie, J and Li, D and Qin, Y and Hale, LE and Wu, L and Deng, Y and He, Z and Van Nostrand, JD and Luo, Y and Tiedje, JM and Zhou, J}, title = {Annual Removal of Aboveground Plant Biomass Alters Soil Microbial Responses to Warming.}, journal = {mBio}, volume = {7}, number = {5}, pages = {}, pmid = {27677789}, issn = {2150-7511}, abstract = {UNLABELLED: Clipping (i.e., harvesting aboveground plant biomass) is common in agriculture and for bioenergy production. However, microbial responses to clipping in the context of climate warming are poorly understood. We investigated the interactive effects of grassland warming and clipping on soil properties and plant and microbial communities, in particular, on microbial functional genes. Clipping alone did not change the plant biomass production, but warming and clipping combined increased the C4 peak biomass by 47% and belowground net primary production by 110%. Clipping alone and in combination with warming decreased the soil carbon input from litter by 81% and 75%, respectively. With less carbon input, the abundances of genes involved in degrading relatively recalcitrant carbon increased by 38% to 137% in response to either clipping or the combined treatment, which could weaken long-term soil carbon stability and trigger positive feedback with respect to warming. Clipping alone also increased the abundance of genes for nitrogen fixation, mineralization, and denitrification by 32% to 39%. Such potentially stimulated nitrogen fixation could help compensate for the 20% decline in soil ammonium levels caused by clipping alone and could contribute to unchanged plant biomass levels. Moreover, clipping tended to interact antagonistically with warming, especially with respect to effects on nitrogen cycling genes, demonstrating that single-factor studies cannot predict multifactorial changes. These results revealed that clipping alone or in combination with warming altered soil and plant properties as well as the abundance and structure of soil microbial functional genes. Aboveground biomass removal for biofuel production needs to be reconsidered, as the long-term soil carbon stability may be weakened.<br><br>IMPORTANCE: Global change involves simultaneous alterations, including those caused by climate warming and land management practices (e.g., clipping). Data on the interactive effects of warming and clipping on ecosystems remain elusive, particularly in microbial ecology. This study found that clipping alters microbial responses to warming and demonstrated the effects of antagonistic interactions between clipping and warming on microbial functional genes. Clipping alone or combined with warming enriched genes degrading relatively recalcitrant carbon, likely reflecting the decreased quantity of soil carbon input from litter, which could weaken long-term soil C stability and trigger positive warming feedback. These results have important implications in assessing and predicting the consequences of global climate change and indicate that the removal of aboveground biomass for biofuel production may need to be reconsidered.}, }
@article {pmid27676396, year = {2016}, author = {Kang, C and Zhang, Y and Zhu, X and Liu, K and Wang, X and Chen, M and Wang, J and Chen, H and Hui, S and Huang, L and Zhang, Q and Zhu, J and Wang, B and Mi, M}, title = {Healthy Subjects Differentially Respond to Dietary Capsaicin Correlating with Specific Gut Enterotypes.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {101}, number = {12}, pages = {4681-4689}, doi = {10.1210/jc.2016-2786}, pmid = {27676396}, issn = {1945-7197}, mesh = {Adult ; Capsaicin/administration &amp; dosage/*pharmacology ; Feces/microbiology ; Female ; Gastric Inhibitory Polypeptide/*blood/drug effects ; Gastrointestinal Microbiome/*drug effects ; Ghrelin/*blood/drug effects ; Glucagon-Like Peptide 1/*blood/drug effects ; Healthy Volunteers ; Humans ; Male ; Sensory System Agents/administration &amp; dosage/*pharmacology ; Young Adult ; }, abstract = {CONTEXT: Previous population studies in evaluating the beneficial effects of capsaicin (CAP) have yielded inconclusive results, and the mechanisms responsible for possible benefit remain unclear.<br><br>OBJECTIVE: The objective was to assess the effect of dietary CAP on metabolic and immune profiles and its potential associations with gut microbial patterns in healthy adults.<br><br>DESIGN: In a 6-week controlled feeding trial, subjects were given the weight maintenance diet sequentially contained with 0, 5, 0, and 10 mg/d CAP from chili powder.<br><br>SETTING AND PARTICIPANTS: The study was conducted in 12 healthy subjects enrolled in Third Military Medical University in Chongqing.<br><br>MAIN OUTCOME MEASURES: At the end of each period, anthropometric and basal metabolism measures together with blood and fecal samples were collected. Plasma metabolic and inflammatory markers and gut microbial ecology of each subject were subsequently assessed.<br><br>RESULT: Dietary CAP increased the Firmicutes/Bacteroidetes ratio and Faecalibacterium abundance, accompanied with increased plasma levels of glucagon-like peptide 1 and gastric inhibitory polypeptide and decreased plasma ghrelin level. Further enterotype analysis revealed that these subjects could be clustered into Bacteroides enterotype (E1) and Prevotella enterotype (E2), and the above beneficial effects were mainly obtained in E1 subjects. Moreover, E1 subjects had significantly higher fecal Faecalibacterium abundance and butyrate concentration after CAP interventions than those in E2 subjects.<br><br>CONCLUSION: Our study showed that gut enterotypes may influence the beneficial effects of dietary CAP, providing new evidence for the personalized nutrition guidance of CAP intervention on health promotion linking with gut microbiota patterns.}, }
@article {pmid27670433, year = {2017}, author = {Wang, L and Li, J and Yang, F and E, Y and Raza, W and Huang, Q and Shen, Q}, title = {Application of Bioorganic Fertilizer Significantly Increased Apple Yields and Shaped Bacterial Community Structure in Orchard Soil.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {404-416}, pmid = {27670433}, issn = {1432-184X}, mesh = {Bacteria/classification/drug effects/genetics ; Base Sequence ; Biodiversity ; Biological Control Agents ; Carbon/metabolism ; China ; DNA, Bacterial/genetics ; *Fertilizers/analysis/microbiology ; Fruit/growth &amp; development ; Malus/*growth &amp; development ; *Microbial Consortia/drug effects/genetics ; Nitrogen/metabolism ; Nitrogen Fixation ; Phylogeny ; Plant Diseases/prevention &amp; control ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Application of bioorganic fertilizers has been reported to improve crop yields and change soil bacterial community structure; however, little work has been done in apple orchard soils where the biological properties of the soils are being degraded due to long-term application of chemical fertilizers. In this study, we used Illumina-based sequencing approach to characterize the bacterial community in the 0-60-cm soil profile under different fertilizer regimes in the Loess Plateau. The experiment includes three treatments: (1) control without fertilization (CK); (2) application of chemical fertilizer (CF); and (3) application of bioorganic fertilizer and organic-inorganic mixed fertilizer (BOF). The results showed that the treatment BOF increased the apple yields by 114 and 67 % compared to the CK and CF treatments, respectively. The treatment BOF also increased the soil organic matter (SOM) by 22 and 16 % compared to the CK and CF treatments, respectively. The Illumina-based sequencing showed that Acidobacteria and Proteobacteria were the predominant phyla and Alphaproteobacteria and Gammaproteobacteria were the most abundant classes in the soil profile. The bacterial richness for ACE was increased after the addition of BOF. Compared to CK and CF treatments, BOF-treated soil revealed higher abundance of Proteobacteria, Alphaproteobacteria and Gammaproteobacteria, Rhizobiales, and Xanthomonadales while Acidobacteria, Gp7, Gp17, and Sphaerobacter were found in lower abundance throughout the soil profile. Bacterial community structure varied with soil depth under different fertilizer treatments, e.g., the bacterial richness, diversity, and the relative abundance of Verruccomicrobia, Candidatus Brocadiales, and Skermanella were decreased with the soil depth in all three treatments. Permutational multivariate analysis showed that the fertilizer regime was the major factor than soil depth in the variations of the bacterial community composition. Two groups, Lysobacter and Rhodospirillaceae, were found to be the significantly increased by the BOF addition and the genus Lysobacter may identify members of this group effective in biological control-based plant disease management and the members of family Rhodospirillaceae had an important role in fixing molecular nitrogen. These results strengthen the understanding of responses to the BOF and possible interactions within bacterial communities in soil that can be associated with disease suppression and the accumulation of carbon and nitrogen. The increase of apple yields after the application of BOF might be attributed to the fact that the application of BOF increased SOM, and soil total nitrogen, and changed the bacterial community by enriching Rhodospirillaceae, Alphaprotreobateria, and Proteobacteria.}, }
@article {pmid27670113, year = {2016}, author = {Lagkouvardos, I and Pukall, R and Abt, B and Foesel, BU and Meier-Kolthoff, JP and Kumar, N and Bresciani, A and Martínez, I and Just, S and Ziegler, C and Brugiroux, S and Garzetti, D and Wenning, M and Bui, TP and Wang, J and Hugenholtz, F and Plugge, CM and Peterson, DA and Hornef, MW and Baines, JF and Smidt, H and Walter, J and Kristiansen, K and Nielsen, HB and Haller, D and Overmann, J and Stecher, B and Clavel, T}, title = {The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota.}, journal = {Nature microbiology}, volume = {1}, number = {10}, pages = {16131}, pmid = {27670113}, issn = {2058-5276}, support = {R01 GM099525/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; *Biological Specimen Banks ; Gastrointestinal Microbiome/genetics/*physiology ; Genome, Bacterial ; *Host Specificity ; Intestines/*microbiology ; Mice ; }, abstract = {Intestinal bacteria influence mammalian physiology, but many types of bacteria are still uncharacterized. Moreover, reference strains of mouse gut bacteria are not easily available, although mouse models are extensively used in medical research. These are major limitations for the investigation of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (miBC), a public repository of bacterial strains and associated genomes from the mouse gut, and studied host-specificity of colonization and sequence-based relevance of the resource. The collection includes several strains representing novel species, genera and even one family. Genomic analyses showed that certain species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50-75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota-host interactions in health and disease, as it will facilitate targeted colonization and molecular studies. The resource is available at www.dsmz.de/miBC.}, }
@article {pmid27669673, year = {2016}, author = {Keisam, S and Romi, W and Ahmed, G and Jeyaram, K}, title = {Quantifying the biases in metagenome mining for realistic assessment of microbial ecology of naturally fermented foods.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {34155}, pmid = {27669673}, issn = {2045-2322}, abstract = {Cultivation-independent investigation of microbial ecology is biased by the DNA extraction methods used. We aimed to quantify those biases by comparative analysis of the metagenome mined from four diverse naturally fermented foods (bamboo shoot, milk, fish, soybean) using eight different DNA extraction methods with different cell lysis principles. Our findings revealed that the enzymatic lysis yielded higher eubacterial and yeast metagenomic DNA from the food matrices compared to the widely used chemical and mechanical lysis principles. Further analysis of the bacterial community structure by Illumina MiSeq amplicon sequencing revealed a high recovery of lactic acid bacteria by the enzymatic lysis in all food types. However, Bacillaceae, Acetobacteraceae, Clostridiaceae and Proteobacteria were more abundantly recovered when mechanical and chemical lysis principles were applied. The biases generated due to the differential recovery of operational taxonomic units (OTUs) by different DNA extraction methods including DNA and PCR amplicons mix from different methods have been quantitatively demonstrated here. The different methods shared only 29.9-52.0% of the total OTUs recovered. Although similar comparative research has been performed on other ecological niches, this is the first in-depth investigation of quantifying the biases in metagenome mining from naturally fermented foods.}, }
@article {pmid27668995, year = {2016}, author = {Maza-Márquez, P and Vilchez-Vargas, R and Kerckhof, FM and Aranda, E and González-López, J and Rodelas, B}, title = {Community structure, population dynamics and diversity of fungi in a full-scale membrane bioreactor (MBR) for urban wastewater treatment.}, journal = {Water research}, volume = {105}, number = {}, pages = {507-519}, doi = {10.1016/j.watres.2016.09.021}, pmid = {27668995}, issn = {1879-2448}, mesh = {Bioreactors/microbiology ; Fungi ; *Membranes, Artificial ; Phylogeny ; Population Dynamics ; *Wastewater ; }, abstract = {Community structure, population dynamics and diversity of fungi were monitored in a full-scale membrane bioreactor (MBR) operated throughout four experimental phases (Summer 2009, Autumn 2009, Summer 2010 and Winter, 2012) under different conditions, using the 18S-rRNA gene and the intergenic transcribed spacer (ITS2-region) as molecular markers, and a combination of temperature-gradient gel electrophoresis and 454-pyrosequencing. Both total and metabolically-active fungal populations were fingerprinted, by amplification of molecular markers from community DNA and retrotranscribed RNA, respectively. Fingerprinting and 454-pyrosequencing evidenced that the MBR sheltered a dynamic fungal community composed of a low number of species, in accordance with the knowledge of fungal diversity in freshwater environments, and displaying a medium-high level of functional organization with few numerically dominant phylotypes. Population shifts were experienced in strong correlation with the changes of environmental variables and operation parameters, with pH contributing the highest level of explanation. Phylotypes assigned to nine different fungal Phyla were detected, although the community was mainly composed of Ascomycota, Basidiomycota and Chytridiomycota/Blastocladiomycota. Prevailing fungal phylotypes were affiliated to Saccharomycetes and Chytridiomycetes/Blastocladiomycetes, which displayed antagonistic trends in their relative abundance throughout the experimental period. Fungi identified in the activated sludge were closely related to genera of relevance for the degradation of organic matter and trace-organic contaminants, as well as genera of dimorphic fungi potentially able to produce plant operational issues such as foaming or biofouling. Phylotypes closely related to genera of human and plant pathogenic fungi were also detected.}, }
@article {pmid27667132, year = {2017}, author = {Meerbergen, K and Van Geel, M and Waud, M and Willems, KA and Dewil, R and Van Impe, J and Appels, L and Lievens, B}, title = {Assessing the composition of microbial communities in textile wastewater treatment plants in comparison with municipal wastewater treatment plants.}, journal = {MicrobiologyOpen}, volume = {6}, number = {1}, pages = {}, pmid = {27667132}, issn = {2045-8827}, mesh = {Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Base Sequence ; *Cities ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Microbiota/*genetics ; Real-Time Polymerase Chain Reaction ; Seasons ; Sequence Analysis, DNA ; Sewage/*microbiology ; *Textile Industry ; Water Purification ; }, abstract = {It is assumed that microbial communities involved in the biological treatment of different wastewaters having a different chemical composition harbor different microbial populations which are specifically adapted to the environmental stresses encountered in these systems. Yet, little is known about the composition of these microbial communities. Therefore, the aim of this study was to assess the microbial community composition over two seasons (winter and summer) in activated sludge from well-operating textile wastewater treatment plants (WWTPs) in comparison with municipal WWTPs, and to explain observed differences by environmental variables. 454-pyrosequencing generated 160 archaeal and 1645 bacterial species-level Operational Taxonomic Units (OTUs), with lower observed richness in activated sludge from textile WWTPs compared to municipal WWTPs. The bacterial phyla Planctomycetes, Chloroflexi, Chlorobi, and Acidobacteria were more abundant in activated sludge samples from textile WWTPs, together with archaeal members of Thaumarchaeota. Nonmetric multidimensional scaling analysis of the microbial communities showed that microbial communities from textile and municipal WWTPs were significantly different, with a seasonal effect on archaea. Nitrifying and denitrifying bacteria as well as phosphate-accumulation bacteria were more abundant in municipal WWTPs, while sulfate-reducing bacteria were almost only detected in textile WWTPs. Additionally, microbial communities from textile WWTPs were more dissimilar than those of municipal WWTPs, possibly due to a wider diversity in environmental stresses to which microbial communities in textile WWTPs are subjected to. High salinity, high organic loads, and a higher water temperature were important potential variables driving the microbial community composition in textile WWTPs. This study provides a general view on the composition of microbial communities in activated sludge of textile WWTPs, and may provide novel insights for identifying key players performing important functions in the purification of textile wastewaters.}, }
@article {pmid27665431, year = {2016}, author = {Maes, S and Claus, M and Verbeken, K and Wallaert, E and De Smet, R and Vanhaecke, F and Boon, N and Hennebel, T}, title = {Platinum recovery from industrial process streams by halophilic bacteria: Influence of salt species and platinum speciation.}, journal = {Water research}, volume = {105}, number = {}, pages = {436-443}, doi = {10.1016/j.watres.2016.09.023}, pmid = {27665431}, issn = {1879-2448}, mesh = {Bacteria ; Industry ; *Platinum ; *Sodium Chloride ; Sodium Chloride, Dietary ; }, abstract = {The increased use and criticality of platinum asks for the development of effective low-cost strategies for metal recovery from process and waste streams. Although biotechnological processes can be applied for the valorization of diluted aqueous industrial streams, investigations considering real stream conditions (e.g., high salt levels, acidic pH, metal speciation) are lacking. This study investigated the recovery of platinum by a halophilic microbial community in the presence of increased salt concentrations (10-80 g L[-1]), different salt matrices (phosphate salts, sea salts and NH4Cl) and a refinery process stream. The halophiles were able to recover 79-99% of the Pt at 10-80 g L[-1] salts and at pH 2.3. Transmission electron microscopy suggested a positive correlation between intracellular Pt cluster size and elevated salt concentrations. Furthermore, the halophiles recovered 46-95% of the Pt-amine complex Pt[NH3]4[2+] from a process stream after the addition of an alternative Pt source (K2PtCl4, 0.1-1.0 g L[-1] Pt). Repeated Pt-tetraamine recovery (from an industrial process stream) was obtained after concomitant addition of fresh biomass and harvesting of Pt saturated biomass. This study demonstrates how aqueous Pt streams can be transformed into Pt rich biomass, which would be an interesting feed of a precious metals refinery.}, }
@article {pmid27660864, year = {2016}, author = {Nejezchlebova, H and Kiewra, D and Žákovská, A and Ovesná, P}, title = {Students' attitudes to tick risks.}, journal = {Annals of agricultural and environmental medicine : AAEM}, volume = {23}, number = {3}, pages = {437-441}, doi = {10.5604/12321966.1219183}, pmid = {27660864}, issn = {1898-2263}, mesh = {Adolescent ; Adult ; Animals ; Czech Republic ; Female ; *Health Knowledge, Attitudes, Practice ; Humans ; Male ; Poland ; Risk Assessment ; Students/statistics &amp; numerical data ; Tick Bites/prevention &amp; control/*psychology ; Tick Control/*methods ; Tick-Borne Diseases/prevention &amp; control/*psychology ; *Ticks ; Young Adult ; }, abstract = {INTRODUCTION AND OBJECTIVES: The ever-increasing number of patients with tick-borne diseases resulted in the presented study investigating the awareness, attitudes and knowledge among students about the threats arising from tick bites and preventive anti-tick practices.<br><br>MATERIALS AND METHOD: Questionnaires concerning these issues were distributed amongst Czech and Polish university students of science. Responses were analyzed by nationality and by gender.<br><br>RESULTS: Nearly all respondents were aware of the risks arising from ticks and could name at least one disease transmitted by ticks. The Czech students felt more threatened by tick-borne diseases, had more frequently suffered from Lyme borreliosis and were vaccinated against tick-borne encephalitis more often than the Polish students. A large number of the participants applied preventive measures against ticks in order to protect themselves. The Czech students believed in the effectiveness of repellents statistically more often than the Polish students, while effectiveness is the main criterion for selection of the right repellent in both groups.<br><br>CONCLUSION: Differences in preferences between the two nations appeared in many areas, e.g. the Czechs felt more threatened by all kind of risks and suffered from Lyme disease more frequently. Gaps can still be found in both the knowledge and behaviour among the respondents. It can be expected that the general public knowledge of this issue is rather limited in comparison with the students participating in the study, who are systematically educated in the field.}, }
@article {pmid27660624, year = {2016}, author = {Tardif, S and Yergeau, &#xc9; and Tremblay, J and Legendre, P and Whyte, LG and Greer, CW}, title = {The Willow Microbiome Is Influenced by Soil Petroleum-Hydrocarbon Concentration with Plant Compartment-Specific Effects.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1363}, pmid = {27660624}, issn = {1664-302X}, abstract = {The interaction between plants and microorganisms, which is the driving force behind the decontamination of petroleum hydrocarbon (PHC) contamination in phytoremediation technology, is poorly understood. Here, we aimed at characterizing the variations between plant compartments in the microbiome of two willow cultivars growing in contaminated soils. A field experiment was set-up at a former petrochemical plant in Canada and after two growing seasons, bulk soil, rhizosphere soil, roots, and stems samples of two willow cultivars (Salix purpurea cv. FishCreek, and Salix miyabeana cv. SX67) growing at three PHC contamination concentrations were taken. DNA was extracted and bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) regions were amplified and sequenced using an Ion Torrent Personal Genome Machine (PGM). Following multivariate statistical analyses, the level of PHC-contamination appeared as the primary factor influencing the willow microbiome with compartment-specific effects, with significant differences between the responses of bacterial, and fungal communities. Increasing PHC contamination levels resulted in shifts in the microbiome composition, favoring putative hydrocarbon degraders, and microorganisms previously reported as associated with plant health. These shifts were less drastic in the rhizosphere, root, and stem tissues as compared to bulk soil, probably because the willows provided a more controlled environment, and thus, protected microbial communities against increasing contamination levels. Insights from this study will help to devise optimal plant microbiomes for increasing the efficiency of phytoremediation technology.}, }
@article {pmid27657355, year = {2017}, author = {Bradford, LL and Ravel, J}, title = {The vaginal mycobiome: A contemporary perspective on fungi in women's health and diseases.}, journal = {Virulence}, volume = {8}, number = {3}, pages = {342-351}, pmid = {27657355}, issn = {2150-5608}, support = {R01 NR015495/NR/NINR NIH HHS/United States ; R25 GM055036/GM/NIGMS NIH HHS/United States ; U19 AI084044/AI/NIAID NIH HHS/United States ; R01 AI116799/AI/NIAID NIH HHS/United States ; }, mesh = {Female ; Fungi/*classification/*isolation &amp; purification ; Humans ; Microbial Interactions ; *Microbiota ; *Mycobiome ; Mycoses/microbiology ; Vagina/*microbiology ; Vaginitis/microbiology ; Women's Health ; }, abstract = {Most of what is known about fungi in the human vagina has come from culture-based studies and phenotypic characterization of single organisms. Though valuable, these approaches have masked the complexity of fungal communities within the vagina. The vaginal mycobiome has become an emerging field of study as genomics tools are increasingly employed and we begin to appreciate the role these fungal communities play in human health and disease. Though vastly outnumbered by its bacterial counterparts, fungi are important constituents of the vaginal ecosystem in many healthy women. Candida albicans, an opportunistic fungal pathogen, colonizes 20% of women without causing any overt symptoms, yet it is one of the leading causes of infectious vaginitis. Understanding its mechanisms of commensalism and patho-genesis are both essential to developing more effective therapies. Describing the interactions between Candida, bacteria (such as Lactobacillus spp.) and other fungi in the vagina is funda-mental to our characterization of the vaginal mycobiome.}, }
@article {pmid27655524, year = {2017}, author = {Panke-Buisse, K and Lee, S and Kao-Kniffin, J}, title = {Cultivated Sub-Populations of Soil Microbiomes Retain Early Flowering Plant Trait.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {394-403}, pmid = {27655524}, issn = {1432-184X}, mesh = {Arabidopsis/*growth &amp; development/*microbiology ; Bacteria/classification/genetics/growth &amp; development ; Base Sequence ; Biomass ; Culture Media ; DNA, Bacterial ; Flowers/growth &amp; development ; Magnoliopsida/*microbiology ; Microbiota/genetics/*physiology ; Plant Leaves/growth &amp; development ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {The collection of microorganisms found in the root zone of soil, termed the rhizosphere microbiome, has been shown to impact plant growth and development. Here, we tease apart the function of the cultivable portion of the microbiome from the whole microbiome in retaining plant traits modified through artificial selection on flowering time. Specifically, the whole microbiome associated with earlier flowering time of Arabidopsis thaliana was cultivated on four types of solid media to create cultivated fractions of the microbiome. These cultivated microbiomes were subsequently preserved in glycerol, frozen, and revived to yield a portion of the cultivable fraction to compare (1) whole microbiome, (2) cultivable microbiome, and (3) revived, cultivable microbiome controls on early flowering time. Plants grown in soils inoculated with bacteria grown on 25 % Luria broth and 10 % tryptic soy agar retained the early flowering trait. An increase in leaf biomass with two of the cultivated microbiomes (49.4 and 38.5 %) contrasted the lowered biomass effect of the whole microbiome. Inoculation with the cultivated microbiomes that were cryopreserved in glycerol showed no effect on flowering time or leaf biomass. The results indicate that the cultivable portion of a plant's microbiome retains the early flowering effect in A. thaliana, but cryopreservation of the cultivated microbiomes disrupts the microbial effects on flowering time. Furthermore, the contrasting effects on leaf biomass (an indirect response from selection on early flowering time), seen with the whole microbiome versus the cultivable portion, suggests versatility in using cultivation methods to modify multiple traits of plants.}, }
@article {pmid27654921, year = {2016}, author = {Roux, S and Brum, JR and Dutilh, BE and Sunagawa, S and Duhaime, MB and Loy, A and Poulos, BT and Solonenko, N and Lara, E and Poulain, J and Pesant, S and Kandels-Lewis, S and Dimier, C and Picheral, M and Searson, S and Cruaud, C and Alberti, A and Duarte, CM and Gasol, JM and Vaqué, D and ,  and Bork, P and Acinas, SG and Wincker, P and Sullivan, MB}, title = {Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses.}, journal = {Nature}, volume = {537}, number = {7622}, pages = {689-693}, pmid = {27654921}, issn = {1476-4687}, support = {P 25111/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {DNA, Viral/analysis ; Datasets as Topic ; Ecology ; *Ecosystem ; Expeditions ; Genes, Viral ; *Genome, Viral ; Geographic Mapping ; Metagenome ; *Metagenomics ; Nitrogen Cycle ; Oceans and Seas ; Seawater/*virology ; Sulfur/metabolism ; Viruses/*genetics/*isolation &amp; purification/metabolism ; }, abstract = {Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting 'global ocean virome' dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.}, }
@article {pmid27654222, year = {2016}, author = {Schoutteten, KVKM and Hennebel, T and Dheere, E and Bertelkamp, C and De Ridder, DJ and Maes, S and Chys, M and Van Hulle, SWH and Vanden Bussche, J and Vanhaecke, L and Verliefde, ARD}, title = {Effect of oxidation and catalytic reduction of trace organic contaminants on their activated carbon adsorption.}, journal = {Chemosphere}, volume = {165}, number = {}, pages = {191-201}, doi = {10.1016/j.chemosphere.2016.09.032}, pmid = {27654222}, issn = {1879-1298}, mesh = {2,4-Dinitrophenol/*analogs &amp; derivatives/metabolism ; Adsorption ; Atrazine/*metabolism ; Carbamazepine/*metabolism ; Catalysis ; Charcoal/chemistry ; Diatrizoate/*metabolism ; Environmental Restoration and Remediation/*methods ; Nitriles/*metabolism ; Oxidation-Reduction ; Ozone/chemistry ; Water Pollutants, Chemical/analysis/*metabolism ; }, abstract = {The combination of ozonation and activated carbon (AC) adsorption is an established technology for removal of trace organic contaminants (TrOCs). In contrast to oxidation, reduction of TrOCs has recently gained attention as well, however less attention has gone to the combination of reduction with AC adsorption. In addition, no literature has compared the removal behavior of reduction vs. ozonation by-products by AC. In this study, the effect of pre-ozonation vs pre-catalytic reduction on the AC adsorption efficiency of five TrOCs and their by-products was compared. All compounds were susceptible to oxidation and reduction, however the catalytic reductive treatment proved to be a slower reaction than ozonation. New oxidation products were identified for dinoseb and new reduction products were identified for carbamazepine, bromoxynil and dinoseb. In terms of compatibility with AC adsorption, the influence of the oxidative and reductive pretreatments proved to be compound dependent. Oxidation products of bromoxynil and diatrizoic acid adsorbed better than their parent TrOCs, but oxidation products of atrazine, carbamazepine and dinoseb showed a decreased adsorption. The reductive pre-treatment showed an enhanced AC adsorption for dinoseb and a major enhancement for diatrizoic acid. For atrazine and bromoxynil, no clear influence on adsorption was noted, while for carbamazepine, the reductive pretreatment resulted in a decreased AC affinity. It may thus be concluded that when targeting mixtures of TrOCs, a trade-off will undoubtedly have to be made towards overall reactivity and removal of the different constituents, since no single treatment proves to be superior to the other.}, }
@article {pmid27645139, year = {2017}, author = {Schimann, H and Bach, C and Lengelle, J and Louisanna, E and Barantal, S and Murat, C and Buée, M}, title = {Diversity and Structure of Fungal Communities in Neotropical Rainforest Soils: The Effect of Host Recurrence.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {310-320}, pmid = {27645139}, issn = {1432-184X}, mesh = {Base Sequence ; *Biodiversity ; Classification ; DNA, Fungal/analysis ; Ecosystem ; French Guiana ; Fungi/*classification/genetics/isolation &amp; purification ; Genetic Heterogeneity ; Polymerase Chain Reaction/methods ; *Rainforest ; Soil/chemistry ; *Soil Microbiology ; Trees/classification/*microbiology ; Tropical Climate ; }, abstract = {The patterns of the distribution of fungal species and their potential interactions with trees remain understudied in Neotropical rainforests, which harbor more than 16,000 tree species, mostly dominated by endomycorrhizal trees. Our hypothesis was that tree species shape the non-mycorrhizal fungal assemblages in soil and litter and that the diversity of fungal communities in these two compartments is partly dependent on the coverage of trees in the Neotropical rainforest. In French Guiana, a long-term plantation and a natural forest were selected to test this hypothesis. Fungal ITS1 regions were sequenced from soil and litter samples from within the vicinity of tree species. A broad range of fungal taxa was found, with 42 orders and 14 classes. Significant spatial heterogeneity in the fungal communities was found without strong variation in the species richness and evenness among the tree plots. However, tree species shaped the fungal assemblages in the soil and litter, explaining up to 18 % of the variation among the communities in the natural forest. These results demonstrate that vegetation cover has an important effect on the structure of fungal assemblages inhabiting the soil and litter in Amazonian forests, illustrating the relative impact of deterministic processes on fungal community structures in these highly diverse ecosystems.}, }
@article {pmid27645137, year = {2017}, author = {Eckford-Soper, LK and Daugbjerg, N}, title = {Interspecific Competition Study Between Pseudochattonella farcimen and P. verruculosa (Dictyochophyceae)-Two Ichthyotoxic Species that Co-occur in Scandinavian Waters.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {259-270}, pmid = {27645137}, issn = {1432-184X}, mesh = {Cell Count ; Cell Culture Techniques ; Coculture Techniques ; DNA/analysis ; DNA Primers ; Diatoms ; Hydrogen-Ion Concentration ; Molecular Probe Techniques ; Nitrates/metabolism ; Phosphates/metabolism ; Phytoplankton/growth &amp; development ; Real-Time Polymerase Chain Reaction/methods ; Scandinavian and Nordic Countries ; Seasons ; Seawater ; Stramenopiles/classification/genetics/*growth &amp; development/*metabolism ; Temperature ; }, abstract = {The genus Pseudochattonella has become a frequent component of late winter-early spring phytoplankton community in Scandinavian waters, causing extensive fish kills and substantial economic losses. One of currently two recognised species, P. farcimen, is often abundant prior to the diatom spring bloom. Recent field studies have revealed that P. farcimen and P. verruculosa have a period of overlap in their temperature ranges and thus their seasonal occurrences. Using laboratory cultures, we investigated the seasonal succession and growth of P. farcimen and P. verruculosa in both mono- and mixed-culture using the recently developed Pseudochattonella 'qPCR subtraction method', which for the first time allowed the simultaneous enumeration of these morphologically indistinguishable species in mixed assemblages. We examined how these species interacted over four different temperatures (5, 8, 11 and 15 °C). The observed growth rates and cell yields varied with temperature revealing their preferred temperature optima. P. farcimen was able to achieve positive net growth over all temperatures, while P. verruculosa failed to grow below 11 °C. Growth responses were statistically different between mono- and mixed-cultures with the outcome of these interactions being temperature-dependent. Nutrients (nitrate and phosphate) and pH levels were also measured throughout the growth experiments to better understand how these factors influenced growth of both species. P. verruculosa was shown to be less sensitive to high pH as growth ceased at pH 9.1, whereas P. farcimen stopped growing at pH 8.4. Understanding the influence of abiotic factors (e.g. temperature, pH and competition) on growth rates allows for a better understanding and prediction of phytoplankton community dynamics.}, }
@article {pmid27639672, year = {2016}, author = {Han, M and Vlaeminck, SE and Al-Omari, A and Wett, B and Bott, C and Murthy, S and De Clippeleir, H}, title = {Uncoupling the solids retention times of flocs and granules in mainstream deammonification: A screen as effective out-selection tool for nitrite oxidizing bacteria.}, journal = {Bioresource technology}, volume = {221}, number = {}, pages = {195-204}, doi = {10.1016/j.biortech.2016.08.115}, pmid = {27639672}, issn = {1873-2976}, mesh = {Ammonia/metabolism ; Bacteria/*metabolism ; Biological Oxygen Demand Analysis ; Bioreactors/*microbiology ; Equipment Design ; Flocculation ; Nitrites/*metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Sewage ; Waste Disposal, Fluid/*instrumentation/*methods ; }, abstract = {This study focused on a physical separator in the form of a screen to out-select nitrite oxidizing bacteria (NOB) for mainstream sewage treatment. This separation relied on the principle that the NOB prefer to grow in flocs, while anammox bacteria (AnAOB) reside in granules. Two types of screens (vacuum and vibrating) were tested for separating these fractions. The vibrating screen was preferred due to more moderate normal forces and additional tangential forces, better balancing retention efficiency of AnAOB granules (41% of the AnAOB activity) and washout of NOB (92% activity washout). This operation resulted in increased NOB out-selection (AerAOB/NOB ratio of 2.3) and a total nitrogen removal efficiency of 70% at influent COD/N ratio of 1.4. An effluent total nitrogen concentration <10mgN/L was achieved using this novel approach combining biological selection with physical separation, opening up the path towards energy positive sewage treatment.}, }
@article {pmid27636701, year = {2016}, author = {Kalams, SA and Rogers, LM and Smith, RM and Barnett, L and Crumbo, K and Sumner, S and Prashad, N and Rybczyk, K and Milne, G and Dowd, SE and Chong, E and Winikoff, B and Aronoff, DM}, title = {Neither vaginal nor buccal administration of 800 μg misoprostol alters mucosal and systemic immune activation or the cervicovaginal microbiome: a pilot study.}, journal = {The European journal of contraception &amp; reproductive health care : the official journal of the European Society of Contraception}, volume = {21}, number = {6}, pages = {436-442}, pmid = {27636701}, issn = {1473-0782}, support = {UL1 TR000445/TR/NCATS NIH HHS/United States ; }, mesh = {Abortifacient Agents, Nonsteroidal/administration &amp; dosage/*pharmacology ; Administration, Buccal ; Administration, Intravaginal ; *Cervix Uteri/drug effects/immunology/microbiology ; Cross-Over Studies ; Elafin/blood ; Enzyme-Linked Immunosorbent Assay ; Female ; Humans ; Immune System/drug effects ; Lymphocytes/drug effects ; Microbiota ; Misoprostol/administration &amp; dosage/*pharmacology ; Pilot Projects ; United States ; *Vagina/drug effects/immunology/microbiology ; }, abstract = {OBJECTIVES: The aim of the study was to assess the extent to which misoprostol alters mucosal or systemic immune responses following either buccal or vaginal administration.<br><br>METHODS: This was a prospective, crossover pilot study of 15 healthy, reproductive-age women. Women first received 800&#x2009;&#x3bc;g misoprostol either via buccal or vaginal administration and were crossed over 1 month later to receive the drug via the other route. Cervicovaginal lavage samples, cervical Cytobrush samples, cervicovaginal swabs, urine and blood were obtained immediately prior to drug administration and the following day. Parameters assessed included urine and cervicovaginal misoprostol levels, whole blood cytokine responses (by ELISA) to immune stimulation with lipopolysaccharide, peripheral blood and cervical lymphocyte phenotyping by flow cytometry, cervicovaginal antimicrobial peptide measurement by ELISA and vaginal microbial ecology assessment by 16S rRNA sequencing.<br><br>RESULTS: Neither buccal nor vaginal misoprostol significantly altered local or systemic immune and microbiological parameters.<br><br>CONCLUSION: In this pilot study, we did not observe significant alteration of mucosal or systemic immunology or vaginal microbial ecology 1&#x2009;day after drug administration following either the buccal or vaginal route.}, }
@article {pmid27636395, year = {2017}, author = {Shade, A}, title = {Diversity is the question, not the answer.}, journal = {The ISME journal}, volume = {11}, number = {1}, pages = {1-6}, pmid = {27636395}, issn = {1751-7370}, mesh = {*Biodiversity ; *Ecology ; Ecosystem ; *Microbiota ; }, abstract = {Local diversity (within-sample or alpha diversity) is often implicated as a cause of success or failure of a microbial community. However, the relationships between diversity and emergent properties of a community, such as its stability, productivity or invasibility, are much more nuanced. I argue that diversity without context provides limited insights into the mechanisms underpinning community patterns. I provide examples from traditional and microbial ecology to discuss common complications and assumptions about within-sample diversity that may prevent us from digging deeper into the more specific mechanisms underpinning community outcomes. I suggest that measurement of diversity should serve as a starting point for further inquiry of ecological mechanisms rather than an 'answer' to community outcomes.}, }
@article {pmid27633927, year = {2016}, author = {Hernández-Zulueta, J and Araya, R and Vargas-Ponce, O and Díaz-Pérez, L and Rodríguez-Troncoso, AP and Ceh, J and Ríos-Jara, E and Rodríguez-Zaragoza, FA}, title = {First deep screening of bacterial assemblages associated with corals of the Tropical Eastern Pacific.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {12}, pages = {}, doi = {10.1093/femsec/fiw196}, pmid = {27633927}, issn = {1574-6941}, mesh = {Ammonium Compounds/metabolism ; Animals ; Anthozoa/*microbiology ; Bacteria/*classification/genetics/isolation &amp; purification ; Base Sequence ; *Coral Reefs ; DNA, Bacterial/genetics ; Geologic Sediments/*microbiology ; Mexico ; Microbiota/*genetics ; Oxygen/metabolism ; Pacific Ocean ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Silicates/metabolism ; Species Specificity ; }, abstract = {Bacterial assemblages associated with the hermatypic corals Pocillopora damicornis and P. verrucosa, the surrounding seawater and the sediment at six coral reef sites in the north section of the Tropical Eastern Pacific were assessed using MiSeq Illumina sequencing of the V4 region of the 16S rDNA. The bacterial microbiota in both coral species, seawater and sediment were stable to seasonal variations. Bacterial assemblages between the same substrates were not significantly different from each other in the six sites sampled. Interestingly, the bacterial composition between substrates within the same site was significantly different, or not, depending on the conservation status of the site. Moreover, we found species-specific bacterial OTUs in both coral species. Analyzing the relationship between bacterial composition and environmental variables revealed a positive correlation between bacterial assemblages and dissolved oxygen, ammonium and silicate.}, }
@article {pmid27632432, year = {2017}, author = {Butler, RN and Kosek, M and Krebs, NF and Loechl, CU and Loy, A and Owino, VO and Zimmermann, MB and Morrison, DJ}, title = {Stable Isotope Techniques for the Assessment of Host and Microbiota Response During Gastrointestinal Dysfunction.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {64}, number = {1}, pages = {8-14}, pmid = {27632432}, issn = {1536-4801}, support = {BB/L004259/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L025418/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; I 2320/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Biomedical Technology ; *Digestion ; Fermentation ; *Gastrointestinal Microbiome ; Growth Disorders ; Humans ; *Intestinal Mucosa ; *Isotopes ; Micronutrients ; *Nutritional Status ; }, abstract = {The International Atomic Energy Agency convened a technical meeting on environmental enteric dysfunction (EED) in Vienna (October 28-30, 2015; https://nucleus.iaea.org/HHW/Nutrition/EED_Technical_Meeting/index.html) to bring together international experts in the fields of EED, nutrition, and stable isotope technologies. Advances in stable isotope-labeling techniques open up new possibilities to improve our understanding of gastrointestinal dysfunction and the role of the microbiota in host health. In the context of EED, little is known about the role gut dysfunction may play in macro- and micronutrient bioavailability and requirements and what the consequences may be for nutritional status and linear growth. Stable isotope labeling techniques have been used to assess intestinal mucosal injury and barrier function, carbohydrate digestion and fermentation, protein-derived amino acid bioavailability and requirements, micronutrient bioavailability and to track microbe-microbe and microbe-host interactions at the single cell level. The noninvasive nature of stable isotope technologies potentially allow for low-hazard, field-deployable tests of gut dysfunction that are applicable across all age groups. The purpose of this review is to assess the state-of-the-art use of stable isotope technologies and to provide a perspective on where these technologies can be exploited to further our understanding of gut dysfunction in EED.}, }
@article {pmid27630624, year = {2016}, author = {Liu, W and Røder, HL and Madsen, JS and Bjarnsholt, T and Sørensen, SJ and Burmølle, M}, title = {Interspecific Bacterial Interactions are Reflected in Multispecies Biofilm Spatial Organization.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1366}, pmid = {27630624}, issn = {1664-302X}, abstract = {Interspecies interactions are essential for the persistence and development of any kind of complex community, and microbial biofilms are no exception. Multispecies biofilms are structured and spatially defined communities that have received much attention due to their omnipresence in natural environments. Species residing in these complex bacterial communities usually interact both intra- and interspecifically. Such interactions are considered to not only be fundamental in shaping overall biomass and the spatial distribution of cells residing in multispecies biofilms, but also to result in coordinated regulation of gene expression in the different species present. These communal interactions often lead to emergent properties in biofilms, such as enhanced tolerance against antibiotics, host immune responses, and other stresses, which have been shown to provide benefits to all biofilm members not only the enabling sub-populations. However, the specific molecular mechanisms of cellular processes affecting spatial organization, and vice versa, are poorly understood and very complex to unravel. Therefore, detailed description of the spatial organization of individual bacterial cells in multispecies communities can be an alternative strategy to reveal the nature of interspecies interactions of constituent species. Closing the gap between visual observation and biological processes may become crucial for resolving biofilm related problems, which is of utmost importance to environmental, industrial, and clinical implications. This review briefly presents the state of the art of studying interspecies interactions and spatial organization of multispecies communities, aiming to support theoretical and practical arguments for further advancement of this field.}, }
@article {pmid27629424, year = {2016}, author = {Val-Moraes, SP and de Macedo, HS and Kishi, LT and Pereira, RM and Navarrete, AA and Mendes, LW and de Figueiredo, EB and La Scala, N and Tsai, SM and de Macedo Lemos, EG and Alves, LM}, title = {Liming in the sugarcane burnt system and the green harvest practice affect soil bacterial community in northeastern São Paulo, Brazil.}, journal = {Antonie van Leeuwenhoek}, volume = {109}, number = {12}, pages = {1643-1654}, doi = {10.1007/s10482-016-0764-8}, pmid = {27629424}, issn = {1572-9699}, mesh = {Agriculture/*methods ; Bacteria/classification/*drug effects/genetics ; Brazil ; Calcium Compounds/*pharmacology ; Fires ; Multivariate Analysis ; Oxides/*pharmacology ; Polymorphism, Restriction Fragment Length ; RNA, Bacterial ; RNA, Ribosomal, 16S/genetics ; *Saccharum ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Here we show that both liming the burnt sugarcane and the green harvest practice alter bacterial community structure, diversity and composition in sugarcane fields in northeastern São Paulo state, Brazil. Terminal restriction fragment length polymorphism fingerprinting and 16S rRNA gene cloning and sequencing were used to analyze changes in soil bacterial communities. The field experiment consisted of sugarcane-cultivated soils under different regimes: green sugarcane (GS), burnt sugarcane (BS), BS in soil amended with lime applied to increase soil pH (BSL), and native forest (NF) as control soil. The bacterial community structures revealed disparate patterns in sugarcane-cultivated soils and forest soil (R = 0.786, P = 0.002), and overlapping patterns were shown for the bacterial community structure among the different management regimes applied to sugarcane (R = 0.194, P = 0.002). The numbers of operational taxonomic units (OTUs) found in the libraries were 117, 185, 173 and 166 for NF, BS, BSL and GS, respectively. Sugarcane-cultivated soils revealed higher bacterial diversity than NF soil, with BS soil accounting for a higher richness of unique OTUs (101 unique OTUs) than NF soil (23 unique OTUs). Cluster analysis based on OTUs revealed similar bacterial communities in NF and GS soils, while the bacterial community from BS soil was most distinct from the others. Acidobacteria and Alphaproteobacteria were the most abundant bacterial phyla across the different soils with Acidobacteria Gp1 accounting for a higher abundance in NF and GS soils than burnt sugarcane-cultivated soils (BS and BSL). In turn, Acidobacteria Gp4 abundance was higher in BS soils than in other soils. These differential responses in soil bacterial community structure, diversity and composition can be associated with the agricultural management, mainly liming practices, and harvest methods in the sugarcane-cultivated soils, and they can be detected shortly after harvest.}, }
@article {pmid27628746, year = {2016}, author = {Prévoteau, A and Ronsse, F and Cid, I and Boeckx, P and Rabaey, K}, title = {The electron donating capacity of biochar is dramatically underestimated.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {32870}, pmid = {27628746}, issn = {2045-2322}, mesh = {Adsorption ; Charcoal/*chemistry ; Electrochemical Techniques ; Electrodes ; Electron Transport ; *Electrons ; Hot Temperature ; Humic Substances/*analysis ; Hydrogen-Ion Concentration ; Kinetics ; Oxidation-Reduction ; Porosity ; Soil ; Temperature ; Wood ; }, abstract = {Biochars have gathered considerable interest for agronomic and engineering applications. In addition to their high sorption ability, biochars have been shown to accept or donate considerable amounts of electrons to/from their environment via abiotic or microbial processes. Here, we measured the electron accepting (EAC) and electron donating (EDC) capacities of wood-based biochars pyrolyzed at three different highest treatment temperatures (HTTs: 400, 500, 600 °C) via hydrodynamic electrochemical techniques using a rotating disc electrode. EACs and EDCs varied with HTT in accordance with a previous report with a maximal EAC at 500 °C (0.4 mmol(e(-)).gchar(-1)) and a large decrease of EDC with HTT. However, while we monitored similar EAC values than in the preceding study, we show that the EDCs have been underestimated by at least 1 order of magnitude, up to 7 mmol(e(-)).gchar(-1) for a HTT of 400 °C. We attribute this existing underestimation to unnoticed slow kinetics of electron transfer from biochars to the dissolved redox mediators used in the monitoring. The EDC of other soil organic constituents such as humic substances may also have been underestimated. These results imply that the redox properties of biochars may have a much bigger impact on soil biogeochemical processes than previously conjectured.}, }
@article {pmid27628741, year = {2017}, author = {Petrovic, A and Kostanjsek, R and Rakhely, G and Knezevic, P}, title = {The First Siphoviridae Family Bacteriophages Infecting Bordetella bronchiseptica Isolated from Environment.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {368-377}, pmid = {27628741}, issn = {1432-184X}, mesh = {Bacteriophages/genetics/growth &amp; development/*isolation &amp; purification/ultrastructure ; Base Sequence ; Bordetella bronchiseptica/genetics/*virology ; DNA, Bacterial/genetics ; DNA, Viral/genetics ; *Environment ; Genes, Viral ; Genome, Viral ; Hot Temperature ; Hydrogen-Ion Concentration ; Microscopy, Electron, Transmission ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Siphoviridae/genetics/growth &amp; development/*isolation &amp; purification/ultrastructure ; Wastewater/virology ; Water Microbiology ; }, abstract = {Bordetella bronchiseptica is a well-known etiological agent of kennel cough in dogs and cats and one of the two causative agents of atrophic rhinitis, a serious swine disease. The aim of the study was to isolate B. bronchiseptica bacteriophages from environmental samples for the first time. A total of 29 phages from 65 water samples were isolated using the strain ATCC 10580 as a host. The lytic spectra of the phages were examined at 25 and 37 °C, using 12 strains of B. bronchiseptica. All phages were able to plaque on 25.0 % to 41.7 % of the strains. The selected phages showed similar morphology (Siphoviridae, morphotype B2), but variation of RFLP patterns and efficacy of plating on various strains. The partial genome sequence of phage vB_BbrS_CN1 showed its similarity to phages from genus Yuavirus. Using PCR, it was confirmed that the phages do not originate from the host strain, and environmental origin was additionally confirmed by the analysis of host genome sequence in silico and plating heated and unheated samples in parallel. Accordingly, this is the first isolation of B. bronchiseptica phages from environment and the first isolation and characterization of phages of B. bronchiseptica belonging to family Siphoviridae.}, }
@article {pmid27628595, year = {2017}, author = {Gomez, A and Nelson, KE}, title = {The Oral Microbiome of Children: Development, Disease, and Implications Beyond Oral Health.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {492-503}, pmid = {27628595}, issn = {1432-184X}, support = {R01 DE019665/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/metabolism/pathogenicity ; Biodiversity ; Biomarkers ; Child ; Dental Caries/microbiology/therapy ; Ecology ; Humans ; Metagenome ; Microbiota/*physiology ; Mouth/*microbiology ; Mouth Diseases/immunology/*microbiology/therapy ; *Oral Health ; Risk Assessment ; Risk Factors ; }, abstract = {In the era of applied meta-omics and personalized medicine, the oral microbiome is a valuable asset. From biomarker discovery to being a powerful source of therapeutic targets and to presenting an opportunity for developing non-invasive approaches to health care, it has become clear that oral microbes may hold the answer for understanding disease, even beyond the oral cavity. Although our understanding of oral microbiome diversity has come a long way in the past 50 years, there are still many areas that need to be fine-tuned for better risk assessment and diagnosis, especially in early developmental stages of human life. Here, we discuss the factors that impact development of the oral microbiome and explore oral markers of disease, with a focus on the early oral cavity. Our ultimate goal is to put different experimental and methodological views into perspective for better assessment of early oral and systemic disease at an early age and discuss how oral microbiomes-at the community level-could provide improved assessment in individuals and populations at risk.}, }
@article {pmid27628594, year = {2017}, author = {Li, S and Peng, C and Wang, C and Zheng, J and Hu, Y and Li, D}, title = {Erratum to: Microbial Succession and Nitrogen Cycling in Cultured Biofilms as Affected by the Inorganic Nitrogen Availability.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {16}, doi = {10.1007/s00248-016-0850-5}, pmid = {27628594}, issn = {1432-184X}, }
@article {pmid27625644, year = {2016}, author = {Rahi, P and Prakash, O and Shouche, YS}, title = {Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1359}, pmid = {27625644}, issn = {1664-302X}, abstract = {Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) based biotyping is an emerging technique for high-throughput and rapid microbial identification. Due to its relatively higher accuracy, comprehensive database of clinically important microorganisms and low-cost compared to other microbial identification methods, MALDI-TOF MS has started replacing existing practices prevalent in clinical diagnosis. However, applicability of MALDI-TOF MS in the area of microbial ecology research is still limited mainly due to the lack of data on non-clinical microorganisms. Intense research activities on cultivation of microbial diversity by conventional as well as by innovative and high-throughput methods has substantially increased the number of microbial species known today. This important area of research is in urgent need of rapid and reliable method(s) for characterization and de-replication of microorganisms from various ecosystems. MALDI-TOF MS based characterization, in our opinion, appears to be the most suitable technique for such studies. Reliability of MALDI-TOF MS based identification method depends mainly on accuracy and width of reference databases, which need continuous expansion and improvement. In this review, we propose a common strategy to generate MALDI-TOF MS spectral database and advocated its sharing, and also discuss the role of MALDI-TOF MS based high-throughput microbial identification in microbial ecology studies.}, }
@article {pmid27624065, year = {2016}, author = {Lenaerts, M and Abid, L and Paulussen, C and Goelen, T and Wäckers, F and Jacquemyn, H and Lievens, B}, title = {Adult Parasitoids of Honeydew-Producing Insects Prefer Honeydew Sugars to Cover their Energetic Needs.}, journal = {Journal of chemical ecology}, volume = {42}, number = {10}, pages = {1028-1036}, pmid = {27624065}, issn = {1573-1561}, mesh = {Animals ; Aphids/*parasitology/physiology ; *Carbohydrate Metabolism ; Carbohydrates/analysis ; Energy Metabolism ; Feeding Behavior ; Female ; Longevity ; Male ; Wasps/*physiology ; }, abstract = {To meet their carbohydrate requirements, adult parasitoids exploit a broad range of sugar resources, including floral and extrafloral nectar and honeydew. Although honeydew might be the predominant sugar source, especially in agricultural systems, it often is nutritionally inferior to sugar sources like nectar. Given its broad availability, it may be expected that sugar-feeding insects have evolved specialized adaptations to deal with this typically inferior sugar source. This would apply especially to organisms that have a close association with honeydew producers. Here, we hypothesized that parasitoids of honeydew-producing insects should show a pronounced response to sugars, such as fructose, sucrose, melezitose, and trehalose, and to a lesser extent glucose. To test this hypothesis, we investigated sugar consumption, feeding behavior and survival of the aphid parasitoid Aphidius ervi on several sugars (equiweight solutions). Our results show that A. ervi adults consumed typical honeydew sugars (sucrose, fructose, trehalose, and melezitose) the most, while consuming considerably less glucose or melibiose. Rhamnose, which does not occur in aphid honeydew, was not, or was only marginally, consumed. When different sugars were provided at the same time, A. ervi adults preferred sucrose or fructose over glucose or melezitose. Furthermore, pre-exposure to sucrose or fructose significantly reduced subsequent intake of glucose, suggesting an acquired distaste for glucose after being previously exposed to highly preferred sugars such as sucrose and fructose. Altogether, this study shows that A. ervi adults prefer sugars (fructose, melezitose, trehalose, and sucrose) that are overrepresented in aphid honeydew and show a lower preference to one (glucose) that is underrepresented in honeydew.}, }
@article {pmid27623966, year = {2017}, author = {Edwards, CL and Byrne, PG and Harlow, P and Silla, AJ}, title = {Dietary Carotenoid Supplementation Enhances the Cutaneous Bacterial Communities of the Critically Endangered Southern Corroboree Frog (Pseudophryne corroboree).}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {435-444}, pmid = {27623966}, issn = {1432-184X}, mesh = {Animal Feed ; Animals ; Animals, Zoo ; Anura/growth &amp; development/*microbiology ; Australia ; Bacteria/classification/*drug effects/growth &amp; development/isolation &amp; purification ; Biological Control Agents ; Carotenoids/*pharmacology ; Chytridiomycota/pathogenicity ; Conservation of Natural Resources ; Diet/*veterinary ; *Dietary Supplements ; *Endangered Species ; Microbiota/drug effects ; Skin/*microbiology ; Stem Cells ; }, abstract = {The rapid spread of infectious disease has resulted in the decline of animal populations globally. Amphibians support a diversity of microbial symbionts on their skin surface that help to inhibit pathogen colonisation and reduce disease susceptibility and virulence. These cutaneous microbial communities represent an important component of amphibian immune defence, however, very little is known about the environmental factors that influence the cutaneous microbiome. Here, we characterise the cutaneous bacterial communities of a captive colony of the critically endangered Australian southern corroboree frog, Pseudophyrne corroboree, and examine the effect of dietary carotenoid supplementation on bacterial abundance, species richness and community composition. Individuals receiving a carotenoid-supplemented diet exhibited significantly higher bacterial abundance and species richness as well as an altered bacterial community composition compared to individuals that did not receive dietary carotenoids. Our findings suggest that dietary carotenoid supplementation enhances the cutaneous bacteria community of the southern corroboree frog and regulates the presence of bacteria species within the cutaneous microbiome. Our study is the second to demonstrate that carotenoid supplementation can improve amphibian cutaneous bacterial community dynamics, drawing attention to the possibility that dietary manipulation may assist with the ex situ management of endangered species and improve resilience to lethal pathogens such as Batrachochytrium dendrobatidis (Bd).}, }
@article {pmid27623965, year = {2018}, author = {Luo, L and Gu, JD}, title = {Influence of Macrofaunal Burrows on Extracellular Enzyme Activity and Microbial Abundance in Subtropical Mangrove Sediment.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {92-101}, pmid = {27623965}, issn = {1432-184X}, mesh = {Acid Phosphatase/analysis ; Animals ; Brachyura/*physiology ; Carbon ; Ecosystem ; *Environmental Microbiology ; Environmental Monitoring ; Enzyme Assays ; Enzymes/*analysis ; Geologic Sediments/*chemistry/*microbiology ; Hong Kong ; Hydrolases/analysis ; Microbiota/*physiology ; Nitrogen ; Oxidoreductases/analysis ; Phenols ; Phosphorus ; Wetlands ; }, abstract = {Bioturbation and bioirrigation induced by burrowing macrofauna are recognized as important processes in aquatic sediment since macrofaunal activities lead to the alteration of sediment characteristics. However, there is a lack of information on how macrofauna influence microbial abundance and extracellular enzyme activity in mangrove sediment. In this study, the environmental parameters, extracellular enzyme activities, and microbial abundance were determined and their relationships were explored. Sediment samples were taken from the surface (S) and lower layer (L) without burrow, as well as crab burrow wall (W) and bottom of crab burrow (B) located at the Mai Po Nature Reserve, Hong Kong. The results showed that the burrowing crabs could enhance the activities of oxidase and hydrolases. The highest activities of phenol oxidase and acid phosphatase were generally observed in B sediment, while the highest activity of N-acetyl-glucosaminidase was found in W sediment. The enzymatic stoichiometry indicated that the crab-affected sediment had similar microbial nitrogen (N) and phosphorous (P) availability relative to carbon (C), lower than S but higher than L sediment. Furthermore, it was found that the highest abundance of both bacteria and fungi was shown in S sediment, and B sediment presented the lowest abundance. Moreover, the concentrations of phosphorus and soluble phenolics in crab-affected sediment were almost higher than the non-affected sediment. The alterations of phenolics, C/P and N/P ratios as well as undetermined environmental factors by the activities of crabs might be the main reasons for the changes of enzyme activity and microbial abundance. Finally, due to the important role of phenol oxidase and hydrolases in sediment organic matter (SOM) decomposition, it is necessary to take macrofaunal activities into consideration when estimating the C budget in mangrove ecosystem in the future.}, }
@article {pmid27623964, year = {2017}, author = {Gao, X}, title = {Scytonemin Plays a Potential Role in Stabilizing the Exopolysaccharidic Matrix in Terrestrial Cyanobacteria.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {255-258}, pmid = {27623964}, issn = {1432-184X}, mesh = {Antioxidants/pharmacology ; Cyanobacteria/*metabolism/radiation effects ; Desiccation ; Indoles/*pharmacology ; Nostoc/metabolism/radiation effects ; Phenols/*pharmacology ; Photosystem II Protein Complex/metabolism/radiation effects ; Pigments, Biological/pharmacology/*physiology ; Polysaccharides, Bacterial/*metabolism/radiation effects ; Sunscreening Agents/pharmacology ; Ultraviolet Rays/adverse effects ; Water Microbiology ; }, abstract = {Cyanobacteria are photosynthetic oxygen-evolving prokaryotes that are distributed in diverse habitats. They synthesize the ultraviolet (UV)-screening pigments, scytonemin (SCY) and mycosporine-like amino acids (MAAs), located in the exopolysaccharide (EPS) matrix. Multiple roles for both pigments have gradually been recognized, such as sunscreen ability, antioxidant activity, and heat dissipation from absorbed UV radiation. In this study, a filamentous terrestrial cyanobacterium Nostoc flagelliforme was used to evaluate the potential stabilizing role of SCY on the EPS matrix. SCY (∼3.7 %) was partially removed from N. flagelliforme filaments by rinsing with 100 % acetone for 5 s. The physiological damage to cells resulting from this treatment, in terms of photosystem II activity parameter Fv/Fm, was repaired after culturing the sample for 40 h. The physiologically recovered sample was further desiccated by natural or rapid drying and then allowed to recovery for 24 h. Compared with the normal sample, a relatively slower Fv/Fm recovery was observed in the SCY-partially removed sample, suggesting that the decreased SCY concentration in the EPS matrix caused cells to suffer further damage upon desiccation. In addition, the SCY-partially removed sample could allow the release of MAAs (∼25 %) from the EPS matrix, while the normal sample did not. Therefore, damage caused by drying of the former resulted from at least the reduction of structural stability of the EPS matrix as well as the loss of partial antioxidant compounds. Considering that an approximately 4 % loss of SCY led to this significant effect, the structurally stabilizing potential of SCY on the EPS matrix is crucial for terrestrial cyanobacteria survival in complex environments.}, }
@article {pmid27623963, year = {2017}, author = {Volova, TG and Prudnikova, SV and Vinogradova, ON and Syrvacheva, DA and Shishatskaya, EI}, title = {Microbial Degradation of Polyhydroxyalkanoates with Different Chemical Compositions and Their Biodegradability.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {353-367}, pmid = {27623963}, issn = {1432-184X}, mesh = {3-Hydroxybutyric Acid/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Base Sequence ; *Biodegradation, Environmental ; Caproates/metabolism ; DNA, Bacterial ; DNA, Fungal ; Fungi/classification/genetics/isolation &amp; purification/*metabolism ; Genes, Bacterial ; Genes, Fungal ; Hydroxybutyrates/metabolism ; Microbial Consortia ; Pentanoic Acids/metabolism ; Phylogeny ; Polyhydroxyalkanoates/biosynthesis/chemistry/*metabolism ; RNA, Ribosomal, 16S/genetics ; Siberia ; Soil/chemistry ; *Soil Microbiology ; Species Specificity ; Temperature ; }, abstract = {The study addresses degradation of polyhydroxyalkanoates (PHA) with different chemical compositions-the polymer of 3-hydroxybutyric acid [P(3HB)] and copolymers of P(3HB) with 3-hydroxyvalerate [P(3HB/3HV)], 4-hydroxybutyrate [P(3HB/4HB)], and 3-hydroxyhexanoate [P(3HB/3HHx)] (10-12 mol%)-in the agro-transformed field soil of the temperate zone. Based on their degradation rates at 21 and 28 °C, polymers can be ranked as follows: P(3HB/4HB) > P(3HB/3HHx) > P(3HB/3HV) > P(3HB). The microbial community on the surface of the polymers differs from the microbial community of the soil with PHA specimens in the composition and percentages of species. Thirty-five isolates of bacteria of 16 genera were identified as PHA degraders by the clear zone technique, and each of the PHA had both specific and common degraders. P(3HB) was degraded by bacteria of the genera Mitsuaria, Chitinophaga, and Acidovorax, which were not among the degraders of the three other PHA types. Roseateles depolymerans, Streptomyces gardneri, and Cupriavidus sp. were specific degraders of P(3HB/4HB). Roseomonas massiliae and Delftia acidovorans degraded P(3HB/3HV), and Pseudoxanthomonas sp., Pseudomonas fluorescens, Ensifer adhaerens, and Bacillus pumilus were specific P(3HB/3HHx) degraders. All four PHA types were degraded by Streptomyces.}, }
@article {pmid27617198, year = {2016}, author = {Greiner, TU and Bäckhed, F}, title = {Microbial regulation of GLP-1 and L-cell biology.}, journal = {Molecular metabolism}, volume = {5}, number = {9}, pages = {753-758}, pmid = {27617198}, issn = {2212-8778}, support = {615362/ERC_/European Research Council/International ; }, abstract = {BACKGROUND: The gut microbiota is associated with several of metabolic diseases, including obesity and type 2 diabetes and affects host physiology through distinct mechanisms. The microbiota produces a vast array of metabolites that signal to host cells in the intestine as well as in more distal organs.<br><br>SCOPE OF REVIEW: Enteroendocrine cells acts as 'chemo sensors' of the intestinal milieu by expressing a large number of receptors, which respond to different metabolites and nutrients, and signal to host by a wide variety of hormones. However, enteroendocrine cells differ along the length of the gut in terms of hormones expressed and receptor repertoire. Also, the microbial ecology and dietary substrates differ along the length of the gut, providing further evidence for unique functions of specific subpopulations among enteroendocrine cells. Here we will review how the gut microbiota interacts with L-cells in the small and large intestine and the resulting effects on the host.<br><br>MAJOR CONCLUSIONS: Microbial metabolites can be sensed differently by specific subpopulations of enteroendocrine cells. Furthermore, hormones such as GLP-1 can have different functions when originating from the small intestine or colon. This article is part of a special issue on microbiota.}, }
@article {pmid27617058, year = {2016}, author = {Bezuidt, OK and Gomri, MA and Pierneef, R and Van Goethem, MW and Kharroub, K and Cowan, DA and Makhalanyane, TP}, title = {Draft genome sequence of Thermoactinomyces sp. strain AS95 isolated from a Sebkha in Thamelaht, Algeria.}, journal = {Standards in genomic sciences}, volume = {11}, number = {1}, pages = {68}, pmid = {27617058}, issn = {1944-3277}, abstract = {The members of the genus Thermoactinomyces are known for their protein degradative capacities. Thermoactinomyces sp. strain AS95 is a Gram-positive filamentous bacterium, isolated from moderately saline water in the Thamelaht region of Algeria. This isolate is a thermophilic aerobic bacterium with the capacity to produce extracellular proteolytic enzymes. This strain exhibits up to 99 % similarity with members of the genus Thermoactinomyces, based on 16S rRNA gene sequence similarity. Here we report on the phenotypic features of Thermoactinomyces sp. strain AS95 together with the draft genome sequence and its annotation. The genome of this strain is 2,558,690 bp in length (one chromosome, but no plasmid) with an average G + C content of 47.95 %, and contains 2550 protein-coding and 60 RNA genes together with 64 ORFs annotated as proteases.}, }
@article {pmid27615066, year = {2017}, author = {Godoy-Vitorino, F and Rodriguez-Hilario, A and Alves, AL and Gonçalves, F and Cabrera-Colon, B and Mesquita, CS and Soares-Castro, P and Ferreira, M and Marçalo, A and Vingada, J and Eira, C and Santos, PM}, title = {The microbiome of a striped dolphin (Stenella coeruleoalba) stranded in Portugal.}, journal = {Research in microbiology}, volume = {168}, number = {1}, pages = {85-93}, doi = {10.1016/j.resmic.2016.08.004}, pmid = {27615066}, issn = {1769-7123}, mesh = {Aerobiosis ; Anaerobiosis ; Animal Structures/microbiology ; Animals ; Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Microbiota ; Phylogeny ; Portugal ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Stenella/*microbiology ; }, abstract = {Infectious diseases with epizootic consequences have not been fully studied in marine mammals. Presently, the unprecedented depth of sequencing, made available by high-throughput approaches, allows detailed comparisons of the microbiome in health and disease. This is the first report of the striped dolphin microbiome in different body sites. Samples from one striped female edematous dolphin were acquired from a variety of body niches, including the blowhole, oral cavity, oral mucosa, tongue, stomach, intestines and genital mucosa. Detailed 16S rRNA analysis of over half a million sequences identified 235 OTUs. Beta diversity analyses indicated that microbial communities vary in structure and cluster by sample origin. Pathogenic, Gram-negative, facultative and obligate anaerobic taxa were significantly detected, including Cetobacterium, Fusobacterium and Ureaplasma. Phocoenobacter and Arcobacter dominated the oral-type samples, while Cardiobacteriaceae and Vibrio were associated with the blowhole and Photobacterium were abundant in the gut. We report for the first time the association of Epulopiscium with a marine mammal gut. The striped dolphin microbiota shows variation in structure and diversity according to the organ type. The high dominance of Gram-negative anaerobic pathogens evidences a cetacean microbiome affected by human-related bacteria.}, }
@article {pmid27614749, year = {2017}, author = {Sarmiento-Vizcaíno, A and González, V and Braña, AF and Palacios, JJ and Otero, L and Fernández, J and Molina, A and Kulik, A and Vázquez, F and Acuña, JL and García, LA and Blanco, G}, title = {Pharmacological Potential of Phylogenetically Diverse Actinobacteria Isolated from Deep-Sea Coral Ecosystems of the Submarine Avilés Canyon in the Cantabrian Sea.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {338-352}, pmid = {27614749}, issn = {1432-184X}, mesh = {Actinobacteria/*chemistry/*classification/genetics/*isolation &amp; purification ; Animals ; Anthozoa/*microbiology ; Anti-Bacterial Agents/pharmacology ; Antineoplastic Agents/pharmacology ; Bacteria/drug effects ; Base Sequence ; Biodiversity ; Biological Products/chemistry/isolation &amp; purification/*pharmacology ; Bioprospecting ; Cell Line, Tumor/drug effects ; Cell Survival/drug effects ; Chromatography, High Pressure Liquid ; Classification ; Coral Reefs ; DNA, Bacterial ; Ecosystem ; Gas Chromatography-Mass Spectrometry ; Genes, Bacterial ; Invertebrates/microbiology ; Marine Biology ; *Phylogeny ; Plant Extracts ; RNA, Ribosomal, 16S/genetics ; Seawater ; Secondary Metabolism ; Spain ; Streptomyces/classification/isolation &amp; purification ; }, abstract = {Marine Actinobacteria are emerging as an unexplored source for natural product discovery. Eighty-seven deep-sea coral reef invertebrates were collected during an oceanographic expedition at the submarine Avilés Canyon (Asturias, Spain) in a range of 1500 to 4700 m depth. From these, 18 cultivable bioactive Actinobacteria were isolated, mainly from corals, phylum Cnidaria, and some specimens of phyla Echinodermata, Porifera, Annelida, Arthropoda, Mollusca and Sipuncula. As determined by 16S rRNA sequencing and phylogenetic analyses, all isolates belong to the phylum Actinobacteria, mainly to the Streptomyces genus and also to Micromonospora, Pseudonocardia and Myceligenerans. Production of bioactive compounds of pharmacological interest was investigated by high-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS) techniques and subsequent database comparison. Results reveal that deep-sea isolated Actinobacteria display a wide repertoire of secondary metabolite production with a high chemical diversity. Most identified products (both diffusible and volatiles) are known by their contrasted antibiotic or antitumor activities. Bioassays with ethyl acetate extracts from isolates displayed strong antibiotic activities against a panel of important resistant clinical pathogens, including Gram-positive and Gram-negative bacteria, as well as fungi, all of them isolated at two main hospitals (HUCA and Cabueñes) from the same geographical region. The identity of the active extracts components of these producing Actinobacteria is currently being investigated, given its potential for the discovery of pharmaceuticals and other products of biotechnological interest.}, }
@article {pmid27613296, year = {2017}, author = {Tessler, M and Brugler, MR and DeSalle, R and Hersch, R and Velho, LFM and Segovia, BT and Lansac-Toha, FA and Lemke, MJ}, title = {A Global eDNA Comparison of Freshwater Bacterioplankton Assemblages Focusing on Large-River Floodplain Lakes of Brazil.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {61-74}, pmid = {27613296}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/growth &amp; development ; Biodiversity ; Brazil ; DNA, Bacterial/genetics ; Ecosystem ; Floods ; Lakes/*microbiology ; Plankton/*classification/genetics/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; }, abstract = {With its network of lotic and lentic habitats that shift during changes in seasonal connection, the tropical and subtropical large-river systems represent possibly the most dynamic of all aquatic environments. Pelagic water samples were collected from Brazilian floodplain lakes (total n = 58) in four flood-pulsed systems (Amazon [n = 21], Araguaia [n = 14], Paraná [n = 15], and Pantanal [n = 8]) in 2011-2012 and sequenced via 454 for bacterial environmental DNA using 16S amplicons; additional abiotic field and laboratory measurements were collected for the assayed lakes. We report here a global comparison of the bacterioplankton makeup of freshwater systems, focusing on a comparison of Brazilian lakes with similar freshwater systems across the globe. The results indicate a surprising similarity at higher taxonomic levels of the bacterioplankton in Brazilian freshwater with global sites. However, substantial novel diversity at the family level was also observed for the Brazilian freshwater systems. Brazilian freshwater bacterioplankton richness was relatively average globally. Ordination results indicate that Brazilian bacterioplankton composition is unique from other areas of the globe. Using Brazil-only ordinations, floodplain system differentiation most strongly correlated with dissolved oxygen, pH, and phosphate. Our data on Brazilian freshwater systems in combination with analysis of a collection of freshwater environmental samples from across the globe offers the first regional picture of bacterioplankton diversity in these important freshwater systems.}, }
@article {pmid27612291, year = {2017}, author = {Props, R and Kerckhof, FM and Rubbens, P and De Vrieze, J and Hernandez Sanabria, E and Waegeman, W and Monsieurs, P and Hammes, F and Boon, N}, title = {Absolute quantification of microbial taxon abundances.}, journal = {The ISME journal}, volume = {11}, number = {2}, pages = {584-587}, pmid = {27612291}, issn = {1751-7370}, mesh = {Bacteria/classification/*genetics/growth &amp; development/isolation &amp; purification ; Biodiversity ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Flow Cytometry ; *Microbiota ; Sequence Analysis, DNA ; }, abstract = {High-throughput amplicon sequencing has become a well-established approach for microbial community profiling. Correlating shifts in the relative abundances of bacterial taxa with environmental gradients is the goal of many microbiome surveys. As the abundances generated by this technology are semi-quantitative by definition, the observed dynamics may not accurately reflect those of the actual taxon densities. We combined the sequencing approach (16S rRNA gene) with robust single-cell enumeration technologies (flow cytometry) to quantify the absolute taxon abundances. A detailed longitudinal analysis of the absolute abundances resulted in distinct abundance profiles that were less ambiguous and expressed in units that can be directly compared across studies. We further provide evidence that the enrichment of taxa (increase in relative abundance) does not necessarily relate to the outgrowth of taxa (increase in absolute abundance). Our results highlight that both relative and absolute abundances should be considered for a comprehensive biological interpretation of microbiome surveys.}, }
@article {pmid27611357, year = {2016}, author = {Zhang, L and Verstraete, W and de Lourdes Mendoza, M and Lu, Z and Liu, Y and Huang, G and Cai, L}, title = {Decrease of dissolved sulfide in sewage by powdered natural magnetite and hematite.}, journal = {The Science of the total environment}, volume = {573}, number = {}, pages = {1070-1078}, doi = {10.1016/j.scitotenv.2016.08.206}, pmid = {27611357}, issn = {1879-1026}, mesh = {Biological Oxygen Demand Analysis ; Ferric Compounds/*chemistry ; Ferrosoferric Oxide/*chemistry ; Models, Theoretical ; Particle Size ; Powders ; Sewage/*chemistry ; Solubility ; Sulfides/*analysis/chemistry ; Water Pollutants, Chemical/*analysis/chemistry ; }, abstract = {UNLABELLED: Natural magnetite and hematite were explored to decrease sulfide in sewage, compared with iron salts (FeCl3 and FeSO4). A particle size of magnetite and hematite ranging from 45 to 60μm was used. The results showed that 40mgL[-1] of powdered magnetite and hematite addition decreased the sulfide in sewage by 79%and 70%, respectively. The achieved decrease of sulfide production capacities were 197.3, 210.6, 317.6 and 283.3mgSg[-1]Fe for magnetite, hematite, FeCl3 and FeSO4 at the optimal dosage of 40mgL[-1], respectively. Magnetite and hematite provided a higher decrease of sulfide production since more iron ions are capable of being released from the solid phase, not because of adsorption capacity of per gram iron. Besides, the impact on pH and oxidation-reduction potential (ORP) of hematite addition was negligible; while magnetite addition resulted in slight increase of 0.3-0.5 on pH and 10-40mV on ORP. Powdered magnetite and hematite thus appear to be suitable for sulfide decrease in sewage, for their sparing solubility, sustained-release, long reactive time in sewage as well as cost-effectiveness, compared with iron salts. Further investigation over long time periods under practical conditions are needed to evaluate the possible settlement in sewers and unwanted (toxic) metal elements presenting as impurities.<br><br>CAPSULE ABSTRACT: Powdered magnetite and hematite were more cost-effective at only 30% costs of iron salts, such as FeCl3 and FeSO4 for decreasing sulfide production in sewage.}, }
@article {pmid27610223, year = {2016}, author = {Balcom, IN and Driscoll, H and Vincent, J and Leduc, M}, title = {Metagenomic analysis of an ecological wastewater treatment plant's microbial communities and their potential to metabolize pharmaceuticals.}, journal = {F1000Research}, volume = {5}, number = {}, pages = {1881}, pmid = {27610223}, issn = {2046-1402}, support = {P20 GM103449/GM/NIGMS NIH HHS/United States ; }, abstract = {Pharmaceuticals and other micropollutants have been detected in drinking water, groundwater, surface water, and soil around the world. Even in locations where wastewater treatment is required, they can be found in drinking water wells, municipal water supplies, and agricultural soils. It is clear conventional wastewater treatment technologies are not meeting the challenge of the mounting pressures on global freshwater supplies. Cost-effective ecological wastewater treatment technologies have been developed in response. To determine whether the removal of micropollutants in ecological wastewater treatment plants (WWTPs) is promoted by the plant-microbe interactions, as has been reported for other recalcitrant xenobiotics, biofilm microbial communities growing on the surfaces of plant roots were profiled by whole metagenome sequencing and compared to the microbial communities residing in the wastewater. In this study, the concentrations of pharmaceuticals and personal care products (PPCPs) were quantified in each treatment tank of the ecological WWTP treating human wastewater at a highway rest stop and visitor center in Vermont. The concentrations of detected PPCPs were substantially greater than values reported for conventional WWTPs likely due to onsite recirculation of wastewater. The greatest reductions in PPCPs concentrations were observed in the anoxic treatment tank where Bacilli dominated the biofilm community. Benzoate degradation was the most abundant xenobiotic metabolic category identified throughout the system. Collectively, the microbial communities residing in the wastewater were taxonomically and metabolically more diverse than the immersed plant root biofilm. However, greater heterogeneity and higher relative abundances of xenobiotic metabolism genes was observed for the root biofilm.}, }
@article {pmid27609499, year = {2016}, author = {Sultanpuram, VR and Mothe, T and Chintalapati, S and Chintalapati, VR}, title = {Tersicoccus solisilvae sp., nov., a bacterium isolated from forest soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {66}, number = {12}, pages = {5061-5065}, doi = {10.1099/ijsem.0.001470}, pmid = {27609499}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; *Forests ; India ; Micrococcaceae/*classification/genetics/isolation &amp; purification ; Nucleic Acid Hybridization ; Peptidoglycan/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {A Gram-stain-positive, aerobic, non-motile, coccoid bacterial strain, 36AT, was isolated from Munnar, in India. Based on the results of 16S rRNA gene sequence analysis, this strain was identified as representing a member of the genus Tersicoccus and was most closely related to the type strain of Tersicoccus phoenicis (98.9 %, sequence similarity), the only other member of the genus, and to members of the related genus Arthrobacter (<96.1 %, sequence similarity). However, the DNA-DNA relatedness of strain 36AT with T. phoenicis DSM 30849T was only 31.9±0.8. The DNA G+C content of strain 36AT was 70.9 mol%. Strain 36AT was an aerobic microbe with optimal growth at 37 °C, pH 6.0-8.0 and NaCl 0.5-3 % (w/v). Cell-wall peptidoglycan of strain 36AT was of type A11.20 (Lys-Ser-Ala2). Polar lipids present were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, two phospholipids, a glycolipid and four unknown lipids. The major isoprenoid quinones were MK-9 (H2) and MK-8 (H2). Major fatty acids of strain 36AT were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. The results of phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strain 36AT, which represents a novel member of the genus Tersicoccus, for which the name Tersicoccus solisilvae sp. nov., is proposed. The type strain is 36AT (=KCTC 33776T=CGMCC 1.15480T).}, }
@article {pmid27605925, year = {2016}, author = {Eren, AM and Sogin, ML and Maignien, L}, title = {Editorial: New Insights into Microbial Ecology through Subtle Nucleotide Variation.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1318}, pmid = {27605925}, issn = {1664-302X}, }
@article {pmid27604258, year = {2016}, author = {Smalla, K and Simonet, P and Tiedje, J and Topp, E}, title = {Editorial: Special section of FEMS Microbiology Ecology on the environmental dimension of antibiotic resistance.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {11}, pages = {}, doi = {10.1093/femsec/fiw172}, pmid = {27604258}, issn = {1574-6941}, }
@article {pmid27603967, year = {2016}, author = {Saad, SA and Welles, L and Abbas, B and Lopez-Vazquez, CM and van Loosdrecht, MCM and Brdjanovic, D}, title = {Denitrification of nitrate and nitrite by 'Candidatus Accumulibacter phosphatis' clade IC.}, journal = {Water research}, volume = {105}, number = {}, pages = {97-109}, doi = {10.1016/j.watres.2016.08.061}, pmid = {27603967}, issn = {1879-2448}, mesh = {Bioreactors ; *Denitrification ; Nitrates ; *Nitrites ; Phosphorus/metabolism ; Sewage ; }, abstract = {Phosphate accumulating organisms (PAO) are assumed to use nitrate as external electron acceptor, allowing an efficient integration of simultaneous nitrogen and phosphate removal with minimal organic carbon (COD) requirements. However, contradicting findings appear in literature regarding the denitrification capacities of PAO due to the lack of clade specific highly enriched PAO cultures. Whereas some studies suggest that only PAO clade I may be capable of using nitrate as external electron acceptor for anoxic P-uptake, other studies indicate that PAO clade II may be responsible for anoxic P-removal. In the present study, a highly enriched PAO clade IC culture (>99% according to FISH) was cultivated in an SBR operated under Anaerobic/Oxic conditions and subsequently exposed to Anaerobic/Anoxic/Oxic conditions using nitrate as electron acceptor. Before and after acclimatization to the presence of nitrate, the aerobic and anoxic (nitrate and nitrite) activities of the PAO I culture were assessed through the execution of batch tests using either acetate or propionate as electron donor. In the presence of nitrate, significant P-uptake by PAO I was not observed before or after acclimatization. Using nitrite as electron acceptor, limited nitrite removal rates were observed before acclimatization with lower rates in the acetate fed reactor without P-uptake and slightly higher in the propionate fed reactor with a marginal anoxic P-uptake. Only after acclimatization to nitrate, simultaneous P and nitrite removal was observed. This study suggests that PAO clade IC is not capable of using nitrate as external electron acceptor for anoxic P-removal. The elucidation of the metabolic capacities for individual PAO clades helps in better understanding and optimization of the relation between microbial ecology and process performance in enhanced biological phosphate removal processes.}, }
@article {pmid27602021, year = {2016}, author = {Ho, A and Angel, R and Veraart, AJ and Daebeler, A and Jia, Z and Kim, SY and Kerckhof, FM and Boon, N and Bodelier, PL}, title = {Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1285}, pmid = {27602021}, issn = {1664-302X}, abstract = {Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes.}, }
@article {pmid27600611, year = {2016}, author = {Kiewra, D and Czułowska, A and Lonc, E}, title = {Winter activity of Dermacentor reticulatus (Fabricius, 1794) in the newly emerging population of Lower Silesia, south-west Poland.}, journal = {Ticks and tick-borne diseases}, volume = {7}, number = {6}, pages = {1124-1127}, doi = {10.1016/j.ttbdis.2016.08.012}, pmid = {27600611}, issn = {1877-9603}, mesh = {Animal Distribution/*physiology ; Animals ; Cat Diseases/epidemiology/parasitology ; Cats ; Dermacentor/*physiology ; Dog Diseases/epidemiology/parasitology ; Dogs ; Female ; Male ; Poland/epidemiology ; *Seasons ; }, abstract = {This paper presents the unexpected winter activity of Dermacentor reticulatus (Fabricius, 1794) ticks in a newly emerging population in south-west Poland. Host-seeking ticks were collected from vegetation in January 2016 in a meadow ecosystem in six sites located in the Wroclaw Agglomeration, as well as from ten companion animals. A total of 238 questing D. reticulatus ticks, comprising 166 females and 72 males, were collected from all examined sites with the highest number of 102 specimens collected in one hour in one locality (Muchobór Wielki, Wrocław). Additionally, two fully-engorged females were collected from two dogs along with one slightly engorged female from a cat. The fact that D. reticulatus can be very active in January indicates a need to take into account the increased threat of tick-bite in the winter time.}, }
@article {pmid27594690, year = {2016}, author = {Rauglas, E and Martin, S and Bailey, K and Magnuson, M and Phillips, R and Harper, WF}, title = {The effect of malathion on the activity, performance, and microbial ecology of activated sludge.}, journal = {Journal of environmental management}, volume = {183}, number = {}, pages = {220-228}, pmid = {27594690}, issn = {1095-8630}, support = {EPA999999/ImEPA/Intramural EPA/United States ; }, mesh = {Ammonia/chemistry ; Biodegradation, Environmental ; Biological Oxygen Demand Analysis ; Bioreactors/microbiology ; Environmental Monitoring ; Malathion/*chemistry ; Microbiota/*drug effects ; Nitrification ; Sewage/*chemistry/*microbiology ; }, abstract = {This study evaluated the effect of a VX (O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothioate) surrogate (malathion) on the activity, performance, and ecology of activated sludge bioreactors. In the presence of malathion, the maximum observed respiration rates varied between 43 and 53 μg/O2 min, generally similar to the 49 μg O2/min rates observed in controls. Malathion did not alter the respiration ratio of O2 consumed-to-CO2 produced nor did it impact the shape of the oxygen consumption curves during respirometry. Shorter term (12 h) batch tests showed that both chemical oxygen demand (COD) and ammonia removal were not negatively impacted by the presence of 0.1-3 mg/L malathion. Longer term continuous addition (i.e. 40 days) of 0.1 mg/L of malathion also had no effect on COD and ammonia removal. In contrast to shorter term exposures, longer term continuous addition of 3 mg/L of malathion negatively impacted both COD and nitrogen removal and was associated with shifts in the abundance of species that are common to activated sludge. These results illustrate the impact that chemicals like malathion may have on COD removal, and nitrification, as well as the robustness of activated sludge microbial communities.}, }
@article {pmid27592346, year = {2017}, author = {Olsson, S and Penacho, V and Puente-Sánchez, F and Díaz, S and Gonzalez-Pastor, JE and Aguilera, A}, title = {Horizontal Gene Transfer of Phytochelatin Synthases from Bacteria to Extremophilic Green Algae.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {50-60}, pmid = {27592346}, issn = {1432-184X}, mesh = {Aminoacyltransferases/*genetics ; Cadmium/*pharmacology ; Chlamydomonas/*genetics/metabolism ; Escherichia coli/*drug effects/*genetics ; Extremophiles/*genetics ; Polymerase Chain Reaction ; Water Pollutants/pharmacology ; Water Pollution, Chemical ; }, abstract = {Transcriptomic sequencing together with bioinformatic analyses and an automated annotation process led us to identify novel phytochelatin synthase (PCS) genes from two extremophilic green algae (Chlamydomonas acidophila and Dunaliella acidophila). These genes are of intermediate length compared to known PCS genes from eukaryotes and PCS-like genes from prokaryotes. A detailed phylogenetic analysis gives new insight into the complicated evolutionary history of PCS genes and provides evidence for multiple horizontal gene transfer events from bacteria to eukaryotes within the gene family. A separate subgroup containing PCS-like genes within the PCS gene family is not supported since the PCS genes are monophyletic only when the PCS-like genes are included. The presence and functionality of the novel genes in the organisms were verified by genomic sequencing and qRT-PCR. Furthermore, the novel PCS gene in Chlamydomonas acidophila showed very strong induction by cadmium. Cloning and expression of the gene in Escherichia coli clearly improves its cadmium resistance. The gene in Dunaliella was not induced, most likely due to gene duplication.}, }
@article {pmid27592345, year = {2017}, author = {McFrederick, QS and Thomas, JM and Neff, JL and Vuong, HQ and Russell, KA and Hale, AR and Mueller, UG}, title = {Flowers and Wild Megachilid Bees Share Microbes.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {188-200}, pmid = {27592345}, issn = {1432-184X}, mesh = {Animals ; Base Sequence ; Bees/*microbiology ; DNA, Bacterial/genetics ; Flowers/*microbiology ; Gastrointestinal Microbiome/*genetics ; Lactobacillus/*classification/*genetics/isolation &amp; purification ; Larva/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Transmission pathways have fundamental influence on microbial symbiont persistence and evolution. For example, the core gut microbiome of honey bees is transmitted socially and via hive surfaces, but some non-core bacteria associated with honey bees are also found on flowers, and these bacteria may therefore be transmitted indirectly between bees via flowers. Here, we test whether multiple flower and wild megachilid bee species share microbes, which would suggest that flowers may act as hubs of microbial transmission. We sampled the microbiomes of flowers (either bagged to exclude bees or open to allow bee visitation), adults, and larvae of seven megachilid bee species and their pollen provisions. We found a Lactobacillus operational taxonomic unit (OTU) in all samples but in the highest relative and absolute abundances in adult and larval bee guts and pollen provisions. The presence of the same bacterial types in open and bagged flowers, pollen provisions, and bees supports the hypothesis that flowers act as hubs of transmission of these bacteria between bees. The presence of bee-associated bacteria in flowers that have not been visited by bees suggests that these bacteria may also be transmitted to flowers via plant surfaces, the air, or minute insect vectors such as thrips. Phylogenetic analyses of nearly full-length 16S rRNA gene sequences indicated that the Lactobacillus OTU dominating in flower- and megachilid-associated microbiomes is monophyletic, and we propose the name Lactobacillus micheneri sp. nov. for this bacterium.}, }
@article {pmid27589234, year = {2016}, author = {Simonin, M and Martins, JM and Uzu, G and Vince, E and Richaume, A}, title = {Combined Study of Titanium Dioxide Nanoparticle Transport and Toxicity on Microbial Nitrifying Communities under Single and Repeated Exposures in Soil Columns.}, journal = {Environmental science &amp; technology}, volume = {50}, number = {19}, pages = {10693-10699}, doi = {10.1021/acs.est.6b02415}, pmid = {27589234}, issn = {1520-5851}, mesh = {Archaea ; Nanoparticles/toxicity ; Nitrification ; *Soil ; *Soil Microbiology ; Titanium/toxicity ; }, abstract = {Soils are exposed to nanoparticles (NPs) as a result of their increasing use in many commercial products. Adverse effects of NPs on soil microorganisms have been reported in several ecotoxicological studies using microcosms. Although repeated exposures are more likely to occur in soils, most of these previous studies were performed as a single exposure to NPs. Contrary to single contamination, the study of multiple NP contaminations in soils requires the use of specialized setups. Using a soil column experiment, we compared the influence of single and repeated exposures (one, two, or three exposures that resulted in the same final concentration applied) on the transport of titanium dioxide (TiO2) NPs through soil and the effect of these different exposure scenarios on the abundance and activity of soil nitrifying microbial communities after a 2 month incubation. The transport of TiO2 NPs was very limited under both single and repeated exposures and was highest for the lowest concentration injected during the first application. Significant decreases in nitrification activity and ammonia-oxidizing archaea and bacteria populations were observed only for the repeated exposure scenario (three TiO2 NP contaminations). These results suggest that, under repeated exposures, the transport of TiO2 NPs to deep soil layers and groundwater is limited and that a chronic contamination is more harmful for the soil microbiological functioning than a single exposure.}, }
@article {pmid27589209, year = {2016}, author = {Rahman, A and Meerburg, FA and Ravadagundhi, S and Wett, B and Jimenez, J and Bott, C and Al-Omari, A and Riffat, R and Murthy, S and De Clippeleir, H}, title = {Bioflocculation management through high-rate contact-stabilization: A promising technology to recover organic carbon from low-strength wastewater.}, journal = {Water research}, volume = {104}, number = {}, pages = {485-496}, doi = {10.1016/j.watres.2016.08.047}, pmid = {27589209}, issn = {1879-2448}, mesh = {Bioreactors ; Carbon ; Oxygen ; Sewage ; *Waste Disposal, Fluid ; *Wastewater ; }, abstract = {A series of pilot-scale studies were performed to compare conventional high-rate activated sludge systems (HRAS) (continuous stirred tank reactor (CSTR) and plug flow (PF) reactor configurations) with high-rate contact-stabilization (CS) technology in terms of carbon recovery potential from chemically enhanced primary treatment effluent at a municipal wastewater treatment plant. This study showed that carbon redirection and recovery could be achieved at short solids retention time (SRT). However, bioflocculation became a limiting factor in the conventional HRAS configurations (total SRT ≤ 1.2 days). At a total SRT ≤1.1 day, the high-rate CS configuration allowed better carbon removal (52-59%), carbon redirection to sludge (0.46-0.55 g COD/g CODadded) and carbon recovery potential (0.33-0.34 gCOD/gCODadded) than the CSTR and PF configurations (28-37% COD removal, carbon redirection of 0.32-0.45 g COD/g CODadded and no carbon harvesting). The presence of a stabilization phase (famine), achieved by aerating the return activated sludge (RAS), followed by low dissolved oxygen contact with the influent (feast) was identified as the main reason for improved biosorption capacity, bioflocculation and settleability in the CS configuration. This study showed that high-rate CS is a promising technology for carbon and energy recovery from low-strength wastewaters.}, }
@article {pmid27586649, year = {2016}, author = {Ralls, MW and Demehri, FR and Feng, Y and Raskind, S and Ruan, C and Schintlmeister, A and Loy, A and Hanson, B and Berry, D and Burant, CF and Teitelbaum, DH}, title = {Bacterial nutrient foraging in a mouse model of enteral nutrient deprivation: insight into the gut origin of sepsis.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {311}, number = {4}, pages = {G734-G743}, pmid = {27586649}, issn = {1522-1547}, support = {P30 DK089503/DK/NIDDK NIH HHS/United States ; R01 AI044076/AI/NIAID NIH HHS/United States ; U24 DK097153/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Disease Models, Animal ; Gastrointestinal Microbiome/*physiology ; Intestinal Mucosa/*metabolism/microbiology ; Jejunum/*metabolism/microbiology ; Male ; Metabolome ; Mice ; Mice, Inbred C57BL ; *Parenteral Nutrition, Total ; Sepsis/*metabolism/microbiology ; }, abstract = {Total parenteral nutrition (TPN) leads to a shift in small intestinal microbiota with a characteristic dominance of Proteobacteria This study examined how metabolomic changes within the small bowel support an altered microbial community in enterally deprived mice. C57BL/6 mice were given TPN or enteral chow. Metabolomic analysis of jejunal contents was performed by liquid chromatography/mass spectrometry (LC/MS). In some experiments, leucine in TPN was partly substituted with [[13]C]leucine. Additionally, jejunal contents from TPN-dependent and enterally fed mice were gavaged into germ-free mice to reveal whether the TPN phenotype was transferrable. Small bowel contents of TPN mice maintained an amino acid composition similar to that of the TPN solution. Mass spectrometry analysis of small bowel contents of TPN-dependent mice showed increased concentration of [13]C compared with fed mice receiving saline enriched with [[13]C]leucine. [[13]C]leucine added to the serosal side of Ussing chambers showed rapid permeation across TPN-dependent jejunum, suggesting increased transmucosal passage. Single-cell analysis by fluorescence in situ hybridization (FISH)-NanoSIMS demonstrated uptake of [[13]C]leucine by TPN-associated bacteria, with preferential uptake by Enterobacteriaceae Gavage of small bowel effluent from TPN mice into germ-free, fed mice resulted in a trend toward the proinflammatory TPN phenotype with loss of epithelial barrier function. TPN dependence leads to increased permeation of TPN-derived nutrients into the small intestinal lumen, where they are predominately utilized by Enterobacteriaceae The altered metabolomic composition of the intestinal lumen during TPN promotes dysbiosis.}, }
@article {pmid27584940, year = {2016}, author = {Al-Rshaidat, MM and Snider, A and Rosebraugh, S and Devine, AM and Devine, TD and Plaisance, L and Knowlton, N and Leray, M}, title = {Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea.}, journal = {Genome}, volume = {59}, number = {9}, pages = {724-737}, doi = {10.1139/gen-2015-0208}, pmid = {27584940}, issn = {1480-3321}, mesh = {Animals ; Anthozoa/*classification/*genetics ; *Biodiversity ; *Coral Reefs ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Geography ; *High-Throughput Nucleotide Sequencing ; Indian Ocean ; Jordan ; Phylogeny ; }, abstract = {High-throughput sequencing (HTS) of DNA barcodes (metabarcoding), particularly when combined with standardized sampling protocols, is one of the most promising approaches for censusing overlooked cryptic invertebrate communities. We present biodiversity estimates based on sequencing of the cytochrome c oxidase subunit 1 (COI) gene for coral reefs of the Gulf of Aqaba, a semi-enclosed system in the northern Red Sea. Samples were obtained from standardized sampling devices (Autonomous Reef Monitoring Structures (ARMS)) deployed for 18 months. DNA barcoding of non-sessile specimens >2 mm revealed 83 OTUs in six phyla, of which only 25% matched a reference sequence in public databases. Metabarcoding of the 2 mm - 500 μm and sessile bulk fractions revealed 1197 OTUs in 15 animal phyla, of which only 4.9% matched reference barcodes. These results highlight the scarcity of COI data for cryptobenthic organisms of the Red Sea. Compared with data obtained using similar methods, our results suggest that Gulf of Aqaba reefs are less diverse than two Pacific coral reefs but much more diverse than an Atlantic oyster reef at a similar latitude. The standardized approaches used here show promise for establishing baseline data on biodiversity, monitoring the impacts of environmental change, and quantifying patterns of diversity at regional and global scales.}, }
@article {pmid27581036, year = {2017}, author = {Wolińska, A and Kuźniar, A and Zielenkiewicz, U and Banach, A and Izak, D and Stępniewska, Z and Błaszczyk, M}, title = {Metagenomic Analysis of Some Potential Nitrogen-Fixing Bacteria in Arable Soils at Different Formation Processes.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {162-176}, pmid = {27581036}, issn = {1432-184X}, mesh = {Agriculture ; Biodiversity ; Cyanobacteria/*classification/genetics/*isolation &amp; purification ; Metagenome/genetics ; Nitrogen-Fixing Bacteria/*classification/genetics/*metabolism ; Poland ; Proteobacteria/*classification/genetics/*isolation &amp; purification ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {The main goal of the study was to determine the diversity of the potential nitrogen-fixing (PNF) bacteria inhabiting agricultural (A) soils versus wastelands serving as controls (C). The soils were classified into three groups based on the formation process: autogenic soils (Albic Luvisols, Brunic Arenosols, Haplic Phaeozem) formed on loess material, hydrogenic soils (Mollic Gleysols, Eutric Fluvisol, Eutric Histosol) formed under the effect of stagnant water and lithogenic soils (Rendzina Leptosols) formed on limestone. In order to determine the preferable conditions for PNF bacteria, the relationships between the soil chemical features and bacterial operational taxonomic units (OTUs) were tested. Additionally, the nitrogen content and fertilisation requirement of the lithogenic (LG), autogenic (AG) and hydrogenic (HG) soils were discussed. The composition of the bacterial communities was analysed with the next-generation sequencing (NGS) by the Ion Torrent™ technology. The sequences were clustered into OTU based on a 99 % similarity threshold. The arable soils tested were distinctly dominated by β-Proteobacteria representatives of PNF bacteria belonging to the genus Burkholderia. Bacteria from the α-Proteobacteria class and Devosia genus were subdominants. A free-living Cyanobacteria population dominated in A rather than in C soils. We have found that both soil agricultural management and soil formation processes are the most conducive factors for PNF bacteria, as a majority of these microorganisms inhabit the AG group of soils, whilst the LG soils with the lowest abundance of PNF bacteria revealed the need for additional mineral fertilisation. Our studies have also indicated that there are close relationships between soil classification with respect to soil formation processes and PNF bacteria preference for occupation of soil niches.}, }
@article {pmid27581035, year = {2017}, author = {Colin, Y and Goñi-Urriza, M and Gassie, C and Carlier, E and Monperrus, M and Guyoneaud, R}, title = {Distribution of Sulfate-Reducing Communities from Estuarine to Marine Bay Waters.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {39-49}, pmid = {27581035}, issn = {1432-184X}, mesh = {Bays/*microbiology ; Biodiversity ; Desulfovibrio/classification/*genetics/*isolation &amp; purification/metabolism ; Ecosystem ; Estuaries ; Fresh Water/microbiology ; Geologic Sediments/*microbiology ; Oxidation-Reduction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Salinity ; Seawater/*microbiology ; Sulfates/*metabolism ; }, abstract = {Estuaries are highly dynamic ecosystems in which freshwater and seawater mix together. Depending on tide and river inflows, particles originating from rivers or from the remobilization of sediments accumulate in the water column. Due to the salinity gradient and the high heterotrophic activity in the estuarine plume, hypoxic and anoxic microniches may form in oxygenated waters, sustaining favorable conditions for resuspended anaerobic microorganisms. In this context, we tested the hypothesis that anaerobic sulfate-reducing prokaryotes may occur in the water column of the Adour River. Using 16S ribosomal RNA (rRNA) and dsrAB-based terminal restriction fragment length polymorphism (T-RFLP) techniques, we characterized total prokaryotic and sulfate-reducing communities along a gradient from estuarine to marine bay waters. Sulfate-reducing prokaryotes were further characterized by the description of dsrB genes and the cultivation of sulfidogenic anaerobic microorganisms. As a result, physical-chemical parameters had a significant effect on water bacterial diversity and community structure along the studied gradient. The concentration of cultured sulfidogenic microorganisms ranged from 1 to 60 × 10[3] cells l[-1] in the water column. Sulfate-reducing prokaryotes occurring in estuarine waters were closely related to microorganisms previously detected in freshwater sediments, suggesting an estuarine origin, mainly by the remobilization of the sediments. In the marine bay station, sediment-derived sulfate-reducing prokaryotes were not cultured anymore, probably due to freshwater dilution, increasing salinity and extended oxic stress. Nevertheless, isolates related to the type strain Desulfovibrio oceani were cultured from the diluted plume and deep marine waters, indicating the occurrence of autochthonous sulfate-reducing bacteria offshore.}, }
@article {pmid27575719, year = {2016}, author = {Doolette, CL and Gupta, VV and Lu, Y and Payne, JL and Batstone, DJ and Kirby, JK and Navarro, DA and McLaughlin, MJ}, title = {Quantifying the Sensitivity of Soil Microbial Communities to Silver Sulfide Nanoparticles Using Metagenome Sequencing.}, journal = {PloS one}, volume = {11}, number = {8}, pages = {e0161979}, pmid = {27575719}, issn = {1932-6203}, mesh = {Bacteria/*drug effects/genetics ; DNA, Bacterial/analysis ; *Metagenome ; Metal Nanoparticles ; Nitrification/drug effects ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA/*methods ; Silver Compounds/*pharmacology ; *Soil Microbiology ; }, abstract = {Soils are a sink for sulfidised-silver nanoparticles (Ag2S-NPs), yet there are limited ecotoxicity data for their effects on microbial communities. Conventional toxicity tests typically target a single test species or function, which does not reflect the broader community response. Using a combination of quantitative PCR, 16S rRNA amplicon sequencing and species sensitivity distribution (SSD) methods, we have developed a new approach to calculate silver-based NP toxicity thresholds (HCx, hazardous concentrations) that are protective of specific members (operational taxonomic units, OTUs) of the soil microbial community. At the HC20 (80% of species protected), soil OTUs were significantly less sensitive to Ag2S-NPs compared to AgNPs and Ag+ (5.9, 1.4 and 1.4 mg Ag kg-1, respectively). However at more conservative HC values, there were no significant differences. These trends in OTU responses matched with those seen in a specific microbial function (rate of nitrification) and amoA-bacteria gene abundance. This study provides a novel molecular-based framework for quantifying the effect of a toxicant on whole soil microbial communities while still determining sensitive genera/species. Methods and results described here provide a benchmark for microbial community ecotoxicological studies and we recommend that future revisions of Soil Quality Guidelines for AgNPs and other such toxicants consider this approach.}, }
@article {pmid27574029, year = {2017}, author = {Mechmeche, M and Kachouri, F and Yaghlane, HB and Ksontini, H and Setti, K and Hamdi, M}, title = {Kinetic analysis and mathematical modeling of growth parameters of Lactobacillus plantarum in protein-rich isolates from tomato seed.}, journal = {Food science and technology international = Ciencia y tecnologia de los alimentos internacional}, volume = {23}, number = {2}, pages = {128-141}, doi = {10.1177/1082013216665706}, pmid = {27574029}, issn = {1532-1738}, mesh = {Biomass ; Bioreactors ; Carbohydrate Metabolism ; Culture Media/chemistry ; Fermentation ; Hydrogen-Ion Concentration ; Lactic Acid/analysis/biosynthesis ; Lactobacillus plantarum/*growth &amp; development/isolation &amp; purification/metabolism ; Solanum lycopersicum/chemistry/metabolism/*microbiology ; *Models, Biological ; Plant Extracts/chemistry/metabolism ; Plant Proteins/analysis/*metabolism ; Seeds/chemistry/microbiology ; }, abstract = {The aim of the present study was to evaluate the applicability of using protein-rich isolates from tomato seed as a sole source of nutrition for the growth of lactic acid bacteria. Unstructured mathematical and logistic models were proposed to describe growth, pH drop, lactic acid production and nutriment consumption by Lactobacillus plantarum in whole and defatted isolates in order to compare their suitability for the production of a fermented beverage. These media have considerable good quantities of nutriment that allowed the growth of L. plantarum, after which the cell numbers begin to decline. The maximum biomass was observed in defatted isolate (1.42 g L[-1]) followed by the whole isolate (1.24 g L[-1]). The lactic acid increased by about 5.5 and 6.5 times respectively in whole and defatted protein isolates. However, significant nutriment consumption occurred during the growth phase as well as stationary phase. A reduction of 61.90% and 95.88% in sugar content, as well as 21.91% and 16.93% reduction in protein content were observed respectively in whole and defatted isolates. In most cases, the proposed models adequately describe the biochemical changes taking place during fermentation and are a promising approach for the formulation of tomato seed-based functional foods.}, }
@article {pmid27573830, year = {2016}, author = {Clayton, JB and Vangay, P and Huang, H and Ward, T and Hillmann, BM and Al-Ghalith, GA and Travis, DA and Long, HT and Tuan, BV and Minh, VV and Cabana, F and Nadler, T and Toddes, B and Murphy, T and Glander, KE and Johnson, TJ and Knights, D}, title = {Captivity humanizes the primate microbiome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {37}, pages = {10376-10381}, pmid = {27573830}, issn = {1091-6490}, support = {T32 DA007097/DA/NIDA NIH HHS/United States ; UL1 TR000114/TR/NCATS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics ; Diet ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; *Genetic Variation ; Humans ; Phylogeny ; Primates/genetics/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The primate gastrointestinal tract is home to trillions of bacteria, whose composition is associated with numerous metabolic, autoimmune, and infectious human diseases. Although there is increasing evidence that modern and Westernized societies are associated with dramatic loss of natural human gut microbiome diversity, the causes and consequences of such loss are challenging to study. Here we use nonhuman primates (NHPs) as a model system for studying the effects of emigration and lifestyle disruption on the human gut microbiome. Using 16S rRNA gene sequencing in two model NHP species, we show that although different primate species have distinctive signature microbiota in the wild, in captivity they lose their native microbes and become colonized with Prevotella and Bacteroides, the dominant genera in the modern human gut microbiome. We confirm that captive individuals from eight other NHP species in a different zoo show the same pattern of convergence, and that semicaptive primates housed in a sanctuary represent an intermediate microbiome state between wild and captive. Using deep shotgun sequencing, chemical dietary analysis, and chloroplast relative abundance, we show that decreasing dietary fiber and plant content are associated with the captive primate microbiome. Finally, in a meta-analysis including published human data, we show that captivity has a parallel effect on the NHP gut microbiome to that of Westernization in humans. These results demonstrate that captivity and lifestyle disruption cause primates to lose native microbiota and converge along an axis toward the modern human microbiome.}, }
@article {pmid27573122, year = {2016}, author = {Girguis, P}, title = {Microbial ecology: Here, there and everywhere.}, journal = {Nature microbiology}, volume = {1}, number = {8}, pages = {16123}, pmid = {27573122}, issn = {2058-5276}, mesh = {*Ecology ; *Environmental Microbiology ; }, }
@article {pmid27572842, year = {2016}, author = {Garren, M}, title = {Microbial ecology: Algae feed a shift on coral reefs.}, journal = {Nature microbiology}, volume = {1}, number = {6}, pages = {16061}, pmid = {27572842}, issn = {2058-5276}, mesh = {Animals ; *Anthozoa ; *Coral Reefs ; Ecology ; Ecosystem ; Eukaryota ; Fishes ; Population Dynamics ; Seaweed ; }, }
@article {pmid27572670, year = {2016}, author = {Pieper, R and Villodre Tudela, C and Taciak, M and Bindelle, J and Pérez, JF and Zentek, J}, title = {Health relevance of intestinal protein fermentation in young pigs.}, journal = {Animal health research reviews}, volume = {17}, number = {2}, pages = {137-147}, doi = {10.1017/S1466252316000141}, pmid = {27572670}, issn = {1475-2654}, mesh = {Animal Nutritional Physiological Phenomena ; Animals ; Dietary Proteins/*metabolism ; Fermentation ; Intestinal Mucosa/*metabolism ; Swine/*metabolism ; }, abstract = {The physiological role of the gastrointestinal microbiota has become an important subject of nutrition research in pigs in the past years, and the importance of intestinal microbial activity in the etiology of disease is doubtless. This review summarizes the recent knowledge related to the microbial ecology of protein fermentation and the appearance of protein-derived metabolites along the pig intestine. The amount of fermentable protein depends on factors such as dietary protein concentration, protein digestibility due to secondary or tertiary structure, the interaction with dietary compounds or anti-nutritional factors, and the secretion of endogenous proteins into the gut lumen. High protein diets increase the luminal concentrations and epithelial exposure to putatively toxic metabolites and increase the risk for post-weaning diarrhea, but the mechanisms are not yet clarified. Although the use of fermentable carbohydrates to reduce harmful protein-derived metabolites in pigs is well-established, recent studies suggest that the inclusion of fermentable carbohydrates into diets with low protein digestibility or high dietary protein level may not ameliorate all negative effects with regard to epithelial response. Based on the current knowledge, the use of diets with low levels of high-quality protein may help to reduce the risk for intestinal disease in young pigs.}, }
@article {pmid27571981, year = {2016}, author = {Schimel, J}, title = {Microbial ecology: Linking omics to biogeochemistry.}, journal = {Nature microbiology}, volume = {1}, number = {}, pages = {15028}, pmid = {27571981}, issn = {2058-5276}, mesh = {*Ecology ; *Ecosystem ; Metagenomics ; Microbial Consortia ; Proteomics ; }, }
@article {pmid27571977, year = {2016}, author = {Kolter, R and van Wezel, GP}, title = {Goodbye to brute force in antibiotic discovery?.}, journal = {Nature microbiology}, volume = {1}, number = {}, pages = {15020}, pmid = {27571977}, issn = {2058-5276}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Drug Discovery ; *Drug Resistance, Bacterial ; }, }
@article {pmid27568187, year = {2017}, author = {Xie, J and Strobel, G and Xu, WF and Chen, J and Ren, HS and An, DJ and Geary, B}, title = {Fungi as Architects of the Rimstone Dams in Huanglong, NSD, Sichuan, China.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {29-38}, pmid = {27568187}, issn = {1432-184X}, mesh = {Ascomycota/classification/*isolation &amp; purification ; Biodiversity ; Calcium Carbonate/*metabolism ; China ; Cold Temperature ; Crystallization ; Diatoms/*isolation &amp; purification ; Microscopy, Electron, Scanning ; Mortierella/classification/*isolation &amp; purification ; Phycomyces/classification/*isolation &amp; purification ; Pseudomonas/classification/*isolation &amp; purification ; Rivers ; Water Microbiology ; }, abstract = {The Huanglong park area of the Sichuan Province of China is a unique scenic area of the world. It is known for its thousands of aquamarine-colored pools that are formed behind naturally formed rimstone dams of travertine (calcite) along a cold water stream. The travertine, based on its crystalline structural analysis, is of biological origin. This makes sense since the temperature of the waters of Huanglong varies from 5 to 7 °C and thus geochemical crystallization does not occur as it does in other locations around the world possessing thermal pools whose structures are primarily formed through cooling processes. Fungi and bacteria were discovered associated with both leaves associated with the calcite dams as well as in the older parts of well-established dams. Several species of Phytium, a phycomycete and an endophyte, accounted for over 45 % of all of the fungi successfully isolated from the well-established dam samples and at least 85 % in the floating leaf samples. Saprolegnia spp. (Phycomycetes) along with Phoma spp. (Ascomycetes) were noted along with Mortierella sp. as other dam-associated fungi. The fungal hyphae observed on dead leaf material as well as in the calcite dams directly served as nucleation points for the formation of crystalline CaCO3. Eventually, these crystals grow large enough to fuse to make calcite plates which form the main structural feature of all of the travertine dams in this area. Interestingly, each of the individual crystals associated with the dams has an associated hole in its core where a fungal hypha used to reside as observed by scanning electron microscopy. While diatoms were present in the analysis, they too seem to contribute to the structure of the dams but in a minor way. The only bacteria isolated from the older dam of this aquatic environment were Pseudomonas spp. and their role in dam formation is uncertain. Huanglong is a unique and beautiful place, and the water features present in this area can definitely be attributed to those fungal architects that encourage calcite crystal formation.}, }
@article {pmid27568186, year = {2017}, author = {Garcia-Mazcorro, JF and Castillo-Carranza, SA and Guard, B and Gomez-Vazquez, JP and Dowd, SE and Brigthsmith, DJ}, title = {Comprehensive Molecular Characterization of Bacterial Communities in Feces of Pet Birds Using 16S Marker Sequencing.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {224-235}, pmid = {27568186}, issn = {1432-184X}, mesh = {Actinobacteria/classification/genetics/*isolation &amp; purification ; Animals ; Birds/*microbiology ; Feces/microbiology ; Firmicutes/classification/genetics/*isolation &amp; purification ; Lactobacillaceae/classification/genetics/*isolation &amp; purification ; Microbiota ; Pets/*microbiology ; Proteobacteria/classification/genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Birds and other animals live and evolve in close contact with millions of microorganisms (microbiota). While the avian microbiota has been well characterized in domestic poultry, the microbiota of other bird species has been less investigated. The aim of this study was to describe the fecal bacterial communities of pet birds. Pooled fecal samples from 22 flocks representing over 150 individual birds of three different species (Melopsittacus undulatus or budgerigars, Nymphicus hollandicus or cockatiels, and Serinus canaria or domestic canaries) were used for analysis using the 16S rRNA gene sequencing in the MiSeq platform (Illumina). Firmicutes was the most abundant phylum (median 88.4 %; range 12.9-98.4 %) followed by other low-abundant phyla such as Proteobacteria (median 2.3 %; 0.1-85.3 %) and Actinobacteria (median 1.7 %; 0-18.3 %). Lactobacillaceae (mostly Lactobacillus spp.) was the most abundant family (median 78.1 %; 1.4-97.5 %), especially in budgerigars and canaries, and it deserves attention because of the ascribed beneficial properties of lactic acid bacteria. Importantly, feces from birds contain intestinal, urinary, and reproductive-associated microbiota thus posing a serious problem to study one anatomical region at a time. Other groups of interest include the family Clostridiaceae that showed very low abundance (overall median <0.1 %) with the exception of two samples from cockatiels (14 and 45.9 %) and one sample from budgerigars (19.9 %). Analysis of UniFrac metrics showed that overall, the microbial communities from the 22 flocks tended to cluster together for each bird species, meaning each species shed distinctive bacterial communities in feces. This descriptive analysis provides insight into the fecal microbiota of pet birds.}, }
@article {pmid27567944, year = {2016}, author = {Kumari, U and Srivastava, N and Shelly, A and Khatri, P and N, S and Singh, DK and Mazumder, S}, title = {Inducible headkidney cytochrome P450 contributes to endosulfan immunotoxicity in walking catfish Clarias gariepinus.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {179}, number = {}, pages = {44-54}, doi = {10.1016/j.aquatox.2016.08.009}, pmid = {27567944}, issn = {1879-1514}, mesh = {Animals ; Biotransformation ; Catfishes/*metabolism ; Cytochrome P-450 Enzyme Inhibitors/metabolism ; Cytochrome P-450 Enzyme System/analysis/genetics/*metabolism ; Endosulfan/analogs &amp; derivatives/metabolism/*toxicity ; Immunoassay ; Kidney/cytology/metabolism/pathology ; Leukocytes/cytology/drug effects/metabolism ; Male ; RNA, Messenger/metabolism ; Real-Time Polymerase Chain Reaction ; Water Pollutants, Chemical/chemistry/metabolism/*toxicity ; }, abstract = {The effect of endosulfan metabolites on fish immune system is not well known. It is also not clear whether endosulfan accumulates in fish immune organs and undergoes metabolic biotransformation in situ. In the present study we investigated the role of headkidney (HK), an important fish immune organ on endosulfan metabolism and the long term effects of endosulfan metabolites on the fish immune system. C. gariepinus (walking catfish) were exposed to 2.884ppb of endosulfan (1/10th LC50) for 30d followed by their maintenance in endosulfan-free water for 30d for recovery. Endosulfan induced time-dependent reduction in the HK somatic index and histo-pathological changes in renal and hemopoietic components of the organ. At cellular level, exposure to endosulfan led to death of HK leucocytes. Gas-liquid-chromatography documented the presence of both α- and β-isomers of endosulfan along with the toxic metabolite endosulfan sulfate (ESS) in the HK of exposed fishes. We report that β-endosulfan accumulates more readily in the HK. Depuration studies suggested the persistence of ESS in the HK. Enzyme-immunoassay and qPCR results demonstrated direct relationship between cytochrome P450 1A (CYP1A) expression and ESS levels in the HK. Pre-treatment of HKL with CYP1A specific inhibitor α-Naphthoflavone (ANF) led to reduction in CYP1A mRNA, protein levels, and inhibited ESS formation together implicating the role of CYP1A on endosulfan metabolism. When the exposed fish were transferred to endosulfan-free water ('recovered fish') it was observed that after 30d of recovery period the concentration of endosulfan and its metabolite in the HK were significantly reduced, compared to 30-d exposed fish. We also observed improvement in HK histo-architecture but no significant recovery in HKL number and viability. Collectively, our findings suggest that HK plays an important role in endosulfan metabolism. We propose that endosulfan induces the activation of CYP1A in HK which led to the generation of persistent metabolite, ESS, resulting in immunotoxicity.}, }
@article {pmid27567683, year = {2016}, author = {Ren, T and Wu, M}, title = {PhyloCore: A phylogenetic approach to identifying core taxa in microbial communities.}, journal = {Gene}, volume = {593}, number = {2}, pages = {330-333}, pmid = {27567683}, issn = {1879-0038}, support = {R01 GM108501/GM/NIGMS NIH HHS/United States ; }, mesh = {*Algorithms ; Microbiota/*genetics ; *Phylogeny ; }, abstract = {BACKGROUND: Identifying core microbiota is an important step for understanding the key components of microbial communities. Traditional approach that identifies core taxa at the OTU level ignores potential ecological coherence of higher rank taxa. There is a need to develop software that can systematically identify core taxa at and above the species level.<br><br>RESULTS: Here we developed PhyloCore, an application that uses a phylogeny-based algorithm to identify core taxa at the proper taxonomic levels. It incorporates a number of features that users can set according to their needs. Using multiple gut microbiota as test cases, we demonstrate that PhyloCore is more powerful and flexible than OTU-based approaches.<br><br>CONCLUSIONS: PhyloCore is a flexible and fast application that identifies core taxa at proper taxonomic levels, making it useful to sequence-based microbial ecology studies. The software is freely available at http://wolbachia.biology.virginia.edu/WuLab/Software.html.}, }
@article {pmid27566409, year = {2016}, author = {Kanoksilapatham, W and Pasomsup, P and Keawram, P and Cuecas, A and Portillo, MC and Gonzalez, JM}, title = {Fervidobacterium thailandense sp. nov., an extremely thermophilic bacterium isolated from a hot spring.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {66}, number = {12}, pages = {5023-5027}, doi = {10.1099/ijsem.0.001463}, pmid = {27566409}, issn = {1466-5034}, mesh = {Bacteria/*chemistry/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Fatty Acids/chemistry ; Geologic Sediments/microbiology ; Hot Springs/*microbiology ; Hot Temperature ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Thailand ; }, abstract = {Strain FC2004T, a strictly anaerobic, extremely thermophilic heterotroph, was isolated from a hot spring in Thailand. Typical cells of strain FC2004T were rod shaped (0.5-0.6×1.1-2.5 µm) with an outer membrane swelling out over an end. Filaments (10-30 µm long) and membrane-bound spheroids containing two or more cells inside (3-8 µm in diameter) were observed. The temperature range for growth was 60-88°C (optimum 78-80°C), pH range was 6.5-8.5 (optimum pH 7.5) and NaCl concentration range was 0 to <5 g l-1 (optimum 0.5 g l-1). S0 stimulated growth yield. S2O32- and NO3- did not influence growth. Glucose, maltose, sucrose, fructose, cellobiose, CM-cellulose and starch were utilized for growth. The membrane was composed mainly of the saturated fatty acids C16:0 and C18:0. The DNA G+C content was 45.8 mol%. The 16S rRNA gene sequence of strain FC2004T revealed highest similarity to species of the genus Fervidobacterium: F. pennivorans DSM 9078T (97-96 %), F. islandicum AW-1 (96 %), F. changbaicum CBS-1T (96 %), F. islandicum H21T (95 %), F. nodosum Rt17-B1T (95 %), F. riparium 1445tT (95 %) and F. gondwanense AB39T (93 %). Phylogenetic analysis of 16S rRNA gene sequences and average nucleotide identity analysis suggested that strain FC2004T represented a novel species within the genus Fervidobacterium, for which the name Fervidobacterium thailandense sp. nov. is proposed. The type strain is FC2004T (=JCM 18757T=ATCC BAA-2483T).}, }
@article {pmid27565613, year = {2016}, author = {Levy, AT and Lee, KH and Hanson, TE}, title = {Chlorobaculum tepidum Modulates Amino Acid Composition in Response to Energy Availability, as Revealed by a Systematic Exploration of the Energy Landscape of Phototrophic Sulfur Oxidation.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {21}, pages = {6431-6439}, pmid = {27565613}, issn = {1098-5336}, support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acids/*chemistry/metabolism ; Biomass ; Chlorobi/growth &amp; development/*metabolism ; Electrons ; Light ; Oxidation-Reduction ; *Phototrophic Processes ; Proteome ; Stress, Physiological ; Sulfur/*metabolism ; }, abstract = {UNLABELLED: Microbial sulfur metabolism, particularly the formation and consumption of insoluble elemental sulfur (S[0]), is an important biogeochemical engine that has been harnessed for applications ranging from bioleaching and biomining to remediation of waste streams. Chlorobaculum tepidum, a low-light-adapted photoautolithotrophic sulfur-oxidizing bacterium, oxidizes multiple sulfur species and displays a preference for more reduced electron donors: sulfide > S[0] > thiosulfate. To understand this preference in the context of light energy availability, an "energy landscape" of phototrophic sulfur oxidation was constructed by varying electron donor identity, light flux, and culture duration. Biomass and cellular parameters of C. tepidum cultures grown across this landscape were analyzed. From these data, a correction factor for colorimetric protein assays was developed, enabling more accurate biomass measurements for C. tepidum, as well as other organisms. C. tepidum's bulk amino acid composition correlated with energy landscape parameters, including a tendency toward less energetically expensive amino acids under reduced light flux. This correlation, paired with an observation of increased cell size and storage carbon production under electron-rich growth conditions, suggests that C. tepidum has evolved to cope with changing energy availability by tuning its proteome for energetic efficiency and storing compounds for leaner times.<br><br>IMPORTANCE: How microbes cope with and adapt to varying energy availability is an important factor in understanding microbial ecology and in designing efficient biotechnological processes. We explored the response of a model phototrophic organism, Chlorobaculum tepidum, across a factorial experimental design that enabled simultaneous variation and analysis of multiple growth conditions, what we term the "energy landscape." C. tepidum biomass composition shifted toward less energetically expensive amino acids at low light levels. This observation provides experimental evidence for evolved efficiencies in microbial proteomes and emphasizes the role that energy flux may play in the adaptive responses of organisms. From a practical standpoint, our data suggest that bulk biomass amino acid composition could provide a simple proxy to monitor and identify energy stress in microbial systems.}, }
@article {pmid27562270, year = {2016}, author = {Boetius, A}, title = {Microbial ecology: Seeing growth without culture.}, journal = {Nature microbiology}, volume = {1}, number = {9}, pages = {16158}, pmid = {27562270}, issn = {2058-5276}, mesh = {Archaea/*growth &amp; development ; Archaeal Proteins/analysis ; Bacteria/*growth &amp; development ; Bacterial Proteins/analysis ; Ecology ; Methane/metabolism ; *Microbial Consortia ; *Microbiological Techniques ; RNA, Ribosomal/analysis ; }, }
@article {pmid27562259, year = {2016}, author = {Weiss, MC and Sousa, FL and Mrnjavac, N and Neukirchen, S and Roettger, M and Nelson-Sathi, S and Martin, WF}, title = {The physiology and habitat of the last universal common ancestor.}, journal = {Nature microbiology}, volume = {1}, number = {9}, pages = {16116}, pmid = {27562259}, issn = {2058-5276}, mesh = {Anaerobiosis ; Archaea/*genetics/physiology ; Autotrophic Processes ; Bacteria/*genetics ; Bacterial Physiological Phenomena ; Biological Evolution ; Cluster Analysis ; DNA Methylation ; Ecology ; Ecosystem ; Genome, Microbial/*genetics ; Origin of Life ; Phylogeny ; Prokaryotic Cells ; Proteins/classification/*genetics ; }, abstract = {The concept of a last universal common ancestor of all cells (LUCA, or the progenote) is central to the study of early evolution and life's origin, yet information about how and where LUCA lived is lacking. We investigated all clusters and phylogenetic trees for 6.1 million protein coding genes from sequenced prokaryotic genomes in order to reconstruct the microbial ecology of LUCA. Among 286,514 protein clusters, we identified 355 protein families (∼0.1%) that trace to LUCA by phylogenetic criteria. Because these proteins are not universally distributed, they can shed light on LUCA's physiology. Their functions, properties and prosthetic groups depict LUCA as anaerobic, CO2-fixing, H2-dependent with a Wood-Ljungdahl pathway, N2-fixing and thermophilic. LUCA's biochemistry was replete with FeS clusters and radical reaction mechanisms. Its cofactors reveal dependence upon transition metals, flavins, S-adenosyl methionine, coenzyme A, ferredoxin, molybdopterin, corrins and selenium. Its genetic code required nucleoside modifications and S-adenosyl methionine-dependent methylations. The 355 phylogenies identify clostridia and methanogens, whose modern lifestyles resemble that of LUCA, as basal among their respective domains. LUCA inhabited a geochemically active environment rich in H2, CO2 and iron. The data support the theory of an autotrophic origin of life involving the Wood-Ljungdahl pathway in a hydrothermal setting.}, }
@article {pmid27561681, year = {2016}, author = {Chowdhury, G and Bhadra, RK and Bag, S and Pazhani, GP and Das, B and Basu, P and Nagamani, K and Nandy, RK and Mukhopadhyay, AK and Ramamurthy, T}, title = {Rugose atypical Vibrio cholerae O1 El Tor responsible for 2009 cholera outbreak in India.}, journal = {Journal of medical microbiology}, volume = {65}, number = {10}, pages = {1130-1136}, doi = {10.1099/jmm.0.000344}, pmid = {27561681}, issn = {1473-5644}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Biofilms ; Cholera/epidemiology/*microbiology ; Disease Outbreaks ; Genotype ; Humans ; India/epidemiology ; Microbial Sensitivity Tests ; Vibrio cholerae O1/classification/genetics/*isolation &amp; purification/physiology ; }, abstract = {Vibrio cholerae causes cholera outbreaks in endemic regions where the water quality and sanitation facilities remain poor. Apart from biotype and serotype changes, V. cholerae undergoes phase variation, which results in the generation of two morphologically different variants termed smooth and rugose. In this study, 12 rugose (R-VC) and 6 smooth (S-VC) V. cholerae O1 Ogawa isolates were identified in a cholera outbreak that occurred in Hyderabad, India. Antimicrobial susceptibility results showed that all the isolates were resistant to ampicillin, furazolidone and nalidixic acid. In addition, R-VC isolates were resistant to ciprofloxacin (92 %), streptomycin (92 %), erythromycin (83 %), trimethoprim-sulfamethoxazole (75 %) and tetracycline (75 %). Based on the ctxB gene analysis, all the isolates were identified as El Tor variant with mutation in two positions of ctxB, similar to the classical biotype. The R-VC isolates specifically showed excessive biofilm formation and were comparatively less motile. In addition, the majority of these isolates (~83 %) displayed random mutations in the hapR gene, which encodes haemagglutinin protease regulatory protein. In the PFGE analysis, R-VC and S-VC were placed in distinct clusters but remained clonally related. In the ribotyping analysis, all the R-VC isolates exhibited R-III pattern, which is a prevailing type among the current El Tor isolates. A hapR deletion mutant generated using an S-VC isolate expressed rugose phenotype. To our knowledge, this is the first report on the association of rugose V. cholerae O1 in a large cholera outbreak with extended antimicrobial resistance and random mutations in the haemagglutinin protease regulatory protein encoding gene (hapR).}, }
@article {pmid27559430, year = {2016}, author = {Everroad, RC and Stuart, RK and Bebout, BM and Detweiler, AM and Lee, JZ and Woebken, D and Prufert-Bebout, L and Pett-Ridge, J}, title = {Permanent draft genome of strain ESFC-1: ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria.}, journal = {Standards in genomic sciences}, volume = {11}, number = {1}, pages = {53}, pmid = {27559430}, issn = {1944-3277}, abstract = {The nonheterocystous filamentous cyanobacterium, strain ESFC-1, is a recently described member of the order Oscillatoriales within the Cyanobacteria. ESFC-1 has been shown to be a major diazotroph in the intertidal microbial mat system at Elkhorn Slough, CA, USA. Based on phylogenetic analyses of the 16S RNA gene, ESFC-1 appears to belong to a unique, genus-level divergence; the draft genome sequence of this strain has now been determined. Here we report features of this genome as they relate to the ecological functions and capabilities of strain ESFC-1. The 5,632,035 bp genome sequence encodes 4914 protein-coding genes and 92 RNA genes. One striking feature of this cyanobacterium is the apparent lack of either uptake or bi-directional hydrogenases typically expected within a diazotroph. Additionally, a large genomic island is found that contains numerous low GC-content genes and genes related to extracellular polysaccharide production and cell wall synthesis and maintenance.}, }
@article {pmid27559027, year = {2016}, author = {Santiago-Rodriguez, TM and Fornaciari, G and Luciani, S and Dowd, SE and Toranzos, GA and Marota, I and Cano, RJ}, title = {Taxonomic and predicted metabolic profiles of the human gut microbiome in pre-Columbian mummies.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {11}, pages = {}, doi = {10.1093/femsec/fiw182}, pmid = {27559027}, issn = {1574-6941}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Adult ; Bacillales/*isolation &amp; purification ; Chagas Disease/diagnosis ; Clostridiales/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Protozoan/genetics ; Female ; Firmicutes/*isolation &amp; purification ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Leishmania donovani/genetics/*isolation &amp; purification ; Male ; Metabolome/genetics ; Metagenome/genetics ; Metagenomics/methods ; Mummies/*microbiology ; RNA, Ribosomal, 16S/genetics ; Trypanosoma cruzi/genetics/*isolation &amp; purification ; Young Adult ; }, abstract = {Characterization of naturally mummified human gut remains could potentially provide insights into the preservation and evolution of commensal and pathogenic microorganisms, and metabolic profiles. We characterized the gut microbiome of two pre-Columbian Andean mummies dating to the 10-15th centuries using 16S rRNA gene high-throughput sequencing and metagenomics, and compared them to a previously characterized gut microbiome of an 11th century AD pre-Columbian Andean mummy. Our previous study showed that the Clostridiales represented the majority of the bacterial communities in the mummified gut remains, but that other microbial communities were also preserved during the process of natural mummification, as shown with the metagenomics analyses. The gut microbiome of the other two mummies were mainly comprised by Clostridiales or Bacillales, as demonstrated with 16S rRNA gene amplicon sequencing, many of which are facultative anaerobes, possibly consistent with the process of natural mummification requiring low oxygen levels. Metagenome analyses showed the presence of other microbial groups that were positively or negatively correlated with specific metabolic profiles. The presence of sequences similar to both Trypanosoma cruzi and Leishmania donovani could suggest that these pathogens were prevalent in pre-Columbian individuals. Taxonomic and functional profiling of mummified human gut remains will aid in the understanding of the microbial ecology of the process of natural mummification.}, }
@article {pmid27558787, year = {2017}, author = {Taketani, RG and Lançoni, MD and Kavamura, VN and Durrer, A and Andreote, FD and Melo, IS}, title = {Dry Season Constrains Bacterial Phylogenetic Diversity in a Semi-Arid Rhizosphere System.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {153-161}, pmid = {27558787}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Biodiversity ; Brazil ; Droughts ; Fabaceae/*microbiology ; Microbiota/*genetics/physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rain ; *Rhizosphere ; Seasons ; *Soil Microbiology ; }, abstract = {The rhizosphere is viewed as a deterministic environment led by the interaction between plants and microorganisms. In the case of semi-arid plants, this interaction is strengthened by the harshness of the environment. We tested the hypothesis that dry season represents a constraint on the bacterial diversity of the rhizosphere from semi-arid plants. To accomplish this, we sampled two leguminous species at five locations during the dry and rainy seasons in the Caatinga biome and characterised bacterial community structures using qPCR and 16S rRNA sequencing. We found that the main differences between seasons were due to reduced phylogenetic diversity caused by dryness. Variation partitioning indicated that environmental characteristics significant impacts in β-diversity. Additionally, distance decay relationship and taxa area relationship indicate a higher spatial turnover at the rainy season. During the dry season, decreased bacterial abundance is likely due to the selection of resistant or resilient microorganisms; with the return of the rain, the sensitive populations start to colonise the rhizosphere by a process that is strongly influenced by environmental characteristics. Thus, we propose that the reduction of PD and strong influence of environmental parameters on the assemblage of these communities make them prone to functional losses caused by climatic disturbances.}, }
@article {pmid27555841, year = {2016}, author = {Ghosh, R and Sharma, NC and Halder, K and Bhadra, RK and Chowdhury, G and Pazhani, GP and Shinoda, S and Mukhopadhyay, AK and Nair, GB and Ramamurthy, T}, title = {Phenotypic and Genetic Heterogeneity in Vibrio cholerae O139 Isolated from Cholera Cases in Delhi, India during 2001-2006.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1250}, pmid = {27555841}, issn = {1664-302X}, abstract = {Incidence of epidemic Vibrio cholerae serogroup O139 has declined in cholera endemic countries. However, sporadic cholera caused by V. cholerae O139 with notable genetic changes is still reported from many regions. In the present study, 42 V. cholerae O139 strains isolated from 2001 to 2006 in Delhi, India, were retrospectively analyzed to understand their phenotype and molecular characteristics. The majority of isolates were resistant to ampicillin, furazolidone and nalidixic acid. Though the integrative conjugative element was detected in all the O139 isolates, the 2004-2006 isolates remained susceptible to co-trimoxazole, chloramphenicol, and streptomycin. Cholera toxin genotype 1 was present in the majority of the O139 isolates while few had type 3 or a novel type 4. In the cholera toxin encoding gene (ctx) restriction fragment length polymorphism, the majority of the isolates harbored three copies of CTX element, of which one was truncated. In this study, the ctx was detected for the first time in the small chromosome of V. cholerae O139 and one isolate harbored 5 copies of CTX element, of which 3 were truncated. The ribotype BII pattern was found in most of the O139 isolates. Three V. cholerae O139 isolated in 2001 had a new ribotype BVIII. Pulsed-field gel electrophoresis analysis revealed clonal variation in 2001 isolates compared to the 2004-2006 isolates. Molecular changes in V. cholerae O139 have to be closely monitored as this information may help in understanding the changing genetic features of this pathogen in relation to the epidemiology of cholera.}, }
@article {pmid27550165, year = {2016}, author = {Trumbo, ST}, title = {Carcass Age and Reproductive Costs for Nicrophorus orbicollis (Coleoptera: Silphidae).}, journal = {Environmental entomology}, volume = {45}, number = {5}, pages = {1178-1183}, doi = {10.1093/ee/nvw114}, pmid = {27550165}, issn = {1938-2936}, mesh = {Animals ; Coleoptera/growth &amp; development/*physiology ; Female ; Longevity ; Reproduction ; }, abstract = {The life history costs of living in microbially dense environments can be high. To assess the importance of these costs for natural selection, it is necessary to know how costs vary with environmental conditions. Adult burying beetles prepare vertebrate carcasses of varying age and states of deterioration as a resource for their young. In the present study, Nicrophorus orbicollis Say females were presented with either fresh or aged (80 h) large carcasses (30-39 g) to examine effects on their lifetime reproductive success (four reproductive attempts) and survival. Reproductive success and survival were also measured for female offspring that developed on fresh and aged carcasses. Carcass age had no measurable effect on lifetime reproductive output or life span of either parents or their adult offspring. In a separate experiment using medium-sized carcasses (22-24 g), the reproductive performance of females in a single reproductive attempt was negatively affected by carcass age (13.9% less brood mass). The results suggest that the costs of using a single older carcass are relatively minor when measured over a lifetime. Alternative costs of using older carcasses and explanations for the complex antimicrobial traits of burying beetles are discussed.}, }
@article {pmid27549116, year = {2016}, author = {Keiblinger, KM and Fuchs, S and Zechmeister-Boltenstern, S and Riedel, K}, title = {Soil and leaf litter metaproteomics-a brief guideline from sampling to understanding.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {11}, pages = {}, pmid = {27549116}, issn = {1574-6941}, support = {P 25438/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Ecosystem ; Environment ; Mass Spectrometry ; *Microbiota ; Plant Leaves/chemistry/*metabolism/*microbiology ; Proteome/*analysis ; Proteomics/*methods ; Soil ; Soil Microbiology ; }, abstract = {The increasing application of soil metaproteomics is providing unprecedented, in-depth characterization of the composition and functionality of in situ microbial communities. Despite recent advances in high-resolution mass spectrometry, soil metaproteomics still suffers from a lack of effective and reproducible protein extraction protocols and standardized data analyses. This review discusses the opportunities and limitations of selected techniques in soil-, and leaf litter metaproteomics, and presents a step-by-step guideline on their application, covering sampling, sample preparation, extraction and data evaluation strategies. In addition, we present recent applications of soil metaproteomics and discuss how such approaches, linking phylogenetics and functionality, can help gain deeper insights into terrestrial microbial ecology. Finally, we strongly recommend that to maximize the insights environmental metaproteomics may provide, such methods should be employed within a holistic experimental approach considering relevant aboveground and belowground ecosystem parameters.}, }
@article {pmid27548377, year = {2016}, author = {Di Cesare, A and Fontaneto, D and Doppelbauer, J and Corno, G}, title = {Fitness and Recovery of Bacterial Communities and Antibiotic Resistance Genes in Urban Wastewaters Exposed to Classical Disinfection Treatments.}, journal = {Environmental science &amp; technology}, volume = {50}, number = {18}, pages = {10153-10161}, doi = {10.1021/acs.est.6b02268}, pmid = {27548377}, issn = {1520-5851}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Disinfection ; Drug Resistance, Microbial/genetics ; Genes, Bacterial/drug effects ; Humans ; Wastewater/*chemistry ; }, abstract = {Antibiotic resistance genes (ARGs) are increasingly appreciated to be important as micropollutants. Indirectly produced by human activities, they are released into the environment, as they are untargeted by conventional wastewater treatments. In order to understand the fate of ARGs and of other resistant forms (e.g., phenotypical adaptations) in urban wastewater treatment plants (WWTPs), we monitored three WWTPs with different disinfection processes (chlorine, peracetic acid (PAA), and ultraviolet light (UV)). We monitored WWTPs influx and pre- and postdisinfection effluent over 24 h, followed by incubation experiments lasting for 96 h. We measured bacterial abundance, size distribution and aggregational behavior, the proportion of intact (active) cells, and the abundances of four ARGs and of the mobile element integron1. While all the predisinfection treatments of all WWTPs removed the majority of bacteria and of associated ARGs, of the disinfection processes only PAA efficiently removed bacterial cells. However, the stress imposed by PAA selected for bacterial aggregates and, similarly to chlorine, stimulated the selection of ARGs during the incubation experiment. This suggests disinfections based on chemically aggressive destruction of bacterial cell structures can promote a residual microbial community that is more resistant to antibiotics and, given the altered aggregational behavior, to competitive stress in nature.}, }
@article {pmid27548162, year = {2016}, author = {Alkhalili, RN and Bernfur, K and Dishisha, T and Mamo, G and Schelin, J and Canbäck, B and Emanuelsson, C and Hatti-Kaul, R}, title = {Antimicrobial Protein Candidates from the Thermophilic Geobacillus sp. Strain ZGt-1: Production, Proteomics, and Bioinformatics Analysis.}, journal = {International journal of molecular sciences}, volume = {17}, number = {8}, pages = {}, pmid = {27548162}, issn = {1422-0067}, mesh = {Anti-Infective Agents/chemistry/metabolism ; Bacterial Proteins/chemistry/metabolism ; Computational Biology/*methods ; Geobacillus/*metabolism ; Hot Temperature ; Proteomics/*methods ; }, abstract = {A thermophilic bacterial strain, Geobacillus sp. ZGt-1, isolated from Zara hot spring in Jordan, was capable of inhibiting the growth of the thermophilic G. stearothermophilus and the mesophilic Bacillus subtilis and Salmonella typhimurium on a solid cultivation medium. Antibacterial activity was not observed when ZGt-1 was cultivated in a liquid medium; however, immobilization of the cells in agar beads that were subjected to sequential batch cultivation in the liquid medium at 60 °C showed increasing antibacterial activity up to 14 cycles. The antibacterial activity was lost on protease treatment of the culture supernatant. Concentration of the protein fraction by ammonium sulphate precipitation followed by denaturing polyacrylamide gel electrophoresis separation and analysis of the gel for antibacterial activity against G. stearothermophilus showed a distinct inhibition zone in 15-20 kDa range, suggesting that the active molecule(s) are resistant to denaturation by SDS. Mass spectrometric analysis of the protein bands around the active region resulted in identification of 22 proteins with molecular weight in the range of interest, three of which were new and are here proposed as potential antimicrobial protein candidates by in silico analysis of their amino acid sequences. Mass spectrometric analysis also indicated the presence of partial sequences of antimicrobial enzymes, amidase, and dd-carboxypeptidase.}, }
@article {pmid27544677, year = {2017}, author = {Kosiba, J and Wilk-Woźniak, E and Krztoń, W and Strzesak, M and Pociecha, A and Walusiak, E and Pudaś, K and Szarek-Gwiazda, E}, title = {What Underpins the Trophic Networks of the Plankton in Shallow Oxbow Lakes?.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {17-28}, pmid = {27544677}, issn = {1432-184X}, mesh = {Animals ; Biomass ; Cyanobacteria/*classification ; Dinoflagellida/*classification ; *Food Chain ; Lakes/microbiology ; Phytoplankton/*classification ; Poland ; Water Microbiology ; Zooplankton/*classification ; }, abstract = {The aim of this study was to determine the relationships in the microbial trophic network underpinning them about communities of plankton ciliates in shallow oxbow lakes of the Vistula River in southern Poland (Jeziorzany 1, Jeziorzany 2, Piekary, Tyniec). The plankton components (phytoplankton, ciliates, zooplankton) were grouped by dietary preference. The studied oxbows differed in physicochemical parameters and in phytoplankton. Cyanobacteria dominated in the total biomass of phytoplankton in the Tyniec oxbow, big green algae (>30 μm) in Piekary and Jeziorzany 1, and euglenoids in Jeziorzany 2 oxbow. The dominance pattern of ciliates and zooplankton were similar in all oxbows. Algivorous ciliates were the main dominant ciliates, and among zooplankton the dominant ones were herbivores that feed on small algae (<30 μm). The oxbows differed significantly in total phytoplankton biomass, cyanobacteria biomass, euglenoid biomass, small green algae (<30 μm) biomass, total biomass of zooplankton, biomass of zooplankton feeding on bacteria + algae, and biomass of zooplankton feeding on big algae (>30 μm). There was no significant differences in ciliate biomass between oxbows. In redundancy analyses, the variability at the trophic groups of plankton was described by explanatory variables in 42.3 %, and positive relationships were found: e.g., between omnivorous zooplankton biomass, the biomass of ciliates feeding on bacteria + algae, and NH4 level; between euglenoid biomass and dinoflagellate biomass; and between cyanobacteria biomass and bacterivorous ciliate biomass. Spearman correlation analysis revealed several relationships between different groups of plankton. In general, phytoplankton group shows more connection among themselves and with different zooplankton groups, e.g., phytoplankton biomass with herbivorous zooplankton biomass (-0.33); and cyanobacteria biomass with dinoflagellate biomass (0.65). Ciliates showed more connections among their trophic groups (e.g., algivorous ciliate biomass with omnivorous ciliate biomass, 0.78) and with zooplankton trophic groups (e.g., biomass of algivorous + bacterivorous ciliates with biomass of predator zooplankton, -0.36). Simple correlations analysis revealed the trophic food web network connectivity among plankton organisms, indicating the flow of organic matter from phytoplankton to zooplankton and from ciliates to zooplankton. Our study sheds light on the trophic relations among plankton ciliates, which are neglected in research but often form a large percentage of zooplankton biomass. In the studied oxbows, ciliate forms 6.7 % of total zooplankton biomass in Jeziorzany 1 and up to 44.5 % of it in the Piekary oxbow.}, }
@article {pmid27543560, year = {2017}, author = {Maher, AMD and Asaiyah, MAM and Brophy, C and Griffin, CT}, title = {An Entomopathogenic Nematode Extends Its Niche by Associating with Different Symbionts.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {211-223}, pmid = {27543560}, issn = {1432-184X}, mesh = {Animals ; DNA, Intergenic/genetics ; Desiccation ; Host-Pathogen Interactions/*physiology ; Ireland ; Photorhabdus/genetics/*isolation &amp; purification/*physiology ; Rhabditoidea/*microbiology ; Symbiosis ; }, abstract = {Bacterial symbionts are increasingly recognised as mediators of ecologically important traits of their animal hosts, with acquisition of new traits possible by uptake of novel symbionts. The entomopathogenic nematode Heterorhabditis downesi associates with two bacterial symbionts, Photorhabdus temperata subsp. temperata and P. temperata subsp. cinerea. At one intensively studied coastal dune site, P. temperata subsp. cinerea is consistently more frequently isolated than P. temperata subsp. temperata in H. downesi recovered from under the bare sand/Ammophila arrenaria of the front dunes (where harsh conditions, including drought, prevail). This is not the case in the more permissive closed dune grassland further from the sea. No differences were detected in ITS1 (internal transcribed spacer) sequence between nematode lines carrying either of the two symbiont subspecies, nor did they differ in their ability to utilise insects from three orders. The two symbionts could be readily swapped between lines, and both were carried in equal numbers within infective juveniles. In laboratory experiments, we tested whether the symbionts differentially affected nematode survival in insect cadavers that were allowed to dry. We assessed numbers of nematode infective juveniles emerging from insects that had been infected with H. downesi carrying either symbiont subspecies and then allowed to desiccate for up to 62 days. In moist conditions, cadavers produced similar numbers of nematodes, irrespective of the symbiont subspecies present, while under desiccating conditions, P. temperata subsp. cinerea cadavers yielded more nematode progeny than P. temperata subsp. temperata cadavers. Desiccating cadavers with the same nematode isolates, carrying either one or the other symbiont subspecies, confirmed that the symbiont was responsible for differences in nematode survival. Moreover, cadavers harbouring P. temperata subsp. cinerea had a reduced rate of drying relative to cadavers harbouring P. temperata subsp. temperata. Our experiments support the hypothesis that H. downesi can extend its niche into harsher conditions by associating with P. temperata subsp. cinerea.}, }
@article {pmid27543321, year = {2016}, author = {Liao, J and Cao, X and Zhao, L and Wang, J and Gao, Z and Wang, MC and Huang, Y}, title = {The importance of neutral and niche processes for bacterial community assembly differs between habitat generalists and specialists.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {11}, pages = {}, doi = {10.1093/femsec/fiw174}, pmid = {27543321}, issn = {1574-6941}, mesh = {Adaptation, Physiological/*physiology ; Bacteria/*classification/genetics/*growth &amp; development/metabolism ; Base Sequence ; Biodiversity ; China ; DNA, Bacterial/genetics ; Ecosystem ; Lakes/*microbiology ; Microbiota/genetics ; Nitrogen ; Oxygen ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sequence Analysis, DNA ; Water Microbiology ; }, abstract = {The mechanisms of community assembly are a central focus in the field of microbial ecology. However, to what extent these mechanisms differ in importance by traits of groups is poorly understood. Here we quantified the importance of neutral and niche processes in community assembly for bacteria, habitat specialists and generalists in 21 plateau lakes of China. Results showed that both neutral and niche processes played a critical role in the assembly of entire bacterial communities, shaping a unique biogeographical pattern. A few habitat generalists and many specialists were identified. Interestingly, habitat specialists were only governed by niche process, with seven significant environmental variables-salinity, dissolved oxygen, water transparency, total phosphorus, ammonium-nitrogen, temperature and total nitrogen-independently explaining 40.3% of the biological variation. By contrast, habitat generalists were strongly driven by neutral process, with 50.9% of the variation of detection frequency explained in neutral community model. Only three environmental variables-salinity, total nitrogen and dissolved oxygen-significantly affected the distribution of habitat generalists, independently explaining 13.6% of the variation. Governed by different assembly mechanisms, habitat specialists and generalists presented disparate biogeographical patterns. Our result emphasizes the importance of investigating the bacterial community assembly at more refined levels than entire communities.}, }
@article {pmid27543320, year = {2016}, author = {Leiva, D and Clavero-León, C and Carú, M and Orlando, J}, title = {Intrinsic factors of Peltigera lichens influence the structure of the associated soil bacterial microbiota.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {11}, pages = {}, doi = {10.1093/femsec/fiw178}, pmid = {27543320}, issn = {1574-6941}, mesh = {Ascomycota/classification/genetics/*physiology ; Bacteria/classification/genetics/*metabolism ; *Bacterial Physiological Phenomena ; Lichens/metabolism/*microbiology ; Microbiota/*physiology ; Soil ; Soil Microbiology ; Symbiosis/*physiology ; }, abstract = {Definition of lichens has evolved from bi(tri)partite associations to multi-species symbioses, where bacteria would play essential roles. Besides, although soil bacterial communities are known to be affected by edaphic factors, when lichens grow upon them these could become less preponderant. We hypothesized that the structure of both the lichen microbiota and the microbiota in the soil underneath lichens is shaped by lichen intrinsic and extrinsic factors. In this work, intrinsic factors corresponded to mycobiont and cyanobiont identities of Peltigera lichens, metabolite diversity and phenoloxidase activity and extrinsic factors involved the site of the forest where lichens grow. Likewise, the genetic and metabolic structure of the lichen and soil bacterial communities were analyzed by fingerprinting. Among the results, metabolite diversity was inversely related to the genetic structure of bacterial communities of lichens and soils, highlighting the far-reaching effect of these substances; while phenoloxidase activity was inversely related to the metabolic structure only of the lichen bacterial microbiota, presuming a more limited effect of the products of these enzymes. Soil bacterial microbiota was different depending on the site and, strikingly, according to the cyanobiont present in the lichen over them, which could indicate an influence of the photobiont metabolism on the availability of soil nutrients.}, }
@article {pmid27542633, year = {2016}, author = {Bengtsson-Palme, J and Hammarén, R and Pal, C and Östman, M and Björlenius, B and Flach, CF and Fick, J and Kristiansson, E and Tysklind, M and Larsson, DGJ}, title = {Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics.}, journal = {The Science of the total environment}, volume = {572}, number = {}, pages = {697-712}, doi = {10.1016/j.scitotenv.2016.06.228}, pmid = {27542633}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/analysis ; Bacteria/drug effects/genetics ; DNA Transposable Elements ; Drug Resistance, Bacterial/drug effects/genetics ; *Drug Resistance, Microbial/drug effects/genetics ; Metagenomics/*methods ; Metals/analysis ; RNA, Ribosomal, 16S ; Selection, Genetic ; Sewage/*microbiology ; Sweden ; Waste Disposal, Fluid/*methods ; Water Pollutants, Chemical/analysis ; }, abstract = {Sewage treatment plants (STPs) have repeatedly been suggested as "hotspots" for the emergence and dissemination of antibiotic-resistant bacteria. A critical question still unanswered is if selection pressures within STPs, caused by residual antibiotics or other co-selective agents, are sufficient to specifically promote resistance. To address this, we employed shotgun metagenomic sequencing of samples from different steps of the treatment process in three Swedish STPs. In parallel, concentrations of selected antibiotics, biocides and metals were analyzed. We found that concentrations of tetracycline and ciprofloxacin in the influent were above predicted concentrations for resistance selection, however, there was no consistent enrichment of resistance genes to any particular class of antibiotics in the STPs, neither for biocide and metal resistance genes. The most substantial change of the bacterial communities compared to human feces occurred already in the sewage pipes, manifested by a strong shift from obligate to facultative anaerobes. Through the treatment process, resistance genes against antibiotics, biocides and metals were not reduced to the same extent as fecal bacteria. The OXA-48 gene was consistently enriched in surplus and digested sludge. We find this worrying as OXA-48, still rare in Swedish clinical isolates, provides resistance to carbapenems, one of our most critically important classes of antibiotics. Taken together, metagenomics analyses did not provide clear support for specific antibiotic resistance selection. However, stronger selective forces affecting gross taxonomic composition, and with that resistance gene abundances, limit interpretability. Comprehensive analyses of resistant/non-resistant strains within relevant species are therefore warranted.}, }
@article {pmid27540075, year = {2016}, author = {Keller-Costa, T and Silva, R and Lago-Lestón, A and Costa, R}, title = {Genomic Insights into Aquimarina sp. Strain EL33, a Bacterial Symbiont of the Gorgonian Coral Eunicella labiata.}, journal = {Genome announcements}, volume = {4}, number = {4}, pages = {}, pmid = {27540075}, issn = {2169-8287}, abstract = {To address the metabolic potential of symbiotic Aquimarina spp., we report here the genome sequence of Aquimarina sp. strain EL33, a bacterium isolated from the gorgonian coral Eunicella labiata This first-described (to our knowledge) animal-associated Aquimarina genome possesses a sophisticated repertoire of genes involved in drug/antibiotic resistance and biosynthesis.}, }
@article {pmid27540061, year = {2016}, author = {Ehsani, E and Barrantes, I and Vandermaesen, J and Geffers, R and Jarek, M and Boon, N and Springael, D and Pieper, DH and Vilchez-Vargas, R}, title = {Draft Genome Sequence of Aeromonas sp. Strain EERV15.}, journal = {Genome announcements}, volume = {4}, number = {4}, pages = {}, pmid = {27540061}, issn = {2169-8287}, abstract = {We report here the draft genome sequence of Aeromonas sp. strain EERV15 isolated from sand filter. The organism most closely related to Aeromonas sp. EERV15 is Aeromonas veronii B565, with an average 83% amino acid sequence similarity of putatively encoded protein open reading frames.}, }
@article {pmid27538875, year = {2017}, author = {De la Cruz-Barrón, M and Cruz-Mendoza, A and Navarro-Noya, YE and Ruiz-Valdiviezo, VM and Ortíz-Gutiérrez, D and Ramírez-Villanueva, DA and Luna-Guido, M and Thierfelder, C and Wall, PC and Verhulst, N and Govaerts, B and Dendooven, L}, title = {The Bacterial Community Structure and Dynamics of Carbon and Nitrogen when Maize (Zea mays L.) and Its Neutral Detergent Fibre Were Added to Soil from Zimbabwe with Contrasting Management Practices.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {135-152}, pmid = {27538875}, issn = {1432-184X}, mesh = {Bacteria/*metabolism ; Carbon/*metabolism ; Fertilizers/*analysis ; Microbiota ; Nitrogen/*metabolism ; Soil/*chemistry ; Soil Microbiology ; Zea mays/metabolism/*microbiology ; Zimbabwe ; }, abstract = {Water infiltration, soil carbon content, aggregate stability and yields increased in conservation agriculture practices compared to conventionally ploughed control treatments at the Henderson research station near Mazowe (Zimbabwe). How these changes in soil characteristics affect the bacterial community structure and the bacteria involved in the degradation of applied organic material remains unanswered. Soil was sampled from three agricultural systems at Henderson, i.e. (1) conventional mouldboard ploughing with continuous maize (conventional tillage), (2) direct seeding with a Fitarelli jab planter and continuous maize (direct seeding with continuous maize) and (3) direct seeding with a Fitarelli jab planter with rotation of maize sunn hemp (direct seeding with crop rotation). Soil was amended with young maize plants or their neutral detergent fibre (NDF) and incubated aerobically for 56 days, while C and N mineralization and the bacterial community structure were monitored. Bacillus (Bacillales), Micrococcaceae (Actinomycetales) and phylotypes belonging to the Pseudomonadales were first degraders of the applied maize plants. At day 3, Streptomyces (Actinomycetales), Chitinophagaceae ([Saprospirales]) and Dyella (Xanthomonadales) participated in the degradation of the applied maize and at day 7 Oxalobacteraceae (Burkholderiales). Phylotypes belonging to Halomonas (Oceanospirillales) were the first degraders of NDF and were replaced by Phenylobacterium (Caulobacterales) and phylotypes belonging to Pseudomonadales at day 3. Afterwards, similar bacterial groups were favoured by application of NDF as they were by the application of maize plants, but there were also clear differences. Phylotypes belonging to the Micrococcaceae and Bacillus did not participate in the degradation of NDF or its metabolic products, while phylotypes belonging to the Acidobacteriaceae participated in the degradation of NDF but not in that of maize plants. It was found that agricultural practices had a limited effect on the bacterial community structure, but application of organic material altered it substantially.}, }
@article {pmid27538874, year = {2017}, author = {Jorquera, MA and Maruyama, F and Ogram, AV and Navarrete, OU and Lagos, LM and Inostroza, NG and Acuña, JJ and Rilling, JI and de La Luz Mora, M}, title = {Erratum to: Rhizobacterial Community Structures Associated with Native Plants Grown in Chilean Extreme Environments.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {253}, doi = {10.1007/s00248-016-0830-9}, pmid = {27538874}, issn = {1432-184X}, }
@article {pmid27538873, year = {2017}, author = {Cutler, NA and Arróniz-Crespo, M and Street, LE and Jones, DL and Chaput, DL and DeLuca, TH}, title = {Long-Term Recovery of Microbial Communities in the Boreal Bryosphere Following Fire Disturbance.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {75-90}, pmid = {27538873}, issn = {1432-184X}, mesh = {Ascomycota/*classification/genetics/growth &amp; development ; Basidiomycota/*classification/genetics/growth &amp; development ; Bryophyta/growth &amp; development/*microbiology ; *Fires ; Microbiota/genetics ; Proteobacteria/*classification/genetics/growth &amp; development ; Sweden ; Taiga ; Trees/growth &amp; development/microbiology ; }, abstract = {Our study used a ∼360-year fire chronosequence in northern Sweden to investigate post-fire microbial community dynamics in the boreal bryosphere (the living and dead parts of the feather moss layer on the forest floor, along with the associated biota). We anticipated systematic changes in microbial community structure and growth strategy with increasing time since fire (TSF) and used amplicon pyrosequencing to establish microbial community structure. We also recorded edaphic factors (relating to pH, C and N accumulation) and the physical characteristics of the feather moss layer. The molecular analyses revealed an unexpectedly diverse microbial community. The structure of the community could be largely explained by just two factors, TSF and pH, although the importance of TSF diminished as the forest recovered from disturbance. The microbial communities on the youngest site (TSF = 14 years) were clearly different from older locations (>100 years), suggesting relatively rapid post-fire recovery. A shift towards Proteobacterial taxa on older sites, coupled with a decline in the relative abundance of Acidobacteria, suggested an increase in resource availability with TSF. Saprotrophs dominated the fungal community. Mycorrhizal fungi appeared to decline in abundance with TSF, possibly due to changing N status. Our study provided evidence for the decadal-scale legacy of burning, with implications for boreal forests that are expected to experience more frequent burns over the course of the next century.}, }
@article {pmid27538871, year = {2017}, author = {Li, S and Peng, C and Wang, C and Zheng, J and Hu, Y and Li, D}, title = {Microbial Succession and Nitrogen Cycling in Cultured Biofilms as Affected by the Inorganic Nitrogen Availability.}, journal = {Microbial ecology}, volume = {73}, number = {1}, pages = {1-15}, pmid = {27538871}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/*metabolism ; Biofilms/*growth &amp; development ; Biomass ; Chlorophyll/analysis ; Chlorophyll A ; Ecosystem ; Eutrophication ; Microbiota ; Nitrogen/chemistry ; Nitrogen Cycle/*physiology ; Phytoplankton/*classification/metabolism ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; }, abstract = {Biofilms play important roles in nutrients and energy cycling in aquatic ecosystems. We hypothesized that as eutrophication could change phytoplankton community and decrease phytoplankton diversity, ambient inorganic nitrogen level will affect the microbial community and diversity of biofilms and the roles of biofilms in nutrient cycling. Biofilms were cultured using a flow incubator either with replete inorganic nitrogen (N-rep) or without exogenous inorganic nitrogen supply (N-def). The results showed that the biomass and nitrogen and phosphorous accumulation of biofilms were limited by N deficiency; however, as expected, the N-def biofilms had significantly higher microbial diversity than that of N-rep biofilms. The microbial community of biofilms shifted in composition and abundance in response to ambient inorganic nitrogen level. For example, as compared between the N-def and the N-rep biofilms, the former consisted of more diazotrophs, while the latter consisted of more denitrifying bacteria. As a result of the shift of the functional microbial community, the N concentration of N-rep medium kept decreasing, while that of N-def medium showed an increasing trend in the late stage. This indicates that biofilms can serve as the source or the sink of nitrogen in aquatic ecosystems, and it depends on the inorganic nitrogen availability.}, }
@article {pmid27536290, year = {2016}, author = {Scoma, A and Yakimov, MM and Boon, N}, title = {Challenging Oil Bioremediation at Deep-Sea Hydrostatic Pressure.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1203}, pmid = {27536290}, issn = {1664-302X}, abstract = {The Deepwater Horizon accident has brought oil contamination of deep-sea environments to worldwide attention. The risk for new deep-sea spills is not expected to decrease in the future, as political pressure mounts to access deep-water fossil reserves, and poorly tested technologies are used to access oil. This also applies to the response to oil-contamination events, with bioremediation the only (bio)technology presently available to combat deep-sea spills. Many questions about the fate of petroleum-hydrocarbons within deep-sea environments remain unanswered, as well as the main constraints limiting bioremediation under increased hydrostatic pressures and low temperatures. The microbial pathways fueling oil bioassimilation are unclear, and the mild upregulation observed for beta-oxidation-related genes in both water and sediments contrasts with the high amount of alkanes present in the spilled oil. The fate of solid alkanes (tar), hydrocarbon degradation rates and the reason why the most predominant hydrocarbonoclastic genera were not enriched at deep-sea despite being present at hydrocarbon seeps at the Gulf of Mexico have been largely overlooked. This mini-review aims at highlighting the missing information in the field, proposing a holistic approach where in situ and ex situ studies are integrated to reveal the principal mechanisms accounting for deep-sea oil bioremediation.}, }
@article {pmid27535039, year = {2016}, author = {Volant, A and Héry, M and Desoeuvre, A and Casiot, C and Morin, G and Bertin, PN and Bruneel, O}, title = {Spatial Distribution of Eukaryotic Communities Using High-Throughput Sequencing Along a Pollution Gradient in the Arsenic-Rich Creek Sediments of Carnoulès Mine, France.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {608-620}, pmid = {27535039}, issn = {1432-184X}, mesh = {Alveolata/classification/genetics/isolation &amp; purification ; Arsenic/*analysis ; Base Sequence ; *Biodiversity ; Classification ; DNA ; Ecology ; Ecosystem ; Environmental Pollution/*analysis ; Eukaryota/*classification/*genetics/*isolation &amp; purification ; France ; Fungi/classification/genetics/isolation &amp; purification ; Geologic Sediments/*chemistry ; *High-Throughput Screening Assays ; Hydrogen-Ion Concentration ; Mining ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Rivers ; Sequence Analysis ; Stramenopiles/classification/genetics/isolation &amp; purification ; Viridiplantae/classification/genetics ; Water Pollutants, Chemical/analysis ; Water Pollution ; }, abstract = {Microscopic eukaryotes play a key role in ecosystem functioning, but their diversity remains largely unexplored in most environments. To advance our knowledge of eukaryotic microorganisms and the factors that structure their communities, high-throughput sequencing was used to characterize their diversity and spatial distribution along the pollution gradient of the acid mine drainage at Carnoulès (France). A total of 16,510 reads were retrieved leading to the identification of 323 OTUs after normalization. Phylogenetic analysis revealed a quite diverse eukaryotic community characterized by a total of eight high-level lineages including 37 classes. The majority of sequences were clustered in four main groups: Fungi, Stramenopiles, Alveolata and Viridiplantae. The Reigous sediments formed a succession of distinct ecosystems hosting contrasted eukaryotic communities whose structure appeared to be at least partially correlated with sediment mineralogy. The concentration of arsenic in the sediment was shown to be a significant factor driving the eukaryotic community structure along this continuum.}, }
@article {pmid27534795, year = {2016}, author = {Tecon, R and Leveau, JH}, title = {Symplasmata are a clonal, conditional, and reversible type of bacterial multicellularity.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {31914}, pmid = {27534795}, issn = {2045-2322}, mesh = {Ecosystem ; Gene Expression Regulation, Bacterial ; Microbiological Phenomena ; Pantoea/genetics/*physiology/*ultrastructure ; }, abstract = {Microorganisms are capable of remarkable social behaviours, such as forming transient multicellular assemblages with properties and adaptive abilities exceeding those of individual cells. Here, we report on the formation and structure of genets known as symplasmata produced by Pantoea eucalypti bacteria. Each symplasmatum develops clonally and stochastically from a single bacterium into a membrane-delimited, capsule-embedded cluster of progeny cells and with a frequency that depends on temperature, pH, and nutrient availability. Transposon mutagenesis identified several gene products required for symplasmata formation, including master regulator LrhA, replication inhibitor CspD, polysaccharide transporter RfbX3, and autoinducer synthase PhzI. We also show that bacteria inside symplasmata are shaped irregularly with punctuated cell-to-cell contacts, metabolically responsive to environmental stimuli, dispersal-ready, and transcriptionally reprogrammed to anticipate multiple alternative futures in terms of carbon source availability. The structured and conditionable nature of symplasmata offers exciting prospects towards a mechanistic understanding of multicellular behaviours and their ecological significance.}, }
@article {pmid27532606, year = {2016}, author = {Franzini, PZ and Ramond, JB and Scholtz, CH and Sole, CL and Ronca, S and Cowan, DA}, title = {The Gut Microbiomes of Two Pachysoma MacLeay Desert Dung Beetle Species (Coleoptera: Scarabaeidae: Scarabaeinae) Feeding on Different Diets.}, journal = {PloS one}, volume = {11}, number = {8}, pages = {e0161118}, pmid = {27532606}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Coleoptera/classification/genetics/*microbiology ; Diet ; Electron Transport Complex IV/genetics ; Fungi/classification/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome/genetics ; Genes, Bacterial ; Genes, Fungal ; Genes, Insect ; Insect Proteins/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; South Africa ; Species Specificity ; }, abstract = {Micro-organisms inhabiting animal guts benefit from a protected and nutrient-rich environment while assisting the host with digestion and nutrition. In this study we compare, for the first time, the bacterial and fungal gut communities of two species of the small desert dung beetle genus Pachysoma feeding on different diets: the detritivorous P. endroedyi and the dry-dung-feeding P. striatum. Whole-gut microbial communities from 5 individuals of each species were assessed using 454 pyrosequencing of the bacterial 16S rRNA gene and fungal ITS gene regions. The two bacterial communities were significantly different, with only 3.7% of operational taxonomic units shared, and displayed intra-specific variation. The number of bacterial phyla present within the guts of P. endroedyi and P. striatum individuals ranged from 6-11 and 4-7, respectively. Fungal phylotypes could only be detected within the gut of P. striatum. Although the role of host phylogeny in Pachysoma microbiome assembly remains unknown, evidence presented in this study suggests that host diet may be a deterministic factor.}, }
@article {pmid27530237, year = {2016}, author = {Chakrabarti, A and Siddharth, J and Lauber, CL and Membrez, M and Betrisey, B and Loyer, C and Chou, CJ and Pataky, Z and Golay, A and Parkinson, SJ}, title = {Resolving microbial membership using Abundance and Variability In Taxonomy ('AVIT).}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {31655}, pmid = {27530237}, issn = {2045-2322}, mesh = {Algorithms ; Animals ; Germ-Free Life ; Humans ; Mice ; *Microbiota ; }, abstract = {Development of NGS has revolutionized the analysis in microbial ecology contributing to our deeper understanding of microbiota in health and disease. However, the quality, quantity and confidence of summarized taxonomic abundances are in need of further scrutiny due to sample dependent and independent effects. In this article we introduce 'AVIT (Abundance and Variability In Taxonomy), an unbiased method to enrich for assigned members of microbial communities. As opposed to using a priori thresholds, 'AVIT uses inherent abundance and variability of taxa in a dataset to determine the inclusion or rejection of each taxa for further downstream analysis. Using in-vitro and in-vivo studies, we benchmarked performance and parameterized 'AVIT to establish a framework for investigating the dynamic range of microbial community membership in clinically relevant scenarios.}, }
@article {pmid27527766, year = {2016}, author = {Chousalkar, K and Gole, V and Caraguel, C and Rault, JL}, title = {Chasing Salmonella Typhimurium in free range egg production system.}, journal = {Veterinary microbiology}, volume = {192}, number = {}, pages = {67-72}, doi = {10.1016/j.vetmic.2016.06.013}, pmid = {27527766}, issn = {1873-2542}, mesh = {Animal Husbandry/*methods ; Animals ; Bacterial Shedding ; *Chickens ; Eggs/microbiology ; Foxes/microbiology ; Housing, Animal ; Humans ; *Oviposition ; Poultry Diseases/*microbiology ; Salmonella Infections, Animal/*microbiology ; *Salmonella typhimurium ; Seasons ; }, abstract = {Free range production systems are becoming a major source of egg production in Australia and worldwide. This study investigated shedding and ecology of Salmonella Typhimurium and Salmonella species in a free range layer flock, wild birds and foxes in the vicinity of the free range farm in different seasons. Shedding of Salmonella was significantly higher in summer. Within the shed, overall, Salmonella prevalence was highest in dust. Corticosterone level in faeces was highest in spring and lowest in winter. There was no direct association between the Salmonella shedding (MPN/gm) and corticosterone levels in faeces. Salmonella Typhimurium MLVA types isolated from fox and wild birds were similar to MLVA types isolated from layer flock and reported during human food borne illness. Wild birds and foxes appear to play an important role in S. Typhimurium ecology and food safety. Environmental factors could play a role in evolution of S. Typhimurium in free range environment.}, }
@article {pmid27523480, year = {2016}, author = {Poirier, I and Kuhn, L and Demortière, A and Mirvaux, B and Hammann, P and Chicher, J and Caplat, C and Pallud, M and Bertrand, M}, title = {Ability of the marine bacterium Pseudomonas fluorescens BA3SM1 to counteract the toxicity of CdSe nanoparticles.}, journal = {Journal of proteomics}, volume = {148}, number = {}, pages = {213-227}, doi = {10.1016/j.jprot.2016.07.021}, pmid = {27523480}, issn = {1876-7737}, mesh = {*Biodegradation, Environmental ; Cadmium Compounds/pharmacokinetics/*toxicity ; Ecosystem ; Industrial Waste ; Metal Nanoparticles/chemistry ; Particle Size ; Proteomics ; Pseudomonas fluorescens/*drug effects/growth &amp; development/metabolism ; Selenium Compounds/pharmacokinetics/*toxicity ; Water Pollutants, Chemical/*toxicity ; }, abstract = {UNLABELLED: In the marine environment, bacteria from estuarine and coastal sediments are among the first targets of nanoparticle pollution; it is therefore relevant to improve the knowledge of interactions between bacteria and nanoparticles. In this work, the response of the marine bacterium Pseudomonas fluorescens BA3SM1 to CdSe nanocrystals (CdSe NPs) of 3nm (NP3) and 8nm (NP8) in diameter was evaluated through microscopic, physiological, biochemical and proteomic approaches. Transmission electron microscopy images showed that NP3 were able to penetrate the bacteria, while NP8 were highly concentrated around the cells, embedded in large exopolysaccharides. In our experimental conditions, both CdSe NP sizes induced a decrease in respiration during the stationary growth phase, while only NP8 caused growth retardation and a decrease in pyoverdine production. Proteomic analyses highlighted that the strain responded to CdSe NP toxicity by inducing various defence mechanisms such as cell aggregation, extracellular CdSe NP sequestration, effective protection against oxidative stress, modifications of envelope organization and properties, and cadmium export. In addition, BA3SM1 presented a biosorption capacity of 1.6×10(16)NP3/g dry weight and 1.7×10(15)NP8/g dry weight. This strain therefore appears as a promising agent for NP bioremediation processes. Proteomic data are available via ProteomeXchange with identifier PXD004012.<br><br>BIOLOGICAL SIGNIFICANCE: To the best of our knowledge, this is the first report focussing on the effects of CdSe colloidal nanocrystals (CdSe NPs) on a marine strain of Pseudomonas fluorescens. CdSe NPs are extensively used in the industry of renewable energies and it is regrettably expected that these pollutants will sometime soon appear in the marine environment through surface runoff, urban effluents and rivers. Bacteria living in estuarine and coastal sediments will be among the first targets of these new pollutants. The pseudomonads are frequently found in these ecosystems. They are involved in several biogeochemical cycles and are known for their high resistance to pollutants. Consequently, this study focussing on the effects of CdSe NPs on the marine strain P. fluorescens BA3SM1 is highly relevant for several reasons. First, it aims at improving knowledge about the interactions between bacteria and NPs. This is fundamental to effectively use NPs against pathogenic bacteria. Secondly, in spite of CdSe NP interactions with the bacterial cells, the strain BA3SM1 can develop various strategies to counteract CdSe NP toxicity and ensure its growth. It exhibits interesting properties to sequester CdSe NPs and it retains its ability to form biofilm. The strain therefore appears as a promising agent for NP bioremediation thanks to biofiltration processes. Finally, this study shows that CdSe NPs of 8nm in diameter cause a decrease in the secretion of siderophore pyoverdine, a secondary metabolite playing a key role in microbial ecology since it drives bacterial survival and competitiveness in ecosystems. Bacteria producing effective siderophores survive better in a Fe-deficient environment where they antagonize the growth of other microbes thought iron deprivation. Furthermore, siderophores are also employed as virulence factors in human pathogenic strains such as P. aeruginosa. Consequently, this study highlights that NPs can impact the secondary metabolism of bacteria with environmental and medical implications. In addition, in this work, Data-Dependant Acquisition (DDA) provided state of the art Mass Spectrometry data by Spectral Counting and MS1 Label-Free. The combination of these two well-known proteomic techniques including manual validations strengthened the identification and quantification of regulated proteins. Moreover, numerous correlations between proteomic analyses and other observations (physiological, biochemical, microscopic) consolidated our interpretations.}, }
@article {pmid27522020, year = {2016}, author = {De Vrieze, J and Raport, L and Roume, H and Vilchez-Vargas, R and Jáuregui, R and Pieper, DH and Boon, N}, title = {The full-scale anaerobic digestion microbiome is represented by specific marker populations.}, journal = {Water research}, volume = {104}, number = {}, pages = {101-110}, doi = {10.1016/j.watres.2016.08.008}, pmid = {27522020}, issn = {1879-2448}, mesh = {Anaerobiosis ; Archaea/*metabolism ; Bacteria, Anaerobic/metabolism ; Bioreactors/*microbiology ; Methane/metabolism ; Microbiota ; }, abstract = {Anaerobic digestion is a well-established microbial-based technology for the treatment of organic waste streams and subsequent biogas recovery. A robust and versatile microbial community to ensure overall stability of the process is essential. Four full-scale anaerobic digestion plants were followed for one year to link operational characteristics with microbial community composition and structure. Similarities between digesters, community dynamics and co-occurrence between bacteria and archaea within each digester were analysed. Free ammonia concentration (>200 mg N L[-1]) and conductivity (>30 mS cm[-1]) hindered acetoclastic methanogenesis by Methanosaetaceae. Thus, methanogenesis was pushed to the hydrogenotrophic pathway carried out by Methanobacteriales and Methanomicrobiales. Firmicutes dominated the overall bacterial community in each of the digesters (>50%), however, principal coordinate analysis of Bray-Curtis indices showed that each of the four digesters hosted a unique microbial community. The uniqueness of this community was related to two phylotypes belonging to the Syntrophomonas genus (Phy32 and Phy34) and to one unclassified bacterium (Phy2), which could both be considered marker populations in the community. A clear differentiation in co-occurrence of methanogens with several bacteria was observed between the different digesters. Our results demonstrated that full-scale anaerobic digestion plants show constant dynamics and co-occurrence patterns in function of time, but are unique in terms of composition, related to the presence of marker populations.}, }
@article {pmid27517880, year = {2016}, author = {Mahfoudhi, A and Grosso, C and Gonçalves, RF and Khelifi, E and Hammami, S and Achour, S and Trabelsi-Ayadi, M and Valentão, P and Andrade, PB and Mighri, Z}, title = {Evaluation of Antioxidant, Anticholinesterase, and Antidiabetic Potential of Dry Leaves and Stems in Tamarix aphylla Growing Wild in Tunisia.}, journal = {Chemistry &amp; biodiversity}, volume = {13}, number = {12}, pages = {1747-1755}, doi = {10.1002/cbdv.201600157}, pmid = {27517880}, issn = {1612-1880}, mesh = {Acetylcholinesterase/*metabolism ; Antioxidants/chemistry/isolation &amp; purification/*pharmacology ; Cholinesterase Inhibitors/chemistry/isolation &amp; purification/*pharmacology ; Dose-Response Relationship, Drug ; Free Radicals/antagonists &amp; inhibitors ; Hypoglycemic Agents/chemistry/isolation &amp; purification/*pharmacology ; Plant Leaves/chemistry ; Plant Stems/chemistry ; Structure-Activity Relationship ; Tamaricaceae/*chemistry/growth &amp; development ; Tunisia ; alpha-Glucosidases/*metabolism ; }, abstract = {Tamarix aphylla (L.) Karst. has a wide geographic distribution and was employed in traditional medicine as astringent, anti-rheumatic and to treat fever. T. aphylla leaves and stems extracts were studied from both chemical and biological points of view to assess the antidiabetic, anticholinesterase and antioxidant potential of this species. The HPLC/Diode Array Detector (DAD) analysis showed the presence of 14 phenolic compounds (gallic, caffeic, p-coumaric, ferulic and ellagic acids, kaempferol, quercetin, quercetin 3-O-galactoside and six flavonol derivatives). This is the first study reporting a comparative study of the biological activities of different extracts from T. aphylla. High activities were obtained against DPPH radical, superoxide anion radical (O2∙-) and nitric oxide radical ([•] NO) in a concentration-dependent manner, the most active extracts being the polar ones. T. aphylla also showed moderate protective effects against acetylcholinesterase, but no effects were observed against butyrylcholinesterase. Against α-glucosidase the MeOH extracts displayed IC50 values from 8.41 to 24.81 μg/ml.}, }
@article {pmid27515514, year = {2016}, author = {Ni, Y and Li, J and Panagiotou, G}, title = {COMAN: a web server for comprehensive metatranscriptomics analysis.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {622}, pmid = {27515514}, issn = {1471-2164}, mesh = {Computational Biology/*methods/statistics &amp; numerical data ; High-Throughput Nucleotide Sequencing ; Humans ; Internet ; Metagenomics/*methods/statistics &amp; numerical data ; Microbiota/*genetics ; Sequence Analysis, RNA ; *Software ; *Transcriptome ; }, abstract = {BACKGROUND: Microbiota-oriented studies based on metagenomic or metatranscriptomic sequencing have revolutionised our understanding on microbial ecology and the roles of both clinical and environmental microbes. The analysis of massive metatranscriptomic data requires extensive computational resources, a collection of bioinformatics tools and expertise in programming.<br><br>RESULTS: We developed COMAN (Comprehensive Metatranscriptomics Analysis), a web-based tool dedicated to automatically and comprehensively analysing metatranscriptomic data. COMAN pipeline includes quality control of raw reads, removal of reads derived from non-coding RNA, followed by functional annotation, comparative statistical analysis, pathway enrichment analysis, co-expression network analysis and high-quality visualisation. The essential data generated by COMAN are also provided in tabular format for additional analysis and integration with other software. The web server has an easy-to-use interface and detailed instructions, and is freely available at http://sbb.hku.hk/COMAN/ CONCLUSIONS: COMAN is an integrated web server dedicated to comprehensive functional analysis of metatranscriptomic data, translating massive amount of reads to data tables and high-standard figures. It is expected to facilitate the researchers with less expertise in bioinformatics in answering microbiota-related biological questions and to increase the accessibility and interpretation of microbiota RNA-Seq data.}, }
@article {pmid27515484, year = {2016}, author = {Scoma, A and Barbato, M and Borin, S and Daffonchio, D and Boon, N}, title = {An impaired metabolic response to hydrostatic pressure explains Alcanivorax borkumensis recorded distribution in the deep marine water column.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {31316}, pmid = {27515484}, issn = {2045-2322}, mesh = {Alcanivoraceae/*growth &amp; development/metabolism ; Amino Acids, Diamino/biosynthesis ; Bacterial Proteins/*genetics/metabolism ; Biosynthetic Pathways ; DNA Replication ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Bacterial ; Hydrostatic Pressure ; Seawater/microbiology ; Water Microbiology ; }, abstract = {Alcanivorax borkumensis is an ubiquitous model organism for hydrocarbonoclastic bacteria, which dominates polluted surface waters. Its negligible presence in oil-contaminated deep waters (as observed during the Deepwater Horizon accident) raises the hypothesis that it may lack adaptive mechanisms to hydrostatic pressure (HP). The type strain SK2 was tested under 0.1, 5 and 10 MPa (corresponding to surface water, 500 and 1000 m depth, respectively). While 5 MPa essentially inactivated SK2, further increase to 10 MPa triggered some resistance mechanism, as indicated by higher total and intact cell numbers. Under 10 MPa, SK2 upregulated the synthetic pathway of the osmolyte ectoine, whose concentration increased from 0.45 to 4.71 fmoles cell(-1). Central biosynthetic pathways such as cell replication, glyoxylate and Krebs cycles, amino acids metabolism and fatty acids biosynthesis, but not β-oxidation, were upregulated or unaffected at 10 MPa, although total cell number was remarkably lower with respect to 0.1 MPa. Concomitantly, expression of more than 50% of SK2 genes was downregulated, including genes related to ATP generation, respiration and protein translation. Thus, A. borkumensis lacks proper adaptation to HP but activates resistance mechanisms. These consist in poorly efficient biosynthetic rather than energy-yielding degradation-related pathways, and suggest that HP does represent a major driver for its distribution at deep-sea.}, }
@article {pmid27514833, year = {2016}, author = {Yagüe, P and Willemse, J and Koning, RI and Rioseras, B and López-García, MT and Gonzalez-Quiñonez, N and Lopez-Iglesias, C and Shliaha, PV and Rogowska-Wrzesinska, A and Koster, AJ and Jensen, ON and van Wezel, GP and Manteca, &#xc1;}, title = {Subcompartmentalization by cross-membranes during early growth of Streptomyces hyphae.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {12467}, pmid = {27514833}, issn = {2041-1723}, support = {280304/ERC_/European Research Council/International ; }, mesh = {Bacterial Proteins/*metabolism ; Cell Compartmentation/*physiology ; Cell Division/physiology ; Cell Membrane/*metabolism ; Cell Wall/metabolism ; Cytoskeletal Proteins/*metabolism ; Hyphae/*physiology ; Microscopy, Fluorescence ; Mutation ; Peptidoglycan/metabolism ; Permeability ; Spores, Bacterial/physiology ; Streptomyces/*physiology ; }, abstract = {Bacteria of the genus Streptomyces are a model system for bacterial multicellularity. Their mycelial life style involves the formation of long multinucleated hyphae during vegetative growth, with occasional cross-walls separating long compartments. Reproduction occurs by specialized aerial hyphae, which differentiate into chains of uninucleoid spores. While the tubulin-like FtsZ protein is required for the formation of all peptidoglycan-based septa in Streptomyces, canonical divisome-dependent cell division only occurs during sporulation. Here we report extensive subcompartmentalization in young vegetative hyphae of Streptomyces coelicolor, whereby 1 μm compartments are formed by nucleic acid stain-impermeable barriers. These barriers possess the permeability properties of membranes and at least some of them are cross-membranes without detectable peptidoglycan. Z-ladders form during the early growth, but cross-membrane formation does not depend on FtsZ. Thus, a new level of hyphal organization is presented involving unprecedented high-frequency compartmentalization, which changes the old dogma that Streptomyces vegetative hyphae have scarce compartmentalization.}, }
@article {pmid27508263, year = {2016}, author = {Myer, PR and Kim, M and Freetly, HC and Smith, TP}, title = {Metagenomic and near full-length 16S rRNA sequence data in support of the phylogenetic analysis of the rumen bacterial community in steers.}, journal = {Data in brief}, volume = {8}, number = {}, pages = {1048-1053}, pmid = {27508263}, issn = {2352-3409}, abstract = {Amplicon sequencing utilizing next-generation platforms has significantly transformed how research is conducted, specifically microbial ecology. However, primer and sequencing platform biases can confound or change the way scientists interpret these data. The Pacific Biosciences RSII instrument may also preferentially load smaller fragments, which may also be a function of PCR product exhaustion during sequencing. To further examine theses biases, data is provided from 16S rRNA rumen community analyses. Specifically, data from the relative phylum-level abundances for the ruminal bacterial community are provided to determine between-sample variability. Direct sequencing of metagenomic DNA was conducted to circumvent primer-associated biases in 16S rRNA reads and rarefaction curves were generated to demonstrate adequate coverage of each amplicon. PCR products were also subjected to reduced amplification and pooling to reduce the likelihood of PCR product exhaustion during sequencing on the Pacific Biosciences platform. The taxonomic profiles for the relative phylum-level and genus-level abundance of rumen microbiota as a function of PCR pooling for sequencing on the Pacific Biosciences RSII platform were provided. For more information, see "Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers" P.R. Myer, M. Kim, H.C. Freetly, T.P.L. Smith (2016) [1].}, }
@article {pmid27507739, year = {2016}, author = {Mouser, PJ and Borton, M and Darrah, TH and Hartsock, A and Wrighton, KC}, title = {Hydraulic fracturing offers view of microbial life in the deep terrestrial subsurface.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {11}, pages = {}, doi = {10.1093/femsec/fiw166}, pmid = {27507739}, issn = {1574-6941}, mesh = {Archaea/*classification/isolation &amp; purification ; Bacteria/*classification/isolation &amp; purification ; Ecosystem ; Environment ; *Hydraulic Fracking ; Natural Gas ; Oil and Gas Fields/*microbiology ; Soil Microbiology ; Wastewater/*microbiology ; }, abstract = {Horizontal drilling and hydraulic fracturing are increasingly used for recovering energy resources in black shales across the globe. Although newly drilled wells are providing access to rocks and fluids from kilometer depths to study the deep biosphere, we have much to learn about microbial ecology of shales before and after 'fracking'. Recent studies provide a framework for considering how engineering activities alter this rock-hosted ecosystem. We first provide data on the geochemical environment and microbial habitability in pristine shales. Next, we summarize data showing the same pattern across fractured shales: diverse assemblages of microbes are introduced into the subsurface, eventually converging to a low diversity, halotolerant, bacterial and archaeal community. Data we synthesized show that the shale microbial community predictably shifts in response to temporal changes in geochemistry, favoring conservation of key microorganisms regardless of inputs, shale location or operators. We identified factors that constrain diversity in the shale and inhibit biodegradation at the surface, including salinity, biocides, substrates and redox. Continued research in this engineered ecosystem is required to assess additive biodegradability, quantify infrastructure biocorrosion, treat wastewaters that return to the surface and potentially enhance energy production through in situ methanogenesis.}, }
@article {pmid27507346, year = {2016}, author = {Auchtung, JM and Robinson, CD and Farrell, K and Britton, RA}, title = {MiniBioReactor Arrays (MBRAs) as a Tool for Studying C. difficile Physiology in the Presence of a Complex Community.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1476}, number = {}, pages = {235-258}, doi = {10.1007/978-1-4939-6361-4_18}, pmid = {27507346}, issn = {1940-6029}, support = {U19 AI090872/AI/NIAID NIH HHS/United States ; }, mesh = {Anaerobiosis ; Anti-Bacterial Agents/pharmacology ; Bioreactors ; Clindamycin/analogs &amp; derivatives/pharmacology ; Clostridioides difficile/*drug effects/growth &amp; development/pathogenicity ; Culture Media/chemistry/*pharmacology ; Equipment Design ; Feces/microbiology ; Fermentation ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Microbial Consortia/*drug effects/physiology ; *Models, Biological ; }, abstract = {The commensal microbiome plays an important role in the dynamics of Clostridium difficile infection. In this chapter, we describe minibioreactor arrays (MBRAs), an in vitro cultivation system that we developed that allows for C. difficile physiology to be assayed in the presence of complex fecal microbial communities. The small size of the bioreactors within the MBRAs allows for dozens of reactors to be run simultaneously and therefore several different variables can be tested with limited time and cost. When coupled with experiments in animal models of C. difficile infection, MBRAs can provide important insights into C. difficile physiology and pathogenesis.}, }
@article {pmid27507334, year = {2016}, author = {Cassona, CP and Pereira, F and Serrano, M and Henriques, AO}, title = {A Fluorescent Reporter for Single Cell Analysis of Gene Expression in Clostridium difficile.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1476}, number = {}, pages = {69-90}, doi = {10.1007/978-1-4939-6361-4_6}, pmid = {27507334}, issn = {1940-6029}, mesh = {Aldehydes/metabolism ; Anaerobiosis/genetics ; Base Sequence ; Benzyl Compounds/chemistry/metabolism ; Clostridioides difficile/*genetics/metabolism/ultrastructure ; Cytosine/chemistry/metabolism ; Fluorescent Dyes/chemistry/metabolism ; *Gene Expression Regulation, Bacterial ; Genes, Reporter ; Guanine/analogs &amp; derivatives/chemistry/metabolism ; Humans ; Indoles/metabolism ; Microscopy, Fluorescence ; O(6)-Methylguanine-DNA Methyltransferase/genetics/metabolism ; Peptides/chemistry/*metabolism ; Plasmids/chemistry/metabolism ; Pyridinium Compounds/metabolism ; Quaternary Ammonium Compounds/metabolism ; Single-Cell Analysis/*methods ; Staining and Labeling/*methods ; }, abstract = {Genetically identical cells growing under homogeneous growth conditions often display cell-cell variation in gene expression. This variation stems from noise in gene expression and can be adaptive allowing for division of labor and bet-hedging strategies. In particular, for bacterial pathogens, the expression of phenotypes related to virulence can show cell-cell variation. Therefore, understanding virulence-related gene expression requires knowledge of gene expression patterns at the single cell level. We describe protocols for the use of fluorescence reporters for single cell analysis of gene expression in the human enteric pathogen Clostridium difficile, a strict anaerobe. The reporters are based on modified versions of the human DNA repair enzyme O (6)-alkylguanine-DNA alkyltransferase, called SNAP-tag and CLIP-tag. SNAP becomes covalently labeled upon reaction with O (6)-benzylguanine conjugated to a fluorophore, whereas CLIP is labeled by O (6)-benzylcytosine conjugates. SNAP and CLIP labeling is orthogonal allowing for dual labeling in the same cells. SNAP and CLIP cassettes optimized for C. difficile can be used for quantitative studies of gene expression at the single cell level. Both the SNAP and CLIP reporters can also be used for studies of protein subcellular localization in C. difficile.}, }
@article {pmid27507000, year = {2016}, author = {Ji, Y and Angel, R and Klose, M and Claus, P and Marotta, H and Pinho, L and Enrich-Prast, A and Conrad, R}, title = {Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types.}, journal = {Environmental microbiology}, volume = {18}, number = {12}, pages = {5082-5100}, doi = {10.1111/1462-2920.13491}, pmid = {27507000}, issn = {1462-2920}, mesh = {Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Geologic Sediments/chemistry/*microbiology ; Lakes/chemistry/*microbiology ; Methane/metabolism ; Phylogeny ; Polymorphism, Restriction Fragment Length ; }, abstract = {Tropical lake sediments are a significant source for the greenhouse gas methane. We studied function (pathway, rate) and structure (abundance, taxonomic composition) of the microbial communities (Bacteria, Archaea) leading to methane formation together with the main physicochemical characteristics in the sediments of four clear water, six white water and three black water lakes of the Amazon River system. Concentrations of sulfate and ferric iron, pH and δ[13] C of organic carbon were usually higher, while concentrations of carbon, nitrogen and rates of CH4 production were generally lower in white water versus clear water or black water sediments. Copy numbers of bacterial and especially archaeal ribosomal RNA genes also tended to be relatively lower in white water sediments. Hydrogenotrophic methanogenesis contributed 58 ± 16% to total CH4 production in all systems. Network analysis identified six communities, of which four were comprised mostly of bacteria found in all sediment types, while two were mostly in clear water sediment. Terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing showed that the compositions of the communities differed between the different sediment systems, statistically related to the particular physicochemical conditions and to CH4 production rates. Among the archaea, clear water, white water, and black water sediments contained relatively more Methanomicrobiales, Methanosarcinaceae and Methanocellales, respectively, while Methanosaetaceae were common in all systems. Proteobacteria, Deltaproteobacteria (Myxococcales, Syntrophobacterales, sulfate reducers) in particular, Acidobacteria and Firmicutes were the most abundant bacterial phyla in all sediment systems. Among the other important bacterial phyla, clear water sediments contained relatively more Alphaproteobacteria and Planctomycetes, whereas white water sediments contained relatively more Betaproteobacteria, Firmicutes, Actinobacteria, and Chloroflexi than the respective other sediment systems. The data showed communities of bacteria common to all sediment types, but also revealed microbial groups that were significantly different between the sediment types, which also differed in physicochemical conditions. Our study showed that function of the microbial communities may be understood on the basis of their structures, which in turn are determined by environmental heterogeneity.}, }
@article {pmid27505348, year = {2017}, author = {Ghai, R and Mehrshad, M and Mizuno, CM and Rodriguez-Valera, F}, title = {Metagenomic recovery of phage genomes of uncultured freshwater actinobacteria.}, journal = {The ISME journal}, volume = {11}, number = {1}, pages = {304-308}, pmid = {27505348}, issn = {1751-7370}, mesh = {Actinobacteria/classification/genetics/*virology ; Bacteriophages/classification/*genetics/*isolation &amp; purification ; Fresh Water/*microbiology/virology ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Phylogeny ; }, abstract = {Low-GC Actinobacteria are among the most abundant and widespread microbes in freshwaters and have largely resisted all cultivation efforts. Consequently, their phages have remained totally unknown. In this work, we have used deep metagenomic sequencing to assemble eight complete genomes of the first tailed phages that infect freshwater Actinobacteria. Their genomes encode the actinobacterial-specific transcription factor whiB, frequently found in mycobacteriophages and also in phages infecting marine pelagic Actinobacteria. Its presence suggests a common and widespread strategy of modulation of host transcriptional machinery upon infection via this transcriptional switch. We present evidence that some whiB-carrying phages infect the acI lineage of Actinobacteria. At least one of them encodes the ADP-ribosylating component of the widespread bacterial AB toxins family (for example, clostridial toxin). We posit that the presence of this toxin reflects a 'trojan horse' strategy, providing protection at the population level to the abundant host microbes against eukaryotic predators.}, }
@article {pmid27503299, year = {2016}, author = {Le, PT and Makhalanyane, TP and Guerrero, LD and Vikram, S and Van de Peer, Y and Cowan, DA}, title = {Comparative Metagenomic Analysis Reveals Mechanisms for Stress Response in Hypoliths from Extreme Hyperarid Deserts.}, journal = {Genome biology and evolution}, volume = {8}, number = {9}, pages = {2737-2747}, pmid = {27503299}, issn = {1759-6653}, mesh = {Actinobacteria/genetics/isolation &amp; purification ; Antarctic Regions ; Bacteroidetes/genetics/isolation &amp; purification ; Cyanobacteria/genetics/isolation &amp; purification ; Desert Climate ; *Extreme Environments ; *Metagenome ; *Microbiota ; Proteobacteria/genetics/isolation &amp; purification ; *Stress, Physiological ; }, abstract = {Understanding microbial adaptation to environmental stressors is crucial for interpreting broader ecological patterns. In the most extreme hot and cold deserts, cryptic niche communities are thought to play key roles in ecosystem processes and represent excellent model systems for investigating microbial responses to environmental stressors. However, relatively little is known about the genetic diversity underlying such functional processes in climatically extreme desert systems. This study presents the first comparative metagenome analysis of cyanobacteria-dominated hypolithic communities in hot (Namib Desert, Namibia) and cold (Miers Valley, Antarctica) hyperarid deserts. The most abundant phyla in both hypolith metagenomes were Actinobacteria, Proteobacteria, Cyanobacteria and Bacteroidetes with Cyanobacteria dominating in Antarctic hypoliths. However, no significant differences between the two metagenomes were identified. The Antarctic hypolithic metagenome displayed a high number of sequences assigned to sigma factors, replication, recombination and repair, translation, ribosomal structure, and biogenesis. In contrast, the Namib Desert metagenome showed a high abundance of sequences assigned to carbohydrate transport and metabolism. Metagenome data analysis also revealed significant divergence in the genetic determinants of amino acid and nucleotide metabolism between these two metagenomes and those of soil from other polar deserts, hot deserts, and non-desert soils. Our results suggest extensive niche differentiation in hypolithic microbial communities from these two extreme environments and a high genetic capacity for survival under environmental extremes.}, }
@article {pmid27502203, year = {2016}, author = {Slaughter, LC and McCulley, RL}, title = {Aboveground Epichloë coenophiala-Grass Associations Do Not Affect Belowground Fungal Symbionts or Associated Plant, Soil Parameters.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {682-691}, pmid = {27502203}, issn = {1432-184X}, mesh = {Carbon/metabolism ; Ecosystem ; Endophytes/physiology ; Epichloe/pathogenicity/*physiology ; Fungi/growth &amp; development/*physiology ; Grassland ; Hyphae/growth &amp; development ; Kentucky ; Mycorrhizae/physiology ; Neotyphodium ; Nitrogen/metabolism ; Plant Roots/microbiology ; Plants/*microbiology ; Poaceae/*microbiology ; Soil/*chemistry ; *Soil Microbiology ; *Symbiosis ; Water/chemistry ; }, abstract = {Cool season grasses host multiple fungal symbionts, such as aboveground Epichloë endophytes and belowground arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSEs). Asexual Epichloë endophytes can influence root colonization by AMF, but the type of interaction-whether antagonistic or beneficial-varies. In Schedonorus arundinaceus (tall fescue), Epichloë coenophiala can negatively affect AMF, which may impact soil properties and ecosystem function. Within field plots of S. arundinaceus that were either E. coenophiala-free (E-), infected with the common, mammal-toxic E. coenophiala strain (CTE+), or infected with one of two novel, non-toxic strains (AR542 NTE+ and AR584 NTE+), we hypothesized that (1) CTE+ would decrease AMF and DSE colonization rates and reduce soil extraradical AMF hyphae compared to E- or NTE+, and (2) this would lead to E- and NTE+ plots having greater water stable soil aggregates and C than CTE+. E. coenophiala presence and strain did not significantly alter AMF or DSE colonization, nor did it affect extraradical AMF hypha length, soil aggregates, or aggregate-associated C and N. Soil extraradical AMF hypha length negatively correlated with root AMF colonization. Our results contrast with previous demonstrations that E. coenophiala symbiosis inhibits belowground AMF communities. In our mesic, relatively nutrient-rich grassland, E. coenophiala symbiosis did not antagonize belowground symbionts, regardless of strain. Manipulating E. coenophiala strains within S. arundinaceus may not significantly alter AMF communities and nutrient cycling, yet we must further explore these relationships under different soils and environmental conditions given that symbiont interactions can be important in determining ecosystem response to global change.}, }
@article {pmid27502158, year = {2016}, author = {Estaki, M and Pither, J and Baumeister, P and Little, JP and Gill, SK and Ghosh, S and Ahmadi-Vand, Z and Marsden, KR and Gibson, DL}, title = {Cardiorespiratory fitness as a predictor of intestinal microbial diversity and distinct metagenomic functions.}, journal = {Microbiome}, volume = {4}, number = {1}, pages = {42}, pmid = {27502158}, issn = {2049-2618}, support = {//CIHR/Canada ; }, mesh = {Adult ; Bacteria/*classification/genetics/isolation &amp; purification ; Base Sequence ; Butyrates/*isolation &amp; purification ; Cardiorespiratory Fitness/*physiology ; Chromatography, Gas ; Exercise/physiology ; Fatty Acids, Volatile/*analysis ; Feces/chemistry/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Intestines/*microbiology ; Male ; Metagenome/genetics ; Pulmonary Gas Exchange ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {BACKGROUND: Reduced microbial diversity in human intestines has been implicated in various conditions such as diabetes, colorectal cancer, and inflammatory bowel disease. The role of physical fitness in the context of human intestinal microbiota is currently not known. We used high-throughput sequencing to analyze fecal microbiota of 39 healthy participants with similar age, BMI, and diets but with varying cardiorespiratory fitness levels. Fecal short-chain fatty acids were analyzed using gas chromatography.<br><br>RESULTS: We showed that peak oxygen uptake (VO2peak), the gold standard measure of cardiorespiratory fitness, can account for more than 20&#xa0;% of the variation in taxonomic richness, after accounting for all other factors, including diet. While VO2peak did not explain variation in beta diversity, it did play a significant role in explaining variation in the microbiomes' predicted metagenomic functions, aligning positively with genes related to bacterial chemotaxis, motility, and fatty acid biosynthesis. These predicted functions were supported by measured increases in production of fecal butyrate, a short-chain fatty acid associated with improved gut health, amongst physically fit participants. We also identified increased abundances of key butyrate-producing taxa (Clostridiales, Roseburia, Lachnospiraceae, and Erysipelotrichaceae) amongst these individuals, which likely contributed to the observed increases in butyrate levels.<br><br>CONCLUSIONS: Results from this study show that cardiorespiratory fitness is correlated with increased microbial diversity in healthy humans and that the associated changes are anchored around a set of functional cores rather than specific taxa. The microbial profiles of fit individuals favor the production of butyrate. As increased microbiota diversity and butyrate production is associated with overall host health, our findings warrant the use of exercise prescription as an adjuvant therapy in combating dysbiosis-associated diseases.}, }
@article {pmid27501384, year = {2016}, author = {Liu, Y and Peng, L and Ngo, HH and Guo, W and Wang, D and Pan, Y and Sun, J and Ni, BJ}, title = {Evaluation of Nitrous Oxide Emission from Sulfide- and Sulfur-Based Autotrophic Denitrification Processes.}, journal = {Environmental science &amp; technology}, volume = {50}, number = {17}, pages = {9407-9415}, doi = {10.1021/acs.est.6b02202}, pmid = {27501384}, issn = {1520-5851}, mesh = {Autotrophic Processes ; Bioreactors ; *Denitrification ; *Nitrous Oxide ; Sulfides ; Sulfur ; }, abstract = {Recent studies have shown that sulfide- and sulfur-based autotrophic denitrification (AD) processes play an important role in contributing to nitrous oxide (N2O) production and emissions. However, N2O production is not recognized in the current AD models, limiting their ability to predict N2O accumulation during AD. In this work, a mathematical model is developed to describe N2O dynamics during sulfide- and sulfur-based AD processes for the first time. The model is successfully calibrated and validated using N2O data from two independent experimental systems with sulfide or sulfur as electron donors for AD. The model satisfactorily describes nitrogen reductions, sulfide/sulfur oxidation, and N2O accumulation in both systems. Modeling results revealed substantial N2O accumulation due to the relatively low N2O reduction rate during both sulfide- and sulfur-based AD processes. Application of the model to simulate long-term operations of activated sludge systems performing sulfide- and sulfur-based AD processes indicates longer sludge retention time reduced N2O emission. For sulfide-based AD process, higher initial S/N ratio also decreased N2O emission but with a higher operational cost. This model can be a useful tool to support process operation optimization for N2O mitigation during AD with sulfide or sulfur as electron donor.}, }
@article {pmid27501305, year = {2016}, author = {Vekeman, B and Kerckhof, FM and Cremers, G and de Vos, P and Vandamme, P and Boon, N and Op den Camp, HJ and Heylen, K}, title = {New Methyloceanibacter diversity from North Sea sediments includes methanotroph containing solely the soluble methane monooxygenase.}, journal = {Environmental microbiology}, volume = {18}, number = {12}, pages = {4523-4536}, doi = {10.1111/1462-2920.13485}, pmid = {27501305}, issn = {1462-2920}, support = {669371/ERC_/European Research Council/International ; }, mesh = {Alphaproteobacteria/enzymology/*genetics/*isolation &amp; purification ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Enzymologic ; Methane/*metabolism ; Molecular Sequence Data ; North Sea ; Oxygenases/genetics/*metabolism ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Marine methylotrophs play a key role in the global carbon cycle by metabolizing reduced one-carbon compounds that are found in high concentrations in marine environments. Genome, physiology and diversity studies have been greatly facilitated by the numerous model organisms brought into culture. However, the availability of marine representatives remains poor. Here, we report the isolation of four novel species from North Sea sediment enrichments closely related to the Alphaproteobacterium Methyloceanibacter caenitepidi. Each of the newly isolated Methyloceanibacter species exhibited a clear genome sequence divergence which was reflected in physiological differences. Notably one strain R-67174 was capable of oxidizing methane as sole source of carbon and energy using solely a soluble methane monooxygenase and represents the first marine Alphaproteobacterial methanotroph brought into culture. Differences in maximum cell density of >1.5 orders of magnitude were observed. Furthermore, three strains were capable of producing nitrous oxide from nitrate. Together, these findings highlight the metabolic and physiologic variability within closely related Methyloceanibacter species and provide a new understanding of the physiological basis of marine methylotrophy.}, }
@article {pmid27500860, year = {2016}, author = {Golda-Cepa, M and Chorylek, A and Chytrosz, P and Brzychczy-Wloch, M and Jaworska, J and Kasperczyk, J and Hakkarainen, M and Engvall, K and Kotarba, A}, title = {Multifunctional PLGA/Parylene C Coating for Implant Materials: An Integral Approach for Biointerface Optimization.}, journal = {ACS applied materials &amp; interfaces}, volume = {8}, number = {34}, pages = {22093-22105}, doi = {10.1021/acsami.6b08025}, pmid = {27500860}, issn = {1944-8252}, mesh = {Coated Materials, Biocompatible ; Lactic Acid/*chemistry ; Polyglycolic Acid/*chemistry ; Polylactic Acid-Polyglycolic Acid Copolymer ; Polymers ; Xylenes ; }, abstract = {Functionalizing implant surfaces is critical for improving their performance. An integrated approach was employed to develop a multifunctional implant coating based on oxygen plasma-modified parylene C and drug-loaded, biodegradable poly(dl-lactide-co-glycolide) (PLGA). The key functional attributes of the coating (i.e., anti-corrosion, biocompatible, anti-infection, and therapeutic) were thoroughly characterized at each fabrication step by spectroscopic, microscopic, and biologic methods and at different scales, ranging from molecular, through the nano- and microscales to the macroscopic scale. The chemistry of each layer was demonstrated separately, and their mutual affinity was shown to be indispensable for the development of versatile coatings for implant applications.}, }
@article {pmid27499582, year = {2016}, author = {Andoh, A and Nishida, A and Takahashi, K and Inatomi, O and Imaeda, H and Bamba, S and Kito, K and Sugimoto, M and Kobayashi, T}, title = {Comparison of the gut microbial community between obese and lean peoples using 16S gene sequencing in a Japanese population.}, journal = {Journal of clinical biochemistry and nutrition}, volume = {59}, number = {1}, pages = {65-70}, pmid = {27499582}, issn = {0912-0009}, abstract = {Altered gut microbial ecology contributes to the development of metabolic diseases including obesity. In this study, we performed 16S rRNA sequence analysis of the gut microbiota profiles of obese and lean Japanese populations. The V3-V4 hypervariable regions of 16S rRNA of fecal samples from 10 obese and 10 lean volunteers were sequenced using the Illumina MiSeq(TM)II system. The average body mass index of the obese and lean group were 38.1 and 16.6 kg/m(2), respectively (p<0.01). The Shannon diversity index was significantly higher in the lean group than in the obese group (p<0.01). The phyla Firmicutes and Fusobacteria were significantly more abundant in obese people than in lean people. The abundance of the phylum Bacteroidetes and the Bacteroidetes/Firmicutes ratio were not different between the obese and lean groups. The genera Alistipes, Anaerococcus, Corpococcus, Fusobacterium and Parvimonas increased significantly in obese people, and the genera Bacteroides, Desulfovibrio, Faecalibacterium, Lachnoanaerobaculum and Olsenella increased significantly in lean people. Bacteria species possessing anti-inflammatory properties, such as Faecalibacterium prausnitzii, increased significantly in lean people, but bacteria species possessing pro-inflammatory properties increased in obese people. Obesity-associated gut microbiota in the Japanese population was different from that in Western people.}, }
@article {pmid27497315, year = {2016}, author = {Harish, A and Abroi, A and Gough, J and Kurland, C}, title = {Did Viruses Evolve As a Distinct Supergroup from Common Ancestors of Cells?.}, journal = {Genome biology and evolution}, volume = {8}, number = {8}, pages = {2474-2481}, pmid = {27497315}, issn = {1759-6653}, support = {BB/G022771/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Archaea/genetics ; Bacteria/genetics ; *Evolution, Molecular ; Genome, Viral ; Models, Genetic ; Phylogeny ; Viral Proteins/genetics ; Viruses/classification/*genetics ; }, abstract = {The evolutionary origins of viruses according to marker gene phylogenies, as well as their relationships to the ancestors of host cells remains unclear. In a recent article Nasir and Caetano-Anollés reported that their genome-scale phylogenetic analyses based on genomic composition of protein structural-domains identify an ancient origin of the "viral supergroup" (Nasir et al. 2015. A phylogenomic data-driven exploration of viral origins and evolution. Sci Adv. 1(8):e1500527.). It suggests that viruses and host cells evolved independently from a universal common ancestor. Examination of their data and phylogenetic methods indicates that systematic errors likely affected the results. Reanalysis of the data with additional tests shows that small-genome attraction artifacts distort their phylogenomic analyses, particularly the location of the root of the phylogenetic tree of life that is central to their conclusions. These new results indicate that their suggestion of a distinct ancestry of the viral supergroup is not well supported by the evidence.}, }
@article {pmid27497120, year = {2016}, author = {Xie, Y and Savell, JW and Arnold, AN and Gehring, KB and Gill, JJ and Taylor, TM}, title = {Prevalence and Characterization of Salmonella enterica and Salmonella Bacteriophages Recovered from Beef Cattle Feedlots in South Texas.}, journal = {Journal of food protection}, volume = {79}, number = {8}, pages = {1332-1340}, doi = {10.4315/0362-028X.JFP-15-526}, pmid = {27497120}, issn = {1944-9097}, mesh = {Animals ; Cattle ; Cattle Diseases/microbiology ; Feces/microbiology ; Kentucky ; Prevalence ; Red Meat ; Salmonella/isolation &amp; purification ; *Salmonella Phages ; Salmonella enterica/*isolation &amp; purification ; Texas ; }, abstract = {Asymptomatic Salmonella carriage in beef cattle is a food safety concern, and the beef feedlot environment may function as a reservoir of this pathogen. The goal of this study was to identify and isolate Salmonella and Salmonella bacteriophages from beef cattle feedlot environments in order to better understand the microbial ecology of Salmonella and identify phages that might be useful as anti-Salmonella beef safety interventions. Three feedlots in south Texas were visited, and 27 distinct samples from each source were collected from dropped feces, feed from feed bunks, drinking water from troughs, and soil in cattle pens (n = 108 samples). Preenrichment, selective enrichment, and selective/differential isolation of Salmonella were performed on each sample. A representative subset of presumptive Salmonella isolates was prepared for biochemical identification and serotyping. Samples were pooled by feedlot and sample type to create 36 samples and enriched to recover phages. Recovered phages were tested for host range against two panels of Salmonella hosts. Salmonella bacteria were identified in 20 (18.5%) of 108 samples by biochemical and/or serological testing. The serovars recovered included Salmonella enterica serovars Anatum, Muenchen, Altona, Kralingen, Kentucky, and Montevideo; Salmonella Anatum was the most frequently recovered serotype. Phage-positive samples were distributed evenly over the three feedlots, suggesting that phage prevalence is not strongly correlated with the presence of culturable Salmonella. Phages were found more frequently in soil and feces than in feed and water samples. The recovery of bacteriophages in the Salmonella-free feedlot suggests that phages might play a role in suppressing the Salmonella population in a feedlot environment.}, }
@article {pmid27495244, year = {2016}, author = {Haq, IU and Calixto, RO and Yang, P and Dos Santos, GM and Barreto-Bergter, E and van Elsas, JD}, title = {Chemotaxis and adherence to fungal surfaces are key components of the behavioral response of Burkholderia terrae BS001 to two selected soil fungi.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {11}, pages = {}, doi = {10.1093/femsec/fiw164}, pmid = {27495244}, issn = {1574-6941}, mesh = {Agaricales/*metabolism ; Bacterial Adhesion/*physiology ; Binding Sites/physiology ; Biofilms/*growth &amp; development ; Burkholderia/*metabolism ; Cell Communication ; Chemotaxis/*physiology ; Glycerol/pharmacology ; Hyphae/metabolism ; Oxalic Acid/pharmacology ; Soil ; Soil Microbiology ; Spores, Fungal/metabolism ; Trichoderma/*metabolism ; }, abstract = {Burkholderia terrae BS001 has previously been proposed to be a 'generalist' associate of soil fungi, but its strategies of interaction have been largely ignored. Here, we studied the chemotactic behavior of B. terrae BS001 towards Lyophyllum sp. strain Karsten and Trichoderma asperellum 302 and the role of fungal surface molecules in their physical interaction with the bacteria. To assess the involvement of the type 3 secretion system (T3SS), wild-type strain BS001 and T3SS mutant strain BS001-ΔsctD were used in the experiments. First, the two fungi showed divergent behavior when confronted with B. terrae BS001 on soil extract agar medium. Lyophyllum sp. strain Karsten revealed slow growth towards the bacterium, whereas T. asperellum 302 grew avidly over it. Both on soil extract and M9 agar, B. terrae BS001 and BS001-ΔsctD moved chemotactically towards the hyphae of both fungi, with a stronger response to Lyophyllum sp. strain Karsten than to T. asperellum 302. The presence of a progressively increasing glycerol level in the M9 agar enhanced the level of movement. Different oxalic acid concentrations exerted varied effects, with a significantly raised chemotactic response at lower, and a subdued response at higher concentrations. Testing of the adherence of B. terrae BS001 and BS001-ΔsctD to Lyophyllum sp. strain Karsten and to cell envelope-extracted ceramide monohexosides (CMHs) revealed that CMHs in both conidia and hyphae could bind strain BS001 cells. As BS001-ΔsctD adhered significantly less to the CMHs than BS001, the T3SS was presumed to have a role in the interaction. In contrast, such avid adherence was not detected with T. asperellum 302. Thus, B. terrae BS001 shows a behavior characterized by swimming towards Lyophyllum sp. strain Karsten and T. asperellum 302 and attachment to the CMH moiety in the cell envelope, in particular of the former.}, }
@article {pmid27488594, year = {2016}, author = {Latorre, E and Pradilla, A and Chueca, B and Pagán, R and Layunta, E and Alcalde, AI and Mesonero, JE}, title = {Listeria monocytogenes Inhibits Serotonin Transporter in Human Intestinal Caco-2 Cells.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {730-739}, pmid = {27488594}, issn = {1432-184X}, mesh = {Caco-2 Cells/*drug effects ; Cell Culture Techniques ; Epithelial Cells/metabolism ; Humans ; Intestinal Mucosa/metabolism/microbiology ; Intestines/*microbiology ; Listeria monocytogenes/drug effects/growth &amp; development/*metabolism/*pathogenicity ; Listeriosis ; Microbiological Techniques ; Myeloid Differentiation Factor 88 ; Serotonin/biosynthesis/metabolism/pharmacology ; Serotonin Plasma Membrane Transport Proteins/biosynthesis/*drug effects ; Selective Serotonin Reuptake Inhibitors/*antagonists &amp; inhibitors ; Toll-Like Receptor 10/antagonists &amp; inhibitors/metabolism ; Toll-Like Receptor 2/metabolism ; }, abstract = {Listeria monocytogenes is a Gram-positive bacterium that can cause a serious infection. Intestinal microorganisms have been demonstrated to contribute to intestinal physiology not only through immunological responses but also by modulating the intestinal serotonergic system. Serotonin (5-HT) is a neuromodulator that is synthesized in the intestinal epithelium and regulates the whole intestinal physiology. The serotonin transporter (SERT), located in enterocytes, controls intestinal 5-HT availability and therefore serotonin's effects. Infections caused by L. monocytogenes are well described as being due to the invasion of intestinal epithelial cells; however, the effect of L. monocytogenes on the intestinal epithelium remains unknown. The main aim of this work, therefore, was to study the effect of L. monocytogenes on SERT. Caco2/TC7 cell line was used as an enterocyte-like in vitro model, and SERT functional and molecular expression assays were performed. Our results demonstrate that living L. monocytogenes inhibits serotonin uptake by reducing SERT expression at the brush border membrane. However, neither inactivated L. monocytogenes nor soluble metabolites were able to affect SERT. The results also demonstrate that L. monocytogenes yields TLR2 and TLR10 transcriptional changes in intestinal epithelial cells and suggest that TLR10 is potentially involved in the inhibitory effect observed on SERT. Therefore, L. monocytogenes, through TLR10-mediated SERT inhibition, may induce increased intestinal serotonin availability and potentially contributing to intestinal physiological changes and the initiation of the inflammatory response.}, }
@article {pmid27486452, year = {2016}, author = {Martinez-Fernandez, G and Denman, SE and Yang, C and Cheung, J and Mitsumori, M and McSweeney, CS}, title = {Methane Inhibition Alters the Microbial Community, Hydrogen Flow, and Fermentation Response in the Rumen of Cattle.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1122}, pmid = {27486452}, issn = {1664-302X}, abstract = {Management of metabolic hydrogen ([H]) in the rumen has been identified as an important consideration when reducing ruminant CH4 emissions. However, little is known about hydrogen flux and microbial rumen population responses to CH4 inhibition when animals are fed with slowly degradable diets. The effects of the anti-methanogenic compound, chloroform, on rumen fermentation, microbial ecology, and H2/CH4 production were investigated in vivo. Eight rumen fistulated Brahman steers were fed a roughage hay diet (Rhode grass hay) or roughage hay:concentrate diet (60:40) with increasing levels (low, mid, and high) of chloroform in a cyclodextrin matrix. The increasing levels of chloroform resulted in an increase in H2 expelled as CH4 production decreased with no effect on dry matter intakes. The amount of expelled H2 per mole of decreased methane, was lower for the hay diet suggesting a more efficient redirection of hydrogen into other microbial products compared with hay:concentrate diet. A shift in rumen fermentation toward propionate and branched-chain fatty acids was observed for both diets. Animals fed with the hay:concentrate diet had both higher formate concentration and H2 expelled than those fed only roughage hay. Metabolomic analyses revealed an increase in the concentration of amino acids, organic, and nucleic acids in the fluid phase for both diets when methanogenesis was inhibited. These changes in the rumen metabolism were accompanied by a shift in the microbiota with an increase in Bacteroidetes:Firmicutes ratio and a decrease in Archaea and Synergistetes for both diets. Within the Bacteroidetes family, some OTUs assigned to Prevotella were promoted under chloroform treatment. These bacteria may be partly responsible for the increase in amino acids and propionate in the rumen. No significant changes were observed for abundance of fibrolytic bacteria, protozoa, and fungi, which suggests that fiber degradation was not impaired. The observed 30% decrease in methanogenesis did not adversely affect rumen metabolism and the rumen microbiota was able to adapt and redirect [H] into other microbial end-products for both diets. However, it is also required dietary supplements or microbial treatments to capture the additional H2 expelled by the animal to further improve rumen digestive efficiency.}, }
@article {pmid27486436, year = {2016}, author = {Buelow, HN and Winter, AS and Van Horn, DJ and Barrett, JE and Gooseff, MN and Schwartz, E and Takacs-Vesbach, CD}, title = {Microbial Community Responses to Increased Water and Organic Matter in the Arid Soils of the McMurdo Dry Valleys, Antarctica.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1040}, pmid = {27486436}, issn = {1664-302X}, abstract = {The soils of the McMurdo Dry Valleys, Antarctica are an extreme polar desert, inhabited exclusively by microscopic taxa. This region is on the threshold of anticipated climate change, with glacial melt, permafrost thaw, and the melting of massive buried ice increasing liquid water availability and mobilizing soil nutrients. Experimental water and organic matter (OM) amendments were applied to investigate how these climate change effects may impact the soil communities. To identify active taxa and their functions, total community RNA transcripts were sequenced and annotated, and amended soils were compared with unamended control soils using differential abundance and expression analyses. Overall, taxonomic diversity declined with amendments of water and OM. The domain Bacteria increased with both amendments while Eukaryota declined from 38% of all taxa in control soils to 8 and 11% in water and OM amended soils, respectively. Among bacterial phyla, Actinobacteria (59%) dominated water-amended soils and Firmicutes (45%) dominated OM amended soils. Three bacterial phyla (Actinobacteria, Proteobacteria, and Firmicutes) were primarily responsible for the observed positive functional responses, while eukaryotic taxa experienced the majority (27 of 34) of significant transcript losses. These results indicated that as climate changes in this region, a replacement of endemic taxa adapted to dry, oligotrophic conditions by generalist, copiotrophic taxa is likely.}, }
@article {pmid27486066, year = {2017}, author = {Schulz-Bohm, K and Tyc, O and de Boer, W and Peereboom, N and Debets, F and Zaagman, N and Janssens, TKS and Garbeva, P}, title = {Fungus-associated bacteriome in charge of their host behavior.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {102}, number = {}, pages = {38-48}, doi = {10.1016/j.fgb.2016.07.011}, pmid = {27486066}, issn = {1096-0937}, mesh = {Alphaproteobacteria/isolation &amp; purification/*physiology ; Anti-Bacterial Agents/pharmacology ; Gammaproteobacteria/isolation &amp; purification/*physiology ; *Microbial Consortia/drug effects ; *Microbial Interactions ; Mucor/drug effects/genetics/growth &amp; development/*physiology ; Secondary Metabolism ; *Soil Microbiology ; }, abstract = {Bacterial-fungal interactions are widespread in nature and there is a growing number of studies reporting distinct fungus-associated bacteria. However, little is known so far about how shifts in the fungus-associated bacteriome will affect the fungal host's lifestyle. In the present study, we describe for the first time the bacterial community associated with the saprotrophic fungus Mucor hiemalis, commonly found in soil and rhizosphere. Two broad-spectrum antibiotics that strongly altered the bacterial community associated with the fungus were applied. Our results revealed that the antibiotic treatment did not significantly reduce the amount of bacteria associated to the fungus but rather changed the community composition by shifting from initially dominating Alpha-Proteobacteria to dominance of Gamma-Proteobacteria. A novel approach was applied for the isolation of fungal-associated bacteria which also revealed differences between bacterial isolates obtained from the original and the antibiotic-treated M. hiemalis. The shift in the composition of the fungal-associated bacterial community led to significantly reduced fungal growth, changes in fungal morphology, behavior and secondary-metabolites production. Furthermore, our results showed that the antibiotic-treated isolate was more attractive and susceptible to mycophagous bacteria as compared to the original isolate. Overall, our study highlights the importance of the fungus-associated bacteriome for the host's lifestyle and interactions and indicate that isolation with antibacterials is not sufficient to eradicate the associated bacteria.}, }
@article {pmid27485508, year = {2016}, author = {Allen, HK and Bayles, DO and Looft, T and Trachsel, J and Bass, BE and Alt, DP and Bearson, SM and Nicholson, T and Casey, TA}, title = {Pipeline for amplifying and analyzing amplicons of the V1-V3 region of the 16S rRNA gene.}, journal = {BMC research notes}, volume = {9}, number = {}, pages = {380}, pmid = {27485508}, issn = {1756-0500}, mesh = {Computational Biology/methods ; DNA, Archaeal/*genetics ; DNA, Bacterial/*genetics ; Data Mining ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Microbial Consortia/*genetics ; Molecular Sequence Annotation ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Profiling of 16S rRNA gene sequences is an important tool for testing hypotheses in complex microbial communities, and analysis methods must be updated and validated as sequencing technologies advance. In host-associated bacterial communities, the V1-V3 region of the 16S rRNA gene is a valuable region to profile because it provides a useful level of taxonomic resolution; however, use of Illumina MiSeq data for experiments targeting this region needs validation.<br><br>RESULTS: Using a MiSeq machine and the version 3 (300&#xa0;&#xd7;&#xa0;2) chemistry, we sequenced the V1-V3 region of the 16S rRNA gene within a mock community. Nineteen bacteria and one archaeon comprised the mock community, and 12 replicate amplifications of the community were performed and sequenced. Sequencing the large fragment (490&#xa0;bp) that encompasses V1-V3 yielded a higher error rate (3.6&#xa0;%) than has been reported when using smaller fragment sizes. This higher error rate was due to a large number of sequences that occurred only one or two times among all mock community samples. Removing sequences that occurred one time among all samples (singletons) reduced the error rate to 1.4&#xa0;%. Diversity estimates of the mock community containing all sequences were inflated, whereas estimates following singleton removal more closely reflected the actual mock community membership. A higher percentage of the sequences could be taxonomically assigned after singleton and doubleton sequences were removed, and the assignments reflected the membership of the input DNA.<br><br>CONCLUSIONS: Sequencing the V1-V3 region of the 16S rRNA gene on the MiSeq platform may require additional sequence curation in silico, and improved error rates and diversity estimates show that removing low-frequency sequences is reasonable. When datasets have a high number of singletons, these singletons can be removed from the analysis without losing statistical power while reducing error and improving microbiota assessment.}, }
@article {pmid27485403, year = {2016}, author = {Wang, X and Zhou, L and Lu, L and Lobo, FL and Li, N and Wang, H and Park, J and Ren, ZJ}, title = {Alternating Current Influences Anaerobic Electroactive Biofilm Activity.}, journal = {Environmental science &amp; technology}, volume = {50}, number = {17}, pages = {9169-9176}, doi = {10.1021/acs.est.6b00813}, pmid = {27485403}, issn = {1520-5851}, mesh = {Bioelectric Energy Sources ; *Biofilms ; Electricity ; Electrodes ; Electron Transport ; *Geobacter ; }, abstract = {Alternating current (AC) is known to inactivate microbial growth in suspension, but how AC influences anaerobic biofilm activities has not been systematically investigated. Using a Geobacter dominated anaerobic biofilm growing on the electrodes of microbial electrochemical reactors, we found that high frequency AC ranging from 1 MHz to 1 kHz (amplitude of 5 V, 30 min) showed only temporary inhibition to the biofilm activity. However, lower frequency (100 Hz, 1.2 or 5 V) treatment led to 47 ± 19% permanent decrease in limiting current on the same biofilm, which is attributed to the action of electrohydrodynamic force that caused biofilm damage and loss of intercellular electron transfer network. Confocal microscopy images show such inactivation mainly occurred at the interface between the biofilm and the electrode. Reducing the frequency further to 1 Hz led to water electrolysis, which generated gas bubbles that flushed all attached cells out of the electrode. These findings provide new references on understanding and regulating biofilm growth, which has broader implications in biofouling control, anaerobic waste treatment, energy and product recovery, and general understanding of microbial ecology and physiology.}, }
@article {pmid27484343, year = {2016}, author = {Wanjugi, P and Fox, GA and Harwood, VJ}, title = {The Interplay Between Predation, Competition, and Nutrient Levels Influences the Survival of Escherichia coli in Aquatic Environments.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {526-537}, pmid = {27484343}, issn = {1432-184X}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/growth &amp; development ; Biota ; Cycloheximide/pharmacology ; Ecosystem ; Environmental Microbiology ; Environmental Monitoring ; Escherichia coli/drug effects/growth &amp; development/*physiology ; Feces/microbiology ; Fresh Water/*microbiology/*parasitology ; Geologic Sediments/microbiology ; Kanamycin/pharmacology ; *Microbial Interactions ; *Nutritional Physiological Phenomena ; *Predatory Behavior ; Survival ; Water Microbiology ; }, abstract = {Nutrient levels, competition from autochthonous microorganisms, and protozoan predation may all influence survival of fecal microorganisms as they transition from the gastrointestinal tract to aquatic habitats. Although Escherichia coli is an important indicator of waterborne pathogens, the effects of environmental stressors on its survival in aquatic environments remain poorly understood. We manipulated organic nutrient, predation, and competition levels in outdoor microcosms containing natural river water, sediments, and microbial populations to determine their relative contribution to E. coli survival. The activities of predator (protozoa) and competitor (indigenous bacteria) populations were inhibited by adding cycloheximide or kanamycin. We developed a statistical model of E. coli density over time that fits with the data under all experimental conditions. Predation and competition had significant negative effects on E. coli survival, while higher nutrient levels increased survival. Among the main effects, predation accounted for the greatest variation (40 %) compared with nutrients (25 %) or competition (15 %). The highest nutrient level mitigated the effect of predation on E. coli survival. Thus, elevated organic nutrients may disproportionately enhance the survival of E. coli, and potentially that of other enteric bacteria, in aquatic habitats.}, }
@article {pmid27484342, year = {2016}, author = {Puente-Sánchez, F and Olsson, S and Aguilera, A}, title = {Comparative Transcriptomic Analysis of the Response of Dunaliella acidophila (Chlorophyta) to Short-Term Cadmium and Chronic Natural Metal-Rich Water Exposures.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {595-607}, pmid = {27484342}, issn = {1432-184X}, mesh = {Base Sequence ; Cadmium/*metabolism/toxicity ; Chlorophyta/*genetics/*metabolism ; Drug Tolerance/genetics ; Gene Expression Regulation, Plant ; Gene Ontology ; Genes, Plant ; Metals, Heavy/*metabolism/toxicity ; Oxidative Stress ; Photosynthesis ; Reactive Oxygen Species/metabolism ; Stress, Physiological/genetics ; Transcriptome/*genetics ; Water/chemistry/*metabolism ; }, abstract = {Heavy metals are toxic compounds known to cause multiple and severe cellular damage. However, acidophilic extremophiles are able to cope with very high concentrations of heavy metals. This study investigated the stress response under natural environmental heavy metal concentrations in an acidophilic Dunaliella acidophila. We employed Illumina sequencing for a de novo transcriptome assembly and to identify changes in response to high cadmium concentrations and natural metal-rich water. The photosynthetic performance was also estimated by pulse amplitude-modulated (PAM) fluorescence. Transcriptomic analysis highlights a number of processes mainly related to a high constitutive expression of genes involved in oxidative stress and response to reactive oxygen species (ROS), even in the absence of heavy metals. Photosynthetic activity seems to be unaltered under short-term exposition to Cd and chronic exposure to natural metal-rich water, probably due to an increase in the synthesis of structural photosynthetic components preserving their functional integrity. An overrepresentation of Gene Ontology (GO) terms related to metabolic activities, transcription, and proteosomal catabolic process was observed when D. acidophila grew under chronic exposure to natural metal-rich water. GO terms involved in carbohydrate metabolic process, reticulum endoplasmic and Golgi bodies, were also specifically overrepresented in natural metal-rich water library suggesting an endoplasmic reticulum stress response.}, }
@article {pmid27484096, year = {2017}, author = {Devriese, S and Eeckhaut, V and Geirnaert, A and Van den Bossche, L and Hindryckx, P and Van de Wiele, T and Van Immerseel, F and Ducatelle, R and De Vos, M and Laukens, D}, title = {Reduced Mucosa-associated Butyricicoccus Activity in Patients with Ulcerative Colitis Correlates with Aberrant Claudin-1 Expression.}, journal = {Journal of Crohn's &amp; colitis}, volume = {11}, number = {2}, pages = {229-236}, doi = {10.1093/ecco-jcc/jjw142}, pmid = {27484096}, issn = {1876-4479}, mesh = {Adult ; Biopsy/methods ; Butyrates/metabolism ; Caco-2 Cells ; Claudin-1/*metabolism ; *Colitis, Ulcerative/metabolism/microbiology/pathology ; *Eubacterium/isolation &amp; purification/physiology ; Feces/microbiology ; Female ; Host-Pathogen Interactions/physiology ; Humans ; *Intestinal Mucosa/microbiology/pathology ; Male ; Occludin/*metabolism ; Patient Acuity ; RNA, Ribosomal, 16S/analysis ; Statistics as Topic ; *Tight Junctions/metabolism/microbiology/pathology ; Tumor Necrosis Factor-alpha/metabolism ; Zonula Occludens-1 Protein/*metabolism ; }, abstract = {BACKGROUND AND AIMS: Butyricicoccus is a butyrate-producing clostridial cluster IV genus whose numbers are reduced in the stool of ulcerative colitis [UC] patients. Conditioned medium of Butyricicoccus [B.] pullicaecorum prevents tumour necrosis factor alpha [TNFα]-induced increase in epithelial permeability in vitro. Since butyrate influences intestinal barrier integrity, we further investigated the relationship between the abundance of mucosa-associated Butyricicoccus and the expression of butyrate-regulated tight junction [TJ] genes.<br><br>METHODS: Tight junction protein 1 [TJP1], occludin [OCLN], claudin-1 [CLDN1], and Butyricicoccus 16S rRNA expression was analysed in a collection of colonic biopsies of healthy controls and UC patients with active disease. The effect of butyrate and B. pullicaecorum conditioned medium on TJ gene expression was investigated in TNF&#x3b1;-stimulated Caco-2 monolayers and inflamed mucosal biopsies of UC patients.<br><br>RESULTS: TJP1 expression was significantly decreased in inflamed UC mucosa, whereas CLDN1 mRNA levels were increased. OCLN did not differ significantly between the groups. Mucosa-associated Butyricicoccus 16S rRNA transcripts were reduced in active UC patients compared with healthy controls. Interestingly, Butyricicoccus activity negatively correlated with CLDN1 expression. Butyrate reversed the inflammation-induced increase of CLDN1 protein levels, and stimulation of inflamed UC biopsies with B. pullicaecorum conditioned medium normalized CLDN1 mRNA levels.<br><br>CONCLUSIONS: Butyricicoccus is a mucosa-associated bacterial genus under-represented in colonic mucosa of patients with active UC, whose activity inversely correlates with CLDN1 expression. Butyrate and B. pullicaecorum conditioned medium reduce CLDN1 expression, supporting its use as a pharmabiotic preserving epithelial TJ integrity.}, }
@article {pmid27482928, year = {2017}, author = {Yan, Y and Kuramae, EE and de Hollander, M and Klinkhamer, PG and van Veen, JA}, title = {Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere.}, journal = {The ISME journal}, volume = {11}, number = {1}, pages = {56-66}, pmid = {27482928}, issn = {1751-7370}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Biodiversity ; Plant Roots/microbiology ; Plants/microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {We studied the impact of community diversity on the selection of bacterial communities in the rhizosphere by comparing the composition and the functional traits of these communities in soil and rhizosphere. Differences in diversity were established by inoculating into sterilized soils diluted suspensions of the same soil. We used 16S ribosomal RNA amplicon sequencing to determine the taxonomical structure of the bacterial communities and a shotgun metagenomics approach to investigate the potential functional diversity of the communities. By comparing the bacterial communities in soil and rhizosphere, the selective power of the plant was observed both at the taxonomic and functional level, although the diversity indices of soil and rhizosphere samples showed a highly variable, irregular pattern. Lesser variation, that is, more homogenization, was found for both the taxonomic structure and the functional profile of the rhizosphere communities as compared to the communities of the bulk soil. Network analysis revealed stronger interactions among bacterial operational taxonomic units in the rhizosphere than in the soil. The enrichment processes in the rhizosphere selected microbes with particular functional genes related to transporters, the Embden-Meyerhof-Parnas pathway and hydrogen metabolism. This selection was not random across bacteria with these functional traits, but it was species specific. Overall, this suggests that functional traits are a key to the assembly of bacterial rhizosphere communities.}, }
@article {pmid27481257, year = {2016}, author = {Foulon, J and Zappelini, C and Durand, A and Valot, B and Blaudez, D and Chalot, M}, title = {Impact of poplar-based phytomanagement on soil properties and microbial communities in a metal-contaminated site.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {10}, pages = {}, doi = {10.1093/femsec/fiw163}, pmid = {27481257}, issn = {1574-6941}, mesh = {*Biodegradation, Environmental ; Ecosystem ; Environment ; High-Throughput Nucleotide Sequencing ; Metals/*analysis/metabolism ; *Microbial Consortia ; Mycorrhizae ; Plant Roots/microbiology ; Populus ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants/analysis/*metabolism ; }, abstract = {Despite a long history of use in phytomanagement strategies, the impacts of poplar trees on the structure and function of microbial communities that live in the soil remain largely unknown. The current study combined fungal and bacterial community analyses from different management regimes using Illumina-based sequencing with soil analysis. The poplar phytomanagement regimes led to a significant increase in soil fertility and a decreased bioavailability of Zn and Cd, in concert with changes in the microbial communities. The most notable changes in the relative abundance of taxa and operational taxonomic units unsurprisingly indicated that root and soil constitute distinct ecological microbial habitats, as exemplified by the dominance of Laccaria in root samples. The poplar cultivar was also an important driver, explaining 12% and 6% of the variance in the fungal and bacterial data sets, respectively. The overall dominance of saprophytic fungi, e.g. Penicillium canescens, might be related to the decomposition activities needed at the experimental site. Our data further highlighted that the mycorrhizal colonization of poplar cultivars varies greatly between the species and genotypes, which is exemplified by the dominance of Scleroderma under Vesten samples. Further interactions between fungal and bacterial functional groups stressed the potential of high-throughput sequencing technologies in uncovering the microbial ecology of disturbed environments.}, }
@article {pmid27480881, year = {2016}, author = {Coelho, FJ and Cleary, DF and Costa, R and Ferreira, M and Polónia, AR and Silva, AM and Simões, MM and Oliveira, V and Gomes, NC}, title = {Multitaxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution.}, journal = {Molecular ecology}, volume = {25}, number = {18}, pages = {4645-4659}, doi = {10.1111/mec.13779}, pmid = {27480881}, issn = {1365-294X}, mesh = {Archaea/*classification ; Climate Change ; Hydrogen-Ion Concentration ; *Petroleum Pollution ; Seawater/*chemistry ; Sulfur-Reducing Bacteria/*classification ; Water Pollutants, Chemical/*adverse effects ; }, abstract = {There is growing concern that predicted changes to global ocean chemistry will interact with anthropogenic pollution to significantly alter marine microbial composition and function. However, knowledge of the compounding effects of climate change stressors and anthropogenic pollution is limited. Here, we used 16S and 18S rRNA (cDNA)-based activity profiling to investigate the differential responses of selected microbial taxa to ocean acidification and oil hydrocarbon contamination under controlled laboratory conditions. Our results revealed that a lower relative abundance of sulphate-reducing bacteria (Desulfosarcina/Desulfococcus clade) due to an adverse effect of seawater acidification and oil hydrocarbon contamination (reduced pH-oil treatment) may be coupled to changes in sediment archaeal communities. In particular, we observed a pronounced compositional shift and marked reduction in the prevalence of otherwise abundant operational taxonomic units (OTUs) belonging to the archaeal Marine Benthic Group B and Marine Hydrothermal Vent Group (MHVG) in the reduced pH-oil treatment. Conversely, the abundance of several putative hydrocarbonoclastic fungal OTUs was higher in the reduced pH-oil treatment. Sediment hydrocarbon profiling, furthermore, revealed higher concentrations of several alkanes in the reduced pH-oil treatment, corroborating the functional implications of the structural changes to microbial community composition. Collectively, our results advance the understanding of the response of a complex microbial community to the interaction between reduced pH and anthropogenic pollution. In future acidified marine environments, oil hydrocarbon contamination may alter the typical mixotrophic and k-/r-strategist composition of surface sediment microbiomes towards a more heterotrophic state with lower doubling rates, thereby impairing the ability of the ecosystem to recover from acute oil contamination events.}, }
@article {pmid27480227, year = {2016}, author = {Zampieri, Bdel B and Pinto, AB and Schultz, L and de Oliveira, MA and de Oliveira, AJ}, title = {Diversity and Distribution of Heavy Metal-Resistant Bacteria in Polluted Sediments of the Araça Bay, São Sebastião (SP), and the Relationship Between Heavy Metals and Organic Matter Concentrations.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {582-594}, pmid = {27480227}, issn = {1432-184X}, mesh = {Bacillus/drug effects/isolation &amp; purification/metabolism ; Bacteria/drug effects/genetics/isolation &amp; purification/*metabolism ; Base Sequence ; Bays/*analysis/*microbiology ; Biodegradation, Environmental ; Biodiversity ; Brazil ; Cadmium/chemistry ; Chromium/chemistry ; Copper/chemistry ; DNA, Bacterial ; *Drug Resistance, Multiple, Bacterial/drug effects ; Environmental Monitoring ; Geologic Sediments/analysis/*microbiology ; Metals, Heavy/*analysis/toxicity ; Microbial Sensitivity Tests ; Microbiological Techniques ; Multivariate Analysis ; Organic Chemicals ; RNA, Ribosomal, 16S/genetics ; Water Pollutants, Chemical/*metabolism ; Zinc/chemistry ; }, abstract = {Heavy metals influence the population size, diversity, and metabolic activity of bacteria. In turn, bacteria can develop heavy metal resistance mechanisms, and this can be used in bioremediation of contaminated areas. The purpose of the present study was to understand how heavy metals concentration influence on diversity and distribution of heavy metal-resistant bacteria in Araça Bay, São Sebastião, on the São Paulo coast of Brazil. The hypothesis is that activities that contribute for heavy metal disposal and the increase of metals concentrations in environment can influence in density, diversity, and distribution of heavy metal-resistant bacteria. Only 12 % of the isolated bacteria were sensitive to all of the metals tested. We observed that the highest percentage of resistant strains were in areas closest to the São Sebastião channel, where port activity occurs and have bigger heavy metals concentrations. Bacterial isolated were most resistant to Cr, followed by Zn, Cd, and Cu. Few strains resisted to Cd levels greater than 200 mg L(-1). In respect to Cr, 36 % of the strains were able to grow in the presence of as much as 3200 mg L(-1). Few strains were able to grow at concentrations of Zn and Cu as high as 1600 mg L(-1), and none grew at the highest concentration of 3200 mg L(-1). Bacillus sp. was most frequently isolated and may be the dominant genus in heavy metal-polluted areas. Staphylococcus sp., Planococcus maritimus, and Vibrio aginolyticus were also isolated, suggesting their potential in bioremediation of contaminated sites.}, }
@article {pmid27480226, year = {2018}, author = {Brower, JL}, title = {The Threat and Response to Infectious Diseases (Revised).}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {19-36}, pmid = {27480226}, issn = {1432-184X}, mesh = {Bioterrorism ; Climate Change ; Communicable Diseases, Emerging/economics/*etiology/*therapy/transmission ; Disaster Planning ; Disasters ; Drug Misuse ; Drug Resistance ; Drug Users ; Forecasting ; Global Warming ; Humans ; Prescription Drug Overuse ; Risk Factors ; Sexual Behavior ; Social Conditions ; Travel ; Urbanization ; Vaccination ; }, abstract = {The threat from microorganisms is complex, and the approaches for reducing the challenges the world is facing are also multifaceted, but a combination approach including several simple steps can make a difference and reduce morbidity and mortality and the economic cost of fighting infectious diseases. This paper discusses the continually evolving infectious disease landscape, contributing factors in the rise of the threat, reasons for optimism, and the policies, technologies, actions, and institutions that might be harnessed to further reduce the dangers introduced by pathogens. It builds upon and updates the work of other authors that have recognized the dangers of emerging and re-emerging pathogens and have explored and documented potential solutions.}, }
@article {pmid27480015, year = {2016}, author = {Meerburg, FA and Boon, N and Van Winckel, T and Pauwels, KT and Vlaeminck, SE}, title = {Live Fast, Die Young: Optimizing Retention Times in High-Rate Contact Stabilization for Maximal Recovery of Organics from Wastewater.}, journal = {Environmental science &amp; technology}, volume = {50}, number = {17}, pages = {9781-9790}, doi = {10.1021/acs.est.6b01888}, pmid = {27480015}, issn = {1520-5851}, mesh = {Biological Oxygen Demand Analysis ; Bioreactors ; Sewage/*chemistry ; Waste Disposal, Fluid ; Wastewater/*chemistry ; }, abstract = {Wastewater is typically treated by the conventional activated sludge process, which suffers from an inefficient overall energy balance. The high-rate contact stabilization (HiCS) has been proposed as a promising primary treatment technology with which to maximize redirection of organics to sludge for subsequent energy recovery. It utilizes a feast-famine cycle to select for bioflocculation, intracellular storage, or both. We optimized the HiCS process for organics recovery and characterized different biological pathways of organics removal and recovery. A total of eight HiCS reactors were operated at 15 °C at short solids retention times (SRT; 0.24-2.8 days), hydraulic contact times (tc; 8 and 15 min), and stabilization times (ts; 15 and 40 min). At an optimal SRT between 0.5 and 1.3 days and tc of 15 min and ts of 40 min, the HiCS system oxidized only 10% of influent chemical oxygen demand (COD) and recovered up to 55% of incoming organic matter into sludge. Storage played a minor role in the overall COD removal, which was likely dominated by aerobic biomass growth, bioflocculation onto extracellular polymeric substances, and settling. The HiCS process recovers enough organics to potentially produce 28 kWh of electricity per population equivalent per year by anaerobic digestion and electricity generation. This inspires new possibilities for energy-neutral wastewater treatment.}, }
@article {pmid27478692, year = {2016}, author = {Fradet, DT and Tavormina, PL and Orphan, VJ}, title = {Members of the methanotrophic genus Methylomarinum inhabit inland mud pots.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e2116}, pmid = {27478692}, issn = {2167-8359}, abstract = {Proteobacteria capable of converting the greenhouse gas methane to biomass, energy, and carbon dioxide represent a small but important sink in global methane inventories. Currently, 23 genera of methane oxidizing (methanotrophic) proteobacteria have been described, although many are represented by only a single validly described species. Here we describe a new methanotrophic isolate that shares phenotypic characteristics and phylogenetic relatedness with the marine methanotroph Methylomarinum vadi. However, the new isolate derives from a terrestrial saline mud pot at the northern terminus of the Eastern Pacific Rise (EPR). This new cultivar expands our knowledge of the ecology of Methylomarinum, ultimately towards a fuller understanding of the role of this genus in global methane cycling.}, }
@article {pmid27476444, year = {2016}, author = {Janus, MM and Crielaard, W and Zaura, E and Keijser, BJ and Brandt, BW and Krom, BP}, title = {A novel compound to maintain a healthy oral plaque ecology in vitro.}, journal = {Journal of oral microbiology}, volume = {8}, number = {}, pages = {32513}, pmid = {27476444}, issn = {2000-2297}, abstract = {OBJECTIVE: Dental caries is caused by prolonged episodes of low pH due to acid production by oral biofilms. Bacteria within such biofilms communicate via quorum sensing (QS). QS regulates several phenotypic biofilm parameters, such as biofilm formation and the production of virulence factors. In this study, we evaluated the effect of several QS modifiers on growth and the cariogenic potential of microcosm oral biofilms.<br><br>METHODS: Biofilms were inoculated with pooled saliva and cultured in the presence of sucrose for 48 and 96 h. QS modifiers (or carrier controls) were continuously present. Lactic acid accumulation capacities were compared to evaluate the cariogenic potential of the biofilms. Subsequently, biofilm growth was quantified by determining colony forming unit counts (CFUs) and their ecology by 16S rDNA-based microbiome analyses. The minimal inhibitory concentration (MIC) for several Streptococcus spp. was determined using microbroth dilution.<br><br>RESULTS: Of the tested QS modifiers only 3-oxo-N-(2-oxocyclohexyl)dodecanamide (3-Oxo-N) completely abolished lactic acid accumulation by the biofilms without affecting biofilm growth. This compound was selected for further investigation. The active range of 3-Oxo-N was 10-100 &#xb5;M. The homologous QS molecule, acyl homoserine lactone C12, did not counteract the reduction in lactic acid accumulation, suggesting a mechanism other than QS inhibition. Microbial ecology analyses showed a reduction in the relative abundance of Streptococcus spp. in favor of the relative abundance of Veillonella spp. in the 3-Oxo-N exposed biofilms. The MIC of 3-Oxo-N for several streptococcal species varied between 8 and 32 &#xb5;M.<br><br>CONCLUSION: 3-Oxo-N changes the ecological homeostasis of in vitro dental plaque. It reduces its cariogenic potential by minimizing lactic acid accumulation. Based on our in vitro data, 3-Oxo-N represents a promising compound in maintaining a healthy, non-cariogenic, ecology in in vivo dental plaque.}, }
@article {pmid27475818, year = {2016}, author = {Korlević, M and Šupraha, L and Ljubešić, Z and Henderiks, J and Ciglenečki, I and Dautović, J and Orlić, S}, title = {Bacterial diversity across a highly stratified ecosystem: A salt-wedge Mediterranean estuary.}, journal = {Systematic and applied microbiology}, volume = {39}, number = {6}, pages = {398-408}, doi = {10.1016/j.syapm.2016.06.006}, pmid = {27475818}, issn = {1618-0984}, mesh = {Actinobacteria/classification/genetics ; Bacteria/*classification/*genetics ; Bacteroidetes/classification/genetics ; Base Sequence ; Betaproteobacteria/classification/genetics ; Croatia ; Cyanobacteria/classification/genetics ; DNA, Bacterial/genetics ; Ecosystem ; *Estuaries ; Gammaproteobacteria/classification/genetics ; In Situ Hybridization, Fluorescence ; Mediterranean Region ; Microbial Consortia/*genetics ; Phytoplankton ; RNA, Ribosomal, 16S/genetics ; Roseobacter/classification/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Highly stratified Mediterranean estuaries are unique environments where the tidal range is low and the tidal currents are almost negligible. The main characteristics of these environments are strong salinity gradients and other environmental parameters. In this study, 454 pyrosequencing of the 16S rRNA gene in combination with catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) was used to estimate the bacterial diversity across the Krka estuary in February and July 2013. The comparison of the data derived from these two techniques resulted in a significant but weak positive correlation (R=0.28) indicating a substantial difference in the bacterial community structure, depending on the applied method. The phytoplankton bloom observed in February was identified as one of the main factors shaping the bacterial community structure between the two environmentally contrasting sampling months. Roseobacter, Bacteroidetes and Gammaproteobacteria differed substantially between February and July. Typical freshwater bacterial classes (Actinobacteria and Betaproteobacteria) showed strong vertical distribution patterns depending on the salinity gradient. Cyanobacteria decreased in abundance in February due to competition with phytoplankton, while the SAR11 clade increased its abundance in July as a result of a better adaptation toward more oligotrophic conditions. The results provided the first detailed insight into the bacterial diversity in a highly stratified Mediterranean karstic estuary.}, }
@article {pmid27468279, year = {2016}, author = {Adam, E and Groenenboom, AE and Kurm, V and Rajewska, M and Schmidt, R and Tyc, O and Weidner, S and Berg, G and de Boer, W and Falcão Salles, J}, title = {Controlling the Microbiome: Microhabitat Adjustments for Successful Biocontrol Strategies in Soil and Human Gut.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1079}, pmid = {27468279}, issn = {1664-302X}, }
@article {pmid27464604, year = {2016}, author = {Cernava, T and Berg, G and Grube, M}, title = {High Life Expectancy of Bacteria on Lichens.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {510-513}, pmid = {27464604}, issn = {1432-184X}, mesh = {Ascomycota/physiology ; *Bacteria/genetics ; *Bacterial Physiological Phenomena ; DNA, Bacterial ; DNA, Ribosomal ; Genes, Bacterial ; Lichens/*microbiology ; *Life Expectancy ; Microscopy, Confocal ; RNA, Ribosomal, 16S/genetics ; Survival ; Symbiosis ; }, abstract = {Self-sustaining lichen symbioses potentially can become very old, sometimes even thousands of years in nature. In the joint structures, algal partners are sheltered between fungal structures that are externally colonized by bacterial communities. With this arrangement lichens survive long periods of drought, and lichen thalli can be revitalized even after decades of dry storage in a herbarium. To study the effects of long-term ex situ storage on viability of indigenous bacterial communities we comparatively studied herbarium-stored material of the lung lichen, Lobaria pulmonaria. We discovered that a significant fraction of the lichen-associated bacterial community survives herbarium storage of nearly 80 years, and living bacteria can still be found in even older material. As the bacteria reside in the upper surface layers of the lichen material, we argue that the extracellular polysaccharides of lichens contribute to superior life expectancy of bacteria. Deeper understanding of underlying mechanisms could provide novel possibilities for biotechnological applications.}, }
@article {pmid27463035, year = {2016}, author = {Beet, CR and Hogg, ID and Collins, GE and Cowan, DA and Wall, DH and Adams, BJ}, title = {Genetic diversity among populations of Antarctic springtails (Collembola) within the Mackay Glacier ecotone.}, journal = {Genome}, volume = {59}, number = {9}, pages = {762-770}, doi = {10.1139/gen-2015-0194}, pmid = {27463035}, issn = {1480-3321}, mesh = {Animals ; Antarctic Regions ; Arthropods/*classification/*genetics ; DNA, Mitochondrial ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; *Genetic Variation ; *Genetics, Population ; Haplotypes ; Phylogeny ; }, abstract = {Climate changes are likely to have major influences on the distribution and abundance of Antarctic terrestrial biota. To assess arthropod distribution and diversity within the Ross Sea region, we examined mitochondrial DNA (COI) sequences for three currently recognized species of springtail (Collembola) collected from sites in the vicinity, and to the north of, the Mackay Glacier (77°S). This area acts as a transition between two biogeographic regions (northern and southern Victoria Land). We found populations of highly divergent individuals (5%-11.3% intraspecific sequence divergence) for each of the three putative springtail species, suggesting the possibility of cryptic diversity. Based on molecular clock estimates, these divergent lineages are likely to have been isolated for 3-5 million years. It was during this time that the Western Antarctic Ice Sheet (WAIS) was likely to have completely collapsed, potentially facilitating springtail dispersal via rafting on running waters and open seaways. The reformation of the WAIS would have isolated newly established populations, with subsequent dispersal restricted by glaciers and ice-covered areas. Given the currently limited distributions for these genetically divergent populations, any future changes in species' distributions can be easily tracked through the DNA barcoding of springtails from within the Mackay Glacier ecotone.}, }
@article {pmid27461253, year = {2016}, author = {Vicente, CS and Nascimento, FX and Barbosa, P and Ke, HM and Tsai, IJ and Hirao, T and Cock, PJ and Kikuchi, T and Hasegawa, K and Mota, M}, title = {Evidence for an Opportunistic and Endophytic Lifestyle of the Bursaphelenchus xylophilus-Associated Bacteria Serratia marcescens PWN146 Isolated from Wilting Pinus pinaster.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {669-681}, pmid = {27461253}, issn = {1432-184X}, mesh = {Animals ; Anti-Infective Agents ; Antinematodal Agents/pharmacology ; Base Sequence ; Classification ; Coleoptera/microbiology ; DNA, Bacterial ; *Endophytes ; Genes, Bacterial ; Host-Parasite Interactions/physiology ; Insect Vectors/microbiology ; *Life Style ; Microscopy, Confocal ; Microscopy, Electron, Scanning ; Molecular Sequence Annotation ; Nematoda/pathogenicity ; *Opportunistic Infections ; Phylogeny ; Pinus/*microbiology/parasitology ; Plant Diseases/microbiology ; Serratia marcescens/genetics/*isolation &amp; purification/*pathogenicity/*physiology ; Trees/microbiology/parasitology ; Tylenchida/drug effects/*microbiology/pathogenicity ; }, abstract = {Pine wilt disease (PWD) results from the interaction of three elements: the pathogenic nematode, Bursaphelenchus xylophilus; the insect-vector, Monochamus sp.; and the host tree, mostly Pinus species. Bacteria isolated from B. xylophilus may be a fourth element in this complex disease. However, the precise role of bacteria in this interaction is unclear as both plant-beneficial and as plant-pathogenic bacteria may be associated with PWD. Using whole genome sequencing and phenotypic characterization, we were able to investigate in more detail the genetic repertoire of Serratia marcescens PWN146, a bacterium associated with B. xylophilus. We show clear evidence that S. marcescens PWN146 is able to withstand and colonize the plant environment, without having any deleterious effects towards a susceptible host (Pinus thunbergii), B. xylophilus nor to the nematode model C. elegans. This bacterium is able to tolerate growth in presence of xenobiotic/organic compounds, and use phenylacetic acid as carbon source. Furthermore, we present a detailed list of S. marcescens PWN146 potentials to interfere with plant metabolism via hormonal pathways and/or nutritional acquisition, and to be competitive against other bacteria and/or fungi in terms of resource acquisition or production of antimicrobial compounds. Further investigation is required to understand the role of bacteria in PWD. We have now reinforced the theory that B. xylophilus-associated bacteria may have a plant origin.}, }
@article {pmid27460793, year = {2016}, author = {Mizuno, CM and Ghai, R and Saghaï, A and López-García, P and Rodriguez-Valera, F}, title = {Genomes of Abundant and Widespread Viruses from the Deep Ocean.}, journal = {mBio}, volume = {7}, number = {4}, pages = {}, pmid = {27460793}, issn = {2150-7511}, support = {322669/ERC_/European Research Council/International ; }, mesh = {Bacteriophages/*classification/genetics/*isolation &amp; purification ; *Genome, Viral ; Metagenomics ; *Oceans and Seas ; Phylogeny ; Prophages/classification/genetics/isolation &amp; purification ; Seawater/*microbiology ; Sequence Homology ; Synteny ; Viral Proteins/genetics ; }, abstract = {UNLABELLED: The deep sea is a massive, largely oligotrophic ecosystem, stretched over nearly 65% of the planet's surface. Deep-sea planktonic communities are almost completely dependent upon organic carbon sinking from the productive surface, forming a vital component of global biogeochemical cycles. However, despite their importance, viruses from the deep ocean remain largely unknown. Here, we describe the first complete genomes of deep-sea viruses assembled from metagenomic fosmid libraries. "Candidatus Pelagibacter" (SAR11) phage HTVC010P and Puniceispirillum phage HMO-2011 are considered the most abundant cultured marine viruses known to date. Remarkably, some of the viruses described here recruited as many reads from deep waters as these viruses do in the photic zone, and, considering the gigantic scale of the bathypelagic habitat, these genomes provide information about what could be some of the most abundant viruses in the world at large. Their role in the viral shunt in the global ocean could be very significant. Despite the challenges encountered in inferring the identity of their hosts, we identified one virus predicted to infect members of the globally distributed SAR11 cluster. We also identified a number of putative proviruses from diverse taxa, including deltaproteobacteria, bacteroidetes, SAR11, and gammaproteobacteria. Moreover, our findings also indicate that lysogeny is the preferred mode of existence for deep-sea viruses inhabiting an energy-limited environment, in sharp contrast to the predominantly lytic lifestyle of their photic-zone counterparts. Some of the viruses show a widespread distribution, supporting the tenet "everything is everywhere" for the deep-ocean virome.<br><br>IMPORTANCE: The deep sea is among the largest known habitats and a critical cog in biogeochemical cycling but remains underexplored in its microbiology. Even more than is the case for its prokaryotic community, our knowledge of its viral component has remained limited by the paucity of information provided by studies dependent upon short sequence fragments. In this work, we attempt to fill this existing gap by using a combination of classical fosmid libraries with next-generation sequencing and assembly to recover long viral genomic fragments. We have sequenced ca. 6,000 fosmids from two metagenomics libraries made from prokaryotic biomass from the deep Mediterranean Sea and recovered twenty-eight complete viral genomes, all of them novel and quite distinct from all previously described viral genomes. They are preferentially found in deeper waters and are widely distributed all over the oceans. To our knowledge, this is the first report on complete and cosmopolitan viral genomes from the bathypelagic habitat.}, }
@article {pmid27460381, year = {2016}, author = {Leray, M and Knowlton, N}, title = {Visualizing Patterns of Marine Eukaryotic Diversity from Metabarcoding Data Using QIIME.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1452}, number = {}, pages = {219-235}, doi = {10.1007/978-1-4939-3774-5_15}, pmid = {27460381}, issn = {1940-6029}, mesh = {Biodiversity ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; Humans ; Microbiota/genetics ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {PCR amplification followed by deep sequencing of homologous gene regions is increasingly used to characterize the diversity and taxonomic composition of marine eukaryotic communities. This approach may generate millions of sequences for hundreds of samples simultaneously. Therefore, tools that researchers can use to visualize complex patterns of diversity for these massive datasets are essential. Efforts by microbiologists to understand the Earth and human microbiomes using high-throughput sequencing of the 16S rRNA gene has led to the development of several user-friendly, open-source software packages that can be similarly used to analyze eukaryotic datasets. Quantitative Insights Into Microbial Ecology (QIIME) offers some of the most helpful data visualization tools. Here, we describe functionalities to import OTU tables generated with any molecular marker (e.g., 18S, COI, ITS) and associated metadata into QIIME. We then present a range of analytical tools implemented within QIIME that can be used to obtain insights about patterns of alpha and beta diversity for marine eukaryotes.}, }
@article {pmid27460335, year = {2016}, author = {Soares, JR and Cassman, NA and Kielak, AM and Pijl, A and Carmo, JB and Lourenço, KS and Laanbroek, HJ and Cantarella, H and Kuramae, EE}, title = {Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {30349}, pmid = {27460335}, issn = {2045-2322}, mesh = {Ammonia/*metabolism ; Fertilizers/*adverse effects ; Greenhouse Gases/*chemistry ; *Microbiota ; Nitrogen Cycle ; Nitrogen Fixation ; Nitrous Oxide/*analysis/metabolism ; Soil/chemistry ; *Soil Microbiology ; Tropical Climate ; Urea/metabolism ; }, abstract = {Nitrous oxide (N2O) from nitrogen fertilizers applied to sugarcane has high environmental impact on ethanol production. This study aimed to determine the main microbial processes responsible for the N2O emissions from soil fertilized with different N sources, to identify options to mitigate N2O emissions, and to determine the impacts of the N sources on the soil microbiome. In a field experiment, nitrogen was applied as calcium nitrate, urea, urea with dicyandiamide or 3,4 dimethylpyrazone phosphate nitrification inhibitors (NIs), and urea coated with polymer and sulfur (PSCU). Urea caused the highest N2O emissions (1.7% of N applied) and PSCU did not reduce cumulative N2O emissions compared to urea. NIs reduced N2O emissions (95%) compared to urea and had emissions comparable to those of the control (no N). Similarly, calcium nitrate resulted in very low N2O emissions. Interestingly, N2O emissions were significantly correlated only with bacterial amoA, but not with denitrification gene (nirK, nirS, nosZ) abundances, suggesting that ammonia-oxidizing bacteria, via the nitrification pathway, were the main contributors to N2O emissions. Moreover, the treatments had little effect on microbial composition or diversity. We suggest nitrate-based fertilizers or the addition of NIs in NH4(+)-N based fertilizers as viable options for reducing N2O emissions in tropical soils and lessening the environmental impact of biofuel produced from sugarcane.}, }
@article {pmid27459857, year = {2016}, author = {de Menezes, AB and Müller, C and Clipson, N and Doyle, E}, title = {The soil microbiome at the Gi-FACE experiment responds to a moisture gradient but not to CO2 enrichment.}, journal = {Microbiology (Reading, England)}, volume = {162}, number = {9}, pages = {1572-1582}, doi = {10.1099/mic.0.000341}, pmid = {27459857}, issn = {1465-2080}, mesh = {Air/*analysis ; Bacteria/classification/genetics/*isolation &amp; purification ; Carbon Dioxide/analysis/*metabolism ; Microbiota ; Soil/*chemistry ; *Soil Microbiology ; Water/*analysis/metabolism ; }, abstract = {The soil bacterial community at the Giessen free-air CO2 enrichment (Gi-FACE) experiment was analysed by tag sequencing of the 16S rRNA gene. No substantial effects of CO2 levels on bacterial community composition were detected. However, the soil moisture gradient at Gi-FACE had a significant effect on bacterial community composition. Different groups within the Acidobacteria and Verrucomicrobia phyla were affected differently by soil moisture content. These results suggest that modest increases in atmospheric CO2 may cause only minor changes in soil bacterial community composition and indicate that the functional responses of the soil community to CO2 enrichment previously reported at Gi-FACE are due to factors other than changes in bacterial community composition. The effects of the moisture gradient revealed new information about the relationships between poorly known Acidobacteria and Verrucomicrobia and soil moisture content. This study contrasts with the relatively small number of other temperate grassland free-air CO2 enrichment microbiome studies in the use of moderate CO2 enrichment and the resulting minor changes in the soil microbiome. Thus, it will facilitate the development of further climate change mitigation studies. In addition, the moisture gradient found at Gi-FACE contributes new knowledge in soil microbial ecology, particularly regarding the abundance and moisture relationships of the soil Verrucomicrobia.}, }
@article {pmid27459256, year = {2016}, author = {Eckert, EM and Di Cesare, A and Stenzel, B and Fontaneto, D and Corno, G}, title = {Daphnia as a refuge for an antibiotic resistance gene in an experimental freshwater community.}, journal = {The Science of the total environment}, volume = {571}, number = {}, pages = {77-81}, doi = {10.1016/j.scitotenv.2016.07.141}, pmid = {27459256}, issn = {1879-1026}, mesh = {Animals ; Antiporters/*analysis ; Bacteria/*genetics ; Bacterial Proteins/*analysis ; Daphnia/*microbiology/physiology ; Feeding Behavior ; Italy ; Lakes/microbiology ; *Microbiota ; Tetracycline/pharmacology ; *Tetracycline Resistance ; }, abstract = {Mechanisms that enable the maintenance of antibiotic resistance genes in the environment are still greatly unknown. Here we show that the tetracycline resistance gene tet(A) is largely removed from the pelagic aquatic bacterial community through filter feeding by Daphnia obtusa while it becomes detectable within the microbiome of the daphniids themselves, where it was not present prior to the experiment. We moreover show that a multitude of Daphnia-associated bacterial taxa are potential carriers of tet(A) and postulated that the biofilm-like structures, where bacteria grow in, may enable horizontal transfer of such genes. This experiment highlights the need to take ecological interactions and a broad range of niches into consideration when studying and discussing the fate of antibiotic resistance genes in nature.}, }
@article {pmid27458442, year = {2016}, author = {Mason, OU and Canter, EJ and Gillies, LE and Paisie, TK and Roberts, BJ}, title = {Mississippi River Plume Enriches Microbial Diversity in the Northern Gulf of Mexico.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1048}, pmid = {27458442}, issn = {1664-302X}, abstract = {The Mississippi River (MR) serves as the primary source of freshwater and nutrients to the northern Gulf of Mexico (nGOM). Whether this input of freshwater also enriches microbial diversity as the MR plume migrates and mixes with the nGOM serves as the central question addressed herein. Specifically, in this study physicochemical properties and planktonic microbial community composition and diversity was determined using iTag sequencing of 16S rRNA genes in 23 samples collected along a salinity (and nutrient) gradient from the mouth of the MR, in the MR plume, in the canyon, at the Deepwater Horizon wellhead and out to the loop current. Analysis of these datasets revealed that the MR influenced microbial diversity as far offshore as the Deepwater Horizon wellhead. The MR had the highest microbial diversity, which decreased with increasing salinity. MR bacterioplankton communities were distinct compared to the nGOM, particularly in the surface where Actinobacteria and Proteobacteria dominated, while the deeper MR was also enriched in Thaumarchaeota. Statistical analyses revealed that nutrients input by the MR, along with salinity and depth, were the primary drivers in structuring the microbial communities. These results suggested that the reduced salinity, nutrient enriched MR plume could act as a seed bank for microbial diversity as it mixes with the nGOM. Whether introduced microorganisms are active at higher salinities than freshwater would determine if this seed bank for microbial diversity is ecologically significant. Alternatively, microorganisms that are physiologically restricted to freshwater habitats that are entrained in the plume could be used as tracers for freshwater input to the marine environment.}, }
@article {pmid27458441, year = {2016}, author = {Labbate, M and Seymour, JR and Lauro, F and Brown, MV}, title = {Editorial: Anthropogenic Impacts on the Microbial Ecology and Function of Aquatic Environments.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1044}, pmid = {27458441}, issn = {1664-302X}, }
@article {pmid27457653, year = {2016}, author = {Vikram, A and Lipus, D and Bibby, K}, title = {Metatranscriptome analysis of active microbial communities in produced water samples from the Marcellus Shale.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {571-581}, pmid = {27457653}, issn = {1432-184X}, mesh = {Alginates/metabolism ; Bacteria/classification/*genetics/metabolism ; Base Sequence ; Biofilms/growth &amp; development ; Biofouling ; DNA, Bacterial ; Disinfectants ; Gene Expression Regulation, Bacterial ; Glucuronic Acid/metabolism ; Hexuronic Acids/metabolism ; Industrial Microbiology ; Metabolic Networks and Pathways/genetics ; Methane/biosynthesis/metabolism ; Microbial Consortia/*genetics ; Osmotic Pressure ; Oxidative Stress ; Pennsylvania ; RNA, Ribosomal, 16S/genetics ; Sulfides/metabolism ; Transcriptome/*genetics ; Wastewater/*microbiology ; Water/metabolism ; *Water Microbiology ; Water Purification ; }, abstract = {Controlling microbial activity is a primary concern during the management of the large volumes of wastewater (produced water) generated during high-volume hydraulic fracturing. In this study we analyzed the transcriptional activity (metatranscriptomes) of three produced water samples from the Marcellus Shale. The goal of this study was to describe active metabolic pathways of industrial concern for produced water management and reuse, and to improve understanding of produced water microbial activity. Metatranscriptome analysis revealed active biofilm formation, sulfide production, and stress management mechanisms of the produced water microbial communities. Biofilm-formation and sulfate-reduction pathways were identified in all samples. Genes related to a diverse array of stress response mechanisms were also identified with implications for biocide efficacy. Additionally, active expression of a methanogenesis pathway was identified in a sample of produced water collected prior to holding pond storage. The active microbial community identified by metatranscriptome analysis was markedly different than the community composition as identified by 16S rRNA sequencing, highlighting the value of evaluating the active microbial fraction during assessments of produced water biofouling potential and evaluation of biocide application strategies. These results indicate biofouling and corrosive microbial processes are active in produced water and should be taken into consideration while designing produced water reuse strategies.}, }
@article {pmid27457652, year = {2016}, author = {Vekeman, B and Speth, D and Wille, J and Cremers, G and De Vos, P and Op den Camp, HJ and Heylen, K}, title = {Genome Characteristics of Two Novel Type I Methanotrophs Enriched from North Sea Sediments Containing Exclusively a Lanthanide-Dependent XoxF5-Type Methanol Dehydrogenase.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {503-509}, pmid = {27457652}, issn = {1432-184X}, mesh = {Alcohol Oxidoreductases/*genetics ; Bacterial Proteins/*genetics/metabolism ; Base Composition ; Calcium ; DNA, Bacterial/genetics ; Ecosystem ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Enzymologic ; Genome, Bacterial ; Geologic Sediments/*microbiology ; Lanthanoid Series Elements/*pharmacology ; Metabolic Networks and Pathways/genetics ; Methane/metabolism ; Methylococcaceae/classification/drug effects/*enzymology/*genetics ; Nitrogen/metabolism ; North Sea ; Oxidation-Reduction ; Oxygenases/genetics ; Phylogeny ; Seawater/microbiology ; Tetrahydrofolates/genetics ; }, abstract = {Microbial methane oxidizers play a crucial role in the oxidation of methane in marine ecosystems, as such preventing the escape of excessive methane to the atmosphere. Despite the important role of methanotrophs in marine ecosystems, only a limited number of isolates are described, with only four genomes available. Here, we report on two genomes of gammaproteobacterial methanotroph cultures, affiliated with the deep-sea cluster 2, obtained from North Sea sediment. Initial enrichments using methane as sole source of carbon and energy and mimicking the in situ conditions followed by serial subcultivations and multiple extinction culturing events over a period of 3 years resulted in a highly enriched culture. The draft genomes of the methane oxidizer in both cultures showed the presence of genes typically found in type I methanotrophs, including genes encoding particulate methane monooxygenase (pmoCAB), genes for tetrahydromethanopterin (H4MPT)- and tetrahydrofolate (H4F)-dependent C1-transfer pathways, and genes of the ribulose monophosphate (RuMP) pathway. The most distinctive feature, when compared to other available gammaproteobacterial genomes, is the absence of a calcium-dependent methanol dehydrogenase. Both genomes reported here only have a xoxF gene encoding a lanthanide-dependent XoxF5-type methanol dehydrogenase. Thus, these genomes offer novel insight in the genomic landscape of uncultured diversity of marine methanotrophs.}, }
@article {pmid27450478, year = {2016}, author = {Martirosyan, V and Unc, A and Miller, G and Doniger, T and Wachtel, C and Steinberger, Y}, title = {Desert Perennial Shrubs Shape the Microbial-Community Miscellany in Laimosphere and Phyllosphere Space.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {659-668}, pmid = {27450478}, issn = {1432-184X}, mesh = {Adaptation, Biological ; Amaranthaceae/microbiology ; Artemisia/microbiology ; Atriplex/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Base Sequence ; *Biodiversity ; *Biota ; DNA, Bacterial ; DNA, Fungal ; *Desert Climate ; Ecology ; Ecosystem ; Fungi/classification/genetics/isolation &amp; purification ; Israel ; *Microbial Consortia ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Plants/classification/*microbiology ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Species Specificity ; Stem Cells ; }, abstract = {Microbial function, composition, and distribution play a fundamental role in ecosystem ecology. The interaction between desert plants and their associated microbes is expected to greatly affect their response to changes in this harsh environment. Using comparative analyses, we studied the impact of three desert shrubs, Atriplex halimus (A), Artemisia herba-alba (AHA), and Hammada scoparia (HS), on soil- and leaf-associated microbial communities. DNA extracted from the leaf surface and soil samples collected beneath the shrubs were used to study associated microbial diversity using a sequencing survey of variable regions of bacterial 16S rRNA and fungal ribosomal internal transcribed spacer (ITS1). We found that the composition of bacterial and fungal orders is plant-type-specific, indicating that each plant type provides a suitable and unique microenvironment. The different adaptive ecophysiological properties of the three plant species and the differential effect on their associated microbial composition point to the role of adaptation in the shaping of microbial diversity. Overall, our findings suggest a link between plant ecophysiological adaptation as a "temporary host" and the biotic-community parameters in extreme xeric environments.}, }
@article {pmid27450202, year = {2017}, author = {Riva, A and Borgo, F and Lassandro, C and Verduci, E and Morace, G and Borghi, E and Berry, D}, title = {Pediatric obesity is associated with an altered gut microbiota and discordant shifts in Firmicutes populations.}, journal = {Environmental microbiology}, volume = {19}, number = {1}, pages = {95-105}, pmid = {27450202}, issn = {1462-2920}, support = {P 26127/FWF_/Austrian Science Fund FWF/Austria ; P 27831/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Adolescent ; Bacteroidetes/classification/genetics/*growth &amp; development ; Child ; Diet ; Dysbiosis/*microbiology ; Fatty Acids, Volatile/*metabolism ; Feces/microbiology ; Female ; Fermentation/genetics ; Firmicutes/classification/genetics/*growth &amp; development ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Molecular Typing ; Pediatric Obesity/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {An altered gut microbiota has been linked to obesity in adulthood, although little is known about childhood obesity. The aim of this study was to characterize the composition of the gut microbiota in obese (n = 42) and normal-weight (n = 36) children aged 6 to 16. Using 16S rRNA gene-targeted sequencing, we evaluated taxa with differential abundance according to age- and sex-normalized body mass index (BMI z-score). Obesity was associated with an altered gut microbiota characterized by elevated levels of Firmicutes and depleted levels of Bacteroidetes. Correlation network analysis revealed that the gut microbiota of obese children also had increased correlation density and clustering of operational taxonomic units (OTUs). Members of the Bacteroidetes were generally better predictors of BMI z-score and obesity than Firmicutes, which was likely due to discordant responses of Firmicutes OTUs. In accordance with these observations, the main metabolites produced by gut bacteria, short chain fatty acids (SCFAs), were higher in obese children, suggesting elevated substrate utilisation. Multiple taxa were correlated with SCFA levels, reinforcing the tight link between the microbiota, SCFAs and obesity. Our results suggest that gut microbiota dysbiosis and elevated fermentation activity may be involved in the etiology of childhood obesity.}, }
@article {pmid27448106, year = {2018}, author = {Lee, KH and Wang, YF and Wang, Y and Gu, JD and Jiao, JJ}, title = {Abundance and Diversity of Aerobic/Anaerobic Ammonia/Ammonium-Oxidizing Microorganisms in an Ammonium-Rich Aquitard in the Pearl River Delta of South China.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {81-91}, pmid = {27448106}, issn = {1432-184X}, support = {HKU 702707P//General Research Fund of the Research Grants Council/ ; }, mesh = {Aerobiosis ; Ammonia/*metabolism ; Ammonium Compounds/*metabolism ; Anaerobiosis ; Archaea/classification/genetics/metabolism ; Bacteria/*classification/genetics/*metabolism ; *Biodiversity ; China ; DNA, Archaeal/genetics/isolation &amp; purification ; DNA, Bacterial/genetics/isolation &amp; purification ; Estuaries ; Genes, Bacterial/genetics ; Geologic Sediments/chemistry/microbiology ; Hydrogen-Ion Concentration ; Microbiota/genetics/physiology ; *Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; *Soil Microbiology ; Wastewater ; }, abstract = {Natural occurring groundwater with abnormally high ammonium concentrations was discovered in the aquifer-aquitard system in the Pearl River Delta, South China. The community composition and abundance of aerobic/anaerobic ammonia/ammonium-oxidizing microorganisms (AOM) in the aquitard were investigated in this study. The alpha subunit of ammonia monooxygenase gene (amoA) was used as the biomarker for the detection of aerobic ammonia-oxidizing archaea (AOA) and bacteria (AOB), and also partial 16S rRNA gene for Plantomycetes and anaerobic ammonium-oxidizing (anammox) bacteria. Phylogenetic analysis showed that AOA in this aquitard were affiliated with those from water columns and wastewater treatment plants; and AOB were dominated by sequences among the Nitrosomonas marina/Nitrosomonas oligotropha lineage, which were affiliated with environmental sequences from coastal eutrophic bay and subtropical estuary. The richness and diversity of both AOA and AOB communities had very little variations with the depth. Candidatus Scalindua-related sequences dominated the anammox bacterial community. AOB amoA gene abundances were always higher than those of AOA at different depths in this aquitard. The Pearson moment correlation analysis showed that AOA amoA gene abundance positively correlated with pH and ammonium concentration, whereas AOB amoA gene abundance negatively correlated with C/N ratio. This is the first report that highlights the presence with low diversity of AOM communities in natural aquitard of rich ammonium.}, }
@article {pmid27447798, year = {2016}, author = {Ben Salem, I and Mezni, M and Boulila, A and Hamdi, M and Saidi, M}, title = {Removal of Penicillin G and Erythromycin with Ionizing Radiation Followed by Biological Treatment.}, journal = {Current microbiology}, volume = {73}, number = {4}, pages = {582-586}, pmid = {27447798}, issn = {1432-0991}, mesh = {Anti-Bacterial Agents/*chemistry/metabolism ; Biodegradation, Environmental ; Cupriavidus/*metabolism/radiation effects ; Erythromycin/*chemistry/metabolism ; Gamma Rays ; Molecular Structure ; Oxidation-Reduction ; Penicillin G/*chemistry/metabolism ; Spectroscopy, Fourier Transform Infrared ; }, abstract = {The decomposition of penicillin G and erythromycin antibiotics at concentration of 0.2 mg ml(-1) by gamma irradiation at 50 kGy followed by biological treatment with Cupriavidus metallidurans CH34 was evaluated. Degradation of penicillin G and erythromycin was analyzed using nuclear magnetic resonance analysis (NMR), fourier transform infrared spectroscopy (FTIR), and chemical oxygen demand (COD). The exposure to the absorbed dose of 50 kGy caused degradation of penicillin G and erythromycin in the aqueous solution. The complete disappearance of NMR and FTIR peaks following irradiation confirmed the breakage of the β-lactam ring in penicillin G, and the decarboxylation and cleavage of the thiazolidine ring and for erythromycin, the complete destruction of the three aromatic rings. Irradiation alone removed 52.8 and 65.5 % of penicillin G and erythromycin, respectively. Further reduction to 12.6 and 14 % of the original penicillin G and erythromycin COD, respectively, was achieved using treatment of the irradiation products with C. metallidurans.}, }
@article {pmid27446028, year = {2016}, author = {Liang, R and Davidova, IA and Marks, CR and Stamps, BW and Harriman, BH and Stevenson, BS and Duncan, KE and Suflita, JM}, title = {Metabolic Capability of a Predominant Halanaerobium sp. in Hydraulically Fractured Gas Wells and Its Implication in Pipeline Corrosion.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {988}, pmid = {27446028}, issn = {1664-302X}, abstract = {Microbial activity associated with produced water from hydraulic fracturing operations can lead to gas souring and corrosion of carbon-steel equipment. We examined the microbial ecology of produced water and the prospective role of the prevalent microorganisms in corrosion in a gas production field in the Barnett Shale. The microbial community was mainly composed of halophilic, sulfidogenic bacteria within the order Halanaerobiales, which reflected the geochemical conditions of highly saline water containing sulfur species (S2O3 (2-), SO4 (2-), and HS(-)). A predominant, halophilic bacterium (strain DL-01) was subsequently isolated and identified as belonging to the genus Halanaerobium. The isolate could degrade guar gum, a polysaccharide polymer used in fracture fluids, to produce acetate and sulfide in a 10% NaCl medium at 37°C when thiosulfate was available. To mitigate potential deleterious effects of sulfide and acetate, a quaternary ammonium compound was found to be an efficient biocide in inhibiting the growth and metabolic activity of strain DL-01 relative to glutaraldehyde and tetrakis (hydroxymethyl) phosphonium sulfate. Collectively, our findings suggest that predominant halophiles associated with unconventional shale gas extraction could proliferate and produce sulfide and acetate from the metabolism of polysaccharides used in hydraulic fracturing fluids. These metabolic products might be returned to the surface and transported in pipelines to cause pitting corrosion in downstream infrastructure.}, }
@article {pmid27445994, year = {2016}, author = {Zhang, M and Brons, JK and van Elsas, JD}, title = {The Complete Sequences and Ecological Roles of Two IncP-1β Plasmids, pHB44 and pBS64, Isolated from the Mycosphere of Laccaria proxima.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {909}, pmid = {27445994}, issn = {1664-302X}, abstract = {Two novel plasmids, coined pHB44 and pBS64, were recently found in Variovorax paradoxus strains HB44 and BS64 isolated from the mycosphere of Laccaria proxima, on two different sampling occasions. We here describe the full sequences of pHB44 and pBS64 and establish their evolutionary placement and ecological function. Both plasmids, unique for mycospheric V. paradoxus, were around 58 kb in size. They possessed, in a very similar fashion, three main plasmid backbone regions, which were predicted to be involved in plasmid replication, central control of maintenance, and conjugational transfer. Phylogenetic inference on the basis of seven selected and concatenated plasmid backbone genes provided solid evidence for the placement of the two plasmids in the IncP-1β1 group, with the recently isolated IncP-1β1 plasmid pMBUI8 as the closest relative. A comparative analysis of the sequences present in each of the recombinational hot spots (RHS) I to III across plasmids pHB44, pBS64, and pMBUI8 revealed the insertions found in plasmids pHB44 and pBS64 to be different from those of pMBUI8. Whereas, in the former two plasmids, RHS I and III were devoid of any major inserts, their RHS II regions contained inserts of 15,043 (pHB44) and 16,406 kb (pBS64), against about 9,3 kb for pMBUI8. Interestingly, these regions were highly similar across plasmids pHB44 and pBS64, and differed from that of pMBUI8. Closer inspection revealed the insert in the former plasmids to contain, next to transposases, an "mmf" gene cassette previously reported to encode metal "responsiveness" in the PromA plasmid pMOL98. Whereas the plasmid pHB44 RHS II contained the canonical mmf sequence, that in pBS64 contained, in addition, a "two-gene duplicated region" flanking the mmf C2 gene. In vitro experiments on the growth and survival of strains with or without plasmid pHB44 suggested this plasmid was involved in the binding and import of Fe(3+) as well as V(3+) ions into the host cells, thus yielding a growth advantage under "metal ion-limiting" conditions. In addition, pHB44 was found to confer a bacitracin resistance phenotype to its host strain HB44. The metal import and bacitracin resistance traits were tentatively attributed to specific genes present in the RHS II inserts.}, }
@article {pmid27441565, year = {2016}, author = {Subramaniam, A and Ptacek, T and Lobashevsky, E and Cliver, S and Lefkowitz, EJ and Morrow, CD and Biggio, JR and Edwards, RK}, title = {Midtrimester Cervicovaginal Microbiota: Identification of Microbial Variations Associated with Puerperal Infection at Term.}, journal = {American journal of perinatology}, volume = {33}, number = {12}, pages = {1165-1175}, pmid = {27441565}, issn = {1098-8785}, support = {P30 AI027767/AI/NIAID NIH HHS/United States ; P30 AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR000165/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Bacteria/*isolation &amp; purification ; Cervix Uteri/*microbiology ; Female ; Humans ; *Microbiota ; Obesity/epidemiology ; Pregnancy ; Pregnancy Trimester, Second ; Proteobacteria/isolation &amp; purification ; Puerperal Infection/*epidemiology ; Vagina/*microbiology ; Young Adult ; }, abstract = {Objective This study aims to evaluate differences in the midtrimester cervicovaginal microbiota between women who developed puerperal infections at term and those who did not, and whether obesity modulates this relationship. Methods Previously, cervicovaginal swabs were collected at 21 to 25 weeks gestation (stored at -80°C). Samples were identified from Black women with normal vaginal flora (Nugent score: 0-2) delivering term singletons. Patients were in one of four equally sized groups (total n = 120) characterized by absence or presence of puerperal infection and maternal obesity. Samples were thawed, DNA extracted, and polymerase chain reaction with primers targeting the 16S rDNA V4 region was used to prepare an amplicon library sequenced and analyzed using Quantitative Insights into Microbial Ecology (QIIME) suite. Microbiota differences were assessed using permutation-based anodis over three β-diversity measures; Kruskal-Wallis test was used for taxa level analysis. Results After quality control measures, 113 samples were analyzed. Overall, there was significant clustering by puerperal infection (p = 0.03), but not by obesity (p > 0.05). Detailed taxa level analysis revealed approximately 66% less Proteobacteria phylum and 400% more BVAB1 genera in the second-trimester microbiota of women who had puerperal infections at term (p < 0.05). Conclusion Women who develop puerperal infections at term have a significantly altered midtrimester cervicovaginal microbiome with less Proteobacteria and greater BVAB1. This finding may represent a potential method to identify women at an increased risk of puerperal infection.}, }
@article {pmid27440168, year = {2017}, author = {Shao, Y and Ding, R and Xu, B and Hua, R and Shen, Q and He, K and Yao, Q}, title = {Alterations of Gut Microbiota After Roux-en-Y Gastric Bypass and Sleeve Gastrectomy in Sprague-Dawley Rats.}, journal = {Obesity surgery}, volume = {27}, number = {2}, pages = {295-302}, pmid = {27440168}, issn = {1708-0428}, mesh = {Animals ; *Gastrectomy/methods ; *Gastric Bypass/methods ; Gastrointestinal Microbiome/*physiology ; Male ; Obesity, Morbid/microbiology/*surgery ; Postoperative Period ; Rats ; Rats, Sprague-Dawley ; }, abstract = {BACKGROUND: The objective of the study was to compare gut microbiota post Roux-en-Y gastric bypass (RYGB) and sleeve gastrectomy (SG).<br><br>METHODS: Sprague-Dawley rats were randomized to RYGB, SG, or sham surgery. Body weight was measured. Fecal samples were collected before and 1, 3, 6, and 9&#xa0;weeks postoperatively. Fecal microbiota was profiled by 16S ribosomal DNA gene sequencing and analyzed using Quantitative Insights into Microbial Ecology (QIIME) to determine the &#x3b1; and &#x3b2; diversities of gut microbiota.<br><br>RESULTS: The body weight of the RYGB and SG group was significantly lower than that of the sham group. Unweighted UniFrac-based principal coordinate analysis of 5,323,091 sequences from 85 fecal samples from 17 rats revealed a distinct cluster of gut microbiota post RYGB from SG and sham surgery. The percentage of Proteobacteria in the SG and sham group remained markedly lower than that of the RYGB group from 3&#xa0;weeks postoperatively, while the proportion of Gammaproteobacteria in the RYGB group was significantly higher than that of the SG group and the sham group from 3&#xa0;weeks postoperatively. Furthermore, the RYGB group was postoperatively enriched for Gammaproteobacteria and Bacteroidaceae, whereas the SG group was postoperatively enriched for Desulfovibrionaceae and Cyanobacteria. Compared to the pre-operative parameters, the RYGB group had a persistent increase in the relative abundance of Gammaproteobacteria and a decrease in the Shannon index, while the SG group only transiently exhibited these changes within the first week after surgery. The relative abundance of Gammaproteobacteria was negatively correlated, whereas the Shannon index was positively correlated with weight after surgery.<br><br>CONCLUSIONS: RYGB, but not SG, alters the gut microbiota of Sprague-Dawley rats. RYGB also reduces the diversity of gut microbiota. Furthermore, the abundance of Gammaproteobacteria negatively correlates with postoperative body weight and may be one of the potential contributors to stable weight loss after bariatric surgery.}, }
@article {pmid27438242, year = {2016}, author = {Han, M and De Clippeleir, H and Al-Omari, A and Wett, B and Vlaeminck, SE and Bott, C and Murthy, S}, title = {Impact of carbon to nitrogen ratio and aeration regime on mainstream deammonification.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {74}, number = {2}, pages = {375-384}, doi = {10.2166/wst.2016.202}, pmid = {27438242}, issn = {0273-1223}, mesh = {Ammonia/*metabolism ; Ammonium Compounds/*metabolism ; Bacteria/*metabolism ; Biological Oxygen Demand Analysis ; Bioreactors ; Carbon/analysis ; *Denitrification ; Environmental Monitoring ; Nitrogen/analysis ; Sewage/analysis ; *Waste Disposal, Fluid ; Wastewater/analysis ; }, abstract = {While deammonification of high-strength wastewater in the sludge line of sewage treatment plants has become well established, the potential cost savings spur the development of this technology for mainstream applications. This study aimed at identifying the effect of aeration and organic carbon on the deammonification process. Two 10 L sequencing bath reactors with different aeration frequencies were operated at 25°C. Real wastewater effluents from chemically enhanced primary treatment and high-rate activated sludge process were fed into the reactors with biodegradable chemical oxygen demand/nitrogen (bCOD/N) of 2.0 and 0.6, respectively. It was found that shorter aerobic solids retention time (SRT) and higher aeration frequency gave more advantages for aerobic ammonium-oxidizing bacteria (AerAOB) than nitrite oxidizing bacteria (NOB) in the system. From the kinetics study, it is shown that the affinity for oxygen is higher for NOB than for AerAOB, and higher dissolved oxygen set-point could decrease the affinity of both AerAOB and NOB communities. After 514 days of operation, it was concluded that lower organic carbon levels enhanced the activity of anoxic ammonium-oxidizing bacteria (AnAOB) over denitrifiers. As a result, the contribution of AnAOB to nitrogen removal increased from 40 to 70%. Overall, a reasonably good total removal efficiency of 66% was reached under a low bCOD/N ratio of 2.0 after adaptation.}, }
@article {pmid27434177, year = {2016}, author = {Fontana, C and Bassi, D and López, C and Pisacane, V and Otero, MC and Puglisi, E and Rebecchi, A and Cocconcelli, PS and Vignolo, G}, title = {Microbial ecology involved in the ripening of naturally fermented llama meat sausages. A focus on lactobacilli diversity.}, journal = {International journal of food microbiology}, volume = {236}, number = {}, pages = {17-25}, doi = {10.1016/j.ijfoodmicro.2016.07.002}, pmid = {27434177}, issn = {1879-3460}, mesh = {Animals ; Argentina ; Bioreactors ; Camelids, New World ; Fermentation ; *Food Microbiology ; Lactobacillus/classification/genetics/*physiology ; Meat Products/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; Random Amplified Polymorphic DNA Technique ; Taste ; }, abstract = {Llama represents for the Andean regions a valid alternative to bovine and pork meat and thanks to the high proteins and low fat content; it can constitute a good product for the novel food market. In this study, culture-dependent and independent methods were applied to investigate the microbial ecology of naturally fermented llama sausages produced in Northwest Argentina. Two different production technologies of llama sausage were investigated: a pilot-plant scale (P) and an artisanal one (A). Results obtained by High-Throughput Sequencing (HTS) of 16S rRNA amplicons showed that the production technologies influenced the development of microbial communities with a different composition throughout the entire fermentation process. Both sequencing and microbiological counts demonstrated that Lactic Acid Bacteria (LAB) contributed largely to the dominant microbiota. When a total of 230 isolates were approached by RAPD-PCR, presumptive LAB strains from P production exhibited an initial variability in RAPD fingerprints switching to a single profile at the final of ripening, while A production revealed a more heterogeneous RAPD pattern during the whole fermentation process. The constant presence of Lactobacillus sakei along the fermentation in both productions was revealed by HTS and confirmed by species-specific PCR from isolated strains. The technological characterization of Lb. sakei isolates evidenced their ability to grow at 15°C, pH4.5 and 5% NaCl (95%). Most strains hydrolyzed myofibrillar and sarcoplasmic proteins. Bacteriocins encoding genes and antimicrobial resistance were found in 35% and 42.5% of the strains, respectively. An appropriate choice of a combination of autochthonous strains in a starter formulation is fundamental to improve and standardize llama sausages safety and quality.}, }
@article {pmid27432448, year = {2016}, author = {Cosgaya, C and Marí-Almirall, M and Van Assche, A and Fernández-Orth, D and Mosqueda, N and Telli, M and Huys, G and Higgins, PG and Seifert, H and Lievens, B and Roca, I and Vila, J}, title = {Acinetobacter dijkshoorniae sp. nov., a member of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex mainly recovered from clinical samples in different countries.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {66}, number = {10}, pages = {4105-4111}, doi = {10.1099/ijsem.0.001318}, pmid = {27432448}, issn = {1466-5034}, mesh = {Acinetobacter/*classification/genetics/isolation &amp; purification ; Acinetobacter Infections/microbiology ; Bacterial Typing Techniques ; Base Composition ; Cluster Analysis ; DNA, Bacterial/genetics ; Genes, Bacterial ; Humans ; Multilocus Sequence Typing ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {The recent advances in bacterial species identification methods have led to the rapid taxonomic diversification of the genus Acinetobacter. In the present study, phenotypic and molecular methods have been used to determine the taxonomic position of a group of 12 genotypically distinct strains belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex, initially described by Gerner-Smidt and Tjernberg in 1993, that are closely related to Acinetobacter pittii. Strains characterized in this study originated mostly from human samples obtained in different countries over a period of 15 years. rpoB gene sequences and multilocus sequence typing were used for comparisons against 94 strains representing all species included in the ACB complex. Cluster analysis based on such sequences showed that all 12 strains grouped together in a distinct clade closest to Acinetobacter pittiithat was supported by bootstrap values of 99 %. Values of average nucleotide identity based on blast between the genome sequence of strain JVAP01T (NCBI accession no. LJPG00000000) and those of other species from the ACB complex were always <91.2 %, supporting the species status of the group. In addition, the metabolic characteristics of the group matched those of the ACB complex and the analysis of their protein signatures by matrix-assisted laser desorption ionization time-of-flight MS identified some specific peaks. Our results support the designation of these strains as representing a novel species, for which the name Acinetobacter dijkshoorniae sp. nov. is proposed. The type strain is JVAP01T (=CECT 9134T=LMG 29605T).}, }
@article {pmid27430632, year = {2016}, author = {Hoostal, MJ and Bouzat, JL}, title = {Spatial Patterns of bphA Gene Diversity Reveal Local Adaptation of Microbial Communities to PCB and PAH Contaminants.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {559-570}, pmid = {27430632}, issn = {1432-184X}, mesh = {Adaptation, Biological/*genetics ; Bacteria/classification/*enzymology/*genetics/metabolism ; Base Sequence ; Biodegradation, Environmental ; *Biphenyl Compounds ; Classification ; DNA, Bacterial ; Dioxygenases/chemistry/*genetics ; Environmental Pollutants ; Gene Library ; Genes, Bacterial/*genetics ; *Genetic Variation ; Geologic Sediments/microbiology ; Phylogeny ; Polychlorinated Biphenyls/metabolism ; Protein Conformation ; RNA, Ribosomal, 16S/genetics ; Rhodococcus/genetics/metabolism ; Substrate Specificity ; }, abstract = {Biphenyl dioxygenases, encoded by the bphA gene, initiate the oxidation of polychlorinated biphenyls (PCBs) and specify the substrate range of PCB congeners metabolized by bacteria. Increased bphA gene diversity within microbial communities may allow a broader range of PCB congeners to be catabolized, thus resulting in greater PCB degradation. To assess the role of PCBs in modulating bphA gene diversity, 16S ribosomal RNA (rRNA) gene and bphA environmental DNA libraries were generated from bacterial communities in sediments with a steep gradient of PCB contamination. Multiple measures of sequence diversity revealed greater heterogeneity of bphA sequences in polluted compared to unpolluted locations. Codon-based signatures of selection in bphA sequences provided evidence of purifying selection. Unifrac analysis of 16S rRNA sequences revealed independent taxonomic lineages from polluted and unpolluted locations, consistent with the presence of locally adapted bacterial communities. Phylogenetic analysis of bphA sequences indicated that dioxygenases from sediments were closely related to previously characterized dioxygenases that metabolize PCBs and polynuclear aromatic hydrocarbons (PAHs), consistent with high levels of these contaminants within the studied sediments. Structural analyses indicated that the BphA protein of Rhodococcus jostii, capable of metabolizing both PCBs and PAHs, provided a more optimal modeling template for bphA sequences reported in this study than a BphA homologue with more restricted substrate specificity. Results from this study suggest that PCBs and PAHs may drive local adaptation of microbial communities by acting as strong selective agents for biphenyl dioxygenases capable of metabolizing a wide range of congeners.}, }
@article {pmid27429647, year = {2016}, author = {Leite, AF and Janke, L and Harms, H and Richnow, HH and Nikolausz, M}, title = {Lessons learned from the microbial ecology resulting from different inoculation strategies for biogas production from waste products of the bioethanol/sugar industry.}, journal = {Biotechnology for biofuels}, volume = {9}, number = {}, pages = {144}, pmid = {27429647}, issn = {1754-6834}, abstract = {BACKGROUND: During strategic planning of a biogas plant, the local availability of resources for start-up and operation should be taken into consideration for a cost-efficient process. Because most bioethanol/sugar industries in Brazil are located in remote areas, the use of fresh cattle manure from local farms could be a solution for the inoculation of the biogas process. This study investigated the diversity and dynamics of bacterial and archaeal communities and the performance of biogas reactors inoculated with manure and a mixed inoculum from different biogas reactors as for a controlled start-up until steady state.<br><br>RESULTS: Laboratory-scale biogas reactors were fed semi-continuously with sugarcane filter cake alone (mono-digestion) or together with bagasse (co-digestion). At the initial start-up, the reactors inoculated with the mixed inoculum displayed a less diverse taxonomic composition, but with higher presence of significant abundances compared to reactors inoculated with manure. However, in the final steady state, the communities of the differently inoculated reactors were very similarly characterized by predominance of the methanogenic genera Methanosarcina and Methanobacterium, the bacterial families Bacteroidaceae, Prevotellaceae and Porphyromonadaceae (phylum Bacteroidetes) and Synergistaceae (phylum Synergistetes). In the mono-digestion reactors, the methanogenic communities varied greater than in the co-digestion reactors independently of the inoculation strategy.<br><br>CONCLUSION: The microbial communities involved in the biogas production from waste products of the Brazilian bioethanol/sugar industry were relatively similar and stable at the reactor's steady phase independently of the inoculum source (manure or mixed inoculum). Therefore, the locally available manure can be used as inoculum for start-up of the biogas process, since it also contains the microbial resources needed. The strong fluctuation of methanogenic communities in mono-digestion reactors indicates higher risk of process instability than in co-digestion reactors.}, }
@article {pmid27428292, year = {2016}, author = {Assié, A and Borowski, C and van der Heijden, K and Raggi, L and Geier, B and Leisch, N and Schimak, MP and Dubilier, N and Petersen, JM}, title = {A specific and widespread association between deep-sea Bathymodiolus mussels and a novel family of Epsilonproteobacteria.}, journal = {Environmental microbiology reports}, volume = {8}, number = {5}, pages = {805-813}, doi = {10.1111/1758-2229.12442}, pmid = {27428292}, issn = {1758-2229}, support = {//European Research Council Advanced Grant/ ; 340535//BathyBiome/ ; GBMF3811//Gordon and Betty Moore Foundation Marine Microbiology Initiative Investigator Award/ ; 264774//European Union (EU) Marie Curie Actions Initial Training Network (ITN) SYMBIOMICS/ ; }, abstract = {Bathymodiolus mussels dominate animal communities at many hydrothermal vents and cold seeps. Essential to the mussels' ecological and evolutionary success is their association with symbiotic methane- and sulfur-oxidizing gammaproteobacteria, which provide them with nutrition. In addition to these well-known gammaproteobacterial endosymbionts, we found epsilonproteobacterial sequences in metatranscriptomes, metagenomes and 16S rRNA clone libraries as well as by polymerase chain reaction screening of Bathymodiolus species sampled from vents and seeps around the world. These epsilonproteobacterial sequences were closely related, indicating that the association is highly specific. The Bathymodiolus-associated epsilonproteobacterial 16S rRNA sequences were at most 87.6% identical to the closest cultured relative, and 91.2% identical to the closest sequences in public databases. This clade therefore represents a novel family within the Epsilonproteobacteria. Fluorescence in situ hybridization and transmission electron microscopy showed that the bacteria are filamentous epibionts associated with the gill epithelia in two Bathymodiolus species. In animals that host highly specific symbioses with one or a few types of endosymbionts, other less-abundant members of the microbiota can be easily overlooked. Our work highlights how widespread and specific associations with less-abundant microbes can be. Possibly, these microbes play an important role in the survival and health of their animal hosts.}, }
@article {pmid27425419, year = {2016}, author = {Urem, M and Świątek-Połatyńska, MA and Rigali, S and van Wezel, GP}, title = {Intertwining nutrient-sensory networks and the control of antibiotic production in Streptomyces.}, journal = {Molecular microbiology}, volume = {102}, number = {2}, pages = {183-195}, doi = {10.1111/mmi.13464}, pmid = {27425419}, issn = {1365-2958}, mesh = {Amino Sugars/metabolism ; Anti-Bacterial Agents/*biosynthesis ; Bacterial Proteins/metabolism ; Biosynthetic Pathways ; Carbon/metabolism ; Nitrogen/metabolism ; Phosphates/metabolism ; Regulon/genetics ; Streptomyces/*metabolism ; }, abstract = {Actinobacteria are producers of a plethora of natural products of agricultural, biotechnological and clinical importance. In an era where mankind has to deal with rapidly spreading antimicrobial resistance, streptomycetes are of particular importance as producers of half of all antibiotics used in the clinic. Genome sequencing efforts revealed that their capacity as antibiotic producers has been underestimated, in particular as many biosynthetic pathways are silent under standard laboratory conditions. Here we review the global regulatory networks that control antibiotic production in streptomycetes, with emphasis on carbon- and aminosugar-related nutrient sensory pathways. Recent research has revealed intriguing connections between these regulons, and overlap and antagonism between the activities of among others the global regulatory proteins AtrA, DasR and Rok7B7 as well as GlnR (nitrogen control) and PhoP (phosphate control), are discussed. Finally, we provide ideas as to how these novel insights might help us to find ways to activate the transcription of silent biosynthetic gene clusters.}, }
@article {pmid27423980, year = {2016}, author = {Damodaram, KJ and Ayyasamy, A and Kempraj, V}, title = {Commensal Bacteria Aid Mate-selection in the Fruit Fly, Bactrocera dorsalis.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {725-729}, pmid = {27423980}, issn = {1432-184X}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/genetics/isolation &amp; purification/pathogenicity ; Bacterial Physiological Phenomena/drug effects ; Base Sequence ; DNA, Ribosomal ; Ejaculation ; Female ; Klebsiella oxytoca/genetics/isolation &amp; purification ; Male ; *Marriage ; Microbiota ; Olfactometry/methods ; *Sexual Behavior, Animal/drug effects ; Sperm Count ; Spermatozoa ; *Symbiosis ; Tephritidae/*microbiology ; }, abstract = {Commensal bacteria influence many aspects of an organism's behaviour. However, studies on the influence of commensal bacteria in insect mate-selection are scarce. Here, we present empirical evidence that commensal bacteria mediate mate-selection in the Oriental fruit fly, Bactrocera dorsalis. Male flies were attracted to female flies, but this attraction was abolished when female flies were fed with antibiotics, suggesting the role of the fly's microbiota in mediating mate-selection. We show that male flies were attracted to and ejaculated more sperm into females harbouring the microbiota. Using culturing and 16S rDNA sequencing, we isolated and identified different commensal bacteria, with Klebsiella oxytoca being the most abundant bacterial species. This preliminary study will enhance our understanding of the influence of commensal bacteria on mate-selection behaviour of B. dorsalis and may find use in devising control operations against this devastating pest.}, }
@article {pmid27423979, year = {2016}, author = {Zheng, Y and Chen, L and Luo, CY and Zhang, ZH and Wang, SP and Guo, LD}, title = {Plant Identity Exerts Stronger Effect than Fertilization on Soil Arbuscular Mycorrhizal Fungi in a Sown Pasture.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {647-658}, pmid = {27423979}, issn = {1432-184X}, mesh = {Animals ; Base Sequence ; *Biodiversity ; Biomass ; China ; DNA, Fungal/isolation &amp; purification ; DNA, Ribosomal ; Ecosystem ; *Fertilizers ; Fungi/classification/*drug effects/genetics/growth &amp; development ; Grassland ; Hyphae/growth &amp; development ; Manure ; Mycorrhizae/classification/*drug effects/genetics/growth &amp; development ; Nitrogen/analysis ; Phylogeny ; Plant Roots/microbiology ; Plants/*drug effects/*microbiology ; Poaceae/microbiology ; Sheep ; Soil/*chemistry ; *Soil Microbiology ; Spores, Fungal/drug effects/growth &amp; development ; Statistics as Topic ; Symbiosis ; Urea/pharmacology ; }, abstract = {Arbuscular mycorrhizal (AM) fungi play key roles in plant nutrition and plant productivity. AM fungal responses to either plant identity or fertilization have been investigated. However, the interactive effects of different plant species and fertilizer types on these symbiotic fungi remain poorly understood. We evaluated the effects of the factorial combinations of plant identity (grasses Avena sativa and Elymus nutans and legume Vicia sativa) and fertilization (urea and sheep manure) on AM fungi following 2-year monocultures in a sown pasture field study. AM fungal extraradical hyphal density was significantly higher in E. nutans than that in A. sativa and V. sativa in the unfertilized control and was significantly increased by urea and manure in A. sativa and by manure only in E. nutans, but not by either fertilizers in V. sativa. AM fungal spore density was not significantly affected by plant identity or fertilization. Forty-eight operational taxonomic units (OTUs) of AM fungi were obtained through 454 pyrosequencing of 18S rDNA. The OTU richness and Shannon diversity index of AM fungi were significantly higher in E. nutans than those in V. sativa and/or A. sativa, but not significantly affected by any fertilizer in all of the three plant species. AM fungal community composition was significantly structured directly by plant identity only and indirectly by both urea addition and plant identity through soil total nitrogen content. Our findings highlight that plant identity has stronger influence than fertilization on belowground AM fungal community in this converted pastureland from an alpine meadow.}, }
@article {pmid27423543, year = {2016}, author = {Westerholm, M and Crauwels, S and Houtmeyers, S and Meerbergen, K and Van Geel, M and Lievens, B and Appels, L}, title = {Microbial community dynamics linked to enhanced substrate availability and biogas production of electrokinetically pre-treated waste activated sludge.}, journal = {Bioresource technology}, volume = {218}, number = {}, pages = {761-770}, doi = {10.1016/j.biortech.2016.07.029}, pmid = {27423543}, issn = {1873-2976}, mesh = {Anaerobiosis ; Archaea/metabolism ; Bacteria/metabolism ; *Biofuels ; Biological Oxygen Demand Analysis ; Bioreactors/*microbiology ; Biota/physiology ; Hydrolysis ; Kinetics ; Sewage/*microbiology ; *Waste Management/methods ; }, abstract = {The restricted hydrolytic degradation rate of complex organic matter presents a considerable challenge in anaerobic digestion of waste activated sludge (WAS). Within this context, application of pre-treatment of digester substrate has potential for improved waste management and enhanced biogas production. Anaerobic degradation of untreated or electrokinetically pre-treated WAS was performed in two pilot-scale digesters for 132days. WAS electrokinetically pre-treated with energy input 0.066kJ/kg sludge was used in a first phase of operation and WAS pre-treated with energy input 0.091kJ/kg sludge was used in a second phase (each phase lasted at least three hydraulic retention times). Substrate characteristics before and after pre-treatment and effects on biogas digester performance were comprehensively analysed. To gain insights into influences of altered substrate characteristics on microbial communities, the dynamics within the bacterial and archaeal communities in the two digesters were investigated using 16S rRNA gene sequencing (pyrosequencing) and quantitative PCR (qPCR). Specific primers targeting dominant operation taxonomic units (OTUs) and members of the candidate phylum Cloacimonetes were designed to further evaluate their abundance and dynamics in the digesters. Electrokinetic pre-treatment significantly improved chemical oxygen demand (COD) and carbohydrate solubility and increased biogas production by 10-11% compared with untreated sludge. Compositional similarity of the bacterial community during initial operation and diversification during later operation indicated gradual adaptation of the community to the higher solubility of organic material in the pre-treated substrate. Further analyses revealed positive correlations between gene abundance of dominant OTUs related to Clostridia and Cloacimonetes and increased substrate availability and biogas production. Among the methanogens, the genus Methanosaeta dominated in both digesters. Overall, the results showed that electrokinetic pre-treatment of WAS increases substrate solubility and biogas production. Changes in bacterial community composition and abundances of dominant bacterial OTUs were observed during anaerobic degradation of pre-treated WAS, whereas the relative abundance of methanogenic community members remained stable.}, }
@article {pmid27423372, year = {2016}, author = {De Vrieze, J and Smet, D and Klok, J and Colsen, J and Angenent, LT and Vlaeminck, SE}, title = {Thermophilic sludge digestion improves energy balance and nutrient recovery potential in full-scale municipal wastewater treatment plants.}, journal = {Bioresource technology}, volume = {218}, number = {}, pages = {1237-1245}, doi = {10.1016/j.biortech.2016.06.119}, pmid = {27423372}, issn = {1873-2976}, mesh = {Anaerobiosis ; Autotrophic Processes ; Bioreactors ; Netherlands ; Sewage/*chemistry ; *Waste Disposal Facilities ; Waste Management/*methods ; Wastewater/*chemistry ; }, abstract = {The conventional treatment of municipal wastewater by means of activated sludge is typically energy demanding. Here, the potential benefits of: (1) the optimization of mesophilic digestion; and (2) transitioning to thermophilic sludge digestion in three wastewater treatment plants (Tilburg-Noord, Land van Cuijk and Bath) in the Netherlands is evaluated, including a full-scale trial validation in Bath. In Tilburg-Noord, thermophilic sludge digestion covered the energy requirements of the plant (102%), whereas 111% of sludge operational treatment costs could be covered in Bath. Thermophilic sludge digestion also resulted in a strong increase in nutrient release. The potential for nutrient recovery was evaluated via: (1) stripping/absorption of ammonium; (2) autotrophic removal of ammonium via partial nitritation/anammox; and (3) struvite precipitation. This research shows that optimization of sludge digestion may lead to a strong increase in energy recovery, sludge treatment costs reduction, and the potential for advanced nutrient management in full-scale sewage treatment plants.}, }
@article {pmid27420812, year = {2016}, author = {Merritt, J and Kuehn, S}, title = {When communities collide.}, journal = {eLife}, volume = {5}, number = {}, pages = {}, pmid = {27420812}, issn = {2050-084X}, mesh = {*Microbial Consortia ; }, abstract = {A new model demonstrates how microbial communities can survive encounters with other communities as a cohesive group, even in the complete absence of cooperation.}, }
@article {pmid27420183, year = {2016}, author = {Forbes, JD and Van Domselaar, G and Sargent, M and Green, C and Springthorpe, S and Krause, DO and Bernstein, CN}, title = {Microbiome profiling of drinking water in relation to incidence of inflammatory bowel disease.}, journal = {Canadian journal of microbiology}, volume = {62}, number = {9}, pages = {781-793}, doi = {10.1139/cjm-2016-0219}, pmid = {27420183}, issn = {1480-3275}, mesh = {Canada/epidemiology ; DNA, Ribosomal/genetics ; Drinking Water/*microbiology ; Humans ; Incidence ; Inflammatory Bowel Diseases/epidemiology/*etiology/microbiology ; Microbiota ; Proteobacteria/genetics ; Pseudomonas/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The etiology of inflammatory bowel disease (IBD) is unknown; current research is focused on determining environmental factors. One consideration is drinking water: water systems harbour considerable microbial diversity, with bacterial concentrations estimated at 10(6)-10(8) cells/L. Perhaps differences in microbial ecology of water sources may impact differential incidence rates of IBD. Regions of Manitoba were geographically mapped according to incidence rates of IBD and identified as high (HIA) or low (LIA) incidence areas. Bulk water, filter material, and pipe wall samples were collected from public buildings in different jurisdictions and their population structure analyzed using 16S rDNA sequencing. At the phylum level, Proteobacteria were observed significantly less frequently (P = 0.02) in HIA versus LIA. The abundance of Proteobacteria was also found to vary according to water treatment distribution networks. Gammaproteobacteria was the most abundant class of bacteria and was observed more frequently (P = 0.006) in LIA. At the genus level, microbes found to associate with HIA include Bradyrhizobium (P = 0.02) and Pseudomonas (P = 0.02). Particular microbes were found to associate with LIA or HIA, based on sample location and (or) type. This work lays out a basis for further studies exploring water as a potential environmental source for IBD triggers.}, }
@article {pmid27420030, year = {2017}, author = {Thompson, LR and Williams, GJ and Haroon, MF and Shibl, A and Larsen, P and Shorenstein, J and Knight, R and Stingl, U}, title = {Metagenomic covariation along densely sampled environmental gradients in the Red Sea.}, journal = {The ISME journal}, volume = {11}, number = {1}, pages = {138-151}, pmid = {27420030}, issn = {1751-7370}, mesh = {Bacteria/classification/*genetics/*isolation &amp; purification ; Environment ; Indian Ocean ; Marine Biology ; Metagenome ; Metagenomics ; Phylogeny ; Salinity ; Seawater/analysis/*microbiology ; Temperature ; }, abstract = {Oceanic microbial diversity covaries with physicochemical parameters. Temperature, for example, explains approximately half of global variation in surface taxonomic abundance. It is unknown, however, whether covariation patterns hold over narrower parameter gradients and spatial scales, and extending to mesopelagic depths. We collected and sequenced 45 epipelagic and mesopelagic microbial metagenomes on a meridional transect through the eastern Red Sea. We asked which environmental parameters explain the most variation in relative abundances of taxonomic groups, gene ortholog groups, and pathways-at a spatial scale of <2000 km, along narrow but well-defined latitudinal and depth-dependent gradients. We also asked how microbes are adapted to gradients and extremes in irradiance, temperature, salinity, and nutrients, examining the responses of individual gene ortholog groups to these parameters. Functional and taxonomic metrics were equally well explained (75-79%) by environmental parameters. However, only functional and not taxonomic covariation patterns were conserved when comparing with an intruding water mass with different physicochemical properties. Temperature explained the most variation in each metric, followed by nitrate, chlorophyll, phosphate, and salinity. That nitrate explained more variation than phosphate suggested nitrogen limitation, consistent with low surface N:P ratios. Covariation of gene ortholog groups with environmental parameters revealed patterns of functional adaptation to the challenging Red Sea environment: high irradiance, temperature, salinity, and low nutrients. Nutrient-acquisition gene ortholog groups were anti-correlated with concentrations of their respective nutrient species, recapturing trends previously observed across much larger distances and environmental gradients. This dataset of metagenomic covariation along densely sampled environmental gradients includes online data exploration supplements, serving as a community resource for marine microbial ecology.}, }
@article {pmid27418359, year = {2016}, author = {Jiménez, DJ and de Lima Brossi, MJ and Schückel, J and Kračun, SK and Willats, WG and van Elsas, JD}, title = {Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {24}, pages = {10463-10477}, pmid = {27418359}, issn = {1432-0614}, mesh = {Aerobiosis ; Bacteria/*classification/enzymology/genetics ; Biotransformation ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Enzymes/metabolism ; Lignin/*metabolism ; *Metagenomics ; *Microbial Consortia ; Panicum/chemistry ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Triticum/chemistry ; Zea mays/chemistry ; }, abstract = {The selection of microbes by enrichment on plant biomass has been proposed as an efficient way to develop new strategies for lignocellulose saccharification. Here, we report an in-depth analysis of soil-derived microbial consortia that were trained to degrade once-used wheat straw (WS1-M), switchgrass (SG-M) and corn stover (CS-M) under aerobic and mesophilic conditions. Molecular fingerprintings, bacterial 16S ribosomal RNA (rRNA) gene amplicon sequencing and metagenomic analyses showed that the three microbial consortia were taxonomically distinct. Based on the taxonomic affiliation of protein-encoding sequences, members of the Bacteroidetes (e.g. Chryseobacterium, Weeksella, Flavobacterium and Sphingobacterium) were preferentially selected on WS1-M, whereas SG-M and CS-M favoured members of the Proteobacteria (e.g. Caulobacter, Brevundimonas, Stenotrophomonas and Xanthomonas). The highest degradation rates of lignin (~59 %) were observed with SG-M, whereas CS-M showed a high consumption of cellulose and hemicellulose. Analyses of the carbohydrate-active enzymes in the three microbial consortia showed the dominance of glycosyl hydrolases (e.g. of families GH3, GH43, GH13, GH10, GH29, GH28, GH16, GH4 and GH92). In addition, proteins of families AA6, AA10 and AA2 were detected. Analysis of secreted protein fractions (metasecretome) for each selected microbial consortium mainly showed the presence of enzymes able to degrade arabinan, arabinoxylan, xylan, β-glucan, galactomannan and rhamnogalacturonan. Notably, these metasecretomes contain enzymes that enable us to produce oligosaccharides directly from wheat straw, sugarcane bagasse and willow. Thus, the underlying microbial consortia constitute valuable resources for the production of enzyme cocktails for the efficient saccharification of plant biomass.}, }
@article {pmid27418177, year = {2016}, author = {Michelland, R and Thioulouse, J and Kyselková, M and Grundmann, GL}, title = {Bacterial Community Structure at the Microscale in Two Different Soils.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {717-724}, pmid = {27418177}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics ; Base Sequence ; *Biodiversity ; DNA, Bacterial ; Ecosystem ; France ; Molecular Typing ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {The spatial distributions of bacteria in the soil matrix have a role in ecosystem function, for example, at the small scale, through gene transfer or xenobiotic degradation. Soil bacterial biogeography has been evidenced at the large scale, but data are scarce at the small scale. The objective of this work was to determine the spatial pattern of bacterial diversity, in spatially referenced microsamples, in order to define bacterial community spatial traits. Two soils with different physical structures, moderately aggregated (La Côte St André (LCSA)) or poorly aggregated (La Dombes (LD)), were studied. The spatial distribution of bacteria was studied in microsamples (diameter 3 mm) along 10- and 20-cm transects, with a taxonomic microarray. 16S rRNA gene sequencing was used to further study the spatial characteristics of the microbial communities in LD soil. The frequency-occupancy plot, in the LCSA and LD soils, using microarray and sequencing data, followed Hanski's core-satellite theory. The frequency-occupancy distribution plots obtained in two different soils showed bimodality and indicated that the microscale spatial distributions were different, particularly core taxa percentage. Core taxa are widespread and abundant, while satellite taxa are restricted in their distribution. The spread of satellite taxa was at a distance range larger than 5 cm, whereas the core taxa were distributed in a distance range less than 3 mm. Besides, there was a positive abundancy-occupancy relationship at this fine scale. It may be interesting to further evaluate the role of the different bacterial spatial distributions at the fine scale on soil function.}, }
@article {pmid27415014, year = {2016}, author = {Romão-Dumaresq, AS and Dourado, MN and Fávaro, LC and Mendes, R and Ferreira, A and Araújo, WL}, title = {Diversity of Cultivated Fungi Associated with Conventional and Transgenic Sugarcane and the Interaction between Endophytic Trichoderma virens and the Host Plant.}, journal = {PloS one}, volume = {11}, number = {7}, pages = {e0158974}, pmid = {27415014}, issn = {1932-6203}, mesh = {Biodiversity ; Crop Production ; DNA, Fungal/genetics ; Endophytes/*physiology ; Herbicide Resistance/genetics ; Phylogeny ; Plant Roots/microbiology/physiology ; Plants, Genetically Modified/genetics/microbiology/physiology ; Rhizosphere ; Saccharum/genetics/*microbiology/physiology ; Sequence Analysis, DNA ; Symbiosis/genetics/physiology ; Trichoderma/genetics/*physiology ; }, abstract = {Plant-associated fungi are considered a vast source for biotechnological processes whose potential has been poorly explored. The interactions and diversity of sugarcane, one of the most important crops in Brazil, have been rarely studied, mainly concerning fungal communities and their interactions with transgenic plants. Taking this into consideration, the purpose of this study was, based on culture dependent strategy, to determine the structure and diversity of the fungal community (root endophytes and rhizosphere) associated with two varieties of sugarcane, a non-genetically modified (SP80-1842) variety and its genetically modified counterpart (IMI-1, expressing imazapyr herbicide resistance). For this, the sugarcane varieties were evaluated in three sampling times (3, 10 and 17 months after planting) under two crop management (weeding and herbicide treatments). In addition, a strain of Trichoderma virens, an endophyte isolated from sugarcane with great potential as a biological control, growth promotion and enzyme production agent, was selected for the fungal-plant interaction assays. The results of the isolation, characterization and evaluation of fungal community changes showed that the sugarcane fungal community is composed of at least 35 different genera, mostly in the phylum Ascomycota. Many genera are observed at very low frequencies among a few most abundant genera, some of which were isolated from specific plant sites (e.g., the roots or the rhizosphere). An assessment of the possible effects upon the fungal community showed that the plant growth stage was the only factor that significantly affected the community's structure. Moreover, if transgenic effects are present, they may be minor compared to other natural sources of variation. The results of interaction studies using the Green fluorescent protein (GFP)-expressing T. virens strain T.v.223 revealed that this fungus did not promote any phenotypic changes in the host plant and was found mostly in the roots where it formed a dense mycelial cover and was able to penetrate the intercellular spaces of the root epidermis upper layers. The ability of T. virens to colonize plant roots suggests a potential for protecting plant health, inhibiting pathogens or inducing systemic resistance.}, }
@article {pmid27412380, year = {2016}, author = {Brandes, J and Kuhajek, JM and Goodwin, E and Wood, SA}, title = {Molecular Characterisation and Co-cultivation of Bacterial Biofilm Communities Associated with the Mat-Forming Diatom Didymosphenia geminata.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {514-525}, pmid = {27412380}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/growth &amp; development/isolation &amp; purification ; Bacterial Physiological Phenomena/genetics ; Base Sequence ; *Biofilms ; Carnobacterium/growth &amp; development ; Cell Adhesion ; *Coculture Techniques ; DNA, Bacterial ; Diatoms/*genetics/growth &amp; development/*microbiology/physiology ; Fresh Water/*microbiology ; High-Throughput Nucleotide Sequencing ; New Zealand ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers/microbiology ; Sphingobacterium ; Water Microbiology ; }, abstract = {Didymosphenia geminata (Lyngbye) M. Schmidt is a stalked freshwater diatom that is expanding its range globally. In some rivers, D. geminata forms thick and expansive polysaccharide-dominated mats. Like other stalked diatoms, D. geminata cells attach to the substratum with a pad of adhesive extracellular polymeric substance. Research on D. geminata and other diatoms suggests that bacterial biofilm composition may contribute to successful attachment. The aim of this study was to investigate the composition and role of bacterial biofilm communities in D. geminata attachment and survival. Bacterial biofilms were collected at four sites in the main stem of a river (containing D. geminata) and in four tributaries (free of D. geminata). Samples were characterised using automated rRNA intergenic spacer analysis and high-throughput sequencing (HTS). Mat-associated bacteria were isolated and their effect on the early establishment of D. geminata cells assessed using co-culturing experiments. ARISA and HTS data showed differences in bacterial communities between samples with and without D. geminata at two of the four sites. Samples with D. geminata had a higher relative abundance of Sphingobacteria (p < 0.01) and variability in community composition was reduced. Analysis of the 76 bacteria isolated from the mat revealed 12 different strains representing 8 genera. Co-culturing of a Carnobacterium sp. with D. geminata reduced survival (p < 0.001) and attachment (p < 0.001) of D. geminata. Attachment was enhanced by Micrococcus sp. and Pseudomonas sp. (p < 0.001 and p < 0.01, respectively). These data provide evidence that bacteria play a role in the initial attachment and on-going survival of D. geminata, and may partly explain observed distribution patterns.}, }
@article {pmid27411538, year = {2016}, author = {Bartlewicz, J and Pozo, MI and Honnay, O and Lievens, B and Jacquemyn, H}, title = {Effects of agricultural fungicides on microorganisms associated with floral nectar: susceptibility assays and field experiments.}, journal = {Environmental science and pollution research international}, volume = {23}, number = {19}, pages = {19776-19786}, pmid = {27411538}, issn = {1614-7499}, mesh = {Bacteria/isolation &amp; purification ; Candida/*drug effects/growth &amp; development ; Flowers/*microbiology ; Fungicides, Industrial/*toxicity ; Linaria/*microbiology ; Metschnikowia/*drug effects/growth &amp; development ; *Plant Nectar ; Pollination ; }, abstract = {Pesticides have become an inseparable element of agricultural intensification. While the direct impact of pesticides on non-target organisms, such as pollinators, has recently received much attention, less consideration has been given to the microorganisms that are associated with them. Specialist yeasts and bacteria are known to commonly inhabit floral nectar and change its chemical characteristics in numerous ways, possibly influencing pollinator attraction. In this study, we investigated the in vitro susceptibility of nectar yeasts Metschnikowia gruessi, Metschnikowia reukaufii, and Candida bombi to six widely used agricultural fungicides (prothioconazole, tebuconazole, azoxystrobin, fenamidone, boscalid, and fluopyram). Next, a commercial antifungal mixture containing tebuconazole and trifloxystrobin was applied to natural populations of the plant Linaria vulgaris and the occurrence, abundance, and diversity of nectar-inhabiting yeasts and bacteria was compared between treated and untreated plants. The results showed that prothioconazole and tebuconazole were highly toxic to nectar yeasts, inhibiting their growth at concentrations varying between 0.06 and 0.5 mg/L. Azoxystrobin, fenamidone, boscalid, and fluopyram on the other hand exhibited considerably lower toxicity, inhibiting yeast growth at concentrations between 1 and 32 mg/L or in many cases not inhibiting microbial growth at all. The application of the antifungal mixture in natural plant populations resulted in a significant decrease in the occurrence and abundance of yeasts in individual flowers, but this did not translate into noticeable changes in bacterial incidence and abundance. Yeast and bacterial species richness and distribution did not also differ between treated and untreated plants. We conclude that the application of fungicides may have negative effects on the abundance of nectar yeasts in floral nectar. The consequences of these effects on plant pollination processes in agricultural systems warrant further investigation.}, }
@article {pmid27411093, year = {2016}, author = {Kirstein, IV and Kirmizi, S and Wichels, A and Garin-Fernandez, A and Erler, R and Löder, M and Gerdts, G}, title = {Dangerous hitchhikers? Evidence for potentially pathogenic Vibrio spp. on microplastic particles.}, journal = {Marine environmental research}, volume = {120}, number = {}, pages = {1-8}, doi = {10.1016/j.marenvres.2016.07.004}, pmid = {27411093}, issn = {1879-0291}, mesh = {*Environmental Monitoring ; North Sea ; Plastics/*analysis ; Polyethylene ; Polymers ; Polystyrenes ; Vibrio parahaemolyticus/*growth &amp; development/isolation &amp; purification ; *Water Microbiology ; Water Pollutants, Chemical/*analysis ; }, abstract = {The taxonomic composition of biofilms on marine microplastics is widely unknown. Recent sequencing results indicate that potentially pathogenic Vibrio spp. might be present on floating microplastics. Hence, these particles might function as vectors for the dispersal of pathogens. Microplastics and water samples collected in the North and Baltic Sea were subjected to selective enrichment for pathogenic Vibrio species. Bacterial colonies were isolated from CHROMagar™Vibrio and assigned to Vibrio spp. on the species level by MALDI-TOF MS (Matrix Assisted Laser Desorption/Ionisation - Time of Flight Mass Spectrometry). Respective polymers were identified by ATR FT-IR (Attenuated Total Reflectance Fourier Transform - Infrared Spectroscopy). We discovered potentially pathogenic Vibrio parahaemolyticus on a number of microplastic particles, e.g. polyethylene, polypropylene and polystyrene from North/Baltic Sea. This study confirms the indicated occurrence of potentially pathogenic bacteria on marine microplastics and highlights the urgent need for detailed biogeographical analyses of marine microplastics.}, }
@article {pmid27406903, year = {2016}, author = {Talukdar, M and Bordoloi, M and Dutta, PP and Saikia, S and Kolita, B and Talukdar, S and Nath, S and Yadav, A and Saikia, R and Jha, DK and Bora, TC}, title = {Structure elucidation and biological activity of antibacterial compound from Micromonospora auratinigra, a soil Actinomycetes.}, journal = {Journal of applied microbiology}, volume = {121}, number = {4}, pages = {973-987}, doi = {10.1111/jam.13233}, pmid = {27406903}, issn = {1365-2672}, mesh = {Anti-Bacterial Agents/*isolation &amp; purification/*pharmacology ; Bacteria/classification/*drug effects ; Humans ; India ; Isonicotinic Acids/*isolation &amp; purification/*pharmacology ; Kinetics ; Microbial Sensitivity Tests ; Micromonospora/*chemistry/classification/ultrastructure ; *Soil Microbiology ; }, abstract = {AIMS: The aim of this study was to isolate and characterize the bioactive compound of Micromonospora auratinigra, HK-10 and its antibacterial inhibitory mechanism.<br><br>METHODS AND RESULTS: An oily bioactive compound was extracted from HK-10 (GenBank accession no. JN381554) and found to have promising antibacterial activity. The compound was characterized as 2-methylheptylisonicotinate (1) by (1) H, (13) C NMR and mass spectroscopy. Minimum inhibitory concentration (MIC) of this molecule was tested by micro broth dilution method and was found to be 70, 40, 80, 60, 60 and 50&#xa0;&#x3bc;g for Staphylococcus aureus, Bacillus subtilis, Proteus vulgaris, Echerichia coli, Pseudomonas aeruginosa and Mycobacterium abscessus respectively. The effects of compound 1 were studied on bacterial membrane structure using scanning electron microscopy. The results indicated a membrane-disrupting mechanism, resulting in the dysfunction of the cytoplasmic membrane structure and cell death of the pathogenic bacterial strains. Kinetics of growth of the test organisms was also analysed and indicated 2-methylheptylisonicotinate 1 as a bactericidal agent. Furthermore, we have studied the binding affinity of 1 towards different membrane proteins of pathogenic bacteria by in silico analysis.<br><br>CONCLUSIONS: 2-methylheptylisonicotinate was isolated from M.&#xa0;auratinigra, a rare actinobacterial strain possessing antibacterial activity through a membrane-disrupting mechanism, and has MICs similar to standard antibiotic neomycin sulphate. It is the first report about a strain of M.&#xa0;auratinigra, isolated from Indo-Burma biodiversity hotspot of North-east India with new antimicrobial activities. In silico studies have also supported these results performed on various membrane targets of pathogenic bacteria.<br><br>The antibacterial potential of M.&#xa0;auratinigra is reported for the first time. The results indicate the possible use of 2-methylheptylisonicotinate as a source of antibacterial agent against dreaded human pathogens.}, }
@article {pmid27406732, year = {2016}, author = {Jorquera, MA and Maruyama, F and Ogram, AV and Navarrete, OU and Lagos, LM and Inostroza, NG and Acuña, JJ and Rilling, JI and de La Luz Mora, M}, title = {Rhizobacterial Community Structures Associated with Native Plants Grown in Chilean Extreme Environments.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {633-646}, pmid = {27406732}, issn = {1432-184X}, mesh = {Actinobacteria/classification/genetics/isolation &amp; purification ; Alphaproteobacteria/classification/genetics/isolation &amp; purification ; Antarctic Regions ; Bacteria/*classification/genetics ; Bacteroidetes/classification/genetics/isolation &amp; purification ; Base Sequence ; Biodiversity ; Chile ; Classification ; Climate ; DNA, Bacterial/isolation &amp; purification ; Denaturing Gradient Gel Electrophoresis ; Desert Climate ; Ecosystem ; *Extreme Environments ; Gammaproteobacteria/classification/genetics/isolation &amp; purification ; Hydrogen-Ion Concentration ; Phylogeny ; Plant Roots/*microbiology ; Plants/*microbiology ; Proteobacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; Species Specificity ; }, abstract = {Chile is topographically and climatically diverse, with a wide array of diverse undisturbed ecosystems that include native plants that are highly adapted to local conditions. However, our understanding of the diversity, activity, and role of rhizobacteria associated with natural vegetation in undisturbed Chilean extreme ecosystems is very poor. In the present study, the combination of denaturing gradient gel electrophoresis and 454-pyrosequencing approaches was used to describe the rhizobacterial community structures of native plants grown in three representative Chilean extreme environments: Atacama Desert (ATA), Andes Mountains (AND), and Antarctic (ANT). Both molecular approaches revealed the presence of Proteobacteria, Bacteroidetes, and Actinobacteria as the dominant phyla in the rhizospheres of native plants. Lower numbers of operational taxonomic units (OTUs) were observed in rhizosphere soils from ATA compared with AND and ANT. Both approaches also showed differences in rhizobacterial community structures between extreme environments and between plant species. The differences among plant species grown in the same environment were attributed to the higher relative abundance of classes Gammaproteobacteria and Alphaproteobacteria. However, further studies are needed to determine which environmental factors regulate the structures of rhizobacterial communities, and how (or if) specific bacterial groups may contribute to the growth and survival of native plants in each Chilean extreme environments.}, }
@article {pmid27402328, year = {2016}, author = {Okazaki, Y and Nakano, SI}, title = {Vertical partitioning of freshwater bacterioplankton community in a deep mesotrophic lake with a fully oxygenated hypolimnion (Lake Biwa, Japan).}, journal = {Environmental microbiology reports}, volume = {8}, number = {5}, pages = {780-788}, doi = {10.1111/1758-2229.12439}, pmid = {27402328}, issn = {1758-2229}, abstract = {In freshwater microbial ecology, extensive studies are attempting to characterize the vast majority of uncultivated bacterioplankton taxa. However, these studies mainly focus on the epilimnion and little is known regarding the bacterioplankton inhabiting the hypolimnion of deep holomictic lakes, despite its biogeochemical importance. In this study, we investigated the bacterioplankton community composition in a deep freshwater lake with a fully oxygenated hypolimnion (Lake Biwa, Japan) using high-throughput 16S rRNA gene amplicon sequencing. Sampling at a pelagic site over 15 months throughout the water column revealed that the community composition in the hypolimnion was significantly different from that in the epilimnion. The bacterial community in the hypolimnion was composed of groups dominating in the whole water layer (e.g., bacI-A1 and acI-B1) and groups that were hypolimnion habitat specialists. Among the hypolimnion specialists, members of Chloroflexi and Planctomycetes were highly represented (e.g., CL500-11, CL500-15 and CL500-37), followed by members of Acidobacteria, Chlorobi and nitrifiers (e.g., Ca. Nitrosoarchaeum, Nitrosospira and Nitrospira). This study identified the number of previously understudied taxa dominating the deep aerobic freshwater habitat, suggesting that the biogeochemical cycling there is driven by the microbial community that are different from that in the epilimnion.}, }
@article {pmid27401822, year = {2016}, author = {Hofmann, K and Lamprecht, A and Pauli, H and Illmer, P}, title = {Distribution of Prokaryotic Abundance and Microbial Nutrient Cycling Across a High-Alpine Altitudinal Gradient in the Austrian Central Alps is Affected by Vegetation, Temperature, and Soil Nutrients.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {704-716}, pmid = {27401822}, issn = {1432-184X}, mesh = {Archaea/classification/enzymology/genetics/growth &amp; development ; Austria ; Bacteria/classification/enzymology/genetics/growth &amp; development ; *Biodiversity ; Biomass ; Carbon/metabolism ; Carbon Cycle ; DNA, Archaeal ; DNA, Bacterial ; Ecological and Environmental Phenomena ; *Food ; Genes, Archaeal ; Genes, Bacterial ; Nitrogen/metabolism ; Phosphorus/metabolism ; Phylogeny ; Plants/microbiology ; Prokaryotic Cells/*classification ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Soil/*chemistry ; *Soil Microbiology ; Sulfur/metabolism ; *Temperature ; *Tundra ; }, abstract = {Studies of the altitudinal distributions of soil microorganisms are rare or have led to contradictory results. Therefore, we studied archaeal and bacterial abundance and microbial-mediated activities across an altitudinal gradient (2700 to 3500 m) on the southwestern slope of Mt. Schrankogel (Central Alps, Austria). Sampling sites distributed over the alpine (2700 to 2900 m), the alpine-nival (3000 to 3100 m), and the nival altitudinal belts (3200 to 3500 m), which are populated by characteristic plant assemblages. Bacterial and archaeal abundances were measured via quantitative real-time PCR (qPCR). Moreover, microbial biomass C, microbial activity (dehydrogenase), and enzymes involved in carbon (CM-cellulase), nitrogen (protease), phosphorus (alkaline phosphatase), and sulfur (arylsulfatase) cycling were determined. Abundances, microbial biomass C, and activities almost linearly decreased along the gradient. Archaeal abundance experienced a sharper decrease, thus pointing to pronounced sensitivity toward environmental harshness. Additionally, abundance and activities were significantly higher in soils of the alpine belt compared with those of the nival belt, whereas the alpine-nival ecotone represented a transitional area with intermediate values, thus highlighting the importance of vegetation. Archaeal abundance along the gradient was significantly related to soil temperature only, whereas bacterial abundance was significantly related to temperature and dissolved organic carbon (DOC). Soil carbon and nitrogen concentrations explained most of the variance in enzyme activities involved in the cycling of C, N, P, and S. Increasing temperature could therefore increase the abundances and activities of microorganisms either directly or indirectly via expansion of alpine vegetation to higher altitudes and increased plant cover.}, }
@article {pmid27399766, year = {2016}, author = {Russo, M and Fabersani, E and Abeijón-Mukdsi, MC and Ross, R and Fontana, C and Benítez-Páez, A and Gauffin-Cano, P and Medina, RB}, title = {Lactobacillus fermentum CRL1446 Ameliorates Oxidative and Metabolic Parameters by Increasing Intestinal Feruloyl Esterase Activity and Modulating Microbiota in Caloric-Restricted Mice.}, journal = {Nutrients}, volume = {8}, number = {7}, pages = {}, pmid = {27399766}, issn = {2072-6643}, mesh = {Animals ; Bacterial Proteins/*metabolism ; Biomarkers/blood ; Blood Glucose/metabolism ; Body Weight ; *Caloric Restriction ; Carboxylic Ester Hydrolases/*metabolism ; *Gastrointestinal Microbiome ; Intestines/*enzymology/*microbiology ; Limosilactobacillus fermentum/*enzymology ; Lipid Peroxidation ; Lipids/blood ; Male ; Mice, Inbred BALB C ; Models, Animal ; Oxidative Stress ; *Probiotics ; Time Factors ; }, abstract = {The purpose of this study was to determine whether the administration of the feruloyl esterase (FE)-producing strain Lactobacillus fermentum CRL1446 enhances metabolic and oxidative parameters in caloric-restricted (CR) mice. Balb/c male mice were divided into ad libitum fed Group (ALF Group), CR diet Group (CR Group) and CR diet plus L. fermentum Group (CR-Lf Group). CR diet was administered during 45 days and CRL1446 strain was given in the dose of 10[8] cells/mL/day/mouse. FE activity was determined in intestinal mucosa and content at Day 1, 20 and 45. Triglyceride, total cholesterol, glucose, thiobarbituric acid reactive substances (TBARS) levels and glutathione reductase activity were determined in plasma. Gut microbiota was evaluated by high-throughput sequencing of 16S rRNA gene amplicons. At Day 45, total intestinal FE activity in CR-Lf Group was higher (p = 0.020) than in CR and ALF groups and an improvement in both metabolic (reductions in triglyceride (p = 0.0025), total cholesterol (p = 0.005) and glucose (p < 0.0001) levels) and oxidative (decrease of TBARS levels and increase of plasmatic glutathione reductase activity (p = 0.006)) parameters was observed, compared to ALF Group. CR diet increased abundance of Bacteroidetes and CRL1446 administration increased abundance of Bifidobacterium and Lactobacillus genus. L. fermentun CRL1446 exerted a bifidogenic effect under CR conditions.}, }
@article {pmid27397563, year = {2016}, author = {Moreno-Indias, I and Torres, M and Sanchez-Alcoholado, L and Cardona, F and Almendros, I and Gozal, D and Montserrat, JM and Queipo-Ortuño, MI and Farré, R}, title = {Normoxic Recovery Mimicking Treatment of Sleep Apnea Does Not Reverse Intermittent Hypoxia-Induced Bacterial Dysbiosis and Low-Grade Endotoxemia in Mice.}, journal = {Sleep}, volume = {39}, number = {10}, pages = {1891-1897}, pmid = {27397563}, issn = {1550-9109}, mesh = {Animals ; *Disease Models, Animal ; Dysbiosis/chemically induced/microbiology/*physiopathology ; Endotoxemia/chemically induced/microbiology/*physiopathology ; Gastrointestinal Microbiome/*physiology ; Hypoxia/chemically induced/microbiology/physiopathology ; Lipopolysaccharides/toxicity ; Male ; Mice ; Mice, Inbred C57BL ; *Recovery of Function ; Sleep Apnea, Obstructive/chemically induced/microbiology/*physiopathology ; Treatment Outcome ; }, abstract = {STUDY OBJECTIVES: Intermittent hypoxia (IH) mimicking obstructive sleep apnea (OSA) significantly modifies gut microbiota in mice. However, whether these IH-induced gut microbiome changes are reversible after restoring normal oxygenation (the equivalent of effective OSA therapy) is unknown. The aim of this study was to investigate gut microbiota composition and circulating endotoxemia after a post-IH normoxic period in a mouse model of OSA.<br><br>METHODS: Ten mice were subjected to IH (40 sec 21% O2-20 sec 5% O2) for 6 h/day for 6 w and 10 mice breathing normoxic air (NM) were used as controls. After exposures, both groups were subjected to 6 w in normoxia. Microbiome composition of fecal samples was determined by 16S ribosomal RNA (rRNA) pyrosequencing. Bioinformatic analysis was performed by Quantitative Insights into Microbial Ecology. Plasma lipopolysaccharide (LPS) levels were measured by endotoxin assay.<br><br>RESULTS: After normoxic recovery, the Chao and Shannon indices of each group suggested similar bacterial richness and diversity. 16S rRNA pyrosequencing analysis showed that IH-exposed mice had a significant decrease in the abundance of Bacteroidetes and a significant increase of Firmicutes and Deferribacteres compared to the NM group. After normoxic recovery, circulating LPS concentrations were higher in the IH group (P < 0.009). Moreover, the IH group showed a negative and significant correlation between the abundance of Lactobacillus and Ruminococcus and significant positive correlations between the abundance of Mucispirillum and Desulfovibrio and plasma LPS levels, respectively.<br><br>CONCLUSIONS: Even after prolonged normoxic recovery after IH exposures, gut microbiota and circulating endotoxemia remain negatively altered, suggesting that potential benefits of OSA treatment for reversing OSA-induced changes in gut microbiota may either require a longer period or alternative interventions.}, }
@article {pmid27397523, year = {2016}, author = {Brandsma, J}, title = {Phytoplankton phenotype plasticity induced by phosphorus starvation may play a significant role in marine microbial ecology and biogeochemistry.}, journal = {The New phytologist}, volume = {211}, number = {3}, pages = {765-766}, doi = {10.1111/nph.14085}, pmid = {27397523}, issn = {1469-8137}, mesh = {Haptophyta/genetics ; Phenotype ; *Phosphorus ; Phytoplankton/*genetics ; }, }
@article {pmid27396978, year = {2016}, author = {May, DH and Timmins-Schiffman, E and Mikan, MP and Harvey, HR and Borenstein, E and Nunn, BL and Noble, WS}, title = {An Alignment-Free "Metapeptide" Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing.}, journal = {Journal of proteome research}, volume = {15}, number = {8}, pages = {2697-2705}, pmid = {27396978}, issn = {1535-3907}, support = {P41 GM103533/GM/NIGMS NIH HHS/United States ; }, mesh = {Aquatic Organisms/*chemistry/genetics ; Biodiversity ; Databases, Protein ; Metagenomics/*methods ; *Microbiota/genetics ; Peptides/*analysis ; Proteomics/*methods ; Sequence Analysis, DNA ; Specimen Handling ; Tandem Mass Spectrometry ; }, abstract = {In principle, tandem mass spectrometry can be used to detect and quantify the peptides present in a microbiome sample, enabling functional and taxonomic insight into microbiome metabolic activity. However, the phylogenetic diversity constituting a particular microbiome is often unknown, and many of the organisms present may not have assembled genomes. In ocean microbiome samples, with particularly diverse and uncultured bacterial communities, it is difficult to construct protein databases that contain the bulk of the peptides in the sample without losing detection sensitivity due to the overwhelming number of candidate peptides for each tandem mass spectrum. We describe a method for deriving "metapeptides" (short amino acid sequences that may be represented in multiple organisms) from shotgun metagenomic sequencing of microbiome samples. In two ocean microbiome samples, we constructed site-specific metapeptide databases to detect more than one and a half times as many peptides as by searching against predicted genes from an assembled metagenome and roughly three times as many peptides as by searching against the NCBI environmental proteome database. The increased peptide yield has the potential to enrich the taxonomic and functional characterization of sample metaproteomes.}, }
@article {pmid27395027, year = {2016}, author = {Feng, H and Liang, Y and Guo, K and Li, N and Shen, D and Cong, Y and Zhou, Y and Wang, Y and Wang, M and Long, Y}, title = {Hybridization of photoanode and bioanode to enhance the current production of bioelectrochemical systems.}, journal = {Water research}, volume = {102}, number = {}, pages = {428-435}, doi = {10.1016/j.watres.2016.06.061}, pmid = {27395027}, issn = {1879-2448}, mesh = {*Bioelectric Energy Sources ; Biofilms ; Electrodes ; Electron Transport ; *Ferric Compounds ; }, abstract = {Bacterial extracellular electron transfer is one of the main bottlenecks in determining the efficiency of bioelectrochemical systems. Here, we report a photobioanode that combines carbon material with a photocatalyst (α-Fe2O3), utilizing visible light to accelerate biofilm formation and extracellular electron transfer in bioelectrochemical systems. Cyclic voltammetric studies of this photobioanode revealed active electron transfer at the anode/biofilm interface. The charge-transfer resistance of the anode/biofilm was ca. 46.6 Ω, which is half that of the unmodified anode. In addition, the results of confocal laser scanning microscopy and bacterial community analysis indicate that the photobioanode and light can accelerate biofilm formation and enrich exoelectrogens. When equipped in photo-bioelectrochemical systems, the start-up time was shortened from about 2.5 days to 1.1 days. The maximum current density of photo-bioelectrochemical systems was almost twice that of a control bioelectrochemical system. In addition, the current density of the photo-bio-electrochemical cell (PBEC) showed almost no decrease after being subjected to 40 d of illumination. This photobioanode is therefore a cost-effective, energy-clean, environment-friendly anode with high electrocatalytic activity and long-term stability, which has broad prospects in various processes, including wastewater treatment, bioelectricity generation, bioelectricity synthesis, and hydrogen production.}, }
@article {pmid27392936, year = {2017}, author = {Huang, YJ and Erb-Downward, JR and Dickson, RP and Curtis, JL and Huffnagle, GB and Han, MK}, title = {Understanding the role of the microbiome in chronic obstructive pulmonary disease: principles, challenges, and future directions.}, journal = {Translational research : the journal of laboratory and clinical medicine}, volume = {179}, number = {}, pages = {71-83}, pmid = {27392936}, issn = {1878-1810}, support = {UL1 TR000433/TR/NCATS NIH HHS/United States ; T32 HL007749/HL/NHLBI NIH HHS/United States ; K23 HL105572/HL/NHLBI NIH HHS/United States ; K23 HL130641/HL/NHLBI NIH HHS/United States ; L30 HL120241/HL/NHLBI NIH HHS/United States ; I01 CX000911/CX/CSRD VA/United States ; }, mesh = {Animals ; Computational Biology ; High-Throughput Nucleotide Sequencing ; Humans ; Inflammation/pathology ; Lung/microbiology/pathology ; *Microbiota ; Pulmonary Disease, Chronic Obstructive/*microbiology ; }, abstract = {In the past several years, advances in sequencing platforms and bioinformatics have transformed our understanding of the relationship between microbial ecology and human health. Both the normal and diseased lung are host to hundreds of bacterial genera, blurring the lines between "colonization" and "infection". However, whereas in health the respiratory microbiome is determined primarily by the dynamic balance of immigration and elimination, in chronic disease conditions become much more favorable for the reproduction of resident bacteria. Recent studies demonstrate that the microbiota of the chronic obstructive pulmonary disease (COPD) lung differ from the healthy lung although significant intrasubject and intersubject heterogeneity are still present with variation impacted by factors such as disease stage and inhaled medications. Changes in the relative abundance of specific bacterial taxa during COPD exacerbations have also been noted although further longitudinal analyses are needed to ascertain the malleability and resilience of this ecological system and its role in the occurrence and frequency of exacerbations. Whether patients with a "frequent exacerbator" phenotype possess specific or greater alterations in their airway microbiome that predispose them to recurrent exacerbations as compared with nonfrequent exacerbators needs to be determined. Although recent data suggest that the presence of bacteria has the potential to influence the host immune response, a key challenge in the next few years will be to continue to move beyond descriptive studies to define the clinical relevance of differences in lung microbiota associated with COPD.}, }
@article {pmid27390131, year = {2016}, author = {Andersen, SJ and Berton, JK and Naert, P and Gildemyn, S and Rabaey, K and Stevens, CV}, title = {Extraction and Esterification of Low-Titer Short-Chain Volatile Fatty Acids from Anaerobic Fermentation with Ionic Liquids.}, journal = {ChemSusChem}, volume = {9}, number = {16}, pages = {2059-2063}, doi = {10.1002/cssc.201600473}, pmid = {27390131}, issn = {1864-564X}, mesh = {Anaerobiosis ; Electrolysis ; Esterification ; Fatty Acids, Volatile/*chemistry/*isolation &amp; purification/metabolism ; *Fermentation ; Hydrogen-Ion Concentration ; Ionic Liquids/*chemistry ; Solvents/chemistry ; Temperature ; }, abstract = {Ionic liquids can both act as a solvent and mediate esterification to valorize low-titer volatile fatty acids and generate organic solvents from renewable carbon sources including biowaste and CO2 . In this study, four phosphonium ionic liquids were tested for single-stage extraction of acetic acid from a dilute stream and esterification to ethyl acetate with added ethanol and heat. The esterification proceeded with a maximum conversion of 85.9±1.3 % after 30 min at 75 °C at a 1:1 stoichiometric ratio of reactants. Extraction and esterification can be tailored using mixed-anion ionic liquids; this is demonstrated herein using a common trihexyl(tetradecyl)phosphonium cation and a mixed chloride and bis(trifluoromethylsulfonyl)imide anion ionic liquid. As a further proof-of-concept, ethyl acetate was generated from an ionic liquid-driven esterification of an acetic acid extractant generated using CO2 as the only carbon source by microbial electrosynthesis.}, }
@article {pmid27389856, year = {2016}, author = {Matassa, S and Boon, N and Pikaar, I and Verstraete, W}, title = {Microbial protein: future sustainable food supply route with low environmental footprint.}, journal = {Microbial biotechnology}, volume = {9}, number = {5}, pages = {568-575}, pmid = {27389856}, issn = {1751-7915}, mesh = {Animals ; Bacteria/*growth &amp; development/metabolism ; Biotechnology/*methods/trends ; *Food Supply ; Fungi/*growth &amp; development/metabolism ; Humans ; Microalgae/*growth &amp; development/metabolism ; Proteins/*metabolism ; }, abstract = {Microbial biotechnology has a long history of producing feeds and foods. The key feature of today's market economy is that protein production by conventional agriculture based food supply chains is becoming a major issue in terms of global environmental pollution such as diffuse nutrient and greenhouse gas emissions, land use and water footprint. Time has come to re-assess the current potentials of producing protein-rich feed or food additives in the form of algae, yeasts, fungi and plain bacterial cellular biomass, producible with a lower environmental footprint compared with other plant or animal-based alternatives. A major driver is the need to no longer disintegrate but rather upgrade a variety of low-value organic and inorganic side streams in our current non-cyclic economy. In this context, microbial bioconversions of such valuable matters to nutritive microbial cells and cell components are a powerful asset. The worldwide market of animal protein is of the order of several hundred million tons per year, that of plant protein several billion tons of protein per year; hence, the expansion of the production of microbial protein does not pose disruptive challenges towards the process of the latter. Besides protein as nutritive compounds, also other cellular components such as lipids (single cell oil), polyhydroxybuthyrate, exopolymeric saccharides, carotenoids, ectorines, (pro)vitamins and essential amino acids can be of value for the growing domain of novel nutrition. In order for microbial protein as feed or food to become a major and sustainable alternative, addressing the challenges of creating awareness and achieving public and broader regulatory acceptance are real and need to be addressed with care and expedience.}, }
@article {pmid27389418, year = {2016}, author = {Oleskin, AV and Shenderov, BA}, title = {Neuromodulatory effects and targets of the SCFAs and gasotransmitters produced by the human symbiotic microbiota.}, journal = {Microbial ecology in health and disease}, volume = {27}, number = {}, pages = {30971}, pmid = {27389418}, issn = {0891-060X}, abstract = {The symbiotic gut microbiota plays an important role in the development and homeostasis of the host organism. Its physiological, biochemical, behavioral, and communicative effects are mediated by multiple low molecular weight compounds. Recent data on small molecules produced by gut microbiota in mammalian organisms demonstrate the paramount importance of these biologically active molecules in terms of biology and medicine. Many of these molecules are pleiotropic mediators exerting effects on various tissues and organs. This review is focused on the functional roles of gaseous molecules that perform neuromediator and/or endocrine functions. The molecular mechanisms that underlie the effects of microbial fermentation-derived gaseous metabolites are not well understood. It is possible that these metabolites produce their effects via immunological, biochemical, and neuroendocrine mechanisms that involve endogenous and microbial modulators and transmitters; of considerable importance are also changes in epigenetic transcriptional factors, protein post-translational modification, lipid and mitochondrial metabolism, redox signaling, and ion channel/gap junction/transporter regulation. Recent findings have revealed that interactivity among such modulators/transmitters is a prerequisite for the ongoing dialog between microbial cells and host cells, including neurons. Using simple reliable methods for the detection and measurement of short-chain fatty acids (SCFAs) and small gaseous molecules in eukaryotic tissues and prokaryotic cells, selective inhibitors of enzymes that participate in their synthesis, as well as safe chemical and microbial donors of pleiotropic mediators and modulators of host intestinal microbial ecology, should enable us to apply these chemicals as novel therapeutics and medical research tools.}, }
@article {pmid27387486, year = {2016}, author = {Junghare, M and Spiteller, D and Schink, B}, title = {Enzymes involved in the anaerobic degradation of ortho-phthalate by the nitrate-reducing bacterium Azoarcus sp. strain PA01.}, journal = {Environmental microbiology}, volume = {18}, number = {9}, pages = {3175-3188}, doi = {10.1111/1462-2920.13447}, pmid = {27387486}, issn = {1462-2920}, mesh = {Acyl Coenzyme A/chemistry/genetics/*metabolism ; Anaerobiosis ; Azoarcus/chemistry/enzymology/genetics/*metabolism ; Bacterial Proteins/chemistry/genetics/*metabolism ; Benzoates/metabolism ; Multigene Family ; Nitrates/*metabolism ; Oxidation-Reduction ; Phthalic Acids/chemistry/*metabolism ; Substrate Specificity ; }, abstract = {The pathway of anaerobic degradation of o-phthalate was studied in the nitrate-reducing bacterium Azoarcus sp. strain PA01. Differential two-dimensional protein gel profiling allowed the identification of specifically induced proteins in o-phthalate-grown compared to benzoate-grown cells. The genes encoding o-phthalate-induced proteins were found in a 9.9 kb gene cluster in the genome of Azoarcus sp. strain PA01. The o-phthalate-induced gene cluster codes for proteins homologous to a dicarboxylic acid transporter, putative CoA-transferases and a UbiD-like decarboxylase that were assigned to be specifically involved in the initial steps of anaerobic o-phthalate degradation. We propose that o-phthalate is first activated to o-phthalyl-CoA by a putative succinyl-CoA-dependent succinyl-CoA:o-phthalate CoA-transferase, and o-phthalyl-CoA is subsequently decarboxylated to benzoyl-CoA by a putative o-phthalyl-CoA decarboxylase. Results from in vitro enzyme assays with cell-free extracts of o-phthalate-grown cells demonstrated the formation of o-phthalyl-CoA from o-phthalate and succinyl-CoA as CoA donor, and its subsequent decarboxylation to benzoyl-CoA. The putative succinyl-CoA:o-phthalate CoA-transferase showed high substrate specificity for o-phthalate and did not accept isophthalate, terephthalate or 3-fluoro-o-phthalate whereas the putative o-phthalyl-CoA decarboxylase converted fluoro-o-phthalyl-CoA to fluoro-benzoyl-CoA. No decarboxylase activity was observed with isophthalyl-CoA or terephthalyl-CoA. Both enzyme activities were oxygen-insensitive and inducible only after growth with o-phthalate. Further degradation of benzoyl-CoA proceeds analogous to the well-established anaerobic benzoyl-CoA degradation pathway of nitrate-reducing bacteria.}, }
@article {pmid27385827, year = {2016}, author = {Hall, JP and Wood, AJ and Harrison, E and Brockhurst, MA}, title = {Source-sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {29}, pages = {8260-8265}, pmid = {27385827}, issn = {1091-6490}, support = {311490/ERC_/European Research Council/International ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Mercury/pharmacology ; Plasmids/*genetics ; Pseudomonas fluorescens/drug effects/*genetics ; Pseudomonas putida/drug effects/*genetics ; *Soil Microbiology ; }, abstract = {Horizontal gene transfer is a fundamental process in bacterial evolution that can accelerate adaptation via the sharing of genes between lineages. Conjugative plasmids are the principal genetic elements mediating the horizontal transfer of genes, both within and between bacterial species. In some species, plasmids are unstable and likely to be lost through purifying selection, but when alternative hosts are available, interspecific plasmid transfer could counteract this and maintain access to plasmid-borne genes. To investigate the evolutionary importance of alternative hosts to plasmid population dynamics in an ecologically relevant environment, we established simple soil microcosm communities comprising two species of common soil bacteria, Pseudomonas fluorescens and Pseudomonas putida, and a mercury resistance (Hg(R)) plasmid, pQBR57, both with and without positive selection [i.e., addition of Hg(II)]. In single-species populations, plasmid stability varied between species: although pQBR57 survived both with and without positive selection in P. fluorescens, it was lost or replaced by nontransferable Hg(R) captured to the chromosome in P. putida A simple mathematical model suggests these differences were likely due to pQBR57's lower intraspecific conjugation rate in P. putida By contrast, in two-species communities, both models and experiments show that interspecific conjugation from P. fluorescens allowed pQBR57 to persist in P. putida via source-sink transfer dynamics. Moreover, the replacement of pQBR57 by nontransferable chromosomal Hg(R) in P. putida was slowed in coculture. Interspecific transfer allows plasmid survival in host species unable to sustain the plasmid in monoculture, promoting community-wide access to the plasmid-borne accessory gene pool and thus potentiating future evolvability.}, }
@article {pmid27383981, year = {2016}, author = {Thaiss, CA and Zmora, N and Levy, M and Elinav, E}, title = {The microbiome and innate immunity.}, journal = {Nature}, volume = {535}, number = {7610}, pages = {65-74}, pmid = {27383981}, issn = {1476-4687}, mesh = {Animals ; Autoimmunity ; Epigenesis, Genetic ; Gastrointestinal Microbiome/immunology/*physiology ; Humans ; Immunity, Innate/genetics/immunology/*physiology ; Infections/genetics/immunology/microbiology ; Inflammation/genetics/microbiology/pathology ; Intestinal Mucosa/cytology/microbiology/physiology ; Lymphocytes/physiology ; Metabolic Syndrome/metabolism/microbiology/pathology ; Myeloid Cells/physiology ; Neoplasms/genetics/microbiology/pathology ; }, abstract = {The intestinal microbiome is a signalling hub that integrates environmental inputs, such as diet, with genetic and immune signals to affect the host's metabolism, immunity and response to infection. The haematopoietic and non-haematopoietic cells of the innate immune system are located strategically at the host-microbiome interface. These cells have the ability to sense microorganisms or their metabolic products and to translate the signals into host physiological responses and the regulation of microbial ecology. Aberrations in the communication between the innate immune system and the gut microbiota might contribute to complex diseases.}, }
@article {pmid27383682, year = {2016}, author = {Hiraoka, S and Yang, CC and Iwasaki, W}, title = {Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond.}, journal = {Microbes and environments}, volume = {31}, number = {3}, pages = {204-212}, pmid = {27383682}, issn = {1347-4405}, mesh = {*Biota ; Computational Biology/*methods ; *Environmental Microbiology ; Metagenomics/*methods ; }, abstract = {Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives.}, }
@article {pmid27381337, year = {2016}, author = {Jo, SJ and Kwon, H and Jeong, SY and Lee, SH and Oh, HS and Yi, T and Lee, CH and Kim, TG}, title = {Effects of Quorum Quenching on the Microbial Community of Biofilm in an Anoxic/Oxic MBR for Wastewater Treatment.}, journal = {Journal of microbiology and biotechnology}, volume = {26}, number = {9}, pages = {1593-1604}, doi = {10.4014/jmb.1604.04070}, pmid = {27381337}, issn = {1738-8872}, mesh = {*Biofilms ; Biofouling/*prevention &amp; control ; Bioreactors/*microbiology ; *Quorum Sensing ; Wastewater ; Water Purification/instrumentation/*methods ; }, abstract = {Recently, bacterial quorum quenching (QQ) has been proven to have potential as an innovative approach for biofouling control in membrane bioreactors (MBRs) for advanced wastewater treatment. Although information regarding the microbial community is crucial for the development of QQ strategies, little information exists on the microbial ecology in QQ-MBRs. In this study, the microbial communities of biofilm were investigated in relation to the effect of QQ on anoxic/oxic MBRs. Two laboratory-scale MBRs were operated with and without QQ-beads (QQ-bacteria entrapped in beads). The transmembrane pressure increase in the QQ-MBRs was delayed by approximately 100-110% compared with conventional- and vacant-MBRs (beads without QQ-bacteria) at 45 kPa. In terms of the microbial community, QQ gradually favored the development of a diverse and even community. QQ had an effect on both the bacterial composition and change rate of the bacterial composition. Proteobacteria and Bacteroidetes were the most dominant phyla in the biofilm, and the average relative composition of Proteobacteria was low in the QQ-MBR. Thiothrix sp. was the dominant bacterium in the biofilm. The relative composition of Thiothrix sp. was low in the QQ-MBR. These findings provide useful information that can inform the development of a new QQ strategy.}, }
@article {pmid27381178, year = {2016}, author = {Sultanpuram, VR and Mothe, T and Mohammed, F and Chintalapati, S and Chintalapati, VR}, title = {Pontibacillus salipaludis sp. nov., a slightly halophilic bacterium isolated from a salt pan.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {66}, number = {10}, pages = {3884-3889}, doi = {10.1099/ijsem.0.001281}, pmid = {27381178}, issn = {1466-5034}, mesh = {Bacillaceae/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Diaminopimelic Acid/chemistry ; Fatty Acids/chemistry ; India ; Nucleic Acid Hybridization ; Peptidoglycan/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {Two novel Gram-stain-positive, facultatively anerobic, rod-shaped, motile, endospore-forming bacterial strains, 9DMT and 6DM, were isolated from Tuticorn, India. The high 16S rRNA gene sequence similarity (99.9 %) and DNA-DNA relatedness (88±2 %) indicated that strains 9DMT and 6DM were members of a single species. Based on 16S rRNA gene sequence analysis these strains were identified as belonging to the genus Pontibacillus and were related most closely to the type strains of Pontibacillus chungwhensis (99.7 % sequence similarity) and Pontibacillus marinus (97.9 %). The DNA G+C content of strains 9DMT and 6DM was 41.6 and 41.4 mol%, respectively. However, the level of DNA-DNA relatedness of these strains with P. chungwhensis KCTC 3890T and P. marinus KCTC 3917T was only 40.9 + 0.8 and 39.8 + 0.9 %, respectively. Strains 9DMT and 6DM were facultative anaerobes with optimal growth at 37 °C, at pH 7.0-8.0 and with 2-3 % (w/v) NaCl. The cell-wall peptidoglycan of strain 9DMT contained meso-diaminopimelic acid. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and three unknown lipids. The isoprenoid quinone was MK-7. Major fatty acids of strain 9DMT were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The results of phylogenetic, chemotaxonomic and biochemical tests allowed the clear differentiation of strains 9DMT and 6DM, which are considered to represent a novel member of the genus Pontibacillus, for which the name Pontibacillus salipaludis sp. nov. is proposed. The type strain is 9DMT (= KCTC 33742T=LMG 29102T= CGMCC 1.15353T).}, }
@article {pmid27380915, year = {2016}, author = {Lee, JC and Kim, SJ and Whang, KS}, title = {Halomonas sediminicola sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {66}, number = {10}, pages = {3865-3872}, doi = {10.1099/ijsem.0.001278}, pmid = {27380915}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Geologic Sediments/*microbiology ; Halomonas/*classification/genetics/isolation &amp; purification ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; Ponds/*microbiology ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Salinity ; Sequence Analysis, DNA ; Ubiquinone/chemistry ; }, abstract = {A Gram-stain-negative, moderately halophilic bacterium, designated strain CPS11T, was isolated from the sediment of a solar pond located in Shinan, Korea. Strain CPS11T was a strictly aerobic, motile, straight rod-shaped bacterium that grew at pH 5.0-9.0 (optimum, pH 7.0-8.0), at 10-37 °C (optimum, 28 °C) and at salinities of 1-20 % (w/v) NaCl (optimum, 10 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain CPS11T belonged to the genus Halomonas, with sequence similarity of 98.5-94.3 % to existing type strains, showing highest sequence similarity to Halomonasfontilapidosi 5CRT (98.5 %), Halomonasventosae Al12T (98.5 %), Halomonascampaniensis 5AGT (98.2 %), Halomonas huangheensis BJGMM-B45T (98.0 %), Halomonas alimentaria YKJ-16T (98.0 %), Halomonas mongoliensis Z-7009T (97.8 %), Halomonas shengliensis SL014B-85T (97.5 %) and Halomonas cupida DSM 4740T (97.5 %). The predominant ubiquinone was Q-9. The major fatty acids were C19 : 0 cyclo ω8c, C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0, C17 : 0 cyclo, C12 : 0 3-OH and C18 : 1ω7c. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid, an unknown phospholipid and unknown lipids. The DNA G+C content of this novel isolate was 64.3 mol%. Levels of DNA-DNA relatedness between strain CPS11T and the type strains of ten other species of the genus ranged from 50 to 21 %. On the basis of the polyphasic analysis conducted in this study, strain CPS11T represents a novel species of the genus Halomonas, for which the name Halomonas sediminicola sp. nov. is proposed. The type strain is CPS11T(=KACC 18262T=NBRC 110636T).}, }
@article {pmid27379042, year = {2016}, author = {Dini-Andreote, F and Brossi, MJ and van Elsas, JD and Salles, JF}, title = {Reconstructing the Genetic Potential of the Microbially-Mediated Nitrogen Cycle in a Salt Marsh Ecosystem.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {902}, pmid = {27379042}, issn = {1664-302X}, abstract = {Coastal ecosystems are considered buffer zones for the discharge of land-derived nutrients without accounting for potential negative side effects. Hence, there is an urgent need to better understand the ecological assembly and dynamics of the microorganisms that are involved in nitrogen (N) cycling in such systems. Here, we employed two complementary methodological approaches (i.e., shotgun metagenomics and quantitative PCR) to examine the distribution and abundance of selected microbial genes involved in N transformations. We used soil samples collected along a well-established pristine salt marsh soil chronosequence that spans over a century of ecosystem development at the island of Schiermonnikoog, The Netherlands. Across the examined soil successional stages, the structure of the populations of genes involved in N cycling processes was strongly related to (shifts in the) soil nitrogen levels (i.e., [Formula: see text], [Formula: see text]), salinity and pH (explaining 73.8% of the total variation, R (2) = 0.71). Quantification of the genes used as proxies for N fixation, nitrification and denitrification revealed clear successional signatures that corroborated the taxonomic assignments obtained by metagenomics. Notably, we found strong evidence for niche partitioning, as revealed by the abundance and distribution of marker genes for nitrification (ammonia-oxidizing bacteria and archaea) and denitrification (nitrite reductase nirK, nirS and nitrous oxide reductase nosZ clades I and II). This was supported by a distinct correlation between these genes and soil physico-chemical properties, such as soil physical structure, pH, salinity, organic matter, total N, [Formula: see text], [Formula: see text] and [Formula: see text], across four seasonal samplings. Overall, this study sheds light on the successional trajectories of microbial N cycle genes along a naturally developing salt marsh ecosystem. The data obtained serve as a foundation to guide the formulation of ecological models that aim to effectively monitor and manage pristine and impacted salt marsh areas. Such models should account for the ecology as well as the historical contingency of N cycling communities.}, }
@article {pmid27378552, year = {2016}, author = {Dorado-Morales, P and Vilanova, C and Peretó, J and Codoñer, FM and Ramón, D and Porcar, M}, title = {A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {29235}, pmid = {27378552}, issn = {2045-2322}, mesh = {Bacteria/*classification/*isolation &amp; purification ; Cities ; *Environmental Microbiology ; Fungi/*classification/*isolation &amp; purification ; Mediterranean Region ; *Microbiota ; Spain ; }, abstract = {Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the panels' surface. This biocenosis proved to be more similar to the ones inhabiting deserts than to any human or urban microbial ecosystem. This unique microbial community shows different day/night proteomic profiles; it is dominated by reddish pigment- and sphingolipid-producers, and is adapted to withstand circadian cycles of high temperatures, desiccation and solar radiation.}, }
@article {pmid27376945, year = {2016}, author = {Welles, L and Lopez-Vazquez, CM and Hooijmans, CM and van Loosdrecht, MCM and Brdjanovic, D}, title = {Prevalence of 'Candidatus Accumulibacter phosphatis' type II under phosphate limiting conditions.}, journal = {AMB Express}, volume = {6}, number = {1}, pages = {44}, pmid = {27376945}, issn = {2191-0855}, abstract = {P-limitation in enhanced biological phosphorus removal (EBPR) systems fed with acetate, has generally been considered as a condition leading to enrichment of organisms of the genotype' Candidatus Competibacter phosphatis' expressing the glycogen-accumulating organisms (GAO) phenotype. Recent studies have demonstrated in short-term experiments that organisms of the genotype 'Candidatus Accumulibacter phosphatis' clade I and II, known to express the polyphosphate-accumulating organisms (PAO) phenotype can switch to the GAO phenotype when poly-P is absent, but are performing the HAc-uptake at lower kinetic rates, where clade I showed the lowest rates. The objective of this study was to verify whether organisms of the genotype 'Candidatus Accumulibacter phosphatis' can also be enriched under P-limiting conditions while expressing a GAO phenotype and more specifically to see which specific clade prevails. A sequencing batch reactor was inoculated with activated sludge to enrich an EBPR culture for a cultivation period of 128 days (16 times the solids retention time) under P-limiting conditions. A mixed culture was obtained comprising of 49 % 'Candidatus Accumulibacter phosphatis' clade II and 46 % 'Candidatus Competibacter phosphatis'. The culture performed a full GAO metabolism for anaerobic HAc-uptake, but was still able to switch to a PAO metabolism, taking up excessive amounts of phosphate during the aerobic phase when it became available in the influent. These findings show that P-limitation, often used as strategy for enrichment of 'Candidatus Competibacter phosphatis', does not always lead to enrichment of only 'Candidatus Competibacter phosphatis'. Furthermore, it demonstrates that 'Candidatus Accumulibacter phosphatis' are able to proliferate in activated sludge systems for periods of up to 128 days or longer when the influent phosphate concentrations are just enough for assimilation purposes and no poly-P is formed. The 'Candidatus Accumulibacter phosphatis' retain the ability to switch to the PAO phenotype, taking up phosphate from the influent as soon as it becomes available.}, }
@article {pmid27376701, year = {2016}, author = {De Vrieze, J and Verstraete, W}, title = {Perspectives for microbial community composition in anaerobic digestion: from abundance and activity to connectivity.}, journal = {Environmental microbiology}, volume = {18}, number = {9}, pages = {2797-2809}, doi = {10.1111/1462-2920.13437}, pmid = {27376701}, issn = {1462-2920}, mesh = {Anaerobiosis ; *Microbial Interactions ; Microbiota ; Nanowires ; Quorum Sensing ; }, abstract = {Microbial management in anaerobic digestion is mainly focused on physically present and metabolically active species. Because of its complexity and operation near the thermodynamic equilibria, it is equally important to address functional regulation, based on spatial organisation and interspecies communication. Further establishment of the knowledge on microbial communication in anaerobic digestion through quorum sensing and nanowires is needed. Methods to detect centres of concentrated activity, related to the presence of highly active and well-connected species that take a central role in the anaerobic digestion process, have to be optimized. Bioaugmentation could serve as a crucial tool to introduce keystone species that may create or sustain such centres. Functional stability can be maintained by keeping the microbial community active. This results in a clear trade-off between functionally active and redundant microorganisms as primary basis for microbial community organization. Finally, a microbial community based prediction strategy for advanced process control is formulated.}, }
@article {pmid27375591, year = {2016}, author = {Herbold, CW and Pelikan, C and Kuzyk, O and Hausmann, B and Angel, R and Berry, D and Loy, A}, title = {Corrigendum: A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {870}, doi = {10.3389/fmicb.2016.00870}, pmid = {27375591}, issn = {1664-302X}, support = {P 25111/FWF_/Austrian Science Fund FWF/Austria ; P 25700/FWF_/Austrian Science Fund FWF/Austria ; P 26127/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {[This corrects the article on p. 731 in vol. 6, PMID: 26236305.].}, }
@article {pmid27375586, year = {2016}, author = {Turroni, S and Rampelli, S and Centanni, M and Schnorr, SL and Consolandi, C and Severgnini, M and Peano, C and Soverini, M and Falconi, M and Crittenden, AN and Henry, AG and Brigidi, P and Candela, M}, title = {Enterocyte-Associated Microbiome of the Hadza Hunter-Gatherers.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {865}, pmid = {27375586}, issn = {1664-302X}, abstract = {By means of a recently developed non-invasive ex vivo minimal model based on the interaction of the human enterocyte-like HT29 cell line and fecal slurries, we explored the enterocyte-associated microbiome of 21 Hadza hunter-gatherers and nine urban living Italians. Though reductionist, this model allows inferring the microbiota structural and functional arrangement as it interacts with enterocytes. Microbial suspensions obtained from Hadza or Italian stools were first evaluated for structural integrity by high resolution-scanning electron microscopy and co-incubated with HT29 cell monolayers. The enterocyte adherent microbiota fraction was then characterized by 16S rRNA gene sequencing and predictive functional profiling using PICRUSt. Compared to Italians, the Hadza enterocyte-associated microbiome was characterized by a greater amount of adhesive microorganisms with pathogenic potential, such as Proteobacteria, Erysipelotrichaceae, Enterococcus, Clostridium and Sarcina. These compositional characteristics were reflected in a functional enrichment in membrane transport, signal transduction, signaling molecules and interaction. Our results depict a new interesting mutualistic configuration of the enterocyte-associated microbiome in Hadza, stressing the importance of microbe-host interaction at the mucosal surface along the course of human evolution.}, }
@article {pmid27375242, year = {2016}, author = {Kerangart, S and Douëllou, T and Delannoy, S and Fach, P and Beutin, L and Sergentet-Thévenot, D and Cournoyer, B and Loukiadis, E}, title = {Variable tellurite resistance profiles of clinically-relevant Shiga toxin-producing Escherichia coli (STEC) influence their recovery from foodstuffs.}, journal = {Food microbiology}, volume = {59}, number = {}, pages = {32-42}, doi = {10.1016/j.fm.2016.05.005}, pmid = {27375242}, issn = {1095-9998}, mesh = {Adhesins, Bacterial ; Animals ; Culture Media ; *Drug Resistance, Bacterial ; Escherichia coli Infections/microbiology ; Escherichia coli O157/isolation &amp; purification ; Escherichia coli Proteins/genetics ; *Food Microbiology ; Humans ; Microbial Sensitivity Tests ; Operon ; Polymerase Chain Reaction ; Serogroup ; Shiga-Toxigenic Escherichia coli/*drug effects/growth &amp; development/*isolation &amp; purification ; Tellurium/*pharmacology ; Virulence/genetics ; }, abstract = {Tellurite (Tel)-amended selective media and resistance (Tel-R) are widely used for detecting Shiga toxin-producing Escherichia coli (STEC) from foodstuffs. Tel-R of 81 O157 and non-O157 STEC strains isolated from animal, food and human was thus investigated. Variations of STEC tellurite minimal inhibitory concentration (MIC) values have been observed and suggest a multifactorial and variable tellurite resistome between strains. Some clinically-relevant STEC were found highly susceptible and could not be recovered using a tellurite-based detection scheme. The ter operon was highly prevalent among highly Tel-R STEC but was not always detected among intermediately-resistant strains. Many STEC serogroup strains were found to harbor sublines showing a gradient of MIC values. These Tel-R sublines showed statistically significant log negative correlations with increasing tellurite concentration. Whatever the tellurite concentration, the highest number of resistant sublines was observed for STEC belonging to the O26 serogroup. Variations in the number of these Tel-R sublines could explain the poor recovery of some STEC serogroups on tellurite-amended media especially from food products with low levels of contamination. Comparison of tellurite MIC values and distribution of virulence-related genes showed Tel-R and virulence to be related.}, }
@article {pmid27374808, year = {2017}, author = {Marzorati, M and Vilchez-Vargas, R and Bussche, JV and Truchado, P and Jauregui, R and El Hage, RA and Pieper, DH and Vanhaecke, L and Van de Wiele, T}, title = {High-fiber and high-protein diets shape different gut microbial communities, which ecologically behave similarly under stress conditions, as shown in a gastrointestinal simulator.}, journal = {Molecular nutrition &amp; food research}, volume = {61}, number = {1}, pages = {}, doi = {10.1002/mnfr.201600150}, pmid = {27374808}, issn = {1613-4133}, mesh = {Chromatography, High Pressure Liquid ; Cluster Analysis ; Dietary Fiber/*pharmacology ; Dietary Proteins/*pharmacology ; Gastrointestinal Microbiome/*drug effects/genetics ; Humans ; RNA, Ribosomal, 16S ; Stress, Physiological ; }, abstract = {The aim of this work was to investigate the relationship between the structure of gut microbial communities fed with different diets (i.e. high-protein-HP- versus high-fiber-HF-diet) and their functional stability when challenged with mild and acute doses of a mix of amoxicillin, ciprofloxacin, and tetracycline. We made use of the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®)-a continuous model of the gastrointestinal tract-coupled with 16S-targeted Illumina and metabolomics (i.e. UHPLC-HRMS) analyses. Independently of the diet, the sudden exposure to an acute stress led to a modification of the microbial community structure, selecting for species belonging to Bacillus spp.; Clostridium cluster XIVa; Enterococci; Bacteroides; and Enterobacteriaceae. The antibiotic treatment led to a decrease in the number of operational taxonomic units (at least -10%). Cluster analysis of untargeted metabolic data showed that the antibiotic treatment affected the microbial activity. The impact on metabolites production was lower when the community was preexposed to mild doses of the antibiotic mix. This effect was stronger in the proximal colon for the HF diet and in the distal colon for the HP diet. Different diets shaped different gut microbial communities, which ecologically behaved similarly under stress conditions.}, }
@article {pmid27358393, year = {2016}, author = {Bálint, M and Bahram, M and Eren, AM and Faust, K and Fuhrman, JA and Lindahl, B and O'Hara, RB and Öpik, M and Sogin, ML and Unterseher, M and Tedersoo, L}, title = {Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes.}, journal = {FEMS microbiology reviews}, volume = {40}, number = {5}, pages = {686-700}, doi = {10.1093/femsre/fuw017}, pmid = {27358393}, issn = {1574-6976}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Biodiversity ; Data Interpretation, Statistical ; Fungi/classification/*genetics ; Genetic Markers/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {With high-throughput sequencing (HTS), we are able to explore the hidden world of microscopic organisms to an unpre-cedented level. The fast development of molecular technology and statistical methods means that microbial ecologists must keep their toolkits updated. Here, we review and evaluate some of the more widely adopted and emerging techniques for analysis of diversity and community composition, and the inference of species interactions from co-occurrence data generated by HTS of marker genes. We emphasize the importance of observational biases and statistical properties of the data and methods. The aim of the review is to critically discuss the advantages and disadvantages of established and emerging statistical methods, and to contribute to the integration of HTS-based marker gene data into community ecology.}, }
@article {pmid27357537, year = {2016}, author = {Di Cesare, A and Losasso, C and Barco, L and Eckert, EM and Conficoni, D and Sarasini, G and Corno, G and Ricci, A}, title = {Diverse distribution of Toxin-Antitoxin II systems in Salmonella enterica serovars.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {28759}, pmid = {27357537}, issn = {2045-2322}, mesh = {Animals ; Bacterial Proteins/genetics ; DNA-Binding Proteins/genetics ; Drug Resistance, Bacterial/*drug effects ; Humans ; Membrane Glycoproteins/genetics ; Plasmids ; Polymerase Chain Reaction ; Salmonella enterica/drug effects/*genetics/*isolation &amp; purification/pathogenicity ; Serogroup ; Toxin-Antitoxin Systems/genetics/*physiology ; }, abstract = {Type II Toxin-Antitoxin systems (TAs), known for their presence in virulent and antibiotic resistant bacterial strains, were recently identified in Salmonella enterica isolates. However, the relationships between the presence of TAs (ccdAB and vapBC) and the epidemiological and genetic features of different non-typhoidal Salmonella serovars are largely unknown, reducing our understanding of the ecological success of different serovars. Salmonella enterica isolates from different sources, belonging to different serovars and epidemiologically unrelated according to ERIC profiles, were investigated for the presence of type II TAs, plasmid content, and antibiotic resistance. The results showed the ubiquitous presence of the vapBC gene in all the investigated Salmonella isolates, but a diverse distribution of ccdAB, which was detected in the most widespread Salmonella serovars, only. Analysis of the plasmid toxin ccdB translated sequence of four selected Salmonella isolates showed the presence of the amino acid substitution R99W, known to impede in vitro the lethal effect of CcdB toxin in the absence of its cognate antitoxin CcdA. These findings suggest a direct role of the TAs in promoting adaptability and persistence of the most prevalent Salmonella serovars, thus implying a wider eco-physiological role for these type II TAs.}, }
@article {pmid27356494, year = {2017}, author = {Neacsu, M and McMonagle, J and Fletcher, RJ and Hulshof, T and Duncan, SH and Scobbie, L and Duncan, GJ and Cantlay, L and Horgan, G and de Roos, B and Duthie, GG and Russell, WR}, title = {Availability and dose response of phytophenols from a wheat bran rich cereal product in healthy human volunteers.}, journal = {Molecular nutrition &amp; food research}, volume = {61}, number = {3}, pages = {}, doi = {10.1002/mnfr.201600202}, pmid = {27356494}, issn = {1613-4133}, mesh = {Adult ; Biological Availability ; Colon/drug effects/metabolism ; Coumaric Acids/urine ; *Dietary Fiber ; Dose-Response Relationship, Drug ; Edible Grain/*chemistry ; Feces/chemistry ; Female ; Humans ; Male ; Middle Aged ; Phenols/*administration &amp; dosage/blood/*pharmacokinetics/urine ; }, abstract = {SCOPE: Phytophenols present in cereals are metabolised to compounds that could be partly responsible for the reduced risk of chronic diseases and all-cause mortality associated with fibre-rich diets. The bioavailability, form and in vivo concentrations of these metabolites require to be established.<br><br>MATERIALS AND METHODS: Eight healthy volunteers consumed a test meal containing a recommended dose (40 g) and high dose (120 g) of ready-to-eat wheat bran cereal and the systemic and colonic metabolites determined quantitatively by LC-MS.<br><br>CONCLUSION: Analysis of the systemic metabolomes demonstrated that a wide range of phytophenols were absorbed/excreted (43 metabolites) within 5 h of consumption. These included 16 of the 21 major parent compounds identified in the intervention product and several of these were also found to be significantly increased in the colon. Not all of the metabolites were increased with the higher dose, suggesting some limitation in absorption due to intrinsic factors and/or the food matrix. Many compounds identified (e.g. ferulic acid and major metabolites) exhibit anti-inflammatory activity and impact on redox pathways. The combination of postprandial absorption and delivery to the colon, as well as hepatic recycling of the metabolites at these concentrations, is likely to be beneficial to both systemic and gut health.}, }
@article {pmid27353382, year = {2016}, author = {Peng, L and Sun, J and Liu, Y and Dai, X and Ni, BJ}, title = {Nitrous Oxide Production in Co- Versus Counter-Diffusion Nitrifying Biofilms.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {28880}, pmid = {27353382}, issn = {2045-2322}, mesh = {*Biofilms ; *Bioreactors ; Diffusion ; Hydroxylamines/metabolism ; Nitrification ; Nitrous Oxide/analysis/*metabolism ; Oxidation-Reduction ; Oxygen/analysis/metabolism ; }, abstract = {For the application of biofilm processes, a better understanding of nitrous oxide (N2O) formation within the biofilm is essential for design and operation of biofilm reactors with minimized N2O emissions. In this work, a previously established N2O model incorporating both ammonia oxidizing bacteria (AOB) denitrification and hydroxylamine (NH2OH) oxidation pathways is applied in two structurally different biofilm systems to assess the effects of co- and counter-diffusion on N2O production. It is demonstrated that the diffusion of NH2OH and oxygen within both types of biofilms would form an anoxic layer with the presence of NH2OH and nitrite (), which would result in a high N2O production via AOB denitrification pathway. As a result, AOB denitrification pathway is dominant over NH2OH oxidation pathway within the co- and counter-diffusion biofilms. In comparison, the co-diffusion biofilm may generate substantially higher N2O than the counter-diffusion biofilm due to the higher accumulation of NH2OH in co-diffusion biofilm, especially under the condition of high-strength ammonium influent (500 mg N/L), thick biofilm depth (300 μm) and moderate oxygen loading (~1-~4 m(3)/d). The effect of co- and counter-diffusion on N2O production from the AOB biofilm is minimal when treating low-strength nitrogenous wastewater.}, }
@article {pmid27352281, year = {2016}, author = {Kim, S and Lee, S and McCormick, M and Kim, JG and Kang, H}, title = {Microbial Community and Greenhouse Gas Fluxes from Abandoned Rice Paddies with Different Vegetation.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {692-703}, pmid = {27352281}, issn = {1432-184X}, mesh = {Agriculture ; Biodiversity ; Biomass ; Carbon Dioxide/chemistry/pharmacology ; Ecology ; Environmental Monitoring ; Enzyme Activation ; Gases/chemistry/*pharmacology ; *Greenhouse Effect ; Methane/chemistry/pharmacology ; Microbial Consortia/*drug effects/genetics/*physiology ; Nitrous Oxide/chemistry/pharmacology ; Oryza/*growth &amp; development/*microbiology ; Seasons ; Soil/chemistry ; *Soil Microbiology ; Wetlands ; }, abstract = {The area of rice paddy fields has declined continuously in East Asian countries due to abandonment of agriculture and concurrent socioeconomic changes. When they are abandoned, rice paddy fields generally transform into wetlands by natural succession. While previous studies have mainly focused on vegetation shifts in abandoned rice paddies, little information is available about how these changes may affect their contribution to wetland functions. As newly abandoned fields proceed through succession, their hydrology and plant communities often change. Moreover, the relationships between these changes, soil microbial characteristics, and emissions of greenhouse gasses are poorly understood. In this study, we examined changes over the course of secondary succession of abandoned rice paddies to wetlands and investigated their ecological functions through changes in greenhouse gas fluxes and microbial characteristics. We collected gas and soil samples in summer and winter from areas dominated by Cyperaceae, Phragmites, and Sphagnum in each site. We found that CO2 emissions in summer were significantly higher than those in winter, but CH4 and N2O emission fluxes were consistently at very low levels and were similar among seasons and locations, due to their low nutrient conditions. These results suggest that microbial activity and abundance increased in summer. Greenhouse gas flux, soil properties, and microbial abundance were not affected by plant species, although the microbial community composition was changed by plant species. This information adds to our basic understanding of the contribution of wetlands that are transformed from abandoned rice paddy systems.}, }
@article {pmid27350881, year = {2016}, author = {Richards, JL and Yap, YA and McLeod, KH and Mackay, CR and Mariño, E}, title = {Dietary metabolites and the gut microbiota: an alternative approach to control inflammatory and autoimmune diseases.}, journal = {Clinical &amp; translational immunology}, volume = {5}, number = {5}, pages = {e82}, pmid = {27350881}, issn = {2050-0068}, abstract = {It is now convincingly clear that diet is one of the most influential lifestyle factors contributing to the rise of inflammatory diseases and autoimmunity in both developed and developing countries. In addition, the modern 'Western diet' has changed in recent years with increased caloric intake, and changes in the relative amounts of dietary components, including lower fibre and higher levels of fat and poor quality of carbohydrates. Diet shapes large-bowel microbial ecology, and this may be highly relevant to human diseases, as changes in the gut microbiota composition are associated with many inflammatory diseases. Recent studies have demonstrated a remarkable role for diet, the gut microbiota and their metabolites-the short-chain fatty acids (SCFAs)-in the pathogenesis of several inflammatory diseases, such as asthma, arthritis, inflammatory bowel disease, colon cancer and wound-healing. This review summarizes how diet, microbiota and gut microbial metabolites (particularly SCFAs) can modulate the progression of inflammatory diseases and autoimmunity, and reveal the molecular mechanisms (metabolite-sensing G protein-coupled receptor (GPCRs) and inhibition of histone deacetylases (HDACs)). Therefore, considerable benefit could be achieved simply through the use of diet, probiotics and metabolites for the prevention and treatment of inflammatory diseases and autoimmunity.}, }
@article {pmid27350093, year = {2016}, author = {Barrett, M and Fitzhenry, K and O'Flaherty, V and Dore, W and Keaveney, S and Cormican, M and Rowan, N and Clifford, E}, title = {Detection, fate and inactivation of pathogenic norovirus employing settlement and UV treatment in wastewater treatment facilities.}, journal = {The Science of the total environment}, volume = {568}, number = {}, pages = {1026-1036}, doi = {10.1016/j.scitotenv.2016.06.067}, pmid = {27350093}, issn = {1879-1026}, mesh = {Bacteriophages/physiology ; Disinfection/*methods ; Norovirus/isolation &amp; purification/*physiology ; *Ultraviolet Rays ; Virus Inactivation ; Waste Disposal, Fluid/*methods ; Wastewater/*virology ; *Water Microbiology ; }, abstract = {It is accepted that discharged wastewaters can be a significant source of pathogenic viruses in receiving water bodies contributing to pollution and may in turn enter the human food chain and pose a risk to human health, thus norovirus (NoV) is often a predominant cause of gastroenteritis globally. Working with NoV poses particular challenges as it cannot be readily identified and detection by molecular methods does not assess infectivity. It has been proposed that the infectivity of NoV may be modelled through the use of an alternative virus; F-specific RNA (FRNA) bacteriophages; GA genotype and other FRNA bacteriophages have been used as a surrogate in studies of NoV inactivation. This study investigated the efficiency of novel pulsed ultraviolet irradiation and low pressure ultraviolet irradiation as a potential pathogen inactivation system for NoV and FRNA bacteriophage (GA) in secondary treated wastewaters. The role of UV dose and the impact of suspended solids concentration on removal efficiency were also examined. The study also investigated the role of settlement processes in wastewater treatment plants in removing NoV. While NoV inactivation could not be determined it was found that at a maximum UV dose of 6.9J/cm(2) (6900mJ/cm(2)) an average 2.4 log removal of FRNA bacteriophage (GA) was observed; indicating the potential need for high UV doses to remove NoV if FRNA bacteriophage prove a suitable indicator for NoV. The study found that increasing concentrations of suspended solids impacted on PUV efficiency however, it appears the extent of the impact may be site specific. Furthermore, the study found that settlement processes can play a significant role in the removal of FRNA bacteriophage, thus potentially NoV.}, }
@article {pmid27349436, year = {2017}, author = {Morris, G and Berk, M and Carvalho, A and Caso, JR and Sanz, Y and Walder, K and Maes, M}, title = {The Role of the Microbial Metabolites Including Tryptophan Catabolites and Short Chain Fatty Acids in the Pathophysiology of Immune-Inflammatory and Neuroimmune Disease.}, journal = {Molecular neurobiology}, volume = {54}, number = {6}, pages = {4432-4451}, pmid = {27349436}, issn = {1559-1182}, mesh = {Animals ; Fatty Acids, Volatile/*metabolism ; Humans ; Inflammation/*metabolism/*microbiology ; *Metabolome ; *Microbiota ; *Neuroimmunomodulation ; Tryptophan/*metabolism ; }, abstract = {There is a growing awareness that gut commensal metabolites play a major role in host physiology and indeed the pathophysiology of several illnesses. The composition of the microbiota largely determines the levels of tryptophan in the systemic circulation and hence, indirectly, the levels of serotonin in the brain. Some microbiota synthesize neurotransmitters directly, e.g., gamma-amino butyric acid, while modulating the synthesis of neurotransmitters, such as dopamine and norepinephrine, and brain-derived neurotropic factor (BDNF). The composition of the microbiota determines the levels and nature of tryptophan catabolites (TRYCATs) which in turn has profound effects on aryl hydrocarbon receptors, thereby influencing epithelial barrier integrity and the presence of an inflammatory or tolerogenic environment in the intestine and beyond. The composition of the microbiota also determines the levels and ratios of short chain fatty acids (SCFAs) such as butyrate and propionate. Butyrate is a key energy source for colonocytes. Dysbiosis leading to reduced levels of SCFAs, notably butyrate, therefore may have adverse effects on epithelial barrier integrity, energy homeostasis, and the T helper 17/regulatory/T cell balance. Moreover, dysbiosis leading to reduced butyrate levels may increase bacterial translocation into the systemic circulation. As examples, we describe the role of microbial metabolites in the pathophysiology of diabetes type 2 and autism.}, }
@article {pmid27347687, year = {2016}, author = {Avellan, A and Auffan, M and Masion, A and Levard, C and Bertrand, M and Rose, J and Santaella, C and Achouak, W}, title = {Remote Biodegradation of Ge-Imogolite Nanotubes Controlled by the Iron Homeostasis of Pseudomonas brassicacearum.}, journal = {Environmental science &amp; technology}, volume = {50}, number = {14}, pages = {7791-7798}, doi = {10.1021/acs.est.6b01455}, pmid = {27347687}, issn = {1520-5851}, mesh = {Biodegradation, Environmental ; Homeostasis ; Iron/*chemistry ; Nanotubes/chemistry ; Pseudomonas/*metabolism ; }, abstract = {The toxicity of high-aspect-ratio nanomaterials (HARNs) is often associated with oxidative stress. The essential nutrient Fe may also be responsible of oxidative stress through the production of reactive oxygen species. In the present study, it has been examined to what extent adding Fenton reaction promoting Fe impacted the toxicity of an alumino-germanate model HARN. Structural addition of only 0.95% wt Fe to Ge-imogolite not only alleviated the toxicity observed in the case of Fe-free nanotubes but also stimulated bacterial growth. This was attributed to the metabolization of siderophore-mobilized Fe from the nanotube structure. This was evidenced by the regulation of the homeostasis-monitoring intracellular Fe levels. This was accompanied by a biodegradation of the nanotubes approaching 40%, whereas the Fe-free nanomaterial remained nearly untouched.}, }
@article {pmid27343575, year = {2016}, author = {Sharma, A and Catanante, G and Hayat, A and Istamboulie, G and Ben Rejeb, I and Bhand, S and Marty, JL}, title = {Development of structure switching aptamer assay for detection of aflatoxin M1 in milk sample.}, journal = {Talanta}, volume = {158}, number = {}, pages = {35-41}, doi = {10.1016/j.talanta.2016.05.043}, pmid = {27343575}, issn = {1873-3573}, mesh = {Aflatoxin M1/*analysis/chemistry ; Animals ; Aptamers, Nucleotide/*chemistry ; Biological Assay ; Fluorescence ; Food Contamination/analysis ; G-Quadruplexes ; Milk/*chemistry ; SELEX Aptamer Technique ; }, abstract = {The discovery of in-vitro systematic evolution of ligands by exponential enrichment (SELEX) process has considerably broaden the utility of aptamer as bio-recognition element, providing the high binding affinity and specificity against the target analytes. Recent research has focused on the development of structure switching signaling aptamer assay, transducing the aptamer- target recognition event into an easily detectable signal. In this paper, we demonstrate the development of structure switching aptamer assay for determination of aflatoxin M1 (AFM1) employing the quenching-dequenching mechanism. Hybridization of fluorescein labelled anti-AFM1 aptamer (F-aptamer) with TAMRA labelled complementary sequences (Q-aptamer) brings the fluorophore and the quencher into close proximity, which results in maximum fluorescence quenching. On addition of AFM1, the target induced conformational formation of antiparallel G-quadruplex aptamer-AFM1 complex results in fluorescence recovery. Under optimized experimental conditions, the developed method showed the good linearity with limit of detection (LOD) at 5.0ngkg(-1) for AFM1. The specificity of the sensing platform was carefully investigated against aflatoxin B1 (AFB1) and ochratoxin A (OTA). The developed assay platform showed the high specificity towards AFM1. The practical application of the developed aptamer assay was verified for detection of AFM1 in spiked milk samples. Good recoveries were obtained in the range from 94.40% to 95.28% (n=3) from AFM1 spiked milk sample.}, }
@article {pmid27341838, year = {2016}, author = {Christian, N and Sullivan, C and Visser, ND and Clay, K}, title = {Plant Host and Geographic Location Drive Endophyte Community Composition in the Face of Perturbation.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {621-632}, pmid = {27341838}, issn = {1432-184X}, mesh = {Animals ; Biodiversity ; *Endophytes/classification/drug effects/isolation &amp; purification ; Face/*microbiology ; Fungi/*classification/drug effects/isolation &amp; purification ; *Herbivory ; Indiana ; Insecta/microbiology ; Microbiota/physiology ; Mining ; Pesticides ; Phylogeny ; Plant Leaves/microbiology ; Plants/*classification/*microbiology ; Soil Microbiology ; Species Specificity ; *Symbiosis ; }, abstract = {All plants form symbioses with endophytic fungi, which affect host plant health and function. Most endophytic fungi are horizontally transmitted, and consequently, local environment and geographic location greatly influence endophyte community composition. Growing evidence also suggests that identity of the plant host (e.g., species, genotype) can be important in shaping endophyte communities. However, little is known about how disturbances to plants affect their fungal symbiont communities. The goal of this study was to test if disturbances, from both natural and anthropogenic sources, can alter endophyte communities independent of geographic location or plant host identity. Using the plant species white snakeroot (Ageratina altissima; Asteraceae), we conducted two experiments that tested the effect of perturbation on endophyte communities. First, we examined endophyte response to leaf mining insect activity, a natural perturbation, in three replicate populations. Second, for one population, we applied fungicide to plant leaves to test endophyte community response to an anthropogenic perturbation. Using culture-based methods and Sanger sequencing of fungal isolates, we then examined abundance, diversity, and community structure of endophytic fungi in leaves subjected to perturbations by leaf mining and fungicide application. Our results show that plant host individual and geographic location are the major determinants of endophyte community composition even in the face of perturbations. Unexpectedly, we found that leaf mining did not impact endophyte communities in white snakeroot, but fungicide treatment resulted in small but significant changes in endophyte community structure. Together, our results suggest that endophyte communities are highly resistant to biotic and anthropogenic disturbances.}, }
@article {pmid27341629, year = {2016}, author = {Tatti, E and McKew, BA and Whitby, C and Smith, CJ}, title = {Simultaneous DNA-RNA Extraction from Coastal Sediments and Quantification of 16S rRNA Genes and Transcripts by Real-time PCR.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {112}, pages = {}, pmid = {27341629}, issn = {1940-087X}, mesh = {DNA ; Geologic Sediments ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*analysis ; Real-Time Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Real Time Polymerase Chain Reaction also known as quantitative PCR (q-PCR) is a widely used tool in microbial ecology to quantify gene abundances of taxonomic and functional groups in environmental samples. Used in combination with a reverse transcriptase reaction (RT-q-PCR), it can also be employed to quantify gene transcripts. q-PCR makes use of highly sensitive fluorescent detection chemistries that allow quantification of PCR amplicons during the exponential phase of the reaction. Therefore, the biases associated with 'end-point' PCR detected in the plateau phase of the PCR reaction are avoided. A protocol to quantify bacterial 16S rRNA genes and transcripts from coastal sediments via real-time PCR is provided. First, a method for the co-extraction of DNA and RNA from coastal sediments, including the additional steps required for the preparation of DNA-free RNA, is outlined. Second, a step-by-step guide for the quantification of 16S rRNA genes and transcripts from the extracted nucleic acids via q-PCR and RT-q-PCR is outlined. This includes details for the construction of DNA and RNA standard curves. Key considerations for the use of RT-q-PCR assays in microbial ecology are included.}, }
@article {pmid27341110, year = {2016}, author = {Lin, X and Mou, R and Cao, Z and Xu, P and Wu, X and Zhu, Z and Chen, M}, title = {Characterization of cadmium-resistant bacteria and their potential for reducing accumulation of cadmium in rice grains.}, journal = {The Science of the total environment}, volume = {569-570}, number = {}, pages = {97-104}, doi = {10.1016/j.scitotenv.2016.06.121}, pmid = {27341110}, issn = {1879-1026}, mesh = {Biodegradation, Environmental ; Cadmium/*metabolism ; DNA, Bacterial/genetics ; Delftia/genetics/*metabolism ; Drug Resistance, Bacterial ; Edible Grain/metabolism ; Oryza/*metabolism ; Pseudomonas aeruginosa/genetics/*metabolism ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Soil Pollutants/*metabolism ; Stenotrophomonas/genetics/*metabolism ; }, abstract = {Cadmium (Cd) pollution is a serious widespread environmental problem that not only destroys the microbial ecology of soil and decreases crop production, but also poses a serious risk to human health. Many methods have been used for the remediation of Cd pollution but none of these is totally satisfactory. Microbial remediation strategies have attracted increasing interest since they are environmentally friendly and cost-effective. In the present study, three Cd-resistant bacteria were isolated and evaluated for potential application in Cd bioremediation. Based on their morphological, physiological and biochemical characteristics, together with 16S rDNA gene sequence analyses, bacteria were identified as Stenotrophomonas acidaminiphila (2#), Pseudomonas aeruginosa (9#) and Delftia tsuruhatensis (12#). Pseudomonas aeruginosa showed very high tolerance to metals, especially Cd (2200mg/L), Zn (1800mg/L) and Pb (1200mg/L), and is thought to be a multi-metal-resistant bacterium. Pseudomonas aeruginosa was also sensitive to 13 different antibiotics. The effects of the bacterial strains on the growth of rice plants and their ability to reduce Cd accumulation from Cd-contaminated soils in pot experiments were also evaluated. For Oryza sativa L. A grown in contaminated soil (3mg/kg Cd), the accumulation of Cd was decreased by 31.2 and 25.5% in brown rice and polished rice, respectively, by strain 9#; Pseudomonas aeruginosa was more effective in reducing Cd accumulation in rice grains than a mixture of strains. For Oryza sativa L. B, a mixture of strains acting synergistically was more effective than a single strain in reducing Cd accumulation; treatment with mixed strains (strains+3mg/kg Cd) resulted in 41.3, 35.9, and 32.6% reductions in Cd accumulation in unhulled rice, brown rice and polished rice, respectively. Although different results were obtained for two rice varieties, it can still be concluded that Cd-resistant bacteria are suitable for reducing Cd accumulation in rice grains and show potential for bioremediation of Cd-contaminated soils.}, }
@article {pmid27339112, year = {2017}, author = {Mao, S and Huo, W and Liu, J and Zhang, R and Zhu, W}, title = {In vitro effects of sodium bicarbonate buffer on rumen fermentation, levels of lipopolysaccharide and biogenic amine, and composition of rumen microbiota.}, journal = {Journal of the science of food and agriculture}, volume = {97}, number = {4}, pages = {1276-1285}, doi = {10.1002/jsfa.7861}, pmid = {27339112}, issn = {1097-0010}, mesh = {Animal Feed ; Animals ; Bacteria/*drug effects/growth &amp; development/metabolism ; Biodiversity ; Biogenic Amines/*metabolism ; Buffers ; Cattle ; Diet ; Dietary Supplements ; Fatty Acids, Volatile/*metabolism ; Female ; Fermentation ; Gastrointestinal Microbiome/*drug effects ; Hydrogen-Ion Concentration ; In Vitro Techniques ; Lipopolysaccharides/*metabolism ; Microbiota ; *Rumen/metabolism/microbiology ; Sodium Bicarbonate/*pharmacology ; }, abstract = {BACKGROUND: Diets containing high levels of carbohydrates provoke a rapid decrease of rumen pH and high levels of biogenic amines and lipopolysaccharides (LPS), which severely impair the health and performance of ruminants. The goal of this study was to evaluate the effects of sodium bicarbonate (BC) buffer on rumen fermentation, levels of LPS and biogenic amine, and composition of rumen microbiota using in vitro rumen cultures.<br><br>RESULTS: Sodium bicarbonate supplementation increased (P < 0.05) the final pH levels and concentrations of total volatile fatty acids and LPS, as well as the proportions of acetate, propionate, isobutyrate, isovalerate and valerate, and it decreased (P < 0.05) the proportion of butyrate and the levels of lactic acid, methylamine, tryptamine, tyramine, histamine and putrescine compared with the control. Pyrosequencing of the 16S rRNA gene showed that BC inclusion increased (P < 0.05) the bacterial diversity index compared with the control. Adding BC also decreased (P < 0.05) the relative abundance of Streptococcus and Butyrivibrio and increased (P < 0.05) the proportions of Ruminococcus, Succinivibrio and Prevotella.<br><br>CONCLUSION: Sodium bicarbonate supplementation has beneficial effects in the reduction of bioamine levels and the increase in ruminal pH, and in modifying the microbial ecology of the rumen; however, it results in an accumulation of LPS under high-grain diet conditions. &#xa9; 2016 Society of Chemical Industry.}, }
@article {pmid27338261, year = {2016}, author = {Huang, XF and Chaparro, JM and Reardon, KF and Judd, TM and Vivanco, JM}, title = {Supplementing Blends of Sugars, Amino Acids, and Secondary Metabolites to the Diet of Termites (Reticulitermes flavipes) Drive Distinct Gut Bacterial Communities.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {497-502}, pmid = {27338261}, issn = {1432-184X}, mesh = {Amino Acids/*metabolism ; Animal Feed/analysis ; Animals ; Bacteria/*classification/genetics ; Base Sequence ; Biodiversity ; *Carbohydrate Metabolism ; DNA, Bacterial/genetics ; Diet ; *Dietary Supplements ; Feeding Behavior ; Gastrointestinal Tract/metabolism/*microbiology ; Isoptera/*metabolism/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Secondary Metabolism ; Sequence Analysis, DNA ; Spirochaeta/genetics ; }, abstract = {Although it is well known that diet is one of the major modulators of the gut microbiome, how the major components of diet shape the gut microbial community is not well understood. Here, we developed a simple system that allows the investigation of the impact of given compounds as supplements of the diet on the termite gut microbiome. The 16S rRNA pyrosequencing analysis revealed that feeding termites different blends of sugars and amino acids did not majorly impact gut community composition; however, ingestion of blends of secondary metabolites caused shifts in gut bacterial community composition. The supplementation of sugars and amino acids reduced the richness significantly, and sugars alone increased the evenness of the gut bacterial community significantly. Secondary metabolites created the most dramatic effects on the microbial community, potentially overriding the effect of other types of compounds. Furthermore, some microbial groups were stimulated specifically by particular groups of compounds. For instance, termites fed with secondary metabolites contained more Firmicutes and Spirochaetes compared to the other treatments. In conclusion, our results suggest that the termite (Reticulitermes flavipes) can be used as a simple and effective system to test the effects of particular chemical compounds in modulating the gut microbiome.}, }
@article {pmid27337977, year = {2017}, author = {Esteves-Oliveira, M and El-Sayed, KF and Dörfer, C and Schwendicke, F}, title = {Impact of combined CO2 laser irradiation and fluoride on enamel and dentin biofilm-induced mineral loss.}, journal = {Clinical oral investigations}, volume = {21}, number = {4}, pages = {1243-1250}, pmid = {27337977}, issn = {1436-3771}, mesh = {Animals ; Bacterial Adhesion/drug effects/radiation effects ; Biofilms/*drug effects/*radiation effects ; Cattle ; Dental Enamel/*drug effects/*radiation effects ; Dentin/*drug effects/*radiation effects ; Fluorides, Topical/*pharmacology ; In Vitro Techniques ; *Lasers, Gas ; Microradiography ; Microscopy, Electron, Scanning ; Random Allocation ; Sodium Fluoride ; Streptococcus mutans/drug effects/radiation effects ; Surface Properties ; Tooth Demineralization/*prevention &amp; control ; }, abstract = {OBJECTIVES: The caries-protective effects of CO2 laser irradiation on dental enamel have been demonstrated using chemical demineralization models. We compared the effect of CO2 laser irradiation, sodium fluoride, or both on biofilm-induced mineral loss (∆Z) and Streptococcus mutans adhesion to enamel and dentin in vitro.<br><br>MATERIALS AND METHODS: Ground, polished bovine enamel, and dentin samples were allocated to four groups (n&#xa0;=&#xa0;12/group): no treatment (C); single 22,600-ppm fluoride (F) varnish (5&#xa0;% NaF) application; single CO2 laser treatment (L) with short pulses (5&#xa0;&#x3bc;s/&#x3bb;&#xa0;=&#xa0;10.6&#xa0;&#x3bc;m); and laser and subsequent fluoride treatment (LF). Samples were sterilized and submitted to an automated mono-species S. mutans biofilm model. Brain heart infusion plus 5&#xa0;% sucrose medium was provided eight times daily, followed by rinses with artificial saliva. After 10&#xa0;days, bacterial numbers in biofilms were enumerated as colony-forming units/ml (CFU/ml) (n&#xa0;=&#xa0;7/group). &#x2206;Z was assessed using transversal microradiography (n&#xa0;=&#xa0;12/group). Univariate ANOVA with post hoc Tukey honestly-significant-difference test was used for statistical analysis.<br><br>RESULTS: Bacterial numbers were significantly higher on dentin than enamel (p&#xa0;<&#xa0;0.01/ANOVA). On dentin, LF yielded significantly lower CFUs than other groups (p&#xa0;=&#xa0;0.03/Tukey), while no differences between groups were found for enamel. The lowest &#x2206;Z in enamel was observed for L (mean/SD 2036/1353&#xa0;vol%&#xd7;&#x3bc;m), which was not only significantly lower than C (9642/2452&#xa0;vol%&#xd7;&#x3bc;m) and F (7713/1489&#xa0;vol%&#xd7;&#x3bc;m) (p&#xa0;<&#xa0;0.05) but also not significantly different from LF (3135/2628&#xa0;vol%&#xd7;&#x3bc;m) (p&#xa0;>&#xa0;0.05). In dentin, only LF (163/227) significantly reduced &#x2206;Z (p&#xa0;<&#xa0;0.05).<br><br>CONCLUSION/CLINICAL RELEVANCE: CO2 laser irradiation did not increase adhesion of S. mutans in vitro. Laser treatment alone protected enamel against biofilm-induced demineralization, while a combined laser-fluoride application was required to protect dentin.}, }
@article {pmid27337482, year = {2016}, author = {Xavier, JB}, title = {Sociomicrobiology and Pathogenic Bacteria.}, journal = {Microbiology spectrum}, volume = {4}, number = {3}, pages = {}, pmid = {27337482}, issn = {2165-0497}, support = {DP2 OD008440/OD/NIH HHS/United States ; }, mesh = {Bacteria/*pathogenicity ; Bacterial Infections/*microbiology ; *Host-Pathogen Interactions ; Humans ; *Microbial Consortia ; *Microbial Interactions ; }, abstract = {The study of microbial pathogenesis has been primarily a reductionist science since Koch's principles. Reductionist approaches are essential to identify the causal agents of infectious disease, their molecular mechanisms of action, and potential drug targets, and much of medicine's success in the treatment of infectious disease stems from that approach. But many bacteria-caused diseases cannot be explained by a single bacterium. Several aspects of bacterial pathogenesis will benefit from a more holistic approach that takes into account social interaction among bacteria of the same species and between species in consortia such as the human microbiome. The emerging discipline of sociomicrobiology provides a framework to dissect microbial interactions in single and multi-species communities without compromising mechanistic detail. The study of bacterial pathogenesis can benefit greatly from incorporating concepts from other disciplines such as social evolution theory and microbial ecology, where communities, their interactions with hosts, and with the environment play key roles.}, }
@article {pmid27332875, year = {2016}, author = {Tan, J and McKenzie, C and Vuillermin, PJ and Goverse, G and Vinuesa, CG and Mebius, RE and Macia, L and Mackay, CR}, title = {Dietary Fiber and Bacterial SCFA Enhance Oral Tolerance and Protect against Food Allergy through Diverse Cellular Pathways.}, journal = {Cell reports}, volume = {15}, number = {12}, pages = {2809-2824}, doi = {10.1016/j.celrep.2016.05.047}, pmid = {27332875}, issn = {2211-1247}, mesh = {Animals ; Antigens, CD/metabolism ; Bacteria/*metabolism ; Dendritic Cells/drug effects/metabolism ; Dietary Fiber/*pharmacology ; Fatty Acids, Volatile/*metabolism ; Feeding Behavior ; Food Hypersensitivity/*immunology/*prevention &amp; control ; Gastrointestinal Microbiome/drug effects ; Immune Tolerance/*drug effects ; Immunoglobulin A/immunology ; Integrin alpha Chains/metabolism ; Mice, Inbred C57BL ; Receptors, G-Protein-Coupled/metabolism ; Receptors, Nicotinic/metabolism ; Signal Transduction/*drug effects ; Vitamin A/metabolism ; }, abstract = {The incidence of food allergies in western countries has increased dramatically in recent decades. Tolerance to food antigens relies on mucosal CD103(+) dendritic cells (DCs), which promote differentiation of regulatory T (Treg) cells. We show that high-fiber feeding in mice improved oral tolerance and protected from food allergy. High-fiber feeding reshaped gut microbial ecology and increased the release of short-chain fatty acids (SCFAs), particularly acetate and butyrate. High-fiber feeding enhanced oral tolerance and protected against food allergy by enhancing retinal dehydrogenase activity in CD103(+) DC. This protection depended on vitamin A in the diet. This feeding regimen also boosted IgA production and enhanced T follicular helper and mucosal germinal center responses. Mice lacking GPR43 or GPR109A, receptors for SCFAs, showed exacerbated food allergy and fewer CD103(+) DCs. Dietary elements, including fiber and vitamin A, therefore regulate numerous protective pathways in the gastrointestinal tract, necessary for immune non-responsiveness to food antigens.}, }
@article {pmid27329450, year = {2016}, author = {Król, N and Obiegala, A and Pfeffer, M and Lonc, E and Kiewra, D}, title = {Detection of selected pathogens in ticks collected from cats and dogs in the Wrocław Agglomeration, South-West Poland.}, journal = {Parasites &amp; vectors}, volume = {9}, number = {1}, pages = {351}, pmid = {27329450}, issn = {1756-3305}, mesh = {Anaplasmataceae/*isolation &amp; purification ; Animals ; Arachnid Vectors/microbiology ; Babesia/*isolation &amp; purification ; Cat Diseases/epidemiology/*parasitology/transmission ; Cats ; Dog Diseases/epidemiology/*parasitology/transmission ; Dogs ; Female ; Ixodidae/*microbiology ; Male ; Poland/epidemiology ; Rickettsia/*isolation &amp; purification ; Tick Infestations/epidemiology/parasitology/veterinary ; Urban Population ; }, abstract = {BACKGROUND: Tick-borne infections are no longer confined to rural areas, they are documented with increasing frequency in urban settlements across the world. They are known to cause diseases in humans as well as in their companion animals.<br><br>METHODS: During a period of 2&#xa0;years, from January 2013 until December 2014, ticks were collected from dogs and cats in 18 veterinary clinics in the Wroc&#x142;aw Agglomeration, Poland. In total, 1455 ticks were found on 931 pets: 760 domestic dogs and 171 cats. For molecular examinations 127 I. ricinus ticks (115 females and 12 males) were randomly selected, all collected I. hexagonus (n&#x2009;=&#x2009;137, 32 females, 98 nymphs, 7 larvae) and all collected D. reticulatus (n&#x2009;=&#x2009;46, 31 females, 15 males) were taken. Ixodes ricinus and I. hexagonus ticks were tested for Rickettsia spp., Anaplasma phagocytophilum, Candidatus Neoehrlichia mikurensis and Babesia spp., while D. reticulatus ticks were investigated for Rickettsia spp. and Babesia spp. only.<br><br>RESULTS: In total, 65.4&#xa0;% I. ricinus ticks were infected with at least one pathogen. Over 50&#xa0;% of I. ricinus were positive for Rickettsia spp. (R. helvetica and R. monacensis). The infection level with A. phagocytophilum was 21.3&#xa0;%. DNA of Cand. N. mikurensis was detected in 8.1&#xa0;% I. ricinus ticks. Interestingly only female ticks were infected. The prevalence of Babesia spp. was confirmed in 9.0&#xa0;% of I. ricinus involving the species B. microti and B. venatorum. A total of nineteen double, one triple and two quadruple infections were found in I. ricinus ticks only. Almost 11&#xa0;% of I. hexagonus ticks were positive for at least one of the tested pathogens. Rickettsia spp. infection was found in 2.2&#xa0;%, while A. phagocytophilum was detected in 8.1&#xa0;% of I. hexagonus ticks. Only one nymph was positive for Cand. N. mikurensis and none of I. hexagonus ticks harbored a Babesia spp. Over 60&#xa0;% of D. reticulatus ticks were positive for rickettsial DNA, exclusively belonging to the species R. raoultii.<br><br>CONCLUSION: The high tick infestation rates and the prevalence of pathogens found in these ticks demonstrate a serious level of encounter to tick-borne diseases in urban dogs in the Wroclaw area, and provide evidence that dogs and cats themselves may substantially contribute to the circulation of the ticks and pathogens in the urban area.}, }
@article {pmid27324654, year = {2016}, author = {Parada, C and Orruño, M and Kaberdin, V and Bravo, Z and Barcina, I and Arana, I}, title = {Changes in the Vibrio harveyi Cell Envelope Subproteome During Permanence in Cold Seawater.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {549-558}, pmid = {27324654}, issn = {1432-184X}, mesh = {Adaptation, Physiological ; Bacterial Proteins/*chemistry/physiology ; Cell Membrane/*chemistry/physiology ; *Cold Temperature ; Colony Count, Microbial ; Cytochrome b Group ; Ferritins ; Membrane Proteins/*chemistry/physiology ; Microbial Viability ; Proteome/*chemistry/physiology ; Seawater/*microbiology ; Time Factors ; Vibrio/chemistry/cytology/*physiology ; }, abstract = {Previous work demonstrated that physiological, morphological, and gene expression changes as well as the time-dependent entry into the viable but not culturable (VBNC) state are used by Vibrio species to survive and cope with diverse stress conditions including seasonal temperature downshifts and starvation. To learn more about the nature and specific contribution of membrane proteins to cell adaptation and survival, we analyzed variations in the protein composition of cell envelope and related them to morphological and physiological changes that were taking place during the long-term permanence of Vibrio harveyi in seawater microcosm at 4 °C. We found that after 21 days of permanence, nearly all population (ca. 99 %) of V. harveyi acquired the VBNC phenotype. Although the size of V. harveyi cells gradually decreased during the incubation time, we found that this morphological change was not directly related to their entry into the VBNC state. Our proteomic study revealed that the level of membrane proteins playing key roles in cellular transport, maintenance of cell structure, and in bioenergetics processes remained unchanged along starvation at low temperature, thus suggesting that V. harveyi might need these proteins for the long-term survival and/or for the resuscitation process. On a contrary, the level of two proteins, elongation factor Tu (EF-TU) and bacterioferritin, greatly increased reaching the maximal values by the end of the incubation period. We further discuss the above data with respect to the putative roles likely exerted by membrane proteins during transition to and maintaining of the VBNC state.}, }
@article {pmid27324653, year = {2016}, author = {Zhang, Y and Deng, CP and Shen, B and Yang, JS and Wang, ET and Yuan, HL}, title = {Syntrophic Interactions Within a Butane-Oxidizing Bacterial Consortium Isolated from Puguang Gas Field in China.}, journal = {Microbial ecology}, volume = {72}, number = {3}, pages = {538-548}, pmid = {27324653}, issn = {1432-184X}, mesh = {Bacteria/growth &amp; development/*isolation &amp; purification/*metabolism ; Bacterial Load ; Bacterial Proteins/genetics ; Base Sequence ; Butanes/analysis/*metabolism ; Butanols/analysis/metabolism ; China ; Chromatography, Gas/methods ; Coculture Techniques ; DNA, Bacterial ; Genes, Bacterial/genetics ; Metabolic Networks and Pathways ; *Microbial Consortia ; Oil and Gas Fields/*microbiology ; *Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction/methods ; Soil Microbiology ; Time Factors ; }, abstract = {Butane oxidation by the hydrocarbon degradation bacteria has long been described, but little is known about the microbial interaction in this process. To investigate this interaction, the efficiency of butane oxidation was estimated in monocultures and co-cultures of six strains of butane-oxidizing bacteria (BOB) and a butanol-oxidizing strain. Results showed that the butane degradation velocity was at least 26 times higher in the co-culture of the seven strains (228.50 nmol h(-1)) than in the six individual monocultures (8.71 nmol h(-1)). Gas chromatographic analysis of metabolites in the cultures revealed the accumulation of butanol in the monocultures of BOB strains but not in the co-culture with the butanol-oxidizing strain. These results evidenced a novel syntrophic association between BOB and butanol-oxidizing bacteria in the butane oxidation. The BOB strains oxidized butane into butanol, but this activity was inhibited by the accumulated butanol in monocultures, whereas the removal of butanol by the butanol-oxidizing strain in co-culture could eliminate the suppression and improve the butane degradation efficiency. In the co-culture, both BOB and butanol-oxidizing bacteria could grow and the time needed for butane complete removal was shortened from more than 192 h to less than 4 h. The unsuppressed effect of the co-culture was also consistent with the results of reverse transcription quantitative real-time PCR (RT-qPCR) of bmoX gene because increased expression of this gene was detected during the syntrophic growth compared with that in monoculture, pointing to the upregulation of bmoX in the syntrophic interaction.}, }
@article {pmid27324572, year = {2016}, author = {Trojan, D and Schreiber, L and Bjerg, JT and Bøggild, A and Yang, T and Kjeldsen, KU and Schramm, A}, title = {A taxonomic framework for cable bacteria and proposal of the candidate genera Electrothrix and Electronema.}, journal = {Systematic and applied microbiology}, volume = {39}, number = {5}, pages = {297-306}, pmid = {27324572}, issn = {1618-0984}, support = {291650/ERC_/European Research Council/International ; }, mesh = {Aquatic Organisms/*classification/*genetics/isolation &amp; purification ; Base Sequence ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Deltaproteobacteria/*classification/*genetics/isolation &amp; purification ; Geologic Sediments/*microbiology ; In Situ Hybridization, Fluorescence ; Microscopy, Atomic Force ; Microscopy, Electron ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Cable bacteria are long, multicellular filaments that can conduct electric currents over centimeter-scale distances. All cable bacteria identified to date belong to the deltaproteobacterial family Desulfobulbaceae and have not been isolated in pure culture yet. Their taxonomic delineation and exact phylogeny is uncertain, as most studies so far have reported only short partial 16S rRNA sequences or have relied on identification by a combination of filament morphology and 16S rRNA-targeted fluorescence in situ hybridization with a Desulfobulbaceae-specific probe. In this study, nearly full-length 16S rRNA gene sequences of 16 individual cable bacteria filaments from freshwater, salt marsh, and marine sites of four geographic locations are presented. These sequences formed a distinct, monophyletic sister clade to the genus Desulfobulbus and could be divided into six coherent, species-level clusters, arranged as two genus-level groups. The same grouping was retrieved by phylogenetic analysis of full or partial dsrAB genes encoding the dissimilatory sulfite reductase. Based on these results, it is proposed to accommodate cable bacteria within two novel candidate genera: the mostly marine "Candidatus Electrothrix", with four candidate species, and the mostly freshwater "Candidatus Electronema", with two candidate species. This taxonomic framework can be used to assign environmental sequences confidently to the cable bacteria clade, even without morphological information. Database searches revealed 185 16S rRNA gene sequences that affiliated within the clade formed by the proposed cable bacteria genera, of which 120 sequences could be assigned to one of the six candidate species, while the remaining 65 sequences indicated the existence of up to five additional species.}, }
@article {pmid27321429, year = {2016}, author = {Lanzén, A and Epelde, L and Blanco, F and Martín, I and Artetxe, U and Garbisu, C}, title = {Multi-targeted metagenetic analysis of the influence of climate and environmental parameters on soil microbial communities along an elevational gradient.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {28257}, pmid = {27321429}, issn = {2045-2322}, mesh = {*Biodiversity ; *Climate Change ; *Metagenomics ; *Soil Microbiology ; Spain ; }, abstract = {Mountain elevation gradients are invaluable sites for understanding the effects of climate change on ecosystem function, community structure and distribution. However, relatively little is known about the impact on soil microbial communities, in spite of their importance for the functioning of the soil ecosystem. Previous studies of microbial diversity along elevational gradients were often limited by confounding variables such as vegetation, pH, and nutrients. Here, we utilised a transect in the Pyrenees established to minimise variation in such parameters, to examine prokaryotic, fungal, protist and metazoan communities throughout three consecutive years. We aimed to determine the influences of climate and environmental parameters on soil microbial community structure; as well as on the relationships between those microbial communities. Further, functional diversity of heterotrophic bacteria was determined using Biolog. Prokaryotic and fungal community structure, but not alpha-diversity, correlated significantly with elevation. However, carbon-to-nitrogen ratio and pH appeared to affect prokaryotic and protist communities more strongly. Both community structure and physicochemical parameters varied considerably between years, illustrating the value of long-term monitoring of the dynamic processes controlling the soil ecosystem. Our study also illustrates both the challenges and strengths of using microbial communities as indicators of potential impacts of climate change.}, }
@article {pmid27321040, year = {2016}, author = {Martini, MC and Wibberg, D and Lozano, M and Torres Tejerizo, G and Albicoro, FJ and Jaenicke, S and van Elsas, JD and Petroni, A and Garcillán-Barcia, MP and de la Cruz, F and Schlüter, A and Pühler, A and Pistorio, M and Lagares, A and Del Papa, MF}, title = {Genomics of high molecular weight plasmids isolated from an on-farm biopurification system.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {28284}, pmid = {27321040}, issn = {2045-2322}, mesh = {Escherichia coli/chemistry/*genetics ; Molecular Weight ; *Plasmids/chemistry/genetics/isolation &amp; purification ; *Replicon ; }, abstract = {The use of biopurification systems (BPS) constitutes an efficient strategy to eliminate pesticides from polluted wastewaters from farm activities. BPS environments contain a high microbial density and diversity facilitating the exchange of information among bacteria, mediated by mobile genetic elements (MGEs), which play a key role in bacterial adaptation and evolution in such environments. Here we sequenced and characterized high-molecular-weight plasmids from a bacterial collection of an on-farm BPS. The high-throughput-sequencing of the plasmid pool yielded a total of several Mb sequence information. Assembly of the sequence data resulted in six complete replicons. Using in silico analyses we identified plasmid replication genes whose encoding proteins represent 13 different Pfam families, as well as proteins involved in plasmid conjugation, indicating a large diversity of plasmid replicons and suggesting the occurrence of horizontal gene transfer (HGT) events within the habitat analyzed. In addition, genes conferring resistance to 10 classes of antimicrobial compounds and those encoding enzymes potentially involved in pesticide and aromatic hydrocarbon degradation were found. Global analysis of the plasmid pool suggest that the analyzed BPS represents a key environment for further studies addressing the dissemination of MGEs carrying catabolic genes and pathway assembly regarding degradation capabilities.}, }
@article {pmid27317862, year = {2016}, author = {Vanwonterghem, I and Jensen, PD and Rabaey, K and Tyson, GW}, title = {Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion.}, journal = {Environmental microbiology}, volume = {18}, number = {9}, pages = {3144-3158}, doi = {10.1111/1462-2920.13382}, pmid = {27317862}, issn = {1462-2920}, mesh = {Anaerobiosis ; Bacteria/classification/*genetics/*metabolism ; Biodiversity ; *Genome, Bacterial ; Metabolic Networks and Pathways ; Metagenomics ; Methane/metabolism ; Phylogeny ; }, abstract = {Our understanding of the complex interconnected processes performed by microbial communities is hindered by our inability to culture the vast majority of microorganisms. Metagenomics provides a way to bypass this cultivation bottleneck and recent advances in this field now allow us to recover a growing number of genomes representing previously uncultured populations from increasingly complex environments. In this study, a temporal genome-centric metagenomic analysis was performed of lab-scale anaerobic digesters that host complex microbial communities fulfilling a series of interlinked metabolic processes to enable the conversion of cellulose to methane. In total, 101 population genomes that were moderate to near-complete were recovered based primarily on differential coverage binning. These populations span 19 phyla, represent mostly novel species and expand the genomic coverage of several rare phyla. Classification into functional guilds based on their metabolic potential revealed metabolic networks with a high level of functional redundancy as well as niche specialization, and allowed us to identify potential roles such as hydrolytic specialists for several rare, uncultured populations. Genome-centric analyses of complex microbial communities across diverse environments provide the key to understanding the phylogenetic and metabolic diversity of these interactive communities.}, }
@article {pmid27315483, year = {2016}, author = {Buffington, SA and Di Prisco, GV and Auchtung, TA and Ajami, NJ and Petrosino, JF and Costa-Mattioli, M}, title = {Microbial Reconstitution Reverses Maternal Diet-Induced Social and Synaptic Deficits in Offspring.}, journal = {Cell}, volume = {165}, number = {7}, pages = {1762-1775}, pmid = {27315483}, issn = {1097-4172}, support = {R01 MH096816/MH/NIMH NIH HHS/United States ; R01 MH112356/MH/NIMH NIH HHS/United States ; R01 NS076708/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Autism Spectrum Disorder/*microbiology ; *Diet, High-Fat ; Dysbiosis/physiopathology ; Female ; *Gastrointestinal Microbiome ; Germ-Free Life ; Housing, Animal ; Limosilactobacillus reuteri ; Male ; Mice ; Mice, Inbred C57BL ; Obesity/*complications ; Oxytocin/analysis/metabolism ; Pregnancy ; *Social Behavior ; Ventral Tegmental Area ; }, abstract = {Maternal obesity during pregnancy has been associated with increased risk of neurodevelopmental disorders, including autism spectrum disorder (ASD), in offspring. Here, we report that maternal high-fat diet (MHFD) induces a shift in microbial ecology that negatively impacts offspring social behavior. Social deficits and gut microbiota dysbiosis in MHFD offspring are prevented by co-housing with offspring of mothers on a regular diet (MRD) and transferable to germ-free mice. In addition, social interaction induces synaptic potentiation (LTP) in the ventral tegmental area (VTA) of MRD, but not MHFD offspring. Moreover, MHFD offspring had fewer oxytocin immunoreactive neurons in the hypothalamus. Using metagenomics and precision microbiota reconstitution, we identified a single commensal strain that corrects oxytocin levels, LTP, and social deficits in MHFD offspring. Our findings causally link maternal diet, gut microbial imbalance, VTA plasticity, and behavior and suggest that probiotic treatment may relieve specific behavioral abnormalities associated with neurodevelopmental disorders. VIDEO ABSTRACT.}, }
@article {pmid27314330, year = {2016}, author = {Azarbad, H and van Gestel, CA and Niklińska, M and Laskowski, R and Röling, WF and van Straalen, NM}, title = {Resilience of Soil Microbial Communities to Metals and Additional Stressors: DNA-Based Approaches for Assessing "Stress-on-Stress" Responses.}, journal = {International journal of molecular sciences}, volume = {17}, number = {6}, pages = {}, pmid = {27314330}, issn = {1422-0067}, mesh = {*Adaptation, Physiological ; Metals/*toxicity ; Microbiota/drug effects/*genetics/physiology ; Mutagens/toxicity ; *Soil Microbiology ; Soil Pollutants/toxicity ; *Stress, Physiological ; }, abstract = {Many microbial ecology studies have demonstrated profound changes in community composition caused by environmental pollution, as well as adaptation processes allowing survival of microbes in polluted ecosystems. Soil microbial communities in polluted areas with a long-term history of contamination have been shown to maintain their function by developing metal-tolerance mechanisms. In the present work, we review recent experiments, with specific emphasis on studies that have been conducted in polluted areas with a long-term history of contamination that also applied DNA-based approaches. We evaluate how the "costs" of adaptation to metals affect the responses of metal-tolerant communities to other stress factors ("stress-on-stress"). We discuss recent studies on the stability of microbial communities, in terms of resistance and resilience to additional stressors, focusing on metal pollution as the initial stress, and discuss possible factors influencing the functional and structural stability of microbial communities towards secondary stressors. There is increasing evidence that the history of environmental conditions and disturbance regimes play central roles in responses of microbial communities towards secondary stressors.}, }
@article {pmid27313569, year = {2016}, author = {Penton, CR and Gupta, VV and Yu, J and Tiedje, JM}, title = {Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {824}, pmid = {27313569}, issn = {1664-302X}, abstract = {We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5, and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs) retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.}, }
@article {pmid27312892, year = {2016}, author = {Miller, AW and Oakeson, KF and Dale, C and Dearing, MD}, title = {Microbial Community Transplant Results in Increased and Long-Term Oxalate Degradation.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {470-478}, pmid = {27312892}, issn = {1432-184X}, support = {F32 DK102277/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria, Anaerobic/isolation &amp; purification/*metabolism ; Biomass ; Feces/chemistry/microbiology ; Female ; *Gastrointestinal Microbiome ; Male ; Oxalates/*metabolism ; Oxalobacter formigenes/isolation &amp; purification/*metabolism ; Probiotics ; Rats ; Rats, Sprague-Dawley ; Sigmodontinae/*microbiology ; }, abstract = {Gut microbes are essential for the degradation of dietary oxalate, and this function may play a role in decreasing the incidence of kidney stones. However, many oxalate-degrading bacteria are susceptible to antibiotics and the use of oxalate-degrading probiotics has only led to an ephemeral reduction in urinary oxalate. The objective of the current study was to determine the efficacy of using whole-community microbial transplants from a wild mammalian herbivore, Neotoma albigula, to increase oxalate degradation over the long term in the laboratory rat, Rattus norvegicus. We quantified the change in total oxalate degradation in lab rats immediately after microbial transplants and at 2- and 9-month intervals following microbial transplants. Additionally, we tracked the fecal microbiota of the lab rats, with and without microbial transplants, using high-throughput Illumina sequencing of a hyper-variable region of the 16S rRNA gene. Microbial transplants resulted in a significant increase in oxalate degradation, an effect that persisted 9 months after the initial transplants. Functional persistence was corroborated by the transfer, and persistence of a group of bacteria previously correlated with oxalate consumption in N. albigula, including an anaerobic bacterium from the genus Oxalobacter known for its ability to use oxalate as a sole carbon source. The results of this study indicate that whole-community microbial transplants are an effective means for the persistent colonization of oxalate-degrading bacteria in the mammalian gut.}, }
@article {pmid27312355, year = {2016}, author = {Subirats, J and Sànchez-Melsió, A and Borrego, CM and Balcázar, JL and Simonet, P}, title = {Metagenomic analysis reveals that bacteriophages are reservoirs of antibiotic resistance genes.}, journal = {International journal of antimicrobial agents}, volume = {48}, number = {2}, pages = {163-167}, doi = {10.1016/j.ijantimicag.2016.04.028}, pmid = {27312355}, issn = {1872-7913}, mesh = {Bacteria/drug effects/*virology ; Bacteriophages/classification/*genetics/isolation &amp; purification ; Caudovirales/classification/genetics/isolation &amp; purification ; *Drug Resistance, Bacterial ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; *Genes, Viral ; Hospitals ; Metagenomics ; Wastewater/*virology ; }, abstract = {A metagenomics approach was applied to explore the presence of antibiotic resistance genes (ARGs) in bacteriophages from hospital wastewater. Metagenomic analysis showed that most phage sequences affiliated to the order Caudovirales, comprising the tailed phage families Podoviridae, Siphoviridae and Myoviridae. Moreover, the relative abundance of ARGs in the phage DNA fraction (0.26%) was higher than in the bacterial DNA fraction (0.18%). These differences were particularly evident for genes encoding ATP-binding cassette (ABC) and resistance-nodulation-cell division (RND) proteins, phosphotransferases, β-lactamases and plasmid-mediated quinolone resistance. Analysis of assembled contigs also revealed that blaOXA-10, blaOXA-58 and blaOXA-24 genes belonging to class D β-lactamases as well as a novel blaTEM (98.9% sequence similarity to the blaTEM-1 gene) belonging to class A β-lactamases were detected in a higher proportion in phage DNA. Although preliminary, these findings corroborate the role of bacteriophages as reservoirs of resistance genes and thus highlight the necessity to include them in future studies on the emergence and spread of antibiotic resistance in the environment.}, }
@article {pmid27310530, year = {2016}, author = {Tikhonov, M}, title = {Community-level cohesion without cooperation.}, journal = {eLife}, volume = {5}, number = {}, pages = {}, pmid = {27310530}, issn = {2050-084X}, mesh = {*Ecosystem ; *Models, Biological ; }, abstract = {Recent work draws attention to community-community encounters ('coalescence') as likely an important factor shaping natural ecosystems. This work builds on MacArthur's classic model of competitive coexistence to investigate such community-level competition in a minimal theoretical setting. It is shown that the ability of a species to survive a coalescence event is best predicted by a community-level 'fitness' of its native community rather than the intrinsic performance of the species itself. The model presented here allows formalizing a macroscopic perspective whereby a community harboring organisms at varying abundances becomes equivalent to a single organism expressing genes at different levels. While most natural communities do not satisfy the strict criteria of multicellularity developed by multi-level selection theory, the effective cohesion described here is a generic consequence of resource partitioning, requires no cooperative interactions, and can be expected to be widespread in microbial ecosystems.}, }
@article {pmid27309848, year = {2016}, author = {Ballhausen, MB and Vandamme, P and de Boer, W}, title = {Trait Differentiation within the Fungus-Feeding (Mycophagous) Bacterial Genus Collimonas.}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0157552}, pmid = {27309848}, issn = {1932-6203}, mesh = {Antibiosis/*physiology ; Antifungal Agents/metabolism ; Bacterial Proteins/*genetics/metabolism ; Chitinases/genetics/metabolism ; DNA Gyrase/genetics/metabolism ; DNA-Directed RNA Polymerases/genetics/metabolism ; Food Chain ; Fungi/*chemistry/growth &amp; development ; Gene Expression ; Herbaspirillum/genetics/metabolism ; Multilocus Sequence Typing ; Oxalobacteraceae/classification/*genetics/metabolism ; Oxidoreductases/genetics/metabolism ; *Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; *Soil Microbiology ; }, abstract = {The genus Collimonas consists of facultative, fungus-feeding (mycophagous) bacteria. To date, 3 species (C. fungivorans, C. pratensis and C. arenae) have been described and over 100 strains have been isolated from different habitats. Functional traits of Collimonas bacteria that are potentially involved in interactions with soil fungi mostly negatively (fungal inhibition e.g.), but also positively (mineral weathering e.g.), affect fungal fitness. We hypothesized that variation in such traits between Collimonas strains leads to different mycophagous bacterial feeding patterns. We investigated a) whether phylogenetically closely related Collimonas strains possess similar traits, b) how far phylogenetic resolution influences the detection of phylogenetic signal (possession of similar traits by related strains) and c) if there is a pattern of co-occurrence among the studied traits. We measured genetically encoded (nifH genes, antifungal collimomycin gene cluster e.g.) as well as phenotypically expressed traits (chitinase- and siderophore production, fungal inhibition and others) and related those to a high-resolution phylogeny (MLSA), constructed by sequencing the housekeeping genes gyrB and rpoB and concatenating those with partial 16S rDNA sequences. Additionally, high-resolution and 16S rDNA derived phylogenies were compared. We show that MLSA is superior to 16SrDNA phylogeny when analyzing trait distribution and relating it to phylogeny at fine taxonomic resolution (a single bacterial genus). We observe that several traits involved in the interaction of collimonads and their host fungus (fungal inhibition e.g.) carry phylogenetic signal. Furthermore, we compare Collimonas trait possession with sister genera like Herbaspirillum and Janthinobacterium.}, }
@article {pmid27309357, year = {2016}, author = {Chai, B and Tsoi, TV and Iwai, S and Liu, C and Fish, JA and Gu, C and Johnson, TA and Zylstra, G and Teppen, BJ and Li, H and Hashsham, SA and Boyd, SA and Cole, JR and Tiedje, JM}, title = {Sphingomonas wittichii Strain RW1 Genome-Wide Gene Expression Shifts in Response to Dioxins and Clay.}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0157008}, pmid = {27309357}, issn = {1932-6203}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, mesh = {Aluminum Silicates/chemistry/metabolism ; *Biodegradation, Environmental ; Cell Movement/drug effects ; Chemotaxis/drug effects ; Clay ; Dioxins/*chemistry/metabolism ; Gene Expression Regulation, Bacterial/drug effects ; Oxygenases/genetics ; Soil Microbiology ; Sphingomonas/*genetics/growth &amp; development/metabolism ; Transcriptome/*genetics ; }, abstract = {Sphingomonas wittichii strain RW1 (RW1) is one of the few strains that can grow on dibenzo-p-dioxin (DD). We conducted a transcriptomic study of RW1 using RNA-Seq to outline transcriptional responses to DD, dibenzofuran (DF), and the smectite clay mineral saponite with succinate as carbon source. The ability to grow on DD is rare compared to growth on the chemically similar DF even though the same initial dioxygenase may be involved in oxidation of both substrates. Therefore, we hypothesized the reason for this lies beyond catabolic pathways and may concern genes involved in processes for cell-substrate interactions such as substrate recognition, transport, and detoxification. Compared to succinate (SUC) as control carbon source, DF caused over 240 protein-coding genes to be differentially expressed, whereas more than 300 were differentially expressed with DD. Stress response genes were up-regulated in response to both DD and DF. This effect was stronger with DD than DF, suggesting a higher toxicity of DD compared to DF. Both DD and DF caused changes in expression of genes involved in active cross-membrane transport such as TonB-dependent receptor proteins, but the patterns of change differed between the two substrates. Multiple transcription factor genes also displayed expression patterns distinct to DD and DF growth. DD and DF induced the catechol ortho- and the salicylate/gentisate pathways, respectively. Both DD and DF induced the shared down-stream aliphatic intermediate compound pathway. Clay caused category-wide down-regulation of genes for cell motility and chemotaxis, particularly those involved in the synthesis, assembly and functioning of flagella. This is an environmentally important finding because clay is a major component of soil microbes' microenvironment influencing local chemistry and may serve as a geosorbent for toxic pollutants. Similar to clay, DD and DF also affected expression of genes involved in motility and chemotaxis.}, }
@article {pmid27306690, year = {2016}, author = {Thomas, T and Moitinho-Silva, L and Lurgi, M and Björk, JR and Easson, C and Astudillo-García, C and Olson, JB and Erwin, PM and López-Legentil, S and Luter, H and Chaves-Fonnegra, A and Costa, R and Schupp, PJ and Steindler, L and Erpenbeck, D and Gilbert, J and Knight, R and Ackermann, G and Victor Lopez, J and Taylor, MW and Thacker, RW and Montoya, JM and Hentschel, U and Webster, NS}, title = {Diversity, structure and convergent evolution of the global sponge microbiome.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {11870}, pmid = {27306690}, issn = {2041-1723}, mesh = {Animals ; Bayes Theorem ; Biodiversity ; *Biological Coevolution ; Ecosystem ; Microbial Consortia/*genetics ; Microbiota/*genetics ; *Phylogeny ; Porifera/classification/genetics/*microbiology ; RNA, Ribosomal, 16S/*genetics ; Symbiosis/physiology ; }, abstract = {Sponges (phylum Porifera) are early-diverging metazoa renowned for establishing complex microbial symbioses. Here we present a global Porifera microbiome survey, set out to establish the ecological and evolutionary drivers of these host-microbe interactions. We show that sponges are a reservoir of exceptional microbial diversity and major contributors to the total microbial diversity of the world's oceans. Little commonality in species composition or structure is evident across the phylum, although symbiont communities are characterized by specialists and generalists rather than opportunists. Core sponge microbiomes are stable and characterized by generalist symbionts exhibiting amensal and/or commensal interactions. Symbionts that are phylogenetically unique to sponges do not disproportionally contribute to the core microbiome, and host phylogeny impacts complexity rather than composition of the symbiont community. Our findings support a model of independent assembly and evolution in symbiont communities across the entire host phylum, with convergent forces resulting in analogous community organization and interactions.}, }
@article {pmid27306031, year = {2016}, author = {Xu, J and Verbrugghe, A and Lourenço, M and Janssens, GP and Liu, DJ and Van de Wiele, T and Eeckhaut, V and Van Immerseel, F and Van de Maele, I and Niu, Y and Bosch, G and Junius, G and Wuyts, B and Hesta, M}, title = {Does canine inflammatory bowel disease influence gut microbial profile and host metabolism?.}, journal = {BMC veterinary research}, volume = {12}, number = {1}, pages = {114}, pmid = {27306031}, issn = {1746-6148}, mesh = {Amino Acids/blood ; Animals ; Dog Diseases/blood/*microbiology ; Dogs ; Feces/microbiology ; Female ; Folic Acid/blood ; *Gastrointestinal Microbiome ; Indican/blood ; Inflammatory Bowel Diseases/blood/microbiology/*veterinary ; Male ; Vitamin B 12/blood ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) refers to a diverse group of chronic gastrointestinal diseases, and gut microbial dysbiosis has been proposed as a modulating factor in its pathogenesis. Several studies have investigated the gut microbial ecology of dogs with IBD but it is yet unclear if this microbial profile can alter the nutrient metabolism of the host. The aim of the present study was to characterize the faecal bacterial profile and functionality as well as to determine host metabolic changes in IBD dogs. Twenty-three dogs diagnosed with IBD and ten healthy control dogs were included. Dogs with IBD were given a clinical score using the canine chronic enteropathy clinical activity index (CCECAI). Faecal short-chain fatty acids (SCFA) and ammonia concentrations were measured and quantitative PCR was performed. The concentration of plasma amino acids, acylcarnitines, serum folate, cobalamin, and indoxyl sulfate was determined.<br><br>RESULTS: No significant differences in the abundance of a selection of bacterial groups and fermentation metabolites were observed between the IBD and control groups. However, significant negative correlations were found between CCECAI and the faecal proportion of Lactobacillus as well as between CCECAI and total SCFA concentration. Serum folate and plasma citrulline were decreased and plasma valine was increased in IBD compared to control dogs. Increased plasma free carnitine and total acylcarnitines were observed in IBD compared with control dogs, whereas short-chain acylcarnitines (butyrylcarnitine&#x2009;+&#x2009;isobutyrylcarnitine and, methylmalonylcarnitine) to free carnitine ratios decreased. Dogs with IBD had a higher 3-hydroxyisovalerylcarnitine&#x2009;+&#x2009;isovalerylcarnitine to leucine ratio compared to control dogs.<br><br>CONCLUSIONS: Canine IBD induced a wide range of changes in metabolic profile, especially for the plasma concentrations of short-chain acylcarnitines and amino acids, which could have evolved from tissue damage and alteration in host metabolism. In addition, dogs with more severe IBD were characterised by a decrease in faecal proportion of Lactobacillus.}, }
@article {pmid27305853, year = {2016}, author = {Van de Wiele, T and Van Praet, JT and Marzorati, M and Drennan, MB and Elewaut, D}, title = {How the microbiota shapes rheumatic diseases.}, journal = {Nature reviews. Rheumatology}, volume = {12}, number = {7}, pages = {398-411}, pmid = {27305853}, issn = {1759-4804}, mesh = {Animals ; Arthritis, Rheumatoid/immunology ; Dysbiosis/immunology ; Evidence-Based Medicine ; Gastrointestinal Microbiome/*immunology ; Homeostasis/*immunology ; Humans ; Lupus Erythematosus, Systemic/immunology ; Microbiota/immunology ; Probiotics/*therapeutic use ; Rheumatic Diseases/*drug therapy/*immunology/microbiology/pathology ; Spondylarthritis/immunology ; Treatment Outcome ; }, abstract = {The human gut harbours a tremendously diverse and abundant microbial community that correlates with, and even modulates, many health-related processes. The mucosal interfaces are particularly active sites of microorganism-host interplay. Growing insight into the characteristic composition and functionality of the mucosal microbiota has revealed that the microbiota is involved in mucosal barrier integrity and immune function. This involvement affects proinflammatory and anti-inflammatory processes not only at the epithelial level, but also at remote sites such as the joints. Here, we review the role of the gut microbiota in shaping local and systemic immune responses and how disturbances in the host-microorganism interplay can potentially affect the development and progression of rheumatic diseases. Increasing our understanding of how to promote host-microorganism homeostasis could therefore reveal novel strategies for the prevention or alleviation of rheumatic disease.}, }
@article {pmid27304953, year = {2016}, author = {Sáez-Lara, MJ and Robles-Sanchez, C and Ruiz-Ojeda, FJ and Plaza-Diaz, J and Gil, A}, title = {Effects of Probiotics and Synbiotics on Obesity, Insulin Resistance Syndrome, Type 2 Diabetes and Non-Alcoholic Fatty Liver Disease: A Review of Human Clinical Trials.}, journal = {International journal of molecular sciences}, volume = {17}, number = {6}, pages = {}, pmid = {27304953}, issn = {1422-0067}, mesh = {Clinical Trials as Topic ; Diabetes Mellitus, Type 2/metabolism/*therapy ; Humans ; *Insulin Resistance ; Metabolic Syndrome/metabolism/therapy ; Non-alcoholic Fatty Liver Disease/metabolism/*therapy ; Obesity/metabolism/*therapy ; Probiotics/*administration &amp; dosage ; Synbiotics/*administration &amp; dosage ; Treatment Outcome ; }, abstract = {The use of probiotics and synbiotics in the prevention and treatment of different disorders has dramatically increased over the last decade. Both probiotics and synbiotics are well known ingredients of functional foods and nutraceuticals and may provide beneficial health effects because they can influence the intestinal microbial ecology and immunity. The present study reviews the effects of probiotics and synbiotics on obesity, insulin resistance syndrome (IRS), type 2 diabetes (T2D) and non-alcoholic fatty liver disease (NAFLD) in human randomized clinical trials. Select probiotics and synbiotics provided beneficial effects in patients with obesity, mainly affecting the body mass index and fat mass. Some probiotics had beneficial effects on IRS, decreasing the cell adhesion molecule-1 levels, and the synbiotics decreased the insulin resistance and plasma lipid levels. Moreover, select probiotics improved the carbohydrate metabolism, fasting blood glucose, insulin sensitivity and antioxidant status and also reduced metabolic stress in subjects with T2D. Some probiotics and synbiotics improved the liver and metabolic parameters in patients with NAFLD. The oral intake of probiotics and synbiotics as co-adjuvants for the prevention and treatment of obesity, IRS, T2D and NAFLD is partially supported by the data shown in the present review. However, further studies are required to understand the precise mechanism of how probiotics and synbiotics affect these metabolic disorders.}, }
@article {pmid27304924, year = {2016}, author = {Dangles, O and Loirat, J and Freour, C and Serre, S and Vacher, J and Le Roux, X}, title = {Research on Biodiversity and Climate Change at a Distance: Collaboration Networks between Europe and Latin America and the Caribbean.}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0157441}, pmid = {27304924}, issn = {1932-6203}, mesh = {*Biodiversity ; Caribbean Region ; *Climate Change ; Conservation of Natural Resources/*methods/statistics &amp; numerical data/trends ; *Cooperative Behavior ; European Union ; Humans ; *International Cooperation ; Latin America ; Research/statistics &amp; numerical data/trends ; Research Personnel/statistics &amp; numerical data ; }, abstract = {Biodiversity loss and climate change are both globally significant issues that must be addressed through collaboration across countries and disciplines. With the December 2015 COP21 climate conference in Paris and the recent creation of the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES), it has become critical to evaluate the capacity for global research networks to develop at the interface between biodiversity and climate change. In the context of the European Union (EU) strategy to stand as a world leader in tackling global challenges, the European Commission has promoted ties between the EU and Latin America and the Caribbean (LAC) in science, technology and innovation. However, it is not clear how these significant interactions impact scientific cooperation at the interface of biodiversity and climate change. We looked at research collaborations between two major regions-the European Research Area (ERA) and LAC-that addressed both biodiversity and climate change. We analysed the temporal evolution of these collaborations, whether they were led by ERA or LAC teams, and which research domains they covered. We surveyed publications listed on the Web of Science that were authored by researchers from both the ERA and LAC and that were published between 2003 and 2013. We also run similar analyses on other topics and other continents to provide baseline comparisons. Our results revealed a steady increase in scientific co-authorships between ERA and LAC countries as a result of the increasingly complex web of relationships that has been weaved among scientists from the two regions. The ERA-LAC co-authorship increase for biodiversity and climate change was higher than those reported for other topics and for collaboration with other continents. We also found strong differences in international collaboration patterns within the LAC: co-publications were fewest from researchers in low- and lower-middle-income countries and most prevalent from researchers in emerging countries like Mexico and Brazil. Overall, interdisciplinary publications represented 25.8% of all publications at the interface of biodiversity and climate change in the ERA-LAC network. Further scientific collaborations should be promoted 1) to prevent less developed countries from being isolated from the global cooperation network, 2) to ensure that scientists from these countries are trained to lead visible and recognized biodiversity and climate change research, and 3) to develop common study models that better integrate multiple scientific disciplines and better support decision-making.}, }
@article {pmid27303740, year = {2016}, author = {Flynn, KJ and Baxter, NT and Schloss, PD}, title = {Metabolic and Community Synergy of Oral Bacteria in Colorectal Cancer.}, journal = {mSphere}, volume = {1}, number = {3}, pages = {}, pmid = {27303740}, issn = {2379-5042}, abstract = {The oral periodontopathic bacterium Fusobacterium nucleatum has been repeatedly associated with colorectal tumors. Molecular analysis has identified specific virulence factors that promote tumorigenesis in the colon. However, other oral community members, such as members of the Porphyromonas spp., are also found with F. nucleatum on colonic tumors, and thus, narrow studies of individual pathogens do not take community-wide virulence properties into account. A broader view of oral bacterial physiology and pathogenesis identifies two factors that could promote colonization and persistence of oral bacterial communities in the colon. The polymicrobial nature of oral biofilms and the asaccharolytic metabolism of many of these species make them well suited to life in the microenvironment of colonic lesions. Consideration of these two factors offers a novel perspective on the role of oral microbiota in the initiation, development, and treatment of colorectal cancer.}, }
@article {pmid27303705, year = {2016}, author = {Braykov, NP and Eisenberg, JN and Grossman, M and Zhang, L and Vasco, K and Cevallos, W and Muñoz, D and Acevedo, A and Moser, KA and Marrs, CF and Foxman, B and Trostle, J and Trueba, G and Levy, K}, title = {Antibiotic Resistance in Animal and Environmental Samples Associated with Small-Scale Poultry Farming in Northwestern Ecuador.}, journal = {mSphere}, volume = {1}, number = {1}, pages = {}, pmid = {27303705}, issn = {2379-5042}, support = {K01 AI103544/AI/NIAID NIH HHS/United States ; R01 AI050038/AI/NIAID NIH HHS/United States ; }, abstract = {The effects of animal agriculture on the spread of antibiotic resistance (AR) are cross-cutting and thus require a multidisciplinary perspective. Here we use ecological, epidemiological, and ethnographic methods to examine populations of Escherichia coli circulating in the production poultry farming environment versus the domestic environment in rural Ecuador, where small-scale poultry production employing nontherapeutic antibiotics is increasingly common. We sampled 262 "production birds" (commercially raised broiler chickens and laying hens) and 455 "household birds" (raised for domestic use) and household and coop environmental samples from 17 villages between 2010 and 2013. We analyzed data on zones of inhibition from Kirby-Bauer tests, rather than established clinical breakpoints for AR, to distinguish between populations of organisms. We saw significantly higher levels of AR in bacteria from production versus household birds; resistance to either amoxicillin-clavulanate, cephalothin, cefotaxime, and gentamicin was found in 52.8% of production bird isolates and 16% of household ones. A strain jointly resistant to the 4 drugs was exclusive to a subset of isolates from production birds (7.6%) and coop surfaces (6.5%) and was associated with a particular purchase site. The prevalence of AR in production birds declined with bird age (P < 0.01 for all antibiotics tested except tetracycline, sulfisoxazole, and trimethoprim-sulfamethoxazole). Farming status did not impact AR in domestic environments at the household or village level. Our results suggest that AR associated with small-scale poultry farming is present in the immediate production environment and likely originates from sources outside the study area. These outside sources might be a better place to target control efforts than local management practices. IMPORTANCE In developing countries, small-scale poultry farming employing antibiotics as growth promoters is being advanced as an inexpensive source of protein and income. Here, we present the results of a large ecoepidemiological study examining patterns of antibiotic resistance (AR) in E. coli isolates from small-scale poultry production environments versus domestic environments in rural Ecuador, where such backyard poultry operations have become established over the past decade. Our previous research in the region suggests that introduction of AR bacteria through travel and commerce may be an important source of AR in villages of this region. This report extends the prior analysis by examining small-scale production chicken farming as a potential source of resistant strains. Our results suggest that AR strains associated with poultry production likely originate from sources outside the study area and that these outside sources might be a better place to target control efforts than local management practices.}, }
@article {pmid27303681, year = {2016}, author = {Zackular, JP and Baxter, NT and Chen, GY and Schloss, PD}, title = {Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis.}, journal = {mSphere}, volume = {1}, number = {1}, pages = {}, pmid = {27303681}, issn = {2379-5042}, support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; R01 CA166879/CA/NCI NIH HHS/United States ; R01 GM099514/GM/NIGMS NIH HHS/United States ; R01 HG005975/HG/NHGRI NIH HHS/United States ; }, abstract = {There is growing evidence that individuals with colonic adenomas and carcinomas harbor a distinct microbiota. Alterations to the gut microbiota may allow the outgrowth of bacterial populations that induce genomic mutations or exacerbate tumor-promoting inflammation. In addition, it is likely that the loss of key bacterial populations may result in the loss of protective functions that are normally provided by the microbiota. We explored the role of the gut microbiota in colon tumorigenesis by using an inflammation-based murine model. We observed that perturbing the microbiota with different combinations of antibiotics reduced the number of tumors at the end of the model. Using the random forest machine learning algorithm, we successfully modeled the number of tumors that developed over the course of the model on the basis of the initial composition of the microbiota. The timing of antibiotic treatment was an important determinant of tumor outcome, as colon tumorigenesis was arrested by the use of antibiotics during the early inflammation period of the murine model. Together, these results indicate that it is possible to predict colon tumorigenesis on the basis of the composition of the microbiota and that altering the gut microbiota can alter the course of tumorigenesis. IMPORTANCE Mounting evidence indicates that alterations to the gut microbiota, the complex community of bacteria that inhabits the gastrointestinal tract, are strongly associated with the development of colorectal cancer. We used antibiotic perturbations to a murine model of inflammation-driven colon cancer to generate eight starting communities that resulted in various severities of tumorigenesis. Furthermore, we were able to quantitatively predict the final number of tumors on the basis of the initial composition of the gut microbiota. These results further bolster the evidence that the gut microbiota is involved in mediating the development of colorectal cancer. As a final proof of principle, we showed that perturbing the gut microbiota in the midst of tumorigenesis could halt the formation of additional tumors. Together, alteration of the gut microbiota may be a useful therapeutic approach to preventing and altering the trajectory of colorectal cancer.}, }
@article {pmid27303369, year = {2016}, author = {Kielak, AM and Barreto, CC and Kowalchuk, GA and van Veen, JA and Kuramae, EE}, title = {The Ecology of Acidobacteria: Moving beyond Genes and Genomes.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {744}, pmid = {27303369}, issn = {1664-302X}, abstract = {The phylum Acidobacteria is one of the most widespread and abundant on the planet, yet remarkably our knowledge of the role of these diverse organisms in the functioning of terrestrial ecosystems remains surprisingly rudimentary. This blatant knowledge gap stems to a large degree from the difficulties associated with the cultivation of these bacteria by classical means. Given the phylogenetic breadth of the Acidobacteria, which is similar to the metabolically diverse Proteobacteria, it is clear that detailed and functional descriptions of acidobacterial assemblages are necessary. Fortunately, recent advances are providing a glimpse into the ecology of members of the phylum Acidobacteria. These include novel cultivation and enrichment strategies, genomic characterization and analyses of metagenomic DNA from environmental samples. Here, we couple the data from these complementary approaches for a better understanding of their role in the environment, thereby providing some initial insights into the ecology of this important phylum. All cultured acidobacterial type species are heterotrophic, and members of subdivisions 1, 3, and 4 appear to be more versatile in carbohydrate utilization. Genomic and metagenomic data predict a number of ecologically relevant capabilities for some acidobacteria, including the ability to: use of nitrite as N source, respond to soil macro-, micro nutrients and soil acidity, express multiple active transporters, degrade gellan gum and produce exopolysaccharide (EPS). Although these predicted properties allude to a competitive life style in soil, only very few of these prediction shave been confirmed via physiological studies. The increased availability of genomic and physiological information, coupled to distribution data in field surveys and experiments, should direct future progress in unraveling the ecology of this important but still enigmatic phylum.}, }
@article {pmid27302652, year = {2016}, author = {Uroz, S and Oger, P and Tisserand, E and Cébron, A and Turpault, MP and Buée, M and De Boer, W and Leveau, JH and Frey-Klett, P}, title = {Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {27756}, pmid = {27302652}, issn = {2045-2322}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biodiversity ; Fagus/*physiology ; Fungi/classification/genetics ; Phylogeny ; Picea/*physiology ; Real-Time Polymerase Chain Reaction ; *Rhizosphere ; Sequence Analysis, DNA ; Soil ; *Soil Microbiology ; Temperature ; }, abstract = {The impacts of plant species on the microbial communities and physico-chemical characteristics of soil are well documented for many herbs, grasses and legumes but much less so for tree species. Here, we investigate by rRNA and ITS amplicon sequencing the diversity of microorganisms from the three domains of life (Archaea, Bacteria and Eukaryota:Fungi) in soil samples taken from the forest experimental site of Breuil-Chenue (France). We discovered significant differences in the abundance, composition and structure of the microbial communities associated with two phylogenetically distant tree species of the same age, deciduous European beech (Fagus sylvatica) and coniferous Norway spruce (Picea abies Karst), planted in the same soil. Our results suggest a significant effect of tree species on soil microbiota though in different ways for each of the three microbial groups. Fungal and archaeal community structures and compositions are mainly determined according to tree species, whereas bacterial communities differ to a great degree between rhizosphere and bulk soils, regardless of the tree species. These results were confirmed by quantitative PCR, which revealed significant enrichment of specific bacterial genera, such as Burkholderia and Collimonas, known for their ability to weather minerals within the tree root vicinity.}, }
@article {pmid27302469, year = {2016}, author = {Harbison, AB and Carson, MA and Lamit, LJ and Basiliko, N and Bräuer, SL}, title = {A novel isolate and widespread abundance of the candidate alphaproteobacterial order (Ellin 329), in southern Appalachian peatlands.}, journal = {FEMS microbiology letters}, volume = {363}, number = {15}, pages = {}, doi = {10.1093/femsle/fnw151}, pmid = {27302469}, issn = {1574-6968}, mesh = {Alphaproteobacteria/*classification/genetics/*isolation &amp; purification/metabolism ; Ecosystem ; Genes, rRNA ; Methane/metabolism ; Microbial Consortia ; Phylogeny ; *Soil Microbiology ; }, abstract = {Peatlands of all latitudes play an integral role in global climate change by serving as a carbon sink and a primary source of atmospheric methane; however, the microbial ecology of mid-latitude peatlands is vastly understudied. Herein, next generation Illumina amplicon sequencing of small subunit rRNA genes was utilized to elucidate the microbial communities in three southern Appalachian peatlands. In contrast to northern peatlands, Proteobacteria dominated over Acidobacteria in all three sites. An average of 11 bacterial phyla was detected at relative abundance values >1%, with three candidate divisions (OP3, WS3 and NC10) represented, indicating high phylogenetic diversity. Physiological traits of isolates within the candidate alphaproteobacterial order, Ellin 329, obtained here and in previous studies indicate that bacteria of this order may be involved in hydrolysis of poly-, di- and monosaccharides. Community analyses indicate that Ellin 329 is the third most abundant order and is most abundant near the surface layers where plant litter decomposition should be primarily occurring. In sum, members of Ellin 329 likely play important roles in organic matter decomposition, in southern Appalachian peatlands and should be investigated further in other peatlands and ecosystem types.}, }
@article {pmid27301322, year = {2016}, author = {Ren, Y and Niu, J and Huang, W and Peng, D and Xiao, Y and Zhang, X and Liang, Y and Liu, X and Yin, H}, title = {Comparison of microbial taxonomic and functional shift pattern along contamination gradient.}, journal = {BMC microbiology}, volume = {16}, number = {1}, pages = {110}, pmid = {27301322}, issn = {1471-2180}, mesh = {Bacteria/*classification/drug effects/genetics/isolation &amp; purification ; Biodiversity ; China ; Classification/*methods ; DNA, Bacterial/genetics ; Ecology ; Ecosystem ; Environmental Microbiology ; Environmental Pollution ; Environmental Restoration and Remediation ; Geologic Sediments/chemistry/microbiology ; Metals, Heavy/administration &amp; dosage/*chemistry/toxicity ; Microbial Interactions/*physiology ; Microbiota/drug effects/genetics/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Soil Pollutants ; }, abstract = {BACKGROUND: The interaction mechanism between microbial communities and environment is a key issue in microbial ecology. Microbial communities usually change significantly under environmental stress, which has been studied both phylogenetically and functionally, however which method is more effective in assessing the relationship between microbial communities shift and environmental changes still remains controversial.<br><br>RESULTS: By comparing the microbial taxonomic and functional shift pattern along heavy metal contamination gradient, we found that both sedimentary composition and function shifted significantly along contamination gradient. For example, the relative abundance of Geobacter and Fusibacter decreased along contamination gradient (from high to low), while Janthinobacterium and Arthrobacter increased their abundances. Most genes involved in heavy metal resistance (e.g., metc, aoxb and mer) showed higher intensity in sites with higher concentration of heavy metals. Comparing the two shift patterns, there were correlations between them, because functional and phylogenetic &#x3b2;-diversities were significantly correlated, and many heavy metal resistance genes were derived from Geobacter, explaining their high abundance in heavily contaminated sites. However, there was a stronger link between functional composition and environmental drivers, while stochasticity played an important role in formation and succession of phylogenetic composition demonstrated by null model test.<br><br>CONCLUSIONS: Overall our research suggested that the responses of functional traits depended more on environmental changes, while stochasticity played an important role in formation and succession of phylogenetic composition for microbial communities. So profiling microbial functional composition seems more appropriate to study the relationship between microbial communities and environment, as well as explore the adaptation and remediation mechanism of microbial communities to heavy metal contamination.}, }
@article {pmid27300277, year = {2016}, author = {Spring, S and Bunk, B and Spröer, C and Schumann, P and Rohde, M and Tindall, BJ and Klenk, HP}, title = {Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum.}, journal = {The ISME journal}, volume = {10}, number = {12}, pages = {2801-2816}, pmid = {27300277}, issn = {1751-7370}, mesh = {Bacterial Proteins/genetics/metabolism ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Fatty Acids/metabolism ; Lakes/chemistry/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Verrucomicrobia/classification/genetics/*isolation &amp; purification/metabolism ; }, abstract = {The recently isolated strain L21-Fru-AB[T] represents moderately halophilic, obligately anaerobic and saccharolytic bacteria that thrive in the suboxic transition zones of hypersaline microbial mats. Phylogenetic analyses based on 16S rRNA genes, RpoB proteins and gene content indicated that strain L21-Fru-AB[T] represents a novel species and genus affiliated with a distinct phylum-level lineage originally designated Verrucomicrobia subdivision 5. A survey of environmental 16S rRNA gene sequences revealed that members of this newly recognized phylum are wide-spread and ecologically important in various anoxic environments ranging from hypersaline sediments to wastewater and the intestine of animals. Characteristic phenotypic traits of the novel strain included the formation of extracellular polymeric substances, a Gram-negative cell wall containing peptidoglycan and the absence of odd-numbered cellular fatty acids. Unusual metabolic features deduced from analysis of the genome sequence were the production of sucrose as osmoprotectant, an atypical glycolytic pathway lacking pyruvate kinase and the synthesis of isoprenoids via mevalonate. On the basis of the analyses of phenotypic, genomic and environmental data, it is proposed that strain L21-Fru-AB[T] and related bacteria are specifically adapted to the utilization of sulfated glycopolymers produced in microbial mats or biofilms.}, }
@article {pmid27300139, year = {2017}, author = {Duvenage, FJ and Duvenage, S and Du Plessis, EM and Volschenk, Q and Korsten, L}, title = {Viable bacterial population and persistence of foodborne pathogens on the pear carpoplane.}, journal = {Journal of the science of food and agriculture}, volume = {97}, number = {4}, pages = {1185-1192}, doi = {10.1002/jsfa.7847}, pmid = {27300139}, issn = {1097-0010}, mesh = {Agriculture/*methods ; Atmosphere ; Bacillaceae/drug effects/growth &amp; development ; Biodiversity ; Chlorine/pharmacology ; Enterobacteriaceae/drug effects/growth &amp; development ; Escherichia coli O157/drug effects/growth &amp; development ; *Food Microbiology ; *Food Safety ; Foodborne Diseases/microbiology/prevention &amp; control ; Fruit/*microbiology ; Humans ; Listeria monocytogenes/drug effects/*growth &amp; development ; Pseudomonadaceae/drug effects/growth &amp; development ; Pyrus/*microbiology ; Salmonella/drug effects/*growth &amp; development ; Seasons ; }, abstract = {BACKGROUND: Knowledge on the culturable bacteria and foodborne pathogen presence on pears is important for understanding the impact of postharvest practices on food safety assurance. Pear fruit bacteria were investigated from the point of harvest, following chlorine drenching and after controlled atmosphere (CA) storage to assess the impact on natural bacterial populations and potential foodborne pathogens.<br><br>RESULTS: Salmonella spp. and Listeria monocytogenes were detected on freshly harvested fruit in season one. During season one, chemical drenching and CA storage did not have a significant effect on the bacterial load of orchard pears, except for two farms where the populations were lower 'after CA storage'. During season two, bacterial populations of orchard pears from three of the four farms increased significantly following drenching; however, the bacterial load decreased 'after CA storage'. Bacteria isolated following enumeration included Enterobacteriaceae, Microbacteriaceae, Pseudomonadaceae and Bacillaceae, with richness decreasing 'after drench' and 'after CA storage'.<br><br>CONCLUSION: Salmonella spp. and L. monocytogenes were not detected after postharvest practices. Postharvest practices resulted in decreased bacterial species richness. Understanding how postharvest practices have an impact on the viable bacterial populations of pear fruit will contribute to the development of crop-specific management systems for food safety assurance. &#xa9; 2016 Society of Chemical Industry.}, }
@article {pmid27298302, year = {2016}, author = {Lee, HJ and Whang, KS}, title = {Streptomyces rhizosphaerihabitans sp. nov. and Streptomyces adustus sp. nov., isolated from bamboo forest soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {66}, number = {9}, pages = {3573-3578}, doi = {10.1099/ijsem.0.001236}, pmid = {27298302}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; *Forests ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sasa/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; Streptomyces/*classification/genetics/isolation &amp; purification ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {Three novel isolates belonging to the genus Streptomyces, designated JR-35T, JR-46 and WH-9T, were isolated from bamboo forest soil in Damyang, Korea. The 16S rRNA gene sequences of strains JR-35T and JR-46 showed highest similarities with Streptomyces olivochromogenes NBRC 3178T (99.1 %), Streptomyces siamensis KC-038T (98.9 %), Streptomyces chartreusis NBRC 12753T (98.9 %), Streptomyces resistomycificus NRRL ISP-5133T (98.9 %) and Streptomyces bobili JCM 4627T (98.8 %), and strain WH-9Tshowed highest sequence similarities with Streptomyces. bobili JCM 4627T (99.2 %), Streptomyces phaeoluteigriseus NRRL ISP-5182T (99.2 %), Streptomyces alboniger NBRC 12738T (99.2 %), Streptomyces galilaeus JCM 4757T (99.1 %) and Streptomyces pseudovenezuelae NBRC 12904T (99.1 %). The predominant menaquinones were MK-9 (H6) and MK-9 (H8). The major fatty acids were anteiso-C15 : 0, iso-C16 : 0, iso-C14 : 0 and iso-C15 : 0 for strains JR-35T and JR-46 and anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0 for strain WH-9T. The G+C content of the genomic DNA of strains JR-35T, JR-46 and WH-9T were 69.4, 74.4 and 74.1 mol%, respectively. Based on the phenotypic and genotypic data, the three strains are assigned to two novel species of the genus Streptomyces, for which the names Streptomyces rhizosphaerihabitans sp. nov. (type stain JR-35T=KACC 17181T=NBRC 109807T) and Streptomyces adustus sp. nov. (type strain WH-9T=KACC 17197T=NBRC 109810T) are proposed.}, }
@article {pmid27296526, year = {2016}, author = {Rideout, JR and Chase, JH and Bolyen, E and Ackermann, G and González, A and Knight, R and Caporaso, JG}, title = {Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets.}, journal = {GigaScience}, volume = {5}, number = {}, pages = {27}, pmid = {27296526}, issn = {2047-217X}, mesh = {Cloud Computing ; Computational Biology/*methods ; Humans ; Information Storage and Retrieval ; Software ; User-Computer Interface ; }, abstract = {BACKGROUND: Bioinformatics software often requires human-generated tabular text files as input and has specific requirements for how those data are formatted. Users frequently manage these data in spreadsheet programs, which is convenient for researchers who are compiling the requisite information because the spreadsheet programs can easily be used on different platforms including laptops and tablets, and because they provide a familiar interface. It is increasingly common for many different researchers to be involved in compiling these data, including study coordinators, clinicians, lab technicians and bioinformaticians. As a result, many research groups are shifting toward using cloud-based spreadsheet programs, such as Google Sheets, which support the concurrent editing of a single spreadsheet by different users working on different platforms. Most of the researchers who enter data are not familiar with the formatting requirements of the bioinformatics programs that will be used, so validating and correcting file formats is often a bottleneck prior to beginning bioinformatics analysis.<br><br>MAIN TEXT: We present Keemei, a Google Sheets Add-on, for validating tabular files used in bioinformatics analyses. Keemei is available free of charge from Google's Chrome Web Store. Keemei can be installed and run on any web browser supported by Google Sheets. Keemei currently supports the validation of two widely used tabular bioinformatics formats, the Quantitative Insights into Microbial Ecology (QIIME) sample metadata mapping file format and the Spatially Referenced Genetic Data (SRGD) format, but is designed to easily support the addition of others.<br><br>CONCLUSIONS: Keemei will save researchers time and frustration by providing a convenient interface for tabular bioinformatics file format validation. By allowing everyone involved with data entry for a project to easily validate their data, it will reduce the validation and formatting bottlenecks that are commonly encountered when human-generated data files are first used with a bioinformatics system. Simplifying the validation of essential tabular data files, such as sample metadata, will reduce common errors and thereby improve the quality and reliability of research outcomes.}, }
@article {pmid27296270, year = {2016}, author = {Vanlancker, E and Vanhoecke, B and Smet, R and Props, R and Van de Wiele, T}, title = {5-Fluorouracil sensitivity varies among oral micro-organisms.}, journal = {Journal of medical microbiology}, volume = {65}, number = {8}, pages = {775-783}, doi = {10.1099/jmm.0.000292}, pmid = {27296270}, issn = {1473-5644}, mesh = {Anti-Bacterial Agents/*pharmacology ; Antimetabolites, Antineoplastic/*pharmacology ; Bacteria/*drug effects/enzymology/growth &amp; development/isolation &amp; purification ; Dihydrouracil Dehydrogenase (NADP)/metabolism ; Fluorouracil/*pharmacology ; Humans ; Microbial Sensitivity Tests ; Microbial Viability/drug effects ; Mouth/*microbiology ; }, abstract = {5-Fluorouracil (5-FU), a commonly used chemotherapeutic agent, often causes oral mucositis, an inflammation and ulceration of the oral mucosa. Micro-organisms in the oral cavity are thought to play an important role in the aggravation and severity of mucositis, but the mechanisms behind this remain unclear. Although 5-FU has been shown to elicit antibacterial effects at high concentrations (>100 µM), its antibacterial effect at physiologically relevant concentrations in the oral cavity is unknown. This study reports the effect of different concentrations of 5-FU (range 0.1-50 µM) on the growth and viability of bacterial monocultures that are present in the oral cavity and the possible role in the activity of dihydropyrimidine dehydrogenase (DPD), an enzyme involved in 5-FU resistance. Our data showed a differential sensitivity among the tested oral species towards physiological concentrations of 5-FU. Klebsiellaoxytoca, Streptococcus salivarius, Streptococcus mitis, Streptococcus oralis, Pseudomonas aeruginosa and Lactobacillus salivarius appeared to be highly resistant to all tested concentrations. In contrast, Lactobacillusoris, Lactobacillus plantarum, Streptococcus pyogenes, Fusobacterium nucleatum and Neisseria mucosa showed a significant reduction in growth and viability starting from very low concentrations (0.2-3.1 µM). We can also provide evidence that DPD is not involved in the 5-FU resistance of the selected species. The observed variability in response to physiological 5-FU concentrations may explain why certain microbiota lead to a community dysbiosis and/or an overgrowth of certain resistant micro-organisms in the oral cavity following cancer treatment.}, }
@article {pmid27292825, year = {2016}, author = {Bunyavanich, S and Shen, N and Grishin, A and Wood, R and Burks, W and Dawson, P and Jones, SM and Leung, DYM and Sampson, H and Sicherer, S and Clemente, JC}, title = {Early-life gut microbiome composition and milk allergy resolution.}, journal = {The Journal of allergy and clinical immunology}, volume = {138}, number = {4}, pages = {1122-1130}, pmid = {27292825}, issn = {1097-6825}, support = {U01 AI066560/AI/NIAID NIH HHS/United States ; UL1 TR000039/TR/NCATS NIH HHS/United States ; UL1 RR025005/RR/NCRR NIH HHS/United States ; R01 AI118833/AI/NIAID NIH HHS/United States ; UL1 TR000154/TR/NCATS NIH HHS/United States ; K08 AI093538/AI/NIAID NIH HHS/United States ; UL1 TR001433/TR/NCATS NIH HHS/United States ; UL1 RR024128/RR/NCRR NIH HHS/United States ; U19 AI066738/AI/NIAID NIH HHS/United States ; P30 DK020541/DK/NIDDK NIH HHS/United States ; UL1 TR000067/TR/NCATS NIH HHS/United States ; UL1 TR001082/TR/NCATS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics ; Child ; Child, Preschool ; Dermatitis, Atopic/physiopathology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Immunoglobulin E/blood ; Infant ; Male ; Milk Hypersensitivity/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Gut microbiota may play a role in the natural history of cow's milk allergy.<br><br>OBJECTIVE: We sought to examine the association between early-life gut microbiota and the resolution of cow's milk allergy.<br><br>METHODS: We studied 226 children with milk allergy who were enrolled at infancy in the Consortium of Food Allergy observational study of food allergy. Fecal samples were collected at age 3 to 16&#xa0;months, and the children were followed longitudinally with clinical evaluation, milk-specific IgE levels, and milk skin prick test performed at enrollment, 6&#xa0;months, 12&#xa0;months, and yearly thereafter up until age 8&#xa0;years. Gut microbiome was profiled by 16s rRNA sequencing and microbiome analyses performed using Quantitative Insights into Microbial Ecology (QIIME), Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt), and Statistical Analysis of Metagenomic Profiles (STAMP).<br><br>RESULTS: Milk allergy resolved by age 8&#xa0;years in 128 (56.6%) of the 226 children. Gut microbiome composition at age 3 to 6&#xa0;months was associated with milk allergy resolution by age 8&#xa0;years (PERMANOVA P&#xa0;=&#xa0;.047), with enrichment of Clostridia and Firmicutes in the infant gut microbiome of subjects whose milk allergy resolved. Metagenome functional prediction supported decreased fatty acid metabolism in the gut microbiome of subjects whose milk allergy resolved (&#x3b7;[2]&#xa0;= 0.43; ANOVA P&#xa0;=&#xa0;.034).<br><br>CONCLUSIONS: Early infancy is a window during which gut microbiota may shape food allergy outcomes in childhood. Bacterial taxa within Clostridia and Firmicutes could be studied as probiotic candidates for milk allergy therapy.}, }
@article {pmid27288569, year = {2016}, author = {Nuñez, H and Covarrubias, PC and Moya-Beltrán, A and Issotta, F and Atavales, J and Acuña, LG and Johnson, DB and Quatrini, R}, title = {Detection, identification and typing of Acidithiobacillus species and strains: a review.}, journal = {Research in microbiology}, volume = {167}, number = {7}, pages = {555-567}, doi = {10.1016/j.resmic.2016.05.006}, pmid = {27288569}, issn = {1769-7123}, mesh = {Acidithiobacillus/*classification/*isolation &amp; purification/metabolism ; *Environmental Microbiology ; *Genetic Variation ; *Industrial Microbiology ; Minerals/metabolism ; Mining/methods ; *Molecular Typing ; }, abstract = {The genus Acidithiobacillus comprises several species of Gram-negative acidophilic bacteria that thrive in natural and man-made low pH environments in a variety of geo-climatic contexts. Beyond their fundamental interest as model extreme acidophiles, these bacteria are involved in the processing of minerals and the desulfurization of coal and natural gas, and are also sources of environmental pollution due to their generation of acid mine drainage and corrosion of cement and concrete structures. Acidithiobacillus spp. are therefore considered a biotechnologically relevant group of bacteria, and their identification and screening in natural and industrial environments is of great concern. Several molecular typing methodologies have been instrumental in improving knowledge of the inherent diversity of acidithiobacilli by providing information on the genetic subtypes sampled in public and private culture collections; more recently, they have provided specific insight into the diversity of acidithiobacilli present in industrial and natural environments. The aim of this review is to provide an overview of techniques used in molecular detection, identification and typing of Acidithiobacillus spp. These methods will be discussed in the context of their contribution to the general and specific understanding of the role of the acidithiobacilli in microbial ecology and industrial biotechnology. Emerging opportunities for industrial and environmental surveillance of acidithiobacilli using next-generation molecular typing methodologies are also reviewed.}, }
@article {pmid27287778, year = {2017}, author = {Portune, KJ and Benítez-Páez, A and Del Pulgar, EM and Cerrudo, V and Sanz, Y}, title = {Gut microbiota, diet, and obesity-related disorders-The good, the bad, and the future challenges.}, journal = {Molecular nutrition &amp; food research}, volume = {61}, number = {1}, pages = {}, doi = {10.1002/mnfr.201600252}, pmid = {27287778}, issn = {1613-4133}, mesh = {Bacteria/metabolism ; Bile Acids and Salts/metabolism ; *Diet ; Diet, High-Fat/adverse effects ; Dietary Fats/*pharmacology ; Dietary Fiber/*pharmacology ; Dietary Proteins/pharmacology ; Fermentation ; *Gastrointestinal Microbiome ; Humans ; Inflammation/microbiology ; Obesity/diet therapy/metabolism/*microbiology ; Whole Grains ; }, abstract = {Diet has been shown to be a major factor in modulating the structure of the mammalian gut microbiota by providing specific nutrient sources and inducing environmental changes (pH, bile acids) in the gut ecosystem. Long-term dietary patterns and short-term interventions have been shown to induce changes in gut microbiota structure and function, with several studies revealing metabolic changes likely resulting from the host microbiota cross-talk, which ultimately could influence host physiology. However, a more precise identification of the specific dietary patterns and food constituents that effectively modulate the gut microbiota and bring a predictable benefit to the host metabolic phenotype is needed to establish microbiome-based dietary recommendations. Here, we briefly review the existing data regarding gut microbiota changes induced by different macronutrients and the resulting metabolites produced via their respective fermentation, including their potential effects on obesity and associated metabolic disorders. We also discuss major limitations of current dietary intervention studies as well as future needs of applying cutting-edge "omic" techniques and of progressing in functional microbiota gene discovery to establish robust causal relationships between the dietary microbiota induced changes and metabolic health or disease.}, }
@article {pmid27287538, year = {2016}, author = {Kanokratana, P and Mhuanthong, W and Laothanachareon, T and Tangphatsornruang, S and Eurwilaichitr, L and Kruetreepradit, T and Mayes, S and Champreda, V}, title = {Comparative Study of Bacterial Communities in Nepenthes Pitchers and Their Correlation to Species and Fluid Acidity.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {381-393}, pmid = {27287538}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; *Biomass ; DNA, Bacterial/genetics ; Hydrogen-Ion Concentration ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Thailand ; Tracheophyta/chemistry/*microbiology ; }, abstract = {Pitchers are specialized digestive organs of carnivorous plants which evolved for trapping prey and represent a unique environment harboring hidden diversity of unexplored microbes forming transient hydrolytic microcosms. In this study, the diversity of bacterial communities in the pitcher fluids of seven local Nepenthes found in Thailand was assessed by tagged 16S ribosomal RNA (rRNA) gene amplicon sequencing on an Ion PGM™ platform. A total of 1,101,000 filtered sequences were obtained which were taxonomically classified into 20 phyla, 48 classes, 72 orders, 153 families, and 442 genera while the remainder (1.43 %) could not be assigned to any existing taxa. Proteobacteria represented the predominant members in closed pitchers and more diversified bacterial taxa particularly Bacteriodetes and Actinobacteria, showed increasing abundance in open pitchers containing insect bodies. Principal coordinate analysis revealed that distribution of bacterial taxa was not significantly related to the Nepenthes species but strongly correlated to the pH of the pitcher fluids (pH 1.7-6.7). Acidicella was a highly dominant bacterial genus in acidic pitcher fluids while Dyella and Mycobacterium were also common genera in most pitchers. A unique microbial community structure was found in Nepenthes ampullaria which could reflect their adaptation to digest leaf litter, in addition to insect prey. The work revealed the highly unexplored nature of bacterial microcosms in Nepenthes pitcher fluids and provides insights into their community structure in this unique ecological system.}, }
@article {pmid27283264, year = {2016}, author = {Daims, H and Lücker, S and Wagner, M}, title = {A New Perspective on Microbes Formerly Known as Nitrite-Oxidizing Bacteria.}, journal = {Trends in microbiology}, volume = {24}, number = {9}, pages = {699-712}, pmid = {27283264}, issn = {1878-4380}, support = {294343/ERC_/European Research Council/International ; P 24101/FWF_/Austrian Science Fund FWF/Austria ; P 25231/FWF_/Austrian Science Fund FWF/Austria ; P 27319/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Ammonia/chemistry ; Nitrification/*physiology ; Nitrite Reductases/genetics/metabolism ; Nitrites/*metabolism ; Nitrobacter/genetics/*metabolism ; Nitrosomonas/genetics/*metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Wastewater/microbiology ; Water Purification ; }, abstract = {Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, nitrite oxidation to nitrate, which is an important process of the biogeochemical nitrogen cycle. NOB were traditionally perceived as physiologically restricted organisms and were less intensively studied than other nitrogen-cycling microorganisms. This picture is in contrast to new discoveries of an unexpected high diversity of mostly uncultured NOB and a great physiological versatility, which includes complex microbe-microbe interactions and lifestyles outside the nitrogen cycle. Most surprisingly, close relatives to NOB perform complete nitrification (ammonia oxidation to nitrate) and this finding will have far-reaching implications for nitrification research. We review recent work that has changed our perspective on NOB and provides a new basis for future studies on these enigmatic organisms.}, }
@article {pmid27282101, year = {2016}, author = {Myer, PR and Kim, M and Freetly, HC and Smith, TPL}, title = {Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers.}, journal = {Journal of microbiological methods}, volume = {127}, number = {}, pages = {132-140}, doi = {10.1016/j.mimet.2016.06.004}, pmid = {27282101}, issn = {1872-8359}, mesh = {Animals ; Cattle/*microbiology ; DNA Primers ; High-Throughput Nucleotide Sequencing/*methods ; Male ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Rumen/*microbiology ; Sequence Analysis, DNA/methods ; }, abstract = {Next generation sequencing technologies have vastly changed the approach of sequencing of the 16S rRNA gene for studies in microbial ecology. Three distinct technologies are available for large-scale 16S sequencing. All three are subject to biases introduced by sequencing error rates, amplification primer selection, and read length, which can affect the apparent microbial community. In this study, we compared short read 16S rRNA variable regions, V1-V3, with that of near-full length 16S regions, V1-V8, using highly diverse steer rumen microbial communities, in order to examine the impact of technology selection on phylogenetic profiles. Short paired-end reads from the Illumina MiSeq platform were used to generate V1-V3 sequence, while long "circular consensus" reads from the Pacific Biosciences RSII instrument were used to generate V1-V8 data. The two platforms revealed similar microbial operational taxonomic units (OTUs), as well as similar species richness, Good's coverage, and Shannon diversity metrics. However, the V1-V8 amplified ruminal community resulted in significant increases in several orders of taxa, such as phyla Proteobacteria and Verrucomicrobia (P < 0.05). Taxonomic classification accuracy was also greater in the near full-length read. UniFrac distance matrices using jackknifed UPGMA clustering also noted differences between the communities. These data support the consensus that longer reads result in a finer phylogenetic resolution that may not be achieved by shorter 16S rRNA gene fragments. Our work on the cattle rumen bacterial community demonstrates that utilizing near full-length 16S reads may be useful in conducting a more thorough study, or for developing a niche-specific database to use in analyzing data from shorter read technologies when budgetary constraints preclude use of near-full length 16S sequencing.}, }
@article {pmid27279447, year = {2016}, author = {Lei, W and Zhang, G and Wu, G and Liu, X}, title = {Cytological Characterization of Anamorphic Fungus Lecanicillium pui and Its Relationship with Chinese Caterpillar Mushroom, Ophiocordyceps sinensis (Ascomycetes).}, journal = {International journal of medicinal mushrooms}, volume = {18}, number = {1}, pages = {75-81}, doi = {10.1615/IntJMedMushrooms.v18.i1.90}, pmid = {27279447}, issn = {1940-4344}, mesh = {Cordyceps/*classification/genetics/growth &amp; development/ultrastructure ; DNA, Fungal/genetics ; Hyphae ; Hypocreales/*classification/genetics/growth &amp; development/ultrastructure ; Medicine, Tibetan Traditional ; Microscopy, Electron, Transmission ; Polymerase Chain Reaction ; }, abstract = {Ophiocordyceps sinensis (syn. Cordyceps sinensis), one of the most valuable medicinal mushrooms, has great economic importance on the Tibetan Plateau. We isolated an anamorphic fungus Lecanicillium pui from natural O. sinensis specimens and found that the optimal temperature for its culture on potato dextrose agar media was 25°C. Cell ultrastructure in L. pui hyphae and spores was characterized by transmission electron microscopy, and it was observed that some primary organelles showed the typical fungal features. Five chemical elements were determined in this fungus and niobium was discovered for the first time even with trace amounts. A species-specific method, nested polymerase chain reaction, was established to investigate the colonization of this fungus. Thus, the extensive distribution of L. pui on O. sinensis, in the shape of hyphae or mycelia, suggested that it may have subtle and chronic effects on the growth of the O. sinensis teleomorphic stage. These findings provide a potential reference, in the view of microbial ecology, for the study on the occurrence and mechanism of development of O. sinensis.}, }
@article {pmid27278778, year = {2016}, author = {Sabino-Pinto, J and Bletz, MC and Islam, MM and Shimizu, N and Bhuju, S and Geffers, R and Jarek, M and Kurabayashi, A and Vences, M}, title = {Composition of the Cutaneous Bacterial Community in Japanese Amphibians: Effects of Captivity, Host Species, and Body Region.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {460-469}, pmid = {27278778}, issn = {1432-184X}, mesh = {Animals ; Anura/classification/*microbiology ; Bacteria/*classification/isolation &amp; purification ; Biomass ; DNA, Bacterial/genetics ; Japan ; Linear Models ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Skin/*microbiology ; Species Specificity ; }, abstract = {The cutaneous microbiota plays a significant role in the biology of their vertebrate hosts, and its composition is known to be influenced both by host and environment, with captive conditions often altering alpha diversity. Here, we compare the cutaneous bacterial communities of 61 amphibians (both wild and captive) from Hiroshima, Japan, using high-throughput amplicon sequencing of a segment of the 16S rRNA gene. The majority of these samples came from a captive breeding facility at Hiroshima University where specimens from six species are maintained under highly standardized conditions for several generations. This allowed to identify host effects on the bacterial communities under near identical environmental conditions in captivity. We found the structure of the cutaneous bacterial community significantly differing between wild and captive individuals of newts, Cynops pyrrhogaster, with a higher alpha diversity found in the wild individuals. Community structure also showed distinct patterns when comparing different species of amphibians kept under highly similar conditions, revealing an intrinsic host effect. Bacterial communities of dorsal vs. ventral skin surfaces did not significantly differ in most species, but a trend of higher alpha diversity on the ventral surface was found in Oriental fire-bellied toads, Bombina orientalis. This study confirms the cutaneous microbiota of amphibians as a highly dynamic system influenced by a complex interplay of numerous factors.}, }
@article {pmid27276347, year = {2016}, author = {McDonald, JE and Larsen, N and Pennington, A and Connolly, J and Wallis, C and Rooks, DJ and Hall, N and McCarthy, AJ and Allison, HE}, title = {Characterising the Canine Oral Microbiome by Direct Sequencing of Reverse-Transcribed rRNA Molecules.}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0157046}, pmid = {27276347}, issn = {1932-6203}, mesh = {Animals ; *Bacteria/classification/genetics ; Dogs ; *High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; Mouth/*microbiology ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {PCR amplification and sequencing of phylogenetic markers, primarily Small Sub-Unit ribosomal RNA (SSU rRNA) genes, has been the paradigm for defining the taxonomic composition of microbiomes. However, 'universal' SSU rRNA gene PCR primer sets are likely to miss much of the diversity therein. We sequenced a library comprising purified and reverse-transcribed SSU rRNA (RT-SSU rRNA) molecules from the canine oral microbiome and compared it to a general bacterial 16S rRNA gene PCR amplicon library generated from the same biological sample. In addition, we have developed BIONmeta, a novel, open-source, computer package for the processing and taxonomic classification of the randomly fragmented RT-SSU rRNA reads produced. Direct RT-SSU rRNA sequencing revealed that 16S rRNA molecules belonging to the bacterial phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and Spirochaetes, were most abundant in the canine oral microbiome (92.5% of total bacterial SSU rRNA). The direct rRNA sequencing approach detected greater taxonomic diversity (1 additional phylum, 2 classes, 1 order, 10 families and 61 genera) when compared with general bacterial 16S rRNA amplicons from the same sample, simultaneously provided SSU rRNA gene inventories of Bacteria, Archaea and Eukarya, and detected significant numbers of sequences not recognised by 'universal' primer sets. Proteobacteria and Spirochaetes were found to be under-represented by PCR-based analysis of the microbiome, and this was due to primer mismatches and taxon-specific variations in amplification efficiency, validated by qPCR analysis of 16S rRNA amplicons from a mock community. This demonstrated the veracity of direct RT-SSU rRNA sequencing for molecular microbial ecology.}, }
@article {pmid27273822, year = {2017}, author = {Paulussen, C and Hallsworth, JE and Álvarez-Pérez, S and Nierman, WC and Hamill, PG and Blain, D and Rediers, H and Lievens, B}, title = {Ecology of aspergillosis: insights into the pathogenic potency of Aspergillus fumigatus and some other Aspergillus species.}, journal = {Microbial biotechnology}, volume = {10}, number = {2}, pages = {296-322}, pmid = {27273822}, issn = {1751-7915}, mesh = {Animals ; Aspergillosis/diagnosis/*microbiology/*pathology ; Aspergillus/*pathogenicity/*physiology ; *Biophysical Phenomena ; Diagnostic Tests, Routine ; Ecosystem ; *Host-Pathogen Interactions ; Humans ; }, abstract = {Fungi of the genus Aspergillus are widespread in the environment. Some Aspergillus species, most commonly Aspergillus fumigatus, may lead to a variety of allergic reactions and life-threatening systemic infections in humans. Invasive aspergillosis occurs primarily in patients with severe immunodeficiency, and has dramatically increased in recent years. There are several factors at play that contribute to aspergillosis, including both fungus and host-related factors such as strain virulence and host pulmonary structure/immune status, respectively. The environmental tenacity of Aspergilllus, its dominance in diverse microbial communities/habitats, and its ability to navigate the ecophysiological and biophysical challenges of host infection are attributable, in large part, to a robust stress-tolerance biology and exceptional capacity to generate cell-available energy. Aspects of its stress metabolism, ecology, interactions with diverse animal hosts, clinical presentations and treatment regimens have been well-studied over the past years. Here, we synthesize these findings in relation to the way in which some Aspergillus species have become successful opportunistic pathogens of human- and other animal hosts. We focus on the biophysical capabilities of Aspergillus pathogens, key aspects of their ecophysiology and the flexibility to undergo a sexual cycle or form cryptic species. Additionally, recent advances in diagnosis of the disease are discussed as well as implications in relation to questions that have yet to be resolved.}, }
@article {pmid27273460, year = {2016}, author = {Liu, Y and Sun, J and Peng, L and Wang, D and Dai, X and Ni, BJ}, title = {Assessment of Heterotrophic Growth Supported by Soluble Microbial Products in Anammox Biofilm using Multidimensional Modeling.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {27576}, pmid = {27273460}, issn = {2045-2322}, mesh = {Ammonium Compounds/*metabolism ; Anaerobiosis/*physiology ; Autotrophic Processes/*physiology ; Bacteria/*growth &amp; development/metabolism ; Biofilms/*growth &amp; development ; Biomass ; Computer Simulation ; Heterotrophic Processes/*physiology ; Kinetics ; Microbial Consortia/physiology ; Models, Chemical ; Oxidation-Reduction ; }, abstract = {Anaerobic ammonium oxidation (anammox) is known to autotrophically convert ammonium to dinitrogen gas with nitrite as the electron acceptor, but little is known about their released microbial products and how these are relative to heterotrophic growth in anammox system. In this work, we applied a mathematical model to assess the heterotrophic growth supported by three key microbial products produced by bacteria in anammox biofilm (utilization associated products (UAP), biomass associated products (BAP), and decay released substrate). Both One-dimensional and two-dimensional numerical biofilm models were developed to describe the development of anammox biofilm as a function of the multiple bacteria-substrate interactions. Model simulations show that UAP of anammox is the main organic carbon source for heterotrophs. Heterotrophs are mainly dominant at the surface of the anammox biofilm with small fraction inside the biofilm. 1-D model is sufficient to describe the main substrate concentrations/fluxes within the anammox biofilm, while the 2-D model can give a more detailed biomass distribution. The heterotrophic growth on UAP is mainly present at the outside of anammox biofilm, their growth on BAP (HetB) are present throughout the biofilm, while the growth on decay released substrate (HetD) is mainly located in the inner layers of the biofilm.}, }
@article {pmid27273325, year = {2016}, author = {Goubert, C and Minard, G and Vieira, C and Boulesteix, M}, title = {Population genetics of the Asian tiger mosquito Aedes albopictus, an invasive vector of human diseases.}, journal = {Heredity}, volume = {117}, number = {3}, pages = {125-134}, pmid = {27273325}, issn = {1365-2540}, mesh = {Aedes/*genetics/virology ; Animals ; Genetic Markers ; Genetic Variation ; *Genetics, Population ; Insect Vectors/*genetics/virology ; *Introduced Species ; }, abstract = {The Asian tiger mosquito Aedes albopictus is currently one of the most threatening invasive species in the world. Native to Southeast Asia, the species has spread throughout the world in the past 30 years and is now present in every continent but Antarctica. Because it was the main vector of recent Dengue and Chikungunya outbreaks, and because of its competency for numerous other viruses and pathogens such as the Zika virus, A. albopictus stands out as a model species for invasive diseases vector studies. A synthesis of the current knowledge about the genetic diversity of A. albopictus is needed, knowing the interplays between the vector, the pathogens, the environment and their epidemiological consequences. Such resources are also valuable for assessing the role of genetic diversity in the invasive success. We review here the large but sometimes dispersed literature about the population genetics of A. albopictus. We first debate about the experimental design of these studies and present an up-to-date assessment of the available molecular markers. We then summarize the main genetic characteristics of natural populations and synthesize the available data regarding the worldwide structuring of the vector. Finally, we pinpoint the gaps that remain to be addressed and suggest possible research directions.}, }
@article {pmid27273090, year = {2016}, author = {Veresoglou, SD and Anderson, IC and de Sousa, NM and Hempel, S and Rillig, MC}, title = {Resilience of Fungal Communities to Elevated CO2.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {493-495}, pmid = {27273090}, issn = {1432-184X}, mesh = {Biodiversity ; Carbon Dioxide/*analysis ; Climate Change ; Ecosystem ; Fungi/*classification/isolation &amp; purification/physiology ; *Soil Microbiology ; }, abstract = {Soil filamentous fungi play a prominent role in regulating ecosystem functioning in terrestrial ecosystems. This necessitates understanding their responses to climate change drivers in order to predict how nutrient cycling and ecosystem services will be influenced in the future. Here, we provide a quantitative synthesis of ten studies on soil fungal community responses to elevated CO2. Many of these studies reported contradictory diversity responses. We identify the duration of the study as an influential parameter that determines the outcome of experimentation. Our analysis reconciles the existing globally distributed experiments on fungal community responses to elevated CO2 and provides a framework for comparing results of future CO2 enrichment studies.}, }
@article {pmid27273089, year = {2016}, author = {Chiu, MC and Kuo, MH and Chang, HY and Lin, HJ}, title = {Bayesian Modeling of the Effects of Extreme Flooding and the Grazer Community on Algal Biomass Dynamics in a Monsoonal Taiwan Stream.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {372-380}, pmid = {27273089}, issn = {1432-184X}, mesh = {Animals ; Bayes Theorem ; *Biomass ; *Climate Change ; Ecosystem ; Eutrophication/*physiology ; *Floods ; Hydrodynamics ; Invertebrates/physiology ; Models, Theoretical ; *Rivers ; Taiwan ; }, abstract = {The effects of grazing and climate change on primary production have been studied widely, but seldom with mechanistic models. We used a Bayesian model to examine the effects of extreme weather and the invertebrate grazer community on epilithic algal biomass dynamics over 10 years (from January 2004 to August 2013). Algal biomass and the invertebrate grazer community were monitored in the upstream drainage of the Dajia River in Taiwan, where extreme floods have been becoming more frequent. The biomass of epilithic algae changed, both seasonally and annually, and extreme flooding changed the growth and resistance to flow detachment of the algae. Invertebrate grazing pressure changes with the structure of the invertebrate grazer community, which, in turn, is affected by the flow regime. Invertebrate grazer community structure and extreme flooding both affected the dynamics of epilithic algae, but in different ways. Awareness of the interactions between algal communities and grazers/abiotic factors can help with the design of future studies and could facilitate the development of management programs for stream ecosystems.}, }
@article {pmid27272205, year = {2016}, author = {Ziemert, N and Alanjary, M and Weber, T}, title = {The evolution of genome mining in microbes - a review.}, journal = {Natural product reports}, volume = {33}, number = {8}, pages = {988-1005}, doi = {10.1039/c6np00025h}, pmid = {27272205}, issn = {1460-4752}, mesh = {Biological Evolution ; Biological Products/chemistry/*metabolism ; Drug Discovery ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing/methods ; Molecular Structure ; Multigene Family ; }, abstract = {Covering: 2006 to 2016The computational mining of genomes has become an important part in the discovery of novel natural products as drug leads. Thousands of bacterial genome sequences are publically available these days containing an even larger number and diversity of secondary metabolite gene clusters that await linkage to their encoded natural products. With the development of high-throughput sequencing methods and the wealth of DNA data available, a variety of genome mining methods and tools have been developed to guide discovery and characterisation of these compounds. This article reviews the development of these computational approaches during the last decade and shows how the revolution of next generation sequencing methods has led to an evolution of various genome mining approaches, techniques and tools. After a short introduction and brief overview of important milestones, this article will focus on the different approaches of mining genomes for secondary metabolites, from detecting biosynthetic genes to resistance based methods and "evo-mining" strategies including a short evaluation of the impact of the development of genome mining methods and tools on the field of natural products and microbial ecology.}, }
@article {pmid27271296, year = {2016}, author = {Walworth, AE and Chai, B and Song, GQ}, title = {Transcript Profile of Flowering Regulatory Genes in VcFT-Overexpressing Blueberry Plants.}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0156993}, pmid = {27271296}, issn = {1932-6203}, mesh = {Blueberry Plants/*genetics ; Flowers/*genetics ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Plant ; Gene Regulatory Networks ; MADS Domain Proteins/*genetics ; Plant Leaves/genetics ; Plant Proteins/genetics ; Sequence Analysis, RNA ; }, abstract = {In order to identify genetic components in flowering pathways of highbush blueberry (Vaccinium corymbosum L.), a transcriptome reference composed of 254,396 transcripts and 179,853 gene contigs was developed by assembly of 72.7 million reads using Trinity. Using this transcriptome reference and a query of flowering pathway genes of herbaceous plants, we identified potential flowering pathway genes/transcripts of blueberry. Transcriptome analysis of flowering pathway genes was then conducted on leaf tissue samples of transgenic blueberry cv. Aurora ('VcFT-Aurora'), which overexpresses a blueberry FLOWERING LOCUS T-like gene (VcFT). Sixty-one blueberry transcripts of 40 genes showed high similarities to 33 known flowering-related genes of herbaceous plants, of which 17 down-regulated and 16 up-regulated genes were identified in 'VcFT-Aurora'. All down-regulated genes encoded transcription factors/enzymes upstream in the signaling pathway containing VcFT. A blueberry CONSTANS-LIKE 5-like (VcCOL5) gene was down-regulated and associated with five other differentially expressed (DE) genes in the photoperiod-mediated flowering pathway. Three down-regulated genes, i.e., a MADS-AFFECTING FLOWERING 2-like gene (VcMAF2), a MADS-AFFECTING FLOWERING 5-like gene (VcMAF5), and a VERNALIZATION1-like gene (VcVRN1), may function as integrators in place of FLOWERING LOCUS C (FLC) in the vernalization pathway. Because no CONSTAN1-like or FLOWERING LOCUS C-like genes were found in blueberry, VcCOL5 and VcMAF2/VcMAF5 or VRN1 might be the major integrator(s) in the photoperiod- and vernalization-mediated flowering pathway, respectively. The major down-stream genes of VcFT, i.e., SUPPRESSOR of Overexpression of Constans 1-like (VcSOC1), LEAFY-like (VcLFY), APETALA1-like (VcAP1), CAULIFLOWER 1-like (VcCAL1), and FRUITFULL-like (VcFUL) genes were present and showed high similarity to their orthologues in herbaceous plants. Moreover, overexpression of VcFT promoted expression of all of these VcFT downstream genes. These results suggest that VcFT's down-stream genes appear conserved in blueberry.}, }
@article {pmid27270755, year = {2016}, author = {Wasielewski, H and Alcock, J and Aktipis, A}, title = {Resource conflict and cooperation between human host and gut microbiota: implications for nutrition and health.}, journal = {Annals of the New York Academy of Sciences}, volume = {1372}, number = {1}, pages = {20-28}, doi = {10.1111/nyas.13118}, pmid = {27270755}, issn = {1749-6632}, mesh = {Energy Metabolism ; *Gastrointestinal Microbiome ; *Health ; Humans ; *Nutritional Status ; Symbiosis ; }, abstract = {Diet has been known to play an important role in human health since at least the time period of the ancient Greek physician Hippocrates. In the last decade, research has revealed that microorganisms inhabiting the digestive tract, known as the gut microbiota, are critical factors in human health. This paper draws on concepts of cooperation and conflict from ecology and evolutionary biology to make predictions about host-microbiota interactions involving nutrients. To optimally extract energy from some resources (e.g., fiber), hosts require cooperation from microbes. Other nutrients can be utilized by both hosts and microbes (e.g., simple sugars, iron) in their ingested form, which may lead to greater conflict over these resources. This framework predicts that some negative health effects of foods are driven by the direct effects of these foods on human physiology and by indirect effects resulting from microbiome-host competition and conflict (e.g., increased invasiveness and inflammation). Similarly, beneficial effects of some foods on host health may be enhanced by resource sharing and other cooperative behaviors between host and microbes that may downregulate inflammation and virulence. Given that some foods cultivate cooperation between hosts and microbes while others agitate conflict, host-microbe interactions may be novel targets for interventions aimed at improving nutrition and human health.}, }
@article {pmid27270282, year = {2016}, author = {van der Aart, LT and Lemmens, N and van Wamel, WJ and van Wezel, GP}, title = {Substrate Inhibition of VanA by d-Alanine Reduces Vancomycin Resistance in a VanX-Dependent Manner.}, journal = {Antimicrobial agents and chemotherapy}, volume = {60}, number = {8}, pages = {4930-4939}, pmid = {27270282}, issn = {1098-6596}, mesh = {Alanine/*metabolism ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/*metabolism ; Carbon-Oxygen Ligases/*metabolism ; Cell Wall/drug effects/metabolism ; Drug Resistance, Microbial/*drug effects ; Enterococcus faecium/drug effects/metabolism ; Glycopeptides/metabolism ; Ligases/metabolism ; Peptidoglycan/metabolism ; Serine-Type D-Ala-D-Ala Carboxypeptidase/*metabolism ; Streptomyces coelicolor/drug effects/metabolism ; Vancomycin/pharmacology ; Vancomycin Resistance/*drug effects ; }, abstract = {The increasing resistance of clinical pathogens against the glycopeptide antibiotic vancomycin, a last-resort drug against infections with Gram-positive pathogens, is a major problem in the nosocomial environment. Vancomycin inhibits peptidoglycan synthesis by binding to the d-Ala-d-Ala terminal dipeptide moiety of the cell wall precursor lipid II. Plasmid-transferable resistance is conferred by modification of the terminal dipeptide into the vancomycin-insensitive variant d-Ala-d-Lac, which is produced by VanA. Here we show that exogenous d-Ala competes with d-Lac as a substrate for VanA, increasing the ratio of wild-type to mutant dipeptide, an effect that was augmented by several orders of magnitude in the absence of the d-Ala-d-Ala peptidase VanX. Liquid chromatography-mass spectrometry (LC-MS) analysis showed that high concentrations of d-Ala led to the production of a significant amount of wild-type cell wall precursors, while vanX-null mutants produced primarily wild-type precursors. This enhanced the efficacy of vancomycin in the vancomycin-resistant model organism Streptomyces coelicolor, and the susceptibility of vancomycin-resistant clinical isolates of Enterococcus faecium (VRE) increased by up to 100-fold. The enhanced vancomycin sensitivity of S. coelicolor cells correlated directly to increased binding of the antibiotic to the cell wall. Our work offers new perspectives for the treatment of diseases associated with vancomycin-resistant pathogens and for the development of drugs that target vancomycin resistance.}, }
@article {pmid27267720, year = {2016}, author = {Strickman, RJS and Fulthorpe, RR and Coleman Wasik, JK and Engstrom, DR and Mitchell, CPJ}, title = {Experimental sulfate amendment alters peatland bacterial community structure.}, journal = {The Science of the total environment}, volume = {566-567}, number = {}, pages = {1289-1296}, doi = {10.1016/j.scitotenv.2016.05.189}, pmid = {27267720}, issn = {1879-1026}, mesh = {Air Pollutants/*analysis ; *Bacteria ; Biodegradation, Environmental ; Deltaproteobacteria ; Methylmercury Compounds/analysis ; *Microbiota ; Minnesota ; Sulfates/*analysis ; *Wetlands ; }, abstract = {As part of a long-term, peatland-scale sulfate addition experiment, the impact of varying sulfate deposition on bacterial community responses was assessed using 16S tag encoded pyrosequencing. In three separate areas of the peatland, sulfate manipulations included an eight year quadrupling of atmospheric sulfate deposition (experimental), a 3-year recovery to background deposition following 5years of elevated deposition (recovery), and a control area. Peat concentrations of methylmercury (MeHg), a bioaccumulative neurotoxin, were measured, the production of which is attributable to a growing list of microorganisms, including many sulfate-reducing Deltaproteobacteria. The total bacterial and Deltaproteobacterial community structures in the experimental treatment differed significantly from those in the control and recovery treatments that were either indistinguishable or very similar to one another. Notably, the relatively rapid return (within three years) of bacterial community structure in the recovery treatment to a state similar to the control, demonstrates significant resilience of the peatland bacterial community to changes in atmospheric sulfate deposition. Changes in MeHg accumulation between sulfate treatments correlated with changes in the Deltaproteobacterial community, suggesting that sulfate may affect MeHg production through changes in the community structure of this group.}, }
@article {pmid27264635, year = {2016}, author = {Shi, S and Nuccio, EE and Shi, ZJ and He, Z and Zhou, J and Firestone, MK}, title = {The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages.}, journal = {Ecology letters}, volume = {19}, number = {8}, pages = {926-936}, doi = {10.1111/ele.12630}, pmid = {27264635}, issn = {1461-0248}, mesh = {Avena/microbiology ; Bacteria/*classification/*genetics ; Biodiversity ; Models, Biological ; Plant Roots ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {While interactions between roots and microorganisms have been intensively studied, we know little about interactions among root-associated microbes. We used random matrix theory-based network analysis of 16S rRNA genes to identify bacterial networks associated with wild oat (Avena fatua) over two seasons in greenhouse microcosms. Rhizosphere networks were substantially more complex than those in surrounding soils, indicating the rhizosphere has a greater potential for interactions and niche-sharing. Network complexity increased as plants grew, even as diversity decreased, highlighting that community organisation is not captured by univariate diversity. Covariations were predominantly positive (> 80%), suggesting that extensive mutualistic interactions may occur among rhizosphere bacteria; we identified quorum-based signalling as one potential strategy. Putative keystone taxa often had low relative abundances, suggesting low-abundance taxa may significantly contribute to rhizosphere function. Network complexity, a previously undescribed property of the rhizosphere microbiome, appears to be a defining characteristic of this habitat.}, }
@article {pmid27263010, year = {2016}, author = {Snyman, M and Gupta, AK and Bezuidenhout, CC and Claassens, S and van den Berg, J}, title = {Gut microbiota of Busseola fusca (Lepidoptera: Noctuidae).}, journal = {World journal of microbiology &amp; biotechnology}, volume = {32}, number = {7}, pages = {115}, pmid = {27263010}, issn = {1573-0972}, mesh = {Animals ; Bacteria/*classification/*genetics/isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; *Gastrointestinal Microbiome ; Larva/microbiology ; Lepidoptera/*microbiology ; Pest Control ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; South Africa ; }, abstract = {Busseola fusca (Fuller) (Lepidoptera: Noctuidae) is a stemborer pest that attacks maize (Zea mays) throughout sub-Saharan Africa. Genetically modified maize has been shown to be effective against B. fusca. However, resistance of B. fusca against Bt-maize has developed and spread throughout South Africa. Previous studies suggested that gut microbiota contribute to mortality across a range of Lepidoptera. To fully assess the role of microbiota within the gut, it is essential to understand the microbiota harboured by natural B. fusca populations. This study aimed to identify the gut-associated bacteria by 16S rRNA gene sequencing. A total of 78 bacterial strains were characterised from the midgut of B. fusca larvae that were collected from 30 sites across the maize producing region of South Africa. Molecular phylogenetic analyses revealed bacteria affiliated to Proteobacteria, Actinobacteria, and Firmicutes. Taxonomic distribution placed these isolates into 15 different genera representing 20 species. The majority of bacteria identified belong to the genera Bacillus, Enterococcus, and Klebsiella. The B. fusca gut represents an intriguing and unexplored niche for analysing microbial ecology. The study could provide opportunities for developing new targets for pest management and contribute to understanding the phenomenon of resistance evolution of this species.}, }
@article {pmid27262549, year = {2016}, author = {Jo, SJ and Kwon, H and Jeong, SY and Lee, CH and Kim, TG}, title = {Comparison of microbial communities of activated sludge and membrane biofilm in 10 full-scale membrane bioreactors.}, journal = {Water research}, volume = {101}, number = {}, pages = {214-225}, doi = {10.1016/j.watres.2016.05.042}, pmid = {27262549}, issn = {1879-2448}, mesh = {*Biofilms ; Biofouling ; Bioreactors/microbiology ; Membranes, Artificial ; Sewage/*microbiology ; Waste Disposal, Fluid ; Wastewater/microbiology ; }, abstract = {Operation of membrane bioreactors (MBRs) for wastewater treatment is hampered by the membrane biofouling resulting from microbial activities. However, the knowledge of the microbial ecology of both biofilm and activated sludge in MBRs has not been sufficient. In this study, we scrutinized microbial communities of biofilm and activated sludge from 10 full-scale MBR plants. Overall, Flavobacterium, Dechloromonas and Nitrospira were abundant in order of abundance in biofilm, whereas Dechloromonas, Flavobacterium and Haliscomenobacter in activated sludge. Community structure was analyzed in either biofilm or activated sludge. Among MBRs, as expected, not only diversity of microbial community but also its composition was different from one another (p < 0.05). Between the biofilm and activated sludge, community composition made significant difference, but its diversity measures (i.e., alpha diversity, e.g., richness, diversity and evenness) did not (p > 0.05). Effects of ten environmental factors on community change were investigated using Spearman correlation. MLSS, HRT, F/M ratio and SADm explained the variation of microbial composition in the biofilm, whereas only MLSS did in the activated sludge. Microbial networks were constructed with the 10 environmental factors. The network results revealed that there were different topological characteristics between the biofilm and activated sludge networks, in which each of the 4 factors had different associations with microbial nodes. These results indicated that the different microbial associations were responsible for the variation of community composition between the biofilm and activated sludge.}, }
@article {pmid27262118, year = {2016}, author = {Matassa, S and Verstraete, W and Pikaar, I and Boon, N}, title = {Autotrophic nitrogen assimilation and carbon capture for microbial protein production by a novel enrichment of hydrogen-oxidizing bacteria.}, journal = {Water research}, volume = {101}, number = {}, pages = {137-146}, doi = {10.1016/j.watres.2016.05.077}, pmid = {27262118}, issn = {1879-2448}, mesh = {Bacteria/metabolism ; Bioreactors/microbiology ; Carbon/*metabolism ; Hydrogen ; Nitrogen/*metabolism ; }, abstract = {Domestic used water treatment systems are currently predominantly based on conventional resource inefficient treatment processes. While resource recovery is gaining momentum it lacks high value end-products which can be efficiently marketed. Microbial protein production offers a valid and promising alternative by upgrading low value recovered resources into high quality feed and also food. In the present study, we evaluated the potential of hydrogen-oxidizing bacteria to upgrade ammonium and carbon dioxide under autotrophic growth conditions. The enrichment of a generic microbial community and the implementation of different culture conditions (sequenced batch resp. continuous reactor) revealed surprising features. At low selection pressure (i.e. under sequenced batch culture at high solid retention time), a very diverse microbiome with an important presence of predatory Bdellovibrio spp. was observed. The microbial culture which evolved under high rate selection pressure (i.e. dilution rate D = 0.1 h(-1)) under continuous reactor conditions was dominated by Sulfuricurvum spp. and a highly stable and efficient process in terms of N and C uptake, biomass yield and volumetric productivity was attained. Under continuous culture conditions the maximum yield obtained was 0.29 g cell dry weight per gram chemical oxygen demand equivalent of hydrogen, whereas the maximum volumetric loading rate peaked 0.41 g cell dry weight per litre per hour at a protein content of 71%. Finally, the microbial protein produced was of high nutritive quality in terms of essential amino acids content and can be a suitable substitute for conventional feed sources such as fishmeal or soybean meal.}, }
@article {pmid27261783, year = {2016}, author = {Morono, Y and Inagaki, F}, title = {Analysis of Low-Biomass Microbial Communities in the Deep Biosphere.}, journal = {Advances in applied microbiology}, volume = {95}, number = {}, pages = {149-178}, doi = {10.1016/bs.aambs.2016.04.001}, pmid = {27261783}, issn = {0065-2164}, mesh = {Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Biomass ; Ecosystem ; Geologic Sediments/*microbiology ; History, 20th Century ; History, 21st Century ; Microbiological Techniques/history/instrumentation/*methods ; Seawater/chemistry/*microbiology ; }, abstract = {Over the past few decades, the subseafloor biosphere has been explored by scientific ocean drilling to depths of about 2.5km below the seafloor. Although organic-rich anaerobic sedimentary habitats in the ocean margins harbor large numbers of microbial cells, microbial populations in ultraoligotrophic aerobic sedimentary habitats in the open ocean gyres are several orders of magnitude less abundant. Despite advances in cultivation-independent molecular ecological techniques, exploring the low-biomass environment remains technologically challenging, especially in the deep subseafloor biosphere. Reviewing the historical background of deep-biosphere analytical methods, the importance of obtaining clean samples and tracing contamination, as well as methods for detecting microbial life, technological aspects of molecular microbiology, and detecting subseafloor metabolic activity will be discussed.}, }
@article {pmid27260155, year = {2016}, author = {Bondoc, KG and Lembke, C and Vyverman, W and Pohnert, G}, title = {Searching for a Mate: Pheromone-Directed Movement of the Benthic Diatom Seminavis robusta.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {287-294}, pmid = {27260155}, issn = {1432-184X}, mesh = {*Chemotaxis ; Diatoms/*physiology ; Diketopiperazines/chemistry ; Models, Biological ; Pheromones/*chemistry ; Reproduction ; }, abstract = {Diatoms are species-rich microalgae that often have a unique life cycle with vegetative cell size reduction followed by size restoration through sexual reproduction of two mating types (MT(+) and MT(-)). In the marine benthic diatom Seminavis robusta, mate-finding is mediated by an L-proline-derived diketopiperazine, a pheromone produced by the attracting mating type (MT(-)). Here, we investigate the movement patterns of cells of the opposite mating type (MT(+)) exposed to a pheromone gradient, using video monitoring and statistical modeling. We report that cells of the migrating mating type (MT(+)) respond to pheromone gradients by simultaneous chemotaxis and chemokinesis. Changes in movement behavior enable MT(+) cells to locate the direction of the pheromone source and to maximize their encounter rate towards it.}, }
@article {pmid27260154, year = {2016}, author = {Soares, MA and Li, HY and Kowalski, KP and Bergen, M and Torres, MS and White, JF}, title = {Functional Role of Bacteria from Invasive Phragmites australis in Promotion of Host Growth.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {407-417}, pmid = {27260154}, issn = {1432-184X}, mesh = {*Antibiosis ; Bacteria/classification/isolation &amp; purification/*metabolism ; Biomass ; Fungi/growth &amp; development ; Indoleacetic Acids/metabolism ; Lipopeptides/biosynthesis ; Nitrogen Fixation ; Phosphates/metabolism ; Plant Roots/*microbiology ; Poaceae/growth &amp; development/*microbiology ; *Soil Microbiology ; Symbiosis ; }, abstract = {We hypothesize that bacterial endophytes may enhance the competitiveness and invasiveness of Phragmites australis. To evaluate this hypothesis, endophytic bacteria were isolated from P. australis. The majority of the shoot meristem isolates represent species from phyla Firmicutes, Proteobacteria, and Actinobacteria. We chose one species from each phylum to characterize further and to conduct growth promotion experiments in Phragmites. Bacteria tested include Bacillus amyloliquefaciens A9a, Achromobacter spanius B1, and Microbacterium oxydans B2. Isolates were characterized for known growth promotional traits, including indole acetic acid (IAA) production, secretion of hydrolytic enzymes, phosphate solubilization, and antibiosis activity. Potentially defensive antimicrobial lipopeptides were assayed for through application of co-culturing experiments and mass spectrometer analysis. B. amyloliquefaciens A9a and M. oxydans B2 produced IAA. B. amyloliquefaciens A9a secreted antifungal lipopeptides. Capability to promote growth of P. australis under low nitrogen conditions was evaluated in greenhouse experiments. All three isolates were found to increase the growth of P. australis under low soil nitrogen conditions and showed increased absorption of isotopic nitrogen into plants. This suggests that the Phragmites microbes we evaluated most likely promote growth of Phragmites by enhanced scavenging of nitrogenous compounds from the rhizosphere and transfer to host roots. Collectively, our results support the hypothesis that endophytic bacteria play a role in enhancing growth of P. australis in natural populations. Gaining a better understanding of the precise contributions and mechanisms of endophytes in enabling P. australis to develop high densities rapidly could lead to new symbiosis-based strategies for management and control of the host.}, }
@article {pmid27259999, year = {2016}, author = {Guerrero-Preston, R and Godoy-Vitorino, F and Jedlicka, A and Rodríguez-Hilario, A and González, H and Bondy, J and Lawson, F and Folawiyo, O and Michailidi, C and Dziedzic, A and Thangavel, R and Hadar, T and Noordhuis, MG and Westra, W and Koch, W and Sidransky, D}, title = {16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment.}, journal = {Oncotarget}, volume = {7}, number = {32}, pages = {51320-51334}, pmid = {27259999}, issn = {1949-2553}, support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; R01 CA121113/CA/NCI NIH HHS/United States ; K01 CA164092/CA/NCI NIH HHS/United States ; P50 DE019032/DE/NIDCR NIH HHS/United States ; RC2 DE020957/DE/NIDCR NIH HHS/United States ; U01 CA084986/CA/NCI NIH HHS/United States ; }, mesh = {Aged ; *Carcinoma, Squamous Cell/genetics/microbiology/surgery/virology ; Cohort Studies ; Female ; Gene Amplification ; Head and Neck Neoplasms/genetics/microbiology/surgery/virology ; Humans ; Longitudinal Studies ; Male ; Microbiota/*genetics ; Middle Aged ; *Mouth Neoplasms/genetics/microbiology/surgery/virology ; *Oral Surgical Procedures ; Papillomaviridae/genetics ; Papillomavirus Infections/*genetics/microbiology/pathology/surgery ; Prognosis ; RNA, Ribosomal, 16S/*genetics ; Risk Factors ; Squamous Cell Carcinoma of Head and Neck ; }, abstract = {Systemic inflammatory events and localized disease, mediated by the microbiome, may be measured in saliva as head and neck squamous cell carcinoma (HNSCC) diagnostic and prognostic biomonitors. We used a 16S rRNA V3-V5 marker gene approach to compare the saliva microbiome in DNA isolated from Oropharyngeal (OPSCC), Oral Cavity Squamous Cell Carcinoma (OCSCC) patients and normal epithelium controls, to characterize the HNSCC saliva microbiota and examine their abundance before and after surgical resection.The analyses identified a predominance of Firmicutes, Proteobacteria and Bacteroidetes, with less frequent presence of Actinobacteria and Fusobacteria before surgery. At lower taxonomic levels, the most abundant genera were Streptococcus, Prevotella, Haemophilus, Lactobacillus and Veillonella, with lower numbers of Citrobacter and Neisseraceae genus Kingella. HNSCC patients had a significant loss in richness and diversity of microbiota species (p<0.05) compared to the controls. Overall, the Operational Taxonomic Units network shows that the relative abundance of OTU's within genus Streptococcus, Dialister, and Veillonella can be used to discriminate tumor from control samples (p<0.05). Tumor samples lost Neisseria, Aggregatibacter (Proteobacteria), Haemophillus (Firmicutes) and Leptotrichia (Fusobacteria). Paired taxa within family Enterobacteriaceae, together with genus Oribacterium, distinguish OCSCC samples from OPSCC and normal samples (p<0.05). Similarly, only HPV positive samples have an abundance of genus Gemellaceae and Leuconostoc (p<0.05). Longitudinal analyses of samples taken before and after surgery, revealed a reduction in the alpha diversity measure after surgery, together with an increase of this measure in patients that recurred (p<0.05). These results suggest that microbiota may be used as HNSCC diagnostic and prognostic biomonitors.}, }
@article {pmid27258395, year = {2016}, author = {Kästner, M and Nowak, KM and Miltner, A and Schäffer, A}, title = {(Multiple) Isotope probing approaches to trace the fate of environmental chemicals and the formation of non-extractable 'bound' residues.}, journal = {Current opinion in biotechnology}, volume = {41}, number = {}, pages = {73-82}, doi = {10.1016/j.copbio.2016.05.002}, pmid = {27258395}, issn = {1879-0429}, mesh = {Environmental Pollutants/analysis/*metabolism ; Isotope Labeling/*methods ; Isotopes/*analysis ; Phylogeny ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {Procedures for the analysis of turnover of chemicals (and of natural compounds) are well developed using radio or stable isotope labelled tracer compounds in various standardized OECD tests. Due to the analytical focus on the isotope label the chemical speciation of the so-called non-extractable residues (NER) in soils and sediments often remains unknown. These NER may stem from parent compounds, metabolites, microbial biomass, or from precipitated carbonates after productive microbial degradation. Fate studies mostly do not describe the link to phylogenetic assignment of degraders and microbial ecology although in these fields various isotope tracer applications are well developed, too. We present several options for integrating both approaches in environmental biotechnology and how they can be used to improve knowledge in microbial ecology.}, }
@article {pmid27255677, year = {2016}, author = {Wüst, PK and Foesel, BU and Geppert, A and Huber, KJ and Luckner, M and Wanner, G and Overmann, J}, title = {Brevitalea aridisoli, B. deliciosa and Arenimicrobium luteum, three novel species of Acidobacteria subdivision 4 (class Blastocatellia) isolated from savanna soil and description of the novel family Pyrinomonadaceae.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {66}, number = {9}, pages = {3355-3366}, doi = {10.1099/ijsem.0.001199}, pmid = {27255677}, issn = {1466-5034}, mesh = {Acidobacteria/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Grassland ; Namibia ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {Three novel strains of the phylum Acidobacteria (Ac_11_E3T, Ac_12_G8T and Ac_16_C4T) were isolated from Namibian semiarid savanna soils by a high-throughput cultivation approach using low-nutrient growth media. 16S rRNA gene sequence analysis placed all three strains in the order Blastocatellales of the class Blastocatellia (Acidobacteria subdivision 4). However, 16S rRNA gene sequence similarities to their closest relative Pyrinomonas methylaliphatogenes K22T were ≤90 %. Cells of strains Ac_11_E3T, Ac_12_G8T and Ac_16_C4T were Gram-staining-negative and non-motile and divided by binary fission. Ac_11_E3T and Ac_16_C4T formed white colonies, while those of Ac_12_G8T were orange-yellowish. All three strains were aerobic chemoorganoheterotrophic mesophiles with a broad pH range for growth. All strains used a very limited spectrum of carbon and energy sources for growth, with a preference for complex proteinaceous substrates. The major respiratory quinone was MK-8. The major shared fatty acid was iso-C15 : 0. The DNA G+C contents of strains Ac_11_E3T, Ac_12_G8T and Ac_16_C4T were 55.9 mol%, 66.9 mol% and 54.7 mol%, respectively. Based on these characteristics, the two novel genera Brevitaleagen. nov. and Arenimicrobiumgen. nov. are proposed, harboring the novel species Brevitaleaaridisoli sp. nov. (Ac_11_E3T=DSM 27934T=LMG 28618T), Brevitalea deliciosa sp. nov. (Ac_16_C4T=DSM 29892T=LMG 28995T) and Arenimicrobium luteum sp. nov. (Ac_12_G8T=DSM 26556T=LMG 29166T), respectively. Since these novel genera are only distantly related to established families, we propose the novel family Pyrinomonadaceaefam. nov. that accommodates the proposed genera and the genus Pyrinomonas(Crowe et al., 2014).}, }
@article {pmid27252690, year = {2016}, author = {Richter-Heitmann, T and Eickhorst, T and Knauth, S and Friedrich, MW and Schmidt, H}, title = {Evaluation of Strategies to Separate Root-Associated Microbial Communities: A Crucial Choice in Rhizobiome Research.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {773}, pmid = {27252690}, issn = {1664-302X}, abstract = {Plants shape distinct, species-specific microbiomes in their rhizospheres. A main premise for evaluating microbial communities associated with root-soil compartments is their successful separation into the rhizosphere (soil-root interface), the rhizoplane (root surface), and the endosphere (inside roots). We evaluated different approaches (washing, sonication, and bleaching) regarding their efficiency to separate microbial cells associated with different root compartments of soil-grown rice using fluorescence microscopy and community fingerprinting of 16S rRNA genes. Vigorous washing detached 45% of the rhizoplane population compared to untreated roots. Additional sonication reduced rhizoplane-attached microorganisms by up to 78% but caused various degrees of root tissue destruction at all sonication intensities tested. Treatment with sodium hypochlorite almost completely (98%) removed rhizoplane-associated microbial cells. Community fingerprinting revealed that microbial communities obtained from untreated, washed, and sonicated roots were not statistically distinguishable. Hypochlorite-treated roots harbored communities significantly different from all other samples, likely representing true endospheric populations. Applying these procedures to other root samples (bean and clover) revealed that treatment efficiencies were strongly affected by root morphological parameters such as root hair density and rigidity of epidermis. Our findings suggest that a careful evaluation of separation strategies prior to molecular community analysis is indispensable, especially when endophytes are the subject of interest.}, }
@article {pmid27252683, year = {2016}, author = {Bezuidt, OK and Pierneef, R and Gomri, AM and Adesioye, F and Makhalanyane, TP and Kharroub, K and Cowan, DA}, title = {The Geobacillus Pan-Genome: Implications for the Evolution of the Genus.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {723}, pmid = {27252683}, issn = {1664-302X}, abstract = {The genus Geobacillus is comprised of a diverse group of spore-forming Gram-positive thermophilic bacterial species and is well known for both its ecological diversity and as a source of novel thermostable enzymes. Although the mechanisms underlying the thermophilicity of the organism and the thermostability of its macromolecules are reasonably well understood, relatively little is known of the evolutionary mechanisms, which underlie the structural and functional properties of members of this genus. In this study, we have compared 29 Geobacillus genomes, with a specific focus on the elements, which comprise the conserved core and flexible genomes. Based on comparisons of conserved core and flexible genomes, we present evidence of habitat delineation with specific Geobacillus genomes linked to specific niches. Our analysis revealed that Geobacillus and Anoxybacillus share a high proportion of genes. Moreover, the results strongly suggest that horizontal gene transfer is a major factor deriving the evolution of Geobacillus from Bacillus, with genetic contributions from other phylogenetically distant taxa.}, }
@article {pmid27252682, year = {2016}, author = {Ganigué, R and Sánchez-Paredes, P and Bañeras, L and Colprim, J}, title = {Low Fermentation pH Is a Trigger to Alcohol Production, but a Killer to Chain Elongation.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {702}, pmid = {27252682}, issn = {1664-302X}, abstract = {Gasification of organic wastes coupled to syngas fermentation allows the recovery of carbon in the form of commodity chemicals, such as carboxylates and biofuels. Acetogenic bacteria ferment syngas to mainly two-carbon compounds, although a few strains can also synthesize four-, and six-carbon molecules. In general, longer carbon chain products have a higher biotechnological (and commercial) value due to their higher energy content and their lower water solubility. However, de-novo synthesis of medium-chain products from syngas is quite uncommon in acetogenic bacteria. An alternative to de-novo synthesis is bioproduction of short-chain products (C2 and C4), and their subsequent elongation to C4, C6, or C8 through reversed β-oxidation metabolism. This two-step synergistic approach has been successfully applied for the production of up to C8 compounds, although the accumulation of alcohols in these mixed cultures remained below detection limits. The present work investigates the production of higher alcohols from syngas by open mixed cultures (OMC). A syngas-fermenting community was enriched from sludge of an anaerobic digester for a period of 109 days in a lab-scale reactor. At the end of this period, stable production of ethanol and butanol was obtained. C6 compounds were only transiently produced at the beginning of the enrichment phase, during which Clostridium kluyveri, a bacterium able to carry out carbon chain elongation, was detected in the community. Further experiments showed pH as a critical parameter to maintain chain elongation activity in the co-culture. Production of C6 compounds was recovered by preventing fermentation pH to decrease below pH 4.5-5. Finally, experiments showed maximal production of C6 compounds (0.8 g/L) and alcohols (1.7 g/L of ethanol, 1.1 g/L of butanol, and 0.6 g/L of hexanol) at pH 4.8. In conclusion, low fermentation pH is critical for the production of alcohols, although detrimental to C. kluyveri. Fine control of fermentation pH to final values around 4.8 could allow sustained production of higher alcohols.}, }
@article {pmid27252681, year = {2016}, author = {Propst, CN and Pylypko, SL and Blower, RJ and Ahmad, S and Mansoor, M and van Hoek, ML}, title = {Francisella philomiragia Infection and Lethality in Mammalian Tissue Culture Cell Models, Galleria mellonella, and BALB/c Mice.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {696}, pmid = {27252681}, issn = {1664-302X}, abstract = {Francisella (F.) philomiragia is a Gram-negative bacterium with a preference for brackish environments that has been implicated in causing bacterial infections in near-drowning victims. The purpose of this study was to characterize the ability of F. philomiragia to infect cultured mammalian cells, a commonly used invertebrate model, and, finally, to characterize the ability of F. philomiragia to infect BALB/c mice via the pulmonary (intranasal) route of infection. This study shows that F. philomiragia infects J774A.1 murine macrophage cells, HepG2 cells and A549 human Type II alveolar epithelial cells. However, replication rates vary depending on strain at 24 h. F. philomiragia infection after 24 h was found to be cytotoxic in human U937 macrophage-like cells and J774A.1 cells. This is in contrast to the findings that F. philomiragia was non-cytotoxic to human hepatocellular carcinoma cells, HepG2 cells and A549 cells. Differential cytotoxicity is a point for further study. Here, it was demonstrated that F. philomiragia grown in host-adapted conditions (BHI, pH 6.8) is sensitive to levofloxacin but shows increased resistance to the human cathelicidin LL-37 and murine cathelicidin mCRAMP when compared to related the Francisella species, F. tularensis subsp. novicida and F. tularensis subsp. LVS. Previous findings that LL-37 is strongly upregulated in A549 cells following F. tularensis subsp. novicida infection suggest that the level of antimicrobial peptide expression is not sufficient in cells to eradicate the intracellular bacteria. Finally, this study demonstrates that F. philomiragia is lethal in two in vivo models; Galleria mellonella via hemocoel injection, with a LD50 of 1.8 × 10(3), and BALB/c mice by intranasal infection, with a LD50 of 3.45 × 10(3). In conclusion, F. philomiragia may be a useful model organism to study the genus Francisella, particularly for those researchers with interest in studying microbial ecology or environmental strains of Francisella. Additionally, the Biosafety level 2 status of F. philomiragia makes it an attractive model for virulence and pathogenesis studies.}, }
@article {pmid27246046, year = {2016}, author = {Gosiewski, T and Mróz, T and Ochońska, D and Pabian, W and Bulanda, M and Brzychczy-Wloch, M}, title = {A study of the effects of therapeutic doses of ionizing radiation in vitro on Lactobacillus isolates originating from the vagina - a pilot study.}, journal = {BMC microbiology}, volume = {16}, number = {}, pages = {99}, pmid = {27246046}, issn = {1471-2180}, mesh = {Dose-Response Relationship, Radiation ; Female ; Gastrointestinal Tract/*microbiology ; Healthy Volunteers ; Humans ; Lactobacillus/classification/*isolation &amp; purification/*radiation effects ; Pilot Projects ; Radiation Dosage ; Radiation Tolerance ; Radiation, Ionizing ; Vagina/*microbiology ; }, abstract = {BACKGROUND: Ionizing radiation is used as a therapeutic option in the treatment of certain neoplastic lesions located, among others, in the pelvic region. The therapeutic doses of radiation employed often result in adverse effects manifesting themselves primarily in the form of genital tract infections in patients or diarrhea. The data available in the literature indicate disorders in the microbial ecosystem caused by ionizing radiation, which leads to the problems mentioned above. In the present study, we examined the influence of ionizing radiation on 52 selected strains of bacteria: Lactobacillus crispatus, L. fermentum, L. plantarum, L. reuteri, L. acidophilus L. amylovorus, L. casei, L. helveticus, L. paracasei, L. rhamnosus, L. salivarius and L. gasseri. This collection of Lactobacillus bacteria isolates of various species, obtained from the genital tract and gastrointestinal tract of healthy women, was tested for resistance to therapeutic doses of ionizing radiation.<br><br>RESULTS: The species studied, were isolated from the genital tract (n = 30) and from the anus (n = 22) of healthy pregnant women. Three doses of 3 Gy (fractionated dose) and 50 Gy (total dose of the whole radiotherapy cycle) were applied. The greatest differences in survival of the tested strains in comparison to the control group (not subjected to radiation) were observed at the dose of 50 Gy. However, the results were not statistically significant. Survival decrease to zero was not demonstrated for any of the tested strains.<br><br>CONCLUSIONS: Therapeutic doses of radiation do not affect the Lactobacillus bacteria significantly.}, }
@article {pmid27245598, year = {2016}, author = {Angel, R and Conrad, R and Dvorsky, M and Kopecky, M and Kotilínek, M and Hiiesalu, I and Schweingruber, F and Doležal, J}, title = {The Root-Associated Microbial Community of the World's Highest Growing Vascular Plants.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {394-406}, pmid = {27245598}, issn = {1432-184X}, mesh = {Bacteria/*classification/isolation &amp; purification ; Biomass ; Brassicaceae/classification/*microbiology ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; India ; Mycorrhizae/*classification/isolation &amp; purification ; Plant Roots/*microbiology ; Poaceae/classification/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Saussurea/classification/*microbiology ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {Upward migration of plants to barren subnival areas is occurring worldwide due to raising ambient temperatures and glacial recession. In summer 2012, the presence of six vascular plants, growing in a single patch, was recorded at an unprecedented elevation of 6150 m.a.s.l. close to the summit of Mount Shukule II in the Western Himalayas (Ladakh, India). Whilst showing multiple signs of stress, all plants have managed to establish stable growth and persist for several years. To learn about the role of microbes in the process of plant upward migration, we analysed the root-associated microbial community of the plants (three individuals from each) using microscopy and tagged amplicon sequencing. No mycorrhizae were found on the roots, implying they are of little importance to the establishment and early growth of the plants. However, all roots were associated with a complex bacterial community, with richness and diversity estimates similar or even higher than the surrounding bare soil. Both soil and root-associated communities were dominated by members of the orders Sphingomonadales and Sphingobacteriales, which are typical for hot desert soils, but were different from communities of temperate subnival soils and typical rhizosphere communities. Despite taxonomic similarity on the order level, the plants harboured a unique set of highly dominant operational taxonomic units which were not found in the bare soil. These bacteria have been likely transported with the dispersing seeds and became part of the root-associated community following germination. The results indicate that developing soils act not only as a source of inoculation to plant roots but also possibly as a sink for plant-associated bacteria.}, }
@article {pmid27245597, year = {2018}, author = {Cundell, AM}, title = {Microbial Ecology of the Human Skin.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {113-120}, pmid = {27245597}, issn = {1432-184X}, mesh = {Age Factors ; Anti-Bacterial Agents ; Axilla/microbiology ; Bacteria/classification/genetics ; Bacterial Physiological Phenomena ; *Biodiversity ; Cosmetics ; *Ecology ; *Ecosystem ; Fungi/classification/genetics/physiology ; Genes, Bacterial/genetics ; Genes, Fungal/genetics ; Health Status ; Homeostasis ; Humans ; Injections ; Microbiota/genetics/*physiology ; Perineum/microbiology ; RNA, Ribosomal, 16S/genetics ; Sex Factors ; Skin/*microbiology ; Toe Joint/microbiology ; Vaccination ; }, abstract = {This review article on the skin microbiota was written in response to recent advances that transitioned from culture methods to PCR amplification and sequencing of bacterial and fungal genes as a result of the Human Microbiome Project. This transition enables the investigation of the full diversity of microorganisms inhabiting human skin. The skin provides a range of habitats with different microbiota associated with the three major regions of the skin, namely the moist axilla, perineum, and toe webs; oily or sebaceous head, neck, and trunk; and dry forearms and legs. These new culture-independent tools are revealing the diversity of the human skin microbiota in the different locations of the body and with skin depth. These tools should lead to a better understanding of the state of homeostasis between the microbiota and the host and the overall functionality of that microbiota.}, }
@article {pmid27243334, year = {2016}, author = {Hamidat, M and Barakat, M and Ortet, P and Chanéac, C and Rose, J and Bottero, JY and Heulin, T and Achouak, W and Santaella, C}, title = {Design Defines the Effects of Nanoceria at a Low Dose on Soil Microbiota and the Potentiation of Impacts by the Canola Plant.}, journal = {Environmental science &amp; technology}, volume = {50}, number = {13}, pages = {6892-6901}, doi = {10.1021/acs.est.6b01056}, pmid = {27243334}, issn = {1520-5851}, mesh = {Microbiota ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Soils act as nanoceria sinks via agricultural spreading and surface waters. Canola plants were grown for one month in soil spiked with nanoceria (1 mg·kg(-1)). To define the role of nanomaterials design on environmental impacts, we studied nanoceria with different sizes (3.5 or 31 nm) and coating (citrate). We measured microbial activities involved in C, N, and P cycling in the rhizosphere and unplanted soil. Bacterial community structure was analyzed in unplanted soil, rhizosphere, and plant roots by 454-pyrosequencing of the 16S rRNA gene. This revealed an impact gradient dependent on nanomaterials design, ranging from decreased microbial enzymatic activities in planted soil to alterations in bacterial community structure in roots. Particle size/aggregation was a key parameter in modulating nanoceria effects on root communities. Citrate coating lowered the impact on microbial enzymatic activities but triggered variability in the bacterial community structure near the plant root. Some nanoceria favored taxa whose closest relatives are hydrocarbon-degrading bacteria and disadvantaged taxa frequently associated in consortia with disease-suppressive activity toward plant pathogens. This work provides a basis to determine outcomes of nanoceria in soil, at a dose close to predicted environmental concentrations, and to design them to minimize these impacts.}, }
@article {pmid27242772, year = {2016}, author = {Scandorieiro, S and de Camargo, LC and Lancheros, CA and Yamada-Ogatta, SF and Nakamura, CV and de Oliveira, AG and Andrade, CG and Duran, N and Nakazato, G and Kobayashi, RK}, title = {Synergistic and Additive Effect of Oregano Essential Oil and Biological Silver Nanoparticles against Multidrug-Resistant Bacterial Strains.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {760}, pmid = {27242772}, issn = {1664-302X}, abstract = {Bacterial resistance to conventional antibiotics has become a clinical and public health problem, making therapeutic decisions more challenging. Plant compounds and nanodrugs have been proposed as potential antimicrobial alternatives. Studies have shown that oregano (Origanum vulgare) essential oil (OEO) and silver nanoparticles have potent antibacterial activity, also against multidrug-resistant strains; however, the strong organoleptic characteristics of OEO and the development of resistance to these metal nanoparticles can limit their use. This study evaluated the antibacterial effect of a two-drug combination of biologically synthesized silver nanoparticles (bio-AgNP), produced by Fusarium oxysporum, and OEO against Gram-positive and Gram-negative bacteria, including multidrug-resistant strains. OEO and bio-AgNP showed bactericidal effects against all 17 strains tested, with minimal inhibitory concentrations (MIC) ranging from 0.298 to 1.193 mg/mL and 62.5 to 250 μM, respectively. Time-kill curves indicated that OEO acted rapidly (within 10 min), while the metallic nanoparticles took 4 h to kill Gram-negative bacteria and 24 h to kill Gram-positive bacteria. The combination of the two compounds resulted in a synergistic or additive effect, reducing their MIC values and reducing the time of action compared to bio-AgNP used alone, i.e., 20 min for Gram-negative bacteria and 7 h for Gram-positive bacteria. Scanning electron microscopy (SEM) revealed similar morphological alterations in Staphylococcus aureus (non-methicillin-resistant S. aureus, non-MRSA) cells exposed to three different treatments (OEO, bio-AgNP and combination of the two), which appeared cell surface blebbing. Individual and combined treatments showed reduction in cell density and decrease in exopolysaccharide matrix compared to untreated bacterial cells. It indicated that this composition have an antimicrobial activity against S. aureus by disrupting cells. Both compounds showed very low hemolytic activity, especially at MIC levels. This study describes for the first time the synergistic and additive interaction between OEO and bio-AgNP produced by F. oxysporum against multidrug-resistant bacteria, such as MRSA, and β-lactamase- and carbapenemase-producing Escherichia coli and Acinetobacter baumannii strains. These results indicated that this combination can be an alternative in the control of infections with few or no treatment options.}, }
@article {pmid27242746, year = {2016}, author = {Scoma, A and Boon, N}, title = {Osmotic Stress Confers Enhanced Cell Integrity to Hydrostatic Pressure but Impairs Growth in Alcanivorax borkumensis SK2.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {729}, pmid = {27242746}, issn = {1664-302X}, abstract = {Alcanivorax is a hydrocarbonoclastic genus dominating oil spills worldwide. While its presence has been detected in oil-polluted seawaters, marine sediment and salt marshes under ambient pressure, its presence in deep-sea oil-contaminated environments is negligible. Recent laboratory studies highlighted the piezosensitive nature of some Alcanivorax species, whose growth yields are highly impacted by mild hydrostatic pressures (HPs). In the present study, osmotic stress was used as a tool to increase HP resistance in the type strain Alcanivorax borkumensis SK2. Control cultures grown under standard conditions of salinity and osmotic pressure with respect to seawater (35.6 ppt or 1136 mOsm kg(-1), respectively) were compared with cultures subjected to hypo- and hyperosmosis (330 and 1720 mOsm kg(-1), or 18 and 62 ppt in salinity, equivalent to brackish and brine waters, respectively), under atmospheric or increased HP (0.1 and 10 MPa). Osmotic stress had a remarkably positive impact on cell metabolic activity in terms of CO2 production (thus, oil bioremediation) and O2 respiration under hyperosmosis, as acclimation to high salinity enhanced cell activity under 10 MPa by a factor of 10. Both osmotic shocks significantly enhanced cell protection by reducing membrane damage under HP, with cell integrities close to 100% under hyposmosis. The latter was likely due to intracellular water-reclamation as no trace of the piezolyte ectoine was found, contrary to hyperosmosis. Notably, ectoine production was equivalent at 0.1 MPa in hyperosmosis-acclimated cells and at 10 MPa under isosmotic conditions. While stimulating cell metabolism and enhancing cell integrity, osmotic stress had always a negative impact on culture growth and performance. No net growth was observed during 4-days incubation tests, and CO2:O2 ratios and pH values indicated that culture performance in terms of hydrocarbon degradation was lowered by the effects of osmotic stress alone or combined with increased HP. These findings confirm the piezosensitive nature of A. borkumensis, which lacks proper resistance mechanisms to improve its metabolic efficiency under increased HP, thus explaining its limited role in oil-polluted deep-sea environments.}, }
@article {pmid27242741, year = {2016}, author = {Trampe, EC and Larsen, JE and Glaring, MA and Stougaard, P and Kühl, M}, title = {In situ Dynamics of O2, pH, Light, and Photosynthesis in Ikaite Tufa Columns (Ikka Fjord, Greenland)-A Unique Microbial Habitat.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {722}, pmid = {27242741}, issn = {1664-302X}, abstract = {The Ikka Fjord (SW Greenland) harbors a unique microbial habitat in the form of several hundred submarine tufa columns composed of ikaite, a special hexahydrate form of calcium carbonate that precipitates when alkaline phosphate- and carbonate-enriched spring water seeping out of the sea floor meets cold seawater. While several unique heterotrophic microbes have been isolated from the tufa columns, the microbial activity, and the boundary conditions for microbial growth in ikaite have remained unexplored. We present the first detailed in situ characterization of the physico-chemical microenvironment and activity of oxygenic phototrophs thriving within the ikaite columns. In situ underwater microsensor measurements of pH, temperature, and irradiance in the porous ikaite crystal matrix, revealed an extreme microenvironment characterized by low temperatures, strong light attenuation, and gradients of pH changing from pH 9 at the outer column surface to above pH 10 over the first 1-2 cm of the ikaite. This outer layer of the freshly deposited ikaite matrix contained densely pigmented yellow and green zones harboring a diverse phototrophic community dominated by diatoms and cyanobacteria, respectively, as shown by amplicon sequencing. In situ O2 measurements, as well as underwater variable chlorophyll fluorescence measurements of photosynthetic activity, demonstrated high levels of oxygenic photosynthesis in this extreme gradient environment with strong irradiance-driven O2 dynamics ranging from anoxia to hyperoxic conditions in the ikaite matrix, albeit the local formation of gas bubbles buffered the day-night dynamics of O2 in the tufa columns. The microbial phototrophs in the ikaite matrix are embedded in exopolymers forming endolithic biofilms that may interact with mineral formation and cementing of ikaite crystals.}, }
@article {pmid27242706, year = {2016}, author = {Hu, YO and Karlson, B and Charvet, S and Andersson, AF}, title = {Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {679}, pmid = {27242706}, issn = {1664-302X}, abstract = {Microbial plankton form the productive base of both marine and freshwater ecosystems and are key drivers of global biogeochemical cycles of carbon and nutrients. Plankton diversity is immense with representations from all major phyla within the three domains of life. So far, plankton monitoring has mainly been based on microscopic identification, which has limited sensitivity and reproducibility, not least because of the numerical majority of plankton being unidentifiable under the light microscope. High-throughput sequencing of taxonomic marker genes offers a means to identify taxa inaccessible by traditional methods; thus, recent studies have unveiled an extensive previously unknown diversity of plankton. Here, we conducted ultra-deep Illumina sequencing (average 10(5) sequences/sample) of rRNA gene amplicons of surface water eukaryotic and bacterial plankton communities sampled in summer along a 2000 km transect following the salinity gradient of the Baltic Sea. Community composition was strongly correlated with salinity for both bacterial and eukaryotic plankton assemblages, highlighting the importance of salinity for structuring the biodiversity within this ecosystem. In contrast, no clear trends in alpha-diversity for bacterial or eukaryotic communities could be detected along the transect. The distribution of major planktonic taxa followed expected patterns as observed in monitoring programs, but groups novel to the Baltic Sea were also identified, such as relatives to the coccolithophore Emiliana huxleyi detected in the northern Baltic Sea. This study provides the first ultra-deep sequencing-based survey on eukaryotic and bacterial plankton biogeography in the Baltic Sea.}, }
@article {pmid27242686, year = {2016}, author = {Beckers, B and Op De Beeck, M and Thijs, S and Truyens, S and Weyens, N and Boerjan, W and Vangronsveld, J}, title = {Performance of 16s rDNA Primer Pairs in the Study of Rhizosphere and Endosphere Bacterial Microbiomes in Metabarcoding Studies.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {650}, pmid = {27242686}, issn = {1664-302X}, abstract = {Next-generation sequencing technologies have revolutionized the methods for studying microbial ecology by enabling high-resolution community profiling. However, the use of these technologies in unraveling the plant microbiome remains challenging. Many bacterial 16S rDNA primer pairs also exhibit high affinity for non-target DNA such as plastid (mostly chloroplast) DNA and mitochondrial DNA. Therefore, we experimentally tested a series of commonly used primers for the analysis of plant-associated bacterial communities using 454 pyrosequencing. We evaluated the performance of all selected primer pairs in the study of the bacterial microbiomes present in the rhizosphere soil, root, stem and leaf endosphere of field-grown poplar trees (Populus tremula × Populus alba) based on (a) co-amplification of non-target DNA, (b) low amplification efficiency for pure chloroplast DNA (real-time PCR), (c) high retrieval of bacterial 16S rDNA, (d) high operational taxonomic unit (OTU) richness and Inverse Simpson diversity and (e) taxonomic assignment of reads. Results indicate that experimental evaluation of primers provide valuable information that could contribute in the selection of suitable primer pairs for 16S rDNA metabarcoding studies in plant-microbiota research. Furthermore, we show that primer pair 799F-1391R outperforms all other primer pairs in our study in the elimination of non-target DNA and retrieval of bacterial OTUs.}, }
@article {pmid27242680, year = {2016}, author = {Le Roux, X and Bouskill, NJ and Niboyet, A and Barthes, L and Dijkstra, P and Field, CB and Hungate, BA and Lerondelle, C and Pommier, T and Tang, J and Terada, A and Tourna, M and Poly, F}, title = {Predicting the Responses of Soil Nitrite-Oxidizers to Multi-Factorial Global Change: A Trait-Based Approach.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {628}, pmid = {27242680}, issn = {1664-302X}, abstract = {Soil microbial diversity is huge and a few grams of soil contain more bacterial taxa than there are bird species on Earth. This high diversity often makes predicting the responses of soil bacteria to environmental change intractable and restricts our capacity to predict the responses of soil functions to global change. Here, using a long-term field experiment in a California grassland, we studied the main and interactive effects of three global change factors (increased atmospheric CO2 concentration, precipitation and nitrogen addition, and all their factorial combinations, based on global change scenarios for central California) on the potential activity, abundance and dominant taxa of soil nitrite-oxidizing bacteria (NOB). Using a trait-based model, we then tested whether categorizing NOB into a few functional groups unified by physiological traits enables understanding and predicting how soil NOB respond to global environmental change. Contrasted responses to global change treatments were observed between three main NOB functional types. In particular, putatively mixotrophic Nitrobacter, rare under most treatments, became dominant under the 'High CO2+Nitrogen+Precipitation' treatment. The mechanistic trait-based model, which simulated ecological niches of NOB types consistent with previous ecophysiological reports, helped predicting the observed effects of global change on NOB and elucidating the underlying biotic and abiotic controls. Our results are a starting point for representing the overwhelming diversity of soil bacteria by a few functional types that can be incorporated into models of terrestrial ecosystems and biogeochemical processes.}, }
@article {pmid27240932, year = {2016}, author = {Gänzle, M and Ripari, V}, title = {Composition and function of sourdough microbiota: From ecological theory to bread quality.}, journal = {International journal of food microbiology}, volume = {239}, number = {}, pages = {19-25}, doi = {10.1016/j.ijfoodmicro.2016.05.004}, pmid = {27240932}, issn = {1879-3460}, mesh = {Bread/*microbiology ; Ecology ; Edible Grain/*microbiology ; Fermentation ; Flour/microbiology ; *Food Microbiology ; Lactobacillus/*classification/*metabolism ; *Microbiota ; }, abstract = {Sourdough has traditionally been used as leavening agent in artisanal baking. The production of baked and steamed cereal products increasingly employs sourdough as baking improver to achieve improved bread quality, or to obtain "clean label" products. Sourdoughs are maintained in bakeries by continuous propagation; composition and metabolic activity of sourdough microbiota and their impact on bread quality are therefore shaped by processing parameters and fermentation substrates. The diversity of fermentation processes leads to diverse compositions of sourdough microbiota. This communication explores whether concepts in community assembly support an improved understanding of the microbial ecology of sourdough. Community assembly is determined by diversification, drift, dispersal, and selection. Evidence for diversification in sourdoughs is inconclusive. Drift has been shown to shape sourdough microbiota only in specific cases. Increasing knowledge on the primary habitat of sourdough lactobacilli indicates that dispersal (limitation) is an important determinant in sourdoughs that are propagated only for short periods of time. In contrast, selection of adapted organisms mainly determines the microbiota of sourdoughs that are propagated for a long time. Bacterial metabolic traits that determine competitiveness in sourdough fermentation, i.e. effective use of maltose, exopolysaccharide formation from sucrose, the use of electron acceptors by heterofermentative lactic acid bacteria, and acid resistance mediated by arginine and glutamine conversion, also determine bread quality. The concepts in community assembly thus provide a valuable tool to understand the influence of the technology of sourdough fermentation on microbial ecology and on bread quality.}, }
@article {pmid27240745, year = {2016}, author = {Bag, S and Saha, B and Mehta, O and Anbumani, D and Kumar, N and Dayal, M and Pant, A and Kumar, P and Saxena, S and Allin, KH and Hansen, T and Arumugam, M and Vestergaard, H and Pedersen, O and Pereira, V and Abraham, P and Tripathi, R and Wadhwa, N and Bhatnagar, S and Prakash, VG and Radha, V and Anjana, RM and Mohan, V and Takeda, K and Kurakawa, T and Nair, GB and Das, B}, title = {An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {26775}, pmid = {27240745}, issn = {2045-2322}, mesh = {DNA/*isolation &amp; purification ; DNA, Bacterial/isolation &amp; purification ; Genome, Microbial ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Soil Microbiology ; }, abstract = {To explore the natural microbial community of any ecosystems by high-resolution molecular approaches including next generation sequencing, it is extremely important to develop a sensitive and reproducible DNA extraction method that facilitate isolation of microbial DNA of sufficient purity and quantity from culturable and uncultured microbial species living in that environment. Proper lysis of heterogeneous community microbial cells without damaging their genomes is a major challenge. In this study, we have developed an improved method for extraction of community DNA from different environmental and human origin samples. We introduced a combination of physical, chemical and mechanical lysis methods for proper lysis of microbial inhabitants. The community microbial DNA was precipitated by using salt and organic solvent. Both the quality and quantity of isolated DNA was compared with the existing methodologies and the supremacy of our method was confirmed. Maximum recovery of genomic DNA in the absence of substantial amount of impurities made the method convenient for nucleic acid extraction. The nucleic acids obtained using this method are suitable for different downstream applications. This improved method has been named as the THSTI method to depict the Institute where the method was developed.}, }
@article {pmid27236402, year = {2016}, author = {Lin, Q and De Vrieze, J and He, G and Li, X and Li, J}, title = {Temperature regulates methane production through the function centralization of microbial community in anaerobic digestion.}, journal = {Bioresource technology}, volume = {216}, number = {}, pages = {150-158}, doi = {10.1016/j.biortech.2016.05.046}, pmid = {27236402}, issn = {1873-2976}, mesh = {Anaerobiosis ; Animals ; Bacteria/*metabolism ; Biofuels ; Bioreactors/microbiology ; Cluster Analysis ; Fatty Acids, Volatile/analysis ; Manure ; Metabolic Networks and Pathways ; Methane/*biosynthesis ; Phylogeny ; Swine ; *Temperature ; }, abstract = {Temperature is crucial for the performance of anaerobic digestion process. In this study of anaerobic digestion of swine manure, the relationship between the microbial gene expression and methane production at different temperatures (25-55°C) was revealed through metatranscriptomic analysis. Daily methane production and total biogas production increased with temperature up to 50°C, but decreased at 55°C. The functional gene expression showed great variation at different temperatures. The function centralization (opposite to alpha-diversity), assessed by the least proportions of functional pathways contributing for at least 50% of total reads positively correlated to methane production. Temperature regulated methane production probably through reducing the diversity of functional pathways, but enhancing central functional pathways, so that most of cellular activities and resource were invested in methanogenesis and related pathways, enhancing the efficiency of conversion of substrates to methane. This research demonstrated the importance of function centralization for efficient system functioning.}, }
@article {pmid27235444, year = {2016}, author = {Wang, X and Wen, X and Deng, Y and Xia, Y and Yang, Y and Zhou, J}, title = {Distance-Decay Relationship for Biological Wastewater Treatment Plants.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {16}, pages = {4860-4866}, pmid = {27235444}, issn = {1098-5336}, mesh = {Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; Bioreactors/*microbiology ; China ; Fungi/genetics/*metabolism ; Oligonucleotide Array Sequence Analysis ; Waste Disposal, Fluid ; Wastewater/*microbiology ; }, abstract = {UNLABELLED: Patterns in the spatial distribution of organisms provide important information about mechanisms underlying biodiversity and the complexity of ecosystems. One of the most well-documented spatial patterns is the distance-decay relationship, which is a universal biogeographic pattern observed repeatedly for plant and animal communities, particularly for microorganisms in natural ecosystems such as soil, ocean, and salt marsh sediment. However, it is uncertain whether the microorganisms exhibit a distance-decay pattern in engineered ecosystems. Therefore, we measured the distance-decay relationship across various microbial functional and phylogenetic groups in 26 biological wastewater treatment plants (WWTPs) in China using a functional gene array (GeoChip 4.2). We found that microbial communities of activated sludge in WWTPs exhibited a significant but very weak distance-decay relationship. The taxon-area z values for different functional and phylogenetic groups were <0.0065, which is about 1 to 2 orders of magnitude lower than those observed in microbial communities elsewhere. Variation-partitioning analysis (VPA) showed that the relationships were driven by both environmental heterogeneity and geographic distance. Collectively, these results provided new insights into the spatial scaling of microbial communities in engineering ecosystems and highlighted the importance of environmental heterogeneity and geographic distance in shaping biogeographic patterns.<br><br>IMPORTANCE: Determining the distance-decay relationship of microbial biodiversity is important but challenging in microbial ecology. All studies to date are based on natural environments; thus, it remains unclear whether there is such a relationship in an engineered ecosystem. The present study shows that there is a very weak distance-decay relationship in an engineered ecosystem (WWTPs) at the regional-to-continental scale. This study makes fundamental contributions to a mechanistic, predictive understanding of microbial biogeography.}, }
@article {pmid27235442, year = {2016}, author = {Sedlacek, CJ and Nielsen, S and Greis, KD and Haffey, WD and Revsbech, NP and Ticak, T and Laanbroek, HJ and Bollmann, A}, title = {Effects of Bacterial Community Members on the Proteome of the Ammonia-Oxidizing Bacterium Nitrosomonas sp. Strain Is79.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {15}, pages = {4776-4788}, pmid = {27235442}, issn = {1098-5336}, support = {S10 RR027015/RR/NCRR NIH HHS/United States ; }, mesh = {Ammonia/*metabolism ; Bacterial Proteins/genetics/metabolism ; Coculture Techniques ; Heterotrophic Processes ; Nitrites/metabolism ; Nitrobacter/genetics/*metabolism ; Nitrosomonas/genetics/*growth &amp; development/*metabolism ; Proteome/*genetics/metabolism ; }, abstract = {UNLABELLED: Microorganisms in the environment do not exist as the often-studied pure cultures but as members of complex microbial communities. Characterizing the interactions within microbial communities is essential to understand their function in both natural and engineered environments. In this study, we investigated how the presence of a nitrite-oxidizing bacterium (NOB) and heterotrophic bacteria affect the growth and proteome of the chemolithoautotrophic ammonia-oxidizing bacterium (AOB) Nitrosomonas sp. strain Is79. We investigated Nitrosomonas sp. Is79 in co-culture with Nitrobacter winogradskyi, in co-cultures with selected heterotrophic bacteria, and as a member of the nitrifying enrichment culture G5-7. In batch culture, N. winogradskyi and heterotrophic bacteria had positive effects on the growth of Nitrosomonas sp. Is79. An isobaric tag for relative and absolute quantification (iTRAQ) liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach was used to investigate the effect of N. winogradskyi and the co-cultured heterotrophic bacteria from G5-7 on the proteome of Nitrosomonas sp. Is79. In co-culture with N. winogradskyi, several Nitrosomonas sp. Is79 oxidative stress response proteins changed in abundance, with periplasmic proteins increasing and cytoplasmic proteins decreasing in abundance. In the presence of heterotrophic bacteria, the abundance of proteins directly related to the ammonia oxidation pathway increased, while the abundance of proteins related to amino acid synthesis and metabolism decreased. In summary, the proteome of Nitrosomonas sp. Is79 was differentially influenced by the presence of either N. winogradskyi or heterotrophic bacteria. Together, N. winogradskyi and heterotrophic bacteria reduced the oxidative stress for Nitrosomonas sp. Is79, which resulted in more efficient metabolism.<br><br>IMPORTANCE: Aerobic ammonia-oxidizing microorganisms play an important role in the global nitrogen cycle, converting ammonia to nitrite. In their natural environment, they coexist and interact with nitrite oxidizers, which convert nitrite to nitrate, and with heterotrophic microorganisms. The presence of nitrite oxidizers and heterotrophic bacteria has a positive influence on the growth of the ammonia oxidizers. Here, we present a study investigating the effect of nitrite oxidizers and heterotrophic bacteria on the proteome of a selected ammonia oxidizer in a defined culture to elucidate how these two groups improve the performance of the ammonia oxidizer. The results show that the presence of a nitrite oxidizer and heterotrophic bacteria reduced the stress for the ammonia oxidizer and resulted in more efficient energy generation. This study contributes to our understanding of microbe-microbe interactions, in particular between ammonia oxidizers and their neighboring microbial community.}, }
@article {pmid27234003, year = {2016}, author = {Cardini, U and van Hoytema, N and Bednarz, VN and Rix, L and Foster, RA and Al-Rshaidat, MM and Wild, C}, title = {Microbial dinitrogen fixation in coral holobionts exposed to thermal stress and bleaching.}, journal = {Environmental microbiology}, volume = {18}, number = {8}, pages = {2620-2633}, doi = {10.1111/1462-2920.13385}, pmid = {27234003}, issn = {1462-2920}, mesh = {Animals ; *Anthozoa/metabolism/microbiology/parasitology ; Bacteria/growth &amp; development/*metabolism ; Dinoflagellida/growth &amp; development/*metabolism ; Global Warming ; Heterotrophic Processes ; Hot Temperature ; Microbiota/physiology ; Nitrogen Fixation/*physiology ; Photosynthesis/physiology ; Stress, Physiological/physiology ; Symbiosis/physiology ; }, abstract = {Coral holobionts (i.e., coral-algal-prokaryote symbioses) exhibit dissimilar thermal sensitivities that may determine which coral species will adapt to global warming. Nonetheless, studies simultaneously investigating the effects of warming on all holobiont members are lacking. Here we show that exposure to increased temperature affects key physiological traits of all members (herein: animal host, zooxanthellae and diazotrophs) of both Stylophora pistillata and Acropora hemprichii during and after thermal stress. S. pistillata experienced severe loss of zooxanthellae (i.e., bleaching) with no net photosynthesis at the end of the experiment. Conversely, A. hemprichii was more resilient to thermal stress. Exposure to increased temperature (+ 6°C) resulted in a drastic increase in daylight dinitrogen (N2) fixation, particularly in A. hemprichii (threefold compared with controls). After the temperature was reduced again to in situ levels, diazotrophs exhibited a reversed diel pattern of activity, with increased N2 fixation rates recorded only in the dark, particularly in bleached S. pistillata (twofold compared to controls). Concurrently, both animal hosts, but particularly bleached S. pistillata, reduced both organic matter release and heterotrophic feeding on picoplankton. Our findings indicate that physiological plasticity by coral-associated diazotrophs may play an important role in determining the response of coral holobionts to ocean warming.}, }
@article {pmid27233797, year = {2016}, author = {Trautwein, K and Will, SE and Hulsch, R and Maschmann, U and Wiegmann, K and Hensler, M and Michael, V and Ruppersberg, H and Wünsch, D and Feenders, C and Neumann-Schaal, M and Kaltenhäuser, S and Ulbrich, M and Schmidt-Hohagen, K and Blasius, B and Petersen, J and Schomburg, D and Rabus, R}, title = {Native plasmids restrict growth of Phaeobacter inhibens DSM 17395: Energetic costs of plasmids assessed by quantitative physiological analyses.}, journal = {Environmental microbiology}, volume = {18}, number = {12}, pages = {4817-4829}, doi = {10.1111/1462-2920.13381}, pmid = {27233797}, issn = {1462-2920}, mesh = {Amino Acids/metabolism ; Energy Metabolism ; *Plasmids ; Replicon ; Rhodobacteraceae/*genetics/growth &amp; development ; Roseobacter/genetics ; }, abstract = {Plasmid carriage is associated with energetic costs, and thus only those plasmids providing fitness benefits are stably maintained in the host lineage. Marine bacteria of the Roseobacter clade harbor up to 11 extrachromosomal replicons, adding lifestyle-relevant and possibly habitat success-promoting functions to their genomic repertoire. Phaeobacter inhibens DSM 17395 is a nutritionally versatile representative, carrying three stable and functionally distinct plasmids (65, 78, and 262 kb). The present study investigates the physiological and energetic consequences of plasmid carriage in P. inhibens DSM 17395, employing mutants cured from all native plasmids in every possible combination (seven different). Cultivation in process-controlled bioreactors with casamino acids as organic substrate revealed a complex physiological response, suggesting existence of functional interconnections between the replicons. Deletion of the 262 kb plasmid boosted growth rate (>3-fold) and growth efficiency (yields for carbon, O2 and CO2), which was not observed for the 65 or 78 kb plasmid. Carriage of the 262 kb plasmid was most costly for the wild type, i.e. contributing ∼50% to its energetic (dissimilatory) expenditures. Cost-benefit analysis of plasmid carriage reflects the high value of plasmids for niche specialization of P. inhibens DSM 17395 and most likely also for related Phaeobacter species.}, }
@article {pmid27231649, year = {2016}, author = {Trubl, G and Solonenko, N and Chittick, L and Solonenko, SA and Rich, VI and Sullivan, MB}, title = {Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e1999}, pmid = {27231649}, issn = {2167-8359}, abstract = {Permafrost stores approximately 50% of global soil carbon (C) in a frozen form; it is thawing rapidly under climate change, and little is known about viral communities in these soils or their roles in C cycling. In permafrost soils, microorganisms contribute significantly to C cycling, and characterizing them has recently been shown to improve prediction of ecosystem function. In other ecosystems, viruses have broad ecosystem and community impacts ranging from host cell mortality and organic matter cycling to horizontal gene transfer and reprogramming of core microbial metabolisms. Here we developed an optimized protocol to extract viruses from three types of high organic-matter peatland soils across a permafrost thaw gradient (palsa, moss-dominated bog, and sedge-dominated fen). Three separate experiments were used to evaluate the impact of chemical buffers, physical dispersion, storage conditions, and concentration and purification methods on viral yields. The most successful protocol, amended potassium citrate buffer with bead-beating or vortexing and BSA, yielded on average as much as 2-fold more virus-like particles (VLPs) g(-1) of soil than other methods tested. All method combinations yielded VLPs g(-1) of soil on the 10(8) order of magnitude across all three soil types. The different storage and concentration methods did not yield significantly more VLPs g(-1) of soil among the soil types. This research provides much-needed guidelines for resuspending viruses from soils, specifically carbon-rich soils, paving the way for incorporating viruses into soil ecology studies.}, }
@article {pmid27228676, year = {2016}, author = {Gapon, MN and Ternovskaya, LN}, title = {[DETECTION OF DEGREE OF MICROECOLOGICAL DISTURBANCE OF INTESTINE BASED ON CALCULATION OF LOCAL ANTIOXIDANT INDEX].}, journal = {Zhurnal mikrobiologii, epidemiologii i immunobiologii}, volume = {}, number = {2}, pages = {80-84}, pmid = {27228676}, issn = {0372-9311}, mesh = {Adult ; Antioxidants/*metabolism ; Catalase/metabolism ; Dysbiosis/*metabolism/microbiology/pathology ; Feces/microbiology ; Female ; Humans ; Intestines/*microbiology/pathology ; Male ; Malondialdehyde/metabolism ; Middle Aged ; Probiotics/metabolism ; Superoxide Dismutase/metabolism ; Superoxide Dismutase-1 ; }, abstract = {AIM: Evaluation of dysbiotic condition of intestine based on determination of local antioxidant index (LAI).<br><br>MATERIALS AND METHODS: 155 patients with bacteriologically confirmed intestine dysbacteriosis were examined: 20 individuals with normobiocenosis of the intestine served as control. Feces dilution 10&#x207b;&#xb2; was used for biochemical study. Catalase, superoxide-dismutase activity and level of malonic dialdehyde was evaluated photometrically by the value of optical density of the samples. Microbial landscape of feces was studied by a bacteriologic method with parallel determination in samples of coprofiltrates of activity of the indicated enzymes and content of malonic dialdehyde. Evaluation of disturbances of microecology of the intestine was carried out by a biochemical method by calculating local antioxidant index in juxtaposition with microbial map data.<br><br>RESULTS: LAI parameter was significantly higher than 20 in coprofiltrates of people with intestine normobiocenosis. In patients with detected intestine dysbacteriosis, depending on its degree, LAI parameter, changes were registered in the range from negative to 20. Dysbacteriosis in a part of patients had a prolonged character, LAI was lower than 14, that reflected the presence of a persistent inflammation. A tendency of normalization of microbial ecology and growth of LAI was observed during administration of a probiotic preparation.<br><br>CONCLUSION: A screening criteria is proposed, that differentiates the degree of severity of intestine dysbacteriosis based on calculation of local antioxidant index.}, }
@article {pmid27226224, year = {2017}, author = {Weller-Stuart, T and Toth, I and De Maayer, P and Coutinho, T}, title = {Swimming and twitching motility are essential for attachment and virulence of Pantoea ananatis in onion seedlings.}, journal = {Molecular plant pathology}, volume = {18}, number = {5}, pages = {734-745}, pmid = {27226224}, issn = {1364-3703}, mesh = {Bacterial Proteins/metabolism ; Fimbriae Proteins/metabolism ; Flagella/metabolism ; Onions/*microbiology ; Pantoea/*pathogenicity ; Plant Diseases/microbiology ; Seedlings/*microbiology ; Virulence ; }, abstract = {Pantoea ananatis is a widespread phytopathogen with a broad host range. Despite its ability to infect economically important crops, such as maize, rice and onion, relatively little is known about how this bacterium infects and colonizes host tissue or spreads within and between hosts. To study the role of motility in pathogenicity, we analysed both swimming and twitching motility in P. ananatis LMG 20103. Genetic recombineering was used to construct four mutants affected in motility. Two flagellar mutants were disrupted in the flgK and motA genes, required for flagellar assembly and flagellar rotation, respectively. Similarly, two twitching motility mutants were generated, impaired in the structure (pilA) and functioning (pilT) of the type IV pili. The role of swimming and twitching motility during the infection cycle of P. ananatis in onion seedlings was determined by comparing the mutant- and wild-type strains using several in vitro and in planta assays. From the results obtained, it was evident that flagella aid P. ananatis in locating and attaching to onion leaf surfaces, as well as in pathogenicity, whereas twitching motility is instrumental in the spread of the bacteria on the surface once attachment has occurred. Both swimming and twitching motility contribute towards the ability of P. ananatis to cause disease in onions.}, }
@article {pmid27221091, year = {2016}, author = {Kayee, P and Sonthiphand, P and Rongsayamanont, C and Limpiyakorn, T}, title = {Retraction Note to: Archaeal amoA Genes Outnumber Bacterial amoA Genes in Municipal Wastewater Treatment Plants in Bangkok.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {262}, doi = {10.1007/s00248-016-0794-9}, pmid = {27221091}, issn = {1432-184X}, }
@article {pmid27221090, year = {2016}, author = {Kerfahi, D and Tripathi, BM and Dong, K and Go, R and Adams, JM}, title = {Rainforest Conversion to Rubber Plantation May Not Result in Lower Soil Diversity of Bacteria, Fungi, and Nematodes.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {359-371}, pmid = {27221090}, issn = {1432-184X}, mesh = {Animals ; Bacteria/*classification/isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; DNA, Helminth/genetics ; Fungi/*classification/isolation &amp; purification ; Malaysia ; Nematoda/*isolation &amp; purification ; *Rainforest ; Rubber ; Sequence Analysis, DNA ; Soil/chemistry/*parasitology ; *Soil Microbiology ; }, abstract = {Large areas of rainforest in Asia have been converted to plantations, with uncertain effects on soil biodiversity. Using standard metagenetic methods, we compared the soil biota of bacteria, fungi, and nematodes at three rainforest sites in Malaysia with two rubber plantation sites with similar soils and geology. We predicted the following: (1) that the rubber sites would have a lower α- and β-diversity than the rainforest sites, due to the monospecific canopy cover and intensive management with herbicides, pesticides, and fertilizers, and (2) that due to differences in the physical and biotic environment associated with cultivation, there would be distinct communities of bacteria, fungi, and nematodes. However, regarding (1), the results showed no consistent difference in α- and β-diversity of bacteria, fungi, or nematodes between rainforest and rubber plantation sites. It appears that conversion of rainforest to rubber plantations does not necessarily result in a decrease in diversity of soil biota. It may be that heterogeneity associated with the cultivation regimen compensates for loss of biotically imposed heterogeneity of the original rainforest. Regarding (2), as predicted there were statistically significant differences in community composition between rainforest and rubber plantation for bacteria, fungi, and nematodes. These differences could be related to a range of factors including light level, litter fall composition, pH, C and N, selecting a distinct set of soil taxa, and it is possible that this in itself would affect long-term soil function.}, }
@article {pmid27220974, year = {2016}, author = {Pylro, VS and Morais, DK and de Oliveira, FS and Dos Santos, FG and Lemos, LN and Oliveira, G and Roesch, LF}, title = {BMPOS: a Flexible and User-Friendly Tool Sets for Microbiome Studies.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {443-447}, pmid = {27220974}, issn = {1432-184X}, mesh = {Bacteriological Techniques ; Brazil ; Databases, Genetic ; Genetic Markers ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; *Microbiota ; Phylogeny ; Sequence Analysis, DNA ; *Software ; }, abstract = {Recent advances in science and technology are leading to a revision and re-orientation of methodologies, addressing old and current issues under a new perspective. Advances in next generation sequencing (NGS) are allowing comparative analysis of the abundance and diversity of whole microbial communities, generating a large amount of data and findings at a systems level. The current limitation for biologists has been the increasing demand for computational power and training required for processing of NGS data. Here, we describe the deployment of the Brazilian Microbiome Project Operating System (BMPOS), a flexible and user-friendly Linux distribution dedicated to microbiome studies. The Brazilian Microbiome Project (BMP) has developed data analyses pipelines for metagenomic studies (phylogenetic marker genes), conducted using the two main high-throughput sequencing platforms (Ion Torrent and Illumina MiSeq). The BMPOS is freely available and possesses the entire requirement of bioinformatics packages and databases to perform all the pipelines suggested by the BMP team. The BMPOS may be used as a bootable live USB stick or installed in any computer with at least 1 GHz CPU and 512 MB RAM, independent of the operating system previously installed. The BMPOS has proved to be effective for sequences processing, sequences clustering, alignment, taxonomic annotation, statistical analysis, and plotting of metagenomic data. The BMPOS has been used during several metagenomic analyses courses, being valuable as a tool for training, and an excellent starting point to anyone interested in performing metagenomic studies. The BMPOS and its documentation are available at http://www.brmicrobiome.org .}, }
@article {pmid27216530, year = {2016}, author = {Song, L and Li, L}, title = {Variations in Bacterial Community in a Temperate Lake Associated with an Agricultural Watershed.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {277-286}, pmid = {27216530}, issn = {1432-184X}, mesh = {Agriculture ; Bacteria/classification/*growth &amp; development ; Biodiversity ; Burkholderiaceae/growth &amp; development ; Carbon/analysis ; DNA, Bacterial/isolation &amp; purification ; Environmental Monitoring ; Hydrogen-Ion Concentration ; Lakes/*chemistry/*microbiology ; Michigan ; Multivariate Analysis ; Mycobacterium/growth &amp; development ; Nitrates/analysis ; Rain ; Seasons ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Terrestrially derived carbon and nutrients are washed into lakes, providing nutritional drivers for both microbial heterotrophy and phototrophy. Changes in the quantity and diversity of carbon and nutrients exported from watersheds in response to alterations in long-term land use have led to a need for evaluation of the linkage between watershed-exported carbon and nutrients and bacterial community structure in watershed associated lakes. To learn more about these interactions, we investigated Muskrat Lake in Michigan, which has a well-defined moderately sized watershed dominated by agriculture. We measured the water chemistry, characterized the dissolved organic carbon, and determined the structure of the bacterial communities at the inlet and center of this lake (five depths per site) over the summer and fall of 2008. The lake had temporal and rain event-based fluctuations in water chemistry, as well as temporal and rain event-dependent shifts in bacterial communities as measured by terminal restriction fragment length polymorphism. Agricultural watershed inputs were observed in the lake during and after rain events. Terminal restriction fragment length polymorphism and 454 pyrosequencing of the bacterial communities indicated that there were differences over time and that the dominant phylotypes shifted between summer and late fall. Some populations (e.g., Polynucleobacter and Mycobacterium) increased during fall, while others (e.g., Gemmatimonas) diminished. Redundancy and partitioning analyses showed that water chemistry is highly correlated with variations in the bacterial community of the lake, which explained 34 % of the variations in the bacterial community. Dissolved organic carbon had the greatest effects on variations in the Muskrat Lake bacterial community (2 %). The results of this study provide information that will enable a better understanding of the interaction between the bacterial community of lakes and changes in chemical properties as a result of nutrient importation from the surrounding watershed.}, }
@article {pmid27214259, year = {2016}, author = {Bosmans, L and Van Calenberge, B and Paeleman, A and Moerkens, R and Wittemans, L and Van Kerckhove, S and De Mot, R and Lievens, B and Rediers, H}, title = {Efficacy of hydrogen peroxide treatment for control of hairy root disease caused by rhizogenic agrobacteria.}, journal = {Journal of applied microbiology}, volume = {121}, number = {2}, pages = {519-527}, doi = {10.1111/jam.13187}, pmid = {27214259}, issn = {1365-2672}, mesh = {Agrobacterium/*drug effects/*physiology ; Biofilms/drug effects ; Catalase/metabolism ; Europe ; Hydrogen Peroxide/*pharmacology ; Solanum lycopersicum/microbiology ; Plant Diseases/*microbiology/prevention &amp; control ; Plant Roots/microbiology ; }, abstract = {AIMS: Rhizogenic Agrobacterium strains are the causative agent of hairy root disease (HRD), an increasing problem in the hydroponic cultivation of tomato and cucumber in Europe. A previous study has demonstrated that different lineages of rhizogenic agrobacteria are able to form biofilms. Although hydrogen peroxide (H2 O2) is a frequently used biocide in hydroponic systems, until now its effectiveness to remove rhizogenic agrobacteria has not been unequivocally demonstrated. Therefore, the main objective of this study was to assess the efficacy of H2 O2 in controlling Agrobacterium-containing biofilms.<br><br>METHODS AND RESULTS: Using lab-scale experiments, we found a huge variation between different rhizogenic Agrobacterium strains in EC50 values, ranging from 18&#xb7;8 to 600&#xa0;ppm H2 O2 , representing the lowest and highest concentration tested respectively. Using pilot-scale experiments in which different H2 O2 concentrations were tested, treatment with 25&#xa0;ppm H2 O2 was found to be ineffective. In contrast, treatment with 50&#xa0;ppm significantly affected a catalase-negative Agrobacterium population, while a catalase-positive population was only marginally affected. For the catalase-positive Agrobacterium population, a treatment of 100&#xa0;ppm H2 O2 was required to be effective. Finally, H2 O2 treatment of HRD in two commercial greenhouses was monitored, and showed that the H2 O2 concentration decreased considerably towards the end of the irrigation circuits. Further, a clear correlation was found between the actual concentration of H2 O2 and the incidence of HRD.<br><br>CONCLUSION: We showed that H2 O2 may be effective to reduce biofilm formation by rhizogenic bacteria. Nevertheless, it was clear from our results that the required H2 O2 concentration depends on the particular Agrobacterium strain(s) present in the greenhouse.<br><br>This is the first study that examined the effectiveness of H2 O2 to control HRD in hydroponic systems, and the effect of catalase activity on H2 O2 effectiveness. Our study has direct relevance for the highly intensive horticultural sector.}, }
@article {pmid27211691, year = {2016}, author = {Hachicha Hbaieb, R and Kotti, F and Cortes-Francisco, N and Caixach, J and Gargouri, M and Vichi, S}, title = {Ripening and storage conditions of Chétoui and Arbequina olives: Part II. Effect on olive endogenous enzymes and virgin olive oil secoiridoid profile determined by high resolution mass spectrometry.}, journal = {Food chemistry}, volume = {210}, number = {}, pages = {631-639}, doi = {10.1016/j.foodchem.2016.05.026}, pmid = {27211691}, issn = {1873-7072}, mesh = {Catechol Oxidase/analysis/metabolism ; Food Preservation/*methods ; Fruit/*enzymology/*growth &amp; development ; Iridoids/*analysis ; Mass Spectrometry/methods ; *Olea ; Olive Oil/*chemistry ; Oxidation-Reduction ; Peroxidase/analysis/metabolism ; Phenols/analysis ; Species Specificity ; Temperature ; beta-Glucosidase/analysis/metabolism ; }, abstract = {Several factors affect virgin olive oil (VOO) phenolic profile. The aim of this study was to monitor olive hydrolytic (β-glucosidase) and oxidative (peroxydase, POX, and polyphenoloxydase, PPO) enzymes during olive ripening and storage and to determine their capacity to shape VOO phenolic profile. To this end, olives from the cultivars Chétoui and Arbequina were stored at 4°C or 25°C for 4weeks and their enzymatic activities and oil phenolic profiles were compared to those of ripening olives. We observed different trends in enzymes activities according to cultivar and storage temperature. Secoiridoid compounds, determined by high resolution mass spectrometry (HRMS), and their deacetoxylated, oxygenated, and deacetoxy-oxygenated derivatives were identified and their contents differed between the cultivars according to olive ripening degree and storage conditions. These differences could be due to β-glucosidase, POX and PPO activities changes during olive ripening and storage. Results also show that oxidised phenolic compounds could be a marker of VOO ''freshness".}, }
@article {pmid27208111, year = {2016}, author = {van der Walt, AJ and Johnson, RM and Cowan, DA and Seely, M and Ramond, JB}, title = {Unique Microbial Phylotypes in Namib Desert Dune and Gravel Plain Fairy Circle Soils.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {15}, pages = {4592-4601}, pmid = {27208111}, issn = {1098-5336}, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Desert Climate ; Ecosystem ; Fungi/classification/genetics/*isolation &amp; purification ; Geologic Sediments/chemistry/*microbiology ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {UNLABELLED: Fairy circles (FCs) are barren circular patches of soil surrounded by grass species. Their origin is poorly understood. FCs feature in both the gravel plains and the dune fields of the Namib Desert. While a substantial number of hypotheses to explain the origin and/or maintenance of fairy circles have been presented, none are completely consistent with either their properties or their distribution. In this study, we investigated the hypothesis that FC formation in dunes and gravel plains is due to microbial phytopathogenesis. Surface soils from five gravel plain and five dune FCs, together with control soil samples, were analyzed using high-throughput sequencing of bacterial/archaeal (16S rRNA gene) and fungal (internal transcribed spacer [ITS] region) phylogenetic markers. Our analyses showed that gravel plain and dune FC microbial communities are phylogenetically distinct and that FC communities differ from those of adjacent vegetated soils. Furthermore, various soil physicochemical properties, particularly the pH, the Ca, P, Na, and SO4 contents, the soil particle size, and the percentage of carbon, significantly influenced the compositions of dune and gravel plain FC microbial communities, but none were found to segregate FC and vegetated soil communities. Nevertheless, 9 bacterial, 1 archaeal, and 57 fungal phylotypes were identified as FC specific, since they were present within the gravel plain and dune FC soils only, not in the vegetated soils. Some of these FC-specific phylotypes were assigned to taxa known to harbor phytopathogenic microorganisms. This suggests that these FC-specific microbial taxa may be involved in the formation and/or maintenance of Namib Desert FCs.<br><br>IMPORTANCE: Fairy circles (FCs) are mysterious barren circular patches of soil found within a grass matrix in the dune fields and gravel plains of the Namib Desert. Various hypotheses attempting to explain this phenomenon have been proposed. To date, however, none have been successful in fully explaining the etiology of FCs, particularly since gravel plain FCs have been largely ignored. In this study, we investigated the hypothesis that microorganisms could be involved in the FC phenomenon through phytopathogenesis. We show that the microbial communities in FC and control vegetated soil samples were significantly different. Furthermore, we detected 67 FC-specific microbial phylotypes, i.e., phylotypes present solely in both gravel plain and dune FC soils, some of which were closely related to known phytopathogens. Our results, therefore, demonstrate that microorganisms may play a role in the formation and/or maintenance of Namib Desert FCs, possibly via phytopathogenic activities.}, }
@article {pmid27207043, year = {2016}, author = {Golda-Cepa, M and Syrek, K and Brzychczy-Wloch, M and Sulka, GD and Kotarba, A}, title = {Primary role of electron work function for evaluation of nanostructured titania implant surface against bacterial infection.}, journal = {Materials science &amp; engineering. C, Materials for biological applications}, volume = {66}, number = {}, pages = {100-105}, doi = {10.1016/j.msec.2016.04.079}, pmid = {27207043}, issn = {1873-0191}, mesh = {Bacterial Adhesion/physiology ; Electrons ; Microscopy, Electron, Scanning ; Microscopy, Fluorescence ; Nanopores/ultrastructure ; Nanostructures/*chemistry ; Prostheses and Implants ; Staphylococcus aureus/physiology ; Surface Properties ; Titanium/*chemistry ; }, abstract = {The electron work function as an essential descriptor for the evaluation of metal implant surfaces against bacterial infection is identified for the first time. Its validity is demonstrated on Staphylococcus aureus adhesion to nanostructured titania surfaces. The established correlation: work function-bacteria adhesion is of general importance since it can be used for direct evaluation of any electrically conductive implant surfaces.}, }
@article {pmid27206480, year = {2016}, author = {De Maayer, P and Cowan, DA}, title = {Flashy flagella: flagellin modification is relatively common and highly versatile among the Enterobacteriaceae.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {377}, pmid = {27206480}, issn = {1471-2164}, mesh = {Enterobacteriaceae/classification/*genetics/*metabolism ; Flagella/*genetics/*metabolism ; Flagellin/*genetics/*metabolism ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Loci ; Glycosylation ; Phylogeny ; Polysaccharides ; Protein Processing, Post-Translational ; }, abstract = {BACKGROUND: Post-translational glycosylation of the flagellin protein is relatively common among Gram-negative bacteria, and has been linked to several phenotypes, including flagellar biosynthesis and motility, biofilm formation, host immune evasion and manipulation and virulence. However to date, despite extensive physiological and genetic characterization, it has never been reported for the peritrichously flagellate Enterobacteriaceae.<br><br>RESULTS: Using comparative genomic approaches we analyzed 2,000 representative genomes of Enterobacteriaceae, and show that flagellin glycosylation islands are relatively common and extremely versatile among members of this family. Differences in the G&#x2009;+&#x2009;C content of the FGIs and the rest of the genome and the presence of mobile genetic elements provide evidence of horizontal gene transfer occurring within the FGI loci. These loci therefore encode highly variable flagellin glycan structures, with distinct sugar backbones, heavily substituted with formyl, methyl, acetyl, lipoyl and amino groups. Additionally, an N-lysine methylase, FliB, previously identified only in the enterobacterial pathogen Salmonella enterica, is relatively common among several distinct taxa within the family. These flagellin methylase island loci (FMIs), in contrast to the FGI loci, appear to be stably maintained within these diverse lineages.<br><br>CONCLUSIONS: The prevalence and versatility of flagellin modification loci, both glycosylation and methylation loci, suggests they play important biological roles among the Enterobacteriaceae.}, }
@article {pmid27199952, year = {2016}, author = {Benítez-Páez, A and Moreno, FJ and Sanz, ML and Sanz, Y}, title = {Genome Structure of the Symbiont Bifidobacterium pseudocatenulatum CECT 7765 and Gene Expression Profiling in Response to Lactulose-Derived Oligosaccharides.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {624}, pmid = {27199952}, issn = {1664-302X}, abstract = {Bifidobacterium pseudocatenulatum CECT 7765 was isolated from stools of a breast-fed infant. Although, this strain is generally considered an adult-type bifidobacterial species, it has also been shown to have pre-clinical efficacy in obesity models. In order to understand the molecular basis of its adaptation to complex carbohydrates and improve its potential functionality, we have analyzed its genome and transcriptome, as well as its metabolic output when growing in galacto-oligosaccharides derived from lactulose (GOS-Lu) as carbon source. B. pseudocatenulatum CECT 7765 shows strain-specific genome regions, including a great diversity of sugar metabolic-related genes. A preliminary and exploratory transcriptome analysis suggests candidate over-expression of several genes coding for sugar transporters and permeases; furthermore, five out of seven beta-galactosidases identified in the genome could be activated in response to GOS-Lu exposure. Here, we also propose that a specific gene cluster is involved in controlling the import and hydrolysis of certain di- and tri-saccharides, which seemed to be those primarily taken-up by the bifidobacterial strain. This was discerned from mass spectrometry-based quantification of different saccharide fractions of culture supernatants. Our results confirm that the expression of genes involved in sugar transport and metabolism and in the synthesis of leucine, an amino acid with a key role in glucose and energy homeostasis, was up-regulated by GOS-Lu. This was done using qPCR in addition to the exploratory information derived from the single-replicated RNAseq approach, together with the functional annotation of genes predicted to be encoded in the B. pseudocatenulatum CETC 7765 genome.}, }
@article {pmid27199914, year = {2016}, author = {Johnston, ER and Rodriguez-R, LM and Luo, C and Yuan, MM and Wu, L and He, Z and Schuur, EA and Luo, Y and Tiedje, JM and Zhou, J and Konstantinidis, KT}, title = {Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {579}, pmid = {27199914}, issn = {1664-302X}, abstract = {How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1-2 g) are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth) by sequencing, and the recovery of 27 high-quality, almost complete (>80% completeness) population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100-530 km apart) tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity). Collectively, our results revealed that Alaska tundra microbial communities are less diverse and more homogenous across spatial scales than previously anticipated, and provided DNA sequences of abundant populations and genes that would be relevant for future studies of the effects of environmental change on tundra ecosystems.}, }
@article {pmid27199093, year = {2016}, author = {Hallam, SJ and Vásquez, M}, title = {Editorial overview: Remapping the body of the world: Exploring interactions at the interface of microbial ecology, biological engineering and information science.}, journal = {Current opinion in microbiology}, volume = {31}, number = {}, pages = {v-vii}, doi = {10.1016/j.mib.2016.05.001}, pmid = {27199093}, issn = {1879-0364}, mesh = {Adaptation, Physiological ; *Bioengineering ; Data Collection ; Ecological and Environmental Phenomena ; *Ecology ; Ecosystem ; Genetic Variation ; *Information Science ; Microbial Consortia/*genetics/physiology ; Phenotype ; }, }
@article {pmid27195106, year = {2016}, author = {Bissett, A and Fitzgerald, A and Court, L and Meintjes, T and Mele, PM and Reith, F and Dennis, PG and Breed, MF and Brown, B and Brown, MV and Brugger, J and Byrne, M and Caddy-Retalic, S and Carmody, B and Coates, DJ and Correa, C and Ferrari, BC and Gupta, VV and Hamonts, K and Haslem, A and Hugenholtz, P and Karan, M and Koval, J and Lowe, AJ and Macdonald, S and McGrath, L and Martin, D and Morgan, M and North, KI and Paungfoo-Lonhienne, C and Pendall, E and Phillips, L and Pirzl, R and Powell, JR and Ragan, MA and Schmidt, S and Seymour, N and Snape, I and Stephen, JR and Stevens, M and Tinning, M and Williams, K and Yeoh, YK and Zammit, CM and Young, A}, title = {Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database.}, journal = {GigaScience}, volume = {5}, number = {}, pages = {21}, pmid = {27195106}, issn = {2047-217X}, mesh = {Archaea/classification/genetics ; Australia ; Bacteria/classification/genetics ; Biodiversity ; *Databases, Factual ; Fungi/classification/genetics ; Metagenomics ; Phylogeny ; Sequence Analysis, DNA/*methods ; *Soil Microbiology ; }, abstract = {BACKGROUND: Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The 'Biomes of Australian Soil Environments' (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function.<br><br>FINDINGS: BASE currently provides amplicon sequences and associated contextual data for over 900 sites encompassing all Australian states and territories, a wide variety of bioregions, vegetation and land-use types. Amplicons target bacteria, archaea and general and fungal-specific eukaryotes. The growing database will soon include metagenomics data. Data are provided in both raw sequence (FASTQ) and analysed OTU table formats and are accessed via the project's data portal, which provides a user-friendly search tool to quickly identify samples of interest. Processed data can be visually interrogated and intersected with other Australian diversity and environmental data using tools developed by the 'Atlas of Living Australia'.<br><br>CONCLUSIONS: Developed within an open data framework, the BASE project is the first Australian soil microbial diversity database. The database will grow and link to other global efforts to explore microbial, plant, animal, and marine biodiversity. Its design and open access nature ensures that BASE will evolve as a valuable tool for documenting an often overlooked component of biodiversity and the many microbe-driven processes that are essential to sustain soil function and ecosystem services.}, }
@article {pmid27193000, year = {2016}, author = {Duarte, S and Cássio, F and Ferreira, V and Canhoto, C and Pascoal, C}, title = {Seasonal Variability May Affect Microbial Decomposers and Leaf Decomposition More Than Warming in Streams.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {263-276}, pmid = {27193000}, issn = {1432-184X}, mesh = {Bacteria/*growth &amp; development ; Biodegradation, Environmental ; Biodiversity ; DNA Fingerprinting ; DNA, Bacterial/isolation &amp; purification ; DNA, Fungal/isolation &amp; purification ; Fungi/*growth &amp; development ; Plant Leaves/*microbiology ; Quercus ; *Seasons ; Temperature ; }, abstract = {Ongoing climate change is expected to affect the diversity and activity of aquatic microbes, which play a key role in plant litter decomposition in forest streams. We used a before-after control-impact (BACI) design to study the effects of warming on a forest stream reach. The stream reach was divided by a longitudinal barrier, and during 1 year (ambient year) both stream halves were at ambient temperature, while in the second year (warmed year) the temperature in one stream half was increased by ca. 3 °C above ambient temperature (experimental half). Fine-mesh bags containing oak (Quercus robur L.) leaves were immersed in both stream halves for up to 60 days in spring and autumn of the ambient and warmed years. We assessed leaf-associated microbial diversity by denaturing gradient gel electrophoresis and identification of fungal conidial morphotypes and microbial activity by quantifying leaf mass loss and productivity of fungi and bacteria. In the ambient year, no differences were found in leaf decomposition rates and microbial productivities either between seasons or stream halves. In the warmed year, phosphorus concentration in the stream water, leaf decomposition rates, and productivity of bacteria were higher in spring than in autumn. They did not differ between stream halves, except for leaf decomposition, which was higher in the experimental half in spring. Fungal and bacterial communities differed between seasons in both years. Seasonal changes in stream water variables had a greater impact on the activity and diversity of microbial decomposers than a warming regime simulating a predicted global warming scenario.}, }
@article {pmid27190163, year = {2016}, author = {Miyambo, T and Makhalanyane, TP and Cowan, DA and Valverde, A}, title = {Plants of the fynbos biome harbour host species-specific bacterial communities.}, journal = {FEMS microbiology letters}, volume = {363}, number = {15}, pages = {}, doi = {10.1093/femsle/fnw122}, pmid = {27190163}, issn = {1574-6968}, mesh = {Actinobacteria/genetics ; Alphaproteobacteria/genetics ; Bacteria/genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; Biodiversity ; DNA, Bacterial/genetics ; *Ecosystem ; Endophytes/classification/genetics/*physiology ; *Host Specificity ; Microbial Consortia/genetics/*physiology ; Phylogeny ; Plants/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; South Africa ; }, abstract = {The fynbos biome in South Africa is globally recognised as a plant biodiversity hotspot. However, very little is known about the bacterial communities associated with fynbos plants, despite interactions between primary producers and bacteria having an impact on the physiology of both partners and shaping ecosystem diversity. This study reports on the structure, phylogenetic composition and potential roles of the endophytic bacterial communities located in the stems of three fynbos plants (Erepsia anceps, Phaenocoma prolifera and Leucadendron laureolum). Using Illumina MiSeq 16S rRNA sequencing we found that different subpopulations of Deinococcus-Thermus, Alphaproteobacteria, Acidobacteria and Firmicutes dominated the endophytic bacterial communities. Alphaproteobacteria and Actinobacteria were prevalent in P. prolifera, whereas Deinococcus-Thermus dominated in L. laureolum, revealing species-specific host-bacteria associations. Although a high degree of variability in the endophytic bacterial communities within hosts was observed, we also detected a core microbiome across the stems of the three plant species, which accounted for 72% of the sequences. Altogether, it seems that both deterministic and stochastic processes shaped microbial communities. Endophytic bacterial communities harboured putative plant growth-promoting bacteria, thus having the potential to influence host health and growth.}, }
@article {pmid27184651, year = {2016}, author = {Verstraete, W and Clauwaert, P and Vlaeminck, SE}, title = {Used water and nutrients: Recovery perspectives in a 'panta rhei' context.}, journal = {Bioresource technology}, volume = {215}, number = {}, pages = {199-208}, doi = {10.1016/j.biortech.2016.04.094}, pmid = {27184651}, issn = {1873-2976}, mesh = {Animals ; Biodegradation, Environmental ; Bioreactors ; Fertilizers/analysis ; Humans ; Manure/analysis ; Recycling ; Wastewater/*analysis/chemistry ; Water/analysis ; Water Pollutants, Chemical/chemistry/*isolation &amp; purification ; Water Purification ; }, abstract = {There is an urgent need to secure global supplies in safe water and proteinaceous food in an eco-sustainable manner, as manifested from tensions in the nexus Nutrients-Energy-Water-Environment-Land. This paper is concept based and provides solutions based on resource recovery from municipal and industrial wastewater and from manure. A set of decisive factors is reviewed facilitating an attractive business case. Our key message is that a robust barrier must clear the recovered product from its original status. Besides refined inorganic fertilizers, a central role for five types of microbial protein is proposed. A resource cycling solution for the extremely confined environment of space habitation should serve as an incentive to assimilate a new user mindset. To achieve the ambitious goal of sustainable food security, the solutions suggested here need a broad implementation, hand in hand with minimizing losses along the entire fertilizer-feed-food-fork chain.}, }
@article {pmid27183997, year = {2016}, author = {Batista, S and Medina, A and Pires, MA and Moriñigo, MA and Sansuwan, K and Fernandes, JM and Valente, LM and Ozório, RO}, title = {Innate immune response, intestinal morphology and microbiota changes in Senegalese sole fed plant protein diets with probiotics or autolysed yeast.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {16}, pages = {7223-7238}, doi = {10.1007/s00253-016-7592-7}, pmid = {27183997}, issn = {1432-0614}, mesh = {Animal Feed ; Animals ; Aquaculture/methods ; Diet ; Dietary Supplements ; Flatfishes/growth &amp; development/immunology/*microbiology ; Gastrointestinal Microbiome/*drug effects ; Immunity, Innate/*immunology ; Intestines/*microbiology ; Plant Proteins, Dietary/*pharmacology ; Probiotics/*pharmacology ; Yeasts ; }, abstract = {The effects of using plant ingredients in Senegalese sole (Solea senegalensis) diet on immune competence and intestine morphology and microbial ecology are still controversial. Probiotics or immunostimulants can potentially alter the intestinal microbiota in a way that protects fish against pathogens. The current study aimed to examine the intestine histology and microbiota and humoral innate immune response in juvenile sole fed diets with low (35 %) or high (72 %) content of plant protein (PP) ingredients supplemented with a multispecies probiotic bacteria or autolysed yeast. Fish fed the probiotic diet had lower growth performance. Lysozyme and complement activities were significantly higher in fish fed PP72 diets than in their counterparts fed PP35 diets after 17 and 38 days of feeding. At 2 days of feeding, fish fed unsupplemented PP72 showed larger intestine section area and longer villus than fish fed unsupplemented PP35. At 17 days of feeding, fish fed unsupplemented PP72 showed more goblet cells than the other dietary groups, except the group fed yeast supplemented PP35 diet. High dietary PP level, acutely stimulate fish innate immune defence of the fish after 2 and 17 days of feeding. However, this effect does not occur after 73 days of feeding, suggesting a habituation to dietary treatments and/or immunosuppression, with a reduction in the number of the goblet cells. Fish fed for 38 days with diets supplemented with autolysed yeast showed longer intestinal villus. The predominant bacteria found in sole intestine were Vibrio sp. and dietary probiotic supplementation caused a reduction in Vibrio content, regardless of the PP level.}, }
@article {pmid27183209, year = {2016}, author = {Meerburg, FA and Vlaeminck, SE and Roume, H and Seuntjens, D and Pieper, DH and Jauregui, R and Vilchez-Vargas, R and Boon, N}, title = {High-rate activated sludge communities have a distinctly different structure compared to low-rate sludge communities, and are less sensitive towards environmental and operational variables.}, journal = {Water research}, volume = {100}, number = {}, pages = {137-145}, doi = {10.1016/j.watres.2016.04.076}, pmid = {27183209}, issn = {1879-2448}, mesh = {Environment ; Sewage/*chemistry ; *Wastewater ; }, abstract = {High-rate activated sludge processes allow for the recovery of organics and energy from wastewaters. These systems are operated at a short sludge retention time and high sludge-specific loading rates, which results in a higher sludge yield and better digestibility than conventional, low-rate activated sludge. Little is known about the microbial ecology of high-rate systems. In this work, we address the need for a fundamental understanding of how high-rate microbial communities differ from low-rate communities. We investigated the high-rate and low-rate communities in a sewage treatment plant in relation to environmental and operational variables over a period of ten months. We demonstrated that (1) high-rate and low-rate communities are distinctly different in terms of richness, evenness and composition, (2) high-rate community dynamics are more variable and less shaped by deterministic factors compared to low-rate communities, (3) sub-communities of continuously core and transitional members are more shaped by deterministic factors than the continuously rare members, both in high-rate and low-rate communities, and (4) high-rate community members showed a co-occurrence pattern similar to that of low-rate community members, but were less likely to be correlated to environmental and operational variables. These findings provide a basis for further optimization of high-rate systems, in order to facilitate resource recovery from wastewater.}, }
@article {pmid27183115, year = {2016}, author = {Hahn, AS and Konwar, KM and Louca, S and Hanson, NW and Hallam, SJ}, title = {The information science of microbial ecology.}, journal = {Current opinion in microbiology}, volume = {31}, number = {}, pages = {209-216}, doi = {10.1016/j.mib.2016.04.014}, pmid = {27183115}, issn = {1879-0364}, mesh = {*Ecological and Environmental Phenomena ; Ecosystem ; Electronic Data Processing/*methods ; High-Throughput Nucleotide Sequencing ; Information Science/*methods ; *Information Services ; Internet ; Microbial Consortia/*genetics ; }, abstract = {A revolution is unfolding in microbial ecology where petabytes of 'multi-omics' data are produced using next generation sequencing and mass spectrometry platforms. This cornucopia of biological information has enormous potential to reveal the hidden metabolic powers of microbial communities in natural and engineered ecosystems. However, to realize this potential, the development of new technologies and interpretative frameworks grounded in ecological design principles are needed to overcome computational and analytical bottlenecks. Here we explore the relationship between microbial ecology and information science in the era of cloud-based computation. We consider microorganisms as individual information processing units implementing a distributed metabolic algorithm and describe developments in ecoinformatics and ubiquitous computing with the potential to eliminate bottlenecks and empower knowledge creation and translation.}, }
@article {pmid27179523, year = {2016}, author = {Pradeep Ram, AS and Chaibi-Slouma, S and Keshri, J and Colombet, J and Sime-Ngando, T}, title = {Functional Responses of Bacterioplankton Diversity and Metabolism to Experimental Bottom-Up and Top-Down Forcings.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {347-358}, pmid = {27179523}, issn = {1432-184X}, mesh = {Bacteria/classification/*metabolism/virology ; Biomass ; Carbon/metabolism ; DNA, Bacterial/genetics ; Fresh Water/*microbiology/virology ; Linear Models ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {We conducted an experimental approach using microcosms to simultaneously examine the functional response of natural freshwater bacterial assemblages to the impact of resources (nutrients) and top-down factors (viruses and grazers) on bacterial physiological state and their community structure. Addition of organic and inorganic nutrients led to the proliferation of high nucleic acid content bacterial cells accompanied by high bacterial growth efficiency (considered as proxy of bacterial carbon metabolism) estimates, suggesting that this subgroup represented the most active fraction of bacterial community and had a high capacity to incorporate carbon into its biomass. However, their rapid growth induced the pressure of viral lytic infection which led to their lysis toward the end of the experiment. In microcosms with flagellates plus viruses, and with viruses alone, the selective removal of metabolically active high nucleic acid cells through viral lysis benefitted the less active low nucleic acid content cells, perhaps via the use of lysis products for its growth and survival. Changes in bacterial physiological state in microcosms were reflected in their community structure which was examined using 16S ribosomal RNA (rRNA) gene sequencing by Illumina's Miseq platform. Chao estimator and Shannon diversity index values suggested that bacterial species richness was highest in the presence of both the top-down factors, indicating a tighter control of bacterioplankton dominants within a relatively stable bacterial community. The increase in bacterial metabolism with nutrient addition followed by subsequent lysis of bacterial dominants indicate that both resources and top-down factors work in concert for the sustenance of stable bacterial communities.}, }
@article {pmid27178181, year = {2016}, author = {Meng, H and Wang, YF and Chan, HW and Wu, RN and Gu, JD}, title = {Co-occurrence of nitrite-dependent anaerobic ammonium and methane oxidation processes in subtropical acidic forest soils.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {17}, pages = {7727-7739}, doi = {10.1007/s00253-016-7585-6}, pmid = {27178181}, issn = {1432-0614}, mesh = {Ammonium Compounds/*metabolism ; Bacteria/classification/genetics/*metabolism ; Forests ; Methane/*metabolism ; Nitrites/*metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {Anaerobic ammonium oxidation (anammox) and nitrite-dependent anaerobic methane oxidation (n-damo) are two new processes of recent discoveries linking the microbial nitrogen and carbon cycles. In this study, 16S ribosomal RNA (rRNA) gene of anammox bacteria and pmoA gene of n-damo bacteria were used to investigate their distribution and diversity in natural acidic and re-vegetated forest soils. The 16S rRNA gene sequences retrieved featured at least three species in two genera known anammox bacteria, namely Candidatus Brocadia anammoxidans, Candidatus Brocadia fulgida, and Candidatus Kuenenia stuttgartiensis while the pmoA gene amplified was affiliated with two species of known n-damo bacteria Candidatus Methylomirabilis oxyfera and a newly established Candidatus Methylomirabilis sp. According to the results, the diversity of anammox bacteria in natural forests was lower than in re-vegetated forests, but no significant difference was observed in n-damo community between them. Quantitative real-time PCR showed that both anammox and n-damo bacteria were more abundant in the lower layer (10-20 cm) than the surface layer (0-5 cm). The abundance of anammox bacteria varied from 2.21 × 10(5) to 3.90 × 10(6) gene copies per gram dry soil, and n-damo bacteria quantities were between 1.69 × 10(5) and 5.07 × 10(6) gene copies per gram dry soil in the two different layers. Both anammox and n-damo bacteria are reported for the first time to co-occur in acidic forest soil in this study, providing a more comprehensive information on more defined microbial processes contributing to C and N cycles in the ecosystems.}, }
@article {pmid27177720, year = {2016}, author = {Scheikl, U and Tsao, HF and Horn, M and Indra, A and Walochnik, J}, title = {Free-living amoebae and their associated bacteria in Austrian cooling towers: a 1-year routine screening.}, journal = {Parasitology research}, volume = {115}, number = {9}, pages = {3365-3374}, pmid = {27177720}, issn = {1432-1955}, support = {TRP 209/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Amoeba/classification/*microbiology ; Austria ; Bacteria/classification/genetics/*isolation &amp; purification ; Disease Outbreaks ; Fresh Water/*microbiology/*parasitology ; }, abstract = {Free-living amoebae (FLA) are widely spread in the environment and known to cause rare but often serious infections. Besides this, FLA may serve as vehicles for bacterial pathogens. In particular, Legionella pneumophila is known to replicate within FLA thereby also gaining enhanced infectivity. Cooling towers have been the source of outbreaks of Legionnaires' disease in the past and are thus usually screened for legionellae on a routine basis, not considering, however, FLA and their vehicle function. The aim of this study was to incorporate a screening system for host amoebae into a Legionella routine screening. A new real-time PCR-based screening system for various groups of FLA was established. Three cooling towers were screened every 2 weeks over the period of 1 year for FLA and Legionella spp., by culture and molecular methods in parallel. Altogether, 83.3 % of the cooling tower samples were positive for FLA, Acanthamoeba being the dominating genus. Interestingly, 69.7 % of the cooling tower samples were not suitable for the standard Legionella screening due to their high organic burden. In the remaining samples, positivity for Legionella spp. was 25 % by culture, but overall positivity was 50 % by molecular methods. Several amoebal isolates revealed intracellular bacteria.}, }
@article {pmid27174263, year = {2016}, author = {Gálvez, EJ and Carrillo-Castro, K and Zárate, L and Güiza, L and Pieper, DH and García-Bonilla, E and Salazar, M and Junca, H}, title = {Draft Genome Sequence of Bacillus licheniformis CG-B52, a Highly Virulent Bacterium of Pacific White Shrimp (Litopenaeus vannamei), Isolated from a Colombian Caribbean Aquaculture Outbreak.}, journal = {Genome announcements}, volume = {4}, number = {3}, pages = {}, pmid = {27174263}, issn = {2169-8287}, abstract = {Bacillus licheniformis strain CG-B52 was isolated as the etiological agent producing a self-limited outbreak of high mortalities in commercial Litopenaeus vannamei culture ponds on the Colombian Caribbean coast in 2005. Here, we report its draft genome and three novel extrachromosomal elements that it harbors.}, }
@article {pmid27170325, year = {2016}, author = {Khor, WC and Roume, H and Coma, M and Vervaeren, H and Rabaey, K}, title = {Acetate accumulation enhances mixed culture fermentation of biomass to lactic acid.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {19}, pages = {8337-8348}, doi = {10.1007/s00253-016-7578-5}, pmid = {27170325}, issn = {1432-0614}, mesh = {Acetates/*metabolism ; Animals ; *Biomass ; Biotransformation ; Fermentation ; Lactic Acid/*metabolism ; Lignin/*metabolism ; *Microbial Consortia ; Rumen/*microbiology ; }, abstract = {Lactic acid is a high-in-demand chemical, which can be produced through fermentation of lignocellulosic feedstock. However, fermentation of complex substrate produces a mixture of products at efficiencies too low to justify a production process. We hypothesized that the background acetic acid concentration plays a critical role in lactic acid yield; therefore, its retention via selective extraction of lactic acid or its addition would improve overall lactic acid production and eliminate net production of acetic acid. To test this hypothesis, we added 10 g/L of acetate to fermentation broth to investigate its effect on products composition and concentration and bacterial community evolution using several substrate-inoculum combinations. With rumen fluid inoculum, lactate concentrations increased by 80 ± 12 % (cornstarch, p < 0.05) and 16.7 ± 0.4 % (extruded grass, p < 0.05) while with pure culture inoculum (Lactobacillus delbrueckii and genetically modified (GM) Escherichia coli), a 4 to 23 % increase was observed. Using rumen fluid inoculum, the bacterial community was enriched within 8 days to >69 % lactic acid bacteria (LAB), predominantly Lactobacillaceae. Higher acetate concentration promoted a more diverse LAB population, especially on non-inoculated bottles. In subsequent tests, acetate was added in a semi-continuous percolation system with grass as substrate. These tests confirmed our findings producing lactate at concentrations 26 ± 5 % (p < 0.05) higher than the control reactor over 20 days operation. Overall, our work shows that recirculating acetate has the potential to boost lactic acid production from waste biomass to levels more attractive for application.}, }
@article {pmid27169388, year = {2016}, author = {Wagner-Döbler, I}, title = {Biofilm transplantation in the deep sea.}, journal = {Molecular ecology}, volume = {25}, number = {9}, pages = {1905-1907}, doi = {10.1111/mec.13612}, pmid = {27169388}, issn = {1365-294X}, mesh = {Bacteria/genetics ; *Biofilms ; Indian Ocean ; *Metagenome ; Microbiota ; }, abstract = {A gold rush is currently going on in microbial ecology, which is powered by the possibility to determine the full complexity of microbial communities through next-generation sequencing. Accordingly, enormous efforts are underway to describe microbiomes worldwide, in humans, animals, plants, soil, air and the ocean. While much can be learned from these studies, only experiments will finally unravel mechanisms. One of the key questions is how a microbial community is assembled from a pool of bacteria in the environment, and how it responds to change - be it the increase in CO2 concentration in the ocean, or antibiotic treatment of the gut microbiome. The study by Zhang et al. () in this issue is one of the very few that approaches this problem experimentally in the natural environment. The authors selected a habitat which is both extremely interesting and difficult to access. They studied the Thuwal Seep in the Red Sea at 850 m depth and used a remotely operated vehicle (ROV) to place a steel frame carrying substrata for biofilm growth into the brine pool and into the adjacent normal bottom water (NBW). Biofilms were allowed to develop for 3 days, and then those that had been growing in the brine pool were transported to normal bottom water and stayed there for another 3 days, and vice versa. The 'switched' biofilms were then compared with their source communities by metagenome sequencing. Strikingly, both 'switched' biofilms were now dominated by the same two species. These species were able to cope with conditions in both source ecosystems, as shown by assembly of their genomes and detection of expression of key genes. The biofilms had adapted to environmental change, rather than to brine pools or NBW. The study shows both the resilience and adaptability of biofilm communities and has implications for microbial ecology in general and even for therapeutic approaches such as transplantation of faecal microbiomes.}, }
@article {pmid27166668, year = {2016}, author = {Bosmans, L and De Bruijn, I and De Mot, R and Rediers, H and Lievens, B}, title = {Agar composition affects in vitro screening of biocontrol activity of antagonistic microorganisms.}, journal = {Journal of microbiological methods}, volume = {127}, number = {}, pages = {7-9}, doi = {10.1016/j.mimet.2016.05.004}, pmid = {27166668}, issn = {1872-8359}, mesh = {Agar/*chemistry ; *Antibiosis ; Bacteriological Techniques/*methods ; Plant Diseases/microbiology/*prevention &amp; control ; Plant Roots/microbiology ; }, abstract = {Agar-based screening assays are the method of choice when evaluating antagonistic potential of bacterial biocontrol-candidates against pathogens. We showed that when using the same medium, but different agar compositions, the activity of a bacterial antagonist against Agrobacterium was strongly affected. Consequently, results from in vitro screenings should be interpreted cautiously.}, }
@article {pmid27164116, year = {2016}, author = {Wichmann, H and Brinkhoff, T and Simon, M and Richter-Landsberg, C}, title = {Dimethylsulfoniopropionate Promotes Process Outgrowth in Neural Cells and Exerts Protective Effects against Tropodithietic Acid.}, journal = {Marine drugs}, volume = {14}, number = {5}, pages = {}, pmid = {27164116}, issn = {1660-3397}, mesh = {Animals ; Cell Line ; Extracellular Signal-Regulated MAP Kinases/metabolism ; Membrane Potential, Mitochondrial/drug effects ; Mice ; Microtubules/drug effects ; Neuroglia/drug effects ; Neurons/*drug effects ; Oxidative Stress/drug effects ; Protective Agents/*pharmacology ; Rats ; Roseobacter/metabolism ; Sulfonium Compounds/*pharmacology ; Tropolone/adverse effects/*analogs &amp; derivatives ; Tubulin/drug effects ; }, abstract = {The marine environment harbors a plethora of bioactive substances, including drug candidates of potential value in the field of neuroscience. The present study was undertaken to investigate the effects of dimethylsulfoniopropionate (DMSP), produced by several algae, corals and higher plants, on cells of the mammalian nervous system, i.e., neuronal N2a and OLN-93 cells as model system for nerve cells and glia, respectively. Additionally, the protective capabilities of DMSP were assessed in cells treated with tropodithietic acid (TDA), a marine metabolite produced by several Roseobacter clade bacteria. Both cell lines, N2a and OLN-93, have previously been shown to be a sensitive target for the action of TDA, and cytotoxic effects of TDA have been connected to the induction of oxidative stress. Our data shows that DMSP promotes process outgrowth and microtubule reorganization and bundling, accompanied by an increase in alpha-tubulin acetylation. Furthermore, DMSP was able to prevent the cytotoxic effects exerted by TDA, including the breakdown of the mitochondrial membrane potential, upregulation of heat shock protein Hsp32 and activation of the extracellular signal-regulated kinases 1/2 (ERK1/2). Our study points to the conclusion that DMSP provides an antioxidant defense, not only in algae but also in mammalian neural cells.}, }
@article {pmid27162369, year = {2016}, author = {Westrich, JR and Ebling, AM and Landing, WM and Joyner, JL and Kemp, KM and Griffin, DW and Lipp, EK}, title = {Saharan dust nutrients promote Vibrio bloom formation in marine surface waters.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {21}, pages = {5964-5969}, pmid = {27162369}, issn = {1091-6490}, mesh = {Africa, Northern ; Aquatic Organisms/*growth &amp; development ; *Dust ; Humans ; Seawater/*microbiology ; Vibrio/*growth &amp; development ; *Water Microbiology ; }, abstract = {Vibrio is a ubiquitous genus of marine bacteria, typically comprising a small fraction of the total microbial community in surface waters, but capable of becoming a dominant taxon in response to poorly characterized factors. Iron (Fe), often restricted by limited bioavailability and low external supply, is an essential micronutrient that can limit Vibrio growth. Vibrio species have robust metabolic capabilities and an array of Fe-acquisition mechanisms, and are able to respond rapidly to nutrient influx, yet Vibrio response to environmental pulses of Fe remains uncharacterized. Here we examined the population growth of Vibrio after natural and simulated pulses of atmospherically transported Saharan dust, an important and episodic source of Fe to tropical marine waters. As a model for opportunistic bacterial heterotrophs, we demonstrated that Vibrio proliferate in response to a broad range of dust-Fe additions at rapid timescales. Within 24 h of exposure, strains of Vibrio cholerae and Vibrio alginolyticus were able to directly use Saharan dust-Fe to support rapid growth. These findings were also confirmed with in situ field studies; arrival of Saharan dust in the Caribbean and subtropical Atlantic coincided with high levels of dissolved Fe, followed by up to a 30-fold increase of culturable Vibrio over background levels within 24 h. The relative abundance of Vibrio increased from ∼1 to ∼20% of the total microbial community. This study, to our knowledge, is the first to describe Vibrio response to Saharan dust nutrients, having implications at the intersection of marine ecology, Fe biogeochemistry, and both human and environmental health.}, }
@article {pmid27162180, year = {2016}, author = {Randle-Boggis, RJ and Helgason, T and Sapp, M and Ashton, PD}, title = {Evaluating techniques for metagenome annotation using simulated sequence data.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {7}, pages = {}, pmid = {27162180}, issn = {1574-6941}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Environmental Microbiology ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Metagenomics/*methods ; Molecular Sequence Annotation/*methods ; Software ; }, abstract = {The advent of next-generation sequencing has allowed huge amounts of DNA sequence data to be produced, advancing the capabilities of microbial ecosystem studies. The current challenge is to identify from which microorganisms and genes the DNA originated. Several tools and databases are available for annotating DNA sequences. The tools, databases and parameters used can have a significant impact on the results: naïve choice of these factors can result in a false representation of community composition and function. We use a simulated metagenome to show how different parameters affect annotation accuracy by evaluating the sequence annotation performances of MEGAN, MG-RAST, One Codex and Megablast. This simulated metagenome allowed the recovery of known organism and function abundances to be quantitatively evaluated, which is not possible for environmental metagenomes. The performance of each program and database varied, e.g. One Codex correctly annotated many sequences at the genus level, whereas MG-RAST RefSeq produced many false positive annotations. This effect decreased as the taxonomic level investigated increased. Selecting more stringent parameters decreases the annotation sensitivity, but increases precision. Ultimately, there is a trade-off between taxonomic resolution and annotation accuracy. These results should be considered when annotating metagenomes and interpreting results from previous studies.}, }
@article {pmid27162101, year = {2016}, author = {Coma, M and Vilchez-Vargas, R and Roume, H and Jauregui, R and Pieper, DH and Rabaey, K}, title = {Product Diversity Linked to Substrate Usage in Chain Elongation by Mixed-Culture Fermentation.}, journal = {Environmental science &amp; technology}, volume = {50}, number = {12}, pages = {6467-6476}, doi = {10.1021/acs.est.5b06021}, pmid = {27162101}, issn = {1520-5851}, mesh = {Acetates/metabolism ; Butyrates/metabolism ; Clostridium/metabolism ; Ethanol/*chemistry ; *Fermentation ; }, abstract = {Acetate and ethanol can be converted to caproic acid by microorganisms through reverse β-oxidation. There is limited insight into the versatility of chain elongation in view of different starting substrates, including even- and odd-carbon carboxylates and alcohols other than ethanol. Thermodynamic analyses show that most elongation pathways are energetically feasible. Through incubations of microbial communities with different substrate-pair combinations, we established that ethanol and propanol were both highly suitable for chain elongation. As an electron acceptor, acetate, propionate, and butyrate readily elongated with ethanol, whereas an adaptation period was necessary for formate. Isobutyrate and longer-chained fatty acids above butyrate were not elongated. The microbial communities converged, and consistent enrichment of Clostridium spp. was observed, independent of the supplied alcohol or carboxylate, with a strain related to Clostridium kluyveri dominating the enrichments. Community analysis also showed phylotypes related to Bacteroidaceae and Microbacteriaceae families in all tests that are capable of converting the base substrates to useful intermediates. These organisms were mainly enriched with methanol or formate. Our overall conclusion is thus that multiple substrates can be used for chain elongation and that this process is carried out by highly similar organisms for direct chain elongation irrespective of the substrate.}, }
@article {pmid27162086, year = {2016}, author = {Oloo, F and Valverde, A and Quiroga, MV and Vikram, S and Cowan, D and Mataloni, G}, title = {Habitat heterogeneity and connectivity shape microbial communities in South American peatlands.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {25712}, pmid = {27162086}, issn = {2045-2322}, mesh = {Antarctic Regions ; Argentina ; Bacteria/classification/*genetics ; Bacterial Proteins/genetics ; *Ecosystem ; *Environmental Microbiology ; Geography ; Oxidoreductases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil ; Species Specificity ; Sphagnopsida/*microbiology ; }, abstract = {Bacteria play critical roles in peatland ecosystems. However, very little is known of how habitat heterogeneity affects the structure of the bacterial communities in these ecosystems. Here, we used amplicon sequencing of the 16S rRNA and nifH genes to investigate phylogenetic diversity and bacterial community composition in three different sub-Antarctic peat bog aquatic habitats: Sphagnum magellanicum interstitial water, and water from vegetated and non-vegetated pools. Total and putative nitrogen-fixing bacterial communities from Sphagnum interstitial water differed significantly from vegetated and non-vegetated pool communities (which were colonized by the same bacterial populations), probably as a result of differences in water chemistry and biotic interactions. Total bacterial communities from pools contained typically aquatic taxa, and were more dissimilar in composition and less species rich than those from Sphagnum interstitial waters (which were enriched in taxa typically from soils), probably reflecting the reduced connectivity between the former habitats. These results show that bacterial communities in peatland water habitats are highly diverse and structured by multiple concurrent factors.}, }
@article {pmid27161356, year = {2016}, author = {Fuentes, S and de Vos, WM}, title = {How to Manipulate the Microbiota: Fecal Microbiota Transplantation.}, journal = {Advances in experimental medicine and biology}, volume = {902}, number = {}, pages = {143-153}, doi = {10.1007/978-3-319-31248-4_10}, pmid = {27161356}, issn = {0065-2598}, mesh = {Clostridioides difficile/pathogenicity/physiology ; Dysbiosis/microbiology/pathology/*therapy ; Enterocolitis, Pseudomembranous/microbiology/pathology/*therapy ; Fecal Microbiota Transplantation/ethics/*methods ; Feces/microbiology ; Gastrointestinal Microbiome/physiology ; Gastrointestinal Tract/microbiology ; Humans ; Inflammatory Bowel Diseases/microbiology/pathology/*therapy ; Tissue Donors ; }, abstract = {Fecal microbiota transplantation (FMT) is a rather straightforward therapy that manipulates the human gastrointestinal (GI) microbiota, by which a healthy donor microbiota is transferred into an existing but disturbed microbial ecosystem. This is a natural process that occurs already at birth; infants are rapidly colonized by a specific microbial community, the composition of which strongly depends on the mode of delivery and which therefore most likely originates from the mother (Palmer et al. 2007; Tannock et al. 1990). Since this early life microbial community already contains most, if not all, of the predominantly anaerobic microbes that are only found in the GI tract, it is reasonable to assume that early life colonization is the ultimate natural fecal transplantation.}, }
@article {pmid27158095, year = {2016}, author = {Mimee, M and Citorik, RJ and Lu, TK}, title = {Microbiome therapeutics - Advances and challenges.}, journal = {Advanced drug delivery reviews}, volume = {105}, number = {Pt A}, pages = {44-54}, pmid = {27158095}, issn = {1872-8294}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 EB017755/EB/NIBIB NIH HHS/United States ; P50 GM098792/GM/NIGMS NIH HHS/United States ; DP2 OD008435/OD/NIH HHS/United States ; }, mesh = {Animals ; Anti-Infective Agents/therapeutic use ; Bioengineering ; Humans ; *Microbiota ; Probiotics/therapeutic use ; }, abstract = {The microbial community that lives on and in the human body exerts a major impact on human health, from metabolism to immunity. In order to leverage the close associations between microbes and their host, development of therapeutics targeting the microbiota has surged in recent years. Here, we discuss current additive and subtractive strategies to manipulate the microbiota, focusing on bacteria engineered to produce therapeutic payloads, consortia of natural organisms and selective antimicrobials. Further, we present challenges faced by the community in the development of microbiome therapeutics, including designing microbial therapies that are adapted for specific geographies in the body, stable colonization with microbial therapies, discovery of clinically relevant biosensors, robustness of engineered synthetic gene circuits and addressing safety and biocontainment concerns. Moving forward, collaboration between basic and applied researchers and clinicians to address these challenges will poise the field to herald an age of next-generation, cellular therapies that draw on novel findings in basic research to inform directed augmentation of the human microbiota.}, }
@article {pmid27157862, year = {2016}, author = {Foxman, B and Luo, T and Srinivasan, U and Ramadugu, K and Wen, A and Goldberg, D and Shedden, K and Crout, R and McNeil, DW and Weyant, R and Marazita, ML}, title = {The effects of family, dentition, and dental caries on the salivary microbiome.}, journal = {Annals of epidemiology}, volume = {26}, number = {5}, pages = {348-354}, pmid = {27157862}, issn = {1873-2585}, support = {R01 DE014899/DE/NIDCR NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aging/physiology ; Appalachian Region/epidemiology ; Child ; Child, Preschool ; Cohort Studies ; Dental Caries/*epidemiology/genetics ; *Dentition ; Family ; Female ; Genetic Predisposition to Disease/epidemiology ; Humans ; Male ; Microbiota/*genetics/physiology ; Middle Aged ; *Oral Health ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; Saliva/microbiology ; Salivary Glands/*microbiology ; Sampling Studies ; Specimen Handling ; }, abstract = {PURPOSE: Family members share genes, environment, and microbial communities. If there is a strong effect of family on the salivary microbiota, controlling for family will enhance identification of microbial communities associated with cariogenesis. The present study was designed to assess the similarity of the salivary microbiome among families and the association between the salivary microbiome and dental decay taking age into account.<br><br>METHODS: We selected families (n&#xa0;=&#xa0;49) participating in the cohort study of oral health conducted by the Center for Oral Health Research in Appalachia. All families where at least two children and at least one parent gave a saliva sample (n&#xa0;= 173) were included. Saliva samples were collected at least 1&#xa0;hour after eating or drinking. After DNA extraction, the V6 region of the 16s rRNA gene was sequenced. Paired ends were joined using fast length adjustment of short reads, sequences were demultiplexed and filtered using Quantitative Insights Into Microbial Ecology 1.9.0, and taxonomy was assigned using the Ribosomal Database Project (RDP; http://rdp.cme.msu.edu/) classifier and sequences aligned with the CORE database using PyNAST.<br><br>RESULTS: The salivary microbiome changed with age and was more similar within families than between families. There was no difference in the diversity of the salivary microbiome by dental decay. After taking into account age and family, signals of dental decay were weak in the saliva, whether examined at the phyla, genus, or operational taxonomic level.<br><br>CONCLUSIONS: The salivary microbiome does not appear to be a good indicator of dental caries.}, }
@article {pmid27155967, year = {2016}, author = {Koopman, JE and Buijs, MJ and Brandt, BW and Keijser, BJ and Crielaard, W and Zaura, E}, title = {Nitrate and the Origin of Saliva Influence Composition and Short Chain Fatty Acid Production of Oral Microcosms.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {479-492}, pmid = {27155967}, issn = {1432-184X}, mesh = {Adult ; Bacteria/*classification/isolation &amp; purification/metabolism ; Biomass ; Butyrates/analysis ; Fatty Acids, Volatile/*biosynthesis ; Female ; Genes, Bacterial ; Genomics ; Humans ; Male ; Neisseria/genetics/isolation &amp; purification/metabolism ; Nitrates/*analysis ; Nitrites/analysis ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; Sequence Analysis, DNA ; Sucrose/analysis ; Veillonella/genetics/isolation &amp; purification/metabolism ; Young Adult ; }, abstract = {Nitrate is emerging as a possible health benefactor. Especially the microbial conversion of nitrate to nitrite in the oral cavity and the subsequent conversion to nitric oxide in the stomach are of interest in this regard. Yet, how nitrate influences the composition and biochemistry of the oral ecosystem is not fully understood. To investigate the effect of nitrate on oral ecology, we performed a 4-week experiment using the multiplaque artificial mouth (MAM) biofilm model. This model was inoculated with stimulated saliva of two healthy donors. Half of the microcosms (n = 4) received a constant supply of nitrate, while the other half functioned as control (n = 4). Additionally, all microcosms received a nitrate and sucrose pulse, each week, on separate days to measure nitrate reduction and acid formation. The bacterial composition of the microcosms was determined by 16S rDNA sequencing. The origin of the saliva (i.e., donor) showed to be the strongest determinant for the development of the microcosms. The supplementation of nitrate was related to a relatively high abundance of Neisseria in the microcosms of both donors, while Veillonella was highly abundant in the nitrate-supplemented microcosms of only one of the donors. The lactate concentration after sucrose addition was similarly high in all microcosms, irrespective of treatment or donor, while the concentration of butyrate was lower after nitrate addition in the nitrate-receiving microcosms. In conclusion, nitrate influences the composition and biochemistry of oral microcosms, although the result is strongly dependent on the inoculum.}, }
@article {pmid27155410, year = {2016}, author = {Chen, Y and Dai, Y and Wang, Y and Wu, Z and Xie, S and Liu, Y}, title = {Distribution of bacterial communities across plateau freshwater lake and upslope soils.}, journal = {Journal of environmental sciences (China)}, volume = {43}, number = {}, pages = {61-69}, doi = {10.1016/j.jes.2015.08.012}, pmid = {27155410}, issn = {1001-0742}, mesh = {Bacteria/classification/*growth &amp; development ; Environmental Monitoring ; Lakes/microbiology ; Soil ; *Soil Microbiology ; *Water Microbiology ; }, abstract = {Microorganisms are involved in a variety of biogeochemical processes in natural environments. The differences between bacterial communities in freshwaters and upslope soils remain unclear. The present study investigated the bacterial distribution in a plateau freshwater lake, Erhai Lake (southwestern China), and its upslope soils. Illumina MiSeq sequencing illustrated high bacterial diversity in lake sediments and soils. Sediment and soil bacterial communities were mainly composed of Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi and Planctomycetes. However, a distinctive difference in bacterial community structure was found between soil and sediment ecosystems. Water content, nitrogen and pH affected the distribution of the bacterial community across Erhai Lake and its upslope soils. Moreover, the soil bacterial community might also be shaped by plant types. This work could provide some new insights into plateau aquatic and terrestrial microbial ecology.}, }
@article {pmid27155348, year = {2016}, author = {Wigley, K and Wakelin, SA and Moot, DJ and Hammond, S and Ridgway, HJ}, title = {Measurements of carbon utilization by single bacterial species in sterile soil: insights into Rhizobium spp.}, journal = {Journal of applied microbiology}, volume = {121}, number = {2}, pages = {495-505}, doi = {10.1111/jam.13170}, pmid = {27155348}, issn = {1365-2672}, mesh = {Carbon/*metabolism ; Rhizobium leguminosarum/*metabolism ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {AIM: The aim of this work was to develop a tool to investigate the influence of soil factors on carbon utilization activity of single micro-organisms.<br><br>METHODS AND RESULTS: The assay for Rhizobium leguminosarum bv.&#xa0;trifolii in &#x3b3;-irradiated soil, using the MicroResp(&#x2122;) system, was optimized for sterility, incubation time, and moisture level. The optimized method was validated with experiments that assessed (i) differences in C utilization of different rhizobia strains and (ii) how this was affected by soil type. Carbon utilization differed among strains of the same species (and symbiovar), but some strains were more responsive to the soil environment than others.<br><br>CONCLUSIONS: This novel modification of the MicroResp(&#x2122;) has enabled the scope of carbon-utilization patterns of single strains of bacteria, such as Rh.&#xa0;leguminosarum bv. trifolii, to be studied in soil.<br><br>The system is a new tool with applications in microbial ecology adaptable to the study of many culturable bacterial and fungal soil-borne taxa. It will allow measurement of a micro-organism's ability to utilize common C sources released in rhizosphere exudates to be measured in a physical soil background. This knowledge may improve selection efficiency and deployment of commercial microbial inoculants.}, }
@article {pmid27152415, year = {2016}, author = {Olesen, SW and Vora, S and Techtmann, SM and Fortney, JL and Bastidas-Oyanedel, JR and Rodríguez, J and Hazen, TC and Alm, EJ}, title = {A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments.}, journal = {PloS one}, volume = {11}, number = {5}, pages = {e0154804}, pmid = {27152415}, issn = {1932-6203}, mesh = {Biodiversity ; *Ecology ; }, abstract = {Many microbial ecology experiments use sequencing data to measure a community's response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samples and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method's validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of "bottle effects".}, }
@article {pmid27152346, year = {2016}, author = {Pandey, R and Usui, K and Livingstone, RA and Fischer, SA and Pfaendtner, J and Backus, EH and Nagata, Y and Fröhlich-Nowoisky, J and Schmüser, L and Mauri, S and Scheel, JF and Knopf, DA and Pöschl, U and Bonn, M and Weidner, T}, title = {Ice-nucleating bacteria control the order and dynamics of interfacial water.}, journal = {Science advances}, volume = {2}, number = {4}, pages = {e1501630}, pmid = {27152346}, issn = {2375-2548}, mesh = {Bacteria/chemistry/*metabolism ; Bacterial Outer Membrane Proteins/*metabolism ; Hydrogen Bonding ; Ice ; Molecular Dynamics Simulation ; Plants/microbiology ; Pseudomonas syringae/*metabolism/pathogenicity ; Temperature ; Water/metabolism ; }, abstract = {Ice-nucleating organisms play important roles in the environment. With their ability to induce ice formation at temperatures just below the ice melting point, bacteria such as Pseudomonas syringae attack plants through frost damage using specialized ice-nucleating proteins. Besides the impact on agriculture and microbial ecology, airborne P. syringae can affect atmospheric glaciation processes, with consequences for cloud evolution, precipitation, and climate. Biogenic ice nucleation is also relevant for artificial snow production and for biomimetic materials for controlled interfacial freezing. We use interface-specific sum frequency generation (SFG) spectroscopy to show that hydrogen bonding at the water-bacteria contact imposes structural ordering on the adjacent water network. Experimental SFG data and molecular dynamics simulations demonstrate that ice-active sites within P. syringae feature unique hydrophilic-hydrophobic patterns to enhance ice nucleation. The freezing transition is further facilitated by the highly effective removal of latent heat from the nucleation site, as apparent from time-resolved SFG spectroscopy.}, }
@article {pmid27150379, year = {2016}, author = {Huber, KJ and Geppert, AM and Wanner, G and Fösel, BU and Wüst, PK and Overmann, J}, title = {The first representative of the globally widespread subdivision 6 Acidobacteria,Vicinamibacter silvestris gen. nov., sp. nov., isolated from subtropical savannah soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {66}, number = {8}, pages = {2971-2979}, doi = {10.1099/ijsem.0.001131}, pmid = {27150379}, issn = {1466-5034}, mesh = {Acidobacteria/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Glycolipids/chemistry ; *Grassland ; Namibia ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {Members of the phylum Acidobacteria are abundant in a wide variety of soil environments. Despite this, previous cultivation attempts have frequently failed to retrieve representative phylotypes of Acidobacteria, which have, therefore, been discovered by culture-independent methods (13175 acidobacterial sequences in the SILVA database version 123; NR99) and only 47 species have been described so far. Strain Ac_5_C6T represents the first isolate of the globally widespread and abundant subdivision 6 Acidobacteria and is described in the present study. Cells of strain Ac_5_C6T were Gram-stain-negative, immotile rods that divided by binary fission. They formed yellow, extremely cohesive colonies and stable aggregates even in rapidly shaken liquid cultures. Ac_5_C6T was tolerant of a wide range of temperatures (12-40 °C) and pH values (4.7-9.0). It grew chemoorganoheterotrophically on a broad range of substrates including different sugars, organic acids, nucleic acids and complex proteinaceous compounds. The major fatty acids of Ac_5_C6T were iso-C17 : 1 ω9c, C18 : 1 ω7c and iso-C15 : 0. Summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), iso-C17 : 0 and C16 : 0 were also detected. Phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid were identified as polar lipids. The major quinone was MK-8. The DNA G+C content of Ac_5_C6T was 65.9 mol%. With 16S rRNA gene sequence similarities of 83-84 %, the closest described relatives were Acidicapsa borealis KA1T, Acidobacterium capsulatum 161T, Granulicella pectinovorans TPB6011T, Occallatibacter riparius 277T and Paludibaculum fermentans P105T. According to the morphological, physiological and molecular characteristics, the novel genus Vicinamibacter gen. nov., and the novel species, Vicinamibacter silvestris sp. nov. (type strain Ac_5_C6T = DSM 29464T = LMG 29035T) are proposed.}, }
@article {pmid27148716, year = {2016}, author = {Seuntjens, D and Bundervoet, BL and Mollen, H and De Mulder, C and Wypkema, E and Verliefde, A and Nopens, I and Colsen, JG and Vlaeminck, SE}, title = {Energy efficient treatment of A-stage effluent: pilot-scale experiences with shortcut nitrogen removal.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {73}, number = {9}, pages = {2150-2158}, doi = {10.2166/wst.2016.005}, pmid = {27148716}, issn = {0273-1223}, mesh = {Bacteria/growth &amp; development ; Biological Oxygen Demand Analysis ; *Bioreactors ; Carbon ; Denitrification ; Netherlands ; Nitrites ; Nitrogen/*chemistry ; Sewage ; Waste Disposal, Fluid/*methods ; Wastewater ; Water Pollutants, Chemical/*chemistry ; Water Purification/*methods ; }, abstract = {Energy autarky of sewage treatment plants, while reaching chemical oxygen demand (COD) and N discharge limits, can be achieved by means of shortcut N-removal. This study presents the results of a shortcut N-removal pilot, located at the biological two-'stage (high/low rate) wastewater treatment plant of Breda, The Netherlands. The pilot treated real effluent of a high-rate activated sludge (COD/N = 3), fed in a continuous mode at realistic loading rates (90-100 g N/(m(3)·d)). The operational strategy, which included increased stress on the sludge settling velocity, showed development of a semi-granular sludge, with average particle size of 280 μm (ø(4,3)), resulting in increased suppression of nitrite-oxidizing bacteria. The process was able to remove part of the nitrogen (51 ± 23%) over nitrite, with COD/N removal ratios of 3.2 ± 0.9. The latter are lower than the current operation of the full-scale B-stage in Breda (6.8-9.4), showing promising results for carbon-efficient N-removal, while producing a well settling sludge (SVI(30) < 100 mL/g).}, }
@article {pmid27149160, year = {2016}, author = {Wang, Y and Huang, WE and Cui, L and Wagner, M}, title = {Single cell stable isotope probing in microbiology using Raman microspectroscopy.}, journal = {Current opinion in biotechnology}, volume = {41}, number = {}, pages = {34-42}, doi = {10.1016/j.copbio.2016.04.018}, pmid = {27149160}, issn = {1879-0429}, support = {BB/M000265/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/*metabolism ; Isotope Labeling/*methods ; Single-Cell Analysis/*methods ; Spectrum Analysis, Raman/*methods ; }, abstract = {Microbial communities are essential for most ecosystem processes and interact in highly complex ways with virtually all eukaryotes. Thus, a detailed understanding of the function of such communities is a fundamental prerequisite for microbial ecologists, applied microbiologists and microbiome researchers. Using single cell Raman microspectroscopy, biochemical fingerprints of individual microbial cells can be obtained in an externally label-free and non-destructive manner. If combined with stable isotope probing (SIP), Raman spectroscopy can directly reveal functions of single microorganisms in their natural habitat. This review provides an update on various SIP-approaches suitable for combination with different Raman scattering techniques and illustrates how single cell Raman SIP can be directly combined with the omics-centric analysis pipelines to investigate microbial communities.}, }
@article {pmid27148222, year = {2016}, author = {Stamps, BW and Lyles, CN and Suflita, JM and Masoner, JR and Cozzarelli, IM and Kolpin, DW and Stevenson, BS}, title = {Municipal Solid Waste Landfills Harbor Distinct Microbiomes.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {534}, pmid = {27148222}, issn = {1664-302X}, abstract = {Landfills are the final repository for most of the discarded material from human society and its "built environments." Microorganisms subsequently degrade this discarded material in the landfill, releasing gases (largely CH4 and CO2) and a complex mixture of soluble chemical compounds in leachate. Characterization of "landfill microbiomes" and their comparison across several landfills should allow the identification of environmental or operational properties that influence the composition of these microbiomes and potentially their biodegradation capabilities. To this end, the composition of landfill microbiomes was characterized as part of an ongoing USGS national survey studying the chemical composition of leachates from 19 non-hazardous landfills across 16 states in the continental U.S. The landfills varied in parameters such as size, waste composition, management strategy, geography, and climate zone. The diversity and composition of bacterial and archaeal populations in leachate samples were characterized by 16S rRNA gene sequence analysis, and compared against a variety of physical and chemical parameters in an attempt to identify their impact on selection. Members of the Epsilonproteobacteria, Gammaproteobacteria, Clostridia, and candidate division OP3 were the most abundant. The distribution of the observed phylogenetic diversity could best be explained by a combination of variables and was correlated most strongly with the concentrations of chloride and barium, rate of evapotranspiration, age of waste, and the number of detected household chemicals. This study illustrates how leachate microbiomes are distinct from those of other natural or built environments, and sheds light on the major selective forces responsible for this microbial diversity.}, }
@article {pmid27148214, year = {2016}, author = {Bouskill, NJ and Wood, TE and Baran, R and Ye, Z and Bowen, BP and Lim, H and Zhou, J and Nostrand, JD and Nico, P and Northen, TR and Silver, WL and Brodie, EL}, title = {Belowground Response to Drought in a Tropical Forest Soil. I. Changes in Microbial Functional Potential and Metabolism.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {525}, pmid = {27148214}, issn = {1664-302X}, abstract = {Global climate models predict a future of increased severity of drought in many tropical forests. Soil microbes are central to the balance of these systems as sources or sinks of atmospheric carbon (C), yet how they respond metabolically to drought is not well-understood. We simulated drought in the typically aseasonal Luquillo Experimental Forest, Puerto Rico, by intercepting precipitation falling through the forest canopy. This approach reduced soil moisture by 13% and water potential by 0.14 MPa (from -0.2 to -0.34). Previous results from this experiment have demonstrated that the diversity and composition of these soil microbial communities are sensitive to even small changes in soil water. Here, we show prolonged drought significantly alters the functional potential of the community and provokes a clear osmotic stress response, including the production of compatible solutes that increase intracellular C demand. Subsequently, a microbial population emerges with a greater capacity for extracellular enzyme production targeting macromolecular carbon. Significantly, some of these drought-induced functional shifts in the soil microbiota are attenuated by prior exposure to a short-term drought suggesting that acclimation may occur despite a lack of longer-term drought history.}, }
@article {pmid27148189, year = {2016}, author = {Wong, K and Shaw, TI and Oladeinde, A and Glenn, TC and Oakley, B and Molina, M}, title = {Rapid Microbiome Changes in Freshly Deposited Cow Feces under Field Conditions.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {500}, pmid = {27148189}, issn = {1664-302X}, abstract = {Although development of next generation sequencing (NGS) has substantially improved our understanding of the microbial ecology of animal feces, previous studies have mostly focused on freshly excreted feces. There is still limited understanding of the aging process dynamics of fecal microbiomes in intact cowpats exposed to natural environments. Fresh cowpats were sampled at multiple time points for 57 days under field conditions; half the samples were exposed to sunlight (unshaded) while the other half was protected from sunlight (shaded). The 16SRNA hypervariable region 4 was amplified from each sample and sequenced on an Illumina MiSeq Platform. While Clostridia, Bacteroidia, and Sphingobacteria were dominant classes of bacteria in fresh cowpats, Alphaproteobacteria, Betaproteobacteria, Actinobacteria, and Bacilli were the dominant classes by the end of the study, indicating a general shift from anaerobic to aerobic bacterial populations. This change was most likely influenced by the shift from cattle gut (anaerobic) to pasture ground (aerobic). Reduced moisture in cowpats may also contribute to the community shift since air can penetrate the dryer cowpat more easily. Twelve genera consisting pathogenic bacteria were detected, with Mycobacterium, Bacillus, and Clostridium being the most abundant; their combined abundance accounts for 90% of the total pathogenic genera. Taxonomic richness and diversity increased throughout the study for most samples, which could be due to bacteria regrowth and colonization of bacteria from the environment. In contrast to the high taxonomic diversity, the changes of PICRUSt inferred function profile were minimal for all cowpats throughout the study, which suggest that core functions predicted by PICRUSt may be too conserved to distinguish differences between aerobe and anaerobe. To the best of our knowledge, this is the first study demonstrating that cowpat exposure to air and sunlight can cause drastic microbiome changes soon after deposition in natural environments. Our findings offer important insights for future research characterizing the microbiome of feces collected in natural environments and the impact of cattle fecal contamination on water resources.}, }
@article {pmid27148188, year = {2016}, author = {Gong, J and Qing, Y and Zou, S and Fu, R and Su, L and Zhang, X and Zhang, Q}, title = {Protist-Bacteria Associations: Gammaproteobacteria and Alphaproteobacteria Are Prevalent as Digestion-Resistant Bacteria in Ciliated Protozoa.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {498}, pmid = {27148188}, issn = {1664-302X}, abstract = {Protistan bacterivory, a microbial process involving ingestion and digestion, is ecologically important in the microbial loop in aquatic and terrestrial ecosystems. While bacterial resistance to protistan ingestion has been relatively well understood, little is known about protistan digestion in which some ingested bacteria could not be digested in cells of major protistan grazers in the natural environment. Here we report the phylogenetic identities of digestion-resistant bacteria (DRB) that could survive starvation and form relatively stable associations with 11 marine and one freshwater ciliate species. Using clone library and sequencing of 16S rRNA genes, we found that the protistan predators could host a high diversity of DRB, most of which represented novel bacterial taxa that have not been cultivated. The localization inside host cells, quantity, and viability of these bacteria were checked using fluorescence in situ hybridization. The DRB were affiliated with Actinobacteria, Bacteroidetes, Firmicutes, Parcubacteria (OD1), Planctomycetes, and Proteobacteria, with Gammaproteobacteria and Alphaproteobacteria being the most frequently occurring classes. The dominance of Gamma- and Alphaproteobacteria corresponds well to a previous study of Global Ocean Sampling metagenomic data showing the widespread types of bacterial type VI and IV secretion systems (T6SS and T4SS) in these two taxa, suggesting a putatively significant role of secretion systems in promoting marine protist-bacteria associations. In the DRB assemblages, opportunistic bacteria such as Alteromonadaceae, Pseudoalteromonadaceae, and Vibrionaceae often presented with high proportions, indicating these bacteria could evade protistan grazing thus persist and accumulate in the community, which, however, contrasts with their well-known rarity in nature. This begs the question whether viral lysis is significant in killing these indigestible bacteria in microbial communities. Taken together, our study on the identity of DRB sheds new light on microbial interactions and generates further hypotheses including the potential importance of bacterial protein secretion systems in structuring bacterial community composition and functioning of "microbial black box" in aquatic environments.}, }
@article {pmid27147245, year = {2016}, author = {Rämä, T and Davey, ML and Nordén, J and Halvorsen, R and Blaalid, R and Mathiassen, GH and Alsos, IG and Kauserud, H}, title = {Fungi Sailing the Arctic Ocean: Speciose Communities in North Atlantic Driftwood as Revealed by High-Throughput Amplicon Sequencing.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {295-304}, pmid = {27147245}, issn = {1432-184X}, mesh = {Adaptation, Physiological ; Ascomycota/*classification/isolation &amp; purification ; Basidiomycota/*classification/isolation &amp; purification ; Biodiversity ; Computational Biology ; DNA, Fungal/genetics ; Ecosystem ; Multivariate Analysis ; Oceans and Seas ; Sequence Analysis, DNA ; Species Specificity ; *Water Microbiology ; Wood/*microbiology ; }, abstract = {High amounts of driftwood sail across the oceans and provide habitat for organisms tolerating the rough and saline environment. Fungi have adapted to the extremely cold and saline conditions which driftwood faces in the high north. For the first time, we applied high-throughput sequencing to fungi residing in driftwood to reveal their taxonomic richness, community composition, and ecology in the North Atlantic. Using pyrosequencing of ITS2 amplicons obtained from 49 marine logs, we found 807 fungal operational taxonomic units (OTUs) based on clustering at 97 % sequence similarity cut-off level. The phylum Ascomycota comprised 74 % of the OTUs and 20 % belonged to Basidiomycota. The richness of basidiomycetes decreased with prolonged submersion in the sea, supporting the general view of ascomycetes being more extremotolerant. However, more than one fourth of the fungal OTUs remained unassigned to any fungal class, emphasising the need for better DNA reference data from the marine habitat. Different fungal communities were detected in coniferous and deciduous logs. Our results highlight that driftwood hosts a considerably higher fungal diversity than currently known. The driftwood fungal community is not a terrestrial relic but a speciose assemblage of fungi adapted to the stressful marine environment and different kinds of wooden substrates found in it.}, }
@article {pmid27144092, year = {2016}, author = {Marques, C and Meireles, M and Norberto, S and Leite, J and Freitas, J and Pestana, D and Faria, A and Calhau, C}, title = {High-fat diet-induced obesity Rat model: a comparison between Wistar and Sprague-Dawley Rat.}, journal = {Adipocyte}, volume = {5}, number = {1}, pages = {11-21}, pmid = {27144092}, issn = {2162-3945}, abstract = {In the past decades, obesity and associated metabolic complications have reached epidemic proportions. For the study of these pathologies, a number of animal models have been developed. However, a direct comparison between Wistar and Sprague-Dawley (SD) Rat as models of high-fat (HF) diet-induced obesity has not been adequately evaluated so far. Wistar and SD rats were assigned for 2 experimental groups for 17 weeks: standard (St) and high-fat (HF) diet groups. To assess some of the features of the metabolic syndrome, oral glucose tolerance tests, systolic blood pressure measurements and blood biochemical analysis were performed throughout the study. The gut microbiota composition of the animals of each group was evaluated at the end of the study by real-time PCR. HF diet increased weight gain, body fat mass, mesenteric adipocyte's size, adiponectin and leptin plasma levels and decreased oral glucose tolerance in both Wistar and SD rats. However, the majority of these effects were more pronounced or earlier detected in Wistar rats. The gut microbiota of SD rats was less abundant in Bacteroides and Prevotella but richer in Bifidobacterium and Lactobacillus comparatively to the gut microbiota of Wistar rats. Nevertheless, the modulation of the gut microbiota by HF diet was similar in both strains, except for Clostridium leptum that was only reduced in Wistar rats fed with HF diet. In conclusion, both Wistar and SD Rat can be used as models of HF diet-induced obesity although the metabolic effects caused by HF diet seemed to be more pronounced in Wistar Rat. Differences in the gut microbial ecology may account for the worsened metabolic scenario observed in Wistar Rat.}, }
@article {pmid27143384, year = {2016}, author = {Wasmund, K and Cooper, M and Schreiber, L and Lloyd, KG and Baker, BJ and Petersen, DG and Jørgensen, BB and Stepanauskas, R and Reinhardt, R and Schramm, A and Loy, A and Adrian, L}, title = {Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling.}, journal = {mBio}, volume = {7}, number = {3}, pages = {}, pmid = {27143384}, issn = {2150-7511}, support = {P 25111/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Chloroflexi/*genetics/isolation &amp; purification/*metabolism ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Denmark ; *Genome, Bacterial ; Geologic Sediments/microbiology ; Hydrocarbons, Aromatic/metabolism ; Hydrogensulfite Reductase/*genetics ; Metabolic Networks and Pathways/*genetics ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfites/*metabolism ; }, abstract = {UNLABELLED: The marine subsurface sediment biosphere is widely inhabited by bacteria affiliated with the class Dehalococcoidia (DEH), phylum Chloroflexi, and yet little is known regarding their metabolisms. In this report, genomic content from a single DEH cell (DEH-C11) with a 16S rRNA gene that was affiliated with a diverse cluster of 16S rRNA gene sequences prevalent in marine sediments was obtained from sediments of Aarhus Bay, Denmark. The distinctive gene content of this cell suggests metabolic characteristics that differ from those of known DEH and Chloroflexi The presence of genes encoding dissimilatory sulfite reductase (Dsr) suggests that DEH could respire oxidized sulfur compounds, although Chloroflexi have never been implicated in this mode of sulfur cycling. Using long-range PCR assays targeting DEH dsr loci, dsrAB genes were amplified and sequenced from various marine sediments. Many of the amplified dsrAB sequences were affiliated with the DEH Dsr clade, which we propose equates to a family-level clade. This provides supporting evidence for the potential for sulfite reduction by diverse DEH species. DEH-C11 also harbored genes encoding reductases for arsenate, dimethyl sulfoxide, and halogenated organics. The reductive dehalogenase homolog (RdhA) forms a monophyletic clade along with RdhA sequences from various DEH-derived contigs retrieved from available metagenomes. Multiple facts indicate that this RdhA may not be a terminal reductase. The presence of other genes indicated that nutrients and energy may be derived from the oxidation of substituted homocyclic and heterocyclic aromatic compounds. Together, these results suggest that marine DEH play a previously unrecognized role in sulfur cycling and reveal the potential for expanded catabolic and respiratory functions among subsurface DEH.<br><br>IMPORTANCE: Sediments underlying our oceans are inhabited by microorganisms in cell numbers similar to those estimated to inhabit the oceans. Microorganisms in sediments consist of various diverse and uncharacterized groups that contribute substantially to global biogeochemical cycles. Since most subsurface microorganisms continue to evade cultivation, possibly due to very slow growth, we obtained and analyzed genomic information from a representative of one of the most widespread and abundant, yet uncharacterized bacterial groups of the marine subsurface. We describe several key features that may contribute to their widespread distribution, such as respiratory flexibility and the potential to use oxidized sulfur compounds, which are abundant in marine environments, as electron acceptors. Together, these data provide important information that can be used to assist in designing enrichment strategies or other postgenomic studies, while also improving our understanding of the diversity and distribution of dsrAB genes, which are widely used functional marker genes for sulfur-cycling microbes.}, }
@article {pmid27140608, year = {2016}, author = {Doblin, MA and van Sebille, E}, title = {Drift in ocean currents impacts intergenerational microbial exposure to temperature.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {20}, pages = {5700-5705}, pmid = {27140608}, issn = {1091-6490}, mesh = {Computer Simulation ; Ecosystem ; *Global Warming ; *Oceans and Seas ; Seasons ; *Water Microbiology ; Weather ; }, abstract = {Microbes are the foundation of marine ecosystems [Falkowski PG, Fenchel T, Delong EF (2008) Science 320(5879):1034-1039]. Until now, the analytical framework for understanding the implications of ocean warming on microbes has not considered thermal exposure during transport in dynamic seascapes, implying that our current view of change for these critical organisms may be inaccurate. Here we show that upper-ocean microbes experience along-trajectory temperature variability up to 10 °C greater than seasonal fluctuations estimated in a static frame, and that this variability depends strongly on location. These findings demonstrate that drift in ocean currents can increase the thermal exposure of microbes and suggests that microbial populations with broad thermal tolerance will survive transport to distant regions of the ocean and invade new habitats. Our findings also suggest that advection has the capacity to influence microbial community assemblies, such that regions with strong currents and large thermal fluctuations select for communities with greatest plasticity and evolvability, and communities with narrow thermal performance are found where ocean currents are weak or along-trajectory temperature variation is low. Given that fluctuating environments select for individual plasticity in microbial lineages, and that physiological plasticity of ancestors can predict the magnitude of evolutionary responses of subsequent generations to environmental change [Schaum CE, Collins S (2014) Proc Biol Soc 281(1793):20141486], our findings suggest that microbial populations in the sub-Antarctic (∼40°S), North Pacific, and North Atlantic will have the most capacity to adapt to contemporary ocean warming.}, }
@article {pmid27138048, year = {2016}, author = {Kelly, LC and Colin, Y and Turpault, MP and Uroz, S}, title = {Mineral Type and Solution Chemistry Affect the Structure and Composition of Actively Growing Bacterial Communities as Revealed by Bromodeoxyuridine Immunocapture and 16S rRNA Pyrosequencing.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {428-442}, pmid = {27138048}, issn = {1432-184X}, mesh = {Bacteria/*classification/isolation &amp; purification ; Biological Assay ; Bromodeoxyuridine ; DNA, Bacterial/genetics ; Hydrogen-Ion Concentration ; Minerals/analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Understanding how minerals affect bacterial communities and their in situ activities in relation to environmental conditions are central issues in soil microbial ecology, as minerals represent essential reservoirs of inorganic nutrients for the biosphere. To determine the impact of mineral type and solution chemistry on soil bacterial communities, we compared the diversity, composition, and functional abilities of a soil bacterial community incubated in presence/absence of different mineral types (apatite, biotite, obsidian). Microcosms were prepared containing different liquid culture media devoid of particular essential nutrients, the nutrients provided only in the introduced minerals and therefore only available to the microbial community through mineral dissolution by biotic and/or abiotic processes. By combining functional screening of bacterial isolates and community analysis by bromodeoxyuridine DNA immunocapture and 16S rRNA gene pyrosequencing, we demonstrated that bacterial communities were mainly impacted by the solution chemistry at the taxonomic level and by the mineral type at the functional level. Metabolically active bacterial communities varied with solution chemistry and mineral type. Burkholderia were significantly enriched in the obsidian treatment compared to the biotite treatment and were the most effective isolates at solubilizing phosphorous or mobilizing iron, in all the treatments. A detailed analysis revealed that the 16S rRNA gene sequences of the OTUs or isolated strains assigned as Burkholderia in our study showed high homology with effective mineral-weathering bacteria previously recovered from the same experimental site.}, }
@article {pmid27138047, year = {2016}, author = {Zelaya-Molina, LX and Hernández-Soto, LM and Guerra-Camacho, JE and Monterrubio-López, R and Patiño-Siciliano, A and Villa-Tanaca, L and Hernández-Rodríguez, C}, title = {Ammonia-Oligotrophic and Diazotrophic Heavy Metal-Resistant Serratia liquefaciens Strains from Pioneer Plants and Mine Tailings.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {324-346}, pmid = {27138047}, issn = {1432-184X}, mesh = {Ammonia/*analysis ; Biofilms ; DNA, Bacterial/genetics ; Genes, Bacterial ; Genetic Variation ; Hydrogen-Ion Concentration ; Indoleacetic Acids/analysis ; Metagenomics ; Metals, Heavy/*analysis ; Mexico ; Microbial Sensitivity Tests ; *Mining ; Nitrogen Fixation ; *Phylogeny ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Serratia liquefaciens/*classification/genetics/isolation &amp; purification ; Soil Microbiology ; Stress, Physiological ; }, abstract = {Mine tailings are man-made environments characterized by low levels of organic carbon and assimilable nitrogen, as well as moderate concentrations of heavy metals. For the introduction of nitrogen into these environments, a key role is played by ammonia-oligotrophic/diazotrophic heavy metal-resistant guilds. In mine tailings from Zacatecas, Mexico, Serratia liquefaciens was the dominant heterotrophic culturable species isolated in N-free media from bulk mine tailings as well as the rhizosphere, roots, and aerial parts of pioneer plants. S. liquefaciens strains proved to be a meta-population with high intraspecific genetic diversity and a potential to respond to these extreme conditions. The phenotypic and genotypic features of these strains reveal the potential adaptation of S. liquefaciens to oligotrophic and nitrogen-limited mine tailings with high concentrations of heavy metals. These features include ammonia-oligotrophic growth, nitrogen fixation, siderophore and indoleacetic acid production, phosphate solubilization, biofilm formation, moderate tolerance to heavy metals under conditions of diverse nitrogen availability, and the presence of zntA, amtB, and nifH genes. The acetylene reduction assay suggests low nitrogen-fixing activity. The nifH gene was harbored in a plasmid of ∼60 kb and probably was acquired by a horizontal gene transfer event from Klebsiella variicola.}, }
@article {pmid27137897, year = {2016}, author = {Chilloux, J and Neves, AL and Boulangé, CL and Dumas, ME}, title = {The microbial-mammalian metabolic axis: a critical symbiotic relationship.}, journal = {Current opinion in clinical nutrition and metabolic care}, volume = {19}, number = {4}, pages = {250-256}, pmid = {27137897}, issn = {1473-6519}, support = {MR/M501797/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animal Nutritional Physiological Phenomena ; Animals ; Diet/adverse effects ; *Diet, Healthy/veterinary ; Dysbiosis/etiology/microbiology/*prevention &amp; control/veterinary ; Fermentation ; *Gastrointestinal Microbiome ; Humans ; Mammals ; Metabolic Diseases/etiology/microbiology/*prevention &amp; control/veterinary ; Prebiotics ; Probiotics ; *Symbiosis ; }, abstract = {PURPOSE OF REVIEW: The microbial-mammalian symbiosis plays a critical role in metabolic health. Microbial metabolites emerge as key messengers in the complex communication between the gut microbiota and their host. These chemical signals are mainly derived from nutritional precursors, which in turn are also able to modify gut microbiota population. Recent advances in the characterization of the gut microbiome and the mechanisms involved in this symbiosis allow the development of nutritional interventions. This review covers the latest findings on the microbial-mammalian metabolic axis as a critical symbiotic relationship particularly relevant to clinical nutrition.<br><br>RECENT FINDINGS: The modulation of host metabolism by metabolites derived from the gut microbiota highlights the importance of gut microbiota in disease prevention and causation. The composition of microbial populations in our gut ecosystem is a critical pathophysiological factor, mainly regulated by diet, but also by the host's characteristics (e.g. genetics, circadian clock, immune system, age). Tailored interventions, including dietary changes, the use of antibiotics, prebiotic and probiotic supplementation and faecal transplantation are promising strategies to manipulate microbial ecology.<br><br>SUMMARY: The microbiome is now considered as an easily reachable target to prevent and treat related diseases. Recent findings in both mechanisms of its interactions with host metabolism and in strategies to modify gut microbiota will allow us to develop more effective treatments especially in metabolic diseases.}, }
@article {pmid27137125, year = {2016}, author = {Kinnunen, M and Dechesne, A and Proctor, C and Hammes, F and Johnson, D and Quintela-Baluja, M and Graham, D and Daffonchio, D and Fodelianakis, S and Hahn, N and Boon, N and Smets, BF}, title = {A conceptual framework for invasion in microbial communities.}, journal = {The ISME journal}, volume = {10}, number = {12}, pages = {2773-2775}, pmid = {27137125}, issn = {1751-7370}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; *Biodiversity ; Ecosystem ; *Microbiota ; Models, Biological ; }, abstract = {There is a growing interest in controlling-promoting or avoiding-the invasion of microbial communities by new community members. Resource availability and community structure have been reported as determinants of invasion success. However, most invasion studies do not adhere to a coherent and consistent terminology nor always include rigorous interpretations of the processes behind invasion. Therefore, we suggest that a consistent set of definitions and a rigorous conceptual framework are needed. We define invasion in a microbial community as the establishment of an alien microbial type in a resident community and argue how simple criteria to define aliens, residents, and alien establishment can be applied for a wide variety of communities. In addition, we suggest an adoption of the community ecology framework advanced by Vellend (2010) to clarify potential determinants of invasion. This framework identifies four fundamental processes that control community dynamics: dispersal, selection, drift and diversification. While selection has received ample attention in microbial community invasion research, the three other processes are often overlooked. Here, we elaborate on the relevance of all four processes and conclude that invasion experiments should be designed to elucidate the role of dispersal, drift and diversification, in order to obtain a complete picture of invasion as a community process.}, }
@article {pmid27137074, year = {2016}, author = {Santos, HF and Carmo, FL and Martirez, N and Duarte, GA and Calderon, EN and Castro, CB and Pires, DO and Rosado, AS and Peixoto, RS}, title = {Cyanobacterial and microeukaryotic profiles of healthy, diseased, and dead Millepora alcicornis from the South Atlantic.}, journal = {Diseases of aquatic organisms}, volume = {119}, number = {2}, pages = {163-172}, doi = {10.3354/dao02972}, pmid = {27137074}, issn = {0177-5103}, mesh = {Animals ; Anthozoa/*microbiology ; Atlantic Ocean ; Cyanobacteria/*isolation &amp; purification ; Eukaryota/classification/*isolation &amp; purification ; Host-Pathogen Interactions ; }, abstract = {Coral reefs are at risk due to events associated with human activities, which have resulted in the increasing occurrence of coral diseases. Corals live in symbiotic relationships with different microorganisms, such as cyanobacteria, a very important group. Members of the phylum Cyanobacteria are found in great abundance in the marine environment and may play an essential role in keeping corals healthy but may also be pathogenic. Furthermore, some studies are showing a rise in cyanobacterial abundance in coral reefs as a result of climate change. The current study aimed to improve our understanding of the relationship between cyanobacteria and coral health. Our results revealed that the cyanobacterial genus GPI (Anabaena) is a possible opportunistic pathogen of the coral species Millepora alcicornis in the South Atlantic Ocean. Furthermore, the bacterial and microeukaryotic profile of healthy, diseased, and post-disease (skeletal) regions of affected coral indicated that a microbial consortium composed of Anabaena sp., Prosthecochloris sp., and microeukaryotes could be involved in this pathogenicity or could be taking advantage of the diseased state.}, }
@article {pmid27135590, year = {2016}, author = {Morris, D and Kavanagh, S and Carney, K and MacDomhnaill, B and Cormican, M}, title = {CapE (capture, amplify, extract): A rapid method for detection of low level contamination of water with Verocytotoxigenic Escherichia coli (VTEC).}, journal = {The Science of the total environment}, volume = {563-564}, number = {}, pages = {267-272}, doi = {10.1016/j.scitotenv.2016.04.075}, pmid = {27135590}, issn = {1879-1026}, mesh = {Antigens, Bacterial/isolation &amp; purification ; Bacterial Load/*methods ; Drinking Water/*microbiology ; Filtration/*methods ; Ireland ; Real-Time Polymerase Chain Reaction/*methods ; Shiga-Toxigenic Escherichia coli/*isolation &amp; purification ; Virulence Factors/isolation &amp; purification ; *Water Microbiology ; }, abstract = {Verocytotoxigenic Escherichia coli (VTEC) is associated with a wide spectrum of disease from mild self-limiting diarrhoea to haemolytic uremic syndrome. Contaminated drinking water is accepted as an important route of transmission in Ireland as elsewhere however established methods for detection of VTEC in drinking water have limitations. We describe a sensitive and rapid method for detection of VTEC from large volumes (20 to 30L) of drinking water based on filtration, enrichment culture of filters and real-time PCR detection of VTEC virulence and O antigen determinants from enrichments. The method has potential applications for other waterborne pathogens.}, }
@article {pmid27130479, year = {2016}, author = {Mysara, M and Leys, N and Raes, J and Monsieurs, P}, title = {IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data.}, journal = {BMC bioinformatics}, volume = {17}, number = {1}, pages = {192}, pmid = {27130479}, issn = {1471-2105}, mesh = {Algorithms ; Animals ; *Genes, rRNA ; High-Throughput Nucleotide Sequencing/*methods ; Machine Learning ; Metagenomics/*methods ; Mice ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {BACKGROUND: The development of high-throughput sequencing technologies has revolutionized the field of microbial ecology via the sequencing of phylogenetic marker genes (e.g. 16S rRNA gene amplicon sequencing). Denoising, the removal of sequencing errors, is an important step in preprocessing amplicon sequencing data. The increasing popularity of the Illumina MiSeq platform for these applications requires the development of appropriate denoising methods.<br><br>RESULTS: The newly proposed denoising algorithm IPED includes a machine learning method which predicts potentially erroneous positions in sequencing reads based on a combination of quality metrics. Subsequently, this information is used to group those error-containing reads with correct reads, resulting in error-free consensus reads. This is achieved by masking potentially erroneous positions during this clustering step. Compared to the second best algorithm available, IPED detects double the amount of errors. Reducing the error rate had a positive effect on the clustering of reads in operational taxonomic units, with an almost perfect correspondence between the number of clusters and the theoretical number of species present in the mock communities.<br><br>CONCLUSION: Our algorithm IPED is a powerful denoising tool for correcting sequencing errors in Illumina MiSeq 16S rRNA gene&#xa0;amplicon sequencing data. Apart from significantly reducing the error rate of the sequencing reads, it has also a beneficial effect on their clustering into operational taxonomic units. IPED is freely available at http://science.sckcen.be/en/Institutes/EHS/MCB/MIC/Bioinformatics/ .}, }
@article {pmid27129319, year = {2016}, author = {Hubert, J and Kamler, M and Nesvorna, M and Ledvinka, O and Kopecky, J and Erban, T}, title = {Comparison of Varroa destructor and Worker Honeybee Microbiota Within Hives Indicates Shared Bacteria.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {448-459}, pmid = {27129319}, issn = {1432-184X}, mesh = {Animals ; Bees/*microbiology/parasitology ; Biodiversity ; DNA, Bacterial/genetics ; Female ; Male ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; Spiroplasma/*classification/isolation &amp; purification ; Symbiosis ; Varroidae/*microbiology ; }, abstract = {The ectoparasitic mite Varroa destructor is a major pest of the honeybee Apis mellifera. In a previous study, bacteria were found in the guts of mites collected from winter beehive debris and were identified using Sanger sequencing of their 16S rRNA genes. In this study, community comparison and diversity analyses were performed to examine the microbiota of honeybees and mites at the population level. The microbiota of the mites and honeybees in 26 colonies in seven apiaries in Czechia was studied. Between 10 and 50 Varroa females were collected from the bottom board, and 10 worker bees were removed from the peripheral comb of the same beehive. Both bees and mites were surface sterilized. Analysis of the 16S rRNA gene libraries revealed significant differences in the Varroa and honeybee microbiota. The Varroa microbiota was less diverse than was the honeybee microbiota, and the relative abundances of bacterial taxa in the mite and bee microbiota differed. The Varroa mites, but not the honeybees, were found to be inhabited by Diplorickettsia. The relative abundance of Arsenophonus, Morganella, Spiroplasma, Enterococcus, and Pseudomonas was higher in Varroa than in honeybees, and the Diplorickettsia symbiont detected in this study is specific to Varroa mites. The results demonstrated that there are shared bacteria between Varroa and honeybee populations but that these bacteria occur in different relative proportions in the honeybee and mite bacteriomes. These results support the suggestion of bacterial transfer via mites, although only some of the transferred bacteria may be harmful.}, }
@article {pmid27127197, year = {2016}, author = {Garcia-Mazcorro, JF and Mills, D and Noratto, G}, title = {Molecular exploration of fecal microbiome in quinoa-supplemented obese mice.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {7}, pages = {}, doi = {10.1093/femsec/fiw089}, pmid = {27127197}, issn = {1574-6941}, mesh = {Animals ; Bacteria/classification/*isolation &amp; purification/metabolism ; Cecum/metabolism/microbiology ; Chenopodium quinoa/*metabolism ; Diabetes Mellitus, Experimental/metabolism/*microbiology ; Dietary Supplements/analysis ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Male ; Mice ; Mice, Obese ; Obesity/metabolism/*microbiology ; }, abstract = {Diet affects gut microorganisms and dietary interventions can help treat obesity and overweight. Our aim was to investigate the effect of quinoa supplementation on fecal microbial ecology of obese diabetic mice. Obese db/db mice were fed commercial diets with and without quinoa supplementation for eight weeks; non-obese mice consuming non-supplemented diet served as lean-control. Fecal bacterial communities were analyzed using marker gene sequencing of 16S rRNA genes. Over 300 000 good-quality sequences were studied and assigned to 5774 different bacterial species (Operational Taxonomic Units at 97% similarity). Significant differences in bacterial abundances were found among the treatment groups, including some associated specifically with quinoa consumption. Analysis of weighted UniFrac distances revealed a distinctive clustering of lean microbial communities independently from obese-control and quinoa-supplemented mice (Analysis of Similarities, P < 0.01). Predicted functional profiles showed significant differences in 38 metabolic functions but most were due to a difference between lean samples compared to both obese-control and quinoa. Quinoa supplementation was associated with lower butyrate and succinic acid concentrations in cecum that were not necessarily more similar to those concentrations in lean mice. This study provides insight into the complex interactions between nutritional supplements and the gut microbiota thus informing future molecular analysis of the health benefits.}, }
@article {pmid27126836, year = {2016}, author = {Moroenyane, I and Chimphango, SB and Wang, J and Kim, HK and Adams, JM}, title = {Deterministic assembly processes govern bacterial community structure in the Fynbos, South Africa.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {313-323}, pmid = {27126836}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; Ecosystem ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; South Africa ; }, abstract = {The Mediterranean Fynbos vegetation of South Africa is well known for its high levels of diversity, endemism, and the existence of very distinct plant communities on different soil types. Studies have documented the broad taxonomic classification and diversity patterns of soil microbial diversity, but none has focused on the community assembly processes. We hypothesised that bacterial phylogenetic community structure in the Fynbos is highly governed by deterministic processes. We sampled soils in four Fynbos vegetation types and examined bacterial communities using Illumina HiSeq platform with the 16S rRNA gene marker. UniFrac analysis showed that the community clustered strongly by vegetation type, suggesting a history of evolutionary specialisation in relation to habitats or plant communities. The standardised beta mean nearest taxon distance (ses. β NTD) index showed no association with vegetation type. However, the overall phylogenetic signal indicates that distantly related OTUs do tend to co-occur. Both NTI (nearest taxon index) and ses. β NTD deviated significantly from null models, indicating that deterministic processes were important in the assembly of bacterial communities. Furthermore, ses. β NTD was significantly higher than that of null expectations, indicating that co-occurrence of related bacterial lineages (over-dispersion in phylogenetic beta diversity) is determined by the differences in environmental conditions among the sites, even though the co-occurrence pattern did not correlate with any measured environmental parameter, except for a weak correlation with soil texture. We suggest that in the Fynbos, there are frequent shifts of niches by bacterial lineages, which then become constrained and evolutionary conserved in their new environments. Overall, this study sheds light on the relative roles of both deterministic and neutral processes in governing bacterial communities in the Fynbos. It seems that deterministic processes play a major role in assembling the bacterial community, with neutral processes playing a more minor role.}, }
@article {pmid27126040, year = {2016}, author = {Zhernakova, A and Kurilshikov, A and Bonder, MJ and Tigchelaar, EF and Schirmer, M and Vatanen, T and Mujagic, Z and Vila, AV and Falony, G and Vieira-Silva, S and Wang, J and Imhann, F and Brandsma, E and Jankipersadsing, SA and Joossens, M and Cenit, MC and Deelen, P and Swertz, MA and ,  and Weersma, RK and Feskens, EJ and Netea, MG and Gevers, D and Jonkers, D and Franke, L and Aulchenko, YS and Huttenhower, C and Raes, J and Hofker, MH and Xavier, RJ and Wijmenga, C and Fu, J}, title = {Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.}, journal = {Science (New York, N.Y.)}, volume = {352}, number = {6285}, pages = {565-569}, pmid = {27126040}, issn = {1095-9203}, support = {310372/ERC_/European Research Council/International ; 322698/ERC_/European Research Council/International ; P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Chromogranin A/analysis/metabolism ; Diet ; Enteroendocrine Cells/metabolism ; Feces/chemistry/microbiology ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; Genetic Markers ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; Netherlands ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Deep sequencing of the gut microbiomes of 1135 participants from a Dutch population-based cohort shows relations between the microbiome and 126 exogenous and intrinsic host factors, including 31 intrinsic factors, 12 diseases, 19 drug groups, 4 smoking categories, and 60 dietary factors. These factors collectively explain 18.7% of the variation seen in the interindividual distance of microbial composition. We could associate 110 factors to 125 species and observed that fecal chromogranin A (CgA), a protein secreted by enteroendocrine cells, was exclusively associated with 61 microbial species whose abundance collectively accounted for 53% of microbial composition. Low CgA concentrations were seen in individuals with a more diverse microbiome. These results are an important step toward a better understanding of environment-diet-microbe-host interactions.}, }
@article {pmid27122124, year = {2016}, author = {Wang, Q and Zhang, H and Liu, X}, title = {Microbial Community Composition Associated with Maotai Liquor Fermentation.}, journal = {Journal of food science}, volume = {81}, number = {6}, pages = {M1485-94}, doi = {10.1111/1750-3841.13319}, pmid = {27122124}, issn = {1750-3841}, mesh = {Air ; Alcoholic Beverages/*microbiology ; Bacteria/genetics/*growth &amp; development ; China ; Denaturing Gradient Gel Electrophoresis ; Edible Grain ; *Fermentation ; Flavoring Agents ; Fungi/genetics/*growth &amp; development ; Humans ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; Soil ; Soil Microbiology ; Sorghum ; }, abstract = {The solid-state fermentation state of Chinese Maotai liquor involves the interaction of several complex microbial communities leading to the generation of the most complex liquor fermentation system in the world and contributes to the unique flavor and aroma of the liquor. In this study, total DNA was extracted from 3 fermented grain samples (FG1, FG2, and FG3) and 12 environmental samples, including Daqu (DA1, DA2, DA3, and DA4), cellar mud (CS1, CS2, and CS3), soil (SL1 and SL2), air (A1 and A2), and sorghum (SH), and the 16S and 18S rRNA genes were amplified. The distribution of typical microorganisms in the samples was analyzed using nested PCR-denaturing gradient gel electrophoresis, while quantitative PCR amplification of 16S rRNA and internal transcribed spacer genes was performed to estimate the microbial abundance present in each sample. The results indicated that Daqu was the primary source of bacteria, followed by the air, soil, and sorghum samples, while the majority of the fungi responsible for Maotai liquor fermentation were from Daqu and sorghum. Highest bacterial concentrations were found in fermented grains, followed by Daqu and sorghum, while the highest fungal concentrations were found in Daqu, followed by sorghum and an air sample from outside the liquor production area. The findings of this study may provide information regarding the mechanisms responsible for flavor development in Maotai liquor, and may be used to further optimize the traditional art of making liquor.}, }
@article {pmid27120706, year = {2016}, author = {Huang, L and Dong, H and Jiang, H and Wang, S and Yang, J}, title = {Relative importance of advective flow versus environmental gradient in shaping aquatic ammonium oxidizers near the Three Gorges Dam of the Yangtze River, China.}, journal = {Environmental microbiology reports}, volume = {8}, number = {5}, pages = {667-674}, doi = {10.1111/1758-2229.12420}, pmid = {27120706}, issn = {1758-2229}, support = {41030211 and 41422208//National Natural Science Foundation of China/ ; //National 1000 Talents Program'/ ; //Fundamental Research Funds for National University/ ; //China University of Geosciences/ ; }, abstract = {Construction of a dam in a large river alters its hydrodynamic condition and geochemical gradient, but the effect of such anthropogenic activity on microbial ecology remains poorly understood. To assess this effect, we investigated the relative importance of advective flow versus environmental condition in shaping ammonia oxidizing bacteria (AOB) and archaea (AOA) community from 110 km upstream to the Three Gorges Dam (TGD) of the Yangtze River, China. Water physicochemical conditions, including turbidity, conductivity, redox state and nutrient level, were fairly constant from 110 to 45 km upstream of the TGD, but significantly oscillated near the dam. AOB and AOA in the Yangtze River were dominated by Nitrosospira- and Nitrosopumilus-affiliated clusters, respectively, and these compositions were invariant throughout the sampled 110 km flow path, suggesting that AOB and AOA communities in the river were largely transported from upstream by advection with minor local and transient inputs from surrounding soils and tributaries. However, the abundance of AOB and AOA was influenced by local geochemical conditions, possibly via the growth/decay mechanisms. The source of AOB in the Yangtze River appeared to be derived from soil near the headwater, but its abundance was enhanced during downstream transport, likely due to survival and growth.}, }
@article {pmid27118254, year = {2016}, author = {Gómez-Sagasti, MT and Barrutia, O and Ribas, G and Garbisu, C and Becerril, JM}, title = {Early transcriptomic response of Arabidopsis thaliana to polymetallic contamination: implications for the identification of potential biomarkers of metal exposure.}, journal = {Metallomics : integrated biometal science}, volume = {8}, number = {5}, pages = {518-531}, doi = {10.1039/c6mt00014b}, pmid = {27118254}, issn = {1756-591X}, mesh = {Arabidopsis/*drug effects/genetics/metabolism ; Biomarkers/*metabolism ; Gene Expression Regulation, Plant/drug effects ; Genes, Plant ; Metals/metabolism/*toxicity ; Oligonucleotide Array Sequence Analysis ; Reverse Transcriptase Polymerase Chain Reaction ; Soil Pollutants/metabolism/*toxicity ; *Transcriptome ; }, abstract = {Heavy metal contaminated sites are frequently characterized by the simultaneous presence of several heavy metals. However, many studies report metal-induced plant responses after long-term exposure to just one metal. By contrast, whole genome expression microarrays were employed here to investigate the early (3 h) transcriptional responses of Arabidopsis thaliana plants exposed to polymetallic treatment (Pb, Hg, Cu, Cd, Co, Ni, Zn, and Mn) at low (L) and high (H) concentrations. After 3 h of exposure to polymetallic treatment, a total of 1315 noticeably (≥2-fold) and significantly (P < 0.05) differentially expressed genes were identified: 656 and 351 upregulated and 314 and 200 downregulated genes in L and H treatments, respectively. Functional analysis revealed that many genes involved in oxidative stress and perception/signalling/regulation systems were activated. Genes encoding proteins involved in hormone regulation (jasmonic acid, abscisic acid, ethylene, and auxins), glucosinolate metabolism and sulphur and nitrogen transport were also modulated. RT-qPCR analysis of four downregulated (AOP2, SAUR16, BBX31, and MTPC3) and upregulated genes (ASN1, DIN2, BT2, and EXL5), markedly responsive to both L and H treatments, validated our microarray data and suggested the potential of some of these genes (AOP2, SAUR16, ASN1, and DIN2) as early biomarkers of metal exposure. Relevant changes in gene expression occur as early as 3 h after exposure to polymetallic treatment. Four genes deserve further studies as novel putative biomarkers of early metal exposure and also owing to their potential implications in stress-related mechanisms: sulphur balance (AOP2), phytohormone regulation of plant growth and development (SAUR16), ammonium detoxification (ASN1) and senescence (DIN2).}, }
@article {pmid27118186, year = {2016}, author = {Sultanpuram, VR and Mothe, T}, title = {Salipaludibacillus aurantiacus gen. nov., sp. nov. a novel alkali tolerant bacterium, reclassification of Bacillus agaradhaerens as Salipaludibacillus agaradhaerens comb. nov. and Bacillus neizhouensis as Salipaludibacillus neizhouensis comb. nov.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {66}, number = {7}, pages = {2747-2753}, doi = {10.1099/ijsem.0.001117}, pmid = {27118186}, issn = {1466-5034}, mesh = {Alkalies ; Bacillus/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; Cell Wall/chemistry ; DNA, Bacterial/genetics ; Diaminopimelic Acid ; Fatty Acids/chemistry ; India ; Lakes/*microbiology ; Nucleic Acid Hybridization ; Peptidoglycan/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {Two novel (S9[T] and S12) Gram-stain-positive, rod shaped, non-motile and endospore forming bacteria were isolated from Narayan Sarovar lake, in India. The high 16S rRNA gene sequence similarity (99.9 %) and DNA-DNA relatedness (86±2 %) indicated that strains S9[T] and S12 were members of a single species. Based on the 16S rRNA gene sequence analysis, these strains were identified as belonging to the class Firmibacteria and were most closely related to Bacillus agaradhaerens PN-105[T] (96.8 % sequence similarity), Bacillus neizhouensis JSM 071004[T] (96.5 %) and Bacillus luteus JC167[T] (96.1 %). However, these strains shared only 90.3 % 16S rRNA gene sequence similarity with Bacillus subtilis subsp. subtilis DSM 10[T], indicating that they might not be members of the genus Bacillus. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unknown phospholipid and an unknown lipid. The predominant isoprenoid quinone was MK-7. Major fatty acids (>5 %) included anteiso-C15 : 0, C16 : 0, iso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and summed feature 3. The results of phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strains S9[T] and S12 from all other members of the family Bacillaceae.The strains therefore represent a novel member of a new genus from the family Bacillaceae, for which the name Salipaludibacillus aurantiacus gen. nov., sp. nov. is proposed. The type strain is S9[T] (=KCTC 33633[T]=LMG 28644[T]). Based on the present study, it is also proposed to transfer Bacillus agaradhaerens and Bacillus neizhouensis to this new genus as Salipaludibacillus agaradhaerens comb. nov. and Salipaludibacillus neizhouensis comb. nov.}, }
@article {pmid27118132, year = {2016}, author = {Ekblad, A and Mikusinska, A and Ågren, GI and Menichetti, L and Wallander, H and Vilgalys, R and Bahr, A and Eriksson, U}, title = {Production and turnover of ectomycorrhizal extramatrical mycelial biomass and necromass under elevated CO2 and nitrogen fertilization.}, journal = {The New phytologist}, volume = {211}, number = {3}, pages = {874-885}, doi = {10.1111/nph.13961}, pmid = {27118132}, issn = {1469-8137}, mesh = {*Biomass ; Carbon/metabolism ; Carbon Dioxide/*pharmacology ; Carbon Isotopes ; Chitin/metabolism ; Ergosterol/metabolism ; *Fertilizers ; Forests ; Models, Biological ; Mycelium/drug effects/*growth &amp; development ; Nitrogen/*pharmacology ; Pinus taeda/drug effects/*physiology ; Time Factors ; }, abstract = {Extramatrical mycelia (EMM) of ectomycorrhizal fungi are important in carbon (C) and nitrogen (N) cycling in forests, but poor knowledge about EMM biomass and necromass turnovers makes the quantification of their role problematic. We studied the impacts of elevated CO2 and N fertilization on EMM production and turnover in a Pinus taeda forest. EMM C was determined by the analysis of ergosterol (biomass), chitin (total bio- and necromass) and total organic C (TOC) of sand-filled mycelium in-growth bags. The production and turnover of EMM bio- and necromass and total C were estimated by modelling. N fertilization reduced the standing EMM biomass C to 57% and its production to 51% of the control (from 238 to 122 kg C ha(-1) yr(-1)), whereas elevated CO2 had no detectable effects. Biomass turnover was high (˜13 yr(-1)) and unchanged by the treatments. Necromass turnover was slow and was reduced from 1.5 yr(-1) in the control to 0.65 yr(-1) in the N-fertilized treatment. However, TOC data did not support an N effect on necromass turnover. An estimated EMM production ranging from 2.5 to 6% of net primary production stresses the importance of its inclusion in C models. A slow EMM necromass turnover indicates an importance in building up forest humus.}, }
@article {pmid27117797, year = {2016}, author = {Xiang, D and Veresoglou, SD and Rillig, MC and Xu, T and Li, H and Hao, Z and Chen, B}, title = {Relative Importance of Individual Climatic Drivers Shaping Arbuscular Mycorrhizal Fungal Communities.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {418-427}, pmid = {27117797}, issn = {1432-184X}, mesh = {China ; *Climate ; Glomeromycota/*classification/isolation &amp; purification ; Grassland ; Mycorrhizae/*classification/isolation &amp; purification ; Soil Microbiology ; Stress, Physiological ; *Symbiosis ; Temperature ; }, abstract = {The physiological tolerance hypothesis (PTH) postulates that it is the tolerance of species to climatic factors that determines overall community richness. Here, we tested whether a group of mutualistic microbes, Glomeromycota, is distributed in semi-arid environments in ways congruent with the PTH. For this purpose, we modeled with climatic predictors the niche of each of the four orders of Glomeromycota and identified predictors of arbuscular mycorrhizal (AM) fungal operational taxonomic unit (OTU) richness. Our dataset consisted of 50 paired grassland and farmland sites in the farming-pastoral ecotone of northern China. We observed shifts in the relative abundance of AM fungal orders in response to climatic variables but also declines in OTU richness in grassland sites that had experienced high precipitation during the preceding year which was incongruous with the PTH. We found pronounced differences across groups of Glomeromycotan fungi in their responses to climatic variables and identified strong dependencies of AM fungal communities on precipitation. Given that precipitation is expected to further decline in the farming-pastoral ecotone over the coming years and that mycorrhiza represents an integral constituent of ecosystem functioning, it is likely that the ecosystem services in the region will change accordingly.}, }
@article {pmid27117796, year = {2018}, author = {Sanmartín, P and DeAraujo, A and Vasanthakumar, A}, title = {Melding the Old with the New: Trends in Methods Used to Identify, Monitor, and Control Microorganisms on Cultural Heritage Materials.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {64-80}, pmid = {27117796}, issn = {1432-184X}, mesh = {Anti-Infective Agents ; Biodegradation, Environmental ; Biofilms ; Ecology ; Environmental Monitoring/*methods ; Enzyme Assays/methods ; Fungi/isolation &amp; purification ; Gene Expression Profiling/methods ; Microbiological Techniques/*methods/trends ; *Microbiota ; Microscopy/methods ; Molecular Typing/methods ; Spectrum Analysis/methods ; }, abstract = {Microbial activity has an important impact on the maintenance of cultural heritage materials, owing to the key role of microorganisms in many deterioration processes. In order to minimize such deleterious effects, there is a need to fine-tune methods that detect and characterize microorganisms. Trends in microbiology indicate that this need can be met by incorporating modern techniques. All of the methods considered in this review paper are employed in the identification, surveillance, and control of microorganisms, and they have two points in common: They are currently used in microbial ecology (only literature from 2009 to 2015 is included), and they are often applied in the cultural heritage sector. More than 75 peer-reviewed journal articles addressing three different approaches were considered: molecular, sensory and morphological, and biocontrol methods. The goal of this review is to highlight the usefulness of the traditional as well as the modern methods. The general theme in the literature cited suggests using an integrated approach.}, }
@article {pmid27116299, year = {2016}, author = {Gao, SH and Fan, L and Peng, L and Guo, J and Agulló-Barceló, M and Yuan, Z and Bond, PL}, title = {Determining Multiple Responses of Pseudomonas aeruginosa PAO1 to an Antimicrobial Agent, Free Nitrous Acid.}, journal = {Environmental science &amp; technology}, volume = {50}, number = {10}, pages = {5305-5312}, doi = {10.1021/acs.est.6b00288}, pmid = {27116299}, issn = {1520-5851}, mesh = {Anti-Infective Agents ; Denitrification/drug effects ; *Nitrous Acid ; Pseudomonas aeruginosa/*drug effects ; Wastewater ; }, abstract = {Free nitrous acid (FNA) has recently been demonstrated as an antimicrobial agent on a range of micro-organisms, especially in wastewater-treatment systems. However, the antimicrobial mechanism of FNA is largely unknown. Here, we report that the antimicrobial effects of FNA are multitargeted. The response of a model denitrifier, Pseudomnas aeruginosa PAO1 (PAO1), common in wastewater treatment, was investigated in the absence and presence of inhibitory level of FNA (0.1 mg N/L) under anaerobic denitrifying conditions. This was achieved through coupling gene expression analysis, by RNA sequencing, and with a suite of physiological analyses. Various transcripts exhibited significant changes in abundance in the presence of FNA. Respiration was likely inhibited because denitrification activity was severely depleted, and decreased transcript levels of most denitrification genes occurred. As a consequence, the tricarboxylic acid (TCA) cycle was inhibited due to the lowered cellular redox state in the FNA-exposed cultures. Meanwhile, during FNA exposure, PAO1 rerouted its carbon metabolic pathway from the TCA cycle to pyruvate fermentation with acetate as the end product as a possible survival mechanism. Additionally, protein synthesis was significantly decreased, and ribosome preservation was evident. These findings improve our understanding of PAO1 in response to FNA and contribute toward the potential application for use of FNA as an antimicrobial agent.}, }
@article {pmid27114874, year = {2016}, author = {Trembath-Reichert, E and Case, DH and Orphan, VJ}, title = {Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e1913}, pmid = {27114874}, issn = {2167-8359}, support = {T32 GM007616/GM/NIGMS NIH HHS/United States ; }, abstract = {Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon-, Delta-, and Gammaproteobacteria in methane seep ecosystems.}, }
@article {pmid27110885, year = {2016}, author = {De Vrieze, J and Coma, M and Debeuckelaere, M and Van der Meeren, P and Rabaey, K}, title = {High salinity in molasses wastewaters shifts anaerobic digestion to carboxylate production.}, journal = {Water research}, volume = {98}, number = {}, pages = {293-301}, doi = {10.1016/j.watres.2016.04.035}, pmid = {27110885}, issn = {1879-2448}, mesh = {Anaerobiosis ; Bioreactors/microbiology ; Methane/biosynthesis ; *Molasses ; Salinity ; Sewage/microbiology ; *Wastewater ; }, abstract = {Biorefinery wastewaters are often treated by means of anaerobic digestion to produce biogas. Alternatively, these wastewaters can be fermented, leading to the formation of carboxylates. Here, we investigated how lab-scale upflow anaerobic sludge blanket reactors could be shifted to fermentation by changing organic loading rate, hydraulic retention time, pH, and salinity. A strong increase in volatile fatty acid concentration up to 40 g COD L(-1) was achieved through increasing salinity above 30 mS cm(-1), as well as a decrease in methane production by more than 90%, which could not be obtained by adjusting the other parameters, thus, indicating a clear shift from methane to carboxylate production. Microbial community analysis revealed a shift in bacterial community to lower evenness and richness values, following the increased salinity and VFA concentration during the fermentation process. A selective enrichment of the hydrogenotrophic Methanomicrobiales took place upon the shift to fermentation, despite a severe decrease in methane production. Particle size distribution revealed a strong degranulation of the sludge in the reactor, related to the high salinity, which resulted in a wash-out of the biomass. This research shows that salinity is a key parameter enabling a shift from methane to carboxylate production in a stable fermentation process.}, }
@article {pmid27109483, year = {2016}, author = {Pylro, VS and Morais, DK and Kalks, KH and Roesch, LF and Hirsch, PR and Tótola, MR and Yotoko, K}, title = {Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases.}, journal = {Journal of microbiological methods}, volume = {126}, number = {}, pages = {18-23}, doi = {10.1016/j.mimet.2016.04.012}, pmid = {27109483}, issn = {1872-8359}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Databases, Nucleic Acid/*standards ; *Denaturing Gradient Gel Electrophoresis/methods ; Genes, rRNA ; *Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Controversy surrounding bacterial phylogenies has become one of the most important challenges for microbial ecology. Comparative analyses with nucleotide databases and phylogenetic reconstruction of the amplified 16S rRNA genes from DGGE (Denaturing Gradient Gel Electrophoresis) excised bands have been used by several researchers for the identification of organisms in complex samples. Here, we individually analyzed DGGE-excised 16S rRNA gene bands from 10 certified bacterial strains of different species, and demonstrated that this kind of approach can deliver erroneous outcomes to researchers, besides causing/emphasizing errors in public databases.}, }
@article {pmid27109371, year = {2016}, author = {Pawłowska, J and Aleksandrzak-Piekarczyk, T and Banach, A and Kiersztyn, B and Muszewska, A and Serewa, L and Szatraj, K and Wrzosek, M}, title = {Preliminary studies on the evolution of carbon assimilation abilities within Mucorales.}, journal = {Fungal biology}, volume = {120}, number = {5}, pages = {752-763}, doi = {10.1016/j.funbio.2016.02.004}, pmid = {27109371}, issn = {1878-6146}, mesh = {*Biological Evolution ; Carbon/*metabolism ; Environment ; Enzymes/*metabolism ; *Metabolic Networks and Pathways ; Microarray Analysis ; Mucorales/*metabolism ; }, abstract = {Representatives of Mucorales belong to one of the oldest lineages of terrestrial fungi. Although carbon is of fundamental importance for fungal growth and functioning, relatively little is known about enzymatic capacities of Mucorales. The evolutionary history and the variability of the capacity to metabolize different carbon sources among representatives of the order Mucorales was studied using Phenotypic Microarray Plates. The ability of 26 strains belonging to 23 nonpathogenic species of Mucorales to use 95 different carbon sources was tested. Intraspecies variability of carbon assimilation profiles was lower than interspecies variation for some selected strains. Although similarities between the phylogenetic tree and the dendrogram created from carbon source utilization data were observed, the ability of the various strains to use the analyzed substrates did not show a clear correlation with the evolutionary history of the group. Instead, carbon assimilation profiles are probably shaped by environmental conditions.}, }
@article {pmid27108138, year = {2016}, author = {Han, SI and Kim, JO and Lee, YR and Ekpeghere, KI and Koh, SC and Whang, KS}, title = {Denitratimonas tolerans gen. nov., sp. nov., a denitrifying bacterium isolated from a bioreactor for tannery wastewater treatment.}, journal = {Antonie van Leeuwenhoek}, volume = {109}, number = {6}, pages = {785-792}, doi = {10.1007/s10482-016-0678-5}, pmid = {27108138}, issn = {1572-9699}, mesh = {Bioreactors/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Denitrification ; Fatty Acids/metabolism ; Phospholipids/metabolism ; Phylogeny ; Quinones/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sodium Chloride/metabolism ; Ubiquinone/metabolism ; Wastewater/*microbiology ; Xanthomonadaceae/*classification/genetics/*isolation &amp; purification/metabolism ; }, abstract = {A denitrifying bacterium, designated strain E4-1(T), was isolated from a bioreactor for tannery wastewater treatment, and its taxonomic position was investigated using a polyphasic approach. Strain E4-1(T), a facultative anaerobic bacterium, was observed to grow between 0 and 12 % (w/v) NaCl, between pH 3.0 and 12.0. Cells were found to be oxidase-positive and catalase-negative. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain E4-1(T) forms a distinct lineage with respect to closely related genera in the family Xanthomonadaceae, and is closely related to Chiayiivirga, Aquimonas and Dokdonella, and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93.9 %. The predominant respiratory quinone was determined to be ubiquinone-8 (Q-8) and the major cellular fatty acids were determined to be iso-C15:0, iso-C17:1 ω9c, iso-C11:0 and iso-C11:0 3OH. Based on physiological, biochemical and chemotaxonomic properties together with results of comparative 16S rRNA gene sequence analysis, strain E4-1(T) is considered to represent a novel species in a new genus, for which the name Denitratimonas tolerans gen. nov., sp. nov. is proposed. The type strain is E4-1(T) (=KACC 17565(T) = NCAIM B 025327(T)).}, }
@article {pmid27107647, year = {2016}, author = {Burges, A and Epelde, L and Benito, G and Artetxe, U and Becerril, JM and Garbisu, C}, title = {Enhancement of ecosystem services during endophyte-assisted aided phytostabilization of metal contaminated mine soil.}, journal = {The Science of the total environment}, volume = {562}, number = {}, pages = {480-492}, doi = {10.1016/j.scitotenv.2016.04.080}, pmid = {27107647}, issn = {1879-1026}, mesh = {*Biodegradation, Environmental ; *Ecosystem ; Endophytes/*physiology ; Metals/analysis/*metabolism ; Mining ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/analysis/*metabolism ; }, abstract = {Endophytic plant growth-promoting bacteria (endophytes) were isolated from a variety of (pseudo)metallophytes growing in an abandoned Zn/Pb mine and then characterized according to their plant growth-promoting traits (i.e. ACC deaminase activity, IAA production, siderophore production, phosphate solubilising capacity, metal and salt tolerance and phenotypic characterization). Initially, under growth chamber conditions, an endophyte-assisted aided phytostabilization study was carried out with Festuca rubra plants (native vs. commercial variety) inoculated with a Pseudomonas sp. isolate and cow slurry as organic amendment. The effect of treatments on soil physicochemical and microbial indicators of soil quality, as well as plant physiological parameters and metal concentrations, was assessed. We performed a complementary interpretation of our data through their grouping within a set of ecosystem services. Although the application of cow slurry had the most pronounced effects on soil quality indicators and ecosystem services, the growth of native F. rubra plants reduced soil bioavailability of Cd and Zn by 19 and 22%, respectively, and enhanced several soil microbial parameters. On the other hand, endophyte (Pseudomonas sp.) inoculation improved the physiological status of F. rubra plants by increasing the content of carotenoids, chlorophylls and Fv/Fm by 69, 65 and 37%, respectively, while also increasing the values of several soil microbial parameters. Finally, a consortium of five endophyte isolates was used for an endophyte-assisted aided phytostabilization field experiment, where lower metal concentrations in native excluder plants were found. Nonetheless, the field inoculation of the endophyte consortium had no effect on the biomass of native plants.}, }
@article {pmid27107125, year = {2016}, author = {Alessandria, V and Ferrocino, I and De Filippis, F and Fontana, M and Rantsiou, K and Ercolini, D and Cocolin, L}, title = {Microbiota of an Italian Grana-Like Cheese during Manufacture and Ripening, Unraveled by 16S rRNA-Based Approaches.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {13}, pages = {3988-3995}, pmid = {27107125}, issn = {1098-5336}, mesh = {Bacteria/*classification/*genetics ; Bacterial Load ; *Biota ; Cheese/*microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; High-Throughput Nucleotide Sequencing ; Italy ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {UNLABELLED: The microbial ecology of cheese involves a rich and complex interaction between starter lactic acid bacteria and nonstarter lactic acid bacteria (NSLAB), mainly originating from raw milk and/or from the environment, that can contribute to the final characteristics of cheese. The aim of the present research was the exploration of the active microbiota by RNA-based approaches during the manufacturing and ripening of a Grana-like cheese. Reverse transcriptase PCR (RT-PCR)-denaturing gradient gel electrophoresis (DGGE) and RNA-based high-throughput sequencing were applied to profile microbial populations, while the enumeration of active bacteria was carried out by using quantitative PCR (qPCR). Three different cheese productions (named D, E, and F) collected in the same month from the same dairy plant were analyzed. The application of the qPCR protocol revealed the presence of 7 log CFU/ml of bacterial load in raw milk, while, during ripening, active bacterial populations ranged from <4 to 8 log CFU/ml. The natural whey starters used in the three productions showed the same microbiota composition, characterized by the presence of Lactobacillus helveticus and Lactobacillus delbrueckii Nevertheless, beta-diversity analysis of the 16S rRNA sequencing data and RT-PCR-DGGE showed a clear clustering of the samples according to the three productions, probably driven by the different milks used. Milk samples were found to be characterized by the presence of several contaminants, such as Propionibacterium acnes, Acidovorax, Acinetobacter, Pseudomonas, and NSLAB. The core genera of the starter tended to limit the development of the spoilage bacteria only in two of the three batches. This study underlines the influence of different factors that can affect the final microbiota composition of the artisanal cheese.<br><br>IMPORTANCE: This study highlights the importance of the quality of the raw milk in the production of a hard cheese. Independent from the use of a starter culture, raw milk with low microbiological quality can negatively affect the populations of lactic acid bacteria and, as a consequence, impact the quality of the final product due to metabolic processes associated with spoilage bacteria.}, }
@article {pmid27102130, year = {2016}, author = {Nakamura, Y and Yamamoto, N and Kino, Y and Yamamoto, N and Kamei, S and Mori, H and Kurokawa, K and Nakashima, N}, title = {Establishment of a multi-species biofilm model and metatranscriptomic analysis of biofilm and planktonic cell communities.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {16}, pages = {7263-7279}, doi = {10.1007/s00253-016-7532-6}, pmid = {27102130}, issn = {1432-0614}, mesh = {Bacteria/classification/*genetics ; Biofilms/*growth &amp; development ; Flagella/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Iron/metabolism ; Japan ; Microbiota/*genetics ; Oligonucleotide Array Sequence Analysis ; Plankton/genetics/*growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Sulfur/metabolism ; Transcriptome/genetics ; }, abstract = {We collected several biofilm samples from Japanese rivers and established a reproducible multi-species biofilm model that can be analyzed in laboratories. Bacterial abundance at the generic level was highly similar between the planktonic and biofilm communities, whereas comparative metatranscriptomic analysis revealed many upregulated and downregulated genes in the biofilm. Many genes involved in iron-sulfur metabolism, stress response, and cell envelope function were upregulated; biofilm formation is mediated by an iron-dependent signaling mechanism and the signal is relayed to stress-responsive and cell envelope function genes. Flagella-related gene expression was regulated depending upon the growth phase, indicating different roles of flagella during the adherence, maturation, and dispersal steps of biofilm formation. Downregulation of DNA repair genes was observed, indicating that spontaneous mutation frequency would be elevated within the biofilm and that the biofilm is a cradle for generating novel genetic traits. Although the significance remains unclear, genes for rRNA methyltransferase, chromosome partitioning, aminoacyl-tRNA synthase, and cysteine, methionine, leucine, thiamine, nucleotide, and fatty acid metabolism were found to be differentially regulated. These results indicate that planktonic and biofilm communities are in different dynamic states. Studies on biofilm and sessile cells, which have received less attention, are important for understanding microbial ecology and for designing tailor-made anti-biofilm drugs.}, }
@article {pmid27100464, year = {2016}, author = {Zhang, Y and Thas, O}, title = {Constrained Ordination Analysis with Enrichment of Bell-Shaped Response Functions.}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0154079}, pmid = {27100464}, issn = {1932-6203}, mesh = {Ecology/*methods ; Likelihood Functions ; *Models, Theoretical ; }, abstract = {Constrained ordination methods aims at finding an environmental gradient along which the species abundances are maximally separated. The species response functions, which describe the expected abundance as a function of the environmental score, are according to the ecological fundamental niche theory only meaningful if they are bell-shaped. Many classical model-based ordination methods, however, use quadratic regression models without imposing the bell-shape and thus allowing for meaningless U-shaped response functions. The analysis output (e.g. a biplot) may therefore be potentially misleading and the conclusions are prone to errors. In this paper we present a log-likelihood ratio criterion with a penalisation term to enforce more bell-shaped response shapes. We report the results of a simulation study and apply our method to metagenomics data from microbial ecology.}, }
@article {pmid27100017, year = {2016}, author = {Harter, J and Weigold, P and El-Hadidi, M and Huson, DH and Kappler, A and Behrens, S}, title = {Soil biochar amendment shapes the composition of N2O-reducing microbial communities.}, journal = {The Science of the total environment}, volume = {562}, number = {}, pages = {379-390}, doi = {10.1016/j.scitotenv.2016.03.220}, pmid = {27100017}, issn = {1879-1026}, mesh = {Charcoal/*chemistry ; Denitrification ; Nitrification ; *Nitrogen Cycle ; Nitrogen Dioxide/analysis/*metabolism ; RNA, Ribosomal, 16S ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N2O) emissions. N2O is a potent greenhouse gas. The main sources of N2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N2O emission mitigation and the abundance and activity of N2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described 'atypical' nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling.}, }
@article {pmid27099947, year = {2016}, author = {Goux, X and Calusinska, M and Fossépré, M and Benizri, E and Delfosse, P}, title = {Start-up phase of an anaerobic full-scale farm reactor - Appearance of mesophilic anaerobic conditions and establishment of the methanogenic microbial community.}, journal = {Bioresource technology}, volume = {212}, number = {}, pages = {217-226}, doi = {10.1016/j.biortech.2016.04.040}, pmid = {27099947}, issn = {1873-2976}, mesh = {Anaerobiosis ; Animals ; Archaea/genetics/growth &amp; development/physiology ; Bacteria/classification/genetics/growth &amp; development ; Biofuels ; Bioreactors/*microbiology ; Cattle ; Euryarchaeota/classification/genetics/physiology ; *Farms ; Manure/microbiology ; Methane/metabolism ; Waste Management/methods ; }, abstract = {The goal of this study was to investigate how the microbial community structure establishes during the start-up phase of a full-scale farm anaerobic reactor inoculated with stale and cold cattle slurry. The 16S/18S high-throughput amplicon sequencing results showed an increase of the bacterial, archaeal and eukaryotic diversity, evenness and richness during the settlement of the mesophilic anaerobic conditions. When a steady performing digestion process was reached, the microbial diversity, evenness and richness decreased, indicating the establishment of a few dominant microbial populations, best adapted to biogas production. Interestingly, among the environmental parameters, the temperature, alkalinity, free-NH3, total solids and O2 content were found to be the main drivers of microbial dynamics. Interactions between eukaryotes, characterized by a high number of unknown organisms, and the bacterial and archaeal communities were also evidenced, suggesting that eukaryotes might play important roles in the anaerobic digestion process.}, }
@article {pmid27098176, year = {2016}, author = {Pakpour, S and Scott, JA and Turvey, SE and Brook, JR and Takaro, TK and Sears, MR and Klironomos, J}, title = {Presence of Archaea in the Indoor Environment and Their Relationships with Housing Characteristics.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {305-312}, pmid = {27098176}, issn = {1432-184X}, mesh = {Archaea/classification/*isolation &amp; purification ; DNA, Archaeal/genetics ; *Environmental Microbiology ; *Housing ; Humans ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Archaea are widespread and abundant in soils, oceans, or human and animal gastrointestinal (GI) tracts. However, very little is known about the presence of Archaea in indoor environments and factors that can regulate their abundances. Using a quantitative PCR approach, and targeting the archaeal and bacterial 16S rRNA genes in floor dust samples, we found that Archaea are a common part of the indoor microbiota, 5.01 ± 0.14 (log 16S rRNA gene copies/g dust, mean ± SE) in bedrooms and 5.58 ± 0.13 in common rooms, such as living rooms. Their abundance, however, was lower than bacteria: 9.20 ± 0.32 and 9.17 ± 0.32 in bedrooms and common rooms, respectively. In addition, by measuring a broad array of environmental factors, we obtained preliminary insights into how the abundance of total archaeal 16S rRNA gene copies in indoor environment would be associated with building characteristics and occupants' activities. Based on the results, Archaea are not equally distributed within houses, and the areas with greater input of outdoor microbiome and higher traffic and material heterogeneity tend to have a higher abundance of Archaea. Nevertheless, more research is needed to better understand causes and consequences of this microbial group in indoor environments.}, }
@article {pmid27094186, year = {2016}, author = {Zhang, FQ and Pan, W and Gu, JD and Xu, B and Zhang, WH and Zhu, BZ and Wang, YX and Wang, YF}, title = {Dominance of ammonia-oxidizing archaea community induced by land use change from Masson pine to eucalypt plantation in subtropical China.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {15}, pages = {6859-6869}, doi = {10.1007/s00253-016-7506-8}, pmid = {27094186}, issn = {1432-0614}, mesh = {Agriculture ; Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Biodiversity ; China ; *Eucalyptus ; Forests ; Nitrification ; Oxidation-Reduction ; *Pinus ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {A considerable proportion of Masson pine forests have been converted into eucalypt plantations in the last 30 years in Guangdong Province, subtropical China, for economic reasons, which may affect the ammonia-oxidizing archaea (AOA) community and the process of ammonia transformation. In order to determine the effects of forest conversion on AOA community, AOA communities in a Masson pine (Pinus massoniana) plantation and a eucalypt (Eucalyptus urophylla) plantation, which was converted from the Masson pine, were compared. Results showed that the land use change from the Masson pine to the eucalypt plantation decreased soil nutrient levels. A significant decrease of the potential nitrification rates (PNR) was also observed after the forest conversion (p < 5 %, n = 6). AOA were the only ammonia oxidizers in both plantations (no ammonia-oxidizing bacteria were detected). The detected AOA are affiliated with the genera Nitrosotalea and Nitrososphaera. A decrease of AOA abundance and an increase of the diversity were evident with the plantation conversion in the surface layer. AOA amoA gene diversity was negatively correlated with organic C and total N, respectively (p < 0.05, n = 12). AOA amoA gene abundance was negatively correlated with NH4 (+) and available P, respectively (p < 0.05, n = 12). However, AOA abundance was positively correlated with PNR, but not significantly (p < 0.05, n = 6), indicating AOA community change was only a partial reason for the decrease of PNR.}, }
@article {pmid27092245, year = {2016}, author = {Wigneswaran, V and Amador, CI and Jelsbak, L and Sternberg, C and Jelsbak, L}, title = {Utilization and control of ecological interactions in polymicrobial infections and community-based microbial cell factories.}, journal = {F1000Research}, volume = {5}, number = {}, pages = {}, pmid = {27092245}, issn = {2046-1402}, abstract = {Microbial activities are most often shaped by interactions between co-existing microbes within mixed-species communities. Dissection of the molecular mechanisms of species interactions within communities is a central issue in microbial ecology, and our ability to engineer and control microbial communities depends, to a large extent, on our knowledge of these interactions. This review highlights the recent advances regarding molecular characterization of microbe-microbe interactions that modulate community structure, activity, and stability, and aims to illustrate how these findings have helped us reach an engineering-level understanding of microbial communities in relation to both human health and industrial biotechnology.}, }
@article {pmid27090902, year = {2016}, author = {Fazi, S and Crognale, S and Casentini, B and Amalfitano, S and Lotti, F and Rossetti, S}, title = {The Arsenite Oxidation Potential of Native Microbial Communities from Arsenic-Rich Freshwaters.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {25-35}, pmid = {27090902}, issn = {1432-184X}, mesh = {Alphaproteobacteria/isolation &amp; purification/metabolism ; Arsenic/*analysis ; Arsenites/*metabolism ; Betaproteobacteria/isolation &amp; purification/metabolism ; Biomass ; Deltaproteobacteria/isolation &amp; purification/metabolism ; Fresh Water/chemistry/*microbiology ; Groundwater/chemistry/microbiology ; *Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Microbiology ; Water Pollutants, Chemical/analysis ; }, abstract = {Microorganisms play an important role in speciation and mobility of arsenic in the environment, by mediating redox transformations of both inorganic and organic species. Since arsenite [As(III)] is more toxic than arsenate [As(V)] to the biota, the microbial driven processes of As(V) reduction and As(III) oxidation may play a prominent role in mediating the environmental impact of arsenic contamination. However, little is known about the ecology and dynamics of As(III)-oxidizing populations within native microbial communities exposed to natural high levels of As. In this study, two techniques for single cell quantification (i.e., flow cytometry, CARD-FISH) were used to analyze the structure of aquatic microbial communities across a gradient of arsenic (As) contamination in different freshwater environments (i.e., groundwaters, surface and thermal waters). Moreover, we followed the structural evolution of these communities and their capacity to oxidize arsenite, when experimentally exposed to high As(III) concentrations in experimental microcosms. Betaproteobacteria and Deltaproteobacteria were the main groups retrieved in groundwaters and surface waters, while Beta and Gammaproteobacteria dominated the bacteria community in thermal waters. At the end of microcosm incubations, the communities were able to oxidize up to 95 % of arsenite, with an increase of Alphaproteobacteria in most of the experimental conditions. Finally, heterotrophic As(III)-oxidizing strains (one Alphaproteobacteria and two Gammaproteobacteria) were isolated from As rich waters. Our findings underlined that native microbial communities from different arsenic-contaminated freshwaters can efficiently perform arsenite oxidation, thus contributing to reduce the overall As toxicity to the aquatic biota.}, }
@article {pmid27090901, year = {2016}, author = {Salerno, C and Benndorf, D and Kluge, S and Palese, LL and Reichl, U and Pollice, A}, title = {Metaproteomics Applied to Activated Sludge for Industrial Wastewater Treatment Revealed a Dominant Methylotrophic Metabolism of Hyphomicrobium zavarzinii.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {9-13}, pmid = {27090901}, issn = {1432-184X}, mesh = {Alcohol Oxidoreductases/metabolism ; Biomass ; Hyphomicrobium/isolation &amp; purification/*metabolism ; Proteomics ; Sewage/chemistry/*microbiology ; Tandem Mass Spectrometry ; Waste Management/*methods ; }, abstract = {In biological wastewater treatments, microbial populations of the so-called activated sludge work together in the abatement of pollutants. In this work, the metabolic behavior of the biomass of a lab-scale plant treating industrial pharmaceutical wastewater was investigated through a metaproteomic approach. The complete treatment process included a membrane biological reactor (MBR) coupled with an advanced oxidation process (AOP) for partial breakdown of non-biodegradable molecules. Proteins from biomass samples collected pre- and post-AOP application were investigated by two-dimensional gel electrophoresis (2DE), mass spectrometry (MS), and finally identified by database search. Results showed that most proteins remained constant between pre- and post-AOP. Methanol dehydrogenase (MDH) belonging to Hyphomicrobium zavarzinii appeared as the most constantly expressed protein in the studied consortium. Other identified proteins belonging to Hyphomicrobium spp. revealed a predominant methylotrophic metabolism, and H. zavarzinii appeared as a key actor in the studied microbial community.}, }
@article {pmid27084981, year = {2016}, author = {Johns, NI and Blazejewski, T and Gomes, AL and Wang, HH}, title = {Principles for designing synthetic microbial communities.}, journal = {Current opinion in microbiology}, volume = {31}, number = {}, pages = {146-153}, pmid = {27084981}, issn = {1879-0364}, support = {DP5 OD009172/OD/NIH HHS/United States ; T32 GM008224/GM/NIGMS NIH HHS/United States ; U01 GM110714/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biodegradation, Environmental ; Biotechnology ; Ecosystem ; Genetic Engineering ; Microbial Consortia/*genetics ; Microbial Interactions/*physiology ; Organisms, Genetically Modified/genetics/growth &amp; development/*metabolism ; Synthetic Biology/*methods ; Systems Biology/*methods ; }, abstract = {Advances in synthetic biology to build microbes with defined and controllable properties are enabling new approaches to design and program multispecies communities. This emerging field of synthetic ecology will be important for many areas of biotechnology, bioenergy and bioremediation. This endeavor draws upon knowledge from synthetic biology, systems biology, microbial ecology and evolution. Fully realizing the potential of this discipline requires the development of new strategies to control the intercellular interactions, spatiotemporal coordination, robustness, stability and biocontainment of synthetic microbial communities. Here, we review recent experimental, analytical and computational advances to study and build multi-species microbial communities with defined functions and behavior for various applications. We also highlight outstanding challenges and future directions to advance this field.}, }
@article {pmid27084554, year = {2016}, author = {Kokurewicz, T and Ogórek, R and Pusz, W and Matkowski, K}, title = {Bats Increase the Number of Cultivable Airborne Fungi in the "Nietoperek" Bat Reserve in Western Poland.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {36-48}, pmid = {27084554}, issn = {1432-184X}, mesh = {*Air Microbiology ; Animals ; Ascomycota/classification/isolation &amp; purification ; Chiroptera/*microbiology ; Colony Count, Microbial ; Fungi/*classification/isolation &amp; purification ; Hibernation ; Humidity ; Poland ; Seasons ; Spores, Fungal/isolation &amp; purification ; Temperature ; }, abstract = {The "Nietoperek" bat reserve located in Western Poland is one of the largest bat hibernation sites in the European Union with nearly 38,000 bats from 12 species. Nietoperek is part of a built underground fortification system from WWII. The aims of the study were (1) to determine the fungal species composition and changes during hibernation season in relation to bat number and microclimatic conditions and (2) evaluate the potential threat of fungi for bat assemblages and humans visiting the complex. Airborne fungi were collected in the beginning, middle and end of hibernation period (9 November 2013 and 17 January and 15 March 2014) in 12 study sites, one outside and 11 inside the complex. Ambient temperature (T a) and relative humidity (RH) were measured by the use of data loggers, and species composition of bats was recorded from the study sites. The collision method (Air Ideal 3P) sampler was used to detect 34 species of airborne fungi including Pseudogymnoascus destructans (Pd). The density of airborne fungi isolated from the outdoor air samples varied from 102 to 242 CFU/1 m(3) of air and from 12 to 1198 CFU in the underground air samples. There was a positive relationship between number of bats and the concentration of fungi. The concentration of airborne fungi increased with the increase of bats number. Analysis of other possible ways of spore transport to the underground indicated that the number of bats was the primary factor determining the number of fungal spores in that hibernation site. Microclimatic conditions where Pd was found (median 8.7 °C, min-max 6.1-9.9 °C and 100 %, min-max 77.5-100.0 %) were preferred by hibernating Myotis myotis and Myotis daubentonii; therefore, these species are most probably especially prone to infection by this fungi species. The spores of fungi found in the underground can be pathogenic for humans and animals, especially for immunocompromised persons, even though their concentrations did not exceed limits and norms established as dangerous for human health. In addition, we showed for the first time that the air in bats hibernation sites can be a reservoir of Pd. Therefore, further study in other underground environments and wintering bats is necessary to find out more about the potential threat of airborne fungi to bats and public health.}, }
@article {pmid27079454, year = {2016}, author = {Chen, L and Luo, Y and Xu, J and Yu, Z and Zhang, K and Brookes, PC}, title = {Assessment of Bacterial Communities and Predictive Functional Profiling in Soils Subjected to Short-Term Fumigation-Incubation.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {240-251}, pmid = {27079454}, issn = {1432-184X}, mesh = {Agriculture/methods ; Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; Firmicutes/*classification/genetics/isolation &amp; purification ; *Fumigation ; Genes, Bacterial ; Grassland ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Previous investigations observed that when soil was fumigated with ethanol-free CHCl3 for 24 h and then incubated under appropriate conditions, after the initial flush of CO2 was over, soil organic carbon (SOC) mineralization continued at the same rate as in the non-fumigated soil. This indicates that, following fumigation, the much diminished microbial population still retained the same ability to mineralize SOC as the much larger non-fumigated population. We hypothesize that although fumigation drastically alters the soil bacterial community abundance, composition, and diversity, it has little influence on the bacterial C-metabolic functions. Here, we conducted a 30-day incubation experiment involving a grassland soil and an arable soil with and without CHCl3 fumigation. At days 0, 7, and 30 of the incubation, the bacterial abundances were determined by quantitative PCR, and the bacterial community composition and diversity were assessed via the 16S rRNA gene amplicon sequencing. PICRUSt was used to predict the metagenome functional content from the sequence data. Fumigation considerably changed the composition and decreased the abundance and diversity of bacterial community at the end of incubation. At day 30, Firmicutes (mainly Bacilli) accounted for 70.9 and 94.6 % of the total sequences in the fumigated grassland and arable soil communities, respectively. The two fumigated soil communities exhibited large compositional and structural differences during incubation. The families Paenibacillaceae, Bacillaceae, and Symbiobacteriaceae dominated the bacterial community in the grassland soil, and Alicyclobacillaceae in the arable soil. Fumigation had little influence on the predicted abundances of KEGG orthologs (KOs) assigned to the metabolism of the main acid esters, saccharides, amino acids, and lipids in the grassland soil community. The saccharide-metabolizing KO abundances were decreased, but the acid ester- and fatty acid-metabolizing KO abundances were elevated by fumigation in the arable soil community. Our study suggests functional redundancy regarding the bacterial genetic potential associated with SOC mineralization.}, }
@article {pmid27079453, year = {2016}, author = {Zhao, L and Wang, X and Huo, H and Yuan, G and Sun, Y and Zhang, D and Cao, Y and Xu, L and Wei, G}, title = {Phylogenetic Diversity of Ammopiptanthus Rhizobia and Distribution of Rhizobia Associated with Ammopiptanthus mongolicus in Diverse Regions of Northwest China.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {231-239}, pmid = {27079453}, issn = {1432-184X}, mesh = {Biodiversity ; China ; DNA, Bacterial/genetics ; Evolution, Molecular ; Fabaceae/*microbiology ; Genes, Bacterial ; Genetic Variation ; Mesorhizobium/genetics/isolation &amp; purification ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Rhizobium/*classification/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Aiming to investigate the diversity and distribution of rhizobia associated with Ammopiptanthus, an endangered evergreen legume widely distributed in deserts, we characterized a total of 219 nodule isolates from nine sampling sites in Northwest China with different soil characteristics based upon restriction fragment length polymorphism (RFLP) analysis of 16S ribosomal RNA (rRNA) and symbiotic genes (nodC and nifH). Ten isolates representing different 16S rRNA-RFLP types were selected for further sequence analyses of 16S rRNA and four housekeeping genes. As results, nine genospecies belonging to the genera Ensifer, Neorhizobium, Agrobacterium, Pararhizobium, and Rhizobium could be defined among the isolates. The nodC and nifH phylogenies of 14 isolates representing different symbiotic-RFLP types revealed five lineages linked to Ensifer fredii, Ensifer meliloti, Rhizobium leguminosarum, Mesorhizobium amorphae, and Rhizobium gallicum, which demonstrated the various origins and lateral transfers of symbiotic genes between different genera and species. The rhizobial diversities of Ammopiptanthus mongolicus varied among regions, and the community compositions of rhizobia associated with A. mongolicus were significantly different in wild and cultured fields. Constrained correspondence analysis showed that the distribution of A. mongolicus rhizobia could be explained by available potassium content and that the assembly of symbiotic types was mainly affected by available phosphorus content and carbon-nitrogen ratio.}, }
@article {pmid27078576, year = {2016}, author = {Grossart, HP and Rojas-Jimenez, K}, title = {Aquatic fungi: targeting the forgotten in microbial ecology.}, journal = {Current opinion in microbiology}, volume = {31}, number = {}, pages = {140-145}, doi = {10.1016/j.mib.2016.03.016}, pmid = {27078576}, issn = {1879-0364}, mesh = {Aquatic Organisms/classification/isolation &amp; purification/metabolism ; *Biodegradation, Environmental ; Biodiversity ; Ecosystem ; Food Chain ; *Fungi/classification/isolation &amp; purification/metabolism ; Microbiota/*physiology ; Secondary Metabolism/physiology ; }, abstract = {Fungi constitute important and conspicuous components of aquatic microbial communities, but their diversity and functional roles remain poorly characterized. New methods and conceptual frameworks are required to accurately describe their ecological roles, involvement in global cycling processes, and utility for human activities, considering both cultivation-independent techniques as well as experiments in laboratory and in natural ecosystems. Here we highlight recent developments and extant knowledge gaps in aquatic mycology, and provide a conceptual model to expose the importance of fungi in aquatic food webs and related biogeochemical processes.}, }
@article {pmid27077011, year = {2016}, author = {Gu, S and Zhang, Y and Wu, Y}, title = {Effects of sound exposure on the growth and intracellular macromolecular synthesis of E. coli k-12.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e1920}, pmid = {27077011}, issn = {2167-8359}, abstract = {Microbes, as one of the primary producers of the biosphere, play an important role in ecosystems. Exploring the mechanism of adaptation and resistance of microbial population to various environmental factors has come into focus in the fields of modern microbial ecology and molecular ecology. However, facing the increasingly serious problem of acoustic pollution, very few efforts have been put forth into studying the relation of single cell organisms and sound field exposure. Herein, we studied the biological effects of sound exposure on the growth of E. coli K-12 with different acoustic parameters. The effects of sound exposure on the intracellular macromolecular synthesis and cellular morphology of E. coli K-12 were also analyzed and discussed. Experimental results indicated that E. coli K-12 exposed to sound waves owned a higher biomass and a faster specific growth rate compared to the control group. Also, the average length of E. coli K-12 cells increased more than 27.26%. The maximum biomass and maximum specific growth rate of the stimulation group by 8000 Hz, 80dB sound wave was about 1.7 times and 2.5 times that of the control group, respectively. Moreover, it was observed that E. coli K-12 can respond rapidly to sound stress at both the transcriptional and posttranscriptional levels by promoting the synthesis of intracellular RNA and total protein. Some potential mechanisms may be involved in the responses of bacterial cells to sound stress.}, }
@article {pmid27075655, year = {2016}, author = {Martínez-García, &#xc1; and Martín-Vivaldi, M and Ruiz-Rodríguez, M and Martínez-Bueno, M and Arco, L and Rodríguez-Ruano, SM and Peralta-Sánchez, JM and Soler, JJ}, title = {The Microbiome of the Uropygial Secretion in Hoopoes Is Shaped Along the Nesting Phase.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {252-261}, pmid = {27075655}, issn = {1432-184X}, mesh = {Animals ; Bacteria/*classification/isolation &amp; purification ; Birds/*microbiology ; DNA, Bacterial/genetics ; Exocrine Glands/*microbiology ; Female ; Genomics ; Male ; *Microbiota ; Nesting Behavior/physiology ; Symbiosis ; }, abstract = {Microbial symbiont acquisition by hosts may determine the effectiveness of the mutualistic relationships. A mix of vertical and horizontal transmission may be advantageous for hosts by allowing plastic changes of microbial communities depending on environmental conditions. Plasticity is well known for gut microbiota but is poorly understood for other symbionts of wild animals. We here explore the importance of environmental conditions experienced by nestling hoopoes (Upupa epops) during the late nesting phase determining microbiota in their uropygial gland. In cross-fostering experiments of 8 days old nestlings, "sibling-sibling" and "mother-offspring" comparisons were used to explore whether the bacterial community naturally established in the uropygial gland of nestlings could change depending on experimental environmental conditions (i.e., new nest environment). We found that the final microbiome of nestlings was mainly explained by nest of origin. Moreover, cross-fostered nestlings were more similar to their siblings and mothers than to their stepsiblings and stepmothers. We also detected a significant effect of nest of rearing, suggesting that nestling hoopoes acquire most bacterial symbionts during the first days of life but that the microbiome is dynamic and can be modified along the nestling period depending on environmental conditions. Estimated effects of nest of rearing, but also most of those of nest of origin are associated to environmental characteristics of nests, which are extended phenotypes of parents. Thus, natural selection may favor the acquisition of appropriated microbial symbionts for particular environmental conditions found in nests.}, }
@article {pmid27075654, year = {2016}, author = {Conlette, OC and Emmanuel, NE and Chijoke, OG}, title = {Methanogen Population of an Oil Production Skimmer Pit and the Effects of Environmental Factors and Substrate Availability on Methanogenesis and Corrosion Rates.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {175-184}, pmid = {27075654}, issn = {1432-184X}, mesh = {Archaea/classification/isolation &amp; purification ; Corrosion ; DNA, Archaeal/genetics ; *Environmental Microbiology ; Euryarchaeota/*classification/isolation &amp; purification ; Hydrogen-Ion Concentration ; Methane/*biosynthesis ; Nigeria ; Oil and Gas Fields/*microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sequence Analysis, DNA ; Temperature ; }, abstract = {Assessment of microbial communities from an oil production skimmer pit using 16S rRNA gene sequencing technique revealed massive dominance of methanogenic archaea in both the skimmer pit water and sediment samples. The dominant genera of methanogens involved are mostly the acetotrophic Methanosaeta (36-83 %), and the hydrogenotrophic Methanococcus (49 %) indicating that methanogenesis is the dominant terminal metabolic process in the skimmer pit. Further studies showed that the methanogens had their optimal activity at pH 6-6.5, salinity of 100 mM, and temperature of 35-45 °C. When appropriate substrates are available and utilized by methanogens, methane production correlates with general corrosion rates (r = +0.927; p < 0.01), and under different conditions of pH, salinity and temperature, methane production showed significantly strong positive correlations (r = +0.824, +0.827, and +0.805; p < 0.01, respectively) with general corrosion rates. To the best of our knowledge, this research work was the first to assess microbial community composition of an oil production skimmer pit at Escravos facility in Nigeria.}, }
@article {pmid27074253, year = {2016}, author = {Salgado, VR and Queiroz, AT and Sanabani, SS and Oliveira, CI and Carvalho, EM and Costa, JM and Barral-Netto, M and Barral, A}, title = {The microbiological signature of human cutaneous leishmaniasis lesions exhibits restricted bacterial diversity compared to healthy skin.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {111}, number = {4}, pages = {241-251}, pmid = {27074253}, issn = {1678-8060}, support = {U01 AI088650/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Female ; Gram-Negative Bacteria/classification/*isolation &amp; purification ; Gram-Positive Bacteria/classification/*isolation &amp; purification ; Humans ; Leishmaniasis, Cutaneous/*microbiology ; Male ; Middle Aged ; Skin/*microbiology/parasitology ; Young Adult ; }, abstract = {Localised cutaneous leishmaniasis (LCL) is the most common form of cutaneous leishmaniasis characterised by single or multiple painless chronic ulcers, which commonly presents with secondary bacterial infection. Previous culture-based studies have found staphylococci, streptococci, and opportunistic pathogenic bacteria in LCL lesions, but there have been no comparisons to normal skin. In addition, this approach has strong bias for determining bacterial composition. The present study tested the hypothesis that bacterial communities in LCL lesions differ from those found on healthy skin (HS). Using a high throughput amplicon sequencing approach, which allows for better populational evaluation due to greater depth coverage and the Quantitative Insights Into Microbial Ecology pipeline, we compared the microbiological signature of LCL lesions with that of contralateral HS from the same individuals.Streptococcus, Staphylococcus,Fusobacterium and other strict or facultative anaerobic bacteria composed the LCL microbiome. Aerobic and facultative anaerobic bacteria found in HS, including environmental bacteria, were significantly decreased in LCL lesions (p < 0.01). This paper presents the first comprehensive microbiome identification from LCL lesions with next generation sequence methodology and shows a marked reduction of bacterial diversity in the lesions.}, }
@article {pmid27073098, year = {2016}, author = {Johnson, TA and Stedtfeld, RD and Wang, Q and Cole, JR and Hashsham, SA and Looft, T and Zhu, YG and Tiedje, JM}, title = {Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e02214-15}, pmid = {27073098}, issn = {2150-7511}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/drug effects/*genetics/isolation &amp; purification ; Bacterial Proteins/*genetics ; China ; Drug Resistance, Bacterial ; Interspersed Repetitive Sequences ; Phylogeny ; Swine/growth &amp; development/*microbiology ; }, abstract = {UNLABELLED: Antibiotic resistance is a worldwide health risk, but the influence of animal agriculture on the genetic context and enrichment of individual antibiotic resistance alleles remains unclear. Using quantitative PCR followed by amplicon sequencing, we quantified and sequenced 44 genes related to antibiotic resistance, mobile genetic elements, and bacterial phylogeny in microbiomes from U.S. laboratory swine and from swine farms from three Chinese regions. We identified highly abundant resistance clusters: groups of resistance and mobile genetic element alleles that cooccur. For example, the abundance of genes conferring resistance to six classes of antibiotics together with class 1 integrase and the abundance of IS6100-type transposons in three Chinese regions are directly correlated. These resistance cluster genes likely colocalize in microbial genomes in the farms. Resistance cluster alleles were dramatically enriched (up to 1 to 10% as abundant as 16S rRNA) and indicate that multidrug-resistant bacteria are likely the norm rather than an exception in these communities. This enrichment largely occurred independently of phylogenetic composition; thus, resistance clusters are likely present in many bacterial taxa. Furthermore, resistance clusters contain resistance genes that confer resistance to antibiotics independently of their particular use on the farms. Selection for these clusters is likely due to the use of only a subset of the broad range of chemicals to which the clusters confer resistance. The scale of animal agriculture and its wastes, the enrichment and horizontal gene transfer potential of the clusters, and the vicinity of large human populations suggest that managing this resistance reservoir is important for minimizing human risk.<br><br>IMPORTANCE: Agricultural antibiotic use results in clusters of cooccurring resistance genes that together confer resistance to multiple antibiotics. The use of a single antibiotic could select for an entire suite of resistance genes if they are genetically linked. No links to bacterial membership were observed for these clusters of resistance genes. These findings urge deeper understanding of colocalization of resistance genes and mobile genetic elements in resistance islands and their distribution throughout antibiotic-exposed microbiomes. As governments seek to combat the rise in antibiotic resistance, a balance is sought between ensuring proper animal health and welfare and preserving medically important antibiotics for therapeutic use. Metagenomic and genomic monitoring will be critical to determine if resistance genes can be reduced in animal microbiomes, or if these gene clusters will continue to be coselected by antibiotics not deemed medically important for human health but used for growth promotion or by medically important antibiotics used therapeutically.}, }
@article {pmid27072664, year = {2016}, author = {Cao, P and Wang, JT and Hu, HW and Zheng, YM and Ge, Y and Shen, JP and He, JZ}, title = {Environmental Filtering Process Has More Important Roles than Dispersal Limitation in Shaping Large-Scale Prokaryotic Beta Diversity Patterns of Grassland Soils.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {221-230}, pmid = {27072664}, issn = {1432-184X}, mesh = {Bacteria/*classification/isolation &amp; purification/metabolism ; Biodiversity ; Chemical Phenomena ; China ; Climate ; DNA, Bacterial/genetics ; Grassland ; Hydrogen-Ion Concentration ; Poaceae/chemistry/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Despite the utmost importance of microorganisms in maintaining ecosystem functioning and their ubiquitous distribution, our knowledge of the large-scale pattern of microbial diversity is limited, particularly in grassland soils. In this study, the microbial communities of 99 soil samples spanning over 3000 km across grassland ecosystems in northern China were investigated using high-throughput sequencing to analyze the beta diversity pattern and the underlying ecological processes. The microbial communities were dominated by Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Planctomycetes across all the soil samples. Spearman's correlation analysis indicated that climatic factors and soil pH were significantly correlated with the dominant microbial taxa, while soil microbial richness was positively linked to annual precipitation. The environmental divergence-dissimilarity relationship was significantly positive, suggesting the importance of environmental filtering processes in shaping soil microbial communities. Structural equation modeling found that the deterministic process played a more important role than the stochastic process on the pattern of soil microbial beta diversity, which supported the predictions of niche theory. Partial mantel test analysis have showed that the contribution of independent environmental variables has a significant effect on beta diversity, while independent spatial distance has no such relationship, confirming that the deterministic process was dominant in structuring soil microbial communities. Overall, environmental filtering process has more important roles than dispersal limitation in shaping microbial beta diversity patterns in the grassland soils.}, }
@article {pmid27072565, year = {2016}, author = {Pedrazzani, R and Menoni, L and Nembrini, S and Manili, L and Bertanza, G}, title = {Suitability of Sludge Biotic Index (SBI), Sludge Index (SI) and filamentous bacteria analysis for assessing activated sludge process performance: the case of piggery slaughterhouse wastewater.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {43}, number = {7}, pages = {953-964}, pmid = {27072565}, issn = {1476-5535}, mesh = {*Abattoirs ; Animals ; Bacteria/classification/*isolation &amp; purification ; Biological Assay ; Biological Oxygen Demand Analysis ; Biomass ; Italy ; Models, Theoretical ; Nitrogen/metabolism ; Sewage/*microbiology ; Swine ; Waste Disposal, Fluid/methods ; }, abstract = {Piggery slaughterhouse wastewater poses serious issues in terms of disposal feasibility and environmental impact, due to its huge organic load and variability. It is commonly treated by means of activated sludge processes, whose performance, in case of municipal wastewater, can be monitored by means of specific analyses, such as Sludge Biotic Index (SBI), Sludge Index (SI) and floc and filamentous bacteria observation. Therefore, this paper was aimed at assessing the applicability of these techniques to piggery slaughterhouse sewage. A plant located in Northern Italy was monitored for 1 year. Physical, chemical and operation parameters were measured; the activated sludge community (ciliates, flagellates, amoebae and small metazoa) was analysed for calculating SBI and SI. Floc and filamentous bacteria were examined and described accordingly with internationally adopted criteria. The results showed the full applicability of the studied techniques for optimizing the operation of a piggery slaughterhouse wastewater treatment plant.}, }
@article {pmid27071849, year = {2016}, author = {Menzel, P and Ng, KL and Krogh, A}, title = {Fast and sensitive taxonomic classification for metagenomics with Kaiju.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {11257}, pmid = {27071849}, issn = {2041-1723}, mesh = {*Algorithms ; Amino Acid Sequence ; Animals ; *Classification ; Humans ; Metagenome ; Metagenomics/*classification ; Proteins/chemistry ; }, abstract = {Metagenomics emerged as an important field of research not only in microbial ecology but also for human health and disease, and metagenomic studies are performed on increasingly larger scales. While recent taxonomic classification programs achieve high speed by comparing genomic k-mers, they often lack sensitivity for overcoming evolutionary divergence, so that large fractions of the metagenomic reads remain unclassified. Here we present the novel metagenome classifier Kaiju, which finds maximum (in-)exact matches on the protein-level using the Burrows-Wheeler transform. We show in a genome exclusion benchmark that Kaiju classifies reads with higher sensitivity and similar precision compared with current k-mer-based classifiers, especially in genera that are underrepresented in reference databases. We also demonstrate that Kaiju classifies up to 10 times more reads in real metagenomes. Kaiju can process millions of reads per minute and can run on a standard PC. Source code and web server are available at http://kaiju.binf.ku.dk.}, }
@article {pmid27069806, year = {2016}, author = {Schloss, PD and Jenior, ML and Koumpouras, CC and Westcott, SL and Highlander, SK}, title = {Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e1869}, pmid = {27069806}, issn = {2167-8359}, support = {U54 HG004973/HG/NHGRI NIH HHS/United States ; R01 GM099514/GM/NIGMS NIH HHS/United States ; T32 GM145304/GM/NIGMS NIH HHS/United States ; R01 HG005975/HG/NHGRI NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; }, abstract = {Over the past 10 years, microbial ecologists have largely abandoned sequencing 16S rRNA genes by the Sanger sequencing method and have instead adopted highly parallelized sequencing platforms. These new platforms, such as 454 and Illumina's MiSeq, have allowed researchers to obtain millions of high quality but short sequences. The result of the added sequencing depth has been significant improvements in experimental design. The tradeoff has been the decline in the number of full-length reference sequences that are deposited into databases. To overcome this problem, we tested the ability of the PacBio Single Molecule, Real-Time (SMRT) DNA sequencing platform to generate sequence reads from the 16S rRNA gene. We generated sequencing data from the V4, V3-V5, V1-V3, V1-V5, V1-V6, and V1-V9 variable regions from within the 16S rRNA gene using DNA from a synthetic mock community and natural samples collected from human feces, mouse feces, and soil. The mock community allowed us to assess the actual sequencing error rate and how that error rate changed when different curation methods were applied. We developed a simple method based on sequence characteristics and quality scores to reduce the observed error rate for the V1-V9 region from 0.69 to 0.027%. This error rate is comparable to what has been observed for the shorter reads generated by 454 and Illumina's MiSeq sequencing platforms. Although the per base sequencing cost is still significantly more than that of MiSeq, the prospect of supplementing reference databases with full-length sequences from organisms below the limit of detection from the Sanger approach is exciting.}, }
@article {pmid27067424, year = {2016}, author = {Kim, GW and Ho, A and Kim, PJ and Kim, SY}, title = {Stimulation of methane oxidation potential and effects on vegetation growth by bottom ash addition in a landfill final evapotranspiration cover.}, journal = {Waste management (New York, N.Y.)}, volume = {55}, number = {}, pages = {306-312}, doi = {10.1016/j.wasman.2016.03.058}, pmid = {27067424}, issn = {1879-2456}, mesh = {Air Pollutants/analysis/*chemistry ; Methane/analysis/*chemistry ; Oxidation-Reduction ; Refuse Disposal/*methods ; *Waste Disposal Facilities ; }, abstract = {The landfilling of municipal solid waste is a significant source of atmospheric methane (CH4), contributing up to 20% of total anthropogenic CH4 emissions. The evapotranspiration (ET) cover system, an alternative final cover system in waste landfills, has been considered to be a promising way to mitigate CH4 emissions, as well as to prevent water infiltration using vegetation on landfill cover soils. In our previous studies, bottom ash from coal-fired power plants was selected among several industrial residues (blast furnace slag, bottom ash, construction waste, steel manufacture slag, stone powder sludge, and waste gypsum) as the best additive for ET cover systems, with the highest mechanical performance achieved for a 35% (wtwt(-1)) bottom ash content in soil. In this study, to evaluate the field applicability of bottom ash mixed soil as ET cover, four sets of lysimeters (height 1.2m×width 2m×length 6m) were constructed in 2007, and four different treatments were installed: (i) soil+bottom ash (35% wtwt(-1)) (SB); (ii) soil+compost (2% wtwt(-1), approximately corresponding to 40Mgha(-1) in arable field scale) (SC); (iii) soil+bottom ash+compost (SBC); and (iv) soil only as the control (S). The effects of bottom ash mixing in ET cover soil on CH4 oxidation potential and vegetation growth were evaluated in a pilot ET cover system in the 5th year after installation by pilot experiments using the treatments. Our results showed that soil properties were significantly improved by bottom ash mixing, resulting in higher plant growth. Bottom ash addition significantly increased the CH4 oxidation potential of the ET cover soil, mainly due to improved organic matter and available copper concentration, enhancing methanotrophic abundances in soil amended with bottom ash. Conclusively, bottom ash could be a good alternative as a soil additive in the ET cover system to improve vegetation growth and mitigate CH4 emission impact in the waste landfill system.}, }
@article {pmid27065991, year = {2016}, author = {Cúcio, C and Engelen, AH and Costa, R and Muyzer, G}, title = {Rhizosphere Microbiomes of European + Seagrasses Are Selected by the Plant, But Are Not Species Specific.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {440}, pmid = {27065991}, issn = {1664-302X}, abstract = {Seagrasses are marine flowering plants growing in soft-body sediments of intertidal and shallow sub-tidal zones. They play an important role in coastal ecosystems by stabilizing sediments, providing food and shelter for animals, and recycling nutrients. Like other plants, seagrasses live intimately with both beneficial and unfavorable microorganisms. Although much is known about the microbiomes of terrestrial plants, little is known about the microbiomes of seagrasses. Here we present the results of a detailed study on the rhizosphere microbiome of seagrass species across the North-eastern Atlantic Ocean: Zostera marina, Zostera noltii, and Cymodocea nodosa. High-resolution amplicon sequencing of 16S rRNA genes showed that the rhizobiomes were significantly different from the bacterial communities of surrounding bulk sediment and seawater. Although we found no significant differences between the rhizobiomes of different seagrass species within the same region, those of seagrasses in different geographical locations differed strongly. These results strongly suggest that the seagrass rhizobiomes are shaped by plant metabolism, but not coevolved with their host. The core rhizobiome of seagrasses includes mostly bacteria involved in the sulfur cycle, thereby highlighting the importance of sulfur-related processes in seagrass ecosystems.}, }
@article {pmid27064484, year = {2016}, author = {Valverde, A and De Maayer, P and Oberholster, T and Henschel, J and Louw, MK and Cowan, D}, title = {Specific Microbial Communities Associate with the Rhizosphere of Welwitschia mirabilis, a Living Fossil.}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0153353}, pmid = {27064484}, issn = {1932-6203}, mesh = {Bacteria/*classification/genetics ; Fossils/*microbiology ; Mirabilis/genetics/*microbiology ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Welwitschia mirabilis is an ancient and rare plant distributed along the western coast of Namibia and Angola. Several aspects of Welwitschia biology and ecology have been investigated, but very little is known about the microbial communities associated with this plant. This study reports on the bacterial and fungal communities inhabiting the rhizosphere of W. mirabilis and the surrounding bulk soil. Rhizosphere communities were dominated by sequences of Alphaproteobacteria and Euromycetes, while Actinobacteria, Alphaproteobacteria, and fungi of the class Dothideomycetes jointly dominated bulk soil communities. Although microbial communities within the rhizosphere and soil samples were highly variable, very few "species" (OTUs defined at a 97% identity cut-off) were shared between these two environments. There was a small 'core' rhizosphere bacterial community (formed by Nitratireductor, Steroidobacter, Pseudonocardia and three Phylobacteriaceae) that together with Rhizophagus, an arbuscular mycorrhizal fungus, and other putative plant growth-promoting microbes may interact synergistically to promote Welwitschia growth.}, }
@article {pmid27063010, year = {2016}, author = {De Vrieze, J and Devooght, A and Walraedt, D and Boon, N}, title = {Enrichment of Methanosaetaceae on carbon felt and biochar during anaerobic digestion of a potassium-rich molasses stream.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {11}, pages = {5177-5187}, doi = {10.1007/s00253-016-7503-y}, pmid = {27063010}, issn = {1432-0614}, mesh = {Anaerobiosis ; Biodegradation, Environmental ; Biological Oxygen Demand Analysis ; Bioreactors ; Carbon/*chemistry ; Carbon Fiber ; Charcoal/*chemistry ; Fatty Acids, Volatile/analysis ; Hydrogen-Ion Concentration ; *Industrial Microbiology ; Methane/metabolism ; Methanosarcinales/classification/*metabolism ; Molasses/*analysis/microbiology ; Potassium/*analysis ; Sewage/microbiology ; Wastewater/chemistry/microbiology ; }, abstract = {Biorefineries allow the production of value-added chemicals, yet this also causes the formation of considerable amounts of wastewater that require suitable treatment. These biorefinery wastewaters often contain a high salinity, which inhibits methanogenesis. In this research, molasses were used to mimic these waste streams to evaluate their treatability by anaerobic digestion. Two different carrier materials, i.e., carbon felt and biochar, with similar surface properties were evaluated for their potential to stabilize anaerobic digestion of these wastewaters via active enrichment of the methanogenic community. Initial stable methane production values between 620 and 640 mL CH4 L(-1) day(-1) were reported in each treatment. At the end of the experiment, methane production decreased with more than 50 %, while VFA increased to values up to 20 g COD L(-1), indicating severe process failure, due to the high potassium concentration in these wastewaters, irrespective of the presence of carrier material. However, an increased relative abundance of Methanosaetaceae both on the biochar and carbon felt was observed. In conclusion, this research demonstrated that carbon felt and biochar are both suitable carrier materials for selective enrichment of Methanosaetaceae, yet this did not lead to stable anaerobic digestion of a potassium-rich molasses waste stream. The increased relative abundance of Methanosaetaceae on both carrier materials can, nonetheless, be considered valuable in terms of alternative applications and warrants further research.}, }
@article {pmid27060777, year = {2016}, author = {Ottesen, EA}, title = {Probing the living ocean with ecogenomic sensors.}, journal = {Current opinion in microbiology}, volume = {31}, number = {}, pages = {132-139}, doi = {10.1016/j.mib.2016.03.012}, pmid = {27060777}, issn = {1879-0364}, mesh = {Archaea/genetics/*isolation &amp; purification/metabolism ; Bacteria/genetics/*isolation &amp; purification/metabolism ; Electronic Data Processing/instrumentation/methods ; Environmental Monitoring/instrumentation/*methods ; Eukaryota/genetics/*isolation &amp; purification/metabolism ; Marine Biology/*methods ; Oceans and Seas ; Seawater/*microbiology ; Viruses/genetics/*isolation &amp; purification/metabolism ; }, abstract = {This review discusses the role of ecogenomic sensors in biological oceanography. Ecogenomic sensors are instruments that can autonomously collect biological samples and perform molecular analyses. This technology reduces logistical constraints on the length and duration of biological data collection. Autonomous, robotic performance of molecular assays shows particular promise in the field of public health. Recent applications include simultaneous detection of harmful algal species and fecal markers paired with same-day remote reporting of test results. Ecogenomic instruments are also showing promise for molecular ecological studies. Autonomous collection and preservation of biological samples is facilitating high-resolution ecological studies that are expanding our understanding of marine microbial ecology and dynamics. This review discusses recent applications of these instruments and makes recommendations for future developments.}, }
@article {pmid27060776, year = {2016}, author = {Cardona, C and Weisenhorn, P and Henry, C and Gilbert, JA}, title = {Network-based metabolic analysis and microbial community modeling.}, journal = {Current opinion in microbiology}, volume = {31}, number = {}, pages = {124-131}, doi = {10.1016/j.mib.2016.03.008}, pmid = {27060776}, issn = {1879-0364}, support = {T32 EB009412/EB/NIBIB NIH HHS/United States ; }, mesh = {Bacteria/*metabolism ; *Bacterial Physiological Phenomena ; Metabolic Networks and Pathways/*physiology ; Microbial Consortia/*physiology ; Microbial Interactions/*physiology ; Models, Biological ; }, abstract = {Network inference is being applied to studies of microbial ecology to visualize and characterize microbial communities. Network representations can allow examination of the underlying organizational structure of a microbial community, and identification of key players or environmental conditions that influence community assembly and stability. Microbial co-association networks provide information on the dynamics of community structure as a function of time or other external variables. Community metabolic networks can provide a mechanistic link between species through identification of metabolite exchanges and species specific resource requirements. When used together, co-association networks and metabolic networks can provide a more in-depth view of the hidden rules that govern the stability and dynamics of microbial communities.}, }
@article {pmid27059740, year = {2016}, author = {Falteisek, L and Duchoslav, V and Čepička, I}, title = {Substantial Variability of Multiple Microbial Communities Collected at Similar Acidic Mine Water Outlets.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {163-174}, pmid = {27059740}, issn = {1432-184X}, mesh = {Acids/chemistry ; Bacteria/*classification/isolation &amp; purification/metabolism ; Biodiversity ; Biofilms ; Cluster Analysis ; DNA, Bacterial/genetics ; *Mining ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Water/chemistry ; *Water Microbiology ; }, abstract = {Deep sequencing of prokaryotic 16S rDNA regularly reveals thousands of microbial species thriving in many common habitats. It is still unknown how this huge microbial diversity, including many potentially competing organisms, may persist at a single site. One of plausible hypotheses is that a large number of spatially separated microcommunities exist within each complex habitat. Smaller subset of the species may exist in each microcommunity and actually interact with each other. We sampled two groups of microbial stalactites growing at a single acidic mine drainage outlet as a model of multiplicated, low-complexity microhabitat. Samples from six other sites were added for comparison. Both tRFLP and 16S rDNA pyrosequencing showed that microbial communities containing 6 to 51 species-level operational taxonomic units (OTU) inhabited all stalactites. Interestingly, most OTUs including the highly abundant ones unpredictably alternated regardless of physical and environmental distance of the stalactites. As a result, the communities clustered independently on sample site and other variables when using both phylogenetic dissimilarity and OTU abundance metrics. Interestingly, artificial communities generated by pooling the biota of several adjacent stalactites together clustered by the locality more strongly than when the stalactites were analyzed separately. The most probable interpretation is that each stalactite contains likely random selection from the pool of plausible species. Such degree of stochasticity in assembly of extremophilic microbial communities is significantly greater than commonly proposed and requires caution when interpreting microbial diversity.}, }
@article {pmid27058515, year = {2016}, author = {Pihl, AF and Fonvig, CE and Stjernholm, T and Hansen, T and Pedersen, O and Holm, JC}, title = {The Role of the Gut Microbiota in Childhood Obesity.}, journal = {Childhood obesity (Print)}, volume = {12}, number = {4}, pages = {292-299}, doi = {10.1089/chi.2015.0220}, pmid = {27058515}, issn = {2153-2176}, mesh = {Child ; Child Nutritional Physiological Phenomena/physiology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology ; Humans ; Pediatric Obesity/*microbiology/*physiopathology ; }, abstract = {BACKGROUND: Childhood and adolescent obesity has reached epidemic proportions worldwide. The pathogenesis of obesity is complex and multifactorial, in which genetic and environmental contributions seem important. The gut microbiota is increasingly documented to be involved in the dysmetabolism associated with obesity.<br><br>METHODS: We conducted a systematic search for literature available before October 2015 in the PubMed and Scopus databases, focusing on the interplay between the gut microbiota, childhood obesity, and metabolism.<br><br>RESULTS: The review discusses the potential role of the bacterial component of the human gut microbiota in childhood and adolescent-onset obesity, with a special focus on the factors involved in the early development of the gut bacterial ecosystem, and how modulation of this microbial community might serve as a basis for new therapeutic strategies in combating childhood obesity. A vast number of variables are influencing the gut microbial ecology (e.g., the host genetics, delivery method, diet, age, environment, and the use of pre-, pro-, and antibiotics); but the exact physiological processes behind these relationships need to be clarified.<br><br>CONCLUSIONS: Exploring the role of the gut microbiota in the development of childhood obesity may potentially reveal new strategies for obesity prevention and treatment.}, }
@article {pmid27058401, year = {2016}, author = {Guo, K and Hidalgo, D and Tommasi, T and Rabaey, K}, title = {Pyrolytic carbon-coated stainless steel felt as a high-performance anode for bioelectrochemical systems.}, journal = {Bioresource technology}, volume = {211}, number = {}, pages = {664-668}, doi = {10.1016/j.biortech.2016.03.161}, pmid = {27058401}, issn = {1873-2976}, mesh = {*Bioelectric Energy Sources ; Biofilms/growth &amp; development ; Carbon/*chemistry ; Catalysis ; Electrochemistry/*methods ; Electrodes ; Spectrometry, X-Ray Emission ; Spectrum Analysis, Raman ; Stainless Steel/*chemistry ; Surface Properties ; *Temperature ; }, abstract = {Scale up of bioelectrochemical systems (BESs) requires highly conductive, biocompatible and stable electrodes. Here we present pyrolytic carbon-coated stainless steel felt (C-SS felt) as a high-performance and scalable anode. The electrode is created by generating a carbon layer on stainless steel felt (SS felt) via a multi-step deposition process involving α-d-glucose impregnation, caramelization, and pyrolysis. Physicochemical characterizations of the surface elucidate that a thin (20±5μm) and homogenous layer of polycrystalline graphitic carbon was obtained on SS felt surface after modification. The carbon coating significantly increases the biocompatibility, enabling robust electroactive biofilm formation. The C-SS felt electrodes reach current densities (jmax) of 3.65±0.14mA/cm(2) within 7days of operation, which is 11 times higher than plain SS felt electrodes (0.30±0.04mA/cm(2)). The excellent biocompatibility, high specific surface area, high conductivity, good mechanical strength, and low cost make C-SS felt a promising electrode for BESs.}, }
@article {pmid27050827, year = {2016}, author = {Huang, LN and Kuang, JL and Shu, WS}, title = {Microbial Ecology and Evolution in the Acid Mine Drainage Model System.}, journal = {Trends in microbiology}, volume = {24}, number = {7}, pages = {581-593}, doi = {10.1016/j.tim.2016.03.004}, pmid = {27050827}, issn = {1878-4380}, mesh = {Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; *Biodegradation, Environmental ; Biodiversity ; Biofilms/growth &amp; development ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Iron/*metabolism ; Mining ; RNA, Ribosomal, 16S/genetics ; Sulfides/*metabolism ; Waste Disposal, Fluid/*methods ; }, abstract = {Acid mine drainage (AMD) is a unique ecological niche for acid- and toxic-metals-adapted microorganisms. These low-complexity systems offer a special opportunity for the ecological and evolutionary analyses of natural microbial assemblages. The last decade has witnessed an unprecedented interest in the study of AMD communities using 16S rRNA high-throughput sequencing and community genomic and postgenomic methodologies, significantly advancing our understanding of microbial diversity, community function, and evolution in acidic environments. This review describes new data on AMD microbial ecology and evolution, especially dynamics of microbial diversity, community functions, and population genomes, and further identifies gaps in our current knowledge that future research, with integrated applications of meta-omics technologies, will fill.}, }
@article {pmid27048467, year = {2016}, author = {Kaul, RB and Kramer, AM and Dobbs, FC and Drake, JM}, title = {Experimental demonstration of an Allee effect in microbial populations.}, journal = {Biology letters}, volume = {12}, number = {4}, pages = {}, pmid = {27048467}, issn = {1744-957X}, mesh = {Aliivibrio fischeri/*growth &amp; development/physiology ; Animals ; Carbon ; *Ecosystem ; Seawater/chemistry ; Stramenopiles ; }, abstract = {Microbial populations can be dispersal limited. However, microorganisms that successfully disperse into physiologically ideal environments are not guaranteed to establish. This observation contradicts the Baas-Becking tenet: 'Everything is everywhere, but the environment selects'. Allee effects, which manifest in the relationship between initial population density and probability of establishment, could explain this observation. Here, we experimentally demonstrate that small populations of Vibrio fischeri are subject to an intrinsic demographic Allee effect. Populations subjected to predation by the bacterivore Cafeteria roenbergensis display both intrinsic and extrinsic demographic Allee effects. The estimated critical threshold required to escape positive density-dependence is around 5, 20 or 90 cells ml(-1)under conditions of high carbon resources, low carbon resources or low carbon resources with predation, respectively. This work builds on the foundations of modern microbial ecology, demonstrating that mechanisms controlling macroorganisms apply to microorganisms, and provides a statistical method to detect Allee effects in data.}, }
@article {pmid27048448, year = {2016}, author = {Liu, L and Salam, N and Jiao, JY and Jiang, HC and Zhou, EM and Yin, YR and Ming, H and Li, WJ}, title = {Diversity of Culturable Thermophilic Actinobacteria in Hot Springs in Tengchong, China and Studies of their Biosynthetic Gene Profiles.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {150-162}, pmid = {27048448}, issn = {1432-184X}, mesh = {Actinobacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; China ; DNA, Bacterial/genetics ; Hot Springs/*microbiology ; Hot Temperature ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The class Actinobacteria has been a goldmine for the discovery of antibiotics and has attracted interest from both academics and industries. However, an absence of novel approaches during the last few decades has limited the discovery of new microbial natural products useful for industries. Scientists are now focusing on the ecological aspects of diverse environments including unexplored or underexplored habitats and extreme environments in the search for new metabolites. This paper reports on the diversity of culturable actinobacteria associated with hot springs located in Tengchong County, Yunnan Province, southwestern China. A total of 58 thermophilic actinobacterial strains were isolated from the samples collected from ten hot springs distributed over three geothermal fields (e.g., Hehua, Rehai, and Ruidian). Phylogenetic positions and their biosynthetic profiles were analyzed by sequencing 16S rRNA gene and three biosynthetic gene clusters (KS domain of PKS-I, KSα domain of PKS-II and A domain of NRPS). On the basis of 16S rRNA gene phylogenetic analysis, the 58 strains were affiliated with 12 actinobacterial genera: Actinomadura Micromonospora, Microbispora, Micrococcus, Nocardiopsis, Nonomuraea, Promicromonospora, Pseudonocardia, Streptomyces, Thermoactinospora, Thermocatellispora, and Verrucosispora, of which the two novel genera Thermoactinospora and Thermocatellisopora were recently described from among these strains. Considering the biosynthetic potential of these actinobacterial strains, 22 were positive for PCR amplification of at least one of the three biosynthetic gene clusters (PKS-I, PKS-II, and NRPS). These actinobacteria were further subjected to antimicrobial assay against five opportunistic human pathogens (Acinetobacter baumannii, Escherichia coli, Micrococcus luteus, Staphylococcus aureus and Streptococcus faecalis). All of the 22 strains that were positive for PCR amplification of at least one of the biosynthetic gene domains exhibited antimicrobial activities against at least one of the five test organisms. Among the remaining 36 actinobacteria that are negative for PCR amplification of the domains for the biosynthetic genes, 33 strains showed antimicrobial activities against at least one of the five test pathogens. In summary, the findings presented in this study emphasized the importance of underexplored habitats such as Tengchong hot springs as potential sources for search of bioactive molecules.}, }
@article {pmid27047609, year = {2016}, author = {Larsen, PE}, title = {More of an Art than a Science: Using Microbial DNA Sequences to Compose Music.}, journal = {Journal of microbiology &amp; biology education}, volume = {17}, number = {1}, pages = {129-132}, pmid = {27047609}, issn = {1935-7877}, abstract = {Bacteria are everywhere. Microbial ecology is emerging as a critical field for understanding the relationships between these ubiquitous bacterial communities, the environment, and human health. Next generation DNA sequencing technology provides us a powerful tool to indirectly observe the communities by sequencing and analyzing all of the bacterial DNA present in an environment. The results of the DNA sequencing experiments can generate gigabytes to terabytes of information, however, making it difficult for the citizen scientist to grasp and the educator to convey this data. Here, we present a method for interpreting massive amounts of microbial ecology data as musical performances, easily generated on any computer and using only commonly available or freely available software and the 'Microbial Bebop' algorithm. Using this approach, citizen scientists and biology educators can sonify complex data in a fun and interactive format, making it easier to communicate both the importance and the excitement of exploring the planet earth's largest ecosystem.}, }
@article {pmid27047584, year = {2016}, author = {Barberán, A and Hammer, TJ and Madden, AA and Fierer, N}, title = {Microbes Should Be Central to Ecological Education and Outreach.}, journal = {Journal of microbiology &amp; biology education}, volume = {17}, number = {1}, pages = {23-28}, pmid = {27047584}, issn = {1935-7877}, abstract = {Our planet is changing rapidly, and responding to the ensuing environmental challenges will require an informed citizenry that can understand the inherent complexity of ecological systems. However, microorganisms are usually neglected in the narratives that we use to understand nature. Here, we advocate for the inclusion of microbial ecology across education levels and delineate the often neglected benefits of incorporating microbes into ecology curricula. We provide examples across education levels, from secondary school (by considering one's self as a microbial ecosystem), to higher education (by incorporating our knowledge of the global ecological role and medical application of microbes), to the general public (by engagement through citizen-science projects). The greater inclusion of microbes in ecological education and outreach will not only help us appreciate the natural world we are part of, but will ultimately aid in building a citizenry better prepared to make informed decisions on health and environmental policies.}, }
@article {pmid27047451, year = {2016}, author = {Learman, DR and Henson, MW and Thrash, JC and Temperton, B and Brannock, PM and Santos, SR and Mahon, AR and Halanych, KM}, title = {Biogeochemical and Microbial Variation across 5500 km of Antarctic Surface Sediment Implicates Organic Matter as a Driver of Benthic Community Structure.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {284}, pmid = {27047451}, issn = {1664-302X}, abstract = {Western Antarctica, one of the fastest warming locations on Earth, is a unique environment that is underexplored with regards to biodiversity. Although pelagic microbial communities in the Southern Ocean and coastal Antarctic waters have been well-studied, there are fewer investigations of benthic communities and most have a focused geographic range. We sampled surface sediment from 24 sites across a 5500 km region of Western Antarctica (covering the Ross Sea to the Weddell Sea) to examine relationships between microbial communities and sediment geochemistry. Sequencing of the 16S and 18S rRNA genes showed microbial communities in sediments from the Antarctic Peninsula (AP) and Western Antarctica (WA), including the Ross, Amundsen, and Bellingshausen Seas, could be distinguished by correlations with organic matter concentrations and stable isotope fractionation (total organic carbon; TOC, total nitrogen; TN, and δ(13)C). Overall, samples from the AP were higher in nutrient content (TOC, TN, and NH4 (+)) and communities in these samples had higher relative abundances of operational taxonomic units (OTUs) classified as the diatom, Chaetoceros, a marine cercozoan, and four OTUs classified as Flammeovirgaceae or Flavobacteria. As these OTUs were strongly correlated with TOC, the data suggests the diatoms could be a source of organic matter and the Bacteroidetes and cercozoan are grazers that consume the organic matter. Additionally, samples from WA have lower nutrients and were dominated by Thaumarchaeota, which could be related to their known ability to thrive as lithotrophs. This study documents the largest analysis of benthic microbial communities to date in the Southern Ocean, representing almost half the continental shoreline of Antarctica, and documents trophic interactions and coupling of pelagic and benthic communities. Our results indicate potential modifications in carbon sequestration processes related to change in community composition, identifying a prospective mechanism that links climate change to carbon availability.}, }
@article {pmid27046099, year = {2016}, author = {Men, Y and Han, P and Helbling, DE and Jehmlich, N and Herbold, C and Gulde, R and Onnis-Hayden, A and Gu, AZ and Johnson, DR and Wagner, M and Fenner, K}, title = {Biotransformation of Two Pharmaceuticals by the Ammonia-Oxidizing Archaeon Nitrososphaera gargensis.}, journal = {Environmental science &amp; technology}, volume = {50}, number = {9}, pages = {4682-4692}, pmid = {27046099}, issn = {1520-5851}, support = {294343/ERC_/European Research Council/International ; T32 HG002536/HG/NHGRI NIH HHS/United States ; }, mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; Bacteria/metabolism ; Biotransformation ; Molecular Sequence Data ; Oxidation-Reduction ; Pharmaceutical Preparations/metabolism ; Phylogeny ; Proteomics ; Soil Microbiology ; }, abstract = {The biotransformation of some micropollutants has previously been observed to be positively associated with ammonia oxidation activities and the transcript abundance of the archaeal ammonia monooxygenase gene (amoA) in nitrifying activated sludge. Given the increasing interest in and potential importance of ammonia-oxidizing archaea (AOA), we investigated the capabilities of an AOA pure culture, Nitrososphaera gargensis, to biotransform ten micropollutants belonging to three structurally similar groups (i.e., phenylureas, tertiary amides, and tertiary amines). N. gargensis was able to biotransform two of the tertiary amines, mianserin (MIA) and ranitidine (RAN), exhibiting similar compound specificity as two ammonia-oxidizing bacteria (AOB) strains that were tested for comparison. The same MIA and RAN biotransformation reactions were carried out by both the AOA and AOB strains. The major transformation product (TP) of MIA, α-oxo MIA was likely formed via a two-step oxidation reaction. The first hydroxylation step is typically catalyzed by monooxygenases. Three RAN TP candidates were identified from nontarget analysis. Their tentative structures and possible biotransformation pathways were proposed. The biotransformation of MIA and RAN only occurred when ammonia oxidation was active, suggesting cometabolic transformations. Consistently, a comparative proteomic analysis revealed no significant differential expression of any protein-encoding gene in N. gargensis grown on ammonium with MIA or RAN compared with standard cultivation on ammonium only. Taken together, this study provides first important insights regarding the roles played by AOA in micropollutant biotransformation.}, }
@article {pmid27037116, year = {2016}, author = {Delport, TC and Power, ML and Harcourt, RG and Webster, KN and Tetu, SG}, title = {Colony Location and Captivity Influence the Gut Microbial Community Composition of the Australian Sea Lion (Neophoca cinerea).}, journal = {Applied and environmental microbiology}, volume = {82}, number = {12}, pages = {3440-3449}, pmid = {27037116}, issn = {1098-5336}, mesh = {Animals ; Animals, Wild ; Animals, Zoo ; Australia ; Bacteria/*classification/*genetics ; *Biota ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Geography ; Sea Lions/*microbiology ; }, abstract = {UNLABELLED: Gut microbiota play an important role in maintenance of mammalian metabolism and immune system regulation, and disturbances to this community can have adverse impacts on animal health. To better understand the composition of gut microbiota in marine mammals, fecal bacterial communities of the Australian sea lion (Neophoca cinerea), an endangered pinniped with localized distribution, were examined. A comparison of samples from individuals across 11 wild colonies in South and Western Australia and three Australian captive populations showed five dominant bacterial phyla: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria The phylum Firmicutes was dominant in both wild (76.4% ± 4.73%) and captive animals (61.4% ± 10.8%), while Proteobacteria contributed more to captive (29.3% ± 11.5%) than to wild (10.6% ± 3.43%) fecal communities. Qualitative differences were observed between fecal communities from wild and captive animals based on principal-coordinate analysis. SIMPER (similarity percentage procedure) analyses indicated that operational taxonomic units (OTU) from the bacterial families Clostridiaceae and Ruminococcaceae were more abundant in wild than in captive animals and contributed most to the average dissimilarity between groups (SIMPER contributions of 19.1% and 10.9%, respectively). Differences in the biological environment, the foraging site fidelity, and anthropogenic impacts may provide various opportunities for unique microbial establishment in Australian sea lions. As anthropogenic disturbances to marine mammals are likely to increase, understanding the potential for such disturbances to impact microbial community compositions and subsequently affect animal health will be beneficial for management of these vulnerable species.<br><br>IMPORTANCE: The Australian sea lion is an endangered species for which there is currently little information regarding disease and microbial ecology. In this work, we present an in-depth study of the fecal microbiota of a large number of Australian sea lions from geographically diverse wild and captive populations. Colony location and captivity were found to influence the gut microbial community compositions of these animals. Our findings significantly extend the baseline knowledge of marine mammal gut microbiome composition and variability.}, }
@article {pmid27036035, year = {2016}, author = {Xie, G and Wang, X and Liu, P and Wei, R and Chen, W and Rajani, C and Hernandez, BY and Alegado, R and Dong, B and Li, D and Jia, W}, title = {Distinctly altered gut microbiota in the progression of liver disease.}, journal = {Oncotarget}, volume = {7}, number = {15}, pages = {19355-19366}, pmid = {27036035}, issn = {1949-2553}, support = {P30 CA071789/CA/NCI NIH HHS/United States ; U01 CA188387/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Animals, Newborn ; Bacteria/classification/genetics ; Carcinoma, Hepatocellular/pathology/*physiopathology ; Disease Models, Animal ; Disease Progression ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Liver Diseases/pathology/physiopathology ; Liver Neoplasms/pathology/*physiopathology ; Male ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/pathology/*physiopathology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Recent studies underscore important roles of intestinal microbiota and the bacterial lipopolysaccharides (LPS) production in the pathogenesis of liver disease. However, how gut microbiota alters in response to the development of steatosis and subsequent progression to nonalcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC) remains unclear. We aimed to study the gut microbial changes over liver disease progression using a streptozotocin-high fat diet (STZ-HFD) induced NASH-HCC C57BL/6J mouse model that is highly relevant to human liver disease. The fecal microbiota at various liver pathological stages was analyzed by 16S rDNA gene pyrosequencing. Both UniFrac analysis and partial least squares-discriminant analysis showed significant structural alterations in gut microbiota during the development of liver disease. Co-abundance network analysis highlighted relationships between genera. Spearman correlation analysis revealed that the bacterial species, Atopobium spp., Bacteroides spp., Bacteroides vulgatus, Bacteroides acidifaciens, Bacteroides uniformis, Clostridium cocleatum, Clostridium xylanolyticum and Desulfovibrio spp., markedly increased in model mice, were positively correlated with LPS levels and pathophysiological features. Taken together, the results showed that the gut microbiota was altered significantly in the progression of liver disease. The connection between the gut microbial ecology and the liver pathology may represent potential targets for the prevention and treatment of chronic liver disease and HCC.}, }
@article {pmid27032029, year = {2016}, author = {Kraler, M and Ghanbari, M and Domig, KJ and Schedle, K and Kneifel, W}, title = {The intestinal microbiota of piglets fed with wheat bran variants as characterised by 16S rRNA next-generation amplicon sequencing.}, journal = {Archives of animal nutrition}, volume = {70}, number = {3}, pages = {173-189}, doi = {10.1080/1745039X.2016.1160534}, pmid = {27032029}, issn = {1477-2817}, mesh = {Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Diet/veterinary ; Dietary Fiber/deficiency/*metabolism ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics/metabolism ; Random Allocation ; Sequence Analysis, DNA/veterinary ; Sus scrofa/*microbiology/*physiology ; }, abstract = {The intestinal microbiota of piglets fed with a Control diet low in dietary fibre and modified wheat bran variants as an additional source of insoluble dietary fibre was characterised. In this context, variances in the microbiota of three different gut segments were assessed. Wheat bran was either included in its native form or modified by fermentation and extrusion before added at 150 g/kg to a basal diet for 48 piglets (12 animals per treatment). Total DNA was extracted from digesta samples from the jejunum, the end of the ileum and the colon ascendens. Samples were prepared accordingly for subsequent sequencing with the Illumina MiSeq. The obtained results revealed distinct location-specific differences in microbial composition. While Firmicutes were most predominant in all three gut segments, Bacteroidetes were additionally found in the colon at high abundance. The parameters of alpha and beta diversity analysis showed significant differences (p < 0.01) between the colon and the other two gut segments. Specialised bacterial groups like Prevotella and Ruminococcaceae were among the most predominant ones found in the colon, as they possess cellulolytic properties to degrade (at least partially) non-starch polysaccharides, while their abundance was negligible in the jejunum and the ileum. Conversely, the genera Lactobacillus, Bifidobacterium and Veillonella, for example, were among the most predominant groups in the jejunum and ileum, while in the colon they were hardly found. Although statistical taxonomical evaluation, following p-value correction, did not reveal pronounced differences in abundance related to bran modification, alpha and beta diversity analysis showed an influence regarding the various feeding strategies applied. Based on these findings, a more in-depth view on intestinal microbial composition within the gastrointestinal tract of young pigs fed with low- and high-fibre diets was generated.}, }
@article {pmid27030361, year = {2016}, author = {Bartlewicz, J and Lievens, B and Honnay, O and Jacquemyn, H}, title = {Microbial diversity in the floral nectar of Linaria vulgaris along an urbanization gradient.}, journal = {BMC ecology}, volume = {16}, number = {}, pages = {18}, pmid = {27030361}, issn = {1472-6785}, mesh = {Biodiversity ; Flowers/*microbiology ; Linaria/*microbiology ; *Plant Nectar ; }, abstract = {BACKGROUND: Microbes are common inhabitants of floral nectar and are capable of influencing plant-pollinator interactions. All studies so far investigated microbial communities in floral nectar in plant populations that were located in natural environments, but nothing is known about these communities in nectar of plants inhabiting urban environments. However, at least some microbes are vectored into floral nectar by pollinators, and because urbanization can have a profound impact on pollinator communities and plant-pollinator interactions, it can be expected that it affects nectar microbes as well. To test this hypothesis, we related microbial diversity in floral nectar to the degree of urbanization in the late-flowering plant Linaria vulgaris. Floral nectar was collected from twenty populations along an urbanization gradient and culturable bacteria and yeasts were isolated and identified by partially sequencing the genes coding for small and large ribosome subunits, respectively.<br><br>RESULTS: A total of seven yeast and 13 bacterial operational taxonomic units (OTUs) were found at 3 and 1% sequence dissimilarity cut-offs, respectively. In agreement with previous studies, Metschnikowia reukaufii and M. gruessi were the main yeast constituents of nectar yeast communities, whereas Acinetobacter nectaris and Rosenbergiella epipactidis were the most frequently found bacterial species. Microbial incidence was high and did not change along the investigated urbanization gradient. However, microbial communities showed a nested subset structure, indicating that species-poor communities were a subset of species-rich communities.<br><br>CONCLUSIONS: The level of urbanization was putatively identified as an important driver of nestedness, suggesting that environmental changes related to urbanization may impact microbial communities in floral nectar of plants growing in urban environments.}, }
@article {pmid27029554, year = {2016}, author = {Speth, DR and In 't Zandt, MH and Guerrero-Cruz, S and Dutilh, BE and Jetten, MS}, title = {Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {11172}, pmid = {27029554}, issn = {2041-1723}, mesh = {Ammonium Compounds/analysis ; Bacteria/classification/*genetics/metabolism ; Biodegradation, Environmental ; Bioreactors/microbiology ; Denitrification ; *Genome, Bacterial ; Metagenomics ; Nitrites/metabolism ; Phylogeny ; Sewage/chemistry/microbiology ; *Wastewater ; Water Purification/*methods ; }, abstract = {Partial-nitritation anammox (PNA) is a novel wastewater treatment procedure for energy-efficient ammonium removal. Here we use genome-resolved metagenomics to build a genome-based ecological model of the microbial community in a full-scale PNA reactor. Sludge from the bioreactor examined here is used to seed reactors in wastewater treatment plants around the world; however, the role of most of its microbial community in ammonium removal remains unknown. Our analysis yielded 23 near-complete draft genomes that together represent the majority of the microbial community. We assign these genomes to distinct anaerobic and aerobic microbial communities. In the aerobic community, nitrifying organisms and heterotrophs predominate. In the anaerobic community, widespread potential for partial denitrification suggests a nitrite loop increases treatment efficiency. Of our genomes, 19 have no previously cultivated or sequenced close relatives and six belong to bacterial phyla without any cultivated members, including the most complete Omnitrophica (formerly OP3) genome to date.}, }
@article {pmid27027301, year = {2016}, author = {Ponziani, FR and Scaldaferri, F and Petito, V and Paroni Sterbini, F and Pecere, S and Lopetuso, LR and Palladini, A and Gerardi, V and Masucci, L and Pompili, M and Cammarota, G and Sanguinetti, M and Gasbarrini, A}, title = {The Role of Antibiotics in Gut Microbiota Modulation: The Eubiotic Effects of Rifaximin.}, journal = {Digestive diseases (Basel, Switzerland)}, volume = {34}, number = {3}, pages = {269-278}, doi = {10.1159/000443361}, pmid = {27027301}, issn = {1421-9875}, mesh = {Anti-Bacterial Agents/*pharmacology/therapeutic use ; DNA, Bacterial/isolation &amp; purification ; Gastrointestinal Microbiome/*drug effects ; Humans ; Lactobacillus/drug effects ; Rifamycins/administration &amp; dosage/*pharmacology ; Rifaximin ; }, abstract = {Antibiotics are mainly used in clinical practice for their activity against pathogens, but they also alter the composition of commensal gut microbial community. Rifaximin is a non-absorbable antibiotic with additional effects on the gut microbiota about which very little is known. It is still not clear to what extent rifaximin can be able to modulate gut microbiota composition and diversity in different clinical settings. Studies based on culture-dependent techniques revealed that rifaximin treatment promotes the growth of beneficial bacteria, such as Bifidobacteria and Lactobacilli. Accordingly, our metagenomic analysis carried out on patients with different gastrointestinal and liver diseases highlighted a significant increase in Lactobacilli after rifaximin treatment, persisting in the short time period. This result was independent of the disease background and was not accompanied by a significant alteration of the overall gut microbial ecology. This suggests that rifaximin can exert important eubiotic effects independently of the original disease, producing a favorable gut microbiota perturbation without changing its overall composition and diversity.}, }
@article {pmid27026101, year = {2016}, author = {Benucci, GMN and Bonito, GM}, title = {The Truffle Microbiome: Species and Geography Effects on Bacteria Associated with Fruiting Bodies of Hypogeous Pezizales.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {4-8}, pmid = {27026101}, issn = {1432-184X}, mesh = {Actinobacteria/genetics/isolation &amp; purification ; Ascomycota/*physiology ; Bacteria/*classification/genetics/isolation &amp; purification ; Bradyrhizobium/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Firmicutes/genetics/isolation &amp; purification ; Fruiting Bodies, Fungal/physiology ; Geography ; *Microbiota ; Proteobacteria/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {Fungi that produce their fruiting bodies underground within the soil profile are known commonly as truffles. Truffle fruiting bodies harbor a diverse but poorly understood microbial community of bacteria, yeasts, and filamentous fungi. In this study, we used next-generation 454 amplicon pyrosequencing of the V1 and V4 region of the bacterial 16S ribosomal DNA (rDNA) in order to characterize and compare effects of truffle species and geographic origin on the truffle microbiome. We compared truffle microbiomes of the glebal tissue for eight truffle species belonging to four distinct genera within the Pezizales: Tuber, Terfezia, Leucangium, and Kalapuya. The bacterial community within truffles was dominated by Proteobacteria, Bacterioides, Actinobacteria, and Firmicutes. Bacterial richness within truffles was quite low overall, with between 2-23 operational taxonomic units (OTUs). Notably, we found a single Bradyrhizobium OTU to be dominant within truffle species belonging to the genus Tuber, irrespective of geographic origin, but not in other truffle genera sampled. This study offers relevant insights into the truffle microbiome and raises questions concerning the recruitment and function of these fungal-associated bacteria consortia.}, }
@article {pmid27026100, year = {2016}, author = {Nasser, NA and Patterson, RT and Roe, HM and Galloway, JM and Falck, H and Palmer, MJ and Spence, C and Sanei, H and Macumber, AL and Neville, LA}, title = {Lacustrine Arcellinina (Testate Amoebae) as Bioindicators of Arsenic Contamination.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {130-149}, pmid = {27026100}, issn = {1432-184X}, mesh = {Amoeba/classification/isolation &amp; purification/*metabolism ; Arsenic/*analysis ; Arsenic Trioxide ; Arsenicals ; Canada ; Cluster Analysis ; *Environmental Monitoring ; Geologic Sediments/*chemistry/*microbiology ; Gold ; Lakes/chemistry ; Mining ; Oxides ; }, abstract = {Arcellininids (testate amoebae) were examined from 61 surface sediment samples collected from 59 lakes in the vicinity of former gold mines, notably Giant Mine, near Yellowknife, Northwest Territories, Canada to determine their utility as bioindicators of arsenic (As), which occurs both as a byproduct of gold extraction at mines in the area and ore-bearing outcrops. Cluster analysis (Q-R-mode) and detrended correspondence analysis (DCA) reveal five arcellininid assemblages, three of which are related to varying As concentrations in the sediment samples. Redundancy analysis (RDA) showed that 14 statistically significant environmental parameters explained 57 % of the variation in faunal distribution, while partial RDA indicated that As had the greatest influence on assemblage variance (10.7 %; p < 0.10). Stress-indicating species (primarily centropyxids) characterized the faunas of samples with high As concentrations (median = 121.7 ppm, max > 10000 ppm, min = 16.1 ppm, n = 32), while difflugiid dominated assemblages were prevalent in substrates with relatively low As concentrations (median = 30.2 ppm, max = 905.2 ppm, min = 6.3 ppm, n = 20). Most of the lakes with very high As levels are located downwind (N and W) of the former Giant Mine roaster stack where refractory ore was roasted and substantial quantities of As were released (as As2O3) to the atmosphere in the first decade of mining. This spatial pattern suggests that a significant proportion of the observed As, in at least these lakes, are industrially derived. The results of this study highlight the sensitivity of Arcellinina to As and confirm that the group has considerable potential for assessing the impact of As contamination on lakes.}, }
@article {pmid27023797, year = {2016}, author = {Law, AD and Fisher, C and Jack, A and Moe, LA}, title = {Tobacco, Microbes, and Carcinogens: Correlation Between Tobacco Cure Conditions, Tobacco-Specific Nitrosamine Content, and Cured Leaf Microbial Community.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {120-129}, pmid = {27023797}, issn = {1432-184X}, mesh = {Bacteria/*classification/enzymology/isolation &amp; purification ; Carcinogens/analysis ; DNA, Bacterial/genetics ; Nitrate Reductase/genetics ; Nitrates/analysis ; Nitrites/analysis ; Nitrosamines/*analysis ; Plant Leaves/*chemistry/microbiology ; RNA, Ribosomal, 16S/genetics ; Temperature ; Nicotiana/chemistry/*microbiology ; }, abstract = {Tobacco-specific nitrosamines are carcinogenic N-nitrosamine compounds present at very low levels in freshly harvested tobacco leaves that accumulate during leaf curing. Formation of N-nitrosamine compounds is associated with high nitrate levels in the leaf at harvest, and nitrate is presumed to be the source from which the N-nitrosation species originates. More specifically, nitrite is considered to be a direct precursor, and nitrite is linked with N-nitrosation in many environmental matrices where it occurs via microbial nitrate reduction. Here, we initiate work exploring the role of leaf microbial communities in formation of tobacco-specific nitrosamines. Leaves from burley tobacco line TN90H were air cured under various temperature and relative humidity levels, and 22 cured tobacco samples were analyzed for their microbial communities and leaf chemistry. Analysis of nitrate, nitrite, and total tobacco-specific nitrosamine levels revealed a strong positive correlation between the three variables, as well as a strong positive correlation with increasing relative humidity during cure conditions. 16S rRNA gene amplicon sequencing was used to assess microbial communities in each of the samples. In most samples, Proteobacteria predominated at the phylum level, accounting for >90 % of the OTUs. However, a distinct shift was noted among members of the high tobacco-specific nitrosamine group, with increases in Firmicutes and Actinobacteria. Several OTUs were identified that correlate strongly (positive and negative) with tobacco-specific nitrosamine content. Copy number of bacterial nitrate reductase genes, obtained using quantitative PCR, did not correlate strongly with tobacco-specific nitrosamine content. Incomplete denitrification is potentially implicated in tobacco-specific nitrosamine levels.}, }
@article {pmid27021396, year = {2016}, author = {Jasim, B and Sreelakshmi, KS and Mathew, J and Radhakrishnan, EK}, title = {Surfactin, Iturin, and Fengycin Biosynthesis by Endophytic Bacillus sp. from Bacopa monnieri.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {106-119}, pmid = {27021396}, issn = {1432-184X}, mesh = {Anti-Infective Agents/isolation &amp; purification/metabolism ; Antineoplastic Agents/isolation &amp; purification/metabolism ; Antioxidants/isolation &amp; purification/metabolism ; Antiviral Agents/isolation &amp; purification/metabolism ; Bacillus/classification/isolation &amp; purification/*metabolism ; Bacopa/*microbiology ; Biological Products/metabolism ; Endophytes/metabolism ; Lipopeptides/*biosynthesis ; Multigene Family ; Peptides, Cyclic/*biosynthesis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tandem Mass Spectrometry ; }, abstract = {Endophytic microorganisms which are ubiquitously present in plants may colonize intracellularly or intercellularly without causing any diseases. By living within the unique chemical environment of a host plant, they produce a vast array of compounds with a wide range of biological activities. Because of this, natural products of endophytic origin have been exploited for antimicrobial, antiviral, anticancer, and antioxidant properties. Also, they can be considered to function as an efficient microbial barrier to protect plants from various pathogens. In the present study, endophytic bacterium BmB 9 with antifungal and antibacterial activity isolated from the stem tissue of Bacopa monnieri was studied for the molecular and chemical basis of its activity. PCR-based genome mining for various biosynthetic gene clusters proved the presence of surfactin, iturin, and type I polyketide synthase (PKS) genes in the isolate. The LC-MS/MS based analysis of the extract further confirmed the production of surfactin derivatives (M + H(+)-1008.6602, 1022.6755), iturin (M + H(+)-1043.5697), and fengycin (M + H(+)-1491.8195, 1477.8055) by the selected bacterial isolate. The 16S rDNA sequence similarity based analysis identified the isolate BmB 9 as Bacillus sp. with 100 % identity to Bacillus sp. LCF1 (KP257289).}, }
@article {pmid27020916, year = {2016}, author = {Cassman, NA and Leite, MF and Pan, Y and de Hollander, M and van Veen, JA and Kuramae, EE}, title = {Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {23680}, pmid = {27020916}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics/*growth &amp; development ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; *Fertilizers ; Fungi/classification/genetics/*physiology ; *Grassland ; Host-Pathogen Interactions ; Microbiota/genetics/*physiology ; Plants/*microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; Soil Microbiology ; Species Specificity ; Time Factors ; }, abstract = {Inorganic fertilization and mowing alter soil factors with subsequent effects-direct and indirect - on above- and below-ground communities. We explored direct and indirect effects of long-term fertilization (N, P, NPK, Liming) and twice yearly mowing on the plant, bacterial and fungal communities and soil factors. We analyzed co-variation using 16S and 18S rRNA genes surveys, and plant frequency and edaphic factors across treatments. The plant and fungal communities were distinct in the NPK and L treatments, while the bacterial communities and soil factors were distinct in the N and L treatments. Plant community diversity and evenness had low diversity in the NPK and high diversity in the liming treatment, while the diversity and evenness of the bacterial and fungal communities did not differ across treatments, except of higher diversity and evenness in the liming treatment for the bacteria. We found significant co-structures between communities based on plant and fungal comparisons but not between plant and bacterial nor bacterial and fungal comparisons. Our results suggested that the plant and fungal communities are more tightly linked than either community with the bacterial community in fertilized soils. We found co-varying plant, bacterial and fungal taxa in different treatments that may indicate ecological interactions.}, }
@article {pmid27020399, year = {2016}, author = {Cagnetta, C and Coma, M and Vlaeminck, SE and Rabaey, K}, title = {Production of carboxylates from high rate activated sludge through fermentation.}, journal = {Bioresource technology}, volume = {217}, number = {}, pages = {165-172}, doi = {10.1016/j.biortech.2016.03.053}, pmid = {27020399}, issn = {1873-2976}, mesh = {*Bioreactors ; *Carboxylic Acids/chemistry/metabolism ; *Fatty Acids, Volatile/chemistry/metabolism ; Fermentation ; *Methane/chemistry/metabolism ; Sewage/*chemistry ; }, abstract = {The aim of this work was to study the key parameters affecting fermentation of high rate activated A-sludge to carboxylates, including pH, temperature, inoculum, sludge composition and iron content. The maximum volatile fatty acids production was 141mgCg(-1) VSSfed, at pH 7. Subsequently the potential for carboxylate and methane production for A-sludge from four different plants at pH 7 and 35°C were compared. Initial BOD of the sludge appeared to be key determining carboxylate yield from A-sludge. Whereas methanogenesis could be correlated linearly to the quantity of ferric used for coagulation, fermentation did not show a dependency on iron presence. This difference may enable a strategy whereby A-stage sludge is separated to achieve fermentation, and iron dosing for phosphate removal is only implemented at the B-stage.}, }
@article {pmid27020160, year = {2016}, author = {Gónzalez, D and Rodriguez-Carres, M and Boekhout, T and Stalpers, J and Kuramae, EE and Nakatani, AK and Vilgalys, R and Cubeta, MA}, title = {Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales.}, journal = {Fungal biology}, volume = {120}, number = {4}, pages = {603-619}, pmid = {27020160}, issn = {1878-6146}, support = {T32 AI052080/AI/NIAID NIH HHS/United States ; T32 AI 52080/AI/NIAID NIH HHS/United States ; }, mesh = {Basidiomycota/*classification/*genetics ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Mitochondrial Proton-Translocating ATPases/genetics ; Peptide Elongation Factor 1/genetics ; *Phylogeny ; RNA Polymerase II/genetics ; Sequence Analysis, DNA ; }, abstract = {Phylogenetic relationships of Rhizoctonia fungi within the order Cantharellales were studied using sequence data from portions of the ribosomal DNA cluster regions ITS-LSU, rpb2, tef1, and atp6 for 50 taxa, and public sequence data from the rpb2 locus for 165 taxa. Data sets were analysed individually and combined using Maximum Parsimony, Maximum Likelihood, and Bayesian Phylogenetic Inference methods. All analyses supported the monophyly of the family Ceratobasidiaceae, which comprises the genera Ceratobasidium and Thanatephorus. Multi-locus analysis revealed 10 well-supported monophyletic groups that were consistent with previous separation into anastomosis groups based on hyphal fusion criteria. This analysis coupled with analyses of a larger sample of 165 rpb2 sequences of fungi in the Cantharellales supported a sister relationship between the Botryobasidiaceae and Ceratobasidiaceae and a sister relationship of the Tulasnellaceae with the rest of the Cantharellales. The inclusion of additional sequence data did not clarify incongruences observed in previous studies of Rhizoctonia fungi in the Cantharellales based on analyses of a single or multiple genes. The diversity of ecological and morphological characters associated with these fungi requires further investigation on character evolution for re-evaluating homologous and homoplasious characters.}, }
@article {pmid27020120, year = {2016}, author = {Scoma, A and Barbato, M and Hernandez-Sanabria, E and Mapelli, F and Daffonchio, D and Borin, S and Boon, N}, title = {Microbial oil-degradation under mild hydrostatic pressure (10 MPa): which pathways are impacted in piezosensitive hydrocarbonoclastic bacteria?.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {23526}, pmid = {27020120}, issn = {2045-2322}, mesh = {Alcanivoraceae/classification/genetics/metabolism ; Bacteria/classification/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Ecosystem ; Gene Expression Profiling/methods ; Gene Expression Regulation, Bacterial ; Geologic Sediments/microbiology ; Hydrocarbons/metabolism ; *Hydrostatic Pressure ; Metabolic Networks and Pathways/genetics ; Petroleum/*metabolism ; *Petroleum Pollution ; RNA, Bacterial/genetics/metabolism ; RNA, Transfer/genetics ; Ribosomal Proteins/genetics/metabolism ; Seawater/microbiology ; Species Specificity ; Spectrophotometry ; }, abstract = {Oil spills represent an overwhelming carbon input to the marine environment that immediately impacts the sea surface ecosystem. Microbial communities degrading the oil fraction that eventually sinks to the seafloor must also deal with hydrostatic pressure, which linearly increases with depth. Piezosensitive hydrocarbonoclastic bacteria are ideal candidates to elucidate impaired pathways following oil spills at low depth. In the present paper, we tested two strains of the ubiquitous Alcanivorax genus, namely A. jadensis KS_339 and A. dieselolei KS_293, which is known to rapidly grow after oil spills. Strains were subjected to atmospheric and mild pressure (0.1, 5 and 10 MPa, corresponding to a depth of 0, 500 and 1000 m, respectively) providing n-dodecane as sole carbon source. Pressures equal to 5 and 10 MPa significantly lowered growth yields of both strains. However, in strain KS_293 grown at 10 MPa CO2 production per cell was not affected, cell integrity was preserved and PO4(3-) uptake increased. Analysis of its transcriptome revealed that 95% of its genes were downregulated. Increased transcription involved protein synthesis, energy generation and respiration pathways. Interplay between these factors may play a key role in shaping the structure of microbial communities developed after oil spills at low depth and limit their bioremediation potential.}, }
@article {pmid27019789, year = {2016}, author = {Coil, DA and Neches, RY and Lang, JM and Brown, WE and Severance, M and Cavalier, D and Eisen, JA}, title = {Growth of 48 built environment bacterial isolates on board the International Space Station (ISS).}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e1842}, pmid = {27019789}, issn = {2167-8359}, abstract = {Background. While significant attention has been paid to the potential risk of pathogenic microbes aboard crewed spacecraft, the non-pathogenic microbes in these habitats have received less consideration. Preliminary work has demonstrated that the interior of the International Space Station (ISS) has a microbial community resembling those of built environments on Earth. Here we report the results of sending 48 bacterial strains, collected from built environments on Earth, for a growth experiment on the ISS. This project was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS). Results. Of the 48 strains sent to the ISS, 45 of them showed similar growth in space and on Earth using a relative growth measurement adapted for microgravity. The vast majority of species tested in this experiment have also been found in culture-independent surveys of the ISS. Only one bacterial strain showed significantly different growth in space. Bacillus safensis JPL-MERTA-8-2 grew 60% better in space than on Earth. Conclusions. The majority of bacteria tested were not affected by conditions aboard the ISS in this experiment (e.g., microgravity, cosmic radiation). Further work on Bacillus safensis could lead to interesting insights on why this strain grew so much better in space.}, }
@article {pmid27019410, year = {2016}, author = {Haichar, FEZ and Heulin, T and Guyonnet, JP and Achouak, W}, title = {Stable isotope probing of carbon flow in the plant holobiont.}, journal = {Current opinion in biotechnology}, volume = {41}, number = {}, pages = {9-13}, doi = {10.1016/j.copbio.2016.02.023}, pmid = {27019410}, issn = {1879-0429}, mesh = {Carbon Isotopes/*analysis ; Isotope Labeling/*methods ; Plant Roots/*metabolism/microbiology ; Plants/*metabolism/microbiology ; *Soil Microbiology ; }, abstract = {Microbial communities associated with a plant host, constituting a holobiont, affect the physiology and growth of the plant via metabolites that are mainly derived from their photosynthates. The structure and function of active microbial communities that assimilate root exudates can be tracked by using stable isotope probing (SIP) approaches. This article reviews results from ongoing SIP research in plant-microbe interactions, with a specific focus on investigating the fate of fresh and recalcitrant carbon in the rhizosphere with [13]C enriched-root exudates, in addition to identifying key players in carbon cycling. Finally, we discuss new SIP applications that have the potential to identify novel enzymes implicated in rhizoremediation or plant genes dedicated to root exudation by combining SIP approaches and genome wide associations studies.}, }
@article {pmid27016562, year = {2016}, author = {Bennke, CM and Reintjes, G and Schattenhofer, M and Ellrott, A and Wulf, J and Zeder, M and Fuchs, BM}, title = {Modification of a High-Throughput Automatic Microbial Cell Enumeration System for Shipboard Analyses.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {11}, pages = {3289-3296}, pmid = {27016562}, issn = {1098-5336}, mesh = {*Aquatic Organisms ; Automation, Laboratory/*methods ; Bacterial Load/*methods ; Image Processing, Computer-Assisted/*methods ; Microscopy/*methods ; Optical Imaging/*methods ; Reproducibility of Results ; }, abstract = {In the age of ever-increasing "-omics" studies, the accurate and statistically robust determination of microbial cell numbers within often-complex samples remains a key task in microbial ecology. Microscopic quantification is still the only method to enumerate specific subgroups of microbial clades within complex communities by, for example, fluorescence in situ hybridization (FISH). In this study, we improved an existing automatic image acquisition and cell enumeration system and adapted it for usage at high seas on board an oceanographic research ship. The system was evaluated by testing settings such as minimal pixel area and image exposure times ashore under stable laboratory conditions before being brought on board and tested under various wind and wave conditions. The system was robust enough to produce high-quality images even with ship heaves of up to 3 m and pitch and roll angles of up to 6.3°. On board the research ship, on average, 25% of the images acquired from plankton samples on filter membranes could be used for cell enumeration. Automated enumeration was highly correlated with manual counts (r(2) > 0.9). Even the smallest of microbial cells in the open ocean, members of the alphaproteobacterial SAR11 clade, could be confidently detected and enumerated. The automated image acquisition and cell enumeration system developed here enables an accurate and reproducible determination of microbial cell counts in planktonic samples and allows insight into the abundance and distribution of specific microorganisms already on board within a few hours.IMPORTANCE In this research article, we report on a new system and software pipeline, which allows for an easy and quick image acquisition and the subsequent enumeration of cells in the acquired images. We put this pipeline through vigorous testing and compared it to manual microscopy counts of microbial cells on membrane filters. Furthermore, we tested this system at sea on board a marine research vessel and counted bacteria on board within a few hours after the retrieval of water samples. The imaging and counting system described here has been successfully applied to a number of laboratory-based studies and allowed the quantification of thousands of samples and FISH preparations (see, e.g., H. Teeling, B. M. Fuchs, D. Becher, C. Klockow, A. Gardebrecht, C. M. Bennke, M. Kassabgy, S. Huang, A. J. Mann, J. Waldmann, M. Weber, A. Klindworth, A. Otto, J. Lange, J. Bernhardt, C. Reinsch, M. Hecker, J. Peplies, F. D. Bockelmann, U. Callies, G. Gerdts, A. Wichels, K. H. Wiltshire, F. O. Glöckner, T. Schweder, and R. Amann, Science 336:608-611, 2012, http://dx.doi.org/10.1126/science.1218344). We adjusted the standard image acquisition software to withstand ship movements. This system will allow for more targeted sampling of the microbial community, leading to a better understanding of the role of microorganisms in the global oceans.}, }
@article {pmid27015005, year = {2016}, author = {Hausmann, B and Knorr, KH and Schreck, K and Tringe, SG and Glavina Del Rio, T and Loy, A and Pester, M}, title = {Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms.}, journal = {The ISME journal}, volume = {10}, number = {10}, pages = {2365-2375}, pmid = {27015005}, issn = {1751-7370}, support = {P 23117/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Ecosystem ; Fermentation ; Methane/metabolism ; *Microbial Consortia ; Oxidation-Reduction ; *Soil Microbiology ; Sulfates/*metabolism ; Sulfur/metabolism ; }, abstract = {Dissimilatory sulfate reduction in peatlands is sustained by a cryptic sulfur cycle and effectively competes with methanogenic degradation pathways. In a series of peat soil microcosms incubated over 50 days, we identified bacterial consortia that responded to small, periodic additions of individual fermentation products (formate, acetate, propionate, lactate or butyrate) in the presence or absence of sulfate. Under sulfate supplementation, net sulfate turnover (ST) steadily increased to 16-174 nmol cm(-3) per day and almost completely blocked methanogenesis. 16S rRNA gene and cDNA amplicon sequencing identified microorganisms whose increases in ribosome numbers strongly correlated to ST. Natively abundant (⩾0.1% estimated genome abundance) species-level operational taxonomic units (OTUs) showed no significant response to sulfate. In contrast, low-abundance OTUs responded significantly to sulfate in incubations with propionate, lactate and butyrate. These OTUs included members of recognized sulfate-reducing taxa (Desulfosporosinus, Desulfopila, Desulfomonile, Desulfovibrio) and also members of taxa that are either yet unknown sulfate reducers or metabolic interaction partners thereof. Most responsive OTUs markedly increased their ribosome content but only weakly increased in abundance. Responsive Desulfosporosinus OTUs even maintained a constantly low population size throughout 50 days, which suggests a novel strategy of rare biosphere members to display activity. Interestingly, two OTUs of the non-sulfate-reducing genus Telmatospirillum (Alphaproteobacteria) showed strongly contrasting preferences towards sulfate in butyrate-amended microcosms, corroborating that closely related microorganisms are not necessarily ecologically coherent. We show that diverse consortia of low-abundance microorganisms can perform peat soil sulfate reduction, a process that exerts control on methane production in these climate-relevant ecosystems.}, }
@article {pmid27014224, year = {2016}, author = {Crits-Christoph, A and Robinson, CK and Ma, B and Ravel, J and Wierzchos, J and Ascaso, C and Artieda, O and Souza-Egipsy, V and Casero, MC and DiRuggiero, J}, title = {Phylogenetic and Functional Substrate Specificity for Endolithic Microbial Communities in Hyper-Arid Environments.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {301}, pmid = {27014224}, issn = {1664-302X}, abstract = {Under extreme water deficit, endolithic (inside rock) microbial ecosystems are considered environmental refuges for life in cold and hot deserts, yet their diversity and functional adaptations remain vastly unexplored. The metagenomic analyses of the communities from two rock substrates, calcite and ignimbrite, revealed that they were dominated by Cyanobacteria, Actinobacteria, and Chloroflexi. The relative distribution of major phyla was significantly different between the two substrates and biodiversity estimates, from 16S rRNA gene sequences and from the metagenomic data, all pointed to a higher taxonomic diversity in the calcite community. While both endolithic communities showed adaptations to extreme aridity and to the rock habitat, their functional capabilities revealed significant differences. ABC transporters and pathways for osmoregulation were more diverse in the calcite chasmoendolithic community. In contrast, the ignimbrite cryptoendolithic community was enriched in pathways for secondary metabolites, such as non-ribosomal peptides (NRP) and polyketides (PK). Assemblies of the metagenome data produced population genomes for the major phyla found in both communities and revealed a greater diversity of Cyanobacteria population genomes for the calcite substrate. Draft genomes of the dominant Cyanobacteria in each community were constructed with more than 93% estimated completeness. The two annotated proteomes shared 64% amino acid identity and a significantly higher number of genes involved in iron update, and NRPS gene clusters, were found in the draft genomes from the ignimbrite. Both the community-wide and genome-specific differences may be related to higher water availability and the colonization of large fissures and cracks in the calcite in contrast to a harsh competition for colonization space and nutrient resources in the narrow pores of the ignimbrite. Together, these results indicated that the habitable architecture of both lithic substrates- chasmoendolithic versus cryptoendolithic - might be an essential element in determining the colonization and the diversity of the microbial communities in endolithic substrates at the dry limit for life.}, }
@article {pmid27014209, year = {2016}, author = {Miyake, S and Ngugi, DK and Stingl, U}, title = {Phylogenetic Diversity, Distribution, and Cophylogeny of Giant Bacteria (Epulopiscium) with their Surgeonfish Hosts in the Red Sea.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {285}, pmid = {27014209}, issn = {1664-302X}, abstract = {Epulopiscium is a group of giant bacteria found in high abundance in intestinal tracts of herbivorous surgeonfish. Despite their peculiarly large cell size (can be up to 600 μm), extreme polyploidy (some with over 100,000 genome copies per cell) and viviparity (whereby mother cells produce live offspring), details about their diversity, distribution or their role in the host gut are lacking. Previous studies have highlighted the existence of morphologically distinct Epulopiscium cell types (defined as morphotypes A to J) in some surgeonfish genera, but the corresponding genetic diversity and distribution among other surgeonfishes remain mostly unknown. Therefore, we investigated the phylogenetic diversity of Epulopiscium, distribution and co-occurrence in multiple hosts. Here, we identified eleven new phylogenetic clades, six of which were also morphologically characterized. Three of these novel clades were phylogenetically and morphologically similar to cigar-shaped type A1 cells, found in a wide range of surgeonfishes including Acanthurus nigrofuscus, while three were similar to smaller, rod-shaped type E that has not been phylogenetically classified thus far. Our results also confirmed that biogeography appears to have relatively little influence on Epulopiscium diversity, as clades found in the Great Barrier Reef and Hawaii were also recovered from the Red Sea. Although multiple symbiont clades inhabited a given species of host surgeonfish and multiple host species possessed a given symbiont clade, statistical analysis of host and symbiont phylogenies indicated significant cophylogeny, which in turn suggests co-evolutionary relationships. A cluster analysis of Epulopiscium sequences from previously published amplicon sequencing dataset revealed a similar pattern, where specific clades were consistently found in high abundance amongst closely related surgeonfishes. Differences in abundance may indicate specialization of clades to certain gut environments reflected by inferred differences in the host diets. Overall, our analysis identified a large phylogenetic diversity of Epulopiscium (up to 10% sequence divergence of 16S rRNA genes), which lets us hypothesize that there are multiple species that are spread across guts of different host species.}, }
@article {pmid27010745, year = {2016}, author = {Wei, H and Dai, J and Xia, M and Romine, MF and Shi, L and Beliav, A and Tiedje, JM and Nealson, KH and Fredrickson, JK and Zhou, J and Qiu, D}, title = {Functional roles of CymA and NapC in reduction of nitrate and nitrite by Shewanella putrefaciens W3-18-1.}, journal = {Microbiology (Reading, England)}, volume = {162}, number = {6}, pages = {930-941}, doi = {10.1099/mic.0.000285}, pmid = {27010745}, issn = {1465-2080}, mesh = {Amino Acid Sequence/genetics ; Aspartic Acid/metabolism ; Cytochrome c Group/metabolism ; Hydroquinones/metabolism ; Lysine/metabolism ; Mutagenesis, Site-Directed ; Nitrate Reductases/*genetics ; Nitrates/*metabolism ; Nitrites/*metabolism ; Oxidation-Reduction ; Sequence Alignment ; Shewanella putrefaciens/genetics/*metabolism ; }, abstract = {Shewanella putrefaciens W3-18-1 harbours two periplasmic nitrate reductase (Nap) gene clusters, NapC-associated nap-alpha (napEDABC) and CymA-dependent nap-beta (napDAGHB), for dissimilatory nitrate respiration. CymA is a member of the NapC/NirT quinol dehydrogenase family and acts as a hub to support different respiratory pathways, including those on iron [Fe(III)] and manganese [Mn(III, IV)] (hydr)oxide, nitrate, nitrite, fumarate and arsenate in Shewanella strains. However, in our analysis it was shown that another NapC/NirT family protein, NapC, was only involved in nitrate reduction, although both CymA and NapC can transfer quinol-derived electrons to a periplasmic terminal reductase or an electron acceptor. Furthermore, our results showed that NapC could only interact specifically with the Nap-alpha nitrate reductase while CymA could interact promiscuously with Nap-alpha, Nap-beta and the NrfA nitrite reductase for nitrate and nitrite reduction. To further explore the difference in specificity, site-directed mutagenesis on both CymA and NapC was conducted and the phenotypic changes in nitrate and nitrite reduction were tested. Our analyses demonstrated that the Lys-91 residue played a key role in nitrate reduction for quinol oxidation and the Asp-166 residue might influence the maturation of CymA. The Asp-97 residue might be one of the key factors that influence the interaction of CymA with the cytochromes NapB and NrfA.}, }
@article {pmid27010358, year = {2016}, author = {Rousk, K and Michelsen, A and Rousk, J}, title = {Microbial control of soil organic matter mineralization responses to labile carbon in subarctic climate change treatments.}, journal = {Global change biology}, volume = {22}, number = {12}, pages = {4150-4161}, doi = {10.1111/gcb.13296}, pmid = {27010358}, issn = {1365-2486}, mesh = {Carbon/*analysis ; *Climate Change ; Nitrogen ; Soil/*chemistry ; *Soil Microbiology ; Sweden ; Temperature ; }, abstract = {Half the global soil carbon (C) is held in high-latitude systems. Climate change will expose these to warming and a shift towards plant communities with more labile C input. Labile C can also increase the rate of loss of native soil organic matter (SOM); a phenomenon termed 'priming'. We investigated how warming (+1.1 °C over ambient using open top chambers) and litter addition (90 g m[-2] yr[-1]) treatments in the subarctic influenced the susceptibility of SOM mineralization to priming, and its microbial underpinnings. Labile C appeared to inhibit the mineralization of C from SOM by up to 60% within hours. In contrast, the mineralization of N from SOM was stimulated by up to 300%. These responses occurred rapidly and were unrelated to microbial successional dynamics, suggesting catabolic responses. Considered separately, the labile C inhibited C mineralization is compatible with previously reported findings termed 'preferential substrate utilization' or 'negative apparent priming', while the stimulated N mineralization responses echo recent reports of 'real priming' of SOM mineralization. However, C and N mineralization responses derived from the same SOM source must be interpreted together: This suggested that the microbial SOM-use decreased in magnitude and shifted to components richer in N. This finding highlights that only considering SOM in terms of C may be simplistic, and will not capture all changes in SOM decomposition. The selective mining for N increased in climate change treatments with higher fungal dominance. In conclusion, labile C appeared to trigger catabolic responses of the resident microbial community that shifted the SOM mining to N-rich components; an effect that increased with higher fungal dominance. Extrapolating from these findings, the predicted shrub expansion in the subarctic could result in an altered microbial use of SOM, selectively mining it for N-rich components, and leading to a reduced total SOM-use.}, }
@article {pmid27010076, year = {2016}, author = {van der Plas, F and Manning, P and Allan, E and Scherer-Lorenzen, M and Verheyen, K and Wirth, C and Zavala, MA and Hector, A and Ampoorter, E and Baeten, L and Barbaro, L and Bauhus, J and Benavides, R and Benneter, A and Berthold, F and Bonal, D and Bouriaud, O and Bruelheide, H and Bussotti, F and Carnol, M and Castagneyrol, B and Charbonnier, Y and Coomes, D and Coppi, A and Bastias, CC and Muhie Dawud, S and De Wandeler, H and Domisch, T and Finér, L and Gessler, A and Granier, A and Grossiord, C and Guyot, V and Hättenschwiler, S and Jactel, H and Jaroszewicz, B and Joly, FX and Jucker, T and Koricheva, J and Milligan, H and Müller, S and Muys, B and Nguyen, D and Pollastrini, M and Raulund-Rasmussen, K and Selvi, F and Stenlid, J and Valladares, F and Vesterdal, L and Zielínski, D and Fischer, M}, title = {Jack-of-all-trades effects drive biodiversity-ecosystem multifunctionality relationships in European forests.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {11109}, pmid = {27010076}, issn = {2041-1723}, mesh = {*Biodiversity ; Europe ; *Forests ; Models, Theoretical ; Species Specificity ; Trees/physiology ; }, abstract = {There is considerable evidence that biodiversity promotes multiple ecosystem functions (multifunctionality), thus ensuring the delivery of ecosystem services important for human well-being. However, the mechanisms underlying this relationship are poorly understood, especially in natural ecosystems. We develop a novel approach to partition biodiversity effects on multifunctionality into three mechanisms and apply this to European forest data. We show that throughout Europe, tree diversity is positively related with multifunctionality when moderate levels of functioning are required, but negatively when very high function levels are desired. For two well-known mechanisms, 'complementarity' and 'selection', we detect only minor effects on multifunctionality. Instead a third, so far overlooked mechanism, the 'jack-of-all-trades' effect, caused by the averaging of individual species effects on function, drives observed patterns. Simulations demonstrate that jack-of-all-trades effects occur whenever species effects on different functions are not perfectly correlated, meaning they may contribute to diversity-multifunctionality relationships in many of the world's ecosystems.}, }
@article {pmid27008566, year = {2016}, author = {Godon, JJ and Arulazhagan, P and Steyer, JP and Hamelin, J}, title = {Vertebrate bacterial gut diversity: size also matters.}, journal = {BMC ecology}, volume = {16}, number = {}, pages = {12}, pmid = {27008566}, issn = {1472-6785}, mesh = {Adolescent ; Adult ; Animals ; Child ; Child, Preschool ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Infant ; Male ; *Microbiota ; Organ Size ; Vertebrates/*microbiology ; Young Adult ; }, abstract = {BACKGROUND: One of the central issues in microbial ecology is to understand the parameters that drive diversity. Among these parameters, size has often been considered to be the main driver in many different ecosystems. Surprisingly, the influence of size on gut microbial diversity has not yet been investigated, and so far in studies reported in the literature only the influences of age, diet, phylogeny and digestive tract structures have been considered. This study explicitly challenges the underexplored relationship connecting gut volume and bacterial diversity.<br><br>RESULTS: The bacterial diversity of 189 faeces produced by 71 vertebrate species covering a body mass range of 5.6 log. The animals comprised mammals, birds and reptiles. The diversity was evaluated based on the Simpson Diversity Index extracted from 16S rDNA gene fingerprinting patterns. Diversity presented an increase along with animal body mass following a power law with a slope z of 0.338 &#xb1; 0.027, whatever the age, phylogeny, diet or digestive tract structure.<br><br>CONCLUSIONS: The results presented here suggest that gut volume cannot be neglected as a major driver of gut microbial diversity. The characteristics of the gut microbiota follow general principles of biogeography that arise in many ecological systems.}, }
@article {pmid27007713, year = {2016}, author = {Matthijs, S and Brandt, N and Ongena, M and Achouak, W and Meyer, JM and Budzikiewicz, H}, title = {Pyoverdine and histicorrugatin-mediated iron acquisition in Pseudomonas thivervalensis.}, journal = {Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine}, volume = {29}, number = {3}, pages = {467-485}, doi = {10.1007/s10534-016-9929-1}, pmid = {27007713}, issn = {1572-8773}, mesh = {Iron/chemistry/*metabolism ; Oligopeptides/*biosynthesis/chemistry ; Pseudomonas/genetics/*metabolism ; Siderophores/*biosynthesis/chemistry ; }, abstract = {The genome of Pseudomonas thivervalensis LMG 21626(T) has been sequenced and a genomic, genetic and structural analysis of the siderophore mediated iron acquisition was undertaken. Pseudomonas thivervalensis produces two structurally new siderophores, pyoverdine PYOthi which is typical for P. thivervalensis strains and a closely related strain, and the lipopeptidic siderophore histicorrugatin which is also detected in P. lini. Histicorrugatin consists out of an eight amino acid long peptide which is linked to octanoic acid. It is structurally related to the siderophores corrugatin and ornicorrugatin. Analysis of the proteome for TonB-dependent receptors identified 25 candidates. Comparison of the TonB-dependent receptors of P. thivervalensis with the 17 receptors of its phylogenetic neighbor, P. brassicacearum subsp. brassicacearum NFM 421, showed that NFM 421 shares the same set of receptors with LMG 21626(T), including the histicorrugatin receptor. An exception was found for their cognate pyoverdine receptor which can be explained by the observation that both strains produce structurally different pyoverdines. Mass analysis showed that NFM 421 did not produce histicorrugatin, but the analogue ornicorrugatin. Growth stimulation assays with a variety of structurally distinct pyoverdines produced by other Pseudomonas species demonstrated that LMG 21626(T) and NFM 421 are able to utilize almost the same set of pyoverdines. Strain NFM 421 is able utilize two additional pyoverdines, pyoverdine of P. fluorescens Pf0-1 and P. citronellolis LMG 18378(T), these pyoverdines are probably taken up by the FpvA receptor of NFM 421.}, }
@article {pmid27005434, year = {2016}, author = {Grunert, O and Reheul, D and Van Labeke, MC and Perneel, M and Hernandez-Sanabria, E and Vlaeminck, SE and Boon, N}, title = {Growing media constituents determine the microbial nitrogen conversions in organic growing media for horticulture.}, journal = {Microbial biotechnology}, volume = {9}, number = {3}, pages = {389-399}, pmid = {27005434}, issn = {1751-7915}, mesh = {Agriculture/methods ; Carbon Dioxide/metabolism ; Culture Media/*chemistry ; *Fertilizers ; Nitrogen/*metabolism ; *Soil Microbiology ; }, abstract = {Vegetables and fruits are an important part of a healthy food diet, however, the eco-sustainability of the production of these can still be significantly improved. European farmers and consumers spend an estimated €15.5 billion per year on inorganic fertilizers and the production of N-fertilizers results in a high carbon footprint. We investigated if fertilizer type and medium constituents determine microbial nitrogen conversions in organic growing media and can be used as a next step towards a more sustainable horticulture. We demonstrated that growing media constituents showed differences in urea hydrolysis, ammonia and nitrite oxidation and in carbon dioxide respiration rate. Interestingly, mixing of the growing media constituents resulted in a stimulation of the function of the microorganisms. The use of organic fertilizer resulted in an increase in amoA gene copy number by factor 100 compared to inorganic fertilizers. Our results support our hypothesis that the activity of the functional microbial community with respect to nitrogen turnover in an organic growing medium can be improved by selecting and mixing the appropriate growing media components with each other. These findings contribute to the understanding of the functional microbial community in growing media and its potential role towards a more responsible horticulture.}, }
@article {pmid26998796, year = {2016}, author = {Coppens, J and Lindeboom, R and Muys, M and Coessens, W and Alloul, A and Meerbergen, K and Lievens, B and Clauwaert, P and Boon, N and Vlaeminck, SE}, title = {Nitrification and microalgae cultivation for two-stage biological nutrient valorization from source separated urine.}, journal = {Bioresource technology}, volume = {211}, number = {}, pages = {41-50}, doi = {10.1016/j.biortech.2016.03.001}, pmid = {26998796}, issn = {1873-2976}, mesh = {Aquaculture ; *Bioreactors ; Microalgae/growth &amp; development/*metabolism ; Nitrification ; Nitrites/metabolism ; Nitrobacter/growth &amp; development/*metabolism ; Oxidation-Reduction ; Sewage/chemistry/microbiology ; Spirulina/growth &amp; development/metabolism ; Urine/*chemistry ; Wastewater/*chemistry ; }, abstract = {Urine contains the majority of nutrients in urban wastewaters and is an ideal nutrient recovery target. In this study, stabilization of real undiluted urine through nitrification and subsequent microalgae cultivation were explored as strategy for biological nutrient recovery. A nitrifying inoculum screening revealed a commercial aquaculture inoculum to have the highest halotolerance. This inoculum was compared with municipal activated sludge for the start-up of two nitrification membrane bioreactors. Complete nitrification of undiluted urine was achieved in both systems at a conductivity of 75mScm(-1) and loading rate above 450mgNL(-1)d(-1). The halotolerant inoculum shortened the start-up time with 54%. Nitrite oxidizers showed faster salt adaptation and Nitrobacter spp. became the dominant nitrite oxidizers. Nitrified urine as growth medium for Arthrospira platensis demonstrated superior growth compared to untreated urine and resulted in a high protein content of 62%. This two-stage strategy is therefore a promising approach for biological nutrient recovery.}, }
@article {pmid26994316, year = {2016}, author = {Tripathi, BM and Edwards, DP and Mendes, LW and Kim, M and Dong, K and Kim, H and Adams, JM}, title = {The impact of tropical forest logging and oil palm agriculture on the soil microbiome.}, journal = {Molecular ecology}, volume = {25}, number = {10}, pages = {2244-2257}, doi = {10.1111/mec.13620}, pmid = {26994316}, issn = {1365-294X}, mesh = {*Agriculture ; Arecaceae/growth &amp; development ; Bacteria/classification ; Biodiversity ; Borneo ; Conservation of Natural Resources ; *Forestry ; Forests ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Selective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land-use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once-logged and twice-logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell-cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land-use changes on the interaction of soil microbes.}, }
@article {pmid26992401, year = {2016}, author = {Rojas, X and Guo, J and Leff, JW and McNear, DH and Fierer, N and McCulley, RL}, title = {Infection with a Shoot-Specific Fungal Endophyte (Epichloë) Alters Tall Fescue Soil Microbial Communities.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {197-206}, pmid = {26992401}, issn = {1432-184X}, mesh = {Archaea/classification/isolation &amp; purification/metabolism ; Bacteria/classification/isolation &amp; purification/metabolism ; Chytridiomycota/classification/isolation &amp; purification/metabolism ; Endophytes/*classification/isolation &amp; purification/metabolism ; Epichloe/*classification/isolation &amp; purification/metabolism ; Festuca/*microbiology ; High-Throughput Nucleotide Sequencing ; Soil/chemistry ; *Soil Microbiology ; Symbiosis ; }, abstract = {Tall fescue (Schedonorus arundinaceus) is a widespread grass that can form a symbiotic relationship with a shoot-specific fungal endophyte (Epichloë coenophiala). While the effects of fungal endophyte infection on fescue physiology and ecology have been relatively well studied, less attention has been given to how this relationship may impact the soil microbial community. We used high-throughput DNA sequencing and phospholipid fatty acid analysis to determine the structure and biomass of microbial communities in both bulk and rhizosphere soils from tall fescue stands that were either uninfected with E. coenophiala or were infected with the common toxic strain or one of several novel strains of the endophyte. We found that rhizosphere and bulk soils harbored distinct microbial communities. Endophyte presence, regardless of strain, significantly influenced soil fungal communities, but endophyte effects were less pronounced in prokaryotic communities. E. coenophiala presence did not change total fungal biomass but caused a shift in soil and rhizosphere fungal community composition, increasing the relative abundance of taxa within the Glomeromycota phylum and decreasing the relative abundance of genera in the Ascomycota phylum, including Lecanicillium, Volutella, Lipomyces, Pochonia, and Rhizoctonia. Our data suggests that tripartite interactions exist between the shoot endophyte E. coenophiala, tall fescue, and soil fungi that may have important implications for the functioning of soils, such as carbon storage, in fescue-dominated grasslands.}, }
@article {pmid26992100, year = {2016}, author = {Koneru, SL and Salinas, H and Flores, GE and Hong, RL}, title = {The bacterial community of entomophilic nematodes and host beetles.}, journal = {Molecular ecology}, volume = {25}, number = {10}, pages = {2312-2324}, pmid = {26992100}, issn = {1365-294X}, support = {SC3 GM105579/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification ; Coleoptera/*microbiology/*parasitology ; DNA, Bacterial/genetics ; DNA, Helminth/genetics ; Host Specificity ; Los Angeles ; *Microbiota ; Nematoda/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Insects form the most species-rich lineage of Eukaryotes and each is a potential host for organisms from multiple phyla, including fungi, protozoa, mites, bacteria and nematodes. In particular, beetles are known to be associated with distinct bacterial communities and entomophilic nematodes. While entomopathogenic nematodes require symbiotic bacteria to kill and reproduce inside their insect hosts, the microbial ecology that facilitates other types of nematode-insect associations is largely unknown. To illuminate detailed patterns of the tritrophic beetle-nematode-bacteria relationship, we surveyed the nematode infestation profiles of scarab beetles in the greater Los Angeles area over a five-year period and found distinct nematode infestation patterns for certain beetle hosts. Over a single season, we characterized the bacterial communities of beetles and their associated nematodes using high-throughput sequencing of the 16S rRNA gene. We found significant differences in bacterial community composition among the five prevalent beetle host species, independent of geographical origin. Anaerobes Synergistaceae and sulphate-reducing Desulfovibrionaceae were most abundant in Amblonoxia beetles, while Enterobacteriaceae and Lachnospiraceae were common in Cyclocephala beetles. Unlike entomopathogenic nematodes that carry bacterial symbionts, insect-associated nematodes do not alter the beetles' native bacterial communities, nor do their microbiomes differ according to nematode or beetle host species. The conservation of Diplogastrid nematodes associations with Melolonthinae beetles and sulphate-reducing bacteria suggests a possible link between beetle-bacterial communities and their associated nematodes. Our results establish a starting point towards understanding the dynamic interactions between soil macroinvertebrates and their microbiota in a highly accessible urban environment.}, }
@article {pmid26989620, year = {2016}, author = {Piché-Choquette, S and Tremblay, J and Tringe, SG and Constant, P}, title = {H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e1782}, pmid = {26989620}, issn = {2167-8359}, abstract = {Soil microbial communities are continuously exposed to H2 diffusing into the soil from the atmosphere. N2-fixing nodules represent a peculiar microniche in soil where H2 can reach concentrations up to 20,000 fold higher than in the global atmosphere (0.530 ppmv). In this study, we investigated the impact of H2 exposure on soil bacterial community structure using dynamic microcosm chambers simulating soil H2 exposure from the atmosphere and N2-fixing nodules. Biphasic kinetic parameters governing H2 oxidation activity in soil changed drastically upon elevated H2 exposure, corresponding to a slight but significant decay of high affinity H2-oxidizing bacteria population, accompanied by an enrichment or activation of microorganisms displaying low-affinity for H2. In contrast to previous studies that unveiled limited response by a few species, the relative abundance of 958 bacterial ribotypes distributed among various taxonomic groups, rather than a few distinct taxa, was influenced by H2 exposure. Furthermore, correlation networks showed important alterations of ribotype covariation in response to H2 exposure, suggesting that H2 affects microbe-microbe interactions in soil. Taken together, our results demonstrate that H2-rich environments exert a direct influence on soil H2-oxidizing bacteria in addition to indirect effects on other members of the bacterial communities.}, }
@article {pmid26981376, year = {2016}, author = {Singh, A and Subudhi, E}, title = {Structural insights of microbial community of Deulajhari (India) hot spring using 16s-rRNA based metagenomic sequencing.}, journal = {Genomics data}, volume = {7}, number = {}, pages = {101-102}, pmid = {26981376}, issn = {2213-5960}, abstract = {Insights about the distribution of the microbial community prove to be the major goal of understanding microbial ecology which remains to be fully deciphered. Hot springs being hub for the thermophilic microbiota attract the attention of the microbiologists. Deulajhari hot spring cluster is located in the Angul district of Odisha. Covered within a wooded area, Deulajhari hot spring is also fed by the plant litter resulting in a relatively high amount of total organic content (TOC). For the first time, Illumina sequencing based biodiversity analysis of microbial composition is studied through amplicon metagenome sequencing of 16s rRNA targeting V3-V4 region using metagenomic DNA from the hot spring sediment. Over 28 phyla were detected through the amplicon metagenome sequencing of which the most dominating phyla at the existing physiochemical parameters like; temperature 69 °C, pH 8.09, electroconductivity 0.025 dSm(- 1) and total organic carbon 0.356%, were Proteobacteria (88.12%), Bacteriodetes (10.76%), Firmicutes (0.35%), Spirochetes (0.18%) and chloroflexi (0.11%). Approximately 713 species were observed at the above physiochemical parameters. The analysis of the metagenome provides the quantitative insights into microbial populations based on the sequence data in Deulajhari hot spring. Metagenome sequence is deposited to SRA database which is available at NCBI with accession no. SRX1459736.}, }
@article {pmid26980802, year = {2016}, author = {Rampal, R and Awasthi, A and Ahuja, V}, title = {Retinoic acid-primed human dendritic cells inhibit Th9 cells and induce Th1/Th17 cell differentiation.}, journal = {Journal of leukocyte biology}, volume = {100}, number = {1}, pages = {111-120}, doi = {10.1189/jlb.3VMA1015-476R}, pmid = {26980802}, issn = {1938-3673}, mesh = {Caco-2 Cells ; Cell Differentiation/*immunology ; Cytokines/metabolism ; Dendritic Cells/cytology/drug effects/*immunology ; Humans ; Interleukin-9/antagonists &amp; inhibitors/*immunology ; Keratolytic Agents/pharmacology ; Monocytes/*immunology ; Th1 Cells/*cytology/immunology ; Th17 Cells/*cytology/immunology ; Transforming Growth Factor beta1 ; Tretinoin/*pharmacology ; }, abstract = {All-trans-retinoic acid plays a central role in mucosal immunity, where it promotes its synthesis by up-regulating CD103 expression on dendritic cells, induces gut tropic (α4β7(+) and CCR9(+)) T cells, and inhibits Th1/Th17 differentiation. Recently, murine studies have highlighted the proinflammatory role of retinoic acid in maintaining inflammation under a variety of pathologic conditions. However, as a result of limited human data, we investigated the effect of retinoic acid on human dendritic cells and CD4(+) T cell responses in the presence of polarizing (Th1/Th9/Th17) and inflammatory (LPS-induced dendritic cells) conditions. We report a novel role of retinoic acid in an inflammatory setup, where retinoic acid-primed dendritic cells (retinoic acid-monocyte-derived dendritic cells) up-regulated CCR9(+)T cells, which were observed to express high levels of IFN-γ in the presence of Th1/Th17 conditions. Retinoic acid-monocyte-derived dendritic cells, under Th17 conditions, also favored the induction of IL-17(+) T cells. Furthermore, in the presence of TGF-β1 and IL-4, retinoic acid-monocyte-derived dendritic cells inhibited IL-9 and induced IFN-γ expression on T cells. Experiments with naïve CD4(+) T cells, activated in the presence of Th1/Th17 conditions and absence of DCs, indicated that retinoic acid inhibited IFN-γ and IL-17 expression on T cells. These data revealed that in the face of inflammatory conditions, retinoic acid, in contrast from its anti-inflammatory role, could maintain or aggravate the intestinal inflammation.}, }
@article {pmid26979952, year = {2016}, author = {van der Plas, F and Manning, P and Soliveres, S and Allan, E and Scherer-Lorenzen, M and Verheyen, K and Wirth, C and Zavala, MA and Ampoorter, E and Baeten, L and Barbaro, L and Bauhus, J and Benavides, R and Benneter, A and Bonal, D and Bouriaud, O and Bruelheide, H and Bussotti, F and Carnol, M and Castagneyrol, B and Charbonnier, Y and Coomes, DA and Coppi, A and Bastias, CC and Dawud, SM and De Wandeler, H and Domisch, T and Finér, L and Gessler, A and Granier, A and Grossiord, C and Guyot, V and Hättenschwiler, S and Jactel, H and Jaroszewicz, B and Joly, FX and Jucker, T and Koricheva, J and Milligan, H and Mueller, S and Muys, B and Nguyen, D and Pollastrini, M and Ratcliffe, S and Raulund-Rasmussen, K and Selvi, F and Stenlid, J and Valladares, F and Vesterdal, L and Zielínski, D and Fischer, M}, title = {Biotic homogenization can decrease landscape-scale forest multifunctionality.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {13}, pages = {3557-3562}, pmid = {26979952}, issn = {1091-6490}, mesh = {*Biodiversity ; Computer Simulation ; Databases, Factual ; Ecosystem ; Europe ; Forestry ; *Forests ; Models, Biological ; Trees ; }, abstract = {Many experiments have shown that local biodiversity loss impairs the ability of ecosystems to maintain multiple ecosystem functions at high levels (multifunctionality). In contrast, the role of biodiversity in driving ecosystem multifunctionality at landscape scales remains unresolved. We used a comprehensive pan-European dataset, including 16 ecosystem functions measured in 209 forest plots across six European countries, and performed simulations to investigate how local plot-scale richness of tree species (α-diversity) and their turnover between plots (β-diversity) are related to landscape-scale multifunctionality. After accounting for variation in environmental conditions, we found that relationships between α-diversity and landscape-scale multifunctionality varied from positive to negative depending on the multifunctionality metric used. In contrast, when significant, relationships between β-diversity and landscape-scale multifunctionality were always positive, because a high spatial turnover in species composition was closely related to a high spatial turnover in functions that were supported at high levels. Our findings have major implications for forest management and indicate that biotic homogenization can have previously unrecognized and negative consequences for large-scale ecosystem multifunctionality.}, }
@article {pmid26979838, year = {2016}, author = {Rocke, E and Jing, H and Xia, X and Liu, H}, title = {Effects of Hypoxia on the Phylogenetic Composition and Species Distribution of Protists in a Subtropical Harbor.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {96-105}, pmid = {26979838}, issn = {1432-184X}, mesh = {*Biodiversity ; Biofilms ; Ciliophora/*classification/isolation &amp; purification ; Cluster Analysis ; Denaturing Gradient Gel Electrophoresis ; Eukaryota/*classification/isolation &amp; purification ; Hong Kong ; Hypoxia/*metabolism ; Nitrogen/analysis ; Oxygen/analysis ; Phosphates/analysis ; *Phylogeny ; Seawater/chemistry/microbiology ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Tolo Harbor, a subtropical semi-enclosed coastal water body, is surrounded by an expanding urban community, which contributes to large concentrations of nutrient runoff, leading to algal blooms and localized hypoxic episodes. Present knowledge of protist distributions in subtropical waters during hypoxic conditions is very limited. In this study, therefore, we combined parallel 454 pyrosequencing technology and denaturing gradient gel electrophoresis (DGGE) fingerprint analyses to reveal the protist community shifts before, during, and after a 2-week hypoxic episode during the summer of 2011. Hierarchical clustering for DGGE demonstrated similar grouping of hypoxic samples separately from oxic samples. Dissolved oxygen (DO) concentration and dissolved inorganic nitrogen:phosphate (DIN:PO4) concentrations significantly affected OTU distribution in 454 sequenced samples, and a shift toward a ciliate and marine alveolate clade II (MALV II) species composition occurred as waters shifted from oxic to hypoxic. These results suggest that protist community shifts toward heterotrophic and parasitic tendencies as well as decreased diversity and richness in response to hypoxic outbreaks.}, }
@article {pmid26976842, year = {2016}, author = {Muziasari, WI and Pärnänen, K and Johnson, TA and Lyra, C and Karkman, A and Stedtfeld, RD and Tamminen, M and Tiedje, JM and Virta, M}, title = {Aquaculture changes the profile of antibiotic resistance and mobile genetic element associated genes in Baltic Sea sediments.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {4}, pages = {fiw052}, doi = {10.1093/femsec/fiw052}, pmid = {26976842}, issn = {1574-6941}, mesh = {Aminoglycosides/pharmacology ; Animals ; Anti-Bacterial Agents/*pharmacology ; Aquaculture/*methods ; Bacteria/*drug effects/*genetics ; Drug Resistance, Bacterial/*genetics ; Finland ; Fisheries ; Genes, Bacterial ; Geologic Sediments/*microbiology ; Integrons ; Interspersed Repetitive Sequences/genetics ; Microbial Sensitivity Tests ; Oceans and Seas ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; beta-Lactam Resistance/genetics ; beta-Lactams/pharmacology ; }, abstract = {Antibiotics are commonly used in aquaculture and they can change the environmental resistome by increasing antibiotic resistance genes (ARGs). Sediment samples were collected from two fish farms located in the Northern Baltic Sea, Finland, and from a site outside the farms (control). The sediment resistome was assessed by using a highly parallel qPCR array containing 295 primer sets to detect ARGs, mobile genetic elements and the 16S rRNA gene. The fish farm resistomes were enriched in transposon and integron associated genes and in ARGs encoding resistance to antibiotics which had been used to treat fish at the farms. Aminoglycoside resistance genes were also enriched in the farm sediments despite the farms not having used aminoglycosides. In contrast, the total relative abundance values of ARGs were higher in the control sediment resistome and they were mainly genes encoding efflux pumps followed by beta-lactam resistance genes, which are found intrinsically in many bacteria. This suggests that there is a natural Baltic sediment resistome. The resistome associated with fish farms can be from native ARGs enriched by antibiotic use at the farms and/or from ARGs and mobile elements that have been introduced by fish farming.}, }
@article {pmid26973627, year = {2016}, author = {Ma, L and Mao, G and Liu, J and Gao, G and Zou, C and Bartlam, MG and Wang, Y}, title = {Spatial-Temporal Changes of Bacterioplankton Community along an Exhorheic River.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {250}, pmid = {26973627}, issn = {1664-302X}, abstract = {To date, few aquatic microbial ecology studies have discussed the variability of the microbial community in exorheic river ecosystems on both the spatial and seasonal scales. In this study, we examined the spatio-temporal variation of bacterioplankton community composition in an anthropogenically influenced exorheic river, the Haihe River in Tianjin, China, using pyrosequencing analysis of 16S rRNA genes. It was verified by one-way ANOVA that the spatial variability of the bacterioplankton community composition over the whole river was stronger than the seasonal variation. Salinity was a major factor leading to spatial differentiation of the microbial community structure into riverine and estuarial parts. A high temperature influence on the seasonal bacterial community variation was only apparent within certain kinds of environments (e.g., the riverine part). Bacterial community richness and diversity both exhibited significant spatial changes, and their seasonal variations were completely different in the two environments studied here. Furthermore, riverine bacterial community assemblages were subdivided into urban and rural groups due to changes in the nutritional state of the river. In addition, the nutrient-loving group including Limnohabitans, Hydrogenophaga, and Polynucleobacter were abundant in the urbanized Haihe River, indicating the environmental factors in these anthropogenic waterbodies heavily influence the core freshwater community composition.}, }
@article {pmid26973611, year = {2016}, author = {Kielak, AM and Scheublin, TR and Mendes, LW and van Veen, JA and Kuramae, EE}, title = {Bacterial Community Succession in Pine-Wood Decomposition.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {231}, pmid = {26973611}, issn = {1664-302X}, abstract = {Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.}, }
@article {pmid26973608, year = {2016}, author = {Keating, C and Chin, JP and Hughes, D and Manesiotis, P and Cysneiros, D and Mahony, T and Smith, CJ and McGrath, JW and O'Flaherty, V}, title = {Biological Phosphorus Removal During High-Rate, Low-Temperature, Anaerobic Digestion of Wastewater.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {226}, pmid = {26973608}, issn = {1664-302X}, abstract = {We report, for the first time, extensive biologically mediated phosphate removal from wastewater during high-rate anaerobic digestion (AD). A hybrid sludge bed/fixed-film (packed pumice stone) reactor was employed for low-temperature (12°C) anaerobic treatment of synthetic sewage wastewater. Successful phosphate removal from the wastewater (up to 78% of influent phosphate) was observed, mediated by biofilms in the reactor. Scanning electron microscopy and energy dispersive X-ray analysis revealed the accumulation of elemental phosphorus (∼2%) within the sludge bed and fixed-film biofilms. 4', 6-diamidino-2-phenylindole (DAPI) staining indicated phosphorus accumulation was biological in nature and mediated through the formation of intracellular inorganic polyphosphate (polyP) granules within these biofilms. DAPI staining further indicated that polyP accumulation was rarely associated with free cells. Efficient and consistent chemical oxygen demand (COD) removal was recorded, throughout the 732-day trial, at applied organic loading rates between 0.4 and 1.5 kg COD m(-3) d(-1) and hydraulic retention times of 8-24 h, while phosphate removal efficiency ranged from 28 to 78% on average per phase. Analysis of protein hydrolysis kinetics and the methanogenic activity profiles of the biomass revealed the development, at 12°C, of active hydrolytic and methanogenic populations. Temporal microbial changes were monitored using Illumina MiSeq analysis of bacterial and archaeal 16S rRNA gene sequences. The dominant bacterial phyla present in the biomass at the conclusion of the trial were the Proteobacteria and Firmicutes and the dominant archaeal genus was Methanosaeta. Trichococcus and Flavobacterium populations, previously associated with low temperature protein degradation, developed in the reactor biomass. The presence of previously characterized polyphosphate accumulating organisms (PAOs) such as Rhodocyclus, Chromatiales, Actinobacter, and Acinetobacter was recorded at low numbers. However, it is unknown as yet if these were responsible for the luxury polyP uptake observed in this system. The possibility of efficient phosphate removal and recovery from wastewater during AD would represent a major advance in the scope for widespread application of anaerobic wastewater treatment technologies.}, }
@article {pmid26972871, year = {2016}, author = {O'Malley, MA}, title = {The ecological virus.}, journal = {Studies in history and philosophy of biological and biomedical sciences}, volume = {59}, number = {}, pages = {71-79}, doi = {10.1016/j.shpsc.2016.02.012}, pmid = {26972871}, issn = {1879-2499}, mesh = {Aquatic Organisms/physiology ; Bacteriophages/*physiology ; *Ecosystem ; *Food Chain ; Seawater/*virology ; }, abstract = {Ecology is usually described as the study of organisms interacting with one another and their environments. From this view of ecology, viruses - not usually considered to be organisms - would merely be part of the environment. Since the late 1980s, however, a growing stream of micrographic, experimental, molecular, and model-based (theoretical) research has been investigating how and why viruses should be understood as ecological actors of the most important sort. Viruses, especially phage, have been revealed as participants in the planet's most crucial food webs, even though viruses technically consume nothing (they do not metabolize by themselves). Even more impressively, viruses have been identified as regulators of planetary biogeochemistry, in which they control cycles such as carbon, nitrogen and phosphorus - cycles on which all life depends. Although much biogeochemical research black-boxes the entities filling functional roles, it is useful to focus a little more closely to understand how viruses can be held responsible for the global processes of life. This paper will give a brief overview of the history of virus ecology and tease out the implications of large-scale ecological modelling with viruses. This analysis suggests that viruses should be conceptualized as ecological actors that are at least comparable and possibly equal to organismal actors. Ecological agency can therefore be distinguished from standard interpretations of biological agency.}, }
@article {pmid26970926, year = {2016}, author = {Lin, Q and De Vrieze, J and Li, J and Li, X}, title = {Temperature affects microbial abundance, activity and interactions in anaerobic digestion.}, journal = {Bioresource technology}, volume = {209}, number = {}, pages = {228-236}, doi = {10.1016/j.biortech.2016.02.132}, pmid = {26970926}, issn = {1873-2976}, mesh = {*Anaerobiosis ; *Biofuels ; Bioreactors ; Euryarchaeota/genetics ; Fermentation ; Manure ; Methane/*biosynthesis ; RNA, Ribosomal, 16S/genetics ; *Temperature ; Waste Management/methods ; }, abstract = {Temperature is a major factor determining the performance of the anaerobic digestion process. The microbial abundance, activity and interactional networks were investigated under a temperature gradient from 25°C to 55°C through amplicon sequencing, using 16S ribosomal RNA and 16S rRNA gene-based approaches. Comparative analysis of past accumulative elements presented by 16S rRNA gene-based analysis, and the in-situ conditions presented by 16S rRNA-based analysis, provided new insights concerning the identification of microbial functional roles and interactions. The daily methane production and total biogas production increased with temperature up to 50°C, but decreased at 55°C. Increased methanogenesis and hydrolysis at 50°C were main factors causing higher methane production which was also closely related with more well-defined methanogenic and/or related modules with comprehensive interactions and increased functional orderliness referred to more microorganisms participating in interactions. This research demonstrated the importance of evaluating functional roles and interactions of microbial community.}, }
@article {pmid26968743, year = {2016}, author = {Obase, K and Douhan, GW and Matsuda, Y and Smith, ME}, title = {Revisiting phylogenetic diversity and cryptic species of Cenococcum geophilum sensu lato.}, journal = {Mycorrhiza}, volume = {26}, number = {6}, pages = {529-540}, pmid = {26968743}, issn = {1432-1890}, mesh = {Ascomycota/*classification/*genetics ; DNA, Fungal/genetics ; DNA, Intergenic/genetics ; Genetic Variation ; *Phylogeny ; Species Specificity ; }, abstract = {The fungus Cenococcum geophilum Fr. (Dothideomycetes, Ascomycota) is one of the most common ectomycorrhizal fungi in boreal to temperate regions. A series of molecular studies has demonstrated that C. geophilum is monophyletic but a heterogeneous species or a species complex. Here, we revisit the phylogenetic diversity of C. geophilum sensu lato from a regional to intercontinental scale by using new data from Florida (USA) along with existing data in GenBank from Japan, Europe, and North America. The combination of internal transcribed spacer (ITS) ribosomal DNA and the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene resolved six well-supported lineages (87-100 % bootstrap values) that are closely related to each other and a seventh lineage that is phylogenetically distinct. A multi-locus analysis (small subunit (SSU), large subunit (LSU), translational elongation factor (TEF), and the largest and second-largest subunits of RNA polymerase II (RPB1 and RPB2)) revealed that the divergent lineage is the sister group to all other known Cenococcum isolates. Isolates of the divergent lineage grow fast on nutrient media and do not form ectomycorrhizas on seedlings of several pine and oak species. Our results indicate that C. geophilum sensu lato includes more phylogenetically distinct cryptic species than have previously been reported. Furthermore, the divergent lineage appears to be a non-mycorrhizal sister group. We discuss the phylogenetic diversity of C. geophilum sensu lato and argue in favor of species recognition based on phylogenetic and ecological information in addition to morphological characteristics. A new genus and species (Pseudocenococcum floridanum gen. et sp. nov.) is proposed to accommodate a divergent and putatively non-mycorrhizal lineage.}, }
@article {pmid26966652, year = {2016}, author = {Forster, D and Dunthorn, M and Stoeck, T and Mahé, F}, title = {Comparison of three clustering approaches for detecting novel environmental microbial diversity.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e1692}, pmid = {26966652}, issn = {2167-8359}, abstract = {Discovery of novel diversity in high-throughput sequencing studies is an important aspect in environmental microbial ecology. To evaluate the effects that amplicon clustering methods have on the discovery of novel diversity, we clustered an environmental marine high-throughput sequencing dataset of protist amplicons together with reference sequences from the taxonomically curated Protist Ribosomal Reference (PR(2)) database using three de novo approaches: sequence similarity networks, USEARCH, and Swarm. The potentially novel diversity uncovered by each clustering approach differed drastically in the number of operational taxonomic units (OTUs) and in the number of environmental amplicons in these novel diversity OTUs. Global pairwise alignment comparisons revealed that numerous amplicons classified as potentially novel by USEARCH and Swarm were more than 97% similar to references of PR(2). Using shortest path analyses on sequence similarity network OTUs and Swarm OTUs we found additional novel diversity within OTUs that would have gone unnoticed without further exploiting their underlying network topologies. These results demonstrate that graph theory provides powerful tools for microbial ecology and the analysis of environmental high-throughput sequencing datasets. Furthermore, sequence similarity networks were most accurate in delineating novel diversity from previously discovered diversity.}, }
@article {pmid26961802, year = {2016}, author = {Tsuchiya, Y and Eda, S and Kiriyama, C and Asada, T and Morisaki, H}, title = {Analysis of Dissolved Organic Nutrients in the Interstitial Water of Natural Biofilms.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {85-95}, pmid = {26961802}, issn = {1432-184X}, mesh = {Bacteria/*chemistry/growth &amp; development ; *Biofilms ; Colony Count, Microbial ; Fresh Water/microbiology ; Hydrogen-Ion Concentration ; Molecular Weight ; Polysaccharides/analysis ; Proteins/analysis ; Temperature ; Water/*chemistry ; }, abstract = {In biofilms, the matrix of extracellular polymeric substances (EPSs) retains water in the interstitial region of the EPS. This interstitial water is the ambient environment for microorganisms in the biofilms. The nutrient condition in the interstitial water may affect microbial activity in the biofilms. In the present study, we measured the concentrations of dissolved organic nutrients, i.e., saccharides and proteins, contained in the interstitial water of biofilms formed on the stones. We also analyzed the molecular weight distribution, chemical species, and availability to bacteria of some saccharides in the interstitial water. Colorimetric assays showed that the concentrations of saccharides and proteins in the biofilm interstitial water were significantly higher (ca. 750 times) than those in the surrounding lake waters (p < 0.05). Chromatographic analyses demonstrated that the saccharides in the interstitial waters were mainly of low molecular-weight saccharides such as glucose and maltose, while proteins in the interstitial water were high molecular-weight proteins (over 7000 Da). Bacterial growth and production of EPS occurred simultaneously with the decrease in the low molecular-weight saccharide concentrations when a small portion of biofilm suspension was inoculated to the collected interstitial water, suggesting that the dissolved saccharides in the interstitial water support bacterial growth and formation of biofilms.}, }
@article {pmid26961712, year = {2016}, author = {Siles, JA and Margesin, R}, title = {Abundance and Diversity of Bacterial, Archaeal, and Fungal Communities Along an Altitudinal Gradient in Alpine Forest Soils: What Are the Driving Factors?.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {207-220}, pmid = {26961712}, issn = {1432-184X}, mesh = {*Altitude ; Archaea/classification/isolation &amp; purification ; Bacteria/classification/isolation &amp; purification ; *Biodiversity ; Chemical Phenomena ; DNA, Archaeal/genetics/isolation &amp; purification ; DNA, Bacterial/genetics/isolation &amp; purification ; DNA, Fungal/genetics/isolation &amp; purification ; Fungi/classification/isolation &amp; purification ; Italy ; RNA, Ribosomal, 16S/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; Temperature ; }, abstract = {Shifts in soil microbial communities over altitudinal gradients and the driving factors are poorly studied. Their elucidation is indispensable to gain a comprehensive understanding of the response of ecosystems to global climate change. Here, we investigated soil archaeal, bacterial, and fungal communities at four Alpine forest sites representing a climosequence, over an altitudinal gradient from 545 to 2000 m above sea level (asl), regarding abundance and diversity by using qPCR and Illumina sequencing, respectively. Archaeal community was dominated by Thaumarchaeota, and no significant shifts were detected in abundance or community composition with altitude. The relative bacterial abundance increased at higher altitudes, which was related to increasing levels of soil organic matter and nutrients with altitude. Shifts in bacterial richness and diversity as well as community structure (comprised basically of Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes) significantly correlated with several environmental and soil chemical factors, especially soil pH. The site at the lowest altitude harbored the highest bacterial richness and diversity, although richness/diversity community properties did not show a monotonic decrease along the gradient. The relative size of fungal community also increased with altitude and its composition comprised Ascomycota, Basidiomycota, and Zygomycota. Changes in fungal richness/diversity and community structure were mainly governed by pH and C/N, respectively. The variation of the predominant bacterial and fungal classes over the altitudinal gradient was the result of the environmental and soil chemical factors prevailing at each site.}, }
@article {pmid26960392, year = {2016}, author = {Reyes, C and Dellwig, O and Dähnke, K and Gehre, M and Noriega-Ortega, BE and Böttcher, ME and Meister, P and Friedrich, MW}, title = {Bacterial communities potentially involved in iron-cycling in Baltic Sea and North Sea sediments revealed by pyrosequencing.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {4}, pages = {fiw054}, doi = {10.1093/femsec/fiw054}, pmid = {26960392}, issn = {1574-6941}, mesh = {Bacillus/*genetics/metabolism ; Base Sequence ; Clostridium/*genetics/metabolism ; DNA, Bacterial/genetics ; Deltaproteobacteria/*genetics/metabolism ; Ferric Compounds/*metabolism ; Geologic Sediments/*microbiology ; Iron/*metabolism ; North Sea ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfates/metabolism ; }, abstract = {To gain insight into the bacterial communities involved in iron-(Fe) cycling under marine conditions, we analysed sediments with Fe-contents (0.5-1.5 wt %) from the suboxic zone at a marine site in the Skagerrak (SK) and a brackish site in the Bothnian Bay (BB) using 16S rRNA gene pyrosequencing. Several bacterial families, including Desulfobulbaceae, Desulfuromonadaceae and Pelobacteraceae and genera, includingDesulfobacterandGeobacter, known to reduce Fe were detected and showed highest abundance near the Fe(III)/Fe(II) redox boundary. Additional genera with microorganisms capable of coupling fermentation to Fe-reduction, includingClostridiumandBacillus, were observed. Also, the Fe-oxidizing families Mariprofundaceae and Gallionellaceae occurred at the SK and BB sites, respectively, supporting Fe-cycling. In contrast, the sulphate (SO4 (2-)) reducing bacteriaDesulfococcusandDesulfobacteriumwere more abundant at greater depths concurring with a decrease in Fe-reducing activity. The communities revealed by pyrosequencing, thus, match the redox stratification indicated by the geochemistry, with the known Fe-reducers coinciding with the zone of Fe-reduction. Not the intensely studied model organisms, such asGeobacterspp., but rather versatile microorganisms, including sulphate reducers and possibly unknown groups appear to be important for Fe-reduction in these marine suboxic sediments.}, }
@article {pmid26959838, year = {2016}, author = {Araújo, WL and Creason, AL and Mano, ET and Camargo-Neves, AA and Minami, SN and Chang, JH and Loper, JE}, title = {Genome Sequencing and Transposon Mutagenesis of Burkholderia seminalis TC3.4.2R3 Identify Genes Contributing to Suppression of Orchid Necrosis Caused by B. gladioli.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {29}, number = {6}, pages = {435-446}, doi = {10.1094/MPMI-02-16-0047-R}, pmid = {26959838}, issn = {0894-0282}, support = {R01GM104977/GM/NIGMS NIH HHS/United States ; }, mesh = {Biological Control Agents ; Burkholderia/*genetics/pathogenicity ; DNA Transposable Elements ; Genes, Bacterial ; *Genome, Bacterial ; Host-Pathogen Interactions ; *Mutagenesis ; Orchidaceae/*microbiology ; Plant Diseases/microbiology ; Plant Leaves/*microbiology ; Saccharum/microbiology ; }, abstract = {From a screen of 36 plant-associated strains of Burkholderia spp., we identified 24 strains that suppressed leaf and pseudobulb necrosis of orchid caused by B. gladioli. To gain insights into the mechanisms of disease suppression, we generated a draft genome sequence from one suppressive strain, TC3.4.2R3. The genome is an estimated 7.67 megabases in size, with three replicons, two chromosomes, and the plasmid pC3. Using a combination of multilocus sequence analysis and phylogenomics, we identified TC3.4.2R3 as B. seminalis, a species within the Burkholderia cepacia complex that includes opportunistic human pathogens and environmental strains. We generated and screened a library of 3,840 transposon mutants of strain TC3.4.2R3 on orchid leaves to identify genes contributing to plant disease suppression. Twelve mutants deficient in suppression of leaf necrosis were selected and the transposon insertions were mapped to eight loci. One gene is in a wcb cluster that is related to synthesis of extracellular polysaccharide, a key determinant in bacterial-host interactions in other systems, and the other seven are highly conserved among Burkholderia spp. The fundamental information developed in this study will serve as a resource for future research aiming to identify mechanisms contributing to biological control.}, }
@article {pmid26959525, year = {2016}, author = {Vogt, C and Lueders, T and Richnow, HH and Krüger, M and von Bergen, M and Seifert, J}, title = {Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {26}, number = {1-3}, pages = {195-210}, doi = {10.1159/000440806}, pmid = {26959525}, issn = {1660-2412}, mesh = {Anaerobiosis ; Bacteria, Anaerobic/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Biodiversity ; Environmental Monitoring/methods ; Hydrocarbons/*metabolism ; Hydrocarbons, Aromatic/chemistry/metabolism ; Isotopes/chemistry ; Molecular Probes ; Phylogeny ; }, abstract = {Stable isotope probing (SIP) techniques have become state-of-the-art in microbial ecology over the last 10 years, allowing for the targeted detection and identification of organisms, metabolic pathways and elemental fluxes active in specific processes within complex microbial communities. For studying anaerobic hydrocarbon-degrading microbial communities, four stable isotope techniques have been used so far: DNA/RNA-SIP, PLFA (phospholipid-derived fatty acids)-SIP, protein-SIP, and single-cell-SIP by nanoSIMS (nanoscale secondary ion mass spectrometry) or confocal Raman microscopy. DNA/RNA-SIP techniques are most frequently applied due to their most meaningful phylogenetic resolution. Especially using 13C-labeled benzene and toluene as model substrates, many new hydrocarbon degraders have been identified by SIP under various electron acceptor conditions. This has extended the current perspective of the true diversity of anaerobic hydrocarbon degraders relevant in the environment. Syntrophic hydrocarbon degradation was found to be a common mechanism for various electron acceptors. Fundamental concepts and recent advances in SIP are reflected here. A discussion is presented concerning how these techniques generate direct insights into intrinsic hydrocarbon degrader populations in environmental systems and how useful they are for more integrated approaches in the monitoring of contaminated sites and for bioremediation.}, }
@article {pmid26957597, year = {2016}, author = {Wexler, AG and Bao, Y and Whitney, JC and Bobay, LM and Xavier, JB and Schofield, WB and Barry, NA and Russell, AB and Tran, BQ and Goo, YA and Goodlett, DR and Ochman, H and Mougous, JD and Goodman, AL}, title = {Human symbionts inject and neutralize antibacterial toxins to persist in the gut.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {13}, pages = {3639-3644}, pmid = {26957597}, issn = {1091-6490}, support = {R01 GM101209/GM/NIGMS NIH HHS/United States ; DP2 GM105456/GM/NIGMS NIH HHS/United States ; //Canadian Institutes of Health Research/Canada ; OD008440/OD/NIH HHS/United States ; GM103574/GM/NIGMS NIH HHS/United States ; R35 GM118038/GM/NIGMS NIH HHS/United States ; DP2 OD008440/OD/NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; GM108657/GM/NIGMS NIH HHS/United States ; AI080609/AI/NIAID NIH HHS/United States ; GM105456/GM/NIGMS NIH HHS/United States ; GM101209/GM/NIGMS NIH HHS/United States ; R01 GM103574/GM/NIGMS NIH HHS/United States ; R01 AI080609/AI/NIAID NIH HHS/United States ; R01 GM108657/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteroides fragilis/genetics/immunology/physiology ; Female ; Gastrointestinal Microbiome/genetics/immunology/*physiology ; Genome, Bacterial ; Germ-Free Life ; Humans ; Male ; Mice ; Models, Animal ; Phylogeny ; Symbiosis/genetics/immunology/physiology ; Type VI Secretion Systems/genetics/immunology/physiology ; }, abstract = {The human gut microbiome is a dynamic and densely populated microbial community that can provide important benefits to its host. Cooperation and competition for nutrients among its constituents only partially explain community composition and interpersonal variation. Notably, certain human-associated Bacteroidetes--one of two major phyla in the gut--also encode machinery for contact-dependent interbacterial antagonism, but its impact within gut microbial communities remains unknown. Here we report that prominent human gut symbionts persist in the gut through continuous attack on their immediate neighbors. Our analysis of just one of the hundreds of species in these communities reveals 12 candidate antibacterial effector loci that can exist in 32 combinations. Through the use of secretome studies, in vitro bacterial interaction assays and multiple mouse models, we uncover strain-specific effector/immunity repertoires that can predict interbacterial interactions in vitro and in vivo, and find that some of these strains avoid contact-dependent killing by accumulating immunity genes to effectors that they do not encode. Effector transmission rates in live animals can exceed 1 billion events per minute per gram of colonic contents, and multiphylum communities of human gut commensals can partially protect sensitive strains from these attacks. Together, these results suggest that gut microbes can determine their interactions through direct contact. An understanding of the strategies human gut symbionts have evolved to target other members of this community may provide new approaches for microbiome manipulation.}, }
@article {pmid26956183, year = {2016}, author = {Geng, H and Sale, KL and Tran-Gyamfi, MB and Lane, TW and Yu, ET}, title = {Longitudinal Analysis of Microbiota in Microalga Nannochloropsis salina Cultures.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {14-24}, pmid = {26956183}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Biofuels ; Biomass ; DNA, Bacterial/genetics ; Gene Library ; Microalgae/*microbiology ; *Microbiota ; Pacific Ocean ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Stramenopiles/microbiology ; Water Microbiology ; }, abstract = {Large-scale open microalgae cultivation has tremendous potential to make a significant contribution to replacing petroleum-based fuels with biofuels. Open algal cultures are unavoidably inhabited with a diversity of microbes that live on, influence, and shape the fate of these ecosystems. However, there is little understanding of the resilience and stability of the microbial communities in engineered semicontinuous algal systems. To evaluate the dynamics and resilience of the microbial communities in microalgae biofuel cultures, we conducted a longitudinal study on open systems to compare the temporal profiles of the microbiota from two multigenerational algal cohorts, which include one seeded with the microbiota from an in-house culture and the other exogenously seeded with a natural-occurring consortia of bacterial species harvested from the Pacific Ocean. From these month-long, semicontinuous open microalga Nannochloropsis salina cultures, we sequenced a time-series of 46 samples, yielding 8804 operational taxonomic units derived from 9,160,076 high-quality partial 16S rRNA sequences. We provide quantitative evidence that clearly illustrates the development of microbial community is associated with microbiota ancestry. In addition, N. salina growth phases were linked with distinct changes in microbial phylotypes. Alteromonadeles dominated the community in the N. salina exponential phase whereas Alphaproteobacteria and Flavobacteriia were more prevalent in the stationary phase. We also demonstrate that the N. salina-associated microbial community in open cultures is diverse, resilient, and dynamic in response to environmental perturbations. This knowledge has general implications for developing and testing design principles of cultivated algal systems.}, }
@article {pmid26952106, year = {2016}, author = {Vacher, C and Cordier, T and Vallance, J}, title = {Phyllosphere Fungal Communities Differentiate More Thoroughly than Bacterial Communities Along an Elevation Gradient.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {1-3}, pmid = {26952106}, issn = {1432-184X}, mesh = {*Altitude ; *Bacterial Physiological Phenomena ; Climate ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Ecosystem ; Fagus/*microbiology ; France ; Fungi/*physiology ; *Microbiota ; Plant Leaves/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, }
@article {pmid26951112, year = {2016}, author = {Sangwan, N and Xia, F and Gilbert, JA}, title = {Recovering complete and draft population genomes from metagenome datasets.}, journal = {Microbiome}, volume = {4}, number = {}, pages = {8}, pmid = {26951112}, issn = {2049-2618}, mesh = {Contig Mapping ; Datasets as Topic ; *Genome, Microbial ; *Metagenome ; Metagenomics/*methods ; Sequence Analysis, DNA ; }, abstract = {Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem of chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution.}, }
@article {pmid26950325, year = {2016}, author = {Yi, Y and de Jong, A and Spoelder, J and Elzenga, JT and van Elsas, JD and Kuipers, OP}, title = {Draft Genome Sequence of Bacillus mycoides M2E15, a Strain Isolated from the Endosphere of Potato.}, journal = {Genome announcements}, volume = {4}, number = {1}, pages = {}, pmid = {26950325}, issn = {2169-8287}, abstract = {We present the draft genome sequence of Bacillus mycoides M2E15, a bacterium isolated from potato endosphere. Analysis of the 6.08-Mbp draft genome sequence identified 6,386 protein-encoding sequences, including potential plant growth promoting genes. Specifically, genes for proteins involved in phosphate utilization, iron acquisition, and bacteriocin production were identified.}, }
@article {pmid26950037, year = {2016}, author = {Taguer, M and Maurice, CF}, title = {The complex interplay of diet, xenobiotics, and microbial metabolism in the gut: Implications for clinical outcomes.}, journal = {Clinical pharmacology and therapeutics}, volume = {99}, number = {6}, pages = {588-599}, doi = {10.1002/cpt.366}, pmid = {26950037}, issn = {1532-6535}, mesh = {Animals ; *Diet ; Drug Resistance, Bacterial ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/immunology/*metabolism/*microbiology ; Humans ; *Microbiota ; Precision Medicine ; Treatment Outcome ; Xenobiotics/*adverse effects ; }, abstract = {From digestion to pathogen resistance and immune system development, the gut microbiota and its collection of microbial genes are redefining what it means to be human. Despite tremendous advances in this field, there is still a limited understanding of how microbial metabolism in the gut impacts human health, which precludes the development of microbiota-targeted therapies. In this article, we discuss the increasing evidence emphasizing the importance of bacterial metabolism in the gut and discuss its intricate links with diet and pharmaceutical compounds leading to altered therapeutic outcomes. We also detail how applying and testing microbial ecology hypotheses will be crucial to fully understand the therapeutic potential of this host-associated community. Going forward, functional and mechanistic studies combining biomedical research, ecology, bioinformatics, statistical modeling, and engineering will be key in our pursuit of personalized medicine.}, }
@article {pmid26948650, year = {2016}, author = {Hachicha Hbaieb, R and Kotti, F and Gargouri, M and Msallem, M and Vichi, S}, title = {Ripening and storage conditions of Chétoui and Arbequina olives: Part I. Effect on olive oils volatiles profile.}, journal = {Food chemistry}, volume = {203}, number = {}, pages = {548-558}, doi = {10.1016/j.foodchem.2016.01.089}, pmid = {26948650}, issn = {1873-7072}, mesh = {*Food Storage ; Fruit/*chemistry/growth &amp; development ; Humans ; Odorants/analysis ; Olea/*chemistry/growth &amp; development ; Olive Oil/*analysis/chemistry ; Oxidation-Reduction ; Phenols/analysis ; Volatile Organic Compounds/*analysis ; }, abstract = {The distinctive aroma of virgin olive oil is mainly attributed to its volatile profile including components responsible for positive attributes and others for sensory defects resulting from chemical oxidation and exogenous enzymes. For this reason, the evolution of volatile compounds from Chétoui and Arbequina virgin olive oils during olive ripening and storage (at 4 and 25 °C during 4 weeks) was investigated. The profile of volatile phenols during olive storage was also studied. Quantitative differences in the volatile compounds during olive storage at 4 and 25 °C according to olive cultivar was determined. Concerning the volatile phenols, the Arbequina olives were the most affected by high storage temperature, as the formation of these compounds, especially 4-ethyl and 4-vinyl derivatives of phenol and guaiacol were more noticeable in Arbequina oils extracted from stored fruits at 25 °C.}, }
@article {pmid26946528, year = {2016}, author = {Jacquemyn, H and Waud, M and Lievens, B and Brys, R}, title = {Differences in mycorrhizal communities between Epipactis palustris, E. helleborine and its presumed sister species E. neerlandica.}, journal = {Annals of botany}, volume = {118}, number = {1}, pages = {105-114}, pmid = {26946528}, issn = {1095-8290}, support = {260601/ERC_/European Research Council/International ; }, mesh = {Ascomycota ; Basidiomycota ; Belgium ; Biodiversity ; Ecosystem ; Forests ; Mycorrhizae/*physiology ; Orchidaceae/*microbiology ; Phylogeny ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {BACKGROUND AND AIMS: In orchid species that have populations occurring in strongly contrasting habitats, mycorrhizal divergence and other habitat-specific adaptations may lead to the formation of reproductively isolated taxa and ultimately to species formation. However, little is known about the mycorrhizal communities associated with recently diverged sister taxa that occupy different habitats.<br><br>METHODS: In this study, 454 amplicon pyrosequencing was used to investigate mycorrhizal communities associating with Epipactis helleborine in its typical forest habitat and with its presumed sister species E. neerlandica that almost exclusively occurs in coastal dune habitats. Samples of the phylogenetically more distant E. palustris, which co-occurred with E. neerlandica, were also included to investigate the role of habitat-specific conditions on mycorrhizal communities.<br><br>RESULTS: A total of 105 operational taxonomic units (OTUs) of putative orchid mycorrhizal fungi were observed in the three studied species. The majority of these fungi were endophytic fungi of Helotiales and ectomycorrhizal fungi belonging to Thelephoraceae, Sebacinaceae and Inocybaceae. In addition, a large number of other ectomycorrhizal taxa were detected, including Cortinarius, Cenococcum, Tuber, Geopora, Wilcoxina, Meliniomyces, Hebeloma, Tricholoma, Russula and Peziza Mycorrhizal communities differed significantly between the three species, but differences were most pronounced between the forest species (E. helleborine) and the two dune slack species (E. neerlandica and E. palustris).<br><br>CONCLUSION: The results clearly showed that recently diverged orchid species that occupy different habitats were characterized by significantly different mycorrhizal communities and call for more detailed experiments that aim at elucidating the contribution of habitat-specific adaptations in general and mycorrhizal divergence in particular to the process of speciation in orchids.}, }
@article {pmid26946500, year = {2016}, author = {Van Goethem, MW and Makhalanyane, TP and Valverde, A and Cary, SC and Cowan, DA}, title = {Characterization of bacterial communities in lithobionts and soil niches from Victoria Valley, Antarctica.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {4}, pages = {fiw051}, doi = {10.1093/femsec/fiw051}, pmid = {26946500}, issn = {1574-6941}, mesh = {Actinobacteria/classification/*genetics ; Antarctic Regions ; Base Sequence ; Cyanobacteria/classification/*genetics ; Ecosystem ; Microbial Consortia/*genetics ; Phylogeny ; Polymorphism, Restriction Fragment Length/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Here we provide the first exploration of microbial diversity from three distinct Victoria Valley edaphic habitats, namely lithobionts (hypoliths, endoliths) and surface soils. Using a combination of terminal restriction fragment length polymorphism (T-RFLP) analysis and 16S rRNA gene amplicon pyrosequencing we assess community structure and diversity patterns, respectively. Our analysis revealed that habitat type (endolithic versus hypolithic versus surface soils) significantly influenced bacterial community composition, even though dominant phyla such as Actinobacteria (41% of total reads) were common to all samples. Consistent with previous surveys in other Dry Valley ecosystems, we found that lithobionts were colonized by a few highly dominant phylotypes (such asGemmatimonasandLeptolyngbya). Our analyses also show that soil bacteria were more diverse and evenly distributed than initially expected based on previous evidence. In contrast to total bacteria, the distribution of Cyanobacteria was not strongly influenced by habitat type, although soil- and endolith-specific cyanobacterial lineages were found. The detection of cyanobacterial lineages in these habitats appears to be influenced by the dispersal of aquatic inocula from lacustrine communities or benthic mats which are abundant in Victoria Valley. Together, our results provide insights into the phylogenetic variation and community structure across niche habitats in Victoria Valley.}, }
@article {pmid26946451, year = {2016}, author = {Macqueen, DJ and Gubry-Rangin, C}, title = {Molecular adaptation of ammonia monooxygenase during independent pH specialization in Thaumarchaeota.}, journal = {Molecular ecology}, volume = {25}, number = {9}, pages = {1986-1999}, doi = {10.1111/mec.13607}, pmid = {26946451}, issn = {1365-294X}, mesh = {Adaptation, Physiological/genetics ; Ammonia/metabolism ; Archaea/enzymology/*genetics ; Archaeal Proteins/*genetics ; Environment ; *Evolution, Molecular ; Hydrogen-Ion Concentration ; Oxidoreductases/*genetics ; Phylogeny ; Selection, Genetic ; }, abstract = {Microbes are abundant in nature and often highly adapted to local conditions. While great progress has been made in understanding the ecological factors driving their distribution in complex environments, the underpinning molecular-evolutionary mechanisms are rarely dissected. Therefore, we scrutinized the coupling of environmental and molecular adaptation in Thaumarchaeota, an abundant archaeal phylum with a key role in ammonia oxidation. These microbes are adapted to a diverse spectrum of environmental conditions, with pH being a key factor shaping their contemporary distribution and evolutionary diversification. We integrated high-throughput sequencing data spanning a broad representation of ammonia-oxidizing terrestrial lineages with codon modelling analyses, testing the hypothesis that ammonia monooxygenase subunit A (AmoA) - a highly conserved membrane protein crucial for ammonia oxidation and classical marker in microbial ecology - underwent adaptation during specialization to extreme pH environments. While purifying selection has been an important factor limiting AmoA evolution, we identified episodic shifts in selective pressure at the base of two phylogenetically distant lineages that independently adapted to acidic conditions and subsequently gained lasting ecological success. This involved nonconvergent selective mechanisms (positive selection vs. selection acting on variants fixed during an episode of relaxed selection) leading to unique sets of amino acid substitutions that remained fixed across the radiation of both acidophilic lineages, highlighting persistent adaptive value in acidic environments. Our data demonstrates distinct trajectories of AmoA evolution despite convergent phenotypic adaptation, suggesting that microbial environmental specialization can be associated with diverse signals of molecular adaptation, even for marker genes employed routinely by microbial ecologists.}, }
@article {pmid26945964, year = {2016}, author = {Di Cesare, A and Eckert, EM and D'Urso, S and Bertoni, R and Gillan, DC and Wattiez, R and Corno, G}, title = {Co-occurrence of integrase 1, antibiotic and heavy metal resistance genes in municipal wastewater treatment plants.}, journal = {Water research}, volume = {94}, number = {}, pages = {208-214}, doi = {10.1016/j.watres.2016.02.049}, pmid = {26945964}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; Bacteria/isolation &amp; purification ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; Integrases/*genetics ; *Integrons ; Metals, Heavy ; *Waste Disposal, Fluid ; Wastewater/*analysis/microbiology ; }, abstract = {The impact of human activities on the spread and on the persistence of antibiotic resistances in the environment is still far from being understood. The natural background of resistances is influenced by human activities, and the wastewater treatment plants (WWTPs) are among the main sources of the release of antibiotic resistance into the environment. The various treatments of WWTPs provide a number of different environmental conditions potentially favoring the selection of antibiotic resistance genes (ARGs) and thereby their well-documented spread in the environment. Although the distribution of different ARGs in WWTPs has been deeply investigated, very little is known on the ecology and on the molecular mechanisms underlying the selection of specific ARGs. This study investigates the fate of diverse ARGs, heavy metal resistance genes (HMRGs) and of a mobile element (the class I integron) in three WWTPs. Abundances of the different genetic markers were correlated to each other and their relation to biotic and abiotic factors (total organic carbon, total nitrogen, prokaryotic cell abundance and its relative distribution in single cells and aggregates) influencing the microbial communities in the different treatment phases in three WWTPs, were investigated. Water samples were analyzed for the abundance of six ARGs (tetA, sulII, blaTEM, blaCTXM,ermB, and qnrS), two HMRGs (czcA and arsB), and of the class I integron (int1). The measured variables clustered in two well-defined groups, the first including tetA, ermB, qnrS and the different biotic and abiotic factors, and a second group around the genes sulII, czcA, arsB and int1. Moreover, the dynamics of sulII, HMRGs, and int1 correlated strongly. Our results suggest a potentially crucial role of HMRGs in the spread, mediated by mobile elements, of some ARGs, i.e. sulII. The possibility of a relation between heavy metal contamination and the spread of ARGs in WWTPs calls for further research to clarify the mechanisms of co-selection and their ecology, in order to implement the removal efficiency of the applied treatments.}, }
@article {pmid26945503, year = {2016}, author = {Song, C and Kidarsa, TA and van de Mortel, JE and Loper, JE and Raaijmakers, JM}, title = {Living on the edge: emergence of spontaneous gac mutations in Pseudomonas protegens during swarming motility.}, journal = {Environmental microbiology}, volume = {18}, number = {10}, pages = {3453-3465}, doi = {10.1111/1462-2920.13288}, pmid = {26945503}, issn = {1462-2920}, mesh = {Bacterial Proteins/*genetics/metabolism ; Chemotaxis ; Flagella/genetics/metabolism ; Gene Expression Profiling ; *Mutation ; Pseudomonas/*cytology/genetics/*metabolism ; }, abstract = {Swarming motility is a flagella-driven multicellular behaviour that allows bacteria to colonize new niches and escape competition. Here, we investigated the evolution of specific mutations in the GacS/GacA two-component regulatory system in swarming colonies of Pseudomonas protegens Pf-5. Experimental evolution assays showed that repeated rounds of swarming by wildtype Pf-5 drives the accumulation of gacS/gacA spontaneous mutants on the swarming edge. These mutants cannot swarm on their own because they lack production of the biosurfactant orfamide A, but they do co-swarm with orfamide-producing wildtype Pf-5. These co-swarming assays further demonstrated that ΔgacA mutant cells indeed predominate on the edge and that initial ΔgacA:wildtype Pf-5 ratios of at least 2:1 lead to a collapse of the swarming colony. Subsequent whole-genome transcriptome analyses revealed that genes associated with motility, resource acquisition, chemotaxis and efflux were significantly upregulated in ΔgacA mutant on swarming medium. Moreover, transmission electron microscopy showed that ΔgacA mutant cells were longer and more flagellated than wildtype cells, which may explain their predominance on the swarming edge. We postulate that adaptive evolution through point mutations is a common feature of range-expanding microbial populations and that the putative fitness benefits of these mutations during dispersal of bacteria into new territories are frequency-dependent.}, }
@article {pmid26944561, year = {2016}, author = {García-Mena, J and Murugesan, S and Pérez-Muñoz, AA and García-Espitia, M and Maya, O and Jacinto-Montiel, M and Monsalvo-Ponce, G and Piña-Escobedo, A and Domínguez-Malfavón, L and Gómez-Ramírez, M and Cervantes-González, E and Núñez-Cardona, MT}, title = {Airborne Bacterial Diversity from the Low Atmosphere of Greater Mexico City.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {70-84}, pmid = {26944561}, issn = {1432-184X}, mesh = {Actinobacteria/genetics/isolation &amp; purification ; *Air Microbiology ; Bacillus/genetics/isolation &amp; purification ; Bacteria/*classification/isolation &amp; purification ; *Biodiversity ; Cities ; Culture Media ; DNA, Bacterial/genetics ; Genomics ; Gluconacetobacter/genetics/isolation &amp; purification ; Mexico ; *Phylogeny ; Proteobacteria/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {Greater Mexico City is one of the largest urban centers in the world, with an estimated population by 2010 of more than 20 million inhabitants. In urban areas like this, biological material is present at all atmospheric levels including live bacteria. We sampled the low atmosphere in several surveys at different points by the gravity method on LB and blood agar media during winter, spring, summer, and autumn seasons in the years 2008, 2010, 2011, and 2012. The colonial phenotype on blood agar showed α, β, and γ hemolytic activities among the live collected bacteria. Genomic DNA was extracted and convenient V3 hypervariable region libraries of 16S rDNA gene were high-throughput sequenced. From the data analysis, Firmicutes, Proteobacteria, and Actinobacteria were the more abundant phyla in all surveys, while the genera from the family Enterobacteriaceae, in addition to Bacillus spp., Pseudomonas spp., Acinetobacter spp., Erwinia spp., Gluconacetobacter spp., Proteus spp., Exiguobacterium spp., and Staphylococcus spp. were also abundant. From this study, we conclude that it is possible to detect live airborne nonspore-forming bacteria in the low atmosphere of GMC, associated to the microbial cloud of its inhabitants.}, }
@article {pmid26943622, year = {2016}, author = {Kuang, J and Huang, L and He, Z and Chen, L and Hua, Z and Jia, P and Li, S and Liu, J and Li, J and Zhou, J and Shu, W}, title = {Predicting taxonomic and functional structure of microbial communities in acid mine drainage.}, journal = {The ISME journal}, volume = {10}, number = {6}, pages = {1527-1539}, pmid = {26943622}, issn = {1751-7370}, mesh = {Acids ; Bacteria/*classification/drug effects/genetics/metabolism ; Biodiversity ; China ; Cluster Analysis ; Ecology ; Extreme Environments ; Groundwater/*microbiology ; Hydrogen-Ion Concentration ; *Microbial Consortia ; Mining ; Nitrogen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/genetics ; Wastewater/chemistry/microbiology ; }, abstract = {Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural acidophilic microbial communities.}, }
@article {pmid26943146, year = {2016}, author = {Larson, CA and Adumatioge, L and Passy, SI}, title = {The number of limiting resources in the environment controls the temporal diversity patterns in the algal benthos.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {64-69}, pmid = {26943146}, issn = {1432-184X}, mesh = {*Biodiversity ; Biofilms ; *Eutrophication ; Fresh Water/microbiology ; Iron/analysis ; Linear Models ; Nitrogen/analysis ; Phosphorus/analysis ; Time Factors ; }, abstract = {The role of the number of limiting resources (NLR) on species richness has been the subject of much theoretical and experimental work. However, how the NLR controls temporal beta diversity and the processes of community assembly is not well understood. To address this knowledge gap, we initiated a series of laboratory microcosm experiments, exposing periphyton communities to a gradient of NLR from 0 to 3, generated by supplementation with nitrogen, phosphorus, iron, and all their combinations. We hypothesized that similarly to alpha diversity, shown to decrease with the NLR in benthic algae, temporal beta diversity would also decline due to filtering. Additionally, we predicted that the NLR would also affect turnover and community nestedness, which would show opposing responses. Indeed, as the NLR increased, temporal beta diversity decreased; turnover, indicative of competition, decreased; and nestedness, suggestive of complementarity, increased. Finally, the NLR determined the role of deterministic versus stochastic processes in community assembly, showing respectively an increasing and a decreasing trend. These results imply that the NLR has a much greater, yet still unappreciated influence on producer communities, constraining not only alpha diversity but also temporal dynamics and community assembly.}, }
@article {pmid26942918, year = {2016}, author = {Kim, SJ and Lee, JC and Han, SI and Whang, KS}, title = {Halobacillus salicampi sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment.}, journal = {Antonie van Leeuwenhoek}, volume = {109}, number = {5}, pages = {713-720}, doi = {10.1007/s10482-016-0672-y}, pmid = {26942918}, issn = {1572-9699}, mesh = {Bacterial Typing Techniques ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Geologic Sediments/chemistry/*microbiology ; Halobacillus/*classification/genetics/*isolation &amp; purification/physiology ; Phenotype ; Phylogeny ; Ponds/*microbiology ; Republic of Korea ; Salinity ; Water Microbiology ; }, abstract = {A Gram-positive, moderately halophilic bacterium, designated strain TGS-15(T), was isolated from the sediment of a solar saltern pond located in Shinan, Korea. Strain TGS-15(T) was found to be a strictly aerobic, non-motile rod which can grow at pH 6.0-10.0 (optimum, pH 9.0), at 20-35 °C (optimum, 28 °C) and at salinities of 1-20 % (w/v) NaCl (optimum, 9 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain TGS-15(T) belongs to the genus Halobacillus, with sequence similarity of 98.5-96.0 % to known type strains, showing high sequence similarity to Halobacillus locisalis MSS-155(T) (98.5 %), Halobacillus faecis IGA7-4(T) (98.2 %) and Halobacillus alkaliphilus FP5(T) (98.0 %), and less than 98.0 % sequence similarity to other currently recognised type strains of the genus. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified glycolipid and an unidentified lipid. The cell wall peptidoglycan was found to be based on L-Orn-D-Asp, the predominant isoprenoid quinone was identified as menaquinone-7 (MK-7) and the major fatty acids were identified as anteiso-C15:0, iso-C15:0, anteiso-C17:0 and C16:1 ω7c alcohol. The DNA G+C content of this novel isolate was determined to be 45.3 mol %. Levels of DNA:DNA relatedness between strain TGS-15(T) and the type strains of 13 other species of the genus ranged from 52 to 9 %. On the basis of the polyphasic analysis conducted in this study, strain TGS-15(T) is concluded to represent a novel species of the genus Halobacillus, for which the name Halobacillus salicampi sp. nov. is proposed. The type strain is TGS-15(T) (=KACC 18264(T) = NBRC 110640(T)).}, }
@article {pmid26941949, year = {2016}, author = {Robinson, HA and Pinharanda, A and Bensasson, D}, title = {Summer temperature can predict the distribution of wild yeast populations.}, journal = {Ecology and evolution}, volume = {6}, number = {4}, pages = {1236-1250}, pmid = {26941949}, issn = {2045-7758}, abstract = {The wine yeast, Saccharomyces cerevisiae, is the best understood microbial eukaryote at the molecular and cellular level, yet its natural geographic distribution is unknown. Here we report the results of a field survey for S. cerevisiae,S. paradoxus and other budding yeast on oak trees in Europe. We show that yeast species differ in their geographic distributions, and investigated which ecological variables can predict the isolation rate of S. paradoxus, the most abundant species. We find a positive association between trunk girth and S. paradoxus abundance suggesting that older trees harbor more yeast. S. paradoxus isolation frequency is also associated with summer temperature, showing highest isolation rates at intermediate temperatures. Using our statistical model, we estimated a range of summer temperatures at which we expect high S. paradoxus isolation rates, and show that the geographic distribution predicted by this optimum temperature range is consistent with the worldwide distribution of sites where S. paradoxus has been isolated. Using laboratory estimates of optimal growth temperatures for S. cerevisiae relative to S. paradoxus, we also estimated an optimum range of summer temperatures for S. cerevisiae. The geographic distribution of these optimum temperatures is consistent with the locations where wild S. cerevisiae have been reported, and can explain why only human-associated S. cerevisiae strains are isolated at northernmost latitudes. Our results provide a starting point for targeted isolation of S. cerevisiae from natural habitats, which could lead to a better understanding of climate associations and natural history in this important model microbe.}, }
@article {pmid26941732, year = {2016}, author = {Graham, EB and Knelman, JE and Schindlbacher, A and Siciliano, S and Breulmann, M and Yannarell, A and Beman, JM and Abell, G and Philippot, L and Prosser, J and Foulquier, A and Yuste, JC and Glanville, HC and Jones, DL and Angel, R and Salminen, J and Newton, RJ and Bürgmann, H and Ingram, LJ and Hamer, U and Siljanen, HM and Peltoniemi, K and Potthast, K and Bañeras, L and Hartmann, M and Banerjee, S and Yu, RQ and Nogaro, G and Richter, A and Koranda, M and Castle, SC and Goberna, M and Song, B and Chatterjee, A and Nunes, OC and Lopes, AR and Cao, Y and Kaisermann, A and Hallin, S and Strickland, MS and Garcia-Pausas, J and Barba, J and Kang, H and Isobe, K and Papaspyrou, S and Pastorelli, R and Lagomarsino, A and Lindström, ES and Basiliko, N and Nemergut, DR}, title = {Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {214}, pmid = {26941732}, issn = {1664-302X}, abstract = {Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.}, }
@article {pmid26941731, year = {2016}, author = {Vavourakis, CD and Ghai, R and Rodriguez-Valera, F and Sorokin, DY and Tringe, SG and Hugenholtz, P and Muyzer, G}, title = {Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {211}, pmid = {26941731}, issn = {1664-302X}, support = {322551/ERC_/European Research Council/International ; }, abstract = {Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration of sodium carbonates in the absence of major divalent cations. Hypersaline soda brines harbor microbial communities with a high species- and strain-level archaeal diversity and a large proportion of still uncultured poly-extremophiles compared to neutral brines of similar salinities. We present the first "metagenomic snapshots" of microbial communities thriving in the brines of four shallow soda lakes from the Kulunda Steppe (Altai, Russia) covering a salinity range from 170 to 400 g/L. Both amplicon sequencing of 16S rRNA fragments and direct metagenomic sequencing showed that the top-level taxa abundance was linked to the ambient salinity: Bacteroidetes, Alpha-, and Gamma-proteobacteria were dominant below a salinity of 250 g/L, Euryarchaeota at higher salinities. Within these taxa, amplicon sequences related to Halorubrum, Natrinema, Gracilimonas, purple non-sulfur bacteria (Rhizobiales, Rhodobacter, and Rhodobaca) and chemolithotrophic sulfur oxidizers (Thioalkalivibrio) were highly abundant. Twenty-four draft population genomes from novel members and ecotypes within the Nanohaloarchaea, Halobacteria, and Bacteroidetes were reconstructed to explore their metabolic features, environmental abundance and strategies for osmotic adaptation. The Halobacteria- and Bacteroidetes-related draft genomes belong to putative aerobic heterotrophs, likely with the capacity to ferment sugars in the absence of oxygen. Members from both taxonomic groups are likely involved in primary organic carbon degradation, since some of the reconstructed genomes encode the ability to hydrolyze recalcitrant substrates, such as cellulose and chitin. Putative sodium-pumping rhodopsins were found in both a Flavobacteriaceae- and a Chitinophagaceae-related draft genome. The predicted proteomes of both the latter and a Rhodothermaceae-related draft genome were indicative of a "salt-in" strategy of osmotic adaptation. The primary catabolic and respiratory pathways shared among all available reference genomes of Nanohaloarchaea and our novel genome reconstructions remain incomplete, but point to a primarily fermentative lifestyle. Encoded xenorhodopsins found in most drafts suggest that light plays an important role in the ecology of Nanohaloarchaea. Putative encoded halolysins and laccase-like oxidases might indicate the potential for extracellular degradation of proteins and peptides, and phenolic or aromatic compounds.}, }
@article {pmid26941724, year = {2016}, author = {Patrone, V and Vajana, E and Minuti, A and Callegari, ML and Federico, A and Loguercio, C and Dallio, M and Tolone, S and Docimo, L and Morelli, L}, title = {Postoperative Changes in Fecal Bacterial Communities and Fermentation Products in Obese Patients Undergoing Bilio-Intestinal Bypass.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {200}, pmid = {26941724}, issn = {1664-302X}, abstract = {We assessed the gut microbial ecology of 11 severely obese patients before and after bilio-intestinal bypass (BIB). Fecal samples were evaluated for microbial communities using 16S rDNA Illumina sequencing, real-time PCR targeting functional genes, and gas chromatography of short chain fatty acids (SCFAs). At 6 months after surgery, subjects exhibited significant improvements in metabolic markers (body weight, glucose, and lipid metabolism) compared with baseline. The fecal microbiota of post-surgery individuals was characterized by an overall decrease of bacterial diversity, with a significant reduction in Lachnospiraceae, Clostridiaceae, Ruminococcaceae, Eubacteriaceae, and Coriobacteriaceae. On the contrary, there were significant increases of genera Lactobacillus, Megasphaera, and Acidaminococcus and the family Enterobacteriaceae. The pH was decreased in fecal samples from patients after BIB and SCFA profiles were altered, with lower percentages of acetate and propionate and higher levels of valerate and hexanoate. Some changes in the bacterial populations were associated with variations in the patients' metabolic health parameters, namely Gemmiger and glucose, Lactobacillus and glucose, and Faecalibacterium and triglycerides. The results from this study of BIB patients furthers our understanding of the composition of gut microbiota and the functional changes that may be involved in improving obesity-related conditions following weight-loss surgery.}, }
@article {pmid26940085, year = {2016}, author = {Hu, SK and Campbell, V and Connell, P and Gellene, AG and Liu, Z and Terrado, R and Caron, DA}, title = {Protistan diversity and activity inferred from RNA and DNA at a coastal ocean site in the eastern North Pacific.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {4}, pages = {fiw050}, doi = {10.1093/femsec/fiw050}, pmid = {26940085}, issn = {1574-6941}, mesh = {Ciliophora/*classification/*genetics ; DNA/*genetics ; Ecosystem ; Pacific Ocean ; Phytoplankton/*genetics ; RNA ; RNA, Ribosomal, 18S/*genetics ; Seawater ; Sequence Analysis, DNA ; }, abstract = {Microbial eukaryotes fulfill key ecological positions in marine food webs. Molecular approaches that connect protistan diversity and biogeography to their diverse metabolisms will greatly improve our understanding of marine ecosystem function. The majority of molecular-based studies to date use 18S rRNA gene sequencing to characterize natural microbial assemblages, but this approach does not necessarily discriminate between active and non-active cells. We incorporated RNA sequencing into standard 18S rRNA gene sequence surveys with the purpose of assessing those members of the protistan community contributing to biogeochemical cycling (active organisms), using the ratio of cDNA (reverse transcribed from total RNA) to 18S rRNA gene sequences within major protistan taxonomic groups. Trophically important phytoplankton, such as diatoms and chlorophytes exhibited seasonal trends in relative activity. Additionally, both radiolaria and ciliates displayed previously unreported high relative activities below the euphotic zone. This study sheds new light on the relative metabolic activity of specific protistan groups and how microbial communities respond to changing environmental conditions.}, }
@article {pmid26937267, year = {2016}, author = {Palmer, M and de Maayer, P and Poulsen, M and Steenkamp, ET and van Zyl, E and Coutinho, TA and Venter, SN}, title = {Draft genome sequences of Pantoea agglomerans and Pantoea vagans isolates associated with termites.}, journal = {Standards in genomic sciences}, volume = {11}, number = {}, pages = {23}, pmid = {26937267}, issn = {1944-3277}, abstract = {The genus Pantoea incorporates many economically and clinically important species. The plant-associated species, Pantoea agglomerans and Pantoea vagans, are closely related and are often isolated from similar environments. Plasmids conferring certain metabolic capabilities are also shared amongst these two species. The genomes of two isolates obtained from fungus-growing termites in South Africa were sequenced, assembled and annotated. A high number of orthologous genes are conserved within and between these species. The difference in genome size between P. agglomerans MP2 (4,733,829 bp) and P. vagans MP7 (4,598,703 bp) can largely be attributed to the differences in plasmid content. The genome sequences of these isolates may shed light on the common traits that enable P. agglomerans and P. vagans to co-occur in plant- and insect-associated niches.}, }
@article {pmid26936255, year = {2016}, author = {Pascual, J and González, I and Estévez, M and Benito, P and Trujillo, ME and Genilloud, O}, title = {Description of Kibdelosporangium banguiense sp. nov., a novel actinomycete isolated from soil of the forest of Pama, on the plateau of Bangui, Central African Republic.}, journal = {Antonie van Leeuwenhoek}, volume = {109}, number = {5}, pages = {685-695}, doi = {10.1007/s10482-016-0669-6}, pmid = {26936255}, issn = {1572-9699}, mesh = {Actinomycetales/*classification/cytology/genetics/*isolation &amp; purification ; Bacterial Typing Techniques ; Central African Republic ; DNA, Bacterial/genetics ; *Forests ; Phenotype ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil ; *Soil Microbiology ; }, abstract = {A novel actinomycete strain F-240,109(T) from the MEDINA collection was isolated from a soil sample collected in the forest of Pama, on the plateau of Bangui, Central African Republic. The strain was identified according to its 16S rRNA gene sequence as a new member of the genus Kibdelosporangium, being closely related to Kibdelosporangium aridum subsp. aridum (98.6 % sequence similarity), Kibledosporangium phytohabitans (98.3 %), Kibdelosporangium aridum subsp. largum (97.7 %), Kibdelosporangium philippinense (97.6 %) and Kibledosporangium lantanae (96.9 %). In order to resolve its precise taxonomic status, the strain was characterised through a polyphasic approach. The strain is a Gram-stain positive, aerobic, non-motile and catalase-positive actinomycete characterised by formation of extensively branched substrate mycelia and sparse brownish grey aerial mycelia with sporangium-like globular structures. The chemotaxonomic characterisation of strain F-240,109(T) corroborated its affiliation into the genus Kibdelosporangium. The peptidoglycan contains meso-diaminopimelic acid; the major menaquinone is MK-9(H4); the phospholipid profile contains high amounts of phosphatidylethanolamine, hydroxyphosphatidylethanolamine, diphosphatidylglycerol and an unidentified phospholipid; and the predominant cellular fatty acid methyl esters are iso-C16:0, iso-C14:0, iso-C15:0 and 2OH iso-C16:0. However, some key phenotypic differences regarding to its close relatives and DNA-DNA hybridization values indicate that strain F-240,109(T) represents a novel Kibdelosporangium species, for which the name Kibdelosporangium banguiense sp. nov. is proposed. The type strain is strain F-240,109(T) (=DSM 46670(T), =LMG 28181(T)).}, }
@article {pmid26932201, year = {2016}, author = {Currie, F and Broadhurst, DI and Dunn, WB and Sellick, CA and Goodacre, R}, title = {Metabolomics reveals the physiological response of Pseudomonas putida KT2440 (UWC1) after pharmaceutical exposure.}, journal = {Molecular bioSystems}, volume = {12}, number = {4}, pages = {1367-1377}, doi = {10.1039/c5mb00889a}, pmid = {26932201}, issn = {1742-2051}, support = {BBC0082191//Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/S/N/2004/11499//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adenosine Triphosphate/metabolism ; Analysis of Variance ; Gas Chromatography-Mass Spectrometry ; *Metabolome ; *Metabolomics/methods ; *Pharmaceutical Preparations ; Propranolol/pharmacology ; Pseudomonas putida/*drug effects/*metabolism ; Spectroscopy, Fourier Transform Infrared ; }, abstract = {Human pharmaceuticals have been detected in wastewater treatment plants, rivers, and estuaries throughout Europe and the United States. It is widely acknowledged that there is insufficient information available to determine whether prolonged exposure to low levels of these substances is having an impact on the microbial ecology in such environments. In this study we attempt to measure the effects of exposing cultures of Pseudomonas putida KT2440 (UWC1) to six pharmaceuticals by looking at differences in metabolite levels. Initially, we used Fourier transform infrared (FT-IR) spectroscopy coupled with multivariate analysis to discriminate between cell cultures exposed to different pharmaceuticals. This suggested that on exposure to propranolol there were significant changes in the lipid complement of P. putida. Metabolic profiling with gas chromatography-mass spectrometry (GC-MS), coupled with univariate statistical analyses, was used to identify endogenous metabolites contributing to discrimination between cells exposed to the six drugs. This approach suggested that the energy reserves of exposed cells were being expended and was particularly evident on exposure to propranolol. Adenosine triphosphate (ATP) concentrations were raised in P. putida exposed to propranolol. Increased energy requirements may be due to energy dependent efflux pumps being used to remove propranolol from the cell.}, }
@article {pmid26931606, year = {2016}, author = {Cydzik-Kwiatkowska, A and Zielińska, M}, title = {Bacterial communities in full-scale wastewater treatment systems.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {32}, number = {4}, pages = {66}, pmid = {26931606}, issn = {1573-0972}, mesh = {Bacteria/classification/*genetics/*isolation &amp; purification ; Biomass ; High-Throughput Nucleotide Sequencing ; Microbial Consortia ; Sequence Analysis, DNA ; Waste Disposal, Fluid/methods ; Wastewater/*microbiology ; Water Microbiology ; }, abstract = {Bacterial metabolism determines the effectiveness of biological treatment of wastewater. Therefore, it is important to define the relations between the species structure and the performance of full-scale installations. Although there is much laboratory data on microbial consortia, our understanding of dependencies between the microbial structure and operational parameters of full-scale wastewater treatment plants (WWTP) is limited. This mini-review presents the types of microbial consortia in WWTP. Information is given on extracellular polymeric substances production as factor that is key for formation of spatial structures of microorganisms. Additionally, we discuss data on microbial groups including nitrifiers, denitrifiers, Anammox bacteria, and phosphate- and glycogen-accumulating bacteria in full-scale aerobic systems that was obtained with the use of molecular techniques, including high-throughput sequencing, to shed light on dependencies between the microbial ecology of biomass and the overall efficiency and functional stability of wastewater treatment systems. Sludge bulking in WWTPs is addressed, as well as the microbial composition of consortia involved in antibiotic and micropollutant removal.}, }
@article {pmid26931390, year = {2016}, author = {Schaeck, M and Duchateau, L and Van den Broeck, W and Van Trappen, S and De Vos, P and Coulombet, C and Boon, N and Haesebrouck, F and Decostere, A}, title = {Vibrio lentus protects gnotobiotic sea bass (Dicentrarchus labrax L.) larvae against challenge with Vibrio harveyi.}, journal = {Veterinary microbiology}, volume = {185}, number = {}, pages = {41-48}, doi = {10.1016/j.vetmic.2016.01.024}, pmid = {26931390}, issn = {1873-2542}, mesh = {Animals ; *Antibiosis ; Aquaculture ; Bacillus/physiology ; Bass/*microbiology ; Fish Diseases/*microbiology/*prevention &amp; control ; Germ-Free Life ; *Probiotics ; Vibrio/*physiology ; Vibrio Infections/microbiology/prevention &amp; control/*veterinary ; }, abstract = {Due to the mounting awareness of the risks associated with the use of antibiotics in aquaculture, treatment with probiotics has recently emerged as the preferred environmental-friendly prophylactic approach in marine larviculture. However, the presence of unknown and variable microbiota in fish larvae makes it impossible to disentangle the efficacy of treatment with probiotics. In this respect, the recent development of a germ-free culture model for European sea bass (Dicentrarchus labrax L.) larvae opened the door for more controlled studies on the use of probiotics. In the present study, 206 bacterial isolates, retrieved from sea bass larvae and adults, were screened in vitro for haemolytic activity, bile tolerance and antagonistic activity against six sea bass pathogens. Subsequently, the harmlessness and the protective effect of the putative probiotic candidates against the sea bass pathogen Vibrio harveyi were evaluated in vivo adopting the previously developed germ-free sea bass larval model. An equivalence trial clearly showed that no harmful effect on larval survival was elicited by all three selected probiotic candidates: Bacillus sp. LT3, Vibrio lentus and Vibrio proteolyticus. Survival of Vibrio harveyi challenged larvae treated with V. lentus was superior in comparison with the untreated challenged group, whereas this was not the case for the larvae supplemented with Bacillus sp. LT3 and V. proteolyticus. In this respect, our results unmistakably revealed the protective effect of V. lentus against vibriosis caused by V. harveyi in gnotobiotic sea bass larvae, rendering this study the first in its kind.}, }
@article {pmid26929931, year = {2016}, author = {Bobrova, O and Kristoffersen, JB and Oulas, A and Ivanytsia, V}, title = {Metagenomic 16s rRNA investigation of microbial communities in the Black Sea estuaries in South-West of Ukraine.}, journal = {Acta biochimica Polonica}, volume = {63}, number = {2}, pages = {315-319}, doi = {10.18388/abp.2015_1145}, pmid = {26929931}, issn = {1734-154X}, mesh = {Biodiversity ; Black Sea ; Metagenome ; Molecular Typing ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; Seawater/microbiology ; Ukraine ; Water Microbiology ; }, abstract = {The Black Sea estuaries represent interfaces of the sea and river environments. Microorganisms that inhabit estuarine water play an integral role in all biochemical processes that occur there and form unique ecosystems. There are many estuaries located in the Southern-Western part of Ukraine and some of them are already separated from the sea. The aim of this research was to determine the composition of microbial communities in the Khadzhibey, Dniester and Sukhyi estuaries by metagenomic 16S rDNA analysis. This study is the first complex analysis of estuarine microbiota based on isolation of total DNA from a biome that was further subjected to sequencing. DNA was extracted from water samples and sequenced on the Illumina Miseq platform using primers to the V4 variable region of the 16S rRNA gene. Computer analysis of the obtained raw sequences was done with QIIME (Quantitative Insights Into Microbial Ecology) software. As the outcome, 57970 nucleotide sequences were retrieved. Bioinformatic analysis of bacterial community in the studied samples demonstrated a high taxonomic diversity of Prokaryotes at above genus level. It was shown that majority of 16S rDNA bacterial sequences detected in the estuarine samples belonged to phyla Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, Planctomycetes. The Khadhzibey estuary was dominated by the Proteobacteria phylum, while Dniester and Sukhyi estuaries were characterized by dominance of Cyanobacteria. The differences in bacterial populations between the Khadzhibey, Dniester and Sukhyi estuaries were demonstrated through the Beta-diversity analysis. It showed that the Khadzhibey estuary's microbial community significantly varies from the Sukhyi and Dniester estuaries. The majority of identified bacterial species is known as typical inhabitants of marine environments, however, for 2.5% of microbial population members in the studied estuaries no relatives were determined.}, }
@article {pmid26925072, year = {2016}, author = {Naqqash, T and Hameed, S and Imran, A and Hanif, MK and Majeed, A and van Elsas, JD}, title = {Differential Response of Potato Toward Inoculation with Taxonomically Diverse Plant Growth Promoting Rhizobacteria.}, journal = {Frontiers in plant science}, volume = {7}, number = {}, pages = {144}, pmid = {26925072}, issn = {1664-462X}, abstract = {Rhizosphere engineering with beneficial plant growth promoting bacteria offers great promise for sustainable crop yield. Potato is an important food commodity that needs large inputs of nitrogen and phosphorus fertilizers. To overcome high fertilizer demand (especially nitrogen), five bacteria, i.e., Azospirillum sp. TN10, Agrobacterium sp. TN14, Pseudomonas sp. TN36, Enterobacter sp. TN38 and Rhizobium sp. TN42 were isolated from the potato rhizosphere on nitrogen-free malate medium and identified based on their 16S rRNA gene sequences. Three strains, i.e., TN10, TN38, and TN42 showed nitrogen fixation (92.67-134.54 nmol h(-1)mg(-1) protein), while all showed the production of indole-3-acetic acid (IAA), which was significantly increased by the addition of L-tryptophan. Azospirillum sp. TN10 produced the highest amount of IAA, as measured by spectrophotometry (312.14 μg mL(-1)) and HPLC (18.3 μg mL(-1)). Inoculation with these bacteria under axenic conditions resulted in differential growth responses of potato. Azospirillum sp. TN10 incited the highest increase in potato fresh and dry weight over control plants, along with increased N contents of shoot and roots. All strains were able to colonize and maintain their population densities in the potato rhizosphere for up to 60 days, with Azospirillum sp. and Rhizobium sp. showing the highest survival. Plant root colonization potential was analyzed by transmission electron microscopy of root sections inoculated with Azospirillum sp. TN10. Of the five test strains, Azospirillum sp. TN10 has the greatest potential to increase the growth and nitrogen uptake of potato. Hence, it is suggested as a good candidate for the production of potato biofertilizer for integrated nutrient management.}, }
@article {pmid26922071, year = {2016}, author = {Keren, R and Lavy, A and Ilan, M}, title = {Erratum to: Increasing the Richness of Culturable Arsenic-Tolerant Bacteria from Theonella swinhoei by Addition of Sponge Skeleton to the Growth Medium.}, journal = {Microbial ecology}, volume = {72}, number = {2}, pages = {496}, doi = {10.1007/s00248-016-0744-6}, pmid = {26922071}, issn = {1432-184X}, }
@article {pmid26921734, year = {2016}, author = {Makhalanyane, TP and Van Goethem, MW and Cowan, DA}, title = {Microbial diversity and functional capacity in polar soils.}, journal = {Current opinion in biotechnology}, volume = {38}, number = {}, pages = {159-166}, doi = {10.1016/j.copbio.2016.01.011}, pmid = {26921734}, issn = {1879-0429}, mesh = {Arctic Regions ; *Bacteria/metabolism ; Metagenomics ; *Soil ; *Soil Microbiology ; }, abstract = {Global change is disproportionately affecting cold environments (polar and high elevation regions), with potentially negative impacts on microbial diversity and functional processes. In most cold environments the combination of low temperatures, and physical stressors, such as katabatic wind episodes and limited water availability result in biotic systems, which are in trophic terms very simple and primarily driven by microbial communities. Metagenomic approaches have provided key insights on microbial communities in these systems and how they may adapt to stressors and contribute towards mediating crucial biogeochemical cycles. Here we review, the current knowledge regarding edaphic-based microbial diversity and functional processes in Antarctica, and the Artic. Such insights are crucial and help to establish a baseline for understanding the impact of climate change on Polar Regions.}, }
@article {pmid26921429, year = {2016}, author = {Staley, C and Sadowsky, MJ}, title = {Regional Similarities and Consistent Patterns of Local Variation in Beach Sand Bacterial Communities throughout the Northern Hemisphere.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {9}, pages = {2751-2762}, pmid = {26921429}, issn = {1098-5336}, mesh = {Bacteria/*classification/genetics ; Bathing Beaches ; Biodiversity ; Ecology ; Ecosystem ; Florida ; Fresh Water ; Great Lakes Region ; Lakes/microbiology ; Microbial Consortia ; Pacific Ocean ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater ; *Soil Microbiology ; Water Microbiology ; }, abstract = {UNLABELLED: Recent characterization of the bacterial community structure in beach sands has revealed patterns of biogeography similar to those observed in aquatic environments. Studies to date, however, have mainly focused on subtidal sediments from marine beaches. Here, we investigate the bacterial diversity, using Illumina-based sequencing of the V5-V6 region of the 16S rRNA gene, at 11 beaches representing those next to the Great Lakes, Florida, and the Pacific Ocean. The alpha diversity differed significantly among regions (P< 0.0001), while the within-region diversity was more similar. The beta diversity also differed by region (P< 0.001), where freshwater sands had significantly higher abundances of taxa within the Actinobacteria, Betaproteobacteria, and Verrucomicrobia than marine environments. In contrast, marine sands harbored greater abundances of Gamma proteobacteria and Planctomycetes, and those from Florida had more Delta proteobacteria and Firmicutes Marine beaches had significantly different phylogenetic community structures (P ≤ 0.018), but freshwater and Florida beaches showed fewer within-region phylogenetic differences. Furthermore, regionally distinct patterns in taxonomic variation were observed in backshore sands, which had communities distinct from those in nearshore sands (P< 0.001). Sample depth minimally influenced the community composition. The results of this study reveal distinct bacterial community structures in sand on a broad geographic scale but moderate regional similarity and suggest that local variation is primarily related to the distance from the shoreline. This study offers a novel comparison of the bacterial communities in freshwater and marine beach sands and provides an important basis for future comparisons and analyses to elucidate factors affecting microbial ecology in this underexplored environment.<br><br>IMPORTANCE: This study presents a large-scale geographic characterization of the bacterial communities present in beach sands. While previous studies have evaluated how environmental factors influence bacterial community composition, few have evaluated bacterial communities in freshwater sands. Furthermore, the use of a consistent methodology to characterize bacterial communities here allowed a novel comparison of communities across geographic regions. We reveal that while the community composition in sands at individual beaches is distinct, beach sands within the same region harbor similar assemblages of bacteria and these assemblages differ greatly between regions. In addition, moisture, associated with distance from the shoreline, strongly influences the bacteria present in sands and more strongly influences the bacteria present than sample depth does. Thus, the data presented here offer an important basis for a broader characterization of the ecology of bacteria in sands, which may also be relevant to public health and resource management initiatives.}, }
@article {pmid26921180, year = {2016}, author = {He, X and So, MJ and de Los Reyes, FL}, title = {Shifts in microbial communities in bioaugmented grease interceptors removing fat, oil, and grease (FOG).}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {16}, pages = {7025-7035}, doi = {10.1007/s00253-016-7398-7}, pmid = {26921180}, issn = {1432-0614}, mesh = {Bacteria/genetics/*metabolism ; Bioreactors ; DNA, Bacterial/genetics ; Fats/*metabolism ; Gene Library ; Oils/*metabolism ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; *Waste Disposal, Fluid ; Water Purification/*methods ; }, abstract = {To understand the effect of daily bioaugmentation in full-scale grease interceptors (GIs), we compared the microbial communities occurring in two full-scale GIs during bioaugmented and non-bioaugmented cycles. The changes in microbial communities were determined using terminal restriction fragment length polymorphism (T-RFLP) and 16S rRNA gene clone library construction. Differences in the microbial community structure between control and bioaugmented cycles were observed in all cases, although the dominant terminal restriction fragments in the biological product were not detected. The addition of bioaugmentation products and changes in the GI microbial ecology were related to differences in GI performance. Understanding the shifts due to bioaugmentation will result in more informed assessments of the benefits of bioadditives on FOG removal in GIs as well as the effects on downstream sewer lines.}, }
@article {pmid26914534, year = {2016}, author = {Crits-Christoph, A and Gelsinger, DR and Ma, B and Wierzchos, J and Ravel, J and Davila, A and Casero, MC and DiRuggiero, J}, title = {Functional interactions of archaea, bacteria and viruses in a hypersaline endolithic community.}, journal = {Environmental microbiology}, volume = {18}, number = {6}, pages = {2064-2077}, doi = {10.1111/1462-2920.13259}, pmid = {26914534}, issn = {1462-2920}, mesh = {Archaea/genetics ; Archaeal Proteins/chemistry ; Bacteria/genetics/*isolation &amp; purification ; Cyanobacteria/genetics/isolation &amp; purification/virology ; *Desert Climate ; Ecosystem ; Euryarchaeota/genetics/*isolation &amp; purification/virology ; Genome, Viral ; Isoelectric Point ; Metagenome ; Microbial Consortia ; Microbial Interactions ; Phylogeny ; *Salinity ; Viruses/genetics/*isolation &amp; purification ; }, abstract = {Halite endoliths in the Atacama Desert represent one of the most extreme ecosystems on Earth. Cultivation-independent methods were used to examine the functional adaptations of the microbial consortia inhabiting halite nodules. The community was dominated by haloarchaea and functional analysis attributed most of the autotrophic CO2 fixation to one unique cyanobacterium. The assembled 1.1 Mbp genome of a novel nanohaloarchaeon, Candidatus Nanopetramus SG9, revealed a photoheterotrophic life style and a low median isoelectric point (pI) for all predicted proteins, suggesting a 'salt-in' strategy for osmotic balance. Predicted proteins of the algae identified in the community also had pI distributions similar to 'salt-in' strategists. The Nanopetramus genome contained a unique CRISPR/Cas system with a spacer that matched a partial viral genome from the metagenome. A combination of reference-independent methods identified over 30 complete or near complete viral or proviral genomes with diverse genome structure, genome size, gene content and hosts. Putative hosts included Halobacteriaceae, Nanohaloarchaea and Cyanobacteria. Despite the dependence of the halite community on deliquescence for liquid water availability, this study exposed an ecosystem spanning three phylogenetic domains, containing a large diversity of viruses and predominance of a 'salt-in' strategy to balance the high osmotic pressure of the environment.}, }
@article {pmid26913851, year = {2016}, author = {Avershina, E and Lundgård, K and Sekelja, M and Dotterud, C and Storrø, O and Øien, T and Johnsen, R and Rudi, K}, title = {Transition from infant- to adult-like gut microbiota.}, journal = {Environmental microbiology}, volume = {18}, number = {7}, pages = {2226-2236}, doi = {10.1111/1462-2920.13248}, pmid = {26913851}, issn = {1462-2920}, mesh = {Adult ; Age Factors ; Bacteria/classification/genetics/*isolation &amp; purification ; Child, Preschool ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Phylogeny ; Young Adult ; }, abstract = {Transition from an infant to an adult associated gut microbiota with age through establishment of strict anaerobic bacteria remains one of the key unresolved questions in gut microbial ecology. Here a comprehensive comparative analysis of stool microbiota in a large cohort of mothers and their children sampled longitudinally up until 2 years of age using sequencing analysis tool was presented that allows realistic microbial diversity estimates. In this work, evidence for the switch from children to adult associated microbial profile between 1 and 2 years of age was provided, suggestively driven by Bifidobacterium breve. An Operational Taxonomic Unit (OTU) belonging to B. breve was highly prevalent in the population throughout the first year of life, and was negatively associated with detection of a range of adult-like OTUs. Although an adult profile was not fully established by 2 years of age, it was demonstrated that with regards to the most prevalent OTUs, their prevalence in the child population by then already resembled that of the adult population. Taken together, it was proposed that late-colonizing OTUs were recruited at a later stage and were not acquired at birth with the recruitment being controlled by gatekeeping OTUs until the age of 1 year.}, }
@article {pmid26909796, year = {2016}, author = {Jia, T and Oberhofer, M and Shymanovich, T and Faeth, SH}, title = {Effects of Hybrid and Non-hybrid Epichloë Endophytes and Their Associated Host Genotypes on the Response of a Native Grass to Varying Environments.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {185-196}, pmid = {26909796}, issn = {1432-184X}, mesh = {Adaptation, Physiological ; Biomass ; Endophytes/*classification/genetics/isolation &amp; purification ; *Environmental Microbiology ; Epichloe/*classification/genetics/isolation &amp; purification ; Festuca/microbiology ; Genotype ; Hybridization, Genetic ; Plant Roots/microbiology ; Poaceae/*microbiology ; Seasons ; Symbiosis ; }, abstract = {Asexual Epichloë endophytes are prevalent in cool season grasses, and many are of hybrid origin. Hybridization of asexual endophytes is thought to provide a rapid influx of genetic variation that may be adaptive to endophyte-host grass symbiota in stressful environments. For Arizona fescue (Festuca arizonica), hybrid symbiota are commonly found in resource-poor environments, whereas non-hybrid symbiota are more common in resource-rich environments. There have been very few experimental tests where infection, hybrid and non-hybrid status, and plant genotype have been controlled to tease apart their effects on host phenotype and fitness in different environments. We conducted a greenhouse experiment where hybrid (H) and non-hybrid (NH) endophytes were inoculated into plant genotypes that were originally uninfected (E-) or once infected with either the H or NH endophytes. Nine endophyte and plant genotypic group combinations were grown under low and high water and nutrient treatments. Inoculation with the resident H endophyte enhanced growth and altered allocation to roots and shoots, but these effects were greatest in resource-rich environments, contrary to expectations. We found no evidence of co-adaptation between endophyte species and their associated host genotypes. However, naturally E- plants performed better when inoculated with the hybrid endophyte, suggesting these plants were derived from H infected lineages. Our results show complex interactions between endophyte species of hybrid and non-hybrid origin with their host plant genotypes and environmental factors.}, }
@article {pmid26909469, year = {2016}, author = {Zhang, MQ and Guo, Y and Powell, CA and Doud, MS and Yang, CY and Zhou, H and Duan, YP}, title = {Zinc treatment increases the titre of 'Candidatus Liberibacter asiaticus' in huanglongbing-affected citrus plants while affecting the bacterial microbiomes.}, journal = {Journal of applied microbiology}, volume = {120}, number = {6}, pages = {1616-1628}, doi = {10.1111/jam.13102}, pmid = {26909469}, issn = {1365-2672}, mesh = {Bacteria/classification/*drug effects/growth &amp; development/isolation &amp; purification ; Citrus/*drug effects/*microbiology ; Microbiota/*drug effects ; Plant Diseases/*microbiology ; Plant Leaves/microbiology ; Rhizobiaceae/drug effects/*physiology ; Zinc/*pharmacology ; }, abstract = {AIMS: Huanglongbing (HLB)-affected citrus often display zinc deficiency symptoms. In this study, supplemental zinc was applied to citrus to determine its effect on Candidatus Liberibacter asiaticus (Las) titre, HLB symptoms, and leaf microbiome.<br><br>METHODS AND RESULTS: HLB-affected citrus were treated with various amounts of zinc. The treatments promoted Las growth and affected microbiomes in citrus leaves. Phylochip(&#x2122;) -based results indicated that 5475 of over 50&#xa0;000 known Operational Taxonomic Units (OTUs) in 52 phyla were detected in the midribs of HLB-affected citrus, of which Proteobacteria was the most abundant, followed by Firmicutes and Actinobacteria. In comparison, the microbiomes of zinc-treated diseased plants had overall more OTUs with higher amounts of Proteobacteria, but decreased percentages of Firmicutes and Actinobacteria. In addition, more OTUs of siderophore-producing bacteria were present. Only zinc-sensitive Staphylococcaceae had higher OTU's in the diseased plants without zinc treatments.<br><br>CONCLUSIONS: Although HLB-affected citrus appear zinc deficient, zinc amendments increased the pathogen levels and shifted the microbiome.<br><br>HLB is currently the most devastating disease of citrus worldwide. Zinc is often applied to HLB-affected citrus due to zinc deficiency symptoms. This study provided new insights into the potential effects of zinc on HLB and the microbial ecology of citrus.}, }
@article {pmid26906468, year = {2016}, author = {Awolusi, OO and Nasr, M and Kumari, S and Bux, F}, title = {Artificial Intelligence for the Evaluation of Operational Parameters Influencing Nitrification and Nitrifiers in an Activated Sludge Process.}, journal = {Microbial ecology}, volume = {72}, number = {1}, pages = {49-63}, pmid = {26906468}, issn = {1432-184X}, mesh = {Ammonia/metabolism ; *Artificial Intelligence ; Bacteria/*classification/isolation &amp; purification ; DNA, Bacterial/genetics ; In Situ Hybridization, Fluorescence ; Models, Theoretical ; *Nitrification ; Nitrobacter/classification ; Real-Time Polymerase Chain Reaction ; Sewage/*microbiology ; Temperature ; Waste Management ; }, abstract = {Nitrification at a full-scale activated sludge plant treating municipal wastewater was monitored over a period of 237 days. A combination of fluorescent in situ hybridization (FISH) and quantitative real-time polymerase chain reaction (qPCR) were used for identifying and quantifying the dominant nitrifiers in the plant. Adaptive neuro-fuzzy inference system (ANFIS), Pearson's correlation coefficient, and quadratic models were employed in evaluating the plant operational conditions that influence the nitrification performance. The ammonia-oxidizing bacteria (AOB) abundance was within the range of 1.55 × 10(8)-1.65 × 10(10) copies L(-1), while Nitrobacter spp. and Nitrospira spp. were 9.32 × 10(9)-1.40 × 10(11) copies L(-1) and 2.39 × 10(9)-3.76 × 10(10) copies L(-1), respectively. Specific nitrification rate (qN) was significantly affected by temperature (r 0.726, p 0.002), hydraulic retention time (HRT) (r -0.651, p 0.009), and ammonia loading rate (ALR) (r 0.571, p 0.026). Additionally, AOB was considerably influenced by HRT (r -0.741, p 0.002) and temperature (r 0.517, p 0.048), while HRT negatively impacted Nitrospira spp. (r -0.627, p 0.012). A quadratic combination of HRT and food-to-microorganism (F/M) ratio also impacted qN (r (2) 0.50), AOB (r (2) 0.61), and Nitrospira spp. (r (2) 0.72), while Nitrobacter spp. was considerably influenced by a polynomial function of F/M ratio and temperature (r (2) 0.49). The study demonstrated that ANFIS could be used as a tool to describe the factors influencing nitrification process at full-scale wastewater treatment plants.}, }
@article {pmid26904675, year = {2016}, author = {Scoma, A and Bertin, L and Reis, MA and Kornaros, M and Coma, M}, title = {Multipurpose, Integrated 2nd Generation Biorefineries.}, journal = {BioMed research international}, volume = {2016}, number = {}, pages = {4327575}, doi = {10.1155/2016/4327575}, pmid = {26904675}, issn = {2314-6141}, mesh = {*Biofuels ; Green Chemistry Technology/*trends ; Humans ; Lignin/*chemistry ; }, }
@article {pmid26904008, year = {2016}, author = {Yang, C and Rooke, JA and Cabeza, I and Wallace, RJ}, title = {Nitrate and Inhibition of Ruminal Methanogenesis: Microbial Ecology, Obstacles, and Opportunities for Lowering Methane Emissions from Ruminant Livestock.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {132}, pmid = {26904008}, issn = {1664-302X}, abstract = {Ruminal methane production is among the main targets for greenhouse gas (GHG) mitigation for the animal agriculture industry. Many compounds have been evaluated for their efficacy to suppress enteric methane production by ruminal microorganisms. Of these, nitrate as an alternative hydrogen sink has been among the most promising, but it suffers from variability in efficacy for reasons that are not understood. The accumulation of nitrite, which is poisonous when absorbed into the animal's circulation, is also variable and poorly understood. This review identifies large gaps in our knowledge of rumen microbial ecology that handicap the further development and safety of nitrate as a dietary additive. Three main bacterial species have been associated historically with ruminal nitrate reduction, namely Wolinella succinogenes, Veillonella parvula, and Selenomonas ruminantium, but others almost certainly exist in the largely uncultivated ruminal microbiota. Indications are strong that ciliate protozoa can reduce nitrate, but the significance of their role relative to bacteria is not known. The metabolic fate of the reduced nitrate has not been studied in detail. It is important to be sure that nitrate metabolism and efforts to enhance rates of nitrite reduction do not lead to the evolution of the much more potent GHG, nitrous oxide. The relative importance of direct inhibition of archaeal methanogenic enzymes by nitrite or the efficiency of capture of hydrogen by nitrate reduction in lowering methane production is also not known, nor are nitrite effects on other members of the microbiota. How effective would combining mitigation methods be, based on our understanding of the effects of nitrate and nitrite on the microbiome? Answering these fundamental microbiological questions is essential in assessing the potential of dietary nitrate to limit methane emissions from ruminant livestock.}, }
@article {pmid26903960, year = {2016}, author = {Nesme, J and Achouak, W and Agathos, SN and Bailey, M and Baldrian, P and Brunel, D and Frostegård, &#xc5; and Heulin, T and Jansson, JK and Jurkevitch, E and Kruus, KL and Kowalchuk, GA and Lagares, A and Lappin-Scott, HM and Lemanceau, P and Le Paslier, D and Mandic-Mulec, I and Murrell, JC and Myrold, DD and Nalin, R and Nannipieri, P and Neufeld, JD and O'Gara, F and Parnell, JJ and Pühler, A and Pylro, V and Ramos, JL and Roesch, LF and Schloter, M and Schleper, C and Sczyrba, A and Sessitsch, A and Sjöling, S and Sørensen, J and Sørensen, SJ and Tebbe, CC and Topp, E and Tsiamis, G and van Elsas, JD and van Keulen, G and Widmer, F and Wagner, M and Zhang, T and Zhang, X and Zhao, L and Zhu, YG and Vogel, TM and Simonet, P}, title = {Back to the Future of Soil Metagenomics.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {73}, pmid = {26903960}, issn = {1664-302X}, }
@article {pmid26899274, year = {2016}, author = {Teshima, T and Reddy, P and Zeiser, R}, title = {Reprint of: Acute Graft-versus-Host Disease: Novel Biological Insights.}, journal = {Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation}, volume = {22}, number = {3 Suppl}, pages = {S3-8}, doi = {10.1016/j.bbmt.2016.01.004}, pmid = {26899274}, issn = {1523-6536}, abstract = {Graft-versus-host disease (GVHD) continues to be a leading cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation. Recent insights into intestinal homeostasis and uncovering of new pathways and targets have greatly reconciled our understanding of GVHD pathophysiology and will reshape contemporary GVHD prophylaxis and treatment. Gastrointestinal (GI) GVHD is the major cause of mortality. Emerging data indicate that intestinal stem cells (ISCs) and their niche Paneth cells are targeted, resulting in dysregulation of the intestinal homeostasis and microbial ecology. The microbiota and their metabolites shape the immune system and intestinal homeostasis, and they may alter host susceptibility to GVHD. Protection of the ISC niche system and modification of the intestinal microbiota and metabolome to restore intestinal homeostasis may, thus, represent a novel approach to modulate GVHD and infection. Damage to the intestine plays a central role in amplifying systemic GVHD by propagating a proinflammatory cytokine milieu. Molecular targeting to inhibit kinase signaling may be a promising approach to treat GVHD, ideally via targeting the redundant effect of multiple cytokines on immune cells and enterocytes. In this review, we discuss insights on the biology of GI GVHD, interaction of microflora and metabolome with the hosts, identification of potential new target organs, and identification and targeting of novel T cell-signaling pathways. Better understanding of GVHD biology will, thus, pave a way to develop novel treatment strategies with great clinical benefits.}, }
@article {pmid26898695, year = {2016}, author = {Christiansen, RH and Madsen, L and Dalsgaard, I and Castillo, D and Kalatzis, PG and Middelboe, M}, title = {Effect of Bacteriophages on the Growth of Flavobacterium psychrophilum and Development of Phage-Resistant Strains.}, journal = {Microbial ecology}, volume = {71}, number = {4}, pages = {845-859}, pmid = {26898695}, issn = {1432-184X}, mesh = {Animals ; Bacteriophages/*physiology ; DNA, Bacterial/genetics ; Fish Diseases/microbiology/prevention &amp; control ; Fishes/microbiology ; Flavobacteriaceae Infections/microbiology/prevention &amp; control/veterinary/virology ; Flavobacterium/genetics/*growth &amp; development/isolation &amp; purification/*virology ; Genome, Bacterial ; Mutation ; Phage Therapy ; Species Specificity ; }, abstract = {The controlling effect of single and multiple phages on the density of Flavobacterium psychrophilum at different initial multiplicity of infection (MOI) was assessed in batch cultures to explore the potential for phage-based treatment of this important fish pathogen. A high initial phage concentration (MOI = 0.3-4) was crucial for efficient viral lysis, resulting in a 10(4)-10(5)-fold reduction of phage-sensitive cells (both single phages and phage cocktails), which was maintained throughout the incubation (>10 days). Following cell lysis, regrowth of phage-resistant strains was examined and resistant strains were isolated for further characterization. The application of a mathematical model allowed simulation of phage-host interactions and resistance development, confirming indications from strain isolations that phage-sensitive strains dominated the regrowing population (>99.8%) at low MOI and phage-resistant strains (>87.8%) dominated at high MOI. A cross-infectivity test covering 68 isolated strains and 22 phages resulted in 23 different host susceptibility patterns, with 20 of the isolates being resistant to all the applied phages. Eleven isolated strains with different susceptibility patterns had lower growth rates (0.093 to 0.31 h(-1)) than the host strain (0.33 h(-1)), while 10 of 14 examined strains had lost the ability to take up specific substrates as shown by BIOLOG profiles. Despite increased selection for phage resistance at high MOI, the results emphasize that high initial MOI is essential for fast and effective control of F. psychrophilum infection and suggest that the small populations of resistant clones had reduced competitive abilities relative to the sensitive ancestral strain.}, }
@article {pmid26897417, year = {2016}, author = {Zaafouri, K and Ben Hassen Trabelsi, A and Krichah, S and Ouerghi, A and Aydi, A and Claumann, CA and André Wüst, Z and Naoui, S and Bergaoui, L and Hamdi, M}, title = {Enhancement of biofuels production by means of co-pyrolysis of Posidonia oceanica (L.) and frying oil wastes: Experimental study and process modeling.}, journal = {Bioresource technology}, volume = {207}, number = {}, pages = {387-398}, doi = {10.1016/j.biortech.2016.02.004}, pmid = {26897417}, issn = {1873-2976}, mesh = {Alismatales/*chemistry ; *Biofuels ; Biomass ; Charcoal ; Conservation of Energy Resources/methods ; Kinetics ; Models, Theoretical ; Waste Management/*methods ; }, abstract = {Energy recovery from lignocellulosic solid marine wastes, Posidonia oceanica wastes (POW) with slow pyrolysis responds to the growing trend of alternative energies as well as waste management. Physicochemical, thermogravimetric (TG/DTG) and spectroscopic (FTIR) characterizations of POW were performed. POW were first converted by pyrolysis at different temperatures (450°C, 500°C, 550°C and 600°C) using a fixed-bed reactor. The obtained products (bio-oil, syngas and bio char) were analyzed. Since the bio-oil yield obtained from POW pyrolysis is low (2wt.%), waste frying oil (WFO) was added as a co-substrate in order to improve of biofuels production. The co-pyrolysis gave a better yield of liquid organic fraction (37wt.%) as well as syngas (CH4,H2…) with a calorific value around 20MJ/kg. The stoichiometric models of both pyrolysis and co-pyrolysis reactions were performed according to the biomass formula: CαHβOγNδSε. The thermal kinetic decomposition of solids was validated through linearized Arrhenius model.}, }
@article {pmid26896159, year = {2016}, author = {Wang, J and Ersan, YC and Boon, N and De Belie, N}, title = {Application of microorganisms in concrete: a promising sustainable strategy to improve concrete durability.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {7}, pages = {2993-3007}, doi = {10.1007/s00253-016-7370-6}, pmid = {26896159}, issn = {1432-0614}, mesh = {Bacillus/chemistry/*metabolism ; Bacillus megaterium/chemistry/*metabolism ; Calcium Carbonate/*chemistry/metabolism ; Chemical Precipitation ; Construction Materials/*microbiology ; Hardness ; Materials Testing ; Metabolic Networks and Pathways/physiology ; Sporosarcina/chemistry/*metabolism ; Surface Properties ; }, abstract = {The beneficial effect of microbially induced carbonate precipitation on building materials has been gradually disclosed in the last decade. After the first applications of on historical stones, promising results were obtained with the respect of improved durability. An extensive study then followed on the application of this environmentally friendly and compatible material on a currently widely used construction material, concrete. This review is focused on the discussion of the impact of the two main applications, bacterial surface treatment and bacteria based crack repair, on concrete durability. Special attention was paid to the choice of suitable bacteria and the metabolic pathway aiming at their functionality in concrete environment. Interactions between bacterial cells and cementitious matrix were also elaborated. Furthermore, recommendations to improve the effectiveness of bacterial treatment are provided. Limitations of current studies, updated applications and future application perspectives are shortly outlined.}, }
@article {pmid26896137, year = {2016}, author = {Wüst, PK and Nacke, H and Kaiser, K and Marhan, S and Sikorski, J and Kandeler, E and Daniel, R and Overmann, J}, title = {Estimates of Soil Bacterial Ribosome Content and Diversity Are Significantly Affected by the Nucleic Acid Extraction Method Employed.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {9}, pages = {2595-2607}, pmid = {26896137}, issn = {1098-5336}, mesh = {Bacteria/*chemistry/genetics ; Bacteriological Techniques/*methods ; Biodiversity ; DNA, Bacterial/genetics/isolation &amp; purification ; Nucleic Acids/chemistry/genetics/*isolation &amp; purification ; Phylogeny ; RNA, Bacterial/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics/isolation &amp; purification ; Real-Time Polymerase Chain Reaction/methods ; Ribosomes/*chemistry/*genetics ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Modern sequencing technologies allow high-resolution analyses of total and potentially active soil microbial communities based on their DNA and RNA, respectively. In the present study, quantitative PCR and 454 pyrosequencing were used to evaluate the effects of different extraction methods on the abundance and diversity of 16S rRNA genes and transcripts recovered from three different types of soils (leptosol, stagnosol, and gleysol). The quality and yield of nucleic acids varied considerably with respect to both the applied extraction method and the analyzed type of soil. The bacterial ribosome content (calculated as the ratio of 16S rRNA transcripts to 16S rRNA genes) can serve as an indicator of the potential activity of bacterial cells and differed by 2 orders of magnitude between nucleic acid extracts obtained by the various extraction methods. Depending on the extraction method, the relative abundances of dominant soil taxa, in particular Actino bacteria and Proteobacteria, varied by a factor of up to 10. Through this systematic approach, the present study allows guidelines to be deduced for the selection of the appropriate extraction protocol according to the specific soil properties, the nucleic acid of interest, and the target organisms.}, }
@article {pmid26894448, year = {2016}, author = {Flury, P and Aellen, N and Ruffner, B and Péchy-Tarr, M and Fataar, S and Metla, Z and Dominguez-Ferreras, A and Bloemberg, G and Frey, J and Goesmann, A and Raaijmakers, JM and Duffy, B and Höfte, M and Blom, J and Smits, TH and Keel, C and Maurhofer, M}, title = {Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics.}, journal = {The ISME journal}, volume = {10}, number = {10}, pages = {2527-2542}, pmid = {26894448}, issn = {1751-7370}, mesh = {Animals ; Genomics ; Host Specificity ; Larva/microbiology ; Lepidoptera/*microbiology ; Phylogeny ; Plants/*microbiology ; Pseudomonas/*genetics/isolation &amp; purification/*pathogenicity/physiology ; Virulence ; }, abstract = {Bacteria of the genus Pseudomonas occupy diverse environments. The Pseudomonas fluorescens group is particularly well-known for its plant-beneficial properties including pathogen suppression. Recent observations that some strains of this group also cause lethal infections in insect larvae, however, point to a more versatile ecology of these bacteria. We show that 26 P. fluorescens group strains, isolated from three continents and covering three phylogenetically distinct sub-clades, exhibited different activities toward lepidopteran larvae, ranging from lethal to avirulent. All strains of sub-clade 1, which includes Pseudomonas chlororaphis and Pseudomonas protegens, were highly insecticidal regardless of their origin (animals, plants). Comparative genomics revealed that strains in this sub-clade possess specific traits allowing a switch between plant- and insect-associated lifestyles. We identified 90 genes unique to all highly insecticidal strains (sub-clade 1) and 117 genes common to all strains of sub-clade 1 and present in some moderately insecticidal strains of sub-clade 3. Mutational analysis of selected genes revealed the importance of chitinase C and phospholipase C in insect pathogenicity. The study provides insight into the genetic basis and phylogenetic distribution of traits defining insecticidal activity in plant-beneficial pseudomonads. Strains with potent dual activity against plant pathogens and herbivorous insects have great potential for use in integrated pest management for crops.}, }
@article {pmid26894446, year = {2016}, author = {Courtens, EN and Spieck, E and Vilchez-Vargas, R and Bodé, S and Boeckx, P and Schouten, S and Jauregui, R and Pieper, DH and Vlaeminck, SE and Boon, N}, title = {A robust nitrifying community in a bioreactor at 50 °C opens up the path for thermophilic nitrogen removal.}, journal = {The ISME journal}, volume = {10}, number = {9}, pages = {2293-2303}, pmid = {26894446}, issn = {1751-7370}, mesh = {Ammonia/metabolism ; Archaea/*metabolism ; Autotrophic Processes ; Bacteria/*metabolism ; Bioreactors/*microbiology ; DNA, Ribosomal/chemistry/genetics ; Fertilizers ; High-Throughput Nucleotide Sequencing ; Hot Temperature ; Nitrification ; Nitrites/metabolism ; Nitrogen/*metabolism ; Phylogeny ; Sequence Analysis, DNA ; Soil Microbiology ; Wastewater/*chemistry ; }, abstract = {The increasing production of nitrogen-containing fertilizers is crucial to meet the global food demand, yet high losses of reactive nitrogen associated with the food production/consumption chain progressively deteriorate the natural environment. Currently, mesophilic nitrogen-removing microbes eliminate nitrogen from wastewaters. Although thermophilic nitrifiers have been separately enriched from natural environments, no bioreactors are described that couple these processes for the treatment of nitrogen in hot wastewaters. Samples from composting facilities were used as inoculum for the batch-wise enrichment of thermophilic nitrifiers (350 days). Subsequently, the enrichments were transferred to a bioreactor to obtain a stable, high-rate nitrifying process (560 days). The community contained up to 17% ammonia-oxidizing archaea (AOAs) closely related to 'Candidatus Nitrososphaera gargensis', and 25% nitrite-oxidizing bacteria (NOBs) related to Nitrospira calida. Incorporation of (13)C-derived bicarbonate into the respective characteristic membrane lipids during nitrification supported their activity as autotrophs. Specific activities up to 198±10 and 894±81 mg N g(-1) VSS per day for AOAs and NOBs were measured, where NOBs were 33% more sensitive to free ammonia. The NOBs were extremely sensitive to free nitrous acid, whereas the AOAs could only be inhibited by high nitrite concentrations, independent of the free nitrous acid concentration. The observed difference in product/substrate inhibition could facilitate the development of NOB inhibition strategies to achieve more cost-effective processes such as deammonification. This study describes the enrichment of autotrophic thermophilic nitrifiers from a nutrient-rich environment and the successful operation of a thermophilic nitrifying bioreactor for the first time, facilitating opportunities for thermophilic nitrogen removal biotechnology.}, }
@article {pmid26893611, year = {2016}, author = {Lai, B and Yu, S and Bernhardt, PV and Rabaey, K and Virdis, B and Krömer, JO}, title = {Anoxic metabolism and biochemical production in Pseudomonas putida F1 driven by a bioelectrochemical system.}, journal = {Biotechnology for biofuels}, volume = {9}, number = {}, pages = {39}, pmid = {26893611}, issn = {1754-6834}, abstract = {BACKGROUND: Pseudomonas putida is a promising host for the bioproduction of chemicals, but its industrial applications are significantly limited by its obligate aerobic character. The aim of this paper is to empower the anoxic metabolism of wild-type Pseudomonas putida to enable bioproduction anaerobically, with the redox power from a bioelectrochemical system (BES).<br><br>RESULTS: The obligate aerobe Pseudomonas putida F1 was able to survive and produce almost exclusively 2-Keto-gluconate from glucose under anoxic conditions due to redox balancing with electron mediators in a BES. 2-Keto-gluconate, a precursor for industrial anti-oxidant production, was produced at an overall carbon yield of over 90&#xa0;% based on glucose. Seven different mediator compounds were tested, and only those with redox potential above 0.207&#xa0;V (vs standard hydrogen electrode) showed interaction with the cells. The productivity increased with the increasing redox potential of the mediator, indicating this was a key factor affecting the anoxic production process. P. putida cells survived under anaerobic conditions, and limited biofilm formation could be observed on the anode's surface. Analysis of the intracellular pools of ATP, ADP and AMP showed that cells had an increased adenylate energy charge suggesting that cells were able to generate energy using the anode as terminal electron acceptor. The analysis of NAD(H) and NADP(H) showed that in the presence of specific extracellular electron acceptors, the NADP(H) pool was more oxidised, while the NAD(H) pool was unchanged. This implies a growth limitation under anaerobic conditions due to a shortage of NADPH and provides a way to limit biomass formation, while allowing cell maintenance and catalysis at high purity and yield.<br><br>CONCLUSIONS: For the first time, this study proved the principle that a BES-driven bioconversion of glucose can be achieved for a wild-type obligate aerobe. This non-growth bioconversion was in high yields, high purity and also could deliver the necessary metabolic energy for cell maintenance. By combining this approach with metabolic engineering strategies, this could prove to be a powerful new way to produce bio-chemicals and fuels from renewables in both high yield and high purity.}, }
@article {pmid26893142, year = {2016}, author = {Zhang, Q and De Clippeleir, H and Su, C and Al-Omari, A and Wett, B and Vlaeminck, SE and Murthy, S}, title = {Deammonification for digester supernatant pretreated with thermal hydrolysis: overcoming inhibition through process optimization.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {12}, pages = {5595-5606}, doi = {10.1007/s00253-016-7368-0}, pmid = {26893142}, issn = {1432-0614}, mesh = {*Ammonium Compounds ; Anaerobiosis ; Bacteria/*metabolism ; Bioreactors ; *Denitrification ; Hydrolysis ; Oxygen ; Sewage/*chemistry/microbiology ; Temperature ; Waste Disposal, Fluid/methods ; Wastewater ; }, abstract = {The thermal hydrolysis process (THP) has been proven to be an excellent pretreatment step for an anaerobic digester (AD), increasing biogas yield and decreasing sludge disposal. The goal of this work was to optimize deammonification for efficient nitrogen removal despite the inhibition effects caused by the organics present in the THP-AD sludge filtrate (digestate). Two sequencing batch reactors were studied treating conventional digestate and THP-AD digestate, respectively. Improved process control based on higher dissolved oxygen set-point (1 mg O2/L) and longer aeration times could achieve successful treatment of THP-AD digestate. This increased set-point could overcome the inhibition effect on aerobic ammonium-oxidizing bacteria (AerAOB), potentially caused by particulate and colloidal organics. Moreover, based on the mass balance, anoxic ammonium-oxidizing bacteria (AnAOB) contribution to the total nitrogen removal decreased from 97 ± 1 % for conventional to 72 ± 5 % for THP-AD digestate treatment, but remained stable by selective AnAOB retention using a vibrating screen. Overall, similar total nitrogen removal rates of 520 ± 28 mg N/L/day at a loading rate of 600 mg N/L/day were achieved in the THP-AD reactor compared to the conventional digestate treatment operating at low dissolved oxygen (DO) (0.38 ± 0.10 mg O2/L).}, }
@article {pmid26888694, year = {2016}, author = {Sankhyan, A and Sharma, C and Dutta, D and Sharma, T and Chosdol, K and Wakita, T and Watashi, K and Awasthi, A and Acharya, SK and Khanna, N and Tiwari, A and Sinha, S}, title = {Inhibition of preS1-hepatocyte interaction by an array of recombinant human antibodies from naturally recovered individuals.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {21240}, pmid = {26888694}, issn = {2045-2322}, mesh = {Antibodies, Neutralizing/*immunology/pharmacology ; Antibodies, Viral/*immunology/pharmacology ; Hep G2 Cells ; *Hepatitis B Surface Antigens/immunology ; Hepatitis B virus/*immunology ; Hepatocytes/*immunology/virology ; Humans ; *Protein Precursors/antagonists &amp; inhibitors/immunology ; Recombinant Proteins/immunology/pharmacology ; Single-Chain Antibodies/*immunology/pharmacology ; }, abstract = {Neutralizing monoclonal antibodies are being found to be increasingly useful in viral infections. In hepatitis B infection, antibodies are proven to be useful for passive prophylaxis. The preS1 region (21-47a.a.) of HBV contains the viral hepatocyte-binding domain crucial for its attachment and infection of hepatocytes. Antibodies against this region are neutralizing and are best suited for immune-based neutralization of HBV, especially in view of their not recognizing decoy particles. Anti-preS1 (21-47a.a.) antibodies are present in serum of spontaneously recovered individuals. We generated a phage-displayed scFv library using circulating lymphocytes from these individuals and selected four preS1-peptide specific scFvs with markedly distinct sequences from this library. All the antibodies recognized the blood-derived and recombinant preS1 containing antigens. Each scFv showed a discrete binding signature, interacting with different amino acids within the preS1-peptide region. Ability to prevent binding of the preS1 protein (N-terminus 60a.a.) to HepG2 cells stably expressing hNTCP (HepG2-hNTCP-C4 cells), the HBV receptor on human hepatocytes was taken as a surrogate marker for neutralizing capacity. These antibodies inhibited preS1-hepatocyte interaction individually and even better in combination. Such a combination of potentially neutralizing recombinant antibodies with defined specificities could be used for preventing/managing HBV infections, including those by possible escape mutants.}, }
@article {pmid26888523, year = {2016}, author = {Rangel, LM and Ger, KA and Silva, LH and Soares, MC and Faassen, EJ and Lürling, M}, title = {Toxicity Overrides Morphology on Cylindrospermopsis raciborskii Grazing Resistance to the Calanoid Copepod Eudiaptomus gracilis.}, journal = {Microbial ecology}, volume = {71}, number = {4}, pages = {835-844}, pmid = {26888523}, issn = {1432-184X}, mesh = {Animals ; Copepoda/*physiology ; Cylindrospermopsis/chemistry/cytology/*metabolism ; Feeding Behavior/physiology ; Fresh Water/*microbiology ; Lakes/microbiology ; Phytoplankton/physiology ; Saxitoxin/biosynthesis/toxicity ; Zooplankton/physiology ; }, abstract = {Toxicity and morphology may function as defense mechanisms of bloom-forming cyanobacteria against zooplankton grazing. Yet, the relative importance of each of these factors and their plasticity remains poorly known. We tested the effects of chemical and morphological traits of the bloom-forming cyanobacterium Cylindrospermopsis raciborskii on the feeding response of the selective feeder Eudiaptomus gracilis (Calanoida, Copepoda), using a saxitoxin-producing strain (STX+) and a non-saxitoxin (STX-)-producing strain as food. From these two chemotypes, we established cultures of three different morphotypes that differed in filament length (short, medium, and long) by incubating the strains at 17, 25, and 32 °C. We hypothesized that the inhibitory effects of saxitoxins determine the avoidance of C. raciborskii, and that morphology would only become relevant in the absence of saxitoxins. Temperature affected two traits: higher temperature resulted in significantly shorter filaments in both strains and led to much higher toxin contents in the STX+ strain (1.7 μg eq STX L(-1) at 17 °C, 7.9 μg eq STX L(-1) at 25 °C, and 25.1 μg eq STX L(-1) at 32 °C). Copepods strongly reduced the ingestion of the STX+ strain in comparison with STX- cultures, regardless of filament length. Conversely, consumption of shorter filaments was significantly higher in the STX- strain. The great plasticity of morphological and chemical traits of C. raciborskii and their resultant contrasting effects on the feeding behavior of zooplankton might explain the success of this cyanobacterium in a variety of aquatic environments.}, }
@article {pmid26887246, year = {2016}, author = {Faten, K and Hamida, K and Soumya, el A and Saad, IS and Hasna, M and Hassan, L and Moktar, H}, title = {Lactobacillus plantarum: Effect of a protective biofilm on the surface of olives during storage.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {47}, number = {1}, pages = {202-209}, pmid = {26887246}, issn = {1678-4405}, mesh = {*Bacterial Adhesion ; Biofilms/*growth &amp; development ; Electron Transport ; *Food Storage ; Hydrophobic and Hydrophilic Interactions ; Lactobacillus plantarum/*physiology ; Microscopy, Electron, Scanning ; Olea/*microbiology ; Surface Properties ; Yeasts/physiology ; }, abstract = {The aim of the present study was to investigate the effect of Lactobacillus plantarum adhesion to the surface of olives during storage through studying the interaction between the surfaces of the olives and L. plantarum. The results showed that the total number of adherent L. plantarum increased exponentially from 1.2×10(6) to 1.3×10(8)cfu/g. Images obtained using environmental scanning electron microscopy (ESEM) after 4 days of storage revealed that the olive surface was covered with a uniform and compact biofilm constituted of L. plantarum and yeast. Physicochemical analysis of surface of L. plantarum revealed that it was hydrophilic (Giwi>0mJ/m(2)). The surface of the olives also appeared to be hydrophilic (Giwi=3.28mJ/m(2)). The electron-donor characteristics of the surfaces of L. plantarum and olive were γ(-)=53.1mJ/m(2) and γ(-)=28.1mJ/m(2), respectively. The formation of a protective biofilm of L. plantarum increased the hydrophilicity (from 3.28 to 46.14mJ/m(2)) and the electron-donor capacity (from 28.1 to 67.2mJ/m(2)) of the olive surface by 1 day of storage. Analysis of the impact of the biofilm that formed on the surface of the olives during storage showed a reduction in the content of undesirable planktonic microorganisms, such as fungi, which could have occurred due to competition for nutrients and oxygen or modifications in the physicochemical properties of the olives. Thus, coating the surface of olives with a natural material, such as L. plantarum, may be a first step in developing strategies to prevent their microbial colonization.}, }
@article {pmid26885935, year = {2016}, author = {Kosina, SM and Danielewicz, MA and Mohammed, M and Ray, J and Suh, Y and Yilmaz, S and Singh, AK and Arkin, AP and Deutschbauer, AM and Northen, TR}, title = {Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism.}, journal = {ACS synthetic biology}, volume = {5}, number = {7}, pages = {569-576}, doi = {10.1021/acssynbio.5b00236}, pmid = {26885935}, issn = {2161-5063}, mesh = {Amino Acids/metabolism ; Coculture Techniques ; Escherichia coli/genetics/*physiology ; Escherichia coli Proteins/genetics/metabolism ; Metabolomics/*methods ; Microbial Consortia/physiology ; Mutation ; Reproducibility of Results ; *Symbiosis ; Synthetic Biology/*methods ; Zymomonas/metabolism/*physiology ; }, abstract = {Synthetic microbial ecology has the potential to enhance the productivity and resiliency of biotechnology processes compared to approaches using single isolates. Engineering microbial consortia is challenging; however, one approach that has attracted significant attention is the creation of synthetic obligate mutualism using auxotrophic mutants that depend on each other for exchange or cross-feeding of metabolites. Here, we describe the integration of mutant library fitness profiling with mass spectrometry based exometabolomics as a method for constructing synthetic mutualism based on cross-feeding. Two industrially important species lacking known ecological interactions, Zymomonas mobilis and Escherichia coli, were selected as the test species. Amino acid exometabolites identified in the spent medium of Z. mobilis were used to select three corresponding E. coli auxotrophs (proA, pheA and IlvA), as potential E. coli counterparts for the coculture. A pooled mutant fitness assay with a Z. mobilis transposon mutant library was used to identify mutants with improved growth in the presence of E. coli. An auxotroph mutant in a gene (ZMO0748) with sequence similarity to cysteine synthase A (cysK), was selected as the Z. mobilis counterpart for the coculture. Exometabolomic analysis of spent E. coli medium identified glutathione related metabolites as potentially available for rescue of the Z. mobilis cysteine synthase mutant. Three sets of cocultures between the Z. mobilis auxotroph and each of the three E. coli auxotrophs were monitored by optical density for growth and analyzed by flow cytometry to confirm high cell counts for each species. Taken together, our methods provide a technological framework for creating synthetic mutualisms combining existing screening based methods and exometabolomics for both the selection of obligate mutualism partners and elucidation of metabolites involved in auxotroph rescue.}, }
@article {pmid26884466, year = {2016}, author = {Aliyu, H and De Maayer, P and Cowan, D}, title = {The genome of the Antarctic polyextremophile Nesterenkonia sp. AN1 reveals adaptive strategies for survival under multiple stress conditions.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {4}, pages = {fiw032}, doi = {10.1093/femsec/fiw032}, pmid = {26884466}, issn = {1574-6941}, mesh = {Antarctic Regions ; Bacterial Proteins/biosynthesis/genetics ; Cold Shock Proteins and Peptides/*genetics ; Cold-Shock Response/*genetics ; Energy Metabolism/*genetics/physiology ; Gene Expression Profiling ; Genome, Bacterial/genetics ; Heat-Shock Proteins/biosynthesis/genetics ; Isocitrate Lyase/biosynthesis/genetics ; Malate Synthase/biosynthesis/genetics ; Micrococcaceae/*genetics/isolation &amp; purification/metabolism ; Osmotic Pressure/physiology ; Oxidative Stress/*genetics ; *Soil Microbiology ; Superoxide Dismutase/biosynthesis/genetics ; }, abstract = {Nesterenkonia sp. AN1 is a polyextremophile isolated from Antarctic desert soil. Genomic analyses and genome comparisons with three mesophilic Nesterenkonia strains indicated that the unique genome fraction of Nesterenkonia sp. AN1 contains adaptive features implicated in the response to cold stress including modulation of membrane fluidity as well as response to cold-associated osmotic and oxidative stress. The core genome also encodes a number of putative cold stress response proteins. RNA-Seq-based transcriptome analyses of Nesterenkonia sp. AN1 grown at 5ºC and 21°C showed that there was significant induction of transcripts that code for antioxidants at 5ºC, demonstrated by the upregulation of sodA, bcp and bpoA2. There was also overexpression of universal stress protein genes related to uspA, along with genes encoding other characterized cold stress features. Genes encoding the two key enzymes of the glyoxylate cycle, isocitrate lyase (ICL) and malate synthase (AceB) were induced at 5ºC, suggesting possible adaptation strategies for energy metabolism in cold habitats. These genomic features may contribute to the survival of Nesterenkonia sp. AN1 in arid Antarctic soils.}, }
@article {pmid26884358, year = {2016}, author = {You, KG and Bong, CW and Lee, CW}, title = {Antibiotic resistance and plasmid profiling of Vibrio spp. in tropical waters of Peninsular Malaysia.}, journal = {Environmental monitoring and assessment}, volume = {188}, number = {3}, pages = {171}, doi = {10.1007/s10661-016-5163-0}, pmid = {26884358}, issn = {1573-2959}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/*genetics ; *Environmental Monitoring ; Malaysia ; Microbial Sensitivity Tests ; Plasmids ; Seawater/*microbiology ; Vibrio/classification/*genetics ; }, abstract = {Vibrio species isolated from four different sampling stations in the west coast of Peninsular Malaysia were screened for their antimicrobial resistance and plasmid profiles. A total of 138 isolates belonging to 15 different species were identified. Vibrio campbellii, V. parahaemolyticus, V. harveyi, and V. tubiashii were found to predominance species at all stations. High incidence of erythromycin, ampicillin, and mecillinam resistance was observed among the Vibrio isolates. In contrast, resistance against aztreonam, cefepime, streptomycin, sulfamethoxazole, and sulfonamides was low. All the Vibrio isolates in this study were found to be susceptible to imipenem, norfloxacin, ofloxacin, chloramphenicol, trimethoprim/sulfamethoxazole, and oxytetracycline. Ninety-five percent of the Vibrio isolates were resistant to one or more different classes of antibiotic, and 20 different resistance antibiograms were identified. Thirty-two distinct plasmid profiles with molecular weight ranging from 2.2 to 24.8 kb were detected among the resistance isolates. This study showed that multidrug-resistant Vibrio spp. were common in the aquatic environments of west coast of Peninsular Malaysia.}, }
@article {pmid26883131, year = {2016}, author = {Stone, BW and Jackson, CR}, title = {Biogeographic Patterns Between Bacterial Phyllosphere Communities of the Southern Magnolia (Magnolia grandiflora) in a Small Forest.}, journal = {Microbial ecology}, volume = {71}, number = {4}, pages = {954-961}, pmid = {26883131}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/*growth &amp; development/isolation &amp; purification ; Bacterial Physiological Phenomena ; Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; *Forests ; Magnolia/*microbiology ; Mississippi ; Phylogeny ; Phylogeography ; Plant Leaves/microbiology ; RNA, Ribosomal, 16S/genetics ; Trees/microbiology ; }, abstract = {The phyllosphere presents a unique system of discrete and easily replicable surfaces colonized primarily by bacteria. However, the biogeography of bacteria in the phyllosphere is little understood, especially at small to intermediate scales. Bacterial communities on the leaves of 91 southern magnolia (Magnolia grandiflora) trees 1-452 m apart in a small forest plot were analyzed and fragments of the 16S ribosomal RNA (rRNA) gene sequenced using the Illumina platform. Assemblages were dominated by members of the Alphaproteobacteria, Bacteroidetes, and Acidobacteria. Patterns in community composition were measured by both relative abundance (theta) and presence-absence (Jaccard) dissimilarity metrics. Distance-based Moran's eigenvector map analyses of the distance-decay relationship found a significant, positive relationship between each dissimilarity metric and significant eigenfunctions derived from geographic distance between trees, indicating trees that were closer together had more similar bacterial phyllosphere communities. Indirect gradient analyses revealed that several environmental parameters (canopy cover, tree elevation, and the slope and aspect of the ground beneath trees) were significantly related to multivariate ordination scores based on relative bacterial sequence abundances; however, these relationships were not significant when looking at the incidence of bacterial taxa. This suggests that bacterial growth and abundance in the phyllosphere is shaped by different assembly mechanisms than bacterial presence or absence. More broadly, this study demonstrates that the distance-decay relationship applies to phyllosphere communities at local scales, and that environmental parameters as well as neutral forces may both influence spatial patterns in the phyllosphere.}, }
@article {pmid26882962, year = {2016}, author = {Xue, B and Xie, J and Huang, J and Chen, L and Gao, L and Ou, S and Wang, Y and Peng, X}, title = {Plant polyphenols alter a pathway of energy metabolism by inhibiting fecal Bacteroidetes and Firmicutes in vitro.}, journal = {Food &amp; function}, volume = {7}, number = {3}, pages = {1501-1507}, doi = {10.1039/c5fo01438g}, pmid = {26882962}, issn = {2042-650X}, mesh = {Bacteroidetes/genetics/growth &amp; development/*metabolism ; Energy Metabolism/*drug effects ; Feces/*microbiology ; Fermentation ; Firmicutes/genetics/growth &amp; development/*metabolism ; Gastrointestinal Microbiome/drug effects ; Gastrointestinal Tract/metabolism/microbiology ; Humans ; Oligosaccharides/metabolism ; Plant Extracts/*pharmacology ; Polyphenols/*pharmacology ; }, abstract = {The function of plant polyphenols in controlling body weight has been in focus for a long time. The aim of this study was to investigate the effect of plant polyphenols on fecal microbiota utilizing oligosaccharides. Three plant polyphenols, quercetin, catechin and puerarin, were added into liquid media for fermenting for 24 h. The pH values, OD600 of the cultures and the content of carbohydrates at 0, 6, 10, 14, 18 and 24 h were determined. The abundance of Bacteroidetes and Firmicutes in each culture was quantified with qPCR after 10 h of fermentation, and the bacterial composition was analyzed using the software Quantitative Insights Into Microbial Ecology. The results revealed that all three plant polyphenols could significantly inhibit the growth of Bacteroidetes (P < 0.01) and Firmicutes (P < 0.01) while at the same time down-regulate the ratio of Bacteroidetes to Firmicutes (P < 0.01). But the fecal bacteria could maintain the ability to hydrolyze fructo-oligosaccharide (FOS) in vitro. Among the tested polyphenols, catechin presented the most intense inhibitory activity towards the growth of Bacteroidetes and Firmicutes, and quercetin was the second. Only the samples with catechin had a significantly lower energy metabolism (P < 0.05). In conclusion, plant polyphenols can change the pathway of degrading FOS or even energy metabolism in vivo by altering gut microbiota composition. It may be one of the mechanisms in which plant polyphenols can lead to body weight loss. It's the first report to study in vitro gastrointestinal microbiota fermenting dietary fibers under the intervention of plant polyphenols.}, }
@article {pmid26882268, year = {2016}, author = {Zilles, JL and Rodríguez, LF and Bartolerio, NA and Kent, AD}, title = {Microbial community modeling using reliability theory.}, journal = {The ISME journal}, volume = {10}, number = {8}, pages = {1809-1814}, pmid = {26882268}, issn = {1751-7370}, mesh = {Bioreactors/microbiology ; Ecosystem ; *Microbial Consortia ; *Models, Biological ; Reproducibility of Results ; }, abstract = {Linking microbial community composition with the corresponding ecosystem functions remains challenging. Because microbial communities can differ in their functional responses, this knowledge gap limits ecosystem assessment, design and management. To develop models that explicitly incorporate microbial populations and guide efforts to characterize their functional differences, we propose a novel approach derived from reliability engineering. This reliability modeling approach is illustrated here using a microbial ecology dataset from denitrifying bioreactors. Reliability modeling is well-suited for analyzing the stability of complex networks composed of many microbial populations. It could also be applied to evaluate the redundancy within a particular biochemical pathway in a microbial community. Reliability modeling allows characterization of the system's resilience and identification of failure-prone functional groups or biochemical steps, which can then be targeted for monitoring or enhancement. The reliability engineering approach provides a new perspective for unraveling the interactions between microbial community diversity, functional redundancy and ecosystem services, as well as practical tools for the design and management of engineered ecosystems.}, }
@article {pmid26879941, year = {2018}, author = {Mittelman, MW and Jones, ADG}, title = {A Pure Life: The Microbial Ecology of High Purity Industrial Waters.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {9-18}, pmid = {26879941}, issn = {1432-184X}, mesh = {Bacteria/cytology/growth &amp; development ; *Bacterial Physiological Phenomena ; Biofilms/growth &amp; development ; Corrosion ; Delivery of Health Care ; *Ecology ; Electrochemistry ; Environment ; Extreme Environments ; Fresh Water/*microbiology ; Hospitals ; *Industrial Microbiology ; Industrial Waste ; Nuclear Power Plants ; Nutrients ; Semiconductors ; Sulfur-Reducing Bacteria ; *Water Microbiology ; Waterborne Diseases ; }, abstract = {The microbial ecology of various natural environments has been an active area of research since the earlier part of the twentieth century. Remote and sometimes extreme environments such as the deep ocean and the deep terrestrial subsurface have revealed a remarkable array of microorganisms. The majority of these environments are nutrient limited, and microorganisms-principally, bacteria-have developed a number of survival strategies that enable their survival and, in some cases, replication. While planktonic microorganisms exist in oligotrophic environments, the predominant mode of survival and growth is associated with biofilms. There are a number of similarities between the physicochemistry of industrial water systems and some natural aquatic ecosystems, and these similarities extend to the microbial populations and the survival mechanisms that are employed. The "starvation-survival" mechanisms, including biofilm formation, may be associated with deleterious effects on industrial water systems. These effects include heat transfer inhibition, microbially influenced corrosion, and contamination of various products manufactured in a wide array of industries. Biological fouling of industrial water systems has significant direct and indirect (through antimicrobial chemical applications) impacts on engineered materials and on the etiology of some waterborne diseases. This review provides an overview of the microbial ecology of purified waters and discusses the impacts of biological activity on industrial systems.}, }
@article {pmid26879940, year = {2016}, author = {Wymore, AS and Liu, CM and Hungate, BA and Schwartz, E and Price, LB and Whitham, TG and Marks, JC}, title = {The Influence of Time and Plant Species on the Composition of the Decomposing Bacterial Community in a Stream Ecosystem.}, journal = {Microbial ecology}, volume = {71}, number = {4}, pages = {825-834}, pmid = {26879940}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; *Ecosystem ; Lignin/chemistry ; Microbial Consortia ; Phylogeny ; Plant Leaves/chemistry/microbiology ; Plants/*chemistry/*microbiology ; Rivers/*chemistry/*microbiology ; Soil Microbiology ; Trees ; Utah ; Water Microbiology ; }, abstract = {Foliar chemistry influences leaf decomposition, but little is known about how litter chemistry affects the assemblage of bacterial communities during decomposition. Here we examined relationships between initial litter chemistry and the composition of the bacterial community in a stream ecosystem. We incubated replicated genotypes of Populus fremontii and P. angustifolia leaf litter that differ in percent tannin and lignin, then followed changes in bacterial community composition during 28 days of decomposition using 16S rRNA gene-based pyrosequencing. Using a nested experimental design, the majority of variation in bacterial community composition was explained by time (i.e., harvest day) (R(2) = 0.50). Plant species, nested within harvest date, explained a significant but smaller proportion of the variation (R(2) = 0.03). Significant differences in community composition between leaf species were apparent at day 14, but no significant differences existed among genotypes. Foliar chemistry correlated significantly with community composition at day 14 (r = 0.46) indicating that leaf litter with more similar phytochemistry harbor bacterial communities that are alike. Bacteroidetes and β-proteobacteria dominated the bacterial assemblage on decomposing leaves, and Verrucomicrobia and α- and δ-proteobacteria became more abundant over time. After 14 days, bacterial diversity diverged significantly between leaf litter types with fast-decomposing P. fremontii hosting greater richness than slowly decomposing P. angustifolia; however, differences were no longer present after 28 days in the stream. Leaf litter tannin, lignin, and lignin: N ratios all correlated negatively with diversity. This work shows that the bacterial community on decomposing leaves in streams changes rapidly over time, influenced by leaf species via differences in genotype-level foliar chemistry.}, }
@article {pmid26879939, year = {2016}, author = {Staley, C and Gould, TJ and Wang, P and Phillips, J and Cotner, JB and Sadowsky, MJ}, title = {Sediments and Soils Act as Reservoirs for Taxonomic and Functional Bacterial Diversity in the Upper Mississippi River.}, journal = {Microbial ecology}, volume = {71}, number = {4}, pages = {814-824}, pmid = {26879939}, issn = {1432-184X}, mesh = {Bacteria/*classification/*genetics ; Biodiversity ; DNA, Bacterial/genetics ; Ecosystem ; Fresh Water/*microbiology ; Geologic Sediments/chemistry/*microbiology ; Minnesota ; Mississippi ; Rivers/*microbiology ; Soil/*chemistry ; }, abstract = {In this study, we utilized Illumina next-generation sequencing of 16S rDNA to characterize the bacterial communities in water, sediments, and soils at four sites along the Mississippi River and Minnesota River, in Minnesota, in order to evaluate community exchanges between these habitats. Communities in water and sediment were hypothesized to show greater taxonomic similarity than those in soil, while microbial communities in sediment and soil would show greater functional similarity. Habitat-specific communities showed significant differences in phylogenetic structure and β-diversity (P < 0.001), but site-specific differences in community structures within a single habitat type did not differ greatly (P ≥ 0.083). Community exchange among habitats generally influenced < 5% of the total community composition in a single sample, with the exception of the sediment community at the Minnesota River site, which contributed to a mean of 14% of the microbial community in the water column. Communities from all habitat types were significantly correlated with each other (r = 0.44-0.64, P ≤ 0.004). Furthermore, approximately 33% of the taxonomic units were found in all samples and comprised at least 40% of the bacterial community. Functional annotation of shotgun sequencing data revealed similar functional profiles for sediment and soil communities that were distinct from those in the water. Results of this study suggest that sediments, when disturbed, contribute significantly to bacterial communities in the water and that a core bacterial community may be supported in the soils and sediments. Furthermore, a high degree of functional redundancy results in similar functional profiles in sediment and soil communities.}, }
@article {pmid26877039, year = {2016}, author = {Margot, J and Lochmatter, S and Barry, DA and Holliger, C}, title = {Role of ammonia-oxidizing bacteria in micropollutant removal from wastewater with aerobic granular sludge.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {73}, number = {3}, pages = {564-575}, doi = {10.2166/wst.2015.514}, pmid = {26877039}, issn = {0273-1223}, mesh = {Aerobiosis ; Ammonia/metabolism ; Bacteria/*metabolism ; Bioreactors ; Nitrification ; Oxidation-Reduction ; Sewage/*chemistry ; Wastewater/*analysis ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Nitrifying wastewater treatment plants (WWTPs) are more efficient than non-nitrifying WWTPs to remove several micropollutants such as pharmaceuticals and pesticides. This may be related to the activity of nitrifying organisms, such as ammonia-oxidizing bacteria (AOBs), which could possibly co-metabolically oxidize micropollutants with their ammonia monooxygenase (AMO). The role of AOBs in micropollutant removal was investigated with aerobic granular sludge (AGS), a promising technology for municipal WWTPs. Two identical laboratory-scale AGS sequencing batch reactors (AGS-SBRs) were operated with or without nitrification (inhibition of AMOs) to assess their potential for micropollutant removal. Of the 36 micropollutants studied at 1 μg l(-1) in synthetic wastewater, nine were over 80% removed, but 17 were eliminated by less than 20%. Five substances (bisphenol A, naproxen, irgarol, terbutryn and iohexol) were removed better in the reactor with nitrification, probably due to co-oxidation catalysed by AMOs. However, for the removal of all other micropollutants, AOBs did not seem to play a significant role. Many compounds were better removed in aerobic condition, suggesting that aerobic heterotrophic organisms were involved in the degradation. As the AGS-SBRs did not favour the growth of such organisms, their potential for micropollutant removal appeared to be lower than that of conventional nitrifying WWTPs.}, }
@article {pmid26876007, year = {2016}, author = {Waud, M and Wiegand, T and Brys, R and Lievens, B and Jacquemyn, H}, title = {Nonrandom seedling establishment corresponds with distance-dependent decline in mycorrhizal abundance in two terrestrial orchids.}, journal = {The New phytologist}, volume = {211}, number = {1}, pages = {255-264}, doi = {10.1111/nph.13894}, pmid = {26876007}, issn = {1469-8137}, support = {260601/ERC_/European Research Council/International ; }, mesh = {Belgium ; Mycorrhizae/genetics/*physiology ; Orchidaceae/*growth &amp; development/*microbiology ; Plant Roots/microbiology ; Seedlings/*growth &amp; development ; *Soil Microbiology ; }, abstract = {In plant species that critically rely on mycorrhizal symbionts for germination and seedling establishment, distance-dependent decline of mycorrhizal fungi in the soil can be hypothesized to lead to significant spatial clustering as a result of nonrandom spatial patterns of seedling establishment. To test this hypothesis, we investigated the abundance and distribution of mycorrhizal fungi in the soil and how they relate to spatial patterns of adults and seedling recruitment in two related orchid species. We combined assessments of spatial variation in fungal abundance using quantitative PCR (qPCR) with spatial point pattern analyses based on long-term demographic data and cluster point process models. qPCR analyses showed that fungal abundance declined rapidly with distance from the adult host plants. Spatial point pattern analyses showed that successful recruitment in both species was clustered significantly around adult plants and that the decline in the neighborhood density of recruits around adults coincided with the decline of fungal abundance around adult plants. Overall, these results indicate that the distribution and abundance of fungal associates in the soil may have a strong impact on the aboveground distribution of its partner.}, }
@article {pmid26875750, year = {2016}, author = {Korenblum, E and Jiménez, DJ and van Elsas, JD}, title = {Succession of lignocellulolytic bacterial consortia bred anaerobically from lake sediment.}, journal = {Microbial biotechnology}, volume = {9}, number = {2}, pages = {224-234}, pmid = {26875750}, issn = {1751-7915}, mesh = {Anaerobiosis ; Bacteria, Anaerobic/*classification/genetics/*metabolism ; *Biota ; Biotransformation ; Carbon/metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; Lignin/*metabolism ; *Microbial Consortia ; Molecular Sequence Data ; Panicum/metabolism ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Anaerobic bacteria degrade lignocellulose in various anoxic and organically rich environments, often in a syntrophic process. Anaerobic enrichments of bacterial communities on a recalcitrant lignocellulose source were studied combining polymerase chain reaction-denaturing gradient gel electrophoresis, amplicon sequencing of the 16S rRNA gene and culturing. Three consortia were constructed using the microbiota of lake sediment as the starting inoculum and untreated switchgrass (Panicum virgatum) (acid or heat) or treated (with either acid or heat) as the sole source of carbonaceous compounds. Additionally, nitrate was used in order to limit sulfate reduction and methanogenesis. Bacterial growth took place, as evidenced from 3 to 4 log unit increases in the 16S rRNA gene copy numbers as well as direct cell counts through three transfers on cleaned and reused substrate placed in fresh mineral medium. After 2 days, Aeromonas bestiarum-like organisms dominated the enrichments, irrespective of the substrate type. One month later, each substrate revealed major enrichments of organisms affiliated with different species of Clostridium. Moreover, only the heat-treated substrate selected Dysgonomonas capnocytophagoides-affiliated bacteria (Bacteroidetes). Towards the end of the experiment, members of the Proteobacteria (Aeromonas, Rhizobium and/or Serratia) became dominant in all three types of substrates. A total of 160 strains was isolated from the enrichments. Most of the strains tested (78%) were able to grow anaerobically on carboxymethyl cellulose and xylan. The final consortia yield attractive biological tools for the depolymerization of recalcitrant lignocellulosic materials and are proposed for the production of precursors of biofuels.}, }
@article {pmid26875613, year = {2016}, author = {Herrero, ER and Slomka, V and Bernaerts, K and Boon, N and Hernandez-Sanabria, E and Passoni, BB and Quirynen, M and Teughels, W}, title = {Antimicrobial effects of commensal oral species are regulated by environmental factors.}, journal = {Journal of dentistry}, volume = {47}, number = {}, pages = {23-33}, doi = {10.1016/j.jdent.2016.02.007}, pmid = {26875613}, issn = {1879-176X}, mesh = {Aggregatibacter actinomycetemcomitans/growth &amp; development/metabolism/*physiology ; Antibiosis ; Bacteriocins/biosynthesis ; Humans ; Hydrogen Peroxide/metabolism/pharmacology ; Mouth/*microbiology ; Periodontium/microbiology ; Porphyromonas gingivalis/growth &amp; development/metabolism/*physiology ; Prevotella intermedia/drug effects/growth &amp; development/metabolism ; Streptococcus/growth &amp; development/metabolism/*physiology ; Symbiosis/*physiology ; }, abstract = {OBJECTIVES: The objectives of this study are to identify oral commensal species which can inhibit the growth of the main periodontopathogens, to determine the antimicrobial substances involved in these inhibitory activities and to evaluate the influence of environmental factors on the magnitude of these inhibitions.<br><br>METHODS: The spotting technique was used to quantify the capacity of 13 commensal species to inhibit the growth of Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis and Prevotella intermedia. By altering experimental conditions (distance between spots and size of spots and concentration of commensal and pathogen) as well as environmental factors (inoculation sequence, oxygen and nutrition availability) the influence of these factors was evaluated. Additionally, the mechanism of inhibition was elucidated by performing inhibition experiments in the presence of peroxidase, trypsin and pepsin and by evaluating acid production.<br><br>RESULTS: Streptococcus sanguinis, Streptococcus cristatus, Streptococcus gordonii, Streptococcus parasanguinis, Streptococcus mitis and Streptococcus oralis significantly inhibit the growth of all pathogens. The volume of the spots and concentration of the commensal have a significant positive correlation with the amount of inhibition whereas distance between the spots and concentration of the pathogen reduced the amount of inhibition. Inhibition is only observed when the commensal species are inoculated 24h before the pathogen and is more pronounced under aerobic conditions. Hydrogen peroxide production by the commensal is the main mechanism of inhibition.<br><br>CONCLUSION: Bacterial antagonism is species specific and depending on experimental as well as environmental conditions. Blocking hydrogen peroxide production neutralizes the inhibitory effect.<br><br>CLINICAL SIGNIFICANCE: Identifying beneficial oral bacteria and understanding how they inhibit pathogens might help to unravel the mechanisms behind dysbiotic oral diseases. In this context, this study points towards an important role for hydrogen peroxide. The latter might lead in the future to novel preventive strategies for oral health based on improving the antimicrobial properties of commensal oral bacteria.}, }
@article {pmid26874778, year = {2016}, author = {Kim, YM and Park, H and Chandran, K}, title = {Nitrification inhibition by hexavalent chromium Cr(VI)--Microbial ecology, gene expression and off-gas emissions.}, journal = {Water research}, volume = {92}, number = {}, pages = {254-261}, doi = {10.1016/j.watres.2016.01.042}, pmid = {26874778}, issn = {1879-2448}, mesh = {Air Pollutants/*analysis ; Bacteria/drug effects/genetics ; Bioreactors/microbiology ; Chromium/*pharmacology ; Denaturing Gradient Gel Electrophoresis ; *Ecosystem ; Gene Expression Regulation, Bacterial/*drug effects ; Nitric Oxide/analysis ; Nitrification/drug effects/*genetics ; Nitrous Oxide/analysis ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The goal of this study was to investigate the responses in the physiology, microbial ecology and gene expression of nitrifying bacteria to imposition of and recovery from Cr(VI) loading in a lab-scale nitrification bioreactor. Exposure to Cr(VI) in the reactor strongly inhibited nitrification performance resulting in a parallel decrease in nitrate production and ammonia consumption. Cr(VI) exposure also led to an overall decrease in total bacterial concentrations in the reactor. However, the fraction of ammonia oxidizing bacteria (AOB) decreased to a greater extent than the fraction of nitrite oxidizing bacteria (NOB). In terms of functional gene expression, a rapid decrease in the transcript concentrations of amoA gene coding for ammonia oxidation in AOB was observed in response to the Cr(VI) shock. In contrast, transcript concentrations of the nxrA gene coding for nitrite oxidation in NOB were relatively unchanged compared to Cr(VI) pre-exposure levels. Therefore, Cr(VI) exposure selectively and directly inhibited activity of AOB, which indirectly resulted in substrate (nitrite) limitation to NOB. Significantly, trends in amoA expression preceded performance trends both during imposition of and recovery from inhibition. During recovery from the Cr(VI) shock, the high ammonia concentrations in the bioreactor resulted in an irreversible shift towards AOB populations, which are expected to be more competitive in high ammonia environments. An inadvertent impact during recovery was increased emission of nitrous oxide (N2O) and nitric oxide (NO), consistent with recent findings linking AOB activity and the production of these gases. Therefore, Cr(VI) exposure elicited multiple responses on the microbial ecology, gene expression and both aqueous and gaseous nitrogenous conversion in a nitrification process. A complementary interrogation of these multiple responses facilitated an understanding of both direct and indirect inhibitory impacts on nitrification.}, }
@article {pmid26872043, year = {2016}, author = {Dyksma, S and Bischof, K and Fuchs, BM and Hoffmann, K and Meier, D and Meyerdierks, A and Pjevac, P and Probandt, D and Richter, M and Stepanauskas, R and Mußmann, M}, title = {Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments.}, journal = {The ISME journal}, volume = {10}, number = {8}, pages = {1939-1953}, pmid = {26872043}, issn = {1751-7370}, support = {294757/ERC_/European Research Council/International ; }, mesh = {Australia ; Carbon/*metabolism ; *Carbon Cycle ; Europe ; Gammaproteobacteria/genetics/isolation &amp; purification/*metabolism ; Gene Expression Profiling ; Geography ; Geologic Sediments/*microbiology ; Metagenomics ; Oceans and Seas ; Oxidation-Reduction ; Sequence Analysis, DNA ; Sulfur/*metabolism ; }, abstract = {Marine sediments are the largest carbon sink on earth. Nearly half of dark carbon fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with (14)C-carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70-86% of dark carbon fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark carbon fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with (14)C-bicarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter, JTB255 and SSr clades) that made up >50% of dark carbon fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and carbon fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria. The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine carbon and sulfur cycles.}, }
@article {pmid26871557, year = {2016}, author = {Auguet, O and Pijuan, M and Borrego, CM and Gutierrez, O}, title = {Control of sulfide and methane production in anaerobic sewer systems by means of Downstream Nitrite Dosage.}, journal = {The Science of the total environment}, volume = {550}, number = {}, pages = {1116-1125}, doi = {10.1016/j.scitotenv.2016.01.130}, pmid = {26871557}, issn = {1879-1026}, abstract = {Bioproduction of hydrogen sulfide (H2S) and methane (CH4) under anaerobic conditions in sewer pipes causes detrimental effects on both sewer facilities and surrounding environment. Among the strategies used to mitigate the production of both compounds, the addition of nitrite (NO2(-)) has shown a greater long-term inhibitory effect compared with other oxidants such as nitrate or oxygen. The aim of this study was to determine the effectiveness of a new method, the Downstream Nitrite Dosage strategy (DNO2D), to control H2S and CH4 emissions in sewers. Treatment effectiveness was assessed on H2S and CH4 abatement on the effluent of a laboratory sewer pilot plant that mimics a full-scale anaerobic rising sewer. The experiment was divided in three different periods: system setup (period 1), nitrite addition (period 2) and system recovery (period 3). Different process and molecular methods were combined to investigate the impact of NO2(-) addition on H2S and CH4 production. Results showed that H2S load was reduced completely during nitrite addition when compared to period 1 due to H2S oxidation but increased immediately after nitrite addition stopped. The H2S overproduction during recovery period was associated with the bacterial reduction of different sulfur species (elemental sulfur/thiosulfate/sulfite) accumulated within the sewer biofilm matrix. Oxidation of CH4 was also detected during period 2 but, contrary to sulfide production, re-establishment of methanogenesis was not immediate after stopping nitrite dosing. The analysis of bulk and active microbial communities along experimental treatment showed compositional changes that agreed with the observed dynamics of chemical processes. Results of this study show that DNO2D strategy could significantly reduce H2S and CH4 emissions from sewers during the addition period but also suggest that microbial agents involved in such processes show a high resilience towards chemical stressors, thus favoring the re-establishment of H2S and CH4 production after stopping nitrite addition.}, }
@article {pmid26870828, year = {2016}, author = {Hua, X and Goedert, JJ and Pu, A and Yu, G and Shi, J}, title = {Allergy associations with the adult fecal microbiota: Analysis of the American Gut Project.}, journal = {EBioMedicine}, volume = {3}, number = {}, pages = {172-179}, pmid = {26870828}, issn = {2352-3964}, support = {ZIA CP010214/ImNIH/Intramural NIH HHS/United States ; ZIA-CP-010214/CP/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Biodiversity ; Databases, Nucleic Acid ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Hypersensitivity/*epidemiology/*etiology ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Odds Ratio ; RNA, Ribosomal, 16S/genetics ; Risk ; Surveys and Questionnaires ; }, abstract = {BACKGROUND: Alteration of the gut microbial population (dysbiosis) may increase the risk for allergies and other conditions. This study sought to clarify the relationship of dysbiosis with allergies in adults.<br><br>METHODS: Publicly available American Gut Project questionnaire and fecal 16S rRNA sequence data were analyzed. Fecal microbiota richness (number of observed species) and composition (UniFrac) were used to compare adults with versus without allergy to foods (peanuts, tree nuts, shellfish, other) and non-foods (drug, bee sting, dander, asthma, seasonal, eczema). Logistic and Poisson regression models adjusted for potential confounders. Odds ratios and 95% confidence intervals (CI) were calculated for lowest vs highest richness tertile. Taxonomy associations considered 122 non-redundant taxa (of 2379 total taxa) with &#x2265; 0.1% mean abundance.<br><br>RESULTS: Self-reported allergy prevalence among the 1879 participants (mean age, 45.5 years; 46.9% male) was 81.5%, ranging from 2.5% for peanuts to 40.5% for seasonal. Fecal microbiota richness was markedly lower with total allergies (P = 10(-9)) and five particular allergies (P &#x2264; 10(-4)). Richness odds ratios were 1.7 (CI 1.3-2.2) with seasonal, 1.8 (CI 1.3-2.5) with drug, and 7.8 (CI 2.3-26.5) with peanut allergy. These allergic participants also had markedly altered microbial community composition (unweighted UniFrac, P = 10(-4) to 10(-7)). Total food and non-food allergies were significantly associated with 7 and 9 altered taxa, respectively. The dysbiosis was most marked with nut and seasonal allergies, driven by higher Bacteroidales and reduced Clostridiales taxa.<br><br>INTERPRETATION: American adults with allergies, especially to nuts and seasonal pollen, have low diversity, reduced Clostridiales, and increased Bacteroidales in their gut microbiota. This dysbiosis might be targeted to improve treatment or prevention of allergy.}, }
@article {pmid26868405, year = {2016}, author = {Franco, T and Califano, G and Gonçalves, AC and Cúcio, C and Costa, R}, title = {Draft Genome Sequence of Vibrio sp. Strain Evh12, a Bacterium Retrieved from the Gorgonian Coral Eunicella verrucosa.}, journal = {Genome announcements}, volume = {4}, number = {1}, pages = {}, pmid = {26868405}, issn = {2169-8287}, abstract = {To shed light on the associations established between Vibrio species and soft corals in coastal ecosystems, we report here the draft genome sequence of Vibrio sp. strain Evh12, a bacterium that has been isolated from the gorgonian coral Eunicella verrucosa and that shows antagonistic activity against Escherichia coli.}, }
@article {pmid26867525, year = {2016}, author = {Lee, JT and Frank, DN and Ramakrishnan, V}, title = {Microbiome of the paranasal sinuses: Update and literature review.}, journal = {American journal of rhinology &amp; allergy}, volume = {30}, number = {1}, pages = {3-16}, pmid = {26867525}, issn = {1945-8932}, support = {CIA13006//PHS HHS/United States ; }, mesh = {Animals ; Bacteria/*genetics ; Biodiversity ; Chronic Disease ; Homeostasis ; Humans ; Microbiota/*genetics ; Paranasal Sinuses/immunology/*microbiology ; RNA, Ribosomal, 16S/analysis ; Rhinitis, Allergic/*microbiology ; Sinusitis/*microbiology ; }, abstract = {BACKGROUND: Our understanding of the resident microbiome of the paranasal sinuses has changed considerably in recent years. Once presumed to be sterile, healthy sinus cavities are now known to harbor a diverse assemblage of microorganisms, and, it is hypothesized that alterations in the kinds and quantities of these microbes may play a role in the pathogenesis of chronic rhinosinusitis (CRS).<br><br>OBJECTIVES: To review the current literature regarding the sinus microbiome and collate research findings from relevant studies published to date.<br><br>METHODS: A systematic literature review was performed on all molecular studies that investigated the microbial communities of the paranasal sinuses. Methods of detection, microbiome composition, and comparative profiling between patients with and without CRS were explored.<br><br>RESULTS: A complex consortium of microorganisms has been demonstrated in the sinuses of both patients with and without CRS. However, the latter generally have been characterized by reduced biodiversity compared with controls, with selective enrichment of particular microbes (e.g., Staphylococcus aureus). Such disruptions in the resident microbiome may contribute to disease pathogenesis by enhancing the virulence of potential pathogens and adversely modulating immune responses.<br><br>CONCLUSION: The advent of culture-independent molecular approaches has led to a greater appreciation of the intricate microbial ecology of the paranasal sinuses. Microbiota composition, distribution, and abundance impact mucosal health and influence pathogen growth and function. A deeper understanding of the host-microbiome relationship and its constituents may encourage development of new treatment paradigms for CRS, which target restoration of microbiome homeostasis and cultivation of optimal microbial communities.}, }
@article {pmid26866046, year = {2015}, author = {Fisher, JC and Newton, RJ and Dila, DK and McLellan, SL}, title = {Urban microbial ecology of a freshwater estuary of Lake Michigan.}, journal = {Elementa (Washington, D.C.)}, volume = {3}, number = {}, pages = {}, pmid = {26866046}, issn = {2325-1026}, support = {R01 AI091829/AI/NIAID NIH HHS/United States ; }, abstract = {Freshwater estuaries throughout the Great Lakes region receive stormwater runoff and riverine inputs from heavily urbanized population centers. While human and animal feces contained in this runoff are often the focus of source tracking investigations, non-fecal bacterial loads from soil, aerosols, urban infrastructure, and other sources are also transported to estuaries and lakes. We quantified and characterized this non-fecal urban microbial component using bacterial 16S rRNA gene sequences from sewage, stormwater, rivers, harbor/estuary, and the lake surrounding Milwaukee, WI, USA. Bacterial communities from each of these environments had a distinctive composition, but some community members were shared among environments. We used a statistical biomarker discovery tool to identify the components of the microbial community that were most strongly associated with stormwater and sewage to describe an "urban microbial signature," and measured the presence and relative abundance of these organisms in the rivers, estuary, and lake. This urban signature increased in magnitude in the estuary and harbor with increasing rainfall levels, and was more apparent in lake samples with closest proximity to the Milwaukee estuary. The dominant bacterial taxa in the urban signature were Acinetobacter, Aeromonas, and Pseudomonas, which are organisms associated with pipe infrastructure and soil and not typically found in pelagic freshwater environments. These taxa were highly abundant in stormwater and sewage, but sewage also contained a high abundance of Arcobacter and Trichococcus that appeared in lower abundance in stormwater outfalls and in trace amounts in aquatic environments. Urban signature organisms comprised 1.7% of estuary and harbor communities under baseflow conditions, 3.5% after rain, and >10% after a combined sewer overflow. With predicted increases in urbanization across the Great Lakes, further alteration of freshwater communities is likely to occur with potential long term impacts on the function of estuarine and nearshore ecosystems.}, }
@article {pmid26865909, year = {2016}, author = {Poehlein, A and Freese, H and Daniel, R and Simeonova, DD}, title = {Genome sequence of Shinella sp. strain DD12, isolated from homogenized guts of starved Daphnia magna.}, journal = {Standards in genomic sciences}, volume = {11}, number = {}, pages = {14}, pmid = {26865909}, issn = {1944-3277}, abstract = {Shinella sp. strain DD12, a novel phosphite assimilating bacterium, has been isolated from homogenized guts of 4 days starved zooplankton Daphnia magna. Here we report the draft genome of this bacterium, which comprises 7,677,812 bp and 7505 predicted protein-coding genes.}, }
@article {pmid26865218, year = {2016}, author = {Gonzales, GB and Smagghe, G and Vissenaekens, H and Grootaert, C and Rajkovic, A and Van de Wiele, T and Raes, K and Van Camp, J}, title = {Quercetin mitigates valinomycin-induced cellular stress via stress-induced metabolism and cell uptake.}, journal = {Molecular nutrition &amp; food research}, volume = {60}, number = {5}, pages = {972-980}, doi = {10.1002/mnfr.201500999}, pmid = {26865218}, issn = {1613-4133}, mesh = {Antioxidants/*pharmacology ; Caco-2 Cells ; Cell Survival/drug effects ; Dose-Response Relationship, Drug ; Humans ; Quercetin/*pharmacology ; Reactive Oxygen Species/metabolism ; Stress, Physiological/*drug effects ; Valinomycin/*toxicity ; }, abstract = {SCOPE: Intestinal cells are constantly exposed to luminal toxins. In this study, we investigated the effect of cellular stress caused by valinomycin, which is structurally and functionally similar to the bacterial toxin cereulide, on quercetin metabolism and cellular localization in undifferentiated cells.<br><br>METHODS AND RESULTS: Coadministration of quercetin and valinomycin (50 &#x3bc;M quercetin/0.05 &#x3bc;M valinomycin) reduced intracellular reactive oxygen species content and increased cell viability (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) of Caco-2 cells compared to valinomycin-only (0.05 &#x3bc;M) treatment. Quercertin was effectively metabolized into methyl, glucuronide, and sulfate conjugates, which were mostly secreted into to the culture medium. Three different O-methylated quercetin isomers were detected. Two were exported from the cells and one remained intracellularly. Further, valinomycin caused an increase in the intracellular accumulation of O-methylated quercetin metabolites compared to cells treated only with quercetin. In valinomycin-untreated cells, quercetin and O-methylated quercetin metabolite were localized in the cell membrane, whereas valinomycin treatment resulted in their uptake by the cells.<br><br>CONCLUSION: This is the first report on the change in metabolism, localization, and accumulation of O-methylated quercetin metabolites in undifferentiated Caco-2 cells as a response during stress caused by valinomycin. These results indicate a potential cellular stress response mechanism in undifferentiated Caco-2 cells, which adds novel insights into the mechanisms of flavonoid cellular bioactivity.}, }
@article {pmid26862140, year = {2016}, author = {Paquet, VE and Charette, SJ}, title = {Amoeba-resisting bacteria found in multilamellar bodies secreted by Dictyostelium discoideum: social amoebae can also package bacteria.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {3}, pages = {}, doi = {10.1093/femsec/fiw025}, pmid = {26862140}, issn = {1574-6941}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Dictyostelium/immunology/*microbiology ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Many bacteria can resist phagocytic digestion by various protozoa. Some of these bacteria (all human pathogens) are known to be packaged in multilamellar bodies produced in the phagocytic pathway of the protozoa and that are secreted into the extracellular milieu. Packaged bacteria are protected from harsh conditions, and the packaging process is suspected to promote bacterial persistence in the environment. To date, only a limited number of protozoa, belonging to free-living amoebae and ciliates, have been shown to perform bacteria packaging. It is still unknown if social amoebae can do bacteria packaging. The link between the capacity of 136 bacterial isolates to resist the grazing of the social amoeba Dictyostelium discoideum and to be packaged by this amoeba was investigated in the present study. The 45 bacterial isolates displaying a resisting phenotype were tested for their capacity to be packaged. A total of seven isolates from Cupriavidus, Micrococcus, Microbacterium and Rathayibacter genera seemed to be packaged and secreted by D. discoideum based on immunofluorescence results. Electron microscopy confirmed that the Cupriavidus and Rathayibacter isolates were formally packaged. These results show that social amoebae can package some bacteria from the environment revealing a new aspect of microbial ecology.}, }
@article {pmid26861660, year = {2016}, author = {ten Hoopen, P and Amid, C and Buttigieg, PL and Pafilis, E and Bravakos, P and Cerdeño-Tárraga, AM and Gibson, R and Kahlke, T and Legaki, A and Narayana Murthy, K and Papastefanou, G and Pereira, E and Rossello, M and Luisa Toribio, A and Cochrane, G}, title = {Value, but high costs in post-deposition data curation.}, journal = {Database : the journal of biological databases and curation}, volume = {2016}, number = {}, pages = {}, pmid = {26861660}, issn = {1758-0463}, support = {BB/I02612X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Computational Biology/*economics ; Data Collection ; Databases, Nucleic Acid/*economics ; Ecosystem ; Europe ; Geography ; Humans ; *Metagenomics ; Microbiota ; Molecular Sequence Annotation ; Semantics ; Sequence Analysis ; }, abstract = {Discoverability of sequence data in primary data archives is proportional to the richness of contextual information associated with the data. Here, we describe an exercise in the improvement of contextual information surrounding sample records associated with metagenomics sequence reads available in the European Nucleotide Archive. We outline the annotation process and summarize findings of this effort aimed at increasing usability of publicly available environmental data. Furthermore, we emphasize the benefits of such an exercise and detail its costs. We conclude that such a third party annotation approach is expensive and has value as an element of curation, but should form only part of a more sustainable submitter-driven approach. Database URL: http://www.ebi.ac.uk/ena.}, }
@article {pmid26861415, year = {2016}, author = {Samanta, B and Bhadury, P}, title = {A comprehensive framework for functional diversity patterns of marine chromophytic phytoplankton using rbcL phylogeny.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {20783}, pmid = {26861415}, issn = {2045-2322}, mesh = {Aquatic Organisms/*classification/genetics/*physiology ; *Genetic Variation ; *Phylogeny ; Phytoplankton/*classification/genetics/*physiology ; Ribulose-Bisphosphate Carboxylase/*genetics ; Sequence Analysis, DNA ; }, abstract = {Marine chromophytes are taxonomically diverse group of algae and contribute approximately half of the total oceanic primary production. To understand the global patterns of functional diversity of chromophytic phytoplankton, robust bioinformatics and statistical analyses including deep phylogeny based on 2476 form ID rbcL gene sequences representing seven ecologically significant oceanographic ecoregions were undertaken. In addition, 12 form ID rbcL clone libraries were generated and analyzed (148 sequences) from Sundarbans Biosphere Reserve representing the world's largest mangrove ecosystem as part of this study. Global phylogenetic analyses recovered 11 major clades of chromophytic phytoplankton in varying proportions with several novel rbcL sequences in each of the seven targeted ecoregions. Majority of OTUs was found to be exclusive to each ecoregion, whereas some were shared by two or more ecoregions based on beta-diversity analysis. Present phylogenetic and bioinformatics analyses provide a strong statistical support for the hypothesis that different oceanographic regimes harbor distinct and coherent groups of chromophytic phytoplankton. It has been also shown as part of this study that varying natural selection pressure on form ID rbcL gene under different environmental conditions could lead to functional differences and overall fitness of chromophytic phytoplankton populations.}, }
@article {pmid26861055, year = {2016}, author = {Selak, M and Rivière, A and Moens, F and Van den Abbeele, P and Geirnaert, A and Rogelj, I and Leroy, F and De Vuyst, L}, title = {Inulin-type fructan fermentation by bifidobacteria depends on the strain rather than the species and region in the human intestine.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {9}, pages = {4097-4107}, doi = {10.1007/s00253-016-7351-9}, pmid = {26861055}, issn = {1432-0614}, mesh = {Bifidobacterium/*metabolism ; Fermentation ; Fructans/*metabolism ; Humans ; Intestines/*microbiology ; }, abstract = {Inulin-type fructans (ITF) are known to cause a health-promoting bifidogenic effect, although the ITF degradation capacity of bifidobacteria in different intestinal regions remains unclear. The present study aims at offering new insights into this link, making use of a collection of 190 bifidobacterial strains, encompassing strains from gut biopsies (terminal ileum and proximal colon; mucosa-associated strains) and the simulator of the human intestinal microbial ecosystem (SHIME®; proximal and distal colon vessels; lumen-associated strains). A multivariate data analysis of all fermentation data revealed four clusters corresponding with different types of ITF degradation fingerprints, which were not correlated with the region in the intestine, suggesting that the degradation of ITF is uniform along the human intestine. Strains from cluster 1 consumed fructose, while strains from cluster 2 consumed more oligofructose than fructose. Higher fructose and oligofructose consumption was characteristic for clusters 3 and 4 strains, which degraded inulin too. In general, the mucosa-associated strains from biopsy origin seemed to be more specialized in the consumption of fructose and oligofructose, while the lumen-associated strains from SHIME origin displayed a higher degradation degree of inulin. Further, intra-species variability in ITF degradation was found, indicating strain-specific variations. The coexistence of different bifidobacterial strains with different ITF degradation fingerprints within the same intestinal region suggests cooperation for the degradation of ITF, with opportunities for cross-feeding on strain and/or species level.}, }
@article {pmid26859516, year = {2016}, author = {Maza-Márquez, P and Vílchez-Vargas, R and Boon, N and González-López, J and Martínez-Toledo, MV and Rodelas, B}, title = {The ratio of metabolically active versus total Mycolata populations triggers foaming in a membrane bioreactor.}, journal = {Water research}, volume = {92}, number = {}, pages = {208-217}, doi = {10.1016/j.watres.2015.12.057}, pmid = {26859516}, issn = {1879-2448}, mesh = {Actinobacteria/genetics/*growth &amp; development/*metabolism ; Bioreactors/*microbiology ; *Membranes, Artificial ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The abundance of total and metabolically active populations of Mycolata was evaluated in a full-scale membrane bioreactor (MBR) experiencing seasonal foaming, using quantitative PCR (qPCR) and retrotranscribed qPCR (RT-qPCR) targeting the 16S rRNA gene sequence. While the abundance of total Mycolata remained stable (10(10) copies of 16S rRNA genes/L activated sludge) throughout four different experimental phases, significant variations (up to one order of magnitude) were observed when the 16S rRNA was targeted. The highest ratios of metabolically active versus total Mycolata populations were observed in samples of two experimental phases when foaming was experienced in the MBR. Non-metric multidimensional scaling and BIO-ENV analyses demonstrated that this ratio was positively correlated to the concentrations of substrates in the influent water, F/M ratio, and pH, and negatively correlated to temperature and solids retention time. It the first time that the ratio of metabolically active versus total Mycolata is found to be a key parameter triggering foaming in the MBR; thus, we propose it as a candidate predictive tool.}, }
@article {pmid26858690, year = {2015}, author = {Jeffries, TC and Schmitz Fontes, ML and Harrison, DP and Van-Dongen-Vogels, V and Eyre, BD and Ralph, PJ and Seymour, JR}, title = {Bacterioplankton Dynamics within a Large Anthropogenically Impacted Urban Estuary.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1438}, pmid = {26858690}, issn = {1664-302X}, abstract = {The abundant and diverse microorganisms that inhabit aquatic systems are both determinants and indicators of aquatic health, providing essential ecosystem services such as nutrient cycling but also causing harmful blooms and disease in impacted habitats. Estuaries are among the most urbanized coastal ecosystems and as a consequence experience substantial environmental pressures, providing ideal systems to study the influence of anthropogenic inputs on microbial ecology. Here we use the highly urbanized Sydney Harbor, Australia, as a model system to investigate shifts in microbial community composition and function along natural and anthopogenic physicochemical gradients, driven by stormwater inflows, tidal flushing and the input of contaminants and both naturally and anthropogenically derived nutrients. Using a combination of amplicon sequencing of the 16S rRNA gene and shotgun metagenomics, we observed strong patterns in microbial biogeography across the estuary during two periods: one of high and another of low rainfall. These patterns were driven by shifts in nutrient concentration and dissolved oxygen leading to a partitioning of microbial community composition in different areas of the harbor with different nutrient regimes. Patterns in bacterial composition were related to shifts in the abundance of Rhodobacteraceae, Flavobacteriaceae, Microbacteriaceae, Halomonadaceae, Acidomicrobiales, and Synechococcus, coupled to an enrichment of total microbial metabolic pathways including phosphorus and nitrogen metabolism, sulfate reduction, virulence, and the degradation of hydrocarbons. Additionally, community beta-diversity was partitioned between the two sampling periods. This potentially reflected the influence of shifting allochtonous nutrient inputs on microbial communities and highlighted the temporally dynamic nature of the system. Combined, our results provide insights into the simultaneous influence of natural and anthropogenic drivers on the structure and function of microbial communities within a highly urbanized aquatic ecosystem.}, }
@article {pmid26854699, year = {2016}, author = {Tella, M and Bravin, MN and Thuriès, L and Cazevieille, P and Chevassus-Rosset, C and Collin, B and Chaurand, P and Legros, S and Doelsch, E}, title = {Increased zinc and copper availability in organic waste amended soil potentially involving distinct release mechanisms.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {212}, number = {}, pages = {299-306}, doi = {10.1016/j.envpol.2016.01.077}, pmid = {26854699}, issn = {1873-6424}, mesh = {Copper/*analysis ; Environmental Monitoring/*methods ; Soil/*chemistry ; Soil Pollutants/*analysis ; Trace Elements/analysis ; Waste Management/*methods ; Waste Products/*analysis ; X-Ray Absorption Spectroscopy ; Zinc/*analysis ; }, abstract = {This study aimed at determining the fate of trace elements (TE) following soil organic waste (OW) application. We used a unique combination of X-ray absorption spectroscopy analyses, to determine TE speciation, with incubation experiments for in situ monitoring of TE availability patterns over a time course with the technique of the diffusive gradients in thin films (DGT). We showed that copper (Cu) and zinc (Zn) availability were both increased in OW-amended soil, but their release was controlled by distinct mechanisms. Zn speciation in OW was found to be dominated by an inorganic species, i.e. Zn sorbed on Fe oxides. Zn desorption from Fe oxides could explain the increase in Zn availability in OW-amended soil. Cu speciation in OW was dominated by organic species. Cu release through the mineralization of organic carbon from OW was responsible for the increase in Cu availability.}, }
@article {pmid26854514, year = {2016}, author = {Maes, S and Props, R and Fitts, JP and Smet, RD and Vilchez-Vargas, R and Vital, M and Pieper, DH and Vanhaecke, F and Boon, N and Hennebel, T}, title = {Platinum Recovery from Synthetic Extreme Environments by Halophilic Bacteria.}, journal = {Environmental science &amp; technology}, volume = {50}, number = {5}, pages = {2619-2626}, doi = {10.1021/acs.est.5b05355}, pmid = {26854514}, issn = {1520-5851}, mesh = {Animals ; Artemia ; Bacteria/drug effects/*metabolism/ultrastructure ; Biomass ; Cell Membrane/drug effects/metabolism ; Chemical Precipitation ; *Environment ; Platinum/*isolation &amp; purification ; Sodium Chloride/*pharmacology ; X-Ray Absorption Spectroscopy ; }, abstract = {Metal recycling based on urban mining needs to be established to tackle the increasing supply risk of critical metals such as platinum. Presently, efficient strategies are missing for the recovery of platinum from diluted industrial process streams, often characterized by extremely low pHs and high salt concentrations. In this research, halophilic mixed cultures were employed for the biological recovery of platinum (Pt). Halophilic bacteria were enriched from Artemia cysts, living in salt lakes, in different salt matrices (sea salt mixture and NH4Cl; 20-210 g L(-1) salts) and at low to neutral pH (pH 3-7). The main taxonomic families present in the halophilic cultures were Halomonadaceae, Bacillaceae, and Idiomarinaceae. The halophilic cultures were able to recover >98% Pt(II) and >97% Pt(IV) at pH 2 within 3-21 h (4-453 mg Ptrecovered h(-1) g(-1) biomass). X-ray absorption spectroscopy confirmed the reduction to Pt(0) and transmission electron microscopy revealed both intra- and extracellular Pt precipitates, with median diameters of 9-30 nm and 11-13 nm, for Pt(II) and Pt(IV), respectively. Flow cytometric membrane integrity staining demonstrated the preservation of cell viability during platinum recovery. This study demonstrates the Pt recovery potential of halophilic mixed cultures in acidic saline conditions.}, }
@article {pmid26853704, year = {2016}, author = {Peck, V and Quiza, L and Buffet, JP and Khdhiri, M and Durand, AA and Paquette, A and Thiffault, N and Messier, C and Beaulieu, N and Guertin, C and Constant, P}, title = {Towards the development of multifunctional molecular indicators combining soil biogeochemical and microbiological variables to predict the ecological integrity of silvicultural practices.}, journal = {Microbial biotechnology}, volume = {9}, number = {3}, pages = {316-329}, pmid = {26853704}, issn = {1751-7915}, mesh = {Bacteria/*classification/*genetics ; *Biota ; *Chemical Phenomena ; DNA, Ribosomal/chemistry/genetics ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {The impact of mechanical site preparation (MSP) on soil biogeochemical structure in young larch plantations was investigated. Soil samples were collected in replicated plots comprising simple trenching, double trenching, mounding and inverting site preparation. Unlogged natural mixed forest areas were used as a reference. Analysis of soil nutrients, abundance of bacteria and gas exchanges unveiled no significant difference among the plots. However, inverting site preparation resulted in higher variations of gas exchanges when compared with trenching, mounding and unlogged natural forest. A combination of the biological and physicochemical variables was used to define a multifunctional classification of the soil samples into four distinct groups categorized as a function of their deviation from baseline ecological conditions. According to this classification model, simple trenching was the approach that represented the lowest ecological risk potential at the microsite level. No relationship was observed between MSP method and soil bacterial community structure as assessed by high-throughput sequencing of bacterial 16S rRNA gene; however, indicator genotypes were identified for each multifunctional soil class. This is the first identification of multifunctional molecular indicators for baseline and disturbed ecological conditions in soil, demonstrating the potential of applied microbial ecology to guide silvicultural practices and ecological risk assessment.}, }
@article {pmid26853591, year = {2016}, author = {Xu, G and Xu, H}, title = {An approach to analyzing environmental drivers to spatial variations in annual distribution of periphytic protozoa in coastal ecosystems.}, journal = {Marine pollution bulletin}, volume = {104}, number = {1-2}, pages = {107-112}, doi = {10.1016/j.marpolbul.2016.01.055}, pmid = {26853591}, issn = {1879-3363}, mesh = {Ammonia/analysis ; Biodiversity ; China ; Ciliophora/*growth &amp; development ; *Ecosystem ; Environmental Monitoring/*methods ; Nitrogen/analysis ; Oceans and Seas ; Salinity ; Seawater/*chemistry ; Water Pollution/*analysis ; Water Quality ; }, abstract = {The environmental drivers to the spatial variation in annual distribution were studied based on an annual dataset of periphytic protozoa using multivariate approaches. Samples were monthly collected at four stations within a pollution gradient in coastal waters of the Yellow Sea, northern China during a 1-year period. The second-stage (2STAGE) analyses showed that the internal patterns of the annual distribution were changed along the pollution gradient in terms of abundance. The dominant species represented different succession dynamics among four sampling stations during a 1-year cycle. Best matching analysis demonstrated that the spatial variations in annual distribution of the protozoa were significantly correlated with ammonium nitrogen (NH4-N), alone or in combination with salinity and dissolved oxygen (DO). Based on the results, we suggest that the nutrients, salinity and DO may be the main drivers to shape the spatial variations in annual distribution of periphytic protozoa.}, }
@article {pmid26853115, year = {2016}, author = {Attar, N}, title = {Microbial ecology: FISHing in the oral microbiota.}, journal = {Nature reviews. Microbiology}, volume = {14}, number = {3}, pages = {132-133}, pmid = {26853115}, issn = {1740-1534}, mesh = {Bacteria/*classification ; Humans ; *Microbiota ; Mouth/*microbiology ; *Phylogeography ; }, }
@article {pmid26851513, year = {2016}, author = {Johnston, AW and Green, RT and Todd, JD}, title = {Enzymatic breakage of dimethylsulfoniopropionate-a signature molecule for life at sea.}, journal = {Current opinion in chemical biology}, volume = {31}, number = {}, pages = {58-65}, doi = {10.1016/j.cbpa.2016.01.011}, pmid = {26851513}, issn = {1879-0402}, support = {BB/H002642/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Bacteria/enzymology/genetics ; Enzymes/chemistry/*metabolism ; Genes, Bacterial ; *Marine Biology ; *Seawater ; Sequence Homology, Amino Acid ; Sulfonium Compounds/*metabolism ; }, abstract = {Largely using gene-based evidence, the last few years have seen real insights on the diverse ways in which different microbes break down dimethylsulfoniopropionate, an abundant anti-stress molecule that is made by marine algae, some corals and a few angiosperms. Here, we review more recent advances in which in vitro biochemical tools-including structural determinations-have shed new light on how the corresponding enzymes act on DMSP. These have revealed how enzymes in very different polypeptide families can act on this substrate, often by novel ways, and with broader implications that extend from enzymatic mechanisms to microbial ecology.}, }
@article {pmid26850162, year = {2016}, author = {Stedtfeld, RD and Williams, MR and Fakher, U and Johnson, TA and Stedtfeld, TM and Wang, F and Khalife, WT and Hughes, M and Etchebarne, BE and Tiedje, JM and Hashsham, SA}, title = {Antimicrobial resistance dashboard application for mapping environmental occurrence and resistant pathogens.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {3}, pages = {}, pmid = {26850162}, issn = {1574-6941}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; 2 P42 ES004911-22A1/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics/isolation &amp; purification ; Bacterial Infections/microbiology/veterinary ; Bacterial Proteins/genetics ; *Databases, Factual ; *Drug Resistance, Bacterial ; Humans ; Microbial Sensitivity Tests ; Prospective Studies ; Rivers/microbiology ; Swine/microbiology ; Wastewater/microbiology ; }, abstract = {An antibiotic resistance (AR) Dashboard application is being developed regarding the occurrence of antibiotic resistance genes (ARG) and bacteria (ARB) in environmental and clinical settings. The application gathers and geospatially maps AR studies, reported occurrence and antibiograms, which can be downloaded for offline analysis. With the integration of multiple data sets, the database can be used on a regional or global scale to identify hot spots for ARGs and ARB; track and link spread and transmission, quantify environmental or human factors influencing presence and persistence of ARG harboring organisms; differentiate natural ARGs from those distributed via human or animal activity; cluster and compare ARGs connections in different environments and hosts; and identify genes that can be used as proxies to routinely monitor anthropogenic pollution. To initially populate and develop the AR Dashboard, a qPCR ARG array was tested with 30 surface waters, primary influent from three waste water treatment facilities, ten clinical isolates from a regional hospital and data from previously published studies including river, park soil and swine farm samples. Interested users are invited to download a beta version (available on iOS or Android), submit AR information using the application, and provide feedback on current and prospective functionalities.}, }
@article {pmid26848031, year = {2016}, author = {Lin, HW and Cejudo-Marín, R and Jeremiasse, AW and Rabaey, K and Yuan, Z and Pikaar, I}, title = {Direct anodic hydrochloric acid and cathodic caustic production during water electrolysis.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {20494}, pmid = {26848031}, issn = {2045-2322}, abstract = {Hydrochloric acid (HCl) and caustic (NaOH) are among the most widely used chemicals by the water industry. Direct anodic electrochemical HCl production by water electrolysis has not been successful as current commercially available electrodes are prone to chlorine formation. This study presents an innovative technology simultaneously generating HCl and NaOH from NaCl using a Mn0.84Mo0.16O2.23 oxygen evolution electrode during water electrolysis. The results showed that protons could be anodically generated at a high Coulombic efficiency (i.e. ≥ 95%) with chlorine formation accounting for 3 ~ 5% of the charge supplied. HCl was anodically produced at moderate strengths at a CE of 65 ± 4% together with a CE of 89 ± 1% for cathodic caustic production. The reduction in CE for HCl generation was caused by proton cross-over from the anode to the middle compartment. Overall, this study showed the potential of simultaneous HCl and NaOH generation from NaCl and represents a major step forward for the water industry towards on-site production of HCl and NaOH. In this study, artificial brine was used as a source of sodium and chloride ions. In theory, artificial brine could be replaced by saline waste streams such as Reverse Osmosis Concentrate (ROC), turning ROC into a valuable resource.}, }
@article {pmid26846217, year = {2016}, author = {Starke, R and Keller, A and Jehmlich, N and Vogt, C and Richnow, HH and Kleinsteuber, S and von Bergen, M and Seifert, J}, title = {Pulsed (13)C2-Acetate Protein-SIP Unveils Epsilonproteobacteria as Dominant Acetate Utilizers in a Sulfate-Reducing Microbial Community Mineralizing Benzene.}, journal = {Microbial ecology}, volume = {71}, number = {4}, pages = {901-911}, pmid = {26846217}, issn = {1432-184X}, mesh = {Acetates/*metabolism ; Anaerobiosis ; Bacterial Proteins/analysis ; Benzene/*metabolism ; Biodegradation, Environmental ; Carbon Isotopes/analysis ; Clostridiales/growth &amp; development/metabolism ; Deltaproteobacteria/metabolism ; Epsilonproteobacteria/*metabolism ; Groundwater/microbiology ; Hydrocarbons/metabolism ; Hydrogen/metabolism ; Microbial Consortia ; Phylogeny ; Proteomics/*methods ; Sulfates/*metabolism ; Sulfur-Reducing Bacteria/metabolism ; }, abstract = {In a benzene-degrading and sulfate-reducing syntrophic consortium, a clostridium affiliated to the genus Pelotomaculum was previously described to ferment benzene while various sulfate-reducing Deltaproteobacteria and a member of the Epsilonproteobacteria were supposed to utilize acetate and hydrogen as key metabolites derived from benzene fermentation. However, the acetate utilization network within this community was not yet unveiled. In this study, we performed a pulsed (13)C2-acetate protein stable isotope probing (protein-SIP) approach continuously spiking low amounts of acetate (10 μM per day) in addition to the ongoing mineralization of unlabeled benzene. Metaproteomics revealed high abundances of Clostridiales followed by Syntrophobacterales, Desulfobacterales, Desulfuromonadales, Desulfovibrionales, Archaeoglobales, and Campylobacterales. Pulsed acetate protein-SIP results indicated that members of the Campylobacterales, the Syntrophobacterales, the Archaeoglobales, the Clostridiales, and the Desulfobacterales were linked to acetate utilization in descending abundance. The Campylobacterales revealed the fastest and highest (13)C incorporation. Previous experiments suggested that the activity of the Campylobacterales was not essential for anaerobic benzene degradation in the investigated community. However, these organisms were consistently detected in various hydrocarbon-degrading and sulfate-reducing consortia enriched from the same aquifer. Here, we demonstrate that this member of the Campylobacterales is the dominant acetate utilizer in the benzene-degrading microbial consortium.}, }
@article {pmid26846216, year = {2016}, author = {Chu, CC and Gill, TA and Hoffmann, M and Pelz-Stelinski, KS}, title = {Inter-Population Variability of Endosymbiont Densities in the Asian Citrus Psyllid (Diaphorina citri Kuwayama).}, journal = {Microbial ecology}, volume = {71}, number = {4}, pages = {999-1007}, pmid = {26846216}, issn = {1432-184X}, mesh = {Alphaproteobacteria/*classification/genetics ; Animals ; Bacterial Load ; Citrus/microbiology ; Female ; Florida ; Helicobacter/classification/genetics ; Hemiptera/*microbiology ; Male ; North America ; Real-Time Polymerase Chain Reaction ; Symbiosis ; Wolbachia/*classification/genetics ; }, abstract = {The Asian citrus psyllid (Diaphorina citri Kuwayama) is an insect pest capable of transmitting Candidatus Liberibacter asiaticus (CLas), the causal agent of citrus greening in North America. D. citri also harbors three endosymbionts, Wolbachia, Candidatus Carsonella ruddii, and Candidatus Profftella armatura, which may influence D. citri physiology and fitness. Although genomic researches on these bacteria have been conducted, much remains unclear regarding their ecology and inter-population variability in D. citri. The present work examined the densities of each endosymbiont in adult D. citri sampled from different populations using quantitative PCR. Under field conditions, the densities of all three endosymbionts positively correlated with each other, and they are associated with D. citri gender and locality. In addition, the infection density of CLas also varied across populations. Although an analysis pooling D. citri from different populations showed that CLas-infected individuals tended to have lower endosymbiont densities compared to uninfected individuals, the difference was not significant when the population was included as a factor in the analysis, suggesting that other population-specific factors may have stronger effects on endosymbiont densities. To determine whether there is a genetic basis to the density differences, endosymbiont densities between aged CLas-negative females of two D. citri populations reared under standardized laboratory conditions were compared. Results suggested that inter-population variability in Wolbachia infection density is associated with the genotypes of the endosymbiont or the host. Findings from this work could facilitate understanding of D. citri-bacterial associations that may benefit the development of approaches for managing citrus greening, such as prevention of CLas transmission.}, }
@article {pmid26843809, year = {2015}, author = {Das, J and Mukherjee, S and Hodge, SE}, title = {Maximum Entropy Estimation of Probability Distribution of Variables in Higher Dimensions from Lower Dimensional Data.}, journal = {Entropy (Basel, Switzerland)}, volume = {17}, number = {7}, pages = {4986-4999}, pmid = {26843809}, issn = {1099-4300}, support = {R01 GM103612/GM/NIGMS NIH HHS/United States ; }, abstract = {A common statistical situation concerns inferring an unknown distribution Q(x) from a known distribution P(y), where X (dimension n), and Y (dimension m) have a known functional relationship. Most commonly, n ≤ m, and the task is relatively straightforward for well-defined functional relationships. For example, if Y1 and Y2 are independent random variables, each uniform on [0, 1], one can determine the distribution of X = Y1 + Y2; here m = 2 and n = 1. However, biological and physical situations can arise where n > m and the functional relation Y→X is non-unique. In general, in the absence of additional information, there is no unique solution to Q in those cases. Nevertheless, one may still want to draw some inferences about Q. To this end, we propose a novel maximum entropy (MaxEnt) approach that estimates Q(x) based only on the available data, namely, P(y). The method has the additional advantage that one does not need to explicitly calculate the Lagrange multipliers. In this paper we develop the approach, for both discrete and continuous probability distributions, and demonstrate its validity. We give an intuitive justification as well, and we illustrate with examples.}, }
@article {pmid26842002, year = {2016}, author = {Berry, D}, title = {The emerging view of Firmicutes as key fibre degraders in the human gut.}, journal = {Environmental microbiology}, volume = {18}, number = {7}, pages = {2081-2083}, doi = {10.1111/1462-2920.13225}, pmid = {26842002}, issn = {1462-2920}, mesh = {*Dietary Fiber ; *Firmicutes ; Humans ; RNA, Ribosomal, 16S ; }, }
@article {pmid26841797, year = {2016}, author = {Tashyreva, D and Elster, J}, title = {Annual Cycles of Two Cyanobacterial Mat Communities in Hydro-Terrestrial Habitats of the High Arctic.}, journal = {Microbial ecology}, volume = {71}, number = {4}, pages = {887-900}, pmid = {26841797}, issn = {1432-184X}, mesh = {Antarctic Regions ; Arctic Regions ; Cyanobacteria/growth &amp; development/metabolism/*physiology/ultrastructure ; *Ecosystem ; Freezing ; Fresh Water/chemistry/*microbiology ; Microbial Viability ; Seasons ; Svalbard ; Temperature ; Water Microbiology ; }, abstract = {Cyanobacteria form extensive macroscopic mats in shallow freshwater environments in the High Arctic and Antarctic. In these habitats, the communities are exposed to seasonal freezing and desiccation as well as to freeze-thawing and drying-rewetting cycles. Here, we characterized the annual cycles of two Phormidium communities in very shallow seepages located in central Svalbard. We observed the structure of the communities and the morphology, ultrastructure, metabolic activity, and viability of filaments and single cells. The communities overwintered as frozen mats, which were formed by long filaments enclosed in thick multilayered polysaccharide sheaths. No morphologically and/or ultrastructurally distinct spore-like cells were produced for surviving the winter, and the winter survival of the communities was not provided by a few resistant cells, which did not undergo visible morphological and ultrastructural transformations. Instead, a high proportion of cells in samples (85%) remained viable after prolonged freezing. The sheaths were the only morphological adaption, which seemed to protect the trichomes from damage due to freezing and freeze-associated dehydration. The cells in the overwintering communities were not dormant, as all viable cells rapidly resumed respiration after thawing, and their nucleoids were not condensed. During the whole vegetative season, defined by the presence of water in a liquid state, the communities were constantly metabolically active and contained <1% of dead and injured cells. The morphology and ultrastructure of the cells remained unaltered during observations throughout the year, except for light-induced changes in thylakoids. The dissemination events are likely to occur in spring as most of the trichomes were split into short fragments (hormogonia), a substantial proportion of which were released into the environment by gliding out of their sheaths, as well as by cracking and dissolving their sheaths. The short fragments subsequently grew longer and gradually produced new polysaccharide sheaths.}, }
@article {pmid26841233, year = {2016}, author = {Courtens, EN and Vandekerckhove, T and Prat, D and Vilchez-Vargas, R and Vital, M and Pieper, DH and Meerbergen, K and Lievens, B and Boon, N and Vlaeminck, SE}, title = {Empowering a mesophilic inoculum for thermophilic nitrification: Growth mode and temperature pattern as critical proliferation factors for archaeal ammonia oxidizers.}, journal = {Water research}, volume = {92}, number = {}, pages = {94-103}, doi = {10.1016/j.watres.2016.01.022}, pmid = {26841233}, issn = {1879-2448}, mesh = {Ammonia/*metabolism ; Archaea/*growth &amp; development/*metabolism ; Base Sequence ; Biodegradation, Environmental ; Biofilms/growth &amp; development ; Biomass ; Bioreactors/microbiology ; Flocculation ; Molecular Sequence Data ; *Nitrification ; Nitrites/metabolism ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; *Temperature ; }, abstract = {Cost-efficient biological treatment of warm nitrogenous wastewaters requires the development of thermophilic nitrogen removal processes. Only one thermophilic nitrifying bioreactor was described so far, achieving 200 mg N L(-1) d(-1) after more than 300 days of enrichment from compost samples. From the practical point of view in which existing plants would be upgraded, however, a more time-efficient development strategy based on mesophilic nitrifying sludge is preferred. This study evaluated the adaptive capacities of mesophilic nitrifying sludge for two linear temperature increase patterns (non-oscillating vs. oscillating), two different slopes (0.25 vs. 0.08 °C d(-1)) and two different reactor types (floc vs. biofilm growth). The oscillating temperature pattern (0.25 °C d(-1)) and the moving bed biofilm reactor (0.08 °C d(-1)) could not reach nitrification at temperatures higher than 46 °C. However, nitrification rates up to 800 mg N L(-1) d(-1) and 150 mg N g(-1) volatile suspended solids d(-1) were achieved at a temperature as high as 49 °C by imposing the slowest linear temperature increase to floccular sludge. Microbial community analysis revealed that this successful transition was related with a shift in ammonium oxidizing archaea dominating ammonia oxidizing bacteria, while for nitrite oxidation Nitrospira spp. was constantly more abundant than Nitrobacter spp.. This observation was accompanied with an increase in observed sludge yield and a shift in maximal optimum temperature, determined with ex-situ temperature sensitivity measurements, predicting an upcoming reactor failure at higher temperature. Overall, this study achieved nitrification at 49 °C within 150 days by gradual adaptation of mesophilic sludge, and showed that ex-situ temperature sensitivity screening can be used to monitor and steer the transition process.}, }
@article {pmid26838999, year = {2016}, author = {Li, H and Xu, Z and Yang, S and Li, X and Top, EM and Wang, R and Zhang, Y and Cai, J and Yao, F and Han, X and Jiang, Y}, title = {Responses of Soil Bacterial Communities to Nitrogen Deposition and Precipitation Increment Are Closely Linked with Aboveground Community Variation.}, journal = {Microbial ecology}, volume = {71}, number = {4}, pages = {974-989}, pmid = {26838999}, issn = {1432-184X}, mesh = {Bacteria/classification/*growth &amp; development/*metabolism ; *Biodiversity ; Carbon/metabolism/pharmacology ; Chemical Precipitation ; China ; Climate ; Ecosystem ; Microbial Consortia ; Nitrogen/*chemistry/metabolism ; Phylogeny ; Plants/microbiology ; Soil/*chemistry ; *Soil Microbiology ; Water/pharmacology ; }, abstract = {It has been predicted that precipitation and atmospheric nitrogen (N) deposition will increase in northern China; yet, ecosystem responses to the interactive effects of water and N remain largely unknown. In particular, responses of belowground microbial community to projected global change and their potential linkages to aboveground macro-organisms are rarely studied. In this study, we examined the responses of soil bacterial diversity and community composition to increased precipitation and multi-level N deposition in a temperate steppe in Inner Mongolia, China, and explored the diversity linkages between aboveground and belowground communities. It was observed that N addition caused the significant decrease in bacterial alpha-diversity and dramatic changes in community composition. In addition, we documented strong correlations of alpha- and beta-diversity between plant and bacterial communities in response to N addition. It was found that N enriched the so-called copiotrophic bacteria, but reduced the oligotrophic groups, primarily by increasing the soil inorganic N content and carbon availability and decreasing soil pH. We still highlighted that increased precipitation tended to alleviate the effects of N on bacterial diversity and dampen the plant-microbe connections induced by N. The counteractive effects of N addition and increased precipitation imply that even though the ecosystem diversity and function are predicted to be negatively affected by N deposition in the coming decades; the combination with increased precipitation may partially offset this detrimental effect.}, }
@article {pmid26834717, year = {2015}, author = {Arrieta, JM and Duarte, CM and Sala, MM and Dachs, J}, title = {Out of Thin Air: Microbial Utilization of Atmospheric Gaseous Organics in the Surface Ocean.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1566}, pmid = {26834717}, issn = {1664-302X}, abstract = {Volatile and semi-volatile gas-phase organic carbon (GOC) is a largely neglected component of the global carbon cycle, with poorly resolved pools and fluxes of natural and anthropogenic GOC in the biosphere. Substantial amounts of atmospheric GOC are exchanged with the surface ocean, and subsequent utilization of specific GOC compounds by surface ocean microbial communities has been demonstrated. Yet, the final fate of the bulk of the atmospheric GOC entering the surface ocean is unknown. Our data show experimental evidence of efficient use of atmospheric GOC by marine prokaryotes at different locations in the NE Subtropical Atlantic, the Arctic Ocean and the Mediterranean Sea. We estimate that between 2 and 27% of the prokaryotic carbon demand was supported by GOC with a major fraction of GOC inputs being consumed within the mixed layer. The role of the atmosphere as a key vector of organic carbon subsidizing marine microbial metabolism is a novel link yet to be incorporated into the microbial ecology of the surface ocean as well as into the global carbon budget.}, }
@article {pmid26833547, year = {2016}, author = {van der Voort, M and Kempenaar, M and van Driel, M and Raaijmakers, JM and Mendes, R}, title = {Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression.}, journal = {Ecology letters}, volume = {19}, number = {4}, pages = {375-382}, doi = {10.1111/ele.12567}, pmid = {26833547}, issn = {1461-0248}, mesh = {*Bacterial Physiological Phenomena ; *Hot Temperature ; Microbial Interactions/*physiology ; Microbiota/*physiology ; Plant Diseases/microbiology ; Plant Roots/microbiology ; Plants/*microbiology ; Rhizoctonia/physiology ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The rhizosphere microbiome offers a range of ecosystem services to the plant, including nutrient acquisition and tolerance to (a)biotic stress. Here, analysing the data by Mendes et al. (2011), we show that short heat disturbances (50 or 80 °C, 1 h) of a soil suppressive to the root pathogenic fungus Rhizoctonia solani caused significant increase in alpha diversity of the rhizobacterial community and led to partial or complete loss of disease protection. A reassembly model is proposed where bacterial families that are heat tolerant and have high growth rates significantly increase in relative abundance after heat disturbance, while temperature-sensitive and slow-growing bacteria have a disadvantage. The results also pointed to a potential role of slow-growing, heat-tolerant bacterial families from Actinobacteria and Acidobacteria phyla in plant disease protection. In conclusion, short heat disturbance of soil results in rearrangement of rhizobacterial communities and this is correlated with changes in the ecosystem service disease suppression.}, }
@article {pmid26832206, year = {2016}, author = {Bradley, JA and Anesio, AM and Arndt, S}, title = {Bridging the divide: a model-data approach to Polar and Alpine microbiology.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {3}, pages = {}, pmid = {26832206}, issn = {1574-6941}, mesh = {Climate Change ; Ecosystem ; Environment ; *Models, Biological ; Soil Microbiology ; }, abstract = {Advances in microbial ecology in the cryosphere continue to be driven by empirical approaches including field sampling and laboratory-based analyses. Although mathematical models are commonly used to investigate the physical dynamics of Polar and Alpine regions, they are rarely applied in microbial studies. Yet integrating modelling approaches with ongoing observational and laboratory-based work is ideally suited to Polar and Alpine microbial ecosystems given their harsh environmental and biogeochemical characteristics, simple trophic structures, distinct seasonality, often difficult accessibility, geographical expansiveness and susceptibility to accelerated climate changes. In this opinion paper, we explain how mathematical modelling ideally complements field and laboratory-based analyses. We thus argue that mathematical modelling is a powerful tool for the investigation of these extreme environments and that fully integrated, interdisciplinary model-data approaches could help the Polar and Alpine microbiology community address some of the great research challenges of the 21st century (e.g. assessing global significance and response to climate change). However, a better integration of field and laboratory work with model design and calibration/validation, as well as a stronger focus on quantitative information is required to advance models that can be used to make predictions and upscale processes and fluxes beyond what can be captured by observations alone.}, }
@article {pmid26832203, year = {2016}, author = {Karkman, A and Johnson, TA and Lyra, C and Stedtfeld, RD and Tamminen, M and Tiedje, JM and Virta, M}, title = {High-throughput quantification of antibiotic resistance genes from an urban wastewater treatment plant.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {3}, pages = {}, doi = {10.1093/femsec/fiw014}, pmid = {26832203}, issn = {1574-6941}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/genetics/*isolation &amp; purification ; Bacterial Proteins/*genetics ; Drug Resistance, Bacterial ; Gene Transfer, Horizontal ; Integrons ; Sewage/microbiology ; Wastewater/*microbiology ; Water Purification/*instrumentation ; }, abstract = {Antibiotic resistance among bacteria is a growing problem worldwide, and wastewater treatment plants have been considered as one of the major contributors to the dissemination of antibiotic resistance to the environment. There is a lack of comprehensive quantitative molecular data on extensive numbers of antibiotic resistance genes (ARGs) in different seasons with a sampling strategy that would cover both incoming and outgoing water together with the excess sludge that is removed from the process. In order to fill that gap we present a highly parallel quantitative analysis of ARGs and horizontal gene transfer potential over four seasons at an urban wastewater treatment plant using a high-throughput qPCR array. All analysed transposases and two-thirds of primer sets targeting ARGs were detected in the wastewater. The relative abundance of most of the genes was highest in influent and lower in effluent water and sludge. The resistance profiles of the samples cluster by sample location with a shift from raw influent through the final effluents and dried sludge to the sediments. Wastewater discharge enriched only a few genes, namely Tn25 type transposase gene and clinical class 1 integrons, in the sediment near the discharge pipe, but those enriched genes may indicate a potential for horizontal gene transfer.}, }
@article {pmid26832092, year = {2016}, author = {Beever, J and Morar, N}, title = {The Porosity of Autonomy: Social and Biological Constitution of the Patient in Biomedicine.}, journal = {The American journal of bioethics : AJOB}, volume = {16}, number = {2}, pages = {34-45}, doi = {10.1080/15265161.2015.1120793}, pmid = {26832092}, issn = {1536-0075}, mesh = {*Brain ; Concept Formation ; Ethical Analysis ; Ethical Theory ; *Feminism ; *Gastrointestinal Microbiome ; Humans ; *Interpersonal Relations ; Moral Obligations ; Obesity/microbiology ; *Patients/psychology ; *Personal Autonomy ; Physician-Patient Relations/ethics ; Weight Gain ; }, abstract = {The nature and role of the patient in biomedicine comprise issues central to bioethical inquiry. Given its developmental history grounded firmly in a backlash against 20th-century cases of egregious human subjects abuse, contemporary medical bioethics has come to rely on a fundamental assumption: the unit of care (and the unit of value) is the autonomous self-directing patient. In this article we examine first the structure of the feminist social critique of autonomy. Then we show that a parallel argument can be made against relational autonomy as well, demonstrating how this second concept of autonomy fails to take sufficiently into account an array of biological determinants, particularly those from microbial biology. Finally, in light of this biological critique, we question whether or to what extent any relevant and meaningful view of autonomy can be recovered in the contemporary landscape of bioethics.}, }
@article {pmid26828626, year = {2016}, author = {Singh, V and Yeoh, BS and Vijay-Kumar, M}, title = {Gut microbiome as a novel cardiovascular therapeutic target.}, journal = {Current opinion in pharmacology}, volume = {27}, number = {}, pages = {8-12}, pmid = {26828626}, issn = {1471-4973}, support = {R01 DK097865/DK/NIDDK NIH HHS/United States ; R01 DK097865-01A1/DK/NIDDK NIH HHS/United States ; T32AI07445/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Cardiovascular Diseases/*etiology/metabolism/*microbiology ; Gastrointestinal Microbiome/*drug effects/*physiology ; Humans ; Intestines/*microbiology ; Risk Factors ; }, abstract = {Over the last two decades, our understanding of gut microbiotal composition and its association with intra-intestinal and extra-intestinal diseases including risk factors of cardiovascular disease (CVD) namely metabolic syndrome and atherosclerosis, have been increased exponentially. A pertinent question which often arises in researchers' community is on how to manipulate the gut microbial ecology to 'cure' the cardiovascular risk factors. Accordingly, in this review we summarized the potential strategies, based on our current knowledge on gut microbiota in modulating CVD, how gut microbiota can be therapeutically exploited by targeting their metabolic activity to alleviate the risk factors of CVD.}, }
@article {pmid26827256, year = {2016}, author = {Vaiopoulou, E and Provijn, T and Prévoteau, A and Pikaar, I and Rabaey, K}, title = {Electrochemical sulfide removal and caustic recovery from spent caustic streams.}, journal = {Water research}, volume = {92}, number = {}, pages = {38-43}, doi = {10.1016/j.watres.2016.01.039}, pmid = {26827256}, issn = {1879-2448}, mesh = {Caustics/*isolation &amp; purification ; Electricity ; Electrochemistry/instrumentation/*methods ; Electrodes ; Hydrogen-Ion Concentration ; Oxidation-Reduction ; Rivers/*chemistry ; Sulfides/*isolation &amp; purification ; Waste Disposal, Fluid ; Water Purification/methods ; }, abstract = {Spent caustic streams (SCS) are produced during alkaline scrubbing of sulfide containing sour gases. Conventional methods mainly involve considerable chemical dosing or energy expenditures entailing high cost but limited benefits. Here we propose an electrochemical treatment approach involving anodic sulfide oxidation preferentially to sulfur coupled to cathodic caustic recovery using a two-compartment electrochemical system. Batch experiments showed sulfide removal efficiencies of 84 ± 4% with concomitant 57 ± 4% efficient caustic production in the catholyte at a final concentration of 6.4 ± 0.1 wt% NaOH (1.6 M) at an applied current density of 100 A m(-2). Subsequent long-term continuous experiments showed that stable cell voltages (i.e. 2.7 ± 0.1 V) as well as constant sulfide removal efficiencies of 67 ± 5% at a loading rate of 47 g(S) L(-1) h(-1) were achieved over a period of 77 days. Caustic was produced at industrially relevant strengths for scrubbing (i.e. 5.1 ± 0.9 wt% NaOH) at current efficiencies of 96 ± 2%. Current density between 0 and 200 A m(-2) and sulfide loading rates of 50-200 g(S) L(-1) d(-1) were tested. The higher the current density the more oxidized the sulfur species produced and the higher the sulfide oxidation. On the contrary, high loading rate resulted in a reduction of sulfide oxidation efficiency. The results obtained in this study together with engineering calculations show that the proposed process could represent a cost-effective approach for sodium and sulfur recovery from SCS.}, }
@article {pmid26826796, year = {2016}, author = {Obeng, N and Pratama, AA and Elsas, JDV}, title = {The Significance of Mutualistic Phages for Bacterial Ecology and Evolution.}, journal = {Trends in microbiology}, volume = {24}, number = {6}, pages = {440-449}, doi = {10.1016/j.tim.2015.12.009}, pmid = {26826796}, issn = {1878-4380}, mesh = {Bacteria/genetics/immunology/metabolism/*virology ; Bacteriophages/genetics/pathogenicity/*physiology ; Biofilms/growth &amp; development ; Biological Coevolution ; CRISPR-Cas Systems ; *Ecology ; *Evolution, Molecular ; Genome, Viral ; Host-Pathogen Interactions/genetics/*physiology ; Phenotype ; *Symbiosis ; Virulence ; }, abstract = {Bacteria and phages have traditionally been viewed as 'antagonists'. However, temperate phages can transfer genes, which can broaden their bacterial hosts' metabolic repertoire, confer or enhance virulence, or eliminate competing organisms, and so enhance bacterial fitness. Recent evidence shows that phages can also promote biofilm formation leading to population-level benefits for their bacterial hosts. Here, we provide a perspective on the ecological and evolutionary consequences for the bacteria interacting with phages, when phage and host interests are aligned. Furthermore, we examine the question whether bacterial hosts can lower immune barriers to phage infection, thereby facilitating infection by beneficial phages. Taking recent evidence together, we suggest that in many cases temperate phages are to be considered as being mutualistic as well as parasitic, at the same time.}, }
@article {pmid26826340, year = {2016}, author = {Zimmermann, J and Wentrup, C and Sadowski, M and Blazejak, A and Gruber-Vodicka, HR and Kleiner, M and Ott, JA and Cronholm, B and De Wit, P and Erséus, C and Dubilier, N}, title = {Closely coupled evolutionary history of ecto- and endosymbionts from two distantly related animal phyla.}, journal = {Molecular ecology}, volume = {25}, number = {13}, pages = {3203-3223}, doi = {10.1111/mec.13554}, pmid = {26826340}, issn = {1365-294X}, mesh = {Animals ; Annelida/*microbiology ; *Biological Evolution ; DNA, Bacterial/genetics ; Gammaproteobacteria/*genetics ; Genetic Markers ; Nematoda/*microbiology ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {The level of integration between associated partners can range from ectosymbioses to extracellular and intracellular endosymbioses, and this range has been assumed to reflect a continuum from less intimate to evolutionarily highly stable associations. In this study, we examined the specificity and evolutionary history of marine symbioses in a group of closely related sulphur-oxidizing bacteria, called Candidatus Thiosymbion, that have established ecto- and endosymbioses with two distantly related animal phyla, Nematoda and Annelida. Intriguingly, in the ectosymbiotic associations of stilbonematine nematodes, we observed a high degree of congruence between symbiont and host phylogenies, based on their ribosomal RNA (rRNA) genes. In contrast, for the endosymbioses of gutless phallodriline annelids (oligochaetes), we found only a weak congruence between symbiont and host phylogenies, based on analyses of symbiont 16S rRNA genes and six host genetic markers. The much higher degree of congruence between nematodes and their ectosymbionts compared to those of annelids and their endosymbionts was confirmed by cophylogenetic analyses. These revealed 15 significant codivergence events between stilbonematine nematodes and their ectosymbionts, but only one event between gutless phallodrilines and their endosymbionts. Phylogenetic analyses of 16S rRNA gene sequences from 50 Cand. Thiosymbion species revealed seven well-supported clades that contained both stilbonematine ectosymbionts and phallodriline endosymbionts. This closely coupled evolutionary history of marine ecto- and endosymbionts suggests that switches between symbiotic lifestyles and between the two host phyla occurred multiple times during the evolution of the Cand. Thiosymbion clade, and highlights the remarkable flexibility of these symbiotic bacteria.}, }
@article {pmid26825820, year = {2016}, author = {Etchebehere, C and Castelló, E and Wenzel, J and del Pilar Anzola-Rojas, M and Borzacconi, L and Buitrón, G and Cabrol, L and Carminato, VM and Carrillo-Reyes, J and Cisneros-Pérez, C and Fuentes, L and Moreno-Andrade, I and Razo-Flores, E and Filippi, GR and Tapia-Venegas, E and Toledo-Alarcón, J and Zaiat, M}, title = {Microbial communities from 20 different hydrogen-producing reactors studied by 454 pyrosequencing.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {7}, pages = {3371-3384}, doi = {10.1007/s00253-016-7325-y}, pmid = {26825820}, issn = {1432-0614}, mesh = {Anaerobiosis ; Bioreactors/*standards ; Clostridium/classification/genetics/metabolism ; Enterobacter/classification/genetics/metabolism ; *Fermentation ; Firmicutes/classification/genetics/metabolism ; High-Throughput Nucleotide Sequencing ; Hydrogen/*metabolism ; Lactobacillus/classification/genetics/metabolism ; Latin America ; Microbial Consortia/*genetics ; Proteobacteria/classification/genetics/metabolism ; RNA, Ribosomal, 16S/*genetics ; Thermotoga maritima/classification/genetics/metabolism ; Veillonellaceae/classification/genetics/metabolism ; }, abstract = {To provide new insight into the dark fermentation process, a multi-lateral study was performed to study the microbiology of 20 different lab-scale bioreactors operated in four different countries (Brazil, Chile, Mexico, and Uruguay). Samples (29) were collected from bioreactors with different configurations, operation conditions, and performances. The microbial communities were analyzed using 16S rRNA genes 454 pyrosequencing. The results showed notably uneven communities with a high predominance of a particular genus. The phylum Firmicutes predominated in most of the samples, but the phyla Thermotogae or Proteobacteria dominated in a few samples. Genera from three physiological groups were detected: high-yield hydrogen producers (Clostridium, Kosmotoga, Enterobacter), fermenters with low-hydrogen yield (mostly from Veillonelaceae), and competitors (Lactobacillus). Inocula, reactor configurations, and substrates influence the microbial communities. This is the first joint effort that evaluates hydrogen-producing reactors and operational conditions from different countries and contributes to understand the dark fermentation process.}, }
@article {pmid26824176, year = {2016}, author = {Dini-Andreote, F and Pylro, VS and Baldrian, P and van Elsas, JD and Salles, JF}, title = {Ecological succession reveals potential signatures of marine-terrestrial transition in salt marsh fungal communities.}, journal = {The ISME journal}, volume = {10}, number = {8}, pages = {1984-1997}, pmid = {26824176}, issn = {1751-7370}, mesh = {Biodiversity ; Ecology ; Ecosystem ; Environment ; Fungi/*classification/genetics/physiology ; Salinity ; Soil ; *Soil Microbiology ; *Wetlands ; }, abstract = {Marine-to-terrestrial transition represents one of the most fundamental shifts in microbial life. Understanding the distribution and drivers of soil microbial communities across coastal ecosystems is critical given the roles of microbes in soil biogeochemistry and their multifaceted influence on landscape succession. Here, we studied the fungal community dynamics in a well-established salt marsh chronosequence that spans over a century of ecosystem development. We focussed on providing high-resolution assessments of community composition, diversity and ecophysiological shifts that yielded patterns of ecological succession through soil formation. Notably, despite containing 10- to 100-fold lower fungal internal transcribed spacer abundances, early-successional sites revealed fungal richnesses comparable to those of more mature soils. These newly formed sites also exhibited significant temporal variations in β-diversity that may be attributed to the highly dynamic nature of the system imposed by the tidal regime. The fungal community compositions and ecophysiological assignments changed substantially along the successional gradient, revealing a clear signature of ecological replacement and gradually transforming the environment from a marine into a terrestrial system. Moreover, distance-based linear modelling revealed soil physical structure and organic matter to be the best predictors of the shifts in fungal β-diversity along the chronosequence. Taken together, our study lays the basis for a better understanding of the spatiotemporally determined fungal community dynamics in salt marshes and highlights their ecophysiological traits and adaptation in an evolving ecosystem.}, }
@article {pmid26823997, year = {2016}, author = {Verstraelen, H and Vilchez-Vargas, R and Desimpel, F and Jauregui, R and Vankeirsbilck, N and Weyers, S and Verhelst, R and De Sutter, P and Pieper, DH and Van De Wiele, T}, title = {Characterisation of the human uterine microbiome in non-pregnant women through deep sequencing of the V1-2 region of the 16S rRNA gene.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e1602}, pmid = {26823997}, issn = {2167-8359}, abstract = {Background. It is widely assumed that the uterine cavity in non-pregnant women is physiologically sterile, also as a premise to the long-held view that human infants develop in a sterile uterine environment, though likely reflecting under-appraisal of the extent of the human bacterial metacommunity. In an exploratory study, we aimed to investigate the putative presence of a uterine microbiome in a selected series of non-pregnant women through deep sequencing of the V1-2 hypervariable region of the 16S ribosomal RNA (rRNA) gene. Methods. Nineteen women with various reproductive conditions, including subfertility, scheduled for hysteroscopy and not showing uterine anomalies were recruited. Subjects were highly diverse with regard to demographic and medical history and included nulliparous and parous women. Endometrial tissue and mucus harvesting was performed by use of a transcervical device designed to obtain endometrial biopsy, while avoiding cervicovaginal contamination. Bacteria were targeted by use of a barcoded Illumina MiSeq paired-end sequencing method targeting the 16S rRNA gene V1-2 region, yielding an average of 41,194 reads per sample after quality filtering. Taxonomic annotation was pursued by comparison with sequences available through the Ribosomal Database Project and the NCBI database. Results. Out of 183 unique 16S rRNA gene amplicon sequences, 15 phylotypes were present in all samples. In some 90% of the women included, community architecture was fairly similar inasmuch B. xylanisolvens, B. thetaiotaomicron, B. fragilis and an undetermined Pelomonas taxon constituted over one third of the endometrial bacterial community. On the singular phylotype level, six women showed predominance of L. crispatus or L. iners in the presence of the Bacteroides core. Two endometrial communities were highly dissimilar, largely lacking the Bacteroides core, one dominated by L. crispatus and another consisting of a highly diverse community, including Prevotella spp., Atopobium vaginae, and Mobiluncus curtisii. Discussion. Our findings are, albeit not necessarily generalizable, consistent with the presence of a unique microbiota dominated by Bacteroides residing on the endometrium of the human non-pregnant uterus. The transcervical sampling approach may be influenced to an unknown extent by endocervical microbiota, which remain uncharacterised, and therefore warrants further validation. Nonetheless, consistent with our understanding of the human microbiome, the uterine microbiota are likely to have a previously unrecognized role in uterine physiology and human reproduction. Further study is therefore warranted to document community ecology and dynamics of the uterine microbiota, as well as the role of the uterine microbiome in health and disease.}, }
@article {pmid26823973, year = {2016}, author = {Benítez-Páez, A and Portune, KJ and Sanz, Y}, title = {Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer.}, journal = {GigaScience}, volume = {5}, number = {}, pages = {4}, pmid = {26823973}, issn = {2047-217X}, mesh = {Bacteria/classification/genetics ; Bacterial Typing Techniques/methods ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Nanopores ; Nucleic Acid Amplification Techniques/*methods ; RNA, Ribosomal, 16S/*genetics ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; Species Specificity ; }, abstract = {BACKGROUND: The miniaturised and portable DNA sequencer MinION™ has been released to the scientific community within the framework of an early access programme to evaluate its application for a wide variety of genetic approaches. This technology has demonstrated great potential, especially in genome-wide analyses. In this study, we tested the ability of the MinION™ system to perform amplicon sequencing in order to design new approaches to study microbial diversity using nearly full-length 16S rDNA sequences.<br><br>RESULTS: Using R7.3 chemistry, we generated more than 3.8 million events (nt) during a single sequencing run. These data were sufficient to reconstruct more than 90&#xa0;% of the 16S rRNA gene sequences for 20 different species present in a mock reference community. After read mapping and 16S rRNA gene assembly, consensus sequences and 2d reads were recovered to assign taxonomic classification down to the species level. Additionally, we were able to measure the relative abundance of all the species present in a mock community and detected a biased species distribution originating from the PCR reaction using 'universal' primers.<br><br>CONCLUSIONS: Although nanopore-based sequencing produces reads with lower per-base accuracy compared with other platforms, the MinION&#x2122; DNA sequencer is valuable for both high taxonomic resolution and microbial diversity analysis. Improvements in nanopore chemistry, such as minimising base-calling errors and the nucleotide bias reported here for 16S amplicon sequencing, will further deliver more reliable information that is useful for the specific detection of microbial species and strains in complex ecosystems.}, }
@article {pmid26822785, year = {2016}, author = {Maruthamuthu, M and Jiménez, DJ and Stevens, P and van Elsas, JD}, title = {A multi-substrate approach for functional metagenomics-based screening for (hemi)cellulases in two wheat straw-degrading microbial consortia unveils novel thermoalkaliphilic enzymes.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {86}, pmid = {26822785}, issn = {1471-2164}, mesh = {Carbohydrate Metabolism/genetics ; Cellulases/chemistry/*genetics/metabolism ; Gene Library ; Gene Order ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; *Microbial Consortia/genetics ; Triticum/*microbiology ; Xylosidases/genetics ; alpha-Galactosidase/genetics ; beta-Galactosidase/genetics ; }, abstract = {BACKGROUND: Functional metagenomics is a promising strategy for the exploration of the biocatalytic potential of microbiomes in order to uncover novel enzymes for industrial processes (e.g. biorefining or bleaching pulp). Most current methodologies used to screen for enzymes involved in plant biomass degradation are based on the use of single substrates. Moreover, highly diverse environments are used as metagenomic sources. However, such methods suffer from low hit rates of positive clones and hence the discovery of novel enzymatic activities from metagenomes has been hampered.<br><br>RESULTS: Here, we constructed fosmid libraries from two wheat straw-degrading microbial consortia, denoted RWS (bred on untreated wheat straw) and TWS (bred on heat-treated wheat straw). Approximately 22,000 clones from each library were screened for (hemi)cellulose-degrading enzymes using a multi-chromogenic substrate approach. The screens yielded 71 positive clones for both libraries, giving hit rates of 1:440 and 1:1,047 for RWS and TWS, respectively. Seven clones (NT2-2, T5-5, NT18-17, T4-1, 10BT, NT18-21 and T17-2) were selected for sequence analyses. Their inserts revealed the presence of 18 genes encoding enzymes belonging to twelve different glycosyl hydrolase families (GH2, GH3, GH13, GH17, GH20, GH27, GH32, GH39, GH53, GH58, GH65 and GH109). These encompassed several carbohydrate-active gene clusters traceable mainly to Klebsiella related species. Detailed functional analyses showed that clone NT2-2 (containing a beta-galactosidase of ~116 kDa) had highest enzymatic activity at 55 &#xb0;C and pH 9.0. Additionally, clone T5-5 (containing a beta-xylosidase of ~86 kDa) showed > 90% of enzymatic activity at 55 &#xb0;C and pH 10.0.<br><br>CONCLUSIONS: This study employed a high-throughput method for rapid screening of fosmid metagenomic libraries for (hemi)cellulose-degrading enzymes. The approach, consisting of screens on multi-substrates coupled to further analyses, revealed high hit rates, as compared with recent other studies. Two clones, 10BT and T4-1, required the presence of multiple substrates for detectable activity, indicating a new avenue in library activity screening. Finally, clones NT2-2, T5-5 and NT18-17 were found to encode putative novel thermo-alkaline enzymes, which could represent a starting point for further biotechnological applications.}, }
@article {pmid26819854, year = {2016}, author = {Lewis, ZT and Davis, JC and Smilowitz, JT and German, JB and Lebrilla, CB and Mills, DA}, title = {The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e1612}, pmid = {26819854}, issn = {2167-8359}, support = {R01 AT007079/AT/NCCIH NIH HHS/United States ; R01 AT008759/AT/NCCIH NIH HHS/United States ; R01 HD061923/HD/NICHD NIH HHS/United States ; }, abstract = {Infant fecal samples are commonly studied to investigate the impacts of breastfeeding on the development of the microbiota and subsequent health effects. Comparisons of infants living in different geographic regions and environmental contexts are needed to aid our understanding of evolutionarily-selected milk adaptations. However, the preservation of fecal samples from individuals in remote locales until they can be processed can be a challenge. Freeze-drying (lyophilization) offers a cost-effective way to preserve some biological samples for transport and analysis at a later date. Currently, it is unknown what, if any, biases are introduced into various analyses by the freeze-drying process. Here, we investigated how freeze-drying affected analysis of two relevant and intertwined aspects of infant fecal samples, marker gene amplicon sequencing of the bacterial community and the fecal oligosaccharide profile (undigested human milk oligosaccharides). No differences were discovered between the fecal oligosaccharide profiles of wet and freeze-dried samples. The marker gene sequencing data showed an increase in proportional representation of Bacteriodes and a decrease in detection of bifidobacteria and members of class Bacilli after freeze-drying. This sample treatment bias may possibly be related to the cell morphology of these different taxa (Gram status). However, these effects did not overwhelm the natural variation among individuals, as the community data still strongly grouped by subject and not by freeze-drying status. We also found that compensating for sample concentration during freeze-drying, while not necessary, was also not detrimental. Freeze-drying may therefore be an acceptable method of sample preservation and mass reduction for some studies of microbial ecology and milk glycan analysis.}, }
@article {pmid26816092, year = {2016}, author = {Westerholm, M and Crauwels, S and Van Geel, M and Dewil, R and Lievens, B and Appels, L}, title = {Microwave and ultrasound pre-treatments influence microbial community structure and digester performance in anaerobic digestion of waste activated sludge.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {12}, pages = {5339-5352}, doi = {10.1007/s00253-016-7321-2}, pmid = {26816092}, issn = {1432-0614}, mesh = {Anaerobiosis/physiology/radiation effects ; Archaea/genetics/physiology/radiation effects ; Bacteroidetes/genetics/physiology/radiation effects ; Biofuels ; Bioreactors/microbiology ; Euryarchaeota/genetics/physiology/radiation effects ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Methane/*biosynthesis ; Microbial Consortia/genetics/*physiology/radiation effects ; *Microwaves ; Proteobacteria/genetics/physiology/radiation effects ; RNA, Ribosomal, 16S ; Real-Time Polymerase Chain Reaction ; Sewage/chemistry/*microbiology ; *Ultrasonic Waves ; }, abstract = {Comparative analyses of bacterial and archaeal community structures and dynamics in three biogas digesters during start-up and subsequent operation using microwaved, ultrasonicated or untreated waste activated sludge were performed based on 454 pyrosequencing datasets of part of 16S ribosomal RNA sequences and quantitative PCR. The pre-treatment increased the solubility, and thus the availability of the substrate for microbial degradation and significantly affected the succession of the anaerobic community structure over the course of the digestion. Bacteroidetes, Proteobacteria and Firmicutes were the dominant phyla in all digesters throughout operation. Proteobacteria decreased in relative abundance from 23-26 % to 11-13 % in association with enhanced substrate availability. Negative correlations between relative abundance of Alpha-, Beta- and Gammaproteobacteria and the substrate availability and/or biogas production were disclosed in statistical analyses. Clostridiales was the dominant order in Firmicutes, and Clostridiales, Clostridia and Firmicutes relative abundance and richness were shown to positively correlate with substrate availability and biogas generation. Methanogenic communities had a fairly restricted structure, highly dominated by Methanosaeta and Methanobrevibacter phylotypes. A gradual decline in Methanobrevibacter and increased representation of Methanosaeta concilii over time were particularly apparent in the digester receiving untreated waste activated sludge, whereas more diversified archaeal communities were maintained in the pre-treatment digesters. The quantitative PCR analyses revealed a methanogenic community distribution that coincided with the 454 pyrosequencing data.}, }
@article {pmid26811460, year = {2016}, author = {Mark Welch, JL and Rossetti, BJ and Rieken, CW and Dewhirst, FE and Borisy, GG}, title = {Biogeography of a human oral microbiome at the micron scale.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {6}, pages = {E791-800}, pmid = {26811460}, issn = {1091-6490}, support = {R01 DE022586/DE/NIDCR NIH HHS/United States ; R13 GM085967/GM/NIGMS NIH HHS/United States ; R37 DE016937/DE/NIDCR NIH HHS/United States ; DE022586/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/*classification ; Dental Plaque/microbiology ; Gingiva/pathology ; Humans ; Metagenomics ; Microbial Consortia ; *Microbiota ; Models, Biological ; Mouth/*microbiology ; *Phylogeography ; Sequence Analysis, DNA ; }, abstract = {The spatial organization of complex natural microbiomes is critical to understanding the interactions of the individual taxa that comprise a community. Although the revolution in DNA sequencing has provided an abundance of genomic-level information, the biogeography of microbiomes is almost entirely uncharted at the micron scale. Using spectral imaging fluorescence in situ hybridization as guided by metagenomic sequence analysis, we have discovered a distinctive, multigenus consortium in the microbiome of supragingival dental plaque. The consortium consists of a radially arranged, nine-taxon structure organized around cells of filamentous corynebacteria. The consortium ranges in size from a few tens to a few hundreds of microns in radius and is spatially differentiated. Within the structure, individual taxa are localized at the micron scale in ways suggestive of their functional niche in the consortium. For example, anaerobic taxa tend to be in the interior, whereas facultative or obligate aerobes tend to be at the periphery of the consortium. Consumers and producers of certain metabolites, such as lactate, tend to be near each other. Based on our observations and the literature, we propose a model for plaque microbiome development and maintenance consistent with known metabolic, adherence, and environmental considerations. The consortium illustrates how complex structural organization can emerge from the micron-scale interactions of its constituent organisms. The understanding that plaque community organization is an emergent phenomenon offers a perspective that is general in nature and applicable to other microbiomes.}, }
@article {pmid26810996, year = {2016}, author = {Silano, M and Agostoni, C and Sanz, Y and Guandalini, S}, title = {Infant feeding and risk of developing celiac disease: a systematic review.}, journal = {BMJ open}, volume = {6}, number = {1}, pages = {e009163}, pmid = {26810996}, issn = {2044-6055}, support = {UL1 TR000430/TR/NCATS NIH HHS/United States ; }, mesh = {*Breast Feeding ; Celiac Disease/epidemiology/*prevention &amp; control ; Glutens/administration &amp; dosage ; Humans ; Infant ; Risk Assessment ; Risk Factors ; Time Factors ; Weaning ; }, abstract = {OBJECTIVE: To review the evidence for the association of breast feeding, breastfeeding duration or the timing of gluten introduction and the later development of celiac disease (CD).<br><br>DESIGN: Systematic review.<br><br>METHODS: We searched MEDLINE, via PubMed, EMBASE and Web of Science, for studies published up to 31 August 2015 investigating the association of breastfeeding duration, breast feeding at the moment of gluten introduction or the timing of gluten introduction and the later development of CD. Prospective studies had to enrol infants/children at high risk of CD. For retrospective studies, participants had to be children or adults with CD. The paper quality was assessed by means of a GRADE score and the bias risk was assessed by the Newcastle-Ottawa Scale (for observational cohort studies) and Cochrane Collaboration's tool (for randomised trials).<br><br>RESULTS: Out of 149 retrieved papers, 48 were considered in depth and 16 were included in this review (9 were prospective and 2 were interventional). We found that neither duration of breastfeeding nor breastfeeding at time of gluten introduction nor the delayed introduction of gluten during weaning were effective in preventing later development of CD.<br><br>CONCLUSIONS: Currently, there is no evidence on the optimal breastfeeding duration or the effects of avoiding early (<4 months of age) or late (&#x2265; 6 or even at 12 months) gluten introduction in children at risk of CD. Accordingly, no specific general recommendations about gluten introduction or optimal breastfeeding duration can be presently provided on evidence-based criteria in order to prevent CD.}, }
@article {pmid26809776, year = {2016}, author = {Keren, R and Lavy, A and Ilan, M}, title = {Increasing the Richness of Culturable Arsenic-Tolerant Bacteria from Theonella swinhoei by Addition of Sponge Skeleton to the Growth Medium.}, journal = {Microbial ecology}, volume = {71}, number = {4}, pages = {873-886}, pmid = {26809776}, issn = {1432-184X}, mesh = {Animals ; Arsenates/*pharmacology ; Arsenic/metabolism ; Arsenites/*pharmacology ; Bacteria/classification/*drug effects/genetics/isolation &amp; purification ; Biodiversity ; Culture Media ; Genes, Bacterial ; Indian Ocean ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater ; Symbiosis ; Theonella/chemistry/*microbiology ; }, abstract = {Theonella swinhoei is an arsenic hyper-accumulator sponge, harboring a multitude of associated bacteria. These bacteria reside in the mesohyl, the dense extracellular matrix of the sponge. Previous elemental analysis of separated cell fractions from the sponge had determined that arsenic is localized to the associated bacteria. Subsequently, sponge-associated arsenic-tolerant bacteria were isolated here and grouped into 15 operational taxonomic units (OTUs, 97% similarity). Both culture-dependent and culture-independent work had revealed that T. swinhoei harbors a highly diverse bacterial community. It was thus hypothesized the acclimation of bacteria in the presence of a sponge skeleton, better mimicking its natural environment, would increase the yield of isolation of sponge-associated bacteria. Using seven modularly designed media, 380 bacteria isolates were grown and grouped into 22 OTUs. Inclusion of sponge skeleton in the growth medium promoted bacterial growth in all seven media, accounting for 20 of the 22 identified OTUs (the other two in a medium without skeleton). Diversity and richness indices were calculated for each treatment or combination of treatments with shared growth parameters. Integrating data inherent in the modularly designed media with the ecological indices led to the formation of new hypotheses regarding the aeration conditions and expected arsenic form in situ. Both aerobic and anoxic conditions are expected to occur in the sponge (temporally and/or spatially). Arsenate is expected to be the dominant (or even the only) arsenic form in the sponge.}, }
@article {pmid26809340, year = {2016}, author = {Rydzanicz, K and Jawień, P and Lonc, E and Modelska, M}, title = {Assessment of productivity of Culex spp. larvae (Diptera: Culicidae) in urban storm water catch basin system in Wrocław (SW Poland).}, journal = {Parasitology research}, volume = {115}, number = {4}, pages = {1711-1720}, pmid = {26809340}, issn = {1432-1955}, mesh = {Animals ; Cities ; Culex/*physiology ; Drainage, Sanitary ; Environment ; Larva/physiology ; Mosquito Control/methods ; Poland ; Pupa ; Seasons ; Temperature ; Water ; }, abstract = {In urban environments, catch basins serve as major developmental and resting sites for anthropophilic and zoophilic mosquitoes. However, the use of this habitat is inconsistent, with abundance of larvae varying significantly across catch basins at a fine spatial scale. During seasonal summer investigations on mosquito species composition, their spatial and temporal distribution and the environmental characteristic of the breeding sites in the underground storm drain systems of the Wrocław urban area (SW Poland) were assessed from May to September in 2012-2013. The study was conducted in order to develop a rational strategy to control mosquito populations and prevent the potential human exposure to mosquito-transmitted pathogens. Mosquito larvae and pupae were collected and identified weekly from 100 regularly inspected street catch basins located in the town center. All existing and potential breeding habitats in the study area were recorded using a GPS receiver (Magellan MobileMapper CX) and transferred to the computer database. Collected data on the geographical location of inspected breeding places, water quality parameters in inspected catch basins, daily temperature, and precipitation were imposed on orthophotomap in ArcGIS (ESRI, USA). Water quality parameters including pH, electrical conductivity, and water temperature were measured by standard methods. Chemical water analysis of cations (Na(+), NH4 (+), K(+), Mg(2+), Ca(2+)) and anions (Cl(-), NO2 (-), NO3 (-), SO4 (2-)) were carried out using Waters Alliance high-performance liquid chromatograph (HPLC) 2695 with 432 Conductivity Detector and 2998 Photodiode Array Detector, an IC-Pak Anion HR column (glauconate/borate eluent) and IC-Pak Cation M/D column (EDTA/HNO3 eluent). Over two seasonal studies and 3739 samplings in total, 3669 mosquito larvae and 274 pupae/1 dip (from 0 to 110 individuals/dip) were collected by dipper. Culex pipiens s.l. (L.) and Cx. torrentium (Martini) prevailed at all catch basins of the study area as the predominant species. In all examined catch basins, autogenous individuals dominated by far. Breeding activity was first detected in early May. Peak abundance of Culex spp. population in many catch basins was observed in June 2012 and August 2013 when average daily temperatures were increasing and rainfall had declined. Dry periods between rainfalls varied during 2 years of the study period and were noted on June 2012 as well as on July and August 2013. Organically enriched catch basins with significant higher concentrations of Na(+) and NO3 (-) were found to be more productive breeding habitats. Differences in the Culex immature stage density based on the variables of habitat type, temperature, and precipitation support the need for ongoing surveillance in communities to guide public health officials in planning for and prioritizing mosquito control efforts.}, }
@article {pmid26805821, year = {2016}, author = {Liu, Y and Zachow, C and Raaijmakers, JM and de Bruijn, I}, title = {Elucidating the Diversity of Aquatic Microdochium and Trichoderma Species and Their Activity against the Fish Pathogen Saprolegnia diclina.}, journal = {International journal of molecular sciences}, volume = {17}, number = {1}, pages = {}, pmid = {26805821}, issn = {1422-0067}, mesh = {Animals ; *Antibiosis ; Aquaculture ; Biodiversity ; Biological Control Agents ; Fish Diseases/parasitology/*therapy ; Infections/parasitology/*therapy ; Phylogeny ; Salmon/microbiology/parasitology ; Saprolegnia/growth &amp; development/*microbiology/pathogenicity ; Spiroplasma/classification/genetics/*growth &amp; development ; Trichoderma/classification/genetics/*growth &amp; development ; Zygote/microbiology/parasitology ; }, abstract = {Animals and plants are increasingly threatened by emerging fungal and oomycete diseases. Amongst oomycetes, Saprolegnia species cause population declines in aquatic animals, especially fish and amphibians, resulting in significant perturbation in biodiversity, ecological balance and food security. Due to the prohibition of several chemical control agents, novel sustainable measures are required to control Saprolegnia infections in aquaculture. Previously, fungal community analysis by terminal restriction fragment length polymorphism (T-RFLP) revealed that the Ascomycota, specifically the genus Microdochium, was an abundant fungal phylum associated with salmon eggs from a commercial fish farm. Here, phylogenetic analyses showed that most fungal isolates obtained from salmon eggs were closely related to Microdochium lycopodinum/Microdochium phragmitis and Trichoderma viride species. Phylogenetic and quantitative PCR analyses showed both a quantitative and qualitative difference in Trichoderma population between diseased and healthy salmon eggs, which was not the case for the Microdochium population. In vitro antagonistic activity of the fungi against Saprolegnia diclina was isolate-dependent; for most Trichoderma isolates, the typical mycoparasitic coiling around and/or formation of papilla-like structures on S. diclina hyphae were observed. These results suggest that among the fungal community associated with salmon eggs, Trichoderma species may play a role in Saprolegnia suppression in aquaculture.}, }
@article {pmid26801570, year = {2016}, author = {Rath, KM and Maheshwari, A and Bengtson, P and Rousk, J}, title = {Comparative Toxicities of Salts on Microbial Processes in Soil.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {7}, pages = {2012-2020}, pmid = {26801570}, issn = {1098-5336}, mesh = {Bacteria/*drug effects/growth &amp; development ; Fungi/*drug effects/growth &amp; development ; Salts/*toxicity ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Soil salinization is a growing threat to global agriculture and carbon sequestration, but to date it remains unclear how microbial processes will respond. We studied the acute response to salt exposure of a range of anabolic and catabolic microbial processes, including bacterial (leucine incorporation) and fungal (acetate incorporation into ergosterol) growth rates, respiration, and gross N mineralization and nitrification rates. To distinguish effects of specific ions from those of overall ionic strength, we compared the addition of four salts frequently associated with soil salinization (NaCl, KCl, Na2SO4, and K2SO4) to a nonsaline soil. To compare the tolerance of different microbial processes to salt and to interrelate the toxicity of different salts, concentration-response relationships were established. Growth-based measurements revealed that fungi were more resistant to salt exposure than bacteria. Effects by salt on C and N mineralization were indistinguishable, and in contrast to previous studies, nitrification was not found to be more sensitive to salt exposure than other microbial processes. The ion-specific toxicity of certain salts could be observed only for respiration, which was less inhibited by salts containing SO4(2-) than Cl(-) salts, in contrast to the microbial growth assessments. This suggested that the inhibition of microbial growth was explained solely by total ionic strength, while ion-specific toxicity also should be considered for effects on microbial decomposition. This difference resulted in an apparent reduction of microbial growth efficiency in response to exposure to SO4(2-) salts but not to Cl(-) salts; no evidence was found to distinguish K(+) and Na(+) salts.}, }
@article {pmid26797794, year = {2016}, author = {Laurent, C and Lekeux, G and Ukuwela, AA and Xiao, Z and Charlier, JB and Bosman, B and Carnol, M and Motte, P and Damblon, C and Galleni, M and Hanikenne, M}, title = {Metal binding to the N-terminal cytoplasmic domain of the PIB ATPase HMA4 is required for metal transport in Arabidopsis.}, journal = {Plant molecular biology}, volume = {90}, number = {4-5}, pages = {453-466}, pmid = {26797794}, issn = {1573-5028}, mesh = {Adenosine Triphosphatases/genetics/*metabolism ; Amino Acid Motifs ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Biological Transport ; Cadmium/metabolism ; Cell Membrane ; Cloning, Molecular ; Gene Expression Regulation, Plant/*physiology ; Magnetic Resonance Spectroscopy ; Metals/*metabolism ; Models, Molecular ; Mutation ; Protein Binding ; Protein Conformation ; Protein Transport ; Zinc/metabolism ; }, abstract = {PIB ATPases are metal cation pumps that transport metals across membranes. These proteins possess N- and C-terminal cytoplasmic extensions that contain Cys- and His-rich high affinity metal binding domains, which may be involved in metal sensing, metal ion selectivity and/or in regulation of the pump activity. The PIB ATPase HMA4 (Heavy Metal ATPase 4) plays a central role in metal homeostasis in Arabidopsis thaliana and has a key function in zinc and cadmium hypertolerance and hyperaccumulation in the extremophile plant species Arabidopsis halleri. Here, we examined the function and structure of the N-terminal cytoplasmic metal-binding domain of HMA4. We mutagenized a conserved CCTSE metal-binding motif in the domain and assessed the impact of the mutations on protein function and localization in planta, on metal-binding properties in vitro and on protein structure by Nuclear Magnetic Resonance spectroscopy. The two Cys residues of the motif are essential for the function, but not for localization, of HMA4 in planta, whereas the Glu residue is important but not essential. These residues also determine zinc coordination and affinity. Zinc binding to the N-terminal domain is thus crucial for HMA4 protein function, whereas it is not required to maintain the protein structure. Altogether, combining in vivo and in vitro approaches in our study provides insights towards the molecular understanding of metal transport and specificity of metal P-type ATPases.}, }
@article {pmid26791510, year = {2016}, author = {Gorgé, O and Bennett, EA and Massilani, D and Daligault, J and Pruvost, M and Geigl, EM and Grange, T}, title = {Analysis of Ancient DNA in Microbial Ecology.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1399}, number = {}, pages = {289-315}, doi = {10.1007/978-1-4939-3369-3_17}, pmid = {26791510}, issn = {1940-6029}, mesh = {Animals ; DNA, Bacterial/*genetics/isolation &amp; purification ; Fossils ; Genome, Microbial/*genetics ; Genomics/methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Paleontology/*methods ; Soil Microbiology ; }, abstract = {The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of the skeletal remains of ancient humans have revolutionized the knowledge of the evolution of our species, including the discovery of a new hominin, and demonstrated admixtures with more distantly related archaic populations such as Neandertals and Denisovans. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes allows the study of their recent evolution, presently over the last several millennia. These spectacular results have been attained despite the degradation of DNA after the death of the host, which results in very short DNA molecules that become increasingly damaged, only low quantities of which remain. The low quantity of ancient DNA molecules renders their analysis difficult and prone to contamination with modern DNA molecules, in particular via contamination from the reagents used in DNA purification and downstream analysis steps. Finally, the rare ancient molecules are diluted in environmental DNA originating from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples and identifying ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota.}, }
@article {pmid26791504, year = {2016}, author = {Van Nostrand, JD and Yin, H and Wu, L and Yuan, T and Zhou, J}, title = {Hybridization of Environmental Microbial Community Nucleic Acids by GeoChip.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1399}, number = {}, pages = {183-196}, doi = {10.1007/978-1-4939-3369-3_11}, pmid = {26791504}, issn = {1940-6029}, mesh = {Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Fungi/classification/genetics ; *Genetic Variation ; Nucleic Acid Hybridization/*methods ; Oligonucleotide Array Sequence Analysis/*methods ; *Soil Microbiology ; Viruses/classification/genetics ; }, abstract = {Functional gene arrays, like the GeoChip, allow for the study of tens of thousands of genes in a single assay. The GeoChip array (5.0) contains probes for genes involved in geochemical cycling (N, C, S, and P), metal homeostasis, stress response, organic contaminant degradation, antibiotic resistance, secondary metabolism, and virulence factors as well as genes specific for fungi, protists, and viruses. Here, we briefly describe GeoChip design strategies (gene selection and probe design) and discuss minimum quantity and quality requirements for nucleic acids. We then provide detailed protocols for amplification, labeling, and hybridization of samples to the GeoChip.}, }
@article {pmid26791496, year = {2016}, author = {Dequiedt, S and Maron, PA and Ranjard, L}, title = {GenoSol Platform: A Logistic and Technical Platform for Conserving and Exploring Soil Microbial Diversity.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1399}, number = {}, pages = {55-60}, doi = {10.1007/978-1-4939-3369-3_3}, pmid = {26791496}, issn = {1940-6029}, mesh = {Bacteria/*genetics/isolation &amp; purification ; Ecology ; Ecosystem ; *Genetic Variation ; *Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {In 2008, the platform "GenoSol" (http://www.dijon.inra.fr/plateforme_genosol) was created at the INRA (French National Institute for Agronomic Research) of Dijon. This platform was launched by several soil microbial ecologist senior scientists to provide a logistics and technical structure dedicated to the acquisition, conservation, characterization, and supply of genetic resources (DNA) of soils from very large-scale samplings (several hundred to several thousand corresponding to large spatial and/or temporal scales). Thanks to this structure metagenomic analysis of soil microbial communities has been standardized as well as a reliable reference system for analysis of the microbial genetic resources of the collected soils (more than 10,000 soil samples to date). This platform also illustrates the usefulness of existing soil archives in providing a readily available source of ecological information that is relevant to microbial ecology, probably more than we can currently fathom.}, }
@article {pmid26790864, year = {2016}, author = {Reitschuler, C and Spötl, C and Hofmann, K and Wagner, AO and Illmer, P}, title = {Archaeal Distribution in Moonmilk Deposits from Alpine Caves and Their Ecophysiological Potential.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {686-699}, pmid = {26790864}, issn = {1432-184X}, mesh = {Ammonia/metabolism ; Archaea/classification/genetics/*isolation &amp; purification ; Austria ; Caves ; DNA, Archaeal/genetics ; Ecosystem ; Geologic Sediments/*microbiology ; Oxidation-Reduction ; Phylogeny ; }, abstract = {(Alpine) caves are, in general, windows into the Earth's subsurface. Frequently occurring structures in caves such as moonmilk (secondary calcite deposits) offer the opportunity to study intraterrestrial microbial communities, adapted to oligotrophic and cold conditions. This is an important research field regarding the dimensions of subsurface systems and cold regions on Earth. On a methodological level, moonmilk deposits from 11 caves in the Austrian Alps were collected aseptically and investigated using a molecular (qPCR and DGGE sequencing-based) methodology in order to study the occurrence, abundance, and diversity of the prevailing native Archaea community. Furthermore, these Archaea were enriched in complex media and studied regarding their physiology, with a media selection targeting different physiological requirements, e.g. methanogenesis and ammonia oxidation. The investigation of the environmental samples showed that all moonmilk deposits were characterized by the presence of the same few habitat-specific archaeal species, showing high abundances and constituting about 50 % of the total microbial communities. The largest fraction of these Archaea was ammonia-oxidizing Thaumarchaeota, while another abundant group was very distantly related to extremophilic Euryarchaeota (Moonmilk Archaea). The archaeal community showed a depth- and oxygen-dependent stratification. Archaea were much more abundant (around 80 %), compared to bacteria, in the actively forming surface part of moonmilk deposits, decreasing to about 5 % down to the bedrock. Via extensive cultivation efforts, it was possible to enrich the enigmatic Moonmilk Archaea and also AOA significantly above the level of bacteria. The most expedient prerequisites for cultivating Moonmilk Archaea were a cold temperature, oligotrophic conditions, short incubation times, a moonmilk surface inoculum, the application of erythromycin, and anaerobic (microaerophilic) conditions. On a physiological level, it seems that methanogenesis is of marginal importance, while ammonia oxidation and a still undiscovered metabolic pathway are vital elements in the (archaeal) moonmilk biome.}, }
@article {pmid26790863, year = {2016}, author = {Sickel, W and Grafe, TU and Meuche, I and Steffan-Dewenter, I and Keller, A}, title = {Bacterial Diversity and Community Structure in Two Bornean Nepenthes Species with Differences in Nitrogen Acquisition Strategies.}, journal = {Microbial ecology}, volume = {71}, number = {4}, pages = {938-953}, pmid = {26790863}, issn = {1432-184X}, mesh = {Acetobacteraceae/isolation &amp; purification ; Animals ; Arthropods/microbiology ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Bacterial Physiological Phenomena ; Biodiversity ; Brunei ; Magnoliopsida/microbiology ; Nitrogen/*metabolism ; Nitrogen-Fixing Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Plant Leaves/microbiology ; Rhizobiaceae/isolation &amp; purification ; Symbiosis ; }, abstract = {Carnivorous plants of the genus Nepenthes have been studied for over a century, but surprisingly little is known about associations with microorganisms. The two species Nepenthes rafflesiana and Nepenthes hemsleyana differ in their pitcher-mediated nutrient sources, sequestering nitrogen from arthropod prey and arthropods as well as bat faeces, respectively. We expected bacterial communities living in the pitchers to resemble this diet difference. Samples were taken from different parts of the pitchers (leaf, peristome, inside, outside, digestive fluid) of both species. Bacterial communities were determined using culture-independent high-throughput amplicon sequencing. Bacterial richness and community structure were similar in leaves, peristomes, inside and outside walls of both plant species. Regarding digestive fluids, bacterial richness was higher in N. hemsleyana than in N. rafflesiana. Additionally, digestive fluid communities were highly variable in structure, with strain-specific differences in community composition between replicates. Acidophilic taxa were mostly of low abundance, except the genus Acidocella, which strikingly reached extremely high levels in two N. rafflesiana fluids. In N. hemsleyana fluid, some taxa classified as vertebrate gut symbionts as well as saprophytes were enriched compared to N. rafflesiana, with saprophytes constituting potential competitors for nutrients. The high variation in community structure might be caused by a number of biotic and abiotic factors. Nitrogen-fixing bacteria were present in both study species, which might provide essential nutrients to the plant at times of low prey capture and/or rare encounters with bats.}, }
@article {pmid26790464, year = {2016}, author = {Alfredsson, H and Clymans, W and Stadmark, J and Conley, D and Rousk, J}, title = {Bacterial and fungal colonization and decomposition of submerged plant litter: consequences for biogenic silica dissolution.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {3}, pages = {}, pmid = {26790464}, issn = {1574-6941}, mesh = {Bacteria/classification/genetics/*growth &amp; development/isolation &amp; purification ; Ecosystem ; Fungi/classification/genetics/*growth &amp; development/isolation &amp; purification ; Nitrogen/analysis/metabolism ; Plants/*microbiology ; Silicon Dioxide/chemistry ; Solubility ; }, abstract = {We studied bacterial and fungal colonization of submerged plant litter, using a known Si-accumulator (Equisetum arvense), in experimental microcosms during one month. We specifically addressed the microbial decomposer role concerning biogenic silica (bSiO2) dissolution from the degrading litter. To vary the rates and level of microbial colonization, the litter was combined with a range of mineral nitrogen (N) and phosphorous (P) supplements. Overall microbial growth on plant litter increased with higher levels of N and P. There was a tendency for higher relative bacterial than fungal stimulation with higher nutrient levels. Differences in microbial colonization of litter between treatments allowed us to test how Si remineralization from plants was influenced by microbial litter decomposition. Contrary to previous results and expectations, we observed a general reduction in Si release from plant litter colonized by a microbial community, compared with sterile control treatments. This suggested that microbial growth resulted in a reduction of dissolved Si concentrations, and we discuss candidate mechanisms to explain this outcome. Hence, our results imply that the microbial role in plant litter associated Si turnover is different from that commonly assumed based on bSiO2 dissolution studies in aquatic ecosystems.}, }
@article {pmid26787693, year = {2016}, author = {Brahmi, S and Touati, A and Cadière, A and Djahmi, N and Pantel, A and Sotto, A and Lavigne, JP and Dunyach-Remy, C}, title = {First Description of Two Sequence Type 2 Acinetobacter baumannii Isolates Carrying OXA-23 Carbapenemase in Pagellus acarne Fished from the Mediterranean Sea near Bejaia, Algeria.}, journal = {Antimicrobial agents and chemotherapy}, volume = {60}, number = {4}, pages = {2513-2515}, pmid = {26787693}, issn = {1098-6596}, mesh = {Acetyltransferases/*genetics/metabolism ; Acinetobacter Infections/epidemiology/microbiology/*veterinary ; Acinetobacter baumannii/classification/drug effects/*genetics/isolation &amp; purification ; Algeria/epidemiology ; Animals ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Fish Diseases/epidemiology/microbiology ; Fish Proteins/*genetics/metabolism ; Gastrointestinal Tract/microbiology ; Gene Expression ; Genotype ; Gills/microbiology ; Mediterranean Sea/epidemiology ; Perciformes ; Phylogeny ; beta-Lactam Resistance/*genetics ; beta-Lactamases/*genetics/metabolism ; }, abstract = {To determine the occurrence of carbapenem-resistantAcinetobacter baumanniiin fish fished from the Mediterranean Sea near the Bejaia coast (Algeria), we studied 300 gills and gut samples that had been randomly and prospectively collected during 1 year. After screening on selective agar media, using PCR arrays and whole-genome sequencing, we identified for the first time two OXA-23-producingA. baumanniistrains belonging to the widespread sequence type 2 (ST2)/international clone II and harboring aminoglycoside-modifying enzymes [aac(6')-Ib andaac(3')-I genes].}, }
@article {pmid26786791, year = {2016}, author = {Paliy, O and Shankar, V}, title = {Application of multivariate statistical techniques in microbial ecology.}, journal = {Molecular ecology}, volume = {25}, number = {5}, pages = {1032-1057}, pmid = {26786791}, issn = {1365-294X}, support = {R03 HD065575/HD/NICHD NIH HHS/United States ; R21 AT003423/AT/NCCIH NIH HHS/United States ; AT003423/AT/NCCIH NIH HHS/United States ; HD065575/HD/NICHD NIH HHS/United States ; }, mesh = {Cluster Analysis ; Discriminant Analysis ; Ecology/*methods ; *Environmental Microbiology ; *Multivariate Analysis ; Principal Component Analysis ; Support Vector Machine ; }, abstract = {Recent advances in high-throughput methods of molecular analyses have led to an explosion of studies generating large-scale ecological data sets. In particular, noticeable effect has been attained in the field of microbial ecology, where new experimental approaches provided in-depth assessments of the composition, functions and dynamic changes of complex microbial communities. Because even a single high-throughput experiment produces large amount of data, powerful statistical techniques of multivariate analysis are well suited to analyse and interpret these data sets. Many different multivariate techniques are available, and often it is not clear which method should be applied to a particular data set. In this review, we describe and compare the most widely used multivariate statistical techniques including exploratory, interpretive and discriminatory procedures. We consider several important limitations and assumptions of these methods, and we present examples of how these approaches have been utilized in recent studies to provide insight into the ecology of the microbial world. Finally, we offer suggestions for the selection of appropriate methods based on the research question and data set structure.}, }
@article {pmid26785934, year = {2016}, author = {Lee, JH and Kim, YG and Lee, K and Kim, CJ and Park, DJ and Ju, Y and Lee, JC and Wood, TK and Lee, J}, title = {Streptomyces-derived actinomycin D inhibits biofilm formation by Staphylococcus aureus and its hemolytic activity.}, journal = {Biofouling}, volume = {32}, number = {1}, pages = {45-56}, doi = {10.1080/08927014.2015.1125888}, pmid = {26785934}, issn = {1029-2454}, mesh = {Anti-Bacterial Agents/pharmacology ; *Biofilms/drug effects/growth &amp; development ; Biofouling/*prevention &amp; control ; Dactinomycin/*pharmacology ; Hemolysis/*drug effects ; Humans ; *Staphylococcus aureus/drug effects/physiology ; Streptomyces/physiology ; Surface-Active Agents/pharmacology ; }, abstract = {Staphylococcus aureus is a versatile human pathogen that produces diverse virulence factors, and its biofilm cells are difficult to eradicate due to their inherent ability to tolerate antibiotics. The anti-biofilm activities of the spent media of 252 diverse endophytic microorganisms were investigated using three S. aureus strains. An attempt was made to identify anti-biofilm compounds in active spent media and to assess their anti-hemolytic activities and hydrophobicities in order to investigate action mechanisms. Unlike other antibiotics, actinomycin D (0.5 μg ml(-1)) from Streptomyces parvulus significantly inhibited biofilm formation by all three S. aureus strains. Actinomycin D inhibited slime production in S. aureus and it inhibited hemolysis by S. aureus and caused S. aureus cells to become less hydrophobic, thus supporting its anti-biofilm effect. In addition, surface coatings containing actinomycin D prevented S. aureus biofilm formation on glass surfaces. Given these results, FDA-approved actinomycin D warrants further attention as a potential antivirulence agent against S. aureus infections.}, }
@article {pmid26784747, year = {2016}, author = {Fernández-Murga, ML and Sanz, Y}, title = {Safety Assessment of Bacteroides uniformis CECT 7771 Isolated from Stools of Healthy Breast-Fed Infants.}, journal = {PloS one}, volume = {11}, number = {1}, pages = {e0145503}, pmid = {26784747}, issn = {1932-6203}, mesh = {Animals ; Bacteroides/isolation &amp; purification/*pathogenicity ; Breast Feeding ; Cytokines/genetics/metabolism ; Feces/microbiology ; Humans ; Infant ; Kidney/microbiology ; Liver/microbiology ; Mice ; Mice, Inbred C57BL ; Nitric Oxide Synthase Type II/genetics/metabolism ; PPAR gamma/genetics/metabolism ; Pancreas/microbiology ; Probiotics/administration &amp; dosage/*adverse effects ; }, abstract = {BACKGROUND: Bacteroides uniformis CECT 7771 is a potential probiotic strain, originally isolated from the stools of healthy breast-feed infants. The strain showed pre-clinical efficacy in a mouse obesity model. The objective of this study was to evaluate its potential toxicity and translocation ability after acute oral administration to mice.<br><br>METHODS AND FINDINGS: A safety study was conducted in immunocompetent and immunosuppressed C57BL-6 mice. Both mouse groups (n = 10 per group) were fed orally 2 x 10(9) colony forming units (cfu)/day of B. uniformis CECT 7771 or placebo by gavage for 6 days. Throughout this time, feed and water intake and body weight were monitored. Afterwards, mice were sacrificed and biological samples were collected to analyze blood and urine biochemistry, inflammatory and immune markers; gut mucosal histology and bacterial translocation to peripheral tissues. The results demonstrated that acute ingestion of this Bacteroides strain had no adverse effects on the animals' general health status or food intake, nor did it affect biochemical indicators of liver, kidney and pancreatic function or gut mucosal histology. Findings also demonstrated that administration did not lead to bacterial translocation to blood, liver or mesenteric lymph nodes. B. uniformis CECT 7771 also downregulated gene and protein expression (iNOS and PPAR-&#x3b3;) and inflammatory cytokines induced by immunosuppression.<br><br>CONCLUSIONS: The findings indicate that the acute oral consumption of B. uniformis CECT 7771 does not raise safety concerns in mice. Further studies in humans should be conducted.}, }
@article {pmid26784356, year = {2016}, author = {Parratt, SR and Laine, AL}, title = {The role of hyperparasitism in microbial pathogen ecology and evolution.}, journal = {The ISME journal}, volume = {10}, number = {8}, pages = {1815-1822}, pmid = {26784356}, issn = {1751-7370}, mesh = {Animals ; *Biological Evolution ; Ecology ; Ecosystem ; *Host-Pathogen Interactions ; Humans ; *Parasites/genetics/pathogenicity/physiology ; Virulence ; }, abstract = {Many micro-organisms employ a parasitic lifestyle and, through their antagonistic interactions with host populations, have major impacts on human, agricultural and natural ecosystems. Most pathogens are likely to host parasites of their own, that is, hyperparasites, but how nested chains of parasites impact on disease dynamics is grossly neglected in the ecological and evolutionary literature. In this minireview we argue that the diversity and dynamics of micro-hyperparasites are an important component of natural host-pathogen systems. We use the current literature from a handful of key systems to show that observed patterns of pathogen virulence and disease dynamics may well be influenced by hyperparasites. Exploring these factors will shed light on many aspects of microbial ecology and disease biology, including resistance-virulence evolution, apparent competition, epidemiology and ecosystem stability. Considering the importance of hyperparasites in natural populations will have applied consequences for the field of biological control and therapeutic science, where hyperparastism is employed as a control mechanism but not necessarily ecologically understood.}, }
@article {pmid26781946, year = {2016}, author = {Lee, MJ and Jeong, HJ and Jang, SH and Lee, SY and Kang, NS and Lee, KH and Kim, HS and Wham, DC and LaJeunesse, TC}, title = {Most Low-Abundance "Background" Symbiodinium spp. Are Transitory and Have Minimal Functional Significance for Symbiotic Corals.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {771-783}, pmid = {26781946}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*parasitology ; Biodiversity ; Dinoflagellida/classification/isolation &amp; purification/*physiology ; Nitrogen/metabolism ; Phylogeny ; Seasons ; Symbiosis ; }, abstract = {Speculation surrounds the importance of ecologically cryptic Symbiodinium spp. (dinoflagellates) that occur at low abundances in reef-building corals and in the surrounding environment. Evidence acquired from extensive sampling, long-term monitoring, and experimental manipulation can allow us to deduce the ecology and functional significance of these populations and whether they might contribute to the response of coral-dinoflagellate mutualisms to climate change. Quantitative PCR was used here to diagnose the prevalence, seasonal variation, and abundances of Symbiodinium spp. within and between colonies of the coral, Alveopora japonica. Consistent with broader geographic sampling, only one species comprised 99.9 %, or greater, the population of symbionts in every sample. However, other Symbiodinium including the non-mutualistic species, Symbiodinium voratum, were often detected, but at estimated cell densities thousands-fold less than the dominant symbiont. The temporal variation in prevalence and abundances of these "background" Symbiodinium could not be definitively related to any particular environmental factor including seasonality and water chemistry. The prevalence (proportion detected among host samples), but not abundance, of S. voratum may weakly correspond to increases in environmental inorganic silica (SiO2) and possibly nitrogen (NO3). When multiple background Symbiodinium occurred within an individual polyp, the average cell densities were positively correlated, suggesting non-specific processes of cell sorting and retention by the animal. While these findings substantiate the existence of a broader, yet uncharacterized, diversity of Symbiodinium, we conclude that only those species which can occur in high abundance and are temporally stable are ultimately important to coral-dinoflagellate mutualisms. Many transient Symbiodinium spp., which occur only at trace abundances in the coral's microbiome, belong to different functional guilds and likely have little, if any, importance to a coral's physiology. The successful integration between host and symbiont into a stable functional unit should therefore be considered when defining host-symbiont specificity.}, }
@article {pmid26780099, year = {2016}, author = {Zarkasi, KZ and Taylor, RS and Abell, GC and Tamplin, ML and Glencross, BD and Bowman, JP}, title = {Atlantic Salmon (Salmo salar L.) Gastrointestinal Microbial Community Dynamics in Relation to Digesta Properties and Diet.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {589-603}, pmid = {26780099}, issn = {1432-184X}, mesh = {Animal Feed/*analysis ; Animals ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Digestion ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/metabolism/*microbiology ; Salmo salar/metabolism/*microbiology ; }, abstract = {To better understand salmon GI tract microbial community dynamics in relation to diet, a feeding trial was performed utilising diets with different proportions of fish meal, protein, lipid and energy levels. Salmon gut dysfunction has been associated with the occurrence of casts, or an empty hind gut. A categorical scoring system describing expressed digesta consistency was evaluated in relation to GI tract community structure. Faster growing fish generally had lower faecal scores while the diet cohorts showed minor differences in faecal score though the overall lowest scores were observed with a low protein, low energy diet. The GI tract bacterial communities were highly dynamic over time with the low protein, low energy diet associated with the most divergent community structure. This included transiently increased abundance of anaerobic (Bacteroidia and Clostridia) during January and February, and facultatively anaerobic (lactic acid bacteria) taxa from February onwards. The digesta had enriched populations of these groups in relation to faecal cast samples. The majority of samples (60-86 %) across all diet cohorts were eventually dominated by the genus Aliivibrio. The results suggest that an interaction between time of sampling and diet is most strongly related to community structure. Digesta categorization revealed microbes involved with metabolism of diet components change progressively over time and could be a useful system to assess feeding responses.}, }
@article {pmid26779222, year = {2015}, author = {Wang, M and Yang, P and Falcão Salles, J}, title = {Distribution of Root-Associated Bacterial Communities Along a Salt-Marsh Primary Succession.}, journal = {Frontiers in plant science}, volume = {6}, number = {}, pages = {1188}, pmid = {26779222}, issn = {1664-462X}, abstract = {Proper quantification of the relative influence of soil and plant host on the root-associated microbiome can only be achieved by studying its distribution along an environmental gradient. Here, we used an undisturbed salt marsh chronosequence to study the bacterial communities associated with the soil, rhizosphere and the root endopshere of Limonium vulgare using 454-pyrosequencing. We hypothesize that the selective force exerted by plants rather than soil would regulate the dynamics of the root-associated bacterial assembly along the chronosequence. Our results showed that the soil and rhizosphere bacterial communities were phylogenetically more diverse than those in the endosphere. Moreover, the diversity of the rhizosphere microbiome followed the increased complexity of the abiotic and biotic factors during succession while remaining constant in the other microbiomes. Multivariate analyses showed that the rhizosphere and soil-associated communities clustered by successional stages, whereas the endosphere communities were dispersed. Interestingly, the endosphere microbiome showed higher turnover, while the bulk and rhizosphere soil microbiomes became more similar at the end of the succession. Overall, we showed that soil characteristics exerted an overriding influence on the rhizosphere microbiome, although plant effect led to a clear diversity pattern along the succession. Conversely, the endosphere microbiome was barely affected by any of the environmental measurements and very distinct from other communities.}, }
@article {pmid26779174, year = {2015}, author = {Yilmaz, P and Yarza, P and Rapp, JZ and Glöckner, FO}, title = {Expanding the World of Marine Bacterial and Archaeal Clades.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1524}, pmid = {26779174}, issn = {1664-302X}, support = {294757/ERC_/European Research Council/International ; }, abstract = {Determining which microbial taxa are out there, where they live, and what they are doing is a driving approach in marine microbial ecology. The importance of these questions is underlined by concerted, large-scale, and global ocean sampling initiatives, for example the International Census of Marine Microbes, Ocean Sampling Day, or Tara Oceans. Given decades of effort, we know that the large majority of marine Bacteria and Archaea belong to about a dozen phyla. In addition to the classically culturable Bacteria and Archaea, at least 50 "clades," at different taxonomic depths, exist. These account for the majority of marine microbial diversity, but there is still an underexplored and less abundant portion remaining. We refer to these hitherto unrecognized clades as unknown, as their boundaries, names, and classifications are not available. In this work, we were able to characterize up to 92 of these unknown clades found within the bacterial and archaeal phylogenetic diversity currently reported for marine water column environments. We mined the SILVA 16S rRNA gene datasets for sequences originating from the marine water column. Instead of the usual subjective taxa delineation and nomenclature methods, we applied the candidate taxonomic unit (CTU) circumscription system, along with a standardized nomenclature to the sequences in newly constructed phylogenetic trees. With this new phylogenetic and taxonomic framework, we performed an analysis of ICoMM rRNA gene amplicon datasets to gain insights into the global distribution of the new marine clades, their ecology, biogeography, and interaction with oceanographic variables. Most of the new clades we identified were interspersed by known taxa with cultivated members, whose genome sequences are available. This result encouraged us to perform metabolic predictions for the novel marine clades using the PICRUSt approach. Our work also provides an update on the taxonomy of several phyla and widely known marine clades as our CTU approach breaks down these randomly lumped clades into smaller objectively calculated subgroups. Finally, all taxa were classified and named following standards compatible with the Bacteriological Code rules, enhancing their digitization, and comparability with future microbial ecological and taxonomy studies.}, }
@article {pmid26779150, year = {2015}, author = {Schmidt, R and Etalo, DW and de Jager, V and Gerards, S and Zweers, H and de Boer, W and Garbeva, P}, title = {Microbial Small Talk: Volatiles in Fungal-Bacterial Interactions.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1495}, pmid = {26779150}, issn = {1664-302X}, abstract = {There is increasing evidence that volatile organic compounds (VOCs) play an important role in the interactions between fungi and bacteria, two major groups of soil inhabiting microorganisms. Yet, most of the research has been focused on effects of bacterial volatiles on suppression of plant pathogenic fungi whereas little is known about the responses of bacteria to fungal volatiles. In the current study we performed a metabolomics analysis of volatiles emitted by several fungal and oomycetal soil strains under different nutrient conditions and growth stages. The metabolomics analysis of the tested fungal and oomycetal strains revealed different volatile profiles dependent on the age of the strains and nutrient conditions. Furthermore, we screened the phenotypic responses of soil bacterial strains to volatiles emitted by fungi. Two bacteria, Collimonas pratensis Ter291 and Serratia plymuthica PRI-2C, showed significant changes in their motility, in particular to volatiles emitted by Fusarium culmorum. This fungus produced a unique volatile blend, including several terpenes. Four of these terpenes were selected for further tests to investigate if they influence bacterial motility. Indeed, these terpenes induced or reduced swimming and swarming motility of S. plymuthica PRI-2C and swarming motility of C. pratensis Ter291, partly in a concentration-dependent manner. Overall the results of this work revealed that bacteria are able to sense and respond to fungal volatiles giving further evidence to the suggested importance of volatiles as signaling molecules in fungal-bacterial interactions.}, }
@article {pmid26779148, year = {2015}, author = {Ho, A and van den Brink, E and Reim, A and Krause, SM and Bodelier, PL}, title = {Recurrence and Frequency of Disturbance have Cumulative Effect on Methanotrophic Activity, Abundance, and Community Structure.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1493}, pmid = {26779148}, issn = {1664-302X}, abstract = {Alternate prolonged drought and heavy rainfall is predicted to intensify with global warming. Desiccation-rewetting events alter the soil quality and nutrient concentrations which drive microbial-mediated processes, including methane oxidation, a key biogeochemical process catalyzed by methanotrophic bacteria. Although aerobic methanotrophs showed remarkable resilience to a suite of physical disturbances induced as a single event, their resilience to recurring disturbances is less known. Here, using a rice field soil in a microcosm study, we determined whether recurrence and frequency of desiccation-rewetting impose an accumulating effect on the methanotrophic activity. The response of key aerobic methanotroph subgroups (type Ia, Ib, and II) were monitored using qPCR assays, and was supported by a t-RFLP analysis. The methanotrophic activity was resilient to recurring desiccation-rewetting, but increasing the frequency of the disturbance by twofold significantly decreased methane uptake rate. Both the qPCR and t-RFLP analyses were congruent, showing the dominance of type Ia/Ib methanotrophs prior to disturbance, and after disturbance, the recovering community was predominantly comprised of type Ia (Methylobacter) methanotrophs. Both type Ib and type II (Methylosinus/Methylocystis) methanotrophs were adversely affected by the disturbance, but type II methanotrophs showed recovery over time, indicating relatively higher resilience to the disturbance. This revealed distinct, yet unrecognized traits among the methanotroph community members. Our results show that recurring desiccation-rewetting before a recovery in community abundance had an accumulated effect, compromising methanotrophic activity. While methanotrophs may recover well following sporadic disturbances, their resilience may reach a 'tipping point' where activity no longer recovered if disturbance persists and increase in frequency.}, }
@article {pmid26779132, year = {2015}, author = {Hanke, A and Berg, J and Hargesheimer, T and Tegetmeyer, HE and Sharp, CE and Strous, M}, title = {Selective Pressure of Temperature on Competition and Cross-Feeding within Denitrifying and Fermentative Microbial Communities.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1461}, pmid = {26779132}, issn = {1664-302X}, support = {242635/ERC_/European Research Council/International ; }, abstract = {In coastal marine sediments, denitrification and fermentation are important processes in the anaerobic decomposition of organic matter. Microbial communities performing these two processes were enriched from tidal marine sediments in replicated, long term chemostat incubations at 10 and 25°C. Whereas denitrification rates at 25°C were more or less stable over time, at 10°C denitrification activity was unstable and could only be sustained either by repeatedly increasing the amount of carbon substrates provided or by repeatedly decreasing the dilution rate. Metagenomic and transcriptomic sequencing was performed at different time points and provisional whole genome sequences (WGS) and gene activities of abundant populations were compared across incubations. These analyses suggested that a temperature of 10°C selected for populations related to Vibrionales/Photobacterium that contributed to both fermentation (via pyruvate/formate lyase) and nitrous oxide reduction. At 25°C, denitrifying populations affiliated with Rhodobacteraceae were more abundant. The latter performed complete denitrification, and may have used carbon substrates produced by fermentative populations (cross-feeding). Overall, our results suggest that a mixture of competition-for substrates between fermentative and denitrifying populations, and for electrons between both pathways active within a single population -, and cross feeding-between fermentative and denitrifying populations-controlled the overall rate of denitrification. Temperature was shown to have a strong selective effect, not only on the populations performing either process, but also on the nature of their ecological interactions. Future research will show whether these results can be extrapolated to the natural environment.}, }
@article {pmid26776474, year = {2016}, author = {Oburger, E and Schmidt, H}, title = {New Methods To Unravel Rhizosphere Processes.}, journal = {Trends in plant science}, volume = {21}, number = {3}, pages = {243-255}, doi = {10.1016/j.tplants.2015.12.005}, pmid = {26776474}, issn = {1878-4372}, mesh = {Bacteria/metabolism ; Botany/*methods ; Isotope Labeling ; Plants/microbiology ; *Rhizosphere ; }, abstract = {Root-triggered processes (growth, uptake and release of solutes) vary in space and time, and interact with heterogeneous soil microenvironments that provide habitats for (micro)biota on various scales. Despite tremendous progress in method development in the past decades, finding a suitable experimental set-up to investigate processes occurring at the dynamic conjunction of biosphere, hydrosphere, and pedosphere in the close vicinity of active plant roots still represents a major challenge. We discuss recent methodological developments in rhizosphere research with a focus on imaging techniques. We further review established concepts that have been updated with novel techniques, highlighting the need for combinatorial approaches to disentangle rhizosphere processes on relevant scales.}, }
@article {pmid26769476, year = {2016}, author = {Ruffini Castiglione, M and Giorgetti, L and Becarelli, S and Siracusa, G and Lorenzi, R and Di Gregorio, S}, title = {Polycyclic aromatic hydrocarbon-contaminated soils: bioaugmentation of autochthonous bacteria and toxicological assessment of the bioremediation process by means of Vicia faba L.}, journal = {Environmental science and pollution research international}, volume = {23}, number = {8}, pages = {7930-7941}, pmid = {26769476}, issn = {1614-7499}, mesh = {Achromobacter/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Pilot Projects ; Polycyclic Aromatic Hydrocarbons/*analysis/toxicity ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Soil Pollutants/*analysis/toxicity ; Sphingomonas/isolation &amp; purification/*metabolism ; Vicia faba/*drug effects/growth &amp; development ; }, abstract = {Two bacterial strains, Achromobacter sp. (ACH01) and Sphingomonas sp. (SPH01), were isolated from a heavily polycyclic aromatic hydrocarbon (PAH)-contaminated soil (5431.3 ± 102.3 ppm) for their capacity to use a mixture of anthracene, pyrene, phenanthrene and fluorene as sole carbon sources for growth and for the capacity to produce biosurfactants. The two strains were exploited for bioaugmentation in a biopile pilot plant to increase the bioavailability and the degradation of the residual PAH contamination (99.5 ± 7.1 ppm) reached after 9 months of treatment. The denaturing gel gradient electrophoresis (DGGE) profile of the microbial ecology of the soil during the experimentation showed that the bioaugmentation approach was successful in terms of permanence of the two strains in the soil in treatment. The bioaugmentation of the two bacterial isolates positively correlated with the PAH depletion that reached 7.9 ± 2 ppm value in 2 months of treatment. The PAH depletion was assessed by the loss of the phyto-genotoxicity of soil elutriates on the model plant Vicia faba L., toxicological assessment adopted also to determine the minimum length of the decontamination process for obtaining both the depletion of the PAH contamination and the detoxification of the soil at the end of the process. The intermediate phases of the bioremediation process were the most significant in terms of toxicity, inducing genotoxic effects and selective DNA fragmentation in the stem cell niche of the root tip. The selective DNA fragmentation can be related to the selective induction of cell death of mutant stem cells that can compromise offsprings.}, }
@article {pmid26764021, year = {2016}, author = {Hiraoka, S and Machiyama, A and Ijichi, M and Inoue, K and Oshima, K and Hattori, M and Yoshizawa, S and Kogure, K and Iwasaki, W}, title = {Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {53}, pmid = {26764021}, issn = {1471-2164}, mesh = {Arthrobacter/*genetics ; Earthquakes ; Ecosystem ; *Genomics ; Japan ; *Metagenomics ; *Soil Microbiology ; Tsunamis ; }, abstract = {BACKGROUND: The Great East Japan Earthquake of 2011 triggered large tsunami waves, which flooded broad areas of land along the Pacific coast of eastern Japan and changed the soil environment drastically. However, the microbial characteristics of tsunami-affected soil at the genomic level remain largely unknown. In this study, we isolated microbes from a soil sample using general low-nutrient and seawater-based media to investigate microbial characteristics in tsunami-affected soil.<br><br>RESULTS: As expected, a greater proportion of strains isolated from the tsunami-affected soil than the unaffected soil grew in the seawater-based medium. Cultivable strains in both the general low-nutrient and seawater-based media were distributed in the genus Arthrobacter. Most importantly, whole-genome sequencing of four of the isolated Arthrobacter strains revealed independent losses of siderophore-synthesis genes from their genomes. Siderophores are low-molecular-weight, iron-chelating compounds that are secreted for iron uptake; thus, the loss of siderophore-synthesis genes indicates that these strains have adapted to environments with high-iron concentrations. Indeed, chemical analysis confirmed the investigated soil samples to be rich in iron, and culture experiments confirmed weak cultivability of some of these strains in iron-limited media. Furthermore, metagenomic analyses demonstrated over-representation of denitrification-related genes in the tsunami-affected soil sample, as well as the presence of pathogenic and marine-living genera and genes related to salt-tolerance.<br><br>CONCLUSIONS: Collectively, the present results would provide an example of microbial characteristics of soil disturbed by the tsunami, which may give an insight into microbial adaptation to drastic environmental changes. Further analyses on microbial ecology after a tsunami are envisioned to develop a deeper understanding of the recovery processes of terrestrial microbial ecosystems.}, }
@article {pmid26763763, year = {2016}, author = {Briki, S and Hamdi, O and Landoulsi, A}, title = {Enzymatic dehairing of goat skins using alkaline protease from Bacillus sp. SB12.}, journal = {Protein expression and purification}, volume = {121}, number = {}, pages = {9-16}, doi = {10.1016/j.pep.2015.12.021}, pmid = {26763763}, issn = {1096-0279}, mesh = {Animals ; Bacillus/*enzymology ; Bacterial Proteins/*chemistry/isolation &amp; purification/pharmacology ; Endopeptidases/*chemistry/isolation &amp; purification/pharmacology ; Enzyme Stability ; Goats ; Hair/drug effects ; Skin/drug effects ; }, abstract = {The present paper reports the production, purification and biochemical characterization of an extracellular alkaline protease from Bacillus sp. SB12. The enzyme has been used as an alternative to conventional chemicals treatment for dehairing of goat skins. The protease was optimally active at 37 °C and pH 9. Starch at 2% (w/v) was used as the best carbon source and the addition of yeast extract and peptone at 1% each supported the maximum level of protease production in the presence of 5 mM Ca(2+). Protease purification was performed with ammonium sulphate precipitation at 70% saturated fraction followed by dialysis and gel filtration chromatography using Sephadex G-100. The purified enzyme was homogeneous on non-denaturing PAGE and appeared as a single band with an apparent molecular weight of 41 kDa. This enzyme was moderately thermostable and has a wide pH stability range extending from pH 7 to 11. It showed high tolerance toward surfactants agents and organic solvents while it was completely inhibited by PMSF indicating the serine protease type. Purified protease was used to remove hair from goat skin proving its potential application in leather processing industry. The results revealed that the protease has enhanced the quality and physico-chemical properties of the skins while reducing the pollution.}, }
@article {pmid26763331, year = {2016}, author = {Hein, AM and Brumley, DR and Carrara, F and Stocker, R and Levin, SA}, title = {Physical limits on bacterial navigation in dynamic environments.}, journal = {Journal of the Royal Society, Interface}, volume = {13}, number = {114}, pages = {20150844}, pmid = {26763331}, issn = {1742-5662}, mesh = {*Bacteria ; *Bacterial Physiological Phenomena ; *Models, Biological ; }, abstract = {Many chemotactic bacteria inhabit environments in which chemicals appear as localized pulses and evolve by processes such as diffusion and mixing. We show that, in such environments, physical limits on the accuracy of temporal gradient sensing govern when and where bacteria can accurately measure the cues they use to navigate. Chemical pulses are surrounded by a predictable dynamic region, outside which bacterial cells cannot resolve gradients above noise. The outer boundary of this region initially expands in proportion to the square root of time before rapidly contracting. Our analysis also reveals how chemokinesis-the increase in swimming speed many bacteria exhibit when absolute chemical concentration exceeds a threshold-may serve to enhance chemotactic accuracy and sensitivity when the chemical landscape is dynamic. More generally, our framework provides a rigorous method for partitioning bacteria into populations that are 'near' and 'far' from chemical hotspots in complex, rapidly evolving environments such as those that dominate aquatic ecosystems.}, }
@article {pmid26762934, year = {2016}, author = {Barrett, M and Khalil, MI and Jahangir, MM and Lee, C and Cardenas, LM and Collins, G and Richards, KG and O'Flaherty, V}, title = {Carbon amendment and soil depth affect the distribution and abundance of denitrifiers in agricultural soils.}, journal = {Environmental science and pollution research international}, volume = {23}, number = {8}, pages = {7899-7910}, pmid = {26762934}, issn = {1614-7499}, mesh = {*Agriculture ; Bacteria/drug effects/genetics ; Carbon/*pharmacology ; Denitrification ; Grassland ; Nitrite Reductases/genetics ; Nitrogen/analysis ; Nitrous Oxide/analysis ; Oxidoreductases/genetics ; Real-Time Polymerase Chain Reaction ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {The nitrite reductase (nirS and nirK) and nitrous oxide reductase-encoding (nosZ) genes of denitrifying populations present in an agricultural grassland soil were quantified using real-time polymerase chain reaction (PCR) assays. Samples from three separate pedological depths at the chosen site were investigated: horizon A (0-10 cm), horizon B (45-55 cm), and horizon C (120-130 cm). The effect of carbon addition (treatment 1, control; treatment 2, glucose-C; treatment 3, dissolved organic carbon (DOC)) on denitrifier gene abundance and N2O and N2 fluxes was determined. In general, denitrifier abundance correlated well with flux measurements; nirS was positively correlated with N2O, and nosZ was positively correlated with N2 (P < 0.03). Denitrifier gene copy concentrations per gram of soil (GCC) varied in response to carbon type amendment (P < 0.01). Denitrifier GCCs were high (ca. 10(7)) and the bac:nirK, bac:nirS, bac:nir (T) , and bac:nosZ ratios were low (ca. 10(-1)/10) in horizon A in all three respective treatments. Glucose-C amendment favored partial denitrification, resulting in higher nir abundance and higher N2O fluxes compared to the control. DOC amendment, by contrast, resulted in relatively higher nosZ abundance and N2 emissions, thus favoring complete denitrification. We also noted soil depth directly affected bacterial, archaeal, and denitrifier abundance, possibly due to changes in soil carbon availability with depth.}, }
@article {pmid26761024, year = {2016}, author = {Adriaenssens, EM and van Zyl, LJ and Cowan, DA and Trindade, MI}, title = {Metaviromics of Namib Desert Salt Pans: A Novel Lineage of Haloarchaeal Salterproviruses and a Rich Source of ssDNA Viruses.}, journal = {Viruses}, volume = {8}, number = {1}, pages = {}, pmid = {26761024}, issn = {1999-4915}, mesh = {Archaeal Viruses/classification/genetics/*isolation &amp; purification/metabolism ; DNA Viruses/classification/genetics/*isolation &amp; purification/metabolism ; DNA, Single-Stranded/genetics/metabolism ; DNA, Viral/genetics/metabolism ; Desert Climate ; *Genome, Viral ; Molecular Sequence Data ; Namibia ; Phylogeny ; Sodium Chloride/*metabolism ; }, abstract = {Viral communities of two different salt pans located in the Namib Desert, Hosabes and Eisfeld, were investigated using a combination of multiple displacement amplification of metaviromic DNA and deep sequencing, and provided comprehensive sequence data on both ssDNA and dsDNA viral community structures. Read and contig annotations through online pipelines showed that the salt pans harbored largely unknown viral communities. Through network analysis, we were able to assign a large portion of the unknown reads to a diverse group of ssDNA viruses. Contigs belonging to the subfamily Gokushovirinae were common in both environmental datasets. Analysis of haloarchaeal virus contigs revealed the presence of three contigs distantly related with His1, indicating a possible new lineage of salterproviruses in the Hosabes playa. Based on viral richness and read mapping analyses, the salt pan metaviromes were novel and most closely related to each other while showing a low degree of overlap with other environmental viromes.}, }
@article {pmid26757676, year = {2016}, author = {Tecon, R and Or, D}, title = {Bacterial flagellar motility on hydrated rough surfaces controlled by aqueous film thickness and connectedness.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {19409}, pmid = {26757676}, issn = {2045-2322}, mesh = {*Bacterial Physiological Phenomena ; Flagella/*physiology ; Models, Biological ; Soil Microbiology ; Surface Properties ; }, abstract = {Recent studies have shown that rates of bacterial dispersion in soils are controlled by hydration conditions that define size and connectivity of the retained aqueous phase. Despite the ecological implications of such constraints, microscale observations of this phenomenon remain scarce. Here, we quantified aqueous film characteristics and bacterial flagellated motility in response to systematic variations in microhydrological conditions on porous ceramic surfaces that mimic unsaturated soils. We directly measured aqueous film thickness and documented its microscale heterogeneity. Flagellar motility was controlled by surface hydration conditions, as cell velocity decreased and dispersion practically ceased at water potentials exceeding -2 kPa (resulting in thinner and disconnected liquid films). The fragmentation of aquatic habitats was delineated indirectly through bacterial dispersal distances within connected aqueous clusters. We documented bacterial dispersal radii ranging from 100 to 10 μm as the water potential varied from 0 to -7 kPa, respectively. The observed decrease of flagellated velocity and dispersal ranges at lower matric potentials were in good agreement with mechanistic model predictions. Hydration-restricted habitats thus play significant role in bacterial motility and dispersal, which has potentially important impact on soil microbial ecology and diversity.}, }
@article {pmid26754847, year = {2016}, author = {Mosquera-Rendón, J and Rada-Bravo, AM and Cárdenas-Brito, S and Corredor, M and Restrepo-Pineda, E and Benítez-Páez, A}, title = {Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {45}, pmid = {26754847}, issn = {1471-2164}, mesh = {Biofilms/growth &amp; development ; *Evolution, Molecular ; Genome, Bacterial ; Genotype ; Humans ; *Phylogeny ; Pseudomonas Infections/*genetics/microbiology ; Pseudomonas aeruginosa/*genetics/pathogenicity ; }, abstract = {BACKGROUND: Drug treatments and vaccine designs against the opportunistic human pathogen Pseudomonas aeruginosa have multiple issues, all associated with the diverse genetic traits present in this pathogen, ranging from multi-drug resistant genes to the molecular machinery for the biosynthesis of biofilms. Several candidate vaccines against P. aeruginosa have been developed, which target the outer membrane proteins; however, major issues arise when attempting to establish complete protection against this pathogen due to its presumably genotypic variation at the strain level. To shed light on this concern, we proposed this study to assess the P. aeruginosa pangenome and its molecular evolution across multiple strains.<br><br>RESULTS: The P. aeruginosa pangenome was estimated to contain more than 16,000 non-redundant genes, and approximately 15&#xa0;% of these constituted the core genome. Functional analyses of the accessory genome indicated a wide presence of genetic elements directly associated with pathogenicity. An in-depth molecular evolution analysis revealed the full landscape of selection forces acting on the P. aeruginosa pangenome, in which purifying selection drives evolution in the genome of this human pathogen. We also detected distinctive positive selection in a wide variety of outer membrane proteins, with the data supporting the concept of substantial genetic variation in proteins probably recognized as antigens. Approaching the evolutionary information of genes under extremely positive selection, we designed a new Multi-Locus Sequencing Typing assay for an informative, rapid, and cost-effective genotyping of P. aeruginosa clinical isolates.<br><br>CONCLUSIONS: We report the unprecedented pangenome characterization of P. aeruginosa on a large scale, which included almost 200 bacterial genomes from one single species and a molecular evolutionary analysis at the pangenome scale. Evolutionary information presented here provides a clear explanation of the issues associated with the use of protein conjugates from pili, flagella, or secretion systems as antigens for vaccine design, which exhibit high genetic variation in terms of non-synonymous substitutions in P. aeruginosa strains.}, }
@article {pmid26753530, year = {2016}, author = {Kwenda, S and Gorshkov, V and Ramesh, AM and Naidoo, S and Rubagotti, E and Birch, PR and Moleleki, LN}, title = {Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {47}, pmid = {26753530}, issn = {1471-2164}, mesh = {Gene Expression Regulation, Bacterial ; Pectobacterium/*genetics/pathogenicity ; Plant Diseases/*genetics/microbiology ; Plants/genetics/microbiology ; RNA, Small Untranslated/*genetics ; Sequence Analysis, RNA ; Stress, Physiological/*genetics ; Transcriptome/genetics ; }, abstract = {BACKGROUND: Small RNAs (sRNAs) have emerged as important regulatory molecules and have been studied in several bacteria. However, to date, there have been no whole-transcriptome studies on sRNAs in any of the Soft Rot Enterobacteriaceae (SRE) group of pathogens. Although the main ecological niches for these pathogens are plants, a significant part of their life cycle is undertaken outside their host within adverse soil environment. However, the mechanisms of SRE adaptation to this harsh nutrient-deficient environment are poorly understood.<br><br>RESULTS: In the study reported herein, by using strand-specific RNA-seq analysis and in silico sRNA predictions, we describe the sRNA pool of Pectobacterium atrosepticum and reveal numerous sRNA candidates, including those that are induced during starvation-activated stress responses. Consequently, strand-specific RNA-seq enabled detection of 137 sRNAs and sRNA candidates under starvation conditions; 25 of these sRNAs were predicted for this bacterium in silico. Functional annotations were computationally assigned to 68 sRNAs. The expression of sRNAs in P. atrosepticum was compared under growth-promoting and starvation conditions: 68 sRNAs were differentially expressed with 47 sRNAs up-regulated under nutrient-deficient conditions. Conservation analysis using BLAST showed that most of the identified sRNAs are conserved within the SRE. Subsequently, we identified 9 novel sRNAs within the P. atrosepticum genome.<br><br>CONCLUSIONS: Since many of the identified sRNAs are starvation-induced, the results of our study suggests that sRNAs play key roles in bacterial adaptive response. Finally, this work provides a basis for future experimental characterization and validation of sRNAs in plant pathogens.}, }
@article {pmid26752633, year = {2016}, author = {Lima-Perim, JE and Romagnoli, EM and Dini-Andreote, F and Durrer, A and Dias, AC and Andreote, FD}, title = {Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest.}, journal = {PloS one}, volume = {11}, number = {1}, pages = {e0146566}, pmid = {26752633}, issn = {1932-6203}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; *Biodiversity ; Ecosystem ; *Rainforest ; *Soil Microbiology ; }, abstract = {The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient-namely, Santa Virginia, Picinguaba and Restinga-we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms-ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning.}, }
@article {pmid26752462, year = {2016}, author = {Naftali, T and Reshef, L and Kovacs, A and Porat, R and Amir, I and Konikoff, FM and Gophna, U}, title = {Distinct Microbiotas are Associated with Ileum-Restricted and Colon-Involving Crohn's Disease.}, journal = {Inflammatory bowel diseases}, volume = {22}, number = {2}, pages = {293-302}, doi = {10.1097/MIB.0000000000000662}, pmid = {26752462}, issn = {1536-4844}, mesh = {Adult ; Case-Control Studies ; Colon/*microbiology/pathology ; Crohn Disease/genetics/*microbiology/pathology ; Female ; Follow-Up Studies ; Humans ; Ileal Diseases/genetics/*microbiology/pathology ; Ileum/*microbiology/pathology ; Inflammation/genetics/*microbiology/pathology ; Male ; Microbiota/*genetics ; Middle Aged ; Prognosis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The etiology of inflammatory bowel disease is believed to involve a shift in the microbiota toward more proinflammatory species. Crohn's disease (CD) usually manifests as one of three phenotypes, involving inflammation of the terminal ileum, the colon, or both. However, what determines the particular phenotype and the level of disease activity remains unknown. In this study, we aim to characterize the intestinal microbiota associated with different CD phenotypes.<br><br>METHODS: DNA was extracted from biopsies of 31 patients with ileal, ileocolic, or colon-restricted CD, and also from 5 non-inflammatory bowel disease control subjects, and analyzed by 16S rRNA gene amplicon pyrosequencing. Data were processed using the Quantitative Insights Into Microbial Ecology pipeline and analyzed using linear discriminant analysis with effect size estimation and PICRUSt algorithms. Two additional recently published cohorts were also analyzed in this study.<br><br>RESULTS: Highly significant separation was observed between bacterial composition of ileal CD compared with CD with colonic involvement (genus level Bray-Curtis P = 0.005, R = 20%). This separation was unaffected by the biopsy's location or its inflammatory state, or by the patients' condition (remission or relapse). Faecalibacterium was strongly reduced in ileal CD compared with CD with colonic involvement, whereas Enterobacteriaceae were more abundant in the former. Fusobacterium relative abundance was strongly correlated with disease activity in patients with ileal-involving, but not in colon-involving, CD.<br><br>CONCLUSIONS: Ileal and colon-involving CD sustain distinct microbiotas, suggesting that different mechanisms underlie the two major manifestations of CD. The potential contribution of Fusobacterium to inflammation in ileal CD should be further investigated.}, }
@article {pmid26748499, year = {2016}, author = {Finley, SJ and Pechal, JL and Benbow, ME and Robertson, BK and Javan, GT}, title = {Microbial Signatures of Cadaver Gravesoil During Decomposition.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {524-529}, pmid = {26748499}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Biodiversity ; Body Remains/*microbiology ; Cadaver ; DNA, Bacterial/genetics ; Humans ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Time Factors ; }, abstract = {Genomic studies have estimated there are approximately 10(3)-10(6) bacterial species per gram of soil. The microbial species found in soil associated with decomposing human remains (gravesoil) have been investigated and recognized as potential molecular determinants for estimates of time since death. The nascent era of high-throughput amplicon sequencing of the conserved 16S ribosomal RNA (rRNA) gene region of gravesoil microbes is allowing research to expand beyond more subjective empirical methods used in forensic microbiology. The goal of the present study was to evaluate microbial communities and identify taxonomic signatures associated with the gravesoil human cadavers. Using 16S rRNA gene amplicon-based sequencing, soil microbial communities were surveyed from 18 cadavers placed on the surface or buried that were allowed to decompose over a range of decomposition time periods (3-303 days). Surface soil microbial communities showed a decreasing trend in taxon richness, diversity, and evenness over decomposition, while buried cadaver-soil microbial communities demonstrated increasing taxon richness, consistent diversity, and decreasing evenness. The results show that ubiquitous Proteobacteria was confirmed as the most abundant phylum in all gravesoil samples. Surface cadaver-soil communities demonstrated a decrease in Acidobacteria and an increase in Firmicutes relative abundance over decomposition, while buried soil communities were consistent in their community composition throughout decomposition. Better understanding of microbial community structure and its shifts over time may be important for advancing general knowledge of decomposition soil ecology and its potential use during forensic investigations.}, }
@article {pmid26746711, year = {2016}, author = {Kanitkar, YH and Stedtfeld, RD and Steffan, RJ and Hashsham, SA and Cupples, AM}, title = {Loop-Mediated Isothermal Amplification (LAMP) for Rapid Detection and Quantification of Dehalococcoides Biomarker Genes in Commercial Reductive Dechlorinating Cultures KB-1 and SDC-9.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {6}, pages = {1799-1806}, pmid = {26746711}, issn = {1098-5336}, mesh = {Bacteriological Techniques/*methods ; Biomarkers/*analysis ; Chloroflexi/genetics/*isolation &amp; purification ; *Gene Dosage ; *Genes, Bacterial ; Groundwater/*microbiology ; Nucleic Acid Amplification Techniques/*methods ; Time Factors ; }, abstract = {Real-time quantitative PCR (qPCR) protocols specific to the reductive dehalogenase (RDase) genes vcrA, bvcA, and tceA are commonly used to quantify Dehalococcoides spp. in groundwater from chlorinated solvent-contaminated sites. In this study, loop-mediated isothermal amplification (LAMP) was developed as an alternative approach for the quantification of these genes. LAMP does not require a real-time thermal cycler (i.e., amplification is isothermal), allowing the method to be performed using less-expensive and potentially field-deployable detection devices. Six LAMP primers were designed for each of three RDase genes (vcrA, bvcA, and tceA) using Primer Explorer V4. The LAMP assays were compared to conventional qPCR approaches using plasmid standards, two commercially available bioaugmentation cultures, KB-1 and SDC-9 (both contain Dehalococcoides species). DNA was extracted over a growth cycle from KB-1 and SDC-9 cultures amended with trichloroethene and vinyl chloride, respectively. All three genes were quantified for KB-1, whereas only vcrA was quantified for SDC-9. A comparison of LAMP and qPCR using standard plasmids indicated that quantification results were similar over a large range of gene concentrations. In addition, the quantitative increase in gene concentrations over one growth cycle of KB-1 and SDC-9 using LAMP was comparable to that of qPCR. The developed LAMP assays for vcrA and tceA genes were validated by comparing quantification on the Gene-Z handheld platform and a real-time thermal cycler using DNA isolated from eight groundwater samples obtained from an SDC-9-bioaugmented site (Tulsa, OK). These assays will be particularly useful at sites subject to bioaugmentation with these two commonly used Dehalococcoides species-containing cultures.}, }
@article {pmid26746710, year = {2016}, author = {Hüpeden, J and Wegen, S and Off, S and Lücker, S and Bedarf, Y and Daims, H and Kühn, C and Spieck, E}, title = {Relative Abundance of Nitrotoga spp. in a Biofilter of a Cold-Freshwater Aquaculture Plant Appears To Be Stimulated by Slightly Acidic pH.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {6}, pages = {1838-1845}, pmid = {26746710}, issn = {1098-5336}, mesh = {*Aquaculture ; *Bacterial Load ; Cold Temperature ; *Filtration ; Fresh Water ; Gallionellaceae/growth &amp; development/*isolation &amp; purification ; Hydrogen-Ion Concentration ; Water Purification/*methods ; }, abstract = {The functioning of recirculation aquaculture systems (RAS) is essential to maintain water quality for fish health, and one crucial process here is nitrification. The investigated RAS was connected to a rainbow trout production system and operated at an average temperature of 13°C and pH 6.8. Community analyses of the nitrifying biofilm revealed a coexistence of Nitrospira and Nitrotoga, and it is hypothesized that a slightly acidic pH in combination with lower temperatures favors the growth of the latter. Modification of the standard cultivation approach toward lower pH values of 5.7 to 6.0 resulted in the successful enrichment (99% purity) of Nitrotoga sp. strain HW29, which had a 16S rRNA sequence similarity of 99.0% to Nitrotoga arctica. Reference cultures of Nitrospira defluvii and the novel Nitrotoga sp. HW29 were used to confirm differentiation of these nitrite oxidizers in distinct ecological niches. Nitrotoga sp. HW29 revealed pH and temperature optima of 6.8 and 22°C, respectively, whereas Nitrospira defluvii displayed the highest nitrite oxidation rate at pH 7.3 and 32°C. We report here the occurrence of Nitrotoga as one of the main nitrite-oxidizing bacteria in freshwater aquaculture systems and indicate that a slightly acidic pH, in addition to temperatures below 20°C, can be applied as a selective isolation criterion for this microorganism.}, }
@article {pmid26743465, year = {2016}, author = {Xia, Y and Hu, M and Wen, X and Wang, X and Yang, Y and Zhou, J}, title = {Diversity and interactions of microbial functional genes under differing environmental conditions: insights from a membrane bioreactor and an oxidation ditch.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {18509}, pmid = {26743465}, issn = {2045-2322}, mesh = {Biodegradation, Environmental ; *Bioreactors ; Carbon/metabolism ; Gene Expression ; *Genes, Bacterial ; *Genes, Fungal ; Humans ; Membranes, Artificial ; Microbial Consortia/*genetics ; Nitrogen/metabolism ; Oxidation-Reduction ; Oxygen/metabolism ; Phosphorus/metabolism ; Waste Disposal, Fluid ; Wastewater/*microbiology ; }, abstract = {The effect of environmental conditions on the diversity and interactions of microbial communities has caused tremendous interest in microbial ecology. Here, we found that with identical influents but differing operational parameters (mainly mixed liquor suspended solid (MLSS) concentrations, solid retention time (SRT) and dissolved oxygen (DO) concentrations), two full-scale municipal wastewater treatment systems applying oxidation ditch (OD) and membrane bioreactor (MBR) processes harbored a majority of shared genes (87.2%) but had different overall functional gene structures as revealed by two datasets of 12-day time-series generated by a functional gene array-GeoChip 4.2. Association networks of core carbon, nitrogen and phosphorus cycling genes in each system based on random matrix theory (RMT) showed different topological properties and the MBR nodes showed an indication of higher connectivity. MLSS and DO were shown to be effective in shaping functional gene structures of the systems by statistical analyses. Higher MLSS concentrations resulting in decreased resource availability of the MBR system were thought to promote positive interactions of important functional genes. Together, these findings show the differences of functional potentials of some bioprocesses caused by differing environmental conditions and suggest that higher stress of resource limitation increased positive gene interactions in the MBR system.}, }
@article {pmid26743115, year = {2016}, author = {Colangelo-Lillis, J and Wing, BA and Whyte, LG}, title = {Low viral predation pressure in cold hypersaline Arctic sediments and limits on lytic replication.}, journal = {Environmental microbiology reports}, volume = {8}, number = {2}, pages = {250-260}, doi = {10.1111/1758-2229.12375}, pmid = {26743115}, issn = {1758-2229}, mesh = {Arctic Regions ; *Biota ; *Cold Temperature ; Geologic Sediments/*virology ; Selection, Genetic ; Virus Replication/*radiation effects ; Viruses/*classification/*radiation effects ; }, abstract = {Viruses are ubiquitous drivers of microbial ecology and evolution and contribute to biogeochemical cycling. Attention to these attributes has been more substantial for marine viruses than viruses of other environments. Microscopy-based investigation of the viral communities from two cold, hypersaline Arctic springs was undertaken to explore the effects of these conditions on microbe-viral ecology. Sediments and water samples were collected along transects from each spring, from anoxic spring outlets through oxygenated downstream channels. Viral abundance, virus-microbe ratios and modelled virus-microbe contact rates were lower than comparable aqueous and sedimentary environments and most similar to deep subsurface sediments. No individual cell from either spring was visibly infected. Viruses in these springs appear to play a smaller role in controlling microbial populations through lytic activity than in marine water column or surface sedimentary environments. Relief from viral predation indicates the microbial communities are primarily controlled by nutrient limitation. The similarity of these springs to deep subsurface sediments suggests a biogeographic divide in viral replication strategy in marine sediments.}, }
@article {pmid26738893, year = {2016}, author = {Reinhart, KO and Rinella, MJ}, title = {A common soil handling technique can generate incorrect estimates of soil biota effects on plants.}, journal = {The New phytologist}, volume = {210}, number = {3}, pages = {786-789}, doi = {10.1111/nph.13822}, pmid = {26738893}, issn = {1469-8137}, mesh = {*Biota ; Computer Simulation ; Confidence Intervals ; Plant Development ; Plants/*metabolism ; *Soil ; }, }
@article {pmid26738552, year = {2016}, author = {Pearman, JK and Kürten, S and Sarma, YV and Jones, BH and Carvalho, S}, title = {Biodiversity patterns of plankton assemblages at the extremes of the Red Sea.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {3}, pages = {}, doi = {10.1093/femsec/fiw002}, pmid = {26738552}, issn = {1574-6941}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Eukaryota/classification/genetics/*isolation &amp; purification ; Indian Ocean ; Molecular Sequence Data ; Phylogeny ; Plankton/classification/genetics/*isolation &amp; purification ; Seawater/*microbiology ; }, abstract = {The diversity of microbial plankton has received limited attention in the main basin of the Red Sea. This study investigates changes in the community composition and structure of prokaryotes and eukaryotes at the extremes of the Red Sea along cross-shelf gradients and between the surface and deep chlorophyll maximum. Using molecular methods to target both the 16S and 18S rRNA genes, it was observed that the dominant prokaryotic classes were Acidimicrobiia, Alphaproteobacteria and Cyanobacteria, regardless of the region and depth. The eukaryotes Syndiniophyceae and Dinophyceae between them dominated in the north, with Bacillariophyceae and Mamiellophyceae more prominent in the southern region. Significant differences were observed for prokaryotes and eukaryotes for region, depth and distance from shore. Similarly, it was noticed that communities became less similar with increasing distance from the shore. Canonical correspondence analysis at the class level showed that Mamiellophyceae and Bacillariophyceae correlated with increased nutrients and chlorophyll a found in the southern region, which is influenced by the input of Gulf of Aden Intermediate Water.}, }
@article {pmid26733999, year = {2015}, author = {Balk, M and Keuskamp, JA and Laanbroek, HJ}, title = {Potential Activity, Size, and Structure of Sulfate-Reducing Microbial Communities in an Exposed, Grazed and a Sheltered, Non-Grazed Mangrove Stand at the Red Sea Coast.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1478}, pmid = {26733999}, issn = {1664-302X}, abstract = {After oxygen, sulfate is the most important oxidant for the oxidation of organic matter in mangrove forest soils. As sulfate reducers are poor competitors for common electron donors, their relative success depends mostly on the surplus of carbon that is left by aerobic organisms due to oxygen depletion. We therefore hypothesized that sulfate-cycling in mangrove soils is influenced by the size of net primary production, and hence negatively affected by mangrove degradation and exploitation, as well as by carbon-exporting waves. To test this, we compared quantitative and qualitative traits of sulfate-reducing communities in two Saudi-Arabian mangrove stands near Jeddah, where co-occurring differences in camel-grazing pressure and tidal exposure led to a markedly different stand height and hence primary production. Potential sulfate reduction rates measured in anoxic flow-through reactors in the absence and presence of additional carbon sources were significantly higher in the samples from the non-grazed site. Near the surface (0-2 cm depth), numbers of dsrB gene copies and culturable cells also tended to be higher in the non-grazed sites, while these differences were not detected in the sub-surface (4-6 cm depth). It was concluded that sulfate-reducing microbes at the surface were indeed repressed at the low-productive site as could be expected from our hypothesis. At both sites, sulfate reduction rates as well as numbers of the dsrB gene copies and viable cells increased with depth suggesting repression of sulfate reduction near the surface in both irrespective of production level. Additionally, sequence analysis of DNA bands obtained from DGGE gels based on the dsrB gene, showed a clear difference in dominance of sulfate-reducing genera belonging to the Deltaproteobacteria and the Firmicutes between sampling sites and depths.}, }
@article {pmid26733981, year = {2015}, author = {Navarrete, AA and Venturini, AM and Meyer, KM and Klein, AM and Tiedje, JM and Bohannan, BJ and Nüsslein, K and Tsai, SM and Rodrigues, JL}, title = {Differential Response of Acidobacteria Subgroups to Forest-to-Pasture Conversion and Their Biogeographic Patterns in the Western Brazilian Amazon.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1443}, pmid = {26733981}, issn = {1664-302X}, abstract = {Members of the phylum Acidobacteria are among the most abundant soil bacteria on Earth, but little is known about their response to environmental changes. We asked how the relative abundance and biogeographic patterning of this phylum and its subgroups responded to forest-to-pasture conversion in soils of the western Brazilian Amazon. Pyrosequencing of 16S rRNA genes was employed to assess the abundance and composition of the Acidobacteria community across 54 soil samples taken using a spatially nested sampling scheme at the landscape level. Numerically, Acidobacteria represented 20% of the total bacterial community in forest soils and 11% in pasture soils. Overall, 15 different Acidobacteria subgroups of the current 26 subgroups were detected, with Acidobacteria subgroups 1, 3, 5, and 6 accounting together for 87% of the total Acidobacteria community in forest soils and 75% in pasture soils. Concomitant with changes in soil chemistry after forest-to-pasture conversion-particularly an increase in properties linked to soil acidity and nutrient availability-we observed an increase in the relative abundances of Acidobacteria subgroups 4, 10, 17, and 18, and a decrease in the relative abundances of other Acidobacteria subgroups in pasture relative to forest soils. The composition of the total Acidobacteria community as well as the most abundant Acidobacteria subgroups (1, 3, 5, and 6) was significantly more similar in composition across space in pasture soils than in forest soils. These results suggest that preponderant responses of Acidobacteria subgroups, especially subgroups 1, 3, 4, 5, and 6, to forest-to-pasture conversion effects in soils could be used to define management-indicators of agricultural practices in the Amazon Basin. These acidobacterial responses are at least in part through alterations on acidity- and nutrient-related properties of the Amazon soils.}, }
@article {pmid26733962, year = {2015}, author = {Ballhausen, MB and van Veen, JA and Hundscheid, MP and de Boer, W}, title = {Methods for Baiting and Enriching Fungus-Feeding (Mycophagous) Rhizosphere Bacteria.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1416}, pmid = {26733962}, issn = {1664-302X}, abstract = {Mycophagous soil bacteria are able to obtain nutrients from living fungal hyphae. However, with exception of the soil bacterial genus Collimonas, occurrence of this feeding strategy has not been well examined. Evaluation of the importance of mycophagy in soil bacterial communities requires targeted isolation methods. In this study, we compared two different approaches to obtain mycophagous bacteria from rhizospheric soil. A short-term method based on baiting for bacteria that can rapidly adhere to fungal hyphae and a long-term method based on the enrichment of bacteria on fungal hyphae via repeated transfer. Hyphae-adhering bacteria were isolated, identified by 16S rDNA sequencing and tested for antifungal activity and the ability to feed on fungi as the sole source of carbon. Both methods yielded a range of potentially mycophagous bacterial isolates with little phylogenetic overlap. We also found indications for feeding preferences among the potentially mycophagous bacteria. Our results indicate that mycophagy could be an important growth strategy for rhizosphere bacteria. To our surprise, we found several potential plant pathogenic bacteria among the mycophagous isolates. We discuss the possible benefits that these bacteria might gain from colonizing fungal hyphae.}, }
@article {pmid26733959, year = {2015}, author = {Tyc, O and Zweers, H and de Boer, W and Garbeva, P}, title = {Volatiles in Inter-Specific Bacterial Interactions.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1412}, pmid = {26733959}, issn = {1664-302X}, abstract = {The importance of volatile organic compounds for functioning of microbes is receiving increased research attention. However, to date very little is known on how inter-specific bacterial interactions effect volatiles production as most studies have been focused on volatiles produced by monocultures of well-described bacterial genera. In this study we aimed to understand how inter-specific bacterial interactions affect the composition, production and activity of volatiles. Four phylogenetically different bacterial species namely: Chryseobacterium, Dyella, Janthinobacterium, and Tsukamurella were selected. Earlier results had shown that pairwise combinations of these bacteria induced antimicrobial activity in agar media whereas this was not the case for monocultures. In the current study, we examined if these observations were also reflected by the production of antimicrobial volatiles. Thus, the identity and antimicrobial activity of volatiles produced by the bacteria were determined in monoculture as well in pairwise combinations. Antimicrobial activity of the volatiles was assessed against fungal, oomycetal, and bacterial model organisms. Our results revealed that inter-specific bacterial interactions affected volatiles blend composition. Fungi and oomycetes showed high sensitivity to bacterial volatiles whereas the effect of volatiles on bacteria varied between no effects, growth inhibition to growth promotion depending on the volatile blend composition. In total 35 volatile compounds were detected most of which were sulfur-containing compounds. Two commonly produced sulfur-containing volatile compounds (dimethyl disulfide and dimethyl trisulfide) were tested for their effect on three target bacteria. Here, we display the importance of inter-specific interactions on bacterial volatiles production and their antimicrobial activities.}, }
@article {pmid26733953, year = {2015}, author = {Björkman, KM and Church, MJ and Doggett, JK and Karl, DM}, title = {Differential Assimilation of Inorganic Carbon and Leucine by Prochlorococcus in the Oligotrophic North Pacific Subtropical Gyre.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1401}, pmid = {26733953}, issn = {1664-302X}, abstract = {The light effect on photoheterotrophic processes in Prochlorococcus, and primary and bacterial productivity in the oligotrophic North Pacific Subtropical Gyre was investigated using (14)C-bicarbonate and (3)H-leucine. Light and dark incubation experiments were conducted in situ throughout the euphotic zone (0-175 m) on nine expeditions to Station ALOHA over a 3-year period. Photosynthetrons were also used to elucidate rate responses in leucine and inorganic carbon assimilation as a function of light intensity. Taxonomic group and cell-specific rates were assessed using flow cytometric sorting. The light:dark assimilation rate ratios of leucine in the top 150 m were ∼7:1 for Prochlorococcus, whereas the light:dark ratios for the non-pigmented bacteria (NPB) were not significant different from 1:1. Prochlorococcus assimilated leucine in the dark at per cell rates similar to the NPB, with a contribution to the total community bacterial production, integrated over the euphotic zone, of approximately 20% in the dark and 60% in the light. Depth-resolved primary productivity and leucine incorporation showed that the ratio of Prochlorococcus leucine:primary production peaked at 100 m then declined steeply below the deep chlorophyll maximum (DCM). The photosynthetron experiments revealed that, for Prochlorococcus at the DCM, the saturating irradiance (E k) for leucine incorporation was reached at approximately half the light intensity required for light saturation of (14)C-bicarbonate assimilation. Additionally, high and low red fluorescing Prochlorococcus populations (HRF and LRF), co-occurring at the DCM, had similar E k values for their respective substrates, however, maximum assimilation rates, for both leucine and inorganic carbon, were two times greater for HRF cells. Our results show that Prochlorococcus contributes significantly to bacterial production estimates using (3)H-leucine, whether or not the incubations are conducted in the dark or light, and this should be considered when making assessments of bacterial production in marine environments where Prochlorococcus is present. Furthermore, Prochlorococcus primary productivity showed rate to light-flux patterns that were different from its light enhanced leucine incorporation. This decoupling from autotrophic growth may indicate a separate light stimulated mechanism for leucine acquisition.}, }
@article {pmid26733293, year = {2016}, author = {Krupovic, M and Dutilh, BE and Adriaenssens, EM and Wittmann, J and Vogensen, FK and Sullivan, MB and Rumnieks, J and Prangishvili, D and Lavigne, R and Kropinski, AM and Klumpp, J and Gillis, A and Enault, F and Edwards, RA and Duffy, S and Clokie, MR and Barylski, J and Ackermann, HW and Kuhn, JH}, title = {Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee.}, journal = {Archives of virology}, volume = {161}, number = {4}, pages = {1095-1099}, doi = {10.1007/s00705-015-2728-0}, pmid = {26733293}, issn = {1432-8798}, support = {HHSN272200700016I//PHS HHS/United States ; }, mesh = {Archaea/*virology ; Archaeal Viruses/*classification ; Classification/methods ; *International Cooperation ; Phylogeny ; *Societies, Scientific ; *Terminology as Topic ; }, }
@article {pmid26728128, year = {2016}, author = {Grunert, O and Hernandez-Sanabria, E and Vilchez-Vargas, R and Jauregui, R and Pieper, DH and Perneel, M and Van Labeke, MC and Reheul, D and Boon, N}, title = {Mineral and organic growing media have distinct community structure, stability and functionality in soilless culture systems.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {18837}, pmid = {26728128}, issn = {2045-2322}, mesh = {Biodiversity ; Culture Media/*chemistry ; Environment ; Microbiota ; *Minerals ; Plant Development ; *Plant Physiological Phenomena ; }, abstract = {The choice of soilless growing medium for plant nutrition, growth and support is crucial for improving the eco-sustainability of the production in horticultural systems. As our current understanding of the functional microbial communities inhabiting this ecosystem is still limited, we examined the microbial community development of the two most important growing media (organic and mineral) used in open soilless horticultural systems. We aimed to identify factors that influence community composition over time, and to compare the distribution of individual taxa across growing media, and their potential functionality. High throughput sequencing analysis revealed a distinctive and stable microbial community in the organic growing medium. Humidity, pH, nitrate-N, ammonium-N and conductivity were uncovered as the main factors associated with the resident bacterial communities. Ammonium-N was correlated with Rhizobiaceae abundance, while potential competitive interactions among both Methylophilaceae and Actinobacteridae with Rhizobiaceae were suggested. Our results revealed that soilless growing media are unique niches for diverse bacterial communities with temporal functional stability, which may possibly impact the resistance to external forces. These differences in communities can be used to develop strategies to move towards a sustainable horticulture with increased productivity and quality.}, }
@article {pmid26725514, year = {2016}, author = {Rossi, O and van Berkel, LA and Chain, F and Tanweer Khan, M and Taverne, N and Sokol, H and Duncan, SH and Flint, HJ and Harmsen, HJ and Langella, P and Samsom, JN and Wells, JM}, title = {Faecalibacterium prausnitzii A2-165 has a high capacity to induce IL-10 in human and murine dendritic cells and modulates T cell responses.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {18507}, pmid = {26725514}, issn = {2045-2322}, mesh = {Adoptive Transfer ; Animals ; CD4-Positive T-Lymphocytes/*immunology/metabolism/microbiology ; Cell Differentiation ; Cells, Cultured ; Coculture Techniques ; Colitis/immunology/metabolism/microbiology ; Colon/microbiology ; Dendritic Cells/*immunology/metabolism/microbiology ; Faecalibacterium prausnitzii/*immunology ; Humans ; Interleukin-10/*biosynthesis/metabolism ; Male ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; NF-kappa B/metabolism ; Toll-Like Receptors/metabolism ; }, abstract = {Faecalibacterium prausnitzii strain A2-165 was previously reported to have anti-inflammatory properties and prevent colitis in a TNBS model. We compared the immunomodulatory properties of strain A2-165 to four different F. prausnitzii isolates and eight abundant intestinal commensals using human dendritic cells (DCs) and mouse BMDCs in vitro. Principal component analysis revealed that the cytokine response to F. prausnitzii A2-165 is distinct from the other strains in eliciting high amounts of IL-10 secretion. The mouse DNBS model of relapsing IBD was used to compare the protective effects of F. prausnitzii A2-165 and Clostridium hathewayi, a low secretor of IL-10, on the Th1-driven inflammatory response to DNBS; attenuation of disease parameters was only observed with F. prausnitzii. In an in vivo mouse model of nasal tolerance to ovalbumin, F. prausnitzii A2-165 enhanced ovalbumin-specific T cell proliferation and reduced the proportion of IFN-γ(+) T cells in CLNs. Similarly, in vitro F. prausnitzii A2-165 stimulated BMDCs increased ovalbumin-specific T cell proliferation and reduced the number of IFN-γ(+) T cells. These mechanisms may contribute to the anti-inflammatory effects of F. prausnitzii in colitis and support the notion that this abundant bacterium might contribute to immune homeostasis in the intestine via its anti-inflammatory properties.}, }
@article {pmid26717555, year = {2016}, author = {Fouquier, J and Schwartz, T and Kelley, ST}, title = {Rapid assemblage of diverse environmental fungal communities on public restroom floors.}, journal = {Indoor air}, volume = {26}, number = {6}, pages = {869-879}, doi = {10.1111/ina.12279}, pmid = {26717555}, issn = {1600-0668}, mesh = {DNA, Fungal/*analysis ; Female ; Fungi/*classification/genetics/*isolation &amp; purification ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Phylogeny ; Sequence Analysis, DNA/*methods ; Surface Properties ; *Toilet Facilities ; }, abstract = {An increasing proportion of humanity lives in urban environments where they spend most of their lives indoors. Recent molecular studies have shown that bacterial assemblages in built environments (BEs) are extremely diverse, but BE fungal diversity remains poorly understood. We applied culture-independent methods based on next-generation sequencing (NGS) of the fungal internal transcribed spacer to investigate the diversity and temporal dynamics of fungi in restrooms. Swab samples were collected weekly from three different surfaces in two public restrooms (male and female) in San Diego, CA, USA, over an 8-week period. DNA amplification and culturing methods both found that the floor samples had significantly higher fungal loads than other surfaces. NGS sequencing of floor fungal assemblages identified a total of 2550 unique phylotypes (~800 per sample), less than half of which were identifiable. Of the known fungi, the majority came from environmental sources and we found little evidence of known human skin fungi. Fungal assemblages reformed rapidly in a highly consistent manner, and the variance in the species diversity among samples was low. Overall, our study contributes to a better understanding of public restroom floor fungal communities.}, }
@article {pmid26714966, year = {2016}, author = {Keita, MB and Padhmanabhan, R and Robert, C and Delaporte, E and Raoult, D and Fournier, PE and Bittar, F}, title = {Non-contiguous-Finished Genome Sequence and Description of Paenibacillus camerounensis sp. nov.}, journal = {Microbial ecology}, volume = {71}, number = {4}, pages = {990-998}, pmid = {26714966}, issn = {1432-184X}, mesh = {Animals ; Bacterial Proteins/genetics ; Base Sequence ; Cameroon ; Chromosome Mapping ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Genes, rRNA ; Gorilla gorilla/microbiology ; Paenibacillus/chemistry/*genetics/isolation &amp; purification ; Phenotype ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Strain G4(T) was isolated from the stool sample of a wild gorilla (Gorilla gorilla gorilla) from Cameroon. It is a facultative anaerobic, Gram-negative, rod-shaped bacterium. This strain exhibits a 16S rRNA nucleotide sequence similarity of 97.48% with Paenibacillus typhae, the phylogenetically closest species with standing nomenclature. Moreover, the strain G4(T) presents some phenotypic differences when compared to other Paenibacillus species and shows a low MALDI-TOF Mass Spectrometry score that does not allow any identification. Thus, it is likely that this strain represents a new species. Here, we describe the characteristics of this organism, complete genome sequence, and annotation. The 6,933,847 bp size genome (1 chromosome but no plasmid) contains 5972 protein-coding genes and 54 RNAs genes, including 44 tRNA genes. In addition, digital DNA-DNA hybridization values for the genome of the strain G4(T) against the closest Paenibacillus genomes range between 19.7 and 22.1, once again confirming its new status as a new species. On the basis of these polyphasic data, consisting of phenotypic and genomic analyses, we propose the creation of Paenibacillus camerounensis sp. nov. that contains the strain G4(T).}, }
@article {pmid26708766, year = {2016}, author = {Proia, L and von Schiller, D and Sànchez-Melsió, A and Sabater, S and Borrego, CM and Rodríguez-Mozaz, S and Balcázar, JL}, title = {Occurrence and persistence of antibiotic resistance genes in river biofilms after wastewater inputs in small rivers.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {210}, number = {}, pages = {121-128}, doi = {10.1016/j.envpol.2015.11.035}, pmid = {26708766}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents/analysis/toxicity ; *Biofilms ; Drug Resistance, Microbial/*genetics ; Rivers/*chemistry ; Wastewater/*chemistry ; }, abstract = {The extensive use of antibiotics in human and veterinary medicine and their subsequent release into the environment may have direct consequences for autochthonous bacterial communities, especially in freshwater ecosystems. In small streams and rivers, local inputs of wastewater treatment plants (WWTPs) may become important sources of organic matter, nutrients and emerging pollutants, such as antibiotic resistance genes (ARGs). In this study, we evaluated the effect of WWTP effluents as a source of ARGs in river biofilms. The prevalence of genes conferring resistance to main antibiotic families, such as beta-lactams (blaCTX-M), fluoroquinolones (qnrS), sulfonamides (sul I), and macrolides (ermB), was determined using quantitative PCR (qPCR) in biofilm samples collected upstream and downstream WWTPs discharge points in four low-order streams. Our results showed that the WWTP effluents strongly modified the hydrology, physico-chemistry and biological characteristics of the receiving streams and favoured the persistence and spread of antibiotic resistance in microbial benthic communities. It was also shown that the magnitude of effects depended on the relative contribution of each WWTP to the receiving system. Specifically, low concentrations of ARGs were detected at sites located upstream of the WWTPs, while a significant increase of their concentrations was observed in biofilms collected downstream of the WWTP discharge points (particularly ermB and sul I genes). These findings suggest that WWTP discharges may favour the increase and spread of antibiotic resistance among streambed biofilms. The present study also showed that the presence of ARGs in biofilms was noticeable far downstream of the WWTP discharge (up to 1 km). It is therefore reasonable to assume that biofilms may represent an ideal setting for the acquisition and spread of antibiotic resistance determinants and thus be considered suitable biological indicators of anthropogenic pollution by active pharmaceutical compounds.}, }
@article {pmid26707136, year = {2016}, author = {Grange, ZL and Gartrell, BD and Biggs, PJ and Nelson, NJ and Anderson, M and French, NP}, title = {Microbial Genomics of a Host-Associated Commensal Bacterium in Fragmented Populations of Endangered Takahe.}, journal = {Microbial ecology}, volume = {71}, number = {4}, pages = {1020-1029}, pmid = {26707136}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/*genetics/isolation &amp; purification ; Biodiversity ; Biological Evolution ; Bird Diseases/*microbiology ; Birds/*microbiology ; Campylobacter/classification/genetics/isolation &amp; purification ; Campylobacter Infections/microbiology/*veterinary ; Endangered Species ; Genomics ; Host-Pathogen Interactions ; Multilocus Sequence Typing ; New Zealand ; Phylogeny ; Symbiosis ; }, abstract = {Isolation of wildlife into fragmented populations as a consequence of anthropogenic-mediated environmental change may alter host-pathogen relationships. Our understanding of some of the epidemiological features of infectious disease in vulnerable populations can be enhanced by the use of commensal bacteria as a proxy for invasive pathogens in natural ecosystems. The distinctive population structure of a well-described meta-population of a New Zealand endangered flightless bird, the takahe (Porphyrio hochstetteri), provided a unique opportunity to investigate the influence of host isolation on enteric microbial diversity. The genomic epidemiology of a prevalent rail-associated endemic commensal bacterium was explored using core genome and ribosomal multilocus sequence typing (rMLST) of 70 Campylobacter sp. nova 1 isolated from one third of the takahe population resident in multiple locations. While there was evidence of recombination between lineages, bacterial divergence appears to have occurred and multivariate analysis of 52 rMLST genes revealed location-associated differentiation of C. sp. nova 1 sequence types. Our results indicate that fragmentation and anthropogenic manipulation of populations can influence host-microbial relationships, with potential implications for niche adaptation and the evolution of micro-organisms in remote environments. This study provides a novel framework in which to explore the complex genomic epidemiology of micro-organisms in wildlife populations.}, }
@article {pmid26705573, year = {2016}, author = {Zhang, M and Yang, P and van Elsas, JD}, title = {Effect of the IncP-1β plasmid pHB44 on the population dynamics of Burkholderia terrae BS001 in the Lyophyllum sp. strain Karsten mycosphere under different iron conditions.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {2}, pages = {}, doi = {10.1093/femsec/fiv167}, pmid = {26705573}, issn = {1574-6941}, mesh = {Agaricales/genetics/*metabolism ; Burkholderia/*genetics/*metabolism ; Comamonadaceae/*genetics/*metabolism ; Ecosystem ; Gene Transfer Techniques ; Iron/metabolism ; Plasmids/*genetics ; Population Dynamics ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Burkholderia terrae strain BS001 is a well-described inhabitant of the mycosphere of diverse fungi. In the interaction between this bacterium and its fungal host in soil, competition for iron might be a key process. Here, we address the capacity of the broad-host-range IncP-1β plasmid pHB44, originally isolated in Variovorax paradoxus HB44, to enhance or modulate the competitiveness of B. terrae BS001 under different soil iron levels when confronted with (young versus ageing) mycelia of Lyophyllum sp. strain Karsten in microcosms. The data revealed that, in most cases, plasmid pHB44 reduced the fitness of its host in the mycosphere, possibly due to a metabolic burden effect. However, an opposite effect was found under low-iron conditions at the extreme tips of the soil-exploring Lyophyllum sp. strain Karsten mycelium. The negative effect of plasmid pHB44 on strain BS001 population sizes was clearly offset by fitness enhancement under these conditions. Moreover, as evidenced by using plasmid pSUP104 as a tracer, plasmid pHB44 was transferred from the B. terrae BS001 host into V. paradoxus BS64 in the ageing mycosphere, but not in bulk soil. Strikingly, successful plasmid establishment in the new host was more prominent in the iron-limited than in the 'high-iron' mycosphere habitat, indicating plasmid pHB44 was required in the V. paradoxus host as a fitness stimulator in the iron-limited condition. Taken together, the data suggest that efficiency of iron acquisition only served as the selective mechanism under certain conditions of iron availability in the soil, specifically promoting the fitness of V. paradoxus transconjugants. Not only is the mycosphere to be regarded as a selective arena in which horizontal gene transfer across the bacterial inhabitants is spurred, but the outcome of the adaptive processes is strongly shaped by competitive events among the local organisms.}, }
@article {pmid26704531, year = {2015}, author = {Song, C and Schmidt, R and de Jager, V and Krzyzanowska, D and Jongedijk, E and Cankar, K and Beekwilder, J and van Veen, A and de Boer, W and van Veen, JA and Garbeva, P}, title = {Exploring the genomic traits of fungus-feeding bacterial genus Collimonas.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {1103}, pmid = {26704531}, issn = {1471-2164}, mesh = {Bacterial Secretion Systems/genetics ; Bacteriophages ; Betaproteobacteria/*genetics/metabolism/virology ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Fungi ; Gene Order ; Genes, Bacterial ; *Genome, Bacterial ; Genomic Islands ; *Genomics/methods ; Metabolome ; Metabolomics ; Microbial Interactions ; Multigene Family ; Phylogeny ; *Quantitative Trait, Heritable ; Secondary Metabolism ; Signal Transduction ; }, abstract = {BACKGROUND: Collimonas is a genus belonging to the class of Betaproteobacteria and consists mostly of soil bacteria with the ability to exploit living fungi as food source (mycophagy). Collimonas strains differ in a range of activities, including swimming motility, quorum sensing, extracellular protease activity, siderophore production, and antimicrobial activities.<br><br>RESULTS: In order to reveal ecological traits possibly related to Collimonas lifestyle and secondary metabolites production, we performed a comparative genomics analysis based on whole-genome sequencing of six strains representing 3 recognized species. The analysis revealed that the core genome represents 43.1 to 52.7% of the genomes of the six individual strains. These include genes coding for extracellular enzymes (chitinase, peptidase, phospholipase), iron acquisition and type II secretion systems. In the variable genome, differences were found in genes coding for secondary metabolites (e.g. tripropeptin A and volatile terpenes), several unknown orphan polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS), nonribosomal peptide synthetase (NRPS) gene clusters, a new lipopeptide and type III and type VI secretion systems. Potential roles of the latter genes in the interaction with other organisms were investigated. Mutation of a gene involved in tripropeptin A biosynthesis strongly reduced the antibacterial activity against Staphylococcus aureus, while disruption of a gene involved in the biosynthesis of the new lipopeptide had a large effect on the antifungal/oomycetal activities.<br><br>CONCLUSIONS: Overall our results indicated that Collimonas genomes harbour many genes encoding for novel enzymes and secondary metabolites (including terpenes) important for interactions with other organisms and revealed genomic plasticity, which reflect the behaviour, antimicrobial activity and lifestylesof Collimonas spp.}, }
@article {pmid26703195, year = {2016}, author = {Álvarez-Pérez, S and de Vega, C and Pozo, MI and Lenaerts, M and Van Assche, A and Herrera, CM and Jacquemyn, H and Lievens, B}, title = {Nectar yeasts of the Metschnikowia clade are highly susceptible to azole antifungals widely used in medicine and agriculture.}, journal = {FEMS yeast research}, volume = {16}, number = {1}, pages = {fov115}, doi = {10.1093/femsyr/fov115}, pmid = {26703195}, issn = {1567-1364}, mesh = {Agriculture/methods ; Animals ; Antifungal Agents/*pharmacology ; Azoles/*pharmacology ; Insecta/microbiology ; Medicine/methods ; Metschnikowia/*drug effects/isolation &amp; purification ; Microbial Sensitivity Tests ; Plants/microbiology ; }, abstract = {The widespread use of azole antifungals in medicine and agriculture and the resulting long-persistent residues could potentially affect beneficial fungi. However, there is very little information on the tolerance of non-target environmental fungi to azoles. In this study, we assessed the susceptibility of diverse plant- and insect-associated yeasts from the Metschnikowia clade, including several ecologically important species, to widely used medical and agricultural azoles (epoxiconazole, imazalil, ketoconazole and voriconazole). A total of 120 strains from six species were tested. Minimum inhibitory concentrations (MICs) were determined by the EUCAST broth microdilution procedure after some necessary modifications were made. The majority of species tested were highly susceptible to epoxiconazole, ketoconazole and voriconazole (>95% of strains showed MICs ≤ 0.125 mg l(-1)). Most strains were also very susceptible to imazalil, although MIC values were generally higher than for the other azoles. Furthermore, certain Metschnikowia reukaufii strains displayed a 'trailing' phenotype (i.e. showed reduced but persistent growth at antifungal concentrations above the MIC), but this characteristic was dependent on test conditions. It was concluded that exposure to azoles may pose a risk for ecologically relevant yeasts from the Metschnikowia clade, and thus could potentially impinge on the tripartite interaction linking these fungi with plants and their insect pollinators.}, }
@article {pmid26700882, year = {2016}, author = {Pitta, DW and Indugu, N and Kumar, S and Vecchiarelli, B and Sinha, R and Baker, LD and Bhukya, B and Ferguson, JD}, title = {Metagenomic assessment of the functional potential of the rumen microbiome in Holstein dairy cows.}, journal = {Anaerobe}, volume = {38}, number = {}, pages = {50-60}, doi = {10.1016/j.anaerobe.2015.12.003}, pmid = {26700882}, issn = {1095-8274}, mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Cattle ; Computational Biology/methods ; Lactation ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Phylogeny ; Rumen/*microbiology/physiology ; }, abstract = {The microbial ecology of the rumen microbiome is influenced by the diet and the physiological status of the dairy cow and can have tremendous influence on the yield and components of milk. There are significant differences in milk yields between first and subsequent lactations of dairy cows, but information on how the rumen microbiome changes as the dairy cow gets older has received little attention. We characterized the rumen microbiome of the dairy cow for phylogeny and functional pathways by lactation group and stage of lactation using a metagenomics approach. Our findings revealed that the rumen microbiome was dominated by Bacteroidetes (70%), Firmicutes (15-20%) and Proteobacteria (7%). The abundance of Firmicutes and Proteobacteria were independently influenced by diet and lactation. Bacteroidetes contributed to a majority of the metabolic functions in first lactation dairy cows while the contribution from Firmicutes and Proteobacteria increased incrementally in second and third lactation dairy cows. We found that nearly 70% of the CAZymes were oligosaccharide breaking enzymes which reflect the higher starch and fermentable sugars in the diet. The results of this study suggest that the rumen microbiome continues to evolve as the dairy cow advances in lactations and these changes may have a significant role in milk production.}, }
@article {pmid26700442, year = {2016}, author = {Dickson, RP}, title = {The microbiome and critical illness.}, journal = {The Lancet. Respiratory medicine}, volume = {4}, number = {1}, pages = {59-72}, pmid = {26700442}, issn = {2213-2619}, support = {UL1 TR000433/TR/NCATS NIH HHS/United States ; T32 HL007749/HL/NHLBI NIH HHS/United States ; UL1TR000433/TR/NCATS NIH HHS/United States ; L30 HL120241/HL/NHLBI NIH HHS/United States ; K23 HL130641/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Asthma/microbiology ; Bronchiectasis/microbiology ; *Critical Illness ; Cystic Fibrosis/microbiology ; Disease Progression ; *Gastrointestinal Microbiome ; Humans ; Lung/*microbiology ; Microbiota ; Pneumonia/microbiology ; Pulmonary Disease, Chronic Obstructive/microbiology ; Respiratory Distress Syndrome/microbiology ; Sepsis/microbiology ; }, abstract = {The central role of the microbiome in critical illness is supported by a half century of experimental and clinical study. The physiological effects of critical illness and the clinical interventions of intensive care substantially alter the microbiome. In turn, the microbiome predicts patients' susceptibility to disease, and manipulation of the microbiome has prevented or modulated critical illness in animal models and clinical trials. This Review surveys the microbial ecology of critically ill patients, presents the facts and unanswered questions surrounding gut-derived sepsis, and explores the radically altered ecosystem of the injured alveolus. The revolution in culture-independent microbiology has provided the tools needed to target the microbiome rationally for the prevention and treatment of critical illness, holding great promise to improve the acute and chronic outcomes of the critically ill.}, }
@article {pmid26697110, year = {2015}, author = {Andersen, SJ and Candry, P and Basadre, T and Khor, WC and Roume, H and Hernandez-Sanabria, E and Coma, M and Rabaey, K}, title = {Electrolytic extraction drives volatile fatty acid chain elongation through lactic acid and replaces chemical pH control in thin stillage fermentation.}, journal = {Biotechnology for biofuels}, volume = {8}, number = {}, pages = {221}, pmid = {26697110}, issn = {1754-6834}, abstract = {BACKGROUND: Volatile fatty acids (VFA) are building blocks for the chemical industry. Sustainable, biological production is constrained by production and recovery costs, including the need for intensive pH correction. Membrane electrolysis has been developed as an in situ extraction technology tailored to the direct recovery of VFA from fermentation while stabilizing acidogenesis without caustic addition. A current applied across an anion exchange membrane reduces the fermentation broth (catholyte, water reduction: H2O + e(-) → ½ H2 + OH(-)) and drives carboxylate ions into a clean, concentrated VFA stream (anolyte, water oxidation: H2O → 2e(-) + 2 H(+) + O2).<br><br>RESULTS: In this study, we fermented thin stillage to generate a mixed VFA extract without chemical pH control. Membrane electrolysis (0.1 A, 3.22&#xa0;&#xb1;&#xa0;0.60&#xa0;V) extracted 28&#xa0;&#xb1;&#xa0;6&#xa0;% of carboxylates generated per day (on a carbon basis) and completely replaced caustic control of pH, with no impact on the total carboxylate production amount or rate. Hydrogen generated from the applied current shifted the fermentation outcome from predominantly C2 and C3 VFA (64&#xa0;&#xb1;&#xa0;3&#xa0;% of the total VFA present in the control) to majority of C4 to C6 (70&#xa0;&#xb1;&#xa0;12&#xa0;% in the experiment), with identical proportions in the VFA acid extract. A strain related to Megasphaera elsdenii (maximum abundance of 57&#xa0;%), a bacteria capable of producing mid-chain VFA at a high rate, was enriched by the applied current, alongside a stable community of Lactobacillus spp. (10&#xa0;%), enabling chain elongation of VFA through lactic acid. A conversion of 30&#xa0;&#xb1;&#xa0;5&#xa0;% VFA produced per sCOD fed (60&#xa0;&#xb1;&#xa0;10&#xa0;% of the reactive fraction) was achieved, with a 50&#xa0;&#xb1;&#xa0;6&#xa0;% reduction in suspended solids likely by electro-coagulation.<br><br>CONCLUSIONS: VFA can be extracted directly from a fermentation broth by membrane electrolysis. The electrolytic water reduction products are utilized in the fermentation: OH(-) is used for pH control without added chemicals, and H2 is metabolized by species such as Megasphaera elsdenii to produce greater value, more reduced VFA. Electro-fermentation displays promise for generating added value chemical co-products from biorefinery sidestreams and wastes.}, }
@article {pmid26697002, year = {2015}, author = {Berry, D and Kuzyk, O and Rauch, I and Heider, S and Schwab, C and Hainzl, E and Decker, T and Müller, M and Strobl, B and Schleper, C and Urich, T and Wagner, M and Kenner, L and Loy, A}, title = {Intestinal Microbiota Signatures Associated with Inflammation History in Mice Experiencing Recurring Colitis.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1408}, pmid = {26697002}, issn = {1664-302X}, support = {P 26127/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Acute colitis causes alterations in the intestinal microbiota, but the microbiota is thought to recover after such events. Extreme microbiota alterations are characteristic of human chronic inflammatory bowel diseases, although alterations reported in different studies are divergent and sometimes even contradictory. To better understand the impact of periodic disturbances on the intestinal microbiota and its compositional difference between acute and relapsing colitis, we investigated the beginnings of recurrent inflammation using the dextran sodium sulfate (DSS) mouse model of chemically induced colitis. Using bacterial 16S rRNA gene-targeted pyrosequencing as well as quantitative fluorescence in situ hybridization, we profiled the intestinal and stool microbiota of mice over the course of three rounds of DSS-induced colitis and recovery. We found that characteristic inflammation-associated microbiota could be detected in recovery-phase mice. Successive inflammation episodes further drove the microbiota into an increasingly altered composition post-inflammation, and signatures of colitis history were detectable in the microbiota more sensitively than by pathology analysis. Bacterial indicators of murine colitis history were identified in intestinal and stool samples, with a high degree of consistency between both sample types. Stool may therefore be a promising non-invasive source of bacterial biomarkers that are highly sensitive to inflammation state and history.}, }
@article {pmid26696989, year = {2015}, author = {Callewaert, C and Van Nevel, S and Kerckhof, FM and Granitsiotis, MS and Boon, N}, title = {Bacterial Exchange in Household Washing Machines.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1381}, pmid = {26696989}, issn = {1664-302X}, abstract = {Household washing machines (WMs) launder soiled clothes and textiles, but do not sterilize them. We investigated the microbial exchange occurring in five household WMs. Samples from a new cotton T-shirt were laundered together with a normal laundry load. Analyses were performed on the influent water and the ingoing cotton samples, as well as the greywater and the washed cotton samples. The number of living bacteria was generally not lower in the WM effluent water as compared to the influent water. The laundering process caused a microbial exchange of influent water bacteria, skin-, and clothes-related bacteria and biofilm-related bacteria in the WM. A variety of biofilm-producing bacteria were enriched in the effluent after laundering, although their presence in the cotton sample was low. Nearly all bacterial genera detected on the initial cotton sample were still present in the washed cotton samples. A selection for typical skin- and clothes-related microbial species occurred in the cotton samples after laundering. Accordingly, malodour-causing microbial species might be further distributed to other clothes. The bacteria on the ingoing textiles contributed for a large part to the microbiome found in the textiles after laundering.}, }
@article {pmid26696977, year = {2015}, author = {Logue, JB and Findlay, SE and Comte, J}, title = {Editorial: Microbial Responses to Environmental Changes.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1364}, pmid = {26696977}, issn = {1664-302X}, }
@article {pmid26696966, year = {2015}, author = {Riquelme, C and Marshall Hathaway, JJ and Enes Dapkevicius, Mde L and Miller, AZ and Kooser, A and Northup, DE and Jurado, V and Fernandez, O and Saiz-Jimenez, C and Cheeptham, N}, title = {Actinobacterial Diversity in Volcanic Caves and Associated Geomicrobiological Interactions.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1342}, pmid = {26696966}, issn = {1664-302X}, support = {P20 GM103452/GM/NIGMS NIH HHS/United States ; }, abstract = {Volcanic caves are filled with colorful microbial mats on the walls and ceilings. These volcanic caves are found worldwide, and studies are finding vast bacteria diversity within these caves. One group of bacteria that can be abundant in volcanic caves, as well as other caves, is Actinobacteria. As Actinobacteria are valued for their ability to produce a variety of secondary metabolites, rare and novel Actinobacteria are being sought in underexplored environments. The abundance of novel Actinobacteria in volcanic caves makes this environment an excellent location to study these bacteria. Scanning electron microscopy (SEM) from several volcanic caves worldwide revealed diversity in the morphologies present. Spores, coccoid, and filamentous cells, many with hair-like or knobby extensions, were some of the microbial structures observed within the microbial mat samples. In addition, the SEM study pointed out that these features figure prominently in both constructive and destructive mineral processes. To further investigate this diversity, we conducted both Sanger sequencing and 454 pyrosequencing of the Actinobacteria in volcanic caves from four locations, two islands in the Azores, Portugal, and Hawai'i and New Mexico, USA. This comparison represents one of the largest sequencing efforts of Actinobacteria in volcanic caves to date. The diversity was shown to be dominated by Actinomycetales, but also included several newly described orders, such as Euzebyales, and Gaiellales. Sixty-two percent of the clones from the four locations shared less than 97% similarity to known sequences, and nearly 71% of the clones were singletons, supporting the commonly held belief that volcanic caves are an untapped resource for novel and rare Actinobacteria. The amplicon libraries depicted a wider view of the microbial diversity in Azorean volcanic caves revealing three additional orders, Rubrobacterales, Solirubrobacterales, and Coriobacteriales. Studies of microbial ecology in volcanic caves are still very limited. To rectify this deficiency, the results from our study help fill in the gaps in our knowledge of actinobacterial diversity and their potential roles in the volcanic cave ecosystems.}, }
@article {pmid26695630, year = {2015}, author = {Case, DH and Pasulka, AL and Marlow, JJ and Grupe, BM and Levin, LA and Orphan, VJ}, title = {Methane Seep Carbonates Host Distinct, Diverse, and Dynamic Microbial Assemblages.}, journal = {mBio}, volume = {6}, number = {6}, pages = {e01348-15}, pmid = {26695630}, issn = {2150-7511}, mesh = {Archaea/*genetics/metabolism/*physiology ; Biodiversity ; Carbonates/*analysis ; Chloroflexi/genetics/metabolism ; Deltaproteobacteria/genetics/metabolism/*physiology ; Ecosystem ; Geologic Sediments/chemistry/*microbiology ; High-Throughput Nucleotide Sequencing ; Methane/*analysis ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; }, abstract = {UNLABELLED: Marine methane seeps are globally distributed geologic features in which reduced fluids, including methane, are advected upward from the subsurface. As a result of alkalinity generation during sulfate-coupled methane oxidation, authigenic carbonates form slabs, nodules, and extensive pavements. These carbonates shape the landscape within methane seeps, persist long after methane flux is diminished, and in some cases are incorporated into the geologic record. In this study, microbial assemblages from 134 native and experimental samples across 5,500 km, representing a range of habitat substrates (carbonate nodules and slabs, sediment, bottom water, and wood) and seepage conditions (active and low activity), were analyzed to address two fundamental questions of seep microbial ecology: (i) whether carbonates host distinct microbial assemblages and (ii) how sensitive microbial assemblages are to habitat substrate type and temporal shifts in methane seepage flux. Through massively parallel 16S rRNA gene sequencing and statistical analysis, native carbonates are shown to be reservoirs of distinct and highly diverse seep microbial assemblages. Unique coupled transplantation and colonization experiments on the seafloor demonstrated that carbonate-associated microbial assemblages are resilient to seep quiescence and reactive to seep activation over 13 months. Various rates of response to simulated seep quiescence and activation are observed among similar phylogenies (e.g., Chloroflexi operational taxonomic units) and similar metabolisms (e.g., putative S oxidizers), demonstrating the wide range of microbial sensitivity to changes in seepage flux. These results imply that carbonates do not passively record a time-integrated history of seep microorganisms but rather host distinct, diverse, and dynamic microbial assemblages.<br><br>IMPORTANCE: Since their discovery in 1984, the global distribution and importance of marine methane seeps have become increasingly clear. Much of our understanding of methane seep microorganisms-from metabolisms to community ecology-has stemmed from detailed studies of seep sediments. However, it has become apparent that carbonates represent a volumetrically significant habitat substrate at methane seeps. Through combined in situ characterization and incubation experiments, this study demonstrates that carbonates host microbial assemblages distinct from and more diverse than those of other seep habitats. This emphasizes the importance of seep carbonates as biodiversity locales. Furthermore, we demonstrate that carbonate-associated microbial assemblages are well adapted to withstand fluctuations in methane seepage, and we gain novel insight into particular taxa that are responsive (or recalcitrant) to changes in seep conditions.}, }
@article {pmid26691516, year = {2016}, author = {Irianni-Renno, M and Akhbari, D and Olson, MR and Byrne, AP and Lefèvre, E and Zimbron, J and Lyverse, M and Sale, TC and De Long, SK}, title = {Comparison of bacterial and archaeal communities in depth-resolved zones in an LNAPL body.}, journal = {Applied microbiology and biotechnology}, volume = {100}, number = {7}, pages = {3347-3360}, doi = {10.1007/s00253-015-7106-z}, pmid = {26691516}, issn = {1432-0614}, mesh = {Archaea/*classification/genetics/metabolism ; Biodegradation, Environmental ; Deltaproteobacteria/*classification/genetics/metabolism ; Groundwater/*microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Hydrocarbons/*metabolism ; Methane/biosynthesis ; Microbial Consortia/genetics ; Oil and Gas Industry ; Oxidation-Reduction ; Oxygen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfates/metabolism ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Advances in our understanding of the microbial ecology at sites impacted by light non-aqueous phase liquids (LNAPLs) are needed to drive development of optimized bioremediation technologies, support longevity models, and develop culture-independent molecular tools. In this study, depth-resolved characterization of geochemical parameters and microbial communities was conducted for a shallow hydrocarbon-impacted aquifer. Four distinct zones were identified based on microbial community structure and geochemical data: (i) an aerobic, low-contaminant mass zone at the top of the vadose zone; (ii) a moderate to high-contaminant mass, low-oxygen to anaerobic transition zone in the middle of the vadose zone; (iii) an anaerobic, high-contaminant mass zone spanning the bottom of the vadose zone and saturated zone; and (iv) an anaerobic, low-contaminant mass zone below the LNAPL body. Evidence suggested that hydrocarbon degradation is mediated by syntrophic fermenters and methanogens in zone III. Upward flux of methane likely contributes to promoting anaerobic conditions in zone II by limiting downward flux of oxygen as methane and oxygen fronts converge at the top of this zone. Observed sulfate gradients and microbial communities suggested that sulfate reduction and methanogenesis both contribute to hydrocarbon degradation in zone IV. Pyrosequencing revealed that Syntrophus- and Methanosaeta-related species dominate bacterial and archaeal communities, respectively, in the LNAPL body below the water table. Observed phylotypes were linked with in situ anaerobic hydrocarbon degradation in LNAPL-impacted soils.}, }
@article {pmid26691315, year = {2016}, author = {Torres, Cde A and Lürling, M and Marinho, MM}, title = {Assessment of the Effects of Light Availability on Growth and Competition Between Strains of Planktothrix agardhii and Microcystis aeruginosa.}, journal = {Microbial ecology}, volume = {71}, number = {4}, pages = {802-813}, pmid = {26691315}, issn = {1432-184X}, mesh = {Cyanobacteria/*growth &amp; development/*radiation effects ; Fresh Water/microbiology ; Light ; Microcystis/*growth &amp; development/*radiation effects ; Phytoplankton/growth &amp; development/radiation effects ; Water Microbiology ; }, abstract = {In this study, we tested the hypothesis that Planktothrix agardhii strains isolated from a tropical water body were better competitors for light than Microcystis aeruginosa strains. These cyanobacteria are common in eutrophic systems, where light is one of the main drivers of phytoplankton, and Planktothrix is considered more shade-adapted and Microcystis more high-light tolerant. First, the effect of light intensities on growth was studied in batch cultures. Next, the minimum requirement of light (I*) and the effect of light limitation on the outcome of competition was investigated in chemostats. All strains showed similar growth at 10 μmol photons m(-2) s(-1), demonstrating the ability of the two species to grow in low light. The optimum light intensity was lower for P. agardhii, but at the highest light intensity, Microcystis strains reached higher biovolume, confirming that P. agardhii has higher sensitivity to high light. Nonetheless, P. agardhii grew in light intensities considered high (500 μmol photons m(-2) s(-1)) for this species. M. aeruginosa showed a higher carrying capacity in light-limited condition, but I* was similar between all the strains. Under light competition, Microcystis strains displaced P. agardhii and dominated. In two cases, there was competitive exclusion and in the other two P. agardhii managed to remain in the system with a low biovolume (≈15%). Our findings not only show that strains of P. agardhii can grow under higher light intensities than generally assumed but also that strains of M. aeruginosa are better competitors for light than supposed. These results help to understand the co-occurrence of these species in tropical environments and the dominance of M. aeruginosa even in low-light conditions.}, }
@article {pmid26690563, year = {2016}, author = {Pechal, JL and Benbow, ME}, title = {Microbial ecology of the salmon necrobiome: evidence salmon carrion decomposition influences aquatic and terrestrial insect microbiomes.}, journal = {Environmental microbiology}, volume = {18}, number = {5}, pages = {1511-1522}, doi = {10.1111/1462-2920.13187}, pmid = {26690563}, issn = {1462-2920}, mesh = {Animals ; Cadaver ; Insecta/*classification ; Larva ; *Microbiota ; RNA, Ribosomal, 16S ; *Salmon/microbiology ; }, abstract = {Carrion decomposition is driven by complex relationships that affect necrobiome community (i.e. all organisms and their genes associated with a dead animal) interactions, such as insect species arrival time to carrion and microbial succession. Little is understood about how microbial communities interact with invertebrates at the aquatic-terrestrial habitat interface. The first objective of the study was to characterize internal microbial communities using high-throughput sequencing of 16S rRNA gene amplicons for aquatic insects (three mayfly species) in streams with salmon carcasses compared with those in streams without salmon carcasses. The second objective was to assess the epinecrotic microbial communities of decomposing salmon carcasses (Oncorhynchus keta) compared with those of terrestrial necrophagous insects (Calliphora terraenovae larvae and adults) associated with the carcasses. There was a significant difference in the internal microbiomes of mayflies collected in salmon carcass-bearing streams and in non-carcass streams, while the developmental stage of blow flies was the governing factor in structuring necrophagous insect internal microbiota. Furthermore, the necrophagous internal microbiome was influenced by the resource on which the larvae developed, and changes in the adult microbiome varied temporally. Overall, these carrion subsidy-driven networks respond to resource pulses with bottom-up effects on consumer microbial structure, as revealed by shifting communities over space and time.}, }
@article {pmid26689997, year = {2016}, author = {Alard, J and Lehrter, V and Rhimi, M and Mangin, I and Peucelle, V and Abraham, AL and Mariadassou, M and Maguin, E and Waligora-Dupriet, AJ and Pot, B and Wolowczuk, I and Grangette, C}, title = {Beneficial metabolic effects of selected probiotics on diet-induced obesity and insulin resistance in mice are associated with improvement of dysbiotic gut microbiota.}, journal = {Environmental microbiology}, volume = {18}, number = {5}, pages = {1484-1497}, doi = {10.1111/1462-2920.13181}, pmid = {26689997}, issn = {1462-2920}, mesh = {Animals ; Diet, High-Fat/*adverse effects ; Gastrointestinal Microbiome/*physiology ; *Insulin Resistance ; Male ; Mice ; Microbiota ; Obesity ; Probiotics/*therapeutic use ; }, abstract = {Alterations in gut microbiota composition and diversity were suggested to play a role in the development of obesity, a chronic subclinical inflammatory condition. We here evaluated the impact of oral consumption of a monostrain or multi-strain probiotic preparation in high-fat diet-induced obese mice. We observed a strain-specific effect and reported dissociation between the capacity of probiotics to dampen adipose tissue inflammation and to limit body weight gain. A multi-strain mixture was able to improve adiposity, insulin resistance and dyslipidemia through adipose tissue immune cell-remodelling, mainly affecting macrophages. At the gut level, the mixture modified the uptake of fatty acids and restored the expression level of the short-chain fatty acid receptor GPR43. These beneficial effects were associated with changes in the microbiota composition, such as the restoration of the abundance of Akkermansia muciniphila and Rikenellaceae and the decrease of other taxa like Lactobacillaceae. Using an in vitro gut model, we further showed that the probiotic mixture favours the production of butyrate and propionate. Our findings provide crucial clues for the design and use of more efficient probiotic preparations in obesity management and may bring new insights into the mechanisms by which host-microbe interactions govern such protective effects.}, }
@article {pmid26687489, year = {2016}, author = {Hines, HN and McCarthy, PJ and Esteban, GF}, title = {The First Record for the Americas of Loxodes rex, a Flagship Ciliate with an Alleged Restricted Biogeography.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {5-8}, pmid = {26687489}, issn = {1432-184X}, mesh = {Body Size ; Ciliophora/growth &amp; development/*isolation &amp; purification ; Florida ; Fresh Water/*parasitology ; }, abstract = {As the foundations of food webs, protozoa are essential to the success of an ecological system. These organisms are often overlooked, and research in the Americas is sparse. Recent samplings conducted in freshwater canals and ponds in Florida, USA, have revealed Loxodes rex, an alleged endemic ciliate species. Originally described as endemic to tropical Africa, L. rex has been considered a prime candidate for proof of microbial endemism. Our studies have shown this giant, non-encysting ciliate to be thriving in subtropical Florida. Our observations are novel and include both the first record of occurrence for the Americas and the first high-quality in vivo images for this charismatic species.}, }
@article {pmid26687343, year = {2016}, author = {Stępień, &#x141; and Waśkiewicz, A and Urbaniak, M}, title = {Wildly Growing Asparagus (Asparagus officinalis L.) Hosts Pathogenic Fusarium Species and Accumulates Their Mycotoxins.}, journal = {Microbial ecology}, volume = {71}, number = {4}, pages = {927-937}, pmid = {26687343}, issn = {1432-184X}, mesh = {Asparagus Plant/*metabolism/*microbiology ; DNA, Fungal/analysis/genetics ; Food Contamination/analysis ; Food Microbiology ; Fusariosis/metabolism/microbiology/pathology ; Fusarium/genetics/growth &amp; development/isolation &amp; purification/*physiology ; Host-Pathogen Interactions ; Mycotoxins/analysis/*biosynthesis/metabolism/toxicity ; Plant Diseases/*microbiology ; }, abstract = {Asparagus officinalis L. is an important crop in many European countries, likely infected by a number of Fusarium species. Most of them produce mycotoxins in plant tissues, thus affecting the physiology of the host plant. However, there is lack of information on Fusarium communities in wild asparagus, where they would definitely have considerable environmental significance. Therefore, the main scientific aim of this study was to identify the Fusarium species and quantify their typical mycotoxins present in wild asparagus plants collected at four time points of the season. Forty-four Fusarium strains of eight species--Fusarium acuminatum, Fusarium avenaceum, Fusarium culmorum, Fusarium equiseti, Fusarium oxysporum, Fusarium proliferatum, Fusarium sporotrichioides, and Fusarium tricinctum--were isolated from nine wild asparagus plants in 2013 season. It is the first report of F. sporotrichioides isolated from this particular host. Fumonisin B1 was the most abundant mycotoxin, and the highest concentrations of fumonisins B1-B3 and beauvericin were found in the spears collected in May. Moniliformin and enniatins were quantified at lower concentrations. Mycotoxins synthesized by individual strains obtained from infected asparagus tissues were assessed using in vitro cultures on sterile rice grain. Most of the F. sporotrichioides strains synthesized HT-2 toxin and F. equiseti strains were found to be effective zearalenone producers.}, }
@article {pmid26687210, year = {2016}, author = {Anderson, KE and Rodrigues, PA and Mott, BM and Maes, P and Corby-Harris, V}, title = {Ecological Succession in the Honey Bee Gut: Shift in Lactobacillus Strain Dominance During Early Adult Development.}, journal = {Microbial ecology}, volume = {71}, number = {4}, pages = {1008-1019}, pmid = {26687210}, issn = {1432-184X}, mesh = {Animals ; Bacterial Load ; Bees/growth &amp; development/*microbiology ; Biodiversity ; *Ecology ; Gastrointestinal Microbiome ; Interpersonal Relations ; Lactobacillus/*classification/genetics/growth &amp; development ; Microbiota ; Phylogeny ; Pollen/microbiology ; Symbiosis ; }, abstract = {In many vertebrates, social interactions and nutrition can affect the colonization of gut symbionts across generations. In the highly social honey bee, it is unknown to what extent the hive environment and older worker individuals contribute to the generational transmission of core gut bacteria. We used high-throughput sequencing to investigate the effect of nest materials and social contact on the colonization and succession of core hindgut microbiota in workers. With only brief exposure to hive materials following natural eclosion, gut bacterial communities at 3 and 7 days contained phylotypes typically found in the guts of mature adults regardless of treatment. Continuous exposure to nest materials or direct social interactions with mature adults did not affect the diversity or abundance of gut bacterial communities at the scale examined. Similarly, a common pollen supplement fed by beekeepers during pollen dearth had no effect. A consideration of unique OTUs revealed extensive microbial succession independent of treatment. The dominant Lactobacillus strain at 3 days was largely replaced by a different strain at day 7, revealing the colonization signature of a pioneer species. Similar but less pronounced patterns were evident in less abundant OTU's, many of which may influence community succession via alteration of the gut environment. Our results indicate that the process of bacterial community colonization in the hindgut is resilient to changes in the nutritional, hive, and social environment. Greater taxonomic resolution is needed to accurately resolve questions of ecological succession and typical proportional variation within and between core members of the gut bacterial community.}, }
@article {pmid26686479, year = {2016}, author = {Deng, D and Weidhaas, JL and Lin, LS}, title = {Kinetics and microbial ecology of batch sulfidogenic bioreactors for co-treatment of municipal wastewater and acid mine drainage.}, journal = {Journal of hazardous materials}, volume = {305}, number = {}, pages = {200-208}, doi = {10.1016/j.jhazmat.2015.11.041}, pmid = {26686479}, issn = {1873-3336}, mesh = {Biological Oxygen Demand Analysis ; Bioreactors/*microbiology ; Industrial Waste ; Kinetics ; Mining ; Oxidation-Reduction ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sulfur-Reducing Bacteria/genetics/isolation &amp; purification/*metabolism ; Waste Disposal, Fluid/methods ; Wastewater ; }, abstract = {The kinetics and microbial ecology in sulfidogenic bioreactors used in a novel two-stage process for co-treatment of acid mine drainage (AMD) and municipal wastewater (MWW) were investigated. Michaelis-Menten modeling of COD oxidation by sulfate reducing bacteria (SRB) (Vmax=0.33mgL(-1)min(-1), Km=4.3mgL(-1)) suggested that the Vmax can be reasonably achieved given the typical COD values in MWW and anticipated mixing with AMD. Non-competitive inhibition modeling (Ki=6.55mgL(-1)) indicated that excessive iron level should be avoided to limit its effects on SRB. The COD oxidation rate was positively correlated to COD/sulfate ratio and SRB population, as evidenced by dsrA gene copies. Phylogenetic analysis revealed diverse microbial communities dominated by sulfate reducing delta-proteobacteria. Microbial community and relative quantities of SRB showed significant differences under different COD/sulfate ratios (0.2, 1 and 2), and the highest dsrA gene concentration and most complex microbial diversity were observed under COD/sulfate ratio 2. Major species were associated with Desulfovirga, Desulfobulbus, Desulfovibrio, and Syntrophus sp. The reported COD kinetics, SRB abundances and the phylogenetic profile provide insights into the co-treatment process and help identify the parameters of concerns for such technology development.}, }
@article {pmid26686411, year = {2016}, author = {Yu, XL and Chan, Y and Zhuang, LF and Lai, HC and Lang, NP and Lacap-Bugler, DC and Leung, WK and Watt, RM}, title = {Distributions of Synergistetes in clinically-healthy and diseased periodontal and peri-implant niches.}, journal = {Microbial pathogenesis}, volume = {94}, number = {}, pages = {90-103}, doi = {10.1016/j.micpath.2015.11.029}, pmid = {26686411}, issn = {1096-1208}, mesh = {Adult ; Aged ; Aged, 80 and over ; Biofilms ; China ; DNA, Bacterial/genetics ; Dental Plaque/microbiology ; Female ; Gram-Negative Anaerobic Bacteria/genetics/*isolation &amp; purification ; Humans ; Male ; Microbiota ; Middle Aged ; Mouth/*microbiology ; Peri-Implantitis/*microbiology ; Periodontal Diseases/*microbiology ; Periodontium/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bacterial taxa belonging to the phylum Synergistetes are commonly detected within diseased periodontal niches, but are rarely found within healthy oral sites. However, as they typically constitute a minor fraction of the oral microbiota, their precise distributions and disease-associations remain to be fully established. Here, we surveyed the Synergistetes taxa present within individual periodontal/subgingival and peri-implant/submucosal sites, within Chinese subjects (n = 18) affected by both peri-implantitis and periodontitis. Four individual, clinically-distinct sites were analyzed in each patient: healthy sulcus; periodontitis lesion; healthy peri-implant space; peri-implantitis lesion. We employed a clone library-based approach, using PCR-primers that specifically amplified ca. 650bp regions of the 16S rRNA gene from oral cluster A and B Synergistetes taxa. Twenty-one of the 72 sites (from 12/18 subjects) yielded Synergistetes 16S rRNA PCR products. Sequencing of cloned amplicon libraries yielded 1338 quality-filtered 16S rRNA sequences, which were assigned to 26 Synergistetes operational taxonomic units (OTUs; oral taxon SH01-SH26) using a 98.5% identity cut-off. We identified 25 Synergistetes oral cluster A OTUs (genus Fretibacterium; corresponding to Human Oral Taxon (HOT) numbers 358, 359, 360, 361, 362, 363, 452, and 453), and one oral cluster B OTU (Pyramidobacter piscolens oral taxon SH04, HOT-357). Three OTUs predominated: Fretibacterium oral taxon SH01 (HOT-360), Fretibacterium oral taxon SH02 (HOT-452), and Fretibacterium fastidiosum oral taxon SH03 (HOT-363). The Synergistetes community compositions within the respective periodontal and peri-implant sites were variable and complex, and no statistically-significant correlations could be established. However, the detection frequency of F. fastidiosum SH03 and Fretibacterium oral taxon SH01 were both positively associated with plaque index at healthy subgingival sites. Taken together, our results show that diverse Synergistetes populations inhabit both diseased and healthy periodontal and peri-implant niches, with considerable site-to-site variations in composition occurring within the same oral cavity.}, }
@article {pmid26685749, year = {2016}, author = {Nunes-Alves, C}, title = {Microbial ecology: Do it yourself nitrification.}, journal = {Nature reviews. Microbiology}, volume = {14}, number = {2}, pages = {61}, pmid = {26685749}, issn = {1740-1534}, mesh = {Ammonia/*metabolism ; Bacteria/*metabolism ; Nitrates/*metabolism ; *Nitrification ; Nitrites/*metabolism ; }, }
@article {pmid26679578, year = {2015}, author = {Bezuidt, OK and Makhalanyane, TP and Gomri, MA and Kharroub, K and Cowan, DA}, title = {Draft Genome Sequence of Thermophilic Geobacillus sp. Strain Sah69, Isolated from Saharan Soil, Southeast Algeria.}, journal = {Genome announcements}, volume = {3}, number = {6}, pages = {}, pmid = {26679578}, issn = {2169-8287}, abstract = {Geobacillus spp. are potential sources of novel enzymes, such as those involved in the degradation of recalcitrant polymers. Here, we report a Geobacillus genome that may help reveal genomic differences between this strain and publicly available representatives of the same genus from diverse niches.}, }
@article {pmid26678139, year = {2016}, author = {Stoops, J and Crauwels, S and Waud, M and Claes, J and Lievens, B and Van Campenhout, L}, title = {Microbial community assessment of mealworm larvae (Tenebrio molitor) and grasshoppers (Locusta migratoria migratorioides) sold for human consumption.}, journal = {Food microbiology}, volume = {53}, number = {Pt B}, pages = {122-127}, doi = {10.1016/j.fm.2015.09.010}, pmid = {26678139}, issn = {1095-9998}, mesh = {Animals ; Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Biodiversity ; Consumer Product Safety ; Food Safety ; Fungi/classification/genetics/growth &amp; development/*isolation &amp; purification ; Humans ; Larva/*microbiology ; Locusta migratoria/*microbiology ; Tenebrio/*microbiology ; }, abstract = {In Western countries, the popularity of edible insects as an alternative animal protein source is increasing. Nevertheless, there is a lack of profound insight into the microbial safety and shelf life of living insects sold for human consumption. The purpose of this study was to characterise the microflora of fresh edible mealworm larvae and grasshoppers in a quantitative and qualitative way. Therefore, culture-dependent analyses (the total viable aerobic count, Enterobacteriaceae, lactic acid bacteria, yeasts and moulds, and bacterial endospores) and next-generation sequencing (454amplicon pyrosequencing) were performed. High microbial counts were obtained for both insect species. Different insect batches resulted in quite similar microbial numbers, except for bacterial endospores. However, the bacterial community composition differed between both insect species. The most abundant operational taxonomic unit in mealworm larvae was Propionibacterium. Also members of the genera Haemophilus, Staphylococcus and Clostridium were found. Grasshoppers were mainly dominated by Weissella, Lactococcus and Yersinia/Rahnella. Overall, a variety of potential spoilage bacteria and food pathogens were characterised. The results of this study suggest that a processing step with a microbiocidal effect is required to avoid or minimize risks involved with the consumption of edible insects.}, }
@article {pmid26677860, year = {2016}, author = {Figueroa, D and Rowe, OF and Paczkowska, J and Legrand, C and Andersson, A}, title = {Allochthonous Carbon--a Major Driver of Bacterioplankton Production in the Subarctic Northern Baltic Sea.}, journal = {Microbial ecology}, volume = {71}, number = {4}, pages = {789-801}, pmid = {26677860}, issn = {1432-184X}, mesh = {Bacteria/*growth &amp; development/*metabolism ; Carbon/chemistry/*metabolism ; North Sea ; Plankton/*growth &amp; development/*metabolism ; Seawater ; Sweden ; }, abstract = {Heterotrophic bacteria are, in many aquatic systems, reliant on autochthonous organic carbon as their energy source. One exception is low-productive humic lakes, where allochthonous dissolved organic matter (ADOM) is the major driver. We hypothesized that bacterial production (BP) is similarly regulated in subarctic estuaries that receive large amounts of riverine material. BP and potential explanatory factors were measured during May-August 2011 in the subarctic Råne Estuary, northern Sweden. The highest BP was observed in spring, concomitant with the spring river-flush and the lowest rates occurred during summer when primary production (PP) peaked. PLS correlations showed that ∼60% of the BP variation was explained by different ADOM components, measured as humic substances, dissolved organic carbon (DOC) and coloured dissolved organic matter (CDOM). On average, BP was threefold higher than PP. The bioavailability of allochthonous dissolved organic carbon (ADOC) exhibited large spatial and temporal variation; however, the average value was low, ∼2%. Bioassay analysis showed that BP in the near-shore area was potentially carbon limited early in the season, while BP at seaward stations was more commonly limited by nitrogen-phosphorus. Nevertheless, the bioassay indicated that ADOC could contribute significantly to the in situ BP, ∼60%. We conclude that ADOM is a regulator of BP in the studied estuary. Thus, projected climate-induced increases in river discharge suggest that BP will increase in subarctic coastal areas during the coming century.}, }
@article {pmid26677166, year = {2016}, author = {Bañares-España, E and del Mar Fernández-Arjona, M and García-Sánchez, MJ and Hernández-López, M and Reul, A and Mariné, MH and Flores-Moya, A}, title = {Sulphide Resistance in the Cyanobacterium Microcystis aeruginosa: a Comparative Study of Morphology and Photosynthetic Performance Between the Sulphide-Resistant Mutant and the Wild-Type Strain.}, journal = {Microbial ecology}, volume = {71}, number = {4}, pages = {860-872}, pmid = {26677166}, issn = {1432-184X}, mesh = {Carotenoids/analysis/metabolism ; Chlorophyll/metabolism ; Fresh Water/microbiology ; Microcystis/*drug effects/genetics/*metabolism/ultrastructure ; Microscopy, Electron, Transmission ; *Mutation ; Oxygen/metabolism ; Photosynthesis ; Photosystem II Protein Complex/metabolism ; Phycocyanin/analysis ; Phycoerythrin/analysis ; Spain ; Sulfides/*pharmacology ; }, abstract = {The cyanobacterium Microcystis aeruginosa is a mesophilic freshwater organism, which cannot tolerate sulphide. However, it was possible to isolate a sulphide-resistant (S(r)) mutant strain that was able to survive in a normally lethal medium sulphide. In order to evaluate the cost of the mutation conferring sulphide resistance in the S(r) strain of M. aeruginosa, the morphology and the photosynthetic performance were compared to that found in the wild-type, sulphide-sensitive (S(s)) strain. An increase in size and a disrupted morphology was observed in S(r) cells in comparison to the S(s) counterpart. Phycoerythrin and phycocyanin levels were higher in the S(r) than in the S(s) cells, whereas a higher carotenoid content, per unit volume, was found in the S(s) strain. The irradiance-saturated photosynthetic oxygen-production rate (GPR max) and the photosynthetic efficiency (measured both by oxygen production and fluorescence, α(GPR) and α(ETR)) were lower in the S(r) strain than in the wild-type. These results appear to be the result of package effect. On the other hand, the S(r) strain showed higher quantum yield of non-photochemical quenching, especially those regulated mechanisms (estimated throughout qN and Y(NPQ)) and a significantly lower slope in the maximum quantum yield of light-adapted samples (Fv'/Fm') compared to the S(s) strain. These findings point to a change in the regulation of the quenching of the transition states (qT) in the S(r) strain which may be generated by a change in the distribution of thylakoidal membranes, which somehow could protect metalloenzymes of the electron transport chain from the lethal effect of sulphide.}, }
@article {pmid26677108, year = {2016}, author = {Bordron, P and Latorre, M and Cortés, MP and González, M and Thiele, S and Siegel, A and Maass, A and Eveillard, D}, title = {Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach.}, journal = {MicrobiologyOpen}, volume = {5}, number = {1}, pages = {106-117}, pmid = {26677108}, issn = {2045-8827}, mesh = {Acidiphilium/*genetics/metabolism ; Acidithiobacillus/*genetics/metabolism ; Clostridiales/*genetics/metabolism ; Copper/*metabolism ; DNA, Bacterial/genetics ; Ecosystem ; Genome, Bacterial/*genetics ; Metabolic Networks and Pathways/*genetics ; Metagenomics ; }, abstract = {Following the trend of studies that investigate microbial ecosystems using different metagenomic techniques, we propose a new integrative systems ecology approach that aims to decipher functional roles within a consortium through the integration of genomic and metabolic knowledge at genome scale. For the sake of application, using public genomes of five bacterial strains involved in copper bioleaching: Acidiphilium cryptum, Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans, we first reconstructed a global metabolic network. Next, using a parsimony assumption, we deciphered sets of genes, called Sets from Genome Segments (SGS), that (1) are close on their respective genomes, (2) take an active part in metabolic pathways and (3) whose associated metabolic reactions are also closely connected within metabolic networks. Overall, this SGS paradigm depicts genomic functional units that emphasize respective roles of bacterial strains to catalyze metabolic pathways and environmental processes. Our analysis suggested that only few functional metabolic genes are horizontally transferred within the consortium and that no single bacterial strain can accomplish by itself the whole copper bioleaching. The use of SGS pinpoints a functional compartmentalization among the investigated species and exhibits putative bacterial interactions necessary for promoting these pathways.}, }
@article {pmid26670292, year = {2015}, author = {Juste-Poinapen, NM and Turner, MS and Rabaey, K and Virdis, B and Batstone, DJ}, title = {Evaluating the potential impact of proton carriers on syntrophic propionate oxidation.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {18364}, pmid = {26670292}, issn = {2045-2322}, mesh = {Bacteria/*metabolism ; Oxidation-Reduction ; Propionates/*metabolism ; Proton-Motive Force/*drug effects ; *Protons ; }, abstract = {Anaerobic propionic acid degradation relies on interspecies electron transfer (IET) between propionate oxidisers and electron acceptor microorganisms, via either molecular hydrogen, formate or direct transfers. We evaluated the possibility of stimulating direct IET, hence enhancing propionate oxidation, by increasing availability of proton carriers to decrease solution resistance and reduce pH gradients. Phosphate was used as a proton carrying anion, and chloride as control ion together with potassium as counter ion. Propionic acid consumption in anaerobic granules was assessed in a square factorial design with ratios (1:0, 2:1, 1:1, 1:2 and 0:1) of total phosphate (TP) to Cl(-), at 1X, 10X, and 30X native conductivity (1.5 mS.cm(-1)). Maximum specific uptake rate, half saturation, and time delay were estimated using model-based analysis. Community profiles were analysed by fluorescent in situ hybridisation and 16S rRNA gene pyrosequencing. The strongest performance was at balanced (1:1) ratios at 10X conductivity where presumptive propionate oxidisers namely Syntrophobacter and Candidatus Cloacamonas were more abundant. There was a shift from Methanobacteriales at high phosphate, to Methanosaeta at low TP:Cl ratios and low conductivity. A lack of response to TP, and low percentage of presumptive electroactive organisms suggested that DIET was not favoured under the current experimental conditions.}, }
@article {pmid26664811, year = {2015}, author = {Westcott, SL and Schloss, PD}, title = {De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units.}, journal = {PeerJ}, volume = {3}, number = {}, pages = {e1487}, pmid = {26664811}, issn = {2167-8359}, support = {P30 DK034933/DK/NIDDK NIH HHS/United States ; R01 GM099514/GM/NIGMS NIH HHS/United States ; }, abstract = {Background. 16S rRNA gene sequences are routinely assigned to operational taxonomic units (OTUs) that are then used to analyze complex microbial communities. A number of methods have been employed to carry out the assignment of 16S rRNA gene sequences to OTUs leading to confusion over which method is optimal. A recent study suggested that a clustering method should be selected based on its ability to generate stable OTU assignments that do not change as additional sequences are added to the dataset. In contrast, we contend that the quality of the OTU assignments, the ability of the method to properly represent the distances between the sequences, is more important. Methods. Our analysis implemented six de novo clustering algorithms including the single linkage, complete linkage, average linkage, abundance-based greedy clustering, distance-based greedy clustering, and Swarm and the open and closed-reference methods. Using two previously published datasets we used the Matthew's Correlation Coefficient (MCC) to assess the stability and quality of OTU assignments. Results. The stability of OTU assignments did not reflect the quality of the assignments. Depending on the dataset being analyzed, the average linkage and the distance and abundance-based greedy clustering methods generated OTUs that were more likely to represent the actual distances between sequences than the open and closed-reference methods. We also demonstrated that for the greedy algorithms VSEARCH produced assignments that were comparable to those produced by USEARCH making VSEARCH a viable free and open source alternative to USEARCH. Further interrogation of the reference-based methods indicated that when USEARCH or VSEARCH were used to identify the closest reference, the OTU assignments were sensitive to the order of the reference sequences because the reference sequences can be identical over the region being considered. More troubling was the observation that while both USEARCH and VSEARCH have a high level of sensitivity to detect reference sequences, the specificity of those matches was poor relative to the true best match. Discussion. Our analysis calls into question the quality and stability of OTU assignments generated by the open and closed-reference methods as implemented in current version of QIIME. This study demonstrates that de novo methods are the optimal method of assigning sequences into OTUs and that the quality of these assignments needs to be assessed for multiple methods to identify the optimal clustering method for a particular dataset.}, }
@article {pmid26662659, year = {2016}, author = {Anderson, OR and Lee, JM and McGuire, K}, title = {Experimental Evidence that Fungi are Dominant Microbes in Carbon Content and Growth Response to Added Soluble Organic Carbon in Moss-rich Tundra Soil.}, journal = {The Journal of eukaryotic microbiology}, volume = {63}, number = {3}, pages = {363-366}, doi = {10.1111/jeu.12286}, pmid = {26662659}, issn = {1550-7408}, mesh = {Archaea/metabolism ; Bacteria/metabolism ; Biomass ; Carbon/*metabolism ; Ecosystem ; Eukaryota/metabolism ; Fungi/classification/genetics/*growth &amp; development/*isolation &amp; purification ; Global Warming ; Glucose/metabolism ; *Soil Microbiology ; Sphagnopsida ; *Tundra ; }, abstract = {Global warming significantly affects Arctic tundra, including permafrost thaw and soluble C release that may differentially affect tundra microbial growth. Using laboratory experiments, we report some of the first evidence for the effects of soluble glucose-C enrichment on tundra soil prokaryotes (bacteria and archaea) and fungi, with comparisons to microbial eukaryotes. Fungal increase in C-biomass was equivalent to 10% (w/w) of the added glucose-C, and for prokaryote biomass 2% (w/w), the latter comparable to prior published results. The C-gain after 14 d was 1.3 mg/g soil for fungi, and ~200 μg/g for prokaryotes.}, }
@article {pmid26662044, year = {2016}, author = {Reilly, C and Goettl, M and Steinmetz, M and Nikrad, J and Jones, RS}, title = {Short-term effects of povidone iodine and sodium fluoride therapy on plaque levels and microbiome diversity.}, journal = {Oral diseases}, volume = {22}, number = {2}, pages = {155-161}, doi = {10.1111/odi.12407}, pmid = {26662044}, issn = {1601-0825}, support = {UL1TR000114/TR/NCATS NIH HHS/United States ; }, mesh = {Anti-Infective Agents, Local/*therapeutic use ; Biofilms/*drug effects ; Cariostatic Agents ; Child ; Dental Plaque/*microbiology/prevention &amp; control ; Dental Plaque Index ; Drug Combinations ; Humans ; Microbiota/*drug effects ; Povidone-Iodine/*therapeutic use ; Sodium Fluoride/*therapeutic use ; }, abstract = {OBJECTIVES: The objective of this study is to evaluate the effect of short-term changes in the oral microbial ecology of dental plaque and plaque levels after topical treatment of a combination of 10% povidone iodine (PI) and 5% sodium fluoride varnish (FV).<br><br>MATERIALS AND METHODS: A single group design intervention study on 12 pediatric patients, who underwent two baseline plaques samplings before the intervention, were enrolled in the study. A modified mixed dentition Silness-L&#xf6;e plaque index score was used to assess plaque accumulation and microbial composition was assessed by amplicon sequencing analysis of the 16S rRNA V4 region.<br><br>RESULTS: Dental plaque accumulation (P = 0.0424) was reduced after 1 week using PI/FV application. This reduction was not observed between the two double-baseline visits. 16S rRNA analysis showed that the single PI/FV therapy did not have dramatic shifts in the plaque microbiome community depicted by hierarchical cluster and principle component analysis. More subtle changes were found when analyzing the Shannon diversity index after the application of PI/FV vs two baselines prior to combination therapy.<br><br>CONCLUSIONS: The bacteria within the dental biofilms showed resilience in maintaining the overall community diversity but reduced biofilm accumulation following PI/FV therapy. Repeated uses of PI/FV may augment plaque control during dental rehabilitation in children.}, }
@article {pmid26661994, year = {2016}, author = {Cotta, SR and Cavalcante Franco Dias, A and Seldin, L and Andreote, FD and van Elsas, JD}, title = {The diversity and abundance of phytase genes (β-propeller phytases) in bacterial communities of the maize rhizosphere.}, journal = {Letters in applied microbiology}, volume = {62}, number = {3}, pages = {264-268}, doi = {10.1111/lam.12535}, pmid = {26661994}, issn = {1472-765X}, mesh = {6-Phytase/*genetics ; Alteromonadaceae/enzymology/*genetics ; Brazil ; Caulobacter/enzymology/*genetics ; Molecular Sequence Data ; Phosphorus/metabolism ; Phylogeny ; Phytic Acid/metabolism ; Pseudomonas/enzymology/*genetics ; *Rhizosphere ; Soil/chemistry ; Soil Microbiology ; Zea mays/*microbiology ; }, abstract = {UNLABELLED: The ecology of microbial communities associated with organic phosphorus (P) mineralization in soils is still understudied. Here, we assessed the abundance and diversity of bacteria harbouring genes encoding β-propeller phytases (BPP) in the rhizosphere of traditional and transgenic maize cultivated in two Brazilian soils. We found a soil-dependent effect towards a higher abundance of phytase genes in the rhizosphere, and an absence of any impact of plant genotype. Phylogenetic analyses indicated members of the genera Pseudomonas, Caulobacter, Idiomarina and Maricaulis, close to 'uncultured bacteria', to constitute the dominant bacteria hosting this gene. The results obtained validate a methodology to target bacteria that are involved in the organic P cycle, and depict the responsiveness of such bacteria to the rhizosphere, albeit in dependency of the soil in which maize is cultivated. The data also identified the major bacterial groups that are associated with the organic P mineralization function.<br><br>Micro-organisms play a key role in nutrient balance in soil ecosystems that are essential to life on the planet. However, some processes such as organic phosphorus mineralization, an important source of phosphorus supply in soil, is poorly studied mainly due the absence of an efficient methodology to assess the phytase-producing micro-organisms. In this study, a method to assess beta-propeller phytase (BPP)-carrying bacteria in soil was validated. This method may contribute to the knowledge of how these micro-organisms behave in the environment and contribute for plant growth promotion.}, }
@article {pmid26661140, year = {2016}, author = {Borschinger, B and Bartoli, C and Chandeysson, C and Guilbaud, C and Parisi, L and Bourgeay, JF and Buisson, E and Morris, CE}, title = {A set of PCRs for rapid identification and characterization of Pseudomonas syringae phylogroups.}, journal = {Journal of applied microbiology}, volume = {120}, number = {3}, pages = {714-723}, doi = {10.1111/jam.13017}, pmid = {26661140}, issn = {1365-2672}, mesh = {Actinidia/microbiology ; DNA Primers/genetics ; Ecosystem ; France ; *Phylogeny ; Plant Diseases/microbiology ; Polymerase Chain Reaction/*methods ; Prunus armeniaca/microbiology ; Pseudomonas syringae/*classification/genetics/*isolation &amp; purification ; }, abstract = {AIMS: The aim of this study was to develop a rapid PCR-based method for the specific detection of individual phylogroups of the Pseudomonas syringae complex.<br><br>METHODS AND RESULTS: Seven primer pairs were developed by analysing whole genomes of 54 Ps.&#xa0;syringae strains. The specificity and sensitivity of these primer pairs were assessed on 236 strains from a large and comprehensive Ps.&#xa0;syringae collection. The method was also validated by characterizing the phylogenetic diversity of 174 putative Ps.&#xa0;syringae isolates from kiwifruit and apricot orchards of southeastern France.<br><br>CONCLUSION: Our PCR-based method allows for the detection and characterization of nine of the 13 Ps.&#xa0;syringae phylogroups (phylogroups 1, 2, 3, 4, 7, 8, 9, 10 and 13).<br><br>To date, phylogenetic affiliation within the Ps.&#xa0;syringae complex was only possible by sequencing housekeeping genes. Here, we propose a rapid PCR-based method for the detection of specific phylogroups of the Ps.&#xa0;syringae complex. Furthermore, for the first time we reveal the presence of Ps.&#xa0;syringae strains belonging to phylogroups 10 and 13 as epiphytes on plants, whereas they had previously only been observed in aquatic habitats.}, }
@article {pmid26660315, year = {2016}, author = {Baltz, RH and Ikeda, H and Katz, L and Kim, ES and van Wezel, GP and Wright, G}, title = {Introduction to the Special Issue: "Natural Product Discovery and Development in the Genomic Era".}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {43}, number = {2-3}, pages = {109}, doi = {10.1007/s10295-015-1715-5}, pmid = {26660315}, issn = {1476-5535}, mesh = {*Biological Products ; *Drug Discovery ; *Genomics ; Humans ; Ivermectin/analogs &amp; derivatives ; Nobel Prize ; Onchocerciasis, Ocular/drug therapy ; }, }
@article {pmid26659563, year = {2016}, author = {Nagy, LG and Riley, R and Tritt, A and Adam, C and Daum, C and Floudas, D and Sun, H and Yadav, JS and Pangilinan, J and Larsson, KH and Matsuura, K and Barry, K and Labutti, K and Kuo, R and Ohm, RA and Bhattacharya, SS and Shirouzu, T and Yoshinaga, Y and Martin, FM and Grigoriev, IV and Hibbett, DS}, title = {Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities.}, journal = {Molecular biology and evolution}, volume = {33}, number = {4}, pages = {959-970}, doi = {10.1093/molbev/msv337}, pmid = {26659563}, issn = {1537-1719}, mesh = {Agaricales/*genetics ; Basidiomycota/genetics ; Evolution, Molecular ; Genome, Fungal ; *Genomics ; Lignin/*genetics ; Molecular Sequence Annotation ; Peroxidases/genetics ; Phylogeny ; }, abstract = {Evolution of lignocellulose decomposition was one of the most ecologically important innovations in fungi. White-rot fungi in the Agaricomycetes (mushrooms and relatives) are the most effective microorganisms in degrading both cellulose and lignin components of woody plant cell walls (PCW). However, the precise evolutionary origins of lignocellulose decomposition are poorly understood, largely because certain early-diverging clades of Agaricomycetes and its sister group, the Dacrymycetes, have yet to be sampled, or have been undersampled, in comparative genomic studies. Here, we present new genome sequences of ten saprotrophic fungi, including members of the Dacrymycetes and early-diverging clades of Agaricomycetes (Cantharellales, Sebacinales, Auriculariales, and Trechisporales), which we use to refine the origins and evolutionary history of the enzymatic toolkit of lignocellulose decomposition. We reconstructed the origin of ligninolytic enzymes, focusing on class II peroxidases (AA2), as well as enzymes that attack crystalline cellulose. Despite previous reports of white rot appearing as early as the Dacrymycetes, our results suggest that white-rot fungi evolved later in the Agaricomycetes, with the first class II peroxidases reconstructed in the ancestor of the Auriculariales and residual Agaricomycetes. The exemplars of the most ancient clades of Agaricomycetes that we sampled all lack class II peroxidases, and are thus concluded to use a combination of plesiomorphic and derived PCW degrading enzymes that predate the evolution of white rot.}, }
@article {pmid26658023, year = {2015}, author = {Fragoso Ados Santos, H and Duarte, GA and Rachid, CT and Chaloub, RM and Calderon, EN and Marangoni, LF and Bianchini, A and Nudi, AH and do Carmo, FL and van Elsas, JD and Rosado, AS and Castro, CB and Peixoto, RS}, title = {Impact of oil spills on coral reefs can be reduced by bioremediation using probiotic microbiota.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {18268}, pmid = {26658023}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics/metabolism ; *Biodegradation, Environmental ; *Biotransformation ; *Coral Reefs ; Hydrocarbons/metabolism ; *Microbiota ; *Petroleum Pollution ; Photochemical Processes ; *Probiotics ; Water Pollutants, Chemical ; }, abstract = {Several anthropogenic factors, including contamination by oil spills, constitute a threat to coral reef health. Current methodologies to remediate polluted marine environments are based on the use of chemical dispersants; however, these can be toxic to the coral holobiont. In this study, a probiotic bacterial consortium was produced from the coral Mussismilia harttii and was trained to degrade water-soluble oil fractions (WSFs). Additionally, we assessed the effect of WSFs on the health of M. harttii in tanks and evaluated the bacterial consortium as a bioremediation agent. The consortium was responsible for the highly efficient degradation of petroleum hydrocarbons, and it minimised the effects of WSFs on coral health, as indicated by raised photosynthetic efficiencies. Moreover, the impact of WSFs on the coral microbiome was diminished by the introduced bacterial consortium. Following introduction, the bacterial consortium thus had a dual function, i.e promoting oil WSF degradation and improving coral health with its probiotic features.}, }
@article {pmid26657897, year = {2016}, author = {Ramanan, R and Kim, BH and Cho, DH and Oh, HM and Kim, HS}, title = {Algae-bacteria interactions: Evolution, ecology and emerging applications.}, journal = {Biotechnology advances}, volume = {34}, number = {1}, pages = {14-29}, doi = {10.1016/j.biotechadv.2015.12.003}, pmid = {26657897}, issn = {1873-1899}, mesh = {Animals ; Anthozoa/microbiology ; Aquaculture ; *Bacterial Physiological Phenomena ; Biodegradation, Environmental ; *Biological Evolution ; Biotechnology/methods ; Ecosystem ; Host-Parasite Interactions ; Lichens/microbiology ; *Microalgae/microbiology ; Phaeophyceae/microbiology ; Phytoplankton/microbiology ; Symbiosis ; }, abstract = {Algae and bacteria have coexisted ever since the early stages of evolution. This coevolution has revolutionized life on earth in many aspects. Algae and bacteria together influence ecosystems as varied as deep seas to lichens and represent all conceivable modes of interactions - from mutualism to parasitism. Several studies have shown that algae and bacteria synergistically affect each other's physiology and metabolism, a classic case being algae-roseobacter interaction. These interactions are ubiquitous and define the primary productivity in most ecosystems. In recent years, algae have received much attention for industrial exploitation but their interaction with bacteria is often considered a contamination during commercialization. A few recent studies have shown that bacteria not only enhance algal growth but also help in flocculation, both essential processes in algal biotechnology. Hence, there is a need to understand these interactions from an evolutionary and ecological standpoint, and integrate this understanding for industrial use. Here we reflect on the diversity of such relationships and their associated mechanisms, as well as the habitats that they mutually influence. This review also outlines the role of these interactions in key evolutionary events such as endosymbiosis, besides their ecological role in biogeochemical cycles. Finally, we focus on extending such studies on algal-bacterial interactions to various environmental and bio-technological applications.}, }
@article {pmid26656884, year = {2016}, author = {Eevers, N and Beckers, B and Op de Beeck, M and White, JC and Vangronsveld, J and Weyens, N}, title = {Comparison between cultivated and total bacterial communities associated with Cucurbita pepo using cultivation-dependent techniques and 454 pyrosequencing.}, journal = {Systematic and applied microbiology}, volume = {39}, number = {1}, pages = {58-66}, doi = {10.1016/j.syapm.2015.11.001}, pmid = {26656884}, issn = {1618-0984}, mesh = {Bacillus/genetics/*growth &amp; development/isolation &amp; purification ; Biodiversity ; Cucurbita/*microbiology ; DNA, Bacterial/genetics ; Endophytes/genetics/*growth &amp; development/isolation &amp; purification ; Enterobacter/genetics/*growth &amp; development/isolation &amp; purification ; Molecular Typing ; Plant Roots/*microbiology ; Plant Shoots/*microbiology ; Pseudomonas/genetics/*growth &amp; development/isolation &amp; purification ; RNA, Ribosomal, 16S ; Rhizobium/genetics/*growth &amp; development/isolation &amp; purification ; }, abstract = {Endophytic bacteria often have beneficial effects on their host plants that can be exploited for bioremediation applications but, according to the literature, only 0.001-1% of all endophytic microbes should be cultivable. This study compared the cultivated endophytic communities of the roots and shoots of Cucurbita pepo with the total endophytic communities as determined by cultivation-dependent techniques and 454 pyrosequencing. The ten most abundant taxa of the total communities aligned well with the cultivated taxa; however, the abundance of these taxa in the two communities differed greatly. Enterobacter showed very low presence in the total communities, whereas they were dominantly present in the cultivated communities. Although Rhizobium dominated in total root and shoot communities, it was poorly cultivable and even then only in growth media containing plant extract. Since endophytes likely contribute to plant-growth promotion, cultivated bacterial strains were tested for their plant-growth promoting capabilities, and the results were correlated with their abundance in the total community. Bacillus and Pseudomonas showed promising results when considering cultivability, abundance in the total community and plant-growth promoting capability. This study demonstrated that, although a limited number of bacterial genera were cultivable, current cultivation-dependent techniques may be sufficient for further isolation and inoculation experiments that aim to improve phytoremediation efficiency.}, }
@article {pmid26656131, year = {2015}, author = {Gunawardana, M and Hyde, ER and Lahmeyer, S and Dorsey, BL and La Val, TP and Mullen, M and Yoo, J and Knight, R and Baum, MM}, title = {Euphorbia plant latex is inhabited by diverse microbial communities.}, journal = {American journal of botany}, volume = {102}, number = {12}, pages = {1966-1977}, doi = {10.3732/ajb.1500223}, pmid = {26656131}, issn = {1537-2197}, mesh = {Bacteria/genetics ; *Bacterial Physiological Phenomena ; DNA, Ribosomal Spacer/genetics ; Endophytes/genetics/*physiology ; Euphorbia/*metabolism/*microbiology ; Fungi/genetics/*physiology ; Latex/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {PREMISE OF THE STUDY: The antimicrobial properties and toxicity of Euphorbia plant latex should make it a hostile environment to microbes. However, when specimens from Euphorbia spp. were propagated in tissue culture, microbial growth was observed routinely, raising the question whether the latex of this diverse plant genus can be a niche for polymicrobial communities.<br><br>METHODS: Latex from a phylogenetically diverse set of Euphorbia species was collected and genomic microbial DNA extracted. Deep sequencing of bar-coded amplicons from taxonomically informative gene fragments was used to measure bacterial and fungal species richness, evenness, and composition.<br><br>KEY RESULTS: Euphorbia latex was found to contain unexpectedly complex bacterial (mean: 44.0 species per sample; 9 plants analyzed) and fungal (mean: 20.9 species per sample; 22 plants analyzed) communities using culture-independent methods. Many of the identified taxa are known plant endophytes, but have not been previously found in latex.<br><br>CONCLUSIONS: Our results suggest that Euphorbia plant latex, a putatively hostile antimicrobial environment, unexpectedly supports diverse bacterial and fungal communities. The ecological roles of these microorganisms and potential interactions with their host plants are unknown and warrant further research.}, }
@article {pmid26655353, year = {2015}, author = {Marion, ZH and Fordyce, JA and Fitzpatrick, BM}, title = {Extending the Concept of Diversity Partitioning to Characterize Phenotypic Complexity.}, journal = {The American naturalist}, volume = {186}, number = {3}, pages = {348-361}, doi = {10.1086/682369}, pmid = {26655353}, issn = {1537-5323}, mesh = {*Biodiversity ; Ecology/*methods ; Genotype ; Models, Biological ; *Phenotype ; }, abstract = {Most components of an organism's phenotype can be viewed as the expression of multiple traits. Many of these traits operate as complexes, where multiple subsidiary parts function and evolve together. As trait complexity increases, so does the challenge of describing complexity in intuitive, biologically meaningful ways. Traditional multivariate analyses ignore the phenomenon of individual complexity and provide relatively abstract representations of variation among individuals. We suggest adopting well-known diversity indices from community ecology to describe phenotypic complexity as the diversity of distinct subsidiary components of a trait. Using a hierarchical framework, we illustrate how total trait diversity can be partitioned into within-individual complexity (α diversity) and between-individual components (β diversity). This approach complements traditional multivariate analyses. The key innovations are (i) addition of individual complexity within the same framework as between-individual variation and (ii) a group-wise partitioning approach that complements traditional level-wise partitioning of diversity. The complexity-as-diversity approach has potential application in many fields, including physiological ecology, ecological and community genomics, and transcriptomics. We demonstrate the utility of this complexity-as-diversity approach with examples from chemical and microbial ecology. The examples illustrate biologically significant differences in complexity and diversity that standard analyses would not reveal.}, }
@article {pmid26655233, year = {2016}, author = {Ma, B and Lv, X and He, Y and Xu, J}, title = {Assessing adsorption of polycyclic aromatic hydrocarbons on Rhizopus oryzae cell wall components with water-methanol cosolvent model.}, journal = {Ecotoxicology and environmental safety}, volume = {125}, number = {}, pages = {55-60}, doi = {10.1016/j.ecoenv.2015.11.032}, pmid = {26655233}, issn = {1090-2414}, mesh = {Adsorption ; Biodegradation, Environmental ; Cell Wall/*metabolism ; Methanol/*chemistry ; *Models, Biological ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Polysaccharides/chemistry/metabolism ; *Rhizopus/cytology/metabolism ; Solvents/*chemistry ; Water/*chemistry ; Water Pollutants, Chemical/*analysis ; }, abstract = {The contribution of different fungal cell wall components in adsorption of polycyclic aromatic hydrocarbons (PAHs) is still unclear. We isolated Rhizopus oryzae cell walls components with sequential extraction, characterized functional groups with NEXAFS spectra, and determined partition coefficients of PAHs on cell walls and cell wall components with cosolvent model. Spectra of NEXAFS indicated that isolated cell walls components were featured with peaks at ~532.7 and ~534.5eV energy. The lipid cosolvent partition coefficients were approximately one order of magnitude higher than the corresponding carbohydrate cosolvent partition coefficients. The partition coefficients for four tested carbohydrates varied at approximate 0.5 logarithmic units. Partition coefficients between biosorbents and water calculated based cosolvent models ranged from 0.8 to 4.2. The present study proved the importance of fungal cell wall components in adsorption of PAHs, and consequently the role of fungi in PAHs bioremediation.}, }
@article {pmid26652666, year = {2015}, author = {Watson, MG and Scardino, AJ and Zalizniak, L and Shimeta, J}, title = {Colonisation and succession of marine biofilm-dwelling ciliate assemblages on biocidal antifouling and fouling-release coatings in temperate Australia.}, journal = {Biofouling}, volume = {31}, number = {9-10}, pages = {709-720}, doi = {10.1080/08927014.2015.1105221}, pmid = {26652666}, issn = {1029-2454}, mesh = {Australia ; Biofilms/*drug effects ; Biofouling/*prevention &amp; control ; *Ciliophora/drug effects/growth &amp; development ; *Diatoms/drug effects/growth &amp; development ; Disinfectants/chemistry/*pharmacology ; *Paint ; }, abstract = {Ciliate assemblages are often overlooked, but ubiquitous components of microbial biofilms which require a better understanding. Ciliate, diatom and bacterial colonisation were evaluated on two fouling-release (FR) coatings, viz. Intersleek 970 and Hempasil X3, and two biocidal antifouling (AF) coatings, viz. Intersmooth 360 and Interspeed 5640, in Port Phillip Bay, Australia. A total of 15 genera were identified during the 10 week deployment. Intersleek 970 displayed the most rapid fouling by ciliates, reaching 63.3(± 5.9) cells cm(-2). After 10 weeks, all four coatings were extensively fouled. However, the toxicity of the AF coatings still significantly inhibited microbial fouling compared to the FR coatings. On all treatments, colonies of sessile peritrichs dominated the ciliate assemblage in the early stage of succession, but as the biofilm matured, vagile ciliates exerted more influence on the assemblage structure. The AF coatings showed selective toxic effects, causing significant differences in the ciliate species assemblages among the treatments.}, }
@article {pmid26651514, year = {2015}, author = {Navarro, E and Fabrègue, O and Scorretti, R and Reboulet, J and Simonet, P and Dawson, L and Demanèche, S}, title = {RisaAligner software for aligning fluorescence data between Agilent 2100 Bioanalyzer chips: Application to soil microbial community analysis.}, journal = {BioTechniques}, volume = {59}, number = {6}, pages = {347, 349-52, 354-6 passim}, doi = {10.2144/000114363}, pmid = {26651514}, issn = {1940-9818}, mesh = {Algorithms ; DNA Fingerprinting/*methods ; DNA, Intergenic/*chemistry ; Nonlinear Dynamics ; Principal Component Analysis ; *Software ; *Soil Microbiology ; }, abstract = {Ribosomal Intergenic Spacer Analysis (RISA) is a high-resolution and highly reproducible fingerprinting technique for discriminating between microbial communities. The community profiles can be visualized using the Agilent 2100 Bioanalyzer. Comparison between fingerprints relies upon precise estimation of all amplified DNA fragment lengths; however, size standard computation can vary between gel runs. For complex samples such as soil microbial communities, discrimination by fragment size is not always sufficient. In such cases, the comparison of whole fluorescence data as a function of time (electrophoregrams) is more appropriate. When electrophoregrams [fluorescence = f (time)] are used, and more than one chip is involved, electrophoregram comparisons are challenging due to experimental variations between chips and the lack of correction by the Agilent software in such situations. Here we present RisaAligner software for analyzing and comparing electrophoregrams from Agilent chips using a nonlinear ladder-alignment algorithm. We demonstrate the robustness and substantial improvement of data analysis by analyzing soil microbial profiles obtained with Agilent DNA 1000 and High Sensitivity chips.}, }
@article {pmid26648929, year = {2015}, author = {Våge, S and Thingstad, TF}, title = {Fractal Hypothesis of the Pelagic Microbial Ecosystem-Can Simple Ecological Principles Lead to Self-Similar Complexity in the Pelagic Microbial Food Web?.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1357}, pmid = {26648929}, issn = {1664-302X}, abstract = {Trophic interactions are highly complex and modern sequencing techniques reveal enormous biodiversity across multiple scales in marine microbial communities. Within the chemically and physically relatively homogeneous pelagic environment, this calls for an explanation beyond spatial and temporal heterogeneity. Based on observations of simple parasite-host and predator-prey interactions occurring at different trophic levels and levels of phylogenetic resolution, we present a theoretical perspective on this enormous biodiversity, discussing in particular self-similar aspects of pelagic microbial food web organization. Fractal methods have been used to describe a variety of natural phenomena, with studies of habitat structures being an application in ecology. In contrast to mathematical fractals where pattern generating rules are readily known, however, identifying mechanisms that lead to natural fractals is not straight-forward. Here we put forward the hypothesis that trophic interactions between pelagic microbes may be organized in a fractal-like manner, with the emergent network resembling the structure of the Sierpinski triangle. We discuss a mechanism that could be underlying the formation of repeated patterns at different trophic levels and discuss how this may help understand characteristic biomass size-spectra that hint at scale-invariant properties of the pelagic environment. If the idea of simple underlying principles leading to a fractal-like organization of the pelagic food web could be formalized, this would extend an ecologists mindset on how biological complexity could be accounted for. It may furthermore benefit ecosystem modeling by facilitating adequate model resolution across multiple scales.}, }
@article {pmid26648926, year = {2015}, author = {Sterngren, AE and Hallin, S and Bengtson, P}, title = {Archaeal Ammonia Oxidizers Dominate in Numbers, but Bacteria Drive Gross Nitrification in N-amended Grassland Soil.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1350}, pmid = {26648926}, issn = {1664-302X}, abstract = {Both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play an important role in nitrification in terrestrial environments. Most often AOA outnumber AOB, but the relative contribution of AOA and AOB to nitrification rates remains unclear. The aim of this experiment was to test the hypotheses that high nitrogen availability would favor AOB and result in high gross nitrification rates, while high carbon availability would result in low nitrogen concentrations that favor the activity of AOA. The hypotheses were tested in a microcosm experiment where sugars, ammonium, or amino acids were added regularly to a grassland soil for a period of 33 days. The abundance of amoA genes from AOB increased markedly in treatments that received nitrogen, suggesting that AOB were the main ammonia oxidizers here. However, AOB could not account for the entire ammonia oxidation activity observed in treatments where the soil was deficient in available nitrogen. The findings suggest that AOA are important drivers of nitrification under nitrogen-poor conditions, but that input of easily available nitrogen results in increased abundance, activity, and relative importance of AOB for gross nitrification in grassland soil.}, }
@article {pmid26648912, year = {2015}, author = {Song, HS and Renslow, RS and Fredrickson, JK and Lindemann, SR}, title = {Integrating Ecological and Engineering Concepts of Resilience in Microbial Communities.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1298}, pmid = {26648912}, issn = {1664-302X}, abstract = {Many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. We argue that the disconnect largely results from the wide variance in microbial community complexity, which range from compositionally simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems that undergo both recoverable and unrecoverable transitions, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the two concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community's functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities and suggest that state changes in response to environmental variation may be a key mechanism driving functional resilience in microbial communities.}, }
@article {pmid26640462, year = {2015}, author = {Lanzén, A and Epelde, L and Garbisu, C and Anza, M and Martín-Sánchez, I and Blanco, F and Mijangos, I}, title = {The Community Structures of Prokaryotes and Fungi in Mountain Pasture Soils are Highly Correlated and Primarily Influenced by pH.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1321}, pmid = {26640462}, issn = {1664-302X}, abstract = {Traditionally, conservation and management of mountain pastures has been managed solely on the basis of visible biota. However, microorganisms play a vital role for the functioning of the soil ecosystem and, hence, pasture sustainability. Here, we studied the links between soil microbial (belowground) community structure (using amplicon sequencing of prokaryotes and fungi), other soil physicochemical and biological properties and, finally, a variety of pasture management practices. To this aim, during two consecutive years, we studied 104 environmental sites characterized by contrasting elevation, habitats, bedrock, and pasture management; located in or near Gorbeia Natural Park (Basque Country/Spain). Soil pH was found to be one of the most important factors in structuring soil microbial diversity. Interestingly, we observed a striking correlation between prokaryotic, fungal and macrofauna diversity, likely caused by interactions between these life forms. Further studies are needed to better understand such interactions and target the influence of different management practices on the soil microbial community, in face of the significant heterogeneity present. However, clearing of bushes altered microbial community structure, and in sites with calcareous bedrock also the use of herbicide vs. mechanical clearing of ferns.}, }
@article {pmid26636067, year = {2015}, author = {Bartholomew, JC and Pearson, AD and Stenseth, NC and LeDuc, JW and Hirschberg, DL and Colwell, RR}, title = {Building Infectious Disease Research Programs to Promote Security and Enhance Collaborations with Countries of the Former Soviet Union.}, journal = {Frontiers in public health}, volume = {3}, number = {}, pages = {271}, pmid = {26636067}, issn = {2296-2565}, abstract = {Addressing the threat of infectious diseases, whether natural, the results of a laboratory accident, or a deliberate act of bioterrorism, requires no corner of the world be ignored. The mobility of infectious agents and their rapid adaptability, whether to climate change or socioeconomic drivers or both, demand the science employed to understand these processes be advanced and tailored to a country or a region, but with a global vision. In many parts of the world, largely because of economic struggles, scientific capacity has not kept pace with the need to accomplish this goal and has left these regions and hence the world vulnerable to infectious disease outbreaks. To build scientific capability in a developing region requires cooperation and participation of experienced international scientists who understand the issues and are committed to educate the next generations of young investigators in the region. These efforts need to be coupled with the understanding and resolve of local governments and international agencies to promote an aggressive science agenda. International collaborative scientific investigation of infectious diseases not only adds significantly to scientific knowledge, but it promotes health security, international trust, and long-term economic benefit to the region involved. This premise is based on the observation that the most powerful human inspiration is that which brings peoples together to work on and solve important global challenges. The republics of the former Soviet Union provide a valuable case study for the need to rebuild scientific capacity as they are located at the crossroads where many of the world's great epidemics began. The scientific infrastructure and disease surveillance capabilities of the region suffered significant decline after the breakup of the Soviet Union. The U.S. Cooperative Threat Reduction (CTR) Program, a part of the U.S. Department of Defense, together with partner countries, have worked diligently to improve the capabilities in this region to guard against the potential future risk from especially dangerous pathogens. The dissolution of the Soviet Union left behind many scientists still working to study pathogens using antiquated protocols in unsafe laboratories. To address this situation, the CTR program began improving laboratory infrastructure, establishing biosafety and biosecurity programs, and training scientists in modern techniques, with emphasis on biosurveillance and safe containment of especially dangerous pathogens. In the Republic of Georgia, this effort culminated in the construction of a modern containment laboratory, the Richard G. Lugar Center for Public Health Research in Tbilisi to house both isolated especially dangerous pathogens as well as the research to be conducted on these agents. The need now is to utilize and sustain the investment made by CTR by establishing strong public and animal health science programs in these facilities tailored to the needs of the region and the goals for which this investment was made. A similar effort is ongoing in other former Soviet Republics. Here, we provide the analysis and recommendations of an international panel of expert scientists appointed by the Cooperative Biological Engagement Program of the Defense Threat Reduction Agency to provide advice to the stakeholders on the scientific path for the future. The emphasis is on an implementation strategy for decision makers and scientists to consider providing a sustainable biological science program in support of the One Health initiative. Opportunities, potential barriers, and lessons learned while meeting the needs of the Republic of Georgia and the Caucasus region are discussed. It is hoped that this effort will serve as a model for similar scientific needs in not only the former Soviet Union republics but also other regions challenged by infectious diseases where the CTR program operates.}, }
@article {pmid26635757, year = {2015}, author = {Posch, T and Eugster, B and Pomati, F and Pernthaler, J and Pitsch, G and Eckert, EM}, title = {Network of Interactions Between Ciliates and Phytoplankton During Spring.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1289}, pmid = {26635757}, issn = {1664-302X}, abstract = {The annually recurrent spring phytoplankton blooms in freshwater lakes initiate pronounced successions of planktonic ciliate species. Although there is considerable knowledge on the taxonomic diversity of these ciliates, their species-specific interactions with other microorganisms are still not well understood. Here we present the succession patterns of 20 morphotypes of ciliates during spring in Lake Zurich, Switzerland, and we relate their abundances to phytoplankton genera, flagellates, heterotrophic bacteria, and abiotic parameters. Interspecific relationships were analyzed by contemporaneous correlations and time-lagged co-occurrence and visualized as association networks. The contemporaneous network pointed to the pivotal role of distinct ciliate species (e.g., Balanion planctonicum, Rimostrombidium humile) as primary consumers of cryptomonads, revealed a clear overclustering of mixotrophic/omnivorous species, and highlighted the role of Halteria/Pelagohalteria as important bacterivores. By contrast, time-lagged statistical approaches (like local similarity analyses, LSA) proved to be inadequate for the evaluation of high-frequency sampling data. LSA led to a conspicuous inflation of significant associations, making it difficult to establish ecologically plausible interactions between ciliates and other microorganisms. Nevertheless, if adequate statistical procedures are selected, association networks can be powerful tools to formulate testable hypotheses about the autecology of only recently described ciliate species.}, }
@article {pmid26635739, year = {2015}, author = {Strejcek, M and Wang, Q and Ridl, J and Uhlik, O}, title = {Hunting Down Frame Shifts: Ecological Analysis of Diverse Functional Gene Sequences.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1267}, pmid = {26635739}, issn = {1664-302X}, abstract = {Functional gene ecological analyses using amplicon sequencing can be challenging as translated sequences are often burdened with shifted reading frames. The aim of this work was to evaluate several bioinformatics tools designed to correct errors which arise during sequencing in an effort to reduce the number of frameshifts (FS). Genes encoding for alpha subunits of biphenyl (bphA) and benzoate (benA) dioxygenases were used as model sequences. FrameBot, a FS correction tool, was able to reduce the number of detected FS to zero. However, up to 44% of sequences were discarded by FrameBot as non-specific targets. Therefore, we proposed a de novo mode of FrameBot for FS correction, which works on a similar basis as common chimera identifying platforms and is not dependent on reference sequences. By nature of FrameBot de novo design, it is crucial to provide it with data as error free as possible. We tested the ability of several publicly available correction tools to decrease the number of errors in the data sets. The combination of maximum expected error filtering and single linkage pre-clustering proved to be the most efficient read processing approach. Applying FrameBot de novo on the processed data enabled analysis of BphA sequences with minimal losses of potentially functional sequences not homologous to those previously known. This experiment also demonstrated the extensive diversity of dioxygenases in soil. A script which performs FrameBot de novo is presented in the supplementary material to the study or available at https://github.com/strejcem/FBdenovo. The tool was also implemented into FunGene Pipeline available at http://fungene.cme.msu.edu/FunGenePipeline/.}, }
@article {pmid26635735, year = {2015}, author = {Gómez Expósito, R and Postma, J and Raaijmakers, JM and De Bruijn, I}, title = {Diversity and Activity of Lysobacter Species from Disease Suppressive Soils.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1243}, pmid = {26635735}, issn = {1664-302X}, abstract = {The genus Lysobacter includes several species that produce a range of extracellular enzymes and other metabolites with activity against bacteria, fungi, oomycetes, and nematodes. Lysobacter species were found to be more abundant in soil suppressive against the fungal root pathogen Rhizoctonia solani, but their actual role in disease suppression is still unclear. Here, the antifungal and plant growth-promoting activities of 18 Lysobacter strains, including 11 strains from Rhizoctonia-suppressive soils, were studied both in vitro and in vivo. Based on 16S rRNA sequencing, the Lysobacter strains from the Rhizoctonia-suppressive soil belonged to the four species Lysobacter antibioticus, Lysobacter capsici, Lysobacter enzymogenes, and Lysobacter gummosus. Most strains showed strong in vitro activity against R. solani and several other pathogens, including Pythium ultimum, Aspergillus niger, Fusarium oxysporum, and Xanthomonas campestris. When the Lysobacter strains were introduced into soil, however, no significant and consistent suppression of R. solani damping-off disease of sugar beet and cauliflower was observed. Subsequent bioassays further revealed that none of the Lysobacter strains was able to promote growth of sugar beet, cauliflower, onion, and Arabidopsis thaliana, either directly or via volatile compounds. The lack of in vivo activity is most likely attributed to poor colonization of the rhizosphere by the introduced Lysobacter strains. In conclusion, our results demonstrated that Lysobacter species have strong antagonistic activities against a range of pathogens, making them an important source for putative new enzymes and antimicrobial compounds. However, their potential role in R. solani disease suppressive soil could not be confirmed. In-depth omics'-based analyses will be needed to shed more light on the potential contribution of Lysobacter species to the collective activities of microbial consortia in disease suppressive soils.}, }
@article {pmid26633470, year = {2015}, author = {Reed, S and Neuman, H and Moscovich, S and Glahn, RP and Koren, O and Tako, E}, title = {Chronic Zinc Deficiency Alters Chick Gut Microbiota Composition and Function.}, journal = {Nutrients}, volume = {7}, number = {12}, pages = {9768-9784}, pmid = {26633470}, issn = {2072-6643}, support = {U24 DK097153/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*genetics ; Biomarkers ; *Chickens ; Gastrointestinal Tract/*microbiology ; Nutritional Status ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Zinc/*deficiency ; }, abstract = {Zinc (Zn) deficiency is a prevalent micronutrient insufficiency. Although the gut is a vital organ for Zn utilization, and Zn deficiency is associated with impaired intestinal permeability and a global decrease in gastrointestinal health, alterations in the gut microbial ecology of the host under conditions of Zn deficiency have yet to be studied. Using the broiler chicken (Gallus gallus) model, the aim of this study was to characterize distinct cecal microbiota shifts induced by chronic dietary Zn depletion. We demonstrate that Zn deficiency induces significant taxonomic alterations and decreases overall species richness and diversity, establishing a microbial profile resembling that of various other pathological states. Through metagenomic analysis, we show that predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways responsible for macro- and micronutrient uptake are significantly depleted under Zn deficiency; along with concomitant decreases in beneficial short chain fatty acids, such depletions may further preclude optimal host Zn availability. We also identify several candidate microbes that may play a significant role in modulating the bioavailability and utilization of dietary Zn during prolonged deficiency. Our results are the first to characterize a unique and dysbiotic cecal microbiota during Zn deficiency, and provide evidence for such microbial perturbations as potential effectors of the Zn deficient phenotype.}, }
@article {pmid26633426, year = {2015}, author = {Wichmann, H and Vocke, F and Brinkhoff, T and Simon, M and Richter-Landsberg, C}, title = {Cytotoxic Effects of Tropodithietic Acid on Mammalian Clonal Cell Lines of Neuronal and Glial Origin.}, journal = {Marine drugs}, volume = {13}, number = {12}, pages = {7113-7123}, pmid = {26633426}, issn = {1660-3397}, mesh = {Actin Cytoskeleton/drug effects/metabolism ; Animals ; Calcium/metabolism ; Cell Death/*drug effects ; Cell Line ; Cell Line, Tumor ; Dose-Response Relationship, Drug ; Membrane Potential, Mitochondrial/drug effects ; Mice ; Microtubules/drug effects/metabolism ; Neuroblastoma/metabolism ; Neuroglia/*drug effects/metabolism ; Neurons/*drug effects/metabolism ; Oligodendroglia/drug effects/metabolism ; Oxidative Stress/drug effects ; Rats ; Roseobacter/metabolism ; Stress, Physiological/drug effects ; Tropolone/administration &amp; dosage/*analogs &amp; derivatives/isolation &amp; purification/toxicity ; }, abstract = {The marine metabolite tropodithietic acid (TDA), produced by several Roseobacter clade bacteria, is known for its broad antimicrobial activity. TDA is of interest not only as a probiotic in aquaculture, but also because it might be of use as an antibacterial agent in non-marine or non-aquatic environments, and thus the potentially cytotoxic influences on eukaryotic cells need to be evaluated. The present study was undertaken to investigate its effects on cells of the mammalian nervous system, i.e., neuronal N2a cells and OLN-93 cells as model systems for nerve cells and glia. The data show that in both cell lines TDA exerted morphological changes and cytotoxic effects at a concentration of 0.3-0.5 µg/mL (1.4-2.4 µM). Furthermore, TDA caused a breakdown of the mitochondrial membrane potential, the activation of extracellular signal-regulated kinases ERK1/2, and the induction of the small heat shock protein HSP32/HO-1, which is considered as a sensor of oxidative stress. The cytotoxic effects were accompanied by an increase in intracellular Ca(2+)-levels, the disturbance of the microtubule network, and the reorganization of the microfilament system. Hence, mammalian cells are a sensitive target for the action of TDA and react by the activation of a stress response resulting in cell death.}, }
@article {pmid26628913, year = {2015}, author = {Jiménez, DJ and Maruthamuthu, M and van Elsas, JD}, title = {Metasecretome analysis of a lignocellulolytic microbial consortium grown on wheat straw, xylan and xylose.}, journal = {Biotechnology for biofuels}, volume = {8}, number = {}, pages = {199}, pmid = {26628913}, issn = {1754-6834}, abstract = {BACKGROUND: Synergistic action of different enzymes is required to complete the degradation of plant biomass in order to release sugars which are useful for biorefining. However, the use of single strains is often not efficient, as crucial parts of the required enzymatic machinery can be absent. The use of microbial consortia bred on plant biomass is a way to overcome this hurdle. In these, secreted proteins constitute sources of relevant enzyme cocktails. Extensive analyses of the proteins secreted by effective microbial consortia will contribute to a better understanding of the mechanism of lignocellulose degradation.<br><br>RESULTS: Here, we report an analysis of the proteins secreted by a microbial consortium (metasecretome) that was grown on either wheat straw (RWS), xylose or xylan as the carbon sources. Liquid chromatography-tandem mass spectrometry was used to analyze the proteins in the supernatants. Totals of 768 (RWS), 477 (xylose) and 103 (xylan) proteins were identified and taxonomically and functionally classified. In RWS, the proteins were mostly affiliated with Sphingobacterium-like consortium members (~50&#xa0;%). Specific abundant protein clusters were predicted to be involved in polysaccharide transport and/or sensing (TonB-dependent receptors). In addition, proteins predicted to degrade plant biomass, i.e. endo-1,4-beta-xylanases, alpha-l-arabinofuranosidases and alpha-l-fucosidases, were prominent. In the xylose-driven consortium, most secreted proteins were affiliated with those from Enterobacteriales (mostly Klebsiella species), whereas in the xylan-driven one, they were related to Flavobacterium-like ones. Notably, the metasecretomes of the consortia growing on xylose and xylan contained proteins involved in diverse metabolic functions (e.g. membrane proteins, isomerases, dehydrogenases and oxidoreductases).<br><br>CONCLUSIONS: An analysis of the metasecretomes of microbial consortia originating from the same source consortium and subsequently bred on three different carbon sources indicated that the major active microorganisms in the three final consortia differed. Importantly, diverse glycosyl hydrolases, predicted to be involved in (hemi)cellulose degradation (e.g. of CAZy families GH3, GH10, GH43, GH51, GH67 and GH95), were identified in the RWS metasecretome. Based on these results, we catalogued the RWS consortium as a true microbial enzyme factory that constitute an excellent source for the production of an efficient enzyme cocktail for the pretreatment of plant biomass.}, }
@article {pmid26627188, year = {2015}, author = {Rhoads, WJ and Ji, P and Pruden, A and Edwards, MA}, title = {Water heater temperature set point and water use patterns influence Legionella pneumophila and associated microorganisms at the tap.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {67}, pmid = {26627188}, issn = {2049-2618}, mesh = {Amoeba/growth &amp; development ; Drinking Water/*microbiology ; Household Articles/instrumentation ; Humans ; Legionella pneumophila/growth &amp; development/*isolation &amp; purification ; Legionnaires' Disease/prevention &amp; control ; Pilot Projects ; Sanitary Engineering ; *Temperature ; *Water Microbiology ; *Water Supply ; }, abstract = {BACKGROUND: Lowering water heater temperature set points and using less drinking water are common approaches to conserving water and energy; yet, there are discrepancies in past literature regarding the effects of water heater temperature and water use patterns on the occurrence of opportunistic pathogens, in particular Legionella pneumophila. Our objective was to conduct a controlled, replicated pilot-scale investigation to address this knowledge gap using continuously recirculating water heaters to examine five water heater set points (39-58 °C) under three water use conditions. We hypothesized that L. pneumophila levels at the tap depend on the collective influence of water heater temperature, flow frequency, and the resident plumbing ecology.<br><br>RESULTS: We confirmed temperature setting to be a critical factor in suppressing L. pneumophila growth both in continuously recirculating hot water lines and at distal taps. For example, at 51 &#xb0;C, planktonic L. pneumophila in recirculating lines was reduced by a factor of 28.7 compared to 39 &#xb0;C and was prevented from re-colonizing biofilm. However, L. pneumophila still persisted up to 58 &#xb0;C, with evidence that it was growing under the conditions of this study. Further, exposure to 51 &#xb0;C water in a low-use tap appeared to optimally select for L. pneumophila (e.g., 125 times greater numbers than in high-use taps). We subsequently explored relationships among L. pneumophila and other ecologically relevant microbes, noting that elevated temperature did not have a general disinfecting effect in terms of total bacterial numbers. We documented the relationship between L. pneumophila and Legionella spp., and noted several instances of correlations with Vermamoeba vermiformis, and generally found that there is a dynamic relationship with this amoeba host over the range of temperatures and water use frequencies examined.<br><br>CONCLUSIONS: Our study provides a new window of understanding into the microbial ecology of potable hot water systems and helps to resolve past discrepancies in the literature regarding the influence of water temperature and stagnation on L. pneumophila, which is the cause of a growing number of outbreaks. This work is especially timely, given society's movement towards "green" buildings and the need to reconcile innovations in building design with public health.}, }
@article {pmid26626912, year = {2016}, author = {David, AS and Seabloom, EW and May, G}, title = {Plant Host Species and Geographic Distance Affect the Structure of Aboveground Fungal Symbiont Communities, and Environmental Filtering Affects Belowground Communities in a Coastal Dune Ecosystem.}, journal = {Microbial ecology}, volume = {71}, number = {4}, pages = {912-926}, pmid = {26626912}, issn = {1432-184X}, mesh = {Biodegradation, Environmental ; Biodiversity ; DNA, Fungal/analysis/genetics ; *Ecosystem ; Endophytes/physiology ; Fungi/growth &amp; development/isolation &amp; purification/*physiology ; Northwestern United States ; Phylogeny ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Plants/*microbiology ; Soil Microbiology ; Species Specificity ; Spores, Fungal/growth &amp; development ; Symbiosis ; }, abstract = {Microbial symbionts inhabit tissues of all plants and animals. Their community composition depends largely on two ecological processes: (1) filtering by abiotic conditions and host species determining the environments that symbionts are able to colonize and (2) dispersal-limitation determining the pool of symbionts available to colonize a given host and community spatial structure. In plants, the above- and belowground tissues represent such distinct habitats for symbionts that we expect different effects of filtering and spatial structuring on their symbiont communities. In this study, we characterized above- and belowground communities of fungal endophytes--fungi living asymptomatically within plants--to understand the contributions of filtering and spatial structure to endophyte community composition. We used a culture-based approach to characterize endophytes growing in leaves and roots of three species of coastal beachgrasses in dunes of the USA Pacific Northwest. For leaves, endophyte isolation frequency and OTU richness depended primarily on plant host species. In comparison, for roots, both isolation frequency and OTU richness increased from the nutrient-poor front of the dune to the higher-nutrient backdune. Endophyte community composition in leaves exhibited a distance-decay relationship across the region. In a laboratory assay, faster growth rates and lower spore production were more often associated with leaf- than root-inhabiting endophytes. Overall, our results reveal a greater importance of biotic filtering by host species and dispersal-limitation over regional geographic distances for aboveground leaf endophyte communities and stronger effects of abiotic environmental filtering and locally patchy distributions for belowground root endophyte communities.}, }
@article {pmid26626911, year = {2016}, author = {Tsiola, A and Pitta, P and Fodelianakis, S and Pete, R and Magiopoulos, I and Mara, P and Psarra, S and Tanaka, T and Mostajir, B}, title = {Nutrient Limitation in Surface Waters of the Oligotrophic Eastern Mediterranean Sea: an Enrichment Microcosm Experiment.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {575-588}, pmid = {26626911}, issn = {1432-184X}, mesh = {Autotrophic Processes ; Bacteria/classification/isolation &amp; purification/*metabolism ; Eukaryota/classification/isolation &amp; purification/*metabolism ; Heterotrophic Processes ; Mediterranean Sea ; Seawater/chemistry/*microbiology ; Viruses/classification/isolation &amp; purification/*metabolism ; }, abstract = {The growth rates of planktonic microbes in the pelagic zone of the Eastern Mediterranean Sea are nutrient limited, but the type of limitation is still uncertain. During this study, we investigated the occurrence of N and P limitation among different groups of the prokaryotic and eukaryotic (pico-, nano-, and micro-) plankton using a microcosm experiment during stratified water column conditions in the Cretan Sea (Eastern Mediterranean). Microcosms were enriched with N and P (either solely or simultaneously), and the PO4 turnover time, prokaryotic heterotrophic activity, primary production, and the abundance of the different microbial components were measured. Flow cytometric and molecular fingerprint analyses showed that different heterotrophic prokaryotic groups were limited by different nutrients; total heterotrophic prokaryotic growth was limited by P, but only when both N and P were added, changes in community structure and cell size were detected. Phytoplankton were N and P co-limited, with autotrophic pico-eukaryotes being the exception as they increased even when only P was added after a 2-day time lag. The populations of Synechococcus and Prochlorococcus were highly competitive with each other; Prochlorococcus abundance increased during the first 2 days of P addition but kept increasing only when both N and P were added, whereas Synechococcus exhibited higher pigment content and increased in abundance 3 days after simultaneous N and P additions. Dinoflagellates also showed opportunistic behavior at simultaneous N and P additions, in contrast to diatoms and coccolithophores, which diminished in all incubations. High DNA content viruses, selective grazing, and the exhaustion of N sources probably controlled the populations of diatoms and coccolithophores.}, }
@article {pmid26626627, year = {2016}, author = {Reddy, MS and Kour, M and Aggarwal, S and Ahuja, S and Marmeisse, R and Fraissinet-Tachet, L}, title = {Metal induction of a Pisolithus albus metallothionein and its potential involvement in heavy metal tolerance during mycorrhizal symbiosis.}, journal = {Environmental microbiology}, volume = {18}, number = {8}, pages = {2446-2454}, doi = {10.1111/1462-2920.13149}, pmid = {26626627}, issn = {1462-2920}, mesh = {Amino Acid Sequence ; Basidiomycota/*metabolism ; Cadmium/*toxicity ; Copper/*toxicity ; Eucalyptus/drug effects/*microbiology ; Metallothionein/*metabolism ; Mycorrhizae/*metabolism ; Plant Development/drug effects/physiology ; Sequence Alignment ; Symbiosis ; }, abstract = {Metallothioneins (MTs) are small, cysteine-rich peptides involved in intracellular sequestration of heavy metals in eukaryotes. We examined the role in metal homeostasis and detoxification of an MT from the ectomycorrhizal fungus Pisolithus albus (PaMT1). PaMT1 encodes a 35 amino acid-long polypeptide, with 7 cysteine residues; most of them part of a C-x-C motif found in other known basidiomycete MTs. The expression levels of PaMT1 increased as a function of increased external Cu and Cd concentrations and were higher with Cu than with Cd. Heterologous complementation assays in metal-sensitive yeast mutants indicated that PaMT1 encodes a polypeptide capable of conferring higher tolerance to both Cu and Cd. Eucalyptus tereticornis plantlets colonized with P. albus grown in the presence of Cu and Cd showed better growth compared with those with non-mycorrhizal plants. Higher PaMT1 expression levels were recorded in mycorrhizal plants grown in the presence of Cu and Cd compared with those in control mycorrhizal plants not exposed to heavy metals. These data provide the first evidence to our knowledge that fungal MTs could protect ectomycorrhizal fungi from heavy metal stress and in turn help the plants to establish in metal-contaminated sites.}, }
@article {pmid26626057, year = {2016}, author = {Gan, XH and Zhang, FQ and Gu, JD and Guo, YD and Li, ZQ and Zhang, WQ and Xu, XY and Zhou, Y and Wen, XY and Xie, GG and Wang, YF}, title = {Differential distribution patterns of ammonia-oxidizing archaea and bacteria in acidic soils of Nanling National Nature Reserve forests in subtropical China.}, journal = {Antonie van Leeuwenhoek}, volume = {109}, number = {2}, pages = {237-251}, doi = {10.1007/s10482-015-0627-8}, pmid = {26626057}, issn = {1572-9699}, mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; China ; Conservation of Natural Resources ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {In addition to ammonia-oxidizing bacteria (AOB) the more recently discovered ammonia-oxidizing archaea (AOA) can also oxidize ammonia, but little is known about AOA community structure and abundance in subtropical forest soils. In this study, both AOA and AOB were investigated with molecular techniques in eight types of forests at surface soils (0-2 cm) and deep layers (18-20 cm) in Nanling National Nature Reserve in subtropical China. The results showed that the forest soils, all acidic (pH 4.24-5.10), harbored a wide range of AOA phylotypes, including the genera Nitrosotalea, Nitrososphaera, and another 6 clusters, one of which was reported for the first time. For AOB, only members of Nitrosospira were retrieved. Moreover, the abundance of the ammonia monooxygenase gene (amoA) from AOA dominated over AOB in most soil samples (13/16). Soil depth, rather than forest type, was an important factor shaping the community structure of AOA and AOB. The distribution patterns of AOA and AOB in soil layers were reversed: AOA diversity and abundances in the deep layers were higher than those in the surface layers; on the contrary, AOB diversity and abundances in the deep layers were lower than those in the surface layers. Interestingly, the diversity of AOA was positively correlated with pH, but negatively correlated with organic carbon, total nitrogen and total phosphorus, and the abundance of AOA was negatively correlated with available phosphorus. Our results demonstrated that AOA and AOB were differentially distributed in acidic soils in subtropical forests and affected differently by soil characteristics.}, }
@article {pmid26625892, year = {2016}, author = {Pelikan, C and Herbold, CW and Hausmann, B and Müller, AL and Pester, M and Loy, A}, title = {Diversity analysis of sulfite- and sulfate-reducing microorganisms by multiplex dsrA and dsrB amplicon sequencing using new primers and mock community-optimized bioinformatics.}, journal = {Environmental microbiology}, volume = {18}, number = {9}, pages = {2994-3009}, doi = {10.1111/1462-2920.13139}, pmid = {26625892}, issn = {1462-2920}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Bacterial Proteins/*genetics/metabolism ; Computational Biology ; DNA Primers/*genetics ; DNA, Bacterial/genetics ; Hydrogensulfite Reductase/genetics/metabolism ; Phylogeny ; Polymerase Chain Reaction ; Sulfates/*metabolism ; Sulfites/*metabolism ; }, abstract = {Genes encoding dissimilatory sulfite reductase (DsrAB) are commonly used as diagnostic markers in ecological studies of sulfite- and sulfate-reducing microorganisms. Here, we developed new high-coverage primer sets for generation of reductive bacterial-type dsrA and dsrB polymerase chain reaction (PCR) products for highly parallel amplicon sequencing and a bioinformatics workflow for processing and taxonomic classification of short dsrA and dsrB reads. We employed two diverse mock communities that consisted of 45 or 90 known dsrAB sequences derived from environmental clones to precisely evaluate the performance of individual steps of our amplicon sequencing approach on the Illumina MiSeq platform. Although PCR cycle number, gene-specific primer mismatches and stringent filtering for high-quality sequences had notable effects on the observed dsrA and dsrB community structures, recovery of most mock community sequences was generally proportional to their relative input abundances. Successful dsrA and dsrB diversity analysis in selected environmental samples further proved that the multiplex amplicon sequencing approach is adequate for monitoring spatial distribution and temporal abundance dynamics of dsrAB-containing microorganisms. Although tested for reductive bacterial-type dsrAB, this method is readily applicable for oxidative-type dsrAB of sulfur-oxidizing bacteria and also provides guidance for processing short amplicon reads of other functional genes.}, }
@article {pmid26619398, year = {2016}, author = {Peng, L and Liu, Y and Gao, SH and Chen, X and Ni, BJ}, title = {Evaluating simultaneous chromate and nitrate reduction during microbial denitrification processes.}, journal = {Water research}, volume = {89}, number = {}, pages = {1-8}, doi = {10.1016/j.watres.2015.11.031}, pmid = {26619398}, issn = {1879-2448}, mesh = {Autotrophic Processes ; Bacteria/metabolism ; Bioreactors/microbiology ; Chromates/*chemistry ; *Denitrification ; Heterotrophic Processes ; *Models, Theoretical ; Nitrates/*chemistry ; Sulfates/chemistry ; Water Pollutants, Chemical/chemistry ; Water Purification/*methods ; }, abstract = {Sulfur-based autotrophic denitrification and heterotrophic denitrification have been demonstrated to be promising technological processes for simultaneous removal of nitrate NO3(-) and chromate (Cr (VI)), two common contaminants in surface and ground waters. In this work, a mathematical model was developed to describe and evaluate the microbial and substrate interactions among sulfur oxidizing denitrifying organism, methanol-based heterotrophic denitrifiers and chromate reducing bacteria in the biofilm systems for simultaneous nitrate and chromate removal. The concomitant multiple chromate reduction pathways by these microbes were taken into account in this model. The validity of the model was tested using experimental data from three independent biofilm reactors under autotrophic, heterotrophic and mixotrophic conditions. The model sufficiently described the nitrate, chromate, methanol, and sulfate dynamics under varying conditions. The modeling results demonstrated the coexistence of sulfur-oxidizing denitrifying bacteria and heterotrophic denitrifying bacteria in the biofilm under mixotrophic conditions, with chromate reducing bacteria being outcompeted. The sulfur-oxidizing denitrifying bacteria substantially contributed to both nitrate and chromate reductions although heterotrophic denitrifying bacteria dominated in the biofilm. The mixotrophic denitrification could improve the tolerance of autotrophic denitrifying bacteria to Cr (VI) toxicity. Furthermore, HRT would play an important role in affecting the microbial distribution and system performance, with HRT of higher than 0.15 day being critical for a high level removal of nitrate and chromate (over 90%).}, }
@article {pmid26617596, year = {2015}, author = {Wang, H and Tomasch, J and Michael, V and Bhuju, S and Jarek, M and Petersen, J and Wagner-Döbler, I}, title = {Identification of Genetic Modules Mediating the Jekyll and Hyde Interaction of Dinoroseobacter shibae with the Dinoflagellate Prorocentrum minimum.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1262}, pmid = {26617596}, issn = {1664-302X}, abstract = {The co-cultivation of the alphaproteobacterium Dinoroseobacter shibae with the dinoflagellate Prorocentrum minimum is characterized by a mutualistic phase followed by a pathogenic phase in which the bacterium kills aging algae. Thus it resembles the "Jekyll-and-Hyde" interaction that has been proposed for other algae and Roseobacter. Here, we identified key genetic components of this interaction. Analysis of the transcriptome of D. shibae in co-culture with P. minimum revealed growth phase dependent changes in the expression of quorum sensing, the CtrA phosphorelay, and flagella biosynthesis genes. Deletion of the histidine kinase gene cckA which is part of the CtrA phosphorelay or the flagella genes fliC or flgK resulted in complete lack of growth stimulation of P. minimum in co-culture with the D. shibae mutants. By contrast, pathogenicity was entirely dependent on one of the extrachromosomal elements of D. shibae, the 191 kb plasmid. The data show that flagella and the CtrA phosphorelay are required for establishing mutualism and prove a cell density dependent killing effect of D. shibae on P. minimum which is mediated by an unknown factor encoded on the 191 kb plasmid.}, }
@article {pmid26617073, year = {2016}, author = {Sutter, M and Faulkner, M and Aussignargues, C and Paasch, BC and Barrett, S and Kerfeld, CA and Liu, LN}, title = {Visualization of Bacterial Microcompartment Facet Assembly Using High-Speed Atomic Force Microscopy.}, journal = {Nano letters}, volume = {16}, number = {3}, pages = {1590-1595}, pmid = {26617073}, issn = {1530-6992}, support = {R01 AI114975/AI/NIAID NIH HHS/United States ; 1R01AI114975-01/AI/NIAID NIH HHS/United States ; BB/M012441/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M024202/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacterial Proteins/analysis/genetics/*ultrastructure ; Crystallography, X-Ray ; Microscopy, Atomic Force/*methods ; Myxococcales/*cytology/genetics/ultrastructure ; Point Mutation ; Protein Conformation ; }, abstract = {Bacterial microcompartments (BMCs) are proteinaceous organelles widespread among bacterial phyla. They compartmentalize enzymes within a selectively permeable shell and play important roles in CO2 fixation, pathogenesis, and microbial ecology. Here, we combine X-ray crystallography and high-speed atomic force microscopy to characterize, at molecular resolution, the structure and dynamics of BMC shell facet assembly. Our results show that preformed hexamers assemble into uniformly oriented shell layers, a single hexamer thick. We also observe the dynamic process of shell facet assembly. Shell hexamers can dissociate from and incorporate into assembled sheets, indicating a flexible intermolecular interaction. Furthermore, we demonstrate that the self-assembly and dynamics of shell proteins are governed by specific contacts at the interfaces of shell proteins. Our study provides novel insights into the formation, interactions, and dynamics of BMC shell facets, which are essential for the design and engineering of self-assembled biological nanoreactors and scaffolds based on BMC architectures.}, }
@article {pmid26616964, year = {2016}, author = {Lavu, RV and Van De Wiele, T and Pratti, VL and Tack, F and Du Laing, G}, title = {Selenium bioaccessibility in stomach, small intestine and colon: Comparison between pure Se compounds, Se-enriched food crops and food supplements.}, journal = {Food chemistry}, volume = {197}, number = {Pt A}, pages = {382-387}, doi = {10.1016/j.foodchem.2015.08.001}, pmid = {26616964}, issn = {1873-7072}, mesh = {Colon/*metabolism ; Crops, Agricultural/chemistry/metabolism ; Dietary Supplements/*analysis ; Digestion ; Food, Fortified/*analysis ; Gastric Mucosa/*metabolism ; Humans ; Intestine, Small/*metabolism ; Selenic Acid/analysis/metabolism ; Selenium Compounds/analysis/*metabolism ; Selenomethionine/analysis/metabolism ; }, abstract = {Selenium (Se) is an essential nutrient for humans as it plays an important role in glutathione peroxidase (GPx) activity. Moreover, it may reduce cancer risks. The objective of this work was to examine in vitro the bioaccessibility of Se in three different Se-enriched food supplements and two different Se-enriched food crops, with reference to two pure Se standards, and changes in its speciation during intestinal digestion. Selenate was found to be stable throughout the entire digestion, whereas incubation of selenomethionine resulted in the chemical and microbial production of minor metabolites. The bioaccessibility of Se in Se-enriched food supplements and food crops was found to be highest in the small intestine. Compared to SelenoPrecise and Se-ACE tablets, a yoghurt-based supplement exhibited a much lower Se bioaccessibility, possibly due to the presence of nano- or microparticles of elemental Se. Colon microbiota were found to primarily affect Se bioaccessibility in the colon environment, with the presence of inactivated microbiota resulting in a higher bioaccessibility. A higher potential of Se to reach the colon and become accessible in this phase may result in beneficial effects on the colon health.}, }
@article {pmid26614069, year = {2016}, author = {Parisot, N and Peyretaillade, E and Dugat-Bony, E and Denonfoux, J and Mahul, A and Peyret, P}, title = {Probe Design Strategies for Oligonucleotide Microarrays.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1368}, number = {}, pages = {67-82}, doi = {10.1007/978-1-4939-3136-1_6}, pmid = {26614069}, issn = {1940-6029}, mesh = {*Algorithms ; Oligonucleotide Array Sequence Analysis/*methods ; *Oligonucleotide Probes/genetics ; Proteins/genetics ; }, abstract = {Oligonucleotide microarrays have been widely used for gene detection and/or quantification of gene expression in various samples ranging from a single organism to a complex microbial assemblage. The success of a microarray experiment, however, strongly relies on the quality of designed probes. Consequently, probe design is of critical importance and therefore multiple parameters should be considered for each probe in order to ensure high specificity, sensitivity, and uniformity as well as potentially quantitative power. Moreover, to assess the complete gene repertoire of complex biological samples such as those studied in the field of microbial ecology, exploratory probe design strategies must be also implemented to target not-yet-described sequences. To design such probes, two algorithms, KASpOD and HiSpOD, have been developed and they are available via two user-friendly web services. Here, we describe the use of this software necessary for the design of highly effective probes especially in the context of microbial oligonucleotide microarrays by taking into account all the crucial parameters.}, }
@article {pmid26613914, year = {2015}, author = {Van Meervenne, E and Van Coillie, E and Van Weyenberg, S and Boon, N and Herman, L and Devlieghere, F}, title = {Low Temperature and Modified Atmosphere: Hurdles for Antibiotic Resistance Transfer?.}, journal = {Journal of food protection}, volume = {78}, number = {12}, pages = {2191-2199}, doi = {10.4315/0362-028X.JFP-15-105}, pmid = {26613914}, issn = {1944-9097}, mesh = {Agar/chemistry ; Air ; Animals ; Carbon Dioxide ; Cold Temperature ; Cooking ; *Drug Resistance, Microbial ; Food Handling ; Food Industry ; *Food Microbiology ; Food Packaging/*methods ; Hydrogen-Ion Concentration ; Lactobacillus ; Listeria monocytogenes ; *Meat ; Nitrogen/chemistry ; Plasmids/metabolism ; Swine ; }, abstract = {Food is an important dissemination route for antibiotic-resistant bacteria. Factors used during food production and preservation may contribute to the transfer of antibiotic resistance genes, but research on this subject is scarce. In this study, the effect of temperature (7 to 37°C) and modified atmosphere packaging (air, 50% CO2-50% N2, and 100% N2) on antibiotic resistance transfer from Lactobacillus sakei subsp. sakei to Listeria monocytogenes was evaluated. Filter mating was performed on nonselective agar plates with high-density inocula. A more realistic setup was created by performing modified atmosphere experiments on cooked ham using high-density and low-density inocula. Plasmid transfer was observed between 10 and 37°C, with plasmid transfer also observed at 7°C during a prolonged incubation period. When high-density inocula were used, transconjugants were detected, both on agar plates and cooked ham, under the three atmospheres (air, 50% CO2-50% N2, and 100% N2) at 7°C. This yielded a median transfer ratio (number of transconjugants/number of recipients) with an order of magnitude of 10(-4) to 10(-6). With low-density inocula, transfer was only detected under the 100% N2 atmosphere after 10-day incubation at 7°C, yielding a transfer ratio of 10(-5). Under this condition, the highest bacterial density was obtained. The results indicate that low temperature and modified atmosphere packaging, two important hurdles in the food industry, do not necessarily prevent plasmid transfer from Lactobacillus sakei subsp. sakei to Listeria monocytogenes.}, }
@article {pmid26613186, year = {2016}, author = {Pauletto, M and Carraro, L and Babbucci, M and Lucchini, R and Bargelloni, L and Cardazzo, B}, title = {Extending RAD tag analysis to microbial ecology: a comparison between MultiLocus Sequence Typing and 2b-RAD to investigate Listeria monocytogenes genetic structure.}, journal = {Molecular ecology resources}, volume = {16}, number = {3}, pages = {823-835}, doi = {10.1111/1755-0998.12495}, pmid = {26613186}, issn = {1755-0998}, mesh = {DNA Restriction Enzymes/metabolism ; DNA, Bacterial/chemistry/genetics ; Environmental Microbiology ; Food Microbiology ; *Genetic Variation ; Genetics, Population ; Listeria monocytogenes/*classification/*genetics ; Molecular Typing/*methods ; }, abstract = {The advent of next-generation sequencing (NGS) has dramatically changed bacterial typing technologies, increasing our ability to differentiate bacterial isolates. Despite it is now possible to sequence a bacterial genome in a few days and at reasonable costs, most genetic analyses do not require whole-genome sequencing, which also remains impractical for large population samples due to the cost of individual library preparation and bioinformatics. More traditional sequencing approaches, however, such as MultiLocus Sequence Typing (mlst) are quite laborious and time-consuming, especially for large-scale analyses. In this study, a genotyping approach based on restriction site-associated (RAD) tag sequencing, 2b-RAD, was applied to characterize Listeria monocytogenes strains. To verify the feasibility of the method, an in silico analysis was performed on 30 available complete genomes. For the same set of strains, in silico mlst analysis was conducted as well. Subsequently, 2b-RAD and mlst analyses were experimentally carried out on 58 isolates collected from food samples or food-processing sites. The obtained results demonstrate that 2b-RAD predicts mlst types and often provides more detailed information on population structure than mlst. Moreover, the majority of variants differentiating identical sequence type isolates mapped against accessory fragments, thus providing additional information to characterize strains. Although mlst still represents a reliable typing method, large-scale studies on molecular epidemiology and public health, as well as bacterial phylogenetics, population genetics and biosafety could benefit of a low cost and fast turnaround time approach such as the 2b-RAD analysis proposed here.}, }
@article {pmid26611863, year = {2015}, author = {Srichandan, S and Kim, JY and Kumar, A and Mishra, DR and Bhadury, P and Muduli, PR and Pattnaik, AK and Rastogi, G}, title = {Interannual and cyclone-driven variability in phytoplankton communities of a tropical coastal lagoon.}, journal = {Marine pollution bulletin}, volume = {101}, number = {1}, pages = {39-52}, doi = {10.1016/j.marpolbul.2015.11.030}, pmid = {26611863}, issn = {1879-3363}, mesh = {Asia ; Biomass ; Cyanobacteria/classification/*growth &amp; development ; *Cyclonic Storms ; Environmental Monitoring ; Fresh Water/*chemistry ; Models, Biological ; Phytoplankton/classification/*growth &amp; development ; Salinity ; Seasons ; Seawater/*chemistry ; Species Specificity ; *Tropical Climate ; }, abstract = {One of the main challenges in phytoplankton ecology is to understand their variability at different spatiotemporal scales. We investigated the interannual and cyclone-derived variability in phytoplankton communities of Chilika, the largest tropical coastal lagoon in Asia and the underlying mechanisms in relation to environmental forcing. Between July 2012 and June 2013, Cyanophyta were most prolific in freshwater northern region of the lagoon. A category-5 very severe cyclonic storm (VSCS) Phailin struck the lagoon on 12th October 2013 and introduced additional variability into the hydrology and phytoplankton communities. Freshwater Cyanophyta further expanded their territory and occupied the northern as well as central region of the lagoon. Satellite remote sensing imagery revealed that the phytoplankton biomass did not change much due to high turbidity prevailing in the lagoon after Phailin. Modeling analysis of species-salinity relationship identified specific responses of phytoplankton taxa to the different salinity regime of lagoon.}, }
@article {pmid26610433, year = {2016}, author = {Lima, MT and Andrade, AC and Oliveira, GP and Calixto, RS and Oliveira, DB and Souza, &#xc9;L and Trindade, GS and Nicoli, JR and Kroon, EG and Martins, FS and Abrahão, JS}, title = {Microbiota is an essential element for mice to initiate a protective immunity against Vaccinia virus.}, journal = {FEMS microbiology ecology}, volume = {92}, number = {2}, pages = {}, doi = {10.1093/femsec/fiv147}, pmid = {26610433}, issn = {1574-6941}, mesh = {Animals ; Cattle ; Cattle Diseases/immunology/virology ; Gastrointestinal Tract/*microbiology ; Host-Pathogen Interactions/*immunology ; Humans ; Mice ; Microbiota/*immunology ; Vaccinia/*immunology/virology ; Vaccinia virus/*immunology ; }, abstract = {The gastrointestinal tract of vertebrates harbors one of the most complex ecosystems known in microbial ecology and this indigenous microbiota almost always has a profound influence on host-parasite relationships, which can enhance or reduce the pathology of the infection. In this context, the impact of the microbiota during the infection of several viral groups remains poorly studied, including the family Poxviridae. Vaccinia virus (VACV) is a member of this family and is the causative agent of bovine vaccinia, responsible for outbreaks that affect bovines and humans. To determine the influence of the microbiota in the development of the disease caused by VACV, a comparative study using a murine model was performed. Germ-free and conventional, 6- to 7-week-old Swiss NIH mice were infected by tail scarification and intranasally with VACV. Moreover, immunosuppression and microbiota reposition were performed, to establish the interactions among the host's immune system, microbiota and VACV. The data demonstrate that the microbiota is essential for the effective immune response of mice against VACV in intranasal inoculation and to control the virus at the primary site of infection. Furthermore, this study is the first to show that Swiss conventional mice are refractory to the intranasal infection of VACV.}, }
@article {pmid26610024, year = {2015}, author = {Daims, H and Lebedeva, EV and Pjevac, P and Han, P and Herbold, C and Albertsen, M and Jehmlich, N and Palatinszky, M and Vierheilig, J and Bulaev, A and Kirkegaard, RH and von Bergen, M and Rattei, T and Bendinger, B and Nielsen, PH and Wagner, M}, title = {Complete nitrification by Nitrospira bacteria.}, journal = {Nature}, volume = {528}, number = {7583}, pages = {504-509}, pmid = {26610024}, issn = {1476-4687}, support = {294343/ERC_/European Research Council/International ; P 25231/FWF_/Austrian Science Fund FWF/Austria ; P 27319/FWF_/Austrian Science Fund FWF/Austria ; T32 HG002536/HG/NHGRI NIH HHS/United States ; }, mesh = {Ammonia/*metabolism ; Bacteria/enzymology/genetics/growth &amp; development/*metabolism ; Evolution, Molecular ; Genome, Bacterial/genetics ; Molecular Sequence Data ; Nitrates/*metabolism ; *Nitrification/genetics ; Nitrites/*metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Phylogeny ; }, abstract = {Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira-contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities.}, }
@article {pmid26608762, year = {2015}, author = {Grijalbo, L and Garbisu, C and Martín, I and Etxebarria, J and Gutierrez-Mañero, FJ and Lucas Garcia, JA}, title = {Functional diversity and dynamics of bacterial communities in a membrane bioreactor for the treatment of metal-working fluid wastewater.}, journal = {Journal of water and health}, volume = {13}, number = {4}, pages = {1006-1019}, doi = {10.2166/wh.2015.079}, pmid = {26608762}, issn = {1477-8920}, mesh = {Bacteria/*classification ; Bioreactors/*microbiology ; DNA, Bacterial/analysis ; Metallurgy ; Phylogeny ; RNA, Ribosomal, 16S/analysis ; Wastewater/*microbiology ; *Water Microbiology ; }, abstract = {An extensive microbiological study has been carried out in a membrane bioreactor fed with activated sludge and metal-working fluids. Functional diversity and dynamics of bacterial communities were studied with different approaches. Functional diversity of culturable bacterial communities was studied with different Biolog™ plates. Structure and dynamics of bacterial communities were studied in culturable and in non-culturable fractions using a 16S rRNA analysis. Among the culturable bacteria, Alphaproteobacteria and Gammaproteobacteria were the predominant classes. However, changes in microbial community structure were detected over time. Culture-independent analysis showed that Betaproteobacteria was the most frequently detected class in the membrane bioreactor (MBR) community with Zoogloea and Acidovorax as dominant genera. Also, among non-culturable bacteria, a process of succession was observed. Longitudinal structural shifts observed were more marked for non-culturable than for culturable bacteria, pointing towards an important role in the MBR performance. Microbial community metabolic abilities assessed with Biolog™ Gram negative, Gram positive and anaerobic plates also showed differences over time for Shannon's diversity index, kinetics of average well colour development, and the intensely used substrates by bacterial community in each plate.}, }
@article {pmid26607213, year = {2015}, author = {Cram, JA}, title = {New insights into relationships between active and dormant organisms, phylogenetic diversity and ecosystem productivity.}, journal = {Molecular ecology}, volume = {24}, number = {23}, pages = {5767-5769}, doi = {10.1111/mec.13449}, pmid = {26607213}, issn = {1365-294X}, mesh = {Bacteria/*classification ; *Biodiversity ; *Ecosystem ; *Phylogeny ; Seawater/*microbiology ; }, abstract = {Marine microbes make up a key part of ocean food webs and drive ocean chemistry through a range of metabolic processes. A fundamental question in ecology is whether the diversity of organisms in a community shapes the ecological functions of that community. While there is substantial evidence to support a positive link between diversity and ecological productivity for macro-organisms in terrestrial environments, this relationship has not previously been verified for marine microbial communities. One factor complicating the understanding of this relationship is that many marine microbes are dormant and are easily dispersed by ocean currents, making it difficult to ensure that the organisms found in a given environmental sample accurately reflect processes occurring in that environment. Another complication is that, due to microbes great range of genotypic and phenotypic variability, communities with distantly related species may have greater range of metabolic functions than communities have the same richness and evenness, but in which the species present are more closely related to each other. In this issue of Molecular Ecology, Galand et al. (2015) provide compelling evidence that the most metabolically active communities are those in which the nondormant portion of the microbial community has the highest phylogenetic diversity. They also illustrate that focusing on the active portion of the community allows for detection of temporal patterns in community structure that would not be otherwise evident. The authors' point out that the presence of many dormant organisms that do not contribute to ecosystem functioning is a feature that makes microbial ecosystems fundamentally different from macro-ecosystems and that this difference needs to be accounted for in microbial ecology theory.}, }
@article {pmid26606090, year = {2015}, author = {Vierheilig, J and Savio, D and Ley, RE and Mach, RL and Farnleitner, AH and Reischer, GH}, title = {Potential applications of next generation DNA sequencing of 16S rRNA gene amplicons in microbial water quality monitoring.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {72}, number = {11}, pages = {1962-1972}, pmid = {26606090}, issn = {0273-1223}, support = {P 22032/FWF_/Austrian Science Fund FWF/Austria ; P 23900/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/*genetics ; Feces/microbiology ; Fresh Water/analysis/*microbiology ; High-Throughput Nucleotide Sequencing/*methods ; RNA, Ribosomal, 16S/*genetics ; Water Pollution ; Water Quality ; }, abstract = {The applicability of next generation DNA sequencing (NGS) methods for water quality assessment has so far not been broadly investigated. This study set out to evaluate the potential of an NGS-based approach in a complex catchment with importance for drinking water abstraction. In this multi-compartment investigation, total bacterial communities in water, faeces, soil, and sediment samples were investigated by 454 pyrosequencing of bacterial 16S rRNA gene amplicons to assess the capabilities of this NGS method for (i) the development and evaluation of environmental molecular diagnostics, (ii) direct screening of the bulk bacterial communities, and (iii) the detection of faecal pollution in water. Results indicate that NGS methods can highlight potential target populations for diagnostics and will prove useful for the evaluation of existing and the development of novel DNA-based detection methods in the field of water microbiology. The used approach allowed unveiling of dominant bacterial populations but failed to detect populations with low abundances such as faecal indicators in surface waters. In combination with metadata, NGS data will also allow the identification of drivers of bacterial community composition during water treatment and distribution, highlighting the power of this approach for monitoring of bacterial regrowth and contamination in technical systems.}, }
@article {pmid26605783, year = {2015}, author = {Sanz, Y}, title = {Microbiome and Gluten.}, journal = {Annals of nutrition &amp; metabolism}, volume = {67 Suppl 2}, number = {}, pages = {28-41}, doi = {10.1159/000440991}, pmid = {26605783}, issn = {1421-9697}, mesh = {Celiac Disease/genetics/*microbiology ; Dysbiosis/complications ; Gastrointestinal Microbiome/*immunology ; Genetic Predisposition to Disease ; Genotype ; Glutens/*adverse effects ; HLA-DQ Antigens ; Humans ; Infant ; Intestines/microbiology ; Prospective Studies ; }, abstract = {Celiac disease (CD) is a frequent chronic inflammatory enteropathy caused by gluten in genetically predisposed individuals that carry disease susceptibility genes (HLA-DQ2/8). These genes are present in about 30-40% of the general population, but only a small percentage of carriers develops CD. Gluten is the key environmental trigger of CD, but its intake does not fully explain disease onset; indeed, an increased number of cases experience gluten intolerance in late adulthood after many years of gluten exposure. Consequently, additional environmental factors seem to be involved in CD. Epidemiological studies indicate that common perinatal and early postnatal factors influence both CD risk and intestinal microbiota structure. Prospective studies in healthy infants at risk of developing CD also reveal that the HLA-DQ genotype, in conjunction with other environmental factors, influences the microbiota composition. Furthermore, CD patients have imbalances in the intestinal microbiota (dysbiosis), which are not fully normalized despite their adherence to a gluten-free diet. Therefore, it is hypothesized that the disease can promote dysbiosis that aggravates CD pathogenesis, and dysbiosis, in turn, can initiate and sustain inflammation through the expansion of proinflammatory pathobionts and decline of anti-inflammatory mutualistic bacteria. Studies in experimental models are also contributing to understand the role of intestinal bacteria and its interactions with a predisposed genotype in promoting CD. Advances in this area could aid in the development of microbiome-informed intervention strategies that optimize the partnership between the gut microbiota and host immunity for improving CD management.}, }
@article {pmid26604364, year = {2015}, author = {Kachouri, F and Ksontini, H and Kraiem, M and Setti, K and Mechmeche, M and Hamdi, M}, title = {Involvement of antioxidant activity of Lactobacillus plantarum on functional properties of olive phenolic compounds.}, journal = {Journal of food science and technology}, volume = {52}, number = {12}, pages = {7924-7933}, pmid = {26604364}, issn = {0022-1155}, abstract = {Eight lactic acid bacteria strains isolated from traditional fermented foods were investigated for their antioxidant activity against DPPH free radicals, β-carotene bleaching assay and linoleic acid test. L. plantarum LAB 1 at a dose of 8.2 10(9) CFU/ml showed the highest DPPH scavenging activity, with inhibition rate of 57.07 ± 0.57 % and an antioxidant activity (TAA = 43.47 ± 0.663 % and AAC = 172.65 ± 5.57), which increase with cell concentrations. When L. plantarum LAB 1 was administered to oxidative enzymes, residual activities decreased significantly with cell concentrations. The use of L. plantarum LAB 1 on olives process, favours the increase of the antioxidant activity (24 %). HPLC results showed a significant increase of orthodiphenols (74 %). Viable cells of strain were implicated directly on minimum media growth with 500 mg/l of olive phenolic compounds. Results showed an increase in their antioxidant activity. CG-SM analysis, identify the presence of compounds with higher antioxidant activity as vinyl phenol and hydroxytyrosol.}, }
@article {pmid26603631, year = {2016}, author = {Desoeuvre, A and Casiot, C and Héry, M}, title = {Diversity and Distribution of Arsenic-Related Genes Along a Pollution Gradient in a River Affected by Acid Mine Drainage.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {672-685}, pmid = {26603631}, issn = {1432-184X}, mesh = {Arsenic/analysis/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/*genetics/metabolism ; Biodegradation, Environmental ; *Biodiversity ; Environmental Pollution ; Mining ; Rivers/chemistry/*microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Some microorganisms have the capacity to interact with arsenic through resistance or metabolic processes. Their activities contribute to the fate of arsenic in contaminated ecosystems. To investigate the genetic potential involved in these interactions in a zone of confluence between a pristine river and an arsenic-rich acid mine drainage, we explored the diversity of marker genes for arsenic resistance (arsB, acr3.1, acr3.2), methylation (arsM), and respiration (arrA) in waters characterized by contrasted concentrations of metallic elements (including arsenic) and pH. While arsB-carrying bacteria were representative of pristine waters, Acr3 proteins may confer to generalist bacteria the capacity to cope with an increase of contamination. arsM showed an unexpected wide distribution, suggesting biomethylation may impact arsenic fate in contaminated aquatic ecosystems. arrA gene survey suggested that only specialist microorganisms (adapted to moderately or extremely contaminated environments) have the capacity to respire arsenate. Their distribution, modulated by water chemistry, attested the specialist nature of the arsenate respirers. This is the first report of the impact of an acid mine drainage on the diversity and distribution of arsenic (As)-related genes in river waters. The fate of arsenic in this ecosystem is probably under the influence of the abundance and activity of specific microbial populations involved in different As biotransformations.}, }
@article {pmid26601194, year = {2015}, author = {Liu, CM and Price, LB and Hungate, BA and Abraham, AG and Larsen, LA and Christensen, K and Stegger, M and Skov, R and Andersen, PS}, title = {Staphylococcus aureus and the ecology of the nasal microbiome.}, journal = {Science advances}, volume = {1}, number = {5}, pages = {e1400216}, pmid = {26601194}, issn = {2375-2548}, support = {R01 AI101371/AI/NIAID NIH HHS/United States ; R15 DE021194/DE/NIDCR NIH HHS/United States ; }, abstract = {The human microbiome can play a key role in host susceptibility to pathogens, including in the nasal cavity, a site favored by Staphylococcus aureus. However, what determines our resident nasal microbiota-the host or the environment-and can interactions among nasal bacteria determine S. aureus colonization? Our study of 46 monozygotic and 43 dizygotic twin pairs revealed that nasal microbiota is an environmentally derived trait, but the host's sex and genetics significantly influence nasal bacterial density. Although specific taxa, including lactic acid bacteria, can determine S. aureus colonization, their negative interactions depend on thresholds of absolute abundance. These findings demonstrate that nasal microbiota is not fixed by host genetics and opens the possibility that nasal microbiota may be manipulated to prevent or eliminate S. aureus colonization.}, }
@article {pmid26599433, year = {2016}, author = {Reboleiro-Rivas, P and Martín-Pascual, J and Morillo, JA and Juárez-Jiménez, B and Poyatos, JM and Rodelas, B and González-López, J}, title = {Interlinkages between bacterial populations dynamics and the operational parameters in a moving bed membrane bioreactor treating urban sewage.}, journal = {Water research}, volume = {88}, number = {}, pages = {796-807}, doi = {10.1016/j.watres.2015.10.059}, pmid = {26599433}, issn = {1879-2448}, mesh = {Bacteria/classification/genetics/*metabolism ; *Bacterial Physiological Phenomena ; Bacterial Proteins/genetics ; Bioreactors ; Membranes, Artificial ; Multivariate Analysis ; Phylogeny ; Sewage/*microbiology ; *Waste Disposal, Fluid ; }, abstract = {Bacteria are key players in biological wastewater treatments (WWTs), thus a firm knowledge of the bacterial population dynamics is crucial to understand environmental/operational factors affecting the efficiency and stability of the biological depuration process. Unfortunately, little is known about the microbial ecology of the advanced biological WWTs combining suspended biomass (SB) and attached biofilms (AB). This study explored in depth the bacterial community structure and population dynamics in each biomass fraction from a pilot-scale moving bed membrane bioreactor (MBMBR) treating municipal sewage, by means of temperature-gradient gel electrophoresis (TGGE) and 454-pyrosequencing. Eight experimental phases were conducted, combining different carrier filling ratios, hydraulic retention times and concentrations of mixed liquor total suspended solids. The bacterial community, dominated by Proteobacteria (20.9-53.8%) and Actinobacteria (20.6-57.6%), was very similar in both biomass fractions and able to maintain its functional stability under all the operating conditions, ensuring a successful and steady depuration process. Multivariate statistical analysis demonstrated that solids concentration, carrier filling ratio, temperature and organic matter concentration in the influent were the significant factors explaining population dynamics. Bacterial diversity increased as carrier filling ratio increased (from 20% to 35%, v/v), and solids concentration was the main factor triggering the shifts of the community structure. These findings provide new insights on the influence of operational parameters on the biology of the innovative MBMBRs.}, }
@article {pmid26598213, year = {2015}, author = {Logares, R and Mangot, JF and Massana, R}, title = {Rarity in aquatic microbes: placing protists on the map.}, journal = {Research in microbiology}, volume = {166}, number = {10}, pages = {831-841}, doi = {10.1016/j.resmic.2015.09.009}, pmid = {26598213}, issn = {1769-7123}, mesh = {Aquatic Organisms/*genetics ; Biodiversity ; *Ecosystem ; Eukaryota/*genetics ; Genes, rRNA ; High-Throughput Nucleotide Sequencing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Most microbial richness at any given time tends to be represented by low-abundance (rare) taxa, which are collectively referred to as the "rare biosphere". Here we review works on the rare biosphere using high-throughput sequencing (HTS), with a particular focus on unicellular eukaryotes or protists. Evidence thus far indicates that the rare biosphere encompasses dormant as well as metabolically active microbes that could potentially play key roles in ecosystem functioning. Rare microbes appear to have biogeography, and sometimes the observed patterns can be similar to what is observed among abundant taxa, suggesting similar community-structuring mechanisms. There is limited evidence indicating that the rare biosphere contains taxa that are phylogenetically distantly related to abundant counterparts; therefore, the rare biosphere may act as a reservoir of deep-branching phylogenetic diversity. The potential role of the rare biosphere as a bank of redundant functions that can help to maintain continuous ecosystem function following oscillations in taxonomic abundances is hypothesized as its main ecological role. Future studies focusing on rare microbes are crucial for advancing our knowledge of microbial ecology and evolution and unveiling their links with ecosystem function.}, }
@article {pmid26597961, year = {2016}, author = {Bor, B and Poweleit, N and Bois, JS and Cen, L and Bedree, JK and Zhou, ZH and Gunsalus, RP and Lux, R and McLean, JS and He, X and Shi, W}, title = {Phenotypic and Physiological Characterization of the Epibiotic Interaction Between TM7x and Its Basibiont Actinomyces.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {243-255}, pmid = {26597961}, issn = {1432-184X}, support = {F32 DE025548/DE/NIDCR NIH HHS/United States ; R01 DE020102/DE/NIDCR NIH HHS/United States ; 1R01DE023810-01/DE/NIDCR NIH HHS/United States ; R00 DE027719/DE/NIDCR NIH HHS/United States ; R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 GM095373/GM/NIGMS NIH HHS/United States ; T90 DE022734/DE/NIDCR NIH HHS/United States ; }, mesh = {Actinomyces/genetics/growth &amp; development/isolation &amp; purification/*physiology ; Bacteria/genetics/growth &amp; development/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Humans ; Mouth/*microbiology ; Phenotype ; Symbiosis ; }, abstract = {Despite many examples of obligate epibiotic symbiosis (one organism living on the surface of another) in nature, such an interaction has rarely been observed between two bacteria. Here, we further characterize a newly reported interaction between a human oral obligate parasitic bacterium TM7x (cultivated member of Candidatus Saccharimonas formerly Candidate Phylum TM7), and its basibiont Actinomyces odontolyticus species (XH001), providing a model system to study epiparasitic symbiosis in the domain Bacteria. Detailed microscopic studies indicate that both partners display extensive morphological changes during symbiotic growth. XH001 cells manifested as short rods in monoculture, but displayed elongated and hyphal morphology when physically associated with TM7x. Interestingly, these dramatic morphological changes in XH001 were also induced in oxygen-depleted conditions, even in the absence of TM7x. Targeted quantitative real-time PCR (qRT-PCR) analyses revealed that both the physical association with TM7x as well as oxygen depletion triggered up-regulation of key stress response genes in XH001, and in combination, these conditions act in an additive manner. TM7x and XH001 co-exist with relatively uniform cell morphologies under nutrient-replete conditions. However, upon nutrient depletion, TM7x-associated XH001 displayed a variety of cell morphologies, including swollen cell body, clubbed-ends, and even cell lysis, and a large portion of TM7x cells transformed from ultrasmall cocci into elongated cells. Our study demonstrates a highly dynamic interaction between epibiont TM7x and its basibiont XH001 in response to physical association or environmental cues such as oxygen level and nutritional status, as reflected by their morphological and physiological changes during symbiotic growth.}, }
@article {pmid26597167, year = {2016}, author = {Selma, MV and Romo-Vaquero, M and García-Villalba, R and González-Sarrías, A and Tomás-Barberán, FA and Espín, JC}, title = {The human gut microbial ecology associated with overweight and obesity determines ellagic acid metabolism.}, journal = {Food &amp; function}, volume = {7}, number = {4}, pages = {1769-1774}, doi = {10.1039/c5fo01100k}, pmid = {26597167}, issn = {2042-650X}, mesh = {Actinobacteria/genetics/isolation &amp; purification/metabolism ; Adult ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodiversity ; Coumarins/chemistry/metabolism ; Ellagic Acid/*metabolism ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; Obesity/*metabolism/*microbiology ; Overweight/*metabolism/*microbiology ; }, abstract = {We recently identified three metabotypes (0, A and B) that depend on the metabolic profile of urolithins produced from polyphenol ellagic acid (EA). The gut microbiota and Gordonibacter spp. recently were identified as species able to produce urolithins. A higher percentage of metabotype B was found in patients with metabolic syndrome or colorectal cancer in comparison with healthy individuals. The aim of the present study was to analyse differences in EA metabolism between healthy overweight-obese and normoweight individuals and evaluate the role of gut microbial composition including Gordonibacter. Although the three metabotypes were confirmed in both groups, metabotype B prevailed in overweight-obese (31%) versus normoweight (20%) individuals while metabotype A was higher in normoweight (70%) than the overweight-obese group (57%). This suggests that weight gain favours the growth of bacteria capable of producing urolithin B and/or isourolithin A with respect to urolithin A-producing bacteria. Gordonibacter spp. levels were not significantly different between normoweight and overweight-obese groups but higher Gordonibacter levels were found in metabotype A individuals than in those with metabotype B. Other bacterial species have been reported to show a much closer relationship to obesity and dysbiosis than Gordonibacter. However, Gordonibacter levels are negatively correlated with metabotype B, which prevails in metabolic syndrome and colorectal cancer. This is the first report that links overweight and obesity with an alteration in the catabolism of EA, and where the correlation of Gordonibacter to this alteration is shown. Future investigation of Gordonibacter and urolithin metabotypes as potential biomarkers or therapeutic targets of obesity-related diseases is warranted.}, }
@article {pmid26597042, year = {2015}, author = {de Bruijn, I and Cheng, X and de Jager, V and Expósito, RG and Watrous, J and Patel, N and Postma, J and Dorrestein, PC and Kobayashi, D and Raaijmakers, JM}, title = {Comparative genomics and metabolic profiling of the genus Lysobacter.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {991}, pmid = {26597042}, issn = {1471-2164}, mesh = {*Genomics ; Lysobacter/*genetics/*metabolism/physiology ; *Metabolomics ; Movement ; Multigene Family ; Rhizoctonia/physiology ; }, abstract = {BACKGROUND: Lysobacter species are Gram-negative bacteria widely distributed in soil, plant and freshwater habitats. Lysobacter owes its name to the lytic effects on other microorganisms. To better understand their ecology and interactions with other (micro)organisms, five Lysobacter strains representing the four species L. enzymogenes, L. capsici, L. gummosus and L. antibioticus were subjected to genomics and metabolomics analyses.<br><br>RESULTS: Comparative genomics revealed a diverse genome content among the Lysobacter species with a core genome of 2,891 and a pangenome of 10,028 coding sequences. Genes encoding type I, II, III, IV, V secretion systems and type IV pili were highly conserved in all five genomes, whereas type VI secretion systems were only found in L. enzymogenes and L. gummosus. Genes encoding components of the flagellar apparatus were absent in the two sequenced L. antibioticus strains. The genomes contained a large number of genes encoding extracellular enzymes including chitinases, glucanases and peptidases. Various nonribosomal peptide synthase (NRPS) and polyketide synthase (PKS) gene clusters encoding putative bioactive metabolites were identified but only few of these clusters were shared between the different species. Metabolic profiling by imaging mass spectrometry complemented, in part, the in silico genome analyses and allowed visualisation of the spatial distribution patterns of several secondary metabolites produced by or induced in Lysobacter species during interactions with the soil-borne fungus Rhizoctonia solani.<br><br>CONCLUSIONS: Our work shows that mining the genomes of Lysobacter species in combination with metabolic profiling provides novel insights into the genomic and metabolic potential of this widely distributed but understudied and versatile bacterial genus.}, }
@article {pmid26595550, year = {2016}, author = {Lopez-Siles, M and Martinez-Medina, M and Surís-Valls, R and Aldeguer, X and Sabat-Mir, M and Duncan, SH and Flint, HJ and Garcia-Gil, LJ}, title = {Changes in the Abundance of Faecalibacterium prausnitzii Phylogroups I and II in the Intestinal Mucosa of Inflammatory Bowel Disease and Patients with Colorectal Cancer.}, journal = {Inflammatory bowel diseases}, volume = {22}, number = {1}, pages = {28-41}, doi = {10.1097/MIB.0000000000000590}, pmid = {26595550}, issn = {1536-4844}, mesh = {Adult ; Case-Control Studies ; Cohort Studies ; Colorectal Neoplasms/diagnosis/epidemiology/genetics/*microbiology ; DNA, Bacterial/genetics ; Female ; Follow-Up Studies ; Gram-Positive Bacteria/*classification/genetics/*isolation &amp; purification ; Gram-Positive Bacterial Infections/diagnosis/epidemiology/genetics/*microbiology ; Humans ; Inflammatory Bowel Diseases/diagnosis/epidemiology/genetics/*microbiology ; Intestinal Mucosa/*microbiology ; Male ; Middle Aged ; Phylogeny ; Prevalence ; Prognosis ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; }, abstract = {BACKGROUND: Faecalibacterium prausnitzii comprises 2 phylogroups, whose abundance in healthy and diseased gut and in conjunction with Escherichia coli has not yet been studied. This work aims to determine the contribution of F. prausnitzii phylogroups I and II in intestinal disease and to assess their potential diagnostic usefulness as biomarkers for gut diseases.<br><br>METHODS: Total F. prausnitzii, its phylogroups, and E. coli loads were determined by quantitative polymerase chain reaction targeting the 16S rRNA gene on biopsies from 31 healthy controls (H), 45 patients with Crohn's disease (CD), 25 patients with ulcerative colitis, 10 patients with irritable bowel syndrome, and 20 patients with colorectal cancer. Data were normalized to total bacterial counts and analyzed according to patients' disease location and clinical characteristics.<br><br>RESULTS: Lower levels of both total F. prausnitzii and phylogroup I were found in subjects with CD, ulcerative colitis, and colorectal cancer (P < 0.001) compared with H subjects. Phylogroup I load was a better biomarker than total F. prausnitzii to discriminate subjects with gut disorders from H. Phylogroup II depletion was observed only in patients with CD (P < 0.001) and can be potentially applied to differentiate ulcerative pancolitis from colonic CD. No statistically significant correlation between E. coli and any of the 2 F. prausnitzii phylogroups was found in any group of patients or by inflammatory bowel disease location. Phylogroup I was lower in active patients with CD, whereas those CD with intestinal resection showed a reduction in phylogroup II. Treatments with mesalazine and immunosuppressants did not result in the recovery of F. prausnitzii phylogroups abundance.<br><br>CONCLUSIONS: F. prausnitzii phylogroup I was depleted in CD, ulcerative colitis, and colorectal cancer, whereas phylogroup II was specifically reduced in CD. Quantification of F. prausnitzii phylogroups and E. coli may help to identify gut disorders and to classify inflammatory bowel disease location.}, }
@article {pmid26590289, year = {2016}, author = {Zablocki, O and Adriaenssens, EM and Cowan, D}, title = {Diversity and Ecology of Viruses in Hyperarid Desert Soils.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {3}, pages = {770-777}, pmid = {26590289}, issn = {1098-5336}, mesh = {Bacteriophages/classification/genetics/isolation &amp; purification/*physiology ; *Desert Climate ; *Ecosystem ; *Genetic Variation ; Genome, Viral ; Phylogeny ; RNA, Ribosomal, 16S ; *Soil Microbiology ; Virus Physiological Phenomena ; Viruses/classification/genetics/isolation &amp; purification ; }, abstract = {In recent years, remarkable progress has been made in the field of virus environmental ecology. In marine ecosystems, for example, viruses are now thought to play pivotal roles in the biogeochemical cycling of nutrients and to be mediators of microbial evolution through horizontal gene transfer. The diversity and ecology of viruses in soils are poorly understood, but evidence supports the view that the diversity and ecology of viruses in soils differ substantially from those in aquatic systems. Desert biomes cover ∼ 33% of global land masses, and yet the diversity and roles of viruses in these dominant ecosystems remain poorly understood. There is evidence that hot hyperarid desert soils are characterized by high levels of bacterial lysogens and low extracellular virus counts. In contrast, cold desert soils contain high extracellular virus titers. We suggest that the prevalence of microbial biofilms in hyperarid soils, combined with extreme thermal regimens, exerts strong selection pressures on both temperate and virulent viruses. Many desert soil virus sequences show low values of identity to virus genomes in public databases, suggesting the existence of distinct and as-yet-uncharacterized soil phylogenetic lineages (e.g., cyanophages). We strongly advocate for amplification-free metavirome analyses while encouraging the classical isolation of phages from dominant and culturable microbial isolates in order to populate sequence databases. This review provides an overview of recent advances in the study of viruses in hyperarid soils and of the factors that contribute to viral abundance and diversity in hot and cold deserts and offers technical recommendations for future studies.}, }
@article {pmid26587819, year = {2015}, author = {Yallapragada, SG and Nash, CB and Robinson, DT}, title = {Early-Life Exposure to Antibiotics, Alterations in the Intestinal Microbiome, and Risk of Metabolic Disease in Children and Adults.}, journal = {Pediatric annals}, volume = {44}, number = {11}, pages = {e265-9}, doi = {10.3928/00904481-20151112-09}, pmid = {26587819}, issn = {1938-2359}, mesh = {Anti-Bacterial Agents/*adverse effects ; Child, Preschool ; Gastrointestinal Microbiome/*drug effects/physiology ; Humans ; Infant ; Metabolic Diseases/*etiology ; }, abstract = {The intestinal microbiome is a complex ecosystem of microorganisms that colonize the human gastrointestinal tract. The microbiome evolves rapidly in early life with contributions from diet, genetics and immunomodulatory factors. Changes in composition of the microbiota due to antibiotics may lead to negative long-term effects including obesity and diabetes mellitus, as evidenced by both animal and large human studies. Inappropriate exposures to antibiotics occur frequently in early childhood. Therefore, an evidence-based system of antimicrobial use should be employed by all providers, especially those who care for pediatric patients. This article explores the natural evolution of the intestinal microbiome from the perinatal period into early childhood, the effect of antibiotics on the microbial ecology, and the implications for future health and disease.}, }
@article {pmid26586902, year = {2015}, author = {Ehsani, E and Jauregui, R and Geffers, R and Jarek, M and Boon, N and Pieper, DH and Vilchez-Vargas, R}, title = {First Draft Genome Sequence of the Acidovorax caeni sp. nov. Type Strain R-24608 (DSM 19327).}, journal = {Genome announcements}, volume = {3}, number = {6}, pages = {}, pmid = {26586902}, issn = {2169-8287}, abstract = {We report the draft genome sequence of the Acidovorax caeni type strain R-24608 that was isolated from activated sludge of an aerobic-anaerobic wastewater treatment plant. The closest strain to Acidovorax caeni strain R-24608 is Acidovorax sp. strain MR-S7 with a 55.4% (amino-acid sequence) open reading frames (ORFs) average similarity.}, }
@article {pmid26586898, year = {2015}, author = {Boukerb, AM and Marti, R and Cournoyer, B}, title = {Genome Sequences of Three Strains of the Pseudomonas aeruginosa PA7 Clade.}, journal = {Genome announcements}, volume = {3}, number = {6}, pages = {}, pmid = {26586898}, issn = {2169-8287}, abstract = {Draft genome sequences of three P. aeruginosa strains from the PA7 clade are presented here. Their lengths are 6.36 (EML528), 6.44 (EML545), and 6.33 Mb (EML548). Comparisons with the PA7 genome showed 5,113 conserved coding sequences (CDSs), and significant numbers of strain-specific CDSs. Their analysis will improve our understanding of this highly divergent clade.}, }
@article {pmid26586809, year = {2016}, author = {Greuter, D and Loy, A and Horn, M and Rattei, T}, title = {probeBase--an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016.}, journal = {Nucleic acids research}, volume = {44}, number = {D1}, pages = {D586-9}, pmid = {26586809}, issn = {1362-4962}, support = {281633/ERC_/European Research Council/International ; I 1628/FWF_/Austrian Science Fund FWF/Austria ; I 2320/FWF_/Austrian Science Fund FWF/Austria ; P 25111/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Computer Simulation ; DNA Primers/*chemistry ; *Databases, Nucleic Acid ; Internet ; Nucleic Acid Hybridization ; Oligonucleotide Probes/*chemistry ; RNA, Ribosomal/*chemistry ; Sequence Analysis, RNA ; }, abstract = {probeBase http://www.probebase.net is a manually maintained and curated database of rRNA-targeted oligonucleotide probes and primers. Contextual information and multiple options for evaluating in silico hybridization performance against the most recent rRNA sequence databases are provided for each oligonucleotide entry, which makes probeBase an important and frequently used resource for microbiology research and diagnostics. Here we present a major update of probeBase, which was last featured in the NAR Database Issue 2007. This update describes a complete remodeling of the database architecture and environment to accommodate computationally efficient access. Improved search functions, sequence match tools and data output now extend the opportunities for finding suitable hierarchical probe sets that target an organism or taxon at different taxonomic levels. To facilitate the identification of complementary probe sets for organisms represented by short rRNA sequence reads generated by amplicon sequencing or metagenomic analysis with next generation sequencing technologies such as Illumina and IonTorrent, we introduce a novel tool that recovers surrogate near full-length rRNA sequences for short query sequences and finds matching oligonucleotides in probeBase.}, }
@article {pmid26585302, year = {2016}, author = {Rungrassamee, W and Klanchui, A and Maibunkaew, S and Karoonuthaisiri, N}, title = {Bacterial dynamics in intestines of the black tiger shrimp and the Pacific white shrimp during Vibrio harveyi exposure.}, journal = {Journal of invertebrate pathology}, volume = {133}, number = {}, pages = {12-19}, doi = {10.1016/j.jip.2015.11.004}, pmid = {26585302}, issn = {1096-0805}, mesh = {Animals ; Biodiversity ; *Disease Resistance ; *Gastrointestinal Microbiome ; Penaeidae/*microbiology ; Vibrio/*physiology ; }, abstract = {The intestinal microbiota play important roles in health of their host, contributing to maintaining the balance and resilience against pathogen. To investigate effects of pathogen to intestinal microbiota, the bacterial dynamics upon a shrimp pathogen, Vibrio harveyi, exposures were determined in two economically important shrimp species; the black tiger shrimp (BT) and the Pacific white shrimp (PW). Both shrimp species were reared under the same diet and environmental conditions. Shrimp survival rates after the V. harveyi exposure revealed that the PW shrimp had a higher resistance to the pathogen than the BT shrimp. The intestinal bacterial profiles were determined by denaturing gradient gel electrophoresis (DGGE) and barcoded pyrosequencing of the 16S rRNA sequences under no pathogen challenge control and under pathogenic V. harveyi challenge. The DGGE profiles showed that the presence of V. harveyi altered the intestinal bacterial patterns in comparison to the control in BT and PW intestines. This implies that bacterial balance in shrimp intestines was disrupted in the presence of V. harveyi. The barcoded pyrosequencing analysis showed the similar bacterial community structures in intestines of BT and PW shrimp under a normal condition. However, during the time course exposure to V. harveyi, the relative abundance of bacteria belong to Vibrio genus was higher in the BT intestines at 12h after the exposure, whereas relative abundance of vibrios was more stable in PW intestines. The principle coordinates analysis based on weighted-UniFrac analysis showed that intestinal bacterial population in the BT shrimp lost their ability to restore their bacterial balance during the 72-h period of exposure to the pathogen, while the PW shrimp were able to reestablish their bacterial population to resemble those seen in the unexposed control group. This observation of bacterial disruption might correlate to different mortality rates observed between the two shrimp species. Our findings provide evidence of intestinal bacterial population altered by a presence of the pathogen in shrimp intestines and intestinal bacterial stability might provide colonization resistance against the invading pathogen in the host shrimp. Hence, intestinal microbial ecology management may potentially contribute to disease prevention in aquaculture.}, }
@article {pmid26585119, year = {2016}, author = {Lucheta, AR and Cannavan, Fde S and Roesch, LF and Tsai, SM and Kuramae, EE}, title = {Fungal Community Assembly in the Amazonian Dark Earth.}, journal = {Microbial ecology}, volume = {71}, number = {4}, pages = {962-973}, pmid = {26585119}, issn = {1432-184X}, mesh = {Biodiversity ; Brazil ; Ecology ; Fungi/classification/genetics/*growth &amp; development ; Phylogeny ; RNA, Ribosomal, 18S ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Here, we compare the fungal community composition and diversity in Amazonian Dark Earth (ADE) and the respective non-anthropogenic origin adjacent (ADJ) soils from four different sites in Brazilian Central Amazon using pyrosequencing of 18S ribosomal RNA (rRNA) gene. Fungal community composition in ADE soils were more similar to each other than their ADJ soils, except for only one site. Phosphorus and aluminum saturation were the main soil chemical factors contributing to ADE and ADJ fungal community dissimilarities. Differences in fungal richness were not observed between ADE and ADJ soil pairs regarding to the most sites. In general, the most dominant subphyla present in the soils were Pezizomycotina, Agaricomycotina, and Mortierellomycotina. The most abundant operational taxonomic units (OTUs) in ADE showed similarities with the entomopathogenic fungus Cordyceps confragosa and the saprobes Fomitopsis pinicola, Acremonium vitellinum, and Mortierellaceae sp., whereas OTUs similar to Aspergillus niger, Lithothelium septemseptatum, Heliocephala gracillis, and Pestalosphaeria sp. were more abundant in ADJ soils. Differences in fungal community composition were associated to soil chemical factors in ADE (P, Ca, Zn, Mg, organic matter, sum of bases, and base saturation) and ADJ (Al, potential acidity, Al saturation, B, and Fe) soils. These results contribute to a deeper view of the fungi communities in ADE and open new perspectives for entomopathogenic fungi studies.}, }
@article {pmid26583015, year = {2015}, author = {Erşan, Y&#xc7; and Gruyaert, E and Louis, G and Lors, C and De Belie, N and Boon, N}, title = {Self-protected nitrate reducing culture for intrinsic repair of concrete cracks.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1228}, pmid = {26583015}, issn = {1664-302X}, abstract = {Attentive monitoring and regular repair of concrete cracks are necessary to avoid further durability problems. As an alternative to current maintenance methods, intrinsic repair systems which enable self-healing of cracks have been investigated. Exploiting microbial induced CaCO3 precipitation (MICP) using (protected) axenic cultures is one of the proposed methods. Yet, only a few of the suggested healing agents were economically feasible for in situ application. This study presents a [Formula: see text] reducing self-protected enrichment culture as a self-healing additive for concrete. Concrete admixtures Ca(NO3)2 and Ca(HCOO)2 were used as nutrients. The enrichment culture, grown as granules (0.5-2 mm) consisting of 70% biomass and 30% inorganic salts were added into mortar without any additional protection. Upon 28 days curing, mortar specimens were subjected to direct tensile load and multiple cracks (0.1-0.6 mm) were achieved. Cracked specimens were immersed in water for 28 days and effective crack closure up to 0.5 mm crack width was achieved through calcite precipitation. Microbial activity during crack healing was monitored through weekly NOx analysis which revealed that 92 ± 2% of the available [Formula: see text] was consumed. Another set of specimens were cracked after 6 months curing, thus the effect of curing time on healing efficiency was investigated, and mineral formation at the inner crack surfaces was observed, resulting in 70% less capillary water absorption compared to healed control specimens. In conclusion, enriched mixed denitrifying cultures structured in self-protecting granules are very promising strategies to enhance microbial self-healing.}, }
@article {pmid26583011, year = {2015}, author = {Balcázar, JL and Subirats, J and Borrego, CM}, title = {The role of biofilms as environmental reservoirs of antibiotic resistance.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1216}, pmid = {26583011}, issn = {1664-302X}, abstract = {Antibiotic resistance has become a significant and growing threat to public and environmental health. To face this problem both at local and global scales, a better understanding of the sources and mechanisms that contribute to the emergence and spread of antibiotic resistance is required. Recent studies demonstrate that aquatic ecosystems are reservoirs of resistant bacteria and antibiotic resistance genes as well as potential conduits for their transmission to human pathogens. Despite the wealth of information about antibiotic pollution and its effect on the aquatic microbial resistome, the contribution of environmental biofilms to the acquisition and spread of antibiotic resistance has not been fully explored in aquatic systems. Biofilms are structured multicellular communities embedded in a self-produced extracellular matrix that acts as a barrier to antibiotic diffusion. High population densities and proximity of cells in biofilms also increases the chances for genetic exchange among bacterial species converting biofilms in hot spots of antibiotic resistance. This review focuses on the potential effect of antibiotic pollution on biofilm microbial communities, with special emphasis on ecological and evolutionary processes underlying acquired resistance to these compounds.}, }
@article {pmid26583008, year = {2015}, author = {Hemme, CL and Tu, Q and Shi, Z and Qin, Y and Gao, W and Deng, Y and Nostrand, JD and Wu, L and He, Z and Chain, PS and Tringe, SG and Fields, MW and Rubin, EM and Tiedje, JM and Hazen, TC and Arkin, AP and Zhou, J}, title = {Comparative metagenomics reveals impact of contaminants on groundwater microbiomes.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1205}, pmid = {26583008}, issn = {1664-302X}, abstract = {To understand patterns of geochemical cycling in pristine versus contaminated groundwater ecosystems, pristine shallow groundwater (FW301) and contaminated groundwater (FW106) samples from the Oak Ridge Integrated Field Research Center (OR-IFRC) were sequenced and compared to each other to determine phylogenetic and metabolic difference between the communities. Proteobacteria (e.g., Burkholderia, Pseudomonas) are the most abundant lineages in the pristine community, though a significant proportion (>55%) of the community is composed of poorly characterized low abundance (individually <1%) lineages. The phylogenetic diversity of the pristine community contributed to a broader diversity of metabolic networks than the contaminated community. In addition, the pristine community encodes redundant and mostly complete geochemical cycles distributed over multiple lineages and appears capable of a wide range of metabolic activities. In contrast, many geochemical cycles in the contaminated community appear truncated or minimized due to decreased biodiversity and dominance by Rhodanobacter populations capable of surviving the combination of stresses at the site. These results indicate that the pristine site contains more robust and encodes more functional redundancy than the stressed community, which contributes to more efficient nutrient cycling and adaptability than the stressed community.}, }
@article {pmid26582318, year = {2016}, author = {Tahon, G and Tytgat, B and Stragier, P and Willems, A}, title = {Analysis of cbbL, nifH, and pufLM in Soils from the Sør Rondane Mountains, Antarctica, Reveals a Large Diversity of Autotrophic and Phototrophic Bacteria.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {131-149}, pmid = {26582318}, issn = {1432-184X}, mesh = {Antarctic Regions ; Autotrophic Processes ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Bacterial Proteins/*genetics ; *Biodiversity ; DNA, Bacterial/genetics ; Dinitrogenase Reductase/*genetics ; Phototrophic Processes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Cyanobacteria are generally thought to be responsible for primary production and nitrogen fixation in the microbial communities that dominate Antarctic ecosystems. Recent studies of bacterial communities in terrestrial Antarctica, however, have shown that Cyanobacteria are sometimes only scarcely present, suggesting that other bacteria presumably take over their role as primary producers and diazotrophs. The diversity of key genes in these processes was studied in surface samples from the Sør Rondane Mountains, Dronning Maud Land, using clone libraries of the large subunit of ribulose-1,5-biphosphate carboxylase/oxygenase (RuBisCO) genes (cbbL, cbbM) and dinitrogenase-reductase (nifH) genes. We recovered a large diversity of non-cyanobacterial cbbL type IC in addition to cyanobacterial type IB, suggesting that non-cyanobacterial autotrophs may contribute to primary production. The nifH diversity recovered was predominantly related to Cyanobacteria, particularly members of the Nostocales. We also investigated the occurrence of proteorhodopsin and anoxygenic phototrophy as mechanisms for non-Cyanobacteria to exploit solar energy. While proteorhodopsin genes were not detected, a large diversity of genes coding for the light and medium subunits of the type 2 phototrophic reaction center (pufLM) was observed, suggesting for the first time, that the aerobic photoheterotrophic lifestyle may be important in oligotrophic high-altitude ice-free terrestrial Antarctic habitats.}, }
@article {pmid26582010, year = {2016}, author = {Foesel, BU and Geppert, A and Rohde, M and Overmann, J}, title = {Parviterribacter kavangonensis gen. nov., sp. nov. and Parviterribacter multiflagellatus sp. nov., novel members of Parviterribacteraceae fam. nov. within the order Solirubrobacterales, and emended descriptions of the classes Thermoleophilia and Rubrobacteria and their orders and families.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {66}, number = {2}, pages = {652-665}, doi = {10.1099/ijsem.0.000770}, pmid = {26582010}, issn = {1466-5034}, abstract = {Two Gram-type-positive, non-spore-forming bacteria, strains D16/0/H6[T] and A22/0/F9_1[T], were isolated from Namibian semiarid savannah soils. 16S rRNA gene sequence analysis revealed 96.6 % identity between the two strains and placed them within the order Solirubrobacterales of the class Thermoleophilia. The closest phylogenetic relatives with validly published names were several strains of the genus Solirubrobacter and the species Conexibacter arvalis, with pairwise sequence similarities of ≤ 94.0 %. Cells of strain D16/0/H6[T] were ovoid to rod-shaped, whereas strain A22/0/F9_1[T] formed regular rods. Cells of both strains were motile and divided by binary fission. Colonies were pink and white to pale yellowish/brownish, respectively. Strains D16/0/H6[T] and A22/0/F9_1[T] were aerobic, chemoheterotrophic mesophiles with broad temperature (13-43 and 17-43 °C, respectively) and pH (pH 4.5-8.5 and 5.0-9.5) ranges for growth. Complex proteinaceous substrates and glucose were the preferred carbon and energy sources. Strain A22/0/F9_1[T] also grew on various carboxylic acids. For both strains, the peptidoglycan diamino acid was meso-2,6-diaminopimelic acid. The major quinone was MK-8. As a minor compound, MK-7 occurred in strain D16/0/H6[T]; strain A22/0F9_1[T] also contained MK-7, MK-7(H2) and MK-8(H2). Major fatty acids of strain D16/0/H6[T] were 10-methyl C17 : 0, iso-C16 : 0 and C18 : 1ω9c. Strain A22/0F9_1[T] contained C18 : 1ω9c, C17 : 1ω8c, C17 : 1ω6c and iso-C16 : 0 as major components. The DNA G+C contents of strains D16/0/H6[T] and A22/0/F9_1[T] were 72.8 and 74.0 mol%, respectively. Based on these characteristics, the two isolates are assigned to novel species of the new genus Parviterribacter gen. nov., the type species Parviterribacter kavangonensis sp. nov. (type strain D16/0/H6[T] = DSM 25205[T] = LMG 26950[T]) and a second species Parviterribacter multiflagellatus sp. nov. (type strain A22/0/F9_1[T] = DSM 25204[T] = LMG 26949[T]). As the novel genus and species cannot be clearly assigned to an established family within the order Solirubrobacterales, the novel family Parviterribacteraceae fam. nov. is proposed. Emended descriptions of the classes Thermoleophilia and Rubrobacteria and their orders and families are also provided.}, }
@article {pmid26579111, year = {2015}, author = {Schulz-Bohm, K and Zweers, H and de Boer, W and Garbeva, P}, title = {A fragrant neighborhood: volatile mediated bacterial interactions in soil.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1212}, pmid = {26579111}, issn = {1664-302X}, abstract = {There is increasing evidence that volatile organic compounds (VOCs) play essential roles in communication and competition between soil microorganisms. Here we assessed volatile-mediated interactions of a synthetic microbial community in a model system that mimics the natural conditions in the heterogeneous soil environment along the rhizosphere. Phylogenetic different soil bacterial isolates (Burkholderia sp., Dyella sp., Janthinobacterium sp., Pseudomonas sp., and Paenibacillus sp.) were inoculated as mixtures or monoculture in organic-poor, sandy soil containing artificial root exudates (ARE) and the volatile profile and growth were analyzed. Additionally, a two-compartment system was used to test if volatiles produced by inter-specific interactions in the rhizosphere can stimulate the activity of starving bacteria in the surrounding, nutrient-depleted soil. The obtained results revealed that both microbial interactions and shifts in microbial community composition had a strong effect on the volatile emission. Interestingly, the presence of a slow-growing, low abundant Paenibacillus strain significantly affected the volatile production by the other abundant members of the bacterial community as well as the growth of the interacting strains. Furthermore, volatiles released by mixtures of root-exudates consuming bacteria stimulated the activity and growth of starved bacteria. Besides growth stimulation, also an inhibition in growth was observed for starving bacteria exposed to microbial volatiles. The current work suggests that volatiles produced during microbial interactions in the rhizosphere have a significant long distance effect on microorganisms in the surrounding, nutrient-depleted soil.}, }
@article {pmid26579098, year = {2015}, author = {Sanli, K and Bengtsson-Palme, J and Nilsson, RH and Kristiansson, E and Alm Rosenblad, M and Blanck, H and Eriksson, KM}, title = {Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1192}, pmid = {26579098}, issn = {1664-302X}, abstract = {Periphyton communities are complex phototrophic, multispecies biofilms that develop on surfaces in aquatic environments. These communities harbor a large diversity of organisms comprising viruses, bacteria, algae, fungi, protozoans, and metazoans. However, thus far the total biodiversity of periphyton has not been described. In this study, we use metagenomics to characterize periphyton communities from the marine environment of the Swedish west coast. Although we found approximately ten times more eukaryotic rRNA marker gene sequences compared to prokaryotic, the whole metagenome-based similarity searches showed that bacteria constitute the most abundant phyla in these biofilms. We show that marine periphyton encompass a range of heterotrophic and phototrophic organisms. Heterotrophic bacteria, including the majority of proteobacterial clades and Bacteroidetes, and eukaryotic macro-invertebrates were found to dominate periphyton. The phototrophic groups comprise Cyanobacteria and the alpha-proteobacterial genus Roseobacter, followed by different micro- and macro-algae. We also assess the metabolic pathways that predispose these communities to an attached lifestyle. Functional indicators of the biofilm form of life in periphyton involve genes coding for enzymes that catalyze the production and degradation of extracellular polymeric substances, mainly in the form of complex sugars such as starch and glycogen-like meshes together with chitin. Genes for 278 different transporter proteins were detected in the metagenome, constituting the most abundant protein complexes. Finally, genes encoding enzymes that participate in anaerobic pathways, such as denitrification and methanogenesis, were detected suggesting the presence of anaerobic or low-oxygen micro-zones within the biofilms.}, }
@article {pmid26579082, year = {2015}, author = {Zwirglmaier, K and Keiz, K and Engel, M and Geist, J and Raeder, U}, title = {Seasonal and spatial patterns of microbial diversity along a trophic gradient in the interconnected lakes of the Osterseen Lake District, Bavaria.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1168}, pmid = {26579082}, issn = {1664-302X}, abstract = {The Osterseen Lake District in Bavaria consists of 19 small interconnected lakes that exhibit a pronounced trophic gradient from eutrophic to oligotrophic. It therefore presents a unique model system to address ecological questions regarding niche adaptation and Baas Becking's long standing hypothesis of "everything is everywhere, but the environment selects." Here, we present the first assessment of the microbial diversity in these lakes. We sampled the lakes in August and December and used 454 pyrosequencing of 16S rRNA amplicons to analyze the microbial diversity. The diversity patterns between lakes and seasons were compared and the bacterial community composition was correlated with key chemical and physical parameters. Distinct patterns of bacterial diversity only emerged at the level of individual OTUs (operational taxonomic units), but not at the level of the major bacterial phyla. This emphasizes the high functional and physiological diversity among bacterial species within a phylum and calls for analysis of biodiversity at the level of OTUs in order to understand fine-scale biogeography. We were able to identify a number of cosmopolitan OTUs as well as specialist OTUs that were restricted to certain lakes or seasons, suggesting adaptation to specific ecological niches.}, }
@article {pmid26578245, year = {2016}, author = {Stone, W and Kroukamp, O and Moes, A and McKelvie, J and Korber, DR and Wolfaardt, GM}, title = {Measuring microbial metabolism in atypical environments: Bentonite in used nuclear fuel storage.}, journal = {Journal of microbiological methods}, volume = {120}, number = {}, pages = {79-90}, doi = {10.1016/j.mimet.2015.11.006}, pmid = {26578245}, issn = {1872-8359}, mesh = {Aluminum Silicates/analysis/chemistry ; Bentonite/*analysis/chemistry ; Biomass ; Clay ; Environmental Microbiology ; Fluorometry ; Geologic Sediments/microbiology ; Hydrogen-Ion Concentration ; *Metabolome ; Microbiological Techniques/*methods ; Nuclear Energy ; Polymerase Chain Reaction ; Radioactive Waste/*analysis ; Silicon Dioxide/chemistry ; *Soil Microbiology ; Water Microbiology ; }, abstract = {Genomics enjoys overwhelming popularity in the study of microbial ecology. However, extreme or atypical environments often limit the use of such well-established tools and consequently demand a novel approach. The bentonite clay matrix proposed for use in Deep Geological Repositories for the long-term storage of used nuclear fuel is one such challenging microbial habitat. Simple, accessible tools were developed for the study of microbial ecology and metabolic processes that occur within this habitat, since the understanding of the microbiota-niche interaction is fundamental to describing microbial impacts on engineered systems such as compacted bentonite barriers. Even when genomic tools are useful for the study of community composition, techniques to describe such microbial impacts and niche interactions should complement these. Tools optimised for assessing localised microbial activity within bentonite included: (a) the qualitative use of the resazurin-resorufin indicator system for redox localisation, (b) the use of a CaCl2 buffer for the localisation of pH, and (c) fluorometry for the localisation of precipitated sulphide. The use of the Carbon Dioxide Evolution Monitoring System was also validated for measuring microbial activity in desiccated and saturated bentonite. Finally, the buffering of highly-basic bentonite at neutral pH improved the success of isolation of microbial populations, but not DNA, from the bentonite matrix. Thus, accessible techniques were optimised for exploring microbial metabolism in the atypical environments of clay matrices and desiccated conditions. These tools have application to the applied field of used nuclear fuel management, as well as for examining the fundamental biogeochemical cycles active in sedimentary and deep geological environments.}, }
@article {pmid26577577, year = {2016}, author = {Wang, P and Yu, Z and Zhao, J and Zhang, H}, title = {Seasonal Changes in Bacterial Communities Cause Foaming in a Wastewater Treatment Plant.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {660-671}, pmid = {26577577}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; China ; Seasons ; Sewage/chemistry/microbiology ; Wastewater/*chemistry/*microbiology ; Water Purification/*instrumentation ; }, abstract = {Bio-foaming is a major problem in solid separation in activated sludge (AS) wastewater treatment systems. Understanding the changes in bacterial communities during sludge foaming is vital for explaining foam formation. Changes in bacterial communities in the foam, corresponding foaming AS, and non-foaming AS in a seasonal foaming wastewater treatment plant (WWTP) in Northern China were investigated by high-throughput pyrosequencing and molecular quantification-based approaches. We found that bacterial communities of the foam and the corresponding foaming AS were similar but markedly different from those of the non-foaming AS. Actinobacteria was the predominant phylum in the foam and the corresponding foaming AS, whereas Proteobacteria was predominant in the non-foaming AS. Similar to the results of most previous studies, our results showed that Candidatus "Microthrix parvicella" was the predominant filamentous bacteria in the foam and the corresponding foaming AS and was significantly enriched in the foam compared to the corresponding foaming AS. Its abundance decreased gradually with a slow disappearance of sludge foaming, indicating that its overgrowth had a direct relationship with sludge foaming. In addition to Candidatus M. parvicella, Tetrasphaera and Trichococcus might play a role in sludge foaming, because they supported the changes in AS microbial ecology for foam formation. The effluent water quality of the surveyed plant remained stable during the period of sludge foaming, but the microbial consortia responsible for nitrogen and phosphorus transformation and removal markedly changed compared to that in the non-foaming AS. This study adds to the previous understanding of bacterial communities causing foaming in WWTPs.}, }
@article {pmid26574687, year = {2016}, author = {Gómez-Consarnau, L and González, JM and Riedel, T and Jaenicke, S and Wagner-Döbler, I and Sañudo-Wilhelmy, SA and Fuhrman, JA}, title = {Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria.}, journal = {The ISME journal}, volume = {10}, number = {5}, pages = {1102-1112}, pmid = {26574687}, issn = {1751-7370}, mesh = {Flavobacteriaceae/*genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Light ; Phylogeny ; Rhodopsins, Microbial/metabolism ; Seawater/microbiology ; Thiamine/*metabolism ; Vitamins/metabolism ; }, abstract = {Proteorhodopsins (PR) are light-driven proton pumps widely distributed in bacterioplankton. Although they have been thoroughly studied for more than a decade, it is still unclear how the proton motive force (pmf) generated by PR is used in most organisms. Notably, very few PR-containing bacteria show growth enhancement in the light. It has been suggested that the presence of specific functions within a genome may define the different PR-driven light responses. Thus, comparing closely related organisms that respond differently to light is an ideal setup to identify the mechanisms involved in PR light-enhanced growth. Here, we analyzed the transcriptomes of three PR-harboring Flavobacteria strains of the genus Dokdonia: Dokdonia donghaensis DSW-1(T), Dokdonia MED134 and Dokdonia PRO95, grown in identical seawater medium in light and darkness. Although only DSW-1(T) and MED134 showed light-enhanced growth, all strains expressed their PR genes at least 10 times more in the light compared with dark. According to their genomes, DSW-1(T) and MED134 are vitamin-B1 auxotrophs, and their vitamin-B1 TonB-dependent transporters (TBDT), accounted for 10-18% of all pmf-dependent transcripts. In contrast, the expression of vitamin-B1 TBDT was 10 times lower in the prototroph PRO95, whereas its vitamin-B1 synthesis genes were among the highest expressed. Our data suggest that light-enhanced growth in DSW-1(T) and MED134 derives from the use of PR-generated pmf to power the uptake of vitamin-B1, essential for central carbon metabolism, including the TCA cycle. Other pmf-generating mechanisms available in darkness are probably insufficient to power transport of enough vitamin-B1 to support maximum growth of these organisms.}, }
@article {pmid26573833, year = {2016}, author = {Steyn, A and Roets, F and Botha, A}, title = {Yeasts Associated with Culex pipiens and Culex theileri Mosquito Larvae and the Effect of Selected Yeast Strains on the Ontogeny of Culex pipiens.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {747-760}, pmid = {26573833}, issn = {1432-184X}, mesh = {Animals ; Culex/*growth &amp; development/*microbiology ; Female ; Larva/growth &amp; development/microbiology ; Male ; Phylogeny ; Species Specificity ; Yeasts/classification/genetics/*isolation &amp; purification ; }, abstract = {The success of mosquitoes in nature has been linked to their microbiota and bacteria in particular. Yet, knowledge on their symbioses with yeasts is lacking. To explore possible associations, culturable yeasts were isolated from wild larvae of Culex pipiens and Culex theileri. These yeasts were classified using restriction fragment length polymorphism (RFLP) analyses and identified by sequencing the D1/D2 region of the 26S rRNA gene. Representative strains of Candida, Cryptococcus, Galactomyces, Hannaella, Meyerozyma, Pichia, Rhodosporidium, Rhodotorula, Trichosporon and Wickerhamomyces were isolated. Our results provide, to our knowledge, the first records of the yeast microbiota from wild mosquito larvae and show that they may harbour potential clinically relevant yeast species, including the well-known opportunistic human pathogen Candida albicans. Also, diminished numbers of yeast isolates originating from adults, compared to larvae, support the hypothesis of microbial reduction/elimination during adult emergence and extend it to include yeasts. In addition, strains of Candida albicans, Candida glabrata, Candida pseudolambica, Cryptococcus gattii, Metschnikowia bicuspidata, Saccharomyces cerevisiae and Wickerhamomyces anomalus were tested as sole feed during a 21-day feeding experiment wherein cumulative larval growth, survival and pupation of Cx. pipiens were recorded. Although most yeasts supported larval growth in a similar manner to the positive control S. cerevisiae strain, the different yeast strains impacted differently on Culex pipiens ontogeny. Notably, survival and pupation of larvae were negatively impacted by a representative strain of the primary pathogen C. gattii - signifying some yeasts to be natural antagonists of mosquitoes.}, }
@article {pmid26573832, year = {2016}, author = {Yang, SJ and Kang, I and Cho, JC}, title = {Expansion of Cultured Bacterial Diversity by Large-Scale Dilution-to-Extinction Culturing from a Single Seawater Sample.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {29-43}, pmid = {26573832}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; *Biodiversity ; Culture Media/metabolism ; DNA, Bacterial/genetics ; Molecular Sequence Data ; Pacific Ocean ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; }, abstract = {High-throughput cultivation (HTC) based on a dilution-to-extinction method has been applied broadly to the cultivation of marine bacterial groups, which has often led to the repeated isolation of abundant lineages such as SAR11 and oligotrophic marine gammaproteobacteria (OMG). In this study, to expand the phylogenetic diversity of HTC isolates, we performed a large-scale HTC with a single surface seawater sample collected from the East Sea, the Western Pacific Ocean. Phylogenetic analyses of the 16S rRNA genes from 847 putative pure cultures demonstrated that some isolates were affiliated with not-yet-cultured clades, including the OPB35 and Puniceicoccaceae marine group of Verrucomicrobia and PS1 of Alphaproteobacteria. In addition, numerous strains were obtained from abundant clades, such as SAR11, marine Roseobacter clade, OMG (e.g., SAR92 and OM60), OM43, and SAR116, thereby increasing the size of available culture resources for representative marine bacterial groups. Comparison between the composition of HTC isolates and the bacterial community structure of the seawater sample used for HTC showed that diverse marine bacterial groups exhibited various growth capabilities under our HTC conditions. The growth response of many bacterial groups, however, was clearly different from that observed with conventional plating methods, as exemplified by numerous isolates of the SAR11 clade and Verrucomicrobia. This study showed that a large number of novel bacterial strains could be obtained by an extensive HTC from even a small number of samples.}, }
@article {pmid26573831, year = {2016}, author = {Duron, O and Cremaschi, J and McCoy, KD}, title = {The High Diversity and Global Distribution of the Intracellular Bacterium Rickettsiella in the Polar Seabird Tick Ixodes uriae.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {761-770}, pmid = {26573831}, issn = {1432-184X}, mesh = {Animals ; *Biodiversity ; Bird Diseases/*microbiology/*parasitology ; Birds/microbiology/parasitology ; Coxiellaceae/classification/genetics/*isolation &amp; purification ; Female ; Ixodes/*microbiology ; Male ; Phylogeny ; }, abstract = {Obligate intracellular bacteria of the Rickettsiella genus are emerging as both widespread and biologically diverse in arthropods. Some Rickettsiella strains are highly virulent entomopathogenic agents, whereas others are maternally inherited endosymbionts exerting very subtle manipulations on host phenotype to promote their own spread. Recently, a variety of Rickettsiella strains have been reported from ticks, but their biology is entirely unknown. In the present study, we examined the incidence and diversity of Rickettsiella in 11 geographically distinct populations of the polar seabird tick Ixodes uriae. We found Rickettsiella in most tick populations with a prevalence ranging from 3 to 24 %. 16S ribosomal RNA (rRNA) and GroEL gene sequences revealed an unexpected diversity of Rickettsiella, with 12 genetically distinct Rickettsiella strains present in populations of I. uriae. Phylogenetic investigations further revealed that these Rickettsiella strains do not cluster within a tick-specific clade but rather exhibit distinct evolutionary origins demonstrating frequent horizontal transfers between distantly related arthropod species. Tick rearing further showed that Rickettsiella are present in eggs laid by infected females with no evidence of abortive development. Using this data set, we discuss the potential biological significance of Rickettsiella in seabird ticks. Most notably, we suggest that these organisms may not be pathogenic forms but rather use more subtle adaptive strategies to persist within tick populations.}, }
@article {pmid26568201, year = {2016}, author = {Knight, SJ and Goddard, MR}, title = {Sporulation in soil as an overwinter survival strategy in Saccharomyces cerevisiae.}, journal = {FEMS yeast research}, volume = {16}, number = {1}, pages = {fov102}, pmid = {26568201}, issn = {1567-1364}, mesh = {*Cold Temperature ; Microbial Viability/*radiation effects ; Saccharomyces cerevisiae/*growth &amp; development ; *Soil Microbiology ; Spores, Fungal/*growth &amp; development ; }, abstract = {Due to its commercial value and status as a research model there is an extensive body of knowledge concerning Saccharomyces cerevisiae's cell biology and genetics. Investigations into S. cerevisiae's ecology are comparatively lacking, and are mostly focused on the behaviour of this species in high sugar, fruit-based environments; however, fruit is ephemeral, and presumably, S. cerevisiae has evolved a strategy to survive when this niche is not available. Among other places, S. cerevisiae has been isolated from soil which, in contrast to fruit, is a permanent habitat. We hypothesize that S. cerevisiae employs a life history strategy targeted at self-preservation rather than growth outside of the fruit niche, and resides in forest niches, such as soil, in a dormant and resistant sporulated state, returning to fruit via vectors such as insects. One crucial aspect of this hypothesis is that S. cerevisiae must be able to sporulate in the 'forest' environment. Here, we provide the first evidence for a natural environment (soil) where S. cerevisiae sporulates. While there are further aspects of this hypothesis that require experimental verification, this is the first step towards an inclusive understanding of the more cryptic aspects of S. cerevisiae's ecology.}, }
@article {pmid26566932, year = {2016}, author = {Benadé, E and Stone, W and Mouton, M and Postma, F and Wilsenach, J and Botha, A}, title = {Binary Interactions of Antagonistic Bacteria with Candida albicans Under Aerobic and Anaerobic Conditions.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {645-659}, pmid = {26566932}, issn = {1432-184X}, mesh = {Aerobiosis ; Anaerobiosis ; *Antibiosis ; Bacteria/growth &amp; development ; *Bacterial Physiological Phenomena ; Candida albicans/growth &amp; development/*physiology ; Coculture Techniques ; }, abstract = {We used both aerobic and anaerobic liquid co-cultures, prepared with Luria Bertani broth, to study the effect of bacteria on the survival of Candida albicans in the external environment, away from an animal host. The bacteria were represented by Aeromonas hydrophila, Bacillus cereus, Bacillus subtilis, Clostridium, Enterobacter, Klebsiella pneumoniae, Kluyvera ascorbata and Serratia marcescens. Under aerobic conditions, the yeast's growth was inhibited in the presence of bacterial growth; however, under anaerobic conditions, yeast and bacterial growth in co-cultures was similar to that observed for pure cultures. Subsequent assays revealed that the majority of bacterial strains aerobically produced extracellular hydrolytic enzymes capable of yeast cell wall hydrolysis, including chitinases and mannan-degrading enzymes. In contrast, except for the A. hydrophila strain, these enzymes were not detected in anaerobic bacterial cultures, nor was the antimicrobial compound prodigiosin found in anaerobic cultures of S. marcescens. When we suspended C. albicans cells in crude extracellular enzyme preparations from K. pneumoniae and S. marcescens, we detected no negative effect on yeast viability. However, we found that these preparations enhance the toxicity of prodigiosin towards the yeast, especially in combination with mannan-degrading enzymes. Analyses of the chitin and mannan content of yeast cell walls revealed that less chitin was produced under anaerobic than aerobic conditions; however, the levels of mannan, known for its low permeability, remained the same. The latter phenomenon, as well as reduced production of the bacterial enzymes and prodigiosin, may contribute to anaerobic growth and survival of C. albicans in the presence of bacteria.}, }
@article {pmid26566425, year = {2015}, author = {Poehlein, A and Daniel, R and Simeonova, DD}, title = {Genome sequence of Pedobacter glucosidilyticus DD6b, isolated from zooplankton Daphnia magna.}, journal = {Standards in genomic sciences}, volume = {10}, number = {}, pages = {100}, pmid = {26566425}, issn = {1944-3277}, abstract = {The phosphite assimilating bacterium, P. glucosidilyticus DD6b, was isolated from the gut of the zooplankton Daphnia magna. Its 3,872,381 bp high-quality draft genome is arranged into 93 contigs containing 3311 predicted protein-coding and 41 RNA-encoding genes. This genome report presents the specific properties and common features of P. glucosidilyticus DD6b genome in comparison with the genomes of P. glucosidilyticus type strain DSM 23,534, and another five Pedobacter type strains with publicly available completely sequenced genomes. Here, we present the first journal report on P. glucosidilyticus genome sequence and provide information on a new specific physiological determinant of P. glucosidilyticus species.}, }
@article {pmid26565889, year = {2016}, author = {Giraldo-Perez, P and Herrera, P and Campbell, A and Taylor, ML and Skeats, A and Aggio, R and Wedell, N and Price, TA}, title = {Winter is coming: hibernation reverses the outcome of sperm competition in a fly.}, journal = {Journal of evolutionary biology}, volume = {29}, number = {2}, pages = {371-379}, pmid = {26565889}, issn = {1420-9101}, mesh = {Animals ; *Cold Temperature ; Drosophila/*physiology ; Female ; Hibernation/*physiology ; Male ; Reproduction ; *Seasons ; Sexual Behavior, Animal ; Spermatozoa/physiology ; Time Factors ; }, abstract = {Sperm commonly compete within females to fertilize ova, but research has focused on short-term sperm storage: sperm that are maintained in a female for only a few days or weeks before use. In nature, females of many species store sperm for months or years, often during periods of environmental stress, such as cold winters. Here we examine the outcome of sperm competition in the fruit fly Drosophila pseudoobscura, simulating the conditions in which females survive winter. We mated females to two males and then stored the female for up to 120 days at 4°C. We found that the outcome of sperm competition was consistent when sperm from two males was stored for 0, 1 or 30 days, with the last male to mate fathering most of the offspring. However, when females were stored in the cold for 120 days, the last male to mate fathered less than 5% of the offspring. Moreover, when sperm were stored long term the first male fathered almost all offspring even when he carried a meiotic driving sex chromosome that drastically reduces sperm competitive success under short-term storage conditions. This suggests that long-term sperm storage can radically alter the outcome of sperm competition.}, }
@article {pmid26565722, year = {2016}, author = {Nemergut, DR and Knelman, JE and Ferrenberg, S and Bilinski, T and Melbourne, B and Jiang, L and Violle, C and Darcy, JL and Prest, T and Schmidt, SK and Townsend, AR}, title = {Decreases in average bacterial community rRNA operon copy number during succession.}, journal = {The ISME journal}, volume = {10}, number = {5}, pages = {1147-1156}, pmid = {26565722}, issn = {1751-7370}, mesh = {Bacteria/*genetics ; Colorado ; Ecosystem ; Gene Dosage ; Operon ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; Soil ; *Soil Microbiology ; Stochastic Processes ; rRNA Operon/*genetics ; }, abstract = {Trait-based studies can help clarify the mechanisms driving patterns of microbial community assembly and coexistence. Here, we use a trait-based approach to explore the importance of rRNA operon copy number in microbial succession, building on prior evidence that organisms with higher copy numbers respond more rapidly to nutrient inputs. We set flasks of heterotrophic media into the environment and examined bacterial community assembly at seven time points. Communities were arrayed along a geographic gradient to introduce stochasticity via dispersal processes and were analyzed using 16 S rRNA gene pyrosequencing, and rRNA operon copy number was modeled using ancestral trait reconstruction. We found that taxonomic composition was similar between communities at the beginning of the experiment and then diverged through time; as well, phylogenetic clustering within communities decreased over time. The average rRNA operon copy number decreased over the experiment, and variance in rRNA operon copy number was lowest both early and late in succession. We then analyzed bacterial community data from other soil and sediment primary and secondary successional sequences from three markedly different ecosystem types. Our results demonstrate that decreases in average copy number are a consistent feature of communities across various drivers of ecological succession. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, ranging from cells to populations and communities, with implications for both microbial ecology and evolution.}, }
@article {pmid26563321, year = {2016}, author = {Modenutti, BE and Balseiro, EG and Bastidas Navarro, MA and Lee, ZM and Souza, MS and Corman, JR and Elser, JJ}, title = {Effects of Volcanic Pumice Inputs on Microbial Community Composition and Dissolved C/P Ratios in Lake Waters: an Experimental Approach.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {18-28}, pmid = {26563321}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; Carbon/*analysis/metabolism ; Lakes/chemistry/*microbiology ; Phosphorus/*analysis/metabolism ; Silicates/*analysis/metabolism ; Volcanic Eruptions/analysis ; }, abstract = {Volcanic eruptions discharge massive amounts of ash and pumice that decrease light penetration in lakes and lead to concomitant increases in phosphorus (P) concentrations and shifts in soluble C/P ratios. The consequences of these sudden changes for bacteria community composition, metabolism, and enzymatic activity remain unclear, especially for the dynamic period immediately after pumice deposition. Thus, the main aim of our study was to determine how ambient bacterial communities respond to pumice inputs in lakes that differ in dissolved organic carbon (DOC) and P concentrations and to what extent these responses are moderated by substrate C/P stoichiometry. We performed an outdoor experiment with natural lake water from two lakes that differed in dissolved organic carbon (DOC) concentration. We measured nutrient concentrations, alkaline phosphatase activity (APA), and DOC consumption rates and assessed different components of bacterial community structure using next-generation sequencing of the 16S rRNA gene. Pumice inputs caused a decrease in the C/P ratio of dissolved resources, a decrease in APA, and an increase in DOC consumption, indicating reduced P limitation. These changes in bacteria metabolism were coupled with modifications in the assemblage composition and an increase in diversity, with increases in bacterial taxa associated with biofilm and sediments, in predatory bacteria, and in bacteria with gliding motility. Our results confirm that volcanic eruptions have the potential to alter nutrient partitioning and light penetration in receiving waterways which can have dramatic impacts on microbial community dynamics.}, }
@article {pmid26563320, year = {2016}, author = {Yasumiba, K and Bell, S and Alford, R}, title = {Cell Density Effects of Frog Skin Bacteria on Their Capacity to Inhibit Growth of the Chytrid Fungus, Batrachochytrium dendrobatidis.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {124-130}, pmid = {26563320}, issn = {1432-184X}, mesh = {Animals ; Antifungal Agents/metabolism/pharmacology ; Australia ; Bacteria/chemistry/*growth &amp; development/isolation &amp; purification/metabolism ; Chytridiomycota/drug effects/*growth &amp; development ; Ranidae/*microbiology ; Skin/*microbiology ; }, abstract = {Bacterial symbionts on frog skin can reduce the growth of the chytrid fungus Batrachochytrium dendrobatidis (Bd) through production of inhibitory metabolites. Bacteria can be effective at increasing the resistance of amphibians to chytridiomycosis when added to amphibian skin, and isolates can be screened for production of metabolites that inhibit Bd growth in vitro. However, some bacteria use density-dependent mechanism such as quorum sensing to regulate metabolite production. It is therefore important to consider cell density effects when evaluating bacteria as possible candidates for bioaugmentation. The aim of our study was to evaluate how the density of cutaneous bacteria affects their inhibition of Bd growth in vitro. We sampled cutaneous bacteria isolated from three frog species in the tropical rainforests of northern Queensland, Australia, and selected ten isolates that were inhibitory to Bd in standardised pilot trials. We grew each isolate in liquid culture at a range of initial dilutions, sub-sampled each dilution at a series of times during the first 48 h of growth and measured spectrophotometric absorbance values, cell counts and Bd-inhibitory activity of cell-free supernatants at each time point. The challenge assay results clearly demonstrated that the inhibitory effects of most isolates were density dependent, with relatively low variation among isolates in the minimum cell density needed to inhibit Bd growth. We suggest the use of minimum cell densities and fast-growing candidate isolates to maximise bioaugmentation efforts.}, }
@article {pmid26562416, year = {2015}, author = {Waghmode, TR and Haque, MM and Kim, SY and Kim, PJ}, title = {Effective Suppression of Methane Emission by 2-Bromoethanesulfonate during Rice Cultivation.}, journal = {PloS one}, volume = {10}, number = {11}, pages = {e0142569}, pmid = {26562416}, issn = {1932-6203}, mesh = {Agriculture/methods ; Alkanesulfonic Acids/*pharmacology ; Biomass ; Dose-Response Relationship, Drug ; Mesna/metabolism ; Methane/*antagonists &amp; inhibitors/metabolism ; Oryza/*drug effects/growth &amp; development/metabolism ; Oxidoreductases/genetics/metabolism ; Polymerase Chain Reaction ; Soil/chemistry ; Soil Microbiology ; }, abstract = {2-bromoethanesulfonate (BES) is a structural analogue of coenzyme M (Co-M) and potent inhibitor of methanogenesis. Several studies confirmed, BES can inhibit CH4 prodcution in rice soil, but the suppressing effectiveness of BES application on CH4 emission under rice cultivation has not been studied. In this pot experiment, different levels of BES (0, 20, 40 and 80 mg kg-1) were applied to study its effect on CH4 emission and plant growth during rice cultivation. Application of BES effectively suppressed CH4 emission when compared with control soil during rice cultivation. The CH4 emission rates were significantly (P<0.001) decreased by BES application possibly due to significant (P<0.001) reduction of methnaogenic biomarkers like Co-M concentration and mcrA gene copy number (i.e. methanogenic abunadance). BES significantly (P<0.001) reduced methanogen activity, while it did not affect soil dehydrogenase activity during rice cultivation. A rice plant growth and yield parameters were not affected by BES application. The maximum CH4 reduction (49% reduction over control) was found at 80 mg kg-1 BES application during rice cultivation. It is, therefore, concluded that BES could be a suitable soil amendment for reducing CH4 emission without affecting rice plant growth and productivity during rice cultivation.}, }
@article {pmid26556275, year = {2015}, author = {Zaura, E and Brandt, BW and Teixeira de Mattos, MJ and Buijs, MJ and Caspers, MP and Rashid, MU and Weintraub, A and Nord, CE and Savell, A and Hu, Y and Coates, AR and Hubank, M and Spratt, DA and Wilson, M and Keijser, BJ and Crielaard, W}, title = {Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces.}, journal = {mBio}, volume = {6}, number = {6}, pages = {e01693-15}, pmid = {26556275}, issn = {2150-7511}, mesh = {Anti-Bacterial Agents/*administration &amp; dosage/pharmacology ; DNA, Ribosomal/chemistry/genetics ; Feces/*microbiology ; Healthy Volunteers ; Humans ; Microbiota/*drug effects ; Placebos/administration &amp; dosage ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; Sequence Analysis, DNA ; Sweden ; Time Factors ; United Kingdom ; }, abstract = {UNLABELLED: Due to the spread of resistance, antibiotic exposure receives increasing attention. Ecological consequences for the different niches of individual microbiomes are, however, largely ignored. Here, we report the effects of widely used antibiotics (clindamycin, ciprofloxacin, amoxicillin, and minocycline) with different modes of action on the ecology of both the gut and the oral microbiomes in 66 healthy adults from the United Kingdom and Sweden in a two-center randomized placebo-controlled clinical trial. Feces and saliva were collected at baseline, immediately after exposure, and 1, 2, 4, and 12 months after administration of antibiotics or placebo. Sequences of 16S rRNA gene amplicons from all samples and metagenomic shotgun sequences from selected baseline and post-antibiotic-treatment sample pairs were analyzed. Additionally, metagenomic predictions based on 16S rRNA gene amplicon data were performed using PICRUSt. The salivary microbiome was found to be significantly more robust, whereas the antibiotics negatively affected the fecal microbiome: in particular, health-associated butyrate-producing species became strongly underrepresented. Additionally, exposure to different antibiotics enriched genes associated with antibiotic resistance. In conclusion, healthy individuals, exposed to a single antibiotic treatment, undergo considerable microbial shifts and enrichment in antibiotic resistance in their feces, while their salivary microbiome composition remains unexpectedly stable. The health-related consequences for the gut microbiome should increase the awareness of the individual risks involved with antibiotic use, especially in a (diseased) population with an already dysregulated microbiome. On the other hand, understanding the mechanisms behind the resilience of the oral microbiome toward ecological collapse might prove useful in combating microbial dysbiosis elsewhere in the body.<br><br>IMPORTANCE: Many health care professionals use antibiotic prophylaxis strategies to prevent infection after surgery. This practice is under debate since it enhances the spread of antibiotic resistance. Another important reason to avoid nonessential use of antibiotics, the impact on our microbiome, has hardly received attention. In this study, we assessed the impact of antibiotics on the human microbial ecology at two niches. We followed the oral and gut microbiomes in 66 individuals from before, immediately after, and up to 12&#xa0;months after exposure to different antibiotic classes. The salivary microbiome recovered quickly and was surprisingly robust toward antibiotic-induced disturbance. The fecal microbiome was severely affected by most antibiotics: for months, health-associated butyrate-producing species became strongly underrepresented. Additionally, there was an enrichment of genes associated with antibiotic resistance. Clearly, even a single antibiotic treatment in healthy individuals contributes to the risk of resistance development and leads to long-lasting detrimental shifts in the gut microbiome.}, }
@article {pmid26554941, year = {2015}, author = {Seyrig, G and Stedtfeld, RD and Tourlousse, DM and Ahmad, F and Towery, K and Cupples, AM and Tiedje, JM and Hashsham, SA}, title = {Selection of fluorescent DNA dyes for real-time LAMP with portable and simple optics.}, journal = {Journal of microbiological methods}, volume = {119}, number = {}, pages = {223-227}, doi = {10.1016/j.mimet.2015.11.004}, pmid = {26554941}, issn = {1872-8359}, mesh = {DNA Primers/genetics ; Fluorescent Dyes/*chemistry ; Mycobacterium tuberculosis/genetics/*isolation &amp; purification ; Nucleic Acid Amplification Techniques/instrumentation/*methods ; Sensitivity and Specificity ; Staphylococcus aureus/genetics/*isolation &amp; purification ; }, abstract = {Loop-mediated isothermal amplification (LAMP) is increasingly used for point-of-care nucleic acid based diagnostics. LAMP can be monitored in real-time by measuring the increase in fluorescence of DNA binding dyes. However, there is little information comparing the effect of various fluorescent dyes on signal to noise ratio (SNR) or threshold time (Tt). This information is critical for implementation with field deployable diagnostic tools that require small, low power consumption, robust, and inexpensive optical components with reagent saving low volume reactions. In this study, SNR and Tt during real-time LAMP was evaluated with eleven fluorescent dyes. Of all dyes tested, SYTO-82, SYTO-84, and SYTOX Orange resulted in the shortest Tt, and SYTO-81 had the widest range of working concentrations. The optimized protocol detected 10 genome copies of Mycobacterium tuberculosis in less than 10 min, 10 copies of Giardia intestinalis in ~20 min, and 10 copies of Staphylococcus aureus or Salmonella enterica in less than 15 min. Results demonstrate that reaction efficiency depends on both dye type and concentration and the selected polymerase. The optimized protocol was evaluated in the Gene-Z™ device, a hand-held battery operated platform characterized via simple and low cost optics, and a multiple assay microfluidic chip with micron volume reaction wells. Compared to the more conventional intercalating dye (SYBR Green), reliable amplification was only observed in the Gene-Z™ when using higher concentrations of SYTO-81.}, }
@article {pmid26553774, year = {2016}, author = {Deshpande, V and Wang, Q and Greenfield, P and Charleston, M and Porras-Alfaro, A and Kuske, CR and Cole, JR and Midgley, DJ and Tran-Dinh, N}, title = {Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences.}, journal = {Mycologia}, volume = {108}, number = {1}, pages = {1-5}, doi = {10.3852/14-293}, pmid = {26553774}, issn = {0027-5514}, mesh = {Bayes Theorem ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Datasets as Topic ; Fungi/*classification/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {Fungi are key organisms in many ecological processes and communities. Rapid and low cost surveys of the fungal members of a community can be undertaken by isolating and sequencing a taxonomically informative genomic region, such as the ITS (internal transcribed spacer), from DNA extracted from a metagenomic sample, and then classifying these sequences to determine which organisms are present. This paper announces the availability of the Warcup ITS training set and shows how it can be used with the Ribosomal Database Project (RDP) Bayesian Classifier to rapidly and accurately identify fungi using ITS sequences. The classifications can be down to species level and use conventional literature-based mycological nomenclature and taxonomic assignments.}, }
@article {pmid26552395, year = {2016}, author = {Llorens-Marès, T and Triadó-Margarit, X and Borrego, CM and Dupont, CL and Casamayor, EO}, title = {High Bacterial Diversity and Phylogenetic Novelty in Dark Euxinic Freshwaters Analyzed by 16S Tag Community Profiling.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {566-574}, pmid = {26552395}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; DNA, Bacterial/genetics ; Lakes/*microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spain ; }, abstract = {Microbial communities growing under extreme low redox conditions are present in anoxic and sulfide-rich (euxinic) environments such as karstic lakes and experience limitation of electron acceptors. The fine natural chemical gradients and the large diversity of organic and inorganic compounds accumulated in bottom waters are impossible to mimic under laboratory conditions, and only a few groups have been cultured. We investigated the bacterial composition in the oxic-anoxic interface and in the deep waters of three sulfurous lakes from the Lake Banyoles karstic area (NE Spain) through 16S rRNA gene tag sequencing and identified the closest GenBank counterpart. High diversity indices were found in most of the samples with >15 phyla/classes and >45 bacterial orders. A higher proportion of operational taxonomic units (OTUs) of the "highest novelty" was found in the hypolimnia (38 % of total sequences) than in the metalimnia (17 %), whereas the percentage of OTUs closer to cultured counterparts (i.e., 97 % identity in the 16S rRNA gene) was 6 to 21 %, respectively. Elusimicrobia, Chloroflexi, Fibrobacteres, and Spirochaetes were the taxa with the highest proportion of novel sequences. Interestingly, tag sequencing results comparison with metagenomics data available from the same dataset, showed a systematic underestimation of sulfur-oxidizing Epsilonproteobacteria with the currently available 907R "universal" primer. Overall, despite the limitation of electron acceptors, a highly diverse and novel assemblage was present in dark and euxinic hypolimnetic freshwaters, unveiling a hotspot of microbial diversity with a remarkable gap with cultured counterparts.}, }
@article {pmid26552394, year = {2016}, author = {Čapková, K and Hauer, T and Řeháková, K and Doležal, J}, title = {Some Like it High! Phylogenetic Diversity of High-Elevation Cyanobacterial Community from Biological Soil Crusts of Western Himalaya.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {113-123}, pmid = {26552394}, issn = {1432-184X}, mesh = {Altitude ; Biodegradation, Environmental ; *Biodiversity ; Cyanobacteria/classification/*genetics/isolation &amp; purification/metabolism ; Geologic Sediments/analysis/*microbiology ; Molecular Sequence Data ; *Phylogeny ; Soil/chemistry ; *Soil Microbiology ; Tibet ; }, abstract = {The environment of high-altitudinal cold deserts of Western Himalaya is characterized by extensive development of biological soil crusts, with cyanobacteria as dominant component. The knowledge of their taxonomic composition and dependency on soil chemistry and elevation is still fragmentary. We studied the abundance and the phylogenetic diversity of the culturable cyanobacteria and eukaryotic microalgae in soil crusts along altitudinal gradients (4600-5900 m) at two sites in the dry mountains of Ladakh (SW Tibetan Plateau and Eastern Karakoram), using both microscopic and molecular approaches. The effects of environmental factors (altitude, mountain range, and soil physico-chemical parameters) on the composition and biovolume of phototrophs were tested by multivariate redundancy analysis and variance partitioning. Both phylogenetic diversity and composition of morphotypes were similar between Karakorum and Tibetan Plateau. Phylogenetic analysis of 16S rRNA gene revealed strains belonging to at least five genera. Besides clusters of common soil genera, e.g., Microcoleus, Nodosilinea, or Nostoc, two distinct clades of simple trichal taxa were newly discovered. The most abundant cyanobacterial orders were Oscillatoriales and Nostacales, whose biovolume increased with increasing elevation, while that of Chroococales decreased. Cyanobacterial species richness was low in that only 15 morphotypes were detected. The environmental factors accounted for 52 % of the total variability in microbial data, 38.7 % of which was explained solely by soil chemical properties, 14.5 % by altitude, and 8.4 % by mountain range. The elevation, soil phosphate, and magnesium were the most important predictors of soil phototrophic communities in both mountain ranges despite their different bedrocks and origin. The present investigation represents a first record on phylogenetic diversity of the cyanobacterial community of biological soil crusts from Western Himalayas and first record from altitudes over 5000 m.}, }
@article {pmid26547568, year = {2016}, author = {Guibert, LM and Loviso, CL and Borglin, S and Jansson, JK and Dionisi, HM and Lozada, M}, title = {Diverse Bacterial Groups Contribute to the Alkane Degradation Potential of Chronically Polluted Subantarctic Coastal Sediments.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {100-112}, pmid = {26547568}, issn = {1432-184X}, mesh = {Alkanes/*metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Biodiversity ; Geologic Sediments/analysis/*microbiology ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Phylogeny ; Seawater/analysis/microbiology ; Water Pollutants, Chemical/analysis/*metabolism ; }, abstract = {We aimed to gain insight into the alkane degradation potential of microbial communities from chronically polluted sediments of a subantarctic coastal environment using a combination of metagenomic approaches. A total of 6178 sequences annotated as alkane-1-monooxygenases (EC 1.14.15.3) were retrieved from a shotgun metagenomic dataset that included two sites analyzed in triplicate. The majority of the sequences binned with AlkB described in Bacteroidetes (32 ± 13 %) or Proteobacteria (29 ± 7 %), although a large proportion remained unclassified at the phylum level. Operational taxonomic unit (OTU)-based analyses showed small differences in AlkB distribution among samples that could be correlated with alkane concentrations, as well as with site-specific variations in pH and salinity. A number of low-abundance OTUs, mostly affiliated with Actinobacterial sequences, were found to be only present in the most contaminated samples. On the other hand, the molecular screening of a large-insert metagenomic library of intertidal sediments from one of the sampling sites identified two genomic fragments containing novel alkB gene sequences, as well as various contiguous genes related to lipid metabolism. Both genomic fragments were affiliated with the phylum Planctomycetes, and one could be further assigned to the genus Rhodopirellula due to the presence of a partial sequence of the 23S ribosomal RNA (rRNA) gene. This work highlights the diversity of bacterial groups contributing to the alkane degradation potential and reveals patterns of functional diversity in relation with environmental stressors in a chronically polluted, high-latitude coastal environment. In addition, alkane biodegradation genes are described for the first time in members of Planctomycetes.}, }
@article {pmid26547567, year = {2016}, author = {Pandit, PS and Rahalkar, MC and Dhakephalkar, PK and Ranade, DR and Pore, S and Arora, P and Kapse, N}, title = {Deciphering Community Structure of Methanotrophs Dwelling in Rice Rhizospheres of an Indian Rice Field Using Cultivation and Cultivation-Independent Approaches.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {634-644}, pmid = {26547567}, issn = {1432-184X}, mesh = {Bacteria/classification/growth &amp; development/*isolation &amp; purification/*metabolism ; India ; Methane/*metabolism ; Oryza/growth &amp; development/*microbiology ; Phylogeny ; Plant Roots/microbiology ; Rhizosphere ; *Soil Microbiology ; }, abstract = {Methanotrophs play a crucial role in filtering out methane from habitats, such as flooded rice fields. India has the largest area under rice cultivation in the world; however, to the best of our knowledge, methanotrophs have not been isolated and characterized from Indian rice fields. A cultivation strategy composing of a modified medium, longer incubation time, and serial dilutions in microtiter plates was used to cultivate methanotrophs from a rice rhizosphere sample from a flooded rice field in Western India. We compared the cultured members with the uncultured community as revealed by three culture-independent methods. A novel type Ia methanotroph (Sn10-6), at the rank of a genus, and a putative novel species of a type II methanotroph (Sn-Cys) were cultivated from the terminal positive dilution (10(-6)). From lower dilution (10(-4)), a strain of Methylomonas spp. was cultivated. All the three culture-independent analyses, i.e., pmoA clone library, terminal restriction fragment length polymorphism (T-RFLP), and metagenomics approach, revealed the dominance of type I methanotrophs. Only metagenomic analysis showed significant presence of type II methanotrophs, albeit in lower proportion (37 %). All the three isolates showed relevance to the methanotrophic community as depicted by uncultured methods; however, the cultivated members might not be the most dominant ones. In conclusion, a combined cultivation and cultivation-independent strategy yielded us a broader picture of the methanotrophic community from rice rhizospheres of a flooded rice field in India.}, }
@article {pmid26547566, year = {2016}, author = {Rahalkar, MC and Pandit, PS and Dhakephalkar, PK and Pore, S and Arora, P and Kapse, N}, title = {Genome Characteristics of a Novel Type I Methanotroph (Sn10-6) Isolated from a Flooded Indian Rice Field.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {519-523}, pmid = {26547566}, issn = {1432-184X}, mesh = {Bacterial Proteins/genetics/metabolism ; Floods ; *Genome, Bacterial ; India ; Methane/*metabolism ; Methylococcaceae/classification/*genetics/isolation &amp; purification/metabolism ; Oryza/*growth &amp; development/microbiology ; Phylogeny ; Plant Roots/growth &amp; development/microbiology ; Rhizosphere ; *Soil Microbiology ; }, abstract = {Flooded rice fields are important sources of atmospheric methane. Aerobic methanotrophs living in the vicinity of rice roots oxidize methane and act as environmental filters. Here, we present genome characteristics of a gammaproteobacterial methanotroph, isolate Sn10-6, which was isolated from a rice rhizosphere of a flooded field in India. Sn10-6 has been identified as a member of a putative novel genus and species within the family Methylococcaceae (Type I methanotrophs). The draft genome of Sn10-6 showed pathways for the following: methane oxidation, formaldehyde assimilation (RuMP), nitrogen fixation, conversion of nitrite to nitrous oxide, and other interesting genes including the ones responsible for survival in the rhizosphere environment. The majority of genes found in this genome were most similar to Methylovulum miyakonese which is a forest isolate. This draft genome provided insight into the physiology, ecology, and phylogeny of this gammaproteobacterial methanotroph.}, }
@article {pmid26546841, year = {2015}, author = {Kurland, CG and Harish, A}, title = {Structural biology and genome evolution: An introduction.}, journal = {Biochimie}, volume = {119}, number = {}, pages = {205-208}, doi = {10.1016/j.biochi.2015.10.023}, pmid = {26546841}, issn = {1638-6183}, mesh = {Animals ; *Evolution, Molecular ; Genomics/*methods/trends ; Humans ; *Models, Genetic ; *Models, Molecular ; Phylogeny ; Protein Isoforms/*chemistry/genetics/metabolism ; Structural Homology, Protein ; }, }
@article {pmid26546424, year = {2016}, author = {Ferrocino, I and Greppi, A and La Storia, A and Rantsiou, K and Ercolini, D and Cocolin, L}, title = {Impact of Nisin-Activated Packaging on Microbiota of Beef Burgers during Storage.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {2}, pages = {549-559}, pmid = {26546424}, issn = {1098-5336}, mesh = {Animals ; Bacteria/classification/drug effects/genetics/*isolation &amp; purification ; Cattle ; Food Additives/*pharmacology ; Food Packaging ; Food Preservation ; Food Storage ; Meat Products/analysis/*microbiology ; Microbiota/*drug effects ; Nisin/*pharmacology ; }, abstract = {Beef burgers were stored at 4°C in a vacuum in nisin-activated antimicrobial packaging. Microbial ecology analyses were performed on samples collected between days 0 and 21 of storage to discover the population diversity. Two batches were analyzed using RNA-based denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. The active packaging retarded the growth of the total viable bacteria and lactic acid bacteria. Culture-independent analysis by pyrosequencing of RNA extracted directly from meat showed that Photobacterium phosphoreum, Lactococcus piscium, Lactobacillus sakei, and Leuconostoc carnosum were the major operational taxonomic units (OTUs) shared between control and treated samples. Beta diversity analysis of the 16S rRNA sequence data and RNA-DGGE showed a clear separation between two batches based on the microbiota. Control samples from batch B showed a significant high abundance of some taxa sensitive to nisin, such as Kocuria rhizophila, Staphylococcus xylosus, Leuconostoc carnosum, and Carnobacterium divergens, compared to control samples from batch A. However, only from batch B was it possible to find a significant difference between controls and treated samples during storage due to the active packaging. Predicted metagenomes confirmed differences between the two batches and indicated that the use of nisin-based antimicrobial packaging can determine a reduction in the abundance of specific metabolic pathways related to spoilage. The present study aimed to assess the viable bacterial communities in beef burgers stored in nisin-based antimicrobial packaging, and it highlights the efficacy of this strategy to prolong beef burger shelf life.}, }
@article {pmid26545170, year = {2015}, author = {Tsilia, V and Uyttendaele, M and Kerckhof, FM and Rajkovic, A and Heyndrickx, M and Van de Wiele, T}, title = {Bacillus cereus Adhesion to Simulated Intestinal Mucus Is Determined by Its Growth on Mucin, Rather Than Intestinal Environmental Parameters.}, journal = {Foodborne pathogens and disease}, volume = {12}, number = {11}, pages = {904-913}, doi = {10.1089/fpd.2014.1926}, pmid = {26545170}, issn = {1556-7125}, mesh = {Bacillus cereus/*growth &amp; development ; Bacterial Adhesion/*physiology ; Colony Count, Microbial ; Gastrointestinal Tract/chemistry/microbiology ; In Vitro Techniques ; Intestinal Mucosa/*microbiology ; Mucins/*metabolism ; }, abstract = {Adhesion of pathogenic bacteria to intestinal mucus, the protective layer of the gastrointestinal epithelium, is often considered a virulence factor. The ability of food-poisoning Bacillus cereus strains to attach to mucus and the factors affecting this interaction have not yet been investigated. Therefore, the role of adhesion in pathogenesis of B. cereus still remains unknown. In the present study, an in vitro assay based on mucin agar was used to simulate adhesion of B. cereus to mucus. Bacterial-associated factors (e.g., strain specificity and microbial competition) known to influence adhesion to different surfaces and a variety of environmental conditions (e.g., pH and oxygen) encountered in the gastrointestinal tract were investigated. The effect of these parameters on B. cereus NVH 0500/00 mucin adhesion was generally limited even in the presence of microbial competition. This suggests that B. cereus NVH 0500/00 is a versatile pathogen. Inoculation of 4 to 5 log colony-forming units (CFU) per milliliter. B. cereus NVH 0500/00 resulted in 5-6 log CFU/mL mucin-associated bacteria after a short incubation period. This indicates that this pathogenic strain could grow in the presence of mucin agar. This growth may potentially mask the effect of the studied conditions. Yet, extensive attachment of B. cereus to mucin is not necessarily a prerequisite for virulence, because other pathogenic strains do not adhere with the same efficiency to mucin. Nevertheless, adhesion may contribute to the disease by providing close contact to nutrient sources, such as mucin, which would not only result in bacterial proliferation, but also in disruption of the protective host mucus surface.}, }
@article {pmid26544541, year = {2016}, author = {de Melo Pereira, GV and Beux, M and Pagnoncelli, MG and Soccol, VT and Rodrigues, C and Soccol, CR}, title = {Isolation, selection and evaluation of antagonistic yeasts and lactic acid bacteria against ochratoxigenic fungus Aspergillus westerdijkiae on coffee beans.}, journal = {Letters in applied microbiology}, volume = {62}, number = {1}, pages = {96-101}, doi = {10.1111/lam.12520}, pmid = {26544541}, issn = {1472-765X}, mesh = {Aflatoxins/*biosynthesis ; Antifungal Agents/*isolation &amp; purification ; Aspergillus/*growth &amp; development ; Biological Control Agents/*isolation &amp; purification/metabolism ; Candida/isolation &amp; purification/metabolism ; Coffee/*microbiology ; Food Contamination/*prevention &amp; control ; Fruit/microbiology ; Lactic Acid/metabolism ; Levilactobacillus brevis/isolation &amp; purification/metabolism ; Ochratoxins/*biosynthesis ; Pichia/isolation &amp; purification/metabolism ; }, abstract = {UNLABELLED: In this study, yeasts and lactic acid bacteria (LAB) were isolated from coffee fruits and identified via biochemical and molecular approaches. The isolates represented the Pichia, Debaryomyces, Candida, Clavispora, Yarrowia, Sporobolomyces, Klyveromyces, Torulaspora and Lactobacillus genera. Four isolates, namely Pichia fermentans LPBYB13, Sporobolomyces roseus LPBY7E, Candida sp. LPBY11B and Lactobacillus brevis LPBB03, were found to have the greatest antagonist activity against an ochratoxigenic strain of Aspergillus westerdijkiae on agar tests and were selected for further characterization. Applications of P. fermentans LPBYB13 in coffee cherries artificially contaminated with A. westerdijkiae showed efficacy in reducing ochratoxin A (OTA) content up to 88%. These results highlight that P. fermentans LPBYB13 fulfils the principle requirements of an efficient biological control of aflatoxigenic fungi in coffee beans and may be seen as a reliable candidate for further validation in field conditions.<br><br>Studies based on microbial ecology and antagonistic interactions are important for the development of new strategies in controlling aflatoxin contamination of crops and are relevant to further biotechnological applications. This study shows that coffee fruit is a potential source for the isolation of microbial strains with antifungal ability. A new yeast strain, Pichia fermentans LPBYB13, showed efficacy in reducing growth and ochratoxin A production of Aspergillus westerdijkiae in coffee beans. Our results should encourage the use of this yeast strain on a large scale for biocontrol of aflatoxigenic fungi in coffee beans.}, }
@article {pmid26543776, year = {2015}, author = {Odeyemi, OA}, title = {Bacteriological safety of packaged drinking water sold in Nigeria: public health implications.}, journal = {SpringerPlus}, volume = {4}, number = {}, pages = {642}, pmid = {26543776}, issn = {2193-1801}, abstract = {BACKGROUND: Over the past years, there has been increase in packaged water consumption in Nigeria. Although, there are several studies on microbial safety of sachet packaged drinking water, there is no information on prevailing pathogens.<br><br>FINDINGS: A comprehensive literature search and meta-analysis of peer reviewed primary studies reported from 2005 for microbiological safety of packaged drinking water sold in Nigeria was conducted using "sachet water", "bottled water" and "packaged water" and Nigeria as search algorithms in public scientific literature databases. It was observed in this study that Escherichia spp., (65.5&#xa0;%), Salmonella spp., (44.8&#xa0;%), Bacillus spp., (44.1&#xa0;%) and Staphylococcus spp. (37.9&#xa0;%) were more prevailing in the samples.<br><br>CONCLUSIONS: The high rate of contamination observed is of public health importance. There is need for use of molecular based methods to understand microbial ecology, epidemiology, virulence factors and survival of isolated water borne pathogens in packaged drinking water sold in Nigeria.}, }
@article {pmid26538122, year = {2016}, author = {Supek, F}, title = {The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function.}, journal = {Journal of molecular evolution}, volume = {82}, number = {1}, pages = {65-73}, pmid = {26538122}, issn = {1432-1432}, mesh = {Archaea ; Bacteria ; *Codon ; Consensus Sequence ; *Evolution, Molecular ; Fungi ; Humans ; Neoplasms/genetics ; *Open Reading Frames ; *Silent Mutation ; }, abstract = {Some mutations in gene coding regions exchange one synonymous codon for another, and thus do not alter the amino acid sequence of the encoded protein. Even though they are often called 'silent,' these mutations may exhibit a plethora of effects on the living cell. Therefore, they are often selected during evolution, causing synonymous codon usage biases in genomes. Comparative analyses of bacterial, archaeal, fungal, and human cancer genomes have found many links between a gene's biological role and the accrual of synonymous mutations during evolution. In particular, highly expressed genes in certain functional categories are enriched with optimal codons, which are decoded by the abundant tRNAs, thus enhancing the speed and accuracy of the translating ribosome. The set of genes exhibiting codon adaptation differs between genomes, and these differences show robust associations to organismal phenotypes. In addition to selection for translation efficiency, other distinct codon bias patterns have been found in: amino acid starvation genes, cyclically expressed genes, tissue-specific genes in animals and plants, oxidative stress response genes, cellular differentiation genes, and oncogenes. In addition, genomes of organisms harboring tRNA modifications exhibit particular codon preferences. The evolutionary trace of codon bias patterns across orthologous genes may be examined to learn about a gene's relevance to various phenotypes, or, more generally, its function in the cell.}, }
@article {pmid26537674, year = {2016}, author = {Douam, F and Bobay, LM and Maurin, G and Fresquet, J and Calland, N and Maisse, C and Durand, T and Cosset, FL and Féray, C and Lavillette, D}, title = {Specialization of Hepatitis C Virus Envelope Glycoproteins for B Lymphocytes in Chronically Infected Patients.}, journal = {Journal of virology}, volume = {90}, number = {2}, pages = {992-1008}, pmid = {26537674}, issn = {1098-5514}, mesh = {B-Lymphocytes/*virology ; Cell Line ; Hepacivirus/isolation &amp; purification/*physiology ; Hepatitis C, Chronic/*virology ; Hepatocytes/virology ; Humans ; Transduction, Genetic ; Viral Envelope Proteins/*metabolism ; *Viral Tropism ; *Virus Internalization ; }, abstract = {UNLABELLED: Hepatitis C virus (HCV) productively infects hepatocytes. Virion surface glycoproteins E1 and E2 play a major role in this restricted cell tropism by mediating virus entry into particular cell types. However, several pieces of evidence have suggested the ability of patient-derived HCV particles to infect peripheral blood mononuclear cells. The viral determinants and mechanisms mediating such events remain poorly understood. Here, we aimed at isolating viral determinants of HCV entry into B lymphocytes. For this purpose, we constructed a library of full E1E2 sequences isolated from serum and B lymphocytes of four chronically infected patients. We observed a strong phylogenetic compartmentalization of E1E2 sequences isolated from B lymphocytes in one patient, indicating that E1E2 glycoproteins can represent important mediators of the strong segregation of two specialized populations in some patients. Most of the E1E2 envelope glycoproteins were functional and allowed transduction of hepatocyte cell lines using HCV-derived pseudoparticles. Strikingly, introduction of envelope glycoproteins isolated from B lymphocytes into the HCV JFH-1 replicating virus switched the entry tropism of this nonlymphotropic virus from hepatotropism to lymphotropism. Significant detection of viral RNA and viral proteins within B cells was restricted to infections with JFH-1 harboring E1E2 from lymphocytes and depended on an endocytic, pH-dependent entry pathway. Here, we achieved for the first time the isolation of HCV viral proteins carrying entry-related lymphotropism determinants. The identification of genetic determinants within E1E2 represents a first step for a better understanding of the complex relationship between HCV infection, viral persistence, and extrahepatic disorders.<br><br>IMPORTANCE: Hepatitis C virus (HCV) mainly replicates within the liver. However, it has been shown that patient-derived HCV particles can slightly infect lymphocytes in vitro and in vivo, highlighting the existence of lymphotropism determinants within HCV viral proteins. We isolated HCV envelope glycoproteins from patient B lymphocytes that conferred to a nonlymphotropic HCV the ability to enter B cells, thus providing a platform for characterization of HCV entry into lymphocytes. This unusual tropism was accompanied by a loss of entry function into hepatocytes, suggesting that HCV lymphotropic variants likely constitute a distinct but parallel source for viral persistence and immune escape within chronically infected patients. Moreover, the level of genetic divergence of B-cell-derived envelopes correlated with their degree of lymphotropism, underlining a long-term specialization of some viral populations for B-lymphocytes. Consequently, the clearance of both hepatotropic and nonhepatotropic HCV populations may be important for effective treatment of chronically infected patients.}, }
@article {pmid26535114, year = {2015}, author = {Crusoe, MR and Alameldin, HF and Awad, S and Boucher, E and Caldwell, A and Cartwright, R and Charbonneau, A and Constantinides, B and Edvenson, G and Fay, S and Fenton, J and Fenzl, T and Fish, J and Garcia-Gutierrez, L and Garland, P and Gluck, J and González, I and Guermond, S and Guo, J and Gupta, A and Herr, JR and Howe, A and Hyer, A and Härpfer, A and Irber, L and Kidd, R and Lin, D and Lippi, J and Mansour, T and McA'Nulty, P and McDonald, E and Mizzi, J and Murray, KD and Nahum, JR and Nanlohy, K and Nederbragt, AJ and Ortiz-Zuazaga, H and Ory, J and Pell, J and Pepe-Ranney, C and Russ, ZN and Schwarz, E and Scott, C and Seaman, J and Sievert, S and Simpson, J and Skennerton, CT and Spencer, J and Srinivasan, R and Standage, D and Stapleton, JA and Steinman, SR and Stein, J and Taylor, B and Trimble, W and Wiencko, HL and Wright, M and Wyss, B and Zhang, Q and Zyme, E and Brown, CT}, title = {The khmer software package: enabling efficient nucleotide sequence analysis.}, journal = {F1000Research}, volume = {4}, number = {}, pages = {900}, pmid = {26535114}, issn = {2046-1402}, support = {R01 HG007513/HG/NHGRI NIH HHS/United States ; }, abstract = {The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/.}, }
@article {pmid26528254, year = {2015}, author = {Wang, J and Mignon, A and Snoeck, D and Wiktor, V and Van Vliergerghe, S and Boon, N and De Belie, N}, title = {Application of modified-alginate encapsulated carbonate producing bacteria in concrete: a promising strategy for crack self-healing.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1088}, pmid = {26528254}, issn = {1664-302X}, abstract = {Self-healing concrete holds promising benefits to reduce the cost for concrete maintenance and repair as cracks are autonomously repaired without any human intervention. In this study, the application of a carbonate precipitating bacterium Bacillus sphaericus was explored. Regarding the harsh condition in concrete, B. sphaericus spores were first encapsulated into a modified-alginate based hydrogel (AM-H) which was proven to have a good compatibility with the bacteria and concrete regarding the influence on bacterial viability and concrete strength. Experimental results show that the spores were still viable after encapsulation. Encapsulated spores can precipitate a large amount of CaCO3 in/on the hydrogel matrix (around 70% by weight). Encapsulated B. sphaericus spores were added into mortar specimens and bacterial in situ activity was demonstrated by the oxygen consumption on the mimicked crack surface. While specimens with free spores added showed no oxygen consumption. This indicates the efficient protection of the hydrogel for spores in concrete. To conclude, the AM-H encapsulated carbonate precipitating bacteria have great potential to be used for crack self-healing in concrete applications.}, }
@article {pmid26528253, year = {2015}, author = {Denman, SE and Martinez Fernandez, G and Shinkai, T and Mitsumori, M and McSweeney, CS}, title = {Metagenomic analysis of the rumen microbial community following inhibition of methane formation by a halogenated methane analog.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1087}, pmid = {26528253}, issn = {1664-302X}, abstract = {Japanese goats fed a diet of 50% Timothy grass and 50% concentrate with increasing levels of the anti-methanogenic compound, bromochloromethane (BCM) were investigated with respect to the microbial population and functional shifts in the rumen. Microbial ecology methods identified species that exhibited positive and negative responses to the increasing levels of BCM. The methane-inhibited rumen appeared to adapt to the higher H2 levels by shifting fermentation to propionate which was mediated by an increase in the population of H2-consuming Prevotella and Selenomonas spp. Metagenomic analysis of propionate production pathways was dominated by genomic content from these species. Reductive acetogenic marker gene libraries and metagenomics analysis indicate that reductive acetogenic species do not play a major role in the BCM treated rumen.}, }
@article {pmid26527841, year = {2015}, author = {Boufahja, F and Semprucci, F and Beyrem, H and Bhadury, P}, title = {Marine Nematode Taxonomy in Africa: Promising Prospects Against Scarcity of Information.}, journal = {Journal of nematology}, volume = {47}, number = {3}, pages = {198-206}, pmid = {26527841}, issn = {0022-300X}, abstract = {From the late 19th century, Africa has faced heavy exploitation of its natural resources with increasing land/water pollution, and several described species have already become extinct or close to extinction. This could also be the case for marine nematodes, which are the most abundant and diverse benthic group in marine sediments, and play major roles in ecosystem functioning. Compared to Europe and North America, only a handful of investigations on marine nematodes have been conducted to date in Africa. This is due to the scarcity of experienced taxonomists, absence of identification guides, as well as local appropriate infrastructures. A pivotal project has started recently between nematologists from Africa (Tunisia), India, and Europe (Italy) to promote taxonomic study and biodiversity estimation of marine nematodes in the African continent. To do this, as a first step, collection of permanent slides of marine nematodes (235 nominal species and 14 new to science but not yet described) was recently established at the Faculty of Sciences of Bizerte (Tunisia). Capacity building of next generation of African taxonomists have been carried out at level of both traditional and molecular taxonomy (DNA barcoding and next-generation sequencing [NGS]), but they need to be implemented. Indeed, the integration of these two approaches appears crucial to overcome lack of information on the taxonomy, ecology, and biodiversity of marine nematodes from African coastal waters.}, }
@article {pmid26527297, year = {2016}, author = {Shah, F and Nicolás, C and Bentzer, J and Ellström, M and Smits, M and Rineau, F and Canbäck, B and Floudas, D and Carleer, R and Lackner, G and Braesel, J and Hoffmeister, D and Henrissat, B and Ahrén, D and Johansson, T and Hibbett, DS and Martin, F and Persson, P and Tunlid, A}, title = {Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors.}, journal = {The New phytologist}, volume = {209}, number = {4}, pages = {1705-1719}, pmid = {26527297}, issn = {1469-8137}, mesh = {Fungal Proteins/genetics/metabolism ; Fungi/genetics/*physiology ; Gene Expression Regulation, Fungal ; Genes, Fungal ; Laccase/metabolism ; Lignin/metabolism ; Mycorrhizae/*physiology ; Organic Chemicals/*analysis ; Oxidation-Reduction ; Phylogeny ; Secondary Metabolism/genetics ; Soil/*chemistry ; Transcription, Genetic ; }, abstract = {Ectomycorrhizal fungi are thought to have a key role in mobilizing organic nitrogen that is trapped in soil organic matter (SOM). However, the extent to which ectomycorrhizal fungi decompose SOM and the mechanism by which they do so remain unclear, considering that they have lost many genes encoding lignocellulose-degrading enzymes that are present in their saprotrophic ancestors. Spectroscopic analyses and transcriptome profiling were used to examine the mechanisms by which five species of ectomycorrhizal fungi, representing at least four origins of symbiosis, decompose SOM extracted from forest soils. In the presence of glucose and when acquiring nitrogen, all species converted the organic matter in the SOM extract using oxidative mechanisms. The transcriptome expressed during oxidative decomposition has diverged over evolutionary time. Each species expressed a different set of transcripts encoding proteins associated with oxidation of lignocellulose by saprotrophic fungi. The decomposition 'toolbox' has diverged through differences in the regulation of orthologous genes, the formation of new genes by gene duplications, and the recruitment of genes from diverse but functionally similar enzyme families. The capacity to oxidize SOM appears to be common among ectomycorrhizal fungi. We propose that the ancestral decay mechanisms used primarily to obtain carbon have been adapted in symbiosis to scavenge nutrients instead.}, }
@article {pmid26527186, year = {2016}, author = {Dickson, RP and Erb-Downward, JR and Martinez, FJ and Huffnagle, GB}, title = {The Microbiome and the Respiratory Tract.}, journal = {Annual review of physiology}, volume = {78}, number = {}, pages = {481-504}, pmid = {26527186}, issn = {1545-1585}, support = {UL1 TR000433/TR/NCATS NIH HHS/United States ; T32 HL007749/HL/NHLBI NIH HHS/United States ; R01 HL114447/HL/NHLBI NIH HHS/United States ; L30 HL120241/HL/NHLBI NIH HHS/United States ; K23 HL130641/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Humans ; Lung Diseases/*microbiology ; Microbiota/*physiology ; Respiratory System/*microbiology ; }, abstract = {Although the notion that "the normal lung is free from bacteria" remains common in textbooks, it is virtually always stated without citation or argument. The lungs are constantly exposed to diverse communities of microbes from the oropharynx and other sources, and over the past decade, novel culture-independent techniques of microbial identification have revealed that the lungs, previously considered sterile in health, harbor diverse communities of microbes. In this review, we describe the topography and population dynamics of the respiratory tract, both in health and as altered by acute and chronic lung disease. We provide a survey of current techniques of sampling, sequencing, and analysis of respiratory microbiota and review technical challenges and controversies in the field. We review and synthesize what is known about lung microbiota in various diseases and identify key lessons learned across disease states.}, }
@article {pmid26526357, year = {2016}, author = {Kevans, D and Tyler, AD and Holm, K and Jørgensen, KK and Vatn, MH and Karlsen, TH and Kaplan, GG and Eksteen, B and Gevers, D and Hov, JR and Silverberg, MS}, title = {Characterization of Intestinal Microbiota in Ulcerative Colitis Patients with and without Primary Sclerosing Cholangitis.}, journal = {Journal of Crohn's &amp; colitis}, volume = {10}, number = {3}, pages = {330-337}, pmid = {26526357}, issn = {1876-4479}, support = {DK-062423/DK/NIDDK NIH HHS/United States ; //Canadian Institutes of Health Research/Canada ; }, mesh = {Adolescent ; Adult ; Aged ; Biodiversity ; Case-Control Studies ; Child ; Cholangitis, Sclerosing/complications/*microbiology ; Colitis, Ulcerative/complications/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; Phenotype ; Principal Component Analysis ; Young Adult ; }, abstract = {BACKGROUND AND AIMS: There is an unexplained association between ulcerative colitis [UC] and primary sclerosing cholangitis [PSC], with the intestinal microbiota implicated as an important factor. The study aim was to compare the structure of the intestinal microbiota of patients with UC with and without PSC.<br><br>METHODS: UC patients with PSC [PSC-UC] and without PSC [UC] were identified from biobanks at Oslo University Hospital, Foothills Hospital Calgary and Mount Sinai Hospital Toronto. Microbial DNA was extracted from colonic tissue and sequencing performed of the V4 region of the 16S rRNA gene on Illumina MiSeq. Sequences were assigned to operational taxonomic units [OTUs] using Quantitative Insights Into Microbial Ecology [QIIME]. Microbial alpha diversity, beta diversity, and relative abundance were compared between PSC-UC and UC phenotypes.<br><br>RESULTS: In all, 31 PSC-UC patients and 56 UC patients were included. Principal coordinate analysis [PCoA] demonstrated that city of sample collection was the strongest determinant of taxonomic profile. In the Oslo cohort, Chao 1 index was modestly decreased in PSC-UC compared with UC [p = 0.04] but did not differ significantly in the Calgary cohort. No clustering by PSC phenotype was observed using beta diversity measures. For multiple microbial genera there were nominally significant differences between UC and PSC-UC, but results were not robust to false-discovery rate correction.<br><br>CONCLUSIONS: No strong PSC-specific microbial associations in UC patients consistent across different cohorts were identified. Recruitment centre had a strong effect on microbial composition. Future studies should include larger cohorts to increase power and the ability to control for confounding factors.}, }
@article {pmid26526132, year = {2016}, author = {Behzad, H and Ibarra, MA and Mineta, K and Gojobori, T}, title = {Metagenomic studies of the Red Sea.}, journal = {Gene}, volume = {576}, number = {2 Pt 1}, pages = {717-723}, doi = {10.1016/j.gene.2015.10.034}, pmid = {26526132}, issn = {1879-0038}, mesh = {Biotechnology ; Indian Ocean ; *Metagenomics ; Microbiota ; }, abstract = {Metagenomics has significantly advanced the field of marine microbial ecology, revealing the vast diversity of previously unknown microbial life forms in different marine niches. The tremendous amount of data generated has enabled identification of a large number of microbial genes (metagenomes), their community interactions, adaptation mechanisms, and their potential applications in pharmaceutical and biotechnology-based industries. Comparative metagenomics reveals that microbial diversity is a function of the local environment, meaning that unique or unusual environments typically harbor novel microbial species with unique genes and metabolic pathways. The Red Sea has an abundance of unique characteristics; however, its microbiota is one of the least studied among marine environments. The Red Sea harbors approximately 25 hot anoxic brine pools, plus a vibrant coral reef ecosystem. Physiochemical studies describe the Red Sea as an oligotrophic environment that contains one of the warmest and saltiest waters in the world with year-round high UV radiations. These characteristics are believed to have shaped the evolution of microbial communities in the Red Sea. Over-representation of genes involved in DNA repair, high-intensity light responses, and osmoregulation were found in the Red Sea metagenomic databases suggesting acquisition of specific environmental adaptation by the Red Sea microbiota. The Red Sea brine pools harbor a diverse range of halophilic and thermophilic bacterial and archaeal communities, which are potential sources of enzymes for pharmaceutical and biotechnology-based application. Understanding the mechanisms of these adaptations and their function within the larger ecosystem could also prove useful in light of predicted global warming scenarios where global ocean temperatures are expected to rise by 1-3°C in the next few decades. In this review, we provide an overview of the published metagenomic studies that were conducted in the Red Sea, and the bio-prospecting potential of the Red Sea microbiota. Furthermore, we discuss the limitations of the previous studies and the need for generating a large and representative metagenomic database of the Red Sea to help establish a dynamic model of the Red Sea microbiota.}, }
@article {pmid26524974, year = {2016}, author = {Lu, S and Peiffer, S and Lazar, CS and Oldham, C and Neu, TR and Ciobota, V and Näb, O and Lillicrap, A and Rösch, P and Popp, J and Küsel, K}, title = {Extremophile microbiomes in acidic and hypersaline river sediments of Western Australia.}, journal = {Environmental microbiology reports}, volume = {8}, number = {1}, pages = {58-67}, doi = {10.1111/1758-2229.12351}, pmid = {26524974}, issn = {1758-2229}, mesh = {Acids/*analysis ; Archaea/*classification/drug effects/metabolism ; Bacteria/*classification/drug effects/metabolism ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/*chemistry/*microbiology ; Iron/metabolism ; Microbiota/*drug effects ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers ; Sequence Analysis, DNA ; Sodium Chloride/*analysis ; Western Australia ; }, abstract = {We investigated the microbial community compositions in two sediment samples from the acidic (pH ∼3) and hypersaline (>4.5% NaCl) surface waters, which are widespread in Western Australia. In West Dalyup River, large amounts of NaCl, Fe(II) and sulfate are brought by the groundwater into the surface run-off. The presence of K-jarosite and schwertmannite minerals in the river sediments suggested the occurrence of microbial Fe(II) oxidation because chemical oxidation is greatly reduced at low pH. 16S rRNA gene diversity analyses revealed that sequences affiliated with an uncultured archaeal lineage named Aplasma, which has the genomic potential for Fe(II) oxidation, were dominant in both sediment samples. The acidophilic heterotrophs Acidiphilium and Acidocella were identified as the dominant bacterial groups. Acidiphilium strain AusYE3-1 obtained from the river sediment tolerated up to 6% NaCl at pH 3 under oxic conditions and cells of strain AusYE3-1 reduced the effects of high salt content by forming filamentous structure clumping as aggregates. Neither growth nor Fe(III) reduction by strain AusYE3-1 was observed in anoxic salt-containing medium. The detection of Aplasma group as potential Fe(II) oxidizers and the inhibited Fe(III)-reducing capacity of Acidiphilium contributes to our understanding of the microbial ecology of acidic hypersaline environments.}, }
@article {pmid26520832, year = {2016}, author = {Babbin, AR and Jayakumar, A and Ward, BB}, title = {Organic Matter Loading Modifies the Microbial Community Responsible for Nitrogen Loss in Estuarine Sediments.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {555-565}, pmid = {26520832}, issn = {1432-184X}, mesh = {Ammonium Compounds/analysis/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Bays/chemistry/*microbiology ; Biodiversity ; Denitrification ; Geologic Sediments/*analysis ; Maryland ; Nitrogen/analysis/*metabolism ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Coastal marine sediments, as locations of substantial fixed nitrogen loss, are very important to the nitrogen budget and to the primary productivity of the oceans. Coastal sediment systems are also highly dynamic and subject to periodic natural and anthropogenic organic substrate additions. The response to organic matter by the microbial community involved in nitrogen loss processes was evaluated using mesocosms of Chesapeake Bay sediments. Over the course of a 50-day incubation, rates of anammox and denitrification were measured weekly using (15)N tracer incubations, and samples were collected for genetic analysis. Rates of both nitrogen loss processes and gene abundances associated with them corresponded loosely, probably because heterogeneities in sediments obscured a clear relationship. The rates of denitrification were stimulated more, and the fraction of nitrogen loss attributed to anammox slightly reduced, by the higher organic matter addition. Furthermore, the large organic matter pulse drove a significant and rapid shift in the denitrifier community composition as determined using a nirS microarray, indicating that the diversity of these organisms plays an essential role in responding to anthropogenic inputs. We also suggest that the proportion of nitrogen loss due to anammox in these coastal estuarine sediments may be underestimated due to temporal dynamics as well as from methodological artifacts related to conventional sediment slurry incubation approaches.}, }
@article {pmid26520831, year = {2016}, author = {Donald, KJ and Clarke, HV and Mitchell, C and Cornwell, RM and Hubbard, SF and Karley, AJ}, title = {Protection of Pea Aphids Associated with Coinfecting Bacterial Symbionts Persists During Superparasitism by a Braconid Wasp.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {1-4}, pmid = {26520831}, issn = {1432-184X}, mesh = {Animals ; Aphids/growth &amp; development/*microbiology/*parasitology/physiology ; Enterobacteriaceae/*physiology ; Female ; Larva/growth &amp; development ; Male ; Nymph/drug effects ; *Symbiosis ; Wasps/*physiology ; }, abstract = {Bacterial endosymbionts that associate facultatively with insect herbivores can influence insect fitness and trophic interactions. The pea aphid, Acyrthosiphon pisum, can be protected from parasitism by the braconid wasp Aphidius ervi when harbouring particular symbiotic bacteria, with specific endosymbiont coinfections providing almost complete protection. However, studies often quantify aphid mummification with no control over parasitoid oviposition per aphid; thus, if mummy production fails or is low, the causes are often unclear. Here, we show that the high level of protection associated with the coinfecting endosymbionts Hamiltonella defensa and X-type is maintained even when pea aphids are superparasitised. This contrasts strongly with the protection provided by H. defensa alone, which has been shown by others to be overcome by superparasitism. By dissecting aphids exposed to two parasitoid attacks, we reveal that A. ervi deposits eggs equally freely in endosymbiont-infected and uninfected nymphs, and lack of mummification in endosymbiont-protected nymphs arises from failure of the wasp eggs to hatch or emerging larvae to develop.}, }
@article {pmid26519142, year = {2015}, author = {Wang, X and Van Nostrand, JD and Deng, Y and Lü, X and Wang, C and Zhou, J and Han, X}, title = {Scale-dependent effects of climate and geographic distance on bacterial diversity patterns across northern China's grasslands.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {12}, pages = {}, doi = {10.1093/femsec/fiv133}, pmid = {26519142}, issn = {1574-6941}, mesh = {Bacteria/*classification/genetics ; *Biodiversity ; China ; *Climate ; Geography ; *Grassland ; Microbial Consortia/*physiology ; Molecular Typing ; Plants/microbiology ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Patterns of variation in plant and animal diversity along precipitation gradients have been extensively studied, but much less is known about how and to what extent precipitation affects the biogeographic distribution of microbial diversity in arid areas across large spatial scales. Here we collected soils from 54 sites along a 3700 km transect covering a wide range of grassland ecosystems with distinct aridity gradients. We quantified the bacterial community diversity and the effects of climate, edaphic parameter and geographic distance on the bacterial community structure using high-throughput 16S rRNA gene sequencing. Of the 35 phyla detected, 6 were dominant: Actinobacteria, Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Bacteroidetes and Planctomycetes. Aridity was a major factor influencing bacterial diversity, community composition and taxon abundance. Although the pattern of bacterial species richness is markedly different from that of plant species richness, most soil bacteria were endemic to particular bioregions like macro-organisms. Community similarity significantly declined with environmental distance and geographic distance (r = -0.579 and -0.773, respectively). Geographic distance (historical contingencies) contributed more to bacterial community variation (36.02%) than combined environmental factors (24.06%). Overall, our results showed that geographic distance and climatic factors concurrently govern bacterial biogeographic patterns in arid and semi-arid grassland.}, }
@article {pmid27682087, year = {2015}, author = {Aguirre, M and Venema, K}, title = {Does the Gut Microbiota Contribute to Obesity? Going beyond the Gut Feeling.}, journal = {Microorganisms}, volume = {3}, number = {2}, pages = {213-235}, pmid = {27682087}, issn = {2076-2607}, abstract = {Increasing evidence suggests that gut microbiota is an environmental factor that plays a crucial role in obesity. However, the aetiology of obesity is rather complex and depends on different factors. Furthermore, there is a lack of consensus about the exact role that this microbial community plays in the host. The aim of this review is to present evidence about what has been characterized, compositionally and functionally, as obese gut microbiota. In addition, the different reasons explaining the so-far unclear role are discussed considering evidence from in vitro, animal and human studies.}, }
@article {pmid27682082, year = {2015}, author = {Lau, E and Iv, EJ and Dillard, ZW and Dague, RD and Semple, AL and Wentzell, WL}, title = {High Throughput Sequencing to Detect Differences in Methanotrophic Methylococcaceae and Methylocystaceae in Surface Peat, Forest Soil, and Sphagnum Moss in Cranesville Swamp Preserve, West Virginia, USA.}, journal = {Microorganisms}, volume = {3}, number = {2}, pages = {113-136}, pmid = {27682082}, issn = {2076-2607}, abstract = {Northern temperate forest soils and Sphagnum-dominated peatlands are a major source and sink of methane. In these ecosystems, methane is mainly oxidized by aerobic methanotrophic bacteria, which are typically found in aerated forest soils, surface peat, and Sphagnum moss. We contrasted methanotrophic bacterial diversity and abundances from the (i) organic horizon of forest soil; (ii) surface peat; and (iii) submerged Sphagnum moss from Cranesville Swamp Preserve, West Virginia, using multiplex sequencing of bacterial 16S rRNA (V3 region) gene amplicons. From ~1 million reads, >50,000 unique OTUs (Operational Taxonomic Units), 29 and 34 unique sequences were detected in the Methylococcaceae and Methylocystaceae, respectively, and 24 potential methanotrophs in the Beijerinckiaceae were also identified. Methylacidiphilum-like methanotrophs were not detected. Proteobacterial methanotrophic bacteria constitute <2% of microbiota in these environments, with the Methylocystaceae one to two orders of magnitude more abundant than the Methylococcaceae in all environments sampled. The Methylococcaceae are also less diverse in forest soil compared to the other two habitats. Nonmetric multidimensional scaling analyses indicated that the majority of methanotrophs from the Methylococcaceae and Methylocystaceae tend to occur in one habitat only (peat or Sphagnum moss) or co-occurred in both Sphagnum moss and peat. This study provides insights into the structure of methanotrophic communities in relationship to habitat type, and suggests that peat and Sphagnum moss can influence methanotroph community structure and biogeography.}, }
@article {pmid27800364, year = {2014}, author = {Chiesa, F and Lomonaco, S and Nucera, D and Garoglio, D and Dalmasso, A and Civera, T}, title = {Distribution of Pseudomonas Species in a Dairy Plant Affected by Occasional Blue Discoloration.}, journal = {Italian journal of food safety}, volume = {3}, number = {4}, pages = {1722}, pmid = {27800364}, issn = {2239-7132}, abstract = {During 2010 many cases of discoloration in mozzarella, popularly termed as blue mozzarella, have been reported to the attention of public opinion. Causes of the alteration were bacteria belonging to the genus Pseudomonas. The strong media impact of such cases has created confusion, not only among consumers, but also among experts. In order to help improving the knowledge on microbial ecology of this microorganism a study has been set up with the collaboration of a medium-sized dairy plant producing fresh mozzarella cheese, with occasional blue discoloration, conducting surveys and sampling in the pre-operational, operational and post-operational process phase, milk before and after pasteurization, water (n=12), environmental surfaces (n=22) and the air (n=27). A shelf life test was conducted on finished products stored at different temperatures (4-8°C). Among the isolates obtained from the microbiological analysis of the samples, 60 were subjected to biomolecular tests in order to confirm the belonging to Pseudomonas genus and to get an identification at species level by the amplification and sequencing of the gyrB gene. The results of microbiological tests demonstrated the presence of microorganisms belonging to the genus Pseudomonas along the entire production lane; molecular tests showed 7 different species among the 40 isolates identified. One particular species (Pseudomonas koreensis) was isolated from blue discolored mozzarella cheese and was indicated as the most relevant for the production plant, both for the distribution along the processing chain and for the consequences on the finished product.}, }
@article {pmid27800358, year = {2014}, author = {Brignardello, S and Sabiu, R and Tedde, T and Cocco, E and Pitzalis, G and Meli, C and Cogoni, MP}, title = {Microbiological Findings in Ready-to-Eat and Precooked Food Distributed in Public Catering Halls in Cagliari Province, Italy.}, journal = {Italian journal of food safety}, volume = {3}, number = {3}, pages = {1733}, pmid = {27800358}, issn = {2239-7132}, abstract = {During this research 159 samples of ready-to-eat and precooked food were examined for the detection of Salmonella spp., Listeria monocytogenes, Escherichia coli, coagulase-positive staphylococci and Enterobacteriaceae, bacterial count. All samples were negative for Salmonella spp. and Listeria monocytogenes; although a low count of coagulase-positive staphylococci (no. 5 samples) and E. coli (no. 3) was found. We proceeded with the identification of the isolates on every sample with high, moderate and low-count of Enterobacteriaceae, to better understand the microbial ecology. The Enterobacteriaceae species most frequently detected were Pantoea spp. (29.62%), Enterobacter cloacae (20.37%) and Serratia liquefaciens (12.96%); other different species of Enterobacteriaceae were detected with a <10% presence. Since there are no legal regulations indicating tolerance or limit values or this kind of microorganisms related to the samples, it would be appropriate, in the presence of high count of Enterobacteriaceae or by type of ready-to-eat and precooked food, to proceed with the identification of every microorganism.}, }
@article {pmid26988190, year = {2014}, author = {Samanta, B and Bhadury, P}, title = {Analysis of diversity of chromophytic phytoplankton in a mangrove ecosystem using rbcL gene sequencing.}, journal = {Journal of phycology}, volume = {50}, number = {2}, pages = {328-340}, doi = {10.1111/jpy.12163}, pmid = {26988190}, issn = {1529-8817}, abstract = {Phytoplankton forms the basis of primary production in mangrove environments. The phylogeny and diversity based on the amplification and sequencing of rbcL, the large subunit encoding the key enzyme ribulose-1, 5-bisphosphate carboxylase/oxygenase was investigated for improved understanding of the community structure and temporal trends of chromophytic eukaryotic phytoplankton assemblages in Sundarbans, the world's largest continuous mangrove. Diatoms (Bacillariophyceae) were by far the most frequently detected group in clone libraries (485 out of 525 clones), consistent with their importance as a major bloom-forming group. Other major chromophytic algal groups including Cryptophyceae, Haptophyceae, Pelagophyceae, Eustigmatophyceae, and Raphidophyceae which are important component of the assemblages were detected for the first time from Sundarbans based on rbcL approach. Many of the sequences from Sundarbans rbcL clone libraries showed identity with key bloom forming diatom genera namely Thalassiosira, Skeletonema and Nitzschia. Similarly, several rbcL sequences which were diatom-like were also detected highlighting the need to explore diatom communities from the study area. Some of the rbcL sequences detected from Sundarbans were ubiquitous in distribution showing 100% identities with uncultured rbcL sequences targeted previously from the Gulf of Mexico and California upwelling system that are geographically separated from study area. Novel rbcL lineages were also detected highlighting the need to culture and sequence phytoplankton from the ecoregion. Principal component analysis revealed that nitrate is an important variable that is associated with observed variation in phytoplankton assemblages (operational taxonomic units). This study applied molecular tools to highlight the ecological significance of diatoms, in addition to other chromophytic algal groups in Sundarbans.}, }
@article {pmid27694764, year = {2013}, author = {Tunin-Ley, A and Lemée, R}, title = {The Genus Neoceratium (Planktonic Dinoflagellates) as a Potential Indicator of Ocean Warming.}, journal = {Microorganisms}, volume = {1}, number = {1}, pages = {58-70}, pmid = {27694764}, issn = {2076-2607}, abstract = {Among the planktonic dinoflagellates, the species-rich genus Neoceratium has particularly remarkable features that include its easily recognizable outline and large size. This ubiquitous genus shows consistent presence in all plankton samples and has been a model for numerous studies since the end of the 19th century. It has already been described as a good candidate to monitor water masses and describe ocean circulation. We argue that the sensitivity displayed by Neoceratium to water temperature also makes it relevant as an indicator of ocean warming. The advantages and interests of using Neoceratium species to monitor climate change on a large scale are reassessed in view of recent advances in understanding their biology and ecology.}, }
@article {pmid27873585, year = {2013}, author = {Elli, M and Arioli, S and Guglielmetti, S and Mora, D}, title = {Biocide susceptibility in bifidobacteria of human origin.}, journal = {Journal of global antimicrobial resistance}, volume = {1}, number = {2}, pages = {97-101}, doi = {10.1016/j.jgar.2013.03.007}, pmid = {27873585}, issn = {2213-7173}, abstract = {Disinfectants have been used in a variety of environmental applications, in products for personal care and in the food industry. The food industry has increased the use of biocides and chemical-based disinfectants to control microbial ecology at production sites in an effort to improve hygiene measures and food safety. However, the susceptibility profile of micro-organisms to disinfectants has been largely neglected. This study therefore aimed to provide this type of information by focusing on the four most commonly used biocides in the food industry, determining their minimum inhibitory concentrations (MICs) and analysing the distribution of MICs across a variety of micro-organisms. In total, 99 different strains of Bifidobacterium spp. were studied. Results showed a unimodal distribution of MICs for chlorhexidine, triclosan (Irgasan) and sodium hypochlorite with no apparent species-specific correlation. Conversely, part of the tested bifidobacteria population (20%) showed reduced susceptibility to benzalkonium chloride compared with the susceptibility exhibited by the majority of the tested bacterial community. The highest MICs were distributed among almost all of the considered Bifidobacterium spp. In generally, the sensitivity of the studied strains to the four tested biocides appeared to be a genus-related trait.}, }
@article {pmid27007041, year = {2013}, author = {Bittar, TB and Lin, Y and Sassano, LR and Wheeler, BJ and Brown, SL and Cochlan, WP and Johnson, ZI}, title = {Carbon allocation under light and nitrogen resource gradients in two model marine phytoplankton(1).}, journal = {Journal of phycology}, volume = {49}, number = {3}, pages = {523-535}, doi = {10.1111/jpy.12060}, pmid = {27007041}, issn = {0022-3646}, abstract = {Marine phytoplankton have conserved elemental stoichiometry, but there can be significant deviations from this Redfield ratio. Moreover, phytoplankton allocate reduced carbon (C) to different biochemical pools based on nutritional status and light availability, adding complexity to this relationship. This allocation influences physiology, ecology, and biogeochemistry. Here, we present results on the physiological and biochemical properties of two evolutionarily distinct model marine phytoplankton, a diatom (cf. Staurosira sp. Ehrenberg) and a chlorophyte (Chlorella sp. M. Beijerinck) grown under light and nitrogen resource gradients to characterize how carbon is allocated under different energy and substrate conditions. We found that nitrogen (N)-replete growth rate increased monotonically with light until it reached a threshold intensity (~200 μmol photons · m(-2) · s(-1)). For Chlorella sp., the nitrogen quota (pg · μm(-3)) was greatest below this threshold, beyond which it was reduced by the effect of N-stress, while for Staurosira sp. there was no trend. Both species maintained constant maximum quantum yield of photosynthesis (mol C · mol photons(-1)) over the range of light and N-gradients studied (although each species used different photophysiological strategies). In both species, C:chl a (g · g(-1)) increased as a function of light and N-stress, while C:N (mol · mol(-1)) and relative neutral lipid:C (rel. lipid · g(-1)) were most strongly influenced by N-stress above the threshold light intensity. These results demonstrated that the interaction of substrate (N-availability) and energy gradients influenced C-allocation, and that general patterns of biochemical responses may be conserved among phytoplankton; they provided a framework for predicting phytoplankton biochemical composition in ecological, biogeochemical, or biotechnological applications.}, }
@article {pmid27478304, year = {2009}, author = {Weinbauer, MG and Bettarel, Y and Cattaneo, R and Luef, B and Maier, C and Motegi, C and Peduzzi, P and Mari, X}, title = {Viral ecology of organic and inorganic particles in aquatic systems: avenues for further research.}, journal = {Aquatic microbial ecology : international journal}, volume = {57}, number = {3}, pages = {321-341}, pmid = {27478304}, issn = {0948-3055}, support = {P 17798/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Viral abundance and processes in the water column and sediments are well studied for some systems; however, we know relatively little about virus-host interactions on particles and how particles influence these interactions. Here we review virus-prokaryote interactions on inorganic and organic particles in the water column. Profiting from recent methodological progress, we show that confocal laser scanning microscopy in combination with lectin and nucleic acid staining is one of the most powerful methods to visualize the distribution of viruses and their hosts on particles such as organic aggregates. Viral abundance on suspended matter ranges from 10[5] to 10[11] ml[-1]. The main factors controlling viral abundance are the quality, size and age of aggregates and the exposure time of viruses to aggregates. Other factors such as water residence time likely act indirectly. Overall, aggregates appear to play a role of viral scavengers or reservoirs rather than viral factories. Adsorption of viruses to organic aggregates or inorganic particles can stimulate growth of the free-living prokaryotic community, e.g. by reducing viral lysis. Such mechanisms can affect microbial diversity, food web structure and biogeochemical cycles. Viral lysis of bacterio- and phytoplankton influences the formation and fate of aggregates and can, for example, result in a higher stability of algal flocs. Thus, viruses also influence carbon export; however, it is still not clear whether they short-circuit or prime the biological pump. Throughout this review, emphasis has been placed on defining general problems and knowledge gaps in virus-particle interactions and on providing avenues for further research, particularly those linked to global change.}, }
@article {pmid26311126, year = {2016}, author = {Norte, AC and Araújo, PM and da Silva, LP and Tenreiro, PQ and Ramos, JA and Núncio, MS and Zé-Zé, L and de Carvalho, IL}, title = {Characterization Through Multilocus Sequence Analysis of Borrelia turdi Isolates from Portugal.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {831-839}, pmid = {26311126}, issn = {1432-184X}, mesh = {Animals ; *Borrelia/classification/genetics/isolation &amp; purification ; DNA, Intergenic/genetics ; Genes, Essential/genetics ; Ixodes/*microbiology ; Multilocus Sequence Typing ; *Passeriformes ; Portugal ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Borrelia turdi is a spirochete from the Borrelia burgdorferi complex, first reported in Japan, that has been increasingly detected in Europe. This genospecies is mostly associated with avian hosts and their ornithophilic ticks such as Ixodes frontalis. In this study, we isolated B. turdi from five I. frontalis feeding on Turdus merula, Turdus philomelos, Parus major and Troglodytes troglodytes, and one Ixodes ricinus feeding on a T. merula in Portugal. These isolates were genetically characterised according to their 5S-23S rRNA intergenic spacer, 16S rRNA and through typing of seven housekeeping genes (multilocus sequence typing). Multilocus sequence analyses revealed that the strains isolated in our study, although belonging to B. turdi genospecies, are not identical to the B. turdi reference strain Ya501. Instead, our strains are separated into a clear defined group, suggesting that the European samples diverged genetically from the strain originally detected in Japan. Population analysis of 5S-23S rRNA sequences can further resolve subpopulations within B. turdi, but more samples from a large geographical scale and host range would be needed to assess potential phylogeographical patterns within this genospecies.}, }
@article {pmid26276409, year = {2016}, author = {France, MT and Remold, SK}, title = {Interference Competition Among Household Strains of Pseudomonas.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {821-830}, pmid = {26276409}, issn = {1432-184X}, mesh = {Bacteriocins/metabolism ; Ecosystem ; Humans ; Microbial Interactions/*physiology ; Phylogeny ; Pseudomonas aeruginosa/classification/*growth &amp; development/isolation &amp; purification ; Pseudomonas fluorescens/classification/*growth &amp; development/isolation &amp; purification ; Pseudomonas putida/classification/*growth &amp; development/isolation &amp; purification ; Pyocins/metabolism ; *Residence Characteristics ; }, abstract = {Bacterial species exhibit biogeographical patterns like those observed in larger organisms. The distribution of bacterial species is driven by environmental selection through abiotic and biotic factors as well dispersal limitations. We asked whether interference competition, a biotic factor, could explain variability in habitat use by Pseudomonas species in the human home. To answer this question, we screened almost 8000 directional, pairwise interactions between 89 Pseudomonas strains including members of the Pseudomonas aeruginosa (n = 29), Pseudomonas fluorescens (n = 21), and Pseudomonas putida (n = 39) species groups for the presence of killing. This diverse set of Pseudomonas strains includes those isolated from several different habitats within the home environment and includes combinations of strains that were isolated from different spatial scales. The use of this strain set not only allowed us to analyze the commonality and phylogenetic scale of interference competition within the genus Pseudomonas but also allowed us to investigate the influence of spatial scale on this trait. Overall, the probability of killing was found to decrease with increasing phylogenetic distance, making it unlikely that interference competition accounts for previously observed differential habitat use among Pseudomonas species and species groups. Strikingly, conspecific P. aeruginosa killing accounted for the vast majority of the observed killing, and this killing was found to differ across the habitat type and spatial scale of the strains' isolation. These data suggest that interference competition likely plays a large role in the within-species dynamics of P. aeruginosa but not other household Pseudomonas species.}, }
@article {pmid26194421, year = {2016}, author = {Lozano, C and Gonzalez-Barrio, D and Camacho, MC and Lima-Barbero, JF and de la Puente, J and Höfle, U and Torres, C}, title = {Characterization of fecal vancomycin-resistant enterococci with acquired and intrinsic resistance mechanisms in wild animals, Spain.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {813-820}, pmid = {26194421}, issn = {1432-184X}, mesh = {Aminoglycosides/pharmacology ; Ampicillin/pharmacology ; Ampicillin Resistance/genetics ; Animals ; Animals, Wild/microbiology ; Bacterial Proteins/genetics ; Carbon-Oxygen Ligases/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Enterococcus faecium/genetics/growth &amp; development/isolation &amp; purification ; Falconiformes/*microbiology ; Feces/microbiology ; Galliformes/*microbiology ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Spain ; Sus scrofa/*microbiology ; Tetracycline/pharmacology ; Tetracycline Resistance/genetics ; Vancomycin/*pharmacology ; Vancomycin-Resistant Enterococci/*genetics/*isolation &amp; purification ; }, abstract = {The objectives were to evaluate the presence of vancomycin-resistant enterococci with acquired (VRE-a) and intrinsic (VRE-i) resistance mechanisms in fecal samples from different wild animals, and analyze their phenotypes and genotypes of antimicrobial resistance. A total of 348 cloacal/rectal samples from red-legged partridges (127), white storks (81), red kites (59), and wild boars (81) (June 2014/February 2015) were inoculated in Slanetz-Bartley agar supplemented with vancomycin (4 μg/mL). We investigated the susceptibility to 12 antimicrobials and the presence of 19 antimicrobial resistance and five virulence genes. In addition, we performed multilocus sequence typing, detection of IS16 and studied Tn1546 structure. One VRE-a isolate was identified in one wild boar. This isolate was identified as Enterococcus faecium, harbored vanA gene included into Tn1546 (truncated with IS1542/IS1216), and belonged to the new ST993. This isolate contained the erm(A), erm(B), tet(M), dfrG, and dfrK genes. Neither element IS16 nor the studied virulence genes were detected. Ninety-six VRE-i isolates were identified (89 Enterococcus gallinarum and seven Enterococcus casseliflavus), with the following prevalence: red kites (71.2 %), white storks (46.9 %), red-legged partridges (7.9 %), and wild boars (4.9 %). Most E. gallinarum isolates showed resistance to tetracycline (66.3 %) and/or erythromycin (46.1 %). High-level resistance to aminoglycosides was present among our VRE-i isolates: kanamycin (22.9 %), streptomycin (11.5 %), and gentamicin (9.4 %). In general, VRE-i isolates of red kites showed higher rates of resistance for non-glycopeptide agents than those of other animal species. The dissemination of acquired resistance mechanisms in natural environments could have implications in the global spread of resistance with public health implications.}, }
@article {pmid26162534, year = {2016}, author = {Fernandez, B and Savard, P and Fliss, I}, title = {Survival and Metabolic Activity of Pediocin Producer Pediococcus acidilactici UL5: Its Impact on Intestinal Microbiota and Listeria monocytogenes in a Model of the Human Terminal Ileum.}, journal = {Microbial ecology}, volume = {72}, number = {4}, pages = {931-942}, pmid = {26162534}, issn = {1432-184X}, mesh = {Azides/pharmacology ; Fermentation ; Gastrointestinal Microbiome/*physiology ; Humans ; Ileum/*microbiology ; Listeria monocytogenes/*growth &amp; development ; Pediocins/*metabolism ; Pediococcus acidilactici/*metabolism ; Probiotics/*metabolism ; Propidium/analogs &amp; derivatives/pharmacology ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; }, abstract = {Pediococcus acidilactici UL5 is a promising probiotic candidate due to its high survival rate under gastric and duodenal conditions and to its ability to produce the antilisterial bacteriocin pediocin PA-1. Its survival, metabolic activity, and impact on Listeria monocytogenes in a continuous stirred tank reactor containing immobilized human intestinal microbiota were studied over a period of 32 days of feeding a nutrient medium simulating ileal chyme. The impact of P. acidilactici UL5 on different bacterial groups of intestinal origin as well as its survival and its impact on L. monocytogenes were quantified using quantitative polymerase chain reaction coupling with propidium monoazide (PMA-qPCR), which was shown to detect and quantify viable bacteria only. P. acidilactici UL5 and its non-pediocin-producing mutant had no effect on the microbiota, but the producing strain induced an increase in the production of acetic and propionic acids. P. acidilactici survived but appeared to be a poor competitor with intestinal microbiota, dropping by 1.3 and 2.8 log10 after 8 h of fermentation to 10[4] colony-forming units (cfu) mL[-1]. A 1.64 log but non-significant reduction of Listeria was observed when P. acidilactici UL5 was added at 10[8] cfu mL[-1]. P. acidilactici UL5 isolated from the reactor after 3 days was still able to produce the active bacteriocin. These data demonstrate that P. acidilactici UL5 is capable of surviving transit through the ileum without losing its ability to produce pediocin PA-1 but seems to not be enough competitive with the great diversity of organisms found in the ileum.}, }
@article {pmid26518432, year = {2016}, author = {Otani, S and Hansen, LH and Sørensen, SJ and Poulsen, M}, title = {Bacterial communities in termite fungus combs are comprised of consistent gut deposits and contributions from the environment.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {207-220}, pmid = {26518432}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Environment ; Fungi/classification/genetics/*isolation &amp; purification ; *Gastrointestinal Microbiome ; Isoptera/classification/*microbiology ; Phylogeny ; Termitomyces/growth &amp; development/physiology ; }, abstract = {Fungus-growing termites (subfamily Macrotermitinae) mix plant forage with asexual spores of their plant-degrading fungal symbiont Termitomyces in their guts and deposit this blend in fungus comb structures, within which the plant matter is degraded. As Termitomyces grows, it produces nodules with asexual spores, which the termites feed on. Since all comb material passes through termite guts, it is inevitable that gut bacteria are also deposited in the comb, but it has remained unknown which bacteria are deposited and whether distinct comb bacterial communities are sustained. Using high-throughput sequencing of the 16S rRNA gene, we explored the bacterial community compositions of 33 fungus comb samples from four termite species (three genera) collected at four South African geographic locations in 2011 and 2013. We identified 33 bacterial phyla, with Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Candidate division TM7 jointly accounting for 92 % of the reads. Analyses of gut microbiotas from 25 of the 33 colonies showed that dominant fungus comb taxa originate from the termite gut. While gut communities were consistent between 2011 and 2013, comb community compositions shifted over time. These shifts did not appear to be due to changes in the taxa present, but rather due to differences in the relative abundances of primarily gut-derived bacteria within fungus combs. This indicates that fungus comb microbiotas are largely termite species-specific due to major contributions from gut deposits and also that environment affects which gut bacteria dominate comb communities at a given point in time.}, }
@article {pmid26516406, year = {2015}, author = {Junghare, M and Patil, Y and Schink, B}, title = {Draft genome sequence of a nitrate-reducing, o-phthalate degrading bacterium, Azoarcus sp. strain PA01(T).}, journal = {Standards in genomic sciences}, volume = {10}, number = {}, pages = {90}, pmid = {26516406}, issn = {1944-3277}, abstract = {Azoarcus sp. strain PA01(T) belongs to the genus Azoarcus, of the family Rhodocyclaceae within the class Betaproteobacteria. It is a facultatively anaerobic, mesophilic, non-motile, Gram-stain negative, non-spore-forming, short rod-shaped bacterium that was isolated from a wastewater treatment plant in Constance, Germany. It is of interest because of its ability to degrade o-phthalate and a wide variety of aromatic compounds with nitrate as an electron acceptor. Elucidation of the o-phthalate degradation pathway may help to improve the treatment of phthalate-containing wastes in the future. Here, we describe the features of this organism, together with the draft genome sequence information and annotation. The draft genome consists of 4 contigs with 3,908,301 bp and an overall G + C content of 66.08 %. Out of 3,712 total genes predicted, 3,625 genes code for proteins and 87 genes for RNAs. The majority of the protein-encoding genes (83.51 %) were assigned a putative function while those remaining were annotated as hypothetical proteins.}, }
@article {pmid26516020, year = {2017}, author = {Jobard, M and Pessiot, J and Nouaille, R and Fonty, G and Sime-Ngando, T}, title = {Microbial diversity in support of anaerobic biomass valorization.}, journal = {Critical reviews in biotechnology}, volume = {37}, number = {1}, pages = {1-10}, doi = {10.3109/07388551.2015.1100584}, pmid = {26516020}, issn = {1549-7801}, mesh = {Anaerobiosis ; Biomass ; Biotechnology ; Fermentation ; Hydrogen/*metabolism ; Methane/*biosynthesis ; *Microbial Consortia ; Waste Management/*methods ; }, abstract = {Microbial diversity provides an immense reservoir of functions and supports key steps in maintaining ecosystem balance through matter decomposition processes and nutrient recycling. The use of microorganisms for biomolecule production is now common, but often involves single-strain cultures. In this review, we highlight the significance of using ecosystem-derived microbial diversity for biotechnological researches. In the context of organic matter mineralization, diversity of microorganisms is essential and enhances the degradation processes. We focus on anaerobic production of biomolecules of interest from discarded biomass, which is an important issue in the context of organic waste valorization and processing. Organic waste represents an important and renewable raw material but remains underused. It is commonly accepted that anaerobic mineralization of organic waste allows the production of diverse interesting molecules within several fields of application. We provide evidence that complex and diversified microbial communities isolated from ecosystems, i.e. microbial consortia, offer considerable advantages in degrading complex organic waste, to yield biomolecules of interest. We defend our opinion that this approach is more efficient and offers enhanced potential compared to the approaches that use single strain cultures.}, }
@article {pmid26512812, year = {2016}, author = {Lu, H and Xue, Z and Saikaly, P and Nunes, SP and Bluver, TR and Liu, WT}, title = {Membrane biofouling in a wastewater nitrification reactor: Microbial succession from autotrophic colonization to heterotrophic domination.}, journal = {Water research}, volume = {88}, number = {}, pages = {337-345}, doi = {10.1016/j.watres.2015.10.013}, pmid = {26512812}, issn = {1879-2448}, mesh = {Autotrophic Processes ; Biofilms ; *Biofouling ; Biopolymers/chemistry/metabolism ; Bioreactors/*microbiology ; Heterotrophic Processes ; Membranes, Artificial ; Microbial Consortia/genetics/*physiology ; Nitrification ; RNA, Ribosomal, 16S ; Ultrafiltration/instrumentation ; Waste Disposal, Fluid/instrumentation/*methods ; }, abstract = {Membrane biofouling is a complex process that involves bacterial adhesion, extracellular polymeric substances (EPS) excretion and utilization, and species interactions. To obtain a better understanding of the microbial ecology of biofouling process, this study conducted rigorous, time-course analyses on the structure, EPS and microbial composition of the fouling layer developed on ultrafiltration membranes in a nitrification bioreactor. During a 14-day fouling event, three phases were determined according to the flux decline and microbial succession patterns. In Phase I (0-2 days), small sludge flocs in the bulk liquid were selectively attached on membrane surfaces, leading to the formation of similar EPS and microbial community composition as the early biofilms. Dominant populations in small flocs, e.g., Nitrosomonas, Nitrobacter, and Acinetobacter spp., were also the major initial colonizers on membranes. In Phase II (2-4 d), fouling layer structure, EPS composition, and bacterial community went through significant changes. Initial colonizers were replaced by fast-growing and metabolically versatile heterotrophs (e.g., unclassified Sphingobacteria). The declining EPS polysaccharide to protein (PS:PN) ratios could be correlated well with the increase in microbial community diversity. In Phase III (5-14 d), heterotrophs comprised over 90% of the community, whereas biofilm structure and EPS composition remained relatively stable. In all phases, AOB and NOB were constantly found within the top 40% of the fouling layer, with the maximum concentrations around 15% from the top. The overall microbial succession pattern from autotrophic colonization to heterotrophic domination implied that MBR biofouling could be alleviated by forming larger bacterial flocs in bioreactor suspension (reducing autotrophic colonization), and by designing more specific cleaning procedures targeting dominant heterotrophs during typical filtration cycles.}, }
@article {pmid26511725, year = {2015}, author = {Xu, H and Liu, W and Zhang, W and Yu, J and Song, Y and Menhe, B and Zhang, H and Sun, Z}, title = {Use of multilocus sequence typing to infer genetic diversity and population structure of Lactobacillus plantarum isolates from different sources.}, journal = {BMC microbiology}, volume = {15}, number = {}, pages = {241}, pmid = {26511725}, issn = {1471-2180}, mesh = {China ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Genes, Essential ; *Genetic Variation ; Genotype ; Lactobacillus plantarum/*classification/*genetics/isolation &amp; purification ; Molecular Sequence Data ; Mongolia ; Multilocus Sequence Typing/*methods ; Phylogeny ; Recombination, Genetic ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {BACKGROUND: Lactobacillus plantarum is a lactic acid bacterium (LAB) of considerable industrial interest since it has an important role in the production of fermented food. In the present study, the genetic diversity and population structure within 186 L. plantarum isolates was determined based on a novel MLST scheme employing eight housekeeping genes. These isolates had originated from different sources and geographic regions: 179 isolates were from our own culture collection and originated from China and Mongolia and seven isolates were type or reference isolates from other collections.<br><br>RESULTS: The results showed that 179 isolates and seven reference isolates could be assigned to 73 different sequence types (STs), forming ten clonal complexes (CCs) and 23 singletons. There were 158 polymorphic sites detected in total, and the nucleotide diversity per site varied from 0.00401 in clpX to 0.03220 in groEL. The minimum spanning tree analyses suggested that the evolution of L. plantarum isolates have little relationship with ecological sources have similar nucleotide diversity. Phylogenetic trees and structure indicated that there were six lineages in the L. plantarum isolates used in our study. Split-decomposition and ClonalFrame analysis indicated that recombination had occurred throughout the population of L. plantarum, but it occurred at a low frequency in these eight loci.<br><br>CONCLUSION: We deduced that L. plantarum isolates from the same ecological niches have similar genetic diversity and population structure. The MLST scheme presented in this study provides abundant sequence data for L. plantarum and enabled global comparisons of isolates associated with various environmental origins to be made. This will further advance our understanding of the microbial ecology of this industrially important LAB.}, }
@article {pmid26511052, year = {2015}, author = {Cardini, U and Bednarz, VN and Naumann, MS and van Hoytema, N and Rix, L and Foster, RA and Al-Rshaidat, MM and Wild, C}, title = {Functional significance of dinitrogen fixation in sustaining coral productivity under oligotrophic conditions.}, journal = {Proceedings. Biological sciences}, volume = {282}, number = {1818}, pages = {20152257}, pmid = {26511052}, issn = {1471-2954}, mesh = {Animals ; Anthozoa/metabolism/*microbiology ; Chlorophyll/analysis ; Chlorophyll A ; Coral Reefs ; Dinoflagellida/*metabolism ; Indian Ocean ; Light ; Nitrogen/metabolism ; *Nitrogen Fixation ; Photosynthesis/physiology ; Seasons ; Symbiosis ; Temperature ; }, abstract = {Functional traits define species by their ecological role in the ecosystem. Animals themselves are host-microbe ecosystems (holobionts), and the application of ecophysiological approaches can help to understand their functioning. In hard coral holobionts, communities of dinitrogen (N2)-fixing prokaryotes (diazotrophs) may contribute a functional trait by providing bioavailable nitrogen (N) that could sustain coral productivity under oligotrophic conditions. This study quantified N2 fixation by diazotrophs associated with four genera of hermatypic corals on a northern Red Sea fringing reef exposed to high seasonality. We found N2 fixation activity to be 5- to 10-fold higher in summer, when inorganic nutrient concentrations were lowest and water temperature and light availability highest. Concurrently, coral gross primary productivity remained stable despite lower Symbiodinium densities and tissue chlorophyll a contents. In contrast, chlorophyll a content per Symbiodinium cell increased from spring to summer, suggesting that algal cells overcame limitation of N, an essential element for chlorophyll synthesis. In fact, N2 fixation was positively correlated with coral productivity in summer, when its contribution was estimated to meet 11% of the Symbiodinium N requirements. These results provide evidence of an important functional role of diazotrophs in sustaining coral productivity when alternative external N sources are scarce.}, }
@article {pmid26507964, year = {2016}, author = {Lee, HJ and Whang, KS}, title = {Catenulispora fulva sp. nov., isolated from forest soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {66}, number = {1}, pages = {271-275}, doi = {10.1099/ijsem.0.000711}, pmid = {26507964}, issn = {1466-5034}, mesh = {Actinomycetales/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Diaminopimelic Acid/chemistry ; Fatty Acids/chemistry ; *Forests ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Peptidoglycan/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {An actinomycete strain, designated SA-246T, was isolated from a forest soil sample collected from Chungnam, South Korea. Applying a polyphasic approach, the isolate was identified as a member of the genus Catenulispora using morphological and chemotaxonomic characteristics, including the presence of ll-diaminopimelic acid, glutamic acid, alanine and glycine in the peptidoglycan. Whole-cell hydrolysates contained predominantly rhamnose, mannose, ribose, arabinose, galactose and glucose. The major menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8). 16S rRNA gene sequence analysis revealed that strain SA-246T belongs to the genus Catenulispora, showing the highest sequence similarity to Catenulispora yoronensis TT N02-20T (98.7 % 16S rRNA gene sequence similarity), Catenulispora subtropica TT 99-48T (98.2 %), Catenulispora graminis BR-34T (97.4 %), Catenulispora rubra Aac-30T (97.4 %) and Catenulispora acidiphila ID139908T (97.3 %). On the basis of polyphasic analysis from this study, strain SA-246T represents a novel species of the genus Catenulispora, for which the name Catenulispora fulva sp. nov. is proposed. The type strain is SA-246T (= KACC 17878T = NBRC 110074T).}, }
@article {pmid26507846, year = {2016}, author = {Schulz, K and Mikhailyuk, T and Dreßler, M and Leinweber, P and Karsten, U}, title = {Biological Soil Crusts from Coastal Dunes at the Baltic Sea: Cyanobacterial and Algal Biodiversity and Related Soil Properties.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {178-193}, pmid = {26507846}, issn = {1432-184X}, mesh = {Baltic States ; *Biodiversity ; Chlorophyta/*classification/genetics ; Cyanobacteria/classification/genetics/*isolation &amp; purification ; Diatoms/classification/genetics/isolation &amp; purification ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Biological soil crusts (BSCs) are known as "ecosystem-engineers" that have important, multifunctional ecological roles in primary production, in nutrient and hydrological cycles, and in stabilization of soils. These communities, however, are almost unstudied in coastal dunes of the temperate zone. Hence, for the first time, the biodiversity of cyanobacterial and algal dominated BSCs collected in five dunes from the southern Baltic Sea coast on the islands Rügen and Usedom (Germany) was investigated in connection with physicochemical soil parameters. The species composition of cyanobacteria and algae was identified with direct determination of crust subsamples, cultural methods, and diatom slides. To investigate the influence of soil properties on species composition, the texture, pH, electrical conductivity, carbonate content, total contents of carbon, nitrogen, phosphorus, and the bioavailable phosphorus-fraction (PO4 (3-)) were analyzed in adjacent BSC-free surface soils at each study site. The data indicate that BSCs in coastal dunes of the southern Baltic Sea represent an ecologically important vegetation form with a surprisingly high site-specific diversity of 19 cyanobacteria, 51 non-diatom algae, and 55 diatoms. All dominant species of the genera Coleofasciculus, Lyngbya, Microcoleus, Nostoc, Hydrocoryne, Leptolyngbya, Klebsormidium, and Lobochlamys are typical aero-terrestrial cyanobacteria and algae, respectively. This first study of coastal sand dunes in the Baltic region provides compelling evidence that here the BSCs were dominated by cyanobacteria, algae, or a mixture of both. Among the physicochemical soil properties, the total phosphorus content of the BSC-free sand was the only factor that significantly influenced the cyanobacterial and algal community structure of BSCs in coastal dunes.}, }
@article {pmid26507767, year = {2015}, author = {Ravi, A and Avershina, E and Foley, SL and Ludvigsen, J and Storrø, O and Øien, T and Johnsen, R and McCartney, AL and L'Abée-Lund, TM and Rudi, K}, title = {The commensal infant gut meta-mobilome as a potential reservoir for persistent multidrug resistance integrons.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {15317}, pmid = {26507767}, issn = {2045-2322}, mesh = {Bacteria/*genetics/metabolism ; Bacterial Physiological Phenomena ; DNA, Bacterial ; Drug Resistance, Multiple, Bacterial/*genetics ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Infant ; Infant, Newborn ; Integrases/*genetics ; *Integrons ; Pregnancy ; *Symbiosis ; }, abstract = {Despite the accumulating knowledge on the development and establishment of the gut microbiota, its role as a reservoir for multidrug resistance is not well understood. This study investigated the prevalence and persistence patterns of an integrase gene (int1), used as a proxy for integrons (which often carry multiple antimicrobial resistance genes), in the fecal microbiota of 147 mothers and their children sampled longitudinally from birth to 2 years. The study showed the int1 gene was detected in 15% of the study population, and apparently more persistent than the microbial community structure itself. We found int1 to be persistent throughout the first two years of life, as well as between mothers and their 2-year-old children. Metagenome sequencing revealed integrons in the gut meta-mobilome that were associated with plasmids and multidrug resistance. In conclusion, the persistent nature of integrons in the infant gut microbiota makes it a potential reservoir of mobile multidrug resistance.}, }
@article {pmid26507513, year = {2015}, author = {Xu, G and Wang, Z and Yang, Z and Xu, H}, title = {Congruency analysis of biofilm-dwelling ciliates as a surrogate of eukaryotic microperiphyton for marine bioassessment.}, journal = {Marine pollution bulletin}, volume = {101}, number = {2}, pages = {600-604}, doi = {10.1016/j.marpolbul.2015.10.046}, pmid = {26507513}, issn = {1879-3363}, mesh = {Biodiversity ; Biofilms ; China ; Ciliophora/*classification/physiology ; Ecosystem ; Environmental Monitoring ; Heterotrophic Processes ; Marine Biology/*methods ; Oceans and Seas ; Water Quality ; }, abstract = {Biofilm-dwelling ciliates are primary components of the eukaryotic microperiphyton in both species composition and community structure. To evaluate the congruency of biofilm-dwelling ciliates as potential surrogates of the eukaryotic microperiphyton, a dataset was collected every month at four stations from the coastal waters of the Yellow Sea, northern China, and assessed. Sufficient species abundance data were obtained for ciliated protozoans at high taxonomic levels up to the family level, indicating a significant variation along the gradient of contamination. Correlation analyses revealed that the taxa richness of these matrices can explain > 85% of the variance in that of the full species dataset. The cost/benefit analysis showed that the protozoan subset at low resolutions up to the family level may be used as a potential surrogate of the original dataset. Thus, we suggest that the protozoan assemblages at genus- and/or family-level resolutions may be useful, cost-efficient surrogates of the original dataset for bioassessment in marine ecosystems.}, }
@article {pmid26507125, year = {2015}, author = {Gunnigle, E and Nielsen, JL and Fuszard, M and Botting, CH and Sheahan, J and O'Flaherty, V and Abram, F}, title = {Functional responses and adaptation of mesophilic microbial communities to psychrophilic anaerobic digestion.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {12}, pages = {}, doi = {10.1093/femsec/fiv132}, pmid = {26507125}, issn = {1574-6941}, mesh = {Acclimatization/genetics/physiology ; Anaerobiosis/physiology ; Base Sequence ; Bioreactors/*microbiology ; In Situ Hybridization, Fluorescence ; Methane/biosynthesis/metabolism ; Methanomicrobiales/genetics/growth &amp; development/*metabolism ; Methanosarcinales/genetics/growth &amp; development/*metabolism ; Microbial Consortia ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; Sewage/*microbiology ; Temperature ; Water Purification/*methods ; }, abstract = {Psychrophilic (<20°C) anaerobic digestion (AD) represents an attractive alternative to mesophilic wastewater treatment. In order to investigate the AD microbiome response to temperature change, with particular emphasis on methanogenic archaea, duplicate laboratory-scale AD bioreactors were operated at 37°C followed by a temperature drop to 15°C. A volatile fatty acid-based wastewater (composed of propionic acid, butyric acid, acetic acid and ethanol) was used to provide substrates representing the later stages of AD. Community structure was monitored using 16S rRNA gene clone libraries, as well as DNA and cDNA-based DGGE analysis, while the abundance of relevant methanogens was followed using qPCR. In addition, metaproteomics, microautoradiography-fluorescence in situ hybridization, and methanogenic activity measurements were employed to investigate microbial activities and functions. Methanomicrobiales abundance increased at low temperature, which correlated with an increased contribution of CH4 production from hydrogenotrophic methanogenesis at 15°C. Methanosarcinales utilized acetate and H2/CO2 as CH4 precursors at both temperatures and a partial shift from acetoclastic to hydrogenotrophic methanogenesis was observed for this archaeal population at 15°C. An upregulation of protein expression was reported at low temperature as well as the detection of chaperones indicating that mesophilic communities experienced stress during long-term exposure to 15°C. Overall, changes in microbial community structure and function were found to underpin the adaptation of mesophilic sludge to psychrophilic AD.}, }
@article {pmid26505627, year = {2015}, author = {Rodrigues, RR and Pineda, RP and Barney, JN and Nilsen, ET and Barrett, JE and Williams, MA}, title = {Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0141424}, pmid = {26505627}, issn = {1932-6203}, mesh = {Actinobacteria/genetics ; Ailanthus/*genetics/microbiology ; Animals ; Fungi/genetics ; Genetic Variation ; *Introduced Species ; Nitrogen Cycle ; Phylogeny ; Plant Roots/metabolism/*microbiology ; Poaceae/*genetics/microbiology ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Rhamnus/*genetics/microbiology ; Soil Microbiology ; Virginia ; }, abstract = {The importance of plant-microbe associations for the invasion of plant species have not been often tested under field conditions. The research sought to determine patterns of change in microbial communities associated with the establishment of invasive plants with different taxonomic and phenetic traits. Three independent locations in Virginia, USA were selected. One site was invaded by a grass (Microstegium vimineum), another by a shrub (Rhamnus davurica), and the third by a tree (Ailanthus altissima). The native vegetation from these sites was used as reference. 16S rRNA and ITS regions were sequenced to study root-zone bacterial and fungal communities, respectively, in invaded and non-invaded samples and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Though root-zone microbial community structure initially differed across locations, plant invasion shifted communities in similar ways. Indicator species analysis revealed that Operational Taxonomic Units (OTUs) closely related to Proteobacteria, Acidobacteria, Actinobacteria, and Ascomycota increased in abundance due to plant invasions. The Hyphomonadaceae family in the Rhodobacterales order and ammonia-oxidizing Nitrospirae phylum showed greater relative abundance in the invaded root-zone soils. Hyphomicrobiaceae, another bacterial family within the phyla Proteobacteria increased as a result of plant invasion, but the effect associated most strongly with root-zones of M. vimineum and R. davurica. Functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed bacteria responsible for nitrogen cycling in soil increased in relative abundance in association with plant invasion. In agreement with phylogenetic and functional analyses, greater turnover of ammonium and nitrate was associated with plant invasion. Overall, bacterial and fungal communities changed congruently across plant invaders, and support the hypothesis that nitrogen cycling bacteria and functions are important factors in plant invasions. Whether the changes in microbial communities are driven by direct plant microbial interactions or a result of plant-driven changes in soil properties remains to be determined.}, }
@article {pmid26503849, year = {2016}, author = {Pant, A and Anbumani, D and Bag, S and Mehta, O and Kumar, P and Saxena, S and Nair, GB and Das, B}, title = {Effect of LexA on Chromosomal Integration of CTXϕ in Vibrio cholerae.}, journal = {Journal of bacteriology}, volume = {198}, number = {2}, pages = {268-275}, pmid = {26503849}, issn = {1098-5530}, mesh = {Bacterial Proteins/genetics/*metabolism ; Bacteriophages ; Chromosomes, Bacterial/genetics ; DNA, Single-Stranded/genetics ; *Genome, Bacterial ; *Genome, Viral ; Serine Endopeptidases/genetics/*metabolism ; Vibrio cholerae ; Virus Integration/*genetics ; }, abstract = {UNLABELLED: The genesis of toxigenic Vibrio cholerae involves acquisition of CTXϕ, a single-stranded DNA (ssDNA) filamentous phage that encodes cholera toxin (CT). The phage exploits host-encoded tyrosine recombinases (XerC and XerD) for chromosomal integration and lysogenic conversion. The replicative genome of CTXϕ produces ssDNA by rolling-circle replication, which may be used either for virion production or for integration into host chromosome. Fine-tuning of different ssDNA binding protein (Ssb) levels in the host cell is crucial for cellular functioning and important for CTXϕ integration. In this study, we mutated the master regulator gene of SOS induction, lexA, of V. cholerae because of its known role in controlling levels of Ssb proteins in other bacteria. CTXϕ integration decreased in cells with a ΔlexA mutation and increased in cells with an SOS-noninducing mutation, lexA (Ind(-)). We also observed that overexpression of host-encoded Ssb (VC0397) decreased integration of CTXϕ. We propose that LexA helps CTXϕ integration, possibly by fine-tuning levels of host- and phage-encoded Ssbs.<br><br>IMPORTANCE: Cholera toxin is the principal virulence factor responsible for the acute diarrheal disease cholera. CT is encoded in the genome of a lysogenic filamentous phage, CTX&#x3d5;. Vibrio cholerae has a bipartite genome and harbors single or multiple copies of CTX&#x3d5; prophage in one or both chromosomes. Two host-encoded tyrosine recombinases (XerC and XerD) recognize the folded ssDNA genome of CTX&#x3d5; and catalyze its integration at the dimer resolution site of either one or both chromosomes. Fine-tuning of ssDNA binding proteins in host cells is crucial for CTX&#x3d5; integration. We engineered the V. cholerae genome and created several reporter strains carrying &#x394;lexA or lexA (Ind(-)) alleles. Using the reporter strains, the importance of LexA control of Ssb expression in the integration efficiency of CTX&#x3d5; was demonstrated.}, }
@article {pmid26500626, year = {2015}, author = {Cordovez, V and Carrion, VJ and Etalo, DW and Mumm, R and Zhu, H and van Wezel, GP and Raaijmakers, JM}, title = {Diversity and functions of volatile organic compounds produced by Streptomyces from a disease-suppressive soil.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1081}, pmid = {26500626}, issn = {1664-302X}, abstract = {In disease-suppressive soils, plants are protected from infections by specific root pathogens due to the antagonistic activities of soil and rhizosphere microorganisms. For most disease-suppressive soils, however, the microorganisms and mechanisms involved in pathogen control are largely unknown. Our recent studies identified Actinobacteria as the most dynamic phylum in a soil suppressive to the fungal root pathogen Rhizoctonia solani. Here we isolated and characterized 300 isolates of rhizospheric Actinobacteria from the Rhizoctonia-suppressive soil. Streptomyces species were the most abundant, representing approximately 70% of the isolates. Streptomyces are renowned for the production of an exceptionally large number of secondary metabolites, including volatile organic compounds (VOCs). VOC profiling of 12 representative Streptomyces isolates by SPME-GC-MS allowed a more refined phylogenetic delineation of the Streptomyces isolates than the sequencing of 16S rRNA and the house-keeping genes atpD and recA only. VOCs of several Streptomyces isolates inhibited hyphal growth of R. solani and significantly enhanced plant shoot and root biomass. Coupling of Streptomyces VOC profiles with their effects on fungal growth, pointed to VOCs potentially involved in antifungal activity. Subsequent assays with five synthetic analogs of the identified VOCs showed that methyl 2-methylpentanoate, 1,3,5-trichloro-2-methoxy benzene and the VOCs mixture have antifungal activity. In conclusion, our results point to a potential role of VOC-producing Streptomyces in disease suppressive soils and show that VOC profiling of rhizospheric Streptomyces can be used as a complementary identification tool to construct strain-specific metabolic signatures.}, }
@article {pmid26500067, year = {2016}, author = {Lavin, P and de Saravia, SG and Guiamet, P}, title = {Scopulariopsis sp. and Fusarium sp. in the Documentary Heritage: Evaluation of Their Biodeterioration Ability and Antifungal Effect of Two Essential Oils.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {628-633}, pmid = {26500067}, issn = {1432-184X}, mesh = {Antifungal Agents/*pharmacology ; Biofilms/drug effects ; Fusarium/*drug effects/physiology ; Oils, Volatile/*pharmacology ; Origanum/*chemistry ; Plant Oils/*pharmacology ; Scopulariopsis/*drug effects/physiology ; Thymus Plant/*chemistry ; }, abstract = {Fungi produce pigments and acids, generating particular local conditions which modify the physicochemical properties of materials. The aims of this work are (i) to investigate bioadhesion, foxing production and biofilm formation by Scopulariopsis sp. and Fusarium sp. isolated from document collections under laboratory conditions; (ii) to verify attack on cellulose fibres and (iii) to study the possibility of reducing fungal growth using natural products. Biofilm formation and extracellular polymeric substance (EPS) production by fungi were demonstrated in laboratory assays and by scanning electron microscopy (SEM) observations. The biocidal activity of two essential oils of Origanum vulgare L. and Thymus vulgaris L. was evaluated using the microatmosphere method. SEM observations showed that these strains were able to attach to paper and form biofilms, causing damage on them, which demonstrates the biodeterioration ability of these microorganisms. Scopulariopsis sp. and Fusarium sp. isolated from paper books showed the formation of fox-like reddish-brown colour spots, attack to the paper structure and pigment production on aged paper samples. The strains tested produced a decrease in the pH of one unit. This would substantiate the effect of the strains in paper biodeterioration. The microatmosphere method showed that volatile compounds of the essential oils have antifungal activity.}, }
@article {pmid26498818, year = {2016}, author = {Rodríguez-Salgado, I and Pérez-Rodríguez, P and Gómez-Armesto, A and Nóvoa-Muñoz, JC and Arias-Estévez, M and Fernández-Calviño, D}, title = {Cu retention in an acid soil amended with perlite winery waste.}, journal = {Environmental science and pollution research international}, volume = {23}, number = {4}, pages = {3789-3798}, pmid = {26498818}, issn = {1614-7499}, mesh = {Adsorption ; Aluminum Oxide/*chemistry ; Copper/*analysis ; Hydrogen-Ion Concentration ; Silicon Dioxide/*chemistry ; Soil/*chemistry ; Soil Pollutants/*analysis ; Vitis/*growth &amp; development ; *Waste Products ; }, abstract = {The effect of perlite waste from a winery on general soil characteristics and Cu adsorption was assessed. The studied soil was amended with different perlite waste concentrations corresponding to 10, 20, 40 and 80 Mg ha(-1). General soil characteristics and Cu adsorption and desorption curves were determined after different incubation times (from 1 day to 8 months). The addition of perlite waste to the soil increased the amounts of organic matter as well as soil nutrients such as phosphorus and potassium, and these increments were stable with time. An increase in Cu adsorption capacity was also detected in the perlite waste-amended soils. The effect of perlite waste addition to the soil had special relevance on its Cu adsorption capacity at low coverage concentrations and on the energy of the soil-Cu bonds.}, }
@article {pmid26497468, year = {2016}, author = {Tsilia, V and Kerckhof, FM and Rajkovic, A and Heyndrickx, M and Van de Wiele, T}, title = {Bacillus cereus NVH 0500/00 Can Adhere to Mucin but Cannot Produce Enterotoxins during Gastrointestinal Simulation.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {1}, pages = {289-296}, pmid = {26497468}, issn = {1098-5336}, mesh = {Bacillus cereus/growth &amp; development/*physiology ; *Bacterial Adhesion ; Colony Count, Microbial ; Enterocytes/microbiology ; Enterotoxins/metabolism ; Gastric Emptying ; Ileum/microbiology ; In Vitro Techniques ; Intestinal Mucosa/*microbiology ; Mucins/*physiology ; }, abstract = {Adhesion to the intestinal epithelium could constitute an essential mechanism of Bacillus cereus pathogenesis. However, the enterocytes are protected by mucus, a secretion composed mainly of mucin glycoproteins. These may serve as nutrients and sites of adhesion for intestinal bacteria. In this study, the food poisoning bacterium B. cereus NVH 0500/00 was exposed in vitro to gastrointestinal hurdles prior to evaluation of its attachment to mucin microcosms and its ability to produce nonhemolytic enterotoxin (Nhe). The persistence of mucin-adherent B. cereus after simulated gut emptying was determined using a mucin adhesion assay. The stability of Nhe toward bile and pancreatin (intestinal components) in the presence of mucin agar was also investigated. B. cereus could grow and simultaneously adhere to mucin during in vitro ileal incubation, despite the adverse effect of prior exposure to a low pH or intestinal components. The final concentration of B. cereus in the simulated lumen at 8 h of incubation was 6.62 ± 0.87 log CFU ml(-1). At that point, the percentage of adhesion was approximately 6%. No enterotoxin was detected in the ileum, due to either insufficient bacterial concentrations or Nhe degradation. Nevertheless, mucin appears to retain B. cereus and to supply it to the small intestine after simulated gut emptying. Additionally, mucin may play a role in the protection of enterotoxins from degradation by intestinal components.}, }
@article {pmid26497463, year = {2016}, author = {Daghio, M and Vaiopoulou, E and Patil, SA and Suárez-Suárez, A and Head, IM and Franzetti, A and Rabaey, K}, title = {Anodes Stimulate Anaerobic Toluene Degradation via Sulfur Cycling in Marine Sediments.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {1}, pages = {297-307}, pmid = {26497463}, issn = {1098-5336}, mesh = {Anaerobiosis ; *Biodegradation, Environmental ; Carbon-Carbon Lyases ; Deltaproteobacteria/*metabolism ; *Electrodes ; Geologic Sediments/*microbiology ; Hydrocarbons/metabolism ; Hydrogensulfite Reductase/genetics/metabolism ; Microbial Consortia/physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfates/metabolism ; Sulfur/*metabolism ; Toluene/*metabolism ; Water Pollutants, Chemical/metabolism ; }, abstract = {Hydrocarbons released during oil spills are persistent in marine sediments due to the absence of suitable electron acceptors below the oxic zone. Here, we investigated an alternative bioremediation strategy to remove toluene, a model monoaromatic hydrocarbon, using a bioanode. Bioelectrochemical reactors were inoculated with sediment collected from a hydrocarbon-contaminated marine site, and anodes were polarized at 0 mV and +300 mV (versus an Ag/AgCl [3 M KCl] reference electrode). The degradation of toluene was directly linked to current generation of up to 301 mA m(-2) and 431 mA m(-2) for the bioanodes polarized at 0 mV and +300 mV, respectively. Peak currents decreased over time even after periodic spiking with toluene. The monitoring of sulfate concentrations during bioelectrochemical experiments suggested that sulfur metabolism was involved in toluene degradation at bioanodes. 16S rRNA gene-based Illumina sequencing of the bulk anolyte and anode samples revealed enrichment with electrocatalytically active microorganisms, toluene degraders, and sulfate-reducing microorganisms. Quantitative PCR targeting the α-subunit of the dissimilatory sulfite reductase (encoded by dsrA) and the α-subunit of the benzylsuccinate synthase (encoded by bssA) confirmed these findings. In particular, members of the family Desulfobulbaceae were enriched concomitantly with current production and toluene degradation. Based on these observations, we propose two mechanisms for bioelectrochemical toluene degradation: (i) direct electron transfer to the anode and/or (ii) sulfide-mediated electron transfer.}, }
@article {pmid26496441, year = {2015}, author = {Humphrey, S and Lacharme-Lora, L and Chaloner, G and Gibbs, K and Humphrey, T and Williams, N and Wigley, P}, title = {Heterogeneity in the Infection Biology of Campylobacter jejuni Isolates in Three Infection Models Reveals an Invasive and Virulent Phenotype in a ST21 Isolate from Poultry.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0141182}, pmid = {26496441}, issn = {1932-6203}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacterial Load ; Caco-2 Cells ; Campylobacter Infections/microbiology/pathology/*veterinary ; Campylobacter jejuni/*pathogenicity/physiology ; Cecum/microbiology ; Chickens ; Female ; Host-Pathogen Interactions ; Humans ; Larva/microbiology ; Lepidoptera/microbiology ; Liver/microbiology ; Male ; *Phenotype ; Poultry ; Poultry Diseases/*microbiology/pathology ; Severity of Illness Index ; Virulence ; }, abstract = {Although Campylobacter is the leading cause of bacterial foodborne gastroenteritis in the world and the importance of poultry as a source of infection is well understood we know relatively little about its infection biology in the broiler chicken. Much of what we know about the biology of Campylobacter jejuni is based on infection of inbred or SPF laboratory lines of chickens with a small number of isolates used in most laboratory studies. Recently we have shown that both the host response and microbial ecology of C. jejuni in the broiler chicken varies with both the host-type and significantly between C. jejuni isolates. Here we describe heterogeneity in infection within a panel of C. jejuni isolates in two broiler chicken breeds, human intestinal epithelial cells and the Galleria insect model of virulence. All C. jejuni isolates colonised the chicken caeca, though colonisation of other parts of the gastrointestinal tract varied between isolates. Extra-intestinal spread to the liver varied between isolates and bird breed but a poultry isolate 13126 (sequence type 21) showed the greatest levels of extra-intestinal spread to the liver in both broiler breeds with over 70% of birds of the fast growing breed and 50% of the slower growing breed having C. jejuni in their livers. Crucially 13126 is significantly more invasive than other isolates in human intestinal epithelial cells and gave the highest mortality in the Galleria infection model. Taken together our findings suggest that not only is there considerable heterogeneity in the infection biology of C. jejuni in avian, mammalian and alternative models, but that some isolates have an invasive and virulent phenotype. Isolates with an invasive phenotype would pose a significant risk and increased difficulty in control in chicken production and coupled with the virulent phenotype seen in 13126 could be an increased risk to public health.}, }
@article {pmid26496191, year = {2015}, author = {Koslicki, D and Chatterjee, S and Shahrivar, D and Walker, AW and Francis, SC and Fraser, LJ and Vehkaperä, M and Lan, Y and Corander, J}, title = {ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0140644}, pmid = {26496191}, issn = {1932-6203}, support = {/WT_/Wellcome Trust/United Kingdom ; G0701039/MRC_/Medical Research Council/United Kingdom ; MR/K012126/1/MRC_/Medical Research Council/United Kingdom ; G1002369/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Algorithms ; Bacteria/classification/*genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Feces/microbiology ; Humans ; Internet ; Metagenomics/*methods ; Microbiota/*genetics ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {MOTIVATION: Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of such large datasets is challenging.<br><br>RESULTS: There has been a recent surge of interest in using compressed sensing inspired and convex-optimization based methods to solve the estimation problem for bacterial community composition. These methods typically rely on summarizing the sequence data by frequencies of low-order k-mers and matching this information statistically with a taxonomically structured database. Here we show that the accuracy of the resulting community composition estimates can be substantially improved by aggregating the reads from a sample with an unsupervised machine learning approach prior to the estimation phase. The aggregation of reads is a pre-processing approach where we use a standard K-means clustering algorithm that partitions a large set of reads into subsets with reasonable computational cost to provide several vectors of first order statistics instead of only single statistical summarization in terms of k-mer frequencies. The output of the clustering is then processed further to obtain the final estimate for each sample. The resulting method is called Aggregation of Reads by K-means (ARK), and it is based on a statistical argument via mixture density formulation. ARK is found to improve the fidelity and robustness of several recently introduced methods, with only a modest increase in computational complexity.<br><br>AVAILABILITY: An open source, platform-independent implementation of the method in the Julia programming language is freely available at https://github.com/dkoslicki/ARK. A Matlab implementation is available at http://www.ee.kth.se/ctsoftware.}, }
@article {pmid26493074, year = {2015}, author = {Palomares-Rius, JE and Tsai, IJ and Karim, N and Akiba, M and Kato, T and Maruyama, H and Takeuchi, Y and Kikuchi, T}, title = {Genome-wide variation in the pinewood nematode Bursaphelenchus xylophilus and its relationship with pathogenic traits.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {845}, pmid = {26493074}, issn = {1471-2164}, mesh = {Animals ; Asia ; Base Sequence ; Europe ; Genome/*genetics ; Japan ; Phenotype ; Pinus/parasitology ; Plant Diseases/genetics/*parasitology ; Polymorphism, Single Nucleotide/*genetics ; Tylenchida/*genetics/pathogenicity ; }, abstract = {BACKGROUND: Bursaphelenchus xylophilus is an emerging pathogenic nematode that is responsible for a devastating epidemic of pine wilt disease across Asia and Europe. In this study, we report the first genome-wide variation analysis of the nematode with an aim to obtain a full picture of its diversity.<br><br>METHODS: We sequenced six key B. xylophilus strains using Illumina HiSeq sequencer. All the strains were isolated in Japan and have been widely used in previous studies. Detection of genomic variations were done by mapping the reads to the reference genome.<br><br>RESULTS: Over 3 Mb of genetic variations, accounting for 4.1 % of the total genome, were detected as single nucleotide polymorphisms or small indels, suggesting multiple introductions of this invaded species from its native area into the country. The high level of genetic diversity of the pine wood nematode was related to its pathogenicity and ecological trait differences. Moreover, we identified a gene set affected by genomic variation, and functional annotation of those genes indicated that some of them had potential roles in pathogenesis.<br><br>CONCLUSIONS: This study provides an important resource for understanding the population structure, pathogenicity and evolutionary ecology of the nematode, and further analysis based on this study with geographically diverse B. xylophilus populations will greatly accelerate our understanding of the complex evolutionary/epidemic history of this emerging pathogen.}, }
@article {pmid26492897, year = {2016}, author = {Zhang, T and Wang, NF and Zhang, YQ and Liu, HY and Yu, LY}, title = {Diversity and Distribution of Aquatic Fungal Communities in the Ny-Ålesund Region, Svalbard (High Arctic): Aquatic Fungi in the Arctic.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {543-554}, pmid = {26492897}, issn = {1432-184X}, mesh = {Arctic Regions ; *Biodiversity ; Climate Change ; Fungi/classification/genetics/*isolation &amp; purification ; Phylogeny ; Svalbard ; *Water Microbiology ; }, abstract = {We assessed the diversity and distribution of fungi in 13 water samples collected from four aquatic environments (stream, pond, melting ice water, and estuary) in the Ny-Ålesund Region, Svalbard (High Arctic) using 454 pyrosequencing with fungi-specific primers targeting the internal transcribed spacer (ITS) region of the ribosomal rRNA gene. Aquatic fungal communities in this region showed high diversity, with a total of 43,061 reads belonging to 641 operational taxonomic units (OTUs) being found. Of these OTUs, 200 belonged to Ascomycota, 196 to Chytridiomycota, 120 to Basidiomycota, 13 to Glomeromycota, and 10 to early diverging fungal lineages (traditional Zygomycota), whereas 102 belonged to unknown fungi. The major orders were Helotiales, Eurotiales, and Pleosporales in Ascomycota; Chytridiales and Rhizophydiales in Chytridiomycota; and Leucosporidiales and Sporidiobolales in Basidiomycota. The common fungal genera Penicillium, Rhodotorula, Epicoccum, Glaciozyma, Holtermanniella, Betamyces, and Phoma were identified. Interestingly, the four aquatic environments in this region harbored different aquatic fungal communities. Salinity, conductivity, and temperature were important factors in determining the aquatic fungal diversity and community composition. The results suggest the presence of diverse fungal communities and a considerable number of potentially novel fungal species in Arctic aquatic environments, which can provide reliable data for studying the ecological and evolutionary responses of fungi to climate change in the Arctic ecosystem.}, }
@article {pmid26490729, year = {2015}, author = {Manoharan, L and Kushwaha, SK and Hedlund, K and Ahrén, D}, title = {Captured metagenomics: large-scale targeting of genes based on 'sequence capture' reveals functional diversity in soils.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {22}, number = {6}, pages = {451-460}, pmid = {26490729}, issn = {1756-1663}, mesh = {*Genes, Bacterial ; *Genes, Microbial ; High-Throughput Nucleotide Sequencing/methods ; *Metagenome ; Metagenomics/methods ; *Soil Microbiology ; }, abstract = {Microbial enzyme diversity is a key to understand many ecosystem processes. Whole metagenome sequencing (WMG) obtains information on functional genes, but it is costly and inefficient due to large amount of sequencing that is required. In this study, we have applied a captured metagenomics technique for functional genes in soil microorganisms, as an alternative to WMG. Large-scale targeting of functional genes, coding for enzymes related to organic matter degradation, was applied to two agricultural soil communities through captured metagenomics. Captured metagenomics uses custom-designed, hybridization-based oligonucleotide probes that enrich functional genes of interest in metagenomic libraries where only probe-bound DNA fragments are sequenced. The captured metagenomes were highly enriched with targeted genes while maintaining their target diversity and their taxonomic distribution correlated well with the traditional ribosomal sequencing. The captured metagenomes were highly enriched with genes related to organic matter degradation; at least five times more than similar, publicly available soil WMG projects. This target enrichment technique also preserves the functional representation of the soils, thereby facilitating comparative metagenomics projects. Here, we present the first study that applies the captured metagenomics approach in large scale, and this novel method allows deep investigations of central ecosystem processes by studying functional gene abundances.}, }
@article {pmid26487679, year = {2015}, author = {Rotem, O and Pasternak, Z and Shimoni, E and Belausov, E and Porat, Z and Pietrokovski, S and Jurkevitch, E}, title = {Cell-cycle progress in obligate predatory bacteria is dependent upon sequential sensing of prey recognition and prey quality cues.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {44}, pages = {E6028-37}, pmid = {26487679}, issn = {1091-6490}, mesh = {Animals ; *Bacterial Physiological Phenomena ; *Cell Cycle ; *Predatory Behavior ; }, abstract = {Predators feed on prey to acquire the nutrients necessary to sustain their survival, growth, and replication. In Bdellovibrio bacteriovorus, an obligate predator of Gram-negative bacteria, cell growth and replication are tied to a shift from a motile, free-living phase of search and attack to a sessile, intracellular phase of growth and replication during which a single prey cell is consumed. Engagement and sustenance of growth are achieved through the sensing of two unidentified prey-derived cues. We developed a novel ex vivo cultivation system for B. bacteriovorus composed of prey ghost cells that are recognized and invaded by the predator. By manipulating their content, we demonstrated that an early cue is located in the prey envelope and a late cue is found within the prey soluble fraction. These spatially and temporally separated cues elicit discrete and combinatory regulatory effects on gene transcription. Together, they delimit a poorly characterized transitory phase between the attack phase and the growth phase, during which the bdelloplast (the invaded prey cell) is constructed. This transitory phase constitutes a checkpoint in which the late cue presumably acts as a determinant of the prey's nutritional value before the predator commits. These regulatory adaptations to a unique bacterial lifestyle have not been reported previously.}, }
@article {pmid26487438, year = {2016}, author = {Heger, TJ and Derungs, N and Theurillat, JP and Mitchell, EA}, title = {Testate Amoebae Like It Hot: Species Richness Decreases Along a Subalpine-Alpine Altitudinal Gradient in Both Natural Calluna vulgaris Litter and Transplanted Minuartia sedoides Cushions.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {725-734}, pmid = {26487438}, issn = {1432-184X}, mesh = {Altitude ; Amoeba/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Calluna/*parasitology ; Caryophyllaceae/*parasitology ; Switzerland ; }, abstract = {Most groups of higher organisms show a decrease in species richness toward high altitude, but the existence of such a pattern is debated for micro-eukaryotes. Existing data are scarce and mostly confounded with the diversity of habitats that also decreases with elevation. In order to disentangle these two factors, one approach is to consider only similar types of habitats occurring across an elevational gradient. We assessed the diversity and community structure of testate amoebae in two specific habitats: (1) natural Calluna vulgaris litter and (2) Minuartia sedoides cushions 7 years after their transplantation along a vertical transect from 1770 to 2430 m in the subalpine and alpine zones of the Swiss Alps. Analyses of co-variance and variance showed that testate amoeba species richness, equitability, and diversity declined with elevation and were significantly correlated to habitat type. In a redundancy analysis, the variation in the relative abundance of the testate amoeba taxa in Calluna vulgaris litter was equally explained by elevation and litter pH. This is the first study documenting a monotonic decrease of protist diversity in similar habitats across an elevational gradient.}, }
@article {pmid26487437, year = {2016}, author = {de Lima Brossi, MJ and Jiménez, DJ and Cortes-Tolalpa, L and van Elsas, JD}, title = {Soil-Derived Microbial Consortia Enriched with Different Plant Biomass Reveal Distinct Players Acting in Lignocellulose Degradation.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {616-627}, pmid = {26487437}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biomass ; Fungi/classification/genetics/isolation &amp; purification/*metabolism ; Lignin/*metabolism ; *Microbial Consortia ; Phylogeny ; Plants/classification/*microbiology ; *Soil Microbiology ; }, abstract = {Here, we investigated how different plant biomass, and-for one substrate-pH, drive the composition of degrader microbial consortia. We bred such consortia from forest soil, incubated along nine aerobic sequential - batch enrichments with wheat straw (WS1, pH 7.2; WS2, pH 9.0), switchgrass (SG, pH 7.2), and corn stover (CS, pH 7.2) as carbon sources. Lignocellulosic compounds (lignin, cellulose and xylan) were best degraded in treatment SG, followed by CS, WS1 and WS2. In terms of composition, the consortia became relatively stable after transfers 4 to 6, as evidenced by PCR-DGGE profiles obtained from each consortium DNA. The final consortia differed by ~40 % (bacteria) and ~60 % (fungi) across treatments. A 'core' community represented by 5/16 (bacteria) and 3/14 (fungi) bands was discerned, next to a variable part. The composition of the final microbial consortia was strongly driven by the substrate, as taxonomically-diverse consortia appeared in the different substrate treatments, but not in the (WS) different pH one. Biodegradative strains affiliated to Sphingobacterium kitahiroshimense, Raoultella terrigena, Pseudomonas putida, Stenotrophomonas rhizophila (bacteria), Coniochaeta ligniaria and Acremonium sp. (fungi) were recovered in at least three treatments, whereas strains affiliated to Delftia tsuruhatensis, Paenibacillus xylanexedens, Sanguibacter inulus and Comamonas jiangduensis were treatment-specific.}, }
@article {pmid26486590, year = {2016}, author = {Foesel, BU and Mayer, S and Luckner, M and Wanner, G and Rohde, M and Overmann, J}, title = {Occallatibacter riparius gen. nov., sp. nov. and Occallatibacter savannae sp. nov., acidobacteria isolated from Namibian soils, and emended description of the family Acidobacteriaceae.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {66}, number = {1}, pages = {219-229}, doi = {10.1099/ijsem.0.000700}, pmid = {26486590}, issn = {1466-5034}, mesh = {Acidobacteria/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Molecular Sequence Data ; Namibia ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {Three Gram-negative, non-spore-forming, encapsulated bacteria were isolated from a Namibian river-bank soil (strains 277T and 307) and a semiarid savannah soil (strain A2-1cT). 16S rRNA gene sequence analyses placed them within subdivision 1 of the Acidobacteria and revealed 100 % similarity between strains 277T and 307 and 98.2 % similarity between A2-1cT and the former two strains. The closest relatives with validly published names were Telmatobacter bradus, Acidicapsa borealis and Acidicapsa ligni (94.7-95.9 % similarity to the type strains). Cells of all three strains were rod-shaped and motile and divided by binary fission. Ultrastructural analyses revealed a thick cell envelope, resulting mainly from a thick periplasmic space. Colonies of strains 277T and 307 were white to cream and light pink, respectively, while strain A2-1cT displayed a bright pink colour. All three strains were aerobic, chemoheterotrophic mesophiles with a broad temperature range for growth and a moderately acidic pH optimum. Sugars and complex proteinaceous substrates were the preferred carbon and energy sources. A few polysaccharides were degraded. The major quinone in all three strains was MK-8; MK-7 occurred in strain A2-1cT as a minor compound. Major fatty acids were iso-C15 : 0 and iso-C17 : 1ω7c. In addition, iso-C17 : 0 occurred in significant amounts. The DNA G+C contents of strains 277T, 307 and A2-1cT were 59.6, 59.9 and 58.5 mol%, respectively. Based on these characteristics, the three isolates are assigned to two novel species of the novel genus Occallatibacter gen. nov., Occallatibacter riparius sp. nov. [type strain 277T (= DSM 25168T = LMG 26948T) and reference strain 307 (= DSM 25169 = LMG 26947)] and Occallatibacter savannae sp. nov. [type strain A2-1cT (= DSM 25170T = LMG 26946T)]. Together with several other recently described taxa, the novel isolates provide the basis for an emended description of the established family Acidobacteriaceae.}, }
@article {pmid26486414, year = {2016}, author = {Xun, W and Zhao, J and Xue, C and Zhang, G and Ran, W and Wang, B and Shen, Q and Zhang, R}, title = {Significant alteration of soil bacterial communities and organic carbon decomposition by different long-term fertilization management conditions of extremely low-productivity arable soil in South China.}, journal = {Environmental microbiology}, volume = {18}, number = {6}, pages = {1907-1917}, doi = {10.1111/1462-2920.13098}, pmid = {26486414}, issn = {1462-2920}, mesh = {Agriculture ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Carbon/*metabolism ; China ; Ecosystem ; Fertilizers/analysis ; Nitrogen/metabolism ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Different fertilization managements of red soil, a kind of Ferralic Cambisol, strongly affected the soil properties and associated microbial communities. The association of the soil microbial community and functionality with long-term fertilization management in the unique low-productivity red soil ecosystem is important for both soil microbial ecology and agricultural production. Here, 454 pyrosequencing analysis of 16S recombinant ribonucleic acid genes and GeoChip4-NimbleGen-based functional gene analysis were used to study the soil bacterial community composition and functional genes involved in soil organic carbon degradation. Long-term nitrogen-containing chemical fertilization-induced soil acidification and fertility decline and significantly altered the soil bacterial community, whereas long-term organic fertilization and fallow management improved the soil quality and maintained the bacterial diversity. Short-term quicklime remediation of the acidified soils did not change the bacterial communities. Organic fertilization and fallow management supported eutrophic ecosystems, in which copiotrophic taxa increased in relative abundance and have a higher intensity of labile-C-degrading genes. However, long-term nitrogen-containing chemical fertilization treatments supported oligotrophic ecosystems, in which oligotrophic taxa increased in relative abundance and have a higher intensity of recalcitrant-C-degrading genes but a lower intensity of labile-C-degrading genes. Quicklime application increased the relative abundance of copiotrophic taxa and crop production, although these effects were utterly inadequate. This study provides insights into the interaction of soil bacterial communities, soil functionality and long-term fertilization management in the red soil ecosystem; these insights are important for improving the fertility of unique low-productivity red soil.}, }
@article {pmid26483764, year = {2015}, author = {Morrissey, EM and Franklin, RB}, title = {Evolutionary history influences the salinity preference of bacterial taxa in wetland soils.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1013}, pmid = {26483764}, issn = {1664-302X}, abstract = {Salinity is a major driver of bacterial community composition across the globe. Despite growing recognition that different bacterial species are present or active at different salinities, the mechanisms by which salinity structures community composition remain unclear. We tested the hypothesis that these patterns reflect ecological coherence in the salinity preferences of phylogenetic groups using a reciprocal transplant experiment of fresh- and saltwater wetland soils. The salinity of both the origin and host environments affected community composition (16S rRNA gene sequences) and activity (CO2 and CH4 production, and extracellular enzyme activity). These changes in community composition and activity rates were strongly correlated, which suggests the effect of environment on function could be mediated, at least in part, by microbial community composition. Based on their distribution across treatments, each phylotype was categorized as having a salinity preference (freshwater, saltwater, or none) and phylogenetic analyses revealed a significant influence of evolutionary history on these groupings. This finding was corroborated by examining the salinity preferences of high-level taxonomic groups. For instance, we found that the majority of α- and γ-proteobacteria in these wetland soils preferred saltwater, while many β-proteobacteria prefer freshwater. Overall, our results indicate the effect of salinity on bacterial community composition results from phylogenetically-clustered salinity preferences.}, }
@article {pmid26479196, year = {2016}, author = {Sun, Y and Hu, D and Li, L and Jing, Z and Wei, C and Zhang, L and Fu, Y and Liu, H}, title = {Influence mechanism of low-dose ionizing radiation on Escherichia coli DH5α population based on plasma theory and system dynamics simulation.}, journal = {Journal of environmental radioactivity}, volume = {151 Pt 1}, number = {}, pages = {185-192}, doi = {10.1016/j.jenvrad.2015.10.007}, pmid = {26479196}, issn = {1879-1700}, mesh = {Biological Evolution ; Dose-Response Relationship, Radiation ; Escherichia coli/growth &amp; development/metabolism/*radiation effects ; Finite Element Analysis ; Models, Theoretical ; Plasma Gases/chemistry ; *Radiation, Ionizing ; Space Simulation ; }, abstract = {It remains a mystery why the growth rate of bacteria is higher in low-dose ionizing radiation (LDIR) environment than that in normal environment. In this study, a hypothesis composed of environmental selection and competitive exclusion was firstly proposed from observed phenomena, experimental data and microbial ecology. Then a LDIR environment simulator (LDIRES) was built to cultivate a model organism of bacteria, Escherichia coli (E. coli) DH5α, the accurate response of bacterial population to ionizing radiation intensity variation was measured experimentally, and then the precise relative dosage of ionizing radiation E. coli DH5α population received was calculated by finite element analysis based on drift-diffusion equations of plasma. Finally, a highly valid mathematical model expressing the relationship between E. coli DH5α population and LDIR intensity was developed by system dynamics based on hypotheses, experimental data and microbial ecology. Both experiment and simulation results clearly showed that the E. coli DH5α individuals with greater specific growth rate and lower substrate consumption coefficient would adapt and survive in LDIR environment and those without such adaptability were finally eliminated under the combined effects of ionizing radiation selection and competitive exclusion.}, }
@article {pmid26479170, year = {2016}, author = {Subramaniam, A and Kumar, R and Cliver, SP and Zhi, D and Szychowski, JM and Abramovici, A and Biggio, JR and Lefkowitz, EJ and Morrow, C and Edwards, RK}, title = {Vaginal Microbiota in Pregnancy: Evaluation Based on Vaginal Flora, Birth Outcome, and Race.}, journal = {American journal of perinatology}, volume = {33}, number = {4}, pages = {401-408}, pmid = {26479170}, issn = {1098-8785}, support = {P30 AI027767/AI/NIAID NIH HHS/United States ; UL1TR000165/TR/NCATS NIH HHS/United States ; P30AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR000165/TR/NCATS NIH HHS/United States ; 5P30AI027767/AI/NIAID NIH HHS/United States ; P30 AR050948/AR/NIAMS NIH HHS/United States ; UL1 TR001417/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Alabama ; DNA, Ribosomal/isolation &amp; purification ; Female ; Humans ; *Microbiota ; Polymerase Chain Reaction ; Pregnancy ; Sequence Analysis, DNA ; Vagina/*microbiology ; Vaginosis, Bacterial/*diagnosis ; Young Adult ; }, abstract = {OBJECTIVE: This study aims to evaluate vaginal microbiota differences by bacterial vaginosis (BV), birth timing, and race, and to estimate parameters to power future vaginal microbiome studies.<br><br>METHODS: Previously, vaginal swabs were collected at 21 to 25 weeks (stored at -80&#xb0;C), and vaginal smears evaluated for BV (Nugent criteria). In a blinded fashion, 40 samples were selected, creating 8 equal-sized groups stratified by race (black/white), BV (present/absent), and birth timing (preterm/term). Samples were thawed, DNA extracted, and prepared. Polymerase chain reaction (PCR) with primers targeting the 16S rDNA V4 region was used to prepare an amplicon library. PCR products were sequenced and analyzed using quantitative insight into microbial ecology; taxonomy was assigned using ribosomal database program classifier (threshold 0.8) against the modified Greengenes database.<br><br>RESULTS: After quality control, 97,720 sequences (mean) per sample, single-end 250 base-reads, were analyzed. BV samples had greater microbiota diversity (p&#x2009;<&#x2009;0.05)-with BVAB1, Prevotella, and unclassified genus, Bifidobacteriaceae family (all p&#x2009;<&#x2009;0.001) more abundant; there was minimal content of Gardnerella or Mobiluncus. Microbiota did not differ by race or birth timing, but there was an association between certain microbial clusters and preterm birth (p&#x2009;=&#x2009;0.07). To evaluate this difference, 159 patients per group are needed.<br><br>CONCLUSIONS: There are differences in the vaginal microbiota between patients with and without BV. Larger studies should assess the relationship between microbiota composition and preterm birth.}, }
@article {pmid26476551, year = {2016}, author = {Pagenkopp Lohan, KM and Fleischer, RC and Carney, KJ and Holzer, KK and Ruiz, GM}, title = {Amplicon-Based Pyrosequencing Reveals High Diversity of Protistan Parasites in Ships' Ballast Water: Implications for Biogeography and Infectious Diseases.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {530-542}, pmid = {26476551}, issn = {1432-184X}, mesh = {Animals ; *Biodiversity ; Communicable Diseases/*parasitology/transmission ; Eukaryota/classification/genetics/*isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Humans ; Parasites/classification/genetics/*isolation &amp; purification ; Phylogeny ; Seawater/*parasitology ; Ships ; Wastewater/*parasitology ; }, abstract = {Ships' ballast water (BW) commonly moves macroorganisms and microorganisms across the world's oceans and along coasts; however, the majority of these microbial transfers have gone undetected. We applied high-throughput sequencing methods to identify microbial eukaryotes, specifically emphasizing the protistan parasites, in ships' BW collected from vessels calling to the Chesapeake Bay (Virginia and Maryland, USA) from European and Eastern Canadian ports. We utilized tagged-amplicon 454 pyrosequencing with two general primer sets, amplifying either the V4 or V9 domain of the small subunit (SSU) of the ribosomal RNA (rRNA) gene complex, from total DNA extracted from water samples collected from the ballast tanks of bulk cargo vessels. We detected a diverse group of protistan taxa, with some known to contain important parasites in marine systems, including Apicomplexa (unidentified apicomplexans, unidentified gregarines, Cryptosporidium spp.), Dinophyta (Blastodinium spp., Euduboscquella sp., unidentified syndinids, Karlodinium spp., Syndinium spp.), Perkinsea (Parvilucifera sp.), Opisthokonta (Ichthyosporea sp., Pseudoperkinsidae, unidentified ichthyosporeans), and Stramenopiles (Labyrinthulomycetes). Further characterization of groups with parasitic taxa, consisting of phylogenetic analyses for four taxa (Cryptosporidium spp., Parvilucifera spp., Labyrinthulomycetes, and Ichthyosporea), revealed that sequences were obtained from both known and novel lineages. This study demonstrates that high-throughput sequencing is a viable and sensitive method for detecting parasitic protists when present and transported in the ballast water of ships. These data also underscore the potential importance of human-aided dispersal in the biogeography of these microbes and emerging diseases in the world's oceans.}, }
@article {pmid26476138, year = {2015}, author = {Prosdocimi, EM and Mapelli, F and Gonella, E and Borin, S and Crotti, E}, title = {Microbial ecology-based methods to characterize the bacterial communities of non-model insects.}, journal = {Journal of microbiological methods}, volume = {119}, number = {}, pages = {110-125}, doi = {10.1016/j.mimet.2015.10.010}, pmid = {26476138}, issn = {1872-8359}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Humans ; Insecta/*microbiology ; Symbiosis ; }, abstract = {Among the animals of the Kingdom Animalia, insects are unparalleled for their widespread diffusion, diversity and number of occupied ecological niches. In recent years they have raised researcher interest not only because of their importance as human and agricultural pests, disease vectors and as useful breeding species (e.g. honeybee and silkworm), but also because of their suitability as animal models. It is now fully recognized that microorganisms form symbiotic relationships with insects, influencing their survival, fitness, development, mating habits and the immune system and other aspects of the biology and ecology of the insect host. Thus, any research aimed at deepening the knowledge of any given insect species (perhaps species of applied interest or species emerging as novel pests or vectors) must consider the characterization of the associated microbiome. The present review critically examines the microbiology and molecular ecology techniques that can be applied to the taxonomical and functional analysis of the microbiome of non-model insects. Our goal is to provide an overview of current approaches and methods addressing the ecology and functions of microorganisms and microbiomes associated with insects. Our focus is on operational details, aiming to provide a concise guide to currently available advanced techniques, in an effort to extend insect microbiome research beyond simple descriptions of microbial communities.}, }
@article {pmid26475440, year = {2016}, author = {Sultanpuram, VR and Mothe, T and Chintalapati, S and Chintalapati, VR}, title = {Pelagirhabdus alkalitolerans gen. nov., sp. nov., an alkali-tolerant and thermotolerant bacterium isolated from beach sediment, and reclassification of Amphibacillus fermentum as Pelagirhabdus fermentum comb. nov.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {66}, number = {1}, pages = {84-90}, doi = {10.1099/ijsem.0.000678}, pmid = {26475440}, issn = {1466-5034}, mesh = {Alkalies ; Bacillaceae/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Diaminopimelic Acid/chemistry ; Fatty Acids/chemistry ; Geologic Sediments/*microbiology ; India ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Peptidoglycan/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {A novel bacterial strain, designated S5T, was isolated from Pingaleshwar beach, in India. Cells were Gram-stain-positive, rod-shaped, non-motile and non-endospore-forming. Based on 16S rRNA gene sequence analysis, the strain was identified as belonging to the class Firmibacteria and was related most closely to Amphibacillus fermentum DSM 13869T (97.6 % sequence similarity). However, it shared only 93.1 % 16S rRNA gene sequence similarity with Amphibacillus xylanus NBRC 15112T, the type species of the genus, indicating that strain S5T might not be a member of the genus Amphibacillus. The DNA-DNA relatedness between strain S5T and Amphibacillus fermentum DSM 13869T was 39 %. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol and two phospholipids. Isoprenoid quinones were absent from strain S5T. Fatty acid analysis revealed that anteiso-C15 : 0, C16 : 0 and iso-C15 : 0 were the predominant fatty acids present. The results of phylogenetic, chemotaxonomic and biochemical tests allowed the clear differentiation of strain S5T, which is considered to represent a novel species of a new genus in the family Bacillaceae, for which the name Pelagirhabdus alkalitolerans gen. nov., sp. nov. is proposed. The type strain of Pelagirhabdus alkalitolerans is S5T (= KCTC 33632T = CGMCC 1.15177T). Based on the present study, it is also suggested to transfer Amphibacillus fermentum to this new genus, as Pelagirhabdus fermentum comb. nov. The type strain of Pelagirhabdus fermentum is Z-7984T = (DSM 13869T = UNIQEM 210T).}, }
@article {pmid26475107, year = {2016}, author = {Guo, J and Cole, JR and Zhang, Q and Brown, CT and Tiedje, JM}, title = {Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes.}, journal = {Applied and environmental microbiology}, volume = {82}, number = {1}, pages = {157-166}, pmid = {26475107}, issn = {1098-5336}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; DNA Primers/genetics ; Metagenome ; Metagenomics ; RNA, Ribosomal/*genetics ; Ribosomes/*genetics ; Soil Microbiology ; }, abstract = {Shotgun metagenomic sequencing does not depend on gene-targeted primers or PCR amplification; thus, it is not affected by primer bias or chimeras. However, searching rRNA genes from large shotgun Illumina data sets is computationally expensive, and no approach exists for unsupervised community analysis of small-subunit (SSU) rRNA gene fragments retrieved from shotgun data. We present a pipeline, SSUsearch, to achieve the faster identification of short-subunit rRNA gene fragments and enabled unsupervised community analysis with shotgun data. It also includes classification and copy number correction, and the output can be used by traditional amplicon analysis platforms. Shotgun metagenome data using this pipeline yielded higher diversity estimates than amplicon data but retained the grouping of samples in ordination analyses. We applied this pipeline to soil samples with paired shotgun and amplicon data and confirmed bias against Verrucomicrobia in a commonly used V6-V8 primer set, as well as discovering likely bias against Actinobacteria and for Verrucomicrobia in a commonly used V4 primer set. This pipeline can utilize all variable regions in SSU rRNA and also can be applied to large-subunit (LSU) rRNA genes for confirmation of community structure. The pipeline can scale to handle large amounts of soil metagenomic data (5 Gb memory and 5 central processing unit hours to process 38 Gb [1 lane] of trimmed Illumina HiSeq2500 data) and is freely available at https://github.com/dib-lab/SSUsearch under a BSD license.}, }
@article {pmid26473972, year = {2015}, author = {Louca, S and Doebeli, M}, title = {Calibration and analysis of genome-based models for microbial ecology.}, journal = {eLife}, volume = {4}, number = {}, pages = {e08208}, pmid = {26473972}, issn = {2050-084X}, mesh = {Acetates/metabolism ; Biological Evolution ; *Biota ; Carbon/metabolism ; Computational Biology/*methods ; Escherichia coli/*genetics/physiology ; *Genome, Bacterial ; Metabolism ; *Microbial Consortia ; Models, Biological ; Oxygen/metabolism ; }, abstract = {Microbial ecosystem modeling is complicated by the large number of unknown parameters and the lack of appropriate calibration tools. Here we present a novel computational framework for modeling microbial ecosystems, which combines genome-based model construction with statistical analysis and calibration to experimental data. Using this framework, we examined the dynamics of a community of Escherichia coli strains that emerged in laboratory evolution experiments, during which an ancestral strain diversified into two coexisting ecotypes. We constructed a microbial community model comprising the ancestral and the evolved strains, which we calibrated using separate monoculture experiments. Simulations reproduced the successional dynamics in the evolution experiments, and pathway activation patterns observed in microarray transcript profiles. Our approach yielded detailed insights into the metabolic processes that drove bacterial diversification, involving acetate cross-feeding and competition for organic carbon and oxygen. Our framework provides a missing link towards a data-driven mechanistic microbial ecology.}, }
@article {pmid26472095, year = {2015}, author = {Barberán, A and McGuire, KL and Wolf, JA and Jones, FA and Wright, SJ and Turner, BL and Essene, A and Hubbell, SP and Faircloth, BC and Fierer, N}, title = {Relating belowground microbial composition to the taxonomic, phylogenetic, and functional trait distributions of trees in a tropical forest.}, journal = {Ecology letters}, volume = {18}, number = {12}, pages = {1397-1405}, doi = {10.1111/ele.12536}, pmid = {26472095}, issn = {1461-0248}, mesh = {*Bacterial Physiological Phenomena ; *Biodiversity ; Fungi/*physiology ; Microbiota ; Panama ; Plant Roots/physiology ; Rainforest ; *Soil Microbiology ; Trees/*physiology ; Tropical Climate ; }, abstract = {The complexities of the relationships between plant and soil microbial communities remain unresolved. We determined the associations between plant aboveground and belowground (root) distributions and the communities of soil fungi and bacteria found across a diverse tropical forest plot. Soil microbial community composition was correlated with the taxonomic and phylogenetic structure of the aboveground plant assemblages even after controlling for differences in soil characteristics, but these relationships were stronger for fungi than for bacteria. In contrast to expectations, the species composition of roots in our soil core samples was a poor predictor of microbial community composition perhaps due to the patchy, ephemeral, and highly overlapping nature of fine root distributions. Our ability to predict soil microbial composition was not improved by incorporating information on plant functional traits suggesting that the most commonly measured plant traits are not particularly useful for predicting the plot-level variability in belowground microbial communities.}, }
@article {pmid26470852, year = {2016}, author = {Bryce, CC and Le Bihan, T and Martin, SF and Harrison, JP and Bush, T and Spears, B and Moore, A and Leys, N and Byloos, B and Cockell, CS}, title = {Rock geochemistry induces stress and starvation responses in the bacterial proteome.}, journal = {Environmental microbiology}, volume = {18}, number = {4}, pages = {1110-1121}, doi = {10.1111/1462-2920.13093}, pmid = {26470852}, issn = {1462-2920}, mesh = {Cupriavidus/*metabolism ; Iron/metabolism ; Phosphorus/metabolism ; Proteome/metabolism ; Soil/*chemistry ; *Soil Microbiology ; *Volcanic Eruptions ; }, abstract = {Interactions between microorganisms and rocks play an important role in Earth system processes. However, little is known about the molecular capabilities microorganisms require to live in rocky environments. Using a quantitative label-free proteomics approach, we show that a model bacterium (Cupriavidus metallidurans CH34) can use volcanic rock to satisfy some elemental requirements, resulting in increased rates of cell division in both magnesium- and iron-limited media. However, the rocks also introduced multiple new stresses via chemical changes associated with pH, elemental leaching and surface adsorption of nutrients that were reflected in the proteome. For example, the loss of bioavailable phosphorus was observed and resulted in the upregulation of diverse phosphate limitation proteins, which facilitate increase phosphate uptake and scavenging within the cell. Our results revealed that despite the provision of essential elements, rock chemistry drives complex metabolic reorganization within rock-dwelling organisms, requiring tight regulation of cellular processes at the protein level. This study advances our ability to identify key microbial responses that enable life to persist in rock environments.}, }
@article {pmid26470632, year = {2016}, author = {Vikram, S and Guerrero, LD and Makhalanyane, TP and Le, PT and Seely, M and Cowan, DA}, title = {Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community.}, journal = {Environmental microbiology}, volume = {18}, number = {6}, pages = {1875-1888}, doi = {10.1111/1462-2920.13088}, pmid = {26470632}, issn = {1462-2920}, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/*genetics/isolation &amp; purification ; Carbon/metabolism ; Desert Climate ; Ecosystem ; Fungi/classification/genetics/*isolation &amp; purification ; Metagenomics ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {In hyperarid ecosystems, macroscopic communities are often restricted to cryptic niches, such as hypoliths (microbial communities found beneath translucent rocks), which are widely distributed in hyperarid desert environments. While hypolithic communities are considered to play a major role in productivity, the functional guilds implicated in these processes remain unclear. Here, we describe the metagenomic sequencing, assembly and analysis of hypolithic microbial communities from the Namib Desert. Taxonomic analyses using Small Subunit phylogenetic markers showed that bacterial phylotypes (93%) dominated the communities, with relatively small proportions of archaea (0.43%) and fungi (5.6%). Refseq-viral database analysis showed the presence of double stranded DNA viruses (7.8% contigs), dominated by Caudovirales (59.2%). Analysis of functional genes and metabolic pathways revealed that cyanobacteria were primarily responsible for photosynthesis with the presence of multiple copies of genes for both photosystems I and II, with a smaller but significant fraction of proteobacterial anoxic photosystem II genes. Hypolithons demonstrated an extensive genetic capacity for the degradation of phosphonates and mineralization of organic sulphur. Surprisingly, we were unable to show the presence of genes representative of complete nitrogen cycles. Taken together, our analyses suggest an extensive capacity for carbon, phosphate and sulphate cycling but only limited nitrogen biogeochemistry.}, }
@article {pmid26467250, year = {2016}, author = {Kothamasi, D and Wannijn, J and van Hees, M and Nauts, R and van Gompel, A and Vanhoudt, N and Cranenbrouck, S and Declerck, S and Vandenhove, H}, title = {Rhizophagus irregularis MUCL 41833 can colonize and improve P uptake of Plantago lanceolata after exposure to ionizing gamma radiation in root organ culture.}, journal = {Mycorrhiza}, volume = {26}, number = {3}, pages = {257-262}, pmid = {26467250}, issn = {1432-1890}, mesh = {Beta Particles ; *Gamma Rays ; Glomeromycota/growth &amp; development/metabolism/*radiation effects ; Mycorrhizae/radiation effects ; Phosphorus/analysis/*metabolism ; Plant Roots/growth &amp; development/metabolism/microbiology ; Plantago/*metabolism/microbiology ; Radiation, Ionizing ; Seedlings/microbiology ; Soil ; Spores, Fungal/metabolism/radiation effects ; Symbiosis ; }, abstract = {Long-lived radionuclides such as (90)Sr and (137)Cs can be naturally or accidentally deposited in the upper soil layers where they emit β/γ radiation. Previous studies have shown that arbuscular mycorrhizal fungi (AMF) can accumulate and transfer radionuclides from soil to plant, but there have been no studies on the direct impact of ionizing radiation on AMF. In this study, root organ cultures of the AMF Rhizophagus irregularis MUCL 41833 were exposed to 15.37, 30.35, and 113.03 Gy gamma radiation from a (137)Cs source. Exposed spores were subsequently inoculated to Plantago lanceolata seedlings in pots, and root colonization and P uptake evaluated. P. lanceolata seedlings inoculated with non-irradiated AMF spores or with spores irradiated with up to 30.35 Gy gamma radiation had similar levels of root colonization. Spores irradiated with 113.03 Gy gamma radiation failed to colonize P. lanceolata roots. P content of plants inoculated with non-irradiated spores or of plants inoculated with spores irradiated with up to 30.35 Gy gamma radiation was higher than in non-mycorrhizal plants or plants inoculated with spores irradiated with 113.03 Gy gamma radiation. These results demonstrate that spores of R. irregularis MUCL 41833 are tolerant to chronic ionizing radiation at high doses.}, }
@article {pmid26467244, year = {2016}, author = {Hollowell, AC and Regus, JU and Gano, KA and Bantay, R and Centeno, D and Pham, J and Lyu, JY and Moore, D and Bernardo, A and Lopez, G and Patil, A and Patel, S and Lii, Y and Sachs, JL}, title = {Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {700-710}, pmid = {26467244}, issn = {1432-184X}, support = {S10 OD016290/OD/NIH HHS/United States ; }, mesh = {Bradyrhizobium/classification/*genetics/isolation &amp; purification/physiology ; California ; Fabaceae/*microbiology ; Genomic Islands ; Genotype ; Phylogeny ; Root Nodules, Plant/microbiology ; *Symbiosis ; }, abstract = {The patterns and drivers of bacterial strain dominance remain poorly understood in natural populations. Here, we cultured 1292 Bradyrhizobium isolates from symbiotic root nodules and the soil root interface of the host plant Acmispon strigosus across a >840-km transect in California. To investigate epidemiology and the potential role of accessory loci as epidemic drivers, isolates were genotyped at two chromosomal loci and were assayed for presence or absence of accessory "symbiosis island" loci that encode capacity to form nodules on hosts. We found that Bradyrhizobium populations were very diverse but dominated by few haplotypes-with a single "epidemic" haplotype constituting nearly 30 % of collected isolates and spreading nearly statewide. In many Bradyrhizobium lineages, we inferred presence and absence of the symbiosis island suggesting recurrent evolutionary gain and or loss of symbiotic capacity. We did not find statistical phylogenetic evidence that the symbiosis island acquisition promotes strain dominance and both symbiotic and non-symbiotic strains exhibited population dominance and spatial spread. Our dataset reveals that a strikingly few Bradyrhizobium genotypes can rapidly spread to dominate a landscape and suggests that these epidemics are not driven by the acquisition of accessory loci as occurs in key human pathogens.}, }
@article {pmid26464069, year = {2015}, author = {Król, N and Kiewra, D and Szymanowski, M and Lonc, E}, title = {The role of domestic dogs and cats in the zoonotic cycles of ticks and pathogens. Preliminary studies in the Wrocław Agglomeration (SW Poland).}, journal = {Veterinary parasitology}, volume = {214}, number = {1-2}, pages = {208-212}, doi = {10.1016/j.vetpar.2015.09.028}, pmid = {26464069}, issn = {1873-2550}, mesh = {Animals ; Borrelia/*isolation &amp; purification ; Cat Diseases/epidemiology/*parasitology ; Cats ; Dermacentor/*microbiology ; Dog Diseases/epidemiology/*microbiology ; Dogs ; Female ; Host-Pathogen Interactions ; Humans ; Ixodes/*microbiology ; Larva/microbiology ; Lyme Disease/epidemiology/transmission/*veterinary ; Male ; Nymph/microbiology ; Pets ; Poland/epidemiology ; Tick Infestations/epidemiology/parasitology/veterinary ; Zoonoses ; }, abstract = {The collection of 729 tick specimens (Ixodes ricinus, 88.6%; Ixodes hexagonus, 9.2%; Dermacentor reticulatus, 2.2%) removed from 373 dogs and 78 cats, along with 201 ticks from vegetation (I. ricinus, 75.6%; D. reticulatus, 24.4%), allows one to say that pets play an important role in maintaining tick life cycles in different urban area. It shows the lack of statistical differences between tick intensity in high-impact anthropogenic areas (HIAA), low-impact anthropogenic areas (LIAA) and mixed areas designed, in an objective way, by GIS techniques. The comparable (statistically insignificant) level of infection with Borrelia spp. of I. ricinus from pets (22.5%) and vegetation (24.8%), shows that dogs and cats do not have zooprophylactic competence for Borrelia spp. in different urban areas. Moreover, Borrelia spp. was detected in I. hexagonues (1.5%) collected from pets, and in D. reticulatus (2%) obtained from vegetation. The presence of D. reticulatus in the Wrocław Agglomeration confirms its expansion and the distribution range in Poland.}, }
@article {pmid26463685, year = {2016}, author = {Ogórek, R and Višňovská, Z and Tančinová, D}, title = {Mycobiota of Underground Habitats: Case Study of Harmanecká Cave in Slovakia.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {87-99}, pmid = {26463685}, issn = {1432-184X}, mesh = {Air/analysis ; *Air Microbiology ; Caves ; Ecosystem ; Fresh Water/analysis/microbiology ; Fungi/classification/genetics/*isolation &amp; purification ; Slovakia ; Temperature ; }, abstract = {Harmanecká Cave is located in the Harmanec Valley to the northwest of Banská Bystrica city, in the southern part of the Great Fatra Mountains, Slovakia. This cave is the most important underground locality of bat occurrence in Slovakia (population of 1000 to 1500 individuals). The study aimed at mycological evaluation of the air, the water, and the rock surface of Harmanecká Cave in Slovakia. The samples were taken on 24 July 2014. To examine the air, the Air Ideal 3P sampler was used. Microbiological evaluation of the rock surface was performed using swab sampling and the water by using the serial dilution technique. The authors observed a relationship between air temperature and the concentration of fungi. The concentration of airborne fungi increased with the increase in the air temperature and decreased with distance from the entrance to the cave. The density of airborne fungi isolated from the outdoor air samples was 810.5 colony-forming units (CFU) per 1 m3 of air and from 27.4 to 128.5 CFU for the indoor air samples. From the rock surface inside the cave, 45.0 to 106.6 CFU per 1 cm2 were isolated, whereas from the water, 29.9 CFU per 1 ml were isolated. Seven species of filamentous fungi were isolated from the external air samples and 12 species of filamentous fungi and 3 species of yeast-like fungi from the internal air samples. From the surface of the rocks inside the cave, 5 species of filamentous fungi and 1 species of yeast-like fungi were cultured, whereas from the water samples, 6 species of filamentous fungi were cultured. Cladosporium spp. were the fungi most frequently isolated from the external air; from the internal air, Penicillium urticae was most frequently isolated; from the rock surface, it was Gliocladium roseum; and from the water, it was P. chrysogenum. The species found in the cave can be pathogenic for humans and animals, especially for immunocompromised persons, and they can also cause biodegradation of the rocks. However, the concentration of airborne fungi inside the cave did not exceed official limits and norms stated as dangerous for the health of tourists.}, }
@article {pmid26462969, year = {2017}, author = {Vinícius de Melo Pereira, G and Soccol, VT and Brar, SK and Neto, E and Soccol, CR}, title = {Microbial ecology and starter culture technology in coffee processing.}, journal = {Critical reviews in food science and nutrition}, volume = {57}, number = {13}, pages = {2775-2788}, doi = {10.1080/10408398.2015.1067759}, pmid = {26462969}, issn = {1549-7852}, mesh = {Beverages ; Coffee/*chemistry ; *Fermentation ; Food Handling/*methods ; Food Microbiology ; Fungi ; Humans ; Taste ; }, abstract = {Coffee has been for decades the most commercialized food product and most widely consumed beverage in the world, with over 600 billion cups served per year. Before coffee cherries can be traded and processed into a final industrial product, they have to undergo postharvest processing on farms, which have a direct impact on the cost and quality of a coffee. Three different methods can be used for transforming the coffee cherries into beans, known as wet, dry, and semi-dry methods. In all these processing methods, a spontaneous fermentation is carried out in order to eliminate any mucilage still stuck to the beans and helps improve beverage flavor by microbial metabolites. The microorganisms responsible for the fermentation (e.g., yeasts and lactic acid bacteria) can play a number of roles, such as degradation of mucilage (pectinolytic activity), inhibition of mycotoxin-producing fungi growth, and production of flavor-active components. The use of starter cultures (mainly yeast strains) has emerged in recent years as a promising alternative to control the fermentation process and to promote quality development of coffee product. However, scarce information is still available about the effects of controlled starter cultures in coffee fermentation performance and bean quality, making it impossible to use this technology in actual field conditions. A broader knowledge about the ecology, biochemistry, and molecular biology could facilitate the understanding and application of starter cultures for coffee fermentation process. This review provides a comprehensive coverage of these issues, while pointing out new directions for exploiting starter cultures in coffee processing.}, }
@article {pmid26460220, year = {2015}, author = {Pascual, J and Wüst, PK and Geppert, A and Foesel, BU and Huber, KJ and Overmann, J}, title = {Novel isolates double the number of chemotrophic species and allow the first description of higher taxa in Acidobacteria subdivision 4.}, journal = {Systematic and applied microbiology}, volume = {38}, number = {8}, pages = {534-544}, doi = {10.1016/j.syapm.2015.08.001}, pmid = {26460220}, issn = {1618-0984}, mesh = {Acidobacteria/*classification/genetics/*isolation &amp; purification/physiology ; Aerobiosis ; Cluster Analysis ; Cytosol/chemistry ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Desert Climate ; Fatty Acids/analysis ; Molecular Sequence Data ; Phospholipids/analysis ; Phylogeny ; Pigments, Biological/metabolism ; Quinones/analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Despite their high phylogenetic diversity and abundance in soils worldwide, Acidobacteria represent an enigmatic bacterial phylum. Four novel Acidobacteria strains were isolated from Namibian semiarid savannah soils using low-nutrient cultivation media and extended incubation periods. 16S rRNA gene sequence analyses placed the isolates within Acidobacteria subdivision 4. Sequence identities with their closest relatives Aridibacter famidurans and Blastocatella fastidiosa were ≤94.9%. The Gram-negative, non-motile, rod-shaped, aerobic, and chemoorganotrophic bacteria grew at minimum doubling times of 5-14h and formed tiny white to pinkish colonies. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, and phosphatidylglycerol. The major isoprenoid quinone was MK-8. The major fatty acid methyl esters comprised iso-C15:0, iso-C15:1H/C13:0 3-OH, and C16:1ω7c/C16:1ω6c. Based on a polyphasic taxonomic characterization, strain Ac_18_E7(T) (=DSM 26557(T)=LMG 28656(T)) represented a novel species and genus, Tellurimicrobium multivorans gen. nov., sp. nov. The other strains constituted three independent species of the novel genus Stenotrophobacter gen. nov., Stenotrophobacter terrae sp. nov. (Ac_28_D10(T)=DSM 26560(T)=LMG 28657(T)), S. roseus sp. nov. (Ac_15_C4(T)=DSM 29891(T)=LMG 28889(T)), and S. namibiensis sp. nov. (Ac_17_F2(T)=DSM 29893(T)=LMG 28890(T)). These isolates doubled the number of established species and permitted the description of higher taxa of Acidobacteria subdivision 4. The family Blastocatellaceae fam. nov. is proposed in order to summarize the currently known oligotrophic, slightly acidophilic to neutrophilic mesophiles from arid soils. The superordinated order Blastocatellales ord. nov. and Blastocatellia classis nov. also include the terrestrial species Pyrinomonas methylaliphatogenes and the anoxygenic photoheterotrophic species Chloracidobacterium thermophilum from microbial mats.}, }
@article {pmid26456925, year = {2015}, author = {Cavicchioli, R}, title = {Microbial ecology of Antarctic aquatic systems.}, journal = {Nature reviews. Microbiology}, volume = {13}, number = {11}, pages = {691-706}, pmid = {26456925}, issn = {1740-1534}, mesh = {Antarctic Regions ; Climate Change ; *Ecosystem ; Lakes/microbiology ; Metagenomics ; Oceans and Seas ; Sunlight ; Temperature ; *Water Microbiology ; }, abstract = {The Earth's biosphere is dominated by cold environments, and the cold biosphere is dominated by microorganisms. Microorganisms in cold Southern Ocean waters are recognized for having crucial roles in global biogeochemical cycles, including carbon sequestration, whereas microorganisms in other Antarctic aquatic biomes are not as well understood. In this Review, I consider what has been learned about Antarctic aquatic microbial ecology from 'omic' studies. I assess the factors that shape the biogeography of Antarctic microorganisms, reflect on some of the unusual biogeochemical cycles that they are associated with and discuss the important roles that viruses have in controlling ecosystem function.}, }
@article {pmid26456581, year = {2015}, author = {Galipeau, HJ and McCarville, JL and Huebener, S and Litwin, O and Meisel, M and Jabri, B and Sanz, Y and Murray, JA and Jordana, M and Alaedini, A and Chirdo, FG and Verdu, EF}, title = {Intestinal microbiota modulates gluten-induced immunopathology in humanized mice.}, journal = {The American journal of pathology}, volume = {185}, number = {11}, pages = {2969-2982}, pmid = {26456581}, issn = {1525-2191}, support = {R01 HD067189/HD/NICHD NIH HHS/United States ; MOP#123282//Canadian Institutes of Health Research/Canada ; R01 DK67189/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/administration &amp; dosage ; Antibodies/*blood ; Celiac Disease/immunology/*microbiology/pathology ; Cell Proliferation ; Cytokines/analysis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Gliadin/adverse effects ; Glutens/*adverse effects ; Humans ; Male ; Mice ; Mice, Inbred NOD ; Specific Pathogen-Free Organisms ; T-Lymphocytes/immunology ; Vancomycin/administration &amp; dosage ; }, abstract = {Celiac disease (CD) is an immune-mediated enteropathy triggered by gluten in genetically susceptible individuals. The recent increase in CD incidence suggests that additional environmental factors, such as intestinal microbiota alterations, are involved in its pathogenesis. However, there is no direct evidence of modulation of gluten-induced immunopathology by the microbiota. We investigated whether specific microbiota compositions influence immune responses to gluten in mice expressing the human DQ8 gene, which confers moderate CD genetic susceptibility. Germ-free mice, clean specific-pathogen-free (SPF) mice colonized with a microbiota devoid of opportunistic pathogens and Proteobacteria, and conventional SPF mice that harbor a complex microbiota that includes opportunistic pathogens were used. Clean SPF mice had attenuated responses to gluten compared to germ-free and conventional SPF mice. Germ-free mice developed increased intraepithelial lymphocytes, markers of intraepithelial lymphocyte cytotoxicity, gliadin-specific antibodies, and a proinflammatory gliadin-specific T-cell response. Antibiotic treatment, leading to Proteobacteria expansion, further enhanced gluten-induced immunopathology in conventional SPF mice. Protection against gluten-induced immunopathology in clean SPF mice was reversed after supplementation with a member of the Proteobacteria phylum, an enteroadherent Escherichia coli isolated from a CD patient. The intestinal microbiota can both positively and negatively modulate gluten-induced immunopathology in mice. In subjects with moderate genetic susceptibility, intestinal microbiota changes may be a factor that increases CD risk.}, }
@article {pmid26454066, year = {2015}, author = {Paranjpye, RN and Nilsson, WB and Liermann, M and Hilborn, ED and George, BJ and Li, Q and Bill, BD and Trainer, VL and Strom, MS and Sandifer, PA}, title = {Environmental influences on the seasonal distribution of Vibrio parahaemolyticus in the Pacific Northwest of the USA.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {12}, pages = {}, doi = {10.1093/femsec/fiv121}, pmid = {26454066}, issn = {1574-6941}, mesh = {Animals ; Diatoms/isolation &amp; purification/microbiology ; Dinoflagellida/chemistry/microbiology ; *Harmful Algal Bloom ; Humans ; Kainic Acid/analogs &amp; derivatives/analysis ; Ostreidae/microbiology ; Phytoplankton/*isolation &amp; purification/pathogenicity ; Salinity ; Seasons ; Seawater/chemistry/*microbiology ; Silicates/analysis/chemistry ; Temperature ; Vibrio Infections/*epidemiology ; Vibrio parahaemolyticus/*isolation &amp; purification/pathogenicity ; Washington/epidemiology ; *Water Microbiology ; }, abstract = {Populations of Vibrio parahaemolyticus in the environment can be influenced by numerous factors. We assessed the correlation of total (tl+) and potentially virulent (tdh+) V. parahaemolyticus in water with three harmful algal bloom (HAB) genera (Pseudo-nitzschia, Alexandrium and Dinophysis), the abundance of diatoms and dinoflagellates, chlorophyll-a and temperature, salinity and macronutrients at five sites in Washington State from 2008-2009. The variability in V. parahaemolyticus density was explained predominantly by strong seasonal trends where maximum densities occurred in June, 2 months prior to the highest seasonal water temperature. In spite of large geographic differences in temperature, salinity and nutrients, there was little evidence of corresponding differences in V. parahaemolyticus density. In addition, there was no evident relationship between V. parahaemolyticus and indices of HAB genera, perhaps due to a lack of significant HAB events during the sampling period. The only nutrient significantly associated with V. parahaemolyticus density after accounting for the seasonal trend was silicate. This negative relationship may be caused by a shift in cell wall structure for some diatom species to a chitinous substrate preferred by V. parahaemolyticus. Results from our study differ from those in other regions corroborating previous findings that environmental factors that trigger vibrio and HAB events may differ depending on geographic locations. Therefore caution should be used when applying results from one region to another.}, }
@article {pmid26453971, year = {2016}, author = {Teshima, T and Reddy, P and Zeiser, R}, title = {Acute Graft-versus-Host Disease: Novel Biological Insights.}, journal = {Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation}, volume = {22}, number = {1}, pages = {11-16}, doi = {10.1016/j.bbmt.2015.10.001}, pmid = {26453971}, issn = {1523-6536}, mesh = {Acute Disease ; Allografts ; Cytokines/immunology ; Gastrointestinal Microbiome/*immunology ; Graft vs Host Disease/etiology/*immunology/mortality/pathology ; *Hematopoietic Stem Cell Transplantation ; Humans ; Intestinal Diseases/etiology/*immunology/mortality/pathology ; Paneth Cells/immunology/pathology ; Signal Transduction/immunology ; Stomach Diseases/etiology/*immunology/mortality/pathology ; T-Lymphocytes/*immunology/pathology ; }, abstract = {Graft-versus-host disease (GVHD) continues to be a leading cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation. Recent insights into intestinal homeostasis and uncovering of new pathways and targets have greatly reconciled our understanding of GVHD pathophysiology and will reshape contemporary GVHD prophylaxis and treatment. Gastrointestinal (GI) GVHD is the major cause of mortality. Emerging data indicate that intestinal stem cells (ISCs) and their niche Paneth cells are targeted, resulting in dysregulation of the intestinal homeostasis and microbial ecology. The microbiota and their metabolites shape the immune system and intestinal homeostasis, and they may alter host susceptibility to GVHD. Protection of the ISC niche system and modification of the intestinal microbiota and metabolome to restore intestinal homeostasis may, thus, represent a novel approach to modulate GVHD and infection. Damage to the intestine plays a central role in amplifying systemic GVHD by propagating a proinflammatory cytokine milieu. Molecular targeting to inhibit kinase signaling may be a promising approach to treat GVHD, ideally via targeting the redundant effect of multiple cytokines on immune cells and enterocytes. In this review, we discuss insights on the biology of GI GVHD, interaction of microflora and metabolome with the hosts, identification of potential new target organs, and identification and targeting of novel T cell-signaling pathways. Better understanding of GVHD biology will, thus, pave a way to develop novel treatment strategies with great clinical benefits.}, }
@article {pmid26453942, year = {2015}, author = {Luther, AK and Desloover, J and Fennell, DE and Rabaey, K}, title = {Electrochemically driven extraction and recovery of ammonia from human urine.}, journal = {Water research}, volume = {87}, number = {}, pages = {367-377}, doi = {10.1016/j.watres.2015.09.041}, pmid = {26453942}, issn = {1879-2448}, mesh = {Ammonia/*analysis ; Electrochemical Techniques/*methods ; Humans ; Urine/*chemistry ; Waste Disposal, Fluid/*methods ; }, abstract = {Human urine contains high concentrations of nitrogen, contributing about 75% of the nitrogen in municipal wastewaters yet only 1% of the volume. Source separation of urine produces an ideal waste stream for nitrogen and phosphorus recovery, reducing downstream costs of nutrient treatment at wastewater treatment facilities. We examined the efficiency and feasibility of ammonia extraction and recovery from synthetic and undiluted human urine using an electrochemical cell (EC). EC processing of synthetic urine produced an ammonium flux of 384 ± 8 g N m(-2) d(-1) with a 61 ± 1% current efficiency at an energy input of 12 kWh kg(-1) N removed. EC processing of real urine displayed similar performance, with an average ammonium flux of 275 ± 5 g N m(-2) d(-1) sustained over 10 days with 55 ± 1% current efficiency for ammonia and at an energy input of 13 kWh kg(-1) N removed. With the incorporation of an ammonia stripping and absorption unit into the real urine system, 57 ± 0.5% of the total nitrogen was recovered as ammonium sulfate. A system configuration additionally incorporating stripping of the influent headspace increased total nitrogen recovery to 79% but led to reduced performance of the EC as the urine ammonium concentration decrease. Direct stripping of ammonia (NH3) from urine with no chemical addition achieved only 12% total nitrogen recovery at hydraulic retention times comparable with the EC systems. Our results demonstrate that ammonia can be extracted via electrochemical means at reasonable energy inputs of approximately 12 kWh kg(-1) N. Considering also that the hydrogen generated is worth 4.3 kWh kg(-1) N, the net electrical input for extraction becomes approximately 8 kWh kg(-1) N if the hydrogen can be used. Critical for further development will be the inclusion of a passive means for ammonia stripping to reduce additional energy inputs.}, }
@article {pmid26451617, year = {2015}, author = {Vanden Bussche, J and Marzorati, M and Laukens, D and Vanhaecke, L}, title = {Validated High Resolution Mass Spectrometry-Based Approach for Metabolomic Fingerprinting of the Human Gut Phenotype.}, journal = {Analytical chemistry}, volume = {87}, number = {21}, pages = {10927-10934}, doi = {10.1021/acs.analchem.5b02688}, pmid = {26451617}, issn = {1520-6882}, mesh = {Chromatography, High Pressure Liquid/methods ; Feces ; Humans ; Intestinal Mucosa/*metabolism ; Intestines/microbiology ; Mass Spectrometry/*methods ; *Metabolomics ; }, abstract = {Fecal samples are an obvious choice for metabolomic approaches, since they can be obtained noninvasively and allow one to study the interactions between the gut microbiota and the host. The use of ultrahigh performance liquid chromatography hyphenated to Orbitrap high-resolution mass spectrometry (UHPLC-Orbitrap HRMS) in this field is unique. Hence, this study relied on Orbitrap HRMS to develop and validate a metabolic fingerprinting workflow for human feces and in vitro digestive fluids. After chemometric sample extraction optimization, an aqueous dilution appeared necessary to comply to the dynamic range of the MS. The method was proven "fit-for-purpose" through a validation procedure that monitored endogenous metabolites in quality control samples, which displayed in both matrices an excellent linearity (R(2) > 0.990), recoveries ranging from 93% to 105%, and precision with coefficients of variation (CVs) < 15%. Finally, feces from 10 healthy individuals and 13 patients diagnosed with inflammatory bowel disease were subjected to metabolomic fingerprinting. 9553 ions were detected, as well as differentiating profiles between Crohn's disease and ulcerative colitis by means of (orthogonal) partial least-square analysis ((O)PLS)-DA (discriminate analysis) models. Additionally, samples from the dynamic gastrointestinal tract simulator (SHIME (Simulator of the Human Intestinal Microbial Ecosystem) platform) were analyzed resulting in 6446 and 5010 ions for the proximal and distal colonic samples, respectively. Supplementing SHIME feed with antibiotics resulted in a significant shift (P < 0.05) of 27.7% of the metabolites from the proximal data set and 34.3% for the distal one. As a result, the presented fingerprinting approach provided predictive modeling of the gastrointestinal metabolome in vivo and in vitro, offering a window to reveal disease related biomarkers and potential insight into the mechanisms behind pathologies.}, }
@article {pmid26449384, year = {2015}, author = {Krause, S and Niklaus, PA and Badwan Morcillo, S and Meima Franke, M and Lüke, C and Reim, A and Bodelier, PL}, title = {Compositional and functional stability of aerobic methane consuming communities in drained and rewetted peat meadows.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {11}, pages = {}, doi = {10.1093/femsec/fiv119}, pmid = {26449384}, issn = {1574-6941}, mesh = {Agriculture ; Biodiversity ; Floods ; *Grassland ; Methane/metabolism ; Methylococcaceae/*classification/metabolism ; Methylocystaceae/metabolism ; Netherlands ; Soil ; *Soil Microbiology ; }, abstract = {The restoration of peatlands is an important strategy to counteract subsidence and loss of biodiversity. However, responses of important microbial soil processes are poorly understood. We assessed functioning, diversity and spatial organization of methanotrophic communities in drained and rewetted peat meadows with different water table management and agricultural practice. Results show that the methanotrophic diversity was similar between drained and rewetted sites with a remarkable dominance of the genus Methylocystis. Enzyme kinetics depicted no major differences, indicating flexibility in the methane (CH4) concentrations that can be used by the methanotrophic community. Short-term flooding led to temporary elevated CH4 emission but to neither major changes in abundances of methane-oxidizing bacteria (MOB) nor major changes in CH4 consumption kinetics in drained agriculturally used peat meadows. Radiolabeling and autoradiographic imaging of intact soil cores revealed a markedly different spatial arrangement of the CH4 consuming zone in cores exposed to near-atmospheric and elevated CH4. The observed spatial patterns of CH4 consumption in drained peat meadows with and without short-term flooding highlighted the spatial complexity and responsiveness of the CH4 consuming zone upon environmental change. The methanotrophic microbial community is not generally altered and harbors MOB that can cover a large range of CH4 concentrations offered due to water-table fluctuations, effectively mitigating CH4 emissions.}, }
@article {pmid26441902, year = {2015}, author = {Sarkar, A and Pazhani, GP and Chowdhury, G and Ghosh, A and Ramamurthy, T}, title = {Attributes of carbapenemase encoding conjugative plasmid pNDM-SAL from an extensively drug-resistant Salmonella enterica Serovar Senftenberg.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {969}, pmid = {26441902}, issn = {1664-302X}, abstract = {A carbapenem resistant Salmonella enterica serovar Senftenberg isolate BCH 2406 was isolated from a diarrheal child attending an outpatient unit of B.C. Roy Hospital in Kolkata, India. This isolate was positive for the bla NDM-1 in the PCR assay, which was confirmed by amplicon sequencing. Except for tetracycline, this isolate was resistant to all the tested antimicrobials. The bla NDM-1 was found to be located on a 146.13-kb mega plasmid pNDM-SAL, which could be conjugally transferred into Escherichia coli and other enteric pathogens such as Vibrio cholerae O1 Ogawa and Shigella flexneri 2a. However, the expression of β-lactam resistance is not the same in different bacteria. The whole genome sequence of pNDM-SAL was determined and compared with other pNDM plasmids available in public domain. This plasmid is an IncA/C incompatibility type composed of 155 predicted coding sequences and shares homology with plasmids of E. coli pNDM-1_Dok01, Klebsiella pNDM-KN, and Citrobacter pNDM-CIT. In pNDM-SAL, gene cluster containing bla NDM-1 was located between IS26 and IS4321 elements. Between the IS26 element and the bla NDM-1, a truncated ISAba125 insertion sequence was identified. Downstream of the bla NDM-1, other genes, such as ble MBL, trpF, tat, and an ISCR1 element with class 1 integron containing aac(6')-Ib were detected. Another β-lactacamase gene, bla CMY -4 was found to be inserted in IS1 element within the type IV conjugative transfer loci of the plasmid. This gene cluster had blc and sugE downstream of the bla CMY -4. From our findings, it appears that the strain S. Senftenberg could have acquired the NDM plasmid from the other members of Enterobacteriaceae. Transfer of NDM plasmids poses a danger in the management of infectious diseases.}, }
@article {pmid26441854, year = {2015}, author = {Orcutt, BN and Sylvan, JB and Rogers, DR and Delaney, J and Lee, RW and Girguis, PR}, title = {Carbon fixation by basalt-hosted microbial communities.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {904}, pmid = {26441854}, issn = {1664-302X}, abstract = {Oceanic crust is a massive potential habitat for microbial life on Earth, yet our understanding of this ecosystem is limited due to difficulty in access. In particular, measurements of rates of microbial activity are sparse. We used stable carbon isotope incubations of crustal samples, coupled with functional gene analyses, to examine the potential for carbon fixation on oceanic crust. Both seafloor-exposed and subseafloor basalts were recovered from different mid-ocean ridge and hot spot environments (i.e., the Juan de Fuca Ridge, the Mid-Atlantic Ridge, and the Loihi Seamount) and incubated with (13)C-labeled bicarbonate. Seafloor-exposed basalts revealed incorporation of (13)C-label into organic matter over time, though the degree of incorporation was heterogeneous. The incorporation of (13)C into biomass was inconclusive in subseafloor basalts. Translating these measurements into potential rates of carbon fixation indicated that 0.1-10 nmol C g(-1) rock d(-1) could be fixed by seafloor-exposed rocks. When scaled to the global production of oceanic crust, this suggests carbon fixation rates of 10(9)-10(12) g C year(-1), which matches earlier predictions based on thermodynamic calculations. Functional gene analyses indicate that the Calvin cycle is likely the dominant biochemical mechanism for carbon fixation in basalt-hosted biofilms, although the reductive acetyl-CoA pathway and reverse TCA cycle likely play some role in net carbon fixation. These results provide empirical evidence for autotrophy in oceanic crust, suggesting that basalt-hosted autotrophy could be a significant contributor of organic matter in this remote and vast environment.}, }
@article {pmid26440298, year = {2016}, author = {Bourceret, A and Cébron, A and Tisserant, E and Poupin, P and Bauda, P and Beguiristain, T and Leyval, C}, title = {The Bacterial and Fungal Diversity of an Aged PAH- and Heavy Metal-Contaminated Soil is Affected by Plant Cover and Edaphic Parameters.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {711-724}, pmid = {26440298}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; Fungi/classification/genetics/*isolation &amp; purification/metabolism ; Medicago sativa/*growth &amp; development ; Metals, Heavy/*analysis/metabolism ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/*analysis/metabolism ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/*analysis/metabolism ; }, abstract = {Industrial wasteland soils with aged PAH and heavy metal contaminations are environments where pollutant toxicity has been maintained for decades. Although the communities may be well adapted to the presence of stressors, knowledge about microbial diversity in such soils is scarce. Soil microbial community dynamics can be driven by the presence of plants, but the impact of plant development on selection or diversification of microorganisms in these soils has not been established yet. To test these hypotheses, aged-contaminated soil samples from a field trial were collected. Plots planted with alfalfa were compared to bare soil plots, and bacterial and fungal diversity and abundance were assessed after 2 and 6 years. Using pyrosequencing of 16S rRNA gene and ITS amplicons, we showed that the bacterial community was dominated by Proteobacteria, Actinobacteria, and Bacteroidetes and was characterized by low Acidobacteria abundance, while the fungal community was mainly represented by members of the Ascomycota. The short-term toxic impact of pollutants usually reduces the microbial diversity, yet in our samples bacterial and fungal species richness and diversity was high suggesting that the community structure and diversity adapted to the contaminated soil over decades. The presence of plants induced higher bacterial and fungal diversity than in bare soil. It also increased the relative abundance of bacterial members of the Actinomycetales, Rhizobiales, and Xanthomonadales orders and of most fungal orders. Multivariate analysis showed correlations between microbial community structure and heavy metal and PAH concentrations over time, but also with edaphic parameters (C/N, pH, phosphorus, and nitrogen concentrations).}, }
@article {pmid26434742, year = {2016}, author = {Smanski, MJ and Schlatter, DC and Kinkel, LL}, title = {Leveraging ecological theory to guide natural product discovery.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {43}, number = {2-3}, pages = {115-128}, pmid = {26434742}, issn = {1476-5535}, mesh = {Animals ; Biological Products/*isolation &amp; purification/*metabolism ; *Drug Discovery ; *Ecosystem ; Humans ; *Microbial Interactions ; Phylogeny ; Phylogeography ; Symbiosis ; }, abstract = {Technological improvements have accelerated natural product (NP) discovery and engineering to the point that systematic genome mining for new molecules is on the horizon. NP biosynthetic potential is not equally distributed across organisms, environments, or microbial life histories, but instead is enriched in a number of prolific clades. Also, NPs are not equally abundant in nature; some are quite common and others markedly rare. Armed with this knowledge, random 'fishing expeditions' for new NPs are increasingly harder to justify. Understanding the ecological and evolutionary pressures that drive the non-uniform distribution of NP biosynthesis provides a rational framework for the targeted isolation of strains enriched in new NP potential. Additionally, ecological theory leads to testable hypotheses regarding the roles of NPs in shaping ecosystems. Here we review several recent strain prioritization practices and discuss the ecological and evolutionary underpinnings for each. Finally, we offer perspectives on leveraging microbial ecology and evolutionary biology for future NP discovery.}, }
@article {pmid26432870, year = {2015}, author = {Dickson, RP and Erb-Downward, JR and Huffnagle, GB}, title = {Homeostasis and its disruption in the lung microbiome.}, journal = {American journal of physiology. Lung cellular and molecular physiology}, volume = {309}, number = {10}, pages = {L1047-55}, pmid = {26432870}, issn = {1522-1504}, support = {UL1 TR000433/TR/NCATS NIH HHS/United States ; T32 HL007749/HL/NHLBI NIH HHS/United States ; R01HL114447/HL/NHLBI NIH HHS/United States ; UL1TR000433/TR/NCATS NIH HHS/United States ; R01 HL114447/HL/NHLBI NIH HHS/United States ; L30 HL120241/HL/NHLBI NIH HHS/United States ; UL1 TR002240/TR/NCATS NIH HHS/United States ; T32HL00774921/HL/NHLBI NIH HHS/United States ; U01 HL098961/HL/NHLBI NIH HHS/United States ; U01HL098961/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; *Homeostasis ; Humans ; Lung/*microbiology/physiology ; Lung Diseases/immunology/metabolism/microbiology ; Microbial Interactions ; *Microbiota ; Signal Transduction ; }, abstract = {The disciplines of physiology and ecology are united by the shared centrality of the concept of homeostasis: the stability of a complex system via internal mechanisms of self-regulation, resilient to external perturbation. In the past decade, these fields of study have been bridged by the discovery of the lung microbiome. The respiratory tract, long considered sterile, is in fact a dynamic ecosystem of microbiota, intimately associated with the host inflammatory response, altered in disease states. If the microbiome is a "newly discovered organ," ecology is the language we use to explain how it establishes, maintains, and loses homeostasis. In this essay, we review recent insights into the feedback mechanisms by which the lung microbiome and the host response are regulated in health and dysregulated in acute and chronic lung disease. We propose three explanatory models supported by recent studies: the adapted island model of lung biogeography, nutritional homeostasis at the host-microbiome interface, and interkingdom signaling and the community stress response.}, }
@article {pmid26432535, year = {2016}, author = {Bertelkamp, C and van der Hoek, JP and Schoutteten, K and Hulpiau, L and Vanhaecke, L and Vanden Bussche, J and Cabo, AJ and Callewaert, C and Boon, N and Löwenberg, J and Singhal, N and Verliefde, AR}, title = {The effect of feed water dissolved organic carbon concentration and composition on organic micropollutant removal and microbial diversity in soil columns simulating river bank filtration.}, journal = {Chemosphere}, volume = {144}, number = {}, pages = {932-939}, doi = {10.1016/j.chemosphere.2015.09.017}, pmid = {26432535}, issn = {1879-1298}, mesh = {Biodegradation, Environmental ; Carbon/chemistry ; Filtration ; Fresh Water/chemistry ; Groundwater/chemistry ; *Models, Theoretical ; Organic Chemicals/*analysis ; Rivers/*chemistry ; Soil/*chemistry ; *Soil Microbiology ; Solubility ; Wastewater/chemistry ; Water Pollutants, Chemical/*analysis ; }, abstract = {This study investigated organic micropollutant (OMP) biodegradation rates in laboratory-scale soil columns simulating river bank filtration (RBF) processes. The dosed OMP mixture consisted of 11 pharmaceuticals, 6 herbicides, 2 insecticides and 1 solvent. Columns were filled with soil from a RBF site and were fed with four different organic carbon fractions (hydrophilic, hydrophobic, transphilic and river water organic matter (RWOM)). Additionally, the effect of a short-term OMP/dissolved organic carbon (DOC) shock-load (e.g. quadrupling the OMP concentrations and doubling the DOC concentration) on OMP biodegradation rates was investigated to assess the resilience of RBF systems. The results obtained in this study imply that - in contrast to what is observed for managed aquifer recharge systems operating on wastewater effluent - OMP biodegradation rates are not affected by the type of organic carbon fraction fed to the soil column, in case of stable operation. No effect of a short-term DOC shock-load on OMP biodegradation rates between the different organic carbon fractions was observed. This means that the RBF site simulated in this study is resilient towards transient higher DOC concentrations in the river water. However, a temporary OMP shock-load affected OMP biodegradation rates observed for the columns fed with the river water organic matter (RWOM) and the hydrophilic fraction of the river water organic matter. These different biodegradation rates did not correlate with any of the parameters investigated in this study (cellular adenosine triphosphate (cATP), DOC removal, specific ultraviolet absorbance (SUVA), richness/evenness of the soil microbial population or OMP category (hydrophobicity/charge).}, }
@article {pmid26431968, year = {2015}, author = {Shah, F and Schwenk, D and Nicolás, C and Persson, P and Hoffmeister, D and Tunlid, A}, title = {Involutin is an Fe3+ reductant secreted by the ectomycorrhizal fungus Paxillus involutus during Fenton-based decomposition of organic matter.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {24}, pages = {8427-8433}, pmid = {26431968}, issn = {1098-5336}, mesh = {Agaricales/*metabolism ; Carbon/metabolism ; Fungal Proteins/*metabolism ; Hydrogen Peroxide/*chemistry ; Hydroxyl Radical/chemical synthesis ; Iron/*chemistry ; Mass Spectrometry ; Mycorrhizae/*metabolism ; Nuclear Magnetic Resonance, Biomolecular ; Reducing Agents/metabolism ; Soil/chemistry ; Wood/microbiology ; }, abstract = {Ectomycorrhizal fungi play a key role in mobilizing nutrients embedded in recalcitrant organic matter complexes, thereby increasing nutrient accessibility to the host plant. Recent studies have shown that during the assimilation of nutrients, the ectomycorrhizal fungus Paxillus involutus decomposes organic matter using an oxidative mechanism involving Fenton chemistry (Fe(2+) + H2O2 + H(+) → Fe(3+) + ˙OH + H2O), similar to that of brown rot wood-decaying fungi. In such fungi, secreted metabolites are one of the components that drive one-electron reductions of Fe(3+) and O2, generating Fenton chemistry reagents. Here we investigated whether such a mechanism is also implemented by P. involutus during organic matter decomposition. Activity-guided purification was performed to isolate the Fe(3+)-reducing principle secreted by P. involutus during growth on a maize compost extract. The Fe(3+)-reducing activity correlated with the presence of one compound. Mass spectrometry and nuclear magnetic resonance (NMR) identified this compound as the diarylcyclopentenone involutin. A major part of the involutin produced by P. involutus during organic matter decomposition was secreted into the medium, and the metabolite was not detected when the fungus was grown on a mineral nutrient medium. We also demonstrated that in the presence of H2O2, involutin has the capacity to drive an in vitro Fenton reaction via Fe(3+) reduction. Our results show that the mechanism for the reduction of Fe(3+) and the generation of hydroxyl radicals via Fenton chemistry by ectomycorrhizal fungi during organic matter decomposition is similar to that employed by the evolutionarily related brown rot saprotrophs during wood decay.}, }
@article {pmid26431725, year = {2015}, author = {Lee, JC and Kim, YS and Yun, BS and Whang, KS}, title = {Halomonas salicampi sp. nov., a halotolerant and alkalitolerant bacterium isolated from a saltern soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {65}, number = {12}, pages = {4792-4799}, doi = {10.1099/ijsem.0.000650}, pmid = {26431725}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Halomonas/*classification/genetics/isolation &amp; purification ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Salinity ; Sequence Analysis, DNA ; *Soil Microbiology ; Ubiquinone/chemistry ; }, abstract = {A Gram-stain-negative, halotolerant and alkalitolerant bacterium, designated strain BH103T, was isolated from saltern soil in Gomso, Korea. Cells of strain BH103T were strictly aerobic, motile, straight rods and grew at pH 7.0-10.8 (optimum, pH 8.5), at 10-55 °C (optimum, 28 °C) and at salinities of 0-23 % (w/v) NaCl (optimum, 14 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BH103T belongs to the genus Halomonas, showing highest sequence similarity to Halomonas boliviensis LC1T (97.7 %), Halomonas neptunia Eplume1T (97.7 %), Halomonas variabilis IIIT (97.7 %), Halomonas alkaliantarctica CRSST (97.7 %), Halomonas olivaria TYRC17T (97.5 %), Halomonas titanicae BH1T (97.2 %) and Halomonas sulfidaeris Esulfide1T (96.2 %). The predominant ubiquinone was Q-9. The major fatty acids were C18 : 1ω7c, C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C12 : 0 3-OH. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and an unknown phospholipid. The DNA G+C content of this novel isolate was 54.7 mol%. DNA-DNA relatedness between strain BH103T and H. boliviensis KACC 16615T, H. neptunia KCTC 2888T, H. variabilis KCTC 2889T, H. alkaliantarctica KCTC 22844T, H. olivaria DSM 19074T, H. titanicae JCM 16411T and H. sulfidaeris DSM 15722T was 45, 41, 39, 32, 38, 45 and 35 %, respectively. On the basis of polyphasic analysis from this study, strain BH103T represents a novel species of the genus Halomonas, for which the name Halomonas salicampi sp. nov. is proposed. The type strain is BH103T (= KACC 17609T = NBRC 109914T = NCAIM B 02528T).}, }
@article {pmid26428446, year = {2015}, author = {Kleiman, SC and Watson, HJ and Bulik-Sullivan, EC and Huh, EY and Tarantino, LM and Bulik, CM and Carroll, IM}, title = {The Intestinal Microbiota in Acute Anorexia Nervosa and During Renourishment: Relationship to Depression, Anxiety, and Eating Disorder Psychopathology.}, journal = {Psychosomatic medicine}, volume = {77}, number = {9}, pages = {969-981}, pmid = {26428446}, issn = {1534-7796}, support = {R01 MH 105684/MH/NIMH NIH HHS/United States ; R01 MH105684/MH/NIMH NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; K01 DK092330/DK/NIDDK NIH HHS/United States ; K01 DK 092330/DK/NIDDK NIH HHS/United States ; P30DK03498/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Affect ; Anorexia Nervosa/*microbiology/psychology/therapy ; Anxiety/microbiology ; Bacteroidetes/isolation &amp; purification ; Body Composition ; Case-Control Studies ; Convalescence ; DNA, Bacterial/genetics ; Depression/microbiology ; Feces/microbiology ; Feeding Behavior ; Female ; Firmicutes/isolation &amp; purification ; Gastrointestinal Microbiome/*physiology ; Humans ; Lactobacillus/isolation &amp; purification ; Methanobrevibacter/isolation &amp; purification ; Ribotyping ; Ruminococcus/isolation &amp; purification ; Surveys and Questionnaires ; Young Adult ; }, abstract = {OBJECTIVE: The relevance of the microbe-gut-brain axis to psychopathology is of interest in anorexia nervosa (AN), as the intestinal microbiota plays a critical role in metabolic function and weight regulation.<br><br>METHODS: We characterized the composition and diversity of the intestinal microbiota in AN, using stool samples collected at inpatient admission (T1; n = 16) and discharge (T2; n = 10). At T1, participants completed the Beck Depression and Anxiety Inventories and the Eating Disorder Examination-Questionnaire. Patients with AN were compared with healthy individuals who participated in a previous study (healthy comparison group; HCG). Genomic DNA was isolated from stool samples, and bacterial composition was characterized by 454 pyrosequencing of the 16S rRNA gene. Sequencing results were processed by the Quantitative Insights Into Microbial Ecology pipeline. We compared T1 versus T2 samples, samples from both points were compared with HCG (n = 12), and associations between psychopathology and T1 samples were explored.<br><br>RESULTS: In patients with AN, significant changes emerged between T1 and T2 in taxa abundance and beta (between-sample) diversity. Patients with AN had significantly lower alpha (within-sample) diversity than did HCG at both T1 (p = .0001) and T2 (p = .016), and differences in taxa abundance were found between AN patients and HCG. Levels of depression, anxiety, and eating disorder psychopathology at T1 were associated with composition and diversity of the intestinal microbiota.<br><br>CONCLUSIONS: We provide evidence of an intestinal dysbiosis in AN and an association between mood and the enteric microbiota in this patient population. Future directions include mechanistic investigations of the microbe-gut-brain axis in animal models and association of microbial measures with metabolic changes and recovery indices.}, }
@article {pmid26425940, year = {2015}, author = {Neumann, AP and Suen, G}, title = {Differences in major bacterial populations in the intestines of mature broilers after feeding virginiamycin or bacitracin methylene disalicylate.}, journal = {Journal of applied microbiology}, volume = {119}, number = {6}, pages = {1515-1526}, doi = {10.1111/jam.12960}, pmid = {26425940}, issn = {1365-2672}, mesh = {Administration, Oral ; Animals ; Anti-Bacterial Agents/administration &amp; dosage/*pharmacology ; Bacitracin/administration &amp; dosage/*pharmacology ; Bacteria/*drug effects ; Chickens ; Gastrointestinal Microbiome/*drug effects ; Intestines/*microbiology ; Salicylates/administration &amp; dosage/*pharmacology ; Virginiamycin/administration &amp; dosage/*pharmacology ; }, abstract = {AIMS: The purpose of this study was to compare the effects of feeding virginiamycin or bacitracin methylene disalicylate (BMD), two in-feed antibiotics typically used by commercial poultry producers in the United States, on the chicken gastrointestinal microbiota.<br><br>METHODS AND RESULTS: 454 pyrosequencing of the V6-V8 region of the 16S rRNA gene and quantitative PCR were employed to examine the bacterial microbiota and Clostridium perfringens, respectively, in the jejunum and caecum of market-age broiler chickens over four replicate grow-outs.<br><br>CONCLUSIONS: Our results suggest that virginiamycin has a more pronounced impact on broiler gastrointestinal tract bacterial communities, relative to BMD, manifested primarily through significant enrichments in the genus Faecalibacterium in the caecum and a distinct population of Lactobacillus, OTU_02, in both the jejunum and caecum. No evidence for a difference among the diets in Cl.&#xa0;perfringens levels in the jejunum or caecum was observed.<br><br>This work represents the highest resolution comparison to date of the jejunum and caecum microbiota in broilers fed either virginiamycin or BMD, and provides evidence for specific bacterial OTUs potentially involved in the health and performance benefits typically attributed to these in-feed antibiotics.}, }
@article {pmid26424812, year = {2015}, author = {Domman, D and Horn, M}, title = {Following the Footsteps of Chlamydial Gene Regulation.}, journal = {Molecular biology and evolution}, volume = {32}, number = {12}, pages = {3035-3046}, pmid = {26424812}, issn = {1537-1719}, support = {281633/ERC_/European Research Council/International ; I 1628/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Biological Evolution ; Chlamydia/*genetics ; *Gene Expression Regulation, Bacterial ; Genomics ; Phylogeny ; Transcription Factors/genetics ; }, abstract = {Regulation of gene expression ensures an organism responds to stimuli and undergoes proper development. Although the regulatory networks in bacteria have been investigated in model microorganisms, nearly nothing is known about the evolution and plasticity of these networks in obligate, intracellular bacteria. The phylum Chlamydiae contains a vast array of host-associated microbes, including several human pathogens. The Chlamydiae are unique among obligate, intracellular bacteria as they undergo a complex biphasic developmental cycle in which large swaths of genes are temporally regulated. Coupled with the low number of transcription factors, these organisms offer a model to study the evolution of regulatory networks in intracellular organisms. We provide the first comprehensive analysis exploring the diversity and evolution of regulatory networks across the phylum. We utilized a comparative genomics approach to construct predicted coregulatory networks, which unveiled genus- and family-specific regulatory motifs and architectures, most notably those of virulence-associated genes. Surprisingly, our analysis suggests that few regulatory components are conserved across the phylum, and those that are conserved are involved in the exploitation of the intracellular niche. Our study thus lends insight into a component of chlamydial evolution that has otherwise remained largely unexplored.}, }
@article {pmid26424434, year = {2016}, author = {Singh, D and Takahashi, K and Park, J and Adams, JM}, title = {Similarities and Contrasts in the Archaeal Community of Two Japanese Mountains: Mt. Norikura Compared to Mt. Fuji.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {428-441}, pmid = {26424434}, issn = {1432-184X}, mesh = {Altitude ; Archaea/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Japan ; *Soil Microbiology ; }, abstract = {The community ecology, abundance, and diversity patterns of soil archaea are poorly understood-despite the fact that they are a major branch of life that is ubiquitous and important in nitrogen cycling in terrestrial ecosystems. We set out to investigate the elevational patterns of archaeal ecology, and how these compare with other groups of organisms. Many studies of different groups of organisms (plants, birds, etc.) have shown a series of distinct communities with elevation, and often a diversity maximum in mid-elevations. We investigated the soil archaeal communities on Mt. Norikura, Japan, using 454 pyrosequencing of the 16S ribosomal RNA (rRNA) gene. There was a strong mid-elevation maximum in diversity, and a mid-elevation maximum in abundance of soil archaea 16S rRNA and amoA genes. These diversity and abundance maximums could not be correlated with any identifiable soil parameter, nor plant diversity. Discrete, predictable communities of archaea occurred at each elevational level, also not explicable in terms of pH or major nutrients. When we compared the archaeal community and diversity patterns with those found in an earlier study of Mt Fuji, both mountains showed mid-elevation maximums in diversity and abundance of archaea, possibly a result of some common environmental factor such as soil disturbance frequency. However, they showed distinct sets of archaeal communities at similar elevational sampling points. Presumably, the difference reflects their distinct geology (Norikura being andesitic, while Fuji is basaltic) and the resulting combinations of soil chemistry and environmental conditions, although no explanatory variable was found. Clearly, many soil archaea have strongly defined niches and will only occur in a narrow subset of the range of possible climate and soil conditions. The findings of a mid-elevation diversity maximum on Norikura provides a further instance of how widespread this unexplained pattern is in nature, in a wide variety of groups of organisms.}, }
@article {pmid26421738, year = {2014}, author = {González-Toril, E and Santofimia, E and López-Pamo, E and García-Moyano, A and Aguilera, &#xc1; and Amils, R}, title = {Comparative microbial ecology of the water column of an extreme acidic pit lake, Nuestra Señora del Carmen, and the Río Tinto basin (Iberian Pyrite Belt).}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {17}, number = {4}, pages = {225-233}, doi = {10.2436/20.1501.01.225}, pmid = {26421738}, issn = {1139-6709}, mesh = {Acids/analysis/metabolism ; Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Ecosystem ; Hydrogen-Ion Concentration ; Lakes/*chemistry/*microbiology ; Phylogeny ; Spain ; }, abstract = {The Iberian Pyrite Belt, located in Southwestern Spain, represents one of the world's largest accumulations of mine wastes and acid mine drainages. This study reports the comparative microbial ecology of the water column of Nuestra Señora del Carmen acid pit lake with the extreme acidic Río Tinto basin. The canonical correspondence analysis identified members of the Leptospirillum, Acidiphilium, Metallibacterium, Acidithiobacillus, Ferrimicrobium and Acidisphaera genera as the most representative microorganisms of both ecosystems. The presence of archaeal members is scarce in both systems. Only sequences clustering with the Thermoplasmata have been retrieved in the bottom layer of Nuestra Señora del Carmen and one station of Río Tinto. Although the photosynthetically active radiation values measured in this lake upper layer were low, they were sufficient to activate photosynthesis in acidophilic microorganisms. All identified photosynthetic microorganisms in Nuestra Señora del Carmen (members of the Chlamydomonas, Zygnemopsis and Klebsormidium genera) are major members of the photosynthetic eukaryotic community characterized in Río Tinto basin. This study demonstrates a close relationship between the microbial diversity of Nuestra Señora del Carmen pit lake and the diversity detected in the Río Tinto basin, which underlain the influence of the shared mineral substrates in the microbial ecology of these ecosystems.}, }
@article {pmid26421736, year = {2014}, author = {Ramió-Pujol, S and Ganigué, R and Bañeras, L and Colprim, J}, title = {Impact of formate on the growth and productivity of Clostridium ljungdahlii PETC and Clostridium carboxidivorans P7 grown on syngas.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {17}, number = {4}, pages = {195-204}, doi = {10.2436/20.1501.01.222}, pmid = {26421736}, issn = {1139-6709}, mesh = {Biofuels/analysis ; Bioreactors/microbiology ; Butanols/metabolism ; Clostridium/chemistry/*growth &amp; development/*metabolism ; Culture Media/chemistry/metabolism ; Ethanol/*metabolism ; Fermentation ; Formates/*metabolism ; Hydrogen-Ion Concentration ; Kinetics ; }, abstract = {The current energy model based on fossil fuels is coming to an end due to the increase in global energy demand. Biofuels such as ethanol and butanol can be produced through the syngas fermentation by acetogenic bacteria. The present work hypothesizes that formate addition would positively impact kinetic parameters for growth and alcohol production in Clostridium ljungdahlii PETC and Clostridium carboxidivorans P7 by diminishing the need for reducing equivalents. Fermentation experiments were conducted using completely anaerobic batch cultures at different pH values and formate concentrations. PETC cultures were more tolerant to formate concentrations than P7, specially at pH 5.0 and 6.0. Complete growth inhibition of PETC occurred at sodium formate concentrations of 30.0 mM; however, no differences in growth rates were observed at pH 7.0 for the two strains. Incubation at formate concentrations lower than 2.0 mM resulted in increased growth rates for both strains. The most recognizable effects of formate addition on the fermentation products were the increase in the total carbon fixed into acids and alcohols at pH 5.0 and pH 6.0, as well as, a higher ethanol to total products ratio at pH 7.0. Taken all together, these results show the ability of acetogens to use formate diminishing the energy demand for growth, and enhancing strain productivity.}, }
@article {pmid26419730, year = {2015}, author = {Bonnichsen, L and Bygvraa Svenningsen, N and Rybtke, M and de Bruijn, I and Raaijmakers, JM and Tolker-Nielsen, T and Nybroe, O}, title = {Lipopeptide biosurfactant viscosin enhances dispersal of Pseudomonas fluorescens SBW25 biofilms.}, journal = {Microbiology (Reading, England)}, volume = {161}, number = {12}, pages = {2289-2297}, pmid = {26419730}, issn = {1465-2080}, mesh = {Bacterial Proteins/genetics/metabolism ; *Biofilms ; Lipopeptides/*metabolism ; Peptide Synthases/genetics/metabolism ; Peptides, Cyclic/*metabolism ; Pseudomonas fluorescens/enzymology/genetics/*physiology ; Surface-Active Agents/*metabolism ; }, abstract = {Pseudomonads produce several lipopeptide biosurfactants that have antimicrobial properties but that also facilitate surface motility and influence biofilm formation. Detailed studies addressing the significance of lipopeptides for biofilm formation and architecture are rare. Hence, the present study sets out to determine the specific role of the lipopeptide viscosin in Pseudomonas fluorescens SBW25 biofilm formation, architecture and dispersal, and to relate viscA gene expression to viscosin production and effect. Initially, we compared biofilm formation of SBW25 and the viscosin-deficient mutant strain SBW25ΔviscA in static microtitre assays. These experiments demonstrated that viscosin had little influence on the amount of biofilm formed by SBW25 during the early stages of biofilm development. Later, however, SBW25 formed significantly less biofilm than SBW25ΔviscA. The indication that viscosin is involved in biofilm dispersal was confirmed by chemical complementation of the mutant biofilm. Furthermore, a fluorescent bioreporter showed that viscA expression was induced in biofilms 4 h prior to dispersal. Subsequent detailed studies of biofilms formed in flow cells for up to 5 days revealed that SBW25 and SBW25ΔviscA developed comparable biofilms dominated by well-defined, mushroom-shaped structures. Carbon starvation was required to obtain biofilm dispersal in this system. Dispersal of SBW25 biofilms was significantly greater than of SBW25ΔviscA biofilms after 3 h and, importantly, carbon starvation strongly induced viscA expression, in particular for cells that were apparently leaving the biofilm. Thus, the present study points to a role for viscosin-facilitated motility in dispersal of SBW25 biofilms.}, }
@article {pmid26419727, year = {2016}, author = {Hernández, SB and Cava, F}, title = {Environmental roles of microbial amino acid racemases.}, journal = {Environmental microbiology}, volume = {18}, number = {6}, pages = {1673-1685}, doi = {10.1111/1462-2920.13072}, pmid = {26419727}, issn = {1462-2920}, mesh = {Amino Acid Isomerases/genetics/*metabolism ; Amino Acids/metabolism ; Bacteria/*enzymology/genetics/metabolism ; Bacterial Proteins/genetics/*metabolism ; Biofilms ; Cell Wall/metabolism ; *Environmental Microbiology ; }, abstract = {Enzymes catalysing the stereo-chemical inter-conversion of amino acids are known as amino acid racemases. In bacteria, these enzymes are fundamental to synthesize the D-Ala and D-Glu that are critical components of the peptidoglycan. In addition to this structural function in cell wall assembly, D-amino acids produced by microbial amino acid racemases have been described as relevant constituents in other prokaryotic structures (e.g. capsule, non-ribosomal peptides) and have been associated to growth fitness and to processes such as biofilm development, spore germination and signalling. The recent discovery of broad spectrum racemases able to produce and release several D-amino acids to the environment suggests that these enzymes might have a great impact in microbial ecology. Consequently, new data on the biochemistry and regulation of racemases is key to understand the biological significance of D-enantiomers in nature, in particular their effect on microbial social networks. This review summarizes current knowledge on the environmental roles of bacterial racemases with an emphasis on the potential roles of the new broad spectrum enzymes in natural environments.}, }
@article {pmid26414296, year = {2015}, author = {Baker, BH and Kröger, R and Brooks, JP and Smith, RK and Czarnecki, JM}, title = {Investigation of denitrifying microbial communities within an agricultural drainage system fitted with low-grade weirs.}, journal = {Water research}, volume = {87}, number = {}, pages = {193-201}, doi = {10.1016/j.watres.2015.09.028}, pmid = {26414296}, issn = {1879-2448}, mesh = {Agriculture/*methods ; Carbon/*analysis ; DNA, Bacterial/analysis ; Denitrification ; *Microbiota ; Mississippi ; Nitrogen/*analysis ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/analysis ; *Soil Microbiology ; }, abstract = {Enhancing wetland characteristics in agricultural drainage ditches with the use of low-grade weirs, has been identified as a best management practice (BMP) to mitigate nutrient runoff from agriculture landscapes. A major objective of utilizing low-grade weirs as a BMP includes fostering environments suitable for the biogeochemical removal of nitrogen via denitrification. This study examined the spatial resolution of microbial communities involved in denitrification in agricultural drainage systems fitted with low-grade weirs. Appropriate sampling scales of microbial communities were investigated using 16S rRNA and denitrification functional genes nosZ, nirS, and nirK via quantitative polymerase chain reaction (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP) analysis. Genes 16S rRNA, nosZ, and nirS were all successfully detected in soil samples, while nirK was below the detection limit throughout the study. Utilizing a combination of three sampling regimes (management, reach, catchment) was found to be effective in capturing microbial community patterns, as ANOVA results revealed nosZ gene abundance was significantly greater at the management rather than reach scale (p = 0.045; F = 3.311), although, no significant differences were observed in 16S rRNA or nirS between sampling scales (p > 0.05). A Pearson correlation matrix confirmed that 16S rRNA and nosZ gene abundances were positively correlated with soil carbon (C), nitrogen (N), and moisture, while nirS abundance was only positively correlated with soil C and soil moisture. This highlights the potential for wetland-like characteristics to be recovered in agricultural drainage systems, as weir proximity is observed to enhance soil moisture and conditions for N remediation. This study provides the basis for additional investigations of these unique environments in the Mississippi Alluvial Valley and a starting point for adaptive management to enhance agricultural drainage systems for microbial communities towards nutrient remediation goals.}, }
@article {pmid26411644, year = {2015}, author = {Brandt, KK and Amézquita, A and Backhaus, T and Boxall, A and Coors, A and Heberer, T and Lawrence, JR and Lazorchak, J and Schönfeld, J and Snape, JR and Zhu, YG and Topp, E}, title = {Ecotoxicological assessment of antibiotics: A call for improved consideration of microorganisms.}, journal = {Environment international}, volume = {85}, number = {}, pages = {189-205}, doi = {10.1016/j.envint.2015.09.013}, pmid = {26411644}, issn = {1873-6750}, mesh = {Animals ; Anti-Bacterial Agents/analysis/*toxicity ; Ecology ; Ecosystem ; *Ecotoxicology ; Environmental Pollutants/analysis/*toxicity ; Humans ; Microbial Consortia/*drug effects ; Risk Assessment ; Soil Microbiology/*standards ; Water Microbiology/*standards ; }, abstract = {Antibiotics play a pivotal role in the management of infectious disease in humans, companion animals, livestock, and aquaculture operations at a global scale. Antibiotics are produced, consumed, and released into the environment at an unprecedented scale causing concern that the presence of antibiotic residues may adversely impact aquatic and terrestrial ecosystems. Here we critically review the ecotoxicological assessment of antibiotics as related to environmental risk assessment (ERA). We initially discuss the need for more specific protection goals based on the ecosystem service concept, and suggest that the ERA of antibiotics, through the application of a mode of toxic action approach, should make more use of ecotoxicological endpoints targeting microorganisms (especially bacteria) and microbial communities. Key ecosystem services provided by microorganisms and associated ecosystem service-providing units (e.g. taxa or functional groups) are identified. Approaches currently available for elucidating ecotoxicological effects on microorganisms are reviewed in detail and we conclude that microbial community-based tests should be used to complement single-species tests to offer more targeted protection of key ecosystem services. Specifically, we propose that ecotoxicological tests should not only assess microbial community function, but also microbial diversity (‘species’ richness) and antibiotic susceptibility. Promising areas for future basic and applied research of relevance to ERA are highlighted throughout the text. In this regard, the most fundamental knowledge gaps probably relate to our rudimentary understanding of the ecological roles of antibiotics in nature and possible adverse effects of environmental pollution with subinhibitory levels of antibiotics.}, }
@article {pmid26409315, year = {2015}, author = {Rashid, M and Stingl, U}, title = {Contemporary molecular tools in microbial ecology and their application to advancing biotechnology.}, journal = {Biotechnology advances}, volume = {33}, number = {8}, pages = {1755-1773}, doi = {10.1016/j.biotechadv.2015.09.005}, pmid = {26409315}, issn = {1873-1899}, mesh = {Bacteria/*genetics/metabolism ; *Biotechnology ; *Genetic Variation ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Single-Cell Analysis ; }, abstract = {Novel methods in microbial ecology are revolutionizing our understanding of the structure and function of microbes in the environment, but concomitant advances in applications of these tools to biotechnology are mostly lagging behind. After more than a century of efforts to improve microbial culturing techniques, about 70-80% of microbial diversity - recently called the "microbial dark matter" - remains uncultured. In early attempts to identify and sample these so far uncultured taxonomic lineages, methods that amplify and sequence ribosomal RNA genes were extensively used. Recent developments in cell separation techniques, DNA amplification, and high-throughput DNA sequencing platforms have now made the discovery of genes/genomes of uncultured microorganisms from different environments possible through the use of metagenomic techniques and single-cell genomics. When used synergistically, these metagenomic and single-cell techniques create a powerful tool to study microbial diversity. These genomics techniques have already been successfully exploited to identify sources for i) novel enzymes or natural products for biotechnology applications, ii) novel genes from extremophiles, and iii) whole genomes or operons from uncultured microbes. More can be done to utilize these tools more efficiently in biotechnology.}, }
@article {pmid26408452, year = {2015}, author = {Maccario, L and Sanguino, L and Vogel, TM and Larose, C}, title = {Snow and ice ecosystems: not so extreme.}, journal = {Research in microbiology}, volume = {166}, number = {10}, pages = {782-795}, doi = {10.1016/j.resmic.2015.09.002}, pmid = {26408452}, issn = {1769-7123}, mesh = {Adaptation, Physiological ; *Bacterial Physiological Phenomena ; Cold Temperature ; *Ecosystem ; Ice ; Microbial Consortia/*physiology ; Microbial Interactions ; Snow/*microbiology ; Ultraviolet Rays ; }, abstract = {Snow and ice environments cover up to 21% of the Earth's surface. They have been regarded as extreme environments because of their low temperatures, high UV irradiation, low nutrients and low water availability, and thus, their microbial activity has not been considered relevant from a global microbial ecology viewpoint. In this review, we focus on why snow and ice habitats might not be extreme from a microbiological perspective. Microorganisms interact closely with the abiotic conditions imposed by snow and ice habitats by having diverse adaptations, that include genetic resistance mechanisms, to different types of stresses in addition to inhabiting various niches where these potential stresses might be reduced. The microbial communities inhabiting snow and ice are not only abundant and taxonomically diverse, but complex in terms of their interactions. Altogether, snow and ice seem to be true ecosystems with a role in global biogeochemical cycles that has likely been underestimated. Future work should expand past resistance studies to understanding the function of these ecosystems.}, }
@article {pmid26408190, year = {2016}, author = {Simachew, A and Lanzén, A and Gessesse, A and Øvreås, L}, title = {Prokaryotic Community Diversity Along an Increasing Salt Gradient in a Soda Ash Concentration Pond.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {326-338}, pmid = {26408190}, issn = {1432-184X}, mesh = {Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; Geologic Sediments/*microbiology ; Phylogeny ; Ponds/analysis/*microbiology ; Sodium Chloride/analysis/metabolism ; }, abstract = {The effect of salinity on prokaryotic community diversity in Abijata-Shalla Soda Ash Concentration Pond system was investigated by using high-throughput 16S rRNA gene 454 pyrosequencing. Surface water and brine samples from five sites spanning a salinity range of 3.4 % (Lake Abijata) to 32 % (SP230F, crystallizer pond) were analyzed. Overall, 33 prokaryotic phyla were detected, and the dominant prokaryotic phyla accounted for more than 95 % of the reads consisting of Planctomycetes, Bacteroidetes, candidate division TM7, Deinococcus-Thermus, Firmicutes, Actinobacteria, Proteobacteria, and Euryarchaeota. Diversity indices indicated that operational taxonomic unit (OTU) richness decreases drastically with increasing salinity in the pond system. A total of 471 OTUs were found at 3.4 % salinity whereas 49 OTUs were detected in pond SP211 (25 % salinity), and only 19 OTUs in the crystallization pond at 32 % salinity (SP230F). Along the salinity gradient, archaeal community gradually replaced bacterial community. Thus, archaeal community accounted for 0.4 % in Lake Abijata while 99.0 % in pond SP230F. This study demonstrates that salinity appears to be the key environmental parameter in structuring the prokaryotic communities of haloalkaline environments. Further, it confirmed that the prokaryotic diversity in Lake Abijata is high and it harbors taxa with low or no phylogenetic similarities to existing prokaryotic taxa and thus represents novel microorganisms.}, }
@article {pmid26408189, year = {2016}, author = {Sánchez-Fernández, RE and Diaz, D and Duarte, G and Lappe-Oliveras, P and Sánchez, S and Macías-Rubalcava, ML}, title = {Antifungal Volatile Organic Compounds from the Endophyte Nodulisporium sp. Strain GS4d2II1a: a Qualitative Change in the Intraspecific and Interspecific Interactions with Pythium aphanidermatum.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {347-364}, pmid = {26408189}, issn = {1432-184X}, mesh = {Antifungal Agents/chemistry/metabolism/*pharmacology ; Endophytes/*chemistry/metabolism ; Plant Diseases/*microbiology ; Pythium/*drug effects/growth &amp; development/physiology ; Volatile Organic Compounds/chemistry/metabolism/*pharmacology ; Xylariales/*chemistry/growth &amp; development/metabolism ; }, abstract = {This study demonstrates volatile organic compounds (VOCs) production as one of the defense mechanisms of the antagonistic endophyte Nodulisporium sp. GS4d2II1a, and the volatile changes in two times of the fungal growth; and, as result of its intra and interspecific interactions with the plant pathogen Pythium aphanidermatum. The antifungal activity of the volatile and diffusible metabolites was evaluated by means of three types of antagonism bioassays and by organic extract agar dilution. VOCs were obtained by gas chromatography coupled to mass spectrometry from 3- and 5-day Nodulisporium sp. cultures, as well as from its interspecific in vitro antagonistic interaction with the oomycete P. aphanidermatum, and its intraspecific Nodulisporium sp.-Nodulisporium sp. interaction. The GS4d2II1a strain completely inhibited the growth of two fungi and seven oomycetes by replacing their mycelia in simple antagonism bioassays and by producing in vitro volatile and diffusible metabolites that acted synergistically in multiple antagonism bioassays. Additionally, VOCs inhibited the growth of three oomycetes and one fungus in antagonism bioassays using divided plates. A total of 70 VOCs were detected, mainly including mono and sesquiterpenes, especially eucalyptol and limonene. Multiple correspondence analysis revealed four different volatile profiles, showing that volatiles changed with the fungus age and its intra and interspecific interactions. The metabolites produced by Nodulisporium sp. GS4d2II1a could be useful for biological control of fungal and oomycetes plant pathogens of economically important crops.}, }
@article {pmid26406384, year = {2015}, author = {Wang, Q and Du, Z and Zhang, H and Zhao, L and Sun, J and Zheng, X and Ren, F}, title = {Modulation of gut microbiota by polyphenols from adlay (Coix lacryma-jobi L. var. ma-yuen Stapf.) in rats fed a high-cholesterol diet.}, journal = {International journal of food sciences and nutrition}, volume = {66}, number = {7}, pages = {783-789}, doi = {10.3109/09637486.2015.1088941}, pmid = {26406384}, issn = {1465-3478}, mesh = {Animals ; Bacteria/*drug effects/growth &amp; development ; Cholesterol, Dietary/*blood ; Coix/*chemistry ; Diet, High-Fat ; Gastrointestinal Microbiome/*drug effects ; *Hypercholesterolemia/blood/microbiology/prevention &amp; control ; Male ; Phytotherapy ; Plant Extracts/*pharmacology/therapeutic use ; Polyphenols/*pharmacology/therapeutic use ; Rats, Wistar ; }, abstract = {This study aimed to evaluate the beneficial effects of polyphenol extract of adlay (Coix lacryma-jobi L. var. ma-yuen Stapf.) (PEA) on gut microbiota in rats fed a high-cholesterol diet (HCD). Rats were fed HCD containing 1% cholesterol (w/w), with or without a daily intragastric supplement of 200 mg/kg body weight PEA. Results showed that PEA significantly ameliorated increases in serum cholesterol and low-density lipoprotein cholesterol values and significantly restored high-density lipoprotein cholesterol values. The HCD-induced imbalance of gut microflora was modulated by the consumption of PEA. Most bacterial strains influenced by PEA are related to host lipid metabolism. The abundances of one Erysipelotrichales strains and two Clostridia strains were lower in the PEA group than in the control. Phenolic compounds in PEA were identified by HPLC. The findings indicate that PEA may be a useful dietary supplement in the treatment of elevated cholesterol levels and the imbalanced gut microbial ecology.}, }
@article {pmid26405832, year = {2016}, author = {Callens, M and Macke, E and Muylaert, K and Bossier, P and Lievens, B and Waud, M and Decaestecker, E}, title = {Food availability affects the strength of mutualistic host-microbiota interactions in Daphnia magna.}, journal = {The ISME journal}, volume = {10}, number = {4}, pages = {911-920}, pmid = {26405832}, issn = {1751-7370}, mesh = {Animals ; Body Size ; Daphnia/*growth &amp; development/*microbiology ; *Diet ; Environment ; Gastrointestinal Tract/*microbiology ; Host-Pathogen Interactions ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Reproduction ; *Symbiosis ; }, abstract = {The symbiotic gut microbial community is generally known to have a strong impact on the fitness of its host. Nevertheless, it is less clear how the impact of symbiotic interactions on the hosts' fitness varies according to environmental circumstances such as changes in the diet. This study aims to get a better understanding of host-microbiota interactions under different levels of food availability. We conducted experiments with the invertebrate, experimental model organism Daphnia magna and compared growth, survival and reproduction of conventionalized symbiotic Daphnia with germ-free individuals given varying quantities of food. Our experiments revealed that the relative importance of the microbiota for the hosts' fitness varied according to dietary conditions. The presence of the microbiota had strong positive effects on Daphnia when food was sufficient or abundant, but had weaker effects under food limitation. Our results indicate that the microbiota can be a potentially important factor in determining host responses to changes in dietary conditions. Characterization of the host-associated microbiota further showed that Aeromonas sp. was the most prevalent taxon in the digestive tract of Daphnia.}, }
@article {pmid26403721, year = {2016}, author = {Mankiewicz-Boczek, J and Jaskulska, A and Pawełczyk, J and Gągała, I and Serwecińska, L and Dziadek, J}, title = {Cyanophages Infection of Microcystis Bloom in Lowland Dam Reservoir of Sulejów, Poland.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {315-325}, pmid = {26403721}, issn = {1432-184X}, mesh = {Bacteriophages/classification/genetics/*isolation &amp; purification/physiology ; Base Sequence ; Ecosystem ; Eutrophication ; Fresh Water/chemistry/*microbiology ; Microcystis/genetics/*growth &amp; development/*virology ; Molecular Sequence Data ; Poland ; Seasons ; Viral Proteins/chemistry/genetics ; Water Resources ; }, abstract = {An increased incidence of cyanobacterial blooms, which are largely composed of toxigenic cyanobacteria from the Microcystis genus, leads to a disruption of aquatic ecosystems worldwide. Therefore, a better understanding of the impact of environmental parameters on the development and collapse of blooms is important. The objectives of the present study were as follows: (1) to investigate the presence and identity of Microcystis-specific cyanophages capable of cyanobacterial cell lysis in a lowland dam reservoir in Central Europe; (2) to investigate Microcystis sensitivity to phage infections with regard to toxic genotypes; and (3) to identify key abiotic parameters influencing phage infections during the summer seasons between 2009 and 2013. Sequencing analysis of selected g91 gene amplification products confirmed that the identified cyanophages belonged to the family Myoviridae (95 % homology). Cyanophages and Microcystis hosts, including toxic genotypes, were positively correlated in 4 of the 5 years analyzed (r = 0.67-0.82). The average percentage of infected Microcystis cells varied between 0.1 and 32 %, and no particular sensitivity of the phages to toxigenic genotypes was recorded. The highest number of cyanophages (>10(4) gene copy number per microliter) was observed in the period preceded by the following: an increase of the water retention time, growth of the water temperature, optimum nutrient concentrations, and the predomination of Microcystis bloom.}, }
@article {pmid26403720, year = {2016}, author = {Li, D and Sharp, JO and Drewes, JE}, title = {Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {78-86}, pmid = {26403720}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Geologic Sediments/chemistry/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers/chemistry/*microbiology ; Wastewater/chemistry/*microbiology ; }, abstract = {To reveal the variation of microbial community functions during water filtration process in river sediments, which has been utilized widely in natural water treatment systems, this study investigates the influence of municipal wastewater discharge to streams on the phylotype and metabolic potential of the microbiome in upstream and particularly various depths of downstream river sediments. Cluster analyses based on both microbial phylogenetic and functional data collectively revealed that shallow upstream sediments grouped with those from deeper subsurface downstream regions. These sediment samples were distinct from those found in shallow downstream sediments. Functional genes associated with carbohydrate, xenobiotic, and certain amino acid metabolisms were overrepresented in upstream and deep downstream samples. In contrast, the more immediate contact with wastewater discharge in shallow downstream samples resulted in an increase in the relative abundance of genes associated with nitrogen, sulfur, purine and pyrimidine metabolisms, as well as restriction-modification systems. More diverse bacterial phyla were associated with upstream and deep downstream sediments, mainly including Actinobacteria, Planctomycetes, and Firmicutes. In contrast, in shallow downstream sediments, genera affiliated with Betaproteobacteria and Gammaproteobacteria were enriched with putative functions that included ammonia and sulfur oxidation, polyphosphate accumulation, and methylotrophic bacteria. Collectively, these results highlight the enhanced capabilities of microbial communities residing in deeper stream sediments for the transformation of water contaminants and thus provide a foundation for better design of natural water treatment systems to further improve the removal of contaminants.}, }
@article {pmid26393509, year = {2015}, author = {de Boer, W and Hundscheid, MP and Klein Gunnewiek, PJ and de Ridder-Duine, AS and Thion, C and van Veen, JA and van der Wal, A}, title = {Antifungal Rhizosphere Bacteria Can increase as Response to the Presence of Saprotrophic Fungi.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0137988}, pmid = {26393509}, issn = {1932-6203}, mesh = {Antibiosis/physiology ; Bacteria/classification/genetics/*growth &amp; development ; Carex Plant/microbiology ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; Fungi/classification/genetics/*physiology ; Microbiota/genetics/physiology ; Models, Biological ; Molecular Sequence Data ; Mucor/genetics/physiology ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; Trichoderma/genetics/physiology ; }, abstract = {Knowledge on the factors that determine the composition of bacterial communities in the vicinity of roots (rhizosphere) is essential to understand plant-soil interactions. Plant species identity, plant growth stage and soil properties have been indicated as major determinants of rhizosphere bacterial community composition. Here we show that the presence of saprotrophic fungi can be an additional factor steering rhizosphere bacterial community composition and functioning. We studied the impact of presence of two common fungal rhizosphere inhabitants (Mucor hiemalis and Trichoderma harzianum) on the composition of cultivable bacterial communities developing in the rhizosphere of Carex arenaria (sand sedge) in sand microcosms. Identification and phenotypic characterization of bacterial isolates revealed clear shifts in the rhizosphere bacterial community composition by the presence of two fungal strains (M. hiemalis BHB1 and T. harzianum PvdG2), whereas another M. hiemalis strain did not show this effect. Presence of both M. hiemalis BHB1 and T. harzianum PvdG2 resulted in a significant increase of chitinolytic and (in vitro) antifungal bacteria. The latter was most pronounced for M. hiemalis BHB1, an isolate from Carex roots, which stimulated the development of the bacterial genera Achromobacter and Stenotrophomonas. In vitro tests showed that these genera were strongly antagonistic against M. hiemalis but also against the plant-pathogenic fungus Rhizoctonia solani. The most likely explanation for fungal-induced shifts in the composition of rhizosphere bacteria is that bacteria are being selected which are successful in competing with fungi for root exudates. Based on the results we propose that measures increasing saprotrophic fungi in agricultural soils should be explored as an alternative approach to enhance natural biocontrol against soil-borne plant-pathogenic fungi, namely by stimulating indigenous antifungal rhizosphere bacteria.}, }
@article {pmid26391805, year = {2016}, author = {Aguirre-Garrido, JF and Ramírez-Saad, HC and Toro, N and Martínez-Abarca, F}, title = {Bacterial Diversity in the Soda Saline Crater Lake from Isabel Island, Mexico.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {68-77}, pmid = {26391805}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; Islands ; Lakes/analysis/*microbiology ; Mexico ; Molecular Sequence Data ; Phylogeny ; Sodium Chloride/analysis/metabolism ; }, abstract = {Isabel Lake is a moderate saline soda crater lake located in Isabel Island in the eastern tropical Pacific coast of Mexico. Lake is mainly formed by rainfall and is strongly affected by evaporation and high input of nutrients derived from excretions of a large bird community inhabiting the island. So far, only the island macrobiota has been studied. The knowledge of the prokaryotic biota inhabiting the upper layers of this meromictic lake can give clues for the maintenance of this ecosystem. We assessed the diversity and composition of prokaryotic community in sediments and water of the lake by DGGE profiling, 16S rRNA gene amplicon pyrosequencing, and cultivation techniques. The bacterial community is largely dominated by halophilic and halotolerant microorganisms. Alpha diversity estimations reveal higher value in sediments than in water (P > 0.005). The lake water is dominated by γ-Proteobacteria belonging to four main families where Halomonadaceae presents the highest abundance. Aerobic, phototrophic, and halotolerant prokaryotes such as Cyanobacteria GPIIa, Halomonas, Alcanivorax, Idiomarina, and Cyclobacterium genera are commonly found. However, in sediment samples, Formosa, Muricauda, and Salegentibacter genera corresponding to Flavobacteriaceae family accounted for 15-20 % of the diversity. Heterotrophs like those involved in sulfur cycle, Desulfotignum, Desulfuromonas, Desulfofustis, and Desulfopila, appear to play an important role in sediments. Finally, a collection of aerobic halophilic bacterial isolates was created from these samples; members of the genus Halomonas were predominantly isolated from lake water. This study contributes to state the bacterial diversity present in this particular soda saline crater lake.}, }
@article {pmid26391804, year = {2016}, author = {Saleem, M and Law, AD and Moe, LA}, title = {Nicotiana Roots Recruit Rare Rhizosphere Taxa as Major Root-Inhabiting Microbes.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {469-472}, pmid = {26391804}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Phylogeny ; Plant Roots/*microbiology ; *Rhizosphere ; *Soil Microbiology ; Nicotiana/*microbiology ; }, abstract = {Root-associated microbes have a profound impact on plant health, yet little is known about the distribution of root-associated microbes among different root morphologies or between rhizosphere and root environments. We explore these issues here with two commercial varieties of burley tobacco (Nicotiana tabacum) using 16S rRNA gene amplicon sequencing from rhizosphere soil, as well as from primary, secondary, and fine roots. While rhizosphere soils exhibited a fairly rich and even distribution, root samples were dominated by Proteobacteria. A comparison of abundant operational taxonomic units (OTUs) between rhizosphere and root samples indicated that Nicotiana roots select for rare taxa (predominantly Proteobacteria, Verrucomicrobia, Actinobacteria, Bacteroidetes, and Acidobacteria) from their corresponding rhizosphere environments. The majority of root-inhabiting OTUs (~80 %) exhibited habitat generalism across the different root morphological habitats, although habitat specialists were noted. These results suggest a specific process whereby roots select rare taxa from a larger community.}, }
@article {pmid26388839, year = {2015}, author = {Ronca, S and Ramond, JB and Jones, BE and Seely, M and Cowan, DA}, title = {Namib Desert dune/interdune transects exhibit habitat-specific edaphic bacterial communities.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {845}, pmid = {26388839}, issn = {1664-302X}, abstract = {The sand dunes and inter-dune zones of the hyper-arid central Namib Desert represent heterogeneous soil habitats. As little is known about their indigenous edaphic bacterial communities, we aimed to evaluate their diversity and factors of assembly and hypothesized that soil physicochemistry gradients would strongly shape dune/interdune communities. We sampled a total of 125 samples from 5 parallel dune/interdune transects and characterized 21 physico-chemical edaphic parameters coupled with 16S rRNA gene bacterial community fingerprinting using T-RFLP and 454 pyrosequencing. Multivariate analyses of T-RFLP data showed significantly different bacterial communities, related to physico-chemical gradients, in four distinct dune habitats: the dune top, slope, base and interdune zones. Pyrosequencing of 16S rRNA gene amplicon sets showed that each dune zone presented a unique phylogenetic profile, suggesting a high degree of environmental selection. The combined results strongly infer that habitat filtering is an important factor shaping Namib Desert dune bacterial communities, with habitat stability, soil texture and mineral and nutrient contents being the main environmental drivers of bacterial community structures.}, }
@article {pmid26386416, year = {2015}, author = {Toumi, J and Miladi, B and Farhat, A and Nouira, S and Hamdi, M and Gtari, M and Bouallagui, H}, title = {Microbial ecology overview during anaerobic codigestion of dairy wastewater and cattle manure and use in agriculture of obtained bio-fertilisers.}, journal = {Bioresource technology}, volume = {198}, number = {}, pages = {141-149}, doi = {10.1016/j.biortech.2015.09.004}, pmid = {26386416}, issn = {1873-2976}, mesh = {*Agriculture ; Anaerobiosis ; Animals ; Bacteria, Anaerobic/genetics ; Biofuels/analysis ; Bioreactors/microbiology ; Cattle ; *Dairying ; Denaturing Gradient Gel Electrophoresis ; Digestion/*physiology ; *Fertilizers ; Hydrogen/analysis ; Manure/*analysis ; Methanobacteriaceae ; Methanosarcina ; Wastewater/*analysis ; Zea mays ; }, abstract = {The anaerobic co-digestion of dairy wastewater (DW) and cattle manure (CM) was examined and associated with microbial community's structures using Denaturing Gradient Gel Electrophoresis (DGGE). The highest volatile solids (VS) reduction yield of 88.6% and biogas production of 0.87 L/g VS removed were obtained for the C/N ratio of 24.7 at hydraulic retention time (HRT) of 20 days. The bacterial DGGE profile showed significant abundance of Uncultured Bacteroidetes, Firmicutes and Synergistetes bacterium. The Syntrophomonas strains were discovered in dependent association to H2-using bacteria such as Methanospirillum sp., Methanosphaera sp. and Methanobacterium formicicum. These syntrophic associations are essential in anaerobic digesters allow them to keep low hydrogen partial pressure. However, high concentrations of VFA produced from dairy wastes acidification allow the growth of Methanosarcina species. The application of the stabilised anaerobic effluent on the agriculture soil showed significant beneficial effects on the forage corn and tomato plants growth and crops.}, }
@article {pmid26385555, year = {2016}, author = {Górz, A and Boroń, P}, title = {The Yeast Fungus Trichosporon lactis Found as an Epizoic Colonizer of Dung Beetle Exoskeletons.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {422-427}, pmid = {26385555}, issn = {1432-184X}, mesh = {Animal Shells/*microbiology ; Animals ; Coleoptera/*microbiology ; Phylogeny ; Trichosporon/classification/genetics/growth &amp; development/*isolation &amp; purification ; }, abstract = {The study on the biology and biodiversity of coprophagous Scarabaeoidea carried out in the Polish Carpathians revealed the occurrence of unusual epizoic excrescences on various dung beetles species of the genus Onthophagus. The excrescences occur on the elytra, prothorax, and head of the studied beetles. Detailed research on this phenomenon determined that the fungus grew in the form of multicellular thalli. The ITS-based identification of fungal material collected from beetles' exoskeletons resulted in a 100 % match with Trichosporon lactis. Until now, only a yeast lifestyle/stage was known for this basidiomycete species. Therefore, in this paper, we describe a new substrate for growth of T. lactis and its unknown and intriguing relationship with dung beetles. The results obtained in this study open up numerous research possibilities on the new role of dung beetles in terrestrial ecosystems, as well as on using the physiological properties of T. lactis to restore soils.}, }
@article {pmid26381785, year = {2015}, author = {Duran, R and Cuny, P and Bonin, P and Cravo-Laureau, C}, title = {Microbial ecology of hydrocarbon-polluted coastal sediments.}, journal = {Environmental science and pollution research international}, volume = {22}, number = {20}, pages = {15195-15199}, pmid = {26381785}, issn = {1614-7499}, }
@article {pmid26381539, year = {2016}, author = {Senra, MV and Dias, RJ and Castelli, M and Silva-Neto, ID and Verni, F and Soares, CA and Petroni, G}, title = {A House for Two--Double Bacterial Infection in Euplotes woodruffi Sq1 (Ciliophora, Euplotia) Sampled in Southeastern Brazil.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {505-517}, pmid = {26381539}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Brazil ; Euplotes/classification/*microbiology/physiology ; Host Specificity ; Molecular Sequence Data ; Phylogeny ; Symbiosis ; }, abstract = {Several ciliated protists form symbiotic associations with a diversity of microorganisms, leading to drastic impact on their ecology and evolution. In this work, two Euplotes spp. sampled in Rio de Janeiro, Brazil, were identified based on morphological and molecular features as Euplotes woodruffi strain Sq1 and E. encysticus strain Sq2 and investigated for the presence of endosymbionts. While E. woodruffi Sq1 stably hosts two bacterial populations, namely Polynucleobacter necessarius (Betaproteobacteria) and a new member of the family "Candidatus Midichloriaceae" (Alphaproteobacteria, Rickettsiales), here described as "Candidatus Bandiella woodruffii," branching with a broad host range bacterial group found in association with cnidarians, sponges, euglenoids, and some arthropods; in E. encysticus Sq2 no symbiotic bacterium could be detected. The dispersion ability of this novel bacterium was tested by co-incubating E. woodruffi Sq1 with three different ciliate species. Among the tested strains "Ca. B. woodruffii" could only be detected in association with E. encysticus Sq2 with a prevalence of 20 % after 1 week and 40 % after 2 weeks, maintaining this level for up to 6 months. Nevertheless, this apparent in vitro association was abolished when E. woodruffi Sq1 donor was removed from the microcosm, suggesting that this bacterium has the capacity for at least a short-term survival outside its natural host and the aptitude to ephemerally interact with other organisms. Together, these findings strongly suggest the need for more detailed investigations to evaluate the host range for "Ca. B. woodruffii" and any possible pathogenic effect of this bacterium on other organisms including humans.}, }
@article {pmid26381538, year = {2016}, author = {Li, Q and Heist, EP and Moe, LA}, title = {Bacterial Community Structure and Dynamics During Corn-Based Bioethanol Fermentation.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {409-421}, pmid = {26381538}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodiversity ; Bioreactors/microbiology ; Ethanol/*metabolism ; Fermentation ; Phylogeny ; Zea mays/metabolism/*microbiology ; }, abstract = {Corn-based fuel ethanol facilities mix enzymatically treated, gelatinized corn starch with water to generate a "mash" that is used as the substrate in large-scale (∼500,000 gallon) yeast-based fermentations. In contrast to other food and beverage fermentations (e.g., cheese, wine), bioethanol production is presumed to be optimal when bacteria are absent from the fermentation-thus maximizing conversion of glucose to ethanol-yet the facilities are not sterilized. Culture-based analysis has suggested that lactic acid bacteria occupy this niche and, under certain circumstances, can outcompete the dedicated fermentation yeast for nutrients. Here, we use 16S rRNA gene amplicon sequencing to probe bacterial community structure during bioethanol fermentation. Nineteen total batches from five corn-based fuel ethanol fermentation facilities were analyzed. From each batch, five samples were taken. This includes the contents of the yeast propagation tank at inoculation, three samples taken at intervals during the fermentation, and a sample taken at the end of fermentation. Bacterial community structure was compared with time, between facility, between fermentor, between batches from the same fermentor, and against environmental variables within each fermentation. Communities were dominated by members of the Firmicutes and Proteobacteria phyla, with lactic acid bacteria dominating the communities in two of the five facilities. In the other facilities, Proteobacteria (largely members of the Pseudomonas and Escherichia-Shigella genera) outcompete the lactic acid bacteria. In most cases, the yeast propagation tank inoculum imparted a rich bacterial community, but the batches vary regarding whether this inoculum was the primary driver of the fermentation community structure.}, }
@article {pmid26379659, year = {2015}, author = {Reis, MP and Ávila, MP and Keijzer, RM and Barbosa, FA and Chartone-Souza, E and Nascimento, AM and Laanbroek, HJ}, title = {The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {898}, pmid = {26379659}, issn = {1664-302X}, abstract = {Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms.}, }
@article {pmid26379473, year = {2015}, author = {Coci, M and Odermatt, N and Salcher, MM and Pernthaler, J and Corno, G}, title = {Ecology and Distribution of Thaumarchaea in the Deep Hypolimnion of Lake Maggiore.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2015}, number = {}, pages = {590434}, pmid = {26379473}, issn = {1472-3654}, mesh = {Ammonia/metabolism ; Archaea/*classification/*genetics/metabolism ; *Biodiversity ; DNA, Archaeal/chemistry/genetics ; Geologic Sediments/*microbiology ; In Situ Hybridization, Fluorescence ; Lakes/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Ammonia-oxidizing Archaea (AOA) play an important role in the oxidation of ammonia in terrestrial, marine, and geothermal habitats, as confirmed by a number of studies specifically focused on those environments. Much less is known about the ecological role of AOA in freshwaters. In order to reach a high resolution at the Thaumarchaea community level, the probe MGI-535 was specifically designed for this study and applied to fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) analysis. We then applied it to a fine analysis of diversity and relative abundance of AOA in the deepest layers of the oligotrophic Lake Maggiore, confirming previous published results of AOA presence, but showing differences in abundance and distribution within the water column without significant seasonal trends with respect to Bacteria. Furthermore, phylogenetic analysis of AOA clone libraries from deep lake water and from a lake tributary, River Maggia, suggested the riverine origin of AOA of the deep hypolimnion of the lake.}, }
@article {pmid26377687, year = {2015}, author = {Lin, HW and Rabaey, K and Keller, J and Yuan, Z and Pikaar, I}, title = {Scaling-Free Electrochemical Production of Caustic and Oxygen for Sulfide Control in Sewers.}, journal = {Environmental science &amp; technology}, volume = {49}, number = {19}, pages = {11395-11402}, doi = {10.1021/acs.est.5b02188}, pmid = {26377687}, issn = {1520-5851}, mesh = {Biofilms ; *Caustics ; Electrochemical Techniques/instrumentation/*methods ; Electrodes ; Equipment Design ; *Oxygen ; *Sulfides ; Wastewater/*chemistry/microbiology ; Water Purification/*methods ; }, abstract = {Caustic shock-loading and oxygen injection are commonly used by the water industry for biofilm and sulfide control in sewers. Caustic can be produced onsite from wastewater using a two-compartment electrochemical cell. This avoids the need for import and storage of caustic soda, which typically represents a cost and a hazard. An issue limiting the practical implementation of this approach is the occurrence of membrane scaling due to the almost universal presence of Ca(2+) and Mg(2+) in wastewater. It results in a rapid increase in the cell voltage, thereby increasing the energy consumption of the system. Here, we propose and experimentally demonstrate an innovative solution for this problem involving the inclusion of a middle compartment between the anode and cathode compartments. Caustic was efficiently produced from wastewater over a period of 12 weeks and had an average Coulombic efficiency (CE) of 84.1 ± 1.1% at practically relevant caustic strengths (∼3 wt %). Neither membrane scaling nor an increase in the cell voltage was observed throughout the experiments. In addition, dissolved oxygen was produced in the anode, resulting in continuously oxygenated wastewater leaving the three-compartment cell. This membrane-scaling control strategy represents a major step forward toward practical implementation of on-site simultaneous electrochemical caustic and oxygen generation for sulfide control in sewers and also has the potential to be applied to other (bio)electrochemical systems receiving wastewater as source for product recovery.}, }
@article {pmid26377599, year = {2015}, author = {Romero-Olivares, AL and Taylor, JW and Treseder, KK}, title = {Neurospora discreta as a model to assess adaptation of soil fungi to warming.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {198}, pmid = {26377599}, issn = {1471-2148}, mesh = {Acclimatization ; Biomass ; *Climate Change ; Models, Biological ; Neurospora/*physiology ; *Soil Microbiology ; Temperature ; }, abstract = {BACKGROUND: Short-term experiments have indicated that warmer temperatures can alter fungal biomass production and CO2 respiration, with potential consequences for soil C storage. However, we know little about the capacity of fungi to adapt to warming in ways that may alter C dynamics. Thus, we exposed Neurospora discreta to moderately warm (16 °C) and warm (28 °C) selective temperatures for 1500 mitotic generations, and then examined changes in mycelial growth rate, biomass, spore production, and CO2 respiration. We tested the hypothesis that strains will adapt to its selective temperature. Specifically, we expected that adapted strains would grow faster, and produce more spores per unit biomass (i.e., relative spore production). In contrast, they should generate less CO2 per unit biomass due to higher efficiency in carbon use metabolism (i.e., lower mass specific respiration, MSR).<br><br>RESULTS: Indeed, N. discreta adapted to warm temperatures, based on patterns of relative spore production. Adapted strains produced more spores per unit biomass than parental strains in the selective temperature. Contrary to our expectations, this increase in relative spore production was accompanied by an increase in MSR and a reduction in mycelial growth rate and biomass, compared to parental strains.<br><br>CONCLUSIONS: Adaptation of N. discreta to warm temperatures may have elicited a tradeoff between biomass production and relative spore production, possibly because relative spore production required higher MSR rates. Therefore, our results do not support the idea that adaptation to warm temperatures will lead to a more efficient carbon use metabolism. Our data might help improve climate change model simulations and provide more concise predictions of decomposition processes and carbon feedbacks to the atmosphere.}, }
@article {pmid26377203, year = {2016}, author = {Kharbush, JJ and Kejriwal, K and Aluwihare, LI}, title = {Distribution and Abundance of Hopanoid Producers in Low-Oxygen Environments of the Eastern Pacific Ocean.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {401-408}, pmid = {26377203}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Oxygen/*analysis/metabolism ; Pacific Ocean ; Phylogeny ; Seawater/analysis/*microbiology ; Triterpenes/*metabolism ; }, abstract = {Hopanoids are bacterial membrane lipid biomarker molecules that feature prominently in the molecular fossil record. In the modern marine water column, recent reports implicate bacteria inhabiting low-oxygen environments as important sources of hopanoids to marine sediments. However, the preliminary biogeography reported by recent studies and the environmental conditions governing such distributions can only be confirmed when the numerical abundance of these organisms is known with more certainty. In this study, we employ two different approaches to examine the quantitative significance of phylogenetically distinct hopanoid producers in low-oxygen environments. First, we develop a novel quantitative PCR (qPCR) assay for the squalene hopene cyclase (sqhC) gene, targeting a subset of hopanoid producers previously identified to be important in the eastern North Pacific Ocean. The results represent the first quantitative gene abundance data of any kind for hopanoid producers in the marine water column and show that these putative alphaproteobacterial hopanoid producers are rare, comprising at most 0.2 % of the total bacterial community in our samples. Second, a complementary analysis of existing low-oxygen metagenomic datasets further examined the generality of the qPCR observation. We find that the dominant sqhC sequences in these metagenomic datasets are associated with phyla such as Nitrospinae rather than Proteobacteria, consistent with the qPCR finding that alphaproteobacterial hopanoid producers are not very abundant in low-oxygen environments. In fact, positive correlations between sqhC gene abundance and environmental parameters in these samples identify nitrite availability as a potentially important factor in the ecology of hopanoid producers that dominate low-oxygen environments.}, }
@article {pmid26375668, year = {2015}, author = {Cerqueira, T and Pinho, D and Egas, C and Froufe, H and Altermark, B and Candeias, C and Santos, RS and Bettencourt, R}, title = {Microbial diversity in deep-sea sediments from the Menez Gwen hydrothermal vent system of the Mid-Atlantic Ridge.}, journal = {Marine genomics}, volume = {24 Pt 3}, number = {}, pages = {343-355}, doi = {10.1016/j.margen.2015.09.001}, pmid = {26375668}, issn = {1876-7478}, mesh = {Archaea/classification/*genetics ; Atlantic Ocean ; Bacteria/classification/*genetics ; DNA/classification/*genetics ; Eukaryota/classification/*genetics ; Geologic Sediments/*microbiology ; Hydrothermal Vents/*microbiology ; RNA/genetics ; RNA, Ribosomal/genetics ; }, abstract = {Deep-sea hydrothermal sediments are known to support remarkably diverse microbial consortia. Cultureindependent sequence-based technologies have extensively been used to disclose the associated microbial diversity as most of the microorganisms inhabiting these ecosystems remain uncultured. Here we provide the first description of the microbial community diversity found on sediments from Menez Gwen vent system. We compared hydrothermally influenced sediments, retrieved from an active vent chimney at 812 m depth, with non-hydrothermally influenced sediments, from a 1400 m depth bathyal plain. Considering the enriched methane and sulfur composition of Menez Gwen vent fluids, and the sediment physicochemical properties in each sampled area, we hypothesized that the site-associated microbes would be different. To address this question, taxonomic profiles of bacterial, archaeal and micro-eukaryotic representatives were studied by rRNA gene tag pyrosequencing. Communities were shown to be significantly different and segregated by sediment geographical area. Specific mesophilic, thermophilic and hyperthermophilic archaeal (e.g., Archaeoglobus, ANME-1) and bacterial (e.g., Caldithrix, Thermodesulfobacteria) taxa were highly abundant near the vent chimney. In contrast, bathyal-associated members affiliated to more ubiquitous phylogroups from deep-ocean sediments (e.g., Thaumarchaeota MGI, Gamma- and Alphaproteobacteria). This study provides a broader picture of the biological diversity and microbial biogeography, and represents a preliminary approach to the microbial ecology associated with the deep-sea sediments from the Menez Gwen hydrothermal vent field.}, }
@article {pmid26373644, year = {2016}, author = {Ergin, &#xc7; and Gök, Y and Bayğu, Y and Gümral, R and Özhak-Baysan, B and Döğen, A and Öğünç, D and Ilkit, M and Seyedmousavi, S}, title = {ATR-FTIR Spectroscopy Highlights the Problem of Distinguishing Between Exophiala dermatitidis and E. phaeomuriformis Using MALDI-TOF MS.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {339-346}, pmid = {26373644}, issn = {1432-184X}, mesh = {Exophiala/*chemistry/classification/isolation &amp; purification ; Humans ; Mycological Typing Techniques/*methods ; Phaeohyphomycosis/*microbiology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Spectroscopy, Fourier Transform Infrared/*methods ; Tandem Mass Spectrometry/*methods ; }, abstract = {The present study compared two chemical-based methods, namely, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, to understand the misidentification of Exophiala dermatitidis and Exophiala phaeomuriformis. The study utilized 44 E. dermatitidis and 26 E. phaeomuriformis strains, which were partially treated with strong acids and bases for further evaluation. MALDI-TOF MS and ATR-FTIR spectroscopy data of the two Exophiala species were compared. Data groupings were observed for the chromic acid- and nitric acid-treated species when the black yeast sources were categorized as creosoted-oak sleepers, concrete sleepers, or dishwasher isolates. The MALDI-TOF MS data for the metalloenzyme-containing regions were consistent with the ATR-FTIR spectroscopy data. These results indicated that environmental isolates might contain metals not found in human isolates and might interfere with chemical-based identification methods. Therefore, MALDI-TOF MS reference libraries should be created for clinical strains and should exclude petroleum-associated environmental isolates.}, }
@article {pmid26373611, year = {2015}, author = {Boers, SA and Hays, JP and Jansen, R}, title = {Micelle PCR reduces chimera formation in 16S rRNA profiling of complex microbial DNA mixtures.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {14181}, pmid = {26373611}, issn = {2045-2322}, mesh = {High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/*genetics ; Reproducibility of Results ; }, abstract = {16S rRNA gene profiling has revolutionized the field of microbial ecology. Many researchers in various fields have embraced this technology to investigate bacterial compositions of samples derived from many different ecosystems. However, it is important to acknowledge the current limitations and drawbacks of 16S rRNA gene profiling. Although sample handling, DNA extraction methods and the choice of universal 16S rRNA gene PCR primers are well known factors that could seriously affect the final results of microbiota profiling studies, inevitable amplification artifacts, such as chimera formation and PCR competition, are seldom appreciated. Here we report on a novel micelle based amplification strategy, which overcomes these limitations via the clonal amplification of targeted DNA molecules. Our results show that micelle PCR drastically reduces chimera formation by a factor of 38 (1.5% vs. 56.9%) compared with traditional PCR, resulting in improved microbial diversity estimates. In addition, compartmentalization during micelle PCR prevents PCR competition due to unequal amplification rates of different 16S template molecules, generating robust and accurate 16S microbiota profiles required for comparative studies (e.g. longitudinal surveys).}, }
@article {pmid26373417, year = {2015}, author = {Sultanpuram, VR and Mothe, T and Chintalapati, S and Chintalapati, VR}, title = {Cellulosimicrobium aquatile sp. nov., isolated from Panagal reservoir, Nalgonda, India.}, journal = {Antonie van Leeuwenhoek}, volume = {108}, number = {6}, pages = {1357-1364}, doi = {10.1007/s10482-015-0588-y}, pmid = {26373417}, issn = {1572-9699}, mesh = {Actinobacteria/*classification/genetics/*isolation &amp; purification/physiology ; Aerobiosis ; Bacterial Typing Techniques ; Base Composition ; Cell Wall/chemistry ; Cluster Analysis ; Cytosol/chemistry ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fatty Acids/analysis ; India ; Lysine/analysis ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Peptidoglycan/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vitamin K 2/analysis ; }, abstract = {A Gram-stain positive, non-spore forming, non-motile, yellow-pigmented, rod shaped and coccoid aerobic strain designated 3bp(T) was isolated from Panagal reservoir, at Nalgonda, Telangana, India. Based on 16S rRNA gene sequence analysis it was identified that strain 3bp(T) belongs to the class Actinobacteria and is closely related to Cellulosimicrobium funkei VTT E-072700(T), Cellulosimicrobium cellulans LMG16221(T) and Cellulosimicrobium terreum KCTC 19206(T). The DNA-DNA relatedness data demonstrated that strain 3bp(T) is distinguishable from the above three species of the genus. Further, the chemotaxonomic properties of strain 3bp(T) were consistent with those of the genus Cellulosimicrobium: MK-9(H4) was the predominant menaquinone, anteiso-C15 : 0, iso-C15:0, anteiso-C17 : 0 and iso- C16:0 were the predominant cellular fatty acids and the cell-wall peptidoglycan contains L-lysine. The DNA G+C content of strain 3bp(T) was 73.8 mol%. The results of the polyphasic analysis allowed a clear differentiation of strain 3bp(T) from all other members of the genus Cellulosimicrobium. Strain 3bp(T) is thus considered to represent a novel member of the genus Cellulosimicrobium, for which the name Cellulosimicrobium aquatile sp. nov. is proposed. The type strain is 3bp(T) (=KCTC 39527(T) = MCC 2761(T) = LMG 28646(T)).}, }
@article {pmid26371074, year = {2015}, author = {Bier, RL and Bernhardt, ES and Boot, CM and Graham, EB and Hall, EK and Lennon, JT and Nemergut, DR and Osborne, BB and Ruiz-González, C and Schimel, JP and Waldrop, MP and Wallenstein, MD}, title = {Linking microbial community structure and microbial processes: an empirical and conceptual overview.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {10}, pages = {}, doi = {10.1093/femsec/fiv113}, pmid = {26371074}, issn = {1574-6941}, mesh = {Archaea/metabolism ; Bacteria/metabolism ; *Ecosystem ; Fungi/metabolism ; Microbial Consortia/*physiology ; }, abstract = {A major goal of microbial ecology is to identify links between microbial community structure and microbial processes. Although this objective seems straightforward, there are conceptual and methodological challenges to designing studies that explicitly evaluate this link. Here, we analyzed literature documenting structure and process responses to manipulations to determine the frequency of structure-process links and whether experimental approaches and techniques influence link detection. We examined nine journals (published 2009-13) and retained 148 experimental studies measuring microbial community structure and processes. Many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant and typically used Spearman or Pearson's correlation analysis (68%). No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure or both structure and process. Together, our findings suggest that few publications report statistically testing structure-process links. However, when links are tested for they often occur but share few commonalities in the processes or structures that were linked and the techniques used for measuring them.}, }
@article {pmid26370112, year = {2016}, author = {Jeanbille, M and Buée, M and Bach, C and Cébron, A and Frey-Klett, P and Turpault, MP and Uroz, S}, title = {Soil Parameters Drive the Structure, Diversity and Metabolic Potentials of the Bacterial Communities Across Temperate Beech Forest Soil Sequences.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {482-493}, pmid = {26370112}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/growth &amp; development/*metabolism ; *Biodiversity ; Carbon/analysis/metabolism ; Fagus/growth &amp; development/*microbiology ; Nitrogen/analysis/metabolism ; Soil/*chemistry ; *Soil Microbiology ; Trees/growth &amp; development/microbiology ; }, abstract = {Soil and climatic conditions as well as land cover and land management have been shown to strongly impact the structure and diversity of the soil bacterial communities. Here, we addressed under a same land cover the potential effect of the edaphic parameters on the soil bacterial communities, excluding potential confounding factors as climate. To do this, we characterized two natural soil sequences occurring in the Montiers experimental site. Spatially distant soil samples were collected below Fagus sylvatica tree stands to assess the effect of soil sequences on the edaphic parameters, as well as the structure and diversity of the bacterial communities. Soil analyses revealed that the two soil sequences were characterized by higher pH and calcium and magnesium contents in the lower plots. Metabolic assays based on Biolog Ecoplates highlighted higher intensity and richness in usable carbon substrates in the lower plots than in the middle and upper plots, although no significant differences occurred in the abundance of bacterial and fungal communities along the soil sequences as assessed using quantitative PCR. Pyrosequencing analysis of 16S ribosomal RNA (rRNA) gene amplicons revealed that Proteobacteria, Acidobacteria and Bacteroidetes were the most abundantly represented phyla. Acidobacteria, Proteobacteria and Chlamydiae were significantly enriched in the most acidic and nutrient-poor soils compared to the Bacteroidetes, which were significantly enriched in the soils presenting the higher pH and nutrient contents. Interestingly, aluminium, nitrogen, calcium, nutrient availability and pH appeared to be the best predictors of the bacterial community structures along the soil sequences.}, }
@article {pmid26370111, year = {2016}, author = {Huang, YL and Devan, MM and U'Ren, JM and Furr, SH and Arnold, AE}, title = {Pervasive Effects of Wildfire on Foliar Endophyte Communities in Montane Forest Trees.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {452-468}, pmid = {26370111}, issn = {1432-184X}, support = {R01 CA090265/CA/NCI NIH HHS/United States ; R01-CA90265/CA/NCI NIH HHS/United States ; }, mesh = {Biodiversity ; Endophytes/classification/genetics/*isolation &amp; purification ; Fires ; Forests ; Fungi/classification/genetics/*isolation &amp; purification ; Plant Leaves/chemistry/*microbiology ; Trees/chemistry/classification/*microbiology ; }, abstract = {Plants in all terrestrial ecosystems form symbioses with endophytic fungi that inhabit their healthy tissues. How these foliar endophytes respond to wildfires has not been studied previously, but is important given the increasing frequency and intensity of severe wildfires in many ecosystems, and because endophytes can influence plant growth and responses to stress. The goal of this study was to examine effects of severe wildfires on endophyte communities in forest trees, with a focus on traditionally fire-dominated, montane ecosystems in the southwestern USA. We evaluated the abundance, diversity, and composition of endophytes in foliage of Juniperus deppeana (Cupressaceae) and Quercus spp. (Fagaceae) collected contemporaneously from areas affected by recent wildfire and paired areas not affected by recent fire. Study sites spanned four mountain ranges in central and southern Arizona. Our results revealed significant effects of fires on endophyte communities, including decreases in isolation frequency, increases in diversity, and shifts in community structure and taxonomic composition among endophytes of trees affected by recent fires. Responses to fire were similar in endophytes of each host in these fire-dominated ecosystems and reflect regional fire-return intervals, with endophytes after fire representing subsets of the regional mycoflora. Together, these findings contribute to an emerging perspective on the responses of diverse communities to severe fire, and highlight the importance of considering fire history when estimating endophyte diversity and community structure for focal biomes.}, }
@article {pmid26370110, year = {2016}, author = {Shilts, MH and Rosas-Salazar, C and Tovchigrechko, A and Larkin, EK and Torralba, M and Akopov, A and Halpin, R and Peebles, RS and Moore, ML and Anderson, LJ and Nelson, KE and Hartert, TV and Das, SR}, title = {Minimally Invasive Sampling Method Identifies Differences in Taxonomic Richness of Nasal Microbiomes in Young Infants Associated with Mode of Delivery.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {233-242}, pmid = {26370110}, issn = {1432-184X}, support = {UL1 TR000445/TR/NCATS NIH HHS/United States ; R01 AI095277/AI/NIAID NIH HHS/United States ; K24 AI077930/AI/NIAID NIH HHS/United States ; U19AI095227/AI/NIAID NIH HHS/United States ; U19 AI070489/AI/NIAID NIH HHS/United States ; AI U19-AI-095277/AI/NIAID NIH HHS/United States ; U19 AI110819/AI/NIAID NIH HHS/United States ; U19-AI-110819/AI/NIAID NIH HHS/United States ; U19 AI095227/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Bacteriological Techniques/instrumentation/*methods ; Cohort Studies ; *Delivery, Obstetric ; Feeding Methods ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; *Microbiota ; Nose/*microbiology ; Phylogeny ; Pregnancy ; Respiratory System/microbiology ; Respiratory Tract Infections/microbiology ; }, abstract = {To date, there is a limited understanding of the role of the airway microbiome in the early life development of respiratory diseases such as asthma, partly due to a lack of simple and minimally invasive sample collection methods. In order to characterize the baseline microbiome of the upper respiratory tract (URT) in infants, a comparatively non-invasive method for sampling the URT microbiome suitable for use in infants was developed. Microbiome samples were collected by placing filter paper in the nostrils of 33 healthy, term infants enrolled as part of the Infant Susceptibility to Pulmonary Infections and Asthma Following RSV Exposure (INSPIRE) study. After bacterial genomic DNA was extracted from the filters, amplicons were generated with universal primers targeting the V1-V3 region of the 16S rRNA gene. This method was capable of capturing a wide variety of taxa expected to inhabit the nasal cavity. Analyses stratifying subjects by demographic and environmental factors previously observed or predicted to influence microbial communities were performed. Microbial community richness was found to be higher in infants who had been delivered via Cesarean section and in those who had been formula-fed; an association was observed between diet and delivery, which confounds this analysis. We have established a baseline URT microbiome using a non-invasive filter paper nasal sampling for this population, and future studies will be performed in this large observational cohort of infants to investigate the relationship between viral infections, the URT microbiota, and the development of childhood wheezing illnesses.}, }
@article {pmid26362980, year = {2015}, author = {Kim, SJ and Lee, JC and Han, SI and Whang, KS}, title = {Halobacillus sediminis sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {65}, number = {12}, pages = {4434-4440}, doi = {10.1099/ijsem.0.000595}, pmid = {26362980}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Halobacillus/*classification/genetics/isolation &amp; purification ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Peptidoglycan/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Salinity ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry ; *Water Microbiology ; }, abstract = {A Gram-staining-positive, moderately halophilic bacterium, designated strain NGS-2T, was isolated from sediment of a solar saltern pond located in Shinan, Korea. Strain NGS-2T was a strictly aerobic, non-motile rod that grew at pH 5.0-10.0 (optimum, pH 8.0), at 10-30 °C (optimum, 28 °C) and in the presence of 1-20 % (w/v) NaCl (optimum, 10 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain NGS-2T belonged to the genus Halobacillus, with sequence similarity of 98.4-95.8 % to existing type strains, showing the highest sequence similarity to Halobacillus dabanensis D-8T (98.4 %), H. litoralis SL-4T (98.4 %), H. trueperi SL-5T (98.2 %), H. faecis IGA7-4T (98.2 %), H. profundi IS-Hb4T (98.1 %) and H. mangrovi MS10T (98.0 %). The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidyl-N-methylethanolamine and an unknown glycolipid. The cell-wall peptidoglycan was based on l-Orn-d-Asp, the predominant isoprenoid quinone was menaquinone 7 (MK-7) and the major fatty acids were anteiso-C15: 0 and anteiso-C17: 0. The DNA G+C content of the novel isolate was 45.0 mol%. Levels of DNA-DNA relatedness between strain NGS-2T and the type strains of 12 other species of the genus ranged from 32 to 3 %. On the basis of the polyphasic analysis conducted in this study, strain NGS-2T represents a novel species of the genus Halobacillus, for which the name Halobacillus sediminis sp. nov. is proposed. The type strain is NGS-2T (= KACC 18263T = NBRC 110639T).}, }
@article {pmid26360455, year = {2016}, author = {Venkidusamy, K and Megharaj, M and Marzorati, M and Lockington, R and Naidu, R}, title = {Enhanced removal of petroleum hydrocarbons using a bioelectrochemical remediation system with pre-cultured anodes.}, journal = {The Science of the total environment}, volume = {539}, number = {}, pages = {61-69}, doi = {10.1016/j.scitotenv.2015.08.098}, pmid = {26360455}, issn = {1879-1026}, mesh = {Bacteria ; Biodegradation, Environmental ; Bioelectric Energy Sources/microbiology ; Biofilms ; Electrodes ; Hydrogen-Ion Concentration ; Oxidation-Reduction ; Petroleum/analysis/*metabolism ; Petroleum Pollution ; Soil Pollutants/analysis/*metabolism ; }, abstract = {Bioelectrochemical remediation (BER) systems such as microbial fuel cells (MFCs) have recently emerged as a green technology for the effective remediation of petroleum hydrocarbon contaminants (PH) coupled with simultaneous energy recovery. Recent research has shown that biofilms previously enriched for substrate degrading bacteria resulted in excellent performance in terms of substrate removal and electricity generation but the effects on hydrocarbon contaminant degradation were not examined. Here we investigate the differences between enriched biofilm anodes and freshly inoculated new anodes in diesel fed single chamber mediatorless microbial fuel cells (DMFC) using various techniques for the enhancement of PH contaminant remediation with concomitant electricity generation. An anodophilic microbial consortium previously selected for over a year through continuous culturing with a diesel concentration of about 800mgl(-1) and which now showed complete removal of this concentration of diesel within 30days was compared to that of a freshly inoculated new anode MFC (showing 83.4% removal of diesel) with a simultaneous power generation of 90.81mW/m(2) and 15.04mW/m(2) respectively. The behaviour of pre-cultured anodes at a higher concentration of PH (8000mgl(-1)) was also investigated. Scanning electron microscopy observation revealed a thick biofilm covering the pre-cultured anodic electrode but not the anode from the freshly inoculated MFC. High resolution imaging showed the presence of thin 60nm diametre pilus-like projections emanating from the cells. Anodic microbial community profiling confirmed that the selection for diesel degrading exoelectrogenic bacteria had occurred. Identification of a biodegradative gene (alkB) provided strong evidence of the catabolic pathway used for diesel degradation in the DMFCs.}, }
@article {pmid26359912, year = {2016}, author = {Robador, A and Müller, AL and Sawicka, JE and Berry, D and Hubert, CR and Loy, A and Jørgensen, BB and Brüchert, V}, title = {Activity and community structures of sulfate-reducing microorganisms in polar, temperate and tropical marine sediments.}, journal = {The ISME journal}, volume = {10}, number = {4}, pages = {796-809}, pmid = {26359912}, issn = {1751-7370}, support = {P 25111/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Deltaproteobacteria/*classification/genetics/isolation &amp; purification/*metabolism ; Ecosystem ; Geologic Sediments/chemistry/*microbiology ; Oxidation-Reduction ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; Sulfates/*metabolism ; Temperature ; }, abstract = {Temperature has a fundamental impact on the metabolic rates of microorganisms and strongly influences microbial ecology and biogeochemical cycling in the environment. In this study, we examined the catabolic temperature response of natural communities of sulfate-reducing microorganisms (SRM) in polar, temperate and tropical marine sediments. In short-term sediment incubation experiments with (35)S-sulfate, we demonstrated how the cardinal temperatures for sulfate reduction correlate with mean annual sediment temperatures, indicating specific thermal adaptations of the dominant SRM in each of the investigated ecosystems. The community structure of putative SRM in the sediments, as revealed by pyrosequencing of bacterial 16S rRNA gene amplicons and phylogenetic assignment to known SRM taxa, consistently correlated with in situ temperatures, but not with sediment organic carbon concentrations or C:N ratios of organic matter. Additionally, several species-level SRM phylotypes of the class Deltaproteobacteria tended to co-occur at sites with similar mean annual temperatures, regardless of geographic distance. The observed temperature adaptations of SRM imply that environmental temperature is a major controlling variable for physiological selection and ecological and evolutionary differentiation of microbial communities.}, }
@article {pmid26358721, year = {2016}, author = {Trottet, A and Leboulanger, C and Vidussi, F and Pete, R and Bouvy, M and Fouilland, E}, title = {Heterotrophic Bacteria Show Weak Competition for Nitrogen in Mediterranean Coastal Waters (Thau Lagoon) in Autumn.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {304-314}, pmid = {26358721}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*metabolism ; Biomass ; Mediterranean Region ; Nitrogen/analysis/*metabolism ; Phytoplankton/classification/metabolism ; Seasons ; Seawater/analysis/*microbiology ; }, abstract = {The importance of heterotrophic bacteria relative to phytoplankton in the uptake of ammonium and nitrate was studied in Mediterranean coastal waters (Thau Lagoon) during autumn, when the Mediterranean Sea received the greatest allochthonous nutrient loads. Specific inhibitors and size-fractionation methods were used in combination with isotopic (15)N tracers. NO3 (-) and NH4 (+) uptake was dominated by phytoplankton (60 % on average) during the study period, which included a flood event. Despite lower biomass specific NH4 (+) and NO3 uptake rates, free-living heterotrophic bacteria contributed significantly (>30 %) to total microbial NH4 (+) and NO3 (-) uptake rates in low chlorophyll waters. Under these conditions, heterotrophic bacteria may be responsible for more than 50 % of primary production, using very little freshly produced phytoplankton exudates. In low chlorophyll coastal waters as reported during the present 3-month study, the heterotrophic bacteria seemed to depend to a greater extent on allochthonous N and C substrates than on autochthonous substrates derived from phytoplankton.}, }
@article {pmid26354829, year = {2015}, author = {Harrison, JP and Dobinson, L and Freeman, K and McKenzie, R and Wyllie, D and Nixon, SL and Cockell, CS}, title = {Aerobically respiring prokaryotic strains exhibit a broader temperature-pH-salinity space for cell division than anaerobically respiring and fermentative strains.}, journal = {Journal of the Royal Society, Interface}, volume = {12}, number = {110}, pages = {0658}, pmid = {26354829}, issn = {1742-5662}, mesh = {Anaerobiosis ; Bacteria/*metabolism ; Cell Division/*physiology ; Fermentation/*physiology ; Hydrogen-Ion Concentration ; *Models, Biological ; *Salinity ; }, abstract = {Biological processes on the Earth operate within a parameter space that is constrained by physical and chemical extremes. Aerobic respiration can result in adenosine triphosphate yields up to over an order of magnitude higher than those attained anaerobically and, under certain conditions, may enable microbial multiplication over a broader range of extremes than other modes of catabolism. We employed growth data published for 241 prokaryotic strains to compare temperature, pH and salinity values for cell division between aerobically and anaerobically metabolizing taxa. Isolates employing oxygen as the terminal electron acceptor exhibited a considerably more extensive three-dimensional phase space for cell division (90% of the total volume) than taxa using other inorganic substrates or organic compounds as the electron acceptor (15% and 28% of the total volume, respectively), with all groups differing in their growth characteristics. Understanding the mechanistic basis of these differences will require integration of research into microbial ecology, physiology and energetics, with a focus on global-scale processes. Critical knowledge gaps include the combined impacts of diverse stress parameters on Gibbs energy yields and rates of microbial activity, interactions between cellular energetics and adaptations to extremes, and relating laboratory-based data to in situ limits for cell division.}, }
@article {pmid26352912, year = {2015}, author = {Marxen, S and Stark, TD and Rütschle, A and Lücking, G and Frenzel, E and Scherer, S and Ehling-Schulz, M and Hofmann, T}, title = {Multiparametric Quantitation of the Bacillus cereus Toxins Cereulide and Isocereulides A-G in Foods.}, journal = {Journal of agricultural and food chemistry}, volume = {63}, number = {37}, pages = {8307-8313}, doi = {10.1021/acs.jafc.5b03705}, pmid = {26352912}, issn = {1520-5118}, mesh = {Bacillus cereus/*metabolism ; Bacterial Toxins/*analysis ; Chromatography, High Pressure Liquid ; Depsipeptides/*analysis/biosynthesis/toxicity ; Food Contamination/*analysis ; Food Microbiology ; Foodborne Diseases/microbiology ; Humans ; Indicator Dilution Techniques ; Isotopes ; Reproducibility of Results ; Sensitivity and Specificity ; Tandem Mass Spectrometry ; }, abstract = {Consumption of food products contaminated with cereulide (1), a toxin produced by Bacillus cereus, might cause intoxications with symptoms reported to range from indigestion pain and emesis to death. Recently, a series of structural variants, coined isocereulides A-G (2-8), were identified for the first time to be produced along with cereulide (1). The observation that isocereulide A (2) shows an ∼ 8-fold increased cytotoxicity when compared to 1 urges the development of analytical tools enabling an accurate quantitation of these toxins. Therefore, a rapid, sensitive, and robust stable isotope dilution assay (SIDA) was developed for the combined quantitation of 1-8 by means of UPLC-MS/MS. On average, trueness and precision of the method were 112.5 ± 1.8% RSD, repeatability and reproducibility were 2 and 4% for cereulide and isocereulides A-G, and the LOD and LOQ of 0.1 and 0.5 ng/g, respectively, demonstrated a high sensitivity for the developed SIDA method. Application of this method to food samples revealed elevated levels of 1-8 in two suspicious noodle samples, for example, ranging from 0.59 (7) to 189.08 ng/g (1) in sample 1 and from 5.77 (7) to 6198.17 ng/g (1) in sample 2, whereas the analysis of 25 randomly selected food samples, which have not been the subject to any complaints, did not contain detectable amounts of any of these toxins. As a consequence, this SIDA method could add an important contribution to the knowledge-based risk assessment of B. cereus toxins in foods.}, }
@article {pmid26348272, year = {2015}, author = {Llirós, M and García-Armisen, T and Darchambeau, F and Morana, C and Triadó-Margarit, X and Inceoğlu, &#xd6; and Borrego, CM and Bouillon, S and Servais, P and Borges, AV and Descy, JP and Canfield, DE and Crowe, SA}, title = {Pelagic photoferrotrophy and iron cycling in a modern ferruginous basin.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {13803}, pmid = {26348272}, issn = {2045-2322}, mesh = {Biodiversity ; Congo ; *Earth, Planet ; Environmental Microbiology ; *Ferric Compounds ; *Iron/chemistry ; Rwanda ; Water/*chemistry ; }, abstract = {Iron-rich (ferruginous) ocean chemistry prevailed throughout most of Earth's early history. Before the evolution and proliferation of oxygenic photosynthesis, biological production in the ferruginous oceans was likely driven by photoferrotrophic bacteria that oxidize ferrous iron {Fe(II)} to harness energy from sunlight, and fix inorganic carbon into biomass. Photoferrotrophs may thus have fuelled Earth's early biosphere providing energy to drive microbial growth and evolution over billions of years. Yet, photoferrotrophic activity has remained largely elusive on the modern Earth, leaving models for early biological production untested and imperative ecological context for the evolution of life missing. Here, we show that an active community of pelagic photoferrotrophs comprises up to 30% of the total microbial community in illuminated ferruginous waters of Kabuno Bay (KB), East Africa (DR Congo). These photoferrotrophs produce oxidized iron {Fe(III)} and biomass, and support a diverse pelagic microbial community including heterotrophic Fe(III)-reducers, sulfate reducers, fermenters and methanogens. At modest light levels, rates of photoferrotrophy in KB exceed those predicted for early Earth primary production, and are sufficient to generate Earth's largest sedimentary iron ore deposits. Fe cycling, however, is efficient, and complex microbial community interactions likely regulate Fe(III) and organic matter export from the photic zone.}, }
@article {pmid26344407, year = {2015}, author = {Boetius, A and Anesio, AM and Deming, JW and Mikucki, JA and Rapp, JZ}, title = {Microbial ecology of the cryosphere: sea ice and glacial habitats.}, journal = {Nature reviews. Microbiology}, volume = {13}, number = {11}, pages = {677-690}, pmid = {26344407}, issn = {1740-1534}, mesh = {*Ecosystem ; Genome, Bacterial ; Ice Cover/*microbiology ; *Water Microbiology ; }, abstract = {The Earth's cryosphere comprises those regions that are cold enough for water to turn into ice. Recent findings show that the icy realms of polar oceans, glaciers and ice sheets are inhabited by microorganisms of all three domains of life, and that temperatures below 0 °C are an integral force in the diversification of microbial life. Cold-adapted microorganisms maintain key ecological functions in icy habitats: where sunlight penetrates the ice, photoautotrophy is the basis for complex food webs, whereas in dark subglacial habitats, chemoautotrophy reigns. This Review summarizes current knowledge of the microbial ecology of frozen waters, including the diversity of niches, the composition of microbial communities at these sites and their biogeochemical activities.}, }
@article {pmid26343383, year = {2015}, author = {Jiménez, DJ and Chaves-Moreno, D and van Elsas, JD}, title = {Unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {13845}, pmid = {26343383}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics/metabolism ; Biomass ; Computational Biology ; Energy Metabolism/genetics ; Gene Order ; Metagenome ; Metagenomics ; *Microbial Consortia/genetics ; Molecular Sequence Annotation ; Open Reading Frames/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Triticum/*microbiology ; }, abstract = {Based on the premise that plant biomass can be efficiently degraded by mixed microbial cultures and/or enzymes, we here applied a targeted metagenomics-based approach to explore the metabolic potential of two forest soil-derived lignocellulolytic microbial consortia, denoted RWS and TWS (bred on wheat straw). Using the metagenomes of three selected batches of two experimental systems, about 1.2 Gb of sequence was generated. Comparative analyses revealed an overrepresentation of predicted carbohydrate transporters (ABC, TonB and phosphotransferases), two-component sensing systems and β-glucosidases/galactosidases in the two consortia as compared to the forest soil inoculum. Additionally, "profiling" of carbohydrate-active enzymes showed significant enrichments of several genes encoding glycosyl hydrolases of families GH2, GH43, GH92 and GH95. Sequence analyses revealed these to be most strongly affiliated to genes present on the genomes of Sphingobacterium, Bacteroides, Flavobacterium and Pedobacter spp. Assembly of the RWS and TWS metagenomes generated 16,536 and 15,902 contigs of ≥10 Kb, respectively. Thirteen contigs, containing 39 glycosyl hydrolase genes, constitute novel (hemi)cellulose utilization loci with affiliation to sequences primarily found in the Bacteroidetes. Overall, this study provides deep insight in the plant polysaccharide degrading capabilities of microbial consortia bred from forest soil, highlighting their biotechnological potential.}, }
@article {pmid26341839, year = {2015}, author = {Cavera, VL and Arthur, TD and Kashtanov, D and Chikindas, ML}, title = {Bacteriocins and their position in the next wave of conventional antibiotics.}, journal = {International journal of antimicrobial agents}, volume = {46}, number = {5}, pages = {494-501}, doi = {10.1016/j.ijantimicag.2015.07.011}, pmid = {26341839}, issn = {1872-7913}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacterial Infections/drug therapy ; Bacteriocins/*pharmacology ; Drug Discovery/trends ; Humans ; }, abstract = {Micro-organisms are capable of producing a range of defence mechanisms, including antibiotics, bacteriocins, lytic agents, protein exotoxins, etc. Such mechanisms have been identified in nearly 99% of studied bacteria. The multiplicity and diversity of bacteriocins and the resultant effects of their interactions with targeted bacteria on microbial ecology has been thoroughly studied and remains an area of investigation attracting many researchers. However, the incorporation of bacteriocins into drug delivery systems used in conjunction with, or as potential alternatives to, conventional antibiotics is only a recent, although rapidly expanding, field. The extensive array of bacteriocins positions them as one of the most promising options in the next wave of antibiotics. The goal of this review was to explore bacteriocins as novel antimicrobials, alone and in combination with established antibiotics, and thus position them as a potential tool for addressing the current antibiotic crisis.}, }
@article {pmid26339932, year = {2016}, author = {Pous, N and Carmona-Martínez, AA and Vilajeliu-Pons, A and Fiset, E and Bañeras, L and Trably, E and Balaguer, MD and Colprim, J and Bernet, N and Puig, S}, title = {Bidirectional microbial electron transfer: Switching an acetate oxidizing biofilm to nitrate reducing conditions.}, journal = {Biosensors &amp; bioelectronics}, volume = {75}, number = {}, pages = {352-358}, doi = {10.1016/j.bios.2015.08.035}, pmid = {26339932}, issn = {1873-4235}, mesh = {Acetates/chemistry ; *Biofilms ; Biosensing Techniques/*methods ; Cell Respiration ; Electrodes ; Electrons ; Geobacter/*chemistry ; Nitrates/chemistry ; Oxidation-Reduction ; }, abstract = {Up to date a few electroactive bacteria embedded in biofilms are described to catalyze both anodic and cathodic reactions in bioelectrochemical systems (i.e. bidirectional electron transfer). How these bacteria transfer electrons to or from the electrode is still uncertain. In this study the extracellular electron transfer mechanism of bacteria within an electroactive biofilm was investigated by using cyclic voltammetry (CV) and differential pulse voltammetry (DPV). First, a mature anodic electroactive biofilm was developed from an activated sludge sample (inoculum), acetate as electron donor and a poised electrode (+397mV vs. SHE). Later, this biofilm was "switched" to biocathodic conditions by feeding it with a medium containing nitrates and poising the electrode at -303mV vs. SHE. The electrochemical characterization indicated that both, acetate oxidation and nitrate reduction took place at a similar formal potential of -175±05 and -175±34mV vs. SHE, respectively. The biofilm was predominantly composed by Geobacter sp. at both experimental conditions. Taken together, the results indicated that both processes could be catalyzed by using the same electron conduit, and most likely by the same bacterial consortium. Hence, this study suggests that electroactive bacteria within biofilms could use the same electron transfer conduit for catalyzing anodic and cathodic reactions.}, }
@article {pmid26339625, year = {2015}, author = {Fedorenko, V and Genilloud, O and Horbal, L and Marcone, GL and Marinelli, F and Paitan, Y and Ron, EZ}, title = {Antibacterial Discovery and Development: From Gene to Product and Back.}, journal = {BioMed research international}, volume = {2015}, number = {}, pages = {591349}, pmid = {26339625}, issn = {2314-6141}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Bacteria/classification/*drug effects/pathogenicity ; Biological Products/therapeutic use ; Drug Resistance, Bacterial/*genetics ; Fermentation ; Humans ; Infections/*drug therapy/genetics/microbiology ; }, abstract = {Concern over the reports of antibiotic-resistant bacterial infections in hospitals and in the community has been publicized in the media, accompanied by comments on the risk that we may soon run out of antibiotics as a way to control infectious disease. Infections caused by Enterococcus faecium, Staphylococcus aureus, Klebsiella species, Clostridium difficile, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, and other Enterobacteriaceae species represent a major public health burden. Despite the pharmaceutical sector's lack of interest in the topic in the last decade, microbial natural products continue to represent one of the most interesting sources for discovering and developing novel antibacterials. Research in microbial natural product screening and development is currently benefiting from progress that has been made in other related fields (microbial ecology, analytical chemistry, genomics, molecular biology, and synthetic biology). In this paper, we review how novel and classical approaches can be integrated in the current processes for microbial product screening, fermentation, and strain improvement.}, }
@article {pmid26338019, year = {2015}, author = {Vishnuvardhan Reddy, S and Thirumala, M and Sasikala, C and Venkata Ramana, C}, title = {Salibacterium halotolerans gen. nov., sp. nov., a bacterium isolated from a salt pan, reclassification of Bacillus qingdaonensis as Salibacterium qingdaonense comb. nov. and Bacillus halochares as Salibacterium halochares comb. nov.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {65}, number = {11}, pages = {4270-4275}, doi = {10.1099/ijsem.0.000572}, pmid = {26338019}, issn = {1466-5034}, mesh = {Bacillaceae/*classification/genetics/isolation &amp; purification ; Bacillus/*classification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Diaminopimelic Acid/chemistry ; Fatty Acids/chemistry ; India ; Nucleic Acid Hybridization ; Peptidoglycan/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Sodium Chloride ; }, abstract = {Two novel Gram-stain-positive, rod-shaped, non-motile, non-endospore-forming bacterial strains, S7T and IB5, were isolated from Khavda, India. Based on 16S rRNA gene sequence analysis they were identified as belonging to the class Bacilli, order Bacillales, family Bacillaceae, and were most closely related to Bacillus qingdaonensis CGMCC 1.6134T (97.3 %, sequence similarity), Bacillus halochares LMG 24571T (96.9 %), Bacillus salarius KCTC 3912T (95.6 %) and Bacillus aidingensis DSM 18341T (95.3 %). However, these strains shared only 88.2 % 16S rRNA gene sequence similarity with Bacillus subtilis subsp. subtilis DSM 10T, indicating that strains S7T and IB5 might not be members of the genus Bacillus. The DNA-DNA relatedness of these strains with B. qingdaonensis CGMCC 1.6134T was 42.9 ± 0.8. The cell-wall peptidoglycan of strains S7T and IB5 contained meso-diaminopimelic acid, while the polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and three unknown lipids. The predominant isoprenoid quinone was MK-7. anteiso-C15 : 0 was the predominant fatty acid. The results of the phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strains S7T and IB5, suggesting that they represent a novel member of the family Bacillaceae, for which the name Salibacterium halotolerans gen. nov., sp. nov. is proposed. The type strain of Salibacterium halotolerans is S7T (= KCTC 33658T = CGMCC 1.15324T). Based on the results of the present study, it is also suggested that B. qingdaonensis and B. halochares should be transferred to this novel genus, as Salibacterium qingdaonense comb. nov. and Salibacterium halochares comb. nov., respectively.}, }
@article {pmid26337826, year = {2016}, author = {Gugliandolo, C and Michaud, L and Lo Giudice, A and Lentini, V and Rochera, C and Camacho, A and Maugeri, TL}, title = {Prokaryotic Community in Lacustrine Sediments of Byers Peninsula (Livingston Island, Maritime Antarctica).}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {387-400}, pmid = {26337826}, issn = {1432-184X}, mesh = {Antarctic Regions ; Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Geologic Sediments/chemistry/*microbiology ; Lakes/chemistry/*microbiology ; Phylogeny ; }, abstract = {Byers Peninsula (Livingston Island, Antarctica), the largest seasonally ice-free region of the Maritime Antarctica, holds a large number of lakes, ponds, and streams. The prokaryotic structure and bacterial diversity in sediment samples collected during the 2008-2009 austral summer from five inland lakes, two coastal lakes, and an estuarine site were analyzed by Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) and 16S rRNA 454 tag pyrosequencing techniques, respectively. Differently from inland lakes, which range around the oligotrophic status, coastal lakes are eutrophic environments, enriched by nutrient inputs from marine animals. Although the prokaryotic abundances (estimated as DAPI stained cells) in sediment samples were quite similar among inland and coastal lakes, Bacteria always far dominated over Archaea. Despite the phylogenetic analysis indicated that most of sequences were affiliated to a few taxonomic groups, mainly referred to Proteobacteria, Bacteroidetes, and Actinobacteria, their relative abundances greatly differed from each site. Differences in bacterial composition showed that lacustrine sediments were more phyla rich than the estuarine sediment. Proteobacterial classes in lacustrine samples were dominated by Betaproteobacteria (followed by Alphaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria), while in the estuarine sample, they were mainly related to Gammaproteobacteria (followed by Deltaproteobacteria, Epsilonproteobacteria, Alphaproteobacteria, and Betaproteobacteria). Higher number of sequences of Alphaproteobacteria, Cyanobacteria, Verrucomicrobia, and Planctomycetes were observed in sediments of inland lakes compared to those of coastal lakes, whereas Chloroflexi were relatively more abundant in the sediments of coastal eutrophic lakes. As demonstrated by the great number of dominant bacterial genera, bacterial diversity was higher in the sediments of inland lakes than that in coastal lakes. Ilumatobacter (Actinobacteria), Gp16 (Acidobacteria), and Gemmatimonas (Gemmatimonadetes) were recovered as dominant genera in both inland and coastal lakes, but not in the estuarine sample, indicating that they may be useful markers of Antarctic lakes. The proximity to the sea, the different lake depths and the external or internal origin of the nutrient sources shape the bacterial communities composition in lacustrine sediments of Byers Peninsula.}, }
@article {pmid26337395, year = {2016}, author = {Pozo, MI and Herrera, CM and Lachance, MA and Verstrepen, K and Lievens, B and Jacquemyn, H}, title = {Species coexistence in simple microbial communities: unravelling the phenotypic landscape of co-occurring Metschnikowia species in floral nectar.}, journal = {Environmental microbiology}, volume = {18}, number = {6}, pages = {1850-1862}, doi = {10.1111/1462-2920.13037}, pmid = {26337395}, issn = {1462-2920}, mesh = {Biodiversity ; Flowers/*microbiology ; Metschnikowia/classification/genetics/*isolation &amp; purification ; Phenotype ; Plant Nectar/*analysis ; }, abstract = {Identifying the ecological processes that underlie the distribution and abundance of species in microbial communities is a central issue in microbial ecology and evolution. Classical trade-off based niche theories of resource competition predict that co-occurrence in microbial communities is more likely when the residing species show trait divergence and complementary resource use. We tested the prediction that niche differentiation explained the co-occurrence of two yeast species (Metschnikowia reukaufii and M. gruessii) in floral nectar. Assessment of the phenotypic landscape showed that both species displayed a significantly different physiological profile. Comparison of utilization profiles in single versus mixed cultures indicated that these two species did not compete for most carbon and nitrogen sources. In mixed cultures, M. reukaufii grew better in sucrose solutions and in the presence of the antimicrobial compound digitonin than when grown as pure culture. M. gruessii, on the other hand, grew better in mixed cultures in glucose and fructose solutions. Overall, these results provide clear evidence that M. reukaufii and M. gruessii frequently co-occur in nectar and that they differ in their phenotypic response to variation in environmental conditions, suggesting that niche differentiation and resource partitioning are important mechanisms contributing to species co-occurrence in nectar yeast communities.}, }
@article {pmid26335567, year = {2016}, author = {Wu, C and Choi, YH and van Wezel, GP}, title = {Metabolic profiling as a tool for prioritizing antimicrobial compounds.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {43}, number = {2-3}, pages = {299-312}, pmid = {26335567}, issn = {1476-5535}, mesh = {Anti-Infective Agents/analysis/isolation &amp; purification/*metabolism ; Biological Products/analysis/isolation &amp; purification/metabolism ; Biomarkers/analysis/metabolism ; Drug Resistance, Microbial ; Humans ; Magnetic Resonance Spectroscopy ; Mass Spectrometry ; *Metabolomics ; Multigene Family ; }, abstract = {Metabolomics is an analytical technique that allows scientists to globally profile low molecular weight metabolites between samples in a medium- or high-throughput environment. Different biological samples are statistically analyzed and correlated to a bioactivity of interest, highlighting differentially produced compounds as potential biomarkers. Here, we review NMR- and MS-based metabolomics as technologies to facilitate the identification of novel antimicrobial natural products from microbial sources. Approaches to elicit the production of poorly expressed (cryptic) molecules are thereby a key to allow statistical analysis of samples to identify bioactive markers, while connection of compounds to their biosynthetic gene cluster is a determining step in elucidating the biosynthetic pathway and allows downstream process optimization and upscaling. The review focuses on approaches built around NMR-based metabolomics, which enables efficient dereplication and guided fractionation of (antimicrobial) compounds.}, }
@article {pmid26334579, year = {2016}, author = {Moratalla, A and Caparrós, E and Juanola, O and Portune, K and Puig-Kröger, A and Estrada-Capetillo, L and Bellot, P and Gómez-Hurtado, I and Piñero, P and Zapater, P and González-Navajas, JM and Such, J and Sanz, Y and Francés, R}, title = {Bifidobacterium pseudocatenulatum CECT7765 induces an M2 anti-inflammatory transition in macrophages from patients with cirrhosis.}, journal = {Journal of hepatology}, volume = {64}, number = {1}, pages = {135-145}, doi = {10.1016/j.jhep.2015.08.020}, pmid = {26334579}, issn = {1600-0641}, mesh = {Aged ; Anti-Inflammatory Agents/*pharmacology ; *Bifidobacterium ; Cell Polarity ; Cytokines/biosynthesis ; Female ; Humans ; Kupffer Cells/immunology ; Lipopolysaccharides/pharmacology ; Liver Cirrhosis/*immunology ; Macrophages/*immunology ; Male ; Middle Aged ; Prospective Studies ; }, abstract = {BACKGROUND &amp; AIMS: Patients with cirrhosis show recurrent access of bacterial products into the bloodstream inducing a multi-altered immunological status leading to relevant complications. We aimed at evaluating Bifidobacterium pseudocatenulatum CECT7765 effect on the host's macrophage function.<br><br>PATIENTS &amp; METHODS: Patients with cirrhosis and ascites were included. Granulocyte-macrophage colony-stimulating factor (GM-CSF) monocyte-derived and ascitic fluid (AF) macrophages were cultured with M-CSF, lipopolysaccharide (LPS) and/or the bifidobacterial strain. Pellets and supernatants were evaluated for gene expression of M1 and M2-related genes and cytokine secretion. Cell surface expression molecules were evaluated by flow cytometry. Kupffer cells from bile duct ligated and CCl4 rats were also evaluated.<br><br>RESULTS: Experiments were run on GM-CSF blood-derived and AF macrophages from 10 patients with cirrhosis and 10 healthy donors. Different macrophage morphology was observed by optical microscopy in cells stimulated with bifidobacteria vs. LPS. M2-like expression of CD206, CD163 and CD16 was significantly increased in macrophages after stimulation with the bifidobacterial strain vs. LPS. B. pseudocatenulatum CECT7765 was able to significantly change the cytokine secretion pattern of blood-derived and AF macrophages and Kupffer cells from bile duct ligated and CCl4 cirrhotic rats compared to that induced by LPS. B. pseudocatenulatum CECT7765 was also effective in inducing a phenotype transition and a functional change from an M1- to an M2-related gene expression and cytokine secretion pattern in AF macrophages even after LPS-pretreatment. B. pseudocatenulatum CECT7765 did not reduce AF macrophage bacterial killing capacity.<br><br>CONCLUSION: B. pseudocatenulatum CECT7765 induces a morphologic, phenotypic and functional transition towards an anti-inflammatory profile in GM-CSF monocyte-derived and AF macrophages from patients with cirrhosis that may help in controlling sustained inflammation in decompensated cirrhosis.}, }
@article {pmid26332409, year = {2015}, author = {Larsen, PE and Collart, FR and Dai, Y}, title = {Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0132837}, pmid = {26332409}, issn = {1932-6203}, mesh = {Biological Transport ; Ecology ; Machine Learning ; Metabolome/*genetics ; *Models, Biological ; Plant Development/*genetics ; *Rhizosphere ; Soil Microbiology ; }, abstract = {The ability to obtain complete genome sequences from bacteria in environmental samples, such as soil samples from the rhizosphere, has highlighted the microbial diversity and complexity of environmental communities. However, new algorithms to analyze genome sequence information in the context of community structure are needed to enhance our understanding of the specific ecological roles of these organisms in soil environments. We present a machine learning approach using sequenced Pseudomonad genomes coupled with outputs of metabolic and transportomic computational models for identifying the most predictive molecular mechanisms indicative of a Pseudomonad's ecological role in the rhizosphere: a biofilm, biocontrol agent, promoter of plant growth, or plant pathogen. Computational predictions of ecological niche were highly accurate overall with models trained on transportomic model output being the most accurate (Leave One Out Validation F-scores between 0.82 and 0.89). The strongest predictive molecular mechanism features for rhizosphere ecological niche overlap with many previously reported analyses of Pseudomonad interactions in the rhizosphere, suggesting that this approach successfully informs a system-scale level understanding of how Pseudomonads sense and interact with their environments. The observation that an organism's transportome is highly predictive of its ecological niche is a novel discovery and may have implications in our understanding microbial ecology. The framework developed here can be generalized to the analysis of any bacteria across a wide range of environments and ecological niches making this approach a powerful tool for providing insights into functional predictions from bacterial genomic data.}, }
@article {pmid26325358, year = {2016}, author = {Hiras, J and Wu, YW and Eichorst, SA and Simmons, BA and Singer, SW}, title = {Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage.}, journal = {The ISME journal}, volume = {10}, number = {4}, pages = {833-845}, pmid = {26325358}, issn = {1751-7370}, mesh = {Bacteroidetes/genetics ; Chlorobi/*classification/cytology/genetics/*metabolism ; Flagella/metabolism ; Genomics ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; United States ; }, abstract = {Recent studies have expanded the phylum Chlorobi, demonstrating that the green sulfur bacteria (GSB), the original cultured representatives of the phylum, are a part of a broader lineage whose members have more diverse metabolic capabilities that overlap with members of the phylum Bacteroidetes. The 16S rRNA gene of an uncultivated clone, OPB56, distantly related to the phyla Chlorobi and Bacteroidetes, was recovered from Obsidian Pool in Yellowstone National Park; however, the detailed phylogeny and function of OPB56 and related clones have remained unknown. Culturing of thermophilic bacterial consortia from compost by adaptation to grow on ionic-liquid pretreated switchgrass provided a consortium in which one of the most abundant members, NICIL-2, clustered with OPB56-related clones. Phylogenetic analysis using the full-length 16S rRNA gene from NICIL-2 demonstrated that it was part of a monophyletic clade, referred to as OPB56, distinct from the Bacteroidetes and Chlorobi. A near complete draft genome (>95% complete) was recovered from metagenomic data from the culture adapted to grow on ionic-liquid pretreated switchgrass using an automated binning algorithm, and this genome was used for marker gene-based phylogenetic analysis and metabolic reconstruction. Six additional genomes related to NICIL-2 were reconstructed from metagenomic data sets obtained from thermal springs at Yellowstone National Park and Nevada Great Boiling Spring. In contrast to the 16S rRNA gene phylogenetic analysis, protein phylogenetic analysis was most consistent with the clustering of the Chlorobea, Ignavibacteria and OPB56 into a single phylum level clade. Metabolic reconstruction of NICIL-2 demonstrated a close linkage with the class Ignavibacteria and the family Rhodothermaceae, a deeply branching Bacteroidetes lineage. The combined phylogenetic and functional analysis of the NICIL-2 genome has refined the membership in the phylum Chlorobi and emphasized the close evolutionary and metabolic relationship between the phyla Chlorobi and the Bacteroidetes.}, }
@article {pmid26324928, year = {2015}, author = {Acosta, F and Zamor, RM and Najar, FZ and Roe, BA and Hambright, KD}, title = {Dynamics of an experimental microbial invasion.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {37}, pages = {11594-11599}, pmid = {26324928}, issn = {1091-6490}, mesh = {Biodiversity ; Chlorophyll/chemistry ; *Climate Change ; Ecology ; Ecosystem ; Fresh Water ; Haptophyta/*physiology ; Introduced Species ; Linear Models ; Population Dynamics ; Time Factors ; *Water Microbiology ; }, abstract = {The ecological dynamics underlying species invasions have been a major focus of research in macroorganisms for the last five decades. However, we still know little about the processes behind invasion by unicellular organisms. To expand our knowledge of microbial invasions, we studied the roles of propagule pressure, nutrient supply, and biotic resistance in the invasion success of a freshwater invasive alga, Prymnesium parvum, using microcosms containing natural freshwater microbial assemblages. Microcosms were subjected to a factorial design with two levels of nutrient-induced diversity and three levels of propagule pressure, and incubated for 7 d, during which P. parvum densities and microbial community composition were tracked. Successful invasion occurred in microcosms receiving high propagule pressure whereas nutrients or community diversity played no role in invasion success. Invaded communities experienced distinctive changes in composition compared with communities where the invasion was unsuccessful. Successfully invaded microbial communities had an increased abundance of fungi and ciliates, and decreased abundances of diatoms and cercozoans. Many of these changes mirrored the microbial community changes detected during a natural P. parvum bloom in the source system. This role of propagule pressure is particularly relevant for P. parvum in the reservoir-dominated southern United States because this species can form large, sustained blooms that can generate intense propagule pressures for downstream sites. Human impact and global climate change are currently causing widespread environmental changes in most southern US freshwater systems that may facilitate P. parvum establishment and, when coupled with strong propagule pressure, could put many more systems at risk for invasion.}, }
@article {pmid26324854, year = {2015}, author = {Eichorst, SA and Strasser, F and Woyke, T and Schintlmeister, A and Wagner, M and Woebken, D}, title = {Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {10}, pages = {}, pmid = {26324854}, issn = {1574-6941}, support = {294343/ERC_/European Research Council/International ; P 25700/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Archaea/classification/isolation &amp; purification/*metabolism ; Bacteria/classification/isolation &amp; purification/*metabolism ; Carbon/metabolism ; Deuterium Oxide/metabolism ; Fungi/classification/isolation &amp; purification/*metabolism ; Isotope Labeling/methods ; RNA, Ribosomal, 16S/genetics ; Single-Cell Analysis/*methods ; *Soil Microbiology ; Spectrometry, Mass, Secondary Ion ; Spectrum Analysis, Raman/*methods ; }, abstract = {The combined approach of incubating environmental samples with stable isotope-labeled substrates followed by single-cell analyses through high-resolution secondary ion mass spectrometry (NanoSIMS) or Raman microspectroscopy provides insights into the in situ function of microorganisms. This approach has found limited application in soils presumably due to the dispersal of microbial cells in a large background of particles. We developed a pipeline for the efficient preparation of cell extracts from soils for subsequent single-cell methods by combining cell detachment with separation of cells and soil particles followed by cell concentration. The procedure was evaluated by examining its influence on cell recoveries and microbial community composition across two soils. This approach generated a cell fraction with considerably reduced soil particle load and of sufficient small size to allow single-cell analysis by NanoSIMS, as shown when detecting active N2-fixing and cellulose-responsive microorganisms via (15)N2 and (13)C-UL-cellulose incubations, respectively. The same procedure was also applicable for Raman microspectroscopic analyses of soil microorganisms, assessed via microcosm incubations with a (13)C-labeled carbon source and deuterium oxide (D2O, a general activity marker). The described sample preparation procedure enables single-cell analysis of soil microorganisms using NanoSIMS and Raman microspectroscopy, but should also facilitate single-cell sorting and sequencing.}, }
@article {pmid26318324, year = {2016}, author = {Yang, Y and Zhao, Q and Cui, Y and Wang, Y and Xie, S and Liu, Y}, title = {Spatio-temporal Variation of Sediment Methanotrophic Microorganisms in a Large Eutrophic Lake.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {9-17}, pmid = {26318324}, issn = {1432-184X}, mesh = {Autotrophic Processes ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics ; Biodiversity ; Eutrophication ; Geologic Sediments/chemistry/microbiology ; Lakes/chemistry/*microbiology ; Methane/*metabolism ; Molecular Sequence Data ; Phylogeny ; Seasons ; }, abstract = {Aerobic methane-oxidizing bacteria (MOB) play a crucial role in mitigating the methane emission from lake ecosystems to the atmosphere. However, the distribution of methanotrophic community in shallow and eutrophic lake and its influential factors remain essentially unclear. The present study investigated sediment methanotrophic microorganisms at different sites in eutrophic freshwater Dianchi Lake (China) in two different seasons. The abundance, diversity, and structure of sediment methanotrophic community showed a profound spatial and seasonal variation. The pmoA gene copy number in lake sediments ranged from 8.71 ± 0.49 × 10(4) to 2.09 ± 0.03 × 10(7) copies per gram of dry sediment. Sediment methanotrophic communities were composed of Methylococcus and Methylobacter (type I methanotrophs) and Methylosinus (type II methanotrophs), while type I MOB usually outnumbered type II MOB. Moreover, ammonia nitrogen was found to be a potential determinant of methanotrophic community structure in Dianchi Lake.}, }
@article {pmid26318323, year = {2016}, author = {Jang, Y and Jang, S and Min, M and Hong, JH and Lee, H and Lee, H and Lim, YW and Kim, JJ}, title = {Erratum to: Comparison of the Diversity of Basidiomycetes from Dead Wood of the Manchurian fir (Abies holophylla) as Evaluated by Fruiting Body Collection, Mycelial Isolation, and 454 Sequencing.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {784-787}, doi = {10.1007/s00248-015-0665-9}, pmid = {26318323}, issn = {1432-184X}, }
@article {pmid26317985, year = {2015}, author = {Liu, Y and Rzeszutek, E and van der Voort, M and Wu, CH and Thoen, E and Skaar, I and Bulone, V and Dorrestein, PC and Raaijmakers, JM and de Bruijn, I}, title = {Diversity of Aquatic Pseudomonas Species and Their Activity against the Fish Pathogenic Oomycete Saprolegnia.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0136241}, pmid = {26317985}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; *Biodiversity ; Eggs/microbiology ; Fish Diseases/microbiology ; Infections/microbiology ; Molecular Sequence Data ; *Pseudomonas/classification/genetics/isolation &amp; purification ; Salmon/microbiology ; Saprolegnia/*microbiology ; *Water Microbiology ; }, abstract = {Emerging fungal and oomycete pathogens are increasingly threatening animals and plants globally. Amongst oomycetes, Saprolegnia species adversely affect wild and cultivated populations of amphibians and fish, leading to substantial reductions in biodiversity and food productivity. With the ban of several chemical control measures, new sustainable methods are needed to mitigate Saprolegnia infections in aquaculture. Here, PhyloChip-based community analyses showed that the Pseudomonadales, particularly Pseudomonas species, represent one of the largest bacterial orders associated with salmon eggs from a commercial hatchery. Among the Pseudomonas species isolated from salmon eggs, significantly more biosurfactant producers were retrieved from healthy salmon eggs than from Saprolegnia-infected eggs. Subsequent in vivo activity bioassays showed that Pseudomonas isolate H6 significantly reduced salmon egg mortality caused by Saprolegnia diclina. Live colony mass spectrometry showed that strain H6 produces a viscosin-like lipopeptide surfactant. This biosurfactant inhibited growth of Saprolegnia in vitro, but no significant protection of salmon eggs against Saprolegniosis was observed. These results indicate that live inocula of aquatic Pseudomonas strains, instead of their bioactive compound, can provide new (micro)biological and sustainable means to mitigate oomycete diseases in aquaculture.}, }
@article {pmid26311623, year = {2015}, author = {Wegener Parfrey, L}, title = {Mock communities highlight the diversity of host-associated eukaryotes.}, journal = {Molecular ecology}, volume = {24}, number = {17}, pages = {4337-4339}, doi = {10.1111/mec.13311}, pmid = {26311623}, issn = {1365-294X}, mesh = {Animals ; Apicomplexa ; *Biodiversity ; Eukaryota ; *High-Throughput Nucleotide Sequencing ; Oligochaeta/microbiology ; *Soil Microbiology ; Symbiosis ; }, abstract = {Host-associated microbes are ubiquitous. Every multicellular eukaryote, and even many unicellular eukaryotes (protists), hosts a diverse community of microbes. High-throughput sequencing (HTS) tools have illuminated the vast diversity of host-associated microbes and shown that they have widespread influence on host biology, ecology and evolution (McFall-Ngai et al.). Bacteria receive most of the attention, but protists are also important components of microbial communities associated with humans (Parfrey et al.) and other hosts. As HTS tools are increasingly used to study eukaryotes, the presence of numerous and diverse host-associated eukaryotes is emerging as a common theme across ecosystems. Indeed, HTS studies demonstrate that host-associated lineages account for between 2 and 12% of overall eukaryotic sequences detected in soil, marine and freshwater data sets, with much higher relative abundances observed in some samples (Ramirez et al. ; Simon et al. ; de Vargas et al.). Previous studies in soil detected large numbers of predominantly parasitic lineages such as Apicomplexa, but did not delve into their origin [e.g. (Ramirez et al.)]. In this issue of Molecular Ecology, Geisen et al. () use mock communities to show that many of the eukaryotic organisms detected by environmental sequencing in soils are potentially associated with animal hosts rather than free-living. By isolating the host-associated fraction of soil microbial communities, Geisen and colleagues help explain the surprisingly high diversity of parasitic eukaryotic lineages often detected in soil/terrestrial studies using high-throughput sequencing (HTS) and reinforce the ubiquity of these host-associated microbes. It is clear that we can no longer assume that organisms detected in bulk environmental sequencing are free-living, but instead need to design studies that specifically enumerate the diversity and function of host-associated eukaryotes. Doing so will allow the field to determine the role host-associated eukaryotes play in soils and other environments and to evaluate hypotheses on assembly of host-associated communities, disease ecology and more.}, }
@article {pmid26311127, year = {2016}, author = {Meisterhans, G and Raymond, N and Girault, E and Lambert, C and Bourrasseau, L and de Montaudouin, X and Garabetian, F and Jude-Lemeilleur, F}, title = {Structure of Manila Clam (Ruditapes philippinarum) Microbiota at the Organ Scale in Contrasting Sets of Individuals.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {194-206}, pmid = {26311127}, issn = {1432-184X}, mesh = {Animal Structures/*microbiology ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bivalvia/*microbiology ; *Microbiota ; Shellfish/*microbiology ; }, abstract = {Marine invertebrate microbiota has a key function in host physiology and health. To date, knowledge about bivalve microbiota is poorly documented except public health concerns. This study used a molecular approach to characterize the microbiota associated with the bivalve Manila clam (Ruditapes philippinarum) by determining (1) the difference among organs either or not under the influence of host habitat, (2) small-scale variability of microbiota, and (3) the experimental response of the Manila clam microbiota submitted to different lateral transmissions. These questions were investigated by sampling two groups of individuals living in contrasting habitats and carrying out a transplant experiment. Manila clam microbiota (i.e., bacterial community structure) was determined at organ-scale (gills, gut, and a pool of remaining tissues) by capillary electrophoresis DNA fingerprinting (CE fingerprinting). The Manila clam microbiota structure differed among organs indicating a selection of Manila clam microbiota at organ scale. Habitat strongly influenced gill and gut microbiota. In contrast, microbiota associated with remaining tissues was similar between group individuals suggesting that these communities are mostly autochthonous, i.e., Manila clam specific. Transplant experiment showed that improving living condition did not induce any change in microbiota associated with remaining tissues. In contrast, the reduction in individual habitat quality led to individuals in declining health as strongly suggested by the increase in phagocytosis activity and decrease in condition index together with the change in internal organ microbiota. This study provides a first description of the Manila clam holobiont which can withstand disturbance and respond opportunistically to improved environmental conditions.}, }
@article {pmid26310700, year = {2015}, author = {Faure, D and Bonin, P and Duran, R and , }, title = {Environmental microbiology as a mosaic of explored ecosystems and issues.}, journal = {Environmental science and pollution research international}, volume = {22}, number = {18}, pages = {13577-13598}, pmid = {26310700}, issn = {1614-7499}, mesh = {Animals ; Archaea/*physiology ; *Bacteria ; Ecosystem ; *Environmental Microbiology ; Environmental Pollutants/pharmacology ; Humans ; Microbial Interactions ; Phylogeny ; *Viruses ; }, abstract = {Microbes are phylogenetically (Archaea, Bacteria, Eukarya, and viruses) and functionally diverse. They colonize highly varied environments and rapidly respond to and evolve as a response to local and global environmental changes, including those induced by pollutants resulting from human activities. This review exemplifies the Microbial Ecology EC2CO consortium's efforts to explore the biology, ecology, diversity, and roles of microbes in aquatic and continental ecosystems.}, }
@article {pmid26310130, year = {2015}, author = {Perin, LM and Dal Bello, B and Belviso, S and Zeppa, G and Carvalho, AF and Cocolin, L and Nero, LA}, title = {Microbiota of Minas cheese as influenced by the nisin producer Lactococcus lactis subsp. lactis GLc05.}, journal = {International journal of food microbiology}, volume = {214}, number = {}, pages = {159-167}, doi = {10.1016/j.ijfoodmicro.2015.08.006}, pmid = {26310130}, issn = {1879-3460}, mesh = {Animals ; Biogenic Amines/*analysis/biosynthesis ; Brazil ; Cattle ; Cheese/analysis/*microbiology ; Coagulase/metabolism ; Female ; Food Microbiology ; Goats ; Lactococcus lactis/*growth &amp; development ; *Microbiota ; Nisin/*biosynthesis ; }, abstract = {Minas cheese is a popular dairy product in Brazil that is traditionally produced using raw or pasteurized cow milk. This study proposed an alternative production of Minas cheese using raw goat milk added of a nisin producer Lactococcus lactis subsp. lactis GLc05. An in situ investigation was carried on to evaluate the interactions between the L. lactis subsp. lactis GLc05 and the autochthonous microbiota of a Minas cheese during the ripening; production of biogenic amines (BAs) was assessed as a safety aspect. Minas cheese was produced in two treatments (A, by adding L. lactis subsp. lactis GLc05, and B, without adding this strain), in three independent repetitions (R1, R2, and R3). Culture dependent (direct plating) and independent (rep-PCR and PCR-DGGE) methods were employed to characterize the microbiota and to assess the possible interferences caused by L. lactis subsp. lactis GLc05. BA amounts were measured using HPLC. A significant decrease in coagulase-positive cocci was observed in the cheeses produced by adding L. lactis subsp. lactis GLc05 (cheese A). The rep-PCR and PCR-DGGE highlighted the differences in the microbiota of both cheeses, separating them into two different clusters. Lactococcus sp. was found as the main microorganism in both cheeses, and the microbiota of cheese A presented a higher number of species. High concentrations of tyramine were found in both cheeses and, at specific ripening times, the BA amounts in cheese B were significantly higher than in cheese A (p<0.05). The interaction of nisin producer L. lactis subsp. lactis GLc05 was demonstrated in situ, by demonstration of its influence in the complex microbiota naturally present in a raw goat milk cheese and by controlling the growth of coagulase-positive cocci. L. lactis subsp. lactis GLc05 influenced also the production of BA determining that their amounts in the cheeses were maintained at acceptable levels for human consumption.}, }
@article {pmid26308033, year = {2015}, author = {Ceuppens, S and Delbeke, S and De Coninck, D and Boussemaere, J and Boon, N and Uyttendaele, M}, title = {Characterization of the Bacterial Community Naturally Present on Commercially Grown Basil Leaves: Evaluation of Sample Preparation Prior to Culture-Independent Techniques.}, journal = {International journal of environmental research and public health}, volume = {12}, number = {8}, pages = {10171-10197}, pmid = {26308033}, issn = {1660-4601}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; *Food Microbiology ; *Food Storage ; *Microbiota ; Ocimum basilicum/*microbiology ; Plant Leaves/microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Temperature ; }, abstract = {Fresh herbs such as basil constitute an important food commodity worldwide. Basil provides considerable culinary and health benefits, but has also been implicated in foodborne illnesses. The naturally occurring bacterial community on basil leaves is currently unknown, so the epiphytic bacterial community was investigated using the culture-independent techniques denaturing gradient gel electrophoresis (DGGE) and next-generation sequencing (NGS). Sample preparation had a major influence on the results from DGGE and NGS: Novosphingobium was the dominant genus for three different basil batches obtained by maceration of basil leaves, while washing of the leaves yielded lower numbers but more variable dominant bacterial genera including Klebsiella, Pantoea, Flavobacterium, Sphingobacterium and Pseudomonas. During storage of basil, bacterial growth and shifts in the bacterial community were observed with DGGE and NGS. Spoilage was not associated with specific bacterial groups and presumably caused by physiological tissue deterioration and visual defects, rather than by bacterial growth.}, }
@article {pmid26305944, year = {2015}, author = {Koch, H and Lücker, S and Albertsen, M and Kitzinger, K and Herbold, C and Spieck, E and Nielsen, PH and Wagner, M and Daims, H}, title = {Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {36}, pages = {11371-11376}, pmid = {26305944}, issn = {1091-6490}, support = {294343/ERC_/European Research Council/International ; T32 HG002536/HG/NHGRI NIH HHS/United States ; }, mesh = {Ammonia/*metabolism ; Bacteria/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Ecosystem ; Formate Dehydrogenases/genetics/metabolism ; Formates/metabolism ; Fresh Water/microbiology ; Genome, Bacterial/genetics ; Metagenome/genetics ; Molecular Sequence Data ; Nitrates/metabolism ; Nitrites/*metabolism ; Nitrogen Cycle ; Oxidation-Reduction ; Oxygen/metabolism ; Sequence Analysis, DNA ; Sewage/microbiology ; Soil Microbiology ; Urea/*metabolism ; Urease/genetics/metabolism ; }, abstract = {Nitrospira are a diverse group of nitrite-oxidizing bacteria and among the environmentally most widespread nitrifiers. However, they remain scarcely studied and mostly uncultured. Based on genomic and experimental data from Nitrospira moscoviensis representing the ubiquitous Nitrospira lineage II, we identified ecophysiological traits that contribute to the ecological success of Nitrospira. Unexpectedly, N. moscoviensis possesses genes coding for a urease and cleaves urea to ammonia and CO2. Ureolysis was not observed yet in nitrite oxidizers and enables N. moscoviensis to supply ammonia oxidizers lacking urease with ammonia from urea, which is fully nitrified by this consortium through reciprocal feeding. The presence of highly similar urease genes in Nitrospira lenta from activated sludge, in metagenomes from soils and freshwater habitats, and of other ureases in marine nitrite oxidizers, suggests a wide distribution of this extended interaction between ammonia and nitrite oxidizers, which enables nitrite-oxidizing bacteria to indirectly use urea as a source of energy. A soluble formate dehydrogenase lends additional ecophysiological flexibility and allows N. moscoviensis to use formate, with or without concomitant nitrite oxidation, using oxygen, nitrate, or both compounds as terminal electron acceptors. Compared with Nitrospira defluvii from lineage I, N. moscoviensis shares the Nitrospira core metabolism but shows substantial genomic dissimilarity including genes for adaptations to elevated oxygen concentrations. Reciprocal feeding and metabolic versatility, including the participation in different nitrogen cycling processes, likely are key factors for the niche partitioning, the ubiquity, and the high diversity of Nitrospira in natural and engineered ecosystems.}, }
@article {pmid26304552, year = {2016}, author = {Bonfim, JA and Vasconcellos, RL and Gumiere, T and de Lourdes Colombo Mescolotti, D and Oehl, F and Nogueira Cardoso, EJ}, title = {Diversity of Arbuscular Mycorrhizal Fungi in a Brazilian Atlantic Forest Toposequence.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {164-177}, pmid = {26304552}, issn = {1432-184X}, mesh = {Altitude ; Biodiversity ; Brazil ; Forests ; Fungi/classification/genetics/*isolation &amp; purification ; Molecular Sequence Data ; Mycorrhizae/classification/genetics/*isolation &amp; purification ; Phylogeny ; Plant Roots/microbiology ; Rhizosphere ; Seasons ; *Soil Microbiology ; }, abstract = {The diversity of arbuscular mycorrhizal fungi (AMF) was studied in the Atlantic Forest in Serra do Mar Park (SE Brazil), based on seven host plants in relationship to their soil environment, altitude and seasonality. The studied plots along an elevation gradient are located at 80, 600, and 1,000 m. Soil samples (0-20 cm) were collected in four seasons from SE Brazilian winter 2012 to autumn 2013. AMF spores in rhizosperic soils were morphologically classified and chemical, physical and microbiological soil caracteristics were determined. AMF diversity in roots was evaluated using the NS31/AM1 primer pair, with subsequent cloning and sequencing. In the rhizosphere, 58 AMF species were identified. The genera Acaulospora and Glomus were predominant. However, in the roots, only 14 AMF sequencing groups were found and all had high similarity to Glomeraceae. AMF species identities varied between altitudes and seasons. There were species that contributed the most to this variation. Some soil characteristics (pH, organic matter, microbial activity and microbial biomass carbon) showed a strong relationship with the occurrence of certain species. The highest AMF species diversity, based on Shannon's diversity index, was found for the highest altitude. Seasonality did not affect the diversity. Our results show a high AMF diversity, higher than commonly found in the Atlantic Forest. The AMF detected in roots were not identical to those detected in rhizosperic soil and differences in AMF communities were found in different altitudes even in geographically close-lying sites.}, }
@article {pmid26298511, year = {2015}, author = {Chabert, N and Amin Ali, O and Achouak, W}, title = {All ecosystems potentially host electrogenic bacteria.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {106}, number = {Pt A}, pages = {88-96}, doi = {10.1016/j.bioelechem.2015.07.004}, pmid = {26298511}, issn = {1878-562X}, mesh = {Bacteria/chemistry/cytology/*metabolism ; Bioelectric Energy Sources/*microbiology ; *Ecosystem ; Electrochemistry ; Electron Transport ; Extracellular Space/chemistry ; }, abstract = {Instead of requiring metal catalysts, MFCs utilize bacteria that oxidize organic matter and either transfer electrons to the anode or take electrons from the cathode. These devices are thus based on a wide microbial diversity that can convert a large array of organic matter components into sustainable and renewable energy. A wide variety of explored environments were found to host electrogenic bacteria, including extreme environments. In the present review, we describe how different ecosystems host electrogenic bacteria, as well as the physicochemical, electrochemical and biological parameters that control the currents from MFCs. We also report how using new molecular techniques allowed characterization of electrochemical biofilms and identification of potentially new electrogenic species. Finally we discuss these findings in the context of future research directions.}, }
@article {pmid26297491, year = {2015}, author = {Pascual, J and Wüst, PK and Geppert, A and Foesel, BU and Huber, KJ and Overmann, J}, title = {Terriglobus albidus sp. nov., a member of the family Acidobacteriaceae isolated from Namibian semiarid savannah soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {65}, number = {10}, pages = {3297-3304}, doi = {10.1099/ijsem.0.000411}, pmid = {26297491}, issn = {1466-5034}, mesh = {Acidobacteria/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; *Grassland ; Molecular Sequence Data ; Namibia ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/chemistry ; }, abstract = {A novel aerobic, chemo-organoheterotrophic bacterium, strain Ac_26_B10T, was isolated from a semiarid savannah soil collected in northern Namibia (Mashare, Kavango region). Based on analysis of its nearly full-length 16S rRNA gene sequence, the isolate belongs to the genus Terriglobus (family Acidobacteriaceae, order Acidobacteriales, class Acidobacteria) and shares 98.3 and 96.9 % 16S rRNA gene sequence similarity with its closest relatives, Terriglobus tenax DRP 35T and T. aquaticus O3SUJ4T. Cells were Gram-negative, coccoid to rod-shaped, non-motile and divided by binary fission. Strain Ac_26_B10T showed weak catalase activity and, in contrast to the other described species of the genus Terriglobus, was oxidase-positive. Compared with the already established species of the genus Terriglobus, the novel strain used a larger range of sugars and sugar alcohols for growth, lacked α-mannosidase activity and exhibited a higher temperature optimum of growth. DNA–DNA hybridization studies with its closest phylogenetic relative, T. tenax DSM 28898T, confirmed that strain Ac_26_B10T represents a distinct genomospecies. Its most abundant fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. Dominant polar lipids were phosphatidylethanolamine and diphosphatidylglycerol. The predominant menaquinone was MK-8; minor amounts of MK-7 and MK-8(H2) were also recorded. The G+C content of the genomic DNA was 58.5 mol%. On the basis of our polyphasic analysis, Ac_26_B10T represents a novel species of the genus Terriglobus, for which the name Terriglobus albidus sp. nov. is proposed. The type strain is Ac_26_B10T (= DSM 26559T = LMG 27984T).}, }
@article {pmid26297346, year = {2015}, author = {Patil, Y and Junghare, M and Pester, M and Müller, N and Schink, B}, title = {Anaerobium acetethylicum gen. nov., sp. nov., a strictly anaerobic, gluconate-fermenting bacterium isolated from a methanogenic bioreactor.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {65}, number = {10}, pages = {3289-3296}, doi = {10.1099/ijsem.0.000410}, pmid = {26297346}, issn = {1466-5034}, mesh = {Bacteria, Anaerobic/classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; Bioreactors/*microbiology ; Clostridiales/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Fermentation ; Germany ; Gluconates/metabolism ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; }, abstract = {A novel strictly anaerobic, mesophilic bacterium was enriched and isolated with gluconate as sole substrate from a methanogenic sludge collected from a biogas reactor. Cells of strain GluBS11T stained Gram-positive and were non-motile, straight rods, measuring 3.0-4.5 × 0.8-1.2 μm. The temperature range for growth was 15-37 °C, with optimal growth at 30 °C, the pH range was 6.5-8.5, with optimal growth at pH 7, and the generation time under optimal conditions was 60 min. API Rapid 32A reactions were positive for α-galactosidase, α-glucosidase and β-glucosidase and negative for catalase and oxidase. A broad variety of substrates was utilized, including gluconate, glucose, fructose, maltose, sucrose, lactose, galactose, melezitose, melibiose, mannitol, erythritol, glycerol and aesculin. Products of gluconate fermentation were ethanol, acetate, formate, H2 and CO2. Neither sulfate nor nitrate served as an electron acceptor. Predominant cellular fatty acids (>10 %) were C14 : 0, C16 : 0, C16 : 1ω7c/iso-C15 : 0 2-OH and C18 : 1ω7c. The DNA G+C content of strain GluBS11T was 44.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequence data revealed that strain GluBS11T is a member of subcluster XIVa within the order Clostridiales. The closest cultured relatives are Clostridium herbivorans (93.1 % similarity to the type strain), Clostridium populeti (93.3 %), Eubacterium uniforme (92.4 %) and Clostridium polysaccharolyticum (91.5 %). Based on this 16S rRNA gene sequence divergence (>6.5 %) as well as on chemotaxonomic and phenotypic differences from these taxa, strain GluBS11T is considered to represent a novel genus and species, for which the name Anaerobium acetethylicum gen. nov., sp. nov. is proposed. The type strain of Anaerobium acetethylicum is GluBS11T (= LMG 28619T = KCTC 15450T = DSM 29698T).}, }
@article {pmid26296733, year = {2015}, author = {Lopez-Siles, M and Martinez-Medina, M and Abellà, C and Busquets, D and Sabat-Mir, M and Duncan, SH and Aldeguer, X and Flint, HJ and Garcia-Gil, LJ}, title = {Mucosa-associated Faecalibacterium prausnitzii phylotype richness is reduced in patients with inflammatory bowel disease.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {21}, pages = {7582-7592}, pmid = {26296733}, issn = {1098-5336}, mesh = {Biopsy ; Clostridiales/*classification/genetics/*isolation &amp; purification ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; *Genetic Variation ; *Genotype ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Intestinal Mucosa/*microbiology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Faecalibacterium prausnitzii depletion in intestinal diseases has been extensively reported, but little is known about intraspecies variability. This work aims to determine if subjects with gastrointestinal disease host mucosa-associated F. prausnitzii populations different from those hosted by healthy individuals. A new species-specific PCR-denaturing gradient gel electrophoresis (PCR-DGGE) method targeting the 16S rRNA gene was developed to fingerprint F. prausnitzii populations in biopsy specimens from 31 healthy control (H) subjects and 36 Crohn's disease (CD), 23 ulcerative colitis (UC), 6 irritable bowel syndrome (IBS), and 22 colorectal cancer (CRC) patients. The richness of F. prausnitzii subtypes was lower in inflammatory bowel disease (IBD) patients than in H subjects. The most prevalent operational taxonomic units (OTUs) consisted of four phylotypes (OTUs with a 99% 16S rRNA gene sequence similarity [OTU99]), which were shared by all groups of patients. Their distribution and the presence of some disease-specific F. prausnitzii phylotypes allowed us to differentiate the populations in IBD and CRC patients from that in H subjects. At the level of a minimum similarity of 97% (OTU97), two phylogroups accounted for 98% of the sequences. Phylogroup I was found in 87% of H subjects but in under 50% of IBD patients (P = 0.003). In contrast, phylogroup II was detected in >75% of IBD patients and in only 52% of H subjects (P = 0.005). This study reveals that even though the main members of the F. prausnitzii population are present in both H subjects and individuals with gut diseases, richness is reduced in the latter and an altered phylotype distribution exists between diseases. This approach may serve as a basis for addressing the suitability of F. prausnitzii phylotypes to be quantified as a putative biomarker of disease and depicting the importance of the loss of these subtypes in disease pathogenesis.}, }
@article {pmid26296731, year = {2015}, author = {Hungate, BA and Mau, RL and Schwartz, E and Caporaso, JG and Dijkstra, P and van Gestel, N and Koch, BJ and Liu, CM and McHugh, TA and Marks, JC and Morrissey, EM and Price, LB}, title = {Quantitative microbial ecology through stable isotope probing.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {21}, pages = {7570-7581}, pmid = {26296731}, issn = {1098-5336}, mesh = {Bacteria/chemistry/*classification/genetics/*metabolism ; *Biota ; Centrifugation, Density Gradient ; DNA, Bacterial/chemistry/genetics/isolation &amp; purification ; *Environmental Microbiology ; Isotope Labeling/*methods ; Sequence Analysis, DNA ; }, abstract = {Bacteria grow and transform elements at different rates, and as yet, quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to stable isotope probing (SIP) that enables the isotopic composition of DNA from individual bacterial taxa after exposure to isotope tracers to be determined. In our modification, after isopycnic centrifugation, DNA is collected in multiple density fractions, and each fraction is sequenced separately. Taxon-specific density curves are produced for labeled and nonlabeled treatments, from which the shift in density for each individual taxon in response to isotope labeling is calculated. Expressing each taxon's density shift relative to that taxon's density measured without isotope enrichment accounts for the influence of nucleic acid composition on density and isolates the influence of isotope tracer assimilation. The shift in density translates quantitatively to isotopic enrichment. Because this revision to SIP allows quantitative measurements of isotope enrichment, we propose to call it quantitative stable isotope probing (qSIP). We demonstrated qSIP using soil incubations, in which soil bacteria exhibited strong taxonomic variations in (18)O and (13)C composition after exposure to [(18)O]water or [(13)C]glucose. The addition of glucose increased the assimilation of (18)O into DNA from [(18)O]water. However, the increase in (18)O assimilation was greater than expected based on utilization of glucose-derived carbon alone, because the addition of glucose indirectly stimulated bacteria to utilize other substrates for growth. This example illustrates the benefit of a quantitative approach to stable isotope probing.}, }
@article {pmid26296574, year = {2015}, author = {Lee, HJ and Whang, KS}, title = {Streptomyces sasae sp. nov., isolated from bamboo (Sasa borealis) rhizosphere soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {65}, number = {10}, pages = {3547-3551}, doi = {10.1099/ijsem.0.000454}, pmid = {26296574}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Diaminopimelic Acid/chemistry ; Fatty Acids/genetics ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Peptidoglycan/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Rhizosphere ; Sasa/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; Streptomyces/*classification/genetics/isolation &amp; purification ; }, abstract = {A novel strain of Gram-staining-positive actinobacterium, designated strain JR-39T, was isolated from the rhizosphere soil of bamboo (Sasa borealis) sampled in Damyang, Korea, and its taxonomic position was investigated by a polyphasic approach. The isolate formed flexuous chains of spores that were cylindrical and smooth-surfaced. Strain JR-39T grew at 4–37 °C (optimum 28 °C). The pH range for growth was pH 5–10 (optimum pH 6–8) and the NaCl range for growth was 0–5 % (w/v) with optimum growth at 1 % NaCl. The cell-wall peptidoglycan contained ll-diaminopimelic acid, glutamic acid, alanine and glycine. Whole-cell hydrolysates mainly contained glucose, mannose, ribose and rhamnose. Predominant menaquinones were MK-9 (H6), MK-9 (H8) and MK-9 (H4). The major cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0, iso-C15 : 0 and iso-C14 : 0. The G+C content of the DNA was 72.3 ± 0.34 mol%. Phylogenetic analyses based on 16S rRNA gene sequence analysis indicated that strain JR-39T belonged to the genus Streptomyces, showing the highest sequence similarity to Streptomyces panaciradicis 1MR-8T (99.4 %), Streptomyces capoamus JCM 4734T (98.8 %), Streptomyces galbus DSM 40089T (98.7 %), Streptomyces longwoodensis LMG 20096T (98.7 %), Streptomyces bungoensis NBRC 15711T (98.7 %) and Streptomyces rhizophilus JR-41T (98.7 %). However, DNA–DNA hybridization assays, as well as physiological and biochemical analyses, showed that strain JR-39T could be differentiated from its closest phylogenetic relatives. On the basis of the phenotypic and genotypic characteristics, strain JR-39T represents a novel species for which the name Streptomyces sasae sp. nov. is proposed. The type strain is JR-39T (= KACC 17182T = NBRC 109809T).}, }
@article {pmid26288654, year = {2015}, author = {Goux, X and Calusinska, M and Lemaigre, S and Marynowska, M and Klocke, M and Udelhoven, T and Benizri, E and Delfosse, P}, title = {Microbial community dynamics in replicate anaerobic digesters exposed sequentially to increasing organic loading rate, acidosis, and process recovery.}, journal = {Biotechnology for biofuels}, volume = {8}, number = {}, pages = {122}, pmid = {26288654}, issn = {1754-6834}, abstract = {BACKGROUND: Volatile fatty acid intoxication (acidosis), a common process failure recorded in anaerobic reactors, leads to drastic losses in methane production. Unfortunately, little is known about the microbial mechanisms underlining acidosis and the potential to recover the process. In this study, triplicate mesophilic anaerobic reactors of 100 L were exposed to acidosis resulting from an excessive feeding with sugar beet pulp and were compared to a steady-state reactor.<br><br>RESULTS: Stable operational conditions at the beginning of the experiment initially led to similar microbial populations in the four reactors, as revealed by 16S rRNA gene T-RFLP and high-throughput amplicon sequencing. Bacteroidetes and Firmicutes were the two dominant phyla, and although they were represented by a high number of operational taxonomic units, only a few were dominant. Once the environment became deterministic (selective pressure from an increased substrate feeding), microbial populations started to diverge between the overfed reactors. Interestingly, most of bacteria and archaea showed redundant functional adaptation to the changing environmental conditions. However, the dominant Bacteroidales were resistant to high volatile fatty acids content and low pH. The severe acidosis did not eradicate archaea and a clear shift in archaeal populations from acetotrophic to hydrogenotrophic methanogenesis occurred in the overfed reactors. After 11&#xa0;days of severe acidosis (pH 5.2&#xa0;&#xb1;&#xa0;0.4), the process was quickly recovered (restoration of the biogas production with methane content above 50&#xa0;%) in the overfed reactors, by adjusting the pH to around 7 using NaOH and NaHCO3.<br><br>CONCLUSIONS: In this study we show that once the replicate reactors are confronted with sub-optimal conditions, their microbial populations start to evolve differentially. Furthermore the alterations of commonly used microbial parameters to monitor the process, such as richness, evenness and diversity indices were unsuccessful to predict the process failure. At the same time, we tentatively propose the replacement of the dominant Methanosaeta sp. in this case by Methanoculleus sp., to be a potential warning indicator of acidosis.}, }
@article {pmid26287281, year = {2015}, author = {Gtari, M and Ghodhbane-Gtari, F and Nouioui, I and Ktari, A and Hezbri, K and Mimouni, W and Sbissi, I and Ayari, A and Yamanaka, T and Normand, P and Tisa, LS and Boudabous, A}, title = {Cultivating the uncultured: growing the recalcitrant cluster-2 Frankia strains.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {13112}, pmid = {26287281}, issn = {2045-2322}, mesh = {Bacterial Proteins/metabolism ; Cell Culture Techniques/*methods ; Cells, Cultured ; Frankia/genetics/*growth &amp; development/isolation &amp; purification ; Genome, Bacterial ; Likelihood Functions ; Magnoliopsida/growth &amp; development ; Phylogeny ; Seedlings/growth &amp; development ; }, abstract = {The repeated failures reported in cultivating some microbial lineages are a major challenge in microbial ecology and probably linked, in the case of Frankia microsymbionts to atypical patterns of auxotrophy. Comparative genomics of the so far uncultured cluster-2 Candidatus Frankia datiscae Dg1, with cultivated Frankiae has revealed genome reduction, but no obvious physiological impairments. A direct physiological assay on nodule tissues from Coriaria myrtifolia infected with a closely-related strain permitted the identification of a requirement for alkaline conditions. A high pH growth medium permitted the recovery of a slow-growing actinobacterium. The strain obtained, called BMG5.1, has short hyphae, produced diazovesicles in nitrogen-free media, and fulfilled Koch's postulates by inducing effective nodules on axenically grown Coriaria spp. and Datisca glomerata. Analysis of the draft genome confirmed its close proximity to the Candidatus Frankia datiscae Dg1 genome with the absence of 38 genes (trehalose synthase, fumarylacetoacetase, etc) in BMG5.1 and the presence of 77 other genes (CRISPR, lanthionine synthase, glutathione synthetase, catalase, Na+/H+ antiporter, etc) not found in Dg1. A multi-gene phylogeny placed the two cluster-2 strains together at the root of the Frankia radiation.}, }
@article {pmid26287240, year = {2015}, author = {Cenit, MC and Olivares, M and Codoñer-Franch, P and Sanz, Y}, title = {Intestinal Microbiota and Celiac Disease: Cause, Consequence or Co-Evolution?.}, journal = {Nutrients}, volume = {7}, number = {8}, pages = {6900-6923}, pmid = {26287240}, issn = {2072-6643}, mesh = {Biological Evolution ; Celiac Disease/genetics/*microbiology ; Diet, Gluten-Free ; Dysbiosis/genetics/microbiology ; Epigenesis, Genetic ; *Gastrointestinal Microbiome ; Glutens/administration &amp; dosage ; Host-Pathogen Interactions ; Humans ; Intestines/*microbiology/physiopathology ; Probiotics ; Risk Factors ; }, abstract = {It is widely recognized that the intestinal microbiota plays a role in the initiation and perpetuation of intestinal inflammation in numerous chronic conditions. Most studies report intestinal dysbiosis in celiac disease (CD) patients, untreated and treated with a gluten-free diet (GFD), compared to healthy controls. CD patients with gastrointestinal symptoms are also known to have a different microbiota compared to patients with dermatitis herpetiformis and controls, suggesting that the microbiota is involved in disease manifestation. Furthermore, a dysbiotic microbiota seems to be associated with persistent gastrointestinal symptoms in treated CD patients, suggesting its pathogenic implication in these particular cases. GFD per se influences gut microbiota composition, and thus constitutes an inevitable confounding factor in studies conducted in CD patients. To improve our understanding of whether intestinal dysbiosis is the cause or consequence of disease, prospective studies in healthy infants at family risk of CD are underway. These studies have revealed that the CD host genotype selects for the early colonizers of the infant's gut, which together with environmental factors (e.g., breast-feeding, antibiotics, etc.) could influence the development of oral tolerance to gluten. Indeed, some CD genes and/or their altered expression play a role in bacterial colonization and sensing. In turn, intestinal dysbiosis could promote an abnormal response to gluten or other environmental CD-promoting factors (e.g., infections) in predisposed individuals. Here, we review the current knowledge of host-microbe interactions and how host genetics/epigenetics and environmental factors shape gut microbiota and may influence disease risk. We also summarize the current knowledge about the potential mechanisms of action of the intestinal microbiota and specific components that affect CD pathogenesis.}, }
@article {pmid26286513, year = {2015}, author = {de Jesus, HE and Peixoto, RS and Cury, JC and van Elsas, JD and Rosado, AS}, title = {Evaluation of soil bioremediation techniques in an aged diesel spill at the Antarctic Peninsula.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {24}, pages = {10815-10827}, doi = {10.1007/s00253-015-6919-0}, pmid = {26286513}, issn = {1432-0614}, mesh = {Antarctic Regions ; Archaea/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Biodegradation, Environmental ; Biota ; Carbon/analysis ; Denaturing Gradient Gel Electrophoresis ; *Environmental Pollution ; *Gasoline ; Hydrocarbons/analysis ; Nitrogen/analysis ; Real-Time Polymerase Chain Reaction ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {Many areas on the Antarctic continent already suffer from the direct and indirect influences of human activities. The main cause of contamination is petroleum hydrocarbons because this compound is used as a source of energy at the many research stations around the continent. Thus, the current study aims to evaluate treatments for bioremediation (biostimulation, bioaugmentation, and bioaugmentation + biostimulation) using soils from around the Brazilian Antarctic Station "Comandante Ferraz" (EACF), King George Island, Antarctic Peninsula. The experiment lasted for 45 days, and at the end of this period, chemical and molecular analyses were performed. Those analyses included the quantification of carbon and nitrogen, denaturing gradient gel electrophoresis (DGGE) analysis (with gradient denaturation), real-time PCR, and quantification of total hydrocarbons and polyaromatics. Molecular tests evaluated changes in the profile and quantity of the rrs genes of archaea and bacteria and also the alkB gene. The influence of the treatments tested was directly related to the type of soil used. The work confirmed that despite the extreme conditions found in Antarctic soils, the bacterial strains degraded hydrocarbons and bioremediation treatments directly influenced the microbial communities present in these soils even in short periods. Although the majority of the previous studies demonstrate that the addition of fertilizer seems to be most effective at promoting bioremediation, our results show that for some conditions, autochthonous bioaugmentation (ABA) treatment is indicated. This work highlights the importance of understanding the processes of recovery of contaminated environments in polar regions because time is crucial to the soil recovery and to choosing the appropriate treatment.}, }
@article {pmid26284671, year = {2015}, author = {Medema, MH and Fischbach, MA}, title = {Computational approaches to natural product discovery.}, journal = {Nature chemical biology}, volume = {11}, number = {9}, pages = {639-648}, pmid = {26284671}, issn = {1552-4469}, support = {R01 AI101018/AI/NIAID NIH HHS/United States ; DP2 OD007290/OD/NIH HHS/United States ; R01 DK101674/DK/NIDDK NIH HHS/United States ; GM081879/GM/NIGMS NIH HHS/United States ; AI101018/AI/NIAID NIH HHS/United States ; DK101674/DK/NIDDK NIH HHS/United States ; P50 GM081879/GM/NIGMS NIH HHS/United States ; OD007290/OD/NIH HHS/United States ; }, mesh = {Algorithms ; Alkaloids/biosynthesis ; Bacteria/*genetics/metabolism ; Biological Products/chemistry/*metabolism ; Computational Biology/instrumentation/*methods ; Data Mining ; Databases, Genetic ; Fungi/*genetics/metabolism ; *Metagenome ; Multigene Family ; Peptide Biosynthesis, Nucleic Acid-Independent ; Peptides/metabolism ; Plants/*genetics/metabolism ; Polyketides/metabolism ; Polysaccharides/biosynthesis ; Terpenes/metabolism ; }, abstract = {Starting with the earliest Streptomyces genome sequences, the promise of natural product genome mining has been captivating: genomics and bioinformatics would transform compound discovery from an ad hoc pursuit to a high-throughput endeavor. Until recently, however, genome mining has advanced natural product discovery only modestly. Here, we argue that the development of algorithms to mine the continuously increasing amounts of (meta)genomic data will enable the promise of genome mining to be realized. We review computational strategies that have been developed to identify biosynthetic gene clusters in genome sequences and predict the chemical structures of their products. We then discuss networking strategies that can systematize large volumes of genetic and chemical data and connect genomic information to metabolomic and phenotypic data. Finally, we provide a vision of what natural product discovery might look like in the future, specifically considering longstanding questions in microbial ecology regarding the roles of metabolites in interspecies interactions.}, }
@article {pmid26284661, year = {2015}, author = {Medema, MH and Kottmann, R and Yilmaz, P and Cummings, M and Biggins, JB and Blin, K and de Bruijn, I and Chooi, YH and Claesen, J and Coates, RC and Cruz-Morales, P and Duddela, S and Düsterhus, S and Edwards, DJ and Fewer, DP and Garg, N and Geiger, C and Gomez-Escribano, JP and Greule, A and Hadjithomas, M and Haines, AS and Helfrich, EJ and Hillwig, ML and Ishida, K and Jones, AC and Jones, CS and Jungmann, K and Kegler, C and Kim, HU and Kötter, P and Krug, D and Masschelein, J and Melnik, AV and Mantovani, SM and Monroe, EA and Moore, M and Moss, N and Nützmann, HW and Pan, G and Pati, A and Petras, D and Reen, FJ and Rosconi, F and Rui, Z and Tian, Z and Tobias, NJ and Tsunematsu, Y and Wiemann, P and Wyckoff, E and Yan, X and Yim, G and Yu, F and Xie, Y and Aigle, B and Apel, AK and Balibar, CJ and Balskus, EP and Barona-Gómez, F and Bechthold, A and Bode, HB and Borriss, R and Brady, SF and Brakhage, AA and Caffrey, P and Cheng, YQ and Clardy, J and Cox, RJ and De Mot, R and Donadio, S and Donia, MS and van der Donk, WA and Dorrestein, PC and Doyle, S and Driessen, AJ and Ehling-Schulz, M and Entian, KD and Fischbach, MA and Gerwick, L and Gerwick, WH and Gross, H and Gust, B and Hertweck, C and Höfte, M and Jensen, SE and Ju, J and Katz, L and Kaysser, L and Klassen, JL and Keller, NP and Kormanec, J and Kuipers, OP and Kuzuyama, T and Kyrpides, NC and Kwon, HJ and Lautru, S and Lavigne, R and Lee, CY and Linquan, B and Liu, X and Liu, W and Luzhetskyy, A and Mahmud, T and Mast, Y and Méndez, C and Metsä-Ketelä, M and Micklefield, J and Mitchell, DA and Moore, BS and Moreira, LM and Müller, R and Neilan, BA and Nett, M and Nielsen, J and O'Gara, F and Oikawa, H and Osbourn, A and Osburne, MS and Ostash, B and Payne, SM and Pernodet, JL and Petricek, M and Piel, J and Ploux, O and Raaijmakers, JM and Salas, JA and Schmitt, EK and Scott, B and Seipke, RF and Shen, B and Sherman, DH and Sivonen, K and Smanski, MJ and Sosio, M and Stegmann, E and Süssmuth, RD and Tahlan, K and Thomas, CM and Tang, Y and Truman, AW and Viaud, M and Walton, JD and Walsh, CT and Weber, T and van Wezel, GP and Wilkinson, B and Willey, JM and Wohlleben, W and Wright, GD and Ziemert, N and Zhang, C and Zotchev, SB and Breitling, R and Takano, E and Glöckner, FO}, title = {Minimum Information about a Biosynthetic Gene cluster.}, journal = {Nature chemical biology}, volume = {11}, number = {9}, pages = {625-631}, pmid = {26284661}, issn = {1552-4469}, support = {BB/J014478/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L014130/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 AI113766/AI/NIAID NIH HHS/United States ; BB/E021611/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M017702/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M028860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 AI037027/AI/NIAID NIH HHS/United States ; R37 AI016935/AI/NIAID NIH HHS/United States ; BBS/B/07071/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; T32 GM067550/GM/NIGMS NIH HHS/United States ; BBS/E/J/00000614/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 GM107550/GM/NIGMS NIH HHS/United States ; R01 GM123998/GM/NIGMS NIH HHS/United States ; R01 CA108874/CA/NCI NIH HHS/United States ; }, mesh = {Alkaloids/biosynthesis ; Bacteria/*genetics/metabolism ; Computational Biology/*standards ; Databases, Genetic ; Fungi/*genetics/metabolism ; Genetic Markers ; International Cooperation ; Metagenome ; *Multigene Family ; Peptide Biosynthesis, Nucleic Acid-Independent ; Peptides/metabolism ; Plants/*genetics/metabolism ; Polyketides/metabolism ; Polysaccharides/biosynthesis ; *Protein Biosynthesis ; Terminology as Topic ; Terpenes/metabolism ; }, }
@article {pmid26284443, year = {2016}, author = {Fillol, M and Auguet, JC and Casamayor, EO and Borrego, CM}, title = {Insights in the ecology and evolutionary history of the Miscellaneous Crenarchaeotic Group lineage.}, journal = {The ISME journal}, volume = {10}, number = {3}, pages = {665-677}, pmid = {26284443}, issn = {1751-7370}, mesh = {*Biological Evolution ; *Ecosystem ; Euryarchaeota/classification/*genetics/isolation &amp; purification ; Fresh Water/*microbiology ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Members of the archaeal Miscellaneous Crenarchaeotic Group (MCG) are among the most successful microorganisms on the planet. During its evolutionary diversification, this very diverse group has managed to cross the saline-freshwater boundary, one of the most important evolutionary barriers structuring microbial communities. However, the current understanding on the ecological significance of MCG in freshwater habitats is scarce and the evolutionary relationships between freshwater and saline MCG remains poorly known. Here, we carried out molecular phylogenies using publicly available 16S rRNA gene sequences from various geographic locations to investigate the distribution of MCG in freshwater and saline sediments and to evaluate the implications of saline-freshwater transitions during the diversification events. Our approach provided a robust ecological framework in which MCG archaea appeared as a core generalist group in the sediment realm. However, the analysis of the complex intragroup phylogeny of the 21 subgroups currently forming the MCG lineage revealed that distinct evolutionary MCG subgroups have arisen in marine and freshwater sediments suggesting the occurrence of adaptive evolution specific to each habitat. The ancestral state reconstruction analysis indicated that this segregation was mainly due to the occurrence of a few saline-freshwater transition events during the MCG diversification. In addition, a network analysis showed that both saline and freshwater MCG recurrently co-occur with archaea of the class Thermoplasmata in sediment ecosystems, suggesting a potentially relevant trophic connection between the two clades.}, }
@article {pmid26284061, year = {2015}, author = {Ganendra, G and Wang, J and Ramos, JA and Derluyn, H and Rahier, H and Cnudde, V and Ho, A and Boon, N}, title = {Biogenic concrete protection driven by the formate oxidation by Methylocystis parvus OBBP.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {786}, pmid = {26284061}, issn = {1664-302X}, abstract = {The effectiveness of Microbiologically Induced Carbonate Precipitation (MICP) from the formate oxidation by Methylocystis parvus OBBP as an alternative process for concrete protection was investigated. MICP was induced on Autoclaved Aerated Concrete (AAC), the model material, by immersing the material in 10(9) M. parvus cells mL(-1) containing 5 g L(-1) of calcium formate. A 2 days immersion of the material gave the maximum weight increase of the specimens (38 ± 19 mg) and this was likely due to the deposition of calcium carbonate, biomass, and unconverted calcium formate. The solid deposition mainly occurred in the micropores of the specimen, close to the outer surface. A significantly lower water absorption was observed in the bacterially treated specimens compared to the non-treated ones (up to 2.92 ± 0.91 kg m(-2)) and this could be attributed to the solid deposition. However, the sonication test demonstrated that the bacterial treatment did not give a consolidating effect to the material. Overall, compared to the currently employed urea hydrolysis process, the formate-based MICP by M. parvus offers a more environmentally friendly approach for the biotechnological application to protect concrete.}, }
@article {pmid26284038, year = {2015}, author = {Penton, CR and St Louis, D and Pham, A and Cole, JR and Wu, L and Luo, Y and Schuur, EA and Zhou, J and Tiedje, JM}, title = {Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {746}, pmid = {26284038}, issn = {1664-302X}, abstract = {Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming is under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.}, }
@article {pmid26282776, year = {2015}, author = {Kim, SY and Park, CK and Gwon, HS and Khan, MI and Kim, PJ}, title = {Optimizing the harvesting stage of rye as a green manure to maximize nutrient production and to minimize methane production in mono-rice paddies.}, journal = {The Science of the total environment}, volume = {537}, number = {}, pages = {441-446}, doi = {10.1016/j.scitotenv.2015.07.061}, pmid = {26282776}, issn = {1879-1026}, mesh = {Agriculture/*methods ; Air Pollutants/*analysis ; *Manure ; Methane/*analysis ; Nitrogen/analysis ; *Oryza ; }, abstract = {Rye (Secale cerealis) has been widely cultivated to improve soil quality in temperate paddies. However, its biomass incorporation can significantly increase greenhouse gas emissions, particularly the emission of methane (CH4), during rice cultivation. The chemical composition and productivity of cover crop biomass may vary at different growing stages. Therefore, nutrient productivity and CH4 production potential might be controlled by selecting the optimum harvesting stage. To investigate the effect of rye harvesting stage on nutrient productivity and CH4 production potential, rye was harvested at different growing stages, from the flowering stage to the maturing stage, for seven weeks. The chemical composition and biomass productivity of rye were investigated. CH4 production was measured by laboratory incubation, and CH4 production potential was estimated to determine the real impact on CH4 dynamics in rice soils. Rye biomass increased with plant maturation, but nutrient productivities such as N (nitrogen), P2O5, and K2O were maximized at the flowering stage. The contents of cellulose and lignin increased significantly as plants matured, but the total N, labile organic carbon (C), and hot and cold water-extractable organic C clearly decreased. Soils were mixed with 0.3% (wt wt(-1) on dry weight) air-dried biomass and incubated to measure the maximum CH4 productivity at 30 °C under flooded conditions. Maximum CH4 productivity was significantly correlated with increasing labile organic C and protein content, but it was negatively correlated with total organic C, cellulose, and lignin content. CH4 production potentials were significantly increased up to the pre-maturing stage (220 DAS) and remained unchanged thereafter. As a result, CH4 production potential per N productivity was the lowest at the late flowering stage (198-205 DAS), which could be the best harvesting stage as well as the most promising stage for increasing nutrient production and decreasing GHG emissions in temperate mono-rice paddy soils.}, }
@article {pmid26280746, year = {2016}, author = {Tu, Q and Zhou, X and He, Z and Xue, K and Wu, L and Reich, P and Hobbie, S and Zhou, J}, title = {The Diversity and Co-occurrence Patterns of N2-Fixing Communities in a CO2-Enriched Grassland Ecosystem.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {604-615}, pmid = {26280746}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; *Biodiversity ; Carbon Dioxide/*metabolism ; Ecosystem ; Grassland ; Nitrogen/*metabolism ; Nitrogen Fixation ; Phylogeny ; *Soil Microbiology ; }, abstract = {Diazotrophs are the major organismal group responsible for atmospheric nitrogen (N2) fixation in natural ecosystems. The extensive diversity and structure of N2-fixing communities in grassland ecosystems and their responses to increasing atmospheric CO2 remain to be further explored. Through pyrosequencing of nifH gene amplicons and extraction of nifH genes from shotgun metagenomes, coupled with co-occurrence ecological network analysis approaches, we comprehensively analyzed the diazotrophic community in a grassland ecosystem exposed to elevated CO2 (eCO2) for 12 years. Long-term eCO2 increased the abundance of nifH genes but did not change the overall nifH diversity and diazotrophic community structure. Taxonomic and phylogenetic analysis of amplified nifH sequences suggested a high diversity of nifH genes in the soil ecosystem, the majority belonging to nifH clusters I and II. Co-occurrence ecological network analysis identified different co-occurrence patterns for different groups of diazotrophs, such as Azospirillum/Actinobacteria, Mesorhizobium/Conexibacter, and Bradyrhizobium/Acidobacteria. This indicated a potential attraction of non-N2-fixers by diazotrophs in the soil ecosystem. Interestingly, more complex co-occurrence patterns were found for free-living diazotrophs than commonly known symbiotic diazotrophs, which is consistent with the physical isolation nature of symbiotic diazotrophs from the environment by root nodules. The study provides novel insights into our understanding of the microbial ecology of soil diazotrophs in natural ecosystems.}, }
@article {pmid26280745, year = {2016}, author = {Mueller, RC and Gallegos-Graves, L and Zak, DR and Kuske, CR}, title = {Assembly of Active Bacterial and Fungal Communities Along a Natural Environmental Gradient.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {57-67}, pmid = {26280745}, issn = {1432-184X}, mesh = {Acer/growth &amp; development/*microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Forests ; Fungi/classification/genetics/*isolation &amp; purification ; Phylogeny ; Plant Leaves/microbiology ; }, abstract = {Dormancy is thought to promote biodiversity within microbial communities, but how assembly of the active community responds to changes in environmental conditions is unclear. To measure the active and dormant communities of bacteria and fungi colonizing decomposing litter in maple forests, we targeted ribosomal genes and transcripts across a natural environmental gradient. Within bacterial and fungal communities, the active and dormant communities were phylogenetically distinct, but patterns of phylogenetic clustering varied. For bacteria, active communities were significantly more clustered than dormant communities, while the reverse was found for fungi. The proportion of operational taxonomic units (OTUs) classified as active and the degree of phylogenetic clustering of the active bacterial communities declined with increasing pH and decreasing C/N. No significant correlations were found for the fungal community. The opposing pattern of phylogenetic clustering in dormant and active communities and the differential response of active communities to environmental gradients suggest that dormancy differentially structures bacterial and fungal communities.}, }
@article {pmid26276410, year = {2016}, author = {Wang, J and Bao, JT and Li, XR and Liu, YB}, title = {Molecular Ecology of nifH Genes and Transcripts Along a Chronosequence in Revegetated Areas of the Tengger Desert.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {150-163}, pmid = {26276410}, issn = {1432-184X}, mesh = {Bacterial Proteins/*genetics ; Biodiversity ; Bryophyta/growth &amp; development/microbiology ; Cyanobacteria/classification/*enzymology/genetics/isolation &amp; purification ; Desert Climate ; Ecosystem ; Lichens/growth &amp; development/microbiology ; Oxidoreductases/*genetics ; Phylogeny ; Soil Microbiology ; }, abstract = {The colonization and succession of diazotrophs are essential for the development of organic soil layers in desert. We examined the succession of diazotrophs in the well-established revegetated areas representing a chronosequence of 0 year (control), 22 years (restored artificially since 1981), 57 years (restored artificially since 1956), and more than 100 years (restored naturally) to determine the community assembly and active expression of diazotrophs. The pyrosequencing data revealed that Alphaproteobacteria-like diazotrophs predominated in the topsoil of our mobile dune site, while cyanobacterial diazotrophs predominated in the revegetated sites. The cyanobacterial diazotrophs were primarily composed of the heterocystous genera Anabaena, Calothrix, Cylindrospermum, Nodularia, Nostoc, Trichormus, and Mastigocladus. Almost all the nifH sequences belonged to the Cyanobacteria phylum (all the relative abundance values >99.1 %) at transcript level and all the active cyanobacterial diazotrophs distributed in the families Nostocaceae and Rivulariaceae. The most dominant active cyanobacterial genus was Cylindrospermum in all the samples. The rank abundance and community analyses demonstrated that most of the diazotrophic diversity originated from the "rare" species, and all the DNA-based diazotrophic libraries were richer and more diverse than their RNA-based counterparts in the revegetated sites. Significant differences in the diazotrophic community and their active population composition were observed among the four research sites. Samples from the 1981-revegetating site (predominated by cyanobacterial crusts) showed the highest nitrogenase activity, followed by samples from the naturally revegetating site (predominated by lichen crusts), the 1956-revegetating site (predominated by moss crusts), and the mobile dune site (without crusts). Collectively, our data highlight the importance of nitrogen fixation by the primary successional desert topsoil and suggest that the N2-fixing cyanobacteria are the key diazotrophs to the nitrogen budget and the development of topsoil in desert, which is critical for the succession of the degraded terrestrial ecosystems.}, }
@article {pmid26276108, year = {2015}, author = {Bååth, E and Kritzberg, E}, title = {pH tolerance in freshwater bacterioplankton: trait variation of the community as measured by leucine incorporation.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {21}, pages = {7411-7419}, pmid = {26276108}, issn = {1098-5336}, mesh = {Bacteria/*drug effects/growth &amp; development/metabolism ; Fresh Water/chemistry/*microbiology ; Hydrogen-Ion Concentration ; Lakes/*microbiology ; Leucine/metabolism ; Microbial Viability/*drug effects ; Rivers/*microbiology ; }, abstract = {pH is an important factor determining bacterial community composition in soil and water. We have directly determined the community tolerance (trait variation) to pH in communities from 22 lakes and streams ranging in pH from 4 to 9 using a growth-based method not relying on distinguishing between individual populations. The pH in the water samples was altered to up to 16 pH values, covering in situ pH ± 2.5 U, and the tolerance was assessed by measuring bacterial growth (Leu incorporation) instantaneously after pH adjustment. The resulting unimodal response curves, reflecting community tolerance to pH, were well modeled with a double logistic equation (mean R(2) = 0.97). The optimal pH for growth (pHopt) among the bacterial communities was closely correlated with in situ pH, with a slope (0.89 ± 0.099) close to unity. The pH interval, in which growth was ≥90% of that at pHopt, was 1.1 to 3 pH units wide (mean 2.0 pH units). Tolerance response curves of communities originating from circum-neutral pH were symmetrical, whereas in high-pH (8.9) and especially in low-pH (<5.5) waters, asymmetric tolerance curves were found. In low-pH waters, decreasing pH was more detrimental for bacterial growth than increasing pH, with a tendency for the opposite for high-pH waters. A pH tolerance index, using the ratio of growth at only two pH values (pH 4 and 8), was closely related to pHopt (R(2) = 0.83), allowing for easy determination of pH tolerance during rapid changes in pH.}, }
@article {pmid26273600, year = {2015}, author = {Merlino, G and Balloi, A and Marzorati, M and Mapelli, F and Rizzi, A and Lavazza, D and de Ferra, F and Carpani, G and Daffonchio, D}, title = {Diverse Reductive Dehalogenases Are Associated with Clostridiales-Enriched Microcosms Dechlorinating 1,2-Dichloroethane.}, journal = {BioMed research international}, volume = {2015}, number = {}, pages = {242856}, pmid = {26273600}, issn = {2314-6141}, mesh = {Biodegradation, Environmental ; Chlorine/chemistry/isolation &amp; purification/metabolism ; Clostridiales/*classification/*enzymology/genetics ; Ethylene Dichlorides/chemistry/isolation &amp; purification/*metabolism ; Groundwater/*microbiology ; Halogenation ; Hydrolases/*metabolism ; Microbiota/physiology ; Oxidation-Reduction ; Species Specificity ; Water Pollutants, Chemical/isolation &amp; purification/*metabolism ; Water Purification/methods ; }, abstract = {The achievement of successful biostimulation of active microbiomes for the cleanup of a polluted site is strictly dependent on the knowledge of the key microorganisms equipped with the relevant catabolic genes responsible for the degradation process. In this work, we present the characterization of the bacterial community developed in anaerobic microcosms after biostimulation with the electron donor lactate of groundwater polluted with 1,2-dichloroethane (1,2-DCA). Through a multilevel analysis, we have assessed (i) the structural analysis of the bacterial community; (ii) the identification of putative dehalorespiring bacteria; (iii) the characterization of functional genes encoding for putative 1,2-DCA reductive dehalogenases (RDs). Following the biostimulation treatment, the structure of the bacterial community underwent a notable change of the main phylotypes, with the enrichment of representatives of the order Clostridiales. Through PCR targeting conserved regions within known RD genes, four novel variants of RDs previously associated with the reductive dechlorination of 1,2-DCA were identified in the metagenome of the Clostridiales-dominated bacterial community.}, }
@article {pmid26272556, year = {2015}, author = {Collingro, A and Kostanjšek, R and Toenshoff, ER and Schulz, F and Schuster, L and Domann, D and Horn, M}, title = {Draft Genome Sequence of "Candidatus Hepatoplasma crinochetorum" Ps, a Bacterial Symbiont in the Hepatopancreas of the Terrestrial Isopod Porcellio scaber.}, journal = {Genome announcements}, volume = {3}, number = {4}, pages = {}, pmid = {26272556}, issn = {2169-8287}, support = {281633/ERC_/European Research Council/International ; P 22533/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {"Candidatus Hepatoplasma crinochetorum" Ps is an extracellular symbiont residing in the hepatopancreas of the terrestrial isopod Porcellio scaber. Its genome is highly similar to that of the close relative "Ca. Hepatoplasma crinochetorum" Av from Armadillidium vulgare. However, instead of a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas system, it encodes a type I restriction modification system.}, }
@article {pmid26272401, year = {2015}, author = {Waldron, D}, title = {Microbial ecology: Sorting out viral dark matter.}, journal = {Nature reviews. Microbiology}, volume = {13}, number = {9}, pages = {526-527}, pmid = {26272401}, issn = {1740-1534}, mesh = {Archaea/*genetics/*virology ; Bacteria/*genetics/*virology ; *Genome, Microbial ; *Host-Pathogen Interactions ; Viruses/*genetics ; }, }
@article {pmid26271741, year = {2016}, author = {Bataille, A and Lee-Cruz, L and Tripathi, B and Kim, H and Waldman, B}, title = {Microbiome Variation Across Amphibian Skin Regions: Implications for Chytridiomycosis Mitigation Efforts.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {221-232}, pmid = {26271741}, issn = {1432-184X}, mesh = {Animals ; Anura/*microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Chytridiomycota/*physiology ; *Microbiota ; Mycoses/microbiology/*veterinary ; Skin/*microbiology ; }, abstract = {Cutaneous bacteria may play an important role in the resistance of amphibians to the pathogenic fungus Batrachochytrium dendrobatidis (Bd). Microbial communities resident on hosts' skin show topographical diversity mapping to skin features, as demonstrated by studies of the human microbiome. We examined skin microbiomes of wild and captive fire-bellied toads (Bombina orientalis) for differences across their body surface. We found that bacterial communities differed between ventral and dorsal skin. Wild toads showed slightly higher bacterial richness and diversity in the dorsal compared to the ventral region. On the other hand, captive toads hosted a higher richness and diversity of bacteria on their ventral than their dorsal skin. Microbial community composition and relative abundance of major bacterial taxonomic groups also differed between ventral and dorsal skin in all populations. Furthermore, microbiome diversity patterns varied as a function of their Bd infection status in wild toads. Bacterial richness and diversity was greater, and microbial community structure more complex, in wild than captive toads. The results suggest that bacterial community structure is influenced by microhabitats associated with skin regions. These local communities may be differentially modified when interacting with environmental bacteria and Bd. A better understanding of microbiome variation across skin regions will be needed to assess how the skin microbiota affects the abilities of amphibian hosts to resist Bd infection, especially in captive breeding programs.}, }
@article {pmid26271740, year = {2016}, author = {Rietl, AJ and Overlander, ME and Nyman, AJ and Jackson, CR}, title = {Microbial Community Composition and Extracellular Enzyme Activities Associated with Juncus roemerianus and Spartina alterniflora Vegetated Sediments in Louisiana Saltmarshes.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {290-303}, pmid = {26271740}, issn = {1432-184X}, mesh = {Bacteria/classification/*enzymology/genetics/*isolation &amp; purification ; Bacterial Proteins/analysis/genetics/metabolism ; Biodiversity ; Fungal Proteins/analysis/genetics/metabolism ; Fungi/classification/*enzymology/genetics/*isolation &amp; purification ; Geologic Sediments/chemistry/*microbiology ; Louisiana ; Magnoliopsida/growth &amp; development/*microbiology ; Phylogeny ; Poaceae/growth &amp; development/*microbiology ; Wetlands ; }, abstract = {Saltmarshes are typically dominated by perennial grasses with large underground rhizome systems that can change local sediment conditions and be important in shaping the sediment microbial community. Factors such as salinity that control plant zonation in saltmarshes are also likely to influence the microbial community, but little is known as to whether microbial communities share distribution patterns with plants in these systems. To determine the extent to which microbial assemblages are influenced by saltmarsh plant communities, as well as to examine patterns in microbial community structure at local and regional scales, we sampled sediments at three saltmarshes in Louisiana, USA. All three systems exhibit a patchy distribution of Juncus roemerianus stands within a Spartina alterniflora marsh. Sediment samples were collected from the interior of several J. roemerianus stands as well as from the S. alterniflora matrix. Samples were assayed for extracellular enzyme activity and DNA extracted to determine microbial community composition. Denaturing gradient gel electrophoresis of rRNA gene fragments was used to determine regional patterns in bacterial, archaeal, and fungal assemblages, while Illumina sequencing was used to examine local, vegetation-driven, patterns in community structure at one site. Both enzyme activity and microbial community structure were primarily influenced by regional site. Within individual saltmarshes, bacterial and archaeal communities differed between J. roemerianus and S. alterniflora vegetated sediments, while fungal communities did not. These results highlight the importance of the plant community in shaping the sediment microbial community in saltmarshes but also demonstrate that regional scale factors are at least as important.}, }
@article {pmid26266896, year = {2015}, author = {Feng, H and Liang, Y and Guo, K and Long, Y and Cong, Y and Shen, D}, title = {Addition of nitrite enhances the electrochemical defluorination of 2-fluoroaniline.}, journal = {Journal of hazardous materials}, volume = {300}, number = {}, pages = {607-614}, doi = {10.1016/j.jhazmat.2015.06.071}, pmid = {26266896}, issn = {1873-3336}, abstract = {This study introduces a novel approach that uses the interaction of pollutants with added nitrite to produce diazonium salts, which cause in situ self-assembly of the pollutants on carbon electrodes, to improve their 2-fluoroaniline (2-FA) defluorination and removal performance. The 2-FA degradation performance, electrode properties, electrochemical properties and degradation pathway were investigated. The reactor containing NO2(-) achieved a 2-FA removal efficiency of 90.1% and a defluorination efficiency of 38% within 48 h, 1.4 and 2.3 times higher than the corresponding results achieved without NO2(-), respectively. The residual NO2(-) was less than 0.5mg/L in the reactor containing added NO2(-), which would not cause serious secondary pollution. Scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS) results proved that the carbon anode surface was successfully modified with benzene polymer, and electrochemical tests confirmed that the electrochemical activity of the modified anode was enhanced significantly. The C-F bond was weakened by the effect of the positive charge of the benzenediazonium groups, and the high electrochemical activity of the carbon anode enhanced the electrochemical performance of the system to accelerate defluorination. Thus, the present electrical method involving nitrite nitrogen is very promising for the treatment of wastewater containing fluoroaniline compounds.}, }
@article {pmid26262816, year = {2016}, author = {Saunders, AM and Albertsen, M and Vollertsen, J and Nielsen, PH}, title = {The activated sludge ecosystem contains a core community of abundant organisms.}, journal = {The ISME journal}, volume = {10}, number = {1}, pages = {11-20}, pmid = {26262816}, issn = {1751-7370}, mesh = {Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Denmark ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Wastewater/*microbiology ; }, abstract = {Understanding the microbial ecology of a system requires that the observed population dynamics can be linked to their metabolic functions. However, functional characterization is laborious and the choice of organisms should be prioritized to those that are frequently abundant (core) or transiently abundant, which are therefore putatively make the greatest contribution to carbon turnover in the system. We analyzed the microbial communities in 13 Danish wastewater treatment plants with nutrient removal in consecutive years and a single plant periodically over 6 years, using Illumina sequencing of 16S ribosomal RNA amplicons of the V4 region. The plants contained a core community of 63 abundant genus-level operational taxonomic units (OTUs) that made up 68% of the total reads. A core community consisting of abundant OTUs was also observed within the incoming wastewater to three plants. The net growth rate for individual OTUs was quantified using mass balance, and it was found that 10% of the total reads in the activated sludge were from slow or non-growing OTUs, and that their measured abundance was primarily because of immigration with the wastewater. Transiently abundant organisms were also identified. Among them the genus Nitrotoga (class Betaproteobacteria) was the most abundant putative nitrite oxidizer in a number of activated sludge plants, which challenges previous assumptions that Nitrospira (phylum Nitrospirae) are the primary nitrite-oxidizers in activated sludge systems with nutrient removal.}, }
@article {pmid26262673, year = {2016}, author = {Kamiloglu, S and Capanoglu, E and Bilen, FD and Gonzales, GB and Grootaert, C and Van de Wiele, T and Van Camp, J}, title = {Bioaccessibility of Polyphenols from Plant-Processing Byproducts of Black Carrot (Daucus carota L.).}, journal = {Journal of agricultural and food chemistry}, volume = {64}, number = {12}, pages = {2450-2458}, doi = {10.1021/acs.jafc.5b02640}, pmid = {26262673}, issn = {1520-5118}, mesh = {Anthocyanins/analysis ; Antioxidants/analysis ; Chromatography, High Pressure Liquid ; Daucus carota/*chemistry ; Digestion/physiology ; Food Handling/methods ; Fruit/chemistry ; Molecular Structure ; Plants, Medicinal/*chemistry ; Polyphenols/*analysis/metabolism ; Turkey ; }, abstract = {Plant-processing byproducts of black carrot represent an important disposal problem for the industry; however, they are also promising sources of polyphenols, especially anthocyanins. The present study focused on the changes in polyphenols from black carrot, peel, and pomace during in vitro gastrointestinal digestion. Total phenolic content (TPC), total monomeric anthocyanin content (TMAC), and total antioxidant capacity (TAC) were determined using spectrophotometric methods, whereas identification and quantification of polyphenols were carried out using UPLC-ESI-MS(E) and HPLC-DAD, respectively. TPC, TMAC, and TAC significantly decreased (23-82%) as a result of in vitro gastrointestinal digestion. Nevertheless, the amount of pomace anthocyanins released at all stages of in vitro gastrointestinal digestion was higher than black carrot anthocyanins, suggesting that pomace may be a better source of bioaccessible anthocyanins. Overall, the current study highlighted black carrot byproducts as substantial sources of polyphenols, which may be used to enrich food products.}, }
@article {pmid26260060, year = {2015}, author = {Gonzalez-Martinez, A and Osorio, F and Morillo, JA and Rodriguez-Sanchez, A and Gonzalez-Lopez, J and Abbas, BA and van Loosdrecht, MC}, title = {Comparison of bacterial diversity in full scale anammox bioreactors operated under different conditions.}, journal = {Biotechnology progress}, volume = {31}, number = {6}, pages = {1464-1472}, doi = {10.1002/btpr.2151}, pmid = {26260060}, issn = {1520-6033}, mesh = {Bioreactors/*microbiology ; Cluster Analysis ; *Microbial Consortia ; Nitrogen/*isolation &amp; purification/metabolism ; Nitrogen Cycle ; Wastewater/*chemistry ; Water Purification/*methods ; }, abstract = {Bacterial community structure of full-scale anammox bioreactor is still mainly unknown. It has never been analyzed whether different anammox bioreactor configurations might result in the development of different bacterial community structures among these systems. In this work, the bacterial community structure of six full-scale autotrophic nitrogen removal bioreactors located in The Netherlands and China operating under three different technologies and with different influent wastewater characteristics was studied by the means of pyrotag sequencing evaluation of the bacterial assemblage yielded a great diversity in all systems. The most represented phyla were the Bacteroidetes and the Proteobacteria, followed by the Planctomycetes. 14 OTUs were shared by all bioreactors, but none of them belonged to the Brocadiales order. Statistical analysis at OTU level showed that differences in the microbial communities were high, and that the main driver of the bacterial assemblage composition was different for the distinct phyla identified in the six bioreactors, depending on bioreactor technology or influent wastewater characteristics.}, }
@article {pmid26257925, year = {2015}, author = {Youssef, NH and Couger, MB and McCully, AL and Criado, AE and Elshahed, MS}, title = {Assessing the global phylum level diversity within the bacterial domain: A review.}, journal = {Journal of advanced research}, volume = {6}, number = {3}, pages = {269-282}, pmid = {26257925}, issn = {2090-1232}, abstract = {Microbial ecology is the study of microbes in the natural environment and their interactions with each other. Investigating the nature of microorganisms residing within a specific habitat is an extremely important component of microbial ecology. Such microbial diversity surveys aim to determine the identity, physiological preferences, metabolic capabilities, and genomic features of microbial taxa within a specific ecosystem. A comprehensive review of various aspects of microbial diversity (phylogenetic, functional, and genomic diversities) in the microbial (bacterial, archaeal, and microeukaryotic) world is clearly a daunting task that could not be aptly summarized in a single review. Here, we focus on one aspect of diversity (phylogenetic diversity) in one microbial domain (the Bacteria). We restrict our analysis to the highest taxonomic rank (phylum) and attempt to investigate the extent of global phylum level diversity within the Bacteria. We present a brief historical perspective on the subject and highlight how the adaptation of molecular biological and phylogenetic approaches has greatly expanded our view of global bacterial diversity. We also summarize recent progress toward the discovery of novel bacterial phyla, present evidences that the scope of phylum level diversity in nature has hardly been exhausted, and propose novel approaches that could greatly facilitate the discovery process of novel bacterial phyla within various ecosystems.}, }
@article {pmid26257872, year = {2015}, author = {Pennekamp, F and Schtickzelle, N and Petchey, OL}, title = {BEMOVI, software for extracting behavior and morphology from videos, illustrated with analyses of microbes.}, journal = {Ecology and evolution}, volume = {5}, number = {13}, pages = {2584-2595}, pmid = {26257872}, issn = {2045-7758}, abstract = {Microbes are critical components of ecosystems and provide vital services (e.g., photosynthesis, decomposition, nutrient recycling). From the diverse roles microbes play in natural ecosystems, high levels of functional diversity result. Quantifying this diversity is challenging, because it is weakly associated with morphological differentiation. In addition, the small size of microbes hinders morphological and behavioral measurements at the individual level, as well as interactions between individuals. Advances in microbial community genetics and genomics, flow cytometry and digital analysis of still images are promising approaches. They miss out, however, on a very important aspect of populations and communities: the behavior of individuals. Video analysis complements these methods by providing in addition to abundance and trait measurements, detailed behavioral information, capturing dynamic processes such as movement, and hence has the potential to describe the interactions between individuals. We introduce BEMOVI, a package using the R and ImageJ software, to extract abundance, morphology, and movement data for tens to thousands of individuals in a video. Through a set of functions BEMOVI identifies individuals present in a video, reconstructs their movement trajectories through space and time, and merges this information into a single database. BEMOVI is a modular set of functions, which can be customized to allow for peculiarities of the videos to be analyzed, in terms of organisms features (e.g., morphology or movement) and how they can be distinguished from the background. We illustrate the validity and accuracy of the method with an example on experimental multispecies communities of aquatic protists. We show high correspondence between manual and automatic counts and illustrate how simultaneous time series of abundance, morphology, and behavior are obtained from BEMOVI. We further demonstrate how the trait data can be used with machine learning to automatically classify individuals into species and that information on movement behavior improves the predictive ability.}, }
@article {pmid26257096, year = {2015}, author = {Bin, Z and Bin, X and Zhigang, Q and Zhiqiang, C and Junwen, L and Taishi, G and Wenci, Z and Jingfeng, W}, title = {Denitrifying capability and community dynamics of glycogen accumulating organisms during sludge granulation in an anaerobic-aerobic sequencing batch reactor.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {12904}, pmid = {26257096}, issn = {2045-2322}, mesh = {Bacteria/*metabolism ; Biomass ; Bioreactors ; Carbon/chemistry/metabolism ; Denaturing Gradient Gel Electrophoresis ; Denitrification ; Glycogen/*metabolism ; In Situ Hybridization, Fluorescence ; Microscopy, Electron, Scanning ; Nitrogen/chemistry/metabolism ; Phosphorus/chemistry/metabolism ; Proteobacteria/genetics/metabolism ; Sewage/*chemistry/microbiology ; }, abstract = {Denitrifying capability of glycogen accumulating organisms (GAOs) has received great attention in environmental science and microbial ecology. Combining this ability with granule processes would be an interesting attempt. Here, a laboratory-scale sequencing batch reactor (SBR) was operated to enrich GAOs and enable sludge granulation. The results showed that the GAO granules were cultivated successfully and the granules had denitrifying capability. The batch experiments demonstrated that all NO3(-)-N could be removed or reduced, some amount of NO2(-)-N were accumulated in the reactor, and N2 was the main gaseous product. SEM analysis suggested that the granules were tightly packed with a large amount of tetrad-forming organisms (TFOs); filamentous bacteria served as the supporting structures for the granules. The microbial community structure of GAO granules was differed substantially from the inoculant conventional activated sludge. Most of the bacteria in the seed sludge grouped with members of Proteobacterium. FISH analysis confirmed that GAOs were the predominant members in the granules and were distributed evenly throughout the granular space. In contrast, PAOs were severely inhibited. Overall, cultivation of the GAO granules and utilizing their denitrifying capability can provide us with a new approach of nitrogen removal and saving more energy.}, }
@article {pmid26254065, year = {2015}, author = {Bertelkamp, C and Schoutteten, K and Vanhaecke, L and Vanden Bussche, J and Callewaert, C and Boon, N and Singhal, N and van der Hoek, JP and Verliefde, ARD}, title = {A laboratory-scale column study comparing organic micropollutant removal and microbial diversity for two soil types.}, journal = {The Science of the total environment}, volume = {536}, number = {}, pages = {632-638}, doi = {10.1016/j.scitotenv.2015.07.056}, pmid = {26254065}, issn = {1879-1026}, mesh = {Biodegradation, Environmental ; Genetic Variation ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants/*analysis ; }, abstract = {UNLABELLED: This study investigated sorption and biodegradation behaviour of 20 organic micropollutants (OMPs) in lab-scale columns filled with two types of soil (fed with the same water quality) simulating river bank filtration (RBF) under oxic conditions. Retardation factors and OMP biodegradation rates were similar for the two soils that were characterised by a different cationic exchange capacity, organic matter and sand/silt/clay content. This result was supported by the microbial community composition (richness, evenness) of the two soils that became more similar as a result of feeding both columns with the same water quality. This indicates that microbial community composition and thereby OMP removal in soils is primarily determined by the composition of the aqueous phase (organic matter quantity and quality, nutrients) rather than the soil phase. These results indicate that different RBF sites located along the same river may show similar OMP removal (in case of similar water quality and residence time).<br><br>CAPSULE: This study shows that the microbial community composition and thus OMP removal is primarily determined by the aqueous phase (water quality) rather than the soil phase.}, }
@article {pmid26253688, year = {2015}, author = {Chatterjee, SS}, title = {From covalent bonds to eco-physiological pharmacology of secondary plant metabolites.}, journal = {Biochemical pharmacology}, volume = {98}, number = {2}, pages = {269-277}, doi = {10.1016/j.bcp.2015.07.037}, pmid = {26253688}, issn = {1873-2968}, mesh = {Central Nervous System Agents/chemistry/pharmacology ; Humans ; Medicine, Ayurvedic ; Plant Extracts/*chemistry/therapeutic use ; Plants, Medicinal/*chemistry/*metabolism ; }, abstract = {Despite the availability of numerous drugs and other therapeutic modalities, the prevention and cure of over- and under-nutrition triggered metabolic and other disease states continues as a major challenge for modern medicine. Such silently progressing and eventually life-threatening diseases often accompany diverse spectrum of comorbid psychiatric disorders. Majority of the global population suffering from metabolic diseases live in economically developing or underdeveloped countries, where due to socioeconomic, cultural, and other reasons, therapies may be unavailable. Evidence from preclinical, clinical, and epidemiological studies of numerous structurally and functionally diverse secondary metabolites of plants suggest that many of these could be promising therapeutic leads for the treatment and prevention of malnutrition-associated diseases and mental health problems. The review discusses the potential therapeutic uses of secondary plant metabolites and their bacterial and mammalian catabolites based on their bioactivity profiles, with special emphasis on their modulating effects on gut microbial ecology and physiological stress responses. Based on concepts in medicinal chemistry and pharmacology considerations that evolved during the author's interactions with David Triggle, secondary plant metabolites may represent an alternative and economically feasible approach to new drugs.}, }
@article {pmid26253681, year = {2015}, author = {Auguet, O and Pijuan, M and Batista, J and Borrego, CM and Gutierrez, O}, title = {Changes in Microbial Biofilm Communities during Colonization of Sewer Systems.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {20}, pages = {7271-7280}, pmid = {26253681}, issn = {1098-5336}, mesh = {Anaerobiosis ; Archaea/*metabolism ; Bacteria/*metabolism ; Biofilms/*growth &amp; development ; Methane/metabolism ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Sulfates/metabolism ; Sulfides/metabolism ; }, abstract = {The coexistence of sulfate-reducing bacteria (SRB) and methanogenic archaea (MA) in anaerobic biofilms developed in sewer inner pipe surfaces favors the accumulation of sulfide (H2S) and methane (CH4) as metabolic end products, causing severe impacts on sewerage systems. In this study, we investigated the time course of H2S and CH4 production and emission rates during different stages of biofilm development in relation to changes in the composition of microbial biofilm communities. The study was carried out in a laboratory sewer pilot plant that mimics a full-scale anaerobic rising sewer using a combination of process data and molecular techniques (e.g., quantitative PCR [qPCR], denaturing gradient gel electrophoresis [DGGE], and 16S rRNA gene pyrotag sequencing). After 2 weeks of biofilm growth, H2S emission was notably high (290.7±72.3 mg S-H2S liter(-1) day(-1)), whereas emissions of CH4 remained low (17.9±15.9 mg COD-CH4 liter(-1) day(-1)). This contrasting trend coincided with a stable SRB community and an archaeal community composed solely of methanogens derived from the human gut (i.e., Methanobrevibacter and Methanosphaera). In turn, CH4 emissions increased after 1 year of biofilm growth (327.6±16.6 mg COD-CH4 liter(-1) day(-1)), coinciding with the replacement of methanogenic colonizers by species more adapted to sewer conditions (i.e., Methanosaeta spp.). Our study provides data that confirm the capacity of our laboratory experimental system to mimic the functioning of full-scale sewers both microbiologically and operationally in terms of sulfide and methane production, gaining insight into the complex dynamics of key microbial groups during biofilm development.}, }
@article {pmid26253507, year = {2015}, author = {Junker, RR and Keller, A}, title = {Microhabitat heterogeneity across leaves and flower organs promotes bacterial diversity.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {9}, pages = {fiv097}, doi = {10.1093/femsec/fiv097}, pmid = {26253507}, issn = {1574-6941}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Flowers/*microbiology ; Hawaii ; Microbiota ; Myrtaceae/*microbiology ; Plant Leaves/*microbiology ; Plant Nectar ; Pollination ; RNA, Ribosomal, 16S/genetics ; Trees/genetics ; }, abstract = {Eukaryote-associated microbiomes interact with their hosts in multiple manners, thereby affecting the hosts' phenotype, physical condition and behaviour. In plants, bacteria have numerous functions, with variable net effects, both in natural and agricultural systems. However, information about the composition and diversity of the bacterial communities associated with different aboveground plant organs, particularly flowers, is lacking. In addition, the relative effects of microhabitat and environmental conditions on community establishment require further attention. Here, using culture-independent methods, we determine that leaves and three floral microhabitats (nectar, stamina and styles) of Metrosideros polymorpha (Myrtaceae), a tree endemic to Hawai'i, host unique indicator communities composed of relatively abundant bacterial taxa. These indicator communities are accompanied by a large number of ubiquitous or rare bacteria with lower abundances. In our study system, the strong effect of microhabitat filtering on plant-associated community composition and bacterial richness and diversity strongly exceeds the influence of environmental effects such as precipitation, altitude, substrate age and geographic distance. Thus, the bacterial richness of aboveground plant organs is strongly underestimated when only one microhabitat, e.g. leaves, is considered. Our study represents a first step towards a comprehensive characterization of the distribution, composition and underlying factors, of plant bacterial communities, with implications for future basic and applied research on plant health, pollination and reproduction.}, }
@article {pmid26251267, year = {2015}, author = {Mariadassou, M and Pichon, S and Ebert, D}, title = {Microbial ecosystems are dominated by specialist taxa.}, journal = {Ecology letters}, volume = {18}, number = {9}, pages = {974-982}, doi = {10.1111/ele.12478}, pmid = {26251267}, issn = {1461-0248}, mesh = {Animals ; *Biodiversity ; Daphnia/microbiology ; *Ecosystem ; Geologic Sediments/microbiology ; Humans ; *Microbial Consortia ; Microbiota ; Models, Biological ; Sequence Analysis, DNA ; Water Microbiology ; Zooplankton/microbiology ; }, abstract = {Abundance and specificity are two key characteristics of species distribution and biodiversity. Theories of species assembly aim to reproduce the empirical joint patterns of specificity and abundance, with the goal to explain patterns of biodiversity across habitats. The specialist-generalist paradigm predicts that specialists should have a local advantage over generalists and thus be more abundant. We developed a specificity index to analyse abundance-specificity relationships in microbial ecosystems. By analysing microbiota spanning 23 habitats from three very different data sets covering a wide range of sequencing depths and environmental conditions, we find that habitats are consistently dominated by specialist taxa, resulting in a strong, positive correlation between abundance and specificity. This finding is consistent over several levels of taxonomic aggregation and robust to errors in abundance measures. The relationship explains why shallow sequencing captures similar β-diversity as deep sequencing, and can be sufficient to capture the habitat-specific functions of microbial communities.}, }
@article {pmid26248298, year = {2015}, author = {Esteban, DJ and Hysa, B and Bartow-McKenney, C}, title = {Temporal and Spatial Distribution of the Microbial Community of Winogradsky Columns.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0134588}, pmid = {26248298}, issn = {1932-6203}, support = {T32 AR007465/AR/NIAMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics/isolation &amp; purification/virology ; Bacteriophages/physiology ; Chloroflexi/genetics/isolation &amp; purification/virology ; Cyanobacteria/genetics/isolation &amp; purification/virology ; Ecosystem ; Geologic Sediments/*microbiology ; Light ; Photography ; RNA, Ribosomal, 16S/analysis/metabolism ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Winogradsky columns are model microbial ecosystems prepared by adding pond sediment to a clear cylinder with additional supplements and incubated with light. Environmental gradients develop within the column creating diverse niches that allow enrichment of specific bacteria. The enrichment culture can be used to study soil and sediment microbial community structure and function. In this study we used a 16S rRNA gene survey to characterize the microbial community dynamics during Winogradsky column development to determine the rate and extent of change from the source sediment community. Over a period of 60 days, the microbial community changed from the founding pond sediment population: Cyanobacteria, Chloroflexi, Nitrospirae, and Planctomycetes increased in relative abundance over time, while most Proteobacteria decreased in relative abundance. A unique, light-dependent surface biofilm community formed by 60 days that was less diverse and dominated by a few highly abundant bacteria. 67-72% of the surface community was comprised of highly enriched taxa that were rare in the source pond sediment, including the Cyanobacteria Anabaena, a member of the Gemmatimonadetes phylum, and a member of the Chloroflexi class Anaerolinea. This indicates that rare taxa can become abundant under appropriate environmental conditions and supports the hypothesis that rare taxa serve as a microbial seed bank. We also present preliminary findings that suggest that bacteriophages may be active in the Winogradsky community. The dynamics of certain taxa, most notably the Cyanobacteria, showed a bloom-and-decline pattern, consistent with bacteriophage predation as predicted in the kill-the-winner hypothesis. Time-lapse photography also supported the possibility of bacteriophage activity, revealing a pattern of colony clearance similar to formation of viral plaques. The Winogradsky column, a technique developed early in the history of microbial ecology to enrich soil microbes, may therefore be a useful model system to investigate both microbial and viral ecology.}, }
@article {pmid26247765, year = {2015}, author = {Saha, S and Badhe, N and Seuntjens, D and Vlaeminck, SE and Biswas, R and Nandy, T}, title = {Effective carbon and nutrient treatment solutions for mixed domestic-industrial wastewater in India.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {72}, number = {4}, pages = {651-657}, doi = {10.2166/wst.2015.254}, pmid = {26247765}, issn = {0273-1223}, mesh = {Anaerobiosis ; *Bioreactors ; Carbon/metabolism ; *Denitrification ; India ; Industrial Waste/analysis ; *Nitrification ; Sewage/*analysis ; Waste Disposal, Fluid/*methods ; *Wetlands ; }, abstract = {The present study evaluates effectiveness of up-flow anaerobic sludge blanket (UASB) reactor followed by two post-anaerobic treatment options, namely free-surface, up-flow constructed wetland (FUP-CW) and oxygen-limited anaerobic nitrification/denitrification (OLAND) processes in treating sewage from the peri-urban areas in India receiving illegal industrial infiltrations. The UASB studies yielded robust results towards fluctuating strength of sewage and consistently removed 87-98% chemical oxygen demand (COD) at a hydraulic retention time of 1.5-2 d. The FUP-CW removed 68.5±13% COD, 68±3% NH4+-N, 38±5% PO4(3-)-P, 97.6±5% suspended particles and 97±13% fecal coliforms. Nutrient removal was found to be limiting in FUP-CW, especially in winter. Nitrogen removal in the OLAND process were 100 times higher than the FUP-CW process. Results show that UASB followed by FUP-CW can be an excellent, decentralized sewage treatment option, except during winter when nutrient removal is limited in FUP-CW. Hence, the study proposes bio-augmentation of FUP-CW with OLAND biomass for overall improvement in the performance of UASB followed by FUP-CW process.}, }
@article {pmid26246963, year = {2015}, author = {Hoyles, L and Murphy, J and Neve, H and Heller, KJ and Turton, JF and Mahony, J and Sanderson, JD and Hudspith, B and Gibson, GR and McCartney, AL and van Sinderen, D}, title = {Klebsiella pneumoniae subsp. pneumoniae-bacteriophage combination from the caecal effluent of a healthy woman.}, journal = {PeerJ}, volume = {3}, number = {}, pages = {e1061}, pmid = {26246963}, issn = {2167-8359}, abstract = {A sample of caecal effluent was obtained from a female patient who had undergone a routine colonoscopic examination. Bacteria were isolated anaerobically from the sample, and screened against the remaining filtered caecal effluent in an attempt to isolate bacteriophages (phages). A lytic phage, named KLPN1, was isolated on a strain identified as Klebsiella pneumoniae subsp. pneumoniae (capsular type K2, rmpA (+)). This Siphoviridae phage presents a rosette-like tail tip and exhibits depolymerase activity, as demonstrated by the formation of plaque-surrounding haloes that increased in size over the course of incubation. When screened against a panel of clinical isolates of K. pneumoniae subsp. pneumoniae, phage KLPN1 was shown to infect and lyse capsular type K2 strains, though it did not exhibit depolymerase activity on such hosts. The genome of KLPN1 was determined to be 49,037 bp (50.53 %GC) in length, encompassing 73 predicted ORFs, of which 23 represented genes associated with structure, host recognition, packaging, DNA replication and cell lysis. On the basis of sequence analyses, phages KLPN1 (GenBank: KR262148) and 1513 (a member of the family Siphoviridae, GenBank: KP658157) were found to be two new members of the genus "Kp36likevirus."}, }
@article {pmid26246894, year = {2015}, author = {Wang, Q and Fish, JA and Gilman, M and Sun, Y and Brown, CT and Tiedje, JM and Cole, JR}, title = {Xander: employing a novel method for efficient gene-targeted metagenomic assembly.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {32}, pmid = {26246894}, issn = {2049-2618}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, abstract = {BACKGROUND: Metagenomics can provide important insight into microbial communities. However, assembling metagenomic datasets has proven to be computationally challenging. Current methods often assemble only fragmented partial genes.<br><br>RESULTS: We present a novel method for targeting assembly of specific protein-coding genes. This method combines a de Bruijn graph, as used in standard assembly approaches, and a protein profile hidden Markov model (HMM) for the gene of interest, as used in standard annotation approaches. These are used to create a novel combined weighted assembly graph. Xander performs both assembly and annotation concomitantly using information incorporated in this graph. We demonstrate the utility of this approach by assembling contigs for one phylogenetic marker gene and for two functional marker genes, first on Human Microbiome Project (HMP)-defined community Illumina data and then on 21 rhizosphere soil metagenomic datasets from three different crops totaling over 800&#xa0;Gbp of unassembled data. We compared our method to a recently published bulk metagenome assembly method and a recently published gene-targeted assembler and found our method produced more, longer, and higher quality gene sequences.<br><br>CONCLUSION: Xander combines gene assignment with the rapid assembly of full-length or near full-length functional genes from metagenomic data without requiring bulk assembly or post-processing to find genes of interest. HMMs used for assembly can be tailored to the targeted genes, allowing flexibility to improve annotation over generic annotation pipelines. This method is implemented as open source software and is available at https://github.com/rdpstaff/Xander_assembler.}, }
@article {pmid26246193, year = {2015}, author = {Song, C and Mazzola, M and Cheng, X and Oetjen, J and Alexandrov, T and Dorrestein, P and Watrous, J and van der Voort, M and Raaijmakers, JM}, title = {Molecular and chemical dialogues in bacteria-protozoa interactions.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {12837}, pmid = {26246193}, issn = {2045-2322}, mesh = {Lipopeptides/genetics/metabolism ; Naegleria/*genetics/*metabolism ; Pseudomonas fluorescens/*genetics/*metabolism ; Putrescine/metabolism ; Transcriptome/physiology ; }, abstract = {Protozoan predation of bacteria can significantly affect soil microbial community composition and ecosystem functioning. Bacteria possess diverse defense strategies to resist or evade protozoan predation. For soil-dwelling Pseudomonas species, several secondary metabolites were proposed to provide protection against different protozoan genera. By combining whole-genome transcriptome analyses with (live) imaging mass spectrometry (IMS), we observed multiple changes in the molecular and chemical dialogues between Pseudomonas fluorescens and the protist Naegleria americana. Lipopeptide (LP) biosynthesis was induced in Pseudomonas upon protozoan grazing and LP accumulation transitioned from homogeneous distributions across bacterial colonies to site-specific accumulation at the bacteria-protist interface. Also putrescine biosynthesis was upregulated in P. fluorescens upon predation. We demonstrated that putrescine induces protozoan trophozoite encystment and adversely affects cyst viability. This multifaceted study provides new insights in common and strain-specific responses in bacteria-protozoa interactions, including responses that contribute to bacterial survival in highly competitive soil and rhizosphere environments.}, }
@article {pmid26236305, year = {2015}, author = {Herbold, CW and Pelikan, C and Kuzyk, O and Hausmann, B and Angel, R and Berry, D and Loy, A}, title = {A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {731}, pmid = {26236305}, issn = {1664-302X}, support = {P 25111/FWF_/Austrian Science Fund FWF/Austria ; P 25700/FWF_/Austrian Science Fund FWF/Austria ; P 26127/FWF_/Austrian Science Fund FWF/Austria ; T32 HG002536/HG/NHGRI NIH HHS/United States ; }, abstract = {High throughput sequencing of phylogenetic and functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we introduce a highly adaptable and economical PCR approach to barcoding and pooling libraries of numerous target genes. In this approach, we replace gene- and sequencing platform-specific fusion primers with general, interchangeable barcoding primers, enabling nearly limitless customized barcode-primer combinations. Compared to barcoding with long fusion primers, our multiple-target gene approach is more economical because it overall requires lower number of primers and is based on short primers with generally lower synthesis and purification costs. To highlight our approach, we pooled over 900 different small-subunit rRNA and functional gene amplicon libraries obtained from various environmental or host-associated microbial community samples into a single, paired-end Illumina MiSeq run. Although the amplicon regions ranged in size from approximately 290 to 720 bp, we found no significant systematic sequencing bias related to amplicon length or gene target. Our results indicate that this flexible multiplexing approach produces large, diverse, and high quality sets of amplicon sequence data for modern studies in microbial ecology.}, }
@article {pmid26236299, year = {2015}, author = {LaRowe, DE and Amend, JP}, title = {Power limits for microbial life.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {718}, pmid = {26236299}, issn = {1664-302X}, abstract = {To better understand the origin, evolution, and extent of life, we seek to determine the minimum flux of energy needed for organisms to remain viable. Despite the difficulties associated with direct measurement of the power limits for life, it is possible to use existing data and models to constrain the minimum flux of energy required to sustain microorganisms. Here, a we apply a bioenergetic model to a well characterized marine sedimentary environment in order to quantify the amount of power organisms use in an ultralow-energy setting. In particular, we show a direct link between power consumption in this environment and the amount of biomass (cells cm(-3)) found in it. The power supply resulting from the aerobic degradation of particular organic carbon (POC) at IODP Site U1370 in the South Pacific Gyre is between ∼10(-12) and 10(-16) W cm(-3). The rates of POC degradation are calculated using a continuum model while Gibbs energies have been computed using geochemical data describing the sediment as a function of depth. Although laboratory-determined values of maintenance power do a poor job of representing the amount of biomass in U1370 sediments, the number of cells per cm(-3) can be well-captured using a maintenance power, 190 zW cell(-1), two orders of magnitude lower than the lowest value reported in the literature. In addition, we have combined cell counts and calculated power supplies to determine that, on average, the microorganisms at Site U1370 require 50-3500 zW cell(-1), with most values under ∼300 zW cell(-1). Furthermore, we carried out an analysis of the absolute minimum power requirement for a single cell to remain viable to be on the order of 1 zW cell(-1).}, }
@article {pmid26236289, year = {2015}, author = {Pepe-Ranney, C and Hall, EK}, title = {The effect of carbon subsidies on marine planktonic niche partitioning and recruitment during biofilm assembly.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {703}, pmid = {26236289}, issn = {1664-302X}, abstract = {The influence of resource availability on planktonic and biofilm microbial community membership is poorly understood. Heterotrophic bacteria derive some to all of their organic carbon (C) from photoautotrophs while simultaneously competing with photoautotrophs for inorganic nutrients such as phosphorus (P) or nitrogen (N). Therefore, C inputs have the potential to shift the competitive balance of aquatic microbial communities by increasing the resource space available to heterotrophs (more C) while decreasing the resource space available to photoautotrophs (less mineral nutrients due to increased competition from heterotrophs). To test how resource dynamics affect membership of planktonic communities and assembly of biofilm communities we amended a series of flow-through mesocosms with C to alter the availability of C among treatments. Each mesocosm was fed with unfiltered seawater and incubated with sterilized microscope slides as surfaces for biofilm formation. The highest C treatment had the highest planktonic heterotroph abundance, lowest planktonic photoautotroph abundance, and highest biofilm biomass. We surveyed bacterial 16S rRNA genes and plastid 23S rRNA genes to characterize biofilm and planktonic community membership and structure. Regardless of resource additions, biofilm communities had higher alpha diversity than planktonic communities in all mesocosms. Heterotrophic plankton communities were distinct from heterotrophic biofilm communities in all but the highest C treatment where heterotrophic plankton and biofilm communities resembled each other after 17 days. Unlike the heterotrophs, photoautotrophic plankton communities were different than photoautotrophic biofilm communities in composition in all treatments including the highest C treatment. Our results suggest that although resource amendments affect community membership and structure, microbial lifestyle (biofilm vs. planktonic) has a stronger influence on community composition.}, }
@article {pmid26234735, year = {2015}, author = {Kurland, CG and Harish, A}, title = {The phylogenomics of protein structures: The backstory.}, journal = {Biochimie}, volume = {119}, number = {}, pages = {284-302}, doi = {10.1016/j.biochi.2015.07.027}, pmid = {26234735}, issn = {1638-6183}, mesh = {Amino Acid Sequence ; Animals ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome ; Humans ; *Models, Genetic ; Mutation ; *Phylogeny ; Protein Conformation ; Protein Isoforms/chemistry/genetics/metabolism ; Protein Structure, Tertiary ; Proteome/*chemistry/genetics/metabolism ; }, abstract = {In this introductory retrospective, evolution as viewed through gene trees is inspected through a lens compounded from its founding operational assumptions. The four assumptions of the gene tree culture that are singularly important to evolutionary interpretations are: a. that protein-coding sequences are molecular fossils; b. that gene trees are equivalent to species trees; c. that the tree of life is assumed to be rooted in a simple akaryote cell implying that akaryotes are primitive, and d. that the notion that all or most incongruities between alignment-based gene trees are due to horizontal gene transfer (HGT), which includes the endosymbiotic models postulated for the origins of eukaryotes. What has been unusual about these particular assumptions is that though each was taken on board explicitly, they are defended in the face of factual challenge by a stolid disregard for the conflicting observations. The factual challenges to the mainstream gene tree-inspired evolutionary view are numerous and most convincingly summarized as: Genome trees tell a very different story. Phylogeny inferred from genomic assortments of homologous protein structural-domains does not support any one of the four principle evolutionary interpretations of gene trees: a. 3D protein domain structures are the molecular fossils of evolution, while coding sequences are transients; b. Species trees are very different from gene trees; c. The ToL is rooted in a surprisingly complex universal common ancestor (UCA) that is distinct from any specific modern descendant and d. HGT including endosymbiosis is a negligible player in genome evolution from UCA to the present.}, }
@article {pmid26234611, year = {2015}, author = {Šulčius, S and Pilkaitytė, R and Mazur-Marzec, H and Kasperovičienė, J and Ezhova, E and Błaszczyk, A and Paškauskas, R}, title = {Increased risk of exposure to microcystins in the scum of the filamentous cyanobacterium Aphanizomenon flos-aquae accumulated on the western shoreline of the Curonian Lagoon.}, journal = {Marine pollution bulletin}, volume = {99}, number = {1-2}, pages = {264-270}, doi = {10.1016/j.marpolbul.2015.07.057}, pmid = {26234611}, issn = {1879-3363}, mesh = {Aphanizomenon/pathogenicity/*physiology ; Cyanobacteria/chemistry/*physiology ; Environmental Monitoring/methods ; *Eutrophication ; Lithuania ; Marine Toxins/*analysis ; Microcystins/*analysis ; Microcystis ; Phytoplankton ; Russia ; }, abstract = {Concentration of toxic cyanobacteria blooms on the downwind shore of high recreational amenity water bodies with largely increases the risk of exposure to cyanotoxins. In this study analysis of phytoplankton structure, cyanotoxin composition and concentration was performed on cyanobacteria scum material, high- and low-density bloom samples in the Curonian Lagoon. We found that the concentration of cyanotoxins in the scum material increased from ∼30 to ∼300-fold compared to bloom samples. In Microcystis aeruginosa dominated samples microcystin-LR was present at the highest concentration, while the dominance of Planktothrix agardhii was associated with the occurrence of dmMC-RR as the major microcystin variant. The toxicological potential of cyanobacterial scums in the Curonian Lagoon is emphasized, and management by removal of these scums is proposed.}, }
@article {pmid26233669, year = {2016}, author = {Hunter-Cevera, KR and Post, AF and Peacock, EE and Sosik, HM}, title = {Diversity of Synechococcus at the Martha's Vineyard Coastal Observatory: Insights from Culture Isolations, Clone Libraries, and Flow Cytometry.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {276-289}, pmid = {26233669}, issn = {1432-184X}, mesh = {*Biodiversity ; Flow Cytometry ; Molecular Sequence Data ; Oceans and Seas ; Phycocyanin/metabolism ; Phycoerythrin/metabolism ; Phylogeny ; Seawater/*microbiology ; Synechococcus/classification/*genetics/*isolation &amp; purification/metabolism ; }, abstract = {The cyanobacterium Synechococcus is a ubiquitous, important phytoplankter across the world's oceans. A high degree of genetic diversity exists within the marine group, which likely contributes to its global success. Over 20 clades with different distribution patterns have been identified. However, we do not fully understand the environmental factors that control clade distributions. These factors are likely to change seasonally, especially in dynamic coastal systems. To investigate how coastal Synechococcus assemblages change temporally, we assessed the diversity of Synechococcus at the Martha's Vineyard Coastal Observatory (MVCO) over three annual cycles with culture-dependent and independent approaches. We further investigated the abundance of both phycoerythrin (PE)-containing and phycocyanin (PC)-only Synechococcus with a flow cytometric setup that distinguishes PC-only Synechococcus from picoeukaryotes. We found that the Synechococcus assemblage at MVCO is diverse (13 different clades identified), but dominated by clade I representatives. Many clades were only isolated during late summer and fall, suggesting more favorable conditions for isolation at this time. PC-only strains from four different clades were isolated, but these cells were only detected by flow cytometry in a few samples over the time series, suggesting they are rare at this site. Within clade I, we identified four distinct subclades. The relative abundances of each subclade varied over the seasonal cycle, and the high Synechococcus cell concentration at MVCO may be maintained by the diversity found within this clade. This study highlights the need to understand how temporal aspects of the environment affect Synechococcus community structure and cell abundance.}, }
@article {pmid26232109, year = {2015}, author = {Morzel, M and Neyraud, E and Brignot, H and Ducoroy, P and Jeannin, A and Lucchi, G and Truntzer, C and Canlet, C and Tremblay-Franco, M and Hirtz, C and Gaillard, S and Peretti, N and Feron, G}, title = {Multi-omics profiling reveals that eating difficulties developed consecutively to artificial nutrition in the neonatal period are associated to specific saliva composition.}, journal = {Journal of proteomics}, volume = {128}, number = {}, pages = {105-112}, doi = {10.1016/j.jprot.2015.07.028}, pmid = {26232109}, issn = {1876-7737}, mesh = {Feeding and Eating Disorders of Childhood/*etiology/*metabolism ; Female ; Glycomics/methods ; Humans ; Infant, Newborn ; Male ; Parenteral Nutrition/*adverse effects ; Proteomics/methods ; Saliva/*chemistry/*metabolism ; }, abstract = {Prolonged enteral or parenteral nutrition in neonatal periods sometimes results in eating difficulties persisting for years, with reduced food intake through the oral route and thereby reduced stimulation of the oral cavity. Aiming at describing the consequences on oral physiology, saliva of 21 children with eating difficulties (ED) was compared to that of 23 healthy controls, using various omics and targeted methods. Overall, despite heterogeneity within the groups (age, medication etc.), the three spectral methods (MALDI-TOF, SELDI-TOF, (1)H NMR) allowed discriminating ED and controls, confirming that oral stimulation by food intake plays a role in shaping the composition of saliva. Saliva of ED patients exhibited a lower antioxidant status and lower levels of the salivary protease inhibitors cystatins. Other discriminant features (IgA1, dimethylamine) may relate to modified oral and/or intestinal microbial ecology. Finally, salivary profiles of ED patients were partly comparable to those of subjects with exacerbated gustatory sensitivities, in particular with reduced abundance of cystatin SN and higher abundance of zinc-alpha-2-glycoprotein. Whether this translates taste hypersensitivity and contributes to the eating difficulties deserves further attention.}, }
@article {pmid26230901, year = {2016}, author = {Patel, AL and Mutlu, EA and Sun, Y and Koenig, L and Green, S and Jakubowicz, A and Mryan, J and Engen, P and Fogg, L and Chen, AL and Pombar, X and Meier, PP and Keshavarzian, A}, title = {Longitudinal Survey of Microbiota in Hospitalized Preterm Very-Low-Birth-Weight Infants.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {62}, number = {2}, pages = {292-303}, pmid = {26230901}, issn = {1536-4801}, support = {R01 NR010009/NR/NINR NIH HHS/United States ; NR010009/NR/NINR NIH HHS/United States ; }, mesh = {Bacteria/*growth &amp; development ; Birth Weight ; DNA, Bacterial/analysis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Gestational Age ; High-Throughput Nucleotide Sequencing ; *Hospitalization ; Humans ; Infant ; Infant, Newborn ; *Infant, Premature ; *Infant, Very Low Birth Weight ; *Intensive Care Units, Neonatal ; Longitudinal Studies ; Male ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {OBJECTIVES: The aim of the present study was to examine the changes in bacteria in hospitalized preterm infants during the first month of life.<br><br>METHODS: Rectal swabs were collected daily from 12 preterm infants. DNA was extracted from swabs from day of birth and weekly thereafter. Bacterial taxa were identified with next generation sequencing using universal bacterial primers targeted at the 16S ribosomal DNA on a 454 Roche titanium platform. Sequences were clustered into operational taxonomic units, and taxonomy was assigned against the Greengenes databank using Quantitative Insights Into Microbial Ecology version 1.4. Quantitative polymerase chain reaction was used to determine the abundance of Bifidobacterium spp. Functional assessment of the microbiome was performed with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt).<br><br>RESULTS: Average birth weight and gestational age were 1055 g and 28 weeks, respectively. There were 6 to 35 different bacterial families identified in the day-of-birth samples, unrelated to the mode of delivery. Richness decreased through hospitalization (week 1, 16.9&#x200a;&#xb1;&#x200a;7.7 vs weeks 3-5, 10.7&#x200a;&#xb1;&#x200a;3.4, P&#x200a;<&#x200a;0.001). The Shannon diversity index demonstrated the lowest diversity at birth, an increase at week 2, followed by a rapid decline at weeks 3 to 5, suggesting the development of a more uniform microbiota composition after 2 weeks of stay at a neonatal intensive care unit. Enterobacteriaceae, Staphylococcaceae, and Enterococcaceae constituted the majority of the bacterial families. Bifidobacterium spp were infrequently detected at extremely low levels. PICRUSt analysis revealed the enhancement of peroxisome, PPAR, and adipocytokine signaling; plant-pathogen interaction; and aminobenzoate degradation pathways in week 1 samples.<br><br>CONCLUSIONS: Our results suggest that although preterm infants have individualized microbiota that are detectable at birth, the differences decrease during the neonatal intensive care unit hospitalization with increasing prominence of pathogenic microbiota.}, }
@article {pmid26228559, year = {2015}, author = {Floudas, D and Hibbett, DS}, title = {Revisiting the taxonomy of Phanerochaete (Polyporales, Basidiomycota) using a four gene dataset and extensive ITS sampling.}, journal = {Fungal biology}, volume = {119}, number = {8}, pages = {679-719}, doi = {10.1016/j.funbio.2015.04.003}, pmid = {26228559}, issn = {1878-6146}, mesh = {Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Molecular Sequence Data ; Phanerochaete/*classification/*genetics ; Phylogeny ; RNA Polymerase II/genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; }, abstract = {We amplified RPB1, RPB2, and the ITS and LSU ribosomal genes from species mostly in the phlebioid clade, focusing heavily in phanerochaetoid taxa. We performed Maximum Likelihood and Bayesian analyses for different combinations of datasets. Our results provide a strongly supported phylogenetic picture of the phlebioid clade, representing 89 species in the four genes analyses, of which 49 represent phanerochaetoid taxa. Phanerochaete sensu lato is polyphyletic and distributed across nine lineages in the phlebioid clade. Six of these lineages are associated to already described genera, while we describe the new genus Phaeophlebiopsis to accommodate Phlebiopsis-like species in one of the remaining lineages. We also propose three taxonomic transfers and describe nine new species, with four of those species currently placed in Phanerochaete sanguinea or Phanerochaete velutina. Finally, the placement of Leptoporus mollis along with other potential brown-rot species in the phlebioid clade suggests that, in addition to the Antrodia clade, brown-rot fungi may have evolved more than once in Polyporales.}, }
@article {pmid26227572, year = {2015}, author = {Li, WW and Yu, HQ}, title = {Electro-assisted groundwater bioremediation: fundamentals, challenges and future perspectives.}, journal = {Bioresource technology}, volume = {196}, number = {}, pages = {677-684}, doi = {10.1016/j.biortech.2015.07.074}, pmid = {26227572}, issn = {1873-2976}, mesh = {*Biodegradation, Environmental ; *Electrochemical Techniques ; Groundwater/*chemistry ; }, abstract = {Bioremediation is envisaged as an important way to abate groundwater contamination, but the need for chemical addition and limited bioavailability of electron donors/acceptors or contaminants hamper its application. As a promising means to enhance such processes, electrochemical system has drawn considerable attention, as it offers distinct advantages in terms of environmental benignity, controllability and treatment efficiency. Meanwhile, there are also potential risks and considerable engineering challenges for its practical application. This review provides a first comprehensive introduction of this emerging technology, discusses its potential applications and current challenges, identifies the knowledge gaps, and outlooks the future opportunities to bring it to field application. The need for a better understanding on the microbiology under electrochemical stimulation and the future requirements on process monitoring, modeling and evaluation protocols and field investigations are highlighted.}, }
@article {pmid26225354, year = {2015}, author = {Prussin, AJ and Garcia, EB and Marr, LC}, title = {Total Virus and Bacteria Concentrations in Indoor and Outdoor Air.}, journal = {Environmental science &amp; technology letters}, volume = {2}, number = {4}, pages = {84-88}, pmid = {26225354}, issn = {2328-8930}, support = {DP2 AI112243/AI/NIAID NIH HHS/United States ; }, abstract = {Viruses play important roles in microbial ecology and some infectious diseases, but relatively little is known about concentrations, sources, transformation, and fate of viruses in the atmosphere. We have measured total airborne concentrations of virus-like and bacteria-like particles (VLPs between 0.02 μm and 0.5 μm in size and BLPs between 0.5 μm and 5 μm) in nine locations: a classroom, a daycare center, a dining facility, a health center, three houses, an office, and outdoors. Indoor concentrations of both VLPs and BLPs were ~10[5] particles m[-3], and the virus-to-bacteria ratio was 0.9 ± 0.1 (mean ± standard deviation across different locations). There were no significant differences in concentration between different indoor environments. VLP and BLP concentrations in outdoor air were 2.6 and 1.6 times higher, respectively, than in indoor air. At the single outdoor site, the virus-to-bacteria ratio was 1.4.}, }
@article {pmid26224165, year = {2016}, author = {Sarmiento-Vizcaíno, A and Braña, AF and González, V and Nava, H and Molina, A and Llera, E and Fiedler, HP and Rico, JM and García-Flórez, L and Acuña, JL and García, LA and Blanco, G}, title = {Atmospheric Dispersal of Bioactive Streptomyces albidoflavus Strains Among Terrestrial and Marine Environments.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {375-386}, pmid = {26224165}, issn = {1432-184X}, mesh = {Animals ; Biological Factors/chemistry/metabolism ; Invertebrates/classification/*microbiology ; Lichens/microbiology ; Seawater/*microbiology ; Streptomyces/chemistry/genetics/*isolation &amp; purification/metabolism ; }, abstract = {Members of the Streptomyces albidoflavus clade, identified by 16S rRNA sequencing and phylogenetic analyses, are widespread among predominant terrestrial lichens (Flavoparmelia caperata and Xanthoria parietina) and diverse intertidal and subtidal marine macroalgae, brown red and green (Phylum Heterokontophyta, Rhodophyta, and Chlorophyta) from the Cantabrian Cornice. In addition to these terrestrial and coastal temperate habitats, similar strains were also found to colonize deep-sea ecosystems and were isolated mainly from gorgonian and solitary corals and other invertebrates (Phylum Cnidaria, Annelida, Echinodermata, Arthropoda, and Porifera) living up to 4700-m depth and at a temperature of 2-4 °C in the submarine Avilés Canyon. Similar strains have been also repeatedly isolated from atmospheric precipitations (rain drops, snow, and hailstone) collected in the same area throughout a year observation time. These ubiquitous strains were found to be halotolerant, psychrotolerant, and barotolerant. Bioactive compounds with diverse antibiotic and cytotoxic activities produced by these strains were identified by high-performance liquid chromatography (HPLC) and database comparison. These include antibacterials (paulomycins A and B), antifungals (maltophilins), antifungals displaying also cytotoxic activities (antimycins and 6-epialteramides), and the antitumor compound fredericamycin. A hypothetical dispersion model is here proposed to explain the biogeographical distribution of S. albidoflavus strains in terrestrial, marine, and atmospheric environments.}, }
@article {pmid26224164, year = {2016}, author = {Rasuk, MC and Fernández, AB and Kurth, D and Contreras, M and Novoa, F and Poiré, D and Farías, ME}, title = {Bacterial Diversity in Microbial Mats and Sediments from the Atacama Desert.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {44-56}, pmid = {26224164}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/genetics ; Desert Climate ; Geologic Sediments/*microbiology ; Lakes/analysis/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The Atacama Desert has extreme environmental conditions that allow the development of unique microbial communities. The present paper reports the bacterial diversity of microbial mats and sediments and its mineralogical components. Some physicochemical conditions of the water surrounding these ecosystems have also been studied trying to determine their influence on the diversity of these communities. In that way, mats and sediments distributed among different hypersaline lakes located in salt flats of the Atacama Desert were subjected to massive parallel sequencing of the V4 region of the 16S rRNA genes of Bacteria. A higher diversity in sediment than in mat samples have been found. Lakes that harbor microbial mats have higher salinity than lakes where mats are absent. Proteobacteria and/or Bacteroidetes are the major phyla represented in all samples. An interesting item is the finding of a low proportion or absence of Cyanobacteria sequences in the ecosystems studied, suggesting the possibility that other groups may be playing an essential role as primary producers in these extreme environments. Additionally, the large proportion of 16S rRNA gene sequences that could not be classified at the level of phylum indicates potential new phyla present in these ecosystems.}, }
@article {pmid26222449, year = {2015}, author = {Khazir, J and Riley, DL and Chashoo, G and Mir, BA and Liles, D and Islam, MA and Singh, SK and Vishwakarma, RA and Pilcher, LA}, title = {Design, synthesis and anticancer activity of Michael-type thiol adducts of α-santonin analogue with exocyclic methylene.}, journal = {European journal of medicinal chemistry}, volume = {101}, number = {}, pages = {769-779}, doi = {10.1016/j.ejmech.2015.07.022}, pmid = {26222449}, issn = {1768-3254}, mesh = {Antineoplastic Agents/*chemical synthesis/chemistry/*pharmacology ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Crystallography, X-Ray ; Dose-Response Relationship, Drug ; *Drug Design ; Drug Screening Assays, Antitumor ; Humans ; Models, Molecular ; Molecular Structure ; Santonin/*analogs &amp; derivatives/chemical synthesis/chemistry/pharmacology ; Structure-Activity Relationship ; Sulfhydryl Compounds/*chemistry/pharmacology ; }, abstract = {A series of Michael-type analogues were generated on the C-ring of α-santonin (α-methylene-γ-butyrolactone) upon reaction with various thiols. All the thiol adducts synthesized were evaluated for their anticancer activity against four human cancer cell lines (PC-3, HCT-15, A-549 and MCF-7). Bioassay results indicated that even though most of the synthesized compounds exhibited a good anticancer activity against various cancer cells in vitro, some of the compounds like 9e, 9g and 9q were found to be the most promising analogues in this series, with compound 9e showing IC50 values of 1.5 μM, 0.6 μM, 2.4 μM and 1.2 μM on PC-3, MCF-7, A-549 and HCT-116 cell lines respectively. Further, flow cytometry studies showed that MCF-7 cells treated with the compounds 9e, 9g and 9q were arrested in the sub G1 phase of the cell cycle in a concentration dependent manner. These lead molecules were further studied for NF-κB, p65 transcription factor inhibitory activity which confirmed concentration dependent inhibition against NF-κB, p65 with analogue 9e showing 57% inhibition at 2 μM, 9g showing 62% inhibition at 3 μM and 9q showing 54% inhibition at 2 μM concentration.}, }
@article {pmid26222307, year = {2015}, author = {Tasoff, J and Mee, MT and Wang, HH}, title = {An Economic Framework of Microbial Trade.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0132907}, pmid = {26222307}, issn = {1932-6203}, support = {DP5 OD009172/OD/NIH HHS/United States ; 7DP5OD009172-03/OD/NIH HHS/United States ; //Canadian Institutes of Health Research/Canada ; }, mesh = {Escherichia coli/*growth &amp; development ; Microbial Consortia/*physiology ; *Models, Biological ; }, abstract = {A large fraction of microbial life on earth exists in complex communities where metabolic exchange is vital. Microbes trade essential resources to promote their own growth in an analogous way to countries that exchange goods in modern economic markets. Inspired by these similarities, we developed a framework based on general equilibrium theory (GET) from economics to predict the population dynamics of trading microbial communities. Our biotic GET (BGET) model provides an a priori theory of the growth benefits of microbial trade, yielding several novel insights relevant to understanding microbial ecology and engineering synthetic communities. We find that the economic concept of comparative advantage is a necessary condition for mutualistic trade. Our model suggests that microbial communities can grow faster when species are unable to produce essential resources that are obtained through trade, thereby promoting metabolic specialization and increased intercellular exchange. Furthermore, we find that species engaged in trade exhibit a fundamental tradeoff between growth rate and relative population abundance, and that different environments that put greater pressure on group selection versus individual selection will promote varying strategies along this growth-abundance spectrum. We experimentally tested this tradeoff using a synthetic consortium of Escherichia coli cells and found the results match the predictions of the model. This framework provides a foundation to study natural and engineered microbial communities through a new lens based on economic theories developed over the past century.}, }
@article {pmid26222031, year = {2015}, author = {Palatinszky, M and Herbold, C and Jehmlich, N and Pogoda, M and Han, P and von Bergen, M and Lagkouvardos, I and Karst, SM and Galushko, A and Koch, H and Berry, D and Daims, H and Wagner, M}, title = {Cyanate as an energy source for nitrifiers.}, journal = {Nature}, volume = {524}, number = {7563}, pages = {105-108}, pmid = {26222031}, issn = {1476-4687}, support = {294343/ERC_/European Research Council/International ; P 25231/FWF_/Austrian Science Fund FWF/Austria ; P 26127/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Aerobiosis ; Ammonia/metabolism ; Ammonium Compounds/metabolism ; Archaea/enzymology/genetics/growth &amp; development/*metabolism ; Carbon Dioxide/metabolism ; Carbon-Nitrogen Lyases/genetics/metabolism ; Cyanates/*metabolism ; Environmental Microbiology ; Metagenome/genetics ; Nitrates/metabolism ; *Nitrification ; Nitrites/metabolism ; Nitrogen/metabolism ; Nitrogen Cycle ; Oxidation-Reduction ; }, abstract = {Ammonia- and nitrite-oxidizing microorganisms are collectively responsible for the aerobic oxidation of ammonia via nitrite to nitrate and have essential roles in the global biogeochemical nitrogen cycle. The physiology of nitrifiers has been intensively studied, and urea and ammonia are the only recognized energy sources that promote the aerobic growth of ammonia-oxidizing bacteria and archaea. Here we report the aerobic growth of a pure culture of the ammonia-oxidizing thaumarchaeote Nitrososphaera gargensis using cyanate as the sole source of energy and reductant; to our knowledge, the first organism known to do so. Cyanate, a potentially important source of reduced nitrogen in aquatic and terrestrial ecosystems, is converted to ammonium and carbon dioxide in Nitrososphaera gargensis by a cyanase enzyme that is induced upon addition of this compound. Within the cyanase gene family, this cyanase is a member of a distinct clade also containing cyanases of nitrite-oxidizing bacteria of the genus Nitrospira. We demonstrate by co-culture experiments that these nitrite oxidizers supply cyanase-lacking ammonia oxidizers with ammonium from cyanate, which is fully nitrified by this microbial consortium through reciprocal feeding. By screening a comprehensive set of more than 3,000 publically available metagenomes from environmental samples, we reveal that cyanase-encoding genes clustering with the cyanases of these nitrifiers are widespread in the environment. Our results demonstrate an unexpected metabolic versatility of nitrifying microorganisms, and suggest a previously unrecognized importance of cyanate in cycling of nitrogen compounds in the environment.}, }
@article {pmid26220947, year = {2016}, author = {Rodrigues Hoffmann, A and Proctor, LM and Surette, MG and Suchodolski, JS}, title = {The Microbiome: The Trillions of Microorganisms That Maintain Health and Cause Disease in Humans and Companion Animals.}, journal = {Veterinary pathology}, volume = {53}, number = {1}, pages = {10-21}, doi = {10.1177/0300985815595517}, pmid = {26220947}, issn = {1544-2217}, mesh = {Animals ; Gastrointestinal Tract/microbiology ; Humans ; Lung/microbiology ; *Microbiota ; Pets ; Respiratory System/microbiology ; Skin/microbiology ; }, abstract = {The microbiome is the complex collection of microorganisms, their genes, and their metabolites, colonizing the human and animal mucosal surfaces, digestive tract, and skin. It is now well known that the microbiome interacts with its host, assisting in digestion and detoxification, supporting immunity, protecting against pathogens, and maintaining health. Studies published to date have demonstrated that healthy individuals are often colonized with different microbiomes than those with disease involving various organ systems. This review covers a brief history of the development of the microbiome field, the main objectives of the Human Microbiome Project, and the most common microbiomes inhabiting the human respiratory tract, companion animal digestive tract, and skin in humans and companion animals. The main changes in the microbiomes in patients with pulmonary, gastrointestinal, and cutaneous lesions are described.}, }
@article {pmid26219267, year = {2016}, author = {Das, S and Liu, CC and Jean, JS and Liu, T}, title = {Dissimilatory Arsenate Reduction and In Situ Microbial Activities and Diversity in Arsenic-rich Groundwater of Chianan Plain, Southwestern Taiwan.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {365-374}, pmid = {26219267}, issn = {1432-184X}, mesh = {Arsenates/analysis/*metabolism ; Arsenic/*analysis/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodiversity ; Groundwater/chemistry/*microbiology ; Oxidation-Reduction ; Sulfates/metabolism ; Taiwan ; Water Pollutants, Chemical/analysis/*metabolism ; }, abstract = {Although dissimilatory arsenic reduction (DAsR) has been recognized as an important process for groundwater arsenic (As) enrichment, its characterization and association with in situ microbial activities and diversity in As-rich groundwater is barely studied. In this work, we collected As-rich groundwater at depths of 23, 300, and 313 m, respectively, from Yenshui-3, Budai-Shinwen, and Budai-4 of Chianan plain, southwestern Taiwan, and conducted incubation experiments using different electron donors, acceptors, and sulfate-reducing bacterial inhibitor (tungstate) to characterize DAsR. Moreover, bacterial diversity was evaluated using 454-pyrosequencing targeting bacterial 16S rRNAs. MPN technique was used to enumerate microorganisms with different in situ metabolic functions. The results revealed that DAsR in groundwater of Chianan plain was a biotic phenomenon (as DAsR was totally inhibited by filter sterilization), enhanced by the type of electron donor (in this case, lactate enhanced DAsR but acetate and succinate did not), and limited by the availability of arsenate. In addition to oxidative recycling of As(III), dissolution of As(V)-saturated manganese and iron minerals by indigenous dissimilatory Mn(IV)- and Fe(III)-reducing bacteria, and abiotic oxidation of As(III) with Mn(IV) regenerated As(V) in the groundwater. Sulfate-respiring bacteria contributed 7.4 and 28.2 % to the observed DAsR in groundwater of Yinshui-3 and Budai-Shinwen, respectively, whereas their contribution was negligible in groundwater of Budai-4. A noticeable variation in dominant genera Acinetobacter and Bacillus was observed within the groundwater. Firmicutes dominated in highly As-rich groundwater of Yenshui-3, whereas Proteobacteria dominated in comparatively less As-rich groundwater of Budai-Shinwen and Budai 4.}, }
@article {pmid26219266, year = {2016}, author = {Resende, JA and Godon, JJ and Bonnafous, A and Arcuri, PB and Silva, VL and Otenio, MH and Diniz, CG}, title = {Seasonal Variation on Microbial Community and Methane Production during Anaerobic Digestion of Cattle Manure in Brazil.}, journal = {Microbial ecology}, volume = {71}, number = {3}, pages = {735-746}, pmid = {26219266}, issn = {1432-184X}, mesh = {Anaerobiosis ; Animals ; Bacteria/classification/isolation &amp; purification/*metabolism ; *Biodiversity ; Brazil ; Cattle ; Manure/analysis/*microbiology ; Methane/analysis/*metabolism ; Phylogeny ; }, abstract = {Anaerobic digestion is an alternative method for the treatment of animal manure and wastewater. The anaerobic bioconversion of biomass requires a multi-step biological process, including microorganisms with distinct roles. The diversity and composition of microbial structure in pilot-scale anaerobic digestion operating at ambient temperature in Brazil were studied. Influence of the seasonal and temporal patterns on bacterial and archaeal communities were assessed by studying the variations in density, dynamic and diversity and structure. The average daily biogas produced in the summer and winter months was 18.7 and 16 L day(-1), respectively, and there was no difference in the average methane yield. Quantitative PCR analysis revealed that no differences in abundances and dynamics were found for bacterial communities and the total number of Archaea in different seasons. Analysis of bacterial clone libraries revealed a predominance of Firmicutes (54.5 %/summer and 46.7 %/winter) and Bacteroidetes (31.4 %/summer and 44.4 %/winter). Within the Archaea, the phylum Euryarchaeota was predominant in both digesters. Phylogenetic distribution showed changes in percentage between the phyla identified, but no alterations were recorded in the quality and amount of produced methane or community dynamics. The results may suggest that redundancy of microbial groups may have occurred, pointing to a more complex microbial community in the ecosystem related to this ambient temperature system.}, }
@article {pmid26218741, year = {2016}, author = {Sun, J}, title = {VDR/vitamin D receptor regulates autophagic activity through ATG16L1.}, journal = {Autophagy}, volume = {12}, number = {6}, pages = {1057-1058}, doi = {10.1080/15548627.2015.1072670}, pmid = {26218741}, issn = {1554-8635}, support = {K01 DK075386/DK/NIDDK NIH HHS/United States ; R01 DK105118/DK/NIDDK NIH HHS/United States ; R03 DK089010/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Autophagy ; Autophagy-Related Proteins/*metabolism ; Colitis/microbiology/pathology ; Gastrointestinal Microbiome ; Humans ; Inflammation/pathology ; Models, Biological ; Receptors, Calcitriol/*metabolism ; }, abstract = {The Paneth cell is a unique intestinal epithelial cell that can sense the gut microbiome and secrete anti-microbial peptides, thereby playing critical roles in the maintenance of homeostasis at the intestinal-microbial interface. These roles in regulating innate immunity and intestinal microbial ecology are dependent on a functional autophagy pathway through ATG16L1. ATG16L1 is a regulator for autophagy and a risk gene for inflammatory bowel disease (IBD). We demonstrated that a low VDR/vitamin D receptor level in the intestine is associated with abnormal Paneth cells, impaired autophagy function, and imbalanced bacterial profile (dysbiosis), accompanied by a reduction of ATG16L1. We determined that VDR transcriptionally regulates ATG16L1 as a VDR target gene. Administration of the bacterial product butyrate increases intestinal VDR expression and suppresses inflammation in a colitis model. Thus, our study indicates that VDR may be a determinant of IBD risk through its actions on ATG16L1. These insights can be leveraged to define therapeutic targets for restoring Paneth cells and autophagy through VDR in chronic inflammation. It may also have applicability for infectious diseases and autoimmune diseases associated with skin or lung, where the host is in contact with bacteria.}, }
@article {pmid26218193, year = {2015}, author = {Acebo-Guerrero, Y and Hernández-Rodríguez, A and Vandeputte, O and Miguélez-Sierra, Y and Heydrich-Pérez, M and Ye, L and Cornelis, P and Bertin, P and El Jaziri, M}, title = {Characterization of Pseudomonas chlororaphis from Theobroma cacao L. rhizosphere with antagonistic activity against Phytophthora palmivora (Butler).}, journal = {Journal of applied microbiology}, volume = {119}, number = {4}, pages = {1112-1126}, doi = {10.1111/jam.12910}, pmid = {26218193}, issn = {1365-2672}, mesh = {*Antibiosis ; Cacao/growth &amp; development/*microbiology ; Molecular Sequence Data ; Phytophthora/*physiology ; Plant Diseases/*microbiology/prevention &amp; control ; Plant Roots/microbiology ; Pseudomonas/genetics/isolation &amp; purification/*physiology ; *Rhizosphere ; }, abstract = {AIM: To isolate and characterize rhizobacteria from Theobroma cacao with antagonistic activity against Phytophthora palmivora, the causal agent of the black pod rot, which is one of the most important diseases of T. cacao.<br><br>METHODS AND RESULTS: Among 127 rhizobacteria isolated from cacao rhizosphere, three isolates (CP07, CP24 and CP30) identified as Pseudomonas chlororaphis, showed in vitro antagonistic activity against P. palmivora. Direct antagonism tested in cacao detached leaves revealed that the isolated rhizobacteria were able to reduce symptom severity upon infection with P. palmivora Mab1, with Ps. chlororaphis CP07 standing out as a potential biocontrol agent. Besides, reduced symptom severity on leaves was also observed in planta where cacao root system was pretreated with the isolated rhizobacteria followed by leaf infection with P. palmivora Mab1. The production of lytic enzymes, siderophores, biosurfactants and HCN, as well as the detection of genes encoding antibiotics, the formation of biofilm, and bacterial motility were also assessed for all three rhizobacterial strains. By using a mutant impaired in viscosin production, derived from CP07, it was found that this particular biosurfactant turned out to be crucial for both motility and biofilm formation, but not for the in vitro antagonism against Phytophthora, although it may contribute to the bioprotection of T. cacao.<br><br>CONCLUSIONS: In the rhizosphere of T. cacao, there are rhizobacteria, such as Ps. chlororaphis, able to protect plants against P. palmivora.<br><br>This study provides a theoretical basis for the potential use of Ps. chlororaphis CP07 as a biocontrol agent for the protection of cacao plants from P. palmivora infection.}, }
@article {pmid26218141, year = {2015}, author = {McFadden, RM and Larmonier, CB and Shehab, KW and Midura-Kiela, M and Ramalingam, R and Harrison, CA and Besselsen, DG and Chase, JH and Caporaso, JG and Jobin, C and Ghishan, FK and Kiela, PR}, title = {The Role of Curcumin in Modulating Colonic Microbiota During Colitis and Colon Cancer Prevention.}, journal = {Inflammatory bowel diseases}, volume = {21}, number = {11}, pages = {2483-2494}, pmid = {26218141}, issn = {1536-4844}, support = {P30 CA023074/CA/NCI NIH HHS/United States ; R01 DK067286/DK/NIDDK NIH HHS/United States ; R01DK67286/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Azoxymethane/administration &amp; dosage ; Carcinogens/pharmacology ; Cell Transformation, Neoplastic/*drug effects ; Colitis/chemically induced/drug therapy ; Colon/microbiology/*pathology ; Colorectal Neoplasms/chemically induced/*drug therapy ; Curcumin/*administration &amp; dosage ; Dietary Supplements ; Disease Models, Animal ; Immunity, Mucosal ; Intestinal Mucosa/*pathology ; Mice ; Mice, 129 Strain ; Mice, Knockout ; Microbiota/*drug effects ; }, abstract = {BACKGROUND: Intestinal microbiota influences the progression of colitis-associated colorectal cancer. With diet being a key determinant of the gut microbial ecology, dietary interventions are an attractive avenue for the prevention of colitis-associated colorectal cancer. Curcumin is the most active constituent of the ground rhizome of the Curcuma longa plant, which has been demonstrated to have anti-inflammatory, antioxidative, and antiproliferative properties.<br><br>METHODS: Il10 mice on 129/SvEv background were used as a model of colitis-associated colorectal cancer. Starting at 10 weeks of age, wild-type or Il10 mice received 6 weekly intraperitoneal injections of azoxymethane (AOM) or phosphate-buffered saline (PBS) and were started on either a control or a curcumin-supplemented diet. Stools were collected every 4 weeks for microbial community analysis. Mice were killed at 30 weeks of age.<br><br>RESULTS: Curcumin-supplemented diet increased survival, decreased colon weight/length ratio, and, at 0.5%, entirely eliminated tumor burden. Although colonic histology indicated improvement with curcumin, no effects of mucosal immune responses have been observed in PBS/Il10 mice and limited effects were seen in AOM/Il10 mice. In wild-type and in Il10 mice, curcumin increased bacterial richness, prevented age-related decrease in alpha diversity, increased the relative abundance of Lactobacillales, and decreased Coriobacterales order. Taxonomic profile of AOM/Il10 mice receiving curcumin was more similar to those of wild-type mice than those fed control diet.<br><br>CONCLUSIONS: In AOM/Il10 model, curcumin reduced or eliminated colonic tumor burden with limited effects on mucosal immune responses. The beneficial effect of curcumin on tumorigenesis was associated with the maintenance of a more diverse colonic microbial ecology.}, }
@article {pmid26217330, year = {2015}, author = {van Agtmaal, M and van Os, GJ and Hol, WH and Hundscheid, MP and Runia, WT and Hordijk, CA and de Boer, W}, title = {Legacy effects of anaerobic soil disinfestation on soil bacterial community composition and production of pathogen-suppressing volatiles.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {701}, pmid = {26217330}, issn = {1664-302X}, abstract = {There is increasing evidence that microbial volatiles (VOCs) play an important role in natural suppression of soil-borne diseases, but little is known on the factors that influence production of suppressing VOCs. In the current study we examined whether a stress-induced change in soil microbial community composition would affect the production by soils of VOCs suppressing the plant-pathogenic oomycete Pythium. Using pyrosequencing of 16S ribosomal gene fragments we compared the composition of bacterial communities in sandy soils that had been exposed to anaerobic disinfestation (AD), a treatment used to kill harmful soil organisms, with the composition in untreated soils. Three months after the AD treatment had been finished, there was still a clear legacy effect of the former anaerobic stress on bacterial community composition with a strong increase in relative abundance of the phylum Bacteroidetes and a significant decrease of the phyla Acidobacteria, Planctomycetes, Nitrospirae, Chloroflexi, and Chlorobi. This change in bacterial community composition coincided with loss of production of Pythium suppressing soil volatiles (VOCs) and of suppression of Pythium impacts on Hyacinth root development. One year later, the composition of the bacterial community in the AD soils was reflecting that of the untreated soils. In addition, both production of Pythium-suppressing VOCs and suppression of Pythium in Hyacinth bioassays had returned to the levels of the untreated soil. GC/MS analysis identified several VOCs, among which compounds known to be antifungal, that were produced in the untreated soils but not in the AD soils. These compounds were again produced 15 months after the AD treatment. Our data indicate that soils exposed to a drastic stress can temporarily lose pathogen suppressive characteristics and that both loss and return of these suppressive characteristics coincides with shifts in the soil bacterial community composition. Our data are supporting the suggested importance of microbial VOCs in the natural buffer of soils against diseases caused by soil-borne pathogens.}, }
@article {pmid26217324, year = {2015}, author = {Van Der Voort, M and Meijer, HJ and Schmidt, Y and Watrous, J and Dekkers, E and Mendes, R and Dorrestein, PC and Gross, H and Raaijmakers, JM}, title = {Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {693}, pmid = {26217324}, issn = {1664-302X}, abstract = {The plant microbiome represents an enormous untapped resource for discovering novel genes and bioactive compounds. Previously, we isolated Pseudomonas sp. SH-C52 from the rhizosphere of sugar beet plants grown in a soil suppressive to the fungal pathogen Rhizoctonia solani and showed that its antifungal activity is, in part, attributed to the production of the chlorinated 9-amino-acid lipopeptide thanamycin (Mendes et al., 2011). To get more insight into its biosynthetic repertoire, the genome of Pseudomonas sp. SH-C52 was sequenced and subjected to in silico, mutational and functional analyses. The sequencing revealed a genome size of 6.3 Mb and 5579 predicted ORFs. Phylogenetic analysis placed strain SH-C52 within the Pseudomonas corrugata clade. In silico analysis for secondary metabolites revealed a total of six non-ribosomal peptide synthetase (NRPS) gene clusters, including the two previously described NRPS clusters for thanamycin and the 2-amino acid antibacterial lipopeptide brabantamide. Here we show that thanamycin also has activity against an array of other fungi and that brabantamide A exhibits anti-oomycete activity and affects phospholipases of the late blight pathogen Phytophthora infestans. Most notably, mass spectrometry led to the discovery of a third lipopeptide, designated thanapeptin, with a 22-amino-acid peptide moiety. Seven structural variants of thanapeptin were found with varying degrees of activity against P. infestans. Of the remaining four NRPS clusters, one was predicted to encode for yet another and unknown lipopeptide with a predicted peptide moiety of 8-amino acids. Collectively, these results show an enormous metabolic potential for Pseudomonas sp. SH-C52, with at least three structurally diverse lipopeptides, each with a different antimicrobial activity spectrum.}, }
@article {pmid26216986, year = {2015}, author = {Abrudan, MI and Smakman, F and Grimbergen, AJ and Westhoff, S and Miller, EL and van Wezel, GP and Rozen, DE}, title = {Socially mediated induction and suppression of antibiosis during bacterial coexistence.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {35}, pages = {11054-11059}, pmid = {26216986}, issn = {1091-6490}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*biosynthesis ; Streptomyces/metabolism/*physiology ; }, abstract = {Despite their importance for humans, there is little consensus on the function of antibiotics in nature for the bacteria that produce them. Classical explanations suggest that bacteria use antibiotics as weapons to kill or inhibit competitors, whereas a recent alternative hypothesis states that antibiotics are signals that coordinate cooperative social interactions between coexisting bacteria. Here we distinguish these hypotheses in the prolific antibiotic-producing genus Streptomyces and provide strong evidence that antibiotics are weapons whose expression is significantly influenced by social and competitive interactions between competing strains. We show that cells induce facultative responses to cues produced by competitors by (i) increasing their own antibiotic production, thereby decreasing costs associated with constitutive synthesis of these expensive products, and (ii) by suppressing antibiotic production in competitors, thereby reducing direct threats to themselves. These results thus show that although antibiotic production is profoundly social, it is emphatically not cooperative. Using computer simulations, we next show that these facultative strategies can facilitate the maintenance of biodiversity in a community context by converting lethal interactions between neighboring colonies to neutral interactions where neither strain excludes the other. Thus, just as bacteriocins can lead to increased diversity via rock-paper-scissors dynamics, so too can antibiotics via elicitation and suppression. Our results reveal that social interactions are crucial for understanding antibiosis and bacterial community dynamics, and highlight the potential of interbacterial interactions for novel drug discovery by eliciting pathways that mediate interference competition.}, }
@article {pmid26215711, year = {2015}, author = {Frias-Lopez, J}, title = {Targeting specific bacteria in the oral microbiome.}, journal = {Trends in microbiology}, volume = {23}, number = {9}, pages = {527-528}, doi = {10.1016/j.tim.2015.07.004}, pmid = {26215711}, issn = {1878-4380}, mesh = {Antimicrobial Cationic Peptides/*pharmacology ; Humans ; Microbiota/*drug effects ; Streptococcus mutans/*drug effects/*physiology ; }, abstract = {A lack of tools that kill selected members of the oral microbiome has hampered the ability to study specific roles of bacteria within bacterial communities. Work by Guo et al. shows the potential of antimicrobial peptides as a tool to assess the role of individual species in the microbial community.}, }
@article {pmid26209674, year = {2015}, author = {Sun, F and Zhang, X and Zhang, Q and Liu, F and Zhang, J and Gong, J}, title = {Seagrass (Zostera marina) Colonization Promotes the Accumulation of Diazotrophic Bacteria and Alters the Relative Abundances of Specific Bacterial Lineages Involved in Benthic Carbon and Sulfur Cycling.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {19}, pages = {6901-6914}, pmid = {26209674}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodiversity ; Carbon/*metabolism ; China ; Ecosystem ; Geologic Sediments/microbiology ; Molecular Sequence Data ; Nitrogen/metabolism ; *Nitrogen Fixation ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Sulfur/*metabolism ; Zosteraceae/*growth &amp; development ; }, abstract = {Seagrass colonization changes the chemistry and biogeochemical cycles mediated by microbes in coastal sediments. In this study, we molecularly characterized the diazotrophic assemblages and entire bacterial community in surface sediments of a Zostera marina-colonized coastal lagoon in northern China. Higher nitrogenase gene (nifH) copy numbers were detected in the sediments from the vegetated region than in the sediments from the unvegetated region nearby. The nifH phylotypes detected were mostly affiliated with the Geobacteraceae, Desulfobulbus, Desulfocapsa, and Pseudomonas. Redundancy analysis based on terminal restriction fragment length polymorphism analysis showed that the distribution of nifH genotypes was mostly shaped by the ratio of total organic carbon to total organic nitrogen, the concentration of cadmium in the sediments, and the pH of the overlying water. High-throughput sequencing and phylogenetic analyses of bacterial 16S rRNA genes also indicated the presence of Geobacteraceae and Desulfobulbaceae phylotypes in these samples. A comparison of these results with those of previous studies suggests the prevalence and predominance of iron(III)-reducing Geobacteraceae and sulfate-reducing Desulfobulbaceae diazotrophs in coastal sedimentary environments. Although the entire bacterial community structure was not significantly different between these two niches, Desulfococcus (Deltaproteobacteria) and Anaerolineae (Chloroflexi) presented with much higher proportions in the vegetated sediments, and Flavobacteriaceae (Bacteroidetes) occurred more frequently in the bare sediments. These data suggest that the high bioavailability of organic matter (indicated by relatively lower carbon-to-nitrogen ratios) and the less-reducing anaerobic condition in vegetated sediments may favor Desulfococcus and Anaerolineae lineages, which are potentially important populations in benthic carbon and sulfur cycling in the highly productive seagrass ecosystem.}, }
@article {pmid26206916, year = {2015}, author = {Huber, JA}, title = {MICROBIAL ECOLOGY. Making methane down deep.}, journal = {Science (New York, N.Y.)}, volume = {349}, number = {6246}, pages = {376-377}, doi = {10.1126/science.aac6673}, pmid = {26206916}, issn = {1095-9203}, mesh = {Aquatic Organisms/*classification ; Archaea/*classification ; Bacteria/*classification ; Coal/*microbiology ; Geologic Sediments/*microbiology ; *Microbial Consortia ; Seawater/*microbiology ; }, }
@article {pmid26205859, year = {2015}, author = {Alkhalili, RN and Hatti-Kaul, R and Canbäck, B}, title = {Genome Sequence of Geobacillus sp. Strain ZGt-1, an Antibacterial Peptide-Producing Bacterium from Hot Springs in Jordan.}, journal = {Genome announcements}, volume = {3}, number = {4}, pages = {}, pmid = {26205859}, issn = {2169-8287}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {This paper reports the draft genome sequence of the firmicute Geobacillus sp. strain ZGt-1, an antibacterial peptide producer isolated from the Zara hot spring in Jordan. This study is the first report on genomic data from a thermophilic bacterial strain isolated in Jordan.}, }
@article {pmid26203654, year = {2015}, author = {Takao, Y and Tomaru, Y and Nagasaki, K and Honda, D}, title = {Ecological Dynamics of Two Distinct Viruses Infecting Marine Eukaryotic Decomposer Thraustochytrids (Labyrinthulomycetes, Stramenopiles).}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0133395}, pmid = {26203654}, issn = {1932-6203}, mesh = {Ecology ; *Ecosystem ; Seawater/*virology ; Stramenopiles/*virology ; *Viruses ; }, abstract = {Thraustochytrids are cosmopolitan osmotrophic or heterotrophic microorganisms that are considered as important decomposers in coastal ecosystems. However, because of a lack of estimation method for each genus or systematic group of them, relatively little is known about their ecology in situ. Previously, we reported two distinct types of virus infecting thraustochytrids (AuRNAV: reported as SssRNAV, and SmDNAV) suggesting they have wide distributions in the host-virus systems of coastal environments. Here we conducted a field survey from 2004 through 2005 to show the fluctuation pattern of thraustochytrids and their viruses in Hiroshima Bay, Japan. During the field survey, we monitored the dynamics of the two types of thraustochytrid-infecting virus: small viruses causing lysis of Aurantiochytrium sp. NIBH N1-27 (identified as AuRNAV) and the large viruses of Sicyoidochytrium minutum NBRC 102975 (similar to SmDNAV in physiology and morphology). Fluctuation patterns of the two distinct types of virus were different from each other. This may reflect the difference in the preference of organic substrates; i.e., it may be likely the host of AuRNAV (Aurantiochytrium sp.) increases utilizing algal dead bodies or feeble cells as the virus shows a large increase in abundance following raphidophyte blooms; whereas, the trophic nutrient supply for S. minutum may primarily depend on other constantly-supplied organic compounds because it did not show any significant change in abundance throughout the survey. Further study concerning the population composition of thraustochytrids and their viruses may demonstrate the microbial ecology (especially concerning the detrital food web) of marine environments.}, }
@article {pmid26203332, year = {2015}, author = {Ten Hoopen, P and Pesant, S and Kottmann, R and Kopf, A and Bicak, M and Claus, S and Deneudt, K and Borremans, C and Thijsse, P and Dekeyzer, S and Schaap, DM and Bowler, C and Glöckner, FO and Cochrane, G}, title = {Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards.}, journal = {Standards in genomic sciences}, volume = {10}, number = {}, pages = {20}, pmid = {26203332}, issn = {1944-3277}, abstract = {Contextual data collected concurrently with molecular samples are critical to the use of metagenomics in the fields of marine biodiversity, bioinformatics and biotechnology. We present here Marine Microbial Biodiversity, Bioinformatics and Biotechnology (M2B3) standards for "Reporting" and "Serving" data. The M2B3 Reporting Standard (1) describes minimal mandatory and recommended contextual information for a marine microbial sample obtained in the epipelagic zone, (2) includes meaningful information for researchers in the oceanographic, biodiversity and molecular disciplines, and (3) can easily be adopted by any marine laboratory with minimum sampling resources. The M2B3 Service Standard defines a software interface through which these data can be discovered and explored in data repositories. The M2B3 Standards were developed by the European project Micro B3, funded under 7(th) Framework Programme "Ocean of Tomorrow", and were first used with the Ocean Sampling Day initiative. We believe that these standards have value in broader marine science.}, }
@article {pmid26202372, year = {2016}, author = {Vanhoecke, BW and De Ryck, TR and De boel, K and Wiles, S and Boterberg, T and Van de Wiele, T and Swift, S}, title = {Low-dose irradiation affects the functional behavior of oral microbiota in the context of mucositis.}, journal = {Experimental biology and medicine (Maywood, N.J.)}, volume = {241}, number = {1}, pages = {60-70}, pmid = {26202372}, issn = {1535-3699}, mesh = {Animals ; Biofilms/*growth &amp; development/*radiation effects ; Candida/physiology/radiation effects ; Disease Models, Animal ; Klebsiella oxytoca/physiology/radiation effects ; Larva/microbiology ; Lepidoptera/microbiology ; Microbiota/*radiation effects ; Mouth Mucosa/*microbiology ; Mucositis/*microbiology ; Streptococcus/physiology/radiation effects ; Virulence/radiation effects ; }, abstract = {The role of host-microbe interactions in the pathobiology of oral mucositis is still unclear; therefore, this study aimed to unravel the effect of irradiation on behavioral characteristics of oral microbial species in the context of mucositis. Using various experimental in vitro setups, the effects of irradiation on growth and biofilm formation of two Candida spp., Streptococcus salivarius and Klebsiella oxytoca in different culture conditions were evaluated. Irradiation did not affect growth of planktonic cells, but reduced the number of K. oxytoca cells in newly formed biofilms cultured in static conditions. Biofilm formation of K. oxytoca and Candida glabrata was affected by irradiation and depended on the culturing conditions. In the presence of mucins, these effects were lost, indicating the protective nature of mucins. Furthermore, the Galleria melonella model was used to study effects on microbial virulence. Irradiated K. oxytoca microbes were more virulent in G. melonella larvae compared to the nonirradiated ones. Our data indicate that low-dose irradiation can have an impact on functional characteristics of microbial species. Screening for pathogens like K. oxytoca in the context of mucosits could be useful to allow early detection and immediate intervention.}, }
@article {pmid26200334, year = {2015}, author = {Bodelier, PL}, title = {Sustainability: Bypassing the methane cycle.}, journal = {Nature}, volume = {523}, number = {7562}, pages = {534-535}, pmid = {26200334}, issn = {1476-4687}, mesh = {Greenhouse Effect/*prevention &amp; control ; Hordeum/*genetics ; Methane/*metabolism ; Oryza/*metabolism ; Plant Proteins/*metabolism ; Starch/*metabolism ; Transcription Factors/*metabolism ; }, }
@article {pmid26198302, year = {2015}, author = {Eriguchi, Y and Nakamura, K and Hashimoto, D and Shimoda, S and Shimono, N and Akashi, K and Ayabe, T and Teshima, T}, title = {Decreased secretion of Paneth cell α-defensins in graft-versus-host disease.}, journal = {Transplant infectious disease : an official journal of the Transplantation Society}, volume = {17}, number = {5}, pages = {702-706}, doi = {10.1111/tid.12423}, pmid = {26198302}, issn = {1399-3062}, mesh = {Animals ; Biomarkers/metabolism ; Dysbiosis/*metabolism/microbiology ; Enzyme-Linked Immunosorbent Assay ; Feces/*chemistry/microbiology ; Female ; Gastrointestinal Microbiome ; Graft vs Host Disease/*metabolism ; Hematopoietic Stem Cell Transplantation ; Intestinal Mucosa/metabolism ; Intestines/microbiology ; LIM Domain Proteins/*metabolism ; Mice ; Mice, Inbred C57BL ; Nuclear Proteins/*metabolism ; Paneth Cells/*metabolism ; Transplantation, Homologous ; alpha-Defensins/*metabolism ; }, abstract = {BACKGROUND: Intestinal microbial ecology is actively regulated by Paneth cell-derived antimicrobial peptides, α-defensins. Graft-versus-host disease (GVHD) is a major complication of allogeneic hematopoietic stem cell transplantation (SCT). We previously demonstrated that Paneth cells are targeted by GVHD, and their expression of antimicrobial peptide α-defensins is impaired, leading to a loss of physiological diversity among the microflora and development of bloodstream infection. Herein, we evaluated whether fecal levels of α-defensins could be surrogate marker of intestinal dysbiosis.<br><br>METHODS: We directly measured &#x3b1;-defensin cryptdin-1 (Crp1) in fecal pellets of mice with GVHD by using a novel enzyme-linked immunosorbent assay.<br><br>RESULTS: Fecal levels of Crp1 were significantly decreased in mice with GVHD but unchanged in mice without GVHD after SCT. These were correlated with intestinal flora diversity.<br><br>CONCLUSION: We demonstrate a link between reduced secretion of Paneth cell &#x3b1;-defensins and dysbiosis of intestinal flora in GVHD. Fecal levels of &#x3b1;-defensins could be surrogate markers for intestinal microbial homeostasis.}, }
@article {pmid26198190, year = {2015}, author = {Smith, VH and Rubinstein, RJ and Park, S and Kelly, L and Klepac-Ceraj, V}, title = {Microbiology and ecology are vitally important to premedical curricula.}, journal = {Evolution, medicine, and public health}, volume = {2015}, number = {1}, pages = {179-192}, pmid = {26198190}, issn = {2050-6201}, abstract = {Despite the impact of the human microbiome on health, an appreciation of microbial ecology is yet to be translated into mainstream medical training and practice. The human microbiota plays a role in the development of the immune system, in the development and function of the brain, in digestion, and in host defense, and we anticipate that many more functions are yet to be discovered. We argue here that without formal exposure to microbiology and ecology-fields that explore the networks, interactions and dynamics between members of populations of microbes-vitally important links between the human microbiome and health will be overlooked. This educational shortfall has significant downstream effects on patient care and biomedical research, and we provide examples from current research highlighting the influence of the microbiome on human health. We conclude that formally incorporating microbiology and ecology into the premedical curricula is invaluable to the training of future health professionals and critical to the development of novel therapeutics and treatment practices.}, }
@article {pmid26197065, year = {2015}, author = {Matteau, D and Baby, V and Pelletier, S and Rodrigue, S}, title = {A Small-Volume, Low-Cost, and Versatile Continuous Culture Device.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0133384}, pmid = {26197065}, issn = {1932-6203}, mesh = {Cell Division/*physiology ; Entomoplasmataceae/cytology/growth &amp; development ; Equipment Design ; Escherichia coli/cytology/growth &amp; development ; Hydrogen-Ion Concentration ; Microbiological Techniques/economics/*instrumentation/*methods ; *Models, Theoretical ; Reproducibility of Results ; Saccharomyces cerevisiae/cytology/growth &amp; development ; }, abstract = {BACKGROUND: Continuous culture devices can be used for various purposes such as establishing reproducible growth conditions or maintaining cell populations under a constant environment for long periods. However, commercially available instruments are expensive, were not designed to handle small volumes in the milliliter range, and can lack the flexibility required for the diverse experimental needs found in several laboratories.<br><br>We developed a versatile continuous culture system and provide detailed instructions as well as a graphical user interface software for potential users to assemble and operate their own instrument. Three culture chambers can be controlled simultaneously with the proposed configuration, and all components are readily available from various sources. We demonstrate that our continuous culture device can be used under different modes, and can easily be programmed to behave either as a turbidostat or chemostat. Addition of fresh medium to the culture vessel can be controlled by a real-time feedback loop or simply calibrated to deliver a defined volume. Furthermore, the selected light-emitting diode and photodetector enable the use of phenol red as a pH indicator, which can be used to indirectly monitor the bulk metabolic activity of a cell population rather than the turbidity.<br><br>CONCLUSIONS/SIGNIFICANCE: This affordable and customizable system will constitute a useful tool in many areas of biology such as microbial ecology as well as systems and synthetic biology.}, }
@article {pmid26195601, year = {2015}, author = {Noguerola, I and Picazo, A and Llirós, M and Camacho, A and Borrego, CM}, title = {Diversity of freshwater Epsilonproteobacteria and dark inorganic carbon fixation in the sulphidic redoxcline of a meromictic karstic lake.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {7}, pages = {}, doi = {10.1093/femsec/fiv086}, pmid = {26195601}, issn = {1574-6941}, mesh = {Arcobacter/genetics/isolation &amp; purification/*metabolism ; Autotrophic Processes/physiology ; Carbon/*metabolism ; Carbon Cycle/*physiology ; Carbon Dioxide/*metabolism ; Chlorobi/genetics/*metabolism ; Fresh Water/microbiology ; In Situ Hybridization, Fluorescence ; Lakes/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Sulfidic redoxclines are a suitable niche for the growth and activity of different chemo- and photolithotrophic sulphide-oxidizing microbial groups such as the Epsilonproteobacteria and the green sulfur bacteria (GSB). We have investigated the diversity, abundance and contribution to inorganic carbon uptake of Epsilonproteobacteria in a meromictic basin of Lake Banyoles. CARD-FISH counts revealed that Epsilonproteobacteria were prevalent at the redoxcline in winter (maximum abundance of 2 × 10(6) cells mL(-1), ≈60% of total cells) but they were nearly absent in summer, when GSB bloomed. This seasonal trend was supported by 16S rRNA gene pyrotag datasets, which revealed that the epsilonproteobacterial community was mainly composed of a member of the genus Arcobacter. In situ incubations using NaH(14)CO3 and MAR-CARD-FISH observations showed that this population assimilated CO2 in the dark, likely being mainly responsible for the autotrophic activity at the redoxcline in winter. Clone libraries targeting the aclB gene provided additional evidence of the potential capacity of these epsilonproteobacteria to fix carbon via rTCA cycle. Our data reinforce the key role of Epsilonproteobacteria in linking carbon and sulphur cycles, extend their influence to freshwater karstic lakes and raise questions about the actual contribution of chemolithotrophy at their redoxcline and euxinic water compartments.}, }
@article {pmid26195343, year = {2015}, author = {Frossard, A and Ramond, JB and Seely, M and Cowan, DA}, title = {Water regime history drives responses of soil Namib Desert microbial communities to wetting events.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {12263}, pmid = {26195343}, issn = {2045-2322}, mesh = {Analysis of Variance ; Bacteria/*metabolism ; *Desert Climate ; Fungi/*metabolism ; Humidity ; Namibia ; *Soil ; *Soil Microbiology ; *Water ; }, abstract = {Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel "dry condition" control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities.}, }
@article {pmid26193074, year = {2015}, author = {Truchado, P and Van den Abbeele, P and Rivière, A and Possemiers, S and De Vuyst, L and Van de Wiele, T}, title = {Bifidobacterium longum D2 enhances microbial degradation of long-chain arabinoxylans in an in vitro model of the proximal colon.}, journal = {Beneficial microbes}, volume = {6}, number = {6}, pages = {849-860}, doi = {10.3920/BM2015.0023}, pmid = {26193074}, issn = {1876-2891}, mesh = {Bifidobacterium/classification/genetics/growth &amp; development/*metabolism ; Biotransformation ; Colon/*chemistry/*microbiology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Gastrointestinal Microbiome ; Glycoside Hydrolases/analysis ; Healthy Volunteers ; Humans ; Models, Theoretical ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Xylans/*metabolism ; }, abstract = {Long-chain arabinoxylans (LC-AX) are degraded in the colon by intestinal bacteria possessing AX-degrading enzymes, such as bifidobacteria. Enzymatic activity of intestinal bacterial might vary depending on the composition of the gut microbiota. To compare the enzymatic activities of the bacterial gut communities of two healthy individuals (donors D1 and D2), these bacterial communities were inoculated into in vitro model M-SHIME(®). Differences in xylanase activities and denaturing gradient gel electrophoresis profiles, in particular a DNA-band corresponding with Bifidobacterium longum, were found in the proximal colon vessel. 16S rRNA gene sequencing analysis demonstrated the presence of two different B. longum species in these bacterial communities, showing 99% gene sequence similarity with B. longum NCC2705 and B. longum. subsp. longum KACC 91563, respectively, further referred to as B. longum D1 and B. longum D2. When grown on LC-AX as the sole added energy source, B. longum D2 displayed significantly higher activities of β-xylanase (5.3-fold), β-xylosidase (2.9-fold), and α-arabinofuranosidase (1.5-fold), respectively, compared to B. longum D1. When B. longum D2 was inoculated in the M-SHIME, inoculated with the bacterial gut communities of the individual with low AX-degrading enzyme activities, the β-xylanase activity increased (1.5-fold) in the proximal vessel. We demonstrated the presence of differences in LC-AX degrading enzyme activities of the bacterial gut communities of two individuals in the in vitro M-SHIME model, which could be linked to the presence of a potent AX-degrading B. longum (D2) strain.}, }
@article {pmid26191049, year = {2015}, author = {Brooks, B and Mueller, RS and Young, JC and Morowitz, MJ and Hettich, RL and Banfield, JF}, title = {Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {654}, pmid = {26191049}, issn = {1664-302X}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; R01 GM103600/GM/NIGMS NIH HHS/United States ; }, abstract = {While there has been growing interest in the gut microbiome in recent years, it remains unclear whether closely related species and strains have similar or distinct functional roles and if organisms capable of both aerobic and anaerobic growth do so simultaneously. To investigate these questions, we implemented a high-throughput mass spectrometry-based proteomics approach to identify proteins in fecal samples collected on days of life 13-21 from an infant born at 28 weeks gestation. No prior studies have coupled strain-resolved community metagenomics to proteomics for such a purpose. Sequences were manually curated to resolve the genomes of two strains of Citrobacter that were present during the later stage of colonization. Proteome extracts from fecal samples were processed via a nano-2D-LC-MS/MS and peptides were identified based on information predicted from the genome sequences for the dominant organisms, Serratia and the two Citrobacter strains. These organisms are facultative anaerobes, and proteomic information indicates the utilization of both aerobic and anaerobic metabolisms throughout the time series. This may indicate growth in distinct niches within the gastrointestinal tract. We uncovered differences in the physiology of coexisting Citrobacter strains, including differences in motility and chemotaxis functions. Additionally, for both Citrobacter strains we resolved a community-essential role in vitamin metabolism and a predominant role in propionate production. Finally, in this case study we detected differences between genome abundance and activity levels for the dominant populations. This underlines the value in layering proteomic information over genetic potential.}, }
@article {pmid26187747, year = {2015}, author = {Anderson, D and Ferreras, E and Trindade, M and Cowan, D}, title = {A novel bacterial Water Hypersensitivity-like protein shows in vivo protection against cold and freeze damage.}, journal = {FEMS microbiology letters}, volume = {362}, number = {15}, pages = {fnv110}, doi = {10.1093/femsle/fnv110}, pmid = {26187747}, issn = {1574-6968}, mesh = {Adaptation, Physiological/*genetics ; Amino Acid Sequence ; Antarctic Regions ; Bacterial Proteins/*genetics/*physiology ; Computational Biology ; Desiccation ; Escherichia coli/genetics ; *Freezing ; Gene Library ; *Genes, Bacterial ; *Metagenome ; Phylogeny ; Pseudomonas/genetics ; Sequence Analysis, DNA ; *Soil ; Soil Microbiology ; Stress, Physiological ; Water ; }, abstract = {Metagenomic library screening, by functional or sequence analysis, has become an established method for the identification of novel genes and gene products, including genetic elements implicated in microbial stress response and adaptation. We have identified, using a sequence-based approach, a fosmid clone from an Antarctic desert soil metagenome library containing a novel gene which codes for a protein homologous to a Water Hypersensitivity domain (WHy). The WHy domain is typically found as a component of specific LEA (Late Embryogenesis Abundant) proteins, particularly the LEA-14 (LEA-8) variants, which occur widely in plants, nematodes, bacteria and archaea and which are typically induced by exposure to stress conditions. The novel WHy-like protein (165 amino acid, 18.6 kDa) exhibits a largely invariant NPN motif at the N-terminus and has high sequence identity to genes identified in Pseudomonas genomes. Expression of this protein in Escherichia coli significantly protected the recombinant host against cold and freeze stress.}, }
@article {pmid26187479, year = {2015}, author = {Bosmans, L and Álvarez-Pérez, S and Moerkens, R and Wittemans, L and Van Calenberge, B and Kerckhove, SV and Paeleman, A and De Mot, R and Rediers, H and Lievens, B}, title = {Assessment of the genetic and phenotypic diversity among rhizogenic Agrobacterium biovar 1 strains infecting solanaceous and cucurbit crops.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {8}, pages = {fiv081}, doi = {10.1093/femsec/fiv081}, pmid = {26187479}, issn = {1574-6941}, mesh = {Agrobacterium/*classification/genetics/isolation &amp; purification ; Base Sequence ; Crops, Agricultural/*microbiology ; Cucurbitaceae/*microbiology ; DNA, Bacterial/genetics ; *Genetic Variation ; Solanum lycopersicum/*microbiology ; Phylogeny ; Plant Diseases/microbiology ; Plant Roots/*microbiology ; Plasmids/genetics ; RNA, Ribosomal, 16S/genetics ; Rec A Recombinases/genetics ; Sequence Analysis, DNA ; }, abstract = {Rhizogenic Agrobacterium biovar 1 strains have been found to cause extensive root proliferation on hydroponically grown Cucurbitaceae and Solanaceae crops, resulting in substantial economic losses. As these agrobacteria live under similar ecological conditions, infecting a limited number of crops, it may be hypothesized that genetic and phenotypic variation among such strains is relatively low. In this study we assessed the phenotypic diversity as well as the phylogenetic and evolutionary relationships of several rhizogenic Agrobacterium biovar 1 strains from cucurbit and solanaceous crops. A collection of 41 isolates was subjected to a number of phenotypic assays and characterized by MLSA targeting four housekeeping genes (16S rRNA gene, recA, rpoB and trpE) and two loci from the root-inducing Ri-plasmid (part of rolB and virD2). Besides phenotypic variation, remarkable genotypic diversity was observed, especially for some chromosomal loci such as trpE. In contrast, genetic diversity was lower for the plasmid-borne loci, indicating that the studied chromosomal housekeeping genes and Ri-plasmid-borne loci might not exhibit the same evolutionary history. Furthermore, phylogenetic and network analyses and several recombination tests suggested that recombination could be contributing in some extent to the evolutionary dynamics of rhizogenic Agrobacterium populations. Finally, a genomospecies-level identification analysis revealed that at least four genomospecies may occur on cucurbit and tomato crops (G1, G3, G8 and G9). Together, this study gives a first glimpse at the genetic and phenotypic diversity within this economically important plant pathogenic bacterium.}, }
@article {pmid26184578, year = {2016}, author = {Mishamandani, S and Gutierrez, T and Berry, D and Aitken, MD}, title = {Response of the bacterial community associated with a cosmopolitan marine diatom to crude oil shows a preference for the biodegradation of aromatic hydrocarbons.}, journal = {Environmental microbiology}, volume = {18}, number = {6}, pages = {1817-1833}, pmid = {26184578}, issn = {1462-2920}, support = {P42 ES005948/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Diatoms/*microbiology ; Hydrocarbons, Aromatic/*metabolism ; Petroleum/metabolism ; Petroleum Pollution ; Phytoplankton/*microbiology ; Polycyclic Aromatic Hydrocarbons/metabolism ; Seawater/microbiology ; }, abstract = {Emerging evidence shows that hydrocarbonoclastic bacteria (HCB) may be commonly found associated with phytoplankton in the ocean, but the ecology of these bacteria and how they respond to crude oil remains poorly understood. Here, we used a natural diatom-bacterial assemblage to investigate the diversity and response of HCB associated with a cosmopolitan marine diatom, Skeletonema costatum, to crude oil. Pyrosequencing analysis and qPCR revealed a dramatic transition in the diatom-associated bacterial community, defined initially by a short-lived bloom of Methylophaga (putative oil degraders) that was subsequently succeeded by distinct groups of HCB (Marinobacter, Polycyclovorans, Arenibacter, Parvibaculum, Roseobacter clade), including putative novel phyla, as well as other groups with previously unqualified oil-degrading potential. Interestingly, these oil-enriched organisms contributed to the apparent and exclusive biodegradation of substituted and non-substituted polycyclic aromatic hydrocarbons (PAHs), thereby suggesting that the HCB community associated with the diatom is tuned to specializing in the degradation of PAHs. Furthermore, the formation of marine oil snow (MOS) in oil-amended incubations was consistent with its formation during the Deepwater Horizon oil spill. This work highlights the phycosphere of phytoplankton as an underexplored biotope in the ocean where HCB may contribute importantly to the biodegradation of hydrocarbon contaminants in marine surface waters.}, }
@article {pmid26184121, year = {2015}, author = {Li, H and Wang, X and Liang, C and Hao, Z and Zhou, L and Ma, S and Li, X and Yang, S and Yao, F and Jiang, Y}, title = {Aboveground-belowground biodiversity linkages differ in early and late successional temperate forests.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {12234}, pmid = {26184121}, issn = {2045-2322}, mesh = {*Biodiversity ; *Ecosystem ; *Forests ; Plants ; Soil/chemistry ; Soil Microbiology ; Trees ; }, abstract = {Understanding ecological linkages between above- and below-ground biota is critical for deepening our knowledge on the maintenance and stability of ecosystem processes. Nevertheless, direct comparisons of plant-microbe diversity at the community level remain scarce due to the knowledge gap between microbial ecology and plant ecology. We compared the α- and β- diversities of plant and soil bacterial communities in two temperate forests that represented early and late successional stages. We documented different patterns of aboveground-belowground diversity relationships in these forests. We observed no linkage between plant and bacterial α-diversity in the early successional forest, and even a negative correlation in the late successional forest, indicating that high bacterial α-diversity is not always linked to high plant α-diversity. Beta-diversity coupling was only found at the late successional stage, while in the early successional forest, the bacterial β-diversity was closely correlated with soil property distances. Additionally, we showed that the dominant competitive tree species in the late successional forest may play key roles in driving forest succession by shaping the soil bacterial community in the early successional stage. This study sheds new light on the potential aboveground-belowground linkage in natural ecosystems, which may help us understand the mechanisms that drive ecosystem succession.}, }
@article {pmid26181436, year = {2015}, author = {Ortiz-Álvarez, R and de Los Ríos, A and Fernández-Mendoza, F and Torralba-Burrial, A and Pérez-Ortega, S}, title = {Ecological Specialization of Two Photobiont-Specific Maritime Cyanolichen Species of the Genus Lichina.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0132718}, pmid = {26181436}, issn = {1932-6203}, mesh = {Ascomycota/classification/*genetics ; Base Sequence ; Bayes Theorem ; Cyanobacteria/classification/*genetics ; Ecosystem ; Fresh Water ; Genetic Speciation ; Haplotypes ; Lichens/classification/*genetics ; Molecular Sequence Data ; Operon ; Phycocyanin/biosynthesis ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Seawater ; Spain ; Symbiosis/physiology ; }, abstract = {All fungi in the class Lichinomycetes are lichen-forming and exclusively associate with cyanobacteria. Two closely related maritime species of the genus Lichina (L. confinis and L. pygmaea) show similar distribution ranges in the Northeast Atlantic, commonly co-occurring at the same rocky shores but occupying different littoral zones. By means of 16S rRNA and phycocyanin operon markers we studied a) the phylogenetic relationships of cyanobionts associated with these species, b) the match of divergence times between both symbionts, and c) whether Lichina species differ in photobiont association and in how geography and ecology affect selectivity. The cyanobionts studied are closely related to both marine and freshwater strains of the genus Rivularia. We found evidence of a high specificity to particular cyanobiont lineages in both species: Lichina pygmaea and L. confinis incorporate specific lineages of Rivularia that do not overlap at the haplotype nor the OTU levels. Dating divergences of the fungal and cyanobacterial partners revealed an asynchronous origin of both lineages. Within each fungal species, selectivity varied across the studied area, influenced by environmental conditions (both atmospheric and marine), although patterns were highly correlated between both lichen taxa. Ecological speciation due to the differential association of photobionts to each littoral zone is suspected to have occurred in marine Lichina.}, }
@article {pmid26175749, year = {2015}, author = {Hol, WH and de Boer, W and de Hollander, M and Kuramae, EE and Meisner, A and van der Putten, WH}, title = {Context dependency and saturating effects of loss of rare soil microbes on plant productivity.}, journal = {Frontiers in plant science}, volume = {6}, number = {}, pages = {485}, pmid = {26175749}, issn = {1664-462X}, abstract = {Land use intensification is associated with loss of biodiversity and altered ecosystem functioning. Until now most studies on the relationship between biodiversity and ecosystem functioning focused on random loss of species, while loss of rare species that usually are the first to disappear received less attention. Here we test if the effect of rare microbial species loss on plant productivity depends on the origin of the microbial soil community. Soils were sampled from three land use types at two farms. Microbial communities with increasing loss of rare species were created by inoculating sterilized soils with serially diluted soil suspensions. After 8 months of incubation, the effects of the different soil communities on abiotic soil properties, soil processes, microbial community composition, and plant productivity was measured. Dilution treatments resulted in increasing species loss, which was in relation to abundance of bacteria in the original field soil, without affecting most of the other soil parameters and processes. Microbial species loss affected plant biomass positively, negatively or not at all, depending on soil origin, but not on land use history. Even within fields the effects of dilution on plant biomass varied between replicates, suggesting heterogeneity in microbial community composition. The effects of medium and severe species loss on plant biomass were similar, pointing toward a saturating effect of species loss. We conclude that changes in the composition of the soil microbial community, including rare species loss, can affect plant productivity, depending on the composition of the initial microbial community. Future work on the relation between function and species loss effects should address this variation by including multiple sampling origins.}, }
@article {pmid26172211, year = {2016}, author = {Kaltenpoth, M and Strupat, K and Svatoš, A}, title = {Linking metabolite production to taxonomic identity in environmental samples by (MA)LDI-FISH.}, journal = {The ISME journal}, volume = {10}, number = {2}, pages = {527-531}, pmid = {26172211}, issn = {1751-7370}, mesh = {Animals ; Anti-Bacterial Agents/chemistry/metabolism ; In Situ Hybridization, Fluorescence/*methods ; Mass Spectrometry/*methods ; Metabolomics/*methods ; Streptomyces/chemistry/classification/*isolation &amp; purification/*metabolism ; *Symbiosis ; Wasps/*microbiology/physiology ; }, abstract = {One of the greatest challenges in microbial ecology remains to link the metabolic activity of individual cells to their taxonomic identity and localization within environmental samples. Here we combined mass-spectrometric imaging (MSI) through (matrix-assisted) laser desorption ionization time-of-flight MSI ([MA]LDI-TOF/MSI) with fluorescence in situ hybridization (FISH) to monitor antibiotic production in the defensive symbiosis between beewolf wasps and 'Streptomyces philanthi' bacteria. Our results reveal similar distributions of the different symbiont-produced antibiotics across the surface of beewolf cocoons, which colocalize with the producing cell populations. Whereas FISH achieves single-cell resolution, MSI is currently limited to a step size of 20-50 μm in the combined approach because of the destructive effects of high laser intensities that are associated with tighter laser beam focus at higher lateral resolution. However, on the basis of the applicability of (MA)LDI-MSI to a broad range of small molecules, its combination with FISH provides a powerful tool for studying microbial interactions in situ, and further modifications of this technique could allow for linking metabolic profiling to gene expression.}, }
@article {pmid26164031, year = {2015}, author = {Gelzinis, A and Verikas, A and Vaiciukynas, E and Bacauskiene, M and Sulcius, S and Simoliunas, E and Staniulis, J and Paskauskas, R}, title = {Automatic detection and morphological delineation of bacteriophages in electron microscopy images.}, journal = {Computers in biology and medicine}, volume = {64}, number = {}, pages = {101-116}, doi = {10.1016/j.compbiomed.2015.06.015}, pmid = {26164031}, issn = {1879-0534}, mesh = {Algorithms ; Aphanizomenon/virology ; Bacteriophages/classification/*ultrastructure ; Capsid/classification/*ultrastructure ; Image Processing, Computer-Assisted/*methods ; Microscopy, Electron/*methods ; Pattern Recognition, Automated/*methods ; }, abstract = {Automatic detection, recognition and geometric characterization of bacteriophages in electron microscopy images was the main objective of this work. A novel technique, combining phase congruency-based image enhancement, Hough transform-, Radon transform- and open active contours with free boundary conditions-based object detection was developed to detect and recognize the bacteriophages associated with infection and lysis of cyanobacteria Aphanizomenon flos-aquae. A random forest classifier designed to recognize phage capsids provided higher than 99% accuracy, while measurable phage tails were detected and associated with a correct capsid with 81.35% accuracy. Automatically derived morphometric measurements of phage capsids and tails exhibited lower variability than the ones obtained manually. The technique allows performing precise and accurate quantitative (e.g. abundance estimation) and qualitative (e.g. diversity and capsid size) measurements for studying the interactions between host population and different phages that infect the same host.}, }
@article {pmid26161548, year = {2015}, author = {Moya-Pérez, A and Neef, A and Sanz, Y}, title = {Bifidobacterium pseudocatenulatum CECT 7765 Reduces Obesity-Associated Inflammation by Restoring the Lymphocyte-Macrophage Balance and Gut Microbiota Structure in High-Fat Diet-Fed Mice.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0126976}, pmid = {26161548}, issn = {1932-6203}, mesh = {Animals ; Bifidobacterium/*immunology ; Diet, High-Fat/adverse effects ; Gastrointestinal Microbiome ; Immunity, Cellular ; Inflammation/complications/immunology/*microbiology/*therapy ; Lymphocytes/*immunology/microbiology ; Macrophages/*immunology/microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Obesity/complications/immunology/*microbiology/*therapy ; Weight Gain ; }, abstract = {BACKGROUND/OBJECTIVES: The role of intestinal dysbiosis in obesity-associated systemic inflammation via the cross-talk with peripheral tissues is under debate. Our objective was to decipher the mechanisms by which intervention in the gut ecosystem with a specific Bifidobacterium strain reduces systemic inflammation and improves metabolic dysfunction in obese high-fat diet (HFD) fed mice.<br><br>METHODS: Adult male wild-type C57BL-6 mice were fed either a standard or HFD, supplemented with placebo or Bifidobacterium pseudocatenulatum CECT 7765, for 14 weeks. Lymphocytes, macrophages and cytokine/chemokine concentrations were quantified in blood, gut, liver and adipose tissue using bead-based multiplex assays. Biochemical parameters in serum were determined by ELISA and enzymatic assays. Histology was assessed by hematoxylin-eosin staining. Microbiota was analyzed by 16S rRNA gene pyrosequencing and quantitative PCR.<br><br>RESULTS: B. pseudocatenulatum CECT 7765 reduced obesity-associated systemic inflammation by restoring the balance between regulatory T cells (Tregs) and B lymphocytes and reducing pro-inflammatory cytokines of adaptive (IL-17A) and innate (TNF-&#x3b1;) immunity and endotoxemia. In the gut, the bifidobacterial administration partially restored the HFD-induced alterations in microbiota, reducing abundances of Firmicutes and of LPS-producing Proteobacteria, paralleled to reductions in B cells, macrophages, and cytokines (IL-6, MCP-1, TNF-&#x3b1;, IL-17A), which could contribute to systemic effects. In adipose tissue, bifidobacterial administration reduced B cells whereas in liver the treatment increased Tregs and shifted different cytokines (MCP-1 plus ILP-10 in adipose tissue and INF-&#x3b3; plus IL-1&#x3b2; in liver). In both tissues, the bifidobacteria reduced pro-inflammatory macrophages and, TNF-&#x3b1; and IL-17A concentrations. These effects were accompanied by reductions in body weight gain and in serum cholesterol, triglyceride, glucose and insulin levels and improved oral glucose tolerance and insulin sensitivity in obese mice.<br><br>CONCLUSIONS: Here, we provide evidence of the immune cellular mechanisms by which the inflammatory cascade associated with diet-induced obesity is attenuated by the administration of a specific Bifidobacterium strain and that these effects are associated with modulation of gut microbiota structure.}, }
@article {pmid26157601, year = {2015}, author = {Coutinho, FH and Meirelles, PM and Moreira, AP and Paranhos, RP and Dutilh, BE and Thompson, FL}, title = {Niche distribution and influence of environmental parameters in marine microbial communities: a systematic review.}, journal = {PeerJ}, volume = {3}, number = {}, pages = {e1008}, pmid = {26157601}, issn = {2167-8359}, abstract = {Associations between microorganisms occur extensively throughout Earth's oceans. Understanding how microbial communities are assembled and how the presence or absence of species is related to that of others are central goals of microbial ecology. Here, we investigate co-occurrence associations between marine prokaryotes by combining 180 new and publicly available metagenomic datasets from different oceans in a large-scale meta-analysis. A co-occurrence network was created by calculating correlation scores between the abundances of microorganisms in metagenomes. A total of 1,906 correlations amongst 297 organisms were detected, segregating them into 11 major groups that occupy distinct ecological niches. Additionally, by analyzing the oceanographic parameters measured for a selected number of sampling sites, we characterized the influence of environmental variables over each of these 11 groups. Clustering organisms into groups of taxa that have similar ecology, allowed the detection of several significant correlations that could not be observed for the taxa individually.}, }
@article {pmid26157420, year = {2015}, author = {Becraft, ED and Wood, JM and Rusch, DB and Kühl, M and Jensen, SI and Bryant, DA and Roberts, DW and Cohan, FM and Ward, DM}, title = {The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {590}, pmid = {26157420}, issn = {1664-302X}, abstract = {Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species [putative ecotypes (PEs)], which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper 1 mm-thick mat layer. Importantly, in most cases variants predicted to belong to the same PE formed unique clusters relative to temperature and depth in the mat in canonical correspondence analysis, supporting the hypothesis that while the PEs are ecologically distinct, the members of each ecotype are ecologically homogeneous. PEs responded differently to experimental perturbations of temperature and light, but the genetic variation within each PE was maintained as the relative abundances of PEs changed, further indicating that each population responded as a set of ecologically interchangeable individuals. Compared to PEs that predominate deeper within the mat photic zone, the timing of transcript abundances for selected genes differed for PEs that predominate in microenvironments closer to upper surface of the mat with spatiotemporal differences in light and O2 concentration. All of these findings are consistent with the hypotheses that Synechococcus species in hot spring mats are sets of ecologically interchangeable individuals that are differently adapted, that these adaptations control their distributions, and that the resulting distributions constrain the activities of the species in space and time.}, }
@article {pmid26156239, year = {2015}, author = {Wang, Y and Liu, L and Chen, H and Yang, J}, title = {Spatiotemporal dynamics and determinants of planktonic bacterial and microeukaryotic communities in a Chinese subtropical river.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {21}, pages = {9255-9266}, doi = {10.1007/s00253-015-6773-0}, pmid = {26156239}, issn = {1432-0614}, mesh = {Ammonia/analysis ; Bacteria/*classification ; *Biota ; China ; Chlorophyll/analysis ; Chlorophyll A ; Denaturing Gradient Gel Electrophoresis ; Eukaryotic Cells/*classification ; Phosphates/analysis ; Plankton/*growth &amp; development ; Rivers/*microbiology ; Seasons ; Spatio-Temporal Analysis ; Temperature ; }, abstract = {The spatiotemporal distribution of microbial diversity, community composition, and their major drivers are fundamental issues in microbial ecology. In this study, the planktonic bacterial and microeukaryotic communities of the Jiulong River were investigated across both wet and dry seasons by using denaturing gradient gel electrophoresis (DGGE). We found evidence of temporal change between wet and dry seasons and distinct spatial patterns of bacterial and microeukaryotic communities. Both bacterial and microeukaryotic communities were strongly correlated with temperature, NH4-N, PO4-P, and chlorophyll a, and these environmental factors were significant but incomplete predictors of microbial community composition. Local environmental factors combined with spatial and temporal factors strongly controlled both bacterial and microeukaryotic communities in complex ways, whereas the direct influence of spatial and temporal factors appeared to be relatively small. Path analysis revealed that the microeukaryotic community played key roles in shaping bacterial community composition, perhaps through grazing effects and multiple interactions. Both Betaproteobacteria and Actinobacteria were the most dominant and diverse taxa in bacterial communities, while the microeukaryotic communities were dominated by Ciliophora (zooplankton) and Chlorophyta (phytoplankton). Our results demonstrated that both bacterial and microeukaryotic communities along the Jiulong River displayed a distinct spatiotemporal pattern; however, microeukaryotic communities exhibited a stronger distance-decay relationship than bacterial communities and their spatial patterns were mostly driven by local environmental variables rather than season or spatial processes of the river. Therefore, we have provided baseline data to support further research on river microbial food webs and integrating different microbial groups into river models.}, }
@article {pmid26156140, year = {2015}, author = {Wallace-Salinas, V and Brink, DP and Ahrén, D and Gorwa-Grauslund, MF}, title = {Cell periphery-related proteins as major genomic targets behind the adaptive evolution of an industrial Saccharomyces cerevisiae strain to combined heat and hydrolysate stress.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {514}, pmid = {26156140}, issn = {1471-2164}, mesh = {Biological Evolution ; Ethanol/metabolism ; Genomics/*methods ; Hot Temperature ; Industrial Microbiology ; *Mutation ; Saccharomyces cerevisiae/genetics/*growth &amp; development/metabolism ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; Selection, Genetic ; Sequence Analysis, DNA ; Stress, Physiological ; }, abstract = {BACKGROUND: Laboratory evolution is an important tool for developing robust yeast strains for bioethanol production since the biological basis behind combined tolerance requires complex alterations whose proper regulation is difficult to achieve by rational metabolic engineering. Previously, we reported on the evolved industrial Saccharomyces cerevisiae strain ISO12 that had acquired improved tolerance to grow and ferment in the presence of lignocellulose-derived inhibitors at high temperature (39 °C). In the current study, we used comparative genomics to uncover the extent of the genomic alterations that occurred during the evolution process and investigated possible associations between the mutations and the phenotypic traits in ISO12.<br><br>RESULTS: Through whole-genome sequencing and variant calling we identified a high number of strain-unique SNPs and INDELs in both ISO12 and the parental strain Ethanol Red. The variants were predicted to have 760 non-synonymous effects in both strains combined and were significantly enriched in Gene Ontology terms related to cell periphery, membranes and cell wall. Eleven genes, including MTL1, FLO9/FLO11, and CYC3 were found to be under positive selection in ISO12. Additionally, the FLO genes exhibited changes in copy number, and the alterations to this gene family were correlated with experimental results of multicellularity and invasive growth in the adapted strain. An independent lipidomic analysis revealed further differences between the strains in the content of nine lipid species. Finally, ISO12 displayed improved viability in undiluted spruce hydrolysate that was unrelated to reduction of inhibitors and changes in cell wall integrity, as shown by HPLC and lyticase assays.<br><br>CONCLUSIONS: Together, the results of the sequence comparison and the physiological characterisations indicate that cell-periphery proteins (e.g. extracellular sensors such as MTL1) and peripheral lipids/membranes are important evolutionary targets in the process of adaptation to the combined stresses. The capacity of ISO12 to develop complex colony formation also revealed multicellularity as a possible evolutionary strategy to improve competitiveness and tolerance to environmental stresses (also reflected by the FLO genes). Although a panel of altered genes with high relevance to the novel phenotype was detected, this study also demonstrates that the observed long-term molecular effects of thermal and inhibitor stress have polygenetic basis.}, }
@article {pmid26156053, year = {2016}, author = {Ozaki, A and Adams, E and Binh, CT and Tong, T and Gaillard, JF and Gray, KA and Kelly, JJ}, title = {One-Time Addition of Nano-TiO2 Triggers Short-Term Responses in Benthic Bacterial Communities in Artificial Streams.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {266-275}, pmid = {26156053}, issn = {1432-184X}, mesh = {Bacteria/classification/drug effects/genetics/metabolism ; Ecosystem ; Nanoparticles/*toxicity ; Rivers/*microbiology ; Titanium/*toxicity ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Nano-TiO2 is an engineered nanomaterial whose production and use are increasing rapidly. Hence, aquatic habitats are at risk for nano-TiO2 contamination due to potential inputs from urban and suburban runoff and domestic wastewater. Nano-TiO2 has been shown to be toxic to a wide range of aquatic organisms, but little is known about the effects of nano-TiO2 on benthic microbial communities. This study used artificial stream mesocosms to assess the effects of a single addition of nano-TiO2 (P25 at a final concentration of 1 mg l(-1)) on the abundance, activity, and community composition of sediment-associated bacterial communities. The addition of nano-TiO2 resulted in a rapid (within 1 day) decrease in bacterial abundance in artificial stream sediments, but bacterial abundance returned to control levels within 3 weeks. Pyrosequencing of partial 16S rRNA genes did not indicate any significant changes in the relative abundance of any bacterial taxa with nano-TiO2 treatment, indicating that nano-TiO2 was toxic to a broad range of bacterial taxa and that recovery of the bacterial communities was not driven by changes in community composition. Addition of nano-TiO2 also resulted in short-term increases in respiration rates and denitrification enzyme activity, with both returning to control levels within 3 weeks. The results of this study demonstrate that single-pulse additions of nano-TiO2 to aquatic habitats have the potential to significantly affect the abundance and activity of benthic microbial communities and suggest that interactions of TiO2 nanoparticles with environmental matrices may limit the duration of their toxicity.}, }
@article {pmid26150458, year = {2015}, author = {Martínez-Lavanchy, PM and Chen, Z and Lünsmann, V and Marin-Cevada, V and Vilchez-Vargas, R and Pieper, DH and Reiche, N and Kappelmeyer, U and Imparato, V and Junca, H and Nijenhuis, I and Müller, JA and Kuschk, P and Heipieper, HJ}, title = {Microbial Toluene Removal in Hypoxic Model Constructed Wetlands Occurs Predominantly via the Ring Monooxygenation Pathway.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {18}, pages = {6241-6252}, pmid = {26150458}, issn = {1098-5336}, mesh = {Anaerobiosis ; Bacteria/classification/genetics ; Biota ; Biotransformation ; Carbon/metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Environmental Pollutants/*metabolism ; Hydrogen/metabolism ; *Metabolic Networks and Pathways ; Microarray Analysis ; Mixed Function Oxygenases/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Toluene/*metabolism ; Wetlands ; }, abstract = {In the present study, microbial toluene degradation in controlled constructed wetland model systems, planted fixed-bed reactors (PFRs), was queried with DNA-based methods in combination with stable isotope fractionation analysis and characterization of toluene-degrading microbial isolates. Two PFR replicates were operated with toluene as the sole external carbon and electron source for 2 years. The bulk redox conditions in these systems were hypoxic to anoxic. The autochthonous bacterial communities, as analyzed by Illumina sequencing of 16S rRNA gene amplicons, were mainly comprised of the families Xanthomonadaceae, Comamonadaceae, and Burkholderiaceae, plus Rhodospirillaceae in one of the PFR replicates. DNA microarray analyses of the catabolic potentials for aromatic compound degradation suggested the presence of the ring monooxygenation pathway in both systems, as well as the anaerobic toluene pathway in the PFR replicate with a high abundance of Rhodospirillaceae. The presence of catabolic genes encoding the ring monooxygenation pathway was verified by quantitative PCR analysis, utilizing the obtained toluene-degrading isolates as references. Stable isotope fractionation analysis showed low-level of carbon fractionation and only minimal hydrogen fractionation in both PFRs, which matches the fractionation signatures of monooxygenation and dioxygenation. In combination with the results of the DNA-based analyses, this suggests that toluene degradation occurs predominantly via ring monooxygenation in the PFRs.}, }
@article {pmid26143359, year = {2016}, author = {Samant, S and Huo, T and Dawson, JO and Hahn, D}, title = {Abundance and Relative Distribution of Frankia Host Infection Groups Under Actinorhizal Alnus glutinosa and Non-actinorhizal Betula nigra Trees.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {473-481}, pmid = {26143359}, issn = {1432-184X}, mesh = {Alnus/*microbiology ; Betula/*microbiology ; Frankia/genetics/*growth &amp; development/isolation &amp; purification ; Plant Roots/microbiology ; Soil Microbiology ; Trees/growth &amp; development/microbiology ; }, abstract = {Quantitative polymerase chain reaction (qPCR) was used to assess the abundance and relative distribution of host infection groups of the root-nodule forming, nitrogen-fixing actinomycete Frankia in four soils with similar physicochemical characteristics, two of which were vegetated with a host plant, Alnus glutinosa, and two with a non-host plant, Betula nigra. Analyses of DAPI-stained cells at three locations, i.e., at a distance of less than 1 m (near stem), 2.5 m (middle crown), and 3-5 m (crown edge) from the stems of both tree species revealed no statistically significant differences in abundance. Frankiae generally accounted for 0.01 to 0.04 % of these cells, with values between 4 and 36 × 10(5) cells (g soil)(-1). In three out of four soils, abundance of frankiae was significantly higher at locations "near stem" and/or "middle crown" compared to "crown edge," while numbers at these locations were not different in the fourth soil. Frankiae of the Alnus host infection group were dominant in all samples accounting for about 75 % and more of the cells, with no obvious differences with distance to stem. In three of the soils, all of these cells were represented by strain Ag45/Mut15. In the fourth soil that was vegetated with older A. glutinosa trees, about half of these cells belonged to a different subgroup represented by strain ArI3. In all soils, the remaining cells belonged to the Elaeagnus host infection group represented by strain EAN1pec. Casuarina-infective frankiae were not found. Abundance and relative distribution of Frankia host infection groups were similar in soils under the host plant A. glutinosa and the non-host plant B. nigra. Results did thus not reveal any specific effects of plant species on soil Frankia populations.}, }
@article {pmid26140529, year = {2016}, author = {Beam, JP and Jay, ZJ and Schmid, MC and Rusch, DB and Romine, MF and Jennings, Rde M and Kozubal, MA and Tringe, SG and Wagner, M and Inskeep, WP}, title = {Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous 'streamer' community.}, journal = {The ISME journal}, volume = {10}, number = {1}, pages = {210-224}, pmid = {26140529}, issn = {1751-7370}, support = {294343/ERC_/European Research Council/International ; }, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Ecosystem ; Genome, Archaeal ; Hot Springs/analysis/*microbiology ; In Situ Hybridization, Fluorescence ; Metagenomics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {The candidate archaeal phylum 'Aigarchaeota' contains microorganisms from terrestrial and subsurface geothermal ecosystems. The phylogeny and metabolic potential of Aigarchaeota has been deduced from several recent single-cell amplified genomes; however, a detailed description of their metabolic potential and in situ transcriptional activity is absent. Here, we report a comprehensive metatranscriptome-based reconstruction of the in situ metabolism of Aigarchaeota in an oxic, hot spring filamentous 'streamer' community. Fluorescence in situ hybridization showed that these newly discovered Aigarchaeota are filamentous, which is consistent with the presence and transcription of an actin-encoding gene. Aigarchaeota filaments are intricately associated with other community members, which include both bacteria (for example, filamentous Thermocrinis spp.) and archaea. Metabolic reconstruction of genomic and metatranscriptomic data suggests that this aigarchaeon is an aerobic, chemoorganoheterotroph with autotrophic potential. A heme copper oxidase complex was identified in the environmental genome assembly and highly transcribed in situ. Potential electron donors include acetate, fatty acids, amino acids, sugars and aromatic compounds, which may originate from extracellular polymeric substances produced by other microorganisms shown to exist in close proximity and/or autochthonous dissolved organic carbon (OC). Transcripts related to genes specific to each of these potential electron donors were identified, indicating that this aigarchaeon likely utilizes several OC substrates. Characterized members of this lineage cannot synthesize heme, and other cofactors and vitamins de novo, which suggests auxotrophy. We propose the name Candidatus 'Calditenuis aerorheumensis' for this aigarchaeon, which describes its filamentous morphology and its primary electron acceptor, oxygen.}, }
@article {pmid26135985, year = {2015}, author = {Crauwels, S and Van Assche, A and de Jonge, R and Borneman, AR and Verreth, C and Troels, P and De Samblanx, G and Marchal, K and Van de Peer, Y and Willems, KA and Verstrepen, KJ and Curtin, CD and Lievens, B}, title = {Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {21}, pages = {9123-9134}, doi = {10.1007/s00253-015-6769-9}, pmid = {26135985}, issn = {1432-0614}, mesh = {Beer/microbiology ; Brettanomyces/classification/*genetics/isolation &amp; purification/*physiology ; Carbon/*metabolism ; Carbonated Beverages/microbiology ; DNA, Fungal/genetics ; *Genetic Variation ; Genomics ; Genotype ; Metabolic Networks and Pathways/*genetics ; Nitrogen/*metabolism ; Phenotype ; Polymerase Chain Reaction ; Sequence Deletion ; Wine/microbiology ; alpha-Glucosidases/genetics/metabolism ; beta-Glucosidase/genetics/metabolism ; }, abstract = {Recent studies have suggested a correlation between genotype groups of Brettanomyces bruxellensis and their source of isolation. To further explore this relationship, the objective of this study was to assess metabolic differences in carbon and nitrogen assimilation between different B. bruxellensis strains from three beverages, including beer, wine, and soft drink, using Biolog Phenotype Microarrays. While some similarities of physiology were noted, many traits were variable among strains. Interestingly, some phenotypes were found that could be linked to strain origin, especially for the assimilation of particular α- and β-glycosides as well as α- and β-substituted monosaccharides. Based upon gene presence or absence, an α-glucosidase and β-glucosidase were found explaining the observed phenotypes. Further, using a PCR screen on a large number of isolates, we have been able to specifically link a genomic deletion to the beer strains, suggesting that this region may have a fitness cost for B. bruxellensis in certain fermentation systems such as brewing. More specifically, none of the beer strains were found to contain a β-glucosidase, which may have direct impacts on the ability for these strains to compete with other microbes or on flavor production.}, }
@article {pmid26127013, year = {2015}, author = {Prévoteau, A and Geirnaert, A and Arends, JBA and Lannebère, S and Van de Wiele, T and Rabaey, K}, title = {Hydrodynamic chronoamperometry for probing kinetics of anaerobic microbial metabolism--case study of Faecalibacterium prausnitzii.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {11484}, pmid = {26127013}, issn = {2045-2322}, mesh = {Anaerobiosis ; Colony Count, Microbial ; Electrochemistry/*methods ; Electrodes ; Glucose/metabolism ; Gram-Positive Bacteria/*metabolism ; *Hydrodynamics ; Kinetics ; Reproducibility of Results ; Riboflavin/metabolism ; Time Factors ; }, abstract = {Monitoring in vitro the metabolic activity of microorganisms aids bioprocesses and enables better understanding of microbial metabolism. Redox mediators can be used for this purpose via different electrochemical techniques that are either complex or only provide non-continuous data. Hydrodynamic chronoamperometry using a rotating disc electrode (RDE) can alleviate these issues but was seldom used and is poorly characterized. The kinetics of Faecalibacterium prausnitzii A2-165, a beneficial gut microbe, were determined using a RDE with riboflavin as redox probe. This butyrate producer anaerobically ferments glucose and reduces riboflavin whose continuous monitoring on a RDE provided highly accurate kinetic measurements of its metabolism, even at low cell densities. The metabolic reaction rate increased linearly over a broad range of cell concentrations (9 × 10(4) to 5 × 10(7) cells.mL(-1)). Apparent Michaelis-Menten kinetics was observed with respect to riboflavin (KM = 6 μM; kcat = 5.3 × 10(5) s(-1), at 37 °C) and glucose (KM = 6 μM; kcat = 2.4 × 10(5) s(-1)). The short temporal resolution allows continuous monitoring of fast cellular events such as kinetics inhibition with butyrate. Furthermore, we detected for the first time riboflavin reduction by another potential probiotic, Butyricicoccus pullicaecorum. The ability of the RDE for fast, accurate, simple and continuous measurements makes it an ad hoc tool for assessing bioprocesses at high resolution.}, }
@article {pmid26126524, year = {2015}, author = {Radecka, D and Mukherjee, V and Mateo, RQ and Stojiljkovic, M and Foulquié-Moreno, MR and Thevelein, JM}, title = {Looking beyond Saccharomyces: the potential of non-conventional yeast species for desirable traits in bioethanol fermentation.}, journal = {FEMS yeast research}, volume = {15}, number = {6}, pages = {}, doi = {10.1093/femsyr/fov053}, pmid = {26126524}, issn = {1567-1364}, mesh = {Anti-Infective Agents/toxicity ; Bioreactors/*microbiology ; Ethanol/*metabolism ; Fermentation ; *Industrial Microbiology ; Stress, Physiological ; Yeasts/growth &amp; development/*metabolism ; }, abstract = {Saccharomyces cerevisiae has been used for millennia in the production of food and beverages and is by far the most studied yeast species. Currently, it is also the most used microorganism in the production of first-generation bioethanol from sugar or starch crops. Second-generation bioethanol, on the other hand, is produced from lignocellulosic feedstocks that are pretreated and hydrolyzed to obtain monomeric sugars, mainly D-glucose, D-xylose and L-arabinose. Recently, S. cerevisiae recombinant strains capable of fermenting pentose sugars have been generated. However, the pretreatment of the biomass results in hydrolysates with high osmolarity and high concentrations of inhibitors. These compounds negatively influence the fermentation process. Therefore, robust strains with high stress tolerance are required. Up to now, more than 2000 yeast species have been described and some of these could provide a solution to these limitations because of their high tolerance to the most predominant stress conditions present in a second-generation bioethanol reactor. In this review, we will summarize what is known about the non-conventional yeast species showing unusual tolerance to these stresses, namely Zygosaccharomyces rouxii (osmotolerance), Kluyveromyces marxianus and Ogataea (Hansenula) polymorpha (thermotolerance), Dekkera bruxellensis (ethanol tolerance), Pichia kudriavzevii (furan derivatives tolerance) and Z. bailii (acetic acid tolerance).}, }
@article {pmid26123782, year = {2015}, author = {Blatchford, P and Bentley-Hewitt, KL and Stoklosinski, H and McGhie, T and Gearry, R and Gibson, G and Ansell, J}, title = {In vitro characterisation of the fermentation profile and prebiotic capacity of gold-fleshed kiwifruit.}, journal = {Beneficial microbes}, volume = {6}, number = {6}, pages = {829-839}, doi = {10.3920/BM2015.0006}, pmid = {26123782}, issn = {1876-2891}, mesh = {Actinidia/*metabolism ; Aerobiosis ; Anaerobiosis ; Carbohydrate Metabolism ; Carboxylic Acids/metabolism ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fermentation ; Fruit/*metabolism ; Gastrointestinal Microbiome/*drug effects ; Humans ; Microbiota/*drug effects ; Models, Theoretical ; *Prebiotics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {A new Actinidia chinensis gold-fleshed kiwifruit cultivar 'Zesy002' was tested to investigate whether it could positively modulate the composition of the human colonic microbiota. Digested Zesy002 kiwifruit was added to in vitro pH-controlled anaerobic batch fermenters that were inoculated with representative human faecal microbiota. Alterations to the gut microbial ecology were determined by 16S rRNA gene sequencing and metabolic end products were measured using gas chromatography and liquid chromatography - mass spectrometry. Results indicated a substantial shift in the composition of bacteria within the gut models caused by kiwifruit supplementation. Zesy002 supplemented microbiota had a significantly higher abundance of Bacteroides spp., Parabacteroides spp. and Bifidobacterium spp. after 48 h of fermentation compared with the start of the fermentation. Organic acids from kiwifruit were able to endure simulated gastrointestinal digestion and were detectable in the first 10 h of fermentation. The fermentable carbohydrates were converted to beneficial organic acids with a particular predilection for propionate production, corresponding with the rise in Bacteroides spp. and Parabacteroides spp. These results support the claim that Zesy002 kiwifruit non-digestible fractions can effect favourable changes to the human colonic microbial community and primary metabolites, and demonstrate a hitherto unknown effect of Zesy002 on colonic microbiota under in vitro conditions.}, }
@article {pmid26120139, year = {2015}, author = {McIlroy, SJ and Saunders, AM and Albertsen, M and Nierychlo, M and McIlroy, B and Hansen, AA and Karst, SM and Nielsen, JL and Nielsen, PH}, title = {MiDAS: the field guide to the microbes of activated sludge.}, journal = {Database : the journal of biological databases and curation}, volume = {2015}, number = {}, pages = {bav062}, pmid = {26120139}, issn = {1758-0463}, mesh = {*Bacteria/classification/genetics ; *Databases, Nucleic Acid ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sewage/*microbiology ; }, abstract = {The Microbial Database for Activated Sludge (MiDAS) field guide is a freely available online resource linking the identity of abundant and process critical microorganisms in activated sludge wastewater treatment systems to available data related to their functional importance. Phenotypic properties of some of these genera are described, but most are known only from sequence data. The MiDAS taxonomy is a manual curation of the SILVA taxonomy that proposes a name for all genus-level taxa observed to be abundant by large-scale 16 S rRNA gene amplicon sequencing of full-scale activated sludge communities. The taxonomy can be used to classify unknown sequences, and the online MiDAS field guide links the identity to the available information about their morphology, diversity, physiology and distribution. The use of a common taxonomy across the field will provide a solid foundation for the study of microbial ecology of the activated sludge process and related treatment processes. The online MiDAS field guide is a collaborative workspace intended to facilitate a better understanding of the ecology of activated sludge and related treatment processes--knowledge that will be an invaluable resource for the optimal design and operation of these systems.}, }
@article {pmid26118321, year = {2015}, author = {Di Cesare, A and Eckert, EM and Teruggi, A and Fontaneto, D and Bertoni, R and Callieri, C and Corno, G}, title = {Constitutive presence of antibiotic resistance genes within the bacterial community of a large subalpine lake.}, journal = {Molecular ecology}, volume = {24}, number = {15}, pages = {3888-3900}, doi = {10.1111/mec.13293}, pmid = {26118321}, issn = {1365-294X}, mesh = {Bacteria/*genetics ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; *Genes, Bacterial ; Italy ; Lakes/*microbiology ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Switzerland ; }, abstract = {The fate of antibiotic resistance genes (ARGs) in environmental microbial communities is of primary concern as prodromal of a potential transfer to pathogenic bacteria. Although of diverse origin, the persistence of ARGs in aquatic environments is highly influenced by anthropic activities, allowing potential control actions in well-studied environments. However, knowledge of abundance and space-time distribution of ARGs in ecosystems is still scarce. Using quantitative real-time PCR, we investigated the presence and the abundance of twelve ARGs (against tetracyclines, β-lactams, aminoglycosides, quinolones and sulphonamides) at different sampling sites, depths and seasons, in Lake Maggiore, a large subalpine lake, and in the area of its watershed. We then evaluated the correlation between each ARG and a number of ecological parameters in the water column in the deepest part of the lake. Our results suggest the constitutive presence of at least four ARGs within the bacterial community with a high proportion of bacteria potentially resistant to tetracyclines and sulphonamides. The presence of these ARGs was independent of the total bacterial density and temperature. The dynamics of tet(A) and sulII genes were, however, positively correlated with dissolved oxygen and negatively to chlorophyll a, suggesting that the resistant microbes inhabit specific niches. These observations indicate that the lake is a reservoir of antibiotic resistances, highlighting the need of a deeper understanding of the sources of ARGs and the factors allowing their persistence in waters.}, }
@article {pmid26113052, year = {2016}, author = {Morris, D and O'Connor, M and Izdebski, R and Corcoran, M and Ludden, CE and McGrath, E and Buckley, V and Cryan, B and Gniadkowski, M and Cormican, M}, title = {Dissemination of clonally related multidrug-resistant Klebsiella pneumoniae in Ireland.}, journal = {Epidemiology and infection}, volume = {144}, number = {2}, pages = {443-448}, doi = {10.1017/S0950268815001041}, pmid = {26113052}, issn = {1469-4409}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Ireland/epidemiology ; Klebsiella Infections/*epidemiology/microbiology ; Klebsiella pneumoniae/*classification/*drug effects/genetics/isolation &amp; purification ; }, abstract = {In October 2012, an outbreak of gentamicin-resistant, ciprofloxacin non-susceptible extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae occurred in a neonatal intensive care unit in Ireland. In order to determine whether the outbreak strain was more widely dispersed in the country, 137 isolates of K. pneumoniae with this resistance phenotype collected from 17 hospitals throughout Ireland between January 2011 and July 2013 were examined. ESBL production was confirmed phenotypically and all isolates were screened for susceptibility to 19 antimicrobial agents and for the presence of genes encoding bla TEM, bla SHV, bla OXA, and bla CTX-M; 22 isolates were also screened for bla KPC, bla NDM, bla VIM, bla IMP and bla OXA-48 genes. All isolates harboured bla SHV and bla CTX-M and were resistant to ciprofloxacin, gentamicin, nalidixic acid, amoxicillin-clavulanate, and cefpodoxime; 15 were resistant to ertapenem, seven to meropenem and five isolates were confirmed as carbapenemase producers. Pulsed-field gel electrophoresis of all isolates identified 16 major clusters, with two clusters comprising 61% of the entire collection. Multilocus sequence typing of a subset of these isolates identified a novel type, ST1236, a single locus variant of ST48. Data suggest that two major clonal groups, ST1236/ST48 (CG43) and ST15/ST14 (CG15) have been circulating in Ireland since at least January 2011.}, }
@article {pmid26112346, year = {2015}, author = {Guo, K and Soeriyadi, AH and Feng, H and Prévoteau, A and Patil, SA and Gooding, JJ and Rabaey, K}, title = {Heat-treated stainless steel felt as scalable anode material for bioelectrochemical systems.}, journal = {Bioresource technology}, volume = {195}, number = {}, pages = {46-50}, doi = {10.1016/j.biortech.2015.06.060}, pmid = {26112346}, issn = {1873-2976}, mesh = {*Bioelectric Energy Sources ; Biofilms ; Catalysis ; Electricity ; Electrochemistry/*methods ; Electrodes ; *Hot Temperature ; Photoelectron Spectroscopy ; Stainless Steel/*chemistry ; Surface Properties ; }, abstract = {This work reports a simple and scalable method to convert stainless steel (SS) felt into an effective anode for bioelectrochemical systems (BESs) by means of heat treatment. X-ray photoelectron spectroscopy and cyclic voltammetry elucidated that the heat treatment generated an iron oxide rich layer on the SS felt surface. The iron oxide layer dramatically enhanced the electroactive biofilm formation on SS felt surface in BESs. Consequently, the sustained current densities achieved on the treated electrodes (1 cm(2)) were around 1.5±0.13 mA/cm(2), which was seven times higher than the untreated electrodes (0.22±0.04 mA/cm(2)). To test the scalability of this material, the heat-treated SS felt was scaled up to 150 cm(2) and similar current density (1.5 mA/cm(2)) was achieved on the larger electrode. The low cost, straightforwardness of the treatment, high conductivity and high bioelectrocatalytic performance make heat-treated SS felt a scalable anodic material for BESs.}, }
@article {pmid26111964, year = {2016}, author = {Yang, Y and Zhang, J and Zhao, Q and Zhou, Q and Li, N and Wang, Y and Xie, S and Liu, Y}, title = {Sediment Ammonia-Oxidizing Microorganisms in Two Plateau Freshwater Lakes at Different Trophic States.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {257-265}, pmid = {26111964}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Biodiversity ; China ; Geologic Sediments/chemistry/*microbiology ; Lakes/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can contribute to ammonia biotransformation in freshwater lake ecosystems. However, the factors shaping the distribution of sediment AOA and AOB in plateau freshwater lake remains unclear. The present study investigated sediment AOA and AOB communities in two freshwater lakes (hypertrophic Dianchi Lake and mesotrophic Erhai Lake) on the Yunnan Plateau (China). A remarkable difference in the abundance, diversity, and composition of sediment AOA and AOB communities was observed between Dianchi Lake and Erhai Lake. AOB usually outnumbered AOA in Dianchi Lake, but AOA showed the dominance in Erhai Lake. Organic matter (OM), total nitrogen (TN), and total phosphorus (TP) might be the key determinants of AOB abundance, while AOA abundance was likely influenced by the ration of OM to TN (C/N). AOA or AOB community structure was found to be relatively similar in the same lake. TN and TP might play important roles in shaping sediment AOA and AOB compositions in Dianchi Lake and Erhai Lake. Moreover, Nitrososphaera-like AOA were detected in Dianchi Lake. Nitrosospira- and Nitrosomonas-like AOB were dominant in Dianchi Lake and Erhai Lake, respectively. Sediment AOA and AOB communities in Dianchi Lake and Erhai Lake were generally regulated by trophic state.}, }
@article {pmid26111963, year = {2016}, author = {Leong, LE and Denman, SE and Hugenholtz, P and McSweeney, CS}, title = {Amino Acid and Peptide Utilization Profiles of the Fluoroacetate-Degrading Bacterium Synergistetes Strain MFA1 Under Varying Conditions.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {494-504}, pmid = {26111963}, issn = {1432-184X}, mesh = {Amino Acids/chemistry/*metabolism ; Bacteria/growth &amp; development/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Chromatography, High Pressure Liquid ; Fluoroacetates/analysis/*metabolism ; Mass Spectrometry ; Peptides/chemistry/*metabolism ; }, abstract = {Synergistetes strain MFA1 is an asaccharolytic ruminal bacterium isolated based on its ability to degrade fluoroacetate, a plant toxin. The amino acid and peptide requirements of the bacterium were investigated under different culturing conditions. The growth of strain MFA1 and its fluoroacetate degradation rate were enhanced by peptide-rich protein hydrolysates (tryptone and yeast extract) compared to casamino acid, an amino acid-rich protein hydrolysate. Complete utilization and preference for arginine, asparagine, glutamate, glycine, and histidine as free amino acids from yeast extract were observed, while the utilization of serine, threonine, and lysine in free form and peptide-bound glutamate was stimulated during growth on fluoroacetate. A predominant peptide in yeast extract preferentially utilized by strain MFA1 was partially characterized by high-liquid performance chromatography-mass spectrometry as a hepta-glutamate oligopeptide. Similar utilization profiles of amino acids were observed between the co-culture of strain MFA1 with Methanobrevibacter smithii without fluoroacetate and pure strain MFA1 culture with fluoroacetate. This suggests that growth of strain MFA1 could be enhanced by a reduction of hydrogen partial pressure as a result of hydrogen removal by a methanogen or reduction of fluoroacetate.}, }
@article {pmid26106383, year = {2015}, author = {Hanif, MK and Hameed, S and Imran, A and Naqqash, T and Shahid, M and Van Elsas, JD}, title = {Isolation and characterization of a β-propeller gene containing phosphobacterium Bacillus subtilis strain KPS-11 for growth promotion of potato (Solanum tuberosum L.).}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {583}, pmid = {26106383}, issn = {1664-302X}, abstract = {Phosphate-solubilizing and phytate-mineralizing bacteria collectively termed as phosphobacteria provide a sustainable approach for managing P-deficiency in agricultural soils by supplying inexpensive phosphate to plants. A phosphobacterium Bacillus subtilis strain KPS-11 (Genbank accession no. KP006655) was isolated from potato (Solanum tuberosum L.) rhizosphere and characterized for potato plant growth promoting potential. The strain utilized both Ca-phosphate and Na-phytate in vitro and produced 6.48 μg mL(-1) indole-3-acetic acid in tryptophan supplemented medium. P-solubilization after 240 h was 66.4 μg mL(-1) alongwith the production of 19.3 μg mL(-1) gluconic acid and 5.3 μg mL(-1) malic acid. The extracellular phytase activity was higher (4.3 × 10(-10) kat mg(-1) protein) than the cell-associated phytase activity (1.6 × 10(-10) kat mg(-1) protein). B. subtilis strain KPS-11 utilized 40 carbon sources and showed resistance against 20 chemicals in GENIII micro-plate system demonstrating its metabolic potential. Phytase-encoding gene β-propeller (BPP) showed 92% amino acid similarity to BPP from B. subtilis (accession no.WP_014114128.1) and 83% structural similarity to BPP from B. subtilis (accession no 3AMR_A). Potato inoculation with B. subtilis strain KPS-11 increased the root/shoot length and root/shoot weight of potato as compared to non-inoculated control plants. Moreover, rifampicin-resistant derivative of KPS-11 were able to survive in the rhizosphere and on the roots of potato up to 60 days showing its colonization potential. The study indicates that B. subtilis strain KPS-11 can be a potential candidate for development of potato inoculum in P-deficient soils.}, }
@article {pmid26106378, year = {2015}, author = {De Maayer, P and Chan, WY and Martin, DA and Blom, J and Venter, SN and Duffy, B and Cowan, DA and Smits, TH and Coutinho, TA}, title = {Integrative conjugative elements of the ICEPan family play a potential role in Pantoea ananatis ecological diversification and antibiosis.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {576}, pmid = {26106378}, issn = {1664-302X}, abstract = {Pantoea ananatis is a highly versatile enterobacterium isolated from diverse environmental sources. The ecological diversity of this species may be attributed, in part, to the acquisition of mobile genetic elements. One such element is an Integrative and Conjugative Element (ICE). By means of in silico analyses the ICE elements belonging to a novel family, ICEPan, were identified in the genome sequences of five P. ananatis strains and characterized. PCR screening showed that ICEPan is prevalent among P. ananatis strains isolated from different environmental sources and geographic locations. Members of the ICEPan family share a common origin with ICEs of other enterobacteria, as well as conjugative plasmids of Erwinia spp. Aside from core modules for ICEPan integration, maintenance and dissemination, the ICEPan contain extensive non-conserved islands coding for proteins that may contribute toward various phenotypes such as stress response and antibiosis, and the highly diverse ICEPan thus plays a major role in the diversification of P. ananatis. An island is furthermore integrated within an ICEPan DNA repair-encoding locus umuDC and we postulate its role in stress-induced dissemination and/or expression of the genes on this island.}, }
@article {pmid26106159, year = {2015}, author = {O'Dwyer, JP and Kembel, SW and Sharpton, TJ}, title = {Backbones of evolutionary history test biodiversity theory for microbes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {27}, pages = {8356-8361}, pmid = {26106159}, issn = {1091-6490}, mesh = {Algorithms ; Bacteria/classification/genetics/*growth &amp; development ; *Biodiversity ; *Biological Evolution ; Ecology/methods ; Ecosystem ; *Models, Biological ; Phylogeny ; Species Specificity ; }, abstract = {Identifying the ecological and evolutionary mechanisms that determine biological diversity is a central question in ecology. In microbial ecology, phylogenetic diversity is an increasingly common and relevant means of quantifying community diversity, particularly given the challenges in defining unambiguous species units from environmental sequence data. We explore patterns of phylogenetic diversity across multiple bacterial communities drawn from different habitats and compare these data to evolutionary trees generated using theoretical models of biodiversity. We have two central findings. First, although on finer scales the empirical trees are highly idiosyncratic, on coarse scales the backbone of these trees is simple and robust, consistent across habitats, and displays bursts of diversification dotted throughout. Second, we find that these data demonstrate a clear departure from the predictions of standard neutral theories of biodiversity and that an alternative family of generalized models provides a qualitatively better description. Together, these results lay the groundwork for a theoretical framework to connect ecological mechanisms to observed phylogenetic patterns in microbial communities.}, }
@article {pmid26104706, year = {2015}, author = {Mandic-Mulec, I and Stefanic, P and van Elsas, JD}, title = {Ecology of Bacillaceae.}, journal = {Microbiology spectrum}, volume = {3}, number = {2}, pages = {TBS-0017-2013}, doi = {10.1128/microbiolspec.TBS-0017-2013}, pmid = {26104706}, issn = {2165-0497}, mesh = {Animals ; Bacillaceae/*classification/*isolation &amp; purification/metabolism/physiology ; *Ecosystem ; *Genetic Variation ; Humans ; Microbial Interactions ; Plants ; }, abstract = {Members of the family Bacillaceae are among the most robust bacteria on Earth, which is mainly due to their ability to form resistant endospores. This trait is believed to be the key factor determining the ecology of these bacteria. However, they also perform fundamental roles in soil ecology (i.e., the cycling of organic matter) and in plant health and growth stimulation (e.g., via suppression of plant pathogens and phosphate solubilization). In this review, we describe the high functional and genetic diversity that is found within the Bacillaceae (a family of low-G+C% Gram-positive spore-forming bacteria), their roles in ecology and in applied sciences related to agriculture. We then pose questions with respect to their ecological behavior, zooming in on the intricate social behavior that is becoming increasingly well characterized for some members of Bacillaceae. Such social behavior, which includes cell-to-cell signaling via quorum sensing or other mechanisms (e.g., the production of extracellular hydrolytic enzymes, toxins, antibiotics and/or surfactants) is a key determinant of their lifestyle and is also believed to drive diversification processes. It is only with a deeper understanding of cell-to-cell interactions that we will be able to understand the ecological and diversification processes of natural populations within the family Bacillaceae. Ultimately, the resulting improvements in understanding will benefit practical efforts to apply representatives of these bacteria in promoting plant growth as well as biological control of plant pathogens.}, }
@article {pmid26104436, year = {2014}, author = {Di Lorenzo, M and Stork, M}, title = {Plasmid-Encoded Iron Uptake Systems.}, journal = {Microbiology spectrum}, volume = {2}, number = {6}, pages = {}, doi = {10.1128/microbiolspec.PLAS-0030-2014}, pmid = {26104436}, issn = {2165-0497}, mesh = {Bacteria/*genetics/*metabolism/pathogenicity ; Bacterial Proteins/genetics ; Biological Transport ; *Genes, Bacterial ; Iron/*metabolism ; *Plasmids ; Virulence ; Virulence Factors/genetics ; }, abstract = {Plasmids confer genetic information that benefits the bacterial cells containing them. In pathogenic bacteria, plasmids often harbor virulence determinants that enhance the pathogenicity of the bacterium. The ability to acquire iron in environments where it is limited, for instance the eukaryotic host, is a critical factor for bacterial growth. To acquire iron, bacteria have evolved specific iron uptake mechanisms. These systems are often chromosomally encoded, while those that are plasmid-encoded are rare. Two main plasmid types, ColV and pJM1, have been shown to harbor determinants that increase virulence by providing the cell with essential iron for growth. It is clear that these two plasmid groups evolved independently from each other since they do not share similarities either in the plasmid backbones or in the iron uptake systems they harbor. The siderophores aerobactin and salmochelin that are found on ColV plasmids fall in the hydroxamate and catechol group, respectively, whereas both functional groups are present in the anguibactin siderophore, the only iron uptake system found on pJM1-type plasmids. Besides siderophore-mediated iron uptake, ColV plasmids carry additional genes involved in iron metabolism. These systems include ABC transporters, hemolysins, and a hemoglobin protease. ColV- and pJM1-like plasmids have been shown to confer virulence to their bacterial host, and this trait can be completely ascribed to their encoded iron uptake systems.}, }
@article {pmid26102291, year = {2015}, author = {Ashbolt, NJ}, title = {Environmental (Saprozoic) Pathogens of Engineered Water Systems: Understanding Their Ecology for Risk Assessment and Management.}, journal = {Pathogens (Basel, Switzerland)}, volume = {4}, number = {2}, pages = {390-405}, pmid = {26102291}, issn = {2076-0817}, abstract = {Major waterborne (enteric) pathogens are relatively well understood and treatment controls are effective when well managed. However, water-based, saprozoic pathogens that grow within engineered water systems (primarily within biofilms/sediments) cannot be controlled by water treatment alone prior to entry into water distribution and other engineered water systems. Growth within biofilms or as in the case of Legionella pneumophila, primarily within free-living protozoa feeding on biofilms, results from competitive advantage. Meaning, to understand how to manage water-based pathogen diseases (a sub-set of saprozoses) we need to understand the microbial ecology of biofilms; with key factors including biofilm bacterial diversity that influence amoebae hosts and members antagonistic to water-based pathogens, along with impacts from biofilm substratum, water temperature, flow conditions and disinfectant residual-all control variables. Major saprozoic pathogens covering viruses, bacteria, fungi and free-living protozoa are listed, yet today most of the recognized health burden from drinking waters is driven by legionellae, non-tuberculous mycobacteria (NTM) and, to a lesser extent, Pseudomonas aeruginosa. In developing best management practices for engineered water systems based on hazard analysis critical control point (HACCP) or water safety plan (WSP) approaches, multi-factor control strategies, based on quantitative microbial risk assessments need to be developed, to reduce disease from largely opportunistic, water-based pathogens.}, }
@article {pmid26097697, year = {2015}, author = {Kopf, A and Bicak, M and Kottmann, R and Schnetzer, J and Kostadinov, I and Lehmann, K and Fernandez-Guerra, A and Jeanthon, C and Rahav, E and Ullrich, M and Wichels, A and Gerdts, G and Polymenakou, P and Kotoulas, G and Siam, R and Abdallah, RZ and Sonnenschein, EC and Cariou, T and O'Gara, F and Jackson, S and Orlic, S and Steinke, M and Busch, J and Duarte, B and Caçador, I and Canning-Clode, J and Bobrova, O and Marteinsson, V and Reynisson, E and Loureiro, CM and Luna, GM and Quero, GM and Löscher, CR and Kremp, A and DeLorenzo, ME and Øvreås, L and Tolman, J and LaRoche, J and Penna, A and Frischer, M and Davis, T and Katherine, B and Meyer, CP and Ramos, S and Magalhães, C and Jude-Lemeilleur, F and Aguirre-Macedo, ML and Wang, S and Poulton, N and Jones, S and Collin, R and Fuhrman, JA and Conan, P and Alonso, C and Stambler, N and Goodwin, K and Yakimov, MM and Baltar, F and Bodrossy, L and Van De Kamp, J and Frampton, DM and Ostrowski, M and Van Ruth, P and Malthouse, P and Claus, S and Deneudt, K and Mortelmans, J and Pitois, S and Wallom, D and Salter, I and Costa, R and Schroeder, DC and Kandil, MM and Amaral, V and Biancalana, F and Santana, R and Pedrotti, ML and Yoshida, T and Ogata, H and Ingleton, T and Munnik, K and Rodriguez-Ezpeleta, N and Berteaux-Lecellier, V and Wecker, P and Cancio, I and Vaulot, D and Bienhold, C and Ghazal, H and Chaouni, B and Essayeh, S and Ettamimi, S and Zaid, el H and Boukhatem, N and Bouali, A and Chahboune, R and Barrijal, S and Timinouni, M and El Otmani, F and Bennani, M and Mea, M and Todorova, N and Karamfilov, V and Ten Hoopen, P and Cochrane, G and L'Haridon, S and Bizsel, KC and Vezzi, A and Lauro, FM and Martin, P and Jensen, RM and Hinks, J and Gebbels, S and Rosselli, R and De Pascale, F and Schiavon, R and Dos Santos, A and Villar, E and Pesant, S and Cataletto, B and Malfatti, F and Edirisinghe, R and Silveira, JA and Barbier, M and Turk, V and Tinta, T and Fuller, WJ and Salihoglu, I and Serakinci, N and Ergoren, MC and Bresnan, E and Iriberri, J and Nyhus, PA and Bente, E and Karlsen, HE and Golyshin, PN and Gasol, JM and Moncheva, S and Dzhembekova, N and Johnson, Z and Sinigalliano, CD and Gidley, ML and Zingone, A and Danovaro, R and Tsiamis, G and Clark, MS and Costa, AC and El Bour, M and Martins, AM and Collins, RE and Ducluzeau, AL and Martinez, J and Costello, MJ and Amaral-Zettler, LA and Gilbert, JA and Davies, N and Field, D and Glöckner, FO}, title = {The ocean sampling day consortium.}, journal = {GigaScience}, volume = {4}, number = {}, pages = {27}, pmid = {26097697}, issn = {2047-217X}, mesh = {Biodiversity ; Database Management Systems ; *Marine Biology ; Metagenomics ; Oceans and Seas ; }, abstract = {Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.}, }
@article {pmid26097471, year = {2015}, author = {Ufarté, L and Potocki-Veronese, G and Laville, &#xc9;}, title = {Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {563}, pmid = {26097471}, issn = {1664-302X}, abstract = {The rapid expansion of new sequencing technologies has enabled large-scale functional exploration of numerous microbial ecosystems, by establishing catalogs of functional genes and by comparing their prevalence in various microbiota. However, sequence similarity does not necessarily reflect functional conservation, since just a few modifications in a gene sequence can have a strong impact on the activity and the specificity of the corresponding enzyme or the recognition for a sensor. Similarly, some microorganisms harbor certain identified functions yet do not have the expected related genes in their genome. Finally, there are simply too many protein families whose function is not yet known, even though they are highly abundant in certain ecosystems. In this context, the discovery of new protein functions, using either sequence-based or activity-based approaches, is of crucial importance for the discovery of new enzymes and for improving the quality of annotation in public databases. This paper lists and explores the latest advances in this field, along with the challenges to be addressed, particularly where microfluidic technologies are concerned.}, }
@article {pmid26096156, year = {2015}, author = {Hauther, KA and Cobaugh, KL and Jantz, LM and Sparer, TE and DeBruyn, JM}, title = {Estimating Time Since Death from Postmortem Human Gut Microbial Communities.}, journal = {Journal of forensic sciences}, volume = {60}, number = {5}, pages = {1234-1240}, doi = {10.1111/1556-4029.12828}, pmid = {26096156}, issn = {1556-4029}, mesh = {Aged ; Aged, 80 and over ; Bacteroides/genetics/physiology ; Bifidobacterium/genetics/physiology ; Female ; Gastrointestinal Microbiome ; Humans ; Intestines/*microbiology ; Lactobacillus/genetics/physiology ; Male ; Middle Aged ; Polymerase Chain Reaction ; *Postmortem Changes ; RNA, Ribosomal, 16S/metabolism ; }, abstract = {Postmortem succession of human-associated microbial communities ("human microbiome") has been suggested as a possible method for estimating postmortem interval (PMI) for forensic analyses. Here we evaluate human gut bacterial populations to determine quantifiable, time-dependent changes postmortem. Gut microflora were repeatedly sampled from the proximal large intestine of 12 deceased human individuals as they decayed under environmental conditions. Three intestinal bacterial genera were quantified by quantitative PCR (qPCR) using group-specific primers targeting 16S rRNA genes. Bacteroides and Lactobacillus relative abundances declined exponentially with increasing PMI at rates of Nt=0.977e(-0.0144t) (r2=0.537, p<0.001) and Nt=0.019e(-0.0087t) (r2=0.396, p<0.001), respectively, where Nt is relative abundance at time (t) in cumulative degree hours. Bifidobacterium relative abundances did not change significantly: Nt=0.003e(-0.002t) (r2=0.033, p=0.284). Therefore, Bacteroides and Lactobacillus abundances could be used as quantitative indicators of PMI.}, }
@article {pmid26095583, year = {2015}, author = {Massana, R}, title = {Getting specific: making taxonomic and ecological sense of large sequencing data sets.}, journal = {Molecular ecology}, volume = {24}, number = {12}, pages = {2904-2906}, doi = {10.1111/mec.13210}, pmid = {26095583}, issn = {1365-294X}, mesh = {*Biodiversity ; Haptophyta/*classification ; *Seasons ; }, abstract = {Eukaryotic microbes comprise a diverse collection of phototrophic and heterotrophic creatures known to play fundamental roles in ecological processes. Some can be identified by light microscopy, generally the largest and with conspicuous shapes, while the smallest can be counted by epifluorescence microscopy or flow cytometry but remain largely unidentified. Microbial diversity studies greatly advanced with the analysis of phylogenetic markers sequenced from natural assemblages. Molecular surveys began in 1990 targeting marine bacterioplankton (Giovannoni et al.) and first approached microbial eukaryotes in three studies published in 2001 (Díez et al. ; López-García et al. ; Moon-van der Staay et al.). These seminal studies, based on cloning and Sanger sequencing the complete 18S rDNA, were critical for obtaining broad pictures of microbial diversity in contrasted habitats and for describing novel lineages by robust phylogenies, but were limited by the number of sequences obtained. So, inventories of species richness in a given sample and community comparisons through environmental gradients were very incomplete. These limitations have been overcome with the advent of high-throughput sequencing (HTS) methods, initially 454-pyrosequencing, today Illumina and soon others to come. In this issue of Molecular Ecology, Egge et al. () show a nice example of the use of HTS to study the biodiversity and seasonal succession of a particularly important group of marine microbial eukaryotes, the haptophytes. Temporal changes were analysed first at the community level, then at the clade level, and finally at the lowest rank comparable to species. Interesting and useful ecological insights were obtained at each taxonomic scale. Haptophyte diversity differed along seasons in a systematic manner, with some species showing seasonal preferences and others being always present. Many of these species had no correspondence with known species, pointing out the high level of novelty in microbial assemblages, only accessible by molecular tools. Moreover, the number of species detected was limited, agreeing with a putative scenario of constrained evolutionary diversification in free-living small eukaryotes. This study illustrates the potential of HTS to address ecological relevant questions in an accessible way by processing large data sets that, nonetheless, need to be treated with a fair understanding of their limitations.}, }
@article {pmid26093964, year = {2016}, author = {Vohník, M and Borovec, O and Kolařík, M}, title = {Communities of Cultivable Root Mycobionts of the Seagrass Posidonia oceanica in the Northwest Mediterranean Sea Are Dominated by a Hitherto Undescribed Pleosporalean Dark Septate Endophyte.}, journal = {Microbial ecology}, volume = {71}, number = {2}, pages = {442-451}, pmid = {26093964}, issn = {1432-184X}, mesh = {Alismatales/*microbiology ; Ascomycota/classification/genetics/growth &amp; development/*isolation &amp; purification ; Endophytes/classification/genetics/growth &amp; development/*isolation &amp; purification ; Mediterranean Sea ; Molecular Sequence Data ; Phylogeny ; Plant Roots/*microbiology ; Spores, Fungal/classification/genetics/growth &amp; development/isolation &amp; purification ; }, abstract = {Seagrasses, a small group of submerged marine macrophytes, were reported to lack mycorrhizae, i.e., the root-fungus symbioses most terrestrial plants use for nutrient uptake. On the other hand, several authors detected fungal endophytes in seagrass leaves, shoots, rhizomes, and roots, and an anatomically and morphologically unique dark septate endophytic (DSE) association has been recently described in the roots of the Mediterranean seagrass Posidonia oceanica. Nevertheless, the global diversity of seagrass mycobionts is not well understood, and it remains unclear what fungus forms the DSE association in P. oceanica roots. We isolated and determined P. oceanica root mycobionts from 11 localities in the northwest Mediterranean Sea with documented presence of the DSE association and compared our results with recent literature. The mycobiont communities were low in diversity (only three species), were dominated by a single yet unreported marine fungal species (ca. 90 % of the total 177 isolates), and lacked common terrestrial and freshwater root mycobionts. Our phylogenetic analysis suggests that the dominating species represents a new monotypic lineage within the recently described Aigialaceae family (Pleosporales, Ascomycota), probably representing a new genus. Most of its examined colonies developed from intracellular microsclerotia occupying host hypodermis and resembling microsclerotia of terrestrial DSE fungi. Biological significance of this hitherto overlooked seagrass root mycobiont remains obscure, but its presence across the NW Mediterranean Sea and apparent root intracellular lifestyle indicate an intriguing symbiotic relationship with the dominant Mediterranean seagrass. Our microscopic observations suggest that it may form the DSE association recently described in P. oceanica roots.}, }
@article {pmid26090504, year = {2015}, author = {Vital, M and Harkema, JR and Rizzo, M and Tiedje, J and Brandenberger, C}, title = {Alterations of the Murine Gut Microbiome with Age and Allergic Airway Disease.}, journal = {Journal of immunology research}, volume = {2015}, number = {}, pages = {892568}, pmid = {26090504}, issn = {2314-7156}, support = {UH3 DK083993/DK/NIDDK NIH HHS/United States ; UH3DK083993/DK/NIDDK NIH HHS/United States ; }, mesh = {Age Factors ; Animals ; Asthma/*immunology/*microbiology ; Disease Models, Animal ; Gastrointestinal Microbiome/*immunology ; Hypersensitivity/*immunology/*microbiology ; Interleukin-17/immunology ; Intestines/*immunology/*microbiology ; Lung/immunology/microbiology ; Male ; Mice ; Mice, Inbred BALB C ; Pneumonia/immunology/microbiology ; Pyroglyphidae/immunology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The gut microbiota plays an important role in the development of asthma. With advanced age the microbiome and the immune system are changing and, currently, little is known about how these two factors contribute to the development of allergic asthma in the elderly. In this study we investigated the associations between the intestinal microbiome and allergic airway disease in young and old mice that were sensitized and challenged with house dust mite (HDM). After challenge, the animals were sacrificed, blood serum was collected for cytokine analysis, and the lungs were processed for histopathology. Fecal pellets were excised from the colon and subjected to 16S rRNA analysis. The microbial community structure changed with age and allergy development, where alterations in fecal communities from young to old mice resembled those after HDM challenge. Allergic mice had induced serum levels of IL-17A and old mice developed a greater allergic airway response compared to young mice. This study demonstrates that the intestinal bacterial community structure differs with age, possibly contributing to the exaggerated pulmonary inflammatory response in old mice. Furthermore, our results show that the composition of the gut microbiota changes with pulmonary allergy, indicating bidirectional gut-lung communications.}, }
@article {pmid26089816, year = {2015}, author = {Febria, CM and Hosen, JD and Crump, BC and Palmer, MA and Williams, DD}, title = {Microbial responses to changes in flow status in temporary headwater streams: a cross-system comparison.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {522}, pmid = {26089816}, issn = {1664-302X}, abstract = {Microbial communities are responsible for the bulk of biogeochemical processing in temporary headwater streams, yet there is still relatively little known about how community structure and function respond to periodic drying. Moreover, the ability to sample temporary habitats can be a logistical challenge due to the limited capability to measure and predict the timing, intensity and frequency of wet-dry events. Unsurprisingly, published datasets on microbial community structure and function are limited in scope and temporal resolution and vary widely in the molecular methods applied. We compared environmental and microbial community datasets for permanent and temporary tributaries of two different North American headwater stream systems: Speed River (Ontario, Canada) and Parkers Creek (Maryland, USA). We explored whether taxonomic diversity and community composition were altered as a result of flow permanence and compared community composition amongst streams using different 16S microbial community methods (i.e., T-RFLP and Illumina MiSeq). Contrary to our hypotheses, and irrespective of method, community composition did not respond strongly to drying. In both systems, community composition was related to site rather than drying condition. Additional network analysis on the Parkers Creek dataset indicated a shift in the central microbial relationships between temporary and permanent streams. In the permanent stream at Parkers Creek, associations of methanotrophic taxa were most dominant, whereas associations with taxa from the order Nitrospirales were more dominant in the temporary stream, particularly during dry conditions. We compared these results with existing published studies from around the world and found a wide range in community responses to drying. We conclude by proposing three hypotheses that may address contradictory results and, when tested across systems, may expand understanding of the responses of microbial communities in temporary streams to natural and human-induced fluctuations in flow-status and permanence.}, }
@article {pmid26085172, year = {2016}, author = {Pérez-Jaramillo, JE and Mendes, R and Raaijmakers, JM}, title = {Impact of plant domestication on rhizosphere microbiome assembly and functions.}, journal = {Plant molecular biology}, volume = {90}, number = {6}, pages = {635-644}, pmid = {26085172}, issn = {1573-5028}, mesh = {Crops, Agricultural/genetics/*microbiology ; Genotype ; *Microbiota ; Plant Roots/*microbiology/physiology ; Plants/genetics/*microbiology ; Rhizosphere ; }, abstract = {The rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. Plants can actively recruit members of the soil microbial community for positive feedbacks, but the underlying mechanisms and plant traits that drive microbiome assembly and functions are largely unknown. Domestication of plant species has substantially contributed to human civilization, but also caused a strong decrease in the genetic diversity of modern crop cultivars that may have affected the ability of plants to establish beneficial associations with rhizosphere microbes. Here, we review how plants shape the rhizosphere microbiome and how domestication may have impacted rhizosphere microbiome assembly and functions via habitat expansion and via changes in crop management practices, root exudation, root architecture, and plant litter quality. We also propose a "back to the roots" framework that comprises the exploration of the microbiome of indigenous plants and their native habitats for the identification of plant and microbial traits with the ultimate goal to reinstate beneficial associations that may have been undermined during plant domestication.}, }
@article {pmid26084447, year = {2015}, author = {Vannecke, TP and Volcke, EI}, title = {Modelling microbial competition in nitrifying biofilm reactors.}, journal = {Biotechnology and bioengineering}, volume = {112}, number = {12}, pages = {2550-2561}, doi = {10.1002/bit.25680}, pmid = {26084447}, issn = {1097-0290}, mesh = {Bacteria/*growth &amp; development/*metabolism ; Biofilms/*growth &amp; development ; Bioreactors/*microbiology ; Culture Media/chemistry ; *Microbial Interactions ; *Models, Theoretical ; *Nitrification ; Nitrogen/metabolism ; Oxygen/metabolism ; }, abstract = {A large variety of microbial parameter values for nitrifying microorganisms has been reported in literature and was revised in this study. Part of the variety was attributed to the variety of analysis methods applied; it also reflects the large biodiversity in nitrifying systems. This diversity is mostly neglected in conventional nitrifying biofilm models. In this contribution, a one-dimensional, multispecies nitrifying biofilm model was set up, taking into account the large variety of the maximum growth rate, the substrate affinity and the yield of nitrifiers reported in literature. Microbial diversity was implemented in the model by considering 60 species of ammonia-oxidizing bacteria (AOB) and 60 species of nitrite-oxidizing bacteria (NOB). A steady-state analysis showed that operational conditions such as the nitrogen loading rate and the bulk liquid oxygen concentration influence both the macroscopic output as well as the microbial composition of the biofilm through the prevailing concentration of substrates throughout the biofilm. Considering two limiting resources (nitrogen and oxygen), the coexistence of two species of the same functional guild (AOB or NOB) was possible at steady state. Their spatial distribution in the biofilm could be explained using the r- and K-selection theory.}, }
@article {pmid26084274, year = {2015}, author = {Wu, L and Wen, C and Qin, Y and Yin, H and Tu, Q and Van Nostrand, JD and Yuan, T and Yuan, M and Deng, Y and Zhou, J}, title = {Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis.}, journal = {BMC microbiology}, volume = {15}, number = {}, pages = {125}, pmid = {26084274}, issn = {1471-2180}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; DNA Primers ; DNA, Archaeal/analysis ; DNA, Bacterial/analysis ; DNA, Ribosomal/*analysis ; Environmental Microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Saliva/microbiology ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Although high-throughput sequencing, such as Illumina-based technologies (e.g. MiSeq), has revolutionized microbial ecology, adaptation of amplicon sequencing for environmental microbial community analysis is challenging due to the problem of low base diversity.<br><br>RESULTS: A new phasing amplicon sequencing approach (PAS) was developed by shifting sequencing phases among different community samples from both directions via adding various numbers of bases (0-7) as spacers to both forward and reverse primers. Our results first indicated that the PAS method substantially ameliorated the problem of unbalanced base composition. Second, the PAS method substantially improved the sequence read base quality (an average of 10 % higher of bases above Q30). Third, the PAS method effectively increased raw sequence throughput (~15 % more raw reads). In addition, the PAS method significantly increased effective reads (9-47 %) and the effective read sequence length (16-96 more bases) after quality trim at Q30 with window 5. In addition, the PAS method reduced half of the sequencing errors (0.54-1.1 % less). Finally, two-step PCR amplification of the PAS method effectively ameliorated the amplification biases introduced by the long barcoded PCR primers.<br><br>CONCLUSION: The developed strategy is robust for 16S rRNA gene amplicon sequencing. In addition, a similar strategy could also be used for sequencing other genes important to ecosystem functional processes.}, }
@article {pmid26079858, year = {2015}, author = {Patil, SA and Arends, JB and Vanwonterghem, I and van Meerbergen, J and Guo, K and Tyson, GW and Rabaey, K}, title = {Selective Enrichment Establishes a Stable Performing Community for Microbial Electrosynthesis of Acetate from CO2.}, journal = {Environmental science &amp; technology}, volume = {49}, number = {14}, pages = {8833-8843}, doi = {10.1021/es506149d}, pmid = {26079858}, issn = {1520-5851}, mesh = {Acetates/*metabolism ; Bacteria/growth &amp; development/*metabolism ; *Bioelectric Energy Sources ; Bioreactors/microbiology ; Carbon Dioxide/*metabolism ; Electrochemical Techniques/*methods ; Electrodes ; Hydrogen-Ion Concentration ; Methane/metabolism ; Reproducibility of Results ; }, abstract = {The advent of renewable energy conversion systems exacerbates the existing issue of intermittent excess power. Microbial electrosynthesis can use this power to capture CO2 and produce multicarbon compounds as a form of energy storage. As catalysts, microbial populations can be used, provided side reactions such as methanogenesis are avoided. Here a simple but effective approach is presented based on enrichment of a robust microbial community via several culture transfers with H2:CO2 conditions. This culture produced acetate at a concentration of 1.29 ± 0.15 g L(-1) (maximum up to 1.5 g L(-1); 25 mM) from CO2 at a fixed current of -5 Am(-2) in fed-batch bioelectrochemical reactors at high N2:CO2 flow rates. Continuous supply of reducing equivalents enabled acetate production at a rate of 19 ± 2 gm(-2)d(-1) (projected cathode area) in several independent experiments. This is a considerably high rate compared with other unmodified carbon-based cathodes. 58 ± 5% of the electrons was recovered in acetate, whereas 30 ± 10% of the electrons was recovered in H2 as a secondary product. The bioproduction was most likely H2 based; however, electrochemical, confocal microscopy, and community analyses of the cathodes suggested the possible involvement of the cathodic biofilm. Together, the enrichment approach and galvanostatic operation enabled instant start-up of the electrosynthesis process and reproducible acetate production profiles.}, }
@article {pmid26079735, year = {2015}, author = {Sabatino, R and Di Cesare, A and Pasquaroli, S and Vignaroli, C and Citterio, B and Amiri, M and Rossi, L and Magnani, M and Mauro, A and Biavasco, F}, title = {Adherence and intracellular survival within human macrophages of Enterococcus faecalis isolates from coastal marine sediment.}, journal = {Microbes and infection}, volume = {17}, number = {9}, pages = {660-664}, doi = {10.1016/j.micinf.2015.06.001}, pmid = {26079735}, issn = {1769-714X}, mesh = {Bacterial Adhesion/*physiology ; Cells, Cultured ; Colony Count, Microbial ; Enterococcus faecalis/*physiology ; Geologic Sediments/*microbiology ; Humans ; Macrophages/*microbiology ; *Microbial Viability ; }, abstract = {Enterococcus faecalis is part of the human intestinal microbiota and an important nosocomial pathogen. It can be found in the marine environment, where it is also employed as a fecal indicator. To assess the pathogenic potential of marine E. faecalis, four strains isolated from marine sediment were analyzed for their ability to survive in human macrophages. Escherichia coli DH5α was used as a negative control. The number of adherent and intracellular bacteria was determined 2.5 h after the infection (T0) and after further 24h (T24) by CFU and qPCR counts. At T24 adherent and intracellular enterococcal CFU counts were increased for all strains, the increment in intracellular bacteria being particularly marked. No CFU of E. coli DH5α were detected. In contrast, qPCR counts of intracellular enterococcal and E. coli bacteria were similar at both time points. These findings suggest that whereas E. coli was killed within macrophages (no CFU, positive qPCR), the E. faecalis isolates not only escaped killing, but actually multiplied, as demonstrated by the increase in the viable cell population. These findings support earlier data by our group, further documenting that marine sediment can be a reservoir of pathogenic enterococci.}, }
@article {pmid26078039, year = {2015}, author = {Martínez-García, &#xc1; and Soler, JJ and Rodríguez-Ruano, SM and Martínez-Bueno, M and Martín-Platero, AM and Juárez-García, N and Martín-Vivaldi, M}, title = {Preening as a Vehicle for Key Bacteria in Hoopoes.}, journal = {Microbial ecology}, volume = {70}, number = {4}, pages = {1024-1033}, pmid = {26078039}, issn = {1432-184X}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics/growth &amp; development/*isolation &amp; purification ; Bacterial Load ; Birds/*microbiology/*physiology ; Egg Shell/microbiology ; Feathers/microbiology ; Female ; *Grooming ; Prevalence ; Species Specificity ; Symbiosis/physiology ; }, abstract = {Oily secretions produced in the uropygial gland of incubating female hoopoes contain antimicrobial-producing bacteria that prevent feathers from degradation and eggs from pathogenic infection. Using the beak, females collect the uropygial gland secretion and smear it directly on the eggshells and brood patch. Thus, some bacterial strains detected in the secretion should also be present on the eggshell, beak, and brood patch. To characterize these bacterial communities, we used Automatic Ribosomal Intergenic Spacer Analysis (ARISA), which distinguishes between taxonomically different bacterial strains (i.e. different operational taxonomic units [OTUs]) by the size of the sequence amplified. We identified a total of 146 different OTUs with sizes between 139 and 999 bp. Of these OTUs, 124 were detected in the uropygial oil, 106 on the beak surface, 97 on the brood patch, and 98 on the eggshell. The highest richness of OTUs appeared in the uropygial oil samples. Moreover, the detection of some OTUs on the beak, brood patch, and eggshells of particular nests depended on these OTUs being present in the uropygial oil of the female. These results agree with the hypothesis that symbiotic bacteria are transmitted from the uropygial gland to beak, brood patch, and eggshell surfaces, opening the possibility that the bacterial community of the secretion plays a central role in determining the communities of special hoopoe eggshell structures (i.e., crypts) that, soon after hatching, are filled with uropygial oil, thereby protecting embryos from pathogens.}, }
@article {pmid26077901, year = {2015}, author = {Philmus, B and Shaffer, BT and Kidarsa, TA and Yan, Q and Raaijmakers, JM and Begley, TP and Loper, JE}, title = {Investigations into the Biosynthesis, Regulation, and Self-Resistance of Toxoflavin in Pseudomonas protegens Pf-5.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {16}, number = {12}, pages = {1782-1790}, doi = {10.1002/cbic.201500247}, pmid = {26077901}, issn = {1439-7633}, mesh = {Biosynthetic Pathways ; Chromatography, Liquid ; Cloning, Molecular ; Molecular Structure ; Multigene Family/genetics ; Pseudomonas/*genetics/*metabolism ; Pyrimidinones/*metabolism ; Triazines/*metabolism ; }, abstract = {Pseudomonas spp. are prolific producers of natural products from many structural classes. Here we show that the soil bacterium Pseudomonas protegens Pf-5 is capable of producing trace levels of the triazine natural product toxoflavin (1) under microaerobic conditions. We evaluated toxoflavin production by derivatives of Pf-5 with deletions in specific biosynthesis genes, which led us to propose a revised biosynthetic pathway for toxoflavin that shares the first two steps with riboflavin biosynthesis. We also report that toxM, which is not present in the well-characterized cluster of Burkholderia glumae, encodes a monooxygenase that degrades toxoflavin. The toxoflavin degradation product of ToxM is identical to that of TflA, the toxoflavin lyase from Paenibacillus polymyxa. Toxoflavin production by P. protegens causes inhibition of several plant-pathogenic bacteria, and introduction of toxM into the toxoflavin-sensitive strain Pseudomonas syringae DC3000 results in resistance to toxoflavin.}, }
@article {pmid26077888, year = {2016}, author = {Gonzalez, OA and Nagarajan, R and Novak, MJ and Orraca, L and Gonzalez-Martinez, JA and Kirakodu, SS and Ebersole, JL}, title = {Immune system transcriptome in gingival tissues of young nonhuman primates.}, journal = {Journal of periodontal research}, volume = {51}, number = {2}, pages = {152-163}, pmid = {26077888}, issn = {1600-0765}, support = {UL1 TR000117/TR/NCATS NIH HHS/United States ; UL1TR000117/TR/NCATS NIH HHS/United States ; P30 GM110788/GM/NIGMS NIH HHS/United States ; P40 RR003640/RR/NCRR NIH HHS/United States ; P20GM103538/GM/NIGMS NIH HHS/United States ; P40RR03640/RR/NCRR NIH HHS/United States ; P20 GM103538/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Gingiva ; Immune System ; Macaca mulatta ; Oligonucleotide Array Sequence Analysis ; Periodontitis ; Transcriptome ; }, abstract = {BACKGROUND AND OBJECTIVE: Young/adolescent humans harbor many microorganisms associated with periodontal disease in adults and show substantial gingival inflammatory responses. However, younger individuals do not demonstrate the soft- and hard-tissue destruction that hallmark periodontitis.<br><br>MATERIAL AND METHODS: This study evaluated responses to the oral microbial ecology in gingival tissues from clinically healthy young Macaca mulatta (<&#xa0;3&#xa0;years of age) compared with older animals (5-23 years of age). RNA was isolated from the tissues and analyzed for the transcriptome using the Rhesus Macaque GeneChip (Affymetrix).<br><br>RESULTS: Global transcriptional profiling of four age groups revealed a subset of 159 genes that were differentially expressed across at least one of the age comparisons. Correlation metrics generated a relevance network abstraction of these genes. Partitioning of the relevance network revealed seven distinct communities comprising functionally related genes associated with host inflammatory and immune responses. A group of genes was identified that were selectively increased/decreased or positively/negatively correlated with gingival profiles in the animals. A principal components analysis created metagenes of expression profiles for classifying the 23 animals.<br><br>CONCLUSION: The results provide novel system-level insights into gene-expression differences in gingival tissues from healthy young animals, weighted toward host responses associated with anti-inflammatory biomolecules or those linked with T-cell regulation of responses. The combination of the regulated microenvironment may help to explain the apparent 'resistance' of younger individuals to developing periodontal disease.}, }
@article {pmid26074892, year = {2015}, author = {Ozuolmez, D and Na, H and Lever, MA and Kjeldsen, KU and Jørgensen, BB and Plugge, CM}, title = {Methanogenic archaea and sulfate reducing bacteria co-cultured on acetate: teamwork or coexistence?.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {492}, pmid = {26074892}, issn = {1664-302X}, abstract = {Acetate is a major product of fermentation processes and an important substrate for sulfate reducing bacteria and methanogenic archaea. Most studies on acetate catabolism by sulfate reducers and methanogens have used pure cultures. Less is known about acetate conversion by mixed pure cultures and the interactions between both groups. We tested interspecies hydrogen transfer and coexistence between marine methanogens and sulfate reducers using mixed pure cultures of two types of microorganisms. First, Desulfovibrio vulgaris subsp. vulgaris (DSM 1744), a hydrogenotrophic sulfate reducer, was cocultured together with the obligate aceticlastic methanogen Methanosaeta concilii using acetate as carbon and energy source. Next, Methanococcus maripaludis S2, an obligate H2- and formate-utilizing methanogen, was used as a partner organism to M. concilii in the presence of acetate. Finally, we performed a coexistence experiment between M. concilii and an acetotrophic sulfate reducer Desulfobacter latus AcSR2. Our results showed that D. vulgaris was able to reduce sulfate and grow from hydrogen leaked by M. concilii. In the other coculture, M. maripaludis was sustained by hydrogen leaked by M. concilii as revealed by qPCR. The growth of the two aceticlastic microbes indicated co-existence rather than competition. Altogether, our results indicate that H2 leaking from M. concilii could be used by efficient H2-scavengers. This metabolic trait, revealed from coculture studies, brings new insight to the metabolic flexibility of methanogens and sulfate reducers residing in marine environments in response to changing environmental conditions and community compositions. Using dedicated physiological studies we were able to unravel the occurrence of less obvious interactions between marine methanogens and sulfate-reducing bacteria.}, }
@article {pmid26074891, year = {2015}, author = {Aguirre-von-Wobeser, E and Eguiarte, LE and Souza, V and Soberón-Chávez, G}, title = {Theoretical analysis of the cost of antagonistic activity for aquatic bacteria in oligotrophic environments.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {490}, pmid = {26074891}, issn = {1664-302X}, abstract = {Many strains of bacteria produce antagonistic substances that restrain the growth of others, and potentially give them a competitive advantage. These substances are commonly released to the surrounding environment, involving metabolic costs in terms of energy and nutrients. The rate at which these molecules need to be produced to maintain a certain amount of them close to the producing cell before they are diluted into the environment has not been explored so far. To understand the potential cost of production of antagonistic substances in water environments, we used two different theoretical approaches. Using a probabilistic model, we determined the rate at which a cell needs to produce individual molecules in order to keep on average a single molecule in its vicinity at all times. For this minimum protection, a cell would need to invest 3.92 × 10(-22) kg s(-1) of organic matter, which is 9 orders of magnitude lower than the estimated expense for growth. Next, we used a continuous model, based on Fick's laws, to explore the production rate needed to sustain minimum inhibitory concentrations around a cell, which would provide much more protection from competitors. In this scenario, cells would need to invest 1.20 × 10(-11) kg s(-1), which is 2 orders of magnitude higher than the estimated expense for growth, and thus not sustainable. We hypothesize that the production of antimicrobial compounds by bacteria in aquatic environments lies between these two extremes.}, }
@article {pmid26074887, year = {2015}, author = {Méndez-García, C and Peláez, AI and Mesa, V and Sánchez, J and Golyshina, OV and Ferrer, M}, title = {Microbial diversity and metabolic networks in acid mine drainage habitats.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {475}, pmid = {26074887}, issn = {1664-302X}, abstract = {Acid mine drainage (AMD) emplacements are low-complexity natural systems. Low-pH conditions appear to be the main factor underlying the limited diversity of the microbial populations thriving in these environments, although temperature, ionic composition, total organic carbon, and dissolved oxygen are also considered to significantly influence their microbial life. This natural reduction in diversity driven by extreme conditions was reflected in several studies on the microbial populations inhabiting the various micro-environments present in such ecosystems. Early studies based on the physiology of the autochthonous microbiota and the growing success of omics-based methodologies have enabled a better understanding of microbial ecology and function in low-pH mine outflows; however, complementary omics-derived data should be included to completely describe their microbial ecology. Furthermore, recent updates on the distribution of eukaryotes and archaea recovered through sterile filtering (herein referred to as filterable fraction) in these environments demand their inclusion in the microbial characterization of AMD systems. In this review, we present a complete overview of the bacterial, archaeal (including filterable fraction), and eukaryotic diversity in these ecosystems, and include a thorough depiction of the metabolism and element cycling in AMD habitats. We also review different metabolic network structures at the organismal level, which is necessary to disentangle the role of each member of the AMD communities described thus far.}, }
@article {pmid26074626, year = {2015}, author = {Larsen, A and Egge, JK and Nejstgaard, JC and Di Capua, I and Thyrhaug, R and Bratbak, G and Thingstad, TF}, title = {Contrasting response to nutrient manipulation in Arctic mesocosms are reproduced by a minimum microbial food web model.}, journal = {Limnology and oceanography}, volume = {60}, number = {2}, pages = {360-374}, pmid = {26074626}, issn = {0024-3590}, abstract = {A minimum mathematical model of the marine pelagic microbial food web has previously shown to be able to reproduce central aspects of observed system response to different bottom-up manipulations in a mesocosm experiment Microbial Ecosystem Dynamics (MEDEA) in Danish waters. In this study, we apply this model to two mesocosm experiments (Polar Aquatic Microbial Ecology (PAME)-I and PAME-II) conducted at the Arctic location Kongsfjorden, Svalbard. The different responses of the microbial community to similar nutrient manipulation in the three mesocosm experiments may be described as diatom-dominated (MEDEA), bacteria-dominated (PAME-I), and flagellated-dominated (PAME-II). When allowing ciliates to be able to feed on small diatoms, the model describing the diatom-dominated MEDEA experiment give a bacteria-dominated response as observed in PAME I in which the diatom community comprised almost exclusively small-sized cells. Introducing a high initial mesozooplankton stock as observed in PAME-II, the model gives a flagellate-dominated response in accordance with the observed response also of this experiment. The ability of the model originally developed for temperate waters to reproduce population dynamics in a 10°C colder Arctic fjord, does not support the existence of important shifts in population balances over this temperature range. Rather, it suggests a quite resilient microbial food web when adapted to in situ temperature. The sensitivity of the model response to its mesozooplankton component suggests, however, that the seasonal vertical migration of Arctic copepods may be a strong forcing factor on Arctic microbial food webs.}, }
@article {pmid26074239, year = {2015}, author = {Chen, X and Song, YQ and Xu, HY and Menghe, BL and Zhang, HP and Sun, ZH}, title = {Genetic relationships among Enterococcus faecalis isolates from different sources as revealed by multilocus sequence typing.}, journal = {Journal of dairy science}, volume = {98}, number = {8}, pages = {5183-5193}, doi = {10.3168/jds.2015-9571}, pmid = {26074239}, issn = {1525-3198}, mesh = {Bacterial Proteins/*genetics/isolation &amp; purification/metabolism ; Dairy Products/*microbiology ; Enterococcus faecalis/*genetics/isolation &amp; purification/metabolism ; *Food Microbiology ; *Genetic Variation ; Molecular Sequence Data ; Multilocus Sequence Typing ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Enterococcus faecalis is part of the natural gut flora of humans and other mammals; some isolates are also used in food production. So, it is important to evaluate the genetic diversity and phylogenetic relationships among E. faecalis isolates from different sources. Multilocus sequence typing protocol was used to compare 39 E. faecalis isolates from Chinese traditional food products (including dairy products, acidic gruel) and 4 published E. faecalis isolates from other sources including human-derived isolates employing 5 housekeeping genes (groEL, clpX, recA, rpoB, and pepC). A total of 23 unique sequence types were identified, which were grouped into 5 clonal complexes and 10 singletons. The value of standardized index of association of the alleles (IA(S)=0.1465) and network structure indicated a high frequency of intraspecies recombination across these isolates. Enterococcus faecalis lineages also exhibited clearly source-clustered distributions. The isolates from dairy source were clustered together. However, the relationship between isolates from acidic gruel and one isolate from a human source was close. The MLST scheme presented in this study provides a sharable and continuously growing sequence database enabling global comparison of strains from different sources, and will further advance our understanding of the microbial ecology of this important species.}, }
@article {pmid26072503, year = {2015}, author = {Yuan, C and Lei, J and Cole, J and Sun, Y}, title = {Reconstructing 16S rRNA genes in metagenomic data.}, journal = {Bioinformatics (Oxford, England)}, volume = {31}, number = {12}, pages = {i35-43}, pmid = {26072503}, issn = {1367-4811}, mesh = {Computational Biology/*methods ; Databases, Nucleic Acid ; Genes, rRNA/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA ; }, abstract = {UNLABELLED: Metagenomic data, which contains sequenced DNA reads of uncultured microbial species from environmental samples, provide a unique opportunity to thoroughly analyze microbial species that have never been identified before. Reconstructing 16S ribosomal RNA, a phylogenetic marker gene, is usually required to analyze the composition of the metagenomic data. However, massive volume of dataset, high sequence similarity between related species, skewed microbial abundance and lack of reference genes make 16S rRNA reconstruction difficult. Generic de novo assembly tools are not optimized for assembling 16S rRNA genes. In this work, we introduce a targeted rRNA assembly tool, REAGO (REconstruct 16S ribosomal RNA Genes from metagenOmic data). It addresses the above challenges by combining secondary structure-aware homology search, zproperties of rRNA genes and de novo assembly. Our experimental results show that our tool can correctly recover more rRNA genes than several popular generic metagenomic assembly tools and specially designed rRNA construction tools.<br><br>The source code of REAGO is freely available at https://github.com/chengyuan/reago.}, }
@article {pmid26072397, year = {2015}, author = {Cleary, DF and de Voogd, NJ and Polónia, AR and Freitas, R and Gomes, NC}, title = {Composition and Predictive Functional Analysis of Bacterial Communities in Seawater, Sediment and Sponges in the Spermonde Archipelago, Indonesia.}, journal = {Microbial ecology}, volume = {70}, number = {4}, pages = {889-903}, pmid = {26072397}, issn = {1432-184X}, mesh = {Animals ; Bacteria/genetics ; Biodiversity ; Coral Reefs ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; Ecosystem ; Geologic Sediments/*microbiology ; Indonesia ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; Xestospongia/microbiology ; }, abstract = {In this study, we used a 16S rRNA gene barcoded pyrosequencing approach to sample bacterial communities from six biotopes, namely, seawater, sediment and four sponge species (Stylissa carteri, Stylissa massa, Xestospongia testudinaria and Hyrtios erectus) inhabiting coral reefs of the Spermonde Archipelago, South Sulawesi, Indonesia. Samples were collected along a pronounced onshore to offshore environmental gradient. Our goals were to (1) compare higher taxon abundance among biotopes, (2) test to what extent variation in bacterial composition can be explained by the biotope versus environment, (3) identify dominant (>300 sequences) bacterial operational taxonomic units (OTUs) and their closest known relatives and (4) assign putative functions to the sponge bacterial communities using a recently developed predictive metagenomic approach. We observed marked differences in bacterial composition and the relative abundance of the most abundant phyla, classes and orders among sponge species, seawater and sediment. Although all biotopes housed compositionally distinct bacterial communities, there were three prominent clusters. These included (1) both Stylissa species and seawater, (2) X. testudinaria and H. erectus and (3) sediment. Bacterial communities sampled from the same biotope, but different environments (based on proximity to the coast) were much more similar than bacterial communities from different biotopes in the same environment. The biotope thus appears to be a much more important structuring force than the surrounding environment. There were concomitant differences in the predicted counts of KEGG orthologs (KOs) suggesting that bacterial communities housed in different sponge species, sediment and seawater perform distinct functions. In particular, the bacterial communities of both Stylissa species were predicted to be enriched for KOs related to chemotaxis, nitrification and denitrification whereas bacterial communities in X. testudinaria and H. erectus were predicted to be enriched for KOs related to the toxin-antitoxin (TA) system, nutrient starvation and heavy metal export.}, }
@article {pmid26072019, year = {2015}, author = {Nansubuga, I and Banadda, N and Ronsse, F and Verstraete, W and Rabaey, K}, title = {Digestion of high rate activated sludge coupled to biochar formation for soil improvement in the tropics.}, journal = {Water research}, volume = {81}, number = {}, pages = {216-222}, doi = {10.1016/j.watres.2015.05.047}, pmid = {26072019}, issn = {1879-2448}, mesh = {Anaerobiosis ; Biodegradation, Environmental ; Charcoal/*chemistry ; Sewage/*chemistry ; *Soil ; Temperature ; Tropical Climate ; Waste Disposal, Fluid/*methods ; }, abstract = {High rate activated sludge (HRAS) is well-biodegradable sludge enabling energy neutrality of wastewater treatment plants via anaerobic digestion. However, even through successful digestion a notable residue still remains. Here we investigated whether this residue can be converted to biochar, for its use as a fertilizer or as a solid fuel, and assessed its characteristics and overall process efficiency. In a first phase, HRAS was anaerobicaly digested under mesophilic conditions at a sludge retention time of 20 days. HRAS digested well (57.9 ± 6.2% VS degradation) producing on average 0.23 ± 0.04 L CH4 per gram VS fed. The digestate particulates were partially air-dried to mimic conditions used in developing countries, and subsequently converted to biochar by fixed-bed slow pyrolysis at a residence time of 15 min and at highest heating temperatures (HHT) of 300 °C, 400 °C and 600 °C. Subsequently, the produced chars were characterized by proximate analysis, CHN-elemental analysis, pH in solution and bomb calorimetry for higher heating value. The yield and volatile matter decreased with increasing HHT while ash content and fixed carbon increased with increasing HHT. The produced biochar showed properties optimal towards soil amendment when produced at a temperature of 600 °C with values of 5.91 wt%, 23.75 wt%, 70.35% on dry basis (db) and 0.44 for volatile matter, fixed carbon, ash content and H/C ratio, respectively. With regard to its use for energy purposes, the biochar represented a lower calorific value than the dried HRAS digestate likely due to high ash content. Based on these findings, it can be concluded that anaerobic digestion of HRAS and its subsequent biochar formation at HHT of 600 °C represents an attractive route for sludge management in tropic settings like in Uganda, coupling carbon capture to energy generation, carbon sequestration and nutrient recovery.}, }
@article {pmid26067226, year = {2015}, author = {Cobaugh, KL and Schaeffer, SM and DeBruyn, JM}, title = {Functional and Structural Succession of Soil Microbial Communities below Decomposing Human Cadavers.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0130201}, pmid = {26067226}, issn = {1932-6203}, mesh = {*Bacteria/classification/isolation &amp; purification ; *Cadaver ; Female ; Humans ; Male ; *Soil Microbiology ; }, abstract = {The ecological succession of microbes during cadaver decomposition has garnered interest in both basic and applied research contexts (e.g. community assembly and dynamics; forensic indicator of time since death). Yet current understanding of microbial ecology during decomposition is almost entirely based on plant litter. We know very little about microbes recycling carcass-derived organic matter despite the unique decomposition processes. Our objective was to quantify the taxonomic and functional succession of microbial populations in soils below decomposing cadavers, testing the hypotheses that a) periods of increased activity during decomposition are associated with particular taxa; and b) human-associated taxa are introduced to soils, but do not persist outside their host. We collected soils from beneath four cadavers throughout decomposition, and analyzed soil chemistry, microbial activity and bacterial community structure. As expected, decomposition resulted in pulses of soil C and nutrients (particularly ammonia) and stimulated microbial activity. There was no change in total bacterial abundances, however we observed distinct changes in both function and community composition. During active decay (7 - 12 days postmortem), respiration and biomass production rates were high: the community was dominated by Proteobacteria (increased from 15.0 to 26.1% relative abundance) and Firmicutes (increased from 1.0 to 29.0%), with reduced Acidobacteria abundances (decreased from 30.4 to 9.8%). Once decay rates slowed (10 - 23 d postmortem), respiration was elevated, but biomass production rates dropped dramatically; this community with low growth efficiency was dominated by Firmicutes (increased to 50.9%) and other anaerobic taxa. Human-associated bacteria, including the obligately anaerobic Bacteroides, were detected at high concentrations in soil throughout decomposition, up to 198 d postmortem. Our results revealed the pattern of functional and compositional succession in soil microbial communities during decomposition of human-derived organic matter, provided insight into decomposition processes, and identified putative predictor populations for time since death estimation.}, }
@article {pmid26066514, year = {2015}, author = {Liu, X and Chen, C and Wang, W and Hughes, JM and Lewis, T and Hou, E and Shen, J}, title = {Vertical Distribution of Soil Denitrifying Communities in a Wet Sclerophyll Forest under Long-Term Repeated Burning.}, journal = {Microbial ecology}, volume = {70}, number = {4}, pages = {993-1003}, pmid = {26066514}, issn = {1432-184X}, mesh = {Ammonium Compounds/analysis ; Bacteria/genetics ; Biodiversity ; Carbon/analysis ; Denitrification ; Ecosystem ; *Fires ; *Forests ; Genes, Bacterial/genetics ; *Genetic Variation ; *Microbial Consortia ; Nitrates/analysis ; Nitrogen/analysis ; Nutrition Assessment ; Oxygen/adverse effects ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Soil biogeochemical cycles are largely mediated by microorganisms, while fire significantly modifies biogeochemical cycles mainly via altering microbial community and substrate availability. Majority of studies on fire effects have focused on the surface soil; therefore, our understanding of the vertical distribution of microbial communities and the impacts of fire on nitrogen (N) dynamics in the soil profile is limited. Here, we examined the changes of soil denitrification capacity (DNC) and denitrifying communities with depth under different burning regimes, and their interaction with environmental gradients along the soil profile. Results showed that soil depth had a more pronounced impact than the burning treatment on the bacterial community size. The abundance of 16S rRNA and denitrification genes (narG, nirK, and nirS) declined exponentially with soil depth. Surprisingly, the nosZ-harboring denitrifiers were enriched in the deeper soil layers, which was likely to indicate that the nosZ-harboring denitrifiers could better adapt to the stress conditions (i.e., oxygen deficiency, nutrient limitation, etc.) than other denitrifiers. Soil nutrients, including dissolved organic carbon (DOC), total soluble N (TSN), ammonium (NH(4)(+)), and nitrate (NO(3)(-)), declined significantly with soil depth, which probably contributed to the vertical distribution of denitrifying communities. Soil DNC decreased significantly with soil depth, which was negligible in the depths below 20 cm. These findings have provided new insights into niche separation of the N-cycling functional guilds along the soil profile, under a varied fire disturbance regime.}, }
@article {pmid26066513, year = {2015}, author = {Gertler, C and Bargiela, R and Mapelli, F and Han, X and Chen, J and Hai, T and Amer, RA and Mahjoubi, M and Malkawi, H and Magagnini, M and Cherif, A and Abdel-Fattah, YR and Kalogerakis, N and Daffonchio, D and Ferrer, M and Golyshin, PN}, title = {Erratum to: Conversion of Uric Acid into Ammonium in Oil-Degrading Marine Microbial Communities: a Possible Role of Halomonads.}, journal = {Microbial ecology}, volume = {70}, number = {4}, pages = {1034}, doi = {10.1007/s00248-015-0631-6}, pmid = {26066513}, issn = {1432-184X}, }
@article {pmid26066028, year = {2015}, author = {Peltoniemi, K and Laiho, R and Juottonen, H and Kiikkilä, O and Mäkiranta, P and Minkkinen, K and Pennanen, T and Penttilä, T and Sarjala, T and Tuittila, ES and Tuomivirta, T and Fritze, H}, title = {Microbial ecology in a future climate: effects of temperature and moisture on microbial communities of two boreal fens.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {7}, pages = {}, doi = {10.1093/femsec/fiv062}, pmid = {26066028}, issn = {1574-6941}, mesh = {Archaea/genetics/physiology ; Arctic Regions ; Basidiomycota/genetics/physiology ; *Climate Change ; Ecosystem ; Microbial Consortia/genetics/*physiology ; Mortierella/genetics/physiology ; Mycorrhizae/genetics ; RNA, Ribosomal, 16S/genetics ; Soil ; *Soil Microbiology ; Temperature ; *Wetlands ; }, abstract = {Impacts of warming with open-top chambers on microbial communities in wet conditions and in conditions resulting from moderate water-level drawdown (WLD) were studied across 0-50 cm depth in northern and southern boreal sedge fens. Warming alone decreased microbial biomass especially in the northern fen. Impact of warming on microbial PLFA and fungal ITS composition was more obvious in the northern fen and linked to moisture regime and sample depth. Fungal-specific PLFA increased in the surface peat in the drier regime and decreased in layers below 10 cm in the wet regime after warming. OTUs representing Tomentella and Lactarius were observed in drier regime and Mortierella in wet regime after warming in the northern fen. The ectomycorrhizal fungi responded only to WLD. Interestingly, warming together with WLD decreased archaeal 16S rRNA copy numbers in general, and fungal ITS copy numbers in the northern fen. Expectedly, many results indicated that microbial response on warming may be linked to the moisture regime. Results indicated that microbial community in the northern fen representing Arctic soils would be more sensitive to environmental changes. The response to future climate change clearly may vary even within a habitat type, exemplified here by boreal sedge fen.}, }
@article {pmid26060984, year = {2015}, author = {Schuerger, AC and Lee, P}, title = {Microbial Ecology of a Crewed Rover Traverse in the Arctic: Low Microbial Dispersal and Implications for Planetary Protection on Human Mars Missions.}, journal = {Astrobiology}, volume = {15}, number = {6}, pages = {478-491}, pmid = {26060984}, issn = {1557-8070}, mesh = {*Ecology ; *Mars ; *Microbiota ; *Models, Theoretical ; Nunavut ; }, abstract = {Between April 2009 and July 2011, the NASA Haughton-Mars Project (HMP) led the Northwest Passage Drive Expedition (NWPDX), a multi-staged long-distance crewed rover traverse along the Northwest Passage in the Arctic. In April 2009, the HMP Okarian rover was driven 496 km over sea ice along the Northwest Passage, from Kugluktuk to Cambridge Bay, Nunavut, Canada. During the traverse, crew members collected samples from within the rover and from undisturbed snow-covered surfaces around the rover at three locations. The rover samples and snow samples were stored at subzero conditions (-20°C to -1°C) until processed for microbial diversity in labs at the NASA Kennedy Space Center, Florida. The objective was to determine the extent of microbial dispersal away from the rover and onto undisturbed snow. Interior surfaces of the rover were found to be associated with a wide range of bacteria (69 unique taxa) and fungi (16 unique taxa). In contrast, snow samples from the upwind, downwind, uptrack, and downtrack sample sites exterior to the rover were negative for both bacteria and fungi except for two colony-forming units (cfus) recovered from one downwind (1 cfu; site A4) and one uptrack (1 cfu; site B6) sample location. The fungus, Aspergillus fumigatus (GenBank JX517279), and closely related bacteria in the genus Brevibacillus were recovered from both snow (B. agri, GenBank JX517278) and interior rover surfaces. However, it is unknown whether the microorganisms were deposited onto snow surfaces at the time of sample collection (i.e., from the clothing or skin of the human operator) or via airborne dispersal from the rover during the 12-18 h layovers at the sites prior to collection. Results support the conclusion that a crewed rover traveling over previously undisturbed terrain may not significantly contaminate the local terrain via airborne dispersal of propagules from the vehicle.}, }
@article {pmid26055111, year = {2016}, author = {Hengge, R and Gründling, A and Jenal, U and Ryan, R and Yildiz, F}, title = {Bacterial Signal Transduction by Cyclic Di-GMP and Other Nucleotide Second Messengers.}, journal = {Journal of bacteriology}, volume = {198}, number = {1}, pages = {15-26}, pmid = {26055111}, issn = {1098-5530}, support = {100289/WT_/Wellcome Trust/United Kingdom ; MR/J006874/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacteria/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Cyclic GMP/*analogs &amp; derivatives/genetics/metabolism ; Gene Expression Regulation, Bacterial/*physiology ; Second Messenger Systems/*physiology ; Signal Transduction/*physiology ; }, abstract = {The first International Symposium on c-Di-GMP Signaling in Bacteria (22 to 25 March 2015, Harnack-Haus, Berlin, Germany)brought together 131 molecular microbiologists from 17 countries to discuss recent progress in our knowledge of bacterial nucleotide second messenger signaling. While the focus was on signal input, synthesis, degradation, and the striking diversity of the modes of action of the current second messenger paradigm, i.e., cyclic di-GMP (c-di-GMP), “classics” like cAMP and (p)ppGpp were also presented, in novel facets, and more recent “newcomers,” such as c-di-AMP and c-AMP-GMP, made an impressive appearance. A number of clear trends emerged during the 30 talks, on the 71 posters, and in the lively discussions, including (i)c-di-GMP control of the activities of various ATPases and phosphorylation cascades, (ii) extensive cross talk between c-di-GMP and other nucleotide second messenger signaling pathways, and (iii) a stunning number of novel effectors for nucleotide second messengers that surprisingly include some long-known master regulators of developmental pathways. Overall, the conference made it amply clear that second messenger signaling is currently one of the most dynamic fields within molecular microbiology,with major impacts in research fields ranging from human health to microbial ecology.}, }
@article {pmid26054703, year = {2015}, author = {Menkis, A and Marčiulynas, A and Gedminas, A and Lynikienė, J and Povilaitienė, A}, title = {High-Throughput Sequencing Reveals Drastic Changes in Fungal Communities in the Phyllosphere of Norway Spruce (Picea abies) Following Invasion of the Spruce Bud Scale (Physokermes piceae).}, journal = {Microbial ecology}, volume = {70}, number = {4}, pages = {904-911}, pmid = {26054703}, issn = {1432-184X}, mesh = {Animals ; Base Sequence ; Biodiversity ; Climate Change ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; Forests ; Fungi/classification/*genetics/pathogenicity ; Lithuania ; Norway ; Phylogeny ; Picea/*microbiology ; Pinus/*microbiology ; Plant Leaves/microbiology ; Plant Shoots/genetics/microbiology ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Trees/*microbiology ; }, abstract = {The aim of this study was to assess the diversity and composition of fungal communities in damaged and undamaged shoots of Norway spruce (Picea abies) following recent invasion of the spruce bud scale (Physokermes piceae) in Lithuania. Sampling was done in July 2013 and included 50 random lateral shoots from ten random trees in each of five visually undamaged and five damaged 40-50-year-old pure stands of P. abies. DNA was isolated from 500 individual shoots, subjected to amplification of the internal transcribed spacer of fungal ribosomal DNA (ITS rDNA), barcoded and sequenced. Clustering of 149,426 high-quality sequences resulted in 1193 non-singleton contigs of which 1039 (87.1 %) were fungal. In total, there were 893 fungal taxa in damaged shoots and 608 taxa in undamaged shoots (p < 0.0001). Furthermore, 431 (41.5 %) fungal taxa were exclusively in damaged shoots, 146 (14.0 %) were exclusively in undamaged shoots, and 462 (44.5 %) were common to both types of samples. Correspondence analysis showed that study sites representing damaged and undamaged shoots were separated from each other, indicating that in these fungal communities, these were largely different and, therefore, heavily affected by P. piceae. In conclusion, the results demonstrated that invasive alien tree pests may have a profound effect on fungal mycobiota associated with the phyllosphere of P. abies, and therefore, in addition to their direct negative effect owing physical damage of the tissue, they may also indirectly determine health, sustainability and, ultimately, distribution of the forest tree species.}, }
@article {pmid26054702, year = {2015}, author = {Ke, X and Lu, W and Conrad, R}, title = {High Oxygen Concentration Increases the Abundance and Activity of Bacterial Rather than Archaeal Nitrifiers in Rice Field Soil.}, journal = {Microbial ecology}, volume = {70}, number = {4}, pages = {961-970}, pmid = {26054702}, issn = {1432-184X}, mesh = {Ammonia/metabolism ; Archaea/growth &amp; development/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Hydrogen-Ion Concentration ; Nitrification ; Nitrites/metabolism ; Nitrobacter/growth &amp; development/*metabolism ; Oryza/*microbiology ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Oxygen/chemistry/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Oxygen is considered as a limiting factor for nitrification in rice paddy soil. However, little is known about how the nitrifying microbial community responds to different oxygen concentrations at community and transcript level. In this study, soil and roots were harvested from 50-day-old rice microcosms and were incubated for up to 45 days under two oxygen concentrations: 2 % O(2) and 20 % O(2) (ambient air). Nitrification rates were measured from the accumulation of nitrite plus nitrate. The population dynamics of bacterial (AOB) and archaeal (AOA) ammonia oxidizers was determined from the abundance (using quantitative PCR (qPCR)) and composition (using terminal restriction fragment length polymorphism and cloning/sequencing) of their amoA genes, that of nitrite oxidizers (NOB) by quantifying the nxrA gene of Nitrobacter spp. and the 16S rRNA gene of Nitrospira spp. The activity of the nitrifiers was determined by quantifying the copy numbers of amoA and nxrA transcripts (using RT-qPCR). Different oxygen concentrations did not affect the community compositions of AOB, AOA, and NOB, which however were different between surface soil, bottom soil, and rice roots. However, nitrification rates were higher under ambient air than 2 % O(2), and abundance and transcript activities of AOB, but not of AOA, were also higher. Abundance and transcript copy numbers of Nitrobacter were also higher at ambient air. These results indicate that AOB and NOB, but not AOA, were sensitive to oxygen availability.}, }
@article {pmid26052662, year = {2015}, author = {Prosser, JI}, title = {Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology.}, journal = {Nature reviews. Microbiology}, volume = {13}, number = {7}, pages = {439-446}, pmid = {26052662}, issn = {1740-1534}, mesh = {Archaea/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; *Gene Expression Profiling ; *Metagenome ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Technological advances are enabling the sequencing of environmental DNA and RNA at increasing depth and with decreasing costs. Metagenomic and transcriptomic analysis of soil microbial communities and the assembly of 'population genomes' from soil DNA are therefore now feasible. Although the value of such 'omic' approaches is limited by the associated technical and bioinformatic difficulties, even if these obstacles were eliminated and 'perfect' metagenomes and metatranscriptomes were available, important conceptual challenges remain. This Opinion article considers these conceptual challenges in the context of the current use of omics in soil microbiology, but the main arguments presented are also relevant to the application of omics to marine, freshwater, gut or other environments.}, }
@article {pmid26048932, year = {2015}, author = {Sapountzis, P and Zhukova, M and Hansen, LH and Sørensen, SJ and Schiøtt, M and Boomsma, JJ}, title = {Acromyrmex Leaf-Cutting Ants Have Simple Gut Microbiota with Nitrogen-Fixing Potential.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {16}, pages = {5527-5537}, pmid = {26048932}, issn = {1098-5336}, support = {323085/ERC_/European Research Council/International ; }, mesh = {Alphaproteobacteria/genetics/*isolation &amp; purification/physiology ; Animals ; Ants/*microbiology ; Entomoplasmatales/*isolation &amp; purification/physiology ; *Gastrointestinal Microbiome ; *Nitrogen Fixation ; Oxidoreductases/genetics ; Symbiosis ; Wolbachia/*isolation &amp; purification/physiology ; }, abstract = {Ants and termites have independently evolved obligate fungus-farming mutualisms, but their gardening procedures are fundamentally different, as the termites predigest their plant substrate whereas the ants deposit it directly on the fungus garden. Fungus-growing termites retained diverse gut microbiota, but bacterial gut communities in fungus-growing leaf-cutting ants have not been investigated, so it is unknown whether and how they are specialized on an exclusively fungal diet. Here we characterized the gut bacterial community of Panamanian Acromyrmex species, which are dominated by only four bacterial taxa: Wolbachia, Rhizobiales, and two Entomoplasmatales taxa. We show that the Entomoplasmatales can be both intracellular and extracellular across different gut tissues, Wolbachia is mainly but not exclusively intracellular, and the Rhizobiales species is strictly extracellular and confined to the gut lumen, where it forms biofilms along the hindgut cuticle supported by an adhesive matrix of polysaccharides. Tetracycline diets eliminated the Entomoplasmatales symbionts but hardly affected Wolbachia and only moderately reduced the Rhizobiales, suggesting that the latter are protected by the biofilm matrix. We show that the Rhizobiales symbiont produces bacterial NifH proteins that have been associated with the fixation of nitrogen, suggesting that these compartmentalized hindgut symbionts alleviate nutritional constraints emanating from an exclusive fungus garden diet reared on a substrate of leaves.}, }
@article {pmid26048370, year = {2015}, author = {Brandes, M and Albach, DC and Vogt, JC and Mayland-Quellhorst, E and Mendieta-Leiva, G and Golubic, S and Palinska, KA}, title = {Supratidal Extremophiles--Cyanobacterial Diversity in the Rock Pools of the Croatian Adria.}, journal = {Microbial ecology}, volume = {70}, number = {4}, pages = {876-888}, pmid = {26048370}, issn = {1432-184X}, mesh = {Biodiversity ; Calcium Carbonate ; Croatia ; Cyanobacteria/*classification/*genetics ; DNA, Bacterial/genetics ; Ecosystem ; *Genetic Variation ; Multigene Family ; Phenotype ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; Seawater/*microbiology ; Sequence Analysis, DNA ; Trees/microbiology ; Water Microbiology ; }, abstract = {Hardly any molecular studies have been done on euendoliths of marine coastal environments, especially along the supratidal ranges of carbonate coasts. In our study, we provide a comparative sequence analysis using 454 pyrosequencing of the 16S ribosomal RNA (rRNA) gene combined with extensive microscopy of the endolithic community from rock pools of the Croatian Adria. Molecular diversity indices and richness estimates showed high level of diversity, particularly in high-salinity samples. The most common cyanobacteria belong to the order Pleurocapsales, similar to observations on limestone coasts in other parts of the world. Using single-cell amplification sequences of Hormathonema spp., Hyella caespitosa, and Kyrtuthrix dalmatica was for the first time introduced to the public GenBank.Microscopic investigations did not show qualitative variances in diversity among sites with different salinity but clear differences in prevalent organisms from similar environments suggesting that most of them are adapted to inhabit extreme, marine endolithic habitats and that similar species inhabit geographically separated but ecologically similar environments. This is a remarkable concordance rather seldom seen in molecular community studies in support of the hypothesis that endolithic ecosystems are seeded from a global meta-community.The relative diversity of the community is greater than those described from harsh endolithic habitats of cold and hot deserts. The maximum likelihood phylogenetic tree consisting of 166 operational taxonomic units (OTUs) at 96 % sequence similarity revealed 11 distinct clusters. Three clusters contained only epilithic or endolithic taxa, and five clusters contained mixed epilithic and endolithic taxa. Organisms clustered according to their taxonomic affiliations and not to their preferences to salt concentrations.}, }
@article {pmid26048196, year = {2015}, author = {Cowan, DA and Ramond, JB and Makhalanyane, TP and De Maayer, P}, title = {Metagenomics of extreme environments.}, journal = {Current opinion in microbiology}, volume = {25}, number = {}, pages = {97-102}, doi = {10.1016/j.mib.2015.05.005}, pmid = {26048196}, issn = {1879-0364}, mesh = {Archaea/*genetics/*physiology ; Bacteria/classification/*genetics ; *Bacterial Physiological Phenomena ; Ecosystem ; Environment ; *Metagenomics ; Microbial Consortia/genetics/*physiology ; }, abstract = {Whether they are exposed to extremes of heat or cold, or buried deep beneath the Earth's surface, microorganisms have an uncanny ability to survive under these conditions. This ability to survive has fascinated scientists for nearly a century, but the recent development of metagenomics and 'omics' tools has allowed us to make huge leaps in understanding the remarkable complexity and versatility of extremophile communities. Here, in the context of the recently developed metagenomic tools, we discuss recent research on the community composition, adaptive strategies and biological functions of extremophiles.}, }
@article {pmid26046429, year = {2015}, author = {Ramió-Pujol, S and Ganigué, R and Bañeras, L and Colprim, J}, title = {Incubation at 25 °C prevents acid crash and enhances alcohol production in Clostridium carboxidivorans P7.}, journal = {Bioresource technology}, volume = {192}, number = {}, pages = {296-303}, doi = {10.1016/j.biortech.2015.05.077}, pmid = {26046429}, issn = {1873-2976}, mesh = {Acetates/metabolism ; Acids/*metabolism ; Biofuels/microbiology ; Bioreactors/microbiology ; Butanols/metabolism ; Caproates/metabolism ; Carbon/metabolism ; Clostridium/*metabolism ; Ethanol/*metabolism ; Fermentation/physiology ; Hexanols/metabolism ; Temperature ; }, abstract = {Incubation of carboxydotrophs at 37 °C provides optimal conditions for their growth. However, a fast accumulation of organic acids, specifically acetate, during the exponential growth phase may result in low alcohol production and substrate consumption due to a phenomenon known as "acid crash". The present work investigates growth and productivity of Clostridium carboxidivorans P7 at two incubation temperatures. At 37 °C the culture was not able to override the "acid crash", resulting in low ethanol titers (1.56 mM). On the other hand, lower metabolic rates at 25 °C enhanced ethanol and butanol production (32.1 and 14.5 mM, respectively). Moreover, at low temperatures, hexanol and caproic acid were also produced at significant concentrations, 8.21 and 9.02 mM respectively, among the highest values reported for P7. Our results demonstrate that production of biofuels with longer carbon chains molecules may be enhanced incubating syngas-fermenting acetogenic bacteria at sub-optimal temperatures.}, }
@article {pmid26046428, year = {2015}, author = {Mechmech, F and Chadjaa, H and Rahni, M and Marinova, M and Ben Akacha, N and Gargouri, M}, title = {Improvement of butanol production from a hardwood hemicelluloses hydrolysate by combined sugar concentration and phenols removal.}, journal = {Bioresource technology}, volume = {192}, number = {}, pages = {287-295}, doi = {10.1016/j.biortech.2015.05.012}, pmid = {26046428}, issn = {1873-2976}, mesh = {Acetic Acid/chemistry ; Acetone/chemistry ; Butanols/*chemistry ; Carbohydrates/*chemistry ; Ethanol/chemistry ; Fermentation ; Ferric Compounds/chemistry ; Hydrolysis ; Phenols/*chemistry ; Polysaccharides/*chemistry ; Wood/*chemistry ; }, abstract = {The feasibility of using hardwood hemicellulosic pre-hydrolysate recovered from a dissolving pulping process for Acetone-Butanol-Ethanol (ABE) fermentation has been investigated. Dilutions and detoxification methods based on flocculation and nanofiltration were tested to determine the inhibitory concentration of phenolic compounds and to evaluate the efficiency of inhibitors removal on fermentation. Flocculation carried out with ferric sulfate was the most effective method for removal of phenolics (56%) and acetic acid (80%). The impact on fermentation was significant, with an ABE production of 6.40 g/L and 4.25 g/L when using flocculation or combined nanofiltration/flocculation respectively, as compared to a non-significant production for the untreated hydrolysate. By decreasing the toxicity effect of inhibitors, this study reports for the first time that the use of these techniques is efficient to increase the inhibitory concentration threshold of phenols, from 0.3g/L in untreated hydrolysate, to 1.1g/L in flocculated and in nanofiltrated and flocculated hydrolysates.}, }
@article {pmid26045158, year = {2015}, author = {Ziganshina, EE and Belostotskiy, DE and Ilinskaya, ON and Boulygina, EA and Grigoryeva, TV and Ziganshin, AM}, title = {Effect of the Organic Loading Rate Increase and the Presence of Zeolite on Microbial Community Composition and Process Stability During Anaerobic Digestion of Chicken Wastes.}, journal = {Microbial ecology}, volume = {70}, number = {4}, pages = {948-960}, pmid = {26045158}, issn = {1432-184X}, mesh = {Ammonia/metabolism ; Anaerobiosis ; Animals ; Bacteria, Anaerobic/*drug effects/*genetics/*metabolism ; Biodiversity ; Biofuels/microbiology ; Bioreactors/*microbiology ; Chickens/*microbiology ; Fatty Acids, Volatile/metabolism ; Hydrogen-Ion Concentration ; Manure/*microbiology ; Microbial Consortia ; RNA, Ribosomal, 16S/genetics ; Waste Disposal, Fluid/*methods ; Zeolites/*chemistry ; }, abstract = {This study investigates the effect of the organic loading rate (OLR) increase from 1.0 to 3.5 g VS L(-1) day(-1) at constant hydraulic retention time (HRT) of 35 days on anaerobic reactors' performance and microbial diversity during mesophilic anaerobic digestion of ammonium-rich chicken wastes in the absence/presence of zeolite. The effects of anaerobic process parameters on microbial community structure and dynamics were evaluated using a 16S ribosomal RNA gene-based pyrosequencing approach. Maximum 12 % of the total ammonia nitrogen (TAN) was efficiently removed by zeolite in the fixed zeolite reactor (day 87). In addition, volatile fatty acids (VFA) in the fixed zeolite reactor accumulated in lower concentrations at high OLR of 3.2-3.5 g VS L(-1) day(-1). Microbial communities in the fixed zeolite reactor and reactor without zeolite were dominated by various members of Bacteroidales and Methanobacterium sp. at moderate TAN and VFA levels. The increase of the OLR accompanied by TAN and VFA accumulation and increase in pH led to the predominance of representatives of the family Erysipelotrichaceae and genera Clostridium and Methanosarcina. Methanosarcina sp. reached relative abundances of 94 and 57 % in the fixed zeolite reactor and reactor without zeolite at the end of the experimental period, respectively. In addition, the diminution of Synergistaceae and Crenarchaeota and increase in the abundance of Acholeplasmataceae in parallel with the increase of TAN, VFA, and pH values were observed.}, }
@article {pmid26045157, year = {2015}, author = {González-Toril, E and Santofimia, E and Blanco, Y and López-Pamo, E and Gómez, MJ and Bobadilla, M and Cruz, R and Palomino, EJ and Aguilera, &#xc1;}, title = {Pyrosequencing-Based Assessment of the Microbial Community Structure of Pastoruri Glacier Area (Huascarán National Park, Perú), a Natural Extreme Acidic Environment.}, journal = {Microbial ecology}, volume = {70}, number = {4}, pages = {936-947}, pmid = {26045157}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/metabolism ; *Biodiversity ; Cold Temperature ; Ecosystem ; Hydrogen-Ion Concentration ; Ice Cover/*microbiology ; Iron/metabolism ; Parks, Recreational ; Peru ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Soil ; Sulfides/metabolism ; Sulfur/metabolism ; Water/analysis/chemistry ; *Water Microbiology ; }, abstract = {The exposure of fresh sulfide-rich lithologies by the retracement of the Nevado Pastoruri glacier (Central Andes, Perú) is increasing the presence of heavy metals in the water as well as decreasing the pH, producing an acid rock drainage (ARD) process in the area. We describe the microbial communities of an extreme ARD site in Huascarán National Park as well as their correlation with the water physicochemistry. Microbial biodiversity was analyzed by FLX 454 sequencing of the 16S rRNA gene. The suggested geomicrobiological model of the area distinguishes three different zones. The proglacial zone is located in the upper part of the valley, where the ARD process is not evident yet. Most of the OTUs detected in this area were related to sequences associated with cold environments (i.e., psychrotolerant species of Cyanobacteria or Bacteroidetes). After the proglacial area, an ARD-influenced zone appeared, characterized by the presence of phylotypes related to acidophiles (Acidiphilium) as well as other species related to acidic and cold environments (i.e., acidophilic species of Chloroflexi, Clostridium and Verrumicrobia). Sulfur- and iron-oxidizing acidophilic bacteria (Acidithiobacillus) were also identified. The post-ARD area was characterized by the presence of OTUs related to microorganisms detected in soils, permafrost, high mountain environments, and deglaciation areas (Sphingomonadales, Caulobacter or Comamonadaceae).}, }
@article {pmid26044435, year = {2015}, author = {Califano, G and Franco, T and Gonçalves, AC and Castanho, S and Soares, F and Ribeiro, L and Mata, L and Costa, R}, title = {Draft Genome Sequence of Aliivibrio fischeri Strain 5LC, a Bacterium Retrieved from Gilthead Sea Bream (Sparus aurata) Larvae Reared in Aquaculture.}, journal = {Genome announcements}, volume = {3}, number = {3}, pages = {}, pmid = {26044435}, issn = {2169-8287}, abstract = {To shed light on the putative host-mediated lifestyle of the quintessential marine symbiont Aliivibrio fischeri, and on the symbiosis versus potentially pathogenic features of bacteria associated with farmed fish, we report the draft genome sequence of A. fischeri strain 5LC, a bacterium retrieved from gilthead sea bream (Sparus aurata) larvae.}, }
@article {pmid26044091, year = {2015}, author = {Nouet, C and Charlier, JB and Carnol, M and Bosman, B and Farnir, F and Motte, P and Hanikenne, M}, title = {Functional analysis of the three HMA4 copies of the metal hyperaccumulator Arabidopsis halleri.}, journal = {Journal of experimental botany}, volume = {66}, number = {19}, pages = {5783-5795}, pmid = {26044091}, issn = {1460-2431}, mesh = {Adenosine Triphosphatases/*genetics/metabolism ; Arabidopsis/*genetics/metabolism ; Arabidopsis Proteins/*genetics/metabolism ; DNA, Complementary/genetics/metabolism ; *Gene Expression Regulation, Plant ; Green Fluorescent Proteins/genetics/metabolism ; Homeostasis ; Metals/metabolism ; Mutation ; Promoter Regions, Genetic ; Sequence Analysis, DNA ; }, abstract = {In Arabidopsis halleri, the HMA4 gene has an essential function in Zn/Cd hypertolerance and hyperaccumulation by mediating root-to-shoot translocation of metals. Constitutive high expression of AhHMA4 results from a tandem triplication and cis-activation of the promoter of all three copies. The three AhHMA4 copies possess divergent promoter sequences, but highly conserved coding sequences, and display identical expression profiles in the root and shoot vascular system. Here, an AhHMA4::GFP fusion was expressed under the control of each of the three A. halleri HMA4 promoters in a hma2hma4 double mutant of A. thaliana to individually examine the function of each AhHMA4 copy. The protein showed non-polar localization at the plasma membrane of the root pericycle cells of both A. thaliana and A. halleri. The expression of each AhHMA4::GFP copy complemented the severe Zn-deficiency phenotype of the hma2hma4 mutant by restoring root-to-shoot translocation of Zn. However, each copy had a different impact on metal homeostasis in the A. thaliana genetic background: AhHMA4 copies 2 and 3 were more highly expressed and provided higher Zn tolerance in roots and accumulation in shoots than copy 1, and AhHMA4 copy 3 also increased Cd tolerance in roots. These data suggest a certain extent of functional differentiation among the three A. halleri HMA4 copies, stemming from differences in expression levels rather than in expression profile. HMA4 is a key node of the Zn homeostasis network and small changes in expression level can have a major impact on Zn allocation to root or shoot tissues.}, }
@article {pmid26043042, year = {2015}, author = {Chang, L and Neu, J}, title = {Early factors leading to later obesity: interactions of the microbiome, epigenome, and nutrition.}, journal = {Current problems in pediatric and adolescent health care}, volume = {45}, number = {5}, pages = {134-142}, doi = {10.1016/j.cppeds.2015.03.003}, pmid = {26043042}, issn = {1538-3199}, mesh = {Adolescent ; Age of Onset ; Cardiovascular Diseases/*etiology/physiopathology/prevention &amp; control ; Child ; Child, Preschool ; Disease Progression ; *Epigenesis, Genetic ; Female ; Humans ; Infant ; Infant, Newborn ; Metabolic Syndrome/*etiology/physiopathology/prevention &amp; control ; *Microbiota ; Musculoskeletal Diseases/*etiology/physiopathology/prevention &amp; control ; Nutritional Physiological Phenomena ; Nutritional Status ; Obesity/*etiology/genetics/physiopathology/prevention &amp; control ; Pregnancy ; Preventive Medicine ; Risk Factors ; Risk Reduction Behavior ; United States ; }, abstract = {Obesity is a major public health problem in the United States and many other countries. Childhood obesity rates have risen extensively over the last several decades with the numbers continuing to rise. Obese and overweight children are at high risk of becoming overweight adolescents and adults. The causes are multifactorial and are affected by various genetic, behavioral, and environmental factors. This review aims to discuss a previously under-recognized antecedent of obesity and related chronic metabolic diseases such as heart disease and diabetes. Specifically, we highlight the relationship of the microbial ecology of the gastrointestinal tract during early development and the consequent effects on metabolism, epigenetics, and inflammatory responses that can subsequently result in metabolic syndrome. Although studies in this area are just beginning, this area of research is rapidly expanding and may lead to early life interventions that may have significant impacts in the prevention of obesity.}, }
@article {pmid26042114, year = {2015}, author = {Sheik, CS and Stevenson, EI and Den Uyl, PA and Arendt, CA and Aciego, SM and Dick, GJ}, title = {Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {495}, pmid = {26042114}, issn = {1664-302X}, abstract = {Glaciers are geologically important yet transient ecosystems that support diverse, biogeochemically significant microbial communities. During the melt season glaciers undergo dramatic physical, geochemical, and biological changes that exert great influence on downstream biogeochemical cycles. Thus, we sought to understand the temporal melt-season dynamics of microbial communities and associated geochemistry at the terminus of Lemon Creek Glacier (LCG) in coastal southern Alaska. Due to late season snowfall, sampling of LCG occurred in three interconnected areas: proglacial Lake Thomas, the lower glacial outflow stream, and the glacier's terminus. LCG associated microbial communities were phylogenetically diverse and varied by sampling location. However, Betaproteobacteria, Alphaproteobacteria, and Bacteroidetes dominated communities at all sampling locations. Strict anaerobic groups such as methanogens, SR1, and OP11 were also recovered from glacier outflows, indicating anoxic conditions in at least some portions of the LCG subglacial environment. Microbial community structure was significantly correlated with sampling location and sodium concentrations. Microbial communities sampled from terminus outflow waters exhibited day-to-day fluctuation in taxonomy and phylogenetic similarity. However, these communities were not significantly different from randomly constructed communities from all three sites. These results indicate that glacial outflows share a large proportion of phylogenetic overlap with downstream environments and that the observed significant shifts in community structure are driven by changes in relative abundance of different taxa, and not complete restructuring of communities. We conclude that LCG glacial discharge hosts a diverse and relatively stable microbiome that shifts at fine taxonomic scales in response to geochemistry and likely water residence time.}, }
@article {pmid26042112, year = {2015}, author = {Pold, G and Melillo, JM and DeAngelis, KM}, title = {Two decades of warming increases diversity of a potentially lignolytic bacterial community.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {480}, pmid = {26042112}, issn = {1664-302X}, abstract = {As Earth's climate warms, the massive stores of carbon found in soil are predicted to become depleted, and leave behind a smaller carbon pool that is less accessible to microbes. At a long-term forest soil-warming experiment in central Massachusetts, soil respiration and bacterial diversity have increased, while fungal biomass and microbially-accessible soil carbon have decreased. Here, we evaluate how warming has affected the microbial community's capability to degrade chemically-complex soil carbon using lignin-amended BioSep beads. We profiled the bacterial and fungal communities using PCR-based methods and completed extracellular enzyme assays as a proxy for potential community function. We found that lignin-amended beads selected for a distinct community containing bacterial taxa closely related to known lignin degraders, as well as members of many genera not previously noted as capable of degrading lignin. Warming tended to drive bacterial community structure more strongly in the lignin beads, while the effect on the fungal community was limited to unamended beads. Of those bacterial operational taxonomic units (OTUs) enriched by the warming treatment, many were enriched uniquely on lignin-amended beads. These taxa may be contributing to enhanced soil respiration under warming despite reduced readily available C availability. In aggregate, these results suggest that there is genetic potential for chemically complex soil carbon degradation that may lead to extended elevated soil respiration with long-term warming.}, }
@article {pmid26041282, year = {2015}, author = {Fénéant, L and Potel, J and François, C and Sané, F and Douam, F and Belouzard, S and Calland, N and Vausselin, T and Rouillé, Y and Descamps, V and Baumert, TF and Duverlie, G and Lavillette, D and Hober, D and Dubuisson, J and Wychowski, C and Cocquerel, L}, title = {New Insights into the Understanding of Hepatitis C Virus Entry and Cell-to-Cell Transmission by Using the Ionophore Monensin A.}, journal = {Journal of virology}, volume = {89}, number = {16}, pages = {8346-8364}, pmid = {26041282}, issn = {1098-5514}, mesh = {Cell Line ; Dose-Response Relationship, Drug ; Drug Resistance, Viral/genetics ; Fluorescent Antibody Technique, Indirect ; Hepacivirus/genetics/*physiology ; Humans ; Hydrogen-Ion Concentration/drug effects ; Ionophores/*pharmacology ; Monensin/*pharmacology ; Mutation, Missense/genetics ; Neutralization Tests ; Viral Envelope Proteins/*genetics ; Viral Proteins/*genetics/metabolism ; Virus Internalization/*drug effects ; }, abstract = {UNLABELLED: In our study, we characterized the effect of monensin, an ionophore that is known to raise the intracellular pH, on the hepatitis C virus (HCV) life cycle. We showed that monensin inhibits HCV entry in a pangenotypic and dose-dependent manner. Monensin induces an alkalization of intracellular organelles, leading to an inhibition of the fusion step between viral and cellular membranes. Interestingly, we demonstrated that HCV cell-to-cell transmission is dependent on the vesicular pH. Using the selective pressure of monensin, we selected a monensin-resistant virus which has evolved to use a new entry route that is partially pH and clathrin independent. Characterization of this mutant led to the identification of two mutations in envelope proteins, the Y297H mutation in E1 and the I399T mutation in hypervariable region 1 (HVR1) of E2, which confer resistance to monensin and thus allow HCV to use a pH-independent entry route. Interestingly, the I399T mutation introduces an N-glycosylation site within HVR1 and increases the density of virions and their sensitivity to neutralization with anti-apolipoprotein E (anti-ApoE) antibodies, suggesting that this mutation likely induces conformational changes in HVR1 that in turn modulate the association with ApoE. Strikingly, the I399T mutation dramatically reduces HCV cell-to-cell spread. In summary, we identified a mutation in HVR1 that overcomes the vesicular pH dependence, modifies the biophysical properties of particles, and drastically reduces cell-to-cell transmission, indicating that the regulation by HVR1 of particle association with ApoE might control the pH dependence of cell-free and cell-to-cell transmission. Thus, HVR1 and ApoE are critical regulators of HCV propagation.<br><br>IMPORTANCE: Although several cell surface proteins have been identified as entry factors for hepatitis C virus (HCV), the precise mechanisms regulating its transmission to hepatic cells are still unclear. In our study, we used monensin A, an ionophore that is known to raise the intracellular pH, and demonstrated that cell-free and cell-to-cell transmission pathways are both pH-dependent processes. We generated monensin-resistant viruses that displayed different entry routes and biophysical properties. Thanks to these mutants, we highlighted the importance of hypervariable region 1 (HVR1) of the E2 envelope protein for the association of particles with apolipoprotein E, which in turn might control the pH dependency of cell-free and cell-to-cell transmission.}, }
@article {pmid26040993, year = {2015}, author = {Cretoiu, MS and Berini, F and Kielak, AM and Marinelli, F and van Elsas, JD}, title = {A novel salt-tolerant chitobiosidase discovered by genetic screening of a metagenomic library derived from chitin-amended agricultural soil.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {19}, pages = {8199-8215}, pmid = {26040993}, issn = {1432-0614}, mesh = {Bacteria/chemistry/*enzymology/genetics ; Bacterial Proteins/*chemistry/*genetics/metabolism ; Base Sequence ; Chitin/metabolism ; Chitinases/*chemistry/*genetics/metabolism ; Cloning, Molecular ; Enzyme Stability ; Gene Library ; Hydrogen-Ion Concentration ; Metagenomics ; Molecular Sequence Data ; Phylogeny ; Sodium Chloride/metabolism ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Here, we report on the construction of a metagenomic library from a chitin-amended disease-suppressive agricultural soil and its screening for genes that encode novel chitinolytic enzymes. The library, constructed in fosmids in an Escherichia coli host, comprised 145,000 clones containing inserts of sizes of 21 to 40 kb, yielding a total of approximately 5.8 GB of cloned soil DNA. Using genetic screenings by repeated PCR cycles aimed to detect gene sequences of the bacterial chitinase A-class (hereby named chi A genes), we identified and characterized five fosmids carrying candidate genes for chitinolytic enzymes. The analysis thus allowed access to the genomic (fosmid-borne) context of these genes. Using the chiA-targeted PCR, which is based on degenerate primers, the five fosmids all produced amplicons, of which the sequences were related to predicted chitinolytic enzyme-encoding genes of four different host organisms, including Stenotrophomonas maltophilia. Sequencing and de novo annotation of the fosmid inserts confirmed that each one of these carried one or more open reading frames that were predicted to encode enzymes active on chitin, including one for a chitin deacetylase. Moreover, the genetic contexts in which the putative chitinolytic enzyme-encoding genes were located were unique per fosmid. Specifically, inserts from organisms related to Burkholderia sp., Acidobacterium sp., Aeromonas veronii, and the chloroflexi Nitrolancetus hollandicus and/or Ktedonobacter racemifer were obtained. Remarkably, the S. maltophilia chiA-like gene was found to occur in two different genetic contexts (related to N. hollandicus/K. racemifer), indicating the historical occurrence of genetic reshufflings in this part of the soil microbiota. One fosmid containing the insert composed of DNA from the N. hollandicus-like organism (denoted 53D1) was selected for further work. Using subcloning procedures, its putative gene for a chitinolytic enzyme was successfully brought to expression in an E. coli host. On the basis of purified protein preparations, the produced protein was characterized as a chitobiosidase of 43.6 kDa, with a pI of 4.83. Given its activity spectrum, it can be typified as a halotolerant chitobiosidase.}, }
@article {pmid26040274, year = {2015}, author = {Mongui, A and Pérez-Llanos, FJ and Yamamoto, MM and Lozano, M and Zambrano, MM and Del Portillo, P and Fernández-Becerra, C and Restrepo, S and Del Portillo, HA and Junca, H}, title = {Development of a genetic tool for functional screening of anti-malarial bioactive extracts in metagenomic libraries.}, journal = {Malaria journal}, volume = {14}, number = {}, pages = {233}, pmid = {26040274}, issn = {1475-2875}, mesh = {Antimalarials/*pharmacology ; Biodiversity ; *Genomic Library ; Malaria, Falciparum/drug therapy ; Metagenome ; *Parasitic Sensitivity Tests ; Plant Extracts/*pharmacology ; Plants/*chemistry ; Plasmodium falciparum/*drug effects/genetics ; }, abstract = {BACKGROUND: The chemical treatment of Plasmodium falciparum for human infections is losing efficacy each year due to the rise of resistance. One possible strategy to find novel anti-malarial drugs is to access the largest reservoir of genomic biodiversity source on earth present in metagenomes of environmental microbial communities.<br><br>METHODS: A bioluminescent P. falciparum parasite was used to quickly detect shifts in viability of microcultures grown in 96-well plates. A synthetic gene encoding the Dermaseptin 4 peptide was designed and cloned under tight transcriptional control in a large metagenomic insert context (30&#xa0;kb) to serve as proof-of-principle for the screening platform.<br><br>RESULTS: Decrease in parasite viability consistently correlated with bioluminescence emitted from parasite microcultures, after their exposure to bacterial extracts containing a plasmid or fosmid engineered to encode the Dermaseptin 4 anti-malarial peptide.<br><br>CONCLUSIONS: Here, a new technical platform to access the anti-malarial potential in microbial environmental metagenomes has been developed.}, }
@article {pmid26038228, year = {2015}, author = {Willis, A and Bunge, J}, title = {Estimating diversity via frequency ratios.}, journal = {Biometrics}, volume = {71}, number = {4}, pages = {1042-1049}, doi = {10.1111/biom.12332}, pmid = {26038228}, issn = {1541-0420}, mesh = {*Biodiversity ; Biometry/methods ; Computer Simulation ; Databases, Genetic ; High-Throughput Nucleotide Sequencing ; *Microbial Consortia ; Nonlinear Dynamics ; Probability Theory ; }, abstract = {We wish to estimate the total number of classes in a population based on sample counts, especially in the presence of high latent diversity. Drawing on probability theory that characterizes distributions on the integers by ratios of consecutive probabilities, we construct a nonlinear regression model for the ratios of consecutive frequency counts. This allows us to predict the unobserved count and hence estimate the total diversity. We believe that this is the first approach to depart from the classical mixed Poisson model in this problem. Our method is geometrically intuitive and yields good fits to data with reasonable standard errors. It is especially well-suited to analyzing high diversity datasets derived from next-generation sequencing in microbial ecology. We demonstrate the method's performance in this context and via simulation, and we present a dataset for which our method outperforms all competitors.}, }
@article {pmid26037816, year = {2015}, author = {Nitzsche, KS and Weigold, P and Lösekann-Behrens, T and Kappler, A and Behrens, S}, title = {Microbial community composition of a household sand filter used for arsenic, iron, and manganese removal from groundwater in Vietnam.}, journal = {Chemosphere}, volume = {138}, number = {}, pages = {47-59}, doi = {10.1016/j.chemosphere.2015.05.032}, pmid = {26037816}, issn = {1879-1298}, mesh = {Archaea/genetics/growth &amp; development ; Arsenic/analysis/*isolation &amp; purification ; Biomass ; Drinking Water/analysis/standards ; Family Characteristics ; Ferric Compounds/chemistry ; Filtration/*instrumentation ; *Groundwater/chemistry/microbiology ; Iron/analysis/*isolation &amp; purification ; Manganese/analysis/*isolation &amp; purification ; Nitrosomonadaceae/genetics/growth &amp; development ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Silicon Dioxide/chemistry ; Vietnam ; Water Pollutants, Chemical/analysis/*isolation &amp; purification ; }, abstract = {Household sand filters are used in rural areas of Vietnam to remove As, Fe, and Mn from groundwater for drinking water purposes. Currently, it is unknown what role microbial processes play in mineral oxide formation and As removal during water filtration. We performed most probable number counts to quantify the abundance of physiological groups of microorganisms capable of catalyzing Fe- and Mn-redox transformation processes in a household sand filter. We found up to 10(4) cells g(-1) dry sand of nitrate-reducing Fe(II)-oxidizing bacteria and Fe(III)-reducing bacteria, and no microaerophilic Fe(II)-oxidizing bacteria, but up to 10(6) cells g(-1) dry sand Mn-oxidizing bacteria. 16S rRNA gene amplicon sequencing confirmed MPN counts insofar as only low abundances of known taxa capable of performing Fe- and Mn-redox transformations were detected. Instead the microbial community on the sand filter was dominated by nitrifying microorganisms, e.g. Nitrospira, Nitrosomonadales, and an archaeal OTU affiliated to Candidatus Nitrososphaera. Quantitative PCR for Nitrospira and ammonia monooxygenase genes agreed with DNA sequencing results underlining the numerical importance of nitrifiers in the sand filter. Based on our analysis of the microbial community composition and previous studies on the solid phase chemistry of sand filters we conclude that abiotic Fe(II) oxidation processes prevail over biotic Fe(II) oxidation on the filter. Yet, Mn-oxidizing bacteria play an important role for Mn(II) oxidation and Mn(III/IV) oxide precipitation in a distinct layer of the sand filter. The formation of Mn(III/IV) oxides contributes to abiotic As(III) oxidation and immobilization of As(V) by sorption to Fe(III) (oxyhydr)oxides.}, }
@article {pmid26034276, year = {2015}, author = {Guo, L and McLean, JS and Yang, Y and Eckert, R and Kaplan, CW and Kyme, P and Sheikh, O and Varnum, B and Lux, R and Shi, W and He, X}, title = {Precision-guided antimicrobial peptide as a targeted modulator of human microbial ecology.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {24}, pages = {7569-7574}, pmid = {26034276}, issn = {1091-6490}, support = {R01 DE020102/DE/NIDCR NIH HHS/United States ; R01 DE023810/DE/NIDCR NIH HHS/United States ; 1-R01-DE020102/DE/NIDCR NIH HHS/United States ; 1-R01-DE023810-01/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Anti-Bacterial Agents/pharmacology ; Antimicrobial Cationic Peptides/*pharmacology ; Biofilms/drug effects/growth &amp; development ; Dental Caries/microbiology ; Humans ; Microbial Sensitivity Tests ; Microbiota/*drug effects ; Mouth/microbiology ; Saliva/microbiology ; Streptococcus mutans/*drug effects/pathogenicity/*physiology ; }, abstract = {One major challenge to studying human microbiome and its associated diseases is the lack of effective tools to achieve targeted modulation of individual species and study its ecological function within multispecies communities. Here, we show that C16G2, a specifically targeted antimicrobial peptide, was able to selectively kill cariogenic pathogen Streptococcus mutans with high efficacy within a human saliva-derived in vitro oral multispecies community. Importantly, a significant shift in the overall microbial structure of the C16G2-treated community was revealed after a 24-h recovery period: several bacterial species with metabolic dependency or physical interactions with S. mutans suffered drastic reduction in their abundance, whereas S. mutans' natural competitors, including health-associated Streptococci, became dominant. This study demonstrates the use of targeted antimicrobials to modulate the microbiome structure allowing insights into the key community role of specific bacterial species and also indicates the therapeutic potential of C16G2 to achieve a healthy oral microbiome.}, }
@article {pmid26033517, year = {2016}, author = {Allais, L and Kerckhof, FM and Verschuere, S and Bracke, KR and De Smet, R and Laukens, D and Van den Abbeele, P and De Vos, M and Boon, N and Brusselle, GG and Cuvelier, CA and Van de Wiele, T}, title = {Chronic cigarette smoke exposure induces microbial and inflammatory shifts and mucin changes in the murine gut.}, journal = {Environmental microbiology}, volume = {18}, number = {5}, pages = {1352-1363}, doi = {10.1111/1462-2920.12934}, pmid = {26033517}, issn = {1462-2920}, mesh = {Animals ; Bacteria/isolation &amp; purification ; Colon/metabolism/microbiology ; Environmental Exposure ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Gene Expression ; Ileum/metabolism ; Inflammation Mediators/*metabolism ; Male ; Mice, Inbred C57BL ; Mucins/genetics/*metabolism ; *Smoking ; Tobacco Products ; }, abstract = {Inflammatory bowel diseases (IBD) are complex multifactorial diseases characterized by an inappropriate host response to an altered commensal microbiome and dysfunctional mucus barrier. Cigarette smoking is the best known environmental risk factor in IBD. Here, we studied the influence of chronic smoke exposure on the gut microbiome, mucus layer composition and immune factors in conventional mice. We compared smoke-exposed with air-exposed mice (n = 12) after a smoke exposure of 24 weeks. Both Illumina sequencing (n = 6) and denaturing gradient gel electrophoresis (n = 12) showed that bacterial activity and community structure were significantly altered in the colon due to smoke exposure. Interestingly, an increase of Lachnospiraceae sp. activity in the colon was observed. Also, the mRNA expression of Muc2 and Muc3 increased in the ileum, whereas Muc4 increased in the distal colon of smoke-exposed mice (n = 6). Furthermore, we observed increased Cxcl2 and decreased Ifn-γ in the ileum, and increased Il-6 and decreased Tgf-β in the proximal colon. Tight junction gene expression remained unchanged. We infer that the modulating role of chronic smoke exposure as a latently present risk factor in the gut may be driven by the altered epithelial mucus profiles and changes in microbiome composition and immune factors.}, }
@article {pmid26031294, year = {2015}, author = {Lee, JC and Whang, KS}, title = {Burkholderia humisilvae sp. nov., Burkholderia solisilvae sp. nov. and Burkholderia rhizosphaerae sp. nov., isolated from forest soil and rhizosphere soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {65}, number = {9}, pages = {2986-2992}, doi = {10.1099/ijs.0.000368}, pmid = {26031294}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; Burkholderia/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; *Forests ; Genes, Bacterial ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; Ubiquinone/chemistry ; }, abstract = {Strains Y-12(T) and Y-47(T) were isolated from mountain forest soil and strain WR43(T) was isolated from rhizosphere soil, at Daejeon, Korea. The three strains grew at 10-55 °C (optimal growth at 28-30 °C), at pH 3.0-8.0 (optimal growth at pH 6.0) and in the presence of 0-4.0% (w/v) NaCl, growing optimally in the absence of added NaCl. On the basis of 16S rRNA gene sequence analysis, the three strains were found to belong to the genus Burkholderia, showing the closest phylogenetic similarity to Burkholderia diazotrophica JPY461(T) (97.2-97.7%); the similarity between the three sequences ranged from 98.3 to 98.7%. Additionally, the three strains formed a distinct group in phylogenetic trees based on the housekeeping genes recA and gyrB. The predominant ubiquinone was Q-8, the major fatty acids were C16 : 0 and C17 : 0 cyclo and the DNA G+C content of the novel isolates was 61.6-64.4 mol%. DNA-DNA relatedness among the three strains and the type strains of the closest species of the genus Burkholderia was less than 50%. On the basis of 16S rRNA, recA and gyrB gene sequence similarities, chemotaxonomic and phenotypic data, the three strains represent three novel species within the genus Burkholderia, for which the names Burkholderia humisilvae sp. nov. (type strain Y-12(T)= KACC 17601(T) = NBRC 109933(T) = NCAIM B 02543(T)), Burkholderia solisilvae sp. nov. (type strain Y-47(T) = KACC 17602(T)= NBRC 109934(T) = NCAIM B 02539(T)) and Burkholderia rhizosphaerae sp. nov. (type strain WR43(T) = KACC 17603(T) = NBRC 109935(T) = NCAIM B 02541(T)) are proposed.}, }
@article {pmid26030887, year = {2015}, author = {Myer, PR and Smith, TP and Wells, JE and Kuehn, LA and Freetly, HC}, title = {Rumen microbiome from steers differing in feed efficiency.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0129174}, pmid = {26030887}, issn = {1932-6203}, mesh = {*Animal Feed ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Cattle ; DNA, Bacterial ; Male ; Mice ; *Microbiota ; Rumen/metabolism/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The cattle rumen has a diverse microbial ecosystem that is essential for the host to digest plant material. Extremes in body weight (BW) gain in mice and humans have been associated with different intestinal microbial populations. The objective of this study was to characterize the microbiome of the cattle rumen among steers differing in feed efficiency. Two contemporary groups of steers (n=148 and n=197) were fed a ration (dry matter basis) of 57.35% dry-rolled corn, 30% wet distillers grain with solubles, 8% alfalfa hay, 4.25% supplement, and 0.4% urea for 63 days. Individual feed intake (FI) and BW gain were determined. Within contemporary group, the four steers within each Cartesian quadrant were sampled (n=16/group) from the bivariate distribution of average daily BW gain and average daily FI. Bacterial 16S rRNA gene amplicons were sequenced from the harvested bovine rumen fluid samples using next-generation sequencing technology. No significant changes in diversity or richness were indicated, and UniFrac principal coordinate analysis did not show any separation of microbial communities within the rumen. However, the abundances of relative microbial populations and operational taxonomic units did reveal significant differences with reference to feed efficiency groups. Bacteroidetes and Firmicutes were the dominant phyla in all ruminal groups, with significant population shifts in relevant ruminal taxa, including phyla Firmicutes and Lentisphaerae, as well as genera Succiniclasticum, Lactobacillus, Ruminococcus, and Prevotella. This study suggests the involvement of the rumen microbiome as a component influencing the efficiency of weight gain at the 16S level, which can be utilized to better understand variations in microbial ecology as well as host factors that will improve feed efficiency.}, }
@article {pmid26029180, year = {2015}, author = {Brumm, PJ and De Maayer, P and Mead, DA and Cowan, DA}, title = {Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {430}, pmid = {26029180}, issn = {1664-302X}, abstract = {In this work we report the whole genome sequences of six new Geobacillus xylanolytic strains along with the genomic analysis of their capability to degrade carbohydrates. The six sequenced Geobacillus strains described here have a range of GC contents from 43.9% to 52.5% and clade with named Geobacillus species throughout the entire genus. We have identified a ~200 kb unique super-cluster in all six strains, containing five to eight distinct carbohydrate degradation clusters in a single genomic region, a feature not seen in other genera. The Geobacillus strains rely on a small number of secreted enzymes located within distinct clusters for carbohydrate utilization, in contrast to most biomass-degrading organisms which contain numerous secreted enzymes located randomly throughout the genomes. All six strains are able to utilize fructose, arabinose, xylose, mannitol, gluconate, xylan, and α-1,6-glucosides. The gene clusters for utilization of these seven substrates have identical organization and the individual proteins have a high percent identity to their homologs. The strains show significant differences in their ability to utilize inositol, sucrose, lactose, α-mannosides, α-1,4-glucosides and arabinan.}, }
@article {pmid26027773, year = {2015}, author = {Besemer, K}, title = {Biodiversity, community structure and function of biofilms in stream ecosystems.}, journal = {Research in microbiology}, volume = {166}, number = {10}, pages = {774-781}, pmid = {26027773}, issn = {1769-7123}, support = {J 3542/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Biodiversity ; *Biofilms/growth &amp; development ; Ecosystem ; Microbial Consortia/genetics/*physiology ; Polymorphism, Restriction Fragment Length ; Rivers/*microbiology ; *Water Microbiology ; }, abstract = {Multi-species, surface-attached biofilms often dominate microbial life in streams and rivers, where they contribute substantially to biogeochemical processes. The microbial diversity of natural biofilms is huge, and may have important implications for the functioning of aquatic environments and the ecosystem services they provide. Yet the causes and consequences of biofilm biodiversity remain insufficiently understood. This review aims to give an overview of current knowledge on the distribution of stream biofilm biodiversity, the mechanisms generating biodiversity patterns and the relationship between biofilm biodiversity and ecosystem functioning.}, }
@article {pmid26024740, year = {2015}, author = {Lopez-Fernandez, M and Cherkouk, A and Vilchez-Vargas, R and Jauregui, R and Pieper, D and Boon, N and Sanchez-Castro, I and Merroun, ML}, title = {Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes.}, journal = {Microbial ecology}, volume = {70}, number = {4}, pages = {922-935}, pmid = {26024740}, issn = {1432-184X}, mesh = {Architectural Accessibility ; Bacteria/*classification/genetics/growth &amp; development/isolation &amp; purification ; Bentonite/*analysis ; Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Radioactive Waste ; Sequence Analysis, DNA ; Soil Microbiology ; Soil Pollutants, Radioactive/analysis ; Spain ; }, abstract = {The long-term disposal of radioactive wastes in a deep geological repository is the accepted international solution for the treatment and management of these special residues. The microbial community of the selected host rocks and engineered barriers for the deep geological repository may affect the performance and the safety of the radioactive waste disposal. In this work, the bacterial population of bentonite formations of Almeria (Spain), selected as a reference material for bentonite-engineered barriers in the disposal of radioactive wastes, was studied. 16S ribosomal RNA (rRNA) gene-based approaches were used to study the bacterial community of the bentonite samples by traditional clone libraries and Illumina sequencing. Using both techniques, the bacterial diversity analysis revealed similar results, with phylotypes belonging to 14 different bacterial phyla: Acidobacteria, Actinobacteria, Armatimonadetes, Bacteroidetes, Chloroflexi, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Gemmatimonadetes, Planctomycetes, Proteobacteria, Nitrospirae, Verrucomicrobia and an unknown phylum. The dominant groups of the community were represented by Proteobacteria and Bacteroidetes. A high diversity was found in three of the studied samples. However, two samples were less diverse and dominated by Betaproteobacteria.}, }
@article {pmid26023875, year = {2016}, author = {Chapelle, E and Mendes, R and Bakker, PA and Raaijmakers, JM}, title = {Fungal invasion of the rhizosphere microbiome.}, journal = {The ISME journal}, volume = {10}, number = {1}, pages = {265-268}, pmid = {26023875}, issn = {1751-7370}, mesh = {*Antibiosis ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Metagenomics ; *Microbiota ; Plant Roots/microbiology ; Plants/microbiology ; Rhizoctonia/*physiology ; Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The rhizosphere is the infection court where soil-borne pathogens establish a parasitic relationship with the plant. To infect root tissue, pathogens have to compete with members of the rhizosphere microbiome for available nutrients and microsites. In disease-suppressive soils, pathogens are strongly restricted in growth by the activities of specific rhizosphere microorganisms. Here, we sequenced metagenomic DNA and RNA of the rhizosphere microbiome of sugar beet seedlings grown in a soil suppressive to the fungal pathogen Rhizoctonia solani. rRNA-based analyses showed that Oxalobacteraceae, Burkholderiaceae, Sphingobacteriaceae and Sphingomonadaceae were significantly more abundant in the rhizosphere upon fungal invasion. Metatranscriptomics revealed that stress-related genes (ppGpp metabolism and oxidative stress) were upregulated in these bacterial families. We postulate that the invading pathogenic fungus induces, directly or via the plant, stress responses in the rhizobacterial community that lead to shifts in microbiome composition and to activation of antagonistic traits that restrict pathogen infection.}, }
@article {pmid26023873, year = {2015}, author = {Schmidt, R and Cordovez, V and de Boer, W and Raaijmakers, J and Garbeva, P}, title = {Volatile affairs in microbial interactions.}, journal = {The ISME journal}, volume = {9}, number = {11}, pages = {2329-2335}, pmid = {26023873}, issn = {1751-7370}, mesh = {Anti-Bacterial Agents/chemistry ; Antifungal Agents/chemistry ; Drug Resistance, Bacterial ; *Ecology ; Eukaryota ; Gene Expression ; *Microbial Interactions ; Quorum Sensing ; Soil/chemistry ; Soil Microbiology ; Volatile Organic Compounds/*chemistry ; }, abstract = {Microorganisms are important factors in shaping our environment. One key characteristic that has been neglected for a long time is the ability of microorganisms to release chemically diverse volatile compounds. At present, it is clear that the blend of volatiles released by microorganisms can be very complex and often includes many unknown compounds for which the chemical structures remain to be elucidated. The biggest challenge now is to unravel the biological and ecological functions of these microbial volatiles. There is increasing evidence that microbial volatiles can act as infochemicals in interactions among microbes and between microbes and their eukaryotic hosts. Here, we review and discuss recent advances in understanding the natural roles of volatiles in microbe-microbe interactions. Specific emphasis will be given to the antimicrobial activities of microbial volatiles and their effects on bacterial quorum sensing, motility, gene expression and antibiotic resistance.}, }
@article {pmid26022715, year = {2018}, author = {Ford, TE and Hamner, S}, title = {A Perspective on the Global Pandemic of Waterborne Disease.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {2-8}, pmid = {26022715}, issn = {1432-184X}, mesh = {Bacterial Infections/epidemiology/transmission ; Biofilms ; Child ; Cholera/epidemiology/microbiology/transmission ; Developing Countries ; Drug Resistance ; Dysentery/epidemiology/microbiology ; Escherichia coli/genetics/pathogenicity ; *Global Health ; Humans ; Hygiene ; *Pandemics ; Public Health ; Risk Assessment ; Sanitation ; Vibrio cholerae/pathogenicity ; Virulence/genetics ; Water Microbiology ; Water Pollution ; Water Supply ; Waterborne Diseases/*epidemiology/microbiology/transmission ; World Health Organization ; }, abstract = {Waterborne diseases continue to take a heavy toll on the global community, with developing nations, and particularly young children carrying most of the burden of morbidity and mortality. Starting with the historical context, this article explores some of the reasons why this burden continues today, despite our advances in public health over the past century or so. While molecular biology has revolutionized our abilities to define the ecosystems and etiologies of waterborne pathogens, control remains elusive. Lack of basic hygiene and sanitation, and failing infrastructure, remain two of the greatest challenges in the global fight against waterborne disease. Emerging risks continue to be the specter of multiple drug resistance and the ease with which determinants of virulence appear to be transmitted between strains of pathogens, both within and outside the human host.}, }
@article {pmid26022714, year = {2015}, author = {Capo, E and Debroas, D and Arnaud, F and Domaizon, I}, title = {Is Planktonic Diversity Well Recorded in Sedimentary DNA? Toward the Reconstruction of Past Protistan Diversity.}, journal = {Microbial ecology}, volume = {70}, number = {4}, pages = {865-875}, pmid = {26022714}, issn = {1432-184X}, mesh = {*Biodiversity ; DNA, Ribosomal/genetics ; Eukaryota/*classification/*genetics ; Fungi/classification/genetics ; Geologic Sediments/*microbiology/*parasitology ; Lakes/microbiology/parasitology ; Phylogeny ; Plankton/*classification/*genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {Studies based on the coupling of a paleolimnological approach and molecular tools (e.g., sequencing of sedimentary DNA) present a promising opportunity to obtain long-term data on past lacustrine biodiversity. However, certain validations are still required, such as the evaluation of DNA preservation in sediments for various planktonic taxa that do not leave any morphological diagnostic features. In this study, we focused on the diversity of planktonic unicellular eukaryotes and verified the presence of their DNA in sediment archives. We compared the molecular inventories (high-throughput sequencing of 18S ribosomal DNA) obtained from monitoring the water column with those obtained for DNA archived in the first 30 cm of sediment. Seventy-one percent of taxonomic units found in the water samples were detected in sediment samples, including pigmented taxa, such as Chlorophyta, Dinophyceae, and Chrysophyceae, phagotrophic taxa, such as Ciliophora, parasitic taxa, such as Apicomplexa and Chytridiomycota, and saprotrophs, such as Cryptomycota. Parallel analysis of 18S ribosomal RNA (rRNA) transcripts revealed the presence of living eukaryotic taxa only in the top 2 cm of sediment; although some limits exist in using RNA/DNA ratio as indicator of microbial activity, these results suggested that the sedimentary DNA mostly represented DNA from past and inactive communities. Only the diversity of a few groups, such as Cryptophyta and Haptophyta, seemed to be poorly preserved in sediments. Our overall results showed that the application of sequencing techniques to sedimentary DNA could be used to reconstruct past diversity for numerous planktonic eukaryotic groups.}, }
@article {pmid26021918, year = {2015}, author = {Gonçalves, AC and Franco, T and Califano, G and Dowd, SE and Pohnert, G and Costa, R}, title = {Draft Genome Sequence of Vibrio sp. Strain Vb278, an Antagonistic Bacterium Isolated from the Marine Sponge Sarcotragus spinosulus.}, journal = {Genome announcements}, volume = {3}, number = {3}, pages = {}, pmid = {26021918}, issn = {2169-8287}, abstract = {We report here the draft genome sequence of Vibrio sp. Vb278, a biofilm-producing strain isolated from the marine sponge Sarcotragus spinosulus, showing in vitro antibacterial activity. The annotated genome displays a range of symbiotic factors and the potential for the biosynthesis of several biologically active natural products.}, }
@article {pmid26020314, year = {2015}, author = {Kerr, BJ and Weber, TE and Ziemer, CJ}, title = {Dietary marker effects on fecal microbial ecology, fecal VFA, nutrient digestibility coefficients, and growth performance in finishing pigs.}, journal = {Journal of animal science}, volume = {93}, number = {5}, pages = {2183-2190}, doi = {10.2527/jas.2014-8633}, pmid = {26020314}, issn = {1525-3163}, mesh = {Ammonia/analysis ; Animals ; Biomarkers/*analysis ; Chromium Compounds/administration &amp; dosage/*pharmacology ; Denaturing Gradient Gel Electrophoresis ; Diet/veterinary ; Digestion/drug effects/physiology ; Fatty Acids, Volatile/*analysis ; Feces/chemistry/*microbiology ; Ferric Compounds/administration &amp; dosage/*pharmacology ; Sus scrofa/*growth &amp; development/metabolism ; Swine ; Titanium/administration &amp; dosage/*pharmacology ; }, abstract = {Use of indigestible markers such as Cr2O3, Fe2O3, and TiO2 are commonly used in animal studies to evaluate digesta rate of passage and nutrient digestibility. Yet, the potential impact of indigestible markers on fecal microbial ecology and subsequent VFA generation is not known. Two experiments utilizing a total of 72 individually fed finishing pigs were conducted to describe the impact of dietary markers on fecal microbial ecology, fecal ammonia and VFA concentrations, nutrient digestibility, and pig performance. All pigs were fed a common diet with no marker or with 0.5% Cr2O3, Fe2O3, or TiO2. In Exp. 1, after 33 d of feeding, fresh fecal samples were collected for evaluation of microbial ecology, fecal ammonia and VFA concentrations, and nutrient digestibility, along with measures of animal performance. No differences were noted in total microbes or bacterial counts in pig feces obtained from pigs fed the different dietary markers while Archaea counts were decreased (P = 0.07) in feces obtained from pigs fed the diet containing Fe2O 3compared to pigs fed the control diet. Feeding Cr2O3, Fe2O3, or TiO2 increased fecal bacterial richness (P = 0.03, 0.01, and 0.10; respectively) when compared to pigs fed diets containing no marker, but no dietary marker effects were noted on fecal microbial evenness or the Shannon-Wiener index. Analysis of denaturing gradient gel electrophoresis gels did not reveal band pattern alterations due to inclusion of dietary markers in pig diets. There was no effect of dietary marker on fecal DM, ammonia, or VFA concentrations. Pigs fed diets containing Cr2O3 had greater Ca, Cu, Fe, and P (P ≤ 0.02), but lower Ti (P= 0.08) digestibility compared to pigs fed the control diet. Pigs fed diets containing Fe2O3 had greater Ca (P = 0.08) but lower Ti (P = 0.01) digestibility compared to pigs fed the control diet. Pigs fed diets containing TiO2 had greater Fe and Zn (P ≤ 0.09), but lower Ti (P= 0.01) digestibility compared to pigs fed the control diet. In Exp. 2, no effect of dietary marker on pig performance was noted. Overall, the data indicate that the inclusion of Cr2O3, Fe2O3, or TiO2 as digestibility markers have little to no impact on microbial ecology, fecal ammonia or VFA concentrations, nutrient digestibility, or pig growth performance indicating they are suitable for use in digestion studies.}, }
@article {pmid26013766, year = {2015}, author = {Kleiner, M and Wentrup, C and Holler, T and Lavik, G and Harder, J and Lott, C and Littmann, S and Kuypers, MM and Dubilier, N}, title = {Use of carbon monoxide and hydrogen by a bacteria-animal symbiosis from seagrass sediments.}, journal = {Environmental microbiology}, volume = {17}, number = {12}, pages = {5023-5035}, pmid = {26013766}, issn = {1462-2920}, mesh = {Animals ; Bacteria/*metabolism ; Carbon Dioxide/metabolism ; Carbon Monoxide/*metabolism ; Energy Metabolism ; Geologic Sediments/*microbiology ; Hydrogen/*metabolism ; Mediterranean Region ; Oligochaeta/*microbiology ; Oxidation-Reduction ; Seawater/*microbiology ; Spectrometry, Mass, Secondary Ion ; Sulfur Compounds/metabolism ; Symbiosis ; }, abstract = {The gutless marine worm Olavius algarvensis lives in symbiosis with chemosynthetic bacteria that provide nutrition by fixing carbon dioxide (CO2) into biomass using reduced sulfur compounds as energy sources. A recent metaproteomic analysis of the O. algarvensis symbiosis indicated that carbon monoxide (CO) and hydrogen (H2) might also be used as energy sources. We provide direct evidence that the O. algarvensis symbiosis consumes CO and H2 . Single cell imaging using nanoscale secondary ion mass spectrometry revealed that one of the symbionts, the γ3-symbiont, uses the energy from CO oxidation to fix CO2 . Pore water analysis revealed considerable in-situ concentrations of CO and H2 in the O. algarvensis environment, Mediterranean seagrass sediments. Pore water H2 concentrations (89-2147 nM) were up to two orders of magnitude higher than in seawater, and up to 36-fold higher than previously known from shallow-water marine sediments. Pore water CO concentrations (17-51 nM) were twice as high as in the overlying seawater (no literature data from other shallow-water sediments are available for comparison). Ex-situ incubation experiments showed that dead seagrass rhizomes produced large amounts of CO. CO production from decaying plant material could thus be a significant energy source for microbial primary production in seagrass sediments.}, }
@article {pmid26013201, year = {2015}, author = {Marxen, S and Stark, TD and Rütschle, A and Lücking, G and Frenzel, E and Scherer, S and Ehling-Schulz, M and Hofmann, T}, title = {Depsipeptide Intermediates Interrogate Proposed Biosynthesis of Cereulide, the Emetic Toxin of Bacillus cereus.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {10637}, pmid = {26013201}, issn = {2045-2322}, mesh = {Amino Acid Sequence ; Bacillus cereus/*metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; Carbon Isotopes/chemistry ; Chromatography, High Pressure Liquid ; Cyclization ; Depsipeptides/analysis/biosynthesis/chemistry/*metabolism ; Molecular Sequence Data ; Multigene Family ; Peptide Synthases/chemistry/genetics/metabolism ; Protein Structure, Tertiary ; Sequence Alignment ; Spectrometry, Mass, Electrospray Ionization ; }, abstract = {Cereulide and isocereulides A-G are biosynthesized as emetic toxins by Bacillus cereus via a non-ribosomal peptide synthetase (NRPS) called Ces. Although a thiotemplate mechanisms involving cyclo-trimerization of ready-made D-O-Leu-D-Ala-L-O-Val-L-Val via a thioesterase (TE) domain is proposed for cereulide biosynthesis, the exact mechanism is far from being understood. UPLC-TOF MS analysis of B. cereus strains in combination with (13)C-labeling experiments now revealed tetra-, octa-, and dodecapeptides of a different sequence, namely (L-O-Val-L-Val-D-O-Leu-D-Ala)1-3, as intermediates of cereulide biosynthesis. Surprisingly, also di-, hexa-, and decadepsipeptides were identified which, together with the structures of the previously reported isocereulides E, F, and G, do not correlate to the currently proposed mechanism for cereulide biosynthesis and violate the canonical NRPS biosynthetic logic. UPLC-TOF MS metabolite analysis and bioinformatic gene cluster analysis highlighted dipeptides rather than single amino or hydroxy acids as the basic modules in tetradepsipeptide assembly and proposed the CesA C-terminal C* domain and the CesB C-terminal TE domain to function as a cooperative esterification and depsipeptide elongation center repeatedly recruiting the action of the C* domain to oligomerize tetradepsipeptides prior to the release of cereulide from the TE domain by macrocyclization.}, }
@article {pmid26005923, year = {2015}, author = {Wang, Y and Wu, Y and Wu, Z and Tam, NF}, title = {Genotypic responses of bacterial community structure to a mixture of wastewater-borne PAHs and PBDEs in constructed mangrove microcosms.}, journal = {Journal of hazardous materials}, volume = {298}, number = {}, pages = {91-101}, doi = {10.1016/j.jhazmat.2015.05.003}, pmid = {26005923}, issn = {1873-3336}, mesh = {Bacteria/*genetics/*metabolism ; Benzo(a)pyrene/chemistry/metabolism ; Biodegradation, Environmental ; DNA, Bacterial/genetics ; Genotype ; Halogenated Diphenyl Ethers/*metabolism ; Molecular Sequence Data ; Phenanthrenes/chemistry/metabolism ; Polycyclic Aromatic Hydrocarbons/*metabolism ; RNA, Ribosomal, 16S/genetics ; Rhizophoraceae/chemistry ; *Waste Disposal, Fluid ; *Water Microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Mangrove microcosms capable of removing polycyclic aromatic hydrocarbons (PAHs) and polybrominated diphenyl ethers (PBDEs) from wastewater were established under everyday tidal and non-tidal flooding regimes, along with two different mangrove species. Defining how bacterial communities change with pollutants or across treatments will contribute to understanding the microbial ecology of in situ bioremediation systems. A semi-nested PCR-DGGE (denaturing gradient gel electrophoresis) approach was employed, with known genus/species-specific primers targeting the 16S rRNA genes of Sphingomonas and Mycobacterium (related to PAH degradation) and Dehalococcoides (related to PBDE degradation). Results showed that the composition of Mycobacterium- and Dehalococcoides-like populations was critically determined by tidal regime during a medium-term (4-8 months) exposure, while that of Sphingomonas-like population, along with total bacterial community, was more dependent on sediment layer and became prominently affected by tidal regime till the end of 8-month treatment. The effect of plant species was relatively small. Canonical correspondence analysis (CCA) further revealed that Sphingomonas- and Mycobacterium-like populations were significantly associated with phenanthrene and benzo(a)pyrene, respectively, while Dehalococcoides-like population was the only group significantly related to the highest PBDE congener (BDE-209) in the mangrove microcosms.}, }
@article {pmid26001060, year = {2015}, author = {Pisacane, V and Callegari, ML and Puglisi, E and Dallolio, G and Rebecchi, A}, title = {Microbial analyses of traditional Italian salami reveal microorganisms transfer from the natural casing to the meat matrix.}, journal = {International journal of food microbiology}, volume = {207}, number = {}, pages = {57-65}, doi = {10.1016/j.ijfoodmicro.2015.04.029}, pmid = {26001060}, issn = {1879-3460}, mesh = {Bacteria/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; *Biodiversity ; Fermentation ; *Food Microbiology ; Meat Products/*microbiology ; Polymerase Chain Reaction ; }, abstract = {In this study the bacterial biodiversity, during the maturation process of traditional sausages (Salame Mantovano), produced with two different kinds of casing (hog middle or "Crespone" and hog bung or "Gentile"), was investigated by means of culture-dependent and -independent methods. In order to assess the natural variability linked to the type of casing used in production, the ingredients, as well as ripening conditions, were identical in both productions. The aim of the study was to understand the contribution of casing microflora during sausage ripening by identifying the dominant species and strains. The bacterial ecology of casings and salami at different ripening stages, as determined by plating, revealed higher staphylococci and enterococci counts for Gentile casing and for the entire ripening period of the salami studied. After molecular identification of 219 Lactobacilli and 225 cocci gram positive catalase positive (GPCP) isolates, the species most frequently isolated were Lactobacillus sakei, Lactobacillus curvatus, Staphylococcus xylosus, and Staphylococcus saprophyticus. Some L. sakei and S. saprophyticus strains, coming from casing, were also found in the salami at different times of ripening. A richer biodiversity was only detected at the beginning of maturation. We also report the first detection, by PCR-DGGE method, of Arcobacter marinus and Brochothrix thermosphacta species in casings and Kokuria salsicia in fresh sausage. Results suggesting that casing can be an important source of bacteria during natural fermentation when starter cultures are not used.}, }
@article {pmid25999470, year = {2015}, author = {Geirnaert, A and Wang, J and Tinck, M and Steyaert, A and Van den Abbeele, P and Eeckhaut, V and Vilchez-Vargas, R and Falony, G and Laukens, D and De Vos, M and Van Immerseel, F and Raes, J and Boon, N and Van de Wiele, T}, title = {Interindividual differences in response to treatment with butyrate-producing Butyricicoccus pullicaecorum 25-3T studied in an in vitro gut model.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {6}, pages = {}, doi = {10.1093/femsec/fiv054}, pmid = {25999470}, issn = {1574-6941}, mesh = {Adult ; Base Sequence ; Butyrates/*metabolism ; Clostridium/genetics/*metabolism ; Colon/*microbiology ; Dysbiosis/prevention &amp; control ; Feces/microbiology ; Humans ; In Vitro Techniques ; Inflammatory Bowel Diseases/microbiology/*therapy ; Male ; Microbiota/genetics ; Probiotics/*therapeutic use ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Butyrate-producing bacteria are promising probiotic candidates to target microbial dysbiosis in gastrointestinal disorders like inflammatory bowel diseases. Butyricicoccus pullicaecorum 25-3(T), a butyrate-producing clostridial cluster IV strain, is such a candidate. Little is known about its abundance in the colon microbiota and its butyrogenic properties. We used the M-SHIME(®), an in vitro simulator for the human intestinal microbial ecosystem, to study the effect of supplementing a single dose of B. pullicaecorum 25-3(T) on lumen- and mucus-associated microbiota of eight individuals. Butyricicoccus pullicaecorum was more abundant in mucus-associated microbiota compared with lumen microbiota. Supplementation with a single dose of B. pullicaecorum 25-3(T) resulted in a temporary increase in B. pullicaecorum bacteria in lumen compartment of all individuals. In two cases, the responders, an increased butyrate production was observed as compared with the control. 16S rRNA gene amplicon sequencing revealed the microbiota of responders to be different as compared to non-responder microbiota. We can conclude that B. pullicaecorum 25-3(T) is a mucus-associated bacterium whose potency to stimulate butyrate production is characterized by a large interindividual variability in terms of composition of the receiving microbial community.}, }
@article {pmid25998810, year = {2015}, author = {Bokulich, NA and Amiranashvili, L and Chitchyan, K and Ghazanchyan, N and Darbinyan, K and Gagelidze, N and Sadunishvili, T and Goginyan, V and Kvesitadze, G and Torok, T and Mills, DA}, title = {Microbial biogeography of the transnational fermented milk matsoni.}, journal = {Food microbiology}, volume = {50}, number = {}, pages = {12-19}, doi = {10.1016/j.fm.2015.01.018}, pmid = {25998810}, issn = {1095-9998}, support = {T32-GM008799/GM/NIGMS NIH HHS/United States ; }, mesh = {Armenia ; Bacteria/growth &amp; development/*isolation &amp; purification ; Biodiversity ; Candida/growth &amp; development/isolation &amp; purification ; Colony Count, Microbial ; Cultured Milk Products/classification/*microbiology ; Fermentation ; Food Microbiology ; Georgia (Republic) ; High-Throughput Nucleotide Sequencing ; Kluyveromyces/growth &amp; development/isolation &amp; purification ; Lactobacillus/isolation &amp; purification ; *Microbiota ; Saccharomyces cerevisiae/growth &amp; development/isolation &amp; purification ; Streptococcus/isolation &amp; purification ; Yeasts/growth &amp; development/*isolation &amp; purification ; }, abstract = {The fermented milk matsoni is a traditional, national food product of both Georgia and Armenia. Little is known about the effects of biogeography and milk type on the microbial biodiversity of matsoni or the fungal composition of matsoni fermentations. High-throughput marker-gene sequencing was used to survey the bacterial and fungal communities of matsoni from different milk types and regions throughout Armenia and Georgia. Results demonstrate that both production region and milk type influence matsoni microbiota, suggesting that the traditional production methods preserve the transfer of unique regional microbiota from batch to batch. Bacterial profiles were dominated by Lactobacillus and Streptococcus species. Yeast profiles varied dramatically, with Kluyveromyces marxianus, Candida famata, Saccharomyces cerevisiae, Lodderomyces elongisporus, and Kluyveromyces lactis being the most important species distinguishing production regions and milk types. This survey will enable more detailed capture and characterization of specific microbiota detected within these fermentations.}, }
@article {pmid25998536, year = {2015}, author = {Mazei, Y and Chernyshov, V and Tsyganov, AN and Payne, RJ}, title = {Testing the Effect of Refrigerated Storage on Testate Amoeba Samples.}, journal = {Microbial ecology}, volume = {70}, number = {4}, pages = {861-864}, pmid = {25998536}, issn = {1432-184X}, mesh = {Amoeba/*growth &amp; development ; *Biodiversity ; Biota ; Cold Temperature ; Ecosystem ; Eukaryota ; *Refrigeration ; Sphagnopsida/growth &amp; development/*parasitology ; }, abstract = {Samples for analysis of testate amoebae and other protists frequently need to be stored for many months before microscopy. This storage commonly involves refrigeration, but we know that testate amoebae can live and reproduce in these conditions. This raises the question: do communities change during storage and how might this effect the data produced? We analysed Sphagnum samples over a 16-week period to address this question. Our results show no evidence for detectable change. This is a reassuring result supporting much current practice although we suggest that frozen storage or the addition of a fixative may be worthwhile precautions where feasible.}, }
@article {pmid25995981, year = {2015}, author = {De Ryck, T and Vanlancker, E and Grootaert, C and Roman, BI and De Coen, LM and Vandenberghe, I and Stevens, CV and Bracke, M and Van de Wiele, T and Vanhoecke, B}, title = {Microbial inhibition of oral epithelial wound recovery: potential role for quorum sensing molecules?.}, journal = {AMB Express}, volume = {5}, number = {}, pages = {27}, pmid = {25995981}, issn = {2191-0855}, abstract = {Awareness of the impact of microbiota in both health and disease is growing. Using a new in vitro oral mucosa co-culture model, we recently showed a clear inhibition of epithelial wound healing in the presence of an oral microbial community. In this paper, we have used the same model in combination with specific oral microbial species to obtain a better insight into the role of the oral microbiota in wound healing. Monocultures of Klebsiella oxytoca and Lactobacillus salivarius significantly inhibited wound healing with ~20%, whereas Streptococcus mitis and S. oralis enhanced the healing process with ~15% in 24 h. Yet, neither S. oralis or S. mitis were able to counteract the inhibitory effects from K. oxytoca on wound healing. Other tested microbial species had no effect on wound healing. Apart from this species-dependency, the inhibitory effect on wound healing depended on a microbial threshold concentration. Further mechanistic experiments with K. oxytoca excluded different microbial factors and hypothesized that quorum sensing molecules might play a role in the inter-kingdom signalling during wound healing. These results are important for the development of new strategies for the management of (infected) wounds and ulcerations.}, }
@article {pmid25995836, year = {2015}, author = {He, Y and Caporaso, JG and Jiang, XT and Sheng, HF and Huse, SM and Rideout, JR and Edgar, RC and Kopylova, E and Walters, WA and Knight, R and Zhou, HW}, title = {Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {20}, pmid = {25995836}, issn = {2049-2618}, abstract = {BACKGROUND: The operational taxonomic unit (OTU) is widely used in microbial ecology. Reproducibility in microbial ecology research depends on the reliability of OTU-based 16S ribosomal subunit RNA (rRNA) analyses.<br><br>RESULTS: Here, we report that many hierarchical and greedy clustering methods produce unstable OTUs, with membership that depends on the number of sequences clustered. If OTUs are regenerated with additional sequences or samples, sequences originally assigned to a given OTU can be split into different OTUs. Alternatively, sequences assigned to different OTUs can be merged into a single OTU. This OTU instability affects alpha-diversity analyses such as rarefaction curves, beta-diversity analyses such as distance-based ordination (for example, Principal Coordinate Analysis (PCoA)), and the identification of differentially represented OTUs. Our results show that the proportion of unstable OTUs varies for different clustering methods. We found that the closed-reference method is the only one that produces completely stable OTUs, with the caveat that sequences that do not match a pre-existing reference sequence collection are discarded.<br><br>CONCLUSIONS: As a compromise to the factors listed above, we propose using an open-reference method to enhance OTU stability. This type of method clusters sequences against a database and includes unmatched sequences by clustering them via a relatively stable de novo clustering method. OTU stability is an important consideration when analyzing microbial diversity and is a feature that should be taken into account during the development of novel OTU clustering methods.}, }
@article {pmid25994609, year = {2015}, author = {Lever, MA and Rogers, KL and Lloyd, KG and Overmann, J and Schink, B and Thauer, RK and Hoehler, TM and Jørgensen, BB}, title = {Life under extreme energy limitation: a synthesis of laboratory- and field-based investigations.}, journal = {FEMS microbiology reviews}, volume = {39}, number = {5}, pages = {688-728}, doi = {10.1093/femsre/fuv020}, pmid = {25994609}, issn = {1574-6976}, mesh = {*Adaptation, Physiological ; *Bacterial Physiological Phenomena ; *Ecosystem ; *Energy Metabolism ; Research/standards ; }, abstract = {The ability of microorganisms to withstand long periods with extremely low energy input has gained increasing scientific attention in recent years. Starvation experiments in the laboratory have shown that a phylogenetically wide range of microorganisms evolve fitness-enhancing genetic traits within weeks of incubation under low-energy stress. Studies on natural environments that are cut off from new energy supplies over geologic time scales, such as deeply buried sediments, suggest that similar adaptations might mediate survival under energy limitation in the environment. Yet, the extent to which laboratory-based evidence of starvation survival in pure or mixed cultures can be extrapolated to sustained microbial ecosystems in nature remains unclear. In this review, we discuss past investigations on microbial energy requirements and adaptations to energy limitation, identify gaps in our current knowledge, and outline possible future foci of research on life under extreme energy limitation.}, }
@article {pmid25994159, year = {2015}, author = {Pozo, MI and Herrera, CM and Van den Ende, W and Verstrepen, K and Lievens, B and Jacquemyn, H}, title = {The impact of nectar chemical features on phenotypic variation in two related nectar yeasts.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {6}, pages = {}, doi = {10.1093/femsec/fiv055}, pmid = {25994159}, issn = {1574-6941}, mesh = {Carbohydrate Metabolism ; Genetic Variation/genetics ; Metschnikowia/*classification/genetics/isolation &amp; purification ; Phenotype ; Plant Nectar/analysis/*chemistry ; Plants/*microbiology ; Pollination ; }, abstract = {Floral nectars become easily colonized by microbes, most often species of the ascomycetous yeast genus Metschnikowia. Although it is known that nectar composition can vary tremendously among plant species, most probably corresponding to the nutritional requirements of their main pollinators, far less is known about how variation in nectar chemistry affects intraspecific variation in nectarivorous yeasts. Because variation in nectar traits probably affects growth and abundance of nectar yeasts, nectar yeasts can be expected to display large phenotypic variation in order to cope with varying nectar conditions. To test this hypothesis, we related variation in the phenotypic landscape of a vast collection of nectar-living yeast isolates from two Metschnikowia species (M. reukaufii and M. gruessii) to nectar chemical traits using non-linear redundancy analyses. Nectar yeasts were collected from 19 plant species from different plant families to include as much variation in nectar chemical traits as possible. As expected, nectar yeasts displayed large variation in phenotypic traits, particularly in traits related to growth performance in carbon sources and inhibitors, which was significantly related to the host plant from which they were isolated. Total sugar concentration and relative fructose content significantly explained the observed variation in the phenotypic profile of the investigated yeast species, indicating that sugar concentration and composition are the key traits that affect phenotypic variation in nectarivorous yeasts.}, }
@article {pmid25992644, year = {2015}, author = {Cavalcante, FS and Abad, ED and Lyra, YC and Saintive, SB and Ribeiro, M and Ferreira, DC and Santos, KR}, title = {High prevalence of methicillin resistance and PVL genes among Staphylococcus aureus isolates from the nares and skin lesions of pediatric patients with atopic dermatitis.}, journal = {Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologicas}, volume = {48}, number = {7}, pages = {588-594}, pmid = {25992644}, issn = {1414-431X}, mesh = {Adolescent ; Bacterial Toxins/*genetics ; Child ; Cross-Sectional Studies ; DNA, Bacterial ; Dermatitis, Atopic/*microbiology ; Electrophoresis, Gel, Pulsed-Field ; Exotoxins/*genetics ; Female ; Humans ; Leukocidins/*genetics ; Male ; Methicillin-Resistant Staphylococcus aureus/*genetics ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Nasal Cavity/*microbiology ; Polymerase Chain Reaction ; Reference Values ; Severity of Illness Index ; Skin/*microbiology ; Staphylococcal Skin Infections/microbiology ; }, abstract = {Staphylococcus aureus is highly prevalent among patients with atopic dermatitis (AD), and this pathogen may trigger and aggravate AD lesions. The aim of this study was to determine the prevalence of S. aureus in the nares of pediatric subjects and verify the phenotypic and molecular characteristics of the isolates in pediatric patients with AD. Isolates were tested for antimicrobial susceptibility, SCCmec typing, and Panton-Valentine Leukocidin (PVL) genes. Lineages were determined by pulsed-field gel electrophoresis and multilocus sequence typing (MLST). AD severity was assessed with the Scoring Atopic Dermatitis (SCORAD) index. Among 106 patients, 90 (85%) presented S. aureus isolates in their nares, and 8 also presented the pathogen in their skin infections. Two patients had two positive lesions, making a total of 10 S. aureus isolates from skin infections. Methicillin-resistant S. aureus (MRSA) was detected in 24 (26.6%) patients, and PVL genes were identified in 21 (23.3%), including 6 (75%) of the 8 patients with skin lesions but mainly in patients with severe and moderate SCORAD values (P=0.0095). All 24 MRSA isolates were susceptible to trimethoprim/sulfamethoxazole, while 8 isolates had a minimum inhibitory concentration (MIC) to mupirocin >1024 μg/mL. High lineage diversity was found among the isolates including USA1100/ST30, USA400/ST1, USA800/ST5, ST83, ST188, ST718, ST1635, and ST2791. There was a high prevalence of MRSA and PVL genes among the isolates recovered in this study. PVL genes were found mostly among patients with severe and moderate SCORAD values. These findings can help clinicians improve the therapies and strategies for the management of pediatric patients with AD.}, }
@article {pmid25991603, year = {2015}, author = {Villegas-Mendoza, J and Cajal-Medrano, R and Maske, H}, title = {INT (2-(4-Iodophenyl)-3-(4-Nitrophenyl)-5-(Phenyl) Tetrazolium Chloride) Is Toxic to Prokaryote Cells Precluding Its Use with Whole Cells as a Proxy for In Vivo Respiration.}, journal = {Microbial ecology}, volume = {70}, number = {4}, pages = {1004-1011}, pmid = {25991603}, issn = {1432-184X}, mesh = {Bacteria, Aerobic/drug effects/metabolism ; Cell Respiration/*drug effects ; Ecosystem ; Eukaryota/drug effects ; Formazans/analysis/metabolism ; Haptophyta/drug effects/metabolism ; Marine Biology/methods ; Oceans and Seas ; Oxidation-Reduction ; Oxygen Consumption/*drug effects ; Plankton/drug effects/metabolism ; Prokaryotic Cells/cytology/*drug effects/metabolism ; Tetrazolium Salts/*toxicity ; Vibrio/drug effects/metabolism ; *Water Microbiology ; }, abstract = {Prokaryote respiration is expected to be responsible for more than half of the community respiration in the ocean, but the lack of a practical method to measure the rate of prokaryote respiration in the open ocean resulted in very few published data leaving the role of organotrophic prokaryotes open to debate. Oxygen consumption rates of oceanic prokaryotes measured with current methods may be biased due to pre-incubation size filtration and long incubation times both of which can change the physiological and taxonomic profile of the sample during the incubation period. In vivo INT reduction has been used in terrestrial samples to estimate respiration rates, and recently, the method was introduced and applied in aquatic ecology. We measured oxygen consumption rates and in vivo INT reduction to formazan in cultures of marine bacterioplankton communities, Vibrio harveyi and the eukaryote Isochrysis galbana. For prokaryotes, we observed a decrease in oxygen consumption rates with increasing INT concentrations between 0.05 and 1 mM. Time series after 0.5 mM INT addition to prokaryote samples showed a burst of in vivo INT reduction to formazan and a rapid decline of oxygen consumption rates to zero within less than an hour. Our data for non-axenic eukaryote cultures suggest poisoning of the eukaryote. Prokaryotes are clearly poisoned by INT on time scales of less than 1 h, invalidating the interpretation of in vivo INT reduction to formazan as a proxy for oxygen consumption rates.}, }
@article {pmid25985770, year = {2015}, author = {Xu, L and Lou, Q and Cheng, C and Lu, M and Sun, J}, title = {Gut-Associated Bacteria of Dendroctonus valens and their Involvement in Verbenone Production.}, journal = {Microbial ecology}, volume = {70}, number = {4}, pages = {1012-1023}, pmid = {25985770}, issn = {1432-184X}, mesh = {Animals ; Anti-Infective Agents/pharmacology ; Bacteria/drug effects/isolation &amp; purification/*metabolism ; Behavior, Animal ; Bicyclic Monoterpenes ; China ; Coleoptera/*metabolism/*microbiology ; Female ; Gastrointestinal Microbiome/drug effects/*physiology ; Male ; Microbial Sensitivity Tests ; Monoterpenes/metabolism/toxicity ; Pest Control, Biological/methods ; Pheromones/biosynthesis ; Terpenes/*metabolism/toxicity ; }, abstract = {Bark beetles are the most important mortality agent in coniferous forests, and pheromones play important roles in their management. Dendroctonus valens LeConte was introduced from North America to China and has killed millions of healthy pines there. Trapping with semiochemicals and pheromones was deployed in D. valens management in the last decade, but little is known about the ability of gut bacteria to produce the pheromone. In this study, we analyzed the volatiles in D. valens guts and frass after antibiotic treatment versus control. Then, we isolated and identified the bacteria in D. valens guts and frass, examined verbenone (a multifunctional pheromone of D. valens) production by 16 gut bacterial isolates from the precursor cis-verbenol at three concentrations, and further compared the cytotoxicities between the cis-verbenol and verbenone to the bacterial isolates. cis-Verbenol was not detected in the frass in the control group, but it was in the antibiotic treatment. The amount of verbenone was significantly suppressed in D. valens guts after antibiotic treatment versus control. Thirteen out of 16 gut bacterial isolates were capable of cis-verbenol to verbenone conversion, and cis-verbenol had stronger cytotoxicities than verbenone to all tested gut bacterial isolates. The bacterial species capable of verbenone production largely exists in D. valens guts and frass, suggesting that gut-associated bacteria may help the bark beetle produce the pheromone verbenone in guts and frass. The bacteria may benefit from the conversion due to the reduced cytotoxicity from the precursor to the beetle pheromone.}, }
@article {pmid25985090, year = {2015}, author = {Lamichhane, S and Yde, CC and Schmedes, MS and Jensen, HM and Meier, S and Bertram, HC}, title = {Strategy for Nuclear-Magnetic-Resonance-Based Metabolomics of Human Feces.}, journal = {Analytical chemistry}, volume = {87}, number = {12}, pages = {5930-5937}, doi = {10.1021/acs.analchem.5b00977}, pmid = {25985090}, issn = {1520-6882}, mesh = {Feces/*chemistry ; Healthy Volunteers ; Humans ; Magnetic Resonance Spectroscopy ; Metabolomics/*methods ; }, abstract = {Metabolomic analyses of fecal material are gaining increasing attention because the gut microbial ecology and activity have an impact on the human phenotype and regulate host metabolism. Sample preparation is a crucial step, and in this study, we recommend a methodology for extraction and analysis of fresh feces by NMR-based metabolomics. The evaluation of extraction solvents showed that buffer extraction is a suitable approach to extract metabolic information in feces. Therefore, the effects of weight-to-buffer (Wf:Vb) combinations and the effect of sonication and freeze-thaw cycles on the reproducibility, chemical shift variability, and signal-to-noise ratio (SNR) of the (1)H NMR spectra were evaluated. On the basis of our results, we suggest that fresh fecal extraction with a Wf:Vb ratio of 1:2 may be the optimum choice to determine the overall metabolite composition of feces. In fact, more than 60 metabolites have been assigned in the NMR spectra obtained from the fresh fecal buffer extract, and assignments of the lipophilic signals are also presented. To our knowledge, some of the metabolites are reported here for the very first time employing (1)H NMR spectroscopy on human fecal extracts.}, }
@article {pmid25983555, year = {2015}, author = {Oulas, A and Pavloudi, C and Polymenakou, P and Pavlopoulos, GA and Papanikolaou, N and Kotoulas, G and Arvanitidis, C and Iliopoulos, I}, title = {Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies.}, journal = {Bioinformatics and biology insights}, volume = {9}, number = {}, pages = {75-88}, pmid = {25983555}, issn = {1177-9322}, abstract = {Advances in next-generation sequencing (NGS) have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field and the establishment of "metagenomics", often defined as the analysis of DNA from microbial communities in environmental samples without prior need for culturing. Many metagenomics statistical/computational tools and databases have been developed in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies. We focus on the currently available bioinformatics techniques, tools, and methodologies for performing each individual step of a typical metagenomic dataset analysis. We also provide future trends in the field with respect to tools and technologies currently under development. Moreover, we discuss data management, distribution, and integration tools that are capable of performing comparative metagenomic analyses of multiple datasets using well-established databases, as well as commonly used annotation standards.}, }
@article {pmid25977143, year = {2015}, author = {Braker, G and Matthies, D and Hannig, M and Brandt, FB and Brenzinger, K and Gröngröft, A}, title = {Impact of Land Use Management and Soil Properties on Denitrifier Communities of Namibian Savannas.}, journal = {Microbial ecology}, volume = {70}, number = {4}, pages = {981-992}, pmid = {25977143}, issn = {1432-184X}, mesh = {Agriculture/*methods ; Carbon/analysis ; Denitrification ; Ecosystem ; Enzyme Assays/methods ; *Grassland ; Hydrogen-Ion Concentration ; *Microbial Consortia ; Namibia ; Nitrates/analysis ; Nitrogen/analysis ; Nitrous Oxide/analysis ; Soil/*chemistry ; *Soil Microbiology ; Water/analysis ; }, abstract = {We studied potential denitrification activity and the underlying denitrifier communities in soils from a semiarid savanna ecosystem of the Kavango region in NE Namibia to help in predicting future changes in N(2)O emissions due to continuing changes of land use in this region. Soil type and land use (pristine, fallow, and cultivated soils) influenced physicochemical characteristics of the soils that are relevant to denitrification activity and N(2)O fluxes from soils and affected potential denitrification activity. Potential denitrification activity was assessed by using the denitrifier enzyme activity (DEA) assay as a proxy for denitrification activity in the soil. Soil type and land use influenced C and N contents of the soils. Pristine soils that had never been cultivated had a particularly high C content. Cultivation reduced soil C content and the abundance of denitrifiers and changed the composition of the denitrifier communities. DEA was strongly and positively correlated with soil C content and was higher in pristine than in fallow or recently cultivated soils. Soil type and the composition of both the nirK- and nirS-type denitrifier communities also influenced DEA. In contrast, other soil characteristics like N content, C:N ratio, and pH did not predict DEA. These findings suggest that due to greater availability of soil organic matter, and hence a more effective N cycling, the natural semiarid grasslands emit more N(2)O than managed lands in Namibia.}, }
@article {pmid25975568, year = {2015}, author = {Ho, A and Reim, A and Kim, SY and Meima-Franke, M and Termorshuizen, A and de Boer, W and van der Putten, WH and Bodelier, PL}, title = {Unexpected stimulation of soil methane uptake as emergent property of agricultural soils following bio-based residue application.}, journal = {Global change biology}, volume = {21}, number = {10}, pages = {3864-3879}, doi = {10.1111/gcb.12974}, pmid = {25975568}, issn = {1365-2486}, mesh = {Bacteria/*metabolism ; *Fertilizers ; Methane/*metabolism ; Netherlands ; Oxidation-Reduction ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Intensification of agriculture to meet the global food, feed, and bioenergy demand entail increasing re-investment of carbon compounds (residues) into agro-systems to prevent decline of soil quality and fertility. However, agricultural intensification decreases soil methane uptake, reducing, and even causing the loss of the methane sink function. In contrast to wetland agricultural soils (rice paddies), the methanotrophic potential in well-aerated agricultural soils have received little attention, presumably due to the anticipated low or negligible methane uptake capacity in these soils. Consequently, a detailed study verifying or refuting this assumption is still lacking. Exemplifying a typical agricultural practice, we determined the impact of bio-based residue application on soil methane flux, and determined the methanotrophic potential, including a qualitative (diagnostic microarray) and quantitative (group-specific qPCR assays) analysis of the methanotrophic community after residue amendments over 2 months. Unexpectedly, after amendments with specific residues, we detected a significant transient stimulation of methane uptake confirmed by both the methane flux measurements and methane oxidation assay. This stimulation was apparently a result of induced cell-specific activity, rather than growth of the methanotroph population. Although transient, the heightened methane uptake offsets up to 16% of total gaseous CO2 emitted during the incubation. The methanotrophic community, predominantly comprised of Methylosinus may facilitate methane oxidation in the agricultural soils. While agricultural soils are generally regarded as a net methane source or a relatively weak methane sink, our results show that methane oxidation rate can be stimulated, leading to higher soil methane uptake. Hence, even if agriculture exerts an adverse impact on soil methane uptake, implementing carefully designed management strategies (e.g. repeated application of specific residues) may compensate for the loss of the methane sink function following land-use change.}, }
@article {pmid25974301, year = {2015}, author = {Fujimura, KE and Lynch, SV}, title = {Microbiota in allergy and asthma and the emerging relationship with the gut microbiome.}, journal = {Cell host &amp; microbe}, volume = {17}, number = {5}, pages = {592-602}, pmid = {25974301}, issn = {1934-6069}, support = {P01 AI089473/AI/NIAID NIH HHS/United States ; UM1 AI114271/AI/NIAID NIH HHS/United States ; 1P01AI089473/AI/NIAID NIH HHS/United States ; UM1AI114271/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Dysbiosis/*complications/*immunology ; *Environmental Microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Hypersensitivity/*microbiology ; Microbiota/*immunology ; Respiratory System/*microbiology ; }, abstract = {Asthma and atopy, classically associated with hyper-activation of the T helper 2 (Th2) arm of adaptive immunity, are among the most common chronic illnesses worldwide. Emerging evidence relates atopy and asthma to the composition and function of the human microbiome, the collection of microbes that reside in and on and interact with the human body. The ability to interrogate microbial ecology of the human host is due in large part to recent technological developments that permit identification of microbes and their products using culture-independent molecular detection techniques. In this review we explore the roles of respiratory, gut, and environmental microbiomes in asthma and allergic disease development, manifestation, and attenuation. Though still a relatively nascent field of research, evidence to date suggests that the airway and/or gut microbiome may represent fertile targets for prevention or management of allergic asthma and other diseases in which adaptive immune dysfunction is a prominent feature.}, }
@article {pmid25970606, year = {2015}, author = {Li, P and Wang, Y and Dai, X and Zhang, R and Jiang, Z and Jiang, D and Wang, S and Jiang, H and Wang, Y and Dong, H}, title = {Microbial community in high arsenic shallow groundwater aquifers in Hetao Basin of Inner Mongolia, China.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0125844}, pmid = {25970606}, issn = {1932-6203}, mesh = {Acinetobacter/genetics/isolation &amp; purification ; Arsenic/*chemistry ; Arthrobacter/genetics/isolation &amp; purification ; China ; Comamonadaceae/genetics/isolation &amp; purification ; Enterobacteriaceae/genetics/isolation &amp; purification ; Groundwater/chemistry/*microbiology ; Microbiota ; Molecular Typing ; Pseudomonas ; Psychrobacter/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Shewanella/genetics/isolation &amp; purification ; *Soil Microbiology ; Thiobacillus/genetics/isolation &amp; purification ; *Water Microbiology ; Water Pollutants, Chemical/*chemistry ; }, abstract = {A survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater) and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes) in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia, using the 454 pyrosequencing approach. A total of 233,704 sequence reads were obtained and classified into 12-267 operational taxonomic units (OTUs). Groundwater and sediment samples were divided into low and high arsenic groups based on measured geochemical parameters and microbial communities, by hierarchical clustering and principal coordinates analysis. Richness and diversity of the microbial communities in high arsenic sediments are higher than those in high arsenic groundwater. Microbial community structure was significantly different either between low and high arsenic samples or between groundwater and sediments. Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella were the top four genera in high arsenic groundwater, while Thiobacillus, Pseudomonas, Hydrogenophaga, Enterobacteriaceae, Sulfuricurvum and Arthrobacter dominated high arsenic sediments. Archaeal sequences in high arsenic groundwater were mostly related to methanogens. Biota-environment matching and co-inertia analyses showed that arsenic, total organic carbon, SO4(2-), SO4(2-)/total sulfur ratio, and Fe(2+) were important environmental factors shaping the observed microbial communities. The results of this study expand our current understanding of microbial ecology in high arsenic groundwater aquifers and emphasize the potential importance of microbes in arsenic transformation in the Hetao Basin, Inner Mongolia.}, }
@article {pmid25970595, year = {2015}, author = {McKenney, EA and Rodrigo, A and Yoder, AD}, title = {Patterns of gut bacterial colonization in three primate species.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0124618}, pmid = {25970595}, issn = {1932-6203}, mesh = {Animals ; Animals, Newborn ; DNA, Bacterial/classification/*genetics ; Diet ; Feces/microbiology ; Female ; Fruit/chemistry ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/growth &amp; development/microbiology/physiology ; Lemur/growth &amp; development/*microbiology/physiology ; Lemuridae/growth &amp; development/*microbiology/physiology ; Male ; Molecular Sequence Annotation ; Phylogeny ; Plant Leaves/chemistry ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Strepsirhini/growth &amp; development/*microbiology/physiology ; Symbiosis/physiology ; Weaning ; }, abstract = {Host fitness is impacted by trillions of bacteria in the gastrointestinal tract that facilitate development and are inextricably tied to life history. During development, microbial colonization primes the gut metabolism and physiology, thereby setting the stage for adult nutrition and health. However, the ecological rules governing microbial succession are poorly understood. In this study, we examined the relationship between host lineage, captive diet, and life stage and gut microbiota characteristics in three primate species (infraorder, Lemuriformes). Fecal samples were collected from captive lemur mothers and their infants, from birth to weaning. Microbial DNA was extracted and the v4 region of 16S rDNA was sequenced on the Illumina platform using protocols from the Earth Microbiome Project. Here, we show that colonization proceeds along different successional trajectories in developing infants from species with differing dietary regimes and ecological profiles: frugivorous (fruit-eating) Varecia variegata, generalist Lemur catta, and folivorous (leaf-eating) Propithecus coquereli. Our analyses reveal community membership and succession patterns consistent with previous studies of human infants, suggesting that lemurs may serve as a useful model of microbial ecology in the primate gut. Each lemur species exhibits distinct species-specific bacterial diversity signatures correlating to life stages and life history traits, implying that gut microbial community assembly primes developing infants at species-specific rates for their respective adult feeding strategies.}, }
@article {pmid25967655, year = {2015}, author = {Ganendra, G and Mercado-Garcia, D and Hernandez-Sanabria, E and Boeckx, P and Ho, A and Boon, N}, title = {Methane biofiltration using autoclaved aerated concrete as the carrier material.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {17}, pages = {7307-7320}, doi = {10.1007/s00253-015-6646-6}, pmid = {25967655}, issn = {1432-0614}, mesh = {Air Filters/*microbiology ; Filtration/*methods ; Methane/*isolation &amp; purification ; Methylococcaceae/growth &amp; development/*metabolism ; Oxidation-Reduction ; }, abstract = {The methane removal capacity of mixed methane-oxidizing bacteria (MOB) culture in a biofilter setup using autoclaved aerated concrete (AAC) as a highly porous carrier material was tested. Batch experiment was performed to optimize MOB immobilization on AAC specimens where optimum methane removal was obtained when calcium chloride was not added during bacterial inoculation step and 10-mm-thick AAC specimens were used. The immobilized MOB could remove methane at low concentration (~1000 ppmv) in a biofilter setup for 127 days at average removal efficiency (RE) of 28.7 %. Unlike a plug flow reactor, increasing the total volume of the filter by adding a biofilter in series did not result in higher total RE. MOB also exhibited a higher abundance at the bottom of the filter, in proximity with the methane gas inlet where a high methane concentration was found. Overall, an efficient methane biofilter performance could be obtained using AAC as the carrier material.}, }
@article {pmid25966981, year = {2015}, author = {Vanhoecke, B and Bateman, E and Mayo, B and Vanlancker, E and Stringer, A and Thorpe, D and Keefe, D}, title = {Dark Agouti rat model of chemotherapy-induced mucositis: establishment and current state of the art.}, journal = {Experimental biology and medicine (Maywood, N.J.)}, volume = {240}, number = {6}, pages = {725-741}, pmid = {25966981}, issn = {1535-3699}, mesh = {Adenocarcinoma/*drug therapy/metabolism/pathology ; Animals ; Antineoplastic Combined Chemotherapy Protocols/*adverse effects/pharmacology ; Camptothecin/adverse effects/analogs &amp; derivatives/pharmacology ; Female ; Fluorouracil/adverse effects/pharmacology ; Humans ; Irinotecan ; Mammary Neoplasms, Experimental/*drug therapy/metabolism/pathology ; Methotrexate/adverse effects/pharmacology ; Mice ; *Mucositis/chemically induced/metabolism/pathology/therapy ; Rats ; }, abstract = {Mucositis is a major oncological problem. The entire gastrointestinal and genitourinary tract and also other mucosal surfaces can be affected in recipients of radiotherapy, and/or chemotherapy. Major progress has been made in recent years in understanding the mechanisms of oral and small intestinal mucositis, which appears to be more prominent than colonic damage. This progress is largely due to the development of representative laboratory animal models of mucositis. This review focuses on the development and establishment of the Dark Agouti rat mammary adenocarcinoma model by the Mucositis Research Group of the University of Adelaide over the past 20 years to characterize the mechanisms underlying methotrexate-, 5-fluorouracil-, and irinotecan-induced mucositis. It also aims to summarize the results from studies using different animal model systems to identify new molecular and cellular markers of mucositis.}, }
@article {pmid25964341, year = {2015}, author = {Franzosa, EA and Huang, K and Meadow, JF and Gevers, D and Lemon, KP and Bohannan, BJ and Huttenhower, C}, title = {Identifying personal microbiomes using metagenomic codes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {22}, pages = {E2930-8}, pmid = {25964341}, issn = {1091-6490}, support = {R01 AI101018/AI/NIAID NIH HHS/United States ; U54HG004969/HG/NHGRI NIH HHS/United States ; HHSN272200900018C/AI/NIAID NIH HHS/United States ; P50 GM098911/GM/NIGMS NIH HHS/United States ; HHSN272200900018C//PHS HHS/United States ; R01 HG005969/HG/NHGRI NIH HHS/United States ; U54 HG004969/HG/NHGRI NIH HHS/United States ; R01HG005969/HG/NHGRI NIH HHS/United States ; P50GM098911/GM/NIGMS NIH HHS/United States ; }, mesh = {Confidentiality/standards/trends ; Genetic Markers/*genetics ; *Genetic Variation ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Models, Genetic ; Precision Medicine/*methods ; }, abstract = {Community composition within the human microbiome varies across individuals, but it remains unknown if this variation is sufficient to uniquely identify individuals within large populations or stable enough to identify them over time. We investigated this by developing a hitting set-based coding algorithm and applying it to the Human Microbiome Project population. Our approach defined body site-specific metagenomic codes: sets of microbial taxa or genes prioritized to uniquely and stably identify individuals. Codes capturing strain variation in clade-specific marker genes were able to distinguish among 100s of individuals at an initial sampling time point. In comparisons with follow-up samples collected 30-300 d later, ∼30% of individuals could still be uniquely pinpointed using metagenomic codes from a typical body site; coincidental (false positive) matches were rare. Codes based on the gut microbiome were exceptionally stable and pinpointed >80% of individuals. The failure of a code to match its owner at a later time point was largely explained by the loss of specific microbial strains (at current limits of detection) and was only weakly associated with the length of the sampling interval. In addition to highlighting patterns of temporal variation in the ecology of the human microbiome, this work demonstrates the feasibility of microbiome-based identifiability-a result with important ethical implications for microbiome study design. The datasets and code used in this work are available for download from huttenhower.sph.harvard.edu/idability.}, }
@article {pmid25963776, year = {2015}, author = {Romi, W and Ahmed, G and Jeyaram, K}, title = {Three-phase succession of autochthonous lactic acid bacteria to reach a stable ecosystem within 7 days of natural bamboo shoot fermentation as revealed by different molecular approaches.}, journal = {Molecular ecology}, volume = {24}, number = {13}, pages = {3372-3389}, doi = {10.1111/mec.13237}, pmid = {25963776}, issn = {1365-294X}, mesh = {Bambusa/*microbiology ; DNA, Bacterial/genetics ; Ecosystem ; *Fermentation ; *Food Microbiology ; India ; Lactic Acid ; Lactobacillaceae/classification/*growth &amp; development ; Leuconostoc/classification/*growth &amp; development ; Leuconostocaceae/classification/*growth &amp; development ; Metagenome ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Microbial community structure and population dynamics during spontaneous bamboo shoot fermentation for production of 'soidon' (indigenous fermented food) in North-east India were studied using cultivation-dependent and cultivation-independent molecular approaches. Cultivation-dependent analyses (PCR-amplified ribosomal DNA restriction analysis and rRNA gene sequencing) and cultivation-independent analyses (PCR-DGGE, qPCR and Illumina amplicon sequencing) were conducted on the time series samples collected from three independent indigenous soidon fermentation batches. The current findings revealed three-phase succession of autochthonous lactic acid bacteria to attain a stable ecosystem within 7 days natural fermentation of bamboo shoots. Weissella spp. (Weissella cibaria, uncultured Weissella ghanensis) and Lactococcus lactis subsp. cremoris predominated the early phase (1-2 days) which was joined by Leuconostoc citreum during the mid-phase (3 days), while Lactobacillus brevis and Lactobacillus plantarum emerged and became dominant in the late phase (5-7 days) with concurrent disappearance of W. cibaria and L. lactis subsp. cremoris. Lactococcus lactis subsp. lactis and uncultured Lactobacillus acetotolerans were predominantly present throughout the fermentation with no visible dynamics. The above identified dominant bacterial species along with their dynamics can be effectively utilized for designing a starter culture for industrialization of soidon production. Our results showed that a more realistic view on the microbial ecology of soidon fermentation could be obtained by cultivation-dependent studies complemented with cultivation-independent molecular approaches. Moreover, the critical issues to be considered for reducing methodological biases while studying the microbial ecology of traditional food fermentation were also highlighted with this soidon fermentation model.}, }
@article {pmid25963669, year = {2015}, author = {Jacquemyn, H and Waud, M and Merckx, VS and Lievens, B and Brys, R}, title = {Mycorrhizal diversity, seed germination and long-term changes in population size across nine populations of the terrestrial orchid Neottia ovata.}, journal = {Molecular ecology}, volume = {24}, number = {13}, pages = {3269-3280}, doi = {10.1111/mec.13236}, pmid = {25963669}, issn = {1365-294X}, mesh = {Belgium ; Biodiversity ; DNA, Fungal/genetics ; *Germination ; Molecular Sequence Data ; Mycorrhizae/*classification ; Orchidaceae/*microbiology ; Phylogeny ; Plant Roots/microbiology ; Population Density ; Seeds/*physiology ; Sequence Analysis, DNA ; Soil ; Soil Microbiology ; Spatio-Temporal Analysis ; Species Specificity ; Symbiosis ; }, abstract = {In plant species that rely on mycorrhizal symbioses for germination and seedling establishment, seedling recruitment and temporal changes in abundance can be expected to depend on fungal community composition and local environmental conditions. However, disentangling the precise factors that determine recruitment success in species that critically rely on mycorrhizal fungi represents a major challenge. In this study, we used seed germination experiments, 454 amplicon pyrosequencing and assessment of soil conditions to investigate the factors driving changes in local abundance in 28 populations of the orchid Neottia ovata. Comparison of population sizes measured in 2003 and 2013 showed that nearly 60% of the studied populations had declined in size (average growth rate across all populations: -0.01). Investigation of the mycorrhizal fungi in both the roots and soil revealed a total of 68 species of putatively mycorrhizal fungi, 21 of which occurred exclusively in roots, 25 that occurred solely in soil and 22 that were observed in both the soil and roots. Seed germination was limited and significantly and positively related to soil moisture content and soil pH, but not to fungal community composition. Large populations or populations with high population growth rates showed significantly higher germination than small populations or populations declining in size, but no significant relationships were found between population size or growth and mycorrhizal diversity. Overall, these results indicate that temporal changes in abundance were related to the ability of seeds to germinate, but at the same time they provided limited evidence that variation in fungal communities played an important role in determining population dynamics.}, }
@article {pmid25960311, year = {2016}, author = {Zabaloy, MC and Carné, I and Viassolo, R and Gómez, MA and Gomez, E}, title = {Soil ecotoxicity assessment of glyphosate use under field conditions: microbial activity and community structure of Eubacteria and ammonia-oxidising bacteria.}, journal = {Pest management science}, volume = {72}, number = {4}, pages = {684-691}, doi = {10.1002/ps.4037}, pmid = {25960311}, issn = {1526-4998}, mesh = {2,4-Dichlorophenoxyacetic Acid/toxicity ; Ammonia/*metabolism ; Bacteria/*drug effects/enzymology/*metabolism ; Drug Interactions ; Glycine/*analogs &amp; derivatives/toxicity ; Oxidation-Reduction ; Oxidoreductases/metabolism ; *Soil Microbiology ; Soil Pollutants/*toxicity ; Glyphosate ; }, abstract = {BACKGROUND: A plot-scale experiment was conducted to assess the impact of field application rates of glyphosate on soil microbial communities by taking measurements of microbial activity (in terms of substrate-induced respiration and enzyme activity) in parallel with culture-independent approaches to assessing both bacterial abundance and diversity. Two rates of glyphosate, alone or in a mixture with 2,4-dichlorophenoxyacetic acid, were applied directly onto the soil surface, simulating normal use in chemical fallow in no-till systems.<br><br>RESULTS: No consistent rate-dependent responses were observed in the microbial activity parameters investigated in the field plots that were exposed to glyphosate. Denaturant gradient gel electrophoresis (DGGE) of the overall bacterial community (Eubacteria) and ammonia-oxidising bacteria (AOB) revealed no effects of the high rate of glyphosate on the structure of the communities in comparison with the control. No treatment effects were observed on the abundance of Eubacteria shortly after treatment in 2010, while a small but significant difference between the high rate and the control was detected in the first sampling in 2011. The abundance of AOB was relatively low during the study, and treatment effects were undetectable.<br><br>CONCLUSIONS: The absence of negative effects on soil microbial communities in this study suggests that glyphosate use at recommended rates poses low risk to the microbiota.}, }
@article {pmid25957311, year = {2015}, author = {Brockhurst, MA}, title = {Experimental evolution can unravel the complex causes of natural selection in clinical infections.}, journal = {Microbiology (Reading, England)}, volume = {161}, number = {6}, pages = {1175-1179}, doi = {10.1099/mic.0.000107}, pmid = {25957311}, issn = {1465-2080}, mesh = {*Adaptation, Biological ; Bacterial Infections/*microbiology ; Cystic Fibrosis/*complications ; Humans ; Models, Theoretical ; *Selection, Genetic ; }, abstract = {It is increasingly clear that rapid evolutionary dynamics are an important process in microbial ecology. Experimental evolution, wherein microbial evolution is observed in real-time, has revealed many instances of appreciable evolutionary change occurring on very short timescales of a few days or weeks in response to a variety of biotic and abiotic selection pressures. From clinical infections, including the chronic bacterial lung infections associated with cystic fibrosis that form a focus of my research, there is now abundant evidence suggesting that rapid evolution by infecting microbes contributes to host adaptation, treatment failure and worsening patient prognosis. However, disentangling the drivers of natural selection in complex infection environments is extremely challenging and limits our understanding of the selective pressures acting upon microbes in infections. Controlled evolution experiments can make a vital contribution to this by determining the causal links between predicted drivers of natural selection and the evolutionary responses of microbes. Integration of experimental evolution into studies of clinical infections is a key next step towards a better understanding of the causes and consequences of rapid microbial evolution in infections, and discovering how these evolutionary processes might be influenced to improve patient health.A video of this Prize Lecture, presented at the Society for General Microbiology Annual Conference 2015, can be viewed via this link: Michael A. Brockhurst https://www.youtube.com/watch?v=N1bodVSl27E.}, }
@article {pmid25956940, year = {2015}, author = {Jung, J and Jang, IA and Ahn, S and Shin, B and Kim, J and Park, C and Jee, SC and Sung, JS and Park, W}, title = {Molecular Mechanisms of Enhanced Bacterial Growth on Hexadecane with Red Clay.}, journal = {Microbial ecology}, volume = {70}, number = {4}, pages = {912-921}, pmid = {25956940}, issn = {1432-184X}, mesh = {Acinetobacter/*growth &amp; development/metabolism ; Alkanes/*metabolism ; *Aluminum Silicates ; Biodegradation, Environmental ; Biota ; Carbon/metabolism ; Clay ; Oxidative Stress ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; Soil Microbiology ; Soil Pollutants/metabolism ; }, abstract = {Red clay was previously used to enhance bioremediation of diesel-contaminated soil. It was speculated that the enhanced degradation of diesel was due to increased bacterial growth. In this study, we selected Acinetobacter oleivorans DR1, a soil-borne degrader of diesel and alkanes, as a model bacterium and performed transcriptional analysis using RNA sequencing to investigate the cellular response during hexadecane utilization and the mechanism by which red clay promotes hexadecane degradation. We confirmed that red clay promotes the growth of A. oleivorans DR1 on hexadecane, a major component of diesel, as a sole carbon source. Addition of red clay to hexadecane-utilizing DR1 cells highly upregulated β-oxidation, while genes related to alkane oxidation were highly expressed with and without red clay. Red clay also upregulated genes related to oxidative stress defense, such as superoxide dismutase, catalase, and glutaredoxin genes, suggesting that red clay supports the response of DR1 cells to oxidative stress generated during hexadecane utilization. Increased membrane fluidity in the presence of red clay was confirmed by fatty acid methyl ester analysis at different growth phases, suggesting that enhanced growth on hexadecane could be due to increased uptake of hexadecane coupled with upregulation of downstream metabolism and oxidative stress defense. The monitoring of the bacterial community in soil with red clay for a year revealed that red clay stabilized the community structure.}, }
@article {pmid25956939, year = {2015}, author = {Yuan, H and Ge, T and Chen, X and Liu, S and Zhu, Z and Wu, X and Wei, W and Whiteley, AS and Wu, J}, title = {Abundance and Diversity of CO2-Assimilating Bacteria and Algae Within Red Agricultural Soils Are Modulated by Changing Management Practice.}, journal = {Microbial ecology}, volume = {70}, number = {4}, pages = {971-980}, pmid = {25956939}, issn = {1432-184X}, mesh = {Agriculture/*methods ; Bacteria/*classification/enzymology/genetics/*metabolism ; Carbon Cycle ; Carbon Dioxide/*metabolism ; China ; DNA, Algal/genetics ; DNA, Bacterial/genetics ; Ecosystem ; Genetic Variation ; Hydrogen-Ion Concentration ; Nitrogen/analysis ; Oryza/microbiology ; Phosphorus/analysis ; Phylogeny ; Phytoplankton/*classification/enzymology/genetics/*metabolism ; Polymorphism, Restriction Fragment Length ; Ribulose-Bisphosphate Carboxylase/genetics/metabolism ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Elucidating the biodiversity of CO(2)-assimilating bacterial and algal communities in soils is important for obtaining a mechanistic view of terrestrial carbon sinks operating at global scales. "Red" acidic soils (Orthic Acrisols) cover large geographic areas and are subject to a range of management practices, which may alter the balance between carbon dioxide production and assimilation through changes in microbial CO(2)-assimilating populations. Here, we determined the abundance and diversity of CO(2)-assimilating bacteria and algae in acidic soils using quantitative PCR and terminal restriction fragment length polymorphism (T-RFLP) of the cbbL gene, which encodes the key CO(2) assimilation enzyme (ribulose-1,5-bisphosphate carboxylase/oxygenase) in the Calvin cycle. Within the framework of a long-term experiment (Taoyuan Agro-ecosystem, subtropical China), paddy rice fields were converted in 1995 to four alternative land management regimes: natural forest (NF), paddy rice (PR), maize crops (CL), and tea plantations (TP). In 2012 (17 years after land use transformation), we collected and analyzed the soils from fields under the original and converted land management regimes. Our results indicated that fields under the PR soil management system harbored the greatest abundance of cbbL copies (4.33 × 10(8) copies g(-1) soil). More than a decade after converting PR soils to natural, rotation, and perennial management systems, a decline in both the diversity and abundance of cbbL-harboring bacteria and algae was recorded. The lowest abundance of bacteria (0.98 × 10(8) copies g(-1) soil) and algae (0.23 × 10(6) copies g(-1) soil) was observed for TP soils. When converting PR soil management to alternative management systems (i.e., NF, CL, and TP), soil edaphic factors (soil organic carbon and total nitrogen content) were the major determinants of bacterial autotrophic cbbL gene diversity. In contrast, soil phosphorus concentration was the major regulator of algal cbbL community composition. Our results provide new insights into the diversity, abundance, and modulation of organisms responsible for microbial autotrophic CO(2) fixation in red acidic soils subjected to changing management regimes.}, }
@article {pmid25955845, year = {2015}, author = {Wang, A and Ling, Z and Yang, Z and Kiela, PR and Wang, T and Wang, C and Cao, L and Geng, F and Shen, M and Ran, X and Su, Y and Cheng, T and Wang, J}, title = {Gut microbial dysbiosis may predict diarrhea and fatigue in patients undergoing pelvic cancer radiotherapy: a pilot study.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0126312}, pmid = {25955845}, issn = {1932-6203}, support = {R01 DK041274/DK/NIDDK NIH HHS/United States ; 5R01-DK041274/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Diarrhea/*etiology/microbiology ; Fatigue/*etiology ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; Microbiota/*physiology/radiation effects ; Middle Aged ; Pelvic Neoplasms/complications/*radiotherapy ; Pilot Projects ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Radiotherapy/*adverse effects ; }, abstract = {Fatigue and diarrhea are the most frequent adverse effects of pelvic radiotherapy, while their etiologies are largely unknown. The aim of this study is to investigate the correlations between fatigue, diarrhea, and alterations in gut microbiota induced by pelvic radiotherapy. During the 5-week treatment of pelvic radiotherapy in 11 cancer patients, the general fatigue score significantly increased and was more prominent in the patients with diarrhea. The fatigue score was closely correlated with the decrease of serum citrulline (an indicator of the functional enterocyte mass) and the increases of systemic inflammatory proteins, including haptoglobin, orosomuoid, α1-antitrypsin and TNF-α. Serum level of lipopolysaccharide (LPS) was also elevated, especially in the patients with diarrhea indicating epithelial barrier breach and endotoxemia. Pyrosequencing analysis of 16S rRNA gene revealed that microbial diversity, richness, and the Firmicutes/Bacteroidetes ratio were significantly altered prior to radiotherapy in patients who later developed diarrhea. Pelvic radiotherapy induced further changes in fecal microbial ecology, some of which were specific to the patients with or without diarrhea. Our results indicate that gut microbial dysbiosis prior to radiation therapy may be exploited to predict development of diarrhea and to guide preventive treatment options. Radiation-induced dysbiosis may contribute to pelvic radiation disease, including mucositis, diarrhea, systemic inflammatory response, and pelvic radiotherapy-associated fatigue in cancer patients.}, }
@article {pmid25953568, year = {2015}, author = {Golda-Cepa, M and Brzychczy-Wloch, M and Engvall, K and Aminlashgari, N and Hakkarainen, M and Kotarba, A}, title = {Microbiological investigations of oxygen plasma treated parylene C surfaces for metal implant coating.}, journal = {Materials science &amp; engineering. C, Materials for biological applications}, volume = {52}, number = {}, pages = {273-281}, doi = {10.1016/j.msec.2015.03.060}, pmid = {25953568}, issn = {1873-0191}, mesh = {Microscopy, Atomic Force ; Microscopy, Electron, Scanning ; Osteoblasts/cytology/drug effects ; Photoelectron Spectroscopy ; Polymers/*chemistry/*pharmacology ; Pseudomonas aeruginosa/drug effects ; Staphylococcus aureus/drug effects ; Staphylococcus epidermidis/drug effects ; Wettability ; Xylenes/*chemistry/*pharmacology ; }, abstract = {Parylene C surface was modified by the use of oxygen plasma treatment and characterized by microscopic and surface-sensitive techniques (E-SEM, AFM, XPS, LDI-TOF-MS, contact angle). The influence of the treatment on surface properties was investigated by calculations of surface free energy (Owens-Wendt method). Moreover, early adhesion (Culture Plate Method, Optical Microscopy Test) and biofilm formation ability (Cristal Violet Assay) on the parylene C surface was investigated. The bacteria strains which are common causative agents of medical device-associated infections (Staphylococcus aureus, Staphylococcus epidermidis and Pseudomonas aeruginosa--reference strains and clinical isolates) were used. It was concluded that chemical (oxygen insertion) and physical (nanotopography generation) changes, have a significant impact on the biocompatibility in terms of increased hydrophilicity (θ w of unmodified sample = 88° ± 2°, θ w of 60 min modified sample = 17.6° ± 0.8°) and surface free energy (SFE of unmodified sample = 42.4 mJ/m(2), and for 60 min modified sample = 70.1 mJ/m(2)). At the same time, no statistical effect on biofilm production and bacteria attachment to the modified surface of any of the tested strains was observed.}, }
@article {pmid25952659, year = {2015}, author = {Sterkenburg, E and Bahr, A and Brandström Durling, M and Clemmensen, KE and Lindahl, BD}, title = {Changes in fungal communities along a boreal forest soil fertility gradient.}, journal = {The New phytologist}, volume = {207}, number = {4}, pages = {1145-1158}, doi = {10.1111/nph.13426}, pmid = {25952659}, issn = {1469-8137}, mesh = {Carbon/analysis ; Ergosterol/metabolism ; Fertility ; Fungi/*physiology ; Hydrogen-Ion Concentration ; Linear Models ; Nitrogen/analysis ; Plant Leaves/microbiology ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; Species Specificity ; *Taiga ; Trees/microbiology ; }, abstract = {Boreal forests harbour diverse fungal communities with decisive roles in decomposition and plant nutrition. Although changes in boreal plant communities along gradients in soil acidity and nitrogen (N) availability are well described, less is known about how fungal taxonomic and functional groups respond to soil fertility factors. We analysed fungal communities in humus and litter from 25 Swedish old-growth forests, ranging from N-rich Picea abies stands to acidic and N-poor Pinus sylvestris stands. 454-pyrosequencing of ITS2 amplicons was used to analyse community composition, and biomass was estimated by ergosterol analysis. Fungal community composition was significantly related to soil fertility at the levels of species, genera/orders and functional groups. Ascomycetes dominated in less fertile forests, whereas basidiomycetes increased in abundance in more fertile forests, both in litter and humus. The relative abundance of mycorrhizal fungi in the humus layer remained high even in the most fertile soils. Tolerance to acidity and nitrogen deficiency seems to be of greater importance than plant carbon (C) allocation patterns in determining responses of fungal communities to soil fertility, in old-growth boreal forests.}, }
@article {pmid25950866, year = {2015}, author = {Na, H and Lever, MA and Kjeldsen, KU and Schulz, F and Jørgensen, BB}, title = {Uncultured Desulfobacteraceae and Crenarchaeotal group C3 incorporate 13C-acetate in coastal marine sediment.}, journal = {Environmental microbiology reports}, volume = {7}, number = {4}, pages = {614-622}, doi = {10.1111/1758-2229.12296}, pmid = {25950866}, issn = {1758-2229}, mesh = {Acetates/*metabolism ; Biota/*drug effects ; Carbon/*metabolism ; Cluster Analysis ; Crenarchaeota/*metabolism ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Deltaproteobacteria/*metabolism ; Denmark ; Geologic Sediments/*microbiology ; Isotope Labeling ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfates/metabolism ; }, abstract = {Stable isotope probing (SIP) of deoxyribonucleic acid (DNA) was used to identify microbes incorporating (13) C-labeled acetate in sulfate-reducing sediment from Aarhus Bay, Denmark. Sediment was incubated in medium containing 10 mM sulfate and different (13) C-acetate (10, 1, 0.1 mM) concentrations. The resultant changes in microbial community composition were monitored in total and SIP-fractionated DNA during long-term incubations. Chemical analyses demonstrated metabolic activity in all sediment slurries, with sulfate-reducing activity largely determined by initial acetate concentrations. Sequencing of 16S rRNA gene PCR amplicons showed that the incubations shifted the bacterial but not the archaeal community composition. After 3 months of incubation, only sediment slurries incubated with 10 mM (13) C-acetate showed detectable (13) C-DNA labeling. Based on 16S rRNA and dsrB gene PCR amplicon sequencing, the (13) C-labeled DNA pool was dominated by a single type of sulfate reducer representing a novel genus in the family Desulfobacteraceae. In addition, members of the uncultivated Crenarchaeotal group C3 were enriched in the (13) C-labeled DNA. Our results were reproducible across biological replicate experiments and provide new information about the identities of uncultured acetate-consuming bacteria and archaea in marine sediments.}, }
@article {pmid25950678, year = {2015}, author = {Caliz, J and Montes-Borrego, M and Triadó-Margarit, X and Metsis, M and Landa, BB and Casamayor, EO}, title = {Influence of edaphic, climatic, and agronomic factors on the composition and abundance of nitrifying microorganisms in the rhizosphere of commercial olive crops.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0125787}, pmid = {25950678}, issn = {1932-6203}, mesh = {Archaea/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Climate ; *Crops, Agricultural ; Hydrogen-Ion Concentration ; *Nitrification ; *Olea ; *Soil Microbiology ; }, abstract = {The microbial ecology of the nitrogen cycle in agricultural soils is an issue of major interest. We hypothesized a major effect by farm management systems (mineral versus organic fertilizers) and a minor influence of soil texture and plant variety on the composition and abundance of microbial nitrifiers. We explored changes in composition (16S rRNA gene) of ammonia-oxidizing archaea (AOA), bacteria (AOB), and nitrite-oxidizing bacteria (NOB), and in abundance of AOA and AOB (qPCR of amoA genes) in the rhizosphere of 96 olive orchards differing in climatic conditions, agricultural practices, soil properties, and olive variety. Majority of archaea were 1.1b thaumarchaeota (soil crenarchaeotic group, SCG) closely related to the AOA genus Nitrososphaera. Most AOB (97%) were identical to Nitrosospira tenuis and most NOB (76%) were closely related to Nitrospira sp. Common factors shaping nitrifiers assemblage composition were pH, soil texture, and olive variety. AOB abundance was positively correlated with altitude, pH, and clay content, whereas AOA abundances showed significant relationships with organic nitrogen content and exchangeable K. The abundances of AOA differed significantly among soil textures and olive varieties, and those of AOB among soil management systems and olive varieties. Overall, we observed minor effects by orchard management system, soil cover crop practices, plantation age, or soil organic matter content, and major influence of soil texture, pH, and olive tree variety.}, }
@article {pmid25947097, year = {2015}, author = {Kúdelová, M and Belvončíková, P and Vrbová, M and Kovaľová, A and Štibrániová, I and Kocáková, P and Slovák, M and Špitalská, E and Lapuníková, B and Matúšková, R and Šupolíková, M}, title = {Detection of Murine Herpesvirus 68 (MHV-68) in Dermacentor reticulatus Ticks.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {785-794}, pmid = {25947097}, issn = {1432-184X}, mesh = {Animals ; Dermacentor/growth &amp; development/*virology ; Female ; Larva/growth &amp; development/virology ; Male ; Nymph/growth &amp; development/virology ; Polymerase Chain Reaction/veterinary ; Polymorphism, Restriction Fragment Length ; Rhadinovirus/*isolation &amp; purification ; Sequence Analysis, DNA/veterinary ; Slovakia ; }, abstract = {Murid herpesvirus 4 (MuHV 4) strain 68 (MHV-68) is a natural pathogen of murid rodents, which serves as hosts to Dermacentor reticulatus ticks. These ticks are known to transmit multiple pathogens, which can cause diseases in humans and animals. Recently, the detection of MHV-68 antibodies in the blood of animals living in the same biotope as virus-infected mice has suggested the role of ticks in pathogen circulation in nature. Herein, to identify MHV-68 in D. reticulatus ticks, DNA samples from 432 adults were collected at two sites in southwestern Slovakia from 2011 to 2014. Samples were examined by polymerase chain reaction (PCR), targeting ORF50 of MHV-68. Ignoring season and locality, we have found 25.9 % of the male and 44.9 % of the female ticks to be positive. Within ticks collected in Vojka, 40 % (125/312) became positive, at a rate of approximately 6.8 times higher in spring than in autumn (66 vs 9.7 %). In addition, in the spring, 1.4 times more females were positive than males. Within ticks collected in Gabčíkovo, 23.3 % (28/120) became positive, with positive females being twice as frequent. The infecting virus was identified by analyzing amplified products via sequencing and restriction fragment length polymorphism (RFLP) analyses. Using an explantation/co-cultivation procedure, we examined the salivary glands, intestines, and ovaries of five females for live MHV-68. In all organs of two ticks, we identified a virus capable of replication in mammalian cells. This is the first report of MHV-68 detection in D. reticulatus ticks and of a live virus in their organs. Findings encourage further study to determine whether this potential arbovirus, found in salivary glands, is transmissible. It further supports the hypothesis regarding the mediating role of ticks in MHV-68 circulation in nature.}, }
@article {pmid25947096, year = {2015}, author = {Mason, OU and Case, DH and Naehr, TH and Lee, RW and Thomas, RB and Bailey, JV and Orphan, VJ}, title = {Comparison of Archaeal and Bacterial Diversity in Methane Seep Carbonate Nodules and Host Sediments, Eel River Basin and Hydrate Ridge, USA.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {766-784}, pmid = {25947096}, issn = {1432-184X}, mesh = {Archaea/*physiology ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; California ; DNA, Archaeal/genetics/metabolism ; DNA, Bacterial/genetics/metabolism ; Environment ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Oregon ; Pacific Ocean ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {Anaerobic oxidation of methane (AOM) impacts carbon cycling by acting as a methane sink and by sequestering inorganic carbon via AOM-induced carbonate precipitation. These precipitates commonly take the form of carbonate nodules that form within methane seep sediments. The timing and sequence of nodule formation within methane seep sediments are not well understood. Further, the microbial diversity associated with sediment-hosted nodules has not been well characterized and the degree to which nodules reflect the microbial assemblage in surrounding sediments is unknown. Here, we conducted a comparative study of microbial assemblages in methane-derived authigenic carbonate nodules and their host sediments using molecular, mineralogical, and geochemical methods. Analysis of 16S rRNA gene diversity from paired carbonate nodules and sediments revealed that both sample types contained methanotrophic archaea (ANME-1 and ANME-2) and syntrophic sulfate-reducing bacteria (Desulfobacteraceae and Desulfobulbaceae), as well as other microbial community members. The combination of geochemical and molecular data from Eel River Basin and Hydrate Ridge suggested that some nodules formed in situ and captured the local sediment-hosted microbial community, while other nodules may have been translocated or may represent a record of conditions prior to the contemporary environment. Taken together, this comparative analysis offers clues to the formation regimes and mechanisms of sediment-hosted carbonate nodules.}, }
@article {pmid25942385, year = {2015}, author = {McKenney, EA and Williamson, L and Yoder, AD and Rawls, JF and Bilbo, SD and Parker, W}, title = {Alteration of the rat cecal microbiome during colonization with the helminth Hymenolepis diminuta.}, journal = {Gut microbes}, volume = {6}, number = {3}, pages = {182-193}, pmid = {25942385}, issn = {1949-0984}, mesh = {Animals ; Bacteria/*classification/*isolation &amp; purification ; Cecum/*microbiology/*parasitology ; Female ; *Gastrointestinal Microbiome ; Hymenolepis diminuta/*growth &amp; development ; Male ; Rats, Sprague-Dawley ; }, abstract = {The microbiome is now widely recognized as being important in health and disease, and makes up a substantial subset of the biome within the ecosystem of the vertebrate body. At the same time, multicellular, eukaryotic organisms such as helminths are being recognized as an important component of the biome that shaped the evolution of our genes. The absence of these macroscopic organisms during the early development and life of humans in Western culture probably leads to a wide range of human immunological diseases. However, the interaction between the microbiome and macroscopic components of the biome remains poorly characterized. In this study, the microbiome of the cecum in rats colonized for 2 generations with the small intestinal helminth Hymenolepis diminuta was evaluated. The introduction of this benign helminth, which is of considerable therapeutic interest, led to several changes in the cecal microbiome. Most of the changes were within the Firmicutes phylum, involved about 20% of the total bacteria, and generally entailed a shift from Bacilli to Clostridia species in the presence of the helminth. The results point toward ecological relationships between various components of the biome, with the observed shifts in the microbiome suggesting potential mechanisms by which this helminth might exert therapeutic effects.}, }
@article {pmid25939371, year = {2015}, author = {Gombeer, S and Ramond, JB and Eckardt, FD and Seely, M and Cowan, DA}, title = {The influence of surface soil physicochemistry on the edaphic bacterial communities in contrasting terrain types of the Central Namib Desert.}, journal = {Geobiology}, volume = {13}, number = {5}, pages = {494-505}, doi = {10.1111/gbi.12144}, pmid = {25939371}, issn = {1472-4669}, mesh = {Bacteria/*classification/*genetics ; *Biota ; Chemical Phenomena ; Desert Climate ; Namibia ; Polymorphism, Restriction Fragment Length ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Notwithstanding, the severe environmental conditions, deserts harbour a high diversity of adapted micro-organisms. In such oligotrophic environments, soil physicochemical characteristics play an important role in shaping indigenous microbial communities. This study investigates the edaphic bacterial communities of three contrasting desert terrain types (gravel plains, sand dunes and ephemeral rivers) with different surface geologies in the Central Namib Desert. For each site, we evaluated surface soil physicochemistries and used explorative T-RFLP methodology to get an indication of bacterial community diversities. While grain size was an important parameter in separating the three terrain types physicochemically and specific surface soil types could be distinguished, the desert edaphic bacterial communities displayed a high level of local spatial heterogeneity. Ten variables contributed significantly (P < 0.05) to the variance in the T-RFLP data sets: fine silt, medium and fine sand content, pH, S, Na, Zn, Al, V and Fe concentrations, and 40% of the total variance could be explained by these constraining variables. The results suggest that local physicochemical conditions play a significant role in shaping the bacterial structures in the Central Namib Desert and stress the importance of recording a wide variety of environmental descriptors to comprehensively assess the role of edaphic parameters in shaping microbial communities.}, }
@article {pmid25936675, year = {2015}, author = {Agathos, SN and Boon, N}, title = {Editorial overview: Environmental biotechnology.}, journal = {Current opinion in biotechnology}, volume = {33}, number = {}, pages = {v-vii}, doi = {10.1016/j.copbio.2015.04.002}, pmid = {25936675}, issn = {1879-0429}, mesh = {Biotechnology/*methods ; Ecosystem ; Humans ; *Periodicals as Topic ; }, }
@article {pmid25933637, year = {2015}, author = {Miura, T and Niswati, A and Swibawa, IG and Haryani, S and Gunito, H and Shimano, S and Fujie, K and Kaneko, N}, title = {Diversity of Fungi on Decomposing Leaf Litter in a Sugarcane Plantation and Their Response to Tillage Practice and Bagasse Mulching: Implications for Management Effects on Litter Decomposition.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {646-658}, pmid = {25933637}, issn = {1432-184X}, mesh = {Agriculture/*methods ; *Biodiversity ; DNA, Intergenic/genetics ; Fungi/*physiology ; Indonesia ; Molecular Sequence Data ; Plant Leaves/*microbiology ; Saccharum/microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {To minimize the degradation of soil organic matter (SOM) content in conventional sugarcane cropping, it is important to understand how the fungal community contributes to SOM dynamics during the decomposition of sugarcane leaf litter. However, our knowledge of fungal diversity in tropical agroecosystems is currently limited. Thus, we determined the fungal community structure on decomposing sugarcane leaf litter and their response to different soil management systems using the internal transcribed spacer region 1 (ITS1) amplicon sequencing method afforded by Ion Torrent Personal Genome Machine (PGM). The results indicate that no-tillage had positive effects on the relative abundance of Zygomycota and of some taxa that may prefer a moist environment over conventional tillage, whereas bagasse mulching decreased the richness of operational taxonomic units (OTUs) and had positive effect on the relative abundance of slow-growing taxa, which may prefer poor nutrient substrates. Furthermore, a combination of no-tillage and bagasse mulching increased the abundance of unique OTUs. We suggest that the alteration of fungal communities through the changes in soil management practices produces an effect on litter decomposition.}, }
@article {pmid25933636, year = {2015}, author = {Bashenkhaeva, MV and Zakharova, YR and Petrova, DP and Khanaev, IV and Galachyants, YP and Likhoshway, YV}, title = {Sub-Ice Microalgal and Bacterial Communities in Freshwater Lake Baikal, Russia.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {751-765}, pmid = {25933636}, issn = {1432-184X}, mesh = {Bacteria/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; Ecosystem ; Ice Cover/microbiology ; Lakes/microbiology ; Microalgae/genetics/*physiology ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Russia ; Seasons ; }, abstract = {The sub-ice environment of Lake Baikal represents a special ecotope where strongly increasing microbial biomass causes an "ice-bloom" contributing therefore to the ecosystem functioning and global element turnover under low temperature in the world's largest freshwater lake. In this work, we analyzed bacterial and microalgal communities and their succession in the sub-ice environment in March-April 2010-2012. It was found out that two dinoflagellate species (Gymnodinium baicalense var. minor and Peridinium baicalense Kisselew et Zwetkow) and four diatom species (Aulacoseira islandica, A. baicalensis, Synedra acus subsp. radians, and Synedra ulna) predominated in the microalgal communities. Interestingly, among all microalgae, the diatom A. islandica showed the highest number of physically attached bacterial cells (up to 67 ± 16 bacteria per alga). Bacterial communities analyzed with pyrosequencing of 16S rRNA gene fragments were diverse and represented by 161 genera. Phyla Proteobacteria, Verrucomicrobia, Actinobacteria, Acidobacteria, Bacteroidetes, and Cyanobacteria represented a core community independently on microalgal composition, although the relative abundance of these bacterial phyla strongly varied across sampling sites and time points; unique OTUs from other groups were rare.}, }
@article {pmid25933635, year = {2015}, author = {Jang, Y and Jang, S and Min, M and Hong, JH and Lee, H and Lee, H and Lim, YW and Kim, JJ}, title = {Comparison of the Diversity of Basidiomycetes from Dead Wood of the Manchurian fir (Abies holophylla) as Evaluated by Fruiting Body Collection, Mycelial Isolation, and 454 Sequencing.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {634-645}, pmid = {25933635}, issn = {1432-184X}, mesh = {Abies/*microbiology ; Basidiomycota/*physiology ; *Biodiversity ; DNA, Fungal/genetics ; DNA, Intergenic/genetics ; Fruiting Bodies, Fungal/chemistry ; Molecular Sequence Data ; Mycelium/chemistry ; Mycology/*methods ; Phylogeny ; Polymerase Chain Reaction ; Republic of Korea ; Sequence Analysis, DNA ; Wood/*microbiology ; }, abstract = {In this study, three different methods (fruiting body collection, mycelial isolation, and 454 sequencing) were implemented to determine the diversity of wood-inhabiting basidiomycetes from dead Manchurian fir (Abies holophylla). The three methods recovered similar species richness (26 species from fruiting bodies, 32 species from mycelia, and 32 species from 454 sequencing), but Fisher's alpha, Shannon-Wiener, Simpson's diversity indices of fungal communities indicated fruiting body collection and mycelial isolation displayed higher diversity compared with 454 sequencing. In total, 75 wood-inhabiting basidiomycetes were detected. The most frequently observed species were Heterobasidion orientale (fruiting body collection), Bjerkandera adusta (mycelial isolation), and Trichaptum fusco-violaceum (454 sequencing). Only two species, Hymenochaete yasudae and Hypochnicium karstenii, were detected by all three methods. This result indicated that Manchurian fir harbors a diverse basidiomycetous fungal community and for complete estimation of fungal diversity, multiple methods should be used. Further studies are required to understand their ecology in the context of forest ecosystems.}, }
@article {pmid25932020, year = {2015}, author = {Zimmermann, M and Escrig, S and Hübschmann, T and Kirf, MK and Brand, A and Inglis, RF and Musat, N and Müller, S and Meibom, A and Ackermann, M and Schreiber, F}, title = {Phenotypic heterogeneity in metabolic traits among single cells of a rare bacterial species in its natural environment quantified with a combination of flow cell sorting and NanoSIMS.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {243}, pmid = {25932020}, issn = {1664-302X}, abstract = {Populations of genetically identical microorganisms residing in the same environment can display marked variability in their phenotypic traits; this phenomenon is termed phenotypic heterogeneity. The relevance of such heterogeneity in natural habitats is unknown, because phenotypic characterization of a sufficient number of single cells of the same species in complex microbial communities is technically difficult. We report a procedure that allows to measure phenotypic heterogeneity in bacterial populations from natural environments, and use it to analyze N2 and CO2 fixation of single cells of the green sulfur bacterium Chlorobium phaeobacteroides from the meromictic lake Lago di Cadagno. We incubated lake water with (15)N2 and (13)CO2 under in situ conditions with and without NH4 (+). Subsequently, we used flow cell sorting with auto-fluorescence gating based on a pure culture isolate to concentrate C. phaeobacteroides from its natural abundance of 0.2% to now 26.5% of total bacteria. C. phaeobacteroides cells were identified using catalyzed-reporter deposition fluorescence in situ hybridization (CARD-FISH) targeting the 16S rRNA in the sorted population with a species-specific probe. In a last step, we used nanometer-scale secondary ion mass spectrometry to measure the incorporation (15)N and (13)C stable isotopes in more than 252 cells. We found that C. phaeobacteroides fixes N2 in the absence of NH4 (+), but not in the presence of NH4 (+) as has previously been suggested. N2 and CO2 fixation were heterogeneous among cells and positively correlated indicating that N2 and CO2 fixation activity interact and positively facilitate each other in individual cells. However, because CARD-FISH identification cannot detect genetic variability among cells of the same species, we cannot exclude genetic variability as a source for phenotypic heterogeneity in this natural population. Our study demonstrates the technical feasibility of measuring phenotypic heterogeneity in a rare bacterial species in its natural habitat, thus opening the door to study the occurrence and relevance of phenotypic heterogeneity in nature.}, }
@article {pmid25930203, year = {2015}, author = {Sengupta, A and Dick, WA}, title = {Bacterial Community Diversity in Soil Under two Tillage Practices as Determined by Pyrosequencing.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {853-859}, pmid = {25930203}, issn = {1432-184X}, mesh = {Agriculture/*methods ; Bacteria/*classification ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Ohio ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The ability of soil to provide ecosystem services is dependent on microbial diversity, with 80-90 % of the processes in soil being mediated by microbes. There still exists a knowledge gap in the types of microorganisms present in soil and how soil management affects them. However, identification of microorganisms is severely limited by classical culturing techniques that have been traditionally used in laboratories. Metagenomic approaches are increasingly becoming common, with current high-throughput sequencing approaches allowing for more in-depth analysis. We conducted a preliminary analysis of bacterial diversity in soils from the longest continuously maintained no-till (NT) plots in the world (52 years) and in adjacent plow-till (PT) plots in Ohio, USA managed similarly except for tillage. Bacterial diversity was determined using a culture-independent approach of high-throughput pyrosequencing of the 16S rRNA gene. Proteobacteria and Acidobacteria were predominant in both samples but the NT soil had a higher number of reads, bacterial richness, and five unique phyla. Four unique phyla were observed in PT and 99 % of the community had relative abundance of <1 %. Plowing and secondary tillage tend to homogenize the soil and reduces the unique (i.e., diverse) microenvironments where microbial populations can reside. We conclude that tillage leads to fewer dominant species being present in soil and that these species contribute to a higher percentage of the total community.}, }
@article {pmid25927833, year = {2015}, author = {Fauteux, L and Cottrell, MT and Kirchman, DL and Borrego, CM and Garcia-Chaves, MC and Del Giorgio, PA}, title = {Patterns in Abundance, Cell Size and Pigment Content of Aerobic Anoxygenic Phototrophic Bacteria along Environmental Gradients in Northern Lakes.}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0124035}, pmid = {25927833}, issn = {1932-6203}, mesh = {Bacteria, Aerobic/*metabolism ; Bacteriochlorophyll A/*metabolism ; Chlorophyll/metabolism ; Chlorophyll A ; Quebec ; }, abstract = {There is now evidence that aerobic anoxygenic phototrophic (AAP) bacteria are widespread across aquatic systems, yet the factors that determine their abundance and activity are still not well understood, particularly in freshwaters. Here we describe the patterns in AAP abundance, cell size and pigment content across wide environmental gradients in 43 temperate and boreal lakes of Québec. AAP bacterial abundance varied from 1.51 to 5.49 x 105 cells mL-1, representing <1 to 37% of total bacterial abundance. AAP bacteria were present year-round, including the ice-cover period, but their abundance relative to total bacterial abundance was significantly lower in winter than in summer (2.6% and 7.7%, respectively). AAP bacterial cells were on average two-fold larger than the average bacterial cell size, thus AAP cells made a greater relative contribution to biomass than to abundance. Bacteriochlorophyll a (BChla) concentration varied widely across lakes, and was not related to AAP bacterial abundance, suggesting a large intrinsic variability in the cellular pigment content. Absolute and relative AAP bacterial abundance increased with dissolved organic carbon (DOC), whereas cell-specific BChla content was negatively related to chlorophyll a (Chla). As a result, both the contribution of AAP bacteria to total prokaryotic abundance, and the cell-specific BChla pigment content were positively correlated with the DOC:Chla ratio, both peaking in highly colored, low-chlorophyll lakes. Our results suggest that photoheterotrophy might represent a significant ecological advantage in highly colored, low-chlorophyll lakes, where DOC pool is chemically and structurally more complex.}, }
@article {pmid25926821, year = {2015}, author = {Nunes da Rocha, U and Cadillo-Quiroz, H and Karaoz, U and Rajeev, L and Klitgord, N and Dunn, S and Truong, V and Buenrostro, M and Bowen, BP and Garcia-Pichel, F and Mukhopadhyay, A and Northen, TR and Brodie, EL}, title = {Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {277}, pmid = {25926821}, issn = {1664-302X}, abstract = {Biological Soil Crusts (BSCs) are organosedimentary assemblages comprised of microbes and minerals in topsoil of terrestrial environments. BSCs strongly impact soil quality in dryland ecosystems (e.g., soil structure and nutrient yields) due to pioneer species such as Microcoleus vaginatus; phototrophs that produce filaments that bind the soil together, and support an array of heterotrophic microorganisms. These microorganisms in turn contribute to soil stability and biogeochemistry of BSCs. Non-cyanobacterial populations of BSCs are less well known than cyanobacterial populations. Therefore, we attempted to isolate a broad range of numerically significant and phylogenetically representative BSC aerobic heterotrophs. Combining simple pre-treatments (hydration of BSCs under dark and light) and isolation strategies (media with varying nutrient availability and protection from oxidative stress) we recovered 402 bacterial and one fungal isolate in axenic culture, which comprised 116 phylotypes (at 97% 16S rRNA gene sequence homology), 115 bacterial and one fungal. Each medium enriched a mostly distinct subset of phylotypes, and cultivated phylotypes varied due to the BSC pre-treatment. The fraction of the total phylotype diversity isolated, weighted by relative abundance in the community, was determined by the overlap between isolate sequences and OTUs reconstructed from metagenome or metatranscriptome reads. Together, more than 8% of relative abundance of OTUs in the metagenome was represented by our isolates, a cultivation efficiency much larger than typically expected from most soils. We conclude that simple cultivation procedures combined with specific pre-treatment of samples afford a significant reduction in the culturability gap, enabling physiological and metabolic assays that rely on ecologically relevant axenic cultures.}, }
@article {pmid25925876, year = {2015}, author = {Hu, W and Zhang, Q and Tian, T and Cheng, G and An, L and Feng, H}, title = {The microbial diversity, distribution, and ecology of permafrost in China: a review.}, journal = {Extremophiles : life under extreme conditions}, volume = {19}, number = {4}, pages = {693-705}, pmid = {25925876}, issn = {1433-4909}, mesh = {*Biodiversity ; China ; *Climate Change ; Humans ; Permafrost/*microbiology ; *Phylogeny ; *Soil Microbiology ; }, abstract = {Permafrost in China mainly located in high-altitude areas. It represents a unique and suitable ecological niche that can be colonized by abundant microbes. Permafrost microbial community varies across geographically separated locations in China, and some lineages are novel and possible endemic. Besides, Chinese permafrost is a reservoir of functional microbial groups involved in key biogeochemical cycling processes. In future, more work is necessary to determine if these phylogenetic groups detected by DNA-based methods are part of the viable microbial community, and their functional roles and how they potentially respond to climate change. This review summaries recent studies describing microbial biodiversity found in permafrost and associated environments in China, and provides a framework for better understanding the microbial ecology of permafrost.}, }
@article {pmid25921519, year = {2015}, author = {Zancolli, G and Mahsberg, D and Sickel, W and Keller, A}, title = {Reptiles as Reservoirs of Bacterial Infections: Real Threat or Methodological Bias?.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {579-584}, pmid = {25921519}, issn = {1432-184X}, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Disease Reservoirs/microbiology/*veterinary ; Feces/microbiology ; *Food Chain ; Lizards/microbiology ; Molecular Sequence Data ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics/metabolism ; Reptiles/*microbiology ; Sequence Analysis, DNA/veterinary ; Snakes/microbiology ; Turtles/microbiology ; }, abstract = {Bacterial infections secondary to snakebites and human pathogens (e.g., Salmonella) have been linked to the oral microbiota of snakes and pet reptiles. Based on culture-dependent studies, it is speculated that snakes' oral microbiota reflects the fecal flora of their ingested preys. However, cultured-based techniques have been shown to be limited as they fail to identify unculturable microorganisms which represent the vast majority of the microbial diversity. Here, we used culture-independent high-throughput sequencing to identify reptile-associated pathogens and to characterize the oral microbial community of five snakes, one gecko, and two terrapins. Few potential human pathogens were detected at extremely low frequencies. Moreover, bacterial taxa represented in the snake's oral cavity bore little resemblance to their preys' fecal microbiota. Overall, we found distinct, highly diverse microbial communities with consistent, species-specific patterns contrary to previous culture-based studies. Our study does not support the widely held assumption that reptiles' oral cavity acts as pathogen reservoir and provides important insights for future research.}, }
@article {pmid25921518, year = {2015}, author = {Esposito, A and Ahmed, E and Ciccazzo, S and Sikorski, J and Overmann, J and Holmström, SJ and Brusetti, L}, title = {Comparison of Rock Varnish Bacterial Communities with Surrounding Non-Varnished Rock Surfaces: Taxon-Specific Analysis and Morphological Description.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {741-750}, pmid = {25921518}, issn = {1432-184X}, mesh = {Bacteria/genetics ; *Bacterial Physiological Phenomena ; DNA, Bacterial/genetics/metabolism ; *Environment ; Italy ; *Microbiota ; Microscopy, Electron, Scanning ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics/metabolism ; Sequence Analysis, DNA ; Substrate Specificity ; }, abstract = {Rock varnish is a thin layer of Fe and Mn oxyhydroxides with embedded clay minerals that contain an increased Mn/Fe ratio compared to that of the Earth's crust. Even if the study of rock varnish has important implications in several fields, the composition of epilithic bacterial communities and the distribution of taxa on varnish surfaces are still not wholly described. The aim of this study was (i) to identify the bacterial taxa which show the greatest variation between varnish and non-varnish environments, collected from the same rock, and (ii) to describe the morphology of epilithic communities through scanning electron microscopy (SEM). Triplicate samples of rock surfaces with varnish and triplicate samples without varnish were collected from five sites in Matsch Valley (South Tyrol, Italy). The V4 region of 16S rRNA gene was analyzed by Illumina sequencing. Fifty-five ubiquitous taxa have been examined to assess variation between varnish and non-varnish. Cyanobacteria, Chloroflexi, Proteobacteria along with minor taxa such as Solirubrobacterales, Conexibaxter, and Rhodopila showed significant variations of abundance, diversity, or both responding to the ecology (presence/absence of varnish). Other taxa, such as the genus Edaphobacter, showed a more marked spatial variation responding to the sampling site. SEM images showed a multitude of bacterial morphologies and structures involved in the process of attachment and creation of a suitable environment for growth. The features emerging from this analysis suggest that the highly oxidative Fe and Mn-rich varnish environment favors anoxigenic autotrophy and establishment of highly specialized bacteria.}, }
@article {pmid25921438, year = {2015}, author = {Hedlund, BP and Dodsworth, JA and Staley, JT}, title = {The changing landscape of microbial biodiversity exploration and its implications for systematics.}, journal = {Systematic and applied microbiology}, volume = {38}, number = {4}, pages = {231-236}, doi = {10.1016/j.syapm.2015.03.003}, pmid = {25921438}, issn = {1618-0984}, mesh = {*Archaea/classification/genetics ; *Bacteria/classification/genetics ; *Metagenomics ; *Single-Cell Analysis ; }, abstract = {A vast diversity of Bacteria and Archaea exists in nature that has evaded axenic culture. Advancements in single-cell genomics, metagenomics, and molecular microbial ecology approaches provide ever-improving insight into the biology of this so-called "microbial dark matter"; however, due to the International Code of Nomenclature of Prokaryotes, yet-uncultivated microorganisms are not accommodated in formal taxonomy regardless of the quantity or quality of data. Meanwhile, efforts to calibrate the existing taxonomy with phylogenetic anchors and genomic data are increasingly robust. The current climate provides an exciting opportunity to leverage rapidly expanding single-cell genomics and metagenomics datasets to improve the taxonomy of Bacteria and Archaea. However, this opportunity must be weighted carefully in light of the strengths and limitations of these approaches. We propose to expand the definition of the Candidatus taxonomy to include taxa, from the phylum level to the species level, that are described genomically, particularly when genomic work is coupled with advanced molecular ecology approaches to probe metabolic functions in situ. This system would preserve the rigor and value of traditional microbial systematics while enabling growth of a provisional taxonomic structure to facilitate communication about "dark" lineages on the tree of life.}, }
@article {pmid25916483, year = {2015}, author = {Gertler, C and Bargiela, R and Mapelli, F and Han, X and Chen, J and Hai, T and Amer, RA and Mahjoubi, M and Malkawi, H and Magagnini, M and Cherif, A and Abdel-Fattah, YR and Kalogerakis, N and Daffonchio, D and Ferrer, M and Golyshin, PN}, title = {Conversion of Uric Acid into Ammonium in Oil-Degrading Marine Microbial Communities: a Possible Role of Halomonads.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {724-740}, pmid = {25916483}, issn = {1432-184X}, mesh = {Ammonium Compounds/*metabolism ; Bacteria/*genetics/metabolism ; Biodegradation, Environmental ; DNA, Bacterial/genetics/metabolism ; Jordan ; Mediterranean Sea ; Microbial Consortia/*genetics ; Petroleum/metabolism ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics/metabolism ; Sequence Analysis, DNA ; Uric Acid/*metabolism ; }, abstract = {Uric acid is a promising hydrophobic nitrogen source for biostimulation of microbial activities in oil-impacted marine environments. This study investigated metabolic processes and microbial community changes in a series of microcosms using sediment from the Mediterranean and the Red Sea amended with ammonium and uric acid. Respiration, emulsification, ammonium and protein concentration measurements suggested a rapid production of ammonium from uric acid accompanied by the development of microbial communities containing hydrocarbonoclastic bacteria after 3 weeks of incubation. About 80 % of uric acid was converted to ammonium within the first few days of the experiment. Microbial population dynamics were investigated by Ribosomal Intergenic Spacer Analysis and Illumina sequencing as well as by culture-based techniques. Resulting data indicated that strains related to Halomonas spp. converted uric acid into ammonium, which stimulated growth of microbial consortia dominated by Alcanivorax spp. and Pseudomonas spp. Several strains of Halomonas spp. were isolated on uric acid as the sole carbon source showed location specificity. These results point towards a possible role of halomonads in the conversion of uric acid to ammonium utilized by hydrocarbonoclastic bacteria.}, }
@article {pmid25914693, year = {2015}, author = {Weimer, PJ}, title = {Redundancy, resilience, and host specificity of the ruminal microbiota: implications for engineering improved ruminal fermentations.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {296}, pmid = {25914693}, issn = {1664-302X}, abstract = {The ruminal microbial community is remarkably diverse, containing 100s of different bacterial and archaeal species, plus many species of fungi and protozoa. Molecular studies have identified a "core microbiome" dominated by phyla Firmicutes and Bacteroidetes, but also containing many other taxa. The rumen provides an ideal laboratory for studies on microbial ecology and the demonstration of ecological principles. In particular, the microbial community demonstrates both redundancy (overlap of function among multiple species) and resilience (resistance to, and capacity to recover from, perturbation). These twin properties provide remarkable stability that maintains digestive function for the host across a range of feeding and management conditions, but they also provide a challenge to engineering the rumen for improved function (e.g., improved fiber utilization or decreased methane production). Direct ruminal dosing or feeding of probiotic strains often fails to establish the added strains, due to intensive competition and amensalism from the indigenous residents that are well-adapted to the historical conditions within each rumen. Known exceptions include introduced strains that can fill otherwise unoccupied niches, as in the case of specialist bacteria that degrade phytotoxins such as mimosine or fluoroacetate. An additional complicating factor in manipulating the ruminal fermentation is the individuality or host specificity of the microbiota, in which individual animals contain a particular community whose species composition is capable of reconstituting itself, even following a near-total exchange of ruminal contents from another herd mate maintained on the same diet. Elucidation of the interactions between the microbial community and the individual host that establish and maintain this specificity may provide insights into why individual hosts vary in production metrics (e.g., feed efficiency or milk fat synthesis), and how to improve herd performance.}, }
@article {pmid25914678, year = {2015}, author = {Chow, CE and Winget, DM and White, RA and Hallam, SJ and Suttle, CA}, title = {Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {265}, pmid = {25914678}, issn = {1664-302X}, abstract = {Viral diversity and virus-host interactions in oxygen-starved regions of the ocean, also known as oxygen minimum zones (OMZs), remain relatively unexplored. Microbial community metabolism in OMZs alters nutrient and energy flow through marine food webs, resulting in biological nitrogen loss and greenhouse gas production. Thus, viruses infecting OMZ microbes have the potential to modulate community metabolism with resulting feedback on ecosystem function. Here, we describe viral communities inhabiting oxic surface (10 m) and oxygen-starved basin (200 m) waters of Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia using viral metagenomics and complete viral fosmid sequencing on samples collected between April 2007 and April 2010. Of 6459 open reading frames (ORFs) predicted across all 34 viral fosmids, 77.6% (n = 5010) had no homology to reference viral genomes. These fosmids recruited a higher proportion of viral metagenomic sequences from Saanich Inlet than from nearby northeastern subarctic Pacific Ocean (Line P) waters, indicating differences in the viral communities between coastal and open ocean locations. While functional annotations of fosmid ORFs were limited, recruitment to NCBI's non-redundant "nr" database and publicly available single-cell genomes identified putative viruses infecting marine thaumarchaeal and SUP05 proteobacteria to provide potential host linkages with relevance to coupled biogeochemical cycling processes in OMZ waters. Taken together, these results highlight the power of coupled analyses of multiple sequence data types, such as viral metagenomic and fosmid sequence data with prokaryotic single cell genomes, to chart viral diversity, elucidate genomic and ecological contexts for previously unclassifiable viral sequences, and identify novel host interactions in natural and engineered ecosystems.}, }
@article {pmid25913884, year = {2015}, author = {Saha, S and Badhe, N and De Vrieze, J and Biswas, R and Nandy, T}, title = {Methanol induces low temperature resilient methanogens and improves methane generation from domestic wastewater at low to moderate temperatures.}, journal = {Bioresource technology}, volume = {189}, number = {}, pages = {370-378}, doi = {10.1016/j.biortech.2015.04.056}, pmid = {25913884}, issn = {1873-2976}, mesh = {Batch Cell Culture Techniques ; Biological Oxygen Demand Analysis ; Bioreactors/microbiology ; *Cold Temperature ; Methane/*biosynthesis ; Methanobacteriales/drug effects/*metabolism ; Methanol/*pharmacology ; Models, Theoretical ; Real-Time Polymerase Chain Reaction ; Sewage/microbiology ; Time Factors ; Wastewater/*microbiology ; }, abstract = {Low temperature (<20 °C) limits bio-methanation of sewage. Literature shows that hydrogenotrophic methanogens can adapt themselves to low temperature and methanol is a preferred substrate by methanogens in cold habitats. The study hypothesizes that methanol can induce the growth of low-temperature resilient, methanol utilizing, hydrogenotrophs in UASB reactor. The hypothesis was tested in field conditions to evaluate the impact of seasonal temperature variations on methane yield in the presence and absence of methanol. Results show that 0.04% (v/v) methanol increased methane up to 15 times and its effect was more pronounced at lower temperatures. The qPCR analysis showed the presence of Methanobacteriales along with Methanosetaceae in large numbers. This indicates methanol induced the growth of both the hydrogenotrophic and acetoclastic groups through direct and indirect routes, respectively. This study thus demonstrated that methanol can impart resistance in methanogenic biomass to low temperature and can improve performance of UASB reactor.}, }
@article {pmid25913208, year = {2015}, author = {Charlop-Powers, Z and Brady, SF}, title = {phylogeo: an R package for geographic analysis and visualization of microbiome data.}, journal = {Bioinformatics (Oxford, England)}, volume = {31}, number = {17}, pages = {2909-2911}, pmid = {25913208}, issn = {1367-4811}, support = {F32 AI110029/AI/NIAID NIH HHS/United States ; U01 GM110714/GM/NIGMS NIH HHS/United States ; AI110029/AI/NIAID NIH HHS/United States ; GM077516/GM/NIGMS NIH HHS/United States ; }, mesh = {*Computer Graphics ; Data Interpretation, Statistical ; Humans ; *Metagenome ; Microbiota/*genetics ; *Phylogeny ; *Programming Languages ; Sequence Analysis, DNA/*methods ; *Software ; Web Browser ; }, abstract = {MOTIVATION: We have created an R package named phylogeo that provides a set of geographic utilities for sequencing-based microbial ecology studies. Although the geographic location of samples is an important aspect of environmental microbiology, none of the major software packages used in processing microbiome data include utilities that allow users to map and explore the spatial dimension of their data. phylogeo solves this problem by providing a set of plotting and mapping functions that can be used to visualize the geographic distribution of samples, to look at the relatedness of microbiomes using ecological distance, and to map the geographic distribution of particular sequences. By extending the popular phyloseq package and using the same data structures and command formats, phylogeo allows users to easily map and explore the geographic dimensions of their data from the R programming language.<br><br>phylogeo is documented and freely available http://zachcp.github.io/phylogeo<br><br>CONTACT: : zcharlop@rockefeller.edu.}, }
@article {pmid25912922, year = {2015}, author = {İnceoğlu, &#xd6; and Llirós, M and Crowe, SA and García-Armisen, T and Morana, C and Darchambeau, F and Borges, AV and Descy, JP and Servais, P}, title = {Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {596-611}, pmid = {25912922}, issn = {1432-184X}, mesh = {Archaea/genetics/*physiology ; Archaeal Proteins/genetics ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; Bacterial Proteins/genetics ; Democratic Republic of the Congo ; Lakes/*microbiology ; *Microbiota ; Phylogeny ; RNA, Archaeal ; RNA, Bacterial ; Real-Time Polymerase Chain Reaction ; Rwanda ; Seasons ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; }, abstract = {The microbial community composition in meromictic Lake Kivu, with one of the largest CH4 reservoirs, was studied using 16S rDNA and ribosomal RNA (rRNA) pyrosequencing during the dry and rainy seasons. Highly abundant taxa were shared in a high percentage between bulk (DNA-based) and active (RNA-based) bacterial communities, whereas a high proportion of rare species was detected only in either an active or bulk community, indicating the existence of a potentially active rare biosphere and the possible underestimation of diversity detected when using only one nucleic acid pool. Most taxa identified as generalists were abundant, and those identified as specialists were more likely to be rare in the bulk community. The overall number of environmental parameters that could explain the variation was higher for abundant taxa in comparison to rare taxa. Clustering analysis based on operational taxonomic units (OTUs at 0.03 cutoff) level revealed significant and systematic microbial community composition shifts with depth. In the oxic zone, Actinobacteria were found highly dominant in the bulk community but not in the metabolically active community. In the oxic-anoxic transition zone, highly abundant potentially active Nitrospira and Methylococcales were observed. The co-occurrence of potentially active sulfur-oxidizing and sulfate-reducing bacteria in the anoxic zone may suggest the presence of an active yet cryptic sulfur cycle.}, }
@article {pmid25912797, year = {2015}, author = {Zhuang, WQ and Fitts, JP and Ajo-Franklin, CM and Maes, S and Alvarez-Cohen, L and Hennebel, T}, title = {Recovery of critical metals using biometallurgy.}, journal = {Current opinion in biotechnology}, volume = {33}, number = {}, pages = {327-335}, pmid = {25912797}, issn = {1879-0429}, support = {P42 ES004705/ES/NIEHS NIH HHS/United States ; }, mesh = {Ecosystem ; Metals/*metabolism ; Solid Waste ; Wastewater/microbiology ; }, abstract = {The increased development of green low-carbon energy technologies that require platinum group metals (PGMs) and rare earth elements (REEs), together with the geopolitical challenges to sourcing these metals, has spawned major governmental and industrial efforts to rectify current supply insecurities. As a result of the increasing critical importance of PGMs and REEs, environmentally sustainable approaches to recover these metals from primary ores and secondary streams are needed. In this review, we define the sources and waste streams from which PGMs and REEs can potentially be sustainably recovered using microorganisms, and discuss the metal-microbe interactions most likely to form the basis of different environmentally friendly recovery processes. Finally, we highlight the research needed to address challenges to applying the necessary microbiology for metal recovery given the physical and chemical complexities of specific streams.}, }
@article {pmid25912513, year = {2015}, author = {Rothballer, M and Picot, M and Sieper, T and Arends, JB and Schmid, M and Hartmann, A and Boon, N and Buisman, CJ and Barrière, F and Strik, DP}, title = {Monophyletic group of unclassified γ-Proteobacteria dominates in mixed culture biofilm of high-performing oxygen reducing biocathode.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {106}, number = {Pt A}, pages = {167-176}, doi = {10.1016/j.bioelechem.2015.04.004}, pmid = {25912513}, issn = {1878-562X}, mesh = {Bioelectric Energy Sources/*microbiology ; Biofilms/*growth &amp; development ; Electrodes ; Gammaproteobacteria/genetics/*metabolism/physiology ; Oxidation-Reduction ; Oxygen/*metabolism ; RNA, Ribosomal, 16S/genetics ; Surface Properties ; }, abstract = {Several mixed microbial communities have been reported to show robust bioelectrocatalysis of oxygen reduction over time at applicable operation conditions. However, clarification of electron transfer mechanism(s) and identification of essential micro-organisms have not been realised. Therefore, the objective of this study was to shape oxygen reducing biocathodes with different microbial communities by means of surface modification using the electrochemical reduction of two different diazonium salts in order to discuss the relation of microbial composition and performance. The resulting oxygen reducing mixed culture biocathodes had complex bacterial biofilms variable in size and shape as observed by confocal and electron microscopy. Sequence analysis of ribosomal 16S rDNA revealed a putative correlation between the abundance of certain microbiota and biocathode performance. The best performing biocathode developed on the unmodified graphite electrode and reached a high current density for oxygen reducing biocathodes at neutral pH (0.9 A/m(2)). This correlated with the highest domination (60.7%) of a monophyletic group of unclassified γ-Proteobacteria. These results corroborate earlier reports by other groups, however, higher current densities and higher presence of these unclassified bacteria were observed in this work. Therefore, members of this group are likely key-players for highly performing oxygen reducing biocathodes.}, }
@article {pmid25911507, year = {2015}, author = {Lossouarn, J and Dupont, S and Gorlas, A and Mercier, C and Bienvenu, N and Marguet, E and Forterre, P and Geslin, C}, title = {An abyssal mobilome: viruses, plasmids and vesicles from deep-sea hydrothermal vents.}, journal = {Research in microbiology}, volume = {166}, number = {10}, pages = {742-752}, doi = {10.1016/j.resmic.2015.04.001}, pmid = {25911507}, issn = {1769-7123}, mesh = {Archaea/genetics/isolation &amp; purification ; Bacteria/genetics/isolation &amp; purification ; Hydrothermal Vents/*microbiology/*virology ; *Interspersed Repetitive Sequences ; Phylogeny ; *Plasmids ; Seawater/microbiology ; Viruses/genetics/isolation &amp; purification ; }, abstract = {Mobile genetic elements (MGEs) such as viruses, plasmids, vesicles, gene transfer agents (GTAs), transposons and transpovirions, which collectively represent the mobilome, interact with cellular organisms from all three domains of life, including those thriving in the most extreme environments. While efforts have been made to better understand deep-sea vent microbial ecology, our knowledge of the mobilome associated with prokaryotes inhabiting deep-sea hydrothermal vents remains limited. Here we focus on the abyssal mobilome by reviewing accumulating data on viruses, plasmids and vesicles associated with thermophilic and hyperthermophilic Bacteria and Archaea present in deep-sea hydrothermal vents.}, }
@article {pmid25911484, year = {2015}, author = {Zhang, B and Penton, CR and Xue, C and Wang, Q and Zheng, T and Tiedje, JM}, title = {Evaluation of the Ion Torrent Personal Genome Machine for Gene-Targeted Studies Using Amplicons of the Nitrogenase Gene nifH.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {13}, pages = {4536-4545}, pmid = {25911484}, issn = {1098-5336}, mesh = {*Biota ; Diagnostic Errors ; Molecular Biology/*methods ; Oxidoreductases/*genetics ; Sequence Analysis, DNA/*methods ; *Soil Microbiology ; Zea mays/growth &amp; development ; }, abstract = {The sequencing chips and kits of the Ion Torrent Personal Genome Machine (PGM), which employs semiconductor technology to measure pH changes in polymerization events, have recently been upgraded. The quality of PGM sequences has not been reassessed, and results have not been compared in the context of a gene-targeted microbial ecology study. To address this, we compared sequence profiles across available PGM chips and chemistries and with 454 pyrosequencing data by determining error types and rates and diazotrophic community structures. The PGM was then used to assess differences in nifH-harboring bacterial community structure among four corn-based cropping systems. Using our suggested filters from mock community analyses, the overall error rates were 0.62, 0.36, and 0.39% per base for chips 318 and 314 with the 400-bp kit and chip 318 with the Hi-Q chemistry, respectively. Compared with the 400-bp kit, the Hi-Q kit reduced indel rates by 28 to 59% and produced one to seven times more reads acceptable for downstream analyses. The PGM produced higher frameshift rates than pyrosequencing that were corrected by the RDP FrameBot tool. Significant differences among platforms were identified, although the diversity indices and overall site-based conclusions remained similar. For the cropping system analyses, a total of 6,182 unique NifH operational taxonomic units at 5% amino acid dissimilarity were obtained. The current crop type, as well as the crop rotation history, significantly influenced the composition of the soil diazotrophic community detected.}, }
@article {pmid25910603, year = {2015}, author = {Wang, Z and Liu, L and Guo, F and Zhang, T}, title = {Deciphering Cyanide-Degrading Potential of Bacterial Community Associated with the Coking Wastewater Treatment Plant with a Novel Draft Genome.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {701-709}, pmid = {25910603}, issn = {1432-184X}, mesh = {Bacteria/*classification/*genetics ; Coke/analysis ; Cyanides/metabolism ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Waste Disposal, Fluid ; Wastewater/analysis/*microbiology ; }, abstract = {Biotreatment processes fed with coking wastewater often encounter insufficient removal of pollutants, such as ammonia, phenols, and polycyclic aromatic hydrocarbons (PAHs), especially for cyanides. However, only a limited number of bacterial species in pure cultures have been confirmed to metabolize cyanides, which hinders the improvement of these processes. In this study, a microbial community of activated sludge enriched in a coking wastewater treatment plant was analyzed using 454 pyrosequencing and Illumina sequencing to characterize the potential cyanide-degrading bacteria. According to the classification of these pyro-tags, targeting V3/V4 regions of 16S rRNA gene, half of them were assigned to the family Xanthomonadaceae, implying that Xanthomonadaceae bacteria are well-adapted to coking wastewater. A nearly complete draft genome of the dominant bacterium was reconstructed from metagenome of this community to explore cyanide metabolism based on analysis of the genome. The assembled 16S rRNA gene from this draft genome showed that this bacterium was a novel species of Thermomonas within Xanthomonadaceae, which was further verified by comparative genomics. The annotation using KEGG and Pfam identified genes related to cyanide metabolism, including genes responsible for the iron-harvesting system, cyanide-insensitive terminal oxidase, cyanide hydrolase/nitrilase, and thiosulfate:cyanide transferase. Phylogenetic analysis showed that these genes had homologs in previously identified genomes of bacteria within Xanthomonadaceae and even presented similar gene cassettes, thus implying an inherent cyanide-decomposing potential. The findings of this study expand our knowledge about the bacterial degradation of cyanide compounds and will be helpful in the remediation of cyanides contamination.}, }
@article {pmid25910602, year = {2015}, author = {Porter, MD and Andrus, JM and Bartolerio, NA and Rodriguez, LF and Zhang, Y and Zilles, JL and Kent, AD}, title = {Seasonal Patterns in Microbial Community Composition in Denitrifying Bioreactors Treating Subsurface Agricultural Drainage.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {710-723}, pmid = {25910602}, issn = {1432-184X}, mesh = {Agriculture ; *Bacterial Physiological Phenomena ; Bioreactors/*microbiology ; Denitrification ; Fungi/*physiology ; Illinois ; *Microbiota ; Seasons ; Water Pollutants, Chemical/metabolism ; }, abstract = {Denitrifying bioreactors, consisting of water flow control structures and a woodchip-filled trench, are a promising approach for removing nitrate from agricultural subsurface or tile drainage systems. To better understand the seasonal dynamics and the ecological drivers of the microbial communities responsible for denitrification in these bioreactors, we employed microbial community "fingerprinting" techniques in a time-series examination of three denitrifying bioreactors over 2 years, looking at bacteria, fungi, and the denitrifier functional group responsible for the final step of complete denitrification. Our analysis revealed that microbial community composition responds to depth and seasonal variation in moisture content and inundation of the bioreactor media, as well as temperature. Using a geostatistical analysis approach, we observed recurring temporal patterns in bacterial and denitrifying bacterial community composition in these bioreactors, consistent with annual cycling. The fungal communities were more stable, having longer temporal autocorrelations, and did not show significant annual cycling. These results suggest a recurring seasonal cycle in the denitrifying bioreactor microbial community, likely due to seasonal variation in moisture content.}, }
@article {pmid25910186, year = {2015}, author = {Rossi, O and Khan, MT and Schwarzer, M and Hudcovic, T and Srutkova, D and Duncan, SH and Stolte, EH and Kozakova, H and Flint, HJ and Samsom, JN and Harmsen, HJ and Wells, JM}, title = {Faecalibacterium prausnitzii Strain HTF-F and Its Extracellular Polymeric Matrix Attenuate Clinical Parameters in DSS-Induced Colitis.}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0123013}, pmid = {25910186}, issn = {1932-6203}, mesh = {Animals ; Antigens, Surface/metabolism ; Colitis/chemically induced/genetics/immunology/metabolism/*microbiology ; Cytokines/genetics/metabolism ; Dendritic Cells/immunology/metabolism ; Dextran Sulfate/adverse effects ; Disease Models, Animal ; Extracellular Matrix/*metabolism ; Female ; Forkhead Transcription Factors/genetics/metabolism ; Inflammation Mediators/metabolism ; Inflammatory Bowel Diseases/etiology/metabolism/pathology ; Intestinal Mucosa/metabolism/microbiology/pathology ; Lymph Nodes/immunology/metabolism ; Mice ; Phenotype ; Ruminococcus/*metabolism/ultrastructure ; Spleen/immunology/metabolism ; Toll-Like Receptor 2/genetics/metabolism ; Transcription, Genetic ; }, abstract = {A decrease in the abundance and biodiversity of intestinal bacteria within the Firmicutes phylum has been associated with inflammatory bowel disease (IBD). In particular, the anti-inflammatory bacterium Faecalibacterium prausnitzii, member of the Firmicutes phylum and one of the most abundant species in healthy human colon, is underrepresented in the microbiota of IBD patients. The aim of this study was to investigate the immunomodulatory properties of F. prausnitzii strain A2-165, the biofilm forming strain HTF-F and the extracellular polymeric matrix (EPM) isolated from strain HTF-F. For this purpose, the immunomodulatory properties of the F. prausnitzii strains and the EPM were studied in vitro using human monocyte-derived dendritic cells. Then, the capacity of the F. prausnitzii strains and the EPM of HTF-F to suppress inflammation was assessed in vivo in the mouse dextran sodium sulphate (DSS) colitis model. The F. prausnitzii strains and the EPM had anti-inflammatory effects on the clinical parameters measured in the DSS model but with different efficacy. The immunomodulatory effects of the EPM were mediated through the TLR2-dependent modulation of IL-12 and IL-10 cytokine production in antigen presenting cells, suggesting that it contributes to the anti-inflammatory potency of F. prausnitzii HTF-F. The results show that F. prausnitzii HTF-F and its EPM may have a therapeutic use in IBD.}, }
@article {pmid25908708, year = {2015}, author = {Vishnuvardhan Reddy, S and Thirumala, M and Farooq, M}, title = {Bacillus caseinilyticus sp. nov., an alkali- and thermotolerant bacterium isolated from a soda lake.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {65}, number = {8}, pages = {2441-2446}, doi = {10.1099/ijs.0.000275}, pmid = {25908708}, issn = {1466-5034}, mesh = {Alkalies/chemistry ; Bacillus/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; Cell Wall/chemistry ; DNA, Bacterial/genetics ; Diaminopimelic Acid/chemistry ; Fatty Acids/chemistry ; India ; Lakes/microbiology ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Peptidoglycan/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry ; *Water Microbiology ; }, abstract = {A novel Gram-stain-positive, rod-shaped, motile, endospore-forming and proteolytic bacterial strain, SPT, was isolated from Lonar soda lake, in India. On the basis of 16S rRNA gene sequence analysis it was identified as belonging to the class Firmibacteria and was most closely related to Bacillus cellulosilyticus DSM 2522T (96.7%) and other members of the genus Bacillus (< 95.9%). Strain SPT was catalase- and oxidase-positive. The cell-wall peptidoglycan of strain SPT contained meso-diaminopimelic acid. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three phospholipids, two aminolipids and two unknown lipids. The predominant isoprenoid quinone was MK-7. Anteiso-C15 : 0 (26.8%) was the predominant fatty acid and significant proportions (>5%) of iso-C15 : 0 (20.9%), C16 : 1ω7c alcohol (6.3%), iso-C16 : 0 (6.3%) and anteiso-C17 : 0 (5.3 %) were also detected in strain SPT. The DNA G+C content of strain SPT was 38.9 mol%. The results of phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strain SPT from all other members of the genus Bacillus. Strain SPT represents a novel member of the genus Bacillus, for which the name Bacilluscaseinilyticus sp. nov. is proposed. The type strain is SPT (= MCC 2612T = JCM 30246T).}, }
@article {pmid25907678, year = {2015}, author = {Lax, S and Gilbert, JA}, title = {Hospital-associated microbiota and implications for nosocomial infections.}, journal = {Trends in molecular medicine}, volume = {21}, number = {7}, pages = {427-432}, doi = {10.1016/j.molmed.2015.03.005}, pmid = {25907678}, issn = {1471-499X}, mesh = {Cross Infection/epidemiology ; Environmental Microbiology ; Hospitals/*statistics &amp; numerical data ; Humans ; Microbiota/*physiology ; }, abstract = {The rise of high-throughput sequencing technologies and culture-independent microbial surveys has the potential to revolutionize our understanding of how microbes colonize, move about, and evolve in hospital environments. Genome analysis of individual organisms, characterization of population dynamics, and microbial community ecology are facilitating the identification of novel pathogens, the tracking of disease outbreaks, and the study of the evolution of antibiotic resistance. Here we review the recent applications of these methods to microbial ecology studies in hospitals and discuss their potential to influence hospital management policy and practice and to reduce nosocomial infections and the spread of antibiotic resistance.}, }
@article {pmid25907143, year = {2015}, author = {Liberti, J and Sapountzis, P and Hansen, LH and Sørensen, SJ and Adams, RM and Boomsma, JJ}, title = {Bacterial symbiont sharing in Megalomyrmex social parasites and their fungus-growing ant hosts.}, journal = {Molecular ecology}, volume = {24}, number = {12}, pages = {3151-3169}, pmid = {25907143}, issn = {1365-294X}, support = {323085/ERC_/European Research Council/International ; }, mesh = {Actinomycetales/*classification ; Animals ; Ants/classification/*microbiology ; DNA, Bacterial/genetics ; Fungi ; Genotype ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; }, abstract = {Bacterial symbionts are important fitness determinants of insects. Some hosts have independently acquired taxonomically related microbes to meet similar challenges, but whether distantly related hosts that live in tight symbiosis can maintain similar microbial communities has not been investigated. Varying degrees of nest sharing between Megalomyrmex social parasites (Solenopsidini) and their fungus-growing ant hosts (Attini) from the genera Cyphomyrmex, Trachymyrmex and Sericomyrmex allowed us to address this question, as both ant lineages rely on the same fungal diet, interact in varying intensities and are distantly related. We used tag-encoded FLX 454 pyrosequencing and diagnostic PCR to map bacterial symbiont diversity across the Megalomyrmex phylogenetic tree, which also contains free-living generalist predators. We show that social parasites and hosts share a subset of bacterial symbionts, primarily consisting of Entomoplasmatales, Bartonellaceae, Acinetobacter, Wolbachia and Pseudonocardia and that Entomoplasmatales and Bartonellaceae can co-infect specifically associated combinations of hosts and social parasites with identical 16S rRNA genotypes. We reconstructed in more detail the population-level infection dynamics for Entomoplasmatales and Bartonellaceae in Megalomyrmex symmetochus guest ants and their Sericomyrmex amabilis hosts. We further assessed the stability of the bacterial communities through a diet manipulation experiment and evaluated possible transmission modes in shared nests such as consumption of the same fungus garden food, eating of host brood by social parasites, trophallaxis and grooming interactions between the ants, or parallel acquisition from the same nest environment. Our results imply that cohabiting ant social parasites and hosts may obtain functional benefits from bacterial symbiont transfer even when they are not closely related.}, }
@article {pmid25906920, year = {2015}, author = {Tzanetakis, GN and Azcarate-Peril, MA and Zachaki, S and Panopoulos, P and Kontakiotis, EG and Madianos, PN and Divaris, K}, title = {Comparison of Bacterial Community Composition of Primary and Persistent Endodontic Infections Using Pyrosequencing.}, journal = {Journal of endodontics}, volume = {41}, number = {8}, pages = {1226-1233}, pmid = {25906920}, issn = {1878-3554}, support = {P30 DK034987/DK/NIDDK NIH HHS/United States ; P30 DK34987/DK/NIDDK NIH HHS/United States ; }, mesh = {Acute Disease ; Adult ; Chronic Disease ; Dental Pulp Cavity/*microbiology ; Female ; Greece ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Microbiota/genetics ; Pulpitis/*microbiology ; }, abstract = {INTRODUCTION: Elucidating the microbial ecology of endodontic infections (EIs) is a necessary step in developing effective intracanal antimicrobials. The aim of the present study was to investigate the bacterial composition of symptomatic and asymptomatic primary and persistent infections in a Greek population using high-throughput sequencing methods.<br><br>METHODS: 16S amplicon pyrosequencing of 48 root canal bacterial samples was conducted, and sequencing data were analyzed using an oral microbiome-specific and a generic (Greengenes) database. Bacterial abundance and diversity were examined by EI type (primary or persistent), and statistical analysis was performed by using non-parametric and parametric tests accounting for clustered data.<br><br>RESULTS: Bacteroidetes was the most abundant phylum in both infection groups. Significant, albeit weak associations of bacterial diversity were found, as measured by UniFrac distances with infection type (analyses of similarity, R = 0.087, P = .005) and symptoms (analyses of similarity, R = 0.055, P = .047). Persistent infections were significantly enriched for Proteobacteria and Tenericutes compared with primary ones; at the genus level, significant differences were noted for 14 taxa, including increased enrichment of persistent infections for Lactobacillus, Streptococcus, and Sphingomonas. More but less abundant phyla were identified using the Greengenes database; among those, Cyanobacteria (0.018%) and Acidobacteria (0.007%) were significantly enriched among persistent infections. Persistent infections showed higher phylogenetic diversity (PD) (asymptomatic: PD = 9.2, standard error [SE] = 1.3; symptomatic: PD = 8.2, SE = 0.7) compared with primary infections (asymptomatic: PD = 5.9, SE = 0.8; symptomatic: PD = 7.4, SE = 1.0).<br><br>CONCLUSIONS: The present study revealed a high bacterial diversity of EI and suggests that persistent infections may have more diverse bacterial communities than primary infections.}, }
@article {pmid25903990, year = {2015}, author = {Kaberdin, VR and Montánchez, I and Parada, C and Orruño, M and Arana, I and Barcina, I}, title = {Unveiling the Metabolic Pathways Associated with the Adaptive Reduction of Cell Size During Vibrio harveyi Persistence in Seawater Microcosms.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {689-700}, pmid = {25903990}, issn = {1432-184X}, mesh = {Adaptation, Biological ; *Gene Expression Regulation, Bacterial ; *Metabolic Networks and Pathways ; Real-Time Polymerase Chain Reaction ; Seawater/*microbiology ; Vibrio/cytology/genetics/*physiology ; }, abstract = {Owing to their ubiquitous presence and ability to act as primary or opportunistic pathogens, Vibrio species greatly contribute to the diversity and evolution of marine ecosystems. This study was aimed at unveiling the cellular strategies enabling the marine gammaproteobacterium Vibrio harveyi to adapt and persist in natural aquatic systems. We found that, although V. harveyi incubation in seawater microcosm at 20 °C for 2 weeks did not change cell viability and culturability, it led to a progressive reduction in the average cell size. Microarray analysis revealed that this morphological change was accompanied by a profound decrease in gene expression affecting the central carbon metabolism, major biosynthetic pathways, and energy production. In contrast, V. harveyi elevated expression of genes closely linked to the composition and function of cell envelope. In addition to triggering lipid degradation via the β-oxidation pathway and apparently promoting the use of endogenous fatty acids as a major energy and carbon source, V. harveyi upregulated genes involved in ancillary mechanisms important for sustaining iron homeostasis, cell resistance to the toxic effect of reactive oxygen species, and recycling of amino acids. The above adaptation mechanisms and morphological changes appear to represent the major hallmarks of the initial V. harveyi response to starvation.}, }
@article {pmid25902536, year = {2015}, author = {Barberán, A and Ladau, J and Leff, JW and Pollard, KS and Menninger, HL and Dunn, RR and Fierer, N}, title = {Continental-scale distributions of dust-associated bacteria and fungi.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {18}, pages = {5756-5761}, pmid = {25902536}, issn = {1091-6490}, mesh = {Aerosols ; Air Microbiology ; Allergens/*analysis ; Animals ; Atmosphere/chemistry ; Bacteria/*isolation &amp; purification ; Biodiversity ; Cities ; Dust/*analysis ; Environmental Monitoring/methods ; Feces ; Fungi/*isolation &amp; purification ; Geography ; Humans ; Multivariate Analysis ; Oceans and Seas ; Seasons ; Skin/microbiology ; Soil Microbiology ; United States ; Water Microbiology ; Wind ; }, abstract = {It has been known for centuries that microorganisms are ubiquitous in the atmosphere, where they are capable of long-distance dispersal. Likewise, it is well-established that these airborne bacteria and fungi can have myriad effects on human health, as well as the health of plants and livestock. However, we have a limited understanding of how these airborne communities vary across different geographic regions or the factors that structure the geographic patterns of near-surface microbes across large spatial scales. We collected dust samples from the external surfaces of ∼1,200 households located across the United States to understand the continental-scale distributions of bacteria and fungi in the near-surface atmosphere. The microbial communities were highly variable in composition across the United States, but the geographic patterns could be explained by climatic and soil variables, with coastal regions of the United States sharing similar airborne microbial communities. Although people living in more urbanized areas were not found to be exposed to distinct outdoor air microbial communities compared with those living in more rural areas, our results do suggest that urbanization leads to homogenization of the airborne microbiota, with more urban communities exhibiting less continental-scale geographic variability than more rural areas. These results provide our first insight into the continental-scale distributions of airborne microbes, which is information that could be used to identify likely associations between microbial exposures in outdoor air and incidences of disease in crops, livestock, and humans.}, }
@article {pmid25900619, year = {2015}, author = {Charlier, JB and Polese, C and Nouet, C and Carnol, M and Bosman, B and Krämer, U and Motte, P and Hanikenne, M}, title = {Zinc triggers a complex transcriptional and post-transcriptional regulation of the metal homeostasis gene FRD3 in Arabidopsis relatives.}, journal = {Journal of experimental botany}, volume = {66}, number = {13}, pages = {3865-3878}, pmid = {25900619}, issn = {1460-2431}, mesh = {5' Untranslated Regions/genetics ; Arabidopsis/drug effects/*genetics ; Arabidopsis Proteins/*genetics/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Plant/*drug effects ; *Genes, Plant ; Genotype ; Homeostasis/drug effects/*genetics ; Membrane Transport Proteins/*genetics/metabolism ; Protein Biosynthesis/drug effects ; RNA Stability/drug effects/genetics ; RNA, Messenger/genetics/metabolism ; Transcription Initiation Site ; Transcription, Genetic/*drug effects ; Zinc/*pharmacology ; }, abstract = {In Arabidopsis thaliana, FRD3 (FERRIC CHELATE REDUCTASE DEFECTIVE 3) plays a central role in metal homeostasis. FRD3 is among a set of metal homeostasis genes that are constitutively highly expressed in roots and shoots of Arabidopsis halleri, a zinc hyperaccumulating and hypertolerant species. Here, we examined the regulation of FRD3 by zinc in both species to shed light on the evolutionary processes underlying the evolution of hyperaccumulation in A. halleri. We combined gene expression studies with the use of β-glucuronidase and green fluorescent protein reporter constructs to compare the expression profile and transcriptional and post-transcriptional regulation of FRD3 in both species. The AtFRD3 and AhFRD3 genes displayed a conserved expression profile. In A. thaliana, alternative transcription initiation sites from two promoters determined transcript variants that were differentially regulated by zinc supply in roots and shoots to favour the most highly translated variant under zinc-excess conditions. In A. halleri, a single transcript variant with higher transcript stability and enhanced translation has been maintained. The FRD3 gene thus undergoes complex transcriptional and post-transcriptional regulation in Arabidopsis relatives. Our study reveals that a diverse set of mechanisms underlie increased gene dosage in the A. halleri lineage and illustrates how an environmental challenge can alter gene regulation.}, }
@article {pmid25898671, year = {2015}, author = {Chen, C and Bai, YH and Liang, JS and Yuan, LJ}, title = {[Application of FISH-NanoSIMS technique in environmental microbial ecology study].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {36}, number = {1}, pages = {244-251}, pmid = {25898671}, issn = {0250-3301}, mesh = {Bacteria/*isolation &amp; purification ; Carbon ; Carbon Isotopes/analysis ; In Situ Hybridization, Fluorescence ; Isotope Labeling ; Nitrogen ; Nitrogen Isotopes/analysis ; Pseudomonas/isolation &amp; purification ; Sewage/*microbiology ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {With the development of microbial ecology techniques, it is possible to analyze the distribution and function of microorganisms simultaneously in complex ecosystems. To explore the application of FISH-NanoSIMS in environmental microbial ecology study, our study used the stable isotope labeled compounds 13C-C6H12O6, and 15N-NH4Cl as C and N sources for cultivating the pure culture (manganese oxidizing bacteria, Pseudomonas sp. QJX-1) and environmental samples (the shallow soil and anaerobic sludge). FISH-NanoSIMS was used to detect the distribution of microorganisms and relatively quantify secondary ions (12C-, 13C-, 12C(14)N-, 12C15N-) in cultivated samples, in order to explore the utilization of C and N isotopes sources by the pure culture and microorganisms in environment samples. The results showed that the contents of 13C and 5N in the area of bacteria were significantly greater than the natural abundance in all samples. It indicated that Pseudomonas sp. QJX-1 and some specific bacteria in environmental samples could metabolize 13C-C6H12O6 and 15N-NH4C1. Furthermore, this study revealed that for Pseudomonas sp. QJX-1, the manganese oxidation only occurred when the carbon and nitrogen were consumed to a low level. For environmental samples, the bacterial nitrification and denitrification were both observed in the shallow soil and anaerobic sludge. In a word, our study demonstrated that the combination of FISH and NanoSIMS could simultaneously examine microbial distribution and microbial metabolic activity in environmental samples, which will help us to obtain the eco-physiology information of microbial community.}, }
@article {pmid25897347, year = {2015}, author = {Raghow, R}, title = {Ménage-à-trois of bariatric surgery, bile acids and the gut microbiome.}, journal = {World journal of diabetes}, volume = {6}, number = {3}, pages = {367-370}, pmid = {25897347}, issn = {1948-9358}, abstract = {Bariatric surgeries have emerged as highly effective treatments for obesity associated type-2 diabetes mellitus. Evidently, the desired therapeutic endpoints such as rates of weight loss, lower levels of glycated hemoglobin and remission of diabetes are achieved more rapidly and last longer following bariatric surgery, as opposed to drug therapies alone. In light of these findings, it has been suspected that in addition to causing weight loss dependent glucose intolerance, bariatric surgery induces other physiological changes that contribute to the alleviation of diabetes. However, the putative post-surgical neuro-hormonal pathways that underpin the therapeutic benefits of bariatric surgery remain undefined. In a recent report, Ryan and colleagues shed new light on the potential mechanisms that determine the salutary effects of bariatric surgery in mice. The authors demonstrated that the improved glucose tolerance and weight loss in mice after vertical sleeve gastrectomy (VSG) surgery were likely to be caused by post-surgical changes in circulating bile acids and farnesoid-X receptor (FXR) signaling, both of which were also mechanistically linked to changes in the microbial ecology of the gut. The authors arrived at this conclusion from a comparison of genome-wide, metabolic consequences of VSG surgery in obese wild type (WT) and FXR knockout mice. Gene expression in the distal small intestines of WT and FXR knockout mice revealed that the pathways regulating bile acid composition, nutrient metabolism and anti-oxidant defense were differentially altered by VSG surgery in WT and FXR(-/-) mice. Based on these data Ryan et al, hypothesized that bile acid homeostasis and FXR signaling were mechanistically linked to the gut microbiota that played a role in modulating post-surgical changes in total body mass and glucose tolerance. The authors' data provide a plausible explanation for putative weight loss-independent benefits of bariatric surgery and its relationship with metabolism of bile acids.}, }
@article {pmid25897029, year = {2015}, author = {Stella, NA and Lahr, RM and Brothers, KM and Kalivoda, EJ and Hunt, KM and Kwak, DH and Liu, X and Shanks, RM}, title = {Serratia marcescens Cyclic AMP Receptor Protein Controls Transcription of EepR, a Novel Regulator of Antimicrobial Secondary Metabolites.}, journal = {Journal of bacteriology}, volume = {197}, number = {15}, pages = {2468-2478}, pmid = {25897029}, issn = {1098-5530}, support = {2T32 EY017271/EY/NEI NIH HHS/United States ; EY08098/EY/NEI NIH HHS/United States ; AI085570/AI/NIAID NIH HHS/United States ; T32 EY017271/EY/NEI NIH HHS/United States ; P30 EY008098/EY/NEI NIH HHS/United States ; R01 AI085570/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Infective Agents/*metabolism ; Cyclic AMP/genetics/*metabolism ; Cyclic AMP Receptor Protein/genetics/*metabolism ; Depsipeptides/genetics/metabolism ; Gene Expression Regulation, Bacterial/*physiology ; Hemolysis ; Humans ; Molecular Sequence Data ; Movement ; Mutation ; Serratia marcescens/genetics/*metabolism ; Transcription Factors/genetics/*metabolism ; }, abstract = {UNLABELLED: Serratia marcescens generates secondary metabolites and secreted enzymes, and it causes hospital infections and community-acquired ocular infections. Previous studies identified cyclic AMP (cAMP) receptor protein (CRP) as an indirect inhibitor of antimicrobial secondary metabolites. Here, we identified a putative two-component regulator that suppressed crp mutant phenotypes. Evidence supports that the putative response regulator eepR was directly transcriptionally inhibited by cAMP-CRP. EepR and the putative sensor kinase EepS were necessary for the biosynthesis of secondary metabolites, including prodigiosin- and serratamolide-dependent phenotypes, swarming motility, and hemolysis. Recombinant EepR bound to the prodigiosin and serratamolide promoters in vitro. Together, these data introduce a novel regulator of secondary metabolites that directly connects the broadly conserved metabolism regulator CRP with biosynthetic genes that may contribute to competition with other microbes.<br><br>IMPORTANCE: This study identifies a new transcription factor that is directly controlled by a broadly conserved transcription factor, CRP. CRP is well studied in its role to help bacteria respond to the amount of nutrients in their environment. The new transcription factor EepR is essential for the bacterium Serratia marcescens to produce two biologically active compounds, prodigiosin and serratamolide. These two compounds are antimicrobial and may allow S. marcescens to compete for limited nutrients with other microorganisms. Results from this study tie together the CRP environmental nutrient sensor with a new regulator of antimicrobial compounds. Beyond microbial ecology, prodigiosin and serratamolide have therapeutic potential; therefore, understanding their regulation is important for both applied and basic science.}, }
@article {pmid25896428, year = {2015}, author = {Grasa, L and Abecia, L and Forcén, R and Castro, M and de Jalón, JA and Latorre, E and Alcalde, AI and Murillo, MD}, title = {Antibiotic-Induced Depletion of Murine Microbiota Induces Mild Inflammation and Changes in Toll-Like Receptor Patterns and Intestinal Motility.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {835-848}, pmid = {25896428}, issn = {1432-184X}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Female ; Gastrointestinal Microbiome/*drug effects ; *Gastrointestinal Motility ; Gene Expression Regulation ; Inflammation/*immunology/microbiology ; Lipopolysaccharides/pharmacology ; Mice ; Mice, Inbred C57BL ; Toll-Like Receptors/*genetics/metabolism ; }, abstract = {We examine the impact of changes in microbiota induced by antibiotics on intestinal motility, gut inflammatory response, and the function and expression of toll-like receptors (TLRs). Alterations in mice intestinal microbiota were induced by antibiotics and evaluated by q-PCR and DGGE analysis. Macroscopic and microscopic assessments of the intestine were performed in control and antibiotic-treated mice. TLR expression was determined in the intestine by q-RT-PCR. Fecal parameter measurements, intestinal transit, and muscle contractility studies were performed to evaluate alterations in intestinal motility. Antibiotics reduced the total bacterial quantity 1000-fold, and diversity was highly affected by treatment. Mice with microbiota depletion had less Peyer's patches, enlarged ceca, and mild gut inflammation. Treatment with antibiotics increased the expression of TLR4, TLR5, and TLR9 in the ileum and TLR3, TLR4, TLR6, TLR7, and TLR8 in the colon, and it reduced the expression of TLR2, TLR3, and TLR6 in the ileum and TLR2 and TLR9 in the colon. Antibiotics decreased fecal output, delayed the whole gut and colonic transit, and reduced the spontaneous contractions and the response to acetylcholine (ACh) in the ileum and colon. Activation of TLR4 by lipopolysaccharide (LPS) reverted the reduction of the spontaneous contractions induced by antibiotics in the ileum. Activation of TLR4 by LPS and TLR5 by flagellin reduced the response to ACh in the ileum in control mice. Our results confirm the role of the microbiota in the regulation of TLRs expression and shed light on the microbiota connection to motor intestinal alterations.}, }
@article {pmid25896427, year = {2015}, author = {Morin, S and Bonet, B and Corcoll, N and Guasch, H and Bottin, M and Coste, M}, title = {Cumulative Stressors Trigger Increased Vulnerability of Diatom Communities to Additional Disturbances.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {585-595}, pmid = {25896427}, issn = {1432-184X}, mesh = {*Biodiversity ; *Climate Change ; Diatoms/*physiology ; Environmental Monitoring ; Fertilizers/adverse effects ; France ; Hot Temperature/adverse effects ; Metals/adverse effects ; Rivers ; Seasons ; *Stress, Physiological ; Water Pollutants, Chemical/*adverse effects ; }, abstract = {Chronic, non-lethal stressors occurring gradually (in space or time) can result in cumulative impacts that are more dramatic than higher intensities or occasional critical levels of any single one of these stressors. The negative effects of the chronic stressors trigger lasting impacts that may grow in intensity and become problematic over time and/or to higher trophic levels. In rivers, aquatic organisms experience this type of cumulative stress along the up- to downstream gradient in natural and anthropogenic contaminants generally observed in inhabited watersheds. Diatoms are a major component of the periphyton in rivers; their richness and diversity in natural communities are directly related to their varied ecological preferences and sensitivity to disturbance. In this study, we monitored from 2003 to 2008 the changes in the diversity of taxonomic and non-taxonomic features along a small river (Riou-Mort, South West France), at three sites: one site upstream considered as a reference for this watershed, one intermediate site with high nutrient load, and one downstream site exposed to both nutrient and metal pollution. The cumulative impacts of nutrients plus metals led to a gradual decrease in species richness and diversity, and in a potential capacity to cope with additional stresses, e.g., climate change-related ones. This is reflected by a decrease in species richness downstream, more dramatic in the hot summer of 2003 than in cooler summers. With the increasingly protective environmental regulations (e.g., Water Framework Directive in Europe), accumulation of stresses on aquatic resources are recommended to receive increasing attention, in particular considering the expected changes in climate.}, }
@article {pmid25894918, year = {2015}, author = {Zakharevich, NV and Averina, OV and Klimina, KM and Kudryavtseva, AV and Kasianov, AS and Makeev, VJ and Danilenko, VN}, title = {Complete Genome Sequence of Bifidobacterium longum GT15: Identification and Characterization of Unique and Global Regulatory Genes.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {819-834}, pmid = {25894918}, issn = {1432-184X}, mesh = {Bifidobacterium/*genetics/metabolism ; Chromosome Mapping ; Chromosomes, Bacterial/*genetics/metabolism ; Epigenesis, Genetic ; *Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; Russia ; Sequence Analysis, DNA ; }, abstract = {In this study, we report the first completely annotated genome sequence of the Russia origin Bifidobacterium longum subsp. longum strain GT15. Comparative genomic analysis of this genome with other available completely annotated genome sequences of B. longum strains isolated from other countries has revealed a high degree of conservation and synteny across the entire genomes. However, it was discovered that the open reading frames to 35 genes were detected only from the B. longum GT15 genome and absent from other genomes B. longum strains (not of Russian origin). These so-called unique genes (UGs) represent a total length of 39,066 bp, with G + C content ranging from 37 to 65 %. Interestingly, certain genes were detected in other B. longum strains of Russian origin. In our analysis, we examined genes for global regulatory systems: proteins of toxin-antitoxin (TA) systems type II, serine/threonine protein kinases (STPKs) of eukaryotic type, and genes of the WhiB-like family proteins. In addition, we have made in silico analysis of all the most significant probiotic genes and considered genes involved in epigenetic regulation and genes responsible for producing various neuromediators. This genome sequence may elucidate the biology of this probiotic strain as a promising candidate for practical (pharmaceutical) applications.}, }
@article {pmid25893957, year = {2015}, author = {Sultanpuram, VR and Mothe, T and Mohammed, F}, title = {Nocardioides solisilvae sp. nov., isolated from a forest soil.}, journal = {Antonie van Leeuwenhoek}, volume = {107}, number = {6}, pages = {1599-1606}, doi = {10.1007/s10482-015-0455-x}, pmid = {25893957}, issn = {1572-9699}, mesh = {Actinobacteria/*classification/genetics/*isolation &amp; purification/physiology ; Aerobiosis ; Bacterial Typing Techniques ; Base Composition ; Cell Wall/chemistry ; Cluster Analysis ; Cytosol/chemistry ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fatty Acids/analysis ; Forests ; India ; Molecular Sequence Data ; Peptidoglycan/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analysis ; }, abstract = {A Gram-stain positive, rod shaped aerobic bacterial strain designated Ka25(T) was isolated from a forest soil sample near Kasol, Himachal Pradesh, India. Based on 16S rRNA gene sequence analysis it was identified that strain Ka25(T) belongs to the class Actinobacteria and is most closely related to Nocardioides daejeonensis KCTC 19772(T) (97.2 %), Nocardioides dubius JCM 13008(T) (96.9 %), Nocardioides psychrotolerans CGMCC 1.11156(T) (96.8 %), Nocardioides pacificus DSM 27278(T)(96.7 %) and Nocardioides daphniae JCM 16608(T)(96.4 %) sequence similarity respectively. The chemotaxonomic properties of strain Ka25(T) are consistent with those of the members of the genus Nocardioides: MK-8(H4) is the predominant menaquinone, iso-C16 : 0, iso-C17 : 0 and C18 : 1ω9c were identified as the predominant cellular fatty acids and the cell-wall peptidoglycan is based on LL-2,6-diaminopimelic acid. The DNA G+C content of strain Ka25(T) was determined to be 71.6 mol %. The results of the polyphasic taxonomic analysis allowed a clear differentiation of strain Ka25(T) from all other members of the genus Nocardioides. Strain Ka25(T) is thus considered to represent a novel member of the genus Nocardioides, for which the name Nocardioides solisilvae sp. nov. is proposed. The type strain is Ka25(T) (=KCTC39528(T) =MCC2762(T)).}, }
@article {pmid25892516, year = {2015}, author = {Park, YS and Dutta, S and Ann, M and Raaijmakers, JM and Park, K}, title = {Promotion of plant growth by Pseudomonas fluorescens strain SS101 via novel volatile organic compounds.}, journal = {Biochemical and biophysical research communications}, volume = {461}, number = {2}, pages = {361-365}, doi = {10.1016/j.bbrc.2015.04.039}, pmid = {25892516}, issn = {1090-2104}, mesh = {Alkenes/chemistry/isolation &amp; purification/metabolism ; *Plant Development ; Pseudomonas fluorescens/chemistry/*physiology ; Triticum/*growth &amp; development/*microbiology ; Volatile Organic Compounds/chemistry/isolation &amp; purification/*metabolism ; }, abstract = {Volatile organic compounds (VOCs) from plant growth-promoting rhizobacteria (PGPR) play key roles in modulating plant growth and induced systemic resistance (ISR) to pathogens. Despite their significance, the physiological functions of the specific VOCs produced by Pseudomonas fluorescens SS101 (Pf.SS101) have not been precisely elucidated. The effects of Pf.SS101 and its VOCs on augmentation of plant growth promotion were investigated in vitro and in planta. A significant growth promotion was observed in plants exposed Pf.SS101 under both conditions, suggesting that its VOCs play a key role in promoting plant growth. Solid-phase micro-extraction (SPME) and a gas chromatography-mass spectrophotometer (GC-MS) system were used to characterize the VOCs emitted by Pf.SS101 and 11 different compounds were detected in samples inoculated this bacterium, including 13-Tetradecadien-1-ol, 2-butanone and 2-Methyl-n-1-tridecene. Application of these compounds resulted in enhanced plant growth. This study suggests that Pf.SS101 promotes the growth of plants via the release of VOCs including 13-Tetradecadien-1-ol, 2-butanone and 2-Methyl-n-1-tridecene, thus increasing understanding of the role of VOCs in plant-bacterial inter-communication.}, }
@article {pmid25889523, year = {2015}, author = {Ho, VT and Zhao, J and Fleet, G}, title = {The effect of lactic acid bacteria on cocoa bean fermentation.}, journal = {International journal of food microbiology}, volume = {205}, number = {}, pages = {54-67}, doi = {10.1016/j.ijfoodmicro.2015.03.031}, pmid = {25889523}, issn = {1879-3460}, mesh = {Acetobacter/growth &amp; development/metabolism ; Anti-Bacterial Agents/pharmacology ; Cacao/*metabolism/*microbiology/*standards ; Ethanol/analysis/metabolism ; *Fermentation ; *Food Microbiology ; Humans ; Lactic Acid/analysis/metabolism ; Lactobacillus/drug effects/growth &amp; development ; Muramidase/pharmacology ; Nisin/pharmacology ; Taste ; }, abstract = {Cocoa beans (Theobroma cacao L.) are the raw material for chocolate production. Fermentation of cocoa pulp by microorganisms is crucial for developing chocolate flavor precursors. Yeasts conduct an alcoholic fermentation within the bean pulp that is essential for the production of good quality beans, giving typical chocolate characters. However, the roles of bacteria such as lactic acid bacteria and acetic acid bacteria in contributing to the quality of cocoa bean and chocolate are not fully understood. Using controlled laboratory fermentations, this study investigated the contribution of lactic acid bacteria to cocoa bean fermentation. Cocoa beans were fermented under conditions where the growth of lactic acid bacteria was restricted by the use of nisin and lysozyme. The resultant microbial ecology, chemistry and chocolate quality of beans from these fermentations were compared with those of indigenous (control) fermentations. The yeasts Hanseniaspora guilliermondii, Pichia kudriavzevii, Kluyveromyces marxianus and Saccharomyces cerevisiae, the lactic acid bacteria Lactobacillus plantarum, Lactobacillus pentosus and Lactobacillus fermentum and the acetic acid bacteria Acetobacter pasteurianus and Gluconobacter frateurii were the major species found in control fermentations. In fermentations with the presence of nisin and lysozyme, the same species of yeasts and acetic acid bacteria grew but the growth of lactic acid bacteria was prevented or restricted. These beans underwent characteristic alcoholic fermentation where the utilization of sugars and the production of ethanol, organic acids and volatile compounds in the bean pulp and nibs were similar for beans fermented in the presence of lactic acid bacteria. Lactic acid was produced during both fermentations but more so when lactic acid bacteria grew. Beans fermented in the presence or absence of lactic acid bacteria were fully fermented, had similar shell weights and gave acceptable chocolates with no differences in sensory rankings. It was concluded that lactic acid bacteria may not be necessary for successful cocoa fermentation.}, }
@article {pmid25889196, year = {2015}, author = {Logan, AC and Katzman, MA and Balanzá-Martínez, V}, title = {Natural environments, ancestral diets, and microbial ecology: is there a modern "paleo-deficit disorder"? Part II.}, journal = {Journal of physiological anthropology}, volume = {34}, number = {1}, pages = {9}, pmid = {25889196}, issn = {1880-6805}, mesh = {Activities of Daily Living ; *Anthropology, Physical ; *Diet, Paleolithic ; Ecology ; *Feeding Behavior ; Humans ; *Microbiota ; Nature ; *Nutritional Sciences ; Probiotics ; *Quality of Life ; Stress, Psychological ; }, abstract = {Famed microbiologist René J. Dubos (1901-1982) was an early pioneer in the developmental origins of health and disease (DOHaD) construct. In the 1960s, he conducted groundbreaking research concerning the ways in which early-life experience with nutrition, microbiota, stress, and other environmental variables could influence later-life health outcomes. He recognized the co-evolutionary relationship between microbiota and the human host. Almost 2 decades before the hygiene hypothesis, he suggested that children in developed nations were becoming too sanitized (vs. our ancestral past) and that scientists should determine whether the childhood environment should be "dirtied up in a controlled manner." He also argued that oft-celebrated growth chart increases via changes in the global food supply and dietary patterns should not be equated to quality of life and mental health. Here in the second part of our review, we reflect the words of Dubos off contemporary research findings in the areas of diet, the gut-brain-axis (microbiota and anxiety and depression) and microbial ecology. Finally, we argue, as Dubos did 40 years ago, that researchers should more closely examine the relevancy of silo-sequestered, reductionist findings in the larger picture of human quality of life. In the context of global climate change and the epidemiological transition, an allergy epidemic and psychosocial stress, our review suggests that discussions of natural environments, urbanization, biodiversity, microbiota, nutrition, and mental health, are often one in the same.}, }
@article {pmid25888294, year = {2015}, author = {Minogue, E and Tuite, NL and Smith, CJ and Reddington, K and Barry, T}, title = {A rapid culture independent methodology to quantitatively detect and identify common human bacterial pathogens associated with contaminated high purity water.}, journal = {BMC biotechnology}, volume = {15}, number = {1}, pages = {6}, pmid = {25888294}, issn = {1472-6750}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Bacterial Typing Techniques/*methods ; Burkholderia/classification/genetics/isolation &amp; purification ; DNA, Bacterial/analysis ; Humans ; Molecular Typing/*methods ; Multiplex Polymerase Chain Reaction ; Pseudomonas aeruginosa/classification/genetics/isolation &amp; purification ; Real-Time Polymerase Chain Reaction ; Serratia marcescens/classification/genetics/isolation &amp; purification ; Stenotrophomonas maltophilia/classification/genetics/isolation &amp; purification ; *Water Microbiology ; Water Purification ; }, abstract = {BACKGROUND: Water and High Purity Water (HPW) distribution systems can be contaminated with human pathogenic microorganisms. This biocontamination may pose a risk to human health as HPW is commonly used in the industrial, pharmaceutical and clinical sectors. Currently, routine microbiological testing of HPW is performed using slow and labour intensive traditional microbiological based techniques. There is a need to develop a rapid culture independent methodology to quantitatively detect and identify biocontamination associated with HPW.<br><br>RESULTS: A novel internally controlled 5-plex real-time PCR Nucleic Acid Diagnostics assay (NAD), was designed and optimised in accordance with Minimum Information for Publication of Quantitative Real-Time PCR Experiments guidelines, to rapidly detect, identify and quantify the human pathogenic bacteria Stenotrophomonas maltophilia, Burkholderia species, Pseudomonas aeruginosa and Serratia marcescens which are commonly associated with the biocontamination of water and water distribution systems. The specificity of the 5-plex assay was tested against genomic DNA isolated from a panel of 95 microorganisms with no cross reactivity observed. The analytical sensitivities of the S. maltophilia, B. cepacia, P. aeruginosa and the S. marcescens assays are 8.5, 5.7, 3.2 and 7.4 genome equivalents respectively. Subsequently, an analysis of HPW supplied by a Millipore Elix 35 water purification unit performed using standard microbiological methods revealed high levels of naturally occurring microbiological contamination. Five litre water samples from this HPW delivery system were also filtered and genomic DNA was purified directly from these filters. These DNA samples were then tested using the developed multiplex real-time PCR NAD assay and despite the high background microbiological contamination observed, both S. maltophilia and Burkholderia species were quantitatively detected and identified. At both sampling points the levels of both S. maltophilia and Burkholderia species present was above the threshold of 10 cfu/100 ml recommended by both EU and US guidelines.<br><br>CONCLUSIONS: The novel culture independent methodology described in this study allows for rapid (<5 h), quantitative detection and identification of these four human pathogens from biocontaminated water and HPW distribution systems. We propose that the described NAD assay and associated methodology could be applied to routine testing of water and HPW distribution systems to assure microbiological safety and high water quality standards.}, }
@article {pmid25888175, year = {2015}, author = {Yan, Y and Kuramae, EE and Klinkhamer, PG and van Veen, JA}, title = {Revisiting the dilution procedure used to manipulate microbial biodiversity in terrestrial systems.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {13}, pages = {4246-4252}, pmid = {25888175}, issn = {1098-5336}, mesh = {Bacteria/*classification/*genetics/growth &amp; development/isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {It is hard to assess experimentally the importance of microbial diversity in soil for the functioning of terrestrial ecosystems. An approach that is often used to make such assessment is the so-called dilution method. This method is based on the assumption that the biodiversity of the microbial community is reduced after dilution of a soil suspension and that the reduced diversity persists after incubation of more or less diluted inocula in soil. However, little is known about how the communities develop in soil after inoculation. In this study, serial dilutions of a soil suspension were made and reinoculated into the original soil previously sterilized by gamma irradiation. We determined the structure of the microbial communities in the suspensions and in the inoculated soils using 454-pyrosequencing of 16S rRNA genes. Upon dilution, several diversity indices showed that, indeed, the diversity of the bacterial communities in the suspensions decreased dramatically, with Proteobacteria as the dominant phylum of bacteria detected in all dilutions. The structure of the microbial community was changed considerably in soil, with Proteobacteria, Bacteroidetes, and Verrucomicrobia as the dominant groups in most diluted samples, indicating the importance of soil-related mechanisms operating in the assembly of the communities. We found unique operational taxonomic units (OTUs) even in the highest dilution in both the suspensions and the incubated soil samples. We conclude that the dilution approach reduces the diversity of microbial communities in soil samples but that it does not allow accurate predictions of the community assemblage during incubation of (diluted) suspensions in soil.}, }
@article {pmid25885431, year = {2015}, author = {Song, C and Sundqvist, G and Malm, E and de Bruijn, I and Kumar, A and van de Mortel, J and Bulone, V and Raaijmakers, JM}, title = {Lipopeptide biosynthesis in Pseudomonas fluorescens is regulated by the protease complex ClpAP.}, journal = {BMC microbiology}, volume = {15}, number = {}, pages = {29}, pmid = {25885431}, issn = {1471-2180}, mesh = {Gene Deletion ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Gene Regulatory Networks ; Lipopeptides/*biosynthesis ; Molecular Chaperones/genetics/*metabolism ; Proteome/analysis ; Pseudomonas fluorescens/*genetics/*metabolism ; Serine Proteases/genetics/*metabolism ; }, abstract = {BACKGROUND: Lipopeptides (LP) are structurally diverse compounds with potent surfactant and broad-spectrum antibiotic activities. In Pseudomonas and other bacterial genera, LP biosynthesis is governed by large multimodular nonribosomal peptide synthetases (NRPS). To date, relatively little is known about the regulatory genetic network of LP biosynthesis.<br><br>RESULTS: This study provides evidence that the chaperone ClpA, together with the serine protease ClpP, regulates the biosynthesis of the LP massetolide in Pseudomonas fluorescens SS101. Whole-genome transcriptome analyses of clpA and clpP mutants showed their involvement in the transcription of the NRPS genes massABC and the transcriptional regulator massAR. In addition, transcription of genes associated with cell wall and membrane biogenesis, energy production and conversion, amino acid transport and metabolism, and pilus assembly were altered by mutations in clpA and clpP. Proteome analysis allowed the identification of additional cellular changes associated to clpA and clpP mutations. The expression of proteins of the citrate cycle and the heat shock proteins DnaK and DnaJ were particularly affected. Combined with previous findings, these results suggest that the ClpAP complex regulates massetolide biosynthesis via the pathway-specific, LuxR-type regulator MassAR, the heat shock proteins DnaK and DnaJ, and proteins of the TCA cycle.<br><br>CONCLUSIONS: Combining transcriptome and proteome analyses provided new insights into the regulation of LP biosynthesis in P. fluorescens and led to the identification of specific missing links in the regulatory pathways.}, }
@article {pmid25880684, year = {2015}, author = {Grizard, S and Versteegh, MA and Ndithia, HK and Salles, JF and Tieleman, BI}, title = {Shifts in bacterial communities of eggshells and antimicrobial activities in eggs during incubation in a ground-nesting passerine.}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0121716}, pmid = {25880684}, issn = {1932-6203}, mesh = {Animals ; Anti-Infective Agents ; *Egg Shell ; *Eggs ; Passeriformes/microbiology/*physiology ; }, abstract = {Microbial invasion of egg contents is a cause of embryonic death. To counter infection risks, the embryo is protected physically by the eggshell and chemically by antimicrobial proteins. If microbial pressure drives embryo mortality, then females may have evolved, through natural selection, to adapt their immune investment into eggs. Although frequently hypothesized, this match between immune allocation and microorganisms has not been explored yet. To examine if correlations between microbes on eggs and immunity in eggs exist, we collected eggs from red-capped larks (Calandrella cinerea) and simultaneously examined their bacterial communities and antimicrobial components--pH, lysozyme and ovotransferrin--during natural incubation. Using molecular techniques, we find that bacterial communities are highly dynamic: bacterial abundance increases from the onset to late incubation, Shannon's α-diversity index increases during early incubation stages, and β-diversity analysis shows that communities from 1 day-old clutches are phylogenetically more similar to each other than the older ones. Regarding the antimicrobials, we notice a decrease of pH and lysozyme concentration, while ovotransferrin concentration increases during incubation. Interestingly, we show that two eggs of the same clutch share equivalent immune protection, independent of clutch age. Lastly, our results provide limited evidence of significant correlation between antimicrobial compounds and bacterial communities. Our study examined simultaneously, for the first time in a wild bird, the dynamics of bacterial communities present on eggshells and of albumen-associated antimicrobial components during incubation and investigated their relationship. However, the link between microorganisms and immunity of eggs remains to be elucidated further. Identifying invading microbes and their roles in embryo mortality, as well as understanding the role of the eggshell microbiome, might be key to better understand avian strategies of immune maternal investment.}, }
@article {pmid25880302, year = {2015}, author = {Kushwaha, SK and Manoharan, L and Meerupati, T and Hedlund, K and Ahrén, D}, title = {MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics.}, journal = {BMC bioinformatics}, volume = {16}, number = {1}, pages = {65}, pmid = {25880302}, issn = {1471-2105}, mesh = {Computational Biology/*methods ; DNA Primers/genetics ; Ecology ; Environment ; *Metagenome ; Metagenomics/*methods ; Sequence Analysis, DNA/methods ; *Software ; Soil/*chemistry ; }, abstract = {BACKGROUND: Massive sequencing of genes from different environments has evolved metagenomics as central to enhancing the understanding of the wide diversity of micro-organisms and their roles in driving ecological processes. Reduced cost and high throughput sequencing has made large-scale projects achievable to a wider group of researchers, though complete metagenome sequencing is still a daunting task in terms of sequencing as well as the downstream bioinformatics analyses. Alternative approaches such as targeted amplicon sequencing requires custom PCR primer generation, and is not scalable to thousands of genes or gene families.<br><br>RESULTS: In this study, we are presenting a web-based tool called MetCap that circumvents the limitations of amplicon sequencing of multiple genes by designing probes that are suitable for large-scale targeted metagenomics sequencing studies. MetCap provides a novel approach to target thousands of genes and genomic regions that could be used in targeted metagenomics studies. Automatic analysis of user-defined sequences is performed, and probes specifically designed for metagenome studies are generated. To illustrate the advantage of a targeted metagenome approach, we have generated more than 400,000 probes that match more than 300,000 [corrected] publicly available sequences related to carbon degradation, and used these probes for target sequencing in a soil metagenome study. The results show high enrichment of target genes and a successful capturing of the majority of gene families. MetCap is freely available to users from: http://soilecology.biol.lu.se/metcap/ .<br><br>CONCLUSION: MetCap is facilitating probe-based target enrichment as an easy and efficient alternative tool compared to complex primer-based enrichment for large-scale investigations of metagenomes. Our results have shown efficient large-scale target enrichment through MetCap-designed probes for a soil metagenome. The web service is suitable for any targeted metagenomics project that aims to study several genes simultaneously. The novel bioinformatics approach taken by the web service will enable researchers in microbial ecology to tap into the vast diversity of microbial communities using targeted metagenomics as a cost-effective alternative to whole metagenome sequencing.}, }
@article {pmid25877793, year = {2015}, author = {Simonin, M and Le Roux, X and Poly, F and Lerondelle, C and Hungate, BA and Nunan, N and Niboyet, A}, title = {Coupling Between and Among Ammonia Oxidizers and Nitrite Oxidizers in Grassland Mesocosms Submitted to Elevated CO2 and Nitrogen Supply.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {809-818}, pmid = {25877793}, issn = {1432-184X}, mesh = {Ammonia/metabolism ; Bacteria/*metabolism ; Carbon Dioxide/*metabolism ; Dactylis/growth &amp; development ; Grassland ; *Nitrification ; Nitrites/metabolism ; Nitrogen/*metabolism ; Oxidation-Reduction ; *Soil Microbiology ; }, abstract = {Many studies have assessed the responses of soil microbial functional groups to increases in atmospheric CO2 or N deposition alone and more rarely in combination. However, the effects of elevated CO2 and N on the (de)coupling between different microbial functional groups (e.g., different groups of nitrifiers) have been barely studied, despite potential consequences for ecosystem functioning. Here, we investigated the short-term combined effects of elevated CO2 and N supply on the abundances of the four main microbial groups involved in soil nitrification: ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (belonging to the genera Nitrobacter and Nitrospira) in grassland mesocosms. AOB and AOA abundances responded differently to the treatments: N addition increased AOB abundance, but did not alter AOA abundance. Nitrobacter and Nitrospira abundances also showed contrasted responses to the treatments: N addition increased Nitrobacter abundance, but decreased Nitrospira abundance. Our results support the idea of a niche differentiation between AOB and AOA, and between Nitrobacter and Nitrospira. AOB and Nitrobacter were both promoted at high N and C conditions (and low soil water content for Nitrobacter), while AOA and Nitrospira were favored at low N and C conditions (and high soil water content for Nitrospira). In addition, Nitrobacter abundance was positively correlated to AOB abundance and Nitrospira abundance to AOA abundance. Our results suggest that the couplings between ammonia and nitrite oxidizers are influenced by soil N availability. Multiple environmental changes may thus elicit rapid and contrasted responses between and among the soil ammonia and nitrite oxidizers due to their different ecological requirements.}, }
@article {pmid25875741, year = {2015}, author = {Hayashi, S and Itoh, K and Suyama, K}, title = {Genes of Bacillus subtilis 168 that Support Growth of the Cyanobacterium, Synechococcus leopoliensis CCAP1405/1 on Agar Media.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {849-852}, pmid = {25875741}, issn = {1432-184X}, mesh = {Bacillus subtilis/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Culture Media/metabolism ; Organisms, Genetically Modified/genetics/metabolism ; Synechococcus/genetics/*growth &amp; development/metabolism ; }, abstract = {Synechococcus leopoliensis CCAP1405/1 cannot grow on common solid media; however, the strain can grow when co-cultured with Bacillus subtilis 168. Gene-disruptant strains of B. subtilis 168 by pMUTINs at the following sites lost the ability to support the growth of S. leopoliensis CCAP1405/1 on agar media: yxeO and yufO (transporter), yxdK (histidine kinase), sdhC (succinate dehydrogenase), yvgQR (sulfite reductase), acoB (acetoin dehydrogenase), yusE (thioredoxin), yrdA (function unknown). Involvement of the assimilatory sulfate reduction pathway was the suggested reason for loss of the function.}, }
@article {pmid25875576, year = {2016}, author = {Lambertini, E and Buchanan, RL and Narrod, C and Pradhan, AK}, title = {Transmission of Bacterial Zoonotic Pathogens between Pets and Humans: The Role of Pet Food.}, journal = {Critical reviews in food science and nutrition}, volume = {56}, number = {3}, pages = {364-418}, doi = {10.1080/10408398.2014.902356}, pmid = {25875576}, issn = {1549-7852}, mesh = {Animal Feed/*microbiology ; Animals ; Bacterial Infections/microbiology/transmission/*veterinary ; *Food Microbiology ; Humans ; *Pets ; Zoonoses/*transmission ; }, abstract = {Recent Salmonella outbreaks associated with dry pet food and treats raised the level of concern for these products as vehicle of pathogen exposure for both pets and their owners. The need to characterize the microbiological and risk profiles of this class of products is currently not supported by sufficient specific data. This systematic review summarizes existing data on the main variables needed to support an ingredients-to-consumer quantitative risk model to (1) describe the microbial ecology of bacterial pathogens in the dry pet food production chain, (2) estimate pet exposure to pathogens through dry food consumption, and (3) assess human exposure and illness incidence due to contact with pet food and pets in the household. Risk models populated with the data here summarized will provide a tool to quantitatively address the emerging public health concerns associated with pet food and the effectiveness of mitigation measures. Results of such models can provide a basis for improvements in production processes, risk communication to consumers, and regulatory action.}, }
@article {pmid25874435, year = {2016}, author = {Wu, J and Franzblau, A and Xi, C}, title = {Molecular characterization of microbial communities and quantification of Mycobacterium immunogenum in metal removal fluids and their associated biofilms.}, journal = {Environmental science and pollution research international}, volume = {23}, number = {5}, pages = {4086-4094}, pmid = {25874435}, issn = {1614-7499}, support = {5-R21-OH-009306-02/OH/NIOSH CDC HHS/United States ; }, mesh = {Adult ; Biofilms/*growth &amp; development ; Gene Library ; Humans ; *Metallurgy ; *Microbial Consortia ; Mycobacterium/genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Wastewater/*microbiology ; Water Microbiology ; }, abstract = {A number of human health effects have been associated with exposure to metal removal fluids (MRFs). Multiple lines of research suggest that a newly identified organism, Mycobacterium immunogenum (MI), appears to have an etiologic role in hypersensitivity pneumonitis (HP) in case of MRFs exposed workers. However, our knowledge of this organism, other possible causative agents (e.g., Pseudomonads), and the microbial ecology of MRFs in general, is limited. In this study, culture-based methods and small subunit ribosomal RNA gene clone library approach were used to characterize microbial communities in MRF bulk fluid and associated biofilm samples collected from fluid systems in an automobile engine plant. PCR amplification data using universal primers indicate that all samples had bacterial and fungal contaminated. Five among 15 samples formed colonies on the Mycobacteria agar 7H9 suggesting the likely presence of Mycobacteria in these five samples. This observation was confirmed with PCR amplification of 16S rRNA gene fragment using Mycobacteria specific primers. Two additional samples, Biofilm-1 and Biofilm-3, were positive in PCR amplification for Mycobacteria, yet no colonies formed on the 7H9 cultivation agar plates. Real-time PCR was used to quantify the abundance of M. immunogenum in these samples, and the data showed that the copies of M. immunogenum 16S rRNA gene in the samples ranges from 4.33 × 10(4) copy/ml to 4.61 × 10(7) copy/ml. Clone library analysis revealed that Paecilomyces sp. and Acremonium sp. and Acremonium-like were dominant fungi in MRF samples. Various bacterial species from the major phylum of proteobacteria were found and Pseudomonas is the dominant bacterial genus in these samples. Mycobacteria (more specifically MI) were found in all biofilm samples, including biofilms collected from inside the MRF systems and from adjacent environmental surfaces, suggesting that biofilms may play an important role in microbial ecology in MRFs. Biofilms may provide a shield or sheltered microenvironment for the growth and/or colonization of Mycobacteria in MRFs.}, }
@article {pmid25874383, year = {2015}, author = {Heyer, R and Kohrs, F and Reichl, U and Benndorf, D}, title = {Metaproteomics of complex microbial communities in biogas plants.}, journal = {Microbial biotechnology}, volume = {8}, number = {5}, pages = {749-763}, pmid = {25874383}, issn = {1751-7915}, mesh = {*Biofuels ; Bioreactors/*microbiology ; Biotechnology/methods/trends ; Ecosystem ; Gene Expression Profiling/methods ; Germany ; Metabolomics/methods ; Metagenomics/methods ; *Microbial Consortia ; Proteomics/*methods ; }, abstract = {Production of biogas from agricultural biomass or organic wastes is an important source of renewable energy. Although thousands of biogas plants (BGPs) are operating in Germany, there is still a significant potential to improve yields, e.g. from fibrous substrates. In addition, process stability should be optimized. Besides evaluating technical measures, improving our understanding of microbial communities involved into the biogas process is considered as key issue to achieve both goals. Microscopic and genetic approaches to analyse community composition provide valuable experimental data, but fail to detect presence of enzymes and overall metabolic activity of microbial communities. Therefore, metaproteomics can significantly contribute to elucidate critical steps in the conversion of biomass to methane as it delivers combined functional and phylogenetic data. Although metaproteomics analyses are challenged by sample impurities, sample complexity and redundant protein identification, and are still limited by the availability of genome sequences, recent studies have shown promising results. In the following, the workflow and potential pitfalls for metaproteomics of samples from full-scale BGP are discussed. In addition, the value of metaproteomics to contribute to the further advancement of microbial ecology is evaluated. Finally, synergistic effects expected when metaproteomics is combined with advanced imaging techniques, metagenomics, metatranscriptomics and metabolomics are addressed.}, }
@article {pmid25872117, year = {2015}, author = {Vanhoecke, B and Stringer, A}, title = {Host-microbe cross talk in cancer therapy.}, journal = {Current opinion in supportive and palliative care}, volume = {9}, number = {2}, pages = {174-181}, doi = {10.1097/SPC.0000000000000133}, pmid = {25872117}, issn = {1751-4266}, mesh = {Animals ; Host-Pathogen Interactions/drug effects/*immunology/radiation effects ; Humans ; Microbiota/drug effects/*immunology/radiation effects ; Neoplasms/*immunology/microbiology/therapy ; Toll-Like Receptors/*immunology/physiology ; }, abstract = {PURPOSE OF REVIEW: Microbiota secrete a multitude of factors that either confer virulence or promote colonization because they are continuously challenged by host immune responses. The dynamic interplay between the host's immune response and microbiota eventually determines the outcome for the host: health or disease. Toll-like receptors (TLRs) play a key role in this interplay as they can recognize both microbial and host-derived ligands on the basis of the context in which recognition occurs.<br><br>RECENT FINDINGS: Evidence is accumulating that conventional cancer therapies alter interactions and cross talks between the host and microbiota. This has been shown for intestinal mucositis, a common side-effect of various cancer therapies. Advances have been made in the development of new and less toxic cancer strategies. One promising field is immunotherapy on the basis of TLR activation through recognition of microbial-associated molecular patterns.<br><br>SUMMARY: Evidence is emerging, indicating that existing cancer therapies have implications on the composition and functionality of the host-microbiota environment. This may favor the colonization of pathogens and build up the overall toxicity of the drug. Exploitation of the host-microbiota cross talks mediated by TLRs is an emerging and promising field in the search for new, less toxic anticancer strategies.}, }
@article {pmid25868615, year = {2015}, author = {Zhang, XH and Sun, ZY and Cao, FL and Ahmad, H and Yang, XH and Zhao, LG and Wang, T}, title = {Effects of dietary supplementation with fermented ginkgo leaves on antioxidant capacity, intestinal morphology and microbial ecology in broiler chicks.}, journal = {British poultry science}, volume = {56}, number = {3}, pages = {370-380}, doi = {10.1080/00071668.2015.1030590}, pmid = {25868615}, issn = {1466-1799}, mesh = {Animal Feed/analysis ; Animal Nutritional Physiological Phenomena/*drug effects ; Animals ; Antioxidants/metabolism ; Aspergillus niger/*chemistry ; Candida/*chemistry ; Chickens/anatomy &amp; histology/*growth &amp; development/*metabolism/microbiology ; Diet/veterinary ; Dietary Supplements/analysis ; Female ; Fermentation ; Ginkgo biloba/*chemistry ; Intestines/anatomy &amp; histology/microbiology ; Male ; Plant Leaves/chemistry ; Random Allocation ; Weight Gain/drug effects ; }, abstract = {1. The purpose of this study was to evaluate the effects of supplementing diets with three types of fermented Ginkgo-leaves (FGL) on growth, antioxidant capacity, intestinal morphology and microbial ecology in broiler chicks. 2. A total of 300 d-old broilers were randomly allocated to 4 dietary treatments with 6 replications of 10 birds each. Birds were fed on basal diets (Control) or basal diets supplemented with 0.5% FGL with Candida utilis (CF group), Aspergillus niger (AF group) or their combined fermentation (CAF group), respectively, for a 42 d feeding trial. 3. AF and CAF supplementation improved body weight gain (BWG) (22-42 d) and feed conversion ratio (22-42 d and 1-42 d). Concentrations of serum α-tocopherol in CAF group, as well as hepatic α-tocopherol in the three FGL groups were increased, while hepatic reactive oxygen species (ROS) levels were greatly decreased in group AF and CAF. Chickens in AF and CAF groups had decreased hepatic protein carbonyls and malondialdehyde (MDA), as well as jejunal and ileal protein carbonyls. The total superoxide dismutase (T-SOD) activities and glutathione (GSH) of both jejunum and ileum of the CAF group were higher than the other groups. 4. Duodenal and jejunal villous height of birds fed on the AF and CAF diets were increased, while jejunal crypt depth (CD) was decreased. Furthermore, birds fed on AF and CAF supplemented diets had increased ileal lactobacilli populations. Decreased ileal and caecal Escherichia coli and Salmonellas populations was found for the birds fed on CAF supplemented diets. 5. The present study may indicate that the improved feed efficiency and intestinal functions in the group supplemented with AF and CAF are directly connected with the improved antioxidant capacity and intestinal microbial ecology.}, }
@article {pmid25864082, year = {2015}, author = {Lim, JH and Lee, CW and Kudo, I}, title = {Temporal variation of phytoplankton growth and grazing loss in the west coast of Peninsular Malaysia.}, journal = {Environmental monitoring and assessment}, volume = {187}, number = {5}, pages = {246}, pmid = {25864082}, issn = {1573-2959}, mesh = {Chlorophyll/analogs &amp; derivatives/analysis ; *Environmental Monitoring ; Malaysia ; Phytoplankton/*growth &amp; development ; Spatio-Temporal Analysis ; }, abstract = {Phytoplankton growth (μ) and grazing loss (g) rates were measured monthly by the Landry-Hassett dilution method over a 2-year period at both estuarine (Klang) and coastal water (Port Dickson) systems along the Straits of Malacca. Chlorophyll a (Chl a) concentration ranged from 0.20 to 4.47 μg L(-1) at Klang except on two occasions when Chl a spiked above 10 μg L(-1). In contrast, Chl a concentrations were relatively stable at Port Dickson (0.14 to 2.76 μg L(-1)). From the rate measurements, μ was higher (t = 2.01, df = 43, p < 0.05) at Klang (0.30 to 2.26 day(-1)) than at Port Dickson (0.18 to 1.66 day(-1)), but g was not significantly different (p > 0.80). g ranged from 0.30 to 1.50 and 0.21 to 1.51 day(-1) at Klang and Port Dickson, respectively. In this study, grazing loss was coupled to phytoplankton growth, and the ratio of g/μ or grazing pressure which estimates the proportion of primary production grazed was 50% at Klang and lower than at Port Dickson (68%; t = 2.213, df = 36, p < 0.05). We found that the higher growth rates in a eutrophic system, i.e., Klang, were not matched by higher grazing loss, and this may have implications for the biogeochemical cycling in coastal waters.}, }
@article {pmid25862577, year = {2015}, author = {Gunnigle, E and Siggins, A and Botting, CH and Fuszard, M and O'Flaherty, V and Abram, F}, title = {Low-temperature anaerobic digestion is associated with differential methanogenic protein expression.}, journal = {FEMS microbiology letters}, volume = {362}, number = {10}, pages = {}, doi = {10.1093/femsle/fnv059}, pmid = {25862577}, issn = {1574-6968}, support = {GR06281AIA//Wellcome Trust/United Kingdom ; }, mesh = {Anaerobiosis ; Archaeal Proteins/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Bacteroidetes/genetics/growth &amp; development/isolation &amp; purification ; Biofuels ; *Bioreactors ; *Cold Temperature ; Deltaproteobacteria/genetics/growth &amp; development/isolation &amp; purification ; Euryarchaeota/genetics/growth &amp; development/isolation &amp; purification/*metabolism ; Firmicutes/genetics/growth &amp; development/isolation &amp; purification ; Methanobacteriales/genetics/growth &amp; development/isolation &amp; purification ; Methanosarcinales/genetics/growth &amp; development/isolation &amp; purification/*metabolism ; Microbial Consortia ; Proteomics/*methods ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sewage/*microbiology ; Temperature ; Wastewater/*microbiology ; }, abstract = {Anaerobic digestion (AD) is an attractive wastewater treatment technology, leading to the generation of recoverable biofuel (methane). Most industrial AD applications, carry excessive heating costs, however, as AD reactors are commonly operated at mesophilic temperatures while handling waste streams discharged at ambient or cold temperatures. Consequently, low-temperature AD represents a cost-effective strategy for wastewater treatment. The comparative investigation of key microbial groups underpinning laboratory-scale AD bioreactors operated at 37, 15 and 7°C was carried out. Community structure was monitored using 16S rRNA clone libraries, while abundance of the most prominent methanogens was investigated using qPCR. In addition, metaproteomics was employed to access the microbial functions carried out in situ. While δ-Proteobacteria were prevalent at 37°C, their abundance decreased dramatically at lower temperatures with inverse trends observed for Bacteroidetes and Firmicutes. Methanobacteriales and Methanosaeta were predominant at all temperatures investigated while Methanomicrobiales abundance increased at 15°C compared to 37 and 7°C. Changes in operating temperature resulted in the differential expression of proteins involved in methanogenesis, which was found to occur in all bioreactors, as corroborated by bioreactors' performance. This study demonstrated the value of employing a polyphasic approach to address microbial community dynamics and highlighted the functional redundancy of AD microbiomes.}, }
@article {pmid25862454, year = {2015}, author = {Gliniewicz, A and Rydzanicz, K and Mikulak, E}, title = {Methods of mosquito plague control in Świnoujście area based on the analysis of species distribution.}, journal = {Przeglad epidemiologiczny}, volume = {69}, number = {1}, pages = {93-8, 185-9}, pmid = {25862454}, issn = {0033-2100}, mesh = {Animals ; Environmental Exposure/*statistics &amp; numerical data ; Environmental Monitoring/*statistics &amp; numerical data ; Humans ; Insecticides/*administration &amp; dosage ; Larva ; Mosquito Control/*organization &amp; administration ; Poland/epidemiology ; Seasons ; }, abstract = {OBJECTIVE: Studies conducted in 2013 in Świnoujście area aimed at determining mosquito species distribution and analyzing sites, productivity and dynamics of larva and adult breeding as well as developing guidelines for effective mosquito control in this area.<br><br>MATERIALAND METHODS: Entomological studies were conducted from March to September 2013. Distribution of mosquito larvae and adults was investigated. Mosquito larvae were observed mainly in April in transient snow-melt pools.<br><br>RESULTS: Ochlerotatus cantans, Oc. communis, Oc. annulipes, Oc. punctor were the most predominant mosquito species. Since July, larvae of the following genera: Culex spp., Culiseta spp., Anopheles spp. were collected in standing water bodies. A total of 17 species adult mosquito were identified. Of them, Oc. communis, Aedes vexans, Culex pipiens/torrentium, Oc. Cantans, Oc. caspius predominated over other species.<br><br>CONCLUSIONS: Mosquito plague in &#x15a;winouj&#x15b;cie area can be controlled if constant actions would be undertaken from April (use of microbial biocides for snow-melt mosquito larva control) to August (use of microbial biocides for polygeneration larva species control and use of chemical biocides for adult mosquito control). Furthermore, there is a need for actions that would make environment less friendly to mosquitoes and would help to identify breeding sites of aggressive mosquito species - Aedes vexans. There is also a necessity to educate the inhabitants of &#x15a;winouj&#x15b;cie area on the danger resulting from uncontrolled use of insecticides in protected areas and those which are unique from a faunistic perspective.}, }
@article {pmid25862231, year = {2015}, author = {Zhang, P and Wu, WM and Van Nostrand, JD and Deng, Y and He, Z and Gihring, T and Zhang, G and Schadt, CW and Watson, D and Jardine, P and Criddle, CS and Brooks, S and Marsh, TL and Tiedje, JM and Arkin, AP and Zhou, J}, title = {Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {12}, pages = {4164-4172}, pmid = {25862231}, issn = {1098-5336}, mesh = {Acetates/metabolism ; *Biodegradation, Environmental ; Emulsions/chemistry ; Groundwater/*microbiology ; Microarray Analysis ; Microbial Consortia/*genetics/*physiology ; Plant Oils ; Sulfates/metabolism ; Time Factors ; Uranium/*metabolism ; Water Pollutants, Radioactive/*metabolism ; }, abstract = {A pilot-scale field experiment demonstrated that a one-time amendment of emulsified vegetable oil (EVO) reduced groundwater U(VI) concentrations for 1 year in a fast-flowing aquifer. However, little is known about how EVO amendment stimulates the functional gene composition, structure, and dynamics of groundwater microbial communities toward prolonged U(VI) reduction. In this study, we hypothesized that EVO amendment would shift the functional gene composition and structure of groundwater microbial communities and stimulate key functional genes/groups involved in EVO biodegradation and reduction of electron acceptors in the aquifer. To test these hypotheses, groundwater microbial communities after EVO amendment were analyzed using a comprehensive functional gene microarray. Our results showed that EVO amendment stimulated sequential shifts in the functional composition and structure of groundwater microbial communities. Particularly, the relative abundance of key functional genes/groups involved in EVO biodegradation and the reduction of NO3 (-), Mn(IV), Fe(III), U(VI), and SO4 (2-) significantly increased, especially during the active U(VI) reduction period. The relative abundance for some of these key functional genes/groups remained elevated over 9 months. Montel tests suggested that the dynamics in the abundance, composition, and structure of these key functional genes/groups were significantly correlated with groundwater concentrations of acetate, NO3 (-), Mn(II), Fe(II), U(VI), and SO4 (2-). Our results suggest that EVO amendment stimulated dynamic succession of key functional microbial communities. This study improves our understanding of the composition, structure, and function changes needed for groundwater microbial communities to sustain a long-term U(VI) reduction.}, }
@article {pmid25860709, year = {2015}, author = {Coma, M and Rovira, S and Canals, J and Colprim, J}, title = {Integrated side-stream reactor for biological nutrient removal and minimization of sludge production.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {71}, number = {7}, pages = {1056-1064}, doi = {10.2166/wst.2015.067}, pmid = {25860709}, issn = {0273-1223}, mesh = {Anaerobiosis ; Bioreactors ; Nitrogen/*metabolism ; Oxidation-Reduction ; Phosphorus/*metabolism ; Pilot Projects ; Sewage/*analysis ; Spain ; Wastewater/analysis ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Integrated processes to reduce in situ the sludge production in wastewater treatment plants are gaining attention in order to facilitate excess sludge management. In contrast to post-treatments, such as anaerobic digestion which is placed between the activated sludge system and dewatering processes, integrated technologies are placed in the sludge return line. This study evaluates the application of an anoxic side-stream reactor (SSR) which creates a physiological shock and uncouples the biomass metabolism and diverts the activity from assimilation for biosynthesis to non-growth activities. The effect of this system in biological nutrient removal for both nitrogen and phosphorus was evaluated for the anaerobic, anoxic and aerobic reactors. The RedOx potential within the SSR was maintained at -150 mV while the sludge loading rate was modified by increasing the percentage of recycled activated sludge feed to the SSR (0 and 40% at laboratory scale and 0, 10, 50 and 100% at pilot scale). The use of the SSR presented a slight reduction of phosphorus removal but maintained the effluent quality to the required discharge values. Nitrogen removal efficiency increased from 75 to 86% while reducing the sludge production rate by 18.3%.}, }
@article {pmid25858310, year = {2015}, author = {Rudnick, MB and van Veen, JA and de Boer, W}, title = {Oxalic acid: a signal molecule for fungus-feeding bacteria of the genus Collimonas?.}, journal = {Environmental microbiology reports}, volume = {7}, number = {5}, pages = {709-714}, doi = {10.1111/1758-2229.12290}, pmid = {25858310}, issn = {1758-2229}, mesh = {Carbon/metabolism ; Energy Metabolism ; Fungi/*metabolism ; Locomotion ; *Microbial Interactions ; Oxalic Acid/*metabolism ; Oxalobacteraceae/*drug effects/*growth &amp; development/*metabolism/physiology ; Signal Transduction ; }, abstract = {Mycophagous (=fungus feeding) soil bacteria of the genus Collimonas have been shown to colonize and grow on hyphae of different fungal hosts as the only source of energy and carbon. The ability to exploit fungal nutrient resources might require a strategy for collimonads to sense fungi in the soil matrix. Oxalic acid is ubiquitously secreted by soil fungi, serving different purposes. In this study, we investigated the possibility that collimonads might use oxalic acid secretion to localize a fungal host and move towards it. We first confirmed earlier indications that collimonads have a very limited ability to use oxalic acid as growth substrate. In a second step, with using different assays, we show that oxalic acid triggers bacterial movement in such a way that accumulation of cells can be expected at micro-sites with high free oxalic acid concentrations. Based on these observations we propose that oxalic acid functions as a signal molecule to guide collimonads to hyphal tips, the mycelial zones that are most sensitive for mycophagous bacterial attack.}, }
@article {pmid25852161, year = {2015}, author = {Liang, Y and Wu, L and Clark, IM and Xue, K and Yang, Y and Van Nostrand, JD and Deng, Y and He, Z and McGrath, S and Storkey, J and Hirsch, PR and Sun, B and Zhou, J}, title = {Over 150 years of long-term fertilization alters spatial scaling of microbial biodiversity.}, journal = {mBio}, volume = {6}, number = {2}, pages = {}, pmid = {25852161}, issn = {2150-7511}, support = {BBS/E/C/00004981/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Agriculture/*methods ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biota ; Fertilizers/*statistics &amp; numerical data ; Fungi/*classification/genetics ; Microarray Analysis ; Oligonucleotide Array Sequence Analysis ; Plants/*classification ; Soil Microbiology ; }, abstract = {UNLABELLED: Spatial scaling is a critical issue in ecology, but how anthropogenic activities like fertilization affect spatial scaling is poorly understood, especially for microbial communities. Here, we determined the effects of long-term fertilization on the spatial scaling of microbial functional diversity and its relationships to plant diversity in the 150-year-old Park Grass Experiment, the oldest continuous grassland experiment in the world. Nested samples were taken from plots with contrasting inorganic fertilization regimes, and community DNAs were analyzed using the GeoChip-based functional gene array. The slopes of microbial gene-area relationships (GARs) and plant species-area relationships (SARs) were estimated in a plot receiving nitrogen (N), phosphorus (P), and potassium (K) and a control plot without fertilization. Our results indicated that long-term inorganic fertilization significantly increased both microbial GARs and plant SARs. Microbial spatial turnover rates (i.e., z values) were less than 0.1 and were significantly higher in the fertilized plot (0.0583) than in the control plot (0.0449) (P < 0.0001). The z values also varied significantly with different functional genes involved in carbon (C), N, P, and sulfur (S) cycling and with various phylogenetic groups (archaea, bacteria, and fungi). Similarly, the plant SARs increased significantly (P < 0.0001), from 0.225 in the control plot to 0.419 in the fertilized plot. Soil fertilization, plant diversity, and spatial distance had roughly equal contributions in shaping the microbial functional community structure, while soil geochemical variables contributed less. These results indicated that long-term agricultural practice could alter the spatial scaling of microbial biodiversity.<br><br>IMPORTANCE: Determining the spatial scaling of microbial biodiversity and its response to human activities is important but challenging in microbial ecology. Most studies to date are based on different sites that may not be truly comparable or on short-term perturbations, and hence, the results observed could represent transient responses. This study examined the spatial patterns of microbial communities in response to different fertilization regimes at the Rothamsted Research Experimental Station, which has become an invaluable resource for ecologists, environmentalists, and soil scientists. The current study is the first showing that long-term fertilization has dramatic impacts on the spatial scaling of microbial communities. By identifying the spatial patterns in response to long-term fertilization and their underlying mechanisms, this study makes fundamental contributions to predictive understanding of microbial biogeography.}, }
@article {pmid25851446, year = {2015}, author = {Chung, CC and Gong, GC and Huang, CY and Lin, JY and Lin, YC}, title = {Changes in the Synechococcus Assemblage Composition at the Surface of the East China Sea Due to Flooding of the Changjiang River.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {677-688}, pmid = {25851446}, issn = {1432-184X}, mesh = {China ; DNA, Bacterial/genetics ; *Floods ; *Microbiota ; Molecular Sequence Data ; Pacific Ocean ; Phycoerythrin/metabolism ; RNA, Ribosomal, 16S/genetics ; Seasons ; Seawater/microbiology ; Sequence Analysis, DNA ; Synechococcus/genetics/*physiology ; }, abstract = {The aim of this study was to elucidate how flooding of the Changjiang River affects the assemblage composition of phycoerythrin-rich (PE-rich) Synechococcus at the surface of the East China Sea (ECS). During non-flooding summers (e.g., 2009), PE-rich Synechococcus usually thrive at the outer edge of the Changjiang River diluted water coverage (CDW; salinity ≤31 PSU). In the summer of 2010, a severe flood occurred in the Changjiang River basin. The plentiful freshwater injection resulted in the expansion of the CDW over half of the ECS and caused PE-rich cells to show a uniform distribution pattern, with decreased abundance compared with the non-flooding summer. The phylogenetic diversity of 16S rRNA gene sequences indicated that the flooding event also shifted the picoplankton community composition from being dominated by Synechococcus, mainly attributed to the clade II lineage, to various orders of heterotrophic bacteria, including Actinobacteria, Flavobacteria, α-Proteobacteria, and γ-Proteobacteria. As an increasing number of studies have proposed that global warming might result in more frequent floods, combining this perspective with the information obtained from our previous [1] and this studies yield a more comprehensive understanding of the relationship between the composition of the marine Synechococcus assemblage and global environmental changes.}, }
@article {pmid25851445, year = {2015}, author = {Hugoni, M and Agogué, H and Taib, N and Domaizon, I and Moné, A and Galand, PE and Bronner, G and Debroas, D and Mary, I}, title = {Temporal Dynamics of Active Prokaryotic Nitrifiers and Archaeal Communities from River to Sea.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {473-483}, pmid = {25851445}, issn = {1432-184X}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/genetics ; DNA, Ribosomal ; Estuaries ; Fresh Water/microbiology ; Phylogeny ; Rivers/microbiology ; Seawater/microbiology ; }, abstract = {To test if different niches for potential nitrifiers exist in estuarine systems, we assessed by pyrosequencing the diversity of archaeal gene transcript markers for taxonomy (16S ribosomal RNA (rRNA)) during an entire year along a salinity gradient in surface waters of the Charente estuary (Atlantic coast, France). We further investigated the potential for estuarine prokaryotes to oxidize ammonia and hydrolyze urea by quantifying thaumarchaeal amoA and ureC and bacterial amoA transcripts. Our results showed a succession of different nitrifiers from river to sea with bacterial amoA transcripts dominating in the freshwater station while archaeal transcripts were predominant in the marine station. The 16S rRNA sequence analysis revealed that Thaumarchaeota marine group I (MGI) were the most abundant overall but other archaeal groups like Methanosaeta were also potentially active in winter (December-March) and Euryarchaeota marine group II (MGII) were dominant in seawater in summer (April-August). Each station also contained different Thaumarchaeota MGI phylogenetic clusters, and the clusters' microdiversity was associated to specific environmental conditions suggesting the presence of ecotypes adapted to distinct ecological niches. The amoA and ureC transcript dynamics further indicated that some of the Thaumarchaeota MGI subclusters were involved in ammonia oxidation through the hydrolysis of urea. Our findings show that ammonia-oxidizing Archaea and Bacteria were adapted to contrasted conditions and that the Thaumarchaeota MGI diversity probably corresponds to distinct metabolisms or life strategies.}, }
@article {pmid25851444, year = {2015}, author = {Calado, Mda L and Carvalho, L and Pang, KL and Barata, M}, title = {Diversity and Ecological Characterization of Sporulating Higher Filamentous Marine Fungi Associated with Spartina maritima (Curtis) Fernald in Two Portuguese Salt Marshes.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {612-633}, pmid = {25851444}, issn = {1432-184X}, mesh = {*Biodiversity ; Environment ; Estuaries ; Fungi/*physiology ; Poaceae/*microbiology ; Portugal ; Seasons ; }, abstract = {Fungal communities associated with early stages of decomposition of Spartina maritima (Curtis) Fernald were assessed in two geographically distinct salt marshes in Portugal by direct observation of fungal sporulating structures. Twenty-three fungal taxa were identified from 390 plant samples, 11 of which were common to both study sites. Natantispora retorquens, Byssothecium obiones, Phaeosphaeria spartinicola, Phoma sp. 1 and Stagonospora sp. were the most frequent fungal taxa in the studied communities. The fungal species Anthostomella spissitecta, Camarosporium roumeguerii, Coniothyrium obiones, Decorospora gaudefroyi, Halosarpheia trullifera, Leptosphaeria marina and Stagonospora haliclysta were recorded for the first time on S. maritima plants; with the exception of C. roumeguerii and L. marina, all of these species were also new records for Portugal. The differences between species composition of the communities associated with S. maritima were attributed to differences in abiotic conditions of the salt marshes. Although the fungal taxa were distributed differently along the host plants, common species to both fungal communities were found on the same relative position, e.g. B. obiones, Lulworthia sp. and N. retorquens occurred on the basal plant portions, Buergenerula spartinae, Dictyosporium pelagicum and Phoma sp. 1 on the middle plant portions and P. spartinicola and Stagonospora sp. on the top plant portions. The distinct vertical distribution patterns reflected species-specific salinity requirements and flooding tolerance, but specially substrate preferences. The most frequent fungi in both communities also exhibited wider distribution ranges and produced a higher number of fruiting structures, suggesting a more active key role in the decay process of S. maritima.}, }
@article {pmid25851443, year = {2015}, author = {Mitbavkar, S and Patil, JS and Rajaneesh, KM}, title = {Picophytoplankton as Tracers of Environmental Forcing in a Tropical Monsoonal Bay.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {659-676}, pmid = {25851443}, issn = {1432-184X}, mesh = {Bays/*microbiology ; *Biodiversity ; Climate ; Environmental Monitoring/*methods ; Estuaries ; India ; Phytoplankton/*physiology ; Seasons ; *Weather ; }, abstract = {In order to better understand the picophytoplankton (PP) dynamics in tropical monsoon influenced coastal regions, samples were collected daily (June-September 2008: monsoon, December 2008: post-monsoon and April 2009: pre-monsoon) from a fixed station in Dona Paula Bay, India. Eight PP abundance peaks comprising Prochlorococcus-like cells, picoeukaryotes, and three groups of Synechococcus occurred. The chlorophyll biomass and PP abundance were negatively influenced by reduced solar radiation, salinity and water transparency due to precipitation and positively influenced by the stabilized waters during precipitation break/non-monsoon periods. Responses to environmental conditions differed with PP groups, wherein the presence of Synechococcus-PEI (phycoerythrin) throughout the year suggested its ability to tolerate salinity and temperature variations and low light conditions. Synechococcus-PEII appearance toward monsoon end and non-monsoon during high water transparency suggests its tidal advection from offshore waters. Dominance of Synechococcus-PC (phycocyanin) at intermediate salinities under low water transparency during MON and high salinities in PrM coinciding with high nitrate concentrations implies a greater influence of light quality or nutrients. Cyanobacteria and not picoeukaryotes were the dominant picophytoplankton in terms of numbers as well as biomass. This study suggests that PP could be used as tracers of environmental forcing driven by tides and freshwater influx and also highlights the importance of high-frequency samplings in dynamic coastal regions through which transient responses can be captured.}, }
@article {pmid25851442, year = {2015}, author = {Tatti, E and Goyer, C and Burton, DL and Wertz, S and Zebarth, BJ and Chantigny, M and Filion, M}, title = {Tillage Management and Seasonal Effects on Denitrifier Community Abundance, Gene Expression and Structure over Winter.}, journal = {Microbial ecology}, volume = {70}, number = {3}, pages = {795-808}, pmid = {25851442}, issn = {1432-184X}, mesh = {Agriculture/*methods ; Bacteria/*genetics/isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; Denitrification ; *Gene Expression ; *Microbiota ; Nitrous Oxide ; Nova Scotia ; Seasons ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Tillage effects on denitrifier communities and nitrous oxide (N2O) emissions were mainly studied during the growing season. There is limited information for the non-growing season, especially in northern countries where winter has prolonged periods with sub-zero temperatures. The abundance and structure of the denitrifier community, denitrification gene expression and N2O emissions in fields under long-term tillage regimes [no-tillage (NT) vs conventional tillage (CT)] were assessed during two consecutive winters. NT exerted a positive effect on nirK and nosZ denitrifier abundance in both winters compared to CT. Moreover, the two contrasting managements had an opposite influence on nirK and nirS RNA/DNA ratios. Tillage management resulted in different denitrifier community structures during both winters. Seasonal changes were observed in the abundance and the structure of denitrifiers. Interestingly, the RNA/DNA ratios were greater in the coldest months for nirK, nirS and nosZ. N2O emissions were not influenced by management but changed over time with two orders of magnitude increase in the coldest month of both winters. In winter of 2009-2010, emissions were mainly as N2O, whereas in 2010-2011, when soil temperatures were milder due to persistent snow cover, most emissions were as dinitrogen. Results indicated that tillage management during the growing season induced differences in denitrifier community structure that persisted during winter. However, management did not affect the active cold-adapted community structure.}, }
@article {pmid25851150, year = {2015}, author = {Zevin, AS and Nam, T and Rittmann, B and Krajmalnik-Brown, R}, title = {Effects of phosphate limitation on soluble microbial products and microbial community structure in semi-continuous Synechocystis-based photobioreactors.}, journal = {Biotechnology and bioengineering}, volume = {112}, number = {9}, pages = {1761-1769}, doi = {10.1002/bit.25602}, pmid = {25851150}, issn = {1097-0290}, mesh = {Biofuels/*microbiology ; DNA, Bacterial ; Microbial Consortia/genetics/physiology ; Phosphates/*metabolism ; Photobioreactors/*microbiology ; Synechocystis/*metabolism ; }, abstract = {All bacteria release organic compounds called soluble microbial products (SMP) as a part of their normal metabolism. In photobioreactor (PBR) settings, SMP produced by cyanobacteria represent a major pool of carbon and electrons available to heterotrophic bacteria. Thus, SMP in PBRs are a major driver for the growth of heterotrophic bacteria, and understanding the distribution of SMP in PBRs is an important step toward proper management of PBR microbial communities. Here, we analyzed the SMP and microbial communities in two Synechocystis sp. PCC6803-based PBRs. The first PBR (PBRP0) became phosphate limited after several days of operation, while the second PBR (PBRP+) did not have phosphate limitation. Heterotrophic bacteria were detected in both PBRs, but PBRP0 had a much higher proportion of heterotrophic bacteria than PBRP+. Furthermore, PBRP+ had greater biomass production and lower SMP production per unit biomass than PBRP0. Carbohydrates that were most likely derived from hydrolysis of extracellular polymeric substances (EPS) dominated the SMP in PBRP0, while products resulting from cell lysis or decay dominated the SMP in PBRP+. Together, our data support that maintaining phosphate availability in Synechocystis-based PBRs is important for managing SMP and, thus, the heterotrophic community.}, }
@article {pmid25850257, year = {2014}, author = {Yuan, XF and Peng, SM and Wang, BL and Ding, ZS}, title = {[Differences of fungal diversity and structure in rhizosphere of Fritillaria thunbergii from different provenances].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {39}, number = {22}, pages = {4304-4310}, pmid = {25850257}, issn = {1001-5302}, mesh = {Ecosystem ; Fritillaria/*genetics/*microbiology ; Fungi/*genetics ; Rhizosphere ; Soil ; Soil Microbiology ; Species Specificity ; }, abstract = {To explore the mechanism of soil microbial ecology, the differences of fungal diversities in rhizosphere of different provenances of Fritillaria thunbergii were analyzed. The diversities and compositions of rhizo-fungi of the samples were analyzed by using DGGE and 454 pyrosequencing. DGGE results showed the Shannon index of Ninbo provenance planted in Ninbo was the highest one. And its dominant fungi were Ascomycota, Deuteromycota and Zygomycota. Except the same fungi, every provenance planted in Ninbo had its own special ones. From the 454 pyrosequencing, the fungal diversity in Panan producing was the highest which was similar with DGGE result. Among the ten phylum detected in its rhizosoil, Fungi_incertae_sedis, Ascomycota, Mucoromycotina, Basidiomycota and Chytridiomycota almost amounted to 90% of the whole community. The fungal types and amounts in Panan were more than those in Ninbo indicating the differences between producing areas and the advantage of macro genome sequencing. There were 10 phyla, 29 families, 28 genus and 159 species of fungi in Panan provenance, 6 phyla, 20 families, 19 genus, 136 species in Ninbo provenance, 8 phyla, 37 families, 47 genus, 289 species in Nantong provenance and 7 phyla, 25 families, 24 genus, 102 species in the bulk soil. Some genus such as Dothidea, Capnobotryella and Conidiobolus were only existed in Nantong provenance, while Pyrenochae- ta, Glomus and Pseudonectria were only in Panan provenance, which implied these species could grew because F. thunbergii influenced the existence of fungi. Experiments of provenance and producing area of F. thunbergii showed that the fungal diversity of indigenous provenance was higher than that of exotic provenance and each provenance had unique fungal species in the rhizosphere, which indicated that the diversity and structure was shaped cooperatively by the species and soil type. These fungal species are interacted with the soil-rhizhosphere-microbe microecological system, which in turn influence the growth of F. thunbergii.}, }
@article {pmid25848874, year = {2015}, author = {Martijn, J and Schulz, F and Zaremba-Niedzwiedzka, K and Viklund, J and Stepanauskas, R and Andersson, SG and Horn, M and Guy, L and Ettema, TJ}, title = {Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution.}, journal = {The ISME journal}, volume = {9}, number = {11}, pages = {2373-2385}, pmid = {25848874}, issn = {1751-7370}, support = {281633/ERC_/European Research Council/International ; 310039/ERC_/European Research Council/International ; }, mesh = {Alphaproteobacteria/classification/*genetics ; Biological Evolution ; Chemotaxis ; *Evolution, Molecular ; Genome, Bacterial ; *Genomics ; Lakes ; Metagenomics ; *Phylogeny ; Rickettsiaceae/classification/*genetics ; Species Specificity ; Water Microbiology ; }, abstract = {The bacterial family Rickettsiaceae includes a group of well-known etiological agents of many human and vertebrate diseases, including epidemic typhus-causing pathogen Rickettsia prowazekii. Owing to their medical relevance, rickettsiae have attracted a great deal of attention and their host-pathogen interactions have been thoroughly investigated. All known members display obligate intracellular lifestyles, and the best-studied genera, Rickettsia and Orientia, include species that are hosted by terrestrial arthropods. Their obligate intracellular lifestyle and host adaptation is reflected in the small size of their genomes, a general feature shared with all other families of the Rickettsiales. Yet, despite that the Rickettsiaceae and other Rickettsiales families have been extensively studied for decades, many details of the origin and evolution of their obligate host-association remain elusive. Here we report the discovery and single-cell sequencing of 'Candidatus Arcanobacter lacustris', a rare environmental alphaproteobacterium that was sampled from Damariscotta Lake that represents a deeply rooting sister lineage of the Rickettsiaceae. Intriguingly, phylogenomic and comparative analysis of the partial 'Candidatus Arcanobacter lacustris' genome revealed the presence chemotaxis genes and vertically inherited flagellar genes, a novelty in sequenced Rickettsiaceae, as well as several host-associated features. This finding suggests that the ancestor of the Rickettsiaceae might have had a facultative intracellular lifestyle. Our study underlines the efficacy of single-cell genomics for studying microbial diversity and evolution in general, and for rare microbial cells in particular.}, }
@article {pmid25848869, year = {2015}, author = {Livermore, JA and Jones, SE}, title = {Local-global overlap in diversity informs mechanisms of bacterial biogeography.}, journal = {The ISME journal}, volume = {9}, number = {11}, pages = {2413-2422}, pmid = {25848869}, issn = {1751-7370}, mesh = {Bacteria ; *Biodiversity ; Ecosystem ; Geography ; Humans ; Intestines/microbiology ; Lakes ; Likelihood Functions ; *Microbiota ; Mouth/microbiology ; Oceans and Seas ; Phylogeny ; Skin/microbiology ; Species Specificity ; *Water Microbiology ; }, abstract = {Spatial variation in environmental conditions and barriers to organism movement are thought to be important factors for generating endemic species, thus enhancing global diversity. Recent microbial ecology research suggested that the entire diversity of bacteria in the global oceans could be recovered at a single site, thus inferring a lack of bacterial endemism. We argue this is not the case in the global ocean, but might be in other bacterial ecosystems with higher dispersal rates and lower global diversity, like the human gut. We quantified the degree to which local and global bacterial diversity overlap in a diverse set of ecosystems. Upon comparison of observed local-global diversity overlap with predictions from a neutral biogeography model, human-associated microbiomes (gut, skin, mouth) behaved much closer to neutral expectations whereas soil, lake and marine communities deviated strongly from the neutral expectations. This is likely a result of differences in dispersal rate among 'patches', global diversity of these systems, and local densities of bacterial cells. It appears that overlap of local and global bacterial diversity is surprisingly large (but likely not one-hundred percent), and most importantly this overlap appears to be predictable based upon traditional biogeographic parameters like community size, global diversity, inter-patch environmental heterogeneity and patch connectivity.}, }
@article {pmid25847522, year = {2015}, author = {Kyung, KH and Medina Pradas, E and Kim, SG and Lee, YJ and Kim, KH and Choi, JJ and Cho, JH and Chung, CH and Barrangou, R and Breidt, F}, title = {Microbial ecology of watery kimchi.}, journal = {Journal of food science}, volume = {80}, number = {5}, pages = {M1031-8}, doi = {10.1111/1750-3841.12848}, pmid = {25847522}, issn = {1750-3841}, mesh = {DNA, Bacterial/chemistry/classification/*isolation &amp; purification ; DNA, Ribosomal/chemistry ; Enterobacteriaceae/classification/genetics/isolation &amp; purification ; *Fermentation ; *Food Microbiology ; Lactobacillus/classification ; Proteobacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Raphanus/microbiology ; Sequence Analysis, DNA ; Temperature ; Vegetables/*microbiology ; }, abstract = {The biochemistry and microbial ecology of 2 similar types of watery (mul) kimchi, containing sliced and unsliced radish and vegetables (nabak and dongchimi, respectively), were investigated. Samples from kimchi were fermented at 4, 10, and 20 °C were analyzed by plating on differential and selective media, high-performance liquid chromatography, and high-throughput DNA sequencing of 16S rDNA. Nabak kimchi showed similar trends as dongchimi, with increasing lactic and acetic acids and decreasing pH for each temperature, but differences in microbiota were apparent. Interestingly, bacteria from the Proteobacterium phylum, including Enterobacteriaceae, decreased more rapidly during fermentation at 4 °C in nabak cabbage fermentations compared with dongchimi. Although changes for Proteobacterium and Enterobacteriaceae populations were similar during fermentation at 10 and 20 °C, the homolactic stage of fermentation did not develop for the 4 and 10 °C samples of both nabak and dongchimi during the experiment. These data show the differences in biochemistry and microbial ecology that can result from preparation method and fermentation conditions of the kimchi, which may impact safety (Enterobacteriaceae populations may include pathogenic bacteria) and quality (homolactic fermentation can be undesirable, if too much acid is produced) of the product. In addition, the data also illustrate the need for improved methods for identifying and differentiating closely related lactic acid bacteria species using high-throughput sequencing methods.}, }
@article {pmid25843944, year = {2015}, author = {Kim, HB and Isaacson, RE}, title = {The pig gut microbial diversity: Understanding the pig gut microbial ecology through the next generation high throughput sequencing.}, journal = {Veterinary microbiology}, volume = {177}, number = {3-4}, pages = {242-251}, doi = {10.1016/j.vetmic.2015.03.014}, pmid = {25843944}, issn = {1873-2542}, mesh = {Age Factors ; Animals ; DNA, Bacterial/chemistry ; Feces/microbiology ; Gene Library ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Intestines/*microbiology ; *Microbiota/genetics ; Probiotics/administration &amp; dosage ; RNA, Ribosomal, 16S/*genetics ; Sus scrofa/*microbiology ; Swine ; Weaning ; }, abstract = {The importance of the gut microbiota of animals is widely acknowledged because of its pivotal roles in the health and well being of animals. The genetic diversity of the gut microbiota contributes to the overall development and metabolic needs of the animal, and provides the host with many beneficial functions including production of volatile fatty acids, re-cycling of bile salts, production of vitamin K, cellulose digestion, and development of immune system. Thus the intestinal microbiota of animals has been the subject of study for many decades. Although most of the older studies have used culture dependent methods, the recent advent of high throughput sequencing of 16S rRNA genes has facilitated in depth studies exploring microbial populations and their dynamics in the animal gut. These culture independent DNA based studies generate large amounts of data and as a result contribute to a more detailed understanding of the microbiota dynamics in the gut and the ecology of the microbial populations. Of equal importance, is being able to identify and quantify microbes that are difficult to grow or that have not been grown in the laboratory. Interpreting the data obtained from this type of study requires using basic principles of microbial diversity to understand importance of the composition of microbial populations. In this review, we summarize the literature on culture independent studies of the pig gut microbiota with an emphasis on its succession and alterations caused by diverse factors.}, }
@article {pmid25842007, year = {2015}, author = {Imangaliyev, S and Keijser, B and Crielaard, W and Tsivtsivadze, E}, title = {Personalized microbial network inference via co-regularized spectral clustering.}, journal = {Methods (San Diego, Calif.)}, volume = {83}, number = {}, pages = {28-35}, doi = {10.1016/j.ymeth.2015.03.017}, pmid = {25842007}, issn = {1095-9130}, mesh = {Algorithms ; *Cluster Analysis ; Computational Biology/*methods ; Humans ; *Microbial Consortia ; Microbiota/*genetics ; }, abstract = {We use Human Microbiome Project (HMP) cohort (Peterson et al., 2009) to infer personalized oral microbial networks of healthy individuals. To determine clustering of individuals with similar microbial profiles, co-regularized spectral clustering algorithm is applied to the dataset. For each cluster we discovered, we compute co-occurrence relationships among the microbial species that determine microbial network per cluster of individuals. The results of our study suggest that there are several differences in microbial interactions on personalized network level in healthy oral samples acquired from various niches. Based on the results of co-regularized spectral clustering we discover two groups of individuals with different topology of their microbial interaction network. The results of microbial network inference suggest that niche-wise interactions are different in these two groups. Our study shows that healthy individuals have different microbial clusters according to their oral microbiota. Such personalized microbial networks open a better understanding of the microbial ecology of healthy oral cavities and new possibilities for future targeted medication. The scripts written in scientific Python and in Matlab, which were used for network visualization, are provided for download on the website http://learning-machines.com/.}, }
@article {pmid25840824, year = {2015}, author = {Baron, JL and Harris, JK and Holinger, EP and Duda, S and Stevens, MJ and Robertson, CE and Ross, KA and Pace, NR and Stout, JE}, title = {Effect of monochloramine treatment on the microbial ecology of Legionella and associated bacterial populations in a hospital hot water system.}, journal = {Systematic and applied microbiology}, volume = {38}, number = {3}, pages = {198-205}, doi = {10.1016/j.syapm.2015.02.006}, pmid = {25840824}, issn = {1618-0984}, mesh = {Anti-Infective Agents/*pharmacology ; Biota/*drug effects ; Chloramines/*pharmacology ; DNA, Bacterial/chemistry/genetics/isolation &amp; purification ; DNA, Ribosomal/chemistry/genetics/isolation &amp; purification ; Hospitals ; Hot Temperature ; Legionella/*drug effects ; Molecular Sequence Data ; Pennsylvania ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Opportunistic pathogens, including Legionella spp. and non-tuberculous mycobacteria, can thrive in building hot water systems despite municipal and traditional on-site chlorine disinfection. Monochloramine is a relatively new approach to on-site disinfection, but the microbiological impact of on-site chloramine use has not been well studied. We hypothesized that comparison of the microbial ecology associated with monochloramine treatment versus no on-site treatment would yield highly dissimilar bacterial communities. Hot water samples were collected monthly from 7 locations for three months from two buildings in a Pennsylvania hospital complex supplied with common municipal water: (1) a hospital administrative building (no on-site treatment) and (2) an adjacent acute-care hospital treated on-site with monochloramine to control Legionella spp. Water samples were subjected to DNA extraction, rRNA PCR, and 454 pyrosequencing. Stark differences in the microbiome of the chloraminated water and the control were observed. Bacteria in the treated samples were primarily Sphingomonadales and Limnohabitans, whereas Flexibacter and Planctomycetaceae predominated in untreated control samples. Serendipitously, one sampling month coincided with dysfunction of the on-site disinfection system that resulted in a Legionella bloom detected by sequencing and culture. This study also demonstrates the potential utility of high-throughput DNA sequencing to monitor microbial ecology in water systems.}, }
@article {pmid25835154, year = {2015}, author = {Volmer, J and Schmid, A and Bühler, B}, title = {Guiding bioprocess design by microbial ecology.}, journal = {Current opinion in microbiology}, volume = {25}, number = {}, pages = {25-32}, doi = {10.1016/j.mib.2015.02.002}, pmid = {25835154}, issn = {1879-0364}, mesh = {Biocatalysis ; Biological Evolution ; *Ecosystem ; Enzymes ; *Industrial Microbiology/economics/methods ; *Metabolic Engineering ; Microbial Consortia/genetics/*physiology ; Synthetic Biology ; }, abstract = {Industrial bioprocess development is driven by profitability and eco-efficiency. It profits from an early stage definition of process and biocatalyst design objectives. Microbial bioprocess environments can be considered as synthetic technical microbial ecosystems. Natural systems follow Darwinian evolution principles aiming at survival and reproduction. Technical systems objectives are eco-efficiency, productivity, and profitable production. Deciphering technical microbial ecology reveals differences and similarities of natural and technical systems objectives, which are discussed in this review in view of biocatalyst and process design and engineering strategies. Strategies for handling opposing objectives of natural and technical systems and for exploiting and engineering natural properties of microorganisms for technical systems are reviewed based on examples. This illustrates the relevance of considering microbial ecology for bioprocess design and the potential for exploitation by synthetic biology strategies.}, }
@article {pmid25833770, year = {2015}, author = {Constancias, F and Terrat, S and Saby, NP and Horrigue, W and Villerd, J and Guillemin, JP and Biju-Duval, L and Nowak, V and Dequiedt, S and Ranjard, L and Chemidlin Prévost-Bouré, N}, title = {Mapping and determinism of soil microbial community distribution across an agricultural landscape.}, journal = {MicrobiologyOpen}, volume = {4}, number = {3}, pages = {505-517}, pmid = {25833770}, issn = {2045-8827}, mesh = {*Agriculture ; Bacteria/classification/genetics ; Biodiversity ; Biomass ; *Ecosystem ; Environment ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km[2]. Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity.}, }
@article {pmid25833176, year = {2016}, author = {Dannemiller, KC and Gent, JF and Leaderer, BP and Peccia, J}, title = {Influence of housing characteristics on bacterial and fungal communities in homes of asthmatic children.}, journal = {Indoor air}, volume = {26}, number = {2}, pages = {179-192}, pmid = {25833176}, issn = {1600-0668}, support = {R01 ES005410/ES/NIEHS NIH HHS/United States ; ES05410/ES/NIEHS NIH HHS/United States ; }, mesh = {*Air Microbiology ; Air Pollution, Indoor/*statistics &amp; numerical data ; Asthma/*epidemiology ; Bacteria ; Child ; Environmental Exposure/*statistics &amp; numerical data ; Fungi ; Housing/statistics &amp; numerical data ; Humans ; }, abstract = {Variations in home characteristics, such as moisture and occupancy, affect indoor microbial ecology as well as human exposure to microorganisms. Our objective was to determine how indoor bacterial and fungal community structure and diversity are associated with the broader home environment and its occupants. Next-generation DNA sequencing was used to describe fungal and bacterial communities in house dust sampled from 198 homes of asthmatic children in southern New England. Housing characteristics included number of people/children, level of urbanization, single/multifamily home, reported mold, reported water leaks, air conditioning (AC) use, and presence of pets. Both fungal and bacterial community structures were non-random and demonstrated species segregation (C-score, P < 0.00001). Increased microbial richness was associated with the presence of pets, water leaks, longer AC use, suburban (vs. urban) homes, and dust composition measures (P < 0.05). The most significant differences in community composition were observed for AC use and occupancy (people, children, and pets) characteristics. Occupant density measures were associated with beneficial bacterial taxa, including Lactobacillus johnsonii as measured by qPCR. A more complete knowledge of indoor microbial communities is useful for linking housing characteristics to human health outcomes. Microbial assemblies in house dust result, in part, from the building's physical and occupant characteristics.}, }
@article {pmid25830022, year = {2015}, author = {Abdul Rahman, N and Parks, DH and Willner, DL and Engelbrektson, AL and Goffredi, SK and Warnecke, F and Scheffrahn, RH and Hugenholtz, P}, title = {A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes.}, journal = {Microbiome}, volume = {3}, number = {}, pages = {5}, pmid = {25830022}, issn = {2049-2618}, abstract = {BACKGROUND: Termites and their microbial gut symbionts are major recyclers of lignocellulosic biomass. This important symbiosis is obligate but relatively open and more complex in comparison to other well-known insect symbioses such as the strict vertical transmission of Buchnera in aphids. The relative roles of vertical inheritance and environmental factors such as diet in shaping the termite gut microbiome are not well understood.<br><br>RESULTS: The gut microbiomes of 66 specimens representing seven higher and nine lower termite genera collected in Australia and North America were profiled by small subunit (SSU) rRNA amplicon pyrosequencing. These represent the first reported culture-independent gut microbiome data for three higher termite genera: Tenuirostritermes, Drepanotermes, and Gnathamitermes; and two lower termite genera: Marginitermes and Porotermes. Consistent with previous studies, bacteria comprise the largest fraction of termite gut symbionts, of which 11 phylotypes (6 Treponema, 1 Desulfarculus-like, 1 Desulfovibrio, 1 Anaerovorax-like, 1 Sporobacter-like, and 1 Pirellula-like) were widespread occurring in &#x2265;50% of collected specimens. Archaea are generally considered to comprise only a minority of the termite gut microbiota (<3%); however, archaeal relative abundance was substantially higher and variable in a number of specimens including Macrognathotermes, Coptotermes, Schedorhinotermes, Porotermes, and Mastotermes (representing up to 54% of amplicon reads). A ciliate related to Clevelandella was detected in low abundance in Gnathamitermes indicating that protists were either reacquired after protists loss in higher termites or persisted in low numbers across this transition. Phylogenetic analyses of the bacterial communities indicate that vertical inheritance is the primary force shaping termite gut microbiota. The effect of diet is secondary and appears to influence the relative abundance, but not membership, of the gut communities.<br><br>CONCLUSIONS: Vertical inheritance is the primary force shaping the termite gut microbiome indicating that species are successfully and faithfully passed from one generation to the next via trophallaxis or coprophagy. Changes in relative abundance can occur on shorter time scales and appear to be an adaptive mechanism for dietary fluctuations.}, }
@article {pmid25827422, year = {2015}, author = {Bautista, MA and Zhang, C and Whitaker, RJ}, title = {Virus-induced dormancy in the archaeon Sulfolobus islandicus.}, journal = {mBio}, volume = {6}, number = {2}, pages = {}, pmid = {25827422}, issn = {2150-7511}, mesh = {Clustered Regularly Interspaced Short Palindromic Repeats ; *Host-Parasite Interactions ; *Microbial Viability ; Sulfolobus/*growth &amp; development/*virology ; Time Factors ; }, abstract = {UNLABELLED: We investigated the interaction between Sulfolobus spindle-shaped virus (SSV9) and its native archaeal host Sulfolobus islandicus. We show that upon exposure to SSV9, S. islandicus strain RJW002 has a significant growth delay where the majority of cells are dormant (viable but not growing) for 24 to 48 hours postinfection (hpi) compared to the growth of controls without virus. We demonstrate that in this system, dormancy (i) is induced by both active and inactive virus particles at a low multiplicity of infection (MOI), (ii) is reversible in strains with active CRISPR-Cas immunity that prevents the establishment of productive infections, and (iii) results in dramatic and rapid host death if virus persists in the culture even at low levels. Our results add a new dimension to evolutionary models of virus-host interactions, showing that the mere presence of a virus induces host cell stasis and death independent of infection. This novel, highly sensitive, and risky bet-hedging antiviral response must be integrated into models of virus-host interactions in this system so that the true ecological impact of viruses can be predicted and understood.<br><br>IMPORTANCE: Viruses of microbes play key roles in microbial ecology; however, our understanding of viral impact on host physiology is based on a few model bacteria that represent a small fraction of the life history strategies employed by hosts or viruses across the three domains that encompass the microbial world. We have demonstrated that rare and even inactive viruses induce dormancy in the model archaeon S.&#xa0;islandicus. Similar virus-induced dormancy strategies in other microbial systems may help to explain several confounding observations in other systems, including the surprising abundance of dormant cell types found in many microbial environments, the difficulty of culturing microorganisms in the laboratory, and the paradoxical virus-to-host abundances that do not match model predictions. A more accurate grasp of virus-host interactions will expand our understanding of the impact of viruses in microbial ecology.}, }
@article {pmid25825684, year = {2015}, author = {Mambanzulua Ngoma, P and Hiligsmann, S and Sumbu Zola, E and Culot, M and Fievez, T and Thonart, P}, title = {Comparative study of the methane production based on the chemical compositions of Mangifera Indica and Manihot Utilissima leaves.}, journal = {SpringerPlus}, volume = {4}, number = {}, pages = {75}, pmid = {25825684}, issn = {2193-1801}, abstract = {Leaves of Mangifera Indica (MI, mango leaves) and Manihot Utilissima (MU, cassava leaves) are available in tropical regions and are the most accessible vegetal wastes of Kinshasa, capital of Democratic Republic of Congo. These wastes are not suitably managed and are not rationally valorized. They are abandoned in full air, on the soil and in the rivers. They thus pollute environment. By contrast, they can be recuperated and treated in order to produce methane (energy source), organic fertilizer and clean up the environment simultaneously. The main objective of this study was to investigate methane production from MI and MU leaves by BMP tests at 30°C. The yields achieved from the anaerobic digestion of up to 61.3 g raw matter in 1 l medium were 0.001 l/g and 0.100 l CH4/g volatile solids of MI and MU leaves, respectively. The yield of MU leaves was in the range mentioned in the literature for other leaves because of a poor presence of bioactive substrates, and low C/N ratio. This methane yield corresponded to 7% of calorific power of wood. By contrast, the methane yield from MI leaves was almost nil suggesting some metabolism inhibition because of their rich composition in carbon and bioactive substrates. Whereas classical acidogenesis and acetogenesis were recorded. Therefore, methane production from the sole MI leaves seems unfavorable by comparison to MU leaves at the ambient temperature in tropical regions. Their solid and liquid residues obtained after anaerobic digestion would be efficient fertilizers. However, the methane productivity of both leaves could be improved by anaerobic co-digestion.}, }
@article {pmid25820471, year = {2015}, author = {Bobrov, AA and Zaitsev, AS and Wolters, V}, title = {Shifts in soil testate amoeba communities associated with forest diversification.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {884-894}, pmid = {25820471}, issn = {1432-184X}, mesh = {Abies/growth &amp; development ; Amoebozoa/*physiology ; *Biota ; Cercozoa/*physiology ; Fagus/growth &amp; development ; Forestry ; *Forests ; Germany ; Picea/growth &amp; development ; Soil/*parasitology ; Trees/growth &amp; development ; }, abstract = {We studied changes of testate amoeba communities associated with the conversion of spruce monocultures into mixed beech-fir-spruce forests in the Southern Black Forest Mountains (Germany). In this region, forest conversion is characterized by a gradual development of beech undergrowth within thinned spruce tree stands leading to multiple age continuous cover forests with a diversified litter layer. Strong shifts in the abundance of testate amoeba observed in intermediate stages levelled off to monoculture conditions again after the final stage of the conversion process had been reached. The average number of species per conversion stage (i.e., local richness) did not respond strongly to forest conversion, but the total number of species (i.e., regional richness) was considerably higher in the initial stage than in the mixed forests, due to the large number of hygrophilous species inhabiting spruce monocultures. Functional diversity of the testate amoeba community, however, significantly increased during the conversion process. This shift was closely associated with improved C and N availability as well as higher niche diversity in the continuous cover stands. Lower soil acidity in these forests coincided with a higher relative abundance of eurytopic species. Our results suggest that testate amoeba communities are much more affected by physicochemical properties of the soil than directly by litter diversity.}, }
@article {pmid25819966, year = {2015}, author = {Feng, H and Zhang, X and Guo, K and Vaiopoulou, E and Shen, D and Long, Y and Yin, J and Wang, M}, title = {Electrical stimulation improves microbial salinity resistance and organofluorine removal in bioelectrochemical systems.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {11}, pages = {3737-3744}, pmid = {25819966}, issn = {1098-5336}, mesh = {*Electric Stimulation ; Halobacterium/*metabolism ; *Microbial Consortia ; Nitrobenzenes/*metabolism ; *Salinity ; Sodium Chloride/*metabolism ; Time Factors ; Wastewater/chemistry ; Water Pollutants, Chemical/metabolism ; Water Purification/methods ; }, abstract = {Fed batch bioelectrochemical systems (BESs) based on electrical stimulation were used to treat p-fluoronitrobenzene (p-FNB) wastewater at high salinities. At a NaCl concentration of 40 g/liter, p-FNB was removed 100% in 96 h in the BES, whereas in the biotic control (BC) (absence of current), p-FNB removal was only 10%. By increasing NaCl concentrations from 0 g/liter to 40 g/liter, defluorination efficiency decreased around 40% in the BES, and in the BC it was completely ceased. p-FNB was mineralized by 30% in the BES and hardly in the BC. Microorganisms were able to store 3.8 and 0.7 times more K(+) and Na(+) intracellularly in the BES than in the BC. Following the same trend, the ratio of protein to soluble polysaccharide increased from 3.1 to 7.8 as the NaCl increased from 0 to 40 g/liter. Both trends raise speculation that an electrical stimulation drives microbial preference toward K(+) and protein accumulation to tolerate salinity. These findings are in accordance with an enrichment of halophilic organisms in the BES. Halobacterium dominated in the BES by 56.8% at a NaCl concentration of 40 g/liter, while its abundance was found as low as 17.5% in the BC. These findings propose a new method of electrical stimulation to improve microbial salinity resistance.}, }
@article {pmid25819646, year = {2015}, author = {Schmidt, VT and Smith, KF and Melvin, DW and Amaral-Zettler, LA}, title = {Community assembly of a euryhaline fish microbiome during salinity acclimation.}, journal = {Molecular ecology}, volume = {24}, number = {10}, pages = {2537-2550}, doi = {10.1111/mec.13177}, pmid = {25819646}, issn = {1365-294X}, mesh = {*Acclimatization ; Animals ; Bacteria/classification ; DNA, Bacterial/genetics ; *Microbiota ; Poecilia/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Stochastic Processes ; Water Microbiology ; }, abstract = {Microbiomes play a critical role in promoting a range of host functions. Microbiome function, in turn, is dependent on its community composition. Yet, how microbiome taxa are assembled from their regional species pool remains unclear. Many possible drivers have been hypothesized, including deterministic processes of competition, stochastic processes of colonization and migration, and physiological 'host-effect' habitat filters. The contribution of each to assembly in nascent or perturbed microbiomes is important for understanding host-microbe interactions and host health. In this study, we characterized the bacterial communities in a euryhaline fish and the surrounding tank water during salinity acclimation. To assess the relative influence of stochastic versus deterministic processes in fish microbiome assembly, we manipulated the bacterial species pool around each fish by changing the salinity of aquarium water. Our results show a complete and repeatable turnover of dominant bacterial taxa in the microbiomes from individuals of the same species after acclimation to the same salinity. We show that changes in fish microbiomes are not correlated with corresponding changes to abundant taxa in tank water communities and that the dominant taxa in fish microbiomes are rare in the aquatic surroundings, and vice versa. Our results suggest that bacterial taxa best able to compete within the unique host environment at a given salinity appropriate the most niche space, independent of their relative abundance in tank water communities. In this experiment, deterministic processes appear to drive fish microbiome assembly, with little evidence for stochastic colonization.}, }
@article {pmid25819618, year = {2015}, author = {De Vrieze, J and Saunders, AM and He, Y and Fang, J and Nielsen, PH and Verstraete, W and Boon, N}, title = {Ammonia and temperature determine potential clustering in the anaerobic digestion microbiome.}, journal = {Water research}, volume = {75}, number = {}, pages = {312-323}, doi = {10.1016/j.watres.2015.02.025}, pmid = {25819618}, issn = {1879-2448}, mesh = {Ammonia/*metabolism ; Anaerobiosis ; Biofuels/*analysis ; *Bioreactors ; DNA, Bacterial/genetics/metabolism ; Microbiota/*genetics ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics/metabolism ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Temperature ; }, abstract = {Anaerobic digestion is regarded as a key environmental technology in the present and future bio-based economy. The microbial community completing the anaerobic digestion process is considered complex, and several attempts already have been carried out to determine the key microbial populations. However, the key differences in the anaerobic digestion microbiomes, and the environmental/process parameters that drive these differences, remain poorly understood. In this research, we hypothesized that differences in operational parameters lead to a particular composition and organization of microbial communities in full-scale installations. A total of 38 samples were collected from 29 different full-scale anaerobic digestion installations, showing constant biogas production in function of time. Microbial community analysis was carried out by means of amplicon sequencing and real-time PCR. The bacterial community in all samples was dominated by representatives of the Firmicutes, Bacteroidetes and Proteobacteria, covering 86.1 ± 10.7% of the total bacterial community. Acetoclastic methanogenesis was dominated by Methanosaetaceae, yet, only the hydrogenotrophic Methanobacteriales correlated with biogas production, confirming their importance in high-rate anaerobic digestion systems. In-depth analysis of operational and environmental parameters and bacterial community structure indicated the presence of three potential clusters in anaerobic digestion. These clusters were determined by total ammonia concentration, free ammonia concentration and temperature, and characterized by an increased relative abundance of Bacteroidales, Clostridiales and Lactobacillales, respectively. None of the methanogenic populations, however, could be significantly attributed to any of the three clusters. Nonetheless, further experimental research will be required to validate the existence of these different clusters, and to which extent the presence of these clusters relates to stable or sub-optimal anaerobic digestion.}, }
@article {pmid25816205, year = {2015}, author = {Matassa, S and Batstone, DJ and Hülsen, T and Schnoor, J and Verstraete, W}, title = {Can direct conversion of used nitrogen to new feed and protein help feed the world?.}, journal = {Environmental science &amp; technology}, volume = {49}, number = {9}, pages = {5247-5254}, doi = {10.1021/es505432w}, pmid = {25816205}, issn = {1520-5851}, mesh = {Agriculture/*methods ; Animal Feed/*analysis ; *Conservation of Natural Resources ; Dietary Proteins/chemistry ; Nitrogen/*metabolism ; Nitrogen Cycle ; *Recycling ; }, abstract = {The increase in the world population, vulnerability of conventional crop production to climate change, and population shifts to megacities justify a re-examination of current methods of converting reactive nitrogen to dinitrogen gas in sewage and waste treatment plants. Indeed, by up-grading treatment plants to factories in which the incoming materials are first deconstructed to units such as ammonia, carbon dioxide and clean minerals, one can implement a highly intensive and efficient microbial resynthesis process in which the used nitrogen is harvested as microbial protein (at efficiencies close to 100%). This can be used for animal feed and food purposes. The technology for recovery of reactive nitrogen as microbial protein is available but a change of mindset needs to be achieved to make such recovery acceptable.}, }
@article {pmid25812998, year = {2015}, author = {Pagès, A and Grice, K and Welsh, DT and Teasdale, PT and Van Kranendonk, MJ and Greenwood, P}, title = {Lipid Biomarker and Isotopic Study of Community Distribution and Biomarker Preservation in a Laminated Microbial Mat from Shark Bay, Western Australia.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {459-472}, pmid = {25812998}, issn = {1432-184X}, mesh = {Bays/*microbiology ; Biomarkers/*analysis ; Cyanobacteria/metabolism ; Geologic Sediments/microbiology ; Lipids/*analysis ; Western Australia ; }, abstract = {Modern microbial mats from Shark Bay present some structural similarities with ancient stromatolites; thus, the functionality of microbial communities and processes of diagenetic preservation of modern mats may provide an insight into ancient microbial assemblages and preservation. In this study, the vertical distribution of microbial communities was investigated in a well-laminated smooth mat from Shark Bay. Biolipid and compound-specific isotopic analyses were performed to investigate the distribution of microbial communities in four distinct layers of the mat. Biomarkers indicative of cyanobacteria were more abundant in the uppermost oxic layer. Diatom markers (e.g. C25 HBI alkene, C20:4ω6 and C20:5ω3 polar lipid fatty acids (PLFAs)) were also detected in high abundance in the uppermost layer, but also in the deepest layer under conditions of permanent darkness and anoxia, where they probably used NO3 (-) for respiration. CycC19:0, an abundant PLFA of purple sulfur bacteria (PSB), was detected in all layers and presented the most (13)C-depleted values of all PLFAs, consistent with photoautotrophic PSB. Sulfur-bound aliphatic and aromatic biomarkers were detected in all layers, highlighting the occurrence of early sulfurisation which may be an important mechanism in the sedimentary preservation of functional biolipids in living and, thus, also ancient mats.}, }
@article {pmid25812434, year = {2015}, author = {Rusconi, R and Stocker, R}, title = {Microbes in flow.}, journal = {Current opinion in microbiology}, volume = {25}, number = {}, pages = {1-8}, doi = {10.1016/j.mib.2015.03.003}, pmid = {25812434}, issn = {1879-0364}, mesh = {*Bacterial Physiological Phenomena ; Biofilms/growth &amp; development ; Ecosystem ; Environmental Microbiology ; *Water Movements ; }, abstract = {Microbes often live in moving fluids. Despite the multitude of implications that flow has on microbial ecology and environmental microbiology, only recently have experimental tools and conceptual frameworks from fluid physics been applied systematically to further our knowledge of the behavior of microbes in flow. This nascent research field, which truly straddles biology and physics, has already produced important contributions to our understanding of the physical interaction between microbes and flow, both in bulk fluid and close to surfaces, at the same time revealing the richness and complexity of the resulting dynamics.}, }
@article {pmid25812092, year = {2015}, author = {Al-Omari, A and Wett, B and Nopens, I and De Clippeleir, H and Han, M and Regmi, P and Bott, C and Murthy, S}, title = {Model-based evaluation of mechanisms and benefits of mainstream shortcut nitrogen removal processes.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {71}, number = {6}, pages = {840-847}, doi = {10.2166/wst.2015.022}, pmid = {25812092}, issn = {0273-1223}, mesh = {Ammonia/metabolism ; Bacteria/*metabolism ; Bioreactors/microbiology ; Denitrification ; Models, Theoretical ; Nitrates/metabolism ; Nitrification ; Nitrites/metabolism ; Nitrogen/*metabolism ; Oxidation-Reduction ; Waste Disposal, Fluid/*methods ; Wastewater/analysis ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The main challenge in implementing shortcut nitrogen removal processes for mainstream wastewater treatment is the out-selection of nitrite oxidizing bacteria (NOB) to limit nitrate production. A model-based approach was utilized to simulate the impact of individual features of process control strategies to achieve NO(-)(2)-N shunt via NOB out-selection. Simulations were conducted using a two-step nitrogen removal model from the literature. Nitrogen shortcut removal processes from two case studies were modeled to illustrate the contribution of NOB out-selection mechanisms. The paper highlights a comparison between two control schemes; one was based on online measured ammonia and the other was based on a target ratio of 1 for ammonia vs. NOx (nitrate + nitrite) (AVN). Results indicated that the AVN controller possesses unique features to nitrify only that amount of nitrogen that can be denitrified, which promotes better management of incoming organics and bicarbonate for a more efficient NOB out-selection. Finally, the model was used in a scenario analysis, simulating hypothetical optimized performance of the pilot process. An estimated potential saving of 60% in carbon addition for nitrogen removal by implementing full-scale mainstream deammonification was predicted.}, }
@article {pmid25809788, year = {2015}, author = {Navarrete, AA and Tsai, SM and Mendes, LW and Faust, K and de Hollander, M and Cassman, NA and Raes, J and van Veen, JA and Kuramae, EE}, title = {Soil microbiome responses to the short-term effects of Amazonian deforestation.}, journal = {Molecular ecology}, volume = {24}, number = {10}, pages = {2433-2448}, doi = {10.1111/mec.13172}, pmid = {25809788}, issn = {1365-294X}, mesh = {Agriculture/methods ; Bacteria/*classification ; *Conservation of Natural Resources ; DNA, Bacterial/genetics ; Forests ; High-Throughput Nucleotide Sequencing ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Slash-and-burn clearing of forest typically results in increase in soil nutrient availability. However, the impact of these nutrients on the soil microbiome is not known. Using next generation sequencing of 16S rRNA gene and shotgun metagenomic DNA, we compared the structure and the potential functions of bacterial community in forest soils to deforested soils in the Amazon region and related the differences to soil chemical factors. Deforestation decreased soil organic matter content and factors linked to soil acidity and raised soil pH, base saturation and exchangeable bases. Concomitant to expected changes in soil chemical factors, we observed an increase in the alpha diversity of the bacterial microbiota and relative abundances of putative copiotrophic bacteria such as Actinomycetales and a decrease in the relative abundances of bacterial taxa such as Chlamydiae, Planctomycetes and Verrucomicrobia in the deforested soils. We did not observe an increase in genes related to microbial nutrient metabolism in deforested soils. However, we did observe changes in community functions such as increases in DNA repair, protein processing, modification, degradation and folding functions, and these functions might reflect adaptation to changes in soil characteristics due to forest clear-cutting and burning. In addition, there were changes in the composition of the bacterial groups associated with metabolism-related functions. Co-occurrence microbial network analysis identified distinct phylogenetic patterns for forest and deforested soils and suggested relationships between Planctomycetes and aluminium content, and Actinobacteria and nitrogen sources in Amazon soils. The results support taxonomic and functional adaptations in the soil bacterial community following deforestation. We hypothesize that these microbial adaptations may serve as a buffer to drastic changes in soil fertility after slash-and-burning deforestation in the Amazon region.}, }
@article {pmid25805726, year = {2015}, author = {Hickey, RJ and Zhou, X and Settles, ML and Erb, J and Malone, K and Hansmann, MA and Shew, ML and Van Der Pol, B and Fortenberry, JD and Forney, LJ}, title = {Vaginal microbiota of adolescent girls prior to the onset of menarche resemble those of reproductive-age women.}, journal = {mBio}, volume = {6}, number = {2}, pages = {}, pmid = {25805726}, issn = {2150-7511}, support = {P30 GM103324/GM/NIGMS NIH HHS/United States ; P30GM103324/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; Bacteria/*classification/*genetics ; *Biota ; Child ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Healthy Volunteers ; Humans ; Longitudinal Studies ; Molecular Sequence Data ; Phylogeny ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vagina/*microbiology ; }, abstract = {UNLABELLED: Puberty is an important developmental stage wherein hormonal shifts mediate the physical and physiological changes that lead to menarche, but until now, the bacterial composition of vaginal microbiota during this period has been poorly characterized. We performed a prospective longitudinal study of perimenarcheal girls to gain insight into the timing and sequence of changes that occur in the vaginal and vulvar microbiota during puberty. The study enrolled 31 healthy, premenarcheal girls between the ages of 10 and 12 years and collected vaginal and vulvar swabs quarterly for up to 3 years. Bacterial composition was characterized by Roche 454 pyrosequencing and classification of regions V1 to V3 of 16S rRNA genes. Contrary to expectations, lactic acid bacteria, primarily Lactobacillus spp., were dominant in the microbiota of most girls well before the onset of menarche in the early to middle stages of puberty. Gardnerella vaginalis was detected at appreciable levels in approximately one-third of subjects, a notable finding considering that this organism is commonly associated with bacterial vaginosis in adults. Vulvar microbiota closely resembled vaginal microbiota but often exhibited additional taxa typically associated with skin microbiota. Our findings suggest that the vaginal microbiota of girls begin to resemble those of adults well before the onset of menarche.<br><br>IMPORTANCE: This study addresses longitudinal changes in vaginal and vulvar microbial communities prior to and immediately following menarche. The research is significant because microbial ecology of the vagina is an integral aspect of health, including resistance to infections. The physiologic changes of puberty and initiation of cyclic menstruation are likely to have profound effects on vaginal microbiota, but almost nothing is known about changes that normally occur during this time. Our understanding has been especially hampered by the lack of thorough characterization of microbial communities using techniques that do not rely on the cultivation of fastidious bacteria, as well as a dearth of studies on girls in the early to middle stages of puberty. This study improves our understanding of the normal development of vaginal microbiota during puberty and onset of menarche and may better inform clinical approaches to vulvovaginal care of adolescent girls.}, }
@article {pmid25805214, year = {2015}, author = {Hu, A and Hou, L and Yu, CP}, title = {Biogeography of Planktonic and Benthic Archaeal Communities in a Subtropical Eutrophic Estuary of China.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {322-335}, pmid = {25805214}, issn = {1432-184X}, mesh = {Archaea/classification/*genetics ; Biodiversity ; China ; DNA, Archaeal/genetics ; Ecosystem ; *Estuaries ; Geologic Sediments/microbiology ; Plankton/classification/*genetics ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Seawater/microbiology ; Water Microbiology ; }, abstract = {Mounting evidence suggests that Archaea are widespread and abundant in aquatic and terrestrial habitats and play fundamental roles in global biogeochemical cycles, yet the pattern and its ecological drivers of biogeographic distribution of archaeal community in estuarine ecosystem are still not well understood. Here, we investigated planktonic and benthic archaeal communities in the human-impacted Jiulong River estuary (JRE), southern China by using real-time PCR (RT-PCR) and Illumina 16S ribosomal RNA (rRNA) amplicon sequencing. RT-PCR analysis indicated that Archaea accounted for an average of 0.79 and 5.31 % of prokaryotic biomass in water and sediment samples of the JRE, respectively. The diversity of planktonic archaeal community decreased gradually from the river runoff to seawater, whereas that of benthic community did not show the similar pattern. The results of taxonomic assignments indicated that Thaumarchaeota (Nitrosopumilus and Cenarchaeum), Methanocorpusculum, and Methanospirillum were significantly more abundant in planktonic than benthic communities, whereas the relative abundances of Miscellaneous Crenarchaeotic Group, Marine Benthic Group-B/-D, anaerobic methane-oxidizing Archaea -1/-2D, and South Africa Gold Mine Euryarchaeotic Group 1 were higher in sediments than in surface waters. Moreover, planktonic archaeal community composition varied significantly at broad and finer-scale taxonomic levels along the salinity gradient. Multivariate statistical analyses revealed that salinity is the main factor structuring the JRE planktonic but not benthic archaeal community at both total community and population level. SourceTrakcer analysis indicated that river might be a major source of archaea in the freshwater zone of the JRE. Overall, this study advances our understanding of the biogeographic patterns and its ecological drivers of estuarine archaeal communities.}, }
@article {pmid25805213, year = {2015}, author = {Sauret, C and Böttjer, D and Talarmin, A and Guigue, C and Conan, P and Pujo-Pay, M and Ghiglione, JF}, title = {Top-Down Control of Diesel-Degrading Prokaryotic Communities.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {445-458}, pmid = {25805213}, issn = {1432-184X}, mesh = {Bacteria/classification/*metabolism ; Biodegradation, Environmental ; Ecosystem ; Microbial Consortia ; Petroleum/microbiology ; Seawater/*microbiology ; Water Microbiology ; }, abstract = {Biostimulation through the addition of inorganic nutrients has been the most widely practiced bioremediation strategy in oil-polluted marine waters. However, little attention has so far been paid to the microbial food web and the impact of top-down control that directly or indirectly influences the success of the bioremediation. We designed a mesocosm experiment using pre-filtered (<50 μm) surface seawater from the Bay of Banyuls-sur-Mer (North-Western Mediterranean Sea) and examined the top-down effect exerted by heterotrophic nanoflagellates (HNF) and virus-like particles (VLP) on prokaryotic abundance, activity and diversity in the presence or absence of diesel fuel. Prokaryotes, HNF and VLP abundances showed a predator-prey succession, with a co-development of HNF and VLP. In the polluted system, we observed a stronger impact of viral lysis on prokaryotic abundances than in the control. Analysis of the diversity revealed that a bloom of Vibrio sp. occurred in the polluted mesocosm. That bloom was rapidly followed by a less abundant and more even community of predation-resistant bacteria, including known hydrocarbon degraders such as Oleispira spp. and Methylophaga spp. and opportunistic bacteria such as Percisivirga spp., Roseobacter spp. and Phaeobacter spp. The shift in prokaryotic dominance in response to viral lysis provided clear evidence of the 'killing the winner' model. Nevertheless, despite clear effects on prokaryotic abundance, activity and diversity, the diesel degradation was not impacted by top-down control. The present study investigates for the first time the functioning of a complex microbial network (including VLP) using a nutrient-based biostimulation strategy and highlights some key processes useful for tailoring bioremediation.}, }
@article {pmid25801599, year = {2015}, author = {Ben Belgacem, Z and Bijttebier, S and Verreth, C and Voorspoels, S and Van de Voorde, I and Aerts, G and Willems, KA and Jacquemyn, H and Ruyters, S and Lievens, B}, title = {Biosurfactant production by Pseudomonas strains isolated from floral nectar.}, journal = {Journal of applied microbiology}, volume = {118}, number = {6}, pages = {1370-1384}, doi = {10.1111/jam.12799}, pmid = {25801599}, issn = {1365-2672}, mesh = {DNA, Bacterial/genetics ; Flowers/chemistry/*microbiology ; Molecular Sequence Data ; Phylogeny ; Plant Nectar/*chemistry ; Pseudomonas/classification/genetics/isolation &amp; purification/*metabolism ; RNA, Ribosomal, 16S/genetics ; Surface-Active Agents/chemistry/*metabolism ; }, abstract = {AIMS: To screen and identify biosurfactant-producing Pseudomonas strains isolated from floral nectar; to characterize the produced biosurfactants; and to investigate the effect of different carbon sources on biosurfactant production.<br><br>METHODS AND RESULTS: Four of eight nectar Pseudomonas isolates were found to produce biosurfactants. Phylogenetic analysis based on three housekeeping genes (16S rRNA gene, rpoB and gyrB) classified the isolates into two groups, including one group closely related to Pseudomonas fluorescens and another group closely related to Pseudomonas fragi and Pseudomonas jessenii. Although our nectar pseudomonads were able to grow on a variety of water-soluble and water-immiscible carbon sources, surface active agents were only produced when using vegetable oil as sole carbon source, including olive oil, sunflower oil or waste frying sunflower oil. Structural characterization based on thin layer chromatography (TLC) and ultra high performance liquid chromatography-accurate mass mass spectrometry (UHPLC-amMS) revealed that biosurfactant activity was most probably due to the production of fatty acids (C16:0; C18:0; C18:1 and C18:2), and mono- and diglycerides thereof.<br><br>CONCLUSIONS: Four biosurfactant-producing nectar pseudomonads were identified. The active compounds were identified as fatty acids (C16:0; C18:0; C18:1 and C18:2), and mono- and diglycerides thereof, produced by hydrolysis of triglycerides of the feedstock.<br><br>Studies on biosurfactant-producing micro-organisms have mainly focused on microbes isolated from soils and aquatic environments. Here, for the first time, nectar environments were screened as a novel source for biosurfactant producers. As nectars represent harsh environments with high osmotic pressure and varying pH levels, further screening of nectar habitats for biosurfactant-producing microbes may lead to the discovery of novel biosurfactants with broad tolerance towards different environmental conditions.}, }
@article {pmid25800495, year = {2015}, author = {Seifried, JS and Wichels, A and Gerdts, G}, title = {Spatial distribution of marine airborne bacterial communities.}, journal = {MicrobiologyOpen}, volume = {4}, number = {3}, pages = {475-490}, pmid = {25800495}, issn = {2045-8827}, mesh = {Bacteria/*classification/genetics ; *Biodiversity ; DNA Barcoding, Taxonomic ; *Ecosystem ; North Sea ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; *Spatial Analysis ; }, abstract = {The spatial distribution of bacterial populations in marine bioaerosol samples was investigated during a cruise from the North Sea to the Baltic Sea via Skagerrak and Kattegat. The analysis of the sampled bacterial communities with a pyrosequencing approach revealed that the most abundant phyla were represented by the Proteobacteria (49.3%), Bacteroidetes (22.9%), Actinobacteria (16.3%), and Firmicutes (8.3%). Cyanobacteria were assigned to 1.5% of all bacterial reads. A core of 37 bacterial OTUs made up more than 75% of all bacterial sequences. The most abundant OTU was Sphingomonas sp. which comprised 17% of all bacterial sequences. The most abundant bacterial genera were attributed to distinctly different areas of origin, suggesting highly heterogeneous sources for bioaerosols of marine and coastal environments. Furthermore, the bacterial community was clearly affected by two environmental parameters - temperature as a function of wind direction and the sampling location itself. However, a comparison of the wind directions during the sampling and calculated backward trajectories underlined the need for more detailed information on environmental parameters for bioaerosol investigations. The current findings support the assumption of a bacterial core community in the atmosphere. They may be emitted from strong aerosolizing sources, probably being mixed and dispersed over long distances.}, }
@article {pmid25799163, year = {2015}, author = {Saillard, C and Sannini, A and Chow-Chine, L and Blache, JL and Brun, JP and Mokart, D}, title = {[Febrile neutropenia in onco-hematology patients hospitalized in Intensive Care Unit].}, journal = {Bulletin du cancer}, volume = {102}, number = {4}, pages = {349-359}, doi = {10.1016/j.bulcan.2014.11.003}, pmid = {25799163}, issn = {1769-6917}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Antifungal Agents/therapeutic use ; Antiviral Agents/therapeutic use ; Catheter-Related Infections/drug therapy ; *Critical Care ; Drug Resistance, Multiple, Bacterial ; Febrile Neutropenia/complications/*drug therapy ; Hematologic Neoplasms/*complications ; Humans ; Intensive Care Units ; Pseudomonas Infections/drug therapy ; Sepsis/complications/*drug therapy ; }, abstract = {Febrile neutropenia in cancer patients is associated with a high mortality. Patients are frequently admitted to Intensive Care Unit (ICU) for severe sepsis or septic shock. Empirical antibiotic treatment, including monotherapy β-lactam covering Pseudomonas aeruginosa, must be prompt. The ICU management is slightly different, due to a particular microbial ecology. A standardized approach to obtain a microbiological documentation is the cornerstone in these patients, leading to an adapted antimicrobial treatment. Systematic reassessment of initial antibiotic regimen should be realised. Neutropenic patients with severe sepsis or septic shock should receive promptly a β-lactam-aminoglycoside combination, as well as glycopeptides in case of severity or absence of documented infection. Early catheter removal should be considered widely. In the actual context of growing resistance, antibiotics saving became a major concern. According to context and microbial documentation, an escalade or de-escalade approach is recommended, to take into account multi-resistant pathogens. The addition of antifugal treatment is also a major issue in these patients and has well-defined indications. In neutropenic patients admitted in the ICU for severe sepsis or septic shock, controlling local microbial epidemiology and the emergence of multi-resistant bacteria are the key issues.}, }
@article {pmid25798439, year = {2015}, author = {Baldwin, SA and Khoshnoodi, M and Rezadehbashi, M and Taupp, M and Hallam, S and Mattes, A and Sanei, H}, title = {The microbial community of a passive biochemical reactor treating arsenic, zinc, and sulfate-rich seepage.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {3}, number = {}, pages = {27}, pmid = {25798439}, issn = {2296-4185}, abstract = {Sulfidogenic biochemical reactors (BCRs) for metal removal that use complex organic carbon have been shown to be effective in laboratory studies, but their performance in the field is highly variable. Successful operation depends on the types of microorganisms supported by the organic matrix, and factors affecting the community composition are unknown. A molecular survey of a field-based BCR that had been removing zinc and arsenic for over 6 years revealed that the microbial community was dominated by methanogens related to Methanocorpusculum sp. and Methanosarcina sp., which co-occurred with Bacteroidetes environmental groups, such as Vadin HA17, in places where the organic matter was more degraded. The metabolic potential for organic matter decomposition by Ruminococcaceae was prevalent in samples with more pyrolyzable carbon. Rhodobium- and Hyphomicrobium-related genera within the Rhizobiales order that have the metabolic potential for dark hydrogen fermentation and methylotrophy, and unclassified Comamonadaceae were the dominant Proteobacteria. The unclassified environmental group Sh765B-TzT-29 was an important Delta-Proteobacteria group in this BCR that co-occurred with the dominant Rhizobiales operational taxonomic units. Organic matter degradation is one driver for shifting the microbial community composition and therefore possibly the performance of these bioreactors over time.}, }
@article {pmid25796498, year = {2018}, author = {Richards, CL and Broadaway, SC and Eggers, MJ and Doyle, J and Pyle, BH and Camper, AK and Ford, TE}, title = {Detection of Pathogenic and Non-pathogenic Bacteria in Drinking Water and Associated Biofilms on the Crow Reservation, Montana, USA.}, journal = {Microbial ecology}, volume = {76}, number = {1}, pages = {52-63}, pmid = {25796498}, issn = {1432-184X}, support = {P20 MD002317/MD/NIMHD NIH HHS/United States ; P20 RR016455/RR/NCRR NIH HHS/United States ; }, mesh = {Alaska Natives ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification/*pathogenicity ; Bacterial Load ; *Biofilms ; Drinking Water/*microbiology ; Environmental Monitoring ; Feces/microbiology ; Groundwater/microbiology ; Helicobacter/classification/isolation &amp; purification ; Heterotrophic Processes ; Humans ; Indians, North American ; Legionella/classification/isolation &amp; purification ; Montana ; Mycobacterium/classification/isolation &amp; purification ; *Water Microbiology ; Water Quality ; Water Supply ; }, abstract = {Private residences in rural areas with water systems that are not adequately regulated, monitored, and updated could have drinking water that poses a health risk. To investigate water quality on the Crow Reservation in Montana, water and biofilm samples were collected from 57 public buildings and private residences served by either treated municipal or individual groundwater well systems. Bacteriological quality was assessed including detection of fecal coliform bacteria and heterotrophic plate count (HPC) as well as three potentially pathogenic bacterial genera, Mycobacterium, Legionella, and Helicobacter. All three target genera were detected in drinking water systems on the Crow Reservation. Species detected included the opportunistic and frank pathogens Mycobacterium avium, Mycobacterium gordonae, Mycobacterium flavescens, Legionella pneumophila, and Helicobacter pylori. Additionally, there was an association between HPC bacteria and the presence of Mycobacterium and Legionella but not the presence of Helicobacter. This research has shown that groundwater and municipal drinking water systems on the Crow Reservation can harbor potential bacterial pathogens.}, }
@article {pmid25794593, year = {2015}, author = {Antúnez, K and Anido, M and Branchiccela, B and Harriet, J and Campa, J and Invernizzi, C and Santos, E and Higes, M and Martín-Hernández, R and Zunino, P}, title = {Seasonal Variation of Honeybee Pathogens and its Association with Pollen Diversity in Uruguay.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {522-533}, pmid = {25794593}, issn = {1432-184X}, mesh = {Animals ; Bees/*virology ; *Pollen ; Seasons ; Uruguay ; }, abstract = {Honeybees are susceptible to a wide range of pathogens, which have been related to the occurrence of colony loss episodes reported mainly in north hemisphere countries. Their ability to resist those infections is compromised if they are malnourished or exposed to pesticides. The aim of the present study was to carry out an epidemiological study in Uruguay, South America, in order to evaluate the dynamics and interaction of honeybee pathogens and evaluate their association with the presence of external stress factors such as restricted pollen diversity and presence of agrochemicals. We monitored 40 colonies in two apiaries over 24 months, regularly quantifying colony strength, parasite and pathogen status, and pollen diversity. Chlorinated pesticides, phosphorus, pyrethroid, fipronil, or sulfas were not found in stored pollen in any colony or season. Varroa destructor was widespread in March (end of summer-beginning of autumn), decreasing after acaricide treatments. Viruses ABPV, DWV, and SBV presented a similar trend, while IAPV and KBV were not detected. Nosema ceranae was detected along the year while Nosema apis was detected only in one sample. Fifteen percent of the colonies died, being associated to high V. destructor mite load in March and high N. ceranae spore loads in September. Although similar results have been reported in north hemisphere countries, this is the first study of these characteristics in Uruguay, highlighting the regional importance. On the other side, colonies with pollen of diverse botanical origins showed reduced viral infection levels, suggesting that an adequate nutrition is important for the development of healthy colonies.}, }
@article {pmid25792281, year = {2015}, author = {Fleischhacker, A and Grube, M and Kopun, T and Hafellner, J and Muggia, L}, title = {Community Analyses Uncover High Diversity of Lichenicolous Fungi in Alpine Habitats.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {348-360}, pmid = {25792281}, issn = {1432-184X}, support = {P 24114/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {DNA, Fungal/genetics ; Ecosystem ; Fungi/classification/*genetics ; Lichens/*microbiology ; Phylogeny ; Symbiosis ; }, abstract = {Lichens are frequently colonized by specialized, lichenicolous fungi. Symptomatic lichenicolous fungi usually display typical phenotypes and reproductive structures on the lichen hosts. The classification based on these structures revealed different host specificity patterns. Other fungi occur asymptomatically in the lichen thalli and are much less known. We aimed at studying the diversity of lichen-associated fungi in specific, lichen-rich communities on rocks in the Alps. We tested whether lichenicolous fungi developing symptomatically on their known hosts also occur asymptomatically in other thalli of the same or of different host species. We collected lichen thalli according to a uniform sampling design comprising individuals adjacent to thalli that showed symptoms of lichenicolous fungal infections. The total fungal communities in the selected lichen thalli were further studied by single-strand conformation polymorphism (SSCP) fingerprinting analyses and sequencing of internal transcribed spacer (ITS) fragments. The systematic, stratified sampling strategy helped to recover 17 previously undocumented lichenicolous fungi and almost exhaustively the species diversity of symptomatic lichenicolous fungi in the studied region. The results from SSCP and the sequencing analyses did not reveal asymptomatic occurrence of normally symptomatic lichenicolous fungi in thalli of both the same and different lichen host species. The fungal diversity did not correlate with the species diversity of the symptomatic lichenicolous fungus-lichen host associations. The complex fingerprint patterns recovered here for fungal communities, in associations of well-delimited lichen thalli, suggest lichen symbiosis as suitable subjects for fungal metacommunity studies.}, }
@article {pmid25791008, year = {2015}, author = {Stoops, J and Ruyters, S and Busschaert, P and Spaepen, R and Verreth, C and Claes, J and Lievens, B and Van Campenhout, L}, title = {Bacterial community dynamics during cold storage of minced meat packaged under modified atmosphere and supplemented with different preservatives.}, journal = {Food microbiology}, volume = {48}, number = {}, pages = {192-199}, doi = {10.1016/j.fm.2014.12.012}, pmid = {25791008}, issn = {1095-9998}, mesh = {Bacteria/drug effects/genetics/*growth &amp; development/isolation &amp; purification ; *Biodiversity ; Food Packaging ; Food Preservation ; Food Preservatives/*pharmacology ; Food Storage ; Meat Products/*microbiology ; }, abstract = {Since minced meat is very susceptible for microbial growth, characterisation of the bacterial community dynamics during storage is important to optimise preservation strategies. The purpose of this study was to investigate the effect of different production batches and the use of different preservatives on the composition of the bacterial community in minced meat during 9 days of cold storage under modified atmosphere (66% O2, 25% CO2 and 9% N2). To this end, both culture-dependent (viable aerobic and anaerobic counts) and culture-independent (454 pyrosequencing) analyses were performed. Initially, microbial counts of fresh minced meat showed microbial loads between 3.5 and 5.0 log cfu/g. The observed microbial diversity was relatively high, and the most abundant bacteria differed among the samples. During storage an increase of microbial counts coincided with a dramatic decrease in bacterial diversity. At the end of the storage period, most samples showed microbial counts above the spoilage level of 7 log cfu/g. A relatively similar bacterial community was obtained regardless of the manufacturing batch and the preservative used, with Lactobacillus algidus and Leuconostoc sp. as the most dominant microorganisms. This suggests that both bacteria played an important role in the spoilage of minced meat packaged under modified atmosphere.}, }
@article {pmid25784903, year = {2015}, author = {Balk, M and Laverman, AM and Keuskamp, JA and Laanbroek, HJ}, title = {Nitrate ammonification in mangrove soils: a hidden source of nitrite?.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {166}, pmid = {25784903}, issn = {1664-302X}, abstract = {Nitrate reduction is considered to be a minor microbial pathway in the oxidation of mangrove-derived organic matter due to a limited supply of nitrate in mangrove soils. At a limited availability of this electron acceptor compared to the supply of degradable carbon, nitrate ammonification is thought to be the preferential pathway of nitrate reduction. Mangrove forest mutually differ in their productivity, which may lead to different available carbon to nitrate ratios in their soil. Hence, nitrate ammonification is expected to be of more importance in high- compared to low-productive forests. The hypothesis was tested in flow-through reactors that contain undisturbed mangrove soils from high-productive Avicennia germinans and Rhizophora mangle forests in Florida and low-productive Avicennia marina forests in Saudi Arabia. Nitrate was undetectable in the soils from both regions. It was assumed that a legacy of nitrate ammonification would be reflected by a higher ammonium production from these soils upon the addition of nitrate. Unexpectedly, the soils from the low-productive forests in Saudi Arabia produced considerably more ammonium than the soils from the high-productive forests in Florida. Hence, other environmental factors than productivity must govern the selection of nitrate ammonification or denitrification. A rather intriguing observation was the 1:1 production of nitrite and ammonium during the consumption of nitrate, more or less independent from sampling region, location, sampling depth, mangrove species and from the absence or presence of additional degradable carbon. This 1:1 ratio points to a coupled production of ammonium and nitrite by one group of nitrate-reducing microorganisms. Such a production of nitrite will be hidden by the presence of active nitrite-reducing microorganisms under the nitrate-limited conditions of most mangrove forest soils.}, }
@article {pmid25784900, year = {2015}, author = {Wisecaver, JH and Rokas, A}, title = {Fungal metabolic gene clusters-caravans traveling across genomes and environments.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {161}, pmid = {25784900}, issn = {1664-302X}, abstract = {Metabolic gene clusters (MGCs), physically co-localized genes participating in the same metabolic pathway, are signature features of fungal genomes. MGCs are most often observed in specialized metabolism, having evolved in individual fungal lineages in response to specific ecological needs, such as the utilization of uncommon nutrients (e.g., galactose and allantoin) or the production of secondary metabolic antimicrobial compounds and virulence factors (e.g., aflatoxin and melanin). A flurry of recent studies has shown that several MGCs, whose functions are often associated with fungal virulence as well as with the evolutionary arms race between fungi and their competitors, have experienced horizontal gene transfer (HGT). In this review, after briefly introducing HGT as a source of gene innovation, we examine the evidence for HGT's involvement on the evolution of MGCs and, more generally of fungal metabolism, enumerate the molecular mechanisms that mediate such transfers and the ecological circumstances that favor them, as well as discuss the types of evidence required for inferring the presence of HGT in MGCs. The currently available examples indicate that transfers of entire MGCs have taken place between closely related fungal species as well as distant ones and that they sometimes involve large chromosomal segments. These results suggest that the HGT-mediated acquisition of novel metabolism is an ongoing and successful ecological strategy for many fungal species.}, }
@article {pmid25783218, year = {2015}, author = {Ding, C and Ma, T and Hu, A and Dai, L and He, Q and Cheng, L and Zhang, H}, title = {Enrichment and Characterization of a Psychrotolerant Consortium Degrading Crude Oil Alkanes Under Methanogenic Conditions.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {433-444}, pmid = {25783218}, issn = {1432-184X}, mesh = {Archaea/classification/*genetics/metabolism ; Biodegradation, Environmental ; Methane/metabolism ; Microbial Consortia/physiology ; Petroleum/*metabolism ; Phylogeny ; Polymorphism, Restriction Fragment Length/genetics ; }, abstract = {Anaerobic alkane degradation via methanogenesis has been intensively studied under mesophilic and thermophilic conditions. While there is a paucity of information on the ability and composition of anaerobic alkane-degrading microbial communities under low temperature conditions. In this study, we investigated the ability of consortium Y15, enriched from Shengli oilfield, to degrade hydrocarbons under different temperature conditions (5-35 °C). The consortium could use hexadecane over a low temperature range (15-30 °C). No growth was detected below 10 °C and above 35 °C, indicating the presence of cold-tolerant species capable of alkane degradation. The preferential degradation of short chain n-alkanes from crude oil was observed by this consortium. The structure and dynamics of the microbial communities were examined using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting and Sanger sequencing of 16S rRNA genes. The core archaeal communities were mainly composed of aceticlastic Methanosaeta spp. Syntrophaceae-related microorganisms were always detected during consecutive transfers and dominated the bacterial communities, sharing 94-96 % sequence similarity with Smithella propionica strain LYP(T). Phylogenetic analysis of Syntrophaceae-related clones in diverse methanogenic alkane-degrading cultures revealed that most of them were clustered into three sublineages. Syntrophaceae clones retrieved from this study were mainly clustered into sublineage I, which may represent psychrotolerant, syntrophic alkane degraders. These results indicate the wide geographic distribution and ecological function of syntrophic alkane degraders.}, }
@article {pmid25781608, year = {2015}, author = {Ptak, A and Bedford, MR and Świątkiewicz, S and Żyła, K and Józefiak, D}, title = {Phytase modulates ileal microbiota and enhances growth performance of the broiler chickens.}, journal = {PloS one}, volume = {10}, number = {3}, pages = {e0119770}, pmid = {25781608}, issn = {1932-6203}, mesh = {6-Phytase/*pharmacology ; Animals ; Calcium/metabolism ; Chickens/growth &amp; development/*microbiology ; Diet/veterinary ; Dietary Supplements ; Female ; Fermentation ; Gastrointestinal Tract/*drug effects/microbiology ; In Situ Hybridization, Fluorescence ; Microbiota/*drug effects ; Phosphorus/metabolism ; }, abstract = {Phytase is well studied and explored, however, little is known about its effects on the microbial ecology of the gastrointestinal tract. In total, 400 one-day-old female Ross 308 chicks were randomly distributed to four experimental groups. The dietary treatments were arranged as a 2 × 2 complete factorial design, with the factors being adequate (PC) or insufficient calcium (Ca) and digestible phosphor (dP)(NC) and with or without 5000 phytase units (FTU)/kg of Escherichia coli 6-phytase. The gastrointestinal tract pH values, ileal microbial communities and short-chain fatty acid concentrations in the digesta were determined. The reduction in Ca and dP concentration significantly affected pH in the crop and caeca, and addition of phytase to the NC resulted in a pH increase in the ileum. The reduction in Ca and dP concentration significantly lowered, while phytase supplementation increased ileal total bacterial counts. Additionally, the deficient diet reduced butyrate- but increased lactate-producing bacteria. The addition of phytase increased Lactobacillus sp./Enterococcus sp. whereas in case of Clostridium leptum subgroup, Clostridium coccoides-Eubacterium rectale cluster, Bifidobacterium sp. and Streptococcus/Lactococcus counts, a significant Ca and dP level x phytase interaction was found. However, the recorded interactions indicated that the effects of phytase and Ca and dP levels were not consistent. Furthermore, the reduction of Ca and dP level lowered Clostridium perfringens and Enterobacteriaceae counts. The analysis of fermentation products showed that reducing the Ca and dP content in the diet reduced total SCFA, DL-lactate, and acetic acid in the ileum whereas phytase increased concentrations of these acids in the NC group. This suggests that P is a factor which limits fermentation in the ileum. It may be concluded that phytase plays a role in modulating the gut microbiota of chicken, however, this is clearly linked with the levels of P and Ca in a diet.}, }
@article {pmid25779926, year = {2015}, author = {Karaś, MA and Turska-Szewczuk, A and Trapska, D and Urbanik-Sypniewska, T}, title = {Growth and Survival of Mesorhizobium loti Inside Acanthamoeba Enhanced Its Ability to Develop More Nodules on Lotus corniculatus.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {566-575}, pmid = {25779926}, issn = {1432-184X}, mesh = {Acanthamoeba/*microbiology ; Lotus/*microbiology ; Mesorhizobium/*growth &amp; development/*physiology ; Symbiosis/physiology ; }, abstract = {The importance of protozoa as environmental reservoirs of pathogens is well recognized, while their impact on survival and symbiotic properties of rhizobia has not been explored. The possible survival of free-living rhizobia inside amoebae could influence bacterial abundance in the rhizosphere of legume plants and the nodulation competitiveness of microsymbionts. Two well-characterized strains of Mesorhizobium: Mesorhizobium loti NZP2213 and Mesorhizobium huakuii symbiovar loti MAFF303099 were assayed for their growth ability within the Neff strain of Acanthamoeba castellanii. Although the association ability and the initial uptake rate of both strains were similar, recovery of viable M. huakuii MAFF303099 after 4 h postinfection decreased markedly and that of M. loti NZP2213 increased. The latter strain was also able to survive prolonged co-incubation within amoebae and to self-release from the amoeba cell. The temperature 28 °C and PBS were established as optimal for the uptake of Mesorhizobium by amoebae. The internalization of mesorhizobia was mediated by the mannose-dependent receptor. M. loti NZP2213 bacteria released from amoebae developed 1.5 times more nodules on Lotus corniculatus than bacteria cultivated in an amoebae-free medium.}, }
@article {pmid25778509, year = {2015}, author = {Ellström, M and Shah, F and Johansson, T and Ahrén, D and Persson, P and Tunlid, A}, title = {The carbon starvation response of the ectomycorrhizal fungus Paxillus involutus.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {4}, pages = {}, pmid = {25778509}, issn = {1574-6941}, mesh = {Autolysis/metabolism ; Basidiomycota/*metabolism ; Biomass ; Carbon/*metabolism ; Carrier Proteins/biosynthesis/metabolism ; Chitinases/biosynthesis ; Gene Expression Profiling ; Hyphae/growth &amp; development/*metabolism ; Laccase/biosynthesis ; Mycelium/*metabolism ; Mycorrhizae/*metabolism ; Peptide Hydrolases/biosynthesis ; Soil/chemistry ; Soil Microbiology ; Transcriptome ; }, abstract = {The amounts of carbon allocated to the fungal partner in ectomycorrhizal associations can vary substantially depending on the plant growth and the soil nutrient conditions, and the fungus may frequently be confronted with limitations in carbon. We used chemical analysis and transcriptome profiling to examine the physiological response of the ectomycorrhizal fungus Paxillus involutus to carbon starvation during axenic cultivation. Carbon starvation induced a decrease in the biomass. Concomitantly, ammonium, cell wall material (chitin) and proteolytic enzymes were released into the medium, which suggest autolysis. Compared with the transcriptome of actively growing hyphae, about 45% of the transcripts analyzed were differentially regulated during C-starvation. Induced during starvation were transcripts encoding extracellular enzymes such as peptidases, chitinases and laccases. In parallel, transcripts of N-transporters were upregulated, which suggest that some of the released nitrogen compounds were re-assimilated by the mycelium. The observed changes suggest that the carbon starvation response in P. involutus is associated with complex cellular changes that involves autolysis, recycling of intracellular compounds by autophagy and reabsorption of the extracellular released material. The study provides molecular markers that can be used to examine the role of autolysis for the turnover and survival of the ectomycorrhizal mycelium in soils.}, }
@article {pmid25778508, year = {2015}, author = {Wolf, AB and Rudnick, MB and de Boer, W and Kowalchuk, GA}, title = {Early colonizers of unoccupied habitats represent a minority of the soil bacterial community.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {5}, pages = {}, doi = {10.1093/femsec/fiv024}, pmid = {25778508}, issn = {1574-6941}, mesh = {Ecosystem ; Enterobacteriaceae/genetics/*growth &amp; development/metabolism ; Genes, rRNA ; Microbiota/genetics ; Oxalobacteraceae/genetics/*metabolism ; Pseudomonas/genetics/*growth &amp; development/metabolism ; Pseudomonas fluorescens/genetics/*metabolism ; RNA, Ribosomal, 16S/genetics ; Soil ; *Soil Microbiology ; }, abstract = {In order to understand (re-)colonization of microhabitats and bacterial succession in soil, it is important to understand which members of soil bacterial communities are most motile in the porous soil matrix. To address this issue, we carried out a series of experiments in sterilized soil microcosms. Using two different model strains, Pseudomonas fluorescens strain Pf0-1 and Collimonas fungivorans strain Ter331, we first determined the influence of nutrient availability on bacterial expansion rates. Based on these results, we then conducted similar microcosm experiments to examine microbial mobility within natural soil bacterial communities under a single nutrient regime. The expansion of bacterial populations within the community was assayed by quantitative PCR and pyrosequencing of 16S rRNA gene fragments. We observed that only a relatively small subset of the total community was able to expand to an appreciable distance (more than 2 cm) within 48 h, with the genera Undibacterium, Pseudomonas and Massilia and especially the family Enterobacteriaceae dominating the communities more distant from the point of inoculation. These results suggest that (re-)colonization of open habitats in soil may be dominated by a few rapidly moving species, which may have important consequences for microbial succession.}, }
@article {pmid25777679, year = {2015}, author = {Reina, LD and Pérez-Díaz, IM and Breidt, F and Azcarate-Peril, MA and Medina, E and Butz, N}, title = {Characterization of the microbial diversity in yacon spontaneous fermentation at 20 °C.}, journal = {International journal of food microbiology}, volume = {203}, number = {}, pages = {35-40}, pmid = {25777679}, issn = {1879-3460}, support = {P30 DK034987/DK/NIDDK NIH HHS/United States ; P30 DK34987/DK/NIDDK NIH HHS/United States ; }, mesh = {Asteraceae/*microbiology ; Bacteria/classification/drug effects/genetics ; Bacterial Load ; Bacterial Physiological Phenomena ; *Biodiversity ; *Fermentation ; Microbiota/drug effects/physiology ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sodium Chloride/pharmacology ; Time Factors ; Yeasts/drug effects/genetics ; }, abstract = {The prebiotic fructooligosaccharide content of yacon makes this root an attractive alternative for the supplementation of a variety of food products. The preservation of yacon by fermentation has been proposed as an alternative to increase the probiotic content of the root concomitantly with its shelf life. Thus the fermented yacon could have significant functional content. The objective of this research was to characterize the biochemistry and microbiology of spontaneous yacon fermentation with 2% NaCl and define the viability of the proposed process. The biochemical analysis of spontaneous heterolactic fermentation of yacon showed a progressive drop in pH with increased lactic and acetic acids, and the production of mannitol during fermentation. The microbial ecology of yacon fermentation was investigated using culture-dependent and culture-independent methods. Bacterial cell counts revealed a dominance of lactic acid bacteria (LAB) over yeasts, which were also present during the first 2 days of the fermentation. Results showed that the heterofermentative LAB were primarily Leuconostoc species, thus it presents a viable method to achieve long term preservation of this root.}, }
@article {pmid25775938, year = {2015}, author = {Maropola, MK and Ramond, JB and Trindade, M}, title = {Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench).}, journal = {Journal of microbiological methods}, volume = {112}, number = {}, pages = {104-117}, doi = {10.1016/j.mimet.2015.03.012}, pmid = {25775938}, issn = {1872-8359}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; DNA/genetics/*isolation &amp; purification ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Endophytes/classification/genetics/*isolation &amp; purification ; Genes, rRNA ; Metagenomics/*methods ; Plant Roots/microbiology ; Plant Stems/microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; Sorghum/*microbiology ; }, abstract = {Culture-independent studies rely on the quantity and quality of the extracted environmental metagenomic DNA (mDNA). To fully access the plant tissue microbiome, the extracted plant mDNA should allow optimal PCR applications and the genetic content must be representative of the total microbial diversity. In this study, we evaluated the endophytic bacterial diversity retrieved using different mDNA extraction procedures. Metagenomic DNA from sorghum (Sorghum bicolor L. Moench) stem and root tissues were extracted using two classical DNA extraction protocols (CTAB- and SDS-based) and five commercial kits. The mDNA yields and quality as well as the reproducibility were compared. 16S rRNA gene terminal restriction fragment length polymorphism (t-RFLP) was used to assess the impact on endophytic bacterial community structures observed. Generally, the classical protocols obtained high mDNA yields from sorghum tissues; however, they were less reproducible than the commercial kits. Commercial kits retrieved higher quality mDNA, but with lower endophytic bacterial diversities compared to classical protocols. The SDS-based protocol enabled access to the highest sorghum endophytic diversities. Therefore, "SDS-extracted" sorghum root and stem microbiome diversities were analysed via 454 pyrosequencing, and this revealed that the two tissues harbour significantly different endophytic communities. Nevertheless, both communities are dominated by agriculturally important genera such as Microbacterium, Agrobacterium, Sphingobacterium, Herbaspirillum, Erwinia, Pseudomonas and Stenotrophomonas; which have previously been shown to play a role in plant growth promotion. This study shows that DNA extraction protocols introduce biases in culture-independent studies of environmental microbial communities by influencing the mDNA quality, which impacts the microbial diversity analyses and evaluation. Using the broad-spectrum SDS-based DNA extraction protocol allows the recovery of the most diverse endophytic communities associated with sorghum tissues and, as such, establishes a reliable basis for future study of endophytic communities.}, }
@article {pmid25774766, year = {2015}, author = {Tyc, O and Wolf, AB and Garbeva, P}, title = {The effect of phylogenetically different bacteria on the fitness of Pseudomonas fluorescens in sand microcosms.}, journal = {PloS one}, volume = {10}, number = {3}, pages = {e0119838}, pmid = {25774766}, issn = {1932-6203}, mesh = {Bacillus/*physiology ; Microbial Consortia/*physiology ; Pedobacter/*physiology ; Pseudomonas fluorescens/*physiology ; *Soil Microbiology ; }, abstract = {In most environments many microorganisms live in close vicinity and can interact in various ways. Recent studies suggest that bacteria are able to sense and respond to the presence of neighbouring bacteria in the environment and alter their response accordingly. This ability might be an important strategy in complex habitats such as soils, with great implications for shaping the microbial community structure. Here, we used a sand microcosm approach to investigate how Pseudomonas fluorescens Pf0-1 responds to the presence of monocultures or mixtures of two phylogenetically different bacteria, a Gram-negative (Pedobacter sp. V48) and a Gram-positive (Bacillus sp. V102) under two nutrient conditions. Results revealed that under both nutrient poor and nutrient rich conditions confrontation with the Gram-positive Bacillus sp. V102 strain led to significant lower cell numbers of Pseudomonas fluorescens Pf0-1, whereas confrontation with the Gram-negative Pedobacter sp. V48 strain did not affect the growth of Pseudomonas fluorescens Pf0-1. However, when Pseudomonas fluorescens Pf0-1 was confronted with the mixture of both strains, no significant effect on the growth of Pseudomonas fluorescens Pf0-1 was observed. Quantitative real-time PCR data showed up-regulation of genes involved in the production of a broad-spectrum antibiotic in Pseudomonas fluorescens Pf0-1 when confronted with Pedobacter sp. V48, but not in the presence of Bacillus sp. V102. The results provide evidence that the performance of bacteria in soil depends strongly on the identity of neighbouring bacteria and that inter-specific interactions are an important factor in determining microbial community structure.}, }
@article {pmid25774156, year = {2015}, author = {Szafranski, KM and Deschamps, P and Cunha, MR and Gaudron, SM and Duperron, S}, title = {Colonization of plant substrates at hydrothermal vents and cold seeps in the northeast Atlantic and Mediterranean and occurrence of symbiont-related bacteria.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {162}, pmid = {25774156}, issn = {1664-302X}, abstract = {Reducing conditions with elevated sulfide and methane concentrations in ecosystems such as hydrothermal vents, cold seeps or organic falls, are suitable for chemosynthetic primary production. Understanding processes driving bacterial diversity, colonization and dispersal is of prime importance for deep-sea microbial ecology. This study provides a detailed characterization of bacterial assemblages colonizing plant-derived substrates using a standardized approach over a geographic area spanning the North-East Atlantic and Mediterranean. Wood and alfalfa substrates in colonization devices were deployed for different periods at 8 deep-sea chemosynthesis-based sites in four distinct geographic areas. Pyrosequencing of a fragment of the 16S rRNA-encoding gene was used to describe bacterial communities. Colonization occurred within the first 14 days. The diversity was higher in samples deployed for more than 289 days. After 289 days, no relation was observed between community richness and deployment duration, suggesting that diversity may have reached saturation sometime in between. Communities in long-term deployments were different, and their composition was mainly influenced by the geographical location where devices were deployed. Numerous sequences related to horizontally-transmitted chemosynthetic symbionts of metazoans were identified. Their potential status as free-living forms of these symbionts was evaluated based on sequence similarity with demonstrated symbionts. Results suggest that some free-living forms of metazoan symbionts or their close relatives, such as Epsilonproteobacteria associated with the shrimp Rimicaris exoculata, are efficient colonizers of plant substrates at vents and seeps.}, }
@article {pmid25773718, year = {2015}, author = {Moore, ML and Six, DL}, title = {Effects of Temperature on Growth, Sporulation, and Competition of Mountain Pine Beetle Fungal Symbionts.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {336-347}, pmid = {25773718}, issn = {1432-184X}, mesh = {Animals ; Coleoptera/*microbiology ; Ophiostomatales/*growth &amp; development/*physiology ; Population Dynamics ; Symbiosis/physiology ; Temperature ; }, abstract = {The mountain pine beetle, Dendroctonus ponderosae, depends on two fungi, Grosmannia clavigera and Ophiostoma montium, to augment a nutrient-poor woody food resource. Because the two fungi exert differential effects on the host beetle, temperature-driven differences in fungal growth and competition outcomes have a strong potential to influence host population dynamics. Weisolated fungi from beetles and wood from three locations in Montana and Utah, USA, and measured their growth rates and sporulation between 5 and 35 °C on artificial media. We also measured growth rates and percent resource capture for each fungus at 10, 15, 21, and 25 °C during inter- and intra-specific competition. G. clavigera excelled at resource capture at most temperatures. Its optimal growth temperature occurs around 20 °C while that of O. montium occurs near 30 °C. There was no effect of collection site on growth or sporulation; however, O. montium exhibited greater variability in response to temperature than did G. clavigera. Sporulation of G. clavigera was greatest at 30 °C while O. montium sporulated at low levels across all temperatures. During competition experiments, G. clavigera captured more resources than O. montium at most temperatures and captured a greater percentage of resources at a greater rate during inter-specific competition than during intra-specific competition. In contrast, O. montium captured a greater percentage of resources during intra-specific competition. These results demonstrate that temperature can differentially affect growth, sporulation, and resource capture of the two symbionts, indicating that it may be an important factor influencing the composition and dynamics of the symbiosis.}, }
@article {pmid25770702, year = {2015}, author = {Guo, K and Prévoteau, A and Patil, SA and Rabaey, K}, title = {Engineering electrodes for microbial electrocatalysis.}, journal = {Current opinion in biotechnology}, volume = {33}, number = {}, pages = {149-156}, doi = {10.1016/j.copbio.2015.02.014}, pmid = {25770702}, issn = {1879-0429}, mesh = {Bacteria/*chemistry/*metabolism ; *Biocatalysis ; Carbon/chemistry ; Electrodes ; Electron Transport ; Nanostructures ; Surface Properties ; }, abstract = {Microbial electrocatalysis refers to the use of microorganisms to catalyze electrode reactions. Many processes have been developed on this principle, ranging from power generation to CO2 conversion using bioelectrochemical systems. The nature of the interface between the microorganisms and the electrodes determines the functioning and efficiency of these systems. This interface can be manipulated in terms of chemical and topographical features to better understand the interaction at nanometer and micrometer scales. Here we discuss how the electrode surface topography and chemistry impact the microorganism-electrode interaction both for direct and indirect electron transfer mechanisms. It appears that composite materials that combine high conductivity with excellent biocompatibility are most attractive towards application. In most cases this implies a combination of a metallic backbone with a carbon coating with a defined topography and chemistry.}, }
@article {pmid25765230, year = {2015}, author = {Patil, SA and Gildemyn, S and Pant, D and Zengler, K and Logan, BE and Rabaey, K}, title = {A logical data representation framework for electricity-driven bioproduction processes.}, journal = {Biotechnology advances}, volume = {33}, number = {6 Pt 1}, pages = {736-744}, doi = {10.1016/j.biotechadv.2015.03.002}, pmid = {25765230}, issn = {1873-1899}, mesh = {*Bioelectric Energy Sources ; *Biotechnology ; Electricity ; Electrodes ; Equipment Design ; }, abstract = {Microbial electrosynthesis (MES) is a process that uses electricity as an energy source for driving the production of chemicals and fuels using microorganisms and CO2 or organics as carbon sources. The development of this highly interdisciplinary technology on the interface between biotechnology and electrochemistry requires knowledge and expertise in a variety of scientific and technical areas. The rational development and commercialization of MES can be achieved at a faster pace if the research data and findings are reported in appropriate and uniformly accepted ways. Here we provide a framework for reporting on MES research and propose several pivotal performance indicators to describe these processes. Linked to this study is an online tool to perform necessary calculations and identify data gaps. A key consideration is the calculation of effective energy expenditure per unit product in a manner enabling cross comparison of studies irrespective of reactor design. We anticipate that the information provided here on different aspects of MES ranging from reactor and process parameters to chemical, electrochemical, and microbial functionality indicators will assist researchers in data presentation and ease data interpretation. Furthermore, a discussion on secondary MES aspects such as downstream processing, process economics and life cycle analysis is included.}, }
@article {pmid25764560, year = {2015}, author = {Nowka, B and Off, S and Daims, H and Spieck, E}, title = {Improved isolation strategies allowed the phenotypic differentiation of two Nitrospira strains from widespread phylogenetic lineages.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {3}, pages = {}, doi = {10.1093/femsec/fiu031}, pmid = {25764560}, issn = {1574-6941}, mesh = {Acriflavine/pharmacology ; Ampicillin/pharmacology ; Anti-Bacterial Agents/pharmacology ; Bacteria/*classification/genetics/isolation &amp; purification ; Biofilms/*growth &amp; development ; Drug Resistance, Multiple, Bacterial ; Ecosystem ; Nitrates/metabolism ; Nitrification ; Nitrites/metabolism ; Optical Tweezers ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; }, abstract = {The second step of nitrification, the oxidation of nitrite to nitrate, is vital for the functioning of the nitrogen cycle, but our understanding of the ecological roles of the involved microorganisms is still limited. The known diversity of Nitrospira, the most widely distributed nitrite-oxidizing bacteria, has increased remarkably by analyses of 16S rRNA and functional gene sequences. However, only few representatives could be brought into laboratory cultures so far. In this study, two Nitrospira from activated sludge were isolated using novel approaches together with established methods. Highly enriched 'Candidatus Nitrospira defluvii' was separated from concomitant heterotrophs by taking advantage of its resistance against ampicillin and acriflavine. Beside this member of lineage I, a novel species of lineage II, named N. lenta, was initially enriched at 10°C and finally purified by using optical tweezers. The tolerance to elevated nitrite levels was much higher in N. defluvii than in the more fastidious N. lenta and was accompanied by pronounced biofilm formation. Phylogenetic classification of 12 additional enrichments indicated that Nitrospira lineage I is common in extreme and moderate ecosystems like lineage II. The new cultures will help to explore physiological and genomic differences affecting niche separation between members of this highly diverse genus.}, }
@article {pmid25764544, year = {2015}, author = {Šulčius, S and Šimoliūnas, E and Staniulis, J and Koreivienė, J and Baltrušis, P and Meškys, R and Paškauskas, R}, title = {Characterization of a lytic cyanophage that infects the bloom-forming cyanobacterium Aphanizomenon flos-aquae.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {2}, pages = {1-7}, doi = {10.1093/femsec/fiu012}, pmid = {25764544}, issn = {1574-6941}, mesh = {Aphanizomenon/isolation &amp; purification/*virology ; Bacteriophages/*genetics/*physiology ; Estuaries ; Water Microbiology ; }, abstract = {Vb-AphaS-CL131 is a novel cyanosiphovirus that infects harmful Aphanizomenon flos-aquae. This cyanophage has an isometric head, 97 nm in diameter and a long, flexible non-contractile tail, 361 nm long. With a genome size of ~120 kb, it is the second largest cyanosiphovirus isolated to date. The latent period was estimated to be ~36 h and a single infected cell produces, on average, 218 infectious cyanophages. Cyanophage infection significantly suppresses host biomass production and alters population phenotype.}, }
@article {pmid25764536, year = {2015}, author = {Mahmoudi, N and Robeson, MS and Castro, HF and Fortney, JL and Techtmann, SM and Joyner, DC and Paradis, CJ and Pfiffner, SM and Hazen, TC}, title = {Microbial community composition and diversity in Caspian Sea sediments.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {1}, pages = {1-11}, pmid = {25764536}, issn = {1574-6941}, mesh = {Archaea/genetics ; Bacteria/genetics ; Base Sequence ; *Biodiversity ; Biomass ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Ecology ; Geologic Sediments/*microbiology ; Microbial Consortia/*genetics ; Oceans and Seas ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Pollution ; }, abstract = {The Caspian Sea is heavily polluted due to industrial and agricultural effluents as well as extraction of oil and gas reserves. Microbial communities can influence the fate of contaminants and nutrients. However, insight into the microbial ecology of the Caspian Sea significantly lags behind other marine systems. Here we describe microbial biomass, diversity and composition in sediments collected from three sampling stations in the Caspian Sea. Illumina sequencing of 16S rRNA genes revealed the presence of a number of known bacterial and archaeal heterotrophs suggesting that organic carbon is a primary factor shaping microbial communities. Surface sediments collected from bottom waters with low oxygen levels were dominated by Gammaproteobacteria while surface sediments collected from bottom waters under hypoxic conditions were dominated by Deltaproteobacteria, specifically sulfate-reducing bacteria. Thaumarchaeota was dominant across all surface sediments indicating that nitrogen cycling in this system is strongly influenced by ammonia-oxidizing archaea. This study provides a baseline assessment that may serve as a point of reference as this system changes or as the efficacy of new remediation efforts are implemented.}, }
@article {pmid25764532, year = {2015}, author = {Epelde, L and Lanzén, A and Blanco, F and Urich, T and Garbisu, C}, title = {Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {1}, pages = {1-11}, doi = {10.1093/femsec/fiu007}, pmid = {25764532}, issn = {1574-6941}, mesh = {Acclimatization ; Aluminum Silicates ; Cadmium/toxicity ; Clay ; *Ecosystem ; Lead/toxicity ; Metals, Heavy/*metabolism ; Microbial Consortia/*drug effects ; Mining ; Soil ; *Soil Microbiology ; Soil Pollutants/*metabolism ; Zinc/toxicity ; }, abstract = {Toxicity of metals released from mine tailings may cause severe damage to ecosystems. A diversity of microorganisms, however, have successfully adapted to such sites. In this study, our objective was to advance the understanding of the indigenous microbial communities of mining-impacted soils. To this end, a metatranscriptomic approach was used to study a heavily metal-contaminated site along a metal concentration gradient (up to 3220 000 and 97 000 mg kg(-1) of Cd, Pb and Zn, respectively) resulting from previous mining. Metal concentration, soil pH and amount of clay were the most important factors determining the structure of soil microbial communities. Interestingly, evenness of the microbial communities, but not its richness, increased with contamination level. Taxa with high metabolic plasticity like Ktedonobacteria and Chloroflexi were found with higher relative abundance in more contaminated samples. However, several taxa belonging to the phyla Actinobacteria and Acidobacteria followed opposite trends in relation to metal pollution. Besides, functional transcripts related to transposition or transfer of genetic material and membrane transport, potentially involved in metal resistance mechanisms, had a higher expression in more contaminated samples. Our results provide an insight into microbial communities in long-term metal-contaminated environments and how they contrast to nearby sites with lower contamination.}, }
@article {pmid25764530, year = {2015}, author = {Pessi, IS and Osorio-Forero, C and Gálvez, EJ and Simões, FL and Simões, JC and Junca, H and Macedo, AJ}, title = {Distinct composition signatures of archaeal and bacterial phylotypes in the Wanda Glacier forefield, Antarctic Peninsula.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {1}, pages = {1-10}, doi = {10.1093/femsec/fiu005}, pmid = {25764530}, issn = {1574-6941}, mesh = {Antarctic Regions ; Archaea/*genetics ; Bacteria/*genetics ; Base Sequence ; Biodiversity ; Climate Change ; Environment ; Ice Cover/*microbiology ; Microbial Consortia/*genetics ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil ; *Soil Microbiology ; }, abstract = {Several studies have shown that microbial communities in Antarctic environments are highly diverse. However, considering that the Antarctic Peninsula is among the regions with the fastest warming rates, and that regional climate change has been linked to an increase in the mean rate of glacier retreat, the microbial diversity in Antarctic soil is still poorly understood. In this study, we analysed more than 40 000 sequences of the V5-V6 hypervariable region of the 16S rRNA gene obtained by 454 pyrosequencing from four soil samples from the Wanda Glacier forefield, King George Island, Antarctic Peninsula. Phylotype diversity and richness were surprisingly high, and taxonomic assignment of sequences revealed that communities are dominated by Proteobacteria, Bacteroidetes and Euryarchaeota, with a high frequency of archaeal and bacterial phylotypes unclassified at the genus level and without cultured representative strains, representing a distinct microbial community signature. Several phylotypes were related to marine microorganisms, indicating the importance of the marine environment as a source of colonizers for this recently deglaciated environment. Finally, dominant phylotypes were related to different microorganisms possessing a large array of metabolic strategies, indicating that early successional communities in Antarctic glacier forefield can be also functionally diverse.}, }
@article {pmid25764468, year = {2015}, author = {Fillol, M and Sànchez-Melsió, A and Gich, F and Borrego, CM}, title = {Diversity of Miscellaneous Crenarchaeotic Group archaea in freshwater karstic lakes and their segregation between planktonic and sediment habitats.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {4}, pages = {}, doi = {10.1093/femsec/fiv020}, pmid = {25764468}, issn = {1574-6941}, mesh = {Base Sequence ; Crenarchaeota/*genetics/growth &amp; development/isolation &amp; purification ; DNA, Archaeal/genetics ; Euryarchaeota/*genetics/growth &amp; development/isolation &amp; purification ; Gene Library ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; Molecular Sequence Data ; Phylogeny ; Plankton/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The Miscellaneous Crenarchaeotic Group (MCG) is an archaeal lineage whose members are widespread and abundant in marine sediments. MCG archaea have also been consistently found in stratified euxinic lakes. In this work, we have studied archaeal communities in three karstic lakes to reveal potential habitat segregation of MCG subgroups between planktonic and sediment compartments. In the studied lakes, archaeal assemblages were strikingly similar to those of the marine subsurface with predominance of uncultured Halobacteria in the plankton and Thermoplasmata and MCG in anoxic, organic-rich sediments. Multivariate analyses identified sulphide and dissolved organic carbon as predictor variables of archaeal community composition. Quantification of MCG using a newly designed qPCR primer pair that improves coverage for MCG subgroups prevalent in the studied lakes revealed conspicuous populations in both the plankton and the sediment. Subgroups MCG-5a and -5b appear as planktonic specialists thriving in euxinic bottom waters, while subgroup MCG-6 emerges as a generalist group able to cope with varying reducing conditions. Besides, comparison of DNA- and cDNA-based pyrotag libraries revealed that rare subgroups in DNA libraries, i.e. MCG-15, were prevalent in cDNA-based datasets, suggesting that euxinic, organic-rich sediments of karstic lakes provide optimal niches for the activity of some specialized MCG subgroups.}, }
@article {pmid25764462, year = {2015}, author = {Daebeler, A and Bodelier, PL and Hefting, MM and Laanbroek, HJ}, title = {Ammonia-limited conditions cause of Thaumarchaeal dominance in volcanic grassland soil.}, journal = {FEMS microbiology ecology}, volume = {91}, number = {3}, pages = {}, doi = {10.1093/femsec/fiv014}, pmid = {25764462}, issn = {1574-6941}, mesh = {Ammonia/*metabolism ; Ammonium Compounds/metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; Grassland ; Nitrification/*physiology ; Oxidation-Reduction ; Soil ; *Soil Microbiology ; Thiourea/analogs &amp; derivatives/metabolism ; }, abstract = {The first step of nitrification is carried out by ammonia-oxidizing bacteria (AOB) and archaea (AOA). It is largely unknown, by which mechanisms these microbes are capable of coexistence and how their respective contribution to ammonia oxidation may differ with varying soil characteristics. To determine how different levels of ammonium availability influence the extent of archaeal and bacterial contributions to ammonia oxidation, microcosm incubations with controlled ammonium levels were conducted. Net nitrification was monitored and ammonia-oxidizer communities were quantified. Additionally, the nitrification inhibitor allylthiourea (ATU) was applied to discriminate between archaeal and bacterial contributions to soil ammonia oxidation. Thaumarchaeota, which were the only ammonia oxidizers detectable at the start of the incubation, grew in all microcosms, but AOB later became detectable in ammonium amended microcosms. Low and high additions of ammonium increasingly stimulated AOB growth, while AOA were only stimulated by the low addition. Treatment with ATU had no effect on net nitrification and sizes of ammonia-oxidizing communities suggesting that the effective concentration of ATU to discriminate between archaeal and bacterial ammonia oxidation is not the same in different soils. Our results support the niche-differentiating potential of ammonium concentration for AOA and AOB, and we conclude that ammonium limitation can be a major reason for absence of detectable AOB in soil.}, }
@article {pmid25763757, year = {2015}, author = {Piccolo, M and De Angelis, M and Lauriero, G and Montemurno, E and Di Cagno, R and Gesualdo, L and Gobbetti, M}, title = {Salivary Microbiota Associated with Immunoglobulin A Nephropathy.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {557-565}, pmid = {25763757}, issn = {1432-184X}, mesh = {Adult ; DNA, Bacterial/genetics ; Female ; Glomerulonephritis, IGA/*microbiology ; Humans ; Male ; Microbiota/genetics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; }, abstract = {This study aimed at investigating the salivary microbiota of 28 patients affected by immunoglobulin A nephropathy (IgAN). Fourteen healthy volunteers (HC) were used as control. Compared to HC, the number of some cultivable bacteria groups (e.g., total anaerobes) significantly (P < 0.05) decreased in the salivary samples of IgAN patients. Total bacteria from salivary samples of IgAN patients and HC subjects were analyzed by pyrosequencing of 16S rRNA gene. Paired t test showed no significant (P > 0.05) differences of alpha-diversity parameters (OTU, ACE, Chao1, and Shannon index) between the salivary samples of HC and IgAN patients. The difference for the community structure was further analyzed using three phylogeny-based beta-diversity measures. Compared to HC, the ratio between Firmicutes/Proteobacteria markedly decreased in IgAN patients. Gemella haemolysins, Granulicatella adiacens, and Veillonella parvula were positively associated (P < 0.05) with HC. Within the phylum Bacteroidetes, Prevotella species (Prevotella nigrescens, Prevotella intermedia, Prevotella pallens, and Prevotella salivae) were the highest in HC. The only exception was for Prevotella aurantiaca. Compared to HC, the percentage of abundance of some species, belonging to Pasteurellaceae family (e.g., Haemophylus parainfluenzae), increased in IgAN patients. Fusobacteriaceae (Fusobacterium) and Corynebacterium sp. also differed between the salivary samples of HC and IgAN patients.}, }
@article {pmid25762992, year = {2015}, author = {Hughes, KA and Cowan, DA and Wilmotte, A}, title = {Protection of Antarctic microbial communities - 'out of sight, out of mind'.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {151}, pmid = {25762992}, issn = {1664-302X}, abstract = {Recent advances in molecular biology techniques have shown the presence of diverse microbial communities and endemic species in Antarctica. Endemic microbes may be a potential source of novel biotechnologically important compounds, including, for example, new antibiotics. Thus, the scientific and biotechnological value of Antarctic terrestrial microbial habitats can be compromised by human visitation to a greater extent than previously realized. The ever-increasing human footprint in Antarctica makes consideration of this topic more pressing, as the number of locations known to be pristine habitats, where increasingly sophisticated cutting-edge research techniques may be used to their full potential, declines. Examination of the Protected Areas system of the Antarctic Treaty shows that microbial habitats are generally poorly protected. No other continent on Earth is dominated to the same degree by microbial species, and real opportunities exist to develop new ways of conceptualizing and implementing conservation of microbial biogeography on a continental scale. Here we highlight potential threats both to the conservation of terrestrial microbial ecosystems, and to future scientific research requiring their study.}, }
@article {pmid25762989, year = {2015}, author = {DeAngelis, KM and Pold, G and Topçuoğlu, BD and van Diepen, LT and Varney, RM and Blanchard, JL and Melillo, J and Frey, SD}, title = {Long-term forest soil warming alters microbial communities in temperate forest soils.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {104}, pmid = {25762989}, issn = {1664-302X}, abstract = {Soil microbes are major drivers of soil carbon cycling, yet we lack an understanding of how climate warming will affect microbial communities. Three ongoing field studies at the Harvard Forest Long-term Ecological Research (LTER) site (Petersham, MA) have warmed soils 5°C above ambient temperatures for 5, 8, and 20 years. We used this chronosequence to test the hypothesis that soil microbial communities have changed in response to chronic warming. Bacterial community composition was studied using Illumina sequencing of the 16S ribosomal RNA gene, and bacterial and fungal abundance were assessed using quantitative PCR. Only the 20-year warmed site exhibited significant change in bacterial community structure in the organic soil horizon, with no significant changes in the mineral soil. The dominant taxa, abundant at 0.1% or greater, represented 0.3% of the richness but nearly 50% of the observations (sequences). Individual members of the Actinobacteria, Alphaproteobacteria and Acidobacteria showed strong warming responses, with one Actinomycete decreasing from 4.5 to 1% relative abundance with warming. Ribosomal RNA copy number can obfuscate community profiles, but is also correlated with maximum growth rate or trophic strategy among bacteria. Ribosomal RNA copy number correction did not affect community profiles, but rRNA copy number was significantly decreased in warming plots compared to controls. Increased bacterial evenness, shifting beta diversity, decreased fungal abundance and increased abundance of bacteria with low rRNA operon copy number, including Alphaproteobacteria and Acidobacteria, together suggest that more or alternative niche space is being created over the course of long-term warming.}, }
@article {pmid25761753, year = {2015}, author = {Gunnigle, E and Ramond, JB and Guerrero, LD and Makhalanyane, TP and Cowan, DA}, title = {Draft genomic DNA sequence of the multi-resistant Sphingomonas sp. strain AntH11 isolated from an Antarctic hypolith.}, journal = {FEMS microbiology letters}, volume = {362}, number = {8}, pages = {fnv037}, doi = {10.1093/femsle/fnv037}, pmid = {25761753}, issn = {1574-6968}, mesh = {Antarctic Regions ; DNA, Bacterial/genetics ; Desert Climate ; Drug Resistance, Multiple, Bacterial ; Ecosystem ; *Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Sphingomonas/drug effects/*genetics/isolation &amp; purification ; }, abstract = {Hypoliths are microbial communities that live underneath translucent rocks in desert ecosystems and represent a key refuge niche in the Antarctic Dry Valleys. These cryptic microbial assemblages are crucial as they mediate numerous ecosystem processes. Here, we present the first draft genome of a hypolith isolate belonging to the α-proteobacterial class and the genus Sphingomonas. The draft genome of Sphingomonas sp. strain AntH11 shows the capacity of this organism to adapt to the extreme cold and arid conditions encountered in Antarctic desert soils. Our result also suggests that its metabolic versatility and multidrug resistance constitutes an opportunistic advantage in competition with other hypolith-colonizing microorganisms.}, }
@article {pmid25761208, year = {2015}, author = {Zachow, C and Jahanshah, G and de Bruijn, I and Song, C and Ianni, F and Pataj, Z and Gerhardt, H and Pianet, I and Lämmerhofer, M and Berg, G and Gross, H and Raaijmakers, JM}, title = {The Novel Lipopeptide Poaeamide of the Endophyte Pseudomonas poae RE*1-1-14 Is Involved in Pathogen Suppression and Root Colonization.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {28}, number = {7}, pages = {800-810}, doi = {10.1094/MPMI-12-14-0406-R}, pmid = {25761208}, issn = {0894-0282}, mesh = {Antibiosis ; Beta vulgaris/microbiology ; Endophytes/*physiology ; Host-Pathogen Interactions ; Lipopeptides/chemistry/isolation &amp; purification/*pharmacology ; Multigene Family ; Mutation ; Oomycetes/drug effects/growth &amp; development ; Phylogeny ; Plant Roots/microbiology ; Pseudomonas/*genetics/*metabolism ; Rhizoctonia/drug effects/*pathogenicity ; Rhizosphere ; }, abstract = {Endophytic Pseudomonas poae strain RE*1-1-14 was originally isolated from internal root tissue of sugar beet plants and shown to suppress growth of the fungal pathogen Rhizoctonia solani both in vitro and in the field. To identify genes involved in its biocontrol activity, RE*1-1-14 random mutagenesis and sequencing led to the identification of a nonribosomal peptide synthetase (NRPS) gene cluster predicted to encode a lipopeptide (LP) with a 10-amino-acid peptide moiety. The two unlinked gene clusters consisted of three NRPS genes, designated poaA (cluster 1) and poaB and poaC (cluster 2), spanning approximately 33.7 kb. In silico analysis followed by chemical analyses revealed that the encoded LP, designated poaeamide, is a structurally new member of the orfamide family. Poaeamide inhibited mycelial growth of R. solani and different oomycetes, including Phytophthora capsici, P. infestans, and Pythium ultimum. The novel LP was shown to be essential for swarming motility of strain RE*1-1-14 and had an impact on root colonization of sugar beet seedlings The poaeamide-deficient mutant colonized the rhizosphere and upper plant cortex at higher densities and with more scattered colonization patterns than the wild type. Collectively, these results indicate that Pseudomonas poae RE*1-1-14 produces a structurally new LP that is relevant for its antagonistic activity against soilborne plant pathogens and for colonization of sugar beet roots.}, }
@article {pmid25758420, year = {2016}, author = {Saha, M and Sarkar, S and Sarkar, B and Sharma, BK and Bhattacharjee, S and Tribedi, P}, title = {Microbial siderophores and their potential applications: a review.}, journal = {Environmental science and pollution research international}, volume = {23}, number = {5}, pages = {3984-3999}, pmid = {25758420}, issn = {1614-7499}, mesh = {Antimalarials/metabolism/pharmacology ; Antineoplastic Agents/metabolism/pharmacology ; Bacteria/growth &amp; development/*metabolism ; Biological Transport ; Biosensing Techniques ; Crops, Agricultural/growth &amp; development/metabolism ; Drug Carriers/metabolism/pharmacology ; Ecology ; Humans ; Iron/*metabolism ; Iron Chelating Agents/metabolism/pharmacology ; Siderophores/*metabolism/*pharmacology ; }, abstract = {Siderophores are small organic molecules produced by microorganisms under iron-limiting conditions which enhance the uptake of iron to the microorganisms. In environment, the ferric form of iron is insoluble and inaccessible at physiological pH (7.35-7.40). Under this condition, microorganisms synthesize siderophores which have high affinity for ferric iron. These ferric iron-siderophore complexes are then transported to cytosol. In cytosol, the ferric iron gets reduced into ferrous iron and becomes accessible to microorganism. In recent times, siderophores have drawn much attention due to its potential roles in different fields. Siderophores have application in microbial ecology to enhance the growth of several unculturable microorganisms and can alter the microbial communities. In the field of agriculture, different types of siderophores promote the growth of several plant species and increase their yield by enhancing the Fe uptake to plants. Siderophores acts as a potential biocontrol agent against harmful phyto-pathogens and holds the ability to substitute hazardous pesticides. Heavy-metal-contaminated samples can be detoxified by applying siderophores, which explicate its role in bioremediation. Siderophores can detect the iron content in different environments, exhibiting its role as a biosensor. In the medical field, siderophore uses the "Trojan horse strategy" to form complexes with antibiotics and helps in the selective delivery of antibiotics to the antibiotic-resistant bacteria. Certain iron overload diseases for example sickle cell anemia can be treated with the help of siderophores. Other medical applications of siderophores include antimalarial activity, removal of transuranic elements from the body, and anticancer activity. The aim of this review is to discuss the important roles and applications of siderophores in different sectors including ecology, agriculture, bioremediation, biosensor, and medicine.}, }
@article {pmid25756301, year = {2015}, author = {De Vrieze, J and Raport, L and Willems, B and Verbrugge, S and Volcke, E and Meers, E and Angenent, LT and Boon, N}, title = {Inoculum selection influences the biochemical methane potential of agro-industrial substrates.}, journal = {Microbial biotechnology}, volume = {8}, number = {5}, pages = {776-786}, pmid = {25756301}, issn = {1751-7915}, mesh = {Anaerobiosis ; Biotransformation ; Manure ; Methane/*metabolism ; *Microbial Consortia ; Molasses ; Sewage/*microbiology ; *Waste Products ; }, abstract = {Obtaining a reliable estimation of the methane potential of organic waste streams in anaerobic digestion, for which a biochemical methane potential (BMP) test is often used, is of high importance. Standardization of this BMP test is required to ensure inter-laboratory repeatability and accuracy of the BMP results. Therefore, guidelines were set out; yet, these do not provide sufficient information concerning origin of and the microbial community in the test inoculum. Here, the specific contribution of the methanogenic community on the BMP test results was evaluated. The biomethane potential of four different substrates (molasses, bio-refinery waste, liquid manure and high-rate activated sludge) was determined by means of four different inocula from full-scale anaerobic digestion plants. A significant effect of the selected inoculum on the BMP result was observed for two out of four substrates. This inoculum effect could be attributed to the abundance of methanogens and a potential inhibiting effect in the inoculum itself, demonstrating the importance of inoculum selection for BMP testing. We recommend the application of granular sludge as an inoculum, because of its higher methanogenic abundance and activity, and protection from bulk solutions, compared with other inocula.}, }
@article {pmid25753824, year = {2015}, author = {Xiong, W and Sun, Y and Zhang, T and Ding, X and Li, Y and Wang, M and Zeng, Z}, title = {Antibiotics, Antibiotic Resistance Genes, and Bacterial Community Composition in Fresh Water Aquaculture Environment in China.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {425-432}, pmid = {25753824}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/*analysis ; *Aquaculture ; China ; Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial ; Environmental Monitoring ; Fresh Water/microbiology ; Genes, Bacterial ; *Water Microbiology ; }, abstract = {Environmental antibiotic resistance has drawn increasing attention due to its great threat to human health. In this study, we investigated concentrations of antibiotics (tetracyclines, sulfonamides and (fluoro)quinolones) and abundances of antibiotic resistance genes (ARGs), including tetracycline resistance genes, sulfonamide resistance genes, and plasmid-mediated quinolone resistance genes, and analyzed bacterial community composition in aquaculture environment in Guangdong, China. The concentrations of sulfametoxydiazine, sulfamethazine, sulfamethoxazole, oxytetracycline, chlorotetracycline, doxycycline, ciprofloxacin, norfloxacin, and enrofloxacin were as high as 446 μg kg(-1) and 98.6 ng L(-1) in sediment and water samples, respectively. The relative abundances (ARG copies/16S ribosomal RNA (rRNA) gene copies) of ARGs (sul1, sul2, sul3, tetM, tetO, tetW, tetS, tetQ, tetX, tetB/P, qepA, oqxA, oqxB, aac(6')-Ib, and qnrS) were as high as 2.8 × 10(-2). The dominant phyla were Proteobacteria, Bacteroidetes, and Firmicutes in sediment samples and Proteobacteria, Actinobacteria and Bacteroidetes in water samples. The genera associated with pathogens were also observed, such as Acinetobacter, Arcobacter, and Clostridium. This study comprehensively investigated antibiotics, ARGs, and bacterial community composition in aquaculture environment in China. The results indicated that fish ponds are reservoirs of ARGs and the presence of potential resistant and pathogen-associated taxonomic groups in fish ponds might imply the potential risk to human health.}, }
@article {pmid25752138, year = {2014}, author = {Zhou, X and Huang, R and Song, G and Pan, X and Jia, Z}, title = {[Restoration of microbial ammonia oxidizers in air-dried forest soils upon wetting].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {54}, number = {11}, pages = {1311-1322}, pmid = {25752138}, issn = {0001-6209}, mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; China ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; Water/analysis ; }, abstract = {OBJECTIVE: This study was aimed to investigate the abundance and community shift of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in air-dried forest soils in response to water addition, to explore the applicability of air-dried soil for microbial ecology study, and to elucidate whether AOA within the marine group 1. 1a dominate ammonia oxidizers communities in the acidic forest soils in China.<br><br>METHODS: Soil samples were collected from 10 forest sites of the China Ecosystem Research Network (CERN) and kept under air-drying conditions in 2010. In 2013 the air-dried soil samples were adjusted to 60% of soil maximum water holding capacity for a 28-day incubation at 28 degrees C in darkness. DGGE fingerprinting, clone library construction, pyrosequencing and quantitative PCR of amoA genes were performed to assess community change of ammonia oxidizers in air-dried and re-wetted soils.<br><br>RESULTS: After incubation for 28 days, the abundance of bacteria and archaea increased significantly, up to 3,230 and 568 times, respectively. AOA increased significantly in 8 samples, and AOB increased significantly in 5 of 10 samples. However, pyrosequencing of amoA genes reveals insignificant changes in composition of AOA and AOB communities. Phylogenetic analysis of amoA genes indicates that archaeal ammonia oxidizers were predominated by AOA within the soil group 1. 1b lineage, while the Nitrosospira-like AOB dominate bacteria ammonia oxidizer communities. There was a significantly positive correlation between AOA/AOB ratio and total nitrogen (r2 = 0.54, P < 0.05), implying that soil ammonia oxidation might be dominated by AOA in association with ammonium released from soil mineralization.<br><br>CONCLUSION: Phylogenetic analysis suggest that AOA members within the soil group 1. 1b lineage were not restricted to non-acidic soils as previously thought. The abundance rather than composition of AOA and AOB changed in response to water addition. This indicates that air-dried soil could be of help for microbial biogeography study.}, }
@article {pmid25750697, year = {2015}, author = {Abram, F}, title = {Systems-based approaches to unravel multi-species microbial community functioning.}, journal = {Computational and structural biotechnology journal}, volume = {13}, number = {}, pages = {24-32}, pmid = {25750697}, issn = {2001-0370}, abstract = {Some of the most transformative discoveries promising to enable the resolution of this century's grand societal challenges will most likely arise from environmental science and particularly environmental microbiology and biotechnology. Understanding how microbes interact in situ, and how microbial communities respond to environmental changes remains an enormous challenge for science. Systems biology offers a powerful experimental strategy to tackle the exciting task of deciphering microbial interactions. In this framework, entire microbial communities are considered as metaorganisms and each level of biological information (DNA, RNA, proteins and metabolites) is investigated along with in situ environmental characteristics. In this way, systems biology can help unravel the interactions between the different parts of an ecosystem ultimately responsible for its emergent properties. Indeed each level of biological information provides a different level of characterisation of the microbial communities. Metagenomics, metatranscriptomics, metaproteomics, metabolomics and SIP-omics can be employed to investigate collectively microbial community structure, potential, function, activity and interactions. Omics approaches are enabled by high-throughput 21st century technologies and this review will discuss how their implementation has revolutionised our understanding of microbial communities.}, }
@article {pmid25750000, year = {2015}, author = {Song, Z and Vail, A and Sadowsky, MJ and Schilling, JS}, title = {Influence of Hyphal Inoculum potential on the Competitive Success of Fungi Colonizing Wood.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {758-767}, pmid = {25750000}, issn = {1432-184X}, mesh = {Basidiomycota/growth &amp; development/*physiology ; Hyphae/physiology ; Polyporales/growth &amp; development/physiology ; Real-Time Polymerase Chain Reaction ; Wood/*microbiology ; }, abstract = {The relative amounts of hyphal inoculum in forest soils may determine the capacity for fungi to compete with and replace early colonizers of wood in ground contact. Our aim in this study was to test the flexibility of priority effects (colonization timing) by varying the timing of inoculum introduction (i.e., precolonization) and amount of inoculum (i.e., inoculum potential). We controlled these variables in soil-block microcosms using fungi with known competitive outcomes in similar conditions, tracking isolate-specific fungal biomass, and residue physiochemistry over time. In the precolonization trial (experiment I), a brown rot fungus Gloeophyllum trabeum was given 1, 3, or 5 weeks to precolonize wood blocks (oak, birch, pine, and spruce) prior the introduction of a white rot fungus, Irpex lacteus, a more aggressive colonizer in this set-up. In the inoculum potential trial (experiment II), the fungi were inoculated simultaneously, but with eightfold higher brown rot inoculum than that of experiment I. As expected, longer precolonization duration increased the chance for the less-competitive brown rot fungus to outcompete its white rot opponent. Higher brown rot fungal inoculum outside of the wood matrix also resulted in competitive success for the brown rot isolate in most cases. These temporal shifts in fungal dominance were detectable in a 'community snapshot' as isolate-specific quantitative PCR, but also as functionally-relevant consequences of wood rot type, including carbohydrate depolymerization and pH. These results from a controlled system reinforce fungal-fungal interaction and suggest that relative inoculum availability beyond the wood matrix (i.e., soils) might regulate the duration of priority effects and shift the functional trajectory of wood decomposition.}, }
@article {pmid25749938, year = {2015}, author = {Purahong, W and Kapturska, D and Pecyna, MJ and Jariyavidyanont, K and Kaunzner, J and Juncheed, K and Uengwetwanit, T and Rudloff, R and Schulz, E and Hofrichter, M and Schloter, M and Krüger, D and Buscot, F}, title = {Effects of forest management practices in temperate beech forests on bacterial and fungal communities involved in leaf litter degradation.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {905-913}, pmid = {25749938}, issn = {1432-184X}, mesh = {Bacteria/*genetics/metabolism ; DNA, Intergenic/genetics/metabolism ; DNA, Ribosomal Spacer/genetics/metabolism ; Forestry/*methods ; *Forests ; Fungi/*genetics/metabolism ; Germany ; Plant Leaves/*chemistry ; *Soil Microbiology ; }, abstract = {Forest management practices (FMPs) significantly influence important ecological processes and services in Central European forests, such as leaf litter decomposition and nutrient cycling. Changes in leaf litter diversity, and thus, its quality as well as microbial community structure and function induced by different FMPs were hypothesized to be the main drivers causing shifts in decomposition rates and nutrient release in managed forests. In a litterbag experiment lasting 473 days, we aimed to investigate the effects of FMPs (even-aged timber management, selective logging and unmanaged) on bacterial and fungal communities involved in leaf litter degradation over time. Our results showed that microbial communities in leaf litter were strongly influenced by both FMPs and sampling date. The results from nonmetric multidimensional scaling (NMDS) ordination revealed distinct patterns of bacterial and fungal successions over time in leaf litter. We demonstrated that FMPs and sampling dates can influence a range of factors, including leaf litter quality, microbial macronutrients, and pH, which significantly correlate with microbial community successions.}, }
@article {pmid25749937, year = {2015}, author = {Santana, RH and Catão, EC and Lopes, FA and Constantino, R and Barreto, CC and Krüger, RH}, title = {The Gut Microbiota of Workers of the Litter-Feeding Termite Syntermes wheeleri (Termitidae: Syntermitinae): Archaeal, Bacterial, and Fungal Communities.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {545-556}, pmid = {25749937}, issn = {1432-184X}, mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Fungi/classification/genetics ; Gastrointestinal Microbiome ; Isoptera/*microbiology ; }, abstract = {The gut microbiota of termites allows them to thrive on a variety of different materials such as wood, litter, and soil. For that reason, they play important roles in the decomposition of biomass in diverse biomes. This function is essential in the savanna, where litter-feeding termites are one of the few invertebrates active during the dry season. In this study, we describe the gut microbiota of workers (third and fourth instars) of the species Syntermes wheeleri, a litter-feeding termite from the Brazilian savanna. Results of 16S and 18S ribosomal RNA (rRNA) gene-targeted pyrosequencing using primers sets specific to each domain have revealed its bacterial, archaeal, and fungal diversities. Firmicutes accounted for more than half of the operational taxonomic units of the Bacteria domain. The most abundant fungal species were from the class Dothideomycetes of the phylum Ascomycota. The methanogenic orders Methanobacteriales, Methanosarcinales, and Methanomicrobiales of the phylum Euryarchaeota accounted for the greatest part of the Archaea detected in this termite. A comparison of the gut microbiota of the two instars revealed a difference in operational taxonomic unit (OTU) abundance but not in species richness. This description of the whole gut microbiota represents the first study to evaluate relationships among bacteria, archaea, fungi, and host in S. wheeleri.}, }
@article {pmid25749323, year = {2015}, author = {Purahong, W and Stempfhuber, B and Lentendu, G and Francioli, D and Reitz, T and Buscot, F and Schloter, M and Krüger, D}, title = {Influence of commonly used primer systems on automated ribosomal intergenic spacer analysis of bacterial communities in environmental samples.}, journal = {PloS one}, volume = {10}, number = {3}, pages = {e0118967}, pmid = {25749323}, issn = {1932-6203}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; DNA Primers ; Genes, Bacterial ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; Software ; Soil Microbiology ; }, abstract = {Due to the high diversity of bacteria in many ecosystems, their slow generation times, specific but mostly unknown nutrient requirements and syntrophic interactions, isolation based approaches in microbial ecology mostly fail to describe microbial community structure. Thus, cultivation independent techniques, which rely on directly extracted nucleic acids from the environment, are a well-used alternative. For example, bacterial automated ribosomal intergenic spacer analysis (B-ARISA) is one of the widely used methods for fingerprinting bacterial communities after PCR-based amplification of selected regions of the operon coding for rRNA genes using community DNA. However, B-ARISA alone does not provide any taxonomic information and the results may be severely biased in relation to the primer set selection. Furthermore, amplified DNA stemming from mitochondrial or chloroplast templates might strongly bias the obtained fingerprints. In this study, we determined the applicability of three different B-ARISA primer sets to the study of bacterial communities. The results from in silico analysis harnessing publicly available sequence databases showed that all three primer sets tested are specific to bacteria but only two primers sets assure high bacterial taxa coverage (1406f/23Sr and ITSF/ITSReub). Considering the study of bacteria in a plant interface, the primer set ITSF/ITSReub was found to amplify (in silico) sequences of some important crop species such as Sorghum bicolor and Zea mays. Bacterial genera and plant species potentially amplified by different primer sets are given. These data were confirmed when DNA extracted from soil and plant samples were analyzed. The presented information could be useful when interpreting existing B-ARISA results and planning B-ARISA experiments, especially when plant DNA can be expected.}, }
@article {pmid25745868, year = {2015}, author = {Agga, GE and Scott, HM and Vinasco, J and Nagaraja, TG and Amachawadi, RG and Bai, J and Norby, B and Renter, DG and Dritz, SS and Nelssen, JL and Tokach, MD}, title = {Effects of chlortetracycline and copper supplementation on the prevalence, distribution, and quantity of antimicrobial resistance genes in the fecal metagenome of weaned pigs.}, journal = {Preventive veterinary medicine}, volume = {119}, number = {3-4}, pages = {179-189}, doi = {10.1016/j.prevetmed.2015.02.008}, pmid = {25745868}, issn = {1873-1716}, mesh = {Animal Feed/analysis ; Animals ; Anti-Bacterial Agents/administration &amp; dosage/*pharmacology ; Cephalosporins/pharmacology ; Chlortetracycline/administration &amp; dosage/*pharmacology ; Copper/administration &amp; dosage/*pharmacology ; Diet/veterinary ; Dietary Supplements/analysis ; *Drug Resistance, Bacterial ; Gastrointestinal Microbiome/*drug effects ; Male ; Polymerase Chain Reaction/veterinary ; Random Allocation ; *Selection, Genetic ; Sus scrofa/*microbiology ; }, abstract = {Use of in-feed antibiotics such as chlortetracycline (CTC) in food animals is fiercely debated as a cause of antimicrobial resistance in human pathogens; as a result, alternatives to antibiotics such as heavy metals have been proposed. We used a total community DNA approach to experimentally investigate the effects of CTC and copper supplementation on the presence and quantity of antimicrobial resistance elements in the gut microbial ecology of pigs. Total community DNA was extracted from 569 fecal samples collected weekly over a 6-week period from groups of 5 pigs housed in 32 pens that were randomized to receive either control, CTC, copper, or copper plus CTC regimens. Qualitative and quantitative PCR were used to detect the presence of 14 tetracycline resistance (tet) genes and to quantify gene copies of tetA, tetB, blaCMY-2 (a 3rd generation cephalosporin resistance gene), and pcoD (a copper resistance gene), respectively. The detection of tetA and tetB decreased over the subsequent sampling periods, whereas the prevalence of tetC and tetP increased. CTC and copper plus CTC supplementation increased both the prevalence and gene copy numbers of tetA, while decreasing both the prevalence and gene copies of tetB. In summary, tet gene presence was initially very diverse in the gut bacterial community of weaned pigs; thereafter, copper and CTC supplementation differentially impacted the prevalence and quantity of the various tetracycline, ceftiofur and copper resistance genes resulting in a less diverse gene population.}, }
@article {pmid25737010, year = {2015}, author = {Moset, V and Poulsen, M and Wahid, R and Højberg, O and Møller, HB}, title = {Mesophilic versus thermophilic anaerobic digestion of cattle manure: methane productivity and microbial ecology.}, journal = {Microbial biotechnology}, volume = {8}, number = {5}, pages = {787-800}, pmid = {25737010}, issn = {1751-7915}, mesh = {Anaerobiosis ; Animals ; Archaea/*classification/genetics/growth &amp; development/metabolism ; Bacteria/*classification/genetics/growth &amp; development/metabolism ; Bioreactors/*microbiology ; *Biota ; Cattle ; Hydrogen-Ion Concentration ; Manure/*microbiology ; Methane/*metabolism ; Molecular Sequence Data ; Sequence Analysis, DNA ; Temperature ; }, abstract = {In this study, productivity and physicochemical and microbiological (454 sequencing) parameters, as well as environmental criteria, were investigated in anaerobic reactors to contribute to the ongoing debate about the optimal temperature range for treating animal manure, and expand the general knowledge on the relation between microbiological and physicochemical process indicators. For this purpose, two reactor sizes were used (10 m(3) and 16 l), in which two temperature conditions (35°C and 50°C) were tested. In addition, the effect of the hydraulic retention time was evaluated (16 versus 20 days). Thermophilic anaerobic digestion showed higher organic matter degradation (especially fiber), higher pH and higher methane (CH4) yield, as well as better percentage of ultimate CH4 yield retrieved and lower residual CH4 emission, when compared with mesophilic conditions. In addition, lower microbial diversity was found in the thermophilic reactors, especially for Bacteria, where a clear intensification towards Clostridia class members was evident. Independent of temperature, some similarities were found in digestates when comparing with animal manure, including low volatile fatty acids concentrations and a high fraction of Euryarchaeota in the total microbial community, in which members of Methanosarcinales dominated for both temperature conditions; these indicators could be considered a sign of process stability.}, }
@article {pmid25733885, year = {2015}, author = {Dini-Andreote, F and Stegen, JC and van Elsas, JD and Salles, JF}, title = {Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {11}, pages = {E1326-32}, pmid = {25733885}, issn = {1091-6490}, mesh = {Computer Simulation ; *Ecosystem ; Models, Biological ; *Soil Microbiology ; *Stochastic Processes ; }, abstract = {Ecological succession and the balance between stochastic and deterministic processes are two major themes within microbial ecology, but these conceptual domains have mostly developed independent of each other. Here we provide a framework that integrates shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. Synthesizing previous work, we devised a conceptual model that links ecosystem development to alternative hypotheses related to shifts in ecological assembly processes. Conceptual model hypotheses were tested by coupling spatiotemporal data on soil bacterial communities with environmental conditions in a salt marsh chronosequence spanning 105 years of succession. Analyses within successional stages showed community composition to be initially governed by stochasticity, but as succession proceeded, there was a progressive increase in deterministic selection correlated with increasing sodium concentration. Analyses of community turnover among successional stages--which provide a larger spatiotemporal scale relative to within stage analyses--revealed that changes in the concentration of soil organic matter were the main predictor of the type and relative influence of determinism. Taken together, these results suggest scale-dependency in the mechanisms underlying selection. To better understand mechanisms governing these patterns, we developed an ecological simulation model that revealed how changes in selective environments cause shifts in the stochastic/deterministic balance. Finally, we propose an extended--and experimentally testable--conceptual model integrating ecological assembly processes with primary and secondary succession. This framework provides a priori hypotheses for future experiments, thereby facilitating a systematic approach to understand assembly and succession in microbial communities across ecosystems.}, }
@article {pmid25732740, year = {2015}, author = {Bosch, TC and Grasis, JA and Lachnit, T}, title = {Microbial ecology in Hydra: why viruses matter.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {53}, number = {3}, pages = {193-200}, pmid = {25732740}, issn = {1976-3794}, support = {5F32AI098418/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteriophages/*physiology ; Biological Evolution ; Cnidaria/*virology ; Hydra/*virology ; Hydrobiology ; Microbiota/physiology ; Species Specificity ; *Symbiosis ; *Virus Physiological Phenomena ; }, abstract = {While largely studied because of their harmful effects on human health, there is growing appreciation that viruses are also important members of the animal holobiont. This review highlights recent findings on viruses associated with Hydra and related Cnidaria. These early evolutionary diverging animals not only select their bacterial communities but also select for viral communities in a species-specific manner. The majority of the viruses associating with these animals are bacteriophages. We demonstrate that the animal host and its virome have evolved into a homeostatic, symbiotic relationship and propose that viruses are an important part of the Hydra holobiont by controlling the species-specific microbiome. We conclude that beneficial virus-bacterial-host interactions should be considered as an integral part of animal development and evolution.}, }
@article {pmid25732544, year = {2015}, author = {Sipkema, D and de Caralt, S and Morillo, JA and Al-Soud, WA and Sørensen, SJ and Smidt, H and Uriz, MJ}, title = {Similar sponge-associated bacteria can be acquired via both vertical and horizontal transmission.}, journal = {Environmental microbiology}, volume = {17}, number = {10}, pages = {3807-3821}, doi = {10.1111/1462-2920.12827}, pmid = {25732544}, issn = {1462-2920}, mesh = {Animals ; Bacteria/genetics/*growth &amp; development ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Microbiota/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {Marine sponges host diverse communities of microorganisms that are often vertically transmitted from mother to oocyte or embryo. Horizontal transmission has often been proposed to co-occur in marine sponges, but the mechanism is poorly understood. To assess the impact of the mode of transmission on the microbial assemblages of sponges, we analysed the microbiota in sympatric sponges that have previously been reported to acquire bacteria via either vertical (Corticium candelabrum and Crambe crambe) or horizontal transmission (Petrosia ficiformis). The comparative study was performed by polymerase chain reaction-denaturing gradient gel electrophoresis and pyrosequencing of barcoded PCR-amplified 16S rRNA gene fragments. We found that P. ficiformis and C. candelabrum each harbour their own species-specific bacteria, but they are similar to other high-microbial-abundance sponges, while the low-microbial-abundance sponge C. crambe hosts microbiota of a very different phylogenetic signature. In addition, nearly 50% of the reads obtained from P. ficiformis were most closely related to bacteria that were previously reported to be vertically transmitted in other sponges and comprised vertical-horizontal transmission phylogenetic clusters (VHT clusters). Therefore, our results provide evidence for the hypothesis that similar sponge-associated bacteria can be acquired via both vertical and horizontal transmission.}, }
@article {pmid25732259, year = {2015}, author = {Cobo-Díaz, JF and Fernández-González, AJ and Villadas, PJ and Robles, AB and Toro, N and Fernández-López, M}, title = {Metagenomic assessment of the potential microbial nitrogen pathways in the rhizosphere of a mediterranean forest after a wildfire.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {895-904}, pmid = {25732259}, issn = {1432-184X}, mesh = {*Fires ; *Forests ; *Metagenome ; Microbiota/*genetics ; Nitrogen/*metabolism ; Quercus/metabolism/microbiology ; Rhizosphere ; *Soil Microbiology ; Spain ; }, abstract = {Wildfires are frequent in the forests of the Mediterranean Basin and have greatly influenced this ecosystem. Changes to the physical and chemical properties of the soil, due to fire and post-fire conditions, result in alterations of both the bacterial communities and the nitrogen cycle. We explored the effects of a holm oak forest wildfire on the rhizospheric bacterial communities involved in the nitrogen cycle. Metagenomic data of the genes involved in the nitrogen cycle showed that both the undisturbed and burned rhizospheres had a conservative nitrogen cycle with a larger number of sequences related to the nitrogen incorporation pathways and a lower number for nitrogen output. However, the burned rhizosphere showed a statistically significant increase in the number of sequences for nitrogen incorporation (allantoin utilization and nitrogen fixation) and a significantly lower number of sequences for denitrification and dissimilatory nitrite reductase subsystems, possibly in order to compensate for nitrogen loss from the soil after burning. The genetic potential for nitrogen incorporation into the ecosystem was assessed through the diversity of the nitrogenase reductase enzyme, which is encoded by the nifH gene. We found that nifH gene diversity and richness were lower in burned than in undisturbed rhizospheric soils. The structure of the bacterial communities involved in the nitrogen cycle showed a statistically significant increase of Actinobacteria and Firmicutes phyla after the wildfire. Both approaches showed the important role of gram-positive bacteria in the ecosystem after a wildfire.}, }
@article {pmid25732258, year = {2015}, author = {Schaffner, I and Hofbauer, S and Krutzler, M and Pirker, KF and Bellei, M and Stadlmayr, G and Mlynek, G and Djinovic-Carugo, K and Battistuzzi, G and Furtmüller, PG and Daims, H and Obinger, C}, title = {Dimeric chlorite dismutase from the nitrogen-fixing cyanobacterium Cyanothece sp. PCC7425.}, journal = {Molecular microbiology}, volume = {96}, number = {5}, pages = {1053-1068}, pmid = {25732258}, issn = {1365-2958}, support = {P 25270/FWF_/Austrian Science Fund FWF/Austria ; W 1224/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Biocatalysis ; Chlorides/*metabolism ; Cyanides/metabolism ; Cyanothece/*enzymology/*genetics/*metabolism ; Escherichia coli/genetics ; Heme ; Kinetics ; Models, Molecular ; Oxidoreductases/*chemistry/isolation &amp; purification/*metabolism ; Oxygen/metabolism ; Phylogeny ; Protein Multimerization ; Recombinant Proteins/chemistry/metabolism ; }, abstract = {It is demonstrated that cyanobacteria (both azotrophic and non-azotrophic) contain heme b oxidoreductases that can convert chlorite to chloride and molecular oxygen (incorrectly denominated chlorite 'dismutase', Cld). Beside the water-splitting manganese complex of photosystem II, this metalloenzyme is the second known enzyme that catalyses the formation of a covalent oxygen-oxygen bond. All cyanobacterial Clds have a truncated N-terminus and are dimeric (i.e. clade 2) proteins. As model protein, Cld from Cyanothece sp. PCC7425 (CCld) was recombinantly produced in Escherichia coli and shown to efficiently degrade chlorite with an activity optimum at pH 5.0 [kcat 1144 ± 23.8 s(-1), KM 162 ± 10.0 μM, catalytic efficiency (7.1 ± 0.6) × 10(6) M(-1) s(-1)]. The resting ferric high-spin axially symmetric heme enzyme has a standard reduction potential of the Fe(III)/Fe(II) couple of -126 ± 1.9 mV at pH 7.0. Cyanide mediates the formation of a low-spin complex with k(on) = (1.6 ± 0.1) × 10(5) M(-1) s(-1) and k(off) = 1.4 ± 2.9 s(-1) (KD ∼ 8.6 μM). Both, thermal and chemical unfolding follows a non-two-state unfolding pathway with the first transition being related to the release of the prosthetic group. The obtained data are discussed with respect to known structure-function relationships of Clds. We ask for the physiological substrate and putative function of these O2 -producing proteins in (nitrogen-fixing) cyanobacteria.}, }
@article {pmid25727763, year = {2015}, author = {Quiroga, MV and Valverde, A and Mataloni, G and Cowan, D}, title = {Understanding diversity patterns in bacterioplankton communities from a sub-Antarctic peatland.}, journal = {Environmental microbiology reports}, volume = {7}, number = {3}, pages = {547-553}, doi = {10.1111/1758-2229.12287}, pmid = {25727763}, issn = {1758-2229}, mesh = {Antarctic Regions ; Argentina ; Bacteria/*classification/*isolation &amp; purification ; *Biota ; Cluster Analysis ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Data ; Phylogeny ; Sequence Homology ; }, abstract = {Bacterioplankton communities inhabiting peatlands have the potential to influence local ecosystem functions. However, most microbial ecology research in such wetlands has been done in ecosystems (mostly peat soils) of the Northern Hemisphere, and very little is known of the factors that drive bacterial community assembly in other regions of the world. In this study, we used high-throughput sequencing to analyse the structure of the bacterial communities in five pools located in a sub-Antarctic peat bog (Tierra del Fuego, Argentina), and tested for relationships between bacterial communities and environmental conditions. Bacterioplankton communities in peat bog pools were diverse and dominated by members of the Proteobacteria, Actinobacteria, Bacteroidetes and Verrucomicrobia. Community structure was largely explained by differences in hydrological connectivity, pH and nutrient status (ombrotrophic versus minerotrophic pools). Bacterioplankton communities in ombrotrophic pools showed phylogenetic clustering, suggesting a dominant role of deterministic processes in shaping these assemblages. These correlations between habitat characteristics and bacterial diversity patterns provide new insights into the factors regulating microbial populations in peatland ecosystems.}, }
@article {pmid25727156, year = {2015}, author = {Schaubroeck, T and De Clippeleir, H and Weissenbacher, N and Dewulf, J and Boeckx, P and Vlaeminck, SE and Wett, B}, title = {Environmental sustainability of an energy self-sufficient sewage treatment plant: improvements through DEMON and co-digestion.}, journal = {Water research}, volume = {74}, number = {}, pages = {166-179}, doi = {10.1016/j.watres.2015.02.013}, pmid = {25727156}, issn = {1879-2448}, mesh = {Air Pollution ; Austria ; Biofuels ; Carbon Footprint ; Climate Change ; *Environment ; Environmental Pollution ; Fertilizers/toxicity ; Greenhouse Effect ; Metals, Heavy/toxicity ; Recycling/*methods ; Sewage/*chemistry ; Waste Disposal, Fluid/*methods ; }, abstract = {It is still not proven that treatment of sewage in a wastewater treatment plant (WWTP) is (in every case) environmentally friendly. To address this matter, we have applied a state-of-the-art life cycle assessment (LCA) to an energy self-sufficient WWTP in Strass (Austria), its supply chain and the valorization of its 'products': produced electricity out of biogas from sludge digestion and the associated stabilized digestate, applied as agricultural fertilizer. Prominent aspects of our study are: a holistic environmental impact assessment, measurement of greenhouse gas emissions (including N2O), and accounting for infrastructure, replacement of conventional fertilizers and toxicity of metals present in the stabilized digestate. Additionally, the environmental sustainability improvement by implementing one-stage partial nitritation/anammox (e.g. DEMON(®)) and co-digestion was also assessed. DEMON on the digesters reject water leads to a considerable saving of natural resources compared to nitritiation/denitritation (about 33% of the life cycle resource input), this through the lowering of sludge consumption for N-removal, and thus increasing electricity production via a higher sludge excess. However, its N2O emission could be restrained through further optimization as it represents a large share (30-66%) of the plants' damaging effect on human health, this through climate change. The co-substrate addition to the digester resulted in no significant improvement of the digestion process but induced net electricity generation. If respective amounts of conventional fertilizers are replaced, the land application of the stabilized digestate is environmentally friendly through prevention of natural resource consumption and diversity loss, but possibly not regarding human health impact due the presence of toxic heavy metals, mainly Zn, in the digestate. The outcomes show that the complete life cycle results in a prevention of resource extraction from nature and a potential mitigation of diversity loss (though for some impact categories no quantification of associated diversity loss is possible) but it also leads to a damaging effect on human health, mainly via climate change and heavy metal toxicity. Since it is for now impossible to aggregate the impact to these different aspects in a sound manner, it is not yet possible to consider in this case the studied system as environmentally friendly. Generally, the field of LCA needs further development to present a better and single outcome.}, }
@article {pmid25725013, year = {2015}, author = {Makhalanyane, TP and Valverde, A and Gunnigle, E and Frossard, A and Ramond, JB and Cowan, DA}, title = {Microbial ecology of hot desert edaphic systems.}, journal = {FEMS microbiology reviews}, volume = {39}, number = {2}, pages = {203-221}, doi = {10.1093/femsre/fuu011}, pmid = {25725013}, issn = {1574-6976}, mesh = {*Biodiversity ; Climate Change ; *Desert Climate ; Plant Roots/microbiology ; *Soil Microbiology ; }, abstract = {A significant proportion of the Earth's surface is desert or in the process of desertification. The extreme environmental conditions that characterize these areas result in a surface that is essentially barren, with a limited range of higher plants and animals. Microbial communities are probably the dominant drivers of these systems, mediating key ecosystem processes. In this review, we examine the microbial communities of hot desert terrestrial biotopes (including soils, cryptic and refuge niches and plant-root-associated microbes) and the processes that govern their assembly. We also assess the possible effects of global climate change on hot desert microbial communities and the resulting feedback mechanisms. We conclude by discussing current gaps in our understanding of the microbiology of hot deserts and suggest fruitful avenues for future research.}, }
@article {pmid25724140, year = {2015}, author = {Flores-Rentería, D and Curiel Yuste, J and Rincón, A and Brearley, FQ and García-Gil, JC and Valladares, F}, title = {Habitat Fragmentation can Modulate Drought Effects on the Plant-soil-microbial System in Mediterranean Holm Oak (Quercus ilex) Forests.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {798-812}, pmid = {25724140}, issn = {1432-184X}, mesh = {Droughts ; *Forests ; Quercus/*microbiology/*physiology ; Soil/chemistry ; *Soil Microbiology ; Spain ; }, abstract = {Ecological transformations derived from habitat fragmentation have led to increased threats to above-ground biodiversity. However, the impacts of forest fragmentation on soils and their microbial communities are not well understood. We examined the effects of contrasting fragment sizes on the structure and functioning of soil microbial communities from holm oak forest patches in two bioclimatically different regions of Spain. We used a microcosm approach to simulate the annual summer drought cycle and first autumn rainfall (rewetting), evaluating the functional response of a plant-soil-microbial system. Forest fragment size had a significant effect on physicochemical characteristics and microbial functioning of soils, although the diversity and structure of microbial communities were not affected. The response of our plant-soil-microbial systems to drought was strongly modulated by the bioclimatic conditions and the fragment size from where the soils were obtained. Decreasing fragment size modulated the effects of drought by improving local environmental conditions with higher water and nutrient availability. However, this modulation was stronger for plant-soil-microbial systems built with soils from the northern region (colder and wetter) than for those built with soils from the southern region (warmer and drier) suggesting that the responsiveness of the soil-plant-microbial system to habitat fragmentation was strongly dependent on both the physicochemical characteristics of soils and the historical adaptation of soil microbial communities to specific bioclimatic conditions. This interaction challenges our understanding of future global change scenarios in Mediterranean ecosystems involving drier conditions and increased frequency of forest fragmentation.}, }
@article {pmid25721729, year = {2015}, author = {Ramond, JB and Lako, JD and Stafford, WH and Tuffin, MI and Cowan, DA}, title = {Evidence of novel plant-species specific ammonia oxidizing bacterial clades in acidic South African fynbos soils.}, journal = {Journal of basic microbiology}, volume = {55}, number = {8}, pages = {1040-1047}, doi = {10.1002/jobm.201400933}, pmid = {25721729}, issn = {1521-4028}, mesh = {Ammonia/*metabolism ; Betaproteobacteria/*classification/genetics/*isolation &amp; purification ; Biodiversity ; Gene Library ; Nitrification ; Nitrogen/metabolism ; Oxidation-Reduction ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; Proteaceae/*microbiology ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; South Africa ; }, abstract = {Ammonia-oxidizing bacteria (AOB) are essential in the biogeochemical cycling of nitrogen as they catalyze the rate-limiting oxidation of ammonia into nitrite. Since their first isolation in the late 19th century, chemolithoautotrophic AOBs have been identified in a wide range of natural (e.g., soils, sediments, estuarine, and freshwaters) and man created or impacted habitats (e.g., wastewater treatment plants and agricultural soils). However, little is known on the plant-species association of AOBs, particularly in the nutrient-starved fynbos terrestrial biome. In this study, we evaluated the diversity of AOBs in the plant canopy of three South African fynbos-specific plant species, namely Leucadendron xanthoconus, Leucospermum truncatulum and Leucadendron microcephalum, through the construction of amoA-gene clone libraries. Our results clearly demonstrate that plant-species specific and monophyletic AOB clades are present in fynbos canopy soils.}, }
@article {pmid25721726, year = {2015}, author = {Bowen, JL and Weisman, D and Yasuda, M and Jayakumar, A and Morrison, HG and Ward, BB}, title = {Marine Oxygen-Deficient Zones Harbor Depauperate Denitrifying Communities Compared to Novel Genetic Diversity in Coastal Sediments.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {311-321}, pmid = {25721726}, issn = {1432-184X}, mesh = {Bacteria/metabolism ; Denitrification ; Ecosystem ; Genetic Variation ; Geologic Sediments/*microbiology ; *Oxygen ; Seawater/microbiology ; }, abstract = {Denitrification is a critically important biogeochemical pathway that removes fixed nitrogen from ecosystems and thus ultimately controls the rate of primary production in nitrogen-limited systems. We examined the community structure of bacteria containing the nirS gene, a signature gene in the denitrification pathway, from estuarine and salt marsh sediments and from the water column of two of the world's largest marine oxygen-deficient zones (ODZs). We generated over 125,000 nirS gene sequences, revealing a large degree of genetic diversity including 1,815 unique taxa, the vast majority of which formed clades that contain no cultured representatives. These results underscore how little we know about the genetic diversity of metabolisms underlying this critical biogeochemical pathway. Marine sediments yielded 1,776 unique taxa when clustered at 95 % sequence identity, and there was no single nirS denitrifier that was a competitive dominant; different samples had different highly abundant taxa. By contrast, there were only 39 unique taxa identified in samples from the two ODZs, and 99 % of the sequences belonged to 5 or fewer taxa. The ODZ samples were often dominated by nirS sequences that shared a 92 % sequence identity to a nirS found in the anaerobic ammonium-oxidizing (anammox) genus Scalindua. This sequence was abundant in both ODZs, accounting for 38 and 59 % of all sequences, but it was virtually absent in marine sediments. Our data indicate that ODZs are remarkably depauperate in nirS genes compared to the remarkable genetic richness found in coastal sediments.}, }
@article {pmid25721725, year = {2015}, author = {Epalle, T and Girardot, F and Allegra, S and Maurice-Blanc, C and Garraud, O and Riffard, S}, title = {Erratum to: Viable but not Culturable Forms of Legionella pneumophila Generated After Heat Shock Treatment are Infectious for Macrophage-like and Alveolar Epithelial cells after Resuscitation on Acanthamoeba polyphaga.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {576-578}, doi = {10.1007/s00248-015-0580-0}, pmid = {25721725}, issn = {1432-184X}, }
@article {pmid25721590, year = {2015}, author = {Amils, R}, title = {Technological challenges to understanding the microbial ecology of deep subsurface ecosystems.}, journal = {Environmental microbiology reports}, volume = {7}, number = {1}, pages = {9-10}, doi = {10.1111/1758-2229.12219}, pmid = {25721590}, issn = {1758-2229}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Earth Sciences ; Ecosystem ; Environmental Microbiology ; Geologic Sediments/chemistry/*microbiology ; Microbiological Techniques ; }, }
@article {pmid25712885, year = {2015}, author = {Duran, R and Bielen, A and Paradžik, T and Gassie, C and Pustijanac, E and Cagnon, C and Hamer, B and Vujaklija, D}, title = {Exploring Actinobacteria assemblages in coastal marine sediments under contrasted Human influences in the West Istria Sea, Croatia.}, journal = {Environmental science and pollution research international}, volume = {22}, number = {20}, pages = {15215-15229}, pmid = {25712885}, issn = {1614-7499}, mesh = {Actinobacteria/*isolation &amp; purification ; Arsenic/analysis ; Croatia ; Environmental Monitoring ; Geologic Sediments/*microbiology ; Metals, Heavy/analysis ; Polycyclic Aromatic Hydrocarbons/analysis ; Water Pollutants, Chemical/analysis ; }, abstract = {The exploration of marine Actinobacteria has as major challenge to answer basic questions of microbial ecology that, in turn, will provide useful information to exploit Actinobacteria metabolisms in biotechnological processes. The ecological functions performed by Actinobacteria in marine sediments are still unclear and belongs to the most burning basic questions. The comparison of Actinobacteria communities inhabiting marine sediments that are under the influence of different contamination types will provide valuable information in the adaptation capacities of Actinobacteria to colonize specific ecological niche. In the present study, the characterization of different Actinobacteria assemblages according to contamination type revealed the ecological importance of Actinobacteria for maintaining both general biogeochemical functions through a "core" Actinobacteria community and specific roles associated with the presence of contaminants. Indeed, the results allowed to distinguish Actinobacteria genera and species operational taxonomic units (OTUs) able to cope with the presence of either (i) As, (ii) metals Ni, Fe, V, Cr, and Mn, or (iii) polycyclic aromatic hydrocarbons (PAHs) and toxic metals (Hg, Cd, Cu, Pb, and Zn). Such observations highlighted the metabolic capacities of Actinobacteria and their potential that should be taken into consideration and advantage during the implementation of bioremediation processes in marine ecosystems.}, }
@article {pmid25712554, year = {2015}, author = {Menzel, P and Gudbergsdóttir, SR and Rike, AG and Lin, L and Zhang, Q and Contursi, P and Moracci, M and Kristjansson, JK and Bolduc, B and Gavrilov, S and Ravin, N and Mardanov, A and Bonch-Osmolovskaya, E and Young, M and Krogh, A and Peng, X}, title = {Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {411-424}, pmid = {25712554}, issn = {1432-184X}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; China ; Ecosystem ; Hot Springs/*microbiology ; Iceland ; Italy ; Metagenomics/*methods ; Russia ; Sequence Analysis, DNA ; Temperature ; United States ; }, abstract = {Hot springs are natural habitats for thermophilic Archaea and Bacteria. In this paper, we present the metagenomic analysis of eight globally distributed terrestrial hot springs from China, Iceland, Italy, Russia, and the USA with a temperature range between 61 and 92 (∘)C and pH between 1.8 and 7. A comparison of the biodiversity and community composition generally showed a decrease in biodiversity with increasing temperature and decreasing pH. Another important factor shaping microbial diversity of the studied sites was the abundance of organic substrates. Several species of the Crenarchaeal order Thermoprotei were detected, whereas no single bacterial species was found in all samples, suggesting a better adaptation of certain archaeal species to different thermophilic environments. Two hot springs show high abundance of Acidithiobacillus, supporting the idea of a true thermophilic Acidithiobacillus species that can thrive in hyperthermophilic environments. Depending on the sample, up to 58 % of sequencing reads could not be assigned to a known phylum, reinforcing the fact that a large number of microorganisms in nature, including those thriving in hot environments remain to be isolated and characterized.}, }
@article {pmid25707714, year = {2015}, author = {Han, XM and Liu, YR and Zhang, LM and He, JZ}, title = {Insight into the Modulation of Dissolved Organic Matter on Microbial Remediation of PAH-Contaminated Soils.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {400-410}, pmid = {25707714}, issn = {1432-184X}, mesh = {*Biodegradation, Environmental ; Polycyclic Aromatic Hydrocarbons/*metabolism ; RNA, Ribosomal, 16S ; Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {Microorganisms play a key role in degradation of polycyclic aromatic hydrocarbons (PAHs) in environments. Dissolved organic matter (DOM) can enhance microbial degradation of PAHs in soils. However, it is not clear how will the soil microbial community respond to addition of DOM during bioremediation of PAH-contaminated soils. In this study, DOMs derived from various agricultural wastes were applied to remediate the aging PAH-contaminated soils in a 90-day microcosm experiment. Results showed that the addition of DOMs offered a more efficient and persistent elimination of soil PAHs compared to the control which had no DOM addition. PAH removal effects were different among treatments with various DOMs; the addition of DOMs with high proportion of hydrophobic fraction could remove PAHs more efficiently from the soil. Low-molecular-weight (LMW) PAHs were more easily eliminated than that with high-molecular-weight (HMW). Addition of DOMs significantly increased abundance of 16S ribosomal RNA (rRNA), pdo1, nah, and C12O genes and obviously changed community compositions of nah and C12O genes in different ways in the PAH-contaminated soil. Phylogenetic analyses of clone libraries exhibited that all of nah sequences and most of C12O sequences were affiliated into Gammaproteobacteria and Betaproteobacteria. These results suggested that external stimuli produced by DOMs could enhance the microbial degradation of PAHs in soils through not only solubilizing PAHs but also altering abundance and composition of indigenous microbial degraders. Our results reinforce the understanding of role of DOMs in mediating degradation of PAHs by microorganims in soils.}, }
@article {pmid25706625, year = {2015}, author = {Kohler, A and Kuo, A and Nagy, LG and Morin, E and Barry, KW and Buscot, F and Canbäck, B and Choi, C and Cichocki, N and Clum, A and Colpaert, J and Copeland, A and Costa, MD and Doré, J and Floudas, D and Gay, G and Girlanda, M and Henrissat, B and Herrmann, S and Hess, J and Högberg, N and Johansson, T and Khouja, HR and LaButti, K and Lahrmann, U and Levasseur, A and Lindquist, EA and Lipzen, A and Marmeisse, R and Martino, E and Murat, C and Ngan, CY and Nehls, U and Plett, JM and Pringle, A and Ohm, RA and Perotto, S and Peter, M and Riley, R and Rineau, F and Ruytinx, J and Salamov, A and Shah, F and Sun, H and Tarkka, M and Tritt, A and Veneault-Fourrey, C and Zuccaro, A and ,  and Tunlid, A and Grigoriev, IV and Hibbett, DS and Martin, F}, title = {Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists.}, journal = {Nature genetics}, volume = {47}, number = {4}, pages = {410-415}, doi = {10.1038/ng.3223}, pmid = {25706625}, issn = {1546-1718}, mesh = {Base Sequence ; Evolution, Molecular ; Gene Deletion ; Gene Expression Regulation, Fungal/genetics ; Genome, Fungal/*genetics ; Molecular Sequence Data ; Mycorrhizae/*genetics/pathogenicity ; Phylogeny ; Plant Diseases/genetics/microbiology ; Plant Roots/microbiology ; *Selection, Genetic ; Symbiosis/*genetics ; Virulence/*genetics ; }, abstract = {To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7-38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.}, }
@article {pmid25706388, year = {2015}, author = {Rachid, CT and Balieiro, FC and Fonseca, ES and Peixoto, RS and Chaer, GM and Tiedje, JM and Rosado, AS}, title = {Intercropped silviculture systems, a key to achieving soil fungal community management in eucalyptus plantations.}, journal = {PloS one}, volume = {10}, number = {2}, pages = {e0118515}, pmid = {25706388}, issn = {1932-6203}, mesh = {Eucalyptus/*microbiology ; Fungi/classification/genetics/*physiology ; RNA, Fungal/genetics ; RNA, Ribosomal, 28S/genetics ; *Soil Microbiology ; Species Specificity ; }, abstract = {Fungi are ubiquitous and important contributors to soil nutrient cycling, playing a vital role in C, N and P turnover, with many fungi having direct beneficial relationships with plants. However, the factors that modulate the soil fungal community are poorly understood. We studied the degree to which the composition of tree species affected the soil fungal community structure and diversity by pyrosequencing the 28S rRNA gene in soil DNA. We were also interested in whether intercropping (mixed plantation of two plant species) could be used to select fungal species. More than 50,000 high quality sequences were analyzed from three treatments: monoculture of Eucalyptus; monoculture of Acacia mangium; and a mixed plantation with both species sampled 2 and 3 years after planting. We found that the plant type had a major effect on the soil fungal community structure, with 75% of the sequences from the Eucalyptus soil belonging to Basidiomycota and 19% to Ascomycota, and the Acacia soil having a sequence distribution of 28% and 62%, respectively. The intercropping of Acacia mangium in a Eucalyptus plantation significantly increased the number of fungal genera and the diversity indices and introduced or increased the frequency of several genera that were not found in the monoculture cultivation samples. Our results suggest that management of soil fungi is possible by manipulating the composition of the plant community, and intercropped systems can be a means to achieve that.}, }
@article {pmid25704317, year = {2015}, author = {Larsen, AM and Bullard, SA and Womble, M and Arias, CR}, title = {Community Structure of Skin Microbiome of Gulf Killifish, Fundulus grandis, Is Driven by Seasonality and Not Exposure to Oiled Sediments in a Louisiana Salt Marsh.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {534-544}, pmid = {25704317}, issn = {1432-184X}, mesh = {Animals ; Cyanobacteria/classification/genetics ; Fundulidae/*microbiology ; Louisiana ; Petroleum Pollution ; Proteobacteria/classification/genetics ; Seasons ; }, abstract = {Mucus of fish skin harbors complex bacterial communities that likely contribute to fish homeostasis. When the equilibrium between the host and its external bacterial symbionts is disrupted, bacterial diversity decreases while opportunistic pathogen prevalence increases, making the onset of pathogenic bacterial infection more likely. Because of that relationship, documenting temporal and spatial microbial community changes may be predictive of fish health status. The 2010 Deepwater Horizon oil spill was a potential stressor to the Gulf of Mexico's coastal ecosystem. Ribosomal intergenic spacer analysis (RISA) and pyrosequencing were used to analyze the bacterial communities (microbiome) associated with the skin and mucus of Gulf killifish (Fundulus grandis) that were collected from oiled and non-oiled salt marsh sites in Barataria Bay, LA. Water samples and fin clips were collected to examine microbiome structure. The microbiome of Gulf killifish was significantly different from that of the surrounding water, mainly attributable to shifts in abundances of Cyanobacteria and Proteobacteria. The Gulf killifish's microbiome was dominated by Gammaproteobacteria, specifically members of Pseudomonas. No significant difference was found between microbiomes of fish collected from oiled and non-oiled sites suggesting little impact of oil contamination on fish bacterial assemblages. Conversely, seasonality significantly influenced microbiome structure. Overall, the high similarity observed between the microbiomes of individual fish observed during this study posits that skin and mucus of Gulf killifish have a resilient core microbiome.}, }
@article {pmid25704316, year = {2015}, author = {Pucciarelli, S and Devaraj, RR and Mancini, A and Ballarini, P and Castelli, M and Schrallhammer, M and Petroni, G and Miceli, C}, title = {Microbial Consortium Associated with the Antarctic Marine Ciliate Euplotes focardii: An Investigation from Genomic Sequences.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {484-497}, pmid = {25704316}, issn = {1432-184X}, mesh = {Adaptation, Physiological ; Antarctic Regions ; Euplotes/*genetics ; Genomics/methods ; Microbial Consortia ; }, abstract = {We report the characterization of the bacterial consortium associated to Euplotes focardii, a strictly psychrophilic marine ciliate that was maintained in laboratory cultures at 4 °C after its first isolation from Terra Nova Bay, in Antarctica. By Illumina genome analyser, we obtained 11,179 contigs of potential prokaryotic origin and classified them according to the NCBI's prokaryotic attributes table. The majority of these sequences correspond to either Bacteroidetes (16 %) or Proteobacteria (78 %). The latter were dominated by gamma- (39 %, including sequences related to the pathogenic genus Francisella), and alpha-proteobacterial (30 %) sequences. Analysis of the Pfam domain family and Gene Ontology term variation revealed that the most frequent terms that appear unique to this consortium correspond to proteins involved in "transmembrane transporter activity" and "oxidoreductase activity". Furthermore, we identified genes that encode for enzymes involved in the catabolism of complex substance for energy reserves. We also characterized members of the transposase and integrase superfamilies, whose role in bacterial evolution is well documented, as well as putative antifreeze proteins. Antibiotic treatments of E. focardii cultures delayed the cell division of the ciliate. To conclude, our results indicate that this consortium is largely represented by bacteria derived from the original Antarctic sample and may contribute to the survival of E. focardii in laboratory condition. Furthermore, our results suggest that these bacteria may have a more general role in E. focardii survival in its natural cold and oxidative environment.}, }
@article {pmid25702162, year = {2015}, author = {Tsilia, V and Van den Abbeele, P and Van de Wiele, T}, title = {Improved in vitro assay for determining the mucin adherence of bacteria sensitive to Triton X-100 treatment.}, journal = {Folia microbiologica}, volume = {60}, number = {5}, pages = {435-442}, pmid = {25702162}, issn = {1874-9356}, mesh = {Animals ; Bacteria/*drug effects/growth &amp; development ; Bacterial Adhesion/*drug effects ; Biological Assay ; Detergents/*pharmacology ; Intestinal Mucosa/*microbiology ; Mucins/*chemistry ; Octoxynol/*pharmacology ; Swine ; }, abstract = {Mucin-associated microbiota are in relatively close contact with the intestinal epithelium and may thus have a more pronounced effect on host health. We have previously developed a simple mucin agar assay to simulate initial mucus colonization by intestinal microbial communities. Adherence of microbiota was estimated using flow cytometry after detachment with Triton X-100. In this study, the effect of this detergent on the cultivability of both virulent and commensal strains was investigated. Mucin attachment of selected strains was evaluated using the mucin adhesion assay. Bacteria were dislodged from the mucin surface by incubation with Triton or from the whole mucin agar layer using a stomacher. Mechanical extraction resulted in 1.24 ± 0.42, 2.69 ± 0.44, and 1.56 ± 0.85 log CFU/mL higher plate counts of Lactobacillus rhamnosus, Bacillus cereus, and Escherichia coli strains, respectively, than the chemical method. The sensitivity of bacteria to Triton varied among microbial species and strains. Among others, Triton inhibited the growth of Salmonella enterica LMG 10396 and Pseudomonas aeruginosa LMG 8029 on laboratory media, although these bacteria maintained their viability during this treatment. Only Gram-positive strains, Enterococcus hirae LMG 6399 and L. rhamnosus GG, were not affected by this detergent. Therefore, the mechanical method is recommended for the extraction of mucin-adhered bacteria that are sensitive to Triton, especially when followed by traditional cultivation techniques. However, this approach can also be recommended for strains that are not affected by this detergent, because it resulted in higher recovery of adhered L. rhamnosus GG compared to the chemical extraction.}, }
@article {pmid25699544, year = {2015}, author = {Dong, Y and Lang, Z and Kong, X and Lu, D and Liu, Z}, title = {Kinetic and multidimensional profiling of accelerated degradation of oil sludge by biostimulation.}, journal = {Environmental science. Processes &amp; impacts}, volume = {17}, number = {4}, pages = {763-774}, doi = {10.1039/c4em00428k}, pmid = {25699544}, issn = {2050-7895}, mesh = {Bacteria/metabolism ; Biodegradation, Environmental ; Carboxylic Acids/analysis/metabolism ; Environmental Pollutants/analysis/*metabolism ; Genes, Bacterial ; Hydrocarbons/analysis/metabolism ; Kinetics ; Petroleum/analysis/*metabolism ; }, abstract = {Biostimulation, which employs nutrients to enhance the proliferation of indigenous microorganisms and therefore the degradation of contaminants, is an effective tool for treatment of oil-contaminated soil. However, the evolution of microbial ecology, which responds directly to stimulation procedures and intrinsically determines the degradation of oil contaminants, has rarely been explored, particularly in the context of biostimulation. In this study, the effects of biostimulation procedures including the regulation of the C : N : P ratio, as well as application of surfactants and electron acceptors in the degradation of crude oil contaminants and the evolution of the microbial community were examined simultaneously to provide ecological insights into the biostimulation. The real-time PCR showed that biostimulation promoted the proliferation of bacteria, with Gammaproteobacteria showing the greatest increase. However, the proliferation of fungi was inhibited by the accumulation of the degradation products. The degradation of polar compounds of crude oil contaminants was characterized by negative-ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (negative-ion ESI FT-ICR MS), showing a biased increase in the relative abundance of naphthenic acids. Principal component analysis (PCA) showed that different species in oil sludge have different degradation rates during biostimulation. The addition of fertilizers with surfactants and electron acceptors profoundly stimulated the indigenous microorganisms with N1, O1 and O2 species as substrates while those with O3 and O4 species were little affected. An enriched abundance of alkB genes was observed during the degradation of saturated hydrocarbons. Monitoring the kinetics of the microbial community, functional genes and degradation offers a comprehensive view for the understanding and optimization of the biostimulation process.}, }
@article {pmid25698567, year = {2015}, author = {Vilajeliu-Pons, A and Puig, S and Pous, N and Salcedo-Dávila, I and Bañeras, L and Balaguer, MD and Colprim, J}, title = {Microbiome characterization of MFCs used for the treatment of swine manure.}, journal = {Journal of hazardous materials}, volume = {288}, number = {}, pages = {60-68}, doi = {10.1016/j.jhazmat.2015.02.014}, pmid = {25698567}, issn = {1873-3336}, mesh = {Anaerobiosis ; Animals ; Bacteria/metabolism ; Biodegradation, Environmental ; Bioelectric Energy Sources/*microbiology ; Biofilms ; DNA Fingerprinting ; Electrochemistry ; Manure/analysis/*microbiology ; *Microbiota ; Swine ; Waste Disposal, Fluid ; Water Microbiology ; }, abstract = {Conventional swine manure treatment is performed by anaerobic digestion, but nitrogen is not treated. Microbial Fuel Cells (MFCs) allow organic matter and nitrogen removal with concomitant electricity production. MFC microbiomes treating industrial wastewaters as swine manure have not been characterized. In this study, a multidisciplinary approach allowed microbiome relation with nutrient removal capacity and electricity production. Two different MFC configurations (C-1 and C-2) were used to treat swine manure. In C-1, the nitrification and denitrification processes took place in different compartments, while in C-2, simultaneous nitrification-denitrification occurred in the cathode. Clostridium disporicum and Geobacter sulfurreducens were identified in the anode compartments of both systems. C. disporicum was related to the degradation of complex organic matter compounds and G. sulfurreducens to electricity production. Different nitrifying bacteria populations were identified in both systems because of the different operational conditions. The highest microbial diversity was detected in cathode compartments of both configurations, including members of Bacteroidetes, Chloroflexiaceae and Proteobacteria. These communities allowed similar removal rates of organic matter (2.02-2.09 kg COD m(-3)d(-1)) and nitrogen (0.11-0.16 kg Nm(-3)d(-1)) in both systems. However, they differed in the generation of electric energy (20 and 2 mW m(-3) in C-1 and C-2, respectively).}, }
@article {pmid25690897, year = {2015}, author = {Esling, P and Lejzerowicz, F and Pawlowski, J}, title = {Accurate multiplexing and filtering for high-throughput amplicon-sequencing.}, journal = {Nucleic acids research}, volume = {43}, number = {5}, pages = {2513-2524}, pmid = {25690897}, issn = {1362-4962}, mesh = {*Algorithms ; Computer Simulation ; DNA Primers/*genetics ; *Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Internet ; Multiplex Polymerase Chain Reaction/*methods ; Reproducibility of Results ; Software ; }, abstract = {Tagging amplicons with tag sequences appended to PCR primers allow the multiplexing of numerous samples for high-throughput sequencing (HTS). This approach is routinely used in HTS-based diversity analyses, especially in microbial ecology and biomedical diagnostics. However, amplicon library preparation is subject to pervasive sample sequence cross-contaminations as a result of tag switching events referred to as mistagging. Here, we sequenced seven amplicon libraries prepared using various multiplexing designs in order to measure the magnitude of this phenomenon and its impact on diversity analyses. Up to 28.2% of the unique sequences correspond to undetectable (critical) mistags in single- or saturated double-tagging libraries. We show the advantage of multiplexing samples following Latin Square Designs in order to optimize the detection of mistags and maximize the information on their distribution across samples. We use this information in designs incorporating PCR replicates to filter the critical mistags and to recover the exact composition of mock community samples. Being parameter-free and data-driven, our approach can provide more accurate and reproducible HTS data sets, improving the reliability of their interpretations.}, }
@article {pmid25687127, year = {2015}, author = {Saravesi, K and Aikio, S and Wäli, PR and Ruotsalainen, AL and Kaukonen, M and Huusko, K and Suokas, M and Brown, SP and Jumpponen, A and Tuomi, J and Markkola, A}, title = {Moth outbreaks alter root-associated fungal communities in subarctic mountain birch forests.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {788-797}, pmid = {25687127}, issn = {1432-184X}, mesh = {Animals ; Betula/growth &amp; development/*microbiology ; Feeding Behavior ; Finland ; Forests ; Molecular Sequence Data ; Moths/*physiology ; Mycorrhizae/genetics/*physiology ; Plant Roots/growth &amp; development/*microbiology ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Climate change has important implications on the abundance and range of insect pests in forest ecosystems. We studied responses of root-associated fungal communities to defoliation of mountain birch hosts by a massive geometrid moth outbreak through 454 pyrosequencing of tagged amplicons of the ITS2 rDNA region. We compared fungal diversity and community composition at three levels of moth defoliation (intact control, full defoliation in one season, full defoliation in two or more seasons), replicated in three localities. Defoliation caused dramatic shifts in functional and taxonomic community composition of root-associated fungi. Differentially defoliated mountain birch roots harbored distinct fungal communities, which correlated with increasing soil nutrients and decreasing amount of host trees with green foliar mass. Ectomycorrhizal fungi (EMF) abundance and richness declined by 70-80 % with increasing defoliation intensity, while saprotrophic and endophytic fungi seemed to benefit from defoliation. Moth herbivory also reduced dominance of Basidiomycota in the roots due to loss of basidiomycete EMF and increases in functionally unknown Ascomycota. Our results demonstrate the top-down control of belowground fungal communities by aboveground herbivory and suggest a marked reduction in the carbon flow from plants to soil fungi following defoliation. These results are among the first to provide evidence on cascading effects of natural herbivory on tree root-associated fungi at an ecosystem scale.}, }
@article {pmid25687126, year = {2015}, author = {Nguyen, NH and Bruns, TD}, title = {The Microbiome of Pinus muricata Ectomycorrhizae: Community Assemblages, Fungal Species Effects, and Burkholderia as Important Bacteria in Multipartnered Symbioses.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {914-921}, pmid = {25687126}, issn = {1432-184X}, mesh = {Burkholderia/genetics/*physiology ; Fungi/genetics/*physiology ; *Microbiota ; Mycorrhizae/*genetics ; Pinus/*microbiology ; Polymerase Chain Reaction ; *Soil Microbiology ; Symbiosis ; }, abstract = {Bacteria have been observed to grow with fungi, and those that associate with ectomycorrhizal fungi have often been thought of as symbionts that may either increase or decrease ectomycorrhizal formation rate or provide other unaccounted benefits. To explore this symbiosis from a community ecology perspective, we sampled ectomycorrhizal root tips over a 3-year period and used 454 pyrosequencing to identify the bacteria that live inside the ectomycorrhizal root tips. The results showed that fungal community composition within the same soil core and fungal taxonomic identity had a stronger effect on bacterial community composition than sample year or site. Members of the Burkholderiales and Rhizobiales were most highly represented, reflecting many previous reports of these bacteria in association with fungi. The repeated occurrences of these two bacterial orders suggest that they may be symbiotic with their fungal hosts, although the nature of such mechanisms, be it symbiotic diazotrophy or otherwise, remains to be thoroughly tested.}, }
@article {pmid25687125, year = {2015}, author = {Moll, J and Goldmann, K and Kramer, S and Hempel, S and Kandeler, E and Marhan, S and Ruess, L and Krüger, D and Buscot, F}, title = {Resource Type and Availability Regulate Fungal Communities Along Arable Soil Profiles.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {390-399}, pmid = {25687125}, issn = {1432-184X}, mesh = {Biomass ; Ecosystem ; Fungi/isolation &amp; purification/metabolism/*physiology ; *Soil Microbiology ; }, abstract = {Soil fungi play an essential role in the decomposition of plant-derived organic material entering soils. The quality and quantity of organic compounds vary seasonally as well as with soil depth. To elucidate how these resources affect fungal communities in an arable soil, a field experiment was set up with two plant species, maize and wheat. Resource availability was experimentally manipulated by maize litter input on one half of these maize and wheat plots after harvest in autumn. Fungal biomass was determined by ergosterol quantification, and community structure was investigated by fungal automated ribosomal intergenic spacer analysis (F-ARISA). An annual cycle was assessed across a depth gradient, distinguishing three soil habitats: the plough layer, rooted soil below the plough layer, and deeper root-free soil. Fungal communities appeared highly dynamic and varied according to soil depth and plant resources. In the plough layer, the availability of litter played a dominant role in shaping fungal communities, whereas in the rooted layer below, community structure and biomass mainly differed between plant species. This plant effect was also extended into the root-free soil at a depth of 70 cm. In winter, the availability of litter also affected fungal communities in deeper soil layers, suggesting vertical transport processes under fallow conditions. These distinct resource effects indicate diverse ecological niches along the soil profile, comprising specific fungal metacommunities. The recorded responses to both living plants and litter point to a central role of fungi in connecting primary production and decomposition within the plant-soil system.}, }
@article {pmid25685915, year = {2015}, author = {Dolfing, J and Feng, Y}, title = {The importance of soil archives for microbial ecology.}, journal = {Nature reviews. Microbiology}, volume = {13}, number = {3}, pages = {1}, doi = {10.1038/nrmicro3382-c1}, pmid = {25685915}, issn = {1740-1534}, mesh = {Animals ; *Biological Specimen Banks ; *Ecology ; *Environmental Microbiology ; Humans ; *Specimen Handling ; }, }
@article {pmid25683328, year = {2015}, author = {Cabezas, A and Pommerenke, B and Boon, N and Friedrich, MW}, title = {Geobacter, Anaeromyxobacter and Anaerolineae populations are enriched on anodes of root exudate-driven microbial fuel cells in rice field soil.}, journal = {Environmental microbiology reports}, volume = {7}, number = {3}, pages = {489-497}, doi = {10.1111/1758-2229.12277}, pmid = {25683328}, issn = {1758-2229}, mesh = {*Bioelectric Energy Sources ; Chloroflexi/genetics/growth &amp; development/*isolation &amp; purification ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrodes/*microbiology ; Exudates and Transudates/*metabolism ; Geobacter/genetics/growth &amp; development/*isolation &amp; purification ; Microbial Consortia ; Molecular Sequence Data ; Myxococcales/genetics/growth &amp; development/*isolation &amp; purification ; Oryza/growth &amp; development/metabolism ; Phylogeny ; Plant Roots/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Plant-based sediment microbial fuel cells (PMFCs) couple the oxidation of root exudates in living rice plants to current production. We analysed the composition of the microbial community on anodes from PMFC with natural rice field soil as substratum for rice by analysing 16S rRNA as an indicator of microbial activity and diversity. Terminal restriction fragment length polymorphism (TRFLP) analysis indicated that the active bacterial community on anodes from PMFCs differed strongly compared with controls. Moreover, clones related to Deltaproteobacteria and Chloroflexi were highly abundant (49% and 21%, respectively) on PMFCs anodes. Geobacter (19%), Anaeromyxobacter (15%) and Anaerolineae (17%) populations were predominant on anodes with natural rice field soil and differed strongly from those previously detected with potting soil. In open circuit (OC) control PMFCs, not allowing electron transfer, Deltaproteobacteria (33%), Betaproteobacteria (20%), Chloroflexi (12%), Alphaproteobacteria (10%) and Firmicutes (10%) were detected. The presence of an electron accepting anode also had a strong influence on methanogenic archaea. Hydrogenotrophic methanogens were more active on PMFC (21%) than on OC controls (10%), whereas acetoclastic Methanosaetaceae were more active on OC controls (31%) compared with PMFCs (9%). In conclusion, electron accepting anodes and rice root exudates selected for distinct potential anode-reducing microbial populations in rice soil inoculated PMFC.}, }
@article {pmid25683239, year = {2015}, author = {Vanwonterghem, I and Jensen, PD and Rabaey, K and Tyson, GW}, title = {Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {8496}, pmid = {25683239}, issn = {2045-2322}, mesh = {Anaerobiosis ; Biodiversity ; Bioreactors/*microbiology ; Fatty Acids, Volatile/*biosynthesis ; Microbiota ; *Temperature ; }, abstract = {Anaerobic digestion is a widely used technology for waste stabilization and generation of biogas, and has recently emerged as a potentially important process for the production of high value volatile fatty acids (VFAs) and alcohols. Here, three reactors were seeded with inoculum from a stably performing methanogenic digester, and selective operating conditions (37°C and 55°C; 12 day and 4 day solids retention time) were applied to restrict methanogenesis while maintaining hydrolysis and fermentation. Replicated experiments performed at each set of operating conditions led to reproducible VFA production profiles which could be correlated with specific changes in microbial community composition. The mesophilic reactor at short solids retention time showed accumulation of propionate and acetate (42 ± 2% and 15 ± 6% of CODhydrolyzed, respectively), and dominance of Fibrobacter and Bacteroidales. Acetate accumulation (>50% of CODhydrolyzed) was also observed in the thermophilic reactors, which were dominated by Clostridium. Under all tested conditions, there was a shift from acetoclastic to hydrogenotrophic methanogenesis, and a reduction in methane production by >50% of CODhydrolyzed. Our results demonstrate that shortening the SRT and increasing the temperature are effective strategies for driving microbial communities towards controlled production of high levels of specific volatile fatty acids.}, }
@article {pmid25681033, year = {2015}, author = {Lis, A and Maryańska-Nadachowska, A and Kajtoch, &#x141;}, title = {Relations of Wolbachia Infection with Phylogeography of Philaenus spumarius (Hemiptera: Aphrophoridae) Populations Within and Beyond the Carpathian Contact Zone.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {509-521}, pmid = {25681033}, issn = {1432-184X}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Hemiptera/*microbiology ; Multilocus Sequence Typing ; Phylogeny ; Wolbachia/drug effects/genetics/*physiology ; }, abstract = {Wolbachia is the most widespread intracellular α-proteobacteria maternally inherited endosymbiont of insects and nematodes. These bacteria are associated with a number of different reproductive phenotypes of their hosts. Relatively few studies have dealt with distribution of infections across populations and with the influence of these bacteria on host genetic diversification and speciation. The aims of this study are to determine the distribution and rate of infection and to characterize the Wolbachia strains associated with Philaenus spumarius spittlebug (Hemiptera) by using multilocus sequencing typing (MLST) analysis and host phylogeography. The results showed that infection rate was significantly different between members of both main mitochondrial phylogenetic lineages of P. spumarius. We detected much higher infection rates of Wolbachia in P. spumarius populations from the north-east clade than the south-west clade. Moreover, the frequency of these infections varied within and outside the contact zone known from the Carpathians. Given the reproductive alterations which are often associated with this endosymbiont, Wolbachia probably maintain genetic differentiation of its hosts in its contact zone in the Carpathians. This is one of the first studies demonstrating the presence of Wolbachia across a large part of the range of insect species, including the contact zone. The spread of Wolbachia in P. spumarius populations can potentially cause speciation by compromising the potential reproductive barrier between infected and uninfected populations. We discuss possible implications of Wolbachia infection inducing cytoplasmic incompatibility in the population dynamics of this spittlebug but confirm that more studies are also required.}, }
@article {pmid25680230, year = {2015}, author = {Schulz, F and Horn, M}, title = {Intranuclear bacteria: inside the cellular control center of eukaryotes.}, journal = {Trends in cell biology}, volume = {25}, number = {6}, pages = {339-346}, doi = {10.1016/j.tcb.2015.01.002}, pmid = {25680230}, issn = {1879-3088}, support = {281633/ERC_/European Research Council/International ; }, mesh = {Animals ; Bacteria/*isolation &amp; purification ; Cell Nucleus/*microbiology ; Cytoplasm/*microbiology ; Eukaryota/*isolation &amp; purification ; Host-Pathogen Interactions/*immunology ; Humans ; Vacuoles/microbiology ; }, abstract = {Intracellular bacteria including major pathogens live in the cytoplasm or in cytoplasmic vacuoles within their host cell. However, some can invade more unusual intracellular niches such as the eukaryotic nucleus. Phylogenetically diverse intranuclear bacteria have been discovered in various protist, arthropod, marine invertebrate, and mammalian hosts. Although targeting the same cellular compartment, they have apparently developed fundamentally-different infection strategies. The nucleus provides a rich pool of nutrients and protection against host cytoplasmic defense mechanisms; intranuclear bacteria can directly manipulate the host by interfering with nuclear processes. The impact on their host cells ranges from stable associations with a neutral or beneficial effect on host fitness to rapid host lysis. The analysis of the intranuclear lifestyle will extend our current framework for understanding host-pathogen interactions.}, }
@article {pmid25678254, year = {2015}, author = {Narayanasamy, S and Muller, EE and Sheik, AR and Wilmes, P}, title = {Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities.}, journal = {Microbial biotechnology}, volume = {8}, number = {3}, pages = {363-368}, pmid = {25678254}, issn = {1751-7915}, mesh = {*Ecosystem ; Gene Expression Profiling/*methods ; Metabolomics/*methods ; Metagenomics/*methods ; *Microbial Consortia ; Proteomics/*methods ; Systems Biology ; Wastewater/*microbiology ; Water Purification ; }, abstract = {Biological wastewater treatment plants harbour diverse and complex microbial communities which prominently serve as models for microbial ecology and mixed culture biotechnological processes. Integrated omic analyses (combined metagenomics, metatranscriptomics, metaproteomics and metabolomics) are currently gaining momentum towards providing enhanced understanding of community structure, function and dynamics in situ as well as offering the potential to discover novel biological functionalities within the framework of Eco-Systems Biology. The integration of information from genome to metabolome allows the establishment of associations between genetic potential and final phenotype, a feature not realizable by only considering single 'omes'. Therefore, in our opinion, integrated omics will become the future standard for large-scale characterization of microbial consortia including those underpinning biological wastewater treatment processes. Systematically obtained time and space-resolved omic datasets will allow deconvolution of structure-function relationships by identifying key members and functions. Such knowledge will form the foundation for discovering novel genes on a much larger scale compared with previous efforts. In general, these insights will allow us to optimize microbial biotechnological processes either through better control of mixed culture processes or by use of more efficient enzymes in bioengineering applications.}, }
@article {pmid25676171, year = {2015}, author = {Liao, J and Wang, J and Huang, Y}, title = {Bacterial Community Features Are Shaped by Geographic Location, Physicochemical Properties, and Oil Contamination of Soil in Main Oil Fields of China.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {380-389}, pmid = {25676171}, issn = {1432-184X}, mesh = {Bacteria/*growth &amp; development/isolation &amp; purification ; Biodegradation, Environmental ; China ; Environmental Monitoring ; Oil and Gas Fields/*microbiology ; Soil Microbiology ; Soil Pollutants ; }, abstract = {Geographic location and physicochemical properties are thought to represent major factors that shape soil bacterial community abundance and diversity. Crude oil contamination is becoming a notable concern with respect to soil property variation; however, the quantifiable influences of geographic location, physicochemical properties, and oil contamination are still poorly understood. In this study, the 16S ribosomal RNA genes of bacteria in the four oil fields in China were analyzed by using pyrosequencing. Results showed that physicochemical properties were the most dominant factor of bacterial community distribution, followed by geographical location. Oil contamination was a driving factor whose indirect influence was stronger than its direct influence. Under the impact of these three factors, different oil fields presented diversified and distinguishable bacterial community features. The soil of sites with the highest total petroleum hydrocarbon content (HB), nitrogen content (DQ), and phosphorus content (XJ) contained the largest proportion of functional groups participating in hydrocarbon degradation, nitrogen turnover, and phosphorus turnover, respectively. The first dominant phylum of the site with loam soil texture (HB) was Actinobacteria instead of Proteobacteria in other sites with sandy or sandy loam soil texture (DQ, SL, XJ). The site with the highest salinization and alkalization (SL) exhibited the largest proportion of unique local bacteria. The site that was located in the desert with extremely low precipitation (XJ) had the most diversified bacteria distribution. The bacterial community diversity was strongly influenced by soil physicochemical properties.}, }
@article {pmid25674080, year = {2015}, author = {Niederberger, TD and Sohm, JA and Gunderson, TE and Parker, AE and Tirindelli, J and Capone, DG and Carpenter, EJ and Cary, SC}, title = {Microbial community composition of transiently wetted Antarctic Dry Valley soils.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {9}, pmid = {25674080}, issn = {1664-302X}, abstract = {During the summer months, wet (hyporheic) soils associated with ephemeral streams and lake edges in the Antarctic Dry Valleys (DVs) become hotspots of biological activity and are hypothesized to be an important source of carbon and nitrogen for arid DV soils. Recent research in the DV has focused on the geochemistry and microbial ecology of lakes and arid soils, with substantially less information being available on hyporheic soils. Here, we determined the unique properties of hyporheic microbial communities, resolved their relationship to environmental parameters and compared them to archetypal arid DV soils. Generally, pH increased and chlorophyll a concentrations decreased along transects from wet to arid soils (9.0 to ~7.0 for pH and ~0.8 to ~5 μg/cm(3) for chlorophyll a, respectively). Soil water content decreased to below ~3% in the arid soils. Community fingerprinting-based principle component analyses revealed that bacterial communities formed distinct clusters specific to arid and wet soils; however, eukaryotic communities that clustered together did not have similar soil moisture content nor did they group together based on sampling location. Collectively, rRNA pyrosequencing indicated a considerably higher abundance of Cyanobacteria in wet soils and a higher abundance of Acidobacterial, Actinobacterial, Deinococcus/Thermus, Bacteroidetes, Firmicutes, Gemmatimonadetes, Nitrospira, and Planctomycetes in arid soils. The two most significant differences at the genus level were Gillisia signatures present in arid soils and chloroplast signatures related to Streptophyta that were common in wet soils. Fungal dominance was observed in arid soils and Viridiplantae were more common in wet soils. This research represents an in-depth characterization of microbial communities inhabiting wet DV soils. Results indicate that the repeated wetting of hyporheic zones has a profound impact on the bacterial and eukaryotic communities inhabiting in these areas.}, }
@article {pmid25666537, year = {2015}, author = {Silva-Lima, AW and Walter, JM and Garcia, GD and Ramires, N and Ank, G and Meirelles, PM and Nobrega, AF and Siva-Neto, ID and Moura, RL and Salomon, PS and Thompson, CC and Thompson, FL}, title = {Multiple Symbiodinium Strains Are Hosted by the Brazilian Endemic Corals Mussismilia spp.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {301-310}, pmid = {25666537}, issn = {1432-184X}, mesh = {Animals ; Anthozoa ; Atlantic Ocean ; Brazil ; *Coral Reefs ; Dinoflagellida/*physiology ; Symbiosis/physiology ; }, abstract = {Corals of genus Mussismilia (Mussidae) are one of the oldest extant clades of scleractinians. These Neogene relicts are endemic to the Brazilian coast and represent the main reef-building corals in the Southwest Atlantic Ocean (SAO). The relatively low-diversity/high-endemism SAO coralline systems are under rapid decline from emerging diseases and other local and global stressors, but have not been severely affected by coral bleaching. Despite the biogeographic significance and importance for understanding coral resilience, there is scant information about the diversity of Symbiodinium in this ocean basin. In this study, we established the first culture collections of Symbiodinium from Mussismilia hosts, comprising 11 isolates, four of them obtained by fluorescent-activated cell sorting (FACS). We also analyzed Symbiodinium diversity directly from Mussismilia tissue samples (N = 16) and characterized taxonomically the cultures and tissue samples by sequencing the dominant ITS2 region. Symbiodinium strains A4, B19, and C3 were detected. Symbiodinium C3 was predominant in the larger SAO reef system (Abrolhos), while Symbiodinium B19 was found only in deep samples from the oceanic Trindade Island. Symbiodinium strains A4 and C3 isolates were recovered from the same Mussismilia braziliensis coral colony. In face of increasing threats, these results indicate that Symbiodinium community dynamics shall have an important contribution for the resilience of Mussismilia spp. corals.}, }
@article {pmid25666536, year = {2015}, author = {Morrow, JL and Frommer, M and Shearman, DC and Riegler, M}, title = {The Microbiome of Field-Caught and Laboratory-Adapted Australian Tephritid Fruit Fly Species with Different Host Plant Use and Specialisation.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {498-508}, pmid = {25666536}, issn = {1432-184X}, mesh = {Animals ; Australia ; Bacteria/classification/genetics ; RNA, Ribosomal, 16S/genetics ; Tephritidae/microbiology/*physiology ; }, abstract = {Tephritid fruit fly species display a diversity of host plant specialisation on a scale from monophagy to polyphagy. Furthermore, while some species prefer ripening fruit, a few are restricted to damaged or rotting fruit. Such a diversity of host plant use may be reflected in the microbial symbiont diversity of tephritids and their grade of dependency on their microbiomes. Here, we investigated the microbiome of six tephritid species from three genera, including species that are polyphagous pests (Bactrocera tryoni, Bactrocera neohumeralis, Bactrocera jarvisi, Ceratitis capitata) and a monophagous specialist (Bactrocera cacuminata). These were compared with the microbiome of a non-pestiferous but polyphagous tephritid species that is restricted to damaged or rotting fruit (Dirioxa pornia). The bacterial community associated with whole fruit flies was analysed by 16S ribosomal DNA (rDNA) amplicon pyrosequencing to detect potential drivers of taxonomic composition. Overall, the dominant bacterial families were Enterobacteriaceae and Acetobacteraceae (both Proteobacteria), and Streptococcaceae and Enterococcaceae (both Firmicutes). Comparisons across species and genera found different microbial composition in the three tephritid genera, but limited consistent differentiation between Bactrocera species. Within Bactrocera species, differentiation of microbial composition seemed to be influenced by the environment, possibly including their diets; beyond this, tephritid species identity or ecology also had an effect. The microbiome of D. pornia was most distinct from the other five species, which may be due to its ecologically different niche of rotting or damaged fruit, as opposed to ripening fruit favoured by the other species. Our study is the first amplicon pyrosequencing study to compare the microbiomes of tephritid species and thus delivers important information about the turnover of microbial diversity within and between fruit fly species and their potential application in pest management strategies.}, }
@article {pmid25666535, year = {2015}, author = {Fulgentini, L and Passini, V and Colombetti, G and Miceli, C and La Terza, A and Marangoni, R}, title = {UV Radiation and Visible Light Induce hsp70 Gene Expression in the Antarctic Psychrophilic Ciliate Euplotes focardii.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {372-379}, pmid = {25666535}, issn = {1432-184X}, mesh = {Acclimatization ; Adaptation, Physiological ; Ciliophora/*physiology/radiation effects ; Euplotes/*physiology/radiation effects ; *Light ; *Ultraviolet Rays ; }, abstract = {The psychrophilic ciliate Euplotes focardii inhabits the shallow marine coastal sediments of Antarctica, where, over millions of years of evolution, it has reached a strict molecular adaptation to such a constant-temperature environment (about -2 °C). This long evolution at sub-zero temperatures has made E. focardii unable to respond to heat stress with the activation of its heat shock protein (hsp) 70 genes. These genes can, however, be expressed in response to other stresses, like the oxidative one, thus indicating that the molecular adaptation has exclusively altered the heat stress signaling pathways, while it has preserved hsp70 gene activation in response to other environmental stressors. Since radiative stress has proved to be affine to oxidative stress in several organisms, we investigated the capability of UV radiation to induce hsp70 transcription. E. focardii cell cultures were exposed to several different irradiation regimes, ranging from visible only to a mixture of visible, UV-A and UV-B. The irradiation values of each spectral band have been set to be comparable with those recorded in a typical Antarctic spring. Using Northern blot analysis, we measured the expression level of hsp70 immediately after irradiation (0-h-labeled samples), 1 h, and 2 h from the end of the irradiation. Surprisingly, our results showed that besides UV radiation, the visible light was also able to induce hsp70 expression in E. focardii. Moreover, spectrophotometric measurements have revealed no detectable endogenous pigments in E. focardii, making it difficult to propose a possible explanation for the visible light induction of its hsp70 genes. Further research is needed to conclusively clarify this point.}, }
@article {pmid25663091, year = {2015}, author = {McLaughlin, RW and Cochran, PA and Dowd, SE}, title = {Metagenomic analysis of the gut microbiota of the Timber Rattlesnake, Crotalus horridus.}, journal = {Molecular biology reports}, volume = {42}, number = {7}, pages = {1187-1195}, pmid = {25663091}, issn = {1573-4978}, mesh = {Actinobacteria/classification/genetics/metabolism ; Animals ; Bacteroides/classification/genetics/metabolism ; Carbohydrate Metabolism ; Colon/microbiology/parasitology/virology ; Crotalus/*microbiology/parasitology/virology ; Eukaryota/classification/genetics/metabolism ; Firmicutes/classification/genetics/metabolism ; Gastrointestinal Microbiome/genetics ; Gene Library ; High-Throughput Nucleotide Sequencing ; Intestine, Small/microbiology/parasitology/virology ; *Metagenome ; *Phylogeny ; Proteobacteria/classification/*genetics/metabolism ; RNA, Ribosomal, 16S/*genetics/isolation &amp; purification ; Stomach/microbiology/parasitology/virology ; Viruses/classification/genetics/metabolism ; }, abstract = {Snakes are capable of surviving long periods without food. In this study we characterized the microbiota of a Timber Rattlesnake (Crotalus horridus), devoid of digesta, living in the wild. Pyrosequencing-based metagenomics were used to analyze phylogenetic and metabolic profiles with the aid of the MG-RAST server. Pyrosequencing of samples taken from the stomach, small intestine and colon yielded 691696, 957756 and 700419 high quality sequence reads. Taxonomic analysis of metagenomic reads indicated Eukarya was the most predominant domain, followed by bacteria and then viruses, for all three tissues. The most predominant phylum in the domain Bacteria was Proteobacteria for the tissues examined. Functional classifications by the subsystem database showed cluster-based subsystems were most predominant (10-15 %). Almost equally predominant (10-13 %) was carbohydrate metabolism. To identify bacteria in the colon at a finer taxonomic resolution, a 16S rRNA gene clone library was created. Proteobacteria was again found to be the most predominant phylum. The present study provides a baseline for understanding the microbial ecology of snakes living in the wild.}, }
@article {pmid25661839, year = {2015}, author = {Schlüter, JP and Czuppon, P and Schauer, O and Pfaffelhuber, P and McIntosh, M and Becker, A}, title = {Classification of phenotypic subpopulations in isogenic bacterial cultures by triple promoter probing at single cell level.}, journal = {Journal of biotechnology}, volume = {198}, number = {}, pages = {3-14}, doi = {10.1016/j.jbiotec.2015.01.021}, pmid = {25661839}, issn = {1873-4863}, mesh = {Bacterial Proteins/genetics ; Galactans/genetics ; Gene Expression Regulation, Bacterial/genetics ; Genes, Reporter/genetics ; Glucans/genetics ; Green Fluorescent Proteins/genetics ; Polysaccharides, Bacterial/genetics ; Promoter Regions, Genetic/*genetics ; Quorum Sensing/genetics ; Sinorhizobium meliloti/*genetics ; }, abstract = {Phenotypic heterogeneity, defined as the unequal behavior of individuals in an isogenic population, is prevalent in microorganisms. It has a significant impact both on industrial bioprocesses and microbial ecology. We introduce a new versatile reporter system designed for simultaneous monitoring of the activities of three different promoters, where each promoter is fused to a dedicated fluorescent reporter gene (cerulean, mCherry, and mVenus). The compact 3.1 kb triple reporter cassette can either be carried on a replicating plasmid or integrated into the genome avoiding artifacts associated with variation in copy number of plasmid-borne reporter constructs. This construct was applied to monitor promoter activities related to quorum sensing (sinI promoter) and biosynthesis of the exopolysaccharide galactoglucan (wgeA promoter) at single cell level in colonies of the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti growing in a microfluidics system. The T5-promoter served as a constitutive and homogeneously active control promoter indicating cell viability. wgeA promoter activity was heterogeneous over the whole period of colony development, whereas sinI promoter activity passed through a phase of heterogeneity before becoming homogeneous at late stages. Although quorum sensing-dependent regulation is a major factor activating galactoglucan production, activities of both promoters did not correlate at single cell level. We developed a novel mathematical strategy for classification of the gene expression status in cell populations based on the increase in fluorescence over time in each individual. With respect to galactoglucan biosynthesis, cells in the population were classified into non-contributors, weak contributors, and strong contributors.}, }
@article {pmid25661475, year = {2015}, author = {Berry, DL and Goleski, JA and Koch, F and Wall, CC and Peterson, BJ and Anderson, OR and Gobler, CJ}, title = {Shifts in Cyanobacterial Strain Dominance during the Onset of Harmful Algal Blooms in Florida Bay, USA.}, journal = {Microbial ecology}, volume = {70}, number = {2}, pages = {361-371}, pmid = {25661475}, issn = {1432-184X}, mesh = {Bays ; Cyanobacteria/*classification/genetics/*growth &amp; development/isolation &amp; purification ; Florida ; *Harmful Algal Bloom ; RNA, Ribosomal, 16S/genetics ; Synechococcus/classification/genetics/growth &amp; development/isolation &amp; purification ; }, abstract = {Cyanobacteria are fundamental components of aquatic phytoplankton communities and some taxa can cause harmful blooms in coastal ecosystems. Harmful cyanobacterial blooms are typically comprised of multiple strains of a single genus or species that cannot be resolved microscopically. Florida Bay, USA, has experienced harmful cyanobacterial blooms that have been associated with the loss of eelgrass, spiny lobsters, and general food web disruption for more than two decades. To identify the strain or strains of cyanobacteria forming blooms in Florida Bay, samples were collected across the system over an annual cycle and analyzed via DNA sequencing using cyanobacterial-specific 16S rRNA gene primers, flow cytometry, and scanning electron microscopy. Analyses demonstrated that the onset of blooms in Florida Bay was coincident with a transformation of the cyanobacterial populations. When blooms were absent, the cyanobacterial population in Florida Bay was dominated by phycoerythrin-containing Synechococcus cells that were most similar to strains within Clade III. As blooms developed, the cyanobacterial community transitioned to dominance by phycocyanin-containing Synechococcus cells that were coated with mucilage, chain-forming, and genetically most similar to the coastal strains within Clade VIII. Clade VIII strains of Synechococcus are known to grow rapidly, utilize organic nutrients, and resist top-down control by protozoan grazers and viruses, all characteristics consistent with observations of cyanobacterial blooms in Florida Bay. Further, the strains of Synechococcus blooming in this system are genetically distinct from the species previously thought to cause blooms in Florida Bay, Synechococcus elongatus. Collectively, this study identified the causative organism of harmful cyanobacterial blooms in Florida Bay, demonstrates the dynamic nature of cyanobacterial stains within genera in an estuary, and affirms factors promoting Synechococcus blooms.}, }
@article {pmid25659305, year = {2015}, author = {Gutiérrez, L and Garbisu, C and Ciprián, E and Becerril, JM and Soto, M and Etxebarria, J and Madariaga, JM and Antigüedad, I and Epelde, L}, title = {Application of ecological risk assessment based on a novel TRIAD-tiered approach to contaminated soil surrounding a closed non-sealed landfill.}, journal = {The Science of the total environment}, volume = {514}, number = {}, pages = {49-59}, doi = {10.1016/j.scitotenv.2015.01.103}, pmid = {25659305}, issn = {1879-1026}, mesh = {Environmental Monitoring/*methods ; Refuse Disposal/methods ; Risk Assessment ; Soil/chemistry ; Soil Pollutants/*analysis ; Spain ; *Waste Disposal Facilities ; }, abstract = {The Ecological Risk Assessment (ERA) is a reliable tool for communicating risk to decision makers in a comprehensive and scientific evidence-based way. In this work, a site-specific ERA methodology based on the TRIAD approach was applied to contaminated soil surrounding a closed non-sealed landfill, as a case study to implement and validate such ERA methodology in the Basque Country (northern Spain). Initially, the procedure consisted of the application of a Parameter Selection Module aimed at selecting the most suitable parameters for the specific characteristics of the landfill contaminated soil, taking into consideration the envisioned land use, intended ecosystem services and nature of contaminants. Afterwards, the selected parameters were determined in soil samples collected from two sampling points located downstream of the abovementioned landfill. The results from these tests were normalized to make them comparable and integrable in a risk index. Then, risk assessment criteria were developed and applied to the two landfill contaminated soil samples. Although the lack of a proper control soil was evidenced, a natural land use was approved by the ERA (at Tier 2) for the two landfill contaminated soils. However, the existence of a potential future risk resulting from a hypothetical soil acidification must be considered.}, }
@article {pmid25651406, year = {2015}, author = {Gildemyn, S and Luther, AK and Andersen, SJ and Desloover, J and Rabaey, K}, title = {Electrochemically and bioelectrochemically induced ammonium recovery.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {95}, pages = {52405}, pmid = {25651406}, issn = {1940-087X}, mesh = {Ammonium Compounds/*isolation &amp; purification ; Electrochemical Techniques/methods ; Electrodes ; Hydrogen-Ion Concentration ; Reproducibility of Results ; Wastewater/*chemistry ; }, abstract = {Streams such as urine and manure can contain high levels of ammonium, which could be recovered for reuse in agriculture or chemistry. The extraction of ammonium from an ammonium-rich stream is demonstrated using an electrochemical and a bioelectrochemical system. Both systems are controlled by a potentiostat to either fix the current (for the electrochemical cell) or fix the potential of the working electrode (for the bioelectrochemical cell). In the bioelectrochemical cell, electroactive bacteria catalyze the anodic reaction, whereas in the electrochemical cell the potentiostat applies a higher voltage to produce a current. The current and consequent restoration of the charge balance across the cell allow the transport of cations, such as ammonium, across a cation exchange membrane from the anolyte to the catholyte. The high pH of the catholyte leads to formation of ammonia, which can be stripped from the medium and captured in an acid solution, thus enabling the recovery of a valuable nutrient. The flux of ammonium across the membrane is characterized at different anolyte ammonium concentrations and currents for both the abiotic and biotic reactor systems. Both systems are compared based on current and removal efficiencies for ammonium, as well as the energy input required to drive ammonium transfer across the cation exchange membrane. Finally, a comparative analysis considering key aspects such as reliability, electrode cost, and rate is made. This video article and protocol provide the necessary information to conduct electrochemical and bioelectrochemical ammonia recovery experiments. The reactor setup for the two cases is explained, as well as the reactor operation. We elaborate on data analysis for both reactor types and on the advantages and disadvantages of bioelectrochemical and electrochemical systems.}, }
@article {pmid25647346, year = {2015}, author = {Mendes, R and Raaijmakers, JM}, title = {Cross-kingdom similarities in microbiome functions.}, journal = {The ISME journal}, volume = {9}, number = {9}, pages = {1905-1907}, pmid = {25647346}, issn = {1751-7370}, }
@article {pmid25645243, year = {2015}, author = {Massimo, NC and Nandi Devan, MM and Arendt, KR and Wilch, MH and Riddle, JM and Furr, SH and Steen, C and U'Ren, JM and Sandberg, DC and Arnold, AE}, title = {Fungal endophytes in aboveground tissues of desert plants: infrequent in culture, but highly diverse and distinctive symbionts.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {61-76}, pmid = {25645243}, issn = {1432-184X}, support = {R01 CA090265/CA/NCI NIH HHS/United States ; R01-CA90265/CA/NCI NIH HHS/United States ; }, mesh = {Arizona ; Ascomycota/*genetics ; Bayes Theorem ; *Biodiversity ; *Biological Evolution ; Computational Biology ; Desert Climate ; Endophytes/*genetics ; Food ; Geography ; Likelihood Functions ; Models, Genetic ; Phylogeny ; Plants/*microbiology ; Polymerase Chain Reaction ; Statistics, Nonparametric ; *Symbiosis ; Temperature ; }, abstract = {In hot deserts, plants cope with aridity, high temperatures, and nutrient-poor soils with morphological and biochemical adaptations that encompass intimate microbial symbioses. Whereas the root microbiomes of arid-land plants have received increasing attention, factors influencing assemblages of symbionts in aboveground tissues have not been evaluated for many woody plants that flourish in desert environments. We evaluated the diversity, host affiliations, and distributions of endophytic fungi associated with photosynthetic tissues of desert trees and shrubs, focusing on nonsucculent woody plants in the species-rich Sonoran Desert. To inform our strength of inference, we evaluated the effects of two different nutrient media, incubation temperatures, and collection seasons on the apparent structure of endophyte assemblages. Analysis of >22,000 tissue segments revealed that endophytes were isolated four times more frequently from photosynthetic stems than leaves. Isolation frequency was lower than expected given the latitude of the study region and varied among species a function of sampling site and abiotic factors. However, endophytes were very species-rich and phylogenetically diverse, consistent with less arid sites of a similar latitudinal position. Community composition differed among host species, but not as a function of tissue type, sampling site, sampling month, or exposure. Estimates of abundance, diversity, and composition were not influenced by isolation medium or incubation temperature. Phylogenetic analyses of the most commonly isolated genus (Preussia) revealed multiple evolutionary origins of desert-plant endophytism and little phylogenetic structure with regard to seasonality, tissue preference, or optimal temperatures and nutrients for growth in vitro. Together, these results provide insight into endophytic symbioses in desert-plant communities and can be used to optimize strategies for capturing endophyte biodiversity at regional scales.}, }
@article {pmid25640844, year = {2015}, author = {Valverde, A and Makhalanyane, TP and Seely, M and Cowan, DA}, title = {Cyanobacteria drive community composition and functionality in rock-soil interface communities.}, journal = {Molecular ecology}, volume = {24}, number = {4}, pages = {812-821}, doi = {10.1111/mec.13068}, pmid = {25640844}, issn = {1365-294X}, mesh = {Bacteria/*classification/genetics ; Cyanobacteria/*classification/genetics ; DNA, Bacterial/genetics ; Desert Climate ; *Ecosystem ; Food Chain ; Heterotrophic Processes ; Namibia ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Most ecological research on hypoliths, significant primary producers in hyperarid deserts, has focused on the diversity of individual groups of microbes (i.e. bacteria). However, microbial communities are inherently complex, and the interactions between cyanobacteria, heterotrophic bacteria, protista and metazoa are likely to be very important for ecosystem functioning. Cyanobacterial and heterotrophic bacterial communities were analysed by pyrosequencing, while metazoan and protistan communities were assessed by T-RFLP analysis. Microbial functionality was estimated using carbon substrate utilization. Cyanobacterial community composition was significant in shaping community structure and function in hypoliths. Ecological network analysis showed that most significant co-occurrences were positive, representing potential synergistic interactions. There were several highly interconnected associations (modules), and specific cyanobacteria were important in driving the modular structure of hypolithic networks. Together, our results suggest that hypolithic cyanobacteria have strong effects on higher trophic levels and ecosystem functioning.}, }
@article {pmid25640407, year = {2015}, author = {Ludden, C and Brennan, G and Morris, D and Austin, B and O'Connell, B and Cormican, M}, title = {Characterization of methicillin-resistant Staphylococcus aureus from residents and the environment in a long-term care facility.}, journal = {Epidemiology and infection}, volume = {143}, number = {14}, pages = {2985-2988}, pmid = {25640407}, issn = {1469-4409}, mesh = {Bacterial Proteins/genetics ; Bacterial Toxins/genetics ; *Environmental Microbiology ; Exotoxins/genetics ; Genotype ; Humans ; Ireland/epidemiology ; Leukocidins/genetics ; *Long-Term Care ; Methicillin-Resistant Staphylococcus aureus/classification/genetics/*isolation &amp; purification ; Molecular Epidemiology ; Molecular Typing ; *Nursing Homes ; Penicillin-Binding Proteins ; Prospective Studies ; Staphylococcal Infections/*epidemiology/*microbiology ; Staphylococcal Protein A/genetics ; }, abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) is a major public health concern associated with residence in a long-term care facility (LTCF). The aim of this prospective study was to characterize MRSA isolated from residents over a 1-year period and their physical environment over a 2-year period. MRSA was recovered from 17/64 residents (R) of a LTCF and from 42 environmental (E) sites. All isolates carried the mecA gene and lacked the mecC and Panton-Valentine leukocidin (PVL) genes. Thirteen spa types were identified with t032 being the most frequent (41% of total; n = 8R, 16E), followed by t727 (22% of total; n = 13E), and t8783 (10% of total; n = 6E). Five spa types were each represented by single isolates. Thirty-nine isolates were of spa types associated with the multilocus sequence type ST22 (t032, 41%; spa-CC22, 68%) and reflect the predominance of ST22 in Irish hospitals. The uncommon spa types t727, t8783, t1372, t3130, t10038 were present in the environment but not detected in residents and are infrequently observed in Ireland.}, }
@article {pmid25639264, year = {2015}, author = {Ruan, A and Zhao, Y and Liu, C and Zong, F and Yu, Z}, title = {Effects of 17β-estradiol on emissions of greenhouse gases in simulative natural water body.}, journal = {Environmental toxicology and chemistry}, volume = {34}, number = {5}, pages = {977-982}, doi = {10.1002/etc.2882}, pmid = {25639264}, issn = {1552-8618}, mesh = {Carbon Dioxide/analysis ; Endocrine Disruptors/*chemistry ; Estradiol/*pharmacology ; Fresh Water ; Gases ; *Greenhouse Effect ; Methane/analysis ; Methylococcaceae/drug effects ; Nitrous Oxide/analysis ; Water Microbiology ; Water Pollutants, Chemical/*chemistry ; }, abstract = {Environmental estrogens are widely spread across the world and are increasingly thought of as serious contaminators. The present study looks at the influence of different concentrations of 17β-estradiol on greenhouse gas emissions (CO2 , CH4 , and N2 O) in simulated systems to explore the relationship between environmental estrogen-pollution and greenhouse gas emissions in natural water bodies. The present study finds that 17β-estradiol pollution in simulated systems has significant promoting effects on the emissions of CH4 and CO2 , although no significant effects on N2 O emissions. The present study indicates that 17β-estradiol has different effects on the different elements cycles; the mechanism of microbial ecology is under review.}, }
@article {pmid25638045, year = {2015}, author = {Sultanpuram, VR and Mothe, T and Mohammed, F}, title = {Salisediminibacterium haloalkalitolerans sp. nov., isolated from Lonar soda lake, India, and a proposal for reclassification of Bacillus locisalis as Salisediminibacterium locisalis comb. nov., and the emended description of the genus Salisediminibacterium and of the species Salisediminibacterium halotolerans.}, journal = {Archives of microbiology}, volume = {197}, number = {4}, pages = {553-560}, doi = {10.1007/s00203-015-1081-8}, pmid = {25638045}, issn = {1432-072X}, mesh = {Bacillus/*classification/*genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; Cell Wall/metabolism ; DNA, Bacterial/genetics ; Diaminopimelic Acid/analogs &amp; derivatives/metabolism ; Fatty Acids/*analysis ; India ; Lakes/*microbiology ; Phospholipids/*analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {A Gram stain-positive, rod-shaped, non-motile, orange-pigmented and non-endospore-forming novel bacterial strain 10nlg(T) was isolated from Lonar soda lake in India. Based on the 16S rRNA gene sequence analysis, it was belonged to the genus Salisediminibacterium and was most closely related to Salisediminibacterium halotolerans CGMCC 1.7654(T) (99.9 %), Bacillus locisalis CGMCC 1.6286(T) (99.1 %) and other members in the Bacillaceae (<93.6 %). Further, DNA-DNA hybridization results demonstrated that strain 10nlg(T) was distantly (<70 %) related to S. halotolerans halo-2(T) (59.6 %) and B. locisalis CGMCC 1.6286(T) (53.2 %). Strain 10nlg(T) was catalase positive and oxidase negative. The cell wall of the strain 10nlg(T) contains meso-diaminopimelic acid as the diagnostic amino acid. Polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, five phospholipids and two unknown lipids. The predominant isoprenoid quinone was MK-7. Anteiso-C15:0 (32.6 %) was the predominant fatty acid, and significant proportions of iso-C15:0 (9.3 %), anteiso-C17:0 (8.3 %), C16:0 (4.3 %) were also detected in the strain 10nlg(T). The DNA G+C content of the strain 10nlg(T) was 45.6 mol %. The results of phylogenetic, physiological and biochemical tests allowed a distinct differentiation of strain 10nlg(T) not only from S. halotolerans halo-2(T), the only member of the genus Salisediminibacterium, but also from the related Bacillaceae members. Strain 10nlg(T) represents a novel species of the genus Salisediminibacterium for which the name Salisediminibacterium haloalkalitolerans sp. nov. is proposed. The type strain is 10nlg(T) (=KCTC 33414(T) = CGMCC 1.12818(T)). B. locisalis CGMCC 1.6286(T) also represents a member of the genus Salisediminibacterium for which the name Salisediminibacterium locisalis CG1(T) is proposed. The type strain is CG1(T) = (CCM 7370(T) = CECT 7152(T) = CGMCC 1.6286(T) = DSM 18085(T)). In accordance with the new polar lipid data collected in this study, emended descriptions of the genus Salisediminibacterium and the species S. halotolerans halo-2(T) are also provided.}, }
@article {pmid25636731, year = {2015}, author = {Logan, AC and Katzman, MA and Balanzá-Martínez, V}, title = {Natural environments, ancestral diets, and microbial ecology: is there a modern "paleo-deficit disorder"? Part I.}, journal = {Journal of physiological anthropology}, volume = {34}, number = {1}, pages = {1}, pmid = {25636731}, issn = {1880-6805}, mesh = {Anxiety ; *Diet, Paleolithic ; Feeding Behavior ; Humans ; *Nature ; *Quality of Life ; *Stress, Psychological ; *Urbanization ; }, abstract = {Famed microbiologist René J. Dubos (1901-1982) was an early pioneer in the developmental origins of health and disease (DOHaD) construct. In the 1960s, he conducted groundbreaking experimental research concerning the ways in which early-life experience with nutrition, microbiota, stress, and other environmental variables could influence later-life health outcomes. He also wrote extensively on potential health consequences of a progressive loss of contact with natural environments (now referred to as green or blue space), arguing that Paleolithic experiences have created needs, particularly in the mental realm, that might not be met in the context of rapid global urbanization. He posited that humans would certainly adapt to modern urban landscapes and high technology, but there might be a toll to be paid in the form of higher psychological distress (symptoms of anxiety and depression) and diminished quality of life. In particular, there might be an erosion of humanness, exemplified by declines in altruism/empathy. Here in the first of a two-part review, we examine contemporary research related to natural environments and question to what extent Dubos might have been correct in some of his 50-year-old assertions.}, }
@article {pmid25636680, year = {2015}, author = {Lee, DH and Choi, SL and Rha, E and Kim, SJ and Yeom, SJ and Moon, JH and Lee, SG}, title = {A novel psychrophilic alkaline phosphatase from the metagenome of tidal flat sediments.}, journal = {BMC biotechnology}, volume = {15}, number = {1}, pages = {1}, pmid = {25636680}, issn = {1472-6750}, mesh = {Alkaline Phosphatase/chemistry/*genetics/*metabolism ; Amino Acid Sequence ; Calcium/metabolism ; Cloning, Molecular ; Enzyme Activation ; Enzyme Stability ; Gene Library ; Geologic Sediments/*microbiology ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Republic of Korea ; Sequence Alignment ; Substrate Specificity ; }, abstract = {BACKGROUND: Alkaline phosphatase (AP) catalyzes the hydrolytic cleavage of phosphate monoesters under alkaline conditions and plays important roles in microbial ecology and molecular biology applications. Here, we report on the first isolation and biochemical characterization of a thermolabile AP from a metagenome.<br><br>RESULTS: The gene encoding a novel AP was isolated from a metagenomic library constructed with ocean-tidal flat sediments from the west coast of Korea. The metagenome-derived AP (mAP) gene composed of 1,824 nucleotides encodes a polypeptide with a calculated molecular mass of 64 kDa. The deduced amino acid sequence of mAP showed a high degree of similarity to other members of the AP family. Phylogenetic analysis revealed that the mAP is shown to be a member of a recently identified family of PhoX that is distinct from the well-studied classical PhoA family. When the open reading frame encoding mAP was cloned and expressed in recombinant Escherichia coli, the mature mAP was secreted to the periplasm and lacks an 81-amino-acid N-terminal Tat signal peptide. Mature mAP was purified to homogeneity as a monomeric enzyme with a molecular mass of 56 kDa. The purified mAP displayed typical features of a psychrophilic enzyme: high catalytic activity at low temperature and a remarkable thermal instability. The optimal temperature for the enzymatic activity of mAP was 37&#xb0;C and complete thermal inactivation of the enzyme was observed at 65&#xb0;C within 15 min. mAP was activated by Ca(2+) and exhibited maximal activity at pH 9.0. Except for phytic acid and glucose 1-phosphate, mAP showed phosphatase activity against various phosphorylated substrates indicating that it had low substrate specificity. In addition, the mAP was able to remove terminal phosphates from cohesive and blunt ends of linearized plasmid DNA, exhibiting comparable efficiency to commercially available APs that have been used in molecular biology.<br><br>CONCLUSIONS: The presented mAP enzyme is the first thermolabile AP found in cold-adapted marine metagenomes and may be useful for efficient dephosphorylation of linearized DNA.}, }
@article {pmid25636185, year = {2015}, author = {Poisnel, E and Roseau, JB and Landais, C and Rodriguez-Nava, V and Bussy, E and Gaillard, T}, title = {Nocardia veterana: disseminated infection with urinary tract infection.}, journal = {The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases}, volume = {19}, number = {2}, pages = {216-219}, pmid = {25636185}, issn = {1678-4391}, mesh = {Humans ; Male ; Middle Aged ; Nocardia/genetics/*isolation &amp; purification ; Nocardia Infections/diagnosis/*microbiology ; RNA, Ribosomal, 16S ; Urinary Tract Infections/diagnosis/*microbiology ; }, abstract = {Nocardia spp. are a group of aerobic actinomycetes widely distributed in soil, and associated with severe opportunistic infections, essentially pulmonary infections. We report the first case of disseminated infection associated with urinary tract infection caused by Nocardia veterana. The diagnosis was difficult; despite the presence of pulmonary nodules, the lung biopsies remained negative while only one aerobic blood culture and the urine culture were positive for N. veterana, identified after a 16S rDNA gene sequence analysis. Few cases of clinical importance due to N. veterana have been published since its characterization. The bacteriological diagnosis of nocardiosis can be difficult to establish because of the delayed growth and the specific techniques that are required. This case illustrates the necessity of performing specific investigations in immunocompromised patients who present with infectious disease because the severity of this infection requires early diagnosis and quick initiation of appropriate antibiotic therapy.}, }
@article {pmid25634943, year = {2015}, author = {Lee, JC and Kim, YS and Yun, BS and Whang, KS}, title = {Idiomarina halophila sp. nov., isolated from a solar saltern sediment.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {65}, number = {Pt 4}, pages = {1268-1273}, doi = {10.1099/ijs.0.000094}, pmid = {25634943}, issn = {1466-5034}, mesh = {Alteromonadaceae/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Salinity ; Sequence Analysis, DNA ; Ubiquinone/chemistry ; *Water Microbiology ; }, abstract = {A Gram-stain-negative, halophilic bacterium, designated strain BH195(T), was isolated from the sediment of the solar saltern pond located in Gomso, Republic of Korea. Strain BH195(T) was a strictly aerobic, non-motile rod, which grew at pH 3.5-10.5 (optimum, pH 7.5), at 4-55 °C (optimum, 30 °C) and at salinities of 0.5-11% (w/v) NaCl [optimum, 2-3% (w/v) NaCl]. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain BH195(T) belongs to the genus Idiomarina , showing the highest sequence similarity to Idiomarina salinarum ISL-52(T) (97.4%), Idiomarina homiensis PO-M2(T) (96.8%), Idiomarina aestuarii KYW314(T) (96.7%), and Idiomarina tainanensis PIN1(T) (96.7%). The major cellular fatty acids of strain BH195(T) were iso-C(11 : 0) 3-OH, iso-C(15 : 0) and iso-C(11 : 0). The DNA G+C content was 51.3 mol% and the major respiratory quinone was ubiquinone 8. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unknown phospholipid. DNA-DNA relatedness between strain BH195(T) and I. salinarum KCTC 12971(T) was 33%. On the basis of this polyphasic analysis, strain BH195(T) represents a novel species of the genus Idiomarina for which the name Idiomarina halophila sp. nov. is proposed. The type strain is BH195(T) (= KACC 17610(T) = NCAIM B 02544(T)).}, }
@article {pmid25633715, year = {2015}, author = {Budd, A and Dinkel, H and Corpas, M and Fuller, JC and Rubinat, L and Devos, DP and Khoueiry, PH and Förstner, KU and Georgatos, F and Rowland, F and Sharan, M and Binder, JX and Grace, T and Traphagen, K and Gristwood, A and Wood, NT}, title = {Ten simple rules for organizing an unconference.}, journal = {PLoS computational biology}, volume = {11}, number = {1}, pages = {e1003905}, pmid = {25633715}, issn = {1553-7358}, mesh = {Communication ; Computational Biology/*organization &amp; administration ; *Congresses as Topic ; Crowdsourcing ; Humans ; }, }
@article {pmid25630351, year = {2015}, author = {Lossouarn, J and Nesbø, CL and Mercier, C and Zhaxybayeva, O and Johnson, MS and Charchuck, R and Farasin, J and Bienvenu, N and Baudoux, AC and Michoud, G and Jebbar, M and Geslin, C}, title = {'Ménage à trois': a selfish genetic element uses a virus to propagate within Thermotogales.}, journal = {Environmental microbiology}, volume = {17}, number = {9}, pages = {3278-3288}, doi = {10.1111/1462-2920.12783}, pmid = {25630351}, issn = {1462-2920}, mesh = {Bacteria/genetics/isolation &amp; purification/*virology ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; DNA, Viral/genetics ; Gene Dosage/drug effects/genetics ; Gene Transfer, Horizontal/*genetics ; Hydrothermal Vents/*microbiology/virology ; Mitomycin/pharmacology ; Plasmids/*genetics ; Siphoviridae/*genetics ; }, abstract = {Prokaryotic viruses play a major role in the microbial ecology and evolution. However, the virosphere associated with deep-sea hydrothermal ecosystems remains largely unexplored. Numerous instances of lateral gene transfer have contributed to the complex and incongruent evolutionary history of Thermotogales, an order well represented in deep-sea hydrothermal vents. The presence of clustered regularly interspaced short palindromic repeats (CRISPR) loci has been reported in all Thermotogales genomes, suggesting that these bacteria have been exposed to viral infections that could have mediated gene exchange. In this study, we isolated and characterized the first virus infecting bacteria from the order Thermotogales, Marinitoga piezophila virus 1 (MPV1). The host, Marinitoga piezophila is a thermophilic, anaerobic and piezophilic bacterium isolated from a deep-sea hydrothermal chimney. MPV1 is a temperate Siphoviridae-like virus with a 43.7 kb genome. Surprisingly, we found that MPV1 virions carry not only the viral DNA but preferentially package a plasmid of 13.3 kb (pMP1) also carried by M. piezophila. This 'ménage à trois' highlights potential relevance of selfish genetic elements in facilitating lateral gene transfer in the deep-sea biosphere.}, }
@article {pmid25626393, year = {2015}, author = {Cass, BN and Yallouz, R and Bondy, EC and Mozes-Daube, N and Horowitz, AR and Kelly, SE and Zchori-Fein, E and Hunter, MS}, title = {Dynamics of the endosymbiont Rickettsia in an insect pest.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {287-297}, pmid = {25626393}, issn = {1432-184X}, mesh = {Animals ; DNA Primers/genetics ; Genetic Fitness/genetics ; *Genetic Variation ; Geography ; Hemiptera/*microbiology ; Insect Control/*methods ; *Introduced Species ; Israel ; Logistic Models ; Microsatellite Repeats/genetics ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Rickettsia/*genetics ; Sex Ratio ; Southwestern United States ; *Symbiosis ; Time Factors ; }, abstract = {A new heritable bacterial association can bring a fresh set of molecular capabilities, providing an insect host with an almost instantaneous genome extension. Increasingly acknowledged as agents of rapid evolution, inherited microbes remain underappreciated players in pest management programs. A Rickettsia bacterium was tracked sweeping through populations of an invasive whitefly provisionally described as the "B" or "MEAM1" of the Bemisia tabaci species complex, in the southwestern USA. In this population, Rickettsia provides strong fitness benefits and distorts whitefly sex ratios under laboratory conditions. In contrast, whiteflies in Israel show few apparent fitness benefits from Rickettsia under laboratory conditions, only slightly decreasing development time. A survey of B. tabaci B samples revealed the distribution of Rickettsia across the cotton-growing regions of Israel and the USA. Thirteen sites from Israel and 22 sites from the USA were sampled. Across the USA, Rickettsia frequencies were heterogeneous among regions, but were generally very high, whereas in Israel, the infection rates were lower and declining. The distinct outcomes of Rickettsia infection in these two countries conform to previously reported phenotypic differences. Intermediate frequencies in some areas in both countries may indicate a cost to infection in certain environments or that the frequencies are in flux. This suggests underlying geographic differences in the interactions between bacterial symbionts and this serious agricultural pest.}, }
@article {pmid25620966, year = {2014}, author = {Clingenpeel, S and Clum, A and Schwientek, P and Rinke, C and Woyke, T}, title = {Reconstructing each cell's genome within complex microbial communities-dream or reality?.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {771}, pmid = {25620966}, issn = {1664-302X}, abstract = {As the vast majority of microorganisms have yet to be cultivated in a laboratory setting, access to their genetic makeup has largely been limited to cultivation-independent methods. These methods, namely metagenomics and more recently single-cell genomics, have become cornerstones for microbial ecology and environmental microbiology. One ultimate goal is the recovery of genome sequences from each cell within an environment to move toward a better understanding of community metabolic potential and to provide substrate for experimental work. As single-cell sequencing has the ability to decipher all sequence information contained in an individual cell, this method holds great promise in tackling such challenge. Methodological limitations and inherent biases however do exist, which will be discussed here based on environmental and benchmark data, to assess how far we are from reaching this goal.}, }
@article {pmid25620958, year = {2014}, author = {Damashek, J and Smith, JM and Mosier, AC and Francis, CA}, title = {Benthic ammonia oxidizers differ in community structure and biogeochemical potential across a riverine delta.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {743}, pmid = {25620958}, issn = {1664-302X}, abstract = {Nitrogen pollution in coastal zones is a widespread issue, particularly in ecosystems with urban or agricultural watersheds. California's Sacramento-San Joaquin Delta, at the landward reaches of San Francisco Bay, is highly impacted by both agricultural runoff and sewage effluent, leading to chronically high nutrient loadings. In particular, the extensive discharge of ammonium into the Sacramento River has altered this ecosystem by vastly increasing ammonium concentrations and thus changing the stoichiometry of inorganic nitrogen stocks, with potential effects throughout the food web. This debate surrounding ammonium inputs highlights the importance of understanding the rates of, and controls on, nitrogen (N) cycling processes across the delta. To date, however, there has been little research examining N biogeochemistry or N-cycling microbial communities in this system. We report the first data on benthic ammonia-oxidizing microbial communities and potential nitrification rates for the Sacramento-San Joaquin Delta, focusing on the functional gene amoA (which codes for the α-subunit of ammonia monooxygenase). There were stark regional differences in ammonia-oxidizing communities, with ammonia-oxidizing bacteria (AOB) outnumbering ammonia-oxidizing archaea (AOA) only in the ammonium-rich Sacramento River. High potential nitrification rates in the Sacramento River suggested these communities may be capable of oxidizing significant amounts of ammonium, compared to the San Joaquin River and the upper reaches of San Francisco Bay. Gene diversity also showed regional patterns, as well as phylogenetically unique ammonia oxidizers in the Sacramento River. The benthic ammonia oxidizers in this nutrient-rich aquatic ecosystem may be important players in its overall nutrient cycling, and their community structure and biogeochemical function appear related to nutrient loadings. Unraveling the microbial ecology and biogeochemistry of N cycling pathways, including benthic nitrification, is a critical step toward understanding how such ecosystems respond to the changing environmental conditions wrought by human development and climate change.}, }
@article {pmid25619404, year = {2015}, author = {Ma, B and Lyu, XF and Zha, T and Gong, J and He, Y and Xu, JM}, title = {Reconstructed metagenomes reveal changes of microbial functional profiling during PAHs degradation along a rice (Oryza sativa) rhizosphere gradient.}, journal = {Journal of applied microbiology}, volume = {118}, number = {4}, pages = {890-900}, doi = {10.1111/jam.12756}, pmid = {25619404}, issn = {1365-2672}, mesh = {Archaea/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Dioxygenases/genetics ; Genome, Archaeal ; Genome, Bacterial ; *Metagenome ; Molecular Sequence Data ; Oryza/*microbiology ; Plant Roots/microbiology ; Polycyclic Aromatic Hydrocarbons/*metabolism ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; *Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {AIMS: The response of microbial metagenome to polycyclic aromatic hydrocarbons (PAHs) degradation in the rice rhizosphere remains poorly understood. We investigated the spatial and temporal variations of microbial communities and reconstructed metagenomes along the rice rhizosphere gradient during PAHs degradation.<br><br>METHODS AND RESULTS: The experiment was performed in rhizoboxes, in which the rhizosphere region was divided into five 1-mm thick layers. Based on denaturant gradient gel electrophoresis profiling and sequencing of bacterial and archaeal 16S rRNA genes, predicted metagenomes were reconstructed. The microbial communities in the rice rhizosphere were influenced by the PAHs concentration and distance from the root surface during PAHs degradation. Correlation network analysis showed that archaea played an important role in PAHs degradation. Predicted metagenomes can be clustered into two groups with high and low PAHs degrading potential, respectively. The relative abundance of genes for defense mechanisms, replication, recombination and reparation was significantly higher in samples with high PAHs degrading potentials. The relative abundance of the dioxygenase gene was greater near the root surface of the rice. However, the abundance of aldolase and dehydrogenase was constant in rhizosphere soils at different distances from the root surface.<br><br>CONCLUSIONS: Distance from root surface and PAH concentrations affected the microbial communities and metagenomes in rice rhizosphere. The abundance of dioxygenase genes relating to PAH degradation in metagenomes mirrored the PAH degradation potential in rice rhizosphere.<br><br>Our findings suggested that the predicted metagenomes reconstructed from 16S rRNA marker gene sequences provide further insights into the spatial variation and dynamics of microbial functioning that occur during bioremediation.}, }
@article {pmid25618377, year = {2015}, author = {Shah, N and Naseby, DC}, title = {Validation of constitutively expressed bioluminescent Pseudomonas aeruginosa as a rapid microbiological quantification tool.}, journal = {Biosensors &amp; bioelectronics}, volume = {68}, number = {}, pages = {447-453}, doi = {10.1016/j.bios.2015.01.008}, pmid = {25618377}, issn = {1873-4235}, mesh = {*Biosensing Techniques ; Limit of Detection ; *Luminescent Measurements ; Pseudomonas aeruginosa/chemistry/*isolation &amp; purification ; }, abstract = {Whole cell biosensors have been extensively used for monitoring toxicity and contamination of various compounds and xenobiotics in environmental biology and microbial ecology; their application in the pharmaceutical and cosmetics industries has been limited. According to several pharmacopoeias, pharmaceutical products must be tested for microbial activity using traditional viable count techniques; the use of whole cell microbial biosensors potentially provides an alternative, fast, and efficient method. However there is a lack of a validated bioluminescence method. Prototype whole cell microbial biosensors have already been developed in Pseudomonas aeruginosa ATCC 9027. Validation of the bioluminescent strains was performed in accordance with the pharmacopoeia, Parenteral Drug Association and International Organisation of Standardisation. These strains demonstrated that the bioluminescent method was accurate, precise and equivalent, as compared with plate counting at a range of 10(3)-10(7) CFU/mL. Percentage recoveries using the bioluminescent method were between 70% and 130% for all bioluminescent strains and therefore the bioluminescent method was accurate according to the criteria set in PDA technical report 33. The method was also more precise (relative standard deviation less than 15%) than the traditional plate counting method or the ATP bioluminescent method. The lower limit of detection was 10(3) CFU/mL. Two-way ANOVA showed no significant difference between the traditional plate counting and the novel bioluminescent method for all bioluminescent strains. The bioluminescent constructs passed/exceeded pharmacopoeia-specified criteria for range, limit of detection, accuracy, precision and equivalence.}, }
@article {pmid25617871, year = {2015}, author = {De Vrieze, J and Plovie, K and Verstraete, W and Boon, N}, title = {Co-digestion of molasses or kitchen waste with high-rate activated sludge results in a diverse microbial community with stable methane production.}, journal = {Journal of environmental management}, volume = {152}, number = {}, pages = {75-82}, doi = {10.1016/j.jenvman.2015.01.029}, pmid = {25617871}, issn = {1095-8630}, mesh = {Anaerobiosis ; Bioreactors/*microbiology ; Methane/*biosynthesis ; Molasses/*analysis ; Sewage/*chemistry ; }, abstract = {Kitchen waste and molasses are organic waste streams with high organic content, and therefore are interesting substrates for renewable energy production by means of anaerobic digestion. Both substrates, however, often cause inhibition of the anaerobic digestion process, when treated separately, hence, co-digestion with other substrates is required to ensure stable methane production. In this research, A-sludge (sludge harvested from a high rate activated sludge system) was used to stabilize co-digestion with kitchen waste or molasses. Lab-scale digesters were fed with A-sludge and kitchen waste or molasses for a total period of 105 days. Increased methane production values revealed a stabilizing effect of concentrated A-sludge on kitchen waste digestion. Co-digestion of molasses with A-sludge also resulted in a higher methane production. Volumetric methane production rates up to 1.53 L L(-1) d(-1) for kitchen waste and 1.01 L L(-1) d(-1) for molasses were obtained by co-digestion with A-sludge. The stabilizing effect of A-sludge was attributed to its capacity to supplement various nutrients. Microbial community results demonstrated that both reactor conditions and substrate composition determined the nature of the bacterial community, although there was no direct influence of micro-organisms in the substrate itself, while the methanogenic community profile remained constant as long as optimal conditions were maintained.}, }
@article {pmid25616799, year = {2015}, author = {Rahkila, R and Johansson, P and Säde, E and Paulin, L and Auvinen, P and Björkroth, J}, title = {Multilocus sequence typing of Leuconostoc gelidum subsp. gasicomitatum, a Psychrotrophic lactic acid bacterium causing spoilage of packaged perishable foods.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {7}, pages = {2474-2480}, pmid = {25616799}, issn = {1098-5336}, mesh = {Cluster Analysis ; Europe ; Genes, Bacterial ; Genes, Essential ; Genotype ; Lactic Acid/metabolism ; Leuconostoc/*classification/*genetics/isolation &amp; purification/metabolism ; Meat/*microbiology ; Molecular Sequence Data ; *Multilocus Sequence Typing ; Sequence Analysis, DNA ; Vegetables/*microbiology ; }, abstract = {Leuconostoc gelidum subsp. gasicomitatum is a psychrotrophic lactic acid bacterium (LAB) that causes spoilage of a variety of modified-atmosphere-packaged (MAP) cold-stored food products. During the past 10 years, this spoilage organism has been increasingly reported in MAP meat and vegetable products in northern Europe. In the present study, the population structure within 252 L. gelidum subsp. gasicomitatum strains was determined based on a novel multilocus sequence-typing (MLST) scheme employing seven housekeeping genes. These strains had been isolated from meat and vegetable sources over a time span of 15 years, and all 68 previously detected pulsed-field gel electrophoresis (PFGE) genotypes were represented. A total of 46 sequence types (STs) were identified, with a majority of the strains (>60%) belonging to three major STs, which were grouped into three clonal complexes (CCs) and 17 singletons by Global Optimal eBURST (goeBURST). The results by Bayesian analysis of population structure (BAPS) mostly correlated with the grouping by goeBURST. Admixture analysis by BAPS indicated a very low level of exchange of genetic material between the subpopulations. Niche specificity was observed within the subpopulations: CC1 and BAPS cluster 1 consisted mostly of strains from a variety of MAP meats, whereas vegetable strains grouped together with strains from MAP poultry within CC2 and BAPS cluster 2. The MLST scheme presented in this study provides a shareable and continuously growing sequence database enabling global comparison of strains associated with spoilage cases. This will further advance our understanding of the microbial ecology of this industrially important LAB.}, }
@article {pmid25614926, year = {2015}, author = {Jacquemyn, H and Brys, R and Waud, M and Busschaert, P and Lievens, B}, title = {Mycorrhizal networks and coexistence in species-rich orchid communities.}, journal = {The New phytologist}, volume = {206}, number = {3}, pages = {1127-1134}, doi = {10.1111/nph.13281}, pmid = {25614926}, issn = {1469-8137}, mesh = {Biodiversity ; Grassland ; Host Specificity ; Italy ; Mycorrhizae/genetics/*physiology ; Orchidaceae/*microbiology ; Phylogeny ; }, abstract = {Multispecies assemblages often consist of a complex network of interactions. Describing the architecture of these networks is a first step in understanding the stability and persistence of these species-rich communities. Whereas a large body of research has been devoted to the description of above-ground interactions, much less attention has been paid to below-ground interactions, probably because of difficulties to adequately assess the nature and diversity of interactions occurring below the ground. In this study, we used 454 amplicon pyrosequencing to investigate the architecture of the network between mycorrhizal fungi and 20 orchid species co-occurring in a species-rich Mediterranean grasslands. We found 100 different fungal operational taxonomic units (OTUs) known to be mycorrhizal in orchids, most of which were members related to the genera Ceratobasidium and Tulasnella. The network of interactions was significantly compartmentalized (M = 0.589, P = 0.001), but not significantly nested (N = 0.74, NODF = 10.58; P > 0.05). Relative nestedness was negative (N* = -0.014), also suggesting the existence of isolated groups of interacting species. Compartmentalization is a typical feature of ecological systems showing high interaction intimacy, and may reflect strong specialization between orchids and fungi resulting from physiological, physical or spatial constraints.}, }
@article {pmid25613225, year = {2015}, author = {Ding, J and Zhang, Y and Deng, Y and Cong, J and Lu, H and Sun, X and Yang, C and Yuan, T and Van Nostrand, JD and Li, D and Zhou, J and Yang, Y}, title = {Integrated metagenomics and network analysis of soil microbial community of the forest timberline.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {7994}, pmid = {25613225}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics ; *Biodiversity ; Carbon Cycle/genetics ; Ecosystem ; Environment ; *Forests ; Gene Regulatory Networks ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Nitrogen Cycle/genetics ; Phosphorus/chemistry ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The forest timberline responds quickly and markedly to climate changes, rendering it a ready indicator. Climate warming has caused an upshift of the timberline worldwide. However, the impact on belowground ecosystem and biogeochemical cycles remain elusive. To understand soil microbial ecology of the timberline, we analyzed microbial communities via 16s rRNA Illumina sequencing, a microarray-based tool named GeoChip 4.0 and a random matrix theory-based association network approach. We selected 24 sampling sites at two vegetation belts forming the timberline of Shennongjia Mountain in Hubei Province of China, a region with extraordinarily rich biodiversity. We found that temperature, among all of measured environmental parameters, showed the most significant and extensive linkages with microbial biomass, microbial diversity and composition at both taxonomic and functional gene levels, and microbial association network. Therefore, temperature was the best predictor for microbial community variations in the timberline. Furthermore, abundances of nitrogen cycle and phosphorus cycle genes were concomitant with NH4(+)-N, NO3(-)-N and total phosphorus, offering tangible clues to the underlying mechanisms of soil biogeochemical cycles. As the first glimpse at both taxonomic and functional compositions of soil microbial community of the timberline, our findings have major implications for predicting consequences of future timberline upshift.}, }
@article {pmid25613091, year = {2015}, author = {White, JA and Richards, NK and Laugraud, A and Saeed, A and Curry, MM and McNeill, MR}, title = {Endosymbiotic candidates for parasitoid defense in exotic and native New Zealand weevils.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {274-286}, pmid = {25613091}, issn = {1432-184X}, mesh = {Animals ; Base Sequence ; DNA Primers/genetics ; Geography ; Likelihood Functions ; Metagenomics ; Models, Genetic ; Molecular Sequence Data ; New Zealand ; Phylogeny ; Polymerase Chain Reaction ; Rickettsia/*genetics ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; Weevils/*microbiology ; Wolbachia/*genetics ; }, abstract = {Some insects are infected with maternally inherited bacterial endosymbionts that protect them against pathogens or parasitoids. The weevil Sitona obsoletus (=Sitona lepidus) is invasive in New Zealand, and suspected to contain such defensive symbionts, because it is particularly resistant to a Moroccan strain of the parasitoid Microctonus aethiopoides (which successfully attacks many other weevil species), and shows geographic variation in susceptibility to an Irish strain of the same parasitoid. Using 454 pyrosequencing, we investigated the bacterial community associated with S. obsoletus, two other exotic weevils (Sitona discoideus and Listronotus bonariensis) and two endemic New Zealand weevils (Irenimus aequalis and Steriphus variabilis). We found that S. obsoletus was infected by one strain of Wolbachia and two strains of Rickettsia, none of which were found in any other weevil species examined. Using diagnostic PCR, we found that S. obsoletus in the Northland region, where parasitism is highly variable, were primarily infected with Wolbachia and Rickettsia strain 2, indicating that these two symbionts should be investigated for potential defensive properties. In comparison, S. discoideus lacked any apparent maternally inherited bacterial endosymbionts. In the other weevil species, we found a different strain of Wolbachia and two different strains of Spiroplasma. Two weevil species (St. variabilis and L. bonariensis) were infected with distinct strains of Nardonella, the ancestral endosymbiont of weevils, whereas three weevil species (S. obsoletus, S. discoideus, and I. aequalis) lacked evidence for Nardonella infection. However, I. aequalis was consistently infected with a novel Enterobacteriaceae strain, suggesting that a symbiont replacement may have taken place, similar to that described for other weevil clades.}, }
@article {pmid25608778, year = {2015}, author = {Vaughan, MJ and Nelson, W and Soderlund, C and Maier, RM and Pryor, BM}, title = {Assessing fungal community structure from mineral surfaces in Kartchner Caverns using multiplexed 454 pyrosequencing.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {175-187}, pmid = {25608778}, issn = {1432-184X}, mesh = {Adaptation, Biological/genetics/*physiology ; Arizona ; Base Sequence ; *Biodiversity ; Carbon Dioxide/analysis ; Carbonates/*chemistry ; Caves/*microbiology ; DNA Primers/genetics ; *Environment ; Fungi/*genetics/physiology ; Molecular Sequence Data ; Sequence Analysis, DNA ; Species Specificity ; Temperature ; }, abstract = {Research on the distribution and structure of fungal communities in caves is lacking. Kartchner Caverns is a wet and mineralogically diverse carbonate cave located in an escarpment of Mississippian Escabrosa limestone in the Whetstone Mountains, Arizona, USA. Fungal diversity from speleothem and rock wall surfaces was examined with 454 FLX Titanium sequencing technology using the Internal Transcribed Spacer 1 as a fungal barcode marker. Fungal diversity was estimated and compared between speleothem and rock wall surfaces, and its variation with distance from the natural entrance of the cave was quantified. Effects of environmental factors and nutrient concentrations in speleothem drip water at different sample sites on fungal diversity were also examined. Sequencing revealed 2,219 fungal operational taxonomic units (OTUs) at the 95% similarity level. Speleothems supported a higher fungal richness and diversity than rock walls. However, community membership and the taxonomic distribution of fungal OTUs at the class level did not differ significantly between speleothems and rock walls. Both OTU richness and diversity decreased significantly with increasing distance from the natural cave entrance. Community membership and taxonomic distribution of fungal OTUs also differed significantly between the sampling sites closest to the entrance and those furthest away. There was no significant effect of temperature, CO2 concentration, or drip water nutrient concentration on fungal community structure on either speleothems or rock walls. Together, these results suggest that proximity to the natural entrance is a critical factor in determining fungal community structure on mineral surfaces in Kartchner Caverns.}, }
@article {pmid25602700, year = {2015}, author = {Hofbauer, S and Hagmüller, A and Schaffner, I and Mlynek, G and Krutzler, M and Stadlmayr, G and Pirker, KF and Obinger, C and Daims, H and Djinović-Carugo, K and Furtmüller, PG}, title = {Structure and heme-binding properties of HemQ (chlorite dismutase-like protein) from Listeria monocytogenes.}, journal = {Archives of biochemistry and biophysics}, volume = {574}, number = {}, pages = {36-48}, pmid = {25602700}, issn = {1096-0384}, support = {P 25270/FWF_/Austrian Science Fund FWF/Austria ; W 1224/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Cyanides/metabolism ; Enzyme Stability ; Heme/*metabolism ; Hydrogen-Ion Concentration ; Listeria monocytogenes/*enzymology ; Oxidoreductases/*chemistry/metabolism ; Protein Binding ; Protein Conformation ; }, abstract = {Chlorite dismutase-like proteins are structurally closely related to functional chlorite dismutases which are heme b-dependent oxidoreductases capable of reducing chlorite to chloride with simultaneous production of dioxygen. Chlorite dismutase-like proteins are incapable of performing this reaction and their biological role is still under discussion. Recently, members of this large protein family were shown to be involved in heme biosynthesis in Gram-positive bacteria, and thus the protein was renamed HemQ in these organisms. In the present work the structural and heme binding properties of the chlorite dismutase-like protein from the Gram-positive pathogen Listeria monocytogenes (LmCld) were analyzed in order to evaluate its potential role as a regulatory heme sensing protein. The homopentameric crystal structure (2.0Å) shows high similarity to chlorite-degrading chlorite dismutases with an important difference in the structure of the putative substrate and heme entrance channel. In solution LmCld is a stable hexamer able to bind the low-spin ligand cyanide. Heme binding is reversible with KD-values determined to be 7.2μM (circular dichroism spectroscopy) and 16.8μM (isothermal titration calorimetry) at pH 7.0. Both acidic and alkaline conditions promote heme release. Presented biochemical and structural data reveal that the chlorite dismutase-like protein from L. monocytogenes could act as a potential regulatory heme sensing and storage protein within heme biosynthesis.}, }
@article {pmid25602160, year = {2015}, author = {Sapkota, R and Nicolaisen, M}, title = {An improved high throughput sequencing method for studying oomycete communities.}, journal = {Journal of microbiological methods}, volume = {110}, number = {}, pages = {33-39}, doi = {10.1016/j.mimet.2015.01.013}, pmid = {25602160}, issn = {1872-8359}, mesh = {Aphanomyces/genetics ; DNA Barcoding, Taxonomic ; DNA Primers ; DNA, Ribosomal Spacer/genetics ; *Daucus carota ; Denmark ; Genetic Variation ; *High-Throughput Nucleotide Sequencing/methods ; Oomycetes/*classification/*genetics ; Peronospora/genetics ; Phytophthora/*classification/genetics ; Polymerase Chain Reaction/*methods ; Pythium/genetics ; Saprolegnia/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Species Specificity ; }, abstract = {Culture-independent studies using next generation sequencing have revolutionized microbial ecology, however, oomycete ecology in soils is severely lagging behind. The aim of this study was to improve and validate standard techniques for using high throughput sequencing as a tool for studying oomycete communities. The well-known primer sets ITS4, ITS6 and ITS7 were used in the study in a semi-nested PCR approach to target the internal transcribed spacer (ITS) 1 of ribosomal DNA in a next generation sequencing protocol. These primers have been used in similar studies before, but with limited success. We were able to increase the proportion of retrieved oomycete sequences dramatically mainly by increasing the annealing temperature during PCR. The optimized protocol was validated using three mock communities and the method was further evaluated using total DNA from 26 soil samples collected from different agricultural fields in Denmark, and 11 samples from carrot tissue with symptoms of Pythium infection. Sequence data from the Pythium and Phytophthora mock communities showed that our strategy successfully detected all included species. Taxonomic assignments of OTUs from 26 soil sample showed that 95% of the sequences could be assigned to oomycetes including Pythium, Aphanomyces, Peronospora, Saprolegnia and Phytophthora. A high proportion of oomycete reads was consistently present in all 26 soil samples showing the versatility of the strategy. A large diversity of Pythium species including pathogenic and saprophytic species were dominating in cultivated soil. Finally, we analyzed amplicons from carrots with symptoms of cavity spot. This resulted in 94% of the reads belonging to oomycetes with a dominance of species of Pythium that are known to be involved in causing cavity spot, thus demonstrating the usefulness of the method not only in soil DNA but also in a plant DNA background. In conclusion, we demonstrate a successful approach for pyrosequencing of oomycete communities using ITS1 as the barcode sequence with well-known primers for oomycete DNA amplification.}, }
@article {pmid25599993, year = {2015}, author = {Van Praet, JT and Donovan, E and Vanassche, I and Drennan, MB and Windels, F and Dendooven, A and Allais, L and Cuvelier, CA and van de Loo, F and Norris, PS and Kruglov, AA and Nedospasov, SA and Rabot, S and Tito, R and Raes, J and Gaboriau-Routhiau, V and Cerf-Bensussan, N and Van de Wiele, T and Eberl, G and Ware, CF and Elewaut, D}, title = {Commensal microbiota influence systemic autoimmune responses.}, journal = {The EMBO journal}, volume = {34}, number = {4}, pages = {466-474}, pmid = {25599993}, issn = {1460-2075}, mesh = {Animals ; Antibodies, Antinuclear/genetics/immunology ; Autoimmunity/genetics/*immunology ; Female ; Flow Cytometry ; Lymphotoxin-alpha/genetics/metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Microbiota/*immunology ; Pregnancy ; Proto-Oncogene Proteins/genetics/metabolism ; }, abstract = {Antinuclear antibodies are a hallmark feature of generalized autoimmune diseases, including systemic lupus erythematosus and systemic sclerosis. However, the processes underlying the loss of tolerance against nuclear self-constituents remain largely unresolved. Using mice deficient in lymphotoxin and Hox11, we report that approximately 25% of mice lacking secondary lymphoid organs spontaneously develop specific antinuclear antibodies. Interestingly, we find this phenotype is not caused by a defect in central tolerance. Rather, cell-specific deletion and in vivo lymphotoxin blockade link these systemic autoimmune responses to the formation of gut-associated lymphoid tissue in the neonatal period of life. We further demonstrate antinuclear antibody production is influenced by the presence of commensal gut flora, in particular increased colonization with segmented filamentous bacteria, and IL-17 receptor signaling. Together, these data indicate that neonatal colonization of gut microbiota influences generalized autoimmunity in adult life.}, }
@article {pmid25594727, year = {2015}, author = {Helbling, DE and Johnson, DR and Lee, TK and Scheidegger, A and Fenner, K}, title = {A framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates.}, journal = {Water research}, volume = {70}, number = {}, pages = {471-484}, doi = {10.1016/j.watres.2014.12.013}, pmid = {25594727}, issn = {1879-2448}, mesh = {Ammonia/*metabolism ; Bacteria/classification/*genetics/*metabolism ; Biotransformation ; DNA, Bacterial/*genetics/metabolism ; Models, Biological ; Molecular Sequence Data ; Multivariate Analysis ; Nitrosomonas/classification/genetics/metabolism ; RNA, Ribosomal, 16S/*genetics/metabolism ; Sequence Analysis, DNA ; Wastewater/*analysis ; }, abstract = {The rates at which wastewater treatment plant (WWTP) microbial communities biotransform specific substrates can differ by orders of magnitude among WWTP communities. Differences in taxonomic compositions among WWTP communities may predict differences in the rates of some types of biotransformations. In this work, we present a novel framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates. We selected ten WWTPs with substantial variation in their environmental and operational metrics and measured the in situ ammonia biotransformation rate constants in nine of them. We isolated total RNA from samples from each WWTP and analyzed 16S rRNA sequence reads. We then developed multivariate models between the measured abundances of specific bacterial 16S rRNA sequence reads and the ammonia biotransformation rate constants. We constructed model scenarios that systematically explored the effects of model regularization, model linearity and non-linearity, and aggregation of 16S rRNA sequences into operational taxonomic units (OTUs) as a function of sequence dissimilarity threshold (SDT). A large percentage (greater than 80%) of model scenarios resulted in well-performing and significant models at intermediate SDTs of 0.13-0.14 and 0.26. The 16S rRNA sequences consistently selected into the well-performing and significant models at those SDTs were classified as Nitrosomonas and Nitrospira groups. We then extend the framework by applying it to the biotransformation rate constants of ten micropollutants measured in batch reactors seeded with the ten WWTP communities. We identified phylogenetic groups that were robustly selected into all well-performing and significant models constructed with biotransformation rates of isoproturon, propachlor, ranitidine, and venlafaxine. These phylogenetic groups can be used as predictive biomarkers of WWTP microbial community activity towards these specific micropollutants. This work is an important step towards developing tools to predict biotransformation rates in WWTPs based on taxonomic composition.}, }
@article {pmid25594131, year = {2015}, author = {Stephens, B and Adams, RI and Bhangar, S and Bibby, K and Waring, MS}, title = {From commensalism to mutualism: integrating the microbial ecology, building science, and indoor air communities to advance research on the indoor microbiome.}, journal = {Indoor air}, volume = {25}, number = {1}, pages = {1-3}, doi = {10.1111/ina.12167}, pmid = {25594131}, issn = {1600-0668}, mesh = {*Air Microbiology ; *Air Pollution, Indoor/adverse effects/analysis ; Ecology ; Environment, Controlled ; Environmental Exposure/analysis ; Humans ; *Interprofessional Relations ; Microbiota ; Research ; }, }
@article {pmid25592637, year = {2015}, author = {Zheng, Y and Hou, L and Liu, M and Gao, J and Yin, G and Li, X and Deng, F and Lin, X and Jiang, X and Chen, F and Zong, H and Zhou, J}, title = {Diversity, Abundance, and Distribution of nirS-Harboring Denitrifiers in Intertidal Sediments of the Yangtze Estuary.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {30-40}, pmid = {25592637}, issn = {1432-184X}, mesh = {Ammonium Compounds/analysis ; Base Sequence ; *Biodiversity ; China ; Cluster Analysis ; Denitrification ; *Estuaries ; Gene Library ; Geologic Sediments/*microbiology ; *Microbiota ; Molecular Sequence Data ; Nitrates/analysis ; Phylogeny ; Population Density ; Real-Time Polymerase Chain Reaction ; *Salinity ; Seasons ; Sequence Analysis, DNA ; }, abstract = {Denitrification plays a critical role in nitrogen removal in estuarine and coastal ecosystems. In this study, the community composition, diversity, abundance, and distribution of cytochrome cd1-type nitrite reductase gene (nirS)-harboring denitrifiers in intertidal sediments of the Yangtze Estuary were analyzed using polymerase chain reaction (PCR)-based clone libraries and quantitative PCR techniques. Clone library analysis showed that the nirS-encoding bacterial biodiversity was significantly higher at the lower salinity sites than at the higher salinity sites. However, there was no significant seasonal difference in the nirS gene diversity between summer and winter. Phylogenetic analysis revealed that the nirS-harboring denitrifier communities at the study area had distinctive spatial heterogeneity along the estuary. At the lower salinity sites, the nirS-harboring bacterial community was co-dominated by clusters III and VII; while at the higher salinity sites, it was dominated by cluster I. Canonical correspondence analysis indicated that the community compositions of nirS-type denitrifiers were significantly correlated with salinity, ammonium, and nitrate. Quantitative PCR results showed that the nirS gene abundance was in the range of 1.01 × 10(6) to 9.00 × 10(7) copies per gram dry sediment, without significant seasonal variation. Among all the environmental factors, the nirS gene abundance was only significantly related to the change of salinity. These results can extend our current knowledge about the composition and dynamics of denitrification microbial community in the estuarine ecosystem.}, }
@article {pmid25592636, year = {2015}, author = {Song, HK and Sonkaria, S and Khare, V and Dong, K and Lee, HT and Ahn, SH and Kim, HK and Kang, HJ and Lee, SH and Jung, SP and Adams, JM}, title = {Pond sediment magnetite grains show a distinctive microbial community.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {168-174}, pmid = {25592636}, issn = {1432-184X}, mesh = {Base Sequence ; DNA Primers/genetics ; Ferrosoferric Oxide/*analysis ; Geobacter/genetics ; Geologic Sediments/chemistry/*microbiology ; Microbiota/*genetics ; Molecular Sequence Data ; Ponds/*microbiology ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Republic of Korea ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Formation of magnetite in anaerobic sediments is thought to be enhanced by the activities of iron-reducing bacteria. Geobacter has been implicated as playing a major role, as in culture its cells are often associated with extracellular magnetite grains. We studied the bacterial community associated with magnetite grains in sediment of a freshwater pond in South Korea. Magnetite was isolated from the sediment using a magnet. The magnetite-depleted fraction of sediment was also taken for comparison. DNA was extracted from each set of samples, followed by PCR for 16S bacterial ribosomal RNA (rRNA) gene and HiSeq sequencing. The bacterial communities of the magnetite-enriched and magnetite-depleted fractions were significantly different. The enrichment of three abundant operational taxonomic units (OTUs) suggests that they may either be dependent upon the magnetite grain environment or may be playing a role in magnetite formation. The most abundant OTU in magnetite-enriched fractions was Geobacter, bolstering the case that this genus is important in magnetite formation in natural systems. Other major OTUs strongly associated with the magnetite-enriched fraction, rather than the magnetite-depleted fraction, include a Sulfuricella and a novel member of the Betaproteobacteria. The existence of distinct bacterial communities associated with particular mineral grain types may also be an example of niche separation and coexistence in sediments and soils, which cannot usually be detected due to difficulties in separating and concentrating minerals.}, }
@article {pmid25592635, year = {2015}, author = {Fahy, A and Giloteaux, L and Bertin, P and Le Paslier, D and Médigue, C and Weissenbach, J and Duran, R and Lauga, B}, title = {16S rRNA and As-Related Functional Diversity: Contrasting Fingerprints in Arsenic-Rich Sediments from an Acid Mine Drainage.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {154-167}, pmid = {25592635}, issn = {1432-184X}, mesh = {Acidobacteria/*genetics ; Arsenic/*analysis ; Arsenite Transporting ATPases/genetics ; Base Sequence ; *Biodiversity ; Cloning, Molecular ; DNA Primers/genetics ; France ; *Mining ; Molecular Sequence Data ; Oxidoreductases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; Soil Pollutants/*analysis ; }, abstract = {To gain an in-depth insight into the diversity and the distribution of genes under the particular evolutionary pressure of an arsenic-rich acid mine drainage (AMD), the genes involved in bacterial arsenic detoxification (arsB, ACR3) and arsenite oxidation (aioA) were investigated in sediment from Carnoulès (France), in parallel to the diversity and global distribution of the metabolically active bacteria. The metabolically active bacteria were affiliated mainly to AMD specialists, i.e., organisms detected in or isolated from AMDs throughout the world. They included mainly Acidobacteria and the non-affiliated "Candidatus Fodinabacter communificans," as well as Thiomonas and Acidithiobacillus spp., Actinobacteria, and unclassified Gammaproteobacteria. The distribution range of these organisms suggested that they show niche conservatism. Sixteen types of deduced protein sequences of arsenite transporters (5 ArsB and 11 Acr3p) were detected, whereas a single type of arsenite oxidase (AioA) was found. Our data suggested that at Carnoulès, the aioA gene was more recent than those encoding arsenite transporters and subjected to a different molecular evolution. In contrast to the 16S ribosomal RNA (16S rRNA) genes associated with AMD environments worldwide, the functional genes aioA, ACR3, and to a lesser extent arsB, were either novel or specific to Carnoulès, raising the question as to whether these functional genes are specific to high concentrations of arsenic, AMD-specific, or site-specific.}, }
@article {pmid25586577, year = {2015}, author = {Zhang, Y and Chen, L and Sun, R and Dai, T and Tian, J and Wen, D}, title = {Ammonia-oxidizing bacteria and archaea in wastewater treatment plant sludge and nearby coastal sediment in an industrial area in China.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {10}, pages = {4495-4507}, doi = {10.1007/s00253-014-6352-9}, pmid = {25586577}, issn = {1432-0614}, mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodiversity ; China ; Geologic Sediments/*microbiology ; Industrial Waste/analysis ; Molecular Sequence Data ; Phylogeny ; Sewage/*microbiology ; Wastewater/chemistry ; Water Purification/instrumentation ; }, abstract = {Under the increasing pressure of human activities, Hangzhou Bay has become one of the most seriously polluted waters along China's coast. Considering the excessive inorganic nitrogen detected in the bay, in this study, the impact of an effluent from a coastal industrial park on ammonia-oxidizing microorganisms (AOMs) of the receiving area was interpreted for the first time by molecular technologies. Revealed by real-time PCR, the ratio of archaeal amoA/bacterial amoA ranged from 5.68 × 10(-6) to 4.79 × 10(-5) in the activated sludge from two wastewater treatment plants (WWTPs) and 0.54-3.44 in the sediments from the effluent receiving coastal area. Analyzed by clone and pyrosequencing libraries, genus Nitrosomonas was the predominant ammonia-oxidizing bacteria (AOB), but no ammonia-oxidizing archaea (AOA) was abundant enough for sequencing in the activated sludge from the WWTPs; genus Nitrosomonas and Nitrosopumilus were the dominant AOB and AOA, respectively, in the coastal sediments. The different abundance of AOA but similar structure of AOB between the WWTPs and nearby coastal area probably indicated an anthropogenic impact on the microbial ecology in Hangzhou Bay.}, }
@article {pmid25586384, year = {2015}, author = {Mendes, LW and Tsai, SM and Navarrete, AA and de Hollander, M and van Veen, JA and Kuramae, EE}, title = {Soil-borne microbiome: linking diversity to function.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {255-265}, pmid = {25586384}, issn = {1432-184X}, mesh = {Agriculture/*methods ; Base Sequence ; Brazil ; Conservation of Natural Resources/methods ; Forests ; Genetic Variation/*physiology ; Metagenomics/*methods ; Microbiota/*genetics/physiology ; Models, Theoretical ; Molecular Sequence Data ; Sequence Analysis, DNA ; *Soil Microbiology ; Glycine max/*growth &amp; development ; Time Factors ; Tropical Climate ; }, abstract = {Soil microorganisms are sensitive to environment disturbances, and such alterations have consequences on microbial diversity and functions. Our hypothesis is that alpha diversity of microbial communities and functional diversity decrease from undisturbed to disturbed soils, with consequences for functional redundancy in the soil ecosystem. To test this hypothesis, we used soil DNA shotgun metagenomics approach to assess the soil microbiome in a chronosequence of land-use from a native tropical forest, followed by deforestation and cultivation of soybean croplands and pasture in different seasons. Agriculture and pasture soils were among the most diverse and presented higher functional redundancy, which is important to maintain the ecosystem functioning after the forest conversion. On the other hand, the ecosystem equilibrium in forest is maintained based on a lower alpha diversity but higher abundance of microorganisms. Our results indicate that land-use change alters the structure and composition of microbial communities; however, ecosystem functionality is overcome by different strategies based on the abundance and diversity of the communities.}, }
@article {pmid25581721, year = {2015}, author = {Gong, J and Shi, F and Ma, B and Dong, J and Pachiadaki, M and Zhang, X and Edgcomb, VP}, title = {Depth shapes α- and β-diversities of microbial eukaryotes in surficial sediments of coastal ecosystems.}, journal = {Environmental microbiology}, volume = {17}, number = {10}, pages = {3722-3737}, doi = {10.1111/1462-2920.12763}, pmid = {25581721}, issn = {1462-2920}, mesh = {Biodiversity ; Ciliophora/classification/*genetics/isolation &amp; purification ; Dinoflagellida/classification/*genetics/isolation &amp; purification ; Geologic Sediments/*parasitology ; Oceans and Seas ; RNA, Ribosomal, 18S/genetics ; Stramenopiles/classification/*genetics/isolation &amp; purification ; Vanadium/pharmacology ; }, abstract = {Little is known about the relative influence of historic processes and environmental gradients on shaping the diversity of single-celled eukaryotes in marine benthos. By combining pyrosequencing of 18S ribosomal RNA genes with data on multiple environmental factors, we investigated the diversity of microeukaryotes in surficial sediments of three basins of the Yellow Sea Large Marine Ecosystem. A considerable proportion (about 20%) of reads was affiliated with known parasitoid protists. Dinophyta and Ciliophora appeared dominant in terms of relative proportion of reads and operational taxonomic unit (OTU) richness. Overall, OTU richness of benthic microeukaryotes decreased with increasing water depth and decreasing pH. While community composition was significantly different among basins, partial Mantel tests indicated a depth-decay pattern of community similarity, whereby water depth, rather than geographic distance or environment, shaped β-diversity of benthic microeukaryotes (including both the abundant and the rare biosphere) on a regional scale. Similar hydrographic and mineralogical factors contributed to the biogeography of both the abundant and the rare OTUs. The trace metal vanadium had a significant effect on the biogeography of the rare biosphere. Our study sheds new light on the composition, diversity patterns and underlying mechanisms of single-celled eukaryote distribution in surficial sediments of coastal oceans.}, }
@article {pmid25581196, year = {2015}, author = {Wheeler, SR and Heard, P and Dufour, C and Thevenot-Sergentet, D and Loukiadis, E and Flowers, RS and McMahon, W}, title = {Detection of non-O157 Shiga toxin-producing Escherichia coli in 375 grams of beef trim enrichments across multiple commercial PCR detection platforms.}, journal = {Journal of food protection}, volume = {78}, number = {1}, pages = {196-202}, doi = {10.4315/0362-028X.JFP-14-263}, pmid = {25581196}, issn = {1944-9097}, mesh = {Agar ; Animals ; Cattle ; Europe ; European Union ; Immunomagnetic Separation/*methods ; Meat/*microbiology ; Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; Shiga-Toxigenic Escherichia coli/*isolation &amp; purification ; United States ; }, abstract = {Although serotype O157:H7 remains the pathogenic Shiga toxin-producing Escherichia coli (STEC) of primary concern worldwide, some focus in the United States has shifted to six particular non-O157 STEC serogroups (O26, O45, O103, O111, O121, and O145). Some of these serogroups have also emerged as concerns elsewhere around the world, including Europe. The objective of this work was to compare commercial detection methods with the U.S. Department of Agriculture (USDA) reference method for detection of non-O157 STEC in 375 g of beef trim using a limit of detection study design. Overall, the commercial platforms performed well, showing similar levels of sensitivity for detection of presumptive positives for O45, O26, O103, and O121 (PCR screen results only). For O111, one method that utilizes an integrated immunomagnetic separation and PCR approach was more sensitive than a PCR-only screen approach. Additionally, one commercial method showed more presumptive and confirmed positives overall. Use of an immunomagnetic separation tool, such as antibody-coated beads, aided considerably with the confirmation procedures and is an important step when confirming suspect samples. A secondary goal of this study was to evaluate isolation and International Organization for Standardization confirmation protocols used in Europe compared with strategies provided by the USDA Microbiology Laboratory Guidebook (MLG). Generally, results from the USDA confirmation plates (modified Rainbow agar) were better than the European Union confirmation plates (MacConkey agar with or without rhamnose). In summary, detection of non-O157 STEC in 375 g of beef trim can be performed by any of the three methods on the market evaluated in the study.}, }
@article {pmid25581131, year = {2015}, author = {He, R and Wooller, MJ and Pohlman, JW and Tiedje, JM and Leigh, MB}, title = {Methane-derived carbon flow through microbial communities in arctic lake sediments.}, journal = {Environmental microbiology}, volume = {17}, number = {9}, pages = {3233-3250}, doi = {10.1111/1462-2920.12773}, pmid = {25581131}, issn = {1462-2920}, mesh = {Actinobacteria/genetics/metabolism ; Arctic Regions ; Carbon/metabolism ; *Carbon Cycle ; Carbon Isotopes/analysis ; Ecosystem ; Fatty Acids/metabolism ; Geologic Sediments/chemistry/*microbiology ; Lakes/*microbiology ; Methane/*metabolism ; Methylobacteriaceae/genetics/metabolism ; Methylomonas/genetics/metabolism ; *Microbial Consortia ; Oxidation-Reduction ; Phospholipids/metabolism ; *Water Microbiology ; }, abstract = {Aerobic methane (CH4) oxidation mitigates CH4 release and is a significant pathway for carbon and energy flow into aquatic food webs. Arctic lakes are responsible for an increasing proportion of global CH4 emissions, but CH4 assimilation into the aquatic food web in arctic lakes is poorly understood. Using stable isotope probing (SIP) based on phospholipid fatty acids (PLFA-SIP) and DNA (DNA-SIP), we tracked carbon flow quantitatively from CH4 into sediment microorganisms from an arctic lake with an active CH4 seepage. When 0.025 mmol CH4 g(-1) wet sediment was oxidized, approximately 15.8-32.8% of the CH4 -derived carbon had been incorporated into microorganisms. This CH4 -derived carbon equated to up to 5.7% of total primary production estimates for Alaskan arctic lakes. Type I methanotrophs, including Methylomonas, Methylobacter and unclassified Methylococcaceae, were most active at CH4 oxidation in this arctic lake. With increasing distance from the active CH4 seepage, a greater diversity of bacteria incorporated CH4 -derived carbon. Actinomycetes were the most quantitatively important microorganisms involved in secondary feeding on CH4 -derived carbon. These results showed that CH4 flows through methanotrophs into the broader microbial community and that type I methanotrophs, methylotrophs and actinomycetes are important organisms involved in using CH4 -derived carbon in arctic freshwater ecosystems.}, }
@article {pmid25576608, year = {2015}, author = {Taylor, AE and Taylor, K and Tennigkeit, B and Palatinszky, M and Stieglmeier, M and Myrold, DD and Schleper, C and Wagner, M and Bottomley, PJ}, title = {Inhibitory effects of C2 to C10 1-alkynes on ammonia oxidation in two Nitrososphaera species.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {6}, pages = {1942-1948}, pmid = {25576608}, issn = {1098-5336}, support = {294343/ERC_/European Research Council/International ; }, mesh = {Alkynes/*metabolism ; Ammonia/*metabolism ; Archaea/*metabolism ; Nitrites/metabolism ; Oxidation-Reduction ; }, abstract = {A previous study showed that ammonia oxidation by the Thaumarchaeota Nitrosopumilus maritimus (group 1.1a) was resistant to concentrations of the C8 1-alkyne, octyne, which completely inhibits activity by ammonia-oxidizing bacteria. In this study, the inhibitory effects of octyne and other C2 to C10 1-alkynes were evaluated on the nitrite production activity of two pure culture isolates from Thaumarchaeota group 1.1b, Nitrososphaera viennensis strain EN76 and Nitrososphaera gargensis. Both N. viennensis and N. gargensis were insensitive to concentrations of octyne that cause complete and irreversible inactivation of nitrite production by ammonia-oxidizing bacteria. However, octyne concentrations (≥20 μM) that did not inhibit N. maritimus partially inhibited nitrite production in N. viennensis and N. gargensis in a manner that did not show the characteristics of irreversible inactivation. In contrast to previous studies with an ammonia-oxidizing bacterium, Nitrosomonas europaea, octyne inhibition of N. viennensis was: (i) fully and immediately reversible, (ii) not competitive with NH4 (+), and (iii) without effect on the competitive interaction between NH4 (+) and acetylene. Both N. viennensis and N. gargensis demonstrated the same overall trend in regard to 1-alkyne inhibition as previously observed for N. maritimus, being highly sensitive to ≤C5 alkynes and more resistant to longer-chain length alkynes. Reproducible differences were observed among N. maritimus, N. viennensis, and N. gargensis in regard to the extent of their resistance/sensitivity to C6 and C7 1-alkynes, which may indicate differences in the ammonia monooxygenase binding and catalytic site(s) among the Thaumarchaeota.}, }
@article {pmid25576328, year = {2015}, author = {Faith, JJ and Colombel, JF and Gordon, JI}, title = {Identifying strains that contribute to complex diseases through the study of microbial inheritance.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {3}, pages = {633-640}, pmid = {25576328}, issn = {1091-6490}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; }, mesh = {DNA, Ribosomal/genetics ; Humans ; *Microbiota/genetics ; Models, Theoretical ; RNA, Ribosomal, 16S/genetics ; }, abstract = {It has been 35 y since Carl Woese reported in PNAS how sequencing ribosomal RNA genes could be used to distinguish the three domains of life on Earth. During the past decade, 16S rDNA sequencing has enabled the now frequent enumeration of bacterial communities that populate the bodies of humans representing different ages, cultural traditions, and health states. A challenge going forward is to quantify the contributions of community members to wellness, disease risk, and disease pathogenesis. Here, we explore a theoretical framework for studies of the inheritance of bacterial strains and discuss the advantages and disadvantages of various study designs for assessing the contribution of strains to complex diseases.}, }
@article {pmid25575888, year = {2015}, author = {Ribeiro, A and Pochart, P and Day, A and Mennuni, S and Bono, P and Baret, JL and Spadoni, JL and Mangin, I}, title = {Microbial diversity observed during hemp retting.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {10}, pages = {4471-4484}, doi = {10.1007/s00253-014-6356-5}, pmid = {25575888}, issn = {1432-0614}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; *Biodiversity ; Cannabis/metabolism/*microbiology ; Fungi/classification/genetics/*isolation &amp; purification/*metabolism ; Molecular Sequence Data ; Phylogeny ; Plant Stems/metabolism/microbiology ; Real-Time Polymerase Chain Reaction ; }, abstract = {Historically used in textile and paper industry, hemp fibres have started to find new applications in composite materials with important economic and ecological advantages. However, their applications are limited since manufacturers have some difficulties to standardise fabrication processes. This study is a first step before selection and isolation of strains that could later be used to optimise microbial retting efficiency and hence fibre quality. We studied six samples harvested on different ground types, at different dates and with different retting durations on field to obtain an exhaustive representation of the process. After DNA extraction, total bacteria and fungi associated with stems during retting were specifically quantified using real-time PCR. Then, using sequence analysis of randomly cloned 16S and 18S ribosomal RNA (rRNA) genes, a phylogenetic characterisation of the dominant microorganisms was carried out. Quantitatively, we showed that there were 8.1-9.5 log10 16S rRNA gene copies per gram of hemp straw for bacteria and 8.6-9.6 log10 18S rRNA gene copies per gram for fungi. Qualitatively, we noticed a higher bacterial diversity in comparison to fungi. This work showed that in the different samples, the same species were present but in significantly different proportions according to ground type, harvest dates and retting durations on field. The most frequent bacterial sequences were affiliated to species Escherichia coli, Pantoea agglomerans, Pseudomonas rhizosphaerae, Rhodobacter sp., Pseudomonas fulva, Rhizobium huautlense and Massilia timonae, whereas fungal sequences were principally related to the genera Cladosporium and Cryptococcus.}, }
@article {pmid25575309, year = {2015}, author = {Dahle, H and Økland, I and Thorseth, IH and Pederesen, RB and Steen, IH}, title = {Energy landscapes shape microbial communities in hydrothermal systems on the Arctic Mid-Ocean Ridge.}, journal = {The ISME journal}, volume = {9}, number = {7}, pages = {1593-1606}, pmid = {25575309}, issn = {1751-7370}, mesh = {Arctic Regions ; Bacteria/*classification ; Hydrothermal Vents/*microbiology ; Models, Theoretical ; Oceans and Seas ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry ; Thermodynamics ; }, abstract = {Methods developed in geochemical modelling combined with recent advances in molecular microbial ecology provide new opportunities to explore how microbial communities are shaped by their chemical surroundings. Here, we present a framework for analyses of how chemical energy availability shape chemotrophic microbial communities in hydrothermal systems through an investigation of two geochemically different basalt-hosted hydrothermal systems on the Arctic Mid-Ocean Ridge: the Soria Moria Vent field (SMVF) and the Loki's Castle Vent Field (LCVF). Chemical energy landscapes were evaluated through modelling of the Gibbs energy from selected redox reactions under different mixing ratios between seawater and hydrothermal fluids. Our models indicate that the sediment-influenced LCVF has a much higher potential for both anaerobic and aerobic methane oxidation, as well as aerobic ammonium and hydrogen oxidation, than the SMVF. The modelled energy landscapes were used to develop microbial community composition models, which were compared with community compositions in environmental samples inside or on the exterior of hydrothermal chimneys, as assessed by pyrosequencing of partial 16S rRNA genes. We show that modelled microbial communities based solely on thermodynamic considerations can have a high predictive power and provide a framework for analyses of the link between energy availability and microbial community composition.}, }
@article {pmid25575307, year = {2015}, author = {Llorens-Marès, T and Yooseph, S and Goll, J and Hoffman, J and Vila-Costa, M and Borrego, CM and Dupont, CL and Casamayor, EO}, title = {Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics.}, journal = {The ISME journal}, volume = {9}, number = {7}, pages = {1648-1661}, pmid = {25575307}, issn = {1751-7370}, mesh = {Ammonia/metabolism ; Archaea/genetics ; Bacteria/*genetics ; *Biodiversity ; Carbon/metabolism ; Carbon Cycle/genetics ; Denitrification/genetics ; Lakes/chemistry/*microbiology ; Metagenomics/*methods ; Nitrates/metabolism ; Nitrification ; Nitrogen/metabolism ; Nitrogen Fixation/genetics ; Oxidation-Reduction ; Spain ; Sulfur/metabolism ; *Water Microbiology ; }, abstract = {Stratified sulfurous lakes are appropriate environments for studying the links between composition and functionality in microbial communities and are potentially modern analogs of anoxic conditions prevailing in the ancient ocean. We explored these aspects in the Lake Banyoles karstic area (NE Spain) through metagenomics and in silico reconstruction of carbon, nitrogen and sulfur metabolic pathways that were tightly coupled through a few bacterial groups. The potential for nitrogen fixation and denitrification was detected in both autotrophs and heterotrophs, with a major role for nitrogen and carbon fixations in Chlorobiaceae. Campylobacterales accounted for a large percentage of denitrification genes, while Gallionellales were putatively involved in denitrification, iron oxidation and carbon fixation and may have a major role in the biogeochemistry of the iron cycle. Bacteroidales were also abundant and showed potential for dissimilatory nitrate reduction to ammonium. The very low abundance of genes for nitrification, the minor presence of anammox genes, the high potential for nitrogen fixation and mineralization and the potential for chemotrophic CO2 fixation and CO oxidation all provide potential clues on the anoxic zones functioning. We observed higher gene abundance of ammonia-oxidizing bacteria than ammonia-oxidizing archaea that may have a geochemical and evolutionary link related to the dominance of Fe in these environments. Overall, these results offer a more detailed perspective on the microbial ecology of anoxic environments and may help to develop new geochemical proxies to infer biology and chemistry interactions in ancient ecosystems.}, }
@article {pmid25573943, year = {2015}, author = {Wu, JJ and de Jager, VC and Deng, WL and Leveau, JH}, title = {Finished Genome Sequence of Collimonas arenae Cal35.}, journal = {Genome announcements}, volume = {3}, number = {1}, pages = {}, pmid = {25573943}, issn = {2169-8287}, abstract = {We announce the finished genome sequence of soil forest isolate Collimonas arenae Cal35, which comprises a 5.6-Mbp chromosome and 41-kb plasmid. The Cal35 genome is the second one published for the bacterial genus Collimonas and represents the first opportunity for high-resolution comparison of genome content and synteny among collimonads.}, }
@article {pmid25573925, year = {2015}, author = {Ronca, S and Frossard, A and Guerrero, LD and Makhalanyane, TP and Aislabie, JM and Cowan, DA}, title = {Draft Genome Sequence of Sphingomonas sp. Strain Ant20, Isolated from Oil-Contaminated Soil on Ross Island, Antarctica.}, journal = {Genome announcements}, volume = {3}, number = {1}, pages = {}, pmid = {25573925}, issn = {2169-8287}, abstract = {Here, we present the draft genome of Sphingomonas sp. strain Ant20, isolated from oil-polluted soil near Scott Base, Ross Island, Antarctica. The genome of this aromatic hydrocarbon-degrading bacterium provides valuable information on the microbially mediated biodegradation of aromatic compounds in cold-climate systems.}, }
@article {pmid25567040, year = {2015}, author = {Huang, YJ and Boushey, HA}, title = {The microbiome in asthma.}, journal = {The Journal of allergy and clinical immunology}, volume = {135}, number = {1}, pages = {25-30}, pmid = {25567040}, issn = {1097-6825}, support = {K23 HL105572/HL/NHLBI NIH HHS/United States ; }, mesh = {Allergens ; Animals ; Asthma/*microbiology ; Environmental Exposure ; Gastrointestinal Tract/*microbiology ; Humans ; *Microbiota ; Respiratory System/microbiology ; Respiratory Tract Infections/microbiology ; Virus Diseases/microbiology ; }, abstract = {The application of recently developed sensitive, specific, culture-independent tools for identification of microbes is transforming concepts of microbial ecology, including concepts of the relationships between the vast complex populations of microbes associated with ourselves and with states of health and disease. Although most work initially focused on the community of microbes (microbiome) in the gastrointestinal tract and its relationship to gastrointestinal disease, interest has expanded to include study of the relationships of the airway microbiome to asthma and its phenotypes and to the relationships between the gastrointestinal microbiome, development of immune function, and predisposition to allergic sensitization and asthma. Here we provide our perspective on the findings of studies of differences in the airway microbiome between asthmatic patients and healthy subjects and of studies of relationships between environmental microbiota, gut microbiota, immune function, and asthma development. In addition, we provide our perspective on how these findings suggest the broad outline of a rationale for approaches involving directed manipulation of the gut and airway microbiome for the treatment and prevention of allergic asthma.}, }
@article {pmid25566210, year = {2014}, author = {Telling, J and Anesio, AM and Tranter, M and Fountain, AG and Nylen, T and Hawkings, J and Singh, VB and Kaur, P and Musilova, M and Wadham, JL}, title = {Spring thaw ionic pulses boost nutrient availability and microbial growth in entombed Antarctic Dry Valley cryoconite holes.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {694}, pmid = {25566210}, issn = {1664-302X}, abstract = {The seasonal melting of ice entombed cryoconite holes on McMurdo Dry Valley glaciers provides oases for life in the harsh environmental conditions of the polar desert where surface air temperatures only occasionally exceed 0°C during the Austral summer. Here we follow temporal changes in cryoconite hole biogeochemistry on Canada Glacier from fully frozen conditions through the initial stages of spring thaw toward fully melted holes. The cryoconite holes had a mean isolation age from the glacial drainage system of 3.4 years, with an increasing mass of aqueous nutrients (dissolved organic carbon, total nitrogen, total phosphorus) with longer isolation age. During the initial melt there was a mean nine times enrichment in dissolved chloride relative to mean concentrations of the initial frozen holes indicative of an ionic pulse, with similar mean nine times enrichments in nitrite, ammonium, and dissolved organic matter. Nitrate was enriched twelve times and dissolved organic nitrogen six times, suggesting net nitrification, while lower enrichments for dissolved organic phosphorus and phosphate were consistent with net microbial phosphorus uptake. Rates of bacterial production were significantly elevated during the ionic pulse, likely due to the increased nutrient availability. There was no concomitant increase in photosynthesis rates, with a net depletion of dissolved inorganic carbon suggesting inorganic carbon limitation. Potential nitrogen fixation was detected in fully melted holes where it could be an important source of nitrogen to support microbial growth, but not during the ionic pulse where nitrogen availability was higher. This study demonstrates that ionic pulses significantly alter the timing and magnitude of microbial activity within entombed cryoconite holes, and adds credence to hypotheses that ionic enrichments during freeze-thaw can elevate rates of microbial growth and activity in other icy habitats, such as ice veins and subglacial regelation zones.}, }
@article {pmid25564681, year = {2014}, author = {Cary, SC and Fierer, N}, title = {The importance of sample archiving in microbial ecology.}, journal = {Nature reviews. Microbiology}, volume = {12}, number = {12}, pages = {789-790}, pmid = {25564681}, issn = {1740-1534}, mesh = {Animals ; *Biological Specimen Banks/standards ; *Ecology ; *Environmental Microbiology ; Humans ; Research ; *Specimen Handling ; }, }
@article {pmid25563415, year = {2015}, author = {Unno, T}, title = {Bioinformatic Suggestions on MiSeq-Based Microbial Community Analysis.}, journal = {Journal of microbiology and biotechnology}, volume = {25}, number = {6}, pages = {765-770}, doi = {10.4014/jmb.1409.09057}, pmid = {25563415}, issn = {1738-8872}, mesh = {*Biota ; Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; }, abstract = {Recent sequencing technology development has revolutionized fields of microbial ecology. MiSeq-based microbial community analysis allows us to sequence more than a few hundred samples at a time, which is far more cost-effective than pyrosequencing. The approach, however, has not been preferably used owing to computational difficulties of processing huge amounts of data as well as known Illumina-derived artefact problems with amplicon sequencing. The choice of assembly software to take advantage of paired-end sequencing and methods to remove Illumina artefacts sequences are discussed. The protocol we suggest not only removed erroneous reads, but also dramatically reduced computational workload, which allows even a typical desktop computer to process a huge amount of sequence data generated with Illumina sequencers. We also developed a Web interface (http://biotech.jejunu.ac.kr/ ~abl/16s/) that allows users to conduct fastq-merging and mothur batch creation. The study presented here should provide technical advantages and supports in applying MiSeq-based microbial community analysis.}, }
@article {pmid25561355, year = {2014}, author = {Eckert, EM and Fontaneto, D and Coci, M and Callieri, C}, title = {Does a barcoding gap exist in prokaryotes? Evidences from species delimitation in cyanobacteria.}, journal = {Life (Basel, Switzerland)}, volume = {5}, number = {1}, pages = {50-64}, pmid = {25561355}, issn = {2075-1729}, abstract = {The amount of information that is available on 16S rRNA sequences for prokaryotes thanks to high-throughput sequencing could allow a better understanding of diversity. Nevertheless, the application of predetermined threshold in genetic distances to identify units of diversity (Operative Taxonomic Units, OTUs) may provide biased results. Here we tests for the existence of a barcoding gap in several groups of Cyanobacteria, defining units of diversity according to clear differences between within-species and among-species genetic distances in 16S rRNA. The application of a tool developed for animal DNA taxonomy, the Automatic Barcode Gap Detector (ABGD), revealed that a barcoding gap could actually be found in almost half of the datasets that we tested. The identification of units of diversity through this method provided results that were not compatible with those obtained with the identification of OTUs with threshold of similarity in genetic distances of 97% or 99%. The main message of our results is a call for caution in the estimate of diversity from 16S sequences only, given that different subjective choices in the method to delimit units could provide different results.}, }
@article {pmid25553568, year = {2015}, author = {Meerburg, FA and Boon, N and Van Winckel, T and Vercamer, JAR and Nopens, I and Vlaeminck, SE}, title = {Toward energy-neutral wastewater treatment: a high-rate contact stabilization process to maximally recover sewage organics.}, journal = {Bioresource technology}, volume = {179}, number = {}, pages = {373-381}, doi = {10.1016/j.biortech.2014.12.018}, pmid = {25553568}, issn = {1873-2976}, mesh = {Biological Oxygen Demand Analysis ; Carbon/analysis ; Chemical Fractionation ; Kinetics ; Methane/biosynthesis ; Organic Chemicals/*isolation &amp; purification ; Sewage/*chemistry ; Thermodynamics ; Wastewater/*chemistry ; Water Purification/*methods ; }, abstract = {The conventional activated sludge process is widely used for wastewater treatment, but to progress toward energy self-sufficiency, the wastewater treatment scheme needs to radically improve energy balances. We developed a high-rate contact stabilization (HiCS) reactor system at high sludge-specific loading rates (>2 kg bCOD kg(-1)TSS d(-1)) and low sludge retention times (<1.2 d) and demonstrate that it is able to recover more chemical energy from wastewater organics than high-rate conventional activated sludge (HiCAS) and the low-rate variants of HiCS and HiCAS. The best HiCS system recovered 36% of the influent chemical energy as methane, due to the combined effects of low production of CO2, high sludge yield, and high methane yield of the produced sludge. The HiCS system imposed a feast-famine cycle and a putative selection pressure on the sludge micro-organisms toward substrate adsorption and storage. Given further optimization, it is a promising process for energy recovery from wastewater.}, }
@article {pmid25550518, year = {2015}, author = {Berry, D and Mader, E and Lee, TK and Woebken, D and Wang, Y and Zhu, D and Palatinszky, M and Schintlmeister, A and Schmid, MC and Hanson, BT and Shterzer, N and Mizrahi, I and Rauch, I and Decker, T and Bocklitz, T and Popp, J and Gibson, CM and Fowler, PW and Huang, WE and Wagner, M}, title = {Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {2}, pages = {E194-203}, pmid = {25550518}, issn = {1091-6490}, support = {294343/ERC_/European Research Council/International ; P 26127/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Archaea/genetics/isolation &amp; purification/metabolism ; Bacteria/genetics/isolation &amp; purification/metabolism ; Base Sequence ; Biomass ; Cecum/microbiology ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Deuterium Oxide/*metabolism ; Escherichia coli/genetics/growth &amp; development/metabolism ; Humans ; In Situ Hybridization, Fluorescence ; Mice ; Mice, Inbred C57BL ; *Microbial Consortia/genetics ; Microbiological Techniques ; Molecular Sequence Data ; Optical Tweezers ; Phylogeny ; Spectrum Analysis, Raman ; }, abstract = {Microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. In this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D2O) combined with Raman microspectroscopy. Incorporation of D2O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labeling pattern was confirmed by nanoscale-resolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D2O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Raman-based cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/or glucosamine were identified, demonstrating the potential of the nondestructive D2O-Raman approach for targeted sorting of microbial cells with defined functional properties for single-cell genomics.}, }
@article {pmid25545295, year = {2015}, author = {Moeller, AH and Peeters, M and Ayouba, A and Ngole, EM and Esteban, A and Hahn, BH and Ochman, H}, title = {Stability of the gorilla microbiome despite simian immunodeficiency virus infection.}, journal = {Molecular ecology}, volume = {24}, number = {3}, pages = {690-697}, pmid = {25545295}, issn = {1365-294X}, support = {R37 AI050529/AI/NIAID NIH HHS/United States ; R01 GM101209/GM/NIGMS NIH HHS/United States ; R01 AI 058715/AI/NIAID NIH HHS/United States ; R01 AI091595/AI/NIAID NIH HHS/United States ; R01 AI058715/AI/NIAID NIH HHS/United States ; R37 AI 050529/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification ; Feces/microbiology ; Gorilla gorilla/*microbiology/virology ; Intestines/*microbiology ; *Microbiota ; Simian Acquired Immunodeficiency Syndrome/*microbiology ; Simian Immunodeficiency Virus ; }, abstract = {Simian immunodeficiency viruses (SIVs) have been discovered in over 45 primate species; however, the pathogenic potential of most SIV strains remains unknown due to difficulties inherent in observing wild populations. Because those SIV infections that are pathogenic have been shown to induce changes in the host's gut microbiome, monitoring the microbiota present in faecal samples can provide a noninvasive means for studying the effects of SIV infection on the health of wild-living primates. Here, we examine the effects of SIVgor, a close relative of SIVcpz of chimpanzees and HIV-1 of humans, on the gut bacterial communities residing within wild gorillas, revealing that gorilla gut microbiomes are exceptionally robust to SIV infection. In contrast to the microbiomes of HIV-1-infected humans and SIVcpz-infected chimpanzees, SIVgor-infected gorilla microbiomes exhibit neither rises in the frequencies of opportunistic pathogens nor elevated rates of microbial turnover within individual hosts. Regardless of SIV infection status, gorilla microbiomes assort into enterotypes, one of which is compositionally analogous to those identified in humans and chimpanzees. The other gorilla enterotype appears specialized for a leaf-based diet and is enriched in environmentally derived bacterial genera. We hypothesize that the acquisition of this gorilla-specific enterotype was enabled by lowered immune system control over the composition of the microbiome. Our results indicate differences between the pathology of SIVgor and SIVcpz/HIV-1 infections, demonstrating the utility of investigating host microbial ecology as a means for studying disease in wild primates of high conservation priority.}, }
@article {pmid25542205, year = {2015}, author = {Bharti, N and Barnawal, D and Maji, D and Kalra, A}, title = {Halotolerant PGPRs Prevent Major Shifts in Indigenous Microbial Community Structure Under Salinity Stress.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {196-208}, pmid = {25542205}, issn = {1432-184X}, mesh = {Adaptation, Biological/*genetics ; Bacillales/genetics/metabolism ; Bacillus/genetics/metabolism ; *Biodiversity ; DNA Primers/genetics ; Halomonas/genetics/metabolism ; Polymorphism, Restriction Fragment Length ; Population Density ; *Rhizosphere ; *Salinity ; Soil/chemistry ; *Soil Microbiology ; Species Specificity ; Stress, Physiological/*physiology ; Zea mays/growth &amp; development/*microbiology ; }, abstract = {The resilience of soil microbial populations and processes to environmental perturbation is of increasing interest as alteration in rhizosphere microbial community dynamics impacts the combined functions of plant-microbe interactions. The present study was conducted to investigate the effect of inoculation with halotolerant rhizobacteria Bacillus pumilus (STR2), Halomonas desiderata (STR8), and Exiguobacterium oxidotolerans (STR36) on the indigenous root-associated microbial (bacterial and fungal) communities in maize under non-saline and salinity stress. Plants inoculated with halotolerant rhizobacteria recorded improved growth as illustrated by significantly higher shoot and root dry weight and elongation in comparison to un-inoculated control plants under both non-saline and saline conditions. Additive main effect and multiplicative interaction ordination analysis revealed that plant growth promoting rhizobacteria (PGPR) inoculations as well as salinity are major drivers of microbial community shift in maize rhizosphere. Salinity negatively impacts microbial community as analysed through diversity indices; among the PGPR-inoculated plants, STR2-inoculated plants recorded higher values of diversity indices. As observed in the terminal-restriction fragment length polymorphism analysis, the inoculation of halotolerant rhizobacteria prevents major shift of the microbial community structure, thus enhancing the resilience capacity of the microbial communities.}, }
@article {pmid25542204, year = {2015}, author = {Schirrmann, MK and Zoller, S and Fior, S and Leuchtmann, A}, title = {Genetic evidence for reproductive isolation among sympatric Epichloë endophytes as inferred from newly developed microsatellite markers.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {51-60}, pmid = {25542204}, issn = {1432-184X}, mesh = {Base Sequence ; Bayes Theorem ; Dactylis/*microbiology ; *Ecosystem ; Epichloe/classification/*genetics ; *Genetic Speciation ; *Genetic Variation ; Genetics, Population ; Holcus/*microbiology ; Microsatellite Repeats/genetics ; Molecular Sequence Data ; Polymorphism, Single Nucleotide/genetics ; Principal Component Analysis ; *Reproductive Isolation ; Sequence Analysis, DNA ; Species Specificity ; Switzerland ; }, abstract = {Reproductive isolation is central to the maintenance of species, and especially in sympatry, effective barriers to prevent interspecific crosses are expected. Host specificity is thought to constitute an effective mechanism for the formation of barriers in different genera of Fungi, but evidence for endophytes is so far lacking. Sexual Epichloë species (Ascomycota, Clavicipitaceae) represent an ideal study system to investigate the mechanisms underlying speciation as mediated by host specificity because they include species complexes with several host-specific taxa. Here, we studied genetic differentiation of three host-specific Epichloë species using microsatellite markers that were newly in silico identified on the genome of Epichloë poae. Among these, 15 were experimentally tested and applied to study an extensive sampling of isolates representing Epichloë typhina infecting Dactylis glomerata and Epichloë clarkii infecting Holcus lanatus from a site with sympatric populations in Switzerland, as well as a reduced sampling of E. poae infecting Poa nemoralis to create a three-taxon dataset. Both principal coordinate analysis and Bayesian clustering algorithm showed three genetically distinct groups representing the three host-specific species. High pairwise F ST values among the three species, as well as sequencing data of the tefA gene revealing diagnostic single nucleotide polymorphisms (SNPs), further support the hypothesis of genetic discontinuities among the taxa. These results provide genotypic evidence of the maintenance of reproductive isolation of the species in a context of sympatry. In silico testing of 885 discovered microsatellites on the genome of Epichloë festucae extend their applicability to a wider taxonomic range of Epichloë.}, }
@article {pmid25542203, year = {2015}, author = {Zhang, M and Warmink, J and Pereira E Silva, MC and Brons, J and Smalla, K and van Elsas, JD}, title = {IncP-1β Plasmids Are Important Carriers of Fitness Traits for Variovorax Species in the Mycosphere--Two Novel Plasmids, pHB44 and pBS64, with Differential Effects Unveiled.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {141-153}, pmid = {25542203}, issn = {1432-184X}, mesh = {Analysis of Variance ; Biofilms/*growth &amp; development ; Blotting, Southern ; Comamonadaceae/*genetics/physiology ; Escherichia coli ; *Laccaria ; Plasmids/*genetics ; Polymerase Chain Reaction/methods ; Population Dynamics ; Pseudomonas fluorescens ; Replicon/genetics ; *Soil Microbiology ; }, abstract = {The Laccaria proxima mycosphere strongly selects Variovorax paradoxus cells. Fifteen independent V. paradoxus strains, isolated from mycospheres sampled at two occasions, were investigated with respect to the occurrence of plasmids of sizes <60-100 kb. Two V. paradoxus strains, HB44 and BS64, were found to contain such plasmids, which were coined pHB44 and pBS64. Replicon typing using a suite of plasmid-specific PCR systems indicated that both plasmids belong to the IncP-1β group. Also, both were able to mobilize selectable IncQ group plasmids into Escherichia coli as well as Pseudomonas fluorescens. Moreover, they showed stable replication in these organisms, confirming their broad host range. Strain BS64 was cured of pBS64 and plasmid pHB44 was subsequently moved into this cured strain by making use of the IncQ group tracer plasmid pSUP104, which was then removed at elevated temperature. Thus, both plasmids could be screened for their ability to confer a phenotype upon strain BS64. No evidence for the presence of genes for xenobiotic degradation and/or antibiotic or heavy metal resistances was found for either of the two plasmids. Remarkably, both could stimulate the production of biofilm material by strain BS64. Also, the population densities of pBS64-containing strain BS64 were temporarily raised in liquid as well as soil systems (versus the plasmid-cured strain), both in the presence of the fungal host Lyophyllum sp. strain Karsten. Strikingly, plasmid pHB44 significantly enhanced the fitness of strain BS64 in soil containing Lyophyllum sp. strain Karsten, but decreased its fitness in soil supplemented with extra FeCl3. The effect was noted both in separate (no inter-strain competition) and joint (competition) inoculations.}, }
@article {pmid25540838, year = {2015}, author = {Ma, Y and Sundar, S and Park, H and Chandran, K}, title = {The effect of inorganic carbon on microbial interactions in a biofilm nitritation-anammox process.}, journal = {Water research}, volume = {70}, number = {}, pages = {246-254}, doi = {10.1016/j.watres.2014.12.006}, pmid = {25540838}, issn = {1879-2448}, mesh = {Ammonium Compounds/metabolism ; Anaerobiosis ; Bacteria/growth &amp; development/metabolism ; *Bacterial Physiological Phenomena ; *Biofilms ; Bioreactors ; Carbon Compounds, Inorganic/*metabolism ; *Microbial Interactions ; Nitrification ; Nitrites ; Nitrogen/metabolism ; Oxidation-Reduction ; *Waste Disposal, Fluid ; }, abstract = {The overarching goal of this study was to determine the role of inorganic carbon (IC) in influencing the microbial ecology, performance and nitrogen turnover by individual microbial communities of a biofilm based combined nitritation-anammox process. IC limitation was transiently imposed by reducing the IC input from 350% to 40% of the stoichiometric requirement for 40 days. The principal impact observed during IC limitation was the overgrowth of nitrite oxidizing bacteria (NOB) at the expense of anaerobic ammonia oxidizing bacteria (AMX). On the other hand, the concentrations of ammonia oxidizing bacteria (AOB) were relatively stable during the imposition of and recovery from IC limitation. The resulting dominance of NOB, in terms of their concentration and contribution to nitrite consumption over AMX, resulted, in turn, in a decrease in overall nitrogen removal from 78 ± 2.0% before IC limitation to 46 ± 2.9% during IC limitation. Upon recovery back to non-limiting IC input, it took an inordinately long time (about 57*HRT) for the N-removal to recover back to pre-limitation conditions. Even after recovery, NOB were still persistent in the biofilm and could not be washed out to pre-limitation concentrations. The emission of nitrous oxide (N2O) and nitric oxide (NO), likely from AOB, transiently increased in concert with transient increases in ammonia and hydroxylamine concentrations during the period of IC limitation. Therefore, an unintended consequence of IC limitation in nitritation-anammox systems can be an increase in their greenhouse gas footprint, in addition to compromised process performance. Most emphasis to date on nitritation and anammox studies has been on the nitrogen cycle. The results of this study demonstrate that the differing strategies used by AOB, NOB and AMX to compete for their preferred assimilative carbon source can also significantly influence the microbial ecology, performance and carbon footprint of such processes.}, }
@article {pmid25538865, year = {2014}, author = {Lang, JM and Eisen, JA and Zivkovic, AM}, title = {The microbes we eat: abundance and taxonomy of microbes consumed in a day's worth of meals for three diet types.}, journal = {PeerJ}, volume = {2}, number = {}, pages = {e659}, pmid = {25538865}, issn = {2167-8359}, abstract = {Far more attention has been paid to the microbes in our feces than the microbes in our food. Research efforts dedicated to the microbes that we eat have historically been focused on a fairly narrow range of species, namely those which cause disease and those which are thought to confer some "probiotic" health benefit. Little is known about the effects of ingested microbial communities that are present in typical American diets, and even the basic questions of which microbes, how many of them, and how much they vary from diet to diet and meal to meal, have not been answered. We characterized the microbiota of three different dietary patterns in order to estimate: the average total amount of daily microbes ingested via food and beverages, and their composition in three daily meal plans representing three different dietary patterns. The three dietary patterns analyzed were: (1) the Average American (AMERICAN): focused on convenience foods, (2) USDA recommended (USDA): emphasizing fruits and vegetables, lean meat, dairy, and whole grains, and (3) Vegan (VEGAN): excluding all animal products. Meals were prepared in a home kitchen or purchased at restaurants and blended, followed by microbial analysis including aerobic, anaerobic, yeast and mold plate counts as well as 16S rRNA PCR survey analysis. Based on plate counts, the USDA meal plan had the highest total amount of microbes at 1.3 × 10(9) CFU per day, followed by the VEGAN meal plan and the AMERICAN meal plan at 6 × 10(6) and 1.4 × 10(6) CFU per day respectively. There was no significant difference in diversity among the three dietary patterns. Individual meals clustered based on taxonomic composition independent of dietary pattern. For example, meals that were abundant in Lactic Acid Bacteria were from all three dietary patterns. Some taxonomic groups were correlated with the nutritional content of the meals. Predictive metagenome analysis using PICRUSt indicated differences in some functional KEGG categories across the three dietary patterns and for meals clustered based on whether they were raw or cooked. Further studies are needed to determine the impact of ingested microbes on the intestinal microbiota, the extent of variation across foods, meals and diets, and the extent to which dietary microbes may impact human health. The answers to these questions will reveal whether dietary microbes, beyond probiotics taken as supplements-i.e., ingested with food-are important contributors to the composition, inter-individual variation, and function of our gut microbiota.}, }
@article {pmid25538691, year = {2014}, author = {Dechesne, A and Badawi, N and Aamand, J and Smets, BF}, title = {Fine scale spatial variability of microbial pesticide degradation in soil: scales, controlling factors, and implications.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {667}, pmid = {25538691}, issn = {1664-302X}, abstract = {Pesticide biodegradation is a soil microbial function of critical importance for modern agriculture and its environmental impact. While it was once assumed that this activity was homogeneously distributed at the field scale, mounting evidence indicates that this is rarely the case. Here, we critically examine the literature on spatial variability of pesticide biodegradation in agricultural soil. We discuss the motivations, methods, and main findings of the primary literature. We found significant diversity in the approaches used to describe and quantify spatial heterogeneity, which complicates inter-studies comparisons. However, it is clear that the presence and activity of pesticide degraders is often highly spatially variable with coefficients of variation often exceeding 50% and frequently displays non-random spatial patterns. A few controlling factors have tentatively been identified across pesticide classes: they include some soil characteristics (pH) and some agricultural management practices (pesticide application, tillage), while other potential controlling factors have more conflicting effects depending on the site or the pesticide. Evidence demonstrating the importance of spatial heterogeneity on the fate of pesticides in soil has been difficult to obtain but modeling and experimental systems that do not include soil's full complexity reveal that this heterogeneity must be considered to improve prediction of pesticide biodegradation rates or of leaching risks. Overall, studying the spatial heterogeneity of pesticide biodegradation is a relatively new field at the interface of agronomy, microbial ecology, and geosciences and a wealth of novel data is being collected from these different disciplinary perspectives. We make suggestions on possible avenues to take full advantage of these investigations for a better understanding and prediction of the fate of pesticides in soil.}, }
@article {pmid25537565, year = {2015}, author = {Moreno-Indias, I and Torres, M and Montserrat, JM and Sanchez-Alcoholado, L and Cardona, F and Tinahones, FJ and Gozal, D and Poroyko, VA and Navajas, D and Queipo-Ortuño, MI and Farré, R}, title = {Intermittent hypoxia alters gut microbiota diversity in a mouse model of sleep apnoea.}, journal = {The European respiratory journal}, volume = {45}, number = {4}, pages = {1055-1065}, doi = {10.1183/09031936.00184314}, pmid = {25537565}, issn = {1399-3003}, mesh = {Analysis of Variance ; Animals ; Disease Models, Animal ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Hypoxia/microbiology/*physiopathology ; Male ; Mice ; Mice, Inbred C57BL ; Periodicity ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics/*metabolism ; Random Allocation ; Severity of Illness Index ; Sleep Apnea, Obstructive/microbiology/*physiopathology ; Statistics, Nonparametric ; }, abstract = {We assessed whether intermittent hypoxia, which emulates one of the hallmarks of obstructive sleep apnoea (OSA), leads to altered faecal microbiome in a murine model. In vivo partial pressure of oxygen was measured in colonic faeces during intermittent hypoxia in four anesthetised mice. 10 mice were subjected to a pattern of chronic intermittent hypoxia (20 s at 5% O2 and 40 s at room air for 6 h·day(-1)) for 6 weeks and 10 mice served as normoxic controls. Faecal samples were obtained and microbiome composition was determined by 16S rRNA pyrosequencing and bioinformatic analysis by Quantitative Insights into Microbial Ecology. Intermittent hypoxia exposures translated into hypoxia/re-oxygenation patterns in the faeces proximal to the bowel epithelium (<200 μm). A significant effect of intermittent hypoxia on global microbial community structure was found. Intermittent hypoxia increased the α-diversity (Shannon index, p<0.05) and induced a change in the gut microbiota (ANOSIM analysis of β-diversity, p<0.05). Specifically, intermittent hypoxia-exposed mice showed a higher abundance of Firmicutes and a smaller abundance of Bacteroidetes and Proteobacteria phyla than controls. Faecal microbiota composition and diversity are altered as a result of intermittent hypoxia realistically mimicking OSA, suggesting the possibility that physiological interplays between host and gut microbiota could be deregulated in OSA.}, }
@article {pmid25534983, year = {2015}, author = {Palesse, S and Colombet, J and Pradeep Ram, AS and Sime-Ngando, T}, title = {Erratum to: Linking Host Prokaryotic Physiology to Viral Lifestyle Dynamics in a Temperate Freshwater Lake (Lake Pavin, France).}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {299-300}, doi = {10.1007/s00248-014-0555-6}, pmid = {25534983}, issn = {1432-184X}, }
@article {pmid25534614, year = {2015}, author = {Gülay, A and Smets, BF}, title = {An improved method to set significance thresholds for β diversity testing in microbial community comparisons.}, journal = {Environmental microbiology}, volume = {17}, number = {9}, pages = {3154-3167}, doi = {10.1111/1462-2920.12748}, pmid = {25534614}, issn = {1462-2920}, mesh = {Algorithms ; Bacteria/*genetics ; Data Interpretation, Statistical ; Microbial Consortia/*genetics/physiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Exploring the variation in microbial community diversity between locations (β diversity) is a central topic in microbial ecology. Currently, there is no consensus on how to set the significance threshold for β diversity. Here, we describe and quantify the technical components of β diversity, including those associated with the process of subsampling. These components exist for any proposed β diversity measurement procedure. Further, we introduce a strategy to set significance thresholds for β diversity of any group of microbial samples using rarefaction, invoking the notion of a meta-community. The proposed technique was applied to several in silico generated operational taxonomic unit (OTU) libraries and experimental 16S rRNA pyrosequencing libraries. The latter represented microbial communities from different biological rapid sand filters at a full-scale waterworks. We observe that β diversity, after subsampling, is inflated by intra-sample differences; this inflation is avoided in the proposed method. In addition, microbial community evenness (Gini > 0.08) strongly affects all β diversity estimations due to bias associated with rarefaction. Where published methods to test β significance often fail, the proposed meta-community-based estimator is more successful at rejecting insignificant β diversity values. Applying our approach, we reveal the heterogeneous microbial structure of biological rapid sand filters both within and across filters.}, }
@article {pmid25533445, year = {2015}, author = {Thorasin, T and Hoyles, L and McCartney, AL}, title = {Dynamics and diversity of the 'Atopobium cluster' in the human faecal microbiota, and phenotypic characterization of 'Atopobium cluster' isolates.}, journal = {Microbiology (Reading, England)}, volume = {161}, number = {Pt 3}, pages = {565-579}, doi = {10.1099/mic.0.000016}, pmid = {25533445}, issn = {1465-2080}, mesh = {Actinobacteria/classification/genetics/*isolation &amp; purification ; Adult ; Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Feces/*microbiology ; Female ; Humans ; Male ; *Microbiota ; Middle Aged ; Molecular Sequence Data ; Phenotype ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {This study monitored the dynamics and diversity of the human faecal 'Atopobium cluster' over a 3-month period using a polyphasic approach. Fresh faecal samples were collected fortnightly from 13 healthy donors (six males and seven females) aged between 26 and 61 years. FISH was used to enumerate total (EUB338mix) and 'Atopobium cluster' (ATO291) bacteria, with counts ranging between 1.12×10(11) and 9.95×10(11), and 1.03×10(9) and 1.16×10(11) cells (g dry weight faeces)(-1), respectively. The 'Atopobium cluster' population represented 0.2-22 % of the total bacteria, with proportions donor-dependent. Denaturing gradient gel electrophoresis (DGGE) using 'Atopobium cluster'-specific primers demonstrated faecal populations of these bacteria were relatively stable, with bands identified as Collinsella aerofaciens, Collinsella intestinalis/Collinsella stercoris, Collinsella tanakaei, Coriobacteriaceae sp. PEAV3-3, Eggerthella lenta, Gordonibacter pamelaeae, Olsenella profusa, Olsenella uli and Paraeggerthella hongkongensis in the DGGE profiles of individuals. Colony PCR was used to identify 'Atopobium cluster' bacteria isolated from faeces (n = 224 isolates). 16S rRNA gene sequence analysis of isolates demonstrated Collinsella aerofaciens represented the predominant (88 % of isolates) member of the 'Atopobium cluster' found in human faeces, being found in nine individuals. Eggerthella lenta was identified in three individuals (3.6 % of isolates). Isolates of Collinsella tanakaei, an 'Enorma' sp. and representatives of novel species belonging to the 'Atopobium cluster' were also identified in the study. Phenotypic characterization of the isolates demonstrated their highly saccharolytic nature and heterogeneous phenotypic profiles, and 97 % of the isolates displayed lipase activity.}, }
@article {pmid25529676, year = {2015}, author = {Hachicha Hbaieb, R and Kotti, F and García-Rodríguez, R and Gargouri, M and Sanz, C and Pérez, AG}, title = {Monitoring endogenous enzymes during olive fruit ripening and storage: correlation with virgin olive oil phenolic profiles.}, journal = {Food chemistry}, volume = {174}, number = {}, pages = {240-247}, doi = {10.1016/j.foodchem.2014.11.033}, pmid = {25529676}, issn = {1873-7072}, mesh = {Catechol Oxidase/metabolism ; Fruit/enzymology/growth &amp; development ; Olea/*enzymology/growth &amp; development ; Olive Oil ; Peroxidase/metabolism ; Phenols/*analysis ; Plant Oils/*chemistry ; Temperature ; beta-Glucosidase/*metabolism ; }, abstract = {The ability of olive endogenous enzymes β-glucosidase, polyphenol oxidase (PPO) and peroxidase (POX), to determine the phenolic profile of virgin olive oil was investigated. Olives used for oil production were stored for one month at 20 °C and 4 °C and their phenolic content and enzymatic activities were compared to those of ripening olive fruits. Phenolic and volatile profiles of the corresponding oils were also analysed. Oils obtained from fruits stored at 4 °C show similar characteristics to that of freshly harvested fruits. However, the oils obtained from fruits stored at 20 °C presented the lowest phenolic content. Concerning the enzymatic activities, results show that the β-glucosidase enzyme is the key enzyme responsible for the determination of virgin olive oil phenolic profile as the decrease in this enzyme activity after 3 weeks of storage at 20 °C was parallel to a dramatic decrease in the phenolic content of the oils.}, }
@article {pmid25524570, year = {2015}, author = {Amato, KR and Leigh, SR and Kent, A and Mackie, RI and Yeoman, CJ and Stumpf, RM and Wilson, BA and Nelson, KE and White, BA and Garber, PA}, title = {The gut microbiota appears to compensate for seasonal diet variation in the wild black howler monkey (Alouatta pigra).}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {434-443}, pmid = {25524570}, issn = {1432-184X}, mesh = {Alouatta/*microbiology ; Animals ; Diet/*veterinary ; Feeding Behavior ; Female ; Fruit ; Gastrointestinal Tract/*microbiology ; Male ; Mexico ; *Microbiota ; Plant Leaves ; Seasons ; }, abstract = {For most mammals, including nonhuman primates, diet composition varies temporally in response to differences in food availability. Because diet influences gut microbiota composition, it is likely that the gut microbiota of wild mammals varies in response to seasonal changes in feeding patterns. Such variation may affect host digestive efficiency and, ultimately, host nutrition. In this study, we investigate the temporal variation in diet and gut microbiota composition and function in two groups (N = 13 individuals) of wild Mexican black howler monkeys (Alouatta pigra) over a 10-month period in Palenque National Park, Mexico. Temporal changes in the relative abundances of individual bacterial taxa were strongly correlated with changes in host diet. For example, the relative abundance of Ruminococcaceae was highest during periods when energy intake was lowest, and the relative abundance of Butyricicoccus was highest when young leaves and unripe fruit accounted for 68 % of the diet. Additionally, the howlers exhibited increased microbial production of energy during periods of reduced energy intake from food sources. Because we observed few changes in howler activity and ranging patterns during the course of our study, we propose that shifts in the composition and activity of the gut microbiota provided additional energy and nutrients to compensate for changes in diet. Energy and nutrient production by the gut microbiota appears to provide an effective buffer against seasonal fluctuations in energy and nutrient intake for these primates and is likely to have a similar function in other mammal species.}, }
@article {pmid25524569, year = {2015}, author = {Hong, PY and Mao, Y and Ortiz-Kofoed, S and Shah, R and Cann, I and Mackie, RI}, title = {Metagenomic-based study of the phylogenetic and functional gene diversity in Galápagos land and marine iguanas.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {444-456}, pmid = {25524569}, issn = {1432-184X}, mesh = {Animals ; Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Ecuador ; Fatty Acids, Volatile/analysis ; Feces/microbiology ; Host-Pathogen Interactions ; Iguanas/*microbiology ; Islands ; *Metagenome ; Metagenomics ; Microbiota ; Multigene Family ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {In this study, a metagenome-based analysis of the fecal samples from the macrophytic algae-consuming marine iguana (MI; Amblyrhynchus cristatus) and terrestrial biomass-consuming land iguanas (LI; Conolophus spp.) was conducted. Phylogenetic affiliations of the fecal microbiome were more similar between both iguanas than to other mammalian herbivorous hosts. However, functional gene diversities in both MI and LI iguana hosts differed in relation to the diet, where the MI fecal microbiota had a functional diversity that clustered apart from the other terrestrial-biomass consuming reptilian and mammalian hosts. A further examination of the carbohydrate-degrading genes revealed that several of the prevalent glycosyl hydrolases (GH), glycosyl transferases (GT), carbohydrate binding modules (CBM), and carbohydrate esterases (CE) gene classes were conserved among all examined herbivorous hosts, reiterating the important roles these genes play in the breakdown and metabolism of herbivorous diets. Genes encoding some classes of carbohydrate-degrading families, including GH2, GH13, GT2, GT4, CBM50, CBM48, CE4, and CE11, as well as genes associated with sulfur metabolism and dehalogenation, were highly enriched or unique to the MI. In contrast, gene sequences that relate to archaeal methanogenesis were detected only in LI fecal microbiome, and genes coding for GH13, GH66, GT2, GT4, CBM50, CBM13, CE4, and CE8 carbohydrate active enzymes were highly abundant in the LI. Bacterial populations were enriched on various carbohydrates substrates (e.g., glucose, arabinose, xylose). The majority of the enriched bacterial populations belong to genera Clostridium spp. and Enterococcus spp. that likely accounted for the high prevalence of GH13 and GH2, as well as the GT families (e.g., GT2, GT4, GT28, GT35, and GT51) that were ubiquitously present in the fecal microbiota of all herbivorous hosts.}, }
@article {pmid25524234, year = {2015}, author = {Lindahl, BD and Tunlid, A}, title = {Ectomycorrhizal fungi - potential organic matter decomposers, yet not saprotrophs.}, journal = {The New phytologist}, volume = {205}, number = {4}, pages = {1443-1447}, doi = {10.1111/nph.13201}, pmid = {25524234}, issn = {1469-8137}, mesh = {Carbon/metabolism ; Gene Expression Profiling ; Genomics ; Mycorrhizae/*metabolism ; Organic Chemicals/*metabolism ; Spectrum Analysis ; }, abstract = {Although hypothesized for many years, the involvement of ectomycorrhizal fungi in decomposition of soil organic matter remains controversial and has not yet been fully acknowledged as an important factor in the regulation of soil carbon (C) storage. Here, we review recent findings, which support the view that some ectomycorrhizal fungi have the capacity to oxidize organic matter, either by 'brown-rot' Fenton chemistry or using 'white-rot' peroxidases. We propose that ectomycorrhizal fungi benefit from organic matter decomposition primarily through increased nitrogen mobilization rather than through release of metabolic C and question the view that ectomycorrhizal fungi may act as facultative saprotrophs. Finally, we discuss how mycorrhizal decomposition may influence organic matter storage in soils and mediate responses of ecosystem C sequestration to environmental changes.}, }
@article {pmid25523930, year = {2015}, author = {Grobbler, C and Virdis, B and Nouwens, A and Harnisch, F and Rabaey, K and Bond, PL}, title = {Use of SWATH mass spectrometry for quantitative proteomic investigation of Shewanella oneidensis MR-1 biofilms grown on graphite cloth electrodes.}, journal = {Systematic and applied microbiology}, volume = {38}, number = {2}, pages = {135-139}, doi = {10.1016/j.syapm.2014.11.007}, pmid = {25523930}, issn = {1618-0984}, mesh = {Bioelectric Energy Sources ; Biofilms/*growth &amp; development ; Electricity ; Electrodes/*microbiology ; Electron Transport ; *Graphite ; Lactates/metabolism ; Mass Spectrometry ; Metabolic Networks and Pathways ; Proteome/*analysis ; Proteomics ; Shewanella/*chemistry/*physiology ; }, abstract = {Quantitative proteomics from low biomass, biofilm samples is not well documented. In this study we show successful use of SWATH-MS for quantitative proteomic analysis of a microbial electrochemically active biofilm. Shewanella oneidensis MR-1 was grown on carbon cloth electrodes under continuous anodic electrochemical polarizations in a bioelectrochemical system (BES). Using lactate as the electron donor, anodes serving as terminal microbial electron acceptors were operated at three different electrode potentials (+0.71 V, +0.21 V &amp; -0.19 V vs. SHE) and the development of catalytic activity was monitored by measuring the current traces over time. Once maximum current was reached (usually within 21-29 h) the electrochemical systems were shut off and biofilm proteins were extracted from the electrodes for proteomic assessment. SWATH-MS analysis identified 704 proteins, and quantitative comparison was made of those associated with tricarboxcylic acid (TCA) cycle. Metabolic differences detected between the biofilms suggested a branching of the S. oneidensis TCA cycle when grown at the different electrode potentials. In addition, the higher abundance of enzymes involved in the TCA cycle at higher potential indicates an increase in metabolic activity, which is expected given the assumed higher energy gains. This study demonstrates high numbers of identifications on BES biofilm samples can be achieved in comparison to what is currently reported. This is most likely due to the minimal preparation steps required for SWATH-MS.}, }
@article {pmid25520714, year = {2014}, author = {Valverde, A and Makhalanyane, TP and Cowan, DA}, title = {Contrasting assembly processes in a bacterial metacommunity along a desiccation gradient.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {668}, pmid = {25520714}, issn = {1664-302X}, abstract = {Understanding the relative influence of deterministic and stochastic processes in driving community assembly is a major goal in microbial ecology. Here, we have investigated the influence of these processes on bacterial community assembly in the lateral sediments of a salt pan along a desiccation gradient over a three-year period. We show that the role of deterministic processes increases in communities distant from the water line (shaped by drought), probably as a result of the interplay between abiotic and biotic factors. By contrast, the influence of stochastic processes on bacterial community assembly was higher in the sediments closest to the water line, more likely due to lower levels of abiotic stress. Our results demonstrate that both deterministic and stochastic processes influence bacterial community assembly in salt pan sediments, and that their relative influence varies along a desiccation gradient.}, }
@article {pmid25517598, year = {2015}, author = {Opipari, A and Franchi, L}, title = {Role of inflammasomes in intestinal inflammation and Crohn's disease.}, journal = {Inflammatory bowel diseases}, volume = {21}, number = {1}, pages = {173-181}, doi = {10.1097/MIB.0000000000000230}, pmid = {25517598}, issn = {1536-4844}, mesh = {Animals ; Crohn Disease/*immunology ; Humans ; Inflammasomes/*immunology ; Inflammation/*immunology ; Intestines/*immunology ; }, abstract = {: Inflammasomes are multiprotein complexes that process procytokines into mature forms of interleukin 1β and interleukin 18 and induce pyroptotic cell death. Evidence linking NLRP3, NLRC4, and NLRP6 inflammasomes to intestinal inflammation is reviewed to provide a basis to understand how the innate immune system discriminates pathogenic bacteria from commensal bacteria and shapes microbial ecology. Inflammasomes have a direct and important role limiting colitis by directing effective immune responses against pathogenic bacterial infections in the intestine. Chronic granulomatous disease is presented to reveal a contrasting proinflammatory effect of inflammasomes. This pathogenic effect is unmasked in a state of immunodeficiency where bacterial growth is poorly controlled increasing inflammasome activity. The role of inflammasomes in inflammation associated with Crohn's disease and ulcerative colitis is discussed. Finally, mechanistic studies linking genetic polymorphisms in ATG16L and NOD2 to inflammasome activation provide a basis for new hypotheses to explain how genetic polymorphism associated with Crohn's disease modulate intestinal inflammation. A deeper understanding of the role of inflammasomes in intestinal inflammation is expected to identify new ways of treating inflammatory bowel disease.}, }
@article {pmid25515425, year = {2015}, author = {Attermeyer, K and Tittel, J and Allgaier, M and Frindte, K and Wurzbacher, C and Hilt, S and Kamjunke, N and Grossart, HP}, title = {Effects of light and autochthonous carbon additions on microbial turnover of allochthonous organic carbon and community composition.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {361-371}, pmid = {25515425}, issn = {1432-184X}, mesh = {Bacteria/*classification/growth &amp; development ; Carbon/*chemistry ; DNA, Bacterial/genetics ; Ecosystem ; *Light ; Phylogeny ; Phytoplankton/growth &amp; development/microbiology ; Plant Leaves/microbiology ; Sequence Analysis, DNA ; }, abstract = {The fate of allochthonous dissolved organic carbon (DOC) in aquatic systems is primarily controlled by the turnover of heterotrophic bacteria. However, the roles that abiotic and biotic factors such as light and DOC release by aquatic primary producers play in the microbial decomposition of allochthonous DOC is not well understood. We therefore tested if light and autochthonous DOC additions would increase allochthonous DOC decomposition rates and change bacterial growth efficiencies and community composition (BCC). We established continuous growth cultures with different inocula of natural bacterial communities and alder leaf leachates (DOCleaf) with and without light exposure before amendment. Furthermore, we incubated DOCleaf together with autochthonous DOC from lysed phytoplankton cultures (DOCphyto). Our results revealed that pretreatments of DOCleaf with light resulted in a doubling of bacterial growth efficiency (BGE), whereas additions of DOCphyto or combined additions of DOCphyto and light had no effect on BGE. The change in BGE was not accompanied by shifts in the phylogenetic structure of the BCC, but BCC was influenced by the DOC source. Our results highlight that a doubling of BGE is not necessarily accompanied by a shift in BCC and that BCC is more strongly affected by resource properties.}, }
@article {pmid25515424, year = {2015}, author = {Amaroli, A}, title = {The Effects of Temperature Variation on the Sensitivity to Pesticides: a Study on the Slime Mould Dictyostelium discoideum (Protozoa).}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {244-254}, pmid = {25515424}, issn = {1432-184X}, mesh = {Analysis of Variance ; Butyrylcholinesterase/metabolism ; Dictyostelium/*drug effects/metabolism/*physiology ; HSP70 Heat-Shock Proteins/metabolism ; Immunoblotting ; Metals, Heavy/*toxicity ; Pesticides/*toxicity ; Reproduction/drug effects ; Spectrophotometry ; *Temperature ; }, abstract = {Slime moulds live in agricultural ecosystems, where they play an important role in the soil fertilization and in the battle against crop pathogens. In an agricultural soil, the amoebae are exposed to different stress factors such as pesticides and weather conditions. The use of pesticides increased up from 0.49 kg per hectare in 1961 to 2 kg in 2004, and the global greenhouse gas emission has grown 70% between 1970 and 2004 leading to a global fluctuation of average surface temperature. Therefore, the European Directive 2009/128/EC has led to a new approach to agriculture, with the transition from an old concept based on high use of pesticides and fossil fuels to an agriculture aware of biodiversity and health issues. We studied the effects of temperature variations and pesticides on Dictyostelium discoideum. We measured the fission rate, the ability to differentiate and the markers of stress such as the activity and presence of pseudocholinesterase and the presence of heat shock protein 70. Our results highlight how the sensitivity to zinc, aluminium, silver, copper, cadmium, mercury, diazinon and dicofol changes for a 2 °C variation from nothing/low to critical. Our work suggests considering, in future regulations, about the use of pesticides as their toxic effect on non-target organisms is strongly influenced by climate temperatures. In addition, there is a need for a new consideration of the protozoa, which takes into account recent researches about the presence in this microorganism of classical neurotransmitters that, similar to those in animals, make protozoa an innocent target of neurotoxic pesticides in the battle against the pest crops.}, }
@article {pmid25506341, year = {2014}, author = {Das, B}, title = {Mechanistic insights into filamentous phage integration in Vibrio cholerae.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {650}, pmid = {25506341}, issn = {1664-302X}, abstract = {Vibrio cholerae, the etiological agent of acute diarrhoeal disease cholera, harbors large numbers of lysogenic filamentous phages, contribute significantly to the host pathogenesis and provide fitness factors to the pathogen that help the bacterium to survive in natural environment. Most of the vibriophage genomes are not equipped with integrase and thus exploit two host-encoded tyrosine recombinases, XerC and XerD, for lysogenic conversion. Integration is site-specific and it occurs at dimer resolution site (dif) of either one or both chromosomes of V. cholerae. Each dif sequence contains two recombinase-binding sequences flanking a central region. The integration follows a sequential strand exchanges between dif and attP sites within a DNA-protein complex consisting of one pair of each recombinase and two DNA fragments. During entire process of recombination, both the DNA components and recombinases of the synaptic complex keep transiently interconnected. Within the context of synaptic complex, both of the actuated enzymes mediate cleavage of phosphodiester bonds. First cleavage generates a phosphotyrosyl-linked recombinase-DNA complex at the recombinase binding sequence and free 5'-hydroxyl end at the first base of the central region. Following the cleavage, the exposed bases with 5'-hydroxyl ends of the central region of dif and attP sites melt from their complementary strands and react with the recombinase-DNA phosphotyrosyl linkage of their recombining partner. Subsequent ligation between dif and attP strands requires complementary base pair interactions at the site of phosphodiester bond formation. Integration mechanism is mostly influenced by the compatibility of dif and attP sequences. dif sites are highly conserved across bacterial phyla. Different phage genomes have different attP sequences; therefore they rely on different mechanisms for integration. Here, I review our current understanding of integration mechanisms used by the vibriophages.}, }
@article {pmid25505456, year = {2014}, author = {Reis, MP and Avila, MP and Costa, PS and Barbosa, FA and Laanbroek, HJ and Chartone-Souza, E and Nascimento, AM}, title = {The influence of human settlement on the distribution and diversity of iron-oxidizing bacteria belonging to the Gallionellaceae in tropical streams.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {630}, pmid = {25505456}, issn = {1664-302X}, abstract = {Among the neutrophilic iron-oxidizing bacteria (FeOB), Gallionella is one of the most abundant genera in freshwater environments. By applying qPCR and DGGE based on 16S rRNA gene-directed primers targeting Gallionellaceae, we delineated the composition and abundance of the Gallionellaceae-related FeOB community in streams differentially affected by metal mining, and explored the relationships between these community characteristics and environmental variables. The sampling design included streams historically impacted by mining activity and a non-impacted stream. The sediment and water samples harbored a distinct community represented by Gallionella, Sideroxydans, and Thiobacillus species. Sequences affiliated with Gallionella were exclusively observed in sediments impacted by mining activities, suggesting an adaptation of this genus to these environments. In contrast, Sideroxydans-related sequences were found in all sediments including the mining impacted locations. The highest and lowest relative frequencies of Gallionellaceae-related FeOB were associated with the lowest and highest concentrations of Fe, respectively. The data enclosed here clearly show distinct species-specific ecological niches, with Gallionella species dominating in sediments impacted by anthropogenic activities over Sideroxydans species.}, }
@article {pmid25502075, year = {2015}, author = {Pautasso, M and Schlegel, M and Holdenrieder, O}, title = {Forest health in a changing world.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {826-842}, pmid = {25502075}, issn = {1432-184X}, mesh = {Climate Change ; Endophytes ; *Forests ; *Plant Diseases/etiology ; Trees/microbiology/*physiology ; }, abstract = {Forest pathology, the science of forest health and tree diseases, is operating in a rapidly developing environment. Most importantly, global trade and climate change are increasing the threat to forest ecosystems posed by new diseases. Various studies relevant to forest pathology in a changing world are accumulating, thus making it necessary to provide an update of recent literature. In this contribution, we summarize research at the interface between forest pathology and landscape ecology, biogeography, global change science and research on tree endophytes. Regional outbreaks of tree diseases are requiring interdisciplinary collaboration, e.g. between forest pathologists and landscape ecologists. When tree pathogens are widely distributed, the factors determining their broad-scale distribution can be studied using a biogeographic approach. Global change, the combination of climate and land use change, increased pollution, trade and urbanization, as well as invasive species, will influence the effects of forest disturbances such as wildfires, droughts, storms, diseases and insect outbreaks, thus affecting the health and resilience of forest ecosystems worldwide. Tree endophytes can contribute to biological control of infectious diseases, enhance tolerance to environmental stress or behave as opportunistic weak pathogens potentially competing with more harmful ones. New molecular techniques are available for studying the complete tree endobiome under the influence of global change stressors from the landscape to the intercontinental level. Given that exotic tree diseases have both ecologic and economic consequences, we call for increased interdisciplinary collaboration in the coming decades between forest pathologists and researchers studying endophytes with tree geneticists, evolutionary and landscape ecologists, biogeographers, conservation biologists and global change scientists and outline interdisciplinary research gaps.}, }
@article {pmid25502074, year = {2015}, author = {Zhang, HH and Huang, TL and Chen, SN and Yang, X and Lv, K and Sekar, R}, title = {Abundance and diversity of bacteria in oxygen minimum drinking water reservoir sediments studied by quantitative PCR and pyrosequencing.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {618-629}, pmid = {25502074}, issn = {1432-184X}, mesh = {Bacteria/*isolation &amp; purification ; China ; DNA, Bacterial/genetics/metabolism ; Drinking Water/*microbiology ; Geologic Sediments/*microbiology ; *Microbiota ; Molecular Sequence Data ; Oxygen/*analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Reservoir sediment is one of the most stressful environments for microorganisms due to periodically oxygen minimum conditions. In this study, the abundance and composition of bacteria associated with sediments from three drinking water reservoirs (Zhoucun, ZCR; Shibianyu, SBYR; and Jinpen, JPR) were investigated by quantitative polymerase chain reaction and 16S rRNA-based 454 pyrosequencing. The results of physico-chemical analysis of sediments showed that the organic matter and total nitrogen were significantly higher in ZCR as compared to JPR (P < 0.01). The bacterial abundance was 9.13 × 10(6), 1.14 × 10(7), and 6.35 × 10(6) copies/ng DNA in sediments of SBYR, ZCR, and JPR, respectively (P < 0.01). The pyrosequencing revealed a total of 9,673 operational taxonomic units, which were affiliated with 17 phyla. The dominant phylum was Firmicutes (56.83%) in JPR; whereas, the dominance of Proteobacteria was observed in SBYR with 40.38% and ZCR with 39.56%. The Shannon-Wiener diversity (H') was high in ZCR; whereas, Chao 1 richness was high in SBYR. The dominant genera were Clostridium with 42.15% and Bacillus with 20.44% in JPR. Meanwhile, Dechloromonas with 14.80% and Smithella with 7.20% were dominated in ZCR, and Bacillus with 45.45% and Acinetobacter with 5.15% in SBYR. The heat map profiles and redundancy analysis indicated substantial differences in sediment bacterial community composition among three reservoirs. Moreover, it appears from the results that physico-chemical variables of sediments including pH, organic matter, total nitrogen, and available phosphorous played key roles in shaping the bacterial community diversity. The results obtained from this study will broaden our understanding on the bacterial community structure of sediments in oxygen minimum and stressful freshwater environments.}, }
@article {pmid25501892, year = {2015}, author = {Liu, J and Liu, X and Wang, M and Qiao, Y and Zheng, Y and Zhang, XH}, title = {Bacterial and archaeal communities in sediments of the north Chinese marginal seas.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {105-117}, pmid = {25501892}, issn = {1432-184X}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Base Sequence ; China ; Chlorophyll/analysis ; Chlorophyll A ; Geography ; Geologic Sediments/chemistry/*microbiology ; *Microbiota ; Molecular Sequence Data ; Oceans and Seas ; Oxygen/analysis ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Seawater/chemistry ; Sequence Analysis, RNA ; Temperature ; }, abstract = {Microbial communities of the Chinese marginal seas have rarely been reported. Here, bacterial and archaeal community structures and abundance in the surface sediment of four sea areas including the Bohai Sea (BS), North Yellow Sea (NYS), South Yellow Sea (SYS), and the north East China Sea (NECS) were surveyed by 16S ribosomal RNA (rRNA) gene pyrosequencing and quantitative PCR. The results showed that microbial communities of the four geographic areas were distinct from each other at the operational taxonomic unit (OTU) level, whereas the microbial communities of the BS, NYS, and SYS were more similar to each other than to the NECS at higher taxonomic levels. Across all samples, Bacteria were numerically dominant relative to Archaea, and among them, Gammaproteobacteria and Euryarchaeota were predominant in the BS, NYS, and SYS, while Deltaproteobacteria and Thaumarchaeota were prevalent in the NECS. The most abundant bacterial genera were putative sulfur oxidizer and sulfate reducer, suggesting that sulfur cycle processes might prevail in these areas, and the high abundance of dsrB (10(7)-10(8) copies g(-1)) in all sites verified the dominance of sulfate reducer in the north Chinese marginal seas. The differences in sediment sources among the sampling areas were potential explanations for the observed microbial community variations. Furthermore, temperature and dissolved oxygen of bottom water were significant environmental factors in determining both bacterial and archaeal communities, whereas chlorophyll a in sediment was significant only in structuring archaeal community. This study presented an outline of benthic microbial communities and provided insights into understanding the biogeochemical cycles in sediments of the north Chinese marginal seas.}, }
@article {pmid25501891, year = {2015}, author = {Siles, JA and Cajthaml, T and Hernández, P and Pérez-Mendoza, D and García-Romera, I and Sampedro, I}, title = {Shifts in soil chemical properties and bacterial communities responding to biotransformed dry olive residue used as organic amendment.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {231-243}, pmid = {25501891}, issn = {1432-184X}, mesh = {Actinobacteria/*growth &amp; development ; Analysis of Variance ; Biodegradation, Environmental ; Biotransformation ; Carbon/analysis ; Chromatography, Gas ; Coriolaceae/metabolism ; Denaturing Gradient Gel Electrophoresis ; Fatty Acids/analysis ; Fusarium/metabolism ; Hydrogen-Ion Concentration ; Nitrogen/analysis ; Olea/*chemistry/metabolism ; Phenols/analysis ; Potassium/analysis ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Soil/*chemistry ; *Soil Microbiology ; Spain ; Time Factors ; Waste Products/analysis ; }, abstract = {Dry olive residue (DOR) is a waste product derived from olive oil extraction and has been proposed as an organic amendment. However, it has been demonstrated that a pre-treatment, such as its transformation by saprophytic fungi, is required before DOR soil application. A greenhouse experiment was designed where 0 and 50 g kg(-1) of raw DOR (DOR), Coriolopsis floccosa-transformed DOR (CORDOR) and Fusarium oxysporum-transformed DOR (FUSDOR) were added to soil. Analyses of the soil chemical properties as well as the structure and relative abundance of bacterial and actinobacterial communities were conducted after 0, 30 and 60 days following amendment. The different amendments produced a slight decrease in soil pH and significant increases in carbon fractions, C/N ratios, phenols and K, with these increases being more significant after DOR application. Quantitative PCR assays of the 16S rRNA gene and PLFA analyses showed that all amendments favoured bacterial growth at 30 and 60 days, although actinobacterial proliferation was more evident after CORDOR and FUSDOR application at 60 days. Bacterial and actinobacterial DGGE multivariate analyses showed that the amendments produced structural changes in both communities, especially after 60 days of amendment. PLFA data analysis identified changes in soil microbial communities according to the amendment considered, with FUSDOR and CORDOR being less disruptive than DOR. Finally, integrated analysis of all data monitored in the present study enabled us to conclude that the greatest impact on soil properties was caused by DOR at 30 days and that soil showed some degree of resilience after this time.}, }
@article {pmid25501890, year = {2015}, author = {Yang, Y and Wang, Z and He, T and Dai, Y and Xie, S}, title = {Sediment bacterial communities associated with anaerobic biodegradation of bisphenol A.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {97-104}, pmid = {25501890}, issn = {1432-184X}, mesh = {Analysis of Variance ; Bacteria, Anaerobic/*metabolism ; Base Sequence ; Beijing ; Benzhydryl Compounds/*metabolism ; Biodegradation, Environmental ; Cell Culture Techniques ; DNA Primers/genetics ; Geologic Sediments/*chemistry/*microbiology ; *Microbiota ; Molecular Sequence Data ; Phenols/*metabolism ; *Rivers ; Sequence Analysis, DNA ; }, abstract = {Bisphenol A (BPA) is one of the endocrine-disrupting chemicals that are ubiquitous in aquatic environments. Biodegradation is a major way to clean up the BPA pollution in sediments. However, information on the effective BPA biodegradation in anaerobic sediments is still lacking. The present study investigated the biodegradation potential of BPA in river sediment under nitrate- or sulfate-reducing conditions. After 120-day incubation, a high removal of BPA (93 or 89%) was found in sediment microcosms (amended with 50 mg kg(-1) BPA) under these two anaerobic conditions. Illumina MiSeq sequencing analysis indicated that Proteobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, and Actinobacteria were the major bacterial groups in BPA-degrading sediments. The shift in bacterial community structure could occur with BPA biodegradation.}, }
@article {pmid25501889, year = {2015}, author = {Stempfhuber, B and Engel, M and Fischer, D and Neskovic-Prit, G and Wubet, T and Schöning, I and Gubry-Rangin, C and Kublik, S and Schloter-Hai, B and Rattei, T and Welzl, G and Nicol, GW and Schrumpf, M and Buscot, F and Prosser, JI and Schloter, M}, title = {pH as a Driver for Ammonia-Oxidizing Archaea in Forest Soils.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {879-883}, pmid = {25501889}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Archaea/*physiology ; *Forests ; Germany ; Hydrogen-Ion Concentration ; *Microbiota ; Oxidation-Reduction ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {In this study, we investigated the impact of soil pH on the diversity and abundance of archaeal ammonia oxidizers in 27 different forest soils across Germany. DNA was extracted from topsoil samples, the amoA gene, encoding ammonia monooxygenase, was amplified; and the amplicons were sequenced using a 454-based pyrosequencing approach. As expected, the ratio of archaeal (AOA) to bacterial (AOB) ammonia oxidizers' amoA genes increased sharply with decreasing soil pH. The diversity of AOA differed significantly between sites with ultra-acidic soil pH (<3.5) and sites with higher pH values. The major OTUs from soil samples with low pH could be detected at each site with a soil pH <3.5 but not at sites with pH >4.5, regardless of geographic position and vegetation. These OTUs could be related to the Nitrosotalea group 1.1 and the Nitrososphaera subcluster 7.2, respectively, and showed significant similarities to OTUs described from other acidic environments. Conversely, none of the major OTUs typical of sites with a soil pH >4.6 could be found in the ultra- and extreme acidic soils. Based on a comparison with the amoA gene sequence data from a previous study performed on agricultural soils, we could clearly show that the development of AOA communities in soils with ultra-acidic pH (<3.5) is mainly triggered by soil pH and is not influenced significantly by the type of land use, the soil type, or the geographic position of the site, which was observed for sites with acido-neutral soil pH.}, }
@article {pmid25501888, year = {2015}, author = {Gonzalez-Gil, G and Sougrat, R and Behzad, AR and Lens, PN and Saikaly, PE}, title = {Microbial community composition and ultrastructure of granules from a full-scale anammox reactor.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {118-131}, pmid = {25501888}, issn = {1432-184X}, mesh = {Ammonium Compounds/*metabolism ; Archaea/*genetics/*metabolism/ultrastructure ; Bacteria, Anaerobic/*genetics/*metabolism/ultrastructure ; Base Sequence ; Bioreactors/*microbiology ; Calcium Phosphates/chemistry ; *Microbiota ; Microscopy, Electron ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Water Purification/methods ; }, abstract = {Granules in anammox reactors contain besides anammox bacteria other microbial communities whose identity and relationship with the anammox bacteria are not well understood. High calcium concentrations are often supplied to anammox reactors to obtain sufficient bacterial aggregation and biomass retention. The aim of this study was to provide the first characterization of bacterial and archaeal communities in anammox granules from a full-scale anammox reactor and to explore on the possible role of calcium in such aggregates. High magnification imaging using backscattered electrons revealed that anammox bacteria may be embedded in calcium phosphate precipitates. Pyrosequencing of 16S rRNA gene fragments showed, besides anammox bacteria (Brocadiacea, 32%), substantial numbers of heterotrophic bacteria Ignavibacteriacea (18%) and Anaerolinea (7%) along with heterotrophic denitrifiers Rhodocyclacea (9%), Comamonadacea (3%), and Shewanellacea (3%) in the granules. It is hypothesized that these bacteria may form a network in which heterotrophic denitrifiers cooperate to achieve a well-functioning denitrification system as they can utilize the nitrate intrinsically produced by the anammox reaction. This network may provide a niche for the proliferation of archaea. Hydrogenotrophic methananogens, which scavenge the key fermentation product H2, were the most abundant archaea detected. Cells resembling the polygon-shaped denitrifying methanotroph Candidatus Methylomirabilis oxyfera were observed by electron microscopy. It is hypothesized that the anammox process in a full-scale reactor triggers various reactions overall leading to efficient denitrification and a sink of carbon as biomass in anammox granules.}, }
@article {pmid25501887, year = {2015}, author = {Porres-Osante, N and Sáenz, Y and Somalo, S and Torres, C}, title = {Characterization of Beta-lactamases in Faecal Enterobacteriaceae Recovered from Healthy Humans in Spain: Focusing on AmpC Polymorphisms.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {132-140}, pmid = {25501887}, issn = {1432-184X}, mesh = {Ampicillin Resistance/*genetics ; Bacterial Proteins/*genetics ; Base Sequence ; Electrophoresis, Gel, Pulsed-Field ; Enterobacteriaceae/*enzymology ; Feces/*microbiology ; Humans ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Phylogeny ; Plasmids/genetics ; Sequence Analysis, DNA ; Spain ; Species Specificity ; beta-Lactamases/*genetics ; }, abstract = {The intestinal tract is a huge reservoir of Enterobacteriaceae, some of which are opportunist pathogens. Several genera of these bacteria harbour intrinsic antibiotic resistance genes, such as ampC genes in species of Citrobacter, Enterobacter or Escherichia genera. In this work, beta-lactamases and other resistance mechanisms have been characterized in Enterobacteriaceae isolates recovered from healthy human faecal samples, focusing on the ampC beta-lactamase genes. Fifty human faecal samples were obtained, and 70 Enterobacteriaceae bacteria were isolated: 44 Escherichia coli, 4 Citrobacter braakii, 9 Citrobacter freundii, 8 Enterobacter cloacae, 1 Proteus mirabilis, 1 Proteus vulgaris, 1 Klebsiella oxytoca, 1 Serratia sp. and 1 Cronobacter sp. A high percentage of resistance to ampicillin was detected (57%), observing the AmpC phenotype in 22 isolates (31%) and the ESBL phenotype in 3 isolates. AmpC molecular characterization showed high diversity into bla CMY and bla ACT genes from Citrobacter and Enterobacter species, respectively, and the pulsed-field gel electrophoresis (PFGE) analysis demonstrated low clonality among them. The prevalence of people colonized by strains carrying plasmid-mediated ampC genes obtained in this study was 2%. The unique plasmid-mediated bla AmpC identified in this study was the bla CMY-2 gene, detected in an E. coli isolate ascribed to the sequence type ST405 which belonged to phylogenetic group D. The hybridization and conjugation experiments demonstrated that the ISEcp1-bla CMY-2-blc structure was carried by a ~78-kb self-transferable IncK plasmid. This study shows a high polymorphism among beta-lactamase genes in Enterobacteriaceae from healthy people microbiota. Extensive AmpC-carrier studies would provide important information and could allow the anticipation of future global health problems.}, }
@article {pmid25501886, year = {2015}, author = {Schaible, GA and Strobel, GA and Mends, MT and Geary, B and Sears, J}, title = {Characterization of an Endophytic Gloeosporium sp. and Its Novel Bioactivity with "Synergistans".}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {41-50}, pmid = {25501886}, issn = {1432-184X}, mesh = {Anti-Infective Agents/analysis/*pharmacology ; Ascomycota/*chemistry/classification/*genetics ; Biological Assay/methods ; Botrytis/drug effects ; DNA Primers/genetics ; DNA, Intergenic/genetics ; Drug Synergism ; Endophytes/chemistry/classification/*genetics ; Furans/analysis ; Isobutyrates/pharmacology ; Phytophthora/drug effects ; Pyrones/analysis/*pharmacology ; RNA, Ribosomal, 18S/genetics ; Rhizoctonia/drug effects ; Terpenes/analysis ; Tsuga/*microbiology ; Verticillium/drug effects ; }, abstract = {Gloeosporium sp. (OR-10) was isolated as an endophyte of Tsuga heterophylla (Western hemlock). Both ITS and 18S sequence analyses indicated that the organism best fits either Hypocrea spp. or Trichoderma spp., but neither of these organisms possess conidiophores associated with acervuli, in which case the endophytic isolate OR-10 does. Therefore, the preferred taxonomic assignment was primarily based on the morphological features of the organism as one belonging to the genus Gloeosporium sp. These taxonomic observations clearly point out that limited ITS and 18S sequence information can be misleading when solely used in making taxonomic assignments. The volatile phase of this endophyte was active against a number of plant pathogenic fungi including Phytophthora palmivora, Rhizoctonia solani, Ceratocystis ulmi, Botrytis cinerea, and Verticillium dahliae. Among several terpenes and furans, the most abundantly produced compound in the volatile phase was 6-pentyl-2H-pyran-2-one, a compound possessing antimicrobial activities. When used in conjunction with microliter amounts of any in a series of esters or isobutyric acid, an enhanced inhibitory response occurred with each test fungus that was greater than that exhibited by Gloeosporium sp. or the compounds tested individually. Compounds behaving in this manner are hereby designated "synergistans." An expression of the "median synergistic effect," under prescribed conditions, has been termed the mSE50. This value describes the amount of a potential synergistan that is required to yield an additional median 50% inhibition of a target organism. In this report, the mSE50s are reported for a series of esters and isobutyric acid. The results indicated that isoamyl acetate, allyl acetate, and isobutyric acid generally possessed the lowest mSE50 values. The value and potential importance of these microbial synergistic effects to the microbial environment are also discussed.}, }
@article {pmid25501483, year = {2015}, author = {Greening, C and Constant, P and Hards, K and Morales, SE and Oakeshott, JG and Russell, RJ and Taylor, MC and Berney, M and Conrad, R and Cook, GM}, title = {Atmospheric hydrogen scavenging: from enzymes to ecosystems.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {4}, pages = {1190-1199}, pmid = {25501483}, issn = {1098-5336}, mesh = {Actinobacteria/enzymology/genetics/*metabolism ; Air Microbiology ; Atmosphere/chemistry ; Bacterial Proteins/genetics/*metabolism ; Ecosystem ; Hydrogen/*metabolism ; Hydrogenase/genetics/*metabolism ; }, abstract = {We have known for 40 years that soils can consume the trace amounts of molecular hydrogen (H2) found in the Earth’s atmosphere.This process is predicted to be the most significant term in the global hydrogen cycle. However, the organisms and enzymes responsible for this process were only recently identified. Pure culture experiments demonstrated that several species of Actinobacteria, including streptomycetes and mycobacteria, can couple the oxidation of atmospheric H2 to the reduction of ambient O2. A combination of genetic, biochemical, and phenotypic studies suggest that these organisms primarily use this fuel source to sustain electron input into the respiratory chain during energy starvation. This process is mediated by a specialized enzyme, the group 5 [NiFe]-hydrogenase, which is unusual for its high affinity, oxygen insensitivity, and thermostability. Atmospheric hydrogen scavenging is a particularly dependable mode of energy generation, given both the ubiquity of the substrate and the stress tolerance of its catalyst. This minireview summarizes the recent progress in understanding how and why certain organisms scavenge atmospheric H2. In addition, it provides insight into the wider significance of hydrogen scavenging in global H2 cycling and soil microbial ecology.}, }
@article {pmid25500508, year = {2015}, author = {Gillings, MR and Gaze, WH and Pruden, A and Smalla, K and Tiedje, JM and Zhu, YG}, title = {Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution.}, journal = {The ISME journal}, volume = {9}, number = {6}, pages = {1269-1279}, pmid = {25500508}, issn = {1751-7370}, mesh = {Anti-Bacterial Agents/chemistry ; Bacteria/drug effects/*genetics ; DNA Transposable Elements ; Drug Resistance, Bacterial ; Environmental Monitoring/*methods ; *Environmental Pollution ; Gene Transfer, Horizontal ; Genetic Variation ; Integrases/*genetics ; Integrons/*genetics ; Metals, Heavy/*analysis ; }, abstract = {Around all human activity, there are zones of pollution with pesticides, heavy metals, pharmaceuticals, personal care products and the microorganisms associated with human waste streams and agriculture. This diversity of pollutants, whose concentration varies spatially and temporally, is a major challenge for monitoring. Here, we suggest that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because: (1) intI1 is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals; (2) it is found in a wide variety of pathogenic and nonpathogenic bacteria; (3) its abundance can change rapidly because its host cells can have rapid generation times and it can move between bacteria by horizontal gene transfer; and (4) a single DNA sequence variant of intI1 is now found on a wide diversity of xenogenetic elements, these being complex mosaic DNA elements fixed through the agency of human selection. Here we review the literature examining the relationship between anthropogenic impacts and the abundance of intI1, and outline an approach by which intI1 could serve as a proxy for anthropogenic pollution.}, }
@article {pmid25500507, year = {2015}, author = {Stevenson, A and Cray, JA and Williams, JP and Santos, R and Sahay, R and Neuenkirchen, N and McClure, CD and Grant, IR and Houghton, JD and Quinn, JP and Timson, DJ and Patil, SV and Singhal, RS and Antón, J and Dijksterhuis, J and Hocking, AD and Lievens, B and Rangel, DE and Voytek, MA and Gunde-Cimerman, N and Oren, A and Timmis, KN and McGenity, TJ and Hallsworth, JE}, title = {Is there a common water-activity limit for the three domains of life?.}, journal = {The ISME journal}, volume = {9}, number = {6}, pages = {1333-1351}, pmid = {25500507}, issn = {1751-7370}, support = {BB/F003471/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/F00351X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBF/00351X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBF/003471/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Archaea/metabolism ; Artifacts ; Ascomycota/metabolism ; Aspergillus/*metabolism ; Bacteria/*metabolism ; Carbohydrates/chemistry ; Fungi/metabolism ; Halobacterium/*metabolism ; Hydrogen-Ion Concentration ; Sodium Chloride/chemistry ; Staphylococcus aureus/metabolism ; Temperature ; Water/physiology ; Water Microbiology ; }, abstract = {Archaea and Bacteria constitute a majority of life systems on Earth but have long been considered inferior to Eukarya in terms of solute tolerance. Whereas the most halophilic prokaryotes are known for an ability to multiply at saturated NaCl (water activity (a(w)) 0.755) some xerophilic fungi can germinate, usually at high-sugar concentrations, at values as low as 0.650-0.605 a(w). Here, we present evidence that halophilic prokayotes can grow down to water activities of <0.755 for Halanaerobium lacusrosei (0.748), Halobacterium strain 004.1 (0.728), Halobacterium sp. NRC-1 and Halococcus morrhuae (0.717), Haloquadratum walsbyi (0.709), Halococcus salifodinae (0.693), Halobacterium noricense (0.687), Natrinema pallidum (0.681) and haloarchaeal strains GN-2 and GN-5 (0.635 a(w)). Furthermore, extrapolation of growth curves (prone to giving conservative estimates) indicated theoretical minima down to 0.611 aw for extreme, obligately halophilic Archaea and Bacteria. These were compared with minima for the most solute-tolerant Bacteria in high-sugar (or other non-saline) media (Mycobacterium spp., Tetragenococcus halophilus, Saccharibacter floricola, Staphylococcus aureus and so on) and eukaryotic microbes in saline (Wallemia spp., Basipetospora halophila, Dunaliella spp. and so on) and high-sugar substrates (for example, Xeromyces bisporus, Zygosaccharomyces rouxii, Aspergillus and Eurotium spp.). We also manipulated the balance of chaotropic and kosmotropic stressors for the extreme, xerophilic fungi Aspergillus penicilloides and X. bisporus and, via this approach, their established water-activity limits for mycelial growth (∼0.65) were reduced to 0.640. Furthermore, extrapolations indicated theoretical limits of 0.632 and 0.636 a(w) for A. penicilloides and X. bisporus, respectively. Collectively, these findings suggest that there is a common water-activity limit that is determined by physicochemical constraints for the three domains of life.}, }
@article {pmid25495929, year = {2015}, author = {Ramond, JB and Makhalanyane, TP and Tuffin, MI and Cowan, DA}, title = {Normalization of environmental metagenomic DNA enhances the discovery of under-represented microbial community members.}, journal = {Letters in applied microbiology}, volume = {60}, number = {4}, pages = {359-366}, doi = {10.1111/lam.12380}, pmid = {25495929}, issn = {1472-765X}, mesh = {Bacteria/classification/*genetics ; Base Sequence ; DNA, Bacterial/*genetics ; Ecosystem ; Gene Library ; Metagenomics/*methods ; Microbial Consortia/*genetics ; Molecular Sequence Data ; Molecular Typing/*methods ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {UNLABELLED: Normalization is a procedure classically employed to detect rare sequences in cellular expression profiles (i.e. cDNA libraries). Here, we present a normalization protocol involving the direct treatment of extracted environmental metagenomic DNA with S1 nuclease, referred to as normalization of metagenomic DNA: NmDNA. We demonstrate that NmDNA, prior to post hoc PCR-based experiments (16S rRNA gene T-RFLP fingerprinting and clone library), increased the diversity of sequences retrieved from environmental microbial communities by detection of rarer sequences. This approach could be used to enhance the resolution of detection of ecologically relevant rare members in environmental microbial assemblages and therefore is promising in enabling a better understanding of ecosystem functioning.<br><br>This study is the first testing 'normalization' on environmental metagenomic DNA (mDNA). The aim of this procedure was to improve the identification of rare phylotypes in environmental communities. Using hypoliths as model systems, we present evidence that this post-mDNA extraction molecular procedure substantially enhances the detection of less common phylotypes and could even lead to the discovery of novel microbial genotypes within a given environment.}, }
@article {pmid25494364, year = {2014}, author = {Kim, SY and Pramanik, P and Bodelier, PL and Kim, PJ}, title = {Cattle Manure Enhances Methanogens Diversity and Methane Emissions Compared to Swine Manure under Rice Paddy.}, journal = {PloS one}, volume = {9}, number = {12}, pages = {e113593}, pmid = {25494364}, issn = {1932-6203}, mesh = {Agriculture ; Animals ; Archaea/genetics ; Carbon/analysis ; *Cattle ; DNA, Archaeal ; *Fertilizers ; *Manure/analysis ; *Methane ; *Oryza/growth &amp; development ; Phylogeny ; *Soil/chemistry ; Soil Microbiology ; *Swine ; }, abstract = {Livestock manures are broadly used in agriculture to improve soil quality. However, manure application can increase the availability of organic carbon, thereby facilitating methane (CH4) production. Cattle and swine manures are expected to have different CH4 emission characteristics in rice paddy soil due to the inherent differences in composition as a result of contrasting diets and digestive physiology between the two livestock types. To compare the effect of ruminant and non-ruminant animal manure applications on CH4 emissions and methanogenic archaeal diversity during rice cultivation (June to September, 2009), fresh cattle and swine manures were applied into experimental pots at 0, 20 and 40 Mg fresh weight (FW) ha-1 in a greenhouse. Applications of manures significantly enhanced total CH4 emissions as compared to chemical fertilization, with cattle manure leading to higher emissions than swine manure. Total organic C contents in cattle (466 g kg-1) and swine (460 g kg-1) manures were of comparable results. Soil organic C (SOC) contents were also similar between the two manure treatments, but dissolved organic C (DOC) was significantly higher in cattle than swine manure. The mcrA gene copy numbers were significantly higher in cattle than swine manure. Diverse groups of methanogens which belong to Methanomicrobiaceae were detected only in cattle-manured but not in swine-manured soil. Methanogens were transferred from cattle manure to rice paddy soils through fresh excrement. In conclusion, cattle manure application can significantly increase CH4 emissions in rice paddy soil during cultivation, and its pretreatment to suppress methanogenic activity without decreasing rice productivity should be considered.}, }
@article {pmid25492472, year = {2015}, author = {Macpherson, AJ and McCoy, KD}, title = {Standardised animal models of host microbial mutualism.}, journal = {Mucosal immunology}, volume = {8}, number = {3}, pages = {476-486}, pmid = {25492472}, issn = {1935-3456}, support = {281785/ERC_/European Research Council/International ; }, mesh = {Animals ; Embryo Transfer ; *Founder Effect ; Genetic Heterogeneity ; Germ-Free Life/*immunology ; Germ-Line Mutation ; Host-Pathogen Interactions ; Humans ; Mice, Transgenic ; Microbiota/*immunology ; Models, Animal ; Symbiosis/*immunology ; }, abstract = {An appreciation of the importance of interactions between microbes and multicellular organisms is currently driving research in biology and biomedicine. Many human diseases involve interactions between the host and the microbiota, so investigating the mechanisms involved is important for human health. Although microbial ecology measurements capture considerable diversity of the communities between individuals, this diversity is highly problematic for reproducible experimental animal models that seek to establish the mechanistic basis for interactions within the overall host-microbial superorganism. Conflicting experimental results may be explained away through unknown differences in the microbiota composition between vivaria or between the microenvironment of different isolated cages. In this position paper, we propose standardised criteria for stabilised and defined experimental animal microbiotas to generate reproducible models of human disease that are suitable for systematic experimentation and are reproducible across different institutions.}, }
@article {pmid25488342, year = {2015}, author = {Song, C and van der Voort, M and van de Mortel, J and Hassan, KA and Elbourne, LD and Paulsen, IT and Loper, JE and Raaijmakers, JM}, title = {The Rsm regulon of plant growth-promoting Pseudomonas fluorescens SS101: role of small RNAs in regulation of lipopeptide biosynthesis.}, journal = {Microbial biotechnology}, volume = {8}, number = {2}, pages = {296-310}, pmid = {25488342}, issn = {1751-7915}, mesh = {Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Lipopeptides/*biosynthesis ; Pseudomonas fluorescens/*genetics/*metabolism ; RNA, Small Untranslated/*metabolism ; *Regulon ; }, abstract = {The rhizobacterium Pseudomonas fluorescens SS101 inhibits growth of oomycete and fungal pathogens, and induces resistance in plants against pathogens and insects. To unravel regulatory pathways of secondary metabolite production in SS101, we conducted a genome-wide search for sRNAs and performed transcriptomic analyses to identify genes associated with the Rsm (repressor of secondary metabolites) regulon. In silico analysis led to the identification of 16 putative sRNAs in the SS101 genome. In frame deletion of the sRNAs rsmY and rsmZ showed that the Rsm system regulates the biosynthesis of the lipopeptide massetolide A and involves the two repressor proteins RsmA and RsmE, with the LuxR-type transcriptional regulator MassAR as their most likely target. Transcriptome analyses of the rsmYZ mutant further revealed that genes associated with iron acquisition, motility and chemotaxis were significantly upregulated, whereas genes of the type VI secretion system were downregulated. Comparative transcriptomic analyses showed that most, but not all, of the genes controlled by RsmY/RsmZ are also controlled by the GacS/GacA two-component system. We conclude that the Rsm regulon of P. fluorescens SS101 plays a critical role in the regulation of lipopeptide biosynthesis and controls the expression of other genes involved in motility, competition and survival in the plant rhizosphere.}, }
@article {pmid25487887, year = {2015}, author = {Benner, J and De Smet, D and Ho, A and Kerckhof, FM and Vanhaecke, L and Heylen, K and Boon, N}, title = {Exploring methane-oxidizing communities for the co-metabolic degradation of organic micropollutants.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {8}, pages = {3609-3618}, doi = {10.1007/s00253-014-6226-1}, pmid = {25487887}, issn = {1432-0614}, mesh = {Copper/metabolism ; *Environmental Microbiology ; Environmental Pollutants/*metabolism ; Enzyme Inhibitors/metabolism ; *Microbial Consortia ; Organic Chemicals/*metabolism ; Oxidation-Reduction ; }, abstract = {Methane-oxidizing cultures from five different inocula were enriched to be used for co-metabolic degradation of micropollutants. In a first screening, 18 different compounds were tested for degradation with the cultures as well as with four pure methane-oxidizing bacterial (MOB) strains. The tested compounds included pharmaceuticals, chemical additives, pesticides, and their degradation products. All enriched cultures were successful in the degradation of at least four different pollutants, but the compounds degraded most often were sulfamethoxazole (SMX) and benzotriazole (BTZ). Addition of acetylene, a specific methane monooxygenase (MMO) inhibitor, revealed that SMX and BTZ were mainly degraded co-metabolically by the present MOB. The pure MOB cultures exhibited less degradation potential, while SMX and BTZ were also degraded by three of the four tested pure strains. For MOB, copper (Cu(2+)) concentration is often an important factor, as several species have the ability to express a soluble MMO (sMMO) if the Cu(2+) concentration is low. In literature, this enzyme is often described to have a broader compound range for co-metabolic degradation of pollutants, in particular when it comes to aromatic structures. However, this study indicated that co-metabolic degradation of the aromatic compounds SMX and BTZ was possible at high Cu(2+) concentration, most probably catalyzed by pMMO.}, }
@article {pmid25487328, year = {2015}, author = {Warinner, C and Speller, C and Collins, MJ}, title = {A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130376}, pmid = {25487328}, issn = {1471-2970}, support = {097829/Z/11/A//Wellcome Trust/United Kingdom ; }, mesh = {Archaeology/*methods/trends ; Dental Calculus/*microbiology ; *Fossils ; High-Throughput Nucleotide Sequencing/methods/trends ; Humans ; Microbiological Techniques/*methods/trends ; Microbiota/*genetics ; Paleodontology/*methods/trends ; }, abstract = {The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes.}, }
@article {pmid25484877, year = {2014}, author = {Ghosh, D and Bhadury, P and Routh, J}, title = {Diversity of arsenite oxidizing bacterial communities in arsenic-rich deltaic aquifers in West Bengal, India.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {602}, pmid = {25484877}, issn = {1664-302X}, abstract = {High arsenic (As) concentration in groundwater has affected human health, particularly in South-East Asia putting millions of people at risk. Biogeochemical cycling of As carried out by different bacterial groups are suggested to control the As fluxes in aquifers. A functional diversity approach in link with As precipitation was adopted to study bacterial community structures and their variation within the As contaminated Bengal Delta Plain (BDP) aquifers of India. Groundwater samples collected from two shallow aquifers in Karimpur II (West Bengal, India), during years 2010 and 2011, were investigated to trace the effects immediately after monsoon period (precipitation) on community structure and diversity of bacterial assemblages with a focus on arsenite oxidizing bacterial phyla for two successive years. The study focused on amplification, clone library generation and sequencing of the arsenite oxidase large sub-unit gene aioA and 16S rRNA marker, with respect to changes in elemental concentrations. New set of primers were designed to amplify the aioA gene as a phylogenetic marker to study taxonomically diverse arsenite oxidizing bacterial groups in these aquifers. The overall narrow distribution of bacterial communities based on aioA and 16S rRNA sequences observed was due to poor nutrient status and anoxic conditions in these As contaminated aquifers. Proteobacteria was the dominant phylum detected, within which Acidovorax, Hydrogenophaga, Albidiferax, Bosea, and Polymorphum were the major arsenite oxidizing bacterial genera based on the number of clones sequenced. The structure of bacterial assemblages including those of arsenite oxidizing bacteria seems to have been affected by increase in major elemental concentrations (e.g., As, Fe, S, and Si) within two sampling sessions, which was supported by statistical analyses. One of the significant findings of this study is detection of novel lineages of 16S rRNA-like bacterial sequences indicating presence of indigenous bacterial communities BDP wells that can play important role in biogeochemical cycling of elements including As.}, }
@article {pmid25483864, year = {2014}, author = {Méthot, PO and Alizon, S}, title = {What is a pathogen? Toward a process view of host-parasite interactions.}, journal = {Virulence}, volume = {5}, number = {8}, pages = {775-785}, pmid = {25483864}, issn = {2150-5608}, mesh = {Animals ; Bacteria/pathogenicity ; Biological Evolution ; Fungi/pathogenicity ; Genetic Variation ; *Host-Parasite Interactions ; *Host-Pathogen Interactions ; Humans ; Virulence/*genetics ; Viruses/pathogenicity ; }, abstract = {Until quite recently and since the late 19(th) century, medical microbiology has been based on the assumption that some micro-organisms are pathogens and others are not. This binary view is now strongly criticized and is even becoming untenable. We first provide a historical overview of the changing nature of host-parasite interactions, in which we argue that large-scale sequencing not only shows that identifying the roots of pathogenesis is much more complicated than previously thought, but also forces us to reconsider what a pathogen is. To address the challenge of defining a pathogen in post-genomic science, we present and discuss recent results that embrace the microbial genetic diversity (both within- and between-host) and underline the relevance of microbial ecology and evolution. By analyzing and extending earlier work on the concept of pathogen, we propose pathogenicity (or virulence) should be viewed as a dynamical feature of an interaction between a host and microbes.}, }
@article {pmid25483618, year = {2015}, author = {Verhagen, P and Destino, C and Boon, N and De Gelder, L}, title = {Spatial heterogeneity in degradation characteristics and microbial community composition of pesticide biopurification systems.}, journal = {Journal of applied microbiology}, volume = {118}, number = {2}, pages = {368-378}, doi = {10.1111/jam.12716}, pmid = {25483618}, issn = {1365-2672}, mesh = {Aniline Compounds/metabolism ; Bacteria/isolation &amp; purification/metabolism ; Biodegradation, Environmental ; Chlorpropham/metabolism ; Pesticides/*metabolism ; Water Pollutants/*metabolism ; Water Purification ; }, abstract = {AIMS: To investigate spatial and temporal differences in degradation characteristics and microbial community composition of pesticide biopurification systems.<br><br>METHODS AND RESULTS: Pilot-scale biofilters were supplemented with the potato-sprouting suppressant chloropropham. Two biofilters were inoculated with a chloropropham-degrading mixed culture, while the other two were not inoculated. Biodegradation rate, size and composition of the microbial community were monitored during 72&#xa0;days at different biofilter depths. First of all, results showed that inoculation was not necessary to obtain efficient degradation although it shortens the biofilter's start-up period. Secondly, a higher biodegradation rate and chloropropham- and 3-chloroaniline-degrading microbial community size could be seen in the top part of the inoculated as well as the noninoculated biofilters. Finally, analysis of the microbial community composition shows that no clear spatial stratification of the microbial community could be found in any biofilter. However, the microbial diversity increases over time in all biofilters and on all biofilter depths, suggesting that during the time of the experiment, the biofilters develop a broad carrying capacity in which a genetically very diverse range of chloropropham- and 3-chloroaniline-degrading species can thrive.<br><br>CONCLUSIONS: In this study, a vertical gradient of the chloropropham- and 3-chloroaniline-degrading community composition, in terms of density and temporal and spatial diversity, was clearly established and was directly connected to a vertical gradient of chloropropham biodegradation activity.<br><br>The major part of degradation activity takes place in the top part of the biofilter, suggesting that it could be possible to use shorter biofilter reactors or higher loading rates to treat chloropropham waste streams, making this type of bioremediation technique economically more feasible.}, }
@article {pmid25482914, year = {2015}, author = {Rodriguez-Mozaz, S and Chamorro, S and Marti, E and Huerta, B and Gros, M and Sànchez-Melsió, A and Borrego, CM and Barceló, D and Balcázar, JL}, title = {Occurrence of antibiotics and antibiotic resistance genes in hospital and urban wastewaters and their impact on the receiving river.}, journal = {Water research}, volume = {69}, number = {}, pages = {234-242}, doi = {10.1016/j.watres.2014.11.021}, pmid = {25482914}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Cities ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; Geography ; *Hospitals ; Rivers/*chemistry ; Wastewater/*chemistry ; }, abstract = {Antibiotic resistance has become a major health concern; thus, there is a growing interest in exploring the occurrence of antibiotic resistance genes (ARGs) in the environment as well as the factors that contribute to their emergence. Aquatic ecosystems provide an ideal setting for the acquisition and spread of ARGs due to the continuous pollution by antimicrobial compounds derived from anthropogenic activities. We investigated, therefore, the pollution level of a broad range of antibiotics and ARGs released from hospital and urban wastewaters, their removal through a wastewater treatment plant (WWTP) and their presence in the receiving river. Several antimicrobial compounds were detected in all water samples collected. Among antibiotic families, fluoroquinolones were detected at the highest concentration, especially in hospital effluent samples. Although good removal efficiency by treatment processes was observed for several antimicrobial compounds, most antibiotics were still present in WWTP effluents. The results also revealed that copy numbers of ARGs, such as blaTEM (resistance to β-lactams), qnrS (reduced susceptibility to fluoroquinolones), ermB (resistance to macrolides), sulI (resistance to sulfonamides) and tetW (resistance to tetracyclines), were detected at the highest concentrations in hospital effluent and WWTP influent samples. Although there was a significant reduction in copy numbers of these ARGs in WWTP effluent samples, this reduction was not uniform across analyzed ARGs. Relative concentration of ermB and tetW genes decreased as a result of wastewater treatment, whereas increased in the case of blaTEM, sulI and qnrS genes. The incomplete removal of antibiotics and ARGs in WWTP severely affected the receiving river, where both types of emerging pollutants were found at higher concentration in downstream waters than in samples collected upstream from the discharge point. Taken together, our findings demonstrate a widespread occurrence of antibiotics and ARGs in urban and hospital wastewater and how these effluents, even after treatment, contribute to the spread of these emerging pollutants in the aquatic environment.}, }
@article {pmid25482369, year = {2015}, author = {McKie-Krisberg, ZM and Gast, RJ and Sanders, RW}, title = {Physiological responses of three species of Antarctic mixotrophic phytoflagellates to changes in light and dissolved nutrients.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {21-29}, pmid = {25482369}, issn = {1432-184X}, mesh = {Adaptation, Biological/*physiology ; Analysis of Variance ; Antarctic Regions ; Chlorophyta/*physiology ; Cryptophyta/*physiology ; Fluorescence ; Food/*statistics &amp; numerical data ; *Light ; Phototrophic Processes/*physiology ; Phytoplankton/*physiology ; Population Dynamics ; }, abstract = {Antarctic phototrophs are challenged by extreme temperatures, ice cover, nutrient limitation, and prolonged periods of darkness. Yet this environment may also provide niche opportunities for phytoplankton utilizing alternative nutritional modes. Mixotrophy, the combination of photosynthesis and particle ingestion, has been proposed as a mechanism for some phytoplankton to contend with the adverse conditions of the Antarctic. We conducted feeding experiments using fluorescent bacteria-sized tracers to compare the effects of light and nutrients on bacterivory rates in three Antarctic marine photosynthetic nanoflagellates representing two evolutionary lineages: Cryptophyceae (Geminigera cryophila) and Prasinophyceae (Pyramimonas tychotreta and Mantoniella antarctica). Only G. cryophila had previously been identified as mixotrophic. We also measured photoautotrophic abilities over a range of light intensities (P vs. I) and used dark survival experiments to assess cell population dynamics in the absence of light. Feeding behavior in these three nanoflagellates was affected by either light, nutrient levels, or a combination of both factors in a species-specific manner that was not conserved by evolutionary lineage. The different responses to environmental factors by these mixotrophs supported the idea of tradeoffs in the use of phagotrophy and phototrophy for growth.}, }
@article {pmid25479086, year = {2015}, author = {Zhang-Sun, W and Augusto, LA and Zhao, L and Caroff, M}, title = {Desulfovibrio desulfuricans isolates from the gut of a single individual: structural and biological lipid A characterization.}, journal = {FEBS letters}, volume = {589}, number = {1}, pages = {165-171}, doi = {10.1016/j.febslet.2014.11.042}, pmid = {25479086}, issn = {1873-3468}, mesh = {Carbohydrate Conformation ; Desulfovibrio desulfuricans/*chemistry/isolation &amp; purification/metabolism ; Humans ; Intestines/*microbiology ; Lipid A/*chemistry/metabolism/toxicity ; }, abstract = {The levels of sulfate-reducing bacteria (SRB), including Desulfovibrionaceae, in the gut increase following a fat-enriched diet. Endotoxins from gut microbiota contribute to the inflammation process, leading to metabolic diseases. Thus, we sought to characterize the lipid A structures of Desulfovibrionaceae lipopolysaccharides (LPS) that are associated with the microbiota inflammatory properties. LPS variants were obtained from two SRB isolates from the gut of a single individual. These LPS variants shared similar lipid A moieties with Enterobacterial LPS, but differed from one another with regard to fatty-acid numbers and endotoxic activity. This first complete structural characterization of Desulfovibrio lipid A gives new insights into previously published data on Desulfovibrio lipid A biosynthesis. LPS microdiversity within SRBs illustrates how adaptation can influence pro-inflammatory potential.}, }
@article {pmid25479061, year = {2014}, author = {Bagchi, S and Vlaeminck, SE and Sauder, LA and Mosquera, M and Neufeld, JD and Boon, N}, title = {Temporal and spatial stability of ammonia-oxidizing archaea and bacteria in aquarium biofilters.}, journal = {PloS one}, volume = {9}, number = {12}, pages = {e113515}, pmid = {25479061}, issn = {1932-6203}, mesh = {Ammonia/metabolism ; Archaea/genetics/*metabolism ; Bacteria/metabolism ; Filtration ; Fresh Water/chemistry/*microbiology ; *Oxidation-Reduction ; Oxidoreductases ; RNA, Ribosomal, 16S/*genetics ; Soil Microbiology ; }, abstract = {Nitrifying biofilters are used in aquaria and aquaculture systems to prevent accumulation of ammonia by promoting rapid conversion to nitrate via nitrite. Ammonia-oxidizing archaea (AOA), as opposed to ammonia-oxidizing bacteria (AOB), were recently identified as the dominant ammonia oxidizers in most freshwater aquaria. This study investigated biofilms from fixed-bed aquarium biofilters to assess the temporal and spatial dynamics of AOA and AOB abundance and diversity. Over a period of four months, ammonia-oxidizing microorganisms from six freshwater and one marine aquarium were investigated at 4-5 time points. Nitrogen balances for three freshwater aquaria showed that active nitrification by aquarium biofilters accounted for ≥ 81-86% of total nitrogen conversion in the aquaria. Quantitative PCR (qPCR) for bacterial and thaumarchaeal ammonia monooxygenase (amoA) genes demonstrated that AOA were numerically dominant over AOB in all six freshwater aquaria tested, and contributed all detectable amoA genes in three aquarium biofilters. In the marine aquarium, however, AOB outnumbered AOA by three to five orders of magnitude based on amoA gene abundances. A comparison of AOA abundance in three carrier materials (fine sponge, rough sponge and sintered glass or ceramic rings) of two three-media freshwater biofilters revealed preferential growth of AOA on fine sponge. Denaturing gel gradient electrophoresis (DGGE) of thaumarchaeal 16S rRNA genes indicated that community composition within a given biofilter was stable across media types. In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time. Nonmetric multidimensional scaling (NMDS) based on denaturing gradient gel electrophoresis (DGGE) fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters. These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater aquarium biofilters, and that AOA community composition within a given aquarium is stable over time and across biofilter support material types.}, }
@article {pmid25478194, year = {2014}, author = {Chambers, DC and Gellatly, SL and Hugenholtz, P and Hansbro, PM}, title = {JTD special edition 'Hot Topics in COPD'-The microbiome in COPD.}, journal = {Journal of thoracic disease}, volume = {6}, number = {11}, pages = {1525-1531}, pmid = {25478194}, issn = {2072-1439}, abstract = {The pathogenesis of chronic obstructive pulmonary disease (COPD) and its exacerbations, are intricately linked to colonisation and infection with bacteria and other microbes. Despite their undeniable importance, we have a poor understanding of the complex relationships between COPD phenotypes, physiology, cellular and molecular biology and the roles of colonising microbe or infecting pathogens. The management algorithms for the care of patients with COPD that include microbial influences, have almost exclusively been developed using microbial methods that were entirely dependent on the ability to grow bacteria on suitable media. The shortcomings of this approach are becoming clear now that it is possible to completely and accurately define the microbial ecology of ecosystems using genomic methods, which do not rely on the ability to cultivate the organisms present. Whilst our appreciation of the relationships between some bacterial ecosystems and the organ in which they reside in humans is now relatively advanced, this is not true for lung. This perspective serves to highlight the growing importance of including an accurate description of bacterial ecology in any attempt to decipher the pathobiology of COPD. While this field is in its infancy, there is significant potential to gain new insights which will translate into more rational and effective treatment algorithms for patients with COPD.}, }
@article {pmid25477871, year = {2014}, author = {Mormile, MR}, title = {Going from microbial ecology to genome data and back: studies on a haloalkaliphilic bacterium isolated from Soap Lake, Washington State.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {628}, pmid = {25477871}, issn = {1664-302X}, abstract = {Soap Lake is a meromictic, alkaline (∼pH 9.8) and saline (∼14-140 g liter(-1)) lake located in the semiarid area of eastern Washington State. Of note is the length of time it has been meromictic (at least 2000 years) and the extremely high sulfide level (∼140 mM) in its monimolimnion. As expected, the microbial ecology of this lake is greatly influenced by these conditions. A bacterium, Halanaerobium hydrogeniformans, was isolated from the mixolimnion region of this lake. Halanaerobium hydrogeniformans is a haloalkaliphilic bacterium capable of forming hydrogen from 5- and 6-carbon sugars derived from hemicellulose and cellulose. Due to its ability to produce hydrogen under saline and alkaline conditions, in amounts that rival genetically modified organisms, its genome was sequenced. This sequence data provides an opportunity to explore the unique metabolic capabilities of this organism, including the mechanisms for tolerating the extreme conditions of both high salinity and alkalinity of its environment.}, }
@article {pmid25477868, year = {2014}, author = {Hardoim, CC and Cardinale, M and Cúcio, AC and Esteves, AI and Berg, G and Xavier, JR and Cox, CJ and Costa, R}, title = {Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {611}, pmid = {25477868}, issn = {1664-302X}, abstract = {Complex and distinct bacterial communities inhabit marine sponges and are believed to be essential to host survival, but our present-day inability to domesticate sponge symbionts in the laboratory hinders our access to the full metabolic breadth of these microbial consortia. We address bacterial cultivation bias in marine sponges using a procedure that enables direct comparison between cultivated and uncultivated symbiont community structures. Bacterial community profiling of the sympatric keratose species Sarcotragus spinosulus and Ircinia variabilis (Dictyoceratida, Irciniidae) was performed by polymerase chain reaction-denaturing gradient gel electrophoresis and 454-pyrosequecing of 16S rRNA gene fragments. Whereas cultivation-independent methods revealed species-specific bacterial community structures in these hosts, cultivation-dependent methods resulted in equivalent community assemblages from both species. Between 15 and 18 bacterial phyla were found in S. spinosulus and I. variabilis using cultivation-independent methods. However, Alphaproteobacteria and Gammaproteobacteria dominated the cultivation-dependent bacterial community. While cultivation-independent methods revealed about 200 and 220 operational taxonomic units (OTUs, 97% gene similarity) in S. spinosulus and I. variabilis, respectively, only 33 and 39 OTUs were found in these species via culturing. Nevertheless, around 50% of all cultured OTUs escaped detection by cultivation-independent methods, indicating that standard cultivation makes otherwise host-specific bacterial communities similar by selectively enriching for rarer and generalist symbionts. This study sheds new light on the diversity spectrum encompassed by cultivated and uncultivated sponge-associated bacteria. Moreover, it highlights the need to develop alternative culturing technologies to capture the dominant sponge symbiont fraction that currently remains recalcitrant to laboratory manipulation.}, }
@article {pmid25475784, year = {2015}, author = {Leng, L and Chang, J and Geng, K and Lu, Y and Ma, K}, title = {Uncultivated Methylocystis Species in Paddy Soil Include Facultative Methanotrophs that Utilize Acetate.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {88-96}, pmid = {25475784}, issn = {1432-184X}, mesh = {Acetates/*metabolism ; Base Sequence ; Carbon Isotopes/metabolism ; Cloning, Molecular ; Computational Biology ; Isotope Labeling ; Methane/metabolism ; Methylocystaceae/*genetics/*metabolism ; Molecular Sequence Data ; Oryza/*growth &amp; development ; Oxidation-Reduction ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Methanotrophs are crucial in regulating methane emission from rice field systems. Type II methanotrophs in particular are often observed in high abundance in paddy soil. Some cultivated species of Methylocystis are able to grow on acetate in the absence of methane. We hypothesize that the dominant type II methanotrophs in paddy soil might facultatively utilize acetate for growth, which we evaluate in the present study. The measurement of methane oxidation rates showed that the methanotrophic activity in paddy soil was inhibited by the addition of acetate compared to the continuous supplementation of methane, but the paddy soil maintained the methane oxidation capacity and recovered following methane supplementation. Terminal restriction fragment length polymorphism analysis (T-RFLP) combined with cloning and sequencing of pmoA genes showed that Methylocystis was enriched after incubation with added acetate, while the type I methanotrophs Methylocaldum/Methylococcus and Methylobacter were enriched by methane supplementation. A comparison of pmoA sequences obtained in this study with those in the public database indicated that they were globally widespread in paddy soils or in associated with rice roots. Furthermore, we performed stable isotope probing (SIP) of pmoA messenger RNA (mRNA) to investigate the assimilation of (13)C-acetate by paddy soil methanotrophs. RNA-SIP revealed that Methylocystis-related methanotrophs which shared the same genotype of the above enriched species were significantly labelled. It indicates that these methanotrophs actively assimilated the labelled acetate in paddy soil. Altogether, these results suggested that uncultivated Methylocystis species are facultative methanotrophs utilizing acetate as a secondary carbon source in paddy soil.}, }
@article {pmid25475614, year = {2015}, author = {Arsène-Ploetze, F and Bertin, PN and Carapito, C}, title = {Proteomic tools to decipher microbial community structure and functioning.}, journal = {Environmental science and pollution research international}, volume = {22}, number = {18}, pages = {13599-13612}, pmid = {25475614}, issn = {1614-7499}, mesh = {Animals ; Bacterial Proteins/metabolism ; *Environmental Microbiology ; Humans ; Metagenomics ; Microbial Interactions ; Microbiota ; Proteome/metabolism ; Proteomics ; }, abstract = {Recent advances in microbial ecology allow studying microorganisms in their environment, without laboratory cultivation, in order to get access to the large uncultivable microbial community. With this aim, environmental proteomics has emerged as an appropriate complementary approach to metagenomics providing information on key players that carry out main metabolic functions and addressing the adaptation capacities of living organisms in situ. In this review, a wide range of proteomic approaches applied to investigate the structure and functioning of microbial communities as well as recent examples of such studies are presented.}, }
@article {pmid25475443, year = {2015}, author = {Courtens, EN and De Clippeleir, H and Vlaeminck, SE and Jordaens, R and Park, H and Chandran, K and Boon, N}, title = {Nitric oxide preferentially inhibits nitrite oxidizing communities with high affinity for nitrite.}, journal = {Journal of biotechnology}, volume = {193}, number = {}, pages = {120-122}, doi = {10.1016/j.jbiotec.2014.11.021}, pmid = {25475443}, issn = {1873-4863}, mesh = {Bioreactors/*microbiology ; Microbial Consortia/drug effects/*physiology ; Nitric Oxide/*metabolism/pharmacology ; Nitrites/*metabolism ; Nitrobacter/metabolism ; Oxidation-Reduction ; Sewage/*microbiology ; }, abstract = {The prerequisite to the development success of the novel mainstream processes partial nitritation/anammox is the out-selection of nitrite oxidizing bacteria (NOB). A recent study suggested that this could be achieved through NO production by ammonium oxidizing bacteria under cyclic oxic-anoxic conditions. Indeed, it is known that among NOB, Nitrobacter species are reversibly inhibited by NO. However, the effect of NO on the activity of the NOB genus Nitrospira is not studied so far. Such an understanding is needed, since Nitrospira related NOB are mostly prevailing in sewage treatment plants. This study quantified the effect of NO on the nitratation activity of sludge types with different Nitrobacter/Nitrospira ratios. In an oxic bubbling column, a dosage of 4.4 mg NO L(-1) d(-1) (∼2 μg NO-N L(-1) in liquid phase) inhibited the Nitrobacter dominated sludge with 24%. For the Nitrospira dominated sludge types, the inhibition was strongly correlated with the nitrite half saturation constant (K(s)) ranging from 0% to 30-50% and 60-80% inhibition of the nitrite oxidation for K(s) of 0.72, 0.36 and 0.06 mg NO2(-)-N L(-1), respectively. This study showed that nitrifying communities with high affinity for nitrite and low specific nitrite oxidation rates (K-strategists) can be strongly inhibited by NO. The degree of inhibition could be confirmed in a set-up with NO dosage through an artificial alginate-based biofilm, ensuring a more direct contact between NO and the microorganisms.}, }
@article {pmid25474262, year = {2014}, author = {Whiteson, KL and Lazarevic, V and Tangomo-Bento, M and Girard, M and Maughan, H and Pittet, D and Francois, P and Schrenzel, J and , }, title = {Noma affected children from Niger have distinct oral microbial communities based on high-throughput sequencing of 16S rRNA gene fragments.}, journal = {PLoS neglected tropical diseases}, volume = {8}, number = {12}, pages = {e3240}, pmid = {25474262}, issn = {1935-2735}, mesh = {Bacteria/classification/*genetics ; Child ; Child, Preschool ; Cross-Sectional Studies ; DNA, Bacterial/genetics ; Female ; Humans ; Male ; Mouth/*microbiology ; Niger/epidemiology ; Noma/epidemiology/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {We aim to understand the microbial ecology of noma (cancrum oris), a devastating ancient illness which causes severe facial disfigurement in>140,000 malnourished children every year. The cause of noma is still elusive. A chaotic mix of microbial infection, oral hygiene and weakened immune system likely contribute to the development of oral lesions. These lesions are a plausible entry point for unidentified microorganisms that trigger gangrenous facial infections. To catalog bacteria present in noma lesions and identify candidate noma-triggering organisms, we performed a cross-sectional sequencing study of 16S rRNA gene amplicons from sixty samples of gingival fluid from twelve healthy children, twelve children suffering from noma (lesion and healthy sites), and twelve children suffering from Acute Necrotizing Gingivitis (ANG) (lesion and healthy sites). Relative to healthy individuals, samples taken from lesions in diseased mouths were enriched with Spirochaetes and depleted for Proteobacteria. Samples taken from healthy sites of diseased mouths had proportions of Spirochaetes and Proteobacteria that were similar to healthy control individuals. Samples from noma mouths did not have a higher abundance of Fusobacterium, casting doubt on its role as a causative agent of noma. Microbial communities sampled from noma and ANG lesions were dominated by the same Prevotella intermedia OTU, which was much less abundant in healthy sites sampled from the same mouths. Multivariate analysis confirmed that bacterial communities in healthy and lesion sites were significantly different. Several OTUs in the Orders Erysipelotrichales, Clostridiales, Bacteroidales, and Spirochaetales were identified as indicators of noma, suggesting that one or more microbes within these Orders is associated with the development of noma lesions. Future studies should include longitudinal sampling of viral and microbial components of this community, before and early in noma lesion development.}, }
@article {pmid25472003, year = {2014}, author = {Pascual-García, A and Tamames, J and Bastolla, U}, title = {Bacteria dialog with Santa Rosalia: Are aggregations of cosmopolitan bacteria mainly explained by habitat filtering or by ecological interactions?.}, journal = {BMC microbiology}, volume = {14}, number = {}, pages = {284}, pmid = {25472003}, issn = {1471-2180}, mesh = {Bacteria/*classification ; *Biota ; *Environmental Microbiology ; Microbial Interactions ; }, abstract = {BACKGROUND: Since the landmark Santa Rosalia paper by Hutchinson, niche theory addresses the determinants of biodiversity in terms of both environmental and biological aspects. Disentangling the role of habitat filtering and interactions with other species is critical for understanding microbial ecology. Macroscopic biogeography explores hypothetical ecological interactions through the analysis of species associations. These methods have started to be incorporated into microbial ecology relatively recently, due to the inherent experimental difficulties and the coarse grained nature of the data.<br><br>RESULTS: Here we investigate the influence of environmental preferences and ecological interactions in the tendency of bacterial taxa to either aggregate or segregate, using a comprehensive dataset of bacterial taxa observed in a wide variety of environments. We assess significance of taxa associations through a null model that takes into account habitat preferences and the global distribution of taxa across samples. The analysis of these associations reveals a surprisingly large number of significant aggregations between taxa, with a marked community structure and a strong propensity to aggregate for cosmopolitan taxa. Due to the coarse grained nature of our data we cannot conclusively reject the hypothesis that many of these aggregations are due to environmental preferences that the null model fails to reproduce. Nevertheless, some observations are better explained by ecological interactions than by habitat filtering. In particular, most pairs of aggregating taxa co-occur in very different environments, which makes it unlikely that these associations are due to habitat preferences, and many are formed by cosmopolitan taxa without well defined habitat preferences. Moreover, known cooperative interactions are retrieved as aggregating pairs of taxa. As observed in similar studies, we also found that phylogenetically related taxa are much more prone to aggregate than to segregate, an observation that may play a role in bacterial speciation.<br><br>CONCLUSIONS: We hope that these results stimulate experimental verification of the putative cooperative interactions between cosmopolitan bacteria, and we suggest several groups of aggregated cosmopolitan bacteria that are interesting candidates for such an investigation.}, }
@article {pmid25469393, year = {2014}, author = {Keim, NL and Martin, RJ}, title = {Dietary whole grain–microbiota interactions: insights into mechanisms for human health.}, journal = {Advances in nutrition (Bethesda, Md.)}, volume = {5}, number = {5}, pages = {556-557}, pmid = {25469393}, issn = {2156-5376}, mesh = {Congresses as Topic ; Dietary Carbohydrates/administration &amp; dosage ; Dietary Fats/administration &amp; dosage ; Dietary Fiber/*administration &amp; dosage ; Dietary Proteins/administration &amp; dosage ; Edible Grain/*chemistry ; Gastrointestinal Tract/drug effects/*microbiology ; Humans ; *Microbiota ; }, abstract = {This article summarizes the presentations from the “Dietary Whole Grain–Microbiota Interactions: Insights into Mechanisms for Human Health” symposium held at the ASN Scientific Sessions and Annual Meeting at Experimental Biology 2014 in San Diego, CA, on 28 April 2014. The symposium focused on the interactive effects of whole grains and nondigestible carbohydrates with the gut microbiota with the goal of identifying the benefits of whole grains that are mediated through their effects on the gut microbiome. This theme was addressed by 4 speakers, each with their own unique perspective. Dr. Michael Lefevre reviewed the impact of whole grains on markers of subclinical inflammation, drawing examples from epidemiologic literature, clinical trials, and animal experiments. Dr. Knud Erik Bach Knudsen discussed data from studies he conducted to identify specific carbohydrates that enhance colonic butyrate production. Dr. Michael Keenan presented a chronology of his research program devoted to understanding the mechanisms underlying the metabolic effects of resistant starch, particularly high-amylose maize. Dr. Jens Walter emphasized that whole grains can impact gut microbial ecology by increasing microbial diversity and inducing compositional alterations, some of which are considered to have beneficial effects on the host.}, }
@article {pmid25468931, year = {2014}, author = {Duarte, M and Jauregui, R and Vilchez-Vargas, R and Junca, H and Pieper, DH}, title = {AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics.}, journal = {Database : the journal of biological databases and curation}, volume = {2014}, number = {}, pages = {bau118}, pmid = {25468931}, issn = {1758-0463}, mesh = {Aerobiosis ; Bacteria/*metabolism ; Biodegradation, Environmental ; *Databases, Factual ; *Genomics ; Hydrocarbons, Aromatic/*metabolism ; Internet ; *Phylogeny ; Search Engine ; User-Computer Interface ; }, abstract = {Understanding prokaryotic transformation of recalcitrant pollutants and the in-situ metabolic nets require the integration of massive amounts of biological data. Decades of biochemical studies together with novel next-generation sequencing data have exponentially increased information on aerobic aromatic degradation pathways. However, the majority of protein sequences in public databases have not been experimentally characterized and homology-based methods are still the most routinely used approach to assign protein function, allowing the propagation of misannotations. AromaDeg is a web-based resource targeting aerobic degradation of aromatics that comprises recently updated (September 2013) and manually curated databases constructed based on a phylogenomic approach. Grounded in phylogenetic analyses of protein sequences of key catabolic protein families and of proteins of documented function, AromaDeg allows query and data mining of novel genomic, metagenomic or metatranscriptomic data sets. Essentially, each query sequence that match a given protein family of AromaDeg is associated to a specific cluster of a given phylogenetic tree and further function annotation and/or substrate specificity may be inferred from the neighboring cluster members with experimentally validated function. This allows a detailed characterization of individual protein superfamilies as well as high-throughput functional classifications. Thus, AromaDeg addresses the deficiencies of homology-based protein function prediction, combining phylogenetic tree construction and integration of experimental data to obtain more accurate annotations of new biological data related to aerobic aromatic biodegradation pathways. We pursue in future the expansion of AromaDeg to other enzyme families involved in aromatic degradation and its regular update. Database URL: http://aromadeg.siona.helmholtz-hzi.de}, }
@article {pmid25467742, year = {2015}, author = {Brasell, KA and Heath, MW and Ryan, KG and Wood, SA}, title = {Successional change in microbial communities of benthic Phormidium-dominated biofilms.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {254-266}, pmid = {25467742}, issn = {1432-184X}, mesh = {Alphaproteobacteria/classification/growth &amp; development/isolation &amp; purification ; Bacteroidetes/classification/growth &amp; development/isolation &amp; purification ; *Biofilms ; Biomass ; Cyanobacteria/*classification/growth &amp; development/*isolation &amp; purification ; DNA, Bacterial/genetics ; Ecosystem ; *Eutrophication ; New Zealand ; Phylogeny ; Phylogeography ; RNA, Ribosomal, 16S/genetics ; Rivers/microbiology ; Sequence Analysis, DNA ; Water Microbiology ; }, abstract = {Benthic cyanobacterial blooms are increasing worldwide and can be harmful to human and animal health if they contain toxin-producing species. Microbial interactions are important in the formation of benthic biofilms and can lead to increased dominance and/or toxin production of one or few taxa. This study investigated how microbial interactions contribute to proliferation of benthic blooms dominated by the neurotoxin-producing Phormidium autumnale. Following a rainfall event that cleared the substrate, biofilm succession was characterised at a site on the Hutt River (New Zealand) by sampling every 2-3 days over 32 days. A combination of morphological and molecular community analyses (automated ribosomal intergenic spacer analysis and Illumina™ MiSeq sequencing) identified three distinct phases of succession in both the micro-algal and bacterial communities within P. autumnale-dominated biofilms. Bacterial composition shifted between the phases, and these changes occurred several days before those of the micro-algal community. Alphaproteobacteria and Betaproteobacteria dominate in the early phase; Alphaproteobacteria, Betaproteobacteria, Sphingobacteria and Flavobacteria in the mid-phase; and Sphingobacteria and Flavobacteria in the late phase. Collectively, the results suggest that succession is driven by bacteria in the early stages but becomes dependent on micro-algae in the mid- and late stages of biofilm formation.}, }
@article {pmid25466308, year = {2015}, author = {Adriaenssens, EM and Edwards, R and Nash, JHE and Mahadevan, P and Seto, D and Ackermann, HW and Lavigne, R and Kropinski, AM}, title = {Integration of genomic and proteomic analyses in the classification of the Siphoviridae family.}, journal = {Virology}, volume = {477}, number = {}, pages = {144-154}, doi = {10.1016/j.virol.2014.10.016}, pmid = {25466308}, issn = {1096-0341}, mesh = {Bacteriophages/chemistry/*classification/genetics ; *Genome, Viral ; Genomics/methods ; Proteome/*analysis ; Proteomics/methods ; Siphoviridae/chemistry/*classification/genetics ; Viral Proteins/*analysis ; Virology/methods ; }, abstract = {Using a variety of genomic (BLASTN, ClustalW) and proteomic (Phage Proteomic Tree, CoreGenes) tools we have tackled the taxonomic status of members of the largest bacteriophage family, the Siphoviridae. In all over 400 phages were examined and we were able to propose 39 new genera, comprising 216 phage species, and add 62 species to two previously defined genera (Phic3unalikevirus; L5likevirus) grouping, in total, 390 fully sequenced phage isolates. Many of the remainders are orphans which the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) chooses not to ascribe genus status at the time being.}, }
@article {pmid25465176, year = {2015}, author = {Li, X and Bossier, P and Dierckens, K and Laureau, S and Defoirdt, T}, title = {Impact of mucin, bile salts and cholesterol on the virulence of Vibrio anguillarum towards gnotobiotic sea bass (Dicentrarchus labrax) larvae.}, journal = {Veterinary microbiology}, volume = {175}, number = {1}, pages = {44-49}, doi = {10.1016/j.vetmic.2014.10.033}, pmid = {25465176}, issn = {1873-2542}, mesh = {Animals ; Bass/*microbiology ; Bile Acids and Salts/*pharmacology ; Cholesterol/*pharmacology ; Fish Diseases/microbiology ; Germ-Free Life ; Larva/microbiology ; Mucins/*pharmacology ; Phenotype ; Vibrio/*drug effects/genetics/pathogenicity ; Vibrio Infections/microbiology/veterinary ; Virulence ; }, abstract = {In this study, we investigated the impact of the host factors mucin, bile salts and cholesterol on the virulence of the economically important aquatic pathogen Vibrio anguillarum towards sea bass larvae. Pretreatment of V. anguillarum with either one of the host factors (at 10 mg l(-1)) prior to inoculation into the sea bass rearing water increased virulence of the bacterium, although the effect of cholesterol was not significant. Each of the three host factors significantly increased several virulence-related phenotypes in V. anguillarum, i.e. protease activity, flagellar motility, biofilm formation and exopolysaccharide production, whereas there was no effect on growth of the bacterium under these conditions. Furthermore, the host factors increased the expression of genes involved in these phenotypes, i.e. the metalloprotease empA, the flagellar transcriptional regulator fleQ, the flagellin gene flaA, the chemotaxis methyltransferase gene cheR, the exopolysaccharide biosynthesis gene wbfD and the exopolysaccharide export gene wza. Our results indicate that V. anguillarum uses host mucin, bile salts, and cholesterol as cues to promote the expression of several important virulence traits that enhance the success of transmission from one host to another.}, }
@article {pmid25463385, year = {2014}, author = {Hoyles, L and McCartney, AL and Neve, H and Gibson, GR and Sanderson, JD and Heller, KJ and van Sinderen, D}, title = {Characterization of virus-like particles associated with the human faecal and caecal microbiota.}, journal = {Research in microbiology}, volume = {165}, number = {10}, pages = {803-812}, doi = {10.1016/j.resmic.2014.10.006}, pmid = {25463385}, issn = {1769-7123}, mesh = {Adult ; Biodiversity ; Cecum/*virology ; Feces/*virology ; Female ; Humans ; Male ; *Microbiota ; Middle Aged ; Viruses/classification/genetics/*isolation &amp; purification ; Young Adult ; }, abstract = {This work represents an investigation into the presence, abundance and diversity of virus-like particles (VLPs) associated with human faecal and caecal samples. Various methodologies for the recovery of VLPs from faeces were tested and optimized, including successful down-stream processing of such samples for the purpose of an in-depth electron microscopic analysis, pulsed-field gel electrophoresis and efficient DNA recovery. The applicability of the developed VLP characterization method beyond the use of faecal samples was then verified using samples obtained from human caecal fluid.}, }
@article {pmid25462753, year = {2015}, author = {Matassa, S and Boon, N and Verstraete, W}, title = {Resource recovery from used water: the manufacturing abilities of hydrogen-oxidizing bacteria.}, journal = {Water research}, volume = {68}, number = {}, pages = {467-478}, doi = {10.1016/j.watres.2014.10.028}, pmid = {25462753}, issn = {1879-2448}, mesh = {Bacteria/growth &amp; development/*metabolism ; Bacterial Proteins/metabolism ; Biomass ; Bioreactors/microbiology ; Cupriavidus necator/growth &amp; development/metabolism ; Hydrogen/*metabolism ; Models, Biological ; Oxidation-Reduction ; Waste Disposal, Fluid/*methods ; Wastewater/*microbiology ; }, abstract = {Resources in used water are at present mainly destroyed rather than reused. Recovered nutrients can serve as raw material for the sustainable production of high value bio-products. The concept of using hydrogen and oxygen, produced by green or off-peak energy by electrolysis, as well as the unique capability of autotrophic hydrogen oxidizing bacteria to upgrade nitrogen and minerals into valuable microbial biomass, is proposed. Both axenic and mixed microbial cultures can thus be of value to implement re-synthesis of recovered nutrients in biomolecules. This process can become a major line in the sustainable "water factory" of the future.}, }
@article {pmid25462724, year = {2015}, author = {Masters, S and Wang, H and Pruden, A and Edwards, MA}, title = {Redox gradients in distribution systems influence water quality, corrosion, and microbial ecology.}, journal = {Water research}, volume = {68}, number = {}, pages = {140-149}, doi = {10.1016/j.watres.2014.09.048}, pmid = {25462724}, issn = {1879-2448}, mesh = {Chloramines/*pharmacology ; Chlorine/*pharmacology ; Corrosion ; Disinfectants/*pharmacology ; Drinking Water/*analysis ; Microbiota/*physiology ; Oxidation-Reduction ; Time Factors ; *Water Quality ; Water Supply/*methods ; }, abstract = {Simulated distribution systems (SDSs) defined the interplay between disinfectant type (free chlorine and chloramines), water age (1-10.2 days), and pipe material (PVC, iron and cement surfaces) on water chemistry, redox zones and infrastructure degradation. Redox gradients developed as a function of water age and pipe material affected the quality of water consumers would receive. Free chlorine was most stable in the presence of PVC while chloramine was most stable in the presence of cement. At a 3.6 day water age the residual in the chlorinated PVC SDS was more than 3.5 times higher than in the chlorinated iron or cement systems. In contrast, the residual in the chloraminated cement SDS was more than 10 times greater than in the chloraminated iron or PVC systems. Near the point of entry to the SDSs where disinfectant residuals were present, free chlorine tended to cause as much as 4 times more iron corrosion when compared to chloramines. Facultative denitrifying bacteria were ubiquitous, and caused complete loss of nitrogen at distal points in systems with iron, and these bacteria co-occurred with very severe pitting attack (1.6-1.9 mm/year) at high water age.}, }
@article {pmid25462016, year = {2015}, author = {McDonald, JA and Fuentes, S and Schroeter, K and Heikamp-deJong, I and Khursigara, CM and de Vos, WM and Allen-Vercoe, E}, title = {Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model.}, journal = {Journal of microbiological methods}, volume = {108}, number = {}, pages = {36-44}, doi = {10.1016/j.mimet.2014.11.007}, pmid = {25462016}, issn = {1872-8359}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/drug effects/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena/drug effects ; Biofilms/*drug effects ; Clindamycin/*pharmacology ; Gastrointestinal Tract/microbiology ; Humans ; Intestinal Mucosa/*microbiology ; Microbiota/*drug effects ; Models, Biological ; Phylogeny ; }, abstract = {In vivo studies of human mucosal gut microbiota are often limited to end-point analyses and confounded by bowel cleansing procedures. Therefore, we used biofilm reactors to incorporate a simulated mucosal environment into an in vitro gut chemostat model. Communities developed were complex, reproducible, distinct, and representative of in vivo communities.}, }
@article {pmid25461045, year = {2015}, author = {Staley, C and Gould, TJ and Wang, P and Phillips, J and Cotner, JB and Sadowsky, MJ}, title = {Species sorting and seasonal dynamics primarily shape bacterial communities in the Upper Mississippi River.}, journal = {The Science of the total environment}, volume = {505}, number = {}, pages = {435-445}, doi = {10.1016/j.scitotenv.2014.10.012}, pmid = {25461045}, issn = {1879-1026}, mesh = {*Ecosystem ; Environmental Monitoring ; Minnesota ; Rivers/chemistry/*microbiology ; Seasons ; *Water Microbiology ; }, abstract = {Bacterial community structure (BCS) in freshwater ecosystems varies seasonally and due to physicochemical gradients, but metacommunity structure of a major river remains understudied. Here we characterize the BCS along the Mississippi River and contributing rivers in Minnesota over three years using Illumina next-generation sequencing, to determine how changes in environmental conditions as well as inputs from surrounding land and confluences impacted community structure. Contributions of sediment to water microbial diversity were also evaluated. Long-term variation in community membership was observed, and significant shifts in relative abundances of major freshwater taxa, including α-Proteobacteria, Burkholderiales, and Actinomycetales, were observed due to temporal and spatial variations. Environmental parameters (e.g. temperature, rainfall, and nutrient concentrations) primarily contributed to differences in phyla abundances (88% of variance), with minimal influence from spatial distance alone (<1% of variance). Furthermore, an annually-recurrent BCS was observed in late summer, further suggesting that seasonal dynamics strongly influence community composition. Sediment communities differed from those in the water, but contributed up to 50% to community composition in the water column. Among water sampling sites, 34% showed significant variability in BCS of replicate samples indicating variability among riverine communities due to heterogeneity in the water column. Results of this study highlight the need for a better understanding of spatial and temporal variations in riverine bacterial diversity associated with physicochemical gradients and reveal how communities in sediments, and potentially other environmental reservoirs, impact waterborne BCS. Techniques used in this study may prove useful to determine sources of microbes from sediments and soils to waterways, which will facilitate best management practices and total maximum daily load determinations.}, }
@article {pmid25461001, year = {2015}, author = {Khor, WC and Rabaey, K and Vervaeren, H}, title = {Low temperature calcium hydroxide treatment enhances anaerobic methane production from (extruded) biomass.}, journal = {Bioresource technology}, volume = {176}, number = {}, pages = {181-188}, doi = {10.1016/j.biortech.2014.11.037}, pmid = {25461001}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Biofuels ; Biomass ; Biotechnology ; Calcium Hydroxide/*chemistry ; Kinetics ; Methane/chemistry/*metabolism ; Poaceae/chemistry/metabolism ; Temperature ; }, abstract = {Ca(OH)2 treatment was applied to enhance methane yield. Different alkali concentration, incubation temperature and duration were evaluated for their effect on methane production and COD conversion efficiency from (non-)extruded biomass during mesophilic anaerobic digestion at lab-scale. An optimum Ca(OH)2 pretreatment for grass is found at 7.5% lime loading at 10°C for 20h (37.3% surplus), while mild (50°C) and high temperatures perform sub-optimal. Ca(OH)2 post-treatment after fast extrusion gives an additional surplus compared to extruded material of 15.2% (grass), 11.2% (maize straw) and 8.2% (sprout stem) regarding methane production. COD conversion improves accordingly, with additional improvements of 10.3% (grass), 9.0% (maize straw) and 6.8% (sprout stem) by Ca(OH)2 post-treatment. Therefore, Ca(OH)2 pretreatment and post-treatment at low temperature generate an additional effect regarding methane production and COD conversion efficiency. Fast extrusion gives a higher energy efficiency ratio compared to slow extrusion.}, }
@article {pmid25460984, year = {2015}, author = {De Francisci, D and Kougias, PG and Treu, L and Campanaro, S and Angelidaki, I}, title = {Microbial diversity and dynamicity of biogas reactors due to radical changes of feedstock composition.}, journal = {Bioresource technology}, volume = {176}, number = {}, pages = {56-64}, doi = {10.1016/j.biortech.2014.10.126}, pmid = {25460984}, issn = {1873-2976}, mesh = {Animals ; Bacteria, Anaerobic/genetics/*physiology ; Base Sequence ; *Biodiversity ; *Biofuels ; Bioreactors/*microbiology ; Carbohydrate Metabolism/physiology ; Cattle ; Computational Biology ; Denmark ; Lipid Metabolism/physiology ; Manure/microbiology ; Metabolic Networks and Pathways/genetics/*physiology ; Molecular Sequence Data ; Principal Component Analysis ; Proteins/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The anaerobic digestion process is often inhibited by alteration of substrates and/or organic overload. This study aimed to elucidate changes of microbial ecology in biogas reactors upon radical changes of substrates and to determine their importance to process imbalance. For this reason, continuously fed reactors were disturbed with pulses of proteins, lipids and carbohydrates and the microbial ecology of the reactors were characterized by 16S rRNA gene sequencing before and after the imposed changes. The microbial composition of the three reactors, initially similar, diverged greatly after substrate change. The greatest increase in diversity was observed in the reactor supplemented with carbohydrates and the microbial community became dominated by lactobacilli, while the lowest corresponded to the reactor overfed with proteins, where only Desulfotomaculum showed significant increase. The overall results suggest that feed composition has a decisive impact on the microbial composition of the reactors, and thereby on their performance.}, }
@article {pmid25460192, year = {2015}, author = {Brablcová, L and Buriánková, I and Badurová, P and Chaudhary, PP and Rulík, M}, title = {Methanogenic archaea diversity in hyporheic sediments of a small lowland stream.}, journal = {Anaerobe}, volume = {32}, number = {}, pages = {24-31}, doi = {10.1016/j.anaerobe.2014.11.009}, pmid = {25460192}, issn = {1095-8274}, mesh = {Archaea/classification/*genetics/*metabolism ; *Biodiversity ; Czech Republic ; Denaturing Gradient Gel Electrophoresis ; Environment ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Phylogeny ; *Rivers/microbiology ; Sequence Analysis, DNA ; }, abstract = {Abundance and diversity of methanogenic archaea were studied at five localities along a longitudinal profile of a Sitka stream (Czech Republic). Samples of hyporheic sediments were collected from two sediment depths (0-25 cm and 25-50 cm) by freeze-core method. Methanogen community was analyzed by fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE) and sequencing method. The proportion of methanogens to the DAPI-stained cells varied among all localities and depths with an average value 2.08 × 10(5) per g of dry sediment with the range from 0.37 to 4.96 × 10(5) cells per g of dry sediment. A total of 73 bands were detected at 19 different positions on the DGGE gel and the highest methanogen diversity was found at the downstream located sites. There was no relationship between methanogen diversity and sediment depth. Cluster analysis of DGGE image showed three main clusters consisting of localities that differed in the number and similarity of the DGGE bands. Sequencing analysis of representative DGGE bands revealed phylotypes affiliated with members belonging to the orders Methanosarcinales, Methanomicrobiales and Methanocellales. The knowledge about occurrence and diversity of methanogenic archaea in freshwater ecosystems are essential for methane dynamics in river sediments and can contribute to the understanding of global warming process.}, }
@article {pmid25459784, year = {2014}, author = {Neu, J}, title = {Probiotics and necrotizing enterocolitis.}, journal = {Clinics in perinatology}, volume = {41}, number = {4}, pages = {967-978}, pmid = {25459784}, issn = {1557-9840}, support = {R01 HD059143/HD/NICHD NIH HHS/United States ; }, mesh = {Enterocolitis, Necrotizing/*prevention &amp; control ; Humans ; Infant, Newborn ; Infant, Premature ; Intestines/*microbiology ; *Microbiota ; *Milk, Human ; Probiotics/*therapeutic use ; }, abstract = {One of the most controversial areas in neonatology is whether probiotics should be provided routinely to preterm infants to prevent necrotizing enterocolitis (NEC). This review provides the reader with a brief overview of NEC and current concepts of its pathophysiology, discusses the microbial ecology of the intestine in preterm infants and factors that may lead to a "dysbiosis", summarizes studies of probiotics in preterm infants, elaborates on the need for regulation in this area, and discusses alternatives to probiotics and what is the future for the prevention of NEC.}, }
@article {pmid25455818, year = {2014}, author = {Zhang, W and Liu, Y and Warren, A and Xu, H}, title = {Insights into assessing water quality using taxonomic distinctness based on a small species pool of biofilm-dwelling ciliate fauna in coastal waters of the Yellow Sea, northern China.}, journal = {Marine pollution bulletin}, volume = {89}, number = {1-2}, pages = {121-127}, doi = {10.1016/j.marpolbul.2014.10.018}, pmid = {25455818}, issn = {1879-3363}, mesh = {Biodiversity ; Biofilms ; Biological Oxygen Demand Analysis ; China ; Ciliophora/classification/*physiology ; Ecosystem ; Environmental Monitoring/*methods ; Seawater/*chemistry ; *Water Quality ; }, abstract = {The aim of this study is to determine the feasibility of using a small species pool from a raw dataset of biofilm-dwelling ciliates for bioassessment based on taxonomic diversity. Samples were collected monthly at four stations within a gradient of environmental stress in coastal waters of the Yellow Sea, northern China from August 2011 to July 2012. A 33-species subset was identified from the raw 137-species dataset using a multivariate method. The spatial patterns of this subset were significantly correlated with the changes in the nutrients and chemical oxygen demand. The taxonomic diversity indices were significantly correlated with nutrients. The pair-wise indices of average taxonomic distinctness (Δ(+)) and the taxonomic distinctness (Λ(+)) showed a clear departure from the expected taxonomic pattern. These findings suggest that this small ciliate assemblage might be used as an adequate species pool for discriminating water quality status based on taxonomic distinctness in marine ecosystems.}, }
@article {pmid25454204, year = {2015}, author = {Herrero, M and Stuckey, DC}, title = {Bioaugmentation and its application in wastewater treatment: A review.}, journal = {Chemosphere}, volume = {140}, number = {}, pages = {119-128}, doi = {10.1016/j.chemosphere.2014.10.033}, pmid = {25454204}, issn = {1879-1298}, support = {BB/K003240/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Biodegradation, Environmental ; *Bioreactors ; Waste Disposal, Fluid/*methods ; Wastewater/*chemistry/microbiology ; }, abstract = {Bioaugmentation (the process of adding selected strains/mixed cultures to wastewater reactors to improve the catabolism of specific compounds, e.g. refractory organics, or overall COD) is a promising technique to solve practical problems in wastewater treatment plants, and enhance removal efficiency. The potential of this option can now be enhanced in order to take advantage of important advances in the fields of microbial ecology, molecular biology, immobilization techniques and advanced bioreactor design. Reports on bioaugmentation in WWT show the difficulties in evaluating the potential parameters involved, leading frequently to inconclusive outcomes. Many studies have been carried out on the basis of trial-and-error approaches, and it has been reported that reactors bioaugmented with pure cultures often fail to perform as well as the pure cultures under laboratory conditions. As an interesting technical challenge, the feasibility of bioaugmentation should ultimately be assessed by data from field implementation, and this review highlights several promising areas to explore in the future.}, }
@article {pmid25450910, year = {2015}, author = {Kowalczyk, A and Martin, TJ and Price, OR and Snape, JR and van Egmond, RA and Finnegan, CJ and Schäfer, H and Davenport, RJ and Bending, GD}, title = {Refinement of biodegradation tests methodologies and the proposed utility of new microbial ecology techniques.}, journal = {Ecotoxicology and environmental safety}, volume = {111}, number = {}, pages = {9-22}, doi = {10.1016/j.ecoenv.2014.09.021}, pmid = {25450910}, issn = {1090-2414}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/metabolism ; *Biodegradation, Environmental ; Genomics ; Metabolomics ; Organisation for Economic Co-Operation and Development ; Proteomics ; Risk Assessment ; Waste Disposal, Fluid ; }, abstract = {Society's reliance upon chemicals over the last few decades has led to their increased production, application and release into the environment. Determination of chemical persistence is crucial for risk assessment and management of chemicals. Current established OECD biodegradation guidelines enable testing of chemicals under laboratory conditions but with an incomplete consideration of factors that can impact on chemical persistence in the environment. The suite of OECD biodegradation tests do not characterise microbial inoculum and often provide little insight into pathways of degradation. The present review considers limitations with the current OECD biodegradation tests and highlights novel scientific approaches to chemical fate studies. We demonstrate how the incorporation of molecular microbial ecology methods (i.e., 'omics') may improve the underlying mechanistic understanding of biodegradation processes, and enable better extrapolation of data from laboratory based test systems to the relevant environment, which would potentially improve chemical risk assessment and decision making. We outline future challenges for relevant stakeholders to modernise OECD biodegradation tests and put the 'bio' back into biodegradation.}, }
@article {pmid25448075, year = {2015}, author = {Claeys, B and Vervaeck, A and Hillewaere, XK and Possemiers, S and Hansen, L and De Beer, T and Remon, JP and Vervaet, C}, title = {Thermoplastic polyurethanes for the manufacturing of highly dosed oral sustained release matrices via hot melt extrusion and injection molding.}, journal = {European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V}, volume = {90}, number = {}, pages = {44-52}, doi = {10.1016/j.ejpb.2014.11.003}, pmid = {25448075}, issn = {1873-3441}, mesh = {Administration, Oral ; Chemistry, Pharmaceutical/methods ; Delayed-Action Preparations/*administration &amp; dosage/*chemistry ; Dosage Forms ; Drug Carriers/administration &amp; dosage/chemistry ; Drug Compounding/methods ; Dyphylline/administration &amp; dosage/chemistry ; Excipients/chemistry ; Hot Temperature ; Humans ; Metoprolol/administration &amp; dosage/chemistry ; Polyethylene Glycols/administration &amp; dosage/chemistry ; Polyurethanes/*administration &amp; dosage/*chemistry ; Porosity ; Tablets/administration &amp; dosage/chemistry ; }, abstract = {This study evaluated thermoplastic polyurethanes (TPUR) as matrix excipients for the production of oral solid dosage forms via hot melt extrusion (HME) in combination with injection molding (IM). We demonstrated that TPURs enable the production of solid dispersions - crystalline API in a crystalline carrier - at an extrusion temperature below the drug melting temperature (Tm) with a drug content up to 65% (wt.%). The release of metoprolol tartrate was controlled over 24h, whereas a complete release of diprophylline was only possible in combination with a drug release modifier: polyethylene glycol 4000 (PEG 4000) or Tween 80. No burst release nor a change in tablet size and geometry was detected for any of the formulations after dissolution testing. The total matrix porosity increased gradually upon drug release. Oral administration of TPUR did not affect the GI ecosystem (pH, bacterial count, short chain fatty acids), monitored via the Simulator of the Human Intestinal Microbial Ecosystem (SHIME). The high drug load (65 wt.%) in combination with (in vitro and in vivo) controlled release capacity of the formulations, is noteworthy in the field of formulations produced via HME/IM.}, }
@article {pmid25440056, year = {2014}, author = {Degnan, PH and Taga, ME and Goodman, AL}, title = {Vitamin B12 as a modulator of gut microbial ecology.}, journal = {Cell metabolism}, volume = {20}, number = {5}, pages = {769-778}, pmid = {25440056}, issn = {1932-7420}, support = {K01 DK089121/DK/NIDDK NIH HHS/United States ; R01 GM103574/GM/NIGMS NIH HHS/United States ; DK089121/DK/NIDDK NIH HHS/United States ; GM103574/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Corrinoids/analysis/metabolism ; Gastrointestinal Tract/metabolism/*microbiology ; Humans ; *Microbiota ; Vitamin B 12/analysis/*metabolism ; }, abstract = {The microbial mechanisms and key metabolites that shape the composition of the human gut microbiota are largely unknown, impeding efforts to manipulate dysbiotic microbial communities toward stability and health. Vitamins, which by definition are not synthesized in sufficient quantities by the host and can mediate fundamental biological processes in microbes, represent an attractive target for reshaping microbial communities. Here, we discuss how vitamin B12 (cobalamin) impacts diverse host-microbe symbioses. Although cobalamin is synthesized by some human gut microbes, it is a precious resource in the gut and is likely not provisioned to the host in significant quantities. However, this vitamin may make an unrecognized contribution in shaping the structure and function of human gut microbial communities.}, }
@article {pmid25435021, year = {2014}, author = {De Fine Licht, HH and Boomsma, JJ and Tunlid, A}, title = {Symbiotic adaptations in the fungal cultivar of leaf-cutting ants.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {5675}, doi = {10.1038/ncomms6675}, pmid = {25435021}, issn = {2041-1723}, mesh = {Agaricus/enzymology/*genetics/metabolism ; Amino Acids, Essential/metabolism ; Animals ; Ants/*microbiology ; Evolution, Molecular ; *Gene Expression Regulation, Fungal ; Hyphae/enzymology/*metabolism ; Symbiosis/*genetics ; Transcriptome ; }, abstract = {Centuries of artificial selection have dramatically improved the yield of human agriculture; however, strong directional selection also occurs in natural symbiotic interactions. Fungus-growing attine ants cultivate basidiomycete fungi for food. One cultivar lineage has evolved inflated hyphal tips (gongylidia) that grow in bundles called staphylae, to specifically feed the ants. Here we show extensive regulation and molecular signals of adaptive evolution in gene trancripts associated with gongylidia biosynthesis, morphogenesis and enzymatic plant cell wall degradation in the leaf-cutting ant cultivar Leucoagaricus gongylophorus. Comparative analysis of staphylae growth morphology and transcriptome-wide expressional and nucleotide divergence indicate that gongylidia provide leaf-cutting ants with essential amino acids and plant-degrading enzymes, and that they may have done so for 20-25 million years without much evolutionary change. These molecular traits and signatures of selection imply that staphylae are highly advanced coevolutionary organs that play pivotal roles in the mutualism between leaf-cutting ants and their fungal cultivars.}, }
@article {pmid25433583, year = {2015}, author = {Koopman, JE and Röling, WF and Buijs, MJ and Sissons, CH and ten Cate, JM and Keijser, BJ and Crielaard, W and Zaura, E}, title = {Stability and resilience of oral microcosms toward acidification and Candida outgrowth by arginine supplementation.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {422-433}, pmid = {25433583}, issn = {1432-184X}, mesh = {Arginine/*pharmacology ; Bacteria/*drug effects/growth &amp; development/isolation &amp; purification ; Biofilms/drug effects/growth &amp; development ; Candida/drug effects/*growth &amp; development ; DNA, Bacterial/genetics ; Dental Caries/drug therapy/microbiology ; Genes, Bacterial ; Humans ; Hydrogen-Ion Concentration ; Hydrolases/genetics/metabolism ; Mouth/*microbiology ; Neisseria/drug effects/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; Sequence Analysis, DNA ; Streptococcus/drug effects/growth &amp; development ; Veillonella/drug effects/growth &amp; development ; }, abstract = {Dysbiosis induced by low pH in the oral ecosystem can lead to caries, a prevalent bacterial disease in humans. The amino acid arginine is one of the pH-elevating agents in the oral cavity. To obtain insights into the effect of arginine on oral microbial ecology, a multi-plaque "artificial mouth" (MAM) biofilm model was inoculated with saliva from a healthy volunteer and microcosms were grown for 4 weeks with 1.6 % (w/v) arginine supplement (Arginine) or without (Control), samples were taken at several time-points. A cariogenic environment was mimicked by sucrose pulsing. The bacterial composition was determined by 16S rRNA gene amplicon sequencing, the presence and amount of Candida and arginine deiminase system genes arcA and sagP by qPCR. Additionally, ammonium and short-chain fatty acid concentrations were determined. The Arginine microcosms were dominated by Streptococcus, Veillonella, and Neisseria and remained stable in time, while the composition of the Control microcosms diverged significantly in time, partially due to the presence of Megasphaera. The percentage of Candida increased 100-fold in the Control microcosms compared to the Arginine microcosms. The pH-raising effect of arginine was confirmed by the pH and ammonium results. The abundances of sagP and arcA were highest in the Arginine microcosms, while the concentration of butyrate was higher in the Control microcosms. We demonstrate that supplementation with arginine serves a health-promoting function; it enhances microcosm resilience toward acidification and suppresses outgrowth of the opportunistic pathogen Candida. Arginine facilitates stability of oral microbial communities and prevents them from becoming cariogenic.}, }
@article {pmid25432577, year = {2015}, author = {Da Silva, ML and Cantão, ME and Mezzari, MP and Ma, J and Nossa, CW}, title = {Assessment of bacterial and archaeal community structure in Swine wastewater treatment processes.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {77-87}, pmid = {25432577}, issn = {1432-184X}, mesh = {Animals ; Archaea/*genetics ; Bacteria/*genetics ; Base Sequence ; DNA, Ribosomal/genetics ; High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; Molecular Sequence Data ; Species Specificity ; Swine ; Waste Disposal, Fluid/*methods ; Wastewater/*microbiology ; }, abstract = {Microbial communities from two field-scale swine wastewater treatment plants (WWTPs) were assessed by pyrosequencing analyses of bacterial and archaeal 16S ribosomal DNA (rDNA) fragments. Effluent samples from secondary (anaerobic covered lagoons and upflow anaerobic sludge blanket [UASB]) and tertiary treatment systems (open-pond natural attenuation lagoon and air-sparged nitrification-denitrification tank followed by alkaline phosphorus precipitation process) were analyzed. A total of 56,807 and 48,859 high-quality reads were obtained from bacterial and archaeal libraries, respectively. Dominant bacterial communities were associated with the phylum Firmicutes, Bacteroidetes, Proteobacteria, or Actinobacteria. Bacteria and archaea diversity were highest in UASB effluent sample. Escherichia, Lactobacillus, Bacteroides, and/or Prevotella were used as indicators of putative pathogen reduction throughout the WWTPs. Satisfactory pathogen reduction was observed after the open-pond natural attenuation lagoon but not after the air-sparged nitrification/denitrification followed by alkaline phosphorus precipitation treatment processes. Among the archaeal communities, 80% of the reads was related to hydrogeno-trophic methanogens Methanospirillum. Enrichment of hydrogenotrophic methanogens detected in effluent samples from the anaerobic covered lagoons and UASB suggested that CO2 reduction with H2 was the dominant methanogenic pathway in these systems. Overall, the results served to improve our current understanding of major microbial communities' changes downgradient from the pen and throughout swine WWTP as a result of different treatment processes.}, }
@article {pmid25431569, year = {2014}, author = {Schmidt, VT and Reveillaud, J and Zettler, E and Mincer, TJ and Murphy, L and Amaral-Zettler, LA}, title = {Oligotyping reveals community level habitat selection within the genus Vibrio.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {563}, pmid = {25431569}, issn = {1664-302X}, support = {P50 ES012742/ES/NIEHS NIH HHS/United States ; }, abstract = {The genus Vibrio is a metabolically diverse group of facultative anaerobic bacteria, common in aquatic environments and marine hosts. The genus contains several species of importance to human health and aquaculture, including the causative agents of human cholera and fish vibriosis. Vibrios display a wide variety of known life histories, from opportunistic pathogens to long-standing symbionts with individual host species. Studying Vibrio ecology has been challenging as individual species often display a wide range of habitat preferences, and groups of vibrios can act as socially cohesive groups. Although strong associations with salinity, temperature and other environmental variables have been established, the degree of habitat or host specificity at both the individual and community levels is unknown. Here we use oligotyping analyses in combination with a large collection of existing Vibrio 16S ribosomal RNA (rRNA) gene sequence data to reveal patterns of Vibrio ecology across a wide range of environmental, host, and abiotic substrate associated habitats. Our data show that individual taxa often display a wide range of habitat preferences yet tend to be highly abundant in either substrate-associated or free-living environments. Our analyses show that Vibrio communities share considerable overlap between two distinct hosts (i.e., sponge and fish), yet are distinct from the abiotic plastic substrates. Lastly, evidence for habitat specificity at the community level exists in some habitats, despite considerable stochasticity in others. In addition to providing insights into Vibrio ecology across a broad range of habitats, our study shows the utility of oligotyping as a facile, high-throughput and unbiased method for large-scale analyses of publically available sequence data repositories and suggests its wide application could greatly extend the range of possibilities to explore microbial ecology.}, }
@article {pmid25429288, year = {2014}, author = {Fierer, N and Barberán, A and Laughlin, DC}, title = {Seeing the forest for the genes: using metagenomics to infer the aggregated traits of microbial communities.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {614}, pmid = {25429288}, issn = {1664-302X}, abstract = {Most environments harbor large numbers of microbial taxa with ecologies that remain poorly described and characterizing the functional capabilities of whole communities remains a key challenge in microbial ecology. Shotgun metagenomic analyses are increasingly recognized as a powerful tool to understand community-level attributes. However, much of this data is under-utilized due, in part, to a lack of conceptual strategies for linking the metagenomic data to the most relevant community-level characteristics. Microbial ecologists could benefit by borrowing the concept of community-aggregated traits (CATs) from plant ecologists to glean more insight from the ever-increasing amount of metagenomic data being generated. CATs can be used to quantify the mean and variance of functional traits found in a given community. A CAT-based strategy will often yield far more useful information for predicting the functional attributes of diverse microbial communities and changes in those attributes than the more commonly used analytical strategies. A more careful consideration of what CATs to measure and how they can be quantified from metagenomic data, will help build a more integrated understanding of complex microbial communities.}, }
@article {pmid25427009, year = {2014}, author = {Claessen, D and van Wezel, GP}, title = {Off the wall.}, journal = {eLife}, volume = {3}, number = {}, pages = {}, pmid = {25427009}, issn = {2050-084X}, mesh = {Bacteria/*cytology ; Cell Wall/*metabolism ; L Forms/*cytology ; }, abstract = {Bacteria that grow and proliferate despite having been stripped of their cell wall may provide insights into how primordial cells could have propagated billions of years ago.}, }
@article {pmid25426111, year = {2014}, author = {Nazir, R and Tazetdinova, DI and van Elsas, JD}, title = {Burkholderia terrae BS001 migrates proficiently with diverse fungal hosts through soil and provides protection from antifungal agents.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {598}, pmid = {25426111}, issn = {1664-302X}, abstract = {Soil bacteria can benefit from co-occurring soil fungi in respect of the acquisition of carbonaceous nutrients released by fungal hyphae and the access to novel territories in soil. Here, we investigated the capacity of the mycosphere-isolated bacterium Burkholderia terrae BS001 to comigrate through soil along with hyphae of the soil fungi Trichoderma asperellum, Rhizoctonia solani, Fusarium oxysporum, F. oxysporum pv lini, Coniochaeta ligniaria, Phanerochaete velutina, and Phallus impudicus. We used Lyophyllum sp. strain Karsten as the reference migration-inciting fungus. Bacterial migration through presterilized soil on the extending fungal hyphae was detected with six of the seven test fungi, with only Phallus impudicus not showing any bacterial transport. Much like with Lyophyllum sp. strain Karsten, intermediate (10(6)-10(8) CFU g(-1) dry soil) to high (>10(8) CFU g(-1) dry soil) strain BS001 cell population sizes were found at the hyphal migration fronts of four fungi, i.e., T. asperellum, Rhizoctonia solani, F. oxysporum and F. oxysporum pv lini, whereas for two fungi, Coniochaeta ligniaria and Phanerochaete velutina, the migration responses were retarded and population sizes were lower (10(3)-10(6) CFU g(-1) dry soil). Consistent with previous data obtained with the reference fungus, migration with the migration-inciting fungi occurred only in the direction of the hyphal growth front. Remarkably, Burkholderia terrae BS001 provided protection from several antifungal agents to the canonical host Lyophyllum sp. strain Karsten. Specifically, this host was protected from Pseudomonas fluorescens strain CHA0 metabolites, as well as from the anti-fungal agent cycloheximide. Similar protection by strain BS001was observed for T. asperellum, and, to a lower extent, F. oxysporum and Rhizoctonia solani. The protective effect may be related to the consistent occurrence of biofilm-like cell layers or agglomerates at the surfaces of the protected fungi. The current study represents the first report of protection of soil fungi against antagonistic agents present in the soil provided by fungal-associated Burkholderia terrae cells.}, }
@article {pmid25426105, year = {2014}, author = {Head, IM and Gray, ND and Larter, SR}, title = {Life in the slow lane; biogeochemistry of biodegraded petroleum containing reservoirs and implications for energy recovery and carbon management.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {566}, pmid = {25426105}, issn = {1664-302X}, abstract = {Our understanding of the processes underlying the formation of heavy oil has been transformed in the last decade. The process was once thought to be driven by oxygen delivered to deep petroleum reservoirs by meteoric water. This paradigm has been replaced by a view that the process is anaerobic and frequently associated with methanogenic hydrocarbon degradation. The thermal history of a reservoir exerts a fundamental control on the occurrence of biodegraded petroleum, and microbial activity is focused at the base of the oil column in the oil water transition zone, that represents a hotspot in the petroleum reservoir biome. Here we present a synthesis of new and existing microbiological, geochemical, and biogeochemical data that expands our view of the processes that regulate deep life in petroleum reservoir ecosystems and highlights interactions of a range of biotic and abiotic factors that determine whether petroleum is likely to be biodegraded in situ, with important consequences for oil exploration and production. Specifically we propose that the salinity of reservoir formation waters exerts a key control on the occurrence of biodegraded heavy oil reservoirs and introduce the concept of palaeopickling. We also evaluate the interaction between temperature and salinity to explain the occurrence of non-degraded oil in reservoirs where the temperature has not reached the 80-90°C required for palaeopasteurization. In addition we evaluate several hypotheses that might explain the occurrence of organisms conventionally considered to be aerobic, in nominally anoxic petroleum reservoir habitats. Finally we discuss the role of microbial processes for energy recovery as we make the transition from fossil fuel reliance, and how these fit within the broader socioeconomic landscape of energy futures.}, }
@article {pmid25425419, year = {2014}, author = {Probst, AJ and Weinmaier, T and Raymann, K and Perras, A and Emerson, JB and Rattei, T and Wanner, G and Klingl, A and Berg, IA and Yoshinaga, M and Viehweger, B and Hinrichs, KU and Thomas, BC and Meck, S and Auerbach, AK and Heise, M and Schintlmeister, A and Schmid, M and Wagner, M and Gribaldo, S and Banfield, JF and Moissl-Eichinger, C}, title = {Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {5497}, doi = {10.1038/ncomms6497}, pmid = {25425419}, issn = {2041-1723}, mesh = {Archaea/classification/genetics/growth &amp; development/*metabolism ; Carbon/*metabolism ; Carbon Cycle ; Groundwater/analysis/*microbiology ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Subsurface microbial life contributes significantly to biogeochemical cycling, yet it remains largely uncharacterized, especially its archaeal members. This 'microbial dark matter' has been explored by recent studies that were, however, mostly based on DNA sequence information only. Here, we use diverse techniques including ultrastuctural analyses to link genomics to biology for the SM1 Euryarchaeon lineage, an uncultivated group of subsurface archaea. Phylogenomic analyses reveal this lineage to belong to a widespread group of archaea that we propose to classify as a new euryarchaeal order ('Candidatus Altiarchaeales'). The representative, double-membraned species 'Candidatus Altiarchaeum hamiconexum' has an autotrophic metabolism that uses a not-yet-reported Factor420-free reductive acetyl-CoA pathway, confirmed by stable carbon isotopic measurements of archaeal lipids. Our results indicate that this lineage has evolved specific metabolic and structural features like nano-grappling hooks empowering this widely distributed archaeon to predominate anaerobic groundwater, where it may represent an important carbon dioxide sink.}, }
@article {pmid25422793, year = {2013}, author = {Neu, J}, title = {The Microbiome and Its Impact on Disease in the Preterm Patient.}, journal = {Current pediatrics reports}, volume = {1}, number = {4}, pages = {215-221}, pmid = {25422793}, issn = {2167-4841}, support = {R01 HD059143/HD/NICHD NIH HHS/United States ; }, abstract = {Emerging technologies derived largely from the Human Genome Project are being applied to evaluating the intestinal microbiota in preterm infants. The microbial ecology of the developing intestine is highly related to health and disease and new discoveries are emerging that will help us understand disorders in the development of the intestinal microbial ecosystem and how to eventually manipulate them to prevent diseases such as necrotizing enterocolitis and late onset sepsis. Here, a brief overview of the developing microbiome as it pertains to several aspects of health and disease in the preterm infant is presented.}, }
@article {pmid25421563, year = {2015}, author = {Wang, Z and Yang, Y and He, T and Xie, S}, title = {Change of microbial community structure and functional gene abundance in nonylphenol-degrading sediment.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {7}, pages = {3259-3268}, doi = {10.1007/s00253-014-6222-5}, pmid = {25421563}, issn = {1432-0614}, mesh = {Bacteria/*genetics/metabolism ; Biodegradation, Environmental ; Biodiversity ; Geologic Sediments/*microbiology ; Microbial Consortia/drug effects/*genetics ; Phenols/*metabolism ; Water Pollutants, Chemical/metabolism ; }, abstract = {Biodegradation by autochthonous microbial community is an important way to clean up nonylphenol (NP) from contaminated river sediment. Knowledge of sediment microbial community can aid in our understanding of biological processes related to NP degradation. However, the change in sediment microbial community associated with NP biodegradation remains unclear. The present study investigated the shift in bacterial community structure and NP-degrading gene abundance in response to NP attenuation in river sediment. Sediment microcosms with different levels of 4-NP (0, 100, or 300 μg/g) were constructed. A nearly complete attenuation of NP occurred in the microcosm with 100 μg/g NP after 9 days' incubation, while a residual NP rate of 8.1 % was observed in the microcosm with 300 μg/g NP after 22 days' incubation. Illumina MiSeq sequencing analysis indicated that Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes predominated in NP-degrading river sediment. Sediment bacterial community structure varied significantly during NP biodegradation and subsequent incubation, which was affected by the level of added NP. The n-alkane biodegradation (alkB) gene abundance showed a significant variation in each NP-amended microcosm (100 or 300 μg/g), while a significant increase in the single component monooxygenase (sMO) gene abundance only occurred in the microcosm spiked with 300 μg/g NP. This study can provide some new insights toward NP-degrading microbial ecology in the environment.}, }
@article {pmid25421389, year = {2015}, author = {Halpern, M and Senderovich, Y}, title = {Chironomid microbiome.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {1-8}, pmid = {25421389}, issn = {1432-184X}, support = {ILB1-7045-HA-11//PHS HHS/United States ; }, mesh = {Aeromonas/genetics/physiology ; Animals ; Chironomidae/*microbiology/physiology ; Life Cycle Stages/*physiology ; Microbiota/*genetics ; Quorum Sensing/physiology ; Species Specificity ; Vibrio cholerae/genetics/physiology ; }, abstract = {Chironomids are abundant insects in freshwater habitats. They undergo a complete metamorphosis of four life stages: eggs, larvae, and pupae in water, and a terrestrial adult stage. Chironomids are known to be pollution-tolerant, but little is known about their resistance mechanisms to toxic substances. Here we review current knowledge regarding the chironomid microbiome. Chironomids were found as natural reservoirs of Vibrio cholerae and Aeromonas spp. A stable bacterial community was found in the egg masses and the larvae when both culture-dependent and -independent methods were used. A large portion of the endogenous bacterial species was closely related to species known as toxicant degraders. Bioassays based on Koch's postulates demonstrated that the chironomid microbiome plays a role in protecting its host from toxic hexavalent chromium and lead. V. cholerae, a stable resident in chironomids, is present at low prevalence. It degrades the egg masses by secreting haemagglutinin/protease, prevents eggs from hatching, and exhibits host pathogen interactions with chironomids. However, the nutrients from the degraded egg masses may support the growth of the other microbiome members and consequently control V. cholerae numbers in the egg mass. V. cholerae, other chironomid endogenous bacteria, and their chironomid host exhibit complex mutualistic relationships.}, }
@article {pmid25413210, year = {2015}, author = {Ruyters, S and Mukherjee, V and Verstrepen, KJ and Thevelein, JM and Willems, KA and Lievens, B}, title = {Assessing the potential of wild yeasts for bioethanol production.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {42}, number = {1}, pages = {39-48}, pmid = {25413210}, issn = {1476-5535}, mesh = {Biofuels/*microbiology ; Candida/metabolism ; Ethanol/*metabolism ; Fermentation ; Lignin/metabolism ; Phenotype ; Saccharomyces cerevisiae/*metabolism ; Saccharomycetales/metabolism ; }, abstract = {Bioethanol fermentations expose yeasts to a new, complex and challenging fermentation medium with specific inhibitors and sugar mixtures depending on the type of carbon source. It is, therefore, suggested that the natural diversity of yeasts should be further exploited in order to find yeasts with good ethanol yield in stressed fermentation media. In this study, we screened more than 50 yeast isolates of which we selected five isolates with promising features. The species Candida bombi, Wickerhamomyces anomalus and Torulaspora delbrueckii showed better osmo- and hydroxymethylfurfural tolerance than Saccharomyces cerevisiae. However, S. cerevisiae isolates had the highest ethanol yield in fermentation experiments mimicking high gravity fermentations (25 % glucose) and artificial lignocellulose hydrolysates (with a myriad of inhibitors). Interestingly, among two tested S. cerevisiae strains, a wild strain isolated from an oak tree performed better than Ethanol Red, a S. cerevisiae strain which is currently commonly used in industrial bioethanol fermentations. Additionally, a W. anomalus strain isolated from sugar beet thick juice was found to have a comparable ethanol yield, but needed longer fermentation time. Other non-Saccharomyces yeasts yielded lower ethanol amounts.}, }
@article {pmid25412983, year = {2015}, author = {Sachsenberg, T and Herbst, FA and Taubert, M and Kermer, R and Jehmlich, N and von Bergen, M and Seifert, J and Kohlbacher, O}, title = {MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics.}, journal = {Journal of proteome research}, volume = {14}, number = {2}, pages = {619-627}, doi = {10.1021/pr500245w}, pmid = {25412983}, issn = {1535-3907}, mesh = {*Automation ; Isotopes/*metabolism ; Proteins/*metabolism ; *Proteomics ; }, abstract = {We propose a joint experimental and theoretical approach to the automated reconstruction of elemental fluxes in microbial communities. While stable isotope probing of proteins (protein-SIP) has been successfully applied to study interactions and elemental carbon and nitrogen fluxes, the volume and complexity of mass spectrometric data in protein-SIP experiments pose new challenges for data analysis. Together with a flexible experimental setup, the novel bioinformatics tool MetaProSIP offers an automated high-throughput solution for a wide range of (13)C or (15)N protein-SIP experiments with special emphasis on the analysis of metaproteomic experiments where differential labeling of organisms can occur. The information calculated in MetaProSIP includes the determination of multiple relative isotopic abundances, the labeling ratio between old and new synthesized proteins, and the shape of the isotopic distribution. These parameters define the metabolic capacities and dynamics within the investigated microbial culture. MetaProSIP features a high degree of reproducibility, reliability, and quality control reporting. The ability to embed into the OpenMS framework allows for flexible construction of custom-tailored workflows. Software and documentation are available under an open-source license at www.openms.de/MetaProSIP.}, }
@article {pmid25412608, year = {2014}, author = {Henne, K and Fuchs, F and Kruth, S and Horz, HP and Conrads, G}, title = {Shifts in Campylobacter species abundance may reflect general microbial community shifts in periodontitis progression.}, journal = {Journal of oral microbiology}, volume = {6}, number = {}, pages = {25874}, pmid = {25412608}, issn = {2000-2297}, abstract = {BACKGROUND: Oral Campylobacter species have been found to be associated with periodontitis progression. While the etiological significance of Campylobacter rectus is quite established, the association of C. gracilis, C. concisus, and C. curvus with health or disease remains contradictory.<br><br>OBJECTIVES: This study hypothesizes that the proportion of species within the Campylobacter genus rather than the absolute abundance of a single species is a suitable indicator for periodontitis progression.<br><br>DESIGN: Subgingival plaque from 90 periodontitis patients and gingival sulcus fluid of 32 healthy individuals were subjected to a newly developed nested PCR approach, in which all Campylobacter spp. were amplified simultaneously. The resulting mixture of 16S-rRNA-gene-amplicons were separated by single-stranded conformation polymorphism (SSCP) gel electrophoresis, followed by sequencing and identification of excised bands and relative quantification of band intensities. In all samples, the abundance of selected periodontitis marker species was determined based on DNA hybridization on a microarray.<br><br>RESULTS: The highly prevalent Campylobacter community was composed of varying proportions of C. rectus, C. gracilis, C. concisus, and C. curvus. Cluster analysis based on SSCP-banding pattern resulted in distinct groups which in turn coincided with significant differences in abundance of established periodontitis marker species (Tannerella forsythia, Porphyromonas gingivalis, and Fusobacterium nucleatum) and progression.<br><br>CONCLUSIONS: The shift in the Campylobacter community composition seems to display the general microbial community shift during clinical progression in a simplified manner. The focus on members of the Campylobacter in this study suggests that this genus can be an indicator of ecological changes in the subgingival oral microflora.}, }
@article {pmid25408227, year = {2015}, author = {Hagemann, M and Henneberg, M and Felde, VJ and Drahorad, SL and Berkowicz, SM and Felix-Henningsen, P and Kaplan, A}, title = {Cyanobacterial Diversity in Biological Soil Crusts along a Precipitation Gradient, Northwest Negev Desert, Israel.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {219-230}, pmid = {25408227}, issn = {1432-184X}, mesh = {Base Sequence ; *Biodiversity ; Cluster Analysis ; Cyanobacteria/*genetics/*physiology ; DNA Primers/genetics ; Desert Climate ; Galactosides ; Indoles ; Israel ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S ; Rain ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Cyanobacteria occur worldwide but play an important role in the formation and primary activity of biological soil crusts (BSCs) in arid and semi-arid ecosystems. The cyanobacterial diversity in BSCs of the northwest Negev desert of Israel was surveyed at three fixed sampling stations situated along a precipitation gradient in the years 2010 to 2012. The three stations also are characterized by marked differences in soil features such as soil carbon, nitrogen, or electrical conductivity. The cyanobacterial biodiversity was analyzed by sequencing inserts of clone libraries harboring partial 16S rRNA gene sequences obtained with cyanobacteria-specific primers. Filamentous, non-diazotrophic strains (subsection III), particularly Microcoleus-like, dominated the cyanobacterial community (30% proportion) in all years. Specific cyanobacterial groups showed increased (e.g., Chroococcidiopsis, Leptolyngbya, and Nostoc strains) or decreased (e.g., unicellular strains belonging to the subsection I and Scytonema strains) abundances with declining water availability at the most arid, southern station, whereas many cyanobacterial strains were frequently found in the soils of all three stations. The cyanobacterial diversity at the three sampling stations appears dependent on the available precipitation, whereas the differences in soil chemistry were of lower importance.}, }
@article {pmid25407899, year = {2015}, author = {Chaib De Mares, M and Hess, J and Floudas, D and Lipzen, A and Choi, C and Kennedy, M and Grigoriev, IV and Pringle, A}, title = {Horizontal transfer of carbohydrate metabolism genes into ectomycorrhizal Amanita.}, journal = {The New phytologist}, volume = {205}, number = {4}, pages = {1552-1564}, doi = {10.1111/nph.13140}, pmid = {25407899}, issn = {1469-8137}, mesh = {Amanita/enzymology/*genetics ; Carbohydrate Metabolism/*genetics ; Fungal Proteins/chemistry/genetics ; *Gene Transfer, Horizontal ; *Genes, Fungal ; Models, Molecular ; Mycorrhizae/*genetics ; Phylogeny ; Physical Chromosome Mapping ; Species Specificity ; }, abstract = {The genus Amanita encompasses both symbiotic, ectomycorrhizal fungi and asymbiotic litter decomposers; all species are derived from asymbiotic ancestors. Symbiotic species are no longer able to degrade plant cell walls. The carbohydrate esterases family 1 (CE1s) is a diverse group of enzymes involved in carbon metabolism, including decomposition and carbon storage. CE1 genes of the ectomycorrhizal A. muscaria appear diverged from all other fungal homologues, and more similar to CE1s of bacteria, suggesting a horizontal gene transfer (HGT) event. In order to test whether AmanitaCE1s were acquired horizontally, we built a phylogeny of CE1s collected from across the tree of life, and describe the evolution of CE1 genes among Amanita and relevant lineages of bacteria. CE1s of symbiotic Amanita were very different from CE1s of asymbiotic Amanita, and are more similar to bacterial CE1s. The protein structure of one CE1 gene of A. muscaria matched a depolymerase that degrades the carbon storage molecule poly((R)-3-hydroxybutyrate) (PHB). Asymbiotic Amanita do not carry sequence or structural homologues of these genes. The CE1s acquired through HGT may enable novel metabolisms, or play roles in signaling or defense. This is the first evidence for the horizontal transfer of carbohydrate metabolism genes into ectomycorrhizal fungi.}, }
@article {pmid25403111, year = {2015}, author = {Rousk, K and Sorensen, PL and Lett, S and Michelsen, A}, title = {Across-habitat comparison of diazotroph activity in the subarctic.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {778-787}, pmid = {25403111}, issn = {1432-184X}, mesh = {Bacteria/*metabolism ; *Ecosystem ; Embryophyta/*metabolism/microbiology ; Lichens/*metabolism/microbiology ; *Nitrogen Fixation ; Soil/chemistry ; *Soil Microbiology ; Sweden ; Taiga ; Wetlands ; }, abstract = {Nitrogen (N) fixation by N2-fixing bacteria (diazotrophs) is the primary N input to pristine ecosystems like boreal forests and subarctic and arctic tundra. However, the contribution by the various diazotrophs to habitat N2 fixation remains unclear. We present results from in situ assessments of N2 fixation of five diazotroph associations (with a legume, lichen, feather moss, Sphagnum moss and free-living) incorporating the ground cover of the associations in five typical habitats in the subarctic (wet and dry heath, polygon-heath, birch forest, mire). Further, we assessed the importance of soil and air temperature, as well as moisture conditions for N2 fixation. Across the growing season, the legume had the highest total as well as the highest fraction of N2 fixation rates at habitat level in the heaths (>85 % of habitat N2 fixation), whereas the free-living diazotrophs had the highest N2 fixation rates in the polygon heath (56 %), the lichen in the birch forest (87 %) and Sphagnum in the mire (100 %). The feather moss did not contribute more than 15 % to habitat N2 fixation in any of the habitats despite its high ground cover. Moisture content seemed to be a major driver of N2 fixation in the lichen, feather moss and free-living diazotrophs. Our results show that the range of N2 fixers found in pristine habitats contribute differently to habitat N2 fixation and that ground cover of the associates does not necessarily mirror contribution.}, }
@article {pmid25403110, year = {2015}, author = {Barthès, A and Ten-Hage, L and Lamy, A and Rols, JL and Leflaive, J}, title = {Resilience of aggregated microbial communities subjected to drought--small-scale studies.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {9-20}, pmid = {25403110}, issn = {1432-184X}, mesh = {Acclimatization/*physiology ; Analysis of Variance ; Biofilms/*growth &amp; development ; *Droughts ; Microbiota/*physiology ; Principal Component Analysis ; Species Specificity ; Stress, Physiological/*physiology ; Time Factors ; }, abstract = {The response of microbial communities to disturbance is a major concern for microbial ecologists since potential modifications in their composition and functioning may affect ecosystems to a larger extent. Microbial ecosystems may be resistant (not affected) or may present engineering (return to initial state) or ecological resilience. In the latter case, when the disturbance is released, the ecosystem evolves towards a new equilibrium state. The aim of this study was to determine if variations in the magnitude of a disturbance could induce either engineering or ecological resilience. We used phototrophic biofilms grown in mesocosms as a model of microbial ecosystem and increasing drought duration (1-8 weeks) as a range of disturbances. Biofilm composition (algal and prokaryotic), photosynthetic activity (PhytoPAM), and potential functional diversity (Biolog) were determined at the end of dry phase and after a 2-week rewetting phase in individual aquaria. We only observed an ecological resilience of the biofilm, with a resistance of phototrophic component for the weakest disturbance. After rewetting, the biofilm could fulfill the same functions, but its species composition was highly modified. We observed a shift from cyanobacteria dominance towards diatom dominance. The disturbance caused a transition towards a new steady state of the biofilm. We also observed a positive effect of stress duration on biofilm productivity after resilience.}, }
@article {pmid25399511, year = {2015}, author = {LeBlanc, N and Kinkel, LL and Kistler, HC}, title = {Soil fungal communities respond to grassland plant community richness and soil edaphics.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {188-195}, pmid = {25399511}, issn = {1432-184X}, mesh = {Analysis of Variance ; Base Sequence ; Fungi/*genetics ; *Grassland ; Metagenomics/methods ; Minnesota ; Molecular Sequence Data ; Population Dynamics ; RNA, Ribosomal/genetics ; *Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Fungal communities in soil have significant influences on terrestrial ecosystem dynamics, yet our understanding of the drivers of fungal diversity and community structure in soil is limited. Fungal communities associated with the rhizosphere of four native perennial grassland plant species, two legumes and two grasses, grown in monoculture and polyculture in a long-term field experiment were characterized. Reference databases were developed for, and amplicon libraries sequenced from, multiple-copy rRNA and single-copy protein-coding loci. Clustering and alignment-based pipelines were utilized to evaluate differences in fungal community structure and diversity in response to plant host, plant community richness, and soil edaphics. Fungal diversity increased in the rhizosphere of plants growing in polyculture plant communities as compared to monoculture plant communities. Fungal community structure was differentiated between legumes and grasses growing in monoculture but not in polyculture. To specifically monitor fungi in the genus Fusarium in the soil, the protein-coding locus was used to increase phylogenetic resolution and enrich for this taxon. These data show that fungal community richness and structure are strongly linked with plant community dynamics and associated soil edaphic characteristics in these grassland soils.}, }
@article {pmid25398863, year = {2015}, author = {Nowka, B and Daims, H and Spieck, E}, title = {Comparison of oxidation kinetics of nitrite-oxidizing bacteria: nitrite availability as a key factor in niche differentiation.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {2}, pages = {745-753}, pmid = {25398863}, issn = {1098-5336}, mesh = {Bacteria/*metabolism ; Environmental Microbiology ; Models, Theoretical ; *Nitrification ; Nitrites/*metabolism ; Oxidation-Reduction ; Temperature ; }, abstract = {Nitrification has an immense impact on nitrogen cycling in natural ecosystems and in wastewater treatment plants. Mathematical models function as tools to capture the complexity of these biological systems, but kinetic parameters especially of nitrite-oxidizing bacteria (NOB) are lacking because of a limited number of pure cultures until recently. In this study, we compared the nitrite oxidation kinetics of six pure cultures and one enrichment culture representing three genera of NOB (Nitrobacter, Nitrospira, Nitrotoga). With half-saturation constants (Km) between 9 and 27 μM nitrite, Nitrospira bacteria are adapted to live under significant substrate limitation. Nitrobacter showed a wide range of lower substrate affinities, with Km values between 49 and 544 μM nitrite. However, the advantage of Nitrobacter emerged under excess nitrite supply, sustaining high maximum specific activities (Vmax) of 64 to 164 μmol nitrite/mg protein/h, contrary to the lower activities of Nitrospira of 18 to 48 μmol nitrite/mg protein/h. The Vmax (26 μmol nitrite/mg protein/h) and Km (58 μM nitrite) of "Candidatus Nitrotoga arctica" measured at a low temperature of 17°C suggest that Nitrotoga can advantageously compete with other NOB, especially in cold habitats. The kinetic parameters determined represent improved basis values for nitrifying models and will support predictions of community structure and nitrification rates in natural and engineered ecosystems.}, }
@article {pmid25395291, year = {2015}, author = {Zhalnina, K and Dias, R and de Quadros, PD and Davis-Richardson, A and Camargo, FA and Clark, IM and McGrath, SP and Hirsch, PR and Triplett, EW}, title = {Soil pH determines microbial diversity and composition in the park grass experiment.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {395-406}, pmid = {25395291}, issn = {1432-184X}, support = {BBS/E/C/00004962/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/C/00004980/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/C/00006004/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Ammonium Sulfate/chemistry ; Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Biomass ; Carbon/chemistry ; Fertilizers/analysis ; Hydrogen-Ion Concentration ; Nitrates/chemistry ; Nitrification ; Nitrogen/chemistry ; Phosphorus/chemistry ; Poaceae/chemistry/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {The Park Grass experiment (PGE) in the UK has been ongoing since 1856. Its purpose is to study the response of biological communities to the long-term treatments and associated changes in soil parameters, particularly soil pH. In this study, soil samples were collected across pH gradient (pH 3.6-7) and a range of fertilizers (nitrogen as ammonium sulfate, nitrogen as sodium nitrate, phosphorous) to evaluate the effects nutrients have on soil parameters and microbial community structure. Illumina 16S ribosomal RNA (rRNA) amplicon sequencing was used to determine the relative abundances and diversity of bacterial and archaeal taxa. Relationships between treatments, measured soil parameters, and microbial communities were evaluated. Clostridium, Bacteroides, Bradyrhizobium, Mycobacterium, Ruminococcus, Paenibacillus, and Rhodoplanes were the most abundant genera found at the PGE. The main soil parameter that determined microbial composition, diversity, and biomass in the PGE soil was pH. The most probable mechanism of the pH impact on microbial community may include mediation of nutrient availability in the soil. Addition of nitrogen to the PGE plots as ammonium sulfate decreases soil pH through increased nitrification, which causes buildup of soil carbon, and hence increases C/N ratio. Plant species richness and plant productivity did not reveal significant relationships with microbial diversity; however, plant species richness was positively correlated with soil microbial biomass. Plants responded to the nitrogen treatments with an increase in productivity and a decrease in the species richness.}, }
@article {pmid25394235, year = {2015}, author = {El Feghaly, RE and Bangar, H and Haslam, DB}, title = {The molecular basis of Clostridium difficile disease and host response.}, journal = {Current opinion in gastroenterology}, volume = {31}, number = {1}, pages = {24-29}, doi = {10.1097/MOG.0000000000000131}, pmid = {25394235}, issn = {1531-7056}, support = {P30 DK078392/DK/NIDDK NIH HHS/United States ; UL1TR000077/TR/NCATS NIH HHS/United States ; }, mesh = {Biomarkers/metabolism ; Clostridioides difficile/*pathogenicity/physiology ; Enterocolitis, Pseudomembranous/diagnosis/*genetics/*microbiology/therapy ; Feces/microbiology ; Host-Pathogen Interactions ; Humans ; Microbiota ; Tissue Transplantation/methods ; }, abstract = {PURPOSE OF REVIEW: Clostridium difficile infection (CDI) ranges from asymptomatic colonization to severe colitis and death. The physiologic and molecular mechanisms determining disease outcome are thus far poorly understood. Here, we review recent advances in the relationship between host response to infection and disease outcome. Furthermore, we review recent studies on the relationship between intestinal microbial ecology and pathogenesis of CDI.<br><br>RECENT FINDINGS: Severe CDI is characterized by toxin-induced epithelial injury and marked intestinal inflammation. Recent studies demonstrate that systemic markers of inflammation correlate with disease outcome. Peripheral neutrophil count, C-reactive protein, and proinflammatory cytokines are elevated in patients with severe disease as compared with asymptomatic controls. Furthermore, fecal inflammatory biomarkers are better predictors of disease severity and diarrhea persistence than C. difficile abundance. A landmark study reported higher than 80% success rate of fecal microbiota transplantation for treatment of recurrent CDI. The commensal microbes responsible for C. difficile protection, and the molecular basis by which microbial ecology impacts disease outcome, are under active investigation.<br><br>SUMMARY: Under conditions of altered microbial ecology, C. difficile incites epithelial injury and marked intestinal inflammation, the primary determinant of disease outcome. Restoration of a diverse intestinal microbial population by fecal microbiota transplantation attenuates disease and prevents recurrence by mechanisms that are yet to be fully elucidated.}, }
@article {pmid25393146, year = {2014}, author = {Zhang, Y and Maignien, L and Stadnitskaia, A and Boeckx, P and Xiao, X and Boon, N}, title = {Stratified community responses to methane and sulfate supplies in mud volcano deposits: insights from an in vitro experiment.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e113004}, pmid = {25393146}, issn = {1932-6203}, mesh = {Archaea/*growth &amp; development ; Bacteria/*growth &amp; development ; Methane/chemistry/*metabolism ; *Models, Biological ; Sulfates/chemistry/*metabolism ; *Volcanic Eruptions ; *Water Microbiology ; }, abstract = {Numerous studies on marine prokaryotic communities have postulated that a process of anaerobic oxidation of methane (AOM) coupled with sulfate reduction (SR) is the main methane sink in the world's oceans. AOM has also been reported in the deep biosphere. But the responses of the primary microbial players in eliciting changes in geochemical environments, specifically in methane and sulfate supplies, have yet to be fully elucidated. Marine mud volcanoes (MVs) expel a complex fluid mixture of which methane is the primary component, forming an environment in which AOM is a common phenomenon. In this context, we attempted to identify how the prokaryotic community would respond to changes in methane and sulfate intensities, which often occur in MV environments in the form of eruptions, diffusions or seepage. We applied an integrated approach, including (i) biochemical surveys of pore water originated from MV, (ii) in vitro incubation of mud breccia, and (iii) prokaryotic community structure analysis. Two distinct AOM regions were clearly detected. One is related to the sulfate methane transition zone (SMTZ) at depth of 30-55 cm below the sea floor (bsf); the second is at 165-205 cm bsf with ten times higher rates of AOM and SR. This finding contrasts with the sulfide concentrations in pore waters and supports the suggestion that potential AOM activity below the SMTZ might be an important methane sink that is largely ignored or underestimated in oceanic methane budget calculations. Moreover, the incubation conditions below the SMTZ favor the growth of methanotrophic archaeal group ANME-2 compared to ANME-1, and promote the rapid growth and high diversity of bacterial communities. These incubation conditions also promote the increase of richness in bacterial communities. Our results provide direct evidence of the mechanisms by which deep AOM processes can affect carbon cycling in the deep biosphere and global methane biochemistry.}, }
@article {pmid25391353, year = {2015}, author = {Sultanpuram, VR and Mothe, T and Mohammed, F}, title = {Streptomyces alkalithermotolerans sp. nov., a novel alkaliphilic and thermotolerant actinomycete isolated from a soda lake.}, journal = {Antonie van Leeuwenhoek}, volume = {107}, number = {2}, pages = {337-344}, doi = {10.1007/s10482-014-0332-z}, pmid = {25391353}, issn = {1572-9699}, mesh = {Bacterial Typing Techniques ; Base Composition ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fatty Acids/analysis ; Hydrogen-Ion Concentration ; India ; Lakes/*microbiology ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Streptomyces/*classification/genetics/*isolation &amp; purification/physiology ; }, abstract = {An alkaliphilic actinomycete, strain AC3(T), was isolated from Lonar soda lake, in India. Based on 16S rRNA gene sequence analysis it was identified that the strain belongs to the class Actinobacteria and was most closely related to Streptomyces sodiiphilus JCM 13581(T) (96.4 % sequence similarity), Streptomyces leeuwenhoekii DSM 42122(T) (96.1 %), Streptomyces albus NRRL B-2365(T) (96.1 %), Streptomyces panacagri Gsoil 519(T) (96.0 %), Streptomyces fimbriatus NBRC 15411(T) (95.9 %) and other members of the genus Streptomyces (<95.9 %).The strain formed a well separated clade in the genus Streptomyces based on the 16S rRNA gene analysis of all of the validly named Streptomyces species. Strain AC3(T) was observed to produce light-cream substrate and white aerial mycelia on most tested media. The optimum pH for growth was determined to be 9.5-10.0 with no growth at pH 7.0. The DNA G+C content of strain AC3(T) was determined to be 71.2 mol %. The results of the polyphasic analysis allowed a clear differentiation of strain AC3(T) from all other members of the genus Streptomyces. Strain AC3(T) is thus considered to represent a novel member of the genus Streptomyces, for which the name Streptomyces alkalithermotolerans sp. nov. is proposed. The type strain is AC3(T) (=KCTC 29497(T) = JCM 30167(T)).}, }
@article {pmid25391238, year = {2015}, author = {Braña, AF and Fiedler, HP and Nava, H and González, V and Sarmiento-Vizcaíno, A and Molina, A and Acuña, JL and García, LA and Blanco, G}, title = {Erratum to: Two Streptomyces Species Producing Antibiotic, Antitumor, and Anti-Inflammatory Compounds Are Widespread Among Intertidal Macroalgae and Deep-Sea Coral Reef Invertebrates from the Central Cantabrian Sea.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {298}, doi = {10.1007/s00248-014-0529-8}, pmid = {25391238}, issn = {1432-184X}, }
@article {pmid25391237, year = {2015}, author = {Xiong, W and Zhao, Q and Zhao, J and Xun, W and Li, R and Zhang, R and Wu, H and Shen, Q}, title = {Different continuous cropping spans significantly affect microbial community membership and structure in a vanilla-grown soil as revealed by deep pyrosequencing.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {209-218}, pmid = {25391237}, issn = {1432-184X}, mesh = {Base Sequence ; China ; Computational Biology ; Crop Production/*methods ; DNA Primers/genetics ; DNA, Ribosomal Spacer/genetics ; Denaturing Gradient Gel Electrophoresis ; Fungi/*genetics/growth &amp; development ; *Microbiota ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; Vanilla/*growth &amp; development ; }, abstract = {In the present study, soil bacterial and fungal communities across vanilla continuous cropping time-series fields were assessed through deep pyrosequencing of 16S ribosomal RNA (rRNA) genes and internal transcribed spacer (ITS) regions. The results demonstrated that the long-term monoculture of vanilla significantly altered soil microbial communities. Soil fungal diversity index increased with consecutive cropping years, whereas soil bacterial diversity was relatively stable. Bray-Curtis dissimilarity cluster and UniFrac-weighted principal coordinate analysis (PCoA) revealed that monoculture time was the major determinant for fungal community structure, but not for bacterial community structure. The relative abundances (RAs) of the Firmicutes, Actinobacteria, Bacteroidetes, and Basidiomycota phyla were depleted along the years of vanilla monoculture. Pearson correlations at the phyla level demonstrated that Actinobacteria, Armatimonadetes, Bacteroidetes, Verrucomicrobia, and Firmicutes had significant negative correlations with vanilla disease index (DI), while no significant correlation for fungal phyla was observed. In addition, the amount of the pathogen Fusarium oxysporum accumulated with increasing years and was significantly positively correlated with vanilla DI. By contrast, the abundance of beneficial bacteria, including Bradyrhizobium and Bacillus, significantly decreased over time. In sum, soil weakness and vanilla stem wilt disease after long-term continuous cropping can be attributed to the alteration of the soil microbial community membership and structure, i.e., the reduction of the beneficial microbes and the accumulation of the fungal pathogen.}, }
@article {pmid25389421, year = {2014}, author = {Tyc, O and van den Berg, M and Gerards, S and van Veen, JA and Raaijmakers, JM and de Boer, W and Garbeva, P}, title = {Impact of interspecific interactions on antimicrobial activity among soil bacteria.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {567}, pmid = {25389421}, issn = {1664-302X}, abstract = {Certain bacterial species produce antimicrobial compounds only in the presence of a competing species. However, little is known on the frequency of interaction-mediated induction of antibiotic compound production in natural communities of soil bacteria. Here we developed a high-throughput method to screen for the production of antimicrobial activity by monocultures and pair-wise combinations of 146 phylogenetically different bacteria isolated from similar soil habitats. Growth responses of two human pathogenic model organisms, Escherichia coli WA321 and Staphylococcus aureus 533R4, were used to monitor antimicrobial activity. From all isolates, 33% showed antimicrobial activity only in monoculture and 42% showed activity only when tested in interactions. More bacterial isolates were active against S. aureus than against E. coli. The frequency of interaction-mediated induction of antimicrobial activity was 6% (154 interactions out of 2798) indicating that only a limited set of species combinations showed such activity. The screening revealed also interaction-mediated suppression of antimicrobial activity for 22% of all combinations tested. Whereas all patterns of antimicrobial activity (non-induced production, induced production and suppression) were seen for various bacterial classes, interaction-mediated induction of antimicrobial activity was more frequent for combinations of Flavobacteria and alpha- Proteobacteria. The results of our study give a first indication on the frequency of interference competitive interactions in natural soil bacterial communities which may forms a basis for selection of bacterial groups that are promising for the discovery of novel, cryptic antibiotics.}, }
@article {pmid25389417, year = {2014}, author = {Parris, DJ and Ganesh, S and Edgcomb, VP and DeLong, EF and Stewart, FJ}, title = {Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {543}, pmid = {25389417}, issn = {1664-302X}, abstract = {Molecular surveys are revealing diverse eukaryotic assemblages in oxygen-limited ocean waters. These communities may play pivotal ecological roles through autotrophy, feeding, and a wide range of symbiotic associations with prokaryotes. We used 18S rRNA gene sequencing to provide the first snapshot of pelagic microeukaryotic community structure in two cellular size fractions (0.2-1.6 μm, >1.6 μm) from seven depths through the anoxic oxygen minimum zone (OMZ) off northern Chile. Sequencing of >154,000 amplicons revealed contrasting patterns of phylogenetic diversity across size fractions and depths. Protist and total eukaryote diversity in the >1.6 μm fraction peaked at the chlorophyll maximum in the upper photic zone before declining by ~50% in the OMZ. In contrast, diversity in the 0.2-1.6 μm fraction, though also elevated in the upper photic zone, increased four-fold from the lower oxycline to a maximum at the anoxic OMZ core. Dinoflagellates of the Dinophyceae and endosymbiotic Syndiniales clades dominated the protist assemblage at all depths (~40-70% of sequences). Other protist groups varied with depth, with the anoxic zone community of the larger size fraction enriched in euglenozoan flagellates and acantharean radiolarians (up to 18 and 40% of all sequences, respectively). The OMZ 0.2-1.6 μm fraction was dominated (11-99%) by Syndiniales, which exhibited depth-specific variation in composition and total richness despite uniform oxygen conditions. Metazoan sequences, though confined primarily to the 1.6 μm fraction above the OMZ, were also detected within the anoxic zone where groups such as copepods increased in abundance relative to the oxycline and upper OMZ. These data, compared to those from other low-oxygen sites, reveal variation in OMZ microeukaryote composition, helping to identify clades with potential adaptations to oxygen-depletion.}, }
@article {pmid25388759, year = {2015}, author = {Liu, Y and Chen, X and Zhang, J and Gao, B}, title = {Hormesis effects of amoxicillin on growth and cellular biosynthesis of Microcystis aeruginosa at different nitrogen levels.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {608-617}, pmid = {25388759}, issn = {1432-184X}, mesh = {Amoxicillin/*pharmacology ; Anti-Bacterial Agents/*pharmacology ; *Hormesis ; Microcystis/*drug effects/growth &amp; development/metabolism ; Nitrogen/metabolism ; }, abstract = {Coexisting antibiotic contaminants have potential to regulate cyanobacterial bloom, and the regulation is likely affected by nitrogen supply. A typical cyanobaterium Microcystis aeruginosa was cultured with 0.05-50 mg L(-1) of nitrogen and exposed to 100-600 ng L(-1) of amoxicillin for 7 days. Algal growth was not significantly (p > 0.05) affected by amoxicillin at the lowest nitrogen level of 0.05 mg L(-1), stimulated by 600 ng L(-1) of amoxicillin at a moderate nitrogen level of 0.5 mg L(-1) and enhanced by 100-600 ng L(-1) of amoxicillin at higher nitrogen levels of 5-50 mg L(-1). Amoxicillin affected chlorophyll-a, psbA gene, and rbcL gene in a similar manner as algal growth, suggesting a regulation of algal growth via the photosynthesis system. At each nitrogen level, synthesis of protein and polysaccharides as well as production and release of microcystins (MCs) increased in response to environmental stress caused by amoxicillin. Expression of ntcA and mcyB showed a positive correlation with the total content of MCs under exposure to amoxicillin at nitrogen levels of 0.05-50 mg L(-1). Nitrogen and amoxicillin significantly (p < 0.05) interact with each other on the regulation of algal growth, synthesis of chlorophyll-a, production and release of MCs, and expression of ntcA and mcyB. The nitrogen-dependent stimulation effect of coexisting amoxicillin contaminant on M. aeruginosa bloom should be fully considered during the combined pollution control of M. aeruginosa and amoxicillin.}, }
@article {pmid25388758, year = {2015}, author = {Grüning, A and Beecroft, NJ and Avignone-Rossa, C}, title = {Low-potential respirators support electricity production in microbial fuel cells.}, journal = {Microbial ecology}, volume = {70}, number = {1}, pages = {266-273}, pmid = {25388758}, issn = {1432-184X}, mesh = {Bacteria, Anaerobic/*metabolism ; Bioelectric Energy Sources/*microbiology ; *Biofilms ; Biomass ; Electrodes/*microbiology ; Linear Models ; Species Specificity ; Waste Management/*methods ; }, abstract = {In this paper, we analyse how electric power production in microbial fuel cells (MFCs) depends on the composition of the anodic biofilm in terms of metabolic capabilities of identified sets of species. MFCs are a promising technology for organic waste treatment and sustainable bioelectricity production. Inoculated with natural communities, they present a complex microbial ecosystem with syntrophic interactions between microbes with different metabolic capabilities. Our results demonstrate that low-potential anaerobic respirators--that is those that are able to use terminal electron acceptors with a low redox potential--are important for good power production. Our results also confirm that community metabolism in MFCs with natural inoculum and fermentable feedstock is a two-stage system with fermentation followed by anode respiration.}, }
@article {pmid25388757, year = {2015}, author = {Vela, AI and Casas-Díaz, E and Fernández-Garayzábal, JF and Serrano, E and Agustí, S and Porrero, MC and Sánchez del Rey, V and Marco, I and Lavín, S and Domínguez, L}, title = {Estimation of cultivable bacterial diversity in the cloacae and pharynx in Eurasian griffon vultures (Gyps fulvus).}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {597-607}, pmid = {25388757}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/*isolation &amp; purification ; Cloaca/microbiology ; Falconiformes/*microbiology ; *Microbiota ; Pharynx/microbiology ; Spain ; Symbiosis ; }, abstract = {In this work, we describe the biodiversity of cloacal and pharynx culture-based bacteria (commensal and pathogenic), in 75 Eurasian griffon vultures (Gyps fulvus) from two geographic areas. We address the question of whether the cultivable microbiota of vultures is organised into assemblages occurring by chance. In addition, we assess bacterial diversity in both anatomic regions and geographic areas. Bacterial diversity was represented by 26 Gram-negative and 20 Gram-positive genera. The most common genera were Escherichia, Enterococcus, Staphylococcus, Clostridium and Lactococcus. Escherichia coli and Enterococcus faecalis were the most common species in cloacal and pharyngeal samples. Staphylococcus and Erysipelothrix were isolated from the pharynx and Salmonella and Corynebacterium from the cloacae, and no Campylobacter was isolated from the cloacal swabs. Ten cloacal swabs were positive for Salmonella, of which five isolates were Salmonella enterica serotype 4,(5),12:i:-, one isolate was S. enterica serotype Derby, three isolates were S. enterica serotype 61:k:1,5,7 and one isolate was S. enterica serotype Infantis. The null modelling approach revealed that the commensal bacteria of vultures are not structured in assemblages. On the other hand, differences in bacterial genus and species richness between cloacal and pharyngeal samples or between geographic areas were clear, with the pharynx in vultures from both geographic areas being richer. The results of this study indicate also that vultures can serve as a reservoir of certain pathogenic zoonotic bacteria. The dissemination of these zoonotic pathogens in wildlife could be prevented by periodic sanitary surveys.}, }
@article {pmid25386170, year = {2014}, author = {Ward, BB and Jensen, MM}, title = {The microbial nitrogen cycle.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {553}, pmid = {25386170}, issn = {1664-302X}, }
@article {pmid25385991, year = {2015}, author = {Lee, JC and Kim, SG and Whang, KS}, title = {Sphingobium subterraneum sp. nov., isolated from ground water.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {65}, number = {Pt 2}, pages = {393-398}, doi = {10.1099/ijs.0.069708-0}, pmid = {25385991}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Groundwater/*microbiology ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Phylogeny ; Pigmentation ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; Sphingomonadaceae/*classification/genetics/isolation &amp; purification ; Ubiquinone/analogs &amp; derivatives/chemistry ; }, abstract = {A Gram-stain-negative, strictly aerobic, non-motile, non-spore-forming, yellow, rod-shaped bacterium, designated S-II-13(T), was isolated from ground water at Daejeon in Korea. Strain S-II-13(T) grew between 15 and 30 °C (optimal growth at 28 °C), between pH 6.0 and 9.0 (optimal growth at pH 7.5) and at salinities of 0.3-1.5 % (w/v) NaCl, growing optimally with 0.5 % (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain S-II-13(T) was found to belong to the genus Sphingobium, showing closest phylogenetic similarity to Rhizorhapis suberifaciens CA1(T) (97.0 % 16S rRNA gene sequence similarity), Sphingobium sufflavum HL-25(T) (96.9 %) and Sphingobium vulgare HU1-GD12(T) (96.6 %). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine and sphingoglycolipid. The predominant ubiquinone was Q-10. The major fatty acids were C18 : 1ω7c, C14 : 0 2-OH, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain S-II-13(T) was 63.5 mol%. DNA-DNA relatedness between strain S-II-13(T) and Rhizorhapis suberifaciens LMG 17323(T), Sphingobium sufflavum KCTC 23953(T) and Sphingobium vulgare KCTC 22289(T) was 24, 52 and 55 %, respectively. On the basis of evidence from this taxonomic study using a polyphasic approach, strain S-II-13(T) represents a novel species of the genus Sphingobium for which the name Sphingobium subterraneum sp. nov. is proposed. The type strain is S-II-13(T) (= KACC 17606(T) = NBRC 109814(T)).}, }
@article {pmid25384908, year = {2014}, author = {Andersson, KM and Kumar, D and Bentzer, J and Friman, E and Ahrén, D and Tunlid, A}, title = {Interspecific and host-related gene expression patterns in nematode-trapping fungi.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {968}, pmid = {25384908}, issn = {1471-2164}, mesh = {Animals ; Ascomycota/pathogenicity/*physiology ; Cluster Analysis ; Fungal Proteins/chemistry/genetics ; Gene Expression Profiling ; *Gene Expression Regulation, Fungal ; Host-Pathogen Interactions/*genetics ; Molecular Sequence Annotation ; Nematoda/*microbiology ; Principal Component Analysis ; Protein Structure, Tertiary ; RNA, Messenger/genetics/metabolism ; Species Specificity ; Transcriptome/genetics ; Up-Regulation/genetics ; Virulence/genetics ; }, abstract = {BACKGROUND: Nematode-trapping fungi are soil-living fungi that capture and kill nematodes using special hyphal structures called traps. They display a large diversity of trapping mechanisms and differ in their host preferences. To provide insights into the genetic basis for this variation, we compared the transcriptome expressed by three species of nematode-trapping fungi (Arthrobotrys oligospora, Monacrosporium cionopagum and Arthrobotrys dactyloides, which use adhesive nets, adhesive branches or constricting rings, respectively, to trap nematodes) during infection of two different plant-pathogenic nematode hosts (the root knot nematode Meloidogyne hapla and the sugar beet cyst nematode Heterodera schachtii).<br><br>RESULTS: The divergence in gene expression between the fungi was significantly larger than that related to the nematode species being infected. Transcripts predicted to encode secreted proteins and proteins with unknown function (orphans) were overrepresented among the highly expressed transcripts in all fungi. Genes that were highly expressed in all fungi encoded endopeptidases, such as subtilisins and aspartic proteases; cell-surface proteins containing the carbohydrate-binding domain WSC; stress response proteins; membrane transporters; transcription factors; and transcripts containing the Ricin-B lectin domain. Differentially expressed transcripts among the fungal species encoded various lectins, such as the fungal fruit-body lectin and the D-mannose binding lectin; transcription factors; cell-signaling components; proteins containing a WSC domain; and proteins containing a DUF3129 domain. A small set of transcripts were differentially expressed in infections of different host nematodes, including peptidases, WSC domain proteins, tyrosinases, and small secreted proteins with unknown function.<br><br>CONCLUSIONS: This is the first study on the variation of infection-related gene expression patterns in nematode-trapping fungi infecting different host species. A better understanding of these patterns will facilitate the improvements of these fungi in biological control programs, by providing molecular markers for screening programs and candidates for genetic manipulations of virulence and host preferences.}, }
@article {pmid25382269, year = {2015}, author = {Coelho, FJ and Cleary, DF and Rocha, RJ and Calado, R and Castanheira, JM and Rocha, SM and Silva, AM and Simões, MM and Oliveira, V and Lillebø, AI and Almeida, A and Cunha, &#xc2; and Lopes, I and Ribeiro, R and Moreira-Santos, M and Marques, CR and Costa, R and Pereira, R and Gomes, NC}, title = {Unraveling the interactive effects of climate change and oil contamination on laboratory-simulated estuarine benthic communities.}, journal = {Global change biology}, volume = {21}, number = {5}, pages = {1871-1886}, doi = {10.1111/gcb.12801}, pmid = {25382269}, issn = {1365-2486}, mesh = {Base Sequence ; *Climate Change ; DNA Primers/genetics ; Deltaproteobacteria/metabolism/radiation effects ; *Estuaries ; Geologic Sediments/*microbiology ; Hydrocarbons/analysis ; Hydrogen-Ion Concentration ; Microbiota/drug effects/*physiology ; *Models, Biological ; Molecular Sequence Data ; Petroleum Pollution/*adverse effects ; Portugal ; Sequence Analysis, DNA ; Ultraviolet Rays ; }, abstract = {There is growing concern that modifications to the global environment such as ocean acidification and increased ultraviolet radiation may interact with anthropogenic pollutants to adversely affect the future marine environment. Despite this, little is known about the nature of the potential risks posed by such interactions. Here, we performed a multifactorial microcosm experiment to assess the impact of ocean acidification, ultraviolet B (UV-B) radiation and oil hydrocarbon contamination on sediment chemistry, the microbial community (composition and function) and biochemical marker response of selected indicator species. We found that increased ocean acidification and oil contamination in the absence of UV-B will significantly alter bacterial composition by, among other things, greatly reducing the relative abundance of Desulfobacterales, known to be important oil hydrocarbon degraders. Along with changes in bacterial composition, we identified concomitant shifts in the composition of oil hydrocarbons in the sediment and an increase in oxidative stress effects on our indicator species. Interestingly, our study identifies UV-B as a critical component in the interaction between these factors, as its presence alleviates harmful effects caused by the combination of reduced pH and oil pollution. The model system used here shows that the interactive effect of reduced pH and oil contamination can adversely affect the structure and functioning of sediment benthic communities, with the potential to exacerbate the toxicity of oil hydrocarbons in marine ecosystems.}, }
@article {pmid25375776, year = {2014}, author = {Golden, S and Dukas, R}, title = {The value of patch-choice copying in fruit flies.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e112381}, pmid = {25375776}, issn = {1932-6203}, mesh = {Animals ; Behavior, Animal/*physiology ; Drosophila melanogaster ; Feeding Behavior/*physiology ; Female ; Male ; *Models, Biological ; }, abstract = {Many animals copy the choices of others but the functional and mechanistic explanations for copying are still not fully resolved. We relied on novel behavioral protocols to quantify the value of patch-choice copying in fruit flies. In a titration experiment, we quantified how much nutritional value females were willing to trade for laying eggs on patches already occupied by larvae (social patches). Females were highly sensitive to nutritional quality, which was positively associated with their offspring success. Females, however, perceived social, low-nutrition patches (33% of the nutrients) as equally valuable as non-social, high-nutrition ones (100% of the nutrients). In follow-up experiments, we could not, however, either find informational benefits from copying others or detect what females' offspring may gain from developing with older larvae. Because patch-choice copying in fruit flies is a robust phenomenon in spite of potential costs due to competition, we suggest that it is beneficial in natural settings, where fruit flies encounter complex dynamics of microbial communities, which include, in addition to the preferred yeast species they feed on, numerous harmful fungi and bacteria. We suggest that microbial ecology underlies many cases of copying in nature.}, }
@article {pmid25373332, year = {2015}, author = {Kuroda, K and Hatamoto, M and Nakahara, N and Abe, K and Takahashi, M and Araki, N and Yamaguchi, T}, title = {Community composition of known and uncultured archaeal lineages in anaerobic or anoxic wastewater treatment sludge.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {586-596}, pmid = {25373332}, issn = {1432-184X}, mesh = {Aerobiosis ; Anaerobiosis ; Archaea/genetics/*isolation &amp; purification/metabolism ; DNA, Archaeal/genetics/metabolism ; Japan ; *Microbiota ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Sequence Analysis, DNA ; Sewage/*microbiology ; Waste Disposal, Fluid ; Wastewater/*microbiology ; }, abstract = {Microbial systems are widely used to treat different types of wastewater from domestic, agricultural, and industrial sources. Community composition is an important factor in determining the successful performance of microbial treatment systems; however, a variety of uncultured and unknown lineages exist in sludge that requires identification and characterization. The present study examined the archaeal community composition in methanogenic, denitrifying, and nitrogen-/phosphate-removing wastewater treatment sludge by Archaea-specific 16S rRNA gene sequencing analysis using Illumina sequencing technology. Phylotypes belonging to Euryarchaeota, including methanogens, were most abundant in all samples except for nitrogen-/phosphate-removing wastewater treatment sludge. High levels of Deep Sea Hydrothermal Vent Group 6 (DHVEG-6), WSA2, Terrestrial Miscellaneous Euryarchaeotal Group, and Miscellaneous Crenarchaeotic Group were also detected. Interestingly, DHVEG-6 was dominant in nitrogen-/phosphate-removing wastewater treatment sludge, indicating that unclear lineages of Archaea still exist in the anaerobic wastewater treatment sludges. These results reveal a previously unknown diversity of Archaea in sludge that can potentially be exploited for the development of more efficient wastewater treatment strategies.}, }
@article {pmid25370887, year = {2015}, author = {Gschwendtner, S and Leberecht, M and Engel, M and Kublik, S and Dannenmann, M and Polle, A and Schloter, M}, title = {Effects of Elevated Atmospheric CO2 on Microbial Community Structure at the Plant-Soil Interface of Young Beech Trees (Fagus sylvatica L.) Grown at Two Sites with Contrasting Climatic Conditions.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {867-878}, pmid = {25370887}, issn = {1432-184X}, mesh = {Carbon Dioxide/*metabolism ; Environment ; Fagus/*metabolism/*microbiology ; Germany ; Molecular Sequence Data ; Polymorphism, Restriction Fragment Length ; *Soil Microbiology ; Trees/*microbiology ; }, abstract = {Soil microbial community responses to elevated atmospheric CO2 concentrations (eCO2) occur mainly indirectly via CO2-induced plant growth stimulation leading to quantitative as well as qualitative changes in rhizodeposition and plant litter. In order to gain insight into short-term, site-specific effects of eCO2 on the microbial community structure at the plant-soil interface, young beech trees (Fagus sylvatica L.) from two opposing mountainous slopes with contrasting climatic conditions were incubated under ambient (360 ppm) CO2 concentrations in a greenhouse. One week before harvest, half of the trees were incubated for 2 days under eCO2 (1,100 ppm) conditions. Shifts in the microbial community structure in the adhering soil as well as in the root rhizosphere complex (RRC) were investigated via TRFLP and 454 pyrosequencing based on 16S ribosomal RNA (rRNA) genes. Multivariate analysis of the community profiles showed clear changes of microbial community structure between plants grown under ambient and elevated CO2 mainly in RRC. Both TRFLP and 454 pyrosequencing showed a significant decrease in the microbial diversity and evenness as a response of CO2 enrichment. While Alphaproteobacteria dominated by Rhizobiales decreased at eCO2, Betaproteobacteria, mainly Burkholderiales, remained unaffected. In contrast, Gammaproteobacteria and Deltaproteobacteria, predominated by Pseudomonadales and Myxococcales, respectively, increased at eCO2. Members of the order Actinomycetales increased, whereas within the phylum Acidobacteria subgroup Gp1 decreased, and the subgroups Gp4 and Gp6 increased under atmospheric CO2 enrichment. Moreover, Planctomycetes and Firmicutes, mainly members of Bacilli, increased under eCO2. Overall, the effect intensity of eCO2 on soil microbial communities was dependent on the distance to the roots. This effect was consistent for all trees under investigation; a site-specific effect of eCO2 in response to the origin of the trees was not observed.}, }
@article {pmid25370886, year = {2015}, author = {Dong, K and Kim, WS and Tripathi, BM and Adams, J}, title = {Generalized soil Thaumarchaeota community in weathering rock and saprolite.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {356-360}, pmid = {25370886}, issn = {1432-184X}, mesh = {Archaea/*classification/genetics/isolation &amp; purification ; Carbon/chemistry ; DNA, Archaeal/genetics ; Genes, Archaeal ; Hydrogen-Ion Concentration ; Nitrogen/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Relatively little is known of the archaeal communities associated with endolithic environments, compared to other microbial groups such as bacteria and fungi. Analyzing the pyrosequenced archaeal 16S ribosomal RNA (rRNA) gene V1-V3 region, we investigated the archaeal community associated with aboveground-exfoliated weathering layers of a granite gneiss, and of the saprolite derived from this rock at 1 m depth below the soil surface, in a forested hilly area south of Seoul, South Korea. In both these sites, an archaeal community dominated by the phylum Thaumarchaeota was identified. The archaeal community in all cases closely resembled that of the surface layer of acidic soils in temperate climates of Korea. It appears that there is no clear distinction in archaeal community composition between a soil and a rock and a saprolite despite a tremendous difference in the concentration of total nitrogen and organic carbon. Of the chemical properties we measured, pH was the best predictor of the archaeal community composition and relative abundance of thaumarchaeal subphyla. These findings reinforce the view that soil archaea are mostly generalists, whose ecology is not closely dependent on nitrogen concentration or soil organic matter status, the presence of living roots, or the abundant presence of any other biota.}, }
@article {pmid25370885, year = {2015}, author = {Yarwood, S and Wick, A and Williams, M and Daniels, WL}, title = {Parent material and vegetation influence soil microbial community structure following 30-years of rock weathering and pedogenesis.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {383-394}, pmid = {25370885}, issn = {1432-184X}, mesh = {Acidobacteria/*classification/genetics/isolation &amp; purification ; Archaea/classification/*genetics/isolation &amp; purification ; Biodiversity ; Carbon/chemistry ; DNA, Ribosomal Spacer/genetics ; Ecosystem ; Fungi/*classification/genetics/isolation &amp; purification ; Hydrogen-Ion Concentration ; Mining ; Nitrogen/chemistry ; Nitrogen Cycle ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Proteobacteria/*classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Weather ; }, abstract = {The process of pedogenesis and the development of biological communities during primary succession begin on recently exposed mineral surfaces. Following 30 years of surface exposure of reclaimed surface mining sites (Appalachian Mountains, USA), it was hypothesized that microbial communities would differ between sandstone and siltstone parent materials and to a lesser extent between vegetation types. Microbial community composition was examined by targeting bacterial and archaeal (16S ribosomal RNA (rRNA)) and fungal (internal transcribed spacer (ITS)) genes and analyzed using Illumina sequencing. Microbial community composition significantly differed between parent materials and between plots established with tall fescue grass or pitch x loblolly pine vegetation types, suggesting that both factors are important in shaping community assembly during early pedogenesis. At the phylum level, Acidobacteria and Proteobacteria differed in relative abundance between sandstone and siltstone. The amount of the heavy fraction carbon (C) was significantly different between sandstone (2.0 mg g(-1)) and siltstone (5.2 mg g(-1)) and correlated with microbial community composition. Soil nitrogen (N) cycling was examined by determining gene copy numbers of ureC, archaeal amoA, and bacterial amoA. Gene quantities tended to be higher in siltstone compared to sandstone but did not differ by vegetation type. This was consistent with differences in extractable ammonium (NH4 (+)) concentrations between sandstone and siltstone (16.4 vs 8.5 μg NH4 (+)-N g(-1) soil), suggesting that nitrification rates may be higher in siltstone. Parent material and early vegetation are important determinants of early microbial community assembly and could be drivers for the trajectory of ecosystem development over longer time scales.}, }
@article {pmid25370884, year = {2015}, author = {Nouhra, E and Pastor, N and Becerra, A and Sarrionandia Areitio, E and Geml, J}, title = {Greenhouse seedlings of Alnus showed low host intrageneric specificity and a strong preference for some Tomentella ectomycorrhizal associates.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {813-825}, pmid = {25370884}, issn = {1432-184X}, mesh = {Alnus/growth &amp; development/*microbiology ; Argentina ; Basidiomycota/genetics/*physiology ; Host Specificity ; Molecular Sequence Data ; Phylogeny ; Seedlings/growth &amp; development/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Ectomycorrhizal (ECM) fungal associates of Alnus are relatively few in comparison with those associated with other tree hosts. The composition of ECM assemblages associated with Alnus seems to change very little across the Northern Hemisphere. However, Alnus-associated ECM assemblages from the Western United States, Mexico, and Argentina tend to differ from those in eastern North America and Europe, presumably due to their different biogeographic histories. Alnus glutinosa is a northern European species subjected to diverse environmental conditions. To address intrageneric host preference within two distantly related Alnus species (Alnus acuminata and A. glutinosa), we tested the ECM colonization on seedlings of both species inoculated with natural soil from A. acuminata forests. Two tomentelloid ECM fungi from A. acuminata natural soils were determined from the anatomotyping and molecular analysis. Both species colonized A. glutinosa seedlings and presented similar relative abundances. Additional soil sequence data from A. acuminata sites suggest that a variety of tomentelloid taxa occur, including several unidentified Tomentella lineages. Maximum-likelihood and Bayesian inference analyses based on internal transcribed spacer (ITS) sequences from various locations do not reflect associations of taxa based on their biogeographic origin, and clades are in general constituted by sequences from diverse regions, including South America, Mexico, USA, and Europe. Results illustrate the probable role of specific tomentelloid fungi in the early colonization of seedlings in A. acuminata forests as well as their importance in the structure of the ECM propagule community at the sites.}, }
@article {pmid25370030, year = {2014}, author = {Canganella, F and Wiegel, J}, title = {Anaerobic thermophiles.}, journal = {Life (Basel, Switzerland)}, volume = {4}, number = {1}, pages = {77-104}, pmid = {25370030}, issn = {2075-1729}, abstract = {The term "extremophile" was introduced to describe any organism capable of living and growing under extreme conditions. With the further development of studies on microbial ecology and taxonomy, a variety of "extreme" environments have been found and an increasing number of extremophiles are being described. Extremophiles have also been investigated as far as regarding the search for life on other planets and even evaluating the hypothesis that life on Earth originally came from space. The first extreme environments to be largely investigated were those characterized by elevated temperatures. The naturally "hot environments" on Earth range from solar heated surface soils and water with temperatures up to 65 °C, subterranean sites such as oil reserves and terrestrial geothermal with temperatures ranging from slightly above ambient to above 100 °C, to submarine hydrothermal systems with temperatures exceeding 300 °C. There are also human-made environments with elevated temperatures such as compost piles, slag heaps, industrial processes and water heaters. Thermophilic anaerobic microorganisms have been known for a long time, but scientists have often resisted the belief that some organisms do not only survive at high temperatures, but actually thrive under those hot conditions. They are perhaps one of the most interesting varieties of extremophilic organisms. These microorganisms can thrive at temperatures over 50 °C and, based on their optimal temperature, anaerobic thermophiles can be subdivided into three main groups: thermophiles with an optimal temperature between 50 °C and 64 °C and a maximum at 70 °C, extreme thermophiles with an optimal temperature between 65 °C and 80 °C, and finally hyperthermophiles with an optimal temperature above 80 °C and a maximum above 90 °C. The finding of novel extremely thermophilic and hyperthermophilic anaerobic bacteria in recent years, and the fact that a large fraction of them belong to the Archaea has definitely made this area of investigation more exciting. Particularly fascinating are their structural and physiological features allowing them to withstand extremely selective environmental conditions. These properties are often due to specific biomolecules (DNA, lipids, enzymes, osmolites, etc.) that have been studied for years as novel sources for biotechnological applications. In some cases (DNA-polymerase, thermostable enzymes), the search and applications successful exceeded preliminary expectations, but certainly further exploitations are still needed.}, }
@article {pmid25368138, year = {2015}, author = {Lee, JC and Kim, YS and Yun, BS and Whang, KS}, title = {Pontibacillus salicampi sp. nov., a moderately halophilic bacterium isolated from saltern soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {65}, number = {Pt 2}, pages = {375-380}, doi = {10.1099/ijs.0.066423-0}, pmid = {25368138}, issn = {1466-5034}, mesh = {Bacillaceae/*classification/genetics/isolation &amp; purification ; Base Composition ; DNA, Bacterial/genetics ; Diaminopimelic Acid/chemistry ; Fatty Acids/chemistry ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Peptidoglycan/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Salinity ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {A Gram-stain-positive, moderately halophilic bacterium, designated BH043(T), was isolated from saltern soil of Gomso in Korea. Cells were motile rods, producing ellipsoidal endospores at a terminal position in swollen sporangia. Strain BH043(T) was strictly aerobic, grew at pH 6.0-10.0 (optimal growth at pH 7.5), at 10-55 °C (optimal growth at 30 °C) and at salinities of 1-20 % (w/v) NaCl, growing optimally with 7 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain BH043(T) belongs to the family Bacillaceae and was most closely related to the type strains of the five recognized species of the genus Pontibacillus, showing sequence similarity to Pontibacillus yanchengensis Y32(T) (97.5 % similarity), Pontibacillus marinus BH030004(T) (97.4 %), Pontibacillus chungwhensis BH030062(T) (97.0 %), Pontibacillus litoralis JSM 072002(T) (96.4 %) and Pontibacillus halophilus JSM 076056(T) (96.2 %). The major cellular fatty acids of strain BH043(T) were iso-C15 : 0 and anteiso-C15 : 0. The genomic DNA G+C content was 42.5 mol%. The major isoprenoid quinone was MK-7 and meso-diaminopimelic acid was present in the cell-wall peptidoglycan as the diagnostic diamino acid. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. DNA-DNA relatedness between strain BH043(T) and the type strains of other species of the genus Pontibacillus, P. yanchengensis CGMCC 1.10680(T) and P. marinus KCTC 3917(T) and P. chungwhensis KCTC 3890(T), was 35, 24 and 18 %, respectively. On the basis of polyphasic analysis from this study, strain BH043(T) represents a novel species of the genus Pontibacillus for which the name Pontibacillus salicampi sp. nov. is proposed. The type strain is BH043(T) (= KACC 17607(T) = NBRC 109831(T) = NCAIM B.02529(T)).}, }
@article {pmid25367428, year = {2015}, author = {Álvarez, R and del Hoyo, A and Díaz-Rodríguez, C and Coello, AJ and del Campo, EM and Barreno, E and Catalá, M and Casano, LM}, title = {Lichen rehydration in heavy metal-polluted environments: Pb modulates the oxidative response of both Ramalina farinacea thalli and its isolated microalgae.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {698-709}, pmid = {25367428}, issn = {1432-184X}, mesh = {Ascomycota/*drug effects/physiology ; Chlorophyll/metabolism ; Chlorophyta/*drug effects/physiology ; Environmental Pollutants/*toxicity ; Fluorometry ; Lead/*toxicity ; Lichens/*drug effects/physiology ; Lipid Peroxidation ; Reactive Oxygen Species/metabolism ; Spain ; Symbiosis ; Water/*metabolism ; }, abstract = {Lichens are adapted to desiccation/rehydration and accumulate heavy metals, which induce ROS especially from the photobiont photosynthetic pigments. Although their mechanisms of abiotic stress tolerance are still to be unravelled, they seem related to symbionts' reciprocal upregulation of antioxidant systems. With the aim to study the effect of Pb on oxidative status during rehydration, the kinetics of intracellular ROS, lipid peroxidation and chlorophyll autofluorescence of whole Ramalina farinacea thalli and its isolated microalgae (Trebouxia TR1 and T. TR9) was recorded. A genetic characterization of the microalgae present in the thalli used was also carried out in order to assess possible correlations among the relative abundance of each phycobiont, their individual physiological responses and that of the entire thallus. Unexpectedly, Pb decreased ROS and lipid peroxidation in thalli and its phycobionts, associated with a lower chlorophyll autofluorescence. Each phycobiont showed a particular pattern, but the oxidative response of the thallus paralleled the TR1's, agreeing with the genetic identification of this strain as the predominant phycobiont. We conclude that: (1) the lichen oxidative behaviour seems to be modulated by the predominant phycobiont and (2) Pb evokes in R. farinacea and its phycobionts strong mechanisms to neutralize its own oxidant effects along with those of rehydration.}, }
@article {pmid25367129, year = {2014}, author = {Tong, M and Jacobs, JP and McHardy, IH and Braun, J}, title = {Sampling of intestinal microbiota and targeted amplification of bacterial 16S rRNA genes for microbial ecologic analysis.}, journal = {Current protocols in immunology}, volume = {107}, number = {}, pages = {7.41.1-7.41.11}, pmid = {25367129}, issn = {1934-368X}, support = {UL1TR000124/TR/NCATS NIH HHS/United States ; DK62413/DK/NIDDK NIH HHS/United States ; DK41301/DK/NIDDK NIH HHS/United States ; U01 DK062413/DK/NIDDK NIH HHS/United States ; T32 DK007180/DK/NIDDK NIH HHS/United States ; CA16042/CA/NCI NIH HHS/United States ; UL1 TR000124/TR/NCATS NIH HHS/United States ; DK46763/DK/NIDDK NIH HHS/United States ; P30 CA016042/CA/NCI NIH HHS/United States ; P30 DK041301/DK/NIDDK NIH HHS/United States ; P01 DK046763/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Gastrointestinal Microbiome/*genetics/immunology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Mice ; Nucleic Acid Amplification Techniques/*methods ; RNA, Bacterial/*genetics/immunology ; RNA, Ribosomal, 16S/*genetics/immunology ; }, abstract = {Dysbiosis of host-associated commensal microbiota is emerging as an important factor in risk and phenotype of immunologic, metabolic, and behavioral diseases. Accurate analysis of microbial composition and functional state in humans or mice requires appropriate collection and pre-processing of biospecimens. Methods to sample luminal and mucosal microbiota from human or mouse intestines and to profile microbial phylogenetic composition using 16S rRNA sequencing are presented here. Data generated using the methods in this unit can be used for downstream quantitative analysis of microbial ecology.}, }
@article {pmid25361394, year = {2015}, author = {Aliaga Goltsman, DS and Comolli, LR and Thomas, BC and Banfield, JF}, title = {Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities.}, journal = {The ISME journal}, volume = {9}, number = {4}, pages = {1014-1023}, pmid = {25361394}, issn = {1751-7370}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biodiversity ; *Biofilms ; Eukaryota/classification/genetics ; Gene Expression Profiling ; Genes, rRNA ; Hydrogen-Ion Concentration ; Mining ; Phylogeny ; *Water Microbiology ; }, abstract = {A fundamental question in microbial ecology relates to community structure, and how this varies across environment types. It is widely believed that some environments, such as those at very low pH, host simple communities based on the low number of taxa, possibly due to the extreme environmental conditions. However, most analyses of species richness have relied on methods that provide relatively low ribosomal RNA (rRNA) sampling depth. Here we used community transcriptomics to analyze the microbial diversity of natural acid mine drainage biofilms from the Richmond Mine at Iron Mountain, California. Our analyses target deep pools of rRNA gene transcripts recovered from both natural and laboratory-grown biofilms across varying developmental stages. In all, 91.8% of the ∼ 254 million Illumina reads mapped to rRNA genes represented in the SILVA database. Up to 159 different taxa, including Bacteria, Archaea and Eukaryotes, were identified. Diversity measures, ordination and hierarchical clustering separate environmental from laboratory-grown biofilms. In part, this is due to the much larger number of rare members in the environmental biofilms. Although Leptospirillum bacteria generally dominate biofilms, we detect a wide variety of other Nitrospira organisms present at very low abundance. Bacteria from the Chloroflexi phylum were also detected. The results indicate that the primary characteristic that has enabled prior extensive cultivation-independent 'omic' analyses is not simplicity but rather the high dominance by a few taxa. We conclude that a much larger variety of organisms than previously thought have adapted to this extreme environment, although only few are selected for at any one time.}, }
@article {pmid25360804, year = {2014}, author = {Li, X and Yang, Q and Dierckens, K and Milton, DL and Defoirdt, T}, title = {RpoS and indole signaling control the virulence of Vibrio anguillarum towards gnotobiotic sea bass (Dicentrarchus labrax) larvae.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e111801}, pmid = {25360804}, issn = {1932-6203}, mesh = {Animals ; Bacterial Proteins/*metabolism ; Bass/*microbiology ; Biofilms/growth &amp; development ; Biopolymers/metabolism ; Gene Deletion ; Genes, Bacterial ; *Germ-Free Life ; Indoles/*metabolism ; Larva ; Oxidative Stress ; Phenotype ; Sigma Factor/*metabolism ; *Signal Transduction ; Vibrio/genetics/*pathogenicity/physiology ; Virulence ; }, abstract = {Quorum sensing, bacterial cell-to-cell communication with small signal molecules, controls the virulence of many pathogens. In contrast to other vibrios, neither the VanI/VanR acylhomoserine lactone quorum sensing system, nor the three-channel quorum sensing system affects virulence of the economically important aquatic pathogen Vibrio anguillarum. Indole is another molecule that recently gained attention as a putative signal molecule. The data presented in this study indicate that indole signaling and the alternative sigma factor RpoS have a significant impact on the virulence of V. anguillarum. Deletion of rpoS resulted in increased expression of the indole biosynthesis gene tnaA and in increased production of indole. Both rpoS deletion and the addition of exogenous indole (50-100 µM) resulted in decreased biofilm formation, exopolysaccharide production (a phenotype that is required for pathogenicity) and expression of the exopolysaccharide synthesis gene wbfD. Further, indole inhibitors increased the virulence of the rpoS deletion mutant, suggesting that indole acts downstream of RpoS. Finally, in addition to the phenotypes found to be affected by indole, the rpoS deletion mutant also showed increased motility and decreased sensitivity to oxidative stress.}, }
@article {pmid25354759, year = {2015}, author = {Suryawanshi, RK and Patil, CD and Borase, HP and Narkhede, CP and Stevenson, A and Hallsworth, JE and Patil, SV}, title = {Towards an understanding of bacterial metabolites prodigiosin and violacein and their potential for use in commercial sunscreens.}, journal = {International journal of cosmetic science}, volume = {37}, number = {1}, pages = {98-107}, doi = {10.1111/ics.12175}, pmid = {25354759}, issn = {1468-2494}, mesh = {Bacteria/*metabolism ; Indoles/*administration &amp; dosage ; Prodigiosin/*administration &amp; dosage ; Sunscreening Agents/*administration &amp; dosage ; }, abstract = {OBJECTIVES: To exploit the microbial ecology of bacterial metabolite production and, specifically, to: (i) evaluate the potential use of the pigments prodigiosin and violacein as additives to commercial sunscreens for protection of human skin, and (ii) determine antioxidant and antimicrobial activities (against pathogenic bacteria) for these two pigments.<br><br>METHODS: Prodigiosin and violacein were used to supplement extracts of Aloe vera leaf and Cucumis sativus (cucumber) fruit which are known to have photoprotective activity, as well as some commercial sunscreen preparations. For each, sunscreen protection factors (SPFs) were determined spectrophotometrically. Assays for antimicrobial activity were carried out using 96-well plates to quantify growth inhibition of Staphylococcus aureus and Escherichia coli.<br><br>RESULTS: For the plant extracts, SPFs were increased by an order of magnitude (i.e. up to ~3.5) and those for the commercial sunscreens increased by 10-22% (for 4% w/w violacein) and 20-65% (for 4% w/w prodigiosin). The antioxidant activities of prodigiosin and violacein were approximately 30% and 20% those of ascorbic acid (a well-characterized, potent antioxidant). Violacein inhibited S.&#xa0;aureus (IC50 6.99&#xa0;&#xb1;&#xa0;0.146&#xa0;&#x3bc;M) but not E.&#xa0;coli, whereas prodigiosin was effective against both of these bacteria (IC50 values were 0.68&#xa0;&#xb1;&#xa0;0.06&#xa0;&#x3bc;M and 0.53&#xa0;&#xb1;&#xa0;0.03&#xa0;&#x3bc;M, respectively).<br><br>CONCLUSION: The bacterial pigments prodigiosin and violacein exhibited antioxidant and antimicrobial activities and were able to increase the SPF of commercial sunscreens as well as the extracts of the two plant species tested. These pigments have potential as ingredients for a new product range of and, indeed, represent a new paradigm for sunscreens that utilize substances of biological origin. We discussed the biotechnological potential of these bacterial metabolites for use in commercial sunscreens, and the need for studies of mammalian cells to determine safety.}, }
@article {pmid25351144, year = {2015}, author = {Cersosimo, LM and Lachance, H and St-Pierre, B and van Hoven, W and Wright, AD}, title = {Examination of the rumen bacteria and methanogenic archaea of wild impalas (Aepyceros melampus melampus) from Pongola, South Africa.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {577-585}, pmid = {25351144}, issn = {1432-184X}, mesh = {Animals ; Antelopes/*microbiology ; Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; *Gastrointestinal Microbiome ; Male ; Molecular Sequence Data ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rumen/microbiology ; South Africa ; }, abstract = {Although the rumen microbiome of domesticated ruminants has been evaluated, few studies have explored the rumen microbiome of wild ruminants, and no studies have identified the rumen microbiome in the impala (Aepyceros melampus melampus). In the present study, next-generation sequencing and real-time polymerase chain reaction were used to investigate the diversity and density of the bacteria and methanogenic archaea residing in the rumen of five adult male impalas, culled during the winter dry season in Pongola, South Africa. A total of 15,323 bacterial 16S rRNA gene sequences (from five impala), representing 3,892 different phylotypes, were assigned to 1,902 operational taxonomic units (OTUs). A total of 20,124 methanogen 16S rRNA gene sequence reads (from four impala), of which 5,028 were unique, were assigned to 344 OTUs. From the total sequence reads, Bacteroidetes, Proteobacteria, and Firmicutes were the most abundant bacterial phyla. While the majority of the bacterial genera found were unclassified, Prevotella and Cupriavidus were the most abundant classified genera. For methanogens, the genera Methanobrevibacter and Methanosphaera represented 94.3% and 4.0% of the classified sequences, respectively. Most notable was the identification of Methanobrevibacter thaueri-like 16S rRNA gene sequence reads in all four impala samples, representing greater than 30% of each individual's total sequences. Both data sets are accessible through NCBI's Sequence Read Archive (SRA), under study accession number SRP [048619]. The densities of bacteria (1.26 × 10(10)-3.82 × 10(10) cells/ml whole rumen contents) and methanogens (4.48 × 10(8)-7.2 × 10(9) cells/ml of whole rumen contents) from five individual impala were similar to those typically observed in domesticated ruminants.}, }
@article {pmid25351143, year = {2015}, author = {Sun, G and Zhang, X and Hu, Q and Zhang, H and Zhang, D and Li, G}, title = {Erratum to: Biodegradation of dichlorodiphenyltrichloroethanes (DDTs) and hexachlorocyclohexanes (HCHsc) with plant and nutrients and their effects on the microbial ecological kinetics.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {721-722}, doi = {10.1007/s00248-014-0520-4}, pmid = {25351143}, issn = {1432-184X}, }
@article {pmid25351142, year = {2015}, author = {Be, NA and Thissen, JB and Fofanov, VY and Allen, JE and Rojas, M and Golovko, G and Fofanov, Y and Koshinsky, H and Jaing, CJ}, title = {Metagenomic analysis of the airborne environment in urban spaces.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {346-355}, pmid = {25351142}, issn = {1432-184X}, mesh = {*Air Microbiology ; Bacillus thuringiensis/isolation &amp; purification ; Bacteria/classification/isolation &amp; purification ; Biomass ; Cities ; DNA Copy Number Variations ; DNA, Bacterial/genetics/*isolation &amp; purification ; District of Columbia ; Environmental Monitoring ; Fungi/classification/isolation &amp; purification ; Metagenome ; Metagenomics/*methods ; Seasons ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The organisms in aerosol microenvironments, especially densely populated urban areas, are relevant to maintenance of public health and detection of potential epidemic or biothreat agents. To examine aerosolized microorganisms in this environment, we performed sequencing on the material from an urban aerosol surveillance program. Whole metagenome sequencing was applied to DNA extracted from air filters obtained during periods from each of the four seasons. The composition of bacteria, plants, fungi, invertebrates, and viruses demonstrated distinct temporal shifts. Bacillus thuringiensis serovar kurstaki was detected in samples known to be exposed to aerosolized spores, illustrating the potential utility of this approach for identification of intentionally introduced microbial agents. Together, these data demonstrate the temporally dependent metagenomic complexity of urban aerosols and the potential of genomic analytical techniques for biosurveillance and monitoring of threats to public health.}, }
@article {pmid25351141, year = {2015}, author = {Amado, AM and Cotner, JB and Cory, RM and Edhlund, BL and McNeill, K}, title = {Disentangling the interactions between photochemical and bacterial degradation of dissolved organic matter: amino acids play a central role.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {554-566}, pmid = {25351141}, issn = {1432-184X}, mesh = {Amino Acids/metabolism/*radiation effects ; Bacteria/*metabolism ; Humic Substances/analysis/*radiation effects ; *Photochemical Processes ; }, abstract = {Photochemical and bacterial degradation are important pathways to carbon mineralization and can be coupled in dissolved organic matter (DOM) decomposition. However, details of several mechanisms of the coupled photochemical and biological processing of DOM remain too poorly understood to achieve accurate predictions of the impact of these processes on DOM fate and reactivity. The aim of this study was to evaluate how photochemical degradation of amino acids affects bacterial metabolism and whether or not photochemical degradation of DOM competes for amino acids with biological processes. We examined the interactions between photochemical and bacterial degradation dynamics using a mixture of 18 amino acids and examined their dynamics and turnover rates within a larger pool of allochthonous or autochthonous DOM. We observed that photochemical exposure of DOM containing amino acids led to delayed biomass production (even though the final biomass did not differ), most likely due to a need for upregulation of biosynthetic pathways for amino acids that were damaged by photochemically produced reactive oxygen species (ROS). This response was most pronounced in bacterial communities where the abundance of photosensitive amino acids was highest (amended treatments and autochthonous DOM) and least pronounced when the abundance of these amino acids was low (unamended and allochthonous DOM), likely because these bacteria already had these biosynthetic pathways functioning. We observed both a cost and benefit associated with photochemical exposure of DOM. We observed a cost associated with photochemically produced ROS that partially degrade key amino acids and a benefit associated with an increase in the availability of other compounds in the DOM. Bacteria growing on DOM sources that are low in labile amino acids, such as those in terrestrially influenced environments, experience more of the benefits associated with photochemical exposure, whereas bacteria growing in more amino acid-rich environments, such as eutrophic and less terrestrially influenced waters, experience a higher cost due to the increased necessity of salvage pathways for these essential amino acids. Finally, we propose a conceptual model whereby the effects of DOM photochemical degradation on microbial metabolism result from the balance between two mechanisms: One is dependent on the DOM sources, and the other is dependent on the DOM concentration in natural systems.}, }
@article {pmid25351140, year = {2015}, author = {Yun, J and Zhang, H and Deng, Y and Wang, Y}, title = {Aerobic methanotroph diversity in Sanjiang wetland, Northeast China.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {567-576}, pmid = {25351140}, issn = {1432-184X}, mesh = {Bacteria/genetics/*isolation &amp; purification/metabolism ; Bacterial Proteins/genetics/metabolism ; China ; DNA, Bacterial/genetics/metabolism ; *Microbiota ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics/metabolism ; Sequence Analysis, DNA ; *Soil Microbiology ; Wetlands ; }, abstract = {Aerobic methanotrophs present in wetlands can serve as a methane filter and thereby significantly reduce methane emissions. Sanjiang wetland is a major methane source and the second largest wetland in China, yet little is known about the characteristics of aerobic methanotrophs in this region. In the present study, we investigated the diversity and abundance of methanotrophs in marsh soils from Sanjiang wetland with three different types of vegetation by 16S ribosomal RNA (rRNA) and pmoA gene analysis. Quantitative polymerase chain reaction analysis revealed the highest number of pmoA gene copies in marsh soils vegetated with Carex lasiocarpa (10(9) g(-1) dry soil), followed by Carex meyeriana, and the least with Deyeuxia angustifolia (10(8) g(-1) dry soil). Consistent results were obtained using Sanger sequencing and pyrosequencing techniques, both indicating the codominance of Methylobacter and Methylocystis species in Sanjiang wetland. Other less abundant methanotrophy, including cultivated Methylomonas and Methylosinus genus, and uncultured clusters such as LP20 and JR-1, were also detected in the wetland. Methanotroph diversity was almost the same in three different vegetation covered soils, suggesting that vegetation types had very little influence on the methanotroph diversity. Our study gives an in-depth insight into the community composition of aerobic methanotrophs in the Sanjiang wetland.}, }
@article {pmid25344857, year = {2015}, author = {Puthiya Veettil, V and Abdulaziz, A and Chekidhenkuzhiyil, J and Kalanthingal Ramkollath, L and Karayadi Hamza, F and Kizhakkepat Kalam, B and Kallungal Ravunnikutty, M and Nair, S}, title = {Bacterial domination over archaea in ammonia oxidation in a monsoon-driven tropical estuary.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {544-553}, pmid = {25344857}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Archaea/genetics/*physiology ; *Bacterial Physiological Phenomena/genetics ; DNA, Bacterial/genetics/metabolism ; Estuaries ; India ; Molecular Sequence Data ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics/metabolism ; Seawater/*microbiology ; Sequence Analysis, DNA ; Tropical Climate ; }, abstract = {Autotrophic ammonia oxidizing microorganisms, which are responsible for the rate-limiting step of nitrification in most aquatic systems, have not been studied in tropical estuaries. Cochin estuary (CE) is one of the largest, productive, and monsoon-driven estuary in India opening into the southeast Arabian Sea. CE receives surplus quantities of ammonia through industrial and domestic discharges. The distribution of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and anaerobic ammonia-oxidizing bacteria (anammox) were studied using fluorescence in situ hybridization (FISH) and their relative contribution to the process as well as the governing factors were examined and reported for the first time from CE. The order of occurrence of these assemblages was β-proteobacteria (0.79 to 2 × 10(5) cells ml(-1)) > γ-proteobacteria (0.9 to 4.6 × 10(4) cells ml(-1)) > anammox (0.49 to 1.9 × 10(4) cells ml(-1)) > AOA (0.56 to 6.3 × 10(3) cells ml(-1)). Phylogenetic analysis of DGGE bands showed major affiliation of AOB to β-proteobacteria, while AOA was affiliated to Crenarchaeota. The abundance of AOB was mostly influenced by ammonia concentrations. The recovered ammonia oxidation rate of AOB was in the range of 45-65%, whereas for AOA, it was 15-45%, indicating that AOB were mostly responsible for the ammonia oxidation in CE during the study period. Overall, the present study provides an insight into the relevance and contribution of different groups of ammonia oxidizing bacteria in CE and emphasizes the need for further in depth studies across space and on season scale.}, }
@article {pmid25343515, year = {2015}, author = {Vital, M and Gao, J and Rizzo, M and Harrison, T and Tiedje, JM}, title = {Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia.}, journal = {The ISME journal}, volume = {9}, number = {4}, pages = {832-843}, pmid = {25343515}, issn = {1751-7370}, support = {UH3 DK083993/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/*isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Birds/metabolism/*microbiology ; Butyrates/*metabolism ; Coenzyme A-Transferases/genetics/metabolism ; Diet ; Feces/*microbiology ; Humans ; Mammals/metabolism/*microbiology ; Phosphotransferases (Carboxyl Group Acceptor)/genetics/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reptiles/metabolism/*microbiology ; }, abstract = {Butyrate-producing bacteria have an important role in maintaining host health. They are well studied in human and medically associated animal models; however, much less is known for other Vertebrata. We investigated the butyrate-producing community in hindgut-fermenting Mammalia (n = 38), Aves (n = 8) and Reptilia (n = 8) using a gene-targeted pyrosequencing approach of the terminal genes of the main butyrate-synthesis pathways, namely butyryl-CoA:acetate CoA-transferase (but) and butyrate kinase (buk). Most animals exhibit high gene abundances, and clear diet-specific signatures were detected with but genes significantly enriched in omnivores and herbivores compared with carnivores. But dominated the butyrate-producing community in these two groups, whereas buk was more abundant in many carnivorous animals. Clustering of protein sequences (5% cutoff) of the combined communities (but and buk) placed carnivores apart from other diet groups, except for noncarnivorous Carnivora, which clustered together with carnivores. The majority of clusters (but: 5141 and buk: 2924) did not show close relation to any reference sequences from public databases (identity <90%) demonstrating a large 'unknown diversity'. Each diet group had abundant signature taxa, where buk genes linked to Clostridium perfringens dominated in carnivores and but genes associated with Ruminococcaceae bacterium D16 were specific for herbivores and omnivores. Whereas 16S rRNA gene analysis showed similar overall patterns, it was unable to reveal communities at the same depth and resolution as the functional gene-targeted approach. This study demonstrates that butyrate producers are abundant across vertebrates exhibiting great functional redundancy and that diet is the primary determinant governing the composition of the butyrate-producing guild.}, }
@article {pmid25343514, year = {2015}, author = {Müller, AL and Kjeldsen, KU and Rattei, T and Pester, M and Loy, A}, title = {Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases.}, journal = {The ISME journal}, volume = {9}, number = {5}, pages = {1152-1165}, pmid = {25343514}, issn = {1751-7370}, support = {P 23117/FWF_/Austrian Science Fund FWF/Austria ; P 25111/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Archaea/*enzymology/genetics ; Bacteria/*enzymology/genetics ; Biodiversity ; DNA Primers ; Databases, Genetic ; Environment ; Genes, Archaeal ; Genes, Bacterial ; Genetic Variation ; Hydrogensulfite Reductase/*genetics ; Oxidoreductases Acting on Sulfur Group Donors/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfates/*chemistry ; Sulfite Dehydrogenase/*genetics ; }, abstract = {The energy metabolism of essential microbial guilds in the biogeochemical sulfur cycle is based on a DsrAB-type dissimilatory (bi)sulfite reductase that either catalyzes the reduction of sulfite to sulfide during anaerobic respiration of sulfate, sulfite and organosulfonates, or acts in reverse during sulfur oxidation. Common use of dsrAB as a functional marker showed that dsrAB richness in many environments is dominated by novel sequence variants and collectively represents an extensive, largely uncharted sequence assemblage. Here, we established a comprehensive, manually curated dsrAB/DsrAB database and used it to categorize the known dsrAB diversity, reanalyze the evolutionary history of dsrAB and evaluate the coverage of published dsrAB-targeted primers. Based on a DsrAB consensus phylogeny, we introduce an operational classification system for environmental dsrAB sequences that integrates established taxonomic groups with operational taxonomic units (OTUs) at multiple phylogenetic levels, ranging from DsrAB enzyme families that reflect reductive or oxidative DsrAB types of bacterial or archaeal origin, superclusters, uncultured family-level lineages to species-level OTUs. Environmental dsrAB sequences constituted at least 13 stable family-level lineages without any cultivated representatives, suggesting that major taxa of sulfite/sulfate-reducing microorganisms have not yet been identified. Three of these uncultured lineages occur mainly in marine environments, while specific habitat preferences are not evident for members of the other 10 uncultured lineages. In summary, our publically available dsrAB/DsrAB database, the phylogenetic framework, the multilevel classification system and a set of recommended primers provide a necessary foundation for large-scale dsrAB ecology studies with next-generation sequencing methods.}, }
@article {pmid25343512, year = {2015}, author = {Vital, M and Chai, B and Østman, B and Cole, J and Konstantinidis, KT and Tiedje, JM}, title = {Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification.}, journal = {The ISME journal}, volume = {9}, number = {5}, pages = {1130-1140}, pmid = {25343512}, issn = {1751-7370}, support = {UH3 DK083993/DK/NIDDK NIH HHS/United States ; }, mesh = {Environment ; Escherichia coli/*genetics ; Escherichia coli Proteins/genetics ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Genome, Bacterial ; Humans ; Intestines/microbiology ; *Phylogeny ; Sequence Analysis, RNA ; Transcriptome ; }, abstract = {Escherichia coli spans a genetic continuum from enteric strains to several phylogenetically distinct, atypical lineages that are rare in humans, but more common in extra-intestinal environments. To investigate the link between gene regulation, phylogeny and diversification in this species, we analyzed global gene expression profiles of four strains representing distinct evolutionary lineages, including a well-studied laboratory strain, a typical commensal (enteric) strain and two environmental strains. RNA-Seq was employed to compare the whole transcriptomes of strains grown under batch, chemostat and starvation conditions. Highly differentially expressed genes showed a significantly lower nucleotide sequence identity compared with other genes, indicating that gene regulation and coding sequence conservation are directly connected. Overall, distances between the strains based on gene expression profiles were largely dependent on the culture condition and did not reflect phylogenetic relatedness. Expression differences of commonly shared genes (all four strains) and E. coli core genes were consistently smaller between strains characterized by more similar primary habitats. For instance, environmental strains exhibited increased expression of stress defense genes under carbon-limited growth and entered a more pronounced survival-like phenotype during starvation compared with other strains, which stayed more alert for substrate scavenging and catabolism during no-growth conditions. Since those environmental strains show similar genetic distance to each other and to the other two strains, these findings cannot be simply attributed to genetic relatedness but suggest physiological adaptations. Our study provides new insights into ecologically relevant gene-expression and underscores the role of (differential) gene regulation for the diversification of the model bacterial species.}, }
@article {pmid25342538, year = {2015}, author = {Liu, Y and Zhang, J and Gao, B}, title = {Cellular and transcriptional responses in Microcystis aeruginosa exposed to two antibiotic contaminants.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {535-543}, pmid = {25342538}, issn = {1432-184X}, mesh = {Amoxicillin/*pharmacology ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Microcystins/drug effects/metabolism ; Microcystis/*drug effects/growth &amp; development/metabolism ; Photosynthesis/drug effects ; Spiramycin/*pharmacology ; Stress, Physiological/drug effects ; Water Pollutants, Chemical/*pharmacology ; }, abstract = {The responses of Microcystis aeruginosa under exposure to spiramycin and amoxicillin were investigated on both cellular and genetic levels through a 7-day exposure test. Algal growth was inhibited by spiramycin while promoted by amoxicillin at test concentrations of 0.6-1.8 μg L(-1), indicating a higher toxicity of spiramycin than amoxicillin. During the whole exposure period, the chlorophyll a content and expression levels of psbA, psaB, and rbcL were significantly inhibited by spiramycin at test concentrations of 1.2 and 1.8 μg L(-1) (p < 0.05) and stimulated by 0.6-1.8 μg L(-1) of amoxicillin (p < 0.05), with respective decreases of up to 26, 75, 72, and 82% compared to the control and respective increases of 20, 70, 135, and 55%. During the 4 to 7 days of exposure, the microcystin-LR content and expression levels of mcyB and grpE were reduced by up to 66, 47, and 72% in spiramycin-treated algal cells, respectively, and stimulated by up to 1.3-, 1.4-, and 1.5-folds in amoxicillin-treated algal cells, respectively. Elevated recA expression was only observed in 1.2 and 1.8 μg L(-1) of spiramycin-treated algal cells, indicating severe DNA damage due to the high toxicity. Target antibiotics were suspected to regulate the growth and microcystin-production in M. aeruginosa via the photosynthesis system.}, }
@article {pmid25342537, year = {2015}, author = {Rampelotto, PH and Barboza, AD and Pereira, AB and Triplett, EW and Schaefer, CE and de Oliveira Camargo, FA and Roesch, LF}, title = {Distribution and interaction patterns of bacterial communities in an ornithogenic soil of Seymour Island, Antarctica.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {684-694}, pmid = {25342537}, issn = {1432-184X}, mesh = {Antarctic Regions ; Bacteria/genetics/*metabolism ; DNA, Bacterial/genetics/metabolism ; Islands ; *Microbiota ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics/metabolism ; *Soil Microbiology ; }, abstract = {Next-generation, culture-independent sequencing offers an excellent opportunity to examine network interactions among different microbial species. In this study, soil bacterial communities from a penguin rookery site at Seymour Island were analyzed for abundance, structure, diversity, and interaction networks to identify interaction patterns among the various taxa at three soil depths. The analysis revealed the presence of eight phyla distributed in different proportions among the surface layer (0-8 cm), middle layer (20-25 cm), and bottom (35-40 cm). The bottom layer presented the highest values of bacterial richness, diversity, and evenness when compared to surface and middle layers. The network analysis revealed the existence of a unique pattern of interactions in which the soil microbial network formed a clustered topology, rather than a modular structure as is usually found in biological communities. In addition, specific taxa were identified as important players in microbial community structure. Furthermore, simulation analyses indicated that the loss of potential keystone groups of microorganisms might alter the patterns of interactions within the microbial community. These findings provide new insights for assessing the consequences of environmental disturbances at the whole-community level in Antarctica.}, }
@article {pmid25342536, year = {2015}, author = {Weidow, CA and Bae, HS and Chauhan, A and Ogram, A}, title = {Diversity and distribution of actinobacterial aromatic ring oxygenase genes across contrasting soil properties.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {676-683}, pmid = {25342536}, issn = {1432-184X}, mesh = {Actinobacteria/enzymology/*genetics ; Bacterial Proteins/*genetics/metabolism ; Fires ; Florida ; Molecular Sequence Data ; Oxygenases/*genetics/metabolism ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants/analysis ; }, abstract = {The diversity of a gene family encoding Actinobacterial aromatic ring oxygenases (AAROs) was detected by the PCR-cloning approach using a newly designed PCR primer set. The distribution of AAROs was investigated in 11 soils representing different land management and vegetation zones and was correlated with several geochemical parameters including pH, organic matter (OM), total Kjeldahl nitrogen (TKN), and nitrogen oxides (NO(x)-N: mostly NO3(-)-N). The distribution of individual clades encoding enzymes with potentially different substrates were correlated with different environmental factors, suggesting differential environmental controls on the distribution of specific enzymes as well as sequence diversity. For example, individual clades associated with phthalate dioxygenases were either strongly negatively correlated with pH, or not correlated with pH but showed strong positive correlation with organic carbon content. A large number of clones clustering in a clade related to PAH oxygenases were positively correlated with pH and nitrogen, but not with organic matter. This analysis may yield insight into the ecological forces driving the distribution of these catabolic genes.}, }
@article {pmid25341787, year = {2014}, author = {McCalley, CK and Woodcroft, BJ and Hodgkins, SB and Wehr, RA and Kim, EH and Mondav, R and Crill, PM and Chanton, JP and Rich, VI and Tyson, GW and Saleska, SR}, title = {Methane dynamics regulated by microbial community response to permafrost thaw.}, journal = {Nature}, volume = {514}, number = {7523}, pages = {478-481}, pmid = {25341787}, issn = {1476-4687}, mesh = {Anaerobiosis ; Arctic Regions ; Atmosphere/*chemistry ; Carbon Dioxide/metabolism ; *Ecosystem ; *Freezing ; Methane/analysis/*metabolism ; *Soil Microbiology ; Sweden ; }, abstract = {Permafrost contains about 50% of the global soil carbon. It is thought that the thawing of permafrost can lead to a loss of soil carbon in the form of methane and carbon dioxide emissions. The magnitude of the resulting positive climate feedback of such greenhouse gas emissions is still unknown and may to a large extent depend on the poorly understood role of microbial community composition in regulating the metabolic processes that drive such ecosystem-scale greenhouse gas fluxes. Here we show that changes in vegetation and increasing methane emissions with permafrost thaw are associated with a switch from hydrogenotrophic to partly acetoclastic methanogenesis, resulting in a large shift in the δ(13)C signature (10-15‰) of emitted methane. We used a natural landscape gradient of permafrost thaw in northern Sweden as a model to investigate the role of microbial communities in regulating methane cycling, and to test whether a knowledge of community dynamics could improve predictions of carbon emissions under loss of permafrost. Abundance of the methanogen Candidatus 'Methanoflorens stordalenmirensis' is a key predictor of the shifts in methane isotopes, which in turn predicts the proportions of carbon emitted as methane and as carbon dioxide, an important factor for simulating the climate feedback associated with permafrost thaw in global models. By showing that the abundance of key microbial lineages can be used to predict atmospherically relevant patterns in methane isotopes and the proportion of carbon metabolized to methane during permafrost thaw, we establish a basis for scaling changing microbial communities to ecosystem isotope dynamics. Our findings indicate that microbial ecology may be important in ecosystem-scale responses to global change.}, }
@article {pmid25339764, year = {2015}, author = {Murphy, L and Varela, M and Desloire, S and Ftaich, N and Murgia, C and Golder, M and Neil, S and Spencer, TE and Wootton, SK and Lavillette, D and Terzian, C and Palmarini, M and Arnaud, F}, title = {The sheep tetherin paralog oBST2B blocks envelope glycoprotein incorporation into nascent retroviral virions.}, journal = {Journal of virology}, volume = {89}, number = {1}, pages = {535-544}, pmid = {25339764}, issn = {1098-5514}, support = {098049/WT_/Wellcome Trust/United Kingdom ; G0801822/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Golgi Apparatus/metabolism ; Jaagsiekte sheep retrovirus/*immunology/*physiology ; Membrane Glycoproteins/*immunology ; Protein Transport ; Sheep ; Viral Envelope Proteins/*antagonists &amp; inhibitors ; Virion/*metabolism ; *Virus Assembly ; }, abstract = {UNLABELLED: Bone marrow stromal cell antigen 2 (BST2) is a cellular restriction factor with a broad antiviral activity. In sheep, the BST2 gene is duplicated into two paralogs termed oBST2A and oBST2B. oBST2A impedes viral exit of the Jaagsiekte sheep retroviruses (JSRV), most probably by retaining virions at the cell membrane, similar to the "tethering" mechanism exerted by human BST2. In this study, we provide evidence that unlike oBST2A, oBST2B is limited to the Golgi apparatus and disrupts JSRV envelope (Env) trafficking by sequestering it. In turn, oBST2B leads to a reduction in Env incorporation into viral particles, which ultimately results in the release of virions that are less infectious. Furthermore, the activity of oBST2B does not seem to be restricted to retroviruses, as it also acts on vesicular stomatitis virus glycoproteins. Therefore, we suggest that oBST2B exerts antiviral activity using a mechanism distinct from the classical tethering restriction observed for oBST2A.<br><br>IMPORTANCE: BST2 is a powerful cellular restriction factor against a wide range of enveloped viruses. Sheep possess two paralogs of the BST2 gene called oBST2A and oBST2B. JSRV, the causative agent of a transmissible lung cancer of sheep, is known to be restricted by oBST2A. In this study, we show that unlike oBST2A, oBST2B impairs the normal cellular trafficking of JSRV envelope glycoproteins by sequestering them within the Golgi apparatus. We also show that oBST2B decreases the incorporation of envelope glycoprotein into JSRV viral particles, which in turn reduces virion infectivity. In conclusion, oBST2B exerts a novel antiviral activity that is distinct from those of BST2 proteins of other species.}, }
@article {pmid25339308, year = {2015}, author = {Velivelli, SL and Kromann, P and Lojan, P and Rojas, M and Franco, J and Suarez, JP and Prestwich, BD}, title = {Identification of mVOCs from Andean rhizobacteria and field evaluation of bacterial and mycorrhizal inoculants on growth of potato in its center of origin.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {652-667}, pmid = {25339308}, issn = {1432-184X}, mesh = {Bacteria/*chemistry/isolation &amp; purification ; Bolivia ; Ecuador ; Fungicides, Industrial/isolation &amp; purification/pharmacology ; Gas Chromatography-Mass Spectrometry ; Mycorrhizae/*chemistry ; Peru ; Plant Roots/chemistry/microbiology ; Rhizoctonia/drug effects ; *Soil Microbiology ; Solanum tuberosum/chemistry/*growth &amp; development/*microbiology ; Solid Phase Microextraction ; Volatile Organic Compounds/isolation &amp; purification/*pharmacology ; }, abstract = {Food security (a pressing issue for all nations) faces a threat due to population growth, land availability for growing crops, a changing climate (leading to increases in both abiotic and biotic stresses), heightened consumer awareness of the risks related to the use of agrichemicals, and also the reliance on depleting fossil fuel reserves for their production. Legislative changes in Europe mean that fewer agrichemicals will be available in the future for the control of crop pests and pathogens. The need for the implementation of a more sustainable agricultural system globally, incorporating an integrated approach to disease management, has never been more urgent. To that end, the Valorizing Andean Microbial Diversity (VALORAM) project (http://valoram.ucc.ie), funded under FP7, examined the role of microbial communities in crop production and protection to improve the sustainability, food security, environmental protection, and productivity for rural Andean farmers. During this work, microbial volatile organic compounds (mVOCs) of 27 rhizobacterial isolates were identified using gas chromatography/mass spectrometry (GC/MS), and their antifungal activity against Rhizoctonia solani was determined in vitro and compared to the activity of a selection of pure volatile compounds. Five of these isolates, Pseudomonas palleroniana R43631, Bacillus sp. R47065, R47131, Paenibacillus sp. B3a R49541, and Bacillus simplex M3-4 R49538 trialled in the field in their respective countries of origin, i.e., Bolivia, Peru, and Ecuador, showed significant increase in the yield of potato. The strategy followed in the VALORAM project may offer a template for the future isolation and determination of putative biocontrol and plant growth-promoting agents, useful as part of a low-input integrated pest management system.}, }
@article {pmid25339307, year = {2015}, author = {They, NH and Ferreira, LM and Marins, LF and Abreu, PC}, title = {Bacterial community composition and physiological shifts associated with the El Niño Southern Oscillation (ENSO) in the Patos Lagoon estuary.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {525-534}, pmid = {25339307}, issn = {1432-184X}, mesh = {Bacteria/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; Brazil ; *El Nino-Southern Oscillation ; Environment ; Estuaries ; *Microbiota ; Seasons ; }, abstract = {The Patos Lagoon estuary is a microtidal system that is strongly regulated by atmospheric forces, including remote large-scale phenomena such as the El Niño Southern Oscillation (ENSO), which affects precipitation patterns in the region. In this study, we investigated whether the bacterial community composition (BCC), community-level physiological profiles (CLPP), and a set of environmental variables were affected by the transition from a moderate El Niño to a strong La Niña event (June 2010 to May 2011). We identified two distinct periods: a period following El Niño that was characterized by low salinity and high concentrations of NO3(-) and PO4(-3) and low molecular weight (LMW) substances and a period following La Niña during which salinity, temperature, and transparency increased and the concentrations of nutrients and LMW substances decreased. The BCC and CLPP were significantly altered in response to this transition. This is the first study addressing the effect of ENSO on bacteria at the community level in an estuarine system. Our results suggest that there is a link between ENSO and bacteria, indicating the role of climate variability in bacterial activities and, hence, the cycling of organic matter by these microorganisms.}, }
@article {pmid25332478, year = {2014}, author = {Ferrario, C and Taverniti, V and Milani, C and Fiore, W and Laureati, M and De Noni, I and Stuknyte, M and Chouaia, B and Riso, P and Guglielmetti, S}, title = {Modulation of fecal Clostridiales bacteria and butyrate by probiotic intervention with Lactobacillus paracasei DG varies among healthy adults.}, journal = {The Journal of nutrition}, volume = {144}, number = {11}, pages = {1787-1796}, doi = {10.3945/jn.114.197723}, pmid = {25332478}, issn = {1541-6100}, mesh = {Adult ; Butyric Acid/*chemistry/metabolism ; Double-Blind Method ; Feces/*chemistry/*microbiology ; Female ; Gram-Positive Endospore-Forming Rods/classification/*isolation &amp; purification ; Humans ; *Lactobacillus ; Male ; Middle Aged ; Probiotics ; Young Adult ; }, abstract = {BACKGROUND: The modulation of gut microbiota is considered to be the first target to establish probiotic efficacy in a healthy population.<br><br>OBJECTIVE: This study was conducted to determine the impact of a probiotic on the intestinal microbial ecology of healthy volunteers.<br><br>METHODS: High-throughput 16S ribosomal RNA gene sequencing was used to characterize the fecal microbiota in healthy adults (23-55 y old) of both sexes, before and after 4 wk of daily consumption of a capsule containing at least 24 billion viable Lactobacillus paracasei DG cells, according to a randomized, double-blind, crossover placebo-controlled design.<br><br>RESULTS: Probiotic intake induced an increase in Proteobacteria (P = 0.006) and in the Clostridiales genus Coprococcus (P = 0.009), whereas the Clostridiales genus Blautia (P = 0.036) was decreased; a trend of reduction was also observed for Anaerostipes (P = 0.05) and Clostridium (P = 0.06). We also found that the probiotic effect depended on the initial butyrate concentration. In fact, participants with butyrate >100 mmol/kg of wet feces had a mean butyrate reduction of 49 &#xb1; 21% and a concomitant decrease in the sum of 6 Clostridiales genera, namely Faecalibacterium, Blautia, Anaerostipes, Pseudobutyrivibrio, Clostridium, and Butyrivibrio (P = 0.021), after the probiotic intervention. In contrast, in participants with initial butyrate concentrations <25 mmol/kg of wet feces, the probiotic contributed to a 329 &#xb1; 255% (mean &#xb1; SD) increment in butyrate concomitantly with an &#x223c;55% decrease in Ruminococcus (P = 0.016) and a 150% increase in an abundantly represented unclassified Bacteroidales genus (P = 0.05).<br><br>CONCLUSIONS: The intake of L. paracasei DG increased the Blautia:Coprococcus ratio, which, according to the literature, can potentially confer a health benefit on the host. The probiotic impact on the microbiota and on short-chain fatty acids, however, seems to strictly depend on the initial characteristics of the intestinal microbial ecosystem. In particular, fecal butyrate concentrations could represent an important biomarker for identifying subjects who may benefit from probiotic treatment. This trial was registered at www.controlled-trials.com/isrctn as ISRCTN56945491.}, }
@article {pmid25331109, year = {2015}, author = {Kivlin, SN and Treseder, KK}, title = {Initial phylogenetic relatedness of saprotrophic fungal communities affects subsequent litter decomposition rates.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {748-757}, pmid = {25331109}, issn = {1432-184X}, mesh = {Alaska ; *Biodiversity ; Fungal Proteins/genetics/metabolism ; Fungi/*classification/*physiology ; Molecular Sequence Data ; *Phylogeny ; Plant Leaves/chemistry/*metabolism/microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; Taiga ; }, abstract = {Ecosystem-level consequences of biodiversity loss of macroorganisms are well understood, while the repercussions of species extirpation in microbial systems are not. We manipulated species richness and phylogenetic relatedness of saprotrophic fungi in situ in a boreal forest to address this issue. Litter decomposition rates (as total mass loss) after 2 months were significantly higher in the least phylogenetically related fungal assemblages. Likewise, cellulose loss was also highest in the most distantly related treatments after 1 year. There were marginal effects of species richness on mass loss that only affected decomposition after 2 months. At the end of 1 year of decomposition, most fungal communities had collapsed from their original diversity to two species, mainly in the Penicillium or Hypocrea clades. Two concurrent processes may explain these results: competition between closely related fungal taxa and phylogenetic conservation in cellulose decomposition. Our results suggest that phylogenetic relatedness of fungal communities may be a more appropriate metric than species richness or community composition to predict functional responses of fungal communities to global change.}, }
@article {pmid25327842, year = {2014}, author = {Barberán, A and Casamayor, EO}, title = {A phylogenetic perspective on species diversity, β-diversity and biogeography for the microbial world.}, journal = {Molecular ecology}, volume = {23}, number = {23}, pages = {5868-5876}, doi = {10.1111/mec.12971}, pmid = {25327842}, issn = {1365-294X}, mesh = {Altitude ; Bacteria/*classification/genetics ; *Biodiversity ; Lakes/microbiology ; Molecular Sequence Data ; *Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Spain ; Water Microbiology ; }, abstract = {There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world, there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high-altitude lakes district data set. We described phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High-altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled 18 lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within the smallest geographical area. The results showed highly diverse communities nonrandomly distributed with phylogenetic β-diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β-diversity shared similar patterns and was primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter- and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies.}, }
@article {pmid25325381, year = {2015}, author = {Eren, AM and Morrison, HG and Lescault, PJ and Reveillaud, J and Vineis, JH and Sogin, ML}, title = {Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences.}, journal = {The ISME journal}, volume = {9}, number = {4}, pages = {968-979}, pmid = {25325381}, issn = {1751-7370}, support = {UH3 DK083993/DK/NIDDK NIH HHS/United States ; }, mesh = {*Algorithms ; Animals ; Biodiversity ; Genetic Markers ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Microbiota ; Mouth/microbiology ; *Phylogeny ; Porifera/microbiology ; Sequence Analysis, DNA/*methods ; }, abstract = {Molecular microbial ecology investigations often employ large marker gene datasets, for example, ribosomal RNAs, to represent the occurrence of single-cell genomes in microbial communities. Massively parallel DNA sequencing technologies enable extensive surveys of marker gene libraries that sometimes include nearly identical sequences. Computational approaches that rely on pairwise sequence alignments for similarity assessment and de novo clustering with de facto similarity thresholds to partition high-throughput sequencing datasets constrain fine-scale resolution descriptions of microbial communities. Minimum Entropy Decomposition (MED) provides a computationally efficient means to partition marker gene datasets into 'MED nodes', which represent homogeneous operational taxonomic units. By employing Shannon entropy, MED uses only the information-rich nucleotide positions across reads and iteratively partitions large datasets while omitting stochastic variation. When applied to analyses of microbiomes from two deep-sea cryptic sponges Hexadella dedritifera and Hexadella cf. dedritifera, MED resolved a key Gammaproteobacteria cluster into multiple MED nodes that are specific to different sponges, and revealed that these closely related sympatric sponge species maintain distinct microbial communities. MED analysis of a previously published human oral microbiome dataset also revealed that taxa separated by less than 1% sequence variation distributed to distinct niches in the oral cavity. The information theory-guided decomposition process behind the MED algorithm enables sensitive discrimination of closely related organisms in marker gene amplicon datasets without relying on extensive computational heuristics and user supervision.}, }
@article {pmid25319239, year = {2015}, author = {Braña, AF and Fiedler, HP and Nava, H and González, V and Sarmiento-Vizcaíno, A and Molina, A and Acuña, JL and García, LA and Blanco, G}, title = {Two Streptomyces species producing antibiotic, antitumor, and anti-inflammatory compounds are widespread among intertidal macroalgae and deep-sea coral reef invertebrates from the central Cantabrian Sea.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {512-524}, pmid = {25319239}, issn = {1432-184X}, mesh = {Animals ; Anti-Bacterial Agents/*adverse effects ; Anti-Inflammatory Agents/*adverse effects ; Antineoplastic Agents/*adverse effects ; Atlantic Ocean ; Bioprospecting ; Coral Reefs ; DNA, Bacterial/genetics/metabolism ; Invertebrates/*microbiology ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics/metabolism ; Seaweed/*microbiology ; Sequence Analysis, DNA ; Spain ; Streptomyces/genetics/isolation &amp; purification/*physiology ; Symbiosis ; }, abstract = {Streptomycetes are widely distributed in the marine environment, although only a few studies on their associations to algae and coral ecosystems have been reported. Using a culture-dependent approach, we have isolated antibiotic-active Streptomyces species associated to diverse intertidal marine macroalgae (Phyllum Heterokontophyta, Rhodophyta, and Chlorophyta), from the central Cantabrian Sea. Two strains, with diverse antibiotic and cytotoxic activities, were found to inhabit these coastal environments, being widespread and persistent over a 3-year observation time frame. Based on 16S rRNA sequence analysis, the strains were identified as Streptomyces cyaneofuscatus M-27 and Streptomyces carnosus M-40. Similar isolates to these two strains were also associated to corals and other invertebrates from deep-sea coral reef ecosystem (Phyllum Cnidaria, Echinodermata, Arthropoda, Sipuncula, and Anelida) living up to 4.700-m depth in the submarine Avilés Canyon, thus revealing their barotolerant feature. These two strains were also found to colonize terrestrial lichens and have been repeatedly isolated from precipitations from tropospheric clouds. Compounds with antibiotic and cytotoxic activities produced by these strains were identified by high-performance liquid chromatography (HPLC) and database comparison. Antitumor compounds with antibacterial activities and members of the anthracycline family (daunomycin, cosmomycin B, galtamycin B), antifungals (maltophilins), anti-inflamatory molecules also with antituberculosis properties (lobophorins) were identified in this work. Many other compounds produced by the studied strains still remain unidentified, suggesting that Streptomyces associated to algae and coral ecosystems might represent an underexplored promising source for pharmaceutical drug discovery.}, }
@article {pmid25319238, year = {2015}, author = {Vishnivetskaya, TA and Hamilton-Brehm, SD and Podar, M and Mosher, JJ and Palumbo, AV and Phelps, TJ and Keller, M and Elkins, JG}, title = {Community analysis of plant biomass-degrading microorganisms from Obsidian Pool, Yellowstone National Park.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {333-345}, pmid = {25319238}, issn = {1432-184X}, mesh = {Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Biofuels ; *Biomass ; Cellulose/chemistry ; Cloning, Molecular ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Hot Springs/*microbiology ; Hot Temperature ; Lignin/chemistry ; Molecular Weight ; *Phylogeny ; Phylogeography ; Populus/chemistry/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Wyoming ; Xylans/chemistry ; }, abstract = {The conversion of lignocellulosic biomass into biofuels can potentially be improved by employing robust microorganisms and enzymes that efficiently deconstruct plant polysaccharides at elevated temperatures. Many of the geothermal features of Yellowstone National Park (YNP) are surrounded by vegetation providing a source of allochthonic material to support heterotrophic microbial communities adapted to utilize plant biomass as a primary carbon and energy source. In this study, a well-known hot spring environment, Obsidian Pool (OBP), was examined for potential biomass-active microorganisms using cultivation-independent and enrichment techniques. Analysis of 33,684 archaeal and 43,784 bacterial quality-filtered 16S rRNA gene pyrosequences revealed that archaeal diversity in the main pool was higher than bacterial; however, in the vegetated area, overall bacterial diversity was significantly higher. Of notable interest was a flooded depression adjacent to OBP supporting a stand of Juncus tweedyi, a heat-tolerant rush commonly found growing near geothermal features in YNP. The microbial community from heated sediments surrounding the plants was enriched in members of the Firmicutes including potentially (hemi)cellulolytic bacteria from the genera Clostridium, Anaerobacter, Caloramator, Caldicellulosiruptor, and Thermoanaerobacter. Enrichment cultures containing model and real biomass substrates were established at a wide range of temperatures (55-85 °C). Microbial activity was observed up to 80 °C on all substrates including Avicel, xylan, switchgrass, and Populus sp. Independent of substrate, Caloramator was enriched at lower (<65 °C) temperatures while highly active cellulolytic bacteria Caldicellulosiruptor were dominant at high (>65 °C) temperatures.}, }
@article {pmid25315832, year = {2015}, author = {Bakhoum, N and Galiana, A and Le Roux, C and Kane, A and Duponnois, R and Ndoye, F and Fall, D and Noba, K and Sylla, SN and Diouf, D}, title = {Phylogeny of nodulation genes and symbiotic diversity of Acacia senegal (L.) Willd. and A. seyal (Del.) Mesorhizobium strains from different regions of Senegal.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {641-651}, pmid = {25315832}, issn = {1432-184X}, mesh = {Acacia/*microbiology ; Acyltransferases/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Mesorhizobium/*genetics/metabolism ; Molecular Sequence Data ; N-Acetylglucosaminyltransferases/*genetics/metabolism ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; Root Nodules, Plant/microbiology ; Senegal ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Acacia senegal and Acacia seyal are small, deciduous legume trees, most highly valued for nitrogen fixation and for the production of gum arabic, a commodity of international trade since ancient times. Symbiotic nitrogen fixation by legumes represents the main natural input of atmospheric N2 into ecosystems which may ultimately benefit all organisms. We analyzed the nod and nif symbiotic genes and symbiotic properties of root-nodulating bacteria isolated from A. senegal and A. seyal in Senegal. The symbiotic genes of rhizobial strains from the two Acacia species were closed to those of Mesorhizobium plurifarium and grouped separately in the phylogenetic trees. Phylogeny of rhizobial nitrogen fixation gene nifH was similar to those of nodulation genes (nodA and nodC). All A. senegal rhizobial strains showed identical nodA, nodC, and nifH gene sequences. By contrast, A. seyal rhizobial strains exhibited different symbiotic gene sequences. Efficiency tests demonstrated that inoculation of both Acacia species significantly affected nodulation, total dry weight, acetylene reduction activity (ARA), and specific acetylene reduction activity (SARA) of plants. However, these cross-inoculation tests did not show any specificity of Mesorhizobium strains toward a given Acacia host species in terms of infectivity and efficiency as stated by principal component analysis (PCA). This study demonstrates that large-scale inoculation of A. senegal and A. seyal in the framework of reafforestation programs requires a preliminary step of rhizobial strain selection for both Acacia species.}, }
@article {pmid25314581, year = {2015}, author = {Sanz, Y and Olivares, M and Moya-Pérez, &#xc1; and Agostoni, C}, title = {Understanding the role of gut microbiome in metabolic disease risk.}, journal = {Pediatric research}, volume = {77}, number = {1-2}, pages = {236-244}, doi = {10.1038/pr.2014.170}, pmid = {25314581}, issn = {1530-0447}, mesh = {Diabetes Mellitus/*epidemiology/*microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; *Microbiota ; *Models, Biological ; Obesity/*epidemiology/*microbiology ; Risk Factors ; }, abstract = {The gut microbiota structure, dynamics, and function result from interactions with environmental and host factors, which jointly influence the communication between the gut and peripheral tissues, thereby contributing to health programming and disease risk. Incidence of both type-1 and type-2 diabetes has increased during the past decades, suggesting that there have been changes in the interactions between predisposing genetic and environmental factors. Animal studies show that gut microbiota and its genome (microbiome) influence alterations in energy balance (increased energy harvest) and immunity (inflammation and autoimmunity), leading to metabolic dysfunction (e.g., insulin resistance and deficiency). Thus, although they have different origins, both disorders are linked by the association of the gut microbiota with the immune-metabolic axis. Human studies have also revealed shifts in microbiome signatures in diseased subjects as compared with controls, and a few of them precede the development of these disorders. These studies contribute to pinpointing specific microbiome components and functions (e.g., butyrate-producing bacteria) that can protect against both disorders. These could exert protective roles by strengthening gut barrier function and regulating inflammation, as alterations in these are a pathophysiological feature of both disorders, constituting common targets for future preventive approaches.}, }
@article {pmid25314312, year = {2014}, author = {Buttigieg, PL and Ramette, A}, title = {A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses.}, journal = {FEMS microbiology ecology}, volume = {90}, number = {3}, pages = {543-550}, doi = {10.1111/1574-6941.12437}, pmid = {25314312}, issn = {1574-6941}, mesh = {Ecology/*statistics &amp; numerical data ; *Guidelines as Topic ; Internet ; *Microbial Consortia ; Multivariate Analysis ; }, abstract = {The application of multivariate statistical analyses has become a consistent feature in microbial ecology. However, many microbial ecologists are still in the process of developing a deep understanding of these methods and appreciating their limitations. As a consequence, staying abreast of progress and debate in this arena poses an additional challenge to many microbial ecologists. To address these issues, we present the GUide to STatistical Analysis in Microbial Ecology (GUSTA ME): a dynamic, web-based resource providing accessible descriptions of numerous multivariate techniques relevant to microbial ecologists. A combination of interactive elements allows users to discover and navigate between methods relevant to their needs and examine how they have been used by others in the field. We have designed GUSTA ME to become a community-led and -curated service, which we hope will provide a common reference and forum to discuss and disseminate analytical techniques relevant to the microbial ecology community.}, }
@article {pmid25313520, year = {2014}, author = {Tian, Z and Cabrol, L and Ruiz-Filippi, G and Pullammanappallil, P}, title = {Microbial ecology in anaerobic digestion at agitated and non-agitated conditions.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e109769}, pmid = {25313520}, issn = {1932-6203}, mesh = {Anaerobiosis ; Archaea/genetics/metabolism ; Biological Oxygen Demand Analysis ; Methane/biosynthesis ; Microbiota ; Molecular Typing ; RNA, Ribosomal, 16S/genetics ; Ruminococcus/genetics/*metabolism ; Volatile Organic Compounds/metabolism ; }, abstract = {To investigate the distribution and dynamics of microbial community in anaerobic digestion at agitated and non-agitated condition, 454 pyrosequencing of 16s rRNA was conducted. It revealed the distinct community compositions between the two digesters and their progressive shifting over time. Methanogens and syntrophic bacteria were found much less abundant in the agitated digester, which was mainly attributed to the presence of bacterial genera Acetanaerobacterium and Ruminococcus with relatively high abundance. The characterization of the microbial community corroborated the digestion performance affected at the agitated condition, where lower methane yield and delayed methane production rate were observed. This was further verified by the accumulation of propionic acid in the agitated digester.}, }
@article {pmid25312606, year = {2014}, author = {Salles, JF and Mallon, CA}, title = {Invasive plant species set up their own niche.}, journal = {The New phytologist}, volume = {204}, number = {3}, pages = {435-437}, doi = {10.1111/nph.13070}, pmid = {25312606}, issn = {1469-8137}, mesh = {Denitrification/*physiology ; Plant Extracts/*chemistry ; Polygonaceae/*metabolism ; Pseudomonas/*drug effects ; }, }
@article {pmid25303712, year = {2015}, author = {Woebken, D and Burow, LC and Behnam, F and Mayali, X and Schintlmeister, A and Fleming, ED and Prufert-Bebout, L and Singer, SW and Cortés, AL and Hoehler, TM and Pett-Ridge, J and Spormann, AM and Wagner, M and Weber, PK and Bebout, BM}, title = {Revisiting N2 fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach.}, journal = {The ISME journal}, volume = {9}, number = {2}, pages = {485-496}, pmid = {25303712}, issn = {1751-7370}, support = {294343/ERC_/European Research Council/International ; P 25700/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodiversity ; Cyanobacteria/classification/genetics/isolation &amp; purification/*metabolism ; Dinitrogenase Reductase/genetics ; Ecosystem ; Mexico ; *Nitrogen Fixation/genetics ; Single-Cell Analysis ; }, abstract = {Photosynthetic microbial mats are complex, stratified ecosystems in which high rates of primary production create a demand for nitrogen, met partially by N2 fixation. Dinitrogenase reductase (nifH) genes and transcripts from Cyanobacteria and heterotrophic bacteria (for example, Deltaproteobacteria) were detected in these mats, yet their contribution to N2 fixation is poorly understood. We used a combined approach of manipulation experiments with inhibitors, nifH sequencing and single-cell isotope analysis to investigate the active diazotrophic community in intertidal microbial mats at Laguna Ojo de Liebre near Guerrero Negro, Mexico. Acetylene reduction assays with specific metabolic inhibitors suggested that both sulfate reducers and members of the Cyanobacteria contributed to N2 fixation, whereas (15)N2 tracer experiments at the bulk level only supported a contribution of Cyanobacteria. Cyanobacterial and nifH Cluster III (including deltaproteobacterial sulfate reducers) sequences dominated the nifH gene pool, whereas the nifH transcript pool was dominated by sequences related to Lyngbya spp. Single-cell isotope analysis of (15)N2-incubated mat samples via high-resolution secondary ion mass spectrometry (NanoSIMS) revealed that Cyanobacteria were enriched in (15)N, with the highest enrichment being detected in Lyngbya spp. filaments (on average 4.4 at% (15)N), whereas the Deltaproteobacteria (identified by CARD-FISH) were not significantly enriched. We investigated the potential dilution effect from CARD-FISH on the isotopic composition and concluded that the dilution bias was not substantial enough to influence our conclusions. Our combined data provide evidence that members of the Cyanobacteria, especially Lyngbya spp., actively contributed to N2 fixation in the intertidal mats, whereas support for significant N2 fixation activity of the targeted deltaproteobacterial sulfate reducers could not be found.}, }
@article {pmid25301499, year = {2015}, author = {Wasserman, RJ and Matcher, GF and Vink, TJ and Froneman, PW}, title = {Preliminary evidence for the organisation of a bacterial community by zooplanktivores at the top of an estuarine planktonic food web.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {245-253}, pmid = {25301499}, issn = {1432-184X}, mesh = {Animals ; Bacteroidetes/*classification/isolation &amp; purification ; Biomass ; Computational Biology ; Cyanobacteria/*classification/isolation &amp; purification ; DNA, Bacterial/genetics ; Estuaries ; *Food Chain ; Multivariate Analysis ; Proteobacteria/*classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Zooplankton ; }, abstract = {As part of a larger investigation, the effect of apex predation on estuarine bacterial community structure, through trophic cascading, was investigated using experimental in situ mesocosms. Through either the removal (filtration) or addition of specific size classes of planktonic groups, four different trophic scenarios were established using estuarine water and its associated plankton. One such treatment represented a "natural" scenario in which stable apex predatory pressure was qualified. Water samples were collected over time from each of the treatments for bacterial community evaluation. These samples were assessed through pyrosequencing of the variable regions 4 and 5 of the bacterial 16S rRNA gene and analysed at the species operational taxonomic unit (OTU) level using a community procedure. The blue-green group dominated the samples, followed by Proteobacteria and Bacteroidetes. Samples were the most similar among treatments at the commencement of the experiment. While the bacterial communities sampled within each treatment changed over time, the deviation from initial appeared to be linked to the treatment trophic scenarios. The least temporal deviation-from-initial in bacterial community was found within the stable apex predatory pressure treatment. These findings are consistent with trophic cascade theory, whereby predators mediate interactions at multiple lower trophic levels with consequent repercussions for diversity.}, }
@article {pmid25301498, year = {2015}, author = {Zhang, M and Jiang, Z and Li, D and Jiang, D and Wu, Y and Ren, H and Peng, H and Lai, Y}, title = {Oral antibiotic treatment induces skin microbiota dysbiosis and influences wound healing.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {415-421}, pmid = {25301498}, issn = {1432-184X}, mesh = {Administration, Oral ; Animals ; Anti-Bacterial Agents/*adverse effects ; Bacterial Load ; Computational Biology ; Down-Regulation ; Dysbiosis/chemically induced/*microbiology ; Interleukin-17/genetics/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; *Microbiota ; Pancreatitis-Associated Proteins ; Proteins/genetics/metabolism ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Skin/*drug effects/microbiology ; Staphylococcus/drug effects ; Vancomycin/adverse effects ; Wound Healing/*drug effects ; }, abstract = {Antibiotic treatment eliminates commensal bacteria and impairs mucosal innate immune defenses in the gut. However, whether oral antibiotic treatment could alter the composition of the microbiota on the skin surface and influence innate immune responses remains unclear. To test this, mice were treated with vancomycin for 7 days and then wounds were made on the back skin of the mice. Five days later, scar tissue from each mouse was collected for bacterial enumeration, the bacterial composition on the scar and unwounded skin was determined using 16S RNA gene-based pyrosequencing analysis, and skin around wounds was collected for RNA extraction. Compared with the control group, the overall density and composition of skin bacteria were altered, and the proportion of Staphylococcus-related sequences was reduced in the vancomycin-treated group. Moreover, vancomycin treatment decreased the expression of RegIIIγ and interleukin (IL)-17 in the wounded skin. Taken together, our data demonstrate that antibiotic treatment decreases the bacterial density and alters the bacterial composition in skin wounds, followed by a decrease in RegIIIγ expression, which may contribute to the delayed wound repair. Our findings also indicate that antibiotic therapy should be carefully considered in the treatment of skin injury.}, }
@article {pmid25301497, year = {2015}, author = {Parker, MA}, title = {The spread of Bradyrhizobium lineages across host legume clades: from Abarema to Zygia.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {630-640}, pmid = {25301497}, issn = {1432-184X}, mesh = {Bacterial Proteins/genetics/metabolism ; *Biological Evolution ; Bradyrhizobium/genetics/*physiology ; DNA, Bacterial/genetics/metabolism ; Fabaceae/*microbiology ; Genomic Islands ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 23S/genetics/metabolism ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {To analyze macroevolutionary patterns in host use by Bradyrhizobium root-nodule bacteria, 420 strains from 75 legume host genera (sampled in 25 countries) were characterized for portions of six housekeeping genes and the nifD locus in the symbiosis island chromosomal region. Most Bradyrhizobium clades utilized very divergent sets of legume hosts. This suggests that Bradyrhizobium spread across the major legume lineages early in its evolution, with only a few derived clades subsequently developing a narrower pattern of host use. Significant modularity existed in the network structure of recent host jumps (inferred from cases where closely related strain pairs were found on different legume taxa). This implies that recent host switching has occurred most often within particular subgroups of legumes. Nevertheless, the observed link structure would allow a bacterial lineage to reach almost any of the 75 legume host genera in a relatively small number of steps. However, permutation tests also showed that symbionts from certain host plant clades were significantly more similar than would be the case if bacteria were distributed at random on the trees. Related legumes thus harbored related sets of symbionts in some cases, indicating some degree of phylogenetic conservatism in partner selection.}, }
@article {pmid25296554, year = {2015}, author = {Kerepesi, C and Szalkai, B and Grolmusz, V}, title = {Visual analysis of the quantitative composition of metagenomic communities: the AmphoraVizu webserver.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {695-697}, pmid = {25296554}, issn = {1432-184X}, mesh = {Artificial Intelligence ; Bacteria/*genetics ; *Genes, Bacterial ; Markov Chains ; *Metagenome ; Metagenomics/*methods ; }, abstract = {Low-cost DNA sequencing methods have given rise to an enormous development of metagenomics in the past few years. One basic--and difficult--task is the phylogenetic annotation of the metagenomic samples studied. The difficulty comes from the fact that the typical environmental sample contains hundreds of unknown and still uncharacterized microorganisms. There are several possible methods to assign at least partial phylogenetic information to these uncharacterized data. Originally, the 16S ribosomal RNA was used as phylogenetic marker, then genome sequence alignments and similarity measures between the unknown genome and the reference genomes were applied (e.g., in the MEGAN software), and more recently, phylogeny-based methods applying suitable sets of marker genes were suggested (AMPHORA, AMPHORA2, and the webserver implementation AmphoraNet). Here, we present a visual analysis tool that is capable of demonstrating the quantitative relations gained from the output of the AMPHORA2 program or the easy-to-use AmphoraNet webserver. Our web-based tool, the AmphoraVizu webserver, makes the phylogenetic distribution of the metagenomic sample clearly visible by using the native output format of AMPHORA2 or AmphoraNet. The user may set the phylogenetic resolution (i.e., superkingdom, phylum, class, order, family, genus, and species) along with the chart type and will receive the distribution data detailed for all relevant marker genes in the sample. For publication quality results, the chart labels can be customized by the user. The visualization webserver is available at the address http://amphoravizu.pitgroup.org. The AmphoraNet webserver is available at http://amphoranet.pitgroup.org. The open-source version of the AmphoraVizu program is available for download at http://pitgroup.org/apps/amphoravizu/AmphoraVizu.pl.}, }
@article {pmid25294189, year = {2015}, author = {Reddy, SV and Thirumala, M and Farooq, M and Sasikala, C and Ramana, CV}, title = {Bacillus lonarensis sp. nov., an alkalitolerant bacterium isolated from a soda lake.}, journal = {Archives of microbiology}, volume = {197}, number = {1}, pages = {27-34}, doi = {10.1007/s00203-014-1040-9}, pmid = {25294189}, issn = {1432-072X}, mesh = {Bacillus/*classification/cytology/*isolation &amp; purification/physiology ; Base Composition ; Cell Wall/chemistry ; DNA, Bacterial/genetics ; Diaminopimelic Acid/analysis ; Fatty Acids/analysis ; Genes, rRNA ; Hydrogen-Ion Concentration ; India ; Lakes/*microbiology ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phospholipids/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sodium Chloride/analysis ; Spores, Bacterial/physiology ; Temperature ; }, abstract = {A novel Gram-stain-positive, rod-shaped, motile and endospore-forming novel bacterial strain 25nlg(T) was isolated from Lonar soda lake, in India. Based on the 16S rRNA gene sequence analysis, it was identified as a member of Firmicutes, being most closely related to Bacillus patagoniensis PAT 05(T) (96.6 %) and other members in the genus Bacillus (<96.0 %). Strain 25nlg(T) was catalase and oxidase-positive. The strain grows optimally at a pH of 9.5 with 4-6 % (w/v) NaCl and temperature of 35-37 °C. The cell wall of the strain 25nlg(T) contains meso-diaminopimelic acid as the diagnostic amino acid. Polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unknown phospholipid (PL2), an aminophospholipid (APL2) and three unknown lipids (L2-4). The predominant isoprenoid quinone was MK-7. iso-C15:0 (41.7 %) was the predominant fatty acid, and significant proportions of anteiso-C15:0 (20.8 %), C12:0 (5.5 %), anteiso-C17:0 (4.9 %), iso-C17:0 (4.5 %) were also detected in the strain 25nlg(T). The DNA G+C content of the strain 25nlg(T) was 40.5 mol%. The results of molecular, physiological and biochemical tests allowed a clear phenotypic differentiation of strain 25nlg(T) from all other members of the genus Bacillus. Strain 25nlg(T) represents a novel member of the genus Bacillus, for which the name Bacillus lonarensis sp. nov. is proposed. The type strain is 25nlg(T) (=KCTC 33413(T) = LMG 27974(T) = CGMCC = 1.12817(T)).}, }
@article {pmid25293875, year = {2015}, author = {Terrat, S and Dequiedt, S and Horrigue, W and Lelievre, M and Cruaud, C and Saby, NP and Jolivet, C and Arrouays, D and Maron, PA and Ranjard, L and Chemidlin Prévost-Bouré, N}, title = {Improving soil bacterial taxa-area relationships assessment using DNA meta-barcoding.}, journal = {Heredity}, volume = {114}, number = {5}, pages = {468-475}, pmid = {25293875}, issn = {1365-2540}, mesh = {Bacteria/*classification/genetics ; *Biodiversity ; DNA Barcoding, Taxonomic/*methods ; DNA Fingerprinting ; DNA, Bacterial/genetics ; France ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {The evaluation of the taxa-area relationship (TAR) with molecular fingerprinting data demonstrated the spatial structuration of soil microorganisms and provided insights into the processes shaping their diversity. The increasing use of massive sequencing technologies in biodiversity investigations has now raised the question of the advantages of such technologies over the fingerprinting approach for elucidation of the determinism of soil microbial community assembly in broad-scale biogeographic studies. Our objectives in this study were to compare DNA fingerprinting and meta-barcoding approaches for evaluating soil bacterial TAR and the determinism of soil bacterial community assembly on a broad scale. This comparison was performed on 392 soil samples from four French geographic regions with different levels of environmental heterogeneity. Both molecular approaches demonstrated a TAR with a significant slope but, because of its more sensitive description of soil bacterial community richness, meta-barcoding provided significantly higher and more accurate estimates of turnover rates. Both approaches were useful in evidencing the processes shaping bacterial diversity variations on a broad scale. When different taxonomic resolutions were considered for meta-barcoding data, they significantly influenced the estimation of turnover rates but not the relative importance of each component process. Altogether, DNA meta-barcoding provides a more accurate evaluation of the TAR and may lead to re-examination of the processes shaping soil bacterial community assembly. This should provide new insights into soil microbial ecology in the context of sustainable use of soil resources.}, }
@article {pmid25293572, year = {2014}, author = {Fonvig, CE and Pihl, AF and Hansen, T and Pedersen, OB and Holm, JC}, title = {[Gut microbiota may influence childhood and adolescent onset obesity].}, journal = {Ugeskrift for laeger}, volume = {176}, number = {34}, pages = {}, pmid = {25293572}, issn = {1603-6824}, mesh = {Adolescent ; Child ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Pediatric Obesity/metabolism/*microbiology ; }, abstract = {Childhood and adolescent onset obesity has reached epidemical proportions worldwide. Recent evidence suggests that obesity is associated with phylogenetic changes in the gut microbiota, which could potentially reveal new avenues for obesity prevention and treatment. A vast number of variables are influencing the gut microbial ecology and though many are proposed, the exact physiological processes behind the relationship are yet to be revealed. This review is focusing on recent advances addressing the potential role of the human gut microbiota in childhood and adolescent onset obesity.}, }
@article {pmid25289188, year = {2014}, author = {Imelfort, M and Parks, D and Woodcroft, BJ and Dennis, P and Hugenholtz, P and Tyson, GW}, title = {GroopM: an automated tool for the recovery of population genomes from related metagenomes.}, journal = {PeerJ}, volume = {2}, number = {}, pages = {e603}, pmid = {25289188}, issn = {2167-8359}, abstract = {Metagenomic binning methods that leverage differential population abundances in microbial communities (differential coverage) are emerging as a complementary approach to conventional composition-based binning. Here we introduce GroopM, an automated binning tool that primarily uses differential coverage to obtain high fidelity population genomes from related metagenomes. We demonstrate the effectiveness of GroopM using synthetic and real-world metagenomes, and show that GroopM produces results comparable with more time consuming, labor-intensive methods.}, }
@article {pmid25285761, year = {2014}, author = {Discart, V and Bilad, MR and Van Nevel, S and Boon, N and Cromphout, J and Vankelecom, IFJ}, title = {Role of transparent exopolymer particles on membrane fouling in a full-scale ultrafiltration plant: feed parameter analysis and membrane autopsy.}, journal = {Bioresource technology}, volume = {173}, number = {}, pages = {67-74}, doi = {10.1016/j.biortech.2014.08.098}, pmid = {25285761}, issn = {1873-2976}, mesh = {Equipment Design ; Equipment Failure Analysis ; Iron Compounds/chemistry/*isolation &amp; purification ; *Membranes, Artificial ; Microalgae/chemistry/*isolation &amp; purification ; Polysaccharides, Bacterial/chemistry/*isolation &amp; purification ; Refractometry ; Ultrafiltration/*instrumentation ; Water Pollutants, Chemical/chemistry/*isolation &amp; purification ; Water Purification/*instrumentation ; }, abstract = {Ultrafiltration (UF) is widely used for water purification, but membrane fouling remains an important issue. In this study, the role of transparent exopolymer particles (TEPs), recently put forward as possible major foulants, was investigated in the fouling process of a full-scale UF installation. Algae, TEPs and other parameters in the UF feed were monitored and correlated during an 8 months long full-scale operation. Results revealed a complex fouling mechanism involving interactions mainly between algae, Fe (flocculant) and TEPs. Algae related parameters rather that TEP concentrations correlated stronger with irreversible fouling rates, suggesting that the overall role of TEPs in membrane fouling seems limited for this application. Finally, membrane autopsy showed the formation of a thick Fe-rich fouling layer on top of the fouled membranes, which could mostly be removed via cleaning-in-place. It remained partly irremovable in the form of some Fe-organic complexes.}, }
@article {pmid25285515, year = {2015}, author = {O'Rorke, R and Cobian, GM and Holland, BS and Price, MR and Costello, V and Amend, AS}, title = {Dining local: the microbial diet of a snail that grazes microbial communities is geographically structured.}, journal = {Environmental microbiology}, volume = {17}, number = {5}, pages = {1753-1764}, doi = {10.1111/1462-2920.12630}, pmid = {25285515}, issn = {1462-2920}, mesh = {Animals ; Base Sequence ; DNA, Bacterial/analysis/genetics ; DNA, Fungal/analysis/genetics ; Diet ; Feces/microbiology ; Fungi/genetics ; Gastrointestinal Tract/*microbiology ; Microbiota/*genetics ; Plant Leaves/microbiology ; Plants/microbiology ; Sequence Analysis, DNA ; Snails/*microbiology ; Trees/microbiology ; }, abstract = {Achatinella mustelina is a critically endangered tree snail that subsists entirely by grazing microbes from leaf surfaces of native trees. Little is known about the fundamental aspects of these microbe assemblages: not taxonomic composition, how this varies with host plant or location, nor whether snails selectively consume microbes. To address these questions, we collected 102 snail faecal samples as a proxy for diet, and 102 matched-leaf samples from four locations. We used Illumina amplicon sequencing to determine bacterial and fungal community composition. Microbial community structure was significantly distinct between snail faeces and leaf samples, but the same microbes occurred in both. We conclude that snails are not 'picky' eaters at the microbial level, but graze the surface of whatever plant they are on. In a second experiment, the gut was dissected from non-endangered native tree snails in the same family as Achatinella to confirm that faecal samples reflect gut contents. Over 60% of fungal reads were shared between faeces, gut and leaf samples. Overall, location, sample type (faeces or leaf) and host plant identity all significantly explained the community composition and variation among samples. Understanding the microbial ecology of microbes grazed by tree snails enables effective management when conservation requires captive breeding or field relocation.}, }
@article {pmid25285494, year = {2014}, author = {Kachouri, F and Ksontini, H and Hamdi, M}, title = {Removal of aflatoxin B1 and inhibition of Aspergillus flavus growth by the use of Lactobacillus plantarum on olives.}, journal = {Journal of food protection}, volume = {77}, number = {10}, pages = {1760-1767}, doi = {10.4315/0362-028X.JFP-13-360}, pmid = {25285494}, issn = {1944-9097}, mesh = {Aflatoxin B1/analysis/*isolation &amp; purification ; Antioxidants/chemistry ; Aspergillus flavus/*growth &amp; development ; Chromatography, High Pressure Liquid ; Fermentation ; Food Contamination/*analysis ; *Food Microbiology ; Food Storage ; Lactobacillus plantarum/*physiology ; Microscopy, Electron, Scanning ; Mycotoxins/analysis ; Olea/*microbiology ; Phenol ; Spectrometry, Fluorescence ; }, abstract = {Olives can be contaminated with a wide variety of molds (Aspergillus and/or Penicillium) that can be occurring naturally on fresh and processed olives and could support mycotoxin production. The aim of this work was to investigate aflatoxin B1 (AFB1) production by fungi and its bioaccumulation in olives during storage and to study the impact of the application of Lactobacillus plantarum on the inhibition of mold development and production of AFB1. Two different treatments were applied: (i) olives with natural microflora and (ii) olives inoculated with Aspergillus flavus after elimination of natural microflora. AFB1 has been extracted from olives and quantitated by high-performance liquid chromatography using a fluorescence detector. Results showed the absence of this metabolite in the olives for the season 2008 to 2009. In 2009 to 2010, AFB1 was detected at the level of 11 μg/kg. The application of L. plantarum during the storage of olives favors the reduction of the level of AFB1 to 5.9 μg/kg correlated with a decrease in the amount of molds (86.3%). The images obtained by environmental scanning electron microscopy showed that L. plantarum was able to adhere to the olive surface and probably produce a biofilm that inhibits the multiplication of yeast and fungi by oxygen competition. Results showed an increase of antioxidant activity and amount of total phenolic compounds of olives, respectively, by 24 and 8.6%. In many olives contaminated with A. flavus, AFB1 was present at an initial level of 5.15 μg/kg and increased to 6.55 μg/kg after 8 days of storage. The biological detoxification of AFB1 in olives by L. plantarum is confirmed by the reduction of the level of AFB1 to 2.12 μg/kg on day 0 and its absence after 4 days of storage.}, }
@article {pmid25282034, year = {2014}, author = {Jobard, M and Pessiot, J and Nouaille, R and Sime-Ngando, T}, title = {Microbial diversity supporting dark fermentation of waste.}, journal = {Trends in biotechnology}, volume = {32}, number = {11}, pages = {549-550}, doi = {10.1016/j.tibtech.2014.09.005}, pmid = {25282034}, issn = {1879-3096}, mesh = {*Biodiversity ; Bioreactors/*microbiology ; Fermentation ; Humans ; Microbial Consortia/*physiology ; Waste Disposal, Fluid/*methods ; }, abstract = {Microbial diversity is essential for human well-being and ecosystem services. Use of microorganisms in biomolecule production is common, but involves single-strain cultures. Microbial consortia provide advantages in the process of degrading organic waste to yield biomolecules of biotechnological interest. Microbial diversity in consortia can be an asset in the context of bioenergy and chemical production, which are key concerns for global energy demands. Improving knowledge of microbial consortia will therefore be important for biotechnology.}, }
@article {pmid25280551, year = {2015}, author = {Pärnänen, K and Karkman, A and Virta, M and Eronen-Rasimus, E and Kaartokallio, H}, title = {Discovery of bacterial polyhydroxyalkanoate synthase (PhaC)-encoding genes from seasonal Baltic Sea ice and cold estuarine waters.}, journal = {Extremophiles : life under extreme conditions}, volume = {19}, number = {1}, pages = {197-206}, pmid = {25280551}, issn = {1433-4909}, mesh = {Acyltransferases/*genetics ; Bacteria/*enzymology/genetics ; Carbon/chemistry ; Cold Temperature ; Ecosystem ; Geography ; Ice Cover ; Macromolecular Substances/chemistry ; Phylogeny ; Seasons ; Seawater/chemistry/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Polyhydroxyalkanoates (PHAs) are macromolecules produced by bacteria as means for storing carbon and energy in intracellular granules. PHAs have physical properties similar to those of plastics and have become of interest to industry as materials for environmentally friendly bioplastic production. There is an ongoing search for new PHA-producing bacterial strains and PHA-synthesizing enzymes tolerating extreme conditions to find ways of producing PHAs at cold temperatures and high solute concentrations. Moreover, the study of PHA producers in the sea-ice biome can aid in understanding the microbial ecology of carbon cycling in ice-associated ecosystems. In this study, PHA producers and PHA synthase genes were examined under the extreme environmental conditions of sea ice and cold seawater to find evidence of PHA production in an environment requiring adaptation to high salinity and cold temperatures. Sea ice and cold estuarine water samples were collected from the northern Baltic Sea and evidence of PHA production was gathered, using microscopy with Nile Blue A staining of PHA-granules and PCR assays detecting PHA-synthesis genes. The PHA granules and PHA synthases were found at all sampling locations, in both sea ice and water, and throughout the sampling period spanning over 10 years. Our study shows, for the first time, that PHA synthesis occurs in Baltic Sea cold-adapted bacteria in their natural environment, which makes the Baltic Sea and its cold environments an interesting choice in the quest for PHA-synthesizing bacteria and synthesis genes.}, }
@article {pmid25279514, year = {2014}, author = {Ramond, JB and Pienaar, A and Armstrong, A and Seely, M and Cowan, DA}, title = {Niche-partitioning of edaphic microbial communities in the Namib Desert gravel plain Fairy Circles.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e109539}, pmid = {25279514}, issn = {1932-6203}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; *Desert Climate ; *Ecosystem ; Environment ; Poaceae/chemistry ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Endemic to the Namib Desert, Fairy Circles (FCs) are vegetation-free circular patterns surrounded and delineated by grass species. Since first reported the 1970's, many theories have been proposed to explain their appearance, but none provide a fully satisfactory explanation of their origin(s) and/or causative agent(s). In this study, we have evaluated an early hypothesis stating that edaphic microorganisms could be involved in their formation and/or maintenance. Surface soils (0-5 cm) from three different zones (FC center, FC margin and external, grass-covered soils) of five independent FCs were collected in April 2013 in the Namib Desert gravel plains. T-RFLP fingerprinting of the bacterial (16S rRNA gene) and fungal (ITS region) communities, in parallel with two-way crossed ANOSIM, showed that FC communities were significantly different to those of external control vegetated soil and that each FC was also characterized by significantly different communities. Intra-FC communities (margin and centre) presented higher variability than the controls. Together, these results provide clear evidence that edaphic microorganisms are involved in the Namib Desert FC phenomenon. However, we are, as yet, unable to confirm whether bacteria and/or fungi communities are responsible for the appearance and development of FCs or are a general consequence of the presence of the grass-free circles.}, }
@article {pmid25279274, year = {2014}, author = {Sato, K and Yoshiga, T and Hasegawa, K}, title = {Activated and inactivated immune responses in Caenorhabditis elegans against Photorhabdus luminescens TT01.}, journal = {SpringerPlus}, volume = {3}, number = {}, pages = {274}, pmid = {25279274}, issn = {2193-1801}, abstract = {The Gram-negative bacterium Photorhabdus luminescens which symbiotically associates with the entomopathogenic nematode Heterorhabditis bacteriophora, has a broad insecticidal and nematicidal activity. The virulence of P. luminescens toward the non-mutualistic nematode Caenorhabditis elegans has not been described. We showed that when fed on P. luminescens, the intestinal cells of C. elegans worms become delicate and some crystal-like structure was developed within the intestinal lumen. Next, we examined the requirement of the p38 mitogen-activated protein kinase (MAPK) and insulin/IGF-1 signaling pathway against P. luminescens. Depletion of pmk-1 by RNAi enhances susceptibility to P. luminescens, and numerous downstream targets regulated by the p38 MAPK pathway were induced when fed on P. luminescens. On the other hand, knockdown of daf-16 has no effects on C. elegans lifespan, but knockdown of daf-2 dramatically increased resistance to P. luminescens in a daf-16-dependent manner. We also revealed one of the daf-2 ligands ins-7 was induced and ins-7 deletion mutant survived longer when fed on P. luminescens. These results suggest the p38 MAPK pathway is activated and required for the host defense against P. luminescens. Insulin/IGF-1 signaling pathway is inactivated by P. luminescens through the overexpression of insulin-like gene.}, }
@article {pmid25278560, year = {2015}, author = {Junghare, M and Schink, B}, title = {Desulfoprunum benzoelyticum gen. nov., sp. nov., a Gram-stain-negative, benzoate-degrading, sulfate-reducing bacterium isolated from a wastewater treatment plant.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {65}, number = {Pt 1}, pages = {77-84}, doi = {10.1099/ijs.0.066761-0}, pmid = {25278560}, issn = {1466-5034}, mesh = {Base Composition ; Benzoates/*metabolism ; DNA, Bacterial/genetics ; Deltaproteobacteria/*classification/genetics/isolation &amp; purification ; Fatty Acids/chemistry ; Germany ; Molecular Sequence Data ; Oxidation-Reduction ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; Sulfates/*metabolism ; Vitamin K 2/chemistry ; }, abstract = {A strictly anaerobic, mesophilic, sulfate-reducing bacterium, strain KoBa311(T), isolated from the wastewater treatment plant at Konstanz, Germany, was characterized phenotypically and phylogenetically. Cells were Gram-stain-negative, non-motile, oval to short rods, 3-5 µm long and 0.8-1.0 µm wide with rounded ends, dividing by binary fission and occurring singly or in pairs. The strain grew optimally in freshwater medium and the optimum temperature was 30 °C. Strain KoBa311(T) showed optimum growth at pH 7.3-7.6. Organic electron donors were oxidized completely to carbon dioxide concomitant with sulfate reduction to sulfide. At excess substrate supply, substrates were oxidized incompletely and acetate (mainly) and/or propionate accumulated. The strain utilized short-chain fatty acids, alcohols (except methanol) and benzoate. Sulfate and DMSO were used as terminal electron acceptors for growth. The genomic DNA G+C content was 52.3 mol% and the respiratory quinone was menaquinone MK-5 (V-H2). The major fatty acids were C16:0, C16:1ω7c/ω6c and C18:1ω7c. Phylogenetic analysis based on 16S rRNA gene sequences placed strain KoBa311(T) within the family Desulfobulbaceae in the class Deltaproteobacteria. Its closest related bacterial species on the basis of the distance matrix were Desulfobacterium catecholicum DSM 3882(T) (93.0% similarity), Desulfocapsa thiozymogenes (93.1%), Desulforhopalus singaporensis (92.9%), Desulfopila aestuarii (92.4%), Desulfopila inferna JS_SRB250Lac(T) (92.3%) and Desulfofustis glycolicus (92.3%). On the basis of phylogenetic, physiological and chemotaxonomic characteristics, strain KoBa311(T) was distinct from any related type species. Therefore, strain KoBa311(T) is considered to represent a novel species of a new genus, for which the name Desulfoprunum benzoelyticum gen. nov., sp. nov. is proposed. The type strain of Desulfoprunum benzoelyticum is KoBa311(T) (=DSM 28570(T) =KCTC 15441(T)).}, }
@article {pmid25273399, year = {2014}, author = {De Maayer, P and Brumm, PJ and Mead, DA and Cowan, DA}, title = {Comparative analysis of the Geobacillus hemicellulose utilization locus reveals a highly variable target for improved hemicellulolysis.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {836}, pmid = {25273399}, issn = {1471-2164}, mesh = {Acetylesterase/genetics/metabolism ; Bacterial Proteins/genetics ; Biomass ; Carbohydrate Metabolism/genetics ; DNA Restriction Enzymes/genetics ; Endo-1,4-beta Xylanases/genetics/metabolism ; Genetic Loci ; Genetic Variation ; Genome, Bacterial ; Geobacillus/classification/*genetics ; Hydrolysis ; Phylogeny ; Polysaccharides/metabolism ; }, abstract = {BACKGROUND: Members of the thermophilic genus Geobacillus can grow at high temperatures and produce a battery of thermostable hemicellulose hydrolytic enzymes, making them ideal candidates for the bioconversion of biomass to value-added products. To date the molecular determinants for hemicellulose degradation and utilization have only been identified and partially characterized in one strain, namely Geobacillus stearothermophilus T-6, where they are clustered in a single genetic locus.<br><br>RESULTS: Using the G. stearothermophilus T-6 hemicellulose utilization locus as genetic marker, orthologous hemicellulose utilization (HUS) loci were identified in the complete and partial genomes of 17/24 Geobacillus strains. These HUS loci are localized on a common genomic island. Comparative analyses of these loci revealed extensive variability among the Geobacillus hemicellulose utilization systems, with only seven out of 41-68 proteins encoded on these loci conserved among the HUS+ strains. This translates into extensive differences in the hydrolytic enzymes, transport systems and metabolic pathways employed by Geobacillus spp. to degrade and utilize hemicellulose polymers.<br><br>CONCLUSIONS: The genetic variability among the Geobacillus HUS loci implies that they have variable capacities to degrade hemicellulose polymers, or that they may degrade distinct polymers, as are found in different plant species and tissues. The data from this study can serve as a basis for the genetic engineering of a Geobacillus strain(s) with an improved capacity to degrade and utilize hemicellulose.}, }
@article {pmid25272964, year = {2015}, author = {Park, HJ and Chae, N and Sul, WJ and Lee, BY and Lee, YK and Kim, D}, title = {Temporal changes in soil bacterial diversity and humic substances degradation in subarctic tundra soil.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {668-675}, pmid = {25272964}, issn = {1432-184X}, mesh = {Alaska ; Archaea/genetics/*isolation &amp; purification/metabolism ; Bacteria/genetics/*isolation &amp; purification/*metabolism ; DNA, Bacterial/genetics ; Humic Substances/*analysis ; Microbiota ; RNA, Ribosomal, 16S/genetics/metabolism ; *Soil Microbiology ; *Tundra ; }, abstract = {Humic substances (HS), primarily humic acids (HA) and fulvic acids (FA), are the largest constituent of soil organic matter. In microcosm systems with subarctic HS-rich tundra soil (site AK 1-75; approximately 5.6 °C during the thawing period) from Council, Alaska, the HA content significantly decreased to 48% after a 99-day incubation at 5 °C as part of a biologically mediated process. Accordingly, levels of FA, a putative byproduct of HA degradation, consistently increased to 172% during an identical incubation process. Culture-independent microbial community analysis showed that during the microcosm experiments, the relative abundance of phyla Proteobacteria (bacteria) and Euryarchaeota (archaea) largely increased, indicating their involvement in HS degradation. When the indigenous bacteria in AK 1-75 were enriched in an artificial mineral medium spiked with HA, the changes in relative abundance were most conspicuous in Proteobacteria (from 60.2 to 79.0%), specifically Betaproteobacteria-related bacteria. One hundred twenty-two HA-degrading bacterial strains, primarily from the genera Paenibacillus (phylum Firmicutes) and Pseudomonas (class Gammaproteobacteria), were cultivated from AK 1-75 and nearby sites. Through culture-dependent analysis with these bacterial isolates, we observed increasing HS-degradation rates in parallel with rising temperatures in a range of 0 °C to 20 °C, with the most notable increase occurring at 8 °C compared to 6 °C. Our results indicate that, although microbial-mediated HS degradation occurs at temperature as low as 5 °C in tundra ecosystems, increasing soil temperature caused by global climate change could enhance HS degradation rates. Extending the thawing period could also increase degradation activity, thereby directly affecting nearby microbial communities and rhizosphere environments.}, }
@article {pmid25272328, year = {2014}, author = {Hardoim, CC and Costa, R}, title = {Microbial communities and bioactive compounds in marine sponges of the family irciniidae-a review.}, journal = {Marine drugs}, volume = {12}, number = {10}, pages = {5089-5122}, pmid = {25272328}, issn = {1660-3397}, mesh = {Animals ; Archaea/physiology ; Bacteria/metabolism ; Fungi/physiology ; Humans ; Porifera/*microbiology ; Quorum Sensing/*physiology ; Symbiosis/*physiology ; }, abstract = {Marine sponges harbour complex microbial communities of ecological and biotechnological importance. Here, we propose the application of the widespread sponge family Irciniidae as an appropriate model in microbiology and biochemistry research. Half a gram of one Irciniidae specimen hosts hundreds of bacterial species-the vast majority of which are difficult to cultivate-and dozens of fungal and archaeal species. The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. Two types of quorum-sensing molecules have been detected in these animals, hinting at microbe-microbe and host-microbe signalling being important processes governing the dynamics of the Irciniidae holobiont. Irciniids are vulnerable to disease outbreaks, and concerns have emerged about their conservation in a changing climate. They are nevertheless amenable to mariculture and laboratory maintenance, being attractive targets for metabolite harvesting and experimental biology endeavours. Several bioactive terpenoids and polyketides have been retrieved from Irciniidae sponges, but the actual producer (host or symbiont) of these compounds has rarely been clarified. To tackle this, and further pertinent questions concerning the functioning, resilience and physiology of these organisms, truly multi-layered approaches integrating cutting-edge microbiology, biochemistry, genetics and zoology research are needed.}, }
@article {pmid25267160, year = {2014}, author = {Mukherjee, V and Steensels, J and Lievens, B and Van de Voorde, I and Verplaetse, A and Aerts, G and Willems, KA and Thevelein, JM and Verstrepen, KJ and Ruyters, S}, title = {Phenotypic evaluation of natural and industrial Saccharomyces yeasts for different traits desirable in industrial bioethanol production.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {22}, pages = {9483-9498}, doi = {10.1007/s00253-014-6090-z}, pmid = {25267160}, issn = {1432-0614}, mesh = {Biodiversity ; Drug Tolerance ; Ethanol/*metabolism/*toxicity ; Industrial Microbiology/*methods ; Saccharomyces cerevisiae/*drug effects/*growth &amp; development/metabolism ; }, abstract = {Saccharomyces cerevisiae is the organism of choice for many food and beverage fermentations because it thrives in high-sugar and high-ethanol conditions. However, the conditions encountered in bioethanol fermentation pose specific challenges, including extremely high sugar and ethanol concentrations, high temperature, and the presence of specific toxic compounds. It is generally considered that exploring the natural biodiversity of Saccharomyces strains may be an interesting route to find superior bioethanol strains and may also improve our understanding of the challenges faced by yeast cells during bioethanol fermentation. In this study, we phenotypically evaluated a large collection of diverse Saccharomyces strains on six selective traits relevant for bioethanol production with increasing stress intensity. Our results demonstrate a remarkably large phenotypic diversity among different Saccharomyces species and among S. cerevisiae strains from different origins. Currently applied bioethanol strains showed a high tolerance to many of these relevant traits, but several other natural and industrial S. cerevisiae strains outcompeted the bioethanol strains for specific traits. These multitolerant strains performed well in fermentation experiments mimicking industrial bioethanol production. Together, our results illustrate the potential of phenotyping the natural biodiversity of yeasts to find superior industrial strains that may be used in bioethanol production or can be used as a basis for further strain improvement through genetic engineering, experimental evolution, or breeding. Additionally, our study provides a basis for new insights into the relationships between tolerance to different stressors.}, }
@article {pmid25266034, year = {2014}, author = {Guttman, DS and McHardy, AC and Schulze-Lefert, P}, title = {Microbial genome-enabled insights into plant-microorganism interactions.}, journal = {Nature reviews. Genetics}, volume = {15}, number = {12}, pages = {797-813}, pmid = {25266034}, issn = {1471-0064}, mesh = {Bacteria/classification ; Bacterial Physiological Phenomena ; Crops, Agricultural/microbiology ; Fungi/classification/physiology ; Genome, Microbial ; Host Specificity ; Host-Pathogen Interactions ; Plant Diseases/immunology/microbiology ; Plants/classification/*microbiology ; }, abstract = {Advances in genome-based studies on plant-associated microorganisms have transformed our understanding of many plant pathogens and are beginning to greatly widen our knowledge of plant interactions with mutualistic and commensal microorganisms. Pathogenomics has revealed how pathogenic microorganisms adapt to particular hosts, subvert innate immune responses and change host range, as well as how new pathogen species emerge. Similarly, culture-independent community profiling methods, coupled with metagenomic and metatranscriptomic studies, have provided the first insights into the emerging field of research on plant-associated microbial communities. Together, these approaches have the potential to bridge the gap between plant microbial ecology and plant pathology, which have traditionally been two distinct research fields.}, }
@article {pmid25261509, year = {2014}, author = {Eichorst, SA and Joshua, C and Sathitsuksanoh, N and Singh, S and Simmons, BA and Singer, SW}, title = {Substrate-Specific Development of Thermophilic Bacterial Consortia by Using Chemically Pretreated Switchgrass.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {23}, pages = {7423-7432}, pmid = {25261509}, issn = {1098-5336}, mesh = {Aerobiosis ; Bacteria/classification/*growth &amp; development/*metabolism ; Biomass ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Lignin/metabolism ; *Microbial Consortia ; Molecular Sequence Data ; Panicum/*metabolism ; Polysaccharides/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Temperature ; }, abstract = {Microbial communities that deconstruct plant biomass have broad relevance in biofuel production and global carbon cycling. Biomass pretreatments reduce plant biomass recalcitrance for increased efficiency of enzymatic hydrolysis. We exploited these chemical pretreatments to study how thermophilic bacterial consortia adapt to deconstruct switchgrass (SG) biomass of various compositions. Microbial communities were adapted to untreated, ammonium fiber expansion (AFEX)-pretreated, and ionic-liquid (IL)-pretreated SG under aerobic, thermophilic conditions using green waste compost as the inoculum to study biomass deconstruction by microbial consortia. After microbial cultivation, gravimetric analysis of the residual biomass demonstrated that both AFEX and IL pretreatment enhanced the deconstruction of the SG biomass approximately 2-fold. Two-dimensional nuclear magnetic resonance (2D-NMR) experiments and acetyl bromide-reactive-lignin analysis indicated that polysaccharide hydrolysis was the dominant process occurring during microbial biomass deconstruction, and lignin remaining in the residual biomass was largely unmodified. Small-subunit (SSU) rRNA gene amplicon libraries revealed that although the dominant taxa across these chemical pretreatments were consistently represented by members of the Firmicutes, the Bacteroidetes, and Deinococcus-Thermus, the abundance of selected operational taxonomic units (OTUs) varied, suggesting adaptations to the different substrates. Combining the observations of differences in the community structure and the chemical and physical structure of the biomass, we hypothesize specific roles for individual community members in biomass deconstruction.}, }
@article {pmid25261127, year = {2015}, author = {De Vrieze, J and Gildemyn, S and Vilchez-Vargas, R and Jáuregui, R and Pieper, DH and Verstraete, W and Boon, N}, title = {Inoculum selection is crucial to ensure operational stability in anaerobic digestion.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {1}, pages = {189-199}, doi = {10.1007/s00253-014-6046-3}, pmid = {25261127}, issn = {1432-0614}, mesh = {Ammonium Compounds/toxicity ; Anaerobiosis ; Archaea/drug effects/growth &amp; development/*metabolism ; Bacteria, Anaerobic/drug effects/growth &amp; development/*metabolism ; *Biota ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Fatty Acids, Volatile/metabolism ; Methane/*metabolism ; *Microbial Consortia ; Molecular Sequence Data ; Sequence Analysis, DNA ; Sewage/*microbiology ; }, abstract = {Anaerobic digestion is considered a key technology for the future bio-based economy. The microbial consortium carrying out the anaerobic digestion process is quite complex, and its exact role in terms of "elasticity", i.e., the ability to rapidly adapt to changing conditions, is still unknown. In this study, the role of the initial microbial community in terms of operational stability and stress tolerance was evaluated during a 175-day experiment. Five different inocula from stable industrial anaerobic digesters were fed a mixture of waste activated sludge and glycerol. Increasing ammonium pulses were applied to evaluate stability and stress tolerance. A different response in terms of start-up and ammonium tolerance was observed among the different inocula. Methanosaetaceae were the dominant acetoclastic methanogens, yet, Methanosarcinaceae increased in abundance at elevated ammonium concentrations. A shift from a Firmicutes to a Proteobacteria dominated bacterial community was observed in failing digesters. Methane production was strongly positively correlated with Methanosaetaceae, but also with Bacteria related to Anaerolinaceae, Clostridiales, and Alphaproteobacteria. Volatile fatty acids were strongly positively correlated with Betaproteobacteria and Bacteroidetes, yet ammonium concentration only with Bacteroidetes. Overall, these results indicate the importance of inoculum selection to ensure stable operation and stress tolerance in anaerobic digestion.}, }
@article {pmid25260923, year = {2015}, author = {Echenique-Subiabre, I and Villeneuve, A and Golubic, S and Turquet, J and Humbert, JF and Gugger, M}, title = {Influence of local and global environmental parameters on the composition of cyanobacterial mats in a tropical lagoon.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {234-244}, pmid = {25260923}, issn = {1432-184X}, mesh = {Biodiversity ; Cloning, Molecular ; Cyanobacteria/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Environment ; Indian Ocean ; *Microbial Consortia ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Tropical Climate ; Water Microbiology ; }, abstract = {Cyanobacteria-dominated microbial mat communities thrive widely and year round in coral reefs and tropical lagoons, with periodic massive development of benthic blooms. We studied the diversity and spatiotemporal variation of the cyanobacterial dominance in mats of the shallow lagoon of La Réunion Island in the Indian Ocean by means of denaturing gradient gel electrophoresis and cloning-sequencing approaches targeting the 16S rRNA gene, combined with macromorphological and micromorphological characterization of corresponding phenotypes. The mat-forming cyanobacteria were highly diversified with at least 67 distinct operational taxonomic units identified in the lagoon, encompassing the entire morphological spectrum of the phylum Cyanobacteria, but with striking dominance of Oscillatoriales and Nostocales. It appeared also that selective pressures acting at different geographical scales have an influence on the structure and composition of these mats dominated by cyanobacteria. First, large changes were observed in their diversity and composition in relation to local changes occurring in their environment. Second, from the data obtained on the richness and composition of the mats and from the comparison with similar studies in the world, tropical mats seem to display wider cyanobacterial richness than in temperate and cold areas. Moreover, these tropical mats share more species with mats in other tropical regions than with those in temperate and cold climatic regions, suggesting that marine cyanobacteria in biofilms and mats display a biogeographic structure.}, }
@article {pmid25260922, year = {2015}, author = {Purkamo, L and Bomberg, M and Nyyssönen, M and Kukkonen, I and Ahonen, L and Itävaara, M}, title = {Heterotrophic communities supplied by ancient organic carbon predominate in deep fennoscandian bedrock fluids.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {319-332}, pmid = {25260922}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Carbon/*chemistry ; Carbon Cycle ; Cloning, Molecular ; DNA, Bacterial/genetics ; Finland ; Gene Library ; Genes, Bacterial ; Genetic Markers ; *Heterotrophic Processes ; Methane/metabolism ; Nitrogen Cycle ; *Phylogeny ; Phylogeography ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The deep subsurface hosts diverse life, but the mechanisms that sustain this diversity remain elusive. Here, we studied microbial communities involved in carbon cycling in deep, dark biosphere and identified anaerobic microbial energy production mechanisms from groundwater of Fennoscandian crystalline bedrock sampled from a deep drill hole in Outokumpu, Finland, by using molecular biological analyses. Carbon cycling pathways, such as carbon assimilation, methane production and methane consumption, were studied with cbbM, rbcL, acsB, accC, mcrA and pmoA marker genes, respectively. Energy sources, i.e. the terminal electron accepting processes of sulphate-reducing and nitrate-reducing communities, were assessed with detection of marker genes dsrB and narG, respectively. While organic carbon is scarce in deep subsurface, the main carbon source for microbes has been hypothesized to be inorganic carbon dioxide. However, our results demonstrate that carbon assimilation is performed throughout the Outokumpu deep scientific drill hole water column by mainly heterotrophic microorganisms such as Clostridia. The source of carbon for the heterotrophic microbial metabolism is likely the Outokumpu bedrock, mainly composed of serpentinites and metasediments with black schist interlayers. In addition to organotrophic metabolism, nitrate and sulphate are other possible energy sources. Methanogenic and methanotrophic microorganisms are scarce, but our analyses suggest that the Outokumpu deep biosphere provides niches for these organisms; however, they are not very abundant.}, }
@article {pmid25259571, year = {2015}, author = {Kip, N and van Veen, JA}, title = {The dual role of microbes in corrosion.}, journal = {The ISME journal}, volume = {9}, number = {3}, pages = {542-551}, pmid = {25259571}, issn = {1751-7370}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Construction Materials/analysis/*microbiology ; Corrosion ; *Microbiota ; Steel/*chemistry ; }, abstract = {Corrosion is the result of a series of chemical, physical and (micro) biological processes leading to the deterioration of materials such as steel and stone. It is a world-wide problem with great societal and economic consequences. Current corrosion control strategies based on chemically produced products are under increasing pressure of stringent environmental regulations. Furthermore, they are rather inefficient. Therefore, there is an urgent need for environmentally friendly and sustainable corrosion control strategies. The mechanisms of microbially influenced corrosion and microbially influenced corrosion inhibition are not completely understood, because they cannot be linked to a single biochemical reaction or specific microbial species or groups. Corrosion is influenced by the complex processes of different microorganisms performing different electrochemical reactions and secreting proteins and metabolites that can have secondary effects. Information on the identity and role of microbial communities that are related to corrosion and corrosion inhibition in different materials and in different environments is scarce. As some microorganisms are able to both cause and inhibit corrosion, we pay particular interest to their potential role as corrosion-controlling agents. We show interesting interfaces in which scientists from different disciplines such as microbiology, engineering and art conservation can collaborate to find solutions to the problems caused by corrosion.}, }
@article {pmid25259528, year = {2014}, author = {Vandini, A and Temmerman, R and Frabetti, A and Caselli, E and Antonioli, P and Balboni, PG and Platano, D and Branchini, A and Mazzacane, S}, title = {Hard surface biocontrol in hospitals using microbial-based cleaning products.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e108598}, pmid = {25259528}, issn = {1932-6203}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Colony Count, Microbial ; Cross Infection/*prevention &amp; control ; Disinfection/*methods ; *Hospitals ; }, abstract = {BACKGROUND: Healthcare-Associated Infections (HAIs) are one of the most frequent complications occurring in healthcare facilities. Contaminated environmental surfaces provide an important potential source for transmission of many healthcare-associated pathogens, thus indicating the need for new and sustainable strategies.<br><br>AIM: This study aims to evaluate the effect of a novel cleaning procedure based on the mechanism of biocontrol, on the presence and survival of several microorganisms responsible for HAIs (i.e. coliforms, Staphyloccus aureus, Clostridium difficile, and Candida albicans) on hard surfaces in a hospital setting.<br><br>METHODS: The effect of microbial cleaning, containing spores of food grade Bacillus subtilis, Bacillus pumilus and Bacillus megaterium, in comparison with conventional cleaning protocols, was evaluated for 24 weeks in three independent hospitals (one in Belgium and two in Italy) and approximately 20000 microbial surface samples were collected.<br><br>RESULTS: Microbial cleaning, as part of the daily cleaning protocol, resulted in a reduction of HAI-related pathogens by 50 to 89%. This effect was achieved after 3-4 weeks and the reduction in the pathogen load was stable over time. Moreover, by using microbial or conventional cleaning alternatively, we found that this effect was directly related to the new procedure, as indicated by the raise in CFU/m2 when microbial cleaning was replaced by the conventional procedure. Although many questions remain regarding the actual mechanisms involved, this study demonstrates that microbial cleaning is a more effective and sustainable alternative to chemical cleaning and non-specific disinfection in healthcare facilities.<br><br>CONCLUSIONS: This study indicates microbial cleaning as an effective strategy in continuously lowering the number of HAI-related microorganisms on surfaces. The first indications on the actual level of HAIs in the trial hospitals monitored on a continuous basis are very promising, and may pave the way for a novel and cost-effective strategy to counteract or (bio)control healthcare-associated pathogens.}, }
@article {pmid25258679, year = {2014}, author = {Tully, BJ and Sachdeva, R and Heidelberg, KB and Heidelberg, JF}, title = {Comparative genomics of planktonic Flavobacteriaceae from the Gulf of Maine using metagenomic data.}, journal = {Microbiome}, volume = {2}, number = {}, pages = {34}, pmid = {25258679}, issn = {2049-2618}, abstract = {BACKGROUND: The Gulf of Maine is an important biological province of the Northwest Atlantic with high productivity year round. From an environmental Sanger-based metagenome, sampled in summer and winter, we were able to assemble and explore the partial environmental genomes of uncultured members of the class Flavobacteria. Each of the environmental genomes represents organisms that compose less than 1% of the total microbial metagenome.<br><br>RESULTS: Four partial environmental genomes were assembled with varying degrees of estimated completeness (37%-84% complete) and were analyzed from a perspective of gathering information regarding niche partitioning between co-occurring organisms. Comparative genomics revealed potentially important niche partitioning genomic variations, including iron transporters and genes associated with cell attachment and polymer degradation. Analysis of large syntenic regions helped reveal potentially ecologically relevant variations for Flavobacteriaceae in the Gulf of Maine, such as arginine biosynthesis, and identify a putative genomic island incorporating novel exogenous genes from the environment.<br><br>CONCLUSIONS: Biogeographic analysis revealed flavobacteria species with distinct abundance patterns suggesting the presence of local blooms relative to the other species, as well as seasonally selected organisms. The analysis of genomic content for the Gulf of Maine Flavobacteria supports the hypothesis of a particle-associated lifestyle and specifically highlights a number of putative coding sequences that may play a role in the remineralization of particulate organic matter. And lastly, analysis of the underlying sequences for each assembled genome revealed seasonal and nonseasonal variants of specific genes implicating a dynamic interaction between individuals within the species.}, }
@article {pmid25256302, year = {2015}, author = {Basak, P and Majumder, NS and Nag, S and Bhattacharyya, A and Roy, D and Chakraborty, A and SenGupta, S and Roy, A and Mukherjee, A and Pattanayak, R and Ghosh, A and Chattopadhyay, D and Bhattacharyya, M}, title = {Spatiotemporal analysis of bacterial diversity in sediments of Sundarbans using parallel 16S rRNA gene tag sequencing.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {500-511}, pmid = {25256302}, issn = {1432-184X}, mesh = {Bacteria/genetics/*isolation &amp; purification/metabolism ; DNA, Bacterial/genetics/metabolism ; Geologic Sediments/*microbiology ; India ; *Microbiota ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics/metabolism ; Sequence Analysis, DNA ; Spatio-Temporal Analysis ; Wetlands ; }, abstract = {The influence of temporal and spatial variations on the microbial community composition was assessed in the unique coastal mangrove of Sundarbans using parallel 16S rRNA gene pyrosequencing. The total sediment DNA was extracted and subjected to the 16S rRNA gene pyrosequencing, which resulted in 117 Mbp of data from three experimental stations. The taxonomic analysis of the pyrosequencing data was grouped into 24 different phyla. In general, Proteobacteria were the most dominant phyla with predominance of Deltaproteobacteria, Alphaproteobacteria, and Gammaproteobacteria within the sediments. Besides Proteobacteria, there are a number of sequences affiliated to the following major phyla detected in all three stations in both the sampling seasons: Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Chloroflexi, Cyanobacteria, Nitrospira, and Firmicutes. Further taxonomic analysis revealed abundance of micro-aerophilic and anaerobic microbial population in the surface layers, suggesting anaerobic nature of the sediments in Sundarbans. The results of this study add valuable information about the composition of microbial communities in Sundarbans mangrove and shed light on possible transformations promoted by bacterial communities in the sediments.}, }
@article {pmid25256301, year = {2015}, author = {Ji, Z and Card, KJ and Dazzo, FB}, title = {CMEIAS JFrad: a digital computing tool to discriminate the fractal geometry of landscape architectures and spatial patterns of individual cells in microbial biofilms.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {710-720}, pmid = {25256301}, issn = {1432-184X}, mesh = {*Bacterial Physiological Phenomena ; Bacteriological Techniques/*methods ; *Biofilms ; *Fractals ; Microscopy ; Software ; }, abstract = {Image analysis of fractal geometry can be used to gain deeper insights into complex ecophysiological patterns and processes occurring within natural microbial biofilm landscapes, including the scale-dependent heterogeneities of their spatial architecture, biomass, and cell-cell interactions, all driven by the colonization behavior of optimal spatial positioning of organisms to maximize their efficiency in utilization of allocated nutrient resources. Here, we introduce CMEIAS JFrad, a new computing technology that analyzes the fractal geometry of complex biofilm architectures in digital landscape images. The software uniquely features a data-mining opportunity based on a comprehensive collection of 11 different mathematical methods to compute fractal dimension that are implemented into a wizard design to maximize ease-of-use for semi-automatic analysis of single images or fully automatic analysis of multiple images in a batch process. As examples of application, quantitative analyses of fractal dimension were used to optimize the important variable settings of brightness threshold and minimum object size in order to discriminate the complex architecture of freshwater microbial biofilms at multiple spatial scales, and also to differentiate the spatial patterns of individual bacterial cells that influence their cooperative interactions, resource use, and apportionment in situ. Version 1.0 of JFrad is implemented into a software package containing the program files, user manual, and tutorial images that will be freely available at http://cme.msu.edu/cmeias/. This improvement in computational image informatics will strengthen microscopy-based approaches to analyze the dynamic landscape ecology of microbial biofilm populations and communities in situ at spatial resolutions that range from single cells to microcolonies.}, }
@article {pmid25252928, year = {2015}, author = {Li, Z and Wright, AD and Liu, H and Bao, K and Zhang, T and Wang, K and Cui, X and Yang, F and Zhang, Z and Li, G}, title = {Bacterial community composition and fermentation patterns in the rumen of sika deer (Cervus nippon) fed three different diets.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {307-318}, pmid = {25252928}, issn = {1432-184X}, mesh = {Animal Feed/analysis ; Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Deer/metabolism/*microbiology ; Diet/*veterinary ; Digestion ; Fatty Acids, Volatile/analysis ; *Fermentation ; High-Throughput Nucleotide Sequencing ; Male ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; Silage/analysis ; Zea mays/chemistry ; }, abstract = {Sika deer (Cervus nippon) rely on microorganisms living in the rumen to convert plant materials into chemical compounds, such as volatile fatty acids (VFAs), but how the rumen bacterial community is affected by different forages and adapt to altered diets remains poorly understood. The present study used 454-pyrosequencing of bacterial 16S ribosomal RNA (rRNA) genes to examine the relationship between rumen bacterial diversity and metabolic phenotypes using three sika deer in a 3 × 3 latin square design. Three sika deer were fed oak leaves (OL), corn stover (CS), or corn silage (CI), respectively. After a 7-day feeding period, when compared to the CS and CI groups, the OL group had a lower proportion of Prevotella spp. and a higher proportion of unclassified bacteria belonging to the families Succinivibrionaceae and Paraprevotellaceae (P<0.05). Meanwhile, the concentration of isobutyrate was significantly lower (P<0.05) in the OL group than in the CS and CI groups. There was no significant change of dominant bacterial genera in the OL group after 28 days of feeding. Conversely, total volatile fatty acids (TVFAs) showed an increase after 28 days of feeding, mainly due to the increasing of acetate, propionate, and valerate (P<0.05). The interplay between bacteria and metabolism in the OL group differed from that in the CS and CI groups, especially for the interaction of TVFAs and acetate/propionate. Overall, the current study suggested that Prevotella spp. played critical roles in the fermentation of feed in the rumen of sika deer. However, the differences in interplay patterns between rumen bacterial community composition and metabolic phenotypes were altered in the native and domesticated diets indicating the changed fermentation patterns in the rumen of sika deer.}, }
@article {pmid25252124, year = {2015}, author = {Loozen, G and Boon, N and Pauwels, M and Slomka, V and Rodrigues Herrero, E and Quirynen, M and Teughels, W}, title = {Effect of Bdellovibrio bacteriovorus HD100 on multispecies oral communities.}, journal = {Anaerobe}, volume = {35}, number = {Pt A}, pages = {45-53}, doi = {10.1016/j.anaerobe.2014.09.011}, pmid = {25252124}, issn = {1095-8274}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Bdellovibrio/genetics/*physiology ; Humans ; *Microbiota ; Mouth/*microbiology ; Periodontitis/*microbiology ; Saliva/microbiology ; }, abstract = {The predation of Bdellovibrio bacteriovorus on different periodontal pathogens has already been described. However, it is necessary to consider the polymicrobial nature of periodontal disease. The current study explores the predation of Bdellovibrio on oral pathogens organized in multispecies communities. The effect of the predator was evaluated on in vitro six species communities with microbial culturing. Additionally, the effect on ex vivo subgingival plaque and saliva samples from periodontitis patients was assessed. In the latter experiment results were examined with microbial culturing, quantitative polymerase chain reaction (qPCR) and denaturing gradient gel electrophoresis (DGGE). The latter technique was used to get an overview of the whole mixed microbial population. Results showed that even in more complex models, B. bacteriovorus was still able to predate on Fusobacterium nucleatum and Aggregatibacter actinomycetemcomitans. However predation on Prevotella intermedia and Porphyromonas gingivalis could not be validated in multispecies models. The effect of Bdellovibrio was not restricted to the target bacteria. Changes in the overall ecology of the different models were evident. It could be concluded that the efficiency of predation decreased when complexity of the models increased. However, B. bacteriovorus was able to attack two important oral pathogens, F. nucleatum, and A. actinomycetemcomitans, even when present in ex vivo clinical samples. These effects still have to be validated in in vivo models to see the impact of Bdellovibrio on the whole bacterial ecology.}, }
@article {pmid25241172, year = {2015}, author = {Mulec, J and Krištůfek, V and Chroňáková, A and Oarga, A and Scharfen, J and Šestauberová, M}, title = {Microbiology of healing mud (fango) from Roman thermae aquae iasae archaeological site (Varaždinske Toplice, Croatia).}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {293-306}, pmid = {25241172}, issn = {1432-184X}, mesh = {Carbon/analysis ; Croatia ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Ecosystem ; Geologic Sediments/*microbiology ; Hydrogen-Ion Concentration ; Metals, Heavy/analysis ; *Mud Therapy ; Phylogeography ; Polymerase Chain Reaction ; Proteobacteria/*classification/isolation &amp; purification ; Sensitivity and Specificity ; Soil Microbiology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Thiobacillus/*classification/isolation &amp; purification ; Water Microbiology ; }, abstract = {We found well-preserved, rocky artefacts that had been buried in the healing mud (fango) for more than 1,500 years at the Roman archaeological site at Varaždinske Toplice. This Roman pool with fango sediments and artefacts is fed from hot sulphidic springs. The fango exhibited nearly neutral pH, a high level of organic C, an elevated concentration of heavy metals and a high total microbial biomass, greater than 10(8) cells per gram of dry weight. The dominant microbes, assessed by molecular profiling (denaturing gradient gel electrophoresis), were affiliated with Thiobacillus, Sulfuricurvum, Polaromonas, and Bdellovibrio. Polymerase chain reaction screening for microbial functional guilds revealed the presence of sulphur oxidizers and methanogens but no sulphate reducers. The dominance of four Proteobacterial classes (α-, β-, δ- and ε-Proteobacteria) was confirmed by fluorescence in situ hybridisation; Actinobacteria were less abundant. Cultivable bacteria represented up to 23.4 % of the total bacterial counts when cultivation media was enriched with fango. These bacteria represented the genera Acinetobacter, Aeromonas, Arthrobacter, Comamonas, Ewingella, Flavobacterium, Pseudomonas, Rahnella and Staphylococcus. This study showed that the heterogeneous nature of fango at neutral pH created various microniches, which largely supported microbial life based on sulphur-driven, autotrophic denitrification.}, }
@article {pmid25238930, year = {2015}, author = {Chehri, K and Salleh, B and Zakaria, L}, title = {Morphological and phylogenetic analysis of Fusarium solani species complex in Malaysia.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {457-471}, pmid = {25238930}, issn = {1432-184X}, mesh = {DNA, Fungal/genetics/metabolism ; DNA, Intergenic/genetics/metabolism ; Fungal Proteins/genetics/metabolism ; Hypocreales/*cytology/*genetics/metabolism ; Malaysia ; Molecular Sequence Data ; RNA, Ribosomal, 28S/genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {Members of Fusarium solani species complex (FSSC) have been known as plant, animal, and human pathogens. Nevertheless, the taxonomic status of such an important group of fungi is still very confusing and many new species as well as lineages have been elucidated recently. Unfortunately, most of the new taxa came from temperate and subtropical regions. Therefore, the objectives of the present study were to identify strains of FSSC recovered from different sources in Malaysia. In the present study, 55 strains belonging to the FSSC were examined and phylogenetically analyzed on the basis of internal transcribed spacer (ITS) regions and partial translation elongation factor-1 (TEF-1α) sequences. Based on morphological features, a total of 55 strains were selected for molecular studies. Based on morphological features, the strains were classified into four described Fusarium species, namely Fusarium keratoplasticum, Fusarium falciforme, FSSC 5, and Fusarium cf. ensiforme, and one unknown phylogenetic species was introduced. Although the data obtained from morphological and molecular studies sufficiently supported each other, the phylogenetic trees based on ITS and TEF-1α dataset clearly distinguished closely related species and distinctly separated all morphological taxa. All members of FSSC in this research were reported for the first time for Malaysian mycoflora.}, }
@article {pmid25236539, year = {2014}, author = {McKenney, EA and Ashwell, M and Lambert, JE and Fellner, V}, title = {Fecal microbial diversity and putative function in captive western lowland gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas) and binturongs (Arctictis binturong).}, journal = {Integrative zoology}, volume = {9}, number = {5}, pages = {557-569}, doi = {10.1111/1749-4877.12112}, pmid = {25236539}, issn = {1749-4877}, mesh = {Animals ; Bacteria/*classification/isolation &amp; purification ; Dietary Fiber ; Feces/*microbiology ; Fermentation ; Gorilla gorilla/*microbiology ; Pan troglodytes/*microbiology ; Papio hamadryas/*microbiology ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Viverridae/*microbiology ; }, abstract = {Microbial populations in the gastrointestinal tract contribute to host health and nutrition. Although gut microbial ecology is well studied in livestock and domestic animals, little is known of the endogenous populations inhabiting primates or carnivora. We characterized microbial populations in fecal cultures from gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas) and binturongs (Arctictis binturong) to compare the microbiomes associated with different gastrointestinal morphologies and different omnivorous feeding strategies. Each species was fed a distinct standardized diet for 2 weeks prior to fecal collection. All diets were formulated to reflect the species' feeding strategies in situ. Fresh fecal samples were pooled within species and used to inoculate in vitro batch cultures. Acetate, propionate, butyrate and valerate were measured after 24 h of incubation. Eubacterial DNA was extracted from individual fecal samples, pooled, and the cpn60 gene region was amplified and then sequenced to identify the major eubacterial constituents associated with each host species. Short chain fatty acids (P < 0.001) and methane (P < 0.001) were significantly different across species. Eubacterial profiles were consistent with fermentation data and suggest an increase in diversity with dietary fiber.}, }
@article {pmid25230887, year = {2015}, author = {Huang, YE and Wang, Y and He, Y and Ji, Y and Wang, LP and Sheng, HF and Zhang, M and Huang, QT and Zhang, DJ and Wu, JJ and Zhong, M and Zhou, HW}, title = {Homogeneity of the vaginal microbiome at the cervix, posterior fornix, and vaginal canal in pregnant Chinese women.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {407-414}, pmid = {25230887}, issn = {1432-184X}, mesh = {Adult ; Asian People ; Bacteria/classification/genetics/isolation &amp; purification ; Cervix Uteri/*microbiology ; DNA, Bacterial/genetics ; Female ; Humans ; Lactobacillus/*classification/genetics/isolation &amp; purification ; *Microbiota ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; Vagina/*microbiology ; Vaginosis, Bacterial/microbiology ; Young Adult ; }, abstract = {The vaginal microbiome is an emerging concern in prenatal health. Because the sampling process of vaginal microbiota may pose potential risks for pregnant women, the choice of sampling site should be carefully considered. However, whether the microbial diversity is different across various sampling sites has been controversial. In the present study, three repeated swabs were collected at the cervix (C), posterior fornix (P), and vaginal canal (V) from 34 Chinese women during different pregnancy stages, and vaginal species were determined using the Illumina sequencing of 16S rRNA tag sequences. The identified microbiomes were classified into four community state types (CSTs): CST I (dominated by L. crispatus), CST II (dominated by L. gasseri), CST III (dominated by L. iners), and CST IV-A (characterized by a low abundance of Lactobacillus, but with proportions of various species previously shown to be associated with bacterial vaginosis). All individuals had consistent CST at the three sampling sites regardless of pregnancy stage and CST group. In addition, there was little heterogeneity across community structures within each individual, as determined by LEfSe, indicating high vaginal microbiome homogeneity at the three sampling sites. The present study also revealed different beta diversity during pregnancy stages. The vaginal microbiome variation among women during trimester T1 (9 ± 2.6 weeks) is larger than that of non-pregnant women and women from other trimesters, as demonstrated by the UniFrac distance (P < 0.05). In particular, the present study is the first one that demonstrates the notably difference of vaginal microbiome of postpartum women compare to women in gestation. These results will be useful for future studies of the vaginal microbiota during pregnancy.}, }
@article {pmid25227214, year = {2014}, author = {Vengerfeldt, V and Špilka, K and Saag, M and Preem, JK and Oopkaup, K and Truu, J and Mändar, R}, title = {Highly diverse microbiota in dental root canals in cases of apical periodontitis (data of illumina sequencing).}, journal = {Journal of endodontics}, volume = {40}, number = {11}, pages = {1778-1783}, doi = {10.1016/j.joen.2014.06.017}, pmid = {25227214}, issn = {1878-3554}, mesh = {Actinobacteria/isolation &amp; purification ; Adult ; Aged ; Bacteroidetes/isolation &amp; purification ; Dental Pulp Cavity/*microbiology ; Enterococcus faecalis/isolation &amp; purification ; Female ; Firmicutes/isolation &amp; purification ; Fusobacteria/isolation &amp; purification ; Gram-Negative Anaerobic Bacteria/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Male ; Microbial Consortia/genetics ; *Microbiota/genetics ; Middle Aged ; Oxalobacteraceae/isolation &amp; purification ; Periapical Abscess/microbiology ; Periapical Periodontitis/*microbiology ; Proteobacteria/isolation &amp; purification ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, RNA/*methods ; Spirochaetales/isolation &amp; purification ; Tenericutes/isolation &amp; purification ; Young Adult ; }, abstract = {INTRODUCTION: Chronic apical periodontitis (CAP) is a frequent condition that has a considerable effect on a patient's quality of life. We aimed to reveal root canal microbial communities in antibiotic-naive patients by applying Illumina sequencing (Illumina Inc, San Diego, CA).<br><br>METHODS: Samples were collected under strict aseptic conditions from 12 teeth (5 with primary CAP, 3 with secondary CAP, and 4 with a periapical abscess [PA]) and characterized by profiling the microbial community on the basis of the V6 hypervariable region of the 16S ribosomal RNA gene by using Illumina HiSeq2000 sequencing combinatorial sequence-tagged polymerase chain reaction products.<br><br>RESULTS: Root canal specimens displayed highly polymicrobial communities in all 3 patient groups. One sample contained 5-8 (mean = 6.5) phyla of bacteria. The most numerous were Firmicutes and Bacteroidetes, but Actinobacteria, Fusobacteria, Proteobacteria, Spirochaetes, Tenericutes, and Synergistetes were also present in most of the patients. One sample contained 30-70 different operational taxonomic units; the mean (&#xb1; standard deviation) was lower in the primary CAP group (36 &#xb1; 4) than in the PA (45 &#xb1; 4) and secondary CAP (43 &#xb1; 13) groups (P < .05). The communities were individually different, but anaerobic bacteria predominated as the rule. Enterococcus faecalis was found only in patients with secondary CAP. One PA sample displayed a significantly high proportion (47%) of Proteobacteria, mainly at the expense of Janthinobacterium lividum.<br><br>CONCLUSIONS: This study provided an in-depth characterization of the microbiota of periapical tissues, revealing highly polymicrobial communities and minor differences between the study groups. A full understanding of the etiology of periodontal disease will only be possible through further in-depth systems-level analyses of the host-microbiome interaction.}, }
@article {pmid25226019, year = {2014}, author = {Sanschagrin, S and Yergeau, E}, title = {Next-generation sequencing of 16S ribosomal RNA gene amplicons.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {90}, pages = {}, pmid = {25226019}, issn = {1940-087X}, mesh = {*Environmental Microbiology ; RNA, Bacterial/chemistry/genetics ; RNA, Ribosomal, 16S/chemistry/genetics ; Sequence Analysis, RNA/*methods ; }, abstract = {One of the major questions in microbial ecology is "who is there?" This question can be answered using various tools, but one of the long-lasting gold standards is to sequence 16S ribosomal RNA (rRNA) gene amplicons generated by domain-level PCR reactions amplifying from genomic DNA. Traditionally, this was performed by cloning and Sanger (capillary electrophoresis) sequencing of PCR amplicons. The advent of next-generation sequencing has tremendously simplified and increased the sequencing depth for 16S rRNA gene sequencing. The introduction of benchtop sequencers now allows small labs to perform their 16S rRNA sequencing in-house in a matter of days. Here, an approach for 16S rRNA gene amplicon sequencing using a benchtop next-generation sequencer is detailed. The environmental DNA is first amplified by PCR using primers that contain sequencing adapters and barcodes. They are then coupled to spherical particles via emulsion PCR. The particles are loaded on a disposable chip and the chip is inserted in the sequencing machine after which the sequencing is performed. The sequences are retrieved in fastq format, filtered and the barcodes are used to establish the sample membership of the reads. The filtered and binned reads are then further analyzed using publically available tools. An example analysis where the reads were classified with a taxonomy-finding algorithm within the software package Mothur is given. The method outlined here is simple, inexpensive and straightforward and should help smaller labs to take advantage from the ongoing genomic revolution.}, }
@article {pmid25225611, year = {2014}, author = {Hong, C and Manimaran, S and Shen, Y and Perez-Rogers, JF and Byrd, AL and Castro-Nallar, E and Crandall, KA and Johnson, WE}, title = {PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples.}, journal = {Microbiome}, volume = {2}, number = {}, pages = {33}, pmid = {25225611}, issn = {2049-2618}, support = {T32 HL007035/HL/NHLBI NIH HHS/United States ; }, abstract = {BACKGROUND: Recent innovations in sequencing technologies have provided researchers with the ability to rapidly characterize the microbial content of an environmental or clinical sample with unprecedented resolution. These approaches are producing a wealth of information that is providing novel insights into the microbial ecology of the environment and human health. However, these sequencing-based approaches produce large and complex datasets that require efficient and sensitive computational analysis workflows. Many recent tools for analyzing metagenomic-sequencing data have emerged, however, these approaches often suffer from issues of specificity, efficiency, and typically do not include a complete metagenomic analysis framework.<br><br>RESULTS: We present PathoScope 2.0, a complete bioinformatics framework for rapidly and accurately quantifying the proportions of reads from individual microbial strains present in metagenomic sequencing data from environmental or clinical samples. The pipeline performs all necessary computational analysis steps; including reference genome library extraction and indexing, read quality control and alignment, strain identification, and summarization and annotation of results. We rigorously evaluated PathoScope 2.0 using simulated data and data from the 2011 outbreak of Shiga-toxigenic Escherichia coli O104:H4.<br><br>CONCLUSIONS: The results show that PathoScope 2.0 is a complete, highly sensitive, and efficient approach for metagenomic analysis that outperforms alternative approaches in scope, speed, and accuracy. The PathoScope 2.0 pipeline software is freely available for download at: http://sourceforge.net/projects/pathoscope/.}, }
@article {pmid25225376, year = {2014}, author = {Kembel, SW and O'Connor, TK and Arnold, HK and Hubbell, SP and Wright, SJ and Green, JL}, title = {Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {38}, pages = {13715-13720}, pmid = {25225376}, issn = {1091-6490}, mesh = {*Ecosystem ; *Forests ; Microbial Consortia/*physiology ; Panama ; *Phylogeny ; Plant Leaves/*microbiology ; Plants/*microbiology ; }, abstract = {The phyllosphere--the aerial surfaces of plants, including leaves--is a ubiquitous global habitat that harbors diverse bacterial communities. Phyllosphere bacterial communities have the potential to influence plant biogeography and ecosystem function through their influence on the fitness and function of their hosts, but the host attributes that drive community assembly in the phyllosphere are poorly understood. In this study we used high-throughput sequencing to quantify bacterial community structure on the leaves of 57 tree species in a neotropical forest in Panama. We tested for relationships between bacterial communities on tree leaves and the functional traits, taxonomy, and phylogeny of their plant hosts. Bacterial communities on tropical tree leaves were diverse; leaves from individual trees were host to more than 400 bacterial taxa. Bacterial communities in the phyllosphere were dominated by a core microbiome of taxa including Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria, and Sphingobacteria. Host attributes including plant taxonomic identity, phylogeny, growth and mortality rates, wood density, leaf mass per area, and leaf nitrogen and phosphorous concentrations were correlated with bacterial community structure on leaves. The relative abundances of several bacterial taxa were correlated with suites of host plant traits related to major axes of plant trait variation, including the leaf economics spectrum and the wood density-growth/mortality tradeoff. These correlations between phyllosphere bacterial diversity and host growth, mortality, and function suggest that incorporating information on plant-microbe associations will improve our ability to understand plant functional biogeography and the drivers of variation in plant and ecosystem function.}, }
@article {pmid25225263, year = {2014}, author = {Das, B and Kumari, R and Pant, A and Sen Gupta, S and Saxena, S and Mehta, O and Nair, GB}, title = {A novel, broad-range, CTXΦ-derived stable integrative expression vector for functional studies.}, journal = {Journal of bacteriology}, volume = {196}, number = {23}, pages = {4071-4080}, pmid = {25225263}, issn = {1098-5530}, mesh = {Attachment Sites, Microbiological ; Chromosomes, Bacterial ; DNA, Single-Stranded/genetics/metabolism ; DNA, Viral/genetics/metabolism ; Escherichia coli/genetics ; Gene Expression ; *Genetic Vectors ; Genetics, Microbial/*methods ; Genome, Viral ; Inovirus/*genetics/isolation &amp; purification ; Klebsiella pneumoniae/genetics ; Molecular Biology/*methods ; Promoter Regions, Genetic ; Recombination, Genetic ; Salmonella enterica/genetics ; Vibrio/*virology ; }, abstract = {CTXΦ, a filamentous vibriophage encoding cholera toxin, uses a unique strategy for its lysogeny. The single-stranded phage genome forms intramolecular base-pairing interactions between two inversely oriented XerC and XerD binding sites (XBS) and generates a functional phage attachment site, attP(+), for integration. The attP(+) structure is recognized by the host-encoded tyrosine recombinases XerC and XerD (XerCD), which enables irreversible integration of CTXΦ into the chromosome dimer resolution site (dif) of Vibrio cholerae. The dif site and the XerCD recombinases are widely conserved in bacteria. We took advantage of these conserved attributes to develop a broad-host-range integrative expression vector that could irreversibly integrate into the host chromosome using XerCD recombinases without altering the function of any known open reading frame (ORF). In this study, we engineered two different arabinose-inducible expression vectors, pBD62 and pBD66, using XBS of CTXΦ. pBD62 replicates conditionally and integrates efficiently into the dif of the bacterial chromosome by site-specific recombination using host-encoded XerCD recombinases. The expression level of the gene of interest could be controlled through the PBAD promoter by modulating the functions of the vector-encoded transcriptional factor AraC. We validated the irreversible integration of pBD62 into a wide range of pathogenic and nonpathogenic bacteria, such as V. cholerae, Vibrio fluvialis, Vibrio parahaemolyticus, Escherichia coli, Salmonella enterica, and Klebsiella pneumoniae. Gene expression from the PBAD promoter of integrated vectors was confirmed in V. cholerae using the well-studied reporter genes mCherry, eGFP, and lacZ.}, }
@article {pmid25224920, year = {2015}, author = {Hosseinkhani, B and Callewaert, C and Vanbeveren, N and Boon, N}, title = {Novel biocompatible nanocapsules for slow release of fragrances on the human skin.}, journal = {New biotechnology}, volume = {32}, number = {1}, pages = {40-46}, doi = {10.1016/j.nbt.2014.09.001}, pmid = {25224920}, issn = {1876-4347}, mesh = {Biocompatible Materials/*chemistry ; Escherichia coli/growth &amp; development ; Fatty Acids, Volatile/analysis ; Humans ; Hydrogen-Ion Concentration ; Lactic Acid/chemistry ; Microbiota ; Microscopy, Fluorescence ; Nanocapsules/*chemistry ; Particle Size ; Perfume/*analysis ; Polyesters ; Polymers/chemistry ; Skin/*chemistry ; Staphylococcus aureus/growth &amp; development ; }, abstract = {There is a growing demand for fragranced products, but due to the poor aqueous solubility and instability of fragrance molecules, their use is limited. Nowadays, fragrance encapsulation in biocompatible nanocontainer material is emerging as a novel strategy to overcome the evaporation of volatile molecules and to prolong the sensory characteristics of fragrance molecules and the longevity of perfumes. The objective of this study was to develop an innovative sustained release system of perfume, by entrapping fragrance molecules in a polymeric nanocarrier; the impact of this strategy on the human axillary microbiome was further assessed. Stabilised poly-l-lactic acid nanocapsules (PLA-NCs) with a diameter of approximately 115 nm were prepared through nanoprecipitation. Size and morphology of the capsules were evaluated using Transmission Electron Microscopy (TEM) and Dynamic Light Scattering (DLS). Two model hydrophobic compounds, chlorobenzene and fluorescein, representing two different types of functionalised molecules, were encapsulated in PLA-NCs with an efficiency rate of 50%. Different release behaviours were seen, dependent on hydrophobicity. For hydrophobic compounds, a steady release was observed over 48hours. The polymeric nanocarriers did not impact the human axillary microbiome. Because of the slow and sustained release of fragrances, encapsulation of molecules in biocompatible NCs can represent a revolutionary contribution to the future of toiletries, body deodorant products, and in washing and cleaning sectors.}, }
@article {pmid25219446, year = {2015}, author = {Silva, KJ and Vidal-Torrado, P and Lambais, MR}, title = {Bacterial and archaeal communities in bleached mottles of tropical podzols.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {372-382}, pmid = {25219446}, issn = {1432-184X}, mesh = {Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Brazil ; Chemical Phenomena ; Crenarchaeota/classification/genetics/isolation &amp; purification ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; *Phylogeny ; Phylogeography ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Podzols frequently show bleached mottles depleted in organic matter, most readily visible in the Bh horizons. Even though the process of bleached mottles development is not understood, it has been suggested that the selective degradation of organic matter by soil microorganisms has a major contribution. In this study, we examined the bacterial and archaeal communities along three Brazilian coastal podzol profiles, as well as in bleached mottles and their immediate vicinity, using 16S rRNA gene profiling. Our results showed that the bacterial and archaeal community structures in the studied podzols varied with depth and that the bacterial communities in the bleached mottles were significantly different from that in their immediate vicinity. In contrast, the archaeal communities in bleached mottles were significantly different from their vicinity only in the Bertioga (BT) profile, based on sequencing of amplicons of the 16S rRNA gene. Redundancy analyses showed that the bacterial community structures in the bleached mottles of BT were negatively associated mostly with the levels of organic carbon, exchangeable-aluminum (Al), exchangeable potassium, and Al-saturation, whereas in the surrounding soil, the opposite was observed. In the Ilha Comprida (IC) profiles, no such relationships were observed, suggesting distinct drivers of the bacterial community structures in bleached mottles of different podzols. In the bleached mottles of the BT profile, operational taxonomic units (OTUs) phylogenetically related to Pseudomonas were the most abundant Bacteria, whereas in the IC profiles, OTUs related to Acidobacteria were predominant. Thermoprotei (Crenarchaeota) were the most abundant Archaea in the bleached mottles and in their immediate vicinity. Based on the diverse metabolic capabilities of Pseudomonas and Acidobacteria, our data suggest that these groups of bacteria may be involved in the development of bleached mottles in the podzols studied and that the selection of specific bacterial populations in the bleached mottles may depend on the local edaphic conditions.}, }
@article {pmid25214308, year = {2014}, author = {Schwendicke, F and Horb, K and Kneist, S and Dörfer, C and Paris, S}, title = {Effects of heat-inactivated Bifidobacterium BB12 on cariogenicity of Streptococcus mutans in vitro.}, journal = {Archives of oral biology}, volume = {59}, number = {12}, pages = {1384-1390}, doi = {10.1016/j.archoralbio.2014.08.012}, pmid = {25214308}, issn = {1879-1506}, mesh = {Animals ; Bifidobacterium/*physiology ; Biofilms/drug effects ; Cariogenic Agents/*pharmacology ; Cattle ; Colony Count, Microbial ; Dental Caries/*microbiology/*prevention &amp; control ; *Hot Temperature ; Hydrogen-Ion Concentration ; In Vitro Techniques ; Microradiography ; Microscopy, Electron, Scanning ; Probiotics/*pharmacology ; Streptococcus mutans ; Tooth Demineralization/microbiology ; }, abstract = {OBJECTIVE: Since some probiotic bacteria are cariogenic themselves, their suitability for caries management is questionable. Inactivated bacteria or their supernatants have been found to exert probiotic effects, whilst having several advantages compared with living bacteria. We hypothesized that viable and heat-inactivated Bifidobacterium animalis BB12 reduces the cariogenicity of Streptococcus mutans (SM) in vitro.<br><br>DESIGN: We assessed mono- and mixed species biofilms of SM and viable or heat-inactivated BB12. Biofilms were grown in a continuous-culture-system under cariogenic conditions on smooth proximal enamel or cavitated dentine. For each of eight experimental subsets (4 biofilms&#xd7;2 hard-tissue conditions), a total of 32 specimens was used. After 10 days, bacterial numbers of 12 biofilms per group were analysed, and all specimens submitted to transversal microradiography.<br><br>RESULTS: Mineral loss was higher in cavitated dentine than smooth enamel for all biofilms (p<0.001, t-test). BB12-monospecies biofilms induced significantly less mineral loss than SM in both enamel (p<0.05) and dentine (p<0.001). Viable BB12 did not significantly reduce cariogenicity of SM (p>0.05), whilst heat-inactivated BB12 decreased cariogenicity of SM in dentinal cavities (p<0.01). Bacterial numbers were higher on dentine than enamel (p<0.05), but not significantly influenced by biofilm species (p>0.05).<br><br>CONCLUSIONS: Heat-inactivated BB12 reduced the cariogenicity of SM in dentinal cavities in vitro. Inactivated probiotics might be suitable for caries control.}, }
@article {pmid25213655, year = {2015}, author = {Xiao, Y and Zheng, Y and Wu, S and Yang, ZH and Zhao, F}, title = {Bacterial community structure of autotrophic denitrification biocathode by 454 pyrosequencing of the 16S rRNA gene.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {492-499}, pmid = {25213655}, issn = {1432-184X}, mesh = {Bacteria/genetics/*isolation &amp; purification/metabolism ; *Bacterial Physiological Phenomena ; *Biofilms ; Bioreactors/microbiology ; DNA, Bacterial/genetics/metabolism ; Denitrification ; Electrodes/microbiology ; *Microbiota ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {Few studies have been conducted to explore the community composition in denitrifying biocathode. Herein, the microbial communities of denitrifying biocathodes yielding current of 1 mA (reactor C1) and 1.5 mA (reactor C2) were characterized by 454 pyrosequencing. The nitrate removal efficiencies in C1 and C2 were about 93 and 85%, respectively. The optimization of data generated high-quality sequences of 18509 in C1 and 14857 in C2. Proteobacteria was the predominant phylum, and Bacteroidetes, Chloroflexi, and Planctomycetes were the subdominant groups. Classes of Alphaproteobacteria, Anaerolineae, and Phycisphaerae may benefit the performance of current production and nitrate removal. Twenty-nine dominant operational taxonomic units (OTUs) accounted for 64 and 65% of sequences in C1 and C2, respectively. A denitrifying pathway was constructed based on the phylogenetic analysis and function inferring of the dominant OTUs. Obviously, the 454 pyrosequencing provided a high-resolution profile of bacteria community in denitrifying biocathode.}, }
@article {pmid25213654, year = {2015}, author = {Sun, G and Zhang, X and Hu, Q and Zhang, H and Zhang, D and Li, G}, title = {Biodegradation of dichlorodiphenyltrichloroethanes (DDTs) and hexachlorocyclohexanes (HCHs) with plant and nutrients and their effects on the microbial ecological kinetics.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {281-292}, pmid = {25213654}, issn = {1432-184X}, mesh = {Bacteria/classification/growth &amp; development/isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Biodiversity ; Biofilms/classification/growth &amp; development ; China ; DDT/*chemistry ; DNA, Bacterial/genetics ; Environmental Monitoring/*methods ; Geologic Sediments/chemistry/microbiology ; Hexachlorocyclohexane/*chemistry ; Hydrocarbons, Chlorinated/chemistry ; Pesticides/chemistry ; Pilot Projects ; Plants ; RNA, Ribosomal, 16S/genetics ; Rivers/chemistry/microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; Soil Pollutants/chemistry ; }, abstract = {Four pilot-scale test mesocosms were conducted for the remediation of organochlorine pesticides (OCPs)-contaminated aged soil. The results indicate that the effects on degradation of hexachlorocyclohexanes (HCHs) and dichlorodiphenyltrichloroethanes (DDTs) were in the following order: nutrients/plant bioaugmentation (81.18 % for HCHs; 85.4 % for DDTs) > nutrients bioaugmentation > plant bioaugmentation > only adding water > control, and nutrients/plant bioaugmentation greatly enhanced the degradation of HCHs (81.18 %) and DDTs (85.4 %). The bacterial community structure, diversity and composition were assessed by 454-pyrosequencing of 16S recombinant RNA (rRNA), whereas the abundance of linA gene was determined by quantitative polymerase chain reaction. Distinct differences in bacterial community composition, structure, and diversity were a function of remediation procedure. Predictability of HCH/DDT degradation in soils was also investigated. A positive correlation between linA gene abundance and the removal ratio of HCHs was indicated by correlation analyses. A similar relationship was also confirmed between the degradation of HCHs/DDTs and the abundance of some assemblages (Gammaproteobacteria and Flavobacteria). Our results offer microbial ecological insight into the degradation of HCHs and DDTs in aged contaminated soil, which is helpful for the intensification of bioremediation through modifying plant-microbe patterns, and cessation of costly and time-consuming assays.}, }
@article {pmid25213653, year = {2015}, author = {Segovia, BT and Pereira, DG and Bini, LM and de Meira, BR and Nishida, VS and Lansac-Tôha, FA and Velho, LF}, title = {The role of microorganisms in a planktonic food web of a floodplain lake.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {225-233}, pmid = {25213653}, issn = {1432-184X}, mesh = {Animals ; Biomass ; Brazil ; Ecosystem ; *Food Chain ; Geologic Sediments/microbiology ; Lakes/*microbiology ; Phytoplankton/*microbiology ; Zooplankton/*microbiology ; }, abstract = {Food webs include complex ecological interactions that define the flow of matter and energy, and are fundamental in understanding the functioning of an ecosystem. Temporal variations in the densities of communities belonging to the planktonic food web (i.e., microbial: bacteria, flagellate, and ciliate; and grazing: zooplankton and phytoplankton) were investigated, aiming to clarify the interactions between these organisms and the dynamics of the planktonic food web in a floodplain lake. We hypothesized that hydrological pulse determines the path of matter and energy flow through the planktonic food web of this floodplain lake. Data were collected monthly from March 2007 to February 2008 at three different sites in Guaraná Lake (Mato Grosso do Sul State, Brazil). The path analysis provided evidence that the dynamics of the planktonic food web was strongly influenced by the hydrological pulse. The high-water period favored interactions among the organisms of the microbial loop, rather than their relationships with zooplankton and phytoplankton. Therefore, in this period, the strong interaction among the organisms of the grazing food chain suggests that the microbial loop functions as a sink of matter and energy. In turn, in the low-water period, higher primary productivity appeared to favor different interactions between the components of the grazing food chain and microorganisms, which would function as a link to the higher trophic levels.}, }
@article {pmid25213652, year = {2015}, author = {Huang, J and Nara, K and Zong, K and Lian, C}, title = {Soil propagule banks of ectomycorrhizal fungi along forest development stages after mining.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {768-777}, pmid = {25213652}, issn = {1432-184X}, mesh = {Biodegradation, Environmental ; *Biodiversity ; China ; *Forests ; Fungal Proteins/genetics/metabolism ; *Mining ; Molecular Sequence Data ; Mycorrhizae/genetics/*physiology ; Pinus/growth &amp; development ; Seasons ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Ectomycorrhizal fungal (EMF) propagules play an important role in seedling establishment following disturbance. However, little is known about how the EMF propagule community changes with forest development. In this study, EMF propagules were examined using seedling bioassays in rhizosphere soils collected from a recently closed Pb-Zn tailing (Taolin Pb-Zn tailing (TLT)), a Cu tailing (Dexing Cu No. 2 tailing (DXT)) that had undergone 21 years of restoration, and a mature Masson pine (Pinus massoniana) forest (DXC) outside the Cu mining areas. The corresponding EMF communities colonizing Masson pine at each site were also investigated for comparison. After 8 months of running bioassays, ectomycorrhizal colonization was poor for seedlings grown in TLT (9.0 % ± 14.9 %) and DXT soils (22.4 % ± 17.7 %), while DXC seedlings were well colonized (47.5 % ± 24.9 %). Internal transcribed spacer sequencing revealed that EMF species richness increased with forest development in both the propagule bank (TLT, 6; DXT, 7; DXC, 12) and in the field (TLT, 8; DXT, 14; DXC, 26), though richness was lower in propagule banks. Several lineages, such as Cenococcum, Rhizopogon, Inocybe, Suillus, and Atheliaceae, were frequently encountered in propagule communities, but species assemblages were different among the three sites. Canonical correspondence analysis revealed that several soil parameters, i.e., N, EC, Cu, Pb, Zn, etc., were responsible for the distribution of EMF in the field and bioassay seedlings. The highest overlap in EMF species composition between the propagule bank and the field community was observed at the recently closed tailing (Morisita-Horn similarity = 0.71 for TLT), whereas the lowest overlap occurred at the mature forest (0.26 for DXC). These results indicate that EMF propagules in soil are less frequent and diverse in early primary succession and become more frequent and diverse along forest development, due mainly to the accumulation of dormant spores of Rhizopogon spp. and sclerotia of Cenococcum spp. Thus, EMF propagule communities in soil may diverge from those root-colonizing EMF communities along a gradient of forest development.}, }
@article {pmid25213651, year = {2015}, author = {Fernando, SC and Wang, J and Sparling, K and Garcia, GD and Francini-Filho, RB and de Moura, RL and Paranhos, R and Thompson, FL and Thompson, JR}, title = {Microbiota of the major South Atlantic reef building coral Mussismilia.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {267-280}, pmid = {25213651}, issn = {1432-184X}, support = {P30-ES002109/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Anthozoa/*microbiology ; Brazil ; Cloning, Molecular ; Coral Reefs ; DNA, Bacterial/genetics ; Gammaproteobacteria/classification/genetics/isolation &amp; purification ; Gene Library ; *Microbiota ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The Brazilian endemic scleractinian corals, genus Mussismilia, are among the main reef builders of the South Atlantic and are threatened by accelerating rates of disease. To better understand how holobiont microbial populations interact with corals during health and disease and to evaluate whether selective pressures in the holobiont or neutral assembly shape microbial composition, we have examined the microbiota structure of Mussismilia corals according to coral lineage, environment, and disease/health status. Microbiota of three Mussismilia species (Mussismilia harttii, Mussismilia hispida, and Mussismilia braziliensis) was compared using 16S rRNA pyrosequencing and clone library analysis of coral fragments. Analysis of biological triplicates per Mussismilia species and reef site allowed assessment of variability among Mussismilia species and between sites for M. braziliensis. From 173,487 V6 sequences, 6,733 coral- and 1,052 water-associated operational taxonomic units (OTUs) were observed. M. braziliensis microbiota was more similar across reefs than to other Mussismilia species microbiota from the same reef. Highly prevalent OTUs were more significantly structured by coral lineage and were enriched in Alpha- and Gammaproteobacteria. Bacterial OTUs from healthy corals were recovered from a M. braziliensis skeleton sample at twice the frequency of recovery from water or a diseased coral suggesting the skeleton is a significant habitat for microbial populations in the holobiont. Diseased corals were enriched with pathogens and opportunists (Vibrios, Bacteroidetes, Thalassomonas, and SRB). Our study examines for the first time intra- and inter-specific variability of microbiota across the genus Mussismilia. Changes in microbiota may be useful indicators of coral health and thus be a valuable tool for coral reef management and conservation.}, }
@article {pmid25212623, year = {2014}, author = {Poehlein, A and Freese, HM and Daniel, R and Simeonova, DD}, title = {Draft Genome Sequence of Serratia sp. Strain DD3, Isolated from the Guts of Daphnia magna.}, journal = {Genome announcements}, volume = {2}, number = {5}, pages = {}, pmid = {25212623}, issn = {2169-8287}, abstract = {We report the draft genome sequence of Serratia sp. strain DD3, a gammaproteobacterium from the family Enterobacteriaceae. It was isolated from homogenized guts of Daphnia magna. The genome size is 5,274 Mb.}, }
@article {pmid25204749, year = {2015}, author = {Meng, F and Gao, G and Jia, Z}, title = {Study on tribological mechanism for multi-layer porous structure of diatom frustule.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {45-58}, pmid = {25204749}, issn = {1432-184X}, mesh = {Diatoms/*cytology/metabolism ; Porosity ; }, abstract = {Tribological mechanism of the diatom frustule with multi-layers of pores is studied with the liquid-solid interaction (FSI) method. Based on the reconstructed representative Coscinodiscus sp. frustule with two-layer porous structure, the tribological performances for the diatom frustule at its different pore diameter ratios, pore depth ratios, and velocities are solved through governing equations involved with FSI method. The numerical result shows that the existence of the two-layer porous structure of the diatom helps to reduce the friction between it and ambient water, and to increase its ability to resist the ambient water pressure. The two-layer porous structure effectively improve the tribological performances for the diatom frustule due to the change in the frustule velocity.}, }
@article {pmid25204748, year = {2015}, author = {Venkatachalam, S and Gowdaman, V and Prabagaran, SR}, title = {Culturable and culture-independent bacterial diversity and the prevalence of cold-adapted enzymes from the Himalayan mountain ranges of India and Nepal.}, journal = {Microbial ecology}, volume = {69}, number = {3}, pages = {472-491}, pmid = {25204748}, issn = {1432-184X}, mesh = {Altitude ; Bacteria/genetics/*isolation &amp; purification/metabolism ; Bioprospecting ; DNA, Bacterial/genetics/metabolism ; India ; *Microbiota ; Molecular Sequence Data ; Nepal ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Bacterial diversity of soil samples collected from different geographical regions of Himalayan mountains was studied through culturable (13 samples) and culture-independent approaches (5 samples based on abundance of diversity indices in each ecological niche). Shannon-Wiener diversity index and total bacterial count ranged from 1.50 ± 0.1 to 2.57 ± 0.15 and 7.8 ± 1.6 × 10(5) to 30.9 ± 1.7 × 10(5) cfu ml(-1) of soil, respectively. Based on morphology and pigmentation, 406 isolates were selected by culturing in different cultivable media at various strengths and concentrations. All the strains were subjected to amplified ribosomal DNA restriction analysis and the representative isolates from each cluster were chosen for 16S rRNA gene sequence-based identification. Soil habitat in Himalayan foot hills was dominated by the genera Arthrobacter, Exiguobacterium, Bacillus, Cedecea, Erwinia, and Pseudomonas. Five 16S rRNA gene libraries from the selected five samples yielded 268 clones and were grouped into 53 phylotypes covering 25 genera including the genus of Ferribacterium, Rothia, and Wautersiella, which were reported for the first time in Himalayan tracks. Principal coordinates analysis indicates that all the clone libraries were clearly separated and found to be significantly different from each other. Further, extracellular investigation of cold-active enzymes showed activity of cellulase (23.71%), pectinase (20.24%), amylase (17.32%), phytase (13.87%), protease (12.72%), and lipase (23.71%) among the isolates. Four isolates namely Exiguobacterium mexicanum (BSa14), Exiguobacterium sibiricum (BZa11), Micrococcus antarcticus (BSb10), and Bacillus simplex (BZb3) showed multiple enzyme activity for five different types of enzymes. In addition, various genera like Exiguobacterium, Erwinia, Mycetecola, Cedecea, Pantoea, and Trichococcus have also shown novel hydrolytic enzyme activity in the Himalayan foothills.}, }
@article {pmid25199986, year = {2014}, author = {Van Cauwenberghe, J and Verstraete, B and Lemaire, B and Lievens, B and Michiels, J and Honnay, O}, title = {Population structure of root nodulating Rhizobium leguminosarum in Vicia cracca populations at local to regional geographic scales.}, journal = {Systematic and applied microbiology}, volume = {37}, number = {8}, pages = {613-621}, doi = {10.1016/j.syapm.2014.08.002}, pmid = {25199986}, issn = {1618-0984}, mesh = {Bacterial Proteins/genetics ; Ecology ; Genetics, Population ; Molecular Sequence Data ; N-Acetylglucosaminyltransferases/genetics ; Phylogeny ; Rhizobium leguminosarum/*classification/*genetics ; Root Nodules, Plant/*microbiology ; Vicia/*microbiology ; }, abstract = {The genetic diversity and population structure of about 350 Rhizobium leguminosarum biovar viciae isolates from Vicia cracca were analysed. A hierarchical sampling design was used covering three regions, one region in Belgium and two in France, in which multiple local V. cracca populations were sampled. Rhizobium isolates were genotyped using RAPD and by sequencing two chromosomal housekeeping genes (glnII and recA) and one plasmid-borne gene (nodC). Twenty-six nodC types and sixty-seven chromosomal types were identified, many of which appeared to be regional or local endemics. We found strong genetic differentiation both among V. cracca populations that are separated by only a few kilometres, and among regions that are 50 to 350km apart. Despite significant plasmid exchange, chromosomal and nod types were similarly structured among host populations and regions. We found two lineages of which one prevailed in the Belgian region while the other dominated the French regions. Although a significant correlation between genetic differentiation and geographic distance was found, it is deemed more likely that the observed biogeographic patterns are rather due to coevolutionary interactions and environmental pressures. Furthermore, the impact of recombination on the chromosomal differentiation was found to be considerable.}, }
@article {pmid25197446, year = {2014}, author = {Field, D and Sterk, P and Kottmann, R and De Smet, JW and Amaral-Zettler, L and Cochrane, G and Cole, JR and Davies, N and Dawyndt, P and Garrity, GM and Gilbert, JA and Glöckner, FO and Hirschman, L and Klenk, HP and Knight, R and Kyrpides, N and Meyer, F and Karsch-Mizrachi, I and Morrison, N and Robbins, R and San Gil, I and Sansone, S and Schriml, L and Tatusova, T and Ussery, D and Yilmaz, P and White, O and Wooley, J and Caporaso, G}, title = {Genomic standards consortium projects.}, journal = {Standards in genomic sciences}, volume = {9}, number = {3}, pages = {599-601}, pmid = {25197446}, issn = {1944-3277}, abstract = {The Genomic Standards Consortium (GSC) is an open-membership community that was founded in 2005 to work towards the development, implementation and harmonization of standards in the field of genomics. Starting with the defined task of establishing a minimal set of descriptions the GSC has evolved into an active standards-setting body that currently has 18 ongoing projects, with additional projects regularly proposed from within and outside the GSC. Here we describe our recently enacted policy for proposing new activities that are intended to be taken on by the GSC, along with the template for proposing such new activities.}, }
@article {pmid25193439, year = {2014}, author = {Pylro, VS and Roesch, LF and Morais, DK and Clark, IM and Hirsch, PR and Tótola, MR}, title = {Data analysis for 16S microbial profiling from different benchtop sequencing platforms.}, journal = {Journal of microbiological methods}, volume = {107}, number = {}, pages = {30-37}, doi = {10.1016/j.mimet.2014.08.018}, pmid = {25193439}, issn = {1872-8359}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Brazil ; *Computational Biology/methods ; *High-Throughput Nucleotide Sequencing ; *Metagenome ; Phylogeny ; *RNA, Ribosomal, 16S ; *Soil Microbiology ; }, abstract = {Progress in microbial ecology is confounded by problems when evaluating results from different sequencing methodologies. Contrary to existing expectations, here we demonstrate that the same biological conclusion is reached using different NGS technologies when stringent sequence quality filtering and accurate clustering algorithms are applied.}, }
@article {pmid25190581, year = {2015}, author = {Chen, H and Mothapo, NV and Shi, W}, title = {Soil moisture and pH control relative contributions of fungi and bacteria to N2O production.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {180-191}, pmid = {25190581}, issn = {1432-184X}, mesh = {Bacteria/*metabolism ; Fungi/*metabolism ; Hydrogen-Ion Concentration ; Nitrous Oxide/*metabolism ; Soil Microbiology ; }, abstract = {Fungal N(2)O production has been progressively recognized, but its controlling factors remain unclear. This study examined the impacts of soil moisture and pH on fungal and bacterial N(2)O production in two ecosystems, conventional farming and plantation forestry. Four treatments, antibiotic-free soil and soil amended with streptomycin, cycloheximide, or both were used to determine N(2)O production of fungi versus bacteria. Soil moisture and pH effects were assessed under 65-90 % water-filled pore space (WFPS) and pH 4.0-9.0, respectively. Irrespective of antibiotic treatments, soil N(2)O fluxes peaked at 85-90 % WFPS and pH 7.0 or 8.0, indicating that both fungi and bacteria preferred more anoxic and neutral or slightly alkaline conditions in producing N(2)O. However, compared with bacteria, fungi contributed more to N(2)O production under sub-anoxic and acidic conditions. Real-time polymerase chain reaction of 16S, ITS rDNA, and denitrifying genes for quantifications of bacteria, fungi, and denitrifying bacteria, respectively, showed that fungi were more abundant at acidic pH, whereas total and denitrifying bacteria favored neutral conditions. Such variations in the abundance appeared to be related to the pH effects on the relative fungal and bacterial contribution to N(2)O production.}, }
@article {pmid25190580, year = {2015}, author = {Rychtecký, P and Řeháková, K and Kozlíková, E and Vrba, J}, title = {Light availability may control extracellular phosphatase production in turbid environments.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {37-44}, pmid = {25190580}, issn = {1432-184X}, mesh = {*Light ; Phosphoric Monoester Hydrolases/*biosynthesis ; Phytoplankton/*enzymology/*radiation effects ; }, abstract = {Extracellular phosphatase production by phytoplankton was investigated in the moderately eutrophic Lipno reservoir, Czech Republic during 2009 and 2010. We hypothesized that production of extracellular phosphatases is an additional mechanism of phosphorus acquisition enabling producers to survive rather than to dominate the phytoplankton. Hence, we examined the relationship between light availability and phosphatase production, as light plays an important role in polymictic environments. Bulk phosphatase activity was measured using a common fluorometric assay, and the production of phosphatases was studied using the Fluorescently Labelled Enzyme Activity technique, which enabled direct microscopic detection of phosphatase-positive cells. In total, 29 taxa of phytoplankton were identified during both years. Only 17 taxa from the total number of 29 showed production of extracellular phosphatases. Species dominating the phytoplankton rarely produced extracellular phosphatases. In contrast, taxa exhibiting phosphatase activity were present in low biomass in the phytoplankton assemblage. Moreover, there was a significant relationship between the proportion of phosphatase positive species in samples and the Z(eu):Z(mix) ratio (a proxy of light availability). A laboratory experiment with different light intensities confirmed the influence of light on production of phosphatases. Our seasonal study confirmed that extracellular phosphatase production is common in low-abundance populations but not in dominant taxa of the phytoplankton. It also suggested the importance of sufficient light conditions for the production of extracellular phosphatases.}, }
@article {pmid25190276, year = {2014}, author = {Niu, Y and Defoirdt, T and Baruah, K and Van de Wiele, T and Dong, S and Bossier, P}, title = {Bacillus sp. LT3 improves the survival of gnotobiotic brine shrimp (Artemia franciscana) larvae challenged with Vibrio campbellii by enhancing the innate immune response and by decreasing the activity of shrimp-associated vibrios.}, journal = {Veterinary microbiology}, volume = {173}, number = {3-4}, pages = {279-288}, doi = {10.1016/j.vetmic.2014.08.007}, pmid = {25190276}, issn = {1873-2542}, mesh = {Analysis of Variance ; Animals ; Antibiosis/*physiology ; Aquaculture/methods ; Artemia/growth &amp; development/*immunology/*microbiology ; Bacillus/immunology/*physiology ; Catechol Oxidase/metabolism ; DNA Primers/genetics ; Enzyme Precursors/metabolism ; Gastrointestinal Tract/*microbiology ; Germ-Free Life/immunology ; HSP70 Heat-Shock Proteins/metabolism ; Immunity, Innate/*immunology ; Larva/immunology/microbiology ; Probiotics/pharmacology ; RNA, Messenger/genetics/metabolism ; Real-Time Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Transglutaminases/metabolism ; Vibrio/drug effects/*immunology ; }, abstract = {Bacteria belonging to the genus Bacillus are amongst the most intensively studied group of bacteria for use as probiotics in aquaculture. However, the exact mechanism of action of these bacteria is often not well described, and the microbiota that are naturally present in cultures of test organisms often compromise the interpretation of the results. The present study aimed to evaluate the putative probiotic effect of Bacillus sp. LT3 in a model system with gnotobiotic brine shrimp Artemia franciscana larvae. The strain significantly increased the survival of brine shrimp larvae challenged with Vibrio campbellii when administered 6h before the challenge. Under these conditions, LT3 was able to colonize the brine shrimp gastrointestinal tract and to decrease the in vivo pathogen activity as indicated by the bioluminescence of the V. campbellii associated with brine shrimp larvae. In order to investigate the effect of the Bacillus strain on the innate immune system of the brine shrimp larvae, prophenoloxidase and transglutaminase mRNA levels were monitored, while heat shock protein 70 mRNA levels were measured as an indicator of physiological stress. Interestingly, 12h after challenge, the prophenoloxidase mRNA level in the larvae pre-treated with LT3 and challenged with V. campbellii was approximately 8-fold higher than in the other treatments. Further, a decreased mRNA level of transglutaminase gene and heat shock protein 70 gene suggested that pretreatment with LT3 results in less stress and tissue damage in the brine shrimp larvae upon V. campbellii challenge. These results indicated that Bacillus sp. LT3 could improve the survival of brine shrimp larvae when challenged with pathogenic V. campbellii, both by decreasing the in vivo activity of the pathogen and by priming the innate immune response through activating the prophenoloxidase system.}, }
@article {pmid25186254, year = {2015}, author = {Narihiro, T and Nobu, MK and Kim, NK and Kamagata, Y and Liu, WT}, title = {The nexus of syntrophy-associated microbiota in anaerobic digestion revealed by long-term enrichment and community survey.}, journal = {Environmental microbiology}, volume = {17}, number = {5}, pages = {1707-1720}, doi = {10.1111/1462-2920.12616}, pmid = {25186254}, issn = {1462-2920}, mesh = {Acetates/metabolism ; Actinobacteria/genetics/metabolism ; Anaerobiosis ; Bacteroidetes/genetics/metabolism ; Base Sequence ; Benzoates/metabolism ; Butyrates/metabolism ; Carbon Dioxide/metabolism ; Chloroflexi/genetics/metabolism ; Euryarchaeota/metabolism ; Formates/metabolism ; Methane/metabolism ; Microbial Consortia/*genetics ; Propionates/metabolism ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Water Purification/*methods ; }, abstract = {Anaerobic digestion (AD) processes are known to effectively convert organic waste to CO2 and CH4 , but much of the microbial ecology remains unclear. Specifically, we have limited insights into symbiotic syntroph and methanogen ('syntrophy') acid degradation, although they are essential for preventing process deterioration. Also, we often observed many uncharacterized or uncultivated organisms, but poorly understood their role(s) in relation to syntrophy. To define syntrophy-associated populations, this study enriched methanogenic communities with propionate, butyrate, benzoate, acetate, formate and H2 from two different inocula over 3 years. 16S pyrotag analysis revealed core populations of known syntrophs (six clades) and methanogens (nine clades) associated with acid degradation, and evidence for substrate- and/or inoculum-dependent specificity in syntrophic partnerships. Based on comprehensive re-evaluation of publically available microbial community data for AD, the known syntrophs and methanogens identified were clearly representatives of the AD-associated syntrophs and methanogens. In addition, uncultivated clades related to Bacteroidetes, Firmicutes, Actinobacteria and Chloroflexi were ubiquitously found in AD and enrichments. These organisms may be universally involved in AD syntrophic degradation, but only represented <23% of the yet-to-be-cultivated organisms (89 of 390 clades). Thus, the contribution of these uncultured organisms in AD remains unclear and warrants further investigation.}, }
@article {pmid25184835, year = {2014}, author = {Tran, H and Bundy, JW and Hinkle, EE and Walter, J and Burkey, TE and Miller, PS}, title = {Effects of a yeast-dried milk product in creep and phase-1 nursery diets on growth performance, circulating immunoglobulin A, and fecal microbiota of nursing and nursery pigs.}, journal = {Journal of animal science}, volume = {92}, number = {10}, pages = {4518-4530}, doi = {10.2527/jas.2014-7574}, pmid = {25184835}, issn = {1525-3163}, mesh = {Animal Feed/*analysis ; *Animal Nutritional Physiological Phenomena ; Animals ; Diet/*veterinary ; Feces/microbiology ; Feeding Methods/veterinary ; Immunoglobulin A/blood ; Microbiota ; Milk/*metabolism ; Sus scrofa/*growth &amp; development/immunology/*microbiology ; Swine ; Yeast, Dried/administration &amp; dosage/*pharmacology ; }, abstract = {Four experiments were conducted to evaluate effects of yeast-dried milk (YDM) product in creep and phase-1 nursery diets. In Exp. 1, 24 parity-4 litters were allotted to 3 dietary treatments (8 litters/treatment) including no creep (NC), control creep (CTL), and experimental creep (EC; 10% YDM). Creep diets were fed twice daily from d 7 after birth until weaning (23.6 ± 1.8 d). In Exp. 2, 108 weaned pigs were selected based on mean BW of pigs from the respective treatments in Exp. 1. For phase 1 (d 0 to 7 postweaning) of Exp. 2, NC and CTL pigs were fed the CTL diet and EC pigs continued to receive the EC diet. For phase 2 and 3 (d 7 to 28 postweaning) of Exp. 2, all pigs received a common diet containing antibiotics. Blood and fecal samples were collected on d 0, 7, 14, and 21 postweaning to evaluate serum IgA and fecal microbiota. In Exp. 1, pigs fed EC and CTL tended to have greater (P < 0.10) weaning BW compared with NC pigs. Pigs fed EC had greater (P < 0.05) ADFI compared with CTL pigs. In Exp. 2, pigs fed EC tended to have greater BW (P < 0.10) and greater ADG (P < 0.05) and ADFI (P < 0.01) compared with CTL and NC pigs (d 0 to 28). For serum IgA, EC and CTL pigs tended (P < 0.10) to have greater IgA compared with NC pigs. For microbial data, EC pigs had greater (P < 0.01) microbial diversity compared with CTL (d 7 postweaning). On d 7 and 21 postweaning, microbial similarity decreased (P < 0.01) in pigs fed EC compared with NC and CTL. Overall (d 0 to 14), lactobacilli gene copy numbers tended (P < 0.10) to be greater in EC (7.3 log10) compared with NC pigs (6.9 log10). In Exp. 3, 23 parity-1 litters were allotted to 3 dietary treatments as described for Exp. 1. In Exp. 4, 108 weaned pigs were selected based on mean BW of all pigs from Exp. 3 and dietary treatments were the same as described for Exp. 2 except no antibiotic was included in phase-2 diet. In Exp. 3, there were no treatment effects on litter ADFI, ADG, and serum IgA, but a tendency (P < 0.10) for lower Lactobacillus reuteri in the CTL (5.1 log10) compared with NC pigs (5.6 log10) was observed. Overall (d 0 to 21) in Exp. 4, pigs fed EC had greater ADG (P < 0.01) and G:F (P < 0.05) and tended to exhibit greater ADFI (P < 0.10) compared with the CTL. For microbial data, pigs fed CTL (4.8 log10) and EC (4.8 log10) had lower (P < 0.01) fecal Lactobacillus johnsonii compared with NC (5.2 log10). Microbial ecology and immune parameters are affected by YDM.}, }
@article {pmid25183073, year = {2014}, author = {Krishnan, M and Bharathiraja, C and Pandiarajan, J and Prasanna, VA and Rajendhran, J and Gunasekaran, P}, title = {Insect gut microbiome - An unexploited reserve for biotechnological application.}, journal = {Asian Pacific journal of tropical biomedicine}, volume = {4}, number = {Suppl 1}, pages = {S16-21}, pmid = {25183073}, issn = {2221-1691}, abstract = {Metagenomics research has been developed over the past decade to elucidate the genomes of the uncultured microorganisms with an aim of understanding microbial ecology. On the other hand, it has also been provoked by the increasing biotechnological demands for novel enzymes, antibiotic and signal mimics. The gut microbiota of insects plays crucial roles in the growth, development and environmental adaptation to the host insects. Very recently, the insect microbiota and their genomes (microbiome), isolated from insects were recognized as a major genetic resources for bio-processing industry. Consequently, the exploitation of insect gut microbiome using metagenomic approaches will enable us to find novel biocatalysts and to develop innovative strategies for identifying smart molecules for biotechnological applications. In this review, we discuss the critical footstep in extraction and purification of metagenomic DNA from insect gut, construction of metagenomic libraries and screening procedure for novel gene identification. Recent innovations and potential applications in bioprocess industries are highlighted.}, }
@article {pmid25180967, year = {2015}, author = {Lücker, S and Schwarz, J and Gruber-Dorninger, C and Spieck, E and Wagner, M and Daims, H}, title = {Nitrotoga-like bacteria are previously unrecognized key nitrite oxidizers in full-scale wastewater treatment plants.}, journal = {The ISME journal}, volume = {9}, number = {3}, pages = {708-720}, pmid = {25180967}, issn = {1751-7370}, support = {P 24101/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Ammonia/metabolism ; Chemoautotrophic Growth ; DNA Primers ; Gallionellaceae/classification/isolation &amp; purification/*metabolism ; Molecular Sequence Data ; Nitrites/*metabolism ; Oxidation-Reduction ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; *Waste Disposal Facilities ; }, abstract = {Numerous past studies have shown members of the genus Nitrospira to be the predominant nitrite-oxidizing bacteria (NOB) in nitrifying wastewater treatment plants (WWTPs). Only recently, the novel NOB 'Candidatus Nitrotoga arctica' was identified in permafrost soil and a close relative was enriched from activated sludge. Still, little is known about diversity, distribution and functional importance of Nitrotoga in natural and engineered ecosystems. Here we developed Nitrotoga 16S rRNA-specific PCR primers and fluorescence in situ hybridization (FISH) probes, which were applied to screen activated sludge samples from 20 full-scale WWTPs. Nitrotoga-like bacteria were detected by PCR in 11 samples and reached abundances detectable by FISH in seven sludges. They coexisted with Nitrospira in most of these WWTPs, but constituted the only detectable NOB in two systems. Quantitative FISH revealed that Nitrotoga accounted for nearly 2% of the total bacterial community in one of these plants, a number comparable to Nitrospira abundances in other WWTPs. Spatial statistics revealed that Nitrotoga coaggregated with ammonia-oxidizing bacteria, strongly supporting a functional role in nitrite oxidation. This activity was confirmed by FISH in combination with microradiography, which revealed nitrite-dependent autotrophic carbon fixation by Nitrotoga in situ. Correlation of the presence or absence with WWTP operational parameters indicated low temperatures as a main factor supporting high Nitrotoga abundances, although in incubation experiments these NOB remained active over an unexpected range of temperatures, and also at different ambient nitrite concentrations. In conclusion, this study demonstrates that Nitrotoga can be functionally important nitrite oxidizers in WWTPs and can even represent the only known NOB in engineered systems.}, }
@article {pmid25180966, year = {2015}, author = {Ju, F and Zhang, T}, title = {Bacterial assembly and temporal dynamics in activated sludge of a full-scale municipal wastewater treatment plant.}, journal = {The ISME journal}, volume = {9}, number = {3}, pages = {683-695}, pmid = {25180966}, issn = {1751-7370}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Ecosystem ; Sewage/*microbiology ; *Waste Disposal Facilities ; }, abstract = {Understanding environmental and biological influences on the dynamics of microbial communities has received great attention in microbial ecology. Here, utilizing large time-series 16S rRNA gene data, we show that in activated sludge of an environmentally important municipal wastewater treatment plant, 5-year temporal dynamics of bacterial community shows no significant seasonal succession, but is consistent with deterministic assemblage by taxonomic relatedness. Biological interactions are dominant drivers in determining the bacterial community assembly, whereas environmental conditions (mainly sludge retention time and inorganic nitrogen) partially explain phylogenetic and quantitative variances and indirectly influence bacterial assembly. We demonstrate a correlation-based statistical method to integrate bacterial association networks with their taxonomic affiliations to predict community-wide co-occurrence and co-exclusion patterns. The results show that although taxonomically closely related bacteria tend to positively co-occur (for example, out of a cooperative relationship), negative co-excluding correlations are deterministically observed between taxonomically less related species, probably implicating roles of competition in determining bacterial assembly. Overall, disclosures of the positive and negative species-species relations will improve our understanding of ecological niches occupied by unknown species and help to predict their biological functions in ecosystems.}, }
@article {pmid25180845, year = {2014}, author = {Brzychczy-Włoch, M and Pabian, W and Majewska, E and Zuk, MG and Kielbik, J and Gosiewski, T and Bulanda, MG}, title = {Dynamics of colonization with group B streptococci in relation to normal flora in women during subsequent trimesters of pregnancy.}, journal = {The new microbiologica}, volume = {37}, number = {3}, pages = {307-319}, pmid = {25180845}, issn = {1121-7138}, mesh = {Adult ; Anal Canal/*microbiology ; Bacteria/classification/genetics/*growth &amp; development/isolation &amp; purification ; Candida/genetics/*growth &amp; development/isolation &amp; purification ; Carrier State/microbiology ; Female ; Humans ; *Microbiota ; Pregnancy ; Pregnancy Trimesters ; Streptococcus/genetics/*growth &amp; development/isolation &amp; purification ; Vagina/*microbiology ; Young Adult ; }, abstract = {The main objective of the study was to compare the qualitative and quantitative composition of vaginal and rectal flora in GBS-positive (n=15) and GBS-negative (n=27) pregnant women examined in three subsequent trimesters of their pregnancy. Study samples consisted of vaginal and rectal smears and urine samples. GBS numbers were determined by the quantitatively cultured method [cfu/ml] and with the use of qPCR. Five GBS colonies were isolated per each positive sample and genotyped by PFGE and serotyping. The normal flora components: Lactobacillus, Bifidobacterium and Candida were quantitatively cultured. Carriage of GBS in subsequent trimesters in vagina/anus was variable and fluctuated between 17% and 28%. Quantitative GBS analyses showed that the vaginal population was at a constant level with the mean value equal to 3.94×104 cfu/ml, in contrast to the rectal population where the highest values appeared in the third trimester 4.37×105. The use of qPCR gave 7% more positive results for vaginal/rectal swabs. Genetic similarity analysis showed that one GBS clone was present in 73% of carriers during pregnancy, while in 27% of patients, 2 clones were found. H2O2-positive vaginal lactobacilli were detected in all women, while H2O2-negative lactobacilli and Bifidobacterium occurred more frequently in the anus in about 50% of women. Candida was present in the vagina in 30% of women. The analysis of women in three consecutive trimesters of pregnancy on the basis of a study group and control group showed no statistically significant differences in either the species (qualitative) or quantitative composition in vaginal and rectal flora in both of the groups. Therefore, GBS should be considered as a component of the microbiota and an opportunistic microorganism rather than a typical pathogen, because it does not distort the composition of women's normal genital tract flora.}, }
@article {pmid25179909, year = {2014}, author = {Geirnaert, A and Steyaert, A and Eeckhaut, V and Debruyne, B and Arends, JB and Van Immerseel, F and Boon, N and Van de Wiele, T}, title = {Butyricicoccus pullicaecorum, a butyrate producer with probiotic potential, is intrinsically tolerant to stomach and small intestine conditions.}, journal = {Anaerobe}, volume = {30}, number = {}, pages = {70-74}, doi = {10.1016/j.anaerobe.2014.08.010}, pmid = {25179909}, issn = {1095-8274}, mesh = {Acetates/metabolism ; Acids/toxicity ; Bile Acids and Salts/metabolism ; Butyrates/*metabolism ; Cytosol/chemistry ; Fatty Acids/analysis/metabolism ; Gram-Positive Bacteria/metabolism/*physiology ; Humans ; Hydrogen-Ion Concentration ; Intestine, Small/*microbiology ; Microbial Viability/*drug effects ; Pancreatic Juice/metabolism ; *Probiotics ; Stomach/*microbiology ; }, abstract = {Butyrate has several beneficial properties that are essential to maintain gastrointestinal health. Therefore butyrate-producing bacteria are seen as the next generation of probiotics. The butyrate-producing bacterium Butyricicoccus pullicaecorum (a clostridial cluster IV strain) is such a promising probiotic candidate for people suffering from inflammatory bowel disease. To exert its beneficial properties, it is crucial that B. pullicaecorum survives the harsh conditions of the upper gastrointestinal tract to arrive in the colon in a viable and metabolically active state. Before developing a stable formulation of B. pullicaecorum for oral administration, it is important to know its intrinsic acid and bile tolerance. We monitored the survival during and short chain fatty acid production after incubation in conditions simulating the stomach and small intestine using in vitro batch experiments. In case of acid conditions (pH 2 and pH 3), B. pullicaecorum was viable and active but not cultivable. Cultivability was restored during subsequent small intestine conditions. Importantly, bile and pancreatic juice had no lethal effect. Milk, as a suspension medium, only had a protective effect on the cultivability during the first hour at pH 2. B. pullicaecorum was still metabolically active after upper gastrointestinal conditions and produced short chain fatty acids, but a shift from butyrate to acetate production was observed. Although the butyrate-producing anaerobe B. pullicaecorum showed good intrinsic acid and bile tolerance in terms of viability and metabolic activity, colonization efficiency and butyrate production under colon conditions is needed to further evaluate its probiotic potential.}, }
@article {pmid25179155, year = {2014}, author = {Bengtsson-Palme, J and Alm Rosenblad, M and Molin, M and Blomberg, A}, title = {Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {749}, pmid = {25179155}, issn = {1471-2164}, mesh = {Bacteria/*genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biotransformation/*genetics ; Cluster Analysis ; Computational Biology/methods ; Datasets as Topic ; *Metagenomics/methods ; Oxidative Stress/genetics ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {BACKGROUND: Environmental shotgun sequencing (metagenomics) provides a new way to study communities in microbial ecology. We here use sequence data from the Global Ocean Sampling (GOS) expedition to investigate toxicant selection pressures revealed by the presence of detoxification genes in marine bacteria. To capture a broad range of potential toxicants we selected detoxification protein families representing systems protecting microorganisms from a variety of stressors, such as metals, organic compounds, antibiotics and oxygen radicals.<br><br>RESULTS: Using a bioinformatics procedure based on comparative analysis to finished bacterial genomes we found that the amount of detoxification genes present in marine microorganisms seems surprisingly small. The underrepresentation is particularly evident for toxicant transporters and proteins involved in detoxifying metals. Exceptions are enzymes involved in oxidative stress defense where peroxidase enzymes are more abundant in marine bacteria compared to bacteria in general. In contrast, catalases are almost completely absent from the open ocean environment, suggesting that peroxidases and peroxiredoxins constitute a core line of defense against reactive oxygen species (ROS) in the marine milieu.<br><br>CONCLUSIONS: We found no indication that detoxification systems would be generally more abundant close to the coast compared to the open ocean. On the contrary, for several of the protein families that displayed a significant geographical distribution, like peroxidase, penicillin binding transpeptidase and divalent ion transport protein, the open ocean samples showed the highest abundance. Along the same lines, the abundance of most detoxification proteins did not increase with estimated pollution. The low level of detoxification systems in marine bacteria indicate that the majority of marine bacteria have a low capacity to adapt to increased pollution. Our study exemplifies the use of metagenomics data in ecotoxicology, and in particular how anthropogenic consequences on life in the sea can be examined.}, }
@article {pmid25177716, year = {2014}, author = {Kuramae, EE and Zhou, JZ and Kowalchuk, GA and van Veen, JA}, title = {Soil-borne microbial functional structure across different land uses.}, journal = {TheScientificWorldJournal}, volume = {2014}, number = {}, pages = {216071}, pmid = {25177716}, issn = {1537-744X}, mesh = {Bacteria/enzymology/genetics/isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; Carbon/analysis ; Cellulase/genetics/metabolism ; Chitinases/genetics/metabolism ; Fungal Proteins/genetics/metabolism ; Fungi/enzymology/genetics/isolation &amp; purification ; Hydrogen-Ion Concentration ; Laccase/genetics/metabolism ; *Microbiota ; Nitrogen/analysis ; Phosphates/analysis ; Polygalacturonase/genetics/metabolism ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was C : N ratio. C : N ratio showed a significant positive correlation with clay and soil pH. Fields with low C : N ratio had an overrepresentation of genes for carbon degradation, carbon fixation, metal reductase, and organic remediation categories, while fields with high C : N ratio had an overrepresentation of genes encoding dissimilatory sulfate reductase, methane oxidation, nitrification, and nitrogen fixation. The most abundant genes related to carbon degradation comprised bacterial and fungal cellulases; bacterial and fungal chitinases; fungal laccases; and bacterial, fungal, and oomycete polygalacturonases. The high number of genes related to organic remediation was probably driven by high phosphate content, while the high number of genes for nitrification was probably explained by high total nitrogen content. The functional gene diversity found in different soils did not group the sites accordingly to land management. Rather, the soil factors, C : N ratio, phosphate, and total N, were the main factors driving the differences in functional genes across the fields examined.}, }
@article {pmid25177538, year = {2014}, author = {Rideout, JR and He, Y and Navas-Molina, JA and Walters, WA and Ursell, LK and Gibbons, SM and Chase, J and McDonald, D and Gonzalez, A and Robbins-Pianka, A and Clemente, JC and Gilbert, JA and Huse, SM and Zhou, HW and Knight, R and Caporaso, JG}, title = {Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.}, journal = {PeerJ}, volume = {2}, number = {}, pages = {e545}, pmid = {25177538}, issn = {2167-8359}, support = {T32 GM008759/GM/NIGMS NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; }, abstract = {We present a performance-optimized algorithm, subsampled open-reference OTU picking, for assigning marker gene (e.g., 16S rRNA) sequences generated on next-generation sequencing platforms to operational taxonomic units (OTUs) for microbial community analysis. This algorithm provides benefits over de novo OTU picking (clustering can be performed largely in parallel, reducing runtime) and closed-reference OTU picking (all reads are clustered, not only those that match a reference database sequence with high similarity). Because more of our algorithm can be run in parallel relative to "classic" open-reference OTU picking, it makes open-reference OTU picking tractable on massive amplicon sequence data sets (though on smaller data sets, "classic" open-reference OTU clustering is often faster). We illustrate that here by applying it to the first 15,000 samples sequenced for the Earth Microbiome Project (1.3 billion V4 16S rRNA amplicons). To the best of our knowledge, this is the largest OTU picking run ever performed, and we estimate that our new algorithm runs in less than 1/5 the time than would be required of "classic" open reference OTU picking. We show that subsampled open-reference OTU picking yields results that are highly correlated with those generated by "classic" open-reference OTU picking through comparisons on three well-studied datasets. An implementation of this algorithm is provided in the popular QIIME software package, which uses uclust for read clustering. All analyses were performed using QIIME's uclust wrappers, though we provide details (aided by the open-source code in our GitHub repository) that will allow implementation of subsampled open-reference OTU picking independently of QIIME (e.g., in a compiled programming language, where runtimes should be further reduced). Our analyses should generalize to other implementations of these OTU picking algorithms. Finally, we present a comparison of parameter settings in QIIME's OTU picking workflows and make recommendations on settings for these free parameters to optimize runtime without reducing the quality of the results. These optimized parameters can vastly decrease the runtime of uclust-based OTU picking in QIIME.}, }
@article {pmid25177534, year = {2014}, author = {Lim, YW and Cuevas, DA and Silva, GG and Aguinaldo, K and Dinsdale, EA and Haas, AF and Hatay, M and Sanchez, SE and Wegley-Kelly, L and Dutilh, BE and Harkins, TT and Lee, CC and Tom, W and Sandin, SA and Smith, JE and Zgliczynski, B and Vermeij, MJ and Rohwer, F and Edwards, RA}, title = {Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition.}, journal = {PeerJ}, volume = {2}, number = {}, pages = {e520}, pmid = {25177534}, issn = {2167-8359}, abstract = {Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phosphonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines.}, }
@article {pmid25176324, year = {2014}, author = {Shah, N and Naseby, DC}, title = {Bioluminescence-based measurement of viability of Pseudomonas aeruginosa ATCC 9027 harbouring plasmid-based lux genes under the control of constitutive promoters.}, journal = {Journal of applied microbiology}, volume = {117}, number = {5}, pages = {1373-1387}, doi = {10.1111/jam.12635}, pmid = {25176324}, issn = {1365-2672}, mesh = {Gene Expression ; Luminescent Measurements/*methods ; Microbial Viability ; Plasmids/genetics ; *Promoter Regions, Genetic ; Pseudomonas aeruginosa/*genetics/growth &amp; development ; }, abstract = {AIMS: Detection of microbial contamination in pharmaceuticals, food and cosmetics has been problematic for several decades. Numerous investigations highlight the urgency for novel methods; development of bioluminescent constructs allows real-time monitoring, rapid analysis and high-throughput screening of products. Microbial growth can be studied by measuring constitutive gene expression. The aim is to develop whole-cell microbial biosensors with Pseudomonas aeruginosa and quantify their growth rate by measuring constitutive expression of lux.<br><br>METHODS AND RESULTS: Pseudomonas aeruginosa cells were genetically modified to produce bioluminescence constitutively. Strains were characterized by assessing their growth kinetics, plasmid stability and gene expression with bacterial replication. Furthermore, cell viability was measured by fluorescence quantification. Promoter strengths were evaluated by comparing bioluminescence (RLU) per colony-forming units (CFU) at various growth stages and related to promoter sequences. Promoter strength decreased in the order of P(lpp) > P(tat) > P(lysS) > P(ldcC) > P(spc) during exponential phase whilst P(tat) was stronger than P(lpp) during stationary phase. Good correlations between RLU and CFU at 24 h indicated a strong relationship for all bioluminescent strains; however, weaker correlations between RLU and CFU and between fluorescence (RFU) and CFU beyond 24 h indicated that a proportion of cells had lost the ability to culture.<br><br>CONCLUSIONS: Equivalence analysis showed no significant difference between bioluminescence and plate counting for all five bioluminescent strains. Pseudomonas aeruginosa-containing P(tat) had steady bioluminescence when correlated to CFU (R > 0&#xb7;9), and together with fluorescence data, it can be concluded that Ps. aeruginosa ATCC 9027 tat-pMElux is preferred for testing microbial viability.<br><br>These whole-cell bioluminescent strains provide a platform for utilization in monitoring toxicity and contamination of compounds in environmental biology and microbial ecology, preservative efficacy testing (PET) in the pharmaceutical cosmetics and food industries; the use of such biosensors provides an alternative, fast and efficient method to traditional methods.}, }
@article {pmid25176132, year = {2014}, author = {De Palma, G and Vida, C and Santacruz, A and De Castro, NM and De la Fuente, M and Sanz, Y}, title = {Impaired responses to gliadin and gut microbes of immune cells from mice with altered stress-related behavior and premature immune senescence.}, journal = {Journal of neuroimmunology}, volume = {276}, number = {1-2}, pages = {47-57}, doi = {10.1016/j.jneuroim.2014.08.007}, pmid = {25176132}, issn = {1872-8421}, mesh = {Aging/*immunology ; Analysis of Variance ; Animals ; Bifidobacteriales Infections/immunology/*pathology ; Celiac Disease/*chemically induced/immunology ; Cytokines/*metabolism ; Disease Models, Animal ; Enzyme-Linked Immunosorbent Assay ; Female ; Flow Cytometry ; Gliadin/*adverse effects ; Mice ; Mice, Inbred ICR ; Stress, Psychological/*pathology ; T-Lymphocytes/*immunology ; }, abstract = {Stress is associated with impaired communication between the nervous and immune systems leading to immunosenescence and increased disease risk. We investigated whether leukocytes from mice with altered stress-related behavior and premature immunosenescence, as well as from chronologically aged mice differently responded ex vivo to celiac disease (CD) triggers (gliadin) and intestinal bacteria by ELISA and flow cytometry and differed in microbiota composition. We found that altered stress-related behavior and premature immunosenescence led to alterations in T lymphocytes and cytokine release of immune cells basally and in response to peptic fragments of gliadin and commensal and pathogenic bacteria, possibly increasing susceptibility to CD in adulthood.}, }
@article {pmid25173951, year = {2014}, author = {Van Geel, M and Busschaert, P and Honnay, O and Lievens, B}, title = {Evaluation of six primer pairs targeting the nuclear rRNA operon for characterization of arbuscular mycorrhizal fungal (AMF) communities using 454 pyrosequencing.}, journal = {Journal of microbiological methods}, volume = {106}, number = {}, pages = {93-100}, doi = {10.1016/j.mimet.2014.08.006}, pmid = {25173951}, issn = {1872-8359}, mesh = {DNA Primers/genetics ; DNA, Fungal/chemistry/*genetics ; DNA, Ribosomal/chemistry/*genetics ; Malus ; Microbiological Techniques/*methods ; Mycology/methods ; Mycorrhizae/*classification/*genetics/isolation &amp; purification ; Plant Roots/microbiology ; Sensitivity and Specificity ; *Sequence Analysis, DNA ; *rRNA Operon ; }, abstract = {In the last few years, 454 pyrosequencing-based analysis of arbuscular mycorrhizal fungal (AMF; Glomeromycota) communities has tremendously increased our knowledge of the distribution and diversity of AMF. Nonetheless, comparing results between different studies is difficult, as different target genes (or regions thereof) and primer combinations, with potentially dissimilar specificities and efficacies, are being utilized. In this study we evaluated six primer pairs that have previously been used in AMF studies (NS31-AM1, AMV4.5NF-AMDGR, AML1-AML2, NS31-AML2, FLR3-LSUmBr and Glo454-NDL22) for their use in 454 pyrosequencing based on both an in silico approach and 454 pyrosequencing of AMF communities from apple tree roots. Primers were evaluated in terms of (i) in silico coverage of Glomeromycota fungi, (ii) the number of high-quality sequences obtained, (iii) selectivity for AMF species, (iv) reproducibility and (v) ability to accurately describe AMF communities. We show that primer pairs AMV4.5NF-AMDGR, AML1-AML2 and NS31-AML2 outperformed the other tested primer pairs in terms of number of Glomeromycota reads (AMF specificity and coverage). Additionally, these primer pairs were found to have no or only few mismatches to AMF sequences and were able to consistently describe AMF communities from apple roots. However, whereas most high-quality AMF sequences were obtained for AMV4.5NF-AMDGR, our results also suggest that this primer pair favored amplification of Glomeraceae sequences at the expense of Ambisporaceae, Claroideoglomeraceae and Paraglomeraceae sequences. Furthermore, we demonstrate the complementary specificity of AMV4.5NF-AMDGR with AML1-AML2, and of AMV4.5NF-AMDGR with NS31-AML2, making these primer combinations highly suitable for tandem use in covering the diversity of AMF communities.}, }
@article {pmid25173917, year = {2014}, author = {Vásquez, GA and Busschaert, P and Haberbeck, LU and Uyttendaele, M and Geeraerd, AH}, title = {An educationally inspired illustration of two-dimensional Quantitative Microbiological Risk Assessment (QMRA) and sensitivity analysis.}, journal = {International journal of food microbiology}, volume = {190}, number = {}, pages = {31-43}, doi = {10.1016/j.ijfoodmicro.2014.07.034}, pmid = {25173917}, issn = {1879-3460}, mesh = {Animals ; Belgium ; Computer Simulation ; Fish Products/microbiology ; Food Microbiology/*methods ; Humans ; Listeria monocytogenes/growth &amp; development ; Listeriosis/*prevention &amp; control ; Models, Theoretical ; Monte Carlo Method ; Risk Assessment ; }, abstract = {Quantitative Microbiological Risk Assessment (QMRA) is a structured methodology used to assess the risk involved by ingestion of a pathogen. It applies mathematical models combined with an accurate exploitation of data sets, represented by distributions and - in the case of two-dimensional Monte Carlo simulations - their hyperparameters. This research aims to highlight background information, assumptions and truncations of a two-dimensional QMRA and advanced sensitivity analysis. We believe that such a detailed listing is not always clearly presented in actual risk assessment studies, while it is essential to ensure reliable and realistic simulations and interpretations. As a case-study, we are considering the occurrence of listeriosis in smoked fish products in Belgium during the period 2008-2009, using two-dimensional Monte Carlo and two sensitivity analysis methods (Spearman correlation and Sobol sensitivity indices) to estimate the most relevant factors of the final risk estimate. A risk estimate of 0.018% per consumption of contaminated smoked fish by an immunocompromised person was obtained. The final estimate of listeriosis cases (23) is within the actual reported result obtained for the same period and for the same population. Variability on the final risk estimate is determined by the variability regarding (i) consumer refrigerator temperatures, (ii) the reference growth rate of L. monocytogenes, (iii) the minimum growth temperature of L. monocytogenes and (iv) consumer portion size. Variability regarding the initial contamination level of L. monocytogenes tends to appear as a determinant of risk variability only when the minimum growth temperature is not included in the sensitivity analysis; when it is included the impact regarding the variability on the initial contamination level of L. monocytogenes is disappearing. Uncertainty determinants of the final risk indicated the need of gathering more information on the reference growth rate and the minimum growth temperature of L. monocytogenes. Uncertainty in the dose-response relationship was not included in the analysis, hence the level of its influence cannot be assessed in the present research. Finally, a baseline global workflow for QMRA and sensitivity analysis is proposed.}, }
@article {pmid25172856, year = {2014}, author = {Zablocki, O and van Zyl, L and Adriaenssens, EM and Rubagotti, E and Tuffin, M and Cary, SC and Cowan, D}, title = {High-level diversity of tailed phages, eukaryote-associated viruses, and virophage-like elements in the metaviromes of antarctic soils.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {22}, pages = {6888-6897}, pmid = {25172856}, issn = {1098-5336}, mesh = {Antarctic Regions ; Bacteriophages/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Ecosystem ; Eukaryota/*virology ; Molecular Sequence Data ; Phylogeny ; Satellite Viruses/classification/genetics/*isolation &amp; purification ; *Soil Microbiology ; }, abstract = {The metaviromes of two distinct Antarctic hyperarid desert soil communities have been characterized. Hypolithic communities, cyanobacterium-dominated assemblages situated on the ventral surfaces of quartz pebbles embedded in the desert pavement, showed higher virus diversity than surface soils, which correlated with previous bacterial community studies. Prokaryotic viruses (i.e., phages) represented the largest viral component (particularly Mycobacterium phages) in both habitats, with an identical hierarchical sequence abundance of families of tailed phages (Siphoviridae > Myoviridae > Podoviridae). No archaeal viruses were found. Unexpectedly, cyanophages were poorly represented in both metaviromes and were phylogenetically distant from currently characterized cyanophages. Putative phage genomes were assembled and showed a high level of unaffiliated genes, mostly from hypolithic viruses. Moreover, unusual gene arrangements in which eukaryotic and prokaryotic virus-derived genes were found within identical genome segments were observed. Phycodnaviridae and Mimiviridae viruses were the second-most-abundant taxa and more numerous within open soil. Novel virophage-like sequences (within the Sputnik clade) were identified. These findings highlight high-level virus diversity and novel species discovery potential within Antarctic hyperarid soils and may serve as a starting point for future studies targeting specific viral groups.}, }
@article {pmid25171544, year = {2014}, author = {Neu, J}, title = {Necrotizing enterocolitis: the mystery goes on.}, journal = {Neonatology}, volume = {106}, number = {4}, pages = {289-295}, doi = {10.1159/000365130}, pmid = {25171544}, issn = {1661-7819}, mesh = {Animals ; Disease Models, Animal ; Dysbiosis ; *Enterocolitis, Necrotizing/classification/diagnosis/immunology/microbiology/physiopathology/therapy ; Host-Pathogen Interactions ; Humans ; Immunity, Innate ; Infant, Newborn ; Infant, Premature ; *Intestines/immunology/microbiology/physiopathology ; Microbiota ; Prognosis ; Risk Factors ; }, abstract = {Necrotizing enterocolitis (NEC) has largely been present in neonatal intensive care units for the past 60 years. NEC prevalence has corresponded with the continued development and sophistication of neonatal intensive care. Despite major efforts towards its eradication, NEC has persisted and appears to be increasing in some centers. The pathophysiology of this disease remains poorly understood. Several issues have hampered our quest to develop a better understanding of this disease. These include the fact that what we have historically termed 'NEC' appears to be several different diseases. Animal models that are commonly used to study NEC pathophysiology and treatment do not directly reflect the most common form of the disease seen in human infants. The pathophysiology appears to be multifactorial, reflecting several different pathways to intestinal necrosis with different inciting factors. Spontaneous intestinal perforations, ischemic bowel disease secondary to cardiac anomalies as well as other entities that are clearly different from the most common form of NEC seen in preterm infants have been put into the same database. Here I describe some of the different forms of what has been called NEC and make some comments on its pathophysiology, where available studies suggest involvement of genetic factors, intestinal immaturity, hemodynamic instability, inflammation and a dysbiotic microbial ecology. Currently utilized approaches for the diagnosis of NEC are presented and innovative technologies for the development of diagnostic and predictive biomarkers are described. Predictions for future strategies are also discussed.}, }
@article {pmid25171437, year = {2015}, author = {Jiménez, DJ and Dini-Andreote, F and Ottoni, JR and de Oliveira, VM and van Elsas, JD and Andreote, FD}, title = {Compositional profile of α / β-hydrolase fold proteins in mangrove soil metagenomes: prevalence of epoxide hydrolases and haloalkane dehalogenases in oil-contaminated sites.}, journal = {Microbial biotechnology}, volume = {8}, number = {3}, pages = {604-613}, pmid = {25171437}, issn = {1751-7915}, mesh = {Biodiversity ; Brazil ; Epoxide Hydrolases/*genetics ; *Genetic Variation ; Hydrolases/*genetics ; *Metagenome ; Oils/*analysis ; Phylogeny ; Sequence Homology, Amino Acid ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants/analysis ; Wetlands ; }, abstract = {The occurrence of genes encoding biotechnologically relevant α/β-hydrolases in mangrove soil microbial communities was assessed using data obtained by whole-metagenome sequencing of four mangroves areas, denoted BrMgv01 to BrMgv04, in São Paulo, Brazil. The sequences (215 Mb in total) were filtered based on local amino acid alignments against the Lipase Engineering Database. In total, 5923 unassembled sequences were affiliated with 30 different α/β-hydrolase fold superfamilies. The most abundant predicted proteins encompassed cytosolic hydrolases (abH08; ∼ 23%), microsomal hydrolases (abH09; ∼ 12%) and Moraxella lipase-like proteins (abH04 and abH01; < 5%). Detailed analysis of the genes predicted to encode proteins of the abH08 superfamily revealed a high proportion related to epoxide hydrolases and haloalkane dehalogenases in polluted mangroves BrMgv01-02-03. This suggested selection and putative involvement in local degradation/detoxification of the pollutants. Seven sequences that were annotated as genes for putative epoxide hydrolases and five for putative haloalkane dehalogenases were found in a fosmid library generated from BrMgv02 DNA. The latter enzymes were predicted to belong to Actinobacteria, Deinococcus-Thermus, Planctomycetes and Proteobacteria. Our integrated approach thus identified 12 genes (complete and/or partial) that may encode hitherto undescribed enzymes. The low amino acid identity (< 60%) with already-described genes opens perspectives for both production in an expression host and genetic screening of metagenomes.}, }
@article {pmid25170152, year = {2014}, author = {Koch, H and Galushko, A and Albertsen, M and Schintlmeister, A and Gruber-Dorninger, C and Lücker, S and Pelletier, E and Le Paslier, D and Spieck, E and Richter, A and Nielsen, PH and Wagner, M and Daims, H}, title = {Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation.}, journal = {Science (New York, N.Y.)}, volume = {345}, number = {6200}, pages = {1052-1054}, doi = {10.1126/science.1256985}, pmid = {25170152}, issn = {1095-9203}, mesh = {Aerobiosis ; Bacteria, Aerobic/genetics/*growth &amp; development/*metabolism ; Chemoautotrophic Growth/genetics/*physiology ; Energy Metabolism ; Genetic Loci ; Hydrogen/*metabolism ; Hydrogenase/genetics ; Molecular Sequence Data ; Nitrates/metabolism ; Nitrification/genetics/physiology ; Nitrites/*metabolism ; *Nitrogen Cycle ; Oxidation-Reduction ; Sequence Analysis, DNA ; }, abstract = {The bacterial oxidation of nitrite to nitrate is a key process of the biogeochemical nitrogen cycle. Nitrite-oxidizing bacteria are considered a highly specialized functional group, which depends on the supply of nitrite from other microorganisms and whose distribution strictly correlates with nitrification in the environment and in wastewater treatment plants. On the basis of genomics, physiological experiments, and single-cell analyses, we show that Nitrospira moscoviensis, which represents a widely distributed lineage of nitrite-oxidizing bacteria, has the genetic inventory to utilize hydrogen (H2) as an alternative energy source for aerobic respiration and grows on H2 without nitrite. CO2 fixation occurred with H2 as the sole electron donor. Our results demonstrate a chemolithoautotrophic lifestyle of nitrite-oxidizing bacteria outside the nitrogen cycle, suggesting greater ecological flexibility than previously assumed.}, }
@article {pmid25158848, year = {2014}, author = {Lee, HJ and Cho, GY and Chung, SH and Whang, KS}, title = {Streptomyces panaciradicis sp. nov., a β-glucosidase-producing bacterium isolated from ginseng rhizoplane.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {64}, number = {Pt 11}, pages = {3816-3820}, doi = {10.1099/ijs.0.061705-0}, pmid = {25158848}, issn = {1466-5034}, mesh = {Base Composition ; Cellulases/genetics ; DNA, Bacterial/genetics ; Diaminopimelic Acid/chemistry ; Fatty Acids/chemistry ; Glucosidases/metabolism ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Panax/*microbiology ; Peptidoglycan/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Sequence Analysis, DNA ; Streptomyces/*classification/genetics/isolation &amp; purification ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {A Gram-staining-positive actinobacterium, designated strain 1MR-8(T), was isolated from the rhizoplane of ginseng and its taxonomic status was determined using a polyphasic approach. The isolate formed long chains of spores that were straight, cylindrical and smooth-surfaced. Strain 1MR-8(T) grew at 10-37 °C (optimum 28 °C), whilst no growth was observed at 45 °C. The pH range for growth was 4.0-11.0 (optimum pH 6.0-8.0) and the NaCl range for growth was 0-7% (w/v) with optimum growth at 1% (w/v). Strain 1MR-8(T) had cell-wall peptidoglycans based on ll-diaminopimelic acid. Glucose, mannose and ribose were the whole-cell sugars. The predominant isoprenoid quinones were MK-9 (H4), MK-9 (H6) and MK-9 (H8) and the major fatty acids were anteiso-C(15:0), iso-C(15:0), anteiso-C(17:0) and iso-C(16:0). 16S rRNA gene sequencing studies showed that the novel strain was closely related to the type strains of Streptomyces caeruleatus GIMN4(T), Streptomyces curacoi NRRL B-2901(T), Streptomyces capoamus JCM 4734(T) and Streptomyces coeruleorubidus NBRC 12761(T) with similarities of 98.8%. However, DNA-DNA relatedness, as well as physiological and biochemical analyses, showed that strain 1MR-8(T) could be differentiated from its closest phylogenetic relatives. It is proposed that this strain should be classified as a representative of a novel species of the genus Streptomyces, with the suggested name Streptomyces panaciradicis sp. nov. The type strain is 1MR-8(T) (= KACC 17632(T) = NBRC 109811(T)).}, }
@article {pmid25157246, year = {2014}, author = {Breider, S and Scheuner, C and Schumann, P and Fiebig, A and Petersen, J and Pradella, S and Klenk, HP and Brinkhoff, T and Göker, M}, title = {Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {416}, pmid = {25157246}, issn = {1664-302X}, abstract = {Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended.}, }
@article {pmid25156547, year = {2015}, author = {Schmidt, TS and Matias Rodrigues, JF and von Mering, C}, title = {Limits to robustness and reproducibility in the demarcation of operational taxonomic units.}, journal = {Environmental microbiology}, volume = {17}, number = {5}, pages = {1689-1706}, doi = {10.1111/1462-2920.12610}, pmid = {25156547}, issn = {1462-2920}, mesh = {Algorithms ; Base Sequence ; Cluster Analysis ; High-Throughput Nucleotide Sequencing ; Humans ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; Reproducibility of Results ; Sequence Analysis/*methods ; Skin/*microbiology ; }, abstract = {The demarcation of operational taxonomic units (OTUs) from complex sequence data sets is a key step in contemporary studies of microbial ecology. However, as biologically motivated 'optimal' OTU-binning algorithms remain elusive, many conceptually distinct approaches continue to be used. Using a global data set of 887 870 bacterial 16S rRNA gene sequences, we objectively quantified biases introduced by several widely employed sequence clustering algorithms. We found that OTU-binning methods often provided surprisingly non-equivalent partitions of identical data sets, notably when clustering to the same nominal similarity thresholds; and we quantified the resulting impact on ecological data description for a well-defined human skin microbiome data set. We observed that some methods were very robust to varying clustering thresholds, while others were found to be highly susceptible even to slight threshold variations. Moreover, we comprehensively quantified the impact of the choice of 16S rRNA gene subregion, as well as of data set scope and context on algorithm performance. Our findings may contribute to an enhanced comparability of results across sequence-processing pipelines, and we arrive at recommendations towards higher levels of standardization in established workflows.}, }
@article {pmid25155235, year = {2014}, author = {Hendrickson, EL and Wang, T and Beck, DA and Dickinson, BC and Wright, CJ and J Lamont, R and Hackett, M}, title = {Proteomics of Fusobacterium nucleatum within a model developing oral microbial community.}, journal = {MicrobiologyOpen}, volume = {3}, number = {5}, pages = {729-751}, pmid = {25155235}, issn = {2045-8827}, support = {R01 DE011111/DE/NIDCR NIH HHS/United States ; DE011111/DE/NIDCR NIH HHS/United States ; DE014372/DE/NIDCR NIH HHS/United States ; R37 DE011111/DE/NIDCR NIH HHS/United States ; R01 DE014372/DE/NIDCR NIH HHS/United States ; R01 DE012505/DE/NIDCR NIH HHS/United States ; DE012505/DE/NIDCR NIH HHS/United States ; R56 DE014372/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/growth &amp; development/isolation &amp; purification ; Bacterial Proteins/chemistry/*genetics/metabolism ; Biodiversity ; Fusobacterium Infections/*microbiology ; Fusobacterium nucleatum/classification/*genetics/isolation &amp; purification/metabolism ; Humans ; Mass Spectrometry ; Models, Biological ; Molecular Sequence Data ; Mouth/microbiology ; Mouth Diseases/*microbiology ; *Proteomics ; }, abstract = {Fusobacterium nucleatum is a common oral organism that can provide adhesive and metabolic support to developing periodontal bacterial communities. It is within the context of these communities that disease occurs. We have previously reported whole cell proteomics analyses of Porphyromonas gingivalis and Streptococcus gordonii in early-stage communities with each other and with F. nucleatum, modeled using 18 h pellets. Here, we report the adaptation of F. nucleatum to the same experimental conditions as measured by differential protein expression. About 1210 F. nucleatum proteins were detected in single species F. nucleatum control samples, 1192 in communities with P. gingivalis, 1224 with S. gordonii, and 1135 with all three species. Quantitative comparisons among the proteomes revealed important changes in all mixed samples with distinct responses to P. gingivalis or S. gordonii alone and in combination. The results were inspected manually and an ontology analysis conducted using DAVID (Database for annotation, visualization, and integrated discovery). Extensive changes were detected in energy metabolism. All multispecies comparisons showed reductions in amino acid fermentation and a shift toward butanoate as a metabolic byproduct, although the two organism model community with S. gordonii showed increases in alanine, threonine, methionine, and cysteine pathways, and in the three species samples there were increases in lysine and methionine. The communities with P. gingivalis or all three organisms showed reduced glycolysis proteins, but F. nucleatum paired with S. gordonii displayed increased glycolysis/gluconeogenesis proteins. The S. gordonii containing two organism model also showed increases in the ethanolamine pathway while the three species sample showed decreases relative to the F. nucleatum single organism control. All of the nascent model communities displayed reduced translation, lipopolysaccharide, and cell wall biosynthesis, DNA replication and DNA repair.}, }
@article {pmid25150724, year = {2014}, author = {Kiewra, D and Stańczak, J and Richter, M}, title = {Ixodes ricinus ticks (Acari, Ixodidae) as a vector of Borrelia burgdorferi sensu lato and Borrelia miyamotoi in Lower Silesia, Poland--preliminary study.}, journal = {Ticks and tick-borne diseases}, volume = {5}, number = {6}, pages = {892-897}, doi = {10.1016/j.ttbdis.2014.07.004}, pmid = {25150724}, issn = {1877-9603}, mesh = {Animals ; Arachnid Vectors/*microbiology ; Base Sequence ; Borrelia/genetics/*isolation &amp; purification ; Borrelia burgdorferi/genetics/isolation &amp; purification ; Coinfection ; DNA, Bacterial/chemistry/genetics ; Female ; Humans ; Ixodes/*microbiology ; Lyme Disease/*epidemiology/microbiology ; Male ; Molecular Sequence Data ; Nymph ; Poland/epidemiology ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; }, abstract = {Ixodes ricinus is the primary vector of Borrelia spirochetes in Europe, including both the Lyme borreliosis (LB) group and the relapsing fever (RF) group. The aim of the study was to estimate the prevalence of different genospecies from the B. burgdorferi s.l. complex and B. miyamotoi in questing I. ricinus collected in chosen areas in Lower Silesia, SW Poland. A total of 599 I. ricinus ticks were investigated using the PCR-RFLP method. The calculated overall minimum infection rate of ticks with Borrelia spirochetes in Lower Silesia was 15.5%. Five different restriction patterns, characteristic of B. afzelii, B. garinii, B. burgdoreri s.s., B. valaisiana, and B. miyamotoi, were obtained and confirmed by DNA sequencing. At least 14% of ticks were infected with B. burgdorferi s.l. while B.afzelii was the dominant genospecies (68.5%). The MIR for B. miyamotoi was calculated at 2%. Four co-infections in single adult ticks were found: B. miyamotoi/B. afzelii, B. miyamotoi/B. burdorferi s.s., B. miyamotoi/B. garinii, and B. afzelii/B. burgdorferi s.s. The results of this study confirm the risk of LB and RF occuring in both urban and protected areas.}, }
@article {pmid25149284, year = {2015}, author = {Zhang, M and Visser, S and Pereira e Silva, MC and van Elsas, JD}, title = {IncP-1 and PromA group plasmids are major providers of horizontal gene transfer capacities across bacteria in the mycosphere of different soil fungi.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {169-179}, pmid = {25149284}, issn = {1432-184X}, mesh = {Bacteria/*genetics ; Fungi/*genetics ; Gene Transfer, Horizontal/*genetics ; Plasmids/*genetics ; Soil Microbiology ; }, abstract = {Plasmids of the IncP-1β group have been found to be important carriers of accessory genes that enhance the ecological fitness of bacteria, whereas plasmids of the PromA group are key agents of horizontal gene transfer in particular soil settings. However, there is still a paucity of knowledge with respect to the diversity, abundance, and involvement in horizontal gene transfer of plasmids of both groups in the mycosphere. Using triparental exogenous isolation based on the IncQ tracer plasmid pSUP104 as well as direct molecular detection, we analyzed the pool of mobilizer and self-transferable plasmids in mycosphere soil. Replicate mushroom types that were related to Russula, Inocybe, Ampulloclitocybe, and Galerina spp. were sampled from a forest soil area, and bulk soil was used as the control. The data showed that the levels of IncP-1β plasmids are significantly raised across several of the mycospheres analyzed, whereas those of PromA group plasmids were similar across the mycospheres and corresponding bulk soil. Moreover, the frequencies of triparental exogenous isolation of mobilizer plasmids into a Pseudomonas fluorescens recipient strain were significantly elevated in communities from several mycospheres as compared with those from bulk soil. Molecular analysis of selected transconjugants, as well as from directly isolated strains, revealed the presence of plasmids of three size groups, i.e., (1) 40-45, (2) 50-60, and (3) ≥60 kb, across all isolations. Replicon typing using IncN, IncW and IncA/C proxies revealed no positive signals. In contrast, a suite of plasmids produced signals with IncP-1β as well as PromA type replicon typing systems. Moreover, a selected subset of plasmids, obtained from the Inocybe and Galerina isolates, was transferred out further, revealing their capacities to transfer and mobilize across a broad host range.}, }
@article {pmid25149283, year = {2015}, author = {McGuire, KL and D'Angelo, H and Brearley, FQ and Gedallovich, SM and Babar, N and Yang, N and Gillikin, CM and Gradoville, R and Bateman, C and Turner, BL and Mansor, P and Leff, JW and Fierer, N}, title = {Responses of soil fungi to logging and oil palm agriculture in Southeast Asian tropical forests.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {733-747}, pmid = {25149283}, issn = {1432-184X}, mesh = {*Agriculture ; Arecaceae/growth &amp; development ; Dipterocarpaceae/growth &amp; development ; Forestry ; *Forests ; Fungi/*physiology ; Malaysia ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Human land use alters soil microbial composition and function in a variety of systems, although few comparable studies have been done in tropical forests and tropical agricultural production areas. Logging and the expansion of oil palm agriculture are two of the most significant drivers of tropical deforestation, and the latter is most prevalent in Southeast Asia. The aim of this study was to compare soil fungal communities from three sites in Malaysia that represent three of the most dominant land-use types in the Southeast Asia tropics: a primary forest, a regenerating forest that had been selectively logged 50 years previously, and a 25-year-old oil palm plantation. Soil cores were collected from three replicate plots at each site, and fungal communities were sequenced using the Illumina platform. Extracellular enzyme assays were assessed as a proxy for soil microbial function. We found that fungal communities were distinct across all sites, although fungal composition in the regenerating forest was more similar to the primary forest than either forest community was to the oil palm site. Ectomycorrhizal fungi, which are important associates of the dominant Dipterocarpaceae tree family in this region, were compositionally distinct across forests, but were nearly absent from oil palm soils. Extracellular enzyme assays indicated that the soil ecosystem in oil palm plantations experienced altered nutrient cycling dynamics, but there were few differences between regenerating and primary forest soils. Together, these results show that logging and the replacement of primary forest with oil palm plantations alter fungal community and function, although forests regenerating from logging had more similarities with primary forests in terms of fungal composition and nutrient cycling potential. Since oil palm agriculture is currently the mostly rapidly expanding equatorial crop and logging is pervasive across tropical ecosystems, these findings may have broad applicability.}, }
@article {pmid25148481, year = {2015}, author = {Gruber-Dorninger, C and Pester, M and Kitzinger, K and Savio, DF and Loy, A and Rattei, T and Wagner, M and Daims, H}, title = {Functionally relevant diversity of closely related Nitrospira in activated sludge.}, journal = {The ISME journal}, volume = {9}, number = {3}, pages = {643-655}, pmid = {25148481}, issn = {1751-7370}, support = {294343/ERC_/European Research Council/International ; P 25231/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Bacterial Proteins/genetics/metabolism ; *Biodiversity ; Ecosystem ; In Situ Hybridization, Fluorescence ; Nitrification ; Nitrite Reductases/genetics/metabolism ; Nitrogen/metabolism ; Oxidoreductases/genetics/metabolism ; Phylogeny ; Sewage/*microbiology ; }, abstract = {Nitrospira are chemolithoautotrophic nitrite-oxidizing bacteria that catalyze the second step of nitrification in most oxic habitats and are important for excess nitrogen removal from sewage in wastewater treatment plants (WWTPs). To date, little is known about their diversity and ecological niche partitioning within complex communities. In this study, the fine-scale community structure and function of Nitrospira was analyzed in two full-scale WWTPs as model ecosystems. In Nitrospira-specific 16S rRNA clone libraries retrieved from each plant, closely related phylogenetic clusters (16S rRNA identities between clusters ranged from 95.8% to 99.6%) within Nitrospira lineages I and II were found. Newly designed probes for fluorescence in situ hybridization (FISH) allowed the specific detection of several of these clusters, whose coexistence in the WWTPs was shown for prolonged periods of several years. In situ ecophysiological analyses based on FISH, relative abundance and spatial arrangement quantification, as well as microautoradiography revealed functional differences of these Nitrospira clusters regarding the preferred nitrite concentration, the utilization of formate as substrate and the spatial coaggregation with ammonia-oxidizing bacteria as symbiotic partners. Amplicon pyrosequencing of the nxrB gene, which encodes subunit beta of nitrite oxidoreductase of Nitrospira, revealed in one of the WWTPs as many as 121 species-level nxrB operational taxonomic units with highly uneven relative abundances in the amplicon library. These results show a previously unrecognized high diversity of Nitrospira in engineered systems, which is at least partially linked to niche differentiation and may have important implications for process stability.}, }
@article {pmid25147548, year = {2014}, author = {Al-Najjar, MA and Ramette, A and Kühl, M and Hamza, W and Klatt, JM and Polerecky, L}, title = {Spatial patterns and links between microbial community composition and function in cyanobacterial mats.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {406}, pmid = {25147548}, issn = {1664-302X}, abstract = {We imaged reflectance and variable fluorescence in 25 cyanobacterial mats from four distant sites around the globe to assess, at different scales of resolution, spatial variabilities in the physiological parameters characterizing their photosynthetic capacity, including the absorptivity by chlorophyll a (A chl), maximum quantum yield of photosynthesis (Y max), and light acclimation irradiance (I k). Generally, these parameters significantly varied within individual mats on a sub-millimeter scale, with about 2-fold higher variability in the vertical than in the horizontal direction. The average vertical profiles of Ymax and I k decreased with depth in the mat, while A chl exhibited a sub-surface maximum. The within-mat variability was comparable to, but often larger than, the between-sites variability, whereas the within-site variabilities (i.e., between samples from the same site) were generally lowest. When compared based on averaged values of their photosynthetic parameters, mats clustered according to their site of origin. Similar clustering was found when the community composition of the mats' cyanobacterial layers were compared by automated ribosomal intergenic spacer analysis (ARISA), indicating a significant link between the microbial community composition and function. Although this link is likely the result of community adaptation to the prevailing site-specific environmental conditions, our present data is insufficient to identify the main factors determining these patterns. Nevertheless, this study demonstrates that the spatial variability in the photosynthetic capacity and light acclimation of benthic phototrophic microbial communities is at least as large on a sub-millimeter scale as it is on a global scale, and suggests that this pattern of variability scaling is similar for the microbial community composition.}, }
@article {pmid25145494, year = {2015}, author = {Li, T and Long, M and Gatesoupe, FJ and Zhang, Q and Li, A and Gong, X}, title = {Comparative analysis of the intestinal bacterial communities in different species of carp by pyrosequencing.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {25-36}, pmid = {25145494}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/*genetics ; Bacteroidetes/classification/genetics ; Carps/*microbiology ; Intestines/*microbiology ; Phylogeny ; Proteobacteria/classification/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Gut microbiota is increasingly regarded as an integral component of the host, due to important roles in the modulation of the immune system, the proliferation of the intestinal epithelium and the regulation of the dietary energy intake. Understanding the factors that influence the composition of these microbial communities is essential to health management, and the application to aquatic animals still requires basic investigation. In this study, we compared the bacterial communities harboured in the intestines and in the rearing water of grass carp (Ctenopharyngodon idellus), crucian carp (Carassius cuvieri), and bighead carp (Hypophthalmichthys nobilis), by using 454-pyrosequencing with barcoded primers targeting the V4 to V5 regions of the bacterial 16S rRNA gene. The specimens of the three species were cohabiting in the same pond. Between 6,218 and 10,220 effective sequences were read from each sample, resulting in a total of 110,398 sequences for 13 samples from gut microbiota and pond water. In general, the microbial communities of the three carps were dominated by Fusobacteria, Firmicutes, Proteobacteria and Bacteroidetes, but the abundance of each phylum was significantly different between species. At the genus level, the overwhelming group was Cetobacterium (97.29 ± 0.46 %) in crucian carp, while its abundance averaged c. 40 and 60 % of the sequences read in the other two species. There was higher microbial diversity in the gut of filter-feeding bighead carp than the gut of the two other species, with grazing feeding habits. The composition of intestine microbiota of grass carp and crucian carp shared higher similarity when compared with bighead carp. The principal coordinates analysis (PCoA) with the weighted UniFrac distance and the heatmap analysis suggested that gut microbiota was not a simple reflection of the microbial community in the local habitat but resulted from species-specific selective pressures, possibly dependent on behavioural, immune and metabolic characteristics.}, }
@article {pmid25136122, year = {2014}, author = {Palovaara, J and Akram, N and Baltar, F and Bunse, C and Forsberg, J and Pedrós-Alió, C and González, JM and Pinhassi, J}, title = {Stimulation of growth by proteorhodopsin phototrophy involves regulation of central metabolic pathways in marine planktonic bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {35}, pages = {E3650-8}, pmid = {25136122}, issn = {1091-6490}, mesh = {Adaptation, Physiological/physiology ; Bicarbonates/metabolism ; Biomass ; Carbon/metabolism ; Carbon Dioxide/metabolism ; Flavobacteriaceae/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Light ; Marine Biology ; Metabolic Networks and Pathways/genetics ; Phototrophic Processes/*physiology ; Plankton/genetics/*metabolism ; Rhodopsin/genetics/*metabolism ; Rhodopsins, Microbial ; Seawater/microbiology ; }, abstract = {Proteorhodopsin (PR) is present in half of surface ocean bacterioplankton, where its light-driven proton pumping provides energy to cells. Indeed, PR promotes growth or survival in different bacteria. However, the metabolic pathways mediating the light responses remain unknown. We analyzed growth of the PR-containing Dokdonia sp. MED134 (where light-stimulated growth had been found) in seawater with low concentrations of mixed [yeast extract and peptone (YEP)] or single (alanine, Ala) carbon compounds as models for rich and poor environments. We discovered changes in gene expression revealing a tightly regulated shift in central metabolic pathways between light and dark conditions. Bacteria showed relatively stronger light responses in Ala compared with YEP. Notably, carbon acquisition pathways shifted toward anaplerotic CO2 fixation in the light, contributing 31 ± 8% and 24 ± 6% of the carbon incorporated into biomass in Ala and YEP, respectively. Thus, MED134 was a facultative double mixotroph, i.e., photo- and chemotrophic for its energy source and using both bicarbonate and organic matter as carbon sources. Unexpectedly, relative expression of the glyoxylate shunt genes (isocitrate lyase and malate synthase) was >300-fold higher in the light--but only in Ala--contributing a more efficient use of carbon from organic compounds. We explored these findings in metagenomes and metatranscriptomes and observed similar prevalence of the glyoxylate shunt compared with PR genes and highest expression of the isocitrate lyase gene coinciding with highest solar irradiance. Thus, regulatory interactions between dissolved organic carbon quality and central metabolic pathways critically determine the fitness of surface ocean bacteria engaging in PR phototrophy.}, }
@article {pmid25135817, year = {2015}, author = {Piñar, G and Sterflinger, K and Ettenauer, J and Quandt, A and Pinzari, F}, title = {A combined approach to assess the microbial contamination of the archimedes palimpsest.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {118-134}, pmid = {25135817}, issn = {1432-184X}, support = {V 194/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Actinobacteria/classification/genetics ; Biodiversity ; *Environmental Microbiology ; Fungi/classification/genetics ; Proteobacteria/classification/genetics ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; }, abstract = {A combined approach, using molecular and microscopic techniques, was used to identify the microbiota associated with the Archimedes Palimpsest, an unusual parchment manuscript. SEM analyses revealed the microbial damage to the collagen fibers and the presence of characteristic cell chains typical of filamentous bacteria and fungal spores. Molecular analysis confirmed a homogeneous bacterial community colonizing the manuscript. The phyla Proteobacteria and Actinobacteria were associated with this ancient parchment; the sequences were most related to uncultured clones detected in the human skin microbiome and in ephitelium, and to cultivated species of the genera Acinetobacter and Nocardiopsis. Nevertheless, a great variation was observed among the different sampled areas indicating fungal diversity. Blumeria spp. dominated in the healthy areas of the parchment while degraded areas showed disparate fungal communities, with dominant members of the genera Mucor and Cladosporium. In addition, the quantification of the β-actin gene by real-time PCR analyses (qPCR) revealed a higher fungal abundance on degraded areas than on the healthy ones.}, }
@article {pmid25135816, year = {2015}, author = {Iasur-Kruh, L and Taha-Salaime, L and Robinson, WE and Sharon, R and Droby, S and Perlman, SJ and Zchori-Fein, E}, title = {Microbial associates of the vine mealybug Planococcus ficus (Hemiptera: Pseudococcidae) under different rearing conditions.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {204-214}, pmid = {25135816}, issn = {1432-184X}, mesh = {Animals ; Hemiptera/*microbiology ; }, abstract = {Sap-feeding insects harbor diverse microbial endosymbionts that play important roles in host ecology and evolution, including contributing to host pest status. The vine mealybug, Planococcus ficus, is a serious pest of grapevines, vectoring a number of pathogenic grape viruses. Previous studies have shown that virus transmission is abolished when mealybugs are raised in the laboratory on potato. To examine the possible role of microbial symbionts in virus transmission, the archaeal, bacterial, and fungal microbiota of field and laboratory P. ficus were characterized using molecular and classical microbiological methods. Lab and field colonies of P. ficus harbored different microbiota. While both were dominated by the bacterial obligate nutritional symbionts Moranella and Tremblaya, field samples also harbored a third bacterium that was allied with cluster L, a lineage of bacterial symbionts previously identified in aphids. Archaea were not found in any of the samples. Fungal communities in field-collected mealybugs were dominated by Metschnikowia and Cladosporium species, while those from laboratory-reared mealybugs were dominated by Alternaria and Cladosporium species. In conclusion, this study has identified a diverse set of microbes, most of which appear to be facultatively associated with P. ficus, depending on environmental conditions. The role of various members of the mealybug microbiome, as well as how the host plant affects microbial community structure, remains to be determined.}, }
@article {pmid25132799, year = {2014}, author = {Mayo, B and Rachid, CT and Alegría, A and Leite, AM and Peixoto, RS and Delgado, S}, title = {Impact of next generation sequencing techniques in food microbiology.}, journal = {Current genomics}, volume = {15}, number = {4}, pages = {293-309}, pmid = {25132799}, issn = {1389-2029}, abstract = {Understanding the Maxam-Gilbert and Sanger sequencing as the first generation, in recent years there has been an explosion of newly-developed sequencing strategies, which are usually referred to as next generation sequencing (NGS) techniques. NGS techniques have high-throughputs and produce thousands or even millions of sequences at the same time. These sequences allow for the accurate identification of microbial taxa, including uncultivable organisms and those present in small numbers. In specific applications, NGS provides a complete inventory of all microbial operons and genes present or being expressed under different study conditions. NGS techniques are revolutionizing the field of microbial ecology and have recently been used to examine several food ecosystems. After a short introduction to the most common NGS systems and platforms, this review addresses how NGS techniques have been employed in the study of food microbiota and food fermentations, and discusses their limits and perspectives. The most important findings are reviewed, including those made in the study of the microbiota of milk, fermented dairy products, and plant-, meat- and fish-derived fermented foods. The knowledge that can be gained on microbial diversity, population structure and population dynamics via the use of these technologies could be vital in improving the monitoring and manipulation of foods and fermented food products. They should also improve their safety.}, }
@article {pmid25131403, year = {2014}, author = {Haq, IU and Zhang, M and Yang, P and van Elsas, JD}, title = {The interactions of bacteria with fungi in soil: emerging concepts.}, journal = {Advances in applied microbiology}, volume = {89}, number = {}, pages = {185-215}, doi = {10.1016/B978-0-12-800259-9.00005-6}, pmid = {25131403}, issn = {0065-2164}, mesh = {Bacteria/genetics ; *Bacterial Physiological Phenomena ; Ecosystem ; Fungi/genetics/*physiology ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {In this chapter, we review the existing literature on bacterial-fungal interactions in soil, exploring the role fungi may play for soil bacteria as providers of hospitable niches. A focus is placed on the mycosphere, i.e., the narrow zone of influence of fungal hyphae on the external soil milieu, in which hypha-associated bacterial cells dwell. Evidence is brought forward for the contention that the hyphae of both mycorrhizal and saprotrophic fungi serve as providers of ecological opportunities in a grossly carbon-limited soil, as a result of their release of carbonaceous compounds next to the provision of a colonizable surface. Soil bacteria of particular nature are postulated to have adapted to such selection pressures, evolving to the extent that they acquired capabilities that allow them to thrive in the novel habitat created by the emerging fungal hyphae. The mechanisms involved in the interactions and the modes of genetic adaptation of the mycosphere dwellers are discussed, with an emphasis on one key mycosphere-adapted bacterium, Burkholderia terrae BS001. In this discussion, we interrogate the positive interactions between soil fungi and bacteria, and refrain from considering negative interactions.}, }
@article {pmid25128346, year = {2014}, author = {Callewaert, C and De Maeseneire, E and Kerckhof, FM and Verliefde, A and Van de Wiele, T and Boon, N}, title = {Microbial odor profile of polyester and cotton clothes after a fitness session.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {21}, pages = {6611-6619}, pmid = {25128346}, issn = {1098-5336}, mesh = {Bacteria/*classification/growth &amp; development/isolation &amp; purification/*metabolism ; *Biota ; *Clothing ; DNA, Bacterial/chemistry/genetics ; *Gossypium ; Humans ; Molecular Sequence Data ; *Odorants ; *Polyesters ; Sequence Analysis, DNA ; }, abstract = {Clothing textiles protect our human body against external factors. These textiles are not sterile and can harbor high bacterial counts as sweat and bacteria are transmitted from the skin. We investigated the microbial growth and odor development in cotton and synthetic clothing fabrics. T-shirts were collected from 26 healthy individuals after an intensive bicycle spinning session and incubated for 28 h before analysis. A trained odor panel determined significant differences between polyester versus cotton fabrics for the hedonic value, the intensity, and five qualitative odor characteristics. The polyester T-shirts smelled significantly less pleasant and more intense, compared to the cotton T-shirts. A dissimilar bacterial growth was found in cotton versus synthetic clothing textiles. Micrococci were isolated in almost all synthetic shirts and were detected almost solely on synthetic shirts by means of denaturing gradient gel electrophoresis fingerprinting. A selective enrichment of micrococci in an in vitro growth experiment confirmed the presence of these species on polyester. Staphylococci were abundant on both cotton and synthetic fabrics. Corynebacteria were not enriched on any textile type. This research found that the composition of clothing fibers promotes differential growth of textile microbes and, as such, determines possible malodor generation.}, }
@article {pmid25125643, year = {2014}, author = {Ferreras, ER and De Maayer, P and Makhalanyane, TP and Guerrero, LD and Aislabie, JM and Cowan, DA}, title = {Draft Genome Sequence of Microbacterium sp. Strain CH12i, Isolated from Shallow Groundwater in Cape Hallett, Antarctica.}, journal = {Genome announcements}, volume = {2}, number = {4}, pages = {}, pmid = {25125643}, issn = {2169-8287}, abstract = {The Antarctic continent is largely covered by an expansive ice sheet, but it harbors diverse terrestrial and aquatic habitats in the coastal ice-free continental margins. Here we present the draft genome of Microbacterium sp. CH12i, which was isolated from hypersaline, alkaline, and nutrient-rich groundwater from Cape Hallett, northern Victoria Land, Antarctica.}, }
@article {pmid25122209, year = {2014}, author = {Zhang, Y and Sun, Y and Cole, JR}, title = {A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data.}, journal = {PLoS computational biology}, volume = {10}, number = {8}, pages = {e1003737}, pmid = {25122209}, issn = {1553-7358}, mesh = {Chromosome Mapping/*methods ; Databases, Genetic ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; Microbiota/genetics ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {Gene assembly, which recovers gene segments from short reads, is an important step in functional analysis of next-generation sequencing data. Lacking quality reference genomes, de novo assembly is commonly used for RNA-Seq data of non-model organisms and metagenomic data. However, heterogeneous sequence coverage caused by heterogeneous expression or species abundance, similarity between isoforms or homologous genes, and large data size all pose challenges to de novo assembly. As a result, existing assembly tools tend to output fragmented contigs or chimeric contigs, or have high memory footprint. In this work, we introduce a targeted gene assembly program SAT-Assembler, which aims to recover gene families of particular interest to biologists. It addresses the above challenges by conducting family-specific homology search, homology-guided overlap graph construction, and careful graph traversal. It can be applied to both RNA-Seq and metagenomic data. Our experimental results on an Arabidopsis RNA-Seq data set and two metagenomic data sets show that SAT-Assembler has smaller memory usage, comparable or better gene coverage, and lower chimera rate for assembling a set of genes from one or multiple pathways compared with other assembly tools. Moreover, the family-specific design and rapid homology search allow SAT-Assembler to be naturally compatible with parallel computing platforms. The source code of SAT-Assembler is available at https://sourceforge.net/projects/sat-assembler/. The data sets and experimental settings can be found in supplementary material.}, }
@article {pmid25117548, year = {2015}, author = {Kim, TG and Jeong, SY and Cho, KS}, title = {Development of droplet digital PCR assays for methanogenic taxa and examination of methanogen communities in full-scale anaerobic digesters.}, journal = {Applied microbiology and biotechnology}, volume = {99}, number = {1}, pages = {445-458}, doi = {10.1007/s00253-014-6007-x}, pmid = {25117548}, issn = {1432-0614}, mesh = {Anaerobiosis ; Archaea/classification/genetics/*isolation &amp; purification ; Biofuels ; Bioreactors/*microbiology ; *Biota ; Methane/*metabolism ; Microbiological Techniques/*methods ; Polymerase Chain Reaction/*methods ; Sewage/*microbiology ; Temperature ; Time Factors ; }, abstract = {Droplet digital PCR (ddPCR) is a new DNA quantification platform without an external DNA calibrator. This study examined methanogen communities in four full-scale anaerobic digesters treating municipal sewage sludge, using ddPCR with taxon-specific primer/TaqMan probe sets (5 orders, 11 families, and 13 genera), many of which were developed in this study. Total methanogen abundance was positively correlated with hydraulic retention time (HRT) and temperature (p < 0.05), though the effect of HRT was stronger (r = 0.864 vs. 0.682, respectively). Moreover, total abundance was strongly correlated with biogas production rate (r = 0.896). HRT was positively correlated with seven methanogenic taxa, while temperature was positively or negatively correlated with 13 taxa (p < 0.05). For instance, the predominant genera Methanosaeta and Methanosarcina were negatively and positively associated, respectively, with temperature only (p < 0.05). Redundancy analysis and principal component analysis using the absolute-abundance dataset indicated that only temperature explained the variability in the methanogen communities at all classification levels. Therefore, HRT was the most important operational factor to influence net methanogen abundance and activity, while temperature governed the composition of the methanogen community. ddPCR enabled absolute quantification of methanogens without the external DNA standards and linked methanogen communities and operational factors, suggesting that it is a promising tool for analyzing the microbial ecology of anaerobic digestion.}, }
@article {pmid25117532, year = {2015}, author = {Davis, TS}, title = {The ecology of yeasts in the bark beetle holobiont: a century of research revisited.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {723-732}, pmid = {25117532}, issn = {1432-184X}, mesh = {Animals ; Larva/growth &amp; development/microbiology ; Ovum/growth &amp; development/microbiology ; Pheromones/physiology ; Pupa/growth &amp; development/microbiology ; *Symbiosis ; Weevils/growth &amp; development/*microbiology ; Yeasts/*physiology ; }, abstract = {Yeasts are extremely common associates of scolytine bark beetles, yet the basic ecology of yeasts in the bark beetle holobiont remains poorly understood. Yeasts are present in all beetle life stages and consistently isolated from adult, larval, and pupal integuments and mycangial structures, but yeasts are also found in oviposition galleries, pupal chambers, larval and adult digestive tracts, as well as phloem and xylem tissues. Yeasts in the Saccharomycetaceae family are the most prevalent associates, and most individual beetles are associated with only one or several yeast species. Kuraishia capsulata and Ogataea pini are the most commonly encountered yeast species in surveys of Dendroctonus and Ips beetles; most beetles that have been surveyed are vectors for one or both yeasts. Yeasts have significant but often overlooked functional roles in bark beetle ecology. Infochemicals resulting from volatile production by yeast have wide-ranging bioactivity for arthropods: Yeast emissions attract beetles at low concentrations but repel beetles at high concentrations, and yeast emissions can also serve as cues to predators and parasites of bark beetles. In some cases, yeasts can modify tree chemistry over time or metabolize toxic terpenoids, though potential consequences for beetle performance or the growth of nutritional fungi remain to be demonstrated. Also, the presence of yeast species can restrict or promote the establishment and growth of filamentous fungi, including mutualists, entomopathogens, and opportunistic saprophytes. The role of yeasts as nutritional symbionts has received mixed support, though a nutritional hypothesis has not been extensively tested. Continued research on the functional ecology of bark beetle-yeast associations is needed to better understand the emergent properties of these complex symbiont assemblages.}, }
@article {pmid25115980, year = {2015}, author = {Park, H and Sundar, S and Ma, Y and Chandran, K}, title = {Differentiation in the microbial ecology and activity of suspended and attached bacteria in a nitritation-anammox process.}, journal = {Biotechnology and bioengineering}, volume = {112}, number = {2}, pages = {272-279}, doi = {10.1002/bit.25354}, pmid = {25115980}, issn = {1097-0290}, mesh = {Ammonia/*metabolism ; Bacteria/classification/genetics/*metabolism ; Biofilms ; Bioreactors/*microbiology ; Nitrification ; Nitrites/*metabolism ; Nitrogen/*metabolism ; Oxidation-Reduction ; }, abstract = {A directed differentiation between the biofilm and suspension was observed in the molecular microbial ecology and gene expression of different bacteria in a biofilm nitritation-anammox process operated at varying hydraulic residence times (HRT) and nitrogen loading rates (NLR). The highest degree of enrichment observed in the biofilm was of anaerobic ammonia-oxidizing bacteria (AMX) followed by that of Nitrospira spp. related nitrite-oxidizing bacteria (NOB). For AMX, a major shift from Candidatus "Brocadia fulgida" to Candidatus "Kuenenia stuttgartiensis" in both suspension and biofilm was observed with progressively shorter HRT, using discriminatory biomarkers targeting the hydrazine synthase (hzsA) gene. In parallel, expression of the hydrazine oxidoreductase gene (hzo), a functional biomarker for AMX energy metabolism, became progressively prominent in the biofilm. A marginal but statistically significant enrichment in the biofilm was observed for Nitrosomonas europaea related ammonia-oxidizing bacteria (AOB). In direct contrast to AMX, the gene expression of ammonia monooxygenase subunit A (amoA), a functional biomarker for AOB energy metabolism, progressively increased in suspension. Using gene expression and biomass concentration measures in conjunction, it was determined that signatures of AOB metabolism were primarily present in the biofilm throughout the study. On the other hand, AMX metabolism gradually shifted from being uniformly distributed in both the biofilm and suspension to primarily the biofilm at shorter HRTs and higher NLRs. These results therefore highlight the complexity and key differences in the microbial ecology, gene expression and activity between the biofilm and suspension of a nitritation-anammox process and the biokinetic and metabolic drivers for such niche segregation.}, }
@article {pmid25113614, year = {2015}, author = {Liu, D and Ishikawa, H and Nishida, M and Tsuchiya, K and Takahashi, T and Kimura, M and Asakawa, S}, title = {Effect of paddy-upland rotation on methanogenic archaeal community structure in paddy field soil.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {160-168}, pmid = {25113614}, issn = {1432-184X}, mesh = {Archaea/classification/*genetics ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {Methanogenic archaea are strict anaerobes and demand highly reduced conditions to produce methane in paddy field soil. However, methanogenic archaea survive well under upland and aerated conditions in paddy fields and exhibit stable community. In the present study, methanogenic archaeal community was investigated in fields where paddy rice (Oryza sativa L.) under flooded conditions was rotated with soybean (Glycine max [L.] Merr.) under upland conditions at different rotation histories, by polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and real-time quantitative PCR methods targeting 16S rRNA and mcrA genes, respectively. Soil samples collected from the fields before flooding or seeding, during crop cultivation and after harvest of crops were analyzed. The abundance of the methanogenic archaeal populations decreased to about one-tenth in the rotational plots than in the consecutive paddy (control) plots. The composition of the methanogenic archaeal community also changed. Most members of the methanogenic archaea consisting of the orders Methanosarcinales, Methanocellales, Methanomicrobiales, and Methanobacteriales existed autochthonously in both the control and rotational plots, while some were strongly affected in the rotational plots, with fatal effect to some members belonging to the Methanosarcinales. This study revealed that the upland conversion for one or longer than 1 year in the rotational system affected the methanogenic archaeal community structure and was fatal to some members of methanogenic archaea in paddy field soil.}, }
@article {pmid25108574, year = {2015}, author = {García-Maldonado, JQ and Bebout, BM and Everroad, RC and López-Cortés, A}, title = {Evidence of novel phylogenetic lineages of methanogenic archaea from hypersaline microbial mats.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {106-117}, pmid = {25108574}, issn = {1432-184X}, mesh = {Archaea/classification/*genetics ; DNA, Archaeal/genetics ; Ecosystem ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; }, abstract = {Methanogenesis in hypersaline and high-sulfate environments is typically dominated by methylotrophic methanogens because sulfate reduction is thermodynamically favored over hydrogenotrophic methanogenesis in these environments. We characterized the community composition of methanogenic archaea in both unmanipulated and incubated microbial mats from different hypersaline environments in Baja California Sur, Mexico. Clone libraries of methyl coenzyme-M reductase (mcrA) sequences and DGGE band patterns of 16S rRNA and mcrA sequences showed that the methanogen community in these microbial mats is dominated by methylotrophic methanogens of the genus Methanohalophilus. However, phylogenetic analyses of mcrA sequences from these mats also revealed two new lineages corresponding to putative hydrogenotrophic methanogens related with the strictly hydrogenotrophic order Methanomicrobiales. Stimulated methane production under decreased salinity and sulfate concentrations also suggested the presence of hydrogenotrophic methanogens in these samples. The relative abundance of mcrA gene and transcripts, estimated by SYBR green I qPCR assays, suggested the activity of different phylogenetic groups of methanogens, including the two novel clusters, in unmanipulated samples of hypersaline microbial mats. Using geochemical and molecular approaches, we show that substrate limitation and values of salinity and sulfate higher than 3 % and 25 mM (respectively) are potential environmental constraints for methanogenesis in these environments. Microcosm experiments with modifications of salinity and sulfate concentrations and TMA addition showed that upper salt and sulfate concentrations for occurrence of methylotrophic methanogenesis were 28 % and 263 mM, respectively. This study provides phylogenetic information about uncultivated and undescribed methanogenic archaea from hypersaline environments.}, }
@article {pmid25107970, year = {2014}, author = {Cotta, SR and Dias, AC and Marriel, IE and Andreote, FD and Seldin, L and van Elsas, JD}, title = {Different effects of transgenic maize and nontransgenic maize on nitrogen-transforming archaea and bacteria in tropical soils.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {20}, pages = {6437-6445}, pmid = {25107970}, issn = {1098-5336}, mesh = {Ammonia/metabolism ; Brazil ; Denaturing Gradient Gel Electrophoresis ; *Microbial Consortia ; Molecular Sequence Data ; Nitrogen Fixation ; Oxidation-Reduction ; Oxidoreductases/genetics ; *Plants, Genetically Modified/growth &amp; development ; Polymerase Chain Reaction ; Rhizosphere ; *Soil Microbiology ; *Zea mays/genetics/growth &amp; development ; }, abstract = {The composition of the rhizosphere microbiome is a result of interactions between plant roots, soil, and environmental conditions. The impact of genetic variation in plant species on the composition of the root-associated microbiota remains poorly understood. This study assessed the abundances and structures of nitrogen-transforming (ammonia-oxidizing) archaea and bacteria as well as nitrogen-fixing bacteria driven by genetic modification of their maize host plants. The data show that significant changes in the abundances (revealed by quantitative PCR) of ammonia-oxidizing bacterial and archaeal communities occurred as a result of the maize host being genetically modified. In contrast, the structures of the total communities (determined by PCR-denaturing gradient gel electrophoresis) were mainly driven by factors such as soil type and season and not by plant genotype. Thus, the abundances of ammonia-oxidizing bacterial and archaeal communities but not structures of those communities were revealed to be responsive to changes in maize genotype, allowing the suggestion that community abundances should be explored as candidate bioindicators for monitoring the possible impacts of cultivation of genetically modified plants.}, }
@article {pmid25106113, year = {2014}, author = {Khoruts, A and Weingarden, AR}, title = {Emergence of fecal microbiota transplantation as an approach to repair disrupted microbial gut ecology.}, journal = {Immunology letters}, volume = {162}, number = {2 Pt A}, pages = {77-81}, pmid = {25106113}, issn = {1879-0542}, support = {UL1 TR000114/TR/NCATS NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/therapeutic use ; Clostridioides difficile/*physiology ; Drug Resistance ; Dysbiosis/*therapy ; Enterocolitis, Pseudomembranous/*therapy ; Feces/microbiology ; Homeostasis ; Humans ; Intestines/microbiology/*physiology ; Microbiota/*physiology ; *Transplantation ; }, abstract = {In the recent years fecal microbiota transplantation (FMT) has emerged as an effective therapeutic option for patients with refractory Clostridium difficile infection that is not responding to antibiotic therapy. It results in implantation of donor microbiota into recipients and restoration of normal distal gut microbial community structure. We anticipate that this form of therapy represents merely the first entry into a new class of therapeutics. There is great interest in application of FMT or defined microbial consortia to treatment of many diseases associated with dysbiosis. However, many challenges remain in development as our understanding of microbial ecology within the human body and microbiota-host interactions remain limited. Future advances in this field will be critically depending on detailed mechanistic understanding.}, }
@article {pmid25105587, year = {2014}, author = {Douterelo, I and Boxall, JB and Deines, P and Sekar, R and Fish, KE and Biggs, CA}, title = {Methodological approaches for studying the microbial ecology of drinking water distribution systems.}, journal = {Water research}, volume = {65}, number = {}, pages = {134-156}, doi = {10.1016/j.watres.2014.07.008}, pmid = {25105587}, issn = {1879-2448}, mesh = {Biofilms/growth &amp; development ; Drinking Water/*microbiology ; Microbiological Techniques/*methods ; Microbiota ; *Water Supply ; }, abstract = {The study of the microbial ecology of drinking water distribution systems (DWDS) has traditionally been based on culturing organisms from bulk water samples. The development and application of molecular methods has supplied new tools for examining the microbial diversity and activity of environmental samples, yielding new insights into the microbial community and its diversity within these engineered ecosystems. In this review, the currently available methods and emerging approaches for characterising microbial communities, including both planktonic and biofilm ways of life, are critically evaluated. The study of biofilms is considered particularly important as it plays a critical role in the processes and interactions occurring at the pipe wall and bulk water interface. The advantages, limitations and usefulness of methods that can be used to detect and assess microbial abundance, community composition and function are discussed in a DWDS context. This review will assist hydraulic engineers and microbial ecologists in choosing the most appropriate tools to assess drinking water microbiology and related aspects.}, }
@article {pmid25105060, year = {2014}, author = {Hargreaves, KR and Kropinski, AM and Clokie, MR}, title = {Bacteriophage behavioral ecology: How phages alter their bacterial host's habits.}, journal = {Bacteriophage}, volume = {4}, number = {}, pages = {e29866}, pmid = {25105060}, issn = {2159-7073}, support = {/WT_/Wellcome Trust/United Kingdom ; G0700855/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Bacteriophages have an essential gene kit that enables their invasion, replication, and production. In addition to this "core" genome, they can carry "accessory" genes that dramatically impact bacterial biology, and presumably boost their own success. The content of phage genomes continue to surprise us by revealing new ways that viruses impact bacterial biology. The genome of a Clostridium difficile myovirus, phiCDHM1, contains homologs of three bacterial accessory gene regulator (agr) genes. The agr system is a type of quorum sensing (QS), via which the phage may modify C. difficile interactions with its environment. Although their mechanism of action is unknown, mutants in bacterial versions of these genes impact sporulation and virulence. To explore how phage QS genes may influence C. difficile biology, we examine the main categories of bacterial behavior that phages have been shown to influence and discuss how interactions via QS could influence behavior at a wider level.}, }
@article {pmid25104950, year = {2014}, author = {Sime-Ngando, T}, title = {Environmental bacteriophages: viruses of microbes in aquatic ecosystems.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {355}, pmid = {25104950}, issn = {1664-302X}, abstract = {Since the discovery 2-3 decades ago that viruses of microbes are abundant in marine ecosystems, viral ecology has grown increasingly to reach the status of a full scientific discipline in environmental sciences. A dedicated ISVM society, the International Society for Viruses of Microorganisms, (http://www.isvm.org/) was recently launched. Increasing studies in viral ecology are sources of novel knowledge related to the biodiversity of living things, the functioning of ecosystems, and the evolution of the cellular world. This is because viruses are perhaps the most diverse, abundant, and ubiquitous biological entities in the biosphere, although local environmental conditions enrich for certain viral types through selective pressure. They exhibit various lifestyles that intimately depend on the deep-cellular mechanisms, and are ultimately replicated by members of all three domains of cellular life (Bacteria, Eukarya, Archaea), as well as by giant viruses of some eukaryotic cells. This establishes viral parasites as microbial killers but also as cell partners or metabolic manipulators in microbial ecology. The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology, focusing primarily on prokaryotic viruses (i.e., phages) in aquatic ecosystems, which form the bulk of our knowledge in modern environmental viral ecology.}, }
@article {pmid25103912, year = {2015}, author = {Abed, RM and Al-Kindi, S and Al-Kharusi, S}, title = {Diversity of bacterial communities along a petroleum contamination gradient in desert soils.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {95-105}, pmid = {25103912}, issn = {1432-184X}, mesh = {Acidobacteria/drug effects/genetics/metabolism ; Actinobacteria/drug effects/genetics/metabolism ; Bacillus/drug effects/genetics/metabolism ; Desert Climate ; Petroleum/*toxicity ; Petroleum Pollution/*adverse effects ; Proteobacteria/drug effects/genetics/metabolism ; RNA, Ribosomal/genetics ; Soil Microbiology ; }, abstract = {Microbial communities in oil-polluted desert soils have been rarely studied compared to their counterparts from freshwater and marine environments. We investigated bacterial diversity and changes therein in five desert soils exposed to different levels of oil pollution. Automated rRNA intergenic spacer (ARISA) analysis profiles showed that the bacterial communities of the five soils were profoundly different (analysis of similarities (ANOSIM), R = 0.45, P < 0.0001) and shared less than 20 % of their operational taxonomic units (OTUs). OTU richness was relatively higher in the soils with the higher oil pollution levels. Multivariate analyses of ARISA profiles revealed that the microbial communities in the S soil, which contains the highest level of contamination, were different from the other soils and formed a completely separate cluster. A total of 16,657 ribosomal sequences were obtained, with 42-89 % of these sequences belonging to the phylum Proteobacteria. While sequences belonging to Betaproteobacteria, Gammaproteobacteria, Bacilli, and Actinobacteria were encountered in all soils, sequences belonging to anaerobic bacteria from the classes Deltaproteobacteria, Clostridia, and Anaerolineae were only detected in the S soil. Sequences belonging to the genus Terriglobus of the class Acidobacteria were only detected in the B3 soil with the lowest level of contamination. Redundancy analysis (RDA) showed that oil contamination level was the most determinant factor that explained variations in the microbial communities. We conclude that the exposure to different levels of oil contamination exerts a strong selective pressure on bacterial communities and that desert soils are rich in aerobic and anaerobic bacteria that could potentially contribute to the degradation of hydrocarbons.}, }
@article {pmid25103911, year = {2015}, author = {Barbosa Lima, A and Cannavan, FS and Navarrete, AA and Teixeira, WG and Kuramae, EE and Tsai, SM}, title = {Amazonian dark Earth and plant species from the Amazon region contribute to shape rhizosphere bacterial communities.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {855-866}, pmid = {25103911}, issn = {1432-184X}, mesh = {Bacteria/genetics/metabolism ; Bacterial Physiological Phenomena ; Brazil ; Fabaceae/*microbiology ; Mimosa/microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics/metabolism ; *Rhizosphere ; Soil/*chemistry ; *Soil Microbiology ; Trees/*microbiology ; }, abstract = {Amazonian Dark Earths (ADE) or Terra Preta de Índio formed in the past by pre-Columbian populations are highly sustained fertile soils supported by microbial communities that differ from those extant in adjacent soils. These soils are found in the Amazon region and are considered as a model soil when compared to the surrounding and background soils. The aim of this study was to assess the effects of ADE and its surrounding soil on the rhizosphere bacterial communities of two leguminous plant species that frequently occur in the Amazon region in forest sites (Mimosa debilis) and open areas (Senna alata). Bacterial community structure was evaluated using terminal restriction fragment length polymorphism (T-RFLP) and bacterial community composition by V4 16S rRNA gene region pyrosequencing. T-RFLP analysis showed effect of soil types and plant species on rhizosphere bacterial community structure. Differential abundance of bacterial phyla, such as Acidobacteria, Actinobacteria, Verrucomicrobia, and Firmicutes, revealed that soil type contributes to shape the bacterial communities. Furthermore, bacterial phyla such as Firmicutes and Nitrospira were mostly influenced by plant species. Plant roots influenced several soil chemical properties, especially when plants were grown in ADE. These results showed that differences observed in rhizosphere bacterial community structure and composition can be influenced by plant species and soil fertility due to variation in soil attributes.}, }
@article {pmid25103759, year = {2014}, author = {Weller-Stuart, T and Chan, WY and Coutinho, TA and Venter, SN and Smits, TH and Duffy, B and Goszczynska, T and Cowan, DA and de Maayer, P}, title = {Draft Genome Sequences of the Onion Center Rot Pathogen Pantoea ananatis PA4 and Maize Brown Stalk Rot Pathogen P. ananatis BD442.}, journal = {Genome announcements}, volume = {2}, number = {4}, pages = {}, pmid = {25103759}, issn = {2169-8287}, abstract = {Pantoea ananatis is an emerging phytopathogen that infects a broad spectrum of plant hosts. Here, we present the genomes of two South African isolates, P. ananatis PA4, which causes center rot of onion, and BD442, isolated from brown stalk rot of maize.}, }
@article {pmid25102857, year = {2015}, author = {Matsen, FA}, title = {Phylogenetics and the human microbiome.}, journal = {Systematic biology}, volume = {64}, number = {1}, pages = {e26-41}, pmid = {25102857}, issn = {1076-836X}, support = {R01 HG005966/HG/NHGRI NIH HHS/United States ; R01-HG005966-01/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Humans ; Microbiota/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of sequencing and genetic analysis of microbiome samples. Much of the analytical work for these sequences involves phylogenetics, at least indirectly, but methodology has developed in a somewhat different direction than for other applications of phylogenetics. In this article, I review the field and its methods from the perspective of a phylogeneticist, as well as describing current challenges for phylogenetics coming from this type of work.}, }
@article {pmid25096989, year = {2015}, author = {Hanshew, AS and McDonald, BR and Díaz Díaz, C and Djiéto-Lordon, C and Blatrix, R and Currie, CR}, title = {Characterization of actinobacteria associated with three ant-plant mutualisms.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {192-203}, pmid = {25096989}, issn = {1432-184X}, support = {T32 GM07215-37/GM/NIGMS NIH HHS/United States ; }, mesh = {Actinobacteria/*physiology ; Animals ; Ants/*physiology ; Ascomycota/*physiology ; Cameroon ; Ecosystem ; Fabaceae/microbiology/physiology ; French Guiana ; }, abstract = {Ant-plant mutualisms are conspicuous and ecologically important components of tropical ecosystems that remain largely unexplored in terms of insect-associated microbial communities. Recent work has revealed that ants in some ant-plant systems cultivate fungi (Chaetothyriales) within their domatia, which are fed to larvae. Using Pseudomyrmex penetrator/Tachigali sp. from French Guiana and Petalomyrmex phylax/Leonardoxa africana and Crematogaster margaritae/Keetia hispida, both from Cameroon, as models, we tested the hypothesis that ant-plant-fungus mutualisms co-occur with culturable Actinobacteria. Using selective media, we isolated 861 putative Actinobacteria from the three systems. All C. margaritae/K. hispida samples had culturable Actinobacteria with a mean of 10.0 colony forming units (CFUs) per sample, while 26 % of P. penetrator/Tachigali samples (mean CFUs 1.3) and 67 % of P. phylax/L. africana samples (mean CFUs 3.6) yielded Actinobacteria. The largest number of CFUs was obtained from P. penetrator workers, P. phylax alates, and C. margaritae pupae. 16S rRNA gene sequencing and phylogenetic analysis revealed the presence of four main clades of Streptomyces and one clade of Nocardioides within these three ant-plant mutualisms. Streptomyces with antifungal properties were isolated from all three systems, suggesting that they could serve as protective symbionts, as found in other insects. In addition, a number of isolates from a clade of Streptomyces associated with P. phylax/L. africana and C. margaritae/K. hispida were capable of degrading cellulose, suggesting that Streptomyces in these systems may serve a nutritional role. Repeated isolation of particular clades of Actinobacteria from two geographically distant locations supports these isolates as residents in ant-plant-fungi niches.}, }
@article {pmid25096988, year = {2015}, author = {Sales, MA and Gonçalves, JF and Dahora, JS and Medeiros, AO}, title = {Influence of leaf quality in microbial decomposition in a headwater stream in the Brazilian cerrado: a 1-year study.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {84-94}, pmid = {25096988}, issn = {1432-184X}, mesh = {Biomass ; Brazil ; Ecosystem ; *Plant Leaves ; Rivers ; }, abstract = {The temporal dynamics of leaf decomposition in a tropical stream were evaluated by measuring the input of leaves from riparian vegetation. The resulting mixture of leaves was processed by decomposer microorganisms and, in particular, by aquatic hyphomycetes, the most important microorganisms associated with leaf litter decomposition. Leaf decomposition and the characteristics and activity of the microbial community were investigated over the course of 1 year; these parameters depended on the composition and availability of leaves in the stream. We assessed the biomass, activity, and community structure of the fungi associated with the decomposing leaf mixtures monthly in a tropical stream with little seasonal variation in water characteristics. The leaf material included 27 riparian species; the amount of leaves of each contributing species varied from month to month, with higher overall values in the rainy season. Leaf decomposition was slow, and leaf mass loss did not occur monthly; however, leaf mass loss was significantly lower in May and September. The values of ATP, the ergosterol concentration, and the sporulation of aquatic hyphomycetes varied during the experiment, and only the ergosterol concentration (fungal biomass) was correlated with leaf mass loss. The sporulation rates of aquatic hyphomycetes peaked at the beginning of the rainy season (October), when only three hyphomycete species were present out of the total of seven that were found during the year. In this tropical stream, where the physical and chemical characteristics of the stream water varied little during the year, we hypothesize that changes related to leaf chemical composition could be the cause of changes in decomposition and the abundance and composition of the fungal assemblages. No significant differences were found for the parameters analyzed (lignin, cellulose, fiber, phosphorous, and polyphenols).}, }
@article {pmid25093819, year = {2014}, author = {Kyrpides, NC and Hugenholtz, P and Eisen, JA and Woyke, T and Göker, M and Parker, CT and Amann, R and Beck, BJ and Chain, PS and Chun, J and Colwell, RR and Danchin, A and Dawyndt, P and Dedeurwaerdere, T and DeLong, EF and Detter, JC and De Vos, P and Donohue, TJ and Dong, XZ and Ehrlich, DS and Fraser, C and Gibbs, R and Gilbert, J and Gilna, P and Glöckner, FO and Jansson, JK and Keasling, JD and Knight, R and Labeda, D and Lapidus, A and Lee, JS and Li, WJ and Ma, J and Markowitz, V and Moore, ER and Morrison, M and Meyer, F and Nelson, KE and Ohkuma, M and Ouzounis, CA and Pace, N and Parkhill, J and Qin, N and Rossello-Mora, R and Sikorski, J and Smith, D and Sogin, M and Stevens, R and Stingl, U and Suzuki, K and Taylor, D and Tiedje, JM and Tindall, B and Wagner, M and Weinstock, G and Weissenbach, J and White, O and Wang, J and Zhang, L and Zhou, YG and Field, D and Whitman, WB and Garrity, GM and Klenk, HP}, title = {Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.}, journal = {PLoS biology}, volume = {12}, number = {8}, pages = {e1001920}, pmid = {25093819}, issn = {1545-7885}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Databases, Genetic ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; *Genomics ; Phylogeny ; *Sequence Analysis, DNA ; }, abstract = {Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.}, }
@article {pmid25093637, year = {2014}, author = {Ghylin, TW and Garcia, SL and Moya, F and Oyserman, BO and Schwientek, P and Forest, KT and Mutschler, J and Dwulit-Smith, J and Chan, LK and Martinez-Garcia, M and Sczyrba, A and Stepanauskas, R and Grossart, HP and Woyke, T and Warnecke, F and Malmstrom, R and Bertilsson, S and McMahon, KD}, title = {Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage.}, journal = {The ISME journal}, volume = {8}, number = {12}, pages = {2503-2516}, pmid = {25093637}, issn = {1751-7370}, support = {T32 GM008349/GM/NIGMS NIH HHS/United States ; 5T32GM08349/GM/NIGMS NIH HHS/United States ; }, mesh = {Actinobacteria/classification/*genetics/growth &amp; development/metabolism ; Actinomycetales/genetics ; Ecosystem ; *Genome, Bacterial ; Genomics ; Heterotrophic Processes ; Lakes/*microbiology ; }, abstract = {Members of the acI lineage of Actinobacteria are the most abundant microorganisms in most freshwater lakes; however, our understanding of the keys to their success and their role in carbon and nutrient cycling in freshwater systems has been hampered by the lack of pure cultures and genomes. We obtained draft genome assemblies from 11 single cells representing three acI tribes (acI-A1, acI-A7, acI-B1) from four temperate lakes in the United States and Europe. Comparative analysis of acI SAGs and other available freshwater bacterial genomes showed that acI has more gene content directed toward carbohydrate acquisition as compared to Polynucleobacter and LD12 Alphaproteobacteria, which seem to specialize more on carboxylic acids. The acI genomes contain actinorhodopsin as well as some genes involved in anaplerotic carbon fixation indicating the capacity to supplement their known heterotrophic lifestyle. Genome-level differences between the acI-A and acI-B clades suggest specialization at the clade level for carbon substrate acquisition. Overall, the acI genomes appear to be highly streamlined versions of Actinobacteria that include some genes allowing it to take advantage of sunlight and N-rich organic compounds such as polyamines, di- and oligopeptides, branched-chain amino acids and cyanophycin. This work significantly expands the known metabolic potential of the cosmopolitan freshwater acI lineage and its ecological and genetic traits.}, }
@article {pmid25085516, year = {2015}, author = {Deveau, A and Barret, M and Diedhiou, AG and Leveau, J and de Boer, W and Martin, F and Sarniguet, A and Frey-Klett, P}, title = {Pairwise transcriptomic analysis of the interactions between the ectomycorrhizal fungus Laccaria bicolor S238N and three beneficial, neutral and antagonistic soil bacteria.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {146-159}, pmid = {25085516}, issn = {1432-184X}, mesh = {Bacteria/*genetics ; Laccaria/*genetics ; Mycorrhizae/genetics ; Soil Microbiology ; }, abstract = {Ectomycorrhizal fungi are surrounded by bacterial communities with which they interact physically and metabolically during their life cycle. These bacteria can have positive or negative effects on the formation and the functioning of ectomycorrhizae. However, relatively little is known about the mechanisms by which ectomycorrhizal fungi and associated bacteria interact. To understand how ectomycorrhizal fungi perceive their biotic environment and the mechanisms supporting interactions between ectomycorrhizal fungi and soil bacteria, we analysed the pairwise transcriptomic responses of the ectomycorrhizal fungus Laccaria bicolor (Basidiomycota: Agaricales) when confronted with beneficial, neutral or detrimental soil bacteria. Comparative analyses of the three transcriptomes indicated that the fungus reacted differently to each bacterial strain. Similarly, each bacterial strain produced a specific and distinct response to the presence of the fungus. Despite these differences in responses observed at the gene level, we found common classes of genes linked to cell-cell interaction, stress response and metabolic processes to be involved in the interaction of the four microorganisms.}, }
@article {pmid25085486, year = {2014}, author = {De Pasquale, I and Di Cagno, R and Buchin, S and De Angelis, M and Gobbetti, M}, title = {Microbial ecology dynamics reveal a succession in the core microbiota involved in the ripening of pasta filata caciocavallo pugliese cheese.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {19}, pages = {6243-6255}, pmid = {25085486}, issn = {1098-5336}, mesh = {Animals ; *Biodiversity ; Cheese/*microbiology ; Computational Biology ; Fatty Acids, Volatile/analysis ; Female ; Food Handling ; *Food Microbiology ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics/*physiology ; Milk/*microbiology ; Proteolysis ; RNA, Bacterial/chemistry/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Pyrosequencing of the 16S rRNA targeting RNA, community-level physiological profiles made with Biolog EcoPlates, proteolysis, and volatile component (VOC) analyses were mainly used to characterize the manufacture and ripening of the pasta filata cheese Caciocavallo Pugliese. Plate counts revealed that cheese manufacture affected the microbial ecology. The results agreed with those from culture-independent approaches. As shown by urea-PAGE, reverse-phase high pressure liquid chromatography (RP-HPLC), and free-amino-acid (FAA) analyses, the extent of secondary proteolysis mainly increased after 30 to 45 days of ripening. VOCs and volatile free fatty acids (VFFA) were identified by a purge-and-trap method (PT) and solid-phase microextraction (SPME) coupled with gas chromatography-mass spectrometry (GC-MS), respectively. Except for aldehydes, the levels of most of VOCs and VFFA mainly increased from 30 to 45 days onwards. As shown through pyrosequencing analysis, raw cows' milk was contaminated by Firmicutes (53%), Proteobacteria (39%), Bacteroidetes (7.8%), Actinobacteria (0.06%), and Fusobacteria (0.03%), with heterogeneity at the genus level. The primary starter Streptococcus thermophilus dominated the curd population. Other genera occurred at low incidence or sporadically. The microbial dynamics reflected on the overall physiological diversity. At 30 days, a microbial succession was clearly highlighted. The relative abundance of Streptococcus sp. and especially St. thermophilus decreased, while that of Lactobacillus casei, Lactobacillus sp., and especially Lactobacillus paracasei increased consistently. Despite the lower relative abundance compared to St. thermophilus, mesophilic lactobacilli were the only organisms positively correlated with the concentration of FAAs, area of hydrophilic peptide peaks, and several VOCs (e.g., alcohols, ketones, esters and all furans). This study showed that a core microbiota was naturally selected during middle ripening, which seemed to be the main factor responsible for cheese ripening.}, }
@article {pmid25085217, year = {2015}, author = {Deepika, S and Kothamasi, D}, title = {Soil moisture--a regulator of arbuscular mycorrhizal fungal community assembly and symbiotic phosphorus uptake.}, journal = {Mycorrhiza}, volume = {25}, number = {1}, pages = {67-75}, pmid = {25085217}, issn = {1432-1890}, mesh = {*Biodiversity ; Fungi/genetics/*physiology ; India ; Molecular Sequence Data ; Mycorrhizae/genetics/*physiology ; Phosphorus/*metabolism ; Plant Roots/microbiology ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Soil/*chemistry ; Sorghum/*microbiology ; Symbiosis ; }, abstract = {Multiple species of arbuscular mycorrhizal fungi (AMF) can colonize roots of an individual plant species but factors which determine the selection of a particular AMF species in a plant root are largely unknown. The present work analysed the effects of drought, flooding and optimal soil moisture (15-20 %) on AMF community composition and structure in Sorghum vulgare roots, using PCR-RFLP. Rhizophagus irregularis (isolate BEG 21), and rhizosphere soil (mixed inoculum) of Heteropogon contortus, a perennial C4 grass, collected from the semi-arid Delhi ridge, were used as AMF inocula. Soil moisture functioned as an abiotic filter and affected AMF community assembly inside plant roots by regulating AMF colonization and phylotype diversity. Roots of plants in flooded soils had lowest AMF diversity whilst root AMF diversity was highest under the soil moisture regime of 15-20 %. Although plant biomass was not affected, root P uptake was significantly influenced by soil moisture. Plants colonized with R. irregularis or mixed AMF inoculum showed higher root P uptake than non-mycorrhizal plants in drought and control treatments. No differences in root P levels were found in the flooded treatment between plants colonized with R. irregularis and non-mycorrhizal plants, whilst under the same treatment, root P uptake was lower in plants colonized with mixed AMF inoculum than in non-mycorrhizal plants.}, }
@article {pmid25081413, year = {2015}, author = {Liu, H and Ibrahim, M and Qiu, H and Kausar, S and Ilyas, M and Cui, Z and Hussain, A and Li, B and Waheed, A and Zhu, B and Xie, G}, title = {Protein profiling analyses of the outer membrane of Burkholderia cenocepacia reveal a niche-specific proteome.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {75-83}, pmid = {25081413}, issn = {1432-184X}, mesh = {Bacterial Outer Membrane Proteins/genetics/*metabolism ; Burkholderia cenocepacia/genetics/*metabolism ; Electrophoresis, Polyacrylamide Gel ; Proteome/*analysis ; Tandem Repeat Sequences/genetics ; }, abstract = {Outer membrane proteins (OMPs) are integral β-barrel proteins of the Gram-negative bacterial cell wall and are crucial to bacterial survival within the macrophages and for eukaryotic cell invasion. Here, we used liquid chromatography tandem mass spectrometry (LC-MS/MS) to comprehensively assess the outer membrane proteome of Burkholderia cenocepacia, an opportunistic pathogen causing cystic fibrosis (CF), in conditions mimicking four major ecological niches: water, CF sputum, soil, and plant leaf. Bacterial cells were harvested at late log phase, and OMPs were extracted following the separation of soluble proteins by one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (1D-SDS-PAGE). Protein bands were excised and identified by LC-MS/MS analysis. The proteins identified under various growth conditions were further subjected to in silico analysis of gene ontology (subcellular localization, structural, and functional analyses). Overall, 72 proteins were identified as common to the four culture conditions, while 33, 37, 20, and 10 proteins were exclusively identified in the water, CF sputum, soil, and plant leaf environments, respectively. The functional profiles of the majority of these proteins revealed significant diversity in protein expression between the four environments studied and may indicate that the protein expression profiles are unique for every condition. Comparison of OMPs from one strain in four distinct ecological niches allowed the elucidation of proteins that are essential for survival in each niche, while the commonly expressed OMPs, such as RND efflux system protein, TonB-dependent siderophore receptor, and ABC transporter-like protein, represent promising targets for drug or vaccine development.}, }
@article {pmid25079685, year = {2015}, author = {Claesen, J and Fischbach, MA}, title = {Synthetic microbes as drug delivery systems.}, journal = {ACS synthetic biology}, volume = {4}, number = {4}, pages = {358-364}, pmid = {25079685}, issn = {2161-5063}, support = {R01 AI101018/AI/NIAID NIH HHS/United States ; DP2 OD007290/OD/NIH HHS/United States ; AI101018/AI/NIAID NIH HHS/United States ; R21 AI101722/AI/NIAID NIH HHS/United States ; GM081879/GM/NIGMS NIH HHS/United States ; AI101722/AI/NIAID NIH HHS/United States ; P50 GM081879/GM/NIGMS NIH HHS/United States ; OD007290/OD/NIH HHS/United States ; }, mesh = {Animals ; *Bacteria ; Cell Engineering/*methods ; Drug Delivery Systems/*methods ; Humans ; Synthetic Biology/methods ; }, abstract = {Synthetic cell therapy is a field that has broad potential for future applications in human disease treatment. Next generation therapies will consist of engineered bacterial strains capable of diagnosing disease, producing and delivering therapeutics, and controlling their numbers to meet containment and safety concerns. A thorough understanding of the microbial ecology of the human body and the interaction of the microbes with the immune system will benefit the choice of an appropriate chassis that engrafts stably and interacts productively with the resident community in specific body niches.}, }
@article {pmid25078442, year = {2014}, author = {Lu, H and Chandran, K and Stensel, D}, title = {Microbial ecology of denitrification in biological wastewater treatment.}, journal = {Water research}, volume = {64}, number = {}, pages = {237-254}, doi = {10.1016/j.watres.2014.06.042}, pmid = {25078442}, issn = {1879-2448}, mesh = {Bacteria/genetics/*metabolism ; DNA, Bacterial/analysis ; *Denitrification ; Environmental Microbiology ; In Situ Hybridization, Fluorescence ; Nitrogen/chemistry ; Sewage/microbiology ; Waste Disposal, Fluid/*methods ; }, abstract = {Globally, denitrification is commonly employed in biological nitrogen removal processes to enhance water quality. However, substantial knowledge gaps remain concerning the overall community structure, population dynamics and metabolism of different organic carbon sources. This systematic review provides a summary of current findings pertaining to the microbial ecology of denitrification in biological wastewater treatment processes. DNA fingerprinting-based analysis has revealed a high level of microbial diversity in denitrification reactors and highlighted the impacts of carbon sources in determining overall denitrifying community composition. Stable isotope probing, fluorescence in situ hybridization, microarrays and meta-omics further link community structure with function by identifying the functional populations and their gene regulatory patterns at the transcriptional and translational levels. This review stresses the need to integrate microbial ecology information into conventional denitrification design and operation at full-scale. Some emerging questions, from physiological mechanisms to practical solutions, for example, eliminating nitrous oxide emissions and supplementing more sustainable carbon sources than methanol, are also discussed. A combination of high-throughput approaches is next in line for thorough assessment of wastewater denitrifying community structure and function. Though denitrification is used as an example here, this synergy between microbial ecology and process engineering is applicable to other biological wastewater treatment processes.}, }
@article {pmid25077936, year = {2014}, author = {Scanlan, PD and Stensvold, CR and Rajilić-Stojanović, M and Heilig, HG and De Vos, WM and O'Toole, PW and Cotter, PD}, title = {The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota.}, journal = {FEMS microbiology ecology}, volume = {90}, number = {1}, pages = {326-330}, doi = {10.1111/1574-6941.12396}, pmid = {25077936}, issn = {1574-6941}, mesh = {Adult ; Blastocystis/classification/genetics/*isolation &amp; purification ; Genetic Variation ; Humans ; Intestines/*microbiology ; *Microbiota ; }, abstract = {To date, the majority of research into the human gut microbiota has focused on the bacterial fraction of the community. Inevitably, this has resulted in a poor understanding of the diversity and functionality of other intestinal microorganisms in the human gut. One such nonbacterial member is the microbial eukaryote Blastocystis, which has been implicated in the aetiology of a range of different intestinal and extra-intestinal diseases. However, prevalence data from different studies are conflicting, and crucially, there is limited information on its incidence and diversity in healthy individuals. Here, we survey the prevalence, genetic diversity and temporal stability of Blastocystis in a group of healthy adults (n = 105) using a sensitive PCR assay. Blastocystis was present in 56% of our sample set, which is much higher than previously reported from an industrialised county (Ireland). Moreover, a diversity of different subtypes (species) were detected, and Blastocystis was present in a subset of individuals sampled over a period of time between 6 and 10 years, indicating that it is capable of long-term host colonisation. These results show that Blastocystis is a common and diverse member of the healthy gut microbiota, thereby extending our knowledge of the microbial ecology of the healthy human intestine.}, }
@article {pmid25077920, year = {2014}, author = {Callewaert, C and Hutapea, P and Van de Wiele, T and Boon, N}, title = {Deodorants and antiperspirants affect the axillary bacterial community.}, journal = {Archives of dermatological research..}, volume = {306}, number = {8}, pages = {701-710}, doi = {10.1007/s00403-014-1487-1}, pmid = {25077920}, issn = {1432-069X}, mesh = {Actinobacteria/*drug effects/physiology ; Aged ; Antiperspirants/*adverse effects ; Belgium ; Biodiversity ; DNA, Bacterial/analysis ; Deodorants/*adverse effects ; Female ; Humans ; Male ; Microbiota/drug effects ; Middle Aged ; Odorants/*prevention &amp; control ; Skin/*drug effects/microbiology ; Species Specificity ; }, abstract = {The use of underarm cosmetics is common practice in the Western society to obtain better body odor and/or to prevent excessive sweating. A survey indicated that 95 % of the young adult Belgians generally use an underarm deodorant or antiperspirant. The effect of deodorants and antiperspirants on the axillary bacterial community was examined on nine healthy subjects, who were restrained from using deodorant/antiperspirant for 1 month. Denaturing gradient gel electrophoresis was used to investigate the individual microbial dynamics. The microbial profiles were unique for every person. A stable bacterial community was seen when underarm cosmetics were applied on a daily basis and when no underarm cosmetics were applied. A distinct community difference was seen when the habits were changed from daily use to no use of deodorant/antiperspirant and vice versa. The richness was higher when deodorants and antiperspirants were applied. Especially when antiperspirants were applied, the microbiome showed an increase in diversity. Antiperspirant usage led toward an increase of Actinobacteria, which is an unfavorable situation with respect to body odor development. These initial results show that axillary cosmetics modify the microbial community and can stimulate odor-producing bacteria.}, }
@article {pmid25074793, year = {2015}, author = {Epalle, T and Girardot, F and Allegra, S and Maurice-Blanc, C and Garraud, O and Riffard, S}, title = {Viable but not culturable forms of Legionella pneumophila generated after heat shock treatment are infectious for macrophage-like and alveolar epithelial cells after resuscitation on Acanthamoeba polyphaga.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {215-224}, pmid = {25074793}, issn = {1432-184X}, mesh = {Acanthamoeba/*physiology ; Cell Line ; Epithelial Cells/*microbiology ; Humans ; Legionella pneumophila/*pathogenicity ; Macrophages/*microbiology ; }, abstract = {Legionella pneumophila, the causative agent of legionellosis is transmitted to human through aerosols from environmental sources and invades lung's macrophages. It also can invade and replicate within various protozoan species in environmental reservoirs. Following exposures to various stresses, L. pneumophila enters a non-replicative viable but non-culturable (VBNC) state. Here, we evaluated whether VBNC forms of three L. pneumophila serogroup 1 strains (Philadelphia GFP 008, clinical 044 and environmental RNN) infect differentiated macrophage-like cell lines (U937 and HL-60), A549 alveolar cells and Acanthamoeba polyphaga. VBNC forms obtained following shocks at temperatures ranging from 50 to 70 °C for 5 to 60 min were quantified using a flow cytometric assay (FCA). Their loss of culturability was checked on BCYE agar medium. VBNC forms were systematically detected upon a 70 °C heat shock for 30 min. When testing their potential to resuscitate upon amoebal infection, VBNC forms obtained after 30 min at 70 °C were re-cultivated except for the clinical strain. No resuscitation or cell lysis was evidenced when using U937, HL-60, or A549 cells despite the use of various contact times and culture media. None of the strains tested could infect A. polyphaga, macrophage-like or alveolar epithelial cells after a 60-min treatment at 70 °C. However, heat-treated VBNC forms were able to infect macrophage-like or alveolar epithelial cells following their resuscitation on A. polyphaga. These results suggest that heat-generated VBNC forms of L. pneumophila (i) are not infectious for macrophage-like or alveolar epithelial cells in vitro although resuscitation is still possible using amoeba, and (ii) may become infectious for human cell lines following a previous interaction with A. polyphaga.}, }
@article {pmid25074792, year = {2015}, author = {Wang, JT and Cao, P and Hu, HW and Li, J and Han, LL and Zhang, LM and Zheng, YM and He, JZ}, title = {Altitudinal distribution patterns of soil bacterial and archaeal communities along mt. Shegyla on the Tibetan Plateau.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {135-145}, pmid = {25074792}, issn = {1432-184X}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Tibet ; }, abstract = {Unraveling the distribution patterns of plants and animals along the elevational gradients has been attracting growing scientific interests of ecologists, whether the microbial communities exhibit similar elevational patterns, however, remains largely less documented. Here, we investigate the biogeographic distribution of soil archaeal and bacterial communities across three vertical climate zones (3,106-4,479 m.a.s.l.) in Mt. Shegyla on the Tibetan Plateau, by combining quantitative PCR and high-throughput barcoded pyrosequencing approaches. Our results found that the ratio of bacterial to archaeal 16S rRNA gene abundance was negatively related with elevation. Acidobacteria dominated in the bacterial communities, Marine benthic group A dominated in the archaeal communities, and the relative abundance of both taxa changed significantly with elevation. At the taxonomic levels of domain, phylum, and class, more bacterial taxa than archaeal exhibited declining trend in diversity along the increasing elevational gradient, as revealed by Shannon and Faith's phylogenetic diversity indices. Unweighted UniFrac distance clustering showed that the bacterial communities from the mountainous temperate zone clustered together, whereas those from the subalpine cool temperate zone clustered together. However, the partitioning effect of elevational zones on the archaeal community was much weaker compared to that on bacteria. Redundancy analysis revealed that soil geochemical factors explained 58.3 % of the bacterial community variance and 75.4 % of the archaeal community variance. Taken together, we provide evidence that soil bacteria exhibited more apparent elevational zonation feature and decreased diversity pattern than archaea with increasing elevation, and distribution patterns of soil microbes are strongly regulated by soil properties along elevational gradient in this plateau montane ecosystem.}, }
@article {pmid25073650, year = {2015}, author = {Busschaert, P and Frans, I and Crauwels, S and Zhu, B and Willems, K and Bossier, P and Michiels, C and Verstrepen, K and Lievens, B and Rediers, H}, title = {Comparative genome sequencing to assess the genetic diversity and virulence attributes of 15 Vibrio anguillarum isolates.}, journal = {Journal of fish diseases}, volume = {38}, number = {9}, pages = {795-807}, doi = {10.1111/jfd.12290}, pmid = {25073650}, issn = {1365-2761}, mesh = {Animals ; Bass/microbiology ; Gene Deletion ; *Genetic Variation ; Genome, Bacterial/*genetics ; Mutagenesis, Insertional ; Polymorphism, Single Nucleotide ; Vibrio/*genetics/*pathogenicity ; Virulence/genetics ; }, abstract = {Vibrio anguillarum is the causative agent of vibriosis, a deadly haemorrhagic septicaemic disease affecting various marine and fresh/brackish water fish, bivalves and crustaceans. However, the diversity and virulence mechanisms of this pathogen are still insufficiently known. In this study, we aimed to increase our understanding of V. anguillarum diversity and virulence through comparative genome analysis of 15 V. anguillarum strains, obtained from different hosts or non-host niches and geographical regions, among which 10 and 5 strains were found to be virulent and avirulent, respectively, against sea bass larvae. First, the 15 draft genomes were annotated and screened for putative virulence factors, including genes encoding iron uptake systems, transport systems and non-ribosomal peptide synthetases. Second, comparative genome analysis was performed, focusing on single nucleotide polymorphisms (SNPs) and small insertions and deletions (InDels). Five V. anguillarum strains showed a remarkably high nucleotide identity. However, these strains comprise both virulent and avirulent strains towards sea bass larvae, suggesting that differences in virulence may be caused by subtle nucleotide variations. Clearly, the draft genome sequence of these 15 strains represents a starting point for further genetic research of this economically important fish pathogen.}, }
@article {pmid25072414, year = {2015}, author = {Larsen, PE and Scott, N and Post, AF and Field, D and Knight, R and Hamada, Y and Gilbert, JA}, title = {Satellite remote sensing data can be used to model marine microbial metabolite turnover.}, journal = {The ISME journal}, volume = {9}, number = {1}, pages = {166-179}, pmid = {25072414}, issn = {1751-7370}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Bacteria/*genetics/metabolism ; England ; Environmental Monitoring/*methods ; Geographic Information Systems ; Humans ; Models, Biological ; *Oceans and Seas ; RNA, Ribosomal, 16S/genetics ; *Satellite Imagery ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {Sampling ecosystems, even at a local scale, at the temporal and spatial resolution necessary to capture natural variability in microbial communities are prohibitively expensive. We extrapolated marine surface microbial community structure and metabolic potential from 72 16S rRNA amplicon and 8 metagenomic observations using remotely sensed environmental parameters to create a system-scale model of marine microbial metabolism for 5904 grid cells (49 km(2)) in the Western English Chanel, across 3 years of weekly averages. Thirteen environmental variables predicted the relative abundance of 24 bacterial Orders and 1715 unique enzyme-encoding genes that encode turnover of 2893 metabolites. The genes' predicted relative abundance was highly correlated (Pearson Correlation 0.72, P-value <10(-6)) with their observed relative abundance in sequenced metagenomes. Predictions of the relative turnover (synthesis or consumption) of CO2 were significantly correlated with observed surface CO2 fugacity. The spatial and temporal variation in the predicted relative abundances of genes coding for cyanase, carbon monoxide and malate dehydrogenase were investigated along with the predicted inter-annual variation in relative consumption or production of ∼3000 metabolites forming six significant temporal clusters. These spatiotemporal distributions could possibly be explained by the co-occurrence of anaerobic and aerobic metabolisms associated with localized plankton blooms or sediment resuspension, which facilitate the presence of anaerobic micro-niches. This predictive model provides a general framework for focusing future sampling and experimental design to relate biogeochemical turnover to microbial ecology.}, }
@article {pmid25071728, year = {2014}, author = {Corno, G and Coci, M and Giardina, M and Plechuk, S and Campanile, F and Stefani, S}, title = {Antibiotics promote aggregation within aquatic bacterial communities.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {297}, pmid = {25071728}, issn = {1664-302X}, abstract = {The release of antibiotics (AB) into the environment poses several threats for human health due to potential development of AB-resistant natural bacteria. Even though the use of low-dose antibiotics has been promoted in health care and farming, significant amounts of AB are observed in aquatic environments. Knowledge on the impact of AB on natural bacterial communities is missing both in terms of spread and evolution of resistance mechanisms, and of modifications of community composition and productivity. New approaches are required to study the response of microbial communities rather than individual resistance genes. In this study a chemostat-based experiment with 4 coexisting bacterial strains has been performed to mimicking the response of a freshwater bacterial community to the presence of antibiotics in low and high doses. Bacterial abundance rapidly decreased by 75% in the presence of AB, independently of their concentration, and remained constant until the end of the experiment. The bacterial community was mainly dominated by Aeromonas hydrophila and Brevundimonas intermedia while the other two strains, Micrococcus luteus and Rhodococcus sp. never exceed 10%. Interestingly, the bacterial strains, which were isolated at the end of the experiment, were not AB-resistant, while reassembled communities composed of the 4 strains, isolated from treatments under AB stress, significantly raised their performance (growth rate, abundance) in the presence of AB compared to the communities reassembled with strains isolated from the treatment without AB. By investigating the phenotypic adaptations of the communities subjected to the different treatments, we found that the presence of AB significantly increased co-aggregation by 5-6 fold. These results represent the first observation of co-aggregation as a successful strategy of AB resistance based on phenotype in aquatic bacterial communities, and can represent a fundamental step in the understanding of the effects of AB in aquatic ecosystems.}, }
@article {pmid25070063, year = {2014}, author = {Volant, A and Bruneel, O and Desoeuvre, A and Héry, M and Casiot, C and Bru, N and Delpoux, S and Fahy, A and Javerliat, F and Bouchez, O and Duran, R and Bertin, PN and Elbaz-Poulichet, F and Lauga, B}, title = {Diversity and spatiotemporal dynamics of bacterial communities: physicochemical and other drivers along an acid mine drainage.}, journal = {FEMS microbiology ecology}, volume = {90}, number = {1}, pages = {247-263}, doi = {10.1111/1574-6941.12394}, pmid = {25070063}, issn = {1574-6941}, mesh = {Arsenic/analysis ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Iron/analysis ; *Mining ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Sulfates/analysis ; *Water Microbiology ; Water Pollutants, Chemical/analysis ; *Water Pollution ; }, abstract = {Deciphering the biotic and abiotic factors that control microbial community structure over time and along an environmental gradient is a pivotal question in microbial ecology. Carnoulès mine (France), which is characterized by acid waters and very high concentrations of arsenic, iron, and sulfate, provides an excellent opportunity to study these factors along the pollution gradient of Reigous Creek. To this end, biodiversity and spatiotemporal distribution of bacterial communities were characterized using T-RFLP fingerprinting and high-throughput sequencing. Patterns of spatial and temporal variations in bacterial community composition linked to changes in the physicochemical conditions suggested that species-sorting processes were at work in the acid mine drainage. Arsenic, temperature, and sulfate appeared to be the most important factors that drove the composition of bacterial communities along this continuum. Time series investigation along the pollution gradient also highlighted habitat specialization for some major members of the community (Acidithiobacillus and Thiomonas), dispersal for Acidithiobacillus, and evidence of extinction/re-thriving processes for Gallionella. Finally, pyrosequencing revealed a broader phylogenetic range of taxa than previous clone library-based diversity. Overall, our findings suggest that in addition to environmental filtering processes, additional forces (dispersal, birth/death events) could operate in AMD community.}, }
@article {pmid25069652, year = {2014}, author = {Domman, D and Collingro, A and Lagkouvardos, I and Gehre, L and Weinmaier, T and Rattei, T and Subtil, A and Horn, M}, title = {Massive expansion of Ubiquitination-related gene families within the Chlamydiae.}, journal = {Molecular biology and evolution}, volume = {31}, number = {11}, pages = {2890-2904}, pmid = {25069652}, issn = {1537-1719}, support = {281633/ERC_/European Research Council/International ; I 1628/FWF_/Austrian Science Fund FWF/Austria ; Y 277/FWF_/Austrian Science Fund FWF/Austria ; 1R01GM097171-01A1/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Secretion Systems/*genetics ; Chlamydiaceae/classification/*genetics/metabolism ; *Evolution, Molecular ; Gene Dosage ; Genetic Variation ; *Genome, Bacterial ; Models, Genetic ; *Multigene Family ; Phylogeny ; Protein Structure, Tertiary ; Ubiquitination/*genetics ; }, abstract = {Gene loss, gain, and transfer play an important role in shaping the genomes of all organisms; however, the interplay of these processes in isolated populations, such as in obligate intracellular bacteria, is less understood. Despite a general trend towards genome reduction in these microbes, our phylogenomic analysis of the phylum Chlamydiae revealed that within the family Parachlamydiaceae, gene family expansions have had pronounced effects on gene content. We discovered that the largest gene families within the phylum are the result of rapid gene birth-and-death evolution. These large gene families are comprised of members harboring eukaryotic-like ubiquitination-related domains, such as F-box and BTB-box domains, marking the largest reservoir of these proteins found among bacteria. A heterologous type III secretion system assay suggests that these proteins function as effectors manipulating the host cell. The large disparity in copy number of members in these families between closely related organisms suggests that nonadaptive processes might contribute to the evolution of these gene families. Gene birth-and-death evolution in concert with genomic drift might represent a previously undescribed mechanism by which isolated bacterial populations diversify.}, }
@article {pmid25062836, year = {2015}, author = {Merbt, SN and Auguet, JC and Blesa, A and Martí, E and Casamayor, EO}, title = {Wastewater treatment plant effluents change abundance and composition of ammonia-oxidizing microorganisms in mediterranean urban stream biofilms.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {66-74}, pmid = {25062836}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Biofilms/*growth &amp; development ; Mediterranean Region ; Nitrosomonas/*metabolism ; Oxidation-Reduction ; Waste Disposal, Fluid/*methods ; Water Purification/*methods ; }, abstract = {Streams affected by wastewater treatment plant (WWTP) effluents are hotspots of nitrification. We analyzed the influence of WWTP inputs on the abundance, distribution, and composition of epilithic ammonia-oxidizing (AO) assemblages in five Mediterranean urban streams by qPCR and amoA gene cloning and sequencing of both archaea (AOA) and bacteria (AOB). The effluents significantly modified stream chemical parameters, and changes in longitudinal profiles of both NH(4)(+) and NO(3)(-) indicated stimulated nitrification activity. WWTP effluents were an allocthonous source of both AOA, essentially from the Nitrosotalea cluster, and mostly of AOB, mainly Nitrosomonas oligotropha, Nitrosomonas communis, and Nitrosospira spp. changing the relative abundance and the natural composition of AO assemblages. Under natural conditions, Nitrososphaera and Nitrosopumilus AOA dominated AO assemblages, and AOB were barely detected. After the WWTP perturbation, epilithic AOB increased by orders of magnitude whereas AOA did not show quantitative changes but a shift in population composition to dominance of Nitrosotalea spp. The foraneous AOB successfully settled in downstream biofilms and probably carried out most of the nitrification activity. Nitrosotalea were only observed downstream and only in biofilms exposed to either darkness or low irradiance. In addition to other potential environmental limitations for AOA distribution, this result suggests in situ photosensitivity as previously reported for Nitrosotalea under laboratory conditions.}, }
@article {pmid25058610, year = {2014}, author = {Siles, JA and Rachid, CT and Sampedro, I and García-Romera, I and Tiedje, JM}, title = {Microbial diversity of a Mediterranean soil and its changes after biotransformed dry olive residue amendment.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e103035}, pmid = {25058610}, issn = {1932-6203}, mesh = {Acidobacteria/classification/genetics/metabolism ; Ascomycota/classification/genetics/metabolism ; Basidiomycota/classification/genetics/metabolism ; Biotransformation ; *Genetic Variation ; Mediterranean Region ; Microbial Consortia/*genetics ; Olea/chemistry/*microbiology ; *Phylogeny ; Proteobacteria/classification/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Soil ; *Soil Microbiology ; Waste Products ; }, abstract = {The Mediterranean basin has been identified as a biodiversity hotspot, about whose soil microbial diversity little is known. Intensive land use and aggressive management practices are degrading the soil, with a consequent loss of fertility. The use of organic amendments such as dry olive residue (DOR), a waste produced by a two-phase olive-oil extraction system, has been proposed as an effective way to improve soil properties. However, before its application to soil, DOR needs a pre-treatment, such as by a ligninolytic fungal transformation, e.g. Coriolopsis floccosa. The present study aimed to describe the bacterial and fungal diversity in a Mediterranean soil and to assess the impact of raw DOR (DOR) and C. floccosa-transformed DOR (CORDOR) on function and phylogeny of soil microbial communities after 0, 30 and 60 days. Pyrosequencing of the 16S rRNA gene demonstrated that bacterial diversity was dominated by the phyla Proteobacteria, Acidobacteria, and Actinobacteria, while 28S-rRNA gene data revealed that Ascomycota and Basidiomycota accounted for the majority of phyla in the fungal community. A Biolog EcoPlate experiment showed that DOR and CORDOR amendments decreased functional diversity and altered microbial functional structures. These changes in soil functionality occurred in parallel with those in phylogenetic bacterial and fungal community structures. Some bacterial and fungal groups increased while others decreased depending on the relative abundance of beneficial and toxic substances incorporated with each amendment. In general, DOR was observed to be more disruptive than CORDOR.}, }
@article {pmid25054627, year = {2014}, author = {Fisher, CK and Mehta, P}, title = {Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e102451}, pmid = {25054627}, issn = {1932-6203}, support = {K25 GM086909/GM/NIGMS NIH HHS/United States ; K25GM086909/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Bacteroides/*genetics ; Bacteroides fragilis/*genetics ; Gastrointestinal Tract/*microbiology ; Humans ; *Linear Models ; Metagenomics/*methods ; Microbial Interactions ; Microbiota/*genetics ; Time Factors ; }, abstract = {Human associated microbial communities exert tremendous influence over human health and disease. With modern metagenomic sequencing methods it is now possible to follow the relative abundance of microbes in a community over time. These microbial communities exhibit rich ecological dynamics and an important goal of microbial ecology is to infer the ecological interactions between species directly from sequence data. Any algorithm for inferring ecological interactions must overcome three major obstacles: 1) a correlation between the abundances of two species does not imply that those species are interacting, 2) the sum constraint on the relative abundances obtained from metagenomic studies makes it difficult to infer the parameters in timeseries models, and 3) errors due to experimental uncertainty, or mis-assignment of sequencing reads into operational taxonomic units, bias inferences of species interactions due to a statistical problem called "errors-in-variables". Here we introduce an approach, Learning Interactions from MIcrobial Time Series (LIMITS), that overcomes these obstacles. LIMITS uses sparse linear regression with boostrap aggregation to infer a discrete-time Lotka-Volterra model for microbial dynamics. We tested LIMITS on synthetic data and showed that it could reliably infer the topology of the inter-species ecological interactions. We then used LIMITS to characterize the species interactions in the gut microbiomes of two individuals and found that the interaction networks varied significantly between individuals. Furthermore, we found that the interaction networks of the two individuals are dominated by distinct "keystone species", Bacteroides fragilis and Bacteroided stercosis, that have a disproportionate influence on the structure of the gut microbiome even though they are only found in moderate abundance. Based on our results, we hypothesize that the abundances of certain keystone species may be responsible for individuality in the human gut microbiome.}, }
@article {pmid25052383, year = {2015}, author = {Olapade, OA and Ronk, AJ}, title = {Isolation, characterization and community diversity of indigenous putative toluene-degrading bacterial populations with catechol-2,3-dioxygenase genes in contaminated soils.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {59-65}, pmid = {25052383}, issn = {1432-184X}, mesh = {Actinobacteria/classification/enzymology/genetics ; Bacillus/classification/enzymology/genetics ; Biodegradation, Environmental ; Catechol 2,3-Dioxygenase/genetics/*metabolism ; Proteobacteria/classification/enzymology/genetics ; Pseudomonas/classification/enzymology/genetics ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Toluene ; }, abstract = {Indigenous bacterial assemblages with putative hydrocarbon-degrading capabilities were isolated, characterized and screened for the presence of the catechol-2,3-dioxygenase (C23O) gene after exposure to toluene in two different (i.e., pristine and conditioned) soil communities. The indigenous bacterial populations were exposed to the hydrocarbon substrate by the addition of toluene concentrations, ranging from 0.5 % to 10 % V/W in 10 g of each soil and incubated at 30 °C for upwards of 12 days. In total, 25 isolates (11 in pristine soil and 14 in conditioned soil) were phenotypically characterized according to standard microbiological methods and also screened for the 238-bp C23O gene fragment. Additionally, 16S rRNA analysis of the isolates identified some of them as belonging to the genera Bacillus, Exiguobacterium, Enterobacter, Pseudomonas and Stenotrophomonas. Furthermore, the two clone libraries that were constructed from these toluene-contaminated soils also revealed somewhat disparate phylotypes (i.e., 70 % Actinobacteria and Firmicutes to 30 % Proteobacteria in conditioned soil, whereas in pristine soil: 66 % Actinobacteria and Firmicutes; 21 % Proteobacteria and 13 % Bacteroidetes). The differences observed in bacterial phylotypes between these two soil communities may probably be associated with previous exposure to hydrocarbon sources by indigenous populations in the conditioned soil as compared to the pristine soil.}, }
@article {pmid25049463, year = {2014}, author = {Mir, BA and Mir, SA and Koul, S}, title = {In vitro propagation and withaferin A production in Withania ashwagandha, a rare medicinal plant of India.}, journal = {Physiology and molecular biology of plants : an international journal of functional plant biology}, volume = {20}, number = {3}, pages = {357-364}, pmid = {25049463}, issn = {0971-5894}, abstract = {Withania ashwagandha, belonging to the family Solanaceae, is an important medicinal herb of India with restricted geographic distribution. It is a rich source of withaferin A (WA) and other bioactive withanolides. In the present study a rapid in vitro mass propagation protocol of W. ashwagandha was developed from nodal explants. Nodal explants were cultured on MS medium supplemented with various concentrations and combinations of plant growth regulators (PGRs). The highest number of regenerated shoots per ex-plant (33 ± 2.7) and highest WA (13.4 ± 1.15 mg/g of DW) production was obtained on MS medium supplemented with 5.0 μM 6-benzyladenine (BA) and 1.0 μM Kinetin (Kn). In vitro raised shoots were further rooted on half-strength MS medium containing 2.0 μM Indole-3-butyric acid (IBA) and analyzed for WA production. The rooted plantlets when transferred to poly bags in the greenhouse showed 90 % survival frequency. Levels of WA were higher in the in vitro and ex vitro derived shoot and root tissues as compared to field grown mother plants. In an attempt to further maximize WA production, shoot cultures were further grown in liquid MS medium supplemented with 5.0 μM 6-benzyladenine (BA) and 1.0 μM Kinetin (Kn). Root cultures were grown on half strength MS liquid medium fortified with 2.0 μM of IBA. WA production in the liquid cultures was significantly higher compared to the static composition of the same media. This protocol, first of its kind in this plant, can be successfully employed for conservation, proliferation and large-scale production of WA. The regenerated plants can also be used in traditional medicine as an alternative to naturally collected plants.}, }
@article {pmid25046442, year = {2014}, author = {Pan, Y and Cassman, N and de Hollander, M and Mendes, LW and Korevaar, H and Geerts, RH and van Veen, JA and Kuramae, EE}, title = {Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil.}, journal = {FEMS microbiology ecology}, volume = {90}, number = {1}, pages = {195-205}, doi = {10.1111/1574-6941.12384}, pmid = {25046442}, issn = {1574-6941}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; *Fertilizers ; *Grassland ; Metagenomics ; Nitrogen ; Phosphates ; Potassium ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Soil abiotic and biotic interactions govern important ecosystem processes. However, the mechanisms behind these interactions are complex, and the links between specific environmental factors, microbial community structures, and functions are not well understood. Here, we applied DNA shotgun metagenomic techniques to investigate the effect of inorganic fertilizers N, P, K, and NPK on the bacterial community composition and potential functions in grassland soils in a 54-year experiment. Differences in total and available nutrients were found in the treatment soils; interestingly, Al, As, Mg, and Mn contents were variable in N, P, K, and NPK treatments. Bacterial community compositions shifted and Actinobacteria were overrepresented under the four fertilization treatments compared to the control. Redundancy analysis of the soil parameters and the bacterial community profiles showed that Mg, total N, Cd, and Al were linked to community variation. Using correlation analysis, Acidobacteria, Bacteroidetes, and Verrucomicrobia were linked similarly to soil parameters, and Actinobacteria and Proteobacteria were linked separately to different suites of parameters. Surprisingly, we found no fertilizers effect on microbial functional profiles which supports functional redundancy as a mechanism for stabilization of functions during changes in microbial composition. We suggest that functional profiles are more resistant to environmental changes than community compositions in the grassland ecosystem.}, }
@article {pmid25041632, year = {2015}, author = {Lievens, B and Hallsworth, JE and Pozo, MI and Belgacem, ZB and Stevenson, A and Willems, KA and Jacquemyn, H}, title = {Microbiology of sugar-rich environments: diversity, ecology and system constraints.}, journal = {Environmental microbiology}, volume = {17}, number = {2}, pages = {278-298}, doi = {10.1111/1462-2920.12570}, pmid = {25041632}, issn = {1462-2920}, mesh = {Acinetobacter/metabolism ; *Carbohydrate Metabolism ; *Carbohydrates ; Ecology ; Enterococcaceae/metabolism ; *Environment ; Flowers/*microbiology ; Fruit/*microbiology ; Metschnikowia/metabolism ; }, abstract = {Microbial habitats that contain an excess of carbohydrate in the form of sugar are widespread in the microbial biosphere. Depending on the type of sugar, prevailing water activity and other substances present, sugar-rich environments can be highly dynamic or relatively stable, osmotically stressful, and/or destabilizing for macromolecular systems, and can thereby strongly impact the microbial ecology. Here, we review the microbiology of different high-sugar habitats, including their microbial diversity and physicochemical parameters, which act to impact microbial community assembly and constrain the ecosystem. Saturated sugar beet juice and floral nectar are used as case studies to explore the differences between the microbial ecologies of low and higher water-activity habitats respectively. Nectar is a paradigm of an open, dynamic and biodiverse habitat populated by many microbial taxa, often yeasts and bacteria such as, amongst many others, Metschnikowia spp. and Acinetobacter spp., respectively. By contrast, thick juice is a relatively stable, species-poor habitat and is typically dominated by a single, xerotolerant bacterium (Tetragenococcus halophilus). A number of high-sugar habitats contain chaotropic solutes (e.g. ethyl acetate, phenols, ethanol, fructose and glycerol) and hydrophobic stressors (e.g. ethyl octanoate, hexane, octanol and isoamyl acetate), all of which can induce chaotropicity-mediated stresses that inhibit or prevent multiplication of microbes. Additionally, temperature, pH, nutrition, microbial dispersion and habitat history can determine or constrain the microbiology of high-sugar milieux. Findings are discussed in relation to a number of unanswered scientific questions.}, }
@article {pmid25040229, year = {2015}, author = {de Menezes, AB and Prendergast-Miller, MT and Richardson, AE and Toscas, P and Farrell, M and Macdonald, LM and Baker, G and Wark, T and Thrall, PH}, title = {Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters.}, journal = {Environmental microbiology}, volume = {17}, number = {8}, pages = {2677-2689}, doi = {10.1111/1462-2920.12559}, pmid = {25040229}, issn = {1462-2920}, mesh = {Bacteria/genetics/*metabolism ; Carbon/analysis ; Ecological and Environmental Phenomena ; Ecosystem ; Fungi/genetics/*metabolism ; *Microbiota ; Nitrogen/analysis ; Phosphorus/analysis ; Polymorphism, Restriction Fragment Length/genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Network and multivariate statistical analyses were performed to determine interactions between bacterial and fungal community terminal restriction length polymorphisms as well as soil properties in paired woodland and pasture sites. Canonical correspondence analysis (CCA) revealed that shifts in woodland community composition correlated with soil dissolved organic carbon, while changes in pasture community composition correlated with moisture, nitrogen and phosphorus. Weighted correlation network analysis detected two distinct microbial modules per land use. Bacterial and fungal ribotypes did not group separately, rather all modules comprised of both bacterial and fungal ribotypes. Woodland modules had a similar fungal : bacterial ribotype ratio, while in the pasture, one module was fungal dominated. There was no correspondence between pasture and woodland modules in their ribotype composition. The modules had different relationships to soil variables, and these contrasts were not detected without the use of network analysis. This study demonstrated that fungi and bacteria, components of the soil microbial communities usually treated as separate functional groups as in a CCA approach, were co-correlated and formed distinct associations in these adjacent habitats. Understanding these distinct modular associations may shed more light on their niche space in the soil environment, and allow a more realistic description of soil microbial ecology and function.}, }
@article {pmid25040202, year = {2014}, author = {Averill, C}, title = {Divergence in plant and microbial allocation strategies explains continental patterns in microbial allocation and biogeochemical fluxes.}, journal = {Ecology letters}, volume = {17}, number = {10}, pages = {1202-1210}, doi = {10.1111/ele.12324}, pmid = {25040202}, issn = {1461-0248}, mesh = {*Carbon Cycle ; Ecology/methods ; *Ecosystem ; Models, Theoretical ; Plants/*metabolism ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Allocation trade-offs shape ecological and biogeochemical phenomena at local to global scale. Plant allocation strategies drive major changes in ecosystem carbon cycling. Microbial allocation to enzymes that decompose carbon vs. organic nutrients may similarly affect ecosystem carbon cycling. Current solutions to this allocation problem prioritise stoichiometric tradeoffs implemented in plant ecology. These solutions may not maximise microbial growth and fitness under all conditions, because organic nutrients are also a significant carbon resource for microbes. I created multiple allocation frameworks and simulated microbial growth using a microbial explicit biogeochemical model. I demonstrate that prioritising stoichiometric trade-offs does not optimise microbial allocation, while exploiting organic nutrients as carbon resources does. Analysis of continental-scale enzyme data supports the allocation patterns predicted by this framework, and modelling suggests large deviations in soil C loss based on which strategy is implemented. Therefore, understanding microbial allocation strategies will likely improve our understanding of carbon cycling and climate.}, }
@article {pmid25038845, year = {2015}, author = {Smith, JM and Mosier, AC and Francis, CA}, title = {Spatiotemporal relationships between the abundance, distribution, and potential activities of ammonia-oxidizing and denitrifying microorganisms in intertidal sediments.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {13-24}, pmid = {25038845}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Denitrification ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Oxidoreductases/metabolism ; }, abstract = {The primary objective of this study was to gain an understanding of how key microbial communities involved in nitrogen cycling in estuarine sediments vary over a 12-month period. Furthermore, we sought to determine whether changes in the size of these communities are related to, or indicative of, seasonal patterns in fixed nitrogen dynamics in Elkhorn Slough--a small, agriculturally impacted estuary with a direct connection to Monterey Bay. We assessed sediment and pore water characteristics, abundance of functional genes for nitrification (bacterial and archaeal amoA, encoding ammonia monooxygenase subunit A) and denitrification (nirS and nirK, encoding nitrite reductase), and measurements of potential nitrification and denitrification activities at six sites. No seasonality in the abundance of denitrifier or ammonia oxidizer genes was observed. A strong association between potential nitrification activity and the size of ammonia-oxidizing bacterial communities was observed across the estuary. In contrast, ammonia-oxidizing archaeal abundances remained relatively constant in space and time. Unlike many other estuaries, salinity does not appear to regulate the distribution of ammonia-oxidizing communities in Elkhorn Slough. Instead, their distributions appear to be governed over two different time scales. Long-term niche characteristics selected for the gross size of archaeal and bacterial ammonia-oxidizing communities, yet covariation in their abundances between monthly samples suggests that they respond in a similar manner to short-term changes in their environment. Abundances of denitrifier and ammonia oxidizer genes also covaried, but site-specific differences in this relationship suggest differing levels of interaction (or coupling) between nitrification and denitrification.}, }
@article {pmid25038317, year = {2014}, author = {Harvey, E and Heys, J and Gedeon, T}, title = {Quantifying the effects of the division of labor in metabolic pathways.}, journal = {Journal of theoretical biology}, volume = {360}, number = {}, pages = {222-242}, pmid = {25038317}, issn = {1095-8541}, support = {P20 RR024237/RR/NCRR NIH HHS/United States ; R01 AG040020/AG/NIA NIH HHS/United States ; }, mesh = {Adaptation, Biological/*physiology ; Biomass ; Computer Simulation ; Escherichia coli/growth &amp; development/metabolism ; Glucose/metabolism ; Metabolic Networks and Pathways/*physiology ; Microbial Consortia/*physiology ; *Models, Biological ; Species Specificity ; }, abstract = {Division of labor is commonly observed in nature. There are several theories that suggest diversification in a microbial community may enhance stability and robustness, decrease concentration of inhibitory intermediates, and increase efficiency. Theoretical studies to date have focused on proving when the stable co-existence of multiple strains occurs, but have not investigated the productivity or biomass production of these systems when compared to a single 'super microbe' which has the same metabolic capacity. In this work we prove that if there is no change in the growth kinetics or yield of the metabolic pathways when the metabolism is specialized into two separate microbes, the biomass (and productivity) of a binary consortia system is always less than that of the equivalent monoculture. Using a specific example of Escherichia coli growing on a glucose substrate, we find that increasing the growth rates or substrate affinities of the pathways is not sufficient to explain the experimentally observed productivity increase in a community. An increase in pathway efficiency (yield) in specialized organisms provides the best explanation of the observed increase in productivity.}, }
@article {pmid25037265, year = {2014}, author = {Haegeman, B and Sen, B and Godon, JJ and Hamelin, J}, title = {Only Simpson diversity can be estimated accurately from microbial community fingerprints.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {169-172}, pmid = {25037265}, issn = {1432-184X}, mesh = {*Biodiversity ; DNA Fingerprinting ; *Microbial Consortia ; }, abstract = {Lalande et al. (Microb. Ecol. 66(3):647-658, 2013) introduced a promising approach to quantify microbial diversity from fingerprinting profiles. Their analysis is based on extrapolating the abundance of the phylotypes detectable in a fingerprint towards the rare phylotypes of the community. By considering a set of reconstructed communities, Lalande et al. obtained a range of estimates for phylotype richness, Shannon diversity and Simpson diversity. They reported narrow ranges indicating accurate estimation, especially for Shannon and Simpson diversities. Here, we show that a much larger set of reconstructed communities than the one considered by Lalande et al. is consistent with the fingerprint. We find that the estimates for phylotype richness and Shannon diversity vary over orders of magnitude, but that the estimates for Simpson diversity are restricted to a narrow range (around 10 %). We conclude that only Simpson diversity can be estimated accurately from fingerprints.}, }
@article {pmid25037159, year = {2014}, author = {Dossi, FC and da Silva, EP and Cônsoli, FL}, title = {Population dynamics and growth rates of endosymbionts during Diaphorina citri (Hemiptera, Liviidae) ontogeny.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {881-889}, pmid = {25037159}, issn = {1432-184X}, mesh = {Animals ; Betaproteobacteria/genetics/growth &amp; development/*physiology ; DNA, Bacterial/genetics/metabolism ; Female ; Halomonadaceae/genetics/growth &amp; development/*physiology ; Hemiptera/growth &amp; development/*microbiology ; Male ; Nymph/growth &amp; development/microbiology ; Ovum/growth &amp; development/microbiology ; Population Dynamics ; RNA, Ribosomal, 16S/genetics/metabolism ; Real-Time Polymerase Chain Reaction ; *Symbiosis ; Wolbachia/genetics/growth &amp; development/*physiology ; }, abstract = {The infection density of symbionts is among the major parameters to understand their biological effects in host-endosymbionts interactions. Diaphorina citri harbors two bacteriome-associated bacterial endosymbionts (Candidatus Carsonella ruddii and Candidatus Profftella armatura), besides the intracellular reproductive parasite Wolbachia. In this study, the density dynamics of the three endosymbionts associated with the psyllid D. citri was investigated by real-time quantitative PCR (qPCR) at different developmental stages. Bacterial density was estimated by assessing the copy number of the 16S rRNA gene for Carsonella and Profftella, and of the ftsZ gene for Wolbachia. Analysis revealed a continuous growth of the symbionts during host development. Symbiont growth and rate curves were estimated by the Gompertz equation, which indicated a negative correlation between the degree of symbiont-host specialization and the time to achieve the maximum growth rate (t*). Carsonella densities were significantly lower than those of Profftella at all host developmental stages analyzed, even though they both displayed a similar trend. The growth rates of Wolbachia were similar to those of Carsonella, but Wolbachia was not as abundant. Adult males displayed higher symbiont densities than females. However, females showed a much more pronounced increase in symbiont density as they aged if compared to males, regardless of the incorporation of symbionts into female oocytes and egg laying. The increased density of endosymbionts in aged adults differs from the usual decrease observed during host aging in other insect-symbiont systems.}, }
@article {pmid25033448, year = {2014}, author = {Baron, JL and Vikram, A and Duda, S and Stout, JE and Bibby, K}, title = {Shift in the microbial ecology of a hospital hot water system following the introduction of an on-site monochloramine disinfection system.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e102679}, pmid = {25033448}, issn = {1932-6203}, mesh = {Actinobacteria/genetics/growth &amp; development ; Base Sequence ; Biofilms/drug effects/growth &amp; development ; Chloramines/*pharmacology ; Cyanobacteria/genetics/growth &amp; development ; DNA, Bacterial/genetics ; Disinfectants/pharmacology ; Disinfection/*methods ; Drinking Water/*microbiology ; *Hospital Distribution Systems ; Proteobacteria/genetics/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Sanitary Engineering ; Sequence Analysis, DNA ; Tertiary Care Centers ; Water Microbiology ; Water Purification/*methods ; Water Quality ; }, abstract = {Drinking water distribution systems, including premise plumbing, contain a diverse microbiological community that may include opportunistic pathogens. On-site supplemental disinfection systems have been proposed as a control method for opportunistic pathogens in premise plumbing. The majority of on-site disinfection systems to date have been installed in hospitals due to the high concentration of opportunistic pathogen susceptible occupants. The installation of on-site supplemental disinfection systems in hospitals allows for evaluation of the impact of on-site disinfection systems on drinking water system microbial ecology prior to widespread application. This study evaluated the impact of supplemental monochloramine on the microbial ecology of a hospital's hot water system. Samples were taken three months and immediately prior to monochloramine treatment and monthly for the first six months of treatment, and all samples were subjected to high throughput Illumina 16S rRNA region sequencing. The microbial community composition of monochloramine treated samples was dramatically different than the baseline months. There was an immediate shift towards decreased relative abundance of Betaproteobacteria, and increased relative abundance of Firmicutes, Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria and Actinobacteria. Following treatment, microbial populations grouped by sampling location rather than sampling time. Over the course of treatment the relative abundance of certain genera containing opportunistic pathogens and genera containing denitrifying bacteria increased. The results demonstrate the driving influence of supplemental disinfection on premise plumbing microbial ecology and suggest the value of further investigation into the overall effects of premise plumbing disinfection strategies on microbial ecology and not solely specific target microorganisms.}, }
@article {pmid25031424, year = {2014}, author = {Reddy, MS and Prasanna, L and Marmeisse, R and Fraissinet-Tachet, L}, title = {Differential expression of metallothioneins in response to heavy metals and their involvement in metal tolerance in the symbiotic basidiomycete Laccaria bicolor.}, journal = {Microbiology (Reading, England)}, volume = {160}, number = {Pt 10}, pages = {2235-2242}, doi = {10.1099/mic.0.080218-0}, pmid = {25031424}, issn = {1465-2080}, mesh = {*Drug Tolerance ; *Gene Expression Profiling ; Laccaria/*drug effects/genetics/physiology ; Metallothionein/genetics/*metabolism ; Metals, Heavy/*metabolism/toxicity ; Molecular Sequence Data ; Oxidative Stress ; Sequence Analysis, DNA ; }, abstract = {Cysteine-rich peptides such as metallothioneins (MTs) are involved in metal homeostasis and detoxification in many eukaryotes. We report the characterization and expression of two MT genes, LbMT1 and LbMT2 from the ectomycorrhizal fungus Laccaria bicolor under metal stress conditions. LbMT1 and LbMT2 differ with respect to the length of the encoded peptides (58 versus 37 aa, respectively) and also by their expression patterns in response to metals. The expression levels of both LbMT1 and LbMT2 increased as a function of increased external Cu concentration, the expression levels for LbMT2 were always significantly higher compared with those of LbMT1. Only LbMT1, but not LbMT2, responded to Cd supply in the range of 25-100 µM while Zn did not affect the transcription of either LbMT1 or LbMT2. Both genes also responded to oxidative stress, but to a lesser extent compared to their responses to either Cu or Cd stress. Heterologous complementation assays in metal-sensitive yeast mutants indicated that both LbMT1 and LbMT2 encode peptides capable of conferring higher tolerance to both Cu and Cd. The present study identified LbMTs as potential determinants of the response of this mycorrhizal fungus to Cu and Cd stress.}, }
@article {pmid25030226, year = {2014}, author = {Chaudhary, PP and Wright, AD and Brablcová, L and Buriánková, I and Bednařík, A and Rulík, M}, title = {Dominance of Methanosarcinales phylotypes and depth-wise distribution of methanogenic community in fresh water sediments of Sitka stream from Czech Republic.}, journal = {Current microbiology}, volume = {69}, number = {6}, pages = {809-816}, pmid = {25030226}, issn = {1432-0991}, mesh = {*Biota ; Cluster Analysis ; Czech Republic ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; Geologic Sediments/*microbiology ; Methanosarcinales/*isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers ; Sequence Analysis, DNA ; }, abstract = {The variation in the diversity of methanogens in sediment depths from Sitka stream was studied by constructing a 16S rRNA gene library using methanogen-specific primers and a denaturing gradient gel electrophoresis (DGGE)-based approach. A total of nine different phylotypes from the 16S rRNA library were obtained, and all of them were clustered within the order Methanosarcinales. These nine phylotypes likely represent nine new species and at least 5-6 new genera. Similarly, DGGE analysis revealed an increase in the diversity of methanogens with an increase in sediment depth. These results suggest that Methanosarcinales phylotypes might be the dominant methanogens in the sediment from Sitka stream, and the diversity of methanogens increases as the depth increases. Results of the present study will help in making effective strategies to monitor the dominant methanogen phylotypes and methane emissions in the environment.}, }
@article {pmid25027277, year = {2014}, author = {Hatje, E and Neuman, C and Stevenson, H and Bowman, JP and Katouli, M}, title = {Population dynamics of Vibrio and Pseudomonas species isolated from farmed Tasmanian Atlantic salmon (Salmo salar L.): a seasonal study.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {679-687}, pmid = {25027277}, issn = {1432-184X}, mesh = {Animals ; Aquaculture ; Fish Diseases/epidemiology/*microbiology ; Molecular Sequence Data ; Polymerase Chain Reaction/veterinary ; Population Dynamics ; Pseudomonas/classification/*isolation &amp; purification ; Pseudomonas Infections/epidemiology/microbiology/*veterinary ; RNA, Ribosomal, 16S/genetics ; Random Amplified Polymorphic DNA Technique/veterinary ; *Salmo salar ; *Seasons ; Sequence Analysis, DNA/veterinary ; Tasmania/epidemiology ; Vibrio/classification/*isolation &amp; purification ; Vibrio Infections/epidemiology/microbiology/*veterinary ; }, abstract = {Vibrio and Pseudomonas species have been shown to be part of the normal microbiota of Atlantic salmon (Salmo salar L.), with some strains causing disease in fish. The factors affecting their prevalence and persistence in the salmon gut, however, have not been well studied. In this study, we collected 340 Vibrio and 150 Pseudomonas isolates from the hindgut of farmed Tasmanian Atlantic salmon, fed with two commercially available diets. Samples were collected every 6-8 weeks between July 2011 and May 2012. Isolates from selective agar were initially identified using biochemical tests and confirmed using genus-specific primers and 16S ribosomal RNA (16S rRNA) sequencing. Random amplified polymorphic DNA (RAPD) PCR was used to type both Pseudomonas and Vibrio; the latter was further typed using a biochemical fingerprinting method (PhP-RV plates). We observed low species diversity with strains comprising Vibrio ichthyoenteri/Vibrio scophthalmi, Vibrio crassostreae/Vibrio splendidus, Aliivibrio finisterrensis, Photobacterium phosphoreum and Pseudomonas fragi. Out of 340 Vibrio isolates, 238 (70 %) belonged to 21 clonal types and were found predominantly during summer when water temperatures reached 15 to 21 °C. Of these, the four major clonal types were found in multiple samples (70 %). P. fragi, on the other hand, was only found during the colder water temperatures and belonged to 18 clonal types. The presence of both groups of bacteria and their clonal types were independent of the fish diets used, suggesting that the water temperature was the main factor of the prevalence and persistence of these bacteria in the gut of Atlantic salmon.}, }
@article {pmid25027276, year = {2014}, author = {Tian, Y and Gao, L}, title = {Bacterial diversity in the rhizosphere of cucumbers grown in soils covering a wide range of cucumber cropping histories and environmental conditions.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {794-806}, pmid = {25027276}, issn = {1432-184X}, mesh = {Agriculture ; Bacteria/classification/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; *Biodiversity ; China ; Cucumis sativus/growth &amp; development/*microbiology ; *Environment ; Plant Roots/growth &amp; development/microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Rhizosphere microorganisms in soils are important for plant growth. However, the importance of rhizosphere microorganisms is still underestimated since many microorganisms associated with plant roots cannot be cultured and since the microbial diversity in the rhizosphere can be influenced by several factors, such as the cropping history, biogeography, and agricultural practice. Here, we characterized the rhizosphere bacterial diversity of cucumber plants grown in soils covering a wide range of cucumber cropping histories and environmental conditions by using pyrosequencing of bacterial 16S rRNA genes. We also tested the effects of compost addition and/or bacterial inoculation on the bacterial diversity in the rhizosphere. We identified an average of approximately 8,883 reads per sample, corresponding to around 4,993 molecular operational taxonomic units per sample. The Proteobacteria was the most abundant phylum in almost all soils. The abundances of the phyla Bacteroidetes, Actinobacteria, Firmicutes, Acidobacteria, and Verrucomicrobia varied among the samples, and together with Proteobacteria, these phyla were the six most abundant phyla in almost all analyzed samples. Analyzing all the sample libraries together, the predominant genera found were Flavobacterium, Ohtaekwangia, Opitutus, Gp6, Steroidobacter, and Acidovorax. Overall, compost and microbial amendments increased shoot biomass when compared to untreated soils. However, compost addition decreased the bacterial α-diversity in most soils (but for three soils compost increased diversity), and no statistical effect of microbial amendment on the bacterial α-diversity was found. Moreover, soil amendments did not significantly influence the bacterial β-diversity. Soil organic content appeared more important than compost and microbial amendments in shaping the structure of bacterial communities in the rhizosphere of cucumber.}, }
@article {pmid25027275, year = {2014}, author = {Gümral, R and Tümgör, A and Saraçlı, MA and Yıldıran, &#x15e;T and Ilkit, M and de Hoog, GS}, title = {Black yeast diversity on creosoted railway sleepers changes with ambient climatic conditions.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {699-707}, pmid = {25027275}, issn = {1432-184X}, mesh = {Altitude ; *Biodiversity ; *Climate ; Creosote/chemistry ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Exophiala/genetics/*physiology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; *Railroads ; Sequence Analysis, DNA ; Turkey ; Wood/*microbiology ; }, abstract = {The environmental isolation of opportunistic pathogenic black yeasts, which are responsible for a wide spectrum of human infections, is essential to understanding the ecology of clinical fungi. Extreme outdoor environments polluted with aromatic hydrocarbons support the growth of black yeasts in unlikely places, such as railway sleepers. However, there are limited data concerning the diversity of these fungi growing on polluted railway sleepers. In this investigation, we examined 845 railway sleeper samples, obtained from 11 Turkish cities representing altitudes from 25 to 1,893 m, and inoculated the samples onto mycological media for the isolation of black yeasts. Ninety-four samples (11.1 %) yielded positive results for black yeast, with creosoted oak sleepers having a significantly higher number of isolates than concrete sleepers (p < 0.05). Identification based on the ribosomal DNA (rDNA) internal transcribed spacer region revealed the highest prevalence of Exophiala phaeomuriformis, followed by Exophiala dermatitidis, Exophiala heteromorpha, Exophiala xenobiotica, and Exophiala crusticola. This study revealed that railway sleepers harboring black yeasts were predominantly (>75 %) populated with thermophilic species. We observed that altitude might have a significant effect on species diversity. Briefly, E. phaeomuriformis exhibited growth over a wide altitude range, from 30 to 1,893 m. In contrast, E. dermatitidis had a remarkable aversion to low altitudes and exhibited maximum growth at 1,285 m. In conclusion, we speculate that one can predict what species will be found on railway sleepers and their probability and that species diversity primarily depends on sleeper type and altitude height. We believe that this study can contribute new insights into the ecology of black yeasts on railway sleepers and the railway factors that influence their diversity.}, }
@article {pmid25026064, year = {2014}, author = {Martens, EC and Kelly, AG and Tauzin, AS and Brumer, H}, title = {The devil lies in the details: how variations in polysaccharide fine-structure impact the physiology and evolution of gut microbes.}, journal = {Journal of molecular biology}, volume = {426}, number = {23}, pages = {3851-3865}, pmid = {25026064}, issn = {1089-8638}, support = {K01 DK084214/DK/NIDDK NIH HHS/United States ; R01 GM099513/GM/NIGMS NIH HHS/United States ; DK084214/DK/NIDDK NIH HHS/United States ; GM099513/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*drug effects/growth &amp; development/*metabolism ; Diet/*methods ; Gastrointestinal Tract/*microbiology ; Humans ; Microbiota/*drug effects ; Polysaccharides/*chemistry/*metabolism ; }, abstract = {The critical importance of gastrointestinal microbes to digestion of dietary fiber in humans and other mammals has been appreciated for decades. Symbiotic microorganisms expand mammalian digestive physiology by providing an armament of diverse polysaccharide-degrading enzymes, which are largely absent in mammalian genomes. By out-sourcing this aspect of digestive physiology to our gut microbes, we maximize our ability to adapt to different carbohydrate nutrients on timescales as short as several hours due to the ability of the gut microbial community to rapidly alter its physiology from meal to meal. Because of their ability to pick up new traits by lateral gene transfer, our gut microbes also enable adaption over time periods as long as centuries and millennia by adjusting their gene content to reflect cultural dietary trends. Despite a vast amount of sequence-based insight into the metabolic potential of gut microbes, the specific mechanisms by which symbiotic gut microorganisms recognize and attack complex carbohydrates remain largely undefined. Here, we review the recent literature on this topic and posit that numerous, subtle variations in polysaccharides diversify the spectrum of available nutrient niches, each of which may be best filled by a subset of microorganisms that possess the corresponding proteins to recognize and degrade different carbohydrates. Understanding these relationships at precise mechanistic levels will be essential to obtain a complete understanding of the forces shaping gut microbial ecology and genomic evolution, as well as devising strategies to intentionally manipulate the composition and physiology of the gut microbial community to improve health.}, }
@article {pmid25025156, year = {2014}, author = {Dong, J and Shi, F and Li, H and Zhang, X and Hu, X and Gong, J}, title = {SSU rDNA sequence diversity and seasonally differentiated distribution of nanoplanktonic ciliates in neritic Bohai and Yellow Seas as revealed by T-RFLP.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e102640}, pmid = {25025156}, issn = {1932-6203}, mesh = {Ciliophora/*genetics ; DNA, Protozoan/*genetics ; DNA, Ribosomal/*genetics ; Oceans and Seas ; Phylogeny ; Plankton/genetics ; Polymorphism, Restriction Fragment Length ; Ribosome Subunits, Small, Eukaryotic/*genetics ; }, abstract = {Nanociliates have been frequently found to be important players in the marine microbial loop, however, little is known about their diversity and distribution in coastal ecosystems. We investigated the molecular diversity and distribution patterns of nanoplanktonic oligotrich and choreotrich (OC) ciliates in surface water of three neritic basins of northern China, the South Yellow Sea (SYS), North Yellow Sea (NYS), and Bohai Sea (BS) in June and November 2011. SSU rRNA gene clone libraries generated from three summertime samples (sites B38, B4 and H8) were analyzed and revealed a large novel ribotype diversity, of which many were low-abundant phylotypes belonging to the subclass Oligotrichia, but divergent from described morphospecies. Based on the data of terminal-restriction fragment length polymorphism (T-RFLP) analysis of all 35 samples, we found that the T-RF richness was generally higher in the SYS than in the BS, and negatively correlated with the molar ratio of P to Si. Overall, multidimensional scaling and permutational multivariate analysis of variance of the community turnover demonstrated a distinct seasonal pattern but no basin-to-basin differentiation across all samples. Nevertheless, significant community differences among basins were recognized in the winter dataset. Mantel tests showed that the environmental factors, P:Si ratio, water temperature and concentration of dissolved oxygen (DO), determined the community across all samples. However, both biogeographic distance and environment shaped the community in winter, with DO being the most important physicochemical factor. Our results indicate that the stoichiometric ratio of P:Si is a key factor, through which the phytoplankton community may be shaped, resulting in a cascade effect on the diversity and community composition of OC nanociliates in the N-rich, Si-limited coastal surface waters, and that the Yellow Sea Warm Current drives the nanociliate community, and possibly the microbial food webs, in the coastal ecosystem in winter.}, }
@article {pmid25015888, year = {2014}, author = {Lin, XB and Gänzle, MG}, title = {Effect of lineage-specific metabolic traits of Lactobacillus reuteri on sourdough microbial ecology.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {18}, pages = {5782-5789}, pmid = {25015888}, issn = {1098-5336}, mesh = {Animals ; DNA, Bacterial/chemistry/genetics ; Fermentation ; *Food Microbiology ; Gene Deletion ; Glutamate Decarboxylase/genetics/metabolism ; Humans ; Hydro-Lyases/genetics/metabolism ; Limosilactobacillus reuteri/enzymology/*growth &amp; development/isolation &amp; purification/*metabolism ; Molecular Sequence Data ; Rodentia ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {This study determined the effects of specific metabolic traits of Lactobacillus reuteri on its competitiveness in sourdoughs. The competitiveness of lactobacilli in sourdough generally depends on their growth rate; acid resistance additionally contributes to competitiveness in sourdoughs with long fermentation times. Glycerol metabolism via glycerol dehydratase (gupCDE) accelerates growth by the regeneration of reduced cofactors; glutamate metabolism via glutamate decarboxylase (gadB) increases acid resistance by generating a proton motive force. Glycerol and glutamate metabolisms are lineage-specific traits in L. reuteri; therefore, this study employed glycerol dehydratase-positive sourdough isolates of human-adapted L. reuteri lineage I, glutamate decarboxylase-positive strains of rodent-adapted L. reuteri lineage II, as well as mutants with deletions in gadB or gupCDE. The competitivenesses of the strains were quantified by inoculation of wheat and sorghum sourdoughs with defined strains, followed by propagation of doughs with a 10% inoculum and 12-h or 72-h fermentation cycles. Lineage I L. reuteri strains dominated sourdoughs propagated with 12-h fermentation cycles; lineage II L. reuteri strains dominated sourdoughs propagated with 72-h fermentation cycles. L. reuteri 100-23ΔgadB was outcompeted by its wild-type strain in sourdoughs fermented with 72-h fermentation cycles; L. reuteri FUA3400ΔgupCDE was outcompeted by its wild-type strain in sourdoughs fermented with both 12-h and 72-h fermentation cycles. Competition experiments with isogenic pairs of strains resulted in a constant rate of strain displacement of the less competitive mutant strain. In conclusion, lineage-specific traits of L. reuteri determine the competitiveness of this species in sourdough fermentations.}, }
@article {pmid25012965, year = {2014}, author = {Smalla, K and Tiedje, JM}, title = {Editorial overview: Ecology and industrial microbiology.}, journal = {Current opinion in microbiology}, volume = {19}, number = {}, pages = {v-vii}, doi = {10.1016/j.mib.2014.06.011}, pmid = {25012965}, issn = {1879-0364}, mesh = {*Ecology ; *Industrial Microbiology ; }, }
@article {pmid25012901, year = {2015}, author = {Mason, MR and Preshaw, PM and Nagaraja, HN and Dabdoub, SM and Rahman, A and Kumar, PS}, title = {The subgingival microbiome of clinically healthy current and never smokers.}, journal = {The ISME journal}, volume = {9}, number = {1}, pages = {268-272}, pmid = {25012901}, issn = {1751-7370}, support = {R01 DE022579/DE/NIDCR NIH HHS/United States ; T32 DE014320/DE/NIDCR NIH HHS/United States ; }, mesh = {Dental Plaque/microbiology ; Female ; Gingiva/*microbiology ; Gingivitis/*microbiology ; Gram-Negative Anaerobic Bacteria/classification/genetics/*isolation &amp; purification ; Humans ; *Microbiota ; Phylogeny ; *Smoking ; }, abstract = {Dysbiotic oral bacterial communities have a critical role in the etiology and progression of periodontal diseases. The goal of this study was to investigate the extent to which smoking increases risk for disease by influencing the composition of the subgingival microbiome in states of clinical health. Subgingival plaque samples were collected from 200 systemically and periodontally healthy smokers and nonsmokers. 16S pyrotag sequencing was preformed generating 1,623,713 classifiable sequences, which were compared with a curated version of the Greengenes database using the quantitative insights into microbial ecology pipeline. The subgingival microbial profiles of smokers and never-smokers were different at all taxonomic levels, and principal coordinate analysis revealed distinct clustering of the microbial communities based on smoking status. Smokers demonstrated a highly diverse, pathogen-rich, commensal-poor, anaerobic microbiome that is more closely aligned with a disease-associated community in clinically healthy individuals, suggesting that it creates an at-risk-for-harm environment that is primed for a future ecological catastrophe.}, }
@article {pmid25008985, year = {2014}, author = {Stroobants, A and Degrune, F and Olivier, C and Muys, C and Roisin, C and Colinet, G and Bodson, B and Portetelle, D and Vandenbol, M}, title = {Diversity of bacterial communities in a profile of a winter wheat field: known and unknown members.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {822-833}, pmid = {25008985}, issn = {1432-184X}, mesh = {Bacteria/*genetics/isolation &amp; purification ; Belgium ; *Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; *Microbiota ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; *Seasons ; Soil/*chemistry ; *Soil Microbiology ; Triticum/growth &amp; development/*microbiology ; }, abstract = {In soils, bacteria are very abundant and diverse. They are involved in various agro-ecosystem processes such as the nitrogen cycle, organic matter degradation, and soil formation. Yet, little is known about the distribution and composition of bacterial communities through the soil profile, particularly in agricultural soils, as most studies have focused only on topsoils or forest and grassland soils. In the present work, we have used bar-coded pyrosequencing analysis of the V3 region of the 16S rRNA gene to analyze bacterial diversity in a profile (depths 10, 25, and 45 cm) of a well-characterized field of winter wheat. Taxonomic assignment was carried out with the Ribosomal Database Project (RDP) Classifier program with three bootstrap scores: a main run at 0.80, a confirmation run at 0.99, and a run at 0 to gain information on the unknown bacteria. Our results show that biomass and bacterial quantity and diversity decreased greatly with depth. Depth also had an impact, in terms of relative sequence abundance, on 81 % of the most represented taxonomic ranks, notably the ranks Proteobacteria, Bacteroidetes, Actinobacteridae, and Acidobacteria. Bacterial community composition differed more strongly between the topsoil (10 and 25 cm) and subsoil (45 cm) than between levels in the topsoil, mainly because of shifts in the carbon, nitrogen, and potassium contents. The subsoil also contained more unknown bacteria, 53.96 % on the average, than did the topsoil, with 42.06 % at 10 cm and 45.59 % at 25 cm. Most of these unknown bacteria seem to belong to Deltaproteobacteria, Actinobacteria, Rhizobiales, and Acidobacteria.}, }
@article {pmid25008984, year = {2014}, author = {Yang, Y and Wang, J and Liao, J and Xie, S and Huang, Y}, title = {Distribution of naphthalene dioxygenase genes in crude oil-contaminated soils.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {785-793}, pmid = {25008984}, issn = {1432-184X}, mesh = {Bacteria/classification/*enzymology/*genetics/isolation &amp; purification ; Bacterial Proteins/*genetics ; China ; Dioxygenases/*genetics ; Molecular Sequence Data ; Multienzyme Complexes/*genetics ; Petroleum/analysis ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; Soil Pollutants/analysis ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are one of the major pollutants in soils in oil exploring areas. Biodegradation is the major process for natural elimination of PAHs from contaminated soils. Functional genes can be used as biomarkers to assess the biodegradation potential of indigenous microbial populations. However, little is known about the distribution of PAH-degrading genes in the environment. The links between environmental parameters and the distribution of PAH metabolic genes remain essentially unclear. The present study investigated the abundance and diversity of naphthalene dioxygenase genes in the oil-contaminated soils in the Shengli Oil Field (China). Spatial variations in the density and diversity of naphthalene dioxygenase genes occurred in this area. Four different sequence genotypes were observed in the contaminated soils, with the predominance of novel PAH-degrading genes. Pearson's correlation analysis illustrated that gene abundance had positive correlations with the levels of total organic carbon and aromatic hydrocarbons, while gene diversity showed a negative correlation with the level of polar aromatics. This work could provide some new insights toward the distribution of PAH metabolic genes and PAH biodegradation potential in oil-contaminated ecosystems.}, }
@article {pmid25008983, year = {2014}, author = {Lu, XM and Lu, PZ}, title = {Effects of farmhouse hotel and paper mill effluents on bacterial community structures in sediment and surface water of Nanxi River, China.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {773-784}, pmid = {25008983}, issn = {1432-184X}, mesh = {Agriculture ; Bacteria/*drug effects ; China ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; Environmental Monitoring ; Geologic Sediments/*microbiology ; Industrial Waste/adverse effects ; Molecular Sequence Data ; Multiplex Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; *Water Microbiology ; Water Pollutants, Chemical/*toxicity ; }, abstract = {The pyrosequencing technique was used to evaluate bacterial community structures in sediment and surface water samples taken from Nanxi River receiving effluents from a paper mill and a farmhouse hotel, respectively. For each sample, 4,610 effective bacterial sequences were selected and used to do the analysis of diversity and abundance, respectively. Bacterial phylotype richness in the sediment sample without effluent input was higher than the other samples, and the surface water sample with addition of effluent from the paper mill contained the least richness. Effluents from both the paper mill and farmhouse hotel have a potential to reduce the bacterial diversity and abundance in the sediment and surface water, especially it is more significant in the sediment. The effect of the paper mill effluent on the sediment and surface water bacterial communities was more serious than that of the farmhouse hotel effluent. Characterization of microbial community structures in the sediment and surface water from two tributaries of the downstream river indicated that various effluents from the paper mill and farmhouse hotel have the similar potential to decrease the natural variability in riverine microbial ecosystems.}, }
@article {pmid25008982, year = {2014}, author = {Baptista, MS and Vasconcelos, VM and Vasconcelos, MT}, title = {Trace metal concentration in a temperate freshwater reservoir seasonally subjected to blooms of toxin-producing cyanobacteria.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {671-678}, pmid = {25008982}, issn = {1432-184X}, mesh = {*Eutrophication ; Geologic Sediments/*chemistry ; Lakes/*chemistry ; Metals, Heavy/*analysis ; Microcystis/*physiology ; Portugal ; Seasons ; Spectrophotometry, Atomic ; Water Pollutants, Chemical/*analysis ; }, abstract = {In situ interactions between cyanobacteria and metals were studied at Torrão reservoir (Tâmega River, North Portugal). The metal content of water and sediments from the reservoir was monitored monthly at Marco de Canaveses (seasonally subjected to toxic blooms of Microcystis aeruginosa) and upstream at Amarante (no blooms recorded), for 16 months. During the 16 months of the study period, M. aeruginosa bloomed twice at Marco de Canaveses, firstly forming a scum, and later with colonies scattered throughout the reservoir. Metals Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb and Zn were analysed in the sediment and in the water column. Cu-binding ligands in water were also determined. When no blooms were taking place, average metal levels for water and sediment were not statistically different at both locations. Therefore, it was considered that the absence of cyanobacteria blooms at Amarante was not due to differences in metal content. When blooms were taking place at Marco de Canaveses, a significant increase of metal levels in the sediment occurred simultaneously. Sediment quality guidelines showed that during this period, Cu and Pb concentrations (32.3 and 43.2 mg kg(-1), respectively) were potentially toxic. However, quantification of the exchangeable metal fraction indicated that these metals were probably not bioavailable. Concentration of Cu-binding ligands in water was higher during the blooms, indicating that cyanobacteria are capable of changing the metal speciation in situ in a reservoir.}, }
@article {pmid25008981, year = {2014}, author = {Cinelli, T and Moscetti, I and Marchi, G}, title = {PsasM2I, a type II restriction-modification system in Pseudomonas savastanoi pv. savastanoi: differential distribution of carrier strains in the environment and the evolutionary history of homologous RM systems in the Pseudomonas syringae complex.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {842-858}, pmid = {25008981}, issn = {1432-184X}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; *Biological Evolution ; DNA Restriction-Modification Enzymes/chemistry/*genetics/metabolism ; DNA Transposable Elements ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Molecular Sequence Data ; Nerium/microbiology ; Olea/microbiology ; Organisms, Genetically Modified/genetics ; Phylogeny ; Pseudomonas/*enzymology/*genetics ; }, abstract = {A type II restriction-modification system was found in a native plasmid of Pseudomonas savastanoi pv. savastanoi MLLI2. Functional analysis of the methyltransferase showed that the enzyme acts by protecting the DNA sequence CTGCAG from cleavage. Restriction endonuclease expression in recombinant Escherichia coli cells resulted in mutations in the REase sequence or transposition of insertion sequence 1A in the coding sequence, preventing lethal gene expression. Population screening detected homologous RM systems in other P. savastanoi strains and in the Pseudomonas syringae complex. An epidemiological survey carried out by sampling olive and oleander knots in two Italian regions showed an uneven diffusion of carrier strains, whose presence could be related to a selective advantage in maintaining the RM system in particular environments or subpopulations. Moreover, carrier strains can coexist in the same orchards, plants, and knot tissues with non-carriers, revealing unexpected genetic variability on a very small spatial scale. Phylogenetic analysis of the RM system and housekeeping gene sequences in the P. syringae complex demonstrated the ancient acquisition of the RM systems. However, the evolutionary history of the gene complex also showed the involvement of horizontal gene transfer between related strains and recombination events.}, }
@article {pmid25008542, year = {2014}, author = {Puentes-Téllez, PE and van Elsas, JD}, title = {Sympatric metabolic diversification of experimentally evolved Escherichia coli in a complex environment.}, journal = {Antonie van Leeuwenhoek}, volume = {106}, number = {3}, pages = {565-576}, doi = {10.1007/s10482-014-0228-y}, pmid = {25008542}, issn = {1572-9699}, mesh = {Adaptation, Biological ; Aerobiosis ; *Biological Evolution ; Culture Media/chemistry ; Escherichia coli/*genetics/*metabolism ; *Genetic Variation ; }, abstract = {Sympatric diversification in bacteria has been found to contravene initial evolutionary theories affirming the selection of the fittest type by competition for the same resource. Studies in unstructured (well-mixed) environments have discovered divergence of an ancestor strain into genomically and phenotypically divergent types growing both on single and mixed energy sources. This study addresses the metabolic diversification in an Escherichia coli population that evolved over ~1,000 generations under aerobic conditions in the nutritional complexity offered by Luria-Bertani (LB) broth. The medium lacked glucose but contained a variety of other resources. Two distinct metabolically-diverged types, coinciding with colony morphologies, were found to dominate the populations. One type was an avid carbohydrate consumer, which could quickly utilize the available (alternative) substrates feeding into glycolysis. The second type was a slow grower, which was able to specifically consume acetate. The capacity to utilize acetate might be providing an advantage to this second type, suggesting an increased capability to deal with adverse conditions that occur in the later stages of growth. The diverged metabolic preferences of the two forms suggested differential and interactive ecological roles within the population. We postulate that these types used different alternative metabolic strategies occupying different niches in a sympatric manner as an outcome of adaptation to the complex environment.}, }
@article {pmid25007331, year = {2014}, author = {Noratto, GD and Garcia-Mazcorro, JF and Markel, M and Martino, HS and Minamoto, Y and Steiner, JM and Byrne, D and Suchodolski, JS and Mertens-Talcott, SU}, title = {Carbohydrate-Free Peach (Prunus persica) and Plum (Prunus salicina) [corrected] Juice Affects Fecal Microbial Ecology in an Obese Animal Model.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e101723}, pmid = {25007331}, issn = {1932-6203}, mesh = {Animals ; Anti-Obesity Agents/*administration &amp; dosage ; *Beverages ; Dietary Carbohydrates/administration &amp; dosage ; Fatty Acids/metabolism ; Feces/microbiology ; Male ; Microbiota/*drug effects/genetics ; Obesity/*drug therapy/microbiology ; Plant Extracts/*administration &amp; dosage ; Prunus/*chemistry ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rats, Zucker ; }, abstract = {BACKGROUND: Growing evidence shows the potential of nutritional interventions to treat obesity but most investigations have utilized non-digestible carbohydrates only. Peach and plum contain high amounts of polyphenols, compounds with demonstrated anti-obesity effects. The underlying process of successfully treating obesity using polyphenols may involve an alteration of the intestinal microbiota. However, this phenomenon is not well understood.<br><br>Obese Zucker rats were assigned to three groups (peach, plum, and control, n&#x200a;=&#x200a;10 each), wild-type group was named lean (n&#x200a;=&#x200a;10). Carbohydrates in the fruit juices were eliminated using enzymatic hydrolysis. Fecal samples were obtained after 11 weeks of fruit or control juice administration. Real-time PCR and 454-pyrosequencing were used to evaluate changes in fecal microbiota. Over 1,500 different Operational Taxonomic Units at 97% similarity were detected in all rats. Several bacterial groups (e.g. Lactobacillus and members of Ruminococcacea) were found to be more abundant in the peach but especially in the plum group (plum juice contained 3 times more total polyphenolics compared to peach juice). Principal coordinate analysis based on Unifrac-based unweighted distance matrices revealed a distinct separation between the microbiota of control and treatment groups. These changes in fecal microbiota occurred simultaneously with differences in fecal short-chain acids concentrations between the control and treatment groups as well as a significant decrease in body weight in the plum group.<br><br>CONCLUSIONS: This study suggests that consumption of carbohydrate-free peach and plum juice has the potential to modify fecal microbial ecology in an obese animal model. The separate contribution of polyphenols and non-polyphenols compounds (vitamins and minerals) to the observed changes is unknown.}, }
@article {pmid25007305, year = {2014}, author = {Courtens, EN and Vlaeminck, SE and Vilchez-Vargas, R and Verliefde, A and Jauregui, R and Pieper, DH and Boon, N}, title = {Trade-off between mesophilic and thermophilic denitrification: rates vs. sludge production, settleability and stability.}, journal = {Water research}, volume = {63}, number = {}, pages = {234-244}, doi = {10.1016/j.watres.2014.06.026}, pmid = {25007305}, issn = {1879-2448}, mesh = {*Bioreactors ; *Denitrification ; Nitrogen/*metabolism ; Sewage/*microbiology ; Temperature ; Waste Disposal, Fluid/*methods ; Wastewater/microbiology ; }, abstract = {The development of thermophilic nitrogen removal strategies will facilitate sustainable biological treatment of warm nitrogenous wastewaters. Thermophilic denitrification was extensively compared to mesophilic denitrification for the first time in this study. Two sequential batch reactors (SBR) at 34 °C and 55 °C were inoculated with mesophilic activated sludge (26 °C), fed with synthetic influent in a first phase. Subsequently, the carbon source was switched from acetate to molasses, whereas in a third phase, the nitrate source was fertilizer industry wastewater. The denitrifying sludge maintained its activity at 55 °C, resulting in an immediate process start-up, obtaining nitrogen removal rates higher than 500 mg N g(-1) VSS d(-1) in less than one week. Although the mesophilic SBR showed twice as high specific nitrogen removal rates, the maximum thermophilic denitrifying activity in this study was nearly 10 times higher than the activities reported thus far. The thermophilic SBR moreover had a 73% lower sludge volume index, a 45% lower sludge production and a higher resilience towards a change in carbon source compared with the mesophilic SBR. The higher resilience was potentially related to a higher microbial diversity and evenness of the thermophilic community at the end of the synthetic feeding period. The thermophilic microbial community showed a higher similarity over the different feeding periods implying a more stable community. Overall, this study showed the capability of mesophilic denitrifiers to maintain their activity after a large temperature increase. Existing mesophilic process systems with cooling for the treatment of warm wastewaters could thus efficiently be converted to thermophilic systems with low sludge production and good settling properties.}, }
@article {pmid25006989, year = {2014}, author = {Pallav, K and Dowd, SE and Villafuerte, J and Yang, X and Kabbani, T and Hansen, J and Dennis, M and Leffler, DA and Newburg, DS and Kelly, CP}, title = {Effects of polysaccharopeptide from Trametes versicolor and amoxicillin on the gut microbiome of healthy volunteers: a randomized clinical trial.}, journal = {Gut microbes}, volume = {5}, number = {4}, pages = {458-467}, doi = {10.4161/gmic.29558}, pmid = {25006989}, issn = {1949-0984}, support = {8UL1TR000170-05/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Amoxicillin/*administration &amp; dosage ; Anti-Bacterial Agents/*administration &amp; dosage ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Healthy Volunteers ; Humans ; Male ; Metagenomics ; Microbiota/*drug effects ; Middle Aged ; *Prebiotics ; Proteoglycans/*administration &amp; dosage/isolation &amp; purification ; Trametes/*chemistry ; Young Adult ; }, abstract = {BACKGROUND: Interactions between the microbial flora of the intestine and the human host play a critical role inmaintaining intestinal health and in the pathophysiology of a wide variety of disorders such as antibiotic associated diarrhea, Clostridium difficile infection, and inflammatory bowel disease. Prebiotics can confer health benefits by beneficial effects on the intestinal microbiome, whereas antibiotics can disrupt the microbiome leading to diarrhea andother side effects.<br><br>AIM: To compare the effects of the prebiotic, polysaccharopeptide from Trametes versicolor, to those of the antibiotic,amoxicillin, on the human gut microbiome<br><br>METHODS: Twenty-four healthy volunteers were randomized to receive PSP, amoxicillin, or no treatment (control).Stool specimens were analyzed using bTEFAP microbial ecology methods on seven occasions over 8 weeks from each participant in the active treatment groups and on three occasions for the controls.<br><br>RESULTS: Twenty-two of 24 participants completed the protocol. PSP led to clear and consistent microbiome changes consistent with its activity as a prebiotic. Despite the diversity of the human microbiome we noted strong microbiome clustering among subjects. Baseline microbiomes tended to remain stable and to overshadow the treatment effects.Amoxicillin treatment caused substantial microbiome changes most notably an increase in Escherichia/Shigella. Antibiotic associated changes persisted to the end of the study, 42 days after antibiotic therapy ended.<br><br>CONCLUSIONS: The microbiomes of healthy individuals show substantial diversity but remain stable over time.The antibiotic amoxicillin alters the microbiome and recovery from this disruption can take several weeks. PSP from T. versicolor acts as a prebiotic to modulate human intestinal microbiome composition.}, }
@article {pmid25004997, year = {2014}, author = {Mennerat, A and Sheldon, BC}, title = {How to deal with PCR contamination in molecular microbial ecology.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {834-841}, pmid = {25004997}, issn = {1432-184X}, mesh = {Bacteria/genetics/isolation &amp; purification ; DNA, Bacterial/*analysis ; DNA, Ribosomal Spacer/analysis ; Decontamination/*methods ; Deoxyribonuclease I/metabolism ; Deoxyribonucleases, Type II Site-Specific/metabolism ; Dithiothreitol/metabolism ; Feces/microbiology ; Humans ; Microbiological Techniques/*methods ; Molecular Biology/*methods ; Mouth/microbiology ; *Polymerase Chain Reaction ; Skin/microbiology ; }, abstract = {Microbial ecology studies often use broad-range PCR primers to obtain community profiles. Contaminant microbial DNA present in PCR reagents may therefore be amplified together with template DNA, resulting in unrepeatable data which may be difficult to interpret, especially when template DNA is present at low levels. One possible decontamination method consists in pre-treating PCR mixes with restriction enzymes before heat-inactivating those enzymes prior to the start of the PCR. However, this method has given contrasting results, including a reduction in PCR sensitivity. In this study, we tested the efficiency of two different enzymes (DNase 1 and Sau3AI) as well as the effect of dithiothreitol (DTT), a strong reducing agent, in the decontamination procedure. Our results indicate that enzymatic treatment does reduce contamination levels. However, DNase 1 caused substantial reductions in the bacterial richness found in communities, which we interpret as a result of its incomplete inactivation by heat treatment. DTT did help maintain bacterial richness in mixes treated with DNase 1. No such issues arose when using Sau3AI, which therefore seems a more appropriate enzyme. In our study, four operational taxonomic units (OTU) decreased in frequency and relative abundance after treatment with Sau3AI and hence are likely to represent contaminant bacterial DNA. We found higher within-sample similarity in community structure after treatment with Sau3AI, probably better reflecting the initial bacterial communities. We argue that the presence of contaminant bacterial DNA may have consequences in the interpretation of ecological data, especially when using low levels of template DNA from highly diverse communities. We advocate the use of such decontaminating approaches as a standard procedure in microbial ecology.}, }
@article {pmid25004996, year = {2014}, author = {Xie, Y and Chen, H and Zhu, B and Qin, N and Chen, Y and Li, Z and Deng, M and Jiang, H and Xu, X and Yang, J and Ruan, B and Li, L}, title = {Effect of intestinal microbiota alteration on hepatic damage in rats with acute rejection after liver transplantation.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {871-880}, pmid = {25004996}, issn = {1432-184X}, mesh = {Animal Feed/analysis ; Animals ; Anti-Bacterial Agents/administration &amp; dosage ; Bacteria/*drug effects/genetics/growth &amp; development ; DNA, Bacterial/genetics/metabolism ; Diet ; Dietary Supplements/analysis ; *Graft Rejection ; Intestines/*microbiology ; Liver/*physiopathology ; *Liver Transplantation ; Male ; Microbiota/genetics/physiology ; Molecular Sequence Data ; Phylogeny ; Probiotics/administration &amp; dosage ; RNA, Ribosomal, 16S/genetics/metabolism ; Rats ; Sequence Analysis, DNA ; }, abstract = {The previous studies all focus on the effect of probiotics and antibiotics on infection after liver transplantation. Here, we focus on the effect of gut microbiota alteration caused by probiotics and antibiotics on hepatic damage after allograft liver transplantation. Brown-Norway rats received saline, probiotics, or antibiotics via daily gavage for 3 weeks. Orthotopic liver transplantation (OLT) was carried out after 1 week of gavage. Alteration of the intestinal microbiota, liver function and histopathology, serum and liver cytokines, and T cells in peripheral blood and Peyer's patch were evaluated. Distinct segregation of fecal bacterial diversity was observed in the probiotic group and antibiotic group when compared with the allograft group. As for diversity of intestinal mucosal microbiota and pathology of intestine at 2 weeks after OLT, antibiotics and probiotics had a significant effect on ileum and colon. The population of Lactobacillus and Bifidobacterium in the probiotic group was significantly greater than the antibiotic group and the allograft group. The liver injury was significantly reduced in the antibiotic group and the probiotic group compared with the allograft group. The CD4/CD8 and Treg cells in Peyer's patch were decreased in the antibiotic group. The intestinal Treg cell and serum and liver TGF-β were increased markedly while CD4/CD8 ratio was significantly decreased in the probiotic group. It suggested that probiotics mediate their beneficial effects through increase of Treg cells and TGF-β and deduction of CD4/CD8 in rats with acute rejection (AR) after OLT.}, }
@article {pmid25004995, year = {2014}, author = {Bracewell, RR and Six, DL}, title = {Broadscale specificity in a bark beetle-fungal symbiosis: a spatio-temporal analysis of the mycangial fungi of the western pine beetle.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {859-870}, pmid = {25004995}, issn = {1432-184X}, mesh = {Animals ; Basidiomycota/genetics/isolation &amp; purification/*physiology ; Body Size ; British Columbia ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fungal Proteins/genetics ; Molecular Sequence Data ; Northwestern United States ; Ophiostomatales/genetics/isolation &amp; purification/*physiology ; Seasons ; Sequence Analysis, DNA ; Southwestern United States ; Species Specificity ; Weevils/genetics/*microbiology/physiology ; }, abstract = {Whether and how mutualisms are maintained through ecological and evolutionary time is a seldom studied aspect of bark beetle-fungal symbioses. All bark beetles are associated with fungi and some species have evolved structures for transporting their symbiotic partners. However, the fungal assemblages and specificity in these symbioses are not well known. To determine the distribution of fungi associated with the mycangia of the western pine beetle (Dendroctonus brevicomis), we collected beetles from across the insect's geographic range including multiple genetically distinct populations. Two fungi, Entomocorticium sp. B and Ceratocystiopsis brevicomi, were isolated from the mycangia of beetles from all locations. Repeated sampling at two sites in Montana found that Entomocorticium sp. B was the most prevalent fungus throughout the beetle's flight season, and that females carrying that fungus were on average larger than females carrying C. brevicomi. We present evidence that throughout the flight season, over broad geographic distances, and among genetically distinct populations of beetle, the western pine beetle is associated with the same two species of fungi. In addition, we provide evidence that one fungal species is associated with larger adult beetles and therefore might provide greater benefit during beetle development. The importance and maintenance of this bark beetle-fungus interaction is discussed.}, }
@article {pmid25004994, year = {2014}, author = {Xu, W and Pang, KL and Luo, ZH}, title = {High fungal diversity and abundance recovered in the deep-sea sediments of the Pacific Ocean.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {688-698}, pmid = {25004994}, issn = {1432-184X}, mesh = {Ascomycota/genetics/physiology ; Basidiomycota/genetics/physiology ; *Biodiversity ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fungi/genetics/*physiology ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Pacific Ocean ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Knowledge about the presence and ecological significance of bacteria and archaea in the deep-sea environments has been well recognized, but the eukaryotic microorganisms, such as fungi, have rarely been reported. The present study investigated the composition and abundance of fungal community in the deep-sea sediments of the Pacific Ocean. In this study, a total of 1,947 internal transcribed spacer (ITS) regions of fungal rRNA gene clones were recovered from five sediment samples at the Pacific Ocean (water depths ranging from 5,017 to 6,986 m) using three different PCR primer sets. There were 16, 17, and 15 different operational taxonomic units (OTUs) identified from fungal-universal, Ascomycota-, and Basidiomycota-specific clone libraries, respectively. Majority of the recovered sequences belonged to diverse phylotypes of Ascomycota (25 phylotypes) and Basidiomycota (18 phylotypes). The multiple primer approach totally recovered 27 phylotypes which showed low similarities (≤97 %) with available fungal sequences in the GenBank, suggesting possible new fungal taxa occurring in the deep-sea environments or belonging to taxa not represented in the GenBank. Our results also recovered high fungal LSU rRNA gene copy numbers (3.52 × 10(6) to 5.23 × 10(7)copies/g wet sediment) from the Pacific Ocean sediment samples, suggesting that the fungi might be involved in important ecological functions in the deep-sea environments.}, }
@article {pmid25004993, year = {2014}, author = {Franco, AR and Sousa, NR and Ramos, MA and Oliveira, RS and Castro, PM}, title = {Diversity and persistence of ectomycorrhizal fungi and their effect on nursery-inoculated Pinus pinaster in a post-fire plantation in Northern Portugal.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {761-772}, pmid = {25004993}, issn = {1432-184X}, mesh = {Agricultural Inoculants/physiology ; *Biodiversity ; DNA, Fungal/genetics/metabolism ; DNA, Ribosomal Spacer/genetics/metabolism ; Denaturing Gradient Gel Electrophoresis ; *Fires ; Forestry ; Fungi/*classification/growth &amp; development/*physiology ; Molecular Sequence Data ; Mycorrhizae/growth &amp; development/*physiology ; Phylogeny ; Pinus/growth &amp; development/*microbiology ; Portugal ; Seedlings/growth &amp; development/microbiology ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Ectomycorrhizal fungi (ECMF) play an important role in forest ecosystems, often mitigating stress factors and increasing seedling performance. The aim of this study was to investigate the effects of a nursery inoculation on Pinus pinaster growth and on the fungal communities established when reforesting burned areas. Inoculated P. pinaster saplings showed 1.5-fold higher stem height than the non-inoculated controls after a 5 year growth period, suggesting that fungal inoculation could potentiate tree growth in the field. Ordination analysis revealed the presence of different ECMF communities on both plots. Among the nursery-inoculated fungi, Laccaria sp., Rhizopogon sp., Suillus bovinus and Pisolithus sp. were detected on inoculated Pinus saplings on both sampling periods, indicating that they persisted after field establishment. Other fungi were also detected in the inoculated plants. Phialocephala sp. was found on the first assessment, while Terfezia sp. was detected on both sampling periods. Laccaria sp. and Rhizopogon sp. were identified in the control saplings, belonging however to different species than those found in the inoculated plot. Inocybe sp., Thelephora sp. and Paxillus involutus were present on both sampling periods in the non-inoculated plots. The results suggest that ECMF inoculation at nursery stage can benefit plant growth after transplantation to a post-fire site and that the inoculated fungi can persist in the field. This approach has great potential as a biotechnological tool to aid in the reforestation of burned areas.}, }
@article {pmid25003508, year = {2014}, author = {Boschker, HT and Vasquez-Cardenas, D and Bolhuis, H and Moerdijk-Poortvliet, TW and Moodley, L}, title = {Chemoautotrophic carbon fixation rates and active bacterial communities in intertidal marine sediments.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e101443}, pmid = {25003508}, issn = {1932-6203}, mesh = {*Bacteria/classification/genetics ; Biodiversity ; Carbon/*chemistry ; Geologic Sediments/*chemistry/*microbiology ; Metagenome ; *Microbiota ; Netherlands ; Oxygen/chemistry ; Phylogeny ; }, abstract = {Chemoautotrophy has been little studied in typical coastal marine sediments, but may be an important component of carbon recycling as intense anaerobic mineralization processes in these sediments lead to accumulation of high amounts of reduced compounds, such as sulfides and ammonium. We studied chemoautotrophy by measuring dark-fixation of 13C-bicarbonate into phospholipid derived fatty acid (PLFA) biomarkers at two coastal sediment sites with contrasting sulfur chemistry in the Eastern Scheldt estuary, The Netherlands. At one site where free sulfide accumulated in the pore water right to the top of the sediment, PLFA labeling was restricted to compounds typically found in sulfur and ammonium oxidizing bacteria. At the other site, with no detectable free sulfide in the pore water, a very different PLFA labeling pattern was found with high amounts of label in branched i- and a-PLFA besides the typical compounds for sulfur and ammonium oxidizing bacteria. This suggests that other types of chemoautotrophic bacteria were also active, most likely Deltaproteobacteria related to sulfate reducers. Maximum rates of chemoautotrophy were detected in first 1 to 2 centimeters of both sediments and chemosynthetic biomass production was high ranging from 3 to 36 mmol C m(-2) d(-1). Average dark carbon fixation to sediment oxygen uptake ratios were 0.22±0.07 mol C (mol O2)(-1), which is in the range of the maximum growth yields reported for sulfur oxidizing bacteria indicating highly efficient growth. Chemoautotrophic biomass production was similar to carbon mineralization rates in the top of the free sulfide site, suggesting that chemoautotrophic bacteria could play a crucial role in the microbial food web and labeling in eukaryotic poly-unsaturated PLFA was indeed detectable. Our study shows that dark carbon fixation by chemoautotrophic bacteria is a major process in the carbon cycle of coastal sediments, and should therefore receive more attention in future studies on sediment biogeochemistry and microbial ecology.}, }
@article {pmid25002514, year = {2014}, author = {Hurwitz, BL and Westveld, AH and Brum, JR and Sullivan, MB}, title = {Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {29}, pages = {10714-10719}, pmid = {25002514}, issn = {1091-6490}, mesh = {Bayes Theorem ; *Gene Regulatory Networks ; Genes, Viral ; *Marine Biology ; *Metagenomics ; Microbiota/*genetics ; *Models, Biological ; *Oceans and Seas ; Pacific Ocean ; Seasons ; Viruses/*genetics ; }, abstract = {Long-standing questions in marine viral ecology are centered on understanding how viral assemblages change along gradients in space and time. However, investigating these fundamental ecological questions has been challenging due to incomplete representation of naturally occurring viral diversity in single gene- or morphology-based studies and an inability to identify up to 90% of reads in viral metagenomes (viromes). Although protein clustering techniques provide a significant advance by helping organize this unknown metagenomic sequence space, they typically use only ∼75% of the data and rely on assembly methods not yet tuned for naturally occurring sequence variation. Here, we introduce an annotation- and assembly-free strategy for comparative metagenomics that combines shared k-mer and social network analyses (regression modeling). This robust statistical framework enables visualization of complex sample networks and determination of ecological factors driving community structure. Application to 32 viromes from the Pacific Ocean Virome dataset identified clusters of samples broadly delineated by photic zone and revealed that geographic region, depth, and proximity to shore were significant predictors of community structure. Within subsets of this dataset, depth, season, and oxygen concentration were significant drivers of viral community structure at a single open ocean station, whereas variability along onshore-offshore transects was driven by oxygen concentration in an area with an oxygen minimum zone and not depth or proximity to shore, as might be expected. Together these results demonstrate that this highly scalable approach using complete metagenomic network-based comparisons can both test and generate hypotheses for ecological investigation of viral and microbial communities in nature.}, }
@article {pmid25002435, year = {2014}, author = {Baptista, JD and Lunn, M and Davenport, RJ and Swan, DL and Read, LF and Brown, MR and Morais, C and Curtis, TP}, title = {Agreement between amoA gene-specific quantitative PCR and fluorescence in situ hybridization in the measurement of ammonia-oxidizing bacteria in activated sludge.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {19}, pages = {5901-5910}, pmid = {25002435}, issn = {1098-5336}, mesh = {Ammonia/metabolism ; Bacteria/enzymology/genetics/*isolation &amp; purification ; Betaproteobacteria/enzymology/genetics/isolation &amp; purification ; DNA, Bacterial/chemistry/isolation &amp; purification ; In Situ Hybridization, Fluorescence/*methods ; Linear Models ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Polymerase Chain Reaction/*methods ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Species Specificity ; Waste Disposal, Fluid ; }, abstract = {Microbial abundance is central to most investigations in microbial ecology, and its accurate measurement is a challenging task that has been significantly facilitated by the advent of molecular techniques over the last 20 years. Fluorescence in situ hybridization (FISH) is considered the gold standard of quantification techniques; however, it is expensive and offers low sample throughput, both of which limit its wider application. Quantitative PCR (qPCR) is an alternative that offers significantly higher throughput, and it is used extensively in molecular biology. The accuracy of qPCR can be compromised by biases in the DNA extraction and amplification steps. In this study, we compared the accuracy of these two established quantification techniques to measure the abundance of a key functional group in biological wastewater treatment systems, the ammonia-oxidizing bacteria (AOB), in samples from a time-series experiment monitoring a set of laboratory-scale reactors and a full-scale plant. For the qPCR analysis, we tested two different sets of AOB-specific primers, one targeting the 16SrRNA gene and one targeting the ammonia monooxygenase (amoA) gene. We found that there was a positive linear logarithmic relationship between FISH and the amoA gene-specific qPCR, where the data obtained from both techniques was equivalent at the order of magnitude level. The 16S rRNA gene-specific qPCR assay consistently underestimated AOB numbers.}, }
@article {pmid25002434, year = {2014}, author = {Perrineau, MM and Le Roux, C and Galiana, A and Faye, A and Duponnois, R and Goh, D and Prin, Y and Béna, G}, title = {Differing courses of genetic evolution of Bradyrhizobium inoculants as revealed by long-term molecular tracing in Acacia mangium plantations.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {18}, pages = {5709-5716}, pmid = {25002434}, issn = {1098-5336}, mesh = {Acacia/*microbiology ; Agriculture/methods ; Bradyrhizobium/*classification/*genetics/isolation &amp; purification/physiology ; DNA, Bacterial/chemistry/genetics ; *Evolution, Molecular ; *Genetic Variation ; Malaysia ; Molecular Sequence Data ; Multilocus Sequence Typing ; Senegal ; *Symbiosis ; Time Factors ; }, abstract = {Introducing nitrogen-fixing bacteria as an inoculum in association with legume crops is a common practice in agriculture. However, the question of the evolution of these introduced microorganisms remains crucial, both in terms of microbial ecology and agronomy. We explored this question by analyzing the genetic and symbiotic evolution of two Bradyrhizobium strains inoculated on Acacia mangium in Malaysia and Senegal 15 and 5 years, respectively, after their introduction. Based on typing of several loci, we showed that these two strains, although closely related and originally sampled in Australia, evolved differently. One strain was recovered in soil with the same five loci as the original isolate, whereas the symbiotic cluster of the other strain was detected with no trace of the three housekeeping genes of the original inoculum. Moreover, the nitrogen fixation efficiency was variable among these isolates (either recombinant or not), with significantly high, low, or similar efficiencies compared to the two original strains and no significant difference between recombinant and nonrecombinant isolates. These data suggested that 15 years after their introduction, nitrogen-fixing bacteria remain in the soil but that closely related inoculant strains may not evolve in the same way, either genetically or symbiotically. In a context of increasing agronomical use of microbial inoculants (for biological control, nitrogen fixation, or plant growth promotion), this result feeds the debate on the consequences associated with such practices.}, }
@article {pmid25001595, year = {2014}, author = {Coppens, J and Decostere, B and Van Hulle, S and Nopens, I and Vlaeminck, SE and De Gelder, L and Boon, N}, title = {Kinetic exploration of nitrate-accumulating microalgae for nutrient recovery.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {19}, pages = {8377-8387}, doi = {10.1007/s00253-014-5854-9}, pmid = {25001595}, issn = {1432-0614}, mesh = {Biodegradation, Environmental ; Diatoms/*chemistry/growth &amp; development/*metabolism ; Kinetics ; Microalgae/*chemistry/growth &amp; development/*metabolism ; Nitrates/*metabolism ; Wastewater/analysis ; }, abstract = {Within sustainable resource management, the recovery of nitrogen and phosphorus nutrients from waste streams is becoming increasingly important. Although the use of microalgae has been described extensively in environmental biotechnology, the potential of nitrate-accumulating microalgae for nutrient recovery has not been investigated yet. The ability of these marine microorganisms to concentrate environmental nitrate within their biomass is remarkable. The aim of this study was to investigate the application potential of nitrate-accumulating diatoms for nutrient recovery from marine wastewaters. The intracellular nitrate storage capacity was quantified for six marine diatom strains in synthetic wastewater. Amphora coffeaeformis and Phaeodactylum tricornutum stored the highest amount of nitrate with respectively 3.15 and 2.10 g N L(-1) of cell volume, which accounted for 17.3 and 4.6 %, respectively, of the total nitrogen content. The growth and nitrate and phosphate uptake of both diatoms were further analyzed and based on these features P. tricornutum showed the highest potential for nutrient recovery. A mathematical model was developed which included intracellular nitrate storage and the kinetic parameters were derived for P. tricornutum. Furthermore, a simulation study was performed to compare the performance of a proposed microalgal nutrient recovery unit with a conventional denitrification system for marine wastewater treatment. Overall, this study demonstrates the potential application of P. tricornutum for saline wastewater treatment with concurrent nitrogen and phosphorus recycling.}, }
@article {pmid25001506, year = {2015}, author = {Oliveira, V and Gomes, NC and Almeida, A and Silva, AM and Silva, H and Cunha, &#xc2;}, title = {Microbe-assisted phytoremediation of hydrocarbons in estuarine environments.}, journal = {Microbial ecology}, volume = {69}, number = {1}, pages = {1-12}, pmid = {25001506}, issn = {1432-184X}, mesh = {*Biodegradation, Environmental ; *Estuaries ; Hydrocarbons/*metabolism ; }, abstract = {Estuaries are sinks for various anthropogenic contaminants, such as petroleum hydrocarbons, giving rise to significant environmental concern. The demand for organisms and processes capable of degrading pollutants in a clean, effective, and less expensive process is of great importance. Phytoremedition approaches involving plant/bacteria interactions have been explored as an alternative, and halophyte vegetation has potential for use in phytoremedition of hydrocarbon contamination. Studies with plant species potentially suitable for microbe-assisted phytoremediation are widely represented in scientific literature. However, the in-depth understanding of the biological processes associated with the re-introduction of indigenous bacteria and plants and their performance in the degradation of hydrocarbons is still the limiting step for the application of these bioremediation solutions in a field context. The intent of the present review is to summarize the sources and effects of hydrocarbon contamination in estuarine environments, the strategies currently available for bioremediation (potential and limitations), and the perspectives of the use of halophyte plants in microbe-assisted phytoremediation approaches.}, }
@article {pmid25001226, year = {2014}, author = {Zhao, J and Zhao, X and Chao, L and Zhang, W and You, T and Zhang, J}, title = {Diversity change of microbial communities responding to zinc and arsenic pollution in a river of northeastern China.}, journal = {Journal of Zhejiang University. Science. B}, volume = {15}, number = {7}, pages = {670-680}, pmid = {25001226}, issn = {1862-1783}, mesh = {Arsenic/*analysis ; China ; Denaturing Gradient Gel Electrophoresis ; Geologic Sediments/microbiology ; Rivers/*chemistry/*microbiology ; Water Pollutants, Chemical/*analysis ; Zinc/*analysis ; }, abstract = {Pollution discharge disturbs the natural functions of water systems. The environmental microbial community composition and diversity are sensitive key indicators to the impact of water pollutant on the microbial ecology system over time. It is meaningful to develop a way to identify the microbial diversity related to heavy metal effects in evaluating river pollution. Water and sediment samples were collected from eight sections along the Tiaozi River where wastewater and sewage were discharged from Siping City in northeastern China. The main pollutants contents and microbial communities were analyzed. As the primary metal pollutants, zinc (Zn) and arsenic (As) were recorded at the maximum concentrations of 420 and 5.72 μg/L in the water, and 1704 and 1.92 mg/kg in the sediment, respectively. These pollutants posed a threat to the microbial community diversity as only a few species of bacteria and eukaryotes with strong resistance were detected through denaturing gradient gel electrophoresis (DGGE). Acinetobacter johnsonii, Clostridium cellulovorans, and Trichococcus pasteurii were the dominant bacteria in the severely polluted areas. The massive reproduction of Limnodrilus hoffmeisteri almost depleted the dissolved oxygen (DO) and resulted in the decline of the aerobic bacteria. It was noted that the pollution reduced the microbial diversity but the L. hoffmeisteri mass increased as the dominant community, which led to the overconsuming of DO and anaerobic stinking water bodies. Water quality, concentrations of heavy metals, and the spatial distribution of microbial populations have obvious consistencies, which mean that the heavy metals in the river pose a serious stress on the microorganisms.}, }
@article {pmid24997040, year = {2014}, author = {Sanz, Y and Moya-Pérez, A}, title = {Microbiota, inflammation and obesity.}, journal = {Advances in experimental medicine and biology}, volume = {817}, number = {}, pages = {291-317}, doi = {10.1007/978-1-4939-0897-4_14}, pmid = {24997040}, issn = {0065-2598}, mesh = {Adaptive Immunity ; Animals ; Humans ; Immunity, Innate ; Inflammation/*etiology ; Intestines/microbiology ; Microbiota/*physiology ; Obesity/*complications ; Toll-Like Receptor 2/physiology ; }, abstract = {Interactions between metabolism and immunity play a pivotal role in the development of obesity-associated chronic co-morbidities. Obesity involves impairment of immune function affecting both the innate and adaptive immune system. This leads to increased risk of infections as well as chronic low-grade inflammation, which in turn causes metabolic dysfunction (e.g. insulin resistance) and chronic disease (e.g. type-2 diabetes). Gut microbiota has emerged as one of the key factors regulating early events triggering inflammation associated with obesity and metabolic dysfunction. This effect seems to be related to diet- and obesity-associated changes in gut microbiota composition and to increased translocation of immunogenic bacterial products, which activate innate and adaptive immunity in the gut and beyond, contributing to an increase in inflammatory tone. Innate immune receptors, like Toll-like receptors (TLRs), are known to be up-regulated in the tissue affected by most inflammatory disorders and activated by both specific microbial components and dietary lipids. This triggers several signaling transduction pathways (e.g. JNK and IKKβ/NF-κB), leading to inflammatory cytokine and chemokine (TNF-α, IL-1, MCP1) production and to inflammatory cell recruitment, causing insulin resistance. T-cell differentiation into effector inflammatory or regulatory T cells also depends on the type of TLR activated and on cytokine production, which in turn depends upon gut microbiota-diet interactions. Here, we update and discuss our current understanding of how gut microbiota could contribute to defining whole-body metabolism by influencing diverse components of the innate and adaptive immune system, both locally and systemically.}, }
@article {pmid24995004, year = {2014}, author = {Parfrey, LW and Walters, WA and Lauber, CL and Clemente, JC and Berg-Lyons, D and Teiling, C and Kodira, C and Mohiuddin, M and Brunelle, J and Driscoll, M and Fierer, N and Gilbert, JA and Knight, R}, title = {Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {298}, pmid = {24995004}, issn = {1664-302X}, support = {R01 HG004872/HG/NHGRI NIH HHS/United States ; T32 GM008759/GM/NIGMS NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; }, abstract = {Eukaryotic microbes (protists) residing in the vertebrate gut influence host health and disease, but their diversity and distribution in healthy hosts is poorly understood. Protists found in the gut are typically considered parasites, but many are commensal and some are beneficial. Further, the hygiene hypothesis predicts that association with our co-evolved microbial symbionts may be important to overall health. It is therefore imperative that we understand the normal diversity of our eukaryotic gut microbiota to test for such effects and avoid eliminating commensal organisms. We assembled a dataset of healthy individuals from two populations, one with traditional, agrarian lifestyles and a second with modern, westernized lifestyles, and characterized the human eukaryotic microbiota via high-throughput sequencing. To place the human gut microbiota within a broader context our dataset also includes gut samples from diverse mammals and samples from other aquatic and terrestrial environments. We curated the SILVA ribosomal database to reflect current knowledge of eukaryotic taxonomy and employ it as a phylogenetic framework to compare eukaryotic diversity across environment. We show that adults from the non-western population harbor a diverse community of protists, and diversity in the human gut is comparable to that in other mammals. However, the eukaryotic microbiota of the western population appears depauperate. The distribution of symbionts found in mammals reflects both host phylogeny and diet. Eukaryotic microbiota in the gut are less diverse and more patchily distributed than bacteria. More broadly, we show that eukaryotic communities in the gut are less diverse than in aquatic and terrestrial habitats, and few taxa are shared across habitat types, and diversity patterns of eukaryotes are correlated with those observed for bacteria. These results outline the distribution and diversity of microbial eukaryotic communities in the mammalian gut and across environments.}, }
@article {pmid24994774, year = {2014}, author = {Lee, JC and Kim, SG and Whang, KS}, title = {Novosphingobium aquiterrae sp. nov., isolated from ground water.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {64}, number = {Pt 9}, pages = {3282-3287}, doi = {10.1099/ijs.0.060749-0}, pmid = {24994774}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Groundwater/*microbiology ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; Spermidine/chemistry ; Sphingomonadaceae/*classification/genetics/isolation &amp; purification ; Ubiquinone/chemistry ; }, abstract = {A Gram-staining-negative, strictly aerobic, non-motile, non-spore-forming, yellow and rod-shaped bacterium, designated E-II-3(T), was isolated from ground water at Daejeon in Korea. Strain E-II-3(T) grew between 4 and 45 °C (optimal growth at 28 °C), between pH 6.0 and 9.0 (optimal growth at pH 7.5) and at salinities of 0-2.0 % (w/v) NaCl, growing optimally with 0.5 % (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain E-II-3(T) was shown to belong to the genus Novosphingobium and showed closest phylogenetic similarity to 'Novosphingobium ginsenosidimutans' FW-6 (97.7 %), Novosphingobium aromaticivorans F199(T) (96.9 %) and Novosphingobium subterraneum B0478(T) (96.5 %). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid. The predominant ubiquinone and polyamine components were Q-10 and spermidine, respectively. The major fatty acids were C18 : 1ω7c (34.0 %), C16 : 1ω7c and/or iso-C15 : 0 2-OH (23.8 %) and C17 : 1ω6c (19.3 %). The DNA G+C content of this novel isolate was 62.7 mol%. DNA-DNA relatedness between strain E-II-3(T) and 'N. ginsenosidimutans' KACC 16615, N. aromaticivorans KCTC 2888(T) and N. capsulatum KCTC 22844(T) was 38, 33 and 29 %, respectively. On the basis of polyphasic analysis from this study, strain E-II-3(T) represents a novel species of the genus Novosphingobium for which the name Novosphingobium aquiterrae sp. nov. is proposed. The type strain is E-II-3(T) (= KACC 17599(T) = NBRC 109812(T) = NCAIM B 02537(T)).}, }
@article {pmid24992679, year = {2014}, author = {Dassa, B and Borovok, I and Ruimy-Israeli, V and Lamed, R and Flint, HJ and Duncan, SH and Henrissat, B and Coutinho, P and Morrison, M and Mosoni, P and Yeoman, CJ and White, BA and Bayer, EA}, title = {Rumen cellulosomics: divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e99221}, pmid = {24992679}, issn = {1932-6203}, mesh = {Bacterial Proteins/*genetics/metabolism ; Cellulose/metabolism ; Genome, Bacterial/*physiology ; *Genome-Wide Association Study ; Ruminococcus/classification/*genetics/metabolism ; }, abstract = {BACKGROUND: A complex community of microorganisms is responsible for efficient plant cell wall digestion by many herbivores, notably the ruminants. Understanding the different fibrolytic mechanisms utilized by these bacteria has been of great interest in agricultural and technological fields, reinforced more recently by current efforts to convert cellulosic biomass to biofuels.<br><br>Here, we have used a bioinformatics-based approach to explore the cellulosome-related components of six genomes from two of the primary fiber-degrading bacteria in the rumen: Ruminococcus flavefaciens (strains FD-1, 007c and 17) and Ruminococcus albus (strains 7, 8 and SY3). The genomes of two of these strains are reported for the first time herein. The data reveal that the three R. flavefaciens strains encode for an elaborate reservoir of cohesin- and dockerin-containing proteins, whereas the three R. albus strains are cohesin-deficient and encode mainly dockerins and a unique family of cell-anchoring carbohydrate-binding modules (family 37).<br><br>CONCLUSIONS/SIGNIFICANCE: Our comparative genome-wide analysis pinpoints rare and novel strain-specific protein architectures and provides an exhaustive profile of their numerous lignocellulose-degrading enzymes. This work provides blueprints of the divergent cellulolytic systems in these two prominent fibrolytic rumen bacterial species, each of which reflects a distinct mechanistic model for efficient degradation of cellulosic biomass.}, }
@article {pmid24992459, year = {2014}, author = {Molineux, CJ and Connop, SP and Gange, AC}, title = {Manipulating soil microbial communities in extensive green roof substrates.}, journal = {The Science of the total environment}, volume = {493}, number = {}, pages = {632-638}, doi = {10.1016/j.scitotenv.2014.06.045}, pmid = {24992459}, issn = {1879-1026}, mesh = {Agricultural Inoculants ; Bacteria ; Biomass ; Conservation of Natural Resources/*methods ; Construction Industry ; *Ecosystem ; Fungi ; Soil ; *Soil Microbiology ; }, abstract = {There has been very little investigation into the soil microbial community on green roofs, yet this below ground habitat is vital for ecosystem functioning. Green roofs are often harsh environments that would greatly benefit from having a healthy microbial system, allowing efficient nutrient cycling and a degree of drought tolerance in dry summer months. To test if green roof microbial communities could be manipulated, we added mycorrhizal fungi and a microbial mixture ('compost tea') to green roof rootzones, composed mainly of crushed brick or crushed concrete. The study revealed that growing media type and depth play a vital role in the microbial ecology of green roofs. There are complex relationships between depth and type of substrate and the biomass of different microbial groups, with no clear pattern being observed. Following the addition of inoculants, bacterial groups tended to increase in biomass in shallower substrates, whereas fungal biomass change was dependent on depth and type of substrate. Increased fungal biomass was found in shallow plots containing more crushed concrete and deeper plots containing more crushed brick where compost tea (a live mixture of beneficial bacteria) was added, perhaps due to the presence of helper bacteria for arbuscular mycorrhizal fungi (AMF). Often there was not an additive affect of the microbial inoculations but instead an antagonistic interaction between the added AM fungi and the compost tea. This suggests that some species of microbes may not be compatible with others, as competition for limited resources occurs within the various substrates. The overall results suggest that microbial inoculations of green roof habitats are sustainable. They need only be done once for increased biomass to be found in subsequent years, indicating that this is a novel and viable method of enhancing roof community composition.}, }
@article {pmid24984515, year = {2014}, author = {Zhou, J and Jin, H and Cai, ZH}, title = {[A review of the role and function of microbes in coral reef ecosystem].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {25}, number = {3}, pages = {919-930}, pmid = {24984515}, issn = {1001-9332}, mesh = {Animals ; Anthozoa ; Biodiversity ; Biological Evolution ; *Coral Reefs ; Eutrophication ; Food Chain ; Temperature ; *Water Microbiology ; }, abstract = {Coral reef is consisted with several kinds of reef-associated organisms, including coral, fish, benthos, algae and microbes, which is an important marine ecosystem. Coral reef lives in the oligotrophic environment, has very highly primary productivity and net productivity, and is called "tropical rain forest in ocean". In corals, diverse microorganisms exert a significant influence on biogeochemical and ecological processes, including food webs, organism life cycles, and nutrient cycling. With the development of molecular biology, the role of microorganisms in a coral system is becoming more outstanding. In this article, we reviewed current understanding on 1) the onset of coral-bacterial associations; 2) the characteristics of microbes in coral (specificity, plasticity and co-evolution) ; 3) the role and signal regulation of microbes in the health and disease of coral; and 4) the response mechanism of microbes for global climatic change and consequent effects, such as temperature rise, ocean acidification and eutrophication. The aims of this article were to summarize the latest theories and achievements, clear the mechanism of microbial ecology in coral reefs and provide a theoretical reference for better protection and maintaining the coral's biodiversity.}, }
@article {pmid24984221, year = {2014}, author = {Lin, XB and Gänzle, MG}, title = {Quantitative high-resolution melting PCR analysis for monitoring of fermentation microbiota in sourdough.}, journal = {International journal of food microbiology}, volume = {186}, number = {}, pages = {42-48}, doi = {10.1016/j.ijfoodmicro.2014.06.010}, pmid = {24984221}, issn = {1879-3460}, mesh = {Bacterial Load ; Biodiversity ; Bread/*microbiology ; *Fermentation ; Food Microbiology/*methods ; Lactobacillus/genetics/isolation &amp; purification/*physiology ; Microbiota/genetics/*physiology ; *Polymerase Chain Reaction ; Sensitivity and Specificity ; Sorghum/microbiology ; Triticum/microbiology ; }, abstract = {Current methods of monitoring the microbial ecology of food fermentation system are generally labor intensive and/or time consuming. This study developed two methods based on high-resolution melting curves (HRM) to monitor sourdough microbiota during fermentation and to investigate the effect of cereal substrate on microbial ecology. A strain cocktail of Lactobacillus fermentum FUA3165, Lactobacillus plantarum FUA3309, Lactobacillus paracasei FUA3166 and Lactobacillus reuteri FUA3168 was used to ferment red (Town and PAN8609) and white (commercial and Segaolane) sorghum sourdough, and wheat sourdough. The microbial composition of sourdoughs was determined by plate count and HRM-qPCR to differentiate at the species level. The resistance of each species to sorghum phenolic extract was measured. There was no difference in microbial composition among the four sorghum sourdoughs, with L. fermentum FUA3165 in all sourdoughs. The competiveness of the strains in sorghum sourdoughs corresponded to their resistance to sorghum phenolic extract. In a second experiment, five L. reuteri strains, the human-lineage strains FUA3400 and 3401 isolated from wheat sourdough, the rodent-lineage strain FUA5448 isolated from rye sourdough and the sorghum isolates FUA3168 and 3324, were used to ferment wheat, rye and sorghum sourdoughs. The microbial composition of sourdoughs was determined by plate counts and HRM-qPCR to different L. reuteri strains representing different host-adapted lineages. No difference among different substrates was observed; indicating cereal type had no selective effect on sourdough microbial ecology. In conclusion, HRM-qPCR assays were established as rapid and highly specific tool for monitoring of sourdough microbiota. The ability to distinguish highly similar microbes in samples containing only few genotypes makes HRM-qPCR suitable for quality control in other food fermentation systems. The presence of phenolic compounds in sorghum sourdough favored organisms with higher resistance.}, }
@article {pmid24976459, year = {2015}, author = {Puentes-Téllez, PE and van Elsas, JD}, title = {Differential stress resistance and metabolic traits underlie coexistence in a sympatrically evolved bacterial population.}, journal = {Environmental microbiology}, volume = {17}, number = {3}, pages = {889-900}, doi = {10.1111/1462-2920.12551}, pmid = {24976459}, issn = {1462-2920}, mesh = {Base Sequence ; Biological Evolution ; DNA, Bacterial/genetics ; Ecology ; Escherichia coli/*genetics ; Escherichia coli Proteins/genetics ; Evolution, Molecular ; Genome, Bacterial/*genetics ; Heat-Shock Response/*genetics ; Oxidative Stress/*genetics ; Phenotype ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Transcription Factors/genetics ; }, abstract = {Following intermittent batch growth in Luria-Bertani (LB) broth for about 1000 generations, differentially evolved forms were found in a population of Escherichia coli cells. Studies on this population revealed the emergence of key polymorphisms, as evidenced by analysis of both whole genome sequences and transcription analysis. Here, we investigated the phenotypic nature of several key forms and found a remarkable (interactive) coexistence of forms which highlights the presence of different ecological roles pointing at a dichotomy in: (i) tolerance to environmental stresses and (ii) the capacity to utilize particular carbon sources such as galactose. Both forms differed from their common ancestor by different criteria. This apparent coexistence of two diverged forms points at the occurrence of niche partitioning as a consequence of dichotomous adaptive evolution. Remarkably, the two forms were shown to continue to coexist - in varying ratio's - in an experiment that cycled them through periods of nutrient feast (plentiful growth substrates) and famine (growth-restrictive - stress conditions). The results further indicated that the equilibrium of the coexistence was destroyed when one of the parameters was high tuned, jeopardizing the stability of the coexisting pair.}, }
@article {pmid24974884, year = {2015}, author = {Dray, S and Pavoine, S and Aguirre de Cárcer, D}, title = {Considering external information to improve the phylogenetic comparison of microbial communities: a new approach based on constrained Double Principal Coordinates Analysis (cDPCoA).}, journal = {Molecular ecology resources}, volume = {15}, number = {2}, pages = {242-249}, doi = {10.1111/1755-0998.12300}, pmid = {24974884}, issn = {1755-0998}, mesh = {*Biota ; DNA, Ribosomal/chemistry/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Statistics as Topic ; }, abstract = {The use of next-generation sequencing technologies is revolutionizing microbial ecology by allowing a deep phylogenetic coverage of tens to thousands of samples simultaneously. Double Principal Coordinates Analysis (DPCoA) is a multivariate method, developed in community ecology, able to integrate a distance matrix describing differences among species (e.g. phylogenetic distances) in the analysis of a species abundance matrix. This ordination technique has been used recently to describe microbial communities taking into account phylogenetic relatedness. In this work, we extend DPCoA to integrate the information of external variables measured on communities. The constrained Double Principal Coordinates Analysis (cDPCoA) is able to enforce a priori classifications to retrieve subtle differences and (or) remove the effect of confounding factors. We describe the main principles of this new approach and demonstrate its usefulness by providing application examples based on published 16S rRNA gene data sets.}, }
@article {pmid24972807, year = {2014}, author = {Monteiro, M and Séneca, J and Magalhães, C}, title = {The history of aerobic ammonia oxidizers: from the first discoveries to today.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {52}, number = {7}, pages = {537-547}, pmid = {24972807}, issn = {1976-3794}, mesh = {Ammonia/*metabolism ; Archaea/*isolation &amp; purification/*metabolism ; Bacteria/*isolation &amp; purification/*metabolism ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Microbiology/*history ; Nitrates/metabolism ; *Nitrification ; Nitrites/metabolism ; }, abstract = {Nitrification, the oxidation of ammonia to nitrite and nitrate, has long been considered a central biological process in the global nitrogen cycle, with its first description dated 133 years ago. Until 2005, bacteria were considered the only organisms capable of nitrification. However, the recent discovery of a chemoautotrophic ammonia-oxidizing archaeon, Nitrosopumilus maritimus, changed our concept of the range of organisms involved in nitrification, highlighting the importance of ammonia-oxidizing archaea (AOA) as potential players in global biogeochemical nitrogen transformations. The uniqueness of these archaea justified the creation of a novel archaeal phylum, Thaumarchaeota. These recent discoveries increased the global scientific interest within the microbial ecology society and have triggered an analysis of the importance of bacterial vs archaeal ammonia oxidation in a wide range of natural ecosystems. In this mini review we provide a chronological perspective of the current knowledge on the ammonia oxidation pathway of nitrification, based on the main physiological, ecological and genomic discoveries.}, }
@article {pmid24968108, year = {2014}, author = {Kougias, PG and De Francisci, D and Treu, L and Campanaro, S and Angelidaki, I}, title = {Microbial analysis in biogas reactors suffering by foaming incidents.}, journal = {Bioresource technology}, volume = {167}, number = {}, pages = {24-32}, doi = {10.1016/j.biortech.2014.05.080}, pmid = {24968108}, issn = {1873-2976}, mesh = {Animals ; Bacterial Proteins/metabolism ; Biofuels/*microbiology ; Bioreactors/*microbiology ; Cattle ; Cluster Analysis ; Gases/*chemistry ; Lipids/analysis ; Manure/analysis ; }, abstract = {Foam formation can lead to total failure of digestion process in biogas plants. In the present study, possible correlation between foaming and the presence of specific microorganisms in biogas reactors was elucidated. The microbial ecology of continuous fed digesters overloaded with proteins, lipids and carbohydrates before and after foaming incidents was characterized using 16S rRNA gene sequencing. Moreover, the microbial diversity between the liquid and foaming layer was assessed. A number of genera that are known to produce biosurfactants, contain mycolic acid in their cell wall, or decrease the surface tension of the media, increased their relative abundance after foam formation. Finally, a microorganism similar to widely known foaming bacteria (Nocardia and Desulfotomaculum) was found to increase its relative abundance in all reactors once foam was observed, regardless of the used substrate. These findings suggest that foaming and specific microorganisms might have direct association which requires to be further investigated.}, }
@article {pmid24966854, year = {2014}, author = {Garbeva, P and Hordijk, C and Gerards, S and de Boer, W}, title = {Volatile-mediated interactions between phylogenetically different soil bacteria.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {289}, pmid = {24966854}, issn = {1664-302X}, abstract = {There is increasing evidence that organic volatiles play an important role in interactions between micro-organisms in the porous soil matrix. Here we report that volatile compounds emitted by different soil bacteria can affect the growth, antibiotic production and gene expression of the soil bacterium Pseudomonas fluorescens Pf0-1. We applied a novel cultivation approach that mimics the natural nutritional heterogeneity in soil in which P. fluorescens grown on nutrient-limited agar was exposed to volatiles produced by 4 phylogenetically different bacterial isolates (Collimonas pratensis, Serratia plymuthica, Paenibacillus sp., and Pedobacter sp.) growing in sand containing artificial root exudates. Contrary to our expectation, the produced volatiles stimulated rather than inhibited the growth of P. fluorescens. A genome-wide, microarray-based analysis revealed that volatiles of all four bacterial strains affected gene expression of P. fluorescens, but with a different pattern of gene expression for each strain. Based on the annotation of the differently expressed genes, bacterial volatiles appear to induce a chemotactic motility response in P. fluorescens, but also an oxidative stress response. A more detailed study revealed that volatiles produced by C. pratensis triggered, antimicrobial secondary metabolite production in P. fluorescens. Our results indicate that bacterial volatiles can have an important role in communication, trophic - and antagonistic interactions within the soil bacterial community.}, }
@article {pmid24964200, year = {2014}, author = {Kardas, M and Gozen, AG and Severcan, F}, title = {FTIR spectroscopy offers hints towards widespread molecular changes in cobalt-acclimated freshwater bacteria.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {155}, number = {}, pages = {15-23}, doi = {10.1016/j.aquatox.2014.05.027}, pmid = {24964200}, issn = {1879-1514}, mesh = {Adaptation, Physiological/*drug effects ; Bacillus/*drug effects ; Bacterial Proteins/genetics/metabolism ; Cobalt/*toxicity ; Escherichia coli/*drug effects ; Fresh Water ; Gene Expression Regulation, Bacterial/drug effects ; Lipid Metabolism/drug effects ; Metals, Heavy/toxicity ; Microbial Sensitivity Tests ; Pseudomonas/*drug effects ; *Spectroscopy, Fourier Transform Infrared ; Water Pollutants, Chemical/toxicity ; }, abstract = {High concentrations of heavy metals can be toxic for bacteria. However, after prolonged exposure, bacteria can become acclimated and begin to be able to grow in the presence of heavy metals. Acclimation can involve alterations of metabolism and molecular structures. Our aim was to examine these alterations in cobalt-acclimated bacteria via attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy on viable samples. Bacillus sp. and Pseudomonas sp. isolated from a temperate shallow lake and a well-established strain of E. coli were investigated. Our results revealed consistent, wide-spread changes in cell membrane and cell wall dynamics of Bacillus sp. and E. coli, including a decrease in peptidoglycan content of Bacillus sp. and increased lipid ordering of the membrane in both bacteria. Furthermore, a decrease in RNA and protein concentrations of Bacillus sp. was measured. All three bacteria studied showed a decrease in conformational freedom of proteins following cobalt acclimation. Interestingly, both Bacillus sp. and E. coli showed slight but significant alterations in their DNA conformations which might imply a methylation-mediated memory formation leading to epigenetic modulation for cobalt adaptation.}, }
@article {pmid24955847, year = {2014}, author = {O'Donnell, DR and Parigi, A and Fish, JA and Dworkin, I and Wagner, AP}, title = {The roles of standing genetic variation and evolutionary history in determining the evolvability of anti-predator strategies.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e100163}, pmid = {24955847}, issn = {1932-6203}, mesh = {Animals ; *Evolution, Molecular ; *Food Chain ; *Genetic Variation ; *Models, Biological ; *Software ; }, abstract = {Standing genetic variation and the historical environment in which that variation arises (evolutionary history) are both potentially significant determinants of a population's capacity for evolutionary response to a changing environment. Using the open-ended digital evolution software Avida, we evaluated the relative importance of these two factors in influencing evolutionary trajectories in the face of sudden environmental change. We examined how historical exposure to predation pressures, different levels of genetic variation, and combinations of the two, affected the evolvability of anti-predator strategies and competitive abilities in the presence or absence of threats from new, invasive predator populations. We show that while standing genetic variation plays some role in determining evolutionary responses, evolutionary history has the greater influence on a population's capacity to evolve anti-predator traits, i.e. traits effective against novel predators. This adaptability likely reflects the relative ease of repurposing existing, relevant genes and traits, and the broader potential value of the generation and maintenance of adaptively flexible traits in evolving populations.}, }
@article {pmid24955113, year = {2014}, author = {Jiménez, DJ and Dini-Andreote, F and van Elsas, JD}, title = {Metataxonomic profiling and prediction of functional behaviour of wheat straw degrading microbial consortia.}, journal = {Biotechnology for biofuels}, volume = {7}, number = {}, pages = {92}, pmid = {24955113}, issn = {1754-6834}, abstract = {BACKGROUND: Mixed microbial cultures, in which bacteria and fungi interact, have been proposed as an efficient way to deconstruct plant waste. The characterization of specific microbial consortia could be the starting point for novel biotechnological applications related to the efficient conversion of lignocellulose to cello-oligosaccharides, plastics and/or biofuels. Here, the diversity, composition and predicted functional profiles of novel bacterial-fungal consortia are reported, on the basis of replicated aerobic wheat straw enrichment cultures.<br><br>RESULTS: In order to set up biodegradative microcosms, microbial communities were retrieved from a forest soil and introduced into a mineral salt medium containing 1% of (un)treated wheat straw. Following each incubation step, sequential transfers were carried out using 1 to 1,000 dilutions. The microbial source next to three sequential batch cultures (transfers 1, 3 and 10) were analyzed by bacterial 16S rRNA gene and fungal ITS1 pyrosequencing. Faith's phylogenetic diversity values became progressively smaller from the inoculum to the sequential batch cultures. Moreover, increases in the relative abundances of Enterobacteriales, Pseudomonadales, Flavobacteriales and Sphingobacteriales were noted along the enrichment process. Operational taxonomic units affiliated with Acinetobacter johnsonii, Pseudomonas putida and Sphingobacterium faecium were abundant and the underlying strains were successfully isolated. Interestingly, Klebsiella variicola (OTU1062) was found to dominate in both consortia, whereas K. variicola-affiliated strains retrieved from untreated wheat straw consortia showed endoglucanase/xylanase activities. Among the fungal players with high biotechnological relevance, we recovered members of the genera Penicillium, Acremonium, Coniochaeta and Trichosporon. Remarkably, the presence of peroxidases, alpha-L-fucosidases, beta-xylosidases, beta-mannases and beta-glucosidases, involved in lignocellulose degradation, was indicated by predictive bacterial metagenome reconstruction. Reassuringly, tests for specific (hemi)cellulolytic enzymatic activities, performed on the consortial secretomes, confirmed the presence of such gene functions.<br><br>CONCLUSION: In an in-depth characterization of two wheat straw degrading microbial consortia, we revealed the enrichment and selection of specific bacterial and fungal taxa that were presumably involved in (hemi) cellulose degradation. Interestingly, the microbial community composition was strongly influenced by the wheat straw pretreatment. Finally, the functional bacterial-metagenome prediction and the evaluation of enzymatic activities (at the consortial secretomes) revealed the presence and enrichment of proteins involved in the deconstruction of plant biomass.}, }
@article {pmid24952818, year = {2014}, author = {Maienza, A and Bååth, E}, title = {Temperature effects on recovery time of bacterial growth after rewetting dry soil.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {818-821}, pmid = {24952818}, issn = {1432-184X}, mesh = {Bacteria/*growth &amp; development/metabolism ; Desiccation ; Grassland ; Leucine/metabolism ; Soil/*chemistry ; *Soil Microbiology ; Sweden ; *Temperature ; Water/analysis/*metabolism ; }, abstract = {The effect of temperature on the recovery of bacterial growth after rewetting dry soil was measured in a soil that responded with bacterial growth increasing immediately upon rewetting in a linear fashion (type (i) response sensu Meisner et al. (Soil Biol Biochem 66: 188-192, 2013)). The soil was air-dried for 4 days and then rewetted at different temperatures. Bacterial growth over time was then estimated using the leucine incorporation method. At 25 °C, the recovery of bacterial growth to levels of a wet control soil was rapid, within 6 h, while at 15 °C, recovery time increased to around 60 h, becoming more than a week at 5 °C. The temperature dependency of the recovery time was well modeled by a square root function. Thus, temperature will not only directly affect growth rates but also affect length of transition periods, like resuscitation after a drying event. The temperature during the rewetting event thus has to be taken into consideration when analyzing the microbial response dynamics.}, }
@article {pmid24952731, year = {2014}, author = {Gómez-Sagasti, MT and Becerril, JM and Martín, I and Epelde, L and Garbisu, C}, title = {cDNA microarray assessment of early gene expression profiles in Escherichia coli cells exposed to a mixture of heavy metals.}, journal = {Cell biology and toxicology}, volume = {30}, number = {4}, pages = {207-232}, doi = {10.1007/s10565-014-9281-6}, pmid = {24952731}, issn = {1573-6822}, mesh = {Escherichia coli/drug effects/genetics/*metabolism ; Escherichia coli Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial/*drug effects ; Metals, Heavy/*pharmacology ; Oligonucleotide Array Sequence Analysis ; Transcription, Genetic ; *Transcriptome ; }, abstract = {Many contaminated sites are characterized by the presence of different metals, thus increasing the complexity of toxic responses in exposed organisms. Within toxicogenomics, transcriptomics can be approached through the use of microarrays aimed at producing a genetic fingerprint for the response of model organisms to the presence of chemicals. We studied temporal changes in the early gene expression profiles of Escherichia coli cells exposed to three metal doses of a polymetallic solution over three exposure times, through the application of cDNA microarray technology. In the absence of metals, many genes belonging to a variety of cellular functions were up- and down-regulated over time. At the lowest metal dose, an activation of metal-specific transporters (Cus and ZraP proteins) and a mobilization of glutathione transporters involved in metal sequestration and trafficking was observed over time; this metal dose resulted in the generation of ROS capable of stimulating the transcription of Mn-superoxide dismutase, the assembly of Fe-S clusters and the synthesis of cysteine. At the intermediate dose, an overexpression of ROS scavengers (AhpF, KatG, and YaaA) and heat shock proteins (ClpP, HslV, DnaK, and IbpAB) was observed. Finally, at the highest dose, E. coli cells showed a repression of genes related with DNA mutation correctors (MutY glycopeptidases).}, }
@article {pmid24952019, year = {2014}, author = {Wanjugi, P and Harwood, VJ}, title = {Protozoan predation is differentially affected by motility of enteric pathogens in water vs. sediments.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {751-760}, pmid = {24952019}, issn = {1432-184X}, mesh = {Escherichia coli O157/*physiology ; Florida ; *Food Chain ; Geologic Sediments/microbiology/*parasitology ; Rivers/microbiology/*parasitology ; Salmonella typhimurium/*physiology ; Tetrahymena pyriformis/*physiology ; }, abstract = {Survival of enteric bacteria in aquatic habitats varies depending upon species, strain, and environmental pressures, but the mechanisms governing their fate are poorly understood. Although predation by protozoa is a known, top-down control mechanism on bacterial populations, its influence on the survival of fecal-derived pathogens has not been systematically studied. We hypothesized that motility, a variable trait among pathogens, can influence predation rates and bacterial survival. We compared the survival of two motile pathogens of fecal origin by culturing Escherichia coli O157 and Salmonella enterica Typhimurium. Each species had a motile and non-motile counterpart and was cultured in outdoor microcosms with protozoan predators (Tetrahymena pyriformis) present or absent. Motility had a significant, positive effect on S. enterica levels in water and sediment in the presence or absence of predators. In contrast, motility had a significant negative effect on E. coli O157 levels in sediment, but did not affect water column levels. The presence/absence of protozoa consistently accounted for a greater proportion of the variability in bacterial levels (>95 %) than in bacterial motility (<4 %) in the water column. In sediments, however, motility was more important than predation for both bacteria. Calculations of total CFU/microcosm showed decreasing bacterial concentrations over time under all conditions except for S. enterica in the absence of predation, which increased ∼0.5-1.0 log over 5 days. These findings underscore the complexity of predicting the survival of enteric microorganisms in aquatic habitats, which has implications for the accuracy of risk assessment and modeling of water quality.}, }
@article {pmid24951561, year = {2014}, author = {Spinler, JK and Sontakke, A and Hollister, EB and Venable, SF and Oh, PL and Balderas, MA and Saulnier, DM and Mistretta, TA and Devaraj, S and Walter, J and Versalovic, J and Highlander, SK}, title = {From prediction to function using evolutionary genomics: human-specific ecotypes of Lactobacillus reuteri have diverse probiotic functions.}, journal = {Genome biology and evolution}, volume = {6}, number = {7}, pages = {1772-1789}, pmid = {24951561}, issn = {1759-6653}, support = {U01CA170930/CA/NCI NIH HHS/United States ; UH3 DK083990/DK/NIDDK NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; R01 DK065075/DK/NIDDK NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 AT004326/AT/NCCIH NIH HHS/United States ; U01 CA170930/CA/NCI NIH HHS/United States ; U54 HG004973/HG/NHGRI NIH HHS/United States ; P30 DK56338/DK/NIDDK NIH HHS/United States ; UH3DK083990/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Cell Line ; *Evolution, Molecular ; *Genomics ; Humans ; Limosilactobacillus reuteri/genetics/*physiology ; Microarray Analysis ; Phylogeny ; *Probiotics ; }, abstract = {The vertebrate gut symbiont Lactobacillus reuteri has diversified into separate clades reflecting host origin. Strains show evidence of host adaptation, but how host-microbe coevolution influences microbial-derived effects on hosts is poorly understood. Emphasizing human-derived strains of L. reuteri, we combined comparative genomic analyses with functional assays to examine variations in host interaction among genetically distinct ecotypes. Within clade II or VI, the genomes of human-derived L. reuteri strains are highly conserved in gene content and at the nucleotide level. Nevertheless, they share only 70-90% of total gene content, indicating differences in functional capacity. Human-associated lineages are distinguished by genes related to bacteriophages, vitamin biosynthesis, antimicrobial production, and immunomodulation. Differential production of reuterin, histamine, and folate by 23 clade II and VI strains was demonstrated. These strains also differed with respect to their ability to modulate human cytokine production (tumor necrosis factor, monocyte chemoattractant protein-1, interleukin [IL]-1β, IL-5, IL-7, IL-12, and IL-13) by myeloid cells. Microarray analysis of representative clade II and clade VI strains revealed global regulation of genes within the reuterin, vitamin B12, folate, and arginine catabolism gene clusters by the AraC family transcriptional regulator, PocR. Thus, human-derived L. reuteri clade II and VI strains are genetically distinct and their differences affect their functional repertoires and probiotic features. These findings highlight the biological impact of microbe:host coevolution and illustrate the functional significance of subspecies differences in the human microbiome. Consideration of host origin and functional differences at the subspecies level may have major impacts on probiotic strain selection and considerations of microbial ecology in mammalian species.}, }
@article {pmid24951430, year = {2014}, author = {Girard-Gagnepain, A and Amirache, F and Costa, C and Lévy, C and Frecha, C and Fusil, F and Nègre, D and Lavillette, D and Cosset, FL and Verhoeyen, E}, title = {Baboon envelope pseudotyped LVs outperform VSV-G-LVs for gene transfer into early-cytokine-stimulated and resting HSCs.}, journal = {Blood}, volume = {124}, number = {8}, pages = {1221-1231}, doi = {10.1182/blood-2014-02-558163}, pmid = {24951430}, issn = {1528-0020}, mesh = {Animals ; Antigens, CD34 ; Betaretrovirus/*genetics ; Cell Line ; Genetic Therapy/*methods ; Genetic Vectors/*genetics ; *Hematopoietic Stem Cells/cytology/metabolism ; Humans ; Lentivirus/*genetics ; Macaca ; Membrane Glycoproteins/genetics ; Mice ; Mice, Inbred NOD ; Mice, Knockout ; Mice, SCID ; *Transduction, Genetic ; Viral Envelope Proteins/*genetics ; }, abstract = {Hematopoietic stem cell (HSC)-based gene therapy holds promise for the cure of many diseases. The field is now moving toward the use of lentiviral vectors (LVs) as evidenced by 4 successful clinical trials. These trials used vesicular-stomatitis-virus-G protein (VSV-G)-LVs at high doses combined with strong cytokine-cocktail stimulation to obtain therapeutically relevant transduction levels; however, they might compromise the HSC character. Summarizing all these disadvantages, alternatives to VSV-G-LVs are urgently needed. We generated here high-titer LVs pseudotyped with a baboon retroviral envelope glycoprotein (BaEV-LVs), resistant to human complement. Under mild cytokine prestimulation to preserve the HSC characteristics, a single BaEV-LV application at a low dose, resulted in up to 90% of hCD34(+) cell transduction. Even more striking was that these new BaEV-LVs allowed, at low doses, efficient transduction of up to 30% of quiescent hCD34(+) cells, whereas high-dose VSV-G-LVs were insufficient. Importantly, reconstitution of NOD/Lt-SCID/γc(-/-) (NSG) mice with BaEV-LV-transduced hCD34(+) cells maintained these high transduction levels in all myeloid and lymphoid lineages, including early progenitors. This transduction pattern was confirmed or even increased in secondary NSG recipient mice. This suggests that BaEV-LVs efficiently transduce true HSCs and could improve HSC-based gene therapy, for which high-level HSC correction is needed for life-long cure.}, }
@article {pmid24947496, year = {2015}, author = {Op De Beeck, M and Lievens, B and Busschaert, P and Rineau, F and Smits, M and Vangronsveld, J and Colpaert, JV}, title = {Impact of metal pollution on fungal diversity and community structures.}, journal = {Environmental microbiology}, volume = {17}, number = {6}, pages = {2035-2047}, doi = {10.1111/1462-2920.12547}, pmid = {24947496}, issn = {1462-2920}, mesh = {Ascomycota/metabolism ; Basidiomycota/*metabolism ; Belgium ; *Biodiversity ; Cadmium/*metabolism ; *Environmental Pollution ; Pinus/microbiology ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/analysis/*metabolism ; Zinc/*metabolism ; }, abstract = {The impact of metal pollution on plant communities has been studied extensively in the past, but little is known about the effects of metal pollution on fungal communities that occur in metal-polluted soils. Metal-tolerant ecotypes of the ectomycorrhizal fungus Suillus luteus are frequently found in pioneer pine forests in the Campine region in Belgium on metal-polluted soils. We hypothesized that metal pollution would play an important role in shaping below-ground fungal communities that occur in these soils and that Suillus luteus would be a dominant player. To test these hypotheses, the fungal communities in a young pine plantation in soil polluted with zinc, and cadmium were studied using 454 amplicon pyrosequencing. Results show that zinc, cadmium and soil organic matter content were strongly correlated with the fungal community composition, but no effects on fungal diversity were observed. As hypothesized, S. luteus was found to be a dominant member of the studied fungal communities. However, other dominant fungal species, such as Sistotrema sp., Wilcoxina mikolae and Cadophora finlandica were found as well. Their presence in metal-polluted sites is discussed.}, }
@article {pmid24947206, year = {2016}, author = {Bai, Y and Eijsink, VG and Kielak, AM and van Veen, JA and de Boer, W}, title = {Genomic comparison of chitinolytic enzyme systems from terrestrial and aquatic bacteria.}, journal = {Environmental microbiology}, volume = {18}, number = {1}, pages = {38-49}, doi = {10.1111/1462-2920.12545}, pmid = {24947206}, issn = {1462-2920}, mesh = {Actinobacteria/*enzymology/*genetics ; Aquatic Organisms/genetics/metabolism ; Chitin/*metabolism ; Chitinases/*genetics ; Genome, Bacterial/*genetics ; Genomics ; Mixed Function Oxygenases/genetics ; }, abstract = {Chitin degradation ability is known for many aquatic and terrestrial bacterial species. However, differences in the composition of chitin resources between aquatic (mainly exoskeletons of crustaceans) and terrestrial (mainly fungal cell walls) habitats may have resulted in adaptation of chitinolytic enzyme systems to the prevalent resources. We screened publicly available terrestrial and aquatic chitinase-containing bacterial genomes for possible differences in the composition of their chitinolytic enzyme systems. The results show significant differences between terrestrial and aquatic bacterial genomes in the modular composition of chitinases (i.e. presence of different types of carbohydrate binding modules). Terrestrial Actinobacteria appear to be best adapted to use a wide variety of chitin resources as they have the highest number of chitinase genes, the highest diversity of associated carbohydrate-binding modules and the highest number of CBM33-type lytic polysaccharide monooxygenases. Actinobacteria do also have the highest fraction of genomes containing β-1, 3-glucanases, enzymes that may reinforce the potential for degrading fungal cell walls. The fraction of bacterial chitinase-containing genomes encoding polyketide synthases was much higher for terrestrial bacteria than for aquatic ones supporting the idea that the combined production of antibiotics and cell-wall degrading chitinases can be an important strategy in antagonistic interactions with fungi.}, }
@article {pmid24946864, year = {2014}, author = {Bialek, K and Cysneiros, D and O'Flaherty, V}, title = {Hydrolysis, acidification and methanogenesis during low-temperature anaerobic digestion of dilute dairy wastewater in an inverted fluidised bioreactor.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {20}, pages = {8737-8750}, doi = {10.1007/s00253-014-5864-7}, pmid = {24946864}, issn = {1432-0614}, mesh = {Anaerobiosis ; Bacteria/classification/genetics ; Bioreactors/*microbiology ; Biota ; Carbon Dioxide/metabolism ; Denaturing Gradient Gel Electrophoresis ; Food Industry ; Hydrogen/metabolism ; Hydrolysis ; Medical Waste Disposal ; Methane/*metabolism ; Polymerase Chain Reaction ; Temperature ; Wastewater/*microbiology ; Water Purification/methods ; }, abstract = {The application of low-temperature (10 °C) anaerobic digestion (LtAD) for the treatment of complex dairy-based wastewater in an inverted fluidised bed (IFB) reactor was investigated. Inadequate mixing intensity provoked poor hydrolysis of the substrate (mostly protein), which resulted in low chemical oxygen demand (COD) removal efficiency throughout the trial, averaging ~69 % at the best operational period. Overgrowth of the attached biomass to the support particles (Extendospheres) induced bed stratification by provoking agglutination of the particles and supporting their washout by sedimentation, which contributed to unstable bioprocess performance at the organic loading rates (OLRs) between 0.5 and 5 kg COD m(-3) day(-1). An applied OLR above 2 kg COD m(-3) day(-1) additionally promoted acidification and strongly influenced the microbial composition and dynamics. Hydrogenotrophic methanogens appeared to be the mostly affected group by the Extendospheres particle washout as a decrease in their abundance was observed by quantitative PCR analysis towards the end of the trial, although the specific methanogenic activity and maximum substrate utilisation rate on H2/CO2 indicated high metabolic activity and preference towards hydrogenotrophic methanogenesis of the reactor biomass at this stage. The bacterial community in the bioreactor monitored via denaturing gradient gel electrophoresis (DGGE) also suggested an influence of OLR stress on bacterial community structure and population dynamics. The data presented in this work can provide useful information in future optimisation of fluidised reactors intended for digestion of complex industrial wastewaters during LtAD.}, }
@article {pmid24939130, year = {2014}, author = {Abraham, PE and Giannone, RJ and Xiong, W and Hettich, RL}, title = {Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities.}, journal = {Current protocols in bioinformatics}, volume = {46}, number = {}, pages = {13.26.1-13.26.14}, doi = {10.1002/0471250953.bi1326s46}, pmid = {24939130}, issn = {1934-340X}, mesh = {Databases, Protein ; Information Storage and Retrieval ; *Microbiota ; Peptides/chemistry ; Proteins/chemistry ; *Proteomics ; }, abstract = {Contemporary microbial ecology studies usually employ one or more "omics" approaches to investigate the structure and function of microbial communities. Among these, metaproteomics aims to characterize the metabolic activities of the microbial membership, providing a direct link between the genetic potential and functional metabolism. The successful deployment of metaproteomics research depends on the integration of high-quality experimental and bioinformatic techniques for uncovering the metabolic activities of a microbial community in a way that is complementary to other "meta-omic" approaches. The essential, quality-defining informatics steps in metaproteomics investigations are: (1) construction of the metagenome, (2) functional annotation of predicted protein-coding genes, (3) protein database searching, (4) protein inference, and (5) extraction of metabolic information. In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool.}, }
@article {pmid24937356, year = {2014}, author = {Lautenschlager, K and Hwang, C and Ling, F and Liu, WT and Boon, N and Köster, O and Egli, T and Hammes, F}, title = {Abundance and composition of indigenous bacterial communities in a multi-step biofiltration-based drinking water treatment plant.}, journal = {Water research}, volume = {62}, number = {}, pages = {40-52}, doi = {10.1016/j.watres.2014.05.035}, pmid = {24937356}, issn = {1879-2448}, mesh = {Bacteria/enzymology/*growth &amp; development ; Biodegradation, Environmental ; *Biodiversity ; Biomass ; Carbon/isolation &amp; purification ; Charcoal/chemistry ; Drinking Water/*microbiology ; Filtration/*methods ; Organic Chemicals/isolation &amp; purification ; Plankton/growth &amp; development ; Switzerland ; Waste Disposal, Fluid ; Water Pollutants, Chemical/isolation &amp; purification ; Water Purification/*methods ; Water Quality ; }, abstract = {Indigenous bacterial communities are essential for biofiltration processes in drinking water treatment systems. In this study, we examined the microbial community composition and abundance of three different biofilter types (rapid sand, granular activated carbon, and slow sand filters) and their respective effluents in a full-scale, multi-step treatment plant (Zürich, CH). Detailed analysis of organic carbon degradation underpinned biodegradation as the primary function of the biofilter biomass. The biomass was present in concentrations ranging between 2-5 × 10(15) cells/m(3) in all filters but was phylogenetically, enzymatically and metabolically diverse. Based on 16S rRNA gene-based 454 pyrosequencing analysis for microbial community composition, similar microbial taxa (predominantly Proteobacteria, Planctomycetes, Acidobacteria, Bacteriodetes, Nitrospira and Chloroflexi) were present in all biofilters and in their respective effluents, but the ratio of microbial taxa was different in each filter type. This change was also reflected in the cluster analysis, which revealed a change of 50-60% in microbial community composition between the different filter types. This study documents the direct influence of the filter biomass on the microbial community composition of the final drinking water, particularly when the water is distributed without post-disinfection. The results provide new insights on the complexity of indigenous bacteria colonizing drinking water systems, especially in different biofilters of a multi-step treatment plant.}, }
@article {pmid24937032, year = {2014}, author = {Kerckhof, FM and Courtens, EN and Geirnaert, A and Hoefman, S and Ho, A and Vilchez-Vargas, R and Pieper, DH and Jauregui, R and Vlaeminck, SE and Van de Wiele, T and Vandamme, P and Heylen, K and Boon, N}, title = {Optimized cryopreservation of mixed microbial communities for conserved functionality and diversity.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e99517}, pmid = {24937032}, issn = {1932-6203}, mesh = {Autotrophic Processes ; *Biofilms ; *Cryopreservation ; Cryoprotective Agents/*pharmacology ; Euryarchaeota/genetics/growth &amp; development ; Feces/microbiology ; Humans ; Microbial Viability ; *Microbiota ; Phylogeny ; Probiotics ; }, abstract = {The use of mixed microbial communities (microbiomes) for biotechnological applications has steadily increased over the past decades. However, these microbiomes are not readily available from public culture collections, hampering their potential for widespread use. The main reason for this lack of availability is the lack of an effective cryopreservation protocol. Due to this critical need, we evaluated the functionality as well as the community structure of three different types of microbiomes before and after cryopreservation with two cryoprotective agents (CPA). Microbiomes were selected based upon relevance towards applications: (1) a methanotrophic co-culture (MOB), with potential for mitigation of greenhouse gas emissions, environmental pollutants removal and bioplastics production; (2) an oxygen limited autotrophic nitrification/denitrification (OLAND) biofilm, with enhanced economic and ecological benefits for wastewater treatment, and (3) fecal material from a human donor, with potential applications for fecal transplants and pre/probiotics research. After three months of cryopreservation at -80 °C, we found that metabolic activity, in terms of the specific activity recovery of MOB, aerobic ammonium oxidizing bacteria (AerAOB) and anaerobic AOB (AnAOB, anammox) in the OLAND mixed culture, resumes sooner when one of our selected CPA [dimethyl sulfoxide (DMSO) and DMSO plus trehalose and tryptic soy broth (DMSO+TT)] was added. However, the activity of the fecal community was not influenced by the CPA addition, although the preservation of the community structure (as determined by 16S rRNA gene sequencing) was enhanced by addition of CPA. In summary, we have evaluated a cryopreservation protocol that succeeded in preserving both community structure and functionality of value-added microbiomes. This will allow individual laboratories and culture collections to boost the use of microbiomes in biotechnological applications.}, }
@article {pmid24935902, year = {2014}, author = {Glinka, C and Hawkes, CV}, title = {Environmental controls on fungal community composition and abundance over 3 years in native and degraded shrublands.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {807-817}, pmid = {24935902}, issn = {1432-184X}, mesh = {*Biodiversity ; *Environment ; Florida ; Fungal Proteins/genetics ; Fungi/genetics/*physiology ; Molecular Sequence Data ; Plants/microbiology ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Soil fungal communities have high local diversity and turnover, but the relative contribution of environmental and regional drivers to those patterns remains poorly understood. Local factors that contribute to fungal diversity include soil properties and the plant community, but there is also evidence for regional dispersal limitation in some fungal communities. We used different plant communities with different soil conditions and experimental manipulations of both vegetation and dispersal to distinguish among these factors. Specifically, we compared native shrublands with former native shrublands that had been disturbed or converted to pasture, resulting in soils progressively more enriched in carbon and nutrients. We tested the role of vegetation via active removal, and we manipulated dispersal by adding living soil inoculum from undisturbed native sites. Soil fungi were tracked for 3 years, with samples taken at ten time points from June 2006 to June 2009. We found that soil fungal abundance, richness, and community composition responded primarily to soil properties, which in this case were a legacy of plant community degradation. In contrast, dispersal had no effect on soil fungi. Temporal variation in soil fungi was partly related to drought status, yet it was much broader in native sites compared to pastures, suggesting some buffering due to the increased soil resources in the pasture sites. The persistence of soil fungal communities over 3 years in this study suggests that soil properties can act as a strong local environmental filter. Largely persistent soil fungal communities also indicate the potential for strong biotic resistance and soil legacies, which presents a challenge for both the prediction of how fungi respond to environmental change and our ability to manipulate fungi in efforts such as ecosystem restoration.}, }
@article {pmid24929088, year = {2014}, author = {Osahor, AN and Tan, CY and Sim, EU and Lee, CW and Narayanan, K}, title = {Short homologies efficiently generate detectable homologous recombination events.}, journal = {Analytical biochemistry}, volume = {462}, number = {}, pages = {26-28}, doi = {10.1016/j.ab.2014.05.030}, pmid = {24929088}, issn = {1096-0309}, mesh = {Base Sequence ; Chromosomes, Artificial, Bacterial/*genetics ; Escherichia coli/genetics ; Genetic Engineering/*methods ; *Homologous Recombination ; Plasmids/genetics ; *Sequence Homology, Nucleic Acid ; Telomere/genetics ; }, abstract = {When recombineering bacterial artificial chromosomes (BACs), it is common practice to design the ends of the donor molecule with 50 bp of homology specifying its insertion site. We demonstrate that desired recombinants can be produced using intermolecular homologies as short as 15 bp. Although the use of shorter donor end regions decreases total recombinants by several fold, the frequency of recombinants with correctly inserted donor molecules was high enough for easy detection by simple polymerase chain reaction (PCR) screening. This observation may have important implications for the design of oligonucleotides for recombineering, including significant cost savings, especially for high-throughput projects that use large quantities of primers.}, }
@article {pmid24929037, year = {2014}, author = {Gunnigle, E and Ramond, JB and Frossard, A and Seeley, M and Cowan, D}, title = {A sequential co-extraction method for DNA, RNA and protein recovery from soil for future system-based approaches.}, journal = {Journal of microbiological methods}, volume = {103}, number = {}, pages = {118-123}, doi = {10.1016/j.mimet.2014.06.004}, pmid = {24929037}, issn = {1872-8359}, mesh = {Chemical Fractionation/methods ; DNA/analysis/*isolation &amp; purification ; Metagenomics ; Proteins/analysis/*isolation &amp; purification ; Proteomics ; RNA/analysis/*isolation &amp; purification ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {A co-extraction protocol that sequentially isolates core biopolymer fractions (DNA, RNA, protein) from edaphic microbial communities is presented. In order to confirm compatibility with downstream analyses, bacterial T-RFLP profiles were generated from the DNA- and RNA-derived fractions of an arid-based soil, with metaproteomics undertaken on the corresponding protein fraction.}, }
@article {pmid24928878, year = {2014}, author = {Sinninghe Damsté, JS and Rijpstra, WI and Hopmans, EC and Foesel, BU and Wüst, PK and Overmann, J and Tank, M and Bryant, DA and Dunfield, PF and Houghton, K and Stott, MB}, title = {Ether- and ester-bound iso-diabolic acid and other lipids in members of acidobacteria subdivision 4.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {17}, pages = {5207-5218}, pmid = {24928878}, issn = {1098-5336}, support = {R01 ES024478/ES/NIEHS NIH HHS/United States ; }, mesh = {Acidobacteria/*chemistry/classification/genetics/isolation &amp; purification ; Chromatography, High Pressure Liquid ; Cytosol/chemistry ; DNA, Bacterial/chemistry/genetics ; Dicarboxylic Acids/*analysis ; Environmental Microbiology ; Esters/analysis ; Ethers/analysis ; Lipids/*analysis ; Mass Spectrometry ; Molecular Sequence Data ; Sequence Analysis, DNA ; }, abstract = {Recently, iso-diabolic acid (13,16-dimethyl octacosanedioic acid) has been identified as a major membrane-spanning lipid of subdivisions 1 and 3 of the Acidobacteria, a highly diverse phylum within the Bacteria. This finding pointed to the Acidobacteria as a potential source for the bacterial glycerol dialkyl glycerol tetraethers that occur ubiquitously in peat, soil, lakes, and hot springs. Here, we examined the lipid composition of seven phylogenetically divergent strains of subdivision 4 of the Acidobacteria, a bacterial group that is commonly encountered in soil. Acid hydrolysis of total cell material released iso-diabolic acid derivatives in substantial quantities (11 to 48% of all fatty acids). In contrast to subdivisions 1 and 3 of the Acidobacteria, 6 out of the 7 species of subdivision 4 (excepting "Candidatus Chloracidobacterium thermophilum") contained iso-diabolic acid ether bound to a glycerol in larger fractional abundance than iso-diabolic acid itself. This is in agreement with the analysis of intact polar lipids (IPLs) by high-performance liquid chromatography-mass spectrometry (HPLC-MS), which showed the dominance of mixed ether-ester glycerides. iso-Diabolic acid-containing IPLs were not identified, because these IPLs are not released with a Bligh-Dyer extraction, as observed before when studying lipid compositions of subdivisions 1 and 3 of the Acidobacteria. The presence of ether bonds in the membrane lipids does not seem to be an adaptation to temperature, because the five mesophilic isolates contained a larger amount of ether lipids than the thermophile "Ca. Chloracidobacterium thermophilum." Furthermore, experiments with Pyrinomonas methylaliphatogenes did not reveal a major influence of growth temperature over the 50 to 69°C range.}, }
@article {pmid24928874, year = {2014}, author = {Hugerth, LW and Wefer, HA and Lundin, S and Jakobsson, HE and Lindberg, M and Rodin, S and Engstrand, L and Andersson, AF}, title = {DegePrime, a program for degenerate primer design for broad-taxonomic-range PCR in microbial ecology studies.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {16}, pages = {5116-5123}, pmid = {24928874}, issn = {1098-5336}, mesh = {Algorithms ; Animals ; Bacteria/classification/*genetics/isolation &amp; purification ; Computers, Molecular ; DNA Primers/*chemistry/genetics ; DNA, Bacterial/genetics ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Rumen/microbiology ; Seawater/microbiology ; *Software ; }, abstract = {The taxonomic composition of a microbial community can be deduced by analyzing its rRNA gene content by, e.g., high-throughput DNA sequencing or DNA chips. Such methods typically are based on PCR amplification of rRNA gene sequences using broad-taxonomic-range PCR primers. In these analyses, the use of optimal primers is crucial for achieving an unbiased representation of community composition. Here, we present the computer program DegePrime that, for each position of a multiple sequence alignment, finds a degenerate oligomer of as high coverage as possible and outputs its coverage among taxonomic divisions. We show that our novel heuristic, which we call weighted randomized combination, performs better than previously described algorithms for solving the maximum coverage degenerate primer design problem. We previously used DegePrime to design a broad-taxonomic-range primer pair that targets the bacterial V3-V4 region (341F-805R) (D. P. Herlemann, M. Labrenz, K. Jurgens, S. Bertilsson, J. J. Waniek, and A. F. Andersson, ISME J. 5:1571-1579, 2011, http://dx.doi.org/10.1038/ismej.2011.41), and here we use the program to significantly increase the coverage of a primer pair (515F-806R) widely used for Illumina-based surveys of bacterial and archaeal diversity. By comparison with shotgun metagenomics, we show that the primers give an accurate representation of microbial diversity in natural samples.}, }
@article {pmid24923325, year = {2014}, author = {Haq, IU and Graupner, K and Nazir, R and van Elsas, JD}, title = {The genome of the fungal-interactive soil bacterium Burkholderia terrae BS001-a plethora of outstanding interactive capabilities unveiled.}, journal = {Genome biology and evolution}, volume = {6}, number = {7}, pages = {1652-1668}, pmid = {24923325}, issn = {1759-6653}, mesh = {Burkholderia/*genetics ; Computational Biology ; *Evolution, Molecular ; Fungi/*genetics ; Genome, Fungal/*genetics ; Phylogeny ; Sequence Alignment ; *Soil Microbiology ; }, abstract = {Burkholderia terrae strain BS001, obtained as an inhabitant of the mycosphere of Laccaria proxima (a close relative of Lyophyllum sp. strain Karsten), actively interacts with Lyophyllum sp. strain Karsten. We here summarize the remarkable ecological behavior of B. terrae BS001 in the mycosphere and add key data to this. Moreover, we extensively analyze the approximately 11.5-Mb five-replicon genome of B. terrae BS001 and highlight its remarkable features. Seventy-nine regions of genomic plasticity (RGP), that is, 16.48% of the total genome size, were found. One 70.42-kb RGP, RGP76, revealed a typical conjugal element structure, including a full type 4 secretion system. Comparative analyses across 24 related Burkholderia genomes revealed that 95.66% of the total BS001 genome belongs to the variable part, whereas the remaining 4.34% constitutes the core genome. Genes for biofilm formation and several secretion systems, under which a type 3 secretion system (T3SS), were found, which is consistent with the hypothesis that T3SSs play a role in the interaction with Lyophyllum sp. strain Karsten. The high number of predicted metabolic pathways and membrane transporters suggested that strain BS001 can take up and utilize a range of sugars, amino acids and organic acids. In particular, a unique glycerol uptake system was found. The BS001 genome further contains genetic systems for the degradation of complex organic compounds. Moreover, gene clusters encoding nonribosomal peptide synthetases (NRPS) and hybrid polyketide synthases/NRPS were found, highlighting the potential role of secondary metabolites in the ecology of strain BS001. The patchwork of genetic features observed in the genome is consistent with the notion that 1) horizontal gene transfer is a main driver of B. terrae BS001 adaptation and 2) the organism is very flexible in its ecological behavior in soil.}, }
@article {pmid24920320, year = {2014}, author = {Lutz, S and Anesio, AM and Jorge Villar, SE and Benning, LG}, title = {Variations of algal communities cause darkening of a Greenland glacier.}, journal = {FEMS microbiology ecology}, volume = {89}, number = {2}, pages = {402-414}, doi = {10.1111/1574-6941.12351}, pmid = {24920320}, issn = {1574-6941}, mesh = {Biomass ; Carbon Cycle ; Chlamydomonas/*metabolism ; Freezing ; Greenland ; *Ice Cover ; Photosynthesis ; Seasons ; Snow ; Streptophyta/*metabolism ; Xanthophylls/metabolism ; Zeaxanthins ; }, abstract = {We have assessed the microbial ecology on the surface of Mittivakkat glacier in SE-Greenland during the exceptional high melting season in July 2012 when the so far most extreme melting rate for the Greenland Ice Sheet has been recorded. By employing a complementary and multi-disciplinary field sampling and analytical approach, we quantified the dramatic changes in the different microbial surface habitats (green snow, red snow, biofilms, grey ice, cryoconite holes). The observed clear change in dominant algal community and their rapidly changing cryo-organic adaptation inventory was linked to the high melting rate. The changes in carbon and nutrient fluxes between different microbial pools (from snow to ice, cryoconite holes and glacial forefronts) revealed that snow and ice algae dominate the net primary production at the onset of melting, and that they have the potential to support the cryoconite hole communities as carbon and nutrient sources. A large proportion of algal cells is retained on the glacial surface and temporal and spatial changes in pigmentation contribute to the darkening of the snow and ice surfaces. This implies that the fast, melt-induced algal growth has a high albedo reduction potential, and this may lead to a positive feedback speeding up melting processes.}, }
@article {pmid24918035, year = {2014}, author = {Beitel, CW and Froenicke, L and Lang, JM and Korf, IF and Michelmore, RW and Eisen, JA and Darling, AE}, title = {Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products.}, journal = {PeerJ}, volume = {2}, number = {}, pages = {e415}, pmid = {24918035}, issn = {2167-8359}, abstract = {Metagenomics is a valuable tool for the study of microbial communities but has been limited by the difficulty of "binning" the resulting sequences into groups corresponding to the individual species and strains that constitute the community. Moreover, there are presently no methods to track the flow of mobile DNA elements such as plasmids through communities or to determine which of these are co-localized within the same cell. We address these limitations by applying Hi-C, a technology originally designed for the study of three-dimensional genome structure in eukaryotes, to measure the cellular co-localization of DNA sequences. We leveraged Hi-C data generated from a simple synthetic metagenome sample to accurately cluster metagenome assembly contigs into groups that contain nearly complete genomes of each species. The Hi-C data also reliably associated plasmids with the chromosomes of their host and with each other. We further demonstrated that Hi-C data provides a long-range signal of strain-specific genotypes, indicating such data may be useful for high-resolution genotyping of microbial populations. Our work demonstrates that Hi-C sequencing data provide valuable information for metagenome analyses that are not currently obtainable by other methods. This metagenomic Hi-C method could facilitate future studies of the fine-scale population structure of microbes, as well as studies of how antibiotic resistance plasmids (or other genetic elements) mobilize in microbial communities. The method is not limited to microbiology; the genetic architecture of other heterogeneous populations of cells could also be studied with this technique.}, }
@article {pmid24912454, year = {2014}, author = {Gulez, G and Altıntaş, A and Fazli, M and Dechesne, A and Workman, CT and Tolker-Nielsen, T and Smets, BF}, title = {Colony morphology and transcriptome profiling of Pseudomonas putida KT2440 and its mutants deficient in alginate or all EPS synthesis under controlled matric potentials.}, journal = {MicrobiologyOpen}, volume = {3}, number = {4}, pages = {457-469}, pmid = {24912454}, issn = {2045-8827}, mesh = {Alginates/*metabolism ; Dehydration ; *Gene Expression Profiling ; Glucuronic Acid/metabolism ; Hexuronic Acids/metabolism ; Polysaccharides, Bacterial/*metabolism ; Pseudomonas putida/*genetics/*metabolism ; Stress, Physiological ; Water/metabolism ; }, abstract = {Pseudomonas putida is a versatile bacterial species adapted to soil and its fluctuations. Like many other species living in soil, P. putida often faces water limitation. Alginate, an exopolysaccharide (EPS) produced by P. putida, is known to create hydrated environments and alleviate the effect of water limitation. In addition to alginate, P. putida is capable of producing cellulose (bcs), putida exopolysaccharide a (pea), and putida exopolysaccharide b (peb). However, unlike alginate, not much is known about their roles under water limitation. Hence, in this study we examined the role of different EPS components under mild water limitation. To create environmentally realistic water limited conditions as observed in soil, we used the Pressurized Porous Surface Model. Our main hypothesis was that under water limitation and in the absence of alginate other exopolysaccharides would be more active to maintain homeostasis. To test our hypothesis, we investigated colony morphologies and whole genome transcriptomes of P. putida KT2440 wild type and its mutants deficient in synthesis of either alginate or all known EPS. Overall our results support that alginate is an important exopolysaccharide under water limitation and in the absence of alginate other tolerance mechanisms are activated.}, }
@article {pmid24912085, year = {2015}, author = {Adriaenssens, EM and Van Zyl, L and De Maayer, P and Rubagotti, E and Rybicki, E and Tuffin, M and Cowan, DA}, title = {Metagenomic analysis of the viral community in Namib Desert hypoliths.}, journal = {Environmental microbiology}, volume = {17}, number = {2}, pages = {480-495}, doi = {10.1111/1462-2920.12528}, pmid = {24912085}, issn = {1462-2920}, mesh = {Africa ; Bacteria/genetics/*virology ; Bacteriophages/*classification/*genetics ; Base Sequence ; Caudovirales/*genetics/isolation &amp; purification ; Cyanobacteria/genetics/*virology ; DNA, Viral/*analysis/genetics ; Desert Climate ; Environment ; Metagenomics ; Phylogeny ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {Hypolithic microbial communities are specialized desert communities inhabiting the underside of translucent rocks. Here, we present the first study of the viral fraction of these communities isolated from the hyperarid Namib Desert. The taxonomic composition of the hypolithic viral communities was investigated and a functional assessment of the sequences determined. Phylotypic analysis showed that bacteriophages belonging to the order Caudovirales, in particular the family Siphoviridae, were most prevalent. Functional analysis and comparison with other metaviromes revealed a relatively high frequency of cell wall-degrading enzymes, ribonucleotide reductases (RNRs) and phage-associated genes. Phylogenetic analyses of terL and phoH marker genes indicated that many of the sequences were novel and distinct from known isolates, and the class distribution of the RNRs suggests that this is a novel environment. The composition of the viral hypolith fraction containing many Bacillus-infecting phages was not completely consistent with Namib hypolith phylotypic surveys of the bacterial hosts, in which the cyanobacterial genus Chroococcidiopsis was found to be dominant. This could be attributed to the lack of sequence information about hypolith viruses/bacteria in public databases or the possibility that hypolithic communities incorporate viruses from the surrounding soil.}, }
@article {pmid24911921, year = {2014}, author = {Guo, K and Donose, BC and Soeriyadi, AH and Prévoteau, A and Patil, SA and Freguia, S and Gooding, JJ and Rabaey, K}, title = {Flame oxidation of stainless steel felt enhances anodic biofilm formation and current output in bioelectrochemical systems.}, journal = {Environmental science &amp; technology}, volume = {48}, number = {12}, pages = {7151-7156}, doi = {10.1021/es500720g}, pmid = {24911921}, issn = {1520-5851}, mesh = {*Bioelectric Energy Sources ; Biofilms/*growth &amp; development ; Bioreactors ; Carbon/*chemistry ; Carbon Fiber ; Catalysis ; *Electricity ; Electrochemical Techniques/*methods ; Electrodes ; Microscopy, Atomic Force ; Microscopy, Electron, Scanning ; Oxidation-Reduction ; Photoelectron Spectroscopy ; Spectrum Analysis, Raman ; Stainless Steel/*chemistry ; Surface Properties ; }, abstract = {Stainless steel (SS) can be an attractive material to create large electrodes for microbial bioelectrochemical systems (BESs), due to its low cost and high conductivity. However, poor biocompatibility limits its successful application today. Here we report a simple and effective method to make SS electrodes biocompatible by means of flame oxidation. Physicochemical characterization of electrode surface indicated that iron oxide nanoparticles (IONPs) were generated in situ on an SS felt surface by flame oxidation. IONPs-coating dramatically enhanced the biocompatibility of SS felt and consequently resulted in a robust electroactive biofilm formation at its surface in BESs. The maximum current densities reached at IONPs-coated SS felt electrodes were 16.5 times and 4.8 times higher than the untreated SS felts and carbon felts, respectively. Furthermore, the maximum current density achieved with the IONPs-coated SS felt (1.92 mA/cm(2), 27.42 mA/cm(3)) is one of the highest current densities reported thus far. These results demonstrate for the first time that flame oxidized SS felts could be a good alternative to carbon-based electrodes for achieving high current densities in BESs. Most importantly, high conductivity, excellent mechanical strength, strong chemical stability, large specific surface area, and comparatively low cost of flame oxidized SS felts offer exciting opportunities for scaling-up of the anodes for BESs.}, }
@article {pmid24910015, year = {2014}, author = {Ju, L and Yang, J and Liu, L and Wilkinson, DM}, title = {Diversity and distribution of freshwater testate amoebae (protozoa) along latitudinal and trophic gradients in China.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {657-670}, pmid = {24910015}, issn = {1432-184X}, mesh = {Amoebida/*physiology ; *Biodiversity ; China ; Fresh Water/*parasitology ; }, abstract = {Freshwater microbial diversity is subject to multiple stressors in the Anthropocene epoch. However, the effects of climate changes and human activities on freshwater protozoa remain poorly understood. In this study, the diversity and distribution of testate amoebae from the surface sediments were investigated in 51 Chinese lakes and reservoirs along two gradients, latitude and trophic status. A total of 169 taxa belonging to 24 genera were identified, and the most diverse and dominant genera were Difflugia (78 taxa), Centropyxis (26 taxa) and Arcella (12 taxa). Our analysis revealed that biomass of testate amoebae decreased significantly along the latitudinal gradient, while Shannon-Wiener indices and species richness presented an opposite trend (P < 0.05). The relationship of diversity and latitude is, we suspect, an artifact of the altitudinal distribution of our sites. Furthermore, biomass-based Shannon-Wiener index and species richness of testate amoebae were significantly unimodally related to trophic status (P < 0.05). This is the first large-scale study showing the effects of latitude and trophic status on diversity and distribution of testate amoebae in China. Therefore, our results provide valuable baseline data on testate amoebae and contribute to lake management and our understanding of the large-scale global patterns in microorganism diversity.}, }
@article {pmid24910014, year = {2014}, author = {Palesse, S and Colombet, J and Pradeep Ram, AS and Sime-Ngando, T}, title = {Linking host prokaryotic physiology to viral lifestyle dynamics in a temperate freshwater lake (Lake Pavin, France).}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {740-750}, pmid = {24910014}, issn = {1432-184X}, mesh = {Bacteria/*virology ; *Bacterial Physiological Phenomena ; Bacteriophages/growth &amp; development/*physiology ; France ; Lakes/*microbiology/*virology ; Lysogeny ; Seasons ; *Virus Integration ; }, abstract = {In aquatic ecosystems, fluctuations in environmental conditions and prokaryotic host physiological states can strongly affect the dynamics of viral life strategies. The influence of prokaryote physiology and environmental factors on viral replication cycles (lytic and lysogeny) was investigated from April to September 2011 at three different strata (epi, meta, and hypolimnion) in the mixolimnion of deep volcanic temperate freshwater Lake Pavin (France). Overall, the euphotic region (epi and metalimnion) was more dynamic and showed significant variation in microbial standing stocks, prokaryotic physiological state, and viral life strategies compared to the aphotic hypolimnion which was stable within sampled months. The prokaryotic host physiology as inferred from the nucleic acid content of prokaryotic cells (high or low nucleic acid) was strongly regulated by the chlorophyll concentration. The predominance of the high nucleic acid (HNA) prokaryotes (cells) over low nucleic acid (LNA) prokaryotes (cells) in the spring (HNA/LNA = 1.2) and vice versa in the summer period (HNA/LNA = 0.4) suggest that the natural prokaryotic communities underwent major shifts in their physiological states during investigated time period. The increase in the percentage of inducible lysogenic prokaryotes in the summer period was associated with the switch in the dominance of LNA over HNA cells, which coincided with the periods of strong resource (nutrient) limitation. This supports the idea that lysogeny represents a maintenance strategy for viruses in unproductive or harsh nutrient/host conditions. A negative correlation of percentage of lysogenic prokaryotes with HNA cell abundance and chlorophyll suggest that lysogenic cycle is closely related to prokaryotic cells which are stressed or starved due to unavailability of resources for its growth and activity. Our results provide support to previous findings that changes in prokaryote physiology are critical for the promotion and establishment of lysogeny in aquatic ecosystems, which are prone to constant environmental fluctuations.}, }
@article {pmid24908577, year = {2014}, author = {Haig, SJ and Quince, C and Davies, RL and Dorea, CC and Collins, G}, title = {Replicating the microbial community and water quality performance of full-scale slow sand filters in laboratory-scale filters.}, journal = {Water research}, volume = {61}, number = {}, pages = {141-151}, doi = {10.1016/j.watres.2014.05.008}, pmid = {24908577}, issn = {1879-2448}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; *Filtration ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Silicon Dioxide/chemistry ; *Water Microbiology ; Water Purification/*methods ; *Water Quality ; }, abstract = {Previous laboratory-scale studies to characterise the functional microbial ecology of slow sand filters have suffered from methodological limitations that could compromise their relevance to full-scale systems. Therefore, to ascertain if laboratory-scale slow sand filters (L-SSFs) can replicate the microbial community and water quality production of industrially operated full-scale slow sand filters (I-SSFs), eight cylindrical L-SSFs were constructed and were used to treat water from the same source as the I-SSFs. Half of the L-SSFs sand beds were composed of sterilized sand (sterile) from the industrial filters and the other half with sand taken directly from the same industrial filter (non-sterile). All filters were operated for 10 weeks, with the microbial community and water quality parameters sampled and analysed weekly. To characterize the microbial community phyla-specific qPCR assays and 454 pyrosequencing of the 16S rRNA gene were used in conjunction with an array of statistical techniques. The results demonstrate that it is possible to mimic both the water quality production and the structure of the microbial community of full-scale filters in the laboratory - at all levels of taxonomic classification except OTU - thus allowing comparison of LSSF experiments with full-scale units. Further, it was found that the sand type composing the filter bed (non-sterile or sterile), the water quality produced, the age of the filters and the depth of sand samples were all significant factors in explaining observed differences in the structure of the microbial consortia. This study is the first to the authors' knowledge that demonstrates that scaled-down slow sand filters can accurately reproduce the water quality and microbial consortia of full-scale slow sand filters.}, }
@article {pmid24906017, year = {2014}, author = {Walker, A and Pfitzner, B and Neschen, S and Kahle, M and Harir, M and Lucio, M and Moritz, F and Tziotis, D and Witting, M and Rothballer, M and Engel, M and Schmid, M and Endesfelder, D and Klingenspor, M and Rattei, T and Castell, WZ and de Angelis, MH and Hartmann, A and Schmitt-Kopplin, P}, title = {Distinct signatures of host-microbial meta-metabolome and gut microbiome in two C57BL/6 strains under high-fat diet.}, journal = {The ISME journal}, volume = {8}, number = {12}, pages = {2380-2396}, pmid = {24906017}, issn = {1751-7370}, mesh = {Animals ; Bacteria/genetics/isolation &amp; purification/metabolism ; Bile Acids and Salts/metabolism ; Cecum/metabolism/microbiology ; Diet, High-Fat ; Gastrointestinal Tract/*microbiology ; Liver/metabolism ; Male ; *Metabolome ; Metabolomics ; Mice, Inbred C57BL ; *Microbiota ; Obesity/*metabolism/*microbiology ; Tandem Mass Spectrometry ; }, abstract = {A combinatory approach using metabolomics and gut microbiome analysis techniques was performed to unravel the nature and specificity of metabolic profiles related to gut ecology in obesity. This study focused on gut and liver metabolomics of two different mouse strains, the C57BL/6J (C57J) and the C57BL/6N (C57N) fed with high-fat diet (HFD) for 3 weeks, causing diet-induced obesity in C57N, but not in C57J mice. Furthermore, a 16S-ribosomal RNA comparative sequence analysis using 454 pyrosequencing detected significant differences between the microbiome of the two strains on phylum level for Firmicutes, Deferribacteres and Proteobacteria that propose an essential role of the microbiome in obesity susceptibility. Gut microbial and liver metabolomics were followed by a combinatory approach using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and ultra performance liquid chromatography time of tlight MS/MS with subsequent multivariate statistical analysis, revealing distinctive host and microbial metabolome patterns between the C57J and the C57N strain. Many taurine-conjugated bile acids (TBAs) were significantly elevated in the cecum and decreased in liver samples from the C57J phenotype likely displaying different energy utilization behavior by the bacterial community and the host. Furthermore, several metabolite groups could specifically be associated with the C57N phenotype involving fatty acids, eicosanoids and urobilinoids. The mass differences based metabolite network approach enabled to extend the range of known metabolites to important bile acids (BAs) and novel taurine conjugates specific for both strains. In summary, our study showed clear alterations of the metabolome in the gastrointestinal tract and liver within a HFD-induced obesity mouse model in relation to the host-microbial nutritional adaptation.}, }
@article {pmid24904563, year = {2014}, author = {Krause, S and Le Roux, X and Niklaus, PA and Van Bodegom, PM and Lennon, JT and Bertilsson, S and Grossart, HP and Philippot, L and Bodelier, PL}, title = {Trait-based approaches for understanding microbial biodiversity and ecosystem functioning.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {251}, pmid = {24904563}, issn = {1664-302X}, abstract = {In ecology, biodiversity-ecosystem functioning (BEF) research has seen a shift in perspective from taxonomy to function in the last two decades, with successful application of trait-based approaches. This shift offers opportunities for a deeper mechanistic understanding of the role of biodiversity in maintaining multiple ecosystem processes and services. In this paper, we highlight studies that have focused on BEF of microbial communities with an emphasis on integrating trait-based approaches to microbial ecology. In doing so, we explore some of the inherent challenges and opportunities of understanding BEF using microbial systems. For example, microbial biologists characterize communities using gene phylogenies that are often unable to resolve functional traits. Additionally, experimental designs of existing microbial BEF studies are often inadequate to unravel BEF relationships. We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. We conclude that such trait-based approaches are a promising framework to increase the understanding of microbial BEF relationships and thus generating systematic principles in microbial ecology and more generally ecology.}, }
@article {pmid24904535, year = {2014}, author = {Berry, D and Widder, S}, title = {Deciphering microbial interactions and detecting keystone species with co-occurrence networks.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {219}, pmid = {24904535}, issn = {1664-302X}, support = {P 26127/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Co-occurrence networks produced from microbial survey sequencing data are frequently used to identify interactions between community members. While this approach has potential to reveal ecological processes, it has been insufficiently validated due to the technical limitations inherent in studying complex microbial ecosystems. Here, we simulate multi-species microbial communities with known interaction patterns using generalized Lotka-Volterra dynamics. We then construct co-occurrence networks and evaluate how well networks reveal the underlying interactions and how experimental and ecological parameters can affect network inference and interpretation. We find that co-occurrence networks can recapitulate interaction networks under certain conditions, but that they lose interpretability when the effects of habitat filtering become significant. We demonstrate that networks suffer from local hot spots of spurious correlation in the neighborhood of hub species that engage in many interactions. We also identify topological features associated with keystone species in co-occurrence networks. This study provides a substantiated framework to guide environmental microbiologists in the construction and interpretation of co-occurrence networks from microbial survey datasets.}, }
@article {pmid24903881, year = {2014}, author = {De Maayer, P and Williamson, CE and Vennard, CT and Danson, MJ and Cowan, DA}, title = {Draft Genome Sequences of Geobacillus sp. Strains CAMR5420 and CAMR12739.}, journal = {Genome announcements}, volume = {2}, number = {3}, pages = {}, pmid = {24903881}, issn = {2169-8287}, abstract = {Thermophilic Geobacillus spp. can efficiently hydrolyze hemicellulose polymers and are therefore of interest in biotechnological applications. Here we report the genome sequences of two hemicellulolytic strains, Geobacillus sp. CAMR12739 and CAMR5420.}, }
@article {pmid24903703, year = {2014}, author = {Meyer-Dombard, DR and Amend, JP}, title = {Geochemistry and microbial ecology in alkaline hot springs of Ambitle Island, Papua New Guinea.}, journal = {Extremophiles : life under extreme conditions}, volume = {18}, number = {4}, pages = {763-778}, pmid = {24903703}, issn = {1433-4909}, mesh = {Alkalies/analysis ; Deinococcus/genetics/*isolation &amp; purification ; Hot Springs/chemistry/*microbiology ; *Microbiota ; Papua New Guinea ; Phylogeny ; Proteobacteria/genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Thermococcales/genetics/*isolation &amp; purification ; }, abstract = {The availability of microbiological and geochemical data from island-based and high-arsenic hydrothermal systems is limited. Here, the microbial diversity in island-based hot springs on Ambitle Island (Papua New Guinea) was investigated using culture-dependent and -independent methods. Waramung and Kapkai are alkaline springs high in sulfide and arsenic, related hydrologically to previously described hydrothermal vents in nearby Tutum Bay. Enrichments were carried out at 24 conditions with varying temperature (45, 80 °C), pH (6.5, 8.5), terminal electron acceptors (O2, SO4 (2-), S(0), NO3 (-)), and electron donors (organic carbon, H2, As(III)). Growth was observed in 20 of 72 tubes, with media targeting heterotrophic metabolisms the most successful. 16S ribosomal RNA gene surveys of environmental samples revealed representatives in 15 bacterial phyla and 8 archaeal orders. While the Kapkai 4 bacterial clone library is primarily made up of Thermodesulfobacteria (74%), no bacterial taxon represents a majority in the Kapkai 3 and Waramung samples (40% Proteobacteria and 39% Aquificae, respectively). Deinococcus/Thermus and Thermotogae are observed in all samples. The Thermococcales dominate the archaeal clone libraries (65-85%). Thermoproteales, Desulfurococcales, and uncultured Eury- and Crenarchaeota make up the remaining archaeal taxonomic diversity. The culturing and phylogenetic results are consistent with the geochemistry of the alkaline, saline, and sulfide-rich fluids. When compared to other alkaline, island-based, high-arsenic, or shallow-sea hydrothermal communities, the Ambitle Island archaeal communities are unique in geochemical conditions, and in taxonomic diversity, richness, and evenness.}, }
@article {pmid24902979, year = {2015}, author = {Pernice, M and Dunn, SR and Tonk, L and Dove, S and Domart-Coulon, I and Hoppe, P and Schintlmeister, A and Wagner, M and Meibom, A}, title = {A nanoscale secondary ion mass spectrometry study of dinoflagellate functional diversity in reef-building corals.}, journal = {Environmental microbiology}, volume = {17}, number = {10}, pages = {3570-3580}, doi = {10.1111/1462-2920.12518}, pmid = {24902979}, issn = {1462-2920}, support = {294343/ERC_/European Research Council/International ; }, mesh = {Ammonium Compounds/metabolism ; Animals ; Anthozoa/*physiology ; Carbon/*metabolism ; *Coral Reefs ; Dinoflagellida/chemistry/genetics/*physiology ; Genetic Variation ; Nitrogen/*metabolism ; Photosynthesis/genetics ; Spectrometry, Mass, Secondary Ion ; Symbiosis/genetics/*physiology ; Temperature ; }, abstract = {Nutritional interactions between corals and symbiotic dinoflagellate algae lie at the heart of the structural foundation of coral reefs. Whilst the genetic diversity of Symbiodinium has attracted particular interest because of its contribution to the sensitivity of corals to environmental changes and bleaching (i.e. disruption of coral-dinoflagellate symbiosis), very little is known about the in hospite metabolic capabilities of different Symbiodinium types. Using a combination of stable isotopic labelling and nanoscale secondary ion mass spectrometry (NanoSIMS), we investigated the ability of the intact symbiosis between the reef-building coral Isopora palifera, and Symbiodinium C or D types, to assimilate dissolved inorganic carbon (via photosynthesis) and nitrogen (as ammonium). Our results indicate that Symbiodinium types from two clades naturally associated with I. palifera possess different metabolic capabilities. The Symbiodinium C type fixed and passed significantly more carbon and nitrogen to its coral host than the D type. This study provides further insights into the metabolic plasticity among different Symbiodinium types in hospite and strengthens the evidence that the more temperature-tolerant Symbiodinium D type may be less metabolically beneficial for its coral host under non-stressful conditions.}, }
@article {pmid24902956, year = {2015}, author = {Hermes, GD and Zoetendal, EG and Smidt, H}, title = {Molecular ecological tools to decipher the role of our microbial mass in obesity.}, journal = {Beneficial microbes}, volume = {6}, number = {1}, pages = {61-81}, doi = {10.3920/BM2014.0016}, pmid = {24902956}, issn = {1876-2891}, mesh = {*Biota ; Fatty Acids/metabolism ; Gastrointestinal Tract/*microbiology ; Gene Expression Profiling/*methods ; Humans ; Metabolomics/*methods ; Metagenomics/*methods ; Microbiota ; Obesity/*microbiology ; Proteomics/*methods ; }, abstract = {After birth, our gastrointestinal (GI) tract is colonised by a highly complex assemblage of microbes, collectively termed the GI microbiota, that develops intimate interactions with our body. Recent evidence indicates that the GI microbiota and its products may contribute to the development of obesity and related diseases. This, coupled with the current worldwide epidemic of obesity, has moved microbiome research into the spotlight of attention. Although the main cause of obesity and its associated metabolic complications is excess caloric intake compared with expenditure, differences in GI tract microbial ecology between individuals might be an important biomarker, mediator or new therapeutic target. This can be investigated using a diverse set of complementary so called -omics technologies, such as 16S ribosomal RNA gene-targeted composition profiling, metabolomics, metagenomics, metatranscriptomics and metaproteomics. This review aims to describe the different molecular approaches and their contributions to our understanding of the role of the GI microbiota in host energy homeostasis. Correspondingly, we highlight their respective strengths, but also try to create awareness for their specific limitations. However, it is currently still unclear which bacterial groups play a role in the development of obesity in humans. This might partly be explained by the heterogeneity in genotype, lifestyle, diet and the complex ethology of obesity and its associated metabolic disorders (OAMD). Nevertheless, recent research on this matter has shown a conceptual shift by focusing on more homogenous subpopulations, through the use of both anthropometric (weight, total body fat) as well as biochemical variables (insulin resistance, hyperlipidaemia) to define categories. Combined with technological advances, recent data suggests that an OAMD associated microbiota can be characterised by a potential pro-inflammatory composition, with less potential for the production of short chain fatty acids and butyrate in particular.}, }
@article {pmid24902875, year = {2015}, author = {Kivelä, M and Arnaud-Haond, S and Saramäki, J}, title = {EDENetworks: a user-friendly software to build and analyse networks in biogeography, ecology and population genetics.}, journal = {Molecular ecology resources}, volume = {15}, number = {1}, pages = {117-122}, doi = {10.1111/1755-0998.12290}, pmid = {24902875}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Ecology/*methods ; Genetics, Population/*methods ; Phylogeography/*methods ; *Software ; }, abstract = {The recent application of graph-based network theory analysis to biogeography, community ecology and population genetics has created a need for user-friendly software, which would allow a wider accessibility to and adaptation of these methods. EDENetworks aims to fill this void by providing an easy-to-use interface for the whole analysis pipeline of ecological and evolutionary networks starting from matrices of species distributions, genotypes, bacterial OTUs or populations characterized genetically. The user can choose between several different ecological distance metrics, such as Bray-Curtis or Sorensen distance, or population genetic metrics such as FST or Goldstein distances, to turn the raw data into a distance/dissimilarity matrix. This matrix is then transformed into a network by manual or automatic thresholding based on percolation theory or by building the minimum spanning tree. The networks can be visualized along with auxiliary data and analysed with various metrics such as degree, clustering coefficient, assortativity and betweenness centrality. The statistical significance of the results can be estimated either by resampling the original biological data or by null models based on permutations of the data.}, }
@article {pmid24893651, year = {2014}, author = {Gosiewski, T and Jurkiewicz-Badacz, D and Sroka, A and Brzychczy-Włoch, M and Bulanda, M}, title = {A novel, nested, multiplex, real-time PCR for detection of bacteria and fungi in blood.}, journal = {BMC microbiology}, volume = {14}, number = {}, pages = {144}, pmid = {24893651}, issn = {1471-2180}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Blood/*microbiology ; Fungi/classification/genetics/*isolation &amp; purification ; Humans ; Multiplex Polymerase Chain Reaction/*methods ; Polymerase Chain Reaction/*methods ; Real-Time Polymerase Chain Reaction/*methods ; Sepsis/*diagnosis/microbiology ; }, abstract = {BACKGROUND: The study describes the application of the PCR method for the simultaneous detection of DNA of Gram-negative bacteria, Gram-positive bacteria, yeast fungi and filamentous fungi in blood and, thus, a whole range of microbial etiological agents that may cause sepsis. Material for the study was sterile blood inoculated with four species of microorganisms (Escherichia coli, Staphylococcus aureus, Candida albicans and Aspergillus fumigatus) and blood collected from patients with clinical symptoms of sepsis. The developed method is based on nested-multiplex real-time PCR .<br><br>RESULTS: Analysis of the obtained data shows that sensitivity of nested-multiplex real-time PCR remained at the level of 10(1) CFU/ml for each of the four studied species of microorganisms and the percentage of positive results of the examined blood samples from the patients was 70% and 19% for the microbiological culture method. The designed primers correctly typed the studied species as belonging to the groups of Gram-positive bacteria, Gram-negative bacteria, yeast fungi, or filamentous fungi.<br><br>CONCLUSIONS: Results obtained by us indicated that the designed PCR methods: (1) allow to detect bacteria in whole blood samples, (2) are much more sensitive than culture method, (3) allow differentiation of the main groups of microorganisms within a few hours.}, }
@article {pmid24893336, year = {2014}, author = {Etto, RM and Cruz, LM and da Conceição Jesus, E and Galvão, CW and Galvão, F and de Souza, EM and de Oliveira Pedrosa, F and Reynaud Steffens, MB}, title = {Seasonal changes in dominant bacterial taxa from acidic peatlands of the Atlantic Rain Forest.}, journal = {Research in microbiology}, volume = {165}, number = {7}, pages = {517-525}, doi = {10.1016/j.resmic.2014.05.036}, pmid = {24893336}, issn = {1769-7123}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; *Biota ; Brazil ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Rainforest ; Seasons ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The acidic peatlands of southern Brazil are essential for maintenance of the Atlantic Rain Forest, one of the 25 hot-spots of biodiversity in the world. While these ecosystems are closely linked to conservation issues, their microbial community ecology and composition remain unknown. In this work, histosol samples were collected from three acidic peatland regions during dry and rainy seasons and their chemical and microbial characteristics were evaluated. Culturing and culture-independent approaches based on SSU rRNA gene pyrosequencing were used to survey the bacterial community and to identify environmental factors affecting the biodiversity and microbial metabolic potential of the Brazilian peatlands. All acidic peatlands were dominated by the Acidobacteria phylum (56-22%) followed by Proteobacteria (28-12%). The OTU richness of these phyla and the abundance of their Gp1, Gp2, Gp3, Gp13, Rhodospirillales and Caulobacteriales members varied according to the period of collection and significantly correlated with the rainy season. However, despite changes in acidobacterial and proteobacterial communities, rainfall did not affect the microbial metabolic potential of the southern Brazilian Atlantic Rain Forest peatlands, as judged by the metabolic capabilities of the microbial community.}, }
@article {pmid24891731, year = {2014}, author = {Prakash, O and Pandey, PK and Kulkarni, GJ and Mahale, KN and Shouche, YS}, title = {Technicalities and Glitches of Terminal Restriction Fragment Length Polymorphism (T-RFLP).}, journal = {Indian journal of microbiology}, volume = {54}, number = {3}, pages = {255-261}, pmid = {24891731}, issn = {0046-8991}, abstract = {Terminal restriction fragment length polymorphism (T-RFLP) is a rapid, robust, inexpensive and simple tool for microbial community profiling. Methods used for DNA extraction, PCR amplification and digestion of amplified products have a considerable impact on the results of T-RFLP. Pitfalls of the method skew the similarity analysis and compromise its high throughput ability. Despite a high throughput method of data generation, data analysis is still in its infancy and needs more attention. Current article highlights the limitations of the methods used for data generation and analysis. It also provides an overview of the recent methodological developments in T-RFLP which will assist the readers in obtaining real and authentic profiles of the microbial communities under consideration while eluding the inherent biases and technical difficulties.}, }
@article {pmid24889288, year = {2014}, author = {Wang, Z and Guo, F and Mao, Y and Xia, Y and Zhang, T}, title = {Metabolic characteristics of a glycogen-accumulating organism in Defluviicoccus cluster II revealed by comparative genomics.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {716-728}, pmid = {24889288}, issn = {1432-184X}, mesh = {China ; DNA, Bacterial/genetics/metabolism ; *Genome, Bacterial ; Genomics ; Glycogen/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Rhodospirillaceae/*genetics/metabolism ; Sequence Analysis, DNA ; Sewage/*microbiology ; }, abstract = {Glycogen-accumulating organisms (GAOs) may compete with phosphate-accumulating organisms (PAOs) for short-chain fatty acids (VFAs) in anaerobic polyhydroxyalkanoates (PHA) synthesis, but no consequently aerobic polyphosphate accumulation in enhanced biological phosphorus removal (EBPR) process, thus deteriorating the EBPR process. They are detected frequently in the deteriorated EBPR process, but their metabolisms are still far from our comprehensions for there is seldom pure culture. In this study, a nearly complete draft genome of a GAOs in Defluviicoccus cluster II, GAO-HK, is recruited from the metagenome of activated sludge in a full-scale industrial anoxic/aerobic wastewater plant. Comparative genomics reveal similar metabolisms of PHA and glycogen in GAOs of GAO-HK, Defluviicoccus tetraformis TFO71 (TFO71) and Competibacter phosphatis clade IIA (CPIIA), and PAOs of Accumulibacter clade IIA UW-1 (UW-1) and Tetrasphaera elongata Lp2 (Lp2). Although there are similar gene cassettes related with polyphosphate metabolism in these GAOs and PAOs, especially for Defluviicoccus-relative bacteria and UW-1, ppk1 in GAOs are diverse from those in the identified PAOs, implying the difference of polyphosphate metabolism in GAOs and PAOs. Additionally, genes related to the dissimilatory denitrification are absent in TFO71 and GAO-HK, implying that additional nitrate or nitrite may favor PAOs over Defluviicoccus-relative GAOs. Therefore, PAOs suffering from competition of Defluviicoccus-relative GAOs might be rescued with the additional nitrate/nitrite, which is important to improve the stability of EBPR processes.}, }
@article {pmid24889287, year = {2014}, author = {Cuecas, A and Portillo, MC and Kanoksilapatham, W and Gonzalez, JM}, title = {Bacterial distribution along a 50 °C temperature gradient reveals a parceled out hot spring environment.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {729-739}, pmid = {24889287}, issn = {1432-184X}, mesh = {*Biodiversity ; Chloroflexi/genetics/*physiology ; Cyanobacteria/genetics/*physiology ; DNA, Bacterial/genetics ; Hot Springs/*microbiology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Thailand ; }, abstract = {Understanding the distribution of bacteria is a major goal of microbial ecology which remains to be fully deciphered. In this study, a model 50 °C temperature gradient at a Northern Thailand hot spring was analyzed to determine how the bacterial communities were structured in the environment. Communities were examined through 16S rRNA gene amplification, denaturing gradient gel electrophoresis, and sequencing. The two major phyla, Cyanobacteria and Chloroflexi, showed characteristic distributions along the temperature gradient. Different clades were allocated at specific portions of the gradient. Comparisons of the bacterial communities along the temperature gradient showed sharp decreases of similarity at increasing temperature difference. Peaks of maximum richness were observed at 50 and 70 °C. This study contributes to explain how environmental conditions and microbial interactions can influence the distribution of specific bacterial clades and phyla shaping the structure of microbial communities in nature.}, }
@article {pmid24889286, year = {2015}, author = {Waring, BG and Hawkes, CV}, title = {Short-term precipitation exclusion alters microbial responses to soil moisture in a wet tropical forest.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {843-854}, pmid = {24889286}, issn = {1432-184X}, mesh = {Biota ; Costa Rica ; *Rain ; *Rainforest ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Many wet tropical forests, which contain a quarter of global terrestrial biomass carbon stocks, will experience changes in precipitation regime over the next century. Soil microbial responses to altered rainfall are likely to be an important feedback on ecosystem carbon cycling, but the ecological mechanisms underpinning these responses are poorly understood. We examined how reduced rainfall affected soil microbial abundance, activity, and community composition using a 6-month precipitation exclusion experiment at La Selva Biological Station, Costa Rica. Thereafter, we addressed the persistent effects of field moisture treatments by exposing soils to a controlled soil moisture gradient in the lab for 4 weeks. In the field, compositional and functional responses to reduced rainfall were dependent on initial conditions, consistent with a large degree of spatial heterogeneity in tropical forests. However, the precipitation manipulation significantly altered microbial functional responses to soil moisture. Communities with prior drought exposure exhibited higher respiration rates per unit microbial biomass under all conditions and respired significantly more CO2 than control soils at low soil moisture. These functional patterns suggest that changes in microbial physiology may drive positive feedbacks to rising atmospheric CO2 concentrations if wet tropical forests experience longer or more intense dry seasons in the future.}, }
@article {pmid24889285, year = {2014}, author = {Hodel, M and Schütz, M and Vandegehuchte, ML and Frey, B and Albrecht, M and Busse, MD and Risch, AC}, title = {Does the aboveground herbivore assemblage influence soil bacterial community composition and richness in subalpine grasslands?.}, journal = {Microbial ecology}, volume = {68}, number = {3}, pages = {584-595}, pmid = {24889285}, issn = {1432-184X}, mesh = {Altitude ; Animals ; Bacteria/*classification ; Biomass ; Carbon/analysis ; *Grassland ; *Herbivory ; Polymorphism, Restriction Fragment Length ; Rhizosphere ; *Soil Microbiology ; Spatio-Temporal Analysis ; Switzerland ; }, abstract = {Grassland ecosystems support large communities of aboveground herbivores that are known to directly and indirectly affect belowground properties such as the microbial community composition, richness, or biomass. Even though multiple species of functionally different herbivores coexist in grassland ecosystems, most studies have only considered the impact of a single group, i.e., large ungulates (mostly domestic livestock) on microbial communities. Thus, we investigated how the exclusion of four groups of functionally different herbivores affects bacterial community composition, richness, and biomass in two vegetation types with different grazing histories. We progressively excluded large, medium, and small mammals as well as invertebrate herbivores using exclosures at 18 subalpine grassland sites (9 per vegetation type). We assessed the bacterial community composition using terminal restriction fragment length polymorphism (T-RFLP) at each site and exclosure type during three consecutive growing seasons (2009-2011) for rhizosphere and mineral soil separately. In addition, we determined microbial biomass carbon (MBC), root biomass, plant carbon:nitrogen ratio, soil temperature, and soil moisture. Even though several of these variables were affected by herbivore exclusion and vegetation type, against our expectations, bacterial community composition, richness, or MBC were not. Yet, bacterial communities strongly differed between the three growing seasons as well as to some extent between our study sites. Thus, our study indicates that the spatiotemporal variability in soil microclimate has much stronger effects on the soil bacterial communities than the grazing regime or the composition of the vegetation in this high-elevation ecosystem.}, }
@article {pmid24889284, year = {2014}, author = {Lambais, MR and Lucheta, AR and Crowley, DE}, title = {Bacterial community assemblages associated with the phyllosphere, dermosphere, and rhizosphere of tree species of the Atlantic forest are host taxon dependent.}, journal = {Microbial ecology}, volume = {68}, number = {3}, pages = {567-574}, pmid = {24889284}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics ; Brazil ; DNA, Bacterial/genetics ; Forests ; Molecular Sequence Data ; *Phylogeny ; Plant Bark/microbiology ; Plant Leaves/microbiology ; Plant Roots/genetics ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; *Soil Microbiology ; Species Specificity ; Trees/*microbiology ; }, abstract = {Bacterial communities associated with tree canopies have been shown to be specific to their plant hosts, suggesting that plant species-specific traits may drive the selection of microbial species that comprise their microbiomes. To further examine the degree to which the plant taxa drive the assemblage of bacterial communities in specific plant microenvironments, we evaluated bacterial community structures associated with the phyllosphere, dermosphere, and rhizosphere of seven tree species representing three orders, four families and four genera of plants from a pristine Dense Ombrophilous Atlantic forest in Brazil, using a combination of PCR-DGGE of 16S rRNA genes and clone library sequencing. Results indicated that each plant species selected for distinct bacterial communities in the phyllosphere, dermosphere, and rhizosphere, and that the bacterial community structures are significantly related to the plant taxa, at the species, family, and order levels. Further characterization of the bacterial communities of the phyllosphere and dermosphere of the tree species showed that they were inhabited predominantly by species of Gammaproteobacteria, mostly related to Pseudomonas. In contrast, the rhizosphere bacterial communities showed greater species richness and evenness, and higher frequencies of Alphaproteobacteria and Acidobacteria Gp1. With individual tree species each selecting for their specific microbiomes, these findings greatly increase our estimates of the bacterial species richness in tropical forests and provoke questions concerning the ecological functions of the microbial communities that exist on different plant parts.}, }
@article {pmid24889097, year = {2015}, author = {Wasmund, K and Algora, C and Müller, J and Krüger, M and Lloyd, KG and Reinhardt, R and Adrian, L}, title = {Development and application of primers for the class Dehalococcoidia (phylum Chloroflexi) enables deep insights into diversity and stratification of subgroups in the marine subsurface.}, journal = {Environmental microbiology}, volume = {17}, number = {10}, pages = {3540-3556}, doi = {10.1111/1462-2920.12510}, pmid = {24889097}, issn = {1462-2920}, mesh = {Aquatic Organisms/*classification/genetics ; Base Sequence ; Biodiversity ; Chloroflexi/*classification/*genetics/isolation &amp; purification ; DNA Primers/*genetics ; DNA, Bacterial/genetics ; Genomics ; Geologic Sediments/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Bacteria of the class Dehalococcoidia (DEH) (phylum Chloroflexi) are widely distributed in the marine subsurface and are especially prevalent in deep marine sediments. Nevertheless, little is known about the specific distributions of DEH subgroups at different sites and depths. This study therefore specifically examined the distributions of DEH through depths of various marine sediment cores by quantitative PCR and pyrosequencing using newly designed DEH 16S rRNA gene targeting primers. Quantification of DEH showed populations may establish in shallow sediments (i.e. upper centimetres), although as low relative proportions of total Bacteria, yet often became more prevalent in deeper sediments. Pyrosequencing revealed pronounced diversity co-exists within single biogeochemical zones, and that clear and sometimes abrupt shifts in relative proportions of DEH subgroups occur with depth. These shifts indicate varying metabolic properties exist among DEH subgroups. The distributional changes in DEH subgroups with depth may be related to a combination of biogeochemical factors including the availability of electron acceptors such as sulfate, the composition of organic matter and depositional regimes. Collectively, the results suggest DEH exhibit wider metabolic and genomic diversity than previously recognized, and this contributes to their widespread occurrence in the marine subsurface.}, }
@article {pmid24886397, year = {2014}, author = {Alsop, EB and Boyd, ES and Raymond, J}, title = {Merging metagenomics and geochemistry reveals environmental controls on biological diversity and evolution.}, journal = {BMC ecology}, volume = {14}, number = {}, pages = {16}, pmid = {24886397}, issn = {1472-6785}, mesh = {Algorithms ; Bacteria/classification/genetics ; *Biodiversity ; *Biological Evolution ; Cluster Analysis ; *Environment ; Hot Springs/chemistry/microbiology ; Markov Chains ; *Metagenomics ; Principal Component Analysis ; Seawater/chemistry/microbiology ; Water Microbiology ; }, abstract = {BACKGROUND: The metabolic strategies employed by microbes inhabiting natural systems are, in large part, dictated by the physical and geochemical properties of the environment. This study sheds light onto the complex relationship between biology and environmental geochemistry using forty-three metagenomes collected from geochemically diverse and globally distributed natural systems. It is widely hypothesized that many uncommonly measured geochemical parameters affect community dynamics and this study leverages the development and application of multidimensional biogeochemical metrics to study correlations between geochemistry and microbial ecology. Analysis techniques such as a Markov cluster-based measure of the evolutionary distance between whole communities and a principal component analysis (PCA) of the geochemical gradients between environments allows for the determination of correlations between microbial community dynamics and environmental geochemistry and provides insight into which geochemical parameters most strongly influence microbial biodiversity.<br><br>RESULTS: By progressively building from samples taken along well defined geochemical gradients to samples widely dispersed in geochemical space this study reveals strong links between the extent of taxonomic and functional diversification of resident communities and environmental geochemistry and reveals temperature and pH as the primary factors that have shaped the evolution of these communities. Moreover, the inclusion of extensive geochemical data into analyses reveals new links between geochemical parameters (e.g. oxygen and trace element availability) and the distribution and taxonomic diversification of communities at the functional level. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial taxonomic and functional composition.<br><br>CONCLUSIONS: Clustering based on the frequency in which orthologous proteins occur among metagenomes facilitated accurate prediction of the ordering of community functional composition along geochemical gradients, despite a lack of geochemical input. The consistency in the results obtained from the application of Markov clustering and multivariate methods to distinct natural systems underscore their utility in predicting the functional potential of microbial communities within a natural system based on system geochemistry alone, allowing geochemical measurements to be used to predict purely biological metrics such as microbial community composition and metabolism.}, }
@article {pmid24884540, year = {2014}, author = {Marzorati, M and Vanhoecke, B and De Ryck, T and Sadaghian Sadabad, M and Pinheiro, I and Possemiers, S and Van den Abbeele, P and Derycke, L and Bracke, M and Pieters, J and Hennebel, T and Harmsen, HJ and Verstraete, W and Van de Wiele, T}, title = {The HMI™ module: a new tool to study the Host-Microbiota Interaction in the human gastrointestinal tract in vitro.}, journal = {BMC microbiology}, volume = {14}, number = {}, pages = {133}, pmid = {24884540}, issn = {1471-2180}, mesh = {Epithelial Cells/*microbiology/*physiology ; Gastrointestinal Tract/*microbiology ; Humans ; Microbiota/*physiology ; *Models, Biological ; }, abstract = {BACKGROUND: Recent scientific developments have shed more light on the importance of the host-microbe interaction, particularly in the gut. However, the mechanistic study of the host-microbe interplay is complicated by the intrinsic limitations in reaching the different areas of the gastrointestinal tract (GIT) in vivo. In this paper, we present the technical validation of a new device--the Host-Microbiota Interaction (HMI) module--and the evidence that it can be used in combination with a gut dynamic simulator to evaluate the effect of a specific treatment at the level of the luminal microbial community and of the host surface colonization and signaling.<br><br>RESULTS: The HMI module recreates conditions that are physiologically relevant for the GIT: i) a mucosal area to which bacteria can adhere under relevant shear stress (3 dynes cm(-2)); ii) the bilateral transport of low molecular weight metabolites (4 to 150 kDa) with permeation coefficients ranging from 2.4 &#xd7; 10(-6) to 7.1 &#xd7; 10(-9) cm sec(-1); and iii) microaerophilic conditions at the bottom of the growing biofilm (PmO2 =&#x2009;2.5 &#xd7; 10(-4) cm sec(-1)). In a long-term study, the host's cells in the HMI module were still viable after a 48-hour exposure to a complex microbial community. The dominant mucus-associated microbiota differed from the luminal one and its composition was influenced by the treatment with a dried product derived from yeast fermentation. The latter--with known anti-inflammatory properties--induced a decrease of pro-inflammatory IL-8 production between 24 and 48 h.<br><br>CONCLUSIONS: The study of the in vivo functionality of adhering bacterial communities in the human GIT and of the localized effect on the host is frequently hindered by the complexity of reaching particular areas of the GIT. The HMI module offers the possibility of co-culturing a gut representative microbial community with enterocyte-like cells up to 48 h and may therefore contribute to the mechanistic understanding of host-microbiome interactions.}, }
@article {pmid24884520, year = {2014}, author = {De Maayer, P and Chan, WY and Rubagotti, E and Venter, SN and Toth, IK and Birch, PR and Coutinho, TA}, title = {Analysis of the Pantoea ananatis pan-genome reveals factors underlying its ability to colonize and interact with plant, insect and vertebrate hosts.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {404}, pmid = {24884520}, issn = {1471-2164}, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; Enterobacteriaceae Infections/microbiology/*veterinary ; Gene-Environment Interaction ; *Genome, Bacterial ; Humans ; Insecta/microbiology ; Pantoea/classification/*genetics/*physiology ; Phylogeny ; Plant Diseases/*microbiology ; Plants/microbiology ; Vertebrates/microbiology ; }, abstract = {BACKGROUND: Pantoea ananatis is found in a wide range of natural environments, including water, soil, as part of the epi- and endophytic flora of various plant hosts, and in the insect gut. Some strains have proven effective as biological control agents and plant-growth promoters, while other strains have been implicated in diseases of a broad range of plant hosts and humans. By analysing the pan-genome of eight sequenced P. ananatis strains isolated from different sources we identified factors potentially underlying its ability to colonize and interact with hosts in both the plant and animal Kingdoms.<br><br>RESULTS: The pan-genome of the eight compared P. ananatis strains consisted of a core genome comprised of 3,876 protein coding sequences (CDSs) and a sizeable accessory genome consisting of 1,690 CDSs. We estimate that ~106 unique CDSs would be added to the pan-genome with each additional P. ananatis genome sequenced in the future. The accessory fraction is derived mainly from integrated prophages and codes mostly for proteins of unknown function. Comparison of the translated CDSs on the P. ananatis pan-genome with the proteins encoded on all sequenced bacterial genomes currently available revealed that P. ananatis carries a number of CDSs with orthologs restricted to bacteria associated with distinct hosts, namely plant-, animal- and insect-associated bacteria. These CDSs encode proteins with putative roles in transport and metabolism of carbohydrate and amino acid substrates, adherence to host tissues, protection against plant and animal defense mechanisms and the biosynthesis of potential pathogenicity determinants including insecticidal peptides, phytotoxins and type VI secretion system effectors.<br><br>CONCLUSIONS: P. ananatis has an 'open' pan-genome typical of bacterial species that colonize several different environments. The pan-genome incorporates a large number of genes encoding proteins that may enable P. ananatis to colonize, persist in and potentially cause disease symptoms in a wide range of plant and animal hosts.}, }
@article {pmid24881215, year = {2014}, author = {Zhang, Y and He, J and Zhou, X and Cao, S and Wu, T and Cao, Y and Xu, X}, title = {[Human buccal mucosa microbiota succession across age].}, journal = {Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology}, volume = {32}, number = {2}, pages = {177-181}, pmid = {24881215}, issn = {1000-1182}, mesh = {Adolescent ; Adult ; Aged ; DNA, Bacterial ; Humans ; Microbiota ; *Mouth Mucosa ; Polymerase Chain Reaction ; *RNA, Ribosomal, 16S ; }, abstract = {OBJECTIVE: This investigation aimed to examine how buccal mucosa microbiome succeeds in a healthy population with different ages and dentition stages.<br><br>METHODS: Twenty-five subjects were recruited and subdivided into five groups: primary dentition group, mixed dentition group, adolescent group, adult group, and elderly group. Individual mucosal microbiota was obtained by gently scraping both sides of the buccal mucosa with a cotton swab. Microbial diversity was analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE).<br><br>RESULTS: 1) The composition of buccal mucosa microbiota has great intra-individual divergence. 2) The average band numbers of the primary dentition group, mixed dentition group, adolescent group, adult group, and elderly group were 21.2 +/- 4.0, 17.8 +/- 3.9, 15.8 +/- 4.3, 16.8 +/- 3.7, and 22.2 +/- 6.5, respectively. No between-group differences was observed (P > 0.05), indicating that predominant strains in the oral cavity may be stable throughout an individual's lifetime. 3) The Shannon indices of primary dentition group, mixed dentition group, adolescent group, adult group, and elderly group were 1.73 +/- 10.2, 1.43 +/- 0.1, 1.05 +/- 0.2, 1.45 +/- 0.2, and 1.63 +/- 0.3, respectively. A significant between-group difference was observed (P = 0.003), indicating that the microbial diversity of the buccal mucosa decreases from childhood through adolescence, but increases from adult through senescence. 4) The clustering analysis showed that most of the samples in the same group clustered together, indicating higher intra-group community structure similarity.<br><br>CONCLUSION: Composition of the buccal mucosa microbiota was different among age groups. Adolescence may be an essential turning point of microbial ecology succession throughout life.}, }
@article {pmid24880500, year = {2014}, author = {de Paula, VA and de Carvalho Ferreira, D and Cavalcante, FS and do Carmo, FL and Rosado, AS and Primo, LG and dos Santos, KR}, title = {Clinical signs and bacterial communities of deciduous necrotic root canals detected by PCR-DGGE analysis: research association.}, journal = {Archives of oral biology}, volume = {59}, number = {8}, pages = {848-854}, doi = {10.1016/j.archoralbio.2014.05.012}, pmid = {24880500}, issn = {1879-1506}, mesh = {Bacterial Typing Techniques ; Child ; Child, Preschool ; Denaturing Gradient Gel Electrophoresis ; Dental Pulp Cavity/*microbiology ; Female ; Humans ; Infant ; Male ; Necrosis/microbiology ; Periapical Diseases/*microbiology ; Polymerase Chain Reaction ; *Root Canal Therapy ; Tooth, Deciduous/*microbiology ; }, abstract = {OBJECTIVE: This study sought to investigate the possible association between clinical and radiographic data of the patients with the bacterial community profiles involved in cases of necrosis in primary root canals.<br><br>METHODS: Microbial community profiles for 25 samples from necrotic deciduous root canals were analyzed using the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprinting approach. These results were related to the clinical and radiographic data of these patients.<br><br>RESULTS: The analysis showed a large diversity of microbial communities in necrotic deciduous root canals. The statistical results pointed out that posterior and anterior teeth were associated with <20 bands and >20 bands in PCR-DGGE method, respectively. A relationship was verified between ages >4 years old and posterior teeth and, ages &#x2264;4 years old and anterior teeth.<br><br>CONCLUSIONS: The data showed a polymicrobial community and pointed out the association of age with necrosis in anterior and posterior teeth.}, }
@article {pmid24880029, year = {2014}, author = {Lopez-Ferraz, C and Ramírez, P and Gordon, M and Marti, V and Gil-Perotin, S and Gonzalez, E and Villarreal, E and Alvarez-Lerma, F and Menendez, R and Bonastre, J and Torres, A}, title = {Impact of microbial ecology on accuracy of surveillance cultures to predict multidrug resistant microorganisms causing ventilator-associated pneumonia.}, journal = {The Journal of infection}, volume = {69}, number = {4}, pages = {333-340}, doi = {10.1016/j.jinf.2014.05.011}, pmid = {24880029}, issn = {1532-2742}, mesh = {Adult ; Aged ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/isolation &amp; purification ; Chi-Square Distribution ; Drug Resistance, Multiple, Bacterial ; *Environmental Microbiology ; Female ; Humans ; Infection Control/*statistics &amp; numerical data ; Male ; Middle Aged ; Pneumonia, Bacterial/epidemiology/*microbiology ; Pneumonia, Ventilator-Associated/epidemiology/*microbiology ; Prospective Studies ; Spain/epidemiology ; }, abstract = {OBJECTIVES: The objective of this study was to assess surveillance cultures (SC) prediction accuracy in two periods and settings of the same Department with a different microbiological epidemiology (high and low prevalence of multi-drug resistant microorganisms (MDRM)).<br><br>METHODS: Prospective and observational study. SC were obtained twice a week in consecutive mechanically ventilated patients. Patients fulfilling VAP criteria were analyzed.<br><br>RESULTS: 440 patients were followed up, 71 patients had VAP (50 in period I and 21 in period II). MDRM causing VAP were more prevalent in the first period (48% vs. 19%; p&#xa0;=&#xa0;0.033). The rate of empirical appropriate treatment in period I was lower than in period II (52% vs.76%; p&#xa0;=&#xa0;0.031). SC prediction accuracy was similar in the two periods (80% vs. 81%; p&#xa0;=&#xa0;0.744). However, if antibiotic treatment had been guided by SC, the percentage of appropriate treatment would have increased by 28% in the first period but only by 5% in the second; p&#xa0;=&#xa0;0.024.<br><br>CONCLUSIONS: SC were able to predict VAP etiology in 80% of cases regardless the prevalence of MDRM. However, the potential benefit of SC in terms of appropriate empirical treatment could be only observed when MDRM were prevalent.}, }
@article {pmid24863131, year = {2014}, author = {Bastidas Navarro, M and Balseiro, E and Modenutti, B}, title = {Bacterial community structure in patagonian Andean Lakes above and below timberline: from community composition to community function.}, journal = {Microbial ecology}, volume = {68}, number = {3}, pages = {528-541}, pmid = {24863131}, issn = {1432-184X}, mesh = {Altitude ; Argentina ; Bacteria/*classification/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; *Ecosystem ; Fresh Water/chemistry/*microbiology ; Lakes/chemistry/microbiology ; Microbial Consortia ; Organic Chemicals/chemistry ; Water Microbiology ; }, abstract = {Lakes located above the timberline are remote systems with a number of extreme environmental conditions, becoming physically harsh ecosystems, and sensors of global change. We analyze bacterial community composition and community-level physiological profiles in mountain lakes located in an altitude gradient in North Patagonian Andes below and above the timberline, together with dissolved organic carbon (DOC) characterization and consumption. Our results indicated a decrease in 71 % of DOC and 65 % in total dissolved phosphorus (TDP) concentration as well as in bacteria abundances along the altitude range (1,380 to 1,950 m a.s.l.). Dissolved organic matter (DOM) fluorescence analysis revealed a low global variability composed by two humic-like components (allochthonous substances) and a single protein-like component (autochthonous substances). Lakes below the timberline showed the presence of all the three components, while lakes above the timberline the protein-like compound constituted the main DOC component. Furthermore, bacterial community composition similarity and ordination analysis showed that altitude and resource concentration (DOC and TDP) were the main variables determining the ordination of groups. Community-level physiological profiles showed a mismatch with bacteria community composition (BCC), indicating the absence of a relationship between genetic and functional diversity in the altitude gradient. However, carbon utilization efficiencies varied according to the presence of different compounds in DOM bulk. The obtained results suggest that the different bacterial communities in these mountain lakes seem to have similar metabolic pathways in order to be able to exploit the available DOC molecules.}, }
@article {pmid24863130, year = {2014}, author = {Wakai, S and Ito, K and Iino, T and Tomoe, Y and Mori, K and Harayama, S}, title = {Corrosion of iron by iodide-oxidizing bacteria isolated from brine in an iodine production facility.}, journal = {Microbial ecology}, volume = {68}, number = {3}, pages = {519-527}, pmid = {24863130}, issn = {1432-184X}, mesh = {Bacteria/classification/isolation &amp; purification/*metabolism ; Corrosion ; DNA, Bacterial/genetics ; Iodides/*metabolism ; Iron/*chemistry ; Japan ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; *Salts ; }, abstract = {Elemental iodine is produced in Japan from underground brine (fossil salt water). Carbon steel pipes in an iodine production facility at Chiba, Japan, for brine conveyance were found to corrode more rapidly than those in other facilities. The corroding activity of iodide-containing brine from the facility was examined by immersing carbon steel coupons in "native" and "filter-sterilized" brine samples. The dissolution of iron from the coupons immersed in native brine was threefold to fourfold higher than that in the filter-sterilized brine. Denaturing gradient gel electrophoresis analyses revealed that iodide-oxidizing bacteria (IOBs) were predominant in the coupon-containing native brine samples. IOBs were also detected in a corrosion deposit on the inner surface of a corroded pipe. These results strongly suggested the involvement of IOBs in the corrosion of the carbon steel pipes. Of the six bacterial strains isolated from a brine sample, four were capable of oxidizing iodide ion (I(-)) into molecular iodine (I(2)), and these strains were further phylogenetically classified into two groups. The iron-corroding activity of each of the isolates from the two groups was examined. Both strains corroded iron in the presence of potassium iodide in a concentration-dependent manner. This is the first report providing direct evidence that IOBs are involved in iron corrosion. Further, possible mechanisms by which IOBs corrode iron are discussed.}, }
@article {pmid24863129, year = {2014}, author = {Van den Wyngaert, S and Vanholsbeeck, O and Spaak, P and Ibelings, BW}, title = {Parasite fitness traits under environmental variation: disentangling the roles of a chytrid's immediate host and external environment.}, journal = {Microbial ecology}, volume = {68}, number = {3}, pages = {645-656}, pmid = {24863129}, issn = {1432-184X}, mesh = {Chytridiomycota/genetics/*physiology ; Diatoms/*parasitology ; *Environment ; Genetic Fitness ; Herbicides ; *Host-Parasite Interactions ; }, abstract = {Parasite environments are heterogeneous at different levels. The first level of variability is the host itself. The second level represents the external environment for the hosts, to which parasites may be exposed during part of their life cycle. Both levels are expected to affect parasite fitness traits. We disentangle the main and interaction effects of variation in the immediate host environment, here the diatom Asterionella formosa (variables host cell volume and host condition through herbicide pre-exposure) and variation in the external environment (variables host density and acute herbicide exposure) on three fitness traits (infection success, development time and reproductive output) of a chytrid parasite. Herbicide exposure only decreased infection success in a low host density environment. This result reinforces the hypothesis that chytrid zoospores use photosynthesis-dependent chemical cues to locate its host. At high host densities, chemotaxis becomes less relevant due to increasing chance contact rates between host and parasite, thereby following the mass-action principle in epidemiology. Theoretical support for this finding is provided by an agent-based simulation model. The immediate host environment (cell volume) substantially affected parasite reproductive output and also interacted with the external herbicide exposed environment. On the contrary, changes in the immediate host environment through herbicide pre-exposure did not increase infection success, though it had subtle effects on zoospore development time and reproductive output. This study shows that both immediate host and external environment as well as their interaction have significant effects on parasite fitness. Disentangling these effects improves our understanding of the processes underlying parasite spread and disease dynamics.}, }
@article {pmid24863128, year = {2014}, author = {Kelly, LC and Cockell, CS and Thorsteinsson, T and Marteinsson, V and Stevenson, J}, title = {Pioneer microbial communities of the Fimmvörðuháls lava flow, Eyjafjallajökull, Iceland.}, journal = {Microbial ecology}, volume = {68}, number = {3}, pages = {504-518}, pmid = {24863128}, issn = {1432-184X}, mesh = {Betaproteobacteria/*classification/isolation &amp; purification ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Gene Library ; Iceland ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; *Volcanic Eruptions ; }, abstract = {Little is understood regarding the phylogeny and metabolic capabilities of the earliest colonists of volcanic rocks, yet these data are essential for understanding how life becomes established in and interacts with the planetary crust, ultimately contributing to critical zone processes and soil formation. Here, we report the use of molecular and culture-dependent methods to determine the composition of pioneer microbial communities colonising the basaltic Fimmvörðuháls lava flow at Eyjafjallajökull, Iceland, formed in 2010. Our data show that 3 to 5 months post eruption, the lava was colonised by a low-diversity microbial community dominated by Betaproteobacteria, primarily taxa related to non-phototrophic diazotrophs such as Herbaspirillum spp. and chemolithotrophs such as Thiobacillus. Although successfully cultured following enrichment, phototrophs were not abundant members of the Fimmvörðuháls communities, as revealed by molecular analysis, and phototrophy is therefore not likely to be a dominant biogeochemical process in these early successional basalt communities. These results contrast with older Icelandic lava of comparable mineralogy, in which phototrophs comprised a significant fraction of microbial communities, and the non-phototrophic community fractions were dominated by Acidobacteria and Actinobacteria.}, }
@article {pmid24863127, year = {2014}, author = {Tugarova, AV and Vetchinkina, EP and Loshchinina, EA and Burov, AM and Nikitina, VE and Kamnev, AA}, title = {Reduction of selenite by Azospirillum brasilense with the formation of selenium nanoparticles.}, journal = {Microbial ecology}, volume = {68}, number = {3}, pages = {495-503}, pmid = {24863127}, issn = {1432-184X}, mesh = {Azospirillum brasilense/*metabolism ; Color ; Culture Media ; Nanoparticles/*chemistry ; Oxidation-Reduction ; Selenious Acid/*chemistry ; Selenium/chemistry ; }, abstract = {The ability to reduce selenite (SeO(3)(2-)) ions with the formation of selenium nanoparticles was demonstrated in Azospirillum brasilense for the first time. The influence of selenite ions on the growth of A. brasilense Sp7 and Sp245, two widely studied wild-type strains, was investigated. Growth of cultures on both liquid and solid (2 % agar) media in the presence of SeO(3)(2-) was found to be accompanied by the appearance of the typical red colouration. By means of transmission electron microscopy (TEM), electron energy loss spectroscopy (EELS) and X-ray fluorescence analysis (XFA), intracellular accumulation of elementary selenium in the form of nanoparticles (50 to 400 nm in diameter) was demonstrated for both strains. The proposed mechanism of selenite-to-selenium (0) reduction could involve SeO(3)(2-) in the denitrification process, which has been well studied in azospirilla, rather than a selenite detoxification strategy. The results obtained point to the possibility of using Azospirillum strains as endophytic or rhizospheric bacteria to assist phytoremediation of, and cereal cultivation on, selenium-contaminated soils. The ability of A. brasilense to synthesise selenium nanoparticles may be of interest to nanobiotechnology for "green synthesis" of bioavailable amorphous red selenium nanostructures.}, }
@article {pmid24859438, year = {2014}, author = {Rasuk, MC and Kurth, D and Flores, MR and Contreras, M and Novoa, F and Poire, D and Farias, ME}, title = {Microbial characterization of microbial ecosystems associated to evaporites domes of gypsum in Salar de Llamara in Atacama desert.}, journal = {Microbial ecology}, volume = {68}, number = {3}, pages = {483-494}, pmid = {24859438}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics ; Biodiversity ; *Calcium Sulfate ; Chile ; DNA, Bacterial/genetics ; *Desert Climate ; *Ecosystem ; Lakes/microbiology ; Phylogeny ; Pigments, Biological/analysis ; RNA, Ribosomal, 16S/genetics ; Seasons ; Water/chemistry ; }, abstract = {The Central Andes in northern Chile contains a large number of closed basins whose central depression is occupied by saline lakes and salt crusts (salars). One of these basins is Salar de Llamara (850 m a.s.l.), where large domed structures of seemingly evaporitic origin forming domes can be found. In this work, we performed a detailed microbial characterization of these domes. Mineralogical studies revealed gypsum (CaSO(4)) as a major component. Microbial communities associated to these structures were analysed by 454 16S rDNA amplicon sequencing and compared between winter and summer seasons. Bacteroidetes Proteobacteria and Planctomycetes remained as the main phylogenetic groups, an increased diversity was found in winter. Comparison of the upper air-exposed part and the lower water-submerged part of the domes in both seasons showed little variation in the upper zone, showing a predominance of Chromatiales (Gammaproteobacteria), Rhodospirillales (Alphaproteobacteria), and Sphingobacteriales (Bacteroidetes). However, the submerged part showed marked differences between seasons, being dominated by Proteobacteria (Alpha and Gamma) and Verrucomicrobia in summer, but with more diverse phyla found in winter. Even though not abundant by sequence, Cyanobacteria were visually identified by scanning electron microscopy (SEM), which also revealed the presence of diatoms. Photosynthetic pigments were detected by high-performance liquid chromatography, being more diverse on the upper photosynthetic layer. Finally, the system was compared with other endoevaporite, mats microbialite and Stromatolites microbial ecosystems, showing higher similitude with evaporitic ecosystems from Atacama and Guerrero Negro. This environment is of special interest for extremophile studies because microbial life develops associated to minerals in the driest desert all over the world. Nevertheless, it is endangered by mining activity associated to copper and lithium extraction; thus, its environmental protection preservation is strongly encouraged.}, }
@article {pmid24858784, year = {2014}, author = {Daebeler, A and Bodelier, PL and Yan, Z and Hefting, MM and Jia, Z and Laanbroek, HJ}, title = {Interactions between Thaumarchaea, Nitrospira and methanotrophs modulate autotrophic nitrification in volcanic grassland soil.}, journal = {The ISME journal}, volume = {8}, number = {12}, pages = {2397-2410}, pmid = {24858784}, issn = {1751-7370}, mesh = {Ammonia/metabolism ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; *Autotrophic Processes ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; *Grassland ; Methane/metabolism ; Microbial Interactions ; *Nitrification ; Oxidation-Reduction ; Soil ; *Soil Microbiology ; Volcanic Eruptions ; }, abstract = {Ammonium/ammonia is the sole energy substrate of ammonia oxidizers, and is also an essential nitrogen source for other microorganisms. Ammonia oxidizers therefore must compete with other soil microorganisms such as methane-oxidizing bacteria (MOB) in terrestrial ecosystems when ammonium concentrations are limiting. Here we report on the interactions between nitrifying communities dominated by ammonia-oxidizing archaea (AOA) and Nitrospira-like nitrite-oxidizing bacteria (NOB), and communities of MOB in controlled microcosm experiments with two levels of ammonium and methane availability. We observed strong stimulatory effects of elevated ammonium concentration on the processes of nitrification and methane oxidation as well as on the abundances of autotrophically growing nitrifiers. However, the key players in nitrification and methane oxidation, identified by stable-isotope labeling using (13)CO2 and (13)CH4, were the same under both ammonium levels, namely type 1.1a AOA, sublineage I and II Nitrospira-like NOB and Methylomicrobium-/Methylosarcina-like MOB, respectively. Ammonia-oxidizing bacteria were nearly absent, and ammonia oxidation could almost exclusively be attributed to AOA. Interestingly, although AOA functional gene abundance increased 10-fold during incubation, there was very limited evidence of autotrophic growth, suggesting a partly mixotrophic lifestyle. Furthermore, autotrophic growth of AOA and NOB was inhibited by active MOB at both ammonium levels. Our results suggest the existence of a previously overlooked competition for nitrogen between nitrifiers and methane oxidizers in soil, thus linking two of the most important biogeochemical cycles in nature.}, }
@article {pmid24858451, year = {2014}, author = {Callewaert, C and Buysschaert, B and Vossen, E and Fievez, V and Van de Wiele, T and Boon, N}, title = {Artificial sweat composition to grow and sustain a mixed human axillary microbiome.}, journal = {Journal of microbiological methods}, volume = {103}, number = {}, pages = {6-8}, doi = {10.1016/j.mimet.2014.05.005}, pmid = {24858451}, issn = {1872-8359}, mesh = {Axilla/*microbiology ; Humans ; Mass Spectrometry ; Metagenome ; *Microbiota ; Odorants/analysis ; Phylogeny ; Sweat/*chemistry/*microbiology ; }, abstract = {A novel artificial sweat composition, Skin Community Interaction simulation, designed to mimic the human axillary sweat, was compared to other artificial sweat compositions. Axillary microbiota grown in the novel composition closely resembled the original community. Volatile organic compound analysis showed good correlations with in vivo axillary (mal)odor components.}, }
@article {pmid24857918, year = {2014}, author = {Tseng, CH and Tang, SL}, title = {Marine microbial metagenomics: from individual to the environment.}, journal = {International journal of molecular sciences}, volume = {15}, number = {5}, pages = {8878-8892}, pmid = {24857918}, issn = {1422-0067}, mesh = {Ecology ; Environment ; Genome, Microbial ; *Metagenomics ; Organophosphonates/metabolism ; Prochlorococcus/metabolism ; Seawater/*microbiology ; Sulfur/metabolism ; }, abstract = {Microbes are the most abundant biological entities on earth, therefore, studying them is important for understanding their roles in global ecology. The science of metagenomics is a relatively young field of research that has enjoyed significant effort since its inception in 1998. Studies using next-generation sequencing techniques on single genomes and collections of genomes have not only led to novel insights into microbial genomics, but also revealed a close association between environmental niches and genome evolution. Herein, we review studies investigating microbial genomics (largely in the marine ecosystem) at the individual and community levels to summarize our current understanding of microbial ecology in the environment.}, }
@article {pmid24852305, year = {2014}, author = {Dige, I and Grønkjær, L and Nyvad, B}, title = {Molecular studies of the structural ecology of natural occlusal caries.}, journal = {Caries research}, volume = {48}, number = {5}, pages = {451-460}, doi = {10.1159/000357920}, pmid = {24852305}, issn = {1421-976X}, mesh = {Actinomyces/cytology ; Bacteria/classification/*cytology ; Bifidobacterium/cytology ; *Biofilms ; Dental Caries/*microbiology ; Dental Enamel/microbiology ; Dental Fissures/microbiology ; Dentin/microbiology/ultrastructure ; Fusobacterium/cytology ; Humans ; In Situ Hybridization, Fluorescence ; Lactobacillus/cytology ; Microbial Consortia ; Microscopy, Confocal ; Molecular Biology ; Plastic Embedding ; Streptococcus/classification/cytology ; Streptococcus mitis/cytology ; Streptococcus mutans/cytology ; Veillonella/cytology ; }, abstract = {Microbiological studies of occlusal dental biofilms have hitherto been hampered by inaccessibility to the sampling site and demolition of the original biofilm architecture. This study shows for the first time the spatial distribution of bacterial taxa in vivo at various stages of occlusal caries, applying a molecular methodology involving preparation of embedded hard dental tissue slices for fluorescence in situ hybridization (FISH) and confocal microscopy. Eleven freshly extracted teeth were classified according to their occlusal caries status. The teeth were fixed, embedded, sectioned and decalcified before FISH was performed using oligonucleotide probes for selected abundant species/genera associated with occlusal caries including Streptococcus, Actinomyces, Veillonella, Fusobacterium, Lactobacillus and Bifidobacterium. The sites showed distinct differences in the bacterial composition between different ecological niches in occlusal caries. Biofilm observed along the entrance of fissures showed an inner layer of microorganisms organized in palisades often identified as Actinomyces, covered by a more loosely structured bacterial layer consisting of diverse genera, similar to supragingival biofilm. Biofilm within the fissure proper seemed less metabolically active, as judged by low fluorescence signal intensity and presence of material of non-bacterial origin. Bacterial invasion (often Lactobacillus and Bifidobacterium spp.) into the dentinal tubules was seen only at advanced stages of caries with manifest cavity formation. It is concluded that the molecular methodology represents a valuable supplement to previous methods for the study of microbial ecology in caries by allowing analysis of the structural composition of the undisturbed biofilm in caries lesions in vivo.}, }
@article {pmid24844669, year = {2014}, author = {Andersen, SJ and Hennebel, T and Gildemyn, S and Coma, M and Desloover, J and Berton, J and Tsukamoto, J and Stevens, C and Rabaey, K}, title = {Electrolytic membrane extraction enables production of fine chemicals from biorefinery sidestreams.}, journal = {Environmental science &amp; technology}, volume = {48}, number = {12}, pages = {7135-7142}, doi = {10.1021/es500483w}, pmid = {24844669}, issn = {1520-5851}, mesh = {Acetic Acid/chemical synthesis ; Biofuels ; *Bioreactors ; Carboxylic Acids/*chemical synthesis ; Electricity ; *Electrolysis ; Esterification ; Fermentation ; *Membranes, Artificial ; Waste Products/*analysis ; }, abstract = {Short-chain carboxylates such as acetate are easily produced through mixed culture fermentation of many biological waste streams, although routinely digested to biogas and combusted rather than harvested. We developed a pipeline to extract and upgrade short-chain carboxylates to esters via membrane electrolysis and biphasic esterification. Carboxylate-rich broths are electrolyzed in a cathodic chamber from which anions flux across an anion exchange membrane into an anodic chamber, resulting in a clean acid concentrate with neither solids nor biomass. Next, the aqueous carboxylic acid concentrate reacts with added alcohol in a water-excluding phase to generate volatile esters. In a batch extraction, 96 ± 1.6% of the total acetate was extracted in 48 h from biorefinery thin stillage (5 g L(-1) acetate) at 379 g m(-2) d(-1) (36% Coulombic efficiency). With continuously regenerated thin stillage, the anolyte was concentrated to 14 g/L acetic acid, and converted at 2.64 g (acetate) L(-1) h(-1) in the first hour to ethyl acetate by the addition of excess ethanol and heating to 70 °C, with a final total conversion of 58 ± 3%. This processing pipeline enables direct production of fine chemicals following undefined mixed culture fermentation, embedding carbon in industrial chemicals rather than returning them to the atmosphere as carbon dioxide.}, }
@article {pmid24843105, year = {2014}, author = {Krom, BP and Oskam, J}, title = {Microbial biofilms and wound healing: an ecological hypothesis.}, journal = {Phlebology}, volume = {29}, number = {1 suppl}, pages = {168-173}, doi = {10.1177/0268355514528845}, pmid = {24843105}, issn = {1758-1125}, abstract = {Man has lived together with microbes for so long that we have become completely dependent on their presence. Most microbes reside in biofilms; structured communities encased in a protective matrix of biopolymers. Under healthy conditions, the microbial biofilm is in balance with itself (endo-balance) and with the host (exo-balance). Integrity of the skin is an important immunological function. Wounds go through a well-orchestrated series of healing steps. However, if for some reason healing times are extended, serious problems related to infection and homeostasis can develop. Based on recent advances in biofilm research and microbiological identification we discuss two hypotheses describing the role of microbial biofilms in chronic wound biology. The first hypothesis describes microbial biofilms as the cause of extended healing times. The second hypothesis is based on the host as cause of extended healing times and basically treats microbial biofilms as a logical consequence of failure to re-build the integrity of the skin.}, }
@article {pmid24840921, year = {2014}, author = {Fukui, Y and Abe, M and Kobayashi, M and Yano, Y and Satomi, M}, title = {Isolation of hyphomonas strains that induce normal morphogenesis in protoplasts of the marine red alga Pyropia yezoensis.}, journal = {Microbial ecology}, volume = {68}, number = {3}, pages = {556-566}, pmid = {24840921}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Morphogenesis ; *Phylogeny ; Protoplasts/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rhodophyta/*growth &amp; development/microbiology ; Sequence Analysis, DNA ; }, abstract = {Marine macroalgae cannot develop normal morphology under axenic conditions although normal morphogenesis can be sustained when certain bacteria are present. In this study, bacteria that induced normal morphogenesis in the red alga Pyropia yezoensis (Nori) were identified. The bacteria were isolated from algal media, thalli, tissue debris, and purified protoplasts during protoplast isolation from P. yezoensis laboratory cultures. 16S rRNA gene sequence analysis showed these bacterial isolates belonged to α-Proteobacteria (12 groups), γ-Proteobacteria (3 groups), and Flavobacteria (2 groups). Axenic protoplasts of P. yezoensis generated by removing epiphytic bacteria were co-cultured along with the bacterial isolates. Most axenic protoplasts showed irregular morphogenetic and anaplastic cells; cells with normal morphology were scarce. However, inoculation with 11 strains of Hyphomonas (α-Proteobacteria) led to significantly higher normal morphogenetic rates (4.5-7.3 %, P < 0.01 or 0.05) compared to axenic protoplasts (0.06 %). These Hyphomonas strains were recovered from all experiments; thus, certain Hyphomonas strains can induce normal morphogenesis in P. yezoensis protoplasts. Direct inoculation of the Hyphomonas strain exhibited higher morphogenetic activity than inoculation of its extracellular and intracellular products. This is the first study demonstrating the influence of specific bacteria on protoplast morphology in marine macroalgae.}, }
@article {pmid24838878, year = {2014}, author = {Bernstein, HC and Carlson, RP}, title = {Design, construction, and characterization methodologies for synthetic microbial consortia.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1151}, number = {}, pages = {49-68}, doi = {10.1007/978-1-4939-0554-6_4}, pmid = {24838878}, issn = {1940-6029}, support = {EB006532/EB/NIBIB NIH HHS/United States ; P20 RR024237/RR/NCRR NIH HHS/United States ; }, mesh = {Biofilms/growth &amp; development ; Cell Culture Techniques/methods ; Chromatography, High Pressure Liquid/methods ; Computer Simulation ; Escherichia coli/genetics/*physiology ; Fermentation ; Metabolic Engineering/*methods ; Metabolic Networks and Pathways ; *Microbial Consortia ; Microscopy/methods ; Mutation ; Oxygen/metabolism ; Synthetic Biology/methods ; Transduction, Genetic ; }, abstract = {Engineered microbial consortia are of growing interest to a range of scientists including bioprocess engineers, systems biologists, and microbiologists because of their ability to simultaneously optimize multiple tasks, to test fundamental systems science, and to understand the microbial ecology of environments like chronic wounds. Metabolic engineering, synthetic biology, and microbial ecology provide a sound scientific basis for designing, building, and analyzing consortium-based microbial platforms.This chapter outlines strategies and protocols useful for (1) in silico network design, (2) experimental strain construction, (3) consortia culturing including biofilm growth methods, and (4) physiological characterization of consortia. The laboratory and computational methods given here may be adapted for synthesis and characterization of other engineered consortia designs.}, }
@article {pmid24837420, year = {2015}, author = {Lee, JZ and Logan, A and Terry, S and Spear, JR}, title = {Microbial response to single-cell protein production and brewery wastewater treatment.}, journal = {Microbial biotechnology}, volume = {8}, number = {1}, pages = {65-76}, pmid = {24837420}, issn = {1751-7915}, mesh = {Bacterial Proteins/genetics/*metabolism ; Biodegradation, Environmental ; Biodiversity ; Bioreactors/microbiology ; Molecular Sequence Data ; Phylogeny ; Prevotella/classification/genetics/isolation &amp; purification/*metabolism ; Waste Products/*analysis ; Wastewater/chemistry/*microbiology ; Water Purification ; }, abstract = {As global fisheries decline, microbial single-cell protein (SCP) produced from brewery process water has been highlighted as a potential source of protein for sustainable animal feed. However, biotechnological investigation of SCP is difficult because of the natural variation and complexity of microbial ecology in wastewater bioreactors. In this study, we investigate microbial response across a full-scale brewery wastewater treatment plant and a parallel pilot bioreactor modified to produce an SCP product. A pyrosequencing survey of the brewery treatment plant showed that each unit process selected for a unique microbial community. Notably, flow equalization basins were dominated by Prevotella, methanogenesis effluent had the highest levels of diversity, and clarifier wet-well samples were sources of sequences for the candidate bacterial phyla of TM7 and BD1-5. Next, the microbial response of a pilot bioreactor producing SCP was tracked over 1 year, showing that two different production trials produced two different communities originating from the same starting influent. However, SCP production resulted generally in enrichment of several clades of rhizospheric diazotrophs of Alphaproteobacteria and Betaproteobacteria in the bioreactor and even more so in the final product. These diazotrophs are potentially useful as the basis of a SCP product for commercial feed production.}, }
@article {pmid24836870, year = {2014}, author = {Wang, Z and Yang, Y and Sun, W and Xie, S and Liu, Y}, title = {Nonylphenol biodegradation in river sediment and associated shifts in community structures of bacteria and ammonia-oxidizing microorganisms.}, journal = {Ecotoxicology and environmental safety}, volume = {106}, number = {}, pages = {1-5}, doi = {10.1016/j.ecoenv.2014.04.019}, pmid = {24836870}, issn = {1090-2414}, mesh = {Archaea/classification/*drug effects/*metabolism ; Bacteria/classification/*drug effects/*metabolism ; Biodegradation, Environmental ; *Biodiversity ; Oxidation-Reduction ; Phenols/*metabolism ; Rivers/*microbiology ; }, abstract = {Nonylphenol (NP) is one of commonly detected contaminants in the environment. Biological degradation is mainly responsible for remediation of NP-contaminated site. Knowledge about the structure of NP-degrading microbial community is still very limited. Microcosms were constructed to investigate the structure of microbial community in NP-contaminated river sediment and its change with NP biodegradation. A high level of NP was significantly dissipated in 6-9 days. Bacteria and ammonia-oxidizing archaea (AOA) were more responsive to NP amendment compared to ammonia-oxidizing bacteria (AOB). Gammaproteobacteria, Alphaproteobacteria and Bacteroidetes were the largest bacterial groups in NP-degrading sediment. Microorganisms from bacterial genera Brevundimonas, Flavobacterium, Lysobacter and Rhodobacter might be involved in NP degradation in river sediment. This study provides some new insights towards NP biodegradation and microbial ecology in NP-contaminated environment.}, }
@article {pmid24830949, year = {2014}, author = {Hosseinkhani, B and Hennebel, T and Boon, N}, title = {Potential of biogenic hydrogen production for hydrogen driven remediation strategies in marine environments.}, journal = {New biotechnology}, volume = {31}, number = {5}, pages = {445-450}, doi = {10.1016/j.nbt.2014.04.005}, pmid = {24830949}, issn = {1876-4347}, mesh = {Alginates/chemistry ; Aquatic Organisms/*metabolism ; Biodegradation, Environmental ; Cells, Immobilized/metabolism ; Glucuronic Acid/chemistry ; Hexuronic Acids/chemistry ; Hydrogen/*metabolism ; Metal Nanoparticles/*chemistry ; Palladium/*chemistry ; Pseudoalteromonas/*metabolism ; Seawater/*microbiology ; Water Microbiology ; }, abstract = {Fermentative production of bio-hydrogen (bio-H2) from organic residues has emerged as a promising alternative for providing the required electron source for hydrogen driven remediation strategies. Unlike the widely used production of H2 by bacteria in fresh water systems, few reports are available regarding the generation of biogenic H2 and optimisation processes in marine systems. The present research aims to optimise the capability of an indigenous marine bacterium for the production of bio-H2 in marine environments and subsequently develop this process for hydrogen driven remediation strategies. Fermentative conversion of organics in marine media to H2 using a marine isolate, Pseudoalteromonas sp. BH11, was determined. A Taguchi design of experimental methodology was employed to evaluate the optimal nutritional composition in batch tests to improve bio-H2 yields. Further optimisation experiments showed that alginate-immobilised bacterial cells were able to produce bio-H2 at the same rate as suspended cells over a period of several weeks. Finally, bio-H2 was used as electron donor to successfully dehalogenate trichloroethylene (TCE) using biogenic palladium nanoparticles as a catalyst. Fermentative production of bio-H2 can be a promising technique for concomitant generation of an electron source for hydrogen driven remediation strategies and treatment of organic residue in marine ecosystems.}, }
@article {pmid24830827, year = {2014}, author = {Santos, HF and Carmo, FL and Duarte, G and Dini-Andreote, F and Castro, CB and Rosado, AS and van Elsas, JD and Peixoto, RS}, title = {Climate change affects key nitrogen-fixing bacterial populations on coral reefs.}, journal = {The ISME journal}, volume = {8}, number = {11}, pages = {2272-2279}, pmid = {24830827}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; *Climate Change ; *Coral Reefs ; Molecular Sequence Data ; *Nitrogen Fixation/genetics ; Oxidoreductases/genetics ; Seawater ; Temperature ; }, abstract = {Coral reefs are at serious risk due to events associated with global climate change. Elevated ocean temperatures have unpredictable consequences for the ocean's biogeochemical cycles. The nitrogen cycle is driven by complex microbial transformations, including nitrogen fixation. This study investigated the effects of increased seawater temperature on bacteria able to fix nitrogen (diazotrophs) that live in association with the mussid coral Mussismilia harttii. Consistent increases in diazotroph abundances and diversities were found at increased temperatures. Moreover, gradual shifts in the dominance of particular diazotroph populations occurred as temperature increased, indicating a potential future scenario of climate change. The temperature-sensitive diazotrophs may provide useful bioindicators of the effects of thermal stress on coral reef health, allowing the impact of thermal anomalies to be monitored. In addition, our findings support the development of research on different strategies to improve the fitness of corals during events of thermal stress, such as augmentation with specific diazotrophs.}, }
@article {pmid24829564, year = {2014}, author = {Barberán, A and Casamayor, EO and Fierer, N}, title = {The microbial contribution to macroecology.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {203}, pmid = {24829564}, issn = {1664-302X}, abstract = {There has been a recent explosion of research within the field of microbial ecology that has been fueled, in part, by methodological improvements that make it feasible to characterize microbial communities to an extent that was inconceivable only a few years ago. Furthermore, there is increasing recognition within the field of ecology that microorganisms play a critical role in the health of organisms and ecosystems. Despite these developments, an important gap still persists between the theoretical framework of macroecology and microbial ecology. We highlight two idiosyncrasies of microorganisms that are fundamental to understanding macroecological patterns and their mechanistic drivers. First, high dispersal rates provide novel opportunities to test the relative importance of niche, stochastic, and historical processes in structuring biological communities. Second, high speciation rates potentially lead to the convergence of ecological and evolutionary time scales. After reviewing these unique aspects, we discuss strategies for improving the conceptual integration of microbes into macroecology. As examples, we discuss the use of phylogenetic ecology as an integrative approach to explore patterns across the tree of life. Then we demonstrate how two general theories of biodiversity (i.e., the recently developed theory of stochastic geometry and the neutral theory) can be adapted to microorganisms. We demonstrate how conceptual models that integrate evolutionary and ecological mechanisms can contribute to the unification of microbial ecology and macroecology.}, }
@article {pmid26504547, year = {2014}, author = {Zhu, Y and Fazio, G and Mazzola, M}, title = {Elucidating the molecular responses of apple rootstock resistant to ARD pathogens: challenges and opportunities for development of genomics-assisted breeding tools.}, journal = {Horticulture research}, volume = {1}, number = {}, pages = {14043}, pmid = {26504547}, issn = {2662-6810}, abstract = {Apple replant disease (ARD) is a major limitation to the establishment of economically viable orchards on replant sites due to the buildup and long-term survival of pathogen inoculum. Several soilborne necrotrophic fungi and oomycetes are primarily responsible for ARD, and symptoms range from serious inhibition of growth to the death of young trees. Chemical fumigation has been the primary method used for control of ARD, and manipulating soil microbial ecology to reduce pathogen density and aggressiveness is being investigated. To date, innate resistance of apple rootstocks as a means to control this disease has not been carefully explored, partly due to the complex etiology and the difficulty in phenotyping the disease resistance. Molecular defense responses of plant roots to soilborne necrotrophic pathogens are largely elusive, although considerable progress has been achieved using foliar disease systems. Plant defense responses to necrotrophic pathogens consist of several interacting modules and operate as a network. Upon pathogen detection by plants, cellular signals such as the oscillation of Ca(2+) concentration, reactive oxygen species (ROS) burst and protein kinase activity, lead to plant hormone biosynthesis and signaling. Jasmonic acid (JA) and ethylene (ET) are known to be fundamental to the induction and regulation of defense mechanisms toward invading necrotrophic pathogens. Complicated hormone crosstalk modulates the fine-tuning of transcriptional reprogramming and metabolic redirection, resulting in production of antimicrobial metabolites, enzyme inhibitors and cell wall refortification to restrict further pathogenesis. Transcriptome profiling of apple roots in response to inoculation with Pythium ultimum demonstrated that there is a high degree of conservation regarding the molecular framework of defense responses compared with those observed with foliar tissues. It is conceivable that the timing and intensity of genotype-specific defense responses may lead to different outcomes between rootstocks in response to invasion by necrotrophic pathogens. Elucidation of host defense mechanisms is critical in developing molecular tools for genomics-assisted breeding of resistant apple rootstocks. Due to their perennial nature, use of resistant rootstocks as a component for disease management might offer a durable and cost-effective benefit to tree performance than the standard practice of soil fumigation for control of ARD.}, }
@article {pmid26458512, year = {2014}, author = {Zablocki, O and van Zyl, L and Adriaenssens, EM and Rubagotti, E and Tuffin, M and Cary, SC and Cowan, D}, title = {Niche-dependent genetic diversity in Antarctic metaviromes.}, journal = {Bacteriophage}, volume = {4}, number = {4}, pages = {e980125}, pmid = {26458512}, issn = {2159-7073}, abstract = {The metaviromes from 2 different Antarctic terrestrial soil niches have been analyzed. Both hypoliths (microbial assemblages beneath transluscent rocks) and surrounding open soils showed a high level diversity of tailed phages, viruses of algae and amoeba, and virophage sequences. Comparisons of other global metaviromes with the Antarctic libraries showed a niche-dependent clustering pattern, unrelated to the geographical origin of a given metavirome. Within the Antarctic open soil metavirome, a putative circularly permuted, ∼42kb dsDNA virus genome was annotated, showing features of a temperate phage possessing a variety of conserved protein domains with no significant taxonomic affiliations in current databases.}, }
@article {pmid26101614, year = {2014}, author = {Eid, N and Enani, S and Walton, G and Corona, G and Costabile, A and Gibson, G and Rowland, I and Spencer, JP}, title = {The impact of date palm fruits and their component polyphenols, on gut microbial ecology, bacterial metabolites and colon cancer cell proliferation.}, journal = {Journal of nutritional science}, volume = {3}, number = {}, pages = {e46}, pmid = {26101614}, issn = {2048-6790}, abstract = {The fruit of the date palm (Phoenix dactylifera L.) is a rich source of dietary fibre and polyphenols. We have investigated gut bacterial changes induced by the whole date fruit extract (digested date extract; DDE) and its polyphenol-rich extract (date polyphenol extract; DPE) using faecal, pH-controlled, mixed batch cultures mimicking the distal part of the human large intestine, and utilising an array of microbial group-specific 16S rRNA oligonucleotide probes. Fluorescence microscopic enumeration indicated that there was a significant increase in the growth of bifidobacteria in response to both treatments, whilst whole dates also increased bacteroides at 24 h and the total bacterial counts at later fermentation time points when compared with DPE alone. Bacterial metabolism of whole date fruit led to the production of SCFA, with acetate significantly increasing following bacterial incubation with DDE. In addition, the production of flavonoid aglycones (myricetin, luteolin, quercetin and apigenin) and the anthocyanidin petunidin in less than 1 h was also observed. Lastly, the potential of DDE, DPE and metabolites to inhibit Caco-2 cell growth was investigated, indicating that both were capable of potentially acting as antiproliferative agents in vitro, following a 48 h exposure. This potential to inhibit growth was reduced following fermentation. Together these data suggest that consumption of date fruits may enhance colon health by increasing beneficial bacterial growth and inhibiting the proliferation of colon cancer cells. This is an early suggestion that date intake by humans may aid in the maintenance of bowel health and even the reduction of colorectal cancer development.}, }
@article {pmid25977791, year = {2014}, author = {Biller, SJ and Berube, PM and Berta-Thompson, JW and Kelly, L and Roggensack, SE and Awad, L and Roache-Johnson, KH and Ding, H and Giovannoni, SJ and Rocap, G and Moore, LR and Chisholm, SW}, title = {Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus.}, journal = {Scientific data}, volume = {1}, number = {}, pages = {140034}, pmid = {25977791}, issn = {2052-4463}, mesh = {*Genome, Bacterial ; Genomics ; Oceans and Seas ; Phylogeny ; Prochlorococcus/*genetics/isolation &amp; purification ; }, abstract = {The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in the oligotrophic oceans, and a model system in marine microbial ecology. Here we report 27 new whole genome sequences (2 complete and closed; 25 of draft quality) of cultured isolates, representing five major phylogenetic clades of Prochlorococcus. The sequenced strains were isolated from diverse regions of the oceans, facilitating studies of the drivers of microbial diversity-both in the lab and in the field. To improve the utility of these genomes for comparative genomics, we also define pre-computed clusters of orthologous groups of proteins (COGs), indicating how genes are distributed among these and other publicly available Prochlorococcus genomes. These data represent a significant expansion of Prochlorococcus reference genomes that are useful for numerous applications in microbial ecology, evolution and oceanography.}, }
@article {pmid25763029, year = {2014}, author = {Rulík, M and Chaudhary, PP}, title = {Molecular identification of the occurrence of magnetotactic bacteria in fresh water sediments (Czech Republic).}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {45}, number = {4}, pages = {1255-1261}, pmid = {25763029}, issn = {1678-4405}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Cluster Analysis ; Czech Republic ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fresh Water/microbiology ; Geologic Sediments/*microbiology ; Locomotion ; Magnetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Magnetotactic bacteria (MTB) are of considerable interest because of their importance in the manufacture of various bioinspired materials. In order to find out the status of magnetotactic bacteria at three different sediment in Czech Republic, samples collected from both standing and running freshwaters were subjected to molecular diversity analysis by using 16S rRNA gene approach. Total community DNA from sediment sample was isolated and used for PCR, cloning and sequence analysis. Of the 24 analyzed sequences, six clones are closely related to Magnetobacterium sp. affiliated with the Nitrospira phylum which showed the dominance of Magnetobacterium phylotypes in the sample. This study will provide useful insight about the community structure of MTB in this particular geographical region. However more detailed and specific studies are warranted in order to properly assess the community structure of MTB's in fresh water sediments.}, }
@article {pmid26184821, year = {2013}, author = {Donnelly, CW}, title = {From Pasteur to Probiotics: A Historical Overview of Cheese and Microbes.}, journal = {Microbiology spectrum}, volume = {1}, number = {1}, pages = {}, doi = {10.1128/microbiolspec.CM-0001-12}, pmid = {26184821}, issn = {2165-0497}, abstract = {Cheese is a food which has been produced for centuries. While cheese was originally developed as a product which extended the shelf life of milk, over time distinct cheese varieties arose, being shaped by geographic, climate, cultural, and economic factors. Global demand for artisan cheeses is creating new economic opportunities. Consumers seeking distinctive products with regional flavor, or terroir, are becoming connoisseurs of hand-crafted cheeses with distinctive tastes and character. These demands have spurred new inquiry into microorganisms used as starter cultures and adjunct cultures, as well as the microbiological consortia of finished cheeses. Such demands have also created new concerns for food safety and international trade. New bacterial pathogens such as Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium DT104 have emerged in the food supply, causing a reevaluation of the efficacy of traditional cheesemaking procedures to control these pathogens. Similarly, pathogens such as Listeria monocytogenes pose problems to susceptible human populations, and cheese can be a vehicle of transmission for this deadly pathogen. With changes in sanitary requirements due to the globalization of the food industry, governments around the world are increasingly requiring assurances of cheese safety. While many governments recognize the safety of traditional artisan cheeses manufactured from raw milk, others are demanding pasteurization of all milk intended for cheesemaking to provide assurance of microbiological safety. In response, new technologies are being proposed to increase cheese safety, but these technologies fundamentally alter the traditional artisan practices and may not enhance microbiological safety. A reevaluation of the safety of traditional artisan practices, validation thereof, and communication of the scientific principles which promote safety will be necessary to enable the continued production of traditional artisan cheeses in global commerce. This also affords the opportunity to more fully explore the microbial diversity and microbial ecology of the great cheeses of the world.}, }
@article {pmid25369810, year = {2013}, author = {Aguilera, A}, title = {Eukaryotic organisms in extreme acidic environments, the río tinto case.}, journal = {Life (Basel, Switzerland)}, volume = {3}, number = {3}, pages = {363-374}, pmid = {25369810}, issn = {2075-1729}, abstract = {A major issue in microbial ecology is to identify the limits of life for growth and survival, and to understand the molecular mechanisms that define these limits. Thus, interest in the biodiversity and ecology of extreme environments has grown in recent years for several reasons. Some are basic and revolve around the idea that extreme environments are believed to reflect early Earth conditions. Others are related to the biotechnological potential of extremophiles. In this regard, the study of extremely acidic environments has become increasingly important since environmental acidity is often caused by microbial activity. Highly acidic environments are relatively scarce worldwide and are generally associated with volcanic activity or mining operations. For most acidic environments, low pH facilitates metal solubility, and therefore acidic waters tend to have high concentrations of heavy metals. However, highly acidic environments are usually inhabited by acidophilic and acidotolerant eukaryotic microorganisms such as algae, amoebas, ciliates, heliozoan and rotifers, not to mention filamentous fungi and yeasts. Here, we review the general trends concerning the diversity and ecophysiology of eukaryotic acidophilic microorganims, as well as summarize our latest results on this topic in one of the largest extreme acidic rivers, Río Tinto (SW, Spain).}, }
@article {pmid25049708, year = {2013}, author = {Wang, WJ and Yang, WR and Wang, Y and Song, EL and Liu, XM and Wan, FC}, title = {Effects of soybean small peptides on rumen fermentation and on intestinal and total tract digestion of luxi yellow cattle.}, journal = {Asian-Australasian journal of animal sciences}, volume = {26}, number = {1}, pages = {72-81}, pmid = {25049708}, issn = {1011-2367}, abstract = {Four Luxi beef cattle (400±10 kg) fitted with ruminal, duodenal and ileal cannulas were used in a 4×4 Latin square to assess the effects of soybean small peptide (SSP) infusion on rumen fermentation, diet digestion and flow of nutrient in the gastrointestinal tract. The ruminal infusion of SSP was 0 (control), 100, 200 and 300 g/d. Ruminal SSP infusion linearly (p<0.01) and quadratically (p<0.01) increased microbial protein synthesis and rumen ammonia-N concentration. Concentrations of total volatile fatty acid were linearly increased (p = 0.029) by infusion SSP. Rumen samples were obtained for analysis of microbial ecology by real-time PCR. Populations of rumen Butyrivibrio fibrisolvens, Streptococcus bovis, Ciliate protozoa, Ruminococcus flavefaciens, and Prevotella ruminicola were expressed as a proportion of total Rumen bacterial 16S ribosomal deoxyribonucleic acid (rDNA). Butyrivibrio fibrisolvens populations which related to total bacterial 16S rDNA were increased (p<0.05), while Streptococcus bovis populations were linearly (p = 0.049) and quadratically (p = 0.020) decreased by infusion of SSP. Apparent rumen digestibility of DM and NDF were (Q, p<0.05; L, p<0.05) increased with infusion SSP. Total tract digestion of DM, OM and NDF were linearly (p<0.01) and quadratically (p<0.01) increased by infusing SSP. The flow of total amino acids (AA), essential amino acids (EAA) and individual amino acids were linearly (p<0.01) and quadratically (p<0.01) increased with infusion SSP. The digestibility of Lysine was quadratically (p = 0.033) increased and apparent degradability of Arginine was linearly (p = 0.032) and quadratically (p = 0.042) increased with infusion SSP. The results indicated that infusion SSP could improve nutrient digestion, ruminal fermentation and AA availability.}, }
@article {pmid24936364, year = {2013}, author = {Nakayama, J and Jiang, J and Watanabe, K and Chen, K and Ninxin, H and Matsuda, K and Kurakawa, T and Tsuji, H and Sonomoto, K and Lee, YK}, title = {Up to Species-level Community Analysis of Human Gut Microbiota by 16S rRNA Amplicon Pyrosequencing.}, journal = {Bioscience of microbiota, food and health}, volume = {32}, number = {2}, pages = {69-76}, pmid = {24936364}, issn = {2186-6953}, abstract = {Pyrosequencing-based 16S rRNA profiling has become a common powerful tool to obtain the community structure of gastrointestinal tract microbiota, but it is still hard to process the massive amount of sequence data into microbial composition data, especially at the species level. Here we propose a new approach in combining the quantitative insights into microbial ecology (QIIME), Mothur and ribosomal database project (RDP) programs to efficiently process 454 pyrosequence data to bacterial composition data up to the species level. It was demonstrated to precisely convert batch sequence data of 16S rRNA V6-V8 amplicons obtained from adult Singaporean fecal samples to taxonomically annotated biota data.}, }
@article {pmid24832664, year = {2013}, author = {Gokul, JK and Valverde, A and Tuffin, M and Cary, SC and Cowan, DA}, title = {Micro-eukaryotic diversity in hypolithons from miers valley, antarctica.}, journal = {Biology}, volume = {2}, number = {1}, pages = {331-340}, pmid = {24832664}, issn = {2079-7737}, abstract = {The discovery of extensive and complex hypolithic communities in both cold and hot deserts has raised many questions regarding their ecology, biodiversity and relevance in terms of regional productivity. However, most hypolithic research has focused on the bacterial elements of the community. This study represents the first investigation of micro-eukaryotic communities in all three hypolith types. Here we show that Antarctic hypoliths support extensive populations of novel uncharacterized bryophyta, fungi and protists and suggest that well known producer-decomposer-predator interactions may create the necessary conditions for hypolithic productivity in Antarctic deserts.}, }
@article {pmid24832663, year = {2013}, author = {Larose, C and Dommergue, A and Vogel, TM}, title = {The dynamic arctic snow pack: an unexplored environment for microbial diversity and activity.}, journal = {Biology}, volume = {2}, number = {1}, pages = {317-330}, pmid = {24832663}, issn = {2079-7737}, abstract = {The Arctic environment is undergoing changes due to climate shifts, receiving contaminants from distant sources and experiencing increased human activity. Climate change may alter microbial functioning by increasing growth rates and substrate use due to increased temperature. This may lead to changes of process rates and shifts in the structure of microbial communities. Biodiversity may increase as the Arctic warms and population shifts occur as psychrophilic/psychrotolerant species disappear in favor of more mesophylic ones. In order to predict how ecological processes will evolve as a function of global change, it is essential to identify which populations participate in each process, how they vary physiologically, and how the relative abundance, activity and community structure will change under altered environmental conditions. This review covers aspects of the importance and implication of snowpack in microbial ecology emphasizing the diversity and activity of these critical members of cold zone ecosystems.}, }
@article {pmid25214102, year = {2011}, author = {Aouidi, F and Ayari, S and Ferhi, H and Roussos, S and Hamdi, M}, title = {Gamma irradiation of air-dried olive leaves: Effective decontamination and impact on the antioxidative properties and on phenolic compounds.}, journal = {Food chemistry}, volume = {127}, number = {3}, pages = {1105-1113}, doi = {10.1016/j.foodchem.2011.01.109}, pmid = {25214102}, issn = {0308-8146}, abstract = {Olive leaves are commercialized for their antioxidative value due to their valuable phenolic compounds. The present study aimed to evaluate the effect of gamma irradiation on microbial load, on antioxidative properties and on phenolic compounds of air-dried olive leaves. Irradiation was applied up to 25kGy (5kGy intervals) to powdered and intact samples. Total aerobic bacteria, yeast and mold, and lactic acid bacteria were counted after gamma irradiation. Decontamination was obtained at 20kGy. The radioresistance of microbial population was high with D10 values between 9.74 and 25.12kGy. Besides, gamma irradiation up to 25kGy was found to maintain the antioxidant capacity, molecular mass distribution of polyphenolics, total phenolics, ortho-diphenols, flavonoids, oleuropein, verbascoside and rutin contents. To conclude, the improvement of the microbial quality of air-dried olive leaves, without affecting phenolic composition and antioxidative properties, can be successively achieved by the application of gamma irradiation treatment.}, }
@article {pmid25213986, year = {2011}, author = {Prat, C and Besalú, E and Bañeras, L and Anticó, E}, title = {Multivariate analysis of volatile compounds detected by headspace solid-phase microextraction/gas chromatography: A tool for sensory classification of cork stoppers.}, journal = {Food chemistry}, volume = {126}, number = {4}, pages = {1978-1984}, doi = {10.1016/j.foodchem.2010.12.057}, pmid = {25213986}, issn = {0308-8146}, abstract = {The volatile fraction of aqueous cork macerates of tainted and non-tainted agglomerate cork stoppers was analysed by headspace solid-phase microextraction (HS-SPME)/gas chromatography. Twenty compounds containing terpenoids, aliphatic alcohols, lignin-related compounds and others were selected and analysed in individual corks. Cork stoppers were previously classified in six different classes according to sensory descriptions including, 2,4,6-trichloroanisole taint and other frequent, non-characteristic odours found in cork. A multivariate analysis of the chromatographic data of 20 selected chemical compounds using linear discriminant analysis models helped in the differentiation of the a priori made groups. The discriminant model selected five compounds as the best combination. Selected compounds appear in the model in the following order; 2,4,6 TCA, fenchyl alcohol, 1-octen-3-ol, benzyl alcohol and benzothiazole. Unfortunately, not all six a priori differentiated sensory classes were clearly discriminated in the model, probably indicating that no measurable differences exist in the chromatographic data for some categories. The predictive analyses of a refined model in which two sensory classes were fused together resulted in a good classification. Prediction rates of control (non-tainted), TCA, musty-earthy-vegetative, vegetative and chemical descriptions were 100%, 100%, 85%, 67.3% and 100%, respectively, when the modified model was used. The multivariate analysis of chromatographic data will help in the classification of stoppers and provide a perfect complement to sensory analyses.}, }
@article {pmid24829553, year = {2014}, author = {Shenderov, BA and Midtvedt, T}, title = {Epigenomic programing: a future way to health?.}, journal = {Microbial ecology in health and disease}, volume = {25}, number = {}, pages = {}, pmid = {24829553}, issn = {0891-060X}, abstract = {It is now generally accepted that the 'central genome dogma' (i.e. a causal chain going from DNA to RNA to proteins and downstream to biological functions) should be replaced by the 'fluid genome dogma', that is, complex feed-forward and feed-back cycles that interconnect organism and environment by epigenomic programing - and reprograming - throughout life and at all levels, sometimes also down the generations. The epigenomic programing is the net sum of interactions derived from own metabolism and microbiota as well as external factors such as diet, pharmaceuticals, environmental compounds, and so on. It is a growing body of results indicating that many chronic metabolic and degenerative disorders and diseases - often called 'civilization diseases' - are initiated and/or influenced upon by non-optimal epigenomic programing, often taking place early in life. In this context, the first 1,000 days of life - from conception into early infancy - is often called the most important period of life. The following sections present some major mechanisms for epigenomic programing as well as some factors assumed to be of importance. The need for more information about own genome and metagenome, as well as a substantial lack of adequate information regarding dietary and environmental databases are also commented upon. However, the mere fact that we can influence epigenomic health programing opens up the way for prophylactic and therapeutic interventions. The authors underline the importance of creating a 'Human Gut Microbiota and Epigenomic Platform' in order to facilitate interdisciplinary collaborations among scientists and clinicians engaged in host microbial ecology, nutrition, metagenomics, epigenomics and metabolomics as well as in disease epidemiology, prevention and treatment.}, }
@article {pmid24827389, year = {2014}, author = {Liu, YR and Wang, JJ and Zheng, YM and Zhang, LM and He, JZ}, title = {Patterns of bacterial diversity along a long-term mercury-contaminated gradient in the paddy soils.}, journal = {Microbial ecology}, volume = {68}, number = {3}, pages = {575-583}, pmid = {24827389}, issn = {1432-184X}, mesh = {Bacteria/*classification ; Biodiversity ; China ; Environmental Monitoring/methods ; Mercury/*analysis ; Methylmercury Compounds/*analysis ; Mining ; Oryza ; Soil Pollutants/*analysis ; }, abstract = {Mercury (Hg) pollution is usually regarded as an environmental stress in reducing microbial diversity and altering bacterial community structure. However, these results were based on relatively short-term studies, which might obscure the real response of microbial species to Hg contamination. Here, we analysed the bacterial abundance and community composition in paddy soils that have been potentially contaminated by Hg for more than 600 years. Expectedly, the soil Hg pollution significantly influenced the bacterial community structure. However, the bacterial abundance was significantly correlated with the soil organic matter content rather than the total Hg (THg) concentration. The bacterial alpha diversity increased at relatively low levels of THg and methylmercury (MeHg) and subsequently approached a plateau above 4.86 mg kg(-1) THg or 18.62 ng g(-1) MeHg, respectively. Contrasting with the general prediction of decreasing diversity along Hg stress, our results seem to be consistent with the intermediate disturbance hypotheses with the peak biological diversity under intermediate disturbance or stress. This result was partly supported by the inconsistent response of bacterial species to Hg stress. For instance, the relative abundance of Nitrospirae decreased, while that of Gemmatimonadetes increased significantly along the increasing soil THg and MeHg concentrations. In addition, the content of SO(4)(2-), THg, MeHg and soil depth were the four main factors influencing bacterial community structures based on the canonical correspondence analysis (CCA). Overall, our findings provide novel insight into the distribution patterns of bacterial community along the long-term Hg-contaminated gradient in paddy soils.}, }
@article {pmid24825893, year = {2014}, author = {Stacy, A and Everett, J and Jorth, P and Trivedi, U and Rumbaugh, KP and Whiteley, M}, title = {Bacterial fight-and-flight responses enhance virulence in a polymicrobial infection.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {21}, pages = {7819-7824}, pmid = {24825893}, issn = {1091-6490}, support = {R01 DE020100/DE/NIDCR NIH HHS/United States ; 1R01DE020100/DE/NIDCR NIH HHS/United States ; }, mesh = {Aggregatibacter actinomycetemcomitans/metabolism/*pathogenicity ; Animals ; Bacterial Proteins/*metabolism ; Biofilms/*growth &amp; development ; Catalase/*metabolism ; Coinfection/microbiology/*physiopathology ; Glycoside Hydrolases/*metabolism ; Hydrogen Peroxide/metabolism ; Lactic Acid/metabolism ; Mice ; Microarray Analysis ; Streptococcus gordonii/*metabolism ; Virulence ; }, abstract = {The oral pathogen Aggregatibacter actinomycetemcomitans (Aa) resides in infection sites with many microbes, including commensal streptococci such as Streptococcus gordonii (Sg). During infection, Sg promotes the virulence of Aa by producing its preferred carbon source, l-lactate, a phenomenon referred to as cross-feeding. However, as with many streptococci, Sg also produces high levels of the antimicrobial hydrogen peroxide (H2O2), leading to the question of how Aa deals with this potent antimicrobial during coinfection. Here, we show that Aa possesses two complementary responses to H2O2: a detoxification or fight response mediated by catalase (KatA) and a dispersion or flight response mediated by Dispersin B (DspB), an enzyme that dissolves Aa biofilms. Using a murine abscess infection model, we show that both of these responses are required for Sg to promote Aa virulence. Although the role of KatA is to detoxify H2O2 during coinfection, 3D spatial analysis of mixed infections revealed that DspB is required for Aa to spatially organize itself at an optimal distance (>4 µm) from Sg, which we propose allows cross-feeding but reduces exposure to inhibitory levels of H2O2. In addition, these behaviors benefit not only Aa but also Sg, suggesting that fight and flight stimulate the fitness of the community. These results reveal that an antimicrobial produced by a human commensal bacterium enhances the virulence of a pathogenic bacterium by modulating its spatial location in the infection site.}, }
@article {pmid24823989, year = {2014}, author = {Lukic, J and Strahinic, I and Milenkovic, M and Nikolic, M and Tolinacki, M and Kojic, M and Begovic, J}, title = {Aggregation factor as an inhibitor of bacterial binding to gut mucosa.}, journal = {Microbial ecology}, volume = {68}, number = {3}, pages = {633-644}, pmid = {24823989}, issn = {1432-184X}, mesh = {Animals ; *Bacterial Adhesion ; Bacterial Proteins/*physiology ; Cell Adhesion Molecules/*physiology ; Cell Line ; Female ; Humans ; Intestinal Mucosa/*microbiology ; Lactobacillus/metabolism ; Lactococcus/*physiology ; Mucins/metabolism ; Rats ; Rats, Wistar ; Swine ; }, abstract = {Modern research in the area of probiotics is largely devoted to discovering factors that promote the adherence of probiotic candidates to host mucosal surfaces. The aim of the present study was to test the role of aggregation factor (AggL) and mucin-binding protein (MbpL) from Lactococcus sp. in adhesion to gastrointestinal mucosa. In vitro, ex vivo, and in vivo experiments in rats were used to assess the adhesive potential of these two proteins expressed in heterologous host Lactobacillus salivarius BGHO1. Although there was no influence of MbpL protein expression on BGHO1 adhesion to gut mucosa, expression of AggL had a negative effect on BGHO1 binding to ileal and colonic rat mucosa, as well as to human HT29-MTX cells and porcine gastric mucin in vitro. Because AggL did not decrease the adhesion of bacteria to intestinal fragments in ex vivo tests, where peristaltic simulation conditions were missing, we propose that intestinal motility could be a crucial force for eliminating aggregation-factor-bearing bacteria. Bacterial strains expressing aggregation factor could facilitate the removal of pathogens through the coaggregation mechanism, thus balancing gut microbial ecosystems in people affected by intestinal bacteria overgrowth.}, }
@article {pmid24821495, year = {2014}, author = {Coutinho, FH and Silveira, CB and Pinto, LH and Salloto, GR and Cardoso, AM and Martins, OB and Vieira, RP and Clementino, MM}, title = {Antibiotic resistance is widespread in urban aquatic environments of Rio de Janeiro, Brazil.}, journal = {Microbial ecology}, volume = {68}, number = {3}, pages = {441-452}, pmid = {24821495}, issn = {1432-184X}, mesh = {Ampicillin ; *Ampicillin Resistance ; Bacteria/classification/*drug effects/genetics ; Bathing Beaches ; Bays ; Brazil ; Cities ; DNA, Bacterial/genetics ; Gene Library ; RNA, Ribosomal, 16S/genetics ; Rivers/microbiology ; Seawater/microbiology ; *Water Microbiology ; }, abstract = {Bacterial resistance to antibiotics has become a public health issue. Over the years, pathogenic organisms with resistance traits have been studied due to the threat they pose to human well-being. However, several studies raised awareness to the often disregarded importance of environmental bacteria as sources of resistance mechanisms. In this work, we analyze the diversity of antibiotic-resistant bacteria occurring in aquatic environments of the state of Rio de Janeiro, Brazil, that are subjected to distinct degrees of anthropogenic impacts. We access the diversity of aquatic bacteria capable of growing in increasing ampicillin concentrations through 16S rRNA gene libraries. This analysis is complemented by the characterization of antibiotic resistance profiles of isolates obtained from urban aquatic environments. We detect communities capable of tolerating antibiotic concentrations up to 600 times higher than the clinical levels. Among the resistant organisms are included potentially pathogenic species, some of them classified as multiresistant. Our results extend the knowledge of the diversity of antibiotic resistance among environmental microorganisms and provide evidence that the diversity of drug-resistant bacteria in aquatic habitats can be influenced by pollution.}, }
@article {pmid24820566, year = {2014}, author = {Kiewra, D and Kryza, M and Szymanowski, M}, title = {Influence of selected meteorological variables on the questing activity of Ixodes ricinus ticks in Lower Silesia, SW Poland.}, journal = {Journal of vector ecology : journal of the Society for Vector Ecology}, volume = {39}, number = {1}, pages = {138-145}, doi = {10.1111/j.1948-7134.2014.12080.x}, pmid = {24820566}, issn = {1948-7134}, mesh = {Adult ; Animals ; Humans ; Ixodes/*physiology ; Poland ; Weather ; }, abstract = {The relationship between climate data and tick questing activity is crucial for estimation of the spatial and temporal distribution of the risk of ticks and tick-borne diseases. This study establishes correlations between selected meteorological variables provided by the Weather Research and Forecasting model (WRF) and the questing activity of Ixodes ricinus nymphs and adults on a regional scale across Lower Silesia, Poland. Application of Generalized Linear Mixed Models (GLMM), built separately for adults and nymphs, showed that solar radiation, air temperature, and saturation deficit appeared to be the meteorological variables of prime importance, whereas the wind speed was less important. However, the effect of meteorological parameters was different for adults and nymphs. The adults are also more influenced by forest cover and the percentage of forest type if compared to nymphs. The WRF model providing meteorological variables separately for each location and day of tick sampling can be useful in studies of questing activity of ticks on a regional scale.}, }
@article {pmid24820221, year = {2014}, author = {Brzychczy-Wloch, M and Gosiewski, T and Bulanda, M}, title = {Multilocus sequence types of invasive and colonizing neonatal group B streptococci in Poland.}, journal = {Medical principles and practice : international journal of the Kuwait University, Health Science Centre}, volume = {23}, number = {4}, pages = {323-330}, pmid = {24820221}, issn = {1423-0151}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/drug effects ; Humans ; Infant, Newborn ; Multilocus Sequence Typing ; Poland ; Serotyping ; Streptococcal Infections/*microbiology ; Streptococcus agalactiae/classification/*genetics/*isolation &amp; purification ; }, abstract = {OBJECTIVES: The present study aimed to investigate the molecular characterization of Streptococcus agalactiae (group B streptococcus; GBS) strains isolated from newborns with invasive neonatal infections and healthy newborns in Poland.<br><br>MATERIALS AND METHODS: Forty-two GBS isolates were characterized by combining different typing methods, i.e. multilocus sequence typing (MLST), molecular serotyping and protein gene profiling.<br><br>RESULTS: Using MLST, a total of 16 sequence types (STs) were identified, and among these, 11 were clustered into the following 5 clonal complexes (CCs): CC23 (20; 49%), CC19 (7; 17%), CC17 (4; 10%), CC10 (4; 10%) and CC1 (1; 2%). A statistically significant relationship between ST-17 and invasive isolates (p = 0.0398) and ST-23 and colonizing strains (p = 0.0034) was detected. Moreover, 2 novel STs were detected (ST-637 and ST-638). Molecular serotyping showed that in the invasive isolates serotype III was predominant (11; 50%), followed by serotypes II (6; 27%), V (3; 14%) and Ia (2; 9%). In healthy newborns, serotype III was also dominant (12; 60%), followed by serotypes Ia (4; 20%), II (2; 10%), V (1; 5%) and Ib (1; 5%). Protein gene profiling indicated that the rib gene was predominant in the invasive strains (11; 59%), followed by bca (5; 22%), alp2 (2; 9%), alp3 (1; 5%) and epsilon (1; 5%), while in colonizing strains the alp2 gene was most common (10; 50%), followed by epsilon (5; 25%), rib (2; 10%), bca (2; 10%) and alp3 (1; 5%). A statistically significant relationship was noted between the rib gene and invasive GBS (p = 0.0329), whereas alp2 was related to the colonizing strains (p = 0.0495).<br><br>CONCLUSIONS: The investigated GBS isolates originating from infections in newborns and healthy neonates represented serotype III in more than half of the cases and differed from one another in terms of resistance to macrolides, ST type affiliation and the presence of genes encoding surface proteins from the Alp family. Further comparative genetic research on a larger number of strains is necessary for epidemiological investigation and vaccine development.}, }
@article {pmid24814796, year = {2014}, author = {Crauwels, S and Zhu, B and Steensels, J and Busschaert, P and De Samblanx, G and Marchal, K and Willems, KA and Verstrepen, KJ and Lievens, B}, title = {Assessing genetic diversity among Brettanomyces yeasts by DNA fingerprinting and whole-genome sequencing.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {14}, pages = {4398-4413}, pmid = {24814796}, issn = {1098-5336}, mesh = {Alleles ; Beer ; Brettanomyces/*classification/genetics/isolation &amp; purification ; *DNA Fingerprinting ; DNA, Fungal/genetics ; Fermentation ; Food Contamination/analysis ; Food Microbiology ; Gene Deletion ; *Genome, Fungal ; Phylogeny ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/*methods ; }, abstract = {Brettanomyces yeasts, with the species Brettanomyces (Dekkera) bruxellensis being the most important one, are generally reported to be spoilage yeasts in the beer and wine industry due to the production of phenolic off flavors. However, B. bruxellensis is also known to be a beneficial contributor in certain fermentation processes, such as the production of certain specialty beers. Nevertheless, despite its economic importance, Brettanomyces yeasts remain poorly understood at the genetic and genomic levels. In this study, the genetic relationship between more than 50 Brettanomyces strains from all presently known species and from several sources was studied using a combination of DNA fingerprinting techniques. This revealed an intriguing correlation between the B. bruxellensis fingerprints and the respective isolation source. To further explore this relationship, we sequenced a (beneficial) beer isolate of B. bruxellensis (VIB X9085; ST05.12/22) and compared its genome sequence with the genome sequences of two wine spoilage strains (AWRI 1499 and CBS 2499). ST05.12/22 was found to be substantially different from both wine strains, especially at the level of single nucleotide polymorphisms (SNPs). In addition, there were major differences in the genome structures between the strains investigated, including the presence of large duplications and deletions. Gene content analysis revealed the presence of 20 genes which were present in both wine strains but absent in the beer strain, including many genes involved in carbon and nitrogen metabolism, and vice versa, no genes that were missing in both AWRI 1499 and CBS 2499 were found in ST05.12/22. Together, this study provides tools to discriminate Brettanomyces strains and provides a first glimpse at the genetic diversity and genome plasticity of B. bruxellensis.}, }
@article {pmid24814756, year = {2014}, author = {Hardoim, CC and Costa, R}, title = {Temporal dynamics of prokaryotic communities in the marine sponge Sarcotragus spinosulus.}, journal = {Molecular ecology}, volume = {23}, number = {12}, pages = {3097-3112}, doi = {10.1111/mec.12789}, pmid = {24814756}, issn = {1365-294X}, mesh = {Animals ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; *Microbiota ; Molecular Sequence Data ; Phylogeny ; Porifera/genetics/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {In spite of their putative relevance to host functioning, in-depth knowledge of sponge microbiome stability over time is scarce. This study tackles the temporal maintenance of bacterial and archaeal assemblages in the model host Sarcotragus spinosulus along three successive years. Prokaryotic communities were profiled by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 454-pyrosequencing of S. spinosulus-derived 16S rRNA gene amplicons. Prevailing bacterial phyla were Actinobacteria, Acidobacteria, Proteobacteria, Poribacteria, PAUC34f, Chloroflexi and Bacteroidetes, with Bacteroidetes, Chloroflexi and Poribacteria showing different abundances over the years. At the approximate species level (operational taxonomic units, OTUs, defined at 97% sequence similarity), no major changes in bacterial richness and composition were found through time. Nearly 50% of all detected bacterial symbionts (96 in 205 OTUs) were recovered from all sampling years, whereas a taxonomically equivalent community of less dominant bacteria characterized the transient sponge microbiota. Despite the evidence for temporal symbiont maintenance, an intriguing cumulative degree of variation between individuals was unravelled, with all the surveyed sponge specimens sharing only 27 bacterial OTUs. Archaeal communities were dominated by one single symbiont of the candidate genus Nitrosopumilus (Thaumarchaeota), known for its ability to aerobically oxidize ammonia to nitrite. Only few bacterial ammonia oxidizers consistently occurred in S. spinosulus across the years as documented by PCR-DGGE fingerprinting. In conclusion, prokaryotic symbionts of S. spinosulus display a state of dynamic stability shaped by the interplay between the maintenance of dominant players and turnover of less prevalent community members, in time and across host individuals, with no apparent consequences to holobiont functioning.}, }
@article {pmid24814336, year = {2014}, author = {Lee, JC and Whang, KS}, title = {Chitinophaga ginsengihumi sp. nov., isolated from soil of ginseng rhizosphere.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {64}, number = {Pt 8}, pages = {2599-2604}, doi = {10.1099/ijs.0.062612-0}, pmid = {24814336}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Bacteroidetes/*classification/genetics/isolation &amp; purification ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Panax/*microbiology ; Phosphatidylethanolamines/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {A novel strain designated SR18(T) was isolated from the rhizosphere soil of a ginseng in Korea. Cells were Gram-staining-negative, motile by gliding, catalase-positive and oxidase-negative, non-spore-forming rods. The isolate grew aerobically at 15-45 °C (optimum 28 °C), pH 5.5-7.5 (optimum pH 7.0) and with 0-3.0% (w/v) NaCl (optimum 1.5% NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SR18(T) belongs to the genus Chitinophaga with sequence similarity of 97.2% and 97.0% to Chitinophaga japonensis 758(T) and Chitinophaga rupis CS5-B1(T), respectively. Similarity to other species of the genus Chitinophaga was 92.8-95.5%. The predominant menaquinone was MK-7. Major fatty acids were iso-C(15 : 0) and C(16 : 1)ω5c. The polar lipids included phosphatidylethanolamine, unidentified phospholipids, unknown aminolipids and unknown lipids. The genomic DNA G+C content was 45.3 mol%. DNA-DNA relatedness between strain SR18(T) and C. japonensis NBRC 16041(T) was 29-32%. On the basis of polyphasic analysis from this study, strain SR18(T) represents a novel species of the genus Chitinophaga, for which the name Chitinophaga ginsengihumi sp. nov. is proposed. The type strain is SR18(T) (= KACC 17604(T) = NBRC 109832(T)).}, }
@article {pmid24814065, year = {2014}, author = {Jansson, JK and Taş, N}, title = {The microbial ecology of permafrost.}, journal = {Nature reviews. Microbiology}, volume = {12}, number = {6}, pages = {414-425}, pmid = {24814065}, issn = {1740-1534}, mesh = {*Adaptation, Physiological ; Bacteria/*classification ; *Biodiversity ; *Cold Climate ; *Soil Microbiology ; }, abstract = {Permafrost constitutes a major portion of the terrestrial cryosphere of the Earth and is a unique ecological niche for cold-adapted microorganisms. There is a relatively high microbial diversity in permafrost, although there is some variation in community composition across different permafrost features and between sites. Some microorganisms are even active at subzero temperatures in permafrost. An emerging concern is the impact of climate change and the possibility of subsequent permafrost thaw promoting microbial activity in permafrost, resulting in increased potential for greenhouse-gas emissions. This Review describes new data on the microbial ecology of permafrost and provides a platform for understanding microbial life strategies in frozen soil as well as the impact of climate change on permafrost microorganisms and their functional roles.}, }
@article {pmid24812360, year = {2014}, author = {Lee, HJ and Whang, KS}, title = {Streptomyces graminifolii sp. nov., isolated from bamboo (Sasa borealis) litter.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {64}, number = {Pt 8}, pages = {2517-2521}, doi = {10.1099/ijs.0.056895-0}, pmid = {24812360}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sasa/*microbiology ; Sequence Analysis, DNA ; Streptomyces/*classification/genetics/isolation &amp; purification ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {The taxonomic position of strain JL-22(T), isolated from litter of a bamboo (Sasa borealis) forest, was determined using a polyphasic approach. The organism had phenotypic and morphological properties consistent with it being a member of the genus Streptomyces. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain JL-22(T) was closely related to Streptomyces prunicolor NRRL B-12281(T) (99.2%), Streptomyces galilaeus JCM 4757(T) (99.0%) and Streptomyces chartreusis NBRC 12753(T) (99.0%). However, the results of DNA-DNA hybridization and physiological and biochemical tests showed that strain JL-22(T) could be differentiated from its closest phylogenetic relatives both genotypically and phenotypically. Based on phenotypic and genotypic data, strain JL-22(T) represents a novel species of the genus Streptomyces, for which the name Streptomyces graminifolii sp. nov. is proposed. The type strain is JL-22(T) (= KACC 17180(T) = NBRC 109806(T)).}, }
@article {pmid24807742, year = {2014}, author = {Zhang, M and Pereira e Silva, Mde C and Chaib De Mares, M and van Elsas, JD}, title = {The mycosphere constitutes an arena for horizontal gene transfer with strong evolutionary implications for bacterial-fungal interactions.}, journal = {FEMS microbiology ecology}, volume = {89}, number = {3}, pages = {516-526}, doi = {10.1111/1574-6941.12350}, pmid = {24807742}, issn = {1574-6941}, mesh = {Bacteria/*genetics ; *Evolution, Molecular ; Fungi/*genetics ; *Gene Transfer, Horizontal ; Microbial Interactions/genetics ; Plasmids/genetics ; *Soil Microbiology ; }, abstract = {In the microhabitat that surrounds fungal hyphae in soil, coined the mycosphere, carbonaceous compounds that are released from the hyphae stimulate the growth of heterotrophic bacteria, and thus activate organism-to-organism contacts through genetic interactions. Therefore, the mycosphere is postulated to constitute a gene transfer arena, in which a plethora of genes, including locally adaptive ones, are swapped across the resident microbial communities. Such genetic transfers may have plasmids, in particular ones with broad host ranges, as the basis. Indeed, evidence is increasing for the contention that plasmids play crucial roles as accelerators of evolution in the mycosphere, serving as a horizontal gene pool and, therefore, providing competence factors to local bacteria as well as fungi. The evidence so far points at mycosphere roles for two major plasmid classes, the IncP-1 and PromA groups. Moreover, recent data indicate that bacterium-to-fungus gene transfers are detectable and have been evolutionarily important. The large gene pool present in the mycosphere, coupled with the chances for cell-to-cell contact between mycosphere dwellers allows enhanced recombination frequencies, and as such, organisms are selected locally for enhanced fitness.}, }
@article {pmid24806706, year = {2014}, author = {Weber, MF and Poxleitner, G and Hebisch, E and Frey, E and Opitz, M}, title = {Chemical warfare and survival strategies in bacterial range expansions.}, journal = {Journal of the Royal Society, Interface}, volume = {11}, number = {96}, pages = {20140172}, pmid = {24806706}, issn = {1742-5662}, mesh = {*Biodiversity ; Biological Evolution ; Ecosystem ; Escherichia coli/drug effects/genetics/*physiology ; Genetic Engineering ; *Models, Biological ; }, abstract = {Dispersal of species is a fundamental ecological process in the evolution and maintenance of biodiversity. Limited control over ecological parameters has hindered progress in understanding of what enables species to colonize new areas, as well as the importance of interspecies interactions. Such control is necessary to construct reliable mathematical models of ecosystems. In our work, we studied dispersal in the context of bacterial range expansions and identified the major determinants of species coexistence for a bacterial model system of three Escherichia coli strains (toxin-producing, sensitive and resistant). Genetic engineering allowed us to tune strain growth rates and to design different ecological scenarios (cyclic and hierarchical). We found that coexistence of all strains depended on three strongly interdependent factors: composition of inoculum, relative strain growth rates and effective toxin range. Robust agreement between our experiments and a thoroughly calibrated computational model enabled us to extrapolate these intricate interdependencies in terms of phenomenological biodiversity laws. Our mathematical analysis also suggested that cyclic dominance between strains is not a prerequisite for coexistence in competitive range expansions. Instead, robust three-strain coexistence required a balance between growth rates and either a reduced initial ratio of the toxin-producing strain, or a sufficiently short toxin range.}, }
@article {pmid24803059, year = {2014}, author = {Cluff, MA and Hartsock, A and MacRae, JD and Carter, K and Mouser, PJ}, title = {Temporal changes in microbial ecology and geochemistry in produced water from hydraulically fractured Marcellus shale gas wells.}, journal = {Environmental science &amp; technology}, volume = {48}, number = {11}, pages = {6508-6517}, doi = {10.1021/es501173p}, pmid = {24803059}, issn = {1520-5851}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; DNA, Bacterial/analysis/genetics ; Extraction and Processing Industry ; Microbial Consortia ; Oil and Gas Fields/*microbiology ; Pennsylvania ; RNA, Ribosomal, 16S/genetics ; Wastewater/*microbiology ; *Water Microbiology ; }, abstract = {Microorganisms play several important roles in unconventional gas recovery, from biodegradation of hydrocarbons to souring of wells and corrosion of equipment. During and after the hydraulic fracturing process, microorganisms are subjected to harsh physicochemical conditions within the kilometer-deep hydrocarbon-bearing shale, including high pressures, elevated temperatures, exposure to chemical additives and biocides, and brine-level salinities. A portion of the injected fluid returns to the surface and may be reused in other fracturing operations, a process that can enrich for certain taxa. This study tracked microbial community dynamics using pyrotag sequencing of 16S rRNA genes in water samples from three hydraulically fractured Marcellus shale wells in Pennsylvania, USA over a 328-day period. There was a reduction in microbial richness and diversity after fracturing, with the lowest diversity at 49 days. Thirty-one taxa dominated injected, flowback, and produced water communities, which took on distinct signatures as injected carbon and electron acceptors were attenuated within the shale. The majority (>90%) of the community in flowback and produced fluids was related to halotolerant bacteria associated with fermentation, hydrocarbon oxidation, and sulfur-cycling metabolisms, including heterotrophic genera Halolactibacillus, Vibrio, Marinobacter, Halanaerobium, and Halomonas, and autotrophs belonging to Arcobacter. Sequences related to halotolerant methanogenic genera Methanohalophilus and Methanolobus were detected at low abundance (<2%) in produced waters several months after hydraulic fracturing. Five taxa were strong indicators of later produced fluids. These results provide insight into the temporal trajectory of subsurface microbial communities after "fracking" and have important implications for the enrichment of microbes potentially detrimental to well infrastructure and natural gas fouling during this process.}, }
@article {pmid24801965, year = {2014}, author = {Noyer, C and Casamayor, EO and Becerro, MA}, title = {Environmental heterogeneity and microbial inheritance influence sponge-associated bacterial composition of Spongia lamella.}, journal = {Microbial ecology}, volume = {68}, number = {3}, pages = {611-620}, pmid = {24801965}, issn = {1432-184X}, mesh = {Animals ; Atlantic Ocean ; Bacteria/*classification/genetics ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Mediterranean Sea ; *Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Sponges are important components of marine benthic communities. High microbial abundance sponges host a large diversity of associated microbial assemblages. However, the dynamics of such assemblages are still poorly known. In this study, we investigated whether bacterial assemblages present in Spongia lamella remained constant or changed as a function of the environment and life cycle. Sponges were collected in multiple locations and at different times of the year in the western Mediterranean Sea and in nearby Atlantic Ocean to cover heterogeneous environmental variability. Co-occurring adult sponges and offsprings were compared at two of the sites. To explore the composition and abundance of the main bacteria present in the sponge mesohyl, embryos, and larvae, we applied both 16S rRNA gene-denaturing gradient gel electrophoresis (DGGE) and sequencing of excised DGGE bands and quantitative polymerase chain reactions (qPCR). On average, the overall core bacterial assemblage showed over 60 % similarity. The associated bacterial assemblage fingerprints varied both within and between sponge populations, and the abundance of specific bacterial taxa assessed by qPCR significantly differed among sponge populations and between adult sponge and offsprings (higher proportions of Actinobacteria in the latter). Sequences showed between 92 and 100 % identity to sequences previously reported in GenBank, and all were affiliated with uncultured invertebrate bacterial symbionts (mainly sponges). Sequences were mainly related to Chloroflexi and Acidobacteria and a few to Actinobacteria and Bacteroidetes. Additional populations may have been present under detection limits. Overall, these results support that both ecological and biological sponge features may shape the composition of endobiont bacterial communities in S. lamella.}, }
@article {pmid24801964, year = {2014}, author = {Liu, WY and Ridgway, HJ and James, TK and James, EK and Chen, WM and Sprent, JI and Young, JP and Andrews, M}, title = {Burkholderia sp. induces functional nodules on the South African invasive legume Dipogon lignosus (Phaseoleae) in New Zealand soils.}, journal = {Microbial ecology}, volume = {68}, number = {3}, pages = {542-555}, pmid = {24801964}, issn = {1432-184X}, mesh = {Burkholderia/genetics/*physiology ; Fabaceae/*microbiology ; Genes, Bacterial ; *Introduced Species ; New Zealand ; Phylogeny ; *Plant Root Nodulation ; RNA, Ribosomal, 16S/genetics ; South Africa ; }, abstract = {The South African invasive legume Dipogon lignosus (Phaseoleae) produces nodules with both determinate and indeterminate characteristics in New Zealand (NZ) soils. Ten bacterial isolates produced functional nodules on D. lignosus. The 16S ribosomal RNA (rRNA) gene sequences identified one isolate as Bradyrhizobium sp., one isolate as Rhizobium sp. and eight isolates as Burkholderia sp. The Bradyrhizobium sp. and Rhizobium sp. 16S rRNA sequences were identical to those of strains previously isolated from crop plants and may have originated from inocula used on crops. Both 16S rRNA and DNA recombinase A (recA) gene sequences placed the eight Burkholderia isolates separate from previously described Burkholderia rhizobial species. However, the isolates showed a very close relationship to Burkholderia rhizobial strains isolated from South African plants with respect to their nitrogenase iron protein (nifH), N-acyltransferase nodulation protein A (nodA) and N-acetylglucosaminyl transferase nodulation protein C (nodC) gene sequences. Gene sequences and enterobacterial repetitive intergenic consensus (ERIC) PCR and repetitive element palindromic PCR (rep-PCR) banding patterns indicated that the eight Burkholderia isolates separated into five clones of one strain and three of another. One strain was tested and shown to produce functional nodules on a range of South African plants previously reported to be nodulated by Burkholderia tuberum STM678(T) which was isolated from the Cape Region. Thus, evidence is strong that the Burkholderia strains isolated here originated in South Africa and were somehow transported with the plants from their native habitat to NZ. It is possible that the strains are of a new species capable of nodulating legumes.}, }
@article {pmid24801158, year = {2014}, author = {Lee, JC and Whang, KS}, title = {Reyranella graminifolii sp. nov., isolated from bamboo (Phyllostachys bambusoides) litter.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {64}, number = {Pt 7}, pages = {2503-2507}, doi = {10.1099/ijs.0.062968-0}, pmid = {24801158}, issn = {1466-5034}, mesh = {Alphaproteobacteria/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phospholipids/chemistry ; *Phylogeny ; Poaceae/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Ubiquinone/chemistry ; }, abstract = {A novel strain designated Wo-34(T) was isolated from bamboo (Phyllostachys bambusoides) litter. Cells were Gram-stain-negative, non-motile, catalase-negative and oxidase-positive rods. The isolate grew aerobically at 15-35 °C (optimum 28 °C), pH 4.0-9.0 (optimum pH 7.0) and in the presence of 0-1.0% (w/v) NaCl (optimum 0.1% NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain Wo-34(T) belonged to the genus Reyranella with the sequence similarities of 97.9% and 97.3% to the other species of the genus Reyranella, Reyranella massiliensis 521(T) and Reyranella soli KIS14-15(T), respectively. The predominant ubiquinone was Q-10. Major fatty acids were C18 : 1ω7c, C18 : 1 2-OH and C19 : 0 cyclo ω8c. The polar lipids contained phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown aminolipid, unidentified phospholipids and unknown lipids. DNA-DNA relatedness values between strain Wo-34(T) and R. massiliensis DSM 23428(T) and R. soli KACC 13034(T) were 35% and 29%, respectively. On the basis of polyphasic analysis from this study, strain Wo-34(T) represents a novel species of the genus Reyranella for which the name Reyranella graminifolii sp. nov. is proposed. The type strain is Wo-34(T) (= KACC 17605(T) = NBRC 109813(T)).}, }
@article {pmid24798298, year = {2014}, author = {Ruiz, V and Ilhan, ZE and Kang, DW and Krajmalnik-Brown, R and Buitrón, G}, title = {The source of inoculum plays a defining role in the development of MEC microbial consortia fed with acetic and propionic acid mixtures.}, journal = {Journal of biotechnology}, volume = {182-183}, number = {}, pages = {11-18}, doi = {10.1016/j.jbiotec.2014.04.016}, pmid = {24798298}, issn = {1873-4863}, mesh = {Acetic Acid/*metabolism ; Bacteria/classification/*genetics/metabolism ; Bioreactors/*microbiology ; DNA, Bacterial/analysis/chemistry/genetics ; Electrodes ; Electrolysis ; Fatty Acids, Volatile/metabolism ; Fermentation ; Hydrogen/metabolism ; Microbial Consortia/*physiology ; Propionates/*metabolism ; }, abstract = {Microbial electrolysis cells (MECs) can be used as a downstream process to dark fermentation to further capture electron in volatile fatty acids that remain after fermentation, improving this way the viability of the overall process. Acetic and propionic acid are common products of dark fermentation. The main objective of this work was to investigate the effect of different initial concentrations of a mixture of acetic and propionic acids on MECs microbial ecology and hydrogen production performance. To link microbial structure and function, we characterized the anode respiring biofilm communities using pyrosequencing and quantitative-PCR. The best hydrogen production rates (265mL/d/Lreactor) were obtained in the first block of experiments by MEC fed with 1500mg/L acetic acid and 250mg/L propionic acid. This reactor presents in the anode biofilm an even distribution of Proteobacteria, Firmicutes and Bacteroidetes and Arcobacter was the dominant genera. The above fact also correlated to the highest electron load among all the reactors. It was evidenced that although defined acetic and propionic acid concentrations fed affected the structure of the microbial consortia that developed at the anode, the initial inoculum played a major role in the development of MEC microbial consortia.}, }
@article {pmid24797710, year = {2014}, author = {Krause, S and van Bodegom, PM and Cornwell, WK and Bodelier, PL}, title = {Weak phylogenetic signal in physiological traits of methane-oxidizing bacteria.}, journal = {Journal of evolutionary biology}, volume = {27}, number = {6}, pages = {1240-1247}, doi = {10.1111/jeb.12401}, pmid = {24797710}, issn = {1420-9101}, mesh = {Genetic Markers ; Methylococcaceae/*genetics/physiology ; *Phylogeny ; Temperature ; }, abstract = {The presence of phylogenetic signal is assumed to be ubiquitous. However, for microorganisms, this may not be true given that they display high physiological flexibility and have fast regeneration. This may result in fundamentally different patterns of resemblance, that is, in variable strength of phylogenetic signal. However, in microbiological inferences, trait similarities and therewith microbial interactions with its environment are mostly assumed to follow evolutionary relatedness. Here, we tested whether indeed a straightforward relationship between relatedness and physiological traits exists for aerobic methane-oxidizing bacteria (MOB). We generated a comprehensive data set that included 30 MOB strains with quantitative physiological trait information. Phylogenetic trees were built from the 16S rRNA gene, a common phylogenetic marker, and the pmoA gene which encodes a subunit of the key enzyme involved in the first step of methane oxidation. We used a Blomberg's K from comparative biology to quantify the strength of phylogenetic signal of physiological traits. Phylogenetic signal was strongest for physiological traits associated with optimal growth pH and temperature indicating that adaptations to habitat are very strongly conserved in MOB. However, those physiological traits that are associated with kinetics of methane oxidation had only weak phylogenetic signals and were more pronounced with the pmoA than with the 16S rRNA gene phylogeny. In conclusion, our results give evidence that approaches based solely on taxonomical information will not yield further advancement on microbial eco-evolutionary interactions with its environment. This is a novel insight on the connection between function and phylogeny within microbes and adds new understanding on the evolution of physiological traits across microbes, plants and animals.}, }
@article {pmid24794950, year = {2014}, author = {Lenaerts, M and Alvarez-Pérez, S and de Vega, C and Van Assche, A and Johnson, SD and Willems, KA and Herrera, CM and Jacquemyn, H and Lievens, B}, title = {Rosenbergiella australoborealis sp. nov., Rosenbergiella collisarenosi sp. nov. and Rosenbergiella epipactidis sp. nov., three novel bacterial species isolated from floral nectar.}, journal = {Systematic and applied microbiology}, volume = {37}, number = {6}, pages = {402-411}, doi = {10.1016/j.syapm.2014.03.002}, pmid = {24794950}, issn = {1618-0984}, support = {260601/ERC_/European Research Council/International ; }, mesh = {Base Composition ; DNA, Bacterial/chemistry/*genetics ; Enterobacteriaceae/*classification/*genetics/isolation &amp; purification ; *Genes, Essential ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Plant Nectar ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The taxonomic status of nine strains of the family Enterobacteriaceae isolated from floral nectar of wild Belgian, French, South African and Spanish insect-pollinated plants was investigated following a polyphasic approach. Confirmation that these strains belonged to the genus Rosenbergiella was obtained from comparative analysis of partial sequences of the 16S rRNA gene and other core housekeeping genes (atpD [ATP synthase β-chain], gyrB [DNA gyrase subunit B] and rpoB [RNA polymerase β-subunit]), DNA-DNA reassociation data, determination of the DNA G+C content and phenotypic profiling. Two strains belonged to the recently described species Rosenbergiella nectarea, while the other seven strains represented three novel species within the genus Rosenbergiella. The names Rosenbergiella australoborealis sp. nov. (with strain CdVSA 20.1(T) [LMG 27954(T)=CECT 8500(T)] as the type strain), Rosenbergiella collisarenosi sp. nov. (with strain 8.8A(T) [LMG 27955(T)=CECT 8501(T)] as the type strain) and Rosenbergiella epipactidis sp. nov. (with strain 2.1A(T) [LMG 27956(T)=CECT 8502(T)] as the type strain) are proposed. Additionally, the description of the genus Rosenbergiella is updated on the basis of new phenotypic and molecular data.}, }
@article {pmid24788211, year = {2014}, author = {Shan, HW and Lu, YH and Bing, XL and Liu, SS and Liu, YQ}, title = {Differential responses of the whitefly Bemisia tabaci symbionts to unfavorable low and high temperatures.}, journal = {Microbial ecology}, volume = {68}, number = {3}, pages = {472-482}, pmid = {24788211}, issn = {1432-184X}, mesh = {Animals ; Enterobacteriaceae/genetics/*physiology ; Female ; Hemiptera/*microbiology/*physiology ; Male ; Rickettsia/genetics/*physiology ; Symbiosis ; *Temperature ; }, abstract = {The whitefly Bemisia tabaci complex contains many cryptic species, of which the Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED) are notorious invasive pests. In our field-collected whitefly samples, MEAM1 harbors an obligate primary symbiont "Candidatus Portiera aleyrodidarum" and two secondary symbionts, "Candidatus Hamiltonella defensa" and Rickettsia sp., whereas MED has only "Ca. Portiera aleyrodidarum" and "Ca. Hamiltonella defensa." Both "Ca. Portiera aleyrodidarum" and "Ca. Hamiltonella defensa" are intracellular endosymbionts residing in the bacteriomes, whereas Rickettsia sp. has a scattered distribution throughout the host body cavity. We examined responses of these symbionts to adverse temperatures as well as survival of the host insects. After cold treatment at 5 or 10 °C or heat treatment at 35 or 40 °C for 24 h, respectively, the infection rates of all symbionts were not significantly decreased based on diagnosis PCR. However, quantitative PCR assays indicated significant reduction of "Ca. Hamiltonella defensa" at 40 °C, and the reduction became greater as the duration increased. Compared with "Ca. Hamiltonella defensa," "Ca. Portiera aleyrodidarum" was initially less affected in the first day but then showed more rapid reduction at days 3-5. The density of Rickettsia sp. fluctuated but was not reduced significantly at 40 °C. Meanwhile, the mortality rates of the host whiteflies elevated rapidly as the duration of exposure to heat treatment increased. The differential responses of various symbionts to adverse temperatures imply complex interactions among the symbionts inside the same host insect and highlight the importance of taking the whole bacterial community into account in studies of symbioses.}, }
@article {pmid24787986, year = {2014}, author = {Zhong, Y and Li, ZX}, title = {Bidirectional cytoplasmic incompatibility induced by cross-order transfection of Wolbachia: implications for control of the host population.}, journal = {Microbial ecology}, volume = {68}, number = {3}, pages = {463-471}, pmid = {24787986}, issn = {1432-184X}, mesh = {Animals ; Crosses, Genetic ; Cytoplasm/*microbiology ; DNA, Bacterial/genetics ; Female ; Fertility ; Hemiptera/*microbiology ; Male ; Pest Control, Biological ; Phenotype ; Phylogeny ; Sequence Analysis, DNA ; Symbiosis ; Wasps/*microbiology ; Wolbachia/genetics/isolation &amp; purification/*physiology ; }, abstract = {Wolbachia are widespread endosymbionts in arthropods and some nematodes. This genus of bacteria is known to manipulate host reproduction by inducing cytoplasmic incompatibility (CI). This important phenotype is implicated in the control of host populations since Wolbachia can suppress host populations through the induction of CI in a way similar to the sterile insect technique. Here, we identified a candidate CI-inducing Wolbachia strain from the parasitic wasp Scleroderma guani (wSguBJ) by sequencing and phylogenetic analysis. This Wolbachia strain was then isolated, purified, and artificially transfected into the new whitefly host Bemisia tabaci through nymphal microinjection. Infection frequency monitoring by molecular detection showed that 60-80 % of the offspring from transfected whitefly populations was infected with wSguBJ six generations after the transfer. Laboratory rearing experiments indicated that the artificial transfection caused no significant difference in the numbers of offspring between the transfected and naturally infected populations and had no significant detrimental effects on the development of transfected males, although the development of transfected females was delayed. Reciprocal crossings revealed that bidirectional CI was induced between the transfected and naturally infected whiteflies. These data indicated that the cross-order transfer of the heterologous Wolbachia strain by nymphal microinjection was successful. Mass release of the transfected males that could stably carry the heterologous Wolbachia without significant compromise of fecundity/development may provide an alternative approach to control of host populations.}, }
@article {pmid24787321, year = {2014}, author = {Gabarró, J and González-Cárcamo, P and Ruscalleda, M and Ganigué, R and Gich, F and Balaguer, MD and Colprim, J}, title = {Anoxic phases are the main N2O contributor in partial nitritation reactors treating high nitrogen loads with alternate aeration.}, journal = {Bioresource technology}, volume = {163}, number = {}, pages = {92-99}, doi = {10.1016/j.biortech.2014.04.019}, pmid = {24787321}, issn = {1873-2976}, mesh = {*Air ; *Bioreactors ; Nitrates/*metabolism ; Nitrous Oxide/*metabolism ; Oxygen/*metabolism ; Pilot Projects ; Wastewater ; }, abstract = {Partial nitritation (PN) reactors treating complex industrial wastewater can be operated by alternating anoxic-aerobic phases to promote heterotrophic denitrification via NO2(-). However, denitrification under stringent conditions can lead to high N2O production. In this study, the suitability of including anoxic phases in a PN-SBR treating real industrial wastewater was assessed in terms of process performance and N2O production. The PN-SBR was operated successfully and, when the HCO3(-):NH4(+) molar ratio was adjusted, produced a suitable effluent for a subsequent anammox reactor. 10-20% of the total influent nitrogen was removed. N2O production accounted for 3.6% of the NLR and took place mainly during the anoxic phases (60%). Specific denitrification batch tests demonstrated that, despite the availability of biodegradable COD, NO2(-) denitrification advanced at a faster rate than N2O denitrification, causing high N2O accumulation. Thus, the inclusion of anoxic phases should be avoided in PN reactors treating industrial wastewaters with high nitrogen loads.}, }
@article {pmid24785568, year = {2014}, author = {Rabaey, K and Ragauskas, AJ}, title = {Editorial overview: energy biotechnology.}, journal = {Current opinion in biotechnology}, volume = {27}, number = {}, pages = {v-vi}, doi = {10.1016/j.copbio.2014.04.001}, pmid = {24785568}, issn = {1879-0429}, mesh = {Biocatalysis ; Biofuels/*supply &amp; distribution ; Biomass ; *Biotechnology/methods/trends ; Electrodes ; }, }
@article {pmid24785289, year = {2014}, author = {Ho, A and de Roy, K and Thas, O and De Neve, J and Hoefman, S and Vandamme, P and Heylen, K and Boon, N}, title = {The more, the merrier: heterotroph richness stimulates methanotrophic activity.}, journal = {The ISME journal}, volume = {8}, number = {9}, pages = {1945-1948}, pmid = {24785289}, issn = {1751-7370}, mesh = {Bacteria/metabolism ; *Biodiversity ; *Heterotrophic Processes ; Methane/*metabolism ; Methylomonas/metabolism ; Oxidation-Reduction ; }, abstract = {Although microorganisms coexist in the same environment, it is still unclear how their interaction regulates ecosystem functioning. Using a methanotroph as a model microorganism, we determined how methane oxidation responds to heterotroph diversity. Artificial communities comprising of a methanotroph and increasing heterotroph richness, while holding equal starting cell numbers were assembled. We considered methane oxidation rate as a functional response variable. Our results showed a significant increase of methane oxidation with increasing heterotroph richness, suggesting a complex interaction in the cocultures leading to a stimulation of methanotrophic activity. Therefore, not only is the methanotroph diversity directly correlated to methanotrophic activity for some methanotroph groups as shown before, but also the richness of heterotroph interacting partners is relevant to enhance methane oxidation too. In this unprecedented study, we provide direct evidence showing how heterotroph richness exerts a response in methanotroph-heterotroph interaction, resulting in increased methanotrophic activity. Our study has broad implications in how methanotroph and heterotroph interact to regulate methane oxidation, and is particularly relevant in methane-driven ecosystems.}, }
@article {pmid24782847, year = {2014}, author = {Hagens, S and Loessner, MJ}, title = {Phages of Listeria offer novel tools for diagnostics and biocontrol.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {159}, pmid = {24782847}, issn = {1664-302X}, abstract = {Historically, bacteriophages infecting their hosts have perhaps been best known and even notorious for being a nuisance in dairy-fermentation processes. However, with the rapid progress in molecular microbiology and microbial ecology, a new dawn has risen for phages. This review will provide an overview on possible uses and applications of Listeria phages, including phage-typing, reporter phage for bacterial diagnostics, and use of phage as biocontrol agents for food safety. The use of phage-encoded enzymes such as endolysins for the detection and as antimicrobial agent will also be addressed. Desirable properties of candidate phages for biocontrol will be discussed. While emphasizing the enormous future potential for applications, we will also consider some of the intrinsic limitations dictated by both phage and bacterial ecology.}, }
@article {pmid24782842, year = {2014}, author = {Cowan, DA and Makhalanyane, TP and Dennis, PG and Hopkins, DW}, title = {Microbial ecology and biogeochemistry of continental Antarctic soils.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {154}, pmid = {24782842}, issn = {1664-302X}, abstract = {The Antarctica Dry Valleys are regarded as the coldest hyperarid desert system on Earth. While a wide variety of environmental stressors including very low minimum temperatures, frequent freeze-thaw cycles and low water availability impose severe limitations to life, suitable niches for abundant microbial colonization exist. Antarctic desert soils contain much higher levels of microbial diversity than previously thought. Edaphic niches, including cryptic and refuge habitats, microbial mats and permafrost soils all harbor microbial communities which drive key biogeochemical cycling processes. For example, lithobionts (hypoliths and endoliths) possess a genetic capacity for nitrogen and carbon cycling, polymer degradation, and other system processes. Nitrogen fixation rates of hypoliths, as assessed through acetylene reduction assays, suggest that these communities are a significant input source for nitrogen into these oligotrophic soils. Here we review aspects of microbial diversity in Antarctic soils with an emphasis on functionality and capacity. We assess current knowledge regarding adaptations to Antarctic soil environments and highlight the current threats to Antarctic desert soil communities.}, }
@article {pmid24780846, year = {2014}, author = {Harms, H and Junca, H}, title = {Editorial overview: environmental biotechnology.}, journal = {Current opinion in biotechnology}, volume = {27}, number = {}, pages = {vii-ix}, doi = {10.1016/j.copbio.2014.04.002}, pmid = {24780846}, issn = {1879-0429}, mesh = {Biodegradation, Environmental ; *Biotechnology ; *Environment ; Environmental Pollutants/classification/metabolism ; }, }
@article {pmid24778240, year = {2014}, author = {Mee, MT and Collins, JJ and Church, GM and Wang, HH}, title = {Syntrophic exchange in synthetic microbial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {20}, pages = {E2149-56}, pmid = {24778240}, issn = {1091-6490}, support = {DP5 OD009172/OD/NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; 1DP5OD009172-01/OD/NIH HHS/United States ; /CAPMC/CIHR/Canada ; }, mesh = {Amino Acids/biosynthesis ; Amino Acids, Essential/*biosynthesis ; Bacteria/*genetics/metabolism ; Coculture Techniques ; Ecology ; Ecosystem ; Escherichia coli/*genetics/*metabolism ; Gene Expression Regulation, Bacterial ; *Microbial Interactions ; Models, Biological ; Phylogeny ; Temperature ; }, abstract = {Metabolic crossfeeding is an important process that can broadly shape microbial communities. However, little is known about specific crossfeeding principles that drive the formation and maintenance of individuals within a mixed population. Here, we devised a series of synthetic syntrophic communities to probe the complex interactions underlying metabolic exchange of amino acids. We experimentally analyzed multimember, multidimensional communities of Escherichia coli of increasing sophistication to assess the outcomes of synergistic crossfeeding. We find that biosynthetically costly amino acids including methionine, lysine, isoleucine, arginine, and aromatics, tend to promote stronger cooperative interactions than amino acids that are cheaper to produce. Furthermore, cells that share common intermediates along branching pathways yielded more synergistic growth, but exhibited many instances of both positive and negative epistasis when these interactions scaled to higher dimensions. In more complex communities, we find certain members exhibiting keystone species-like behavior that drastically impact the community dynamics. Based on comparative genomic analysis of >6,000 sequenced bacteria from diverse environments, we present evidence suggesting that amino acid biosynthesis has been broadly optimized to reduce individual metabolic burden in favor of enhanced crossfeeding to support synergistic growth across the biosphere. These results improve our basic understanding of microbial syntrophy while also highlighting the utility and limitations of current modeling approaches to describe the dynamic complexities underlying microbial ecosystems. This work sets the foundation for future endeavors to resolve key questions in microbial ecology and evolution, and presents a platform to develop better and more robust engineered synthetic communities for industrial biotechnology.}, }
@article {pmid24774752, year = {2014}, author = {Vo, AT and Jedlicka, JA}, title = {Protocols for metagenomic DNA extraction and Illumina amplicon library preparation for faecal and swab samples.}, journal = {Molecular ecology resources}, volume = {14}, number = {6}, pages = {1183-1197}, doi = {10.1111/1755-0998.12269}, pmid = {24774752}, issn = {1755-0998}, mesh = {Animals ; Cloaca/*microbiology ; DNA/*isolation &amp; purification ; DNA, Ribosomal/chemistry/genetics ; Feces/*microbiology ; *Gene Library ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; Mouth Mucosa/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Songbirds/microbiology ; }, abstract = {Next-generation sequencing (NGS) technology has extraordinarily enhanced the scope of research in the life sciences. To broaden the application of NGS to systems that were previously difficult to study, we present protocols for processing faecal and swab samples into amplicon libraries amenable to Illumina sequencing. We developed and tested a novel metagenomic DNA extraction approach using solid phase reversible immobilization (SPRI) beads on Western Bluebird (Sialia mexicana) samples stored in RNAlater. Compared with the MO BIO PowerSoil Kit, the current standard for the Human and Earth Microbiome Projects, the SPRI-based method produced comparable 16S rRNA gene PCR amplification from faecal extractions but significantly greater DNA quality, quantity and PCR success for both cloacal and oral swab samples. We furthermore modified published protocols for preparing highly multiplexed Illumina libraries with minimal sample loss and without post-adapter ligation amplification. Our library preparation protocol was successfully validated on three sets of heterogeneous amplicons (16S rRNA gene amplicons from SPRI and PowerSoil extractions as well as control arthropod COI gene amplicons) that were sequenced across three independent, 250-bp, paired-end runs on Illumina's MiSeq platform. Sequence analyses revealed largely equivalent results from the SPRI and PowerSoil extractions. Our comprehensive strategies focus on maximizing efficiency and minimizing costs. In addition to increasing the feasibility of using minimally invasive sampling and NGS capabilities in avian research, our methods are notably not avian-specific and thus applicable to many research programmes that involve DNA extraction and amplicon sequencing.}, }
@article {pmid24774670, year = {2014}, author = {Olivares, M and Castillejo, G and Varea, V and Sanz, Y}, title = {Double-blind, randomised, placebo-controlled intervention trial to evaluate the effects of Bifidobacterium longum CECT 7347 in children with newly diagnosed coeliac disease.}, journal = {The British journal of nutrition}, volume = {112}, number = {1}, pages = {30-40}, doi = {10.1017/S0007114514000609}, pmid = {24774670}, issn = {1475-2662}, mesh = {Anti-Inflammatory Agents, Non-Steroidal/*therapeutic use ; Bacteroides fragilis/growth &amp; development/*immunology/isolation &amp; purification ; *Bifidobacterium/immunology ; Celiac Disease/blood/*diet therapy/immunology/microbiology ; Child ; Child Development ; Child, Preschool ; Combined Modality Therapy ; Cytokines/blood ; Diet, Gluten-Free ; Double-Blind Method ; Feces/chemistry/microbiology ; Female ; Gram-Negative Bacteria/growth &amp; development/immunology/isolation &amp; purification ; Gram-Positive Bacteria/growth &amp; development/immunology/isolation &amp; purification ; Humans ; *Immunity, Mucosal ; Immunoglobulin A, Secretory/analysis/metabolism ; Intestinal Mucosa/*immunology/metabolism/microbiology ; Male ; Microbial Viability ; Probiotics/*therapeutic use ; }, abstract = {Interactions between the immune system and the intestinal microbiota may play a role in coeliac disease (CD). In the present study, the potential effects of Bifidobacterium longum CECT 7347 in children with newly diagnosed CD were evaluated. A double-blind, randomised, placebo-controlled trial was conducted in thirty-three children who received a capsule containing either B. longum CECT 7347 (10[9] colony-forming units) or placebo (excipients) daily for 3 months together with a gluten-free diet (GFD). Outcome measures (baseline and post-intervention) included immune phenotype of peripheral blood cells, serum cytokine concentration, faecal secretory IgA (sIgA) content, anthropometric parameters and intestinal microbiota composition. Comparisons between the groups revealed greater height percentile increases (P= 0·048) in the B. longum CECT 7347 group than in the placebo group, as well as decreased peripheral CD3[+] T lymphocytes (P= 0·004) and slightly reduced TNF-α concentration (P= 0·067). Within-group comparisons of baseline and final values did not reveal any differences in T lymphocytes and cytokines in the placebo group, while decreased CD3[+] (P =0·013) and human leucocyte antigen (HLA)-DR[+] T lymphocytes (P =0·029) and slightly reduced TNF-α concentration (P= 0·085) were detected in the B. longum CECT 7347 group. Comparison between the groups showed that the administration of B. longum CECT 7347 reduced the numbers of the Bacteroides fragilis group (P= 0·020) and the content of sIgA in stools (P= 0·011) compared with the administration of placebo. Although this is a first exploratory intervention with limitations, the findings suggest that B. longum CECT 7347 could help improve the health status of CD patients who tend to show alterations in gut microbiota composition and a biased immune response even on a GFD.}, }
@article {pmid24773019, year = {2014}, author = {Rusconi, R and Garren, M and Stocker, R}, title = {Microfluidics expanding the frontiers of microbial ecology.}, journal = {Annual review of biophysics}, volume = {43}, number = {}, pages = {65-91}, pmid = {24773019}, issn = {1936-1238}, support = {R01 GM100473/GM/NIGMS NIH HHS/United States ; 1R01GM100473-0/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacterial Physiological Phenomena ; Ecology/*methods ; *Microbiological Techniques ; Microfluidics/*methods ; }, abstract = {Microfluidics has significantly contributed to the expansion of the frontiers of microbial ecology over the past decade by allowing researchers to observe the behaviors of microbes in highly controlled microenvironments, across scales from a single cell to mixed communities. Spatially and temporally varying distributions of organisms and chemical cues that mimic natural microbial habitats can now be established by exploiting physics at the micrometer scale and by incorporating structures with specific geometries and materials. In this article, we review applications of microfluidics that have resulted in insightful discoveries on fundamental aspects of microbial life, ranging from growth and sensing to cell-cell interactions and population dynamics. We anticipate that this flexible multidisciplinary technology will continue to facilitate discoveries regarding the ecology of microorganisms and help uncover strategies to control microbial processes such as biofilm formation and antibiotic resistance.}, }
@article {pmid24772289, year = {2014}, author = {Grizard, S and Dini-Andreote, F and Tieleman, BI and Salles, JF}, title = {Dynamics of bacterial and fungal communities associated with eggshells during incubation.}, journal = {Ecology and evolution}, volume = {4}, number = {7}, pages = {1140-1157}, pmid = {24772289}, issn = {2045-7758}, abstract = {Microorganisms are closely associated with eggs and may play a determinant role in embryo survival. Yet, the majority of studies focusing on this association relied on culture-based methodology, eventually leading to a skewed assessment of microbial communities. By targeting the 16S rRNA gene and internal transcribed spacer (ITS) region, we, respectively, described bacterial and fungal communities on eggshells of the homing pigeon Columba livia. We explored their structure, abundance, and composition. Firstly, we showed that sampling technique affected the outcome of the results. While broadly used, the egg swabbing procedure led to a lower DNA extraction efficiency and provided different profiles of bacterial communities than those based on crushed eggshell pieces. Secondly, we observed shifts in bacterial and fungal communities during incubation. At late incubation, bacterial communities showed a reduction in diversity, while their abundance increased, possibly due to the competitive advantage of some species. When compared to their bacterial counterparts, fungal communities also decreased in diversity at late incubation. In that case, however, the decline was associated with a diminution of their overall abundance. Conclusively, our results showed that although incubation might inhibit microbial growth when compared to unincubated eggs, we observed the selective growth of specific bacterial species during incubation. Moreover, we showed that fungi are a substantial component of the microbial communities associated with eggshells and require further investigations in avian ecology. Identifying the functional roles of these microorganisms is likely to provide news insights into the evolutionary strategies that control embryo survival. We aimed to describe the dynamics of bacterial and fungal communities on homing pigeon eggshell surfaces. We investigated these communities at early and late incubation stages.}, }
@article {pmid24771032, year = {2014}, author = {De Pasquale, I and Calasso, M and Mancini, L and Ercolini, D and La Storia, A and De Angelis, M and Di Cagno, R and Gobbetti, M}, title = {Causal relationship between microbial ecology dynamics and proteolysis during manufacture and ripening of protected designation of origin (PDO) cheese Canestrato Pugliese.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {14}, pages = {4085-4094}, pmid = {24771032}, issn = {1098-5336}, mesh = {Animals ; Carnobacterium/growth &amp; development/isolation &amp; purification ; Cheese/*microbiology ; Colony Count, Microbial ; Food Handling/*methods ; Food Microbiology/*methods ; Lactobacillus/growth &amp; development/isolation &amp; purification ; Lactococcus/growth &amp; development/isolation &amp; purification ; Leuconostoc/growth &amp; development/isolation &amp; purification ; Milk/microbiology ; *Proteolysis ; RNA, Ribosomal, 16S/genetics/isolation &amp; purification ; }, abstract = {Pyrosequencing of the 16S rRNA gene, community-level physiological profiles determined by the use of Biolog EcoPlates, and proteolysis analyses were used to characterize Canestrato Pugliese Protected Designation of Origin (PDO) cheese. The number of presumptive mesophilic lactococci in raw ewes' milk was higher than that of presumptive mesophilic lactobacilli. The numbers of these microbial groups increased during ripening, showing temporal and numerical differences. Urea-PAGE showed limited primary proteolysis, whereas the analysis of the pH 4.6-soluble fraction of the cheese revealed that secondary proteolysis increased mainly from 45 to 75 days of ripening. This agreed with the concentration of free amino acids. Raw ewes' milk was contaminated by several bacterial phyla: Proteobacteria (68%; mainly Pseudomonas), Firmicutes (30%; mainly Carnobacterium and Lactococcus), Bacteroidetes (0.05%), and Actinobacteria (0.02%). Almost the same microbial composition persisted in the curd after molding. From day 1 of ripening onwards, the phylum Firmicutes dominated. Lactococcus dominated throughout ripening, and most of the Lactobacillus species appeared only at 7 or 15 days. At 90 days, Lactococcus (87.2%), Lactobacillus (4.8%; mainly Lactobacillus plantarum and Lactobacillus sakei), and Leuconostoc (3.9%) dominated. The relative utilization of carbon sources by the bacterial community reflected the succession. This study identified strategic phases that characterized the manufacture and ripening of Canestrato Pugliese cheese and established a causal relationship between mesophilic lactobacilli and proteolysis.}, }
@article {pmid24766220, year = {2014}, author = {Pourabedin, M and Xu, Z and Baurhoo, B and Chevaux, E and Zhao, X}, title = {Effects of mannan oligosaccharide and virginiamycin on the cecal microbial community and intestinal morphology of chickens raised under suboptimal conditions.}, journal = {Canadian journal of microbiology}, volume = {60}, number = {5}, pages = {255-266}, doi = {10.1139/cjm-2013-0899}, pmid = {24766220}, issn = {1480-3275}, mesh = {Animals ; Anti-Bacterial Agents/administration &amp; dosage ; Cecum/cytology/drug effects/*microbiology ; Chickens/*growth &amp; development/*microbiology ; Denaturing Gradient Gel Electrophoresis ; Dietary Supplements/analysis ; Intestines/cytology/drug effects/microbiology ; Lactobacillus ; Male ; Mannans/*administration &amp; dosage ; *Prebiotics ; Virginiamycin/administration &amp; dosage ; }, abstract = {There is an increasing movement against use of antibiotic growth promoters in animal feed. Prebiotic supplementation is a potential alternative to enhance the host's natural defense through modulation of gut microbiota. In the present study, the effect of mannan oligosaccharide (MOS) and virginiamycin (VIRG) on cecal microbial ecology and intestinal morphology of broiler chickens raised under suboptimal conditions was evaluated. MOS and VIRG induced different bacterial community structures, as revealed by denaturing gradient gel electrophoresis of 16S rDNA. The antibiotic treatment reduced cecal microbial diversity while the community equitability increased. A higher bacterial diversity was observed in the cecum of MOS-supplemented birds. Quantitative polymerase chain reaction results indicated that MOS changed the cecal microbiota in favor of the Firmicutes population but not the Bacteroidetes population. No difference was observed in total bacterial counts among treatments. MOS promoted the growth of Lactobacillus spp. and Bifidobacterium spp. in the cecum and increased villus height and goblet cell numbers in the ileum and jejunum. These results provide a deeper insight into the microbial ecological changes after supplementation of MOS prebiotic in poultry diets.}, }
@article {pmid24765642, year = {2014}, author = {Wu, B and Lan, T and Lu, D and Liu, Z}, title = {Ecological and enzymatic responses to petroleum contamination.}, journal = {Environmental science. Processes &amp; impacts}, volume = {16}, number = {6}, pages = {1501-1509}, doi = {10.1039/c3em00731f}, pmid = {24765642}, issn = {2050-7895}, mesh = {Bacteria/*drug effects/enzymology ; Ecosystem ; Petroleum/*toxicity ; *Petroleum Pollution ; Polycyclic Aromatic Hydrocarbons/toxicity ; *Soil Microbiology ; }, abstract = {The changes in microbial ecology interpreted from taxonomic and functional genes and biological functions represented by urease and dehydrogenase activities were monitored in soil contaminated with different petroleum hydrocarbons including crude oil, diesel, n-hexadecane and poly-aromatic hydrocarbons (PAHs). It was shown that the presence of n-hexadecane stimulated the activity of indigenous microorganisms, especially alkane degrading bacteria, and led to over 20% degradation of n-hexadecane within one month. No obvious degradation of the other three types of petroleum hydrocarbons was observed. The stimulation effect was most marked in the soil spiked with a medium concentration (2500 mg kg(-1) dry soil) of n-hexadecane. However, the presence of PAHs completely inhibited the previously-mentioned bioactivities of the soil. The content of PAH degrading bacteria, however, increased more than 10-fold, indicating the selection effect of PAHs on soil bacteria. The impacts of diesel and crude oil on the microbial ecology and biological functions varied significantly with their concentration. The disclosure of the ecological and enzymatic responses could be helpful in soil bioremediation.}, }
@article {pmid24763979, year = {2014}, author = {Folland, I and Trione, D and Dazzo, F}, title = {Accuracy of biovolume formulas for CMEIAS computer-assisted microscopy and body size analysis of morphologically diverse microbial populations and communities.}, journal = {Microbial ecology}, volume = {68}, number = {3}, pages = {596-610}, pmid = {24763979}, issn = {1432-184X}, mesh = {Algorithms ; Bacteria/*cytology ; Biofilms ; Biomass ; Microscopy/*methods ; *Models, Biological ; *Software ; }, abstract = {Cell biovolume is a commonly used metric of microbial abundance analyzed by computer-assisted microscopy, but the accuracies of most biovolume formulas have not been validated by ground truth data. We examined the accuracy of 17 biovolume formulas by comparing the computed volumes of 3D models representing 11 microbial morphotypes (cocci, spirals, curved rods, U-shaped rods, regular straight rods, unbranched filaments, ellipsoids, clubs, prosthecates, rudimentary branched rods, and branched filaments) to the volume displacement of the same objects as ground truth. As anticipated, formula accuracy was significantly influenced by the morphotype examined. A few formulas performed very accurately (> 95 %), especially those that adapted to the cell's shape, whereas others were consistently inaccurate or only accurate for one or two morphotypes. As an example of application, indices of morphological diversity in a freshwater biofilm assemblage were shown to be significantly different when microbial abundance among morphotype classes was measured as biovolume body mass rather than cell counts. Spatial analysis of biovolume body mass can also provide insights on the in situ ecophysiological attributes among individuals in microbial populations and communities, including their spatially autocorrelated allometric scaling interrelationships between body size, metabolic activity, resource apportionment and use, food web dynamics, and various cell-cell interactions affecting their growth and colonization behavior within spatially structured biofilm landscapes. This improved computing technology of biovolume algorithms with proven accuracy identifies which formula(s) should be used to compute microbial biovolumes in 2D images of morphologically diverse communities acquired by conventional phase-contrast light microscopy at single-cell resolution.}, }
@article {pmid24763225, year = {2014}, author = {Ghosh, TS and Gupta, SS and Bhattacharya, T and Yadav, D and Barik, A and Chowdhury, A and Das, B and Mande, SS and Nair, GB}, title = {Gut microbiomes of Indian children of varying nutritional status.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e95547}, pmid = {24763225}, issn = {1932-6203}, mesh = {Bacteria/genetics ; Child ; Child Nutrition Disorders/*microbiology ; Gastrointestinal Tract/*microbiology ; Genes, Bacterial ; Humans ; India ; Microbiota/*genetics ; Molecular Typing ; Nutritional Status ; Sequence Analysis, DNA ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Malnutrition is a global health problem affecting more than 300 million pre-school children worldwide. It is one of the major health concerns in India since around 50% of children below the age of two suffer from various forms of malnutrition. The gut microbiome plays an important role in nutrient pre-processing, assimilation and energy harvest from food. Consequently, dysbiosis of the gut microbiota has been implicated in malnutrition.<br><br>Metagenomics approach was adopted to investigate the gut microbiome sampled from 20 rural Indian children with varying nutritional status. The changes in the abundances of various taxonomic and functional groups were investigated across these gut microbiomes. A core set of 23 genera were observed across samples, with some showing differential abundances with varying nutritional status. One of the findings of the current study is the positive/negative associations of specific taxonomic and functional groups with the nutritional status of the children. Notable alterations in the architecture of the inter-microbial co-occurrence networks were also observed with changes in nutritional status. A key example is the clustering of potentially pathogenic groups into a distinct hub in severely malnourished gut. Our data does not demonstrate causality with the microbiome patterns that we observed, rather a description of some interesting patterns, whose underlying mechanism remains to be uncovered.<br><br>CONCLUSIONS: The present study envisioned interrelationships between the pattern of gut microbiome and the nutritional status of children. The cause of this pattern needs to be explored. However, insights obtained from the present study form the basis for further metagenomic investigations on larger population of children. Results of such studies will be useful in identifying the key microbial groups that can be utilized for targeted therapeutic interventions for managing severe acute malnutrition.}, }
@article {pmid24760171, year = {2014}, author = {Fahrenfeld, N and Cozzarelli, IM and Bailey, Z and Pruden, A}, title = {Insights into biodegradation through depth-resolved microbial community functional and structural profiling of a crude-oil contaminant plume.}, journal = {Microbial ecology}, volume = {68}, number = {3}, pages = {453-462}, pmid = {24760171}, issn = {1432-184X}, mesh = {Azoarcus/genetics/metabolism ; Bacteria/*classification/metabolism ; Biodegradation, Environmental ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Genes, Bacterial ; Geologic Sediments/microbiology ; Groundwater/chemistry/*microbiology ; Petroleum/*metabolism ; Petroleum Pollution ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Water Pollutants, Chemical/*metabolism ; Wetlands ; }, abstract = {Small-scale geochemical gradients are a key feature of aquifer contaminant plumes, highlighting the need for functional and structural profiling of corresponding microbial communities on a similar scale. The purpose of this study was to characterize the microbial functional and structural diversity with depth across representative redox zones of a hydrocarbon plume and an adjacent wetland, at the Bemidji Oil Spill site. A combination of quantitative PCR, denaturing gradient gel electrophoresis, and pyrosequencing were applied to vertically sampled sediment cores. Levels of the methanogenic marker gene, methyl coenzyme-M reductase A (mcrA), increased with depth near the oil body center, but were variable with depth further downgradient. Benzoate degradation N (bzdN) hydrocarbon-degradation gene, common to facultatively anaerobic Azoarcus spp., was found at all locations, but was highest near the oil body center. Microbial community structural differences were observed across sediment cores, and bacterial classes containing known hydrocarbon degraders were found to be low in relative abundance. Depth-resolved functional and structural profiling revealed the strongest gradients in the iron-reducing zone, displaying the greatest variability with depth. This study provides important insight into biogeochemical characteristics in different regions of contaminant plumes, which will aid in improving models of contaminant fate and natural attenuation rates.}, }
@article {pmid24760170, year = {2014}, author = {Gao, ZM and Wang, Y and Lee, OO and Tian, RM and Wong, YH and Bougouffa, S and Batang, Z and Al-Suwailem, A and Lafi, FF and Bajic, VB and Qian, PY}, title = {Pyrosequencing reveals the microbial communities in the Red Sea sponge Carteriospongia foliascens and their impressive shifts in abnormal tissues.}, journal = {Microbial ecology}, volume = {68}, number = {3}, pages = {621-632}, pmid = {24760170}, issn = {1432-184X}, mesh = {Animals ; Bacteria/*classification/genetics ; DNA, Bacterial/genetics ; Indian Ocean ; *Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; }, abstract = {Abnormality and disease in sponges have been widely reported, yet how sponge-associated microbes respond correspondingly remains inconclusive. Here, individuals of the sponge Carteriospongia foliascens under abnormal status were collected from the Rabigh Bay along the Red Sea coast. Microbial communities in both healthy and abnormal sponge tissues and adjacent seawater were compared to check the influences of these abnormalities on sponge-associated microbes. In healthy tissues, we revealed low microbial diversity with less than 100 operational taxonomic units (OTUs) per sample. Cyanobacteria, affiliated mainly with the sponge-specific species "Candidatus Synechococcus spongiarum," were the dominant bacteria, followed by Bacteroidetes and Proteobacteria. Intraspecies dynamics of microbial communities in healthy tissues were observed among sponge individuals, and potential anoxygenic phototrophic bacteria were found. In comparison with healthy tissues and the adjacent seawater, abnormal tissues showed dramatic increase in microbial diversity and decrease in the abundance of sponge-specific microbial clusters. The dominated cyanobacterial species Candidatus Synechococcus spongiarum decreased and shifted to unspecific cyanobacterial clades. OTUs that showed high similarity to sequences derived from diseased corals, such as Leptolyngbya sp., were found to be abundant in abnormal tissues. Heterotrophic Planctomycetes were also specifically enriched in abnormal tissues. Overall, we revealed the microbial communities of the cyanobacteria-rich sponge, C. foliascens, and their impressive shifts under abnormality.}, }
@article {pmid24760169, year = {2014}, author = {Guevara, R and Ikenaga, M and Dean, AL and Pisani, C and Boyer, JN}, title = {Changes in sediment bacterial community in response to long-term nutrient enrichment in a subtropical seagrass-dominated estuary.}, journal = {Microbial ecology}, volume = {68}, number = {3}, pages = {427-440}, pmid = {24760169}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; *Estuaries ; Fertilizers ; Florida ; Geologic Sediments/*microbiology ; Nitrogen/*chemistry ; Phosphorus/*chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/microbiology ; Sequence Analysis, DNA ; Water Microbiology ; }, abstract = {Florida Bay exhibits a natural gradient of strong P limitation in the east which shifts to weak P or even N limitation at the western boundary. This nutrient gradient greatly affects seagrass abundance and productivity across the bay. We assessed the effects of N and P additions on sediment bacterial community structure in relation to the existing nutrient gradient in Florida Bay. Sediment samples from 24 permanent 0.25 m(2) plots in each of six sites across Florida Bay were fertilized with granular N and P in a factorial design for 26 months. Sediment bacterial community structure was analyzed using PCR-denaturing gradient gel electrophoresis (DGGE) analysis of 16S ribosomal RNA (rRNA) genes and a cloning strategy from DGGE bands. The phylogenetic positions of 16S rRNA sequences mostly fell into common members found in marine sediments such as sulfate-reducing Deltaproteobacteria, Gammaproteobacteria, Spirochaetes, and Bacteriodetes. Twenty-eight common DGGE bands were found in all sediment samples; however, some DGGE bands were only found or were better represented in eastern sites. Bacterial community diversity (Shannon-Weiner index) showed similar values throughout all sediment samples. The N treatment had no effect on the bacterial community structures across the bay. Conversely, the addition of P significantly influenced the bacterial community structure at all but the most western site, where P is least limiting due to inputs from the Gulf of Mexico. P additions enhanced DGGE band sequences related to Cytophagales, Ectothiorhodospiraceae, and Desulfobulbaceae, suggesting a shift toward bacterial communities with increased capability to degrade polymeric organic matter. In addition, a band related to Deferribacteres was enhanced in eastern sites. Thus, indigenous environmental conditions were the primary determining factors controlling the bacterial communities, while the addition of P was a secondary determining factor. This P-induced change in community composition tended to be proportional to the amount of P limitation obviated by the nutrient additions.}, }
@article {pmid24760168, year = {2014}, author = {Trujillo, CA and Ochoa, JC and Mideros, MF and Restrepo, S and López, C and Bernal, A}, title = {A complex population structure of the cassava pathogen Xanthomonas axonopodis pv. manihotis in recent years in the Caribbean Region of Colombia.}, journal = {Microbial ecology}, volume = {68}, number = {1}, pages = {155-167}, pmid = {24760168}, issn = {1432-184X}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Colombia ; DNA, Bacterial/genetics ; Evolution, Molecular ; Genes, Bacterial ; Genetic Markers ; *Genetics, Population ; Haplotypes ; Manihot/*microbiology ; Plant Diseases/*microbiology ; Polymorphism, Genetic ; Selection, Genetic ; Virulence/genetics ; Xanthomonas axonopodis/*genetics/pathogenicity ; }, abstract = {Cassava bacterial blight, caused by Xanthomonas axonopodis pv. manihotis (Xam), is the most important bacterial disease affecting this crop. A continuous surveillance of the pathogen population dynamics is required to develop an efficient disease management program. During the 1990s, Xam populations showed high levels of genetic variation and relevant migratory processes that were important determinants of the distribution of the pathogen diversity in Colombia. Aiming to characterize the current population structure of the pathogen and the evolutionary forces that shape these populations, sampling collections were carried out from September 2008 until November 2010 in the Colombian Caribbean Region. One hundred and sixty bacterial isolates were characterized using amplified fragment length polymorphism (AFLP) markers. Additionally, a subset of effector genes were sequenced in some isolates to determine their usefulness in Xam population studies and to provide additional information to that obtained with AFLPs. Virulence patterns of ten isolates were determined in nine cassava accessions. Our results show a complex architecture of population and confirm migratory process previously reported in the Caribbean Region. Chinú, one of the locations sampled, presented remarkable features in population dynamics such as longer genetic distances, higher diversity indices, and a genetically differentiated population when it was compared with other locations. Virulence tests showed that MCOL2215, one of the most cultivated cassava varieties in the Caribbean coast, was susceptible to the majority of Xam isolates tested. This study shows the current condition of populations of Xam in the Caribbean Region of Colombia, and it contributes to improve the existing bacterial blight control practices.}, }
@article {pmid24760167, year = {2014}, author = {Aedo, S and Ivanova, L and Tomova, A and Cabello, FC}, title = {Plasmid-related quinolone resistance determinants in epidemic Vibrio parahaemolyticus, uropathogenic Escherichia coli, and marine bacteria from an aquaculture area in Chile.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {324-328}, pmid = {24760167}, issn = {1432-184X}, mesh = {Amino Acid Sequence ; Anti-Bacterial Agents/*pharmacology ; Aquaculture ; Chile ; Cloning, Molecular ; DNA, Bacterial/genetics ; Drug Resistance, Bacterial/*genetics ; Genes, Bacterial ; Molecular Sequence Data ; Mutation ; Plasmids/genetics ; Quinolones/*pharmacology ; Uropathogenic Escherichia coli/*drug effects/genetics ; Vibrio parahaemolyticus/*drug effects/genetics ; }, abstract = {Marine bacteria from aquaculture areas with industrial use of quinolones have the potential to pass quinolone resistance genes to animal and human pathogens. The VPA0095 gene, related to the quinolone resistance determinant qnrA, from clinical isolates of epidemic Vibrio parahaemolyticus conferred reduced susceptibility to quinolone after cloning into Escherichia coli K-12 either when acting alone or synergistically with DNA gyrase mutations. In addition, a plasmid-mediated quinolone resistance gene from marine bacteria, aac(6')-Ib-cr, was identical to aac(6')-Ib-cr from urinary tract isolates of E. coli, suggesting a recent flow of this gene between these bacteria isolated from different environments. aac(6')-Ib-cr from E. coli also conferred reduced susceptibility to quinolone and kanamycin when cloned into E. coli K-12.}, }
@article {pmid24759534, year = {2014}, author = {Courtens, EN and Meerburg, F and Mausen, V and Vlaeminck, SE}, title = {When the smoke disappears: dealing with extinguishing chemicals in firefighting wastewater.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {69}, number = {8}, pages = {1720-1727}, doi = {10.2166/wst.2014.081}, pmid = {24759534}, issn = {0273-1223}, mesh = {Bioreactors ; Chlorides ; Ferric Compounds ; *Fires ; Nitrogen/*chemistry ; Phosphorus/*chemistry ; Waste Disposal, Fluid/*methods ; Water Pollutants, Chemical/*chemistry ; }, abstract = {Water is not enough. Nowadays, numerous chemicals are used for fire extinction. After use, however, these may unintentionally enter sewerage systems. In order to safely treat firefighting wastewater (FFWW), knowledge of the potential effects of these chemicals on biological treatment processes is essential. This study characterized and mimicked the composition of FFWW containing two powders, three foams and one foam degrader. Nitrogen (162-370 mg NH4(+)-N L(-1)) and phosphorus (173-320 mg PO4(3-)-P L(-1)) concentrations exceeded discharge limits, whereas chemical and biological oxygen demand, suspended solids and detergent concentrations remained sufficiently low. Adequate nutrient removal could be obtained through FeCl3 addition and nitrification/denitrification with acetate as substrate. In batch tests, residual nitrifying activities of 84, 81, 89, 95 and 93% were observed in the presence of powders, foams, foam degrader, synthetic and real FFWW, respectively. All categories showed higher denitrification rates than the control. Although the powders at first seemed to inhibit anammox activity at 82%, after pH correction anammox was fully feasible, allowing nitrogen removal through oxygen-limited nitrification/denitrification (OLAND). Detailed cost calculations indicated that OLAND could save 11% of capital and 68% of operational costs compared to nitrification/denitrification, identifying OLAND as the most recommendable process for nitrogen removal from firefighting wastewaters.}, }
@article {pmid24751377, year = {2014}, author = {Verhoeven, JT and Laanbroek, HJ and Rains, MC and Whigham, DF}, title = {Effects of increased summer flooding on nitrogen dynamics in impounded mangroves.}, journal = {Journal of environmental management}, volume = {139}, number = {}, pages = {217-226}, doi = {10.1016/j.jenvman.2014.02.035}, pmid = {24751377}, issn = {1095-8630}, mesh = {Ammonium Compounds/analysis ; Avicennia/*growth &amp; development ; Ecosystem ; Florida ; Insect Control/*methods ; Nitrogen/analysis ; *Nitrogen Cycle ; Seasons ; Wetlands ; }, abstract = {Mangroves are important for coastal protection, carbon sequestration and habitat provision for plants and animals in the tropics and subtropics. Mangroves are threatened by habitat destruction and sea level rise, but management activities such as impounding for mosquito control can also have negative effects. We studied the effects of Rotational Impoundment Management (RIM) on nitrogen dynamics in impoundments dominated by three types of Black mangrove (Avicennia germinans) stands along the Indian River Lagoon (Florida). RIM, designed for noxious insect control, involves pumping estuarine water into impoundments in this area during spring and summer to raise water levels by 30 cm. We compared aspects of the nitrogen cycle before and after the start of the RIM and measured the same variables in an impoundment without RIM management. RIM led to the accumulation of ammonium in the substrate which coincided with a lowering of nitrification rates and decreased denitrification rates. Salt pan habitats dominated by dwarf mangroves became less saline following RIM initiation. Shoot growth of mangroves increased in response to higher nitrogen availability and lower pore water salinity. Mangrove responses were greatest in areas with dwarf and sparse mangrove cover. Overall, RIM resulted in lower nitrification and denitrification leading to lower nitrogen losses and increased Black mangrove growth, all benefits of RIM beyond those associated with noxious insect control.}, }
@article {pmid24751288, year = {2014}, author = {Barberán, A and Ramirez, KS and Leff, JW and Bradford, MA and Wall, DH and Fierer, N}, title = {Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria.}, journal = {Ecology letters}, volume = {17}, number = {7}, pages = {794-802}, doi = {10.1111/ele.12282}, pmid = {24751288}, issn = {1461-0248}, mesh = {Bacteria/classification/genetics/metabolism ; *Bacterial Physiological Phenomena ; Biodiversity ; *Ecosystem ; Genome, Bacterial ; Phylogeny ; Population Density ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Identifying the traits that determine spatial distributions can be challenging when studying organisms, like bacteria, for which phenotypic information is limited or non-existent. However, genomic data provide another means to infer traits and determine the ecological attributes that account for differences in distributions. We determined the spatial distributions of ~124 000 soil bacterial taxa across a 3.41 km(2) area to determine whether we could use phylogeny and/or genomic traits to explain differences in habitat breadth. We found that occupancy was strongly correlated with environmental range; taxa that were more ubiquitous were found across a broader range of soil conditions. Across the ~500 taxa for which genomic information was available, genomic traits were more useful than phylogeny alone in explaining the variation in habitat breadth; bacteria with larger genomes and more metabolic versatility were more likely to have larger environmental and geographical distributions. Just as trait-based approaches have proven to be so useful for understanding the distributions of animals and plants, we demonstrate that we can use genomic information to infer microbial traits that are difficult to measure directly and build trait-based predictions of the biogeographical patterns exhibited by microbes.}, }
@article {pmid24747512, year = {2014}, author = {Alemany, L and Barbera, R and Alegría, A and Laparra, JM}, title = {Plant sterols from foods in inflammation and risk of cardiovascular disease: a real threat?.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {69}, number = {}, pages = {140-149}, doi = {10.1016/j.fct.2014.03.038}, pmid = {24747512}, issn = {1873-6351}, mesh = {Atherosclerosis/etiology ; Biological Availability ; Cardiovascular Diseases/chemically induced/*etiology ; Cholesterol/metabolism ; Food/*adverse effects ; Food Handling ; Humans ; Inflammation/chemically induced/*etiology/metabolism ; Phytosterols/adverse effects/metabolism/pharmacokinetics/*pharmacology ; Risk Factors ; }, abstract = {High dietary intakes of cholesterol together with sedentary habits have been identified as major contributors to atherosclerosis. The latter has long been considered a cholesterol storage disease; however, today atherosclerosis is considered a more complex disease in which both innate and adaptive immune-inflammatory mechanisms as well as bacteria play a major role, in addition to interactions between the arterial wall and blood components. This scenario has promoted nutritional recommendations to enrich different type of foods with plant sterols (PS) because of their cholesterol-lowering effects. In addition to cholesterol, PS can also be oxidized during food processing or storage, and the oxidized derivatives, known as phytosterol oxidation products (POPs), can make an important contribution to the negative effects of both cholesterol and cholesterol oxidation oxides (COPs) in relation to inflammatory disease onset and the development of atherosclerosis. Most current research efforts have focused on COPs, and evaluations of the particular role and physiopathological implications of specific POPs have been only inferential. Appreciation of the inflammatory role described for both COPs and POPs derived from foods also provides additional reasons for safety studies after long-term consumption of PS. The balance and relevance for health of all these effects deserves further studies in humans. This review summarizes current knowledge about the presence of sterol oxidation products (SOPs) in foods and their potential role in inflammatory process and cardiovascular disease.}, }
@article {pmid24743885, year = {2014}, author = {Jung, J and Choi, S and Hong, H and Sung, JS and Park, W}, title = {Effect of red clay on diesel bioremediation and soil bacterial community.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {314-323}, pmid = {24743885}, issn = {1432-184X}, mesh = {*Aluminum Silicates ; Bacteria/classification/*growth &amp; development ; Bacteriological Techniques ; Biodegradation, Environmental ; Clay ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; Gasoline/*microbiology ; Microbial Consortia ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {Red clay is a type of soil, the red color of which results from the presence of iron oxide. It is considered an eco-friendly material, with many industrial, cosmetic, and architectural uses. A patented method was applied to red clay in order to change its chemical composition and mineral bioavailability. The resulting product was designated processed red clay. This study evaluates the novel use of red clay and processed red clay as biostimulation agents in diesel-contaminated soils. Diesel biodegradation was enhanced in the presence of red clay and processed red clay by 4.9- and 6.7-fold, respectively, and the number of culturable bacterial cells was correlated with the amount of diesel biodegradation. The growth of Acinetobacter oleivorans DR1, Pseudomonas putida KT2440, and Cupriavidus necator was promoted by both types of red clays. Culture-independent community analysis determined via barcoded pyrosequencing indicated that Nocardioidaceae, Xanthomonadaceae, Pseudomonadaceae, and Caulobacteraceae were enriched by diesel contamination. Bacterial strain isolation from naphthalene- and liquid paraffin-amended media was affiliated with enriched taxa based on 16S rRNA gene sequence identity. We suggest that the biostimulating mechanism of red clay and processed red clay is able to support bacterial growth without apparent selection for specific bacterial species.}, }
@article {pmid24743884, year = {2014}, author = {Vila-Costa, M and Bartrons, M and Catalan, J and Casamayor, EO}, title = {Nitrogen-cycling genes in epilithic biofilms of oligotrophic high-altitude lakes (central Pyrenees, Spain).}, journal = {Microbial ecology}, volume = {68}, number = {1}, pages = {60-69}, pmid = {24743884}, issn = {1432-184X}, mesh = {Altitude ; Archaea/genetics/growth &amp; development ; Bacteria/*genetics/growth &amp; development ; *Biofilms ; *Denitrification ; Genes, Archaeal ; Genes, Bacterial ; Lakes/*microbiology ; Nitrogen/metabolism ; Oxidoreductases/genetics ; Spain ; }, abstract = {Microbial biofilms in oligotrophic environments are the most reactive component of the ecosystem. In high-altitude lakes, exposed bedrock, boulders, gravel, and sand in contact with highly oxygenated water and where a very thin epilithic biofilm develops usually dominate the littoral zone. Traditionally, these surfaces have been considered unsuitable for denitrification, but recent investigations have shown higher biological diversity than expected, including diverse anaerobic microorganisms. In this study, we explored the presence of microbial N-cycling nirS and nirK (denitrification through the conversion of NO2(-) to NO), nifH (N2 fixation), anammox (anaerobic ammonium oxidation), and amoA (aerobic ammonia oxidation, both bacterial and archaeal) genes in epilithic biofilms of a set of high-altitude oligotrophic lakes in the Pyrenees. The concentrations of denitrifying genes determined by quantitative PCR were two orders of magnitude higher than those of ammonia-oxidizing genes. Both types of genes were significantly correlated, suggesting a potential tight coupling nitrification-denitrification in these biofilms that deserves further confirmation. The nifH gene was detected after nested PCR, and no signal was detected for the anammox-specific genes used. The taxonomic composition of denitrifying and nitrogen-fixing genes was further explored by cloning and sequencing. Interestingly, both microbial functional groups were richer and more genetically diverse than expected. The nirK gene, mostly related to Alphaproteobacteria (Bradyrhizobiaceae), dominated the denitrifying gene pool as expected for oxygen-exposed habitats, whereas Deltaproteobacteria (Geobacter like) and Cyanobacteria were the most abundant among nitrogen fixers. Overall, these results suggest an epilithic community more metabolically diverse than previously thought and with the potential to carry out an active role in the biogeochemical nitrogen cycling of high-altitude ecosystems. Measurements of activity rates should be however carried out to substantiate and further explore these findings.}, }
@article {pmid24743883, year = {2014}, author = {McHugh, TA and Koch, GW and Schwartz, E}, title = {Minor changes in soil bacterial and fungal community composition occur in response to monsoon precipitation in a semiarid grassland.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {370-378}, pmid = {24743883}, issn = {1432-184X}, mesh = {Arizona ; Bacteria/*classification/genetics ; Biomass ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fungi/*classification/genetics ; *Grassland ; Humidity ; RNA, Ribosomal, 16S/genetics ; *Rain ; Seasons ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Arizona and New Mexico receive half of their annual precipitation during the summer monsoon season, making this large-scale rain event critical for ecosystem productivity. We used the monsoon rains to explore the responses of soil bacterial and fungal communities to natural moisture pulses in a semiarid grassland. Through 454 pyrosequencing of the 16S rRNA gene and ITS region, we phylogenetically characterized these communities at 22 time points during a summer season. Relative humidity increased before the rains arrived, creating conditions in soil that allowed for the growth of microorganisms. During the course of the study, the relative abundances of most bacterial phyla showed little variation, though some bacterial populations responded immediately to an increase in soil moisture once the monsoon rains arrived. The Firmicutes phylum experienced over a sixfold increase in relative abundance with increasing water availability. Conversely, Actinobacteria, the dominant taxa at our site, were negatively affected by the increase in water availability. No relationship was found between bacterial diversity and soil water potential. Bacterial community structure was unrelated to all environmental variables that we measured, with the exception of a significant relationship with atmospheric relative humidity. Relative abundances of fungal phyla fluctuated more throughout the season than bacterial abundances did. Variation in fungal community structure was unrelated to soil water potential and to most environmental variables. However, ordination analysis showed a distinct fungal community structure late in the season, probably due to plant senescence.}, }
@article {pmid24743166, year = {2014}, author = {Sarmiento-Ramírez, JM and van der Voort, M and Raaijmakers, JM and Diéguez-Uribeondo, J}, title = {Unravelling the microbiome of eggs of the endangered sea turtle Eretmochelys imbricata identifies bacteria with activity against the emerging pathogen Fusarium falciforme.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e95206}, pmid = {24743166}, issn = {1932-6203}, mesh = {Animals ; Bacteria ; *Endangered Species ; *Fusarium ; Microbiota/*physiology ; Ovum ; Turtles/*microbiology ; }, abstract = {Habitat bioaugmentation and introduction of protective microbiota have been proposed as potential conservation strategies to rescue endangered mammals and amphibians from emerging diseases. For both strategies, insight into the microbiomes of the endangered species and their habitats is essential. Here, we sampled nests of the endangered sea turtle species Eretmochelys imbricata that were infected with the fungal pathogen Fusarium falciforme. Metagenomic analysis of the bacterial communities associated with the shells of the sea turtle eggs revealed approximately 16,664 operational taxonomic units, with Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes as the most dominant phyla. Subsequent isolation of Actinobacteria from the eggshells led to the identification of several genera (Streptomyces, Amycolaptosis, Micromomospora Plantactinospora and Solwaraspora) that inhibit hyphal growth of the pathogen F. falciforme. These bacterial genera constitute a first set of microbial indicators to evaluate the potential role of microbiota in conservation of endangered sea turtle species.}, }
@article {pmid24739627, year = {2014}, author = {Vanwonterghem, I and Jensen, PD and Dennis, PG and Hugenholtz, P and Rabaey, K and Tyson, GW}, title = {Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters.}, journal = {The ISME journal}, volume = {8}, number = {10}, pages = {2015-2028}, pmid = {24739627}, issn = {1751-7370}, mesh = {Anaerobiosis ; Archaea/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Bioreactors/*microbiology ; Cellulose/metabolism ; Phylogeny ; }, abstract = {A replicate long-term experiment was conducted using anaerobic digestion (AD) as a model process to determine the relative role of niche and neutral theory on microbial community assembly, and to link community dynamics to system performance. AD is performed by a complex network of microorganisms and process stability relies entirely on the synergistic interactions between populations belonging to different functional guilds. In this study, three independent replicate anaerobic digesters were seeded with the same diverse inoculum, supplied with a model substrate, α-cellulose, and operated for 362 days at a 10-day hydraulic residence time under mesophilic conditions. Selective pressure imposed by the operational conditions and model substrate caused large reproducible changes in community composition including an overall decrease in richness in the first month of operation, followed by synchronised population dynamics that correlated with changes in reactor performance. This included the synchronised emergence and decline of distinct Ruminococcus phylotypes at day 148, and emergence of a Clostridium and Methanosaeta phylotype at day 178, when performance became stable in all reactors. These data suggest that many dynamic functional niches are predictably filled by phylogenetically coherent populations over long time scales. Neutral theory would predict that a complex community with a high degree of recognised functional redundancy would lead to stochastic changes in populations and community divergence over time. We conclude that deterministic processes may play a larger role in microbial community dynamics than currently appreciated, and under controlled conditions it may be possible to reliably predict community structural and functional changes over time.}, }
@article {pmid24739625, year = {2014}, author = {Dini-Andreote, F and de Cássia Pereira e Silva, M and Triadó-Margarit, X and Casamayor, EO and van Elsas, JD and Salles, JF}, title = {Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning.}, journal = {The ISME journal}, volume = {8}, number = {10}, pages = {1989-2001}, pmid = {24739625}, issn = {1751-7370}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Phylogeny ; Proteobacteria/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Salinity ; Soil ; *Soil Microbiology ; *Wetlands ; }, abstract = {The mechanisms underlying community assembly and promoting temporal succession are often overlooked in microbial ecology. Here, we studied an undisturbed salt marsh chronosequence, spanning over a century of ecosystem development, to understand bacterial succession in soil. We used 16S rRNA gene-based quantitative PCR to determine bacterial abundance and multitag 454 pyrosequencing for community composition and diversity analyses. Despite 10-fold lower 16S rRNA gene abundances, the initial stages of soil development held higher phylogenetic diversities than the soil at late succession. Temporal variations in phylogenetic β-diversity were greater at initial stages of soil development, possibly as a result of the great dynamism imposed by the daily influence of the tide, promoting high immigration rates. Allogenic succession of bacterial communities was mostly driven by shifts in the soil physical structure, as well as variations in pH and salinity, which collectively explained 84.5% of the variation concerning community assemblage. The community assembly data for each successional stage were integrated into a network co-occurrence analysis, revealing higher complexity at initial stages, coinciding with great dynamism in turnover and environmental variability. Contrary to a spatial niche-based perspective of bacterial community assembly, we suggest temporal niche partitioning as the dominant mechanism of assembly (promoting more phylotype co-occurrence) in the initial stages of succession, where continuous environmental change results in the existence of multiple niches over short periods of time.}, }
@article {pmid24739623, year = {2014}, author = {Giovannoni, SJ and Cameron Thrash, J and Temperton, B}, title = {Implications of streamlining theory for microbial ecology.}, journal = {The ISME journal}, volume = {8}, number = {8}, pages = {1553-1565}, pmid = {24739623}, issn = {1751-7370}, mesh = {Bacteria/genetics/growth &amp; development ; Ecological and Environmental Phenomena ; *Evolution, Molecular ; Genetic Drift ; *Genome Size ; Genome, Archaeal ; *Genome, Bacterial ; }, abstract = {Whether a small cell, a small genome or a minimal set of chemical reactions with self-replicating properties, simplicity is beguiling. As Leonardo da Vinci reportedly said, 'simplicity is the ultimate sophistication'. Two diverging views of simplicity have emerged in accounts of symbiotic and commensal bacteria and cosmopolitan free-living bacteria with small genomes. The small genomes of obligate insect endosymbionts have been attributed to genetic drift caused by small effective population sizes (Ne). In contrast, streamlining theory attributes small cells and genomes to selection for efficient use of nutrients in populations where Ne is large and nutrients limit growth. Regardless of the cause of genome reduction, lost coding potential eventually dictates loss of function. Consequences of reductive evolution in streamlined organisms include atypical patterns of prototrophy and the absence of common regulatory systems, which have been linked to difficulty in culturing these cells. Recent evidence from metagenomics suggests that streamlining is commonplace, may broadly explain the phenomenon of the uncultured microbial majority, and might also explain the highly interdependent (connected) behavior of many microbial ecosystems. Streamlining theory is belied by the observation that many successful bacteria are large cells with complex genomes. To fully appreciate streamlining, we must look to the life histories and adaptive strategies of cells, which impose minimum requirements for complexity that vary with niche.}, }
@article {pmid24736315, year = {2014}, author = {Uyeno, Y and Katayama, S and Nakamura, S}, title = {Changes in mouse gastrointestinal microbial ecology with ingestion of kale.}, journal = {Beneficial microbes}, volume = {5}, number = {3}, pages = {345-349}, doi = {10.3920/BM2013.0073}, pmid = {24736315}, issn = {1876-2891}, mesh = {Animal Feed ; Animals ; Bacterial Typing Techniques ; Bacteroidetes/classification/isolation &amp; purification ; *Brassica ; *Diet ; Dietary Supplements ; Fatty Acids, Volatile/*analysis ; Feces/microbiology ; Intestines/*microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Microbiota ; }, abstract = {Kale, a cultivar of Brassica oleracea, has attracted a great deal of attention because of its health-promoting effects, which are thought to be exerted through modulation of the intestinal microbiota. The present study was performed to investigate the effects of kale ingestion on the gastrointestinal microbial ecology of mice. 21 male C57BL/6J mice were divided into three groups and housed in a specific pathogen-free facility. The animals were fed either a control diet or experimental diets supplemented with different commercial kale products for 12 weeks. Contents of the caecum and colon of the mice were processed for the determination of active bacterial populations by a bacterial rRNA-based quantification method and short-chain fatty acids by HPLC. rRNAs of Bacteroides-Prevotella, the Clostridium coccoides-Eubacterium rectale group, and Clostridium leptum subgroup constituted the major fraction of microbiota regardless of the composition of the diet. The ratio of Firmicutes to Bacteroidetes was higher in the colon samples of one of the kale diet groups than in the control. The colonic butyrate level was also higher with the kale-supplemented diet. Overall, the ingestion of kale tended to either increase or decrease the activity of specific bacterial groups in the mouse gastrointestinal tract, however, the effect might vary depending on the nutritional composition.}, }
@article {pmid24735853, year = {2014}, author = {Bachy, C and Worden, AZ}, title = {Microbial ecology: finding structure in the rare biosphere.}, journal = {Current biology : CB}, volume = {24}, number = {8}, pages = {R315-7}, doi = {10.1016/j.cub.2014.03.029}, pmid = {24735853}, issn = {1879-0445}, mesh = {*Biodiversity ; Eukaryota/*genetics/*physiology ; Marine Biology/*statistics &amp; numerical data ; Microbiota/*genetics ; *Phylogeny ; }, abstract = {Protists (unicellular eukaryotes) play important roles in marine ecosystems but are tremendously diverse and many remain uncharacterized. Deep-sequencing of a universal marker gene has helped resolve community composition patterns among rare and abundant protistan sequence groups in coastal European waters.}, }
@article {pmid24732021, year = {2014}, author = {Mir, BA and Mewalal, R and Mizrachi, E and Myburg, AA and Cowan, DA}, title = {Recombinant hyperthermophilic enzyme expression in plants: a novel approach for lignocellulose digestion.}, journal = {Trends in biotechnology}, volume = {32}, number = {5}, pages = {281-289}, doi = {10.1016/j.tibtech.2014.03.003}, pmid = {24732021}, issn = {1879-3096}, mesh = {Enzyme Stability ; Hot Temperature ; Hydrolases/*chemistry/genetics/*metabolism ; Hydrolysis ; Lignin/*metabolism ; Plants/*enzymology/genetics ; Recombinant Proteins/chemistry/genetics/metabolism ; }, abstract = {Plant biomass, as an abundant renewable carbon source, is a promising alternative to fossil fuels. However, the enzymes most commonly used for depolymerization of lignocellulosic biomass are expensive, and the development of cost-effective alternative conversion technologies would be desirable. One possible option is the heterologous expression of genes encoding lignocellulose-digesting enzymes in plant tissues. To overcome simultaneously issues of toxicity and incompatibility with high-temperature steam explosion processes, the use of heterologous genes encoding hyperthermophilic enzymes may be an attractive alternative. This approach could reduce the need for exogenous enzyme additions prior to fermentation, reducing the cost of the complete processing operation. This review highlights recent advances and future prospects for using hyperthermophilic enzymes in the biofuels industry.}, }
@article {pmid24728758, year = {2014}, author = {Wang, YF and Zhang, FQ and Gu, JD}, title = {Improvement of DGGE analysis by modifications of PCR protocols for analysis of microbial community members with low abundance.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {12}, pages = {5655-5663}, doi = {10.1007/s00253-014-5734-3}, pmid = {24728758}, issn = {1432-0614}, mesh = {*Biota ; Denaturing Gradient Gel Electrophoresis/*methods ; *Environmental Microbiology ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA ; }, abstract = {Denaturing gradient gel electrophoresis (DGGE) is a powerful technique to reveal the community structures and composition of microorganisms in complex natural environments and samples. However, positive and reproducible polymerase chain reaction (PCR) products, which are difficult to acquire for some specific samples due to low abundance of the target microorganisms, significantly impair the effective applications of DGGE. Thus, nested PCR is often introduced to generate positive PCR products from the complex samples, but one problem is also introduced: The total number of thermocycling in nested PCR is usually unacceptably high, which results in skewed community structures by generation of random or mismatched PCR products on the DGGE gel, and this was demonstrated in this study. Furthermore, nested PCR could not resolve the uneven representative issue with PCR products of complex samples with unequal richness of microbial population. In order to solve the two problems in nested PCR, the general protocol was modified and improved in this study. Firstly, a general PCR procedure was used to amplify the target genes with the PCR primers without any guanine cytosine (GC) clamp, and then, the resultant PCR products were purified and diluted to 0.01 μg ml(-1). Subsequently, the diluted PCR products were utilized as templates to amplify again with the same PCR primers with the GC clamp for 17 cycles, and the products were finally subjected to DGGE analysis. We demonstrated that this is a much more reliable approach to obtain a high quality DGGE profile with high reproducibility. Thus, we recommend the adoption of this improved protocol in analyzing microorganisms of low abundance in complex samples when applying the DGGE fingerprinting technique to avoid biased results.}, }
@article {pmid24728526, year = {2014}, author = {Roe, HM and Patterson, RT}, title = {Arcellacea (testate amoebae) as bio-indicators of road salt contamination in lakes.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {299-313}, pmid = {24728526}, issn = {1432-184X}, mesh = {Amoeba/*growth &amp; development/isolation &amp; purification ; Cluster Analysis ; Environmental Monitoring/*methods ; Lakes/chemistry/microbiology ; Ontario ; Sodium Chloride/*analysis ; Water Pollutants, Chemical/*analysis ; }, abstract = {Winter deicing operations occur extensively in mid- to high-latitude metropolitan regions around the world and result in a significant reduction in road accidents. Deicing salts can, however, pose a major threat to water quality and aquatic organisms. In this paper, we examine the utility of Arcellacea (testate amoebae) for monitoring lakes that have become contaminated by winter deicing salts, particularly sodium chloride. We analysed 50 sediment samples and salt-related water property variables (chloride concentrations; conductivity) from 15 lakes in the Greater Toronto Area and adjacent areas of southern Ontario, Canada. The sampled lakes included lakes in proximity to major highways and suburban roads and control lakes in forested settings away from road influences. Samples from the most contaminated lakes, with chloride concentrations in excess of 400 mg/l and conductivities of >800 μS/cm, were dominated by species typically found in brackish and/or inhospitable lake environments and by lower faunal diversities (lowest Shannon diversity index values) than samples with lower readings. Q-R-mode cluster analysis and detrended correspondence analysis (DCA) resulted in the recognition of four assemblage groupings. These reflect varying levels of salt contamination in the study lakes, along with other local influences, including nutrient loading. The response to nutrients can, however, be isolated if the planktic eutrophic indicator species Cucurbitella tricuspis is removed from the counts. The findings show that the group has considerable potential for biomonitoring in salt-contaminated lakes, and their presence in lake sediment cores may provide significant insights into long-term benthic community health, which is integral for remedial efforts.}, }
@article {pmid24723922, year = {2014}, author = {Röling, WF and van Bodegom, PM}, title = {Toward quantitative understanding on microbial community structure and functioning: a modeling-centered approach using degradation of marine oil spills as example.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {125}, pmid = {24723922}, issn = {1664-302X}, abstract = {Molecular ecology approaches are rapidly advancing our insights into the microorganisms involved in the degradation of marine oil spills and their metabolic potentials. Yet, many questions remain open: how do oil-degrading microbial communities assemble in terms of functional diversity, species abundances and organization and what are the drivers? How do the functional properties of microorganisms scale to processes at the ecosystem level? How does mass flow among species, and which factors and species control and regulate fluxes, stability and other ecosystem functions? Can generic rules on oil-degradation be derived, and what drivers underlie these rules? How can we engineer oil-degrading microbial communities such that toxic polycyclic aromatic hydrocarbons are degraded faster? These types of questions apply to the field of microbial ecology in general. We outline how recent advances in single-species systems biology might be extended to help answer these questions. We argue that bottom-up mechanistic modeling allows deciphering the respective roles and interactions among microorganisms. In particular constraint-based, metagenome-derived community-scale flux balance analysis appears suited for this goal as it allows calculating degradation-related fluxes based on physiological constraints and growth strategies, without needing detailed kinetic information. We subsequently discuss what is required to make these approaches successful, and identify a need to better understand microbial physiology in order to advance microbial ecology. We advocate the development of databases containing microbial physiological data. Answering the posed questions is far from trivial. Oil-degrading communities are, however, an attractive setting to start testing systems biology-derived models and hypotheses as they are relatively simple in diversity and key activities, with several key players being isolated and a high availability of experimental data and approaches.}, }
@article {pmid24723913, year = {2014}, author = {Scott, NM and Hess, M and Bouskill, NJ and Mason, OU and Jansson, JK and Gilbert, JA}, title = {The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {108}, pmid = {24723913}, issn = {1664-302X}, abstract = {During hydrocarbon exposure, the composition and functional dynamics of marine microbial communities are altered, favoring bacteria that can utilize this rich carbon source. Initial exposure of high levels of hydrocarbons in aerobic surface sediments can enrich growth of heterotrophic microorganisms having hydrocarbon degradation capacity. As a result, there can be a localized reduction in oxygen potential within the surface layer of marine sediments causing anaerobic zones. We hypothesized that increasing exposure to elevated hydrocarbon concentrations would positively correlate with an increase in denitrification processes and the net accumulation of dinitrogen. This hypothesis was tested by comparing the relative abundance of genes associated with nitrogen metabolism and nitrogen cycling identified in 6 metagenomes from sediments contaminated by polyaromatic hydrocarbons from the Deepwater Horizon (DWH) oil spill in the Gulf of Mexico, and 3 metagenomes from sediments associated with natural oil seeps in the Santa Barbara Channel. An additional 8 metagenomes from uncontaminated sediments from the Gulf of Mexico were analyzed for comparison. We predicted relative changes in metabolite turnover as a function of the differential microbial gene abundances, which showed predicted accumulation of metabolites associated with denitrification processes, including anammox, in the contaminated samples compared to uncontaminated sediments, with the magnitude of this change being positively correlated to the hydrocarbon concentration and exposure duration. These data highlight the potential impact of hydrocarbon inputs on N cycling processes in marine sediments and provide information relevant for system scale models of nitrogen metabolism in affected ecosystems.}, }
@article {pmid24723703, year = {2014}, author = {Adriaenssens, EM and Guerrero, LD and Makhalanyane, TP and Aislabie, JM and Cowan, DA}, title = {Draft Genome Sequence of the Aromatic Hydrocarbon-Degrading Bacterium Sphingobium sp. Strain Ant17, Isolated from Antarctic Soil.}, journal = {Genome announcements}, volume = {2}, number = {2}, pages = {}, pmid = {24723703}, issn = {2169-8287}, abstract = {Here, we present the draft genome sequence of Sphingobium sp. strain Ant17, an aromatic hydrocarbon-degrading bacterium that was isolated from Antarctic oil-contaminated soil. An analysis of this genome can lead to insights into the mechanisms of xenobiotic degradation processes at low temperatures and potentially aid in bioremediation applications.}, }
@article {pmid24721211, year = {2014}, author = {Jacquiod, S and Demanèche, S and Franqueville, L and Ausec, L and Xu, Z and Delmont, TO and Dunon, V and Cagnon, C and Mandic-Mulec, I and Vogel, TM and Simonet, P}, title = {Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library.}, journal = {Journal of biotechnology}, volume = {190}, number = {}, pages = {18-29}, doi = {10.1016/j.jbiotec.2014.03.036}, pmid = {24721211}, issn = {1873-4863}, mesh = {Bacteria/enzymology/*genetics ; Bacterial Proteins/genetics ; Base Sequence ; Chitin/metabolism ; Cloning, Molecular ; DNA, Bacterial/genetics ; Gene Library ; *Genes, Bacterial ; Integrases/genetics ; Laccase/genetics ; Metagenomics/*methods ; Nucleic Acid Hybridization/genetics ; *Soil Microbiology ; }, abstract = {A mix of oligonucleotide probes was used to hybridize soil metagenomic DNA from a fosmid clone library spotted on high density membranes. The pooled radio-labeled probes were designed to target genes encoding glycoside hydrolases GH18, dehalogenases, bacterial laccases and mobile genetic elements (integrases from integrons and insertion sequences). Positive hybridizing spots were affiliated to the corresponding clones in the library and the metagenomic inserts were sequenced. After assembly and annotation, new coding DNA sequences related to genes of interest were identified with low protein similarity against the closest hits in databases. This work highlights the sensitivity of DNA/DNA hybridization techniques as an effective and complementary way to recover novel genes from large metagenomic clone libraries. This study also supports that some of the identified catabolic genes might be associated with horizontal transfer events.}, }
@article {pmid24720232, year = {2014}, author = {Li, X and Liu, YR and Zheng, YM and He, JZ}, title = {[Characterization and soil environmental safety assessment of super absorbent polymers in agricultural application].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {35}, number = {1}, pages = {394-400}, pmid = {24720232}, issn = {0250-3301}, mesh = {*Agriculture ; Polymers/*chemistry ; Soil/*chemistry ; Water ; }, abstract = {Super absorbent polymers (SAPs) are compounds that can absorb a lot of water which can be several folds of their original size and weight. They can increase soil water content and aggregates, promote fertilizer utilization efficiency, and stimulate crop growth. Therefore, SAPs have been widely regarded as a potential agent for water-saving agriculture. In this paper, we reviewed the advances of SAPs in materials, properties and applications in agriculture and pointed out that the absence of influences of SAPs on soil microbial ecology was the main issue in current studies. In regard to the adverse effects on soil environment caused by misuse of SAPs, we should address the systematic safety assessment of SAPs application in the soil, especially the effects on the soil microorganisms, which should be an important part of chemicals risk assessment in the soil application.}, }
@article {pmid24719854, year = {2014}, author = {D'Argenio, V and Casaburi, G and Precone, V and Salvatore, F}, title = {Comparative metagenomic analysis of human gut microbiome composition using two different bioinformatic pipelines.}, journal = {BioMed research international}, volume = {2014}, number = {}, pages = {325340}, pmid = {24719854}, issn = {2314-6141}, mesh = {Bacteria/classification/*genetics ; Computational Biology/*methods ; Gastrointestinal Tract/microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Technological advances in next-generation sequencing-based approaches have greatly impacted the analysis of microbial community composition. In particular, 16S rRNA-based methods have been widely used to analyze the whole set of bacteria present in a target environment. As a consequence, several specific bioinformatic pipelines have been developed to manage these data. MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights Into Microbial Ecology (QIIME) are two freely available tools for metagenomic analyses that have been used in a wide range of studies. Here, we report the comparative analysis of the same dataset with both QIIME and MG-RAST in order to evaluate their accuracy in taxonomic assignment and in diversity analysis. We found that taxonomic assignment was more accurate with QIIME which, at family level, assigned a significantly higher number of reads. Thus, QIIME generated a more accurate BIOM file, which in turn improved the diversity analysis output. Finally, although informatics skills are needed to install QIIME, it offers a wide range of metrics that are useful for downstream applications and, not less important, it is not dependent on server times.}, }
@article {pmid24718907, year = {2014}, author = {Yun, J and Ju, Y and Deng, Y and Zhang, H}, title = {Bacterial community structure in two permafrost wetlands on the Tibetan Plateau and Sanjiang Plain, China.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {360-369}, pmid = {24718907}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics ; China ; DNA, Bacterial/genetics ; Genes, Bacterial ; *Permafrost ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; *Wetlands ; }, abstract = {Permafrost wetlands are important methane emission sources and fragile ecosystems sensitive to climate change. Presently, there remains a lack of knowledge regarding bacterial communities, especially methanotrophs in vast areas of permafrost on the Tibetan Plateau in Northwest China and the Sanjiang Plain (SJ) in Northeast China. In this study, 16S rRNA-based quantitative PCR (qPCR) and 454 pyrosequencing were used to identify bacterial communities in soils sampled from a littoral wetland of Lake Namco on the Tibetan Plateau (NMC) and an alluvial wetland on the SJ. Additionally, methanotroph-specific primers targeting particulate methane monooxygenase subunit A gene (pmoA) were used for qPCR and pyrosequencing analysis of methanotrophic community structure in NMC soils. qPCR analysis revealed the presence of 10(10) 16S rRNA gene copies per gram of wet soil in both wetlands, with 10(8) pmoA copies per gram of wet soil in NMC. The two permafrost wetlands showed similar bacterial community compositions, which differed from those reported in other cold environments. Proteobacteria, Actinobacteria , and Chloroflexi were the most abundant phyla in both wetlands, whereas Acidobacteria was prevalent in the acidic wetland SJ only. These four phyla constituted more than 80 % of total bacterial community diversity in permafrost wetland soils, and Methylobacter of type I methanotrophs was overwhelmingly dominant in NMC soils. This study is the first major bacterial sequencing effort of permafrost in the NMC and SJ wetlands, which provides fundamental data for further studies of microbial function in extreme ecosystems under climate change scenarios.}, }
@article {pmid24715147, year = {2014}, author = {Abraham, WR}, title = {Applications and impacts of stable isotope probing for analysis of microbial interactions.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {11}, pages = {4817-4828}, doi = {10.1007/s00253-014-5705-8}, pmid = {24715147}, issn = {1432-0614}, mesh = {*Food Chain ; Isotope Labeling/*methods ; Microbial Consortia/*physiology ; *Microbial Interactions ; Microbiological Techniques/*methods ; }, abstract = {Probing the interactions between microbes and their environment with stable isotopes became a powerful technique over the last years. While quadruple mass spectrometry or isotope ratio mass spectrometry (IRMS) require at least 300,000 bacterial cells, analysis at the single-cell level is possible with secondary ion mass spectrometry (SIMS) or Raman microspectrometry. While SIMS needs enrichments of more than 0.1 and Raman microscopy of more than 25 at.-%, IRMS can deal with 0.0001 at.-%. To find out who eats what, one has to discern between the different species in a community. Several methods have been introduced to discern between the different taxa in microbial communities, e.g., by using fatty acids as biomarkers, density centrifugation of DNA/RNA, or fluorescent in situ hybridization (FISH) with phylogenetic probes. While the biomarker approach can be coupled with the high sensitivity of the IRMS, the DNA approach gives in general a better phylogenetic resolution of the metabolic active microbes. A combination of both is the separation via coupling of FISH-probes to magnetic beads or fluorescent assisted cell sorting (FACS) of stained cells leading to fractions which can be analyzed by IRMS. Applying these techniques over a time course can reveal the metabolic kinetics and food webs. In this review, the different methods are presented with examples and their advantages and disadvantages are discussed. An outlook on the combination of the various techniques and their applications in microbial ecology is given.}, }
@article {pmid24713080, year = {2014}, author = {Porcellato, D and Brighton, C and McMahon, DJ and Oberg, CJ and Lefevre, M and Broadbent, JR and Steele, JL}, title = {Application of ARISA to assess the influence of salt content and cation type on microbiological diversity of Cheddar cheese.}, journal = {Letters in applied microbiology}, volume = {59}, number = {2}, pages = {207-216}, doi = {10.1111/lam.12263}, pmid = {24713080}, issn = {1472-765X}, mesh = {Bacteria/genetics ; Cations ; Cheese/*microbiology ; Denaturing Gradient Gel Electrophoresis ; Limit of Detection ; Microbiota/*genetics ; Molecular Typing/*methods ; Salt Tolerance ; Sodium Chloride/chemistry ; }, abstract = {UNLABELLED: The structure and dynamics of microbial populations play a significant role during cheese manufacture and ripening. Therefore, fast and accurate methods for identification and characterization of the microbial populations are of fundamental importance to the cheese industry. In this study, we investigate the application of the automated ribosomal intergenic spacer analysis (ARISA) for the assessment of the microbial dynamics in cheeses differing in salt cation level and type. We developed a database of the observed and theoretical length of the 16S-23S intergenic spacer of common lactic acid bacteria (LAB) found in cheese and used the database to describe the structure and dynamics of microbial populations during ripening. Salt content and cation concentration did not significantly influence the overall bacteria structure, except that lower salt levels resulted in enhanced starter survival. Presence of nonstarter LAB was detected by ARISA and denaturing gradient gel electrophoresis (DGGE) after 3 months for all the cheeses analysed. ARISA used as fingerprinting method, proved to be a rapid and inexpensive technique for the discrimination of LAB in cheese and demonstrated higher resolution and performance in comparison with DGGE.<br><br>Microbial communities play important roles during cheese making and ripening, hence rapid inexpensive methods to characterize this microbiota are of great interest to both academic and industrial scientists. The application of automated ribosomal intergenic spacer analysis (ARISA) was used to examine the microbial ecology of Cheddar cheese differing in salt level and type. ARISA is well suited to the analysis of the microbial ecology of cheese during ripening. Additionally, the results confirm that salt concentration influences starter culture survival in the cheese matrix, while significant differences were not observed in the nonstarter lactic acid bacteria.}, }
@article {pmid24711012, year = {2014}, author = {Kovachev, SM}, title = {Obstetric and gynecological diseases and complications resulting from vaginal dysbacteriosis.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {173-184}, pmid = {24711012}, issn = {1432-184X}, mesh = {*Dysbiosis ; Female ; Genital Diseases, Female/*microbiology ; Humans ; Lactobacillus ; Pregnancy ; Pregnancy Complications, Infectious/*microbiology ; Vagina/*microbiology ; }, abstract = {Accurate knowledge of the composition and ecology of vaginal microbial environment of a healthy woman is necessary for the understanding of normal flora and how to reduce the risk for diseases. Vagina and its microflora form a balanced ecosystem in which dominated bacteria are vaginal lactobacilli. There are dynamic changes in this ecosystem having structure and composition depending on many factors. The term dysbacteriosis defines any movement outside the normal range for the given biotope of obligate and/or facultative microflora. Such a change in the quantity and quality of the respective microbial balance is fraught with danger and requires correction and recovery. The purpose of this overview is to examine obstetric and gynecological diseases that can cause vaginal impaired microbial balance. Vaginal dysbacteriosis is a cause, predecessor, and often also consequence of vaginal infections. In essence, any vaginal infection can be seen as dysbacteriosis, developed to the most severe extent. Here, there is a dominant microorganism other than lactic acid bacteria in the vagina (clinically manifested or not, respectively), depletion of defense mechanisms of the vagina associated with the shift of lactobacilli from their dominant role in the vaginal balance, decrease in their number and species diversity, and a resulting change in the healthy status of the vagina. Vaginal dysbacteriosis can be found in pathogenetic mechanism, whereby many obstetric and gynecological diseases develop. Most of these diseases lead directly to increased maternal and infant morbidity and mortality, so it is important to understand the reasons for them and the arrangements for their prevention.}, }
@article {pmid24710002, year = {2014}, author = {Somboonna, N and Wilantho, A and Jankaew, K and Assawamakin, A and Sangsrakru, D and Tangphatsornruang, S and Tongsima, S}, title = {Microbial ecology of Thailand tsunami and non-tsunami affected terrestrials.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e94236}, pmid = {24710002}, issn = {1932-6203}, mesh = {Biodiversity ; *Ecological and Environmental Phenomena ; Ecosystem ; Metagenomics ; *Microbiota ; Thailand ; *Tsunamis ; }, abstract = {The effects of tsunamis on microbial ecologies have been ill-defined, especially in Phang Nga province, Thailand. This ecosystem was catastrophically impacted by the 2004 Indian Ocean tsunami as well as the 600 year-old tsunami in Phra Thong island, Phang Nga province. No study has been conducted to elucidate their effects on microbial ecology. This study represents the first to elucidate their effects on microbial ecology. We utilized metagenomics with 16S and 18S rDNA-barcoded pyrosequencing to obtain prokaryotic and eukaryotic profiles for this terrestrial site, tsunami affected (S1), as well as a parallel unaffected terrestrial site, non-tsunami affected (S2). S1 demonstrated unique microbial community patterns than S2. The dendrogram constructed using the prokaryotic profiles supported the unique S1 microbial communities. S1 contained more proportions of archaea and bacteria domains, specifically species belonging to Bacteroidetes became more frequent, in replacing of the other typical floras like Proteobacteria, Acidobacteria and Basidiomycota. Pathogenic microbes, including Acinetobacter haemolyticus, Flavobacterium spp. and Photobacterium spp., were also found frequently in S1. Furthermore, different metabolic potentials highlighted this microbial community change could impact the functional ecology of the site. Moreover, the habitat prediction based on percent of species indicators for marine, brackish, freshwater and terrestrial niches pointed the S1 to largely comprise marine habitat indicating-species.}, }
@article {pmid24709538, year = {2014}, author = {Van Den Hende, S and Carré, E and Cocaud, E and Beelen, V and Boon, N and Vervaeren, H}, title = {Treatment of industrial wastewaters by microalgal bacterial flocs in sequencing batch reactors.}, journal = {Bioresource technology}, volume = {161}, number = {}, pages = {245-254}, doi = {10.1016/j.biortech.2014.03.057}, pmid = {24709538}, issn = {1873-2976}, mesh = {Aquaculture ; Biomass ; *Bioreactors ; Chemical Industry ; Food Industry ; Industrial Waste ; *Microalgae ; Waste Disposal, Fluid/*methods ; Wastewater ; Water Purification/*instrumentation ; }, abstract = {Microalgal bacterial flocs in sequencing batch reactors (MaB-floc SBRs) represent a novel approach to wastewater treatment. In this approach, mechanical aeration is replaced by photosynthetic aeration and MaB-floc settling separates the treated wastewater from the produced biomass. However, its technical potential for industrial wastewaters needs to be shown. Therefore, wastewaters of aquaculture, manure treatment, food-processing and chemical industry were treated in MaB-floc SBRs. This treatment resulted in significantly different nutrient removal rates and effluent qualities among wastewaters. A high MaB-floc production was obtained for all wastewaters, ranging from 0.14 to 0.26g total suspended solids Lreactor(-1)day(-1). A major advantage of MaB-flocs is the harvesting via a filter press with a large pore size of 200μm, resulting in MaB-floc recoveries of 79-99% and cakes containing 12-21% dry matter. These results may contribute to evolving MaB-floc SBRs as a valuable remediation strategy, especially for aquaculture and food-processing wastewaters.}, }
@article {pmid24704907, year = {2014}, author = {Brooks, JP and Adeli, A and McLaughlin, MR}, title = {Microbial ecology, bacterial pathogens, and antibiotic resistant genes in swine manure wastewater as influenced by three swine management systems.}, journal = {Water research}, volume = {57}, number = {}, pages = {96-103}, doi = {10.1016/j.watres.2014.03.017}, pmid = {24704907}, issn = {1879-2448}, mesh = {Animal Husbandry/*methods ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics/*isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; Manure/*microbiology ; Methicillin-Resistant Staphylococcus aureus/drug effects/genetics/isolation &amp; purification ; *Microbiota ; RNA, Ribosomal, 16S/genetics/metabolism ; Real-Time Polymerase Chain Reaction ; Southeastern United States ; Sus scrofa ; Wastewater/*microbiology ; }, abstract = {The environmental influence of farm management in concentrated animal feeding operations (CAFO) can yield vast changes to the microbial biota and ecological structure of both the pig and waste manure lagoon wastewater. While some of these changes may not be negative, it is possible that CAFOs can enrich antibiotic resistant bacteria or pathogens based on farm type, thereby influencing the impact imparted by the land application of its respective wastewater. The purpose of this study was to measure the microbial constituents of swine-sow, -nursery, and -finisher farm manure lagoon wastewater and determine the changes induced by farm management. A total of 37 farms were visited in the Mid-South USA and analyzed for the genes 16S rRNA, spaQ (Salmonella spp.), Camp-16S (Campylobacter spp.), tetA, tetB, ermF, ermA, mecA, and intI using quantitative PCR. Additionally, 16S rRNA sequence libraries were created. Overall, it appeared that finisher farms were significantly different from nursery and sow farms in nearly all genes measured and in 16S rRNA clone libraries. Nearly all antibiotic resistance genes were detected in all farms. Interestingly, the mecA resistance gene (e.g. methicillin resistant Staphylococcus aureus) was below detection limits on most farms, and decreased as the pigs aged. Finisher farms generally had fewer antibiotic resistance genes, which corroborated previous phenotypic data; additionally, finisher farms produced a less diverse 16S rRNA sequence library. Comparisons of Camp-16S and spaQ GU (genomic unit) values to previous culture data demonstrated ratios from 10 to 10,000:1 depending on farm type, indicating viable but not cultivatable bacteria were dominant. The current study indicated that swine farm management schemes positively and negatively affect microbial and antibiotic resistant populations in CAFO wastewater which has future "downstream" implications from both an environmental and public health perspective.}, }
@article {pmid24703617, year = {2014}, author = {Moon-van der Staay, SY and van der Staay, GW and Michalowski, T and Jouany, JP and Pristas, P and Javorský, P and Kišidayová, S and Varadyova, Z and McEwan, NR and Newbold, CJ and van Alen, T and de Graaf, R and Schmid, M and Huynen, MA and Hackstein, JH}, title = {The symbiotic intestinal ciliates and the evolution of their hosts.}, journal = {European journal of protistology}, volume = {50}, number = {2}, pages = {166-173}, doi = {10.1016/j.ejop.2014.01.004}, pmid = {24703617}, issn = {1618-0429}, mesh = {Animals ; Biodiversity ; Ciliophora/*classification/genetics/*physiology ; Feces/parasitology ; Intestines/*parasitology ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; Rumen/parasitology ; Ruminants/*classification/genetics/*parasitology ; }, abstract = {The evolution of sophisticated differentiations of the gastro-intestinal tract enabled herbivorous mammals to digest dietary cellulose and hemicellulose with the aid of a complex anaerobic microbiota. Distinctive symbiotic ciliates, which are unique to this habitat, are the largest representatives of this microbial community. Analyses of a total of 484 different 18S rRNA genes show that extremely complex, but related ciliate communities can occur in the rumen of cattle, sheep, goats and red deer (301 sequences). The communities in the hindgut of equids (Equus caballus, Equus quagga), and elephants (Elephas maximus, Loxodonta africanus; 162 sequences), which are clearly distinct from the ruminant ciliate biota, exhibit a much higher diversity than anticipated on the basis of their morphology. All these ciliates from the gastro-intestinal tract constitute a monophyletic group, which consists of two major taxa, i.e. Vestibuliferida and Entodiniomorphida. The ciliates from the evolutionarily older hindgut fermenters exhibit a clustering that is specific for higher taxa of their hosts, as extant species of horse and zebra on the one hand, and Africa and Indian elephant on the other hand, share related ciliates. The evolutionary younger ruminants altogether share the various entodiniomorphs and the vestibuliferids from ruminants.}, }
@article {pmid24701142, year = {2014}, author = {Ali Shah, F and Mahmood, Q and Maroof Shah, M and Pervez, A and Ahmad Asad, S}, title = {Microbial ecology of anaerobic digesters: the key players of anaerobiosis.}, journal = {TheScientificWorldJournal}, volume = {2014}, number = {}, pages = {183752}, pmid = {24701142}, issn = {1537-744X}, mesh = {*Anaerobiosis ; *Ecology ; Fermentation ; Methane/metabolism ; *Waste Management ; }, abstract = {Anaerobic digestion is the method of wastes treatment aimed at a reduction of their hazardous effects on the biosphere. The mutualistic behavior of various anaerobic microorganisms results in the decomposition of complex organic substances into simple, chemically stabilized compounds, mainly methane and CO2. The conversions of complex organic compounds to CH4 and CO2 are possible due to the cooperation of four different groups of microorganisms, that is, fermentative, syntrophic, acetogenic, and methanogenic bacteria. Microbes adopt various pathways to evade from the unfavorable conditions in the anaerobic digester like competition between sulfate reducing bacteria (SRB) and methane forming bacteria for the same substrate. Methanosarcina are able to use both acetoclastic and hydrogenotrophic pathways for methane production. This review highlights the cellulosic microorganisms, structure of cellulose, inoculum to substrate ratio, and source of inoculum and its effect on methanogenesis. The molecular techniques such as DGGE (denaturing gradient gel electrophoresis) utilized for dynamic changes in microbial communities and FISH (fluorescent in situ hybridization) that deal with taxonomy and interaction and distribution of tropic groups used are also discussed.}, }
@article {pmid24700375, year = {2015}, author = {Olivares, M and Albrecht, S and De Palma, G and Ferrer, MD and Castillejo, G and Schols, HA and Sanz, Y}, title = {Human milk composition differs in healthy mothers and mothers with celiac disease.}, journal = {European journal of nutrition}, volume = {54}, number = {1}, pages = {119-128}, pmid = {24700375}, issn = {1436-6215}, mesh = {Adult ; Bacteroides fragilis/classification/genetics/growth &amp; development/*isolation &amp; purification ; Bifidobacterium/classification/genetics/growth &amp; development/*isolation &amp; purification ; Case-Control Studies ; Celiac Disease/diet therapy/immunology/*metabolism/microbiology ; Cytokines/*analysis/metabolism ; Diet, Gluten-Free ; Family Health ; Female ; Gene Dosage ; Genes, Bacterial ; Humans ; Immunoglobulin A, Secretory/*analysis/metabolism ; Interferon-gamma/analysis/metabolism ; Interleukin-12/analysis/metabolism ; Lewis Blood Group Antigens/metabolism ; Maternal Nutritional Physiological Phenomena ; Milk, Human/*chemistry/microbiology ; Molecular Typing ; Oligosaccharides/*analysis/metabolism ; Transforming Growth Factor beta1/analysis/metabolism ; }, abstract = {PURPOSE: To investigate whether breast-milk composition and microbiota differ in healthy mothers and mothers with celiac disease (CD) to ultimately contribute to identify additional factors determining CD risk.<br><br>METHODS: Breast-milk samples from healthy mothers (n = 12) and mothers with CD (n = 12) were collected. Cytokines and secretory immunoglobulin A (sIgA) were analyzed by bead-arrays and flow cytometry and human milk oligosaccharides (HMOs) were assessed by capillary electrophoresis with laser-induced fluorescence (CE-LIF) detection. Breast-milk microbiota composition was analyzed by conventional and quantitative real-time PCR.<br><br>RESULT: Breast milk from CD mothers showed significantly lower levels of interleukin (IL) 12p70 (P < 0.042), transforming growth factor (TGF)-&#x3b2;1 (P < 0.018) and sIgA (P < 0.003) and almost significantly lower levels of interferon (IFN)-&#x3b3; (P < 0.058). Six mothers in each group belonged to the secretor Le(a-b+) type, one to the secretor Le(a-b-) type and five to the non-secretor Le(a+b-) type. CD mothers of non-secretor Le(a+b-) type showed increased Lacto-N-tetraose content (P < 0.042) compared with healthy mothers. CD mothers' milk showed reduced gene copy numbers of Bifidobacterium spp. (P < 0.026) and B. fragilis group (P < 0.044).<br><br>CONCLUSION: CD mothers' breast milk is characterized by a reduced abundance of immunoprotective compounds (TGF-&#x3b2;1 and sIgA) and bifidobacteria. The reduction in these components could theoretically diminish the protective effects of breast-feeding on the child's future risk of developing CD.}, }
@article {pmid24699870, year = {2014}, author = {Penton, CR and Gupta, VV and Tiedje, JM and Neate, SM and Ophel-Keller, K and Gillings, M and Harvey, P and Pham, A and Roget, DK}, title = {Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e93893}, pmid = {24699870}, issn = {1932-6203}, mesh = {Bacteria/*genetics ; DNA, Fungal/genetics ; Fungi/*genetics ; Phylogeny ; *Rhizosphere ; *Soil ; Soil Microbiology ; South Australia ; }, abstract = {Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils 'suppressive' or 'non-suppressive' for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ∼ 994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and non-suppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria, Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression.}, }
@article {pmid24697310, year = {2014}, author = {Santaella, C and Allainmat, B and Simonet, F and Chanéac, C and Labille, J and Auffan, M and Rose, J and Achouak, W}, title = {Aged TiO2-based nanocomposite used in sunscreens produces singlet oxygen under long-wave UV and sensitizes Escherichia coli to cadmium.}, journal = {Environmental science &amp; technology}, volume = {48}, number = {9}, pages = {5245-5253}, doi = {10.1021/es500216t}, pmid = {24697310}, issn = {1520-5851}, mesh = {Cadmium/*toxicity ; Electron Spin Resonance Spectroscopy ; Escherichia coli/*drug effects/metabolism/*radiation effects ; Hydroxyl Radical/chemistry ; Microscopy, Electron, Scanning ; *Nanocomposites ; Oxidative Stress ; Reactive Oxygen Species/metabolism ; Singlet Oxygen/*chemistry ; Sunscreening Agents/*chemistry ; Titanium/*chemistry ; *Ultraviolet Rays ; }, abstract = {TiO2-based nanocomposite (NC) are widely used as invisible UV protectant in cosmetics. These nanomaterials (NMs) end in the environment as altered materials. We have investigated the properties of T-Lite SF, a TiO2-NC used as sunscreen, after weathering in water and under light. We have examined the formation of ROS and their consequences on cell physiology of Escherichia coli. Our results show that aged-T-Lite SF produced singlet oxygen under low intensity long wave UV and formed hydroxyl radicals at high intensity. Despite the production of these ROS, T-Lite SF had neither effect on the viability of E. coli nor on mutant impaired in oxidative stress, did not induce mutagenesis and did not impair the integrity of membrane lipids, thus seemed safe to bacteria. However, when pre-exposed to T-Lite SF under low intensity UV, cells turned out to be more sensitive to cadmium, a priority pollutant widely disseminated in soil and surface waters. This effect was not a Trojan horse: sensitization of cells was dependent on the formation of singlet oxygen. These results provide a basis for caution, especially on NMs that have no straight environmental toxicity. It is crucial to anticipate indirect and combined effects of environmental pollutants and NMs.}, }
@article {pmid24694563, year = {2014}, author = {Kouzuma, A and Watanabe, K}, title = {Microbial ecology pushes frontiers in biotechnology.}, journal = {Microbes and environments}, volume = {29}, number = {1}, pages = {1-3}, pmid = {24694563}, issn = {1347-4405}, mesh = {Bacteria/genetics/*metabolism ; Biodegradation, Environmental ; Bioelectric Energy Sources ; Biotechnology/*trends ; Ecology/*trends ; Fermentation ; Water Purification ; }, }
@article {pmid24691849, year = {2014}, author = {Lou, QZ and Lu, M and Sun, JH}, title = {Yeast diversity associated with invasive Dendroctonus valens killing Pinus tabuliformis in China using culturing and molecular methods.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {397-415}, pmid = {24691849}, issn = {1432-184X}, mesh = {Animals ; Ascomycota/*classification ; Basidiomycota/*classification ; China ; DNA, Fungal/genetics ; Ecosystem ; Female ; Genetic Variation ; Phylogeny ; *Pinus ; Sequence Analysis, DNA ; Weevils/*microbiology ; }, abstract = {Bark beetle-associated yeasts are much less studied than filamentous fungi, yet they are also considered to play important roles in beetle nutrition, detoxification, and chemical communication. The red turpentine beetle, Dendroctonus valens, an invasive bark beetle introduced from North America, became one of the most destructive pests in China, having killed more than 10 million Pinus tabuliformis as well as other pine species. No investigation of yeasts associated with this bark beetle in its invaded ranges has been conducted so far. The aim of this study was to assess the diversity of yeast communities in different microhabitats and during different developmental stages of Den. valens in China using culturing and denaturing gradient gel electrophoresis (DGGE) approaches and to compare the yeast flora between China and the USA. The yeast identity was confirmed by sequencing the D1/D2 domain of LSU ribosomal DNA (rDNA). In total, 21 species (13 ascomycetes and eight basidiomycetes) were detected by culturing method, and 12 species (11 ascomycetes and one basidiomycetes) were detected by molecular methods from China. The most frequent five species in China were Candida piceae (Ogataea clade), Cyberlindnera americana, Candida oregonensis (Metschnikowia clade), Candida nitratophila (Ogataea clade) and an undescribed Saccharomycopsis sp., detected by both methods. Seven species were exclusively detected by DGGE. Ca. oregonensis (Metschnikowia clade) was the most frequently detected species by DGGE method. Eight species (all were ascomycetes) from the USA were isolated; seven of those were also found in China. We found significant differences in yeast total abundance as well as community composition between different developmental stages and significant differences between the surface and the gut. The frass yeast community was more similar to that of Den. valens surface or larvae than to the community of the gut or adults. Possible functions of the yeast associates are discussed.}, }
@article {pmid24691848, year = {2014}, author = {Swindles, GT and Reczuga, M and Lamentowicz, M and Raby, CL and Turner, TE and Charman, DJ and Gallego-Sala, A and Valderrama, E and Williams, C and Draper, F and Honorio Coronado, EN and Roucoux, KH and Baker, T and Mullan, DJ}, title = {Ecology of testate amoebae in an Amazonian peatland and development of a transfer function for palaeohydrological reconstruction.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {284-298}, pmid = {24691848}, issn = {1432-184X}, mesh = {Amoeba/classification/*growth &amp; development/isolation &amp; purification ; Environmental Monitoring ; Groundwater ; Hydrology ; Models, Theoretical ; Peru ; Population Dynamics ; Soil ; Sphagnopsida/*microbiology ; *Water Microbiology ; *Wetlands ; }, abstract = {Tropical peatlands represent globally important carbon sinks with a unique biodiversity and are currently threatened by climate change and human activities. It is now imperative that proxy methods are developed to understand the ecohydrological dynamics of these systems and for testing peatland development models. Testate amoebae have been used as environmental indicators in ecological and palaeoecological studies of peatlands, primarily in ombrotrophic Sphagnum-dominated peatlands in the mid- and high-latitudes. We present the first ecological analysis of testate amoebae in a tropical peatland, a nutrient-poor domed bog in western (Peruvian) Amazonia. Litter samples were collected from different hydrological microforms (hummock to pool) along a transect from the edge to the interior of the peatland. We recorded 47 taxa from 21 genera. The most common taxa are Cryptodifflugia oviformis, Euglypha rotunda type, Phryganella acropodia, Pseudodifflugia fulva type and Trinema lineare. One species found only in the southern hemisphere, Argynnia spicata, is present. Arcella spp., Centropyxis aculeata and Lesqueresia spiralis are indicators of pools containing standing water. Canonical correspondence analysis and non-metric multidimensional scaling illustrate that water table depth is a significant control on the distribution of testate amoebae, similar to the results from mid- and high-latitude peatlands. A transfer function model for water table based on weighted averaging partial least-squares (WAPLS) regression is presented and performs well under cross-validation (r(2)(apparent)= 0.76, RMSE = 4.29; r(2)(jack)= 0.68, RMSEP =5.18). The transfer function was applied to a 1-m peat core, and sample-specific reconstruction errors were generated using bootstrapping. The reconstruction generally suggests near-surface water tables over the last 3,000 years, with a shift to drier conditions at c. cal. 1218-1273 AD.}, }
@article {pmid24691115, year = {2014}, author = {Ghishan, FK and Kiela, PR}, title = {Epithelial transport in inflammatory bowel diseases.}, journal = {Inflammatory bowel diseases}, volume = {20}, number = {6}, pages = {1099-1109}, pmid = {24691115}, issn = {1536-4844}, support = {5R37DK033209/DK/NIDDK NIH HHS/United States ; R37 DK033209/DK/NIDDK NIH HHS/United States ; R01 DK041274/DK/NIDDK NIH HHS/United States ; R01 DK073638/DK/NIDDK NIH HHS/United States ; 5R01DK041274/DK/NIDDK NIH HHS/United States ; }, mesh = {Biological Transport/physiology ; Colitis, Ulcerative/complications/*metabolism ; Crohn Disease/complications/*metabolism ; Epithelial Cells/*metabolism ; Humans ; Intestinal Mucosa/*metabolism ; Malnutrition/etiology/*metabolism ; }, abstract = {The epithelium of the gastrointestinal tract is one of the most versatile tissues in the organism, responsible for providing a tight barrier between dietary and bacterial antigens and the mucosal and systemic immune system while maintaining efficient digestive and absorptive processes to ensure adequate nutrient and energy supply. Inflammatory bowel diseases (Crohn's disease and ulcerative colitis) are associated with a breakdown of both functions, which in some cases are clearly interrelated. In this updated literature review, we focus on the effects of intestinal inflammation and the associated immune mediators on selected aspects of the transepithelial transport of macronutrients and micronutrients. The mechanisms responsible for nutritional deficiencies are not always clear and could be related to decreased intake, malabsorption, and excess losses. We summarize the known causes of nutrient deficiencies and the mechanism of inflammatory bowel disease-associated diarrhea. We also overview the consequences of impaired epithelial transport, which infrequently transcend its primary purpose to affect the gut microbial ecology and epithelial integrity. Although some of those regulatory mechanisms are relatively well established, more work needs to be done to determine how inflammatory cytokines can alter the transport process of nutrients across the gastrointestinal and renal epithelia.}, }
@article {pmid24689975, year = {2014}, author = {Delgado-Serrano, L and López, G and Bohorquez, LC and Bustos, JR and Rubiano, C and Osorio-Forero, C and Junca, H and Baena, S and Zambrano, MM}, title = {Neotropical Andes hot springs harbor diverse and distinct planktonic microbial communities.}, journal = {FEMS microbiology ecology}, volume = {89}, number = {1}, pages = {56-66}, doi = {10.1111/1574-6941.12333}, pmid = {24689975}, issn = {1574-6941}, mesh = {Altitude ; Chloroflexi/genetics ; Cluster Analysis ; Colombia ; Cyanobacteria/genetics ; Ecosystem ; Euryarchaeota/genetics ; Genes, Archaeal ; Genes, Bacterial ; Gram-Negative Bacteria/genetics ; Hot Springs/chemistry/*microbiology ; Hydrogen-Ion Concentration ; Molecular Typing ; Phytoplankton/genetics ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Sulfates/chemistry ; *Water Microbiology ; }, abstract = {Microbial explorations of hot springs have led to remarkable discoveries and improved our understanding of life under extreme conditions. The Andean Mountains harbor diverse habitats, including an extensive chain of geothermal heated water sources. In this study, we describe and compare the planktonic microbial communities present in five high-mountain hot springs with distinct geochemical characteristics, at varying altitudes and geographical locations in the Colombian Andes. The diversity and structure of the microbial communities were assessed by pyrosequencing the V5 - V6 region of the 16S rRNA gene. The planktonic communities varied in terms of diversity indexes and were dominated by the bacterial phyla Proteobacteria, Aquificae, Chloroflexi, Cyanobacteria, Firmicutes, Nitrospirae, and Thermotogae, with site-specific bacterial taxa also observed in some cases. Statistical analyses showed that these microbial communities were distinct from one another and that they clustered in a manner consistent with physicochemical parameters of the environment sampled. Multivariate analysis suggested that pH and sulfate were among the main variables influencing population structure and diversity. The results show that despite their geographical proximity and some shared geochemical characteristics, there were few shared operational taxonomic units (OTUs) and that community structure was influenced mainly by environmental factors that have resulted in different microbial populations.}, }
@article {pmid24682342, year = {2014}, author = {Sun, W and Zhang, F and He, L and Li, Z}, title = {Pyrosequencing reveals diverse microbial community associated with the zoanthid Palythoa australiae from the South China Sea.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {942-950}, pmid = {24682342}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology ; Archaea/classification/genetics/isolation &amp; purification/*physiology ; Bacteria/classification/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; China ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Eukaryota/classification/genetics/isolation &amp; purification/*physiology ; *Microbiota ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Diverse sessile organisms inhabit the coral reef ecosystems, including corals, sponges, and sea anemones. In the past decades, scleractinian corals (Cnidaria, Anthozoa, Scleractinia) and their associated microorganisms have attracted much attention. Zoanthids (Cnidaria, Anthozoa, Zoanthidea) are commonly found in coral reefs. However, little is known about the community structure of zoanthid-associated microbiota. In this study, the microbial community associated with the zoanthid Palythoa australiae in the South China Sea was investigated by 454 pyrosequencing. As a result, 2,353 bacterial, 583 archaeal, and 36 eukaryotic microbial ribotypes were detected, respectively. A total of 22 bacterial phyla (16 formally described phyla and six candidate phyla) were recovered. Proteobacteria was the most abundant group, followed by Chloroflexi and Actinobacteria. High-abundance Rhizobiales and diverse Chloroflexi were observed in the bacterial community. The archaeal population was composed of Crenarchaeota and Euryarchaeota, with Marine Group I as the dominant lineage. In particular, Candidatus Nitrosopumilus dominated the archaeal community. Besides bacteria and archaea, the zoanthid harbored eukaryotic microorganisms including fungi and algae though their diversity was very low. This study provided the first insights into the microbial community associated with P. australiae by 454 pyrosequencing, consequently laid a basis for the understanding of the association of P. australiae-microbes symbioses.}, }
@article {pmid24682341, year = {2014}, author = {Li, J and Zheng, YM and Liu, YR and Ma, YB and Hu, HW and He, JZ}, title = {Initial copper stress strengthens the resistance of soil microorganisms to a subsequent copper stress.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {931-941}, pmid = {24682341}, issn = {1432-184X}, mesh = {Archaea/*drug effects/genetics/metabolism ; Archaeal Proteins/genetics ; Bacteria/*drug effects/genetics/metabolism ; Bacterial Proteins/genetics ; China ; Copper/*toxicity ; Molecular Sequence Data ; Oxidoreductases/genetics ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil Pollutants/*toxicity ; }, abstract = {To improve the prediction of essential ecosystem functioning under future environmental disturbances, it is of significance to identify responses of soil microorganisms to environmental stresses. In this study, we collected polluted soil samples from field plots with eight copper levels ranging from 0 to 3,200 mg Cu kg(-1) soil. Then, the soils with 0 and 3,200 mg Cu kg(-1) were selected to construct a microcosm experiment. Four treatments were set up including Cu0-C and Cu3200-C without further Cu addition, and Cu0-A and Cu3200-A with addition of 57.5 mg Cu kg(-1) soil. We measured substrate-induced respiration (SIR) and potential nitrification rate (PNR). Furthermore, the abundance of bacterial, archaeal 16S rRNA genes, ammonia-oxidizing bacteria and archaea amoA genes were determined through quantitative PCR. The soil microbial communities were investigated by terminal restriction fragment length polymorphism (T-RFLP). For the field samples, the SIR and PNR as well as the abundance of soil microorganisms varied significantly between eight copper levels. Soil microbial communities highly differed between the low and high copper stress. In the microcosm experiment, the PNR and SIR both recovered while the abundance of soil microorganisms varied irregularly during the 90-day incubation. The differences of microbial communities measured by pairwise Bray-Curtis dissimilarities between Cu0-A and Cu0-C on day 0 were significantly higher after subsequent stress than before. However, the differences of microbial communities between Cu3200-A and Cu3200-C on day 0 changed little between after subsequent stress and before. Therefore, initial copper stress could increase the resistance of soil microorganisms to subsequent copper stress.}, }
@article {pmid24682340, year = {2014}, author = {Al-Mailem, D and Eliyas, M and Khanafer, M and Radwan, S}, title = {Culture-dependent and culture-independent analysis of hydrocarbonoclastic microorganisms indigenous to hypersaline environments in Kuwait.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {857-865}, pmid = {24682340}, issn = {1432-184X}, mesh = {Archaea/genetics/growth &amp; development/*isolation &amp; purification ; Bacteria/genetics/growth &amp; development/*isolation &amp; purification ; Colony Count, Microbial ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; *Environment ; Kuwait ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Sequence Analysis, DNA ; *Soil Microbiology ; *Water Microbiology ; }, abstract = {The halophilic, hydrocarbonoclastic bacteria and archaea inhabiting two hypersaline coastal areas in Kuwait, one in the north and the other in the south, were counted and characterized. Environmental parameters in both areas were similar, with the exception of the soil organic carbon content, which was in the north higher than in the south. The hydrocarbonoclastic bacterial and haloarchaeal numbers and identities as analyzed using nutrient media of various salinities were similar in soil and pond water samples from both areas. The bacterial species recorded by this culture-dependent method belonged to the genera Halomonas, Chromohalobacter, Marinobacter, Exiguobacterium, Stenotrophomonas, Pseudomonas, Salinivibrio, and Bacillus. The haloarchaeal species belonged to the genera Haloferax and Halobacterium. When analyzed by fingerprinting of their amplified genomic DNA followed by sequencing of the electrophoresis-resolved bands, the same environmental samples revealed a different microbial composition. Bacterial phylotypes recorded by this culture-independent method were affiliated with the genera Ochrobactrum, Stenotrophomonas, Rhodococcus, and "Halomicrobium," whereas the archaeal phylotypes were affiliated with Halorussus, Halomicrobium, and Halorientalis. The observed diversity and composition similarity of the hydrocarbonocalastic microflora in both hypersaline areas suggest an effective potential for oil mineralization therein. This potential has been confirmed experimentally.}, }
@article {pmid24682339, year = {2014}, author = {Yingkajorn, M and Sermwitayawong, N and Palittapongarnpimp, P and Nishibuchi, M and Robins, WP and Mekalanos, JJ and Vuddhakul, V}, title = {Vibrio parahaemolyticus and its specific bacteriophages as an indicator in cockles (Anadara granosa) for the risk of V. parahaemolyticus infection in Southern Thailand.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {849-856}, pmid = {24682339}, issn = {1432-184X}, support = {GM068851/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Arcidae/*microbiology/virology ; Bacteriophages/*isolation &amp; purification ; Colony Count, Microbial ; Disease Reservoirs/*microbiology ; Food Microbiology/*methods ; Humans ; Incidence ; Polymerase Chain Reaction ; Risk Factors ; Serotyping ; Shellfish/*microbiology/virology ; Thailand/epidemiology ; Vibrio Infections/*epidemiology/microbiology ; Vibrio parahaemolyticus/genetics/*isolation &amp; purification/pathogenicity/*virology ; Viral Plaque Assay ; Virulence Factors ; }, abstract = {Correlation between the numbers of Vibrio parahaemolyticus and its specific bacteriophages in cockles was investigated from June 2009 to May 2010 in Hat Yai, Songkhla, Thailand. Cockles obtained monthly from a local market were sampled to determine the numbers of V. parahaemolyticus and bacteriophages that could form plaques on ten strains of pandemic and nonpandemic V. parahaemolyticus. In addition, V. parahaemolyticus isolates from clinical samples from Hat Yai hospital over the same period were investigated. All 139 cockles sampled were positive for V. parahaemolyticus. However, only 76 of them were positive for bacteriophages. During the testing period, the number of bacteriophages was not significantly correlated with the incidence of V. parahaemolyticus-infected patients, but the numbers of V. parahaemolyticus isolates from the cockle samples were closely related to the number of infected patients. The bacteriophages isolated from V. parahaemolyticus also infected Vibrio alginolyticus and Vibrio mimicus, suggesting that the broad host range of phages may be a factor of providing the possibility of their participation in the processes of genetic exchange between V. parahaemolyticus and closely related Vibrio spp. In conclusion, this study indicated that the number of V. parahaemolyticus in cockles may be a useful tool for predicting the relative risk of infection by V. parahaemolyticus in this area of Thailand.}, }
@article {pmid24682309, year = {2014}, author = {Ahn, JH and Choi, MY and Kim, BY and Lee, JS and Song, J and Kim, GY and Weon, HY}, title = {Effects of water-saving irrigation on emissions of greenhouse gases and prokaryotic communities in rice paddy soil.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {271-283}, pmid = {24682309}, issn = {1432-184X}, mesh = {Agricultural Irrigation/*methods ; Archaea/classification/growth &amp; development ; Bacteria/classification/growth &amp; development ; Genes, Archaeal ; Genes, Bacterial ; *Greenhouse Effect ; Methane/*metabolism ; Nitrous Oxide/*metabolism ; *Oryza ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Seasons ; Sequence Analysis, DNA ; *Soil Microbiology ; Water ; }, abstract = {The effects of water-saving irrigation on emissions of greenhouse gases and soil prokaryotic communities were investigated in an experimental rice field. The water layer was kept at 1-2 cm in the water-saving (WS) irrigation treatment and at 6 cm in the continuous flooding (CF) irrigation treatment. WS irrigation decreased CH(4) emissions by 78 % and increased N(2)O emissions by 533 %, resulting in 78 % reduction of global warming potential compared to the CF irrigation. WS irrigation did not affect the abundance or phylogenetic distribution of bacterial/archaeal 16S rRNA genes and the abundance of bacterial/archaeal 16S rRNAs. The transcript abundance of CH(4) emission-related genes generally followed CH(4) emission patterns, but the difference in abundance between mcrA transcripts and amoA/pmoA transcripts best described the differences in CH(4) emissions between the two irrigation practices. WS irrigation increased the relative abundance of 16S rRNAs and functional gene transcripts associated with Anaeromyxobacter and Methylocystis spp., suggesting that their activities might be important in emissions of the greenhouse gases. The N(2)O emission patterns were not reflected in the abundance of N(2)O emission-related genes and transcripts. We showed that the alternative irrigation practice was effective for mitigating greenhouse gas emissions from rice fields and that it did not affect the overall size and structure of the soil prokaryotic community but did affect the activity of some groups.}, }
@article {pmid24681301, year = {2014}, author = {Li, H and Zhou, S and Ma, W and Huang, P and Huang, G and Qin, Y and Xu, B and Ouyang, H}, title = {Long-term performance and microbial ecology of a two-stage PN-ANAMMOX process treating mature landfill leachate.}, journal = {Bioresource technology}, volume = {159}, number = {}, pages = {404-411}, doi = {10.1016/j.biortech.2014.02.054}, pmid = {24681301}, issn = {1873-2976}, mesh = {Air ; Ammonium Compounds/*metabolism ; Anaerobiosis ; Bacteria/*metabolism ; Biodegradation, Environmental ; Bioreactors/microbiology ; Hydrogen-Ion Concentration ; Nitrification ; Nitrogen/isolation &amp; purification ; Oxidation-Reduction ; Phylogeny ; Temperature ; Water Pollutants, Chemical/*isolation &amp; purification ; Water Purification/*methods ; }, abstract = {Long-term performance of a two-stage partial nitritation (PN)-anaerobic ammonium oxidation (ANAMMOX) process treating mature landfill leachate was investigated. Stable partial nitritation performance was achieved in a sequencing batch reactor (SBR) using endpoint pH control, providing an effluent with a ratio of NO2(-)-N/NH4(+)-N at 1.23 ± 0.23. High rate nitrogen removal over 4 kg N/m(3)/d was observed in the ANAMMOX reactor in the first three months. However, during long-term operation, the ANAMMOX reactor can only stably operate under nitrogen load of 1 kg N/m(3)/d, with 85 ± 1% of nitrogen removal. The ammonium oxidizing bacteria (AOB) in the PN-SBR were mainly affiliated to Nitrosomonas sp. IWT514, Nitrosomonas eutropha and Nitrosomonas eutropha, the anaerobic ammonium oxidizing bacteria (AnAOB) in the ANAMMOX reactor were mainly affiliated to Kuenenia stuttgartiensis.}, }
@article {pmid24676728, year = {2014}, author = {Hoefman, S and van der Ha, D and Iguchi, H and Yurimoto, H and Sakai, Y and Boon, N and Vandamme, P and Heylen, K and De Vos, P}, title = {Methyloparacoccus murrellii gen. nov., sp. nov., a methanotroph isolated from pond water.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {64}, number = {Pt 6}, pages = {2100-2107}, doi = {10.1099/ijs.0.057760-0}, pmid = {24676728}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Genes, Bacterial ; Japan ; Methylococcaceae/*classification/genetics/isolation &amp; purification ; Molecular Sequence Data ; Nitrogenase/genetics ; Oxygenases/genetics ; *Phylogeny ; Ponds/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; South Africa ; }, abstract = {Two novel methanotrophic strains, R-49797(T) and OS501, were isolated from pond water in South Africa and Japan, respectively. Strains R-49797(T) and OS501 shared 99.7% 16S rRNA gene sequence similarity. Cells were Gram-stain-negative, non-motile cocci with a diplococcoid tendency and contained type I methanotroph intracytoplasmic membranes. The pmoA gene encoding particulate methane monooxygenase was present. Soluble methane monoooxygenase (sMMO) activity, the mmoX gene encoding sMMO and the nifH gene encoding nitrogenase were not detected. Methane and methanol were utilized as sole carbon source. The strains grew optimally at 25-33 °C (range 20-37 °C) and at pH 6.3-6.8 (range 5.8-9.0). The strains did not support growth in media supplemented with 1% (w/v) NaCl. For both strains, the two major fatty acids were C(16 : 1)ω7c and C(16 : 0) and the DNA G+C content was 65.6 mol%. The isolates belong to the family Methylococcaceae of the class Gammaproteobacteria and cluster most closely among the genera Methylocaldum, Methylococcus and Methylogaea, with a 16S rRNA gene sequence similarity of 94.2% between strain R-49797(T) and its closest related type strain (Methylocaldum gracile VKM 14L(T)). Based on the low 16S rRNA gene sequence similarities with its nearest phylogenetic neighbouring genera, the formation of a separate lineage based on 16S rRNA and pmoA gene phylogenetic analysis, and the unique combination of phenotypic characteristics of the two isolated strains compared with the genera Methylocaldum, Methylococcus and Methylogaea, we propose to classify these strains as representing a novel species of a new genus, Methyloparacoccus murrellii gen. nov., sp. nov., within the family Methylococcaceae. The type strain of Methyloparacoccus murrellii is R-49797(T) (= LMG 27482(T) = JCM 19379(T)).}, }
@article {pmid24675854, year = {2014}, author = {Aliyu, H and De Maayer, P and Rees, J and Tuffin, M and Cowan, DA}, title = {Draft Genome Sequence of the Antarctic Polyextremophile Nesterenkonia sp. Strain AN1.}, journal = {Genome announcements}, volume = {2}, number = {2}, pages = {}, pmid = {24675854}, issn = {2169-8287}, abstract = {Nesterenkonia sp. strain AN1 was isolated from Antarctic soil and is a polyextremophile, being tolerant of low temperatures, high salt concentrations, and high alkalinity. Here we report the draft genome sequence of this strain.}, }
@article {pmid24672519, year = {2014}, author = {Rousk, J and Bengtson, P}, title = {Microbial regulation of global biogeochemical cycles.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {103}, pmid = {24672519}, issn = {1664-302X}, }
@article {pmid24671755, year = {2014}, author = {Yung, CC and Chan, Y and Lacap, DC and Pérez-Ortega, S and de Los Rios-Murillo, A and Lee, CK and Cary, SC and Pointing, SB}, title = {Characterization of chasmoendolithic community in Miers Valley, McMurdo Dry Valleys, Antarctica.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {351-359}, pmid = {24671755}, issn = {1432-184X}, mesh = {Antarctic Regions ; Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biodiversity ; Cyanobacteria/classification/genetics ; *Ecosystem ; Fungi/classification/genetics ; Lichens/classification/genetics ; Microbial Consortia ; Microclimate ; Phylogeny ; Sequence Analysis, DNA ; Silicon Dioxide ; *Soil Microbiology ; }, abstract = {The Antarctic Dry Valleys are unable to support higher plant and animal life and so microbial communities dominate biotic ecosystem processes. Soil communities are well characterized, but rocky surfaces have also emerged as a significant microbial habitat. Here, we identify extensive colonization of weathered granite on a landscape scale by chasmoendolithic microbial communities. A transect across north-facing and south-facing slopes plus valley floor moraines revealed 30-100 % of available substrate was colonized up to an altitude of 800 m. Communities were assessed at a multidomain level and were clearly distinct from those in surrounding soils and other rock-inhabiting cryptoendolithic and hypolithic communities. All colonized rocks were dominated by the cyanobacterial genus Leptolyngbya (Oscillatoriales), with heterotrophic bacteria, archaea, algae, and fungi also identified. Striking patterns in community distribution were evident with regard to microclimate as determined by aspect. Notably, a shift in cyanobacterial assemblages from Chroococcidiopsis-like phylotypes (Pleurocapsales) on colder-drier slopes, to Synechococcus-like phylotypes (Chroococcales) on warmer-wetter slopes. Greater relative abundance of known desiccation-tolerant bacterial taxa occurred on colder-drier slopes. Archaeal phylotypes indicated halotolerant taxa and also taxa possibly derived from nearby volcanic sources. Among the eukaryotes, the lichen photobiont Trebouxia (Chlorophyta) was ubiquitous, but known lichen-forming fungi were not recovered. Instead, fungal assemblages were dominated by ascomycetous yeasts. We conclude that chasmoendoliths likely constitute a significant geobiological phenomenon at lower elevations in granite-dominated Antarctic Dry Valley systems.}, }
@article {pmid24671087, year = {2014}, author = {Liu, Y and de Bruijn, I and Jack, AL and Drynan, K and van den Berg, AH and Thoen, E and Sandoval-Sierra, V and Skaar, I and van West, P and Diéguez-Uribeondo, J and van der Voort, M and Mendes, R and Mazzola, M and Raaijmakers, JM}, title = {Deciphering microbial landscapes of fish eggs to mitigate emerging diseases.}, journal = {The ISME journal}, volume = {8}, number = {10}, pages = {2002-2014}, pmid = {24671087}, issn = {1751-7370}, support = {BB/G012075/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Communicable Diseases, Emerging/microbiology/*veterinary ; Fish Diseases/*microbiology ; Microbiota ; Oomycetes/classification/isolation &amp; purification ; Ovum/*microbiology ; Salmo salar/embryology/*microbiology ; *Saprolegnia/isolation &amp; purification ; }, abstract = {Animals and plants are increasingly suffering from diseases caused by fungi and oomycetes. These emerging pathogens are now recognized as a global threat to biodiversity and food security. Among oomycetes, Saprolegnia species cause significant declines in fish and amphibian populations. Fish eggs have an immature adaptive immune system and depend on nonspecific innate defences to ward off pathogens. Here, meta-taxonomic analyses revealed that Atlantic salmon eggs are home to diverse fungal, oomycete and bacterial communities. Although virulent Saprolegnia isolates were found in all salmon egg samples, a low incidence of Saprolegniosis was strongly correlated with a high richness and abundance of specific commensal Actinobacteria, with the genus Frondihabitans (Microbacteriaceae) effectively inhibiting attachment of Saprolegniato salmon eggs. These results highlight that fundamental insights into microbial landscapes of fish eggs may provide new sustainable means to mitigate emerging diseases.}, }
@article {pmid24671086, year = {2014}, author = {Malkin, SY and Rao, AM and Seitaj, D and Vasquez-Cardenas, D and Zetsche, EM and Hidalgo-Martinez, S and Boschker, HT and Meysman, FJ}, title = {Natural occurrence of microbial sulphur oxidation by long-range electron transport in the seafloor.}, journal = {The ISME journal}, volume = {8}, number = {9}, pages = {1843-1854}, pmid = {24671086}, issn = {1751-7370}, mesh = {Deltaproteobacteria/genetics/isolation &amp; purification/*metabolism/ultrastructure ; Electron Transport ; Geologic Sediments/*microbiology ; Oxidation-Reduction ; Sulfur/*metabolism ; }, abstract = {Recently, a novel mode of sulphur oxidation was described in marine sediments, in which sulphide oxidation in deeper anoxic layers was electrically coupled to oxygen reduction at the sediment surface. Subsequent experimental evidence identified that long filamentous bacteria belonging to the family Desulfobulbaceae likely mediated the electron transport across the centimetre-scale distances. Such long-range electron transfer challenges some long-held views in microbial ecology and could have profound implications for sulphur cycling in marine sediments. But, so far, this process of electrogenic sulphur oxidation has been documented only in laboratory experiments and so its imprint on the seafloor remains unknown. Here we show that the geochemical signature of electrogenic sulphur oxidation occurs in a variety of coastal sediment environments, including a salt marsh, a seasonally hypoxic basin, and a subtidal coastal mud plain. In all cases, electrogenic sulphur oxidation was detected together with an abundance of Desulfobulbaceae filaments. Complementary laboratory experiments in intertidal sands demonstrated that mechanical disturbance by bioturbating fauna destroys the electrogenic sulphur oxidation signal. A survey of published geochemical data and 16S rRNA gene sequences identified that electrogenic sulphide oxidation is likely present in a variety of marine sediments with high sulphide generation and restricted bioturbation, such as mangrove swamps, aquaculture areas, seasonally hypoxic basins, cold sulphide seeps and possibly hydrothermal vent environments. This study shows for the first time that electrogenic sulphur oxidation occurs in a wide range of marine sediments and that bioturbation may exert a dominant control on its natural distribution.}, }
@article {pmid24671034, year = {2014}, author = {De Maayer, P and Anderson, D and Cary, C and Cowan, DA}, title = {Some like it cold: understanding the survival strategies of psychrophiles.}, journal = {EMBO reports}, volume = {15}, number = {5}, pages = {508-517}, pmid = {24671034}, issn = {1469-3178}, mesh = {*Adaptation, Physiological ; *Antifreeze Proteins ; Cell Survival ; *Cold Temperature ; Cold-Shock Response ; Gene Expression Regulation/physiology ; Stress, Physiological ; }, abstract = {Much of the Earth's surface, both marine and terrestrial, is either periodically or permanently cold. Although habitats that are largely or continuously frozen are generally considered to be inhospitable to life, psychrophilic organisms have managed to survive in these environments. This is attributed to their innate adaptive capacity to cope with cold and its associated stresses. Here, we review the various environmental, physiological and molecular adaptations that psychrophilic microorganisms use to thrive under adverse conditions. We also discuss the impact of modern "omic" technologies in developing an improved understanding of these adaptations, highlighting recent work in this growing field.}, }
@article {pmid24662311, year = {2014}, author = {Van Den Hende, S and Beelen, V and Bore, G and Boon, N and Vervaeren, H}, title = {Up-scaling aquaculture wastewater treatment by microalgal bacterial flocs: from lab reactors to an outdoor raceway pond.}, journal = {Bioresource technology}, volume = {159}, number = {}, pages = {342-354}, doi = {10.1016/j.biortech.2014.02.113}, pmid = {24662311}, issn = {1873-2976}, mesh = {*Aquaculture ; Bacteria/*metabolism ; Batch Cell Culture Techniques/instrumentation ; Biodegradation, Environmental ; Biological Oxygen Demand Analysis ; Biomass ; Bioreactors/*microbiology ; Electric Conductivity ; Flocculation ; Hydrogen-Ion Concentration ; Microalgae/*metabolism ; Nitrogen/analysis ; Oxygen/analysis ; Phosphorus/analysis ; Photons ; Photosynthesis ; Ponds/*microbiology ; Waste Disposal, Fluid ; Wastewater/*chemistry/microbiology ; Water Purification/*methods ; }, abstract = {Sequencing batch reactors with microalgal bacterial flocs (MaB-floc SBRs) are a novel approach for photosynthetic aerated wastewater treatment based on bioflocculation. To assess their technical potential for aquaculture wastewater treatment in Northwest Europe, MaB-floc SBRs were up-scaled from indoor photobioreactors of 4 L over 40 and 400 L to a 12 m(3) outdoor raceway pond. Scale-up decreased the nutrient removal efficiencies with a factor 1-3 and the volumetric biomass productivities with a factor 10-13. Effluents met current discharge norms, except for nitrite and nitrate. Flue gas sparging was needed to decrease the effluent pH. Outdoor MaB-flocs showed enhanced settling properties and an increased ash and chlorophyll a content. Bioflocculation enabled successful harvesting by gravity settling and dewatering by filtering at 150-250 μm. Optimisation of nitrogen removal and biomass valorisation are future challenges towards industrial implementation of MaB-floc SBRs for aquaculture wastewater treatment.}, }
@article {pmid24658546, year = {2014}, author = {Taddei, CR and Oliveira, FF and Duarte, RT and Talarico, ST and Takagi, EH and Ramos Carvalho, II and Gomes, FM and Brandt, K and Martinez, MB}, title = {High abundance of Escherichia during the establishment of fecal microbiota in Brazilian children.}, journal = {Microbial ecology}, volume = {67}, number = {3}, pages = {624-634}, pmid = {24658546}, issn = {1432-184X}, mesh = {Bifidobacterium/genetics/isolation &amp; purification ; Brazil ; Escherichia coli/genetics/isolation &amp; purification/*physiology ; Feces/*microbiology ; Female ; Humans ; Infant ; Male ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {The sequence of bacterial events that occurs during the colonization of the gastrointestinal tract may affect the future health of the host. A clear understanding of the colonization process of the human neonatal gut in developing countries is lacking because the few available studies were mostly performed using culture techniques. Using molecular approaches, this study analyzed the fecal microbiota of children of low socioeconomic status in São Paulo, Brazil, during their first year of life. We collected fecal samples of healthy children at 3, 6, and 12 months of life. Total DNA was extracted directly from feces, and the bacteria-specific primers 27F-1492R were used to construct 16S rRNA libraries. Clones were randomly selected and partially sequenced. The main phylogenetic groups identified at 3 months were Streptococcus, unidentified bacteria, and Escherichia. At 6 months, Escherichia remained predominant, while the unidentified bacterial population increased significantly. At 12 months, a more complex composition of fecal microbiota was observed, represented by unidentified bacteria and microorganisms found at low rates at earlier ages. The genus Escherichia remained the most abundant microorganism (34% relative abundance and 75% prevalence). Principal component analysis (PCA) revealed changes in the composition of the microbiota at 6 months and an increase of diversity at 12 months of life. Bifidobacterium was identified by quantitative PCR (qPCR) and showed a high incidence in the microbiota at 3 months. The present results corroborate the global observation of inter-individual variability with an early establishment of microbial complexity at the end of the first year of life and highlight the presence of the Escherichia as abundant in microbiota composition of this group of children.}, }
@article {pmid24658457, year = {2014}, author = {Peralta, AL and Matthews, JW and Kent, AD}, title = {Habitat specialization along a wetland moisture gradient differs between ammonia-oxidizing and denitrifying microorganisms.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {339-350}, pmid = {24658457}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics ; *Denitrification ; Genes, Archaeal ; Hydrology ; Illinois ; Microbial Consortia ; Oxidation-Reduction ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; *Soil Microbiology ; Water ; *Wetlands ; }, abstract = {Gradients in abiotic parameters, such as soil moisture,can strongly influence microbial community structure and function. Denitrifying and ammonia-oxidizing microorganisms,in particular, have contrasting physiological responses to abiotic factors such as oxygen concentration and soil moisture. Identifying abiotic factors that govern the composition and activity of denitrifying and ammonia-oxidizing communities is critical for understanding the nitrogen cycle.The objectives of this study were to (i) examine denitrifier andarchaeal ammonia oxidizer community composition and (ii) assess the taxa occurring within each functional group related to soil conditions along an environmental gradient. Soil was sampled across four transects at four locations along a dry to saturated environmental gradient at a restored wetland. Soil pH and soil organic matter content increased from dry to saturated plots. Composition of soil denitrifier and ammonia oxidizer functional groups was assessed by terminal restriction fragment length polymorphism (T-RFLP) community analysis, and local soil factors were also characterized. Microbial community composition of denitrifiers and ammonia oxidizers differed along the moisture gradient (denitrifier:ANOSIM R = 0.739, P < 0.001; ammonia oxidizers: ANOSIMR = 0.760, P < 0.001). Individual denitrifier taxa were observed over a larger range of moisture levels than individual archaeal ammonia oxidizer taxa (Wilcoxon rank sum, W = 2413, P value = 0.0002). Together, our data suggest that variation in environmental tolerance of microbial taxa have potential to influence nitrogen cycling in terrestrial ecosystems.}, }
@article {pmid24658414, year = {2014}, author = {Tripathi, BM and Lee-Cruz, L and Kim, M and Singh, D and Go, R and Shukor, NA and Husni, MH and Chun, J and Adams, JM}, title = {Spatial scaling effects on soil bacterial communities in Malaysian tropical forests.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {247-258}, pmid = {24658414}, issn = {1432-184X}, mesh = {Bacteria/classification/*growth &amp; development ; *Biodiversity ; DNA, Bacterial/genetics ; *Forests ; Malaysia ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Spatial Analysis ; }, abstract = {Spatial scaling to some extent determines biodiversity patterns in larger organisms, but its role in microbial diversity patterns is much less understood. Some studies have shown that bacterial community similarity decreases with distance, whereas others do not support this. Here, we studied soil bacterial communities of tropical rainforest in Malaysia at two spatial scales: a local scale with samples spaced every 5 mover a 150-m transect, and a regional scale with samples 1 to 1,800 km apart. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1–V3 region was pyrosequenced using Roche/454 GS FLX Titanium platform. A ranked partial Mantel test showed a weak correlation between spatial distance and whole bacterial community dissimilarity, but only at the local scale. In contrast, environmental distance was highly correlated with community dissimilarity at both spatial scales,stressing the greater role of environmental variables rather than spatial distance in determining bacterial community variation at different spatial scales. Soil pH was the only environmental parameter that significantly explained the variance in bacterial community at the local scale, whereas total nitrogen and elevation were additional important factors at the regional scale.We obtained similar results at both scales when only the most abundant OTUs were analyzed. A variance partitioning analysis showed that environmental variables contributed more to bacterial community variation than spatial distance at both scales. In total, our results support a strong influence of the environment in determining bacterial community composition in the rainforests of Malaysia. However, it is possible that the remaining spatial distance effect is due to some of the myriad of other environmental factors which were not considered here, rather than dispersal limitation.}, }
@article {pmid24658413, year = {2014}, author = {Pan, Y and Abell, GC and Bodelier, PL and Meima-Franke, M and Sessitsch, A and Bodrossy, L}, title = {Remarkable recovery and colonization behaviour of methane oxidizing bacteria in soil after disturbance is controlled by methane source only.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {259-270}, pmid = {24658413}, issn = {1432-184X}, mesh = {Biodiversity ; DNA, Bacterial/genetics ; Genes, Bacterial ; Methane/*metabolism ; Methylococcaceae/*classification/genetics/growth &amp; development ; *Microbial Consortia ; Netherlands ; Oxidation-Reduction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Little is understood about the relationship between microbial assemblage history, the composition and function of specific functional guilds and the ecosystem functions they provide. To learn more about this relationship we used methane oxidizing bacteria (MOB) as model organisms and performed soil microcosm experiments comprised of identical soil substrates, hosting distinct overall microbial diversities(i.e., full, reduced and zero total microbial and MOB diversities). After inoculation with undisturbed soil, the recovery of MOB activity, MOB diversity and total bacterial diversity were followed over 3 months by methane oxidation potential measurements and analyses targeting pmoA and 16S rRNA genes. Measurement of methane oxidation potential demonstrated different recovery rates across the different treatments. Despite different starting microbial diversities, the recovery and succession of the MOB communities followed a similar pattern across the different treatment microcosms. In this study we found that edaphic parameters were the dominant factor shaping microbial communities over time and that the starting microbial community played only a minor role in shaping MOB microbial community.}, }
@article {pmid24647480, year = {2014}, author = {Paulander, W and Wang, Y and Folkesson, A and Charbon, G and Løbner-Olesen, A and Ingmer, H}, title = {Bactericidal antibiotics increase hydroxyphenyl fluorescein signal by altering cell morphology.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e92231}, pmid = {24647480}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/*pharmacology ; Escherichia coli/*cytology/*drug effects ; Flow Cytometry ; Fluorescein/*metabolism ; Fluoresceins/*metabolism ; Fluorescence ; Green Fluorescent Proteins/metabolism ; Microscopy, Interference ; }, abstract = {It was recently proposed that for bactericidal antibiotics a common killing mechanism contributes to lethality involving indirect stimulation of hydroxyl radical (OH•) formation. Flow cytometric detection of OH• by hydroxyphenyl fluorescein (HPF) probe oxidation was used to support this hypothesis. Here we show that increased HPF signals in antibiotics-exposed bacterial cells are explained by fluorescence associated with increased cell size, and do not reflect reactive oxygen species (ROS) concentration. Independently of antibiotics, increased fluorescence was seen for elongated cells expressing the oxidative insensitive green fluorescent protein (GFP). Although our data question the role of ROS in lethality of antibiotics other research approaches point to important interplays between basic bacterial metabolism and antibiotic susceptibility. To underpin such relationships, methods for detecting bacterial metabolites at a cellular level are needed.}, }
@article {pmid24646314, year = {2014}, author = {Weissbrodt, DG and Shani, N and Holliger, C}, title = {Linking bacterial population dynamics and nutrient removal in the granular sludge biofilm ecosystem engineered for wastewater treatment.}, journal = {FEMS microbiology ecology}, volume = {88}, number = {3}, pages = {579-595}, doi = {10.1111/1574-6941.12326}, pmid = {24646314}, issn = {1574-6941}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; *Biofilms ; Bioreactors/*microbiology ; Ecosystem ; Nitrogen/analysis ; Phosphorus/analysis ; Phylogeny ; Sewage/*microbiology ; *Wastewater ; Water Purification/*methods ; }, abstract = {Intensive nutrient removal from wastewater in anaerobic-aerobic systems using granular sludge should rely on optimal balances at biofilm and microbial ecology levels. This study targets the impacts of reactor characteristics and fluctuations in operation conditions on nutrient removal and bacterial community structures by means of microbial and numerical ecology methods. The dynamics of both predominant and accompanying populations were investigated with high resolution on temporal and phylogenetic scales in two reactors operated during 5 months with synthetic wastewater. Multivariate analyses highlighted significant correlations from process to microbial scales in the first reactor, whereas nitrification and phosphorus removal might have been affected by oxygen mass transfer limitations with no impact at population level in the second system. The bacterial community continuum of the first reactor was composed of two major antagonistic Accumulibacter-Nitrosomonas-Nitrospira and Competibacter-Cytophaga-Intrasporangiaceae clusters that prevailed under conditions leading to efficient P- (> 95%) and N-removal (> 65%) and altered P- (< 90%) and N-removal (< 60%), respectively. A third cluster independent of performances was dominated by Xanthomonadaceae affiliates that were on average more abundant at 25 °C (31 ± 5%) than at 20 °C (22 ± 4%). Starting from the physiological traits of the numerous phylotypes identified, a conceptual model is proposed as a base for functional analysis in the granular sludge microbiome and for future investigations with complex real wastewater.}, }
@article {pmid24643714, year = {2014}, author = {Burgos-Caraballo, S and Cantrell, SA and Ramírez, A}, title = {Diversity of benthic biofilms along a land use gradient in tropical headwater streams, Puerto Rico.}, journal = {Microbial ecology}, volume = {68}, number = {1}, pages = {47-59}, pmid = {24643714}, issn = {1432-184X}, mesh = {Agriculture ; *Biodiversity ; *Biofilms ; Forests ; *Microbial Consortia ; Nitrates/chemistry ; Polymorphism, Restriction Fragment Length ; Puerto Rico ; Rivers/chemistry/*microbiology ; Urbanization ; Water/chemistry ; Water Microbiology ; }, abstract = {The properties of freshwater ecosystems can be altered, directly or indirectly, by different land uses (e.g., urbanization and agriculture). Streams heavily influenced by high nutrient concentrations associated with agriculture or urbanization may present conditions that can be intolerable for many aquatic species such as macroinvertebrates and fishes. However, information with respect to how benthic microbial communities may respond to changes in stream ecosystem properties in relation to agricultural or urban land uses is limited, in particular for tropical ecosystems. In this study, diversity of benthic biofilms was evaluated in 16 streams along a gradient of land use at the Turabo watershed in Puerto Rico using terminal restriction fragment length polymorphism. Diversity indices and community structure descriptors (species richness, Shannon diversity, dominance and evenness) were calculated for both bacteria and eukaryotes for each stream. Diversity of both groups, bacteria and eukaryotes, did not show a consistent pattern with land use, since it could be high or low at streams dominated by different land uses. This suggests that diversity of biofilms may be more related to site-specific conditions rather than watershed scale factors. To assess this contention, the relationship between biofilm diversity and reach-scale parameters (i.e., nutrient concentrations, canopy cover, conductivity, and dissolved oxygen) was determined using the Akaike Information Criterion (AIC(c)) for small sample size. Results indicated that nitrate was the variable that best explained variations in biofilm diversity. Since nitrate concentrations tend to increase with urban land use, our results suggest that urbanization may indeed increase microbial diversity indirectly by increasing nutrients in stream water.}, }
@article {pmid24643713, year = {2014}, author = {Kaplan, A and Kaplan, CW and He, X and McHardy, I and Shi, W and Lux, R}, title = {Characterization of aid1, a novel gene involved in Fusobacterium nucleatum interspecies interactions.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {379-387}, pmid = {24643713}, issn = {1432-184X}, support = {R01 DE021108/DE/NIDCR NIH HHS/United States ; DE021108/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacterial Adhesion/*genetics ; Bacterial Proteins/*genetics ; *Biofilms ; DNA, Bacterial/genetics ; Fusobacterium nucleatum/*genetics/physiology ; Genes, Bacterial ; *Microbial Interactions ; Streptococcus/physiology ; }, abstract = {The oral opportunistic pathogen Fusobacterium nucleatum is known to interact with a large number of different bacterial species residing in the oral cavity. It adheres to a variety of Gram-positive bacteria, including oral streptococci via the arginine-inhibitable adhesin RadD. In this study, we describe a novel protein encoded by the predicted open reading frame FN1253 that appears to play a role in interspecies interactions of F. nucleatum, particularly with oral streptococci and related Gram-positive species. We designated FN1253 as aid1 (Adherence Inducing Determinant 1). Expression analyses demonstrated that this gene was induced in F. nucleatum single species biofilms, while the presence of representative members of the oral microbiota known to adhere to F. nucleatum triggered its suppression. Inactivation as well as overexpression of aid1 affected the ability of F. nucleatum to coaggregate with oral streptococci and the closely related Enterococcus faecalis, but not other Gram-positive oral species tested. Furthermore, overexpression of aid1 led to a drastic change in the structure of dual species biofilms of F. nucleatum with oral streptococci. Aid1 function was abolished in the presence of arginine and found to be dependent on RadD. Interestingly, differential expression of aid1 did not affect messenger RNA and protein levels of RadD. These findings indicate that RadD-mediated adhesion to oral streptococci involves more complex cellular processes than the simple interaction of adhesins on the surface of partner strains. Aid1 could potentially play an important role in facilitating RadD-mediated interaction with oral streptococci by increasing binding specificity of F. nucleatum to other microbial species.}, }
@article {pmid24642546, year = {2014}, author = {Sköld-Chiriac, S and Nord, A and Nilsson, J&#xc5; and Hasselquist, D}, title = {Physiological and behavioral responses to an acute-phase response in zebra finches: immediate and short-term effects.}, journal = {Physiological and biochemical zoology : PBZ}, volume = {87}, number = {2}, pages = {288-298}, doi = {10.1086/674789}, pmid = {24642546}, issn = {1537-5293}, mesh = {*Acute-Phase Reaction ; Animals ; Basal Metabolism ; Body Temperature ; Body Weight ; Finches/immunology/*physiology ; *Immunity, Humoral ; Immunoglobulins/blood ; Injections, Intramuscular ; Lipopolysaccharides/administration &amp; dosage/*pharmacology ; Male ; Motor Activity ; }, abstract = {Activation of the immune system to clear pathogens and mitigate infection is a costly process that might incur fitness costs. When vertebrates are exposed to pathogens, their first line of defense is the acute-phase response (APR), which consists of a suite of physiological and behavioral changes. The dynamics of the APR are relatively well investigated in mammals and domesticated birds but still rather unexplored in passerine birds. In this study, we injected male zebra finches (Taeniopygia guttata) with a bacterial endotoxin (lipopolysaccharide [LPS]) to assess the potential physiological, immunological, and behavioral responses during the time course of an APR and also to record any potential short-term effects by measuring the birds during the days after the expected APR. We found that LPS-injected zebra finches decreased activity and gained less body mass during the APR, compared to control individuals. In addition, LPS-injected birds increased their production of LPS-reactive antibodies and reduced their metabolic rate during the days after the expected APR. Our results show that zebra finches demonstrate sickness behaviors during an APR but also that physiological effects persist after the expected time course of an APR. These delayed effects might be either a natural part of the progression of an APR, which is probably true for the antibody response, or a short-term carryover effect, which is probably true for the metabolic response.}, }
@article {pmid24641281, year = {2014}, author = {Crane, JM and Frodyma, ME and Bergstrom, GC}, title = {Nutrient-induced spore germination of a Bacillus amyloliquefaciens biocontrol agent on wheat spikes.}, journal = {Journal of applied microbiology}, volume = {116}, number = {6}, pages = {1572-1583}, doi = {10.1111/jam.12480}, pmid = {24641281}, issn = {1365-2672}, mesh = {Alanine/pharmacology ; Asparagine/pharmacology ; Bacillus/*physiology ; *Biological Control Agents ; Fructose/pharmacology ; Glucose/pharmacology ; Potassium Chloride/pharmacology ; Spores, Bacterial/*growth &amp; development ; Triticum/*microbiology ; }, abstract = {AIMS: In this study, we investigated the feasibility of applying nutrient germinants to plant surfaces to stimulate the spore germination of the plant disease biocontrol agent Bacillus amyloliquefaciens strain TrigoCor.<br><br>METHODS AND RESULTS: Using the terbium chloride assay and phase-contrast microscopy, we screened potential germinants of TrigoCor spores and found that a combination of d-glucose, d-fructose and potassium chloride (GFK), in addition to either l-asparagine (Asn-GFK) or l-alanine (Ala-GFK), induced maximal levels of TrigoCor spore germination in vitro. The germinant mixture Asn-GFK was also able to significantly stimulate Bacillus spore germination on wheat surfaces.<br><br>CONCLUSIONS: The successful in vivo stimulation of Bacillus spore germination suggests that nutrient-induced spore germination on plant surfaces is a feasible strategy for improving Bacillus biocontrol.<br><br>One of the challenges of applying Bacillus biological control agents to aboveground plant parts is that Bacillus cells transition to a metabolically dormant spore state on plant surfaces, making them unable to prevent subsequent pathogen attacks. This study demonstrates that using nutrients to stimulate Bacillus spore germination in vivo is a promising option for improving disease control and should be pursued further.}, }
@article {pmid24639675, year = {2014}, author = {Cardinale, M}, title = {Scanning a microhabitat: plant-microbe interactions revealed by confocal laser microscopy.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {94}, pmid = {24639675}, issn = {1664-302X}, abstract = {No plant or cryptogam exists in nature without microorganisms associated with its tissues. Plants as microbial hosts are puzzles of different microhabitats, each of them colonized by specifically adapted microbiomes. The interactions with such microorganisms have drastic effects on the host fitness. Since the last 20 years, the combination of microscopic tools and molecular approaches contributed to new insights into microbe-host interactions. Particularly, confocal laser scanning microscopy (CLSM) facilitated the exploration of microbial habitats and allowed the observation of host-associated microorganisms in situ with an unprecedented accuracy. Here I present an overview of the progresses made in the study of the interactions between microorganisms and plants or plant-like organisms, focusing on the role of CLSM for the understanding of their significance. I critically discuss risks of misinterpretation when procedures of CLSM are not properly optimized. I also review approaches for quantitative and statistical analyses of CLSM images, the combination with other molecular and microscopic methods, and suggest the re-evaluation of natural autofluorescence. In this review, technical aspects were coupled with scientific outcomes, to facilitate the readers in identifying possible CLSM applications in their research or to expand their existing potential. The scope of this review is to highlight the importance of confocal microscopy in the study of plant-microbe interactions and also to be an inspiration for integrating microscopy with molecular techniques in future researches of microbial ecology.}, }
@article {pmid24633338, year = {2014}, author = {Ylla, I and Canhoto, C and Romaní, AM}, title = {Effects of warming on stream biofilm organic matter use capabilities.}, journal = {Microbial ecology}, volume = {68}, number = {1}, pages = {132-145}, pmid = {24633338}, issn = {1432-184X}, mesh = {*Biofilms ; Biomass ; Carbon/*metabolism ; Extracellular Space/enzymology ; Organic Chemicals/metabolism ; Portugal ; Rivers/*chemistry ; *Temperature ; Water/chemistry ; Water Microbiology ; }, abstract = {The understanding of ecosystem responses to changing environmental conditions is becoming increasingly relevant in the context of global warming. Microbial biofilm communities in streams play a key role in organic matter cycling which might be modulated by shifts in flowing water temperature. In this study, we performed an experiment at the Candal stream (Portugal) longitudinally divided into two reaches: a control half and an experimental half where water temperature was 3 °C above that of the basal stream water. Biofilm colonization was monitored during 42 days in the two stream halves. Changes in biofilm function (extracellular enzyme activities and carbon substrate utilization profiles) as well as chlorophyll a and prokaryote densities were analyzed. The biofilm in the experimental half showed a higher capacity to decompose cellulose, hemicellulose, lignin, and peptidic compounds. Total leucine-aminopeptidase, cellobiohydrolase and β-xylosidase showed a respective 93, 66, and 61% increase in activity over the control; much higher than would be predicted by only the direct temperature physical effect. In contrast, phosphatase and lipase activity showed the lowest sensitivity to temperature. The biofilms from the experimental half also showed a distinct functional fingerprint and higher carbon usage diversity and richness, especially due to a wider use of polymers and carbohydrates. The changes in the biofilm functional capabilities might be indirectly affected by the higher prokaryote and chlorophyll density measured in the biofilm of the experimental half. The present study provides evidence that a realistic stream temperature increase by 3 °C changes the biofilm metabolism to a greater decomposition of polymeric complex compounds and peptides but lower decomposition of lipids. This might affect stream organic matter cycling and the transfer of carbon to higher trophic levels.}, }
@article {pmid24633337, year = {2014}, author = {Ju, F and Zhang, T}, title = {Novel microbial populations in ambient and mesophilic biogas-producing and phenol-degrading consortia unraveled by high-throughput sequencing.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {235-246}, pmid = {24633337}, issn = {1432-184X}, mesh = {Archaea/*classification/genetics/growth &amp; development ; Bacteria/*classification/genetics/growth &amp; development ; Biofuels/microbiology ; Bioreactors/microbiology ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Metagenome ; Methane/*biosynthesis ; *Microbial Consortia ; Phenols/*metabolism ; Sequence Analysis, DNA ; }, abstract = {Methanogenesis from wastewater-borne organics and organic solid wastes (e.g., food residues) can be severely suppressed by the presence of toxic phenols. In this work, ambient (20 °C) and mesophilic (37 °C) methane-producing and phenol-degrading consortia were enriched and characterized using high-throughput sequencing (HTS). 454 Pyrosequencing indicated novel W22 (25.0 % of bacterial sequences) in the WWE1 and Sulfurovum-resembled species (32.0 %) in the family Campylobacterales were the most abundant in mesophilic and ambient reactors, respectively, which challenges previous knowledge that Syntrophorhabdus was the most predominant. Previous findings may underestimate bacterial diversity and low-abundance bacteria, but overestimate abundance of Syntrophorhabdus. Illumina HTS revealed that archaeal populations were doubled in ambient reactor and tripled in mesophilic reactor, respectively, compared to the ∼4.9 % (of the bacteria and archaea sequences) in the seed sludge. Moreover, unlike the dominance of Methanosarcina in seed sludge, acetotrophic Methanosaeta predominated both (71.4-76.5 % of archaeal sequences) ambient and mesophilic enrichments. Noteworthy, this study, for the first time, discovered the co-occurrence of green sulfur bacteria Chlorobia, sulfur-reducing Desulfovibrio, and Sulfurovum-resembling species under ambient condition, which could presumably establish mutualistic relationships to compete with syntrophic bacteria and methanogens, leading to the deterioration of methanogenic activity. Taken together, this HTS-based study unravels the high microbial diversity and complicated bacterial interactions within the biogas-producing and phenol-degrading bioreactors, and the identification of novel bacterial species and dominant methanogens involved in the phenol degradation provides novel insights into the operation of full-scale bioreactors for maximizing biogas generation.}, }
@article {pmid24631878, year = {2014}, author = {Lackner, S and Gilbert, EM and Vlaeminck, SE and Joss, A and Horn, H and van Loosdrecht, MC}, title = {Full-scale partial nitritation/anammox experiences--an application survey.}, journal = {Water research}, volume = {55}, number = {}, pages = {292-303}, doi = {10.1016/j.watres.2014.02.032}, pmid = {24631878}, issn = {1879-2448}, mesh = {Biofilms ; *Bioreactors ; Waste Disposal, Fluid/*standards ; Water Purification/*standards ; }, abstract = {Partial nitritation/anammox (PN/A) has been one of the most innovative developments in biological wastewater treatment in recent years. With its discovery in the 1990s a completely new way of ammonium removal from wastewater became available. Over the past decade many technologies have been developed and studied for their applicability to the PN/A concept and several have made it into full-scale. With the perspective of reaching 100 full-scale installations in operation worldwide by 2014 this work presents a summary of PN/A technologies that have been successfully developed, implemented and optimized for high-strength ammonium wastewaters with low C:N ratios and elevated temperatures. The data revealed that more than 50% of all PN/A installations are sequencing batch reactors, 88% of all plants being operated as single-stage systems, and 75% for sidestream treatment of municipal wastewater. Additionally an in-depth survey of 14 full-scale installations was conducted to evaluate practical experiences and report on operational control and troubleshooting. Incoming solids, aeration control and nitrate built up were revealed as the main operational difficulties. The information provided gives a unique/new perspective throughout all the major technologies and discusses the remaining obstacles.}, }
@article {pmid24631458, year = {2014}, author = {Asselin, C and Gendron, FP}, title = {Shuttling of information between the mucosal and luminal environment drives intestinal homeostasis.}, journal = {FEBS letters}, volume = {588}, number = {22}, pages = {4148-4157}, doi = {10.1016/j.febslet.2014.02.049}, pmid = {24631458}, issn = {1873-3468}, mesh = {Animals ; Endoplasmic Reticulum Stress ; Environment ; *Homeostasis ; Humans ; Intestinal Mucosa/cytology/immunology/*metabolism/microbiology ; Microbiota ; Receptors, Aryl Hydrocarbon/metabolism ; }, abstract = {The gastrointestinal tract is a passageway for dietary nutrients, microorganisms and xenobiotics. The gut is home to diverse bacterial communities forming the microbiota. While bacteria and their metabolites maintain gut homeostasis, the host uses innate and adaptive immune mechanisms to cope with the microbiota and luminal environment. In recent years, multiple bi-directional instructive mechanisms between microbiota, luminal content and mucosal immune systems have been uncovered. Indeed, epithelial and immune cell-derived mucosal signals shape microbiota composition, while microbiota and their by-products shape the mucosal immune system. Genetic and environmental perturbations alter gut mucosal responses which impact on microbial ecology structures. On the other hand, changes in microbiota alter intestinal mucosal responses. In this review, we discuss how intestinal epithelial Paneth and goblet cells interact with the microbiota, how environmental and genetic disorders are sensed by endoplasmic reticulum stress and autophagy responses, how specific bacteria, bacterial- and diet-derived products determine the function and activation of the mucosal immune system. We will also discuss the critical role of HDAC activity as a regulator of immune and epithelial cell homeostatic responses.}, }
@article {pmid24628845, year = {2015}, author = {Donn, S and Kirkegaard, JA and Perera, G and Richardson, AE and Watt, M}, title = {Evolution of bacterial communities in the wheat crop rhizosphere.}, journal = {Environmental microbiology}, volume = {17}, number = {3}, pages = {610-621}, doi = {10.1111/1462-2920.12452}, pmid = {24628845}, issn = {1462-2920}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; *Biological Evolution ; Microbial Consortia ; Microbiota ; Plant Roots/*microbiology ; Plants/genetics/*microbiology ; *Rhizosphere ; Seasons ; Soil ; Soil Microbiology ; Triticum/*microbiology ; }, abstract = {The gap between current average global wheat yields and that achievable through best agronomic management and crop genetics is large. This is notable in intensive wheat rotations which are widely used. Expectations are that this gap can be reduced by manipulating soil processes, especially those that involve microbial ecology. Cross-year analysis of the soil microbiome in an intensive wheat cropping system revealed that rhizosphere bacteria changed much more than the bulk soil community. Dominant factors influencing populations included binding to roots, plant age, site and planting sequence. We demonstrated evolution of bacterial communities within the field rhizosphere. Early in the season, communities tightly bound to the root were simplest. These increased in diversity with plant age and senescence. Loosely bound communities also increased in diversity from vegetative to reproductive plant stages but were more stable than those tightly bound to roots. Planting sequence and, to a lesser extent, wheat genotype also significantly affected rhizosphere bacteria. Plasticity in the rhizosphere generated from crop root system management and genetics offers promise for manipulating the soil ecology of intense cereal systems. Analyses of soil microbiomes for the purpose of developing agronomic benefit should include roots as well as soil loosely adhered to the roots, and the bulk soil.}, }
@article {pmid24623528, year = {2014}, author = {Kuppardt, A and Kleinsteuber, S and Vogt, C and Lüders, T and Harms, H and Chatzinotas, A}, title = {Phylogenetic and functional diversity within toluene-degrading, sulphate-reducing consortia enriched from a contaminated aquifer.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {222-234}, pmid = {24623528}, issn = {1432-184X}, mesh = {Biodegradation, Environmental ; DNA, Bacterial/genetics ; Deltaproteobacteria/*classification/genetics ; Ecosystem ; Genes, Bacterial ; Germany ; Groundwater/*microbiology ; Microbial Consortia/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfur-Reducing Bacteria/classification/genetics ; Toluene/*metabolism ; Water Microbiology ; Water Pollutants, Chemical/metabolism ; }, abstract = {Three toluene-degrading microbial consortia were enriched under sulphate-reducing conditions from different zones of a benzene, toluene, ethylbenzene and xylenes (BTEX) plume of two connected contaminated aquifers. Two cultures were obtained from a weakly contaminated zone of the lower aquifer, while one culture originated from the highly contaminated upper aquifer. We hypothesised that the different habitat characteristics are reflected by distinct degrader populations. Degradation of toluene with concomitant production of sulphide was demonstrated in laboratory microcosms and the enrichment cultures were phylogenetically characterised. The benzylsuccinate synthase alpha-subunit (bssA) marker gene, encoding the enzyme initiating anaerobic toluene degradation, was targeted to characterise the catabolic diversity within the enrichment cultures. It was shown that the hydrogeochemical parameters in the different zones of the plume determined the microbial composition of the enrichment cultures. Both enrichment cultures from the weakly contaminated zone were of a very similar composition, dominated by Deltaproteobacteria with the Desulfobulbaceae (a Desulfopila-related phylotype) as key players. Two different bssA sequence types were found, which were both affiliated to genes from sulphate-reducing Deltaproteobacteria. In contrast, the enrichment culture from the highly contaminated zone was dominated by Clostridia with a Desulfosporosinus-related phylotype as presumed key player. A distinct bssA sequence type with high similarity to other recently detected sequences from clostridial toluene degraders was dominant in this culture. This work contributes to our understanding of the niche partitioning between degrader populations in distinct compartments of BTEX-contaminated aquifers.}, }
@article {pmid24623527, year = {2014}, author = {Prewitt, L and Kang, Y and Kakumanu, ML and Williams, M}, title = {Fungal and bacterial community succession differs for three wood types during decay in a forest soil.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {212-221}, pmid = {24623527}, issn = {1432-184X}, mesh = {Bacteria/genetics/*growth &amp; development ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; *Forests ; Fungi/genetics/*growth &amp; development ; Microbial Consortia ; Pinus taeda/microbiology ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Thuja/microbiology ; Wood/*microbiology ; }, abstract = {Wood decomposition by soil microorganisms is vital to carbon and nutrient cycles of forested ecosystems. Different wood types decompose at different rates; however, it is not known if there are differences in microbial community succession associated with the decay of different wood types. In this study, the microbial community associated with the decay of pine (decay-susceptible wood), western red cedar (decay resistant) and ACQ-treated pine (Ammoniacal Copper Quaternary, preservative-treated pine for decay resistance) in forest soil was characterized using DNA sequencing, phospholipid fatty acid (PLFA) analysis, and microbial activity over a 26-month period. Bray-Curtis ordination using an internal transcribed spacer (ITS) sequence and PLFA data indicated that fungal communities changed during succession and that wood type altered the pattern of succession. Nondecay fungi decreased over the 26 months of succession; however, by 18 months of decay, there was a major shift in the fungal communities. By this time, Trametes elegans dominated cedar and Phlebia radiata dominated pine and ACQ-treated pine. The description of PLFA associated with ACQ-treated pine resembled cedar more than pine; however, both PLFA and ITS descriptions indicated that fungal communities associated with ACQ-treated pine were less dynamic, perhaps a result of the inhibition by the ACQ preservative, compared with pine and cedar. Overall, fungal community composition and succession were associated with wood type. Further research into the differences in community composition will help to discern their functional importance to wood decay.}, }
@article {pmid24619233, year = {2014}, author = {Zaragoza, WJ and Krediet, CJ and Meyer, JL and Canas, G and Ritchie, KB and Teplitski, M}, title = {Outcomes of infections of sea anemone Aiptasia pallida with Vibrio spp. pathogenic to corals.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {388-396}, pmid = {24619233}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/microbiology ; Host-Pathogen Interactions ; Melanins/biosynthesis ; Microbial Consortia ; Sea Anemones/metabolism/*microbiology ; Stress, Physiological ; Temperature ; Vibrio/*pathogenicity ; Virulence ; }, abstract = {Incidents of coral disease are on the rise. However, in the absence of a surrogate animal host, understanding of the interactions between coral pathogens and their hosts remains relatively limited, compared to other pathosystems of similar global importance. A tropical sea anemone, Aiptasia pallida, has been investigated as a surrogate model to study certain aspects of coral biology. Therefore, to test whether the utility of this surrogate model can be extended to study coral diseases, in the present study, we tested its susceptibility to common coral pathogens (Vibrio coralliilyticus and Vibrio shiloi) as well as polymicrobial consortia recovered from the Caribbean Yellow Band Disease (CYBD) lesions. A. pallida was susceptible to each of the tested pathogens. A. pallida responded to the pathogens with darkening of the tissues (associated with an increased melanization) and retraction of tentacles, followed by complete disintegration of polyp tissues. Loss of zooxanthellae was not observed; however, the disease progression pattern is consistent with the behavior of necrotizing pathogens. Virulence of some coral pathogens in Aiptasia was paralleled with their glycosidase activities.}, }
@article {pmid24619121, year = {2014}, author = {Kamika, I and Coetzee, M and Mamba, BB and Msagati, T and Momba, MN}, title = {The impact of microbial ecology and chemical profile on the enhanced biological phosphorus removal (EBPR) process: a case study of Northern Wastewater Treatment Works, Johannesburg.}, journal = {International journal of environmental research and public health}, volume = {11}, number = {3}, pages = {2876-2898}, pmid = {24619121}, issn = {1660-4601}, mesh = {*Microbial Consortia ; Phosphorus/*isolation &amp; purification/metabolism ; Polyphosphates/metabolism ; Sewage/chemistry/*microbiology ; South Africa ; *Waste Management ; }, abstract = {The impact of polyphosphate-accumulating organism (PAO) and glycogen-accumulating organism (GAO) populations as well as of the chemical profile on the performance of Unit-3 (open elutriation tanks) and Unit-5 (covered elutriation tank) of the City of Johannesburg Northern Wastewater Treatment Works was determined. Physicochemical parameters of wastewater samples were measured using standard methods. Bacterial diversity was determined using 16S rRNA gene amplicon pyrosequencing of the variable region V1-3. Results showed soluble COD concentrations from settled sewage for Unit-3 at 192.8 mg COD/L and for Unit-5 at 214.6 mg COD/L, which increased to 301.8 mg COD/L and 411.6 mg COD/L in the overflow from elutriation tanks and decreased to 170.9 mg COD/L and 256.3 mg COD/L at the division boxes, respectively. Both long-chain volatile fatty acids (heptanoic acid, isobutyric acid, 3-methylbutanoic acid, pentanoic acid, 4-methylpentanoic acid, methylheptanoic acid) and short-chain volatile fatty acids (acetic acid, propionic acid, isobutyric acid) were present within concentration ranges of 17.19 mg/L to 54.98 mg/L and 13.64 mg/L to 87.6 mg/L for Unit 3 and 38.61 mg/L to58.85 mg/L and 21.63 mg/L to 92.39 mg/L for Unit 5, respectively. In the secondary settling tanks, the phosphate-removal efficiency in Unit-5 appeared to be slightly higher (0.08 mg P/L) compared to that of Unit-3 (0.11 mg P/L). The average DO concentrations (2.1 mg/L and 2.2 mg/L) as well as the pH values (pH 7 to pH 7.5) were found to be slightly higher in Unit-5 in the aerobic zones. The high presence of PAOs in the bioreactors (Unit-5: Dechloromonas (14.96%), Acinetobacter (6.3%), Zoogloea (4.72%) in the anaerobic zone and Dechloromonas (22.37 %) in the aerobic zone; Unit-3: Dechloromonas (37.25%) in the anaerobic zone and Dechloromonas (23.97%) in the aerobic zone) confirmed the phosphate-removal efficiencies of both units. Negligible GAOs were found in the aerobic zones (Defluviicoccus spp.: 0.33% for Unit-5 and 0.68% for Unit-3) and in the anaerobic zones (Defluviicoccus: 9.8% for Unit-3). The high microbial diversity and a negligible percentage of GAOs in Unit-5 could contribute to its high phosphate-removal efficiency, although results did not indicate statistically significant differences between the unit with a covered elutriation tank (Unit-5) and that with open elutriation tanks (Unit-3).}, }
@article {pmid24618462, year = {2014}, author = {Angly, FE and Fields, CJ and Tyson, GW}, title = {The Bio-Community Perl toolkit for microbial ecology.}, journal = {Bioinformatics (Oxford, England)}, volume = {30}, number = {13}, pages = {1926-1927}, pmid = {24618462}, issn = {1367-4811}, mesh = {Computational Biology/methods ; *Ecosystem ; Humans ; Microbiological Techniques ; Microbiology ; Software Design ; }, abstract = {The development of bioinformatic solutions for microbial ecology in Perl is limited by the lack of modules to represent and manipulate microbial community profiles from amplicon and meta-omics studies. Here we introduce Bio-Community, an open-source, collaborative toolkit that extends BioPerl. Bio-Community interfaces with commonly used programs using various file formats, including BIOM, and provides operations such as rarefaction and taxonomic summaries. Bio-Community will help bioinformaticians to quickly piece together custom analysis pipelines and develop novel software. Availability an implementation: Bio-Community is cross-platform Perl code available from http://search.cpan.org/dist/Bio-Community under the Perl license. A readme file describes software installation and how to contribute.}, }
@article {pmid24618403, year = {2014}, author = {Shafquat, A and Joice, R and Simmons, SL and Huttenhower, C}, title = {Functional and phylogenetic assembly of microbial communities in the human microbiome.}, journal = {Trends in microbiology}, volume = {22}, number = {5}, pages = {261-266}, pmid = {24618403}, issn = {1878-4380}, support = {R01 HG005969/HG/NHGRI NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; R01HG005969/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; Microbiota/*physiology ; *Phylogeny ; }, abstract = {Microbial communities associated with the human body, that is, the human microbiome, are complex ecologies critical for normal development and health. The taxonomic and phylogenetic composition of these communities tends to significantly differ among individuals, precluding the definition of a simple, shared set of 'core' microbes. Here, we review recent evidence and ecological theory supporting the assembly of host-associated microbial communities in terms of functional traits rather than specific organisms. That is, distinct microbial species may be responsible for specific host-associated functions and phenotypes in distinct hosts. We discuss how ecological processes (selective and stochastic forces) governing the assembly of metazoan communities can be adapted to describe microbial ecologies in host-associated environments, resulting in both niche-specific and 'core' metabolic and other pathways maintained throughout the human microbiome. The extent to which phylogeny and functional traits are linked in host-associated microbes, as opposed to unlinked by mechanisms, such as lateral transfer, remains to be determined. However, the definition of these functional assembly rules within microbial communities using controlled model systems and integrative 'omics' represents a fruitful opportunity for molecular systems ecology.}, }
@article {pmid24616839, year = {2014}, author = {Keen, EC}, title = {Tradeoffs in bacteriophage life histories.}, journal = {Bacteriophage}, volume = {4}, number = {1}, pages = {e28365}, pmid = {24616839}, issn = {2159-7073}, abstract = {Viruses are the most abundant biological entities on the planet, yet most classical principles of evolutionary biology and ecology were not developed with viruses in mind. Here, the concept of biological tradeoffs, a fundamental tenet of life history theory, is examined in the context of bacteriophage biology. Specifically, several important parameters of phage life histories-replication, persistence, host range, and adsorption-are evaluated for tradeoffs. Available data indicate that replication rate is strongly negatively correlated with both persistence and host range, suggesting that the well-documented tradeoff in macroorganisms between offspring production and offspring quality also applies to phages. The biological tradeoffs that appear to characterize viruses' life histories have potential importance for viral evolution, ecology, and pathogenesis.}, }
@article {pmid24613921, year = {2014}, author = {Jacobs, JP and Braun, J}, title = {Immune and genetic gardening of the intestinal microbiome.}, journal = {FEBS letters}, volume = {588}, number = {22}, pages = {4102-4111}, pmid = {24613921}, issn = {1873-3468}, support = {U01 DK062413/DK/NIDDK NIH HHS/United States ; T32 DK007180/DK/NIDDK NIH HHS/United States ; R01 DK085691/DK/NIDDK NIH HHS/United States ; R01 AI078885/AI/NIAID NIH HHS/United States ; P01 DK046763/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; P30 CA016042/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Genetic Variation ; Humans ; *Immunity ; Intestinal Mucosa/immunology/metabolism/microbiology ; Intestines/immunology/*microbiology ; *Microbiota ; Receptors, Pattern Recognition/metabolism ; }, abstract = {The mucosal immune system - consisting of adaptive and innate immune cells as well as the epithelium - is profoundly influenced by its microbial environment. There is now growing evidence that the converse is also true, that the immune system shapes the composition of the intestinal microbiome. During conditions of health, this bidirectional interaction achieves a homeostasis in which inappropriate immune responses to non-pathogenic microbes are averted and immune activity suppresses blooms of potentially pathogenic microbes (pathobionts). Genetic alteration in immune/epithelial function can affect host gardening of the intestinal microbiome, contributing to the diversity of intestinal microbiota within a population and in some cases allowing for unfavorable microbial ecologies (dysbiosis) that confer disease susceptibility.}, }
@article {pmid24612310, year = {2014}, author = {Clements, KD and Angert, ER and Montgomery, WL and Choat, JH}, title = {Intestinal microbiota in fishes: what's known and what's not.}, journal = {Molecular ecology}, volume = {23}, number = {8}, pages = {1891-1898}, doi = {10.1111/mec.12699}, pmid = {24612310}, issn = {1365-294X}, mesh = {Animals ; Digestion ; Fishes/*microbiology/physiology ; Intestines/*microbiology ; *Microbiota ; }, abstract = {High-throughput sequencing approaches have enabled characterizations of the community composition of numerous gut microbial communities, which in turn has enhanced interest in their diversity and functional relationships in different groups of vertebrates. Although fishes represent the greatest taxonomic and ecological diversity of vertebrates, our understanding of their gut microbiota and its functional significance has lagged well behind that of terrestrial vertebrates. In order to highlight emerging issues, we provide an overview of research on fish gut microbiotas and the biology of their hosts. We conclude that microbial community composition must be viewed within an informed context of host ecology and physiology, and that this is of particular importance with respect to research planning and sampling design.}, }
@article {pmid24607969, year = {2014}, author = {Cole, JR and Tiedje, JM}, title = {History and impact of RDP: a legacy from Carl Woese to microbiology.}, journal = {RNA biology}, volume = {11}, number = {3}, pages = {239-243}, pmid = {24607969}, issn = {1555-8584}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; UH2 DK083993/DK/NIDDK NIH HHS/United States ; UH3 DK083993/DK/NIDDK NIH HHS/United States ; P42-ES004911/ES/NIEHS NIH HHS/United States ; }, mesh = {*Databases, Genetic ; Microbiological Phenomena ; Phylogeny ; RNA, Ribosomal/*genetics ; Sequence Analysis, RNA ; }, abstract = {The Ribosomal Database Project (RDP) grew out of Carl Woese's vision of how rRNA comparative methods could transform biology. First at the University of Illinois Urbana-Champaign, and later at Michigan State University's Center for Microbial Ecology, the project has grown from a few hundred to several million rRNA gene sequences. In the years since Woese started the RDP, publications describing the database and related tools have been cited over 11,000 times in journals spanning a wide range of disciplines, while the RDP website is accessed by 10,000 researchers in over 20,000 analysis sessions each month. This article describes the history of RDP's development over the last two decades.}, }
@article {pmid24604428, year = {2014}, author = {Bajer, A and Welc-Falęciak, R and Bednarska, M and Alsarraf, M and Behnke-Borowczyk, J and Siński, E and Behnke, JM}, title = {Long-term spatiotemporal stability and dynamic changes in the haemoparasite community of bank voles (Myodes glareolus) in NE Poland.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {196-211}, pmid = {24604428}, issn = {1432-184X}, mesh = {Animals ; Arvicolinae/blood/microbiology/*parasitology ; Babesia microti ; Bartonella ; Female ; Male ; Mycoplasma ; Poland ; Population Dynamics ; Spatio-Temporal Analysis ; Trypanosoma ; }, abstract = {Long-term field studies on parasite communities are rare but provide a powerful insight into the ecological and evolutionary processes shaping host-parasite interactions. The aim of our study was to identify the principal factors regulating long-term trends in the haemoparasite communities of bank voles, and to this end, we sampled three semi-isolated populations of bank voles (n = 880) in 1999, 2002, 2006 and 2010 in the Mazury lake district region of NE Poland. Overall, 90.8 % of the bank voles harboured at least one of the species of haemoparasites studied. Whilst overall prevalence (all species combined) did not vary significantly between the surveys, different temporal changes were detected among voles in each of the three sites. In voles from Urwitałt, prevalence increased consistently with successive surveys, whereas in Tałty, the peak years were 2002 and 2006, and in Pilchy, prevalence oscillated without a clear pattern. Across the study, bank voles harboured a mean of 1.75 ± 0.034 haemoparasite species, and species richness remained stable with no significant between-year fluctuations or trends. However, each of the five constituent species/genera showed a different pattern of spatio-temporal changes. The overall prevalence of Babesia microti was 4.9 %, but this varied significantly between years peaking in 2006 and declining again by 2010. For Bartonella spp., overall prevalence was 38.7 %, and this varied with year of study, but the temporal pattern of changes differed among the three sites. The overall prevalence of Haemobartonella (Mycoplasma) was 68.3 % with an increase in prevalence with year of study in all three sites. Hepatozoon erhardovae had an overall prevalence of 46.8 % but showed a marked reduction with each successive year of the study, and this was consistent in all three sites. The overall prevalence of Trypanosoma evotomys was 15.4 % varying significantly between sites, but showing temporal stability. While overall prevalence of all haemoparasites combined and species richness remained stable over the period of study, among the five haemoparasites, the pattern of spatiotemporal changes in prevalence and abundance of infections differed depending on parasite species. For some genera, host age was shown to play an important role, but a significant effect of host sex was found only for Haemobartonella spp.}, }
@article {pmid24602907, year = {2014}, author = {Manso, S and De Muynck, W and Segura, I and Aguado, A and Steppe, K and Boon, N and De Belie, N}, title = {Bioreceptivity evaluation of cementitious materials designed to stimulate biological growth.}, journal = {The Science of the total environment}, volume = {481}, number = {}, pages = {232-241}, doi = {10.1016/j.scitotenv.2014.02.059}, pmid = {24602907}, issn = {1879-1026}, mesh = {Conservation of Natural Resources/*methods ; Construction Materials/*analysis/microbiology ; Microalgae/*growth &amp; development ; *Porosity ; }, abstract = {Ordinary Portland cement (OPC), the most used binder in construction, presents some disadvantages in terms of pollution (CO2 emissions) and visual impact. For this reason, green roofs and façades have gain considerable attention in the last decade as a way to integrate nature in cities. These systems, however, suffer from high initial and maintenance costs. An alternative strategy to obtain green facades is the direct natural colonisation of the cementitious construction materials constituting the wall, a phenomenon governed by the bioreceptivity of such material. This work aims at assessing the suitability of magnesium phosphate cement (MPC) materials to allow a rapid natural colonisation taking carbonated OPC samples as a reference material. For that, the aggregate size, the w/c ratio and the amount of cement paste of mortars made of both binders were modified. The assessment of the different bioreceptivities was conducted by means of an accelerated algal fouling test. MPC samples exhibited a faster fouling compared to OPC samples, which could be mainly attributed to the lower pH of the MPC binder. In addition to the binder, the fouling rate was governed by the roughness and the porosity of the material. MPC mortar with moderate porosity and roughness appears to be the most feasible material to be used for the development of green concrete walls.}, }
@article {pmid24599071, year = {2014}, author = {Borgdorff, H and Tsivtsivadze, E and Verhelst, R and Marzorati, M and Jurriaans, S and Ndayisaba, GF and Schuren, FH and van de Wijgert, JH}, title = {Lactobacillus-dominated cervicovaginal microbiota associated with reduced HIV/STI prevalence and genital HIV viral load in African women.}, journal = {The ISME journal}, volume = {8}, number = {9}, pages = {1781-1793}, pmid = {24599071}, issn = {1751-7370}, mesh = {Adolescent ; Adult ; Cervix Uteri/*microbiology/virology ; Female ; HIV Infections/epidemiology/*microbiology/virology ; HIV-1/genetics/isolation &amp; purification ; Humans ; Lactobacillus/genetics/*isolation &amp; purification ; *Microbiota ; Middle Aged ; Phylogeny ; Pregnancy ; Prevalence ; Rwanda ; Sexually Transmitted Diseases, Bacterial/epidemiology ; Sexually Transmitted Diseases, Viral/epidemiology ; Vagina/*microbiology/virology ; Viral Load ; Young Adult ; }, abstract = {Cervicovaginal microbiota not dominated by lactobacilli may facilitate transmission of HIV and other sexually transmitted infections (STIs), as well as miscarriages, preterm births and sepsis in pregnant women. However, little is known about the exact nature of the microbiological changes that cause these adverse outcomes. In this study, cervical samples of 174 Rwandan female sex workers were analyzed cross-sectionally using a phylogenetic microarray. Furthermore, HIV-1 RNA concentrations were measured in cervicovaginal lavages of 58 HIV-positive women among them. We identified six microbiome clusters, representing a gradient from low semi-quantitative abundance and diversity dominated by Lactobacillus crispatus (cluster R-I, with R denoting 'Rwanda') and L. iners (R-II) to intermediate (R-V) and high abundance and diversity (R-III, R-IV and R-VI) dominated by a mixture of anaerobes, including Gardnerella, Atopobium and Prevotella species. Women in cluster R-I were less likely to have HIV (P=0.03), herpes simplex virus type 2 (HSV-2; P<0.01), and high-risk human papillomavirus (HPV; P<0.01) and had no bacterial STIs (P=0.15). Statistically significant trends in prevalence of viral STIs were found from low prevalence in cluster R-I, to higher prevalence in clusters R-II and R-V, and highest prevalence in clusters R-III/R-IV/R-VI. Furthermore, only 10% of HIV-positive women in clusters R-I/R-II, compared with 40% in cluster R-V, and 42% in clusters R-III/R-IV/R-VI had detectable cervicovaginal HIV-1 RNA (Ptrend=0.03). We conclude that L. crispatus-dominated, and to a lesser extent L. iners-dominated, cervicovaginal microbiota are associated with a lower prevalence of HIV/STIs and a lower likelihood of genital HIV-1 RNA shedding.}, }
@article {pmid24596290, year = {2014}, author = {Luo, H and Swan, BK and Stepanauskas, R and Hughes, AL and Moran, MA}, title = {Comparing effective population sizes of dominant marine alphaproteobacteria lineages.}, journal = {Environmental microbiology reports}, volume = {6}, number = {2}, pages = {167-172}, doi = {10.1111/1758-2229.12129}, pmid = {24596290}, issn = {1758-2229}, mesh = {Alphaproteobacteria/classification/genetics/*isolation &amp; purification/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Ecosystem ; Heterotrophic Processes ; Molecular Sequence Data ; Phylogeny ; Seawater/*microbiology ; }, abstract = {A fundamental question in marine microbial ecology is how microbes adapt to ocean environments. Although numerically dominant populations are typically considered more successful, higher census population sizes (Nc) do not equate directly to a greater capability for adaptation. Instead, effective population size (Ne) determines the fate of deleterious and favourable mutations, and thus is a key parameter for determining the adaptive potential of a population. In the case of the SAR11 and Roseobacter lineages, two abundant heterotrophic bacteria in ocean surface waters with contrasting life history strategies, culture-independent population surveys suggest that SAR11s have greater Nc than Roseobacters. To determine relative Ne, we compared the ratio of nonsynonymous to synonymous substitution rates (ω) of recently diverged lineages of these taxa. Values of ω associated with several of the Roseobacter subclades were lower than for SAR11 subclades, suggesting greater Ne in these cases. Most Roseobacter lineages also had smaller ω values compared with an atypical basal Roseobacter lineage with a large Nc. This finding provides insight into variability in Ne across two important marine bacterial lineages, and provides an evolutionary context for considering how heterotrophic marine bacteria may differ in their ability to adapt to changing ocean habitats.}, }
@article {pmid24596259, year = {2014}, author = {Garcia, SL and McMahon, KD and Grossart, HP and Warnecke, F}, title = {Successful enrichment of the ubiquitous freshwater acI Actinobacteria.}, journal = {Environmental microbiology reports}, volume = {6}, number = {1}, pages = {21-27}, doi = {10.1111/1758-2229.12104}, pmid = {24596259}, issn = {1758-2229}, mesh = {Actinobacteria/classification/genetics/*growth &amp; development/*isolation &amp; purification ; Ecosystem ; Fresh Water/*microbiology ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Actinobacteria of the acI lineage are often the numerically dominant bacterial phylum in surface freshwaters, where they can account for > 50% of total bacteria. Despite their abundance, there are no described isolates. In an effort to obtain enrichment of these ubiquitous freshwater Actinobacteria, diluted freshwater samples from Lake Grosse Fuchskuhle, Germany, were incubated in 96-well culture plates. With this method, a successful enrichment containing high abundances of a member of the lineage acI was established. Phylogenetic classification showed that the acI Actinobacteria of the enrichment belonged to the acI-B2 tribe, which seems to prefer acidic lakes. This enrichment grows to low cell densities and thus the oligotrophic nature of acI-B2 was confirmed.}, }
@article {pmid24595908, year = {2014}, author = {Ishaq, SL and Wright, AD}, title = {High-throughput DNA sequencing of the ruminal bacteria from moose (Alces alces) in Vermont, Alaska, and Norway.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {185-195}, pmid = {24595908}, issn = {1432-184X}, mesh = {Alaska ; Animals ; Bacteria/*classification ; DNA, Bacterial/genetics ; Deer/*microbiology ; Female ; High-Throughput Nucleotide Sequencing ; Male ; Norway ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; Vermont ; }, abstract = {In the present study, the rumen bacteria of moose (Alces alces) from three distinct geographic locations were investigated. Moose are large, browsing ruminants in the deer family, which subsist on fibrous, woody browse, and aquatic plants. Subspecies exist which are distinguished by differing body and antler size, and these are somewhat geographically isolated. Seventeen rumen samples were collected from moose in Vermont, Alaska, and Norway, and bacterial 16S ribosomal RNA genes were sequenced using Roche 454 pyrosequencing with titanium chemistry. Overall, 109,643 sequences were generated from the 17 individual samples, revealing 33,622 unique sequences. Members of the phylum Bacteroidetes were dominant in samples from Alaska and Norway, but representatives of the phylum Firmicutes were dominant in samples from Vermont. Within the phylum Bacteroidetes, Prevotellaceae was the dominant family in all three sample locations, most of which belonged to the genus Prevotella. Within the phylum Firmicutes, the family Lachnospiraceae was the most prevalent in all three sample locations. The data set supporting the results of this article is available in the Sequence Read Archive (SRA), available through NCBI [study accession number SRP022590]. Samples clustered by geographic location and by weight and were heterogenous based on gender, location, and weight class (p < 0.05). Location was a stronger factor in determining the core microbiome than either age or weight, but gender did not appear to be a strong factor. There were no shared operational taxonomic units across all 17 samples, which indicates that these moose may have been isolated long enough to preclude a core microbiome among moose. Other potential factors discussed include differences in climate, food quality and availability, gender, and life cycle.}, }
@article {pmid24595907, year = {2014}, author = {Le Roux, C and Muller, F and Bouvet, JM and Dreyfus, B and Béna, G and Galiana, A and Bâ, AM}, title = {Genetic diversity patterns and functional traits of Bradyrhizobium strains associated with Pterocarpus officinalis Jacq. in Caribbean islands and Amazonian forest (French Guiana).}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {329-338}, pmid = {24595907}, issn = {1432-184X}, mesh = {Bradyrhizobium/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Forests ; French Guiana ; *Genetic Variation ; *Phylogeny ; Pterocarpus/*microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Root Nodules, Plant/microbiology ; Sequence Analysis, DNA ; Symbiosis ; West Indies ; }, abstract = {Pterocarpus officinalis Jacq. is a legume tree native to the Caribbean islands and South America growing as a dominant species in swamp forests. To analyze (i) the genetic diversity and (ii) the symbiotic properties of its associated nitrogen-fixing soil bacteria, root nodules were collected from P. officinalis distributed in 16 forest sites of the Caribbean islands and French Guiana. The sequencing of the 16S-23S ribosomal RNA intergenic spacer region (ITS) showed that all bacteria belonged to the Bradyrhizobium genus. Bacteria isolated from insular zones showed very close sequence homologies with Bradyrhizobium genospecies V belonging to the Bradyrhizobium japonicum super-clade. By contrast, bacteria isolated from continental region displayed a larger genetic diversity and belonged to B. elkanii super-clade. Two strains from Puerto Rico and one from French Guiana were not related to any known sequence and could be defined as a new genospecies. Inoculation experiments did not show any host specificity of the Bradyrhizobium strains tested in terms of infectivity. However, homologous Bradyrhizobium sp. strain-P. officinalis provenance associations were more efficient in terms of nodule production, N acquisition, and growth than heterologous ones. The dominant status of P. officinalis in the islands may explain the lower bacterial diversity compared to that found in the continent where P. officinalis is associated with other leguminous tree species. The specificity in efficiency found between Bradyrhizobium strains and host tree provenances could be due to a coevolution process between both partners and needs to be taken in consideration in the framework of rehabilitation plantation programs.}, }
@article {pmid24588891, year = {2014}, author = {Fritsche, K and van den Berg, M and de Boer, W and van Beek, TA and Raaijmakers, JM and van Veen, JA and Leveau, JH}, title = {Biosynthetic genes and activity spectrum of antifungal polyynes from Collimonas fungivorans Ter331.}, journal = {Environmental microbiology}, volume = {16}, number = {5}, pages = {1334-1345}, doi = {10.1111/1462-2920.12440}, pmid = {24588891}, issn = {1462-2920}, mesh = {Antifungal Agents/isolation &amp; purification/*pharmacology ; Aspergillus niger/drug effects ; Fatty Acid Desaturases/genetics ; Genes, Bacterial ; Microbial Interactions ; Oxalobacteraceae/*genetics/metabolism ; Polyketide Synthases/genetics ; Polyynes/isolation &amp; purification/*pharmacology ; }, abstract = {The antifungal activity of bacteria from the genus Collimonas has been well documented, but the chemistry and gene functions that underlie this phenotype are still poorly understood. Screening of a random plasposon insertion library of Collimonas fungivorans Ter331 for loss-of-function mutants revealed the importance of gene cluster K, which is annotated to code for the biosynthesis of a secondary metabolite and which features genes for fatty acid desaturases and polyketide synthases. Mutants in gene cluster K had lost the ability to inhibit hyphal growth of the fungus Aspergillus niger and were no longer able to produce and secrete several metabolites that after extraction and partial purification from wildtype strain Ter331 were shown to share a putative ene-triyne moiety. Some but not all of these metabolites were able to inhibit growth of A. niger, indicating functional variation within this group of Collimonas-produced polyyne-like 'collimomycins'. Polymerase chain reaction analysis of isolates representing different Collimonas species indicated that the possession of cluster K genes correlated positively with antifungal ability, further strengthening the notion that this cluster is involved in collimomycin production. We discuss our findings in the context of other bacterially produced polyynes and the potential use of collimomycins for the control of harmful fungi.}, }
@article {pmid24586961, year = {2014}, author = {Gruninger, RJ and Sensen, CW and McAllister, TA and Forster, RJ}, title = {Diversity of rumen bacteria in canadian cervids.}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e89682}, pmid = {24586961}, issn = {1932-6203}, mesh = {Animals ; Bacteria/*classification/genetics ; *Biodiversity ; Canada ; DNA, Bacterial ; Deer ; Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Rumen/*microbiology ; Ruminants ; Sequence Analysis, DNA ; }, abstract = {Interest in the bacteria responsible for the breakdown of lignocellulosic feedstuffs within the rumen has increased due to their potential utility in industrial applications. To date, most studies have focused on bacteria from domesticated ruminants. We have expanded the knowledge of the microbial ecology of ruminants by examining the bacterial populations found in the rumen of non-domesticated ruminants found in Canada. Next-generation sequencing of 16S rDNA was employed to characterize the liquid and solid-associated bacterial communities in the rumen of elk (Cervus canadensis), and white tailed deer (Odocoileus virginianus). Despite variability in the microbial populations between animals, principle component and weighted UniFrac analysis indicated that bacterial communities in the rumen of elk and white tail deer are distinct. Populations clustered according to individual host animal and not the association with liquid or solid phase of the rumen contents. In all instances, Bacteroidetes and Firmicutes were the dominant bacterial phyla, although the relative abundance of these differed among ruminant species and between phases of rumen digesta, respectively. In the elk samples Bacteroidetes were more predominant in the liquid phase whereas Firmicutes was the most prevalent phyla in the solid digesta (P = 1×10(-5)). There were also statistically significant differences in the abundance of OTUs classified as Fibrobacteres (P = 5×10(-3)) and Spirochaetes (P = 3×10(-4)) in the solid digesta of the elk samples. We identified a number of OTUs that were classified as phylotypes not previously observed in the rumen environment. Our results suggest that although the bacterial diversity in wild North American ruminants shows overall similarities to domesticated ruminants, we observed a number of OTUs not previously described. Previous studies primarily focusing on domesticated ruminants do not fully represent the microbial diversity of the rumen and studies focusing on non-domesticated ruminants should be expanded.}, }
@article {pmid24584416, year = {2014}, author = {Zhang, M and Liu, N and Qian, C and Wang, Q and Wang, Q and Long, Y and Huang, Y and Zhou, Z and Yan, X}, title = {Phylogenetic and functional analysis of gut microbiota of a fungus-growing higher termite: Bacteroidetes from higher termites are a rich source of β-glucosidase genes.}, journal = {Microbial ecology}, volume = {68}, number = {2}, pages = {416-425}, pmid = {24584416}, issn = {1432-184X}, mesh = {Animals ; Bacteroidetes/enzymology/*genetics ; DNA, Bacterial/genetics ; Digestive System/microbiology ; Genes, Bacterial ; Isoptera/*microbiology ; *Microbiota ; Molecular Sequence Annotation ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; beta-Glucosidase/*genetics/metabolism ; }, abstract = {Fungus-growing termites, their symbiotic fungi, and microbiota inhibiting their intestinal tract comprise a highly efficient cellulose-hydrolyzing system; however, little is known about the role of gut microbiota in this system. Twelve fosmid clones with β-glucosidase activity were previously obtained by functionally screening a metagenomic library of a fungus-growing termite, Macrotermes annandalei. Ten contigs containing putative β-glucosidase genes (bgl1-10) were assembled by sequencing data of these fosmid clones. All these contigs were binned to Bacteroidetes, and all these β-glucosidase genes were phylogenetically closed to those from Bacteroides or Dysgonomonas. Six out of 10 β-glucosidase genes had predicted signal peptides, indicating a transmembrane capability of these enzymes to mediate cellulose hydrolysis within the gut of the termites. To confirm the activities of these β-glucosidase genes, three genes (bgl5, bgl7, and bgl9) were successfully expressed and purified. The optimal temperature and pH of these enzymes largely resembled the environment of the host's gut. The gut microbiota composition of the fungus-growing termite was also determined by 454 pyrosequencing, showing that Bacteroidetes was the most dominant phylum. The diversity and the enzyme properties of β-glucosidases revealed in this study suggested that Bacteroidetes as the major member in fungus-growing termites contributed to cello-oligomer degradation in cellulose-hydrolyzing process and represented a rich source for β-glucosidase genes.}, }
@article {pmid24581391, year = {2014}, author = {Staley, C and Dunny, GM and Sadowsky, MJ}, title = {Environmental and animal-associated enterococci.}, journal = {Advances in applied microbiology}, volume = {87}, number = {}, pages = {147-186}, doi = {10.1016/B978-0-12-800261-2.00004-9}, pmid = {24581391}, issn = {0065-2164}, mesh = {Animals ; Ecology ; Enterococcus/drug effects/genetics/*physiology ; *Environmental Microbiology ; Fresh Water/microbiology ; Geologic Sediments/microbiology ; Humans ; Seawater/microbiology ; Virulence ; }, abstract = {Enterococci are generally commensal bacteria inhabiting the gastrointestinal tract of humans and animals. They have, however, been implicated as the etiological agent of a variety of illnesses and nosocomial infections. In addition to pathogenic potential, there is growing concern regarding the incidence of antibiotic resistance and genetic exchange among Enterococcus spp. within and among a variety of animal hosts. While primarily considered an enteric group, extra-enteric habitats in which enterococci persist and potentially grow have been studied for decades. Although many biotic (e.g., predation) and abiotic (e.g., sunlight, nutrients, and salinity) stressors have been thought to limit the success of enterococci in these secondary habitats, a growing body of evidence suggests that certain strains may become naturalized to environmental habitats. Enterococci have also been used for decades as indicators of fecal contamination in recreational waters where increased concentrations of this group have been linked to the incidence of illness in humans following recreational use of these waters. Persistence of enterococci in secondary habitats, however, suggests that their presence in ambient waters may prove to be a poor indicator of actual risks to public health. In this chapter, we provide a review of the existing body of literature concerning animal host associations, genetic exchange is reviewed, and emphasis is placed on the growing body of evidence for the persistence and growth of enterococci in secondary habitats.}, }
@article {pmid24581365, year = {2013}, author = {Kiewra, D and Zaleśny, G}, title = {Relationship between temporal abundance of ticks and incidence of Lyme borreliosis in Lower Silesia regions of Poland.}, journal = {Journal of vector ecology : journal of the Society for Vector Ecology}, volume = {38}, number = {2}, pages = {345-352}, doi = {10.1111/j.1948-7134.2013.12050.x}, pmid = {24581365}, issn = {1948-7134}, mesh = {Animals ; Humans ; Incidence ; Lyme Disease/*epidemiology/transmission ; Poland ; Ticks/*pathogenicity ; }, abstract = {The aim of this study was to identify the factors determining the incidence of Lyme borreliosis (LB) in south-western Poland by estimating the prevalence of B. burgdorferi s. l. in I. ricinus, and to analyze the temporal abundance of ticks in relation to epidemiological data on LB incidence. Host-seeking ticks collected in 2011 in four districts in southwestern Poland were examined by nested PCR for the presence of B. burgdorferi s.l. In total, 2,507 host-seeking I. ricinus were collected. The temporal abundance of ticks varied between districts. The minimal infection rates with B. burgdorferi s.l. were 11.5% for nymphs and 37.7% for adults. There were no statistical differences in the level of infection between districts either for nymphs or for adults. Five different genospecies were identified within the B. burgdorferi s.l. complex: B. garinii, B. afzelii, B. lusitaniae, B. valasiana, and B. burgdorferi s.s., and additionally B. miyamotoi. Our results point to a relationship between tick temporal abundance and LB incidence both for adults and nymphs. The high abundance of ticks is positively correlated with the number of LB cases in humans. The tick's abundance may be considered as a major factor in determining the LB risk in southwestern Poland.}, }
@article {pmid24580036, year = {2014}, author = {van Dorst, J and Bissett, A and Palmer, AS and Brown, M and Snape, I and Stark, JS and Raymond, B and McKinlay, J and Ji, M and Winsley, T and Ferrari, BC}, title = {Community fingerprinting in a sequencing world.}, journal = {FEMS microbiology ecology}, volume = {89}, number = {2}, pages = {316-330}, doi = {10.1111/1574-6941.12308}, pmid = {24580036}, issn = {1574-6941}, mesh = {Antarctic Regions ; Arctic Regions ; Bacteria/classification/*genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; High-Throughput Nucleotide Sequencing ; Molecular Typing ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Sensitivity and Specificity ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Despite decreasing costs, generating large-scale, well-replicated and multivariate microbial ecology investigations with sequencing remains an expensive and time-consuming option. As a result, many microbial ecology investigations continue to suffer from a lack of appropriate replication. We evaluated two fingerprinting approaches - terminal restriction fragment length polymorphism (T-RFLP) and automated ribosomal intergenic spacer analysis (ARISA) against 454 pyrosequencing, by applying them to 225 polar soil samples from East Antarctica and the high Arctic. By incorporating local and global spatial scales into the dataset, our aim was to determine whether various approaches differed in their ability and hence utility, to identify ecological patterns. Through the reduction in the 454 sequencing data to the most dominant OTUs, we revealed that a surprisingly small proportion of abundant OTUs (< 0.25%) was driving the biological patterns observed. Overall, ARISA and T-RFLP had a similar capacity as sequencing to separate samples according to distance at a local scale, and to correlate environmental variables with microbial community structure. Pyrosequencing had a greater resolution at the global scale but all methods were capable of significantly differentiating the polar sites. We conclude fingerprinting remains a legitimate approach to generating large datasets as well as a cost-effective rapid method to identify samples for elucidating taxonomic information or diversity estimates with sequencing methods.}, }
@article {pmid24579975, year = {2014}, author = {Geyer, KM and Altrichter, AE and Takacs-Vesbach, CD and Van Horn, DJ and Gooseff, MN and Barrett, JE}, title = {Bacterial community composition of divergent soil habitats in a polar desert.}, journal = {FEMS microbiology ecology}, volume = {89}, number = {2}, pages = {490-494}, doi = {10.1111/1574-6941.12306}, pmid = {24579975}, issn = {1574-6941}, mesh = {Acidobacteria/*genetics ; Actinobacteria/*genetics ; Antarctic Regions ; Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; Desert Climate ; Ecosystem ; Hydrogen-Ion Concentration ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Edaphic factors such as pH, organic matter, and salinity are often the most significant drivers of diversity patterns in soil bacterial communities. Desert ecosystems in particular are model locations for examining such relationships as food web complexity is low and the soil environment is biogeochemically heterogeneous. Here, we present the findings from a 16S rRNA gene sequencing approach used to observe the differences in diversity and community composition among three divergent soil habitats of the McMurdo Dry Valleys, Antarctica. Results show that alpha diversity is significantly lowered in high pH soils, which contain higher proportions of the phyla Acidobacteria and Actinobacteria, while mesic soils with higher soil organic carbon (and ammonium) content contain high proportions of Nitrospira, a nitrite-oxidizing bacteria. Taxonomic community resolution also had a significant impact on our conclusions, as pH was the primary predictor of phylum-level diversity, while moisture was the most significant predictor of diversity at the genus level. Predictive power also increased with increasing taxonomic resolution, suggesting a potential increase in niche-based drivers of bacterial community composition at such levels.}, }
@article {pmid24577741, year = {2014}, author = {Ghadakpour, M and Bester, E and Liss, SN and Gardam, M and Droppo, I and Hota, S and Wolfaardt, GM}, title = {Integration and proliferation of Pseudomonas aeruginosa PA01 in multispecies biofilms.}, journal = {Microbial ecology}, volume = {68}, number = {1}, pages = {121-131}, pmid = {24577741}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Load ; *Biofilms/drug effects ; Genes, Reporter ; Green Fluorescent Proteins/genetics ; *Intensive Care Units ; Microscopy, Confocal ; Pseudomonas aeruginosa/drug effects/*growth &amp; development ; Toilet Facilities ; Water Microbiology ; Water Supply ; }, abstract = {Despite an increased awareness of biofilm formation by pathogens and the role of biofilms in human infections, the potential role of environmental biofilms as an intermediate stage in the host-to-host cycle is poorly described. To initiate infection, pathogens in biofilms on inanimate environmental surfaces must detach from the biofilm and be transmitted to a susceptible individual in numbers large enough to constitute an infectious dose. Additionally, while detachment has been recognized as a discrete event in the biofilm lifestyle, it has not been studied to the same extent as biofilm development or biofilm physiology. Successful integration of Pseudomonas aeruginosa strain PA01 expressing green fluorescent protein (PA01GFP), employed here as a surrogate pathogen, into multispecies biofilm communities isolated and enriched from sink drains in public washrooms and a hospital intensive care unit is described. Confocal laser scanning microscopy indicated that PA01GFP cells were most frequently located in the deeper layers of the biofilm, near the attachment surface, when introduced into continuous flow cells before or at the same time as the multispecies drain communities. A more random integration pattern was observed when PA01GFP was introduced into established multispecies biofilms. Significant numbers of single PA01GFP cells were continuously released from the biofilms to the bulk liquid environment, regardless of the order of introduction into the flow cell. Challenging the multispecies biofilms containing PA01GFP with sub-lethal concentrations of an antibiotic, chelating agent and shear forces that typically prevail at distances away from the point of treatment showed that environmental biofilms provide a suitable habitat where pathogens are maintained and protected, and from where they are continuously released.}, }
@article {pmid24577740, year = {2014}, author = {He, L and Liu, F and Karuppiah, V and Ren, Y and Li, Z}, title = {Comparisons of the fungal and protistan communities among different marine sponge holobionts by pyrosequencing.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {951-961}, pmid = {24577740}, issn = {1432-184X}, mesh = {Animals ; China ; DNA, Fungal/genetics ; DNA, Protozoan/genetics ; Eukaryota/genetics/physiology ; Fungi/genetics/physiology ; Molecular Sequence Data ; Phylogeny ; Porifera/genetics/*microbiology/*parasitology ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; Symbiosis ; }, abstract = {To date, the knowledge of eukaryotic communities associated with sponges remains limited compared with prokaryotic communities. In a manner similar to prokaryotes, it could be hypothesized that sponge holobionts have phylogenetically diverse eukaryotic symbionts, and the eukaryotic community structures in different sponge holobionts were probably different. In order to test this hypothesis, the communities of eukaryota associated with 11 species of South China Sea sponges were compared with the V4 region of 18S ribosomal ribonucleic acid gene using 454 pyrosequencing. Consequently, 135 and 721 unique operational taxonomic units (OTUs) of fungi and protists were obtained at 97 % sequence similarity, respectively. These sequences were assigned to 2 phyla of fungi (Ascomycota and Basidiomycota) and 9 phyla of protists including 5 algal phyla (Chlorophyta, Haptophyta, Streptophyta, Rhodophyta, and Stramenopiles) and 4 protozoal phyla (Alveolata, Cercozoa, Haplosporidia, and Radiolaria) including 47 orders (12 fungi, 35 protists). Entorrhizales of fungi and 18 orders of protists were detected in marine sponges for the first time. Particularly, Tilletiales of fungi and Chlorocystidales of protists were detected for the first time in marine habitats. Though Ascomycota, Alveolata, and Radiolaria were detected in all the 11 sponge species, sponge holobionts have different fungi and protistan communities according to OTU comparison and principal component analysis at the order level. This study provided the first insights into the fungal and protistan communities associated with different marine sponge holobionts using pyrosequencing, thus further extending the knowledge on sponge-associated eukaryotic diversity.}, }
@article {pmid24576697, year = {2014}, author = {De Vrieze, J and Gildemyn, S and Arends, JB and Vanwonterghem, I and Verbeken, K and Boon, N and Verstraete, W and Tyson, GW and Hennebel, T and Rabaey, K}, title = {Biomass retention on electrodes rather than electrical current enhances stability in anaerobic digestion.}, journal = {Water research}, volume = {54}, number = {}, pages = {211-221}, doi = {10.1016/j.watres.2014.01.044}, pmid = {24576697}, issn = {1879-2448}, mesh = {Anaerobiosis ; Bacteria/genetics/metabolism ; Base Sequence ; *Biomass ; Bioreactors/microbiology ; *Electricity ; Electrochemical Techniques ; Electrodes ; Methane/biosynthesis ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Water Purification/*methods ; }, abstract = {Anaerobic digestion (AD) is a well-established technology for energy recovery from organic waste streams. Several studies noted that inserting a bioelectrochemical system (BES) inside an anaerobic digester can increase biogas output, however the mechanism behind this was not explored and primary controls were not executed. Here, we evaluated whether a BES could stabilize AD of molasses. Lab-scale digesters were operated in the presence or absence of electrodes, in open (no applied potential) and closed circuit conditions. In the control reactors without electrodes methane production decreased to 50% of the initial rate, while it remained stable in the reactors with electrodes, indicating a stabilizing effect. After 91 days of operation, the now colonized electrodes were introduced in the failing AD reactors to evaluate their remediating capacity. This resulted in an immediate increase in CH4 production and VFA removal. Although a current was generated in the BES operated in closed circuit, no direct effect of applied potential nor current was observed. A high abundance of Methanosaeta was detected on the electrodes, however irrespective of the applied cell potential. This study demonstrated that, in addition to other studies reporting only an increase in methane production, a BES can also remediate AD systems that exhibited process failure. However, the lack of difference between current driven and open circuit systems indicates that the key impact is through biomass retention, rather than electrochemical interaction with the electrodes.}, }
@article {pmid24575403, year = {2014}, author = {Roca, M and Nofrarías, M and Majó, N and Pérez de Rozas, AM and Segalés, J and Castillo, M and Martín-Orúe, SM and Espinal, A and Pujols, J and Badiola, I}, title = {Changes in bacterial population of gastrointestinal tract of weaned pigs fed with different additives.}, journal = {BioMed research international}, volume = {2014}, number = {}, pages = {269402}, pmid = {24575403}, issn = {2314-6141}, mesh = {Animals ; Bacteria/drug effects ; Biodiversity ; Colony Count, Microbial ; Diet ; Feeding Behavior/*drug effects ; Food Additives/*pharmacology ; Gastrointestinal Tract/drug effects/*microbiology ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sus scrofa ; *Weaning ; }, abstract = {This study aimed to provide novel insights into the gastrointestinal microbial diversity from different gastrointestinal locations in weaning piglets using PCR-restriction fragment length polymorphism (PCR-RFLP). Additionally, the effect of different feed additives was analyzed. Thirty-two piglets were fed with four different diets: a control group and three enriched diets, with avilamycin, sodium butyrate, and a plant extract mixture. Digesta samples were collected from eight different gastrointestinal segments of each animal and the bacterial population was analysed by a PCR-RFLP technique that uses 16S rDNA gene sequences. Bacterial diversity was assessed by calculating the number of bands and the Shannon-Weaver index. Dendrograms were constructed to estimate the similarity of bacterial populations. A higher bacterial diversity was detected in large intestine compared to small intestine. Among diets, the most relevant microbial diversity differences were found between sodium butyrate and plant extract mixture. Proximal jejunum, ileum, and proximal colon were identified as those segments that could be representative of microbial diversity in pig gut. Results indicate that PCR-RFLP technique allowed detecting modifications on the gastrointestinal microbial ecology in pigs fed with different additives, such as increased biodiversity by sodium butyrate in feed.}, }
@article {pmid24573163, year = {2014}, author = {Huber, KJ and Wüst, PK and Rohde, M and Overmann, J and Foesel, BU}, title = {Aridibacter famidurans gen. nov., sp. nov. and Aridibacter kavangonensis sp. nov., two novel members of subdivision 4 of the Acidobacteria isolated from semiarid savannah soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {64}, number = {Pt 6}, pages = {1866-1875}, doi = {10.1099/ijs.0.060236-0}, pmid = {24573163}, issn = {1466-5034}, mesh = {Acidobacteria/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Molecular Sequence Data ; Namibia ; Nucleic Acid Hybridization ; *Phylogeny ; Pigmentation ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {Acidobacteria constitute an abundant fraction of the soil microbial community and are currently divided into 26 subdivisions. Most cultivated members of the Acidobacteria are affiliated with subdivision 1, while only a few representatives of subdivisions 3, 4, 8, 10 and 23 have been isolated and described so far. Two novel isolates of subdivision 4 of the Acidobacteria were isolated from subtropical savannah soils and are characterized in the present work. Cells of strains A22_HD_4H(T) and Ac_23_E3(T) were immotile rods that divided by binary fission. Colonies were pink and white, respectively. The novel strains A22_HD_4H(T) and Ac_23_E3(T) were aerobic mesophiles with a broad range of tolerance towards pH (4.0-9.5 and 3.5-10.0, respectively) and temperature (15-44 and 12-47 °C, respectively). Both showed chemo-organoheterotrophic growth on some sugars, the amino sugar N-acetylgalactosamine, a few amino acids, organic acids and various complex protein substrates. Major fatty acids of A22_HD_4H(T) and Ac_23_E3(T) were iso-C(15 : 0), summed feature 1 (C(13 : 0) 3-OH/iso-C(15 : 1) H), summed feature 3 (C(16 : 1)ω7c/C(16 : 1)ω6c) and anteiso-C(17 : 0). The major quinone was MK-8; in addition, MK-7 occurred in small amounts. The DNA G+C contents of A22_HD_4H(T) and Ac_23_E3(T) were 53.2 and 52.6 mol%, respectively. The closest described relative was Blastocatella fastidiosa A2-16(T), with 16S rRNA gene sequence identity of 93.2 and 93.3%, respectively. Strains A22_HD_4H(T) and Ac_23_E3(T) displayed 16S rRNA gene sequence similarity of 97.4% to each other. On the basis of the low DNA-DNA hybridization value, the two isolates represent different species. Based on morphological, physiological and molecular characteristics, the new genus Aridibacter gen. nov. is proposed, with two novel species, the type species Aridibacter famidurans sp. nov. (type strain A22_HD_4H(T) = DSM 26555(T) = LMG 27985(T)) and a second species, Aridibacter kavangonensis sp. nov. (type strain Ac_23_E3(T) = DSM 26558(T) = LMG 27597(T)).}, }
@article {pmid24573161, year = {2014}, author = {Sorokin, DY and Vejmelkova, D and Lücker, S and Streshinskaya, GM and Rijpstra, WIC and Sinninghe Damsté, JS and Kleerbezem, R and van Loosdrecht, M and Muyzer, G and Daims, H}, title = {Nitrolancea hollandica gen. nov., sp. nov., a chemolithoautotrophic nitrite-oxidizing bacterium isolated from a bioreactor belonging to the phylum Chloroflexi.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {64}, number = {Pt 6}, pages = {1859-1865}, doi = {10.1099/ijs.0.062232-0}, pmid = {24573161}, issn = {1466-5034}, mesh = {Base Composition ; Bioreactors/*microbiology ; Chemoautotrophic Growth ; Chloroflexi/*classification/genetics/isolation &amp; purification/ultrastructure ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Molecular Sequence Data ; Netherlands ; Nitrification ; Nitrites/*metabolism ; Oxidation-Reduction ; Peptidoglycan/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {A novel nitrite-oxidizing bacterium (NOB), strain Lb(T), was isolated from a nitrifying bioreactor with a high loading of ammonium bicarbonate in a mineral medium with nitrite as the energy source. The cells were oval (lancet-shaped) rods with pointed edges, non-motile, Gram-positive (by staining and from the cell wall structure) and non-spore-forming. Strain Lb(T) was an obligately aerobic, chemolitoautotrophic NOB, utilizing nitrite or formate as the energy source and CO2 as the carbon source. Ammonium served as the only source of assimilated nitrogen. Growth with nitrite was optimal at pH 6.8-7.5 and at 40 °C (maximum 46 °C). The membrane lipids consisted of C20 alkyl 1,2-diols with the dominant fatty acids being 10MeC18 and C(18 : 1)ω9. The peptidoglycan lacked meso-DAP but contained ornithine and lysine. The dominant lipoquinone was MK-8. Phylogenetic analyses of the 16s rRNA gene sequence placed strain Lb(T) into the class Thermomicrobia of the phylum Chloroflexi with Sphaerobacter thermophilus as the closest relative. On the basis of physiological and phylogenetic data, it is proposed that strain Lb(T) represents a novel species of a new genus, with the suggested name Nitrolancea hollandica gen. nov., sp. nov. The type strain of the type species is Lb(T) (= DSM 23161(T) = UNIQEM U798(T)).}, }
@article {pmid24572567, year = {2014}, author = {Reid, A}, title = {From Woese to Wired: the unexpected payoffs of basic research.}, journal = {RNA biology}, volume = {11}, number = {3}, pages = {205-206}, doi = {10.4161/rna.27701}, pmid = {24572567}, issn = {1555-8584}, mesh = {Biological Evolution ; History, 20th Century ; Metagenomics/methods ; Phylogeny ; RNA, Ribosomal, 16S/analysis/*genetics ; Ribotyping/*history ; }, abstract = {Fundamental observations about nature sometimes take a circuitous and utterly unpredictable course from bright idea to demonstrably practical impact. The tale of how Carl Woese's basic insights about microbial diversity eventually contributed to the emergence of a new field of science with numerous potential applications is just such a story.}, }
@article {pmid24569274, year = {2014}, author = {Berjaga, X and Coma, M and Meléndez, J and Puig, S and Colprim, J and Colomer, J}, title = {Granularity determination of activated sludge through on-line profiles by means of case-based reasoning.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {69}, number = {4}, pages = {760-767}, doi = {10.2166/wst.2013.776}, pmid = {24569274}, issn = {0273-1223}, mesh = {*Bioreactors ; Facility Design and Construction ; Filtration ; Models, Theoretical ; Principal Component Analysis ; *Sewage ; *Waste Disposal, Fluid ; }, abstract = {Aerobic granulation from floccular sludge is difficult to detect in first stages with the naked eye. This work proposes a combination of multi-way principal components and case-based reasoning to predict the granulation state of a sequencing batch reactor, based solely on the on-line registered profiles of common sensors (i.e. pH, dissolved oxygen and oxidation-reduction potential). The methodology is able to discriminate between two active sludge granularities (floccular and granular). Two different scenarios are presented: one in which both granularities are present, and another scenario for which the granular state is not initially available. Analysis reported pH as the key variable in the transition between both states according to its variation, and that, in general, the granularity of the process can be correctly predicted at the end of the anaerobic phase. This methodology improves process monitoring capabilities during granulation and is an on-line alternative to a microscope analysis before the batch release.}, }
@article {pmid24568033, year = {2013}, author = {Plasencia, A and Gich, F and Fillol, M and Borrego, CM}, title = {Phylogenetic characterization and quantification of ammonia-oxidizing archaea and bacteria from Lake Kivu in a long-term microcosm incubation.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {16}, number = {3}, pages = {177-189}, doi = {10.2436/20.1501.01.192}, pmid = {24568033}, issn = {1139-6709}, mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/*classification/genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics ; Lakes/chemistry/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; *Phylogeny ; Spain ; }, abstract = {A microcosm cultivation-based method was set up to investigate the growth of ammonia-oxidizing archaea (AOA), isolated from a water sample acquired at a depth of 50 m from the northern basin of Lake Kivu. For this purpose, both CARD-FISH and qPCR targeting of archaeal 16S rRNA and amoA genes were used. Archaeal cell growth at the end of the 246-day microcosm experiment accounted for 35% of the SybrGold-stained cells, which corresponded to 6.61 x 10(6) cells/ml and 1.76 +/- 0.09 x 10(6) archaeal 16S rRNA gene copies/ml. Clone libraries and DGGE fingerprinting confirmed the dominance of AOA phylotypes in the archaeal community microcosm. The majority of the identified archaeal 16S rRNA gene sequences in the clone libraries were affiliated with Thaumarchaeota Marine Group 1 .1a. Subsequent cultivation of the AOA community on deep-well microtiter plates in medium containing different carbon sources to stimulate archaeal growth failed to show significant differences in archaeal abundance (ANOVA t14 = -1.058, P = 0.308 and ANOVA t14= 1.584, P = 0.135 for yeast extract and simple organic acids, respectively). The lack of growth stimulation by organic compounds is in concordance with the oligotrophic status of Lake Kivu. Finally, the addition of antibiotics to the growth medium resulted in archaeal cell counts that were significantly lower than those obtained from cultures in antibiotic-free medium (ANOVA t14 = 12.12, P < 0.001).}, }
@article {pmid24567836, year = {2013}, author = {Semenov, AV and Elsas, JD and Glandorf, DC and Schilthuizen, M and Boer, WF}, title = {The use of statistical tools in field testing of putative effects of genetically modified plants on nontarget organisms.}, journal = {Ecology and evolution}, volume = {3}, number = {8}, pages = {2739-2750}, pmid = {24567836}, issn = {2045-7758}, abstract = {To fulfill existing guidelines, applicants that aim to place their genetically modified (GM) insect-resistant crop plants on the market are required to provide data from field experiments that address the potential impacts of the GM plants on nontarget organisms (NTO's). Such data may be based on varied experimental designs. The recent EFSA guidance document for environmental risk assessment (2010) does not provide clear and structured suggestions that address the statistics of field trials on effects on NTO's. This review examines existing practices in GM plant field testing such as the way of randomization, replication, and pseudoreplication. Emphasis is placed on the importance of design features used for the field trials in which effects on NTO's are assessed. The importance of statistical power and the positive and negative aspects of various statistical models are discussed. Equivalence and difference testing are compared, and the importance of checking the distribution of experimental data is stressed to decide on the selection of the proper statistical model. While for continuous data (e.g., pH and temperature) classical statistical approaches - for example, analysis of variance (ANOVA) - are appropriate, for discontinuous data (counts) only generalized linear models (GLM) are shown to be efficient. There is no golden rule as to which statistical test is the most appropriate for any experimental situation. In particular, in experiments in which block designs are used and covariates play a role GLMs should be used. Generic advice is offered that will help in both the setting up of field testing and the interpretation and data analysis of the data obtained in this testing. The combination of decision trees and a checklist for field trials, which are provided, will help in the interpretation of the statistical analyses of field trials and to assess whether such analyses were correctly applied. We offer generic advice to risk assessors and applicants that will help in both the setting up of field testing and the interpretation and data analysis of the data obtained in field testing.}, }
@article {pmid24565802, year = {2014}, author = {Zhao, HP and Ontiveros-Valencia, A and Tang, Y and Kim, BO and Vanginkel, S and Friese, D and Overstreet, R and Smith, J and Evans, P and Krajmalnik-Brown, R and Rittmann, B}, title = {Removal of multiple electron acceptors by pilot-scale, two-stage membrane biofilm reactors.}, journal = {Water research}, volume = {54}, number = {}, pages = {115-122}, doi = {10.1016/j.watres.2014.01.047}, pmid = {24565802}, issn = {1879-2448}, mesh = {Bacteria/growth &amp; development ; *Biofilms ; *Bioreactors ; *Electrons ; *Membranes, Artificial ; Nitrates/isolation &amp; purification ; Oxygen/isolation &amp; purification ; Perchlorates/isolation &amp; purification ; Pilot Projects ; Sulfates/isolation &amp; purification ; Time Factors ; Waste Disposal, Fluid ; Water Purification/*instrumentation/*methods ; }, abstract = {We studied the performance of a pilot-scale membrane biofilm reactor (MBfR) treating groundwater containing four electron acceptors: nitrate (NO3(-)), perchlorate (ClO4(-)), sulfate (SO4(2-)), and oxygen (O2). The treatment goal was to remove ClO4(-) from ∼200 μg/L to less than 6 μg/L. The pilot system was operated as two MBfRs in series, and the positions of the lead and lag MBfRs were switched regularly. The lead MBfR removed at least 99% of the O2 and 63-88% of NO3(-), depending on loading conditions. The lag MBfR was where most of the ClO4(-) reduction occurred, and the effluent ClO4(-) concentration was driven to as low as 4 μg/L, with most concentrations ≤10 μg/L. However, SO4(2-) reduction occurred in the lag MBfR when its NO3(-) + O2 flux was smaller than ∼0.18 g H2/m(2)-d, and this was accompanied by a lower ClO4(-) flux. We were able to suppress SO4(2-) reduction by lowering the H2 pressure and increasing the NO3(-) + O2 flux. We also monitored the microbial community using the quantitative polymerase chain reaction targeting characteristic reductase genes. Due to regular position switching, the lead and lag MBfRs had similar microbial communities. Denitrifying bacteria dominated the biofilm when the NO3(-) + O2 fluxes were highest, but sulfate-reducing bacteria became more important when SO4(2-) reduction was enhanced in the lag MBfR due to low NO3(-) + O2 flux. The practical two-stage strategy to achieve complete ClO4(-) and NO3(-) reduction while suppressing SO4(2-) reduction involved controlling the NO3(-) + O2 surface loading between 0.18 and 0.34 g H2/m(2)-d and using a low H2 pressure in the lag MBfR.}, }
@article {pmid24565058, year = {2013}, author = {Shang, L and Gardner, DP and Xu, W and Cannone, JJ and Miranker, DP and Ozer, S and Gutell, RR}, title = {Two accurate sequence, structure, and phylogenetic template-based RNA alignment systems.}, journal = {BMC systems biology}, volume = {7 Suppl 4}, number = {Suppl 4}, pages = {S13}, pmid = {24565058}, issn = {1752-0509}, support = {R01 GM067317/GM/NIGMS NIH HHS/United States ; R01 GM085337/GM/NIGMS NIH HHS/United States ; GM085337/GM/NIGMS NIH HHS/United States ; GM067317/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Computational Biology/*methods ; Databases, Genetic ; *Phylogeny ; RNA/*genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment/*methods ; *Templates, Genetic ; }, abstract = {BACKGROUND: The analysis of RNA sequences, once a small niche field for a small collection of scientists whose primary emphasis was the structure and function of a few RNA molecules, has grown most significantly with the realizations that 1) RNA is implicated in many more functions within the cell, and 2) the analysis of ribosomal RNA sequences is revealing more about the microbial ecology within all biological and environmental systems. The accurate and rapid alignment of these RNA sequences is essential to decipher the maximum amount of information from this data.<br><br>METHODS: Two computer systems that utilize the Gutell lab's RNA Comparative Analysis Database (rCAD) were developed to align sequences to an existing template alignment available at the Gutell lab's Comparative RNA Web (CRW) Site. Multiple dimensions of cross-indexed information are contained within the relational database--rCAD, including sequence alignments, the NCBI phylogenetic tree, and comparative secondary structure information for each aligned sequence. The first program, CRWAlign-1 creates a phylogenetic-based sequence profile for each column in the alignment. The second program, CRWAlign-2 creates a profile based on phylogenetic, secondary structure, and sequence information. Both programs utilize their profiles to align new sequences into the template alignment.<br><br>RESULTS: The accuracies of the two CRWAlign programs were compared with the best template-based rRNA alignment programs and the best de-novo alignment programs. We have compared our programs with a total of eight alternative alignment methods on different sets of 16S rRNA alignments with sequence percent identities ranging from 50% to 100%. Both CRWAlign programs were superior to these other programs in accuracy and speed.<br><br>CONCLUSIONS: Both CRWAlign programs can be used to align the very extensive amount of RNA sequencing that is generated due to the rapid next-generation sequencing technology. This latter technology is augmenting the new paradigm that RNA is intimately implicated in a significant number of functions within the cell. In addition, the use of bacterial 16S rRNA sequencing in the identification of the microbiome in many different environmental systems creates a need for rapid and highly accurate alignment of bacterial 16S rRNA sequences.}, }
@article {pmid24564823, year = {2014}, author = {Stephenson, RE and Gutierrez, D and Peters, C and Nichols, M and Boles, BR}, title = {Elucidation of bacteria found in car interiors and strategies to reduce the presence of potential pathogens.}, journal = {Biofouling}, volume = {30}, number = {3}, pages = {337-346}, pmid = {24564823}, issn = {1029-2454}, support = {R01 AI099065/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Infective Agents/*pharmacology ; *Automobiles ; Biofouling/*prevention &amp; control ; Colony Count, Microbial ; Environmental Exposure/analysis ; *Microbiota ; Silver/*pharmacology ; Surface Properties ; }, abstract = {The human microbiome is influenced by a number of factors, including environmental exposure to microbes. Because many humans spend a large amount of time in built environments, it can be expected that the microbial ecology of these environments will influence the human microbiome. In an attempt to further understand the microbial ecology of built environments, the microbiota of car interiors was analyzed using culture dependent and culture independent methods. While it was found that the number and type of bacteria varied widely among the cars and sites tested, Staphylococcus and Propionibacterium were nearly always the dominant genera found at the locations sampled. Because Staphylococcus is of particular concern to human health, the characteristics of this genus found in car interiors were investigated. Staphylococcus epidermidis, S. aureus, and S. warnerii were the most prevalent staphylococcal species found, and 22.6% of S. aureus strains isolated from shared community vehicles were resistant to methicillin. The reduction in the prevalence of pathogenic bacteria in cars by using silver-based antimicrobial surface coatings was also evaluated. Coatings containing 5% silver ion additives were applied to steering wheels, placed in cars for five months and were found to eliminate the presence of culturable pathogenic bacteria recovered from these sites relative to controls. Together, these results provide new insight into the microbiota found in an important built environment, the automobile, and potential strategies for controlling the presence of human pathogens.}, }
@article {pmid24564164, year = {2013}, author = {Ding, YL and Liu, J and Wang, YY}, title = {[Effects of biochar on microbial ecology in agriculture soil: a review].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {24}, number = {11}, pages = {3311-3317}, pmid = {24564164}, issn = {1001-9332}, mesh = {Charcoal/*chemistry ; Conservation of Natural Resources/methods ; Crops, Agricultural/*growth &amp; development ; *Ecosystem ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Biochar, as a new type of soil amendment, has been obtained considerable attention in the research field of environmental sciences worldwide. The studies on the effects of biochar in improving soil physical and chemical properties started quite earlier, and already covered the field of soil microbial ecology. However, most of the studies considered the soil physical and chemical properties and the microbial ecology separately, with less consideration of their interactions. This paper summarized and analyzed the interrelationships between the changes of soil physical and chemical properties and of soil microbial community after the addition of biochar. Biochar can not only improve soil pH value, strengthen soil water-holding capacity, increase soil organic matter content, but also affect soil microbial community structure, and alter the abundance of soil bacteria and fungi. After the addition of biochar, the soil environment and soil microorganisms are interacted each other, and promote the improvement of soil microbial ecological system together. This review was to provide a novel perspective for the in-depth studies of the effects of biochar on soil microbial ecology, and to promote the researches on the beneficial effects of biochar to the environment from ecological aspect. The methods to improve the effectiveness of biochar application were discussed, and the potential applications of biochar in soil bioremediation were further analyzed.}, }
@article {pmid24563192, year = {2014}, author = {Qadri, M and Rajput, R and Abdin, MZ and Vishwakarma, RA and Riyaz-Ul-Hassan, S}, title = {Diversity, molecular phylogeny, and bioactive potential of fungal endophytes associated with the Himalayan blue pine (Pinus wallichiana).}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {877-887}, pmid = {24563192}, issn = {1432-184X}, mesh = {Anti-Infective Agents/pharmacology ; Antifungal Agents/pharmacology ; Bacteria/drug effects ; *Biodiversity ; Conservation of Natural Resources ; DNA, Fungal/genetics ; DNA, Intergenic/genetics ; Endophytes/classification/drug effects/genetics/isolation &amp; purification/*physiology ; Fungi/classification/drug effects/genetics/isolation &amp; purification/*physiology ; India ; Molecular Sequence Data ; *Phylogeny ; Pinus/*microbiology ; Plant Leaves/microbiology ; Plant Stems/microbiology ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {In this study, we investigated the diversity of fungal endophytes associated with Pinus wallichiana from the Western Himalayas, with emphasis on comparison of endophytic communities harbored by the stem and needle tissues of the host and their antimicrobial potential. A total number of 130 isolates, comprising of 38 different genera, were recovered from 210 fragments of the plant. Among the isolated fungi, only a single isolate, Tritirachium oryzae, belonged to the Phylum Basidiomycota whereas the rest belonged to Ascomycota. Dothideomycetes was the dominant class with the highest isolation frequency of 49.2 %. The most frequent colonizers of the host were Alternaria spp., Pestalotiopsis spp., Preussia spp., and Sclerostagonospora spp. The diversity and species richness were higher in needle tissues than in the stems. Antimicrobial activities were displayed by extracts from a total number of 22 endophytes against one or more pathogens. Endophytes designated as P1N13 (Coniothyrium carteri), P2N8 (Thielavia subthermophila), P4S6b (Truncatella betulae), P7N10 (Cochliobolus australiensis), and P8S4 (Tritirachium oryzae) were highly active against Candida albicans. Broad spectrum antimicrobial activities were obtained with the extracts of P8-S4 (Tritirachium oryzae) and P5-N26 (Coniochaeta gigantospora) that were potentially active against the Gram-positive and Gram-negative bacteria as well as the fungal pathogen, Candida albicans. The most prominent antagonistic activity against fungal pathogens was shown by P8-S4 (Tritirachium oryzae), P5-N31a (Truncatella spadicea), and P5-N20 (Fusarium larvarum). Our findings indicate that Pinus wallichiana harbors a rich endophytic fungal community with potential antimicrobial activities. Further studies are needed to understand the ecology and evolutionary context of the associations between the Himalayan pine and its endophytes.}, }
@article {pmid24563191, year = {2014}, author = {Abell, GC and Ross, DJ and Keane, J and Holmes, BH and Robert, SS and Keough, MJ and Eyre, BD and Volkman, JK}, title = {Niche differentiation of ammonia-oxidising archaea (AOA) and bacteria (AOB) in response to paper and pulp mill effluent.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {758-768}, pmid = {24563191}, issn = {1432-184X}, mesh = {Archaea/classification/*drug effects/genetics/metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/classification/*drug effects/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Biota/*drug effects ; *Industrial Waste ; Molecular Sequence Data ; Oxidoreductases/genetics/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Rivers/*microbiology ; Sequence Analysis, DNA ; Tasmania ; Water Pollutants, Chemical/*pharmacology ; }, abstract = {Sediment organic loading has been shown to affect estuarine nitrification and denitrification, resulting in changes to sediment biogeochemistry and nutrient fluxes detrimental to estuarine health. This study examined the effects of organic loading on nutrient fluxes and microbial communities in sediments receiving effluent from a paper and pulp mill (PPM) by applying microcosm studies and molecular microbial ecology techniques. Three sites near the PPM outfall were compared to three control sites, one upstream and two downstream of the outfall. The control sites showed coupled nitrification-denitrification with minimal ammonia release from the sediment. In contrast, the impacted sites were characterised by nitrate uptake and substantial ammonia efflux from the sediments, consistent with a decoupling of nitrification and denitrification. Analysis of gene diversity demonstrated that the composition of nitrifier communities was not significantly different at the impacted sites compared to the control sites; however, analysis of gene abundance indicated that whilst there was no difference in total bacteria, total archaea or ammonia-oxidising archaea (AOA) abundance between the control and impacted sites, there was a significant reduction in ammonia-oxidising bacteria (AOB) at the impacted sites. The results of this study demonstrate an effect of organic loading on estuarine sediment biogeochemistry and highlight an apparent niche differentiation between AOA and AOB.}, }
@article {pmid24560870, year = {2014}, author = {Nieuwdorp, M and Gilijamse, PW and Pai, N and Kaplan, LM}, title = {Role of the microbiome in energy regulation and metabolism.}, journal = {Gastroenterology}, volume = {146}, number = {6}, pages = {1525-1533}, doi = {10.1053/j.gastro.2014.02.008}, pmid = {24560870}, issn = {1528-0012}, support = {P30 DK040561/DK/NIDDK NIH HHS/United States ; DK088661/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/*metabolism ; Bile Acids and Salts/metabolism ; Diabetes Mellitus/metabolism/microbiology ; *Energy Metabolism ; Gastrointestinal Diseases/metabolism/microbiology/therapy ; Homeostasis ; Host-Pathogen Interactions ; Humans ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; *Microbiota ; Obesity/metabolism/microbiology ; Probiotics/therapeutic use ; }, abstract = {Intestinal microbes regulate metabolic function and energy balance; an altered microbial ecology is believed to contribute to the development of several metabolic diseases. Relative species abundance and metabolic characteristics of the intestinal microbiota change substantially in those who are obese or have other metabolic disorders and in response to ingested nutrients or therapeutic agents. The mechanisms through which the intestinal microbiota and its metabolites affect host homeostasis are just beginning to be understood. We review the relationships between the intestinal microbiota and host metabolism, including energy intake, use, and expenditure, in relation to glucose and lipid metabolism. These associations, along with interactions among the intestinal microbiota, mucus layer, bile acids, and mucosal immune responses, reveal potential mechanisms by which the microbiota affect metabolism. We discuss how controlled studies involving direct perturbations of microbial communities in human and animal models are required to identify effective therapeutic targets in the microbiota.}, }
@article {pmid24557506, year = {2014}, author = {Castillo, D and Christiansen, RH and Espejo, R and Middelboe, M}, title = {Diversity and geographical distribution of Flavobacterium psychrophilum isolates and their phages: patterns of susceptibility to phage infection and phage host range.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {748-757}, pmid = {24557506}, issn = {1432-184X}, mesh = {Aquaculture ; Bacteriophages/genetics/isolation &amp; purification/*physiology ; Chile/epidemiology ; DNA, Bacterial/genetics ; Denmark/epidemiology ; Flavobacterium/classification/*genetics/isolation &amp; purification/*virology ; *Genetic Variation ; Geography ; Host Specificity ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; United States/epidemiology ; }, abstract = {Flavobacterium psychrophilum is an important fish pathogen worldwide that causes cold water disease (CWD) or rainbow trout fry syndrome (RTFS). Phage therapy has been suggested as an alternative method for the control of this pathogen in aquaculture. However, effective use of bacteriophages in disease control requires detailed knowledge about the diversity and dynamics of host susceptibility to phage infection. For this reason, we examined the genetic diversity of 49 F. psychrophilum strains isolated in three different areas (Chile, Denmark, and USA) through direct genome restriction enzyme analysis (DGREA) and their susceptibility to 33 bacteriophages isolated in Chile and Denmark, thus covering large geographical (>12,000 km) and temporal (>60 years) scales of isolation. An additional 40 phage-resistant isolates obtained from culture experiments after exposure to specific phages were examined for changes in phage susceptibility against the 33 phages. The F. psychrophilum and phage populations isolated from Chile and Denmark clustered into geographically distinct groups with respect to DGREA profile and host range, respectively. However, cross infection between Chilean phage isolates and Danish host isolates and vice versa was observed. Development of resistance to certain bacteriophages led to susceptibility to other phages suggesting that "enhanced infection" is potentially an important cost of resistance in F. psychrophilum, possibly contributing to the observed co-existence of phage-sensitive F. psychrophilum strains and lytic phages across local and global scales. Overall, our results showed that despite the identification of local communities of phages and hosts, some key properties determining phage infection patterns seem to be globally distributed.}, }
@article {pmid24555997, year = {2014}, author = {Tschurtschenthaler, M and Wang, J and Fricke, C and Fritz, TM and Niederreiter, L and Adolph, TE and Sarcevic, E and Künzel, S and Offner, FA and Kalinke, U and Baines, JF and Tilg, H and Kaser, A}, title = {Type I interferon signalling in the intestinal epithelium affects Paneth cells, microbial ecology and epithelial regeneration.}, journal = {Gut}, volume = {63}, number = {12}, pages = {1921-1931}, doi = {10.1136/gutjnl-2013-305863}, pmid = {24555997}, issn = {1468-3288}, support = {P 21530/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Antimicrobial Cationic Peptides ; Cell Proliferation/genetics ; *Colitis/etiology/immunology ; *Crohn Disease/genetics/immunology/pathology ; Dextran Sulfate/pharmacology ; Genetic Predisposition to Disease ; *Goblet Cells/metabolism/pathology ; Immunity, Mucosal/genetics ; Inflammation Mediators ; Intracellular Signaling Peptides and Proteins ; Mice ; Mice, Inbred C57BL ; Microbiota ; *Paneth Cells/metabolism/pathology ; Receptor, Interferon alpha-beta/*genetics ; Transcription, Genetic ; }, abstract = {OBJECTIVE: Intestinal epithelial cells (IECs) at the internal/external interface orchestrate the mucosal immune response. Paneth cells secrete antimicrobial peptides and inflammatory mediators, protect from pathogens and shape the commensal microbiota. Prompted by the genetic association of the locus harbouring the type I interferon (IFN) receptor (IFNAR1) with Crohn's disease, and a transcriptional signature for type I IFN signalling in Paneth cells, we studied the function of IFNAR1 in IECs.<br><br>DESIGN: Type I IFN signalling was studied in mice with conditional deletion of Ifnar1 in IECs. Phenotype was characterised at baseline, and gut microbiota composition was assessed by 16S rDNA ribotyping. The role of IFNAR1 was also investigated in experimental colitis induced by dextran sodium sulfate (DSS) and colitis-associated cancer induced by DSS in conjunction with azoxymethane (AOM).<br><br>RESULTS: Ifnar1(-/-(IEC)) mice displayed expansion of Paneth cell numbers and epithelial hyperproliferation compared with Ifnar1-sufficient littermates. While Ifnar1(-/-(IEC)) mice did not exhibit spontaneous inflammation or increased severity in DSS colitis compared with Ifnar1(+/+(IEC)) mice, they exhibited an increased tumour burden in the AOM/DSS model. Both hyperproliferation and tumour promotion were dependent on the microbial flora, as the differences between genotypes were marked upon separately housing mice, but disappeared when Ifnar1(-/-(IEC)) and Ifnar1(+/+(IEC)) mice were co-housed. Accordingly, ribotyping revealed marked differences between Ifnar1(-/-(IEC)) and Ifnar1(+/+(IEC)) mice that where diminished upon co-housing.<br><br>CONCLUSIONS: IFNAR1 in IECs, and Paneth cells in particular, contributes to the regulation of the host-microbiota relationship, with consequences for intestinal regeneration and colitis-associated tumour formation.}, }
@article {pmid24554641, year = {2014}, author = {Zhang, YQ and Lee, JC and Park, DJ and Lu, XX and Mou, XZ and Kim, CJ}, title = {Roseivivax roseus sp. nov., an alphaproteobacterium isolated from a solar saltern soil sample.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {64}, number = {Pt 5}, pages = {1743-1746}, doi = {10.1099/ijs.0.061630-0}, pmid = {24554641}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Molecular Sequence Data ; Phospholipids/chemistry ; *Phylogeny ; Pigmentation ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Rhodobacteraceae/*classification/genetics/isolation &amp; purification ; Salinity ; Sequence Analysis, DNA ; Sodium Chloride/analysis ; *Soil Microbiology ; Ubiquinone/chemistry ; }, abstract = {A pink, Gram-stain-negative, motile, halotolerant bacterium with subpolar flagellum, designated strain BH87090T, was isolated from a saline soil sample collected from the south-west coastal area of South Korea (125° 58' 58.08″ E 34° 45' 37.32″ N). The isolate formed opaque pink to red colonies on marine agar plates at 30 °C. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sulfoquinovosyl diacylglycerol, phosphatidylcholine and one unidentified phospholipid. The sole respiratory quinone was ubiquinone-10 (Q-10). The major cellular fatty acids were C18:1ω7c, C19:0 cyclo ω8c, C16:0 and 11-methyl C18:1ω7c. The genomic DNA G+C content was 61.8 mol%. These chemotaxonomic characteristics were all consistent with specific properties of the genus Roseivivax. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate affiliated to the cluster with members of the genus Roseivivax in the Roseobacter clade, which suggested that the strain belonged to the genus Roseivivax. However, the low 16S rRNA gene similarities (93.5-95.3%) of strain BH87090T with all the members of the genus Roseivivax indicated that it represented a novel species of the genus Roseivivax. On the basis of phenotypic and genotypic data, strain BH87090T should be classified as a novel species of the genus Roseivivax. The name Roseivivax roseus sp. nov. is proposed, with strain BH87090T (=DSM 23042T=KCTC 22650T) as the type strain.}, }
@article {pmid24553914, year = {2014}, author = {Xiong, J and Chu, H and Sun, H and Xue, X and Peng, F and Zhang, H}, title = {Divergent responses of soil fungi functional groups to short-term warming.}, journal = {Microbial ecology}, volume = {68}, number = {4}, pages = {708-715}, pmid = {24553914}, issn = {1432-184X}, mesh = {Basidiomycota/classification/genetics/physiology ; *Climate Change ; DNA Barcoding, Taxonomic ; Fungi/classification/genetics/*physiology ; *Hot Temperature ; Molecular Sequence Data ; RNA, Ribosomal, 18S/genetics ; Seasons ; *Soil Microbiology ; Tibet ; }, abstract = {Soil fungi fill pivotal ecological roles in biogeochemical processes, particularly dominating decomposition of lignin. Little is known, however, about the responses of different fungal groups to climate warming with respect to bacteria. In this study, using barcode pyrosequencing, we showed that short-term (15 months) of field exposure of an alpine meadow to warming (elevated 1 and 2 °C) did not markedly alter the overall soil fungal community structures and α-diversity on Tibetan Plateau, but the average β-diversity dramatically decreased in response to warming. However, soil respiration rates were stimulated in the growing season, which significantly (P < 0.001) correlated with soil temperature. Particularly, warming triggered dramatic shifts in the community structure of dominate Ascomycota and rare taxa (relative abundance < 0.1 %). In addition, the abundances of specific Basidiomycota-affiliated members significantly increased, while Ascomycota showed a range of responses to warming. Collectively, we conclude that the fungal communities are resistant to short-term warming, though variations are observed in certain species and rare taxa. This report indicates that changes in a relatively small subset of the soil fungal community are sufficient to produce substantial changes in function, such as CO(2) efflux rates.}, }
@article {pmid24553913, year = {2014}, author = {Nacke, H and Fischer, C and Thürmer, A and Meinicke, P and Daniel, R}, title = {Land use type significantly affects microbial gene transcription in soil.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {919-930}, pmid = {24553913}, issn = {1432-184X}, mesh = {Archaea/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Eukaryota/classification/genetics/isolation &amp; purification ; *Forests ; Grassland ; *Microbiota ; Molecular Sequence Data ; Phylogeny ; RNA, Messenger/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; *Transcriptome ; }, abstract = {Soil microorganisms play an essential role in sustaining biogeochemical processes and cycling of nutrients across different land use types. To gain insights into microbial gene transcription in forest and grassland soil, we isolated mRNA from 32 sampling sites. After sequencing of generated complementary DNA (cDNA), a total of 5,824,229 sequences could be further analyzed. We were able to assign nonribosomal cDNA sequences to all three domains of life. A dominance of bacterial sequences, which were affiliated to 25 different phyla, was found. Bacterial groups capable of aromatic compound degradation such as Phenylobacterium and Burkholderia were detected in significantly higher relative abundance in forest soil than in grassland soil. Accordingly, KEGG pathway categories related to degradation of aromatic ring-containing molecules (e.g., benzoate degradation) were identified in high abundance within forest soil-derived metatranscriptomic datasets. The impact of land use type forest on community composition and activity is evidently to a high degree caused by the presence of wood breakdown products. Correspondingly, bacterial groups known to be involved in lignin degradation and containing ligninolytic genes such as Burkholderia, Bradyrhizobium, and Azospirillum exhibited increased transcriptional activity in forest soil. Higher solar radiation in grassland presumably induced increased transcription of photosynthesis-related genes within this land use type. This is in accordance with high abundance of photosynthetic organisms and plant-infecting viruses in grassland.}, }
@article {pmid24553470, year = {2014}, author = {Williams, TJ and Allen, MA and DeMaere, MZ and Kyrpides, NC and Tringe, SG and Woyke, T and Cavicchioli, R}, title = {Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea.}, journal = {The ISME journal}, volume = {8}, number = {8}, pages = {1645-1658}, pmid = {24553470}, issn = {1751-7370}, mesh = {ATP-Binding Cassette Transporters/genetics ; Antarctic Regions ; Carbohydrate Metabolism ; Ecotype ; Genome, Archaeal ; Genomics ; Halobacteriaceae/classification/genetics/*metabolism ; Lakes/*microbiology ; Nitrogen/metabolism ; Salinity ; }, abstract = {Deep Lake in Antarctica is a cold, hypersaline system where four types of haloarchaea representing distinct genera comprise >70% of the lake community: strain tADL ∼44%, strain DL31 ∼18%, Halorubrum lacusprofundi ∼10% and strain DL1 ∼0.3%. By performing comparative genomics, growth substrate assays, and analyses of distribution by lake depth, size partitioning and lake nutrient composition, we were able to infer important metabolic traits and ecophysiological characteristics of the four Antarctic haloarchaea that contribute to their hierarchical persistence and coexistence in Deep Lake. tADL is characterized by a capacity for motility via flagella (archaella) and gas vesicles, a highly saccharolytic metabolism, a preference for glycerol, and photoheterotrophic growth. In contrast, DL31 has a metabolism specialized in processing proteins and peptides, and appears to prefer an association with particulate organic matter, while lacking the genomic potential for motility. H. lacusprofundi is the least specialized, displaying a genomic potential for the utilization of diverse organic substrates. The least abundant species, DL1, is characterized by a preference for catabolism of amino acids, and is the only one species that lacks genes needed for glycerol degradation. Despite the four haloarchaea being distributed throughout the water column, our analyses describe a range of distinctive features, including preferences for substrates that are indicative of ecological niche partitioning. The individual characteristics could be responsible for shaping the composition of the haloarchaeal community throughout the lake by enabling selection of ecotypes and maintaining sympatric speciation.}, }
@article {pmid24553469, year = {2014}, author = {Seyler, LM and McGuinness, LM and Kerkhof, LJ}, title = {Crenarchaeal heterotrophy in salt marsh sediments.}, journal = {The ISME journal}, volume = {8}, number = {7}, pages = {1534-1543}, pmid = {24553469}, issn = {1751-7370}, mesh = {Carbon Isotopes ; Crenarchaeota/classification/genetics/*metabolism ; Genes, rRNA ; Geologic Sediments/microbiology ; Heterotrophic Processes/*genetics ; Isotope Labeling ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Archaeal/*genetics ; RNA, Ribosomal, 16S/*genetics ; Salinity ; *Wetlands ; }, abstract = {Mesophilic Crenarchaeota (also known as Thaumarchaeota) are ubiquitous and abundant in marine habitats. However, very little is known about their metabolic function in situ. In this study, salt marsh sediments from New Jersey were screened via stable isotope probing (SIP) for heterotrophy by amending with a single (13)C-labeled compound (acetate, glycine or urea) or a complex (13)C-biopolymer (lipids, proteins or growth medium (ISOGRO)). SIP incubations were done at two substrate concentrations (30-150 μM; 2-10 mg ml(-1)), and (13)C-labeled DNA was analyzed by terminal restriction fragment length polymorphism (TRFLP) analysis of 16S rRNA genes. To test for autotrophy, an amendment with (13)C-bicarbonate was also performed. Our SIP analyses indicate salt marsh crenarchaea are heterotrophic, double within 2-3 days and often compete with heterotrophic bacteria for the same organic substrates. A clone library of (13)C-amplicons was screened to find matches to the (13)C-TRFLP peaks, with seven members of the Miscellaneous Crenarchaeal Group and seven members from the Marine Group 1.a Crenarchaeota being discerned. Some of these crenarchaea displayed a preference for particular carbon sources, whereas others incorporated nearly every (13)C-substrate provided. The data suggest salt marshes may be an excellent model system for studying crenarchaeal metabolic capabilities and can provide information on the competition between crenarchaea and other microbial groups to improve our understanding of microbial ecology.}, }
@article {pmid24553468, year = {2014}, author = {Mendes, LW and Kuramae, EE and Navarrete, AA and van Veen, JA and Tsai, SM}, title = {Taxonomical and functional microbial community selection in soybean rhizosphere.}, journal = {The ISME journal}, volume = {8}, number = {8}, pages = {1577-1587}, pmid = {24553468}, issn = {1751-7370}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; *Metagenome ; Nitrogen/analysis ; Phosphorus ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; *Glycine max ; }, abstract = {This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors.}, }
@article {pmid24553467, year = {2014}, author = {Reichardt, N and Duncan, SH and Young, P and Belenguer, A and McWilliam Leitch, C and Scott, KP and Flint, HJ and Louis, P}, title = {Phylogenetic distribution of three pathways for propionate production within the human gut microbiota.}, journal = {The ISME journal}, volume = {8}, number = {6}, pages = {1323-1335}, pmid = {24553467}, issn = {1751-7370}, mesh = {Acrylates/metabolism ; Bacteria/classification/isolation &amp; purification/*metabolism ; Fermentation ; Gastrointestinal Tract/*microbiology ; Gram-Positive Bacteria/classification/isolation &amp; purification/metabolism ; Humans ; *Microbiota ; Phylogeny ; Propionates/*metabolism ; Propylene Glycols/metabolism ; Succinates/metabolism ; }, abstract = {Propionate is produced in the human large intestine by microbial fermentation and may help maintain human health. We have examined the distribution of three different pathways used by bacteria for propionate formation using genomic and metagenomic analysis of the human gut microbiota and by designing degenerate primer sets for the detection of diagnostic genes for these pathways. Degenerate primers for the acrylate pathway (detecting the lcdA gene, encoding lactoyl-CoA dehydratase) together with metagenomic mining revealed that this pathway is restricted to only a few human colonic species within the Lachnospiraceae and Negativicutes. The operation of this pathway for lactate utilisation in Coprococcus catus (Lachnospiraceae) was confirmed using stable isotope labelling. The propanediol pathway that processes deoxy sugars such as fucose and rhamnose was more abundant within the Lachnospiraceae (based on the pduP gene, which encodes propionaldehyde dehydrogenase), occurring in relatives of Ruminococcus obeum and in Roseburia inulinivorans. The dominant source of propionate from hexose sugars, however, was concluded to be the succinate pathway, as indicated by the widespread distribution of the mmdA gene that encodes methylmalonyl-CoA decarboxylase in the Bacteroidetes and in many Negativicutes. In general, the capacity to produce propionate or butyrate from hexose sugars resided in different species, although two species of Lachnospiraceae (C. catus and R. inulinivorans) are now known to be able to switch from butyrate to propionate production on different substrates. A better understanding of the microbial ecology of short-chain fatty acid formation may allow modulation of propionate formation by the human gut microbiota.}, }
@article {pmid24552056, year = {2013}, author = {Kim, J and Kim, W and Lee, C}, title = {Absolute dominance of hydrogenotrophic methanogens in full-scale anaerobic sewage sludge digesters.}, journal = {Journal of environmental sciences (China)}, volume = {25}, number = {11}, pages = {2272-2280}, doi = {10.1016/s1001-0742(12)60299-x}, pmid = {24552056}, issn = {1001-0742}, mesh = {Anaerobiosis ; *Bioreactors ; Euryarchaeota/classification/*metabolism ; Phylogeny ; Sewage/*microbiology ; }, abstract = {Anaerobic digestion (AD) is gaining increasing attention due to the ability to covert organic pollutants into energy-rich biogas and, accordingly, growing interest is paid to the microbial ecology of AD systems. Despite extensive efforts, AD microbial ecology is still limitedly understood, especially due to the lack of quantitative information on the structures and dynamics of AD microbial communities. Such knowledge gap is particularly pronounced in sewage sludge AD processes although treating sewage sludge is among the major practical applications of AD. Therefore, we examined the microbial communities in three full-scale sewage sludge digesters using qualitative and quantitative molecular techniques in combination: denaturing gradient gel electrophoresis (DGGE) and real-time polymerase chain reaction (PCR). Eight out of eleven bacterial sequences retrieved from the DGGE analysis were not affiliated to any known species while all eleven archaeal sequences were assigned to known methanogen species. Quantitative real-time PCR analysis revealed that, based on the 16S rRNA gene abundance, the hydrogenotrophic order Methanomicrobiales is the most dominant methanogen group (> 94% of the total methanogen population) in all digesters. This corresponds well to the prevailing occurrence of the DGGE bands related to Methanolinea and Methanospirillum, both belonging to the order Methanomicrobiales, in all sludge samples. It is therefore suggested that hydrogenotrophic methanogens, especially Methanomicrobiales strains, are likely the major players responsible for biogas production in the digesters studied. Our observation is contrary to the conventional understanding that aceticlastic methanogens generally dominate methanogen communities in stable AD environments, suggesting the need for further studies on the dominance relationship in various AD systems.}, }
@article {pmid24549747, year = {2014}, author = {Al Kassaa, I and Hamze, M and Hober, D and Chihib, NE and Drider, D}, title = {Identification of vaginal lactobacilli with potential probiotic properties isolated from women in North Lebanon.}, journal = {Microbial ecology}, volume = {67}, number = {3}, pages = {722-734}, pmid = {24549747}, issn = {1432-184X}, mesh = {Adult ; *Antibiosis ; Bacteria/genetics/isolation &amp; purification ; Candida albicans/physiology ; DNA Fingerprinting ; Female ; Humans ; Lactobacillus/genetics/*isolation &amp; purification/*physiology ; Lebanon ; Middle Aged ; Polymerase Chain Reaction ; Probiotics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Vagina/*microbiology ; Young Adult ; }, abstract = {The aim of this work was to study the diversity of vaginal lactobacilli in Lebanese women and to evaluate the antagonism, hydrophobicity, and safety characteristics of these strains. This study was performed on samples from 135 women who visited a gynecology clinic in the north of Lebanon, between September 2012 and January 2013. From these samples, 53 different isolates of vaginal lactobacilli were collected from vaginal swabs and identified using biochemical and molecular methods. The use of genotypic Rep-PCR fingerprinting allowed for the organization of these isolates into 23 different groups. Seven of the isolated lactobacilli were antagonistic against the following vaginal pathogens: Gardnerella vaginalis CIP7074T, Staphylococcus aureus ATCC33862, Escherichia coli CIP103982, and Candida albicans ATCC10231. The antagonistic lactobacilli strains were then identified using 16S rDNA sequence. The data of this study show that the antagonistic lactobacilli were non-hemolytic, sensitive to most antibiotic tests, free of plasmid DNA, and exhibited interesting hydrophobicity and autoaggregation properties positioning them as potential candidates for probiotic design.}, }
@article {pmid24549746, year = {2014}, author = {Murugan, R and Loges, R and Taube, F and Sradnick, A and Joergensen, RG}, title = {Changes in soil microbial biomass and residual indices as ecological indicators of land use change in temperate permanent grassland.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {907-918}, pmid = {24549746}, issn = {1432-184X}, mesh = {*Agriculture ; *Bacterial Physiological Phenomena ; Biomass ; *Biota ; Carbon/metabolism ; Ergosterol/metabolism ; Fertilizers/analysis ; Fungi/*physiology ; Germany ; *Grassland ; Manure/analysis ; Microbiota ; Nitrogen/metabolism ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The relationship between microbial biomass, residues and their contribution to microbial turnover is important to understand ecosystem C storage. The effects of permanent grassland (100 % ryegrass--PG), conversion to modified grassland (mixture of grass and clover--MG) or maize monoculture (MM) on the dynamics of soil organic C (SOC), microbial biomass, fungal ergosterol and microbial residues (bacterial muramic acid and fungal glucosamine) were investigated. Cattle slurry was applied to quantify the effects of fertilisation on microbial residues and functional diversity of microbial community across land use types. Slurry application significantly increased the stocks of microbial biomass C and S and especially led to a shift in microbial residues towards bacterial tissue. The MM treatment decreased the stocks of SOC, microbial biomass C, N and S and microbial residues compared with the PG and MG treatments at 0-40 cm depth. The MM treatment led to a greater accumulation of saprotrophic fungi, as indicated by the higher ergosterol-to-microbial biomass C ratio and lower microbial biomass C/S ratio compared with the grassland treatments. The absence of a white clover population in the PG treatment caused a greater accumulation of fungal residues (presumably arbuscular mycorrhizal fungi (AMF), which do not contain ergosterol but glucosamine), as indicated by the significantly higher fungal C-to-bacterial C ratio and lower ergosterol-to-microbial biomass C ratio compared with the MG treatment. In addition to these microbial biomass and residual indices, the community level physiological profiles (CLPP) demonstrated distinct differences between the PG and MG treatments, suggesting the potential of these measurements to act as an integrative indicator of soil functioning.}, }
@article {pmid24549745, year = {2014}, author = {Kim, M and Kim, WS and Tripathi, BM and Adams, J}, title = {Distinct bacterial communities dominate tropical and temperate zone leaf litter.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {837-848}, pmid = {24549745}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/genetics ; *Forests ; Malaysia ; Molecular Sequence Data ; Plant Leaves/*microbiology ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, RNA ; *Soil Microbiology ; Tropical Climate ; }, abstract = {Little is known of the bacterial community of tropical rainforest leaf litter and how it might differ from temperate forest leaf litter and from the soils underneath. We sampled leaf litter in a similarly advanced stage of decay, and for comparison, we also sampled the surface layer of soil, at three tropical forest sites in Malaysia and four temperate forest sites in South Korea. Illumina sequencing targeting partial bacterial 16S ribosomal ribonucleic acid (rRNA) gene revealed that the bacterial community composition of both temperate and tropical litter is quite distinct from the soils underneath. Litter in both temperate and tropical forest was dominated by Proteobacteria and Actinobacteria, while soil is dominated by Acidobacteria and, to a lesser extent, Proteobacteria. However, bacterial communities of temperate and tropical litter clustered separately from one another on an ordination. The soil bacterial community structures were also distinctive to each climatic zone, suggesting that there must be a climate-specific biogeographical pattern in bacterial community composition. The differences were also found in the level of diversity. The temperate litter has a higher operational taxonomic unit (OTU) diversity than the tropical litter, paralleling the trend in soil diversity. Overall, it is striking that the difference in community composition between the leaf litter and the soil a few centimeters underneath is about the same as that between leaf litter in tropical and temperate climates, thousands of kilometers apart. However, one substantial difference was that the leaf litter of two tropical forest sites, Meranti and Forest Research Institute Malaysia (FRIM), was overwhelmingly dominated by the single genus Burkholderia, at 37 and 23 % of reads, respectively. The 454 sequencing result showed that most Burkholderia species in tropical leaf litter belong to nonpathogenic "plant beneficial" lineages. The differences from the temperate zone in the bacterial community of tropical forest litter may be partly a product of its differing chemistry, although the unvarying climate might also play a role, as might interactions with other organisms such as fungi. The single genus Burkholderia may be seen as potentially playing a major role in decomposition and nutrient cycling in tropical forests, but apparently not in temperate forests.}, }
@article {pmid24535161, year = {2014}, author = {Guo, F and Zhang, T}, title = {Detecting the nonviable and heat-tolerant bacteria in activated sludge by minimizing DNA from dead cells.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {829-836}, pmid = {24535161}, issn = {1432-184X}, mesh = {Azides/metabolism ; Bacteria/genetics/growth &amp; development/*isolation &amp; purification ; Bacteriological Techniques/*methods ; DNA, Bacterial/genetics ; Environmental Monitoring/*methods ; Feces/microbiology ; Hot Temperature ; Humans ; *Microbial Viability ; Polymerase Chain Reaction ; Propidium/analogs &amp; derivatives/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; Sewage/*microbiology ; }, abstract = {Propidium monoazide (PMA) has been used to determine viable microorganisms for clinical and environmental samples since selected naked DNA which was covalently cross-linked by this dye could not be PCR-amplified. In this study, we applied PMA to the activated sludge samples composed of complex bacterial populations to investigate the viability of human fecal bacteria and to determine the heat-tolerant bacteria by high-throughput sequencing of 16S ribosomal DNA (rDNA) V3 region. The methodological evaluation suggested the validity, and about 2-3 magnitude signals decreasing from the stained DNA were observed. However, the nest PCR, which was previously conducted to further minimize signals from dead cells, seemed not suitable perhaps due to the limitation of the primers. On one hand, for typical human fecal bacteria, less than half of them were viable, and most genera exhibited the similar viable percentages. It was interesting that many "unclassified bacteria" showed low viability, implying their sensitivity to environmental change. On the other hand, after heating at 60 °C for 4 h, the bacteria with high survival rate in activated sludge samples included those reported thermophiles or heat-tolerant lineages, such as Anoxybacillus and diverse species in Actinobacteria, and some novel ones, such as Gp16 subdivision in Acidobacteria. In summary, our results took a glance at the fate of fecal bacteria during sewage treatment and established an example for identifying tolerant species to lethal shocks in a complex community.}, }
@article {pmid24533086, year = {2014}, author = {Keller-Costa, T and Jousset, A and van Overbeek, L and van Elsas, JD and Costa, R}, title = {The freshwater sponge Ephydatia fluviatilis harbours diverse Pseudomonas species (Gammaproteobacteria, Pseudomonadales) with broad-spectrum antimicrobial activity.}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e88429}, pmid = {24533086}, issn = {1932-6203}, mesh = {Animals ; *Antibiosis ; Biofilms ; Gene Expression Regulation, Bacterial ; Genome, Bacterial ; Genotype ; Likelihood Functions ; Microbial Sensitivity Tests ; Multivariate Analysis ; Phylogeny ; Polymerase Chain Reaction ; Porifera/*microbiology ; Principal Component Analysis ; Pseudomonas/*physiology ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {Bacteria are believed to play an important role in the fitness and biochemistry of sponges (Porifera). Pseudomonas species (Gammaproteobacteria, Pseudomonadales) are capable of colonizing a broad range of eukaryotic hosts, but knowledge of their diversity and function in freshwater invertebrates is rudimentary. We assessed the diversity, structure and antimicrobial activities of Pseudomonas spp. in the freshwater sponge Ephydatia fluviatilis. Polymerase Chain Reaction--Denaturing Gradient Gel Electrophoresis (PCR-DGGE) fingerprints of the global regulator gene gacA revealed distinct structures between sponge-associated and free-living Pseudomonas communities, unveiling previously unsuspected diversity of these assemblages in freshwater. Community structures varied across E. fluviatilis specimens, yet specific gacA phylotypes could be detected by PCR-DGGE in almost all sponge individuals sampled over two consecutive years. By means of whole-genome fingerprinting, 39 distinct genotypes were found within 90 fluorescent Pseudomonas isolates retrieved from E. fluviatilis. High frequency of in vitro antibacterial (49%), antiprotozoan (35%) and anti-oomycetal (32%) activities was found among these isolates, contrasting less-pronounced basidiomycetal (17%) and ascomycetal (8%) antagonism. Culture extracts of highly predation-resistant isolates rapidly caused complete immobility or lysis of cells of the protozoan Colpoda steinii. Isolates tentatively identified as P. jessenii, P. protegens and P. oryzihabitans showed conspicuous inhibitory traits and correspondence with dominant sponge-associated phylotypes registered by cultivation-independent analysis. Our findings suggest that E. fluviatilis hosts both transient and persistent Pseudomonas symbionts displaying antimicrobial activities of potential ecological and biotechnological value.}, }
@article {pmid24531645, year = {2014}, author = {Zhang, XZ and Xie, JJ and Sun, FL}, title = {Effects of three polycyclic aromatic hydrocarbons on sediment bacterial community.}, journal = {Current microbiology}, volume = {68}, number = {6}, pages = {756-762}, pmid = {24531645}, issn = {1432-0991}, mesh = {Bacteria/*classification/*metabolism ; Biota/*drug effects ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Mangrove sediment is susceptible to anthropogenic pollutants, including polycyclic aromatic hydrocarbons (PAHs). However, the effects of PAHs on the bacterial diversity in mangrove sediment have been rarely studied. In the present study, the effects of three types of PAHs (Naphthalene, Fluorene, and Pyrene) at three doses on sediment microbial populations were investigated by using denaturing gradient gel electrophoresis (DGGE). After 7 and 24 days of incubation of the three types of PAHs, markedly different patterns were observed in the bacterial communities. Overall, the diversity of bacterial community was suppressed before 7 days but was promoted after 24 days. Multidimensional scaling analysis suggested that the composition of bacterial communities after 7 days was distinctly distant from that after 24 days. Also despite a slight shift of bacterial abundance, the bacterial communities were relatively steady in these sediments after exposure to PAHs. In addition, DGGE suggested that the applications of three PAHs (especially PYR) had considerable effects on bacterial communities. For phylogenetic analysis, bacteria species belonging to Proteobacteria (α-, β-, and γ-), Actinobacteria, Chloroflexi, Bacteroidetes, and Planctomycetes were changed dramatically after treatment with PAHs. These results suggest that PAHs play key roles in the change of bacterial community, which may be important for understanding the relationship between PAHs and sediment microbial ecology.}, }
@article {pmid24531374, year = {2014}, author = {Vestergaard, G and Garrett, RA and Shah, SA}, title = {CRISPR adaptive immune systems of Archaea.}, journal = {RNA biology}, volume = {11}, number = {2}, pages = {156-167}, pmid = {24531374}, issn = {1555-8584}, mesh = {Adaptation, Physiological ; Archaea/classification/*immunology ; CRISPR-Associated Proteins/classification/genetics ; CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; DNA, Archaeal ; Evolution, Molecular ; Genes, Archaeal ; Genome, Archaeal ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {CRISPR adaptive immune systems were analyzed for all available completed genomes of archaea, which included representatives of each of the main archaeal phyla. Initially, all proteins encoded within, and proximal to, CRISPR-cas loci were clustered and analyzed using a profile-profile approach. Then cas genes were assigned to gene cassettes and to functional modules for adaptation and interference. CRISPR systems were then classified primarily on the basis of their concatenated Cas protein sequences and gene synteny of the interference modules. With few exceptions, they could be assigned to the universal Type I or Type III systems. For Type I, subtypes I-A, I-B, and I-D dominate but the data support the division of subtype I-B into two subtypes, designated I-B and I-G. About 70% of the Type III systems fall into the universal subtypes III-A and III-B but the remainder, some of which are phyla-specific, diverge significantly in Cas protein sequences, and/or gene synteny, and they are classified separately. Furthermore, a few CRISPR systems that could not be assigned to Type I or Type III are categorized as variant systems. Criteria are presented for assigning newly sequenced archaeal CRISPR systems to the different subtypes. Several accessory proteins were identified that show a specific gene linkage, especially to Type III interference modules, and these may be cofunctional with the CRISPR systems. Evidence is presented for extensive exchange having occurred between adaptation and interference modules of different archaeal CRISPR systems, indicating the wide compatibility of the functionally diverse interference complexes with the relatively conserved adaptation modules.}, }
@article {pmid24527795, year = {2014}, author = {Nunez, M and Hammer, H}, title = {Microbial specialists in below-grade foundation walls in Scandinavia.}, journal = {Indoor air}, volume = {24}, number = {5}, pages = {543-551}, doi = {10.1111/ina.12095}, pmid = {24527795}, issn = {1600-0668}, mesh = {Construction Materials/*microbiology ; *Environmental Microbiology ; *Microbial Consortia ; Norway ; }, abstract = {Below-grade foundation walls are often exposed to excessive moisture by water infiltration, condensation, leakage, or lack of ventilation. Microbial growth in these structures depends largely on environmental factors, elapsed time, and the type of building materials and construction setup. The ecological preferences of Actinomycetes (Actinobacteria) and the molds Ascotricha chartarum, Myxotrichum chartarum (Ascomycota), Geomyces pannorum, and Monocillium sp. (Hyphomycetes) have been addressed based on analyses of 1764 samples collected in below-grade spaces during the period of 2001-2012. Our results show a significant correlation between these taxa and moist foundation walls as ecological niches. Substrate preference was the strongest predictor of taxa distribution within the wall, but the taxa's physiological needs, together with gradients of abiotic factors within the wall structure, also played a role. Our study describes for the first time how the wall environment affects microbial growth.}, }
@article {pmid24526362, year = {2014}, author = {Courtens, EN and Boon, N and De Schryver, P and Vlaeminck, SE}, title = {Increased salinity improves the thermotolerance of mesophilic nitrification.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {10}, pages = {4691-4699}, doi = {10.1007/s00253-014-5540-y}, pmid = {24526362}, issn = {1432-0614}, mesh = {Bacteria/drug effects/*metabolism/radiation effects ; Bioreactors/microbiology ; Hot Temperature ; Nitrification/*drug effects/*radiation effects ; *Salinity ; Sodium Chloride/metabolism ; }, abstract = {Nitrification is a well-studied and established process to treat ammonia in wastewater. Although thermophilic nitrification could avoid cooling costs for the treatment of warm wastewaters, applications above 40 °C remain a significant challenge. This study tested the effect of salinity on the thermotolerance of mesophilic nitrifying sludge (34 °C). In batch tests, 5 g NaCl L(-1) increased the activity of aerobic ammonia-oxidizing bacteria (AerAOB) by 20-21 % at 40 and 45 °C. For nitrite-oxidizing bacteria (NOB), the activity remained unaltered at 40 °C, yet decreased by 83 % at 45 °C. In a subsequent long-term continuous reactor test, temperature was increased from 34 to 40, 42.5, 45, 47.5 and 50 °C. The AerAOB activity showed 65 and 37 % higher immediate resilience in the salt reactor (7.5 g NaCl L(-1)) for the first two temperature transitions and lost activity from 45 °C onwards. NOB activity, in contrast to the batch tests, was 37 and 21 % more resilient in the salt reactor for the first two transitions, while no difference was observed for the third temperature transition. The control reactor lost NOB activity at 47.5 °C, while the salt reactor only lost activity at 50 °C. Overall, this study demonstrates salt amendment as a tool for a more efficient temperature transition for mesophilic sludge (34 °C) and eventually higher nitrification temperatures.}, }
@article {pmid24525216, year = {2014}, author = {Diamantis, V and Eftaxias, A and Bundervoet, B and Verstraete, W}, title = {Performance of the biosorptive activated sludge (BAS) as pre-treatment to UF for decentralized wastewater reuse.}, journal = {Bioresource technology}, volume = {156}, number = {}, pages = {314-321}, doi = {10.1016/j.biortech.2014.01.061}, pmid = {24525216}, issn = {1873-2976}, mesh = {Adsorption ; Ammonia/analysis ; Biodegradation, Environmental ; Biological Oxygen Demand Analysis ; Costs and Cost Analysis ; Membranes, Artificial ; Permeability ; Phosphorus/analysis ; *Recycling ; Sewage/*chemistry ; Solubility ; Ultrafiltration/economics/*methods ; Waste Disposal, Fluid ; Wastewater/*chemistry/economics ; }, abstract = {A biosorptive activated sludge (BAS) was operated at lab-scale with diluted and concentrated municipal wastewater to study the efficiency of removal of organics (particulate and soluble COD) and recovery of nutrients (TKN, ammonia, phosphorus). The system performed significantly better with concentrated wastewater, where COD removal efficiency was 80% at organic loading rates between 10 and 20kg m(-3)d(-1). Supplementation of ferrous iron at 20mg L(-1), significantly improved both the removal of particulate, soluble COD and phosphorus. The effluent from the BAS was further treated using an ultrafiltration process with backwashing. The average permeate flux (at constant TMP=0.3bar) increased from 23 to 28 and 34L m(-2)h(-1) when raw sewage, BAS without iron, and iron respectively were tested. The proposed technology is compact, efficient and suitable for decentralized water reuse, while the capital and operational expenses were calculated as 0.64 and 0.43€ m(-3), respectively.}, }
@article {pmid24525065, year = {2014}, author = {Huang, P and Li, L and Kotay, SM and Goel, R}, title = {Carbon mass balance and microbial ecology in a laboratory scale reactor achieving simultaneous sludge reduction and nutrient removal.}, journal = {Water research}, volume = {53}, number = {}, pages = {153-167}, doi = {10.1016/j.watres.2013.12.035}, pmid = {24525065}, issn = {1879-2448}, mesh = {Ammonia/metabolism ; Betaproteobacteria/genetics/*metabolism ; *Bioreactors ; Carbon/*metabolism ; DNA, Bacterial/genetics ; Molecular Sequence Data ; Oxidation-Reduction ; Oxygen/*metabolism ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Polyphosphates/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*chemistry ; }, abstract = {Solids reduction in activated sludge processes (ASP) at source using process manipulation has been researched widely over the last two-decades. However, the absence of nutrient removal component, lack of understanding on the organic carbon, and limited information on key microbial community in solids minimizing ASP preclude the widespread acceptance of sludge minimizing processes. In this manuscript, we report simultaneous solids reduction through anaerobiosis along with nitrogen and phosphorus removals. The manuscript also reports carbon mass balance using stable isotope of carbon, microbial ecology of nitrifiers and polyphosphate accumulating organisms (PAOs). Two laboratory scale reactors were operated in anaerobic-aerobic-anoxic (A(2)O) mode. One reactor was run in the standard mode (hereafter called the control-SBR) simulating conventional A(2)O type of activated sludge process and the second reactor was run in the sludge minimizing mode (called the modified-SBR). Unlike other research efforts where the sludge minimizing reactor was maintained at nearly infinite solids retention time (SRT). To sustain the efficient nutrient removal, the modified-SBR in this research was operated at a very small solids yield rather than at infinite SRT. Both reactors showed consistent NH3-N, phosphorus and COD removals over a period of 263 days. Both reactors also showed active denitrification during the anoxic phase even if there was no organic carbon source available during this phase, suggesting the presence of denitrifying PAOs (DNPAOs). The observed solids yield in the modified-SBR was 60% less than the observed solids yield in the control-SBR. Specific oxygen uptake rate (SOUR) for the modified-SBR was almost 44% more than the control-SBR under identical feeding conditions, but was nearly the same for both reactors under fasting conditions. The modified-SBR showed greater diversity of ammonia oxidizing bacteria and PAOs compared to the control-SBR. The diversity of PAOs in the modified-SBR was even more interesting in which case novel clades of Candidatus Accumulibacter phosphatis (CAP), an uncultured but widely found PAOs, were found.}, }
@article {pmid24523444, year = {2014}, author = {Han, SI and Lee, JC and Ohta, H and Whang, KS}, title = {Sphingomonas oligoaromativorans sp. nov., an oligotrophic bacterium isolated from a forest soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {64}, number = {Pt 5}, pages = {1679-1684}, doi = {10.1099/ijs.0.052894-0}, pmid = {24523444}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Molecular Sequence Data ; *Phylogeny ; Pigmentation ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; *Soil Microbiology ; Spermidine/analogs &amp; derivatives/chemistry ; Sphingomonas/*classification/genetics/isolation &amp; purification ; Trees/microbiology ; Ubiquinone/chemistry ; }, abstract = {A halo- and organo-sensitive oligotrophic bacterium, designated strain SY-6T, was isolated from humus forest soil at Gyeryong mountain in Korea. Cells of the strain were Gram-negative, strictly aerobic, non-motile rods and the strain formed yellow-pigmented colonies on 100-fold-diluted nutrient broth. Strain SY-6T grew at pH 6.0-7.0 (optimal growth at pH 7.0), at 10-37 °C (optimal growth at 28 °C) and at salinities of 0-0.5% (w/v) NaCl, growing optimally at 0.01% (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain SY-6T was shown to belong to the genus Sphingomonas and showed the closest phylogenetic similarity to Sphingomonas polyaromaticivorans B2-7T (96.7%). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. The predominant ubiquinone and polyamine were Q-10 and sym-homospermidine, respectively. The major fatty acids were C18:1ω7c and C16:0. The DNA G+C content of the novel isolate was 65.3 mol%. On the basis of the evidence from this polyphasic study, strain SY-6T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas oligoaromativorans sp. nov. is proposed. The type strain is SY-6T (=KACC 12948T=NBRC 105508T).}, }
@article {pmid24517495, year = {2014}, author = {Bukowska, A and Bielczyńska, A and Karnkowska, A and Chróst, RJ and Jasser, I}, title = {Molecular (PCR-DGGE) versus morphological approach: analysis of taxonomic composition of potentially toxic cyanobacteria in freshwater lakes.}, journal = {Aquatic biosystems}, volume = {10}, number = {1}, pages = {2}, pmid = {24517495}, issn = {2046-9063}, abstract = {BACKGROUND: The microscopic Utermöhl method is commonly used for the recognition of the presence and taxonomic composition of potentially toxic cyanobacteria and is especially useful for monitoring reservoirs used as drinking water, recreation and fishery resources. However, this method is time-consuming and does not allow potentially toxic and nontoxic cyanobacterial strains to be distinguished. We have developed a method based on denaturing gradient gel electrophoresis (DGGE) of the marker gene ITS and the mcy-gene cluster, and DNA sequencing. We have attempted to calibrate the DGGE-method with a microscopic procedure, using water samples taken in 2011 from four lakes of the Great Mazurian Lakes system.<br><br>RESULTS: Results showed that the classic microscopic method was much more precise and allowed the classification of the majority of cyanobacterial taxa to the species or genus. Using the molecular approach, most of the sequences could only be assigned to a genus or family. The results of DGGE and microscopic analyses overlapped in the detection of the filamentous cyanobacteria. For coccoid cyanobacteria, we only found two taxa using the molecular method, which represented 17% of the total taxa identified using microscopic observations. The DGGE method allowed the identification of two genera of cyanobacteria (Planktothrix and Microcystis) in the studied samples, which have the potential ability to produce toxins from the microcystins group.<br><br>CONCLUSIONS: The results confirmed that the molecular approach is useful for the rapid detection and taxonomic distinction of potentially toxic cyanobacteria in lake-water samples, also in very diverse cyanobacterial communities. Such rapid detection is unattainable by other methods. However, with still limited nucleotide sequences deposited in the public databases, this method is currently not sufficient to evaluate the entire taxonomic composition of cyanobacteria in lakes.}, }
@article {pmid24517489, year = {2015}, author = {David, MM and Cecillon, S and Warne, BM and Prestat, E and Jansson, JK and Vogel, TM}, title = {Microbial ecology of chlorinated solvent biodegradation.}, journal = {Environmental microbiology}, volume = {17}, number = {12}, pages = {4835-4850}, doi = {10.1111/1462-2920.12413}, pmid = {24517489}, issn = {1462-2920}, mesh = {*Biodegradation, Environmental ; Bromodeoxyuridine/metabolism ; Chloroflexi/genetics/*metabolism ; DNA, Bacterial/genetics ; Dichloroethylenes/metabolism ; Ethylenes/biosynthesis ; Halogenation ; Microbiota/physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Solvents/*metabolism ; Tetrachloroethylene/*metabolism ; Trichloroethylene/metabolism ; Vinyl Chloride/metabolism ; Water Pollutants, Chemical/*metabolism ; }, abstract = {This study focused on the microbial ecology of tetrachloroethene (PCE) degradation to trichloroethene, cis-1,2-dichloroethene and vinyl chloride to evaluate the relationship between the microbial community and the potential accumulation or degradation of these toxic metabolites. Multiple soil microcosms supplied with different organic substrates were artificially contaminated with PCE. A thymidine analogue, bromodeoxyuridine (BrdU), was added to the microcosms and incorporated into the DNA of actively replicating cells. We compared the total and active bacterial communities during the 50-day incubations by using phylogenic microarrays and 454 pyrosequencing to identify microorganisms and functional genes associated with PCE degradation to ethene. By use of this integrative approach, both the key community members and the ecological functions concomitant with complete PCE degradation could be determined, including the presence and activity of microbial community members responsible for producing hydrogen and acetate, which are critical for Dehalococcoides-mediated PCE degradation. In addition, by correlation of chemical data and phylogenic microarray data, we identified several bacteria that could potentially oxidize hydrogen. These results demonstrate that PCE degradation is dependent on some microbial community members for production of appropriate metabolites, while other members of the community compete for hydrogen in soil at low redox potentials.}, }
@article {pmid24515357, year = {2014}, author = {Gillings, MR}, title = {Rapid extraction of PCR-competent DNA from recalcitrant environmental samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1096}, number = {}, pages = {17-23}, doi = {10.1007/978-1-62703-712-9_2}, pmid = {24515357}, issn = {1940-6029}, mesh = {*Environmental Microbiology ; Molecular Typing/methods ; *Polymerase Chain Reaction/methods ; }, abstract = {Advances in sequencing technologies have made the investigation of microbial ecology and community dynamics more tractable. The critical first step in such analyses is the efficient and representative recovery of PCR-competent DNA from complex environmental samples. All extraction protocols contain inherent biases, meaning that choice of method involves compromise between various factors, including efficiency, yield, universality, and representative extraction. Here, details are given for a routine method used in our laboratory to extract DNA from soils, sediments, biofilms, roots, and fungi.}, }
@article {pmid24509922, year = {2014}, author = {Ayrapetyan, M and Williams, TC and Oliver, JD}, title = {Interspecific quorum sensing mediates the resuscitation of viable but nonculturable vibrios.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {8}, pages = {2478-2483}, pmid = {24509922}, issn = {1098-5336}, mesh = {Animals ; Homoserine/*analogs &amp; derivatives/metabolism ; Lactones/*metabolism ; Microbial Viability/*drug effects ; Ostreidae/microbiology ; *Quorum Sensing ; Seawater/microbiology ; Vibrio vulnificus/*drug effects/growth &amp; development/*physiology ; }, abstract = {Entry and exit from dormancy are essential survival mechanisms utilized by microorganisms to cope with harsh environments. Many bacteria, including the opportunistic human pathogen Vibrio vulnificus, enter a form of dormancy known as the viable but nonculturable (VBNC) state. VBNC cells can resuscitate when suitable conditions arise, yet the molecular mechanisms facilitating resuscitation in most bacteria are not well understood. We discovered that bacterial cell-free supernatants (CFS) can awaken preexisting dormant vibrio populations within oysters and seawater, while CFS from a quorum sensing mutant was unable to produce the same resuscitative effect. Furthermore, the quorum sensing autoinducer AI-2 could induce resuscitation of VBNC V. vulnificus in vitro, and VBNC cells of a mutant unable to produce AI-2 were unable to resuscitate unless the cultures were supplemented with exogenous AI-2. The quorum sensing inhibitor cinnamaldehyde delayed the resuscitation of wild-type VBNC cells, confirming the importance of quorum sensing in resuscitation. By monitoring AI-2 production by VBNC cultures over time, we found quorum sensing signaling to be critical for the natural resuscitation process. This study provides new insights into the molecular mechanisms stimulating VBNC cell exit from dormancy, which has significant implications for microbial ecology and public health.}, }
@article {pmid24509720, year = {2014}, author = {Glad, T and Barboza, P and Mackie, RI and Wright, AD and Brusetti, L and Mathiesen, SD and Sundset, MA}, title = {Dietary supplementation of usnic acid, an antimicrobial compound in lichens, does not affect rumen bacterial diversity or density in reindeer.}, journal = {Current microbiology}, volume = {68}, number = {6}, pages = {724-728}, pmid = {24509720}, issn = {1432-0991}, mesh = {Animals ; Anti-Infective Agents/*administration &amp; dosage ; Archaea/*drug effects/isolation &amp; purification ; Bacteria/classification/*drug effects/genetics/isolation &amp; purification ; Benzofurans/*administration &amp; dosage ; Biota/*drug effects ; Denaturing Gradient Gel Electrophoresis ; Dietary Supplements ; Molecular Sequence Data ; Reindeer ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Reindeer (Rangifer tarandus tarandus) may include large proportions of lichens in their winter diet. These dietary lichens are rich in phenolic secondary compounds, the most well-known being the antimicrobial usnic acid. Previous studies have shown that reindeer host rumen bacteria resistant to usnic acid and that usnic acid is quickly detoxified in their rumen. In the present study, reindeer (n = 3) were sampled before, during, and after usnic acid supplementation to determine the effect on their rumen microbial ecology. Ad libitum intake of usnic acid averaged up to 278 mg/kg body mass. Population densities of rumen bacteria and methanogenic archaea determined by real-time PCR, ranged from 1.36 × 10(9) to 11.8 × 10(9) and 9.0 × 10(5) to 1.35 × 10(8) cells/g wet weight, respectively, and the two populations did not change significantly during usnic acid supplementation (repeated measures ANOVA) or vary significantly between the rumen liquid and particle fraction (paired t test). Rumen bacterial community structure determined by denaturing gradient gel electrophoresis did not change in response to intake of usnic acid. Firmicutes (38.7 %) and Bacteriodetes (27.4 %) were prevalent among the 16S rRNA gene sequences (n = 62) from the DGGE gels, but representatives of the phyla Verrucomicrobia (14.5 %) and Proteobacteria (1.6 %) were also detected. Rapid detoxification of the usnic acid or resistance to usnic acid may explain why the diversity of the dominant bacterial populations and the bacterial density in the reindeer rumen does not change during usnic acid supplementation.}, }
@article {pmid24509705, year = {2014}, author = {Furbino, LE and Godinho, VM and Santiago, IF and Pellizari, FM and Alves, TM and Zani, CL and Junior, PA and Romanha, AJ and Carvalho, AG and Gil, LH and Rosa, CA and Minnis, AM and Rosa, LH}, title = {Diversity patterns, ecology and biological activities of fungal communities associated with the endemic macroalgae across the Antarctic peninsula.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {775-787}, pmid = {24509705}, issn = {1432-184X}, mesh = {Antarctic Regions ; *Biodiversity ; Chlorophyta/*microbiology ; DNA, Intergenic/genetics ; Fungi/genetics/isolation &amp; purification/metabolism/*physiology ; Geography ; Molecular Sequence Data ; Rhodophyta/*microbiology ; Sequence Analysis, DNA ; }, abstract = {We surveyed diversity patterns and engaged in bioprospecting for bioactive compounds of fungi associated with the endemic macroalgae, Monostroma hariotii and Pyropia endiviifolia, in Antarctica. A total of 239 fungal isolates were obtained, which were identified to represent 48 taxa and 18 genera using molecular methods. The fungal communities consisted of endemic, indigenous and cold-adapted cosmopolitan taxa, which displayed high diversity and richness, but low dominance indices. The extracts of endemic and cold-adapted fungi displayed biological activities and may represent sources of promising prototype molecules to develop drugs. Our results suggest that macroalgae along the marine Antarctic Peninsula provide additional niches where fungal taxa can survive and coexist with their host in the extreme conditions. We hypothesise that the dynamics of richness and dominance among endemic, indigenous and cold-adapted cosmopolitan fungal taxa might be used to understand and model the influence of climate change on the maritime Antarctic mycota.}, }
@article {pmid24504329, year = {2014}, author = {Jiang, W and Ling, Z and Lin, X and Chen, Y and Zhang, J and Yu, J and Xiang, C and Chen, H}, title = {Pyrosequencing analysis of oral microbiota shifting in various caries states in childhood.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {962-969}, pmid = {24504329}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/*isolation &amp; purification ; Child ; Child, Preschool ; China ; DNA, Bacterial/genetics ; Dental Caries/*microbiology ; Dental Plaque/microbiology ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Dental caries is one of the most prevalent childhood diseases worldwide, but little is known about the dynamic characteristics of oral microbiota in the development of dental caries. To investigate the shifting bacterial profiles in different caries states, 60 children (3-7-year-old) were enrolled in this study, including 30 caries-free subjects and 30 caries-active subjects. Supragingival plaques were collected from caries-active subjects on intact enamel, white spot lesions and carious dentin lesions. Plaques from caries-free subjects were used as a control. All samples were analyzed by 454 pyrosequencing based on 16S rRNA gene V1-V3 hypervariable regions. A total of 572,773 pyrosequencing reads passed the quality control and 25,444 unique phylotypes were identified, which represented 18 phyla and 145 genera. Reduced bacterial diversity in the cavitated dentin was observed as compared with the other groups. Thirteen genera (including Capnocytophaga, Fusobacterium, Porphyromonas, Abiotrophia, Comamonas, Tannerella, Eikenella, Paludibacter, Treponema, Actinobaculum, Stenotrophomonas, Aestuariimicrobium, and Peptococcus) were found to be associated with dental health, and the bacterial profiles differed considerably depending on caries status. Eight genera (including Cryptobacterium, Lactobacillus, Megasphaera, Olsenella, Scardovia, Shuttleworthia, Cryptobacterium, and Streptococcus) were increased significantly in cavitated dentin lesions, and Actinomyces and Corynebacterium were present at significant high levels in white spot lesions (P < 0.05), while Flavobacterium, Neisseria, Bergeyella, and Derxia were enriched in the intact surfaces of caries individuals (P < 0.05). Our results showed that oral bacteria were specific at different stages of caries progression, which contributes to informing the prevention and treatment of childhood dental caries.}, }
@article {pmid24503131, year = {2014}, author = {Britton, RA and Young, VB}, title = {Role of the intestinal microbiota in resistance to colonization by Clostridium difficile.}, journal = {Gastroenterology}, volume = {146}, number = {6}, pages = {1547-1553}, pmid = {24503131}, issn = {1528-0012}, support = {U19AI090871/AI/NIAID NIH HHS/United States ; U19 AI090871/AI/NIAID NIH HHS/United States ; U19 AI090872/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; U19090872//PHS HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/adverse effects ; Bile Acids and Salts/metabolism ; Biological Therapy/methods ; Clostridioides difficile/*growth &amp; development/metabolism/pathogenicity ; Disease Models, Animal ; Dysbiosis ; Enterocolitis, Pseudomembranous/metabolism/*microbiology/prevention &amp; control ; Feces/microbiology ; Host-Pathogen Interactions ; Humans ; Intestinal Mucosa/metabolism ; Intestines/drug effects/*microbiology ; *Microbiota/drug effects ; Probiotics/therapeutic use ; }, abstract = {Antibiotic-associated infection with the bacterial pathogen Clostridium difficile is a major cause of morbidity and increased health care costs. C difficile infection follows disruption of the indigenous gut microbiota by antibiotics. Antibiotics create an environment within the intestine that promotes C difficile spore germination, vegetative growth, and toxin production, leading to epithelial damage and colitis. Studies of patients with C difficile infection and animal models have shown that the indigenous microbiota can inhibit expansion and persistence of C difficile. Although the specific mechanisms of these processes are not known, they are likely to interfere with key aspects of the pathogen's physiology, including spore germination and competitive growth. Increasing our understanding of how the intestinal microbiota manage C difficile could lead to better means of controlling this important nosocomial pathogen.}, }
@article {pmid24500618, year = {2014}, author = {Schulz, F and Lagkouvardos, I and Wascher, F and Aistleitner, K and Kostanjšek, R and Horn, M}, title = {Life in an unusual intracellular niche: a bacterial symbiont infecting the nucleus of amoebae.}, journal = {The ISME journal}, volume = {8}, number = {8}, pages = {1634-1644}, pmid = {24500618}, issn = {1751-7370}, support = {281633/ERC_/European Research Council/International ; }, mesh = {Acanthamoeba/microbiology ; Alphaproteobacteria/*classification/genetics/isolation &amp; purification ; Cell Nucleus/*microbiology ; Hartmannella/*microbiology/ultrastructure ; Host Specificity ; Phylogeny ; Symbiosis ; }, abstract = {Amoebae serve as hosts for various intracellular bacteria, including human pathogens. These microbes are able to overcome amoebal defense mechanisms and successfully establish a niche for replication, which is usually the cytoplasm. Here, we report on the discovery of a bacterial symbiont that is located inside the nucleus of its Hartmannella sp. host. This symbiont, tentatively named 'Candidatus Nucleicultrix amoebiphila', is only moderately related to known bacteria (∼90% 16S and 23S rRNA sequence similarity) and member of a novel clade of protist symbionts affiliated with the Rickettsiales and Rhodospirillales. Screening of 16S rRNA amplicon data sets revealed a broad distribution of these bacteria in freshwater and soil habitats. 'Candidatus Nucleicultrix amoebiphila' traffics within 6 h post infection to the host nucleus. Maximum infection levels are reached after 96-120 h, at which time point the nucleus is pronouncedly enlarged and filled with bacteria. Transmission of the symbionts occurs vertically upon host cell division but may also occur horizontally through host cell lysis. Although we observed no impact on the fitness of the original Hartmannella sp. host, the bacteria are rather lytic for Acanthamoeba castellanii. Intranuclear symbiosis is an exceptional phenomenon, and amoebae represent an ideal model system to further investigate evolution and underlying molecular mechanisms of these unique microbial associations.}, }
@article {pmid24499292, year = {2014}, author = {Huse, SM and Mark Welch, DB and Voorhis, A and Shipunova, A and Morrison, HG and Eren, AM and Sogin, ML}, title = {VAMPS: a website for visualization and analysis of microbial population structures.}, journal = {BMC bioinformatics}, volume = {15}, number = {}, pages = {41}, pmid = {24499292}, issn = {1471-2105}, mesh = {*Bacteria/classification/genetics/metabolism ; Computational Biology/*methods ; Computer Graphics ; High-Throughput Nucleotide Sequencing ; Internet ; Microbiota ; *Software ; User-Computer Interface ; }, abstract = {BACKGROUND: The advent of next-generation DNA sequencing platforms has revolutionized molecular microbial ecology by making the detailed analysis of complex communities over time and space a tractable research pursuit for small research groups. However, the ability to generate 10[5]-10[8] reads with relative ease brings with it many downstream complications. Beyond the computational resources and skills needed to process and analyze data, it is difficult to compare datasets in an intuitive and interactive manner that leads to hypothesis generation and testing.<br><br>RESULTS: We developed the free web service VAMPS (Visualization and Analysis of Microbial Population Structures, http://vamps.mbl.edu) to address these challenges and to facilitate research by individuals or collaborating groups working on projects with large-scale sequencing data. Users can upload marker gene sequences and associated metadata; reads are quality filtered and assigned to both taxonomic structures and to taxonomy-independent clusters. A simple point-and-click interface allows users to select for analysis any combination of their own or their collaborators' private data and data from public projects, filter these by their choice of taxonomic and/or abundance criteria, and then explore these data using a wide range of analytic methods and visualizations. Each result is extensively hyperlinked to other analysis and visualization options, promoting data exploration and leading to a greater understanding of data relationships.<br><br>CONCLUSIONS: VAMPS allows researchers using marker gene sequence data to analyze the diversity of microbial communities and the relationships between communities, to explore these analyses in an intuitive visual context, and to download data, results, and images for publication. VAMPS obviates the need for individual research groups to make the considerable investment in computational infrastructure and bioinformatic support otherwise necessary to process, analyze, and interpret massive amounts of next-generation sequence data. Any web-capable device can be used to upload, process, explore, and extract data and results from VAMPS. VAMPS encourages researchers to share sequence and metadata, and fosters collaboration between researchers of disparate biomes who recognize common patterns in shared data.}, }
@article {pmid24493462, year = {2014}, author = {Yannarell, AC and Menning, SE and Beck, AM}, title = {Influence of shrub encroachment on the soil microbial community composition of remnant hill prairies.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {897-906}, pmid = {24493462}, issn = {1432-184X}, mesh = {*Biodiversity ; Conservation of Natural Resources ; DNA, Ribosomal Spacer/genetics ; Environment ; *Grassland ; Illinois ; Polymerase Chain Reaction ; Seasons ; *Soil Microbiology ; }, abstract = {Hill prairies are remnant grasslands perched on the bluffs of major river valleys, and because their steep slopes make them unsuitable for traditional row crop agriculture, they have some of the lowest levels of anthropogenic disturbance of any prairie ecosystems in the Midwestern USA. However, many decades of fire suppression have allowed for shrub encroachment from the surrounding forests. While shrub encroachment of grasslands can modify soil respiration rates and nutrient storage, it is not known whether shrubs also alter the community composition of soil microorganisms. We conducted transect sampling of nine different hill prairie remnants showing varying degrees of shrub encroachment, and we used DNA-based community profiling (automated ribosomal intergenic spacer analysis) to characterize the composition of bacterial and fungal communities in the open prairie habitat, the shrub-encroached border, and the surrounding forest. While both bacterial and fungal communities showed statistically significant variation across these habitats, their predominant patterns were different. Bacterial communities of forest soils were distinct from those of the open prairie and the shrub-encroached areas, while fungal communities of the open prairie were distinct from those of the forest and the shrub-encroached border. Shrub encroachment significantly altered the community composition of soil fungal communities. Furthermore, fungal communities of heavily encroached prairie remnants more closely resembled those of the surrounding forest than those of lightly encroached prairies. Thus, shrub encroachment can cause soil fungi to shift from a "grassland" community to a "woody" community, with potential consequences for soil processes and plant-microbe interactions.}, }
@article {pmid24493461, year = {2014}, author = {Kerfahi, D and Hall-Spencer, JM and Tripathi, BM and Milazzo, M and Lee, J and Adams, JM}, title = {Shallow water marine sediment bacterial community shifts along a natural CO2 gradient in the Mediterranean Sea off Vulcano, Italy.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {819-828}, pmid = {24493461}, issn = {1432-184X}, mesh = {Bacteria/classification/*metabolism ; *Biodiversity ; Carbon Dioxide/*metabolism ; Genes, Bacterial/genetics ; Geologic Sediments/*microbiology ; Hydrogen-Ion Concentration ; Italy ; Mediterranean Sea ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The effects of increasing atmospheric CO(2) on ocean ecosystems are a major environmental concern, as rapid shoaling of the carbonate saturation horizon is exposing vast areas of marine sediments to corrosive waters worldwide. Natural CO(2) gradients off Vulcano, Italy, have revealed profound ecosystem changes along rocky shore habitats as carbonate saturation levels decrease, but no investigations have yet been made of the sedimentary habitat. Here, we sampled the upper 2 cm of volcanic sand in three zones, ambient (median pCO(2) 419 μatm, minimum Ω(arag) 3.77), moderately CO(2)-enriched (median pCO(2) 592 μatm, minimum Ω(arag) 2.96), and highly CO(2)-enriched (median pCO(2) 1611 μatm, minimum Ω(arag) 0.35). We tested the hypothesis that increasing levels of seawater pCO(2) would cause significant shifts in sediment bacterial community composition, as shown recently in epilithic biofilms at the study site. In this study, 454 pyrosequencing of the V1 to V3 region of the 16S rRNA gene revealed a shift in community composition with increasing pCO(2). The relative abundances of most of the dominant genera were unaffected by the pCO(2) gradient, although there were significant differences for some 5 % of the genera present (viz. Georgenia, Lutibacter, Photobacterium, Acinetobacter, and Paenibacillus), and Shannon Diversity was greatest in sediments subject to long-term acidification (>100 years). Overall, this supports the view that globally increased ocean pCO(2) will be associated with changes in sediment bacterial community composition but that most of these organisms are resilient. However, further work is required to assess whether these results apply to other types of coastal sediments and whether the changes in relative abundance of bacterial taxa that we observed can significantly alter the biogeochemical functions of marine sediments.}, }
@article {pmid24489847, year = {2014}, author = {Küng, D and Bigler, L and Davis, LR and Gratwicke, B and Griffith, E and Woodhams, DC}, title = {Stability of microbiota facilitated by host immune regulation: informing probiotic strategies to manage amphibian disease.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e87101}, pmid = {24489847}, issn = {1932-6203}, mesh = {Amphibian Proteins/physiology ; Animals ; Antimicrobial Cationic Peptides/physiology ; Anura/*immunology/microbiology ; Bacillus/*physiology ; Chytridiomycota/*immunology ; Dermatomycoses/immunology/*veterinary ; Disease Resistance ; Host-Pathogen Interactions ; Microbiota/*immunology ; Probiotics ; Skin/metabolism/microbiology ; Weight Loss/immunology ; }, abstract = {Microbial communities can augment host immune responses and probiotic therapies are under development to prevent or treat diseases of humans, crops, livestock, and wildlife including an emerging fungal disease of amphibians, chytridiomycosis. However, little is known about the stability of host-associated microbiota, or how the microbiota is structured by innate immune factors including antimicrobial peptides (AMPs) abundant in the skin secretions of many amphibians. Thus, conservation medicine including therapies targeting the skin will benefit from investigations of amphibian microbial ecology that provide a model for vertebrate host-symbiont interactions on mucosal surfaces. Here, we tested whether the cutaneous microbiota of Panamanian rocket frogs, Colostethus panamansis, was resistant to colonization or altered by treatment. Under semi-natural outdoor mesocosm conditions in Panama, we exposed frogs to one of three treatments including: (1) probiotic - the potentially beneficial bacterium Lysinibacillus fusiformis, (2) transplant - skin washes from the chytridiomycosis-resistant glass frog Espadarana prosoblepon, and (3) control - sterile water. Microbial assemblages were analyzed by a culture-independent T-RFLP analysis. We found that skin microbiota of C. panamansis was resistant to colonization and did not differ among treatments, but shifted through time in the mesocosms. We describe regulation of host AMPs that may function to maintain microbial community stability. Colonization resistance was metabolically costly and microbe-treated frogs lost 7-12% of body mass. The discovery of strong colonization resistance of skin microbiota suggests a well-regulated, rather than dynamic, host-symbiont relationship, and suggests that probiotic therapies aiming to enhance host immunity may require an approach that circumvents host mechanisms maintaining equilibrium in microbial communities.}, }
@article {pmid24487184, year = {2014}, author = {Stephen, AS and Naughton, DP and Pizzey, RL and Bradshaw, DJ and Burnett, GR}, title = {In vitro growth characteristics and volatile sulfur compound production of Solobacterium moorei.}, journal = {Anaerobe}, volume = {26}, number = {}, pages = {53-57}, doi = {10.1016/j.anaerobe.2014.01.007}, pmid = {24487184}, issn = {1095-8274}, mesh = {Chromatography, Gas ; Culture Media/chemistry ; Cysteine/metabolism ; Gram-Positive Bacteria/*growth &amp; development/isolation &amp; purification/*metabolism ; Halitosis/microbiology ; Humans ; Hydrogen Sulfide/*metabolism ; }, abstract = {Solobacterium moorei has recently been implicated as a causative agent of halitosis. In vitro experiments to evaluate the role of S. moorei in halitosis have, however, been complicated by a paucity of information on the ideal conditions for culturing this organism. This work aimed to optimize a liquid culture medium for S. moorei, and to determine the growth-curve of the organism. Further, the ability of S. moorei to generate volatile sulfur compounds was investigated and compared quantitatively to other oral anaerobes by an optimized head-space gas chromatography method. Serum-supplementation of standard liquid growth media gave greater growth of S. moorei than non-supplemented broths, with the best medium found to be serum-supplemented tryptone soya broth. S. moorei was able to metabolize cysteine directly to hydrogen sulfide, but was unable to produce methanethiol from methionine. S. moorei produced 2-3 times more hydrogen sulfide (normalized for colony forming units) than Porphyromonas gingivalis and Veillonella dispar, but considerably less than Fusobacterium nucleatum. The study has identified reliable growth conditions for culture of S. moorei, which were employed to show that S. moorei has the requisite biochemistry consistent with a potential role in halitosis.}, }
@article {pmid24487179, year = {2014}, author = {Spirito, CM and Richter, H and Rabaey, K and Stams, AJ and Angenent, LT}, title = {Chain elongation in anaerobic reactor microbiomes to recover resources from waste.}, journal = {Current opinion in biotechnology}, volume = {27}, number = {}, pages = {115-122}, doi = {10.1016/j.copbio.2014.01.003}, pmid = {24487179}, issn = {1879-0429}, support = {323009/ERC_/European Research Council/International ; }, mesh = {Acetates/metabolism ; Anaerobiosis ; Bioreactors/*microbiology ; Carbon Dioxide/metabolism ; Carboxylic Acids/metabolism ; Electrodes ; Microbiota/*physiology ; Oxidation-Reduction ; *Recycling ; Succinic Acid/metabolism ; Waste Management/*methods ; }, abstract = {Different microbial pathways can elongate the carbon chains of molecules in open cultures of microbial populations (i.e. reactor microbiomes) under anaerobic conditions. Here, we discuss three such pathways: 1. homoacetogenesis to combine two carbon dioxide molecules into acetate; 2. succinate formation to elongate glycerol with one carbon from carbon dioxide; and 3. reverse β oxidation to elongate short-chain carboxylates with two carbons into medium-chain carboxylates, leading to more energy-dense and insoluble products (e.g. easier to separate from solution). The ability to use reactor microbiomes to treat complex substrates can simultaneously address two pressing issues: 1. providing proper waste management; and 2. producing renewable chemicals and fuels.}, }
@article {pmid24482762, year = {2014}, author = {Darling, AE and Jospin, G and Lowe, E and Matsen, FA and Bik, HM and Eisen, JA}, title = {PhyloSift: phylogenetic analysis of genomes and metagenomes.}, journal = {PeerJ}, volume = {2}, number = {}, pages = {e243}, pmid = {24482762}, issn = {2167-8359}, abstract = {Like all organisms on the planet, environmental microbes are subject to the forces of molecular evolution. Metagenomic sequencing provides a means to access the DNA sequence of uncultured microbes. By combining DNA sequencing of microbial communities with evolutionary modeling and phylogenetic analysis we might obtain new insights into microbiology and also provide a basis for practical tools such as forensic pathogen detection. In this work we present an approach to leverage phylogenetic analysis of metagenomic sequence data to conduct several types of analysis. First, we present a method to conduct phylogeny-driven Bayesian hypothesis tests for the presence of an organism in a sample. Second, we present a means to compare community structure across a collection of many samples and develop direct associations between the abundance of certain organisms and sample metadata. Third, we apply new tools to analyze the phylogenetic diversity of microbial communities and again demonstrate how this can be associated to sample metadata. These analyses are implemented in an open source software pipeline called PhyloSift. As a pipeline, PhyloSift incorporates several other programs including LAST, HMMER, and pplacer to automate phylogenetic analysis of protein coding and RNA sequences in metagenomic datasets generated by modern sequencing platforms (e.g., Illumina, 454).}, }
@article {pmid24481860, year = {2014}, author = {Marcisz, K and Fournier, B and Gilbert, D and Lamentowicz, M and Mitchell, EA}, title = {Response of sphagnum peatland testate amoebae to a 1-year transplantation experiment along an artificial hydrological gradient.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {810-818}, pmid = {24481860}, issn = {1432-184X}, mesh = {Amoebozoa/*physiology ; *Biodiversity ; France ; Hydrology ; Rhizaria/*physiology ; Sphagnopsida ; *Wetlands ; }, abstract = {Peatland testate amoebae (TA) are well-established bioindicators for depth to water table (DWT), but effects of hydrological changes on TA communities have never been tested experimentally. We tested this in a field experiment by placing Sphagnum carpets (15 cm diameter) collected in hummock, lawn and pool microsites (origin) at three local conditions (dry, moist and wet) using trenches dug in a peatland. One series of samples was seeded with microorganism extract from all microsites. TA community were analysed at T0: 8-2008, T1: 5-2009 and T2: 8-2009. We analysed the data using conditional inference trees, principal response curves (PRC) and DWT inferred from TA communities using a transfer function used for paleoecological reconstruction. Density declined from T0 to T1 and then increased sharply by T2. Species richness, Simpson diversity and Simpson evenness were lower at T2 than at T0 and T1. Seeded communities had higher species richness in pool samples at T0. Pool samples tended to have higher density, lower species richness, Simpson diversity and Simpson Evenness than hummock and/or lawn samples until T1. In the PRC, the effect of origin was significant at T0 and T1, but the effect faded away by T2. Seeding effect was strongest at T1 and lowest vanished by T2. Local condition effect was strong but not in line with the wetness gradient at T1 but started to reflect it by T2. Likewise, TA-inferred DWT started to match the experimental conditions by T2, but more so in hummock and lawn samples than in pool samples. This study confirmed that TA responds to hydrological changes over a 1-year period. However, sensitivity of TA to hydrological fluctuations, and thus the accuracy of inferred DWT changes, was habitat specific, pool TA communities being least responsive to environmental changes. Lawns and hummocks may be thus better suited than pools for paleoecological reconstructions. This, however, contrasts with the higher prediction error and species' tolerance for DWT with increasing dryness observed in transfer function models.}, }
@article {pmid24481066, year = {2014}, author = {Almstrand, R and Persson, F and Daims, H and Ekenberg, M and Christensson, M and Wilén, BM and Sörensson, F and Hermansson, M}, title = {Three-dimensional stratification of bacterial biofilm populations in a moving bed biofilm reactor for nitritation-anammox.}, journal = {International journal of molecular sciences}, volume = {15}, number = {2}, pages = {2191-2206}, pmid = {24481066}, issn = {1422-0067}, mesh = {Anaerobiosis ; *Bacterial Physiological Phenomena ; *Biofilms ; *Bioreactors ; In Situ Hybridization, Fluorescence ; *Nitrification ; Wastewater/microbiology ; }, abstract = {Moving bed biofilm reactors (MBBRs) are increasingly used for nitrogen removal with nitritation-anaerobic ammonium oxidation (anammox) processes in wastewater treatment. Carriers provide protected surfaces where ammonia oxidizing bacteria (AOB) and anammox bacteria form complex biofilms. However, the knowledge about the organization of microbial communities in MBBR biofilms is sparse. We used new cryosectioning and imaging methods for fluorescence in situ hybridization (FISH) to study the structure of biofilms retrieved from carriers in a nitritation-anammox MBBR. The dimensions of the carrier compartments and the biofilm cryosections after FISH showed good correlation, indicating little disturbance of biofilm samples by the treatment. FISH showed that Nitrosomonas europaea/eutropha-related cells dominated the AOB and Candidatus Brocadia fulgida-related cells dominated the anammox guild. New carriers were initially colonized by AOB, followed by anammox bacteria proliferating in the deeper biofilm layers, probably in anaerobic microhabitats created by AOB activity. Mature biofilms showed a pronounced three-dimensional stratification where AOB dominated closer to the biofilm-water interface, whereas anammox were dominant deeper into the carrier space and towards the walls. Our results suggest that current mathematical models may be oversimplifying these three-dimensional systems and unless the multidimensionality of these systems is considered, models may result in suboptimal design of MBBR carriers.}, }
@article {pmid24478213, year = {2014}, author = {Lee, HJ and Whang, KS}, title = {Streptomyces graminisoli sp. nov. and Streptomyces rhizophilus sp. nov., isolated from bamboo (Sasa borealis) rhizosphere soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {64}, number = {Pt 5}, pages = {1546-1551}, doi = {10.1099/ijs.0.055210-0}, pmid = {24478213}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Diaminopimelic Acid/chemistry ; Fatty Acids/chemistry ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Peptidoglycan/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Rhizosphere ; Sasa/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; Streptomyces/*classification/genetics/isolation &amp; purification ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {Four strains of actinomycete, designated strains JR-19T, JR-12, JR-29 and JR-41T were isolated from bamboo (Sasa borealis) rhizosphere soil. Phylogenetic, morphological, chemotaxonomic and phenotypic analysis demonstrated that the four strains belong to the genus Streptomyces. Microscopic observation revealed that the four strains produced spirales spore chains with spiny surfaces. The cell-wall peptidoglycan of the four strains contained ll-diaminopimelic acid, glutamic acid, alanine and glycine. Whole-cell hydrolysates mainly contained glucose and ribose. The predominant menaquinones were MK-9 (H6) and MK-9 (H8). Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that these strains and the members of the genus Streptomyces exhibited moderately high 16S rRNA gene sequence similarities of 98.3-99.3%, with the most closely related strains being Streptomyces shenzhenensis 172115T and Streptomyces gramineus JR-43T. Based on the phenotypic and genotypic data, the four strains are considered to represent two novel species of the genus Streptomyces, for which the names Streptomyces graminisoli sp. nov. [to accommodate strains JR-19T (type strain; =KACC 16472T=NBRC 108883T), JR-12 (=KACC 16471) and JR-29 (=KACC 16473)] and Streptomyces rhizophilus sp. nov. [for strain JR-41T (=KACC 16580T=NBRC 108885T)] are proposed.}, }
@article {pmid24477925, year = {2014}, author = {Lu, XM and Lu, PZ}, title = {Characterization of bacterial communities in sediments receiving various wastewater effluents with high-throughput sequencing analysis.}, journal = {Microbial ecology}, volume = {67}, number = {3}, pages = {612-623}, pmid = {24477925}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; *Biodiversity ; China ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Rivers/*microbiology ; Sequence Analysis, DNA ; Wastewater/*microbiology ; }, abstract = {454 Pyrosequencing was applied to examine bacterial communities in sediment samples collected from a river receiving effluent discharge from rural domestic sewage (RDS) and various factories, including a tannery (TNS), clothing plant (CTS), and button factory (BTS), respectively. For each sample, 4,510 effective sequences were selected and utilized to do the bacterial diversity and abundance analysis, respectively. In total, 1,288, 2,036, 1,800, and 2,150 operational taxonomic units were obtained at 3% distance cutoff in TNS, CTS, BTS, and RDS, respectively. Bacterial phylotype richness in RDS was higher than the other samples, and TNS had the least richness. The most predominant class in the TNS, CTS, and BTS samples is Betaproteobacteria. Cyanobacteria (no_rank) is the most predominant one in the RDS sample. Circa 31% sequences in TNS were affiliated with the Rhodocyclales order. In the four samples, Aeromonas, Arcobacter, Clostridium, Legionella, Leptospira, Mycobacterium, Pseudomonas, and Treponema genera containing pathogenic bacteria were detected. Characterization of bacterial communities in sediments from various downstream branches indicated that distinct wastewater effluents have similar potential to reduce the natural variability in river ecosystems and contribute to the river biotic homogenization.}, }
@article {pmid24477924, year = {2014}, author = {Wu, L and Zhang, G and Lan, S and Zhang, D and Hu, C}, title = {Longitudinal photosynthetic gradient in crust lichens' thalli.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {888-896}, pmid = {24477924}, issn = {1432-184X}, mesh = {China ; Chlorophyll/*metabolism ; Desert Climate ; Fluorometry ; Lichens/*metabolism ; *Photosynthesis ; *Soil Microbiology ; Species Specificity ; }, abstract = {In order to evaluate the self-shading protection for inner photobionts, the photosynthetic activities of three crust lichens were detected using Microscope-Imaging-PAM. The false color images showed that longitudinal photosynthetic gradient was found in both the green algal lichen Placidium sp. and the cyanolichen Peltula sp. In longitudinal direction, all the four chlorophyll fluorescence parameters Fv/Fm, Yield, qP, and rETR gradually decreased with depth in the thalli of both of these two lichens. In Placidium sp., qN values decreased with depth, whereas an opposite trend was found in Peltula sp. However, no such photosynthetic heterogeneity was found in the thalli of Collema sp. in longitudinal direction. Microscope observation showed that photobiont cells are compactly arranged in Placidium sp. and Peltula sp. while loosely distributed in Collema sp. It was considered that the longitudinal photosynthetic heterogeneity was ascribed to the result of gradual decrease of incidence caused by the compact arrangement of photobiont cells in the thalli. The results indicate a good protection from the self-shading for the inner photobionts against high radiation in crust lichens.}, }
@article {pmid24477923, year = {2014}, author = {Polónia, AR and Cleary, DF and Duarte, LN and de Voogd, NJ and Gomes, NC}, title = {Composition of Archaea in seawater, sediment, and sponges in the Kepulauan Seribu reef system, Indonesia.}, journal = {Microbial ecology}, volume = {67}, number = {3}, pages = {553-567}, pmid = {24477923}, issn = {1432-184X}, mesh = {Animals ; Archaea/classification/genetics/isolation &amp; purification/metabolism/*physiology ; *Biodiversity ; *Coral Reefs ; Geologic Sediments/*microbiology ; Indonesia ; Molecular Sequence Data ; Phylogeny ; Porifera/*microbiology ; Seawater/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Coral reefs are among the most diverse and productive ecosystems in the world. Most research has, however, focused on eukaryotes such as corals and fishes. Recently, there has been increasing interest in the composition of prokaryotes, particularly those inhabiting corals and sponges, but these have mainly focused on bacteria. There have been very few studies of coral reef Archaea, despite the fact that Archaea have been shown to play crucial roles in nutrient dynamics, including nitrification and methanogenesis, of oligotrophic environments such as coral reefs. Here, we present the first study to assess Archaea in four different coral reef biotopes (seawater, sediment, and two sponge species, Stylissa massa and Xestospongia testudinaria). The archaeal community of both sponge species and sediment was dominated by Crenarchaeota, while the seawater community was dominated by Euryarchaeota. The biotope explained more than 72% of the variation in archaeal composition. The number of operational taxonomic units (OTUs) was highest in sediment and seawater biotopes and substantially lower in both sponge hosts. No "sponge-specific" archaeal OTUs were found, i.e., OTUs found in both sponge species but absent from nonhost biotopes. Despite both sponge species hosting phylogenetically distinct microbial assemblages, there were only minor differences in Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways. In contrast, most functional pathways differed significantly between microbiomes from sponges and nonhost biotopes including all energy metabolic pathways. With the exception of the methane and nitrogen metabolic pathway, all energy metabolic pathways were enriched in sponges when compared to nonhost biotopes.}, }
@article {pmid24477922, year = {2014}, author = {Grimes, DJ and Ford, TE and Colwell, RR and Baker-Austin, C and Martinez-Urtaza, J and Subramaniam, A and Capone, DG}, title = {Viewing marine bacteria, their activity and response to environmental drivers from orbit: satellite remote sensing of bacteria.}, journal = {Microbial ecology}, volume = {67}, number = {3}, pages = {489-500}, pmid = {24477922}, issn = {1432-184X}, support = {R01 AI039129/AI/NIAID NIH HHS/United States ; 2R01A1039129-11A2//PHS HHS/United States ; }, mesh = {Aquatic Organisms/*physiology ; Cyanobacteria/*physiology ; *Environment ; Environmental Monitoring/*methods ; Oceans and Seas ; *Remote Sensing Technology ; Spacecraft ; Vibrio/*physiology ; }, abstract = {Satellite-based remote sensing of marine microorganisms has become a useful tool in predicting human health risks associated with these microscopic targets. Early applications were focused on harmful algal blooms, but more recently methods have been developed to interrogate the ocean for bacteria. As satellite-based sensors have become more sophisticated and our ability to interpret information derived from these sensors has advanced, we have progressed from merely making fascinating pictures from space to developing process models with predictive capability. Our understanding of the role of marine microorganisms in primary production and global elemental cycles has been vastly improved as has our ability to use the combination of remote sensing data and models to provide early warning systems for disease outbreaks. This manuscript will discuss current approaches to monitoring cyanobacteria and vibrios, their activity and response to environmental drivers, and will also suggest future directions.}, }
@article {pmid24477921, year = {2014}, author = {Tout, J and Jeffries, TC and Webster, NS and Stocker, R and Ralph, PJ and Seymour, JR}, title = {Variability in microbial community composition and function between different niches within a coral reef.}, journal = {Microbial ecology}, volume = {67}, number = {3}, pages = {540-552}, pmid = {24477921}, issn = {1432-184X}, mesh = {Archaea/classification/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; *Biodiversity ; *Coral Reefs ; *Environment ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Queensland ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {To explore how microbial community composition and function varies within a coral reef ecosystem, we performed metagenomic sequencing of seawater from four niches across Heron Island Reef, within the Great Barrier Reef. Metagenomes were sequenced from seawater samples associated with (1) the surface of the coral species Acropora palifera, (2) the surface of the coral species Acropora aspera, (3) the sandy substrate within the reef lagoon and (4) open water, outside of the reef crest. Microbial composition and metabolic function differed substantially between the four niches. The taxonomic profile showed a clear shift from an oligotroph-dominated community (e.g. SAR11, Prochlorococcus, Synechococcus) in the open water and sandy substrate niches, to a community characterised by an increased frequency of copiotrophic bacteria (e.g. Vibrio, Pseudoalteromonas, Alteromonas) in the coral seawater niches. The metabolic potential of the four microbial assemblages also displayed significant differences, with the open water and sandy substrate niches dominated by genes associated with core house-keeping processes such as amino acid, carbohydrate and protein metabolism as well as DNA and RNA synthesis and metabolism. In contrast, the coral surface seawater metagenomes had an enhanced frequency of genes associated with dynamic processes including motility and chemotaxis, regulation and cell signalling. These findings demonstrate that the composition and function of microbial communities are highly variable between niches within coral reef ecosystems and that coral reefs host heterogeneous microbial communities that are likely shaped by habitat structure, presence of animal hosts and local biogeochemical conditions.}, }
@article {pmid24475755, year = {2014}, author = {Marine, R and McCarren, C and Vorrasane, V and Nasko, D and Crowgey, E and Polson, SW and Wommack, KE}, title = {Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome.}, journal = {Microbiome}, volume = {2}, number = {1}, pages = {3}, pmid = {24475755}, issn = {2049-2618}, support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: Shotgun metagenomics has become an important tool for investigating the ecology of microorganisms. Underlying these investigations is the assumption that metagenome sequence data accurately estimates the census of microbial populations. Multiple displacement amplification (MDA) of microbial community DNA is often used in cases where it is difficult to obtain enough DNA for sequencing; however, MDA can result in amplification biases that may impact subsequent estimates of population census from metagenome data. Some have posited that pooling replicate MDA reactions negates these biases and restores the accuracy of population analyses. This assumption has not been empirically tested.<br><br>RESULTS: Using mock viral communities, we examined the influence of pooling on population-scale analyses. In pooled and single reaction MDA treatments, sequence coverage of viral populations was highly variable and coverage patterns across viral genomes were nearly identical, indicating that initial priming biases were reproducible and that pooling did not alleviate biases. In contrast, control unamplified sequence libraries showed relatively even coverage across phage genomes.<br><br>CONCLUSIONS: MDA should be avoided for metagenomic investigations that require quantitative estimates of microbial taxa and gene functional groups. While MDA is an indispensable technique in applications such as single-cell genomics, amplification biases cannot be overcome by combining replicate MDA reactions. Alternative library preparation techniques should be utilized for quantitative microbial ecology studies utilizing metagenomic sequencing approaches.}, }
@article {pmid24468528, year = {2014}, author = {Pardo, T and Clemente, R and Epelde, L and Garbisu, C and Bernal, MP}, title = {Evaluation of the phytostabilisation efficiency in a trace elements contaminated soil using soil health indicators.}, journal = {Journal of hazardous materials}, volume = {268}, number = {}, pages = {68-76}, doi = {10.1016/j.jhazmat.2014.01.003}, pmid = {24468528}, issn = {1873-3336}, mesh = {Atriplex/*growth &amp; development ; *Biodegradation, Environmental ; Biomass ; Fertilizers ; Soil/*chemistry ; Soil Microbiology ; Soil Pollutants/*isolation &amp; purification ; Trace Elements/*isolation &amp; purification ; }, abstract = {The efficiency of a remediation strategy was evaluated in a mine soil highly contaminated with trace elements (TEs) by microbiological, ecotoxicological and physicochemical parameters of the soil and soil solution (extracted in situ), as a novel and integrative methodology for assessing recovery of soil health. A 2.5-year field phytostabilisation experiment was carried out using olive mill-waste compost, pig slurry and hydrated lime as amendments, and a native halophytic shrub (Atriplex halimus L.). Comparing with non-treated soil, the addition of the amendments increased soil pH and reduced TEs availability, favoured the development of a sustainable vegetation cover (especially the organic materials), stimulated soil microorganisms (increasing microbial biomass, activity and functional diversity, and reducing stress) and reduced direct and indirect soil toxicity (i.e., its potential associated risks). Therefore, under semi-arid conditions, the use of compost and pig slurry with A. halimus is an effective phytostabilisation strategy to improve soil health of nutrient-poor soils with high TEs concentrations, by improving the habitat function of the soil ecosystem, the reactivation of the biogeochemical cycles of essential nutrients, and the reduction of TEs dissemination and their environmental impact.}, }
@article {pmid24467551, year = {2015}, author = {Héry, M and Rizoulis, A and Sanguin, H and Cooke, DA and Pancost, RD and Polya, DA and Lloyd, JR}, title = {Microbial ecology of arsenic-mobilizing Cambodian sediments: lithological controls uncovered by stable-isotope probing.}, journal = {Environmental microbiology}, volume = {17}, number = {6}, pages = {1857-1869}, doi = {10.1111/1462-2920.12412}, pmid = {24467551}, issn = {1462-2920}, mesh = {Acetates/metabolism ; Arsenic/*metabolism/toxicity ; Cambodia ; Desulfovibrio/genetics/metabolism ; Drinking Water/*chemistry ; Geobacter/genetics/metabolism ; Geologic Sediments/*microbiology ; Groundwater/*microbiology ; Isotope Labeling ; Lactates/metabolism ; Molecular Sequence Data ; Proteobacteria/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Water Pollution, Chemical ; }, abstract = {Microbially mediated arsenic release from Holocene and Pleistocene Cambodian aquifer sediments was investigated using microcosm experiments and substrate amendments. In the Holocene sediment, the metabolically active bacteria, including arsenate-respiring bacteria, were determined by DNA stable-isotope probing. After incubation with (13) C-acetate and (13) C-lactate, active bacterial community in the Holocene sediment was dominated by different Geobacter spp.-related 16S rRNA sequences. Substrate addition also resulted in the enrichment of sequences related to the arsenate-respiring Sulfurospirillum spp. (13) C-acetate selected for ArrA related to Geobacter spp. whereas (13) C-lactate selected for ArrA which were not closely related to any cultivated organism. Incubation of the Pleistocene sediment with lactate favoured a 16S rRNA-phylotype related to the sulphate-reducing Desulfovibrio oxamicus DSM1925, whereas the ArrA sequences clustered with environmental sequences distinct from those identified in the Holocene sediment. Whereas limited As(III) release was observed in Pleistocene sediment after lactate addition, no arsenic mobilization occurred from Holocene sediments, probably because of the initial reduced state of As, as determined by X-ray Absorption Near Edge Structure. Our findings demonstrate that in the presence of reactive organic carbon, As(III) mobilization can occur in Pleistocene sediments, having implications for future strategies that aim to reduce arsenic contamination in drinking waters by using aquifers containing Pleistocene sediments.}, }
@article {pmid24466294, year = {2014}, author = {Wittmann, J and Dreiseikelmann, B and Rohde, C and Rohde, M and Sikorski, J}, title = {Isolation and characterization of numerous novel phages targeting diverse strains of the ubiquitous and opportunistic pathogen Achromobacter xylosoxidans.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e86935}, pmid = {24466294}, issn = {1932-6203}, mesh = {Achromobacter denitrificans/*drug effects/*genetics/*virology ; Anti-Bacterial Agents/*pharmacology ; Blotting, Southern ; Caudovirales/*ultrastructure ; Drug Resistance, Bacterial/*genetics ; Germany ; Microarray Analysis ; Microscopy, Electron ; Multilocus Sequence Typing ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Species Specificity ; }, abstract = {The clinical relevance of nosocomially acquired infections caused by multi-resistant Achromobacter strains is rapidly increasing. Here, a diverse set of 61 Achromobacter xylosoxidans strains was characterized by MultiLocus Sequence Typing and Phenotype MicroArray technology. The strains were further analyzed in regard to their susceptibility to 35 antibiotics and to 34 different and newly isolated bacteriophages from the environment. A large proportion of strains were resistant against numerous antibiotics such as cephalosporines, aminoglycosides and quinolones, whereas piperacillin-tazobactam, ticarcillin, mezlocillin and imipenem were still inhibitory. We also present the first expanded study on bacteriophages of the genus Achromobacter that has been so far a blank slate with respect to phage research. The phages were isolated mainly from several waste water treatment plants in Germany. Morphological analysis of all of these phages by electron microscopy revealed a broad diversity with different members of the order Caudovirales, including the families Siphoviridae, Myoviridae, and Podoviridae. A broad spectrum of different host ranges could be determined for several phages that lysed up to 24 different and in part highly antibiotic resistant strains. Molecular characterisation by DNA restriction analysis revealed that all phages contain linear double-stranded DNA. Their restriction patterns display distinct differences underlining their broad diversity.}, }
@article {pmid24465722, year = {2014}, author = {D'Adamo, S and Jinkerson, RE and Boyd, ES and Brown, SL and Baxter, BK and Peters, JW and Posewitz, MC}, title = {Evolutionary and biotechnological implications of robust hydrogenase activity in halophilic strains of Tetraselmis.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e85812}, pmid = {24465722}, issn = {1932-6203}, mesh = {Acclimatization/drug effects/radiation effects ; *Biotechnology ; Carbohydrate Metabolism/drug effects/radiation effects ; Carbon Dioxide/metabolism ; Cell Count ; Chlorophyta/drug effects/*enzymology/*genetics/radiation effects ; *Evolution, Molecular ; Fermentation/drug effects/radiation effects ; Gene Expression Regulation, Enzymologic/drug effects/radiation effects ; Hydrogen/metabolism ; Hydrogenase/*genetics/isolation &amp; purification ; Light ; Likelihood Functions ; Metabolome/drug effects/radiation effects ; Molecular Sequence Data ; Paraquat/pharmacology ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; RNA, Messenger/genetics/metabolism ; *Salinity ; Transcriptome/drug effects/radiation effects ; }, abstract = {Although significant advances in H2 photoproduction have recently been realized in fresh water algae (e.g. Chlamydomonas reinhardtii), relatively few studies have focused on H2 production and hydrogenase adaptations in marine or halophilic algae. Salt water organisms likely offer several advantages for biotechnological H2 production due to the global abundance of salt water, decreased H2 and O2 solubility in saline and hypersaline systems, and the ability of extracellular NaCl levels to influence metabolism. We screened unialgal isolates obtained from hypersaline ecosystems in the southwest United States and identified two distinct halophilic strains of the genus Tetraselmis (GSL1 and QNM1) that exhibit both robust fermentative and photo H2-production activities. The influence of salinity (3.5%, 5.5% and 7.0% w/v NaCl) on H2 production was examined during anoxic acclimation, with the greatest in vivo H2-production rates observed at 7.0% NaCl. These Tetraselmis strains maintain robust hydrogenase activity even after 24 h of anoxic acclimation and show increased hydrogenase activity relative to C. reinhardtii after extended anoxia. Transcriptional analysis of Tetraselmis GSL1 enabled sequencing of the cDNA encoding the FeFe-hydrogenase structural enzyme (HYDA) and its maturation proteins (HYDE, HYDEF and HYDG). In contrast to freshwater Chlorophyceae, the halophilic Tetraselmis GSL1 strain likely encodes a single HYDA and two copies of HYDE, one of which is fused to HYDF. Phylogenetic analyses of HYDA and concatenated HYDA, HYDE, HYDF and HYDG in Tetraselmis GSL1 fill existing knowledge gaps in the evolution of algal hydrogenases and indicate that the algal hydrogenases sequenced to date are derived from a common ancestor. This is consistent with recent hypotheses that suggest fermentative metabolism in the majority of eukaryotes is derived from a common base set of enzymes that emerged early in eukaryotic evolution with subsequent losses in some organisms.}, }
@article {pmid24463414, year = {2014}, author = {Arends, JB and Van Denhouwe, S and Verstraete, W and Boon, N and Rabaey, K}, title = {Enhanced disinfection of wastewater by combining wetland treatment with bioelectrochemical H(2)O(2) production.}, journal = {Bioresource technology}, volume = {155}, number = {}, pages = {352-358}, doi = {10.1016/j.biortech.2013.12.058}, pmid = {24463414}, issn = {1873-2976}, mesh = {Disinfection/methods ; Electrochemistry/methods ; Filtration/methods ; Flow Cytometry ; Hydrogen Peroxide/*chemical synthesis ; Wastewater/*chemistry ; Water Purification/*methods ; *Wetlands ; }, abstract = {A highly-loaded constructed wetland (up to 44±21gCODm(-2)d(-1)) was connected to a bioelectrochemical system (BES) to produce hydrogen peroxide for disinfection purposes. The anode delivered a current from the wetland effluent up to 3.5Am(-2) (maximum 62% anodic efficiency) but was limited in the supply of organic carbon. Hydrogen peroxide could be produced in situ in wetland effluent. Production rates were tested at various current densities with a maximum rate of 2.7gmelectrode(-2)h(-1) (4h at 10Am(-2), 41% cathodic efficiency). Little difference was observed between production rate in wetland effluent or a 0.3% NaCl solution. The resulting hydrogen peroxide (0.1%) was used to disinfect wetland effluent successfully (<75CFUml(-1) after 1h contact time). The combination of wetland water treatment with peroxide production in a BES thus enables generating higher water qualities, including disinfected water, without external input of chemicals.}, }
@article {pmid24462909, year = {2014}, author = {Banerjee, R and Das, B and Balakrish Nair, G and Basak, S}, title = {Dynamics in genome evolution of Vibrio cholerae.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {23}, number = {}, pages = {32-41}, doi = {10.1016/j.meegid.2014.01.006}, pmid = {24462909}, issn = {1567-7257}, mesh = {Biological Evolution ; Cholera/*epidemiology ; DNA Transposable Elements ; Drug Resistance, Bacterial ; Genetic Variation ; *Genome, Bacterial ; Humans ; Phylogeny ; Vibrio cholerae/*classification/*genetics/pathogenicity ; }, abstract = {Vibrio cholerae, the etiological agent of the acute secretary diarrheal disease cholera, is still a major public health concern in developing countries. In former centuries cholera was a permanent threat even to the highly developed populations of Europe, North America, and the northern part of Asia. Extensive studies on the cholera bug over more than a century have made significant advances in our understanding of the disease and ways of treating patients. V. cholerae has more than 200 serogroups, but only few serogroups have caused disease on a worldwide scale. Until the present, the evolutionary relationship of these pandemic causing serogroups was not clear. In the last decades, we have witnessed a shift involving genetically and phenotypically varied pandemic clones of V. cholerae in Asia and Africa. The exponential knowledge on the genome of several representatives V. cholerae strains has been used to identify and analyze the key determinants for rapid evolution of cholera pathogen. Recent comparative genomic studies have identified the presence of various integrative mobile genetic elements (IMGEs) in V. cholerae genome, which can be used as a marker of differentiation of all seventh pandemic clones with very similar core genome. This review attempts to bring together some of the important researches in recent times that have contributed towards understanding the genetics, epidemiology and evolution of toxigenic V. cholerae strains.}, }
@article {pmid24462702, year = {2014}, author = {Ho, VT and Zhao, J and Fleet, G}, title = {Yeasts are essential for cocoa bean fermentation.}, journal = {International journal of food microbiology}, volume = {174}, number = {}, pages = {72-87}, doi = {10.1016/j.ijfoodmicro.2013.12.014}, pmid = {24462702}, issn = {1879-3460}, mesh = {Acetic Acid/metabolism ; Acetobacter/genetics/metabolism ; Adult ; Antifungal Agents/pharmacology ; Cacao/chemistry/*microbiology/*standards ; DNA, Ribosomal/genetics ; Ethanol/metabolism ; *Fermentation ; *Food Microbiology ; Genes, Bacterial/genetics ; Genes, Fungal/genetics ; Humans ; Limosilactobacillus fermentum/genetics/metabolism ; Lactobacillus plantarum/genetics/metabolism ; Middle Aged ; Taste ; Yeasts/drug effects/growth &amp; development/metabolism/*physiology ; Young Adult ; }, abstract = {Cocoa beans (Theobroma cacao) are the major raw material for chocolate production and fermentation of the beans is essential for the development of chocolate flavor precursors. In this study, a novel approach was used to determine the role of yeasts in cocoa fermentation and their contribution to chocolate quality. Cocoa bean fermentations were conducted with the addition of 200ppm Natamycin to inhibit the growth of yeasts, and the resultant microbial ecology and metabolism, bean chemistry and chocolate quality were compared with those of normal (control) fermentations. The yeasts Hanseniaspora guilliermondii, Pichia kudriavzevii and Kluyveromyces marxianus, the lactic acid bacteria Lactobacillus plantarum and Lactobacillus fermentum and the acetic acid bacteria Acetobacter pasteurianus and Gluconobacter frateurii were the major species found in the control fermentation. In fermentations with the presence of Natamycin, the same bacterial species grew but yeast growth was inhibited. Physical and chemical analyses showed that beans fermented without yeasts had increased shell content, lower production of ethanol, higher alcohols and esters throughout fermentation and lesser presence of pyrazines in the roasted product. Quality tests revealed that beans fermented without yeasts were purplish-violet in color and not fully brown, and chocolate prepared from these beans tasted more acid and lacked characteristic chocolate flavor. Beans fermented with yeast growth were fully brown in color and gave chocolate with typical characters which were clearly preferred by sensory panels. Our findings demonstrate that yeast growth and activity were essential for cocoa bean fermentation and the development of chocolate characteristics.}, }
@article {pmid24460947, year = {2014}, author = {Waud, M and Busschaert, P and Ruyters, S and Jacquemyn, H and Lievens, B}, title = {Impact of primer choice on characterization of orchid mycorrhizal communities using 454 pyrosequencing.}, journal = {Molecular ecology resources}, volume = {14}, number = {4}, pages = {679-699}, doi = {10.1111/1755-0998.12229}, pmid = {24460947}, issn = {1755-0998}, mesh = {*Biota ; Cluster Analysis ; DNA Primers/*genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Molecular Sequence Data ; Mycorrhizae/*classification/*genetics ; Orchidaceae/*microbiology ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {Although the number of studies investigating mycorrhizal associations in orchids has increased in recent years, the fungal communities associating with orchids and how they differ between species and sites remain unclear. Recent research has indicated that individual orchid plants may associate with several fungi concurrently, implying that to study mycorrhizal associations in orchids the fungal community should be assessed, rather than the presence of individual dominant fungal species or strains. High-throughput sequencing methods, such as 454 pyrosequencing, are increasingly used as the primary tool for such analyses. However, many studies combine universal primers from previous phylogenetic or ecological studies to generate amplicons suitable for 454 pyrosequencing without first critically evaluating their performance, potentially resulting in biased fungal community descriptions. Here, following in silico primer analysis we evaluated the performance of different combinations of existing PCR primers to characterize orchid mycorrhizal communities using 454 pyrosequencing by analysis of both an artificially assembled community of mycorrhizal fungi isolated from diverse orchid species and root samples from three different orchid species (Anacamptis morio, Ophrys tenthredinifera and Serapias lingua). Our results indicate that primer pairs ITS3/ITS4OF and ITS86F/ITS4, targeting the internal transcribed spacer-2 (ITS-2) region, outperformed other tested primer pairs in terms of number of reads, number of operational taxonomic units recovered from the artificial community and number of different orchid mycorrhizal associating families detected in the orchid samples. Additionally, we show the complementary specificity of both primer pairs, making them highly suitable for tandem use when studying the diversity of orchid mycorrhizal communities.}, }
@article {pmid24460707, year = {2014}, author = {Zhuang, LF and Watt, RM and Steiner, S and Lang-Hua, BH and Wang, R and Ramseier, CA and Lang, NP}, title = {Subgingival microbiota of Sri Lankan tea labourers naïve to oral hygiene measures.}, journal = {Journal of clinical periodontology}, volume = {41}, number = {5}, pages = {433-441}, doi = {10.1111/jcpe.12230}, pmid = {24460707}, issn = {1600-051X}, mesh = {Aged ; Bacteria/*classification/genetics ; Cohort Studies ; Dental Plaque/*microbiology ; Food Industry ; Fusobacteria/classification ; Gram-Positive Bacteria/classification ; Humans ; Male ; Middle Aged ; Molecular Sequence Data ; *Oral Hygiene ; Periodontal Pocket/classification/microbiology ; Polymerase Chain Reaction ; Proteobacteria/classification ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, RNA/classification ; Sri Lanka ; Tea ; }, abstract = {AIM: To characterize the subgingival microbiota within a cohort of adult males (n = 32) naïve to oral hygiene practices, and to compare the composition of bacterial taxa present in periodontal sites with various probing depths.<br><br>MATERIAL AND METHODS: Subgingival plaque samples were collected from single shallow pocket [pocket probing depth (PPD)&#x2264;3&#xa0;mm] and deep pocket (PPD&#x2265;6&#xa0;mm) sites from each subject. A polymerase chain reaction based strategy was used to construct a clone library of 16S ribosomal RNA (rRNA) genes for each site. The sequences of ca. 30-60 plasmid clones were determined for each site to identify resident taxa. Microbial composition was compared using a variety of statistical and bioinformatics approaches.<br><br>RESULTS: A total of 1887 cloned 16S rRNA gene sequences were analysed, which were assigned to 318 operational taxonomic units (98% identity cut-off). The subgingival microbiota was dominated by Firmicutes (69.8%), Proteobacteria (16.3%), and Fusobacteria (8.0%). The overall composition of microbial communities in shallow sites was significantly different from those within deep sites (&#x222b;-Libshuff, p&#xa0;<&#xa0;0.001).<br><br>CONCLUSIONS: A taxonomically diverse subgingival microbiota was present within this cohort; however, the structures of the microbial communities present in the respective subjects exhibited limited variation. Deep and shallow sites contained notably different microbial compositions, but this was not correlated with the rate of periodontal progression.}, }
@article {pmid24459282, year = {2014}, author = {Guerrero, LD and Makhalanyane, TP and Aislabie, JM and Cowan, DA}, title = {Draft Genome Sequence of Williamsia sp. Strain D3, Isolated From the Darwin Mountains, Antarctica.}, journal = {Genome announcements}, volume = {2}, number = {1}, pages = {}, pmid = {24459282}, issn = {2169-8287}, abstract = {Actinobacteria are the dominant taxa in Antarctic desert soils. Here, we describe the first draft genome of a member of the genus Williamsia (strain D3) isolated from Antarctic soil. The genome of this psychrotolerant bacterium may help to elucidate crucial survival mechanisms for organisms inhabiting cold desert soil systems.}, }
@article {pmid24457304, year = {2014}, author = {Courtens, EN and Boon, N and De Clippeleir, H and Berckmoes, K and Mosquera, M and Seuntjens, D and Vlaeminck, SE}, title = {Control of nitratation in an oxygen-limited autotrophic nitrification/denitrification rotating biological contactor through disc immersion level variation.}, journal = {Bioresource technology}, volume = {155}, number = {}, pages = {182-188}, doi = {10.1016/j.biortech.2013.12.108}, pmid = {24457304}, issn = {1873-2976}, mesh = {Ammonium Compounds/*metabolism ; Autotrophic Processes/*physiology ; Biofilms ; Biological Oxygen Demand Analysis ; *Bioreactors ; Models, Chemical ; Nitrification/*physiology ; Oxygen/*metabolism ; Polymerase Chain Reaction ; Water Pollutants, Chemical/*metabolism ; Water Purification/instrumentation/*methods ; }, abstract = {With oxygen supply playing a crucial role in an oxygen-limited autotrophic nitrification/denitrification (OLAND) rotating biological contactor (RBC), its controlling factors were investigated in this study. Disc rotation speeds (1.8 and 3.6rpm) showed no influence on the process performance of a lab-scale RBC, although abiotic experiments showed a significant effect on the oxygenation capacity. Estimations of the biological oxygen uptake rate revealed that 85-89% of the oxygen was absorbed by the microorganisms during the air exposure of the discs. Indeed, increasing the disc immersion (50 to 75-80%) could significantly suppress undesired nitratation, on the short and long term. The presented results demonstrated that nitratation could be controlled by the immersion level and revealed that oxygen control in an OLAND RBC should be predominantly based on the atmospheric exposure percentage of the discs.}, }
@article {pmid24456144, year = {2015}, author = {Vanhoecke, B and De Ryck, T and Stringer, A and Van de Wiele, T and Keefe, D}, title = {Microbiota and their role in the pathogenesis of oral mucositis.}, journal = {Oral diseases}, volume = {21}, number = {1}, pages = {17-30}, doi = {10.1111/odi.12224}, pmid = {24456144}, issn = {1601-0825}, mesh = {Humans ; Microbiota/*physiology ; Mouth/*microbiology ; Mouth Mucosa/microbiology ; Risk Factors ; Stomatitis/*etiology/microbiology ; }, abstract = {Oral mucositis in patients undergoing cancer therapy is a significant problem. Its prevalence ranges between 20 and 100%, depending on treatment type and protocols and patient-based variables. Mucositis is self-limiting when uncomplicated by infection. Unfortunately, the incidence of developing a local or systemic infection during the course of the treatment is very high. At this stage, it is unclear which role oral microbiota play in the onset, duration, and severity of oral mucositis. Nevertheless, there is growing interest in this underexplored topic, and new studies are being undertaken to unravel their impact on the pathogenesis of mucositis.}, }
@article {pmid24452996, year = {2014}, author = {Gião, MS and Keevil, CW}, title = {Listeria monocytogenes can form biofilms in tap water and enter into the viable but non-cultivable state.}, journal = {Microbial ecology}, volume = {67}, number = {3}, pages = {603-611}, pmid = {24452996}, issn = {1432-184X}, mesh = {Biofilms/*growth &amp; development ; Colony Count, Microbial ; Drinking Water/*microbiology ; Listeria monocytogenes/growth &amp; development/*physiology ; *Microbial Viability ; *Stainless Steel ; Temperature ; }, abstract = {Listeria monocytogenes is a foodborne pathogen that can be transmitted through contaminated raw food or by ready-to-eat products that have been in contact with contaminated surfaces. Tap water (TW) is used to wash produce, as a processed food constituent and to wash processing surfaces and floors. The main aim of this work was to investigate the formation and survival of L. monocytogenes biofilms on stainless steel (SS) coupons in TW at 4, 22, 30 and 37 °C. For that, coupons with biofilm were visualised in situ while other coupons were scraped to quantify total cells by SYTO 9, cultivable numbers by plating onto brain heart infusion agar and viable numbers by the direct viable count method. Results showed that L. monocytogenes can form biofilms on SS surfaces in TW at any temperature, including at 4 °C. The number of total cells was similar for all the conditions tested while cultivable numbers varied between the level of detection (<8.3 CFU cm(-2)) and 3.5 × 10(5) CFU cm(-2), meaning between 7.0 × 10(4) and 1.1 × 10(7) cells cm(-2) have entered the viable but non-cultivable (VBNC) state. This work clearly demonstrates that L. monocytogenes can form biofilms in TW and that sessile cells can remain viable and cultivable in some conditions for at least the 48 h investigated. On the other hand, VBNC adaptation suggests that the pathogen can remain undetectable using traditional culture recovery techniques, which may give a false indication of processing surface hygiene status, leading to potential cross-contamination of food products.}, }
@article {pmid24451334, year = {2013}, author = {Vital, M and Penton, CR and Wang, Q and Young, VB and Antonopoulos, DA and Sogin, ML and Morrison, HG and Raffals, L and Chang, EB and Huffnagle, GB and Schmidt, TM and Cole, JR and Tiedje, JM}, title = {A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community.}, journal = {Microbiome}, volume = {1}, number = {1}, pages = {8}, pmid = {24451334}, issn = {2049-2618}, support = {R01 DK097268/DK/NIDDK NIH HHS/United States ; }, abstract = {BACKGROUND: Butyrate, which is produced by the human microbiome, is essential for a well-functioning colon. Bacteria that produce butyrate are phylogenetically diverse, which hinders their accurate detection based on conventional phylogenetic markers. As a result, reliable information on this important bacterial group is often lacking in microbiome research.<br><br>RESULTS: In this study we describe a gene-targeted approach for 454 pyrotag sequencing and quantitative polymerase chain reaction for the final genes in the two primary bacterial butyrate synthesis pathways, butyryl-CoA:acetate CoA-transferase (but) and butyrate kinase (buk). We monitored the establishment and early succession of butyrate-producing communities in four patients with ulcerative colitis who underwent a colectomy with ileal pouch anal anastomosis and compared it with three control samples from healthy colons. All patients established an abundant butyrate-producing community (approximately 5% to 26% of the total community) in the pouch within the 2-month study, but patterns were distinctive among individuals. Only one patient harbored a community profile similar to the healthy controls, in which there was a predominance of but genes that are similar to reference genes from Acidaminococcus sp., Eubacterium sp., Faecalibacterium prausnitzii and Roseburia sp., and an almost complete absence of buk genes. Two patients were greatly enriched in buk genes similar to those of Clostridium butyricum and C. perfringens, whereas a fourth patient displayed abundant communities containing both genes. Most butyrate producers identified in previous studies were detected and the general patterns of taxa found were supported by 16S rRNA gene pyrotag analysis, but the gene-targeted approach provided more detail about the potential butyrate-producing members of the community.<br><br>CONCLUSIONS: The presented approach provides quantitative and genotypic insights into butyrate-producing communities and facilitates a more specific functional characterization of the intestinal microbiome. Furthermore, our analysis refines but and buk reference annotations found in central databases.}, }
@article {pmid24451205, year = {2014}, author = {Thrash, JC and Temperton, B and Swan, BK and Landry, ZC and Woyke, T and DeLong, EF and Stepanauskas, R and Giovannoni, SJ}, title = {Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype.}, journal = {The ISME journal}, volume = {8}, number = {7}, pages = {1440-1451}, pmid = {24451205}, issn = {1751-7370}, mesh = {Alphaproteobacteria/classification/*genetics ; DNA, Intergenic/classification ; Ecotype ; *Genes, rRNA ; Genomics ; Metagenome ; *Phylogeny ; RNA, Ribosomal, 16S/classification/*genetics ; Seawater/*microbiology ; Single-Cell Analysis ; Synteny ; }, abstract = {Bacterioplankton of the SAR11 clade are the most abundant microorganisms in marine systems, usually representing 25% or more of the total bacterial cells in seawater worldwide. SAR11 is divided into subclades with distinct spatiotemporal distributions (ecotypes), some of which appear to be specific to deep water. Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%-86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets. Subclade Ic genomes dominated metagenomic fragment recruitment below the euphotic zone. They had similar COG distributions, high local synteny and shared a large number (69%) of orthologous clusters with SAR11 surface genomes, yet were distinct at the 16S rRNA gene and amino-acid level, and formed a separate, monophyletic group in phylogenetic trees. Subclade Ic genomes were enriched in genes associated with membrane/cell wall/envelope biosynthesis and showed evidence of unique phage defenses. The majority of subclade Ic-specfic genes were hypothetical, and some were highly abundant in deep ocean metagenomic data, potentially masking mechanisms for niche differentiation. However, the evidence suggests these organisms have a similar metabolism to their surface counterparts, and that subclade Ic adaptations to the deep ocean do not involve large variations in gene content, but rather more subtle differences previously observed deep ocean genomic data, like preferential amino-acid substitutions, larger coding regions among SAR11 clade orthologs, larger intergenic regions and larger estimated average genome size.}, }
@article {pmid24451012, year = {2013}, author = {Links, MG and Chaban, B and Hemmingsen, SM and Muirhead, K and Hill, JE}, title = {mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences.}, journal = {Microbiome}, volume = {1}, number = {1}, pages = {23}, pmid = {24451012}, issn = {2049-2618}, abstract = {BACKGROUND: Formation of operational taxonomic units (OTU) is a common approach to data aggregation in microbial ecology studies based on amplification and sequencing of individual gene targets. The de novo assembly of OTU sequences has been recently demonstrated as an alternative to widely used clustering methods, providing robust information from experimental data alone, without any reliance on an external reference database.<br><br>RESULTS: Here we introduce mPUMA (microbial Profiling Using Metagenomic Assembly, http://mpuma.sourceforge.net), a software package for identification and analysis of protein-coding barcode sequence data. It was developed originally for Cpn60 universal target sequences (also known as GroEL or Hsp60). Using an unattended process that is independent of external reference sequences, mPUMA forms OTUs by DNA sequence assembly and is capable of tracking OTU abundance. mPUMA processes microbial profiles both in terms of the direct DNA sequence as well as in the translated amino acid sequence for protein coding barcodes. By forming OTUs and calculating abundance through an assembly approach, mPUMA is capable of generating inputs for several popular microbiota analysis tools. Using SFF data from sequencing of a synthetic community of Cpn60 sequences derived from the human vaginal microbiome, we demonstrate that mPUMA can faithfully reconstruct all expected OTU sequences and produce compositional profiles consistent with actual community structure.<br><br>CONCLUSIONS: mPUMA enables analysis of microbial communities while empowering the discovery of novel organisms through OTU assembly.}, }
@article {pmid24450397, year = {2014}, author = {Martineau, C and Pan, Y and Bodrossy, L and Yergeau, E and Whyte, LG and Greer, CW}, title = {Atmospheric methane oxidizers are present and active in Canadian high Arctic soils.}, journal = {FEMS microbiology ecology}, volume = {89}, number = {2}, pages = {257-269}, doi = {10.1111/1574-6941.12287}, pmid = {24450397}, issn = {1574-6941}, mesh = {Air ; Arctic Regions ; Bacterial Proteins/*genetics ; Canada ; Genes, Bacterial ; Genetic Variation ; Methane/*metabolism ; Methylococcaceae/enzymology/*genetics ; Molecular Sequence Data ; Oxidation-Reduction ; Oxygenases/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The melting of permafrost and the associated potential for methane emissions to the atmosphere are major concerns in the context of global warming. However, soils can also represent a significant sink for methane through the activity of methane-oxidizing bacteria (MOB). In this study, we looked at the activity, diversity, and community structure of MOB at two sampling depths within the active layer in three soils from the Canadian high Arctic. These soils had the capacity to oxidize methane at low (15 ppm) and high (1000 ppm) methane concentrations, but rates differed greatly depending on the sampling date, depth, and site. The pmoA gene sequences related to two genotypes of uncultured MOB involved in atmospheric methane oxidation, the 'upland soil cluster gamma' and the 'upland soil cluster alpha', were detected in soils with near neutral and acidic pH, respectively. Other groups of MOB, including Type I methanotrophs and the 'Cluster 1' genotype, were also detected, indicating a broader diversity of MOB than previously reported for Arctic soils. Overall, the results reported here showed that methane oxidation at both low and high methane concentrations occurs in high Arctic soils and revealed that different groups of atmospheric MOB inhabit these soils.}, }
@article {pmid24449851, year = {2014}, author = {Reed, DC and Algar, CK and Huber, JA and Dick, GJ}, title = {Gene-centric approach to integrating environmental genomics and biogeochemical models.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {5}, pages = {1879-1884}, pmid = {24449851}, issn = {1091-6490}, mesh = {Computer Simulation ; Genes/*genetics ; Hydrogen Sulfide/metabolism ; *Metagenomics ; *Models, Biological ; Nitrates/metabolism ; Nitrogen Cycle/genetics ; Oceans and Seas ; Oxidation-Reduction ; Oxygen/metabolism ; }, abstract = {Rapid advances in molecular microbial ecology have yielded an unprecedented amount of data about the evolutionary relationships and functional traits of microbial communities that regulate global geochemical cycles. Biogeochemical models, however, are trailing in the wake of the environmental genomics revolution, and such models rarely incorporate explicit representations of bacteria and archaea, nor are they compatible with nucleic acid or protein sequence data. Here, we present a functional gene-based framework for describing microbial communities in biogeochemical models by incorporating genomics data to provide predictions that are readily testable. To demonstrate the approach in practice, nitrogen cycling in the Arabian Sea oxygen minimum zone (OMZ) was modeled to examine key questions about cryptic sulfur cycling and dinitrogen production pathways in OMZs. Simulations support previous assertions that denitrification dominates over anammox in the central Arabian Sea, which has important implications for the loss of fixed nitrogen from the oceans. Furthermore, cryptic sulfur cycling was shown to attenuate the secondary nitrite maximum often observed in OMZs owing to changes in the composition of the chemolithoautotrophic community and dominant metabolic pathways. Results underscore the need to explicitly integrate microbes into biogeochemical models rather than just the metabolisms they mediate. By directly linking geochemical dynamics to the genetic composition of microbial communities, the method provides a framework for achieving mechanistic insights into patterns and biogeochemical consequences of marine microbes. Such an approach is critical for informing our understanding of the key role microbes play in modulating Earth's biogeochemistry.}, }
@article {pmid24448554, year = {2014}, author = {Mejía-León, ME and Petrosino, JF and Ajami, NJ and Domínguez-Bello, MG and de la Barca, AM}, title = {Fecal microbiota imbalance in Mexican children with type 1 diabetes.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {3814}, pmid = {24448554}, issn = {2045-2322}, mesh = {Adolescent ; Bacteria/*classification/*genetics ; Case-Control Studies ; Child ; Computational Biology ; Cross-Sectional Studies ; DNA, Bacterial/genetics ; Diabetes Mellitus, Type 1/*microbiology ; Feces/*microbiology ; Female ; Follow-Up Studies ; Gastrointestinal Tract/microbiology ; Humans ; Male ; Mexico ; *Microbiota ; Prognosis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Dysbiosis of the intestinal microbiota affecting the gut barrier could be triggering Type 1 Diabetes (T1D), the second most frequent autoimmune disease in childhood. This study compared the structure of the fecal microbiota in 29 mestizo children aged 7-18 years, including 8 T1D at onset, 13 T1D after 2 years treatment, and 8 healthy controls. Clinical information was collected, predisposing haplotypes were determined; the fecal DNA was extracted, the V4 region of the 16S rRNA gene amplified and 454-pyrosequenced. The newly diagnosed T1D cases had high levels of the genus Bacteroides (p < 0.004), whereas the control group had a gut microbiota dominated by Prevotella. Children with T1D treated for ≥2 years had levels of Bacteroides and Prevotella compared to those of the control group. The gut microbiota of newly diagnosed T1D cases is altered, but whether it is involved in disease causation or is a consequence of host selection remains unclear.}, }
@article {pmid24447520, year = {2014}, author = {Desloover, J and Roobroeck, D and Heylen, K and Puig, S and Boeckx, P and Verstraete, W and Boon, N}, title = {Pathway of nitrous oxide consumption in isolated Pseudomonas stutzeri strains under anoxic and oxic conditions.}, journal = {Environmental microbiology}, volume = {16}, number = {10}, pages = {3143-3152}, doi = {10.1111/1462-2920.12404}, pmid = {24447520}, issn = {1462-2920}, mesh = {Acetylene/metabolism ; Aerobiosis ; Ammonium Compounds/metabolism ; Anaerobiosis ; Denitrification ; Nitrogen/metabolism ; Nitrogen Fixation ; Nitrous Oxide/*metabolism ; Pseudomonas stutzeri/isolation &amp; purification/*metabolism ; Sewage/microbiology ; }, abstract = {The microbial consumption of nitrous oxide (N2O) has gained great interest since it was revealed that this process could mitigate the greenhouse effect of N2O. The consumption of N2O results from its reduction to dinitrogen gas (N2) as part of the denitrification process. However, there is ongoing debate regarding an alternative pathway, namely reduction of N2O to NH4(+), or assimilatory N2O consumption. To date, this pathway is poorly investigated and lacks unambiguous evidence. Enrichment of denitrifying activated sludge using a mineral nitrogen-free medium rendered a mixed culture capable of anoxic and oxic N2O consumption. Dilution plating, isolation and deoxyribonucleic acid fingerprinting identified a collection of Pseudomonas stutzeri strains as dominant N2O consumers in both anaerobic and aerobic enrichments. A detailed isotope tracing experiment with a Pseudomonas stutzeri isolate showed that consumption of N2O via assimilatory reduction to NH4(+) was absent. Conversely, respiratory N2O reduction was directly coupled to N2 fixation.}, }
@article {pmid24437399, year = {2014}, author = {Walters, WA and Knight, R}, title = {Technology and techniques for microbial ecology via DNA sequencing.}, journal = {Annals of the American Thoracic Society}, volume = {11 Suppl 1}, number = {Suppl 1}, pages = {S16-20}, pmid = {24437399}, issn = {2325-6621}, support = {T32 GM008759/GM/NIGMS NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA, Bacterial/*analysis ; DNA, Ribosomal/*analysis ; Humans ; Metagenome/*genetics ; Microbiota/*genetics ; *Phylogeny ; Sequence Analysis, DNA/instrumentation/*methods ; Software ; }, abstract = {High-throughput sequencing technology, coupled with the use of conserved marker genes, has allowed for the understanding of communities of microbes (both culturable and unculturable) as well as their phylogenetic placement. The recent explosion of sequencing data prompted the development of software that could process the vast amount of data generated and phylogenetically differentiate groups of samples. Host-associated microbial studies have revealed that microbes are highly varied between individuals and fluctuate within an individual. Large-scale studies are being undertaken that include collection of extensive environmental data to help uncover the forces that shape microbial communities.}, }
@article {pmid24436212, year = {2014}, author = {Van Meervenne, E and De Weirdt, R and Van Coillie, E and Devlieghere, F and Herman, L and Boon, N}, title = {Biofilm models for the food industry: hot spots for plasmid transfer?.}, journal = {Pathogens and disease}, volume = {70}, number = {3}, pages = {332-338}, doi = {10.1111/2049-632X.12134}, pmid = {24436212}, issn = {2049-632X}, mesh = {Biofilms/*growth &amp; development ; Biomass ; Bioreactors ; Conjugation, Genetic ; Escherichia coli/physiology ; *Food Industry ; Plasmids/genetics ; Pseudomonas putida/physiology ; }, abstract = {Biofilms represent a substantial problem in the food industry, with food spoilage, equipment failure, and public health aspects to consider. Besides, biofilms may be a hot spot for plasmid transfer, by which antibiotic resistance can be disseminated to potential foodborne pathogens. This study investigated biomass and plasmid transfer in dual-species (Pseudomonas putida and Escherichia coli) biofilm models relevant to the food industry. Two different configurations (flow-through and drip-flow) and two different inoculation procedures (donor-recipient and recipient-donor) were tested. The drip-flow configuration integrated stainless steel coupons in the setup while the flow-through configuration included a glass flow cell and silicone tubing. The highest biomass density [10 log (cells cm-[2])] was obtained in the silicone tubing when first the recipient strain was inoculated. High plasmid transfer ratios, up to 1/10 (transconjugants/total bacteria), were found. Depending on the order of inoculation, a difference in transfer efficiency between the biofilm models could be found. The ease by which the multiresistance plasmid was transferred highlights the importance of biofilms in the food industry as hot spots for the acquisition of multiresistance plasmids. This can impede the treatment of foodborne illnesses if pathogens acquire this multiresistance in or from the biofilm.}, }
@article {pmid24435863, year = {2014}, author = {O'Donnell, MM and Harris, HM and O'Toole, PW and Ross, RP}, title = {The Genome of the Predominant Equine Lactobacillus Species, Lactobacillus equi, Is Reflective of Its Lifestyle Adaptations to an Herbivorous Host.}, journal = {Genome announcements}, volume = {2}, number = {1}, pages = {}, pmid = {24435863}, issn = {2169-8287}, abstract = {We report the draft genome sequence of Lactobacillus equi strain DPC6820, isolated from equine feces. L. equi is a predominant Lactobacillus species in the horse hindgut microbiota. An examination of the genome identified genes and enzymes highlighting L. equi adaptations to the herbivorous gastrointestinal tract of the horse, including fructan hydrolases. This genome sequence may help us further understand the microbial ecology of the equine hindgut and the influence lactobacilli have on it.}, }
@article {pmid24435545, year = {2014}, author = {Musafer, HK and Kuchma, SL and Naimie, AA and Schwartzman, JD and Al-Mathkhury, HJ and O'Toole, GA}, title = {Investigating the link between imipenem resistance and biofilm formation by Pseudomonas aeruginosa.}, journal = {Microbial ecology}, volume = {68}, number = {1}, pages = {111-120}, pmid = {24435545}, issn = {1432-184X}, support = {R01 AI083256/AI/NIAID NIH HHS/United States ; R01AI083256/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; *Biofilms ; Cystic Fibrosis/microbiology ; Drug Resistance, Bacterial/*genetics ; Genes, Bacterial ; Humans ; Imipenem/*pharmacology ; Mutation ; Porins/*genetics/physiology ; Pseudomonas aeruginosa/*drug effects/genetics/physiology ; Sputum/microbiology ; }, abstract = {Pseudomonas aeruginosa, a ubiquitous environmental organism, is a difficult-to-treat opportunistic pathogen due to its broad-spectrum antibiotic resistance and its ability to form biofilms. In this study, we investigate the link between resistance to a clinically important antibiotic, imipenem, and biofilm formation. First, we observed that the laboratory strain P. aeruginosa PAO1 carrying a mutation in the oprD gene, which confers resistance to imipenem, showed a modest reduction in biofilm formation. We also observed an inverse relationship between imipenem resistance and biofilm formation for imipenem-resistant strains selected in vitro, as well as for clinical isolates. We identified two clinical isolates of P. aeruginosa from the sputum of cystic fibrosis patients that formed robust biofilms, but were sensitive to imipenem (MIC ≤ 2 μg/ml). To test the hypothesis that there is a general link between imipenem resistance and biofilm formation, we performed transposon mutagenesis of these two clinical strains to identify mutants defective in biofilm formation, and then tested these mutants for imipenem resistance. Analysis of the transposon mutants revealed a role for previously described biofilm factors in these clinical isolates of P. aeruginosa, including mutations in the pilY1, pilX, pilW, algC, and pslI genes, but none of the biofilm-deficient mutants became imipenem resistant (MIC ≥ 8 μg/ml), arguing against a general link between biofilm formation and resistance to imipenem. Thus, assessing biofilm formation capabilities of environmental isolates is unlikely to serve as a good predictor of imipenem resistance. We also discuss our findings in light of the limited literature addressing planktonic antibiotic resistance factors that impact biofilm formation.}, }
@article {pmid24435544, year = {2014}, author = {Corneo, PE and Pellegrini, A and Cappellin, L and Gessler, C and Pertot, I}, title = {Moderate warming in microcosm experiment does not affect microbial communities in temperate vineyard soils.}, journal = {Microbial ecology}, volume = {67}, number = {3}, pages = {659-670}, pmid = {24435544}, issn = {1432-184X}, mesh = {Agriculture ; Bacteria/classification/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Climate Change ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; Fungi/classification/genetics/isolation &amp; purification/*physiology ; *Hot Temperature ; Italy ; Seasons ; *Soil Microbiology ; }, abstract = {Changes in the soil microbial community structure can lead to dramatic changes in the soil ecosystem. Temperature, which is projected to increase with climate change, is commonly assumed to affect microbial communities, but its effects on agricultural soils are not fully understood. We collected soil samples from six vineyards characterised by a difference of about 2 °C in daily soil temperature over the year and simulated in a microcosm experiment different temperature regimes over a period of 1 year: seasonal fluctuations in soil temperature based on the average daily soil temperature measured in the field; soil temperature warming (2 °C above the normal seasonal temperatures); and constant temperatures normally registered in these temperate soils in winter (3 °C) and in summer (20 °C). Changes in the soil bacterial and fungal community structures were analysed by automated ribosomal intergenic spacer analysis (ARISA). We did not find any effect of warming on soil bacterial and fungal communities, while stable temperatures affected the fungal more than the bacterial communities, although this effect was soil dependent. The soil bacterial community exhibited soil-dependent seasonal fluctuations, while the fungal community was mainly stable. Each soil harbours different microbial communities that respond differently to seasonal temperature fluctuations; therefore, any generalization regarding the effect of climate change on soil communities should be made carefully.}, }
@article {pmid24425229, year = {2014}, author = {Hanson, BT and Hewson, I and Madsen, EL}, title = {Metaproteomic survey of six aquatic habitats: discovering the identities of microbial populations active in biogeochemical cycling.}, journal = {Microbial ecology}, volume = {67}, number = {3}, pages = {520-539}, pmid = {24425229}, issn = {1432-184X}, mesh = {Bacterial Proteins/*genetics/metabolism ; Biodiversity ; Chromatography, Liquid ; Cyanobacteria/classification/genetics/*physiology ; Fresh Water/microbiology ; Molecular Sequence Data ; Pacific Ocean ; Phylogeny ; Phylogeography ; Proteobacteria/classification/genetics/*physiology ; *Proteomics ; Seawater/microbiology ; Sequence Analysis, DNA ; Tandem Mass Spectrometry ; United States ; }, abstract = {Our goal is to strengthen the foundations of metaproteomics as a microbial community analysis tool that links the functional identity of actively expressed gene products with host phylogeny. We used shotgun metaproteomics to survey waters in six disparate aquatic habitats (Cayuga Lake, NY; Oneida Lake, NY; Gulf of Maine; Chesapeake Bay, MD; Gulf of Mexico; and the South Pacific). Peptide pools prepared from filter-gathered microbial biomass, analyzed by nano-liquid chromatography-mass spectrometry (MS/MS) generating 9,693 ± 1,073 mass spectra identified 326 ± 107 bacterial proteins per sample. Distribution of proteobacterial (Alpha and Beta) and cyanobacterial (Prochlorococcus and Synechococcus spp.) protein hosts across all six samples was consistent with the previously published biogeography for these microorganisms. Marine samples were enriched in transport proteins (TRAP-type for dicarboxylates and ATP binding cassette (ABC)-type for amino acids and carbohydrates) compared with the freshwater samples. We were able to match in situ expression of many key proteins catalyzing C-, N-, and S-cycle processes with their bacterial hosts across all six habitats. Pelagibacter was identified as the host of ABC-type sugar-, organic polyanion-, and glycine betaine-transport proteins; this extends previously published studies of Pelagibacter's in situ biogeochemical role in marine C- and N-metabolism. Proteins matched to Ruegeria confirmed these organism's role in marine waters oxidizing both carbon monoxide and sulfide. By documenting both processes expressed in situ and the identity of host cells, metaproteomics tested several existing hypotheses about ecophysiological processes and provided fodder for new ones.}, }
@article {pmid24419542, year = {2014}, author = {Siles, JA and González-Menéndez, V and Platas, G and Sampedro, I and García-Romera, I and Bills, GF}, title = {Effects of dry olive residue transformed by Coriolopsis floccosa (Polyporaceae) on the distribution and dynamic of a culturable fungal soil community.}, journal = {Microbial ecology}, volume = {67}, number = {3}, pages = {648-658}, pmid = {24419542}, issn = {1432-184X}, mesh = {Cluster Analysis ; Colony Count, Microbial ; DNA, Fungal/chemistry/genetics ; Filtration ; Fungi/classification/genetics/growth &amp; development/*pathogenicity ; Molecular Sequence Data ; Olea/*metabolism ; Phylogeny ; Sequence Analysis, DNA ; *Soil Microbiology ; Spain ; }, abstract = {Dry olive residue (DOR) is an abundant waste product resulting from a two-phase olive oil extraction system. Due to its high organic and mineral content, this material has been proposed as an organic soil amendment; however, it presents phytotoxic and microtoxic properties. Thus, a pretreatment is necessary before its application to soil. Among the strategies for the bioremediation of DOR is treatment with ligninolytic fungi, e.g. Coriolopsis floccosa. This work aimed to assess the diversity of culturable fungi in a soil of the southeast Iberian Peninsula and to evaluate the short-term impact of untransformed and C. floccosa-transformed DOR on soil mycobiota. A total of 1,733 strains were isolated by the particle filtration method and were grouped among 109 different species using morphological and molecular methods. The majority of isolates were ascomycetes and were concentrated among three orders: Hypocreales, Eurotiales and Capnodiales. The soil amendment with untransformed DOR was associated with a depression in fungal diversity at 30 days and changes in the proportions of the major species. However, when C. floccosa-transformed DOR was applied to the soil, changes in fungal diversity were less evident, and species composition was similar to unamended soil.}, }
@article {pmid24419541, year = {2014}, author = {Hawkins, AN and Johnson, KW and Bräuer, SL}, title = {Southern Appalachian peatlands support high archaeal diversity.}, journal = {Microbial ecology}, volume = {67}, number = {3}, pages = {587-602}, pmid = {24419541}, issn = {1432-184X}, mesh = {Archaea/classification/genetics/isolation &amp; purification/*physiology ; *Biodiversity ; Gene Library ; Molecular Sequence Data ; North Carolina ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Wetlands ; }, abstract = {Mid-latitude peatlands with a temperate climate are sparsely studied and as such represent a gap in the current knowledge base regarding archaeal populations present and their roles in these environments. Phylogenetic analysis of the archaeal populations among three peatlands in the Southern Appalachians reveal not only methanogenic species but also significant populations of thaumarchaeal and crenarchaeal-related organisms of the uncultured miscellaneous crenarchaeotal group (MCG) and the terrestrial group 1.1c, as well as deep-branching Euryarchaeota primarily within the Lake Dagow sediment and rice cluster V lineages. The Thaum/Crenarchaea and deep-branching Euryarchaea represented approximately 24-83% and 2-18%, respectively, of the total SSU rRNA clones retrieved in each library, and methanogens represented approximately 14-72% of the clones retrieved. Several taxa that are either rare or novel to acidic peatlands were detected including the euryarchaeal SM1K20 cluster and thaumarchaeal/crenarchaeal-related clusters 1.1a, C3, SAGMCG-1, pSL12, and AK59. All three major groups (methanogens, Thaumarchaea/Crenarchaea, and deep-branching Euryarchaea) were detected in the RNA library, suggesting at least a minimum level of maintenance activity. Compared to their northern counterparts, Southern Appalachian peatlands appear to harbor a relatively high diversity of Archaea and exhibit a high level of intra-site heterogeneity.}, }
@article {pmid24416931, year = {2013}, author = {Maity, C and Adak, A and Halder, SK and Jana, A and Ghosh, K and Das Mohapatra, PK and Pati, BR and Mondal, KC}, title = {Analysis of alteration of gut microbial population under the exposure of graded hyperbaric pressures: application of metagenomic approach.}, journal = {Indian journal of experimental biology..}, volume = {51}, number = {11}, pages = {960-968}, pmid = {24416931}, issn = {0019-5189}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Base Sequence ; DNA Primers ; Intestines/*microbiology ; Male ; *Metagenomics ; Microscopy, Electron, Scanning ; Polymerase Chain Reaction ; *Pressure ; Rats ; Species Specificity ; }, abstract = {Gastroenterological disorders are very common at hyperbaric conditions. The present study was conducted to find out the impact of gut flora on the gastrointestinal disorders created at such environmental circumstances. For this, male albino rat were exposed to graded hyperbaric pressures (915 and 1277 mmHg) and large intestinal content was examined for microbial composition using culture based and PCR-DGGE tools. After 30 day exposure, total aerobes (38.54 and 375.57 folds, 1.35 and 1.58 gdi) and E. coli (126.05 and 873.23 folds, 1.31 and 1.44 gdi) were increased whereas total anaerobes (7.01 x 10(4) and 8.84 x 10(3) folds, -1.56 and -1.39 gdi), Enterobacter spp. (-2.45 and -1.00 gdi) and Clostridium perfringens (12.88 and 54.16 folds, -1.38 and -1.75 gdi) were decreased significantly in respect to control after exposure of simulated hyperbaric pressures like at 915 and 1277 mmHg, respectively. Metagenomics study revealed an overall reduction in total microbial profile was noted than control at higher level hyperbaric pressure, i.e., 1277 mmHg air pressure for highest duration of exposure. Though, some new bands also appeared which indicated the expansion of dormant or new microbiota, Variation in the numbers of these newly dominated bacteria was correlated to dose and duration of hyperbaric treatment. The histological results clearly indicated that hyperbaric environment induced severe inflammation in the mucosal and submucosal layer of large intestine. Thus, the result suggest that hyperbaric pressure is an important exogenous factor that strongly modulated the intestinal morphology and microbial ecology, and induced several gastrointestinal ailments during hyperbarism.}, }
@article {pmid24416370, year = {2014}, author = {Sommer, F and Adam, N and Johansson, ME and Xia, L and Hansson, GC and Bäckhed, F}, title = {Altered mucus glycosylation in core 1 O-glycan-deficient mice affects microbiota composition and intestinal architecture.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e85254}, pmid = {24416370}, issn = {1932-6203}, support = {R01 DK085691/DK/NIDDK NIH HHS/United States ; U01 AI095473/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification ; Colitis/chemically induced/*enzymology/immunology/microbiology ; Dextran Sulfate ; Female ; Galactosemias/enzymology/genetics/immunology/microbiology ; Glycosylation ; Intestinal Mucosa/enzymology/immunology/microbiology/*pathology ; Intestines/enzymology/immunology/microbiology/*pathology ; Male ; Mice ; Mice, Knockout ; Microbiota/immunology ; Mucus/*enzymology/immunology/microbiology ; Organ Size ; Polysaccharides/*metabolism ; }, abstract = {A functional mucus layer is a key requirement for gastrointestinal health as it serves as a barrier against bacterial invasion and subsequent inflammation. Recent findings suggest that mucus composition may pose an important selection pressure on the gut microbiota and that altered mucus thickness or properties such as glycosylation lead to intestinal inflammation dependent on bacteria. Here we used TM-IEC C1galt (-/-) mice, which carry an inducible deficiency of core 1-derived O-glycans in intestinal epithelial cells, to investigate the effects of mucus glycosylation on susceptibility to intestinal inflammation, gut microbial ecology and host physiology. We found that TM-IEC C1galt (-/-) mice did not develop spontaneous colitis, but they were more susceptible to dextran sodium sulphate-induced colitis. Furthermore, loss of core 1-derived O-glycans induced inverse shifts in the abundance of the phyla Bacteroidetes and Firmicutes. We also found that mucus glycosylation impacts intestinal architecture as TM-IEC C1galt(-/-) mice had an elongated gastrointestinal tract with deeper ileal crypts, a small increase in the number of proliferative epithelial cells and thicker circular muscle layers in both the ileum and colon. Alterations in the length of the gastrointestinal tract were partly dependent on the microbiota. Thus, the mucus layer plays a role in the regulation of gut microbiota composition, balancing intestinal inflammation, and affects gut architecture.}, }
@article {pmid24412527, year = {2014}, author = {Petrof, EO and Khoruts, A}, title = {From stool transplants to next-generation microbiota therapeutics.}, journal = {Gastroenterology}, volume = {146}, number = {6}, pages = {1573-1582}, pmid = {24412527}, issn = {1528-0012}, support = {R21 AI091907/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Biological Therapy/*methods ; Clostridioides difficile/*growth &amp; development/pathogenicity ; Dysbiosis ; Enterocolitis, Pseudomembranous/epidemiology/microbiology/*therapy ; Epidemics ; Feces/*microbiology ; Host-Pathogen Interactions ; Humans ; Intestines/*microbiology ; *Microbiota ; Recurrence ; Risk Factors ; Treatment Outcome ; }, abstract = {The epidemic of Clostridium difficile infection fueled by new virulent strains of the organism has led to increased use of fecal microbiota transplantation (FMT). The procedure is effective for even the most desperate cases after failure of multiple courses of antibiotics. The approach recognizes microbiota to be integral to normal human physiology, and microbiota being used in FMT represents a new class of therapeutics. Imbalance in the composition and altered activity of the microbiota are associated with many diseases. Consequently, there is growing interest in applying FMT to non-C difficile indications. However, this may succeed only if microbiota therapeutics are developed systematically, based on mechanistic understanding, and applying up-to-date principles of microbial ecology. We discuss 2 pathways in the development of this new therapeutic class: whole microbial communities separated from donor stool and an assembly of specific fecal microorganisms grown in vitro.}, }
@article {pmid24411459, year = {2014}, author = {Bhattacharya, A and Pletschke, BI}, title = {Review of the enzymatic machinery of Halothermothrix orenii with special reference to industrial applications.}, journal = {Enzyme and microbial technology}, volume = {55}, number = {}, pages = {159-169}, doi = {10.1016/j.enzmictec.2013.10.011}, pmid = {24411459}, issn = {1879-0909}, mesh = {Bacteria, Anaerobic/drug effects/*enzymology/growth &amp; development ; Bacterial Proteins/metabolism ; Fermentation ; Forecasting ; Hot Temperature ; Hydrolases/metabolism ; Hydrolysis ; Industrial Microbiology/*methods ; Lakes ; Solvents/pharmacology ; Starch/metabolism ; Tunisia ; Water Microbiology ; }, abstract = {Over the past few decades the extremes at which life thrives has continued to challenge our understanding of physiology, biochemistry, microbial ecology and evolution. Innovative culturing approaches, environmental genome sequencing, and whole genome sequencing have provided new opportunities for the biotechnological exploration of extremophiles. The whole genome sequencing of H. orenii has provided valuable insights not only into the survival and adaptation strategies of thermohalophiles but has also led to the identification of genes encoding biotechnologically relevant enzymes. The present review focuses on the purified and characterized enzymes from H. orenii including amylases, β-glucosidase, fructokinase, and ribokinase--along with uncharacterized but industrially important enzymes encoded by the genes identified in the genome such as β-galactosidases, mannosidases, pullulanases, chitinases, α-L-arabinofuranosidases and other glycosyl hydrolases of commercial interest. This review highlights the importance of the enzymes and their applications in different sectors and why future research for exploring the enzymatic machinery of H. orenii should focus on the expression, purification, and characterization of the novel proteins in H. orenii and their feasible application to pertinent industrial sectors. H. orenii is an anaerobe; genome sequencing studies have also revealed the presence of enzymes for gluconeogenesis and fermentation to ethanol and acetate, making H. orenii an attractive strain for the conversion of starch into bioethanol.}, }
@article {pmid24407313, year = {2014}, author = {Ortiz, R and Párraga, M and Navarrete, J and Carrasco, I and de la Vega, E and Ortiz, M and Herrera, P and Jurgens, JA and Held, BW and Blanchette, RA}, title = {Investigations of biodeterioration by fungi in historic wooden churches of Chiloé, Chile.}, journal = {Microbial ecology}, volume = {67}, number = {3}, pages = {568-575}, pmid = {24407313}, issn = {1432-184X}, mesh = {Ascomycota/classification/genetics/*isolation &amp; purification/*metabolism ; Basidiomycota/classification/genetics/*isolation &amp; purification/*metabolism ; Chile ; Construction Materials/microbiology ; DNA, Fungal/genetics/metabolism ; DNA, Ribosomal Spacer/genetics ; Molecular Sequence Data ; Sequence Analysis, DNA ; Wood/*microbiology ; }, abstract = {The use of wood in construction has had a long history and Chile has a rich cultural heritage of using native woods for building churches and other important structures. In 2000, UNESCO designated a number of the historic churches of Chiloé, built entirely of native woods, as World Heritage Sites. These unique churches were built in the late 1700 s and throughout the 1800 s, and because of their age and exposure to the environment, they have been found to have serious deterioration problems. Efforts are underway to better understand these decay processes and to carryout conservation efforts for the long-term preservation of these important structures. This study characterized the types of degradation taking place and identified the wood decay fungi obtained from eight historic churches in Chiloé, seven of them designated as UNESCO World Heritage sites. Micromorphological observations identified white, brown and soft rot in the structural woods and isolations provided pure cultures of fungi that were identified by sequencing of the internal transcribed region of rDNA. Twenty-nine Basidiomycota and 18 Ascomycota were found. These diverse groups of fungi represent several genera and species not previously reported from Chile and demonstrates a varied microflora is causing decay in these historic buildings.}, }
@article {pmid24402370, year = {2014}, author = {Duchet, C and Tetreau, G and Marie, A and Rey, D and Besnard, G and Perrin, Y and Paris, M and David, JP and Lagneau, C and Després, L}, title = {Persistence and recycling of bioinsecticidal Bacillus thuringiensis subsp. israelensis spores in contrasting environments: evidence from field monitoring and laboratory experiments.}, journal = {Microbial ecology}, volume = {67}, number = {3}, pages = {576-586}, pmid = {24402370}, issn = {1432-184X}, mesh = {Animals ; *Bacillus thuringiensis ; Culicidae/microbiology ; *Environment ; France ; Larva ; *Mosquito Control ; Spores, Bacterial ; }, abstract = {Sprays of commercial preparations of the bacterium Bacillus thuringiensis subsp. israelensis are widely used for the control of mosquito larvae. Despite an abundant literature on B. thuringiensis subsp. israelensis field efficiency on mosquito control, few studies have evaluated the fate of spores in the environment after treatments. In the present article, two complementary experiments were conducted to study the effect of different parameters on B. thuringiensis subsp. israelensis persistence and recycling, in field conditions and in the laboratory. First, we monitored B. thuringiensis subsp. israelensis persistence in the field in two contrasting regions in France: the Rhône-Alpes region, where mosquito breeding sites are temporary ponds under forest cover with large amounts of decaying leaf matter on the ground and the Mediterranean region characterized by open breeding sites such as brackish marshes. Viable B. thuringiensis subsp. israelensis spores can persist for months after a treatment, and their quantity is explained both by the vegetation type and by the number of local treatments. We found no evidence of B. thuringiensis subsp. israelensis recycling in the field. Then, we tested the effect of water level, substrate type, salinity and presence of mosquito larvae on the persistence/recycling of B. thuringiensis subsp. israelensis spores in controlled laboratory conditions (microcosms). We found no effect of change in water level or salinity on B. thuringiensis subsp. israelensis persistence over time (75 days). B. thuringiensis subsp. israelensis spores tended to persist longer in substrates containing organic matter compared to sand-only substrates. B. thuringiensis subsp. israelensis recycling only occurred in presence of mosquito larvae but was unrelated to the presence of organic matter.}, }
@article {pmid24402369, year = {2014}, author = {Perlman, SJ and Dowdy, NJ and Harris, LR and Khalid, M and Kelly, SE and Hunter, MS}, title = {Factors affecting the strength of Cardinium-induced cytoplasmic incompatibility in the parasitic wasp Encarsia pergandiella (Hymenoptera: Aphelinidae).}, journal = {Microbial ecology}, volume = {67}, number = {3}, pages = {671-678}, pmid = {24402369}, issn = {1432-184X}, mesh = {Animals ; Bacteroidetes/genetics/*physiology ; Cytoplasm/physiology ; Female ; Male ; Reproduction ; *Symbiosis ; Wasps/genetics/growth &amp; development/*microbiology/*physiology ; }, abstract = {Bacteria that cause cytoplasmic incompatibility (CI) are among the most common maternally transmitted parasites of insects. In CI, uninfected females produce few or no offspring when they mate with infected males and, as a result, are often at a reproductive disadvantage relative to infected females. Two different bacteria are known to cause CI, Wolbachia and Cardinium. CI Cardinium was discovered more recently and has been little studied. Here, factors that could influence the reduction in reproductive output in a CI cross, or CI "strength," were explored in the parasitic wasp Encarsia pergandiella. Cardinium in this wasp exhibits variable CI strength. Experiments tested the effect of male age, male size, male host species, Cardinium density, and male development time on CI strength. We found a striking effect of male development time, with males that took longer to develop exhibiting stronger CI when mated to uninfected females. Male age had little effect; although in one experiment, the oldest males exhibited stronger CI. Male size, host species, and bacterial density had no effect on the strength of CI. Identifying the factors that control CI are crucial for understanding the dynamics of infection, as well as the success of strategies that aim to use CI microbes to control insect pests and disease vectors.}, }
@article {pmid24402368, year = {2014}, author = {Soto, W and Rivera, FM and Nishiguchi, MK}, title = {Ecological diversification of Vibrio fischeri serially passaged for 500 generations in novel squid host Euprymna tasmanica.}, journal = {Microbial ecology}, volume = {67}, number = {3}, pages = {700-721}, pmid = {24402368}, issn = {1432-184X}, support = {R25 GM061222/GM/NIGMS NIH HHS/United States ; T34 GM007667/GM/NIGMS NIH HHS/United States ; 1SC1AI081659/AI/NIAID NIH HHS/United States ; R25GM061222/GM/NIGMS NIH HHS/United States ; GM07667-35/GM/NIGMS NIH HHS/United States ; 3SC1AI081659-02S1/AI/NIAID NIH HHS/United States ; SC1 AI081659/AI/NIAID NIH HHS/United States ; }, mesh = {Aliivibrio fischeri/genetics/*physiology ; Animals ; Biofilms ; *Biological Evolution ; Carbon/*metabolism ; Decapodiformes/*microbiology ; Luminescent Measurements ; Selection, Genetic ; }, abstract = {Vibrio fischeri isolated from Euprymna scolopes (Cephalopoda: Sepiolidae) was used to create 24 lines that were serially passaged through the non-native host Euprymna tasmanica for 500 generations. These derived lines were characterized for biofilm formation, swarming motility, carbon source utilization, and in vitro bioluminescence. Phenotypic assays were compared between "ES" (E. scolopes) and "ET" (E. tasmanica) V. fischeri wild isolates to determine if convergent evolution was apparent between E. tasmanica evolved lines and ET V. fischeri. Ecological diversification was observed in utilization of most carbon sources examined. Convergent evolution was evident in motility, biofilm formation, and select carbon sources displaying hyperpolymorphic usage in V. fischeri. Convergence in bioluminescence (a 2.5-fold increase in brightness) was collectively evident in the derived lines relative to the ancestor. However, dramatic changes in other properties--time points and cell densities of first light emission and maximal light output and emergence of a lag phase in growth curves of derived lines--suggest that increased light intensity per se was not the only important factor. Convergent evolution implies that gnotobiotic squid light organs subject colonizing V. fischeri to similar selection pressures. Adaptation to novel hosts appears to involve flexible microbial metabolism, establishment of biofilm and swarmer V. fischeri ecotypes, and complex changes in bioluminescence. Our data demonstrate that numerous alternate fitness optima or peaks are available to V. fischeri in host adaptive landscapes, where novel host squids serve as habitat islands. Thus, V. fischeri founder flushes occur during the initiation of light organ colonization that ultimately trigger founder effect diversification.}, }
@article {pmid24402367, year = {2014}, author = {Montassier, E and Batard, E and Massart, S and Gastinne, T and Carton, T and Caillon, J and Le Fresne, S and Caroff, N and Hardouin, JB and Moreau, P and Potel, G and Le Vacon, F and de La Cochetière, MF}, title = {16S rRNA gene pyrosequencing reveals shift in patient faecal microbiota during high-dose chemotherapy as conditioning regimen for bone marrow transplantation.}, journal = {Microbial ecology}, volume = {67}, number = {3}, pages = {690-699}, pmid = {24402367}, issn = {1432-184X}, mesh = {Adult ; Antineoplastic Agents/*therapeutic use ; Bacteria/*drug effects/*genetics/isolation &amp; purification ; *Bone Marrow Transplantation ; Chromatography, High Pressure Liquid ; DNA, Bacterial/*genetics/isolation &amp; purification ; Denaturing Gradient Gel Electrophoresis ; Feces/*microbiology ; Female ; France ; High-Throughput Nucleotide Sequencing ; Humans ; Lymphoma, Non-Hodgkin/drug therapy/*therapy ; Male ; Microbiota/*drug effects ; Middle Aged ; Molecular Sequence Data ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA ; }, abstract = {Gastrointestinal disturbances are a side-effect frequently associated with haematological malignancies due to the intensive cytotoxic treatment given in connection with bone marrow transplantation (BMT). However, intestinal microbiota changes during chemotherapy remain poorly described, probably due to the use of culture-based and low-resolution molecular methods in previous studies. The objective of our study was to apply a next generation DNA sequencing technology to analyse chemotherapy-induced changes in faecal microbiota. We included eight patients with non-Hodgkin's lymphoma undergoing one course of BMT conditioning chemotherapy. We collected a prechemotherapy faecal sample, the day before chemotherapy was initiated, and a postchemotherapy sample, collected 1 week after the initiation of chemotherapy. Total DNA was extracted from faecal samples, denaturing high-performance liquid chromatography based on amplification of the V6 to V8 region of the 16S ribosomal RNA (rRNA) gene, and 454-pyrosequencing of the 16 S rRNA gene, using PCR primers targeting the V5 and V6 hypervariable 16S rRNA gene regions were performed. Raw sequence data were screened, trimmed, and filtered using the QIIME pipeline. We observed a steep reduction in alpha diversity and significant differences in the composition of the intestinal microbiota in response to chemotherapy. Chemotherapy was associated with a drastic drop in Faecalibacterium and accompanied by an increase of Escherichia. The chemotherapy-induced shift in the intestinal microbiota could induce severe side effects in immunocompromised cancer patients. Our study is a first step in identifying patients at risk for gastrointestinal disturbances and to promote strategies to prevent this drastic shift in intestinal microbiota.}, }
@article {pmid24402366, year = {2014}, author = {Brinkmann, CM and Neuman, C and Katouli, M and Kurtböke, DI}, title = {Detection of thermoactinomyces species in selected agricultural substrates from Queensland.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {804-809}, pmid = {24402366}, issn = {1432-184X}, mesh = {Agriculture ; Bacterial Adhesion ; Bryophyta/microbiology ; Cell Line ; DNA, Bacterial/genetics ; Geologic Sediments/microbiology ; Manure/microbiology ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Queensland ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Thermoactinomyces/classification/genetics/*isolation &amp; purification/*physiology ; }, abstract = {Selected overheated substrates commercially available for public use in sub-tropical Queensland, Australia were screened for the presence of Thermoactinomyces species using an air sampler. All substrates with the exception of tea tree mulch were found to contain Thermoactinomyces species. Subsequent 16S rDNA oligonucleotide sequencing of the selected eight isolates indicated that some of these species were closely related to previously reported allergenic Thermoactinomyces vulgaris and Laceyella sacchari. In view of this, the isolates were tested to determine their adhesion ability and cytotoxicity to human lung cells (calu-3 cells). The results indicated that all eight isolates were highly adherent and showed cytotoxicity to this cell line. These findings might indicate that the presence of such species in overheated agricultural materials may constitute a public health risk if storage and handling conditions are not optimal and do not meet criteria defined for sub-tropical climates.}, }
@article {pmid24402365, year = {2014}, author = {Menkis, A and Ihrmark, K and Stenlid, J and Vasaitis, R}, title = {Root-associated fungi of Rosa rugosa grown on the frontal dunes of the Baltic Sea Coast in Lithuania.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {769-774}, pmid = {24402365}, issn = {1432-184X}, mesh = {Biodiversity ; DNA, Ribosomal Spacer/genetics ; Endophytes/physiology ; Environment ; Fungi/*physiology ; Lithuania ; Molecular Sequence Data ; Mycorrhizae/physiology ; Plant Roots/microbiology/physiology ; RNA, Fungal/genetics ; Rosa/*microbiology/*physiology ; Sequence Analysis, DNA ; }, abstract = {The aim of the present study was to assess fungal communities associated with fine living roots of Rosa rugosa Thunb grown on the frontal dunes of Curonian Spit at the Baltic Sea coast in Lithuania. The roots of R. rugosa were sampled at five sites (Nida, Preila, Pervalka, Juodkrante and Smiltyne) situated at a distance ca. 5-15 km from each other. Direct amplification, cloning and sequencing of fungal ITS rRNA from the fine roots resulted in 134 high-quality sequences, representing 31 fungal taxa among which saprotrophs and endophytes Mycena sp. (14.2 %), Tumularia sp. (14.2 %), Penicillium spinulosum (11.9 %) and Cadophora malorum (9.0 %) were most common. Arbuscular mycorrhizal fungi including Entrophospora baltica (0.7 %) and Rhizophagus irregularis (0.7 %) and potentially root pathogenic fungi--Ceratobasidium sp. (4.5 %), Fusarium oxysporum (3.0 %), Fusarium culmorum (0.7 %) and Ilyonectria crassa (0.7 %)--were also detected at low proportions. In conclusion, the results demonstrated that the fine roots of R. rugosa are inhabited by various groups of fungi. Although saprotrophs and endophytes were dominant, the detection of arbuscular mycorrhizal fungi indicated that these may be important for mineral nutrition of R. rugosa established on dry and poor fertility coastal dunes.}, }
@article {pmid24402364, year = {2014}, author = {Monticelli, LS and Caruso, G and Decembrini, F and Caroppo, C and Fiesoletti, F}, title = {Role of prokaryotic biomasses and activities in carbon and phosphorus cycles at a coastal, thermohaline front and in offshore waters (Gulf of Manfredonia, Southern Adriatic Sea).}, journal = {Microbial ecology}, volume = {67}, number = {3}, pages = {501-519}, pmid = {24402364}, issn = {1432-184X}, mesh = {Archaea/*physiology ; *Autotrophic Processes ; Bacteria/*metabolism ; Biomass ; *Carbon Cycle ; Environment ; *Heterotrophic Processes ; Italy ; Mediterranean Sea ; Phosphorus/*metabolism ; Seasons ; }, abstract = {The Western areas of the Adriatic Sea are subjected to inputs of inorganic nutrients and organic matter that can modify the trophic status of the waters and consequently, the microbiological processes involved in the carbon and phosphorus biogeochemical cycles, particularly in shallow coastal environments. To explore this topic, a survey was carried out during the spring of 2003 in a particular hydrodynamic area of the Gulf of Manfredonia, where the potential (P) and real (R) rates of four different microbial exoenzymatic activities (EEA) (α [αG] and ß glucosidases [ßG], leucine aminopeptidase [LAP], and alkaline phosphatase [AP]) as well as the P and R rates of prokaryotic heterotrophic production (PHP), AP as well as the P and R rates of PHP, primary production (PPnet), the prokaryotic and phototrophic stocks and basic hydrological parameters were examined. Three different water masses were found, with a thermohaline front (THF) being detected between the warmer and less saline coastal waters and colder and saltier offshore Adriatic waters. Under the general oligotrophic conditions of the entire Gulf, a decreasing gradient from the coastal toward the offshore areas was detected, with PHP, PPnet, stocks and EEA (αG, ßG, AP) being directly correlated with the temperature and inversely correlated with the salinity, whereas opposite relationships were observed for LAP activity. No enhancement of microbiological activities or stocks was observed at the THF. The use of P or R rates of microbiological activities, which decrease particularly for EEA, could result in discrepancies in interpreting the efficiency of several metabolic processes.}, }
@article {pmid24402363, year = {2014}, author = {Lou, Y and Clay, SA and Davis, AS and Dille, A and Felix, J and Ramirez, AH and Sprague, CL and Yannarell, AC}, title = {An affinity-effect relationship for microbial communities in plant-soil feedback loops.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {866-876}, pmid = {24402363}, issn = {1432-184X}, mesh = {Ambrosia/growth &amp; development/*microbiology ; *Bacterial Physiological Phenomena ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; DNA, Intergenic/genetics ; Fungi/*physiology ; Helianthus/growth &amp; development/*microbiology ; *Microbiota ; Midwestern United States ; Oregon ; Polymerase Chain Reaction ; *Soil Microbiology ; Species Specificity ; }, abstract = {Feedback loops involving soil microorganisms can regulate plant populations. Here, we hypothesize that microorganisms are most likely to play a role in plant-soil feedback loops when they possess an affinity for a particular plant and the capacity to consistently affect the growth of that plant for good or ill. We characterized microbial communities using whole-community DNA fingerprinting from multiple "home-and-away" experiments involving giant ragweed (Ambrosia trifida L.) and common sunflower (Helianthus annuus L.), and we looked for affinity-effect relationships in these microbial communities. Using canonical ordination and partial least squares regression, we developed indices expressing each microorganism's affinity for ragweed or sunflower and its putative effect on plant biomass, and we used linear regression to analyze the relationship between microbial affinity and effect. Significant linear affinity-effect relationships were found in 75 % of cases. Affinity-effect relationships were stronger for ragweed than for sunflower, and ragweed affinity-effect relationships showed consistent potential for negative feedback loops. The ragweed feedback relationships indicated the potential involvement of multiple microbial taxa, resulting in strong, consistent affinity-effect relationships in spite of large-scale microbial variability between trials. In contrast, sunflower plant-soil feedback may involve just a few key players, making it more sensitive to underlying microbial variation. We propose that affinity-effect relationship can be used to determine key microbial players in plant-soil feedback against a low "signal-to-noise" background of complex microbial datasets.}, }
@article {pmid24402362, year = {2014}, author = {Lee, OO and Chung, HC and Yang, J and Wang, Y and Dash, S and Wang, H and Qian, PY}, title = {Molecular techniques revealed highly diverse microbial communities in natural marine biofilms on polystyrene dishes for invertebrate larval settlement.}, journal = {Microbial ecology}, volume = {68}, number = {1}, pages = {81-93}, pmid = {24402362}, issn = {1432-184X}, mesh = {Animals ; Aquatic Organisms ; Bacteria/*classification/growth &amp; development ; Biodiversity ; *Biofilms ; Cyanobacteria/classification/growth &amp; development ; DNA, Bacterial/genetics ; Gene Library ; Invertebrates/*physiology ; Larva/physiology ; Microbial Consortia ; Phylogeny ; Polystyrenes ; Proteobacteria/classification/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Seasons ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Biofilm microbial communities play an important role in the larval settlement response of marine invertebrates. However, the underlying mechanism has yet to be resolved, mainly because of the uncertainties in characterizing members in the communities using traditional 16S rRNA gene-based molecular methods and in identifying the chemical signals involved. In this study, pyrosequencing was used to characterize the bacterial communities in intertidal and subtidal marine biofilms developed during two seasons. We revealed highly diverse biofilm bacterial communities that varied with season and tidal level. Over 3,000 operational taxonomic units with estimates of up to 8,000 species were recovered in a biofilm sample, which is by far the highest number recorded in subtropical marine biofilms. Nineteen phyla were found, of which Cyanobacteria and Proteobacteria were the most dominant one in the intertidal and subtidal biofilms, respectively. Apart from these, Actinobacteria, Bacteroidetes, and Planctomycetes were the major groups recovered in both intertidal and subtidal biofilms, although their relative abundance varied among samples. Full-length 16S rRNA gene clone libraries were constructed for the four biofilm samples and showed similar bacterial compositions at the phylum level to those revealed by pyrosequencing. Laboratory assays confirmed that cyrids of the barnacle Balanus amphitrite preferred to settle on the intertidal rather than subtidal biofilms. This preference was independent of the biofilm bacterial density or biomass but was probably related to the biofilm community structure, particularly, the Proteobacterial and Cyanobacterial groups.}, }
@article {pmid24402361, year = {2014}, author = {Li, W and Han, L and Yu, P and Ma, C and Wu, X and Moore, JE and Xu, J}, title = {Molecular characterization of skin microbiota between cancer cachexia patients and healthy volunteers.}, journal = {Microbial ecology}, volume = {67}, number = {3}, pages = {679-689}, pmid = {24402361}, issn = {1432-184X}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/*genetics/isolation &amp; purification ; Cachexia/etiology/*microbiology ; China ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Female ; Humans ; Male ; Metagenome/genetics ; Middle Aged ; Molecular Sequence Data ; Neoplasms/etiology/*microbiology ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Skin/*microbiology ; }, abstract = {Systemic inflammation contributes to both the development of cancer and of cachexia. The microenvironment of bacterial habitats might be changed during the progression of cancer cachexia. The aim of this study was to quantitatively and qualitatively compare the composition of the skin microbiota between cancer cachexia patients and healthy volunteers. Cutaneous bacteria were swabbed at the axillary fossa of 70 cancer cachexia patients and 34 healthy individuals from China. Nested-PCR-denaturing gradient gel electrophoresis (PCR-DGGE) with primers specifically targeting V3 region and quantitative PCR (qPCR) for total bacteria, Corynebacterium spp., Staphylococcus spp., and Staphylococcus epidermidis were performed on all samples. Barcoded 454 pyrosequencing of the V3-V4 regions was performed on 30 randomly selected samples. By comparing diversity and richness indices, we found that the skin microbiome of cachectic cancer patients is less diverse than that of healthy participants, though these differences were not significant. The main microbes that reside on human skin were divided into four phyla: Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes. Staphylococcus spp. and Corynebacterium spp. were the dominant bacteria at the genus level. Significantly fewer Corynebacterium spp. had been observed in cachexia patients compared to healthy subjects. These results suggest that the presence of cancer and cachexia alters human skin bacterial communities. Understanding the changes in microbiota during cancer cachexia may lead to new insights into the syndrome.}, }
@article {pmid24402360, year = {2014}, author = {Gołębiewski, M and Deja-Sikora, E and Cichosz, M and Tretyn, A and Wróbel, B}, title = {16S rDNA pyrosequencing analysis of bacterial community in heavy metals polluted soils.}, journal = {Microbial ecology}, volume = {67}, number = {3}, pages = {635-647}, pmid = {24402360}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Environmental Monitoring ; Metals, Heavy/*analysis ; Molecular Sequence Data ; Poland ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/*analysis ; }, abstract = {Soil contamination with heavy metals is a widespread problem, especially prominent on grounds lying in the vicinity of mines, smelters, and other industrial facilities. Many such areas are located in Southern Poland; they are polluted mainly with Pb, Zn, Cd, or Cu, and locally also with Cr. As for now, little is known about most bacterial species thriving in such soils and even less about a core bacterial community--a set of taxa common to polluted soils. Therefore, we wanted to answer the question if such a set could be found in samples differing physicochemically and phytosociologically. To answer the question, we analyzed bacterial communities in three soil samples contaminated with Pb and Zn and two contaminated with Cr and lower levels of Pb and Zn. The communities were assessed with 16S rRNA gene fragments pyrosequencing. It was found that the samples differed significantly and Zn decreased both diversity and species richness at species and family levels, while plant species richness did not correlate with bacterial diversity. In spite of the differences between the samples, they shared many operational taxonomic units (OTUs) and it was possible to delineate the core microbiome of our sample set. The core set of OTUs comprised members of such taxa as Sphingomonas, Candidatus Solibacter, or Flexibacter showing that particular genera might be shared among sites ~40 km distant.}, }
@article {pmid24402359, year = {2014}, author = {Brian-Jaisson, F and Ortalo-Magné, A and Guentas-Dombrowsky, L and Armougom, F and Blache, Y and Molmeret, M}, title = {Identification of bacterial strains isolated from the Mediterranean Sea exhibiting different abilities of biofilm formation.}, journal = {Microbial ecology}, volume = {68}, number = {1}, pages = {94-110}, pmid = {24402359}, issn = {1432-184X}, mesh = {Bacteria/*classification/isolation &amp; purification ; Bacterial Adhesion ; *Biofilms ; DNA, Bacterial/genetics ; Ecosystem ; France ; Mediterranean Sea ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The Mediterranean Sea has rarely been investigated for the characterization of marine bacteria as compared to other marine environments such as the Atlantic or Pacific Ocean. Bacteria recovered from inert surfaces are poorly studied in these environments, when it has been shown that the community structure of attached bacteria can be dissimilar from that of planktonic bacteria present in the water column. The objectives of this study were to identify and characterize marine bacteria isolated from biofilms developed on inert surfaces immersed in the Mediterranean Sea and to evaluate their capacity to form a biofilm in vitro. Here, 13 marine bacterial strains have been isolated from different supports immersed in seawater in the Bay of Toulon (France). Phylogenetic analysis and different biological and physico-chemical properties have been investigated. Among the 13 strains recovered, 8 different genera and 12 different species were identified including 2 isolates of a novel bacterial species that we named Persicivirga mediterranea and whose genus had never been isolated from the Mediterranean Sea. Shewanella sp. and Pseudoalteromonas sp. were the most preponderant genera recovered in our conditions. The phenotypical characterization revealed that one isolate belonging to the Polaribacter genus differed from all the other ones by its hydrophobic properties and poor ability to form biofilms in vitro. Identifying and characterizing species isolated from seawater including from Mediterranean ecosystems could be helpful for example, to understand some aspects of bacterial biodiversity and to further study the mechanisms of biofilm (and biofouling) development in conditions approaching those of the marine environment.}, }
@article {pmid24402358, year = {2014}, author = {Sandberg, DC and Battista, LJ and Arnold, AE}, title = {Fungal endophytes of aquatic macrophytes: diverse host-generalists characterized by tissue preferences and geographic structure.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {735-747}, pmid = {24402358}, issn = {1432-184X}, support = {R01 CA090265/CA/NCI NIH HHS/United States ; }, mesh = {Arizona ; Biodiversity ; Endophytes/classification/*physiology ; Fungi/classification/*physiology ; Geography ; Lakes/microbiology ; Plants/*microbiology ; *Symbiosis ; }, abstract = {Most studies of endophytic symbionts have focused on terrestrial plants, neglecting the ecologically and economically important plants present in aquatic ecosystems. We evaluated the diversity, composition, host and tissue affiliations, and geographic structure of fungal endophytes associated with common aquatic plants in lentic waters in northern Arizona, USA. Endophytes were isolated in culture from roots and photosynthetic tissues during two growing seasons. A total of 226 isolates representing 60 putative species was recovered from 9,600 plant tissue segments. Although isolation frequency was low, endophytes were phylogenetically diverse and species-rich. Comparisons among the most thoroughly sampled species and reservoirs revealed that isolation frequency and diversity did not differ significantly between collection periods, among species, among reservoirs, or as a function of depth. However, community structure differed significantly among reservoirs and tissue types. Phylogenetic analyses of a focal genus (Penicillium) corroborated estimates of species boundaries and informed community analyses, highlighting clade- and genotype-level affiliations of aquatic endophytes with both sediment- and waterborne fungi, and endophytes of proximate terrestrial plants. Together these analyses provide a first quantitative examination of endophytic associations in roots and foliage of aquatic plants and can be used to optimize survey strategies for efficiently capturing fungal biodiversity at local and regional scales.}, }
@article {pmid24401855, year = {2014}, author = {Schwab, C and Berry, D and Rauch, I and Rennisch, I and Ramesmayer, J and Hainzl, E and Heider, S and Decker, T and Kenner, L and Müller, M and Strobl, B and Wagner, M and Schleper, C and Loy, A and Urich, T}, title = {Longitudinal study of murine microbiota activity and interactions with the host during acute inflammation and recovery.}, journal = {The ISME journal}, volume = {8}, number = {5}, pages = {1101-1114}, pmid = {24401855}, issn = {1751-7370}, support = {P 25369/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Bacteria/*classification/genetics ; Butyrates/metabolism ; Colitis/chemically induced/genetics/*microbiology ; Dextran Sulfate ; Disease Models, Animal ; Flagellin/genetics ; Longitudinal Studies ; Mice ; *Microbiota ; Mucins/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Although alterations in gut microbiota composition during acute colitis have been repeatedly observed, associated functional changes and the recovery from dysbiosis received little attention. In this study, we investigated structure and function of the gut microbiota during acute inflammation and recovery in a dextran sodium sulfate (DSS)-colitis mouse model using metatranscriptomics, bacterial 16S rRNA gene amplicon sequencing and monitoring of selected host markers. Parallel to an increase of host markers of inflammation during acute colitis, we observed relative abundance shifts and alterations in phylotype composition of the dominant bacterial orders Clostridiales and Bacteroidales, and an increase of the low abundant Enterobacteriales, Deferribacterales, Verrucomicrobiales and Erysipelotrichales. During recovery, the microbiota began to resume, but did not reach its original composition until the end of the experiment. Microbial gene expression was more resilient to disturbance, with pre-perturbation-type transcript profiles appearing quickly after acute colitis. The decrease of Clostridiales during inflammation correlated with a reduction of transcripts related to butyrate formation, suggesting a disturbance in host-microbe signalling and mucosal nutrient provision. The impact of acute inflammation on the Clostridiales was also characterized by a significant downregulation of their flagellin-encoding genes. In contrast, the abundance of members of the Bacteroidales increased along with an increase in transcripts related to mucin degradation. We propose that acute inflammation triggered a selective reaction of the immune system against flagella of commensals and temporarily altered murine microbiota composition and functions relevant for the host. Despite changes in specific interactions, the host-microbiota homeostasis revealed a remarkable ability for recovery.}, }
@article {pmid24394564, year = {2014}, author = {Dolan, JR and Pierce, RW and Bachy, C}, title = {Cyttarocylis ampulla, a polymorphic tintinnid ciliate of the marine plankton.}, journal = {Protist}, volume = {165}, number = {1}, pages = {66-80}, doi = {10.1016/j.protis.2013.11.002}, pmid = {24394564}, issn = {1618-0941}, mesh = {*Aquatic Organisms ; Ciliophora/*classification/*cytology/isolation &amp; purification/physiology ; Phylogeography ; *Plankton ; *Polymorphism, Genetic ; Seawater/*parasitology ; }, abstract = {Tintinnid species are traditionally distinguished via lorica features. Recently, sequencing has revealed polymorphism, i.e., genetically identical individuals with distinct lorica morphologies. One such polymorphic species is Cyttarocylis ampulla; individuals can display lorica morphologies of formally different species of Cyttarocylis and Petalotricha, well-represented in the literature. We compiled and analysed a global database of species records to determine if there is a main form and if different morphotypes have distinct temporal or spatial distributions. The two genera show very similar widespread distributions but with some statistical evidence of spatial segregation. Examining co-occurrence among the common 'species' we found most were rarely found alone, only 6-14% of the records for all species except for 2 forms: C. eucecryphalus and P. ampulla reported alone in 34% and 43%, respectively, of their records. We identify them as the main forms and analysed data of global distributions, spatial distribution across the Mediterranean in summer and winter and temporal distributions from a site in the Adriatic. The two main forms show frequent co-occurrence, similar lack of strong seasonality and widespread geographic distributions. We tentatively conclude that the different lorica morphologies may only reflect conditions of high temporally variability such as quantities and composition of prey. Directions for further research are suggested.}, }
@article {pmid24391809, year = {2013}, author = {Siddharth, J and Holway, N and Parkinson, SJ}, title = {A Western diet ecological module identified from the 'humanized' mouse microbiota predicts diet in adults and formula feeding in children.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e83689}, pmid = {24391809}, issn = {1932-6203}, mesh = {Adult ; Animals ; Bacteria/classification/genetics/*growth &amp; development ; *Bottle Feeding ; Breast Feeding ; Child, Preschool ; *Diet ; Feces/*microbiology ; *Feeding Behavior ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenome ; Mice ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The interplay between diet and the microbiota has been implicated in the growing frequency of chronic diseases associated with the Western lifestyle. However, the complexity and variability of microbial ecology in humans and preclinical models has hampered identification of the molecular mechanisms underlying the association of the microbiota in this context. We sought to address two key questions. Can the microbial ecology of preclinical models predict human populations? And can we identify underlying principles that surpass the plasticity of microbial ecology in humans? To do this, we focused our study on diet; perhaps the most influential factor determining the composition of the gut microbiota. Beginning with a study in 'humanized' mice we identified an interactive module of 9 genera allied with Western diet intake. This module was applied to a controlled dietary study in humans. The abundance of the Western ecological module correctly predicted the dietary intake of 19/21 top and 21/21 of the bottom quartile samples inclusive of all 5 Western and 'low-fat' diet subjects, respectively. In 98 volunteers the abundance of the Western module correlated appropriately with dietary intake of saturated fatty acids, fat-soluble vitamins and fiber. Furthermore, it correlated with the geographical location and dietary habits of healthy adults from the Western, developing and third world. The module was also coupled to dietary intake in children (and piglets) correlating with formula (vs breast) feeding and associated with a precipitous development of the ecological module in young children. Our study provides a conceptual platform to translate microbial ecology from preclinical models to humans and identifies an ecological network module underlying the association of the gut microbiota with Western dietary habits.}, }
@article {pmid24391805, year = {2013}, author = {Wolf, AB and Vos, M and de Boer, W and Kowalchuk, GA}, title = {Impact of matric potential and pore size distribution on growth dynamics of filamentous and non-filamentous soil bacteria.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e83661}, pmid = {24391805}, issn = {1932-6203}, mesh = {Bacillus/*growth &amp; development ; Models, Biological ; Porosity ; Soil/*chemistry ; *Soil Microbiology ; Streptomyces/*growth &amp; development ; Surface Properties ; Water/*chemistry ; }, abstract = {The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores in unsaturated soils. In particular, fungi perform better than bacteria in soils during drought, a property that has been ascribed to the hyphal growth form of fungi. However, it is unknown if, and to what extent, filamentous bacteria may also display similar advantages over non-filamentous bacteria in soils with low hydraulic connectivity. In addition to allowing for microbial interactions and competition across connected micro-sites, water films also facilitate the motility of non-filamentous bacteria. To examine these issues, we constructed and characterized a series of quartz sand microcosms differing in matric potential and pore size distribution and, consequently, in connection of micro-habitats via water films. Our sand microcosms were used to examine the individual and competitive responses of a filamentous bacterium (Streptomyces atratus) and a motile rod-shaped bacterium (Bacillus weihenstephanensis) to differences in pore sizes and matric potential. The Bacillus strain had an initial advantage in all sand microcosms, which could be attributed to its faster growth rate. At later stages of the incubation, Streptomyces became dominant in microcosms with low connectivity (coarse pores and dry conditions). These data, combined with information on bacterial motility (expansion potential) across a range of pore-size and moisture conditions, suggest that, like their much larger fungal counterparts, filamentous bacteria also use this growth form to facilitate growth and expansion under conditions of low hydraulic conductivity. The sand microcosm system developed and used in this study allowed for precise manipulation of hydraulic properties and pore size distribution, thereby providing a useful approach for future examinations of how these properties influence the composition, diversity and function of soil-borne microbial communities.}, }
@article {pmid24387850, year = {2014}, author = {Justé, A and Malfliet, S and Waud, M and Crauwels, S and De Cooman, L and Aerts, G and Marsh, TL and Ruyters, S and Willems, K and Busschaert, P and Lievens, B}, title = {Bacterial community dynamics during industrial malting, with an emphasis on lactic acid bacteria.}, journal = {Food microbiology}, volume = {39}, number = {}, pages = {39-46}, doi = {10.1016/j.fm.2013.10.010}, pmid = {24387850}, issn = {1095-9998}, mesh = {*Biodiversity ; Food Handling ; Hordeum/chemistry/*microbiology ; Lactic Acid/metabolism ; Lactobacillaceae/classification/genetics/*isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; }, abstract = {Characterization of the microflora during malting is an essential step towards process management and optimization. Up till now, however, microbial characterization in the malting process has mostly been done using culture-dependent methods, probably leading to biased estimates of microbial diversity. The aim of this study was to characterize the bacterial communities using two culture-independent methods, including Terminal Restriction Fragment Length Polymorphism (T-RFLP) and 454 pyrosequencing, targeting the 16S rRNA gene. Studied samples originated from two harvest years and two malting houses malting the same batch of barley. Besides targeting the entire bacterial community (T-RFLP), emphasis was put on lactic acid bacteria (LAB) (T-RFLP and 454 pyrosequencing). The overall bacterial community richness was limited, but the community structure changed during the process. Zooming in on the LAB community using 454 pyrosequencing revealed a total of 47 species-level operational taxonomic units (OTUs). LAB diversity appeared relatively limited since 88% of the sequences were covered by the same five OTUs (representing members of Weissella, Lactobacillus and Leuconostoc) present in all samples investigated. Fluctuations in the relative abundances of the dominant LAB were observed with the process conditions. In addition, both the year of harvest and malting house influenced the LAB community structure.}, }
@article {pmid24386174, year = {2013}, author = {Torrazza, RM and Ukhanova, M and Wang, X and Sharma, R and Hudak, ML and Neu, J and Mai, V}, title = {Intestinal microbial ecology and environmental factors affecting necrotizing enterocolitis.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e83304}, pmid = {24386174}, issn = {1932-6203}, support = {R01 HD059143/HD/NICHD NIH HHS/United States ; R01 HD 059143/HD/NICHD NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Bifidobacterium/classification/genetics ; Biodiversity ; Case-Control Studies ; Cluster Analysis ; Enterocolitis, Necrotizing/drug therapy/*etiology/microbiology ; *Environment ; Female ; Humans ; Infant, Newborn ; Infant, Premature ; Infant, Premature, Diseases/drug therapy/*etiology/microbiology ; Intestines/drug effects/*microbiology/*pathology ; Male ; Metagenome ; Microbiota ; RNA, Ribosomal, 16S ; Risk Factors ; }, abstract = {Necrotizing enterocolitis (NEC) is the most devastating intestinal disease affecting preterm infants. In addition to being associated with short term mortality and morbidity, survivors are left with significant long term sequelae. The cost of caring for these infants is high. Epidemiologic evidence suggests that use of antibiotics and type of feeding may cause an intestinal dysbiosis important in the pathogenesis of NEC, but the contribution of specific infectious agents is poorly understood. Fecal samples from preterm infants ≤ 32 weeks gestation were analyzed using 16S rRNA based methods at 2, 1, and 0 weeks, prior to diagnosis of NEC in 18 NEC cases and 35 controls. Environmental factors such as antibiotic usage, feeding type (human milk versus formula) and location of neonatal intensive care unit (NICU) were also evaluated. Microbiota composition differed between the three neonatal units where we observed differences in antibiotic usage. In NEC cases we observed a higher proportion of Proteobacteria (61%) two weeks and of Actinobacteria (3%) 1 week before diagnosis of NEC compared to controls (19% and 0.4%, respectively) and lower numbers of Bifidobacteria counts and Bacteroidetes proportions in the weeks before NEC diagnosis. In the first fecal samples obtained during week one of life we detected a novel signature sequence, distinct from but matching closest to Klebsiella pneumoniae, that was strongly associated with NEC development later in life. Infants who develop NEC exhibit a different pattern of microbial colonization compared to controls. Antibiotic usage correlated with these differences and combined with type of feeding likely plays a critical role in the development of NEC.}, }
@article {pmid24386128, year = {2013}, author = {Mir, K and Neuhaus, K and Bossert, M and Schober, S}, title = {Short barcodes for next generation sequencing.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e82933}, pmid = {24386128}, issn = {1932-6203}, mesh = {DNA/*chemistry ; High-Throughput Nucleotide Sequencing/*methods ; Sequence Analysis, DNA ; }, abstract = {We consider the design and evaluation of short barcodes, with a length between six and eight nucleotides, used for parallel sequencing on platforms where substitution errors dominate. Such codes should have not only good error correction properties but also the code words should fulfil certain biological constraints (experimental parameters). We compare published barcodes with codes obtained by two new constructions methods, one based on the currently best known linear codes and a simple randomized construction method. The evaluation done is with respect to the error correction capabilities, barcode size and their experimental parameters and fundamental bounds on the code size and their distance properties. We provide a list of codes for lengths between six and eight nucleotides, where for length eight, two substitution errors can be corrected. In fact, no code with larger minimum distance can exist.}, }
@article {pmid24385973, year = {2013}, author = {Fabisch, M and Beulig, F and Akob, DM and Küsel, K}, title = {Surprising abundance of Gallionella-related iron oxidizers in creek sediments at pH 4.4 or at high heavy metal concentrations.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {390}, pmid = {24385973}, issn = {1664-302X}, abstract = {We identified and quantified abundant iron-oxidizing bacteria (FeOB) at three iron-rich, metal-contaminated creek sites with increasing sediment pH from extremely acidic (R1, pH 2.7), to moderately acidic (R2, pH 4.4), to slightly acidic (R3, pH 6.3) in a former uranium-mining district. The geochemical parameters showed little variations over the 1.5 year study period. The highest metal concentrations found in creek sediments always coincided with the lowest metal concentrations in creek water at the slightly acidic site R3. Sequential extractions of R3 sediment revealed large portions of heavy metals (Ni, Cu, Zn, Pb, U) bound to the iron oxide fraction. Light microscopy of glass slides exposed in creeks detected twisted stalks characteristic of microaerobic FeOB of the family Gallionellaceae at R3 but also at the acidic site R2. Sequences related to FeOB such as Gallionella ferruginea, Sideroxydans sp. CL21, Ferritrophicum radicicola, and Acidovorax sp. BrG1 were identified in the sediments. The highest fraction of clone sequences similar to the acidophilic "Ferrovum myxofaciens" was detected in R1. Quantitative PCR using primer sets specific for Gallionella spp., Sideroxydans spp., and "Ferrovum myxofaciens" revealed that ~72% (R2 sediment) and 37% (R3 sediment) of total bacterial 16S rRNA gene copies could be assigned to groups of FeOB with dominance of microaerobic Gallionella spp. at both sites. Gallionella spp. had similar and very high absolute and relative gene copy numbers in both sediment communities. Thus, Gallionella-like organisms appear to exhibit a greater acid and metal tolerance than shown before. Microaerobic FeOB from R3 creek sediment enriched in newly developed metal gradient tubes tolerated metal concentrations of 35 mM Co, 24 mM Ni, and 1.3 mM Cd, higher than those in sediments. Our results will extend the limited knowledge of FeOB at contaminated, moderately to slightly acidic environments.}, }
@article {pmid24376878, year = {2013}, author = {Józefiak, D and Kierończyk, B and Juśkiewicz, J and Zduńczyk, Z and Rawski, M and Długosz, J and Sip, A and Højberg, O}, title = {Dietary nisin modulates the gastrointestinal microbial ecology and enhances growth performance of the broiler chickens.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e85347}, pmid = {24376878}, issn = {1932-6203}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Load/veterinary ; Chickens/*growth &amp; development ; Dietary Supplements ; Dose-Response Relationship, Drug ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Tract/*microbiology ; Male ; Microbiota/*drug effects ; Nisin/*pharmacology ; Pyrans ; Species Specificity ; }, abstract = {Due to antimicrobial properties, nisin is one of the most commonly used and investigated bacteriocins for food preservation. Surprisingly, nisin has had limited use in animal feed as well as there are only few reports on its influence on microbial ecology of the gastrointestinal tract (GIT). The present study therefore aimed at investigating effects of dietary nisin on broiler chicken GIT microbial ecology and performance in comparison to salinomycin, the widely used ionophore coccidiostat. In total, 720 one-day-old male Ross 308 chicks were randomly distributed to six experimental groups. The positive control (PC) diet was supplemented with salinomycin (60 mg/kg). The nisin (NI) diets were supplemented with increasing levels (100, 300, 900 and 2700 IU nisin/g, respectively) of the bacteriocin. The negative control (NC) diet contained no additives. At slaughter (35 days of age), activity of specific bacterial enzymes (α- and β-glucosidases, α-galactosidases and β-glucuronidase) in crop, ileum and caeca were significantly higher (P<0.05) in the NC group, and nisin supplementation decreased the enzyme activities to levels observed for the PC group. A similar inhibitory influence on bacterial activity was reflected in the levels of short-chain fatty acids (SCFA) and putrefactive SCFA (PSCFA) in digesta from crop and ileum; no effect was observed in caeca. Counts of Bacteroides and Enterobacteriacae in ileum digesta were significantly (P<0.001) decreased by nisin and salinomycin, but no effects were observed on the counts of Clostridium perfringens, Lactobacillus/Enterococcus and total bacteria. Like salinomycin, nisin supplementation improved broiler growth performance in a dose-dependent manner; compared to the NC group, the body weight gain of the NI900 and NI2700 groups was improved by 4.7 and 8.7%, respectively. Our findings suggest that dietary nisin exerts a mode of action similar to salinomycin and could be considered as a dietary supplement for broiler chickens.}, }
@article {pmid24376864, year = {2013}, author = {Gonçalves, PF and Klepac-Ceraj, V and Huang, H and Paster, BJ and Aukhil, I and Wallet, SM and Shaddox, LM}, title = {Correlation of Aggregatibacter actinomycetemcomitans detection with clinical/immunoinflammatory profile of localized aggressive periodontitis using a 16S rRNA microarray method: a cross-sectional study.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e85066}, pmid = {24376864}, issn = {1932-6203}, support = {R01 DE019456/DE/NIDCR NIH HHS/United States ; R01DE019456/DE/NIDCR NIH HHS/United States ; }, mesh = {Aggregatibacter actinomycetemcomitans/*genetics ; Aggressive Periodontitis/*genetics ; Brazil ; Cross-Sectional Studies ; Cytokines/analysis ; Gingival Crevicular Fluid/chemistry ; Humans ; Lipopolysaccharides/blood ; Microarray Analysis/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVE: The objective of this study was to determine whether the detection of Aggregatibacter actinomycetemcomitans (Aa) correlates with the clinical and immunoinflammatory profile of Localized Aggressive Periodontitis (LAP), as determined by by 16S rRNA gene-based microarray.<br><br>SUBJECTS AND METHODS: Subgingival plaque samples from the deepest diseased site of 30 LAP patients [PD &#x2265; 5 mm, BoP and bone loss] were analyzed by 16S rRNA gene-based microarrays. Gingival crevicular fluid (GCF) samples were analyzed for 14 cyto/chemokines. Peripheral blood was obtained and stimulated in vitro with P.gingivalis and E.coli to evaluate inflammatory response profiles. Plasma lipopolysaccharide (LPS) levels were also measured.<br><br>RESULTS: Aa was detected in 56% of LAP patients and was shown to be an indicator for different bacterial community structures (p<0.01). Elevated levels of pro-inflammatory cyto/chemokines were detected in LPS-stimulated blood samples in both Aa-detected and Aa-non-detected groups (p>0.05). Clinical parameters and serum LPS levels were similar between groups. However, Aa-non-detected GCF contained higher concentration of IL-8 than Aa-detected sites (p<0.05). TNF&#x3b1; and IL1&#x3b2; were elevated upon E.coli LPS stimulation of peripheral blood cells derived from patients with Aa-detected sites.<br><br>CONCLUSIONS: Our findings demonstrate that the detection of Aa in LAP affected sites, did not correlate with clinical severity of the disease at the time of sampling in this cross-sectional study, although it did associate with lower local levels of IL-8, a different subgingival bacterial profile and elevated LPS-induced levels of TNF&#x3b1; and IL1&#x3b2;.}, }
@article {pmid24373130, year = {2014}, author = {Scheublin, TR and Deusch, S and Moreno-Forero, SK and Müller, JA and van der Meer, JR and Leveau, JH}, title = {Transcriptional profiling of Gram-positive Arthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds.}, journal = {Environmental microbiology}, volume = {16}, number = {7}, pages = {2212-2225}, doi = {10.1111/1462-2920.12375}, pmid = {24373130}, issn = {1462-2920}, mesh = {Agar ; Arbutin/biosynthesis ; Arthrobacter/*genetics/metabolism ; Biodegradation, Environmental ; Chlorophenols/metabolism ; *Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; *Genome, Bacterial ; Hydroquinones/metabolism ; Molecular Sequence Annotation ; Phaseolus/metabolism/*microbiology ; Phenol/metabolism ; Plant Leaves/metabolism/*microbiology ; Transcriptome ; }, abstract = {Arthrobacter chlorophenolicus A6 is a Gram-positive, 4-chlorophenol-degrading soil bacterium that was recently shown to be an effective colonizer of plant leaf surfaces. The genetic basis for this phyllosphere competency is unknown. In this paper, we describe the genome-wide expression profile of A.chlorophenolicus on leaves of common bean (Phaseolus vulgaris) compared with growth on agar surfaces. In phyllosphere-grown cells, we found elevated expression of several genes known to contribute to epiphytic fitness, for example those involved in nutrient acquisition, attachment, stress response and horizontal gene transfer. A surprising result was the leaf-induced expression of a subset of the so-called cph genes for the degradation of 4-chlorophenol. This subset encodes the conversion of the phenolic compound hydroquinone to 3-oxoadipate, and was shown to be induced not only by 4-chlorophenol but also hydroquinone, its glycosylated derivative arbutin, and phenol. Small amounts of hydroquinone, but not arbutin or phenol, were detected in leaf surface washes of P.vulgaris by gas chromatography-mass spectrometry. Our findings illustrate the utility of genomics approaches for exploration and improved understanding of a microbial habitat. Also, they highlight the potential for phyllosphere-based priming of bacteria to stimulate pollutant degradation, which holds promise for the application of phylloremediation.}, }
@article {pmid24370864, year = {2014}, author = {Winkelströter, LK and Teixeira, FB and Silva, EP and Alves, VF and De Martinis, EC}, title = {Unraveling microbial biofilms of importance for food microbiology.}, journal = {Microbial ecology}, volume = {68}, number = {1}, pages = {35-46}, pmid = {24370864}, issn = {1432-184X}, mesh = {Bacteria/*growth &amp; development ; Bacterial Adhesion ; *Biofilms ; Food Contamination/*prevention &amp; control ; Food Handling ; *Food Microbiology ; }, abstract = {The presence of biofilms is a relevant risk factors in the food industry due to the potential contamination of food products with pathogenic and spoilage microorganisms. The majority of bacteria are able to adhere and to form biofilms, where they can persist and survive for days to weeks or even longer, depending on the microorganism and the environmental conditions. The biological cycle of biofilms includes several developmental phases such as: initial attachment, maturation, maintenance, and dispersal. Bacteria in biofilms are generally well protected against environmental stress, consequently, extremely difficult to eradicate and detect in food industry. In the present manuscript, some techniques and compounds used to control and to prevent the biofilm formation are presented and discussed. Moreover, a number of novel techniques have been recently employed to detect and evaluate bacteria attached to surfaces, including real-time polymerase chain reaction (PCR), DNA microarray and confocal laser scanning microscopy. Better knowledge on the architecture, physiology and molecular signaling in biofilms can contribute for preventing and controlling food-related spoilage and pathogenic bacteria. The present study highlights basic and applied concepts important for understanding the role of biofilms in bacterial survival, persistence and dissemination in food processing environments.}, }
@article {pmid24370863, year = {2014}, author = {Frydenborg, BR and Krediet, CJ and Teplitski, M and Ritchie, KB}, title = {Temperature-dependent inhibition of opportunistic Vibrio pathogens by native coral commensal bacteria.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {392-401}, pmid = {24370863}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology ; Chitinases/metabolism ; Coculture Techniques ; Glycoside Hydrolases/metabolism ; Peptide Hydrolases/metabolism ; Symbiosis ; *Temperature ; Vibrio/*growth &amp; development/isolation &amp; purification/*metabolism ; Virulence Factors/metabolism ; }, abstract = {Bacteria living within the surface mucus layer of corals compete for nutrients and space. A number of stresses affect the outcome of this competition. The interactions between native microorganisms and opportunistic pathogens largely determine the coral holobiont's overall health and fitness. In this study, we tested the hypothesis that commensal bacteria isolated from the mucus layer of a healthy elkhorn coral, Acropora palmata, are capable of inhibition of opportunistic pathogens, Vibrio shiloi AK1 and Vibrio coralliilyticus. These vibrios are known to cause disease in corals and their virulence is temperature dependent. Elevated temperature (30 °C) increased the cell numbers of one commensal and both Vibrio pathogens in monocultures. We further tested the hypothesis that elevated temperature favors pathogenic organisms by simultaneously increasing the fitness of vibrios and decreasing the fitness of commensals by measuring growth of each species within a co-culture over the course of 1 week. In competition experiments between vibrios and commensals, the proportion of Vibrio spp. increased significantly under elevated temperature. We finished by investigating several temperature-dependent mechanisms that could influence co-culture differences via changes in competitive fitness. The ability of Vibrio spp. to utilize glycoproteins found in A. palmata mucus increased or remained stable when exposed to elevated temperature, while commensals' tended to decrease utilization. In both vibrios and commensals, protease activity increased at 30 °C, while chiA expression increased under elevated temperatures for Vibrio spp. These results provide insight into potential mechanisms through which elevated temperature may select for pathogenic bacterial dominance and lead to disease or a decrease in coral fitness.}, }
@article {pmid24368315, year = {2014}, author = {François, IE and Lescroart, O and Veraverbeke, WS and Marzorati, M and Possemiers, S and Hamer, H and Windey, K and Welling, GW and Delcour, JA and Courtin, CM and Verbeke, K and Broekaert, WF}, title = {Effects of wheat bran extract containing arabinoxylan oligosaccharides on gastrointestinal parameters in healthy preadolescent children.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {58}, number = {5}, pages = {647-653}, doi = {10.1097/MPG.0000000000000285}, pmid = {24368315}, issn = {1536-4801}, mesh = {Abdominal Pain/etiology ; Ammonia/analysis ; Bifidobacterium/isolation &amp; purification ; Child ; Cross-Over Studies ; *Dietary Fiber/analysis ; Double-Blind Method ; Fatty Acids/analysis ; Fatty Acids, Volatile/analysis ; Feces/chemistry/microbiology ; Female ; Flatulence/chemically induced ; Gastrointestinal Tract/drug effects/*microbiology ; Humans ; Hydrogen-Ion Concentration ; Male ; Microbiota/*drug effects ; Oligosaccharides/*administration &amp; dosage/analysis ; Patient Compliance ; Placebos ; Plant Extracts/*administration &amp; dosage/adverse effects ; Prebiotics ; Xylans/*administration &amp; dosage/analysis ; }, abstract = {OBJECTIVES: We assessed whether wheat bran extract (WBE) containing arabinoxylan-oligosaccharides (AXOS) elicited a prebiotic effect and modulated gastrointestinal (GI) parameters in healthy preadolescent children upon consumption in a beverage.<br><br>METHODS: This double-blind randomized placebo-controlled crossover trial evaluated the effects of consuming WBE at 0 (control) or 5.0 g/day for 3 weeks in 29 healthy children (8-12 years). Fecal levels of microbiota, short-chain fatty acids, branched-chain fatty acids, ammonia, moisture, and fecal pH were assessed at the end of each treatment and at the end of a 1-week run-in (RI) period. In addition, the subjects completed questionnaires scoring distress severity of 3 surveyed GI symptoms. Finally, subjects recorded defecation frequency and stool consistency.<br><br>RESULTS: Nominal fecal bifidobacteria levels tended to increase after 5 g/day WBE consumption (P = 0.069), whereas bifidobacteria expressed as percentage of total fecal microbiota was significantly higher upon 5 g/day WBE intake (P = 0.002). Additionally, 5 g/day WBE intake induced a significant decrease in fecal content of isobutyric acid and isovaleric acid (P < 0.01), markers of protein fermentation. WBE intake did not cause a change in distress severity of the 3 surveyed GI symptoms (flatulence, abdominal pain/cramps, and urge to vomit) (P > 0.1).<br><br>CONCLUSIONS: WBE is well tolerated at doses up to 5 g/day in healthy preadolescent children. In addition, the intake of 5 g/day exerts beneficial effects on gut parameters, in particular an increase in fecal bifidobacteria levels relative to total fecal microbiota, and reduction of colonic protein fermentation.}, }
@article {pmid24367073, year = {2014}, author = {Marino, S and Baxter, NT and Huffnagle, GB and Petrosino, JF and Schloss, PD}, title = {Mathematical modeling of primary succession of murine intestinal microbiota.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {1}, pages = {439-444}, pmid = {24367073}, issn = {1091-6490}, support = {U19AI090871/AI/NIAID NIH HHS/United States ; U19 AI090871/AI/NIAID NIH HHS/United States ; R01 HG005975/HG/NHGRI NIH HHS/United States ; R01GM095356/GM/NIGMS NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; R01HG005975/HG/NHGRI NIH HHS/United States ; P30DK034933/DK/NIDDK NIH HHS/United States ; R01 GM099514/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Bacteroidetes ; Computational Biology/methods ; DNA, Bacterial/genetics ; Female ; Genes, rRNA ; Intestines/*microbiology ; Lactobacillus ; Mice ; Mice, Inbred C57BL ; *Microbiota ; *Models, Theoretical ; RNA, Ribosomal, 16S/metabolism ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Understanding the nature of interpopulation interactions in host-associated microbial communities is critical to understanding gut colonization, responses to perturbations, and transitions between health and disease. Characterizing these interactions is complicated by the complexity of these communities and the observation that even if populations can be cultured, their in vitro and in vivo phenotypes differ significantly. Dynamic models are the cornerstone of computational systems biology and a key objective of computational systems biologists is the reconstruction of biological networks (i.e., network inference) from high-throughput data. When such computational models reflect biology, they provide an opportunity to generate testable hypotheses as well as to perform experiments that are impractical or not feasible in vivo or in vitro. We modeled time-series data for murine microbial communities using statistical approaches and systems of ordinary differential equations. To obtain the dense time-series data, we sequenced the 16S ribosomal RNA (rRNA) gene from DNA isolated from the fecal material of germfree mice colonized with cecal contents of conventionally raised animals. The modeling results suggested a lack of mutualistic interactions within the community. Among the members of the Bacteroidetes, there was evidence for closely related pairs of populations to exhibit parasitic interactions. Among the Firmicutes, the interactions were all competitive. These results suggest future animal and in silico experiments. Our modeling approach can be applied to other systems to provide a greater understanding of the dynamics of communities associated with health and disease.}, }
@article {pmid24362769, year = {2014}, author = {Chen, Y and Zhen, Y and He, H and Lu, X and Mi, T and Yu, Z}, title = {Diversity, abundance, and spatial distribution of ammonia-oxidizing β-proteobacteria in sediments from Changjiang Estuary and its adjacent area in East China Sea.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {788-803}, pmid = {24362769}, issn = {1432-184X}, mesh = {Bacterial Proteins/*genetics ; Betaproteobacteria/classification/enzymology/genetics/*physiology ; *Biodiversity ; China ; Estuaries ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Oceans and Seas ; Oxidoreductases/*genetics/*metabolism ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Changjiang Estuary, the largest estuary in China, encompasses a wide range of nutrient loading and trophic levels from the rivers to the sea, providing an ideal natural environment to explore relationships between functional diversity, physical/chemical complexity, and ecosystem function. In this study, molecular biological techniques were used to analyze the community structure and diversity of ammonia-oxidizing bacteria (AOB) in the sediments of Changjiang Estuary and its adjacent waters in East China Sea. The amoA gene (encoding ammonia monooxygenase subunit A) libraries analysis revealed extensive diversity within the β-Proteobacteria group of AOB, which were grouped into Nitrosospira-like and Nitrosomonas-like lineages. The majority of amoA gene sequences fell within Nitrosospira-like clade, and only a few sequences were clustered with the Nitrosomonas-like clade, indicating that Nitrosospira-like lineage may be more adaptable than Nitrosomonas-like lineage in this area. Multivariate statistical analysis indicated that the spatial distribution of the sedimentary β-Proteobacterial amoA genotype assemblages correlated significantly with nitrate, nitrite, and salinity. The vertical profile of amoA gene copies in gravity cores showed that intense sediment resuspension led to a deeper mixing layer. The horizontal distribution pattern of amoA gene copies was nearly correlated with the clayey mud belt in Changjiang Estuary and its adjacent area in East China Sea, where higher β-Proteobacteria phylogenetic diversity was observed. Meanwhile, those areas with high amoA copies in the surface sediments nearly matched those with low concentrations of dissolved oxygen and ammonium in the bottom water.}, }
@article {pmid24362427, year = {2014}, author = {Corcoran, M and Morris, D and De Lappe, N and O'Connor, J and Lalor, P and Dockery, P and Cormican, M}, title = {Commonly used disinfectants fail to eradicate Salmonella enterica biofilms from food contact surface materials.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {4}, pages = {1507-1514}, pmid = {24362427}, issn = {1098-5336}, mesh = {Bacterial Load ; Benzalkonium Compounds/pharmacology ; Biofilms/*drug effects ; Disinfectants/*pharmacology ; *Environmental Microbiology ; *Food Handling ; Microbial Viability/drug effects ; Salmonella enterica/*drug effects/*physiology ; Sodium Hydroxide/pharmacology ; Sodium Hypochlorite/pharmacology ; }, abstract = {Salmonellosis is the second most common cause of food-borne illness worldwide. Contamination of surfaces in food processing environments may result in biofilm formation with a risk of food contamination. Effective decontamination of biofilm-contaminated surfaces is challenging. Using the CDC biofilm reactor, the activities of sodium hypochlorite, sodium hydroxide, and benzalkonium chloride were examined against an early (48-h) and relatively mature (168-h) Salmonella biofilm. All 3 agents result in reduction in viable counts of Salmonella; however, only sodium hydroxide resulted in eradication of the early biofilm. None of the agents achieved eradication of mature biofilm, even at the 90-min contact time. Studies of activity of chemical disinfection against biofilm should include assessment of activity against mature biofilm. The difficulty of eradication of established Salmonella biofilm serves to emphasize the priority of preventing access of Salmonella to postcook areas of food production facilities.}, }
@article {pmid24361532, year = {2014}, author = {Anterrieu, S and Quadri, L and Geurkink, B and Dinkla, I and Bengtsson, S and Arcos-Hernandez, M and Alexandersson, T and Morgan-Sagastume, F and Karlsson, A and Hjort, M and Karabegovic, L and Magnusson, P and Johansson, P and Christensson, M and Werker, A}, title = {Integration of biopolymer production with process water treatment at a sugar factory.}, journal = {New biotechnology}, volume = {31}, number = {4}, pages = {308-323}, doi = {10.1016/j.nbt.2013.11.008}, pmid = {24361532}, issn = {1876-4347}, mesh = {Ammonia/isolation &amp; purification ; Biological Oxygen Demand Analysis ; Biomass ; Biopolymers/*biosynthesis ; Bioreactors/microbiology ; Biotechnology/*methods ; Carbohydrates/*analysis ; *Industrial Waste ; Nitrogen/isolation &amp; purification ; Phylogeny ; Pilot Projects ; Polyhydroxyalkanoates ; Solubility ; *Water Purification ; }, abstract = {The present investigation has focused on generating a surplus denitrifying biomass with high polyhydroxyalkanoate (PHA) producing potential while maintaining water treatment performance in biological nitrogen removal. The motivation for the study was to examine integration of PHA production into the water treatment and residuals management needs at the Suiker Unie sugar beet factory in Groningen, the Netherlands. At the factory, process waters are treated in nitrifying-denitrifying sequencing batch reactors (SBRs) to remove nitrogen found in condensate. Organic slippage (COD) in waters coming from beet washing is the substrate used for denitrification. The full-scale SBR was mimicked at laboratory scale. In two parallel laboratory scale SBRs, a mixed-culture biomass selection strategy of anoxic-feast and aerobic-famine was investigated using the condensate and wash water from Suiker Unie. One laboratory SBR was operated as conventional activated sludge with long solids retention time similar to the full-scale (SRT >16 days) while the other SBR was a hybrid biofilm-activated sludge (IFAS) process with short SRT (4-6 days) for the suspended solids. Both SBRs were found to produce biomass with augmented PHA production potential while sustaining process water treatment for carbon, nitrogen and phosphorus for the factory process waters. PHA producing potential in excess of 60 percent g-PHA/g-VSS was achieved with the lab scale surplus biomass. Surplus biomass of low (4-6 days) and high (>16 days) solids retention time yielded similar results in PHA accumulation potential. However, nitrification performance was found to be more robust for the IFAS SBR. Assessment of the SBR microbial ecology based on 16sDNA and selected PHA synthase genes at full-scale in comparison to biomass from the laboratory scale SBRs suggested that the full-scale process was enriched with a PHA storing microbial community. However, structure-function relationships based on RNA levels for the selected PHA synthases could not be established and, towards this ambition, it is speculated that a wider representation of PHA synthesases would need to be monitored. Additionally at the factory, beet tail press waters coming from the factory beet residuals management activities are available as a carbon source for PHA accumulation. At pilot scale, beet tail press waters were shown to provide a suitable carbon source for mixed culture PHA production in spite of otherwise being of relatively low organic strength (≤ 10 g-COD/L). A copolymer of 3-hydroxybutyrate with 3-hydroxyvalerate (PHBV with 15% HV on a molar basis) of high thermal stability and high weight average molecular mass (980 kDa) was produced from the beet tail press water. The mixed culture accumulation process sustained PHA storage with parallel biomass growth of PHA storing bacteria suggesting a strategy to further leverage the utilization of surplus functional biomass from biological treatment systems. Integration of PHA production into the existing factory water management by using surplus biomass from condensate water treatment and press waters from beet residuals processing was found to be a feasible strategy for biopolymer production.}, }
@article {pmid24361423, year = {2014}, author = {Mathieu, A and Vogel, TM and Simonet, P}, title = {The future of skin metagenomics.}, journal = {Research in microbiology}, volume = {165}, number = {2}, pages = {69-76}, doi = {10.1016/j.resmic.2013.12.002}, pmid = {24361423}, issn = {1769-7123}, mesh = {Humans ; Metagenomics/*methods/trends ; *Microbiota ; Skin/*microbiology ; }, abstract = {Metagenomics, the direct exploitation of environmental microbial DNA, is complementary to traditional culture-based approaches for deciphering taxonomic and functional microbial diversity in a plethora of ecosystems, including those related to the human body such as the mouth, saliva, teeth, gut or skin. DNA extracted from human skin analyzed by sequencing the PCR-amplified rrs gene has already revealed the taxonomic diversity of microbial communities colonizing the human skin ("skin microbiome"). Each individual possesses his/her own skin microbial community structure, with marked taxonomic differences between different parts of the body and temporal evolution depending on physical and chemical conditions (sweat, washing etc.). However, technical limitations due to the low bacterial density at the surface of the human skin or contamination by human DNA still has inhibited extended use of the metagenomic approach for investigating the skin microbiome at a functional level. These difficulties have been overcome in part by the new generation of sequencing platforms that now provide sequences describing the genes and functions carried out by skin bacteria. These methodological advances should help us understand the mechanisms by which these microorganisms adapt to the specific chemical composition of each skin and thereby lead to a better understanding of bacteria/human host interdependence. This knowledge will pave the way for more systemic and individualized pharmaceutical and cosmetic applications.}, }
@article {pmid24359473, year = {2013}, author = {Brzychczy-Wloch, M and Borszewska-Kornacka, M and Gulczynska, E and Wojkowska-Mach, J and Sulik, M and Grzebyk, M and Luchter, M and Heczko, PB and Bulanda, M}, title = {Prevalence of antibiotic resistance in multi-drug resistant coagulase-negative staphylococci isolated from invasive infection in very low birth weight neonates in two Polish NICUs.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {12}, number = {}, pages = {41}, pmid = {24359473}, issn = {1476-0711}, mesh = {Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Multiple, Bacterial ; Genes, Bacterial ; Humans ; Infant, Newborn ; *Infant, Very Low Birth Weight ; Intensive Care Units, Neonatal ; Microbial Sensitivity Tests ; Multiplex Polymerase Chain Reaction ; Poland ; Prevalence ; Staphylococcal Infections/*epidemiology/*microbiology ; Staphylococcus/classification/*drug effects/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Multi-drug resistant coagulaso-negative staphylococci (CNS) have become an increasing problem in nosocomial infections connected with the presence of medical devices. The paper aimed to analyze the prevalence of antibiotic resistance in CNS isolated from invasive infection in very low birth weight (VLBW) neonates.<br><br>METHODS: Continuous prospective target surveillance of infections was conducted in 2009 at two Polish NICUs that participated in the Polish Neonatology Surveillance Network (PNSN). The study covered 386 neonates with VLBW (&#x2264;1500&#xa0;g), among which 262 cases of invasive infection were detected with predominance of CNS (123; 47%). Altogether, 100 CNS strains were analyzed. The resistance phenotypes were determined according to EUCAST. Resistance genes: mecA, ermA, ermB, ermC, msrA, aac(6')/aph(2''), ant(4')-Ia and aph(3')-IIIa were detected using multiplex PCR.<br><br>RESULTS: The most common species was S. epidermidis (63%), then S. haemolyticus (28%) and other CNS (9%). Among S. epidermidis, 98% of isolates were resistant to methicillin, 90% to erythromycin, 39% to clindamycin, 95% to gentamicin, 60% to amikacin, 36% to ofloxacin, 2% to tigecycline, 3% to linezolid and 13% to teicoplanin. Among S. haemolyticus isolates, 100% were resistant to methicillin, erythromycin and gentamicin, 18% to clindamycin, 50% to amikacin, 86% to ofloxacin, 14% to tigecycline and 4% to teicoplanin. No resistance to linezolid was detected for S. haemolyticus isolates. Moreover, all isolates of S. epidermidis and S. haemolyticus were susceptible to vancomycin. The mecA gene was detected in 98% of S. epidermidis isolates and all of S. haemolyticus ones. Among macrolide resistance isolates, the ermC was most common in S. epidermidis (60%) while msrA was prevalent in S. haemolyticus (93%). The ermC gene was indicated in all isolates with cMLSB, whereas mrsA was found in isolates with MSB phenotype. Of the aminoglycoside resistance genes, aac(6')/aph(2'') were present alone in 83% of S. epidermidis, whereas aac(6')/aph(2'') with aph(3')-IIIa were predominant in 84% of S. haemolyticus.<br><br>CONCLUSIONS: Knowing the epidemiology and antibiotic resistance of CNS isolated from invasive infection in VLBW neonates is a key step in developing targeted prevention strategies and reducing antibiotic consumption.}, }
@article {pmid24358364, year = {2013}, author = {Walker, CR and Hautefort, I and Dalton, JE and Overweg, K and Egan, CE and Bongaerts, RJ and Newton, DJ and Cruickshank, SM and Andrew, EM and Carding, SR}, title = {Intestinal intraepithelial lymphocyte-enterocyte crosstalk regulates production of bactericidal angiogenin 4 by Paneth cells upon microbial challenge.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e84553}, pmid = {24358364}, issn = {1932-6203}, support = {/WT_/Wellcome Trust/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Cell Communication ; Cell Line ; Enterocytes/*metabolism ; Interleukin-23/biosynthesis ; Interleukins/pharmacology ; Intestinal Mucosa/*immunology/*metabolism/microbiology ; Lymphocytes/drug effects/immunology/*metabolism ; Mice ; Mice, Knockout ; Paneth Cells/*metabolism ; Receptors, Antigen, T-Cell, gamma-delta/metabolism ; Ribonuclease, Pancreatic/*biosynthesis ; Salmonella/immunology ; Stress, Physiological ; Interleukin-22 ; }, abstract = {Antimicrobial proteins influence intestinal microbial ecology and limit proliferation of pathogens, yet the regulation of their expression has only been partially elucidated. Here, we have identified a putative pathway involving epithelial cells and intestinal intraepithelial lymphocytes (iIELs) that leads to antimicrobial protein (AMP) production by Paneth cells. Mice lacking γδ iIELs (TCRδ(-/-)) express significantly reduced levels of the AMP angiogenin 4 (Ang4). These mice were also unable to up-regulate Ang4 production following oral challenge by Salmonella, leading to higher levels of mucosal invasion compared to their wild type counterparts during the first 2 hours post-challenge. The transfer of γδ iIELs from wild type (WT) mice to TCRδ(-/-) mice restored Ang4 production and Salmonella invasion levels were reduced to those obtained in WT mice. The ability to restore Ang4 production in TCRδ(-/-) mice was shown to be restricted to γδ iIELs expressing Vγ7-encoded TCRs. Using a novel intestinal crypt co-culture system we identified a putative pathway of Ang4 production initiated by exposure to Salmonella, intestinal commensals or microbial antigens that induced intestinal epithelial cells to produce cytokines including IL‑23 in a TLR-mediated manner. Exposure of TCR-Vγ7(+) γδ iIELs to IL-23 promoted IL‑22 production, which triggered Paneth cells to secrete Ang4. These findings identify a novel role for γδ iIELs in mucosal defence through sensing immediate epithelial cell cytokine responses and influencing AMP production. This in turn can contribute to the maintenance of intestinal microbial homeostasis and epithelial barrier function, and limit pathogen invasion.}, }
@article {pmid24358254, year = {2013}, author = {Anderson, KE and Sheehan, TH and Mott, BM and Maes, P and Snyder, L and Schwan, MR and Walton, A and Jones, BM and Corby-Harris, V}, title = {Microbial ecology of the hive and pollination landscape: bacterial associates from floral nectar, the alimentary tract and stored food of honey bees (Apis mellifera).}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e83125}, pmid = {24358254}, issn = {1932-6203}, mesh = {Animals ; Bacteria/*isolation &amp; purification ; Bacteriological Techniques ; Bees/*microbiology/*physiology ; DNA, Bacterial/genetics ; Ecology ; Endophytes/isolation &amp; purification ; Gastrointestinal Tract/*microbiology ; Honey/*microbiology ; Plant Nectar ; *Pollination ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Nearly all eukaryotes are host to beneficial or benign bacteria in their gut lumen, either vertically inherited, or acquired from the environment. While bacteria core to the honey bee gut are becoming evident, the influence of the hive and pollination environment on honey bee microbial health is largely unexplored. Here we compare bacteria from floral nectar in the immediate pollination environment, different segments of the honey bee (Apis mellifera) alimentary tract, and food stored in the hive (honey and packed pollen or "beebread"). We used cultivation and sequencing to explore bacterial communities in all sample types, coupled with culture-independent analysis of beebread. We compare our results from the alimentary tract with both culture-dependent and culture-independent analyses from previous studies. Culturing the foregut (crop), midgut and hindgut with standard media produced many identical or highly similar 16S rDNA sequences found with 16S rDNA clone libraries and next generation sequencing of 16S rDNA amplicons. Despite extensive culturing with identical media, our results do not support the core crop bacterial community hypothesized by recent studies. We cultured a wide variety of bacterial strains from 6 of 7 phylogenetic groups considered core to the honey bee hindgut. Our results reveal that many bacteria prevalent in beebread and the crop are also found in floral nectar, suggesting frequent horizontal transmission. From beebread we uncovered a variety of bacterial phylotypes, including many possible pathogens and food spoilage organisms, and potentially beneficial bacteria including Lactobacillus kunkeei, Acetobacteraceae and many different groups of Actinobacteria. Contributions of these bacteria to colony health may include general hygiene, fungal and pathogen inhibition and beebread preservation. Our results are important for understanding the contribution to pollinator health of both environmentally vectored and core microbiota, and the identification of factors that may affect bacterial detection and transmission, colony food storage and disease susceptibility.}, }
@article {pmid24355817, year = {2014}, author = {Minervini, F and De Angelis, M and Di Cagno, R and Gobbetti, M}, title = {Ecological parameters influencing microbial diversity and stability of traditional sourdough.}, journal = {International journal of food microbiology}, volume = {171}, number = {}, pages = {136-146}, doi = {10.1016/j.ijfoodmicro.2013.11.021}, pmid = {24355817}, issn = {1879-3460}, mesh = {*Biodiversity ; Bread/*microbiology ; *Ecology ; Fermentation ; Flour/microbiology ; *Food Microbiology ; Lactobacillaceae/physiology ; Yeasts/physiology ; }, abstract = {The quality of some leavened, sourdough baked goods is not always consistent, unless a well propagated sourdough starter culture is used for the dough fermentation. Among the different types of sourdough used, the traditional sourdough has attracted the interest of researchers, mainly because of its large microbial diversity, especially with respect to lactic acid bacteria. Variation in this diversity and the factors that cause it will impact on quality and is the subject of this review. Sourdough microbial diversity is mainly caused by the following factors: (i) sourdough is obtained through spontaneous, multi-step fermentation; (ii) it is propagated using flour, whose nutrient content may vary according to the batch and to the crop, and which is naturally contaminated by microorganisms; and (iii) it is propagated under peculiar technological parameters, which vary depending on the historical and cultural background and type of baked good. In the population dynamics leading from flour to mature sourdough, lactic acid bacteria (several species of Lactobacillus sp., Leuconostoc sp., and Weissella sp.) and yeasts (mainly Saccharomyces cerevisiae and Candida sp.) outcompete other microbial groups contaminating flour, and interact with each other at different levels. Ecological parameters qualitatively and quantitatively affecting the dominant sourdough microbiota may be classified into specific technological parameters (e.g., percentage of sourdough used as inoculum, time and temperature of fermentation) and parameters that are not fully controlled by those who manage the propagation of sourdough (e.g., chemical, enzyme and microbial composition of flour). Although some sourdoughs have been reported to harbour a persistent dominant microbiota, the stability of sourdough ecosystem during time is debated. Indeed, several factors may interfere with the persistence of species and strains associations that are typical of a given sourdough: metabolic adaptability to the stressing conditions of sourdough, nutritional and antagonistic interactions among microorganisms, intrinsic robustness of microorganisms, and existence of a stable house microbiota. Further studies have to be performed in order to highlight hidden mechanisms underlying the microbial structure and stability of sourdough. The comprehension of such mechanisms would be helpful to assess the most appropriate conditions that allow keeping a given traditional sourdough as a stable microbial ecosystem, thus preserving, during time, the typical traits of the resulting product.}, }
@article {pmid24355291, year = {2014}, author = {Jenni, S and Vlaeminck, SE and Morgenroth, E and Udert, KM}, title = {Successful application of nitritation/anammox to wastewater with elevated organic carbon to ammonia ratios.}, journal = {Water research}, volume = {49}, number = {}, pages = {316-326}, doi = {10.1016/j.watres.2013.10.073}, pmid = {24355291}, issn = {1879-2448}, mesh = {Ammonia/*analysis ; Anaerobiosis ; Biodegradation, Environmental ; Bioreactors/microbiology ; Carbon/*analysis ; *Nitrification ; Nitrogen/metabolism ; Organic Chemicals/*analysis/isolation &amp; purification ; Oxidation-Reduction ; Particle Size ; Sewage/chemistry/microbiology ; Time Factors ; Wastewater/*chemistry/microbiology ; }, abstract = {The nitritation/anammox process has been mainly applied to high-strength nitrogenous wastewaters with very low biodegradable organic carbon content (<0.5 g COD∙g N(-1)). However, several wastewaters have biodegradable organic carbon to nitrogen (COD/N) ratios between 0.5 and 1.7 g COD∙g N(-1) and thus, contain elevated amounts of organic carbon but not enough for heterotrophic denitrification. In this study, the influence of elevated COD/N ratios was studied on a nitritation/anammox process with suspended sludge. In a step-wise manner, the influent COD/N ratio was increased to 1.4 g COD∙g N(-1) by supplementing digester supernatant with acetate. The increasing availability of COD led to an increase of the nitrogen removal efficiency from around 85% with pure digester supernatant to >95% with added acetate while the nitrogen elimination rate stayed constant (275 ± 40 mg N∙L(-1)∙d(-1)). Anammox activity and abundance of anammox bacteria (AMX) were strongly correlated, and with increasing influent COD/N ratio both decreased steadily. At the same time, heterotrophic denitrification with nitrite and the activity of ammonia oxidising bacteria (AOB) gradually increased. Simultaneously, the sludge retention time (SRT) decreased significantly with increasing COD loading to about 15 d and reached critical values for the slowly growing AMX. When the SRT was increased by reducing biomass loss with the effluent, AMX activity and abundance started to rise again, while the AOB activity remained unaltered. Fluorescent in-situ hybridisation (FISH) showed that the initial AMX community shifted within only 40 d from a mixed AMX community to "Candidatus Brocadia fulgida" as the dominant AMX type with an influent COD/N ratio of 0.8 g COD∙g N(-1) and higher. "Ca. Brocadia fulgida" is known to oxidise acetate, and its ability to outcompete other types of AMX indicates that AMX participated in acetate oxidation. In a later phase, glucose was added to the influent instead of acetate. The new substrate composition did not significantly influence the nitrogen removal nor the AMX activity, and "Ca. Brocadia fulgida" remained the dominant type of AMX. Overall, this study showed that AMX can coexist with heterotrophic bacteria at elevated influent COD/N ratios if a sufficiently high SRT is maintained.}, }
@article {pmid24354737, year = {2014}, author = {Ali, S and Gladieux, P and Rahman, H and Saqib, MS and Fiaz, M and Ahmad, H and Leconte, M and Gautier, A and Justesen, AF and Hovmøller, MS and Enjalbert, J and de Vallavieille-Pope, C}, title = {Inferring the contribution of sexual reproduction, migration and off-season survival to the temporal maintenance of microbial populations: a case study on the wheat fungal pathogen Puccinia striiformis f.sp. tritici.}, journal = {Molecular ecology}, volume = {23}, number = {3}, pages = {603-617}, doi = {10.1111/mec.12629}, pmid = {24354737}, issn = {1365-294X}, mesh = {Basidiomycota/*genetics ; Bayes Theorem ; Berberis/microbiology ; Cluster Analysis ; DNA, Fungal/genetics ; Genetic Variation ; *Genetics, Population ; Genotype ; Microsatellite Repeats ; Multilocus Sequence Typing ; Pakistan ; Plant Diseases/*microbiology ; Population Density ; Seasons ; Sequence Analysis, DNA ; Triticum/*microbiology ; }, abstract = {Understanding the mode of temporal maintenance of plant pathogens is an important domain of microbial ecology research. Due to the inconspicuous nature of microbes, their temporal maintenance cannot be studied directly through tracking individuals and their progeny. Here, we suggest a series of population genetic analyses on molecular marker variation in temporally spaced samples to infer about the relative contribution of sexual reproduction, off-season survival and migration to the temporal maintenance of pathogen populations. We used the proposed approach to investigate the temporal maintenance of wheat yellow rust pathogen, Puccinia striiformis f.sp. tritici (PST), in the Himalayan region of Pakistan. Multilocus microsatellite genotyping of PST isolates revealed high genotypic diversity and recombinant population structure across all locations, confirming the existence of sexual reproduction in this region. The genotypes were assigned to four genetic groups, revealing a clear differentiation between zones with and without Berberis spp., the alternate host of PST, with an additional subdivision within the Berberis zone. The lack of any differentiation between samples across two sampling years, and the very infrequent resampling of multilocus genotypes over years at a given location was consistent with limited over-year clonal survival, and a limited genetic drift. The off-season oversummering population in the Berberis zone, likely to be maintained locally, served as a source of migrants contributing to the temporal maintenance in the non-Berberis zone. Our study hence demonstrated the contribution of both sexual recombination and off-season oversummering survival to the temporal maintenance of the pathogen. These new insights into the population biology of PST highlight the general usefulness of the analytical approach proposed.}, }
@article {pmid24351936, year = {2014}, author = {Müller, AL and de Rezende, JR and Hubert, CR and Kjeldsen, KU and Lagkouvardos, I and Berry, D and Jørgensen, BB and Loy, A}, title = {Endospores of thermophilic bacteria as tracers of microbial dispersal by ocean currents.}, journal = {The ISME journal}, volume = {8}, number = {6}, pages = {1153-1165}, pmid = {24351936}, issn = {1751-7370}, support = {P 20185/FWF_/Austrian Science Fund FWF/Austria ; P 25111/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Arctic Regions ; Bacteria/*classification/genetics/isolation &amp; purification ; Geologic Sediments/microbiology ; Oceans and Seas ; Phylogeny ; Phylogeography ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Spores, Bacterial/genetics ; Temperature ; Water Movements ; }, abstract = {Microbial biogeography is influenced by the combined effects of passive dispersal and environmental selection, but the contribution of either factor can be difficult to discern. As thermophilic bacteria cannot grow in the cold seabed, their inactive spores are not subject to environmental selection. We therefore conducted a global experimental survey using thermophilic endospores that are passively deposited by sedimentation to the cold seafloor as tracers to study the effect of dispersal by ocean currents on the biogeography of marine microorganisms. Our analysis of 81 different marine sediments from around the world identified 146 species-level 16S rRNA phylotypes of endospore-forming, thermophilic Firmicutes. Phylotypes showed various patterns of spatial distribution in the world oceans and were dispersal-limited to different degrees. Co-occurrence of several phylotypes in locations separated by great distances (west of Svalbard, the Baltic Sea and the Gulf of California) demonstrated a widespread but not ubiquitous distribution. In contrast, Arctic regions with water masses that are relatively isolated from global ocean circulation (Baffin Bay and east of Svalbard) were characterized by low phylotype richness and different compositions of phylotypes. The observed distribution pattern of thermophilic endospores in marine sediments suggests that the impact of passive dispersal on marine microbial biogeography is controlled by the connectivity of local water masses to ocean circulation.}, }
@article {pmid24350777, year = {2014}, author = {Hosseinkhani, B and Hennebel, T and Van Nevel, S and Verschuere, S and Yakimov, MM and Cappello, S and Blaghen, M and Boon, N}, title = {Biogenic nanopalladium based remediation of chlorinated hydrocarbons in marine environments.}, journal = {Environmental science &amp; technology}, volume = {48}, number = {1}, pages = {550-557}, doi = {10.1021/es403047u}, pmid = {24350777}, issn = {1520-5851}, mesh = {Biodegradation, Environmental ; Catalysis ; Desulfovibrio desulfuricans/*metabolism ; Halogenation ; Hydrocarbons, Chlorinated/*isolation &amp; purification ; Italy ; Metal Nanoparticles/*chemistry ; Microscopy, Electron, Transmission ; Palladium/*chemistry/isolation &amp; purification ; Particle Size ; Shewanella/*metabolism ; Trichloroethylene/isolation &amp; purification ; Water Microbiology ; Water Pollutants, Chemical/*isolation &amp; purification ; X-Ray Diffraction ; }, abstract = {Biogenic catalysts have been studied over the last 10 years in freshwater and soil environments, but neither their formation nor their application has been explored in marine ecosystems. The objective of this study was to develop a biogenic nanopalladium-based remediation method for reducing chlorinated hydrocarbons from marine environments by employing indigenous marine bacteria. Thirty facultative aerobic marine strains were isolated from two contaminated sites, the Lagoon of Mar Chica, Morocco, and Priolo Gargallo Syracuse, Italy. Eight strains showed concurrent palladium precipitation and biohydrogen production. X-ray diffraction and thin section transmission electron microscopy analysis indicated the presence of metallic Pd nanoparticles of various sizes (5-20 nm) formed either in the cytoplasm, in the periplasmic space, or extracellularly. These biogenic catalysts were used to dechlorinate trichloroethylene in simulated marine environments. Complete dehalogenation of 20 mg L(-1) trichloroethylene was achieved within 1 h using 50 mg L(-1) biogenic nanopalladium. These biogenic nanoparticles are promising developments for future marine bioremediation applications.}, }
@article {pmid24349285, year = {2013}, author = {Nunes da Rocha, U and Plugge, CM and George, I and van Elsas, JD and van Overbeek, LS}, title = {The rhizosphere selects for particular groups of acidobacteria and verrucomicrobia.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e82443}, pmid = {24349285}, issn = {1932-6203}, mesh = {*Acidobacteria/classification/genetics ; Biodiversity ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; RNA, Ribosomal, 16S ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; *Verrucomicrobia/classification/genetics ; }, abstract = {There is a lack in our current understanding on the putative interactions of species of the phyla of Acidobacteria and Verrucomicrobia with plants. Moreover, progress in this area is seriously hampered by the recalcitrance of members of these phyla to grow as pure cultures. The purpose of this study was to investigate whether particular members of Acidobacteria and Verrucomicrobia are avid colonizers of the rhizosphere. Based on previous work, rhizosphere competence was demonstrated for the Verrucomicrobia subdivision 1 groups of Luteolibacter and Candidatus genus Rhizospheria and it was hypothesized that the rhizosphere is a common habitat for Acidobacteria subdivision 8 (class Holophagae). We assessed the population densities of Bacteria, Verrucomicrobia subdivision 1 groups Luteolibacter and Candidatus genus Rhizospheria and Acidobacteria subdivisions 1, 3, 4, 6 and Holophagae in bulk soil and in the rhizospheres of grass, potato and leek in the same field at different points in time using real-time quantitative PCR. Primers of all seven verrucomicrobial, acidobacterial and holophagal PCR systems were based on 16S rRNA gene sequences of cultivable representatives of the different groups. Luteolibacter, Candidatus genus Rhizospheria, subdivision 6 acidobacteria and Holophaga showed preferences for one or more rhizospheres. In particular, the Holophaga 16S rRNA gene number were more abundant in the leek rhizosphere than in bulk soil and the rhizospheres of grass and potato. Attraction to, and colonization of, leek roots by Holophagae strain CHC25 was further shown in an experimental microcosm set-up. In the light of this remarkable capacity, we propose to coin strain CHC25 Candidatus Porrumbacterium oxyphilus (class Holophagae, Phylum Acidobacteria), the first cultured representative with rhizosphere competence.}, }
@article {pmid24349190, year = {2013}, author = {Neteler, M and Metz, M and Rocchini, D and Rizzoli, A and Flacio, E and Engeler, L and Guidi, V and Lüthy, P and Tonolla, M}, title = {Is Switzerland suitable for the invasion of Aedes albopictus [corrected]?.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e82090}, pmid = {24349190}, issn = {1932-6203}, mesh = {Aedes/growth &amp; development/*physiology ; Animals ; Ecosystem ; Geography ; *Introduced Species ; Models, Theoretical ; Seasons ; Switzerland ; Temperature ; }, abstract = {BACKGROUND: Over the last 30 years, the Asian tiger mosquito, Aedes albopictus, has rapidly spread around the world. The European distribution comprises the Mediterranean basin with a first appearance in Switzerland in 2003. Early identification of the most suitable areas in Switzerland allowing progressive invasion by this species is considered crucial to suggest adequate surveillance and control plans.<br><br>We identified the most suitable areas for invasion and establishment of Ae. albopictus in Switzerland. The potential distribution areas linked to the current climatic suitability were assessed using remotely sensed land surface temperature data recorded by the MODIS satellite sensors. Suitable areas for adult survival and overwintering of diapausing eggs were also identified for future climatic conditions, considering two different climate change scenarios (A1B, A2) for the periods 2020-2049 and 2045-2074. At present, the areas around Lake Geneva in western Switzerland provide suitable climatic conditions for Ae. albopictus. In northern Switzerland, parts of the Rhine valley, around Lake Constance, as well as the surroundings of Lake Neuch&#xe2;tel, appear to be suitable for the survival at least of adult Ae. albopictus. However, these areas are characterized by winters currently being too cold for survival and development of diapausing eggs. In southern Switzerland, Ae. albopictus is already well-established, especially in the Canton of Ticino. For the years 2020-2049, the predicted possible spread of the tiger mosquito does not differ significantly from its potential current distribution. However, important expansions are obtained if the period is extended to the years 2045-2074, when Ae. albopictus may invade large new areas.<br><br>CONCLUSIONS/SIGNIFICANCE: Several parts of Switzerland provide suitable climatic conditions for invasion and establishment of Ae. albopictus. The current distribution and rapid spread in other European countries suggest that the tiger mosquito will colonize new areas in Switzerland in the near future.}, }
@article {pmid24348281, year = {2013}, author = {Midtvedt, T}, title = {Society for microbial ecology, microbial ecology in health and disease, and the future.}, journal = {Microbial ecology in health and disease}, volume = {24}, number = {}, pages = {}, doi = {10.3402/mehd.v24i0.23315}, pmid = {24348281}, issn = {0891-060X}, }
@article {pmid24341984, year = {2014}, author = {Vannette, RL and Fukami, T}, title = {Historical contingency in species interactions: towards niche-based predictions.}, journal = {Ecology letters}, volume = {17}, number = {1}, pages = {115-124}, pmid = {24341984}, issn = {1461-0248}, mesh = {*Ecosystem ; Mimulus/microbiology ; Plant Nectar ; Yeasts ; }, abstract = {The way species affect one another in ecological communities often depends on the order of species arrival. The magnitude of such historical contingency, known as priority effects, varies across species and environments, but this variation has proven difficult to predict, presenting a major challenge in understanding species interactions and consequences for community structure and function. Here, we argue that improved predictions can be achieved by decomposing species' niches into three components: overlap, impact and requirement. Based on classic theories of community assembly, three hypotheses that emphasise related, but distinct influences of the niche components are proposed: priority effects are stronger among species with higher resource use overlap; species that impact the environment to a greater extent exert stronger priority effects; and species whose growth rate is more sensitive to changes in the environment experience stronger priority effects. Using nectar-inhabiting microorganisms as a model system, we present evidence that these hypotheses complement the conventional hypothesis that focuses on the role of environmental harshness, and show that niches can be twice as predictive when separated into components. Taken together, our hypotheses provide a basis for developing a general framework within which the magnitude of historical contingency in species interactions can be predicted.}, }
@article {pmid24341371, year = {2014}, author = {Nikel, PI and Silva-Rocha, R and Benedetti, I and de Lorenzo, V}, title = {The private life of environmental bacteria: pollutant biodegradation at the single cell level.}, journal = {Environmental microbiology}, volume = {16}, number = {3}, pages = {628-642}, doi = {10.1111/1462-2920.12360}, pmid = {24341371}, issn = {1462-2920}, mesh = {Biodegradation, Environmental ; *Environmental Microbiology ; Environmental Pollutants/*metabolism ; Genetic Variation ; Genotype ; Phenotype ; Plasmids/genetics ; Pseudomonas putida/*genetics/*metabolism ; }, abstract = {Bacteria display considerable cell-to-cell heterogeneity in a number of genetic and physiological traits. Stochastic differences in regulatory patterns (e.g. at the transcriptional level) propagate into the metabolic and physiological status of otherwise isogenic cells, which ultimately results in appearance of sub-populations within the community. As new technologies emerge and because novel single cell strategies are constantly being refined, our knowledge on microbial individuality is in burgeoning and constant expansion. These approaches encompass not only molecular biology tools (e.g. fluorescent-protein based reporters) but also a suite of sophisticated, non-invasive technologies to gain insight into the metabolic state of individual cells. Defining the role of individual heterogeneities is thus instrumental for the population-level understanding of macroscopic processes in both environmental and industrial set-ups. The present article reviews the state-of-the-art methodologies for the investigation of single bacteria at both the genetic and metabolic level, and places the application of currently available tools in the context of microbial ecology and environmental microbiology. As a case example, we examine the stochastic and multi-stable behaviour of the TOL-encoded pathway of Pseudomonas putida mt-2 for the biodegradation of aromatic compounds. Bet-hedging strategies and division of labour are considered as factors pushing forward the evolution of environmental microorganisms.}, }
@article {pmid24337806, year = {2014}, author = {Enitan, AM and Kumari, S and Swalaha, FM and Adeyemo, J and Ramdhani, N and Bux, F}, title = {Kinetic modelling and characterization of microbial community present in a full-scale UASB reactor treating brewery effluent.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {358-368}, pmid = {24337806}, issn = {1432-184X}, mesh = {Bacteria/*isolation &amp; purification ; Biofuels/analysis ; Bioreactors/*microbiology ; DNA, Archaeal/isolation &amp; purification ; DNA, Bacterial/isolation &amp; purification ; Euryarchaeota/*isolation &amp; purification ; Fatty Acids, Volatile/analysis ; In Situ Hybridization, Fluorescence ; Methane/analysis ; Models, Chemical ; Polymerase Chain Reaction ; Sewage/*microbiology ; Waste Disposal, Fluid/*methods ; }, abstract = {The performance of a full-scale upflow anaerobic sludge blanket (UASB) reactor treating brewery wastewater was investigated by microbial analysis and kinetic modelling. The microbial community present in the granular sludge was detected using fluorescent in situ hybridization (FISH) and further confirmed using polymerase chain reaction. A group of 16S rRNA based fluorescent probes and primers targeting Archaea and Eubacteria were selected for microbial analysis. FISH results indicated the presence and dominance of a significant amount of Eubacteria and diverse group of methanogenic Archaea belonging to the order Methanococcales, Methanobacteriales, and Methanomicrobiales within in the UASB reactor. The influent brewery wastewater had a relatively high amount of volatile fatty acids chemical oxygen demand (COD), 2005 mg/l and the final COD concentration of the reactor was 457 mg/l. The biogas analysis showed 60-69% of methane, confirming the presence and activities of methanogens within the reactor. Biokinetics of the degradable organic substrate present in the brewery wastewater was further explored using Stover and Kincannon kinetic model, with the aim of predicting the final effluent quality. The maximum utilization rate constant U max and the saturation constant (K(B)) in the model were estimated as 18.51 and 13.64 g/l/day, respectively. The model showed an excellent fit between the predicted and the observed effluent COD concentrations. Applicability of this model to predict the effluent quality of the UASB reactor treating brewery wastewater was evident from the regression analysis (R(2) = 0.957) which could be used for optimizing the reactor performance.}, }
@article {pmid24337805, year = {2014}, author = {Armada, E and Roldán, A and Azcon, R}, title = {Differential activity of autochthonous bacteria in controlling drought stress in native Lavandula and Salvia plants species under drought conditions in natural arid soil.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {410-420}, pmid = {24337805}, issn = {1432-184X}, mesh = {Antioxidants/metabolism ; Ascorbate Peroxidases/metabolism ; Bacillus/growth &amp; development/isolation &amp; purification ; *Droughts ; Enterobacter/growth &amp; development/isolation &amp; purification ; Glutathione Reductase/metabolism ; Lavandula/microbiology/*physiology ; Mycorrhizae/metabolism ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Salvia/microbiology/*physiology ; *Soil Microbiology ; *Stress, Psychological ; Water/metabolism ; }, abstract = {The effectiveness of autochthonous plant growth-promoting rhizobacteria was studied in Lavandula dentata and Salvia officinalis growing in a natural arid Mediterranean soil under drought conditions. These bacteria identified as Bacillus megaterium (Bm), Enterobacter sp. (E), Bacillus thuringiensis (Bt), and Bacillus sp. (Bsp). Each bacteria has different potential to meliorate water limitation and alleviating drought stress in these two plant species. B. thuringiensis promoted growth and drought avoidance in Lavandula by increasing K content, by depressing stomatal conductance, and it controlled shoot proline accumulation. This bacterial effect on increasing drought tolerance was related to the decrease of glutathione reductase (GR) and ascorbate peroxidase (APX) that resulted sensitive indexes of lower cellular oxidative damage involved in the adaptative drought response in B. thuringiensis-inoculated Lavandula plants. In contrast, in Salvia, having intrinsic lower shoot/root ratio, higher stomatal conductance and lower APX and GR activities than Lavandula, the bacterial effects on nutritional, physiological and antioxidant enzymatic systems were lower. The benefit of bacteria depended on intrinsic stress tolerance of plant involved. Lavadula demonstrated a greater benefit than Salvia to control drought stress when inoculated with B. thuringiensis. The bacterial drought tolerance assessed as survival, proline, and indolacetic acid production showed the potential of this bacteria to help plants to grow under drought conditions. B. thuringiensis may be used for Lavandula plant establishment in arid environments. Particular characteristic of the plant species as low shoot/root ratio and high stomatal conductance are important factors controlling the bacterial effectiveness improving nutritional, physiological, and metabolic plant activities.}, }
@article {pmid24337804, year = {2014}, author = {Ren, D and Madsen, JS and de la Cruz-Perera, CI and Bergmark, L and Sørensen, SJ and Burmølle, M}, title = {High-throughput screening of multispecies biofilm formation and quantitative PCR-based assessment of individual species proportions, useful for exploring interspecific bacterial interactions.}, journal = {Microbial ecology}, volume = {68}, number = {1}, pages = {146-154}, pmid = {24337804}, issn = {1432-184X}, mesh = {Bacteria/*classification/growth &amp; development ; *Biofilms ; Culture Media/chemistry ; DNA, Bacterial/genetics ; High-Throughput Screening Assays/*methods ; Microbial Consortia ; Polymerase Chain Reaction/methods ; }, abstract = {Multispecies biofilms are predominant in almost all natural environments, where myriads of resident microorganisms interact with each other in both synergistic and antagonistic manners. The interspecies interactions among different bacteria are, despite the ubiquity of these communities, still poorly understood. Here, we report a rapid, reproducible and sensitive approach for quantitative screening of biofilm formation by bacteria when cultivated as mono- and multispecies biofilms, based on the Nunc-TSP lid system and crystal violet staining. The relative proportion of the individual species in a four-species biofilm was assessed using quantitative PCR based on SYBR Green I fluorescence with specific primers. The results indicated strong synergistic interactions in a four-species biofilm model community with a more than 3-fold increase in biofilm formation and demonstrated the strong dominance of two strains, Xanthomonas retroflexus and Paenibacillus amylolyticus. The developed approach can be used as a standard procedure for evaluating interspecies interactions in defined microbial communities. This will be of significant value in the quantitative study of the microbial composition of multispecies biofilms both in natural environments and infectious diseases to increase our understanding of the mechanisms that underlie cooperation, competition and fitness of individual species in mixed-species biofilms.}, }
@article {pmid24337222, year = {2014}, author = {Ganendra, G and De Muynck, W and Ho, A and Hoefman, S and De Vos, P and Boeckx, P and Boon, N}, title = {Atmospheric methane removal by methane-oxidizing bacteria immobilized on porous building materials.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {8}, pages = {3791-3800}, doi = {10.1007/s00253-013-5403-y}, pmid = {24337222}, issn = {1432-0614}, mesh = {Carbon Dioxide/metabolism ; Cells, Immobilized/*metabolism ; Construction Materials/*microbiology ; Methane/*metabolism ; Methylococcaceae/*metabolism ; Oxidation-Reduction ; }, abstract = {Biological treatment using methane-oxidizing bacteria (MOB) immobilized on six porous carrier materials have been used to mitigate methane emission. Experiments were performed with different MOB inoculated in building materials at high (~20 % (v/v)) and low (~100 ppmv) methane mixing ratios. Methylocystis parvus in autoclaved aerated concrete (AAC) exhibited the highest methane removal rate at high (28.5 ± 3.8 μg CH4 g[-1] building material h[-1]) and low (1.7 ± 0.4 μg CH4 g[-1] building material h[-1]) methane mixing ratio. Due to the higher volume of pores with diameter >5 μm compared to other materials tested, AAC was able to adsorb more bacteria which might explain for the higher methane removal observed. The total methane and carbon dioxide-carbon in the headspace was decreased for 65.2 ± 10.9 % when M. parvus in Ytong was incubated for 100 h. This study showed that immobilized MOB on building materials could be used to remove methane from the air and also act as carbon sink.}, }
@article {pmid24337178, year = {2014}, author = {Watanabe, M and Yukuhiro, F and Maeda, T and Miura, K and Kageyama, D}, title = {Novel strain of Spiroplasma found in flower bugs of the genus Orius (Hemiptera: Anthocoridae): transovarial transmission, coexistence with Wolbachia and varied population density.}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {219-228}, pmid = {24337178}, issn = {1432-184X}, mesh = {Animals ; DNA, Bacterial/genetics ; Female ; Hemiptera/*microbiology ; Japan ; Male ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spiroplasma/*classification/growth &amp; development/isolation &amp; purification ; Symbiosis ; Wolbachia/*growth &amp; development ; }, abstract = {Spiroplasma, a group of small, wall-less, helical, and motile bacteria belonging to the Mollicutes, contains species with diverse life histories. To date, all the Spiroplasma strains that are known to be transmitted vertically in arthropod lineages belong to either the Spiroplasma ixodetis group or the Spiroplasma poulsonii group. Here, we found that a unique strain of Spiroplasma vertically transmitted in predatory flower bugs of the genus Orius belongs to the Spiroplasma insolitum group, which is a group of bacteria phylogenetically closely related to S. insolitum derived from the tickseed sunflower, Bidens sp. (Asterales: Asteraceae). The infection frequencies in natural populations were16.0% in Orius sauteri (n = 75), 40.5% in Orius nagaii (n = 37), and 8.0% in Orius minutus (n = 87). Orius strigicollis was not infected with Spiroplasma (n = 147). In the early stage of oogenesis (i.e., within the germarium), a large number of bacteria with the typical morphology of Spiroplasma existed, keeping a distance from Wolbachia bacteria. The Spiroplasma population seemed to increase during host development but Wolbachia population did not.}, }
@article {pmid24337146, year = {2014}, author = {Doud, CW and Scott, HM and Zurek, L}, title = {Role of house flies in the ecology of Enterococcus faecalis from wastewater treatment facilities.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {380-391}, pmid = {24337146}, issn = {1432-184X}, mesh = {Animals ; Cities ; Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus faecalis/drug effects/*genetics/*isolation &amp; purification ; Houseflies/*microbiology ; Logistic Models ; Phenotype ; Virulence Factors/*genetics ; Waste Disposal Facilities ; Wastewater/*microbiology ; }, abstract = {Enterococci are important nosocomial pathogens, with Enterococcus faecalis most commonly responsible for human infections. In this study, we used several measures to test the hypothesis that house flies, Musca domestica (L.), acquire and disseminate antibiotic-resistant and potentially virulent E. faecalis from wastewater treatment facilities (WWTF) to the surrounding urban environment. House flies and sludge from four WWTF (1-4) as well as house flies from three urban sites close to WWTF-1 were collected and cultured for enterococci. Enterococci were identified, quantified, screened for antibiotic resistance and virulence traits, and assessed for clonality. Of the 11 antibiotics tested, E. faecalis was most commonly resistant to tetracycline, doxycycline, streptomycin, gentamicin, and erythromycin, and these traits were intra-species horizontally transferrable by in vitro conjugation. Profiles of E. faecalis (prevalence, antibiotic resistance, and virulence traits) from each of WWTF sludge and associated house flies were similar, indicating that flies successfully acquired these bacteria from this substrate. The greatest number of E. faecalis with antibiotic resistance and virulence factors (i.e., gelatinase, cytolysin, enterococcus surface protein, and aggregation substance) originated from WWTF-1 that processed meat waste from a nearby commercial meat-processing plant, suggesting an agricultural rather than human clinical source of these isolates. E. faecalis from house flies collected from three sites 0.7-1.5 km away from WWTF-1 were also similar in their antibiotic resistance profiles; however, antibiotic resistance was significantly less frequent. Clonal diversity assessment using pulsed-field gel electrophoresis revealed the same clones of E. faecalis from sludge and house flies from WWTF-1 but not from the three urban sites close to WWTF-1. This study demonstrates that house flies acquire antibiotic-resistant enterococci from WWTF and potentially disseminate them to the surrounding environment.}, }
@article {pmid24337108, year = {2014}, author = {Hong, H and Ko, HJ and Choi, IG and Park, W}, title = {Previously undescribed plasmids recovered from activated sludge confer tetracycline resistance and phenotypic changes to Acinetobacter oleivorans DR1.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {369-379}, pmid = {24337108}, issn = {1432-184X}, mesh = {Acinetobacter/*genetics/isolation &amp; purification ; Alkanes/chemistry ; Anti-Bacterial Agents/pharmacology ; Biodegradation, Environmental ; Biofilms ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Oxidative Stress ; Phenotype ; Plasmids/*isolation &amp; purification ; Polymorphism, Restriction Fragment Length ; Quorum Sensing ; Salts/metabolism ; Sequence Analysis, DNA ; Sewage/*microbiology ; Tetracycline/pharmacology ; Tetracycline Resistance/*genetics ; }, abstract = {We used culture-dependent and culture-independent methods to extract previously undescribed plasmids harboring tetracycline (TC) resistance genes from activated sludge. The extracted plasmids were transformed into naturally competent Acinetobacter oleivorans DR1 to recover a non-Escherichia coli-based plasmid. The transformed cells showed 80-100-fold higher TC resistance than the wild-type strain. Restriction length polymorphism performed using 30 transformed cells showed four different types of plasmids. Illumina-based whole sequencing of the four plasmids identified three previously unreported plasmids and one previously reported plasmid. All plasmids carried TC resistance-related genes (tetL, tetH), tetracycline transcriptional regulators (tetR), and mobilization-related genes. As per expression analysis, TC resistance genes were functional in the presence of TC. The recovered plasmids showed mosaic gene acquisition through horizontal gene transfer. Membrane fluidity, hydrophobicity, biofilm formation, motility, growth rate, sensitivity to stresses, and quorum sensing signals of the transformed cells were different from those of the wild-type cells. Plasmid-bearing cells seemed to have an energy burden for maintaining and expressing plasmid genes. Our data showed that acquisition of TC resistance through plasmid uptake is related to loss of biological fitness. Thus, cells acquiring antibiotic resistance plasmids can survive in the presence of antibiotics, but must pay ecological costs.}, }
@article {pmid24337107, year = {2014}, author = {Caragata, EP and Rancès, E and O'Neill, SL and McGraw, EA}, title = {Competition for amino acids between Wolbachia and the mosquito host, Aedes aegypti.}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {205-218}, pmid = {24337107}, issn = {1432-184X}, mesh = {Aedes/*microbiology/*physiology ; Amino Acids/*metabolism ; Animals ; Cholesterol/metabolism ; Female ; Fertility ; Humans ; Ovum/physiology ; Rats ; Rats, Inbred Lew ; Sheep ; Symbiosis ; Wolbachia/*physiology ; }, abstract = {The endosymbiont Wolbachia represents a promising method of dengue control, as it reduces the ability of the primary vector, the mosquito Aedes aegypti, to transmit viruses. When mosquitoes infected with the virulent Wolbachia strain wMelPop are fed non-human blood, there is a drastic reduction in mosquito fecundity and egg viability. Wolbachia has a reduced genome and is clearly dependent on its host for a wide range of nutritional needs. The fitness defects seen in wMelPop-infected A. aegypti could be explained by competition between the mosquito and the symbiont for essential blood meal nutrients, the profiles of which are suboptimal in non-human blood. Here, we examine cholesterol and amino acids as candidate molecules for competition, as they have critical roles in egg structural development and are known to vary between blood sources. We found that Wolbachia infection reduces total cholesterol levels in mosquitoes by 15-25%. We then showed that cholesterol supplementation of a rat blood meal did not improve fecundity or egg viability deficits. Conversely, amino acid supplementation of sucrose before and after a sheep blood meal led to statistically significant increases in fecundity of approximately 15-20 eggs per female and egg viability of 30-40%. This mosquito system provides the first empirical evidence of competition between Wolbachia and a host over amino acids and may suggest a general feature of Wolbachia-insect associations. These competitive processes could affect many aspects of host physiology and potentially mosquito fitness, a key concern for Wolbachia-based mosquito biocontrol.}, }
@article {pmid24335827, year = {2014}, author = {Wang, FP and Zhang, Y and Chen, Y and He, Y and Qi, J and Hinrichs, KU and Zhang, XX and Xiao, X and Boon, N}, title = {Methanotrophic archaea possessing diverging methane-oxidizing and electron-transporting pathways.}, journal = {The ISME journal}, volume = {8}, number = {5}, pages = {1069-1078}, pmid = {24335827}, issn = {1751-7370}, mesh = {Acetates/metabolism ; Archaea/enzymology/genetics/*metabolism ; Electrons ; Gene Expression Regulation, Archaeal ; Genome, Archaeal ; Geologic Sediments/*microbiology ; Hydrogen/metabolism ; Methane/*metabolism ; Oxidation-Reduction ; Oxidoreductases ; }, abstract = {Anaerobic oxidation of methane (AOM) is a crucial process limiting the flux of methane from marine environments to the atmosphere. The process is thought to be mediated by three groups of uncultivated methane-oxidizing archaea (ANME-1, 2 and 3). Although the responsible microbes have been intensively studied for more than a decade, central mechanistic details remain unresolved. On the basis of an integrated analysis of both environmental metatranscriptome and single-aggregate genome of a highly active AOM enrichment dominated by ANME-2a, we provide evidence for a complete and functioning AOM pathway in ANME-2a. All genes required for performing the seven steps of methanogenesis from CO2 were found present and actively expressed. Meanwhile, genes for energy conservation and electron transportation including those encoding F420H2 dehydrogenase (Fpo), the cytoplasmic and membrane-associated Coenzyme B-Coenzyme M heterodisulfide (CoB-S-SCoM) reductase (HdrABC, HdrDE), cytochrome C and the Rhodobacter nitrogen fixation (Rnf) complex were identified and expressed, whereas genes encoding for hydrogenases were absent. Thus, ANME-2a is likely performing AOM through a complete reversal of methanogenesis from CO2 reduction without involvement of canonical hydrogenase. ANME-2a is demonstrated to possess versatile electron transfer pathways that would provide the organism with more flexibility in substrate utilization and capacity for rapid adjustment to fluctuating environments. This work lays the foundation for understanding the environmental niche differentiation, physiology and evolution of different ANME subgroups.}, }
@article {pmid24334281, year = {2014}, author = {Wandermur, G and Rodrigues, D and Allil, R and Queiroz, V and Peixoto, R and Werneck, M and Miguel, M}, title = {Plastic optical fiber-based biosensor platform for rapid cell detection.}, journal = {Biosensors &amp; bioelectronics}, volume = {54}, number = {}, pages = {661-666}, doi = {10.1016/j.bios.2013.11.030}, pmid = {24334281}, issn = {1873-4235}, mesh = {Antibodies, Immobilized/chemistry ; Biosensing Techniques/*instrumentation ; Equipment Design ; Escherichia coli/*isolation &amp; purification ; Escherichia coli Infections/diagnosis/microbiology ; Humans ; Immunoassay/instrumentation ; *Optical Fibers ; Plastics/chemistry ; Sensitivity and Specificity ; }, abstract = {This work presents a novel, fast response time, plastic optic fiber (POF) biosensor to detect Escherichia coli. It discloses the technique for the development, calibration and measurement of this robust and simple-to-construct POF biosensor. The probes in U-shaped format were manufactured with a specially developed device. The calibration process led to the evaluation of the sensitivity, accuracy and repeatability by using solutions of sucrose for obtaining refractive indices (RI) in the range 1.33-1.39 IR equivalent of water and bacteria, respectively. The POF probes were functionalized with antibody anti-E. coli serotype O55 and tested firstly with saline and then with bacterial concentrations of 10(4), 10(6), and 10(8) colony forming units/ml (CFU/ml). The optoelectronic setup consists of an 880 nm LED connected to the U-shaped probe driven by a sine waveform generated by the Simulink (from Matlab(®)). On the other side of the probe a photodetector generates a photocurrent which is amplified by a transconductance amplifier. The output voltage signal is read by the analog-to-digital (A/D) input of the microcontroller. In all tested concentrations, the results presented a tendency of a decrease in the output signal with time, due to the attachment of the bacteria to the POF probe and consequent increase in the RI close to the sensitive area of the fiber surface. It has been shown that the system is capable of providing positive response to the bacterial concentration in less than 10 min, demonstrating good possibilities to be commercially developed as a portable field sensor.}, }
@article {pmid24329759, year = {2014}, author = {Garbeva, P and Hordijk, C and Gerards, S and de Boer, W}, title = {Volatiles produced by the mycophagous soil bacterium Collimonas.}, journal = {FEMS microbiology ecology}, volume = {87}, number = {3}, pages = {639-649}, doi = {10.1111/1574-6941.12252}, pmid = {24329759}, issn = {1574-6941}, mesh = {Antibiosis ; Fungi/*growth &amp; development ; Oxalobacteraceae/*metabolism ; Plant Roots/microbiology ; Silicon Dioxide ; Soil ; *Soil Microbiology ; Volatile Organic Compounds/*metabolism ; }, abstract = {It is increasingly recognized that volatile organic compounds play an import role during interactions between soil microorganisms. Here, we examined the possible involvement of volatiles in the interaction of Collimonas bacteria with soil fungi. The genus Collimonas is known for its ability to grow at the expense of living fungi (mycophagy), and antifungal volatiles may contribute to the attack of fungi by these bacteria. We analyzed the composition of volatiles produced by Collimonas on agar under different nutrient conditions and studied the effect on fungal growth. The volatiles had a negative effect on the growth of a broad spectrum of fungal species. Collimonas bacteria did also produce volatiles in sand microcosms supplied with artificial root exudates. The production of volatiles in sand microcosms was enhanced by the presence of fungi. The overall picture that we get from our study is that antifungal volatiles produced by Collimonas could play an important role in realizing its mycophagous lifestyle. The current work is also interesting for understanding the ecological relevance of volatile production by soil bacteria in general as we found strong influences of root exudates composition and incubation conditions on the spectrum of volatiles produced.}, }
@article {pmid24325257, year = {2014}, author = {Jacquemyn, H and Brys, R and Merckx, VSFT and Waud, M and Lievens, B and Wiegand, T}, title = {Coexisting orchid species have distinct mycorrhizal communities and display strong spatial segregation.}, journal = {The New phytologist}, volume = {202}, number = {2}, pages = {616-627}, doi = {10.1111/nph.12640}, pmid = {24325257}, issn = {1469-8137}, mesh = {*Basidiomycota/classification ; *Ecosystem ; *Mycorrhizae/classification ; *Orchidaceae/classification ; Species Specificity ; *Symbiosis ; }, abstract = {Because orchids are dependent on mycorrhizal fungi for germination and establishment of seedlings, differences in the mycorrhizal communities associating with orchids can be expected to mediate the abundance, spatial distribution and coexistence of terrestrial orchids in natural communities. We assessed the small-scale spatial distribution of seven orchid species co-occurring in 25 × 25 m plots in two Mediterranean grasslands. In order to characterize the mycorrhizal community associating with each orchid species, 454 pyrosequencing was used. The extent of spatial clustering was assessed using techniques of spatial point pattern analysis. The community of mycorrhizal fungi consisted mainly of members of the Tulasnellaceae, Thelephoraceae and Ceratobasidiaceae, although sporadically members of the Sebacinaceae, Russulaceae and Cortinariaceae were observed. Pronounced differences in mycorrhizal communities were observed between species, whereas strong clustering and significant segregation characterized the spatial distribution of orchid species. However, spatial segregation was not significantly related to phylogenetic dissimilarity of fungal communities. Our results indicate that co-occurring orchid species have distinctive mycorrhizal communities and show strong spatial segregation, suggesting that mycorrhizal fungi are important factors driving niche partitioning in terrestrial orchids and may therefore contribute to orchid coexistence.}, }
@article {pmid24317898, year = {2014}, author = {Peralta-Sánchez, JM and Soler, JJ and Martín-Platero, AM and Knight, R and Martínez-Bueno, M and Møller, AP}, title = {Eggshell bacterial load is related to antimicrobial properties of feathers lining barn swallow nests.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {480-487}, pmid = {24317898}, issn = {1432-184X}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Bacillus/*isolation &amp; purification ; *Bacterial Load ; Egg Shell/*microbiology ; Feathers/*microbiology ; Pigmentation ; Swallows/*microbiology ; }, abstract = {The use of feathers to line bird's nests has traditionally been interpreted as having a thermoregulatory function. Feather-degrading bacteria growing on feathers lining nests may have antimicrobial properties, which may provide an additional benefit to lining nests with feathers. We test the hypothesis that the production of antimicrobial substances by feather bacteria affects the microbiological environment of the nest, and therefore the bacterial density on eggshells and, indirectly, hatching success. These effects would be expected to differ between nests lined with pigmented and white feathers, because bacteria grow differently on feathers of different colors. We experimentally manipulated the composition of pigmented and unpigmented feathers in nests of the barn swallow (Hirundo rustica) and studied the antimicrobial properties against the keratin-degrading bacterium Bacillus licheniformis of bacteria isolated from feathers of each color. Analyzed feathers were collected at the end of the incubation period, and antimicrobial activity was defined as the proportion of bacteria from the feathers that produce antibacterial substances effective against B. licheniformis. Our experimental manipulation affected antimicrobial activity, which was higher in nests with only white feathers at the beginning of incubation. Moreover, white feathers showed higher antimicrobial activity than black ones. Interestingly, antimicrobial activity in feathers of one of the colors correlated negatively with bacterial density on feather of the opposite color. Finally, antimicrobial activity of white feathers was negatively related to eggshell bacterial load. These results suggest that antimicrobial properties of feathers in general and of white feathers in particular affect the bacterial environment in nests. This environment in turn affects the bacterial load on eggshells, which may affect hatching success.}, }
@article {pmid24312088, year = {2013}, author = {Laanbroek, HJ and Keijzer, RM and Verhoeven, JT and Whigham, DF}, title = {Changes in community composition of ammonia-oxidizing betaproteobacteria from stands of Black mangrove (Avicennia germinans) in response to ammonia enrichment and more oxic conditions.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {343}, pmid = {24312088}, issn = {1664-302X}, abstract = {In flooded and non-flooded impounded forests of Black mangrove (Avicennia germinans), the community structure of the ammonia-oxidizing betaproteobacteria (β-AOB) differed among distinct mangrove vegetation cover types and hydrological regimes. This had been explained by a differential response of lineages of β-AOB to the prevailing soil conditions that included increased levels of moisture and ammonium. To test this hypothesis, slurries of soils collected from a flooded and a non-flooded impoundment were subjected to enhanced levels of ammonium in the absence and presence of additional shaking. After a period of 6 days, the community composition of the β-AOB based on the 16S rRNA gene was determined and compared with the original community structures. Regardless of the incubation conditions and the origin of the samples, sequences belonging to the Nitrosomonas aestuarii lineage became increasingly dominant, whereas the number of sequences of the lineages of Nitrosospira (i.e., Cluster 1) and Nitrosomonas sp. Nm143 declined. Changes in community structure were related to changes in community sizes determined by quantitative PCR based on the amoA gene. The amoA gene copy numbers of β-AOB were compared to those of the ammonia-oxidizing archaea (AOA). Gene copy numbers of the bacteria increased irrespective of incubation conditions, but the numbers of archaea declined in the continuously shaken cultures. This observation is discussed in relation to the distribution of the β-AOB lineages in the impounded Black mangrove forests.}, }
@article {pmid24311313, year = {2013}, author = {De Weirdt, R and Coenen, E and Vlaeminck, B and Fievez, V and Van den Abbeele, P and Van de Wiele, T}, title = {A simulated mucus layer protects Lactobacillus reuteri from the inhibitory effects of linoleic acid.}, journal = {Beneficial microbes}, volume = {4}, number = {4}, pages = {299-312}, doi = {10.3920/BM2013.0017}, pmid = {24311313}, issn = {1876-2891}, mesh = {Anti-Bacterial Agents/*metabolism ; Bacterial Adhesion/drug effects ; Colony Count, Microbial ; Humans ; Limosilactobacillus reuteri/*drug effects/*physiology ; Linoleic Acid/*pharmacology ; Microbial Viability/*drug effects ; Models, Theoretical ; Mucus/*metabolism/*microbiology ; }, abstract = {Lactobacillus reuteri is a commensal, beneficial gut microbe that colonises the intestinal mucus layer, where it makes close contact with the human host and may significantly affect human health. Here, we investigated the capacity of linoleic acid (LA), the most common polyunsaturated fatty acid (PUFA) in a Western-style diet, to affect L. reuteri ATCC PTA 6475 prevalence and survival in a simulated mucus layer. Short-term (1 h) survival and mucin-agar adhesion assays of a log-phase L. reuteri suspension in intestinal water demonstrated that the simulated mucus layer protected L. reuteri against the inhibitory effects of LA by lowering its contact with the bacterial cell membrane. The protective effect of the simulated mucus layer was further evaluated using a more complex and dynamic model of the colon microbiota (SHIME®), in which L. reuteri survival was monitored during 6 days of daily exposure to LA in the absence (L-SHIME) and presence (M-SHIME) of a simulated mucus layer. After 6 days, luminal L- and M-SHIME L. reuteri plate counts had decreased by 3.1±0.5 and 2.6±0.9 log cfu/ml, respectively. Upon supplementation of 1.0 g/l LA, the decline in the luminal L. reuteri population started earlier than was observed for the control. In contrast, mucin-agar levels of L. reuteri (in the M-SHIME) remained unaffected throughout the experiment even in the presence of high concentrations of LA. Overall, the results of this study indicate the importance of the mucus layer as a protective environment for beneficial gut microbes to escape from stress by high loads of the antimicrobial PUFA LA to the colon, i.e. due to a Western-style diet.}, }
@article {pmid24306831, year = {2014}, author = {Xiong, J and Zhu, J and Wang, K and Wang, X and Ye, X and Liu, L and Zhao, Q and Hou, M and Qiuqian, L and Zhang, D}, title = {The temporal scaling of bacterioplankton composition: high turnover and predictability during shrimp cultivation.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {256-264}, pmid = {24306831}, issn = {1432-184X}, mesh = {Animals ; Aquaculture/*methods ; Bacteria/growth &amp; development/*isolation &amp; purification ; Biodiversity ; Biomass ; DNA, Bacterial/genetics ; Linear Models ; Penaeidae/*microbiology ; Plankton/growth &amp; development/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Water/chemistry ; *Water Microbiology ; }, abstract = {The spatial distribution of microbial communities has recently been reliably documented in the form of a distance-similarity decay relationship. In contrast, temporal scaling, the pattern defined by the microbial similarity-time relationships (STRs), has received far less attention. As a result, it is unclear whether the spatial and temporal variations of microbial communities share a similar power law. In this study, we applied the 454 pyrosequencing technique to investigate temporal scaling in patterns of bacterioplankton community dynamics during the process of shrimp culture. Our results showed that the similarities decreased significantly (P = 0.002) with time during the period over which the bacterioplankton community was monitored, with a scaling exponent of w = 0.400. However, the diversities did not change dramatically. The community dynamics followed a gradual process of succession relative to the parent communities, with greater similarities between samples from consecutive sampling points. In particular, the variations of the bacterial communities from different ponds shared similar successional trajectories, suggesting that bacterial temporal dynamics are predictable to a certain extent. Changes in bacterial community structure were significantly correlated with the combination of Chl a, TN, PO4 (3-), and the C/N ratio. In this study, we identified predictable patterns in the temporal dynamics of bacterioplankton community structure, demonstrating that the STR of the bacterial community mirrors the spatial distance-similarity decay model.}, }
@article {pmid24296350, year = {2013}, author = {Hannigan, GD and Grice, EA}, title = {Microbial ecology of the skin in the era of metagenomics and molecular microbiology.}, journal = {Cold Spring Harbor perspectives in medicine}, volume = {3}, number = {12}, pages = {a015362}, pmid = {24296350}, issn = {2157-1422}, support = {P30 AR057217/AR/NIAMS NIH HHS/United States ; R00 AR060873/AR/NIAMS NIH HHS/United States ; AR060873/AR/NIAMS NIH HHS/United States ; AR057217/AR/NIAMS NIH HHS/United States ; }, mesh = {Alphapapillomavirus/physiology ; Biodiversity ; Fungi/physiology ; Humans ; Malassezia/physiology ; Metagenomics/trends ; Microbiology/trends ; Microbiota/physiology ; Skin/*microbiology ; Skin Diseases, Infectious/diagnosis/*microbiology ; }, abstract = {The skin is the primary physical barrier between the body and the external environment and is also a substrate for the colonization of numerous microbes. Previously, dermatological microbiology research was dominated by culture-based techniques, but significant advances in genomic technologies have enabled the development of less-biased, culture-independent approaches to characterize skin microbial communities. These molecular microbiology approaches illustrate the great diversity of microbiota colonizing the skin and highlight unique features such as site specificity, temporal dynamics, and interpersonal variation. Disruptions in skin commensal microbiota are associated with the progression of many dermatological diseases. A greater understanding of how skin microbes interact with each other and with their host, and how we can therapeutically manipulate those interactions, will provide powerful tools for treating and preventing dermatological disease.}, }
@article {pmid24294263, year = {2013}, author = {Procópio, L and de Cassia Pereira e Silva, M and van Elsas, JD and Seldin, L}, title = {Transcriptional profiling of genes involved in n-hexadecane compounds assimilation in the hydrocarbon degrading Dietzia cinnamea P4 strain.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {44}, number = {2}, pages = {633-641}, pmid = {24294263}, issn = {1678-4405}, mesh = {Actinomycetales/*genetics/growth &amp; development/*metabolism ; Alkanes/*metabolism ; Biotransformation ; *Gene Expression Profiling ; *Genes, Bacterial ; Hydrocarbons/*metabolism ; Hydrogen-Ion Concentration ; Metabolic Networks and Pathways/*genetics ; Real-Time Polymerase Chain Reaction ; Temperature ; }, abstract = {The petroleum-derived degrading Dietzia cinnamea strain P4 recently had its genome sequenced and annotated. This allowed employing the data on genes that are involved in the degradation of n-alkanes. To examine the physiological behavior of strain P4 in the presence of n-alkanes, the strain was grown under varying conditions of pH and temperature. D. cinnamea P4 was able to grow at pH 7.0-9.0 and at temperatures ranging from 35 ºC to 45 ºC. Experiments of gene expression by real-time quantitative RT-PCR throughout the complete growth cycle clearly indicated the induction of the regulatory gene alkU (TetR family) during early growth. During the logarithmic phase, a large increase in transcriptional levels of a lipid transporter gene was noted. Also, the expression of a gene that encodes the protein fused rubredoxin-alkane monooxygenase was enhanced. Both genes are probably under the influence of the AlkU regulator.}, }
@article {pmid24292901, year = {2014}, author = {Abd El Razak, A and Ward, AC and Glassey, J}, title = {Screening of marine bacterial producers of polyunsaturated fatty acids and optimisation of production.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {454-464}, pmid = {24292901}, issn = {1432-184X}, mesh = {Bacteria/*isolation &amp; purification/*metabolism ; Colorimetry ; Culture Media ; Ecosystem ; Fatty Acids, Unsaturated/*biosynthesis ; Gas Chromatography-Mass Spectrometry ; Mediterranean Sea ; Models, Biological ; Seawater/microbiology ; *Water Microbiology ; }, abstract = {Water samples from three different environments including Mid Atlantic Ridge, Red Sea and Mediterranean Sea were screened in order to isolate new polyunsaturated fatty acids (PUFAs) bacterial producers especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). Two hundred and fifty-one isolates were screened for PUFA production and among them the highest number of producers was isolated from the Mid-Atlantic Ridge followed by the Red Sea while no producers were found in the Mediterranean Sea samples. The screening strategy included a simple colourimetric method followed by a confirmation via GC/MS. Among the tested producers, an isolate named 66 was found to be a potentially high PUFA producer producing relatively high levels of EPA in particular. A Plackett-Burman statistical design of experiments was applied to screen a wide number of media components identifying glycerol and whey as components of a production medium. The potential low-cost production medium was optimised by applying a response surface methodology to obtain the highest productivity converting industrial by-products into value-added products. The maximum achieved productivity of EPA was 20 mg/g, 45 mg/l, representing 11% of the total fatty acids, which is approximately five times more than the amount produced prior to optimisation. The production medium composition was 10.79 g/l whey and 6.87 g/l glycerol. To our knowledge, this is the first investigation of potential bacteria PUFA producers from Mediterranean and Red Seas providing an evaluation of a colourimetric screening method as means of rapid screening of a large number of isolates.}, }
@article {pmid24292151, year = {2013}, author = {Pilhofer, M and Aistleitner, K and Biboy, J and Gray, J and Kuru, E and Hall, E and Brun, YV and VanNieuwenhze, MS and Vollmer, W and Horn, M and Jensen, GJ}, title = {Discovery of chlamydial peptidoglycan reveals bacteria with murein sacculi but without FtsZ.}, journal = {Nature communications}, volume = {4}, number = {}, pages = {2856}, pmid = {24292151}, issn = {2041-1723}, support = {R01 GM051986/GM/NIGMS NIH HHS/United States ; GM094800B/GM/NIGMS NIH HHS/United States ; BB/I020012/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 281633/ERC_/European Research Council/International ; R01 AI059327/AI/NIAID NIH HHS/United States ; R01 GM094800/GM/NIGMS NIH HHS/United States ; AI059327/AI/NIAID NIH HHS/United States ; GM051986/GM/NIGMS NIH HHS/United States ; R21 AI059327/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; Cell Wall/chemistry/metabolism/ultrastructure ; Chlamydiales/chemistry/classification/*metabolism/ultrastructure ; Cytoskeletal Proteins/genetics/*metabolism ; Peptidoglycan/chemistry/*metabolism ; }, abstract = {Chlamydiae are important pathogens and symbionts with unique cell biological features. They lack the cell-division protein FtsZ, and the existence of peptidoglycan (PG) in their cell wall has been highly controversial. FtsZ and PG together function in orchestrating cell division and maintaining cell shape in almost all other bacteria. Using electron cryotomography, mass spectrometry and fluorescent labelling dyes, here we show that some environmental chlamydiae have cell wall sacculi consisting of a novel PG type. Treatment with fosfomycin (a PG synthesis inhibitor) leads to lower infection rates and aberrant cell shapes, suggesting that PG synthesis is crucial for the chlamydial life cycle. Our findings demonstrate for the first time the presence of PG in a member of the Chlamydiae. They also present a unique example of a bacterium with a PG sacculus but without FtsZ, challenging the current hypothesis that it is the absence of a cell wall that renders FtsZ non-essential.}, }
@article {pmid24292081, year = {2014}, author = {Regueiro, L and Veiga, P and Figueroa, M and Lema, JM and Carballa, M}, title = {Influence of transitional states on the microbial ecology of anaerobic digesters treating solid wastes.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {5}, pages = {2015-2027}, doi = {10.1007/s00253-013-5378-8}, pmid = {24292081}, issn = {1432-0614}, mesh = {Anaerobiosis ; Archaea/*classification/growth &amp; development/metabolism ; Bacteria/*classification/growth &amp; development/metabolism ; Bioreactors/*microbiology ; *Biota ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fermentation ; Genes, rRNA ; *Industrial Waste ; Methane/metabolism ; Molecular Sequence Data ; *Phase Transition ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; *Solid Waste ; Time Factors ; Waste Management ; }, abstract = {A better understanding of the microbial ecology of anaerobic processes during transitional states is important to achieve a long-term efficient reactor operation. Five wastes (pig manure, biodiesel residues, ethanol stillage, molasses residues, and fish canning waste) were treated in five anaerobic reactors under the same operational conditions. The influence of the type of substrate and the effect of modifying feeding composition on the microbial community structure was evaluated. The highest biomethanation efficiency was observed in reactors fed with fish canning waste, which also presented the highest active archaeal population and the most diverse microbial communities. Only two Bacteria populations could be directly related to a particular substrate: Ilyobacter with biodiesel residues and Trichococcus with molasses residues. Results showed that the time to achieve steady-state performance after these transitional states was not dependent on the substrate treated. But reactors needed more time to handle the stress conditions derived from the start-up compared to the adaptation to a new feeding. Cluster analyses showed that the type of substrate had a clear influence on the microbiology of the reactors, and that segregation was related to the reactors performance. Finally, we conclude that the previous inoculum history treating solid waste and higher values of active Archaea population are important factors to face a successful change in substrate not entailing stability failure.}, }
@article {pmid24290824, year = {2014}, author = {Gatti, M and Bottari, B and Lazzi, C and Neviani, E and Mucchetti, G}, title = {Invited review: Microbial evolution in raw-milk, long-ripened cheeses produced using undefined natural whey starters.}, journal = {Journal of dairy science}, volume = {97}, number = {2}, pages = {573-591}, doi = {10.3168/jds.2013-7187}, pmid = {24290824}, issn = {1525-3198}, mesh = {Animals ; Cheese/*analysis/*microbiology ; *Food Microbiology ; Milk/*microbiology ; }, abstract = {The robustness of the starter culture during cheese fermentation is enhanced by the presence of a rich consortium of microbes. Natural starters are consortia of microbes undoubtedly richer than selected starters. Among natural starters, natural whey starters (NWS) are the most common cultures currently used to produce different varieties of cheeses. Undefined NWS are typically used for Italian cooked, long-ripened, extra-hard, raw milk cheeses, such as Parmigiano Reggiano and Grana Padano. Together with raw milk microbiota, NWS are responsible for most cheese characteristics. The microbial ecology of these 2 cheese varieties is based on a complex interaction among starter lactic acid bacteria (SLAB) and nonstarter lactic acid bacteria (NSLAB), which are characterized by their different abilities to grow in a changing substrate. This review aims to summarize the latest findings on Parmigiano Reggiano and Grana Padano to better understand the dynamics of SLAB, which mainly arise from NWS, and NSLAB, which mainly arise from raw milk, and their possible role in determining the characteristics of these cheeses. The review is presented in 4 main sections. The first summarizes the main microbiological and chemical properties of the ripened cheese as determined by cheese-making process variables, as these variables may affect microbial growth. The second describes the microbiota of raw milk as affected by specific milk treatments, from milking to the filling of the cheese milk vat. The third describes the microbiota of NWS, and the fourth reviews the knowledge available on microbial dynamics from curd to ripened cheese. As the dynamics and functionality of complex undefined NWS is one of the most important areas of focus in current food microbiology research, this review may serve as a good starting point for implementing future studies on microbial diversity and functionality of undefined cheese starter cultures.}, }
@article {pmid24290642, year = {2014}, author = {Quero, GM and Fusco, V and Cocconcelli, PS and Owczarek, L and Borcakli, M and Fontana, C and Skapska, S and Jasinska, UT and Ozturk, T and Morea, M}, title = {Microbiological, physico-chemical, nutritional and sensory characterization of traditional Matsoni: selection and use of autochthonous multiple strain cultures to extend its shelf-life.}, journal = {Food microbiology}, volume = {38}, number = {}, pages = {179-191}, doi = {10.1016/j.fm.2013.09.004}, pmid = {24290642}, issn = {1095-9998}, mesh = {Animals ; Cattle ; Cultured Milk Products/*chemistry/*microbiology ; Fermentation ; Food Preservation ; Food Storage ; Humans ; Lactobacillales/classification/genetics/*isolation &amp; purification/*metabolism ; *Nutritive Value ; *Taste ; }, abstract = {Matsoni, a traditional Georgian fermented milk, has variable quality and stability besides a short shelf-life (72-120 h at 6 °C) due to inadequate production and storage conditions. To individuate its typical traits as well as select and exploit autochthonous starter cultures to standardize its overall quality without altering its typicality, we carried out a thorough physico-chemical, sensorial and microbial characterization of traditional Matsoni. A polyphasic approach, including a culture-independent (PCR-DGGE) and two PCR culture-dependent methods, was employed to study the ecology of Matsoni. Overall, the microbial ecosystem of Matsoni resulted largely dominated by Streptococcus (S.) thermophilus and Lactobacillus (Lb.) delbrueckii subsp. bulgaricus. High loads of other lactic acid bacteria species, including Lb. helveticus, Lb. paracasei and Leuconostoc (Leuc.) lactis were found to occur as well. A selected autochthonous multiple strain culture (AMSC) composed of one Lb. bulgaricus, one Lb. paracasei and one S. thermophilus strain, applied for the pilot-scale production of traditional Matsoni, resulted the best in terms of enhanced shelf-life (one month), sensorial and nutritional quality without altering its overall typical quality. This AMSC is at disposal of SMEs who need to exploit and standardize the overall quality of this traditional fermented milk, preserving its typicality.}, }
@article {pmid24288368, year = {2014}, author = {Cole, JR and Wang, Q and Fish, JA and Chai, B and McGarrell, DM and Sun, Y and Brown, CT and Porras-Alfaro, A and Kuske, CR and Tiedje, JM}, title = {Ribosomal Database Project: data and tools for high throughput rRNA analysis.}, journal = {Nucleic acids research}, volume = {42}, number = {Database issue}, pages = {D633-42}, pmid = {24288368}, issn = {1362-4962}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; UH3 DK083993/DK/NIDDK NIH HHS/United States ; U01 HL098961/HL/NHLBI NIH HHS/United States ; }, mesh = {Archaea/classification ; Bacteria/classification ; *Databases, Nucleic Acid ; Fungi/classification ; Genes, Archaeal ; Genes, Bacterial ; Genes, Fungal ; *Genes, Microbial ; *Genes, rRNA ; *High-Throughput Nucleotide Sequencing ; Internet ; Oligonucleotide Probes ; Sequence Alignment ; Software ; }, abstract = {Ribosomal Database Project (RDP; http://rdp.cme.msu.edu/) provides the research community with aligned and annotated rRNA gene sequence data, along with tools to allow researchers to analyze their own rRNA gene sequences in the RDP framework. RDP data and tools are utilized in fields as diverse as human health, microbial ecology, environmental microbiology, nucleic acid chemistry, taxonomy and phylogenetics. In addition to aligned and annotated collections of bacterial and archaeal small subunit rRNA genes, RDP now includes a collection of fungal large subunit rRNA genes. RDP tools, including Classifier and Aligner, have been updated to work with this new fungal collection. The use of high-throughput sequencing to characterize environmental microbial populations has exploded in the past several years, and as sequence technologies have improved, the sizes of environmental datasets have increased. With release 11, RDP is providing an expanded set of tools to facilitate analysis of high-throughput data, including both single-stranded and paired-end reads. In addition, most tools are now available as open source packages for download and local use by researchers with high-volume needs or who would like to develop custom analysis pipelines.}, }
@article {pmid24286373, year = {2014}, author = {Deng, J and Brettar, I and Luo, C and Auchtung, J and Konstantinidis, KT and Rodrigues, JL and Höfle, M and Tiedje, JM}, title = {Stability, genotypic and phenotypic diversity of Shewanella baltica in the redox transition zone of the Baltic Sea.}, journal = {Environmental microbiology}, volume = {16}, number = {6}, pages = {1854-1866}, doi = {10.1111/1462-2920.12344}, pmid = {24286373}, issn = {1462-2920}, mesh = {Cluster Analysis ; Genetic Variation ; Genome, Bacterial ; Genotype ; Microbiota/genetics ; Molecular Sequence Annotation ; Multilocus Sequence Typing ; Oceans and Seas ; Oxidation-Reduction ; Phylogeny ; Seawater/chemistry/*microbiology ; Selection, Genetic ; Shewanella/*genetics ; *Water Microbiology ; }, abstract = {Studying how bacterial strains diverge over space and time and how divergence leads to ecotype formation is important for understanding structure and dynamics of environmental communities. Here we assess the ecological speciation and temporal dynamics of a collection of Shewanella baltica strains from the redox transition zone of the central Baltic Sea, sampled at three time points over a course of 12 years, with a subcollection containing 46 strains subjected to detailed genetic and physiological characterization. Nine clades were consistently recovered by three different genotyping approaches: gyrB gene sequencing, multilocus sequence typing (MLST) and whole genome clustering of data from comparative genomic hybridization, and indicated specialization according to nutrient availability, particle association and temporal distribution. Genomic analysis suggested higher intra- than inter-clade recombination that might result from niche partitioning. Substantial heterogeneity in carbon utilization and respiratory capabilities suggested rapid diversification within the same 'named' species and physical habitat and showed consistency with genetic relatedness. At least two major ecotypes, represented by MLST clades A and E, were proposed based on genetic, ecological and physiological distinctiveness. This study suggests that genetic analysis in conjunction with phenotypic evaluation can provide better understanding of the ecological framework and evolutionary trajectories of microbial species.}, }
@article {pmid24284397, year = {2013}, author = {McLean, RJ and Kakirde, KS}, title = {Enhancing metagenomics investigations of microbial interactions with biofilm technology.}, journal = {International journal of molecular sciences}, volume = {14}, number = {11}, pages = {22246-22257}, pmid = {24284397}, issn = {1422-0067}, mesh = {Biofilms/*growth &amp; development ; Computational Biology ; Ecology ; Environment ; *Metagenomics ; *Microbial Interactions ; }, abstract = {Investigations of microbial ecology and diversity have been greatly enhanced by the application of culture-independent techniques. One such approach, metagenomics, involves sample collections from soil, water, and other environments. Extracted nucleic acids from bulk environmental samples are sequenced and analyzed, which allows microbial interactions to be inferred on the basis of bioinformatics calculations. In most environments, microbial interactions occur predominately in surface-adherent, biofilm communities. In this review, we address metagenomics sampling and biofilm biology, and propose an experimental strategy whereby the resolving power of metagenomics can be enhanced by incorporating a biofilm-enrichment step during sample acquisition.}, }
@article {pmid24281733, year = {2014}, author = {Golby, S and Ceri, H and Marques, LL and Turner, RJ}, title = {Mixed-species biofilms cultured from an oil sand tailings pond can biomineralize metals.}, journal = {Microbial ecology}, volume = {68}, number = {1}, pages = {70-80}, pmid = {24281733}, issn = {1432-184X}, mesh = {Alberta ; Bacteria/drug effects/*growth &amp; development ; Biodegradation, Environmental ; Biofilms/drug effects/*growth &amp; development ; DNA, Bacterial/genetics ; Industrial Waste ; Metals/*metabolism ; Petroleum ; Ponds/microbiology ; Rhodococcus/drug effects/growth &amp; development ; Sequence Analysis, DNA ; Sewage/microbiology ; }, abstract = {Here, we used an in vitro biofilm approach to study metal resistance and/or tolerance of mixed-species biofilms grown from an oil sand tailings pond in northern Alberta, Canada. Metals can be inhibitory to microbial hydrocarbon degradation. If microorganisms are exposed to metal concentrations above their resistance levels, metabolic activities and hydrocarbon degradation can be slowed significantly, if not inhibited completely. For this reason, bioremediation strategies may be most effective if metal-resistant microorganisms are used. Viability was measured after exposure to a range of concentrations of ions of Cu, Ag, Pb, Ni, Zn, V, Cr, and Sr. Mixed-species biofilms were found to be extremely metal resistant; up to 20 mg/L of Pb, 16 mg/L of Zn, 1,000 mg/L of Sr, and 3.2 mg/L of Ni. Metal mineralization was observed by visualization with scanning electron microscopy with metal crystals of Cu, Ag, Pb, and Sr exuding from the biofilms. Following metal exposure, the mixed-species biofilms were analyzed by molecular methods and were found to maintain high levels of species complexity. A single species isolated from the community (Rhodococcus erythropolis) was used as a comparison against the mixed-community biofilm and was seen to be much less tolerant to metal stress than the community and did not biomineralize the metals.}, }
@article {pmid24281732, year = {2014}, author = {Cregut, M and Durand, MJ and Thouand, G}, title = {The diversity and functions of choline sulphatases in microorganisms.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {350-357}, pmid = {24281732}, issn = {1432-184X}, mesh = {Archaea/enzymology/*genetics ; Ecology ; Fungi/enzymology/*genetics ; *Genetic Variation ; Membrane Transport Proteins ; Operon ; Rhizobiaceae/enzymology/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; *Soil Microbiology ; Sulfatases/*genetics/metabolism ; }, abstract = {Choline sulphates have two putative roles in microorganisms: as a reservoir of C, N and S and as osmoprotectants. Although there is no established connection to date regarding the relative distribution of these two functions in microbial communities, this information is crucial in determining the role of choline sulphate in soils, particularly in cultivated soils where S is limiting. Therefore, in order to establish such a connection, the diversity of choline sulphatase (betC) genes was investigated in this study using numerous fully sequenced microbes available in GenBank. Our genomic analyses revealed unequivocally that the betICBA operon is restricted to Rhizobiaceae family members, which live under symbiotic conditions that prevent elemental depletion. Together with the uniform genetic organisation of the betICBA operon in Rhizobiaceae, BetC appears to be both utilised for osmoprotection or S replenishment. In contrast, betC in a wide variety of free-living microbes (including fungi, archaea and bacteria) was found in a cassette encoding only BetC and a choline sulphate transporter, a configuration that appears to be responsible for fulfilling elemental S requirements. Lastly, the relatively high number of BetC sequences available allowed the identification of a specific signature sequence that discriminates between these two functions and also globally defines some conserved motifs in microbial choline sulphatases. Due to the widespread presence of BetC in microbes and the wide repartition of the betC cassette system, the potential importance of choline sulphatase in global S recycling requires further clarification.}, }
@article {pmid24278322, year = {2013}, author = {Buriánková, I and Brablcová, L and Mach, V and Dvořák, P and Chaudhary, PP and Rulík, M}, title = {Identification of methanogenic archaea in the hyporheic sediment of Sitka stream.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e80804}, pmid = {24278322}, issn = {1932-6203}, mesh = {Archaea/*genetics ; Czech Republic ; Environmental Microbiology ; Gene Library ; Genes, Archaeal ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Molecular Sequence Data ; Phylogeny ; Rivers/*microbiology ; }, abstract = {Methanogenic archaea produce methane as a metabolic product under anoxic conditions and they play a crucial role in the global methane cycle. In this study molecular diversity of methanogenic archaea in the hyporheic sediment of the lowland stream Sitka (Olomouc, Czech Republic) was analyzed by PCR amplification, cloning and sequencing analysis of the methyl coenzyme M reductase alpha subunit (mcrA) gene. Sequencing analysis of 60 clones revealed 24 different mcrA phylotypes from hyporheic sedimentary layers to a depth of 50 cm. Phylotypes were affiliated with Methanomicrobiales, Methanosarcinales and Methanobacteriales orders. Only one phylotype remains unclassified. The majority of the phylotypes showed higher affiliation with uncultured methanogens than with known methanogenic species. The presence of relatively rich assemblage of methanogenic archaea confirmed that methanogens may be an important component of hyporheic microbial communities and may affect CH4 cycling in rivers.}, }
@article {pmid24276540, year = {2014}, author = {Tugarova, AV and Burov, AM and Burashnikova, MM and Kamnev, AA}, title = {Gold(III) reduction by the rhizobacterium Azospirillum brasilense with the formation of gold nanoparticles.}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {155-160}, pmid = {24276540}, issn = {1432-184X}, mesh = {Azospirillum brasilense/*metabolism ; Gold/*metabolism ; Microscopy, Electron, Transmission ; *Nanoparticles ; Polysaccharides, Bacterial/chemistry ; Spectrometry, X-Ray Emission ; }, abstract = {For the soil nitrogen-fixing bacterium Azospirillum brasilense, the ability to reduce [AuCl4](-) and to form gold nanoparticles (GNPs) has been demonstrated, with the appearance of a mauve tint of the culture. To validate the shapes and chemical nature of nanoparticles, transmission electron microscopy (TEM) and X-ray fluorescence analysis were used. For the widely studied agriculturally important wild-type strains A. brasilense Sp7 and Sp245, GNPs formed after 10 days of incubation of cell biomass with 0.25 mM [AuCl4](-) were shown (using TEM) to be mainly of spherical form (5 to 20 nm in diameter), with rare occasional triangles. In the course of cultivation with [AuCl4](-), after 5 days, a mauve tint was already visible for cells of strain Sp245.5, after 6 days for Sp245 and after 10 days for Sp7. Thus, for the mutant strain Sp245.5 (which has significant differences in the structure and composition of cell-surface polysaccharides as compared with Sp245), a more rapid formation of GNPs was observed. Moreover, their TEM images (also obtained after 10 days) showed different shapes: nano-sized spheres, triangles, hexagons and rods, as well as larger round-shaped flower-like nanoparticles about 100 nm in size. Since by the time of GNP formation in our experiments the cells were found to be already not viable, this confirms the dominating role of cell surface structure and chemical composition in shaping the GNPs formed in the course of [AuCl4](-) reduction to Au(0). This finding may be useful for understanding the natural biogeochemical mechanisms of gold reduction and formation of GNPs involving microorganisms. The data obtained may also help in developing protocols for environmentally friendly synthesis of nanoparticles and possible use of bacterial cells with modified surface structure and composition for their fabrication.}, }
@article {pmid24276539, year = {2014}, author = {Zhao, J and Zhang, R and Xue, C and Xun, W and Sun, L and Xu, Y and Shen, Q}, title = {Pyrosequencing reveals contrasting soil bacterial diversity and community structure of two main winter wheat cropping systems in China.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {443-453}, pmid = {24276539}, issn = {1432-184X}, mesh = {Agriculture/methods ; *Biodiversity ; China ; Crops, Agricultural/microbiology ; DNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; *Soil Microbiology ; Triticum/*microbiology ; Zea mays/microbiology ; }, abstract = {Microbes are key components of the soil environment, playing an important role in maintaining soil health, sustainability, and productivity. The composition and structure of soil bacterial communities were examined in winter wheat-rice (WR) and winter wheat-maize (WM) cropping systems derived from five locations in the Low-Middle Yangtze River plain and the Huang-Huai-Hai plain by pyrosequencing of the 16S ribosomal RNA gene amplicons. A total of 102,367 high quality sequences were used for multivariate statistical analysis and to test for correlation between community structure and environmental variables such as crop rotations, soil properties, and locations. The most abundant phyla across all soil samples were Proteobacteria, Acidobacteria, and Bacteroidetes. Similar patterns of bacterial diversity and community structure were observed within the same cropping systems, and a higher relative abundance of anaerobic bacteria was found in WR compared to WM cropping systems. Variance partitioning analysis revealed complex relationships between bacterial community and environmental variables. The effect of crop rotations was low but significant, and interactions among soil properties, locations, and crop rotations accounted for most of the explained variation in the structure of bacterial communities. Soil properties such as pH, available P, and available K showed higher correlations (positive or negative) with the majority of the abundant taxa. Bacterial diversity (the Shannon index) and richness (Chao1 and ACE) were higher under WR than WM cropping systems.}, }
@article {pmid24276538, year = {2014}, author = {Vega, LM and Alvarez, PJ and McLean, RJ}, title = {Bacterial signaling ecology and potential applications during aquatic biofilm construction.}, journal = {Microbial ecology}, volume = {68}, number = {1}, pages = {24-34}, pmid = {24276538}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/pharmacology ; Aquatic Organisms ; Bacteria/drug effects/*growth &amp; development ; Biofilms/drug effects/*growth &amp; development ; *Quorum Sensing/drug effects/genetics ; }, abstract = {In their natural environment, bacteria and other microorganisms typically grow as surface-adherent biofilm communities. Cell signal processes, including quorum signaling, are now recognized as being intimately involved in the development and function of biofilms. In contrast to their planktonic (unattached) counterparts, bacteria within biofilms are notoriously resistant to many traditional antimicrobial agents and so represent a major challenge in industry and medicine. Although biofilms impact many human activities, they actually represent an ancient mode of bacterial growth as shown in the fossil record. Consequently, many aquatic organisms have evolved strategies involving signal manipulation to control or co-exist with biofilms. Here, we review the chemical ecology of biofilms and propose mechanisms whereby signal manipulation can be used to promote or control biofilms.}, }
@article {pmid24276537, year = {2014}, author = {Mei, L and Zhu, M and Zhang, DZ and Wang, YZ and Guo, J and Zhang, HB}, title = {Geographical and temporal changes of foliar fungal endophytes associated with the invasive plant Ageratina adenophora.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {402-409}, pmid = {24276537}, issn = {1432-184X}, mesh = {Ascomycota/classification/growth &amp; development/*isolation &amp; purification ; Asteraceae/*microbiology ; Biodiversity ; China ; Colletotrichum/genetics/growth &amp; development/*isolation &amp; purification ; DNA, Fungal/genetics ; Endophytes/genetics/growth &amp; development/*isolation &amp; purification ; Genetic Variation ; Geography ; *Introduced Species ; Phylogeny ; Plant Leaves/microbiology ; Symbiosis ; }, abstract = {Endophytes may gradually accumulate in the new geographic range of a non-native plant, just as pathogens do. To test this hypothesis, the dynamics of colonization and diversity of foliar fungal endophytes of non-native Ageratina adenophora were investigated. Previous reports showed that the time since the initial introduction (1930s) of A. adenophora into China varied among populations. Endophytes were sampled in three provinces of Southwest China in 21 sites that varied from 20 to 70 years since the introduction of A. adenophora from its native Central America. Endophyte isolation frequencies varied from 1.87% to 60.23% overall in a total of 4,032 leaf fragments. Based on ITS sequence variations, 463 fungal endophytes were distinguished as 112 operational taxonomic units (OTUs) belonging to the Sordariomycetes (77 OTUs, 373 isolates), Dothideomycetes (18 OTUs, 38 isolates), and Agaricomycetes (17 OTUs, 52 strains) classes. Colletotrichum (28.51%), Nemania (14.90%), Phomopsis (13.17%), and Xylaria (4.97%) were the most abundant genera. Both endophyte diversity and overall isolation frequency increased with time since introduction. The genetic differentiation of the fungus Colletotrichum gloeosporioides indicated that the dispersal of endophytes was likely affected by a combination of geographic factors and the invasion history of the host A. adenophora.}, }
@article {pmid24276536, year = {2014}, author = {Balboa, S and Bastardo, A and Romalde, JL}, title = {Disentangling the population structure and evolution of the clam pathogen Vibrio tapetis.}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {145-154}, pmid = {24276536}, issn = {1432-184X}, mesh = {Animals ; Bacterial Typing Techniques ; Bivalvia/*microbiology ; DNA, Bacterial/genetics ; *Evolution, Molecular ; Gene Flow ; Genetic Variation ; Multilocus Sequence Typing ; *Phylogeny ; Recombination, Genetic ; Sequence Analysis, DNA ; Vibrio/classification/*genetics ; Vibrio Infections/microbiology/veterinary ; }, abstract = {Vibrio tapetis is a fastidious slow-growing microorganism that causes the Brown Ring Disease in clams. Recently, two subspecies for this bacterial pathogen have been proposed. We have developed a multilocus sequence typing scheme and performed evolutionary studies of V. tapetis population using the great majority of isolates of V. tapetis obtained worldwide until now (30 isolates). V. tapetis constitutes a high polymorphic population, showing low diversity indexes and some genetic discontinuity among the isolates. Mutation events are more frequent than recombination, although both are approximately equally important for genetic diversification. In fact, the divergence between subspecies occurred exclusively by mutation but the diversity observed among isolates of the same subspecies appeared to be generated mostly by recombination. Between the subspecies, genetic distance is very high and almost no recurrent gene flow exists. This pathogen displays a non-clonal population structure with an ancient spatial segregation population and some degree of geographical isolation, followed by a population expansion, at least for V. tapetis subsp. tapetis. A database from this study was created and hosted on publmlst.org (http://pubmlst.org/vtapetis/).}, }
@article {pmid24274586, year = {2014}, author = {De Roy, K and Marzorati, M and Van den Abbeele, P and Van de Wiele, T and Boon, N}, title = {Synthetic microbial ecosystems: an exciting tool to understand and apply microbial communities.}, journal = {Environmental microbiology}, volume = {16}, number = {6}, pages = {1472-1481}, doi = {10.1111/1462-2920.12343}, pmid = {24274586}, issn = {1462-2920}, mesh = {Animals ; Bacteria/*metabolism ; Bacterial Physiological Phenomena ; Biodegradation, Environmental ; Biofilms ; Bioreactors ; *Ecosystem ; Humans ; Microbial Consortia ; *Models, Biological ; }, abstract = {Many microbial ecologists have described the composition of microbial communities in a plenitude of environments, which has greatly improved our basic understanding of microorganisms and ecosystems. However, the factors and processes that influence the behaviour and functionality of an ecosystem largely remain black boxes when using conventional approaches. Therefore, synthetic microbial ecology has gained a lot of interest in the last few years. Because of their reduced complexity and increased controllability, synthetic communities are often preferred over complex communities to examine ecological theories. They limit the factors that influence the microbial community to a minimum, allowing their management and identifying specific community responses. However, besides their use for basic research, synthetic ecosystems also found their way towards different applications, like industrial fermentation and bioremediation. Here, we review why and how synthetic microbial communities are applied for research purposes and for which applications they have been and could be successfully used.}, }
@article {pmid24273587, year = {2013}, author = {Scharschmidt, TC and Fischbach, MA}, title = {What Lives On Our Skin: Ecology, Genomics and Therapeutic Opportunities Of the Skin Microbiome.}, journal = {Drug discovery today. Disease mechanisms}, volume = {10}, number = {3-4}, pages = {}, pmid = {24273587}, issn = {1740-6765}, support = {R01 AI101018/AI/NIAID NIH HHS/United States ; DP2 OD007290/OD/NIH HHS/United States ; UL1 TR000149/TR/NCATS NIH HHS/United States ; UL1 TR001120/TR/NCATS NIH HHS/United States ; M01 RR001346/RR/NCRR NIH HHS/United States ; }, abstract = {Our skin is home to a rich community of microorganisms. Recent advances in sequencing technology have allowed more accurate enumeration of these human-associated microbiota and investigation of their genomic content. Staphylococcus, Corynebacterium and Propionibacterium represent the dominant bacterial genera on skin and illustrate how bacteria adapt to life in this harsh environment and also provide us with unique benefits. In healthy states, our skin peacefully co-exists with commensal bacteria while fending off potentially dangerous invaders. Disruption of this equilibrium, termed "dysbiosis", can result from changes in the composition of our skin bacteria, an altered immune response to them, or both and may be a driving factor in certain types of inflammatory skin disease. Engineering topical therapeutics to favourably influence the composition of our skin flora and optimize interactions with them represents a real therapeutic opportunity for the field of dermatology and warrants additional investigation into skin microbial ecology and disease mechanisms related to host-microbe dysbiosis.}, }
@article {pmid24272281, year = {2014}, author = {Shen, LD and Liu, S and Zhu, Q and Li, XY and Cai, C and Cheng, DQ and Lou, LP and Xu, XY and Zheng, P and Hu, BL}, title = {Distribution and diversity of nitrite-dependent anaerobic methane-oxidising bacteria in the sediments of the Qiantang River.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {341-349}, pmid = {24272281}, issn = {1432-184X}, mesh = {Anaerobiosis ; Bacteria/genetics/*isolation &amp; purification ; *Biodiversity ; China ; DNA, Bacterial/genetics ; Ecosystem ; Geologic Sediments/*microbiology ; Methane/chemistry ; Nitrites/chemistry ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Nitrite-dependent anaerobic methane oxidation (n-damo) process was reported to be mediated by "Candidatus Methylomirabilis oxyfera", which belongs to the candidate phylum NC10. M. oxyfera-like bacteria have been detected in lake ecosystems, while their distribution, diversity and abundance in river ecosystems have not been well studied. In this study, both the 16S rRNA and the pmoA molecular biomarkers confirmed the presence of diverse NC10 phylum bacteria related to M. oxyfera in a river ecosystem-the Qiantang River, Zhejiang Province (China). Phylogenetic analysis of 16S rRNA genes demonstrated that the recovered M. oxyfera-like sequences could be grouped into several distinct clusters that exhibited 89.8% to 98.9% identity to the M. oxyfera 16S rRNA gene. Similarly, several different clusters of pmoA gene sequences were observed, and these clusters displayed 85.1-95.4% sequence identity to the pmoA gene of M. oxyfera. Quantitative PCR showed that the abundance of M. oxyfera-like bacteria varied from 1.32 ± 0.16 × 10(6) to 1.03 ± 0.12 × 10(7) copies g (dry weight)(-1). Correlation analysis demonstrated that the total inorganic nitrogen content, the ammonium content and the organic content of the sediment were important factors affecting the distribution of M. oxyfera-like bacterial groups in the examined sediments. This study demonstrated the distribution of diverse M. oxyfera-like bacteria and their correlation with environmental factors in Qiantang River sediments.}, }
@article {pmid24272280, year = {2014}, author = {Sjöqvist, C and Kremp, A and Lindehoff, E and Båmstedt, U and Egardt, J and Gross, S and Jönsson, M and Larsson, H and Pohnert, G and Richter, H and Selander, E and Godhe, A}, title = {Effects of grazer presence on genetic structure of a phenotypically diverse diatom population.}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {83-95}, pmid = {24272280}, issn = {1432-184X}, mesh = {Animals ; *Biodiversity ; Copepoda ; Diatoms/*genetics/*growth &amp; development ; *Food Chain ; Genetic Variation ; Genotype ; Phenotype ; }, abstract = {Studies of predator-prey systems in both aquatic and terrestrial environments have shown that grazers structure the intraspecific diversity of prey species, given that the prey populations are phenotypically variable. Populations of phytoplankton have traditionally considered comprising only low intraspecific variation, hence selective grazing as a potentially structuring factor of both genetic and phenotypic diversity has not been comprehensively studied. In this study, we compared strain specific growth rates, production of polyunsaturated aldehydes, and chain length of the marine diatom Skeletonema marinoi in both grazer and non-grazer conditions by conducting monoclonal experiments. Additionally, a mesocosm experiment was performed with multiclonal experimental S. marinoi populations exposed to grazers at different levels of copepod concentration to test effects of grazer presence on diatom diversity in close to natural conditions. Our results show that distinct genotypes of a geographically restricted population exhibit variable phenotypic traits relevant to grazing interactions such as chain length and growth rates. Grazer presence affected clonal richness and evenness of multiclonal Skeletonema populations in the mesocosms, likely in conjunction with intrinsic interactions among the diatom strains. Only the production of polyunsaturated aldehydes was not affected by grazer presence. Our findings suggest that grazing can be an important factor structuring diatom population diversity in the sea and emphasize the importance of considering clonal differences when characterizing species and their role in nature.}, }
@article {pmid24272279, year = {2014}, author = {Im, H and Kim, D and Ghim, CM and Mitchell, RJ}, title = {Shedding light on microbial predator-prey population dynamics using a quantitative bioluminescence assay.}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {167-176}, pmid = {24272279}, issn = {1432-184X}, mesh = {Bdellovibrio/*physiology ; *Escherichia coli/genetics ; Fluorescence ; *Food Chain ; Genes, Reporter ; Luciferases/genetics ; *Luminescent Measurements ; Microscopy, Fluorescence ; Plasmids/genetics ; Population Dynamics ; Transformation, Bacterial ; }, abstract = {This study assessed the dynamics of predation by Bdellovibrio bacteriovorus HD 100. Predation tests with two different bioluminescent strains of Escherichia coli, one expressing a heat-labile bacterial luciferase and the other a heat-stable form, showed near identical losses from both, indicating that protein expression and stability are not responsible for the "shutting-off" of the prey bioluminescence (BL). Furthermore, it was found that the loss in the prey BL was not proportional with the predator-to-prey ratio (PPR), with significantly greater losses seen as this value was increased. This suggests that other factors also play a role in lowering the prey BL. The loss in BL, however, was very consistent within nine independent experiments to the point that we were able to reliably estimate the predator numbers within only 1 h when present at a PPR of 6 or higher, Using a fluorescent prey, we found that premature lysis of the prey occurs at a significant level and was more prominent as the PPR ratio increased. Based upon the supernatant fluorescent signal, even a relatively low PPR of 10-20 led to approximately 5% of the prey population being prematurely lysed within 1 h, while a PPR of 90 led to nearly 15% lysis. Consequently, we developed a modified Lotka-Volterra predator-prey model that accounted for this lysis and is able to reliably estimate the prey and bdelloplast populations for a wide range of PPRs.}, }
@article {pmid24270897, year = {2014}, author = {Wang, YF and Gu, JD}, title = {Effects of allylthiourea, salinity, and pH on ammonia/ammonium-oxidizing prokaryotes in mangrove sediment incubated in laboratory microcosms.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {7}, pages = {3257-3274}, doi = {10.1007/s00253-013-5399-3}, pmid = {24270897}, issn = {1432-0614}, mesh = {Ammonia/*metabolism ; Ammonium Compounds/*metabolism ; Anaerobiosis ; Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biota ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Geologic Sediments/*microbiology ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Oxidation-Reduction ; *Salinity ; Seawater/*chemistry ; Sequence Analysis, DNA ; Thiourea/*analogs &amp; derivatives/analysis ; }, abstract = {Anaerobic ammonium-oxidizing (anammox) bacteria, aerobic ammonia-oxidizing archaea (AOA) and bacteria (AOB) are three groups of ammonia/ammonium-oxidizing prokaryotes (AOPs) involved in the biochemical nitrogen cycling. In this study, the effects of allylthiourea (ATU), pH, and salinity on these three groups from mangrove sediment were investigated through microcosm incubation in laboratory. ATU treatments (50, 100, and 500 mg L(-1)) obviously affected the community structure of anammox bacteria and AOB, but only slightly for AOA. ATU began to inhibit anammox bacteria growth slightly from day 10, but had an obvious inhibition on AOA growth from the starting of the study. At 100 mg L(-1) of ATU or higher, AOB growth was inhibited, but only lasted for 5 days. The pH treatments showed that acidic condition (pH 5) had a slight effect on the community structure of anammox bacteria and AOA, but an obvious effect on AOB. Acidic condition promoted the growth of all groups of AOPs in different extent, but alkaline condition (pH 9) had a weak effect on AOB community structure and a strong effect on both anammox bacteria and AOA. Alkaline condition obviously inhibited anammox bacteria growth, slightly promoted AOA, and slightly promoted AOB in the first 20 days, but inhibited afterward. Salinity treatment showed that higher salinity (20 and 40 ‰) resulted in higher anammox bacteria diversity, and both AOA and AOB might have species specificity to salinity. High salinity promoted the growth of both anammox bacteria and AOB, inhibited AOA between 5 and 10 days, but promoted afterward. The results help to understand the role of these microbial groups in biogeochemical nitrogen cycling and their responses to the changing environments.}, }
@article {pmid24260458, year = {2013}, author = {Tong, M and Li, X and Wegener Parfrey, L and Roth, B and Ippoliti, A and Wei, B and Borneman, J and McGovern, DP and Frank, DN and Li, E and Horvath, S and Knight, R and Braun, J}, title = {A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e80702}, pmid = {24260458}, issn = {1932-6203}, support = {UL1TR000124/TR/NCATS NIH HHS/United States ; U01 DK062413/DK/NIDDK NIH HHS/United States ; HG005964/HG/NHGRI NIH HHS/United States ; R21 DK084554/DK/NIDDK NIH HHS/United States ; UL1 TR000124/TR/NCATS NIH HHS/United States ; P01DK046763/DK/NIDDK NIH HHS/United States ; DK46763/DK/NIDDK NIH HHS/United States ; R21 HG005964/HG/NHGRI NIH HHS/United States ; R01 AI078885/AI/NIAID NIH HHS/United States ; P01 DK046763/DK/NIDDK NIH HHS/United States ; AI078885/AI/NIAID NIH HHS/United States ; DK062413/DK/NIDDK NIH HHS/United States ; DK084554/DK/NIDDK NIH HHS/United States ; }, mesh = {Cluster Analysis ; Cohort Studies ; Humans ; Inflammatory Bowel Diseases/etiology/*microbiology ; Intestinal Mucosa/*microbiology/pathology ; Metagenome ; *Microbiota ; Phenotype ; RNA, Ribosomal, 16S ; }, abstract = {Abnormalities of the intestinal microbiota are implicated in the pathogenesis of Crohn's disease (CD) and ulcerative colitis (UC), two spectra of inflammatory bowel disease (IBD). However, the high complexity and low inter-individual overlap of intestinal microbial composition are formidable barriers to identifying microbial taxa representing this dysbiosis. These difficulties might be overcome by an ecologic analytic strategy to identify modules of interacting bacteria (rather than individual bacteria) as quantitative reproducible features of microbial composition in normal and IBD mucosa. We sequenced 16S ribosomal RNA genes from 179 endoscopic lavage samples from different intestinal regions in 64 subjects (32 controls, 16 CD and 16 UC patients in clinical remission). CD and UC patients showed a reduction in phylogenetic diversity and shifts in microbial composition, comparable to previous studies using conventional mucosal biopsies. Analysis of weighted co-occurrence network revealed 5 microbial modules. These modules were unprecedented, as they were detectable in all individuals, and their composition and abundance was recapitulated in an independent, biopsy-based mucosal dataset 2 modules were associated with healthy, CD, or UC disease states. Imputed metagenome analysis indicated that these modules displayed distinct metabolic functionality, specifically the enrichment of oxidative response and glycan metabolism pathways relevant to host-pathogen interaction in the disease-associated modules. The highly preserved microbial modules accurately classified IBD status of individual patients during disease quiescence, suggesting that microbial dysbiosis in IBD may be an underlying disorder independent of disease activity. Microbial modules thus provide an integrative view of microbial ecology relevant to IBD.}, }
@article {pmid24256454, year = {2014}, author = {Ni, J and Yan, Q and Yu, Y and Zhang, T}, title = {Factors influencing the grass carp gut microbiome and its effect on metabolism.}, journal = {FEMS microbiology ecology}, volume = {87}, number = {3}, pages = {704-714}, doi = {10.1111/1574-6941.12256}, pmid = {24256454}, issn = {1574-6941}, mesh = {Amino Acids/metabolism ; Animal Feed ; Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Carbohydrate Metabolism ; Carps/*metabolism/*microbiology ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Feeding Behavior ; Gastrointestinal Tract/*microbiology ; Metagenome ; *Microbiota ; Open Reading Frames ; Phylogeny ; }, abstract = {Gut microbiota have attracted extensive attention recently because of their important role in host metabolism, immunity and health maintenance. The present study focused on factors affecting the gut microbiome of grass carp (Ctenopharyngodon idella) and further explored the potential effect of the gut microbiome on metabolism. Totally, 43.39 Gb of screened metagenomic sequences obtained from 24 gut samples were fully analysed. We detected 1228 phylotypes (116 Archaea and 1112 Bacteria), most of which belonged to the phyla Firmicutes, Proteobacteria and Fusobacteria. Totally, 41335 of the detected open reading frames (ORFs) were matched to Kyoto Encyclopedia of Genes and Genomes pathways, and carbohydrate and amino acid metabolism was the main matched pathway deduced from the annotated ORFs. Redundancy analysis based on the phylogenetic composition and gene composition of the gut microbiome indicated that gut fullness and feeding (i.e. ryegrass vs. commercial feed, and pond-cultured vs. wild) were significantly related to the gut microbiome. Moreover, many biosynthesis and metabolism pathways of carbohydrates, amino acids and lipids were significantly enhanced by the gut microbiome in ryegrass-fed grass carp. These findings suggest that the metabolic role played by the gut microbiome in grass carp can be affected by feeding. These findings contribute to the field of fish gut microbial ecology and also provide a basis for follow-up functional studies.}, }
@article {pmid24253663, year = {2014}, author = {Bibby, K}, title = {Improved bacteriophage genome data is necessary for integrating viral and bacterial ecology.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {242-244}, pmid = {24253663}, issn = {1432-184X}, mesh = {Bacteriophages/*genetics ; Databases, Factual ; Ecology ; *Genome, Bacterial ; *Genome, Viral ; Sequence Analysis, DNA ; }, abstract = {The recent rise in "omics"-enabled approaches has lead to improved understanding in many areas of microbial ecology. However, despite the importance that viruses play in a broad microbial ecology context, viral ecology remains largely not integrated into high-throughput microbial ecology studies. A fundamental hindrance to the integration of viral ecology into omics-enabled microbial ecology studies is the lack of suitable reference bacteriophage genomes in reference databases-currently, only 0.001% of bacteriophage diversity is represented in genome sequence databases. This commentary serves to highlight this issue and to promote bacteriophage genome sequencing as a valuable scientific undertaking to both better understand bacteriophage diversity and move towards a more holistic view of microbial ecology.}, }
@article {pmid24253662, year = {2014}, author = {Zhong, X and Ram, AS and Colombet, J and Jacquet, S}, title = {Variations in abundance, genome size, morphology, and functional role of the virioplankton in Lakes Annecy and Bourget over a 1-year period.}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {66-82}, pmid = {24253662}, issn = {1432-184X}, mesh = {Bacteria/virology ; DNA Viruses/genetics/*isolation &amp; purification/ultrastructure ; *Ecosystem ; France ; Fresh Water/*virology ; *Genome Size ; Lakes/*virology ; Microscopy, Electron, Transmission ; Plankton/virology ; Seasons ; }, abstract = {We sampled the surface waters (2-50 m) of two deep peri-alpine lakes over a 1-year period in order to examine (1) the abundance, vertical distribution, genome size, and morphology structures of the virioplankton; (2) the virus-mediated bacterial mortality; and (3) the specific genome size range of double-stranded DNA (dsDNA) phytoplankton viruses. Virus-like particle (VLP) concentrations varied between 4.16 × 10(7) (January) and 2.08 × 10(8) part mL(-1) (May) in Lake Bourget and between 2.7 × 10(7) (June) and 8.39 × 10(7) part mL(-1) (November) in Lake Annecy. Our flow cytometry analysis revealed at least three viral groups (referred to as virus-like particles 1, 2, and 3) that exhibited distinctive dynamics suggestive of different host types. Phage-induced bacterial mortality varied between 6.1% (June) and 33.2% (October) in Lake Bourget and between 7.4% (June) and 52.6% (November) in Lake Annecy, suggesting that viral lysis may be a key cause of mortality of the bacterioplankton. Virioplankton genome size ranged from 27 to 486 kb in Lake Bourget, while it reached 620 kb in Lake Annecy for which larger genome sizes were recorded. Our analysis of pulsed field gel electrophoresis bands using different PCR primers targeting both cyanophages and algal viruses showed that (1) dsDNA viruses infecting phytoplankton may range from 65 to 486 kb, and (2) both cyanophage and algal "diversity" were higher in Lake Annecy. Lakes Annecy and Bourget also differed regarding the proportions of both viral families (with the dominance of myoviruses vs. podoviruses) and infected bacterial morphotypes (short rods vs. elongated rods), in each of these lakes, respectively. Overall, our results reveal that (1) viruses displayed distinct temporal and vertical distribution, dynamics, community structure in terms of genome size and morphology, and viral activity in the two lakes; (2) the Myoviridae seemed to be the main cause of bacterial mortality in both lakes and this group seemed to be related to VLP2; and (3) phytoplankton viruses may have a broader range of genome size than previously thought. This study adds to growing evidence that viruses are diverse and play a significant role in freshwater microbial dynamics and more globally lake functioning. It highlights the importance of further considering this biological compartment for a better understanding of plankton ecology in peri-alpine lakes.}, }
@article {pmid24251832, year = {2014}, author = {Ramond, JB and Welz, PJ and Le Roes-Hill, M and Tuffin, MI and Burton, SG and Cowan, DA}, title = {Selection of Clostridium spp. in biological sand filters neutralizing synthetic acid mine drainage.}, journal = {FEMS microbiology ecology}, volume = {87}, number = {3}, pages = {678-690}, doi = {10.1111/1574-6941.12255}, pmid = {24251832}, issn = {1574-6941}, mesh = {Acids/*metabolism ; Biodegradation, Environmental ; Clostridium/genetics/*isolation &amp; purification ; Ferric Compounds/metabolism ; Ferrous Compounds/metabolism ; Filtration ; Microbial Consortia ; *Mining ; Oxidation-Reduction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Silicon Dioxide ; Sulfates/metabolism ; }, abstract = {In this study, three biological sand filter (BSF) were contaminated with a synthetic iron- [1500 mg L[-1] Fe(II), 500 mg L[-1] Fe(III)] and sulphate-rich (6000 mg L[-1] SO4[2-]) acid mine drainage (AMD) (pH = 2), for 24 days, to assess the remediation capacity and the evolution of autochthonous bacterial communities (monitored by T-RFLP and 16S rRNA gene clone libraries). To stimulate BSF bioremediation involving sulphate-reducing bacteria, a readily degradable carbon source (glucose, 8000 mg L[-1]) was incorporated into the influent AMD. Complete neutralization and average removal efficiencies of 81.5 (±5.6)%, 95.8 (±1.2)% and 32.8 (±14.0)% for Fe(II), Fe(III) and sulphate were observed, respectively. Our results suggest that microbial iron reduction and sulphate reduction associated with iron precipitation were the main processes contributing to AMD neutralization. The effect of AMD on BSF sediment bacterial communities was highly reproducible. There was a decrease in diversity, and notably a single dominant operational taxonomic unit (OTU), closely related to Clostridium beijerinckii, which represented up to 65% of the total community at the end of the study period.}, }
@article {pmid24250784, year = {2013}, author = {Zhang, M and Powell, CA and Benyon, LS and Zhou, H and Duan, Y}, title = {Deciphering the bacterial microbiome of citrus plants in response to 'Candidatus Liberibacter asiaticus'-infection and antibiotic treatments.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e76331}, pmid = {24250784}, issn = {1932-6203}, mesh = {Ampicillin/pharmacology ; Bacteria/classification/*isolation &amp; purification ; Citrus/genetics/*microbiology ; Gentamicins/pharmacology ; Microbiota/genetics ; Plant Diseases/genetics/*microbiology/prevention &amp; control ; Plant Leaves/*microbiology ; }, abstract = {The bacterial microbiomes of citrus plants were characterized in response to 'Candidatus Liberibacter asiaticus' (Las)-infection and treatments with ampicillin (Amp) and gentamicin (Gm) by Phylochip-based metagenomics. The results revealed that 7,407 of over 50,000 known Operational Taxonomic Units (OTUs) in 53 phyla were detected in citrus leaf midribs using the PhyloChip™ G3 array, of which five phyla were dominant, Proteobacteria (38.7%), Firmicutes (29.0%), Actinobacteria (16.1%), Bacteroidetes (6.2%) and Cyanobacteria (2.3%). The OTU62806, representing 'Candidatus Liberibacter', was present with a high titer in the plants graft-inoculated with Las-infected scions treated with Gm at 100 mg/L and in the water-treated control (CK1). However, the Las bacterium was not detected in the plants graft-inoculated with Las-infected scions treated with Amp at 1.0 g/L or in plants graft-inoculated with Las-free scions (CK2). The PhyloChip array demonstrated that more OTUs, at a higher abundance, were detected in the Gm-treated plants than in the other treatment and the controls. Pairwise comparisons indicated that 23 OTUs from the Achromobacter spp. and 12 OTUs from the Methylobacterium spp. were more abundant in CK2 and CK1, respectively. Ten abundant OTUs from the Stenotrophomonas spp. were detected only in the Amp-treatment. These results provide new insights into microbial communities that may be associated with the progression of citrus huanglongbing (HLB) and the potential effects of antibiotics on the disease and microbial ecology.}, }
@article {pmid24246941, year = {2014}, author = {Yang, Y and Wang, Z and Xie, S}, title = {Aerobic biodegradation of bisphenol A in river sediment and associated bacterial community change.}, journal = {The Science of the total environment}, volume = {470-471}, number = {}, pages = {1184-1188}, doi = {10.1016/j.scitotenv.2013.10.102}, pmid = {24246941}, issn = {1879-1026}, mesh = {Aerobiosis ; Bacteria/classification/growth &amp; development ; Benzhydryl Compounds/*analysis/metabolism ; Biodegradation, Environmental ; Geologic Sediments/*chemistry ; Phenols/*analysis/metabolism ; Rivers/chemistry ; *Water Microbiology ; Water Pollutants, Chemical/*analysis/metabolism ; }, abstract = {Bisphenol A (BPA) is one of the commonly detected endocrine-disrupting chemicals in the environment. Biodegradation plays a major role in elimination of BPA pollution in the environment. However, information on the structure of BPA-degrading microbial community is still lacking. In this study, microcosms with different treatments were constructed to investigate the microbial community structure in river sediment and its shift during BPA biodegradation. BPA could be quickly depleted in the BPA-spiked sediment. BPA amendment had a significant impact on sediment bacterial community, influenced by dosage levels. Gammaproteobacteria and Alphaproteobacteria were the predominant bacterial groups in BPA-degrading sediment microcosm. A consortium of microorganisms from different bacterial genera might be involved in BPA biodegradation in river sediment. This study provides some new insights towards BPA biodegradation and microbial ecology in BPA-degrading environment.}, }
@article {pmid24244185, year = {2013}, author = {Meerupati, T and Andersson, KM and Friman, E and Kumar, D and Tunlid, A and Ahrén, D}, title = {Genomic mechanisms accounting for the adaptation to parasitism in nematode-trapping fungi.}, journal = {PLoS genetics}, volume = {9}, number = {11}, pages = {e1003909}, pmid = {24244185}, issn = {1553-7404}, mesh = {Animals ; Ascomycota/genetics/physiology ; *Biological Evolution ; Fungal Proteins/*genetics ; Fungi/*genetics/physiology ; Gene Expression Regulation, Fungal ; *Genome, Fungal ; Genomics ; Nematoda ; Phylogeny ; Point Mutation/genetics ; Sequence Analysis, DNA ; Species Specificity ; Symbiosis/genetics ; }, abstract = {Orbiliomycetes is one of the earliest diverging branches of the filamentous ascomycetes. The class contains nematode-trapping fungi that form unique infection structures, called traps, to capture and kill free-living nematodes. The traps have evolved differently along several lineages and include adhesive traps (knobs, nets or branches) and constricting rings. We show, by genome sequencing of the knob-forming species Monacrosporium haptotylum and comparison with the net-forming species Arthrobotrys oligospora, that two genomic mechanisms are likely to have been important for the adaptation to parasitism in these fungi. Firstly, the expansion of protein domain families and the large number of species-specific genes indicated that gene duplication followed by functional diversification had a major role in the evolution of the nematode-trapping fungi. Gene expression indicated that many of these genes are important for pathogenicity. Secondly, gene expression of orthologs between the two fungi during infection indicated that differential regulation was an important mechanism for the evolution of parasitism in nematode-trapping fungi. Many of the highly expressed and highly upregulated M. haptotylum transcripts during the early stages of nematode infection were species-specific and encoded small secreted proteins (SSPs) that were affected by repeat-induced point mutations (RIP). An active RIP mechanism was revealed by lack of repeats, dinucleotide bias in repeats and genes, low proportion of recent gene duplicates, and reduction of recent gene family expansions. The high expression and rapid divergence of SSPs indicate a striking similarity in the infection mechanisms of nematode-trapping fungi and plant and insect pathogens from the crown groups of the filamentous ascomycetes (Pezizomycotina). The patterns of gene family expansions in the nematode-trapping fungi were more similar to plant pathogens than to insect and animal pathogens. The observation of RIP activity in the Orbiliomycetes suggested that this mechanism was present early in the evolution of the filamentous ascomycetes.}, }
@article {pmid24241584, year = {2014}, author = {Gągała, I and Izydorczyk, K and Jurczak, T and Pawełczyk, J and Dziadek, J and Wojtal-Frankiewicz, A and Jóźwik, A and Jaskulska, A and Mankiewicz-Boczek, J}, title = {Role of environmental factors and toxic genotypes in the regulation of microcystins-producing cyanobacterial blooms.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {465-479}, pmid = {24241584}, issn = {1432-184X}, mesh = {Biomass ; Chemical Phenomena ; DNA, Bacterial/genetics ; Environmental Monitoring ; *Eutrophication ; Fresh Water/microbiology ; *Genotype ; Microcystins/biosynthesis ; Microcystis/*genetics/*isolation &amp; purification ; Poland ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; Temperature ; Water Microbiology ; }, abstract = {The aim of this study was to understand: (1) how environmental conditions can contribute to formation of Microcystis-dominated blooms in lowland, dam reservoirs in temperate climate-with the use of quantitative molecular monitoring, and (2) what is the role of toxic Microcystis genotypes in the bloom functioning. Monitoring of the Sulejow Reservoir in 2009 and 2010 in two sites Tresta (TR) and Bronislawow BR), which have different morphometry, showed that physicochemical conditions were always favorable for cyanobacterial bloom formation. In 2009, the average biomass of cyanobacteria reached 13 mg L(-1) (TR) and 8 mg L(-1) (BR), and in the second year, it decreased to approximately 1 mg L(-1) (TR and BR). In turns, the mean number of toxic Microcystis genotypes in the total Microcystis reached 1% in 2009, both in TR and BR, and in 2010, the number increased to 70% in TR and 14 % in BR. Despite significant differences in the biomass of cyanobacteria in 2009 and 2010, the mean microcystins (MCs) concentration and toxicity stayed at a similar level of approximately 1 μg L(-1). Statistical analysis indicated that water retention time was a factor that provided a significant difference between the two monitoring seasons and was considered a driver of the changes occurring in the Sulejow Reservoir. Hydrologic differences, which occurred between two studied years due to heavy flooding in Poland in 2010, influenced the decrease in number of Microcystis biomass by causing water disturbances and by lowering water temperature. Statistical analysis showed that Microcystis aeruginosa biomass and 16S rRNA gene copy number representing Microcystis genotypes in both years of monitoring could be predicted on the basis of total and dissolved phosphorus concentrations and water temperature. In present study, the number of mcyA gene copies representing toxic Microcystis genotypes could be predicted based on the biomass of M. aeruginosa. Moreover, MCs toxicity and concentration could be predicted on the basic of mcyA gene copy number and M. aeruginosa (biomass, 16S rRNA), respectively. Present findings may indicate that Microcystis can regulate the number of toxic genotypes, and in this way adjust the whole bloom to be able to produce MCs at the level which is necessary for its maintenance in the Sulejow Reservoir under stressful hydrological conditions.}, }
@article {pmid24238386, year = {2013}, author = {Doll, HM and Armitage, DW and Daly, RA and Emerson, JB and Goltsman, DS and Yelton, AP and Kerekes, J and Firestone, MK and Potts, MD}, title = {Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {259}, pmid = {24238386}, issn = {1471-2180}, mesh = {*Biota ; Computational Biology/methods ; Ecology/*methods ; }, abstract = {BACKGROUND: Microbial ecologists often employ methods from classical community ecology to analyze microbial community diversity. However, these methods have limitations because microbial communities differ from macro-organismal communities in key ways. This study sought to quantify microbial diversity using methods that are better suited for data spanning multiple domains of life and dimensions of diversity. Diversity profiles are one novel, promising way to analyze microbial datasets. Diversity profiles encompass many other indices, provide effective numbers of diversity (mathematical generalizations of previous indices that better convey the magnitude of differences in diversity), and can incorporate taxa similarity information. To explore whether these profiles change interpretations of microbial datasets, diversity profiles were calculated for four microbial datasets from different environments spanning all domains of life as well as viruses. Both similarity-based profiles that incorporated phylogenetic relatedness and naïve (not similarity-based) profiles were calculated. Simulated datasets were used to examine the robustness of diversity profiles to varying phylogenetic topology and community composition.<br><br>RESULTS: Diversity profiles provided insights into microbial datasets that were not detectable with classical univariate diversity metrics. For all datasets analyzed, there were key distinctions between calculations that incorporated phylogenetic diversity as a measure of taxa similarity and na&#xef;ve calculations. The profiles also provided information about the effects of rare species on diversity calculations. Additionally, diversity profiles were used to examine thousands of simulated microbial communities, showing that similarity-based and na&#xef;ve diversity profiles only agreed approximately 50% of the time in their classification of which sample was most diverse. This is a strong argument for incorporating similarity information and calculating diversity with a range of emphases on rare and abundant species when quantifying microbial community diversity.<br><br>CONCLUSIONS: For many datasets, diversity profiles provided a different view of microbial community diversity compared to analyses that did not take into account taxa similarity information, effective diversity, or multiple diversity metrics. These findings are a valuable contribution to data analysis methodology in microbial ecology.}, }
@article {pmid24233286, year = {2014}, author = {Kitzing, C and Pröschold, T and Karsten, U}, title = {UV-induced effects on growth, photosynthetic performance and sunscreen contents in different populations of the green alga Klebsormidium fluitans (Streptophyta) from alpine soil crusts.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {327-340}, pmid = {24233286}, issn = {1432-184X}, mesh = {Italy ; Nucleic Acid Conformation ; Photosynthesis/radiation effects ; Soil/*chemistry ; Streptophyta/genetics/*growth &amp; development/*radiation effects ; Sunscreening Agents/pharmacology ; *Ultraviolet Rays ; }, abstract = {Members of the green algal genus Klebsormidium (Klebsormidiales, Streptophyta) are typical components of biological soil crust communities worldwide, which exert important ecological functions. Klebsormidium fluitans (F. Gay) Lokhorst was isolated from an aeroterrestrial biofilm as well as from four different biological soil crusts along an elevational gradient between 600 and 2350 m in the Tyrolean and South Tyrolean Alps (Austria, Italy), which are characterised by seasonally high solar radiation. Since the UVtolerance of Klebsormidium has not been studied in detail, an ecophysiological and biochemical study was applied. The effects of controlled artificial ultraviolet radiation (UVR; <9 W m(-2) UV-A, <0.5 W m(-2) UV-B) on growth, photosynthetic performance and the capability to synthesise mycosporine-like amino acids (MAAs) as potential sunscreen compounds were comparatively investigated to evaluate physiological plasticity and possible ecotypic differentiation within this Klebsormidium species. Already under control conditions, the isolates showed significantly different growth rates ranging from 0.42 to 0.74 μm day(-1). The UVR effects on growth were isolate specific, with only two strains affected by the UV treatments. Although all photosynthetic and respiratory data indicated strain-specific differences under control conditions, UV-A and UV-B treatment led only to rather minor effects. All physiological results clearly point to a high UV tolerance in the K. fluitans strains studied, which can be explained by their biochemical capability to synthesize and accumulate a putative MAA after exposure to UV-A and UV-B. Using HPLC, a UV-absorbing compound with an absorption maximum at 324 nm could be identified in all strains. The steady-state concentrations of this Klebsormidium MAA under control conditions ranged from 0.09 to 0.93 mg g(-1) dry weight (DW). While UV-A led to a slight stimulation of MAA accumulation, exposure to UV-B was accompanied by a strong but strain-specific increase of this compound (5.34-12.02 mg(-1) DW), thus supporting its function as UV sunscreen. Although ecotypic differences in the UVR response patterns of the five K. fluitans strains occurred, this did not correlate with the altitude of the respective sampling location. All data indicate a generally high UV tolerance which surely contributes to the aeroterrestrial lifestyle of K. fluitans in soil crusts of the alpine regions of the European Alps.}, }
@article {pmid24233285, year = {2014}, author = {Brady, CM and Asplen, MK and Desneux, N and Heimpel, GE and Hopper, KR and Linnen, CR and Oliver, KM and Wulff, JA and White, JA}, title = {Worldwide populations of the aphid Aphis craccivora are infected with diverse facultative bacterial symbionts.}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {195-204}, pmid = {24233285}, issn = {1432-184X}, mesh = {Animals ; Aphids/genetics/*microbiology ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Haplotypes ; Medicago sativa ; Mitochondria/genetics ; Molecular Sequence Data ; Robinia ; *Symbiosis ; }, abstract = {Facultative bacterial endosymbionts can play an important role in the evolutionary trajectory of their hosts. Aphids (Hemiptera: Aphididae) are infected with a wide variety of facultative endosymbionts that can confer ecologically relevant traits, which in turn may drive microevolutionary processes in a dynamic selective environment. However, relatively little is known about how symbiont diversity is structured in most aphid species. Here, we investigate facultative symbiont species richness and prevalence among world-wide populations of the cowpea aphid, Aphis craccivora Koch. We surveyed 44 populations of A. craccivora, and detected 11 strains of facultative symbiotic bacteria, representing six genera. There were two significant associations between facultative symbiont and aphid food plant: the symbiont Arsenophonus was found at high prevalence in A. craccivora populations collected from Robinia sp. (locust), whereas the symbiont Hamiltonella was almost exclusively found in A. craccivora populations from Medicago sativa (alfalfa). Aphids collected from these two food plants also had divergent mitochondrial haplotypes, potentially indicating the formation of specialized aphid lineages associated with food plant (host-associated differentiation). The role of facultative symbionts in this process remains to be determined. Overall, observed facultative symbiont prevalence in A. craccivora was lower than that of some other well-studied aphids (e.g., Aphis fabae and Acyrthosiphon pisum), possibly as a consequence of A. craccivora's almost purely parthenogenetic life history. Finally, most (70 %) of the surveyed populations were polymorphic for facultative symbiont infection, indicating that even when symbiont prevalence is relatively low, symbiont-associated phenotypic variation may allow population-level evolutionary responses to local selection.}, }
@article {pmid24231291, year = {2014}, author = {Gong, J and Qing, Y and Guo, X and Warren, A}, title = {"Candidatus Sonnebornia yantaiensis", a member of candidate division OD1, as intracellular bacteria of the ciliated protist Paramecium bursaria (Ciliophora, Oligohymenophorea).}, journal = {Systematic and applied microbiology}, volume = {37}, number = {1}, pages = {35-41}, doi = {10.1016/j.syapm.2013.08.007}, pmid = {24231291}, issn = {1618-0984}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification/ultrastructure ; China ; Cluster Analysis ; Cytoplasm/microbiology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fresh Water ; In Situ Hybridization, Fluorescence ; Microbial Consortia ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Paramecium/*microbiology ; Phylogeny ; Ponds/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {An intracellular bacterium was discovered in an isolate of Paramecium bursaria from a freshwater pond in Yantai, China. The bacteria were abundant and exclusively found in the cytoplasm of the host which, along with the green alga Chlorella, formed a three-partner consortium that could survive in pure water for at least one week. Cloning, sequencing and phylogenetic analysis of the bacterial 16S rRNA gene showed that the bacterium belonged to the uncultured candidate division OD1, which usually forms part of the rare biosphere. Transmission electron microscopy and fluorescence in situ hybridization (FISH) with specific probes showed that the bacteria were usually located close to the perialgal membranes of endosymbiotic Chlorella cells, and occasionally irregularly distributed throughout the host cytoplasm. The name "Candidatus Sonnebornia yantaiensis" gen. nov., sp. nov. is proposed for the new bacterium. A strongly supported monophyletic subclade, OD1-p, which included the new species, was recognized and this study highlights that protists can be important hosts for rare bacterial taxa.}, }
@article {pmid24230469, year = {2014}, author = {De Vuyst, L and Van Kerrebroeck, S and Harth, H and Huys, G and Daniel, HM and Weckx, S}, title = {Microbial ecology of sourdough fermentations: diverse or uniform?.}, journal = {Food microbiology}, volume = {37}, number = {}, pages = {11-29}, doi = {10.1016/j.fm.2013.06.002}, pmid = {24230469}, issn = {1095-9998}, mesh = {Biodiversity ; Bread/analysis/*microbiology ; Ecosystem ; Edible Grain/chemistry/*microbiology ; Fermentation ; Flour/analysis/*microbiology ; Lactobacillus/classification/genetics/isolation &amp; purification/*metabolism ; Yeasts/classification/genetics/isolation &amp; purification/*metabolism ; }, abstract = {Sourdough is a specific and stressful ecosystem inhabited by yeasts and lactic acid bacteria (LAB), mainly heterofermentative lactobacilli. On the basis of their inocula, three types of sourdough fermentation processes can be distinguished, namely backslopped ones, those initiated with starter cultures, and those initiated with a starter culture followed by backslopping. Typical sourdough LAB species are Lactobacillus fermentum, Lactobacillus paralimentarius, Lactobacillus plantarum, and Lactobacillus sanfranciscensis. Typical sourdough yeast species are Candida humilis, Kazachstania exigua, and Saccharomyces cerevisiae. Whereas region specificity is claimed in the case of artisan backslopped sourdoughs, no clear-cut relationship between a typical sourdough and its associated microbiota can be found, as this is dependent on the sampling, isolation, and identification procedures. Both simple and very complex consortia may occur. Moreover, a series of intrinsic and extrinsic factors may influence the composition of the sourdough microbiota. For instance, an influence of the flour (type, quality status, etc.) and the process parameters (temperature, pH, dough yield, backslopping practices, etc.) occurs. In this way, the presence of Lb. sanfranciscensis during sourdough fermentation depends on specific environmental and technological factors. Also, Triticum durum seems to select for obligately heterofermentative LAB species. Finally, there are indications that the sourdough LAB are of intestinal origin.}, }
@article {pmid24229782, year = {2013}, author = {Störmer, R and Wichels, A and Gerdts, G}, title = {Geo-Chip analysis reveals reduced functional diversity of the bacterial community at a dumping site for dredged Elbe sediment.}, journal = {Marine pollution bulletin}, volume = {77}, number = {1-2}, pages = {113-122}, doi = {10.1016/j.marpolbul.2013.10.022}, pmid = {24229782}, issn = {1879-3363}, mesh = {Bacteria/*classification/growth &amp; development ; Ecosystem ; *Environmental Monitoring ; Geologic Sediments/chemistry/*microbiology ; Multivariate Analysis ; Oligonucleotide Array Sequence Analysis ; *Refuse Disposal ; Rivers/chemistry/microbiology ; }, abstract = {The dumping of dredged sediments represents a major stressor for coastal ecosystems. The impact on the ecosystem function is determined by its complexity not easy to assess. In the present study, we evaluated the potential of bacterial community analyses to act as ecological indicators in environmental monitoring programmes. We investigated the functional structure of bacterial communities, applying functional gene arrays (GeoChip4.2). The relationship between functional genes and environmental factors was analysed using distance-based multivariate multiple regression. Apparently, both the function and structure of the bacterial communities are impacted by dumping activities. The bacterial community at the dumping centre displayed a significant reduction of its entire functional diversity compared with that found at a reference site. DDX compounds separated bacterial communities of the dumping site from those of un-impacted sites. Thus, bacterial community analyses show great potential as ecological indicators in environmental monitoring.}, }
@article {pmid24229735, year = {2014}, author = {Richter, JF and Pieper, R and Zakrzewski, SS and Günzel, D and Schulzke, JD and Van Kessel, AG}, title = {Diets high in fermentable protein and fibre alter tight junction protein composition with minor effects on barrier function in piglet colon.}, journal = {The British journal of nutrition}, volume = {111}, number = {6}, pages = {1040-1049}, doi = {10.1017/S0007114513003498}, pmid = {24229735}, issn = {1475-2662}, mesh = {Animals ; Colon/chemistry/*physiology ; Diet/veterinary ; Dietary Fiber/*administration &amp; dosage ; Dietary Proteins/*administration &amp; dosage ; Female ; *Fermentation ; Intestinal Absorption ; Intestinal Mucosa/physiology ; Male ; Sus scrofa/*physiology ; Tight Junction Proteins/*analysis ; }, abstract = {Protein fermentation end products may damage the colonic mucosa, which could be counteracted by dietary inclusion of fermentable carbohydrates (fCHO). Although fermentable crude protein (fCP) and fCHO are known to affect microbial ecology, their interactive effects on epithelial barrier function are unknown. In the present study, in a 2 × 2 factorial experiment, thirty-two weaned piglets were fed low-fCP/low-fCHO (14·5 % crude protein (CP)/14·5 % total dietary fibre (TDF)), low-fCP/high-fCHO (14·8 % CP/16·6 % TDF), high-fCP/low-fCHO (19·8 % CP/14·5 % TDF) and high-fCP/high-fCHO (20·1 % CP/18·0 % TDF) diets. After 21-23 d, samples of proximal and distal colonic mucosae were investigated in Ussing chambers with respect to the paracellular and transcytotic passages of macromolecules and epithelial ion transport. The high-fCHO diets were found to reduce the permeability of the distal colon to the transcytotic marker horseradish peroxidase (HRP, 44 kDa; P <0·05) and also reduce the paracellular permeation of N-hydroxysuccinimide-biotin into the submucosa (443 Da; P <0·05), whereas that of HRP was decreased by the high-fCP diets (P <0·01). Short-circuit current (active ion transport), transepithelial resistance (barrier function) and charge selectivity were largely unaffected in both the segments. However, the high-fCP diets were found to suppress the aldosterone-induced epithelial Na channel activity (P <0·01) irrespective of fCHO inclusion. The high-fCP diets generally reduced the expression of colonic claudin-1, claudin-2 and claudin-3 (P <0·01), while that of claudin-4 was increased by the high-fCHO diets (P <0·01). The high-fCHO diets also altered the ratio between occludin forms (P <0·05) and increased the expression of tricellulin in the proximal colon, which was not observed with high-fCP diets. In conclusion, dietary fCHO and fCP exerted few and largely independent effects on functional measurements, but altered tight junction protein composition in a compensatory way, so that colonic transport and barrier properties were only marginally affected.}, }
@article {pmid24216233, year = {2013}, author = {Wuertz, S and Nielsen, PH}, title = {Editorial: Microbial ecology.}, journal = {Water research}, volume = {47}, number = {19}, pages = {6957}, doi = {10.1016/j.watres.2013.10.039}, pmid = {24216233}, issn = {1879-2448}, mesh = {Arsenic/metabolism ; Bioelectric Energy Sources ; Cyanobacteria ; *Ecology ; Nitrous Oxide ; Sulfates/metabolism ; *Water Microbiology ; }, }
@article {pmid24216229, year = {2013}, author = {Pervin, HM and Dennis, PG and Lim, HJ and Tyson, GW and Batstone, DJ and Bond, PL}, title = {Drivers of microbial community composition in mesophilic and thermophilic temperature-phased anaerobic digestion pre-treatment reactors.}, journal = {Water research}, volume = {47}, number = {19}, pages = {7098-7108}, doi = {10.1016/j.watres.2013.07.053}, pmid = {24216229}, issn = {1879-2448}, mesh = {Anaerobiosis ; Bioreactors/*microbiology ; Gram-Negative Anaerobic Bacteria/genetics ; Gram-Positive Endospore-Forming Rods/genetics ; In Situ Hybridization, Fluorescence ; Microbial Consortia/genetics/*physiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S ; Sewage/microbiology ; Temperature ; Time Factors ; Waste Disposal, Fluid/instrumentation/*methods ; }, abstract = {Temperature-phased anaerobic digestion (TPAD) is an emerging technology that facilitates improved performance and pathogen destruction in anaerobic sewage sludge digestion by optimising conditions for 1) hydrolytic and acidogenic organisms in a first-stage/pre-treatment reactor and then 2) methogenic populations in a second stage reactor. Pre-treatment reactors are typically operated at 55-65 °C and as such select for thermophilic bacterial communities. However, details of key microbial populations in hydrolytic communities and links to functionality are very limited. In this study, experimental thermophilic pre-treatment (TP) and control mesophilic pre-treatment (MP) reactors were operated as first-stages of TPAD systems treating activated sludge for 340 days. The TP system was operated sequentially at 50, 60 and 65 °C, while the MP rector was held at 35 °C for the entire period. The composition of microbial communities associated with the MP and TP pre-treatment reactors was characterised weekly using terminal-restriction fragment length polymorphism (T-RFLP) supported by clone library sequencing of 16S rRNA gene amplicons. The outcomes of this approach were confirmed using 454 pyrosequencing of gene amplicons and fluorescence in-situ hybridisation (FISH). TP associated bacterial communities were dominated by populations affiliated to the Firmicutes, Thermotogae, Proteobacteria and Chloroflexi. In particular there was a progression from Thermotogae to Lutispora and Coprothermobacter and diversity decreased as temperature and hydrolysis performance increased. While change in the composition of TP associated bacterial communities was attributable to temperature, that of MP associated bacterial communities was related to the composition of the incoming feed. This study determined processes driving the dynamics of key microbial populations that are correlated with an enhanced hydrolytic functionality of the TPAD system.}, }
@article {pmid24210739, year = {2014}, author = {Subtil, A and Collingro, A and Horn, M}, title = {Tracing the primordial Chlamydiae: extinct parasites of plants?.}, journal = {Trends in plant science}, volume = {19}, number = {1}, pages = {36-43}, doi = {10.1016/j.tplants.2013.10.005}, pmid = {24210739}, issn = {1878-4372}, support = {281633/ERC_/European Research Council/International ; }, mesh = {Adaptation, Physiological ; Biological Evolution ; Chlamydia/genetics/metabolism/*physiology ; Host Specificity ; Plants/*microbiology ; Plastids ; Symbiosis ; }, abstract = {Chlamydiae are obligate intracellular bacteria found as symbionts and pathogens in a wide range of eukaryotes, including protists, invertebrates, and vertebrates. It was recently proposed that an ancient chlamydial symbiont facilitated the establishment of primary plastids in a tripartite symbiosis with cyanobacteria and early eukaryotes. In this review, we summarize recent advances in understanding of the lifestyle and the evolutionary history of extant Chlamydiae. We reconstruct and describe key features of the ancient chlamydial symbiont. We propose that it was already adapted to an intracellular lifestyle before the emergence of Archaeplastida, and that several observations are compatible with an essential contribution of Chlamydiae to the evolution of algae and plants.}, }
@article {pmid24210153, year = {2014}, author = {Avrillon, V and Ny, C and Chan, S and Souquet, PJ and Couraud, S}, title = {[First epidemiologic data on pneumonia in Cambodia].}, journal = {Revue de pneumologie clinique}, volume = {70}, number = {3}, pages = {133-141}, doi = {10.1016/j.pneumo.2013.09.003}, pmid = {24210153}, issn = {1776-2561}, mesh = {Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/therapeutic use ; Cambodia/epidemiology ; Cough/etiology ; Drug Resistance, Multiple, Bacterial ; Dyspnea/etiology ; Female ; Hemoptysis/etiology ; Humans ; Male ; Middle Aged ; Pneumonia, Bacterial/drug therapy/*epidemiology/microbiology ; Retrospective Studies ; Young Adult ; }, abstract = {About 15% of deaths in adults are related to lung infections in Cambodia. Some knowledge on microbial epidemiology is crucial for deciding first-line antibiotic treatment. However, to date, these data are not available in Cambodia. Consequently, antibiotic prescription relies on French or neighborhood's countries guidelines, which are possibly not suitable. This cases-series aimed to provide data on microbial ecology in pneumonia. Medical charts of patients newly admitted for lung infection in the pulmonology unit of Preah Kossamak Hospital were retrospectively reviewed. Ninety-four patients were included and 29% had a complete microbiological diagnosis. Main germs isolated were: Gram-negative bacilli (n=20; 70.4%) and M. tuberculosis infections (n=7; 25.9%). There was one case of myeloïdosis. No S. pneumonia was isolated, possibly due to sample shipping tropical conditions. Antibiograms showed high resistance profiles. Although this study bring new data in the field, it also showed that European guidelines for antibiotic are not relevant in such countries and stress the need for further dedicated and prospective studies.}, }
@article {pmid24201892, year = {2014}, author = {Arends, JB and Speeckaert, J and Blondeel, E and De Vrieze, J and Boeckx, P and Verstraete, W and Rabaey, K and Boon, N}, title = {Greenhouse gas emissions from rice microcosms amended with a plant microbial fuel cell.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {7}, pages = {3205-3217}, doi = {10.1007/s00253-013-5328-5}, pmid = {24201892}, issn = {1432-0614}, mesh = {Archaea/*growth &amp; development/metabolism ; Bacteria/*growth &amp; development/metabolism ; *Bioelectric Energy Sources ; Carbon/metabolism ; Electricity ; Electrodes/microbiology ; *Greenhouse Effect ; Methane/*metabolism ; Oryza/*microbiology ; Rhizosphere ; }, abstract = {Methane (CH4) release from wetlands is an important source of greenhouse gas emissions. Gas exchange occurs mainly through the aerenchyma of plants, and production of greenhouse gases is heavily dependent on rhizosphere biogeochemical conditions (i.e. substrate availability and redox potential). It is hypothesized that by introducing a biocatalyzed anode electrode in the rhizosphere of wetland plants, a competition for carbon and electrons can be invoked between electrical current-generating bacteria and methanogenic Archaea. The anode electrode is part of a bioelectrochemical system (BES) capable of harvesting electrical current from microbial metabolism. In this work, the anode of a BES was introduced in the rhizosphere of rice plants (Oryza sativa), and the impact on methane emissions was monitored. Microbial current generation was able to outcompete methanogenic processes when the bulk matrix contained low concentrations of organic carbon, provided that the electrical circuit with the effective electroactive microorganisms was in place. When interrupting the electrical circuit or supplying an excess of organic carbon, methanogenic metabolism was able to outcompete current generating metabolism. The qPCR results showed hydrogenotrophic methanogens were the most abundant methanogenic group present, while mixotrophic or acetoclastic methanogens were hardly detected in the bulk rhizosphere or on the electrodes. Competition for electron donor and acceptor were likely the main drivers to lower methane emissions. Overall, electrical current generation with BESs is an interesting option to control CH4 emissions from wetlands but needs to be applied in combination with other mitigation strategies to be successful and feasible in practice.}, }
@article {pmid24194099, year = {2014}, author = {Kalia, VC and Wood, TK and Kumar, P}, title = {Evolution of resistance to quorum-sensing inhibitors.}, journal = {Microbial ecology}, volume = {68}, number = {1}, pages = {13-23}, pmid = {24194099}, issn = {1432-184X}, support = {R01 GM089999/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/genetics ; Drug Resistance, Bacterial/*genetics ; *Evolution, Molecular ; Pseudomonas aeruginosa/drug effects/genetics ; Quorum Sensing/*drug effects/genetics ; Virulence ; }, abstract = {The major cause of mortality and morbidity in human beings is bacterial infection. Bacteria have developed resistance to most of the antibiotics primarily due to large-scale and "indiscriminate" usage. The need is to develop novel mechanisms to treat bacterial infections. The expression of pathogenicity during bacterial infections is mediated by a cell density-dependent phenomenon known as quorum sensing (QS). A wide array of QS systems (QSS) is operative in expressing the virulent behavior of bacterial pathogens. Each QSS may be mediated largely by a few major signals along with others produced in minuscule quantities. Efforts to target signal molecules and their receptors have proved effective in alleviating the virulent behavior of such pathogenic bacteria. These QS inhibitors (QSIs) have been reported to be effective in influencing the pathogenicity without affecting bacterial growth. However, evidence is accumulating that bacteria may develop resistance to QSIs. The big question is whether QSIs will meet the same fate as antibiotics.}, }
@article {pmid24194098, year = {2014}, author = {Stabili, L and Giangrande, A and Pizzolante, G and Caruso, G and Alifano, P}, title = {Characterization of vibrios diversity in the mucus of the polychaete Myxicola infundibulum (Annellida, Polichaeta).}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {186-194}, pmid = {24194098}, issn = {1432-184X}, mesh = {Animals ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Italy ; Mediterranean Sea ; Mucus/microbiology ; *Phylogeny ; Polychaeta/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vibrio/*classification/genetics/isolation &amp; purification ; }, abstract = {Vibrios are among the most abundant culturable microbes in aquatic environments. They can be either free-living in the water column or associated with several marine organisms as mutualists, saprophytes, or parasites. In the present study we analysed vibrios abundance and diversity in the mucus of the polychaete Myxicola infundibulum, complementing culture-based with molecular methods. Vibrios reached 4.6 × 10(3) CFU mL(-1) thus representing a conspicuous component of the heterotrophic culturable bacteria. In addition, luminous vibrios accounted for about 60% of the total culturable vibrios in the mucus. The isolates were assigned to: Vibrio gigantis, Vibrio fischeri, Vibrio jasicida, Vibrio crassostreae, Vibrio kanaloae, and Vibrio xuii. Two Vibrio isolates (MI-13 and MI-15) may belong to a new species. We also tested the ability of the Vibrio isolates to grow on M. infundibulum mucus as the sole carbon source. All strains showed appreciable growth in the presence of mucus, leading us to conclude that this matrix, which is abundant and covers the animal entirely, may represent a microcosm and a food source for some bacteria, playing a crucial role in the structuring of a mucus-associated beneficial microbial community. Moreover, the trophic relationship between vibrios and M. infundibulum mucus could be enhanced by the protection that mucus offers to vibrios. The results of this study represent a contribution to the growing evidence for complex and dynamic invertebrate-microbe associations present in nature and highlight the importance of exploring relationships that Vibrio species establish with marine invertebrates.}, }
@article {pmid24194097, year = {2014}, author = {Reardon, CL and Magnuson, TS and Boyd, ES and Leavitt, WD and Reed, DW and Geesey, GG}, title = {Hydrogenase activity of mineral-associated and suspended populations of Desulfovibrio desulfuricans Essex 6.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {318-326}, pmid = {24194097}, issn = {1432-184X}, mesh = {Biofilms ; DNA, Bacterial/genetics ; Desulfovibrio desulfuricans/*enzymology/isolation &amp; purification ; Ferric Compounds/*chemistry ; Hydrogen/chemistry ; Hydrogenase/genetics/*metabolism ; Iron/chemistry ; Minerals/chemistry ; Oxidation-Reduction ; Sequence Analysis, DNA ; Sulfates/chemistry ; }, abstract = {The interactions between sulfate-reducing microorganisms and iron oxides influence a number of important redox-sensitive biogeochemical processes including the formation of iron sulfides. Enzymes, such as hydrogenase which catalyze the reversible oxidation of molecular hydrogen, are known to mediate electron transfer to metals and may contribute to the formation and speciation of ferrous sulfides formed at the cell-mineral interface. In the present study, we compared the whole cell hydrogenase activity of Desulfovibrio desulfuricans strain Essex 6 growing as biofilms on hematite (hematite-associated) or as suspended populations using different metabolic pathways. Hematite-associated cells exhibited significantly greater hydrogenase activity than suspended populations during sulfate respiration but not during pyruvate fermentation. The enhanced activity of the hematite-associated, sulfate-grown cells appears to be dependent on iron availability rather than a general response to surface attachment since the activity of glass-associated cells did not differ from that of suspended populations. Hydrogenase activity of pyruvate-fermenting cells was stimulated by addition of iron as soluble Fe(II)Cl2 and, in the absence of added iron, both sulfate-reducing and pyruvate-fermenting cells displayed similar rates of hydrogenase activity. These data suggest that iron exerts a stronger influence on whole cell hydrogenase activity than either metabolic pathway or mode of growth. The location of hydrogenase to the cell envelope and the enhanced activity at the hematite surface in sulfate-reducing cells may influence the redox conditions that control the species of iron sulfides on the mineral surface.}, }
@article {pmid24704840, year = {2011}, author = {De Jesús-Laboy, KM and Godoy-Vitorino, F and Piceno, YM and Tom, LM and Pantoja-Feliciano, IG and Rivera-Rivera, MJ and Andersen, GL and Domínguez-Bello, MG}, title = {Comparison of the fecal microbiota in feral and domestic goats.}, journal = {Genes}, volume = {3}, number = {1}, pages = {1-18}, pmid = {24704840}, issn = {2073-4425}, abstract = {Animals have co-evolved with mutualistic microbial communities, known as the microbiota, which are essential for organ development and function. We hypothesize that modern animal husbandry practices exert an impact on the intestinal microbiota. In this study, we compared the structure of the fecal microbiota between feral and domestic goats using the G2 PhyloChip and assessed the presence of five tetracycline resistance genes [tet(M), tet(S), tet(O), tet(Q) and tet(W)] by PCR. Feces were collected from 10 goats: 5 domestic from a farm in the main island of Puerto Rico and 5 feral from the remote dry island of Mona. There were 42 bacterial phyla from 153 families detected in the goats' feces. A total of 84 PhyloChip-OTUs were different in the fecal microbiota of feral and domestic goat. Both feral and domestic goats carried antibiotic resistance genes tet(O) and tet(W), but domestic goats additionally carried tet(Q). Diet, host genetics and antibiotic exposure are likely determinant factors in shaping the intestinal microbiota and may explain the differences observed between feral and domestic goats fecal microbiota.}, }
@article {pmid24193496, year = {1996}, author = {Nollet, L and Verstraete, W}, title = {Gastro-enteric methane versus sulphate and volatile fatty acid production.}, journal = {Environmental monitoring and assessment}, volume = {42}, number = {1-2}, pages = {113-131}, pmid = {24193496}, issn = {0167-6369}, abstract = {The breakdown of low digestible components present in food during passage through the human and animal gastro-intestinal (GI) tract is performed by the highly diverse microbial community present in this ecosystem. Fermentation of these substances yields, besides CO2 and volatile fatty acids, H2, which is used as a substrate by three different H2-consuming bacteria. Sulphate-reducing bacteria (SRB) use H2 to reduce SO inf4 (sup2-) to H2S, hydrogenotrophic methane-producing bacteria (MPB) use H2 to reduce CO2 to CH4 and reductive acetogens (RAC) use H2 to reduce CO2 to CH3COOH. A competition between these three bacterial groups exists for the common H2 substrate. This results generally in the dominance of one group above the other two.}, }
@article {pmid24415089, year = {1996}, author = {Parada, JL and Zapata, E and de Fabrizio, SV and Martínez, A}, title = {Microbiological and technological aspects of cassava-starch fermentation.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {12}, number = {1}, pages = {53-56}, pmid = {24415089}, issn = {0959-3993}, abstract = {The major genera found in the microflora of fermented, sour, cassava-starch were Streptococcus, Bacillus, Lactobacillus and Saccharomyces with amylase activity. Lactic acid bacteria predominated whereas the presence of moulds was not significant. No coliforms were detected. Electron microscopy showed bacteria and yeasts in contact with the starch granules and signs of erosion on the granule surface. Lactic acid was the main metabolite; no oligosaccharides, maltose or glucose were detected, indicating their rapid utilization. The degree of acidification, which correlated with the decrease in viscosity and the final quality of the product, was influenced by the variable microbial ecology.}, }
@article {pmid24414908, year = {1995}, author = {Arif, MA and Verstraete, W}, title = {Methane dosage to soil and its effect on plant growth.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {11}, number = {5}, pages = {529-535}, pmid = {24414908}, issn = {0959-3993}, abstract = {Two protocols for following soil methane enrichment were used, one with methane dosed as a carbon source ([C]-soil) and one with methane plus minerals ([C+M]-soil). Methane oxidation occurred much faster in soil receiving minerals in addition to methane than in the control soil receiving only methane. In both treatments, only a small fraction of methane (2% to 14%) was converted into microbial biomass C. Nevertheless, a strong increase in soil microbial biomass (up to 1.5 to 2.0-fold) was achieved in the [C+M]-soil in a 3-week period. Due to methane application, the NO3 (-) content of the soil was significantly decreased, by 83% to 90% in the [C]-soil and by 56% to 83% in the [C+M]-soil. Soil enzymatic activities were slightly increased in the [C+M]-soil only. The soil-methane incubation did not alter the composition of the monitored microbial populations in the soil or in rhizosphere of plants. In the [C]-soil, methane incubation resulted in reduction of the shoot dry wt of maize by 8% to 12%. In the [C+M]-soil under non-limiting mineral-nutrient status, a significant increase in shoot dry wt was observed for maize (13%), a neutral effect was registered for spinach and a negative effect was observed for wheat.}, }
@article {pmid24425665, year = {1992}, author = {Kjøller, A}, title = {A view on microbial ecology.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {8 Suppl 1}, number = {}, pages = {117-119}, doi = {10.1007/BF02421512}, pmid = {24425665}, issn = {0959-3993}, abstract = {In the research areas referred to above the Department of General Microbiology in Copenhagen is involved directly or indirectly. Microbial ecology in Denmark is wider in its scope and other departments or groups are active in different research areas.Marine and limnic sediments have been studied with great success in the Department of Ecology and Genetics in Aarhus, and in recent years several microelectrodes for detailed studies of microbial processes have been developed.A new research group on rhizosphere studies has been established at the Agricultural University, Section for Microbiology. New detection systems are being developed for study of specific bacterial strains (Pseudomonas spp) and their functional role.All of these research areas are simultaneously being studied all over the world and often in cooperation between different research groups. Some of the important global themes are connected with: the microbial response to climate change; the production of toxins in food for man and animals; the dispersal, growth and survival of pathogenic organisms in the environment; the microorganisms in pollution control and bioremidiation; and microbiological control with pathogenic organisms.With the introduction of molecular methods in microbial ecology it seems as if a series of ecological themes will be addressed with appropriate methods. The stability of strains and of populations will be examined, the exchange of genetic material, the adaptation to changing environmental conditions will find new microbial ecology and also of interest for the use of microorganisms by society is expected. *** DIRECT SUPPORT *** AAK17001 00013.}, }
@article {pmid24193210, year = {1992}, author = {Polz, MF and Felbeck, H and Novak, R and Nebelsick, M and Ott, JA}, title = {Chemoautotrophic, sulfur-oxidizing symbiotic bacteria on marine nematodes: Morphological and biochemical characterization.}, journal = {Microbial ecology}, volume = {24}, number = {3}, pages = {313-329}, pmid = {24193210}, issn = {0095-3628}, abstract = {The marine, free-living Stilbonematinae (Nematoda: Desmodorida) inhabit the oxygen sulfide chemocline in marine sands. They are characterized by an association with ectosymbiotic bacteria. According to their ultrastructure the bacteria are Gram-negative and form morphologically uniform coats that cover the entire body surface of the worms. They are arranged in host-genus or host-species specific patterns: cocci form multilayered sheaths, rods, and crescent- or filament-shaped bacteria form monolayers. The detection of enzymes associated with sulfur metabolism and of ribulose-1,5 bisphosphate carboxylase oxygenase, as well as elemental sulfur in the bacteria indicate a chemolithoautotrophic nature of the symbionts. Their reproductive patterns appear to optimize space utilization on the host surface: vertically standing rods divide by longitudinal fission, whereas other bacteria form non-septate filaments of up to 100 μm length.}, }
@article {pmid24193209, year = {1992}, author = {Völksch, B and Ullrich, M and Fritsche, W}, title = {Identification and population dynamics of bacteria in leaf spots of soybean.}, journal = {Microbial ecology}, volume = {24}, number = {3}, pages = {305-311}, pmid = {24193209}, issn = {0095-3628}, abstract = {The qualitative and quantitative composition of bacterial flora occurring inside the leaf spots of field grown soybeans was studied during the growing seasons (June to October) of 1989 and 1990. As a rule these leaf spots (necrotic lesions with chlorotic haloes) were caused by Pseudomonas syringae pv. glycinea. This pathogenic bacterium was predominantly found during the whole season in the symptomatic leaf tissue. Other species, mainly Erwinia herbicola, were also found in the same habitat. The population sizes of P. s. pv. glycinea increased from the beginning of symptom occurrence until July, stabilized until September, and then decreased a little. In general, the size of saprophytic populations was orders of magnitude lower than that of the pathogenic populations. The number of different bacterial genera per sample increased up to four genera per leaf spot by the end of the season. No significant influence of the occurring saprophytes on the population dynamics of the pathogen in planta could be observed.}, }
@article {pmid24193208, year = {1992}, author = {Kandel, A and Nybroe, O and Rasmussen, OF}, title = {Survival of 2,4-dichlorophenoxyacetic acid degrading Alcaligenes eutrophus AE0106(pR0101) in lake water microcosms.}, journal = {Microbial ecology}, volume = {24}, number = {3}, pages = {291-303}, pmid = {24193208}, issn = {0095-3628}, abstract = {Survival of the 2,4-dichlorophenoxyacetic acid (2,4-D) degrading Alcaligenes eutrophus strain AEO 106 harboring the catabolic plasmid pRO101 was studied in lake water from the eutrophic lake Frederiksborg Slotssø. Survival experiments were performed for periods of 7 days in laboratory microcosms containing filtered (0.2-µm pore size) or natural lake water amended with increasing concentrations of 2,4-D. A. eutrophus AE0106 was detected by combining the fluorescent antibody method with selective and nonselective plating followed by colony blotting and colony hybridization. Comparison of colony blotting and colony hybridization demonstrated that the A. eutrophus AE0106 host organism and the catabolic plasmid pRO101 had similar fates in the model system employed. In all experiments culturable counts of A. eutrophus AE0106 were lower than fluorescent antibody counts and frequently a decline in culturable counts occurred at times when the fluorescent antibody method showed an increasing population size. Amendment with 2,4-D increased survival of A. eutrophus AE0106 both in filtered and in natural lake water. Survival was always poorer in model systems with natural water than in 0.2 µm-filtered water.}, }
@article {pmid24193207, year = {1992}, author = {Liessens, J and Vanbrabant, J and De Vos, P and Kersters, K and Verstraete, W}, title = {Mixed culture hydrogenotrophic nitrate reduction in drinking water.}, journal = {Microbial ecology}, volume = {24}, number = {3}, pages = {271-290}, pmid = {24193207}, issn = {0095-3628}, abstract = {Isolation and identification of the bacteria from a hydrogenotrophic reactor for the denitrification of drinking water revealed that several microorganisms are involved. Acinetobacter sp., Aeromonas sp., Pseudomonas sp. and Shewanella putrefaciens were repeatedly isolated from the hydrogenotrophic sludge and postulated to be of primary importance in the process. Nitrate reduction to nitrite appears to be a property of a diverse group of organisms. Nitrite reduction was found to be stimulated by the presence of organic growth factors. Thus, in a mixed culture, hydrogenotrophic denitrification reactor, NO inf2 (sup-) formed by NO inf3 (sup-) -reducers can be converted by true denitrifiers thriving on organic growth factors either present in the raw water, or excreted by the microbial community. Mixotrophic growth also contributes to NO inf2 (sup-) reduction. Finally, chemolithotrophic bacteria participate in the nitrite to nitrogen gas conversion.}, }
@article {pmid24193206, year = {1992}, author = {Sinke, AJ and Cottaar, FH and Buis, K and Keizer, P}, title = {Methane oxidation by methanotrophs and its effects on the phosphate flux over the sediment-water interface in a eutrophic lake.}, journal = {Microbial ecology}, volume = {24}, number = {3}, pages = {259-269}, pmid = {24193206}, issn = {0095-3628}, abstract = {The effect of methane oxidation in aerobic sediment on oxygen consumption and phosphate flux was investigated in diffusion chambers. The diffusion chambers consisted of two compartments separated by a Teflon membrane. In the upper chamber a thin sediment layer was present and the lower chamber was continuously flushed with gas. The hydrophobic membrane allowed for diffusion of gases from the lower chamber through the sediment layer toward the headspace of the upper chamber. In experiments with a methane oxidation rate of 9.8 mmol m(-2) day(-1), the oxygen consumption rate increased by a factor of two compared with controls without methane oxidation (8.6 vs 17.7 mmol m(-2) day(-1)). Methane oxidation significantly decreased oxygen penetration depth (2.5-4.0 vs 1.0-2.0 mm). However, despite the shrinkage of the oxidized microlayer, no differences were found in phosphate flux across the sediment water interface. Batch experiments with standard additions of methane revealed that the growth of methanotrophic bacteria contributes to the phosphate uptake of aerobic sediment. From the batch experiments a molar ratio of carbon to phosphate of 45 mol:mol was calculated for the growth of methanotrophs. Results suggest that a decrease in chemical phosphate adsorption caused by a decrease in the oxygen penetration depth could be compensated for entirely by the growth of methanotrophic bacteria.}, }
@article {pmid24193205, year = {1992}, author = {Karner, M and Fuks, D and Herndl, GJ}, title = {Bacterial activity along a trophic gradient.}, journal = {Microbial ecology}, volume = {24}, number = {3}, pages = {243-257}, pmid = {24193205}, issn = {0095-3628}, abstract = {Bacterial biomass, secondary production, and extracellular enzymatic activity [α-glucosidase and leucine-aminopeptidase, measured as cleavage of artificial fluorogenic substrates 4-methyl umbelliferyl (MVF) α-D-glucopyranoside and L-leucine 7-amido-4-methyl coumarin (MCA)] were measured along a trophic gradient in the Northern Adriatic Sea in four ecologically different situations. Bacterial parameters were compared with chlorophyll a and inorganic and organic nutrient concentrations. Bacterial secondary production and extracellular enzymatic activity markedly changed among different seasons and along the trophic gradient. Average bacterial secondary production increased from 0.61 to 2.09 µg Cl(-1) hour(-1) preceding a bloom, to 2.09 µg Cl(-1) hour(-1) during the bloom, decreasing again to 0.81 and 0.83 µg Cl(-1) hour(-1) in the post-bloom and summer periods, respectively (values from 0.5 m depth). Leucine-aminopeptidase activity showed more consistent trends than α-glucosidase activity. Average values of leucine-aminopeptidase activity, measured by enzymatic release of MCA, increased from a pre-bloom value of 164.0 to 1,712.0 (nM MCA) hour(-1) released during a bloom, decreasing to 298.5 and 133.7 (nM MCA) hour(-1) released for the post-bloom and summer situation, respectively (values from 0.5 m depth). Average growth rates decreased during the bloom, whereas average extracellular enzymatic activity levels expressed on a cell basis increased by an average factor of 2. Along the trophic gradient, a consistent increase in bacterial secondary production could be observed in all but the summer situation (values from 0.5 m depth). Leucine-aminopeptidase activity also showed positive trends along the gradient, while α-glucosidase activity did not exhibit such a clear trend. Bacterial biomass trends were less obvious considering both seasonal changes and the tropic gradient. Highly significant interrelations were detected between bacterial proteolytic activity, secondary production, chlorophyll a content, and nitrate concentrations, especially in the surface horizon.}, }
@article {pmid24193204, year = {1992}, author = {Kinkel, LL and Nordheim, EV and Andrews, JH}, title = {Microbial community analysis in incompletely or destructively sampled systems.}, journal = {Microbial ecology}, volume = {24}, number = {3}, pages = {227-242}, pmid = {24193204}, issn = {0095-3628}, abstract = {Analyses of microbial community dynamics are often constrained by the destructive, indirect, and incomplete nature of most sampling techniques. These methodological constraints compel assumptions that are rarely verified about the relationships among separate communities. We evaluated the consequences for community analysis of the common assumption that separate microbial communities are described by the same species abundance distribution. Sample data were generated from simulated communities in which the species abundance distributions were the same or were different. Samples from communities that had the same number of species or were described by the same species abundance distribution sometimes had significantly different numbers of species. Samples from simulated communities that had different species number-species abundance distribution combinations sometimes contained indistinguishable numbers of species. When sampling from independent communities described by unknown distributions (e.g., microbial communities on plant surfaces), the simulations showed that standardization of sample size (number of individuals or colony-forming units) does not guarantee samples of equal proportions of the total species in a community. Sample sizes that are logistically feasible for many microbial systems will provide only limited information for differentiating species numbers or species abundance distributions among separate communities over time. For ecologists studying destructively or incompletely sampled communities this seriously influences both the sample designs that are reasonable and the questions that can be addressed in such systems.}, }
@article {pmid24193138, year = {1992}, author = {Cahill, MM and Macrae, IC}, title = {Characteristics of 0/129-sensitive motile Aeromonas strains isolated from freshwater on starch-ampicillin agar.}, journal = {Microbial ecology}, volume = {24}, number = {2}, pages = {215-226}, pmid = {24193138}, issn = {0095-3628}, abstract = {Motile Aeromonas hydrophila strains were recovered from several freshwater sources by spread-plating water samples on starch-ampicillin agar, originally described as a medium for recovering Aeromonas hydrophila quantitatively from foods. Starch-ampicillin agar was compared with membrane Aeromonas medium and Rimler-Shotts medium for selectivity for, and recovery of, Aeromonas strains from freshwater. Thirty-four Aeromonas strains thus isolated were identified to species level by their phenotypic characteristics, and the Mol% G+C of representative strains was determined. Although resistant to 10 μg of the vibriostatic agent 0/129, all these strains showed sensitivity to 150 μg 0/129, which brings into question the use of this agent for distinguishing aeromonads from vibrios. The ability of these strains to produce extracellular virulence factors was generally similar to that reported for environmental strains isolated by other methods from various geographical locations within and beyond Australia. Ten of the 20 A. sobria strains, but none of the A. hydrophila or A. caviae strains, produced enterotoxin as shown by the suckling mouse test. Haemolysin was produced by 9/10 of the enterotoxigenic A. sobria strains and 2/9 A. hydrophila strains. Hemagglutinating activity was detected in 5/20 A. sobria and 7/9 A. hydrophila strains, and was inhibited by fucose and mannose, but not by galactose. The characteristics of these strains were comparable with those of Aeromonas strains isolated from other freshwater environments apart from their sensitivity to 0/129.}, }
@article {pmid24193137, year = {1992}, author = {Madsen, EL and Winding, A and Malachowsky, K and Thomas, CT and Ghiorse, WC}, title = {Contrasts between subsurface microbial communities and their metabolic adaptation to polycyclic aromatic hydrocarbons at a forested and an urban coal-tar disposal site.}, journal = {Microbial ecology}, volume = {24}, number = {2}, pages = {199-213}, pmid = {24193137}, issn = {0095-3628}, abstract = {The abundance and distribution of microorganisms and their potential for mineralizing polycyclic aromatic hydrocarbons (PAHs) were measured in subsurface sediment samples at two geographically separate buried coal-tar sites. At a relatively undisturbed forested site in the northeastern United States, metabolic adaptation to the PAHs was evident: Radiolabeled naphthalene and phenanthrene were converted to (14)CO2 in core material from inside but not outside a plume of groundwater contamination. However, at the urban site in the midwestern United States these PAHs were mineralized in sediments from both contaminated and uncontaminated boreholes. Thus, clear qualitative evidence showing an adaptational response by the subsurface microbial community was not obtained at the urban site. Instead, subtler clues suggesting metabolic adaptation by subsurface microorganisms from the urban site were discerned by comparing lag periods and extents of (14)CO2 production from radiolabeled PAHs added to samples from contaminated and uncontaminated boreholes. Despite slightly higher PAH mineralization activity in contaminated borehole samples, p-hydroxybenzoate was mineralized equally in all samples from the urban site regardless of location. No striking trends in the abundances of actinomycetes, fungi, and either viable or total bacteria were encountered. However, colonies of the soil bacterium, Bacillus mycoides, were detected on enumeration plates of several samples from unsaturated and saturated zones in both urban boreholes. Furthermore, other common soil bacteria, Myxococcus xanthus and Chromobacterium violaceum, were identified in samples from the uncontaminated urban borehole. The occurrence of bacteria usually restricted to surface soil, combined with the observation of fragments of building materials in many of the core samples, suggested that past excavation and backfilling operations may have caused mixing of surface soil with subsurface materials at the urban site. We speculate that this mixing, as well as non-coal-tar-derived sources of PAHs, contributed to the PAH-mineralizing activity present in the sediment samples from the uncontaminated urban borehole.}, }
@article {pmid24193136, year = {1992}, author = {Corpe, WA and Jensen, TE}, title = {An electron microscopic study of picoplanktonic organisms from a Small Lake.}, journal = {Microbial ecology}, volume = {24}, number = {2}, pages = {181-197}, pmid = {24193136}, issn = {0095-3628}, abstract = {Picoplankton, both prokaryotic and eukaryotic, are distinguished from other aquatic organisms by their small size (0.1-2.0 μm). Such organisms were recovered from waters of a small oligotrophic lake using screens, filters, and high-speed centrifugation. The majority of the picoplankton were unable to form visible colonies on common media. Cells examined in thin sections by electron microscopy showed that 60-75% of the cells had an average diameter after dehydration of 0.48-0.51 μm. The maximum dimensions of the rest of the cells ranged from 0.56-1.81 μm. Using details of ultrastructure, cells were classified as prokaryotic or eukaryotic. Phototrophs present included two cyanobacterial morphotypes (5-6%) and two eukaryotic algae (less than I%). The arrays of intracytoplasmic membranes in 18-20% of the cells were suggestive of methanotrophic rods and chemoautotrophs. Relatively few prosthecate bacteria were observed in the water column samples. The smallest cells (1-2%) contained magnetosomes, the presence of which were confirmed by x-ray spectroscopy. Iron was also detected in the envelopes of some rod shaped cells by the same technique. The study of in situ picoplankton populations using TEM coupled with other techniques may provide better understanding of picoplankton biomass.}, }
@article {pmid24193135, year = {1992}, author = {Gaju, N and Esteve, I and Guerrero, R}, title = {Distribution of predatory bacteria that attack chromatiaceae in a sulfurous lake.}, journal = {Microbial ecology}, volume = {24}, number = {2}, pages = {171-179}, pmid = {24193135}, issn = {0095-3628}, abstract = {Predatory bacteria that attack Chromatiaceae (purple sulfur bacteria) recovered from Lake Cisó (a mostly anaerobic holomictic lake) have been studied over two annual cycles. During the mixing period the lake was completely anaerobic; both predator and prey populations were found along the water column, and even at the surface. Throughout the stratification period maximum Chromatiaceae occurred between a depth of 1 and 3 m depth. The maximum numbers of predators and prey (Chromatiaceae) also occurred in this range.A collapse took place in the lake during the second annual cycle in 1986. It brought about changes in the physicochemical parameters of the lake, thus altering the population dynamics. Nevertheless, during both cycles the number of predatory bacteria was maximum immediately below the depth at which the maximum number of prey bacteria occurred.}, }
@article {pmid24193134, year = {1992}, author = {Moran, MA and Hodson, RE}, title = {Contributions of three subsystems of a freshwater marsh to total bacterial secondary productivity.}, journal = {Microbial ecology}, volume = {24}, number = {2}, pages = {161-170}, pmid = {24193134}, issn = {0095-3628}, abstract = {Rates of bacterial production were measured in the water column, on the surface of plant detritus, and in the surface sediments of a freshwater marsh in the Okefenokee Swamp, Georgia, USA. Bacterioplankton production rates were not correlated with several measures of quantity and quality of dissolved organic matter, including an index of the relative importance of vascular plant derivatives. Bacterioplankton productivity was high (mean: 63 μg C liter(-1) day(-1)) compared with rates reported for other aquatic ecosystems. Somewhat paradoxically, bacterial productivity on plant detritus (mean: 13 μg C g(-1) day(-1)) and sediments (mean: 15 μg C g(-1) day(-1)) was low relative to other locations. On an a real basis, total bacterial productivity in this marsh ecosystem averaged 22 mg C m(-2) day(-1), based on sample dates in May 1990 and February 1991. Marsh sediments supported the bulk of the production, accounting for 46% (May) and 88% (February) of the total. The remainder was contributed approximately equally by bacteria in the water column and on accumulated stores of plant detritus.}, }
@article {pmid24193133, year = {1992}, author = {Kristiansen, K and Nielsen, H and Riemann, B and Fuhrman, JA}, title = {Growth efficiencies of freshwater bacterioplankton.}, journal = {Microbial ecology}, volume = {24}, number = {2}, pages = {145-160}, pmid = {24193133}, issn = {0095-3628}, abstract = {The growth efficiency of freshwater bacteria was examined in continuous cultures. One series of experiments was carried out using generation times from 50 to 200 hours and aged, normal, and enriched media, all of natural origin. Another series of experiments examined the bacterial growth efficiency during the growth season in eutrophic Frederiksborg Slotssø, in relation to changes in the planktonic communities and to factors controlling the bacterial incorporation of (3)H-thymidine. Attachment of bacteria to the inner surfaces of the experimental flasks was examined using various types of bottles, adding glass tubes to the bottles, and measuring (3)H-thymidine incorporation and direct cell counts of attached and free-living bacteria. Attachment of bacteria varied, and in one example up to 36% of the thymidine incorporation was by attached bacteria after 4 days. It was calculated that 36% of attached bacteria caused an underestimation of the growth efficiency of 11%. The mean growth efficiency tended to decrease with generation time using enriched medium (47 to 19%) and aged medium (35 to 12%), and tended to decrease with medium quality (enriched > normal > aged media) from 37% to 27%. The only significant difference in growth efficiency occurred in relation to generation time, in samples with enriched medium (unpaired t-test, P < 0.05). The overall mean value for all generation times and media was 30% (SEM = 3%, n = 24). From April to October, the growth efficiency was determined 5 times in samples from Frederiksborg Slotssø. The overall mean value was 31% (SEM = 3%, n = 30), and there was no significant change in the growth efficiency during the period measured. In June, three bioassay experiments revealed that carbon limitation controlled bacterial incorporation of (3)H-thymidine, whereas additions of phosphate and nitrate did not change the incorporation rates. The narrow range of growth efficiencies obtained in this study (mean 31%, SEM = 2%, n = 54) suggests that changes in substratequality in the media applied and in the eutrophic samples examined causes only subtle changes in the growth efficiency.}, }
@article {pmid24193132, year = {1992}, author = {Ducklow, HW and Kirchman, DL and Quinby, HL}, title = {Bacterioplankton cell growth and macromolecular synthesis in seawater cultures during the North Atlantic Spring Phytoplankton Bloom, May, 1989.}, journal = {Microbial ecology}, volume = {24}, number = {2}, pages = {125-144}, pmid = {24193132}, issn = {0095-3628}, abstract = {We performed a series of seawater culture experiments on surface mixed layer samples during the spring phytoplankton bloom in the North Atlantic Ocean. Diluted (20% unfiltered + 80% 0.22 μm filtered) and untreated "whole" seawater samples were incubated up to 40 hour and sampled periodically for cell numbers, biovolume, and incorporation of (3)H-thymidine and -leucine. Abundance and biovolume increased exponentially at similar rates in diluted and whole samples, suggesting that removal by bacteriovores was low compared with growth. The exponential increase in biovolume was due to increases in cell numbers and mean cell volume. Generation times (i.e., 0.693/μ) averaged 36-53 hour in these surface (10 m) samples. Ninety percent of the tritiated thymidine incorporation (TTI) into cold trichloroacetic acid-insoluble cell fractions was recovered after extraction with NaOH and phenolchloroform, indicating that catabolism of thymidine and its appearance in RNA or protein was very low. The percentage of thymidine recovered in DNA did not change over the 40 hour of incubation and was the same as in water column samples. Rates of thymidine and leucine incorporation also increased exponentially. Incorporation rates tended to increase more rapidly than cell numbers or biovolume, though the differences were not significantly different, due to the small number of samples and variability over the time courses. Differential rates of increase in cellular properties during growth might indicate a lack of coupling between incorporation and production over time scales of hours-days. This in turn may reflect unbalanced growth of bacterial assemblages, which is an adaptation to variable conditions in the upper ocean in this season. Nonequality of rate constants for cells and incorporation yields conversion factors that are either higher or lower than would be calculated from balanced growth (i.e., rates of increase in numbers and incorporation rates equal), depending on the calculation approach chosen. An alternative approach to calculating conversion factors (the modified derivative approach) is proposed, which is insensitive to differential rates of increase of abundance and incorporation.}, }
@article {pmid24193131, year = {1992}, author = {Amblard, C and Rachiq, S and Bourdier, G}, title = {Photolithotrophy, photoheterotrophy and chemoheterotrophy during spring phytoplankton development (Lake Pavin).}, journal = {Microbial ecology}, volume = {24}, number = {2}, pages = {109-123}, pmid = {24193131}, issn = {0095-3628}, abstract = {In order to determine the relative importance of autotrophic and heterotrophic activities in both bacterial and phytoplanktonic communities in an oligomesotrophic lake, the size fractionation by differential filtration and the use of a bacterial inhibitor (gentamycin) were combined. The study was carried out at Lake Pavin during the spring planktonic bloom. Photosynthetic and photo- and chemoheterotrophic activities were measured from the assimilation of NaH(14)CO3 and glucose-(3)H, using a double labeling technique. The bacterial community was at low cell concentration (0.6 to 7 × 10(5) cells ml(-)) and represented very low biomass values (0.9 to 11.5 μgC liter(-1)). The abundance of the phytoplankton varied between 0.5 and 1.8 × 10(6) cells liter(-1), and biomass values ranged between 19 and 118 μgC liter(-1). The diatom Melosira italica sp. subarctica (O. Mueller) was the largely dominant species in the meta- and hypolimnion. Inorganic fixation by photolithotrophy (mean value: 1.66 mg C m(-3) hour(-1)) largely predominates over assimilation by photoheterotrophy (mean value: 0.93 μg C m(-3) hour(-1)) or chemoheterotrophy (mean value: 2.42 μg C m(-3) hour(-1)). However, because of the considerable underestimation of heterotrophic assimilation due to the experimental methods used, and because of the spatial and temporal separation of photolithotrophic and photo- and chemoheterotrophic activities, it is likely that the fixation of organic carbon by microalgae plays an important role in the survival of species and/or in competitive interactions, as the results with Monoraphidium contortum (Pasch. et Korschik.), the prevailing species in the epilimnion, would suggest.}, }
@article {pmid24193042, year = {1992}, author = {Vandenabeele, J and de Beer, D and Germonpré, R and Verstraete, W}, title = {Manganese oxidation by microbial consortia from sand filters.}, journal = {Microbial ecology}, volume = {24}, number = {1}, pages = {91-108}, pmid = {24193042}, issn = {0095-3628}, abstract = {The role of microbial consortia on the removal of manganese (Mn) was examined on sand from three different Belgian rapid sand filters for the treatment of ground water. Microorganisms closely associated with deposits of Fe and amorphous Mn precipitates were observed by SEM and EDAX techniques on sand from the filters able to remove Mn efficiently. Bacterial counts were performed. Of the CFU enumerated on PYM-medium, 25-33% displayed Mn-oxidizing activity.Batch cultures were set up by inoculating a Mn-containing, low organic medium with sand from one of the filters. Microbial growth resulted in the formation of Mn-removing bacterial flocs and a pH increase. Suppression of microbial growth by addition of azide, kanamycin, or by autoclaving reduced removal of Mn(2+) from 0.5 mM/day to 0.05-0.11 mM/day. Buffering the pH of the medium at 7.5 (0.1 mM Hepes) decelerated the Mn removal but did not halt it, whereas microelectrode measurements revealed a clear pH drop of about 0.7 units inside bacterial flocs. In the absence of Mn(2+), the pH drop was only 0.4 units. The auto-catalytic removal of Mn by the Mn oxide coated filter sand was not sufficient to explain the Mn removal observed. Inactivated cells were not capable of a pronounced autocatalytic Mn removal. Experiments with enrichment cultures indicated that the Mn-removing capacity of the microbial sand filter consortia was not constitutive but was promoted by preadaptation and the presence of a substratum. These results clearly link Mn oxidation in rapid sand filters to microbial processes.}, }
@article {pmid24193041, year = {1992}, author = {Karl, DM}, title = {The grounding of the Bahia Paraiso: Microbial ecology of the 1989 Antarctic oil spill.}, journal = {Microbial ecology}, volume = {24}, number = {1}, pages = {77-89}, pmid = {24193041}, issn = {0095-3628}, abstract = {On 28 January 1989 the Bahia Paraiso ran aground and sank near Palmer Station, Antarctica. At least 6.8 × 10(5) liters of diesel fuel arctic (DFA) were released into semi-enclosed Arthur Harbor and deposited in the nearby intertidal regions. Approximately 6 weeks later, a group of scientists was deployed to evaluate the impact of the oil spill on the surrounding coastal marine ecosystem.Microbial hydrocarbon oxidation potential ((14)CO2 evolved from (14)C-labeled hexadecane) was detected throughout both the oil-impacted and control regions. Hexadecane was mineralized at extremely low rates (0.13-1.21 pmol g(-1) sediment dry weight day(-1)); microbiological turnover time exceeded 2 years. The acute effects of DFA (measured over exposure periods of 3-7 days) on the metabolic activities of sedimentary microorganisms appear to be negligible even at seawater saturation concentrations of DFA. Long-term exposure (120 days) to varying concentrations of DFA resulted in significant decreases (>90%) in total ATP, but had either no effect or a slight stimulatory effect on metabolic activity and production. In contrast to planktonic microbial communities, increasing incubation temperatures of between 0 and 30°C had a positive effect on rates of metabolism and production of sedimentary assemblages. These results may influence the overall weathering rates of hydrocarbons deposited in the intertidal and supratidal regions of Arthur Harbor and other polar regions.}, }
@article {pmid24193040, year = {1992}, author = {Bernadsky, G and Rosenberg, E}, title = {Drag-reducing properties of bacteria from the skin mucus of the cornetfish (Fistularia commersonii).}, journal = {Microbial ecology}, volume = {24}, number = {1}, pages = {63-76}, pmid = {24193040}, issn = {0095-3628}, abstract = {Scanning electron microscopy and fluorescence microscopy after scanning with DAPI indicated that the skin mucus of the cornetfish contained large numbers of bacteria, 4 × 10(8) per cm3. However, viable counts yielded only 2 × 104 per cm(3). Twelve bacterial strains were isolated directly from the mucus and another ten strains were obtained following enrichment on pasteurized mucus medium. Most of the isolates belonged to the genus Pseudomonas; a smaller number were classified as Micrococcaceae. Cultures of 13 of the isolates were active in reducing friction in a turbulent flow rheometer. The surface active and drag-reducing properties of three strains-JR5, JR8, and GB7-were studied further. The drag-reducing activities, which were extracellular, were concentrated by ultra-filtration. The chemical composition of the concentrated preparations consisted of 14-24% protein and 38-75% polysaccharide. The major components of the polysaccharide fraction were galacturonic acid, galactosamine, and glucosamine, with lesser amounts of glucose and galactose. The most active preparation, from strain JR8, had a specific drag-reducing activity of 77 units per mg. Strain JR5 was the most hydrophobic as measured by the DOS and BATH tests. JR8 gave intermediate values, and GB8 showed low hydrophobicity values in both tests. The hydrocarbon-in-water emulsifying ability of the concentrated polymer fractions from JR8, GB7, and JR5 were high, intermediate, and low, respectively. The emulsifying and drag-reducing activities of the polymer fraction from strain JR8 were separated from each other by extraction with hydrocarbons. The emulsifying activity was due to a carbohydrate-protein complex, whereas the drag-reducing activity was associated with a uronic acid-containing polysaccharide.}, }
@article {pmid24193039, year = {1992}, author = {Brunel, B and Janse, JD and Laanbroek, HJ and Woldendorp, JW}, title = {Effect of transient oxic conditions on the composition of the nitrate-reducing community from the rhizosphere of Typha angustifolia.}, journal = {Microbial ecology}, volume = {24}, number = {1}, pages = {51-61}, pmid = {24193039}, issn = {0095-3628}, abstract = {Within a nitrate-reducing bacterial community, a niche differentiation between denitrifying and nitrate ammonifying bacteria may be determinated by a complex of environmental parameters, such as the availability of carbon, nitrate, and oxygen. Hence, oxygen- and carbon-releasing aerenchymatous plants may affect the composition of the nitrate-reducing community in waterlogged sediment. The composition of the nitrate-reducing community in the rhizosphere of the aerenchymatous plant species Typha angustifolia was compared with the community in nonrhizospheric sediment. All three functional groups (NO2 (-) accumulators, N2O producers, and presumed NH4 (+) producers) were present at both sites with an ratio of 36:45:12 and 43:22:18 for nonrhizospheric and rhizospheric sediments, respectively. Most of the isolated were gram-negative, and approximately 50% of these strains demonstrated an obligatory oxidative metabolism.In the absence of nitrate, Enterobacteriaceae (belonging to the NO2 (-) accumulating group) became dominant during enrichment of bacteria from the rhizosphere of T. angustifolia in a chemostat with glycerol (20 mM) as substrate, both under strictly anoxic and transient oxic conditions. Addition of nitrate to the chemostats led to the predominance of denitrifying pseudomonads, irrespective of the presence or absence of oxygen. However, in the presence of nitrate under anoxic conditions, enterobacteria persisted in the medium together with pseudomonads.It was concluded that oxidative bacteria such as pseudomonads are the better competitors for limiting amounts of glycerol, provided oxygen or nitrate is present. In the absence of these electron acceptors, fermentative bacteria become dominant.}, }
@article {pmid24193038, year = {1992}, author = {Powell, SJ and Prosser, JI}, title = {Inhibition of biofilm populations of Nitrosomonas europaea.}, journal = {Microbial ecology}, volume = {24}, number = {1}, pages = {43-50}, pmid = {24193038}, issn = {0095-3628}, abstract = {The influence of surface attachment and growth on inhibition of the ammonia oxidizing bacterium, Nitrosomonas europaea, by nitrapyrin was investigated in liquid culture in the presence and absence of glass slides. Significant attachment to glass slides occurred in the absence of ammonia, but the extent of attachment was not affected by nitrapyrin, nor by previous culture of cells in medium containing nitrapyrin. The presence of glass slides affected neither the specific growth rate of N. europaea, measured by changes in nitrite concentration, nor inhibition by nitrapyrin. Inhibitory effects of nitrapyrin on increases in nitrite concentration and in free cell concentration were similar, but greater effects were observed on changes in attached cell concentration. Established biofilms on glass slides grew at a lower specific growth rate than freely suspended cells. Both biofilm cells, and those detached from the biofilm, were protected from inhibition. A mechanism for protection of biofilm populations is proposed involving reduced sensitivity of slowly growing cells producing extracellular polymeric material.}, }
@article {pmid24193037, year = {1992}, author = {Lindgvist, R and Enfield, CG}, title = {Cell density and non-equilibrium sorption effects on bacterial dispersal in groundwater microcosms.}, journal = {Microbial ecology}, volume = {24}, number = {1}, pages = {25-41}, pmid = {24193037}, issn = {0095-3628}, abstract = {The relative importance of dispersion, physical straining, non-equilibrium sorption, and cell density on the dispersal of bacteria was examined in saturated, flow-dynamic sand columns. The bacterial breakthrough as a result of different size distributions of sand particles was followed by measuring the effluent concentration of 3H-adenosine-labelled cells of a Bacillus sp. and an Enterobacter sp. strain suspended in groundwater. The breakthrough curves were compared with theoretical curves predicted from an advective-dispersioe equilibrium sorption model (ADS), an ADS model with a first order sink term for irreversible cell reactions, a two-site model (equilibrium and nonequilibrium sorption sites), and a filtration model. Bacterial sand: water isotherms were linear in the experimental concentration range but had positive intercepts. The partition coefficients ranged from 15 to 0.4 for the Bacillus sp., and 120 to 0.4 for a Pseudomonas sp., and decreased with increasing particle size of the dominant fraction. In a kinetic study, the partition coefficient for the Enterobacter sp. in the smaller particle sand was 63 after one hour, but had decreased to 9 after 19 hours. Bacteria were detected in the effluent after one pore volume, which was earlier than predicted by the sand : water partition coefficients, and displayed an apparent nonequilibrium breakthrough. Dispersion effects and physical straining appeared to be insignificant in the experiments, but tailing of the elution part of the curves indicated slow reversible sorption, and nonequilibrium sorption may have been the main determinant of dispersal retardation. The reversible non-equilibrium sorption invalidated some of the assumptions behind all models except, possibly, the two-site model. Consequently, the models described the large particle sand data better where sorption was of less importance for the dispersal. The dispersal retardation was also affected by the bacterial cell density, both in the pore water and on the sand, suggesting that population characteristics may be an important factor for the bacterial distribution between the water and sand habitats. The retardation factor decreased from 13.7 to 7.8 when the cell density in the loading solution was increased from 3× 10(8) to 1.2 × 10(9) cells ml(-1). Presaturation of the sand with bacteria had a similar effect.}, }
@article {pmid24193036, year = {1992}, author = {Leff, LG and Vaun McArthur, J and Shimkets, LJ}, title = {Information spiraling: Movement of bacteria and their genes in streams.}, journal = {Microbial ecology}, volume = {24}, number = {1}, pages = {11-24}, pmid = {24193036}, issn = {0095-3628}, abstract = {Bacteria in transport in streams are largely derived from other parts of the ecosystem. Here we review factors that influence transport of bacteria and their movement between habitats (such as sediment, water column, rocks, wood, and leaves) and consider the role of these movements in ecosystem processes. Bacteria enter the water column by sloughing, scouring, as a consequence of changes in morphology or hydrophobicity, or dislodgment by invertebrates and fish or other aquatic vertebrates. Transported cells (which may be planktonic or particle-associated) that colonize surfaces may establish new gene pools through cell division (vertical transfer) or genetic exchange (lateral transfer). Genetic information is also transported in streams as free or protected DNA or in bacteriophages. Movement of these vectors causes genetic information to spiral along a stream in a manner analogous to that of nutrients and organic carbon. Spiraling refers to the pattern of transport, uptake or attachment, and release of a molecule or cell. The flow of water in streams causes this cycle of attachment and release to be displaced downstream resulting in a spiral rather than a closed, stationary loop.}, }
@article {pmid24193035, year = {1992}, author = {Crawford, DW}, title = {Metabolic cost of motility in planktonic protists: Theoretical considerations on size scaling and swimming speed.}, journal = {Microbial ecology}, volume = {24}, number = {1}, pages = {1-10}, pmid = {24193035}, issn = {0095-3628}, abstract = {The metabolic cost of swimming for planktonic protists is calculated, on theoretical grounds, from a simple model based upon Stokes' law. Energetic expenditure is scaled over both typically encountered size ranges (1-100 µm) and swimming speeds (100-5,000 µm/sec). In agreement with previous estimates for typical flagellates, these estimates generally suggest a low (<1%) cost for motility, related to total metabolic rate of growing cells. However, the cost of motility in small, fast-moving forms, such as some ciliates and flagellates, may be significant (1-10%) and even substantial (10-100%+) for certain species. In accordance with these predictions, many fast-moving ciliates restrict motility to bursts of activity or "jumps." In the absence of a reduction in swimming speed or in the frequency of jumps, it is predicted that this relative cost of motility will be significantly increased in starving heterotrophs or light-limited autotrophs, if such cells reduce cell volumes and specific rates of respiration.}, }
@article {pmid24192863, year = {1992}, author = {Hackett, KJ and Whitcomb, RF and Tully, JG and Lloyd, JE and Anderson, JJ and Clark, TB and Henegar, RB and Roset, DL and Clark, EA and Vaughn, JL}, title = {Lampyridae (Coleoptera): A plethora of mollicute associations.}, journal = {Microbial ecology}, volume = {23}, number = {2}, pages = {181-193}, pmid = {24192863}, issn = {0095-3628}, abstract = {Beetles (Coleoptera) harbor many species ofAcholeplasma andSpiroplasma (division Tenericutes, class Mollicutes). Mollicutes were isolated from guts and/or hemocoels of firefly beetles (Lampyridae) from the United States (Maryland and West Virginia), Ecuador, and Tobago. Firefly beetles were frequent hosts for the group XIV spiroplasma, isolated from Ellychnia corrusca, and the group XIX spiroplasma, isolated fromPhoturis spp. The most unusual feature of the firefly-mollicute association is the carriage of four Mycoplasma species. Recent phylogenetic studies indicate that these species are members of a clade that includes a vertebrate pathogen,Mycoplasma mycoides. The high rate of occurrence ofMycoplasma species (which are, otherwise, infrequent in insects) in lampyrid beetles suggests that the association is significant. The unusual light-producing physiology of lampyrids (which is dependent on large pools of energy) and the production of large amounts of cardenolides from cholesterol (a critical growth factor for many mollicutes) may favor colonization by mollicutes.}, }
@article {pmid24192862, year = {1992}, author = {Park, YH and Kenerley, CM and Stack, JP}, title = {Inoculum dynamics ofGliocladium virens associated with roots of cotton seedlings.}, journal = {Microbial ecology}, volume = {23}, number = {2}, pages = {169-179}, doi = {10.1007/BF00172638}, pmid = {24192862}, issn = {0095-3628}, abstract = {A system was developed to evaluate the effects of root growth of cotton seedlings on the inoculum dynamics ofGliocladium virens in nonsterile soil. In soil infested withG. virens, inoculum densities of the fungus increased when plants remained alive. After 30 days, shoots were excised and the roots allowed to deteriorate. During this portion of the experiment (30-60 days) soil inoculum densities ofG. virens declined. In infested soil without a seedling, inoculum densities remained constant throughout the duration of the experiments. Colonization of roots byG. virens was found to increase throughout the duration of the experiments. At 60 daysG. virens was recovered from approximately 60% of the root pieces (1-cm) sampled. The percentage of primary, secondary, or tertiary roots colonized was different (P = 0.01), but the total colonization of roots at three depths (0-10, 10-20, and 20-30 cm) was not different (P = 0.64). In noninfested soil, colonization of roots by indigenous propagules ofG. virens was never greater than 3%.}, }
@article {pmid24192861, year = {1992}, author = {Bergbauer, M and Moran, MA and Hodson, RE}, title = {Decomposition of lignocellulose from a freshwater macrophyte by aero-aquatic fungi.}, journal = {Microbial ecology}, volume = {23}, number = {2}, pages = {159-167}, pmid = {24192861}, issn = {0095-3628}, abstract = {Mineralization of uniformly radiolabeled [(14)C]lignocellulose and specifically radiolabeled [(14)C-lignin]lignocellulose from the freshwater sedgeCarex walteriana by five aero-aquatic fungi was investigated. The extent of mineralization varied among the five species from 2.2 to 4.2% for the lignin component and from 3.3 to 20.6% for the polysaccharide component. The extent of mineralization of both lignin and polysaccharide moieties by a mixed culture of the five fungi were generally markedly lower than by pure cultures, possibly due to the production of antimicrobial compounds.Spirosphaera foriformis, the most active strain in lignin as well as in polysaccharide mineralization, degraded ferulic acid faster than p-coumaric acid. Decomposition ofCarex walteriana lignocellulose by this strain resulted in decreased cinnamyl/vanillyl (C/V) and syringyl/vanillyl (S/V) ratios.}, }
@article {pmid24192860, year = {1992}, author = {Kroer, N and Coffin, RB}, title = {Microbial trophic interactions in aquatic microcosms designed for testing genetically engineered microorganisms: A field comparison.}, journal = {Microbial ecology}, volume = {23}, number = {2}, pages = {143-157}, pmid = {24192860}, issn = {0095-3628}, abstract = {Microcosms may potentially be used as tools for evaluating the fate and effects of genetically engineered microorganisms released into the environment. Extrapolation of data to the field, however, requires that the correspondence between microcosm and field is known. Microbial trophic interactions within the microbial loop were compared quantitatively and qualitatively between field and microcosms containing estuarine water with and without intact sediment cores. The comparison showed that whereas proportions between trophic levels in microcosms were qualitatively similar to those in the field, rates of microbial processes were from 25 to 40% lower in microcosms. Nitrogen cycling was disrupted in microcosms incubated in the dark to eliminate primary production. Examination of the microbial parameters further suggests that sediment in microcosms may be an important factor regulating the bacterial trophic level. These results demonstrate that analysis of microbial trophic interactions is a sensitive method for the field comparison of aquatic microcosms and a potentially useful tool in the risk assessment of genetically engineered microorganisms.}, }
@article {pmid24192859, year = {1992}, author = {Schmidt, SK and Smith, R and Sheker, D and Hess, TF and Silverstein, J and Radehaus, PM}, title = {Interactions of bacteria and microflagellates in sequencing batch reactors exhibiting enhanced mineralization of toxic organic chemicals.}, journal = {Microbial ecology}, volume = {23}, number = {2}, pages = {127-142}, pmid = {24192859}, issn = {0095-3628}, abstract = {Community level interactions were studied in non-axenic sequencing batch reactors (SBRs) being used to treat 2,4-dinitrophenol (DNP). Increasing the influent DNP concentrations from 1 to 10 µg ml(-1) eliminated large predatory organisms such as rotifers and ciliated protozoa from the SBRs. Under steady-state conditions at a DNP concentration of 10 µg ml(-1), supplemental additions of glucose enhanced DNP degradation and led to the establishment of a microbial community consisting of five species of bacteria and a variety of microflagellates. The bacteria and flagellates exhibited oscillating population dynamics in this system, possibly indicating predator-prey interactions between these two groups. Only two of the five bacteria isolated from this system could utilize glucose as a growth substrate, and one of these two species was the only organism that could mineralize DNP in the system. The other three bacteria could grow using metabolic by-products of one of the glucose-utilizing strains (Bacillus cereus) found in the reactors. Supplemental glucose additions increased the average size of bacterial floc particles to 172 µm, compared with 41 µm in SBRs not receiving glucose. It is theorized that the enhanced mineralization of DNP in this non-axenic system was attributable to increased community interactions resulting in increased bacterial flocculation in SBRs receiving supplemental glucose additions.}, }
@article {pmid24192858, year = {1992}, author = {Benoit, L and Cailliez, C and Petitdemange, E and Gitton, J}, title = {Isolation of cellulolytic mesophilic clostridia from a municipal solid waste digestor.}, journal = {Microbial ecology}, volume = {23}, number = {2}, pages = {117-125}, pmid = {24192858}, issn = {0095-3628}, abstract = {Ten obligately anaerobic, cellulolytic mesophilic bacteria were isolated from a municipal solid waste digestor used for biogas production. The isolates were rod-shaped, spore-forming bacteria in anaerobic conditions, and stained Gram-positive in young cultures, and hence were identified asClostridium. Small regular translucent and unpigmented colonies were observed on cellulose plates. The strains were gelatinase-negative, hydrolyzed esculin and starch, and fermented xylose and arabinose. The lecithinase, lipase, and indole tests were negative. The major fermentation products from cellulose included ethanol and acetate. The morphological and other biochemical characteristics indicated that these clostridia did not correspond to any previously described species. All the strains produced high activities of extracellular cellulases in cellulose media and degraded paper.}, }
@article {pmid24192857, year = {1992}, author = {Hadas, O and Pinkas, R and Wynne, D}, title = {Nitrate reductase activity, ammonium regeneration, and orthophosphate uptake in protozoa isolated from Lake Kinneret, Israel.}, journal = {Microbial ecology}, volume = {23}, number = {2}, pages = {107-115}, pmid = {24192857}, issn = {0095-3628}, abstract = {Nitrate reductase (NR) activity and nutrient (N, P) recycling in the ciliatesColpoda steinii andStylonychia sp. and two unidentified flagellates (I and II), isolated from Lake Kinneret, have been studied. When grown on a bacterium also isolated from the lake, all species, except flagellate I, exhibited NR activity. Activity was higher in the presence of nitrate than in its absence, and in the case ofC. steinii showed a dependence on initial ambient NO3 concentrations in the cultures. NR activity was inversely proportional to body size, suggesting that the larger protozoan species have decreased specific metabolic rates. A net increase in ammonium concentrations and a decrease in orthophosphate levels was observed, but both phenomena were much less sensitive to ambient NO3 concentrations than NR activity. Similar trends in NR activity and NH4 production were also observed whenC. steinii was grown on the picocyanobacteriumSynechococcus sp. Our results suggest that NH4 excretion is the outcome of N remineralization from the food supply but is also partially due to dissimilatory nitrate reduction. These data imply that protozoa may have an important role in nutrient recycling in Lake Kinneret and that some species could use NO3 respiration in anoxic regions of the water column.}, }
@article {pmid24192937, year = {1992}, author = {Albrechtsen, HJ and Winding, A}, title = {Microbial biomass and activity in subsurface sediments from Vejen, Denmark.}, journal = {Microbial ecology}, volume = {23}, number = {3}, pages = {303-317}, pmid = {24192937}, issn = {0095-3628}, abstract = {Subsurface sediment samples were collected from 4 to 31 m below landsurface in glacio-fluvial sediments from the Quaternary period. The samples were described in terms of pH, electrical conductivity, chloride concentration, organic matter content, and grain size distribution. Viable counts of bacteria varied from 0.5 to 1,203 x 103 colony forming units/g dry weight (gdw); total numbers of bacteria acridine orange direct counts (AODC) varied from 1.7 to 147 × 10(7) cells/gdw; growth rates (incorporation of [(3)H]-thymidine) varied from 1.4 to 60.7 × 10(4) cells/(gdw · day); and rate constants for mineralization of (14)C-labelled compounds varied from 0.2 to 2.3 × 10(-3) ml/(dpm · day) for acetate, and from 0 to 2.0 × 10(-3) ml/(dpm · day) for phenol. Sediment texture influenced the total number of bacteria and potential for mineralization; with increasing content of clay and silt and decreasing content of sand, AODC increased and the mineralization rate declined. Intrinsic permeability calculated from grain size correlated positively with mineralization rate for acetate. Statistical correlation analysis showed high correlations between some of the abiotic parameters, but it was not possible to point out a single abiotic parameter that could explain the variation of size and activity of the microbial population. The microbial data obtained in these geologically young sediments were compared to literature data from older sediments, and this comparison showed that age and type of geological formation might be important for the size and activity of the microbial populations.}, }
@article {pmid24192936, year = {1992}, author = {Brockman, FJ and Kieft, TL and Fredrickson, JK and Bjornstad, BN and Li, SM and Spangenburg, W and Long, PE}, title = {Microbiology of vadose zone paleosols in south-central Washington State.}, journal = {Microbial ecology}, volume = {23}, number = {3}, pages = {279-301}, pmid = {24192936}, issn = {0095-3628}, abstract = {Three unsaturated subsurface paleosols influenced by moisture recharge, including a highly developed calcic paleosol, were studied to investigate the microbiology of paleosols. Two near-surface paleosols, one impacted by moisture recharge and the other beyond the influence of recharge, were also sampled to directly assess the effect of moisture recharge on the activity and composition of the microbial community associated with paleosols. The highly developed paleosol had a higher population of culturable heterotrophs, a greater glucose mineralization potential, a higher microbial diversity based on colony morphology, and a more than 20-fold higher concentration of ATP than the two weakly developed paleosols. The recharged near-surface paleosol, as compared to the near-surface paleosol unaffected by recharge, had a lower population of culturable heterotrophs, smaller mineralization rate constant, and lower richness based on colony morphology. The recharged paleosols contained predominantly gram-negative isolates, whereas the paleosol unaffected by recharge contained predominantly gram-positive isolates. Storage at 4°C of subsurface and near-surface paleosol samples containing high water potential increased the population of culturable aerobic heterotrophs, decreased diversity in colony morphology, and increased first-order rate constants and decreased lag times for glucose mineralization. These results indicate that aerobic heterotrophs are present in deep vadose zone paleosols and that there is potential for stimulation of their in situ growth and activity.}, }
@article {pmid24192935, year = {1992}, author = {Plante, C and Jumars, P}, title = {The microbial environment of marine deposit-feeder guts characterized via microelectrodes.}, journal = {Microbial ecology}, volume = {23}, number = {3}, pages = {257-277}, pmid = {24192935}, issn = {0095-3628}, abstract = {Microbial viability and growth in animal guts are dependent upon conditions influenced by both the physiological activities of the animal and the activities of the microbes themselves. To examine the relative contribution of these influences, the guts of Molpadia intermedia (a subtidal holothuroid) and a variety of other marine deposit feeders from diverse habitats were probed with mini- or microelectrodes to measure oxygen, Eh, and pH. In general, bulk oxygen and pH conditions of the gut mimicked those of ambient sediments, revealing nearly neutral pH and zero oxygen in sub- and intertidal animals, with more oxygen in bathyal animals ingesting oxygenated sediments. Eh in guts of subsurface deposit feeders that likely subduct and aerate sediments before ingestion did not mimic sediments. Axial Eh profiles, in contrast to those of pH and oxygen, revealed significant changes along the gut. In most deposit feeders, values decreased from mouth to midgut, suggesting high rates of microbial metabolism within the gut. Increases in Eh were observed in the most distal portion of guts, however, likely due to anal intake of aerated water, and throughout the guts of terebellid polychaetes that feed on highly reducing sediments. This addition of a strong oxidant by the animal may be necessary to avoid sulfide poisoning and may provide access to organic products by stimulating chemoautotrophy. Radial profiles of the gut revealed sharp gradients of Eh and oxygen. In general, steep redox gradients stimulate bacterial metabolism and may lead to exceptionally high respiratory rates. Radial diffusion calculations made using oxygen profiles surrounding the gut reveal that, as predicted by digestion theory, oxygen consumption rates are rapid and are higher in the hindgut, where the digestive products of the animal are available to microbes, than in the foregut.}, }
@article {pmid24192934, year = {1992}, author = {Petersen, SO and Nielsen, AL and Haarder, K and Henriksen, K}, title = {Factors controlling nitrification and denitrification: A laboratory study with gel-stabilized liquid cattle manure.}, journal = {Microbial ecology}, volume = {23}, number = {3}, pages = {239-255}, pmid = {24192934}, issn = {0095-3628}, abstract = {Nitrification and denitrification were studied in a millimeterscale microenvironment using a two-phase system with a liquid manure-saturated layer. Samples consisted of liquid cattle manure and air-dried soil stabilized with silica gel, placed between two aerobic soil phases with a water content near field capacity. A high potential for NH4 (+) oxidation developed within 0-2 mm distance from the interface, and NH4 (+) diffused only 10-20 mm into the soil. Some NH4 (+) was probably immobilized by microorganisms in the soil between 0 and 4 days, after which nitrification was the only sink for NH4 (+). A potential for denitrification developed within the manure-saturated zone. Maximum rates of both potential and actual denitrification were recorded by Day 4, but denitrification continued for at least 2-3 weeks. The potential for nitrification peaked after 14 days. When the pH of the manure was adjusted to 5.5, nitrification was reduced close to the interface, and NH4 (+) penetrated further into the soil before it was oxidized. The pH adjustment had an inhibitory effect on denitrification: Both potential and actual rates of denitrification were almost eliminated for several days. The size of the manure-saturated layer strongly affected denitrification losses. With layers of 8 and 16 mm thickness, losses equivalent to 33 and 40% of the original NH4 (+) pool, respectively, were estimated. When manure corresponding to a 12 mm layer was homogeneously mixed with the soil, only 0.3% was lost.}, }
@article {pmid24192933, year = {1992}, author = {Hassani, L and Imziln, B and Boussaid, A and Gauthier, MJ}, title = {Seasonal incidence of and antibiotic resistance among Aeromonas species isolated from domestic wastewater before and after treatment in stabilization ponds.}, journal = {Microbial ecology}, volume = {23}, number = {3}, pages = {227-237}, pmid = {24192933}, issn = {0095-3628}, abstract = {The efficiency of stabilization pond treatment of domestic wastewater in removing culturable cells of motile Aeromonas and its influence on the incidence of resistance to seven antibiotics were investigated in this study. Removal efficiency was higher (P < 0.001) in the warm months (98.8%) than in the cold months (97%). Among the 264 isolates, 163 were Aeromonas caviae, 24 were A. hydrophila, and 54 were A. sobria. Twenty-three isolates could not be identified to the species level. In the influent, A. caviae dominated in both cold and warm months. In the water samples originating from the influent, A. sobria was present at higher percentages in the warm period. All the isolates were resistant to amoxicillin and most of them (73%) exhibited resistance to cephalothin. Of the three species tested, A. sobria was more susceptible to antibiotics than either A. caviae or A. hydrophila. The most striking difference among the species was seen in resistance to cephalothin. There were 91 % of A. caviae strains and 96% of A. hydrophila isolates that were resistant to cephalothin. However, only 9% of A. sobria strains exhibited resistance to this drug. The high incidence of resistance in raw sewage was connected with a high proportion of A. caviae, whereas in the water samples collected from the effluent during the warm months, a high proportion of A. sobria decreased the total amount of multiple-resistant bacteria. Results demonstrated the need for identification to the species level.}, }
@article {pmid24192932, year = {1992}, author = {Epstein, SS and Shiaris, MP}, title = {Size-selective grazing of coastal bacterioplankton by natural assemblages of pigmented flagellates, colorless flagellates, and ciliates.}, journal = {Microbial ecology}, volume = {23}, number = {3}, pages = {211-225}, pmid = {24192932}, issn = {0095-3628}, abstract = {Fluorescently-labelled bacteria (FLB) were used to study the feeding strategies of a natural assemblage of estuarine protozoans and to examine whether the protozoan grazing could account for the in situ size structure of the bacterioplankton. The FLB, DTAF-stained enterococci, ranging in volume from 0.01 to 0.30 × 10(-1) µm(3), were added to a natural planktonic assemblage at a density of 5.5% of the natural bacterioplankton. Initial densities (individuals ml(-1)) were as follows: total natural bacteria, 2.2 × 10(6); FLB, 1.2 × 10(5); pigmented flagellates, 300; colorless flagellates, 250; and ciliates, 30. FLB consumption rates were determined by examining the contents of protozoan food vacuoles, and the long-term effect of grazing (over a period of 100 hours) was determined by monitoring the decline in the FLB density in experimental vessels. The average consumption rates of FLB by pigmented flagellates were similar to those by flagellates that lacked chloroplasts (0.9 and 0.6 FLB protozoan(-1) hour(-1), respectively). The ciliates consumed bacteria at an average rate that was 17-fold higher (per cell) than flagellates, and they displayed a greater preference for larger bacteria than did the flagellates. FLB of the mid-size classes (0.025-0.100 µm(3)) were heavily grazed by the entire protozoan assemblage; the smallest (<0.025 µm(3)) and the largest (>0.100 µm(3)) FLB escaped protozoan grazing. This had a profound effect on the resulting size distribution of FLB. At the end of a 100-hour incubation, the percentage of mid-size FLB (0.025 to 0.100 µm(3)) decreased 2.0-2.2-fold, while the percentage of the smallest and the largest FLB increased 2.0-2.5-fold. Resultant densities of FLB were consistent with initial clearance rates determined for the protozoan groups. The grazing rates of protozoans on FLB were species-specific; whereas some species consumed FLB, others did not demonstrate bacterivory. The results suggest that protozoan grazing has a major effect on the size distribution of coastal bacterioplankton. By selectively feeding on a particular size-class of bacteria, planktonic ciliates may consume 15-90% day(-1) of the standing stock of largest size classes of bacterioplankton. Thus, ciliates, which were present in low abundance in the field, could not balance the production of the entire bacterial community, but they may strongly influence the portion of the bacterial community represented by the largest bacterial class. The direct effect of flagellates (e.g., grazing) was limited to smaller bacteria.}, }
@article {pmid24192931, year = {1992}, author = {Tibbles, BJ and Davis, CL and Harris, JM and Lucas, MI}, title = {Estimates of bacterial productivity in marine sediments and water from a temperate saltmarsh lagoon.}, journal = {Microbial ecology}, volume = {23}, number = {3}, pages = {195-209}, pmid = {24192931}, issn = {0095-3628}, abstract = {Tritiated thymidine incorporation (TTI) into DNA was used to estimate bacterial productivity in sediment and water samples from two sites in Langebaan Lagoon, South Africa. Routine analysis of isotope dilution showed seasonal variations of approximately threefold in the thymidine precursor pool sizes for bacterial assemblages from each site. Dual label incorporation of [(3)H]-thymidine and (14)C-leucine into DNA and protein, respectively, showed that pelagic but not sediment assemblages were in a balanced state of growth during TTI. This is the first report of dual label measurements of bacterial production in sediments. Sediments supported bacterial productivities that exceeded those in the water column by factors from five- to 950-fold, whereas bacterial abundance supported by sediments exceeded that in the water column by more than 3 orders of magnitude. Estimates of bacterial productivities in sediments were coincident with levels of organic content in sediments, but not with bacterial abundance. Measurements of TTI activity for 5 different benthic microhabitats at one lagoon site showed highest activity associated with seagrass beds (2.11 ± 0.84 nmol thymidine hours(-1) g-1 dry weight), whereas activities decreased with depth (0.46 ± 0.21 nmol thymidine hours(-1) g(-I) dry weight) below sediment surface.}, }
@article {pmid24192832, year = {1992}, author = {Maki, JS and Rittschof, D and Mitchell, R}, title = {Inhibition of larval barnacle attachment to bacterial films: An investigation of physical properties.}, journal = {Microbial ecology}, volume = {23}, number = {1}, pages = {97-106}, pmid = {24192832}, issn = {0095-3628}, abstract = {The effects of films of two strains of a marine bacterium, Deleya marina (ATCC 25374 and 27129) on the attachment response of cypris larvae of the balanomorph barnacle, Balanus amphitrite, were examined in the laboratory. Tests showed that the cell-surface hydrophobicities of the two bacteria in suspension were different. In contrast, films derived from these cells were both highly wettable (i.e., displayed high surface free energy). Assays (22 hours) compared permanent attachment of larval barnacles to films derived from exponential and stationary phase cells for both bacteria. These films either had no effect or inhibited attachment of both 0-day- and 4-day-old cypris larvae when compared with unfilmed controls. Our data indicate that inhibition of larval barnacle attachment by films of the two bacteria is the result of factors other than surface free energy. Production of chemical barnacle settlement inhibitors by the bacteria is hypothesized.}, }
@article {pmid24192831, year = {1992}, author = {Krecek, RC and Els, HJ and de Wet, SC and Henton, MM}, title = {Studies on ultrastructure and cultivation of microorganisms associated with zebra nematodes.}, journal = {Microbial ecology}, volume = {23}, number = {1}, pages = {87-95}, pmid = {24192831}, issn = {0095-3628}, abstract = {Nematodes recovered from the hindgut of zebras were examined with scanning and transmission electron microscopy for microorganisms. Microorganisms were observed attached to the posterior extremities of two groups of nematodes, atractids and cyathostomes. Novel techniques were used to culture the microorganisms, and these included rinses to reduce contamination from hindgut flora and the design of the culture media. Electron microscopy revealed a flat bacterium not previously observed, as well as small rods and segmented filamentous bacteria. Culturing techniques resulted in isolation of a Propionibacterium species.}, }
@article {pmid24192830, year = {1992}, author = {McGinness, S and Johnson, DB}, title = {Grazing of acidophilic bacteria by a flagellated protozoan.}, journal = {Microbial ecology}, volume = {23}, number = {1}, pages = {75-86}, pmid = {24192830}, issn = {0095-3628}, abstract = {A biflagellated protozoan was isolated from an acidic drainage stream located inside a disused pyrite mine. The stream contained copious amounts of "acid streamer" bacterial growths, and the flagellate was observed in situ apparently grazing the streamer bacteria. The protozoan was obligately acidophilic, growing between pH 1.8 and 4.5, but not at pH 1.6 or 5.0, with optimum growth between pH 3 and 4. It was highly sensitive to copper, molybdenum, silver, and uranium, but tolerated ferrous and ferric iron up to 50 and 25 mM, respectively. In the laboratory, the protozoan was found to graze a range of acidophilic bacteria, including the chemolithotrophs Thiobacillus ferrooxidans, Leptospirillum ferrooxidans, and the heterotroph Acidiphilium cryptum. Thiobacillus thiooxidans and Thiobacillus acidophilus were not grazed. Filamentous growth of certain acidophiles afforded some protection against being grazed by the flagellate. In mixed cultures of T. ferrooxidans and L. ferrooxidans, the protozoan isolate displayed preferential grazing of the former. The possibility of using acidophilic protozoa as a means of controlling bacteria responsible for the production of acid mine drainage is discussed.}, }
@article {pmid24192829, year = {1992}, author = {Strycek, T and Acreman, J and Kerry, A and Leppard, GG and Nermut, MV and Kushner, DJ}, title = {Extracellular fibril production by freshwater algae and cyanobacteria.}, journal = {Microbial ecology}, volume = {23}, number = {1}, pages = {53-74}, pmid = {24192829}, issn = {0095-3628}, abstract = {In order to study the ability of freshwater algae and cyanobacteria to form extracellular fibrils, a screening test using ruthenium red (RR) staining was carried out on 28 species. Five of these were examined for growth and production of fibrillar material in culture media of different phosphate (P;) contents. RR-staining and uronic acid determinations at various stages of algal growth were complemented by electron microscopy of the cells and of fibrillar material released into the medium. The lower Pi concentrations enhanced growth of Micrasterias radiata, Eremosphaera sp., and Microcystis aeruginosa, and had little or no effect on growth of a Xanthidium sp. and Scenedesmus quadricauda. Extracellular uronic acid production, which was higher in low Pi medium in M. radiata, M. aeruginosa, and Xanthidium sp., could reach levels of 50 mg/liter or more. Algae with high proportions of RR-positive cells (M. radiata, Eremosphaera sp., Xanthidium sp., and M. aeruginosa) produced high levels of slime-like material and distinct fibrils that were often seen attached to the cell surface and only slowly released into the medium. No such material was found in cultures (or supernatants) of Sc. quadricauda, which also produced relatively low amounts of polyuronic acids. Specific types of filaments, often forming "fascicles" with rectangular arrays of globular particles were observed by negative staining electron microscopy of some algal cultures. RR-positive material was also observed in the cytoplasm and on the cell walls and surfaces of M. radiata and M. aeruginosa.}, }
@article {pmid24192828, year = {1992}, author = {Dik, AJ and Fokkema, NJ and van Pelt, JA}, title = {Influence of climatic and nutritional factors on yeast population dynamics in the phyllosphere of wheat.}, journal = {Microbial ecology}, volume = {23}, number = {1}, pages = {41-52}, pmid = {24192828}, issn = {0095-3628}, abstract = {The role of saprophytic phyllosphere yeasts in removing aphid honeydew and other nutrients from wheat leaves was evaluated in growth cabinet experiments at different temperatures and relative humidities. Population densities of both pink and white yeasts (Sporobolomyces roseus and Cryptococcus laurentii, respectively) increased between 12 and 24°C, if nutrients were supplied. White yeast numbers increased rapidly at a constant vapor pressure deficit (VPD) of 0.10 kPa and alternating VPDs of 0.10 and 0.61 kPa (each 12 hours per day) but decreased at a constant VPD of 0.61 kPa. In growth cabinet experiments with aphids on wheat plants, the amount of aphid honeydew on the leaves was lower when yeast population densities were high. Addition of amino acids to leaves with honeydew had no effect on yeast population density or the rate of honeydew consumption. This indicated that low concentrations of amino acids in aphid honeydew are not a limiting factor for honeydew consumption by the yeasts. The naturally occurring saprophytes efficiently removed fructose, sucrose, and melezitose from the phyllosphere of field-grown wheat plants.}, }
@article {pmid24192827, year = {1992}, author = {Unanue, M and Ayo, B and Azúa, I and Barcina, I and Iriberri, J}, title = {Temporal variability of attached and free-living bacteria in coastal waters.}, journal = {Microbial ecology}, volume = {23}, number = {1}, pages = {27-39}, pmid = {24192827}, issn = {0095-3628}, abstract = {The temporal variability of the abundance and the incorporation of (3)H-thymidine and (14)C-glucose by attached and free-living bacteria, as well as their relation with environmental factors, were analyzed in a coastal marine ecosystem during a year. Both communities were quantitatively very different. Attached bacteria represented only 6.8% of the total bacterial abundance, whereas free-living bacteria represented 93.2%. The environmental factors most closely linked to the abundance and activity of free-living bacteria were temperature and the concentration of dissolved nutrients. Moreover, the free-living community showed similar temporal variations in abundance and in activity, with lower values in the cold months (from October to May). The attached community did not present the same pattern of variation as the free-living one. The abundance of the attached bacteria was mainly correlated to the concentration of particulate material, whereas their activity was correlated to temperature. We did not find a significant correlation between the abundance and the activity of the attached community. On the other hand, the activity per cell of the two communities did not present a clear temporal variation. Attached bacteria were more active than free-living ones in the incorporation of radiolabeled substrates on a per cell basis (five times more in the case of glucose incorporation and twice as active in thymidine incorporation). However, both communities showed similar specific growth rates. The results suggest that the two aquatic bacterial communities must not be considered as being independent of each other. There appears to be a dynamic equilibrium between the two communities, regulated by the concentrations of particulate matter and nutrients and by other environmental factors.}, }
@article {pmid24194346, year = {1991}, author = {Butow, B and Dan, TB}, title = {Effects of growth conditions of acetate utilization byRhodopseudomonas palustris isolated from a freshwater lake.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {317-328}, pmid = {24194346}, issn = {0095-3628}, abstract = {Rhodopseudomonas palustris, a purple non-sulfur bacterium, was recently found throughout the water column in Lake Kinneret. It was demonstrated to be of a versatile nature, growing under both aerobic and anaerobic conditions at different light intensities. A comparison of C-acetate uptake byR. palustris andChlorobium phaeobacterioides, a green sulfur bacterium, showed that, under identical growth conditions, C-acetate assimilation byR. palustris was greater. Furthermore, C-acetate uptake forR. palustris was greater than C-CO2 uptake at all light intensities. Depending on the prevailing conditions, acetate can be used byR. palustris as both an electron donor and carbon source. Malate synthase was used as an indicator of activity of the glyoxylic acid cycle. It was found that enzyme activity was higher (i.e., acetate was used mainly as a carbon source) under anaerobic conditions, in the dark, or in the absence of HCO3 (-). Acetate was used preferably as an electron donor under photosynthetic microaerophillic conditions.}, }
@article {pmid24194345, year = {1991}, author = {Shanker, R and Kaiser, JP and Bollag, JM}, title = {Microbial transformation of heterocyclic molecules in deep subsurface sediments.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {305-316}, pmid = {24194345}, issn = {0095-3628}, abstract = {Recently attempts have been made to establish the presence and to determine the metabolic versatility of microorganisms in the terrestrial deep subsurface at the Savannah River Plant, Aiken, SC, USA. Sediment samples obtained at 20 different depths of up to 526 m were examined to determine carbon mineralization under aerobic, sulfate-reducing, and methanogenic conditions. The evolution of(14)CO2 from radiolabelled glucose was observed under aerobic conditions in all sediments, whereas pyridine was transformed in 50% of the 20 sediments and indole was metabolized in 85% of the sediments. Glucose mineralization in certain sediments was comparable to that in the surface environment. Sulfate was reduced in only five sediments, and two were carbon limited. Methane production was detected in ten sediments amended with formate only after long-term incubations. The transformation of indole and pyridine was only rarely observed under sulfate-reducing conditions and was never detected in methanogenic incubations. This study provides information concerning the metabolic capability of both aerobic and anaerobic microorganisms in the deep subsurface and may prove useful in determining the feasibility of microbial decontamination of such environments.}, }
@article {pmid24194344, year = {1991}, author = {Hazen, TC and Jiménez, L and López de Victoria, G and Fliermans, CB}, title = {Comparison of bacteria from deep subsurface sediment and adjacent groundwater.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {293-304}, pmid = {24194344}, issn = {0095-3628}, abstract = {Samples of groundwater and the enclosing sediments were compared for densities of bacteria using direct (acridine orange direct staining) and viable (growth on 1% PTYG medium) count methodology. Sediments to a depth of 550 m were collected from boreholes at three sites on the Savannah River Site near Aiken, South Carolina, using techniques to insure a minimum of surface contamination. Clusters of wells screened at discreet intervals were established at each site. Bacterial densities in sediment were higher, by both direct and viable count, than in groundwater samples. Differences between direct and viable counts were much greater for groundwater samples than for sediment samples. Densities of bacteria in sediment ranged from less than 1.00×10(6) bacteria/g dry weight (gdw) up to 5.01 ×10(8) bacteria/gdw for direct counts, while viable counts were less than 1.00×10(3) CFU/gdw to 4.07×10(7) CFU/gdw. Bacteria densities in groundwater were 1.00×10(3)-6.31×10(4) bacteria/ml and 5.75-4.57×10(2) CFU/ml for direct and viable counts, respectively. Isolates from sediment were also found to assimilate a wider variety of carbon compounds than groundwater bacteria. The data suggest that oligotrophic aquifer sediments have unique and dense bacterial communities that are attached and not reflected in groundwater found in the strata. Effective in situ bioremediation of contaimination in these aquifers may require sampling and characterization of sediment communities.}, }
@article {pmid24194343, year = {1991}, author = {Gessner, MO and Bauchrowitz, MA and Escautier, M}, title = {Extraction and quantification of ergosterol as a measure of fungal biomass in leaf litter.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {285-291}, pmid = {24194343}, issn = {0095-3628}, abstract = {Homogenization in methanol, two hours of refluxing in methanol, and direct saponification in alcoholic KOH were equally efficient at extracting ergosterol from fungally colonized leaf litter. A 25-cm Li-Chrosphere RP18 HPLC column gave excellent resolution of ergosterol in leaf extracts. Recovery of ergosterol added to leaf powder and methylcellulose ranged between 88 and 97%, but differences among leaf species were not significant. Conditions for liquid-liquid extraction from saponified extracts are critical in ergosterol analysis. Dark storage of samples does not lead to dramatic losses of ergosterol. Extensive sample clean up before HPLC injection is nonessential.}, }
@article {pmid24194342, year = {1991}, author = {Scherer, S and Zhong, ZP}, title = {Desiccation independence of terrestrialNostoc commune ecotypes (cyanobacteria).}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {271-283}, pmid = {24194342}, issn = {0095-3628}, abstract = {The subspeciesNostoc commune var.flagelliforme andN. commune var.commune are found in China (Ningxia Province, Inner Mongolia) as two morphologically different ecotypes of the desiccation-independent cyanobacteriumN. commune. The first ecotype, but not the second, colonizes arid areas. Various biochemical parameters and water dependence of photosynthesis and nitrogen fixation were compared for both ecotypes. Different patterns of water stress proteins were found in the two ecotypes. Repeated desiccation resulted in an enhanced desiccation independence for photosynthesis and, in the case of the ecotypecommune, for nitrogen fixation. The different response of nitrogenase of both ecotypes towards repeated cycles of rewetting and desiccation under conditions simulating the natural environment is discussed in terms of the energy balance of the colonies that are adapted to different environmental conditions.}, }
@article {pmid24194341, year = {1991}, author = {Bashan, Y}, title = {Airborne transmission of the rhizosphere bacteriumAzospirillum.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {257-269}, pmid = {24194341}, issn = {0095-3628}, abstract = {In controlled environments, plants inoculated withAzospirillum brasilense caused the contamination of noninoculated plants via air transmission. This was detected up to 6 m from the inoculation source. In the temperate agricultural zone studied in field experiments, localAzospirillum strains were detected year-round. Other diazotrophs showed a similar distribution pattern. It is proposed that (1) contamination fromAzospirillum-inoculated plants may occur via airborne bacteria, (2) local azospirilla and other diazotrophs have an airborne phase in temperate agricultural zones, and (3) because of the existence of an airborne phase for Gram-negative rhizosphere bacteria, inoculation presents a risk of uncontrolled airborne contamination.}, }
@article {pmid24194340, year = {1991}, author = {Atlas, RM and Horowitz, A and Krichevsky, M and Bej, AK}, title = {Response of microbial populations to environmental disturbance.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {249-256}, pmid = {24194340}, issn = {0095-3628}, abstract = {Taxonomic and genetic diversities of microbial communities disturbed by chemical pollutants were lower than in undisturbed reference communities. The dominant populations within the disturbed communities had enhanced physiological tolerances and substrate utilization capabilities, indicating that generalized physiological versatility is an adaptive characteristic of populations that successfully compete within disturbed communities.}, }
@article {pmid24194339, year = {1991}, author = {Semenov, AM}, title = {Physiological bases of oligotrophy of microorganisms and the concept of microbial community.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {239-247}, pmid = {24194339}, issn = {0095-3628}, abstract = {Three groups of physiological processes in microorganisms are considered the physiological basis of oligotrophy: the greater substrate affinity of the oligotrophs' transport systems, efficient or "economical" metabolism, and existence of a "master reaction" or "rate-determining steps" controlling the rate of metabolism. Heterotrophic microorganisms are divided into three unequal groups according to "reaction norma." Two groups representing the extremes are small groups with the "narrow" reaction norma, regarding the concentrations and structure of the assimilated organic compounds and variability limits of the physiological characteristics mentioned above. The third, intermediate group includes the majority of microorganisms with the "wide" reaction norma.}, }
@article {pmid24194338, year = {1991}, author = {Mitchell, JG}, title = {The influence of cell size on marine bacterial motility and energetics.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {227-238}, pmid = {24194338}, issn = {0095-3628}, abstract = {The influence of Brownian motion on marine bacteria was examined. Due to their small size, marine bacteria rotate up to 1,400 degrees in one second. This rapid rotation makes directional swimming difficult or impossible, as a bacterium may point in a particular direction for only a few tens of milliseconds on average. Some directional movement, however, was found to be possible if swimming speed is sufficiently great, over approximately 100 μm sec(-1). This led to the testable hypothesis that marine bacteria with radiii less than about 0.75 μm should exceed this speed. The result of the increased speed is that marine bacteria may spend in excess of 10% of their total energy budget on movement. This expenditure is 100 times greater than values for enteric bacteria, and indicates that marine bacteria are likely to be immotile below critical size-specific nutrient concentrations.}, }
@article {pmid24194337, year = {1991}, author = {Smith, HL and Waltman, P}, title = {The gradostat: A model of competition along a nutrient gradient.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {207-226}, pmid = {24194337}, issn = {0095-3628}, abstract = {The general mathematical theory of the gradostat is presented for two competitors. The gradostat provides a mechanism for studying competition along a nutrient gradient. In the two vessel case, the results are complete and the conditions are testable. In then-vessel case, the relevant conditions are stated in terms of the stability modulii of certain matrices and are testable for any specific case.}, }
@article {pmid24194336, year = {1991}, author = {Simonsen, L}, title = {The existence conditions for bacterial plasmids: Theory and reality.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {187-205}, pmid = {24194336}, issn = {0095-3628}, abstract = {Bacteria abound with conjugative and nonconjugative plasmids that often carry genes determining a number of environmental adaptations. Plasmids may also encode genes that enable them to transmit themselves infectiously to new host cells, by conjugation or mobilization. The question of whether plasmids can be maintained in a bacterial community as parasitic DNA, that is, while conferring a selective disadvantage to their host, serves as a basic hypothesis in theoretical studies of the population biology of plasmids. The conditions necessary for the establishment and maintenance of plasmids have been determined analytically for the simplest possible models. Based on these a priori conditions, on some reconsiderations and extensions of these models, and on recent estimates of transfer rates of liquid and surface bacterial populations, it will be argued that within a bacterial population, a parasitic lifestyle is unlikely for most naturally occurring plasmids. This result raises anew the problem of how cryptic plasmids are maintained and why plasmids encode costly and elaborate genes for horizontal transfer.}, }
@article {pmid24194335, year = {1991}, author = {Lauffenburger, DA}, title = {Quantitative studies of bacterial chemotaxis and microbial population dynamics.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {175-185}, pmid = {24194335}, issn = {0095-3628}, abstract = {Although there is a long history of conjecture regarding the role and significance of bacterial chemotaxis in microbial ecology, only recently has a significant body of work appeared attempting to address this issue. The purpose of this paper is to provide a concise overview of this work, which combined mathematical modeling of bacterial population migration and experimental measurement of the model parameters with modeling of competitive microbial population dynamics in a nonmixed environment. Predictions from the population dynamics models, based on experimental estimates of the various motility and growth parameter values, are related to the small number of experimental observations available to date dealing with the effects of bacterial motility on competition in a nonmixed environment. Current results indicate that cell motility and chemotaxis properties can be as important to population dynamics as cell growth kinetic properties, so that greater attention to this aspect of microbial behavior is warranted in future studies of microbial ecology.}, }
@article {pmid24194334, year = {1991}, author = {Goodwin, S and Giraldo-Gomez, E and Mobarry, B and Switzenbaum, MS}, title = {Comparison of diffusion and reaction rates in anaerobic microbial aggregates.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {161-174}, pmid = {24194334}, issn = {0095-3628}, abstract = {The ability of hydrogen diffusion to account for the rates of methane production in microbial aggregates was studied in a defined coculture consisting of a sulfate reducer grown as a syntrophic hydrogen producer in the absence of sulfate and a methanogen. The hydrogen uptake kinetics of the methanogen were determined using the infinite dilution technique. The maximum hydrogen uptake velocity was 7.1 nmol/min/μg protein and the half saturation constant for hydrogen uptake was 386 nmol/liter. A threshold of 28 nmol/liter below which no further hydrogen consumption occurred was observed. The reconstituted co-culture was shown to produce methane at rates similar to mixed culture enrichments grown on lactate. The diffusion model demonstrated that for the particular system studied, the rates of hydrogen diffusion could account for the overall rate of methane production.}, }
@article {pmid24194333, year = {1991}, author = {Fredrickson, AG}, title = {Segregated, structured, distributed models and their role in microbial ecology: A case study based on work done on the filter-feeding ciliateTetrahymena pyriformis.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {139-159}, pmid = {24194333}, issn = {0095-3628}, abstract = {Microbial populations are composed of individual organisms each of which, if environmental circumstances are favorable, is undergoing change of its internal state through the operation of the set of processes that we call the cell cycle. The rate of progression through the cycle is subject to internal controls as well as external influences, and exhibits random as well as deterministic features. Microorganisms of the same species in different stages of the cell cycle have different internal states, and thus, the operation of the cell cycle is by itself sufficient to produce a distribution of states among the individual organisms of a population. In turn, the distribution of states produces distributions of the rates at which the cells of a population carry on their activities. Mathematical models of microbial growth that take the operation of the cell cycle and its consequences into account are more complicated than the kinds of models that are often used in microbial ecology. This paper gives some account of the nature, formulation, and uses of complex growth models. The account is illustrated by work done by the author and his collaborators H. M. Tsuchiya and more recently F. Srienc, as well as by others, on the filter-feeding ciliateTetrahymena pyriformis.}, }
@article {pmid24194332, year = {1991}, author = {Ford, RM and Phillips, BR and Quinn, JA and Lauffenburger, DA}, title = {Stopped-flow chamber and image analysis system for quantitative characterization of bacterial population migration: Motility and chemotaxis ofEscherichia coli K12 to fucose.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {127-138}, pmid = {24194332}, issn = {0095-3628}, abstract = {The directed movement of a bacterial population in response to a chemical gradient is known as bacterial chemotaxis and plays a critical role in the distribution and dynamic interaction of bacterial populations. A quantitative characterization of the chemotactic response in terms of intrinsic cell properties is necessary for making reliable predictions about the migratory behavior of bacterial populations within the environment.The design of the stopped-flow diffusion chamber (SFDC) provides a well-characterized chemical gradient and reliable method for measuring bacterial migration behavior. During flow through the chamber a step change in the chemical concentration is imposed on a uniform suspension of bacteria. Once flow is stopped a transient chemical gradient forms due to diffusion; bacteria respond by forming a band of high cell density that travels toward higher concentrations of the attractant. Sequential observations of bacterial spatial distributions over a period of about ten minutes are recorded on photomicrographs. Computer-aided image analysis of the photographic negatives converts light-scattering information to a digital representation of the bacterial density profiles. A mathematical model is used to quantitatively characterize these observations in terms of intrinsic cell parameters: a chemotactic sensitivity coefficient, χ0, from the aggregate cell density accumulated in the band and a random motility coefficient, μ0, from population dispersion in the absence of a chemical gradient.Using the SFDC assay and an individual cell-based mathematical model we successfully determined values for both of these population parameters forEscherichia coli K12 responding to fucose. The values we obtained were μ0=1.1 ± 0.4 x 10(-5) cm(2)/sec and χ0=8 ± 3 x 10(-5) cm(2)/sec. These parameters will be useful for predicting population behavior in application systems such as biofilm development, population dynamics of genetically-engineered bacteria released into the environment, and in situ bioremediation technologies.}, }
@article {pmid24194331, year = {1991}, author = {Christian, RR and Wetzel, RL}, title = {Synergism between research and simulation models of estuarine microbial food webs.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {111-125}, pmid = {24194331}, issn = {0095-3628}, abstract = {Construction of mathematical simulation models helps to organize current information and extend inferences from available data. During the past two decades, microbial ecology has undergone rapid developments in both quantity and quality of available data. In particular, considerable advances have been made in our knowledge of microbial food web dynamics in the Duplin River watershed at Sapelo Island, Georgia. Here we provide examples of how modeling and microbial ecology have interfaced. In the early 1970s, construction of a 14-compartment model of carbon flow through a salt marsh ecosystem aided in directing method development and field experiments on the sediment microbial community. In turn, the results of field experiments corroborated the model's postulated controls on the community. Also, during the past 12 years we have developed a series of simulation models reflecting the growing information on the aquatic microbial food web. Early models provided evidence for the microbial loop but illustrated the paucity of knowledge concerning controls for bacterial growth on detritus. Results from newer methods in microbial ecology and studies from the Duplin River have allowed us to construct a model which provides realistic simulations but is also highly sensitive to certain parameter value changes (e.g., in organic matter availability and grazing by protozoans). Thus improvements in model structure and corroboration of the models with extant data have been closely tied to methodological and conceptual advances in microbial ecology. The relationship is viewed as synergistic, as needs for model parameter values and equation forms have directed further development of methods, experimentation, and field observations.}, }
@article {pmid24194330, year = {1991}, author = {Hoppensteadt, F and Lauffenburger, DA and Waltman, P}, title = {Editorial.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {109-110}, doi = {10.1007/BF02540217}, pmid = {24194330}, issn = {0095-3628}, }
@article {pmid24194329, year = {1991}, author = {Elmholt, S}, title = {Side effects of propiconazole (tilt 250 EC(TM)) on non-target soil fungi in a field trial compared with natural stress effects.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {99-108}, pmid = {24194329}, issn = {0095-3628}, abstract = {The present study was performed as a dose-response field experiment using a trade marked formulation of the ergosterol biosynthesis inhibiting fungicide, propiconazole, applied at the recommended and ten times the recommended application rates. The soil dilution plate method was used to isolate fungi from 0-1 and 1-2 cm soil depth. Soil samples were taken 10 times during the period from May 22 to August 11, 1986. The numbers of yeasts and filamentous fungi were enumerated, the latter includingCladosporium andPenicillium, which were also enumerated separately. The fluctuations in fungal occurrence due to the propiconazole treatment were smaller than seasonal fluctuations, these most likely being caused by variations in the soil matric potential and by soil invasion of phyllosphere fungi. Fungicide treatment had significant inhibitory effects on the filamentous fungi, especially on theCladosporium, whereas no significant effects were found on the yeasts and onPenicillium spp. From an ecotoxicological point of view, it is important that the effects were considerably delayed, with respect to the time of fungicide application.}, }
@article {pmid24194328, year = {1991}, author = {Russell, NJ and Anderson, DJ and Day, MJ and White, GF}, title = {Colonization of biofilms by bacteria capable of biodegrading sodium dodecyl sulphate (SDS) at clean and polluted riverine sites.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {85-98}, pmid = {24194328}, issn = {0095-3628}, abstract = {Biofilm formation on presterile slate-discs placed at a pristine source site and at three polluted sites located upstream from, at, and down-stream from a sewage-works outfall in a South Wales river, was monitored over 14 days. Viable bacterial cell densities in biofilms increased with time at all sites but more rapidly at the polluted sites, and stabilized after 1-4 days at levels equal to those of stones indigenous to the corresponding sites, and similar to those seen in other comparable pristine and polluted rivers. Biofilm cell densities were elevated about 1,000-fold at the sewage works outfall compared with the site immediately upstream. Downstream from the outfall, the cell densities were intermediate between the upstream and outfall values. Epilithon resuspended from the slates during colonization was tested for its capacity to biodegrade the surfactant sodium dodecyl sulphate (SDS) in die-away tests. No biodegradation of this common pollutant was observed for the samples from the pristine source. In contrast, even after only 1 day, all polluted sites produced samples capable of biodegrading SDS. Longer exposure in the river led to more rapid onset of biodegradation in the die-away tests, indicating an adaptation mechanism(s). Die-away kinetics were fitted by computerized non-linear regression analysis to one of several models. The model of best fit involved biodegradation of SDS by a bacterial population growing at the expense of endogenous carbon. The regression parameter reflecting SDS-degrading activity of the epilithic samples increased markedly during Days 0-4 for all three polluted sites. The stabilized values (Days 4-14) increased from the upstream site to the outfall, then decreased to intermediate values downstream. Although this pattern corresponded to the changes in viable cell numbers, the effect of the sewage input was less marked for the SDS-degrading activities than for bacterial cell densities. In addition, there was little variation in growth characteristics throughout colonization at all three polluted sites. Collectively the results indicate that the observed adaptation during exposure in the river is attributable to colonization of the epilithon by an existing SDS-degrading population, rather than the acquisition or adaptation of this biodegradative capability.}, }
@article {pmid24194327, year = {1991}, author = {Paszko-Kolva, C and Shahamat, M and Yamamoto, H and Sawyer, T and Vives-Rego, J and Colwell, RR}, title = {Survival ofLegionella pneumophila in the aquatic environment.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {75-83}, pmid = {24194327}, issn = {0095-3628}, abstract = {Survival ofLegionella pneumophila SG 1 in seawater and river water was assessed using plate counts on buffered charcoal yeast extract agar amended with α-ketoglutarate (BCYEα) and [(3)H]thymidine-labeling. The [(3)H]thymidine-labeling method for assessing survival ofL. pneumophila in aquatic environments was compared with viable counts, direct fluorescent microscopy (DFA), and acridine orange direct counts (AODC). Protozoa were isolated from the samples employed in the study and identified by characteristic trophozite and cyst morphology. Selective filtration employing 2.0 μm Nucleopore filters was used to determine the effect of grazing on survival ofL. pneumophila in seawater and river water.Legionella viability as measured by plate counts (CFU/ml), declined to a greater extent than cell lysis, assessed by thymidine, DFA, and AODC counts, suggesting thatL. pneumophila survives in aquatic habitats to a greater extent than revealed through culturable counts.}, }
@article {pmid24194326, year = {1991}, author = {McFeters, GA and Terzieva, SI}, title = {Survival ofEscherichia coli andYersinia enterocolitica in stream water: Comparison of field and laboratory exposure.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {65-74}, pmid = {24194326}, issn = {0095-3628}, abstract = {Experiments were done to compare the influence of three aquatic exposure methods on the behavior of pathogenic and nonpathogenic enteric bacteria (Yersinia enterocolitica andEscherichia coli). Bacterial suspensions were exposed to stream water in membrane diffusion chambers in situ as well as in the laboratory using a large vessel of stream water and in enclosed bottles. The persistence of culturability of the bacterial suspensions was dependent upon the method of aquatic exposure. This difference was most apparent during the initial six days of each experiment. A steady decline in colony forming units was seen after a short stationary period in chambers in situ, while there was an abrupt increase in bacteria within chambers exposed in the laboratory. A rapid initial decrease was observed in the experimental variation using bottles, accompanied by higher levels of injury inE. coli and reduced expression of plasmid-borne virulence phenotypes inY. enterocolitica. However, there were no changes in the plasmid profiles of either organism throughout the 21-day duration of the experiments. In addition, the survival and injury of pathogenic and nonpathogenic strains of both test bacteria was very similar with aquatic exposure. These results suggest that the response of enteric bacteria in aquatic environments is influenced by experimental design as well as other factors and that the comparison of survival data should only be attempted when similar methods are used.}, }
@article {pmid24194325, year = {1991}, author = {O'Donohue, MJ and Moriarty, DJ and Rae, IC}, title = {Nitrogen fixation in sediments and the rhizosphere of the seagrassZostera capricorni.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {53-64}, pmid = {24194325}, issn = {0095-3628}, abstract = {Rates of nitrogen fixation in seagrass beds (Zostera capricorni) were determined with(15)N and reduction of acetylene in intact cores of sediment and seagrass. There was good agreement in the results from the two techniques, with a molar ratio of 3∶1.9 ethylene: ammonia produced. Fixed nitrogen was rapidly utilized by the plants, with significant amounts of(15)N found in the roots and rhizomes and 50% of fixed(15)N apparently translocated to the leaves. Rates of fixation were high in summer (25 to 40 mg N m(-2) day(-1)) and lower in winter (10 mg N m(-2) day(-1)) and were estimated to supply between one-third and one-half of the nitrogen requirements of the seagrass. Rates of nitrogen fixation were greater in the light than in the dark, and in cores of intact seagrass than in defoliated cores, indicating that the bacteria were dependent on organic compounds secreted by the plants.}, }
@article {pmid24194324, year = {1991}, author = {Boon, PI}, title = {Bacterial assemblages in rivers and billabongs of Southeastern Australia.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {27-52}, pmid = {24194324}, issn = {0095-3628}, abstract = {Billabongs, lentic waterbodies common to the floodplain of Australian rivers, differ considerably from the lotic riverine environment in terms of hydrology, physiochemical characteristics, and biological assemblages present. As little is known regarding the bacterial ecology of billabong habitats, a comparison was made of the bacterial assemblages in the water column of seven paired river/billabong sites in the Murray-Darling Basin of southeastern Australia. Billabongs supported larger populations of bacteria (1-157×10(9) cells liter(-1); 11-10,270 μg C liter(-1)) than did rivers (1-10×10(9) cells liter(-1); 6-143 μg C liter(-1)). Phospholipid analyses confirmed that billabongs (14-111 μg phospholipid fatty acid liter(-1)) had larger bacterial populations than rivers (<12 μg liter(-1)). Bacterial production, measured with(3)H-leucine, was also greater in billabongs (0.28-3.05 μg C liter(-1) hour(-1)) than rivers (0.05-0.62 μg C liter(-1) hour(-1)). Production calculated from the frequency of dividing cells confirmed this conclusion, and suggested bacterial production in some billabongs could exceed 100 μg C liter(-1) hour(-1). An INT-formazan method indicated that usually <25% of bacterial cells were active in either habitat, but this was probably an underestimate of the bona fide value. Turnover times of glucose were usually shorter in billabongs, and the cell-specific activity greater for billabong than river assemblages. The factors most likely to be responsible for the differences between the bacterial assemblages in rivers and billabongs relate to hydrological regime and the availability of organic carbon substrates.}, }
@article {pmid24194323, year = {1991}, author = {Jones, GW and Baines, L and Genthner, FJ}, title = {Heterotrophic bacteria of the freshwater neuston and their ability to act as plasmid recipients under nutrient deprived conditions.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {15-25}, pmid = {24194323}, issn = {0095-3628}, abstract = {Significantly higher numbers of Gram-negative heterotrophic bacteria were present at the air-water interface (neston) of freshwater lakes than in the bulk water. Neuston bacteria were distinguished as a population distinct from bacteria in the bulk water by a higher incidence of pigmented colony types and significantly greater levels of multiple resistance to antibiotics and heavy metals. The incidence of plasmids in 236 neuston and 229 bulk water strains were similar (14 and 16.2%, respectively). Nine of 168 plasmid-free strains and 2 of 14 plasmid carrying strains, isolated from both bulk water and neuston, acted as recipients of plasmid R68.45 in plate matings with aPseudomonas aeruginosa donor strain PAO4032 at 21°C, but at frequencies below that of matings with a restriction-minus recipient strain ofP. aeruginosa, strain PAO1168. In a model system composed of nutrient-free synthetic lake water, plasmid R68.45 was shown to transfer betweenP. aeruginosa strains at frequencies between 10(-3) and 10(-5). Transconjugants were detected about 100 times more frequently at the interface than in the bulk water, which in part reflected a greater enrichment of the donor at this site. None of the aquatic isolates were able to act as recipients of plasmid R68.45 in this model system with strain PAO4032 as donor. The results suggest that under nutrient deprived conditions, the spread of plasmid R68.45 and similar plasmids by lateral transfer into this particular aquatic population would be a rare event.}, }
@article {pmid24194322, year = {1991}, author = {Wimpenny, JW and Abdollahi, H}, title = {Growth of mixed cultures ofParacoccus denitrificans andDesulfovibrio desulfuricans in homogeneous and in heterogeneous culture systems.}, journal = {Microbial ecology}, volume = {22}, number = {1}, pages = {1-13}, pmid = {24194322}, issn = {0095-3628}, abstract = {Obligate aerobes and anaerobes coexist closely in natural ecosystems. One species representative of each class (Desulfovibrio desulfuricans andParacoccus denitrificans) were selected for investigation in different laboratory growth systems. When incubated together, the aerobe protected the anaerobe against oxygen poisoning allowing the latter to grow and to reduce sulfate. When gas phase oxygen tension was systematically altered in stirred batch cultures, both species grew over a broad range of oxygen concentrations. Similar experiments in a chemostat indicated that conditions were far more exacting. No steady state was possible; however, at one critical oxygen tension the two species entered a stable oscillating cycle that lasted for 12 days. When the two organisms were grown in a gradostat in opposing gradients of sulfate plus oxygen and lactate, they coexisted but at different positions in the system. The actual position of the sulfate reducer was determined by the sulfate concentration in the reservoir.}, }
@article {pmid24194216, year = {1991}, author = {Harris, JM and Seiderer, LJ and Lucas, MI}, title = {Gut microflora of two saltmarsh detritivore thalassinid prawns,Upogebia africana andCallianassa kraussi.}, journal = {Microbial ecology}, volume = {21}, number = {1}, pages = {277-296}, pmid = {24194216}, issn = {0095-3628}, abstract = {The presence and digestive capabilities of bacteria associated with the digestive systems and habitats of two saltmarsh-burrowing detritivore thalassinid prawns (Upogebia africana andCallianassa kraussi) was examined.U. africana is a filter-feeding prawn inhabiting muddy deposits, whereasC. kraussi, a deposit feeder, inhabits coarser more sandy deposits. Scanning electron microscopy was used to examine the gut lining and associated microflora and the nature of the ingested food of both prawns. The gut contents of both prawns included plant fragments, fragmented diatoms, partially degraded protozoa, and bacteria attached to organic matter. In bothU. africana andC. kraussi the midgut walls and gut contents were extensively coated by filamentous bacteria which were absent in the hindgut. The hindgut epithelium ofU. africana was coated by mats of rodshaped bacteria, not reported in marine invertebrates previously. The digestive glands of both species contained bacteria in the lumen. Isolation of gut and habitat bacteria suggests that bothU. africana andC. kraussi maintain a gut microflora distinct from the habitat microflora. Bacteria isolated from the guts of both species of prawn differed from those isolated from their respective habitats with regards to both the genera isolated and their digestive capabilities. The dominant genera isolated from the guts of bothU. africana andC. kraussi wereVibrio andPseudomonas, with an unidentified fermenter andPseudomonas, respectively dominating in the digestive glands. Bacteria of the genusAcinetobacter dominated the isolates from the habitats of both species of prawn. Resident gut bacteria isolated from the guts of both species of prawn exhibited lipase, protease, chitinase, and lysozyme, but not cellulase activity, and may contribute to nitrogen aquisition by the prawns. Isolates from the prawns' habitat exhibited alginase, gelatinase, and lipase activity, a few (3%) fromU. africana habitat having cellulases. In this study a distinction between resident gut bacteria and transient gut bacteria was made. Results suggest that some habitat bacteria remain viable in the guts ofU. africana, but not inC. kraussi.}, }
@article {pmid24194215, year = {1991}, author = {Underwood, GJ}, title = {Note: Colonization and invasion of leaves of the aquatic macrophyteCeratophyllum demersum L. by epiphytic bacteria.}, journal = {Microbial ecology}, volume = {21}, number = {1}, pages = {267-275}, pmid = {24194215}, issn = {0095-3628}, abstract = {The colonization of leaves of the aquatic macrophyteCeratophyllum demersum L. by epiphytic bacteria, and the hypothesis that bacterial invasion causes leaf senescence, was studied using transmission and scanning electron microscopy and light microscopy. Population densities of epiphytic bacterial communities onCeratophyllum leaves were positively correlated with leaf age. Initial settlement of bacteria on young leaves appeared to favour the boundaries between epidermal cells. On older leaves, large populations of bacteria were present over the whole surface. One third of senescentCeratophyllum leaves examined by transmission electron microscopy showed signs of bacterial invasion. Of these, up to 54% of the leaf's epidermal cells contained bacteria. Areas of cell wall degradation were associated with invasive bacteria in senescent leaves. In healthy, nonsenescent leaves, no bacterial invasion was observed. These results suggest that epiphytic bacteria did not cause leaf senescence but probably colonized the internal tissues of leaves once senescence had occurred.}, }
@article {pmid24194214, year = {1991}, author = {Palmer, RJ and Siebert, J and Hirsch, P}, title = {Biomass and organic acids in sandstone of a weathering building: Production by bacterial and fungal isolates.}, journal = {Microbial ecology}, volume = {21}, number = {1}, pages = {253-266}, pmid = {24194214}, issn = {0095-3628}, abstract = {Ten fungal and nine bacterial strains were isolated from a weathering sandstone building. Their growth, organic acid production, and acidification capacity were assessed in culture under nutritional conditions similar to those in situ. Biomass (10-50 nmol phospholipid-PO4g(-1)) within the rock was small compared to soils. The isolated organisms were able to produce high amounts of those acids found in the sandstone, but acid production did not cause a drastic reduction in culture pH. It is suggested that the importance of acidification in microbial degradation of sandstone has been overestimated and that, under in situ pH and nutritional conditions, cation chelation by microbially produced organic acid anions may be more relevant to the weathering process.}, }
@article {pmid24194213, year = {1991}, author = {Kämpfer, P and Steiof, M and Dott, W}, title = {Microbiological characterization of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria.}, journal = {Microbial ecology}, volume = {21}, number = {1}, pages = {227-251}, pmid = {24194213}, issn = {0095-3628}, abstract = {Seven soil samples and seven groundwater samples from a site contaminated with fuel-oil were investigated using several chemical and microbiological techniques. In soil samples, 500 to 7,500 mg/kg of total hydrocarbons were found. These samples contained no n-alkanes but iso- and branched chain alkanes. No polychlorinated biphenyls could be detected. Microbiological investigations included estimations of total cell counts, viable cell counts on different media, and numbers of methylotrophic, denitrifying, sulphate reducing, anaerobic (with the exception of methanogenic organisms), and hydrocarbon degrading bacteria. Viable and hydrocarbon degrading bacteria were found in all samples. A total of 1,366 pure cultures was characterized morphologically and physiologically and identified by numerical identification using a data base of more than 4,000 reference strains. Groundwater samples were dominated by gram-negative bacteria of the generaPseudomonas, Comamonas, Alcaligenes, andAcinetobacter, which were also found in soil samples. In addition, more grampositive bacteria belonging to the generaArthrobacter, Nocardia, andBacillus could be isolated from soil samples.}, }
@article {pmid24194212, year = {1991}, author = {Sime-Ngande, T and Bourdier, G and Amblard, C and Pinel-Alloul, B}, title = {Short-term variations in specific biovolumes of different bacterial forms in aquatic ecosystems.}, journal = {Microbial ecology}, volume = {21}, number = {1}, pages = {211-226}, pmid = {24194212}, issn = {0095-3628}, abstract = {Short-term and spatial fluctuations in specific biovolumes (volume x cell(-1)) of different morphological categories of planktonic bacteria were estimated microscopically. Samples were taken from two lakes occurring in two different climatic systems: Lake Aydat (France) and Lake Cromwell (Canada). The study was done in summer, using 24-hour cycles of sampling.Due to their large size, the specific volume of filamentous bacteria constituted, on average, the major part (>70%) of the total specific volume of all bacterial forms considered. Greatest variations in specific biovolumes were recorded for filamentous bacteria (coefficients of variation ranged from 16 to 109%). These variations were more pronounced in the oxygenated and microaerophilic strata (DOC ≈1.5 mg liter(-1)). Fluctuations in cell volume were high (coefficients of variation =12-80%) for coccal bacteria, whereas no marked fluctuations were found for the rod and vibrio bacteria (coefficients of variation =4-10%).Evidence of diel patterns of cell volume of filamentous bacteria is provided. These cells displayed their maximum size during the day until early night, indicating cell division was occurring at night. Homogeneous circadian patterns were not provided by specific volume variations of coccal, rod, and vibrio bacteria.Statistical relationships between bacterial specific biovolumes and the biotic and abiotic parameters considered are discussed.}, }
@article {pmid24194211, year = {1991}, author = {Zimmerman, WJ and Culley, DE}, title = {Genetic variation at theapcAB,cpcAB,gvpA1, andnifH loci and in DNA methylation among N2-fixing cyanobacteria designatedNostoc punctiforme.}, journal = {Microbial ecology}, volume = {21}, number = {1}, pages = {199-209}, pmid = {24194211}, issn = {0095-3628}, abstract = {Genetic similarity among cyanobacteria of a morphological subgroup ofNostoc was evaluated through a comparison of several specific genes and the extent of DNA methylation. Four of six cyanobacteria were originally cultured from facultative symbioses with higher plants (Gunnera andEncephalartos); these and one free-living isolate had been identified or reputed to beN. punctiforme. No consistent correlation to species or symbiotic history was found from DNA hybridizations to genes coding for phycocyanin (cpcAB), allophycocyanin (apcAB), gas vesicle protein (gvpA1), and dinitrogenase reductase (nifH). One gene (gvpC) was not present, andgvpA1 was a single-copy gene in all strains. The gas vesicle genes were concluded to be potentially useful for broadly characterizingNostoc or at least this subgroup. Incubations ofNostoc genomic DNA with 22 restriction endonucleases indicated a high degree of methylation and similarity of its methylated DNA to that of other heterocystous cyanobacteria. The genetic variation of theNostoc isolates was judged to reflect primarily different soil origins.}, }
@article {pmid24194210, year = {1991}, author = {Liesack, W and Weyland, H and Stackebrandt, E}, title = {Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria.}, journal = {Microbial ecology}, volume = {21}, number = {1}, pages = {191-198}, pmid = {24194210}, issn = {0095-3628}, abstract = {The 16S rDNA genes of an apparently pure culture of a psychrophilic and strict barophilic bacterium (WHB 46) were studied by PCR-mediated amplification and cloning into phage M13 mp18. Sequence analysis of five individual clones revealed the presence of two different 16S rDNA types. The homology value of 90% indicates that culture WHB 46 is actually composed of two closely related species (WHB 46-1 and 46-2). Both strains are members of the γ-subdivision of proteobacteria. Analysis of a sixth clone (WHB 46-1/2) leads to the conclusion that it represents a 16S rDNA hybrid molecule assembled during the PCR reaction. This hypothesis was confirmed by secondary structure analysis of the chimeric rDNA. The appearance of such hybrid molecules point to a potential risk in studies on the diversity of bacterial populations by analysis of rDNA pattern via PCR-mediated amplification because they suggest the existence of organisms that do not actually exist in the sample investigated.}, }
@article {pmid24194209, year = {1991}, author = {Bolton, H and Fredrickson, JK and Thomas, JM and Li, SM and Workman, DJ and Bentjen, SA and Smith, JL}, title = {Field calibration of soil-core microcosms: Ecosystem structural and functional comparisons.}, journal = {Microbial ecology}, volume = {21}, number = {1}, pages = {175-189}, pmid = {24194209}, issn = {0095-3628}, abstract = {Microcosms containing intact soil-cores are a potential biotechnology risk assessment tool for assessing the ecological effects of genetically engineered microorganisms before they are released to the field; however, microcosms must first be calibrated to ensure that they adequately simulate key field parameters. Soil-core microcosms were compared with the field in terms of ecological response to the introduction of a large inoculum of a rifampicin-resistant rhizobacterium,Pseudomonas sp. RC1. RC1 was inoculated into intact soil-core microcosms incubated in the laboratory at ambient temperature (22°C) and in a growth chamber with temperature fluctuations that mimicked a verage field values, as well as into field lysimeters and plots. The effect of the introduced bacterium on ecosystem structure, including wheat rhizoplane populations of total and fluorescent pseudomonads, total heterotrophic bacteria, and the diversity of total heterotrophic bacteria, was determined. Fluorescent pseudomonads were present on the rhizoplane in significantly lower numbers in soil inoculated with RC1, in both microcosms and the field. Conditions for microbial growth appeared to be most favorable in the growth chamber microcosm, as evidenced by higher populations of heterotrophs and a greater species diversity on the rhizoplane at the three-leaf stage of wheat growth. Ecosystem functional parameters, as determined by soil dehydrogenase activity, plant biomass production, and(15)N-fertilizer uptake by wheat, were different in the four systems. The stimulation of soil dehydrogenase activity by the addition of alfalfa was greater in the microcosms than in the field. In general, growth chamber microcosms, which simulated average field temperatures, were better predictors of field behavior than microcosms incubated continuously at 22°C.}, }
@article {pmid24194208, year = {1991}, author = {Bolton, H and Fredrickson, JK and Bentjen, SA and Workman, DJ and Li, SM and Thomas, JM}, title = {Field calibration of soil-core microcosms: Fate of a genetically altered rhizobacterium.}, journal = {Microbial ecology}, volume = {21}, number = {1}, pages = {163-173}, pmid = {24194208}, issn = {0095-3628}, abstract = {Microcosms containing intact soil-cores are a potential tool for assessing the risks of the release of genetically engineered microorganisms (GEMs) to the environment. Before microcosms become a standard assessment tool, however, they must first be calibrated to ensure that they adequately simulate key parameters in the field. Four systems were compared: intact soil-core microcosms located in the laboratory at ambient temperature and in a growth chamber with temperature fluctuations that simulated average conditions in the field, field lysimeters, and field plots. These four systems were inoculated with rifampicin-resistantPseudomonas sp. and planted to winter wheat. Populations of thePseudomonas sp. in soil decreased more rapidly at ambient temperature, but population size at the three-leaf stage of wheat growth was the same in all four systems. Populations of thePseudomonas sp. on the rhizoplane of wheat were the same at the three-leaf stage in all four systems, and colonization with depth at the final boot stage-sampling was also similar. In general, microcosms incubated at ambient temperature in the laboratory or in the growth chamber were similar to those in the field with respect to survival of and colonization of the rhizoplane by the introducedPseudomonas sp.}, }
@article {pmid24194207, year = {1991}, author = {Barkay, T and Turner, RR and Vandenbrook, A and Liebert, C}, title = {The relationships of Hg(II) volatilization from a freshwater pond to the abundance ofmer genes in the gene pool of the indigenous microbial community.}, journal = {Microbial ecology}, volume = {21}, number = {1}, pages = {151-161}, pmid = {24194207}, issn = {0095-3628}, abstract = {The role of biological activities in the reduction and volatilization of Hg(II) from a polluted pond was investigated. Elemental mercury was evolved from pond water immediately following spiking with(203)Hg(NO3)2, whereas an acclimation period of 36 hours was required in control samples collected from a nearby, unpolluted river before onset of volatilization. Genes encoding the bacterial mercuric reductase enzyme (mer genes) were abundant in DNA fractions extracted from biomass of the pond microbial community, but not in samples extracted from control communities. Thus, evolution of Hg(0) was probably due to activities mediated by the bacterial mercuric reductase. Of four characterizedmer operons, the system encoded by transposon 501 (mer(Tn501)) dominated and likely contributed to the majority of the observed Hg(II) volatilization. Thus,mer-mediated reduction and volatilization could be used to reduce Hg(II) concentrations in polluted waters, in turn decreasing rates of methylmercury formation by limiting substrate availability.}, }
@article {pmid24194206, year = {1991}, author = {Liebert, CA and Barkay, T and Turner, RR}, title = {Acclimation of aquatic microbial communities to Hg(II) and CH3Hg (+) in polluted freshwater ponds.}, journal = {Microbial ecology}, volume = {21}, number = {1}, pages = {139-149}, pmid = {24194206}, issn = {0095-3628}, abstract = {The relationship of mercury resistance to the concentration and chemical speciation of mercurial compounds was evaluated for microbial communities of mercury-polluted and control waters. Methodologies based on the direct viable counting (DVC) method were adapted to enumerate mercury-resistant communities. Elevated tolerance to Hg(II) was observed for the microbial community of one mercury-polluted pond as compared to the community of control waters. These results suggest an in situ acclimation to Hg(II). The results of the methylmercury resistance-DVC assay suggested that minimal acclimation to CH3Hg(+) occurred since similar concentrations of CH3HgCl inhibited growth of 50% of organisms in both the control and polluted communities. Analyses of different mercury species in pond waters suggested that total mercury, but not CH3Hg(+) concentrations, approached toxic levels in the polluted ponds. Thus, microbial acclimation was specific to the chemical species of mercury present in the water at concentrations high enough to cause toxic effects to nonacclimated bacterial communities.}, }
@article {pmid24194205, year = {1991}, author = {Müller, H and Schöne, A and Pinto-Coelho, RM and Schweizer, A and Weisse, T}, title = {Seasonal succession of ciliates in lake constance.}, journal = {Microbial ecology}, volume = {21}, number = {1}, pages = {119-138}, pmid = {24194205}, issn = {0095-3628}, abstract = {We found a recurrent seasonal pattern in abundance and composition of planktonic ciliates in Lake Constance, FRG, over a three-year period. Abundance peaks occurred in early spring and summer/autumn, while ciliate numbers were low in late spring (clear-water phase) and winter. Prostomatida and Oligotrichida dominated in early spring. They responded immediately to the phytoplankton spring bloom, while Haptorida, Peritrichida, and large Scuticociliatida (Histiobalantium) were delayed by 1 to 2 weeks. The spring community broke down at the onset of the clear-water phase.Pelagohalteria viridis containing symbiontic algae appeared shortly after this event. A highly diverse community was recorded in summer/autumn. Peritrichida, small Oligotrichida, and large Scuticociliatida reached their maxima during this season. Small Scuticociliatida were rare throughout the year and contributed moderately to total ciliate numbers only during the cold season. The observed seasonal sequence of pelagic ciliates in Lake Constance is discussed in relation to simultaneously collected data on potential food organisms and grazers.}, }
@article {pmid24194204, year = {1991}, author = {White, PA and Kalff, J and Rasmussen, JB and Gasol, JM}, title = {The effect of temperature and algal biomass on bacterial production and specific growth rate in freshwater and marine habitats.}, journal = {Microbial ecology}, volume = {21}, number = {1}, pages = {99-118}, pmid = {24194204}, issn = {0095-3628}, abstract = {We analyzed heterotrophic, pelagic bacterial production and specific growth rate data from 57 studies conducted in fresh, marine and estuarine/coastal waters. Strong positive relationships were identified between 1) bacterial production and bacterial abundance and 2) bacterial production and algal biomass. The relationship between bacterial production and bacterial abundance was improved by also considering water temperature. The analysis of covariance model revealed consistent differences between fresh, marine and estuarine/coastal waters, with production consistently high in estuarine/coastal environments. The log-linear regression coefficient of abundance was not significantly different from 1.00, and this linear relationship permitted the use of specific growth rate (SGR in day(-1)) as a dependent variable. A strong relationship was identified between specific growth rate and temperature. This relationship differed slightly across the three habitats. A substantial portion of the residual variation from this relationship was accounted for by algal biomass, including the difference between marine and estuarine/coastal habitats. A small but significant difference between the fresh- and saltwater habitats remained. No significant difference between the chlorophyll effect in different habitats was identified. The model of SGR against temperature and chlorophyll was much weaker for freshwater than for marine environments. For a small subset of the data set, mean cell volume accounted for some of the residual variation in SGR. Pronounced seasonality, fluctuations in nutrient quality, and variation of the grazing environment may contribute to the unexplained variation in specific growth.}, }
@article {pmid24194203, year = {1991}, author = {Whitton, BA and Grainger, SL and Hawley, GR and Simon, JW}, title = {Cell-bound and extracellular phosphatase activities of cyanobacterial isolates.}, journal = {Microbial ecology}, volume = {21}, number = {1}, pages = {85-98}, pmid = {24194203}, issn = {0095-3628}, abstract = {Fifty cyanobacterial strains (10 genera) were tested in batch culture for their ability to use organic phosphorus compounds (1 mg liter(-1) P) as their sole P source. Two monoesters, Na2-β-glycerophosphate and π-nitrophenyl phosphate (πNPP), supported growth of all strains, and the diester bis-π-nitrophenyl phosphate (bis-π-NPP) and herring sperm DNA supported almost all strains. ATP was either a very favorable or poor P source and failed to support growth of nine strains, seven of which were Rivulariaceae with trichomes ending in a hair or long tapered region. Phytic acid was in general the least favorable P source.P-limited cultures grown initially with inorganic phosphate to conditions of P limitation were also tested for cell-bound and extracellular phosphomonoesterase (PMEase) and phosphodiesterase (PDEase) activities at two pH values (7.6, 10.3) using πNPP and bis-πNPP as substrates. Cell-bound PMEase was inducible in all strains and cell-bound PDEase in most strains. Most showed extracellular PMEase, but not extracellular PDEase. The highest values (μM πNPP or bis-πNPP hydrolyzed mg dry weight(-1) hour(-1)) all occurred in strains ofGloeotrichia as follows: cell-bound PMEase at pH 7.6, 2.7 μM in strain D602; cell-bound PMEase at pH 10.3, 5.2 μM in D602; extracellular PMEase at pH 7.6, 0.73 μM in D281; extracellular PMEase at pH 10.3, 6.6 μM in D281; cell-bound PDEase at 7.6, 0.40 μM in D613; cell-bound PDEase at pH 10.3, 1.0 μM in D613.The results were compared to see if they indicated possible relationships between phosphatase activity and taxonomic or ecological grouping. The following differences were significant (P<0.05). Rivulariaceae produced higher yields than filamentous non-Rivulariaceae with β-glycerophosphate, πNPP, and DNA. Rivulariaceae with the ability to form hairs in culture showed poorer growth in ATP than non-hair-forming Rivulariaceae, but were more effective at utilizing phytic acid. Strains from calcareous environments had higher PMEase activity at pH 10.3 than strains from noncalcareous environments (P<0.01).}, }
@article {pmid24194202, year = {1991}, author = {Bergbauer, M}, title = {Degradation and oligomerization of syringic acid by distinctive ecological groups of fungi.}, journal = {Microbial ecology}, volume = {21}, number = {1}, pages = {73-84}, pmid = {24194202}, issn = {0095-3628}, abstract = {Forty-four terrestrial and aeroaquatic and aquatic fungi, including fifteen species causing white-rot, four species causing brown-rot, and some species causing soft-rot of wood, were tested for their ability to degrade the monomer syringic acid, which is released during decay of angiosperm lignin. None of the white- or brown-rot species caused any detectable degradation of syringic acid under the test conditions; however, six typical white-rot fungi strongly oligomerized syringic acid, both with and without cosubstrate. The main polymerization product was identified as a 1,3-dimethylpyrogallol oligomer by(13)C-NMR. Other minor metabolic products were methylated and hydroxylated derivatives. Oligomerization depended on the presence of 1 or 2 methoxy groups in ortho position to the hydroxy group of the substrate.Among the remaining fungi,Exophiala jeanselmei, Fusarium eumartii, andPaecilomyces variotii completely and rapidly degraded syringic acid (5 g/liter) within 48 to 100 hours. A further seven species were able to degrade syringic acid to some extent when glucose was added. Methylated and demethylated metabolic intermediates were identified by GC/MS.}, }
@article {pmid24194201, year = {1991}, author = {Lindqvist, R and Bengtsson, G}, title = {Dispersal dynamics of groundwater bacteria.}, journal = {Microbial ecology}, volume = {21}, number = {1}, pages = {49-72}, pmid = {24194201}, issn = {0095-3628}, abstract = {Dispersal of bacteria in saturated, porous soils can be characterized by the partitioning of cells between the aqueous and solid phases, as a result of the physical and chemical nature of the soil and water and cell surface modifications. The purpose of this work is to understand variations in partitioning as a consequence of the nutrient conditions and to use this information in mathematical models to predict the dispersal rate of bacteria in aquifer material. Two different models were used to describe dispersal: an advective-dispersive-sorptive model with a first order kinetic sink term to account for irreversible cell reactions, such as death and sorption; and a two-site reaction model, in which the retardation was assumed to be determined by two types of sites, one characterized by instantaneous equilibrium sorption reactions and the other by kinetic nonequilibrium reactions. Water-saturated sand columns were used as continuous-flow groundwater microcosms to test the models under different nutrient regimes. Two strains of indigenous groundwater bacteria were isolated from aquifer material and labelled with(3)H-alanine,(14)C-pyruvic acid,(3)H-glucose, and(3)H-adenosine for different measurements of sorption and dispersal, which were estimated from breakthrough curves. Both experimental data and model variables showed that dispersal of bacteria was a dynamic nonequilibrium process, possibly shaped by two subpopulations, one strongly, even irreversibly, adsorbing to the solid particles, and one with very slow adsorption kinetics. The cell surfaces were modified in response to the growth conditions, which was demonstrated by hydrophobic and electrostatic interaction chromatography. Cell surface hydrophobicity was about eight times higher in groundwater than in eutrophic lake water. The partition coefficient varied between 12.6 in the groundwater and 6.4 in the lake water, indicating the prime importance of hydrophobic binding for attachment in low nutrient conditions. The partitioning was also sensitive to the hydrodynamics of the system and the oxygen supply, as demonstrated by comparison of sorption in agitated test tubes, gently shaken vials, and air-flushed bottles. Sorption kinetics were demonstrated in a continuous flow cell. About 45% of a population was associated with sand particles with a continuous flow of pure groundwater and as little as 20% in lake water. However, more than 50% of the bacteria in the aqueous phase were associated with suspended material of less than 60 μm in diameter. This association may enhance dispersal for example, by size exclusion of the colloidal material in the interstitial pores.}, }
@article {pmid24194200, year = {1991}, author = {Ercolani, GL}, title = {Distribution of epiphytic bacteria on olive leaves and the influence of leaf age and sampling time.}, journal = {Microbial ecology}, volume = {21}, number = {1}, pages = {35-48}, pmid = {24194200}, issn = {0095-3628}, abstract = {Mesophilic heterotrophic, aerobic or facultatively anaerobic bacteria that grow on yeast tryptone glucose extract agar were isolated from the surface of olive leaves of 3 or 4 different ages in January, April, July, and October from 1984 to 1989. Unweighted average linkage cluster analysis on either the Jaccard coefficient or the simple matching coefficient recovered 1,701 representative strains in 32 phena defined at the 70% and 80% similarity level, respectively. Of these, 25 were identified to genus or lower level. From the identity of the representative strains, the frequency of occurrence among the phylloplane bacteria over the 6-year period was estimated at 51% forPseudomonas syringae, followed byXanthomonas campestris (6.7%),Erwinia herbicola (6%),Acetobacter aceti (4.7%),Gluconobacter oxydans (4.3%),Pseudomonas fluorescens (3.9%),Bacillus megaterium (3.8%),Leuconostoc mesenteroides subsp.dextranicum (3.1%),Lactobacillus plantarum (2.8%),Curtobacterium plantarum (2.2%),Micrococcus luteus (2.2%),Arthrobacter globiformis (1.4%),Klebsiella planticola (1.2%),Streptococcus faecium (1.2%),Clavibacter sp. (0.98%),Micrococcus sp. (0.82%),Serratia marcescens (0.81%),Bacillus subtilis (0.57%),Cellulomonas flavigena (0.4%),Erwinia sp. (0.37%),Zymomonas mobilis (0.3%),Bacillus sp. (0.29%),Alcaligenes faecalis (0.27%),Erwinia carotovora (0.08%), andPseudomonas aeruginosa (0.04%). Bacterial communities on leaves of a given age at a given time during any one year displayed a very similar structure but differed significantly from those on the leaves of the same age at a different time or on the leaves of a different age at any time during any one year. Communities on the leaves of a given age at a given time of the year were invariably dominated by one or another of only 9 taxa, which accounted for 22 to 98.5% of the isolates from those leaves. The communities on 10- and 13-month-old leaves were invariably made up of fewer taxa than those on younger leaves at the same time of the year.}, }
@article {pmid24194199, year = {1991}, author = {Pillai, SD and Pepper, IL}, title = {Transposon Tn5 as an identifiable marker in rhizobia: Survival and genetic stability of Tn5 mutant bean rhizobia under temperature stressed conditions in desert soils.}, journal = {Microbial ecology}, volume = {21}, number = {1}, pages = {21-33}, pmid = {24194199}, issn = {0095-3628}, abstract = {Five transposon Tn5 insertion mutants of a beanRhizobium strain (Rhizobium leguminosarum b. v.phaseoli) were used in an ecological study to evaluate the extent to which transposon Tn5 was stable to serve as an identifiable marker in rhizobia under a high temperature stress condition in two Sonoran Desert soils. All the mutants possessed single chromosomal insertions of the transposon. In both soils, under the temperature stress conditions that were employed (40°C), both wild type and mutant populations possessing functional transposable elements declined rapidly. After 12 days, mutant cells, when screened using the Tn5 coded antibiotic resistance markers, were significantly less in number than when they were screened using only their intrinsic antibiotic resistance markers. There were no significant differences in numbers between the mutant cell population and the wild type when the mutant cells were screened using only the intrinsic antibiotic resistance markers. DNA-DNA hybridizations using a probe indicated neither deletion nor transposition of the transposable element. The results indicate that transposon DNA sequences are present within cells under high temperature stress conditions, but kanamycin/neomycin resistance is not expressed by some of these cells, suggesting that Tn5 undergoes a possible functional inactivation under these conditions. The possible implications of these findings are discussed.}, }
@article {pmid24194198, year = {1991}, author = {Boussaid, A and Baleux, B and Hassani, L and Lesne, J}, title = {Aeromonas species in stabilization ponds in the arid region of Marrakesh, Morocco, and relation to fecal-pollution and climatic factors.}, journal = {Microbial ecology}, volume = {21}, number = {1}, pages = {11-20}, pmid = {24194198}, issn = {0095-3628}, abstract = {During the period 12 July 1985 to 23 December 1987, water samples were collected in two-week intervals for estimates ofAeromonas species in a waste treatment system located in the arid region of Marrakech, Morocco. Fecal coliforms, temperature, and chemical oxygen demand were measured simultaneously withAeromonas species densities. Statistical methods were utilized to analyze the significance of average differences and temporal patterns ofAeromonas species numbers.Removal ofAeromonas in the whole system did not exceed 1.14 log.Aeromonas densities showed significantly higher resistance to the treatment process when compared with fecal coliforms; however, abundance of the two groups presented a similar seasonal change. The highest numbers occurred during the cold months, while the lowest appeared in the warm months. Statistical time-series analyses of the densities data showed the seasonal and cyclic distribution ofAeromonas in this treatment plant.These temporal changes were simultaneously observed in all the stations investigated and were negatively correlated with water temperature values.Aeromonas populations were dominated byA. caviae andA. hydrophila in the inlet samples. These two species were rapidly eliminated in the treatment plant. The temporal distribution ofA. caviae was similar to the change in densities ofAeromonas and fecal coliforms. The seasonal fluctuations of abundance ofAeromonas were probably related to this species, which dominated in the winter samples but dropped during the summer. Meanwhile,A. sobria dominated all the final effluent samples. This greater survival ofA. sobria and its known pathogenicity may limit the re-use of treated water for irrigation of fodder plants.}, }
@article {pmid24194197, year = {1991}, author = {Svetlichny, VA and Sokolova, TG and Gerhardt, M and Kostrikina, NA and Zavarzin, GA}, title = {Anaerobic extremely thermophilic carboxydotrophic bacteria in hydrotherms of Kuril Islands.}, journal = {Microbial ecology}, volume = {21}, number = {1}, pages = {1-10}, pmid = {24194197}, issn = {0095-3628}, abstract = {A new group of extremely thermophilic, obligately anaerobic, carboxydotrophic eubacteria is described. The organisms are characterized by a novel type of chemotrophic metabolism in thermophilic environments. They grow at temperatures up to 80-85°C chemolithotrophically with 100% CO in the gas phase as the sole energy source. The CO oxidation is coupled to H2 and CO2 formation according to the equation CO+H2O → H2+CO2. No other products of metabolism are produced. The group of CO-utilizing, H2-producing anaerobes includes diverse bacteria. They are non-sporeforming rods differing in morphology, CO uptake rates, habitats, and maximum growth temperatures. The new carboxydotrophic thermophilic anaerobes are widely distributed in freshwater and coastal marine hydrotherms of the Kuril Islands.}, }
@article {pmid24193982, year = {1990}, author = {Federle, TW and Ventullo, RM and White, DC}, title = {Spatial distribution of microbial biomass, activity, community structure, and the biodegradation of linear alkylbenzene sulfonate (LAS) and linear alcohol ethoxylate (LAE) in the subsurface.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {297-313}, pmid = {24193982}, issn = {0095-3628}, abstract = {The vertical distribution of microbial biomass, activity, community structure and the mineralization of xenobiotic chemicals was examined in two soil profiles in northern Wisconsin. One profile was impacted by infiltrating wastewater from a laundromat, while the other served as a control. An unconfined aquifer was present 14 meters below the surface at both sites. Biomass and community structure were determined by acridine orange direct counts and measuring concentrations of phospholipid-derived fatty acids (PLFA). Microbial activity was estimated by measuring fluorescein diacetate (FDA) hydrolysis, thymidine incorporation into DNA, and mixed amino acid (MAA) mineralization. Mineralization kinetics of linear alkylbenzene sulfonate (LAS) and linear alcohol ethoxylate (LAE) were determined at each depth. Except for MAA mineralization rates, measures of microbial biomass and activity exhibited similar patterns with depth. PLFA concentration and rates of FDA hydrolysis and thymidine incorporation decreased 10-100 fold below 3 m and then exhibited little variation with depth. Fungal fatty acid markers were found at all depths and represented from 1 to 15% of the total PLFAs. The relative proportion of tuberculostearic acid (TBS), an actinomycete marker, declined with depth and was not detected in the saturated zone. The profile impacted by wastewater exhibited higher levels of PLFA but a lower proportion of TBS than the control profile. This profile also exhibited faster rates of FDA hydrolysis and amino acid mineralization at most depths. LAS was mineralized in the upper 2 m of the vadose zone and in the saturated zone of both profiles. Little or no LAS biodegradation occurred at depths between 2 and 14 m. LAE was mineralized at all depths in both profiles, and the mineralization rate exhibited a similar pattern with depth as biomass and activity measurements. In general, biomass and biodegradative activities were much lower in groundwater than in soil samples obtained from the same depth.}, }
@article {pmid24193981, year = {1990}, author = {Donnelly, PK and Entry, JA and Crawford, DL and Cromack, K}, title = {Cellulose and lignin degradation in forest soils: Response to moisture, temperature, and acidity.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {289-295}, pmid = {24193981}, issn = {0095-3628}, abstract = {The concentration of lignin in plant tissue is a major factor controlling organic matter degradation rates in forest ecosystems. Microbial biomass and lignin and cellulose decomposition were measured for six weeks in forest soil microcosms in order to determine the influence of pH, moisture, and temperature on organic matter decomposition. Microbial biomass was determined by chloroform fumigation; lignin and cellulose decomposition were measured radiometrically. The experiment was designed as a Latin square with soils of pH of 4.5, 5.5, and 6.5 adjusted to 20, 40, or 60% moisture content, and incubated at temperatures of 4, 12, or 24°C. Microbial biomass and lignin and cellulose decomposition were not significantly affected by soil acidity. Microbial biomass was greater at higher soil moisture contents. Lignin and cellulose decomposition significantly increased at higher soil temperatures and moisture contents. Soil moisture was more important in affecting microbial biomass than either soil temperature or soil pH.}, }
@article {pmid24193980, year = {1990}, author = {Genthner, FJ and Upadhyay, J and Campbell, RP and Genthner, BR}, title = {Anomalies in the enumeration of starved bacteria on culture media containing nalidic acid and tetracycline.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {283-288}, pmid = {24193980}, issn = {0095-3628}, abstract = {Culturable counts of antibiotic resistant, genetically engineeredPseudomonas fluorescens were determined on antibiotic-containing plate count agar during starvation in water. Prior to starvation, colony counts obtained on all media separated into two groups. The mean of the colony counts on plate count agar with or without tetracycline (4.9 × 10(6) ml(-1)) was significantly higher than the mean colony counts on plate count agar containing either nalidixic acid or nalidixic acid plus tetraclycline (2.5×10(6) ml(-1)). After 20 days of starvation the highest mean colony counts continued to be obtained on plate count agar (7.2 × 10(6) ml(-1)) with slightly, but significantly, lower counts obtained on plate count agar containing either nalidixic acid (5.6 × 10(6) ml(-1)) or tetraclycline (1.5×10(6) ml(-1)). A combination of nalidixic acid and tetracycline in plate count agar, however, dramatically reduced colony counts (8.3 × 10(2) ml(-1)) after this starvation period. The addition of catalase to plate count agar containing nalidixic acid and tetracycline negated the effect caused by this combination of antibiotics. When colony counts obtained over the entire 20 day incubation were considered, the addition of MgSO4 to plate count agar containing nalidixic acid and tetracycline resulted in a significant increase in colony counts. Other combinations of antibiotics, nalidixic acid+carbenicillin, nalidixic acid+kanamycin, streptomycin+tetracycline, streptomycin+carbenicillin, rifampicin+tetracycline, rifampicin+carbenicillin, and rifampicin+kanamycin, did not inhibit colony formation of starved cells. Antibiotic resistant strains ofP. putida andEscherichia coli also displayed sensitivity to the combination of nalidixic acid and tetracycline in plate count agar after starvation.}, }
@article {pmid24193979, year = {1990}, author = {Eckert, W and Yacobi, YZ and Trüper, HG}, title = {A bloom of a brown phototrophic sulfur bacterium in lake kinneret: Hydrochemical aspects.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {273-282}, pmid = {24193979}, issn = {0095-3628}, abstract = {During a bloom of the brown phototrophic sulfur bacteriumChlorobium phaeobacteroides in Lake Kinneret the decisive hydrochemical parameters, pH, pH2S and pe (p=-log activity) were monitored in situ and related to the phototrophic bacterial bloom. The measured data in dicate a strong influence of the phototrophic bacteria on the metalimnic sulfide concentration and on the prevailing redox conditions. The intensity of theC. phaeobacteroides bloom, which appeared in two distinct peaks, could be related to vertical changes of the thermocline.}, }
@article {pmid24193978, year = {1990}, author = {Christoffersen, K and Riemann, B and Hansen, LR and Klysner, A and Sørensen, HB}, title = {Qualitative importance of the microbial loop and plankton community structure in a eutrophic lake during a bloom of cyanobacteria.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {253-272}, pmid = {24193978}, issn = {0095-3628}, abstract = {Plankton community structure and major pools and fluxes of carbon were observed before and after culmination of a bloom of cyanobacteria in eutrophic Frederiksborg Slotssø, Denmark. Biomass changes of heterotrophic nanoflagellates, ciliates, microzooplankton (50 to 140 μm), and macrozooplankton (larger than 140 μm) were compared to phytoplankton and bacterial production as well as micro- and macrozooplankton ingestion rates of phytoplankton and bacteria. The carbon budget was used as a means to examine causal relationships in the plankton community. Phytoplankton biomass decreased and algae smaller than 20 μm replacedAphanizomenon after the culmination of cyanobacteria. Bacterial net production peaked shortly after the culmination of the bloom (510 μg C liter(-1) d(-1) and decreased thereafter to a level of approximately 124 μg C liter(-1) d(-1). Phytoplankton extracellular release of organic carbon accounted for only 4-9% of bacterial carbon demand. Cyclopoid copepods and small-sized cladocerans started to grow after the culmination, but food limitation probably controlled the biomass after the collapse of the bloom. Grazing of micro- and macrozooplankton were estimated from in situ experiments using labeled bacteria and algae. Macrozooplankton grazed 22% of bacterial net production during the bloom and 86% after the bloom, while microzooplankton (nauplii, rotifers and ciliates larger than 50 μm) ingested low amounts of bacteria and removed 10-16% of bacterial carbon. Both macro-and microzooplankton grazed algae smaller than 20 μm, although they did not control algal biomass. From calculated clearance rates it was found that heterotrophic nanoflagellates (40-440 ml(-1)) grazed 3-4% of the bacterial production, while ciliates smaller than 50 μm removed 19-39% of bacterial production, supporting the idea that ciliates are an important link between bacteria and higher trophic levels. During and after the bloom ofAphanizomenon, major fluxes of carbon between bacteria, ciliates and crustaceans were observed, and heterotrophic nanoflagellates played a minor role in the pelagic food web.}, }
@article {pmid24193977, year = {1990}, author = {Gauthier, MJ and Flatau, GN and Clément, RL}, title = {Influence of phosphate ions and alkaline phosphatase activity of cells on survival ofEscherichia coli in seawater.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {245-251}, pmid = {24193977}, issn = {0095-3628}, abstract = {When grown in a minimal medium and suspended for 2 hours in distilled water, seawater, phosphate buffer or a polyphosphate solution,E. coli MC4100 cells with high alkaline phosphatase activity survived in seawater for longer periods than cells with low or no activity. However, mutant cells totally deprived of alkaline phosphatase activity held in phosphate-containing media before transfer to seawater showed survival almost as high as the wild type strain, indicating that alkaline phosphatase activity is not the only factor influencing survival. Alkaline phosphatase activity also increased the protection of cells provided by glycine betaine. Survival was enhanced when cells were preincubated in the presence of phosphate or polyphosphate. Thus, the transfer of cells in wastewater could influence their subsequent survival in seawater.}, }
@article {pmid24193976, year = {1990}, author = {Gurijala, KR and Alexander, M}, title = {Explanation for the decline of bacteria introduced into lake water.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {231-244}, pmid = {24193976}, issn = {0095-3628}, abstract = {The sizes of the populations of individual bacterial species diminished following their addition to water from lakes with different trophic levels at temperatures of 5, 10, 15, and 30°C. Some species persisted after their initial reduction in cell numbers, but others were undetectable after 3 to 15 days. The decline of these introduced bacteria was not a result of their inoculation at higher densities than are found in nature. The death of most of the test species was not the result of starvation, abiotic factors, bdellovibrios, or bacteriophages. Despite the presence of lytic bacteria, the lake water did not have lytic activity against the test species. Protozoan predation was a significant factor in the fall in bacterial population sizes because protozoa increased in numbers as the bacterial density fell, the suppression of protozoa led to the elimination or delay of the decline of the bacteria, and the addition of protozoa to lake water in which indigenous protozoa were suppressed produced the same pattern of bacterial elimination as in untreated lake water.}, }
@article {pmid24193975, year = {1990}, author = {Osgood, MP and Boylen, CW}, title = {Seasonal variations in bacterial communities in adirondack streams exhibiting pH gradients.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {211-230}, pmid = {24193975}, issn = {0095-3628}, abstract = {Measurements of microbial biomass, bacterial numbers, and microbial production were determined for three small woodland streams located in the Adirondack Mountain region of New York State, USA. These streams exhibited spatial and temporal gradients in water pH ranging from a high of 7.0 to a low of 4.5. Twelve sites along these streams were used for comparative analyses of the effects of pH and related water chemistry parameters on the planktonic, sedimentary, and epilithic bacterial communities. The planktonic bacterial communities were not influenced by water pH or related water chemistry parameters. For sedimentary populations, the organic content of the sediment was more important than the chemistry of the overlying water. The epilithic bacterial communities, however, were influenced significantly by the pH of the water column, showing decreased bacterial production at lower pH.}, }
@article {pmid24193974, year = {1990}, author = {Aust, SD}, title = {Degradation of environmental pollutants byPhanerochaete chrysosporium.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {197-209}, pmid = {24193974}, issn = {0095-3628}, abstract = {The white rot fungi appear to be unique in their ability to degrade lignin by the secretion of hydrogen peroxide and a family of peroxidases now referred to as lignin peroxidases or simply ligninases. The fact that these enzymes are naturally secreted and seem to be capable of initiating the oxidation of lignin by a free-radical mechanism led to the proposal and demonstration that the white rot fungi are able to degrade a wide variety of normally very recalcitrant environmental pollutants. The mineralization of chemicals byPhanerochaete chrysosporium does seem to be dependent upon the lignin degrading system. Thus it should be possible to at least initiate degradation extracellularly, eliminating the need for absorption of the chemical. The nonspecific nature of the system gives the potential for oxidation of a wide variety of chemicals and even mixtures of chemicals. As the lignin peroxidases are synthesized and secreted in response to nutrient starvation there is no requirement for conditioning of the organism. Mineralization can occur in either a water or soil matrix using very economical agricultural or wood wastes as nutrients. The lignin peroxidases can be purified from the extracellular fluid quite easily by fast protein liquid chromatography. They are somewhat typical peroxidases but also have some unique properties. The oxidation of some xenobiotics has been demonstrated and cooxidation is also a possible mechanism.}, }
@article {pmid24193973, year = {1990}, author = {Hale, DD and Rogers, JE and Wiegel, J}, title = {Reductive dechlorination of dichlorophenols by nonadapted and adapted microbial communities in pond sediments.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {185-196}, pmid = {24193973}, issn = {0095-3628}, abstract = {Fresh and dichlorophenol (DCP)-adapted sediments from two ponds near Athens, Georgia exhibited distinctly different dechlorinating activities. These differences centered on the relative rates of reductive dehlorination in both fresh and adapted sediments and on the substrate specificity of the adapted sediments. Fresh Cherokee Trailer Park Pond sediment dechlorinated 2,3-, 2,4-, and 2,6-DCP to monochlorophenols at a faster rate and after a shorter lag period than fresh Bolton's Pond sediment. Lag periods were not observed in either Cherokee or Bolton's sediments that had been adapted to dechlorinate either 2,3-, 2,4-or 2,6-DCP. Adapted Cherokee sediments exhibited faster dechlorinating rates and a broader substrate specificity than the adapted Bolton's sediments. The broad substrate specificity of each of the adapted Cherokee sediments contrasted sharply with the narrow specificity of the 2,6-DCP-adapted Bolton's sediment. The preference for reductive dechlorination wasortho>meta orpara in sediments from both ponds.}, }
@article {pmid24193972, year = {1990}, author = {Shanker, R and Bollag, JM}, title = {Transformation of indole by methanogenic and sulfate-reducing microorganisms isolated from digested sludge.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {171-183}, pmid = {24193972}, issn = {0095-3628}, abstract = {In the present study, mineralization of an aromaticN-heterocyclic molecule, indole, by microorganisms present in anaerobically digested sewage sludge was examined. The first step in indole mineralization was the formation of a hydroxylated intermediate, oxindole. The rate of transformation of indole to oxindole and its subsequent disappearance was dependent on the concentration of inoculum and indole and the incubation temperature. Methanogenesis appeared to be the dominant process in the mineralization of indole in 10% digested sludge even in the presence of high concentrations of sulfate. Enrichment of the digested sludge with sulfate as an electron acceptor allowed the isolation of a metabolically stable mixed culture of anaerobic bacteria which transformed indole to oxindole and acetate, and ultimately to methane and carbon dioxide. This mixed culture exhibited a predominance of sulfate-reducers over methanogens with more than 75% of the substrate mineralized to carbon dioxide. The investigation demonstrates that indole can be transformed by both methanogenic and sulfate-reducing microbial populations.}, }
@article {pmid24193971, year = {1990}, author = {Henry, SM and Grbic-Galic, D}, title = {Effect of mineral media on trichloroethylene oxidation by aquifer methanotrophs.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {151-169}, pmid = {24193971}, issn = {0095-3628}, abstract = {The effect of growth in different mineral media on subsequent oxidation of trichloroethylene (TCE) by type I and type II aquifer methanotrophs was evaluated. Mixed culture MM1, containing a type II methanotroph, and a type I pure culture tentatively identified as aMethylomonas sp., were enriched and isolated from an uncontaminated groundwater aquifer. The second-order rate coefficients (k/Ks) for TCE oxidation by these cultures varied by more than an order of magnitude when the cultures were grown in different mineral media. The presence of a chelator (NaEDTA) in one of these media, termed Whittenbury, significantly enhanced rates of TCE oxidation by all the cultures tested. When pregrown in this mineral medium, the resting cells of the pure cultureMethylomonas sp. MM2 exhibited second-order TCE oxidation rates as great as 0.78 liter/mg·day, whereas when pregrown in Whittenbury lacking the chelator, the rates did not exceed 0.018 liter/mg·day. The rate of TCE oxidation byMethylomonas sp. MM2 pregrown in another mineral medium formulation, devoid of chelators (termed Fogel), was intermediate in value (0.26 liter/mg·day), and adding EDTA to this medium did not affect the rate. Adding 1.6 μM copper to both Whittenbury and Fogel mineral media reduced the TCE oxidation rates about an order of magnitude; subsequent addition of 84 μM EDTA partially alleviated this effect. The maximal rate coefficients (k) for TCE oxidation byMethylomonas sp. MM2 were significantly higher, and the half saturation coefficients (Ks) for TCE significantly lower, following growth in the presence of EDTA. Stationary phase TCE oxidation rates as great as 2.3 liter/mg·day were achieved whenMethylomonas sp. MM2, grown in Whittenbury medium was provided formate as a source of reducing power. Omitting EDTA from Whittenbury medium also significantly reduced the methane oxidation rate and the growth yield. Copper addition did not significantly affect the methane oxidation rate or growth yield. The internal membrane structures ofMethylomonas sp. MM2 evaluated by transmission electron microscopy showed the presence of internal membranes, the ultrastructure of which was the same regardless of growth medium or TCE oxidation rate. The methane monooxygenase responsible for TCE oxidation inMethylomonas sp. MM2 under the conditions of this study appears to be associated with the particulate fraction.}, }
@article {pmid24193970, year = {1990}, author = {Häggblom, MM and Rivera, MD and Bossert, ID and Rogers, JE and Young, LY}, title = {Anaerobic biodegradation ofPara-cresol under three reducing conditions.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {141-150}, pmid = {24193970}, issn = {0095-3628}, abstract = {The anaerobic degradation ofp-cresol was studied with one sediment source under three reducing conditions-denitrifying, sulfidogenic, and methanogenic. Loss ofp-cresol (1 mM) in all the anaerobic systems took initially 3 to 4 weeks. In acclimated culturesp-cresol was degraded in less than a week.p-Cresol was completely metabolized under denitrifying, sulfidogenic, and methanogenic conditions, with formation of nitrogen gas, loss of sulfate, and formation of methane and carbon dioxide, respectively.p-Cresol metabolism proceeded throughp-hydroxybenzal-dehyde andp-hydroxybenzoate under denitrifying and methanogenic conditions. These compounds were rapidly degraded in cultures acclimated top-cresol under all three reducing conditions. These results suggest that the initial pathway ofp-cresol degradation is the same under denitryfying, sulfidogenic, and methanogenic conditions and proceeds via oxidation of the methyl substituent top-hydroxybenzaldehyde andp-hydroxybenzoate. The initial rate ofp-hydroxybenzaldehyde degradation was high in both the unacclimated cultures and in the cultures acclimated top-cresol, suggesting that this step is nonspecific. Benzoate was additionally detected as a metabolite followingp-hydroxybenzoate in the methanogenic cultures, but not in the denitrifying or sulfidogenic cultures. The degradation pathway therefore may diverge afterp-hydroxybenzoate formation depending on which electron acceptor is available.}, }
@article {pmid24193969, year = {1990}, author = {Middeldorp, PJ and Briglia, M and Salkinoja-Salonen, MS}, title = {Biodegradation of pentachlorophenol in natural soil by inoculatedRhodococcus chlorophenolicus.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {123-139}, pmid = {24193969}, issn = {0095-3628}, abstract = {Rhodococcus chlorophenolicus PCP-1, a mineralizer of polychlorinated phenols, was inoculated into natural sandy loam and peaty soils with pentachlorophenol (PCP) at concentrations usually found at lightly and heavily polluted industrial sites (30 to 600 mg PCP/kg). A single inoculum of 10(5) to 10(8) cells per g of peat soil and as little as 500 cells/g sandy soil initiated mineralization of(14)C-PCP. The mineralization rates of PCP were 130 to 250 mg mineralized per kg soil in 4 months in the heavily (600 mg/kg) polluted soils and 13 to 18 mg/kg in the lightly (30 mg/kg) polluted soils. There were no detectable PCP mineralizing organisms in the soils prior to inoculation, and also there was no significant adaptation of the indigenous microbial population to degrade PCP during 4 months observation in the uninoculated soils. The inoculum-induced mineralization continued for longer than 4 months after a single inoculation. Uninoculated, lightly polluted soils (30 mg PCP/kg) also showed loss of PCP, but some of this reappeared as pentachloroanisol and other organic chlorine compounds (EOX). Such products did not accumulate in theR. chlorophenolicus-inoculated soils, where instead EOX was mineralized 90 to 98%.R. chlorophenolicus mineralized PCP unhindered by the substrate competition offered by the PCP-methylating bacteria indigenously occurring in the soils or by simultaneously inoculated O-methylatingR. rhodochrous.}, }
@article {pmid24193968, year = {1990}, author = {Zhang, X and Wiegel, J}, title = {Isolation and partial characterization of aClostridium species transforming para-hydroxybenzoate and 3,4-dihydroxybenzoate and producing phenols as the final transformation products.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {103-121}, pmid = {24193968}, issn = {0095-3628}, abstract = {Organisms present in methanogenic freshwater lake sediments from the vicinity of Athens, Georgia, were adapted to mineralize 2,4-dichlorophenol. Repeated addition of 0.5 to 2.7 mmol/liter of phenol, and later of 0.5-6.2 mmol/liter p-hydroxybenzoate (p-OHB), to such enrichments led to the conversion of p-OHB to phenol at a rate of up to 100 mmol p-OHB per liter per day. Subsequently, a spore-forming, obligately anaerobic bacterium, strain JW/Z-1, was isolated which transformed p-OHB to phenol and 3,4-dihydroxybenzoate (3,4-OHB) to catechol (1,2-dihydroxybenzene) stoichiometrically without further metabolism of the phenols. The strain did not transform benzoate, 4-chlorophenol, 2,4-dichlorophenol, 4-chlorobenzoate, o- and m-hydroxybenzoate, 2,4- and 3,5-dihydroxybenzoate, 2,3,4- and 3,4,5-trihydroxybenzoate, or 4-aminobenzoate. Yeast extract was required for growth of strain JW/Z-1 and only high concentrations of casein hydrolysate or tryptone could substitute it, to some extent. Except for sodium acetate, and some amino acids together with a 20-fold increased concentration of vitamins, no single carbohydrate or defined organic compound has been found to support growth of this strain in the presence (or in the absence) of 0.2 to 0.5% (w/v) yeast extract. The fermentation products during growth on yeast extract indicated that the metabolism of amino acid degradation was the major source for growth. The decarboxylating activity was inducible by p-OHB for the decarboxylation of p-OHB, and at a lower rate for 3,4-OHB, and by 3,4-OHB only for 3,4-OHB, suggesting that two different enzyme systems exist. The addition of the aromatic amino acids phenol or benzoate did not induce the decarboxylation activity in cultures growing with yeast extract. Growth was observed at temperatures ranging from 12-41°C (Topt, 33-34°C) and at pH-values ranging from 6.0-10.0 (pHopt, 7.2-8.2). The shortest doubling time observed for strain JW/Z-1 was 3.2 hours.}, }
@article {pmid24193967, year = {1990}, author = {Bedard, DL and Haberl, ML}, title = {Influence of chroline substitution pattern on the degradation of polychlorinated biphenyls by eight bacterial strains.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {87-102}, pmid = {24193967}, issn = {0095-3628}, abstract = {We compared the metabolism of eight di- and trichlorobiphenyls by eight bacterial strains chosen to represent a broad range of degradative activity against polychlorinated biphenyls (PCBs). The PCB congeners used were 2,3-, 2,3'-, 2,4'-, 3,3'-, 2,3,3'-, 2,4,4'-, 2,5,3'-, and 3,4,2'-chlorobiphenyl. The bacterial strains used wereCorynebacterium sp. MB1,Alcaligenes strainsA. eutrophus H850 andA. faecalis Pi434, andPseudomonas strains LB400 and H1130,P. testosteroni H430 and H336, andP. cepacia H201. The results indicated that both the relative rates of primary degradation of PCBs and the choice of the ring attacked were dependent on the bacterial strain used. The bacterial strains exhibited considerable differences in their relative reactivity preferences for attack on mono- and dichlorophenyl groups and in the degree to which the attack was affected by the chlorine substitution pattern on the nonreacting ring. For MB1 the reactivity pattern was 3-≥4-≫2-chlorophenyl with no attack on 2,4- or 2,5-chlorophenyl groups. This strain was relatively insensitive to the chlorine substitution pattern on the nonreacting ring. Strains H1130, H430, H201, and Pi434 exhibited the same reactivity preferences as MB1, but for these strains (and for all others tested) the chlorination pattern on the nonreacting ring had a strong effect. For strain H336 the reactivity preference was 4-≥2->2,4-≥3-chlorophenyl, with no evidence of attack on 2,5-chlorophenyl rings. For strains H850 and LB400 the relative reactivity was 2->2,5->3-≫2,4->4-chlorophenyl. On this basis we propose that the eight bacterial strains represent four distinct classes of biphenyl/PCB-dioxygenase activity.The types of products formed were largely strain-independent and were determined primarily by the chlorine substitution pattern on the reacting ring. When the reacting ring was an unsubstituted phenyl or a 2-chlorophenyl group, the products were chlorobenzoic acids in high yields; for a 3-chlorophenyl ring, both chlorobenzoic acids and chloroacetophenones in moderate yields; and for a 4- or 2,4-chlorophenyl group, chlorobenzoic acids in low yields with an apparent accumulation ofmeta ring-fission product. Strains H850 and LB400 were able to degrade the 3-chlorobenzoic acid that they produced from the degradation of 2,3'-chlorobiphenyl. We conclude that despite differences among strains in the specificity of the initial dioxygenase, the specificities of the enzymes responsible for the subsequent degradation to chlorobenzoic acid and/or chloroacetophenone are quite similar for all strains.}, }
@article {pmid24193966, year = {1990}, author = {Young, LY and Salkinoja-Salonen, M}, title = {Editorial.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {85-86}, doi = {10.1007/BF02543869}, pmid = {24193966}, issn = {0095-3628}, }
@article {pmid24193965, year = {1990}, author = {Shikano, S and Luckinbill, LS and Kurihara, Y}, title = {Changes of traits in a bacterial population associated with protozoal predation.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {75-84}, pmid = {24193965}, issn = {0095-3628}, abstract = {In an attempt to understand the significance of predation in the evolution of prey species, the ecological and morphological characteristics of bacterial species under predation by a ciliated protozoa,Cyclidium sp., were investigated. Serial transfer at 7 day intervals was applied to the bacterial populations in the presence or absence ofCyclidium. Although cells of the parental bacterial strain are typically short rods up to 1.5 μm long, cells of much greater length, up to 20 μm long (type L) were found in populations exposed to predation fromCyclidium. However, the wildtype, shorter length bacteria persisted even after the appearance of type L. Type L was not observed in the singl bacterial culture throughout the serial transfers. Type L appeared to improve the ability to escape predation by elongating cell size, but growth rate and saturation density were decreased.}, }
@article {pmid24193964, year = {1990}, author = {Sukiman, HI and New, PB}, title = {Relationship between root colonization and initial adsorption ofAzospirillum to plant roots.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {65-74}, pmid = {24193964}, issn = {0095-3628}, abstract = {Four strains ofAzospirillum were ranked according to numbers of cells adsorbed on the roots of seedlings in liquid medium, and the rankings were evaluated for their usefulness in predicting success of colonization of the roots of pot-grown plants.Different rankings were observed on different parts of the roots and on different host plants. Rhizosphere colonization results for rice were similar to those for clover and showed little difference between bacterial strains. The population densities were approximately equal to those of the most dense strains in the wheat rhizosphere, whereas the highest concentrations in the root interior of clover and rice were only about one-tenth of those in wheat.Rankings of initial adsorptive ability on various parts of the roots showed potential for predicting the best strains for colonizing the root interiors of wheat and clover. On wheat, the two strains (Cd and SpBr14) which showed best initial adsorption to the root cap were best at colonizing the endorhizosphere of pot-grown plants. For rice, strains Cd and SpBr14 gave lowest and highest values, respectively, both for adsorption to the terminal 2 cm of roots and for subsequent colonization of the root interior. Data on initial adsorption were of no value in predicting the relative success of strains in colonizing the root surface of any host plants or the interior of clover roots.}, }
@article {pmid24193963, year = {1990}, author = {Di-Ruggiero, J and Gounot, AM}, title = {Microbial manganese reduction mediated by bacterial strains isolated from aquifer sediments.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {53-63}, pmid = {24193963}, issn = {0095-3628}, abstract = {One hundred and five strains isolated from aquifer sediments andEscherichia coli ML30S were tested for their ability to reduce manganese oxides. Eighty-two strains, includingE. coli, reduced manganese. In most cases the bacterial activity decreased the pH and Eh below 6.75 and 350 mV, respectively, enhancing a spontaneous and nonspecific reduction of manganese. However, for 12 strains the reduction was specifically catalyzed by bacteria; the high pH and Eh values would not permit a spontaneous reduction of manganese. Some of the most active strains were identified as genera common in soils and waters, i.e.,Pseudomonas, Bacillus, Corynebacterium, andAcinetobacter. Two strains were studied in detail. One of the strains, identified asPseudomonas fluorescens, required contact between the cells and the manganese oxides for reduction to occur. The reduction was inhibited by 15 mM of sodium azide. The other strain, identified asAcinetobacter johnsonii, catalyzed manganese reduction by an inductive and dialyzable substance which was excreted by the bacteria. The mechanism involved has not been previously demonstrated.}, }
@article {pmid24193962, year = {1990}, author = {Pedersen, K and Ekendahl, S}, title = {Distribution and activity of bacteria in deep granitic groundwaters of southeastern sweden.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {37-52}, pmid = {24193962}, issn = {0095-3628}, abstract = {This study investigated the distribution of bacteria in groundwater from 16 different levels in five boreholes in granite bedrock down to a maximum of 860 m. Enrichment cultures were used to assay the groups of bacteria present. Autoradiographic studies with(14)C- or(3)H-labeled formate, methanol, acetate, lactate, glucose, sodium bicarbonate, leucine, glutamine, thymidine, orN-acetyl-glucosamine were used to obtain information about bacteria active in substrate uptake. The biofilm formation potential was studied in one borehole. The chemical environment in the groundwater was anaerobic with an Eh between -112 and -383 mV, a pH usually around 8, and a temperature range of 10.2 to 20.5°C, depending on the depth. The organic content ranged between <0.5 and 9.5 mg total organic carbon liter(-1). Carbon dioxide, hydrogen, hydrogen sulfide, and methane were present in the water. The nitrate, nitrite, and phosphate concentrations were close to, or below, the detection limits, while there were detectable amounts of NH4 (+) in the range of 4 to 330 μg liter(-1). The average total number of bacteria was 2.6×10(5) bacteria ml(-1), as determined with an acridine organge direct-count (AODC) technique. The average number of bacteria that grew on a medium with 1.5 g liter(-1) of organic substrate was 7.7×10(3) colony-forming units (CFU) ml(-1). The majority of these were facultatively anaerobic, gram-negative, nonfermenting heterotrophs. Enrichment cultures indicated the presence of anaerobic bacteria capable of growth on C-1 compounds and hydrogen, presumably methanogenic bacteria. Most probable number assays with sulfate and lactate revealed up to 5.6×10(4) viable sulfate-reducing bacteria per ml. A biofilm development experiment indicated an active attached microbial population. Active substrate uptake could not be registered with the bulk water populations, except for an uptake of leucine not associated with growth. The bulk water microbial cells in deep groundwater may be inactive cells detached from active biofilms on the rock surface.}, }
@article {pmid24193961, year = {1990}, author = {Jeffrey, WH and Paul, JH and Cazares, LH and Deflaun, MF and David, AW}, title = {Correlation of nonspecific macromolecular labeling with environmental parameters during [(3)H]Thymidine incorporation in the waters of southwest florida.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {21-35}, pmid = {24193961}, issn = {0095-3628}, abstract = {During routine [(3)H]thymidine incorporation measurements of environmental samples, significant amounts of radioactivity are often incorporated into macromolecules other than DNA. Although the percentage of nonspecific labeling varies both temporally and spatially, the cause(s) of these variations remain unknown. Correlations between the percent incorporated radioactivity in DNA and a variety of experimental and environmental parameters measured in the Alfia River, Crystal River, Medard Reservoir, and Bayboro Harbor were examined. The amount of radioactivity incorporated into DNA ranged from 6 to 95% ([Formula: see text]; n=121). Nonspecific labeling began immediately upon the addition of [(3)H]thymidine and was linear over time. Labeling patterns were independent of both the amount of thymidine added and cell-size fraction. A two year study of Bayboro Harbor indicated no conclusive relationship between nonspecific labeling and seasonality. The amount of radioactivity incorporated into DNA was inversely correlated with total rates of thymidine incorporation and a strong diurnal pattern was observed in the Crystal River. No consistent relationship was observed between labeling patterns and primary productivity, chlorophylla, particulate DNA, dissolved DNA, bacterial cell numbers, temperature, salinity, and dissolved organic carbon. The only relationship with dissolved inorganic nutrients (N and P) occurred in the Crystal River. In this phosphate limited river, the percent of radioactivity incorporated into DNA was positively correlated with phosphate concentrations. These results indicate that nonspecific labeling is not dependent on any one parameter but may be a function of many interacting environmental factors or a function of the specific ambient bacterial population.}, }
@article {pmid24193960, year = {1990}, author = {Scanferlato, VS and Lacy, GH and Cairns, J}, title = {Persistence of genetically engineeredErwinia carotovora in perturbed and unperturbed aquatic microcosms and effect on recovery of indigenous bacteria.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {11-20}, pmid = {24193960}, issn = {0095-3628}, abstract = {Genetically engineeredErwinia carotovora persisted significantly longer in thermally perturbed microcosms (35 days) than in nonstressed microcosms (5 days). Decreased pressure of competitors and predators and increased nutrient availability were examined as the most probable reasons for greater vulnerability of perturbed microcosms to colonization by genetically engineered microorganisms (GEMs). Indigenous bacteria that competed with GEMs for the same nutrient sources (protein, cellulose, pectate) were present immediately after perturbation in densities one to two orders of magnitude lower than in unperturbed microcosms, but their populations increased to densities significantly higher than in unperturbed microscosms 10 to 15 days after inoculation. Predators of bacteria (protozoans, cladocerans, nematodes, and rotifers) were present during the experiment in unperturbed microcosms, while dense populations of bacteriovorous nanoflagellates developed in perturbed microcosms. Preemptive inoculation of perturbed microcosms with GEMs did not have a longlasting effect on the recovery of total, proteolytic, cellulolytic, and pectolytic bacteria in perturbed microscosms, indicating the absence of competitive exclusion.}, }
@article {pmid24193959, year = {1990}, author = {Kangatharalingam, N and Wang, L and Priscu, JC}, title = {An in situ technique to measure bacterial chemotaxis in natural aquatic environments.}, journal = {Microbial ecology}, volume = {20}, number = {1}, pages = {3-10}, pmid = {24193959}, issn = {0095-3628}, abstract = {A simple and reliable technique to study bacterial chemotaxis in natural aquatic environments is reported. This technique uses the test chemicals in known volumes of semi-solid agar media placed in double layered, highly porous, polyester tubes. Following in situ incubation, bacteria attracted by the test chemicals are enumerated with fluorescence microscopy following acridine orange staining. Studies in an eutrophic reservoir showed that significant numbers of bacteria were attracted to D-glucose and glycine; no significant effects were observed with L-serine, sodium succinate, or sodium chloride.}, }
@article {pmid24196368, year = {1990}, author = {Florin-Christensen, J and Florin-Christensen, M and Tiedtke, A and Rasmussen, L}, title = {The role of secreted acid hydrolases in the utilization of complex nutrients byTetrahymena.}, journal = {Microbial ecology}, volume = {19}, number = {3}, pages = {311-316}, pmid = {24196368}, issn = {0095-3628}, abstract = {In an attempt to extend our knowledge of the biology of feeding of the ciliateTetrahymena thermophila, this organism was grown axenically on complex organic material. The nutrient substrate was based on autoclaved wheat grains and adjusted to either pH 5.5 or 7.5. In wild type cultures the cells grew and multiplied only under acidic conditions. In cultures of a mutant cell line blocked in the secretion of acid hydrolases the cells did not grow at either pH value. Thus released acid hydrolases may play a key role in the utilization of complex nutrients in combination with uptake of small organic molecules. Mechanisms in the feeding biology ofTetrahymena thermophila andParamecium tetraurelia are compared.}, }
@article {pmid24196367, year = {1990}, author = {Op den Camp, HJ and Stumm, CK and Straatsma, G and Derikx, PJ and van Griensven, LJ}, title = {Hyphal and mycelial interactions betweenAgaricus bisporus andScytalidium thermophilum on agar media.}, journal = {Microbial ecology}, volume = {19}, number = {3}, pages = {303-309}, doi = {10.1007/BF02017174}, pmid = {24196367}, issn = {0095-3628}, abstract = {The interaction betweenAgaricus bisporus andScytalidium thermophilum on agar media was studied by differential interference contrast and phase contrast microscopy.A. bisporus combatively replacesS. thermophilum in culture on agar media. The antagonistic effect ofA. bisporus is transmissible through a cellophane membrane and causes irreversible disintegration ofS. thermophilum protoplasm, resulting in a total loss of viability after prolonged interaction between the two fungi. On compost extract agar, but not on other media, the growth rate ofA. bisporus increased from 2.7 to 5.3 mm·d(-1) following contact withS. thermophilum mycelium.}, }
@article {pmid24196366, year = {1990}, author = {Zimmerman, WJ and Bergman, B}, title = {TheGunnera symbiosis: DNA restriction fragment length polymorphism and protein comparisons ofNostoc symbionts.}, journal = {Microbial ecology}, volume = {19}, number = {3}, pages = {291-302}, pmid = {24196366}, issn = {0095-3628}, abstract = {Cyanobacteria separated from symbiosis with several species of the angiospermGunnera were comparatively characterized and correlated with the locales and taxonomy of their host plants. All were identified as strains ofNostoc. Protein profiles and DNA restriction fragment length polymorphisms (from hybridizations with heterologousnifH andglnA probes) determined that three of the four cyanobacteria fromGunnera grown at one site in Sweden, each from a different host species, were very similar or identical. Plants of one species,G. manicata, grown in a second location at the site were infected with a different cyanobiont. Among five isolates from two species ofGunnera, collected in the same locale in New Zealand, three subgroups were documented. Isolates from three differentGunnera species grown in separate locations in the United States were each uniquely different. None of the cyanobacteria differed in the molecular weights of their glutamine synthetase and Fe-nitrogenase proteins. The diversity and accessibility of compatibleNostoc populations present in the soil micro-environment, not a critical selective factor required byGunnera, were concluded to be a major determinant in symbiont selection.}, }
@article {pmid24196365, year = {1990}, author = {Carman, KR}, title = {Radioactive labeling of a natural assemblage of marine sedimentary bacteria and microalgae for trophic studies: An autoradiographic study.}, journal = {Microbial ecology}, volume = {19}, number = {3}, pages = {279-290}, pmid = {24196365}, issn = {0095-3628}, abstract = {Autoradiography was used to examine critical questions for trophic studies concerning the uptake of radioactive tracers by a natural assemblage of sedimentary microorganisms. Labeled organic substrates ([(3)H]-acetate and [(3)H]-thymidine) were taken up only by heterotrophic bacteria, and [(14)C]-bicarbonate was taken up only by microalgae. Only approximately 2% of the bacterial assemblage took up detectable quantities of either [(3)H]-acetate or [(3)H]-thymidine, regardless of whether labeled substrates were delivered to sediments via slurries or by injection with a microliter syringe. Significantly more diatoms were labeled when [(14)C]-bicarbonate was delivered to sediments by the injection method (75%) as compared to the slurry method (50%). These results indicate that radio-active tracers can be used in natural sediments to selectively label potential microbial food of invertebrate grazers. Only a small proportion of bacteria, however, may actually use a labeled substrate, which introduces a large uncertainty into the conversion of radioactivity in grazers to the number of bacteria consumed. Finally, the use of disruptive methods (e.g., slurries) to deliver labels to sediments does not increase the proportion of microorganisms that become labeled. Thus, given the variety of artifacts that may be associated with the use of sediment slurries, it is probably advisable to use nondisruptive methods to deliver substrates to sediments.}, }
@article {pmid24196364, year = {1990}, author = {Mittelman, MW and Nivens, DE and Low, C and White, DC}, title = {Differential adhesion, activity, and carbohydrate: Protein ratios ofPseudomonas atlantica monocultures attaching to stainless steel in a linear shear gradient.}, journal = {Microbial ecology}, volume = {19}, number = {3}, pages = {269-278}, pmid = {24196364}, issn = {0095-3628}, abstract = {Biofilm formation on metallic surfaces in marine and freshwater environments often precedes corrosion and other biofouling conditions. Attachment is mediated by such environmental factors as the presence of surface conditioning films, fluid dynamics, bulk-phase nutrient levels, and surface chemistry. In this study, we utilized a Fowler Cell Adhesion Measurement Module to demonstrate that the changes in cellular concentration and composition of a monoculture ofPseudomonas atlantica biofilms on stainless steel were a function of the applied shear force. At shear forces in the range of 3-10 dynes cm(-2) (1.0 liter min(-1)), attachment as measured by acridine orange direct microscopic counts was greatest at the higher shear forces.(14)C-Acetate uptake activity on the stainless steel surfaces increased with shear stress. Acetate incorporation ranged from 1×10(-5) to 19×10(-5) μmol cm(-2) between 0.15 and 30 dynes cm(-2) for 30 min uptake periods. On a per cell basis, however, activity decreased with shear, indicating a shift in metabolism. Fourier transform infrared spectroscopy revealed that protein and carbohydrate concentrations also increased with the applied shear. Increased biofilm C∶N ratios and total fatty acids were associated with the higher shear stresses. Neither radius of interaction nor biofilm age appeared to significantly influence the relationship between fluid shear and attachment and cellular composition ofP. atlantica biofilms in the range of 1-10 dynes cm(-2).}, }
@article {pmid24196363, year = {1990}, author = {Jeffrey, WH and Paul, JH and Stewart, GJ}, title = {Natural transformation of a marineVibrio species by plasmid DNA.}, journal = {Microbial ecology}, volume = {19}, number = {3}, pages = {259-268}, pmid = {24196363}, issn = {0095-3628}, abstract = {Vibrio sp. DI9, recently isolated from Tampa Bay, FL, has been found to be naturally transformed by the broad host range plasmid pKT230 in both filter transformation assays and sterile sediment microcosms. This is the first report of natural transformation by plasmid DNA of aVibrio sp. and of a marine bacterial isolate. Transformation frequencies ranged from 0.3 to 3.1×10(-8) transformants per recipient. Transformants were detected by both plating and by selection for growth in liquid medium in the presence of streptomycin and kanamycin and confirmed by probing of southern transfers. Transformation was enhanced by multimeric forms of the plasmid. A technique using sediment microcosms, mixed populations ofVibrio sp. DI9 and another antibiotic resistant organism, and enrichment in liquid media has been developed which allows detection of transformation at frequencies too low to be detected by plating. This technique may serve as a model for the detection of natural transformation in the environment. These results suggest that natural transformation may be one mechanism of horizontal plasmid transfer in the marine environment, and may provide the methodology with which to detect this process in natural populations of bacteria.}, }
@article {pmid24196362, year = {1990}, author = {Griffiths, RP and Moyer, CL and Caldwell, BA and Ye, C and Morita, RY}, title = {Long-term starvation-induced loss of antibiotic resistance in bacteria.}, journal = {Microbial ecology}, volume = {19}, number = {3}, pages = {251-257}, pmid = {24196362}, issn = {0095-3628}, abstract = {Escherichia coli, Pseudomonas fluorescens, and aPseudomonas sp. strain 133B containing the pSa plasmid were starved in well water for up to 523 days. There were two patterns of apparent antibiotic resistance loss observed. InPseudomonas sp. strain 133B, there was no apparent loss of antibiotic resistance even after starvation for 340 days. InE. coli, by day 49 there was a ten-fold difference between the number of cells that would grow on antibiotic- and nonantibiotic-containing plates. However, over 76% of the cells that apparently lost their antibiotic resistance were able to express antibiotic resistance after first being resuscitated on non-selective media. By day 523, only 12% of these cells were able to express their antibiotic resistance after being resuscitated. After starvation for 49 days, cells that could not grow on antibiotic medium even after resuscitation, showed a permanent loss of chloramphenicol (Cm) resistance but retained resistance to kanamycin (Km) and streptomycin (Sm). Restriction enzyme digests show that a 2.5 to 3.0 Kb region from map location 12.5 to 15.5 Kb was deleted. This coincides with the 2.5 Kb reduction in plasmid size observed in 3 isolates that had lost antibiotic resistance after starvation for 49 days.}, }
@article {pmid24196361, year = {1990}, author = {van Overbeek, LS and van Elsas, JD and Trevors, JT and Starodub, ME}, title = {Long-term survival of and plasmid stability inPseudomonas andKlebsiella species and appearance of nonculturable cells in agricultural drainage water.}, journal = {Microbial ecology}, volume = {19}, number = {3}, pages = {239-249}, pmid = {24196361}, issn = {0095-3628}, abstract = {One year after introduction into agricultural drainage waterPseudomonas fluorescens R2f (RP4),Pseudomonas putida CYM318 (pRK2501), andKlebsiella aerogenes NCTC418 (pBR322) could be recovered on agar media. Survival of the introduced strains depended on competition with the indigenous microflora, the presence of nutrients, and the availability of air.In contrast toK. aerogenes NCTC418 (pBR322), bothPseudomonas species lost their plasmids, as indicated by the consistently lower colony counts on selective medium compared with the counts on nonselective medium. The plasmid loss did not depend on nutrient status and oxygen supply. P. fluorescens R2f cells could be detected with the immunofluorescence (IF) technique. Total cell counts determined by IF were consistently higher than corresponding colony counts. Even in samples where no colonies were recovered, R2f cells could be detected by IF. This indicated the occurrence of nonculturable R2f cells in drainage water. Homology with(32)P-labelled plasmid RP4 DNA was found in several drainage water samples that originally receivedP. fluorescens R2f (RP4), by using the cell suspension filter hybridization technique. P. putida CYM318 andK. aerogenes NCTC418 cells could also be detected in sterile drainage water samples, after nonspecific staining with fluorescein isothiocyanate. Cell counts of both strains were consistently higher than corresponding plate counts.}, }
@article {pmid24196360, year = {1990}, author = {Tezuka, Y}, title = {Bacterial regeneration of ammonium and phosphate as affected by the carbon:nitrogen:phosphorus ratio of organic substrates.}, journal = {Microbial ecology}, volume = {19}, number = {3}, pages = {227-238}, pmid = {24196360}, issn = {0095-3628}, abstract = {The effect of carbon∶nitrogen∶phosphorus (C∶N∶P) ratio of organic substrates on the regeneration of ammonium and phosphate was investigated by growing natural assemblages of freshwater bacteria in mineral media supplemented with the simple organic C, N, and P sources (glucose, asparagine, and sodium glycerophosphate, respectively) to give 25 different substrate C∶N∶P ratios. Both ammonium and phosphate were regenerated when C∶N and N∶P atomic ratios of organic substrates were ≤10∶1 and ≤16∶1, respectively. Only ammonium was regenerated when C∶N and N∶P ratios were ≤10∶1 and ≥10-20∶1, respectively. On the other hand, neither ammonium nor phosphate was regenerated when C∶N and N∶P ratios were ≥15∶1 and ≥5∶1, respectively. In no case was phosphate alone regenerated. As bacteria were able to alter widely the C∶N∶P ratio of their biomass, the growth yield of bacteria appeared primarily dependent on the substrate carbon concentration, irrespective of a wide variation in the substrate C∶N∶P ratio.}, }
@article {pmid24196359, year = {1990}, author = {Ward, BB}, title = {Kinetics of ammonia oxidation by a marine nitrifying bacterium: Methane as a substrate analogue.}, journal = {Microbial ecology}, volume = {19}, number = {3}, pages = {211-225}, pmid = {24196359}, issn = {0095-3628}, abstract = {In pure culture, the marine ammonia oxidizer,Nitrosococcus oceanus, exhibits normal Michaelis Menten kinetics with respect to its primary substrate, ammonia.N. oceanus also exhibits a kinetic response to methane. In the absence of methane, oxidation of ammonia is first order with respect to ammonia concentration under atmospheric oxygen concentrations at seawater pH. In the presence of methane, ammonia oxidation is inhibited, and the amount of inhibition is related to the relative concentrations of methane and ammonia. Using semicontinuous batch cultures as a source of organisms for short-term kinetic experiments, I investigated the relationship between ammonia and methane oxidation inN. oceanus by varying the absolute and relative concentration of both substrates. Methane appeared to act as a substrate analogue, and its effect on ammonia oxidation was modeled as a permutation of competitive inhibition involving a cooperative enzyme system. Methane was oxidized byN. oceanus, even in the absence of measurable ammonia oxidation, but the process was inhibited at increasing methane concentrations. Of the two product pools analyzed, an average of 37% of methane oxidized was detected in particulate (cell) material and the remainder was detected in(14)CO2. The contribution of methane to total carbon assimilation varied with the ratio [CH4]/[NH3] and may be significant under substrate concentrations typical of a dilute aquatic environment.}, }
@article {pmid24196312, year = {1990}, author = {Debiase, AE and Sanders, RW and Porter, KG}, title = {Relative nutritional value of ciliate protozoa and algae as food forDaphnia.}, journal = {Microbial ecology}, volume = {19}, number = {2}, pages = {199-210}, pmid = {24196312}, issn = {0095-3628}, abstract = {The relative importance of autotrophic flagellates, desmids, cyanobacteria, and ciliates as food forDaphnia magna was examined using cohort life tables. Each cohort was fed a single food type at a given concentration, and comparisons among each type were made. Algal feeding treatments included three levels of young (7 to 14 days old)Chlamydomonas reinhardi (Chlorophyta, Chlamydomonadacae), two levels of senescent (> 14 days old)C. reinhardi, two levels ofCryptomonas sp. (Chlorophyta, Cryptomonadacae), two levels ofStaurastrum sp. (Chlorophyta, Desmidacae), four levels of young (7 to 15 days old) or senescent (> 15 days old)Microcystis aeruginosa (Cyanophyta, Chlorococcacae), and a no-food treatment. The ciliatesCyclidium sp. andParamecium caudatum were also presented at concentrations of 1 or 10(2) cells/ml, as well as mixtures ofC. reinhardi (10(3)/ml) andCyclidium (1/ml) orP. caudatum (1/ml).Daphnia growth, reproduction, and survivorship were highest whenC. reinhardi orCryptomonas were the food source, while those starved or fedM. aeruginosa had shorter survivorship and lower growth and reproduction.Daphnia grew and had high survivorship when fedP. caudatum, but even though eggs were produced, most were aborted after 2 or 3 days.Staurastrum andCyclidium produced intermediate growth and survivorship, but reproduction was seen only in the 10(3) Staurastrum/ml treatment. Carbon and nitrogen content were general indicators of nutritional value. However, growth, reproduction, and survivorship were higher in some cohorts fed treatments containing relatively low levels of carbon and nitrogen. Other cohorts were short-lived and did not reproduce, despite being fed much higher levels of carbon and nitrogen. The results also suggest that green algae are nutritionally valuable forDaphnia, whereas cyanobacteria are not. As measured by life-table parameters, the nutritional value of ciliates was variable, with some being poor food sources. Thus, the potential of ciliates as a trophic link between microbial production and higher trophic levels may vary with the ciliate community structure. Our results suggest that ciliates alone were insufficient as a food source to supportDaphnia population growth.}, }
@article {pmid24196311, year = {1990}, author = {Els, HJ and Krecek, RC}, title = {Ultrastructure of filamentous microorganisms associated with zebra cyathostomes.}, journal = {Microbial ecology}, volume = {19}, number = {2}, pages = {187-198}, pmid = {24196311}, issn = {0095-3628}, abstract = {Filamentous microorganisms were observed colonizing the cuticle of cyathostomes (Nematoda: Strongylidae) collected from the large intestine of Burchell's zebra (Equus burchelli antiquorum). Scanning (SEM) and transmission (TEM) electron microscopy revealed three filamentous microorganisms, designated as segmented, continuous multicellular, and helical. The segmented and continuous multicellular morphotypes each revealed a process of segmentation in their developmental stages, and those of the segmented filaments are demonstrated in this report. In contrast, the helical types of filaments appeared to be complexes of spiraling rodshaped organisms. In addition to these filaments, the cyathostome cuticle was also colonized by other smaller microorganisms.}, }
@article {pmid24196310, year = {1990}, author = {Ogunseitan, OA and Sayler, GS and Miller, RV}, title = {Dynamic interactions ofPseudomonas aeruginosa and bacteriophages in lake water.}, journal = {Microbial ecology}, volume = {19}, number = {2}, pages = {171-185}, pmid = {24196310}, issn = {0095-3628}, abstract = {The persistence and interaction between newly isolated strains ofPseudomonas aeruginosa and resident bacteriophages indigenous to a freshwater environment was monitored over 45 days in lake water microcosms. The interaction between susceptible and resistant bacteria with pure phage (UT1) particles or a mixed phage population (M1) was investigated by following temporal changes in host density, phage-to-bacteria ratio (PBR), and the appearance of apparent prophage carriers within the host population. Decay rates of the phage (UT1) ranged from 0.054 hour(-1) in natural water to 0.027 hour(-1) in filtered lake water. About 45% of sensitive bacteria incubated with phase UT1 were pseudolysogenic within 12 hours of incubation in natural lake water. This process was delayed until 72 hours in the steile lake water control, suggesting that host-phage interaction is promoted in the presence of a viable natural microbial community. Phage UT1 appeared to stabilize the density of host bacteria in lake water at a level of 10(4) colony-forming units (cfu) ml(-1). Bacterial coexistence with the mixed phage (M1) population resulted in an oscillating equilibrium with the PBR stabilizing at about 3. The presence of extraneous homoimmune phages appeared to be detrimental to the stability of the pseudolysogens, which were maintained at a lower population density than prophage-free cells in lake water containing the mixed phage (M1) population.}, }
@article {pmid24196309, year = {1990}, author = {Brunel, B and Boeufgras, JM and Bernillon, D and Bardin, R}, title = {Phenotypic drift inBradyrhizobium japonicum populations after introduction into soils as established by numerical analysis.}, journal = {Microbial ecology}, volume = {19}, number = {2}, pages = {163-170}, pmid = {24196309}, issn = {0095-3628}, abstract = {The degree of phenotypic variation of the bacterial strains USDA 125-Sp, USDA 138 and USDA 138-SmBradyrhizobium japonicum a long time after introduction was studied in three experimental fields. A total of 54 phenotypic characters were analyzed by constructing a dendrogram based on an hierarchic classification. Strong similarities (92.6, 94 and 95%) were found between the isolates introduced into soil 8, 10 and 13 years ago and between their respectiveB. japonicum parental clones. The dendrogrammic analysis detected a small amount of phenotypic drift, however, between soil isolates and parental clones belonging to the same serogroup (selective effects were found to have generated 0 to 3.9% variation for the USDA 125-Sp inoculum introduced 8 years ago, and 3.2-3.5% after 10 and 13 years, respectively, for the USDA 138 and USDA 138-Sm bacterial inocula) and within the serogroup 125 soil isolates (2.7%). We found a similar evolution of serogroup 125 isolates when compared with parental clones conserved on slant agar at 4°C. When a drift was observed, the isolates from soil presented a lower activity for several enzymes and lower diversity compared with the parental clones.}, }
@article {pmid24196308, year = {1990}, author = {Postma, J and van Veen, JA}, title = {Habitable pore space and survival ofRhizobium leguminosarum biovartrifolii introduced into soil.}, journal = {Microbial ecology}, volume = {19}, number = {2}, pages = {149-161}, pmid = {24196308}, issn = {0095-3628}, abstract = {The hypothesis that the population size of introduced bacteria is affected by habitable pore space was studied by varying moisture content and bulk density in sterilized, as well as in natural loamy sand and silt loam. The soils were inoculated withRhizobium leguminosarum biovartrifolii and established and maintained at soil water potentials between -5 and -20 kPa (pF 1.7 and 2.3). Rhizobial cells were enumerated when population sizes were expected to be more or less stable. In sterilized soils, the rhizobial numbers were not affected or decreased only slightly when water potentials increased from -20 to -5 kPa. In natural soils, the decrease in rhizobial numbers with increasing water potentials was more pronounced. Bulk density had only minor effects on the population sizes of rhizobia or total bacteria. Soil water retention curves of both soils were used to calculate volume and surface area of pores from different diameter classes, and an estimation of the habitable pore space was made. Combining these values of the theoretical habitable pore space with the measured rhizobial numbers showed that only 0.37 and 0.44% of the habitable pore space was occupied in the sterilized loamy sand and silt loam, respectively. The situation in natural soil is more complicated, since a whole variety of microorganisms is present. Nevertheless, it was suggested that, in general, pore space does not limit proliferation and growth of soil microorganisms.}, }
@article {pmid24196307, year = {1990}, author = {Smith, JJ and Quintero, EJ and Geesey, GG}, title = {A sensitive chromatographic method for the detection of pyruvyl groups in microbial polymers from sediments.}, journal = {Microbial ecology}, volume = {19}, number = {2}, pages = {137-147}, pmid = {24196307}, issn = {0095-3628}, abstract = {A method was developed for the quantitation of pyruvyl groups in microbial polymers using mild acid hydrolysis, o-phenylenediamine labeling, reversed-phase high-performance liquid chromatography (RP-HPLC), and fluorescence detection. The method was used to determine the pyruvate content of various microbial exopolysaccharides and to estimate the abundance of polymeric pyruvate in freshwater sediments. The results of this method were compared with those of several other pyruvate assays. The detection limit of the method was 1.6 nmol pyruvate. As little as 3.7μg of the bacterial polysaccharide xanthan gum, or from 5 to 22 mg of sediment (depending on polymeric pyruvate content), were needed for detection and quantitation of polymeric pyruvate. The results should be useful in determining the contribution of polymeric pyruvate to total metal-binding ligands in sediments.}, }
@article {pmid24196306, year = {1990}, author = {Yacobi, YZ and Eckert, W and Trüper, HG and Berman, T}, title = {High performance liquid chromatography detection of phototrophic bacterial pigments in aquatic environments.}, journal = {Microbial ecology}, volume = {19}, number = {2}, pages = {127-136}, pmid = {24196306}, issn = {0095-3628}, abstract = {Pigment extracts of phototrophic bacteria isolated from Lake Kinneret (Rhodopseudomonas palustris, Thiocapsa roseopersicina, Prosthecochloris aestuaris andChlorobium phaeobacteroides) were studied by means of high performance liquid chromatography (HPLC). An absorption wavelength of 360 nm provided the best resolution among the pigments of the species tested and between them and chlorophylla. Signature pigments were identified for each of these species, and their presence was thereby monitored in lake water samples.C. phaeobacteroides, which was observed in the anaerobic hypolimnion and predominated in the metalimnion, was recognized by a characteristic cluster of major chlorophyllous pigment peaks. The spectral qualities of these pigments were close but not identical to published data on bacteriochlorophylle, presumably due to the use of different solvents for extraction. The intensity of these pigment peaks was employed to determine the depth of the greatest phototrophic bacterial biomass, which was not related to that of algae.}, }
@article {pmid24196259, year = {1990}, author = {Helander, ML and Rantio-Lehtimäki, A}, title = {Effects of watering and simulated acid rain on quantity of phyllosphere fungi of birch leaves.}, journal = {Microbial ecology}, volume = {19}, number = {1}, pages = {119-125}, pmid = {24196259}, issn = {0095-3628}, abstract = {The effects of simulated acid rain on the population of birch phyllosphere fungi and species/genera/group composition of fungi on birch leaves were investigated in a field study in the subarctic region of northern Finland. The acid rain treatments consisted of a mixture of H2SO4 and HNO3 with a mass ratio of 2.86∶1 (S∶N) with acidities of pH 4 (A4) and pH 3 (A3). Dry control (DC) plots received only natural precipitation; irrigated control (IC) plots received spring water (pH 6) in a volume equal to the acid treatment plots. Treatments began in 1985. Culturing of the fungi inhabiting the birch leaves was performed five times during the summer of 1988. The number of fungal colonies was significantly decreased on one of five sampling dates in the pH 4 treatment and on three of five sampling dates in the pH 3 treatment. Irrigation with spring water did not have a significant effect. The acid rain treatments affected the microflora of the upper branches (at a height of 2 m) and of the lower branches (at a height of 0.5 m) equally. The lower branches had significantly more fungi than the upper ones on three of five sampling dates. The number of phyllosphere fungi isolated from birch leaves was greater in late summer than in early summer. The most abundant taxon (∼80%) wasAureobasidium pullulons, followed byHormonema sp. and zygomycetes.}, }
@article {pmid24196258, year = {1990}, author = {Palmer, RJ and Friedmann, EI}, title = {Water relations and photosynthesis in the cryptoendolithic microbial habitat of hot and cold deserts.}, journal = {Microbial ecology}, volume = {19}, number = {1}, pages = {111-118}, pmid = {24196258}, issn = {0095-3628}, abstract = {Two cryptoendolithic microbial communities, lichens in the Ross Desert of Antarctica and cyanobacteria in the Negev Desert, inhabit porous sandstone rocks of similar physical structure. Both rock types adsorb water vapor by physical mechanisms unrelated to biological processes. Yet the two microbial communities respond differently to water stress: cryp-toendolithic lichens begin to photosynthesize at a matric water potential of -46.4 megaPascals (MPa) [70% relative humidity (RH) at 8°C], resembling thallose desert lichens. Cryptoendolithic cyanobacteria, like other prokaryotes, photosynthesize only at very high matric water potentials [> -6.9 MPa, 90% RH at 20°C].}, }
@article {pmid24196257, year = {1990}, author = {Sanders, RW and Porter, KG and Caron, DA}, title = {Relationship between phototrophy and phagotrophy in the mixotrophic chrysophytePoterioochromonas malhamensis.}, journal = {Microbial ecology}, volume = {19}, number = {1}, pages = {97-109}, pmid = {24196257}, issn = {0095-3628}, abstract = {The time scales involved in the transition between phototrophic and phagotrophic modes of nutrition were examined in the mixotrophic chrysophytePoterioochromonas malhamensis. Phagotrophy began almost immediately when bacteria were added to phototrophically growing cultures of the alga, and chlorophylla concentration per cell in these cultures decreased over a 24-hour period. Chlorophyll concentrations per cell began to increase when bacteria were grazed to a density of approximately 10(6) ml(-1), but after more than 24 hours they had not returned to the higher chlorophyll concentrations observed in the phototrophically grown cultures. Bacterivory was the dominant mode of nutrition in all cultures containing heat-killed bacteria. Photosynthesis did not contribute more than ≈7% of the total carbon budget of the alga when in the presence of abundant heat-killed bacteria. Bacterial density was the primary factor influencing the ability ofP. malhamensis to feed phagotrophically, while light intensity, pH, and the presence of dissolved organic matter had no effect on phagotrophy. We conclude thatP. malhamensis is capable of phagotrophy at all times. In contrast, phototrophy is inducible in the light during starvation and is a long-term survival strategy for this mixotrophic alga (i.e., it operates on time scales greater than a diel cycle).}, }
@article {pmid24196256, year = {1990}, author = {Mancuso, CA and Franzmann, PD and Burton, HR and Nichols, PD}, title = {Microbial community structure and biomass estimates of a methanogenic Antarctic Lake ecosystem as determined by phospholipid analyses.}, journal = {Microbial ecology}, volume = {19}, number = {1}, pages = {73-95}, pmid = {24196256}, issn = {0095-3628}, abstract = {Phospholipid analyses were performed on water column particulate and sediment samples from Ace Lake, a meromictic lake in the Vestfold Hills, Antarctica, to estimate the viable microbial biomass and community structure in the lake. In the water column, methanogenic bacterial phospholipids were present below 17 m in depth at concentrations which converted to a biomass of between 1 and 7×10(8) cells/liter. Methanogenic biomass in the sediment ranged from 17.7×10(9) cells/g dry weight of sediment at the surface to 0.1×10(9) cells/g dry weight at 2 m in depth. This relatively high methanogenic biomass implies that current microbial degradation of organic carbon in Ace Lake sediments may occur at extremely slow rates. Total microbial biomass increased from 4.4×10(8) cells/ liter at 2 m in depth to 19.4×10(8) cells/liter at 23 m, near the bottom of the water column. Total nonarchaebacterial biomass decreased from 4.2 ×10(9) cells/g dry weight in the surface sediment (1/4 the biomass of methanogens) to 0.06×10(8) cells/g dry weight at 2 m in depth in the sediment. Phospholipid fatty acid profiles showed that microeukaryotes were the major microbial group present in the oxylimnion of the lake, while bacteria dominated the lower, anoxic zone. Sulfate-reducing bacteria (SRB) comprised 25% of the microbial population at 23 m in depth in the water column particulates and were present in the surface sediment but to a lesser extent. Biomass estimates and community structure of the Ace Lake eco-system are discussed in relation to previously measured metabolic rates for this and other antarctic and temperate ecosystems. This is the first instance, to our knowledge, in which the viable biomass of methanogenic and SRB have been estimated for an antarctic microbial community.}, }
@article {pmid24196255, year = {1990}, author = {Nielsen, LP and Christensen, PB and Revsbech, NP and Sørensen, J}, title = {Denitrification and oxygen respiration in biofilms studied with a microsensor for nitrous oxide and oxygen.}, journal = {Microbial ecology}, volume = {19}, number = {1}, pages = {63-72}, pmid = {24196255}, issn = {0095-3628}, abstract = {Depth distributions of O2 respiration and denitrification activity were studied in 1- to 2-mm thick biofilms from nutrient-rich Danish streams. Acetylene was added to block the reduction of N2O, and micro-profiles of O2 and N2O in the biofilm were measured simultaneously with a polarographic microsensor. The specific activities of the two respiratory processes were calculated from the microprofiles using a one-dimensional diffusion-reaction model. Denitrification only occurred in layers where O2 was absent or present at low concentrations (of a fewμM). Introduction of O2 into deeper layers inhibited denitrification, but the process started immediately after anoxic conditions were reestablished. Denitrification activity was present at greater depth in the biofilm when the NO3 (-) concentration in the overlying water was elevated, and the deepest occurrence of denitrification was apparently determined by the depth penetration of NO3 (-). The denitrification rate within each specific layer was not affected by an increase in NO3 (-) concentration, and the half-saturation concentration (Km) for NO3 (-) therefore considered to be low (<25μM). Addition of 0.2% yeast extract stimulated denitrification only in the uppermost 0.2 mm of the denitrification zone indicating a very efficient utilization of the dissolved organic matter within the upper layers of the biofilm.}, }
@article {pmid24196254, year = {1990}, author = {Fallon, RD and Boylen, CW}, title = {Bacterial production in freshwater sediments: Cell specific versus system measures.}, journal = {Microbial ecology}, volume = {19}, number = {1}, pages = {53-62}, pmid = {24196254}, issn = {0095-3628}, abstract = {Estimates of bacterial production based on total trichloroacetic acid (TCA)-precipitable [methyl-(3)H]thymidine incorporation and frequency of dividing cell (FDC) techniques were compared to sediment respiration rates in Lake George, New York. Bacterial growth rates based on thymidine incorporation ranged from 0.024 to 0.41 day(-1), while rates based on FDC ranged from 1.78 to 2.48 day(-1). Respiration rates ranged from 0.11 to 1.8μmol O2·hour(-1)·g dry weight sediment(-1). Thymidine incorporation yielded production estimates which were in reasonable agreement with respiration rates. Production estimates based on FDC were 4- to 190-fold higher than those predicted from respiration rates.}, }
@article {pmid24196253, year = {1990}, author = {Oren, A}, title = {Thymidine incorporation in saltern ponds of different salinities: Estimation of in situ growth rates of halophilic archaeobacteria and eubacteria.}, journal = {Microbial ecology}, volume = {19}, number = {1}, pages = {43-51}, pmid = {24196253}, issn = {0095-3628}, abstract = {Incorporation of [methyl-(3)H]thymidine was measured in solar saltern ponds of different salinities. Estimated doubling times of the bacterial communities were in the range of 1.1 to 22.6 days. Even at the highest salt concentrations (NaCl saturation), relatively rapid thymidine incorporation was observed. In an attempt to differentiate between activity of halophilic archaeobacteria (theHalobacterium group) and halophilic eubacteria, taurocholate, which causes lysis of the halobacteria without affecting eubacteria, was used. At salt concentrations exceeding 250 g/liter all thymidine incorporation activity could be attributed to halobacteria. Aphidicolin, a potent inhibitor of DNA synthesis in halobacteria, completely abolished thymidine incorporation at the highest salinities, but also caused significant inhibition at salinities at which halobacteria are expected to be absent. Attempts to use nalidixic acid to selectively inhibit DNA synthesis by the eubacterial communities were unsuccessful.}, }
@article {pmid24196252, year = {1990}, author = {Cahill, MM}, title = {Bacterial flora of fishes: A review.}, journal = {Microbial ecology}, volume = {19}, number = {1}, pages = {21-41}, pmid = {24196252}, issn = {0095-3628}, abstract = {Bacterial floras isolated from eggs, skin, gills, and intestines have been described for a limited number of fish species. Generally, the range of bacterial genera isolated is related to the aquatic habitat of the fish and varies with factors such as the salinity of the habitat and the bacterial load in the water. In many investigations, identification of isolates to the genus level only makes it difficult to determine the precise relationships of aquatic and fish microfloras. Bacteria recovered from the skin and gills may be transient rather than resident on the fish surfaces. Microfloras of fish intestines appear to vary with the complexity of the fish digestive system. The genera present in the gut generally seem to be those from the environment or diet which can survive and multiply in the intestinal tract, although there is evidence for a distinct intestinal microflora in some species. While obligate anaerobes have been recovered from carp and tilapia intestines, low ambient temperatures may prevent colonization by anaerobes in species such as rainbow trout.}, }
@article {pmid24196251, year = {1990}, author = {Sayler, GS and Hooper, SW and Layton, AC and King, JM}, title = {Catabolic plasmids of environmental and ecological significance.}, journal = {Microbial ecology}, volume = {19}, number = {1}, pages = {1-20}, pmid = {24196251}, issn = {0095-3628}, abstract = {The environmental and ecological significance of catabolic plasmids and their host strains are discussed in the context of their potential application for environmental biotechnology. Included is a comprehensive list of naturally occurring discrete catabolic plasmids isolated from either natural habitats or selective enrichment studies. General properties, such as plasmid maintenance, stability and transfer, are discussed together with the techniques for plasmid detection and monitoring in the environment. The issues concerning the construction of catabolic strains with new or broader substrate ranges and the uses of monocultures or consortia for in situ treatment are addressed.}, }
@article {pmid24196208, year = {1989}, author = {Schmidt, SK and Gier, MJ}, title = {Dynamics of microbial populations in soil: Indigenous microorganisms degrading 2,4-dinitrophenol.}, journal = {Microbial ecology}, volume = {18}, number = {3}, pages = {285-296}, pmid = {24196208}, issn = {0095-3628}, abstract = {The mineralization of 2,4-dinitrophenol (DNP) and changes in the DNP-mineralizing population over a wide range of DNP concentrations were monitored to evaluate the dynamics of the DNP-mineralizing populations in two soils (soils 1 and 2). Curves of CO2 evolution were analyzed using nonlinear regression analysis and models incorporating parameters for population size and growth rate. The results of these analyses were compared to independent estimates of the DNP-mineralizing population from most-probable-number (MPN) determinations. The combined results of these analyses showed that 0.1μg of DNP g(-1) of soil was too low a concentration to support maintenance or growth of the DNP-mineralizing population, whereas all higher concentrations supported either maintenance or growth of the population in soil 1. Independent estimates of population size showed good agreement between the nonlinear regression and MPN techniques, especially at initial DNP concentrations below 100μg g(-1). Estimates of both population size and maximum specific growth rate varied with concentration, possibly indicating the existence of two different DNP-mineralizing populations in soil 1. In the other soil tested (soil 2), the population of DNP-mineralizers was much lower than in the first soil, and no evidence of two populations was obtained. In soil 2, good agreement between the nonlinear regression and MPN estimates of population size was also obtained. Results of this study demonstrate the power of using testable models of population dynamics to obtain useful estimates of parameters of microbial growth and survival in soil.}, }
@article {pmid24196207, year = {1989}, author = {Messer, AC and Lee, MJ}, title = {Effect of chemical treatments on methane emission by the hindgut microbiota in the termiteZootermopsis angusticollis.}, journal = {Microbial ecology}, volume = {18}, number = {3}, pages = {275-284}, pmid = {24196207}, issn = {0095-3628}, abstract = {Selective removal of symbiotic hindgut microorganisms by chemical treatments reduced methane emission by the termiteZootermopsis angusticollis. Methane emission from untreated termites incubated in 25% H2 increased 123%, from 10.3 nmol/termite/hour (U) to 22.9 U. Though linear with time, methane emission was not correlated with termite mass. Hyperbaric oxygen treatments reduced methane emission to unquantifiable levels and eliminated all but the protozoaTricercomitus andHexamastix. Exogenous H2 restored 5% of methane emission to 1.3 U. 2-bromoethanesulfonic acid, fed on filter papers to termites, eliminated methane production. Epifluorescence microscopy showed that this treatment selectively removed methanogens from symbioses withTricercomitus, Hexamastix, andTrichomitopsis, but the protozoa did not appear to be affected. The insect molting hormone 20-hydroxyecdysone reduced methane production 86% to 1.6 U from an initial level of 11.4 U. Hydrogen incubation increased this rate to 77% of the initial rate, 8.8 U. Hormone treatment reduced the number ofTrichonympha in the hindgut and induced sexuality in these protozoa. A model suggests thatTrichonympha evolve most of the hydrogen and that methanogenic bacteria symbiotic withTrichomitopsis produce most of the methane in this hindgut ecosystem.}, }
@article {pmid24196206, year = {1989}, author = {Müller, H}, title = {The relative importance of different ciliate taxa in the pelagic food web of lake constance.}, journal = {Microbial ecology}, volume = {18}, number = {3}, pages = {261-273}, pmid = {24196206}, issn = {0095-3628}, abstract = {Abundance, biovolume, and species composition of pelagic ciliates in Lake Constance were recorded over two annual cycles (1987/88). Production was estimated from mean annual biovolumes and size-specific growth rates obtained from the literature. Cell concentrations and biovolumes ranged from 0.1 to 120 cells ml(-1) and from 3 to 1,200 mm(3) m(-3), respectively. Mean annual values were, respectively, 6.8 cells ml(-1) and 94 mm(3) m(-3) in 1987, and 12.0 cells ml(-1) and 130 mm(3) m(-3) in 1988. In both years, prostome nanociliates (<20μm) dominated numerically, while strobiliids in the size range 20-35μm contributed most significantly to ciliate production. Ciliate community production, according to a crude calculation, yielded approximately 10-15 g C m(-2) year(-1).}, }
@article {pmid24196205, year = {1989}, author = {Shieh, WY and Simidu, U and Maruyama, Y}, title = {Enumeration and characterization of nitrogen-fixing bacteria in an eelgrass (Zostera marina) bed.}, journal = {Microbial ecology}, volume = {18}, number = {3}, pages = {249-259}, pmid = {24196205}, issn = {0095-3628}, abstract = {Marine nitrogen-fixing bacteria distributed in the eelgrass bed and seawater of Aburatsubo Inlet, Kanagawa, Japan were investigated using anaerobic and microaerobic enrichment culture methods. The present enrichment culture methods are simple and efficient for enumeration and isolation of nitrogen-fixing bacteria from marine environments. Mostprobable-number (MPN) values obtained for nitrogen-fixing bacteria ranged from 1.1×10(2) to 4.6×10(2)/ml for seawater, 4.0×10(4) to 4.3×10(5)/g wet wt for eelgrass-bed sediment, and 2.1 × 10(5) to 1.2 × 10(7)/g wet wt for eelgrass-root samples. More than 100 strains of halophilic, nitrogen-fixing bacteria belonging to the family Vibrionaceae were isolated from the MPN tubes. These isolates were roughly classified into seven groups on the basis of their physiological and biochemical characteristics. The majority of the isolates were assigned to the genusVibrio and one group to the genusPhotobacterium. However, there was also a group that could not be identified to the generic level. All isolates expressed nitrogen fixation activities under anaerobic conditions, and no organic growth factors were required for their activities.}, }
@article {pmid24196204, year = {1989}, author = {Bengtsson, G}, title = {Growth and metabolic flexibility in groundwater bacteria.}, journal = {Microbial ecology}, volume = {18}, number = {3}, pages = {235-248}, pmid = {24196204}, issn = {0095-3628}, abstract = {Groundwater bacteria isolated from an oligotrophic-saturated soil showed a mixed strategy of economized metabolism and migration when grown in a continuous-flow column system simulating poor or nutrient-amended growth conditions. The cells were generally <0.5μm in diameter in pure groundwater, but doubled in size when the concentration of dissolved organic carbon and phosphate in groundwater was increased 10-fold. The biomass, estimated from analysis of muramic acid (MuAc) in cell wall peptidoglucans, increased at the same time by a factor of 5 when the solid support in the columns was gravel and by a factor of 10 when it was glass beads. Bacteria in pure groundwater stored 10 times more of the energy-rich polysaccharide, poly-β-hydroxybutyric acid (PHB), than bacteria in enriched groundwater, and those cells that were attached to the gravel stored 10 times as much as cells in the interstitial pore water. Once phosphate was added to groundwater, stored PHB was metabolized. The proportion of free-living to attached bacteria was 2 to 10 times higher in enriched compared with pure groundwater indicating a mass transport of cells as the carrying capacity of their habitat rose.}, }
@article {pmid24196203, year = {1989}, author = {Breen, A and Stahl, DA and Flesher, B and Sayler, G}, title = {Characterization ofPseudomonas geomorphus: A novel groundwater bacterium.}, journal = {Microbial ecology}, volume = {18}, number = {3}, pages = {221-233}, pmid = {24196203}, issn = {0095-3628}, abstract = {Strain ABS10, a Gram-negative, pleomorphic bacterium isolated from a pristine aquifer in Ada, Oklahoma, was studied as a candidate for the introduction and expression of plasmid DNA in a native ground water isolate. This organism was originally typed as anArthrobacter sp. due to its morphological phase change and Gram-variable reaction upon Gram staining. The fatty acid methyl ester profile of ABS10 revealed a high similarity withPseudomonas putida. DNA-DNA hybridization showed 81% homology between ABS10 andP. putida. 16S rRNA sequence analysis showed ABS 10 to be a member of the Gamma division of the purple photosynthetic bacteria. The organism has been designatedPseudomonas geomorphus due to its isolation from a subterranean sample and the morphological phase change from rods in young cultures to cocci in older cultures. The broad host range plasmid RP4 was introduced into ABS10 and stably maintained, indicating that RP4 may serve as a vehicle for the introduction of catabolic genes into this organism.}, }
@article {pmid24196202, year = {1989}, author = {Pickup, RW}, title = {Related plasmids found in an English Lake district stream.}, journal = {Microbial ecology}, volume = {18}, number = {3}, pages = {211-220}, pmid = {24196202}, issn = {0095-3628}, abstract = {An examination of the distribution of plasmids carried by copper-tolerant bacteria from a freshwater stream revealed that >60% carried at least one plasmid, and that large plasmids (>100 kb) were predominant. A total of 10 copper-tolerant bacteria carrying the 54-kb plasmid, pFBA20, were detected at four sampling sites within the stream and, on consecutive occasions, at one site throughout a 1-year sampling period. The detection of this plasmid provides evidence that related plasmids can, under no apparent selective pressure, survive and disperse within the bacterial community. Two of the isolates that carried pFBA20 were phenotypically distinguishable. This would suggest that pFBA20 is transmissible.}, }
@article {pmid24196201, year = {1989}, author = {Delaquis, PJ and Caldwell, DE and Lawrence, JR and McCurdy, AR}, title = {Detachment ofPseudomonas fluorescens from biofilms on glass surfaces in response to nutrient stress.}, journal = {Microbial ecology}, volume = {18}, number = {3}, pages = {199-210}, pmid = {24196201}, issn = {0095-3628}, abstract = {The effects of glucose and nitrogen depletion on the colonization of glass Petri plates byPseudomonas fluorescens were studied in batch culture. Colonization of the surfaces was initiated before colonization of the bulk phase, and biofilm formation was observed. This resulted in an apparent lag in the batch growth curve for the cell suspension. The lag phase was an artifact caused by the partitioning of cells between the bulk and solid phase of the culture and was not due to a reduction in the growth rate of unattached cells. The specific growth rate of the unattached cells (0.331 hour(-1)) was almost twice that determined for the total population (0.171 hour(-1)). Consequently the growth rate of biofilm-forming bacteria cannot be determined in batch culture unless the growth of both attached and unattached cells is monitored, and batch growth curves may contain artifacts due to the formation and dispersion of biofilms. The depletion of either glucose or nitrogen led to the active detachment of cells from the biofilm. An increase in the hydrophobicity of unattached cells was noted on depletion of carbon. This increase was the result of emigration of cells from the surface into the bulk phase.}, }
@article {pmid24196200, year = {1989}, author = {Duxbury, T and McIntyre, R}, title = {Population density-dependent metal tolerance: One possible basis and its ecological implications.}, journal = {Microbial ecology}, volume = {18}, number = {3}, pages = {187-197}, pmid = {24196200}, issn = {0095-3628}, abstract = {A population density-dependent copper (Cu) resistance mechanism in a gram-negative soil bacterium, strain TDCd1, was shown to be inducible and was accompanied by changes in the protein composition of the outer membrane of the cell envelope. Characteristically, following inoculation of TDCd1 into Cu-supplemented growth media, there was a period of growth inhibition during which the number of individuals tolerant to Cu gradually increased, even though microcultural experiments indicated that some cells died during this period. We concluded that the population density dependency of the resistance mechanism resulted from the interactions between the rate of cell death, the time taken for Cu resistance to develop, and the size of the initial population. Therefore, the ability of relatively large populations of microorganisms to grow in metal-supplemented media under laboratory conditions may have little ecological significance for sparse populations in natural environments.}, }
@article {pmid24196132, year = {1989}, author = {Van Outryve, MF and Gosselé, F and Swings, J}, title = {The bacterial microflora of witloof chicory (Cichorium intybus L. var.foliosum Hegi) leaves.}, journal = {Microbial ecology}, volume = {18}, number = {2}, pages = {175-186}, pmid = {24196132}, issn = {0095-3628}, abstract = {The bacterial flora on the heads of four different witloof chicory varieties was examined. The 590 isolates were characterized by their SDS-PAGE protein profiles; they revealed 149 different protein fingerprint types. The fluorescentPseudomonas fingerprint type CH001 was abundantly found on all heads examined. Fourteen other fingerprint types occurred in high densities more than twice. Among these, the following were identified: fluorescentPseudomonas, nonfluorescentPseudomonas sp.,Erwinia herbicola, Erwinia sp., andFlavobacterium sp. The majority of the fingerprint types (90%) was found only once. It was also our objective to isolate bacteria applicable in the biological control of chicory phytopathogens. Isolates of all fingerprint types were tested for in vitro antagonistic activity and for possible deleterious effect on plant growth. FluorescentPseudomonas andSerratia liquefaciens isolates were antagonistic against fungi. Among the 161 fluorescentPseudomonas strains, five were able to produce disease symptoms on chicory leaves upon inoculation. Comparison of the results of this study with those obtained in two previous analyses revealed that the leaf microflora showed some similarities with the bacterial flora of chicory roots. The chicory seed microflora differed from that of both leaves and roots.}, }
@article {pmid24196131, year = {1989}, author = {Kinkel, LL and Andrews, JH and Nordheim, EV}, title = {Microbial introductions to apple leaves: Influences of altered immigration on fungal community dynamics.}, journal = {Microbial ecology}, volume = {18}, number = {2}, pages = {161-173}, pmid = {24196131}, issn = {0095-3628}, abstract = {Fungal immigration to apple leaves in the field was altered by the introduction of populations ofChaetomium globosum orAureobasidium pullulans to surface-disinfested leaves either immediately following, or 6 days after, disinfestation. Total numbers of fungal individuals and numbers of filamentous fungal and yeast individuals were estimated and compared over time for 4-7 weeks on control leaves (leaves disinfested but no populations applied), onAureobasidium-treated, and onChaetomium-treated leaves. Fungal communities developing on leaves during three experiments in two different time frames (experiment 1: July 9-August 27; experiments 2 and 3: July 29-August 27), and thus under different immigration regimes, were also compared. Survival of introduced populations was not related to the presence of prior fungal immigrants. Rates of increase in total numbers of fungi and numbers of filamentous fungi and yeasts per leaf varied among experiments, apparently in relation to differences in immigration and environmental history. Differences among leaves in immigration had a short-term (days) influence on community size. However, no long-term effects of altered immigration on phylloplane fungal community size were evident.}, }
@article {pmid24196130, year = {1989}, author = {Häggblom, MM and Janke, D and Salkinoja-Salonen, MS}, title = {Transformation of chlorinated phenolic compounds in the genusRhodococcus.}, journal = {Microbial ecology}, volume = {18}, number = {2}, pages = {147-159}, pmid = {24196130}, issn = {0095-3628}, abstract = {The ability of strains of the genusRhodococcus to transform chlorinated phenolic compounds was studied. Noninduced cells of several strains ofRhodococcus, covering at least eight species, were found to attack mono-, di-, and trichlorophenols by hydroxylation at theortho position to chlorocatechols. 3-chlorophenol and 4-chlorophenol were converted to 4-chlorocatechol, 2,3-dichlorophenol to 3,4-dichlorocatechol, and 3,4-di-chlorophenol to 4,5-dichlorocatechol. The chlorocatechols accumulated to nearly stoichiometric amounts. Other mono- and dichlorophenols were not transformed. The ability of the strains to hydroxylate chlorophenols correlated with the ability to grow on unsubstituted phenol as the sole source of carbon and energy. SeveralRhodococcus strains attacked chlorophenolic compounds by both hydroxylation and O-methylation. 2,3,4-, 2,3,5- and 3,4,5-trichlorophenol were hydroxylated to trichlorocatechol and then sequentially O-methylated to chloroguaiacol and chloroveratrole. Tetrachlo-rohydroquinone was O-methylated sequentially to tetrachloro-4-methoxy-phenol and tetrachloro-1,4-dimethoxybenzene. Several of the active strains had no known history of exposure to any chloroaromatic compound. Rhodococci are widely distributed in soil and sludge and these results suggest that this genus may play an important role in transformation of chlorinated phenolic compounds in the environment.}, }
@article {pmid24196129, year = {1989}, author = {Shiaris, MP}, title = {Phenanthrene mineralization along a natural salinity gradient in an Urban Estuary, Boston Harbor, Massachusetts.}, journal = {Microbial ecology}, volume = {18}, number = {2}, pages = {135-146}, pmid = {24196129}, issn = {0095-3628}, abstract = {The effect of varying salinity on phenanthrene and glutamate mineralization was examined in sediments along a natural salinity gradient in an urban tidal river. Mineralization was measured by trapping(14)CO2 from sediment slurries dosed with trace levels of [(14)C]phenanthrene or [(14)C]glutamate. Sediments from three sites representing three salinity regimes (0, 15, and 30%.) were mixed with filtered column water from each site. Ambient phenanthrene concentrations were also determined to calculate phenanthrene mineralization rates. Rates of phenanthrene mineralization related significantly to increasing salinity along the transect as determined by linear regression analysis. Rates ranged from 1 ng/hour/g dry sediment at the freshwater site to > 16 ng/hour/g dry sediment at the 30‰ salinity site. Glutamate mineralization also increased from the freshwater to the marine site; however, the relationship to salinity was not statistically significant.To examine the effect of salinity on mineralizing activities, individual sediments were mixed with filtered water of the other two sites. Slurries were also made with artificial seawater composed of 0, 15, or 30 g NaCl/ liter to substitute for overlying water. Rates of phenanthrene mineralization in the 0‰ ambient salinity sediments were not affected by higher salinity waters. Activities in the 15 and 30‰ ambient salinity sediments, however, were significantly inhibited by incubation with 0‰ salinity water. The inhibition, in large part, appears to be due to the decreased NaCl concentration of the water phase. Glutamate mineralization was affected in a similar manner, but not as dramatically as phenanthrene mineralization. The results suggest that phenanthrene degraders in low salinity estuarine sediments subject to salt water intrusion are tolerant to a wide range of salinities but phenanthrene degradation in brackish waters is mainly a function of obligate marine microorganisms.}, }
@article {pmid24196128, year = {1989}, author = {Muñiz, I and Jiménez, L and Toranzos, GA and Hazen, TC}, title = {Survival and activity ofStreptococcus faecalis andEscherichia coli in tropical freshwater.}, journal = {Microbial ecology}, volume = {18}, number = {2}, pages = {125-134}, pmid = {24196128}, issn = {0095-3628}, abstract = {The survival ofStreptococcus faecalis andEscherichia coli was studied in situ in a tropical rain forest watershed using membrane diffusion chambers. Densities were determined by acridine orange direct count and Coulter Counter. Population activity was determined by microautoradiography, cell respiration, and by nucleic acid composition. Densities ofS. faecalis andE. coli decreased less than 1 log unit after 105 hours as measured by direct count methods. Activity as measured by respiration, acridine orange activity, and microautoradiography indicated that both bacteria remained moderately active during the entire study. After 12 hours,E. coli was more active thanS. faecalis as measured by nucleic acid composition. In this tropical rain forest watershed,E. coli andS. faecalis survived and remained active for more than 5 days; consequently, both would seem to be unsuitable as indicators of recent fecal contamination in tropical waters.}, }
@article {pmid24196127, year = {1989}, author = {Delille, D and Perret, E}, title = {Influence of temperature on the growth potential of Southern polar marine bacteria.}, journal = {Microbial ecology}, volume = {18}, number = {2}, pages = {117-123}, pmid = {24196127}, issn = {0095-3628}, abstract = {Regular surveys of heterotrophic microflora from seawater were conducted in the subantarctic (Kerguelen archipelago) and Antarctic (Terre Adélie area). Although a predominance of psychrophilic bacteria could be expected for such polar marine environments, there were no significant differences between results obtained after incubation at two different temperatures (4°C for 21 days or 18°C for 6 days). To investigate this further, four sets of bacterial strains were isolated from the subantarctic area (early fall, late fall, spring, and summer) and one set of Antarctic bacteria was isolated in summer. The growth rates of the 143 strains collected were determined at four different temperatures (4, 7, 20, and 30°C). The results clearly indicated that a large majority of the isolated bacteria must be considered psychrotrophic and not truly psychrophilic strains.}, }
@article {pmid24196126, year = {1989}, author = {Austin, HK and Findlay, SE}, title = {Benthic bacterial biomass and production in the Hudson River estuary.}, journal = {Microbial ecology}, volume = {18}, number = {2}, pages = {105-116}, pmid = {24196126}, issn = {0095-3628}, abstract = {Bacterial biomass, production, and turnover were determined for two freshwater marsh sites and a site in the main river channel along the tidally influenced Hudson River. The incorporation of [methyl-(3)H]thymidine into DNA was used to estimate the growth rate of surface and anaerobic bacteria. Bacterial production at marsh sites was similar to, and in some cases considerably higher than, production estimates reported for other aquatic wetland and marine sediment habitats. Production averaged 1.8-2.8 mg C·m(-2)·hour(-1) in marsh sediments. Anaerobic bacteria in marsh sediment incorporated significant amounts of [methyl-(3)H]thymidine into DNA. Despite differences in dominant vegetation and tidal regime, bacterial biomass was similar (1×10(3)±0.08 mg C·m(-2)) inTrapa, Typha, andNuphar aquatic macrophyte communities. Bacterial abundance and productivity were lower in sandy sediments associated withScirpus communities along the Hudson River (0.2×10(3)±0.05 mg C·m(-2) and 0.3±0.23 mg C·m(-2)·hour(-1), respectively).}, }
@article {pmid24196125, year = {1989}, author = {Caron, DA and Davis, PG and Sieburth, JM}, title = {Factors responsible for the differences in cultural estimates and direct microscopical counts of populations of bacterivorous nanoflagellates.}, journal = {Microbial ecology}, volume = {18}, number = {2}, pages = {89-104}, pmid = {24196125}, issn = {0095-3628}, abstract = {Bacterivorous nanoflagellates (microflagellates) have been routinely enumerated in marine and freshwater samples using either a Most Probable Number (MPN) culture method or by a direct microscopical counting method (DC). These two techniques typically yield highly disparate estimates of the density of nanoflagellates in natural samples. We compared these methods with seawater and marine snow (macroscopic detrital aggregate) samples collected from surface waters throughout the North Atlantic and in freshwater samples collected at three stations in Lake Ontario. Densities of nanoflagellates determined by the two methods differed by as much as four orders of magnitude; the MPN estimate rarely exceeded 10% of the microscopical count, and averaged ≈ 1% of this count. The MPN estimate constituted a higher percentage of the DC value in environments with high concentrations of nanoflagellates relative to environments with low concentrations of nanoflagellates. The ratio of the culture count to the microscopical count (MPN∶DC) increased along an environmental gradient from oligotrophy to eutrophy, and was positively correlated with the density of bacteria in the samples. In laboratory experiments with two species of bacterivorous nanoflagellates, the MPN count constituted a much greater percentage of the DC count during the exponential growth phase of the nanoflagellate than during the stationary growth phase. Differences in the estimates of nanoflagellate density obtained with these two techniques probably can be explained by the trophic mode of these protozoa, their growth stage, and the amenability of these species to laboratory culture.}, }
@article {pmid24196124, year = {1989}, author = {Abedon, ST}, title = {Selection for bacteriophage latent period length by bacterial density: A theoretical examination.}, journal = {Microbial ecology}, volume = {18}, number = {2}, pages = {79-88}, pmid = {24196124}, issn = {0095-3628}, abstract = {In bacteriophage (phage), rapid and efficient intracellular progeny production is of obvious benefit. A short latent period is not. All else being equal, a longer latent period utilizes host cell resources more completely. Using established parameters of phage growth, a simulation of three successive phage lysis cycles is presented. I have found that high, but not low, host cell densities can select for short phage latent periods. This results from phage with short latent periods more rapidly establishing multiple parallel infections at high host cell concentrations, whereas phage with long latent periods are restricted to growth within a single cell over the same period. This implies that phage with short latent periods habitually grow in environments that are rich in host cells.}, }
@article {pmid24196022, year = {1989}, author = {Johnstone, BH and Jones, RD}, title = {A Study on the lack of [methyl-(3)H] thymidine uptake and incorporation by chemolithotrophic bacteria.}, journal = {Microbial ecology}, volume = {18}, number = {1}, pages = {73-77}, pmid = {24196022}, issn = {0095-3628}, abstract = {Five chemolithotrophic bacteria were tested for their ability to incorporate [methyl-(3)H] thymidine. None of the bacteria incorporated the label, even after incubation for 24 hours. The inability of these bacteria to incorporate thymidine appears to be due to an absence of transport mechanisms for exogenous nucleosides. As a result of these findings, it is concluded that activities deduced from labeled thymidine incorporation measurements probably do not include the activity of chemolithotrophic bacteria.}, }
@article {pmid24196021, year = {1989}, author = {Miller, FC}, title = {Matric water potential as an ecological determinant in compost, a substrate dense system.}, journal = {Microbial ecology}, volume = {18}, number = {1}, pages = {59-71}, pmid = {24196021}, issn = {0095-3628}, abstract = {Water is a critical ecological factor in substrate dense matric ecosystems, of which composting systems are an example. Excessive moisture inhibits aerobic metabolism because of oxygen diffusion limitations. How a lack of water impedes composting activity has not been previously considered. An investigation of the relationship of matric water potential (water held by physical attractions) to gravimetric water content was carried out in a laboratory composting system using a sewage sludge and wood chip substrate. The gravimetric-matric water relationship was best fit by a 2∘ polynomial regression of y=64.049-0.142 x, andR= 0.95. It is proposed that the commonly observed failure of composting to occur under drier conditions is a physical limitation, that is bacteria progressively fail to physically colonize the substrate as matric potential decreases below approximately -20 kPa. In physically mixed systems, agitation and introduction of inoculum may promote colonization, permitting composting to be initiated and proceed at lower moisture contents. In nonmixed systems, promotion of thorough initial colonization may permit composting to continue in the presence of significant drying.}, }
@article {pmid24196020, year = {1989}, author = {Kinkel, LL and Andrews, JH and Nordheim, EV}, title = {Fungal immigration dynamics and community development on apple leaves.}, journal = {Microbial ecology}, volume = {18}, number = {1}, pages = {45-58}, pmid = {24196020}, issn = {0095-3628}, abstract = {Fungal immigration dynamics and community development were followed over time on sets of surface-disinfested apple leaves in the field. Immigration was defined as the arrival of viable propagules on the leaf surface. In three separate experiments (May, June, July), total numbers of fungal immigrants, numbers of filamentous fungal immigrants, and numbers of yeast immigrants per leaf were estimated for successive 12-hour immigration periods. Communities developing over 2-14 immigration periods (1-7 days) were compared with the corresponding estimates of cumulative immigration. There were significant differences among both experiments and immigration periods within each experiment in mean numbers of immigrants per leaf. Leaf area was often significantly correlated with numbers of immigrants. Developing communities supported progressively fewer individuals than the corresponding sums of immigrants, suggesting that losses due to emigration and/or death play a critical role in shaping these communities.}, }
@article {pmid24196019, year = {1989}, author = {Plante, CJ and Jumars, PA and Baross, JA}, title = {Rapid bacterial growth in the hindgut of a marine deposit feeder.}, journal = {Microbial ecology}, volume = {18}, number = {1}, pages = {29-44}, pmid = {24196019}, issn = {0095-3628}, abstract = {Antibiotic-insensitive mutants of natural sedimentary bacteria from an intertidal site were selected on gradient plates. Two of these strains, anAeromonas sp. andVibrio alginolyticus, were mixed with natural sediments from the field and fed toAbarenicola vagabunda, an intertidal lugworm characteristic of sandy beaches in the Pacific Northwest. Digestive removal was apparent in the midgut, 97% efficiency being seen forAeromonas sp. Both strains showed rapid growth in the hindgut, increasing between 2 and 3 orders of magnitude in abundance between the midgut and rectum of the polychaete, corresponding with a doubling time of about 50 min for each strain. Direct epifluorescence counts of natural bacteria in guts of animals freshly collected from the field suggest a mean doubling time that is only slightly greater (66 min) for all ingested bacteria that survive midgut digestion. These bacterial growth rates exceed by orders of magnitude the greatest rates reported for ambient marine sediments and suggest that hindgut bacterial growth, though of little immediate importance in the energetics of the animals, may strongly influence both population dynamics of marine bacteria and diagenesis of sedimentary organic matter.}, }
@article {pmid24196018, year = {1989}, author = {Deflaun, MF and Paul, JH}, title = {Detection of exogenous gene sequences in dissolved DNA from aquatic environments.}, journal = {Microbial ecology}, volume = {18}, number = {1}, pages = {21-28}, pmid = {24196018}, issn = {0095-3628}, abstract = {A method for the concentration and detection of gene sequences in the dissolved DNA from freshwater and marine environments has been developed. The limit of detection in the dot blot format was 167 fg/ml (100 ml sample) for exogenous herpes simplex thymidine kinase (TK) gene that was added to artificial seawater or river water. This procedure has been used to determine the longevity and monitor progressive changes in molecular weight of a plasmid containing the TK gene added to eutrophic estuarine water. The onset of plasmid degradation as determined by change in molecular weight was rapid (within 5 min). Intact plasmid was detected for at least 4 hours and sequences hybridizable to the TK gene probe were present for up to 24 hours.}, }
@article {pmid24196017, year = {1989}, author = {Korber, DR and Lawrence, JR and Sutton, B and Caldwell, DE}, title = {Effect of laminar flow velocity on the kinetics of surface recolonization by Mot(+) and Mot (-) Pseudomonas fluorescens.}, journal = {Microbial ecology}, volume = {18}, number = {1}, pages = {1-19}, pmid = {24196017}, issn = {0095-3628}, abstract = {Computer-enhanced microscopy (CEM) was used to monitor bacteria colonizing the inner surfaces of a 1×3 mm glass flow cell. Image analysis provided a rapid and reliable means of measuring microcolony count, microcolony area, and cell motility. The kinetics of motile and nonmotilePseudomonas fluorescens surface colonization were compared at flow velocities above (120μm sec(-1)) and below (8μm sec(-1)) the strain's maximum motility rate (85μm sec(-1)). A direct attachment assay confirmed that flagellated cells undergo initial attachment more rapidly than nonflagellated cells at high and low flow. During continuous-flow slide culture, neither the rate of growth nor the timing of recolonization (cell redistribution within surface microenvironments) were influenced by flow rate or motility. However, the amount of reattachment of recolonizing cells was both flow and motility dependent. At 8μm sec(-1) flow, motility increased reattachment sixfold, whereas at 120μm sec(-1) flow, motility increased reattachment fourfold. The spatial distribution of recolonizing cells was also influenced by motility. Motile cells dispersed over surfaces more uniformly (mean distance to the nearest neighbor was 47.0μm) than nonmotile cells (mean distance was 14.2μm) allowing uniform biofilm development through more effective redistribution of cells over the surface during recolonization. In addition, motile cell backgrowth (where cells colonize against laminar flow) occurred four times more rapidly than nonmotile cell backgrowth at low flow (where rate of motility exceeded flow), and twice as rapidly at high flow (where flow exceeded the rate of motility). The observed backgrowth of Mot(+) cells against high flow could only have occurred as the result of motile attachment behavior. These results confirm the importance of motility as a behavioral mechanism in colonization and provides an explanation for enhanced colonization by motile cells in environments lacking concentration gradients necessary for chemotactic behavior.}, }
@article {pmid24197289, year = {1989}, author = {Towne, G and Nagaraja, TG and Cochran, RC}, title = {Ruminal microbial populations and fermentation characteristics in bison and cattle fed high- and low-quality forage.}, journal = {Microbial ecology}, volume = {17}, number = {3}, pages = {311-316}, pmid = {24197289}, issn = {0095-3628}, abstract = {Ruminal microbial populations and fermentation products were compared between two ruminally cannulated bison (375 kg) and two ruminally cannulated Hereford steers (567 kg) on alfalfa or prairie hay diets. Differential media were used to enumerate carbohydrate-specific bacterial subgroups. Voluntary dry matter intake was higher (P=0.006) for cattle than for bison fed alfalfa, but prairie hay intake was not different (P=0.16) between the two species. Volatile fatty acid concentrations, pH, and ruminal ammonia were similar between bison and cattle on both diets. Total anaerobic bacteria and xylanolytic bacterial counts were higher (P<0.02) in bison than in cattle fed alfalfa. However, with the prairie hay diet, no differences in bacterial counts on any medium were observed between ruminant species. Both bison and cattle possessed a mixed A-B protozoan population with nearly identical protozoan numbers and distribution of genera. The similarities between bison and cattle consuming either high-or low-quality forage suggest that any differences in putative forage digestibility between the species are not due to differences in microbial counts.}, }
@article {pmid24197288, year = {1989}, author = {New, PB and Kennedy, IR}, title = {Regional distribution and pH sensitivity ofAzospirillum associated with wheat roots in Eastern Australia.}, journal = {Microbial ecology}, volume = {17}, number = {3}, pages = {299-309}, pmid = {24197288}, issn = {0095-3628}, abstract = {In a survey ofAzospirillum spp. on the roots and associated soil of wheat grown in eastern Australia, azospirilla were isolated from approximately 40% of samples from areas of soil pH between 5.0 and 6.6. However, azospirilla isolates were rare in soil between pH 4.5 and 5.0 and absent below pH 4.5. Of 25 independent isolates, 17 wereA. brasiliense and eight wereA. lipoferum. No selection forA. brasiliense Nir(-) strains by wheat roots was observed. Only one of six endorhizosphere isolates wereA. brasiliense Nir(-), compared with three of nine from unsterilized roots plus associated soil, and three of eight from soil. With a medium buffered with 0.05 M malate and 0.05 M phosphate, it was found that allAzospirillum isolates had a lower minimum pH for growth when supplied with fixed nitrogen than when grown under nitrogen-fixing conditions. Strains isolated from soils had a minimum pH for growth that was less than the pH of the soil from which they were isolated. However, a significant proportion of strains isolated from roots had a minimum pH for growth that was higher than the pH of the associated soil suggesting that the wheat roots provided an ecological niche protecting against soil acidity.}, }
@article {pmid24197287, year = {1989}, author = {Fitt, WK and Labare, MP and Fuqua, WC and Walch, M and Coon, SL and Bonar, DB and Colwell, RR and Weiner, RM}, title = {Factors influencing bacterial production of inducers of settlement behavior of larvae of the oysterCrassostrea gigas.}, journal = {Microbial ecology}, volume = {17}, number = {3}, pages = {287-298}, pmid = {24197287}, issn = {0095-3628}, abstract = {Dissolved chemical inducers of settlement behavior of veliger larvae of the oysterCrassostrea gigas are found in supernatants of both pigmented species of bacteria (Alteromonas colwelliana, Vibrio cholerae strain HTX) as well as nonpigmented bacteria (Excherichia coli, Vibrio cholerae strain 596-B). Usually less than 10% of veligers exhibited settlement behavior in response to supernatants from the early bacterial growth phases, whereas 30-90% of larvae responded when exposed to supernatant from late-log and stationary phase cultures. Percentages of larvae exhibiting settlement behavior were inversely correlated with oxygen levels in the culture. Furthermore, the behavioral response decreased with pigment formation, suggesting that quantities of noxious compounds such as quinones may build up in the supernatants of cultures of pigmented bacteria. Tyrosinase, an enzyme that converts L-tyrosine to L-DOPA in the first step of melanogenesis, was detected both in the bacterial pellet and the supernatant during growth of the pigmented species. The enzyme is not required for the production of settlement inducer as the nonpigmented speciesE. coli andV. cholerae (596-B) also released inducer into the supernatant and had no detectable tyrosinase. The data suggest either that there is more than one inducer of settlement behavior found in bacterial supernatants or that the inducer is not L-DOPA or an L-DOPA-mimetic associated with the melanin biochemical pathway.}, }
@article {pmid24197286, year = {1989}, author = {Laurence, OS and Cooney, JJ and Gadd, GM}, title = {Toxicity of organotins towards the marine yeastDebaryomyces hansenii.}, journal = {Microbial ecology}, volume = {17}, number = {3}, pages = {275-285}, pmid = {24197286}, issn = {0095-3628}, abstract = {Of nine organotin compounds tested towards the marine yeastDebaryomyces hansenii, only triphenyltin chloride (Ph3SnCl) and mono-, di-, and tributyltin chloride induced significant K(+) release from cells which was symptomatic of viability loss. The general order of toxicity of the butylated compounds was tributyltin chloride (Bu3SnCl) > monobutyltin chloride (BuSnCl3) ≫ dibutyltin chloride (Bu2SnCl2). The overall toxicity of Ph3SnCl was similar to BuSnCl3. Release of K(+) induced by butylated tin compounds or by Ph3SnCl was strongly dependent on the external pH. Maximal toxicity occurred at pH 6.5 for Bu3SnCl, BuSnCl3, and Ph3SnCl, whereas maximal toxicity of Bu2SnCl2 occurred at pH 5.0. Toxicity was decreased above or below these values. The toxicity of BuSnCl3, Bu3SnCl, and Ph3SnCl was reduced at salinity levels approximating to sea water conditions. Prior growth ofD. hansenii in 3% (w/v) NaCl also resulted in reduced sensitivity to Bu3SnCl as evidenced by a decreased rate and extent of K(+) efflux. Bu3SnCl-induced Na(+) release from cells grown in the absence or presence of 3% (w/v) NaCl was low and similar in both cases. It appeared that the monovalent cation was important in the reduction of Bu3SnCl toxicity since Na2SO4 had a similar protective effect as NaCl while CsCl completely prevented K(+) efflux. Thus, the effects of external NaCl were related both to Na(+) and to Cl(-). These results emphasize that cellular and environmental factors influence the toxic effects of organotins and suggests that these compounds may be more effective antimicrobial agents in some environmental niches than in others.}, }
@article {pmid24197285, year = {1989}, author = {Baldi, F and Filippelli, M and Olson, GJ}, title = {Biotransformation of mercury by bacteria isolated from a river collecting cinnabar mine waters.}, journal = {Microbial ecology}, volume = {17}, number = {3}, pages = {263-274}, pmid = {24197285}, issn = {0095-3628}, abstract = {One hundred six strains of aerobic bacteria were isolated from the Fiora River which drains an area of cinnabar deposits in southern Tuscany, Italy. Thirty-seven of the strains grew on an agar medium containing 10μg/ml Hg (as HgCl2) with all of these strains producing elemental mercury. Seven of the 37 strains also degraded methylmercury. None of 106 sensitive and resistant strains produced detectable monomethylmercury although 15 strains produced a benzene-soluble mercury species. Two strains of alkylmercury (methyl-, ethyl- and phenylmercury) degrading bacteria were tested for the ability to degrade several other analogous organometals and organic compounds, but no activity was detected toward these compounds. Mercury methylation is not a mechanism of Hg resistance in aerobic bacteria from this environment. Growth of bacteria on the agar medium containing 10μg/ml HgCl2 was diagnostic for Hg detoxification based on reduction.}, }
@article {pmid24197284, year = {1989}, author = {Andersson, A and Falk, S and Samuelsson, G and Hagström, A}, title = {Nutritional characteristics of a mixotrophic nanoflagellate,Ochromonas sp.}, journal = {Microbial ecology}, volume = {17}, number = {3}, pages = {251-262}, pmid = {24197284}, issn = {0095-3628}, abstract = {Autotrophic and heterotrophic growth characteristics of a nano-flagellate were investigated. The flagellate,Ochromonas sp., was isolated from the northern Baltic Sea. Autotrophic growth was poor. Axenically pregrown flagellates did not increase significantly in cell number during incubation in different inorganic media. The number of flagellates remained constant 3-5 weeks in cultures kept in the light (100μmol m(-2) sec(-1)), whereas in the dark, a high mortality rate was found. Uptake of inorganic(14)C into an acid-stable fraction indicated thatOchromonas had a functional photosynthetic apparatus. Heterotrophic growth in both liquid medium and medium containing bacteria was rapid. The maximum growth rate corresponded to a generation time of 5.3 hours. Light had no effect on heterotrophic growth. Cells pregrown onEscherichia coli minicells survived without additional bacteria as food when kept in the light, but rapid death occurred in darkness. In conclusion, heterotrophy is the major mechanism to support growth in this species ofOchromonas, but under poor environmental conditions photoautotrophy might be a strategy for survival rather than growth.}, }
@article {pmid24197283, year = {1989}, author = {Dobbs, FC and Guckert, JB and Carman, KR}, title = {Comparison of three techniques for administering radiolabeled substrates to sediments for trophic studies: Incorporation by microbes.}, journal = {Microbial ecology}, volume = {17}, number = {3}, pages = {237-250}, pmid = {24197283}, issn = {0095-3628}, abstract = {Three principal methods have been used to administer substrates to sediments: injection, porewater replacement, and slurry. Here we assess how each of these techniques affects incorporation of radiolabels into macromolecules of marine sedimentary microbes. Eighty-five cores of intertidal sand were collected in a randomized-block, factorial design. One set of cores received(14)C-bicarbonate/(3)H-thymidine and was incubated in the light; another set received(14)C-acetate/(3)H-thymidine and was incubated in the dark. Following a 5-hour incubation, sediments were analyzed for incorporation of radiolabel into lipid fractions (neutral, glyco-, and polar) and DNA. The three methods of isotope administration were also applied to cores subsequently analyzed for polar lipid phosphates and phospholipid fatty-acid (PLFA) profiles. In general, incorporation was greatest when injections were made, consistent with the prediction that incorporation would decrease as specific activity of the radiolabeled substrate was diminished by dilution. The ratio of(14)C from acetate incorporated into polar and glycolipid fractions indicated that a significant disturbance accompanied the porewater and slurry techniques. Substantial amounts of(3)H were recovered in the neutral-lipid fraction, indicating that thymidine was catabolized by sedimentary microbes and tritiated products were incorporated by eukaryotes. There were no significant differences in PLFA profiles or estimates of microbial biomass among methods or controls. Incorporation of(3)H into DNA was similar with all combinations of methods and radiocarbon substrates.(14)C was extensively incorporated into DNA, indicating that photoautotrophs and heterotrophs utilized radiocarbon from bicarbonate and acetate, respectively, for de novo synthesis of DNA. Injection is suggested as the method of choice, as it presents more flexibility in its application than porewater replacement and disturbs the consortia of gradients in sediments to a significantly lesser degree than porewater replacement and slurry.}, }
@article {pmid24197282, year = {1989}, author = {Troussellier, M and Legendre, P}, title = {Dynamics of fecal coliform and culturable heterotroph densities in an eutrophic ecosystem: Stability of models and evolution of these bacterial groups.}, journal = {Microbial ecology}, volume = {17}, number = {3}, pages = {227-235}, pmid = {24197282}, issn = {0095-3628}, abstract = {Time series of a population of fecal coliforms and a community of total viable counts were recorded during years 5 and 6 after the "birth" of an eutrophic aquatic ecosystem (sewage treatment lagoons). These time series were used to re-examine models, previously published, describing their temporal dynamics as well as the relationships between bacterial and environmental variables. The dynamics of the fecal coliforms and their relationships to the environment were unchanged; the fecal coliform abundances displayed an annual cycle with maximum reduction in numbers during the summer, which would be due at least partly to environmental variables (hypotheses of control by irradiance and pH, which have a seasonal behavior, are supported by the data). On the contrary, the total viable count dynamics moved towards a closer dependence on phytoplankton, from a situation of relative independence with respect to other biotic components of the ecosystem. Indeed during the first two years, only one of the abiotic variables in the model (the biological oxygen demand, which is an indicator of available organic matter) seemed to have an effect on the total viable counts. The behavior of these bacterial groups, measured during 1980-1982 and 1984-1986, shows that demographic and ecological laws founded on the observation of other organisms also apply to heterotrophic bacteria. A population, such as the fecal coliforms in the present study, has a limited ecological amplitude and is then more likely to react to environmental variables such as irradiance, pH, and phytoplanktonic metabolic products, whose bactericidal action is highest during the summer months and lowest during winter. On the other hand, a community such as that detected by the total viable counts of the present study is composed of many species and thus has a larger ecological amplitude. This makes it easier for the species to occupy the various available habitats and to maintain themselves through ecological succession and endogenous rhythms.}, }
@article {pmid24197281, year = {1989}, author = {Martinez, J and Garcia-Lara, J and Vives-Rego, J}, title = {Estimation ofEscherichia coli mortality in seawater by the decrease in(3)H-label and electron transport system activity.}, journal = {Microbial ecology}, volume = {17}, number = {3}, pages = {219-225}, pmid = {24197281}, issn = {0095-3628}, abstract = {The mortality ofEscherichia coli in seawater was assessed by viable counts, electron transport system activity, and cellular(3)H-labelling. Filtration was used to assess the grazing mortality. Cellular radiolabelling and electron transport system activity were useful methods for assessingE. coli survival in seawater. The decrease in the(3)H-label as a method to assess bacterial mortality was validated by using viable counts and metabolic activity assays. The particulate fraction that passed 2 μm but was retained on 0.2 μm pore-size filters was the primary reason forE. coli mortality in seawater.}, }
@article {pmid24197249, year = {1989}, author = {Cowley, HM and Hill, RH}, title = {Spirochetes autochthonous to the rat gastrointestinal tract.}, journal = {Microbial ecology}, volume = {17}, number = {2}, pages = {207-217}, pmid = {24197249}, issn = {0095-3628}, abstract = {Spirochetes are structurally unique microorganisms found in the gastrointestinal tracts of most mammals. In an attempt to determine the ecological status of these bacteria, enumeration and distribution of morphologically distinct spirochetes were studied in the tracts of conventional laboratory rats. Five different types were seen to colonize infant rats between 19 and 26 days of age and subsequently to form stable communities in all 15 adults examined. Two types were found predominantly in lumen contents of the large bowel. The other three were consistently seen in the mucous blanket, attached to enterocyte surfaces or deep in the glands of the cecum and proximal colon. One type inhabiting the mucosal environment was also seen to pass into and through epithelial cells with no detectable host response. We conclude that spirochetes fulfill all the criteria for autochthonicity to the rat gastrointestinal tract.}, }
@article {pmid24197248, year = {1989}, author = {Tibbles, BJ and Baecker, AA}, title = {Effects and fate of phenol in simulated landfill sites.}, journal = {Microbial ecology}, volume = {17}, number = {2}, pages = {201-206}, pmid = {24197248}, issn = {0095-3628}, abstract = {Phenol was administered to landfill waste in concentrations from 150 to 1,000 ppm via the feed-liquor of lysimeter systems over an 18-week incubation period. Biotic contributions to phenol removal in the landfill waste were of greater significance than abiotic removal. The addition of phenol did not cause the isolation of thermophilic phenol degraders. Plates inoculated from the test lysimeter receiving phenol were eventually predominated by mesophilic phenol-degradingMicrococcus, Nocardia, andArthrobacter spp.; plates inoculated from the control lysimeter, receiving water, were predominated by species incapable of utilizing phenol.}, }
@article {pmid24197247, year = {1989}, author = {Jaffee, BA and Gaspard, JT and Ferris, H}, title = {Density-dependent parasitism of the soil-borne nematodeCriconemella xenoplax by the nematophagous fungusHirsutella rhossiliensis.}, journal = {Microbial ecology}, volume = {17}, number = {2}, pages = {193-200}, pmid = {24197247}, issn = {0095-3628}, abstract = {Spatial sampling was used to investigate temporal density-dependent parasitism of the plant-parasitic nematodeCriconemella xenoplax byHirsutella rhossiliensis in three peach orchards on eight sample dates. The patches of soil in which the nematode and fungus interacted were assumed to possess similar density-dependent dynamics and to be small, independent, and asynchronous. Furthermore, sampling of separate patches was assumed to provide similar information with respect to density dependence as would temporal (repeated) sampling of the same patch. Percent parasitism was dependent on the number ofC. xenoplax/100 cm(3) soil (P=0.0001). The slope was unaffected by orchard or date but ranged from 0.0001 to 0.0043 depending on distance from the irrigation furrow. The relative shallowness of the slope and the large variation in percent parasitism not explained by nematode density suggest thatH. rhossiliensis is a weak regulator ofC. xenoplax population density.}, }
@article {pmid24197246, year = {1989}, author = {Sørheim, R and Torsvik, VL and Goksøyr, J}, title = {Phenotypical divergences between populations of soil bacteria isolated on different media.}, journal = {Microbial ecology}, volume = {17}, number = {2}, pages = {181-192}, pmid = {24197246}, issn = {0095-3628}, abstract = {Bacterial strains were randomly isolated from soil using three different media with glucose (TG), Tryptone Soya Broth (TTS), and succinate (TS) as carbon sources. Plate counts obtained were 12.0×10(7), 4.5 ×10(7), and 1.5×10(7) g(-1) soil dry weight, respectively. The strains were characterized phenotypically by the API 20B test system. A cluster analysis of all isolates revealed 40 biotypes at 80% similarity, 23 in TG, 29 in TTS, and 27 in TS. Each of the 10 most common biotypes contained 10 to 2.5% of the isolates, and 17 biotypes contained one or two isolates. The common biotypes were unevenly distributed among the isolates from the different media. About 20% of the isolates from TG and TTS were unique for the particular medium, whereas among the isolates from TS, about 60% were unique. Thirty percent of the isolates belonged to biotypes that were common to all three populations. All media gave approximately the same high diversity measured as Shannon index and Equitability, indicating no direct correlation between plate count and diversity.}, }
@article {pmid24197245, year = {1989}, author = {Henis, Y and Gurijala, KR and Alexander, M}, title = {Factors involved in multiplication and survival ofEscherichia coli in lake water.}, journal = {Microbial ecology}, volume = {17}, number = {2}, pages = {171-180}, pmid = {24197245}, issn = {0095-3628}, abstract = {The population of a strain ofEscherichia coli that was resistant to nalidixic acid and streptomycin declined rapidly in samples of sterile and nonsterile Cayuga Lake water and reached an undetectable level in nonsterile water at 24 and 72 hours when counted on eosin-methylene blue (EMB) agar and half-strength trypticase soy agar (TSA), respectively. In sterile lake water amended with 10μg amino acids per ml or 0.1 M phosphate,E. coli multiplied exponentially for more than 24 hours. The addition ofRhizobium leguminosarum biovarphaseoli to unamended sterile lake water prevented the decline ofE. coli, and its addition to amended sterile lake water preventedE. coli multiplication. The cell density of this strain ofE. coli declined in the first 8 hours after its introduction into an inorganic salts solution, but the bacterium then grew extensively. This increase in abundance was not observed in the presence ofR. phaseoli, andE. coli counts on half-strength TSA remained unchanged between 8 hours and 6 days. When counted on EMB agar, the abundance of the antibiotic-resistant strain ofE. coli and a strain not selected for resistance increased in solutions containing phosphate and amino acids but declined in the presence of high densities ofR. phaseoli. Many of the cells of the antibiotic-resistantE. coli strain failed to grow on antibiotic-amended EMB agar after introduction of the organism into nonsterile or sterile lake water or into an inorganic salts solution containingR. phaseoli, although colonies appeared on TSA. The data suggest thatE. coli cells grown on rich media suffer a shock when introduced into lake water because of low hypotonicity, the indigenous competing flora, or both. This shock is prevented by either phosphate buffer or by amino acids at low concentration. The shocked bacteria formed colonies on half-strength TSA. Depending on environmental conditions, the presence of a second organism either has no effect or results in an increase or decrease inE. coli numbers.}, }
@article {pmid24197244, year = {1989}, author = {Sallis, PJ and Burns, RG}, title = {The characterization of amidohydrolases in a freshwater lake sediment.}, journal = {Microbial ecology}, volume = {17}, number = {2}, pages = {159-170}, pmid = {24197244}, issn = {0095-3628}, abstract = {The properties of three amidohydrolases, i.e., urease (I) EC 3.5.1.5, L-asparaginase (II) EC 3.5.1.1, and L-glutaminase (III) EC 3.5.1.2, were studied in sediment samples taken from a shallow eutrophic freshwater lake.Sediment samples were air dried (ADS) and stored for at least 3 months before being enzymically characterized. The pH optimum of I, II, and III were pH 7.0, 8.4, and 6.5-7.0, respectively, while III in soluble extracts from ADS was most active between pH 8.0 and 9.0. The temperature response of the three enzymes in ADS gave Ea values of 38.9, 41.6, and 35.9 kJmol(-1) for I, II, and III, respectively. Km and Vmax values for ADS I, II, and III were 1.2 mM and 1.9μmol NH3 g(-1)h(-1); 0.8 mM and 4.1μmol NH3 g(-1)h(-1); and 1.25 mM and 17.4μmol NH3 g(-1)h(-1). Km values for all three enzymes in ADS extracts were at least an order of magnitude greater than those of the ADS. The susceptability of each enzyme to proteolysis was followed in ADS and fresh wet sediment and compared with that of III in an ADS extract. All sediment enzymes were found to be more resistant than the commercial preparation of bacterial L-glutaminase subjected to the same treatment. These results suggested that I, II, and III all exist to some extent as colloid-immobilized enzyme fractions in freshwater sediments and are analogous to the stable enzyme fractions in soils.}, }
@article {pmid24197243, year = {1989}, author = {Slater, JM and Capone, DG}, title = {Nitrate requirement for acetylene inhibition of nitrous oxide reduction in marine sediments.}, journal = {Microbial ecology}, volume = {17}, number = {2}, pages = {143-157}, pmid = {24197243}, issn = {0095-3628}, abstract = {The inhibition of nitrous oxide (N2O) reduction by acetylene (C2H2) in saltmarsh sediment was temporary; we investigated this phenomenon and possible causes. The reduction of N2O in the presence of C2H2 was biological. N2O consumption in the presence of C2H2 began when nitrate concentration became very low. The time course of N2O consumption after periods of N2O accumulation was unaffected by initial nitrate concentrations between 16 and 200μM, or C2H2 concentrations between 10 and 100% of the gas phase. Sulfide had no effect on the kinetics of N2O reduction in the presence of C2H2. In more dilute slurries of saltmarsh sediments and in estuarine sediment, N2O persisted in the presence of C2H2 unless sufficient organic carbon was added to deplete nitrate. In saltmarsh sediments, the rate of N2O consumption in the presence of C2H2 was not changed by preincubation with C2H2. Initial positive rates of N2O production in the presence of C2H2 occurred only when the block was apparently effective (i.e., at nitrate concentrations greater than about 5-10μM) and appeared to represent a valid estimate of denitrification. Conversely, and in agreement with previous studies, concentrations of NO3 (-) below these levels resulted in reduced efficiency of C2H2 blockage of N2O reductase.}, }
@article {pmid24197242, year = {1989}, author = {Bianchi, M}, title = {Unusual bloom of star-like prosthecate bacteria and filaments as a consequence of grazing pressure.}, journal = {Microbial ecology}, volume = {17}, number = {2}, pages = {137-141}, pmid = {24197242}, issn = {0095-3628}, abstract = {In seawater used for shrimp aquaculture in French Polynesia, the grazing of small bacteria (rods and coccoids) allowed the growth ofAncalomicrobium cells (to more than 2×10(6) cells ml(-1)) and large filaments > 10μm in length (5×10(6) cells ml(-1)). Their contribution to the increase in total bacterial number after grazing was 27.8 and 9.8%, respectively. These large bacteria are not grazed on by microflagellates, but are available for mesoplankton larvae.}, }
@article {pmid24197241, year = {1989}, author = {Beaver, JR and Crisman, TL}, title = {The role of ciliated protozoa in pelagic freshwater ecosystems.}, journal = {Microbial ecology}, volume = {17}, number = {2}, pages = {111-136}, pmid = {24197241}, issn = {0095-3628}, abstract = {The abundance and biomass of ciliates are both strongly related to lake trophic status as measured by chlorophylla concentrations. Taxonomic replacements occur with increasing eutrophication such that large-bodied forms (predominantly oligotrichs) are progressively replaced by smaller-bodied ciliates (mainly scuticociliates). Highly acidic lakes display a more pronounced dominance of large-bodied forms when contrasted with less acidic lakes of comparable trophy. Community structure of ciliate populations is determined largely by lake trophy with acidic oligotrophic systems being characterized by reduced diversity and species richness compared with hypereutrophic systems. The temporal and spatial distribution of small (< 100μm) ciliate populations is ascribed to lake thermal regimes which provide localized concentrations of food resources. Likewise, in extremely productive lakes, very large (> 100μm) meroplanktonic ciliates enter the water column during midsummer after the development of thermal stratification and associated profundal deoxygenation. Laboratory studies indicate that large zooplankton (crustaceans) are capable of utilizing ciliates as a food source, but there is little direct evidence from field studies documenting this trophic link. Ciliates can be voracious grazers of both bacterioplankton and phytoplankton, and each species has a distinct range of preferred particle size which is a function of both mouth size and morphology. Myxotrophic ciliates may be important components in some plankton communities, particularly during periods of nutrient limitation or after their displacement from the benthos of eutrophic lakes. Evidence regarding the importance of planktonic ciliated protozoa in nutrient regeneration and as intermediaries in energy flow is discussed.}, }
@article {pmid24197127, year = {1989}, author = {Blake, LA and West, BC and Lary, CH and Fowler, ME and Todd, JR}, title = {Earthworms near leprosy patients' homes are negative for acid-fast bacilli by fite stain, providing no link between leprous armadillos (Dasypus novemcinctus) and human leprosy.}, journal = {Microbial ecology}, volume = {17}, number = {1}, pages = {105-110}, pmid = {24197127}, issn = {0095-3628}, abstract = {Enzootic leprosy has been recognized in armadillos in Louisiana since 1975. Contact with armadillos is being assessed as a risk factor for leprosy in three white women, lifelong residents of separate rural areas in northern Louisiana, which is a region without endemic leprosy. None has had any known exposure to human leprosy. Each was aware of armadillos (Dasypus novemcinctus) near or under her home for decades. In considering Possible environmental sources forMycobacterium leprae, we observed that all three had earthworm growth areas for fishing bait where soil was kept moist near their homes. The worms attracted armadillos. Since armadillos subsist on worms, grubs, and insects and because of the common feature of a "worm farm" near each home, we reasoned that earthworms might containM. leprae and be part of a cycle involving the armadillo and human beings. Worms from each home worm farm were studied. One site was sampled twice at patient 1's home, five sites were sampled once at patient 2's home, and three sites were sampled once at patient 3's home. A sample consisted of 3-4 worms, which were washed, purged, fixed live in 10% formalin, embedded in paraffin, sectioned, and stained with the Fite stain. Each was sagittally sectioned and examined by three independent observers. No acid-fast bacilli or other acid-fast structures were identified. We conclude that it is unlikely that earthworms are an environmental source or reservoir ofM. leprae.}, }
@article {pmid24197126, year = {1989}, author = {Guerin, WF}, title = {Phenanthrene degradation by estuarine surface microlayer and bulk water microbial populations.}, journal = {Microbial ecology}, volume = {17}, number = {1}, pages = {89-104}, pmid = {24197126}, issn = {0095-3628}, abstract = {Paired surface microlayer and bulk water samples from five sites in the Great Bay Estuary, New Hampshire, were examined with regard to numbers of bacteria,(14)C-phenanthrene biodegradation potentials, and organic and inorganic chemical characteristics. Microlayer samples were generally enriched in nutrients (N and P), dissolved organic matter, and culturable heterotrophic bacteria compared with their corresponding bulk waters. Microlayer samples from marina environments were also enriched in aromatic hydrocarbons, as determined by UV spectrophotometric and fluorometric analyses, and demonstrated substantial phenanthrene biodegradation activity in the assay employed. Biodegradation activity of marina bulk water samples ranged from nil to levels exceeding those exhibited by microlayer samples. No diminution of biodegradation activity was observed after filtration (1.2 μm effective retention) of microlayer water, indicating that the responsible organisms were not particle-associated. Phenanthrene-degrading bacteria, enumerated by counting clearing zones in a crystalline phenanthrene overlay after colony development on a phenanthrene/toluene agar (PTA) medium, were superior to epifluorescence direct counts or standard plate counts on PTA or estuarine nutrient agar in predicting(14)C-phenanthrene biodegradative activity.}, }
@article {pmid24197125, year = {1989}, author = {Geider, RJ}, title = {Use of radiolabeled tracers in dilution grazing experiments to estimate bacterial growth and loss rates.}, journal = {Microbial ecology}, volume = {17}, number = {1}, pages = {77-87}, pmid = {24197125}, issn = {0095-3628}, abstract = {Dilution grazing experiments were conducted to determine growth and loss rates of glucose-metabolizing and total bacteria. Bacterial growth rates were low and losses to grazers negligible in samples collected from the Celtic Sea in June 1986. Growth and loss rates of glucose-metabolizing bacteria were higher than growth and loss rates of total bacteria in a sample collected from the North Sea in October 1986.}, }
@article {pmid24197124, year = {1989}, author = {Smith, RE and Clement, P and Cota, GF}, title = {Population dynamics of bacteria in Arctic sea ice.}, journal = {Microbial ecology}, volume = {17}, number = {1}, pages = {63-76}, pmid = {24197124}, issn = {0095-3628}, abstract = {The dynamics of bacterial populations in annual sea ice were measured throughout the vernal bloom of ice algae near Resolute in the Canadian Arctic. The maximum concentration of bacteria was 6.0·10(11) cells·m(-2) (about 2.0·10(10) cells·l(-1)) and average cell volume was 0.473 μm(3) in the lower 4 cm of the ice sheet. On average, 37% of the bacteria were epiphytic and were most commonly attached (70%) to the dominant alga,Nitzschia frigida (58% of total algal numbers). Bacterial population dynamics appeared exponential, and specific growth rates were higher in the early season (0.058 day(-1)), when algal biomass was increasing, than in the later season (0.0247 day(-1)), when algal biomass was declining. The proportion of epiphytes and the average number of epiphytes per alga increased significantly (P<0.05) through the course of the algal bloom. The net production of bacteria was 67.1 mgC·m(-2) throughout the algal bloom period, of which 45.5 mgC·m(-2) occurred during the phase of declining algal biomass. Net algal production was 1942 mgC·m(-2). Sea ice bacteria (both arctic and antarctic) are more abundant than expected on the basis of relationships between bacterioplankton and chlorophyll concentrations in temperate waters, but ice bacteria biomass and net production are nonetheless small compared with the ice algal blooms that presumably support them.}, }
@article {pmid24197123, year = {1989}, author = {Schütt, C}, title = {Plasmids in the bacterial assemblage of a dystrophic Lake: Evidence for plasmid-encoded nickel resistance.}, journal = {Microbial ecology}, volume = {17}, number = {1}, pages = {49-62}, pmid = {24197123}, issn = {0095-3628}, abstract = {Sixty-two aerobic bacterial strains isolated from the unproductive dystrophic Lake Skärshultsjön (South Sweden) were screened for plasmids. The lake is considered to be an extreme environment because of its high concentration of persistent but nontoxic humic compounds. One-third of the isolates harbored multiple plasmids usually of similar high molecular weights (>25 Mdal). The plasmid-bearing strains were members of the common aquatic taxaPseudomonas spp.,Acinetobacter sp.,Alcaligenes sp.,Aeromonas/Vibrio group, andEnterobacteriaceae (taxonomy is tentative). The majority of isolates displayed multiple resistance to antibiotics and heavy metals. Some of them were capable of degrading aromatic compounds. Three isolates were chosen for curing experiments. Only strain S-68, anAlcaligenes sp., could be cured of one of its two plasmids. It harbored the two cryptic plasmids pQQ32 and pQQ70 of 32 and ca. 70 Mdal, and the latter was segregated during ethidium bromide treatment. Parental strain S-68 was capable of degrading some of nonchlorinated phenolic compounds and displayed resistance to a broad spectrum of antibiotics and the heavy metals Co(2+), Ni(2+), Zn(2+), Cd(2+), and Hg(2+). Derivative strain S-68-41 lost its resistance to nickel, suggesting segregated plasmid PQQ70 coded for nickel resistance. Transformation experiments to restore nickel resistance in the cured derivative strain were not successful.}, }
@article {pmid24197122, year = {1989}, author = {Dillon, PS and Maki, JS and Mitchell, R}, title = {Adhesion ofEnteromorpha swarmers to microbial films.}, journal = {Microbial ecology}, volume = {17}, number = {1}, pages = {39-47}, pmid = {24197122}, issn = {0095-3628}, abstract = {Laboratory experiments were conducted to determine the effect of bacterial films on adhesion ofEnteromorpha sp. reproductive swarmer cells. Swarmers always attached in greater numbers to filmed than to unfilmed polystyrene surfaces. Surface energy measurements produced higher values on filmed surfaces than on unfilmed surfaces. Our data indicate that this higher surface energy may contribute to the increased adhesion by the algal swarmers.}, }
@article {pmid24197121, year = {1989}, author = {Sar, N and Rosenberg, E}, title = {Fish skin bacteria: Production of friction-reducing polymers.}, journal = {Microbial ecology}, volume = {17}, number = {1}, pages = {27-38}, pmid = {24197121}, issn = {0095-3628}, abstract = {The supernatant fluids of cultures of four bacterial strains isolated from the skin of barracuda contained extracellular polymer concentrations of 0.2-0.5 mg/ml and reduced factional drag by 2.5-22% in a turbulent flow rheometer. The production and properties of one of the drag-reducing polymers, referred to as PS-6, were studied further. Polymer PS-6 was produced by strain NS-31 in minimal salts medium supplemented with ethanol or glucose. The polymer began to accumulate in the culture medium during exponential phase and continued to be produced during stationary phase. It reduced drag by 55% at a concentration of 0.75 mg/ ml. Acid-base titration of the deproteinized polymer PS-6A gave two inflection points: pK1=3.26 (2.4 μeq/mg) and pK2=9.66 (0.8 μeq/mg).(13)C-NMR spectroscopy of PS-6A resolved 25 peaks, including three methyl groups, three carbonyl groups, and four signals in the anomeric region (99-103 ppm), indicating the presence of four different monosaccharides. Strong acid hydrolysis of PS-6A yielded an amino acid, pyruvate, and four reducing sugars: a hexosamine, a uronic acid, and two hexoses which migrated on TLC similarly to glucose and galactose. The possible role of bacteria in production of drag-reducing mucus is discussed.}, }
@article {pmid24197120, year = {1989}, author = {Eisen, A and Reid, G}, title = {Effect of culture media onLactobacillus hydrophobicity and electrophoretic mobility.}, journal = {Microbial ecology}, volume = {17}, number = {1}, pages = {17-25}, pmid = {24197120}, issn = {0095-3628}, abstract = {The hydrophobicity of six strains representing three species ofLactobacillus was measured using dextran-polyethylene glycol contact angle measurements. These ranged from 123.6° forLactobacillus casei douche to 26.2° forL. casei RC-17 under identical growth conditions. The results indicated that the nutritional environment affected bacterial hydrophobicity. Electrophoretic mobilities of the lactobacilli were also determined and found to be negative for all specimens, and to vary with growth media, especially when sugars were added to urine. The electrophoretic mobility histograms showed one main peak for all strains, exceptLactobacillus acidophilus T-13 which had two peaks, suggesting two morphological sizes or types within its population. In addition, strain T-13 was more positively charged than the other five strains after growth in agar, urine, and supplemented urine. The use of contact angle and electrophoretic mobility techniques allows examination of cell surface properties of lactobacilli that may have importance in the colonization of mucosal epithelia.}, }
@article {pmid24197119, year = {1989}, author = {van Loosdrecht, MC and Lyklema, J and Norde, W and Zehnder, AJ}, title = {Bacterial adhesion: A physicochemical approach.}, journal = {Microbial ecology}, volume = {17}, number = {1}, pages = {1-15}, pmid = {24197119}, issn = {0095-3628}, abstract = {The adhesion of bacteria to solid surfaces was studied using a physicochemical approach. Adhesion to negatively charged polystyrene was found to be reversible and could be described quantitatively using the DLVO theory for colloidal stability, i.e., in terms of Van der Waals and electrostatic interactions. The influence of the latter was assessed by varying the electrolyte strength. Adhesion increased with increasing electrolyte strength. The adhesion Gibbs energy for a bacterium and a negatively charged polystyrene surface was estimated from adhesion isotherms and was found to be 2-3 kT per cell. This low value corresponds to an adhesion in the secondary minimum of interaction as described by the DLVO theory. The consequences of these findings for adhesion in the natural environment are discussed.}, }
@article {pmid24201719, year = {1988}, author = {Van Outryve, MF and Gosselé, V and Gosselé, F and Swings, J}, title = {Composition of the microflora of witloof chicory seeds.}, journal = {Microbial ecology}, volume = {16}, number = {3}, pages = {339-348}, pmid = {24201719}, issn = {0095-3628}, abstract = {The bacterial microflora of nine varieties of witloof chicory (Cichorium intybus L. var.foliosum Hegi) seeds was studied. The 184 isolates were characterized by protein profiles determined by SDS-protein polyacrylamide gel electrophoresis of the total cell proteins. Isolates with identical protein profiles were grouped into one fingerprint type. Sixty-seven fingerprint types were distinguished. Two quantitatively major fingerprint types,Erwinia herbicola and an arthrobacter, represented 52% of the total number of isolates and were found on different chicory varieties. The latter organism was inhibited at seed germination. Other isolates, i.e.,Xanthomonas maltophilia, Pseudomonas paucimobilis, Agrobacterium radiobacter, Pseudomonas syringae, and a fluorescentPseudomonas, were only occasionally found. A minority were gram-positive isolates, i.e.,Bacillus sp.,Streptomyces sp., and coryneforms. In vitro activity of the isolates was tested against five fungi. Isolates with strong antifungal activity were found amongErwinia herbicola andBacillus sp.}, }
@article {pmid24201718, year = {1988}, author = {Bonjour, F and Graber, A and Aragno, M}, title = {Isolation ofBacillus schlegelii, a thermophilic, hydrogen oxidizing, aerobic autotroph, from geothermal and nongeothermal environments.}, journal = {Microbial ecology}, volume = {16}, number = {3}, pages = {331-337}, pmid = {24201718}, issn = {0095-3628}, abstract = {Thermophilic hydrogen-oxidizing strains forming round, terminal endospores were isolated from geothermal areas. They were neutrophilic and facultatively autotrophic. They resembledBacillus schlegelii, a thermophilic hydrogen bacterium found so far only in cold environments. Phenotypic similarities, as well as DNA G+C content and DNA:DNA homologies, clearly revealed that the isolated strains belonged to the taxospeciesB. schlegelii. Hence, the strains ofB. schlegelii found in cold environments are probably allochthonous, their origin being geothermal and volcanic areas.}, }
@article {pmid24201717, year = {1988}, author = {Benner, R and McArthur, JV}, title = {Effects of temperature on microbial utilization of lignocellulosic detritus in a thermally impacted stream.}, journal = {Microbial ecology}, volume = {16}, number = {3}, pages = {323-330}, pmid = {24201717}, issn = {0095-3628}, abstract = {The effects of temperature on rates of mineralization of [(14)C]lignocellulose were investigated in water and sediment from a thermally impacted stream and from a nearby unimpacted swamp at the Savannah River Plant, South Carolina. The temperature optimum for lignocellulose mineralization remained near 35°C at the unimpacted site throughout the sampling period from November 1986 to May 1987. The temperature optimum for lignocellulose mineralization in the thermally impacted stream was near 45°C when thermal effluents from a nuclear reactor were released to the stream, and was near 35°C when the reactor was not operating. Microbial populations capable of rapidly degrading lignocellulose at higher temperatures (45-55°C) developed between 9 and 27 days under conditions of thermal stress, indicating that under favorable conditions thermophilic microorganisms became dominant components of the microbiota. Removal of thermal stress for periods of 75 days or less resulted in a collapse of the thermophilic degrading population.}, }
@article {pmid24201716, year = {1988}, author = {Tranvik, LJ}, title = {Availability of dissolved organic carbon for planktonic bacteria in oligotrophic lakes of differing humic content.}, journal = {Microbial ecology}, volume = {16}, number = {3}, pages = {311-322}, pmid = {24201716}, issn = {0095-3628}, abstract = {Bacterioplankton from 10 oligotrophic lakes, representing a gradient from clearwater to polyhumic, were grown in dilution cultures of sterile filtered lake water. The bacterial biomass achieved in the stationary phase of the dilution cultures was positively correlated with the amount of both humic matter and dissolved organic carbon (DOC) in the lakes. About the same fraction of the total DOC pool was consumed in the dilution cultures of all lakes (average 9.5%, coefficient of variation (CV) 24%), with approximately the same growth efficiency (average 26%, CV 28%). Thus, humic lakes could support a higher bacterial biomass than clearwater lakes due to their larger DOC pools. The relevance of the results to planktonic food webs of humic and clearwater lakes is discussed.}, }
@article {pmid24201715, year = {1988}, author = {Healey, MJ and Moll, RA and Diallo, CO}, title = {Abundance and distribution of bacterioplankton in the Gambia River, West Africa.}, journal = {Microbial ecology}, volume = {16}, number = {3}, pages = {291-310}, pmid = {24201715}, issn = {0095-3628}, abstract = {Four ecological zones of the Gambia River were sampled during four different hydrologic seasons for determination of microbial, nutrient, and physical parameters. A Greco-Latin Square experimental design was used to define the particular transect, station, depth, and tide/time-of-day of samples taken. Ranges of total bacterioplankton densities (10(6) cells/ml) were similar to those of tropical and temperate environments. Numbers of free bacteria were similar temporally, whereas attached bacteria numbers were greater during periods of high stream flows when suspended solids concentrations were higher. Free bacteria were usually twice as numerous in the freshwater zones than in the estuarine zones. Attached bacterial densities were approximately four times greater in the estuarine zones than in the freshwater zones. Uptake of(3)H-glucose on both a sample volume and per-cell basis increased from the early stages of the flood (6.95±SE 1.37 ng/liter/hour and 3.8 pg/hour/10(6) cells, respectively) and reached observed annual maximums during the dry season (21.01±SE 3.05 ng/ liter/hour and 13.0 pg/hour/10(6) cells, respectively). Spatially,(3)H-glucose uptake per sample volume and per cell was highest in the upper river zone and lowest in the lower estuary zone. The lower estuary zone consistently acted out of concert with the other river zones in terms of(3)H-glucose and(14)C-bicarbonate uptake. Analysis of variance (ANOVA) indicated that free and attached bacterioplankton densities were not homogeneous among transects, stations, depths, and tide/time-of-day at the different zones during the four hydrologic seasons. The results suggested that heterotrophy overshadowed autotrophy in the river and that the bacterial abundance, distribution, and glucose uptake activity in this tropical floodplain river were greatly influenced by the annual flood and the presence of extensive mangrove forests in the estuary.}, }
@article {pmid24201714, year = {1988}, author = {Nienow, JA and McKay, CP and Friedmann, EI}, title = {The cryptoendolithic microbial environment in the Ross Desert of Antarctica: Light in the photosynthetically active region.}, journal = {Microbial ecology}, volume = {16}, number = {3}, pages = {271-289}, pmid = {24201714}, issn = {0095-3628}, abstract = {The vertical zonation of the Antarctic cryptoendolithic community appears to form in response to the light regime in the habitat. However, because of the structure of the habitat, the light regime is difficult to study directly. Therefore, a mathematical model of the light regime was constructed, which was used to estimate the total photon flux in different zones of the community. Maximum fluxes range from about 150μm photons m(-2) s(-1) at the upper boundary of the community to about 0.1μm photons m(-2) s(-1). Estimates of the annual productivity in the community indicate that the lowest zone of the community is light limited, with the maximal annual carbon uptake equivalent to less than the carbon content of one algal (Hemichloris) cell.}, }
@article {pmid24201713, year = {1988}, author = {Nienow, JA and McKay, CP and Friedmann, EI}, title = {The cryptoendolithic microbial environment in the Ross Desert of Antarctica: Mathematical models of the thermal regime.}, journal = {Microbial ecology}, volume = {16}, number = {3}, pages = {253-270}, pmid = {24201713}, issn = {0095-3628}, abstract = {Microbial activity in the Antarctic cryptoendolithic habitat is regulated primarily by temperature. Previous field studies have provided some information on the thermal regime in this habitat, but this type of information is limited by the remoteness of the site and the harsh climatic conditions. Therefore, a mathematical model of the endolithic thermal regime was constructed to augment the field data. This model enabled the parameters affecting the horizontal and altitudinal distribution of the community to be examined. The model predicts that colonization should be possible on surfaces with zenith angle less than 15°. At greater zenith angles, colonization should be restricted to surfaces with azimuth angles less than 135° or greater than 225°. The upper elevational limit of the community should be less than 2,500 m. The thermal regime probably does not influence the zonation of the community within a rock.}, }
@article {pmid24201712, year = {1988}, author = {Reid, G and Hawthorn, LA and Mandatori, R and Cook, RL and Beg, HS}, title = {Adhesion of lactobacilli to polymer surfaces in vivo and in vitro.}, journal = {Microbial ecology}, volume = {16}, number = {3}, pages = {241-251}, pmid = {24201712}, issn = {0095-3628}, abstract = {The ability of bacteria to attach to surfaces has been recognized as an important phenomenon, particularly for pathogenic organisms that utilize this capacity to initiate disease. The present investigation was undertaken to determine whether indigenous urogenital bacteria, lactobacilli, colonized prosthetic devices in vivo and in vitro and attached to specific polymer surfaces in vitro. Polyethylene intrauterine devices (IUDs) in place for 2 years were removed from six women who were asymptomatic and free of signs of cervical or uterine infection. Lactobacilli were found attached to the IUDs, as determined by culture, and fluorescent antibody and acridine orange staining techniques. This demonstrated that bacterial biofilms consisting of indigenous bacteria can occur on prosthetic devices without inducing a symptomatic infection. In vitro studies were then undertaken with well-documented lactobacilli strainsL. acidophilus T-13,L. casei GR-1, GR-2, and RC-17, andL. fermentum A-60. These organisms were found to adhere to IUDs and urinary catheters within 24 hours. A quantitative assay was designed to examine the mechanisms of adhesion ofL. acidophilus T-13 to specific polymer surfaces that are commonly used as prosthetic devices. The lactobacilli adhered optimally to fluorinated ethylene propylene when 10(8) bacteria were incubated for 9 hours at 37°C in phosphate buffered saline, pH 7.1. Additional experiments verified that the lactobacilli adhered to polyethyleneterephthalate, polystyrene, and sulfonated polystyrene and to silkolatex catheter material. There was a linear relationship found between polymer hydrophobicity and bacterial adherence. These results demonstrate that lactobacilli bind to various surfaces in vivo and in vitro, and that the nature of the substratum can affect the colonization.}, }
@article {pmid24201574, year = {1988}, author = {Noeth, C and Britz, TJ and Joubert, WA}, title = {The isolation and characterization of the aerobic endospore-forming bacteria present in the liquid phase of an anaerobic fixed-bed digester, while treating a petrochemical effluent.}, journal = {Microbial ecology}, volume = {16}, number = {2}, pages = {233-240}, pmid = {24201574}, issn = {0095-3628}, abstract = {Sixty-nine gram-positive endospore-forming rods were isolated from the liquid phase of an anaerobic digester, while treating a fatty acid-rich petrochemical effluent. These strains, including eight reference strains, were characterized and the similarities between the different strains were calculated using Sokal and Michener's simple matching coefficient. Phenotypic characteristics, determined by the API 20E and API 50CHB galleries, other biochemical tests, and morphological characteristics, were used for the numerical analysis. The strains were grouped into 12 (five major and seven minor) clusters. Nine of the clusters were positively identified asBacillus pumilus, B. subtilis, B. sphaericus, B. laterosporus, B. brevis, B. cereus, B. coagulans, B. megaterium, andB. circulans. Three clusters could not be identified using Gordon's classical system or the API identification system. Most of the aerobic endospore-forming rods (72%) utilized both acetic and propionic acid, and 17% utilized acetic acid as carbon source, but only under aerobic conditions. A small percentage of the strains studied (11%) was unable to utilize the fatty acids present in the petrochemical substrate, and no explanation could be given as to how they obtained their carbon source. Seventy-eight percent of the strains did not show growth in anaerobic agar. It was possible that sufficient oxygen, required for growth by these members of the genusBacillus, was introduced by the substrate. Since ample time had been allowed for population selection, their presence indicates that these aerobic strains can survive, grow, and compete in the digester environment but their relative importance and role in the primary digestion reactions is not clear.}, }
@article {pmid24201573, year = {1988}, author = {Nakatsu, C and Hutchinson, TC}, title = {Extreme metal and acid tolerance ofEuglena mutabilis and an associated yeast from Smoking Hills, Northwest Territories, and their apparent mutualism.}, journal = {Microbial ecology}, volume = {16}, number = {2}, pages = {213-231}, pmid = {24201573}, issn = {0095-3628}, abstract = {In isolates ofEuglena mutabilis and an associated yeast from strongly acidic tundra ponds (pH 1.8-2.0) at the Smoking Hills, North West Territories (N.W.T.), and in isolates from acidic ponds in the Yukon, a remarkable degree of tolerance to a number of toxic elements and to very low pH has been found. Growth was used as a measure of tolerance. The tolerances to both low pH and to elevated metal concentrations were markedly enhanced when both organisms were present together. This mutualism occurred even betweenE. mutabilis from one field location and a yeast from another. In every field collection we made ofEuglena, the yeast was also found. The tolerances to metals are 10-100 times higher than the highest reported previously for algae, and include tolerance to some metals not elevated in the ponds from which isolations were made. Reciprocal combinations of algal-yeast partners suggest a generalized benefit of association and an increased benefit for co-selected pairs from a specific site. This algal-yeast association may be a major factor in allowing colonization of these extreme acid habitats, paralleling the cyanobacteria-bacterial associations of extremely alkaline waters.}, }
@article {pmid24201572, year = {1988}, author = {Sambanis, A and Fredrickson, AG}, title = {Peristance of bacteria in the presence of viable, nonencysting, bacterivorous ciliates.}, journal = {Microbial ecology}, volume = {16}, number = {2}, pages = {197-211}, pmid = {24201572}, issn = {0095-3628}, abstract = {Laboratory studies of the interactions between a bacterial population and a population of bacterivorous ciliates consistently show that the bacteria are able to persist in the presence of viable ciliates. Reproduction of the bacteria, presumably at the expense of substrates produced by death and lysis of the ciliates and/or by their metabolic activity, has been suggested to be a factor involved in the observed bacterial persistence. Rates and extents of growth ofEscherichia coli in broths of mixed cultures of this bacterium and the ciliateTetrahymena pyriformis were determined in order to provide some data necessary to assess the importance of the suggested factor. In addition, an attempt was made to suppress bacterial growth on produced substrates so that feeding of the ciliates could be studied free of this complication. However, the procedure tested-addition of the antibiotic chloramphenicol (CM) at a concentration of 150μg/ml-led to other complications that made it impossible to obtain the desired information about feeding.}, }
@article {pmid24201571, year = {1988}, author = {McEldowney, S and Fletcher, M}, title = {Effect of pH, temperature, and growth conditions on the adhesion of a gliding bacterium and three nongliding bacteria to polystyrene.}, journal = {Microbial ecology}, volume = {16}, number = {2}, pages = {183-195}, pmid = {24201571}, issn = {0095-3628}, abstract = {The effect of growth rate, growth phase, pH, and temperature on the permanent adhesion of a glidingFlexibacter sp. and three nongliding bacteria,Pseudomonas fluorescens, Enterobacter cloacae, andChromobacterium sp., to polystyrene substrata was investigated. The permanent adhesion of the flexibacter appeared to be related to growth, as levels of adhesion increased with increased growth rate in continuous culture and declined rapidly with death phase in batch culture. With the three nongliding bacteria, there was no relationship between growth rate and levels of permanent adhesion. The permanent adhesion of the nongliding bacteria was maximum between pH 5.5 and pH 7 and between 20 and 30°C, whereas the adhesion of the flexibacter progressively decreased with increasing temperature and pH. The effect of different nutrient conditions on the gliding motility of the flexibacter across agar was also investigated. Gliding motility was inhibited by increased nutrient concentration and was affected by carbon source. Inhibition appeared to be related to the accumulation of a viscous exopolymer. It is proposed that the differences in the permanent adhesion of the gliding and nongliding bacteria may be related to their adaptation to different ecological niches.}, }
@article {pmid24201570, year = {1988}, author = {Haack, SK and Burton, T and Ulrich, K}, title = {Effects of whole-tree harvest on epilithic bacterial populations in headwater streams.}, journal = {Microbial ecology}, volume = {16}, number = {2}, pages = {165-181}, pmid = {24201570}, issn = {0095-3628}, abstract = {Bacteria attached to rock and glass surfaces were studied in streams draining a whole-tree harvested watershed (WTH) and a nonharvested (CONTROL) watershed in the Hubbard Brook Experimental Forest, New Hampshire, U.S.A. Seasonal trends in numbers of cells/cm(2), mean cell volume, cell size-frequency distribution, and bacterial biomass were determined using 4'6-diamidino-2-phenylindole (DAPI) epifluorescent microscopy and scanning electron microscopy (SEM); the response of these parameters to decreased pH and increased nitrate concentration in the WTH stream was assessed via controlled manipulation of stream water chemistry in artificial channels placed in the CONTROL stream. Bacterial distribution varied significantly between the two streams and seasonally within each stream in apparent response to differential availability of dissolved organic carbon from algae and autumn-shed leaves. Decreased pH similar to that in the WTH stream had a significant effect on cell numbers, mean cell volume, and biomass in the CONTROL stream. Decreased pH accounted for some aspects of the altered bacterial distributions observed in the WTH stream. Nitrate at concentrations similar to those in the WTH stream had no effect on bacterial distribution in the CONTROL stream suggesting that headwater stream epilithic bacteria were carbon limited.}, }
@article {pmid24201569, year = {1988}, author = {Chrzanowski, TH and Crotty, RD and Hubbard, GJ}, title = {Seasonal variation in cell volume of epilimnetic bacteria.}, journal = {Microbial ecology}, volume = {16}, number = {2}, pages = {155-163}, pmid = {24201569}, issn = {0095-3628}, abstract = {The relationship between bacterial cell volume and temperature was examined for field data collected over a 4-year period and through controlled chemostat incubations of aPseudomonas sp. Volumes of planktonic bacteria were found to decrease as water temperature increased. Changes in temperature accounted for 38% of the variation in average cell volume (P<0.001). Average planktobacterial cell volume fell 42% from 0.217μm(3) in mid-winter to 0.127μm(3) in mid-summer. Similar results were found for the size distribution of epibacterial cells. Controlled chemostat incubations of aPseudomonas sp. indicated that cell volume was significantly affected by temperature, growth rate, and the interaction of temperature and growth rate. The data suggest that a change in cell volume as a result of a change in temperature is an intrinsic property of planktonic bacteria.}, }
@article {pmid24201568, year = {1988}, author = {Bisoyi, RN and Singh, PK}, title = {Effect of seasonal changes on cyanobacterial production and nitrogen-yield.}, journal = {Microbial ecology}, volume = {16}, number = {2}, pages = {149-154}, doi = {10.1007/BF02018910}, pmid = {24201568}, issn = {0095-3628}, abstract = {A mixed culture of cyanobacteria (BGA) containingAulosira sp.,Aphanothece sp., andGloeotrichia sp. were grown throughout the year to assess the influence of seasonal variables on their biomass production and nitrogen (N)-yield under field conditions. The seasonal variables considered in this study, i.e., water temperature (maximum, minimum), solar radiation, sunshine hours, and rainfall, fluctuated widely. Attempts were made to establish a relationship between seasonal changes as independent variables and BGA productivity and N-yield as dependent variables. The analysis indicated that solar radiation was the prime factor. Estimates of BGA biomass production varied from 3.3 to 366.5 kg (dry wt)/ha/month, and N-yield ranged from 0.1 to 11.8 kg N/ha/month. The nitrogen accumulated during the study period was 71.2 kg N/ha. The variations explained by seasonal changes were 52.3 and 50.3% for biomass production and N-yield of BGA, respectively.}, }
@article {pmid24201567, year = {1988}, author = {Jørgensen, BB and Nelson, DC}, title = {Bacterial zonation, photosynthesis, and spectral light distribution in hot spring microbial mats of Iceland.}, journal = {Microbial ecology}, volume = {16}, number = {2}, pages = {133-147}, pmid = {24201567}, issn = {0095-3628}, abstract = {The zonation and structure of phototrophic microbial mats were studied along two thermal gradients in sulfide-rich hot springs of southwest Iceland. The green, filamentous bacteriumChloroflexus and the unicellular, "high-temperature form" (HTF) ofMastigocladus formed mats growing up to a temperature limit of 62-66°C. The dominant phototrophs wereChloroflexus sp.,Mastigocladus laminosus, andPhormidium laminosum, respectively, at the three temperature intervals: >60°C, 60°C to 55-50°C, and <55-50°C. AChloroflexus mat growing at 60°C under 60μM H2S was anoxic in the light with the exception of a 0.5 mm thick band of HTFMastigocladus which produced oxygen. The oxygenic photosynthesis of these H2S-sensitive cyanobacteria was probably dependent on a preceding sulfide depletion by the anoxygenicChloroflexus. Measurements of spectral radiance gradients with a fiberoptic microprobe showed maximum light attenuation by carotenoids and bacteriochlorophyllC. AM. laminosus mat growing at 52°C was oxic throughout and showed maximum light attenuation by carotenoids, chlorophyllA, and phycocyanin, but no detectable phycoerythrocyanin absorption.}, }
@article {pmid24201566, year = {1988}, author = {Kelly, FX and Dapsis, KJ and Lauffenburger, DA}, title = {Effect of bacterial chemotaxis on dynamics of microbial competition.}, journal = {Microbial ecology}, volume = {16}, number = {2}, pages = {115-131}, pmid = {24201566}, issn = {0095-3628}, abstract = {Although the dynamic behavior of microbial populations in nonmixed systems is a central aspect of many problems in biochemical engineering and microbiology, the factors that govern this behavior are not well understood. In particular, the effects of bacterial chemotaxis (biased migration of cells in the direction of chemical concentration gradients) have been the subject of much speculation but very little quantitative investigation. In this paper, we provide the first theoretical analysis of the effects of bacterial chemotaxis on the dynamics of competition between two microbial populations for a single rate-limiting nutrient in a confined nonmixed system. We use a simple unstructured model for cell growth and death, and the most soundly based current model for cell population migration. Using numerical finite element techniques, we examine both transient and steady-state behavior of the competing populations, focusing primarily on the influence of the cell random motility coefficient,μ, and the cell chemotaxis coefficient, χ. We find that, in general, there are four possible steady-state outcomes: both populations die out, population 1 exists alone, population 2 exists alone, and the two populations coexist. We find that, in contrast to well-mixed systems, the slower-growing population can coexist and even exist alone if it possesses sufficiently superior motility and chemotaxis properties. Our results allow estimation of the value of χ necessary to allow coexistence and predominance for reasonable values of growth and random motility parameters in common systems. An especially intriguing finding is that there is a minimum value of χ necessary for a chemotactic population to have a competitive advantage over an immotile population in a confined nonmixed system. Further, for typical system parameter values, this minimum value of χ is the range of values that can be estimated from independent experimental assays for chemotaxis.Thus, in typical nonmixed systems, cell motility and chemotaxis properties can be the determining factors in governing population dynamics.}, }
@article {pmid24201536, year = {1988}, author = {Hirsch, P and Rades-Rohkohl, E}, title = {Some special problems in the determination of viable counts of groundwater microorganisms.}, journal = {Microbial ecology}, volume = {16}, number = {1}, pages = {99-113}, pmid = {24201536}, issn = {0095-3628}, abstract = {Factors affecting viable cell counts in groundwater or sediments were studied with samples from the Segeberg Forest test area in northern Germany. There was very little variation in results with the season (April, August, November) or depth of sampling; generally there were 10(3)-10(4) aerobic cells per ml or g sediment. Long incubation times resulted in higher cell counts; groundwater samples required 4-5 weeks, and sediment extracts had to be cultured for 7 weeks. Total cell counts in sediment were 10(2)-10(4) cell/g higher than viable cell counts of aerobes. This was explained partly by the additional presence of anaerobes and partly by the observation that some morphotypes may not have grown under our conditions. Viable cell counts were not influenced by cell extraction from the sediment with either Na-pyrophosphate or groundwater extracts. However, iron-precipitating or manganese-oxidizing bacteria were better extracted with sterile groundwater. The microflora of wells was more numerous than that of the free aquifer; consequently it was better to pump off all well water before aquifer water was sampled. The diameter of the well was also important; thinner tubes had higher cell counts than those with wider diameter. For sampling, wells should be at least 1 year old, since young wells contain higher numbers of microorganisms due to underground disturbances from the drilling. Turbid water samples could be clarified by filtration, but this reduced the viable counts by 1-2 orders of magnitude. Two different media inoculated with a sample dilution resulted in the same cell counts, but their microbial diversity was different. Storage of groundwater samples before processing resulted in up to 17-fold increases in cell counts and loss of diversity in the first 24 hours. Cell numbers decreased slowly during longer storage.}, }
@article {pmid24201535, year = {1988}, author = {Beloin, RM and Sinclair, JL and Ghiorse, WC}, title = {Distribution and activity of microorganisms in subsurface sediments of a pristine study site in Oklahoma.}, journal = {Microbial ecology}, volume = {16}, number = {1}, pages = {85-97}, pmid = {24201535}, issn = {0095-3628}, abstract = {Distribution and activity of microorganisms in surface soil and subsurface sediments were studied in depth profiles of six different microbial biomass and activity indicators (total direct counts, number of cells capable of electron transport system activity, viable cell plate counts, most Probable numbers of protozoa, and 4-hydroxybenzoate-degrading microorganisms, and ATP content). The profiles showed the same general trends on two different dates (January and June 1985). Seasonal variations were noted, but they were not extreme. Biomass and activity values declined sharply with depth in the unsaturated zone, reaching minima in a clay confining layer in the interface zone between 3 and 4 m. Contiguous 10-cm samples from the interface zone showed significant textural and microbiological variability. Higher and more stable biomass and activity values were detected in the saturated zone, the highest being a very permeable gravelly loamy sand layer at approximately 7.5 m. In this layer, viable counts were nearly equal to total counts and they approached the viable counts in surface soil. Surface-type protozoa and cyanobacteria also were detected in this layer, suggesting that it was connected hydrologically to a nearby river. Lowest values were detected in an underlying bedrock clay layer at 8 m, which, despite its impermeability and low viable counts, did contain measurable total counts, 4-hydroxybenzoate-degrading microorganisms, and ATP. Correlations were noted between sediment texture and microbial activity (i.e., sandy texture=high activity, clayey texture=low activity), but other hydrogeological and geochemical factors probably also influenced microbial distribution and activity in the profile.}, }
@article {pmid24201534, year = {1988}, author = {Balkwill, DL and Leach, FR and Wilson, JT and McNabb, JF and White, DC}, title = {Equivalence of microbial biomass measures based on membrane lipid and cell wall components, adenosine triphosphate, and direct counts in subsurface aquifer sediments.}, journal = {Microbial ecology}, volume = {16}, number = {1}, pages = {73-84}, pmid = {24201534}, issn = {0095-3628}, abstract = {An uncontaminated subsurface aquifer sediment contains a sparse microbial community consisting primarily of coccobacillary bacteria of relatively uniform size which can be counted directly with appropriate staining. The morphological simplicity and the relatively decreased cell numbers, when compared with surface soils and sediments, make the subsurface an ideal natural community with which to compare the utility of chemical measures of microbial biomass to direct microscopic counts. The membrane phospholipids (estimated as the polar lipid fatty acids, the lipid phosphate, and phosopholipid glycerol phosphate), lipopolysaccharide lipid A (estimated as the LPS hydroxy fatty acids), cell walls (estimated as the muramic acid), and adenosine triphosphate all give essentially identical estimates of cell numbers and dry weight as the direct counts, using conversion factors determined on subsurface microorganism monocultures. Assays of microbial cell components are thus validated by comparison with the classical direct count in at least one soil/sediment.}, }
@article {pmid24201533, year = {1988}, author = {Marxsen, J}, title = {Investigations into the number of respiring bacteria in groundwater from sandy and gravelly deposits.}, journal = {Microbial ecology}, volume = {16}, number = {1}, pages = {65-72}, pmid = {24201533}, issn = {0095-3628}, abstract = {Samples were collected from organically polluted and unpolluted groundwater of sandy and gravelly deposits. After filtration onto polycarbonate filters (0.2μm pore size) the number of respiring bacteria was recorded by microscopically counting cells containing red INT-formazan spots, which characterize respiring bacteria. The total number of bacteria was simultaneously recorded by epifluorescence microscopy after staining with acridine orange. The number of respiring bacteria in the groundwater samples (55-490×10(3)/cm(3)) is within the range of values for other aquatic biotopes, but as the total number of bacteria in groundwater was usually higher, the proportion of respiring groundwater bacteria (0.66-7. 4%) was lower. Mainly larger bacteria, rods, and bacteria on particles could be identified as being active, whereas hardly any respiratory activity could be detected among small cocci and free interstitial bacteria. If the supply of dissolved organic matter (DOM) is adequate, the biomass of respiring bacteria correlates well with oxygen concentration, but there is no direct correlation between DOM concentration in groundwater and active bacterial biomass. Nor could any relationship be observed between the biomass of total and respiring bacteria, or between the quantity of respiring bacteria and heterotrophic bacterial activity.}, }
@article {pmid24201532, year = {1988}, author = {Bone, TL and Balkwill, DL}, title = {Morphological and cultural comparison of microorganisms in surface soil and subsurface sediments at a pristine study site in Oklahoma.}, journal = {Microbial ecology}, volume = {16}, number = {1}, pages = {49-64}, pmid = {24201532}, issn = {0095-3628}, abstract = {Surface-soil and subsurface microfloras at the site of a shallow aquifer in Oklahoma were examined and compared with respect to (1) total and viable cell numbers, (2) colony and cell types that grew on various plating media, (3) cell morphologies seen in flotation films stripped from sample particles, and (4) cellular ultrastructure. Appreciable numbers of microbial cells were present in the subsurface (total counts: 10(6)-10(7) cellsg(-1); viable counts up to 10(6) cells · g(-1)), but the subsurface microflora was considerably less populous than that of the surface soil (total counts: 10(9) cells·g(-1); viable counts: 10(7)-10(8) cells · g(-1)). The subsurface microflora (especially that of the saturated zone) also appeared to be much less diverse, containing fewer microbial types that would grow on enumeration plates (on nutrient-rich media, 3-4 colony types versus 19-22 for the surface soil) and fewer cell types that could be distinguished by direct microscopy (3-4 types versus 17 for the surface soil). The specific types of microorganisms that were numerically predominant in the aquifer sediments were entirely different from those that were predominant in the surface soil. Moreover, the predominant types varied from one depth to another within the saturated zone. The potential metabolic capability of the subsurface microflora, as indicated by its readiness to grow rapidly on nutrient-rich media, also varied with depth.}, }
@article {pmid24201531, year = {1988}, author = {Kölbel-Boelke, J and Anders, EM and Nehrkorn, A}, title = {Microbial communities in the saturated groundwater environment II: Diversity of bacterial communities in a Pleistocene sand aquifer and their in vitro activities.}, journal = {Microbial ecology}, volume = {16}, number = {1}, pages = {31-48}, pmid = {24201531}, issn = {0095-3628}, abstract = {Bacterial cell numbers obtained from 103 water and sediment samples from a Pleistocene sandy aquifer in the Lower Rhine region (Bocholt, FRG) were determinated on P-agar and by direct count. Below 5 m under the surface, colony-forming unit (cfu) numbers in water samples were less than 100/ml, and in many cases less than 50/ml. In sediment samples, they were 10- to 100-fold higher (10(2)-10(4) cfu/g dry wt), but changing markedly between different depths. Direct cell counts yielded numbers two to three orders of magnitude higher.About 2,700 strains of bacteria from 60 samples were isolated randomly and characterized by morphological and physiological properties. Of all the isolates, 71.6% were gram-negative, and 52.2% were gram-negative straight rods. Water communities, with one exception, had low proportions of gram-positive bacteria (<11%), whereas in all but one of the sediment communities percentages of gram-positive isolates were three- to sevenfold higher (35-43%). Water and sediment communities, as well as communities from different sampling sites and communities from different depths of the same sampling site, differed in their qualitative and quantitative morphotype composition and physiological capabilities.The in vitro activities of strains within a single community were quite different, indicating that each community is composed of many diverse bacteria, several having extremely different capabilities. Thus, each community has its own specific activity pattern. Gram-positive bacteria showed on an average lower total activities than did gram-negative bacteria. Grampositive bacteria as well as gram-negative bacteria from sediment had higher values of in vitro activities than the corresponding groups isolated from water. Many water and sediment bacteria preferred the same substrates which were utilized at high rates. However, there were differences in the degradation of the various other substrates present, and each community showed preferences for particular substrates, which they degraded best.The results of cell morphology and physiology studies indicated that all eight characterized communities were very different from one another and very diversely structured.}, }
@article {pmid24201530, year = {1988}, author = {Kölbel-Boelke, J and Tienken, B and Nehrkorn, A}, title = {Microbial communities in the saturated groundwater environment I: Methods of isolation and characterization of heterotrophic bacteria.}, journal = {Microbial ecology}, volume = {16}, number = {1}, pages = {17-29}, pmid = {24201530}, issn = {0095-3628}, abstract = {In this paper we present a method of isolation and morphological and physiological characterization of groundwater bacteria based on numerical taxonomy and cluster analysis, and using a miniaturized test system (microtiter plates). Bacteria were isolated randomly on P-agar, and each strain was characterized in regard to 155 features. The media for biochemical differentiation are listed as well as methods of morphological discrimination. 246 strains of heterotrophic and oligotrophic bacteria, isolated from five water samples from different depths of the saturated groundwater area, were used for optimizing media and test reactions.}, }
@article {pmid24201529, year = {1988}, author = {Thorn, PM and Ventullo, RM}, title = {Measurement of bacterial growth rates in subsurface sediments using the incorporation of tritiated thymidine into DNA.}, journal = {Microbial ecology}, volume = {16}, number = {1}, pages = {3-16}, pmid = {24201529}, issn = {0095-3628}, abstract = {Microbial growth rates in subsurface sediment from three sites were measured using incorporation of tritiated thymidine into DNA. Sampling sites included Lula, Oklahoma, Traverse City, Michigan, and Summit Lake, Wisconsin. Application of the thymidine method to subsurface sediments required (1) thymidine concentrations greater than 125 nM, (2) incubation periods of less than 4 hours, (3) addition of SDS and EDTA for optimum macromolecular extraction, and (4) DNA purification, in order to accurately measure the rate of thymidine incorporation into DNA. Macromolecule extraction recoveries, as well as the percentage of tritium label incorporated into the DNA fraction, were variable and largely dependent upon sediment composition. In general, sandy sediments yielded higher extraction recoveries and demonstrated a larger percentage of label incorporated into DNA than sediments that contained a high silt-clay component. Reported results also indicate that the acid-base hydrolysis procedure routinely used for macromolecular fractionation in water samples may not be routinely applicable to the modified sediment procedure where addition of SDS and EDTA are required for macromolecule extraction. Growth rates exhibited by subsurface communities are relatively slow, ranging from 5.1 to 10.2×10(5) cells g(-1) day(-1). These rates are 2-1,000-fold lower than growth rates measured in surface sediments. These data lend support to the supposition that subsurface microbial communities are nutritionally stressed.}, }
@article {pmid24201528, year = {1988}, author = {Hirsch, P}, title = {Editorial.}, journal = {Microbial ecology}, volume = {16}, number = {1}, pages = {1-2}, doi = {10.1007/BF02097400}, pmid = {24201528}, issn = {0095-3628}, }
@article {pmid24201411, year = {1988}, author = {Bolinches, J and Lemos, ML and Barja, JL}, title = {Population dynamics of heterotrophic bacterial communities associated withFucus vesiculosus andUlva rigida in an estuary.}, journal = {Microbial ecology}, volume = {15}, number = {3}, pages = {345-357}, pmid = {24201411}, issn = {0095-3628}, abstract = {The heterotrophic bacterial communities associated with the seaweedsFucus vesiculosus andUlva rigida in an estuary were studied. Changes in these communities were monitored by monthly sampling during the year. The isolated strains were identified at the genus level and grouped into 14 clusters by their similarities. Seasonal changes in genera and clusters as well as variations in diversity were related to primary production periods and fluctuation of salinity levels. TheFlavobacterium group was the major inhabitant of algal surfaces, being dominant after the primary production peaks occurred in spring and autumn. The decrease of dissolved organic matter after these peaks yielded an increase in diversity. Important alterations in these bacterial communities were observed during a period of large decrease in the salinity of estuarine water. In general, the epiphytic communities of both seaweeds were similar in their composition and dynamics, but they were very different from the surrounding water communities.}, }
@article {pmid24201410, year = {1988}, author = {Sugita, H and Tsunohara, M and Ohkoshi, T and Deguchi, Y}, title = {The establishment of an intestinal microflora in developing goldfish (Carassius auratus) of culture ponds.}, journal = {Microbial ecology}, volume = {15}, number = {3}, pages = {333-344}, pmid = {24201410}, issn = {0095-3628}, abstract = {The bacterial flora in the intestinal tract of goldfish (Carassius auratus) was investigated at different stages of fish development. The floras of the diets and the water and sediment of a culture pond were also analyzed. The total counts in the intestine ranged from 2.2 × 10(6)-2.1 × 10(8) cells g(-1) wet weight.Aeromonas hydrophila, A. punctata, Pseudomonas, Bacteroidaceae andClostridium species were the common components in the intestinal tract of goldfish from larvae to adult stage.Bacteroides type A appeared at 44 days with a density of 10(3) cells g(-1) and then predominated with densities of 10(5)-10(7) cells g(-1). The intestinal microflora of goldfish become relatively stable after 67 days of hatching. These observations suggest that the intestinal microflora of adult goldfish becomes established approximately 2 months after hatching.}, }
@article {pmid24201409, year = {1988}, author = {Austin, DA and Baker, JH}, title = {Fate of bacteria ingested by larvae of the freshwater mayfly,Ephemera danica.}, journal = {Microbial ecology}, volume = {15}, number = {3}, pages = {323-332}, pmid = {24201409}, issn = {0095-3628}, abstract = {The fate of bacteria in the food of a common freshwater invertebrate has been studied both in controlled laboratory experiments and in a stream sediment. The animal chosen was the larva of the burrowing mayfly,Ephemera danica. It ingested all available bacteria nonselectively. More bacteria were found associated with the hindgut than with the mesenteron despite continuous plug flow of food through the alimentary canal. Species of bacteria were affected in different ways.Aeromonas hydrophila andCitrobacter freundii were both digested, the former selectively.Flavobacterium sp. and other unidentified species appeared to attach to the hindgut wall. Digestion of bacteria was not due to a sudden change in pH.}, }
@article {pmid24201408, year = {1988}, author = {Reichardt, W}, title = {Impact of the Antarctic benthic fauna on the enrichment of biopolymer degrading psychrophilic bacteria.}, journal = {Microbial ecology}, volume = {15}, number = {3}, pages = {311-321}, pmid = {24201408}, issn = {0095-3628}, abstract = {Stenothermic cold adaptation was a predominant growth characteristic among biopolymer degrading bacteria from Antarctic shelf sediments. Psychrophilic decomposers of protein (gelatin), chitin, and cellulose accounted for up to 84, 93, and 68%, respectively, of 0°C-isolates from selected compartments of the sediments. Macroinvertebrates were recognized as a selective pressure on these fast-growing (zymogenous) psychrophiles. Psychrophilic properties of growth and biopolymer degradation coincided most in the case of proteolytic isolates. On the other hand, the majority of psychrophilic chitin- and cellulose-decomposers showed less efficient biopolymer degradation at environmental temperatures (0°C). Temperature optima of the activities of pertinent depolymerizing enzymes (e.g., scleroprotease) exceeded by far the temperature optima for growth (between 4 and 12°C). Therefore, it appears likely that enhanced rates of enzyme synthesis at low temperatures play a crucial role for the degradation of detrital organic matter in this permanently cold environment.}, }
@article {pmid24201407, year = {1988}, author = {Delille, D and Bouvy, M and Cahet, G}, title = {Short-term variations of bacterioplankton in Antarctic zone: Terre Adelie area.}, journal = {Microbial ecology}, volume = {15}, number = {3}, pages = {293-309}, pmid = {24201407}, issn = {0095-3628}, abstract = {Previous studies on Antarctic seawater have demonstrated the presence of significant numbers of bacteria, but their in situ activity has not been demonstrated. In order to demonstrate this hypothetical activity, a scheduled survey was conducted from January to February 1986 in a coastal area of Adelie Land. Seawater samples were collected in a selected station every day or every hour during a 17 hour period. Bacterial communities in each sample were studied by measuring direct and viable counts, frequency of dividing cells estimation, taxonomic analysis, and heterotrophic potential. Complementary studies used batch cultures with artificial nutrient supplements. The results clearly suggest a strong potential activity of the natural Antarctic bacterial microflora.}, }
@article {pmid24201406, year = {1988}, author = {Kiene, RP and Capone, DG}, title = {Microbial transformations of methylated sulfur compounds in anoxic salt marsh sediments.}, journal = {Microbial ecology}, volume = {15}, number = {3}, pages = {275-291}, pmid = {24201406}, issn = {0095-3628}, abstract = {Anoxic salt marsh sediments were amended with several methylated sulfur compounds. Sediment microbes transformed the added compounds into other volatile methylated sulfur compounds and eventually mineralized the compounds to CH4 and presumably to CO2 and H2S. The principal methyl-sulfur product of dimethylsulfoniopropionate (DMSP) was found to be dimethylsulfide (DMS), with only small amounts of methane thiol (MSH) produced. By contrast, methionine and S-methyl cysteine were degraded mostly to MSH and to lesser amounts of DMS. Dimethylsulfoxide (DMSO) was biologically converted to DMS. Dimethyldisulfide (DMDS) was rapidly reduced to MSH by the sediment microflora, and some DMS was also produced. DMS, whether added directly or when derived from other precursors, was metabolized with the production of MSH. Methane thiol was also metabolized, and evidence suggests that MSH may be biologically methylated to form DMS. Experiments with selective microbial inhibitors were used to ascertain which microbial groups were responsible for the observed transformations. Based on these experiments, it appears that both sulfate-reducing and methane-producing bacteria may be involved in transforming and mineralizing methylated sulfur compounds. A simple scheme of how methylated sulfur compounds may be transformed in the environment is presented.}, }
@article {pmid24201405, year = {1988}, author = {Dobbins, DC and Pfaender, FK}, title = {Methodology for assessing respiration and cellular incorporation of radiolabeled substrates by soil microbial communities.}, journal = {Microbial ecology}, volume = {15}, number = {3}, pages = {257-273}, pmid = {24201405}, issn = {0095-3628}, abstract = {A method is described for determining biodegradation kinetics of both naturally occurring and xenobiotic compounds in surface and sub-surface soil samples. The method measures both respiration and uptake into cellular biomass of(14)C-labeled substrates. The estimation of biomass incorporation entailed removal of cells from soil particles by washing the soil with a polyvinyl-pyrrolidone/pyrophosphate solution and H2O2. After separation of the cells and the soil particles by centrifugation, the cells were trapped on membrane filters for liquid scintillation counting. Mass balances were easily obtained. The technique was used to measure metabolic activity in soil profiles, including unsaturated and saturated zones. First order rate constants (K1) were in the range of 10(-3)-10(-2) hour(-1) for amino acid metabolism and 10(-5)-10(-4) hour(-1) for m-cresol metabolism. Saturation kinetics were observed for amino acids and m-cresol. m-Cresol K1 values for uptake often exceeded those for respiration by greater than a factor of ten. Vmax values were low (amino acids, 10(1)-10(2) ng g(-1) hour(-1); m-cresol, 10(-1) ng g(-1) hour(-1)), whereas Km values were quite high (amino acids, 10(3)-10(4) ng g(-1); m-cresol 10(3)-10(5) ng g(-1)). Saturation was not observed in many horizons even at 10(5) ng g(-1) dry soil. Frequently, respiration obeyed saturation kinetics whereas uptake was first order. It is concluded that measuring only kinetics of respiration may lead to severe underestimations of biodegradation rates.}, }
@article {pmid24201404, year = {1988}, author = {Tannock, GW}, title = {Mini review: Molecular genetics: A new tool for investigating the microbial ecology of the gastrointestinal tract?.}, journal = {Microbial ecology}, volume = {15}, number = {3}, pages = {239-256}, pmid = {24201404}, issn = {0095-3628}, }
@article {pmid24203003, year = {1988}, author = {McEldowney, S and Fletcher, M}, title = {Bacterial desorption from food container and food processing surfaces.}, journal = {Microbial ecology}, volume = {15}, number = {2}, pages = {229-237}, pmid = {24203003}, issn = {0095-3628}, abstract = {The desorption ofStaphylococcus aureus, Acinetobacter calcoaceticus, and a coryneform from the surfaces of materials used for manufacturing food containers (glass, tin plate, and polypropylene) or postprocess canning factory conveyor belts (stainless steel and nylon) was investigated. The effect of time, pH, temperature, and adsorbed organic layers on desorption was studied.S. aureus did not detach from the substrata at any pH investigated (between pH 5 and 9).A. calcoaceticus and the coryneform in some cases detached, depending upon pH and substratum composition. The degree of bacterial detachment from the substrata was not related to bacterial respiration at experimental pH values. Bacterial desorption was not affected by temperature (4-30°C) nor by an adsorbed layer of peptone and yeast extract on the substrata. The results indicate that bacterial desorption, hence bacterial removal during cleaning or their transfer via liquids flowing over colonized surfaces, is likely to vary with the surface composition and the bacterial species colonizing the surfaces.}, }
@article {pmid24203002, year = {1988}, author = {Morikawa, K}, title = {Differences in plating efficiency of bacteria from river epilithon sampled from upper and lower surfaces of artificial substrata.}, journal = {Microbial ecology}, volume = {15}, number = {2}, pages = {217-228}, pmid = {24203002}, issn = {0095-3628}, abstract = {The bacterial generic composition of biofilms was investigated by determining colony-forming units on 1/2 PYG (peptone, yeast extract, and glucose medium) agar plates. The biofilms developed on the upper and lower surfaces of artificial substrata submerged in river water at Unazawa in the Tamagawa River in Tokyo, Japan. Greater variation in the number and generic composition in platable colonies was obtained on the upper surface of an artificial substratum than on the lower surface. This variation corresponded to the variation in algal biomass. Accompanying the growth of the algae, specific bacteria commensal with the algae proliferated on the upper surface. The biofilm exfoliated when the surface density of chlorophyll was 11.2 μg·cm(-2). When the biofilm exfoliated, the bacterial community accompanying the algae also exfoliated, and the bacterial composition altered. The bacterial composition after exfoliation resembled that observed on the lower surface. The generic composition on the upper surface soon after it was initially submerged resembled that observed in the river water. The bacterial generic composition on the lower surface of the artificial substrata did not change greatly throughout the investigation because of the constant environmental conditions. The difference between the bacterial generic composition on the upper and lower surfaces was due to the fact that bacteria commensal with algae proliferated on the upper surface but not on the lower.}, }
@article {pmid24203001, year = {1988}, author = {Nair, GB and Sarkar, BL and De, SP and Chakrabarti, MK and Bhadra, RK and Pal, SC}, title = {Ecology ofVibrio cholerae in the freshwater environs of Calcutta, India.}, journal = {Microbial ecology}, volume = {15}, number = {2}, pages = {203-215}, pmid = {24203001}, issn = {0095-3628}, abstract = {Seasonal incidence ofVibrio cholerae was monitored for a year in a man-made freshwater lake, an open sewage canal, and a pond composed of rainwater accumulations, located in Calcutta.V. cholerae was found in all sites. It exhibited a distinct bimodal seasonal cycle in the lake with a primary peak in August-September and a secondary peak in May-June. Correlation with environmental parameters revealed that temperature and, to a certain extent, pH were the important factors governing the densities ofV. cholerae. In the lake, sediment samples harbored high densities ofV. cholerae immediately after months when peak counts were observed in plankton, suggesting a cycle of cells between sediment and water. At the other sampling areas, no defined seasonality was observed. Instead, high counts ofV. cholerae were observed at these severely polluted sites throughout the study period, including the winter months. All the 15 water samples passed via the ligated loop of rabbits yielded pure cultures ofV. cholerae, indicating that the rabbit intestine selects outV. cholerae from a mixed flora. Uniformly high isolation rates ofV. cholerae were observed from brackish water and freshwater species of export quality prawns.V. cholerae was found to be abundant and was represented by 32 individual Louisiana State University (LSU) serovars, including two new serovars. The 01 serovar could not be isolated from any of the samples examined in this study. It was concluded thatV. cholerae non-01 is common in the freshwater environs of Calcutta.}, }
@article {pmid24203000, year = {1988}, author = {Glaser, D}, title = {Simultaneous consumption of bacteria and dissolved organic matter byTetrahymena pyriformis.}, journal = {Microbial ecology}, volume = {15}, number = {2}, pages = {189-201}, pmid = {24203000}, issn = {0095-3628}, abstract = {The addition of ciliated protozoa to aquatic microcosms and bench-scale sewage treatment plants increases decomposition rates. This is surprising, inasmuch as protozoa consume bacteria, which are the primary decomposers. One possible mechanism of the increase in decomposition rate is the direct consumption of dissolved organic matter by protozoa that are feeding primarily on bacteria. This possibility was explored experimentally in two-stage continuous cultures, with glucose limitingEscherichia coli in the first stage andE. coli limitingTetrahymena pyriformis in the second. Glycine and histidine were the test nutrients. The results of adding them to the second stages suggested that direct uptake by ciliates does not affect the dynamics of dissolved amino acids in pelagic environments or activated sludge plants. Ciliates might, however, affect the dynamics of amino acid pools in environments high in nutrients and ciliates, perhaps including some microenvironments near decomposing material or in benthic sediments. Direct uptake of dissolved amino acids by ciliates probably does not affect ciliate or bacterial populations substantially.}, }
@article {pmid24202999, year = {1988}, author = {Insam, H and Domsch, KH}, title = {Relationship between soil organic carbon and microbial biomass on chronosequences of reclamation sites.}, journal = {Microbial ecology}, volume = {15}, number = {2}, pages = {177-188}, pmid = {24202999}, issn = {0095-3628}, abstract = {The interrelationship between soil microorganisms and soil organic carbon was studied on an agricultural and on a forest chronosequence of open-pit mine reclamation soils. Thirty years after reclamation, soil carbon levels of 0.8% on the agricultural sites and 1.7% on the forest sites (A-horizon) were reached. Microbial biomass rose very fast to levels characteristic of undisturbed soils. Microbial carbon (Cmier) was 57 mg·100 g(-1) soil after 15 years on the agricultural sites and 43 mg·100 g(-1) on the forest sites. The contribution of Cmier to the total organic carbon (Corg) decreased with time, more rapidly on the forest sites than on the agricultural ones. From the Cmierr/Corg ratio it became evident that both chronosequences had not yet reached a steady state within the 50 years of reclamation. A significant decrease of the metabolic quotient qCO2 (microbial respiration per unit biomass) with time was observed on the agricultural sites but not on the forest sites. The Cmier/Corg ratio proved to be a reliable soil microbial parameter for describing changes in man-made ecosystems. For evaluating reclamation efforts, the Cmier/Corg ratio can be considered superior to its single components (Cmier or Corg) and to other parameters.}, }
@article {pmid24202998, year = {1988}, author = {Simon, M}, title = {Growth characteristics of small and large free-living and attached bacteria in Lake Constance.}, journal = {Microbial ecology}, volume = {15}, number = {2}, pages = {151-163}, pmid = {24202998}, issn = {0095-3628}, abstract = {The growth characteristics of small (0.2-1.0μm) and large (1.0-3.0 (μm) free-living and attached bacteria were studied in Lake Constance by comparing the spatial and seasonal dynamics of their biomass turnover time (ratio of biomass/production). The biomass of small free-living bacteria usually turned over significantly faster than that of large free-living bacteria throughout the water column. The turnover of attached bacterial biomass was characterized by large fluctuations. Occasionally, in aphotic water layers, it was as long as that of large free-living bacteria, but when large amounts of decaying organic particles were present, it was shorter than that of small free-living cells. Biomass turnover times of free-living bacteria were in the same range as their generation times, which were estimated from the increase in bacterial abundance in 3μm prefiltered samples. The biomass turnover time of actively metabolizing bacteria was comparable to the generation time of actively metabolizing cells. These results indicate that the biomass turnover time is a useful indicator of the growth of different bacterial fractions, as it reflects their different amounts of participation in microbial processes of aquatic ecosystems.}, }
@article {pmid24202997, year = {1988}, author = {Heinen, W and Lauwers, AM}, title = {Leaching of silica and uranium and other quantitative aspects of the lithobiontic colonization in a radioactive thermal spring.}, journal = {Microbial ecology}, volume = {15}, number = {2}, pages = {135-149}, pmid = {24202997}, issn = {0095-3628}, abstract = {The formation of microbial mats by thermophilic organisms on submerged rocks in radioactive thermal springs was followed quantitatively in situ as well as under experimental conditions, by determining the change in dry weight and organic matter as a function of time. Furthermore, the decay of the rock occurring in the springs could be shown to be directly related to the microbial colonization. Early in that process the formation of silicious gels, facilitating the settling of the organisms, could be observed. Simultaneously, this was accompanied by the leaching of silica from the underlying rock. This resulted in the destruction of the rock, which had been altered to a fine-grained dust underneath the colonizing mats; the microorganisms were found to move further downward within this layer. From the heavy metals present in the rock-iron (Fe), copper (Cu), manganese (Mn), uranium (U)- the leaching of uranium could be demonstrated, leading to the acquisition of this metal in the microbial mats in concentrations up to 15.34μg/mg dry weight. Direct evidence for the leaching of Si (silicon) and U could be obtained by measurement of these elements after their release from ground rock chips in cultures with microorganisms from the hot springs at 50°C. X-ray analysis of the biomats strongly suggested that Cu, Mn, and Fe are also accumulated.}, }
@article {pmid24202996, year = {1988}, author = {Mason, J and Kelly, DP}, title = {Thiosulfate oxidation by obligately heterotrophic bacteria.}, journal = {Microbial ecology}, volume = {15}, number = {2}, pages = {123-134}, pmid = {24202996}, issn = {0095-3628}, abstract = {Thiosulfate was oxidized stoichiometrically to tetrathionate during growth on glucose byKlebsiella aerogenes, Bacillus globigii, B. megaterium, Pseudomonas putida, two strains each ofP. fluorescens andP. aeruginosa, and anAeromonas sp. A gram-negative, rod-shaped soil isolate, Pseudomonad Hw, converted thiosulfate to tetrathionate during growth on acetate. None of the organisms could use thiosulfate as sole energy source. The quantitative recovery of all the thiosulfate supplied to heterotrophic cultures either as tetrathionate alone or as tetrathionate and unused thiosulfate demonstrated that no oxidation to sulfate occurred with any of the strains tested. Two strains ofEscherichia coli did not oxidize thiosulfate. Thiosulfate oxidation in batch culture occurred at different stages of the growth cycle for different organisms:P. putida oxidized thiosulfate during lag and early exponential phase,K. aerogenes oxidized thiosulfate at all stages of growth, andB. megaterium andAeromonas oxidized thiosulfate during late exponential phase. The relative rates of oxidation byP. putida andK. aerogenes were apparently determined by different concentrations of thiosulfate oxidizing enzyme. Thiosulfate oxidation byP. aeruginosa grown in chemostat culture was inducible, since organisms pregrown on thiosulfate-containing media oxidized thiosulfate, but those pregrown on glucose only could not oxidize thiosulfate. Steady state growth yield ofP. aeruginosa in glucose-limited chemostat culture increased about 23% in the presence of 5-22 mM thiosulfate, with complete or partial concomitant oxidation to tetrathionate. The reasons for this stimulation are unclear. The results suggest that heterotrophic oxidation of thiosulfate to tetrathionate is widespread across several genera and may even stimulate bacterial growth in some organisms.}, }
@article {pmid24202995, year = {1988}, author = {Macmichael, GJ}, title = {The response of gram-negative, thermophilic bacteria to oxygen.}, journal = {Microbial ecology}, volume = {15}, number = {2}, pages = {115-122}, pmid = {24202995}, issn = {0095-3628}, abstract = {Nine gram-negative, thermophilic bacteria (LEH-1, CC-6, BI-1, NR-9, K-2,Thermus aquaticus, T. thermophilus, T. sp. X-1, andThermomicrobium roseum) tolerated increased oxygen tensions (0.6-1.0 atm). All of the strains demonstrated catalase, peroxidase, and superoxide dismutase activity. Except forT. roseum, the specific activity of one or more of these enzymes was higher under aerated culture, as compared to static conditions. Polyacrylamide gel electrophoresis (PAGE) indicated that each organism possessed only one superoxide dismutase, and each was tentatively identified as having a manganese prosthetic group. PAGE also demonstrated that the number of isozymes of catalase varied from one to three, depending on the organism. Finally, the characterization of these enzymes supported previous tentative groupings of these thermophiles.}, }
@article {pmid24202865, year = {1988}, author = {Pfender, WF and Wootke, SL}, title = {Microbial communities ofPyrenophora-infested wheat straw as examined by multivariate analysis.}, journal = {Microbial ecology}, volume = {15}, number = {1}, pages = {95-113}, pmid = {24202865}, issn = {0095-3628}, abstract = {Winter wheat straw naturally infested withPyrenophora triticirepentis andSeptoria nodorum was incubated in the field in one of three placements: buried in the soil, placed directly on the soil surface, or placed 2 cm above the soil within a straw layer. Periodically between June and April, straws from each treatment were collected and assayed by dilution plating to determine microbial populations in the following categories: total yeasts, total actinomycetes, total other bacteria, and genera or species of fungi. The data were analyzed by the multivariate procedures of ordination and classification, using detrended correspondence analysis (DCA) and cluster analysis, respectively. The major DCA axis displayed a gradient starting with pioneer colonizer communities of above-soil straw (dominated byPyrenophora, Septoria, Alternaria, andCladosporium), through on-soil straws (colonized by secondary saprophytes such asAcremonium strictum, Diplodia, Fusarium, and bacteria) to buried straws (dominated by actinomycetes, bacteria, and soil-inhabiting fungi). The second DCA axis showed a gradient separating different types of late secondary communities. In vitro tests for degradative abilities of straw-inhabiting organisms showed that low-temperature cellulolysis is characteristic of pioneer and early secondary colonizers, whereas chitin degradation is limited to secondary colonizers, particularly soil inhabitants. The results suggest the vulnerability ofPyrenophora andSeptoria to displacement by secondary colonists in an active microbial community, and indicate a number of organisms that may be useful in biological control of these plant parasites through exploitative or interference competition in plant residues.}, }
@article {pmid24202864, year = {1988}, author = {Coûteaux, MM and Ogden, CG}, title = {The growth ofTracheleuglypha dentata (Rhizopoda: Testacea) in clonal cultures under different trophic conditions.}, journal = {Microbial ecology}, volume = {15}, number = {1}, pages = {81-93}, pmid = {24202864}, issn = {0095-3628}, abstract = {Twenty-four clones ofTracheleuglypha dentata were cultivated under different trophic conditions. Half were cultivated with soil extract which induced low bacterial growth. The other 12 were cultivated in the same medium with the addition of Cerophyl to enhance bacterial growth. The dynamics of each clone was followed for about 3 months by counting both live animals and empty shells. The rate of decomposition of empty shells was negligible. The number of empty shells are a direct measure for mortality. Parameters measured were densities, intrinsic rate of growth, generation time, production, and mortality. The densities increased in most of the clones until about the third week; it then reached a plateau or decreased slowly until the end of the experiment. After this initial period, the live animals closed their pseudostome with a thin membrane and remained quiescent until fresh food was given. The level of the plateau was significantly six times higher in the well-fed than in the starved clones, a difference due to a higher rate of growth induced by a shorter generation time during the first 10 days. This high growth produced giant shells, teratological forms created by the fusion of several shells. Mortality appeared at about the 20th day. Because it was higher in the well-fed clones than in the starved clones, it brought the densities of both clones to the same level after 3 months. The first empty shells were produced by either precocious mortality or abortion, as they did not contain reserve plates necessary for a new shell prior to reproduction. The mortality of adults came later and was probably linked with the age of the culture. The starved cells had an unusual morphology which disappeared when the medium was renewed.}, }
@article {pmid24202863, year = {1988}, author = {Alongi, DM}, title = {Bacterial productivity and microbial biomass in tropical mangrove sediments.}, journal = {Microbial ecology}, volume = {15}, number = {1}, pages = {59-79}, pmid = {24202863}, issn = {0095-3628}, abstract = {Bacterial productivity ((3)H-thymidine incorporation into DNA) and intertidal microbenthic communities were examined within five mangrove estuaries along the tropical northeastern coast of Australia. Bacteria in mangrove surface sediments (0-2 cm depth) were enumerated by epifluorescence microscopy and were more abundant (mean and range: 1.1(0.02-3.6)×10(11) cells·g DW(-1)) and productive (mean: 1.6 gC·m(-2)· d(-1)) compared to bacterial populations in most other benthic environments. Specific growth rates (¯x=1.1) ranged from 0.2-5.5 d(-1), with highest rates of growth in austral spring and summer. Highest bacterial numbers occurred in winter (June-August) in estuaries along the Cape York peninsula north of Hinchinbrook Island and were significantly different among intertidal zones and estuaries. Protozoa (10(5)-10(6)·m(-2), pheopigments (0.0-24.1μg·gDW(-1)) and bacterial productivity (0.2-5.1 gC·m(-2)·d(-1)) exhibited significant seasonality with maximum densities and production in austral spring and summer. Algal biomass (chlorophylla) was low (mean: 1.6μg·gDW(-1)) compared to other intertidal sediments because of low light intensity under the dense forest canopy, especially in the mid-intertidal zone. Partial correlation analysis and a study of possible tidal effects suggest that microbial biomass and bacterial growth in tropical intertidal sediments are regulated primarily by physicochemical factors and by tidal flushing and exposure. High microbial biomass and very high rates of bacterial productivity coupled with low densities of meiofaunal and macroinfaunal consumers observed in earlier studies suggest that microbes may be a sink for carbon in intertidal sediments of tropical mangrove estuaries.}, }
@article {pmid24202862, year = {1988}, author = {Lopez-Torres, AJ and Prieto, L and Hazen, TC}, title = {Comparison of the in situ survival and activity ofKlebsiella pneumoniae andEscherichia coli in tropical marine environments.}, journal = {Microbial ecology}, volume = {15}, number = {1}, pages = {41-57}, pmid = {24202862}, issn = {0095-3628}, abstract = {A near-shore coastal mangrove island receiving untreated sewage and a coastal cove receiving rum distillery effluent in Puerto Rico were examined for their ability to support survival and activity ofKlebsiella pneumoniae andEscherichia coli. Pure cultures of both bacteria were monitored for 96 hours in situ at both locations using membrane diffusion chambers.K. pneumoniae survived at all sites as measured by AODC and Coulter Counter direct counts. However, at the mangrove island less than 20% of theK. pneumoniae population was active (AODC) after the first 3 hours and less than 10% of this population was respiring (INT). In contrast, the coastal area which was receiving rum distillery effluent was able to maintain 40% of theK. pneumoniae population in an active state with 90% respiring. TheE. coli population declined by two orders of magnitude at the mangrove island, but remained unchanged at the rum distillery outfall. TheE. coli population had a higher proportion of active cells and respiring cells thanK. pneumoniae at all sites. At the rum distillery site, theE. coli population was remarkable in that 95% remained active and 99% were respiring. This study suggests that, when sufficient organic loading exists,E. coli, a "nonsurvivor," can overcome the bactericidal effects of tropical marine waters.K. pneumoniae, a "survivor," could survive under all conditions but could not maintain the activity or respiration that theE. coli population could, even when high organic loads were present. Morphological changes related to nutrient stress in the tropical marine environment were apparent inE. coli, but not inK. pneumoniae. Based on physiological activityE. coli is just as much a "survivor" asK. pneumoniae in tropical marine waters.}, }
@article {pmid24202861, year = {1988}, author = {Keen, GA and Prosser, JI}, title = {The surface growth and activity ofNitrobacter.}, journal = {Microbial ecology}, volume = {15}, number = {1}, pages = {21-39}, pmid = {24202861}, issn = {0095-3628}, abstract = {The effect of surface attachment on oxidation of nitrite to nitrate byNitrobacter was studied in batch culture, on glass coverslips, and in continuous culture on glass beads and anion exchange resin beads in an air-lift column fermenter. In batch culture, the surfaces stimulated specific growth rate, while in continuous culture, activity of attached cells was less than that of freely suspended cells. Nitrate productivity, free cell productivity, and attached cell concentration increased exponentially at the same specific rate, termed the colonization rate, and nitrate productivity was found to be a convenient estimate of biomass concentration. Permanent attachment was mediated by production of slime material. Surface growth resulted in multiple steady states and the ability to respond quickly to changes in dilution rate. The air-lift column fermenter system provided a convenient system for the study of growth and activity of attached cells and was most suitable when using ion exchange resins as a substratum for attachment.}, }
@article {pmid24202860, year = {1988}, author = {Williams, HN}, title = {A study of the occurrence and distribution of bdellovibrios in estuarine sediment over an annual cycle.}, journal = {Microbial ecology}, volume = {15}, number = {1}, pages = {9-20}, pmid = {24202860}, issn = {0095-3628}, abstract = {The recovery of bdellovibrios from estuarine sediments over an annual cycle was studied. Greater numbers of the predators were recovered in sediment than in the water column. Increases in the number of bdellovibrios recovered from sediment over various periods of time suggest that multiplication of the predators occurred. Sediment was observed to be an important ecosystem for the survival of bdellovibrios in the winter months. As has been observed in water, the number of bdellovibrios in sediment fluctuated, with seasonal and temperature changes declining to very low numbers during the winter months. In the colder months, low numbers of the predators appeared to winter-over in sediment, with greater numbers of the organisms being recovered from deeper sediment. As the water temperature warmed in the spring, increases in the number of bdellovibrios occurred first in sediment and subsequently in water. This increase of bdellovibrios in sediment may have resulted in the shedding of the organisms into the water column where their numbers subsequently increased. Population fluctuations of bdellovibrios were similar in both water and sediment. Although the temperature may account for much of the observed fluctuation in the number of bdellovibrios, other factors, including salinity and the number of host bacteria, may also play a major role. The number of bdellovibrios recovered from sediment correlated positively with the water temperature, and negatively with the water salinity and the number of bacterial colony-forming units from sediment. The results of this study revealed the significance of sediment to the seasonal cycle, survival, and growth of the bdellovibrios in an estuarine environment.}, }
@article {pmid24202859, year = {1988}, author = {Casida, LE}, title = {Minireview: Nonobligate bacterial predation of bacteria in soil.}, journal = {Microbial ecology}, volume = {15}, number = {1}, pages = {1-8}, pmid = {24202859}, issn = {0095-3628}, }
@article {pmid24202721, year = {1987}, author = {Andrews, JH and Kinkel, LL and Berbee, FM and Nordheim, EV}, title = {Fungi, leaves, and the theory of island biogeography.}, journal = {Microbial ecology}, volume = {14}, number = {3}, pages = {277-290}, pmid = {24202721}, issn = {0095-3628}, abstract = {Species dynamics of fungi (filamentous fungi and yeasts) on apple leaves were studied within the framework of the theory of island biogeography by following "immigration" and "extinction" patterns on individual apple leaf "islands" over time. Total fungi were censused on unmanipulated leaves collected throughout two seasons; filamentous fungi only were monitored additionally for several weeks in one season on newly created, axenic, model (seedling) islands introduced to the orchard, and on surface-sterilized, preexisting leaves. Analyses based on both the natural and the surface-sterilized systems showed that an equilibrium in species number was reached and turnover in species composition occurred in both. Immigration and extinction events were strongly related to number of species present on each island. The balance between immigration and extinction implies that species number on leaves and "real" (oceanic) islands is determined by a common mechanism, and emphasizes the need to regard leaf microbial communities as dynamic.}, }
@article {pmid24202720, year = {1987}, author = {Barker, JS and Starmer, WT and Vacek, DC}, title = {Analysis of spatial and temporal variation in the community structure of yeasts associated with decayingOpuntia cactus.}, journal = {Microbial ecology}, volume = {14}, number = {3}, pages = {267-276}, pmid = {24202720}, issn = {0095-3628}, abstract = {The microbial structure within, between, and over time in decaying cladodes of the common prickly pearOpuntia stricta was studied at each of two separate localities. In general, the effective number of yeast species and yeast species diversity increased as the rot aged to the observed maximum time of 4 weeks. Yeast heterogeneity at the two localities differed in the mode of environmental influence, with spatial variability (among rots) most important at one and temporal variability (within rots over time) most important at the other. Differences in cactus density and quality (age) are most likely determinants of the differences in yeast community structure.}, }
@article {pmid24202719, year = {1987}, author = {Millner, PD and Powers, KE and Enkiri, NK and Burge, WD}, title = {Microbially mediated growth suppression and death of salmonella in composted sewage sludge.}, journal = {Microbial ecology}, volume = {14}, number = {3}, pages = {255-265}, pmid = {24202719}, issn = {0095-3628}, abstract = {The role of compost microflora in the suppression of salmonella regrowth in composted sewage sludge was investigated. Microbial inhibition studies of salmonella growth were conducted on nutrient agar, in composts that had been subjected to different temperatures in compost piles, and in radiation sterilized composts inoculated with selected fractions of the compost microflora. Agar assays of inhibition indicated that bacteria and actinomycetes were not suppressive to salmonellae, but a few fungi were. However, compost inoculation assays showed consistently that fungi were not suppressive, but bacteria and actinomycetes were. In compost inoculation assays, microbial antagonists, when present, either killed salmonellae or reduced their growth rate. No suppression of salmonellae occurred in compost taken from 70°C compost-pile zones despite the presence and growth of many types of microbes. With greater numbers and kinds of microbes in 55°C compost, salmonella growth was suppressed 100-10,000-fold. Salmonellae died when inoculated into compost from unheated zones (25-40°C) of piles. Prior colonization of compost with only noncoliform gram-negative bacteria suppressed salmonellae growth 3,000-fold. Coliforms when inoculated prior to salmonellae accounted for 75% of salmonella die-off. Mesophilic curing to allow colonization of curing piles in their entirety by gram-negative bacteria, especially coliforms, should be an effective way to prevent repopulation by salmonellae.}, }
@article {pmid24202718, year = {1987}, author = {Burge, WD and Enkiri, NK and Hussong, D}, title = {Salmonella regrowth in compost as influenced by substrate (salmonella regrowth in compost).}, journal = {Microbial ecology}, volume = {14}, number = {3}, pages = {243-253}, pmid = {24202718}, issn = {0095-3628}, abstract = {Composting can eliminate pathogenic organisms, including salmonellae, from sewage sludge. However, if salmonellae are present in the compost at undetectable levels or are inoculated into the compost by infected animals or from other sources, they may regrow presenting a health hazard for certain uses of compost. In this study, we examined dilute mineral-salt extracts of three composts from widely separate composting sites in the United States and found that they supported growth ofSalmonella typhimurium. From kinetic studies of the growth of the organism on these extracts, we concluded that each compost produced on extraction a single water-soluble substrate and that the substrates from the different composts were very similar, if not identical.}, }
@article {pmid24202717, year = {1987}, author = {Gilmour, CC and Tuttle, JH and Means, JC}, title = {Anaerobic microbial methylation of inorganic tin in estuarine sediment slurries.}, journal = {Microbial ecology}, volume = {14}, number = {3}, pages = {233-242}, pmid = {24202717}, issn = {0095-3628}, abstract = {Estuarine sediment slurries and microorganisms were examined for the ability to methylate inorganic tin. Under controlled redox conditions, tin was methylated only in oxygen-free sediment slurries. Monomethyltin usually comprised greater than 90% of the alkyltin products formed, although dimethyltin was also produced. Autoclaved anoxic sediments did not produce organotins. Several bacterial cultures, most notably sulfate-reducing bacteria isolated from anoxic estuarine sediments, formed monoand dimethyltin from inorganic tin in the absence of sediment. The results suggest that inorganic tin methylation in estuarine environments is an anaerobic process catalyzed primarily by sulfate-reducing microorganisms.}, }
@article {pmid24202716, year = {1987}, author = {Mills, AL and Mallory, LM}, title = {The community structure of sessile heterotrophic bacteria stressed by acid mine drainage.}, journal = {Microbial ecology}, volume = {14}, number = {3}, pages = {219-232}, pmid = {24202716}, issn = {0095-3628}, abstract = {Microbial communities that developed on glass slides suspended in acid-polluted (pH=2.9) and nonpolluted (pH=6.5) but otherwise similar waters showed evidence of stress when suspended at the opposite station. Glucose incorporation was inhibited in both translocated communities, but the inhibition was not as severe and recovery of activity was faster for the acid-developed community as compared to the circumneutral community. The communities contained a substantially different set of members with little overlap. The range of pH values at which the members of the acid-developed community could function suggested that the members of that community were generalists, as opposed to narrowly constrained members of the community from the circumneutral station. Based on the proportion of test characters that received positive responses, the organisms from the acidic site were more general in their abilities (47.6% positive) as compared with the neutral counterparts (18.7% positive). The results support the concept that communities developed in extreme environments tend to be generalists, whereas those from mesic environments, due to the higher levels of competition present, tend to be specialists. Furthermore, the study of microbial communities in dynamic systems such as streams and reservoir inflows is facilitated by the use of solid surfaces which allow an assemblage of nontransient microbes to develop.}, }
@article {pmid24202715, year = {1987}, author = {Moran, MA and Maccubbin, AE and Benner, R and Hodson, RE}, title = {Dynamics of microbial biomass and activity in five habitats of the Okefenokee Swamp ecosystem.}, journal = {Microbial ecology}, volume = {14}, number = {3}, pages = {203-217}, pmid = {24202715}, issn = {0095-3628}, abstract = {A variety of freshwater marsh and swamp habitats are found interspersed in a mosaic pattern throughout the Okefenokee Swamp, Georgia, USA. We examined spatial and temporal patterns in standing stocks and activity in the microbial community of five habitats within this heterogeneous ecosystem. Standing stock dynamics were studied by measuring microbial biomass (ATP) and bacterial numbers (AODC) in both water and sediments over a 14 month period. Abundance varied temporally, being generally lower in winter months than in spring and summer months. However, a large proportion of the measured variability was not correlated with temporal patterns in temperature or with bulk nutrient levels. Spatial variability was characteristic of the Okefenokee at a variety of large and small scales. Habitat-level heterogeneity was evident when microbial standing stocks and activity (measured as [(14)C]lignocellulose mineralization) were compared across the five communities, although abundance differences among sites were restricted to nonwinter months when microbial biomass was high. Spatial variation within habitats was also found; patches of surface sediment with differing microbial activity or abundance were measured at scales from 30 cm to 150 m.}, }
@article {pmid24202714, year = {1987}, author = {Rogers, AH and Zilm, PS and Gully, NJ}, title = {Influence of arginine on the coexistence ofStreptococcus mutans andS. milleri in glucose-limited mixed continuous culture.}, journal = {Microbial ecology}, volume = {14}, number = {3}, pages = {193-202}, pmid = {24202714}, issn = {0095-3628}, abstract = {Dental plaque is a complex community of bacteria coexisting in an environment frequently limited by carbon and energy sources. UnlikeStreptococcus mutans, other oral streptococci such asS. milleri andS. sanguis have an absolute requirement for and actually consume all available arginine when grown glucose limited in a chemically defined medium. The conditions, particularly in terms of arginine concentration, under which the dental plaque bacteriaS. mutans andS. milleri would coexist under glucose-limiting conditions were investigated. The minimum level of arginine supporting optimal growth ofS. milleri was found to be ca. 50μM, and above this level these strains outcompetedS. mutans. However, coexistence withS. mutans could be achieved at arginine levels of 14-40μM, depending upon theS. milleri andS. mutans strains used. Under such dual limitation,S. milleri was unable to respond to glucose pulses but did respond to pulses of arginine and arginine plus glucose. One of the twoS. milleri strains did not tolerate low pH. In contrast,S. mutans did not tolerate high pH whereasS. milleri was unaffected. This is relevant to dental plaque where arginine catabolism produces a pH rise. Additionally, arginine is an important nutrient since it can be used as an energy source by some oral streptococci.}, }
@article {pmid24202645, year = {1987}, author = {Starmer, WT and Lachance, MA and Phaff, HJ}, title = {A comparison of yeast communities found in necrotic tissue of cladodes and fruits ofOpuntia stricta on Islands in the Caribbean Sea and where introduced into Australia.}, journal = {Microbial ecology}, volume = {14}, number = {2}, pages = {179-192}, pmid = {24202645}, issn = {0095-3628}, abstract = {Yeast communities growing in the decaying tissues (cladodes and fruits) ofOpuntia stricta (prickly pear cactus) and associated yeast vectors (Drosophila species) were compared in two geographic regions (Caribbean and eastern Australia). The Australian yeast community provides an interesting comparison to the Caribbean community, because the host plantO. stricta was introduced to Australia over 100 years ago. Many of the yeasts found in the Australian system also were introduced during a period of biological control (1926-1935) when they accompanied rotting prickly pear cladodes and insects shipped to Australia from the Americas. The yeast community composition (proportion of each species) is compared at several levels of organization: (1) within and between regions, (2) across seasons and years, and (3) within and between tissue types. The yeast species composition of the cladode communities are similar from locality to locality, season to season, and year to year, with the region-to-region similarity slightly less. The composition of the fruit-yeast communities are distinct from region to region and only show some overlap with the cladodes within regions when collected simultaneously in the same locality. It is suggested that the cladode-microorganism-Drosophila system is relatively closed (little extrinsic influence) whereas the fruit-microorganism-Drosophila system is open (large extrinsic influence).}, }
@article {pmid24202644, year = {1987}, author = {De Haast, J and Britz, TJ}, title = {Characterization of some anaerobic bacteria from the liquid phase of a mesophilic anaerobic digester fed with a prefermented cheese whey substrate.}, journal = {Microbial ecology}, volume = {14}, number = {2}, pages = {167-177}, pmid = {24202644}, issn = {0095-3628}, abstract = {Bacterial counts on the contents of an anaerobic fixed-bed digester receiving a whey substrate were conducted using the modified roll tube technique. Average anaerobic counts after 48 hours incubation on lactate containing media were 3.12 × 10(9) and 3.7 × 10(9) ml(-1), respectively. These counts were between 140 and 190 times higher than aerobic counts on the same media. Seventy-four strains from both media were isolated and characterized, and the relationship between the organisms was calculated according to the similarity coefficient of Sokal and Michener [20]. The organisms were clustered using the unweighted pair group method and the results were presented in the form of a simplified dendrogram. The isolates clustered in three major groups (A, B, and C) at a similarity level of 76%. A small diffuse group of five organisms was also found. The organisms in two (A and B) of the major clusters were obligate anaerobes. Cluster A represented 34% of the isolates, cluster B represented 50%, and the facultative streptococci in cluster C, 11%. The isolates in clusters A and B could only tentatively be identified as members of the generaBacteroides andPeptostreptococcus, respectively. The isolates could not be positively identified.}, }
@article {pmid24202643, year = {1987}, author = {Mayasich, SA and Smucker, RA}, title = {Role ofCristispira sp. and other bacteria in the chitinase and chitobiase activities of the crystalline style ofCrassostrea virginica (Gmelin).}, journal = {Microbial ecology}, volume = {14}, number = {2}, pages = {157-166}, pmid = {24202643}, issn = {0095-3628}, abstract = {Activity was found for chitinase and chitobiase in the crystalline styles of American oysters (Crassostrea virginica Gmelin) collected from the Chesapeake Bay (Maryland, USA). The oysters were maintained in tanks on natural food from a constant flow of unfiltered estuarine water. Chitinase and chitobiase specific activities were compared with total, viable, and chitinoclastic bacterial counts andCristispira counts. Regression analyses revealed that one correlation, chitobiase vsCristispira, was significant (P < 0.05). Several oysters were fed chitin in the presence or absence of chloramphenicol. Although no chitinoclasts were present in the antibiotic-treated oysters, the treatment means did not differ significantly (P > 0.05) for either chitinase or chitobiase activity. In several cases with both chitin-fed and naturally fed oysters, enzyme activity was found when noCristispira were present. The results of the investigations suggest that the oyster produces chitinase and chitobiase endogenously.}, }
@article {pmid24202642, year = {1987}, author = {Miller, CL and Landa, ER and Updegraff, DM}, title = {Ecological aspects of microorganisms inhabiting uranium mill tailings.}, journal = {Microbial ecology}, volume = {14}, number = {2}, pages = {141-155}, pmid = {24202642}, issn = {0095-3628}, abstract = {Numbers and types of microorganisms in uranium mill tailings were determined using culturing techniques.Arthrobacter were found to be the predominant microorganism inhabiting the sandy tailings, whereasBacillus and fungi predominated in the slime tailings. Sulfate-reducing bacteria, capable of leaching radium, were isolated in low numbers from tailings samples but were isolated in significantly high numbers from topsoil in contact with the tailings. The results are placed in the context of the magnitude of uranium mill tailings in the United States, the hazards posed by the tailings, and how such hazards could be enhanced or diminished by microbial activities. Patterns in the composition of the microbial population are evaluated with respect to the ecological variables that influence microbial growth.}, }
@article {pmid24202641, year = {1987}, author = {Underhill, SE and Prosser, JI}, title = {Surface attachment of nitrifying bacteria and their inhibition by potassium ethyl xanthate.}, journal = {Microbial ecology}, volume = {14}, number = {2}, pages = {129-139}, pmid = {24202641}, issn = {0095-3628}, abstract = {Ion exchange resins and glass microscope slides were used to investigate factors affecting attachment of nitrifying bacteria to solid surfaces and the effect of attachment on inhibition ofNitrobacter by potassium ethyl xanthate. The ammonium oxidizerNitrosomonas attached preferentially to cation exchange resins while the nitrite oxidizerNitrobacter colonized anion exchange resins more extensively. Colonization was always associated with growth, and the site of substrate (NH4 (+) or NO2 (-)) adsorption was the major factor in attachment and colonization. The specific growth rate of cells colonizing either ion exchange resin beads or glass surfaces was greater than that of freely suspended cells, butNitrobacter populations colonizing glass surfaces were more sensitive to the inhibitor potassium ethyl xanthate. The findings indicate that surface growth alone does not protect soil nitrifying bacteria from inhibition by potassium ethyl xanthate and explain different patterns of inhibition for ammonium and nitrite oxidizers in the soil.}, }
@article {pmid24202640, year = {1987}, author = {Hood, MA and Macdonell, MT}, title = {Distribution of ultramicrobacteria in a gulf coast estuary and induction of ultramicrobacteria.}, journal = {Microbial ecology}, volume = {14}, number = {2}, pages = {113-127}, pmid = {24202640}, issn = {0095-3628}, abstract = {The abundance of ultramicrobacteria (i.e., bacteria that pass through a 0.2μm filter) in a subtropical Alabama estuary was determined during a 1-year period. Although phenotypic and molecular characterization indicated that the population of ultramicrobacteria was dominated byVibrio species, species ofListonella andPseudomonas were also abundant. Vibrios occurred with the greatest frequency in waters whose salinities were less than 14‰, and were the most abundant species of the total ultramicrobacterial population year-round, whilePseudomonas species were absent or considerably reduced during the winter months. The total number of ultramicrobacteria showed an inverse relationship to total heterotrophic bacteria as measured by colony-forming units (CFU)/ml and to water quality as measured by several parameters. Analysis by generic composition indicated that both salinity and temperature significantly affected the distribution of these organisms. Laboratory studies revealed that strains of vibrios under starvation in both static and continuous-flow microcosms could be induced to form cells that passed through 0.2 and/or 0.4μm filters. Cells exposed to low nutrients became very small; some grew on both oligotrophic (5.5 mg carbon/liter) and eutrophic (5.5 g carbon/liter) media; and some few cells grew only on oligotrophic media. By passing selected vibrio strains on progressively diluted nutrient media, cells were also obtained that were small, that passed through 0.4μm filters, and that could grow in oligotrophic media. These results suggest that ultramicrobacteria in estuaries (at least some portion of the population) may be nutrientstarved or low nutrient-induced forms of certain heterotrophic, eutrophic, autochthonous, estuarine bacteria.}, }
@article {pmid24202639, year = {1987}, author = {Rashit, E and Bazin, M}, title = {Environmental fluctuations, productivity, and species diversity: An experimental study.}, journal = {Microbial ecology}, volume = {14}, number = {2}, pages = {101-112}, pmid = {24202639}, issn = {0095-3628}, abstract = {Seemingly opposing hypotheses concerning the effects of environmental fluctuations on species diversity were shown to complement one another. Studies were made on naturally occurring microbial communities growing in continuous cultures, under both low and high productivity levels. The communities consisted of species of bacteria, protozoan flagellates, and protozoan predators (sarcodinians and ciliates). Fluctuations were imposed by periodically removing a portion of the culture and refilling with sterilized medium. They were designed to mimic the effect of fluctuations periodically decreasing the demand/supply ratio of the community for the available resources. It was found that when growth rates were low (either because of low productivity levels or because of low intrinsic growth rates of the organisms concerned), fluctuations decreased species diversity, whereas when growth rates were high, fluctuations increased species diversity. It is suggested that fluctuations decrease diversity when growth rates are low because they prevent slower growing species from surviving, and increase diversity when growth rates are high because they decrease the extent of competitive domination and exclusion.}, }
@article {pmid24202610, year = {1987}, author = {Dodds, WK and Jones, RD}, title = {Potential rates of nitrification and denitrification in an oligotrophic freshwater sediment system.}, journal = {Microbial ecology}, volume = {14}, number = {1}, pages = {91-100}, pmid = {24202610}, issn = {0095-3628}, abstract = {Potential rates of nitrification and denitrification were measured in an oligotrophic sediment system. Nitrification potential was estimated using the CO oxidation technique, and potential denitrification was measured by the acetylene blockage technique. The sediments demonstrated both nitrifying and denitrifying activity. Eh, O2, and organic C profiles showed two distinct types of sediment. One type was low in organic C, had high O2 and Eh, and had rates of denitrification 1,000 times lower than the other which had high organic C, low O2, and low Eh. Potential nitrification and denitrification rates were negatively correlated with Eh. This suggests that environmental heterogeneity in denitrifier and nitrifier populations in oligotrophic sediment systems may be assessed using Eh before sampling protocols for nitrification or denitrification rates are established. There was no correlation between denitrification and nitrification rates or between either of these processes and NH4 (+) or NO3 (-) concentrations. The maximum rate of denitrification was 0.969 nmole N cm(-3) hour(-1), and the maximum rate of nitrification was 23.6 nmole cm(-3) hour(-1), suggesting nitrification does not limit denitrification in these oligotrophic sediments. Some sediment cores had mean concentrations of 6.0 mg O2/liter and still showed both nitrification and denitrification activity.}, }
@article {pmid24202609, year = {1987}, author = {Jansson, M}, title = {Anaerobic dissolution of iron-phosphorus complexes in sediment due to the activity of nitrate-reducing bacteria.}, journal = {Microbial ecology}, volume = {14}, number = {1}, pages = {81-89}, pmid = {24202609}, issn = {0095-3628}, abstract = {Nitrate-reducing bacteria (Pseudomonas fluorescens andAlcaligenes sp.) as well as extracellular compounds from these bacteria increased the dissolution rate of iron and phosphorus sorbed to iron precipitates during anaerobic, nitrate-free conditions in experimental sediment-water systems. It is suggested that the influence of the bacteria is due to enzymatic catalyzation of chemical iron reduction.}, }
@article {pmid24202608, year = {1987}, author = {Thomas, JM and Alexander, M}, title = {Colonization and mineralization of palmitic acid byPseudomonas pseudoflava.}, journal = {Microbial ecology}, volume = {14}, number = {1}, pages = {75-80}, pmid = {24202608}, issn = {0095-3628}, abstract = {Pseudomonas pseudoflava and palmitic acid were used to investigate the role of bacterial colonization in the degradation of waterinsoluble organic compounds. Mineralization was measured by trapping the(14)CO2 produced from the labeled substrate, and colonization of the surface of the solid organic chemical was determined by epifluorescence microscopy. In a medium containing solid palmitic acid,P. pseudoflava mineralized the organic substrate at a logarithmic rate. Mineralization was evident before colonization of the surface of the chemical was detected. The rate of appearance of single cells and/or aggregations of cells on the surface of the palmitic acid was essentially the same as the doubling time of free cells in solution. At about 50 hours, mineralization and colonization of the surface stopped. In a salts solution containing solid palmitic acid,P. pseudoflava grew logarithmically in the solution and biphasically on the surface of the palmitic acid. We suggest that the bacterium first metabolizes soluble palmitic acid and later colonizes the solid when the substrate in solution has been depleted.}, }
@article {pmid24202607, year = {1987}, author = {Tang, YJ and Alexander, M}, title = {Absence of a role for lytic microorganisms in the decline of bacteria andSaccharomyces introduced into soil.}, journal = {Microbial ecology}, volume = {14}, number = {1}, pages = {67-73}, pmid = {24202607}, issn = {0095-3628}, abstract = {The populations ofKlebsieila pneumoniae, Escherichia coli, Enterobacter aerogenes, andPseudomonas sp. fell following their addition to soil, but species lysing these gram-negative bacteria were not detected. The numbers ofStaphylococcus aureus andMicrococcus flavus fell by more than four orders of magnitude and ofSaccharomyces cerevisiae by more than two orders after their addition to soil. Organisms lysing these gram-positive bacteria were present in soil, but their numbers did not increase as a result of the additions. Lytic activity againstS. aureus was detected in soil filtrates, but this activity was not enhanced by inoculation of soil with the bacterium. Addition of cycloheximide to soil suspensions delayed the fall in abundance ofM. flavus but did not suppress the lytic populations. We conclude that lysis is not responsible for the decline of bacteria orS. cerevisiae added to soil.}, }
@article {pmid24202606, year = {1987}, author = {Kusano, H and Kusano, T and Watanabe, Y}, title = {Seasonal succession of a microphagotroph community in a small pond during litter decomposition.}, journal = {Microbial ecology}, volume = {14}, number = {1}, pages = {55-66}, pmid = {24202606}, issn = {0095-3628}, abstract = {Temporal dynamics of a lentic microphagotroph community were studied during leaf litter decomposition from December to May. Small plastic vessels containing leaf litter were placed on a pond bottom. They were sampled periodically to collect microphagotrophs. Three abiotic factors and abundance of two food items were also measured to analyze the autogenic and allogenic phenomena during a microphagotroph succession. Three behavior types were recognized in dominant taxa: a free-swimming type, a vagile (creeps on substratum, sometimes swims) type, and a voluntarily fixed type. Dominant taxa changed from the free-swimming to the vagile type up to mid-March, and the reverse change occurred from mid-April. Principal component analysis (PCA) indicated four factors affecting the dynamics of the community: water temperature as a seasonal factor, detritus volume on the litter surface as a habitat factor, and densities of bacteria and small flagellates as food factors. Taxa replacement appeared to occur through two mechanisms. (1) Dominance of small holotrichs, a free-swimming type, was brought about by a high bacterial density caused by seasonal events, i.e., leaf fall in December and detritus formation by litter feeders in mid-April. This is an allogenic aspect of community dynamics. (2) The free-swimming type was replaced by the vagile one during the period with high taxa diversity. This replacement occurred through intertaxa competition for scarce food and/or selective predation by larger microphagotrophs. It is an autogenic process within the community.}, }
@article {pmid24202605, year = {1987}, author = {Beeman, RE and Suflita, JM}, title = {Microbial ecology of a shallow unconfined ground water aquifer polluted by municipal landfill leachate.}, journal = {Microbial ecology}, volume = {14}, number = {1}, pages = {39-54}, pmid = {24202605}, issn = {0095-3628}, abstract = {The microflora of a shallow anoxic aquifer underlying a municipal landfill in Oklahoma was characterized by direct light microscopy, most probable number determinations of sulfate reducers and methanogens, and measurements of methanogenesis in aquifer samples containing either endogenous or exogenous electron donors and various sulfate concentrations. Acridine orange direct counts of bacteria did not vary significantly with time or between 2 major sampling areas (1.70±0.16×10(7) to 11.2±2.1×10(7) cells/gdw). One site (B) was high in organic matter and low in sulfate, and methanogens generally outnumbered sulfate-reducers at most times of the year, whereas the opposite was true for another site (A). Greater than 75% of the theoretical amount of methane was detected within 7 weeks in both site A and B aquifer slurries amended with noncompetitive electron donors like methanol and trimethylamine. However, only site B slurries efficiently converted competitive donors like acetate, H2, and formate to the expected amount of methane. A mapping of sulfate and methane levels indicated that site A is relatively localized. These results suggest that the predominant flow of carbon and energy is through methanogenesis at aquifer site B whereas sulfate reduction predominated at site A. However, both methanogens and sulfate reducers could be isolated from either site.}, }
@article {pmid24202604, year = {1987}, author = {Kremer, RJ}, title = {Identity and properties of bacteria inhabiting seeds of selected broadleaf weed species.}, journal = {Microbial ecology}, volume = {14}, number = {1}, pages = {29-37}, pmid = {24202604}, issn = {0095-3628}, abstract = {Seeds of five weed species were examined for the presence of seedborne bacteria. A total of 459 isolates were obtained from 1,740 seeds. The bacteria were identified and examined for distribution among seed viability classes, antifungal activity, and potential phytopathogenicity. Weed seeds varied for the prevalence of bacteria and in the types of bacteria associated with each plant species. Antifungal activity exhibited by 80% of the bacteria may limit seed deterioration by potential fungal seed pathogens. Some of the seedborne bacteria (15%) were potentially phytopathogenic. It is suggested that the complex nature of the weed seed-bacteria associations may be an obstacle to the development of biotic agents for manipulating weed seed activity in soil.}, }
@article {pmid24202603, year = {1987}, author = {Lawrence, JR and Caldwell, DE}, title = {Behavior of bacterial stream populations within the hydrodynamic boundary layers of surface microenvironments.}, journal = {Microbial ecology}, volume = {14}, number = {1}, pages = {15-27}, pmid = {24202603}, issn = {0095-3628}, abstract = {Phase and computer-enhanced microscopy were used to observe the surface microenvironment of continuous-flow slide cultures during microbial colonization and to document the diversity of bacterial colonization maneuvers among natural stream populations. Surface colonization involved 4 discrete types of cell movement, which were designated as packing, spreading, shedding, and rolling maneuvers. Each maneuver appeared to be associated with a specific species population within the community. The packing maneuver resulted in the formation of a monolayer of contiguous cells, while spreading maneuvers resulted in a monolayer of adjacent cells. During the shedding maneuver, cells attached perpendicular to the surface and the daughter cells were released. The rate of growth of new daughter cells gradually decreased as the attached mother cell aged. During the rolling maneuver, cells were loosely attached and continuously somersaulted across the surface as they grew and divided. Only those populations with a packing maneuver conformed fully to the assumptions of kinetics used previously to calculate growth and attachment rates from cell number and distribution. Consequently, these kinetics are not applicable to stream communities unless fluorescent antisera are used to study specific species populations within natural communities. Virtually all of the cells that attached to the surface were viable and underwent cell division. The abundance of unicells on surfaces incubated in situ was thus primarily the consequence of bacterial colonization behavior (shedding and spreading maneuvers) rather than the adhesion of dead or moribund cells.}, }
@article {pmid24202602, year = {1987}, author = {Lawrence, JR and Delaquis, PJ and Korber, DR and Caldwell, DE}, title = {Behavior ofPseudomonas fluorescens within the hydrodynamic boundary layers of surface microenvironments.}, journal = {Microbial ecology}, volume = {14}, number = {1}, pages = {1-14}, pmid = {24202602}, issn = {0095-3628}, abstract = {Phase, darkfield, and computer-enhanced microscopy were used to observe the surface microenvironment of flow cells during bacterial colonization. Microbial behavior was consistent with the assumptions used previously to derive surface colonization kinetics and to calculate surface growth and attachment rates from cell number and distribution. Surface microcolonies consisted of closely packed cells. Each colony contained 2(n) cells, where n is the number of cell divisions following attachment. Initially, cells were freely motile while attached, performing circular looping movements within the plane of the solid-liquid interface. Subsequently, cells attached apically, maintained a fixed position on the surface, and rotated. This type of attachment was reversible and did not necessarily lead to the formation of microcolonies. Cells became irreversibly attached by progressing from apical to longitudinal attachment. Longitudinally attached cells increased in length, then divided, separated, moved apart laterally, and slid next to one another. This resulted in tight cell packing and permitted simultaneous growth and adherence. After approximately 4 generations, individual cells emigrated from developing microcolonies to recolonize the surface at new locations. Surface colonization byPseudomonas fluorescens can thus be subdivided into the following sequential colonization phases: motile attachment phase, reversible attachment phase, irreversible attachment phase, growth phase, and recolonization phase.}, }
@article {pmid24213300, year = {1987}, author = {Sallal, AK and Nimr, ND and Al-Sharif, HF}, title = {Isolation ofNostoc muscorum cyanophages from a domestic sewage.}, journal = {Microbial ecology}, volume = {13}, number = {3}, pages = {261-268}, pmid = {24213300}, issn = {0095-3628}, abstract = {TwoNostoc muscorum cyanophages were isolated from a domestic sewage in Kuwait. N-1L cyanophage had a hexagonal head with a long tail, while N-2S cyanophage was a short-tailed virus. N-1L cyanophage was active at 50°C and at acidic pH, compared with N-2S, which was more heat stable and active at pH 7.0. Seasonal variations in the total number of plaque-forming units ofN. muscorum cyanophages were determined for sewage samples collected at each treatment step.}, }
@article {pmid24213299, year = {1987}, author = {Ignatiades, L and Karydis, M and Pagou, K}, title = {Patterns of dark(14)CO 2 incorporation by natural marine phytoplankton communities.}, journal = {Microbial ecology}, volume = {13}, number = {3}, pages = {249-259}, pmid = {24213299}, issn = {0095-3628}, abstract = {The rates of dark(14)CO2 fixation by natural phytoplankton communities growing in eutrophic and oligotrophic waters were studied with short-term in situ experiments. Three aspects were investigated: (1) the time course incorporation of(14)CO2 in darkness, (2) the depth variability in dark(14)CO2 fixation, and (3) the variability in(14)CO2 fixation within a year. The highest dark(14)CO2 incorporation rates were observed during the first interval of incubation (20 min) after which they approached a constant rate with time. The observed differences in dark(14)CO2 fixation rates between populations from different depths were associated with differences in species composition as well as with physiological differences caused by exposure to different illumination conditions prior to their exposure to darkness. Autocorrelation coefficients were computed for the analysis of variability of dark(14)CO2 fixation rates within a year. It was suggested that dark(14)CO2 incorporation might be a periodic phenomenon depending mainly on the productive capacity of the phytoplankton community.}, }
@article {pmid24213298, year = {1987}, author = {Chróst, RJ and Overbeck, J}, title = {Kinetics of alkaline phosphatase activity and phosphorus availability for phytoplankton and bacterioplankton in lake plu\see (North German Eutrophic Lake).}, journal = {Microbial ecology}, volume = {13}, number = {3}, pages = {229-248}, pmid = {24213298}, issn = {0095-3628}, abstract = {Annual studies of kinetics of alkaline phosphatase (APA) activity and phosphorus availability for microplankton in the photic zone of an eutrophic lake are reported. The total APA activity of microplankton varied strongly. Vmax was highest during summer P depletion, and in autumn and winter total APA activity was low. The total APA specific activity of the microplankton was also highest (average 3.55 pmole PO4 (3-) ng ATP(-1) min(-1)) when ambient orthophosphate concentrations were very low. Both Vmax and specific APA activity were not dependent on the biomass of microplankton; they were strongly affected by P available for microplankton. A differential filtration technique was used for separation of microplankton into two size classes, i.e., algal, larger than 3μm, and bacterial fraction with size 0.2-3.0μm. The algal size fraction had lower specific APA activity (average 1.224 pmole PO4 (3-) ng ATP(-1) min(-1)) and higher KM values (38.8μmole × liter(-1)) than microorganisms which were smaller than 3μm (2.011 pmole PO4 (3-) ng ATP(-1) min(-1) and 25.4μmole liter(-1), respectively). The KM values of free, dissolved APA (36.8μmole liter(-1)) indicated that free APA was probably released by algae. Phytoplankton were major APA activity producers in the photic zone of the lake from March to November, and their activity constituted, on the average, 48.6% of the total APA activity in the water. Bacteria were the dominant APA activity producers in winter (41.3-44.9%); however, during other periods they contributed significantly (average 21.7%) to total APA activity. When surplus constituted less than 10% of particulate P in seston, phytoplankton produced high specific APA activity, and when surplus P was higher than 15%, the specific APA activity of phytoplankton size fraction rapidly decreased. APA of the bacterial size fraction of the seston was not affected by P concentrations. Orthophosphate was a competitive inhibitor of APA produced by microorganisms of the size fraction larger than 3.0μm, and increasing concentrations of inorganic phosphate caused an increase in KM values. The hypothetical metabolic-coupling between phytoplankton and bacterioplankton in the phosphorus cycle in conjunction with carbon metabolism in the lake is discussed.}, }
@article {pmid24213297, year = {1987}, author = {Fuerst, JA and McGregor, A and Dickson, MR}, title = {Negative staining of freshwater bacterioneuston sampled directly with electron microscope specimen support grids.}, journal = {Microbial ecology}, volume = {13}, number = {3}, pages = {219-228}, pmid = {24213297}, issn = {0095-3628}, abstract = {A technique for observation of surface microlayer bacteria (bacterioneuston) is described, utilizing direct sampling of the air-water interface with carbon-stabilized electron microscope specimen support grids, followed by negative staining and transmission electron microscopy. The method resulted in excellent preservation of forms of microcolonial association, regular surface arrays, surface appendages, and prosthecae in the bacterioneuston of a freshwater pond.}, }
@article {pmid24213296, year = {1987}, author = {Caron, DA}, title = {Grazing of attached bacteria by heterotrophic microflagellates.}, journal = {Microbial ecology}, volume = {13}, number = {3}, pages = {203-218}, pmid = {24213296}, issn = {0095-3628}, abstract = {Four species of heterotrophic microflagellates were examined for their ability to graze attached and unattached bacteria. The species tested displayed pronounced differences in their ability to graze the bacteriumPseudomonas halodurans attached to chitin particles. Two species of microflagellates (Monas andCryptobia sp.) efficiently grazed unattached bacteria but showed little or no ability to graze attached or aggregated cells. In contrast,Rhynchomonas nasuta andBodo sp. showed marked preferences for attached and aggregated bacteria and a limited ability to graze unattached cells. The density of attached bacteria was reduced by an order of magnitude due to grazing byBodo andR. nasuta, even though the density of unattached bacteria was ∼5-90× the density of attached cells. The maximum densities attained by microflagellates in the cultures were related to the density of unattached bacteria forMonas andCryptobia but not forBodo andR. nasuta. Growth of the latter two species appeared to be related to the density of attached or aggregated bacteria. Based on the results of these experiments, it is concluded that the pelagic existence of microflagellates that graze attached bacteria may be strongly linked to the distribution of suspended particles and their associated bacteria. In addition, the removal of attached bacteria by microflagellates can significantly affect the density of bacteria attached to particles in the plankton. This activity may have important implications for the controversy concerning the relative importance of attached and free-living bacteria in the plankton.}, }
@article {pmid24213295, year = {1987}, author = {Sar, N and Rosenberg, E}, title = {Fish skin bacteria: Colonial and cellular hydrophobicity.}, journal = {Microbial ecology}, volume = {13}, number = {3}, pages = {193-202}, pmid = {24213295}, issn = {0095-3628}, abstract = {Bacteria were desorbed from the skin of healthy, fast-swimming fish by several procedures, including brief exposure to sonic oscillation and treatment with nontoxic surface active agents. The surface properties of these bacteria were studied by measuring their adhesion to hexadecane, as well as by a newly developed, simple method for studying the hydrophobicity of bacterial lawns. This method, referred to as the "Direction of Spreading" (DOS) method, consists of recording the direction to which a water drop spreads when introduced at the border between bacterial lawns and other surfaces. Of the 13 fish skin isolates examined, two strains were as hydrophobic as polystyrene by the DOS method. Suspended cells of one of these strains adhered strongly to hexadecane (84%), whereas cells of the other strain adhered poorly (13%). Another strain which was almost as hydrophobic as polystyrene by the DOS method did not adhere to hexadecane at all. Similarly, lawns of three other strains were more hydrophobic than glass by the DOS method, but cell suspensions prepared from these colonies showed little or no adhesion to hexadecane. The high colonial but relatively low cellular hydrophobicity could be due to a hydrophobic slime that is removed during the suspension and washing procedures. The possibility that specific bacteria assist in fish locomotion by changing the surface properties of the fish skin and by producing drag-reducing polymers is discussed.}, }
@article {pmid24213294, year = {1987}, author = {Jacques, M and Marrie, TJ and Costerton, JW}, title = {Review: Microbial colonization of prosthetic devices.}, journal = {Microbial ecology}, volume = {13}, number = {3}, pages = {173-191}, pmid = {24213294}, issn = {0095-3628}, abstract = {The threat of bacterial colonization and biofilm formation poses the most important limitation on the use and development of prosthetic devices in human medicine. Data from the literature suggest that microbial adherence effected by the glycocalyx is a fundamental factor in sepsis involving biomaterials and that it may explain the resistance of such infections to host defense mechanisms and to antibiotherapy. A full appreciation of the existence and the consequences of the biofilm mode of bacterial growth is required so that we can both prevent and eliminate these protected microbial reservoirs.}, }
@article {pmid24213213, year = {1987}, author = {Joubert, WA and Britz, TJ}, title = {Characterization of aerobic, facultative anaerobic, and anaerobic bacteria in an acidogenic phase reactor and their metabolite formation.}, journal = {Microbial ecology}, volume = {13}, number = {2}, pages = {159-168}, pmid = {24213213}, issn = {0095-3628}, abstract = {Fifty-two aerobic and facultative anaerobic and 57 anaerobic bacterial isolates were obtained from an acidogenic phase digestion system. These isolates were characterized and the similarities between the different strains were calculated using Sokal and Michener's similarity coefficient. The aerobic and facultative anaerobic strains clustered in two major groups with the strains of the first main group being gram-negative fermentative rods, representing the generaKlebsiella, Enterobacter, Escherichia andAeromonas. Isolates of the second group were gram-positive streptococci similar toStreptococcus lactis. The strict anaerobic isolates also clustered into two main groups with strains of cluster A being identified as members of the genusFusobacterium while strains in cluster B were members of the genusBacteroides. Hypothetical mean organisms were calculated for each cluster and used in further culture studies. The major products of the continuously fed acidogenic phase reactor were ethanol and acetic, propionic, and butyric acids. In batch cultures, ethanol, acetic acid, diacetyl, and 2,3-butanediol were formed by the strains as major products both under aerobic and anaerobic conditions. The ability of the aerobic and facultative anaerobic strains to be metabolically active under anaerobic conditions indicates a prominent role in acidogenic reactors.}, }
@article {pmid24213212, year = {1987}, author = {Matavulj, M and Flint, KP}, title = {A model for acid and alkaline phosphatase activity in a small pond.}, journal = {Microbial ecology}, volume = {13}, number = {2}, pages = {141-158}, pmid = {24213212}, issn = {0095-3628}, abstract = {Acid and alkaline phosphatase activity were determined in a small pond over a period of 24 months (64 samples). Activity of each phosphatase enzyme was positively correlated with chlorophyll concentration, viable bacterial count, total phosphate concentration, inorganic phosphate concentration, and temperature. Multiple regression analysis was used to formulate equations that described phosphatase activity in terms of these physical, chemical, and biotic factors. Corrected coefficients of determination were calculated, and the highest values were obtained when all parameters were included in the equation (r (2)=0.776 and 0.659 for alkaline and acid phosphatase activity, respectively). However, there was little improvement in ther (2) value obtained when only chlorophyll was used in the equation (r (2)=0.654 and 0.624, respectively). Samples were then taken over a further 12 months (25 samples), and observed activity was compared with the activity predicted by application of the previously derived equations. For alkaline phosphatase, the best fit between observed and expected activity was seen with the equation containing all parameters, but for acid phosphatase the best fit was seen with the equation containing only chlorophyll and temperature as the determinants. In both cases there was a good fit between observed and expected data using the equation containing chlorophyll as the sole determinant. From this we have concluded that phytoplankton were the chief producers of phosphatase activity in this pond, although the influence of physical and chemical factors on enzyme activity could not be ignored.}, }
@article {pmid24213211, year = {1987}, author = {Gaill, F and Desbruyères, D and Prieur, D}, title = {Bacterial communities associated with "Pompei worms" from the East Pacific rise hydrothermal vents: SEM, TEM observations.}, journal = {Microbial ecology}, volume = {13}, number = {2}, pages = {129-139}, pmid = {24213211}, issn = {0095-3628}, abstract = {A morphological study of bacteria associated with the "Pompei worm,"Alvinella pompejana, collected from East Pacific rise hydrothermal vents, revealed four types of epidermal associations on the dorsal part of the animals: various single cells distributed on the animal tegument; clump-like associations located in the intertegumentary spaces; and filamentous bacteria associated with epidermal expansions, or inserted on the posterior parapodia. The bacterial morphologies were illustrated by SEM and TEM pictures and compared to bacteria previously described. The functional significance of these associations is discussed.}, }
@article {pmid24213210, year = {1987}, author = {Lynn, DH and Montagnes, DJ and Riggs, W}, title = {Divider size and the cell cycle after prolonged starvation ofTetrahymena corlissi.}, journal = {Microbial ecology}, volume = {13}, number = {2}, pages = {115-127}, pmid = {24213210}, issn = {0095-3628}, abstract = {Cell growth and division of the ciliateTetrahymena corlissi were examined upon refeeding after prolonged starvation of up to 12 days. Division did not automatically occur when a certain critical cell size was reached. Rather, it varied both with the nutritional history of the cell and the nutrient conditions in which the cell was growing. Upon refeeding, cells starved for 12 days divided at a smaller size and later than cells starved for 6 days. Cells refed at high density took longer to begin division than cells refed at low density. The results are discussed with respect to the "relative starvation" and "critical constituent" models of the cell cycle and in terms of the polymorphic life cycle ofTetrahymena species.}, }
@article {pmid24213209, year = {1987}, author = {Bakken, LR and Olsen, RA}, title = {The relationship between cell size and viability of soil bacteria.}, journal = {Microbial ecology}, volume = {13}, number = {2}, pages = {103-114}, pmid = {24213209}, issn = {0095-3628}, abstract = {The number of bacterial cells in soil that form colonies on nutrient agar represent a small fraction of the direct microscopic counts (DMC). The colony-forming cells have larger cell dimensions than the very small ("dwarf") cells which represent the majority of the DMC. This may indicate that the dwarf cells are species unable to form visible colonies on agar, or that they swell to normal dimensions when growing. Indigenous bacterial cells were separated from soil by density gradient centrifugation and fractionated according to diameter by filtration through polycarbonate filters. Each filtrate was studied with respect to DMC, cell dimensions, colony-forming cells (visible colonies and microcolonies), and cell dimensions during growth on the agar. The calculated average percent viability was only 0.2% for cells with diameters below 0.4μm, about 10% for cells with diameters between 0.4 and 0.6μm, and 30-40% for cells with diameters above 0.6μm. Only 10-20% of the viable cells with diameters <0.4μm increased their diameter to >0.4μm prior to growth. Thus, size change during starvation and growth cycles did not explain the high numbers of dwarf cells observed by microscopy. The results show that despite the relatively low number of colony-forming bacteria in soil, the species that form colonies may be fairly representative for the medium size and large cells, which constitute a major part of the bacterial biovolume. Thus plate counting could be a useful method to count and isolate the bacteria accounting for much of the biovolume in soil. The origin of the dwarf cells is still unclear, but the low number of small cells that increased in size seems to indicate that the majority of these bacterial cells are not small forms of ordinary sized bacteria.}, }
@article {pmid24213208, year = {1987}, author = {Norland, S and Heldal, M and Tumyr, O}, title = {On the relation between dry matter and volume of bacteria.}, journal = {Microbial ecology}, volume = {13}, number = {2}, pages = {95-101}, pmid = {24213208}, issn = {0095-3628}, abstract = {Dry matter and volumes of 337 individual bacterial cells with volumes in the range 0.01-7μm(3) from different origins were measured. An allometric relation was established between dry matter and volume, such that smaller bacteria tended to have a higher dry matter to volume ratio than larger bacteria. The results are compared to results from similar work on algae. The implications for the use of conversion factors are discussed.}, }
@article {pmid24213105, year = {1987}, author = {Dackman, C and Olsson, S and Jansson, HB and Lundgren, B and Nordbring-Hertz, B}, title = {Quantification of predatory and endoparasitic nematophagous fungi in soil.}, journal = {Microbial ecology}, volume = {13}, number = {1}, pages = {89-93}, pmid = {24213105}, issn = {0095-3628}, abstract = {Methods were developed to quantify predatory and endoparasitic fungi in soil. The methods were based on previously developed detection techniques and combined with a most probable number estimation. The methods were applied to an agricultural soil fertilized with farmyard manure. Large amounts of farmyard manure resulted in increased amounts of organic matter, numbers of propagules of predatory and endoparasitic fungi, and numbers of bacteria and nematodes.}, }
@article {pmid24213104, year = {1987}, author = {Berg, P and Rosswall, T}, title = {Seasonal variations in abundance and activity of nitrifiers in four arable cropping systems.}, journal = {Microbial ecology}, volume = {13}, number = {1}, pages = {75-87}, pmid = {24213104}, issn = {0095-3628}, abstract = {Ammonium and nitrite oxidizers were counted with the most probable number (MPN) method and potential ammonium- and nitrite-oxidation rates were determined with a chlorate inhibition technique in an arable soil over a 3-year period. Samples were taken from the topsoil once a month for 2 years and a few times during a third year in four cropping systems: unfertilized lucerne ley and barley, and nitrate fertilized grass ley and barley. The distribution of nitrifiers was determined and their activities measured at various soil depths and between and within plant rows of fertilized barley.The numbers and activities of ammonium oxidizers were highest in the spring and autumn samples. Numbers of ammonium oxidizers ranged from 0.2 to 19×10(4) and nitrite oxidizers from 3 to 870×10(4) cells g(-1) dry soil. Potential ammonium-oxidizer activities ranged from 120 to 1,060 and nitrite-oxidizer activities ranged from 280 to 680 ng N g(-1) dry soil hour(-1). Lucerne and grass leys generally showed the highest, whereas unfertilized barley had the lowest, abundances and activities.Abundance estimates and activities were 10-20 times higher in the plow layer than in underlying sand and clay layers. A strong correlation was found between organic matter content vs numbers and activities of both ammonium and nitrite oxidizers. Only nitrite oxidizer counts were significantly higher within plant rows compared to between plant rows.}, }
@article {pmid24213103, year = {1987}, author = {Olsen, RA and Bakken, LR}, title = {Viability of soil bacteria: Optimization of plate-counting technique and comparison between total counts and plate counts within different size groups.}, journal = {Microbial ecology}, volume = {13}, number = {1}, pages = {59-74}, pmid = {24213103}, issn = {0095-3628}, abstract = {Viable counts of heterotropic soil bacteria were 3-5 times higher on low-nutrient agar media compared with a series of conventional agar media. Substantial amounts of monosaccharides and amino acids were present in solid media made from distilled water and agar powder, and a salt-solution agar medium (without organic substrates added) gave practically the same colony counts as the low nutrient soil extract agar medium. MPN values were comparable to or lower than plate counts. A search for slow-growing cells in the negative MPN tubes by fluorescence microscopical examination after 3 months incubation was negative.The viable counts were 2-4% of the total microscopical counts in different soils. Assuming that the colony-forming cells did not derive from the numerous "dwarf" cells present in soil, a calculated percent viability of the larger cells was about 10%. The ecological significance of the plate-counting technique is discussed.}, }
@article {pmid24213102, year = {1987}, author = {Kanagawa, T and Kelly, DP}, title = {Degradation of substituted thiophenes by bacteria isolated from activated sludge.}, journal = {Microbial ecology}, volume = {13}, number = {1}, pages = {47-57}, pmid = {24213102}, issn = {0095-3628}, abstract = {Actinomycetes were isolated from activated sludge acclimated to thiophene-2-carboxylic acid (T2C) or 5-methyl-thiophene-2-carboxylic acid (T5M2C). These isolates were apparently identical and were identified as strains ofRhodococcus. The strains could grow on T2C, T5M2C, or thiophene-2-acetic acid as sole sources of carbon and energy, but could not use thiophene, methyl thiophenes, several other substituted thiophenes, dibenzothiophene, dimethyl sulfide, or pyrrole-2-carboxylic acid. T2C was degraded quantitatively to sulfate, and its carbon was converted almost entirely to cell biomass and carbon dioxide. Growth yields indicated about 25% conversion of T2C-carbon to cell-carbon. Growth was not supported by thiosulfate or methionine, nor were these compounds oxidized.Rhodococcus strain TTD-1 grown on T2C oxidized both T2C and T5M2C with an apparent Km of 1.3×10(-5) M. Sulfide was also oxidized by T2C-grown organisms. This is the first demonstration of an actinomycete capable of the complete degradation of thiophene derivatives and of their use by it as sole substrates for growth.}, }
@article {pmid24213101, year = {1987}, author = {Davidson, AM and Fry, JC}, title = {A mathematical model for the growth of bacterial microcolonies on marine sediment.}, journal = {Microbial ecology}, volume = {13}, number = {1}, pages = {31-45}, pmid = {24213101}, issn = {0095-3628}, abstract = {Counts of bacterial microcolonies attached to deep-sea sediment particles showed 4-, 8-, 16-, and 32-celled microcolonies to be very rare. This was investigated with a mathematical model in which microcolonies grew from single cells at a constant growth rate (μ), detached from particles at constant rate (λ), and reattached as single cells. Terms for attachment of foreign bacteria (a) and death of single cells (d) were also included. The best method of fitting the model to the microcolony counts was a weighted least-squares approach by whichλ(0.83 hour(-1)) was estimated to be about 20 times greater thanμ(0.038 hour(-1)). This showed that the bacteria were very mobile between sediment particles and this mobility was explained in terms of attachment by reversible sorption. The implications of the results for the frequency of dividing cell method for estimating growth rates of sediment bacteria are discussed. The ratio ofλ andμ was found to be very robust both in terms of the errors associated with the microcolony counts and the range of microcolony sizes used to obtain the solution.}, }
@article {pmid24213100, year = {1987}, author = {Meyer, JL and Edwards, RT and Risley, R}, title = {Bacterial growth on dissolved organic carbon from a blackwater river.}, journal = {Microbial ecology}, volume = {13}, number = {1}, pages = {13-29}, pmid = {24213100}, issn = {0095-3628}, abstract = {Different nominal molecular weight (nMW) fractions of DOC from a southeastern blackwater river were concentrated by ultrafiltration and added to sieved river water to assess each fraction's ability to stimulate bacterial growth. Bacterial growth was measured using change in bacterial biomass from direct counts and using(3)H-thymidine incorporated into DNA. Bacterial growth and amount of DOC used was greatest in the low MW enrichment (< 1,000 nMW) and least in the intermediate MW enrichment (1,000-10,000 nMW). The high MW fraction (> 10,000 nMW) supported more growth than did the intermediate MW fraction, apparently because of lower MW compounds complexed with a high MW refractory core. The low MW fraction of DOC from a clearwater mountain stream, a boreal blackwater river, and leachate from water oak and willow leaves also stimulated more bacterial growth than did other fractions. However, the high MW DOC from these other sources was not as biologically available as high MW DOC from a blackwater river. Bacteria converted blackwater river DOC to bacterial biomass with an efficiency of 31%. Bacteria produced at the expense of abundant riverine DOC provide a trophic resource for protozoa and higher levels of the microbial food web of a blackwater river.}, }
@article {pmid24213099, year = {1987}, author = {Schmaljohann, R and Pollingher, U and Berman, T}, title = {Natural populations of bacteria in Lake Kinneret: Observations with scanning electron and epifluorescence microscopy.}, journal = {Microbial ecology}, volume = {13}, number = {1}, pages = {1-12}, pmid = {24213099}, issn = {0095-3628}, abstract = {The bacterioplankton assemblage in Lake Kinneret, Israel, sampled on 6 occasions representative of different seasonal conditions was studied with scanning electron microscopy (SEM) and epifluorescence microscopy after acridine-orange staining. In near-surface (1-3 m) samples taken in October 1981 and March 1983, several unusual types of budding, appendaged, and filamentous cells were found. During lake stratification, typical large anaerobic forms (including photosynthetic green sulphur bacteria) were observed in samples from the metalimnion and deep (40 m) hypolimnion. Epifluorescence counts indicated that bacteria in the water column ranged from 0.55 to 2.67 × 10(6) cells ml(-1).}, }
@article {pmid24212926, year = {1986}, author = {Troussellier, M and Legendre, P and Baleux, B}, title = {Modeling of the evolution of bacterial densities in an eutrophic ecosystem (sewage lagoons).}, journal = {Microbial ecology}, volume = {12}, number = {4}, pages = {355-379}, pmid = {24212926}, issn = {0095-3628}, abstract = {The process of wastewater treatment was studied by modeling the relationships between physical, chemical, and biological (bacteria, phytoplankton, zooplankton) components of the sewage treatment lagoons of an urban wastewater center, based upon a two-year sampling program. The models of interactions between variables were tested by path analysis. The path coefficients were computed from the results of ridge regression, instead of linear multiple regression. The results show that fecal coliforms were effectively controlled by the environmental variables included in the model, which have a cyclic seasonal behavior. This control grew stronger with distance from the input (R (2)=0.71) to the output (R (2)=0.88) of the treatment plant, resulting in effective elimination of most enteric bacteria. Simultaneously, the ecosystem's community of aerobic heterotrophic bacteria became more independent from the model's predictive variables, with increased distance from the sewage input, thus demonstrating its maturation as an autonomous community in the lagoon ecosystem. Consequences of modeling are discussed, with respect to the understanding of biological wastewater treatment mechanisms and ecosystem dynamics and to plant management.}, }
@article {pmid24212925, year = {1986}, author = {Sharma, VK and Hobson, PN}, title = {Interactions among cellulolytic bacteria from an anaerobic digester.}, journal = {Microbial ecology}, volume = {12}, number = {4}, pages = {343-353}, pmid = {24212925}, issn = {0095-3628}, abstract = {High cellulolytic activity of particular strains did not cause dominance of one, or a few, species of fiber-digesting bacteria in a cattlewaste anaerobic digester. The population contained a large number of species and varieties with different cellulolytic and fiber-digesting activities. Although mixed cultures of some of these bacteria showed no intereffects, with others, cellulolysis was less or in some cases greater than that shown by individual components of the cultures. The interactions were probably related to effects on growth of the bacteria rather than on activities of components of the cellulase enzyme complex, and culture filtrates of two of the more numerous cellulolytic species ofClostridium affected growth of other cellulolytic bacteria. The inhibitory factor(s) appeared to be of bacteriocin type, but the stimulatory factor(s) was unknown. It was suggested that these interactions are localized or short-lived in the digester, and so the population remains in a "dynamic" steady state.Some inhibitions of growth of rumen cellulolytic bacteria were caused by the digester bacteria, but it was suggested that factors other than these inhibitions are responsible for the absence of rumen bacteria from anaerobic digesters.}, }
@article {pmid24212924, year = {1986}, author = {Hirsch, P and Müller, M}, title = {Methods and sources for the enrichment and isolation of budding, nonprosthecate bacteria from freshwater.}, journal = {Microbial ecology}, volume = {12}, number = {4}, pages = {331-341}, pmid = {24212924}, issn = {0095-3628}, abstract = {Methods are described for the observation, enrichment and isolation (from various freshwater samples) of bacteria of the generaPlanctomyces andPirella. Because immature buds were easily dislodged by shearing forces, slide culture techniques and direct microscopy of the budding process are recommended. An "auxanographic" technique to detect possible stimulation by soluble substrates was based on the diffusion of these substrates from peripherally placed crystals into the agar of a slide culture. Nearly every water sample investigated contained representatives of the generaPlanctomyces, Pirella, andBlastobacter, as well as budding cocci. Six enrichment techniques were tried; some enrichment experiments lasted several months. Allowing samples without added substrate to stand for a long time or generally employing nutrient-poor media were most successful. The "petri dish method," taking advantage of attachment of many budding bacteria to glass surfaces, was especially useful for increasing the numbers ofPlanctomyces spp. Pure cultures obtained from freshwater samples were tentatively placed in the generaPlanctomyces, Pirella, andBlastobacter. One strain appeared to represent a new genus of gram-positive, budding, and nonprosthecate bacteria.}, }
@article {pmid24212923, year = {1986}, author = {Jones, JG and Simon, BM}, title = {Nutritional strategy of a benthic filamentous bacterium.}, journal = {Microbial ecology}, volume = {12}, number = {4}, pages = {323-330}, pmid = {24212923}, issn = {0095-3628}, abstract = {Filibacter limicola is a filamentous gliding bacterium isolated from the profundal sediment of a eutrophic lake. It is an obligate amino acid utilizer. The kinetic parameters for the metabolism of four amino acids byF. limicola, Vitreoscilla spp. and the bacterial populations of water and sediment samples were compared.F. limicola exhibited low half-saturation constants (K) which were of the same order as those obtained with water samples. The K values for theVitreoscilla spp. and the sediment were an order of magnitude higher. It would appear that the bacterium is a specialist, inhabiting a niche which is sufficiently nutrient rich to support an organism with a limited substrate range. It also possesses a high affinity uptake system for some amino acids which may permit it to compete effectively during periods of nutrient depletion.}, }
@article {pmid24212922, year = {1986}, author = {Kefford, B and Marshall, KC}, title = {The role of bacterial surface and substratum hydrophobicity in adhesion ofLeptospira biflexa serovarpatoc 1 to inert surfaces.}, journal = {Microbial ecology}, volume = {12}, number = {4}, pages = {315-322}, pmid = {24212922}, issn = {0095-3628}, abstract = {Adhesion of the hydrophilicLeptospira biflexa serovarpatoc 1 (L. patoc) was consistently greater on inert hydrophobic surfaces than on hydrophilic surfaces (glass and plastic). When inert substrata were coated with fetal calf serum (FCS) or bovine serum albumin fraction V (BSA), however, surface hydrophobicity was reduced compared to untreated surfaces, but adhesion ofL. patoc increased. The mechanism of adhesion at protein-coated surfaces is likely to be different than that at untreated surfaces, but it is suggested that the adhesion is nonspecific, as the level of adhesion is similar for different protein coatings. Increased adhesion to FCS- and BSA-coated surfaces was apparently not associated with substrate utilization (scavenging of fatty acids) from the coatings, as essentially fatty acid-free BSA-coated surfaces had similar levels of adhesion. The presence of FCS in the diluent lowered the adhesion ofL. patoc regardless of the original nature of the substratum. This may result from the mutual repulsion of the bacterium and the substratum caused by the exclusion volumes of similar macromolecules adsorbed to both surfaces from the FCS solution.}, }
@article {pmid24212683, year = {1986}, author = {Caldwell, DE and Lawrence, JR}, title = {Growth kinetics ofPseudomonas fluorescens microcolonies within the hydrodynamic boundary layers of surface microenvironments.}, journal = {Microbial ecology}, volume = {12}, number = {3}, pages = {299-312}, pmid = {24212683}, issn = {0095-3628}, abstract = {Computer-enhanced microscopy (CEM) was used to study the growth kinetics of bacterial microcolonies attached to the wall of a continuous-flow slide culture. Image processing increased effective microscope resolution and quantitated colony growth at 10 min intervals. Three growth parameters were used to determine growth rate: the time required for cell fission, the specific rate of increase in cell number, and the specific rate of increase in cell area. Growth rate was initially constant regardless of colony size, as assumed previously in deriving colonization kinetics. However, at low substrate concentrations growth rate varied depending on laminar flow velocity. Growth was flow-dependent at a glucose concentration of 100 mg/liter and flow-independent at a concentration of 1 g/liter. This indicated that the surface microenvironment became substrate-depleted in the absence of sufficient laminar flow velocities and that glucose rather than oxygen was rate limiting.}, }
@article {pmid24212682, year = {1986}, author = {Benner, R and Maccubbin, AE and Hodson, RE}, title = {Temporal relationship between the deposition and microbial degradation of lignocellulosic detritus in a Georgia salt marsh and the Okefenokee Swamp.}, journal = {Microbial ecology}, volume = {12}, number = {3}, pages = {291-298}, pmid = {24212682}, issn = {0095-3628}, abstract = {Temperature dependence and seasonal variations in rates of microbial degradation of the lignin and polysaccharide components of specifically radiolabeled lignocelluloses were determined in sediment and water samples from a Georgia salt marsh and the nearby Okefenokee Swamp. Although temperature regimes in the two ecosystems were similar, rates of mineralization ofSpartina alterniflora lignocellulose in salt marsh sediments increased eightfold between winter and summer, whereas rates of mineralization of lignocellulose from an analogous freshwater macrophyte,Carex walteriana, in Okefenokee sediments increased only twofold between winter and summer. Temperature was the major factor influencing seasonal variations in rates of lignocellulose degradation in both environments. At any given temperature, no substantial differences in lignocellulolytic potential were observed with sediment samples collected at each season. In both ecosystems, the bulk of the lignocellulosic detritus was not degraded at the time of its peak deposition during the fall and winter. Instead, the periods of maximal decomposition occurred during the following spring and summer. These results suggest that periods of maximal nutrient regeneration from the mineralization of lignocellulosic detritus coincide with periods of highest primary production, and that, depending on hydrologic conditions, significant horizontal transport of essentially intact lignocellulosic material is possible due to the lag period between deposition and microbial degradation.}, }
@article {pmid24212681, year = {1986}, author = {Esteves, JL and Mille, G and Blanc, F and Bertrand, JC}, title = {Nitrate reduction activity in a continuous flow-through system in marine sediments.}, journal = {Microbial ecology}, volume = {12}, number = {3}, pages = {283-290}, pmid = {24212681}, issn = {0095-3628}, abstract = {Nitrate reduction in a non-polluted, coastal marine sediment was measured with an open flow-through system. The recorded rates depended upon nitrate concentration but were largely independent of the weight of sediment (14-35 g) and the dilution rate (0.7-5 h(-1)). Rate of nitrate uptake followed classical Michaelis-Menten kinetics, and km and Vmax values were equal to 78μM and 0.168μm mol g(-1) hour(-1), respectively. These values are in good agreement with those found by the other authors for the same biotope but by different methods. This technique of the open flow-through system is fast, simple, and inexpensive and involves small quantities of sediment (∼10 g).}, }
@article {pmid24212680, year = {1986}, author = {Turley, C and Lochte, K}, title = {Diel changes in the specific growth rate and mean cell volume of natural bacterial communities in two different water masses in the Irish sea.}, journal = {Microbial ecology}, volume = {12}, number = {3}, pages = {271-282}, pmid = {24212680}, issn = {0095-3628}, abstract = {Diel changes in the specific growth rates of natural bacterial communities as a whole and of different groups within the communities were followed over 2 days during July 1982, in stratified waters in the vicinity of a shallow sea tidal mixing front in the Irish Sea. Waters well above (4 m) and below (60 m) the thermocline were enclosed in dialysis bags and incubated in situ. The results show that there were periods of altered growth rates of the whole bacterial community and synchronous cell division of morphological groups. An increase in mean cell volume within both 4 and 60 m communities preceded an increase in specific growth rates, with a resultant decrease in the mean cell volume. Above the thermocline the whole bacterial community, as well as the rod and coccoid forms, doubled in number once a day. The doubling time of the whole bacterial community at 60 m was 2 days and slower than that at 4 m. This was due to a slower doubling time (3 days) for the coccoid forms. Rod forms at the two depths had a similar doubling time (1 day). The time of day when maximum division rate occurred was also different in the two water masses. At 4 m more coccoid forms divided during the night, whereas at 60 m more divided during the day. Conversely, at 4 m more rod forms divided during the day, whereas at 60 m more divided at night.These data indicate that the bacterial community and members of the community may be adapted to exploit the diurnal rhythms of dissolved organic carbon (DOC) release by other organisms and that portions of the bacterial community may therefore be more active at certain times of the day. The diurnal growth of the bacterial community may thus vary between different water masses and largely reflects the differences in the chemical and biological characteristics of the two water masses investigated.}, }
@article {pmid24212679, year = {1986}, author = {Moriarty, DJ}, title = {Bacterial productivity in ponds used for culture of penaeid prawns.}, journal = {Microbial ecology}, volume = {12}, number = {3}, pages = {259-269}, pmid = {24212679}, issn = {0095-3628}, abstract = {The quantitative role of bacteria in the carbon cycle of ponds used for culture of penaeid prawns has been studied. Bacterial biomass was measured using epifluorescence microscopy and muramic acid determinations. Bacterial growth rates were estimated from the rate of tritiated thymidine incorporation into DNA. In the water column, bacterial numbers ranged from 8.3×10(9) 1(-1) to 2.57×10(10) 1(-1) and production ranged from 0.43 to 2.10 mg Cl(-1) d(-1). In the 0-10 mm zone in sediments, bacterial biomass was 1.4 to 5.8 g C m(-2) and production was 250 to 500 mg C m(-2) d(-1). The results suggested that most organic matter being supplied to the ponds as feed for the prawns was actually being utilized by the bacteria. When the density of meiofauna increased after chicken manure was added, bacterial biomass decreased and growth rates increased.}, }
@article {pmid24212678, year = {1986}, author = {Riemann, B and Jørgensen, NO and Lampert, W and Fuhrman, JA}, title = {Zooplankton induced changes in dissolved free amino acids and in production rates of freshwater bacteria.}, journal = {Microbial ecology}, volume = {12}, number = {3}, pages = {247-258}, pmid = {24212678}, issn = {0095-3628}, abstract = {This study examined the importance of zooplankton in the flux of dissolved free amino acids (DFAA) in the water and into bacteria. DFAA release rates were followed in laboratory grazing experiments usingDaphnia galeata andEudiaptomus graciloides as grazers, andScenedesmus acutus andSynechococcus elongatus as food sources. Except for minor initial peaks, DFAAs were released continuously during the first 2 hours and made up 6-12% (in one experiment 50%) of the calculated ingestion rates. During three diel studies in lakes, effects of removal and increase of the density of zooplankton (>200μm) on the pools of DFAA as well as on the bacterial production were followed. During two of the diel studies, higher DFAA pools were measured when 3-4 times the natural zooplankton density was present, and in one study a minor increase also occurred in the bacterial production, compared with results from experiments without zooplankton and with a natural zooplankton density. The increase in bacterial growth coincided with a decline in DFAA. During the third study, neither DFAA nor the bacterial production changed significantly when the zooplankton density was increased 3 times. Removal of zooplankton, however, caused a decline in both DFAA and bacterial production. Our data suggest a close relationship between occurrence of zooplankton and release of DFAA, but the factors regulating the amount of DFAA released and its effect on bacterial growth are not yet understood.}, }
@article {pmid24212541, year = {1986}, author = {Leufvén, A and Nehls, L}, title = {Quantification of different yeasts associated with the bark beetle,Ips typographus, during its attack on a spruce tree.}, journal = {Microbial ecology}, volume = {12}, number = {2}, pages = {237-243}, pmid = {24212541}, issn = {0095-3628}, abstract = {There were different amounts and types of yeasts associated with individuals ofIps typographus spruce bark beetles during different phases of their attack on a healthy spruce tree. The yeasts were isolated on Sabouraud agar medium in order to identify them and estimate their numbers.Hansenula holstii andCandida diddensii type yeasts were most frequently isolated. The increase in number of these two yeast types probably accounted for most of the total yeast increase found during the later attack phases of the bark beetles. Lesser amounts ofHansenula capsulata, Pichia pinus, Candida nitratophila, and twoCryptococcus type yeasts were also found.}, }
@article {pmid24212540, year = {1986}, author = {Ramesh, A and Nandakumar, R and Venugopalan, VK}, title = {Enteric luminous microflora of the pond-cultured milk fishChanos chanos (Forskal).}, journal = {Microbial ecology}, volume = {12}, number = {2}, pages = {231-235}, pmid = {24212540}, issn = {0095-3628}, abstract = {Qualitative and quantitative investigations were made on the luminous bacteria associated with the gut of pond cultured milk fishChanos chanos. Significant differences in luminous bacterial numbers were found between gut and pond water and between gut and pond sediment, but not between pond water and sediment. No significant variation in luminous bacterial population among the gut regions was observed. The quantity of ingesta in the fish gut does not appear to influence the biomass of luminous bacteria.Vibrio harveyi andV. fischeri were the 2 most commonly encountered species, and of the 2 luminous species,V. harveyi was predominant.}, }
@article {pmid24212539, year = {1986}, author = {Schnürer, J and Clarholm, M and Boström, S and Rosswall, T}, title = {Effects of moisture on soil microorganisms and nematodes: A field experiment.}, journal = {Microbial ecology}, volume = {12}, number = {2}, pages = {217-230}, pmid = {24212539}, issn = {0095-3628}, abstract = {The effects of soil moisture changes on bacteria, fungi, protozoa, and nematodes and changes in oxygen consumption were studied in a field experiment. In one plot the soil was drip-irrigated daily for 10 days, while an adjacent plot experienced one rainfall and was then allowed to dry out. Oxygen consumption was the parameter measured which responded most rapidly to changes in soil moisture content. Lengths of fluorescein diacetate-active hyphae paralleled oxygen consumption in both plots. Total hyphal length was not affected by one rainfall but increased from 700 mg(-1) dry weight soil to more than 1,600 m in less than 10 days in the irrigated plot. In the rain plot, bacterial numbers doubled within 3 days and declined during the following period of drought. In the irrigated plot, numbers increased by 50% and then remained constant over the duration of the study. Only small changes in protozoan numbers were observed, with the exception of the last sampling date in the irrigated plot when large numbers of naked amoebae were recorded 2 days after a large natural rainfall. Nematode numbers, especially obligate root feeders, increased in both treatments. The increases were caused by decoiling rather than growth. The results indicate that fungal respiration was dominating, while bacteria, lacking a suitable source of energy, were less active, except for the first days.}, }
@article {pmid24212538, year = {1986}, author = {Kanazawa, S and Filip, Z}, title = {Distribution of microorganisms, total biomass, and enzyme activities in different particles of brown soil.}, journal = {Microbial ecology}, volume = {12}, number = {2}, pages = {205-215}, pmid = {24212538}, issn = {0095-3628}, abstract = {A soil sample from the Ap horizon of an arable brown soil was fractionated by wet sieving, and seven size fractions of organic and mineral soil particles were separated. The organic fractions formed only 2.2% of the soil dry mass, but contained 41.5 and 29.12% of the total soil content of carbon and nitrogen, respectively, and thus represented an important reservoir of readily utilizable nutrients. Organic particles also accumulated most of the soil enzyme activities, determined asβ-glucosidase,β-acetylglucosaminidase, and proteinase activity. The highest counts of bacteria, actinomycetes, and fungi per gram of the soil fractions were obtained with the organic particles, but for the most part microorganisms accumulated in the silt-clay fraction. All soil fractions except the coarsest organic particles contained higher counts of oligotrophic bacteria than copiotrophic ones. Microbial counts, ATP contents, and enzyme activities decreased significantly with decrease in size of the organic soil particles, and increased with decrease in size of the mineral soil particles. Thus, the coarse organic particles >5 mm and the silt-clay fraction <0.05 mm represent the sites with the highest concentrations of microorganisms, ATP contents, and enzyme activities in the arable brown soil under test.}, }
@article {pmid24212537, year = {1986}, author = {Baker, JH}, title = {Relationship between microbial activity of stream sediments, determined by three different methods, and abiotic variables.}, journal = {Microbial ecology}, volume = {12}, number = {2}, pages = {193-203}, pmid = {24212537}, issn = {0095-3628}, abstract = {Microbial activity of stream sediments has been determined by three distinct methods: phosphatase levels, maximum uptake velocity of radiolabeled glucose, and carbon dioxide production rates. These methods have been applied to different types of sediment (mud, sand, gravel) from the same stream and to 5 samples from two different streams for comparison. Temperature, discharge, and 8 other abiotic variables for each sample were also determined. The 3 activity methods correlated closely with each other and were measured with a similar precision. Phosphatase activity could be predicted for all sites from bulk density. The largest proportion of the variance associated with carbon dioxide production was explained by variations in percent of organic matter, but the relationship did not hold for all streams. Maximum uptake velocity, compared with the other 2 activity measurements, was poorly explained by any of the abiotic variables.}, }
@article {pmid24212536, year = {1986}, author = {Baldock, BM}, title = {A method for enumerating protozoa in a variety of freshwater habitats.}, journal = {Microbial ecology}, volume = {12}, number = {2}, pages = {187-191}, pmid = {24212536}, issn = {0095-3628}, abstract = {A method for enumerating protozoa (ciliates, flagellates, and amoebae) in fine, freshwater sediments is described. The results, using fixed material, are compared with two published techniques: a culture method (most probable number) and a direct count method.}, }
@article {pmid24212535, year = {1986}, author = {Patel, BK and Morgan, HW and Daniel, RM}, title = {Unusual microorganisms observed in New Zealand hot springs.}, journal = {Microbial ecology}, volume = {12}, number = {2}, pages = {181-186}, pmid = {24212535}, issn = {0095-3628}, abstract = {A technique is described for studying hot spring microbial morphotypes by using electron microscope grids incubatedin situ. Such studies revealed the presence of filaments bearing swollen saclike structures in a number of New Zealand hot springs. There was considerable variation in the size, structure, and morphology of the filaments and the saclike structures.}, }
@article {pmid24212534, year = {1986}, author = {de Haast, J and Britz, TJ}, title = {Characterization of aerobic and facultative anaerobic bacteria from the liquid phase of an anaerobic fixed-bed digester treating a cheese whey substrate.}, journal = {Microbial ecology}, volume = {12}, number = {2}, pages = {173-179}, pmid = {24212534}, issn = {0095-3628}, abstract = {Bacterial counts on the liquid phase of an anaerobic, fixed-bed digester, treating a deproteinated, prefermented cheese whey substrate, were conducted on two different media under aerobic and facultative conditions. Average counts of 16.6×10(6) and 26.5×10(6) ml(-1) were obtained on the two media, with the nutritionally poorer of the two media giving the highest average count. Seventy-five isolates from both media, incubated aerobically as well as in anaerobic jars, were obtained. These isolates as well as 13 reference strains were phenotypically characterized. The similarities between cultures were calculated using the similarity coefficient of Sokal and Michener [16]. The organisms were clustered using the unweighted pair group method, and the results presented as a simplified dendrogram. The isolates could be divided into 3 main groups: gram-negative fermentative rods, mainlyEnterobacter, Klebsiella, andCitrobacter, withKlebsiella as the predominant genus; gram-positive bacteria, mainly enterococci; and gram-negative nonfermentive rods of the generaPseudomonas, Alcaligenes, andAcinetobacter. All the enterobacteria and enterococci were able to produce acetic acid, an intermediate in methanogenesis.}, }
@article {pmid24212466, year = {1986}, author = {Bartha, R}, title = {Biotechnology of petroleum pollutant biodegradation.}, journal = {Microbial ecology}, volume = {12}, number = {1}, pages = {155-172}, pmid = {24212466}, issn = {0095-3628}, abstract = {Procedures designed to meet the physiological needs of petroleum hydrocarbon (PHC) degrading microorganisms are useful in mitigating environmental damage caused by marine and terrestrial PHC spills. By similar approaches, soil can be utilized as a cost-effective biological incinerator for hazardous PHC wastes. Physiological ecology needs to complement genetic engineering efforts for an effective attack on environmental pollution problems.}, }
@article {pmid24212465, year = {1986}, author = {Sahm, H and Brunner, M and Schoberth, SM}, title = {Anaerobic degradation of halogenated aromatic compounds.}, journal = {Microbial ecology}, volume = {12}, number = {1}, pages = {147-153}, pmid = {24212465}, issn = {0095-3628}, abstract = {Recent microbiological findings show how compounds, regarded hitherto as unusual substrates for anaerobic bacteria, are degraded under anaerobic conditions. The complete conversion of halobenzoic acids and halophenolic compounds to methane by lake sediment and sewage sludge microorganisms has been demonstrated. Since haloaromatic compounds are widely used and may be found in such effluents as those from the forest industry, these studies could stimulate a broader interest in anaerobic treatment of industrial waste waters which contain unusual organic compounds.}, }
@article {pmid24212464, year = {1986}, author = {Kilbane, JJ}, title = {Genetic aspects of toxic chemical degradation.}, journal = {Microbial ecology}, volume = {12}, number = {1}, pages = {135-145}, pmid = {24212464}, issn = {0095-3628}, abstract = {All naturally occurring molecules are continuously being recycled in nature, constantly being synthesized, and constantly being degraded. Synthetic molecules on the other hand, often are unable to enter nature's recycling scheme because organisms that have an ability to degrade these xenobiotic compounds simply do not exist. Moreover, many synthetic chemicals are not only recalcitrant to biodegradation, but also are toxic and therefore can cause significant pollution problems even at very low concentrations. The chemical industry will continue to produce an evergrowing number of molecules, even though severe environmental problems have resulted from synthetic molecules already produced. We must find a means of bringing synthetic molecules back into nature's recycling systems if we are to preserve the environment. Biotechnology, through the genetic manipulation of microorganisms, provides a means of accomplishing this goal.}, }
@article {pmid24212463, year = {1986}, author = {Omenn, GS}, title = {Genetic control of environmental pollutants: A conference review.}, journal = {Microbial ecology}, volume = {12}, number = {1}, pages = {129-134}, doi = {10.1007/BF02153228}, pmid = {24212463}, issn = {0095-3628}, }
@article {pmid24212462, year = {1986}, author = {Hunter-Cevera, JC and Sotos, L}, title = {Screening for a "new" enzyme in nature: Haloperoxidase production by Death Valley dematiaceous hyphomycetes.}, journal = {Microbial ecology}, volume = {12}, number = {1}, pages = {121-127}, pmid = {24212462}, issn = {0095-3628}, abstract = {Haloperoxidases are enzymes that have the ability to halogenate a broad range of substrates [10]. To find a biologically produced haloperoxidase that could function at a pH greater than 3.0 and at a temperature greater than 19°C, dematiaceous hyphomycetes were isolated from the Death Valley desert and screened for their ability to produce such an enzyme. A qualitative assay using bromophenol red was employed in situ over a 12-day fermentation period. Several dematiaceous hyphomycetes, such asDreschlera haloides andUlocladium chartarum, produced haloperoxidases that were active in broth culture at 19, 25, and 34°C at pH 7.0 and 8.0.}, }
@article {pmid24212461, year = {1986}, author = {Deming, JW}, title = {The biotechnological future for newly described, extremely thermophilic bacteria.}, journal = {Microbial ecology}, volume = {12}, number = {1}, pages = {111-119}, pmid = {24212461}, issn = {0095-3628}, abstract = {Recent explorations of aquatic volcanic environments have led to the isolation of novel microorganisms with optimal growth temperatures of 80°C or higher. Expectations of equally novel, highly thermostable biocatalysts and specialty chemicals from such organisms remain high but must be tempered with the laboratory realities of manipulating unusual bacteria whose growth characteristics are as yet poorly defined. Advancing the biotechnological future of "super-thermophiles" will require new cultivation methods, including the use of highly thermostable gels and pressurized bioreactors.}, }
@article {pmid24212460, year = {1986}, author = {Bonar, DB and Weiner, RM and Colwell, RR}, title = {Microbial-invertebrate interactions and potential for biotechnology.}, journal = {Microbial ecology}, volume = {12}, number = {1}, pages = {101-110}, pmid = {24212460}, issn = {0095-3628}, abstract = {As the interactions between marine invertebrates and their bacterial commensals and symbionts are better understood, the application of biotechnology will enhance both environmental and economic benefit. In the immediate future, marine bacteria, either selected or genetically engineered, will play a significant role in enhancing the development of selected invertebrates in aquaculture and in the field. Luck may also favor discovery of mechanisms to suppress the development of biofouling species, perhaps by making it possible to coat submerged surfaces with bacterial films designed to repell larvae and/or interfere with larval morphogenesis. In any case, the future is appealing.}, }
@article {pmid24212459, year = {1986}, author = {Staley, JT and Stanley, PM}, title = {Potential commercial applications in aquatic microbiology.}, journal = {Microbial ecology}, volume = {12}, number = {1}, pages = {79-100}, pmid = {24212459}, issn = {0095-3628}, }
@article {pmid24212458, year = {1986}, author = {Okami, Y}, title = {Marine microorganisms as a source of bioactive agents.}, journal = {Microbial ecology}, volume = {12}, number = {1}, pages = {65-78}, pmid = {24212458}, issn = {0095-3628}, abstract = {Several ecological factors of the marine environment were used in developing a strategy for discovering useful bioactive agents from marine microorganisms. By consideration of sea water requirements, production and degradation of marine polymers, and plasmid content, several novel anti-malarial antibiotics, anti-tumor polysaccharides, glucan-degrading enzymes, and aminoglycoside antibiotics were found.}, }
@article {pmid24212457, year = {1986}, author = {Robrish, SA}, title = {Biotechnology and ecological studies on the oral cavity.}, journal = {Microbial ecology}, volume = {12}, number = {1}, pages = {53-64}, pmid = {24212457}, issn = {0095-3628}, }
@article {pmid24212456, year = {1986}, author = {Williams, ST and Vickers, JC}, title = {The ecology of antibiotic production.}, journal = {Microbial ecology}, volume = {12}, number = {1}, pages = {43-52}, pmid = {24212456}, issn = {0095-3628}, abstract = {Over the last 40 years, there has been a steady supply of novel, useful antibiotics produced by microbes isolated from soil and other natural environments. The increased efficiency of screening procedures in the last decade has played a major part in maintaining this supply. However, the selection and sampling of natural environments are still essentially random processes. The main reasons for this are an almost total lack of knowledge of the significance of antibiotics in nature, deficiencies in the taxonomy of antibiotic-producing microbes and its application, and lack of information about the distribution and ecology of known or potential antibiotic producers. The origins of these problems are discussed and some possible solutions are suggested.}, }
@article {pmid24212455, year = {1986}, author = {Phaff, HJ}, title = {Ecology of yeasts with actual and potential value in biotechnology.}, journal = {Microbial ecology}, volume = {12}, number = {1}, pages = {31-42}, pmid = {24212455}, issn = {0095-3628}, }
@article {pmid24212454, year = {1986}, author = {Hobbs, G}, title = {Ecology of food microorganisms.}, journal = {Microbial ecology}, volume = {12}, number = {1}, pages = {15-30}, pmid = {24212454}, issn = {0095-3628}, abstract = {The behavior of microorganisms in foods is governed by the constraints applied to the microflora by a variety of environmental and ecological factors. These include water activity, pH, Eh, chemical composition, the presence of natural or added antimicrobial compounds, and storage temperature, as well as processing factors such as the application of heat and physical manipulation. Control of these factors will govern whether the food spoils or not, whether any microbial health hazard arises, and whether desired microbial processes are successful or not. While much is known about the effects of individual environmental factors, the effects due to their interactions are less understood. The two main problems now facing the food microbiologist are optimization of environmental parameters and the selection of strains with specific properties. A better understanding of the mechanisms of action and interactions between the various environmental factors, coupled with the application of modern techniques to produce strains with particular properties, will lead to optimum use of food supplies and improvements in quality. There is also potential for the development of new and novel foods.}, }
@article {pmid24212453, year = {1986}, author = {Stellwag, EJ and Brenchley, JE}, title = {Genetic engineering of microorganisms for biotechnology.}, journal = {Microbial ecology}, volume = {12}, number = {1}, pages = {3-13}, pmid = {24212453}, issn = {0095-3628}, }
@article {pmid24212452, year = {1986}, author = {Colwell, RR and Demain, AL}, title = {Editorial.}, journal = {Microbial ecology}, volume = {12}, number = {1}, pages = {1-2}, doi = {10.1007/BF02153217}, pmid = {24212452}, issn = {0095-3628}, }
@article {pmid24221503, year = {1985}, author = {Sohier, LP and Bianchi, MA}, title = {Development of a heterotrophic bacterial community within a closed prawn aquaculture system.}, journal = {Microbial ecology}, volume = {11}, number = {4}, pages = {353-369}, pmid = {24221503}, issn = {0095-3628}, abstract = {The quantitative and qualitative development of a heterotrophic bacterial community in seawater was studied throughout an experimental rearing of the prawnPenaeus japonicus. The maturation of juvenile prawns had been carried out for 8 months in aerated tanks of seawater without any water renewal. Bacteria (337 strains) were isolated from seawater, which had been sampled at different times. Samples from one of the mussels used to feed the prawns and from the digestive tract of one prawn each supplied 40 more strains. 101 tests were performed on each strain, and cluster analysis showed the existence of 4 different groups containing 95% of the sampled strains. Characteristics of the various samples and groups were described in terms of ecotype diversities, catabolic potentialities, nutritional capacities, and morpho-physiological groups. Until nitrification attained a steady state, the heterotrophic community clearly decreased in number and was composed mostly of auxotrophic bacteria (pseudomonads andMoraxella-Acinetobacter groups). These bacteria needed growth factors and were unable to use amino acids (group B). At the end of the experiment (7 months) the bacteria isolated from the water were vibrios and enterobacteria, as were those isolated from the prawn and the mussel. They clustered together in group A. The number of strains that clustered with those of natural seawater (group E) decreased steadily during the experimental period.}, }
@article {pmid24221502, year = {1985}, author = {Lee, K and Wong, CS and Cretney, WJ and Whitney, FA and Parsons, TR and Lalli, CM and Wu, J}, title = {Microbial response to crude oil and Corexit 9527: SEAFLUXES enclosure study.}, journal = {Microbial ecology}, volume = {11}, number = {4}, pages = {337-351}, pmid = {24221502}, issn = {0095-3628}, abstract = {The response of marine bacteria to Corexit 9527, with and without Prudhoe Bay crude oil labeled withn-(1-(14)C)hexadecane, in a temperate pelagic environment was monitored over 22 days using controlled ecosystem enclosures. The results indicated that Corexit and Corexit-dispersed crude oil stimulated bacterial production by serving as substrates and/or by inducing the release of organic compounds from the indigenous phytoplankton population. Highest bacterial standing stock was observed in the enclosure treated with a mixture of Corexit and crude oil, in which a large fraction of the predominant bacterivores were eliminated. Biodegradation appeared to be more significant than abiotic processes in contributing to the loss of low volatility n-alkanes in Corexit-dispersed oil. Twenty-two days following its addition, 50% of the radiotracer was recovered: 3% in the suspended particulate fraction, 10% in sedimentary material, 36% as CO2, and less than 1% in the dissolved organic pool.}, }
@article {pmid24221501, year = {1985}, author = {Dicker, HJ and Smith, DW}, title = {Metabolism of low molecular weight organic compounds by sulfate-reducing bacteria in a Delaware salt marsh.}, journal = {Microbial ecology}, volume = {11}, number = {4}, pages = {317-335}, pmid = {24221501}, issn = {0095-3628}, abstract = {Oxidation of acetate, lactate, pyruvate, and ethanol to CO2 in anaerobic salt marsh sediments was rapid, with the oxidation rate being significantly inhibited (60-90% decrease) in the presence of 2 mM sodium molybdate, an inhibitor of sulfate-reducing bacteria (SRB). 2-Bromoethanesulfonic acid (BES), an inhibitor of methanogenic bacteria, generally had no effect on the oxidation rate. Acetate was the only intermediate product detected in the oxidation of lactate and ethanol. Competition studies with lactate, acetate, and ethanol indicated that the preferred order of substrate utilization was lactate, then acetate, then ethanol. The turnover times of these three compounds in salt marsh sediments via the combined CO2 plus acetate pool was rapid (10-13 hours) with a two- to threefold increase in the turnover time in the presence of molybdate. These results strongly suggest that SRB play a major role in the terminal metabolism of low molecular weight organic compounds in anaerobic salt marsh sediment.}, }
@article {pmid24221500, year = {1985}, author = {Dicker, HJ and Smith, DW}, title = {Effects of organic amendments on sulfate reduction activity, H2 consumption, and H 2 production in salt marsh sediments.}, journal = {Microbial ecology}, volume = {11}, number = {4}, pages = {299-315}, pmid = {24221500}, issn = {0095-3628}, abstract = {Sulfate reduction activity (SRA) was measured via the radioactive tracer ((35)SO4 (=)) technique in sediment samples from the Canary Creek Marsh in Lewes, Delaware. Basal levels of SRA ranged from 130 to 319 nmoles of sulfate reduced/gram dry sediment/hour. With the exception of lactate and formate, all organic acids tested resulted in no stimulation of SRA, whereas straight chain alcohols (C1-C4) all gave a significant increase in SRA. In addition, H2, glucose, and cellobiose caused a twofold or greater increase in SRA, while cellulose amendments did not alter SRA. Molybdate, an inhibitor of sulfate-reducing bacteria (SRB), caused a total inhibition in SRA. 2-Bromoethanesulfonic acid (BES), an inhibitor of methanogenic bacteria, caused a slight decrease in SRA. Hydrogen was not produced in detectable quantities in unamended samples but was produced in large amounts in glucose-amended samples. Hydrogen was rapidly consumed in unamended samples with molybdate additions causing a significant decrease in the rate of H2 consumption. A variety of organic amendments was found to stimulate H2 uptake. These studies suggest that SRB are stimulated by a large variety of organic amendments in situ and that SRB play a major role in maintaining low partial pressures of H2 in marsh sediments.}, }
@article {pmid24221499, year = {1985}, author = {Gordon, AS and Millero, FJ}, title = {Adsorption mediated decrease in the biodegradation rate of organic compounds.}, journal = {Microbial ecology}, volume = {11}, number = {4}, pages = {289-298}, pmid = {24221499}, issn = {0095-3628}, abstract = {A negative correlation between adsorption of low molecular weight organic acids and sugars onto a hydroxyapatite surface and biodegradation rates of the compounds in the presence of the mineral was observed. Qualitatively, the effect was the same whether the organics were equilibrated with the surface prior to the addition of organisms or the organisms were preattached to the surface. Glucose, acetic acid, succinic acid, glutamic acid, and citric acid showed equilibrium adsorption values ranging from 0-94% from a 2μM solution. Changes in both respiration and assimilation of the substrates in the presence of hydroxyapatite were inversely correlated with adsorption.}, }
@article {pmid24221498, year = {1985}, author = {Cynar, FJ and Estep, KW and Sieburth, JM}, title = {The detection and characterization of bacteria-sized protists in "Protist-free" filtrates and their potential impact on experimental marine ecology.}, journal = {Microbial ecology}, volume = {11}, number = {4}, pages = {281-288}, pmid = {24221498}, issn = {0095-3628}, abstract = {Nuclepore filters of 0.6-1.0μm pore size have been used to prepare "protist-free" water for a number of studies in microbial ecology. This procedure has been called into question by a recent study claiming that a significant portion of bacterial loss in filtrates could be due to uncharacterized predators passing through 0.6μm filters. We were unable to directly observe protists in 0.6μm filtrates using phase contrast, epifluorescence, or transmission electron microscopy. Using the culture techniques of rice grain enrichment and most probable number, however, we were able to observe and quantify several species of bacterivorous nanoflagellates that developed not only in 0.6μm, but also in 0.4μm seawater filtrates. The ability of predacious nanoflagellates to squeeze through bacteria-sized pores questions studies of bacterial production and chemical cycling that have assumed protist-free filtrates.}, }
@article {pmid24221367, year = {1985}, author = {Rahim, Z and Aziz, KM and Islam, S and Huq, MI}, title = {A preliminary survey of the relative abundance of fecal coliform bacteria in water and sediment and in the fresh water bivalve,Lamellidens marginalis, of the Buriganga river, Bangladesh.}, journal = {Microbial ecology}, volume = {11}, number = {3}, pages = {277-280}, pmid = {24221367}, issn = {0095-3628}, abstract = {Studies on the concentration of fecal coliforms in freshwater bivalves were carried out using a spread plate method and membrane fecal coliform medium. Water, sediment, and bivalves collected from the Buriganga River at Dhaka, Bangladesh, were examined. As demonstrated in many previous studies, fecal coliform counts were consistently higher for the bivalve tissue than those for water and sediment samples; in the bivalveLamellidens marginalis, they were ∼10.0- to 87.0-fold higher than those in water, and 2.0- to 11.0-fold higher than those in sediment.}, }
@article {pmid24221366, year = {1985}, author = {Haanstad, JO and Norris, DM}, title = {Microbial symbiotes of the ambrosia beetleXyloterinus politus.}, journal = {Microbial ecology}, volume = {11}, number = {3}, pages = {267-276}, pmid = {24221366}, issn = {0095-3628}, abstract = {Progression in the understanding of the microecology of ambrosia beetles and their associated microorganisms is briefly reviewed. Between the 1840s and the early 1960s the concept of one ambrosial fungus per ambrosia beetle was emphasized. Some subsequent research has supported the view that each ambrosia beetle plus several associated microorganisms constitute a highly co-evolved symbiotic community. It was hypothesized in this study that such a community of symbiotic microbial species, not just one ambrosial fungus, is actively cultivated and perpetuated by the ambrosia beetleXyloterinus politus. Experimental results indicated that bacteria, yeasts, a yeastlike fungus, and ambrosial fungi compose such a symbiotic microbial complex in association withX. politus. The microecology of the ectosymbiotic microorganisms in relation to this insect is discussed.}, }
@article {pmid24221365, year = {1985}, author = {Nohrstedt, H&#xd6;}, title = {Biological activity in soil from forest stands in Central Sweden, as related to site properties.}, journal = {Microbial ecology}, volume = {11}, number = {3}, pages = {259-266}, doi = {10.1007/BF02010604}, pmid = {24221365}, issn = {0095-3628}, abstract = {The relationship between biological activities in samples from the forest floor and, respectively, stand (site quality class, tree age, and latitude) and soil (pH, carbon, carbon/nitrogen, and available phosphorus) properties was examined in a multi-site study performed in Central Sweden. The biological activities measured were respiration and phosphatase and dehydrogenase activity. The incubations were made in the laboratory on sieved and homogenized samples. When the biological activities were expressed on a dry matter weight basis, the concentration of organic C was the strongest predictor of respiration and phosphatase activity. In contrast, the strongest predictor of dehydrogenase activity was the pH value. Respiration and dehydrogenase activity were not significantly correlated. When excluding the influence of C concentration by expressing the activities on a C weight basis, respiration and phosphatase activity were not significantly correlated with any of the independent variables studied. Curvilinear models (polynomial equations of second and third order) gave significantly better descriptions of the relationship between respiration and, respectively, pH and C/N ratio, than linear models. Optimum conditions for respiration were indicated at intermediate pH (4-5 in 0.01 M CaCl2) and C/N ratio (20-30). The dehydrogenase activity on a C weight basis was correlated with the pH value even more strongly than it was on a dry matter basis. The phosphatase activity was not significantly correlated with the content of available P either on a dry matter basis or on a C weight basis.}, }
@article {pmid24221364, year = {1985}, author = {Smith, MJ and Walton, DW}, title = {A statistical analysis of the relationships among viable microbial populations, vegetation, and environment in a subantarctic tundra.}, journal = {Microbial ecology}, volume = {11}, number = {3}, pages = {245-257}, doi = {10.1007/BF02010603}, pmid = {24221364}, issn = {0095-3628}, abstract = {Parametric and nonparametric analyses were used to investigate the relationships between the populations of viable microbes and 4 edaphic variables - soil moisture, rainfall, temperature, and pH. Microbial populations were sampled over a 2-year period in contrasting grass and moss stands on the subantarctic island of South Georgia. Moisture was found to be the most significant edaphic variable, but there were highly significant correlations between bacterial and fungal populations at both sites. Individual plant species showed clear correlations with both bacterial and fungal populations.}, }
@article {pmid24221363, year = {1985}, author = {Moss, MO and Bryant, TN}, title = {A numerical analysis of counts of diatom frustules, and other algae, in water samples from the River Wey.}, journal = {Microbial ecology}, volume = {11}, number = {3}, pages = {231-243}, pmid = {24221363}, issn = {0095-3628}, abstract = {During May 1978, samples of water were collected from 24 sites on, or associated with, the River Wey between its source south of Haslemere and Send just downstream of Guildford (approx. 57.5 km). Counts of diatom frustules, and other algae surviving the sampling technique, were analyzed by numerical taxonomic techniques. On the basis of community structure, the river was clearly separated into two regions. The seven sites along the first 18 km formed a cluster, and those of the remaining stretch formed a second cluster, which was more similar to Broadwater, a large shallow pond that discharges into the river between Godalming and Guildford (approx. 34.2 km below the source). Two methods are compared for reducing the counts obtained for each sample to a single index.}, }
@article {pmid24221362, year = {1985}, author = {Lewis, TE and Garland, CD and McMeekin, TA}, title = {The bacterial biota on crustose (nonarticulated) coralline algae from Tasmanian waters.}, journal = {Microbial ecology}, volume = {11}, number = {3}, pages = {221-230}, pmid = {24221362}, issn = {0095-3628}, abstract = {The bacterial biota associated with the cuticle surface of healthy benthic samples of crustose nonarticulated coralline algae from the east coast of Tasmania (Australia) was examined by bacteriological cultivation and electron microscopy. In 32 samples studied, the viable count on Zobell's marine agar (supplemented with vitamins) was 3.3×10(6) bacteria g(-1) wet wt. (range 2.9×10(4)-2.7×10(7)). Of 732 strains isolated from 16 out of 32 samples and identified to genus level,Moraxella was the predominant genus (66%). In contrast,Moraxella comprised only 11% of 217 strains isolated from benthic seawater samples collected at the same time as coralline algae. In 22 out of 32 algal samples examined by scanning electron microscopy, the total count was 1.6 × 10(7) bacteria g(-1) wet wt. (range 5.1× 10(6)-3.8×107); the major morphotype was cocco-bacilli (80%). Several environmental factors did not significantly influence the viable count or generic distribution, or the total count or morphotypic distribution of bacteria on the cuticle. These factors included geographical site, season, storage of samples in aquarium conditions, and the presence or absence of abalone from shells that the coralline algae encrusted. The microbiota, consisting mostly of the nonmotile bacterial genusMoraxella, appeared to be highly adapted to its calcerous plant host.}, }
@article {pmid24221361, year = {1985}, author = {Gehlen, M and Trampisch, HJ and Dott, W}, title = {Physiological characterization of heterotrophic bacterial communities from selected aquatic environments.}, journal = {Microbial ecology}, volume = {11}, number = {3}, pages = {205-219}, pmid = {24221361}, issn = {0095-3628}, abstract = {Three different biotopes, groundwater, surface water, and activated sludge, were examined and the total colony count on nutrient agar determined. The bacteria that could be isolated from the agar plates were identified and their in vitro activities investigated. Three principal approaches were used: (1) isolates were identified and the results used in a numerical analysis to determine their similarity; (2) the different physiological properties of isolates originating from a single biotope were compiled and used to characterize the community (collective total activity); and (3) the diversity of the physiological properties of the isolates of all populations was determined; on the basis of main characters a "heterotrophic" diversity index was calculated. The possibility of using a polyphasic ecological study to characterize aquatic bacterial communities is considered.}, }
@article {pmid24221360, year = {1985}, author = {Güde, H}, title = {Influence of phagotrophic processes on the regeneration of nutrients in two-stage continuous culture systems.}, journal = {Microbial ecology}, volume = {11}, number = {3}, pages = {193-204}, pmid = {24221360}, issn = {0095-3628}, abstract = {Regeneration of nutrients in aquatic ecosystems may be affected by autolysis, bacterial degradation, and activities of phagotrophic organisms. To examine the relative importance of these processes, mineralization of carbon, nitrogen, and phosphorus was studied in a two-stage continuous culture system. In the first stage (production compartment), aChlorella sp. was grown either axenically or in the presence of bacteria under P-limited conditions. In the presence of bacteria, the biomass of algae decreased due to efficient competition for P by bacteria. In the second stage (remineralization compartment), which was kept continuously in the dark, the nutrients incorporated by the organisms in the first stage were remineralized only slightly (0-25%) irrespective of the presence or absence of bacteria. However, remineralization of all nutrients tested was strongly increased (60-80%) after addition of zooflagellates, which grazed on algae and bacteria. These observations suggest that a net regeneration of nutrients was provided by phagotrophic organisms, whereas nutrients were trapped rather than released by bacteria. It is concluded that nutrient cycling could probably not proceed at the high velocities observed in the field without the participation of phagotrophic organisms.}, }
@article {pmid24221359, year = {1985}, author = {Boyer, JN and Kator, HI}, title = {Method for measuring microbial degradation and mineralization of(14)C-labeled chitin obtained from the blue crab,Callinectes sapidus.}, journal = {Microbial ecology}, volume = {11}, number = {3}, pages = {185-192}, pmid = {24221359}, issn = {0095-3628}, abstract = {A method for measuring microbial degradation and mineralization of radiolabeled native chitin is described.(14)C-labeled chitin was synthesized in vivo by injecting shed blue crabs (Callinectes sapidus) with N-acetyl-D-[1-(14)C]-glucosamine and allowing for its incorporation into the exoskeleton. The cuticle had a total organic carbon content of 0.48 mg C mg(-1) with a specific radioactivity of 6,356 CPM mg(-1). Glucosamine, i.e., chitin content as determined colorimetrically, was 22% (w/w). Microbial degradation and mineralization rates were assessed in batch culture using(14)C-chitin as substrate and York River water as inoculum. Replicate flasks were sampled daily for enumeration of chitinoclastic bacteria and the radiolabel recovered as particulate(14)C-chitin or(14)CO2. The amount of(14)CO2 generated was directly proportional to the loss of particulate(14)C-chitin, with 96% of the added label recovered as the sum of both phases. The maximum rate of mineralization was 207 mg day(-1) g(-1) seeded(14)C-chitin at 20°C. Highest chitinoclastic bacterial counts corresponded to the period of maximum rate of chitinolysis. It is suggested that the rate of chitin mineralization is limited by exoenzymatic depolymerization and not by chitin concentration.}, }
@article {pmid24221305, year = {1985}, author = {Lussenhop, J and Wicklow, DT}, title = {Interaction of competing fungi with fly larvae.}, journal = {Microbial ecology}, volume = {11}, number = {2}, pages = {175-182}, pmid = {24221305}, issn = {0095-3628}, abstract = {Saprophytic fungi have degradative abilities and interspecific interactions which suggest that resource use and yield should increase as species number increases, but previous studies show the opposite. As a test of the possibility that invertebrate activity changes fungal resource use patterns, we grew coprophilous fungi on rabbit feces at the same initial density singly or in mixtures of 2, 4, or 6 species, with or without activity of larvalLycoriella mali (Diptera: Sciaridae). Fungi in mixtures without larvae caused less weight loss in one mixture, and greater weight loss in 2 mixtures than when growing alone; fungi in 4 of 6 mixtures produced fewer spores than when growing alone. Overall, without larvae, weight loss did not increase as number of fungal species increased. Larvae did not change the pattern of weight loss or proportions of spores caused by mixing fungal species. Numbers of larvae surviving to pupate rose as fungal species numbers increased; as a result, weight loss increased with fungal species number in cultures with larvae.}, }
@article {pmid24221304, year = {1985}, author = {Fogleman, JC and Starmer, WT}, title = {Analysis of the community structure of yeasts associated with the decaying stems of cactus. III.Stenocereus thurberi.}, journal = {Microbial ecology}, volume = {11}, number = {2}, pages = {165-173}, pmid = {24221304}, issn = {0095-3628}, abstract = {Yeast communities in necroses of organpipe cactus (Stenocereus thurberi) were surveyed at 3 localities in Arizona. Quantitative analysis of random samples allows comparisons of the types and numbers of yeasts at 3 levels: within plants, between plants within a locality, and between localities. The analysis shows that the major source of variability is between plants. This pattern is identical with the pattern shown by agria cactus (Stenocereus gummosus) and is thought to be due to sampling different successional stages. No significant differences in estimates of the effective number of yeast species (ENS) in agria and organpipe samples were found. Comparisons of agria, organpipe, and prickly pear (Opuntia) cacti support the hypothesis that cactus chemistry is an important determinant of the yeast community structure which, in turn, is an important determinant of the diversity ofDrosophila species which utilize necrotic cacti as feeding and breeding substrates.}, }
@article {pmid24221303, year = {1985}, author = {Lemos, ML and Toranzo, AE and Barja, JL}, title = {Antibiotic activity of epiphytic bacteria isolated from intertidal seaweeds.}, journal = {Microbial ecology}, volume = {11}, number = {2}, pages = {149-163}, pmid = {24221303}, issn = {0095-3628}, abstract = {A survey of antibiotic-producing bacteria from the microbial flora attached to seaweeds and the study of their antibiotic capacities were carried out. From 5 species of green and brown marine algae, 224 bacterial strains were isolated and tested for antibiotic production. A total of 38 strains displayed antibiotic activity, withEnteromorpha intestinalis being the source of the highest number of producer strains. All epiphytic bacteria with antibiotic activity were assigned to thePseudomonas-Alteromonas group. Antagonism assays among the isolates demonstrated that each producer strain inhibits the growth of the other producers, as well as of some nonproducer strains also isolated from seaweeds. Likewise, an autoinhibitory effect was observed in all antibiotic-producing strains. Antibacterial spectra of all the strains include activity againstStaphylococcus, Alcaligenes, Pseudomonas, Vibrio, Pasteurella, andAchromobacter. A preliminary characterization of the antibiotic substances produced by these epiphytic bacteria demonstrated that they are low molecular weight compounds, thermolabile, and anionic and are not affected by proteolytic enzymes. The role that these inhibitory substances can play in the natural environment is discussed.}, }
@article {pmid24221302, year = {1985}, author = {Jardim, WF and Pearson, HW}, title = {Copper toxicity to cyanobacteria and its dependence on extracellular ligand concentration and degradation.}, journal = {Microbial ecology}, volume = {11}, number = {2}, pages = {139-148}, pmid = {24221302}, issn = {0095-3628}, abstract = {Copper toxicity to the cyanobacteriumPlectonema boryanum (UTEX 594) has been investigated in the presence of citrate and nitrilotriacetic acid (NTA) using a copper-saturated culture medium. The coppercitrate complex was biodegradable, and toxicity was dependent on the free ligand concentration. The ratio of citrate to copper also affected the extent of metal toxicity. NTA was not degraded byP. boryanum. Ligand degradation in the cyanobacterial culture increased the ionic copper concentration and caused a concomitant reduction in growth. The ecological implications of these findings are discussed.}, }
@article {pmid24221301, year = {1985}, author = {Cooney, JJ and Silver, SA and Beck, EA}, title = {Factors influencing hydrocarbon degradation in three freshwater lakes.}, journal = {Microbial ecology}, volume = {11}, number = {2}, pages = {127-137}, pmid = {24221301}, issn = {0095-3628}, abstract = {The mixed microbial flora of 3 lakes in Ohio with differing histories of hydrocarbon pollution was examined in relation to the ability to use hydrocarbons. Weathered kerosene was spiked with naphthalene, pristane, 1,13-tetradecadiene, andn-hexadecane and added to water-sediment mixtures from the 3 lakes, and utilization of the 4 marker hydrocarbons was measured. Each of the marker hydrocarbons was metabolized; naphthalene was the most readily used and pristane was the most resistant. Values for dissolved oxygen suggest that oxygen did not limit hydrocarbon degradation in the water column at any site examined. Nutrient addition studies indicated that nitrogen and phosphorus limited hydrocarbon degradation at all sites examined. Maximum numbers of heterotrophic bacteria were detected when the water temperature was 10°C or higher. The data indicate that temperature limits hydrocarbon degradation in the winter, except at a site which had been impacted by an oil spill and which received chronic inputs of hydrocarbons and nutrients. In samples from that site, all 4 marker hydrocarbons were degraded at 0°C. Results of temperature and nutrient-addition experiments suggest that different seasonal populations of hydrocarbon users are selected at that site, but not at other lake sites.}, }
@article {pmid24221300, year = {1985}, author = {Laanbroek, HJ and Blok, JP and Steenhuis, L}, title = {Variability in fermentation patterns of sugar-utilizing bacteria isolated from anaerobic, intertidal sediments.}, journal = {Microbial ecology}, volume = {11}, number = {2}, pages = {117-125}, pmid = {24221300}, issn = {0095-3628}, abstract = {Three dominant types of sugar-fermenting bacteria were isolated from the anaerobic, intertidal sediments of the Eems-Dollard estuary by applying techniques involving anaerobic agar shake tubes. One of the isolated types was tentatively identified as aStreptococcus species, the other two asBacteroides species. All types were versatile with respect to the utilization of sugars. The fermentation patterns of two types were dependent upon conditions of cultivation. In glucose-limited cultures ofStreptococcus strain NS.G52, the production of lactate was suppressed in favor of formate, acetate, and ethanol. In glucose-limited syntrophic cultures withMethanospirillum hungatei, Bacteroides strain NS.G42 was forced to produce acetate and hydrogen at the expense of ethanol. The fermentation pattern ofBacteroides strain NS.S42, which consisted of acetate, propionate, and succinate, was not affected by conditions of cultivation.}, }
@article {pmid24221299, year = {1985}, author = {Rodriguez-Valera, F and Ventosa, A and Juez, G and Imhoff, JF}, title = {Variation of environmental features and microbial populations with salt concentrations in a multi-pond saltern.}, journal = {Microbial ecology}, volume = {11}, number = {2}, pages = {107-115}, pmid = {24221299}, issn = {0095-3628}, abstract = {A multi-pond saltern that creates a gradient of salt concentrations has been studied with respect to some characteristics of the resulting environments and their microbial populations. The increase in salt concentration was correlated with increase in diurnal temperature and biomass present and with decrease in oxygen concentrations. Many types of organisms below 15% (w/v) total salts, were found, many of them normal inhabitants of seawater and even freshwater. Most organisms over 15% salts were halophilic. The salt concentrations comprised two ranges, each characterized by different microbial populations. First, between 15 and 30% salts, the populations ofDunaliella increased, reaching large numbers; moderately halophilic eubacteria and some fast-growing halobacteria predominated as heterotrophic microorganisms and, among the first, thePseudomonas-Alteromonas-Alcaligenes group andVibrio were the more abundant taxonomic groups; and gram-positive cocci appeared mainly over 25% salts. Phototrophic bacteria, both oxygenic and anoxygenic, were also found in this range, and among the anoxygenic type,Chromatium species andRodospirillum salexigens were probably predominant. Second, over 30% salts the diversity decreased greatly, all organisms found at the lower salt concentrations disappeared, and instead large populations of halobacteria developed. Over 50% salts, only three species of halobacteria were found.}, }
@article {pmid24221298, year = {1985}, author = {Hermansson, M and Marshall, KC}, title = {Utilization of surface localized substrate by non-adhesive marine bacteria.}, journal = {Microbial ecology}, volume = {11}, number = {2}, pages = {91-105}, pmid = {24221298}, issn = {0095-3628}, abstract = {Thirty-four marine bacteria were isolated from the eluate of seawater passed through a column of glass beads coated with stearic acid. Irreversible attachment of these isolates to stearic acid-coated glass surfaces ranged from 7.6-100% of the total attached population, with 7 isolates exhibiting less than 10% irreversible adhesion. All 14 isolates tested were able to utilize surface bound(14)C-stearic acid, even though some showed mostly reversible adhesion to the surface. More detailed studies were made comparing the reversibly adheringVibrio MH3 with the irreversibly adheringPseudomonas NCMB2021. MH3 cells were readily removed from the surface by a gentle shear force, and a significant degree of(14)C-labeling of MH3 cells, but not of NCMB2021 cells, in the bulk phase was observed. The ecological significance of nutrient scavenging at solid surfaces by reversibly attached bacteria is considered.}, }
@article {pmid24221242, year = {1985}, author = {Molitoris, E and McKinley, G and Krichevsky, MI and Fagerberg, DJ}, title = {Comparison of conventional and miniaturized biochemical techniques for identification of animal streptococcal isolates.}, journal = {Microbial ecology}, volume = {11}, number = {1}, pages = {81-90}, pmid = {24221242}, issn = {0095-3628}, abstract = {Human clinical streptococcal isolates can be identified rapidly by means of commercially available miniaturized biochemical systems, in contrast to animal and environmental isolates which may require extensive characterization using conventional methods. Streptococcal isolates (n=548) from fresh animal feces of cattle, swine, and broiler chickens were tested by means of conventional biochemical and physiological techniques, and also with a miniaturized technique in which conventional formulations were dispensed in 0.1 ml volume into microtiter plates. Agreement of the positive feature frequencies of the two methods were compared. Results from the tolerance tests in the two methods were generally in good agreement. However, the miniaturized method tended to give false negative results in some carbohydrate fermentation tests. Agreement between the 2 methods ranged from 100% for bile esculin tests to 71% for raffinose fermentation. Cluster analysis of the conventional method data indicated that there were 11 biochemically related groups of isolates, 2 of which were identified asStreptococcus faecalis, andS. morbillorum. Half of the isolates biochemically resembledS. faecium. Errors of miniaturized tests occurred mainly in certain tests and in certain biochemically related clusters of isolates. The data indicate that further investigation of experimental conditions such as medium formulation and inoculum size could lead to a successful miniaturized technique for testing animal streptococcal isolates.}, }
@article {pmid24221241, year = {1985}, author = {Srivastava, AC and Turner, J and Hughes, DE and Griffiths, AJ}, title = {A taxonomic and ecological study of candidosis.}, journal = {Microbial ecology}, volume = {11}, number = {1}, pages = {71-79}, pmid = {24221241}, issn = {0095-3628}, abstract = {A total of 450 yeast isolates were obtained from up to 34 sites on 59 human subjects. The yeasts were characterized using morphological features and assimilation tests. Ten species were identified but, of these,Candida albicans andCandida parapsilosis were the most common and accounted for 84% of the isolates. An examination of the biotypes of the various species indicated a much greater diversity in the yeast microflora than that detected by species identifications alone. Fifty-five biotypes were differentiated and it is suggested that these could be regarded as distinct taxonomic or ecological entities.}, }
@article {pmid24221240, year = {1985}, author = {Orpin, CG}, title = {Association of rumen ciliate populations with plant particles in vitro.}, journal = {Microbial ecology}, volume = {11}, number = {1}, pages = {59-69}, pmid = {24221240}, issn = {0095-3628}, abstract = {Seven known species of rumen ciliates and mixedEntodinium spp. showed association with plant particles in rumen fluid in vitro. Association was greater with fresh particles than with hay, and substantially decreased when the water-soluble components of the particles were removed, suggesting that the water-soluble components may be responsible for the association. The association was rapid and maximal between 5 and 35 min (depending on the ciliate species) after exposure to the particles, and involved major transfers of ciliate populations and biomass from the liquid phase to the solid phase of the system. The most rapid and largest population transfers to the particles from the rumen fluid were shown by the holotrich ciliates, where transfers of up to 97% of the population were recorded. Association with plant particles by all species examined occurred within the pH range 5.5-7.5, and decreased with time when the particles were incubated in rumen contents in vivo. The ciliate biomass transferring from the liquid to the solid phase varied with the composition of the ciliate population.}, }
@article {pmid24221239, year = {1985}, author = {Sandhu, DK and Waraich, MK}, title = {Yeasts associated with pollinating bees and flower nectar.}, journal = {Microbial ecology}, volume = {11}, number = {1}, pages = {51-58}, pmid = {24221239}, issn = {0095-3628}, abstract = {A study of the yeast flora of 328 honey stomachs from 7 different pollinating bee species, and 342 flower nectar samples of 9 different flower species yielded 766 yeast isolates composed of 16 genera and 47 species. Most of the yeast species from both the sources belonged to the genusCandida, while the most frequently isolated yeasts wereDekkera intermedia from honey stomach andCandida blankii from flower nectar. Among the honey bees,Xylocopa sp., and among flowers,Citrus medica, yielded the highest number of yeast species. Nineteen species of yeasts belonging to 9 genera were common to both the sources.}, }
@article {pmid24221238, year = {1985}, author = {Ercolani, GL}, title = {Factor analysis of fluctuation in populations ofPseudomonas syringae pv.savastanoi on the phylloplane of the olive.}, journal = {Microbial ecology}, volume = {11}, number = {1}, pages = {41-49}, pmid = {24221238}, issn = {0095-3628}, abstract = {Populations ofPseudomonas syringae pv.savastanoi on the surface of olive leaves were monitored quarterly from 1974 to 1981. Seven microbiological parameters were measured: the density of the bacteria on the leaves unfolded in March, in June, and in September; the density of the bacteria on random leaves; the mean vigor of bacterial isolates obtained at each sampling time; and the similarity between the isolates, based on both the simple matching coefficient and the pattern coefficient. Seven environmental parameters were also recorded: the mean temperature, the rainfall, and the frequency and velocity of east and west winds during a period of 30 days before each sampling; the rate of turnover of the leaves during the same period; the number of pollen grains on the leaves at the time of sampling; and the 5-day biochemical oxygen demand of the wash water of leaves in each sample. Factor analysis led to extraction of 7 factors that accounted for 70.69%-92.80% of the maximum variance of every microbiological parameter and 68.92%-96.62% of the maximum variance of every environmental parameter. The factors were identified as "cambial activity", "leaf age", "summertime", "time of blossoming", "summer rains", "winter rains", and "warm weather fronts." More than 43% of the total parameter variance was loaded in the first 2 factors. Higher communality values (>86% of maximum variance) were obtained for the microbiological parameters based on the distribution of phenotypic characters among the bacterial isolates than for those based on bacterial densities on the phylloplane.}, }
@article {pmid24221237, year = {1985}, author = {Fuhs, GW and Chen, M and Sturman, LS and Moore, RS}, title = {Virus adsorption to mineral surfaces is reduced by microbial overgrowth and organic coatings.}, journal = {Microbial ecology}, volume = {11}, number = {1}, pages = {25-39}, pmid = {24221237}, issn = {0095-3628}, abstract = {In experiments with strains of poliovirus, reovirus, echovirus, and Coxsackievirus, overgrowth with exopolymer-forming bacteria reduced virus adsorption to mineral surfaces. Adsorption was improved when organic materials adsorbed to minerals were removed by low-temperature ashing. In a soil series, virus adsorption increased with soil depth. This paralleled a decrease in organic content, but differences in charge development of the soil particles may also be involved. Prolonged (40-year) irrigation with treated sewage effluents, leading to a buildup of organic coatings, also decreased adsorption. However, saturation of the virus-binding capacity of the soil as a result of continuous exposure to virus-containing effluents was not apparent.}, }
@article {pmid24221236, year = {1985}, author = {Li, WK and Dickie, PM}, title = {Metabolic inhibition of size-fractionated marine plankton radiolabeled with amino acids, glucose, bicarbonate, and phosphate in the light and dark.}, journal = {Microbial ecology}, volume = {11}, number = {1}, pages = {11-24}, pmid = {24221236}, issn = {0095-3628}, abstract = {The effects of various metabolic inhibitors (dichlorophenyl dimethylurea, chloramphenicol, cycloheximide, carbonyl cyanide m-chlorophenyl hydrazone) on the accumulation of radiolabeled substrates (amino acids, glucose, bicarbonate, phosphate) by size-fractionated marine microbial plankton from the Sargasso Sea and the eastern Canadian arctic were studied in time-course fashion during experimental incubations either exposed to or shielded from ambient solar radiation. Picoplankton accounted for ≥65% of the organic substrates and phosphate accumulated by the assemblages. The rate of organic substrate accumulation was stimulated by solar radiation in some cases but inhibited in other cases. Presumably, stimulation and inhibition co-occur and the measured response is the net result arising from these counteracting tendencies. Approximately 40% of H(14) CO3 (-) accumulation in the Sargasso Sea was associated with the picoplankton. The insensitivity of picoplankton(14)C-labeling to cycloheximide suggested active prokaryotic photosynthesis rather than heterotrophic assimilation of(14)C-labeled algal photosynthates as the route of labeling. The usefulness of some inhibitors was restricted in this study because of inconsistent correlations between the intended primary metabolic effect and the measured ecological response within the duration of the experiment.}, }
@article {pmid24221235, year = {1985}, author = {Lovell, CR and Konopka, A}, title = {Excretion of photosynthetically fixed organic carbon by metalimnetic phytoplankton.}, journal = {Microbial ecology}, volume = {11}, number = {1}, pages = {1-9}, pmid = {24221235}, issn = {0095-3628}, abstract = {The effects of light intensity, oxygen concentration, and pH on the rates of photosynthesis and net excretion by metalimnetic phytoplankton populations of Little Crooked Lake, Indiana, were studied. Photosynthetic rates increased from 1.42 to 3.14 mg C·mg(-1) chlorophylla·hour(-1) within a range of light intensities from 65 to 150μE·m(-2)·sec(-1), whereas net excretion remained constant at 0.05 mg C·mg(-1) chlorophylla·hour(-1). Bacteria assimilated approximately 50% of the carbon released by the phytoplankton under these conditions. Excreted carbon (organic compounds either assimilated by bacteria or dissolved in the lake water) was produced by phytoplankton at rates of 0.02-0.15 mg C·mg(-1) chlorophylla·hour(-1). These rates were 6%-13% of the photosynthetic rates of the phytoplankton. Both total excretion of carbon and bacterial assimilation of excreted carbon increased at high light intensities whereas net excretion remained fairly constant. Elevated oxygen concentrations in samples incubated at 150μE· m(-2)·sec(-1) decreased rates of both photosynthesis and net excretion. The photosynthetic rate increased from 3.0 to 5.0 mg C·mg(-1) chlorophylla· hour(-1) as the pH was raised from 7.5 to 8.8. Net excretion within this range decreased slightly. Calculation of total primary production using a numerical model showed that whereas 225.8 g C·m(-2) was photosynthetically fixed between 12 May and 24 August 1982, a maximum of about 9.3 g C·m(-2) was released extracellularly.}, }
@article {pmid24221180, year = {1984}, author = {Barker, JS and East, PD and Phaff, HJ and Miranda, M}, title = {The ecology of the yeast flora in necroticOpuntia cacti and of associatedDrosophila in Australia.}, journal = {Microbial ecology}, volume = {10}, number = {4}, pages = {379-399}, pmid = {24221180}, issn = {0095-3628}, abstract = {A survey was made of the yeast communities isolated from necrotic tissue of 4 species of prickly-pear cacti (Opuntia stricta, O. tomentosa, O. monacantha, andO. streptacantha) which have colonized in Australia. Yeast communities were sampled from a number of localities and at different times. Cactus specific yeasts accounted for 80% of the total isolates, and the 3 most common species contributed 63% of the total. Comparisons of the species compositions of the yeast communities indicated that the differences among communities were greater betweenOpuntia species than between different localities within a single cactus species, and also that differences between years were greater than average differences between localities within years. Multivariate statistical tests of association between yeast community and physical features of rots indicated that temperature, pH, and age of rot all exerted some influence on the structure of the yeast community. Similar analyses involvingDrosophila species inhabiting these cactus rots suggested the existence of complex associations betweenDrosophila community, yeast community, and physical and chemical attributes of the cactus necroses.}, }
@article {pmid24221179, year = {1984}, author = {Blackwell, M and Gilbertson, RL}, title = {Distribution and sporulation phenology of myxomycetes in the Sonoran Desert of Arizona.}, journal = {Microbial ecology}, volume = {10}, number = {4}, pages = {369-377}, pmid = {24221179}, issn = {0095-3628}, abstract = {All pith samples from 68 dead saguaro cacti in 3 plots and 11 isolated dead plants in Saguaro National Monument, Arizona, produced at least one species of myxomycete upon incubation at 20 or 30°C. Three species,Badhamia gracilis (Macbr.) Macbr.,Physarum straminipes Lister, andDidymium eremophilum M. Blackwell et Gilbertson, developed at high frequencies on the substrates in moist chamber culture.Perichaena corticalis (Batsch) Rost, andProtophysarum phloiogenum M. Blackwell et Alexopoulos were also present. Although previous literature reports [9] indicated that Myxomycetes grow best at low pH, these species all tolerated substrates of pH 8.7-10.4.Didymium eremophilum andP. phloiogenum had peaks in sporulation within 6 days; other species were slower. There was no difference in time of sporulation ofB. gracilis orD. eremophilum at 20 and 30°C; however, sporulation ofP. straminipes was significantly later at 30°C. Reduced spore germination and slower buildup of critically sized amoebal populations ofP. straminipes at 30°C may be a factor.}, }
@article {pmid24221178, year = {1984}, author = {Apajalahti, JH and Salkinoja-Salonen, MS}, title = {Absorption of pentachlorophenol (PCP) by bark chips and its role in microbial PCP degradation.}, journal = {Microbial ecology}, volume = {10}, number = {4}, pages = {359-367}, pmid = {24221178}, issn = {0095-3628}, abstract = {A pentachlorophenol (PCP)-degrading mixed bacterial population was enriched in a biofilter filled with soft wood bark chips. We found that bark chips were essential for the degradation to proceed at PCP concentrations higher than 10μM. PCP-degrading bacteria were found to be extremely sensitive to PCP. Bark chips absorbed PCP reversibly, thus detoxifying the medium and allowing degradation to proceed at higher concentrations of PCP (beyond 200μM).}, }
@article {pmid24221177, year = {1984}, author = {Ingham, ER and Coleman, DC}, title = {Effects of streptomycin, cycloheximide, Fungizone, captan, carbofuran, cygon, and PCNB on soil microorganisms.}, journal = {Microbial ecology}, volume = {10}, number = {4}, pages = {345-358}, pmid = {24221177}, issn = {0095-3628}, abstract = {Eight biocides were chosen to determine whether they had any effects on nontarget organisms in soil and to what extent they would reduce their target populations under laboratory experimental conditions. A simplified microcosm system was utilized in which reduced species arrays that included field populations of either only bacteria and fungi, or bacteria, fungi, and protozoa (no nematodes, arthropods, or plants) were inoculated into sterilized soil. In a second set of experiments, plants were grown in sterilized soil. A bactericide-streptomycin-four fungicides-cycloheximide, Fungizone (amphotericin B), captan, and PCNB (quintozene)-an acaricide-cygon-an insecticide-nematicide-carbofuran-and an insecticide-diazinon-were used. Each biocide had effects on nontarget organisms although the increases or decreases, with respect to the control, were of only limited duration. Reductions in target groups were typically of longer duration. Streptomycin, applied at 1 mg·g(-1) soil, did not decrease bacterial populations during the experimental incubation. At 3 mg·g(-1) soil, streptomycin decreased the numbers of bacteria that grew on tryptone agar, but also reduced active hyphae. Fungizone was the most effective of the 4 fungicides tested in reducing active hyphae. Increased bacterial populations were usually observed following fungal reductions. Carbofuran had the fewest effects on the test organisms (bacteria, fungi, and protozoa). Only an initial stimulation of bacterial and fungal populations was observed with cygon although it also increased NH4 (+)-N concentrations in soil during most of the incubation, as did streptomycin and cycloheximide. A transitory increase in fungal populations following a decrease in ciliate numbers was observed in the cygon with grazers treatments. Diazinon reduced all microbial populations and inorganic nitrogen concentrations measured. Cygon and PCNB decreased growth of blue grama plants, while streptomycin reduced shoot weights of blue grama. These results should be useful in assessing the effects of these biocides when applied to more complex systems.}, }
@article {pmid24221176, year = {1984}, author = {Bott, TL and Kaplan, LA and Kuserk, FT}, title = {Benthic bacterial biomass supported by streamwater dissolved organic matter.}, journal = {Microbial ecology}, volume = {10}, number = {4}, pages = {335-344}, pmid = {24221176}, issn = {0095-3628}, abstract = {Bacterial biomass in surface sediments of a headwater stream was measured as a function of dissolved organic carbon (DOC) flux and temperature. Bacterial biomass was estimated using epifluorescence microscopic counts (EMC) and ATP determinations during exposure to streamwater containing 1,788μg DOC/liter and after transfer to groundwater containing 693μg DOC/liter. Numbers of bacteria and ATP concentrations averaged 1.36×10(9) cells and 1,064 ng per gram dry sediment, respectively, under initial DOC exposure. After transfer to low DOC water, biomass estimates dropped by 53 and 55% from EMC and ATP, respectively. The decline to a new steady state occurred within 4 days from ATP assays and within 11 days from EMC measures. A 4°C difference during these exposures had little effect on generation times. The experiment indicated that 27.59 mg/hour of natural DOC supported a steady state bacterial biomass of approximately 10μg C/g dry weight of sediment (from EMC determinations). Steady state bacterial biomass estimates on sediments that were previously muffled to remove organic matter were approximately 20-fold lower. The ratio of GTP∶ATP indicated differences in physiological condition or community composition between natural and muffled sediments.}, }
@article {pmid24221175, year = {1984}, author = {Cooper, AB}, title = {Activities of benthic nitrifiers in streams and their role in oxygen consumption.}, journal = {Microbial ecology}, volume = {10}, number = {4}, pages = {317-334}, pmid = {24221175}, issn = {0095-3628}, abstract = {The in situ rates of oxygen consumption by benthic nitrifiers were estimated at 11 study sites in 4 streams. Two methods were used: an in situ respiration chamber method and a method involving conversion of nitrifying potential measurements to in situ rates. Estimates of benthic nitrogenous oxygen consumption (BNOC) rate ranged from 0-380 mmol of O2 m(-2)·day(-1), and BNOC contributed between 0-85% of the total benthic oxygen consumption rate. The activity of nitrifiers residing in the sediments was influenced by O2 availability, temperature, pH, and substrate. Depending upon site, nitrification could approximate either first-order or zero-order kinetics with respect to ammonium concentration. The source of ammonium for benthic nitrifiers could be either totally from within the sediment or totally from the overlying water. Nitrate produced in the sediments could flux to the water above or be lost within the sediment. The sediments could act as a source (positive flux) or sink (negative flux) for both ammonium (-185 mmol·m(-2)·day(-1) to +195 mmol·m(-2)·day(-1)) and nitrate (-135 mmol·m(-2)·day(-1) to +185 mmol·m(-2)·day(-1)).This study provides evidence to suggest that measurements of down-stream mass flow changes in inorganic nitrogen forms may give poor estimates of in situ rates of nitrification in flowing waters.}, }
@article {pmid24221174, year = {1984}, author = {Jørgensen, NO and Søndergaard, M}, title = {Are dissolved free amino acids free?.}, journal = {Microbial ecology}, volume = {10}, number = {4}, pages = {301-316}, pmid = {24221174}, issn = {0095-3628}, abstract = {Microbial assimilation of 3 amino acids (glutamic acid, alanine, and ornithine) was characterized in 3 lakes and 2 marine stations using the Michaelis-Menten kinetic approach. The calculated Kt + Sn concentrations were related to chemical concentration measurements of dissolved free amino acids (DFAA) to evaluate the biological and the chemical determinations of the DFAA pools. Concentrations of Kt + Sn always were larger than chemical measurements of the Sn concentrations. Kt + Sn and Sn varied from 11.5 and 9.5 nM (alanine, oligotrophic lake) to 288.7 and 89.9 nM (ornithine, marine harbor station), respectively. Subtracting Sn from the Kt + Sn concentrations, Kt was found to range from 12-897% of the chemically measured Sn concentrations. To test whether the DFAA actually were free, dissolved molecules, dissolved material in the water samples was separated into various molecular size classes by means of gel permeation chromatography. From 47-116% of the DFAA in the untreated water samples was recovered in the low molecular fraction (<700 Daltons). Variation in recoveries mainly appeared to be due to an incomplete chromatographic separation and difficulties in obtaining proper blank levels. The present observations suggest that labeled tracers can be used in the study of DFAA assimilation and that the DFAA are free, dissolved molecules. This partly conflicts with previously published reports.}, }
@article {pmid24221173, year = {1984}, author = {Brock, TD}, title = {How sensitive is the light microscope for observations on microorganisms in natural habitats?.}, journal = {Microbial ecology}, volume = {10}, number = {4}, pages = {297-300}, doi = {10.1007/BF02015555}, pmid = {24221173}, issn = {0095-3628}, abstract = {Theoretical calculations based on the depth of field of standard microscope objectives and the visual acuity of normal observors show that direct microscopy of natural samples is rarely able to reveal the presence of small microorganisms at the densities found in natural systems. Over-estimation of the importance of bacterial aggregates is also likely from an uncritical use of light microscopy.}, }
@article {pmid24221149, year = {1984}, author = {Mallory, LM and Sayler, GS}, title = {Application of FAME (fatty acid methyl ester) analysis in the numerical taxonomic determination of bacterial guild structure.}, journal = {Microbial ecology}, volume = {10}, number = {3}, pages = {283-296}, pmid = {24221149}, issn = {0095-3628}, abstract = {Comparative numerical taxonomic analyses, using fatty acid methyl ester (FAME) profiles and phenetic characteristics, were conducted to examine bacterial guild structure in freshwater sediments. Both approaches were used to examine a subset of 60 OTUs obtained from a previously well characterized microbial community in sediments of a shallow fast flowing stream. For both classifications, greater than 80% of the OTUs were recovered in 11 and 12 major groups for FAME and phenetics approaches. However, there was not complete correspondence for the groupings of the 2 classifications, with most FAME groups being distributed among the phenetic groups and 2 phenetic groups not providing usable characteristics for FAME analysis. The results did demonstrate significant taxonomic variation in bacteria capable of occupying the same or a similar fundamental niche.}, }
@article {pmid24221148, year = {1984}, author = {Grimes, DJ and Stemmler, J and Hada, H and May, EB and Maneval, D and Hetrick, FM and Jones, RT and Stoskopf, M and Colwell, RR}, title = {Vibrio species associated with mortality of sharks held in captivity.}, journal = {Microbial ecology}, volume = {10}, number = {3}, pages = {271-282}, pmid = {24221148}, issn = {0095-3628}, abstract = {Two urease-positiveVibrio spp. were isolated from a brown shark (Carcharhinus plumbeus) that died in captivity at a national aquarium. Morphological, biochemical, and molecular genetic studies revealed one of the isolates to beV. damsela; the other isolate was unique and has been classified asV. carchariae sp. nov. BothV. damsela andV. carchariae were found to be virulent for spiny dogfish (Squalus acanthias), causing death in less than 18 hours after intraperitoneal injection of ca. 4×10(6) cells.V. damsela was strongly cytotoxic for Y1 adrenal cell monolayers;V. carchariae exhibited weak cytotoxicity for Y1 cells.V. damsela contained cryptic plasmids and both isolates were urease positive.V. carchariae was able to utilize urea as sole source of carbon and nitrogen.}, }
@article {pmid24221147, year = {1984}, author = {Weber, FH and Rosenberg, FA}, title = {Interactions of carbaryl with estuarine bacterial communities.}, journal = {Microbial ecology}, volume = {10}, number = {3}, pages = {257-269}, pmid = {24221147}, issn = {0095-3628}, abstract = {The addition of carbaryl (100μg/ml) to a model estuarine ecosystem did not affect the number of bacteria in the sediment, but reduced the diversity (as measured by the rarefaction technique) of the microbial community as compared with a control model ecosystem. Two carbaryltolerant strains of bacteria were isolated from the carbaryl-treated system, but none were isolated from the control system. Bacterial growth and filter paper decomposition in mixed cultures was prevented by 100μg/ml carbaryl, but this amount had no effect on the extracellular cellulase of an estuarine isolate. Increasing the amount of organic matter in the medium attenuated the toxicity of carbaryl to pure cultures of an estuarine isolate. The addition of 1, 10, or 100μg/ml carbaryl to field plots had no effect on bacterial numbers, diversity, or filter paper decomposition. The amount of carbaryl in sediments exposed to 100μg/ml fell below the limit of detection by thin-layer chromatography within 12 hours. In sterile and nonsterile model systems, carbaryl rapidly adsorbed to sediment, and hydrolyzed to 1-naphthol in both sediment and water. Although carbaryl may be toxic to bacteria under some conditions, the amounts that might enter and persist in an estuary are insufficient to have a significant impact on the sediment microbial community.}, }
@article {pmid24221146, year = {1984}, author = {Rublee, PA and Merkel, SM and Faust, MA and Miklas, J}, title = {Distribution and activity of bacteria in the headwaters of the Rhode River Estuary, Maryland, USA.}, journal = {Microbial ecology}, volume = {10}, number = {3}, pages = {243-255}, pmid = {24221146}, issn = {0095-3628}, abstract = {A transect along the axis of the headwaters of a tidal estuary was sampled for microbial, nutrient, and physical parameters. Chlorophylla averaged 42μg 1(-1) and phytoplankton comprised an estimated 80% of the total microbial biomass as determined by adenosine triphosphate (ATP). Bacterial concentrations ranged from 0.3-53.9×10(6) cells ml(-1) and comprised about 4% of the total living microbial biomass. Bacterial production, determined by(3)H-methyl-thymidine incorporation was about 0.05-2.09× 10(9) cells 1(-1) h(-1), with specific growth rates of 0.26-1.69 d(-1). Most bacterial production was retained on 0.2μm pore size filters, but passed through 1.0μm filters. Significant positive correlations were found between all biomass measures and most nutrient measures with the exception of dissolved inorganic nitrogen nutrients where correlations were negative. Seasonal variability was evident in all parameters and variability among the stations was evident in most. The results suggest that bacterial production requires a significant carbon input, likely derived from autotrophic production, and that microbial trophic interactions are important.}, }
@article {pmid24221145, year = {1984}, author = {McGrath Grossi, S and Kottmeier, ST and Sullivan, CW}, title = {Sea ice microbial communities. III. Seasonal abundance of microalgae and associated bacteria, Mcmurdo Sound, Antarctica.}, journal = {Microbial ecology}, volume = {10}, number = {3}, pages = {231-242}, pmid = {24221145}, issn = {0095-3628}, abstract = {Numbers of bacteria in annual sea ice increased directly with numbers of algae during the 1981 spring ice diatom bloom in McMurdo Sound, Antarctica. Algae and bacteria in a control site grew at rates of 0.10 and 0.05 day(-1), respectively, whereas in an experimentally darkened area neither increased after six weeks. Epiphytic bacteria grew at a rate twice that of the nonattached bacteria and were significantly larger, contributing approximately 30% of the total bacterial biomass after October. The microalgal assemblage was dominated by two species of pennate diatoms, anAmphiprora sp. andNitzschia stellata. Greater than 65% of epiphytic bacteria were associated withAmphiprora sp. after October.N. stellata, however, remained largely uncolonized throughout the study. We hypothesize that microalgae stimulate bacterial growth in sea ice, possibly by providing the bacteria with organic substrates.}, }
@article {pmid24221144, year = {1984}, author = {Bell, WH}, title = {Bacterial adaptation to low-nutrient conditions as studied with algal extracellular products.}, journal = {Microbial ecology}, volume = {10}, number = {3}, pages = {217-230}, pmid = {24221144}, issn = {0095-3628}, abstract = {Kinetic analyses indicate that members of natural bacterial populations from 2 marine environments near Woods Hole, MA, possess enzyme-mediated transport systems which permit utilization of(14)C-labeled extracellular organic C ((14)C-EOC) prepared from the algae,Skeletonema costatum, Thalassiosira pseudonana, andDunaliella tertiolecta, and supplied over a concentration range of 15-150μC·liter(-1). It is shown that previous exposure of the bacteria to the EOC from these algae cannot explain the linear kinetic patterns obtained. Therefore, the ability to utilize algal EOC at low concentrations is a general feature of metabolically active bacterial populations. Further, as the native bacteria do not restrict this ability to a specific EOC pool, the results are consistent with the hypothesis that bacteria adapted to low nutrient environments possess uptake systems of high substrate affinity and low substrate specificity. Elevation of substrate levels with as little as 10 mg·1(-1) peptone is shown to favor development of a bacterial population that lacks these adaptations. Standard enrichment techniques typically result in the isolation of bacteria that are poor models for evaluating the ecology of native microbiota.}, }
@article {pmid24221143, year = {1984}, author = {Currie, DJ and Kalff, J}, title = {Can bacteria outcompete phytoplankton for phosphorus? a chemostat test.}, journal = {Microbial ecology}, volume = {10}, number = {3}, pages = {205-216}, pmid = {24221143}, issn = {0095-3628}, abstract = {Although the bacterioplankton of lakes are usually considered primarily in terms of mineralization processes, recent studies suggest that they may also strongly compete for phosphorus with the phytoplankton. In the present study, we have tested in chemostat culture, and found support for the hypotheses that (1) a freshwater bacterium (Pseudomonas paucimobilis), whose carbon source is excretion from a phosphorus-limited alga (Synedra ulna var.danica), can outcompete that alga for phosphorus (P) under widely varied P supply rates; (2) exogenously-supplied organic carbon positively influences bacterial biomass and negatively influences algal biomass; (3) the ratio of bacterial to algal phosphorus uptake in short-term(32)P orthophosphate uptake experiments is an accurate predictor of their relative long-term phosphorus assimilation (i.e., growth) in mixed culture.}, }
@article {pmid24221142, year = {1984}, author = {Bååth, E and Lundgren, B and Söderström, B}, title = {Fungal populations in podzolic soil experimentally acidified to simulate acid rain.}, journal = {Microbial ecology}, volume = {10}, number = {3}, pages = {197-203}, pmid = {24221142}, issn = {0095-3628}, abstract = {The effect of experimental acidification on the soil microfungal community was studied in the humus layer of a coniferous forest in northern Sweden. The study was made 4 years after the last application of sulfuric acid. Fungal species composition was altered by treatments of 100 and 150 kg sulfuric acid ha(-1) each year for 6 years, yet no differences were found between the control treatment and an application of 50 kg ha(-1). The abundance ofPenicillium spinulosum andOidiodendron cf.echinulatum II increased with increasing rates of acid application, whereas only small changes were found for other isolated fungal taxa. Soil respiration rate and fluorescein diacetate (FDA)-active fungal biomass were significantly different from the control treatment at all 3 levels of acidification.}, }
@article {pmid24221141, year = {1984}, author = {France, RC and Reid, CP}, title = {Pure culture growth of ectomycorrhizal fungi on inorganic nitrogen sources.}, journal = {Microbial ecology}, volume = {10}, number = {3}, pages = {187-195}, pmid = {24221141}, issn = {0095-3628}, abstract = {Four ectomycorrhizal fungi were tested for their ability to grow (i.e., mycelial mat radial extension and fungal biomass) on nutrient media either supplemented with ammonium-nitrogen or nitrate-nitrogen or in the absence of an inorganic nitrogen source.Pisolithus tinctorius, Cenococcum geophilum andThelephora terrestris exhibited greater growth on ammonium-nitrogen.Suillus granulatus grew better on the nitrate-nitrogen nutrient medium. Regardless of inorganic nitrogen form preference (i.e., ammonium-nitrogen or nitrate-nitrogen), all 4 species showed some growth on each of the 3 nutrient media. Growth rate maxima varied by fungal species as well as by inorganic nitrogen source. Maximum growth rate forT. terrestris exceeded rates exhibited by the other 3 fungi by 2-5 times.}, }
@article {pmid24221097, year = {1984}, author = {Chrzanowski, TH and Crotty, RD and Hubbard, JG and Welch, RP}, title = {Applicability of the fluorescein diacetate method of detecting active bacteria in freshwater.}, journal = {Microbial ecology}, volume = {10}, number = {2}, pages = {179-185}, pmid = {24221097}, issn = {0095-3628}, abstract = {Fluorescein diacetate (FDA) hydrolysis was evaluated as a means to detect actively metabolizing bacteria in freshwater. Fluorescein diacetate, a nonfluorescent derivative of fluorescein, can be transported across cell membranes and deacetylated by nonspecific esterases. Resultant fluorescein accumulates within cells and allows direct visualization by epifluorescent microscopy. Application of FDA to a variety of freshwater habitats yielded estimates of active cells ranging from 6-24% of the total population. These estimates were 49-61% lower than estimates of active cells obtained from measures of electron transport activity. The difference was attributed to low permeability of the fluorogen through the outer membrane of heterotrophic gram-negative cells. Data suggest that FDA hydrolysis as a means of detecting active bacteria may be limited to environments rich in eucaryotes and gram-positive cells.}, }
@article {pmid24221096, year = {1984}, author = {Robinson, JA and Characklis, WG}, title = {Simultaneous estimation ofV max, K m, and the rate of endogenous substrate production (R) from substrate depletion data.}, journal = {Microbial ecology}, volume = {10}, number = {2}, pages = {165-178}, pmid = {24221096}, issn = {0095-3628}, abstract = {The nonlinear and 3 linearized forms of the integrated Michaelis-Menten equation were evaluated for their ability to provide reliable estimates of uptake kinetic parameters, when the initial substrate concentration (S0) is not error-free. Of the 3 linearized forms, the one where t/(S0-S) is regressed against ln(S0/S)/(S0-S) gave estimates ofV max and Km closest to the true population means of these parameters. Further, this linearization was the least sensitive of the 3 to errors (±1%) in S0. Our results illustrate the danger of relying on r(2) values for choosing among the 3 linearized forms of the integrated Michaelis-Menten equation. Nonlinear regression analysis of progress curve data, when S0 is not free of error, was superior to even the best of the 3 linearized forms. The integrated Michaelis-Menten equation should not be used to estimateV max and Km when substrate production occurs concomitant with consumption of added substrate. We propose the use of a new equation for estimation of these parameters along with a parameter describing endogenous substrate production (R) for kinetic studies done with samples from natural habitats, in which the substrate of interest is an intermediate. The application of this new equation was illustrated for both simulated data and previously obtained H2 depletion data. The only means by whichV max, Km, and R may be evaluated from progress curve data using this new equation is via nonlinear regression, since a linearized form of this equation could not be derived. Mathematical components of computer programs written for fitting data to either of the above nonlinear models using nonlinear least squares analysis are presented.}, }
@article {pmid24221095, year = {1984}, author = {Griffiths, RP and Caldwell, BA and Morita, RY}, title = {Observations on microbial percent respiration values in arctic and subarctic marine waters and sediments.}, journal = {Microbial ecology}, volume = {10}, number = {2}, pages = {151-164}, pmid = {24221095}, issn = {0095-3628}, abstract = {Percent respiration was measured in over 1,100 arctic and subarctic marine water and sediment samples using(14)C-labeled glucose and glutamate. These measurements were made at different times of the year in 4 regions. Percent respiration values were typically lower in regions where the waters of large rivers mixed with seawater. They were also lower in sediments and in waters collected near the bottom than in surface waters. They were higher in winter arctic waters than water samples collected in the summer; however, a similar seasonal trend was not observed in subarctic waters. There were a number of studies in which there were significant positive rank correlations between percent respiration and salinity and between percent respiration and temperature. From what is known about the range of temperature and salinity encountered in samples collected during these studies and the results of temperature and salinity effects experiments, it was concluded that changes in these 2 variables did not explain the variation observed in percent respiration. Correlations between percent respiration and the inorganic nutrients PO4 (-3), NH4 (+) and NO3 (-) showed that of the 3 variables, only NO3 (-) showed relatively high correlations with all the same sign. From this it was concluded that there may be situations in which NO3 (-) levels may influence percent respiration in nearshore marine waters. It is also likely that qualitative characteristics of the available organic nutrients may also influence percent respiration levels. Although no organic nutrient data is available for statistical analysis, the patterns of percent respiration near river plumes and the relatively strong negative correlation often observed between uptake rates (heterotrophic activity) and percent respiration suggests that organic nutrients may be a factor in controlling percent respiration. It is suggested that there are situations in which percent respiration measurements may be used to document stress in natural microbial populations due to nutrient deficiencies.}, }
@article {pmid24221094, year = {1984}, author = {Wright, RT and Coffin, RB}, title = {Measuring microzooplankton grazing on planktonic marine bacteria by its impact on bacterial production.}, journal = {Microbial ecology}, volume = {10}, number = {2}, pages = {137-149}, pmid = {24221094}, issn = {0095-3628}, abstract = {Grazing on planktonic bacteria by microzooplankton was estimated by separating bacteria from the larger plankton with 1μm pore Nuclepore filtration and measuring changes in bacteria in filtered and unfiltered samples over 24 hours. In the absence of grazers, bacteria increased linearly. The regression coefficient of linear increase was used to estimatein situ bacterial production. When grazers were present, the changes in bacteria concentration usually took the form of a linear decline, and grazing was estimated by subtracting the regression coefficient of the unfiltered sample from that of the 1μm filtrate. Results from the Essex estuary-coastal system of northern Massachusetts show grazing and production at rates that indicate a daily turnover of the standing crop of bacteria, with highest values in mid-estuarine waters. Experiments on the size distribution of grazing showed that microzooplankton from 1-3μm were responsible for most of the observed decrease in bacteria. It was suggested that the basic pattern of linear increase of the bacteria in the absence of grazing reflects density-dependent limitation by substrate present at the outset of the incubation and is indicative of a population that has been maintained around the mid-point of the logistic growth curve by grazing.}, }
@article {pmid24221093, year = {1984}, author = {Keast, D and Rowe, P and Bowra, B and Sanfelieu, L and Stapley, EO and Woodruff, HB}, title = {Studies on the ecology of West Australian actinomycetes: Factors which influence the diversity and types of actionomycetes in Australian soils.}, journal = {Microbial ecology}, volume = {10}, number = {2}, pages = {123-136}, pmid = {24221093}, issn = {0095-3628}, abstract = {A statistical technique has been employed to study the effects of various environmental factors in altering the actinomycete populations of soils located in the western part of Australia. Over 12,000 actinomycetes obtained at 28 different locations were included in the evaluation. Among factors that had a significant influence were the geographic area at which the sample was taken, the nature of plant rhizosphere, and a rainstorm. Seasonal changes in population did occur, but there was considerable stability of population with time. Although marked differences occurred in types of actinomycetes present among different geographic locations, multiple samples taken within a location at distances of 30 cm or greater showed marked similarity in populations. There were varied degrees of diversity among the populations studied. The population that developed after a rainstorm was low in diversity, whereas the populations of root rhizospheres were as diverse as those of plant-free soil-litter areas. In assessing the ecology of soil actinomycetes, it is important to consider the degree of change in population induced by an environmental factor and also its effect on diversity, since the effects may be complementary or may be opposite in nature.}, }
@article {pmid24221092, year = {1984}, author = {Heritage, AD and Foster, RC}, title = {Catalase and sulfur in the rice rhizosphere: An ultrastructural histochemical demonstration of a symbiotic relationship.}, journal = {Microbial ecology}, volume = {10}, number = {2}, pages = {115-121}, pmid = {24221092}, issn = {0095-3628}, abstract = {An ultrastructural study has been made of a symbiotic association between a sulfur bacterium and the roots of the rice plant (Oryza saliva L.). This association is proposed to have useful economic consequences in ameliorating hydrogen sulfide toxicity and associated Akiochi or Straighthead disease in lowland rice cultivation. The presence of catalase (E.C. 1.11.1.6) in rice roots and in some rhizosphere bacteria has been demonstrated in ultrathin sections of field-grown rice using a catalasespecific medium. Catalase was detected in capsules surrounding the catalase-negative S-bacteria. These capsules were of a novel fibrillar structure. Two sizes of inclusion bodies were present in these large bacteria. The disappearance of the smaller inclusions during carbon disulfide treatment suggests that they are the sulfur granules. The name "thiosome" is proposed for these membrane-bound structures.}, }
@article {pmid24221091, year = {1984}, author = {Casella, S and Leporini, C and Nuti, MP}, title = {Nitrous oxide production by nitrogen-fixing, fast-growing Rhizobia.}, journal = {Microbial ecology}, volume = {10}, number = {2}, pages = {107-114}, pmid = {24221091}, issn = {0095-3628}, abstract = {Rhizobium trifolii, R. leguminosarum, andR. "hedysarum", grownex planta under anoxic conditions in a chemically defined medium, evolve N2O from NO3 (-), NO2 (-), and (NH4)2NO3. The amount of nitrous oxide formed after 96 hours is about 0.2μM×mg(-1) cells d.w. Large availability of organic matter enhances the production of N2O from nitrate by free-livingR. trifolii in peat/sand mixtures. Denitrification of the above species andR. meliloti was detected also in planta. Nitrous oxide production increases almost linearly from 10-45μM×mg(-1) nodules d.w. when nitrogen-fixing plants are exposed to increasing concentrations of nitrate (1-12μM).}, }
@article {pmid24221090, year = {1984}, author = {Gay, G and Corman, A}, title = {Comparative study of the growth of two strains ofNitrobacter in batch and continuous culture.}, journal = {Microbial ecology}, volume = {10}, number = {2}, pages = {99-105}, pmid = {24221090}, issn = {0095-3628}, abstract = {Growth kinetics of 2Nitrobacter strains (N.w. and L) coexisting in the same soil are studied in batch and continuous culture. Monod's parameters are estimated numerically from experimental data in the case of the batch experiment, and from steady-state equations in the case of the chemostat. In both cases, the 2 strains show different values for their growth parameters. N.w. may be characterized by its highμ max-Ks values, relative to strain L. But for each strain,μ max is significantly lowered between batch and continuous culture. In this latter case, at N-NO2 (-) concentrations less than 1.5μg·ml(-1), the 2 strains exhibit similar growth rates showing that for concentrations of the limiting substrate prevailing in the soil, they may compete for this substrate.}, }
@article {pmid24221089, year = {1984}, author = {Varon, M and Fine, M and Stein, A}, title = {The maintenance ofBdellovibrio at low prey density.}, journal = {Microbial ecology}, volume = {10}, number = {2}, pages = {95-98}, pmid = {24221089}, issn = {0095-3628}, abstract = {A mathematical model for the interaction ofBdellovibrio and its prey predicted that a relatively high prey density (7×10(5) cells ml(-1)) would be required for the establishment of an equilibrium in a mixed population [8]. The present report shows thatBdellovibrio can be maintained in a continuous culture when the prey cell density is much lower (2-5×10(4) cells ml(-1)), and closer to that of naturally occurring bacterial populations in sea waters.}, }
@article {pmid24221088, year = {1984}, author = {Hurst, JL and Pugh, GJ and Walton, DW}, title = {The effect of temperature on the growth ofCandida saké isolated from the leaves of a subantarctic grass.}, journal = {Microbial ecology}, volume = {10}, number = {2}, pages = {89-93}, pmid = {24221088}, issn = {0095-3628}, abstract = {During a survey of microfungi on the subantarctic island of South Georgia, large numbers of phylloplane yeasts were isolated in late spring from leaves of a tussock grass. The dominant yeast was identified asCandida saké, this being the first record for the Antarctic region. Isolates in liquid culture had a temperature optimum for growth of 20-25°C. It was capable of assimilation of a range of simple carbohydrates, similar to those found in leachates from new leaves of the tussock grass. The seasonal decline of yeasts on the phylloplane is discussed in terms of the availability of leachate and the growth of filamentous microfungi on new leaves.}, }
@article {pmid24221052, year = {1984}, author = {Phillips, MW and Lee, A}, title = {Microbial colonization of rat colonic mucosa following intestinal perturbation.}, journal = {Microbial ecology}, volume = {10}, number = {1}, pages = {79-88}, pmid = {24221052}, issn = {0095-3628}, abstract = {An allochthonous population of spiral-shaped bacteria was found colonizing the surfaces of the colonic mucosa of rats after they had been given magnesium sulphate (MgSO4)-induced diarrhea. These organisms were rarely seen in normal control rats and were not displaced when the treatment was ceased, remaining associated with the tissue for periods of up to 180 days. Similar bacteria were also found when specific pathogen-free rats, lacking mucosa-associated populations, were inoculated with homogenized rat intestine from conventional animals. Light and electron microscopic observations showed that the organisms were attached to the surface of the colon, orientated at right angles to the tissue, with one end inserted into the microvillus border. This is the first report of long-term colonization, following perturbation of the gut ecosystem, of a site on the gastrointestinal mucosa not normally associated with bacteria. The ultrastructure and mode of attachment of these organisms were very similar to that of spiral-shaped bacteria known to associate with the colonic mucosa in monkeys and man.}, }
@article {pmid24221051, year = {1984}, author = {Nealson, KH and Haygood, MG and Tebo, BM and Roman, M and Miller, E and McCosker, JE}, title = {Contribution by symbiotically luminous fishes to the occurrence and bioluminescence of luminous bacteria in seawater.}, journal = {Microbial ecology}, volume = {10}, number = {1}, pages = {69-77}, pmid = {24221051}, issn = {0095-3628}, abstract = {Seawater samples from a variety of locations contained viable luminous bacteria, but luminescence was not detectable although the system used to measure light was sensitive enough to measure light from a single, fully induced luminous bacterial cell. When the symbiotically luminous fishCleidopus gloriamaris was placed in a sterile aquarium, plate counts of water samples showed an increase in luminous colony-forming units. Luminescence also increased, decreasing when the fish was removed. Light measurements of water samples from a sterile aquarium containingPhotoblepharon palpebratus, another symbiotically luminous fish, whose bacterial symbionts have not been cultured, showed a similar pattern of increasing light which rapidly decreased upon removal of the fish. These experiments suggest that symbiotically luminous fishes release brightly luminous bacteria from light organs into their environment and may be a source of planktonic luminous bacteria. Although planktonic luminous bacteria are generally not bright when found in seawater, water samples from environments with populations of symbiotically luminous fish may show detectable levels of light.}, }
@article {pmid24221050, year = {1984}, author = {Baltzis, BC and Fredrickson, AG}, title = {Competition of two suspension-feeding protozoan populations for a growing bacterial population in continuous culture.}, journal = {Microbial ecology}, volume = {10}, number = {1}, pages = {61-68}, pmid = {24221050}, issn = {0095-3628}, abstract = {Mathematical studies for ecosystems involving 2 predators competing for a growing prey population have shown that the 2 competitors can coexist in a state of sustained oscillations for a range of values of the system parameters. For the case of 1 suspension-feeding protozoan population, recent experimental observations suggest that the predator-prey interaction is complicated by the ability of the bacteria to grow on products produced by the lysis of protozoan cells. This situation is studied here for the case where 2 suspension-feeding protozoan populations compete for a growing bacterial population in a chemostat. Computer simulations show that the 2 protozoan populations can coexist over a range of the operating parameters. Some necessary conditions for coexistence are presented as are some speculations regarding the possible physical explanations of results.}, }
@article {pmid24221049, year = {1984}, author = {Jackson, KM and Berger, J}, title = {Survival of ciliate protozoa under starvation conditions and at low bacterial levels.}, journal = {Microbial ecology}, volume = {10}, number = {1}, pages = {47-59}, pmid = {24221049}, issn = {0095-3628}, abstract = {Under starvation conditions, 50% survivorship times displayed no significant relationship with cell size in 2 ciliate species in this study and 5 protozoan species from the literature. Differences in survival ability were attributed to differences in weight-specific respiratory rate and relative motility among these 7 species. At low bacterial levels, 4 ciliate species in this study displayed significant differences in survivorship. High survivorship ofEuplotes patella relative to that ofParamecium caudatum andParaurostyla sp. at low ciliate densities was attributed to the lower individual energy requirements of this smaller species. High survivorship ofStentor coeruleus was interpreted as an effect of its large quantity of reserves and low respiratory rate. The survivorship ofE. patella was reduced at a higher population density. Four ciliate species survived longer at 15‡C than at 22‡C. Q10 values based on 50% survivorship times at these 2 temperatures were much lower than Q10 values based on respiratory rates and growth rates of well-fed ciliates over a similar temperature range.}, }
@article {pmid24221048, year = {1984}, author = {Hall, GH and Jeffries, C}, title = {The contribution of nitrification in the water column and profundal sediments to the total oxygen deficit of the hypolimnion of a mesotrophic lake (Grasmere, English Lake District).}, journal = {Microbial ecology}, volume = {10}, number = {1}, pages = {37-46}, pmid = {24221048}, issn = {0095-3628}, abstract = {Estimates ofin situ nitrifying activity have been made in the hypolimnetic water column and surface 1.0 cm of profundal sediments at 2 sites in Grasmere, a mesotrophic lake in the English Lake District. Increases of nitrate concentrations were used to estimate nitrification in the water column whereas a mini-core technique, involving the use of a nitrification inhibitor (allylthiourea), was used to estimate the rate in surface sediments. The pattern of oxygen depletion in the water column was used to estimate the maximum depth to which sediments affect the overlying water. Nitrification in the sediment and in the water column made approximately equal contributions to the total areal oxygen deficit and, as a whole, nitrification accounted for 15-20% of the total oxygen depletion. There was no significant difference in oxygen depletion due to nitrification between the 2 sites. Attempts were made, using the nitrification potential technique, to determine the depth distribution of nitrifying activity in the surface 1.0 cm of sediment.}, }
@article {pmid24221047, year = {1984}, author = {Hall, GH}, title = {Measurement of nitrification rates in lake sediments: Comparison of the nitrification inhibitors nitrapyrin and allylthiourea.}, journal = {Microbial ecology}, volume = {10}, number = {1}, pages = {25-36}, pmid = {24221047}, issn = {0095-3628}, abstract = {A method for measuring rates of nitrification in intact marine sediment cores has been modified and adapted for use in freshwater sediments. The technique involves subsampling a sediment core into minicores. Half of these cores are treated with an inhibitor of chemolithotrophic nitrification and, after incubation, differences in ammonia and nitrate concentration between inhibited and uninhibited systems are calculated. The within-treatment variability of ammonia and nitrate concentrations could be reduced by storing the cores overnight prior to subsampling. Estimates of the nitrification rate using the difference in ammonia concentrations between the inhibited and uninhibited mini-cores were always greater than the rate estimate using the difference in nitrate concentrations. Comparison between the results using the nitrification inhibitors allylthiourea (ATU) and nitrapyrin (N-Serve) indicated that the former appeared to give larger values for the nitrification rate than did the latter. Differences in the efficiency of these inhibitors in the control of nitrification under the conditions used partly explain these results. Data are also presented on the effect of N-Serve and ATU on some other nitrogen transformations affecting ammonia and nitrate concentrations.}, }
@article {pmid24221046, year = {1984}, author = {Varel, VH}, title = {Characteristics of some fermentative bacteria from a thermophilic methane-producing fermenter.}, journal = {Microbial ecology}, volume = {10}, number = {1}, pages = {15-24}, pmid = {24221046}, issn = {0095-3628}, abstract = {Anaerobic bacteria from a 55‡C methane-producing beef waste fermenter were enumerated, isolated, and characterized. Direct microscopic bacterial counts were 5.2-6.8×10(10) per g fermenter effluent. Using a nonselective roll-tube medium which contained 40% fermenter effluent, 8.5-14.1% of the microscopic count was culturable. Deletion of fermenter effluent significantly reduced the viable count. Sixty-four randomly picked strains were characterized. All were pleomorphic, gram-negative, anaerobic rods, many of which were difficult to grow in liquid media. The strains were divided into 5 major groups based on glucose fermentation, hydrogen sulfide production, starch hydrolysis, fermentation products, and morphology. Glucose was fermented by 75% of the isolates, 76% utilized starch, 25% produced hydrogen sulfide, 76% produced hydrogen, 37% produced indole, 21% hydrolyzed gelatin, and 13% were sporeformers. Ethanol, lactate, formate, acetate, and hydrogen were common fermentation products. Twenty-four representative strains had 1-12 flagella. Growth was observed between 35 and 73‡C. These studies indicate that species diversity among the isolated organisms was low.}, }
@article {pmid24221045, year = {1984}, author = {Gowland, PC and Slater, JH}, title = {Transfer and stability of drug resistance plasmids inEscherichia coli K12.}, journal = {Microbial ecology}, volume = {10}, number = {1}, pages = {1-13}, pmid = {24221045}, issn = {0095-3628}, abstract = {Mating experiments between pairs of strains ofEscherichia coli containing either the compatible plasmids TP120 (Inc N) and R1 (Inc FII) or the incompatible plasmids TP125 (Inc B) and TP113 (Inc B) were undertaken in mixed continuous-flow cultures and in dialysis sacs suspended in pond water. Plasmid transfer was readily demonstrated between strains carrying compatible plasmids TP120 and R1 in both continuous-flow culture and pond water. In mixed cultures of strains carrying plasmids TP125 and TP113, transfer was only observed in continuous-flow culture systems. Strains ofE. coli containing aggregates of plasmids TP120 and R1 were shown to be stable over 5 months continuous cultivation under carbon limited conditions at a growth rate of 0.1 hours(-1) in the presence of drugs which select for the maintenance of both plasmids. In the strains containing plasmid aggregates, a gene dosage effect was observed with respect to the levels of resistance to drugs whose resistance was encoded by both plasmids. Chemostat experiments showed that no cointegrate plasmids were found from the strains ofE. coli initially containing both plasmid TP120 and plasmid R1.}, }
@article {pmid24221824, year = {1983}, author = {Brown, KW and Donnelly, KC and Deuel, LE}, title = {Effects of mineral nutrients, sludge application rate, and application frequency on biodegradation of two oily sludges.}, journal = {Microbial ecology}, volume = {9}, number = {4}, pages = {363-373}, pmid = {24221824}, issn = {0095-3628}, abstract = {A continuous flow soil respirometer was used to evaluate the effect of nutrient addition, application rate, and application frequency on biodegradation of 2 complex oily sludges in soil. The most rapid biodegradation of the refinery sludge occurred when nitrogen was added to reduce the carbon to nitrogen (C∶N) ratio to 9∶1. The petrochemical sludge was degraded most rapidly when nitrogen, phosphorus, and potassium were added at a rate of 124∶1, C∶NPK; CO2evolution from both wastes increased with increasing application rates, but the fraction of applied sludge which degraded decreased with increasing application rates. Small frequent applications resulted in a slight increase in respiration rate per unit applied over a single equivalent application, indicating that repeated applications of smaller amounts of sludge result in a more rapid rate of decomposition. The population of total soil bacteria was greatest when 1% of either sludge was added to the soil, whereas 5 and 10% sludge additions resulted in slightly lower microbial populations.}, }
@article {pmid24221823, year = {1983}, author = {Tarn, TY and Mayfield, CI and Inniss, WE}, title = {Microbial decomposition of leaf material at 0°C.}, journal = {Microbial ecology}, volume = {9}, number = {4}, pages = {355-362}, pmid = {24221823}, issn = {0095-3628}, abstract = {The microbial decomposition of leaves (both fresh and autumnshed) at 0°C using stream sediment-water was investigated. The maximum rates of loss of leaf carbohydrate and protein at 0°C were considerable, being about 40% of those at 20°C. These rates were only slightly affected by the type of leaf material present being 1.3-fold higher with fresh leaves as compared with autumn-shed leaves. In addition, an epifluorescence microscopic counting technique was developed and utilized to enumerate the microbial populations colonizing the decomposing leaves. The average microbial densities on fresh and autumn-shed leaves after 35 days of incubation were 1.3 × 10(6) and 9.0 × 10(5) microorganisms cm(-2) at 0°C as compared with 5.5 × 10(6) and 3.3 × 10(6) microorganisms cm(-2) at 20°C, respectively. Antibacterial and antifungal antibiotics were used to estimate the comparative involvement of sediment bacteria and fungi in leaf degradation.}, }
@article {pmid24221822, year = {1983}, author = {Laanbroek, HJ and Geerligs, HJ and Peijnenburg, AA and Siesling, J}, title = {Competition for L-lactate betweenDesulfovibrio, Veillonella, andAcetobacterium species isolated from anaerobic intertidal sediments.}, journal = {Microbial ecology}, volume = {9}, number = {4}, pages = {341-354}, pmid = {24221822}, issn = {0095-3628}, abstract = {Almost equal numbers ofDesulfovibrio, Veillonella, andAcetobacterium species were found in agar shake dilutions of anaerobic intertidal brackish sediments applying L-lactate as the only energy source and sulfate as electron acceptor. Pure cultures of these bacteria were studied in more detail in batch cultures as well as in L-lactate-limited chemostats. The maximal specific growth rates on L-lactate were determined in washout experiments and amounted to 0.16, 0.30, and 0.06 h(-1) forDesulfovibrio baculatus H.L21,Veillonella alcalescens NS.L49, andAcetobacterium NS.L40, respectively. Competition for L-lactate was studied in energy-limited chemostats at a dilution rate of 0.02 h(-1).D. baculatus H.L21 turned out to be the best competitor at low L-lactate concentrations provided that sufficient sulfate and iron were present.V. alcalescens NS.L49 was favored by the absence of sulfate and iron. Coexistence ofD. baculatus H.L21 andV. alcalescens NS.L49 was observed in a L-lactate-limited chemostat with additional sulfate and citrate. Syntrophic growth ofV. alcalescens NS.L49 andAcetobacterium NS.L40 occurred in a L-lactate-limited chemostat in the absence of sulfate. No coexistence betweenD. baculatus H.L21 andAcetobacterium NS.L40 was observed in a L-lactate-limited chemostat without sulfate. Addition of calcium-saturated illite to an energy-limited mixed culture ofV. alcalescens NS.L49 andAcetobacterium NS.L40 induced iron limitation and subsequent washout of theAcetobacterium species. Finally, the ecological niches of the 3 species in relation to the consumption of lactate were discussed.}, }
@article {pmid24221821, year = {1983}, author = {Morley, CR and Trofymow, JA and Coleman, DC and Cambardella, C}, title = {Effects of freeze-thaw stress on bacterial populations in soil microcosms.}, journal = {Microbial ecology}, volume = {9}, number = {4}, pages = {329-340}, pmid = {24221821}, issn = {0095-3628}, abstract = {To test the effect of freezing on soil biota, isolated from the shortgrass prairie of northeastern Colorado, a series of experiments were performed using gnotobiotic soil microcosms.Pseudomonas paucimobilis was used to examine the effects of freezing on bacteria of different growth stages. Secondly, the effect of multiple freeze-thaw cycles was tested on an assemblage of bacterial species. Lastly, the effect of freezing on predator-prey interactions was studied usingP. paucimobilis and an amoebal predator,Acanthamoeba polyphaga. A temperature of -9°C was not detrimental toP. paucimobilis at any growth stage. A single severe freeze-thaw cycle (-27°C to 23°C) resulted in 40-60% mortality ofP. paucimobilis and the mixed bacteria, although additional freezing events did not reduce the populations further. Multiple freeze-thaw cycles (-9°C to 23°C) gave 40-60% mortality ofP. paucimobilis and the mixed bacteria. Predator-prey population cycles were possibly desynchronized by freeze-thaw events.}, }
@article {pmid24221820, year = {1983}, author = {Hermansson, M and Dahlbäck, B}, title = {Bacterial activity at the air/water interface.}, journal = {Microbial ecology}, volume = {9}, number = {4}, pages = {317-328}, pmid = {24221820}, issn = {0095-3628}, abstract = {By using substrate molecules of varying degrees of surface activity, we were able to measure some features of bacterial activity in the surface microlayers (SM) and in the subsurface (bulk) water. The fraction of active cells was determined by a combined microautoradiography-epifluorescence (ME) method. Measurements were made of(14)CO2 evolution to determine the rate of respiration. Results from in situ measurements showed no significant difference between fraction of active cells in the SM and in the bulk. This may be due to an exchange of bacteria between SM and bulk. This exchange was assessed by spreading a film of(3)H-palmitic acid on the surface and, after incubation, measuring the amount of labeled cells at the surface and in the bulk. Test bacteria showing a high accumulation at the surface also showed a low exchange between the 2 strata. When low concentrations of added(14)C-protein were used, the respiration measurements showed a lower value for bulk than for interface localized protein. At higher concentrations, the evolved(14)CO2 was the same whether the protein was mixed in the bulk or spread at the surface. When 2.4-12 ng·cm(-2) of(14)C-palmitic acid was spread on the surface, there was a linear relation between turnover time and amount of added substrate. At higher substrate concentrations there was a deviation from the straight line. Results are discussed in terms of the unique habitat found at an interface.}, }
@article {pmid24221819, year = {1983}, author = {Salas, SD and Geesey, GG}, title = {Surface attachment of a sediment isolate ofEnterobacter cloacae.}, journal = {Microbial ecology}, volume = {9}, number = {4}, pages = {307-315}, pmid = {24221819}, issn = {0095-3628}, abstract = {Enterobacter cloacae was recovered from surface sediments of a flood control channel in an area where freshwater runoff mixed with coastal seawater. Cells of this bacterium elaborated an extensive capsule when cultured under laboratory conditions designed to promote extracellular polysaccharide production. Colonization of glass surfaces by cells was similar under aerobic and anaerobic conditions. Temperature exerted little effect on maximum adherent cell density in the range of 15-25°C. The availability of organic nutrients also had little influence on the tendency of cells to adhere to surfaces. Maximum adherent cell densities decreased (76%) as salinity increased from 0 to 12‰ The results suggest that cells ofE. cloacae are suitably adapted to maintain a sessile existence in brackish water sediments of temperate coastal areas.}, }
@article {pmid24221818, year = {1983}, author = {Malone, JA and Caldwell, DE}, title = {Evaluation of surface colonization kinetics in continuous culture.}, journal = {Microbial ecology}, volume = {9}, number = {4}, pages = {299-305}, pmid = {24221818}, issn = {0095-3628}, abstract = {Two equations, describing surface colonization, were evaluated and compared using suspended glass slides in a continuous culture ofPseudomonas aeruginosa. These equations were used to determine surface growth rates from the number and distribution of cells present on the surface after incubation. One of these was the colonization equation which accounts for simultaneous attachment and growth of bacteria on surfaces:[Formula: see text] where N=number of cells on surface (cells field(-1)); A=attachment rate (cells field(-1)h(-1));μ=specific growth rate (h(-1)); t=incubation period (h). The other was the surface growth rate equation which assumes that the number of colonies of a given size (Ci) will reach a constant value (Cmax) which is equal to A divided byμ:[Formula: see text] Both equations gave similar results and the time required to approximate Cmax may not be as long as was previously thought. In all cases both A andμ continuously decreased throughout the incubation period. These decreases may be due to various effects of microbial accumulation on the surface. Both equations accurately determined surface growth rates despite highly variable attachment rates. Growth rates were similar for both the liquid phase of the culture and the solid-liquid interface (0.4 h(-1)). Use of the surface growth rate equation is favored over the use of the colonization equation since the former does not require a computer to solve forμ and the counting procedure is simplified.}, }
@article {pmid24221707, year = {1983}, author = {Roberts, NC and Siebeling, RJ and Kaper, JB and Bradford, HB}, title = {Vibrios in the Louisiana gulf coast environment.}, journal = {Microbial ecology}, volume = {9}, number = {3}, pages = {296}, doi = {10.1007/BF02097744}, pmid = {24221707}, issn = {0095-3628}, }
@article {pmid24221706, year = {1983}, author = {Reichardt, W and Gunn, B and Colwell, RR}, title = {Ecology and taxonomy of chitinoclasticCytophaga and related chitin-degrading bacteria isolated from an estuary.}, journal = {Microbial ecology}, volume = {9}, number = {3}, pages = {273-294}, pmid = {24221706}, issn = {0095-3628}, abstract = {A total of 103 strains of estuarine, Chitinoclastic bacteria isolated from water, and sediment samples collected from the upper Chesapeake Bay, including 17 freshwater and 11 seawater isolates, were subjected to numerical taxonomy analysis. The isolates included 44 yellow-orange pigmented strains classified asCytophaga-like bacteria (CLB) of theCytophagaceae. Salt requirement of the strains ranged from tolerance to ≤1% NaCl to an absolute requirement for NaCl, with 1% NaCl satisfying this requirement. The largest phenon consisted of facultatively anaerobic, oligo-nitrophilic, and flexirubin pigment-producing freshwater and estuarine isolates, and included reference strains of bothCytophaga johnsonae Stanier andCytophaga aquatilis Strohl and Tait. Other phena, containing a smaller number of strains, comprised marine and estuarine isolates which did not produce flexirubin pigments, and required organic nitrogen for growth and for production of chitinolytic enzymes. Salt-requiring, flexirubin pigment-producing, chitin-degrading strains were, on occasion, isolated from estuarine samples and represented phena found in estuaries. Most of theCytophaga isolates, as well as chitin-degrading species not of the genusCytophaga that were isolated from Chesapeake Bay, clustered in phena representing previously described species of aerobic, zymogenic, chitinoclastic bacteria. When the frequency of occurrence of features related to environmental parameters, viz., pH, salinity, temperature range of growth, and growth on media lacking organic nitrogen, was calculated, ecological groupings of strains in the 2 major phena of CLB could be distinguished among the estuarine, chitin-degrading bacteria.}, }
@article {pmid24221705, year = {1983}, author = {Rudd, T and Sterritt, RM and Lester, JN}, title = {Mass balance of heavy metal uptake by encapsulated cultures ofKlebsiella aerogenes.}, journal = {Microbial ecology}, volume = {9}, number = {3}, pages = {261-272}, pmid = {24221705}, issn = {0095-3628}, abstract = {Dialysis was employed as a method of speciating heavy metals in cultures of an extracellular polymer forming strain ofKlebsiella aerogenes. A noncapsulated strain of the same bacterium was used as a control, and a mass balance of copper, cadmium, cobalt, nickel, and manganese in batch culture at pH 4.5 and pH 6.8 and in continuous culture at pH 6.8 was constructed. Copper and cadmium were accumulated by the cell during rapid proliferation whereas all 5 metals were bound nonspecifically by extracellular polymer produced during stationary phase and at low dilution rates. The presence of extracellular polymer appeared to inhibit cellular uptake of nickel. At the lower pH, metal uptake was considerably reduced. The results are discussed in the context of metal removal in the activated sludge process of waste water treatment.}, }
@article {pmid24221704, year = {1983}, author = {Starmer, WT and Phaff, HJ}, title = {Analysis of the community structure of yeasts associated with the decaying stems of cactus. II.Opuntia species.}, journal = {Microbial ecology}, volume = {9}, number = {3}, pages = {247-259}, pmid = {24221704}, issn = {0095-3628}, abstract = {A survey was made of yeast species associated with the decaying pads of 3 prickly pear cacti (Opuntia phaeacantha, O. ficus-indica, andO. lindheimeri) in Arizona and Texas. Yeast communities from 12 localities were compared among localities, amongOpuntia species, and with previous data on yeast communities associated with columnar cacti. The results indicate thatOpuntia necroses contain relatively more yeast species with broader physiological abilities in their communities than columnar necroses. It is argued that differences in chemistry of the opuntias and columnar forms in concert with the insect vectors specific for these cacti account for the differences in yeast community structure. It is further hypothesized that the differences in yeast community structure have been important in the evolution and maintenance of species diversity forDrosophila species which live in the decaying stems or cladodes of various cacti. Most of the yeast community evolution in the cacti is postulated to have proceeded by evolution in situ and not by additions and replacements from outside of the system.}, }
@article {pmid24221703, year = {1983}, author = {Taylor-George, S and Palmer, F and Staley, JT and Borns, DJ and Curtiss, B and Adams, JB}, title = {Fungi and bacteria involved in desert varnish formation.}, journal = {Microbial ecology}, volume = {9}, number = {3}, pages = {227-245}, pmid = {24221703}, issn = {0095-3628}, abstract = {Desert varnish is a coating of ferromanganese oxides and clays that develops on rock surfaces in arid to semi-arid regions. Active respiration but not photosynthesis was detected on varnished rock surfaces from the Sonoran Desert. Light microscopy, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) observations, and cultivation experiments indicate that both fungi, primarily dematiaceous hyphomycetes, and bacteria are found on and within desert varnish coatings from the arid regions studied. Some fungi grow as microcolonial fungi (MCF) on rocks, and microscopic observations suggest MCF become incorporated in the varnish coating. SEM-EDAX (energy dispersive X-ray systems) analyses indicate the MCF contain 3 of the characteristic elements of varnish: iron, aluminum, and silicon. In some locations, MCF are also enriched in manganese relative to the rock substratum. Furthermore, some of the dematiaceous hyphomycetes that have been cultivated are able to oxidize manganese under laboratory conditions. It is possible that manganese-oxidizing bacteria, which are found in varnish, also play an important role in varnish formation.}, }
@article {pmid24221702, year = {1983}, author = {Bright, JJ and Fletcher, M}, title = {Amino acid assimilation and respiration by attached and free-living populations of a marinePseudomonas sp.}, journal = {Microbial ecology}, volume = {9}, number = {3}, pages = {215-226}, pmid = {24221702}, issn = {0095-3628}, abstract = {The uptake kinetics of leucine and the assimilation and respiration of leucine, glycine, glutamate and arginine by a marinePseudomonas sp. was evaluated to determine whether the uptake and efficiency of substrate utilization of free-living bacteria differed from that of bacteria associated with surfaces. Bacteria were allowed to attach to plastic substrata with known hydrophilicities, as measured by advancing water contact angle (θ A); these were Thermanox, poly(vinylidene fluoride), poly(ethelene) and poly(tetrafluoroethylene). The assimilation and respiration of surface-associated bacteria depended on the amino acid and substratumθ A, but assimilation by surface-associated cells was generally greater than and respiration was generally less than that by free-living bacteria. The uptake kinetics with leucine demonstrated that the half saturation constant (K) of surface-associated bacteria was greater than that for free-living cells. The Vmax values for surface-associated and free-living bacteria were similar, except for cells associated with poly(tetrafluoroethylene), which had a higher Vmax value.}, }
@article {pmid24221701, year = {1983}, author = {Williams, RT and Crawford, RL}, title = {Microbial diversity of Minnesota peatlands.}, journal = {Microbial ecology}, volume = {9}, number = {3}, pages = {201-214}, pmid = {24221701}, issn = {0095-3628}, abstract = {Microbial diversity, numbers, and metabolic activities in Minnesota peatlands were investigated using a variety of microbial enrichment and enumeration procedures together with radioisotopic measurements of microbial degradative processes. Minnesota peatlands were shown to contain large microbial populations of wide metabolic diversity. Direct counts of bacteria using epifluorescence microscopy indicated bacterial populations of about 10(8) ml(-1) of peatland water, irrespective of depth. Radioisotopic most-probable-number (MPN) counts of heterotrophs able to mineralize(14)C-labeled substrates to(14)CO2 showed significant populations of glucose degraders (10(4)-10(6) ml(-1)) as well as degraders of benzoate (10(2)-10(3) ml(-1)), 2,4-dichlorophenoxyacetate (10(2)-10(5) ml(-1)), and sphagnum (10(3)-10(7) ml(-1)) in the various peatlands examined. The MPNs of NO3 (-) reducers varied from 10(3)-10(6) ml(-1), SO4 (-) reducers from 10(2)-10(3) ml(-1), methanogenic bacteria from 10(3)-10(6) ml(-1), and methane oxidizers from 10(3)-10(4) ml(-1), depending on sampling site and depth. Eighty pure cultures of aerobic bacteria and fungi were isolated from Minnesota peats. Most of those cultures tested were able to grow on at least 20 organic compounds (carbohydrates, aromatic molecules, hydrocarbons, etc.) as sole sources of carbon and energy. One isolate, aBacillus, was able to fix atmospheric N2. Several of the isolates were able to mineralize(14)C-labeled lignin.}, }
@article {pmid24221700, year = {1983}, author = {Thompson, LA and Nedwell, DB and Balba, MT and Banat, IM and Senior, E}, title = {The use of multiple-vessel, open flow systems to investigate carbon flow in anaerobic microbial communities.}, journal = {Microbial ecology}, volume = {9}, number = {3}, pages = {189-199}, pmid = {24221700}, issn = {0095-3628}, abstract = {Five vessels, connected in series, were used for a continuous flow system to model carbon flow in anaerobic microbial communities. Two such 5-vessel systems were constructed, the inflows containing 10 mM sulfate and either 10 mM glucose or benzoate. Dilution was slow (D=0.0018 h(-1) for the whole system).Analyses of dissolved organic and inorganic carbon, and of CO2 and CH4, showed that the systems attained steady states in which biomass was constant, although there was net biosynthesis in the early vessels and net mineralization in succeeding vessels.Examination of the distributions of sulfate reduction, methanogenesis, and of H2+CO2-utilizing fatty acid-forming bacteria revealed spatial separation of these functional groups of bacteria in different vessels of the array, resembling the vertical spatial separation found in many natural sediments. Such model systems should, therefore, prove valuable in investigating the many microbial activities that contribute to the flow of carbon in anaerobic microbial communities.}, }
@article {pmid24221654, year = {1983}, author = {Elad, Y and Sadovski, Z and Chet, I}, title = {Detection of mycoparasitism by infrared photomicrography.}, journal = {Microbial ecology}, volume = {9}, number = {2}, pages = {185-187}, pmid = {24221654}, issn = {0095-3628}, abstract = {The fungusTrichoderma harzianum which parasitizes its hostRhizoctonia solani (AG 1-6) was observed under a light microscope and the interaction sites photomicrographed with infrared film. Bright regions indicating infrared irradiation were observed at the interaction sites, apparently due to the high parasitic activity occurring there. The possible use of infrared photomicrography in cell-cell interactions is discussed.}, }
@article {pmid24221653, year = {1983}, author = {Maki, JS and Remsen, CC}, title = {A membrane adsorption-SEM technique for observing neuston organisms.}, journal = {Microbial ecology}, volume = {9}, number = {2}, pages = {177-183}, pmid = {24221653}, issn = {0095-3628}, abstract = {A technique to observe neuston organisms, combining membrane adsorption and scanning electron microscopy, is described. Bacteria, algae, and protozoa collected from the surface of 2 freshwater ponds using this methodology appeared well preserved by the fixation and dehydration procedures used.}, }
@article {pmid24221652, year = {1983}, author = {Buck, JD}, title = {Occurrence ofCandida albicans in fresh gull feces in temperate and subtropical areas.}, journal = {Microbial ecology}, volume = {9}, number = {2}, pages = {171-176}, pmid = {24221652}, issn = {0095-3628}, abstract = {The occurrence ofCandida albicans in fresh gull (Larus spp.) feces was compared in temperate and subtropical locations. Of 239 fresh samples, 133 were obtained in southeastern Connecticut and 106 from different sites on the southeastern and central western coasts of Florida. Overall, 60% of all feces containedC. albicans. Of the Connecticut samples, 78% were positive, whereas 38% of the Florida samples revealed the presence of the yeast. Only 1 of 24 samples of fresh brown pelican feces containedC. albicans. Differences inC. albicans occurrence in birds in various locations was ascribed to variations in habitat and feeding behavior. Samples of water from a municipal reservoir in Connecticut were routinely positive, with an average cell density of 20/liter. Two fresh gull samples obtained on the reservoir bank containedC. albicans at an average cell concentration of 5, 200/g. The frequency ofC. albicans in gull droppings was higher than reported by others, and the yeast is common in temperate waters. These findings have important public health implications.}, }
@article {pmid24221651, year = {1983}, author = {Wassel, RA and Mills, AL}, title = {Changes in water and sediment bacterial community structure in a lake receiving acid mine drainage.}, journal = {Microbial ecology}, volume = {9}, number = {2}, pages = {155-169}, pmid = {24221651}, issn = {0095-3628}, abstract = {Water and sediment bacterial communities in a freshwater impoundment were studied over a 13-month period for stress-related responses to a point source of acid mine drainage (AMD). Comparisons of community structure were made on collections taken at the mouth of the acid stream, at a point 2 km downstream, and at the mouth of an uncontaminated stream. Monthly measurements of pH and specific conductance indicated the expected decrease in the AMD pollution with increasing distance from the source. Acridine orange direct counts did not differ significantly among the sites; however significantly fewer viable heterotrophs were observed by plate counts at the acid impacted station relative to the uncontaminated site. The diversity of the communities was significantly lower at the sites receiving mine drainage as compared with the unaffected station, and comparisons of community similarity showed that collections from the impacted sites were more like each other than like the control site. The assemblage at the latter site contained many bacterial guilds not found at the contaminated sites. The guilds unique to the control site showed a reduced in vitro ability to tolerate heavy metals as compared with the general community.}, }
@article {pmid24221650, year = {1983}, author = {Hazen, TC}, title = {A model for the density ofAeromonas hydrophila in Albemarle Sound, North Carolina.}, journal = {Microbial ecology}, volume = {9}, number = {2}, pages = {137-153}, pmid = {24221650}, issn = {0095-3628}, abstract = {The abundance ofAeromonas hydrophila was measured monthly at 29 sites in Albemarle Sound, North Carolina and its tributaries from April 1977 through July 1979. Simultaneous measurements included heterotrophic plate count bacteria, fecal coliform bacteria, and 18 physical and chemical parameters. Using only 6 water quality parameters, multiple correlation and regression analysis of the data produced a best-fit regression which explained 38% of the variation observed inA. hydrophila density. The 6 water quality parameters included dissolved oxygen, temperature, orthophosphate, chlorophyll A trichromatic, total Kjeldahl nitrogen, and ammonia. Heterotrophic plate count bacteria and fecal coliform densities were highly correlated withA. hydrophila density, but made the model very unstable. The model was successfully tested against similar data collected for 2 other North Carolina reservoirs, Lake Norman and Badin Lake. Data from 10 sites in Badin Lake over 18 months and from 7 sites on Lake Norman over 5 months were not significantly different from the Albemarle Sound model. Conditions of water quality that may give rise to "blooms" ofA. hydrophila will simultaneously contribute to the probability of increased epizootics in fish in the southeastern United States.}, }
@article {pmid24221649, year = {1983}, author = {Simmons, GM and Wharton, RA and Parker, BC and Andersen, D}, title = {Chlorophylla and adenosine triphosphate levels in Antarctic and temperate lake sediments.}, journal = {Microbial ecology}, volume = {9}, number = {2}, pages = {123-135}, pmid = {24221649}, issn = {0095-3628}, abstract = {Analysis of adenosine triphosphate (ATP) from surficial sediment layers in two antarctic lakes and two temperate lakes showed a high degree of similarity in spite of differences between trophic state, mictic state, or geographic location. Adenosine triphosphate was found at all levels sampled in temperate lake sediment cores but occasionally was present only in surficial layers of antarctic cores. Surficial sediment layers from antarctic lakes contained high chlorophylla (Chla) levels due to the extensive benthic algal mats which occur there. In some antarctic cores, Chla was detectable in deep, old mat layers, whereas Chla was not found in any of the temperate lake cores. Antarctic lake sediments appear to be unique environments where Chla molecules can remain intact for long periods of time due to low light, temperature, and microbial activity. As such, these lakes are important natural laboratories where a long history of microbial interactions can be studied without metazoan perturbation effects. Although there was much variability in concentration of Chla and ATP between samples, there appears to be no relationship between Chla or ATP levels to mictic or trophic states of the lakes. These data suggest that sediment microbial communities may be independent of environmental and biological properties of the overlying water masses.}, }
@article {pmid24221648, year = {1983}, author = {Fenchel, T and Finlay, BJ}, title = {Respiration rates in heterotrophic, free-living protozoa.}, journal = {Microbial ecology}, volume = {9}, number = {2}, pages = {99-122}, pmid = {24221648}, issn = {0095-3628}, abstract = {Published estimates of protozoan respiratory rates are reviewed with the object of clarifying their value in ecological studies. The data show a surprisingly large variance when similarly sized cells or individual species are compared. This is attributed to the range of physiological states in the cells concerned. The concept of basal metabolism has little meaning in protozoa. During balanced growth, energy metabolism is nearly linearly proportional to the growth rate constant; at the initiation of starvation, metabolic rate rapidly declines. Motility requires an insignificant fraction of the energy budget of protozoans. For growing cells, metabolic rate is approximately proportional to weight(0.75) and the data fall nearly exactly on a curve extrapolated from that describing the respiration rates of poikilotherm metazoans as a function of body weight. It is conceivable that protozoan species exist with lower maximum potential growth and metabolic rates than those predicted from cell volume and the equations derived from the available data. However, the lack of information concerning the state of the cells studied prevents verification of this idea. Laboratory measurements of protozoan respiratory rates have no predictive value for protozoa in nature other than delimiting a potential range. For small protozoans, this range may, on an individual basis, represent a factor of 50.}, }
@article {pmid24221647, year = {1983}, author = {Paerl, HW}, title = {Environmental regulation of H2 utilization ((3)H 2 exchange) among natural and laboratory populations of N2 and non-N 2 fixing phytoplankton.}, journal = {Microbial ecology}, volume = {9}, number = {2}, pages = {79-97}, pmid = {24221647}, issn = {0095-3628}, abstract = {Regulation of H2 utilization, as monitored by the hydrogenase-mediated(3)H2 exchange reaction, was examined among phytoplankton communitiesin situ and populations in culture. During a 2-year study in the Chowan River, North Carolina, at least 2 major groups of phytoplankton dominated(3)H2 exchange rates. They included N2 fixing cyanobacteria and NO3 (})- utilizing genera. Utilization of(3)H2 by N2 fixers was mainly dark-mediated, whereas(3)H2 utilization associated with periods of NO3 (})- abundance revealed an increasing dependence on light. Inhibitors of N2 fixation (C2H2 and NH4 (+)) negatively affected(3)H2 utilization, substantiating previous findings that close metabolic coupling of both processes exists among N2 fixing cyanobacteria. Conversely, NO3 (})- stimulated(3)H2 utilization among N2 and non-N2 fixing genera, particularly under illuminated conditions. A variety of environmental factors were shown to control(3)H2 exchange. In addition to the nitrogen sources discussed above, dissolved O2, photosynthetically available radiation (PAR), temperature, and pH changes altered(3)H2 exchange rates. It is likely that other factors not addressed here could also affect(3)H2 exchange rates. At least 2 ecological benefits from H2 utilization in natural phytoplankton can be offered. They include the simultaneous generation of adenosine triphosphate (ATP) and consumption of O2 during the oxidation of H2 via an oxyhydrogen or "Knallgas" reaction. Both processes could help sustain phytoplankton, and particularly cyanobacterial, bloom intensity under natural conditions when O2 supersaturation is common in surface waters. H2 utilization appeared to be a general feature of natural and laboratory phytoplankton populations. The magnitudes of(3)H2 utilization rates were directly related to community biomass. Although it can be shown that utilization rates are controlled by specific environmental factors, the potential relationships between H2 utilization and phytoplankton primary production remain poorly understood.}, }
@article {pmid24221617, year = {1983}, author = {Hood, MA and Ness, GE and Rodrick, GE and Blake, NJ}, title = {Distribution ofVibrio cholerae in two Florida estuaries.}, journal = {Microbial ecology}, volume = {9}, number = {1}, pages = {65-75}, pmid = {24221617}, issn = {0095-3628}, abstract = {The distribution ofVibrio cholerae was examined in 2 Florida estuaries, Apalachicola and Tampa Bay.Vibrio cholerae serotype non-01 was the most abundant serotype, being isolated from 45% of the oyster samples, 30% of the sediments, 50% of the waters, and 75% of the blue crabs.Vibrio cholerae serotype 01 was isolated from only one oyster sample. Strong linear correlations betweenV. cholerae and temperature, salinity, or the other physical/chemical parameters measured,Escherichia coli, or fecal coliforms were not observed, but a range of temperatures and salinities appeared relevant to the distribution of the organism. The organism was present in the highest concentrations when salinities were 10‰-25‰ and temperatures were 20‡C-35‡C.In vitro growth curves of 95V. cholerae environmental isolates further supported that 10‰-25‰ was an ideal salinity range for the organisms. The results suggest thatV. cholerae is a widely distributed organism in the nutrient-rich warm waters of the Gulf Coast estuaries.}, }
@article {pmid24221616, year = {1983}, author = {Esteve, I and Guerrero, R and Montesinos, E and Abellà, C}, title = {Electron microscope study of the interaction of epibiontic bacteria withChromatium minus in natural habitats.}, journal = {Microbial ecology}, volume = {9}, number = {1}, pages = {57-64}, pmid = {24221616}, issn = {0095-3628}, abstract = {Epibiontic cells on the surface of the photosynthetic purple sulfur bacteriumChromatium minus, collected several times during the year from 3 different Spanish lakes, were examined using scanning and transmission electron microscopy. The cells attached to theC. minus cell wall by an electron-dense pad, but did not enter the cell. They were ovoidal (about 0.6Μm wide) when free, and slightly curved rods (0.3×0.6Μm) when undergoing division. Division only occurred when cells remained attached toChromatium. A septum was formed, resulting in 2 or 3 curved rods surrounded by a common capsule. Detached daughter cells became ovoidal.The host ultrastructure changed as a result of epibiontic attachment, showing symptoms of cellular degradation. Simultaneously, plaques could be detected on cell lawns formed spontaneously upon cell sedimentation from field samples.}, }
@article {pmid24221615, year = {1983}, author = {Mallory, LM and Sayler, GS}, title = {Heterotrophic bacterial guild structure: Relationship to biodegradative populations.}, journal = {Microbial ecology}, volume = {9}, number = {1}, pages = {41-55}, pmid = {24221615}, issn = {0095-3628}, abstract = {Numerical taxonomic analysis of a freshwater bacterial guild demonstrated that the bacteria capable of growth on phenanthrene and polychlorinated biphenyl media were representative of the taxa obtained from low nutrient oligotrophic media. The diversity of heterotrophic bacteria and members of new taxa recovered from the guild followed a poisson distribution relative to the number of isolation media used. Moderately high nutrient, yeast extract peptone and glucose agar was found to be the most selective isolation medium relative to the total number of taxa recovered whereas low nutrient, lake water agar was the least selective medium used. Carbon source utilization patterns of the isolated taxa indicated that taxa within the guild had broad niche ranges and could potentially occupy many niches within a dynamic environment. The structure of the bacterial guild was dominated by mesophilic oligotrophs.The results of this investigation demonstrate that potential biodegradative populations are representative of the diverse taxa found in uncontaminated freshwater environments.}, }
@article {pmid24221614, year = {1983}, author = {Marinucci, AC and Hobbie, JE and Helfrich, JV}, title = {Effect of litter nitrogen on decomposition and microbial biomass inSpartina alterniflora.}, journal = {Microbial ecology}, volume = {9}, number = {1}, pages = {27-40}, pmid = {24221614}, issn = {0095-3628}, abstract = {The effect on decomposition of 4 different levels of nitrogen in aerial tissue ofSpartina alterniflora, collected at the end of its growing season litter, was studied in laboratory percolators for 56 days at 20‡C. The CO2 evolution and the release of organic nitrogen and organic carbon were monitored. From these data, the ash-free dry weight (AFDW), nitrogen (N) content, and carbon∶nitrogen (C/N) ratio were calculated at various times during decomposition. Fungal biomass, bacterial biomass, and the relative autoradiographic activity of bacteria were measured at the end of the study. Decomposition was significantly affected by the nitrogen content of the litter. A 55% increase in plant N increased overall weight loss and k by 50% and 40%, respectively. Furthermore, k (calculated from time course weight loss data) responded linearly to the 4 different levels of nitrogen inSpartina tissue. Fungi appear to dominate the microbial community. At the end of the experiment, fungal biomass was between 2.23 and 3.08% of the AFDW, and was calculated to contain 12 to 22% of the nitrogen in the litter. Bacterial biomass was 1/10 of the fungal biomass, and 12-17% of the bacteria were active. The total microbial biomass was not affected by increased plant nitrogen. In the course of decomposition, the organic nitrogen and carbon were highest in the effluent water in all treatments during the first 8 days. The respiration rate (CO2 evolution) first increased to a maximum at day 18 and then decreased to a constant rate (1-2 mg C/day/g detritus). Respiration was highest in the high N litter. The C/N ratio in all treatments increased from the start to day 8, then decreased to day 20. In low N litter, C/N then increased again as a result of increased total organic nitrogen (TON) loss relative to carbon mineralization. In the high N, this was reversed.}, }
@article {pmid24221613, year = {1983}, author = {Bengtsson, G}, title = {Habitat selection in two species of aquatic hyphomycetes.}, journal = {Microbial ecology}, volume = {9}, number = {1}, pages = {15-26}, pmid = {24221613}, issn = {0095-3628}, abstract = {Two species of aquatic hyphomycetes,Tetracladium marchalianum andTricladium splendens, were isolated from decaying leaves in a stream.T. marchalianum was abundant on alder leaves but absent on beech leaves, which were dominated byT. splendens. It was hypothesized that differences in some chemical key factors in the leaves would account for differences in the distribution of the 2 species. In the experiment designed to test the hypothesis, combinations of sterilized leaves and isolated fungi were used. Differences in growth of FDA active mycelium were related to differences in leaf weight loss;T. splendens decomposed beech leaves andT. marchalianum decomposed alder leaves. Extracellular protease activity corresponded with these trends but there was no detectable protein loss in the leaves. Both fungi showed a nitrogen demand, and hydrolysis of leaf proteins was complemented with absorption of free amino acids and ammonium. High concentrations of free amino acids modified the pattern for habitat selection so thatT. splendens grew substantially on alder leaves andT. marchalianum colonized beech leaves. No protease activity was, however, found fromT. marchalianum on beech leaves, and it is concluded that a more general metabolic inhibition prevents extensive growth of this species on beech leaves. The low natural abundance ofT. splendens on alder leaves, where it may grow well, may be a consequence of a specific protease inhibition and competition from other species.}, }
@article {pmid24221612, year = {1983}, author = {Kieft, TL and Caldwell, DE}, title = {A computer simulation of surface microcolony formation during microbial colonization.}, journal = {Microbial ecology}, volume = {9}, number = {1}, pages = {7-13}, pmid = {24221612}, issn = {0095-3628}, abstract = {Several models of microbial surface colonization have been devised to quantitate growth and attachment rates on surfaces. One of these, the surface growth rate equation, is based on the assumption that the number of microcolonies of a given size (Ci) reaches a constant value (Cmax) that is equal to the attachment rate (A) divided by the specific growth rate (Μ). In this study, a computer simulation was used to determine the time required to reach Cmax. It was shown that Ci approaches Cmax asymptotically. The time required is dependent solely upon the growth rate and size of microcolonies. The number of one-celled microcolonies reaches 95% of Cmax after 4.3 generations. At low growth rates, a relatively long incubation period is required. Alternate methods that shorten the incubation time are considered.}, }
@article {pmid24221611, year = {1983}, author = {Caldwell, DE and Malone, JA and Kieft, TL}, title = {Derivation of a growth rate equation describing microbial surface colonization.}, journal = {Microbial ecology}, volume = {9}, number = {1}, pages = {1-6}, pmid = {24221611}, issn = {0095-3628}, abstract = {A surface growth rate equation is derived which describes simultaneous growth and attachment during microbial surface colonization. The equation simplifies determination of attachment and growth rate, and does not require a computer program for solution. This rate equation gives the specific growth rate (Μ) as a function of the number of cells on the surface (N), the incubation period (t), and the number of colonies (Ci) containing either one cell, two cells, four cells, etc, as shown below.[Formula: see text] The attachment rate (A) is given by the following relationship:[Formula: see text] The proposed colonization kinetics are compared with exponential growth kinetics using 3-dimensional computer plots. Colonization kinetics diverged most from exponential kinetics when the growth rate was low or the attachment rate was high. Using these kinetics, it is possible to isolate the effects of growth and attachment on microbial surface colonization.}, }
@article {pmid24226056, year = {1982}, author = {Clark, TB and Whitcomb, RF and Tully, JG}, title = {Spiroplasmas from coleopterous insects: New ecological dimensions.}, journal = {Microbial ecology}, volume = {8}, number = {4}, pages = {401-409}, pmid = {24226056}, issn = {0095-3628}, abstract = {The genusSpiroplasma (helical wall-less prokaryotes) is a recently described group of microorganisms that cause disease in plants, arthropods, and experimentally, in vertebrates. Two spiroplasmas from beetles have now been discovered in a search for microorganisms suitable for biological control of economically important coleopterous insects. Colorado potato beetles (CPB) infected with spiroplasma were commonly found on potato and other solanaceous plants in Maryland. Although this spiroplasma occurred in high concentration in gut fluids and sputum, it could not be cultivated in conventional spiroplasma media. However, another spiroplasma (CN-5 and related strains) reported here to occur commonly in association with larvae and adults of the green June beetle,Cotinus nitida, could be cultivated readily in the SM-1 formulation and several other conventional spiroplasma media. The CN-5 spiroplasma was serologically distinct from representative members of all 8 major groups now recognized. Thus, it represents a ninth major spiroplasma serogroup (IX), and can be considered to be an unnamed species. The CPB spiroplasma is apparently maintained in plant surface-insect gut cycles, but details of maintenance of the CN-5 spiroplasma are incompletely understood. Isolation of CN-5 spiroplasma from soil in which host larvae had fed suggests that transmission of this agent may occur in the soil. Both CN-5 and CPB spiroplasmas exhibited unusually active translational motility in natural fluids, and CN-5 organisms exhibited such motility in culture media. Although we have no evidence that either spiroplasma is pathogenic to its usual host, the pathogenicity of spiroplasmas to many hosts, including the beetle,Melolontha melolontha, suggests possible application for biological control.}, }
@article {pmid24226055, year = {1982}, author = {Mouches, C and Bové, JM and Albisetti, J and Clark, TB and Tully, JG}, title = {A spiroplasma of serogroup IV causes a May-disease-like disorder of honeybees in Southwestern France.}, journal = {Microbial ecology}, volume = {8}, number = {4}, pages = {387-399}, pmid = {24226055}, issn = {0095-3628}, abstract = {Honeybees affected by a disorder resembling the classical "May disease" in southwestern France contained numerous helical, motile organisms in their digestive tracts and hemolymph. Two strains of the organism (B31 and B39) were cultured and triply cloned in the BSR spiroplasma medium. The electrophoretic patterns of spiroplasmal proteins in 1 - and 2-dimensional polyacrylamide gels were similar to those of group IV spiroplasmas F1 and F2, cultured previously from flower surfaces in France. The organism could be introduced into adult bees by injection or food ingestion at various stages after emergence. Agent administered by either route multiplied to high titers in the hemolymph and killed the bees. Both multiplication and the induced lethal effect of the agent could be prevented by tetracycline but not penicillin. Spiroplasmas that were nearly identical to the B31 and B39 strains were also recovered from the surface of flowers collected within the area visited by the bees from the diseased hives.}, }
@article {pmid24226054, year = {1982}, author = {Daggett, PM and Sawyer, TK and Nerad, TA}, title = {Distribution and possible interrelationships of pathogenic and nonpathogenicAcanthamoeba from aquatic environments.}, journal = {Microbial ecology}, volume = {8}, number = {4}, pages = {371-386}, pmid = {24226054}, issn = {0095-3628}, abstract = {Among the more recently discovered agents of human disease are small, free-living amebae belonging to the generaNaegleria andAcanthamoeba. An overview of the distribution ofAcanthamoeba in recent surveys of the near shore waters of the northeastern United States is presented. There appears to be a particular association between the presence ofAcanthamoeba in marine sediments and the sites of oceanic sludge dumping. Amebae belonging to the genusNaegleria have not been isolated from these marine sediments which routinely yieldedAcanthamoeba. Starch gel electrophoretic analysis of enzymes suggests that some isolates ofAcanthamoeba from oceanic sludge dump-sites are not members of previously recognized pathogenic species.}, }
@article {pmid24226053, year = {1982}, author = {Mundt, JO}, title = {The ecology of the streptococci.}, journal = {Microbial ecology}, volume = {8}, number = {4}, pages = {355-369}, pmid = {24226053}, issn = {0095-3628}, abstract = {All species of streptococci are divided into several groups according to the ecological niches they occupy. Members of the lactic acid group are found only in the plant environment and the dairy. Members of the pyogenic group and the buccal and intestinal residents of the subthermophilic group are found in intimate association only with homeothermic hosts. Members of the virulent pyogenic group, such asStreptococcus pyogenes, S. equi, andS. infrequens, are restricted to single hosts-the human, the horse, and the pig-whereas others, such asS. agalactiae can be found in several hosts. The intestinal dwellers of the subthermophilic group,S. bovis andS. equinus, occur in several animal species and are not isolated from other sources. The superficially homogeneousS. faecalis of the "enteric" group may actually consist of a group specifically restricted to the human host, and of a second group distributed among wild animals, insects, and plants. The latter group differs from the human type by the ability to hydrolyze starch and to produce a rennin-proteolytic type of curd in milk.Streptococcus faecium is widely distributed in both the homeothermic and poikilothermic environments, but no properties which differentiate the sources are known.Streptococcus faecium biot.casseliflavus has been isolated only from insects and plants.Streptococcus uberis occurs on the bovine lips and skin. Unidentified streptococci from all environments vary widely in properties. Many resembleS. lactis, S. faecalis, andS. faecium.}, }
@article {pmid24226052, year = {1982}, author = {Taylor, DN and Brown, M and McDermott, KT}, title = {Waterborne transmission ofCampylobacter enteritis.}, journal = {Microbial ecology}, volume = {8}, number = {4}, pages = {347-354}, pmid = {24226052}, issn = {0095-3628}, abstract = {Campylobacter jejuni is an important cause of human diarrheal disease throughout the world and likeSalmonella enteritidis, has a large animal reservoir which includes most of man's domestic animals. Until recently, it has been difficult to trace the chain of transmission from animals to man because of inadequate environmental sampling techniques and means to distinguish strains. Recent improvements in these techniques have made environmental studies more feasible in 2 water-related out-breaks.In 1 study,C. jejuni was found to be an important cause of sporadic, summertime diarrheal disease among hikers in national wilderness areas of Wyoming. In this setting, illness was significantly associated with drinking untreated surface water. SubsequentlyC. jejuni was isolated from surface water, including mountian streams, and from animals in the area. Some of the environmental isolates were serotypically identical to strains isolated from humans.A second study occurred as a result of an outbreak of Campylobacter enteritis in a community in northern Illinois which was epidemiologically associated with the community water system.Campylobacter jejuni was isolated from several surface water sources and from the implicated water system. These studies demonstrate that environmental isolation ofC. jejuni is now possible and may add to our understanding of disease transmission.}, }
@article {pmid24226051, year = {1982}, author = {Janda, JM and Sheehan, DJ and Das, A and Bottone, EJ}, title = {Gentamicin-resistantPseudomonas aeruginosa: Concepts regarding their evolution and attenuated virulence.}, journal = {Microbial ecology}, volume = {8}, number = {4}, pages = {335-346}, pmid = {24226051}, issn = {0095-3628}, abstract = {Pseudomonas aeruginosa, a free-living bacterial species, is a major nosocomial pathogen, especially of compromised patients within medical facilities. Numerous factors contribute to the ecological selection of this bacterial species within the hospital environment, among which the expression of newly acquired or quiescent enzymatic capability seems par-amount. The emergence of pathogenic strains ofP. aeruginosa appears to be gradual, embodying a transition of strains from their natural aquatic environment, to establishing inanimate (hospital) and animate (human) reservoirs. In this stepwise transition, subsets ofP. aeruginosa may evolve which express a survival trait, for example, gentamicin resistance, but concomitantly suffer a loss of invasive potential. In this study,P. aeruginosa strains from natural [22], hospital [11], and stool [17] sources were evaluated for their physiological and exoenzymatic activity and compared with gentamicin-resistantP. aeruginosa (GRPA) strains [49] of clinical origin. As a whole, environmental and hospital isolates showed reduced enzymatic potential, for example, frequency of production of elastase, lipase, deoxyribonuclease, and pyocyanin production. Human fecal isolates most closely resembled the prototype of human invasiveP. aeruginosa in their gentamicin susceptibility (95%) and increased frequencies of exoenzymes, including elastase production. On the other hand, GRPA were frequently apyocyanogenic (9/49), lacked extracellular enzymes correlated with pathogenicity, and were rarely isolated from systemic sites. When encountered, these strains appeared to represent colonization of a body site rather than incitants of overt infection. As a "subset" ofP. aeruginosa, gentamicin resistance was seen predominantly among serotype 11 strains, and encountered most frequently from patients with localized urinary tract infections.}, }
@article {pmid24226050, year = {1982}, author = {Lechevallier, MW and Evans, TM and Seidler, RJ and Daily, OP and Merrell, BR and Rollins, DM and Joseph, SW}, title = {Aeromonas sobria in chlorinated drinking water supplies.}, journal = {Microbial ecology}, volume = {8}, number = {4}, pages = {325-333}, pmid = {24226050}, issn = {0095-3628}, abstract = {Aeromonas species were recovered from over 27% of 183 chlorinated drinking water samples collected during an 18-month period. Sixteen of 20 isolates tested elicited a cytotoxic response by Y-1 mouse adrenal cells. None of the strains was either enterotoxigenic by the rabbit ligated ileal loop assay, exhibited piliation, or showed significant mannose resistant adherence to human buccal cells. TheAeromonas isolates were further identified to beA. sobria and were resistant to ampicillin and susceptible to chloramphenicol, kanamycin, streptomycin, and tetracycline. Total coliform levels did not correlate withAeromonas densities in distribution water. With 85% of the samplings,Aeromonas occurred in distribution water when no coliforms were detectable by either the membrane filter or most-probable-number techniques. A significant correlation (P<.001) existed between standard plate count levels andAeromonas.}, }
@article {pmid24226049, year = {1982}, author = {Xu, HS and Roberts, N and Singleton, FL and Attwell, RW and Grimes, DJ and Colwell, RR}, title = {Survival and viability of nonculturableEscherichia coli andVibrio cholerae in the estuarine and marine environment.}, journal = {Microbial ecology}, volume = {8}, number = {4}, pages = {313-323}, pmid = {24226049}, issn = {0095-3628}, abstract = {Plating methods for estimating survival of indicator organisms, such asEscherichia coli, and water-borne pathogens includingVibrio cholerae, have severe limitations when used to estimate viable populations of these organisms in the aquatic environment. By combining the methods of immunofluorescent microscopy, acridine orange direct counting, and direct viable counting, with culture methods such as indirect enumeration by most probable number (MPN) estimation and direct plating, it was shown that bothE. coli andV. cholerae undergo a "nonrecoverable" stage of existence, but remain viable. Following 2-week incubations in saltwater (5-25%o NaCl) microcosms, total counts, measured by direct microscopic examination of fluorescent antibody and acridine orange stained cells, remained unchanged, whereas MPN estimates and plate counts exhibited rapid decline. Results of direct viable counting, a procedure permitting estimate of substrate-responsive viable cells by microscopic examination, revealed that a significant proportion of the nonculturable cells were, indeed, viable. Thus, survival of pathogens in the aquatic environment must be re-assessed. The "die-off" or "decay" concept may not be completely valid. Furthermore, the usefulness of the coliform and fecal coliform indices for evaluating water quality for public health purposes may be seriously compromised, in the light of the finding reported here.}, }
@article {pmid24226048, year = {1982}, author = {Roberts, NC and Siebeling, RJ and Kaper, JB and Bradford, HB}, title = {Vibrios in the Louisiana gulf coast environment.}, journal = {Microbial ecology}, volume = {8}, number = {4}, pages = {299-312}, pmid = {24226048}, issn = {0095-3628}, abstract = {A polyphasic approach, using bacteriological, immunological, and molecular biological techniques was used to elucidate the distribution of pathogenicVibrio species in the Louisiana coastal environment. A variety ofVibrio species pathogenic for man, includingV. cholerae, V. parahaemolyticus, V. fluvialis, andV. vulnificus, were found to be ubiquitous in Louisiana.Vibrio species monitored were shown to fluctuate in response to environmental factors of temperature, salinity, and nutrient level, and to vary independently of fecal coliform counts. A comprehensive serological screening system, based on species specific H antigens, was developed to identify pathogenicVibrio sp. 1 step after primary isolation.Vibrio sp. were correctly identified with accuracies ranging from 93-100%, depending on the specific H antiserum. Over 2,500V. cholerae isolates were rapidly screened for production of cholera toxin by DNA hybridization of specific toxin gene probes to colonies inoculated on nitrocellulose filter paper. The toxin gene probes, together with O antigen analysis, revealed that enterotoxigenicV. cholerae 01 serovars were recovered only from sewage stations or human disease, whereas enterotoxigenicV. cholerae non 01 serovars were recovered from environmental samples in addition to clinical and sewage samples. The results of this study indicate that techniques of immunology and molecular biology are very valuable supplements to conventional bacteriological techniques in studying the epidemiology and ecology of pathogenicVibrio sp.}, }
@article {pmid24226047, year = {1982}, author = {Westfall, HN and Myers, WF and Weiss, E}, title = {Detection ofLegionella antibodies by enzyme-linked immunosorbent assay (ELISA) using whole cell and carbohydrate antigens.}, journal = {Microbial ecology}, volume = {8}, number = {4}, pages = {287-298}, pmid = {24226047}, issn = {0095-3628}, abstract = {The systematic study ofLegionella as a human pathogen and a bacterium widely disseminated in the environment requires simplification of present methodology. We describe a highly sensitive enzyme-linked immunosorbent assay (ELISA) for the detection of serum antibodies that can also be used for the detection of antigen.Legionella pneumophila serogroups 1 and 3 (Philadelphia 2 and Bloomington 2),L. bozemanii (WIGA), andL. micdadei (TATLOCK) were grown in diphasic medium consisting of charcoal yeast extract agar (CYE) overlayed with yeast extract medium (YEM) for the production of whole cell antigen and CYE for the extraction of carbohydrate antigen. The whole cells were inactivated with 0.5% formalin. The carbohydrate was obtained from the supernatant of cells resuspended twice in phosphate buffered saline (PBS). The antigen was sterilized and concentrated by filtration and purified by chromatography through a Sepharose 4B column. The highest molecular weight fractions were used for chemical characterization, which confirmed the carbohydrate nature of the antigen, and for micro-ELISA. Titers ranging from 5×10(3) to 3×10(5) (inverse of serum dilutions) were obtained from rabbit sera collected after 1, 2, or 3 injections of whole cells. The titers were somewhat higher and more consistent with the higher of 2 antigen concentrations used (5 or 15μg/ml protein or dry weight), and with the carbohydrate rather than the whole cell antigen. The reactions were serogroup and species specific and only low titers were obtained with some of the heterologous antigens. The sensitivity and specificity of the reactions were not diminished when as many as 4 antigens were mixed in the same well. Thus, the micro-ELISA can be used as a test of highly specific antigens as well as a screening test with mixtures of antigens. A preliminary test withLegionella containing water specimen concentrates and high-titer rabbit sera indicated that the micro-ELISA can also be used for the detection of antigen. This investigation appears to have paved the way for the simplification of the serological methodology for the study ofLegionella.}, }
@article {pmid24226046, year = {1982}, author = {Joseph, SW}, title = {Editorial.}, journal = {Microbial ecology}, volume = {8}, number = {4}, pages = {285}, doi = {10.1007/BF02010668}, pmid = {24226046}, issn = {0095-3628}, }
@article {pmid24225894, year = {1982}, author = {Rasool, KA and Wimpenny, JW}, title = {Mixed continuous culture experiments with an antibiotic-producing streptomycete andEscherichia coli.}, journal = {Microbial ecology}, volume = {8}, number = {3}, pages = {267-277}, pmid = {24225894}, issn = {0095-3628}, abstract = {Four strains ofStreptomyces aureofaciens capable of producing different amounts of tetracycline have been grown in continuous culture with either of two strains ofEscherichia coli orBacillus pumillus. Each of the bacteria had faster specific growth rates than any of the streptomycetes.E. coli NTCT 5993 had a higher affinity for sucrose than didS. aureofaciens SR 11. In mixed culture experiments, the bacteria displaced the streptomycete under the following conditions: (a) when the streptomycete produced no tetracycline; (b) in tetracycline-producing cultures after a fraction of the bacteria had died-the bacterial population that subsequently developed was resistant to the drug; and (c) when using tetracycline-resistant bacteria. Under nutrient conditions leading to high antibiotic levels, it was possible to kill all the bacteria, and the streptomycete survived after a transient fall in mycelium and tetracycline levels. No stable mixed population was ever seen. Once tetracycline-resistant bacteria had displaced the streptomycete, and tetracycline concentrations had fallen, a sensitive bacterial population reappeared. Competition between sensitive and resistantE. coli NCTC 5993 in the chemostat confirmed the selective advantage of the sensitive strain. Results were discussed in terms of the role of antibiotics in nature.}, }
@article {pmid24225893, year = {1982}, author = {Smith, VR and Steyn, MG}, title = {Soil microbial counts in relation to site characteristics at a subantarctic Island.}, journal = {Microbial ecology}, volume = {8}, number = {3}, pages = {253-266}, pmid = {24225893}, issn = {0095-3628}, abstract = {Enumerations of colony-forming units of aerobic bacteria and fungi at Marion Island (46°54'S, 37°45'E) showed that the mire and bog peats investigated possessed greater numbers of microorganisms on a dry soil weight basis than did the slope fernbrake soils but that counts from both sites were similar per unit soil volume. Afjaeldmark soil of an exposed rocky ridge contained very low microbial populations. Manuring by sea-birds and seals caused an increase in levels of soil N and P and in the numbers of bacteria and fungi. Regression analyses indicated that inorganic N and soil pH explained more of the variation in bacterial and fungal counts respectively than all other soil parameters included in the regression. Variation in botanical composition between the sites was examined using multivariate analysis and the resulting pattern compared with the soil microorganism and nutrient levels. This analysis emphasized the importance of manuring influences in elevating NH4-N and bacterial levels in the soil and allowing the occurrence of a vegetation cover dominated by copriphilous species. No correlation occurred between site botanical factors and soil fungi counts.}, }
@article {pmid24225892, year = {1982}, author = {Blair, WR and Olson, GJ and Brinckman, FE and Iverson, WP}, title = {Accumulation and fate of tri-n-butyltin cation in estuarine bacteria.}, journal = {Microbial ecology}, volume = {8}, number = {3}, pages = {241-251}, pmid = {24225892}, issn = {0095-3628}, abstract = {The accumulation and possible metabolic transformation of tri-n-butyltin cation by tin-resistant estuarine bacteria was studied. The bacterial isolates accumulated tributyltin to 3.7-7.7 mg tin per g dry weight of cells by a nonenergy requiring process, probably by adsorption to the cell envelope. Chemical speciation of cell extracts and culture media by combined liquid chromatography-atomic absorption spectrophotometry and tin-selective purge and trap flame photometric gas chromatography for possible tributyltin degradation products revealed no significant biotransformations of tributyltin cation by the tributyltin-resistant isolates. Apparently the isolates accumulate, but do not metabolize tributyltin.}, }
@article {pmid24225891, year = {1982}, author = {Jansson, HB}, title = {Predacity by nematophagous fungi and its relation to the attraction of nematodes.}, journal = {Microbial ecology}, volume = {8}, number = {3}, pages = {233-240}, pmid = {24225891}, issn = {0095-3628}, abstract = {Predacity, the ability of nematophagous fungi to destroy nematodes, was investigated for eight species of fungi by a method using sterilized soil and the nematodePanagrellus redivivus. In addition, the ability of the fungi to attract nematodes was investigated using an agar plate technique. Predacity and attraction were highly correlated (r=0.98) in these tests. The presence of traps in cultures ofArthrobotrys oligospora increased the ability to attract nematodes by a factor of 2.}, }
@article {pmid24225890, year = {1982}, author = {Graham, JM and Canale, RP}, title = {Experimental and modeling studies of a four-trophic level predator-prey system.}, journal = {Microbial ecology}, volume = {8}, number = {3}, pages = {217-232}, pmid = {24225890}, issn = {0095-3628}, abstract = {Experimental studies of a microbial food chain involving organic carbon substrates,Enterobacter aerogenes, and ciliate protozoansParamecium primaurelia andDldinium nasutum were conducted in stirred, aerated batch cultures. Quantitative measurements were made of organic carbon levels and of cell numbers, mean cell volumes, and total biovolumes for all three microbial populations. A mathematical model based on Monod kinetics was developed to describe this four-trophic level predator-prey system. The model was formulated in terms of biovolume, which is the product of cell numbers and mean cell size, and includes terms for bio-volume decay. Batch culture data were used to derive parameter values, and model simulations were compared to experimental results. Despite the significance ofParamecium-Didinium studies in ecological literature, the entire food chain has not been previously studied or modeled.}, }
@article {pmid24225889, year = {1982}, author = {Swift, ST and Najita, IY and Ohtaguchi, K and Fredrickson, AG}, title = {Some physiological aspects of the autecology of the suspension-feeding protozoanTetrahymena pyriformis.}, journal = {Microbial ecology}, volume = {8}, number = {3}, pages = {201-215}, pmid = {24225889}, issn = {0095-3628}, abstract = {Feeding, growth, and reproductive responses of the suspension-feeding protozoanTetrahymena pyriformis to shifts up or down of the density of its bacterial food were observed. The rates of feeding, growth, and reproduction were determined by measuring the rates of uptake of viable bacterial cells, of change of mean volume of the protozoan cells, and of change of number of protozoan cells, respectively. The effects of the nutritional status of the protozoans at the time of shifting were observed also. Results are interpreted in terms of the limited polymorphism exhibited in the life cycle of this organism. Responses in all cases seem to reflect a strategy for exploiting a patchy, transient environment, a conclusion already reached by several earlier investigators.}, }
@article {pmid24225814, year = {1982}, author = {Brannan, DK and Caldwell, DE}, title = {Evaluation of a proposed surface colonization equation usingThermothrix thiopara as a model organism.}, journal = {Microbial ecology}, volume = {8}, number = {2}, pages = {200}, doi = {10.1007/BF02010454}, pmid = {24225814}, issn = {0095-3628}, }
@article {pmid24225813, year = {1982}, author = {Lachance, MA and Metcalf, BJ and Starmer, WT}, title = {Yeasts from exudates ofQuercus, Ulmus, Populus, andPseudotsuga: New isolations and elucidation of some factors affecting ecological specificity.}, journal = {Microbial ecology}, volume = {8}, number = {2}, pages = {191-198}, pmid = {24225813}, issn = {0095-3628}, abstract = {The yeast flora associated with exudates ofQuercus, Ulmus, Populus, andPseudotsuga was examined in the light of new isolations in geographic areas different from those in previous reports. Application of multivariate analytic methods indicated that geographic distance, although a meaningful ecological factor, is largely overshadowed by host tree specificity, provided that yeast community physiological profiles and not yeast taxa, are used as ecological descriptors. Some physiological attributes used in classifying yeasts were identified as particularly important in shaping the yeast communities of those trees. The possible divergence between these attributes and those generally considered taxonomically useful is discussed.}, }
@article {pmid24225812, year = {1982}, author = {Garland, CD and Lee, A and Dickson, MR}, title = {Segmented filamentous bacteria in the rodent small intestine: Their colonization of growing animals and possible role in host resistance toSalmonella.}, journal = {Microbial ecology}, volume = {8}, number = {2}, pages = {181-190}, pmid = {24225812}, issn = {0095-3628}, abstract = {The establishment and proliferation of a model population of autochthonous surface-associated microorganisms in the small bowel of growing rats (2-12 weeks of age) was studied. Segmented filamentous bacteria on the distal ileal villi were examined by scanning electron microscopy (SEM) and countedin situ by transect line analysis. In young animals, these bacteria first colonized the villous base, but occupied all areas on the villus by adult age. Their distribution on Peyer's patches was also noted.In growing animals, colonization of the ileal villi by filamentous bacteria was significantly correlated to the development of host resistance to fatal infection by orally-dosedSalmonella enteritidis. In animals givenSalmonella and examined by SEM and transmission EM (TEM), the pathogen was seen only on ileal tissue surfaces, predominantly the villous base, from which the autochthonous population was absent. Conversely, in animals with filamentous bacteria,Salmonella surface colonization was not observed. The results suggest a possible protective role for the surface flora in the small bowel.}, }
@article {pmid24225811, year = {1982}, author = {McCoy, RE and Basham, HG and Davis, RE}, title = {Powder puff spiroplasma: A new epiphytic mycoplasma.}, journal = {Microbial ecology}, volume = {8}, number = {2}, pages = {169-180}, pmid = {24225811}, issn = {0095-3628}, abstract = {A spiroplasma (strain PPS1) isolated from healthy flowers ofCalliandra haematocephala in Florida has been found to be a member of a serogroup of the Spiroplasmataceae. It is distinct fromSpiroplasma citri and from other described spiroplasmas as determined by growth inhibition, fluorescent antibody, and ELISA serological tests. PPS1 was also distinguished fromS. citri and several other spiroplasmas by the guanine + cytosine content of its DNA. PPS1 requires sterol for growth, is inhibited by digitonin, grows at 20-30°C, and does not hydrolyze arginine or urea. The ready isolation of this and similar organisms from surfaces of healthy plants emphasizes that caution should be exercised in attempts to isolate cell wall-less prokaryotes from the interior of diseased plants. Although some strains of spiroplasmas are known as insect pathogens in nature, the ecological role(s) of the flower-inhabiting spiroplasmas has yet to be fully determined.}, }
@article {pmid24225810, year = {1982}, author = {Trevors, JT and Mayfield, CI and Inniss, WE}, title = {Measurement of Electron Transport System (ETS) activity in soil.}, journal = {Microbial ecology}, volume = {8}, number = {2}, pages = {163-168}, pmid = {24225810}, issn = {0095-3628}, abstract = {Electron transport system (ETS) activity was measured in amended and nonamended soil by measuring the reduction of 2-(p-iodophenyl)-3-(p-nitrophenyl)-5-phenyl tetrazolium chloride (INT) to iodonitrotetrazolium formazan (INT-formazan), which can be easily extracted with methanol without interference from other compounds found in soil. A high correlation between ETS activity and oxygen consumption was observed. This technique allows rapid quantitative measurements of microbial ETS activity in soil.}, }
@article {pmid24225809, year = {1982}, author = {Rushforth, SR and Felix, EA}, title = {Biotic adjustments to changing salinities in the Great Salt Lake, Utah, USA.}, journal = {Microbial ecology}, volume = {8}, number = {2}, pages = {157-161}, pmid = {24225809}, issn = {0095-3628}, abstract = {The salinity of the Great Salt Lake, Utah has changed greatly over the past 23 years. The north arm of the lake has increased in salinity and decreased in overall biological diversity, whereas the south arm has decreased in salinity and increased markedly in biological diversity.}, }
@article {pmid24225808, year = {1982}, author = {Chrzanowski, TH and Stevenson, LH and Spurrier, JD}, title = {Transport of microbial biomass through the North Inlet ecosystem.}, journal = {Microbial ecology}, volume = {8}, number = {2}, pages = {139-156}, pmid = {24225808}, issn = {0095-3628}, abstract = {Tidal fluctuations and transports of total microbial biomass (measured as adenosine triphosphate [ATP]) were investigated at three marsh creeks comprising the major transfer points between the North Inlet marsh and the adjoining aquatic ecosystems. Two creeks, Town Creek and North Jones Creek, form the inlet mouth and are the only marsh-ocean exchange points. The third creek, South Jones Creek, connects to a brackish water embayment. The creeks were simultaneously sampled every 1.5 hours for 50 consecutive hours during neap tides (four tidal cycles) and 50 consecutive hours during spring tides of each season. At the inlet, ATP concentration fluctuated in phase with the tide during winter and fall and out of phase with the tide during the spring. Fluctuation patterns at South Jones Creek were irregular. The highest ATP concentrations were during the spring (mean=2.17 mg of ATP per m(3)) and the lowest concentrations were during the winter (mean=0.65 mg of ATP per m(3)). Net transports of ATP varied from tidal cycle to tidal cycle with regard to direction of transport (import or export) and magnitude. Net transports were small compared to large instantaneous transports and only 4 of 22 determinations of net transport were different from zero transport.}, }
@article {pmid24225807, year = {1982}, author = {Federle, TW and McKinley, VL and Vestal, JR}, title = {Physical determinants of microbial colonization and decomposition of plant litter in an Arctic Lake.}, journal = {Microbial ecology}, volume = {8}, number = {2}, pages = {127-138}, pmid = {24225807}, issn = {0095-3628}, abstract = {Physical effects on the microbial colonization and decomposition of plant litter in an oligotrophic lake were studied in Toolik Lake, Alaska. Colonization, measured by adenosine triphosphate (ATP) analysis, and decomposition, measured by weight loss, were correlated with depth of incubation, light, and temperature. The effects of turbulence, light, and temperature were studied in microcosm experiments. A 10°C increase (above ambient) in temperature caused a doubling in the amount of microbial colonization and a 50% increase in decomposition. Light intensity had no quantitative effect on either colonization or decomposition. Turbulence experiments conducted in Toolik Lake showed significant differences in decomposition between natural turbulence and no turbulence. Elevated temperature (20°C, which was 10°C above ambient), high turbulence, and total darkness changed the composition of the litter microbiota, causing a shift from a bacterially dominated microbiota to one dominated by large filamentous forms, as revealed by scanning electron microscopy. This study shows the importance of these physical factors in determining the rate at which plant litter is colonized and degraded in aquatic environments.}, }
@article {pmid24225806, year = {1982}, author = {Haack, TK and McFeters, GA}, title = {Nutritional relationships among microorganisms in an epilithic biofilm community.}, journal = {Microbial ecology}, volume = {8}, number = {2}, pages = {115-126}, pmid = {24225806}, issn = {0095-3628}, abstract = {Previous studies of an epilithic algal-bacterial community in a pristine mountain stream suggested that heterotrophic bacteria were responding to the metabolic activities of the phototrophic population. Subsequent studies were performed to follow the flow of labeled carbon, from its initial inorganic form, through the trophic levels of the mat community. A majority of primary production metabolites were excreted by the algal population during active growth; this shifted to an incorporation into cellular material as phototrophic activity declined. Results suggest that there was a direct flux of soluble algal products to the bacterial population, with little heterotrophic utilization of dissolved organics from the overlying stream water. Both phototrophic productivity and bacterial utilization of algal products peaked at approximately the same time of year. Activity of the diatom-dominated algal population declined as silica concentrations in the stream water dropped, leading to a situation in which the sessile bacteria were substrate limited. These events resulted in an almost complete disappearance of the community in early September.}, }
@article {pmid24225805, year = {1982}, author = {Riemann, B and Fuhrman, J and Azam, F}, title = {Bacterial secondary production in freshwater measured by(3)H-thymidine incorporation method.}, journal = {Microbial ecology}, volume = {8}, number = {2}, pages = {101-113}, pmid = {24225805}, issn = {0095-3628}, abstract = {Bacterial secondary production in lake water was measured by(3)H-thymidine incorporation into DNA. The application of the method to freshwater systems studied required (1) thymidine concentration > 10 nM (10-25 nM) evaluated from isotope dilution by varying the specific activity of labeled thymidine, (2) short incubation periods less than 1 hour, and (3) partial purification of the DNA fraction for measuring(3)H-thymidine incorporation. During 2 diel studies, bacterial productivity was compared to phytoplankton primary production and extracellular release of organic carbon. Diel changes in bacterial growth suggested substantial activity during the morning and evening. Possible mechanisms of control of bacterial growth, such as extracellular release of organic carbon, are discussed.}, }
@article {pmid24225702, year = {1982}, author = {Arianoutsou-Faraggitaki, M and Margaris, NS}, title = {Decomposers and the fire cycle in a phryganic (East Mediterranean) ecosystem.}, journal = {Microbial ecology}, volume = {8}, number = {1}, pages = {91-98}, pmid = {24225702}, issn = {0095-3628}, abstract = {Dehydrogenase activity, cellulose decomposition, nitrification, and CO2 release were measured for 2 years to estimate the effects of a wildfire over a phryganic ecosystem. In decomposers' subsystem we found that fire mainly affected the nitrification process during the whole period, and soil respiration for the second post-fire year, when compared with the control site. Our data suggest that after 3-4 months the activity of microbial decomposers is almost the same at the two sites, suggesting that fire is not a catastrophic event, but a simple perturbation common to Mediterranean-type ecosystems.}, }
@article {pmid24225701, year = {1982}, author = {Rosini, G and Federici, F and Martini, A}, title = {Yeast flora of grape berries during ripening.}, journal = {Microbial ecology}, volume = {8}, number = {1}, pages = {83-89}, pmid = {24225701}, issn = {0095-3628}, abstract = {The yeast flora associated with the surface of grapes during ripening was studied with regard to different sectors of the grape skin and the position in the bunch by means of traditional as well as more vigorous preisolation and precounting treatments. The yeast number per square centimeter of skin increases with ripening and is highest in the area immediately surrounding the stem. The cluster sector closer to the peduncle seems to constitute a favorable substrate for yeasts, hosting a resident flora about 10 and 100 times higher than the central and lower parts of the bunch, respectively.Kloeckera apiculata was the normal resident species of grapes regardless of the sector or the ripening period, and constitutes the fermenting flora of mature grapes. The ecological implications of the results of this survey are discussed.}, }
@article {pmid24225700, year = {1982}, author = {Starmer, WT}, title = {Analysis of the community structure of yeasts associated with the decaying stems of cactus. I.Stenocereus gummosus.}, journal = {Microbial ecology}, volume = {8}, number = {1}, pages = {71-81}, pmid = {24225700}, issn = {0095-3628}, abstract = {Yeast communities of decayingStenocereus gummosus were analyzed for spatial, temporal, and physiological characteristics. Analysis of random samples within plants, between plants, and between localities shows that the species proportions of the yeast community are relatively constant within plants and between localities, but that there is significant variability between rotting plants. It is suggested that the increased variability between plants represents sampling of different stages of succession. The physiological abilities of the yeast community also show a relatively constant pattern within plants and between localities yet more variability between plants.The variablity profiles of species proportions and community physiological characters are demonstrated to be correlated within and between plants. This observation is an extension of the Kluge-Kerfoot phenomenon to the level of the community. The correlation of within and between plant variability profiles is suggested to be a result of the temporal and spatial availability of resources during the stages of rotting plant succession. The community structure is thus postulated to result from a set of possible future resource states of the habitat.}, }
@article {pmid24225699, year = {1982}, author = {Bianchi, MA and Bianchi, AJ}, title = {Statistical sampling of bacterial strains and its use in bacterial diversity measurement.}, journal = {Microbial ecology}, volume = {8}, number = {1}, pages = {61-69}, pmid = {24225699}, issn = {0095-3628}, abstract = {The cultural bacterial strains of two sediment samples, i.e., 260 strains, were submitted to numerical taxonomy to determine "ecological profiles." From these profiles several calculations of bacterial diversity were done with increasing number of strains (between 10 and 130). Studying 20-30 strains was sufficient to obtain a diversity of bacterial community.Number of tests could be reduced from 62 to 30 without any influence on bacterial diversity. Similarity between studied tests was shown by using numerical taxonomy.}, }
@article {pmid24225698, year = {1982}, author = {Baldock, BM and Rogerson, A and Berger, J}, title = {Further studies on respiratory rates of freshwater amoebae (Rhizopoda, Gymnamoebia).}, journal = {Microbial ecology}, volume = {8}, number = {1}, pages = {55-60}, pmid = {24225698}, issn = {0095-3628}, abstract = {The respiration rates of axenically culturedAcanthamoeba castellanii (Gymnamoebia) and of the test organismTetrahymena pyriformis (Ciliophora) were compared using both Warburg and cartesian diver respirometer techniques at 20°C. Furthermore, the latter procedure was employed to measure the oxygen consumption of the amoebae,Polychaos fasciculatum, Saccamoeba limax, andAmoeba sp. The linear relationship between respiration rate and mean cell volume in amoebae was reassessed in view of these additional estimates. The importance of this regression in ecological studies is discussed.}, }
@article {pmid24225697, year = {1982}, author = {Jensen, LM and Søndergaard, M}, title = {Abiotic formation of particles from extracellular organic carbon released by phytoplankton.}, journal = {Microbial ecology}, volume = {8}, number = {1}, pages = {47-54}, pmid = {24225697}, issn = {0095-3628}, abstract = {(14)C-labeled extracellular organic carbon (EOC) released by the phytoplankton in a Danish Estuary was shown immediately to form particles (>0.2μm) when the products were added to a natural water sample. About 14%-20% of the added activity could be recovered as particles. Any bacterial assimilation of the extracellular products was thus masked. The abiotic origin of the particulate EOC was verified, and it was shown that the particle formation was due to some factors present in the estuarine water with a nominal diameter >0.2μm. Precaution must be taken to avoid misinterpretations in studies concerning carbon flow from algae to bacteria.}, }
@article {pmid24225696, year = {1982}, author = {Newell, SY and Fallon, RD}, title = {Bacterial productivity in the water column and sediments of the Georgia (USA) coastal zone: Estimates via direct counting and parallel measurement of thymidine incorporation.}, journal = {Microbial ecology}, volume = {8}, number = {1}, pages = {33-46}, pmid = {24225696}, issn = {0095-3628}, abstract = {Three methods of estimating bacterial productivity were compared using parallel samples of Atlantic Ocean water (within 0.25-15 km of the Georgia coast). The frequency-of-dividing cells (FDC) method and the [(3)H]thymidine incorporation method gave results which were strongly correlated (r=0.97), but the FDC estimates were always higher (X2 to X7) than the [(3)H]thymidine estimates. Estimates of bacterial productivity ranged from 2-4×10(8) cells·l(-1)·h(-1) at 0.25 km from shore to 1-9×10(7)cells·l(-1)·h(-1) at 15 km. A method involving incubation of 3-μm filtrates and direct counting gave results that could not be easily translated into estimates of bacterial productivity. Application of the FDC method to sediment samples gave high productivity estimates, which could be not reconciled with productivity estimates based on sediment oxygen uptake.}, }
@article {pmid24225695, year = {1982}, author = {Ishida, Y and Imai, I and Miyagaki, T and Kadota, H}, title = {Growth and uptake kinetics of a facultatively oligotrophic bacterium at low nutrient concentrations.}, journal = {Microbial ecology}, volume = {8}, number = {1}, pages = {23-32}, pmid = {24225695}, issn = {0095-3628}, abstract = {In oligotrophic waters, not only community structure but also physiological properties of heterotrophic bacteria are influenced by the concentration of organic matter.The relationship between growth rate of two facultatively oligotrophic strains ofAeromonas sp. No. 6 andFlavobacterium sp. M1 was studied in comparison with that of two eutrophic strains ofEscherichia coli 7020 andFlavobacterium sp. M2. These strains had two or three different substrate constants (Ks values) depending on substrate concentrations: Ks values for the two former were remarkably lower than those for the two latter. For instance, Ks value forAeromonas sp. No. 6 was about 8.9μM when substrate concentration was greater than 53μM and about 1.1μM when substrate concentration was less man 53μM. InE. coli the Ks value was about 260μM at greater than 5600μM and about 47μM at less than 5600μM substrate concentration.Uptake kinetics ofAeromonas sp. grown in a medium containing 2.7 mM glutamate (H-cell) and 0.11μM glutamate (L-cell) have been determined for the intact cells. H-cell had two distinct values of Km for glutamate assimilation and respiration, and L-cell had three distinct values of Km for glutamate assimilation and respiration: In H-cell Km of assimilation was 2.8×10(-7) M and 1.5×10(-4) M, and Km of respiration was 2.3×10(-7) M and 1.7×10(-4) M; in L-cell Km of assimilation was 7.4×10(-8) M, 8.3×10(-6) M, and 1.3×10(-4) M, and Km of respiration was 2.5×10(-7), 8.9×10(-6)M, and 1.7×10(-4) M. More than 60% of glutamate taken up by the H- and L-cells was respired when the substrate concentration was less than 10(-6) M, although at greater than 10(-6) M, 50% and 30% of glutamate was respired by H-cells and L-cells, respectively. These results suggest that the facultatively oligotrophic bacteria grow with high efficiency in environments with extremely low nutrient concentration, such as oligotrophic waters of lakes and ocean, as compared with in their growth in conditions of high nutrient concentraton, such as nutrient broth.}, }
@article {pmid24225694, year = {1982}, author = {Brannan, DK and Caldwell, DE}, title = {Evaluation of a proposed surface colonization equation usingThermothrix thiopara as a model organism.}, journal = {Microbial ecology}, volume = {8}, number = {1}, pages = {15-21}, pmid = {24225694}, issn = {0095-3628}, abstract = {The colonization equation shown below was evaluated usingThermothrix thiopara as a model organism.[Formula: see text] where: N=number of cells on surface (cells field(-1)); A = attachment rate (cells field(-1) h(-1)); M=specific growth rate (h(-1)); t=incubation period (h).Previous studies of microbial surface colonization consider attachment and growth independently. However, the proposed colonization equation integrates the effects of simultaneous attachment and growth. Using this equation, the specific growth rate ofT. thiopara was found to be 0.38±0.3 h(-1) during in situ colonization. Estimates ofμ were independent of incubation period after 4 h (2 generations). Shorter incubations were inadequate to produce sufficient microcolonies for accurate determination of specific growth rate. Empirical data for the time course of colonization fell within the 95% confidence interval of predicted values. The attachment rate, although assumed to be constant, was found to continuously increase with time. This increase may have been an artifact due to the continuous deposition of travertine on the surface, or may indicate the need for a function to replace A in the colonization equation. Using the exponential growth equation, the progeny of cells that attach during incubation are considered to be progeny of cells that attach initially. This erroneously inflated the growth rate by 55%.}, }
@article {pmid24225693, year = {1982}, author = {Moriarty, DJ and Hayward, AC}, title = {Ultrastructure of bacteria and the proportion of Gram-negative bacteria in marine sediments.}, journal = {Microbial ecology}, volume = {8}, number = {1}, pages = {1-14}, pmid = {24225693}, issn = {0095-3628}, abstract = {Bacteria in sediments from the surface aerobic layer (0-1 cm) and a deeper anaerobic layer (20-21 cm) of a seagrass bed were examined in section by transmission electron microscopy. Bacteria with a Gram-negative ultrastructure made up 90% of bacteria in the surface layer, and Gram-positive bacteria comprised 10%. In the anaerobic zone, Gram-negative bacteria comprised 70% and Gram-positive bacteria 30% of the bacterial population. These differences were highly significant and support predictions of these proportions made from muramic acid measurements and direct counting with fluorescence microscopy. Most cells were enveloped in extracellular slime layers or envelopes, some with considerable structural complexity. The trophic value to animals of these envelopes is discussed. A unique organism with spines was observed.}, }
@article {pmid24227552, year = {1981}, author = {Sewell, LM and Bitton, G and Bays, JS}, title = {Evaluation of membrane adsorption-epifluorescence microscopy for the enumeration of bacteria in coastal surface films.}, journal = {Microbial ecology}, volume = {7}, number = {4}, pages = {365-369}, pmid = {24227552}, issn = {0095-3628}, abstract = {We have evaluated a method for enumerating surface slick bacteria by combining a membrane adsorption procedure with epifluorescence microscopy. Various chemicals were investigated for their ability to enhance bacterial elution from the membrane filters. The results of the elution-epifluorescence method were compared to plate counts and to direct epifluorescence counts of the sampling membrane filters. In all tests, the elution-epifluorescence technique yielded significantly higher bacterial concentrations.}, }
@article {pmid24227551, year = {1981}, author = {Rogers, KH and Breen, CM}, title = {Effects of epiphyton onPotamogeton crispus L. leaves.}, journal = {Microbial ecology}, volume = {7}, number = {4}, pages = {351-363}, pmid = {24227551}, issn = {0095-3628}, abstract = {Potamogeton crispus L. grows as a winter producing annual in the shallow lakes of the Pongolo Floodplain, South Africa. Colonization of leaves by algal and bacterial epiphytes, as seen by scanning electron microscopy, followed the established pattern of increasing diversity and density with leaf age. It was apparent from the micrographs that the primary and subsequent colonizers were present even after death of the host leaf. Cross sections of leaves, viewed by transmission electron microscopy, illustrated that bacterial attachment did not damage the surface of young leaves. There was, however, extensive inward swelling and disorganization of the epidermal walls, characteristic of a reaction to invasion by pathogens. In older leaves the swelling was also present in mesophyll cells, while bacteria had invaded and degraded the epidermal cell wall. The bacterial invasion was concomitant with signs of senescence, and in dead leaves the organisms had penetrated and degraded the epidermis and mesophyll cell walls. The epiphyton/ host relationship may therefore be considered necrotrophic with important consequences for the transfer of energy from producers to consumers during decomposition.}, }
@article {pmid24227550, year = {1981}, author = {Clarholm, M}, title = {Protozoan grazing of bacteria in soil-impact and importance.}, journal = {Microbial ecology}, volume = {7}, number = {4}, pages = {343-350}, pmid = {24227550}, issn = {0095-3628}, abstract = {Interactions between bacteria and protozoa in soil were studied over 2-week periods in the field and in a pot experiment. Under natural conditions the total biological activity was temporarily synchronized by a large rainfall, and in the laboratory by the addition of water to dried-out soil, with or without plants. In the field, peaks in numbers and biomass of bacteria appeared after the rain, and a peak of naked amoebae quickly followed. Of the three investigated groups-flagellates, ciliates, and amoebae-only populations of the latter were large enough and fluctuated in a way that indicated a role as bacterial regulators. The bacterial increase was transient, and the amoebae alone were calculated to be able to cause 60% of the bacterial decrease. The same development of bacteria and protozoa was observed in the pot experiment: in the presence of roots, amoebic numbers increased 20 times and became 5 times higher than in the unplanted soil. In the planted pots, the amoebic increase was large enough to cause the whole bacterial decrease observed; but in the unplanted soil, consumption by the amoebae caused only one-third of the bacterial decrease.}, }
@article {pmid24227549, year = {1981}, author = {Haskå, G}, title = {Activity of bacteriolytic enzymes adsorbed to clays.}, journal = {Microbial ecology}, volume = {7}, number = {4}, pages = {331-341}, pmid = {24227549}, issn = {0095-3628}, abstract = {Myxococcus virescens is able to produce extracellular bacteriolytic enzymes that are rapidly adsorbed on montmorillonite. These adsorbed enzymes are active and can be assayed by measuring the release of UV-absorbing materials in mixtures containingMicrococcus luteus cells. The activity of the clay-adsorbed enzymes is, however, considerably lower than that of the unadsorbed enzymes. Both unadsorbed and adsorbed enzymes have their maximum activity at approximately the same pH. At lower clay-enzyme concentrations, the activity is proportional to the concentration. If, however, increasing amounts of clay are added to a fixed volume of clay-enzyme suspension, the activity remains almost unchanged until a definite limit is reached, then the activity decreases rapidly. This limit was dependent only on the ratio of the amounts of enzyme and clay and not on the absolute concentration of the enzyme. The montmorillonite-adsorbed bacteriolytic enzymes fromM. virescens were not active against gram-negative bacteria, and no activity against purified cell walls fromM. luteus could be measured. Montmorillonite-adsorbed egg white lysozyme was not active onM. luteus cells.}, }
@article {pmid24227548, year = {1981}, author = {Trentham, JN and James, TR}, title = {Seasonal selection in a freshwater heterotrophic bacterial community.}, journal = {Microbial ecology}, volume = {7}, number = {4}, pages = {323-330}, pmid = {24227548}, issn = {0095-3628}, abstract = {The objective of this study was to determine if a seasonal selection could be demonstrated in the heterotrophic component of a freshwater bacterial community. Surface samples were taken at approximately monthly intervals covering an annual seasonal cycle, and counts were made of the numbers of bacteria capable of growing at each of 10 incubation temperatures from 0° to 45°C at 5°C intervals. Evidence for seasonal selection was provided by a 6°C shift in the mean temperature of the counts from the summer sample to the winter sample. The selection was even more evident when the number of organisms capable of growing at 10°C and those capable of growing at 35°C were compared over the seasonal cycle. The counts at these two incubation temperatures varied inversely to each other. Although a negligible number of organisms from a representative summer sample grew at 10°C, 18% of the organisms from a representative winter sample grew at this temperature. The data of this study indicate that, although seasonal selection does occur, the magnitude of that selection is not great enough to permit the growth of bacteria during the coldest month to approach the levels of growth observed during the summer months. However, the selection appears to be adequate to permit significant activity during the spring and fall transition months.}, }
@article {pmid24227547, year = {1981}, author = {Mills, AL and Maubrey, R}, title = {Effect of mineral composition on bacterial attachment to submerged rock surfaces.}, journal = {Microbial ecology}, volume = {7}, number = {4}, pages = {315-322}, pmid = {24227547}, issn = {0095-3628}, abstract = {A direct microscopic count technique employing fluorescein isothiocyanate stain was used to compare microbial colonization on the exposed surfaces of rocks and minerals suspended in several ponds for various time intervals. Hematitic sandstone was never colonized at a rate greater than limestone, but quartz was always colonized more rapidly than calcite. The use of single-crystal minerals (quartz and calcite) in a nested factor experiment showed that the effect of the minerals on colonization was statistically significant, but that differences among the immersion sites were also significant. Sandstone samples placed in a pond outflow accumulated microbial colonizers more rapidly than those placed in the still waters of the same pond. The results indicate that the composition of the mineral substrate, in concert with the immersion environment, controls the formation of primary slime layers in aquatic systems.}, }
@article {pmid24227546, year = {1981}, author = {Nedwell, DB and Banat, IM}, title = {Hydrogen as an electron donor for sulfate-reducing bacteria in slurries of salt marsh sediment.}, journal = {Microbial ecology}, volume = {7}, number = {4}, pages = {305-313}, pmid = {24227546}, issn = {0095-3628}, abstract = {Experiments with a Warburg respirometer showed that a sediment slurry consumed hydrogen from a hydrogen atmosphere, and this consumption was not due to the activity of methanogenic bacteria. The hydrogren uptake was inhibited by the addition of 20 mM molybdate. Further experiments with sediment slurry held in conical flasks under an atmosphere of nitrogen showed that hydrogen accumulated in the headspace when bacterial sulfate reduction was inhibited either by the addition of 20 mM molybdate or by low (<5 mM) sulfate concentrations in the slurry. Methanogenesis was stimulated in the presence of a hydrogen atmosphere or by the addition of 20 mM molybdate. The results confirmed that hydrogren was an important electron donor for sulfate-reducing bacteria present in the sediment. The stimulation of methanogenesis by molybdate could be explained in part by a competition for hydrogen between sulfate-reducing bacteria and hydrogen-metabolizing methanogenic bacteria, but competition for another common substrate, possibly acetate, could also be significant.}, }
@article {pmid24227545, year = {1981}, author = {Hansen, JI and Henriksen, K and Blackburn, TH}, title = {Seasonal distribution of nitrifying bacteria and rates of nitrification in coastal marine sediments.}, journal = {Microbial ecology}, volume = {7}, number = {4}, pages = {297-304}, pmid = {24227545}, issn = {0095-3628}, abstract = {The distribution of nitrification potential (NP) with depth in sediment and season was investigated in a shallow sandy sediment (0.5 m water) and a deeper muddy sediment (17m water). In both sediments, nitrifying bacteria were present in the anoxic strata (oxygen penetration was 5 mm below the surface). The NP at 6-8 cm depth in the sediment was 50% and 10% of the surface NP at the sandy and muddy sediment, respectively. It is suggested that bioturbation and physical disturbance of the sediment were the most likely reasons for this distribution. The NP increased as sediment temperature decreased. This effect was less marked in the muddy sediment. It is concluded that during the summer, the numbers or specific activity of nitrifying bacteria diminished for the following reasons: There was decreased O2 penetration into the sediment and increased competition for O2 by heterotrophs; there was increased competition for NH4 (+) and there was inhibition by H2S. These effects counteracted the potentially higher growth rates and increased rates of NH4 (+) production at the elevated summer temperatures. The potential nitrification rates in the upper 1 cm, which were measured at 22°C, were converted to calculated rates at the in situ temperature (Q10=2.5) and in situ oxygen penetration. These calculated rates were shown to closely resemble the measured in situ rates of nitrification. The relationship between the in situ rates of nitrification and the nitrification potential is discussed.}, }
@article {pmid24227544, year = {1981}, author = {Troussellier, M and Legendre, P}, title = {A functional evenness index for microbial ecology.}, journal = {Microbial ecology}, volume = {7}, number = {4}, pages = {283-296}, pmid = {24227544}, issn = {0095-3628}, abstract = {Microbial ecologists attempting to describe community structures through the use of synthetic parameters face enormous difficulties. These stem in part from the necessity of using standard taxonomic reference levels in a field where the species level is poorly defined. This paper presents an attempt to obviate this problem. A "functional evenness" index (E) is defined using information measures; it is based directly on the characteristics of the bacteria, as determined, for example, with the API 20B method. Comparisons of this index with classic structure indices, such as taxonomic evenness (Pielou) or systematic dominance (Hulburt), show that it behaves like an evenness index, while bypassing the taxonomic study required before computation of the classic indices. Its use is illustrated with samples of aerobic heterotrophic bacteria obtained from brackish lagoon sediments.}, }
@article {pmid24227501, year = {1981}, author = {Josserand, A and Gay, G and Faurie, G}, title = {Ecological study of twoNitrobacter serotypes coexisting in the same soil.}, journal = {Microbial ecology}, volume = {7}, number = {3}, pages = {275-280}, pmid = {24227501}, issn = {0095-3628}, abstract = {The problem of competition betweenNitrobacter strains was posed by the fact that two serotypes (N.w and L) coexisted in a soil, as shown by immunofluorescence. The L serotype had a lower growth rate in pure culture than serotype N.w, as well as a slower nitrifying activity when inoculated to a sterilized soil percolated with NO2 (-) solution. When both serotypes were inoculated together, only N.w was observed by immunofluorescence at the end of the percolation; when in the control soil the two serotypes were identified, strain L always adhered to particles. Maintenance of the two serotypes in the soil could be explained as their exploitation of distinct ecological niches. Thus the relative in situ importance of the two strains is governed by environmental conditions.}, }
@article {pmid24227500, year = {1981}, author = {Ducklow, HW and Clausen, K and Mitchell, R}, title = {Ecology of bacterial communities in the schistosomiasis vector snailBiomphalaria glabrata.}, journal = {Microbial ecology}, volume = {7}, number = {3}, pages = {253-274}, pmid = {24227500}, issn = {0095-3628}, abstract = {The internal colony-forming bacterial flora of the schistosome intermediate host snailBiomphalaria glabrata (Say) has been characterized in ca. 500 individual snails from Puerto Rico, Guadeloupe, and St. Lucia, and from laboratory aquaria. Freshly captured wild snails harbor 2-40×10(6) CFU·g(-1), and healthy aquarium snails harbor 4-16×10(7) CFU·g(-1), whereas moribund individuals have 4-10 times as many bacteria as healthy individuals from the same habitats.Pseudomonas spp. are the most common predominant bacteria in normal snails, whereasAcinetobacter, Aeromonas, andMoraxella spp. predominate in moribund snails. External bacterial populations in water appear to have little effect on the composition and size of the flora in any snail. In addition to normal (healthy) and moribund snails, a third group of snails has been distinguished on the basis of internal bacterial density and predominating genera. These "high-density" snails may have undergone stresses and may harbor opportunistic pathogens. The microfloras of wild and laboratory-reared snails can be altered and stimulated to increase in density by crowding the snails or treating them with antibiotics.}, }
@article {pmid24227499, year = {1981}, author = {Johnson, I and Flower, N and Loutit, MW}, title = {Contribution of periphytic bacteria to the concentration of chromium in the crabHelice crassa.}, journal = {Microbial ecology}, volume = {7}, number = {3}, pages = {245-252}, pmid = {24227499}, issn = {0095-3628}, abstract = {Periphytic bacteria found on the carapace and gills of crabs collected from near a tannery effluent outlet were shown to be able to concentrate chromium. By concentrating Cr, the bacteria contributed to the total Cr concentration of the crabs. Since crabs and other crustaceans are eaten by bottom feeding fish, bacteria may be contributing to the passage of Cr up the food chain.}, }
@article {pmid24227498, year = {1981}, author = {Rodriguez-Valera, F and Ruiz-Berraquero, F and Ramos-Cormenzana, A}, title = {Characteristics of the heterotrophic bacterial populations in hypersaline environments of different salt concentrations.}, journal = {Microbial ecology}, volume = {7}, number = {3}, pages = {235-243}, pmid = {24227498}, issn = {0095-3628}, abstract = {Solar salterns, based on a multi-pond system, give a discontinuous gradient of salt concentrations. The heterotrophic bacterial populations of ponds containing from 10% salt to saturation have been studied. Saltern samples were spread on agar plates containing different media for halophilic bacteria and one medium made with water of the pond plus nutrients. Replica plating was done to determine the salt range for growth of the colonies. We studied 150 strains to determine the salt spectra of growth, the morphology, and nutrient requirements. The following conclusions were reached: (a) In salt concentrations above 10% (total salts), most bacteria are halophilic and few are halotolerant; (b) the two types of halophilic bacteria, moderate and extreme, show different distributions; in these ponds a narrow overlap exists between 25% and 32% salts with moderate halophiles predominating below this interval and extreme halophiles above it; (c) the populations of moderate halophiles are highly heterogeneous, and the salt concentration of their habitat affects their taxonomic composition, salt range for growth, and nutrient requirements. The population composition of extreme halophiles is less affected by the salt concentrations at which these bacteria are found.}, }
@article {pmid24227497, year = {1981}, author = {Lynch, JM and Panting, LM}, title = {Measurement of the microbial biomass in intact cores of soil.}, journal = {Microbial ecology}, volume = {7}, number = {3}, pages = {229-234}, pmid = {24227497}, issn = {0095-3628}, abstract = {The fumigation/respiration technique was used to estimate the size of the soil microbial biomass. Sieving decreased the biomass in winter but increased it in summer; we suggest that this was a consequence of the different substrates available and the different microbial populations during the year. The flush in respiration following fumigation correlated significantly with the CO2-C produced 10 days after fumigation (X), so that in the soils studied by us the biomass (B) can be calculated from Bk=0.673X-3.53, wherek is the fraction of fumigated organisms mineralized to CO2, thus avoiding the need to measure CO2 production from unfumigated cores.}, }
@article {pmid24227496, year = {1981}, author = {Lauffenburger, D and Aris, R and Keller, KH}, title = {Effects of random motility on growth of bacterial populations.}, journal = {Microbial ecology}, volume = {7}, number = {3}, pages = {207-227}, pmid = {24227496}, issn = {0095-3628}, abstract = {A spatially distributed mathematical model is developed to elucidate the effects of chemical diffusion and cell motility as well as cell growth, death, and substrate uptake on steady-state bacterial population growth in a finite, one-dimensional, nonmixed region. The situation considered is growth limited by a diffusing substrate from an adjacent phase not accessible to the bacteria. Chemotactic movement is not considered in this paper; we consider only "randomwalk"-type random motility behavior here. The following important general concepts are suggested by the results of our theoretical analysis: (a) The significance of random motility effects depends on the magnitude of the ratioμ/kL (2), whereμ is the bacterial random motility coefficient,k is the growth rate constant, andL is the linear dimension of the confined growth region. (b) In steady-state growth in a confined region, the bacterial population size decreases asμ increases. (c) The effect ofμ on population size can be great; in fact, sometimes relative population sizes of two species can be governed primarily by the relative values ofμ rather than by the relative values ofk.}, }
@article {pmid24227495, year = {1981}, author = {Brown, EJ and Button, DK and Lang, DS}, title = {Competition between heterotrophic and autotrophic microplankton for dissolved nutrients.}, journal = {Microbial ecology}, volume = {7}, number = {3}, pages = {199-206}, pmid = {24227495}, issn = {0095-3628}, abstract = {When a heterotrophic (Rhodotorula rubra) and a phototrophic (Selenastrum capricornutum) plankton were grown together in dilute phosphate (Pi) continuous cultures, coexistence occurred only when the heterotroph was growthrate limited by organic carbon (C). Because of its higher affinity for Pi, and because C starvation does not affect the heterotrophic yeast's ability to transport Pi, the concentration of organic carbon indirectly controlled the biomass of the phototroph. The results support a threshold model of microbial growth.}, }
@article {pmid24227427, year = {1981}, author = {Massalski, A and Laube, VM and Kushner, DJ}, title = {Effects of cadmium and copper on the ultrastructure ofAnkistrodesmus braunii andAnabaena 7120.}, journal = {Microbial ecology}, volume = {7}, number = {2}, pages = {183-193}, pmid = {24227427}, issn = {0095-3628}, abstract = {The effects of brief exposure to, or growth in the presence of, lethal and sublethal concentrations of Cu(NO)2 and Cd(NO3) on the ultrastructure of the blue-green algaAnabaena 7120 and the green algaAnkistrodesmus braunii were studied. Exposure to increasing amount of both metal ions led to the appearance of larger proportions of electron-dense cells whose organelles were less well defined than those of untreated cells. Metal-treated cells ofAnabaena 7120 became distorted. Some had a corrugated appearance. Others lysed, leaving a much larger proportion of heterocysts. Such heterocysts were often empty or had a curious collapsed appearance. Growth ofA. braunii in the presence of 10(-4) M Cu(NO2)2 produced substantial numbers of multinucleate giant cells with thick walls; such cells result from repeated mitotic division without subsequent cytokinesis. The giant cells contained centrioles, structures not as yet found in normal cells of the genusAnkistrodesmus. Some nuclei of giant, but not of normal, cells contained deep indentations that appeared as "holes" in cross section. Some giant cells also contained triple parallel strands of endoplasmic reticulum which extended across much of the cell, connecting to the nuclear envelope. Some ultrastructural changes were also noted in algal cells grown over sediment containing Cu or Cd, but these were generally less severe than those occurring when metal ions were added directly to the algal cultures.}, }
@article {pmid24227426, year = {1981}, author = {Hauxhurst, JD and Kaneko, T and Atlas, RM}, title = {Characteristics of bacterial communities in the Gulf of Alaska.}, journal = {Microbial ecology}, volume = {7}, number = {2}, pages = {167-182}, pmid = {24227426}, issn = {0095-3628}, abstract = {Taxonomic diversity, physiological tolerance ranges, and nutrient utilization capabilities were determined for bacterial communities in Gulf of Alaska surface waters and sediments. Taxonomic diversity was assessed using Shannon Weaver (H') and equitability (J') indices. Physiological tolerance and nutritional versatility indices were developed to further assess the state of "informational heterogeneity" within the bacterial communities. The Gulf of Alaska bacterial communities were characteristically diverse; the bacterial populations in these marine ecosystems generally were eurytolerant and nutritionally versatile. The maintenance of a high degree of informational heterogeneity was found to be characteristic of these bacterial communities. It appears to be of adaptive advantage to maintain diverse populations with physiological tolerances whose ranges exceed those experienced within the natural habitat, and for the bacterial communities to possess a high degree of nutritional versatility within these marine ecosystems.}, }
@article {pmid24227425, year = {1981}, author = {Tison, DL and Wilde, EW and Pope, DH and Fliermans, CB}, title = {Productivity and species composition of algal mat communities exposed to a fluctuating thermal regime.}, journal = {Microbial ecology}, volume = {7}, number = {2}, pages = {151-165}, pmid = {24227425}, issn = {0095-3628}, abstract = {Algal mat communities growing in thermal effluents of production nuclear reactors at the Savannah River Plant, near Aiken, SC, are exposed to large temperature fluctuations resulting from reactor operations. Rates of primary production and species composition were monitored at 4 sites along a thermal gradient in a trough microcosm to determine how these large temperature fluctuations affected productivity and algal community structure. Blue-green algae (cyanobacteria) were the only phototrophic primary producers growing in water above 45°C. These thermophiles were able to survive and apparently adapt to ambient temperatures when the reactor was shut down. The algal mat communities exposed to <45°C were composed of blue-green and eukaryotic algae that adapted rapidly to ambient temperatures. An increase in the percentage extracellular release (PER) of(14)C-labeled dissolved organic compounds and a decrease in primary production were observed during periods of thermal fluctuation. The results show that the dominant phototrophs in this artificially heated aquatic habitat have been selected for their ability to survive large temperature fluctuations and are similar to those of natural hot springs.}, }
@article {pmid24227424, year = {1981}, author = {Moss, MO and Ryall, C}, title = {Distribution of chromobacteria in a lowland river.}, journal = {Microbial ecology}, volume = {7}, number = {2}, pages = {139-149}, pmid = {24227424}, issn = {0095-3628}, abstract = {A selective medium was used to estimate the numbers of purple pigmented bacteria in the River Wey. Chromobacteria were never isolated from the springs at the source of the river, but they appeared within a short distance and their numbers generally increased over the first 30 km. Counts were always low but were much higher during the winter than during the summer.Records of water temperature and turbidity, as well as daily rainfall, were maintained during the sampling period. An unweighted multiple regression analysis of some of the results has shown that much of the variability in the counts of chromobacteria was correlated with turbidity (r=0.67,P<0.001). After turbidity was allowed for, a significant inverse correlation with temperature (r=0.60,P < 0.001) became apparent and these two factors together accounted for 64.7% of the variation in counts. Allowing for these two factors revealed a significant correlation with rainfall during the previous 4 days (r=0.27,P<0.05), and the three factors together accounted for 67.2% of the variability in counts.In an attempt to discover the source of chromobacteria, samples of silt, soil, and storm overflow effluents were studied. In general, chromobacteria were present in highest numbers in soil or silt containing substantial quantities of organic material.}, }
@article {pmid24227423, year = {1981}, author = {Bridges, JR}, title = {Nitrogen-fixing bacteria associated with bark beetles.}, journal = {Microbial ecology}, volume = {7}, number = {2}, pages = {131-137}, pmid = {24227423}, issn = {0095-3628}, abstract = {Nitrogen-fixingEnterobacter agglomerans andEnterobacter spp. were consistently isolated from the bark beetleDendroctonus terebrans. Large populations of nitrogen-fixing bacteria were found with the beetle, although no in situ acetylene reduction was demonstrated. The constant occurrence of nitrogenfixing bacteria withD. terebrans suggests a symbiotic relationship. Nitrogen-fixing bacteria were also isolated from the bark beetlesDendroctonus frontalis andIps avulsus.}, }
@article {pmid24227422, year = {1981}, author = {Ishida, Y and Kadota, H}, title = {Growth patterns and substrate requirements of naturally occurring obligate oligotrophs.}, journal = {Microbial ecology}, volume = {7}, number = {2}, pages = {123-130}, pmid = {24227422}, issn = {0095-3628}, abstract = {Eighteen strains of obligately oligotrophic bacteria that grow in a medium containing 1 mg of organic carbon per liter and do not grow in a rich medium (5 g/liter of nutrient) were isolated as dominant organisms from the oligotrophic water of Lake Biwa. The growth properties of these, especially of five strains, were examined. The maximum cell yield ranged from 8.5×10(4)/ml to 2.3×10(6)/ml, and their doubling times ranged from 6.6/h to 11.8/h in LT10(-4) medium (0.5 mg trypticase and 0.05 mg yeast extract in 1 liter of filtered and aged lake water). They also showed good growth in lake water medium without adding nutrients. The optimum concentrations for their growth were 5 mg/1, 5-50 mg/1, 50 mg/1, or 500 mg/1, depending on the strains. They utilized glutamate, glycine, serine, and glycolate, but not acetate, proline, or leucine. Several properties were examined. Their growth properties were very different from those of oligotrophs or oligocarbophiles isolated by other researchers.}, }
@article {pmid24227421, year = {1981}, author = {Li, WK and Goldman, JC}, title = {Problems in estimating growth rates of marine phytoplankton from short-term(14)C assays.}, journal = {Microbial ecology}, volume = {7}, number = {2}, pages = {113-121}, pmid = {24227421}, issn = {0095-3628}, abstract = {Growth rate estimates (μ') of phytoplankton populations that were sampled from nitrogen-limited continuous cultures and then incubated for short durations in batch culture with added(14)C-HCO3 (-) were significantly different than steady-state growth rates (μ) for 3 of 5 marine phytoplankton species. Two diatoms,Thalassiosira weissflogii andChaetoceros simplex, displayed virtually identical growth rates (μ=μ') over a wide range ofμ, whereasμ' for a third diatom,Phaeodactylum tricornutum, was overestimated by an average of 40% compared toμ. In contrast,μ' was underestimated by the(14)C technique for the two remaining species: up to 40% at a steady-stateμ of 1.0 day(-1) for the chlorophyteDunaliella tertiolecta and up to 100% atμ of 1.4 day(-1) for the haptophytePavlova lutheri. For the latter two species the divergence betweenμ andμ' appeared to increase with increasing steady-stateμ. A simple model of labeled and total carbon flow between the aqueous phase and cellular biomass was constructed to demonstrate that respiration was negligible whenμ=μ', but was significant whenμ'>μ. In the cases in whichμ'<μ, a rapid physiological alteration presumably took place once the steady state was disturbed and cells were placed in the incubation chambers, which perhaps was related to the nutritional state of the cultures at the time of sampling. Questions thus are raised regarding our ability to measure accurately primary productivity from shipboard experiments with confined samples of phytoplankton from nutrient-impoverished waters that probably are less hardy than the laboratory cultures used in these studies.}, }
@article {pmid24227420, year = {1981}, author = {Varon, M and Shilo, M}, title = {Inhibition of the predatory activity ofBdellovibrio by various environmental pollutants.}, journal = {Microbial ecology}, volume = {7}, number = {2}, pages = {107-111}, pmid = {24227420}, issn = {0095-3628}, abstract = {The predatory activity of bdellovibrios is affected by various environmental pollutants such as detergents, heavy metals, and pesticides. This was shown in a two-membered system ofBdellovibrio andPhotobacterium, in which the effect of the predator on the bioluminescence of the prey indicated the activity of the former. The high sensitivity of the bdellovibrios toward certain chemicals (e.g., CdCl2) indicates the possibility of using the system for biological monitoring of those chemicals.}, }
@article {pmid24227419, year = {1981}, author = {Varon, M}, title = {Interaction ofBdellovibrio with Its prey in mixed microbial populations.}, journal = {Microbial ecology}, volume = {7}, number = {2}, pages = {97-105}, pmid = {24227419}, issn = {0095-3628}, abstract = {The interaction ofBdellovibrio with its prey can be affected by the presence of other microorganisms regardless of whether they serve as a prey for the bdellovibrios. This was shown in a system in which the fate of one prey could be followed in mixed bacterial populations thanks to a specific trait, bioluminescence. The attacking bdellovibrio causes decay of bioluminescence, and the rate of light decay of the population indicates the rate at which the luminous bacteria are attacked. Using this system it was found that different bacteria affected the predatorprey interaction in different ways: some "competed" with the original prey for the predator; others enhanced the activity of the predator toward the original prey, and others inhibited it. The significance of these findings in relation to the distribution and activity ofBdellovibrio in the natural ecosystem is discussed.}, }
@article {pmid24420598, year = {1981}, author = {Paul, VJ and Frautschy, S and Fenical, W and Nealson, KH}, title = {Antibiotics in microbial ecology : Isolation and structure assignment of several new antibacterial compounds from the insect-symbiotic bacteriaXenorhabdus spp.}, journal = {Journal of chemical ecology}, volume = {7}, number = {3}, pages = {589-597}, pmid = {24420598}, issn = {0098-0331}, abstract = {Nine strains of the terrestrial bacterial genusXenorhabdus, all isolated as symbionts of nematodes, were examined for their abilities to produce substances with antibiotic activites when grown in pure culture. All nine produced measurable antibiotic activities against one or more of the test strains utilized. The inhibition patterns indicated that different compounds were being produced by the various bacteria. Two of the species that showed particularly strong inhibition patterns were studied in detail. The inhibitory compounds were purified and identified. Strain R produced a mixture of active substances, the major components of which were hydroxyl- and acetoxyl-bearing indole derivatives, presumably produced via tryptophan. Strain Hb, on the other hand, produced only two antibiotics, 4-ethyl- and 4-isopropyl-3,5-dihydroxy-trans-stilbenes, which are presumed to arise via polyketide pathways.}, }
@article {pmid24227321, year = {1981}, author = {Deming, JW and Tabor, PS and Colwell, RR}, title = {Barophilic growth of bacteria from intestinal tracts of deep-sea invertebrates.}, journal = {Microbial ecology}, volume = {7}, number = {1}, pages = {85-94}, pmid = {24227321}, issn = {0095-3628}, abstract = {Digestive tracts of abyssal scavenging amphipods and a deep-sea holothurian were examined for the presence of intestinal microflora capable of rapid proliferation under in situ pressures of 430 to 520 atmospheres (atm) and temperatures of 3-5°C. For two amphipod specimens, population doubling times of 5 and 6 hours were observed under in situ conditions, compared to 8 and 6 hours, respectively, at 1 atm. Growth enhancement under pressure was related inversely to initial population size and directly to concentration of available nutrient. In the case of the deposit-feeding holothurian, attached bacteria scraped from the intestinal lining showed a doubling time, under pressure, of 11 hours, compared to 36 hours for transient sediment bacteria that comprised the gut contents. These data suggest that deep-sea animals possess a commensal gut flora capable of responding to increased nutrient levels, via feeding of the host, without inhibition by the elevated hydrostatic pressures encountered in the deep ocean environment.}, }
@article {pmid24227320, year = {1981}, author = {Tabor, PS and Ohwada, K and Colwell, RR}, title = {Filterable marine bacteria found in the deep sea: Distribution, taxonomy, and response to starvation.}, journal = {Microbial ecology}, volume = {7}, number = {1}, pages = {67-83}, pmid = {24227320}, issn = {0095-3628}, abstract = {A significant number of viable colony-forming bacteria were recovered from deep-ocean bottom water samples passed through a 0.45μm filter. However, these bacteria small enough to pass through a 0.45μm membrane filter and termed "filterable bacteria" were less abundant in open-ocean surface water and coastal water samples. The reduced size of bacterial cells present in deep-ocean bottom water samples was documented by scanning electron microscopy. The concentration of ATP in the water samples was found to be correlated with results of direct counts of bacteria.Numerical taxonomy of bacterial strains isolated from water samples collected at two stations in the deep sea yielded taxonomic clusters grouped according to sample and size fraction. The generic composition of bacterial populations of bottom water filtrates was compared with that of bacteria retained by 0.45μ m filters. Strains ofAlcaligenes, Flavobacterium, Pseudomonas, andVibrio spp. were identified among those retained by, as well as passing through, 0.45μm filters.Two marine isolates obtained from the filtrate of a deep-ocean water sample were incubated for 9 weeks in nutrient-free artificial seawater, during which the cells became rounded and reduced in size. After the 9-week incubation period, more than 10% of the viable cells of both cultures were able to pass through a 0.4μm filter. The viable count at 9 weeks wasca. 10% of that of the initial population, although from direct counts the total population number remained relatively constant throughout the incubation period. From the observed reduction in cell size and increased starvation resistance of cells held under low nutrient conditions, it is concluded that a significant relationship exists between decreased cell size and increased survival of marine bacteria in the deep sea.}, }
@article {pmid24227319, year = {1981}, author = {Tabor, PS and Deming, JW and Ohwada, K and Davis, H and Waxman, M and Colwell, RR}, title = {A pressure-retaining deep ocean sampler and transfer system for measurement of microbial activity in the deep sea.}, journal = {Microbial ecology}, volume = {7}, number = {1}, pages = {51-65}, pmid = {24227319}, issn = {0095-3628}, abstract = {A deep ocean sampler (DOS) has been developed for microbiological sampling and is capable of aseptically collecting 400-ml water samples from any depth in the world oceans. The instrument maintains samples under in situ pressure and temperature. A hyperbaric transfer system has also been developed, enabling transfer of sample volumes up to 150 ml, without decompression or dilution, to pressurized incubation chambers. Utilization of(14)C-glutamate (21 to 96μg/l) and(14)C-acetate (4.6μg/l) by microbial populations in undecompressed water samples from the N.W. Atlantic and the Cape and Angola Basins was recorded over incubation periods of 2 to 18 weeks. Rates of substrate utilization ranged from 1 to 38×10(-2) μg/l/day.}, }
@article {pmid24227318, year = {1981}, author = {Olson, GJ and McFeters, GA and Temple, KL}, title = {Occurrence and activity of iron- and sulfur-oxidizing microorganisms in alkaline coal strip mine spoils.}, journal = {Microbial ecology}, volume = {7}, number = {1}, pages = {39-50}, pmid = {24227318}, issn = {0095-3628}, abstract = {Spoils samples collected from a coal strip mine in southeastern Montana were examined for populations and activities of iron- and sulfur-oxidizing bacteria. Spoils examined were of three types: (a) acidic pyrite-rich waste coal, (b) oxidation halo material, and (c) alkaline material, which was the most widespread type. Bacterial numbers, sulfur oxidation, and(14)CO2 uptake activity declined to low levels in the summer when spoils were dry. Even in wetter spring months pyritic spoils contained relatively low numbers of acidophilic iron- and sulfur-oxidizing bacteria, probably indicative of water stress since the same spoils incubated with excess water or dilute mineral salts showed considerably greater bacterial numbers and activity. Certain wells in coal and spoils aquifers contained substantial populations of iron-oxidizing acidophilic bacteria. However, these wells were always of alkaline or neutral pH, indicating that bacterial pyrite oxidation occurred where groundwaters contacted either replaced spoils or coal that contained pyrite or other metal sulfides. Bacterial activity may contribute to trace metal and sulfate leaching in the area.}, }
@article {pmid24227317, year = {1981}, author = {Chet, I and Harman, GE and Baker, R}, title = {Trichoderma hamatum: Its hyphal interactions withRhizoctonia solani andPythium spp.}, journal = {Microbial ecology}, volume = {7}, number = {1}, pages = {29-38}, pmid = {24227317}, issn = {0095-3628}, abstract = {The mode of hyphal interaction and parasitism ofPythium spp. andRhizoctonia solani byTrichoderma hamatum was studied by both phase-contrast and Nomarski differential interference-contrast microscopy. Directed growth of the mycoparasite toward its host was observed. In the area of interaction,T. hamatum produced appressorial-like structures attached to the host cell wall. Subsequently, several different types of interactions occurred.T. hamatum either grew parallel to and along the host hypha or coiled around its host. In the contrast regions the parasite formed bulbular or hook-like structures that contained granular cytoplasm. In other cases the parasite penetrated into and grew within the mycelium ofR. solani orP. ultimum. As a consequence of the attack, the host hypha became vacuolated, shrank, collapsed, and finally disintegrated. These observations suggest the involvement of parasitism followed by lysis rather than involvement of antibiotics in this host-mycoparasite relationship.}, }
@article {pmid24227316, year = {1981}, author = {Kuriger, WE and Roane, CW}, title = {Identification and population dynamics of bacteria in symptomatic oat leaves.}, journal = {Microbial ecology}, volume = {7}, number = {1}, pages = {23-28}, pmid = {24227316}, issn = {0095-3628}, abstract = {Bacteria isolated from symptomatic oat leaves included pseudomonads,Erwinia herbicola, and others.Pseudomonas coronafaciens was isolated predominantly from leaves with halo blight symptoms or necrotic spots. Leaves with red leaf symptoms yielded many types of bacteria, including saprophytic pseudomonads,P. syringae, E. herbicola, Bacillus sp.,Micrococcus sp.,Corynebacterium sp., a yeast, and other unidentified species. Only isolates ofP. coronafaciens were pathogenic on the plant hosts tested. The bacteria associated with red leaf symptoms exist as saprophytes and/or epiphytes on leaves with those symptoms. It is concluded that bacteria do not contribute to red leaf symptom development in oats, but symptomatic leaves provide an environment for their growth.}, }
@article {pmid24227315, year = {1981}, author = {Wilkinson, CR and Nowak, M and Austin, B and Colwell, RR}, title = {Specificity of bacterial symbionts in Mediterranean and Great Barrier Reef sponges.}, journal = {Microbial ecology}, volume = {7}, number = {1}, pages = {13-21}, pmid = {24227315}, issn = {0095-3628}, abstract = {Bacteria were isolated from marine sponges from the Mediterranean and the Great Barrier Reef and characterized using numerical taxonomy techniques. A similar sponge-specific bacterial symbiont was found in 9 of 10 sponges examined from both geographic regions. This symbiont occurred in sponges of two classes and seven orders, and it probably has been associated with sponges over a long geological time scale. Another symbiont apparently specific to the spongeVerongia aerophoba was found. This sponge is yellow-orange, similar in color to the bacterial symbiont. These symbionts are two of a large mixed bacterial population present in many sponges.}, }
@article {pmid24227314, year = {1981}, author = {Caldwell, DE and Brannan, DK and Morris, ME and Betlach, MR}, title = {Quantitation of microbial growth on surfaces.}, journal = {Microbial ecology}, volume = {7}, number = {1}, pages = {1-11}, pmid = {24227314}, issn = {0095-3628}, abstract = {An equation describing the initial phases of microbial surface colonization is presented. Simultaneous microbial attachment and growth are considered as the primary components of colonization. A table is given that permits determination of growth rate from the density and distribution of cells present on surfaces after incubation in situ. Other methods used to calculate microbial growth rate on surfaces are evaluated. The new procedure is more accurate and less time consuming than those used previously. Published data on microbial surface colonization more closely follow the proposed colonization equation than the exponential growth equation, which overestimates the growth rate.}, }
@article {pmid24232520, year = {1980}, author = {Tate, RL}, title = {Effect of several environmental parameters on carbon metabolism in histosols.}, journal = {Microbial ecology}, volume = {5}, number = {4}, pages = {329-336}, pmid = {24232520}, issn = {0095-3628}, abstract = {High specific activity(14)C-labeled glucose, succinate, acetate, salicylate, and amino acids were used to examine carbon metabolism by the microbial community of Pahokee muck (aLithic medisaprist), a drained, cultivated soil of the Florida Everglades. Variations in carbon oxidation were observed from the end of the wet season through the dry season in a fallow (bare) field. Evolution of(14)CO2 varied with the substrate added and time. Calculation of(14)CO2 evolution for each substrate as a proportion of total respiration of the microbial community which was measured by succinate oxidation (relative oxidation) allowed for determination of the proportion of metabolic activity contributed by the oxidation of each carbon source. Except for the May sample when an approximate 30% decline in relative salicylate oxidation activity was observed, the proportion of total catabolic activity contributed by salicylate oxidation and acetate degradation was constant with time. Relative oxidation of glucose and amino acids ranged from 0.12 to 0.52 and 0.10 to 0.23, respectively. At two times during the dry season, the effect of depth of soil and crop on the carbon oxidation was examined. Relative acetate and amino acid oxidation were constant with depth whereas statistically significant variation was observed in glucose and salicylate oxidation. Generally, with the latter substrates, the activity declined with increased soil depth. Greatest effect of crop on these metabolic activities was noted with oxidation of salicylate in soils from a St. Augustinegrass [Stenatophrum secundatum (Walt.) Kuntz] pasture. In these soils, oxidation of salicylate was nearly double that of the fallow field or of soil planted with sugarcane (Saccharum sp.).}, }
@article {pmid24232519, year = {1980}, author = {Tu, CM}, title = {Influence of five pyrethroid insecticides on microbial populations and activities in soil.}, journal = {Microbial ecology}, volume = {5}, number = {4}, pages = {321-327}, pmid = {24232519}, issn = {0095-3628}, abstract = {Laboratory tests were conducted to determine the effects of five pyrethroid insecticides-permethrin (FMC 33297) [3-phenoxybenzyl (±)-3-(2,2-dichlorovinyl)-2,2-dimethylcyclopropanecarboxylate]; FMC 45498 [(S)-α-cyano-3-phenoxybenzyl-(R)-cis-2-(2,2-dibromovinyl)-3,3-dimethylcyclopropanecarboxylate]; Shell WL 41706 [(±)-α-cyano-3-phenoxybenzyl 2,2,3,3-tetramethylcyclopropane-carboxylate]; Shell WL 43467 [(±)-α-cyano-3-phenoxy benzyl (±)-cis,trans-2-(2,2-dichlorovinyl)-3,3-dimethylcyclopropanecarboxylate]; and Shell WL 43775 [(±)-α-cyano-3-phenoxybenzyl (±)-2-(4-chlorophenyl)-3-methylbutyrate]-at 0.5 and 5μg/g on microbial populations and activities in a sandy loam. The insecticides had antimicrobial activity in early stages of incubation. The populations recovered after 2 to 4 weeks and stimulatory effects on populations were also observed in later stages. No inhibition of acetylene (C2H2) reduction was evident with any of the insecticides. However, WL 43467 at both concentrations and permethrin and WL 41706 at 5 μg/g increased nitrification after 4 weeks. Soil microbial respiration, as indicated by oxygen consumption, increased with increasing concentration of insecticides, suggesting the possibility of microbial degradation of the insecticides. Dehydrogenase activity showed that none of the insecticides inhibited formazan (2,3,5-triphenyltetrazolium formazan) formation, whereas urease activity was stimulated in most cases. The studies indicated that some of the pyrethroid insecticides may exert transient effects on populations and activities of the microflora in a sandy loam, but these were short-lived and minor in nature.}, }
@article {pmid24232518, year = {1980}, author = {Piearce, TG and Phillips, MJ}, title = {Fate of ciliates in the earthworm gut: An in vitro study.}, journal = {Microbial ecology}, volume = {5}, number = {4}, pages = {313-319}, pmid = {24232518}, issn = {0095-3628}, abstract = {The behavior of the ciliateColpidium campylum was unaffected by exposure in vitro to high concentrations of pharyngeal and hindgut fluids from the earthwormLumbricus terrestris, but movement became abnormal and ceased in concentrations of midgut fluid as low as 1.5%. On mixingC. campylum culture with an equal volume of midgut fluid, which often contained resident astomatous ciliates, the.C. campylum cells were immediately immobilized and frequently disintegrated, while the astomatous ciliates continued to behave normally. Possible causes of the hostility of the midgut environment, and implications for earthworm nutrition, are discussed.}, }
@article {pmid24232517, year = {1980}, author = {Tan, TL}, title = {Effect of long-term lead exposure on the seawater and sediment bacteria from heterogeneous continuous flow cultures.}, journal = {Microbial ecology}, volume = {5}, number = {4}, pages = {295-311}, pmid = {24232517}, issn = {0095-3628}, abstract = {Lead-influenced changes of the composition of seawater and sediment bacteria were studied in two flow cultures run with lead-contaminated artificial seawater (1 mg Pb(2+)1(-1)) and one control culture. During the experiment viable counts of physiological groups of bacteria from the control culture were not significantly different from that of the lead-contaminated cultures. Lead tolerance of seawater and sediment bacteria strains was investigated. Comparisons of growth yields showed that lead tolerance of seawater and sediment bacteria was lost again if the bacteria were cultivated in a medium without lead. Lead tolerance could not be demonstrated for the sediment bacteria of one lead-contaminated culture. Heterotrophic uptake measurements with radioactive glucose indicated that seawater bacteria from the lead-contaminated cultures became adapted to lead pollution. The sediment bacteria, however, did not reveal lead tolerance by this method. Fluctuations in lead content of the sediment as well as of the overlying seawater gave indications of adsorption-desorption processes between seawater and sediment. Lead was not homogeneously distributed at the sediment surface.}, }
@article {pmid24232516, year = {1980}, author = {Karydis, M}, title = {Uptake of hydrocarbons by the marine diatomCyclotella cryptica.}, journal = {Microbial ecology}, volume = {5}, number = {4}, pages = {287-293}, pmid = {24232516}, issn = {0095-3628}, abstract = {The accumulation of exogenous hydrocarbons by the marine diatomCyclotella cryptica grown in culture has been studied using gas chromatography. Exposure of the alga to paraffins for 10 days results in accumulation of n-alkanes having between C13 and C16 carbon atoms. The C16 level in the accumulated fraction is twice as high as that in the original oil.}, }
@article {pmid24232515, year = {1980}, author = {Healey, FP}, title = {Slope of the Monod equation as an indicator of advantage in nutrient competition.}, journal = {Microbial ecology}, volume = {5}, number = {4}, pages = {281-286}, pmid = {24232515}, issn = {0095-3628}, abstract = {Apparently by analogy with enzyme kinetics, the half-saturation value (K) for nutrient uptake or growth has frequently been overemphasized in discussions of competition, and the role of maximum rates (Rm) has not been given sufficient emphasis. The ratio Rm/K, which is the slope of the Monod equation at lowest substrate concentration, offers a simple way of emphasizing both factors. Several examples from the literature are cited to show that this ratio better reflects rates at lowest concentrations, and therefore competitive position in the process being considered, than do K values alone.}, }
@article {pmid24232514, year = {1980}, author = {Martin, YP and Bianchi, MA}, title = {Structure, diversity, and catabolic potentialities of aerobic heterotrophic bacterial populations associated with continuous cultures of natural marine phytoplankton.}, journal = {Microbial ecology}, volume = {5}, number = {4}, pages = {265-279}, pmid = {24232514}, issn = {0095-3628}, abstract = {Variations of structure (probable taxonomic generic groups; ecological profiles), diversity (Shannon index, ¯H), and average catabolic potentialities (strain's average exoenzyme equipment, EAI; average carbonaceous compound utilization, UAI) of bacterial populations during two experimental phytoplankton blooms are described and show a certain overall unity. Oligotrophic conditions are characterized by high diversity levels (¯H from 3.60 to 4) and moderate catabolic potentialities (EAI and UAI close to 40%). During phytoplankton exponential growth phase bacteria show an EAI stability, but there is an increase of UAI with maximal values at the beginning of chlorophyll plateau (52-57%) and higher values of diversity (¯H greater than 4). Phytoplankton mortalities appear to cause an EAI increase and a decrease of both UAI and ¯H (1.50 to 2). Vibrio-like organisms seem to be closely related to this period.In spite of these similar patterns, many differences appear between both experiments from a taxonomic point of view, the autumnal population being more diversified than the spring one.The results obtained show the value of simultaneous analysis of these different aspects and of this ecological methodology allowing spatial or temporal comparisons.}, }
@article {pmid24232513, year = {1980}, author = {Ansbaek, J and Blackburn, TH}, title = {A method for the analysis of acetate turnover in a coastal marine sediment.}, journal = {Microbial ecology}, volume = {5}, number = {4}, pages = {253-264}, pmid = {24232513}, issn = {0095-3628}, abstract = {The concentrations of volatile fatty acids were measured in the pore water of sediment from the Limfjorden, Denmark. The pore water was freeze-dried and the acids, which were redissolved in formic acid, were analyzed by gas chromatography on a Carbopack column. The limit of detection was 0.1 μmol l(-1) pore water. The concentration ranges (μmol l(-1) pore water) were as follows: 0.1 to 6.0 for acetate; <0.1 to 0.6 for propionate, and <0.1 to 0.5 for butyrate. The rate constants for the disappearance of injected tracer concentrations of U-(14)C-acetate were measured at 2 cm depth intervals in sediment strata (0 to 10 cm). The rate constant for acetate turnover at 4 to 6 cm depth did not vary greatly with season, 2.1 h(-1), SD 0.6 for 7 values. In spring, the rate constants were highest in the 0 to 2 cm stratum and decreased with sediment depth. The calculated rates for acetate turnover of 7.2 mmol m(-2) day(-1) for early spring (2°C) and of 19.6 mmol m(-2) day(-1) for late autumn (7°C) were higher than would be expected from published values for carbon oxidation by sulfate in these sediments.}, }
@article {pmid24232512, year = {1980}, author = {Staley, JT and Marshall, KC and Skerman, VB}, title = {Budding and prosthecate bacteria from freshwater habitats of various trophic states.}, journal = {Microbial ecology}, volume = {5}, number = {4}, pages = {245-251}, pmid = {24232512}, issn = {0095-3628}, abstract = {Budding and prosthecate bacteria were enumerated in spring and summer by viable counting procedures in several freshwater habitats in Australia including oligotrophic lakes, a mesotrophic lake, and eutrophic ponds.Caulobacter spp. were the most numerous type encountered. They were present in the highest concentrations (exceeding 1000/ml) in the mesotrophic lake during the summer. Their proportion to total viable heterotrophic bacteria was also highest (35.1 to 37.7) in this habitat. From 17 to 330/mlCaulobacter spp. were counted in the eutrophic habitats where their proportion to total viable numbers was less than 1.0%. In the oligotrophic lakes they varied from 5 to 23/ml and comprised greater than 5% of the total viable count.Hyphomicrobium- like bacteria were also numerous in the mesotrophic lake and in one oligotrophic lake during the summer sampling period.Ancalomicrobium spp. occurred in high concentrations (130/ml) in the mesotrophic lake. Budding bacteria of thePlanctomyces-Pasteuria group were most numerous in the eutrophic habitats where as many as 240/ml were counted; their proportion to total heterotrophs remained relatively constant regardless of trophic state, however. A similar pattern was observed withProsthecobacter spp.}, }
@article {pmid24227231, year = {1980}, author = {Orndorff, SA and Colwell, RR}, title = {Effect of Kepone on estuarine microbial activity.}, journal = {Microbial ecology}, volume = {6}, number = {4}, pages = {357-368}, pmid = {24227231}, issn = {0095-3628}, abstract = {In situ heterotrophic uptake of mixed(14)C-amino acids and direct viable cell (DVC) count of Chesapeake Bay water samples were not significantly affected by the insecticide Kepone at concentrations [Symbol: see text]0.01 mg/1. Maximum inhibition of heterotrophic uptake,ca. 85-90%, and DVC count, 45-97%, was evident at concentrations of Kepone exceeding 0.2 mg/1. A specific activity index (Metabolic Activity/DVC or Kepone-resistant DVC), heterotrophic uptake, and DVC count were found to be statistically correlated (a=0.05) to one another, but negatively correlated with concentration of Kepone. The direct viable cell count proved to be a rapid, simple method for estimating the effect of Kepone on in situ estuarine microbial activity.}, }
@article {pmid24227230, year = {1980}, author = {Roskoski, JP}, title = {N2 Fixation (C2H 2 reduction) by epiphylls on coffee,Coffea arabica.}, journal = {Microbial ecology}, volume = {6}, number = {4}, pages = {349-355}, pmid = {24227230}, issn = {0095-3628}, abstract = {Nitrogen fixation (C2H2 reduction) by epiphylls on coffee,Coffea arabica, grown in sites with different degrees of shade, was determined. Coffee leaves with nitrogen-fixing epiphylls were found in all sites in approximately equal numbers. Rates of C2H2 reduction were similar for all sites and throughout the year, averaging 3.21 nmoles C2H2 reduced leaf with epiphylls(-1) day(-1). Apparently, neither rates of activity nor abundance of leaves with nitrogen-fixing epiphylls is related to the degree of shade in a site. No correlation was found between percent epiphyll cover and the presence or magnitude of nitrogen-fixing activity. Calculated annual fixation by epiphylls on coffee was low, ranging from 0.7 g N2 ha(-1) year(-1) for the shadeless site to 1.4 g N2 ha(-1) year(-1) for the site withIngajinicuil shade trees. These results suggest that epiphyll fixation is not an important source of nitrogen for the coffee ecosystem studied.}, }
@article {pmid24227229, year = {1980}, author = {Jones, RD and Hood, MA}, title = {Effects of temperature, ph, salinity, and inorganic nitrogen on the rate of ammonium oxidation by nitrifiers isolated from wetland environments.}, journal = {Microbial ecology}, volume = {6}, number = {4}, pages = {339-347}, pmid = {24227229}, issn = {0095-3628}, abstract = {Ammonium-oxidizing bacteria were examined in two wetland environments, a freshwater marsh and an estuarine bay, during a 2-year period. Two predominant types were consistently isolated, one from each environment. Both isolates were identified as species ofNitrosomonas. Using a closed culture, high cell density assay, the effects of temperature, pH, salinity, Na(+), K(+), nitrite, nitrate, and ammonium concentrations on ammonium oxidation were determined. Maximum activity was observed for the freshwater isolate at 35°C, pH 8.5, salinities of 0.3 to 0.5% Na(+) and K(+), and ammonium concentrations greater than 0.5 g/l. For the estuarine isolate, maximum activity was observed at 40°C, pH 8.0, salinities of 0.5 to 1.0%, 1.0% Na(+) and K(+), and 0.2 g/l ammonium. The estuarine isolate had a Na(+) requirement which could be partially substituted by the K(+), suggesting that the organism is a true estuarine bacterium. Nitrite inhibited both isolates at concentrations greater than 5 mg/l, whereas nitrate had no significant effect on either isolate.}, }
@article {pmid24227228, year = {1980}, author = {Henriksen, K}, title = {Measurement of in situ rates of nitrification in sediment.}, journal = {Microbial ecology}, volume = {6}, number = {4}, pages = {329-337}, pmid = {24227228}, issn = {0095-3628}, abstract = {A method has been developed for the measurement of nitrification rates in intact sediment cores without disturbing the concentration gradients of oxygen and ammonium. N-serve (2-chloro-6-trichloromethyl-pyridine), a specific inhibitor of the autotrophic ammonium oxidation, was injected into a 0-2 cm surface layer of the sediment (20 ppm) and added to the water column of sediment cores (5 ppm). N-serve in these concentrations was sufficient to inhibit nitrification, but did not change the rate of ammonium production or incorporation in sediment suspensions, which were incubated aerobically and anaerobically. The ammonium accumulation in cores injected with N-serve was thus equal to the amount of ammonium which was oxidized to nitrate in the control cores. Nitrification rates were in the range of 0-3 mmol N m(-2) (-1.)}, }
@article {pmid24227227, year = {1980}, author = {Aumen, NG}, title = {Microbial succession on a chitinous substrate in a woodland stream.}, journal = {Microbial ecology}, volume = {6}, number = {4}, pages = {317-327}, pmid = {24227227}, issn = {0095-3628}, abstract = {Plate counts, scanning electron microscopy, and direct observations were utilized to determine successional trends of different groups of microorganisms onProcambarus versutus (Hagen) exoskeletons incubatedin situ in a second-order, acidic woodland stream in Northwest Florida. Plate counts and SEM observations indicated a definite successional pattern dominated in numbers initially by the nonbranching bacteria, followed by the actinomycetes. The greatest number of fungal propagules coincided with the least number of bacterial colony-forming units. Chitinoclastic bacterial colonizers increased on the substrate throughout the study, comprising as much as 88% of the total bacterial community during the final stages of chitin decomposition. Scanning electron micrographs taken over the duration of the study revealed the abundance of an actinomycete, identified as a species ofStreptomyces, on the exoskeleton. Enumeration of microorganisms in the stream sediment was also performed in conjunction with the exoskeleton analysis. Relatively constant numbers of bacteria and fungi were observed, with chitinoclastic bacteria comprising between 3 and 11% of the total sediment bacterial community.}, }
@article {pmid24227226, year = {1980}, author = {Wickstrom, CE and Wiegert, RG}, title = {Response of thermal algal-bacterial mat to grazing by brine flies.}, journal = {Microbial ecology}, volume = {6}, number = {4}, pages = {303-315}, pmid = {24227226}, issn = {0095-3628}, abstract = {Gelatinous mats of blue-green algae (cyanobacteria) and bacteria in alkaline thermal springs of Yellowstone National Park add biomass at the surface more rapidly than material is degraded in the anaerobic layers underneath. This inequality leads to flow diversion and exposure of mat surface. The microenvironment of these cool exposed "islands" is drastically altered as adults and larvae of ephydrid fly species invade, feed on, and solubilize the mat. We studied the effect of this grazing by comparing hot and cool ungrazed controls with mat that was cooled and remained open to invasion by ephydrid flies. Mat community biomass changes (ash free dry weight-AFDW) and changes in bacterial numbers were determined. Mat biomass was essentially unchanged for 3 weeks in the controls. Numbers of bacteria remained unchanged in the cool ungrazed control but decreased by more than 90% in the hot-ungrazed control. Grazing by ephydrid flies initially increased both mat biomass and numbers of unicellular heterotrophic bacteria. When grazed mat was reexposed to flowing hot water, biomass and bacterial numbers per mg AFDW declined immediately and significantly. The long-term effect of grazing on the mat is solubilization with downstream biomass export and subsequent initiation of successional algal-bacterial mat regrowth. Our experimental results suggest an initial stimulation of net photosynthesis by grazing, possibly related to the promotion of bacterial activity resulting in the release of essential mineral nutrients and/or free CO2.}, }
@article {pmid24227225, year = {1980}, author = {Konopka, A and Schnur, M}, title = {Effect of light intensity on macromolecular synthesis in cyanobacteria.}, journal = {Microbial ecology}, volume = {6}, number = {4}, pages = {291-301}, pmid = {24227225}, issn = {0095-3628}, abstract = {The light-dependent incorporation of NaH(14)CO3 into low molecular weight compounds, polysaccharide, or protein was determined in cultures of the cyanobacteriumMerismopedia tenuissima incubated at a series of light intensities. There was an inverse relationship between incorporation into polysaccharide and protein. At light intensities of 90 μE/m(2)/sec or above, relative incorporation of radioisotope into polysaccharide was greatest and relative incorporation into protein was lowest. Optimal relative protein accumulation occurred in samples incubated at 20 μE/m(2)/sec. A broader optimum of light intensity for maximal protein accumulation was found if ammonia rather than nitrate was the nitrogen source. Physiological adaptation of cultures to growth at a particular light intensity did not alter the pattern of macromolecular incorporation when those cultures were tested over the series of light intensities. The response of cultures ofOscillatoria rubescens to light intensity was similar to that ofM. tenuissima, although incorporation into low molecular weight compounds was significantly greater.The effect of light intensity on macromolecular synthesis in a natural population ofOscillatoria rubescens was also determined. A pattern similar to that observed in batch cultures ofO. rubescens was occasionally found, but in other experiments there was no increase in relative protein incorporation when light intensity was decreased.}, }
@article {pmid24227224, year = {1980}, author = {Karydis, M and Fogg, GE}, title = {Physiological effects of hydrocarbons on the marine diatomCyclotella cryptica.}, journal = {Microbial ecology}, volume = {6}, number = {4}, pages = {281-290}, pmid = {24227224}, issn = {0095-3628}, abstract = {Effects of hydrocarbons on the marine diatomCyclotella cryptica have been studied in laboratory experiments. Low hydrocarbon concentrations (100 μg· l(-1)) stimulate growth whereas higher concentrations (l mg· l(-1)) inhibit growth. The aromatics are most toxic among the hydrocarbons, whereas the paraffins do not seem to have any serious effect on growth or photosynthesis of the algae. Both aromatic and paraffin fractions affected the chlorophyll a, protein, and sugar contents of the cells. Toxicity levels were affected by the presence of dissolved organic material in the medium. Studies on the ultrastructure ofC. cryptica have shown that paraffins affect the thickness of the cell wall.}, }
@article {pmid24227135, year = {1980}, author = {Okon, Y and Cakmakci, L and Nur, I and Chet, I}, title = {Aerotaxis and chemotaxis ofAzospirillum brasilense: A note.}, journal = {Microbial ecology}, volume = {6}, number = {3}, pages = {277-280}, pmid = {24227135}, issn = {0095-3628}, abstract = {Azospirillum brasilense was attracted to capillaries containing either phosphate buffer, distilled water, or saline. The number of bacteria in these capillaries was 3-4×10(4), after 1 h of incubation. In the presence of phosphate buffer + attractants, the number of cells accumulated in the capillary increased only to 5×10(4)-1.1×10(5) cells. It was not possible, therefore, to measure chemotaxis inA. brasilense as distinct from aerotaxis by the capillary method. Chemotaxis was observed in semi-solid agar plates and was determined by a growth band oriented towards the attractant. Positive chemotactic response was obtained with peptone, tryptone, yeast extract, amino acids, organic acids, arabinose and galactose.}, }
@article {pmid24227134, year = {1980}, author = {Jones, RD and Hood, MA}, title = {Interaction between an ammonium-oxidizer,Nitrosomonas sp., and two heterotrophic bacteria,Nocardia atlantica andPseudomonas sp.: A note.}, journal = {Microbial ecology}, volume = {6}, number = {3}, pages = {271-275}, pmid = {24227134}, issn = {0095-3628}, abstract = {Closed culture experiments showed that the ability of an estuarine chemolithotrophic ammonium-oxidizer,Nitrosomonas sp., to convert ammonium to nitrite was substantially increased by as much as 150% and 50% when grown in the presence of two heterotrophs isolated from the same environment. The heterotrophs were identified asNocardia atlantica andPseudomonas sp. The growth of the heterotrophs was stimulated by as much as one order of magnitude in the presence of the ammonium-oxidizer.}, }
@article {pmid24227133, year = {1980}, author = {Kilpi, S}, title = {Degradation of some phenoxy acid herbicides by mixed cultures of bacteria isolated from soil treated with 2-(2-methyl-4-chloro)phenoxypropionic acid.}, journal = {Microbial ecology}, volume = {6}, number = {3}, pages = {261-270}, pmid = {24227133}, issn = {0095-3628}, abstract = {Mixed bacterial cultures capable of using 2-methyl-4-chIorophenoxyacetic acid (MCPA) and 2, 4-dichlorophenoxyacetic acid (2, 4-D) as the sole source of carbon and energy were isolated from field soil treated with the herbicide (±)2-(2-methyl-4-chloro)phenoxypropionic acid (mecoprop). An enrichment technique with two aromatic compounds as sources of carbon was used. Effects of temperature and substrate concentration were studied. The mixed cultures retained their ability to degrade MCPA although the bacteria were grown for 3 months (32 successive passages) with glucose as the sole source of carbon and energy. With benzoic acid as co-substrate, one of the cultures was also able to degrade mecoprop and (±)2-(2, 4-dichloro)phenoxypropionic acid (dichlorprop). This ability was not maintained, however, over more than 10 passages.}, }
@article {pmid24227132, year = {1980}, author = {Hutchins, AS}, title = {In vitro inhibition of root-rot pathogensPhellinus weirii, Armillariella mellea, Fomes annosus, andPhytophthora cinnamomi by a newly isolatedBacillus sp.}, journal = {Microbial ecology}, volume = {6}, number = {3}, pages = {253-259}, pmid = {24227132}, issn = {0095-3628}, abstract = {A Gram-positive bacterium that inhibits several root-rot pathogens was isolated from alder forest soil on the Oregon coast. This organism, similar toBacillus cereus, produces in culture media a heat-stable, broad-spectrum antibiotic which inhibits growth of four important Northwest conifer root disease fungi:Phellinus weirii (Murr.) Gilbertson,Fomes annosus (Fr.) Cke.,Armillariella mellea (Fr.) Karst., andPhytophthora cinnamomi Rands.}, }
@article {pmid24227131, year = {1980}, author = {Nordbring-Hertz, B and Odham, G}, title = {Determination of volatile nematode exudates and their effects on a nematode-trapping fungus.}, journal = {Microbial ecology}, volume = {6}, number = {3}, pages = {241-251}, pmid = {24227131}, issn = {0095-3628}, abstract = {Volatile compounds exuded from axenically grown free-living nematodes were determined with gas chromatographic and mass spectrometric techniques. Carbon dioxide evolved from 5-200 nematodes was determined with an ampoule technique, whereas total ammonia (NH3 + NH4 (+)) and acetic and propionic acids were determined by direct injection of water in which nematodes had been suspended for 1-3 days. CO2 amounted to about 80 ng nematode(-1) d(-1), total ammonia to 1-5 ng, and acetic and propionic acids to 0.5 and 1.0 pg nematode(-1) d(-1).The effects of these compounds on induction of trap formation in the nematodetrapping fungusArthrobotrys oligospora were tested. CO2 inhibited trap formation at 5-10% CO2 in air (v/v), whereas ammonia stimulated trap formation in a certain concentration range. No effects of acetic and propionic acids were noted for the concentrations tested. The combined effects of these volatiles in the aqueous environment are discussed on the basis of stoichiometric considerations.}, }
@article {pmid24227130, year = {1980}, author = {Bewley, RJ and Campbell, R}, title = {Influence of zinc, lead, and cadmium pollutants on the microflora of hawthorn leaves.}, journal = {Microbial ecology}, volume = {6}, number = {3}, pages = {227-240}, pmid = {24227130}, issn = {0095-3628}, abstract = {Transect studies were conducted to determine the relative effects of zinc, lead, and cadmium pollution on microorganisms occurring on hawthorn leaves at varying distances from a smelting complex.Sporobolomyces roseus was absent from the most heavily contaminated leaves but, although lead was inhibitory, other environmental factors were also important in determining its overall population level. Conversely,Aureobasidium pullulans and nonpigmented yeasts showed a significant partial positive correlation with lead but were inhibited by zinc and/or cadmium. Numbers of bacterial colonies were only slightly reduced by the combined effect of all three metals, but total numbers of bacteria were highly negatively correlated with lead. Filamentous fungi, isolated by leaf washing, were only slightly inhibited by all three metals, and the degree of mycelial proliferation on senescent leaves was little affected by heavy metal pollution. Computer-generated maps were produced of the distribution ofA. pullulans in relation to zinc and lead fallout.}, }
@article {pmid24227129, year = {1980}, author = {Swisher, R and Carroll, GC}, title = {Fluorescein diacetate hydrolysis as an estimator of microbial biomass on coniferous needle surfaces.}, journal = {Microbial ecology}, volume = {6}, number = {3}, pages = {217-226}, pmid = {24227129}, issn = {0095-3628}, abstract = {Estimating microbial standing crops and microbial production in natural habitats has been difficult for microbial ecologists. The present paper describes a simple spectrophotometric assay based on the hydrolysis of fluorescein diacetate which estimates well the standing crops of microbial cells on coniferous needles and twigs. A technique is also presented for correlating optical density readings with actual dry weights of microbial cells epiphytic on needles, and thus for standardizing the assay. The assay shows promise of broad applicability to other microbial habitats.}, }
@article {pmid24227128, year = {1980}, author = {Laybourn-Parry, J and Baldock, B and Kingmill-Robinson, C}, title = {Respiratory studies on two small freshwater amoebae.}, journal = {Microbial ecology}, volume = {6}, number = {3}, pages = {209-216}, pmid = {24227128}, issn = {0095-3628}, abstract = {The changes in respiration rate and mean cell volume induced by temperature within the range 10°C-25°C were investigated in two small species of freshwater amoebae,Saccamoeba limax Page andVannella sp. Mean cell volume varied in response to temperature, with maxima at 20°C inVannella sp. (10.15× 10(3) (±1.80)μm(3) and 15°C inS. limax (9.08×10(3) (±0.93)μm(3). Respiration rate increased over the temperature range investigated. The highest rates and the greatest rate of increase between temperatures occurred inVannella sp. Q10 ranged between 0.12 and 1.33 inS. limax and between 1.77 and 7.36 inVannella sp. A regression of log oxygen uptake versus log cell volume incorporating the data of the present investigation and the data of other workers on amoeba respiration is presented, and the ecological significance and application of such data discussed.}, }
@article {pmid24227127, year = {1980}, author = {Nalewajko, C and Lee, K and Fay, P}, title = {Significance of algal extracellular products to bacteria in lakes and in cultures.}, journal = {Microbial ecology}, volume = {6}, number = {3}, pages = {199-207}, pmid = {24227127}, issn = {0095-3628}, abstract = {In simulated diurnal experiments withChlorella pyrenoidosa andPseudomonas fluorescens, bacterial growth was virtually confined to the daylight period and occurred at the expense of glycolate, the predominant extracellular product of the alga. Both glycolate levels and(14)C-DOC excretion rates were much lower in mixed algal-bacterial than in axenicChlorella cultures.This close coupling of bacterial growth to algal photosynthesis and extracellular release was also observed in Jack's Lake, but not in Lake Erie. Experimental enrichment with lake water particulates >30μm suppressed the daytime growth of bacteria in Jack's Lake, but increased it dramatically in Lake Erie. Daylight doubling times for bacteria in lakewater ranged from 2 to 19 days. In mixed culture withChlorella, Pseudomonas had a doubling time of about 2 hours in the light.}, }
@article {pmid24227126, year = {1980}, author = {Berman, T and Gerber, C}, title = {Differential filtration studies of carbon flux from living algae to microheterotrophs, microplankton size distribution and respiration in Lake Kinneret.}, journal = {Microbial ecology}, volume = {6}, number = {3}, pages = {189-198}, pmid = {24227126}, issn = {0095-3628}, abstract = {The flux of newly photosynthetically fixed, dissolved organic carbon (PDOC) from phototrophs to microheterotrophs in Lake Kinneret was examined by differential (3 and 0.4μm) filtration after samples were incubated with(14)C-bicarbonate for 3 hours (in the light) and subsequently for 21 hours (in darkness). Only a small proportion (average about 10%) of the carbon fixed from(14)C-bicarbonate in the light was associated with particulate matter <3μm. In 14 out of 16 experiments there was no significant decrease in the relative proportion of radioactivity associated with larger (>3μm) organisms after the dark period, suggesting that the amount of PDOC taken up by unclumped, single bacteria (<3μm) was not very great. Respiration rates, estimated by the decrease in(14)C particulate counts in the dark period, ranged from 3.4 to 21.2% of daylight net photosynthesis. In almost all cases, parallel experiments with additions of radioactive glucose or amino acids indicated that the majority of active heterotrophs passed through 3μm filters. Apparent residence times for glucose and amino acids were 20 to 168 hours and 20 to 152 hours, respectively.}, }
@article {pmid24226969, year = {1980}, author = {Simidu, U and Tsukamoto, K}, title = {A method of the selective isolation and enumeration of marine Vibrionaceae.}, journal = {Microbial ecology}, volume = {6}, number = {2}, pages = {181-184}, pmid = {24226969}, issn = {0095-3628}, abstract = {A noninhibitory medium and GasPack anaerobic culture system were employed for the selective enumeration and isolation of Vibrionaceae in seawater and marine sediments.Vibrio counts obtained by the new method for seawater and sediment samples were compared with vibrio numbers in the heterotrophic bacterial population appearing on a medium routinely employed in the laboratory for such counts. The ratio of the former to the latter counts ranged from 0.5 to 1.3, the average being 0.96. The seawater and sediment bacteria that grew and produced visible colonies on the medium under anaerobic conditions for 3 days at 20°C were almost exclusively vibrios.From the results reported here it is concluded that most of the vibrios present in seawater and sediment samples can be recovered by the new method developed in this study.}, }
@article {pmid24226968, year = {1980}, author = {Lavoie, KH}, title = {Toxicity of carbide waste to heterotrophic microorganisms in caves.}, journal = {Microbial ecology}, volume = {6}, number = {2}, pages = {173-179}, pmid = {24226968}, issn = {0095-3628}, abstract = {The spent carbide from acetylene-generating lamps used by spelunkers has long been assumed to be toxic. Pure cultures ofE. coli, S. cerevisiae, andB. subtilis were inhibited within 15 minutes by addition of a 1% solution of waste carbide. The heterotrophic microorganisms which form the food base in caves were depressed 81% in 1 hour by the application of fresh carbide waste to a cave stream mudbank. The effects were temporary as the toxicity was lost when the extremely alkaline pH of the waste was neutralized. The reduction in pH occurs naturally over time by atmospheric and substrate buffering and is probably related to soil type and available moisture.}, }
@article {pmid24226967, year = {1980}, author = {Dicker, HJ and Smith, DW}, title = {Physiological ecology of acetylene reduction (nitrogen fixation) in a Delaware salt marsh.}, journal = {Microbial ecology}, volume = {6}, number = {2}, pages = {161-171}, pmid = {24226967}, issn = {0095-3628}, abstract = {The effects of several fixed nitrogen compounds on acetylene reduction activity (nitrogen fixation) of surface sediments from a Delaware salt marsh were studied. Ammonia addition caused little decrease in activity early in the summer but resulted in a considerable decrease (85-95%) in activity late in the summer and early in the fall. Nitrate caused a near complete suppression of activity at all times. Other compounds such as glutamate, urea, and yeast extract caused a slight increase in activity in tallSpartina sediments and caused more than a 2.5-fold increase in shortSpartina sediments. There was a lag period (1-2 days) before the commencement of in vitro acetylene reduction activity during the spring and early summer, but this lag period was not present in the late summer. The addition of chloramphenicol to samples from a shortSpartina zone caused decreases in activity similar to those obtained with ammonia, whereas chlorate amendments yielded results which, when compared on an electron basis, were comparable to those obtained with nitrate. These results indicated that the observed lag period may be the result of a physiological response to the in situ levels of ammonia and/or nitrate. It is suggested here that in situ nitrogenase activity may be controlled by two processes: (a) repression and derepression of nitrogenase synthesis mediated by the levels of ammonia, and (b) competition for reducing power (electrons) and energy (ATP) between the processes of nitrate reduction and nitrogen fixation.}, }
@article {pmid24226966, year = {1980}, author = {Kent, EB}, title = {Effect of food level on reproduction and metamorphosis in the suctorian protozoanTokophrya lemnarum stein.}, journal = {Microbial ecology}, volume = {6}, number = {2}, pages = {153-159}, pmid = {24226966}, issn = {0095-3628}, abstract = {A sessile predator, the ciliated protozoanTokophrya lemnarum, produces a motile embryo. The embryo attaches to a substrate and secretes a stalk at metamorphosis. Production of the offspring is closely synchronized with the feeding schedule, so that fecundity per individual varies directly with the food level. Some embryos produced by an adult do not attach at metamorphosis but become freely floating adults. The percentage of nonattaching embryos is compared between adults fed high or low level diets. Adults on the low level diet produce 25% or more nonattaching embryos compared to 10% or less produced by adults on a high level diet. If the adult is switched from a low level diet to a high level diet, or from high to low, the percentage of nonattaching embryos produced on each diet remains relatively constant. It is suggested that nonattachment provides one means for individuals to escape areas of low prey density and availability.}, }
@article {pmid24226965, year = {1980}, author = {Sjoblad, RD and Coleman, BA}, title = {Chemotactic responses ofThiobacillus thioparus.}, journal = {Microbial ecology}, volume = {6}, number = {2}, pages = {147-151}, pmid = {24226965}, issn = {0095-3628}, abstract = {A capillary assay was employed to quantify chemotactic responses in the chemoautotrophic bacterium,Thiobacillus thioparus. NH4Cl, KNO3, and Na2S2O3 were strong attractants. The minimum concentration of each of these inorganic chemicals needed to elicit an observable response was approximately 10(-4) M.T. thioparus did not respond to carbohydrates or amino acids.}, }
@article {pmid24226964, year = {1980}, author = {Rüger, HJ and Koploy, JA}, title = {DNA base compositions of halophilic and nonhalophilicBacillus firmus strains of marine origin.}, journal = {Microbial ecology}, volume = {6}, number = {2}, pages = {141-146}, pmid = {24226964}, issn = {0095-3628}, abstract = {The mineral salt requirements of 27 strains ofBacillus firmus were determined. Twenty-six of these strains were of marine origin and one terrestrial strain was used as a reference. Three strains demonstrated strictly halophilic behavior, i.e., they showed no growth in media prepared without sodium chloride. Seven strains were nonhalophilic. The growth of 17 strains was stimulated by the addition of sodium chloride, but the cells were able to grow without it. These results were compared with the DNA base compositions of the strains. In contrast to literature data, relationships between the DNA base ratios and the halophilic or nonhalophilic behavior of the cells could not be detected. But strains with guanine plus cytosine values above 41 mol% did grow well at 44°C, and those strains showing poor growth at this temperature had lower guanine plus cytosine percentages.}, }
@article {pmid24226963, year = {1980}, author = {Gregory, E and Perry, RS and Staley, JT}, title = {Characterization, distribution, and significance ofMetallogenium in Lake Washington.}, journal = {Microbial ecology}, volume = {6}, number = {2}, pages = {125-140}, pmid = {24226963}, issn = {0095-3628}, abstract = {During summer stratification,Metallogenium personatun was found exclusively in the hypolimnion of Lake Washington where the oxygen tension was below 8 ppm. Numbers of the organism decreased in the lake immediately following turnover in October. Significant concentrations ofMetallogenium microcolonies did not recur until spring, after the lake had stratified. During stratification the distribution of particulate manganese closely followed the distribution ofMetallogenium. EDAX analysis, confirmed by electron microprobe analyses of the encrustation, showed that the primary component was manganese. Iron and some trace elements were also precipitated on the organism but to a lesser degree. In addition, phosphate, the primary substance limiting phytoplankton growth in Lake Washington, was found in the encrustation, indicatingMetallogenium maybe important in limiting algal blooms in the lake. Attempts to growMetallogenium in the laboratory were unsuccessful. This inability, combined with the negative results of thin-sectioning and acridine orange staining ofMetallogenium microcolonies, suggests that the microcolonial structures seen in Lake Washington are not a living form of an organism.}, }
@article {pmid24226962, year = {1980}, author = {Lund, V and Goksøyr, J}, title = {Effects of water fluctuations on microbial mass and activity in soil.}, journal = {Microbial ecology}, volume = {6}, number = {2}, pages = {115-123}, pmid = {24226962}, issn = {0095-3628}, abstract = {When previously dried soil was remoistened, a series of microbial events occurred. The bacterial plate count population increased rapidly, with a doubling time of 4-5 h. The length of fungal hyphae and microscopic counts of bacteria increased more slowly. The microscopically counted bacterial population was estimated to have a doubling time of about 90 h. The respiratory burst occurring after 2-3 days coincided with the maximal growth rate of the bacterial plate count population. From the respiratory data, plate count bacteria were estimated to have a cell mass of 0.4 pg dry weight, whereas the mass of microscopically counted bacteria was only 10% of this. Changes in bacterial DNA content corresponded to changes in the microscopic count, whereas changes in soil catalase activity mainly corresponded to changes in the fungal biomass, which was dominant.It is suggested that bacterial plate counts and microscopic counts represent two distinct populations of bacteria, which for practical purposes may be termed zymogenous and autochthonous, respectively.}, }
@article {pmid24226961, year = {1980}, author = {Bentley, BL and Carpenter, EJ}, title = {Effects of desiccation and rehydration on nitrogen fixation by epiphylls in a tropical rainforest.}, journal = {Microbial ecology}, volume = {6}, number = {2}, pages = {109-113}, pmid = {24226961}, issn = {0095-3628}, abstract = {Nitrogen fixation rates by epiphyllous microorganisms are affected by desiccation. Rates from leaf samples which had been dried for 12 h were 0.66 ng N/10 cm(2)/h. In contrast, rates from leaves which had been kept continuously wet were 18.69 ng N/10 cm(2)/h. Leaf samples which had been rehydrated for 2 and 4 h showed intermediate fixation rates (4.26 and 9.76 ng N/10 cm(2)/h, respectively). Epiphyllous bryophytes maintain moist conditions on the leaf surface and thus create a microenvironment suitable for prolonged fixation by the microorganisms.}, }
@article {pmid24226960, year = {1980}, author = {Friedmann, EI and Kibler, AP}, title = {Nitrogen economy of endolithic microbial communities in hot and cold deserts.}, journal = {Microbial ecology}, volume = {6}, number = {2}, pages = {95-108}, pmid = {24226960}, issn = {0095-3628}, abstract = {The source of combined nitrogen in endolithic microbial communities was studied in samples from desert localities in North and South America, the Middle East, South Africa, and Antarctica. Nitrogen fixation (acetylene reduction) seems to occur only exceptionally. Evidence suggests that, in general, the nitrogen source for endolithic microorganisms in deserts is abiotically fixed nitrogen produced by atmospheric electric discharges (lightning or aurorae), conveyed to the rock by atmospheric precipitation. Nitrogen is apparently not a limiting factor in these low-productivity communities. An incomplete nitrogen cycle seems to be present which includes the following pathways: supply of nitrates and ammonia from the atmosphere; decomposition of organic matter to ammonia; reassimilation of ammonia; ammonia volatilization; loss of organic matter through weathering (only in certain Antarctic rocks); biological nitrogen fixation (exceptional).}, }
@article {pmid24226837, year = {1980}, author = {Wilkerson, FP}, title = {Bacterial symbionts on green hydra and their effect on phosphate uptake.}, journal = {Microbial ecology}, volume = {6}, number = {1}, pages = {85-92}, pmid = {24226837}, issn = {0095-3628}, abstract = {Gram-negative rod-shaped bacteria (1.5-2μm long and 0.5μm wide) have been found associated with green hydra. They are always present on the hydra surface delineating the ectodermal cells, on animals in culture, and also on those sampled from a natural habitat. The bacteria could be removed by a 30-min treatment with antibiotics (50μ/ml polymyxin B and 50μ/ml streptomycin). Antibiotic-treated hydra took up 55% less phosphate from the medium than control hydra. The nutritional relationship between the bacteria and green hydra and possible routes of infection of the hydra by these prokaryotic symbionts are discussed. Their importance in interpreting results of certain types of physiological experiments using aquatic organisms is emphasized.}, }
@article {pmid24226836, year = {1980}, author = {Andrews, JH and Kenerley, CM and Nordheim, EV}, title = {Positional variation in phylloplane microbial populations within an apple tree canopy.}, journal = {Microbial ecology}, volume = {6}, number = {1}, pages = {71-84}, pmid = {24226836}, issn = {0095-3628}, abstract = {Variation in density of epiphytic yeasts, filamentous fungi, and bacteria on apple leaves collected from eight trees at nine dates for two seasons was determined with respect to three positional factors: height, compass direction from the center of the tree, and lateral proximity to the canopy periphery. Univariate analyses of variance were performed on each of the microbial classes for each date according to a model that excluded tree effect but accounted for the positional factors with interactions. The assumption of no tree effect was explored by residual analysis and examination of the seasonal pattern of microbial densities for each tree. No persuasive evidence was obtained to invalidate this assumption. For filamentous fungi and yeasts, height and lateral position were the most significant factors withp<0.05 for yeasts at several periods. The two factors appeared to be of equal importance. Trends were less clear for bacteria, but all three positional factors and some two-way interactions seemed of some importance. For filamentous fungi and bacteria, frequently no factors were significant at a level of 0.10, but at almost all sampling dates certain positional factors and interactions were significant at a level of 0.25. Inspection of partial correlation coefficients indicated no apparent linear association between densities of most pairs of microbial classes. Implications of these results for experimental design and for the microbial ecology of the phylloplane community are discussed.}, }
@article {pmid24226835, year = {1980}, author = {Houba, C and Remacle, J}, title = {Composition of the saprophytic bacterial communities in freshwater systems contaminated by heavy metals.}, journal = {Microbial ecology}, volume = {6}, number = {1}, pages = {55-69}, pmid = {24226835}, issn = {0095-3628}, abstract = {The bacterial communities of three aquatic systems were analyzed in order to compare the influence of heavy metals. The first system was a sedimentation pond in a zinc-copper factory. The second was the bank of the Belgian river Meuse covered by the mossPlatyhypnidium riparioides (Hedw.) Dix. contaminated with heavy metals. The third was the bank of the same river covered by the same uncontaminated moss.The study was focused mainly on cadmium.The reciprocal averaging method showed that some bacterial strains could develop in very high concentrations of cadmium, but their physiological characteristics were not the same as those of the sensitive strains. In addition, the characteristics of the resistant strains depended on the environment. Correlation between resistance to heavy metals and to antibiotics was observed but was not the same in all communities. The density of resistant strains was roughly related to the level of toxicity in the environment.}, }
@article {pmid24226834, year = {1980}, author = {Rippey, SR and Cabelli, VJ}, title = {Occurrence ofAeromonas hydrophila in limnetic environments: Relationship of the organism to trophic state.}, journal = {Microbial ecology}, volume = {6}, number = {1}, pages = {45-54}, pmid = {24226834}, issn = {0095-3628}, abstract = {The densities ofAeromonas hydrophila in various natural waters were found to be strongly correlated with a relative index proposed for use in trophic state assessments of fresh waters. No such correlation was found with the recoverable heterotrophic population of whichA. hydrophila is a part.A. hydrophila was found to be seasonally distributed with maximal densities occurring during summer through early fall. It was also found to be spatially distributed within a pond with the most consistent densities occurring from 1 m depth down to that depth in the water column where the temperature reaches 16°C. The densities of the organism correlated most strongly with total phosphorus, chlorophylla, and Secchi depth. Moderate correlations were found with dissolved phosphorus, Kjeldahl nitrogen, and dissolved organic carbon. Little or no correlation was obtained with ammonia, orthophosphate, pH, alkalinity, or dissolved oxygen. The discriminating ability that theA. hydrophila density measurements provide in the oligotrophic through mesotrophic range appears to exceed those of presently available methods. The facility and sensitivity of the enumeration method forA. hydrophila should make it a useful tool for trophic state assessments.}, }
@article {pmid24226833, year = {1980}, author = {Griffiths, AJ and Lovitt, R}, title = {Use of numerical profiles for studying bacterial diversity.}, journal = {Microbial ecology}, volume = {6}, number = {1}, pages = {35-43}, pmid = {24226833}, issn = {0095-3628}, abstract = {A total of 308 bacteria were isolated from oil-storage tanks. Of these 20% were unidentifiable, even at the generic level. A numerical scoring method differentiated between the isolates and was used to estimate the diversity of the bacterial communities in the tanks over a period of 11 months. Although the scoring method suggested a higher diversity than did conventional identification, there was some consistency in the results produced by the two approaches. It is suggested that a scoring method based on only nine tests could be useful for estimating and comparing bacterial diversity in other habitats.}, }
@article {pmid24226832, year = {1980}, author = {Taylor, WD and Berger, J}, title = {Microspatial heterogeneity in the distribution of ciliates in a small pond.}, journal = {Microbial ecology}, volume = {6}, number = {1}, pages = {27-34}, pmid = {24226832}, issn = {0095-3628}, abstract = {Five transects of contiguous samples from the surface of a small pond and one transect from its bottom were collected in order to quantify microspatial heterogeneity in the distribution of ciliated protozoa. Examination of the frequency-abundance relations for these transects suggests that they can be approximated by negative binomial distributions with a commonk of 1.87. Contagiousness or crowding increases with population density.Mean patch size and mean interpatch distance were measured for 4 transects as 1.5 to 2 cm and 3 to 4 cm, respectively. This heterogeneity is suggested to arise from behavioral aggregation about discrete food sources and be very ephemeral.Blocking of adjacent contiguous samples was used to investigate the effect of sample size on the apparent correlation between the numbers of pairs of taxa. In all cases examined, taxa were relatively independent in their distribution at small sample sizes and became more negatively or positively associated as samples were combined. This may reflect that the small scale patches are essentially monospecific.}, }
@article {pmid24226831, year = {1980}, author = {Fenchel, T}, title = {Suspension feeding in ciliated protozoa: Feeding rates and their ecological significance.}, journal = {Microbial ecology}, volume = {6}, number = {1}, pages = {13-25}, pmid = {24226831}, issn = {0095-3628}, abstract = {The quantitative uptake of suspended particles has been studied in 14 species of ciliated protozoa in terms of the maximum rate of water cleared at low particle concentrations and of the maximum ingestion rate at high particle concentrations. The results, supported by data from the literature, show that ciliates which feed on larger particles (> 1-5μm) compare favorably with metazoan suspension feeders with respect to the ability to concentrate dilute suspensions of particles. Species specialized on smaller food particles (0.2-1μm), the size range of most bacteria in natural environments, require a higher concentration of particles. Bacterial population densities which can sustain ciliate growth are found in sediments, waters rich in organic material, and in the early successional stages of decomposing organic material. This is not the case in open waters in general where bacterivorous ciliates cannot play a role as grazers of bacteria.}, }
@article {pmid24226830, year = {1980}, author = {Fenchel, T}, title = {Suspension feeding in ciliated protozoa: Functional response and particle size selection.}, journal = {Microbial ecology}, volume = {6}, number = {1}, pages = {1-11}, pmid = {24226830}, issn = {0095-3628}, abstract = {The quantitative uptake of latex beads of different sizes and of live cells by 14 species of ciliates was studied. The functional response (uptake rate as function of food particle concentration) can be fitted to a hyperbolic function and this can be explained in terms of the function of the mouth apparatus. Each species shows a distinct size spectrum of particles which are retained and ingested. These size spectra may be explained by mouth morphology, and particle size selection may play a role for niche separation of coexisting ciliates. Most bacterivorous holotrich ciliates retain particles down to 0.2μm and in one case down to 0.1μm; they retain particles between 0.3 and 1μm most efficiently. The spirotrich ciliates investigated do not retain particles smaller than 1-2μm.}, }
@article {pmid24232496, year = {1979}, author = {Güde, H}, title = {Grazing by protozoa as selection factor for activated sludge bacteria.}, journal = {Microbial ecology}, volume = {5}, number = {3}, pages = {225-237}, pmid = {24232496}, issn = {0095-3628}, abstract = {In continuous culture enrichments that were inoculated with activated sludge and were fed with polymeric substrates, freely dispersed single-celled bacteria belonging to theCytophaga group dominated among the initial populations, irrespective of the activated sludge source. These populations were grazed by flagellated protozoa which after several days reached high cell densities. Other morphologic bacterial groups such as spiral-shaped or filamentous bacteria then became dominant. In defined mixed culture experiments with bacterial isolates from the enrichment cultures, it was shown that a "grazing-resistant"Microcyclus strain outgrew aCytophaga strain in the presence of grazing protozoa. In contrast, theCytophaga strain competed successfully with theMicrocyclus strain and with other "grazing-resistant" strains under protozoa-free conditions. Furthermore, it was demonstrated that assumed grazing resistance factors such as floccing or filamentous growth were lost by some of the strains when they were grown for several generations in continuous culture under the same conditions, but in the absence of protozoa.}, }
@article {pmid24232495, year = {1979}, author = {Ducklow, HW and Mitchell, R}, title = {Observations on naturally and artificially diseased tropical corals: A scanning electron microscope study.}, journal = {Microbial ecology}, volume = {5}, number = {3}, pages = {215-223}, pmid = {24232495}, issn = {0095-3628}, abstract = {Scanning electron microscopic (SEM) observations of naturally and artificially diseased corals reveal that the disease is characterized by a filamentous matrix of cyanobacterial andBeggiatoa filaments. Spiral bacteria are commonly embedded in the matrix. The artificial disease is not manifested as the characteristic "black line disease" and does not contain filaments of cyanobacteria. This suggests that cyanobacteria are necessary for the black line phenomenon. The colorless, sulfide-oxidizing bacteriumBeggiatoa, however, is always associated with the disease.}, }
@article {pmid24232494, year = {1979}, author = {Makboul, HE and Ottow, JC}, title = {Michaelis constant (K m) of acid phospatase as affected by montmorillonite, illite, and kaolinite clay minerals.}, journal = {Microbial ecology}, volume = {5}, number = {3}, pages = {207-213}, pmid = {24232494}, issn = {0095-3628}, abstract = {The influence of Ca homoionic clay minerals (montmorillonite, illite, and kaolinite) on the activity,K m , andV m values of acid phosphatase was examined in model experiments. At each substrate (p-nitrophenyl phosphate) level tested, the addition of increasing amounts of clays (50, 100, and 150 mg, respectively) decreased the activity and increased theK m value from 1.43×10(-3) M PNP (in the soluble state) to 82.3×10(-3)M (montmorillonite), 8.02×10(-3) M (kaolinite), and 7.65×10(-3) M (illite) at the 150 mg level. The maximum enzyme reaction velocity (V m) remained nearly constant at different amounts of kaolinite and illite, but increased remarkably with rising quantities of montmorillonite. Apparently, the substrate affinity of sorbed acid phosphatase is significantly lower with montmorillonite than with kaolinite or illite. This may be ascribed to an intensive sorption of both substrate and enzyme to the surface as well as to interlattice sites of montmorillonite.}, }
@article {pmid24232493, year = {1979}, author = {Josserand, A and Cleyet-Marel, JC}, title = {Isolation from soils ofNitrobacter and evidence for novel serotypes using immunofluorescence.}, journal = {Microbial ecology}, volume = {5}, number = {3}, pages = {197-205}, pmid = {24232493}, issn = {0095-3628}, abstract = {To study the ecology of chemoautotrophic nitrifying bacteria (Nitrobacter), the immunofluorescence technique has been used. Fluorescent antibodies againstNitrobacter winogradskyi andNitrobacter agilis, the two known serotypes, have not labeled strains isolated from soils of the Lyon region (pH 8.1 and pH 4.7). The pure-culture isolates appeared to belong to the same genus, but to be serologically different from the reference strains. These results led us to question the diversity of strains ofNitrobacter in soils.}, }
@article {pmid24232492, year = {1979}, author = {Hazen, TC}, title = {Ecology ofAeromonas hydrophila in a South Carolina cooling reservoir.}, journal = {Microbial ecology}, volume = {5}, number = {3}, pages = {179-195}, pmid = {24232492}, issn = {0095-3628}, abstract = {Densities ofAeromonas hydrophila were determined monthly from December 1975 to December 1977 in a South Carolina cooling reservoir which receives heated effluent from a single nuclear production reactor. Selected water quality parameters and prevalence of red-sore disease among largemouth bass were monitored simultaneously.Higher densities ofA. hydrophila were observed in areas of the reservoir receiving effluent from the reactor. Densities ofA. hydrophila generally were heterogeneous in the water column. The sediments had lower densities ofA. hydrophila than water immediately above.A. hydrophila could not be isolated from sediments greater than 1 cm from the water interface. Temperature, redox potential, pH, and conductivity were all significantly correlated with densities ofA. hydrophila in the water column. The temporal and spatial distribution and abundance ofA. hydrophila in water were not related to total organic carbon, dissolved organic carbon, particulate organic carbon, inorganic carbon, or dissolved oxygen. High densities ofA. hydrophila were observed in mats of decomposingMyriophyllum spicatum and, enterically, in largemouth bass, several other species of fish, turtles, alligators, and snails. The greatest densities ofA. hydrophila in water occurred during March and June with a second peak in October. The mean monthly densities ofA. hydrophila were positively correlated with the incidence of infection in largemouth bass. Largemouth bass from thermally altered parts of the reservoir had a significantly higher incidence of infection. It is concluded that thermal effluent significantly affects the ecology ofA. hydrophila and the epizootiology of red-sore disease within Par Pond.}, }
@article {pmid24232491, year = {1979}, author = {Robb, F and Davies, BR and Cross, R and Kenyon, C and Howard-Williams, C}, title = {Cellulolytic bacteria as primary colonizers ofPotamogeton pectinatus L. (Sago Pond Weed) from a Brackish South-Temperate Coastal Lake.}, journal = {Microbial ecology}, volume = {5}, number = {3}, pages = {167-177}, pmid = {24232491}, issn = {0095-3628}, abstract = {Bacteria adhering to newly emerged and decomposing leaves ofPotamogeton pectinatus L. were examined using scanning electron microscopy. Bacteria obtained from mature leaves were isolated, grown in pure culture, and allowed to infect bacteria-free leaves. Infected leaves and individual isolates were examined by scanning electron microscopy. The method provided detail of the forms of bacterial attachment to leaf surfaces.Supernatants from isolate cultures were assayed for cellulase activity. Six out of eight isolates produced extracellular cellulase in medium containing carboxymethyl cellulose. In one isolate cellulase was produced at discrete intervals, at the beginning and end of the growth cycle. The adhesion of the isolates toP. pectinatus leaves, as well as their possession of cellulase, are considered as evidence of an active role of bacteria in the degradation ofP. pectinatus foliage. The system is unusual in that bacteria, as opposed to fungi, are primary colonizers of the leaves.}, }
@article {pmid24232490, year = {1979}, author = {Goldman, JC}, title = {Temperature effects on steady-state growth, phosphorus uptake, and the chemical composition of a marine phytoplankter.}, journal = {Microbial ecology}, volume = {5}, number = {3}, pages = {153-166}, pmid = {24232490}, issn = {0095-3628}, abstract = {The marine chrysophyteMonochrysis lutheri was grown in phosphorus-limited continuous cultures at temperatures of 15°, 18.8° and 23°C. The effect of temperature on the maximum growth rate was well-defined by the Arrhenius equation, but the Q10 for this alga (1.7) was somewhat lower than has been determined previously for many other phytoplankton species (2.0-2.2). The minimum phosphorus cell quota was relatively unaffected by temperature at 18.8°C and 23°C, but doubled in magnitude at 15°C. As a result, the internal nutrient equation of Droop described the relationship between specific growth rate and phosphorus cell quota well at 18.8° and 23°C, but was less successful at 15°C. The major limitation in using the Droop equation is that the ratio between the minimum and maximum cell quotas must be known, thus necessitating the need to establish the true maximum growth rate by the cell washout technique. In addition, the phosphorus uptake rate on a cell basis at a given steady state growth rate (=specific uptake rate) increased dramatically at 15°C, whereas the turnover rate of total available phosphorus was unaffected by temperature. Both the nitrogen and carbon cell quotas were relatively unaffected by growth rate at a given temperature, but the average values increased slightly with decreasing temperature. The overall conclusion is that phytoplankton growth and limiting-nutrient uptake rates are only synchronous at or near the optimum temperature. Because these types of responses are species specific, much additional data on temperature effects will be required before the importance of including such effects in phytoplankton-nutrient models can be determined.}, }
@article {pmid24232421, year = {1979}, author = {Zevenhuizen, LP and Dolfing, J and Eshuis, EJ and Scholten-Koerselman, IJ}, title = {Inhibitory effects of copper on bacteria related to the free ion concentration.}, journal = {Microbial ecology}, volume = {5}, number = {2}, pages = {139-146}, pmid = {24232421}, issn = {0095-3628}, abstract = {Cu(2+) ion determinations were carried out in complex and in inorganic salts-glycerol media, to which increasing amounts of Cu(II) had been added, with the ion-specific Cu(II)-Selectrode. Likewise, complexing capacity of bacterial suspensions was estimated by titration with CuSO4.Copper-sensitive bacteria, e.g.,Klebsiella aerogenes, were inhibited in their growth and survival in the range of 10(-8)-10(-6) M Cu(2+) ion concentrations. In copper-buffered complex media, high copper loads could be tolerated, as growth proceeded with most of the copper bound to medium components. In low-complexing mineral salts media, in which high Cu(2+) ion concentrations exist at low copper loads, there was competition of Cu(2+) for binding sites of the cells. Total allowed copper was then determined by the ratio of copper to biomass.Copper-resistant bacteria could be isolated from a stock solution of CuSO4, containing 100 ppm Cu(II). They were of thePseudomonas type and showed a much higher tolerance towards Cu(2+), up to 10(-3) M.}, }
@article {pmid24232420, year = {1979}, author = {Eiland, F and Nielsen, BS}, title = {Influence of cation content on adenosine triphosphate determinations in soil.}, journal = {Microbial ecology}, volume = {5}, number = {2}, pages = {129-137}, pmid = {24232420}, issn = {0095-3628}, abstract = {Adenosine triphosphate in soil is measured by the luciferin-luciferase bioluminescence method. Cation exchange in the ATP extraction procedure is used to reduce the content of, e.g., Fe, Al, and Cations in extracts. The efficiency of the cation exchange is determined by measuring the concentration of Fe by X-ray fluorescence spectrometry. The time dependence of the light emission from the bioluminescence process is investigated, and a method for correlating the ATP content and the light emission is proposed.}, }
@article {pmid24232419, year = {1979}, author = {Gates, JE and Pham, KD}, title = {An indirect fluorescent antibody staining technique for determining population levels ofThiobacillus ferrooxidans in acid mine drainage waters.}, journal = {Microbial ecology}, volume = {5}, number = {2}, pages = {121-127}, pmid = {24232419}, issn = {0095-3628}, abstract = {Thiobacillus ferrooxidans is believed to be responsible for the oxidation of ferrous ion at low pH, the rate-limiting step in the oxidation of pyrite ores and subsequent formation of acid mine drainage (AMD). It has been suggested that efforts to control this environmental problem include procedures that would inhibit this bacterium. At present, a most probable number (MPN) procedure requiring a minimum of 10 days is used to enumerate this microorganism in natural waters. If control of AMD through inhibition ofT. ferrooxidans is to be feasible, it will be necessary to develop a more rapid method to determine population levels to facilitate application of control measures.An indirect fluorescent antibody (FA) staining technique was developed for this purpose which provided reliable estimates within a few hours. Artificial samples containing approximated numbers ofT. ferrooxidans were analyzed using the FA and MPN procedures, and the FA technique more closely approximated expected numbers of cells. The MPN method was excessively conservative, detecting only 3% to 21% of the cells enumerated by the FA procedure.}, }
@article {pmid24232418, year = {1979}, author = {Maier, S and Preissner, WC}, title = {Occurrence ofThioploca in Lake Constance and Lower Saxony, Germany.}, journal = {Microbial ecology}, volume = {5}, number = {2}, pages = {117-119}, doi = {10.1007/BF02010502}, pmid = {24232418}, issn = {0095-3628}, abstract = {Thioploca had been encountered in several locations in Central Europe. Five of these were revisited to find out ifT. schmidlei andT. ingrica were still present in these locations. Of the three locations in Lake Constance with abundant populations, one (Staad) contained a sparse population of small specimens ofT. ingrica only; from the others (Ermatingen and Mainau) neither species was recovered. In Lower Saxony two spots reportedly containedT. ingrica. The first of these (Bückeburg) has been destroyed by human stream improvement. The description of the other (Bad Nenndorf) was insufficient for relocation. During the search a new location containingT. ingrica was discovered, Crater Spring, across highway B65 from Bad Nenndorf.}, }
@article {pmid24232417, year = {1979}, author = {Sørensen, J and Jørgensen, BB and Revsbech, NP}, title = {A comparison of oxygen, nitrate, and sulfate respiration in coastal marine sediments.}, journal = {Microbial ecology}, volume = {5}, number = {2}, pages = {105-115}, pmid = {24232417}, issn = {0095-3628}, abstract = {Aerobic respiration with oxygen and anaerobic respiration with nitrate (denitrification) and sulfate (sulfate reduction) were measured during winter and summer in two coastal marine sediments (Denmark). Both aerobic respiration and denitrification took place in the oxidized surface layer, whereas sulfate reduction was most significant in the deeper, reduced sediment. The low availability of nitrate apparently limited the activity of denitrification during summer to less than 0.2 mmoles NO 3 (-) m(-2) day(-1), whereas activities of 1.0-3.0 mmoles NO 3 (-) m(-2) day(-1) were measured during winter. Sulfate reduction, on the contrary, increased from 2.6-7.6 mmoles SO 4 (2-) m(-2) day(-1) during winter to 9.8-15.1 mmoles SO 4 (2-) m(-2) day(-1) during summer. The aerobic respiration was high during summer, 135-140 mmoles O2 m(-2) day(-1), as compared to estimated winter activities of about 30 mmoles O2 m(-2) day(-1). The little importance of denitrification relative to aerobic respiration and sulfate reduction is discussed in relation to the availability and distribution of oxygen, nitrate, and sulfate in the sediments and to the detritus mineralization.}, }
@article {pmid24232416, year = {1979}, author = {Caldwell, BA and Hagedorn, C and Denison, WC}, title = {Bacterial ecology of an old-growth douglas fir canopy.}, journal = {Microbial ecology}, volume = {5}, number = {2}, pages = {91-103}, pmid = {24232416}, issn = {0095-3628}, abstract = {Microbial populations associated with the major substrates of the canopy of a single 70 m old-growth Douglas fir were studied to determine potential activities. Seasonal samples from bark, foliage, epiphytic moss, lichens, and litter accumulations were collected to: (a) obtain population data, (b) isolate the major groups of microorganisms present, (c) measure enzymatic activities associated with cellulose and xylan degradation, and (d) examine the potential for nitrogen fixation. We tested 562 bacterial isolates for utilization of 25 compounds associated with the canopy substrates, and for activities in nitrogen and sulfur cycle transformations. Total bacterial populations, reflecting seasonal temperature and moisture conditions, were lowest on bark and foliage [21-266×10(3) colony-forming units (CFU/g)] and highest on moss and lodged litter (19-610×10(5) CFU/g). Lichens contained intermediate numbers of bacteria (3.3-270×10(5) CFU/g). The majority of the bacteria were classified as species ofArthrobacter, Bacillus, Flavobacterium, andXanthomonas. Isolates ofAlcaligenes (Achromobacter), Aeromonas, Chromobacterium, Micrococcus, andPseudomonas were less common. No measurable rates of nitrogen fixation attributable to free-living bacteria were detected by acetylene reduction. Eleven species in six genera of lichens containing a blue-green algal phycobiont showed positive acetylene reduction. One species,Lobaria oregana, accounted for 51% of the total lichen biomass of the canopy. Cellulase and xylanase activity was routinely detected in moss and litter samples, and less frequently in lichens. There was a strong correlation between the two activities for moss (r=0.94) and litter (r=0.81).}, }
@article {pmid24232415, year = {1979}, author = {Grant, IF and Bancroft, K and Alexander, M}, title = {SO2 and NO2 effects on microbial activity in an acid forest soil.}, journal = {Microbial ecology}, volume = {5}, number = {2}, pages = {85-89}, pmid = {24232415}, issn = {0095-3628}, abstract = {The rate of glucose decomposition and the pH fell in a forest soil (initial pH 4.06) exposed to 1.0 ppm SO2. No such effect was noted if the soil was exposed to 1.0 ppm nitrogen dioxide (NO2). Nitrite but not bisulfite (5μg N or S/g of soil) inhibited O2 consumption and CO2 evolution in the glucose-amended forest soil, and nitrite and bisulfite acted synergistically in inhibiting these processes. Iron and manganese were solubilized when the soil was exposed to 10 ppm SO2, but NO2 caused no such change.}, }
@article {pmid24232302, year = {1979}, author = {Abdollahi, H and Nedwell, DB}, title = {Seasonal temperature as a factor influencing bacterial sulfate reduction in a saltmarsh sediment.}, journal = {Microbial ecology}, volume = {5}, number = {1}, pages = {73-79}, pmid = {24232302}, issn = {0095-3628}, abstract = {The population of sulfate-reducing bacteria in saltmarsh sediment was examined at monthly intervals by plate-counting and by determining the response of sulfate reduction rates to environmental temperature using(35)SO 4 (2-) . The sulfate reduction rate was shown to be related to temperature by an Arrhenius function.The temperature characteristic of the population of sulfate-reducing bacteria did not vary significantly with season, and was shown to be equivalent to 20.4 kcals mole(-1), a Q10 of 3.5. Apart from one anomolous result, the monthly value for the Arrhenius constant also did not show any significant variation throughout the year. There was no seasonal trend of optimum temperature for sulfate reduction.The results suggested that, although environmental temperature was the dominant variable influencing sulfate reduction rates in the sediment, there was no detectable response or adaptation of the sulfate-reducing population to seasonally changing environmental temperature.}, }
@article {pmid24232301, year = {1979}, author = {Nedwell, DB and Abram, JW}, title = {Relative influence of temperature and electron donor and electron acceptor concentrations on bacterial sulfate reduction in saltmarsh sediment.}, journal = {Microbial ecology}, volume = {5}, number = {1}, pages = {67-72}, pmid = {24232301}, issn = {0095-3628}, abstract = {The relative importance of three environmental variables known to influence the rate of bacterial sulfate reduction was examined using sediment from a saltmarsh pan. The variables investigated were temperature, electron donor concentration, and electron acceptor concentration. Their relative influence on the rate of bacterial sulfate reduction was examined with multiple replicate sediment samples in which the variables were experimentally adjusted. Sulfate reduction rates were measured with(35)SO 4 (2-) .The relative importance of each variable to sulfate reduction rate was assessed with multiple regression analysis by calculating the standardized partial regression coefficients, and the results were compared with the ranges of the three variables encountered in the natural sediment. Temperature proved to have the greatest influence, followed by electron donor and electron acceptor concentrations, in that order. The sulfate concentration was shown to have little influence on sulfate reduction rate at seawater concentrations of sulfate, but its effect increased if sulfate concentrations were diminished compared to those of seawater.}, }
@article {pmid24232300, year = {1979}, author = {Tuovinen, OH and Nurmiaho, EL}, title = {Microscopic examination of bacteria in Fe(III)-oxide deposited from ground water.}, journal = {Microbial ecology}, volume = {5}, number = {1}, pages = {57-66}, pmid = {24232300}, issn = {0095-3628}, abstract = {Ochreous sludge deposited in the course of aeration of ground water contained an assortment of bacterial forms and structures which were investigated by light microscopy, scanning electron microscopy, and transmission electron microscopy. Bacterial structures were often covered by iron deposition which could be removed by acidification of the samples. Sulfuric acid treatment was consistently better than hydrochloric acid to dissolve iron without a considerable damage to the bacterial cells. Partial dissolution of amorphous ferric iron was achieved by acidifying the samples with oxalic acid or citric acid prior to the preparation for electron microscopy.}, }
@article {pmid24232299, year = {1979}, author = {Inniss, WE and Mayfield, CI}, title = {Effect of temperature on violacein production in a psychrotrophicChromobacterium from Lake Ontario sediment.}, journal = {Microbial ecology}, volume = {5}, number = {1}, pages = {51-56}, pmid = {24232299}, issn = {0095-3628}, abstract = {A truly psychrotrophic strain ofChromobacterium, which was isolated from Lake Ontario sediment and characterized asChromobacterium lividum, was found to be capable of pigment production that was completely prevented at 0°C, although growth readily occurred. Normal pigment formation occurred at 15°C, 20°C, and 25°C. The prevention of synthesis of the pigment at 0°C, which was confirmed spectrophotometrically to be violacein, was not reversed by the presence of various carbon sources, although all except one acted as growth substrates. In addition, some of the carbon sources actually inhibited pigment production at 20°C, preventing violacein synthesis in the presence of pyruvate which was shown to allow pigmentation. Similar results were obtained under both liquid and solid media cultivation conditions.}, }
@article {pmid24232298, year = {1979}, author = {Vacek, DC and Starmer, WT and Heed, WB}, title = {Relevance of the ecology ofCitrus yeasts to the diet ofDrosophila.}, journal = {Microbial ecology}, volume = {5}, number = {1}, pages = {43-49}, pmid = {24232298}, issn = {0095-3628}, abstract = {A study of the yeast flora of necrotic oranges and associatedDrosophila yielded a total of 221 isolates composed ofKloeckera apiculata (75),Pichia fermentans (75),Pichia kluyveri (50),Torulopsis stellata (17),Hanseniaspora uvarum (2),P. membranaefaciens (1), andCandida vini (1). The yeast species of all samples of oranges and adultDrosophila were very similar; however, the speciesof Drosophila contained a higher proportion ofP. fermentans and a lower proportion ofK. apiculata than was found in the rotting oranges.P. fermentans was subsequently found more frequently on the surface of the necrotic tissue, where the flies feed, than was found internally. SinceP. fermentans characteristically produces a pellicle and pseudomycelium andK. apiculata does not, it is concluded that the growth characteristics of the yeasts are an important factor determining adultDrosophila diets.}, }
@article {pmid24232297, year = {1979}, author = {Wesney, E and Tannock, GW}, title = {Association of rat, pig, and fowl biotypes of lactobacilli with the stomach of gnotobiotic mice.}, journal = {Microbial ecology}, volume = {5}, number = {1}, pages = {35-42}, pmid = {24232297}, issn = {0095-3628}, abstract = {We grouped 20 isolates of lactobacilli from the stomach of conventional rats, 21 isolates from pig stomachs, and 19 isolates from the crop of fowls according to their ability to ferment N-acetylglucosamine, dextrin, cellobiose, gum arabic, and xylan. Most of the isolates did not resemble previously describedLactobacillus species. Representative group A isolates were associated with germ-free mice. Only a rat isolate was able to colonize the keratinized squamous epithelium of the stomach of gnotobiotic mice.}, }
@article {pmid24232296, year = {1979}, author = {Tannock, GW}, title = {Coliforms and enterococci isolated from the intestinal tract of conventional mice.}, journal = {Microbial ecology}, volume = {5}, number = {1}, pages = {27-34}, pmid = {24232296}, issn = {0095-3628}, abstract = {Coliforms and enterococci were isolated from the intestinal tract of infant (12-day-old) and adult (6-to 8-week-old) conventional mice. Eighty coliform isolates and eighty enterococcal strains were grouped according to their ability to ferment or hydrolyze various substrates. Sixty-one of the coliform isolates were identified asEscherichia coli. The remaining 19 strains were similar toE. coli, but did not produceβ-galactosidase. The enterococci belonged to two species:Streptococcus faecium andS. faecalis. Four biotypes ofS. faecium and two biotypes ofS. faecalis were detected. Xylosefermenting enterococci were isolated with a higher frequency from infant mice than from adults.}, }
@article {pmid24232295, year = {1979}, author = {Höfle, MG}, title = {Effects of sudden temperature shifts on pure cultures of four strains of freshwater bacteria.}, journal = {Microbial ecology}, volume = {5}, number = {1}, pages = {17-26}, pmid = {24232295}, issn = {0095-3628}, abstract = {Three psychrotrophic and one mesophilic strains were isolated from winter water samples of different freshwater biotopes and identified asCytophaga johnsonae (C-21),Cytophaga sp. (M-17),Pseudomonas fluorescens (KD), andEnterobacter cloacae (BS-2). Temperature shift-up experiments with emphasis on low temperatures were carried out with aerated pure batch cultures in glucose mineral medium. The effects of sudden temperature increases on growth rates and substrate conversion were investigated. All three psychrotrophic strains in the temperature increase experiments at low temperatures showed differing reactions within the linear zone of the Arrhenius plot. TheC. johnsonae (C-21) shift-up cultures adjusted the growth rate immediately to the rate of the temperature adapted cultures, whereasCytophaga sp. (M-17) shift-up cultures showed a lower andP. fluorescens (KD) a higher growth rate. The mesophilicE. cloacae (BS-2), likeC. johnsonae (C-21), adjusted immediately to the new growth rate. Substrate conversion increased in all experiments immediately after the shift-up. The extracellular substrate conversion byP. fluorescens (KD) of glucose to gluconate and 2-ketogluconate was particularly affected by the sudden temperature increase.}, }
@article {pmid24232294, year = {1979}, author = {McKinley, KR and Wetzel, RG}, title = {Photolithotrophy, photoheterotrophy, and chemoheterotrophy: Patterns of resource utilization on an annual and a diurnal basis within a pelagic microbial community.}, journal = {Microbial ecology}, volume = {5}, number = {1}, pages = {1-15}, pmid = {24232294}, issn = {0095-3628}, abstract = {An annual investigation of rates of photolithotrophy, photoheterotrophy, and chemoheterotrophy utilizing glucose and bicarbonate was made within the pelagic zone of a small, hardwater, southwestern Michigan lake. Sampling proceeded on a monthly, diurnal, and depth-wise basis. Annual mean photoheterotrophic uptake was estimated at 2.6μg C m(-3)h(-1). Two periods of relatively high activity were observed: one during spring overturn and the second during the late summer period. In general, greatest contributions to overall carbon cycling occurred during morning to midday incubation periods and at intermediate depths within the water column. Rates of chemoheterotrophy averaged 6.9μg C m(-3)h(-1) and were relatively uniform throughout the annual period. Greatest overall chemoheterotrophic activity was associated with periods of overturn. In general, this activity increased throughout the day and with increasing depth within the water column. The annual mean for photolithotrophic fixation was 1.33 mg C m(-3)h(-1). Greatest contributions to rates of photosynthesis were associated with epilimnetic waters during early morning and midday incubations. Relatively minor contributions to inorganic fixation were made by waters below the 6-meter contour. Spring overturn and late summer represented periods of particularly great photolithotrophic activity. Quantitative comparisons among carbon pathways indicate that rates of pelagic heterotrophy, both photo- and chemoheterotrophy combined, contribute small quantities of carbon to overall carbon metabolism in this oligotrophic system. Qualitative comparisons among pathways indicate strong spatial and temporal separation. The late summer period showed greatest seasonal separation of the three pathways. Spring values represented a period of relatively high activity for all three pathways. On a depth-wise basis, photolithotrophic activity was greatest near the surface and chemolithotrophic activity greatest near the bottom. Photoheterotrophy took an intermediate position between the two. Diurnally, photoheterotrophy and photolithotrophy showed greatest activity during midday and early morning periods, whereas chemoheterotrophy increased throughout the daylight period and reached maximal values in sunset incubations.}, }
@article {pmid24233670, year = {1977}, author = {Mouraret, M and Baldensperger, J}, title = {Use of membrane filters for the enumeration of autotrophic thiobacilli.}, journal = {Microbial ecology}, volume = {3}, number = {4}, pages = {345-358}, pmid = {24233670}, issn = {0095-3628}, abstract = {A new membrane filter technique for field use was developed for the enumeration of either aerobic or anaerobic, autotrophic, sulfur-oxidizing bacteria in waters and soils. Immediately after collection, samples were filtered through sulfur-coated filters and incubated in selective media. Acidification or gas evolution was used as a growth indicator of aerobic and anaerobic thiobacilli, respectively, and related to the initial number of cells deposited on the filter.}, }
@article {pmid24233669, year = {1977}, author = {Smith, EA and Mayfield, CI}, title = {Effects of paraquat on selected microbial activities in soil.}, journal = {Microbial ecology}, volume = {3}, number = {4}, pages = {333-343}, pmid = {24233669}, issn = {0095-3628}, abstract = {Paraquat, applied as Gramoxone, to a nonamended sandy loam soil at five times the suggested field application rate (10 lb/A ≈ 115μg/cm(2)) increased the numbers of bacteria, actinomycetes, and fungi during a 14-day incubation at 25°C. This increase was attributed to the use of compounds in the Gramoxone formulation rather than the use of paraquat. Treatment at one and five times the normal rate reduced CO2 evolution by 44% and 67%, respectively, in soil amended with 2% glucose during a 12-day incubation. Similar treatments reduced CO2 evolution in 1% straw-amended soil by 39% and 58%, respectively, during a 28-day incubation. Cellulose decomposition of cotton duck containing 13 and 176μg of paraquat per milligram of material was inhibited for 15 and 28 days, respectively, in soil containing a large population of cellulolytic microorganisms. A concentration of 5000μg/gm of paraquat was necessary to inhibit nitrification in soil by 44% druing a 28-day incubation at 20°C. Paraquat inhibited C2H2 reduction in artificial aggregates of soil amended with 2% glucose and incubated anaerobically at 25°C. Nitrogenase activity in aggregates was inhibited by 43% and 52% at concentrations of 580 and 720μg/gm of paraquat respectively. The inhibitory effects of the herbicide were reduced when soil was amended with organic matter in the form of peat or straw. The availability of paraquat controlled the toxicity of the herbicide to soil microorganisms.}, }
@article {pmid24233668, year = {1977}, author = {Tchan, YT and Chiou, AC and New, PB and Funnell, GR}, title = {The photobioluminometer, an instrument for the study of ecological factors affecting photosynthesis.}, journal = {Microbial ecology}, volume = {3}, number = {4}, pages = {327-332}, doi = {10.1007/BF02010739}, pmid = {24233668}, issn = {0095-3628}, abstract = {An instrument for measurement of bioluminescence and photosynthesis is described. It may be used to detect chemicals toxic to luminous bacteria or to measure photosynthetic oxygen production of algae in mixed culture with bacteria. The latter technique has been used to study the effect on algal photosynthesis of environmental factors such as light quality, temperature, and salinity, and to study the factors affecting chlorophyll synthesis. The technique is ideal for rapid detection of photosynthesis-inhibiting herbicides and other toxic substances in water.}, }
@article {pmid24233667, year = {1977}, author = {Zavarzin, GA and Nozhevnikova, AN}, title = {Aerobic carboxydobacteria.}, journal = {Microbial ecology}, volume = {3}, number = {4}, pages = {305-326}, pmid = {24233667}, issn = {0095-3628}, abstract = {Bacterial consumption of CO, a major atmospheric pollutant, has been described in the literature long ago, but often with controversial data. Attempts were made, therefore, to isolate and study a broader spectrum of aerobic CO bacteria in order to better understand their ecology.About 100 samples from various locations in the USSR (water, mud, junkyard, or garden, soil etc.) were inoculated into mineral medium and incubated under 80% CO and 20% O2. Such enrichments yielded a large number of strains representing 5-6 different bacterial species. The highest number of CO utilizers came from fresh samples of polluted, moist soil or mud. Some mixed cultures were composed of vitamin-dependent bacteria living together in a state of protocooperation. Seven strains (previously already partially described) were studied in greater detail. They are regarded as "carboxydobacteria." Six carboxydobacteria also utilized hydrogen, but none of the 7 cultures grew with methane or formate. The optimal concentration of, and sensitivity to, CO varied with the strains. Reducedvs. oxidized spectra revealed in all cultures the presence ofb-, c-, anda-type cytochromes, indicating a functioning electron transport chain when grown under CO. Isotope experiments with(14)C indicated that CO was assimilated only after oxidation to CO2, the pathway being the normal Calvin cycle reaction sequence as observed in other chemolithotrophs. The key enzymes of this sequence were shown to be present and active.Organotrophic growth of carboxydobacteria was obtained with a number of compounds such as organic acids, primary alcohols, carbohydrates, and amino acids. A description of properties of the 7 test strains is given. Their ecological niche(s) seem to be where facultatively anaerobic bacteria produce organic intermediates as well as H2 and CO. Pellicle formation indicates their presence on the water surface (neuston layer). Relationships with hydrogen-oxidizing bacteria are discussed and explained on ecological grounds.}, }
@article {pmid24233666, year = {1977}, author = {Ballester, M and Ballester, JM and Belaich, JP}, title = {Isolation and characterization of a high molecular weight antibiotic produced by a marine bacterium.}, journal = {Microbial ecology}, volume = {3}, number = {4}, pages = {289-303}, pmid = {24233666}, issn = {0095-3628}, abstract = {Many marine bacteria demonstrate antibiotic activity against organisms of terrestrial origin. Low molecular weight antibiotics have been extracted and, in some cases, purified, but few attempts have been made to isolate high molecular weight antibiotics produced by marine bacteria. In the study reported here, a high molecular weight antibiotic was extracted from whole cells ofAlteromonas strain P18 (NCMB 1890) grown on 2216E medium. Purification included ammonium sulfate precipitation, ultracentrifugation, chromatography on DEAE cellulose, and gel filtration on Ultrogel. A rapid method for measuring specific activity of the antibiotic was developed.}, }
@article {pmid24233665, year = {1977}, author = {Berman, T and Stiller, M}, title = {Simultaneous measurement of phosphorus and carbon uptake in Lake Kinneret by multiple isotopic labeling and differential filtration.}, journal = {Microbial ecology}, volume = {3}, number = {4}, pages = {279-288}, pmid = {24233665}, issn = {0095-3628}, abstract = {Differential filtration and multiple isotopic labeling were combined to study the uptake of [(14)C]bicarbonate, [(14)C]glucose, and [(32)P]orthophosphate by microplakton in Lake Kinneret, Israel. Short-term (4 hr) uptake experiments showed seasonal changes in the size distributions of organisms taking up inorganic carbon, glucose carbon, and orthophosphate in the lake water. In a time-course experiment of 48 hr (Jan 1976) most, but not all, of the photosynthetic activity (average 72%) and a similar fraction of chlorophyll (72%) were associated with organisms retained on 3-μm Nuclepore filters (retention on 0.4-μm filters was 100%). About 90% of the organisms that assimilated glucose passed through 3-μm filters. Photosynthetic carbon fixation, dark carbon uptake, and heterotrophic uptake of glucose carbon accounted for 99%, 1%, and 1%, respectively, of the total net carbon assimilated during the first 6 hours. Radioactive phosphorus showed an initial rapid uptake into particles, which was not affected by light or dark. We suggest that this methodology has a wide potential for elucidating the flux of nutrients into various components of the microplankton and in characterizing different aquatic environments.}, }
@article {pmid24233664, year = {1977}, author = {Hunt, HW and Cole, CV and Klein, DA and Coleman, DC}, title = {A simulation model for the effect of predation on bacteria in continuous culture.}, journal = {Microbial ecology}, volume = {3}, number = {4}, pages = {259-278}, pmid = {24233664}, issn = {0095-3628}, abstract = {A simulation model was developed for the carbon (C), nitrogen (N), and phosphorus (P) content of bacteria and their medium in a chemostat. Cell components distinguished included the structural component, synthetic machinery, building blocks and intermediates, C reserves, ammonium (NH4), orthophosphate (PO4), and polyphosphate. Growth, incorporation of substrates, and production of waste products were related to physiological status, as indicated by the amounts of various cell components. The model was fitted to data from chemostats on the chemical composition of bacteria growing in C-, N-, and P-limiting media and was used to explore the consequences of predation on bacterial populations. In C-limiting media predation (without the return of nutrients to the medium by the predator) increased NH4 uptake in spite of a decrease in bacterial biomass. In N-limiting media predation decreased both biomass and the rate of N uptake. These results were accounted for by the effect of growth rate on bacterial N demand. In C-limiting media the return of NH4 and PO4 by the predator did not change the effect of predation on bacteria. But in N-limiting media the return of nutrients decreased the effect of predation on biomass, and stimulated respiration and NH4 uptake by the bacteria. The effect of growth rate on the chemical composition of bacteria was proposed as a possible explanation of the stimulatory effect of predators on bacteria.}, }
@article {pmid24232229, year = {1977}, author = {Cole, CV and Elliott, ET and Hunt, HW and Coleman, DC}, title = {Trophic interactions in soils as they affect energy and nutrient dynamics. V. Phosphorus transformations.}, journal = {Microbial ecology}, volume = {4}, number = {4}, pages = {381-387}, pmid = {24232229}, issn = {0095-3628}, abstract = {Regeneration of nutrients from relatively nutrient-poor organic residues is essential for overall operation of an ecosystem. Nutrients thus released are, however, inadequate for the needs of the decomposer populations, and a much faster nutrient turnover involving bacterial immobilization and release occurs concurrently. Evidence from aquatic ecosystems indicates that bacteria release little phosphorus, for which they have high demand, whereas bacterial grazers play an important role in regeneration of bacterial phosphorus. Our studies extend these relationships to terrestrial ecosystems. We studied phosphorus immobilization and mineralization in soil incubations, simulating rhizospheres with combinations of bacterial, amoebal, and nematode populations. Bacteria quickly assimilated and retained much of the labile inorganic phosphorus as carbon substrates were metabolized. Most of this bacterial phosphorus was mineralized and returned to the inorganic phosphorus pool by the amoebae. Nematode effects on phosphorus mineralization were small, except for indirect effects on amoebal activity. The observed remineralization may reflect direct excretion by the amoebae, physiological effects on the bacterial populations, or both. These results suggest a major role of microfauna in nutrient cycling.}, }
@article {pmid24232228, year = {1977}, author = {Coleman, DC and Anderson, RV and Cole, CV and Elliott, ET and Woods, L and Campion, MK}, title = {Trophic interactions in soils as they affect energy and nutrient dynamics. IV. Flows of metabolic and biomass carbon.}, journal = {Microbial ecology}, volume = {4}, number = {4}, pages = {373-380}, pmid = {24232228}, issn = {0095-3628}, abstract = {Flows of biomass and respiratory carbon were studied in a series of propylene-oxide sterilized soil microcosms. One-half of the microcosms received three pulsed additions of 200 ppm glucose-carbon to mimic rhizosphere carbon inputs. Biotic variables were: bacteria (Pseudomonas) alone, or amoebae (Acanthamoeba) and nematodes (Mesodiplogaster) singly, or both combined in the presence of bacteria.Over the 24-day experiment, respiration was significantly higher in the microcosms containing the bacterial grazers. Biomass accumulation by amoebae was significantly higher than that by nematodes. The nematodes respired up to 30-fold more CO2 per unit biomass than did amoebae. Similar amounts of carbon flowed into both respiratory and biomass carbon in microcosms with fauna, compared with the bacteria-alone microcosms. However, partitioning of available carbon by the microfauna varied considerably, with little biomass production and relatively more CO2-C produced in the nematode-containing microcosms. The amoebae, in contrast, allocated more carbon to tissue production (about 40% assimilation efficiency) and correspondingly less to CO2.}, }
@article {pmid24232227, year = {1977}, author = {Anderson, RV and Elliott, ET and McClellan, JF and Coleman, DC and Cole, CV and Hunt, HW}, title = {Trophic interactions in soils as they affect energy and nutrient dynamics. III. Biotic interactions of bacteria, amoebae, and nematodes.}, journal = {Microbial ecology}, volume = {4}, number = {4}, pages = {361-371}, pmid = {24232227}, issn = {0095-3628}, abstract = {Bacteria (Pseudomonas), amoebae (Acanthamoeba), and nematodes (Mesodiplogaster) were raised in soil microcosms with and without glucose additions. Nematode and amoebal grazing on bacteria significantly reduced bacterial populations by the end of a 24-day incubation period. Amoebal numbers decreased in the presence of nematodes with a corresponding increase in nematode numbers which reached a maximum of 230 nematodes/g of soil in the treatment with amoebae and glucose additions. After 24 days the nematode populations in the treatments without carbon additions were dominated by resistant dauer larvae indicating the unavailability of food. Although larval numbers were high in the treatments with glucose additions, the adult component of the population was still increasing at the end of the 24-day experiment. The effect of the presence of amoebae on nematode abundance was of the same magnitude as addition of 600Μg glucose-C.}, }
@article {pmid24232226, year = {1977}, author = {Herzberg, MA and Klein, DA and Coleman, DC}, title = {Trophic interactions in soils as they affect energy and nutrient dynamics. II. Physiological responses of selected rhizosphere bacteria.}, journal = {Microbial ecology}, volume = {4}, number = {4}, pages = {351-359}, pmid = {24232226}, issn = {0095-3628}, abstract = {Comparative microbial functions in the plant root zone were studied by evaluating rhizosphere-derivedPseudomonas andArthrobacter growth in chemostat culture and responses to root-exudate-related nutrients after varied starvation periods. These organisms were chosen to represent zymogenous and autochthonous microbes, respectively. In chemostat culture, thePseudomonas isolate showed increased energy charge and decreased populations with higher growth rates, whereas theArthrobacter had lower energy charge and cell population values which did not change appreciably with growth rate. The responses of these two types of organisms also differed with starvation. ThePseudomonas lost its ability to respire efficiently in the presence of several known root exudate components, whereas theArthrobacter isolate, in comparison, maintained a lower but more consistent ability to utilize these nutrients with increased starvation. TheArthrobacter also showed increased utilization of several substrates after starvation, suggesting its potential ability to function under restricted nutrient availability conditions. These results suggest thatPseudomonas-type organisms in the rhizosphere may best function in periods of more intense exudate release, whereas organisms of theArthrobacter- type may be more efficient at nutrient utilization during periods of lesser nutrient flux. Based on these data the rhizosphere-derivedPseudomonas isolate was considered to be an appropriate bacterium to use in more complex rhizosphere microcosm experiments where nutrient flux dynamics would be emphasized.}, }
@article {pmid24232225, year = {1977}, author = {Coleman, DC and Cole, CV and Hunt, HW and Klein, DA}, title = {Trophic interactions in soils as they affect energy and nutrient dynamics. I. Introduction.}, journal = {Microbial ecology}, volume = {4}, number = {4}, pages = {345-349}, pmid = {24232225}, issn = {0095-3628}, abstract = {The dynamics of nutrient transformations at the soil-root interface are complex but amenable to controlled experimental study. Using a conceptual model we introduce a series of papers which ascertain the role of microfloral-faunal trophic interactions in carbon, nitrogen, and phosphorus transformations in soil microcosms.}, }
@article {pmid24232224, year = {1977}, author = {Mayfield, CI and Inniss, WE}, title = {Interactions between freshwater bacteria andAnkistrodesmus braunii in batch and continuous culture.}, journal = {Microbial ecology}, volume = {4}, number = {4}, pages = {331-344}, pmid = {24232224}, issn = {0095-3628}, abstract = {Batch and continuous cultures ofAnkistrodesmus braunii were established in an inorganic medium with growth rate limited by P. In batch culture, inoculation of lake water bacterial isolates ofPseudomonas sp. andFlavobacterium sp. showed that thePseudomonas isolate was capable of more rapid growth on algal exudates of lytic products than was theFlavobacterium isolate. When inoculated singly into a continuous culture (D=0.267 day(-1); P level, 2ΜM), theFlavobacterium isolate initially caused a decrease in the population density of the alga, but then steady states for both organisms were obtained. ThePseudomonas isolate under the same conditions caused a rapid washout of the algal culture, and steady-state conditions were never obtained. When thePseudomonas isolate was added to the two-member, steady-state system ofA. braunii andFlavobacterium, the algal population again washed out of the vessel, followed by theFlavobacterium and then thePseudomonas isolate. A transient increase in the P concentration to 200ΜM in the culture vessel caused the low algal population level to increase, followed by increases in the bacterial isolates when the algal population was high enough to supply the required organic carbon source. The system demonstrated that competition for P between the alga and the bacteria can occur, and the results were dependent on the algal and bacterial relative growth rates. The bacterial growth rates were limited initially by organic substrates produced by the alga, and the different bacterial isolates competed for these substrates.}, }
@article {pmid24232223, year = {1977}, author = {Berk, SG and Mills, AL and Hendricks, DL and Colwell, RR}, title = {Effects of ingesting mercury-containing bacteria on mercury tolerance and growth rates of ciliates.}, journal = {Microbial ecology}, volume = {4}, number = {4}, pages = {319-330}, pmid = {24232223}, issn = {0095-3628}, abstract = {The ciliateUronema nigricans was found to acquire tolerance to mercury after being fed mercury-laden bacteria followed by exposure of washed suspensions of these ciliates to various concentrations of mercury in solution. Significant differences in percent mortality were observed for ciliates fed mercury-laden bacteria compared with control suspensions fed mercury-free bacteria. The phenomenon of acquired mercury tolerance was demonstrated within a single generation time. Ciliates fed mercury-free bacteria and subsequently exposed to increasing levels of mercury in solution showed an elevated tolerance to concentrations which, on initial testing, resulted in mortality of 83% of the ciliate population. The effect of ingesting mercury-laden bacteria on growth rate ofUronema was examined, and results showed no significant differences in growth rates of both 3- and 14-day-old cultures of protozoa that had been fed mercury-laden and mercury-free bacteria under controlled conditions.}, }
@article {pmid24232222, year = {1977}, author = {Gadd, GM and Griffiths, AJ}, title = {Microorganisms and heavy metal toxicity.}, journal = {Microbial ecology}, volume = {4}, number = {4}, pages = {303-317}, pmid = {24232222}, issn = {0095-3628}, abstract = {The environmental and microbiological factors that can influence heavy metal toxicity are discussed with a view to understanding the mechanisms of microbial metal tolerance. It is apparent that metal toxicity can be heavily influenced by environmental conditions. Binding of metals to organic materials, precipitation, complexation, and ionic interactions are all important phenomena that must be considered carefully in laboratory and field studies. It is also obvious that microbes possess a range of tolerance mechanisms, most featuring some kind of detoxification. Many of these detoxification mechanisms occur widely in the microbial world and are not only specific to microbes growing in metal-contaminated environments.}, }
@article {pmid24232221, year = {1977}, author = {Buck, JD}, title = {Comparison ofin Situ andin Vitro survival ofCandida albicans in seawater.}, journal = {Microbial ecology}, volume = {4}, number = {4}, pages = {291-302}, pmid = {24232221}, issn = {0095-3628}, abstract = {The survival in seawater of several laboratory and field isolates ofCandida albicans was investigated. Initial studies were madein vitro (flasks) to confirm previous reports. Frequent sampling of viable cells showed that flask experiments, even repeated, produced varied patterns of survival in this closed system. As an alternative, multiple experiments were run in untreated seawater in dialysis bags and plexiglas chambers at ambient temperature (17‡ to 22‡C) in flowing seawater. Die-off rates of all cultures tested in dialysis bags were very rapid in the first day and may have been related to high levels of dissolved organic carbon in the tubing. Distilled water-or acid-washed bags did not yield significantly higher survival rates in all cases. When plexiglas chambers closed with Nuclepore membranes were used, survival rates decreased to 5% to 15% of the original population after 6 days. Chamber data were more uniform and represented approximately a twofold increase in survival over that shown previously inin vitro (flask) studies. Some evidence was obtained in all three test systems for the greater survival rate of a field isolate ofC. albicans compared with that noted for a laboratory (ATCC) strain. The results are considered to more accurately depict the survival ofC. albicans in summer temperate recreational waters.}, }
@article {pmid24232220, year = {1977}, author = {Roper, MM and Marshall, KC}, title = {Effects of a clay mineral on microbial predation and parasitism ofEscherichia coli.}, journal = {Microbial ecology}, volume = {4}, number = {4}, pages = {279-289}, pmid = {24232220}, issn = {0095-3628}, abstract = {Montmorillonitic clay influences the biological control ofEscherichia coli in aquatic systems, the magnitude of the effects being dependent on the state of the clay and the type of host-antagonist interaction. The interaction ofBdellovibrio andE. coli was partially inhibited by the presence of montmorillonite. Because it is highly motile,Bdellovibrio apparently could penetrate any colloidal clay barrier aroundE. coli if the clay envelope was thin enough. Colloidal clay had little effect on predation ofE. coli by the myxobacteriumPolyangium, and had no effect on the activity of the amoebaVexillifera. Crude clay, on the other hand, resulted in a physical separation of predator and prey, and this completely inhibited theE. coli-Polyangium interaction and slowed the rate of engulfment ofE. coli byVexillifera.The interference of natural biological control by clays may alter the microbial balance favoring survival of fecal microorganisms and resulting in their accumulation in saline sediments. This could constitute a health hazard if these organisms were released by upwelling of bottom waters or were desorbed in estuarine systems by dilution during heavy rains.}, }
@article {pmid24233577, year = {1977}, author = {Sayler, GS and Shon, M and Colwell, RR}, title = {Growth of an estuarinePseudomonas sp. on polychlorinated biphenyl.}, journal = {Microbial ecology}, volume = {3}, number = {3}, pages = {241-255}, pmid = {24233577}, issn = {0095-3628}, abstract = {In the course of a study of the microbial degradation of polychlorinated biphenyls (PCB), 16 cultures, representing 5 genera of bacteria, were isolated. APseudomonas sp. was found to degrade mixtures of PCB (Aroclor 1254) and pure isomers, i.e., hexachlorobiphenyl (HCB). Degradation was found to be variable, depending on length of incubation, purity, and degree of chlorination of the biphenyl molecule. In addition to apparent degradation of PCB, it was observed that PCB stimulated growth and oxygen uptake. Bioaccumulation of PCB residues was suggested since(14)-Clabeled material derived from(14)C-PCB accumulated on or in the bacterial cells. The potential degradation and utilization of PCB by microorganisms suggests that this may be an important mechanism for removal or mobilization of PCB into food chains in the estuarine environment.}, }
@article {pmid24233576, year = {1977}, author = {Smith, WH}, title = {Influence of heavy metal leaf contaminants on the in vitro growth of urban-tree phylloplane-fungi.}, journal = {Microbial ecology}, volume = {3}, number = {3}, pages = {231-239}, pmid = {24233576}, issn = {0095-3628}, abstract = {The surfaces of urban woody vegetation are contaminated with varying amounts of numerous metallic compounds, including Cd, Cu, Mn, Al, Cr, Ni, Fe, Pb, Na, and Zn. To examine the possibility that these metals may affect phylloplane fungi, the above cations were tested in vitro for their ability to influence the growth of numerous saprophytic and parasitic fungi isolated from the leaves of London plane trees. Considerable variation in growth inhibition by the metals was observed. GenerallyAureobasidium pullulans, Epicoccum sp., andPhialophora verrucosa were relatively tolerant;Gnomonia platani, Cladsporium sp., andPleurophomella sp. were intermediate; andPestalotiopsis andChaetomium sp. were relatively sensitive to the incorporation of certain metals into solid and liquid media. If similar growth inhibitions occur in nature, competitive abilities or population structures of plant surface microbes may be altered by surface metal contamination. Metals causing the greatest and broadest spectrum growth suppression included Ni, Zn, Pb, Al, Fe, and Mn.}, }
@article {pmid24233575, year = {1977}, author = {Gibson, WP and Burns, RG}, title = {The breakdown of malathion in soil and soil components.}, journal = {Microbial ecology}, volume = {3}, number = {3}, pages = {219-230}, pmid = {24233575}, issn = {0095-3628}, abstract = {The disappearance of the organophosphorus insecticide, malathion, from a silt loam soil and from its organic and inorganic components was examined. Half-lives and the time taken for 90% decomposition in nonsterile, sodium azide-treated, and 2.5 Mrad-irradiated soils were similar (3/4-1 1/2 days and 4-6 days, respectively) but breakdown in autoclaved soils was negligible. Decay in nonsterile sand, silt, and clay minus organic matter fractions was 3-6 times slower than that recorded in the original soil. Breakdown of malathion in the clay plus organic matter fraction (organo-mineral complex) was rapid (half-life, 1 day), as was the case in the separated organic matter (half-life, 1 3/4 days). Filter-sterilized organic matter was not as effective in catalyzing the breakdown of malathion (half-life, 4 days), and no loss occurred from any of the autoclaved components. Irradiation doses of 2.5 and 5.0 Mrad had little influence on the ability of soil to degrade malathion. Thereafter, increases up to 20 Mrad had a more drastic, though far from totally inhibitory, effect. Our results suggest that either the colloidal organic matter itself, or a fraction associated with it, is the most important single factor concerned with the rapid breakdown of malathion in the soil studied. Direct microbial metabolism is a slower process and may have a significant role in malathion disappearance in coarsetextured soils low in colloidal organic matter. The catalytic component of the organic matter is suggested to be a stable exoenzyme and is supportive of reports by other workers. The quantitative effect of organo-mineral complex (containing the active degradative ingredient) additions to sand and silt fractions on the rate of subsequent malathion decay is also described.}, }
@article {pmid24233574, year = {1977}, author = {Jacobs, R and Lind, O}, title = {The combined relationship of temperature and molybdenum concentration to nitrogen fixation byAnabaena cylindrica.}, journal = {Microbial ecology}, volume = {3}, number = {3}, pages = {205-217}, pmid = {24233574}, issn = {0095-3628}, abstract = {The joint effects of growth temperature, incubation temperature, and molybdenum concentration on the nitrogen fixation rate ofAnabaena cylindrica were determined using the acetylene-reduction technique. The nitrogen-fixation response to increased molybdenum concentration varied among three growth temperatures (15°, 23°, and 30° C). The pattern of rate change was similar within a growth temperature but increased overall in magnitude with the three incubation temperatures (also 15°, 23°, and 30° C). The maximum rate of nitrogen fixation occurred at 30°C regardless of previous growth temperature. The minimum molybdenum concentration necessary to yield substantial acetylene reduction varied with growth temperature: at 15°C, 15μg 1(-1) was effective; at 23°C, less than 5μg 1(-1) was effective; and at 30°C, 50μg 1(-1) was effective. At all three growth temperatures, increases in molybdenum concentration above the minimum effective concentration produced increases in acetylene reduction. However, at higher molybdenum concentrations inhibition of nitrogen fixation occurred.}, }
@article {pmid24233573, year = {1977}, author = {Kaplan, WA and Teal, JM and Valiela, I}, title = {Denitrification in salt marsh sediments: Evidence for seasonal temperature selection among populations of denitrifiers.}, journal = {Microbial ecology}, volume = {3}, number = {3}, pages = {193-204}, pmid = {24233573}, issn = {0095-3628}, abstract = {Direct measurements of bacterial denitrification in salt marsh sediments near Woods Hole, Massachusetts were made over a 10-month period using a simple and precise gas-chromatographic technique. Based on laboratory experiments at 5°, 10°, and 20°C, it is shown that seasonal temperature variations select for at least two distinct populations of denitrifiers.In situ incubations suggest that resident populations of denitrifying bacteria are cold-sensitive. Salt marsh denitrifying bacteria are not optimally adapted to their thermal environment, but to temperatures 5°-10°C higher. In these water-logged muds, rates of bacterial denitrification (0.3-1.5μg N2/gm sediment-hr) are up to three orders of magnitude greater than maximum potential rates of insitu bacterial and algal nitrogen fixation.}, }
@article {pmid24233572, year = {1977}, author = {Simidu, U and Kaneko, E and Taga, N}, title = {Microbiological studies of Tokyo Bay.}, journal = {Microbial ecology}, volume = {3}, number = {3}, pages = {173-191}, pmid = {24233572}, issn = {0095-3628}, abstract = {The generic composition of the heterotrophic bacterial population of Tokyo Bay, which is now highly polluted and eutrophic, was compared with that of the adjacent, less polluted regions of Sagami Bay and Suruga Bay. Members of Vibrionaceae predominated in the bacterial flora of seawater and zooplankton samples from Sagami Bay, Suruga Bay, and the mouth of Tokyo Bay. However,Vibrio spp. formed only a small proportion of the bacterial population of the water and sediment samples from the inner Tokyo Bay; there the Gram-negative, nonmotile, nonpigmented bacteria, which were tentatively identified asAcinetobacter, were predominant. The result of experiments, in which seawater samples from Tokyo Bay were incubated under various experimental conditions, indicated that two significant factors apparently control the growth ofVibrio spp. in seawater; (1) a direct antagonism betweenVibrios and phytoplankton undergoing rapid growth, and (2) a limiting organic nutrient forvibrios.}, }
@article {pmid24232166, year = {1977}, author = {Young, LY}, title = {Bacterioneuston examined with critical point drying and transmission electron microscopy.}, journal = {Microbial ecology}, volume = {4}, number = {3}, pages = {267-277}, pmid = {24232166}, issn = {0095-3628}, abstract = {Morphological details of bacteria collected at the air/seawater interface are greatly enhanced when transmission electron microscopy is coupled with critical point dried preparations. Few artifacts and minimal distortion permit a more accurate appraisal of an organism's cell characteristics and its relationship to its microenvironment. Cell surface and extracellular polymer materials are clearly distinguished in a manner not feasible with other preparations.}, }
@article {pmid24232165, year = {1977}, author = {Digeronimo, MJ and Nikaido, M and Alexander, M}, title = {Most-probable-number technique for the enumeration of aromatic degraders in natural environments.}, journal = {Microbial ecology}, volume = {4}, number = {3}, pages = {263-266}, pmid = {24232165}, issn = {0095-3628}, abstract = {A most-probable-number (MPN) method is described for the enumeration of heterotrophic populations capable of utilizing chlorinated and nonchlorinated benzoates and phenols as sole carbon sources. A correlation coefficient of 0.91 was obtained between the numbers determined by the MPN technique and the standard plate count. The MPN method gave realistic cell counts when population densities were low, and the presence of oligocarbophiles did not give spurious results.}, }
@article {pmid24232164, year = {1977}, author = {Shlomi, ER and Lankhorst, A and Prins, RA}, title = {Methanogenic fermentation of benzoate in an enrichment culture.}, journal = {Microbial ecology}, volume = {4}, number = {3}, pages = {249-261}, pmid = {24232164}, issn = {0095-3628}, abstract = {Enrichment cultures inoculated with black mud fermented benzoate according to the stoichiometric equation: 4 C6H5CO2H+18 H2O → 15 CH4+13 CO2.Trans-2-hydroxycyclohexanecarboxylate, 2-oxo-cyclohexanecarboxylate, pimelate, caproate, butyrate, acetate, and molecular hydrogen were shown to be regular components of the culture fluid occurring in low concentrations. Inhibition of methanogenesis by chloroform, 4-chlorobutyrate, or 2-bromooctanoate resulted in a cessation of the benzoate breakdown after all intermediates had accumulated. It is proposed that benzoate is fermented via a direct reductive pathway to butyrate, acetate, H2, and CO2, whereafter butyrate is converted to acetate and H2, and the latter substrates are fermented to CH4 and CO2 by methane producers.}, }
@article {pmid24232163, year = {1977}, author = {Kaspar, HF and Wuhrmann, K}, title = {Product inhibition in sludge digestion.}, journal = {Microbial ecology}, volume = {4}, number = {3}, pages = {241-248}, pmid = {24232163}, issn = {0095-3628}, abstract = {Hydrogen and acetate inhibit the microbial degradation of propionate and ethanol in digesting sludge. Propionate oxidation is more sensitive than ethanol oxidation to product activities. This difference can be explained on thermodynamic grounds. It is concluded that the limiting factors for complete anaerobic mineralization of biodegradable organic matter in digesting sludge are to be sought in the boundary conditions for the exergonic oxidation of propionate. The different ecological significances of hydrogen and acetate as inhibitory agents of fatty acid degradation in sludge digestion are discussed. Hydrogen partial pressure and alkalinity are recommended as parameters in monitoring sludge digestion.}, }
@article {pmid24232162, year = {1977}, author = {Ghiorse, WC and Alexander, M}, title = {Nitrifying populations and the destruction of nitrogen dioxide in soil.}, journal = {Microbial ecology}, volume = {4}, number = {3}, pages = {233-240}, pmid = {24232162}, issn = {0095-3628}, abstract = {The nitrite formed from nitrogen dioxide (NO2) was oxidized more readily in soil that had been treated previously with the gas than in soil not so pre-exposed. The reaction was inhibited by 1.0 but not by 0.01 mM chlorate. The population of nitrite-oxidizing autotrophs estimated by the most-probable-number procedure was too small and often grew too late to account for oxidation of the nitrite generated from NO2. The reaction also proceeded in soil heated to 42° to 45°C or treated with 0.16 mM chlorate, although the countable autotrophs did not increase during the transformation or grew only late in the active period of nitrite oxidation. The data suggest that unknown populations are responsible for metabolism of the nitrite produced from NO2 entering soil.}, }
@article {pmid24232161, year = {1977}, author = {Paerl, HW}, title = {Role of heterotrophic bacteria in promoting N2 fixation byAnabaena in aquatic habitats.}, journal = {Microbial ecology}, volume = {4}, number = {3}, pages = {215-231}, pmid = {24232161}, issn = {0095-3628}, abstract = {Anabaena species are commonly colonized by bacteria, especially during N2-fixing blooms. Generally these associations do not represent bacterial attack on algal hosts. Instead, the algal N2-fixing capabilities are increased in the presence of the bacteria. Possible mechanisms promoting the mutual growth of algae and attached bacteria were investigated by observing specific sites of bacterial attachment, by noting reduced microzones created by the bacteria, and by locating sites of bacterial uptake of organics representative of algal excretion products.Attached bacteria show preference for typical algal excretion products and their growth is enhanced by such products. In return, enhancement of algal nitrogenase activity occurs when bacteria create O2-consuming microzones around the nitrogenase-bearing heterocysts.}, }
@article {pmid24232160, year = {1977}, author = {Taylor, WD}, title = {Growth responses of ciliate protozoa to the abundance of their bacterial prey.}, journal = {Microbial ecology}, volume = {4}, number = {3}, pages = {207-214}, pmid = {24232160}, issn = {0095-3628}, abstract = {The growth rate or numerical response of five species of bactivorous ciliates to the abundance ofEnterobacter aerogenes was examined in monoxenic culture. The ciliatesColpidium campylum, C. colpoda, Glaucoma scintillons, G. frontata, andCyclidium glaucoma were isolated from a small pond. Four were grown in shaken cultures, while three were grown in cultures in which the bacteria were allowed to settle on the bottom of the culture vessel. Of the seven response curves generated, four had distinct thresholds, so that the Michaelis-Menten model usually fitted to ciliate numerical response curves was not appropriate. In shaken cultures, half-saturation prey densities ranged from 5.5 × 10(6) to 42.9 × 10(6) bacteria/ml. In unshaken cultures, half-saturation densities ranged from 0.057 × 10(6) to 14.6 × 10(6) bacteria/cm(2). Two species grown on both suspended and settled bacteria attained higher growth rates and had lower half-saturation prey densities feeding on settled bacteria.}, }
@article {pmid24232159, year = {1977}, author = {Rades-Rohkohl, E and Fränzle, O and Hirsch, P}, title = {Behavior, activities, and effects of bacteria on synthetic quartz monocrystal surfaces.}, journal = {Microbial ecology}, volume = {4}, number = {3}, pages = {189-205}, pmid = {24232159}, issn = {0095-3628}, abstract = {Two strains ofBacillus sp. and a strain ofBrevibacterium sp., originally isolated from a natural quartzite surface, were characterized and employed as test strains with several methods: acridine orange fluorochromation and epifluorescence microscopy were used for detection of individual cells; scanning and transmission microscopy for studying attachment behavior; replica techniques in combination with electron microscopy for following surface interaction effects; and chemical analysis of SiO2 for detecting possible silica leaching activities. The experimental results clearly showed that the three test strains were able to attach to and grow on the precleaned quartz surfaces. Attachment modes were either by direct sorption mechanisms (Brevibacterium sp. S) or the production of adhesive polymers (Bacillus sp. U andBacillus sp. W). In short-term contact incubation experiments with rich media, neither quartz crystal surface structures nor bacterial cell surfaces appeared to be changed. Likewise, significant biochemical dissolution and mechanical dislocation of SiO2 (which would have indicated rapid bacterial weathering activities) could not be detected. The importance of quartz purity and crystalline structure for the initiation of weathering processes is discussed.}, }
@article {pmid24232158, year = {1977}, author = {Weise, W and Rheinheimer, G}, title = {Scanning electron microscopy and epifluorescence investigation of bacterial colonization of marine sand sediments.}, journal = {Microbial ecology}, volume = {4}, number = {3}, pages = {175-188}, pmid = {24232158}, issn = {0095-3628}, abstract = {Scanning electron microscopy (SEM) was employed for the investigation of microorganisms living in marine sand sediments. Epifluorescence, as well as sediment analyses, gave further data on the parameters of the sediment samples.SEM revealed a correlation between the site and density of bacterial colonization and the microtopography of the individual sand grains.Sand grains with a medium roundness showed the greatest density of bacterial colonization. Protected surface sites were favored in the colonization process. The mode of bacterial attachment varied; mostly the barren sand grain surface was colonized. However, bacteria were also observed close to or within detritus or attached to diatoms. Many of the attaching bacteria observed were found to produce polymer strands.In some cases special structures were discovered which could serve bacterial attachment. Entire colonies attached by means of polymer nets, and disc-shaped bacteria were observed.}, }
@article {pmid24233468, year = {1977}, author = {Roper, MM and Marshall, KC}, title = {Lysis ofEscherichia coli by a marine myxobacter.}, journal = {Microbial ecology}, volume = {3}, number = {2}, pages = {167-171}, pmid = {24233468}, issn = {0095-3628}, }
@article {pmid24233467, year = {1977}, author = {Post, FJ}, title = {The microbial ecology of the Great Salt Lake.}, journal = {Microbial ecology}, volume = {3}, number = {2}, pages = {143-165}, pmid = {24233467}, issn = {0095-3628}, abstract = {The Great Salt Lake is actually two lakes. A highly saline (330-gml(-1)) northern arm and a moderately saline (120-gml(-1)) southern arm separated by a semipermeable rock causeway. The lake, particularly the northern arm, has a massive accumulation of organic matter resulting from more than 100,000 years of productivity, cycling from a freshwater to a saline lake, plus the influence of human industry and agriculture in more recent times. The north arm planktonic and attached community consists principally of, in order of biomass: bacteria of at least two genera,Halobacterium andHalococcus; two algae,Dunaliella salina andD. viridis; the brine shrimp,Anemia salina; and, two species of brine fly,Ephydra gracilis andE. hians and possibly one more species. The algae and the bacteria appear to depend on each other for nutrients. The bacteria use organic matter produced by the algae and the algae use ammonia produced by the bacteria and possibly the brine shrimp. The production of ammonia appears to be the rate-limiting step although there is no shortage of other forms of nitrogen in the north arm. Based on aquarium studies, the potential for biomass production of algae and bacteria is much higher than actually observed in the north arm, leading to the postulation of two additional factors controlling population; the grazing of the algae by invertebrates with the excretion of compounds rich in nitrogen, and the effect of a low habitat temperature and winter cold on the bacteria, reducing their metabolic activities to nearly zero. Some aspects of the various organisms and their metabolism are discussed. A comparison is made with recent work on the Dead Sea.}, }
@article {pmid24233466, year = {1977}, author = {Villarreal, E and Canale, RR and Akcasu, Z}, title = {Transport equations for a microbial predator-prey community.}, journal = {Microbial ecology}, volume = {3}, number = {2}, pages = {131-142}, pmid = {24233466}, issn = {0095-3628}, abstract = {A transport equation is used which describes the temporal behavior of interacting populations in changing environments. The formulation takes into account the internal state variables of the individuals. The general theory is applied to the transient analysis of a microbial predator-prey system using an approximate model for the specific cell growth rate and multigroup formulism to approximate the mass distribution within the population. Experimental results in aTetrahymena pyriformis- Aerobacter aerogenes system have been used to evaluate the group parameters and test the validity of the theoretical predictions.}, }
@article {pmid24233465, year = {1977}, author = {Kuenen, JG and Boonstra, J and Schröder, HG and Veldkamp, H}, title = {Competition for inorganic substrates among chemoorganotrophic and chemolithotrophic bacteria.}, journal = {Microbial ecology}, volume = {3}, number = {2}, pages = {119-130}, pmid = {24233465}, issn = {0095-3628}, abstract = {In aerobic enrichment experiments with a chemostat, using phosphate-limited lactate medium, aSpirillum sp. predominated at the lower range of dilution rates. At the higher dilution rates an (chemoorganotrophic) unidentified rod-shaped bacterium came to the fore. The same result was obtained in competition experiments with pure cultures of the two bacteria. Growth parameters were: Rod,Μ max=0.48 hr(-1),k s(PO4 (3-))=6.6×10(-N) M;Spirillum, Μ max=0.24 hr(-1)· ks(PO4 (3-)) =2.7×10(-8) M. TheSpirillum grew faster than the rod at low dilution rates, not only under phosphate-limitation but also in K(+)-,Mg(2+)-, NH4 (+)-, aspartate-, succinate-, and lactate-limited cultures. Both organisms showed little substrate specificity and could utilize a similar range of carbon and energy sources. The results support the view that part of the diversity among bacteria in the natural environment is based on selection toward substrate concentration. Another set of competition experiments was carried out with pure cultures of two marine obligately chemolithotrophic colorless sulfur bacteria,Thiobacillus thioparus andThiomicrospira pelophila. Tms. pelophila outgrewT. thioparus at low dilution rates under iron limitation, while the reverse was true at high dilution rates. It is concluded that the relatively fast growth ofTms. pelophila at low iron concentration may explain its higher sulfide tolerance. Organisms showing a selection advantage at very low concentrations of limiting substrates appear to have a relatively high surface to volume ratio.}, }
@article {pmid24233464, year = {1977}, author = {Peduzzi, R and Bizzozero, S}, title = {Immunochemical investigation of four Saprolegnia species with parasitic activity in fish: Serological and kinetic characterization of a chymotrypsin-like activity.}, journal = {Microbial ecology}, volume = {3}, number = {2}, pages = {107-118}, pmid = {24233464}, issn = {0095-3628}, abstract = {The antigenic structure of four aquatic Phycomycetes of the genusSaprolegnia with parasitic activity in fish was analyzed with immunoelectrophoresis and double diffusion techniques. It is shown that these serological tests might represent a valuable criterion for the identification of the fourSaprolegnia species:S. parasitica, S. ferax, S. delica, andS. diclina. A specific chromogenic reaction revealed the presence of a protease with chymotrypsin-like activity among the precipitation arcs obtained after immunoelectrophoresis. Analysis of this proteolytic activity by kinetic assay methods confirmed the results of the serological tests. Moreover estimates of the quantity of enzyme present in the cellular extract and in the culture medium were obtained. A possible relationship between the proteolytic activity and the host-parasite interaction was discussed.}, }
@article {pmid24233463, year = {1977}, author = {Castenholz, RW}, title = {The effect of sulfide on the blue-green algae of hot springs II. Yellowstone National Park.}, journal = {Microbial ecology}, volume = {3}, number = {2}, pages = {79-105}, pmid = {24233463}, issn = {0095-3628}, abstract = {In the Mammoth Springs (Yellowstone National Park) waters with near neutral pH and soluble sulfide (H2S, HS(-), S(2-)) of over 1-2 mg/liter (30-60ΜM) are characterized by substrate covers of phototrophic bacteria (Chloroflexus and aChlorobium-like unicell) above 50‡C and by a blue-green alga (Spirulina labyrinthiformis) below this temperature.Synechococcus. Mastigocladus, and other blue-green algae typical of most hot springs of western North America are excluded, apparently by sulfide. The sulfide-adaptedSpirulina photosynthesized at maximum rates at 45‡C and at approximately 300 to 700ΜEin/m(2)/sec of "visible" radiation. Sulfide (0.6-1.2 mM) severely poisoned photosynthesis of nonadapted populations, but those continuously exposed to over 30ΜM tolerated at least 1 mM without inhibition. A normal(14)C-HCO3 photoincorporation rate was sustained with 0.6-1 mM sulfide in the presence of DCMU (7ΜM) or NH2OH (0.2 mM), although both of these photosystem II inhibitors prevented photoincorporation without sulfide. Other sulfur-containing compounds (S2O3 (2-) SO3 (2-), S2O4 (2-) thioglycolic acid cysteine) were unable to relieve DCMU inhibition. The lowering of the photoincorporation rate by preferentially irradiating photosystem I was also relieved by sulfide. The most tenable explanation of these results is that sulfide is used as a photo-reductant of CO2, at least when photosystem II is inhibited. It is suggested that in some blue-green algae photosystem II is poisoned by a low sulfide concentration, thus making these algae sulfidedependent if they are to continue photosynthesizing in a sulfide environment. Presumably a sulfidecytochrome reductase enzyme system must be synthesized for sulfide to be used as a photo-reductant.}, }
@article {pmid24231974, year = {1977}, author = {Walsh, F and Mitchell, R}, title = {Bacterial chemotactic responses in flowing water.}, journal = {Microbial ecology}, volume = {4}, number = {2}, pages = {165-168}, pmid = {24231974}, issn = {0095-3628}, abstract = {Chemotaxis in marine bacteria is shown to be the basis for instream location in flowing water. The response is of importance in the location of prey by motile bacterial predators.}, }
@article {pmid24231973, year = {1977}, author = {Barron, GL}, title = {Nematophagous fungi: Endoparasites ofRhabditis terricola.}, journal = {Microbial ecology}, volume = {4}, number = {2}, pages = {157-163}, pmid = {24231973}, issn = {0095-3628}, abstract = {Three techniques were compared for the recovery of endoparasitic nematophagous fungi from soil. The Baermann funnel technique (32 species) was superior to differential centrifugation (19 species) or soil sprinkling (21 species) in terms of number of species found. The main advantage of the Baermann funnel was in the recovery of lower fungi, especially those with flagellate states. In all, 40 species of endoparasites (70% of the known flora) were recorded. Thirty-two of those were found capable of attacking the soil nematodeRhabditis terricola Dujardin.}, }
@article {pmid24231972, year = {1977}, author = {Kaneko, T and Colwell, RR}, title = {The annual cycle ofVibrio Parahaemolyticus in chesapeake bay.}, journal = {Microbial ecology}, volume = {4}, number = {2}, pages = {135-155}, pmid = {24231972}, issn = {0095-3628}, abstract = {An ecological study ofVibrio parahaemolyticus was carried out from December 1970 to December 1971 in the Rhode River of Chesapeake Bay. The annual cycle of the organism was elucidated and factors restricting its distribution in the estuary were described, including the association of the organism with zooplankton. Numerical taxonomy was employed for identification and classification ofV. parahaemolyticus and related organisms on the basis of substrate utilization tests. From characteristics recorded forV. parahaemolyticus, it is concluded to be an estuarine organism.}, }
@article {pmid24231971, year = {1977}, author = {Stevenson, LH}, title = {A case for bacterial dormancy in aquatic systems.}, journal = {Microbial ecology}, volume = {4}, number = {2}, pages = {127-133}, pmid = {24231971}, issn = {0095-3628}, }
@article {pmid24231970, year = {1977}, author = {Bitton, G and Freihofer, V}, title = {Influence of extracellular polysaccharides on the toxicity of copper and cadmium towardKlebsiella aerogenes.}, journal = {Microbial ecology}, volume = {4}, number = {2}, pages = {119-125}, pmid = {24231970}, issn = {0095-3628}, }
@article {pmid24231969, year = {1977}, author = {Smith, EA and Mayfield, CI and Wong, PT}, title = {Naturally occurring apatite as a source of orthophosphate for growth of bacteria and algae.}, journal = {Microbial ecology}, volume = {4}, number = {2}, pages = {105-117}, pmid = {24231969}, issn = {0095-3628}, abstract = {Several naturally occurring calcium-phosphate apatites which varied in crystalline structure and ionic composition were added as crystals of different particle size to P-free (<1μg/liter total P) nutrient media. Sufficient ortho-PO 4 (3-) was released by the partial dissolution of apatite crystals at limnetic pH levels (pH 7.8) to support growth of several unialgal-mixed bacterial cultures. The biomass produced by mixed populations increased as the amount of available apatite was increased and as the pH of the media and the particle size of the apatite crystals were decreased. These findings suggest that although apatite characteristically displays reduced solubility under alkaline conditions, the tons of apatite which are continuously entering aquatic environments as erosion material may be contributing to the P loading of those ecosystems.}, }
@article {pmid24231968, year = {1977}, author = {Blumershine, RV and Savage, DC}, title = {Filamentous microbes indigenous to the murine small bowel: A scanning electron microscopic study of their morphology and attachment to the epithelium.}, journal = {Microbial ecology}, volume = {4}, number = {2}, pages = {95-103}, pmid = {24231968}, issn = {0095-3628}, abstract = {Segmented, filamentous prokaryotic microorganisms colonize and attach to the cells in the epithelium of the mucosa of the small bowels of mice and rats. Scanning electron micrographs, derived from specimens of mouse small intestine, reveal microbial filaments of at least two types. One type is thin (0.8μm) with only faint lines suggesting septa; the other is thicker (1.4μm) and has distinct segments with pronounced septa. Most of the segments are rounded; a few are thin and elongated. Immediately surrounding the attachment site of these organisms, the surface of the epithelial cells appears roughened and occasionally stringy. The filaments may differ morphologically because they represent different phases in the life cycle of a single microbial type. Alternatively, however, they may differ because they are the cells of different microbial types colonizing the same epithelial habitat.}, }
@article {pmid24231887, year = {1977}, author = {Cundell, AM and Sleeter, TD and Mitchell, R}, title = {Microbial populations associated with the surface of the brown algaAscophyllum nodosum.}, journal = {Microbial ecology}, volume = {4}, number = {1}, pages = {81-91}, pmid = {24231887}, issn = {0095-3628}, abstract = {The microorganisms on the surface of the brown algaAscophyllum nodosum, collected from an intertidal area in Nahant, Massachusetts, were examined using scanning electron microscopy. Differences in the microbial populations on the holdfast, internodal regions of the stipe, and the apical tips were apparent. The populations ranged from a lawn of end-attached bacteria above the holdfast to microcolonies of yeast cells near the apical tips. The greatest diversity of microorganisms was noted in the internodal region representing the fourth year of growth where a dense lawn of end-attached bacteria was overlaid by filamentous bacteria, pennate diatoms, and filamentous blue-green algae. A simple procedure was developed to estimate the number of bacteria on the surface of the seaweed using the scanning electron microscope. The observed distribution of epiphytes may be explained in terms of the age of the algal surface, differences in light intensity, and the differential secretion of tannin by various parts ofAscophyllum.}, }
@article {pmid24231886, year = {1977}, author = {Peterson, EW and Lighthart, B}, title = {Estimation of downwind viable airborne microbes from a wet cooling tower-Including settling.}, journal = {Microbial ecology}, volume = {4}, number = {1}, pages = {67-79}, pmid = {24231886}, issn = {0095-3628}, abstract = {In recent years, reuse of municipal waste water as the coolant in drift-producing cooling towers at electrical generating plants has become increasingly common. A hueristic model is presented that can be used to estimate the concentrations of viable airborne microbes in the drift from a wet cooling tower given the concentration of microbes in the cooling tower. The purpose of this presentation is to allow the nonmeteorologist to understand the factors affecting airborne concentration and to make crude estimates of ground-level concentrations of airborne microorganisms. Concentrations are calculated using a standard meterological method, the Gaussian dispersion model, in which terms have been included for droplet settling and microbial death rate.}, }
@article {pmid24231885, year = {1977}, author = {Baleux, B}, title = {A computer study of the evolution of aerobic heterotrophic bacterial populations in sewage and river waters.}, journal = {Microbial ecology}, volume = {4}, number = {1}, pages = {53-65}, pmid = {24231885}, issn = {0095-3628}, abstract = {The biodegradation of six surface active agents tested. The biochemical characteristics of the aerobic heterotrophic bacteria present in Montpellier waste waters and in Rhône water, before and after degradation, were studied by a standardized microbiological method. Four hundred strains isolated from these populations were compared to 29 reference strains by computer analysis. The reference strains were first grouped in classes (single linkage). Then the strains were compared first to these classes, and then to each reference strain. Whereas the bacterial populations were widely distributed before biodegradation, after degradation they were restricted to a few prevailing genera:Pseudomonas, Alcaligenes, andKlebsiella.}, }
@article {pmid24231884, year = {1977}, author = {Bernstein, ME and Carroll, GC}, title = {Microbial populations on Douglas fir needle surfaces.}, journal = {Microbial ecology}, volume = {4}, number = {1}, pages = {41-52}, pmid = {24231884}, issn = {0095-3628}, abstract = {The surface microflora on Douglas fir (Pseudotsuga menziesii (Mirb.) Franco.) foliage from old-growth trees in western Oregon has been examined by epifluorescence and scanning electron microscopy. Colonies of microorganisms on both upper and lower surfaces of 1-, 3-, 5-, and 8-year-old needles from three heights in the canopy of a single tree have been counted in belt transects, and the relative abundance of various categories of microorganisms has been computed. Aggregations of microbial cells are prevalent in the midrib depression along the upper surface and in stomatal cavities and gutters between rows of epidermal cells on the lower surface. Darkly pigmented hyphae and clumps of cells occur, in general, more frequently on the upper needle surface, a habitat more subject to desiccation and UV exposure.Protococcus colonies become abundant on both upper and lower surfaces of older needles. Microbial cover was found to be significantly higher on the bottom of the needle than on the top. The factors involved in this effect are considered and discussed.}, }
@article {pmid24231883, year = {1977}, author = {Berk, SG and Brownlee, DC and Heinle, DR and Kling, HJ and Colwell, RR}, title = {Ciliates as a food source for marine planktonic copepods.}, journal = {Microbial ecology}, volume = {4}, number = {1}, pages = {27-40}, pmid = {24231883}, issn = {0095-3628}, abstract = {Copepods of the genusEurytemora, isolated from the Patuxent River, a tributary of Chesapeake Bay, were fed suspensions of the ciliateUronema isolated from the Rhode River, a subestuary of Chesapeake Bay. Grazing by copepods was determined by the decrease in numbers of ciliates, which were monitored by both direct counting and particle size analysis. Results from both methods of analysis showed significant reduction in the numbers ofUronema in the suspension whenEurytemora was present. Survival of copepods with ciliates added as food source was significantly longer than without ciliates. Analysis of field samples collected in the fall showed that ciliates comprised approximately 20% of the total plankton biomass at selected sampling sites. The results of the laboratory and field studies indicate that copepods can feed on ciliates and suggest that, in nature, ciliates may comprise an important source of food for copepods.}, }
@article {pmid24231882, year = {1977}, author = {Tuttle, JH and Jannasch, HW}, title = {Thiosulfate stimulation of microbial dark assimilation of carbon dioxide in shallow marine waters.}, journal = {Microbial ecology}, volume = {4}, number = {1}, pages = {9-25}, pmid = {24231882}, issn = {0095-3628}, abstract = {The effect of thiosulfate on dark assimilation of carbon dioxide in shallow marine environments was investigated in order to explain the recent discovery of bacterial thiosulfate oxidation in aerobic, open ocean seawater. The results demonstrate that the potential exists for microbial thiosulfate oxidation to increase both dark assimilation of carbon dioxide and the utilization of organic compounds in the sea. Thiosulfate-stimulated microbial activity may be caused not only by chemoautotrophic sulfur bacteria, but also by heterotrophic species which oxidize thiosulfate to tetrathionate. Measurements of dark assimilation of carbon dioxide made at different incubation times indicate that great care must be taken both in experimental procedure and in interpretation of results obtained with the dark assimilation technique.}, }
@article {pmid24231881, year = {1977}, author = {Wiebe, WJ and Smith, DF}, title = {(14)C-labeling of the compounds excreted by phytoplankton for employment as a realistic tracer in secondary productivity measurements.}, journal = {Microbial ecology}, volume = {4}, number = {1}, pages = {1-8}, pmid = {24231881}, issn = {0095-3628}, abstract = {Preparations of the dissolved organic compounds released by photosynthesizing marine phytoplankton have been obtained with(14)carbon activities as high as 1.5 × 10(5) dpm/ml. The radioisotope content of the preparations resides wholly in dissolved organic compounds of low molecular weight (MW<3500), which are uncontaminated by residual(14)C-labeled inorganic carbon. The labeled compunds arise through photosynthetic fixation and do not appear to be products of cell lysis during the incubation or to originate from cell damage during the filtration step employed.}, }
@article {pmid24233398, year = {1976}, author = {Chet, I and Mitchell, R}, title = {An enrichment technique for isolation of marine chemotactic bacteria.}, journal = {Microbial ecology}, volume = {3}, number = {1}, pages = {75-78}, pmid = {24233398}, issn = {0095-3628}, }
@article {pmid24233397, year = {1976}, author = {Bollag, JM and Russel, S}, title = {Aerobic versus anaerobic metabolism of halogenated anilines by aParacoccus sp.}, journal = {Microbial ecology}, volume = {3}, number = {1}, pages = {65-73}, pmid = {24233397}, issn = {0095-3628}, abstract = {AParacoccus sp. which transforms aniline and different halogen-substituted derivatives under aerobic and anaerobic conditions was isolated from the soil. In experiments with(14)C-ring-labeled 4-chloroaniline, approximately 60% of the radioactive material disappeared from the growth medium after incubation under anaerobiosis within 48 hr, but under aerobic conditions no decrease of radioactivity in the growth medium was observed, although 4-chloroaniline was completely metabolized. Acetylation appears to constitute, especially under aerobic conditions, a major transformation mechanism by the bacterium, since almost 50% of the acetylated compound could be detected and identified if aniline, 2-, 3-, and 4-chloroaniline served as substrate. The formation of different metabolites under aerobic and anaerobic conditions clearly indicates the existence of two separate pathways in the metabolism of aniline compounds depending on the oxygen status of the environment.}, }
@article {pmid24233396, year = {1976}, author = {Gibbs, CF and Davis, SJ}, title = {The rate of microbial degradation of oil in a beach gravel column.}, journal = {Microbial ecology}, volume = {3}, number = {1}, pages = {55-64}, pmid = {24233396}, issn = {0095-3628}, abstract = {An automatic, continuous flow respirometer was used to follow the bio-oxidation of a crude oil in a column of fairly coarse beach material. A number of water percolation rates were employed, with and without inorganic nutrient supplementation (nitrate and phosphate). Initially, nutrient supplementation was required to allow significant oxidation rates, but a capacity for biodegradation in the absence of continued supplementation developed slowly. The increase in oxidation rate with nutrient supplementation was in the proportion 0.23 mg oxygen perμmol nitrate. This proportionality was similar to previous results in this laboratory (using different systems), as was the effect of temperature. The mean of two Q10 values in this work was 2.7.}, }
@article {pmid24233395, year = {1976}, author = {Antia, NJ}, title = {Effects of temperature on the darkness survival of marine microplanktonic algae.}, journal = {Microbial ecology}, volume = {3}, number = {1}, pages = {41-54}, pmid = {24233395}, issn = {0095-3628}, abstract = {Thirty-seven species of marine microplanktonic algae from 10 taxonomic classes were tested for their viability in axenic culture after prolonged exposure to darkness at 2°, 10°, and 20°C. The darkness test periods were prolonged in weekly installments up to a maximum of 1 year, and viability retention (survival) was judged from the capability for resuming growth after replacement in light. The 2°C-tests showed 32% of the species reaching the limits of survival with 5-6 months of darkness exposure, but another similar percentage continued to tolerate darkness for double this period. These darkness toleration limits were considerably shorter at 20°C for the strains known to be isolated from cold marine regions, whereas the warm-water strains showed the reverse temperature effect in surviving significantly longer at 10°-20°C than at 2°C. Irrespective of temperature or algal class, the bulk of the more resistant survivors was formed by the strains qualifying as benthic types, about 70% of which tolerated 11-12 months and the rest at least 5-6 months of darkness. A few randomly chosen benthic strains extended this toleration to 3 years of darkness. It was concluded that phytoplankters retain darkness-endurance capacity determined by their ecological origin and with no obvious taxonomic correspondence. The concept of ecological races, characterized by temperature control of darkness survival, is discussed.}, }
@article {pmid24233394, year = {1976}, author = {Doores, S and Cook, TM}, title = {Occurrence ofVibrio and other bacteria on the sea nettle,Chrysaora quinquecirrha.}, journal = {Microbial ecology}, volume = {3}, number = {1}, pages = {31-40}, pmid = {24233394}, issn = {0095-3628}, abstract = {Sixty-two specimens of the sea nettle,Chrysaora quinquecirrha, were caught in the lower Chesapeake Bay, homogenized, and samples plated on a yeast extract-Bay water agar. Bacterial colonies were selected randomly, purified, and tested for 180 characteristics. Computer analysis permitted clustering of the 208 isolates into 15 groups (comprised of 133 strains) plus 75 nongrouped strains which failed to associate with any group at the 70% similarity level. The majority of the isolates (68.8%) wereVibrio species. These included 110 of the grouped strains (forming 12 of the 15 groups) and 33 of the nongrouped strains. The remainder of the isolates were distributed as follows:Pseudomonas (11.6%),Bacillus (8.2%),Flavobacterium (2.4%),Acinetobacter (2.4%),Moraxella (1.9%),Cytophaga (1.9%), Gram-positive cocci (1.4%), and miscellaneous (1.4%). All theBacillus were isolated from a group of moribund nettles and reflect an abnormal condition.Vibrio species predominated in the five "catches" of healthy nettles, but were distinctly different for each catch.}, }
@article {pmid24233393, year = {1976}, author = {Starmer, WT and Heed, WB and Miranda, M and Miller, MW and Phaff, HJ}, title = {The ecology of yeast flora associated with cactiphilic Drosophila and their host plants in the Sonoran desert.}, journal = {Microbial ecology}, volume = {3}, number = {1}, pages = {11-30}, pmid = {24233393}, issn = {0095-3628}, abstract = {Yeasts were isolated from the rotting stems of 7 species of cereoid cacti and 4 species ofDrosophila which utilize them as host plants. The yeast most common among 132 nonidentical isolates from the cacti and 187 nonidentical isolates from the flies, respectively, were:Pichia membranaefaciens (59 and 126),Candida ingens (22 and 8),Torulopsis sonorensis (16 and 20), andCryptococcus cereanus (11 and 14). Isolates capable of utilizingD-xylose were recovered primarily fromD. pachea andL. schotti. Adult flies were present on the substrates whenP. membranaefaciens was at high concentrations. As the pH of the substrates increased, the percent ofC. ingens cells increased relative to other yeast species. Larvae were detected mainly in alkaline substrates, and since adults did not yieldC. ingens to the extent the substrates did,C. ingens may be important in larval nutrition.Torulopsis sonorensis was recovered mainly fromD. mojavensis and its host plants,M. gummosus andL. thurberi. The concentration ofT. sonorensis in the substrates was negatively correlated with the temperature of the substrate.Cryptococcus cereanus was found in high concentrations in suitable tissues for adult flies but most adults did not yield this species to any extent. The yeast habitat diversities from the substrates had the following order:L. thurberi > C. gigantea > C. gigantea soils ≫ M. gummosus > L. schotti > others. Habitat diversity is discussed in relation to the variation of the physical conditions and chemical composition of the substrates. The yeast habitat diversities from the flies had the orderD. pachea > D. mojavensis ≫ D. nigrospiracula > undescribed Species M. The degree of habitat diversity is possibly a function of the surface feeding behavior of the flies.}, }
@article {pmid24233392, year = {1976}, author = {Imhoff, JF and Trüper, HG}, title = {Marine sponges as habitats of anaerobic phototrophic bacteria.}, journal = {Microbial ecology}, volume = {3}, number = {1}, pages = {1-9}, pmid = {24233392}, issn = {0095-3628}, abstract = {Enrichment cultures were prepared with different media for phototrophic bacteria from four species of marine sponges, collected from oxic coastal waters near Split (Yugoslavia). We obtained pure cultures of six strains ofChromatiaceae and two strains ofRhodospirillaceae by agar shake dilution. TheRhodospirillaceae were identified asRhodopseudomonas sulfidophila and a marine form ofRhodopseudomonas palustris. TheChromatiaceae were identified asChromatium vinosum, Chromatium gracile, Chromatium minutissimum. Ectothiorhodospira mobilis, and a Chromatium species, which in some respects resemblesChromatium minus. The occurrence of strictly anaerobic phototrophic bacteria in aerobic sponges is discussed with respect to nutrition and possible syntrophism.}, }
@article {pmid24241392, year = {1975}, author = {Hankin, L and Poincelot, RP and Anagnostakis, SL}, title = {Microorganisms from composting leaves: Ability to produce extracellular degradative enzymes.}, journal = {Microbial ecology}, volume = {2}, number = {4}, pages = {296-308}, pmid = {24241392}, issn = {0095-3628}, abstract = {Mixed populations of bacteria, fungi, and actinomycetes in a leaf compost pile were examined over a 100-day test period for their ability to produce extracellular proteolytic, lipolytic, amylolytic, cellulolytic, pectolytic, and ureolytic enzymes and ability to utilize alkanes. Urea was added to the leaves to adjust the carbon to nitrogen ratio but was of little value in maintaining the proper ratio since it was degraded within the first few days. The degradative enzymes excreted by microorganisms was dependent on the temperature of the pile. In many cases organisms able to produce specific extracellular enzymes at medium temperatures were able to grow at high temperatures, but either did not excrete the specific enzymes or the enzymes were inactivated by the high temperature.}, }
@article {pmid24241391, year = {1975}, author = {Marbach, A and Varon, M and Shilo, M}, title = {Properties of marine bdellovibrios.}, journal = {Microbial ecology}, volume = {2}, number = {4}, pages = {284-295}, pmid = {24241391}, issn = {0095-3628}, abstract = {Marine bdellovibrio isolates from the Israeli littoral of the Mediterranean Sea were screened and characterized in terms of host range, temperature and salinity ranges, cation requirement, mutation frequency, and G + C% mole content. Ten types of isolates were distinguished on the basis of these parameters.}, }
@article {pmid24241390, year = {1975}, author = {Law, AT and Robertson, BR and Dunker, SS and Button, DK}, title = {On describing microbial growth kinetics from continuous culture data: Some general considerations, observations, and concepts.}, journal = {Microbial ecology}, volume = {2}, number = {4}, pages = {261-283}, pmid = {24241390}, issn = {0095-3628}, abstract = {Analysis of continuous culture methodology suggests that this potentially powerful tool for kinetic analysis can be improved by minimizing several inherent shortcomings. Medium background substrates - organic carbon, phosphate, and manganese - were shown to dominate kinetic observations at concentrations below chemical detection methods. Reactor wall growth, culture size distribution changes, sample removal-induced steady state perturbations, and limiting substrate leakage from organisms are treated in terms of kinetic measurement errors. Large variations in maximal growth rates and substrate uptake rates found are attributed to experimental protocol-induced transient states. Relationships are presented for correcting limiting substrate concentrations for lability during sampling, contamination with unreacted medium, and background substrate effects. Analytical procedures are discussed for improved measurement of limiting substrate kinetics involving enzymes, isotopes, and material balance manipulation. Relaxation methods as applied to continuous culture are introduced as a means for isolating separate rate constants describing net substrate transport and for evaluating cellular metabolite leakage. Low velocity growth, multiple substrate metabolism, and endogenous metabolism are discussed along with measurements showing that 1-month generation times for aquatic microorganisms can be quite normal and that the kinetics are compatible withμg/liter limiting substrate concentrations. The concept of regarding growth kinetics as the sum of several net accumulation processes is suggested.}, }
@article {pmid24241389, year = {1975}, author = {Pollingher, U and Berman, T}, title = {Autoradiographic screening for potential heterotrophs in natural algal populations of Lake Kinneret.}, journal = {Microbial ecology}, volume = {2}, number = {4}, pages = {252-260}, pmid = {24241389}, issn = {0095-3628}, abstract = {Microautoradiography was used to screen natural phytoplankton populations from Lake Kinneret for their ability to take up radioactive organic substrates (glucose, acetic acid, amino acids, and glycollic acid. Several of the important Chlorophyta (Pediastrum spp.,Actinastrum hantzschii, Kirchncriella spp.,Coelastrum spp.,Scenedesmus spp., andTetraëdron spp.) and Cyanophyta (Microcystis spp.,Merismopedia sp.,Chroococcus spp., andAnabaena spp.) showed consistent organic uptake. However, the principal bloom former, the dinoflagellatePeridinium cinctum fawestii and most of the pelagic algae observed, never assimilated any of the above substrates. Autoradiographic surveys permit rapid screening of algal populations for species which are capable of taking up organic matter and can indicate potential facultative heterotrophs.}, }
@article {pmid24241388, year = {1975}, author = {Jordan, TL and Staley, JT}, title = {Electron microscopic study of succession in the periphyton community of lake Washington.}, journal = {Microbial ecology}, volume = {2}, number = {4}, pages = {241-251}, pmid = {24241388}, issn = {0095-3628}, abstract = {Microbial succession has been observed on electron microscope grids immersed in lake water for 1, 3, 6, and 10 days. As predicted by ecological theory, the biomass, numbers, and diversity of attached microorganisms increased as succession proceeded. The diversity index of Shannon showed a marked increase from 3.1 at day 1 to 4.2 at day 3. It continued to rise at day 6 and attained the maximum value calculated on day 10 of 4.8. Bacteria were the major pioneer colonizers in this mesotrophic community. Based on these results and the results of other microbiologists who have found bacteria to be the dominant component during the pioneer stage of succession in periphyton communities of varying trophic status, we suggest that microbial heterotrophs may commonly, and perhaps always, be the major component of the early pioneer community of autogenic successions.}, }
@article {pmid24241338, year = {1975}, author = {Disalvo, LH and Daniels, GW}, title = {Observations on estuarine microfouling using the scanning electron microscope.}, journal = {Microbial ecology}, volume = {2}, number = {3}, pages = {234-240}, pmid = {24241338}, issn = {0095-3628}, abstract = {Scanning electron microscopy was used to observe microbiological primary fouling of glass surfaces exposed in estuarine waters. Observations on clean glass, and glass treated with water-repellent coatings, showed that bacterial slimes adhered less strongly to the waterrepellent glass. An experiment using pure cultures of bacteria and latex particles showed that attached bacteria promoted the settlement of latex particles on the glass.}, }
@article {pmid24241337, year = {1975}, author = {Mitchell, R and Chet, I}, title = {Bacterial attack of corals in polluted seawater.}, journal = {Microbial ecology}, volume = {2}, number = {3}, pages = {227-233}, pmid = {24241337}, issn = {0095-3628}, abstract = {Coral heads of the genusPlatigyra exposed to low concentrations of crude oil, copper sulfate, potassium phosphate, or dextrose were killed in periods of 5 to 10 days in aquarium studies. The chemicals stimulated the production of large quantities of mucus by the corals. In aquaria treated with antibiotics to prevent microbial growth,Platigyra survived the presence of these chemicals in the water, indicating a role of the microflora in the death of the corals. Evidence was obtained implicating predatory bacteria,Desulfovibrio andBeggiatoa, in the destruction of the stressed coral colonies.}, }
@article {pmid24241336, year = {1975}, author = {Mack, WN and Mack, JP and Ackerson, AO}, title = {Microbial film development in a trickling filter.}, journal = {Microbial ecology}, volume = {2}, number = {3}, pages = {215-226}, pmid = {24241336}, issn = {0095-3628}, abstract = {The transmission and scanning electron microscopes were employed to visualize the sequence of the biofilm development in the trickling wastewater filter. After the deposit of a small amount of debris upon a hard surface, the bacterial cells attach and develop the matrix on which the biofilm is formed. Protozoa invade the basic layer where they feed on the bacteria. The algae are seeded upon the bacterial matrix and grow so profusely that the bacteria must develop aerial colonies in the competition for food and oxygen. Destruction of the bacteria in the matrix and the weight and hydraulic pressure cause detachment of the biofilm and a new matrix must be developed.}, }
@article {pmid24241335, year = {1975}, author = {Meinert, JC and Ehret, CF and Antipa, GA}, title = {Circadian chronotypic death in heat-synchronized infradian mode cultures ofTetrahymena pyriformis W.}, journal = {Microbial ecology}, volume = {2}, number = {3}, pages = {201-214}, pmid = {24241335}, issn = {0095-3628}, abstract = {Continuous cultures ofTetrahymena pyriformis in the infradian ("slow-exponential") growth mode can be entrained to give circadian rhythms of cell division by the application of thermal cycles with periods of 24 hr. The degree of synchronization (phasing index) is dependent on the cycling of other environmental agents, particularly food in the form of the defined medium used. The phase angles of these multiple zeitgebers to one another and to the circadian cell cycle markedly influence the quality of synchronization achieved. In wellsynchronized oxygen-limited cultures, a circadian cytotoxia (circadian chronotypic death) is observed when the culture's oxygen requirements periodically exceed the oxygen support limit of the environment.}, }
@article {pmid24241334, year = {1975}, author = {Chet, I}, title = {Ultrastructural basis of sclerotial survival in soil.}, journal = {Microbial ecology}, volume = {2}, number = {3}, pages = {194-200}, pmid = {24241334}, issn = {0095-3628}, abstract = {The ultrastructure of developing and mature sclerotia ofSclerotium rolfsii was studied with a scanning electron microscope. The mature sclerotium is disconnected from the mycelium and well differentiated. The rind is composed of rather thick-walled empty cells. The cortex cells are large and almost completely filled with vesicles, whereas the medullar cells are smaller and some of them are very thickwalled.}, }
@article {pmid24241333, year = {1975}, author = {Cherry, DS and Guthrie, RK}, title = {Effects ofFlavobacterium lutescens growth on populations ofEscherichia coli andStreptococcus faecalis in water following thermal loading.}, journal = {Microbial ecology}, volume = {2}, number = {3}, pages = {186-193}, pmid = {24241333}, issn = {0095-3628}, abstract = {Flavobacterium lutescens has been observed to constitute a major segment of the aerobic, heterotrophic bacterial populations in nonpolluted aquatic systems. It is present in lesser numbers in the presence of municipal sewage and higher concentrations of organic wastes. In laboratory tests, in water from nonpolluted systems, this species became the predominant bacterial type following thermal addition. When temperature was increased in water from polluted sources,F. lutescens became a major component of the bacterial populations. In the laboratory, the numbers ofEscherichia coli andStreptococcus faecalis were observed to decrease in proportion to the increase inF. lutescens after thermal addition. Similar results were observed when water from three aquatic systems of differing nutrient content was tested. A greater amount of organic material present in the water reduced the predominance ofF. lutescens. These results indicate that, without use of chemical additives, this method may be useful for restoration of natural aquatic bacterial populations and reduction of undesirable microbial populations in water supplies.}, }
@article {pmid24241332, year = {1975}, author = {Rovira, AD and Campbell, R}, title = {A scanning electron microscope study of interactions between micro-organisms andGaeumannomyces graminis (Syn.Ophiobolus graminis) on wheat roots.}, journal = {Microbial ecology}, volume = {2}, number = {3}, pages = {177-185}, pmid = {24241332}, issn = {0095-3628}, abstract = {Roots of wheat grown in unsterilized sand inoculated withGaeumannomyces graminis (Sacc.) von Arx and Olivier were examined by scanning electron microscopy. Healthy roots had a mucilaginous covering and were sparsely colonized by bacteria, but asG. graminis colonized the roots the mucilage disappeared and the numbers of bacteria on the surface increased. Lysis of the hyphae occurred, apparently caused by bacteria that colonized the hyphae. Inoculation of wheat in axenic culture with a strain ofPseudomonas fluorescens that was antagonistic toG. graminis in agar gave some protection against the pathogen; lysis of hyphae was observed where protection occurred.}, }
@article {pmid24241236, year = {1975}, author = {Ramamoorthy, S and Kushner, DJ}, title = {Binding of mercuric and other heavy metal ions by microbial growth media.}, journal = {Microbial ecology}, volume = {2}, number = {2}, pages = {162-176}, pmid = {24241236}, issn = {0095-3628}, abstract = {Ion-specific electrodes were used to study the binding of Hg(2+), Pb(2+), Cu(2+), and Cd(2+) ions to widely used bacterial growth media (Nutrient broth, trypticase soy broth, the medium of Foot and Taylor [6] and of Nelsonet al.[12]) and to media components [yeast extract, peptone, tryptone, proteose peptone, and casamino acids (acid hydrolyzed casein)]. Volatilization of Hg(2+) from aqueous solutions could be prevented by any of the growth media or their components. All media bound large amounts of Hg(2+), Pb(2+), and Cu(2+), but much less Cd(2+). Of the media components, casamino acids showed the most binding activity for all metal ions; the relative affinity of other media components to different ions varied with the cation studied. In general, the Irving-Williams [8] series for cation affinity to organic ligands was followed: Hg(2+)>Pa(2+)≫ Cu(2+)≫ Cd(2+).After adding 20 ppm of Hg(2+), Pb(2+), or Cu(2+) (concentrations inhibitory to the growth of most microorganisms) to the growth media, 80 ppb or less remained as free cations in the solution. This might suggest that such ions enter bacterial cells as organic complexes, or that bacterial cells can compete successfully with growth media for the bound ions.}, }
@article {pmid24241235, year = {1975}, author = {Nissenbaum, A}, title = {The microbiology and biogeochemistry of the Dead Sea.}, journal = {Microbial ecology}, volume = {2}, number = {2}, pages = {139-161}, pmid = {24241235}, issn = {0095-3628}, abstract = {The Dead Sea is a hypersaline water body. Its total dissolved salts content is on the average 322.6 gm/liter. The dominant cation is Mg (40.7 gm/liter), followed by Na (39.2 gm/liter), Ca (17 gm/liter) and K (7 gm/liter). The major anion is Cl (212 gm/liter), followed by Br (5 gm/liter); SO4 and HCO3, are very minor. The lake contains a limited variety of microorganisms and no higher organisms. The number of recorded species is very low, but the total biomass is reasonably high (about 10(5) bacteria/ml and 10(4) algal cells/ml). The indigenous flora is comprised mainly of obligate halophylic bacteria, such as the pink, pleomorphicHalobacterium sp., aSarcina-like coccus, and the facultative halophilic green alga,Dunaliella. Sulfate reducers can be isolated from bottom sediments. Recently a unique obligate magnesiophile bacteria was isolated from Dead Sea sediment. Several of the Dead Sea organisms possess unusual properties. TheHalobacterium sp. has extremely high intercellular K(+) concentration (up to 4.8M) and extraordinary specificity for K(+) over Na. TheDunaliella has very high intracellular concentration of glycerol (up to 2.1M). The microorganisms exert marked influence on some biogeochemical processes occurring in the lake, such as the control of the sulfur cycle and the formation and diagenesis of organic matter in the sediments. The Dead Sea is an excellent example of the development of two different mechanisms for adjusting to a hostile environment. The algae adjust to the high salinity by developing a mechanism for the exclusion of salts from the intracellular fluid and using glycerol for osmotic regulation. On the other hand, the bacteria adapt to the environment by adjusting their internal inorganic ionic strength, but not composition, to that of the medium. The problem of population dynamics and limiting factors for algal and bacterial productivity are discussed in view of the total absence of zooplankton and other consumers other than bacteria.}, }
@article {pmid24241234, year = {1975}, author = {Fuhs, GW and Chen, M}, title = {Microbiological basis of phosphate removal in the activated sludge process for the treatment of wastewater.}, journal = {Microbial ecology}, volume = {2}, number = {2}, pages = {119-138}, pmid = {24241234}, issn = {0095-3628}, abstract = {Several strains resembling members of theAcinetobacter-Moraxella-Mima group of bacteria were isolated from activated sludge-type sewage treatment plants designed for phosphate removal. The bacteria are obligate aerobes but utilize as carbon and energy sources low-molecular intermediates generated anaerobically, particularly acetate and ethanol. These bacteria can be shown to be responsible for the phosphate luxury uptake occurring in these treatment plants. The bacteria are physiologically unusual in that they perform luxury uptake of phosphates in a complete growth medium. Phosphate release occurs on addition of a carbon source to the carbon-starved bacteria, lowering pH or both. The bacteria persist in the system by virtue of their ability to form floc.}, }
@article {pmid24241233, year = {1975}, author = {Mishustin, EN}, title = {Microbial associations of soil types.}, journal = {Microbial ecology}, volume = {2}, number = {2}, pages = {97-118}, pmid = {24241233}, issn = {0095-3628}, abstract = {Microorganisms are characterized by wide ranges of distribution. Some groups, however, are known to have zones of active proliferation, and the development of specific populations in discrete zones results in rather specific microbial associations in some soil types. The soils formed in warm climates are richer in microorganisms and contain more bacilli and actinomycetes. The spectrum of dominant microbial groups varies in different soil types.}, }
@article {pmid24241164, year = {1975}, author = {Larock, PA and Ehrlich, HL}, title = {Observations of bacterial microcolonies on the surface of ferromanganese nodules from blake plateau by scanning electron microscopy.}, journal = {Microbial ecology}, volume = {2}, number = {1}, pages = {84-96}, pmid = {24241164}, issn = {0095-3628}, abstract = {Examination of the surface of freshly collected ferromanganese nodules by scanning electron microscopy revealed the presence of microcolonies of rod- and coccus-shaped bacteria which appeared to be anchored to the nodule surface by slime. The attachment of microcolonies by slime to the surface of freshly collected nodules argues against their being contaminants introduced during nodule collection or processing. These results corroborate cultural and biochemical detection of bacteria on ferromanganese nodules.}, }
@article {pmid24241163, year = {1975}, author = {Paerl, HW}, title = {Microbial attachment to particles in marine and freshwater ecosystems.}, journal = {Microbial ecology}, volume = {2}, number = {1}, pages = {73-83}, pmid = {24241163}, issn = {0095-3628}, abstract = {Scanning electron microscopy observations ofin situ suspended marine and freshwater particles show diverse but similar modes of bacterial and fungal attachment. A survey of Sierra Nevada mountain lakes and pelagic and near-shore waters in the Pacific Ocean indicates that attachment is most noticeable in the near-surface waters where fresh dissolved and particulate input of carbon from phytoplankton and elevated temperatures favor microbial growth. The most common modes of attachment are: adhesive stalk formation, growth on adhesive webs, attachment by the use of pili-like appendages and slimy capsular secretions, and molecular or chemical sorption without the use of visualized structural appendages. Attached microbial growth is accelerated when particulate substrates are supplied, even when they are not rich in organic nutrients. This is the case in the Lake Tahoe basin, where microflora attached to eroded silts can significantly modify the organic carbon and nutrient content of such minerogenous particles.}, }
@article {pmid24241162, year = {1975}, author = {Cappenberg, TE}, title = {A study of mixed continuous cultures of sulfate-reducing and methane-producing bacteria.}, journal = {Microbial ecology}, volume = {2}, number = {1}, pages = {60-72}, pmid = {24241162}, issn = {0095-3628}, abstract = {Ecological relationships between sulfate-reducing and methane-producing bacteria in mud of Lake Vechten have been studied by continuous culture studies using the chemostat technique. The maximum specific growth rate (μ max) and saturation constant (K s) were, respectively, 0.36 hr(-1) and 0.047 mM for lactate-limited growth ofDesulfovibrio desulfuricans and 0,011 hr(-1) and 0.17 mM for acetate-limited growth ofMethanobacterium sp. Calculated values for the true molar growth yieldsY G) and maintenance coefficients (m) were 30.6 g bacterial mass/mole of lactate and 0.53 g substrate/g dry wt hr forD. desulfuricans and 37.8 g bacterial mass/mole of acetate and 0.54 g substrate/g dry wt hr forMethanobacterium.No growth ofMethanobacterium was observed at apS(2-) value (the hydrogen sulfide potential) of more than 11 and there was no effect on the growth atpS(2-) values above 13. In mixed continuous culture experiments the concentration of acetate decreased in the secondstage growth vessel, whereas that of methane increased stoichiometrically. If the substrate concentration in the reservoirs (S r) was increased from 0.1 to 0.5 mg/ml, the population ofDesulfovibrio increased and that ofMethanobacterium was washed out of the culture vessel, since the concentration of hydrogen sulfide reached apS(2-) value of 10.5. From the mixed continuous culture experiments a commensalism between the two species can be described, i.e., the acetate-fermentingMethanobacterium benefits from the acetate released byDesulfovibrio which is, in turn, not affected in the presence of the former.}, }
@article {pmid24241161, year = {1975}, author = {Grimes, DJ and Morrison, SM}, title = {Bacterial bioconcentration of chlorinated hydrocarbon insecticides from aqueous systems.}, journal = {Microbial ecology}, volume = {2}, number = {1}, pages = {43-59}, pmid = {24241161}, issn = {0095-3628}, abstract = {The prevalence of chlorinated hydrocarbon insecticide uptake by chemoorganotrophic bacteria has been investigated. Thirteen bacterial species were observed to sorb and concentrate (bioconcentratc)α-chlordane,β-chlordane, dieldrin, heptachlor epoxide, and lindane from aqueous systems. Bioconcentration, as expressed by the ratio of cellular insecticide in ng/mg (dry wt) to supernatant insecticide in ng/μl, ranged from 10 for lindane byEnterobacter aerogenes to a high of 55,900 forβ-chlordane byCaulobacter vibrioides var.limonus. Amounts of cellular chlorinated hydrocarbon insecticides (CHI) detected and the bioconcentration ratios were observed to have the following order in magnitude:α- orβ-chlordane > dieldrin > heptachlor epoxide > lindane. This decreasing order was the inverse of reported water solubilities for the CHI and the inverse relationship was mathematically defined. The CHI were not easily removed from cells by washing (desorbing) and desorption was directly proportional to insecticide water solubility. Uptake of the CHI was rapid, near-maximum amounts being sorbed within 15 min, and pH 7 appeared optimal for bioconcentration as examined over the range pH 6 to 8. Implications of this investigation are that bioconcentration of CHI by bacteria might serve as a means of introducing these toxic compounds into aquatic food chains and that the bioconcentration phenomenon might lend itself as a treatment procedure for the intentional removal of residual CHI from water supplies and wastewater.}, }
@article {pmid24241160, year = {1975}, author = {Caparello, DM and Larock, PA}, title = {A radioisotope assay for the quantification of hydrocarbon biodegradation potential in environmental samples.}, journal = {Microbial ecology}, volume = {2}, number = {1}, pages = {28-42}, pmid = {24241160}, issn = {0095-3628}, abstract = {An enrichment culture method is described for quantifying the activity of hydrocarbon oxidizing bacteria in water and sediments. Application of the procedure indicated that the hydrocarbon oxidizing potential of environmental samples reflects the hydrocarbon burden of the area, the ability of the microflora to utilize hydrocarbons, and that lakes with large aquatic plant communities contain populations of hydrocarbon bacteria comparable to those found in oil-polluted harbors.}, }
@article {pmid24241159, year = {1975}, author = {Alexander, M}, title = {Environmental and microbiological problems arising from recalcitrant molecules.}, journal = {Microbial ecology}, volume = {2}, number = {1}, pages = {17-27}, pmid = {24241159}, issn = {0095-3628}, }
@article {pmid24241158, year = {1975}, author = {Pope, DH}, title = {Effects of light intensity, oxygen concentration, and carbon dioxide concentration on photosynthesis in algae.}, journal = {Microbial ecology}, volume = {2}, number = {1}, pages = {1-16}, pmid = {24241158}, issn = {0095-3628}, abstract = {The effects of various combinations of light intensity, oxygen concentration, and CO2 concentration on photosynthesis and growth in several algal types were studied. The results suggest the following. (1) Different algae show different responses to high oxygen concentrations and high light intensities. (2) Inhibition of photosynthesis (CO2 fixation and growth), if seen, increases with increasing oxygen concentration and with increasing light intensity (at light intensities greater than saturation). (3) The inhibition of net photosynthesis observed cannot be attributed to high light intensity alone. (4) The inhibition cannot be attributed to increased rates of excretion of organic materials under conditions of high oxygen concentration and high light intensity. (5) Increased concentrations of CO2 can decrease the effect of high oxygen and light in some algae. (6) The decrease in net photosynthesis observed is probably the result of photorespiration. (7) The effect of light intensity, oxygen concentration, or CO2 concentration on algal photosynthesis should not be studied without considering the effect of the other factors. Some implications of these results, as related to primary productivity measurements, are also discussed.}, }
@article {pmid24241032, year = {1974}, author = {Hauser, DC and Levandowsky, M and Hutner, SH and Chunosoff, L and Hollwitz, JS}, title = {Chemosensory responses by the heterotrophic marine dinoflagellateCrypthecodinium cohnii.}, journal = {Microbial ecology}, volume = {1}, number = {1}, pages = {246-254}, pmid = {24241032}, issn = {0095-3628}, abstract = {Chemosensory responses by the colorles inshore marine dinoflagellateCrypthecodinium cohnii were observed in quadrant-divided Petri plates containing an agar layer + liquid overlay. A suspension of organisms in salt solution was poured onto this and allowed to stand 3 hr. A differential tendency of the cells to become firmly attached or embedded in the substratum was observed when various substances were incorporated in the gel. A positive response (tendency to attach) occurred with: α-L-fucose, dimethyl-β-propiothetin, betaine, sucrose, glycine, L-alanine, hemin, and fructose; negative response: formalin, glutathione, acid hydrolyzed agar, protamine SO4, L-glutamic acid, lactose, glutamine, taurine, L-aspartic acid, putrescine 2 HCl, choline citrate, choline bitartrate, K citrate, and choline HCl. γ-Aminobutyric acid was negative or positive dependeng on concentration. Dead or immotile cells did not become attached. The following compounds elicited no response: α-D-fucose, dimethyl acetothetin chloride, cyclic AMP, and glucose.}, }
@article {pmid24241031, year = {1974}, author = {Haskå, G}, title = {Influence of clay minerals on sorption of bacteriolytic enzymes.}, journal = {Microbial ecology}, volume = {1}, number = {1}, pages = {234-245}, pmid = {24241031}, issn = {0095-3628}, abstract = {Myxobacteria presumably produce extracellular bacteriolytic enzymes when they are growing in soil. In order to study their ecological significance, adsorption experiments were performed with lytic enzymes produced byMyxococcus virescens in casitone media. Different soils as well as montmorillonite and kaolinite can rapidly adsorb the bacteriolytic but not the proteolytic enzymes. About 1 gm of montmorillonite per liter of cell-free culture solution is enough for the adsorption of 97% of the bacteriolytic enzymes. The adsorption per unit weight is about 100 times greater on montmorillonite than on kaolinite. About 40% of the adsorbed enzymes can be eluted with solutions of high pH or high ionic strength. The only desorbed bacteriolytic enzyme is the alanyl-∈-N-lysine endopeptidase.}, }
@article {pmid24241030, year = {1974}, author = {Litchfield, CD and Rake, JB and Zindulis, J and Watanabe, RT and Stein, DJ}, title = {Optimization of procedures for the recovery of heterotrophic bacteria from marine sediments.}, journal = {Microbial ecology}, volume = {1}, number = {1}, pages = {219-233}, pmid = {24241030}, issn = {0095-3628}, abstract = {A study was undertaken of the various factors affecting the recovery of heterotrophic bacteria from marine sediments. The dilution medium and culture medium were found to be of great importance in the recovery of heterotrophic colony forming units (CFU). Statistical analysis of the total viable counts obtained under the test conditions showed that artificial seawater (ASW) without further supplementation was equal to or superior to ASW plus 0.1% peptone or ASW plus 0.1% peptone and 0.1% glycerol. The addition of a surfactive agent, on the other hand, resulted in 95% inhibition of the recoverable CFU. The elapsed time (up to 12 hr) between recovery of a sedimentary core and completion of plating procedures was found to have little effect provided the sedimentary sample was removed from the core, placed in ASW, and stored in a refrigerator until actual plating occurred. It was further noted that lower organic nutrient concentrations, approximately one-tenth of those generally in use, resulted in significantly higher total viable counts. Finally, replicate contiguous sampling at three depths in a core resulted in no significant changes in the number of CFU from the surface samples, indicating a greater surface homogeneity than that previously suspected. The same pattern was not true, however, for samples obtained a lower positions in the core, thus indicating pockets of microbial concentration.}, }
@article {pmid24241029, year = {1974}, author = {Nelson, JD and Colwell, RR}, title = {The ecology of mercury-resistant bacteria in Chesapeake Bay.}, journal = {Microbial ecology}, volume = {1}, number = {1}, pages = {191-218}, pmid = {24241029}, issn = {0095-3628}, abstract = {Total ambient mercury concentrations and numbers of mercury resistant, aerobic heterotrophic bacteria at six locations in Chesapeake Bay were monitored over a 17 month period. Mercury resistance expressed as the proportion of the total, viable, aerobic, heterotrophic bacterial population reached a reproducible maximum in spring and was positively correlated with dissolved oxygen concentration and sediment mercury concentration and negatively correlated with water turbidity. A relationship between mercury resistance and metabolic capability for reduction of mercuric ion to the metallic state was established by surveying a number of HgCl2-resistant cultures. The reaction was also observed in microrganisms isolated by differential centrifugation of water and sediment samples. Mercuric ion exhibited an average half-life of 12.5 days in the presence of approximately 10(5) organisms/ml. Cultures resistant to 6 ppm of mercuric chloride and 3 ppm of phenylmercuric acetate (PMA) were classified into eight generic categories.Pseudomonas spp. were the most numerous of those bacteria capable of metabolizing both compounds; however, PMA was more toxic and was more selective forPseudomonas. The mercury-resistant generic distribution was distinct from that of the total bacterial generic distribution and differed significantly between water and sediment, positionally and seasonally. The proportion of nonglucose-utilizing mercury-resistantPsuedomonas spp. was found to be positively correlated with total bacterial mercury resistance. It is concluded from this study that numbers of mercury-resistant bacteria as established by plate count can serve as a valid index ofin situ Hg(2+) metabolism.}, }
@article {pmid24241028, year = {1974}, author = {Matsumura, P and Keller, DM and Marquis, RE}, title = {Restricted pH ranges and reduced yields for bacterial growth under pressure.}, journal = {Microbial ecology}, volume = {1}, number = {1}, pages = {176-189}, pmid = {24241028}, issn = {0095-3628}, abstract = {Hydrostatic pressure was found to cause a marked narrowing of pH ranges for growth and reductions in growth yields for a variety of bacteria. In many cases, reduced yields under pressure could be directly related to increased sensitivities to metabolic acids that accumulated in the enclosed culture vessels used. Magnesium and calcium ions partially reversed increases in sensitivities of representative gram-positive and gram-negative bacteria to low, but not high, pH. Growth inhibition of these organisms at both extremes of pH was associated with enhanced loss of K(+) from pressurized cells. Inhibited cells in alkaline media also lysed under pressure, but microscopically observable lysis was clearly a secondary phenomenon because it occurred slowly. Apparent volumes for growth-inhibitory protonation-deprotonation reactions were calculated on the basis of measured shifts in inhibitory pH with pressure. The values ranged from 99 to 431 ml/mole, and their magnitudes indicated that growth inhibition by acids or bases involves cooperative changes in polymeric interactions such as those which accompany protein denaturation.}, }
@article {pmid24241027, year = {1974}, author = {Chen, M}, title = {Kinetics of phosphorus absorption byCorynebacterium bovis.}, journal = {Microbial ecology}, volume = {1}, number = {1}, pages = {164-175}, pmid = {24241027}, issn = {0095-3628}, abstract = {The initial rate of phosphorus uptake by phosphorus-limited cells ofCorynebacterium bovis grown in batch culture and in a chemostat was measured with [(32)P] orthophosphate. It was dependent on the external phosphorus concentration and was inversely related to the amount of intracellular phosphorus. The relationship between the initial rate of uptake, intracellular phosphorus, and phosphorus concentration in the medium can be expressed in terms of Haldane's modification of the Michaelis-Menten equation.}, }
@article {pmid24241026, year = {1974}, author = {Atlas, RM and Hubbard, JS}, title = {Applicability of radiotracer methods of measuring(14)CO 2 assimilation for determining microbial activity in soil including a newin situ method.}, journal = {Microbial ecology}, volume = {1}, number = {1}, pages = {145-163}, pmid = {24241026}, issn = {0095-3628}, abstract = {The applicability of two methods (pyrolysis gas chromatography and acidification-wet oxidation) for determining(14)CO2 incorporation into soil microorganisms was investigated. Both methods were able to distinguish biologically incorporated(14)C from abiotically adsorbed(14)C, but to varying degrees, there being a larger carryover of abiotic(14)C into the organic fraction and a higher percentage of assimilated(14)C in the organic fraction with the wet oxidation method. Using(14)C assimilation as a measure, it was possible to determine microbial activities in soils of diverse properties under a variety of conditions, including polar soils under harsh environmental conditions. Both light and dark(14)CO2 fixation was measurable.(14)CO2 assimilation was not always proportional to the enumerable microorganisms. A new design for measurement of microbial activityin situ enabled measurement of total C influx (primary productivity) into soils with minimal perturbation to the natural soil ecosystem.}, }
@article {pmid24241025, year = {1974}, author = {Cox, DP and Alexander, M}, title = {Factors affecting trimethylarsine and dimethylselenide formation byCandida humicola.}, journal = {Microbial ecology}, volume = {1}, number = {1}, pages = {136-144}, pmid = {24241025}, issn = {0095-3628}, abstract = {Selenite, selenate, and tellurate inhibited the conversion of arsenate to trimethylarsine byCandida humicola. Trimethylarsine disappeared from the gas phase when incubated withC. humicola in the presence of selenium or tellurium salts. The fungus generated dimethyl-selenide from selenite and selenate and an unidentified gas from tellurate. Sulfate but not arsenate, tellurate, or phosphate inhibited the conversion of selenate to dimethylselenide. Arsenate-grown cells generated trimethylarsine from arsenate, and selenate-grown cells formed dimethylselenide from selenate with almost no lag phase. Cells grown in media with selenate or with no additions only formed the alkylarsine from arsenate after a lag phase, and those grown in solutions with arsenate or no additions produced dimethylselenide slowly from selenate.}, }
@article {pmid24241024, year = {1974}, author = {Ulitzur, S}, title = {Vibrio parahaemolyticus andVibrio alginolyticus: Short generation-time marine bacteria.}, journal = {Microbial ecology}, volume = {1}, number = {1}, pages = {127-135}, pmid = {24241024}, issn = {0095-3628}, abstract = {The growth rates of 30 different strains ofVibrio parahaemolyticus andVibrio alginolyticus at 37°C was determined. Each species consists of two major groups, one having a short generation time (12-14 min) and one with a longer generation time (20-25 min). The diversity in generation times of different strains belonging to the same species is discussed. The effect of temperature, salt, and nutrient concentrations on the growth rate of oneV. alginolyticus strain (NCMB 1803) was studied. The most striking is the effect of the temperature; at 39°C the generation time is 10-11 min, while at 21°C it is 60 min. The heat of activation for growth calculating from such data is 22,580 kcal/mole/hr(-1). The ecological significance of these results is discussed.}, }
@article {pmid24241023, year = {1974}, author = {Fuhs, GW and Chen, M}, title = {Refractive index of uranyl-treated bacterial cytoplasm as related to ribonucleic-acid content and growth rate.}, journal = {Microbial ecology}, volume = {1}, number = {1}, pages = {120-125}, pmid = {24241023}, issn = {0095-3628}, abstract = {After fixation and treatment with uranyl acetate solutions, the refractive index (n D) of the cytoplasm ofCorynebacterium bovis varies with substrate-dependent growth rate and RNA content. The effect, which presumably is due to quantitative binding of uranyl ions by RNA, permits a measurement of the growth rate of single cells in a single-species system by interference microscopy. Temperature-induced changes in growth rate are not reflected in changes ofn D or RNA content.}, }
@article {pmid24241022, year = {1974}, author = {van Gemerden, H}, title = {Coexistence of organisms competing for the same substrate: An example among the purple sulfur bacteria.}, journal = {Microbial ecology}, volume = {1}, number = {1}, pages = {104-119}, pmid = {24241022}, issn = {0095-3628}, abstract = {The purpose of this study was to find a possible explanation for the coexistence of large and small purple sulfur bacteria in natural habitats. Experiments were carried out withChromatium vinosum SMG 185 andChromatium weissei SMG 171, grown in both batch and continuous cultures. The data may be summarized as follows: (a) In continuous light, with sulfide as growth rate-limiting substrate, the specific growth rate ofChr. vinosum exceeds that ofChr. weissei regardless of the sulfide concentration employed. Consequently,Chr. weissei is unable to compete successfully and is washed out in continuous cultures. (b) With intermittant light-dark illumination, the organisms showed balanced coexistence when grown in continuous cultures. The "steady-state" abundance ofChr. vinosum was found to be positively related to the length of the light period, and that ofChr. weissei to the length of the dark period. (c) Sulfide added during darkness is rapidly oxidized on subsequent illumination, resulting in the intracellular storage of reserve substances, which are later utilized for growth. The rate of sulfide oxidation/mg cell N/hr was found to be over twice as high inChr. weissei as inChr. vinosum. The observed coexistence may be explained as follows. In the light, with both strains growing, most of the sulfide will be oxidized byChr. vinosum [see (a)]. In the dark, sulfide accumulates. On illumination, the greater part of the accumulated sulfide will be oxidized byChr. weissei [see (c)]. A changed light-dark regimen should then have the effect as observed [see (b)]. These observations suggest that intermittant illumination may, at least in part explain the observed coexistence of both types of purple sulfur bacteria in nature.}, }
@article {pmid24241021, year = {1974}, author = {Suberkropp, KF and Klug, MJ}, title = {Decomposition of deciduous leaf litter in a woodland stream : I. A. Scanning electron microscopic study.}, journal = {Microbial ecology}, volume = {1}, number = {1}, pages = {96-103}, pmid = {24241021}, issn = {0095-3628}, abstract = {Microorganisms associated with decomposing deciduous leaf litter in a woodland stream were examined by scanning electron microscopy. The use of a critical point drying method allowed the preservation of a wide variety of microorganisms as well as the decomposing litter with a minimum of distortion. The micrographs provide evidence that the aquatic hyphomycetes are the major fungal flora present during decomposition. Two distinct groups of these fungi were found during the seasonal cycle with one group occurring only in the summer while the other occurred throughout the rest of the year. The presence of all developmental stages of these organisms in the environment is considered further evidence of their active role in the decomposition of litter.}, }
@article {pmid24241020, year = {1974}, author = {Walker, JD and Colwell, RR}, title = {Microbial degradation of model petroleum at low temperatures.}, journal = {Microbial ecology}, volume = {1}, number = {1}, pages = {63-95}, pmid = {24241020}, issn = {0095-3628}, abstract = {Two areas of Chesapeake Bay, Colgate Creek in Baltimore Harbor and Eastern Bay, are presently under study, with routine sampling of water and sediment for petroleum-degrading microorganisms (bacteria, yeasts, and fungi) by direct plating and enrichment culture. Selected physical and chemical parameters are recorded for each sampling site, and water and sediment samples are extracted for hydrocarbons. Numbers of petroleum-degrading microorganisms enumerated by direct plating were found to correlate with the concentration of benzene-extractable material and were higher for the Colgate Creek than for the Eastern Bay site. Petroleum-degrading microorganisms were isolated from water and sediment samples at environmental temperatures of 0°, 5°, and 10°C.A salts medium supplemented with nitrate and phosphate was used to provide optimum conditions for petroleum degradation, whereas Chesapeake Bay water was used to simulate natural environmental conditions. Use of a model petroleum permitted quantitative measurement of utilization of individual hydrocarbons ranging in complexity from simple alkanes to polynuclear aromatic hydrocarbons. Higher growth yields and maximum hydrocarbon degradation was observed for microorganisms in the salts medium at 0°, 5°, and 10°C, although significant quantities of hydrocarbons were utilized in some samples grown in a medium for which Chesapeake Bay water was the diluent. Bacterial hydrocarbon degradation accounted for most of the model petroleum utilization at 0° and 5°C. However, oscillations of bacterial populations, with significant growth of yeasts, was observed at 10°C. Photomicroscopy and scanning electron microscopy revealed aggregates of bacteria, yeasts, and fungi associated with oil globules. From preliminary identification and classification of the hydrocarbon-utilizing bacteria, members of the generaVibrio, Aeromonas, Pseudomonas, andAcinetobacter were present in the enrichment cultures. From results of this study, it is concluded that utilization of model petroleum at low temperatures is a function of the types and numbers of microorganisms present in an original inoculum taken from the natural environment.}, }
@article {pmid24241019, year = {1974}, author = {Walsby, AE}, title = {The identification of gas vacuoles and their abundance in the hypolimnetic bacteria of Arco Lake, Minnesota.}, journal = {Microbial ecology}, volume = {1}, number = {1}, pages = {51-61}, pmid = {24241019}, issn = {0095-3628}, abstract = {Bright refractile granules in bacterial cells are identified as gas vacuoles if they disappear on application of a few atmospheres pressure. This paper describes a simple method for observing individual cells under the light microscope before and after application of pressure and the use of this method in making a comprehensive survey of gas-vacuolate organisms in a sample. In water samples from the hypolimnion of a stratified lake (Arco Lake) in Northern Minnesota, gas vacuoles were found in nearly 30 different bacteria, representing possibly 60% or more of those present. The pressure sensitivity of gas vacuoles in these organisms is illustrated by micrograph pairs. Gas vacuoles, which are otherwise uncommon in bacteria, are evidently of great selective value in the hypolimnia of stratified lakes, perhaps by regulating cell buoyancy.}, }
@article {pmid24241018, year = {1974}, author = {Fisher, NS and Carpenter, EJ and Remsen, CC and Wurster, CF}, title = {Effects of PCB on interspecific competition in natural and gnotobiotic phytoplankton communities in continuous and batch cultures.}, journal = {Microbial ecology}, volume = {1}, number = {1}, pages = {39-50}, pmid = {24241018}, issn = {0095-3628}, abstract = {The toxicity of polychlorinated biphenyls (PCB) to the diatomThalassiosira pseudonana (formerlyCyclotella nana), grown in pure and mixed cultures, was greatest when in competition with other species. Continuous cultures were superior to batch cultures for studying competitive interactions, and PCB caused greater alteration of species composition in continuous cultures than it did in batch cultures. Natural phytoplankton communities from Vineyard Sound, maintained in continuous culture, responded to PCB stress the same as did gnotobiotic communities, withT. pseudonana showing similar responses in both communities.A PCB concentration of 0.1 μg/liter (0.1 part per billion), a level not uncommon in natural waters, did not affect algal growth in pure cultures but caused substantial disruption of continuous culture communities. The possible impact of PCB pollution on natural phytoplankton communities is discussed.}, }
@article {pmid24241017, year = {1974}, author = {Wirsen, CO and Jannasch, HW}, title = {Microbial transformations of some(14)C-labeled substrates in coastal water and sediment.}, journal = {Microbial ecology}, volume = {1}, number = {1}, pages = {25-37}, pmid = {24241017}, issn = {0095-3628}, abstract = {In order to complement data obtained from earlier deep-sea studies on microbial transformations, similarin situ incubation experiments were done in shallow coastal waters. Compared to laboratory controls,in situ activities were reduced about 50%, in contrast to about 99% previously reported for samples incubated in the deep sea.}, }
@article {pmid24241016, year = {1974}, author = {Rovira, AD and Campbell, R}, title = {Scanning electron microscopy of microorganisms on the roots of wheat.}, journal = {Microbial ecology}, volume = {1}, number = {1}, pages = {15-23}, doi = {10.1007/BF02512376}, pmid = {24241016}, issn = {0095-3628}, abstract = {The scanning electron microscope was used to study the microorganisms on wheat roots grown in both soil and sand. Bacteria became common on the root surface only in the root hair region of young roots; nearer the tip of the root they were rare. Older roots had relatively high populations of bacteria. Bacteria were sometimes embedded in mucilage, of either plant or microbial origin, which seemed to bind the bacteria firmly to the root surface. Mineral grains on or near the roots of wheat were generally free of mucilage.}, }
@article {pmid24241015, year = {1974}, author = {Roper, MM and Marshall, KC}, title = {Modification of the interaction betweenEscherichia coli and bacteriophage in saline sediment.}, journal = {Microbial ecology}, volume = {1}, number = {1}, pages = {1-13}, pmid = {24241015}, issn = {0095-3628}, abstract = {The effects of sorption phenomena on the interaction between a parasite and its host bacterium have been investigated using anEscherichia coli-bacteriophage-saline sediment system. The sediment contained organic matter and a high proportion of clay, predominantly montmorillonoid. BothE. coli and phage remained firmly sorbed to saline sediments or montmorillonite, but were rapidly desorbed following dilution of the electrolyte below a critical concentration. This desorption coincided with the dispersal of sediment colloids.Escherichia coli was protected from phage attack by the presence of sediment, montmorillonite, or organic matter at salinty levels both above and below this critical point for dispersal and desorption. Evidence is presented indicating thatE. coli is protected from phage attack at low electrolyte concentrations by an envelope of sorbed colloidal materials around the cell, whereas at high electrolyte concentrations protection results both from the colloid envelope around the cells as well as from the sorption of cells and phages to solid particles. The protection ofE. coli and possibly other fecal bacteria may result in their accumulation in saline sediments, producing a possible health hazard in estuaries and lagoons if the bacteria are desorbed following dilution as a result of heavy rainfall.}, }
@article {pmid24189653, year = {2014}, author = {Cébron, A and Arsène-Ploetze, F and Bauda, P and Bertin, PN and Billard, P and Carapito, C and Devin, S and Goulhen-Chollet, F and Poirel, J and Leyval, C}, title = {Rapid impact of phenanthrene and arsenic on bacterial community structure and activities in sand batches.}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {129-144}, pmid = {24189653}, issn = {1432-184X}, mesh = {Arsenic/*chemistry ; Bacteria/classification/*isolation &amp; purification/metabolism ; Genes, Bacterial ; Metabolome ; Phenanthrenes/*chemistry ; Plant Exudates/chemistry ; Proteome ; RNA, Ribosomal, 16S/genetics ; Silicon Dioxide/chemistry ; *Soil Microbiology ; Soil Pollutants/*chemistry ; Stress, Physiological ; }, abstract = {The impact of both organic and inorganic pollution on the structure of soil microbial communities is poorly documented. A short-time batch experiment (6 days) was conducted to study the impact of both types of pollutants on the taxonomic, metabolic and functional diversity of soil bacteria. For this purpose sand spiked with phenanthrene (500 mg kg(-1) sand) or arsenic (arsenite 0.66 mM and arsenate 12.5 mM) was supplemented with artificial root exudates and was inoculated with bacteria originated from an aged PAH and heavy-metal-polluted soil. The bacterial community was characterised using bacterial strain isolation, TTGE fingerprinting and proteomics. Without pollutant, or with phenanthrene or arsenic, there were no significant differences in the abundance of bacteria and the communities were dominated by Pseudomonas and Paenibacillus genera. However, at the concentrations used, both phenanthrene or arsenic were toxic as shown by the decrease in mineralisation activities. Using community-level physiological profiles (Biolog Ecoplates™) or differential proteomics, we observed that the pollutants had an impact on the community physiology, in particular phenanthrene induced a general cellular stress response with changes in the central metabolism and membrane protein synthesis. Real-time PCR quantification of functional genes and transcripts revealed that arsenic induced the transcription of functional arsenic resistance and speciation genes (arsB, ACR3 and aioA), while no transcription of PAH-degradation genes (PAH-dioxygenase and catechol-dioxygenase) was detected with phenanthrene. Altogether, in our tested conditions, pollutants do not have a major effect on community abundance or taxonomic composition but rather have an impact on metabolic and functional bacterial properties.}, }
@article {pmid24185849, year = {2014}, author = {Lagkouvardos, I and Jehl, MA and Rattei, T and Horn, M}, title = {Signature protein of the PVC superphylum.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {2}, pages = {440-445}, pmid = {24185849}, issn = {1098-5336}, support = {281633/ERC_/European Research Council/International ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics ; Biological Evolution ; Chlamydia/*genetics ; Conserved Sequence ; Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; Planctomycetales/*genetics ; Verrucomicrobia/*genetics ; }, abstract = {The phyla Planctomycetes, Verrucomicrobia, Chlamydiae, Lentisphaerae, and "Candidatus Omnitrophica (OP3)" comprise bacteria that share an ancestor but show highly diverse biological and ecological features. Together, they constitute the PVC superphylum. Using large-scale comparative genome sequence analysis, we identified a protein uniquely shared among all of the known members of the PVC superphylum. We provide evidence that this signature protein is expressed by representative members of the PVC superphylum. Its predicted structure, physicochemical characteristics, and overexpression in Escherichia coli and gel retardation assays with purified signature protein suggest a housekeeping function with unspecific DNA/RNA binding activity. Phylogenetic analysis demonstrated that the signature protein is a suitable phylogenetic marker for members of the PVC superphylum, and the screening of published metagenome data indicated the existence of additional PVC members. This study provides further evidence of a common evolutionary history of the PVC superphylum and presents a unique case in which a single protein serves as an evolutionary link among otherwise highly diverse members of major bacterial groups.}, }
@article {pmid24180241, year = {2013}, author = {Poehlein, A and Daniel, R and Schink, B and Simeonova, DD}, title = {Life based on phosphite: a genome-guided analysis of Desulfotignum phosphitoxidans.}, journal = {BMC genomics}, volume = {14}, number = {1}, pages = {753}, pmid = {24180241}, issn = {1471-2164}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/metabolism ; Carbon Dioxide/metabolism ; Deltaproteobacteria/*genetics/metabolism ; Energy Metabolism ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Lyases/genetics/metabolism ; Molecular Sequence Data ; Multigene Family ; Nitrogen/metabolism ; Phosphites/chemistry/*metabolism ; Proton-Translocating ATPases/chemistry/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sulfur/metabolism ; }, abstract = {BACKGROUND: The Delta-Proteobacterium Desulfotignum phosphitoxidans is a type strain of the genus Desulfotignum, which comprises to date only three species together with D. balticum and D. toluenicum. D. phosphitoxidans oxidizes phosphite to phosphate as its only source of electrons, with either sulfate or CO2 as electron acceptor to gain its metabolic energy, which is of exclusive interest. Sequencing of the genome of this bacterium was undertaken to elucidate the genomic basis of this so far unique type of energy metabolism.<br><br>RESULTS: The genome contains 4,998,761 base pairs and 4646 genes of which 3609 were assigned to a function, and 1037 are without function prediction. Metabolic reconstruction revealed that most biosynthetic pathways of Gram negative, autotrophic sulfate reducers were present. Autotrophic CO2 assimilation proceeds through the Wood-Ljungdahl pathway. Additionally, we have found and confirmed the ability of the strain to couple phosphite oxidation to dissimilatory nitrate reduction to ammonia, which in itself is a new type of energy metabolism. Surprisingly, only two pathways for uptake, assimilation and utilization of inorganic and organic phosphonates were found in the genome. The unique for D. phosphitoxidans Ptx-Ptd cluster is involved in inorganic phosphite oxidation and an atypical C-P lyase-coding cluster (Phn) is involved in utilization of organophosphonates.<br><br>CONCLUSIONS: We present the whole genome sequence of the first bacterium able to gain metabolic energy via phosphite oxidation. The data obtained provide initial information on the composition and architecture of the phosphite-utilizing and energy-transducing systems needed to live with phosphite as an unusual electron donor.}, }
@article {pmid24173537, year = {2014}, author = {Pylro, VS and Roesch, LF and Ortega, JM and do Amaral, AM and Tótola, MR and Hirsch, PR and Rosado, AS and Góes-Neto, A and da Costa da Silva, AL and Rosa, CA and Morais, DK and Andreote, FD and Duarte, GF and de Melo, IS and Seldin, L and Lambais, MR and Hungria, M and Peixoto, RS and Kruger, RH and Tsai, SM and Azevedo, V and , }, title = {Brazilian Microbiome Project: revealing the unexplored microbial diversity--challenges and prospects.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {237-241}, pmid = {24173537}, issn = {1432-184X}, mesh = {Advisory Committees/*organization &amp; administration ; Animals ; *Biodiversity ; Brazil ; Databases, Factual ; *Metagenome ; *Microbiota ; Plants/microbiology ; Soil Microbiology ; }, abstract = {The Brazilian Microbiome Project (BMP) aims to assemble a Brazilian Metagenomic Consortium/Database. At present, many metagenomic projects underway in Brazil are widely known. Our goal in this initiative is to co-ordinate and standardize these together with new projects to come. It is estimated that Brazil hosts approximately 20 % of the entire world's macroorganism biological diversity. It is 1 of the 17 countries that share nearly 70 % of the world's catalogued animal and plant species, and is recognized as one of the most megadiverse countries. At the end of 2012, Brazil has joined GBIF (Global Biodiversity Information Facility), as associated member, to improve the access to the Brazilian biodiversity data in a free and open way. This was an important step toward increasing international collaboration and clearly shows the commitment of the Brazilian government in directing national policies toward sustainable development. Despite its importance, the Brazilian microbial diversity is still considered to be largely unknown, and it is clear that to maintain ecosystem dynamics and to sustainably manage land use, it is crucial to understand the biological and functional diversity of the system. This is the first attempt to collect and collate information about Brazilian microbial genetic and functional diversity in a systematic and holistic manner. The success of the BMP depends on a massive collaborative effort of both the Brazilian and international scientific communities, and therefore, we invite all colleagues to participate in this project.}, }
@article {pmid24169949, year = {2014}, author = {Wang, YF and Li, XY and Gu, JD}, title = {Differential responses of ammonia/ammonium-oxidizing microorganisms in mangrove sediment to amendment of acetate and leaf litter.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {7}, pages = {3165-3180}, doi = {10.1007/s00253-013-5318-7}, pmid = {24169949}, issn = {1432-0614}, mesh = {Acetates/*metabolism ; Ammonia/*metabolism ; Ammonium Compounds/*metabolism ; Archaea/classification/genetics/*growth &amp; development/metabolism ; Bacteria/classification/genetics/*growth &amp; development/metabolism ; Biota ; Cluster Analysis ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; Plant Leaves/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The effects of acetate and leaf litter powder on ammonia/ammonium-oxidizing microorganisms (AOMs) in mangrove sediment were investigated in a laboratory incubation study for a period of 60 days. The results showed that different AOMs responded differently to the addition of acetate and leaf litter. A higher diversity of anaerobic ammonium-oxidizing (anammox) bacteria was observed when acetate or leaf litter was added than the control. However, acetate and leaf litter generally inhibited the growth of anammox bacteria despite that leaf litter promoted their growth in the first 5 days. The inhibitory effects on anammox bacteria were more pronounced by acetate than by leaf litter. Neither acetate nor leaf litter affected ammonia-oxidizing archaea (AOA) community structures, but promoted their growth. For ammonia-oxidizing bacteria (AOB), the addition of acetate or leaf litter resulted in changes of community structures and promoted their growth in the early phase of the incubation. In addition, the promoting effects by leaf litter on AOB growth were more obvious than acetate. These results indicated that organic substances affect AOM community structures and abundances. The study suggests that leaf litter has an important influence on the community structures and abundances of AOMs in mangrove sediment and affects the nitrogen cycle in such ecosystem.}, }
@article {pmid24164959, year = {2014}, author = {Zaman, C and Osaki, T and Hanawa, T and Yonezawa, H and Kurata, S and Kamiya, S}, title = {Analysis of the microbial ecology between Helicobacter pylori and the gastric microbiota of Mongolian gerbils.}, journal = {Journal of medical microbiology}, volume = {63}, number = {Pt 1}, pages = {129-137}, doi = {10.1099/jmm.0.061135-0}, pmid = {24164959}, issn = {1473-5644}, mesh = {Animals ; Antibiosis ; Disease Models, Animal ; Female ; Gerbillinae/*microbiology ; Helicobacter Infections/*microbiology ; Helicobacter pylori/*growth &amp; development ; Lactobacillus/*growth &amp; development ; Stomach/*microbiology ; }, abstract = {Animal models are essential for in vivo analysis of Helicobacter-related diseases. Mongolian gerbils are used frequently to study Helicobacter pylori-induced gastritis and its consequences. The presence of some gastric microbiota with a suppressive effect on H. pylori suggests inhibitory gastric bacteria against H. pylori infection. The aim of the present study was to analyse the microbial ecology between H. pylori and the gastric microbiota of Mongolian gerbils. Gastric mucosa samples of H. pylori-negative and -positive gerbils were orally inoculated to five (Group 1) and six (Group 2) gerbils, respectively, and the gerbils were challenged with H. pylori infection. The colonization rate (40 %) of H. pylori in Group 1 gerbils was lower than the rate (67 %) in Group 2 gerbils. Culture filtrate of the gastric mucosa samples of Group 1 gerbils inhibited the in vitro growth of H. pylori. Three lactobacilli species, Lactobacillus reuteri, Lactobacillus johnsonii and Lactobacillus murinus, were isolated by anaerobic culture from the gerbils in Groups 1 and 2, and identified by genomic sequencing. It was demonstrated that the three different strains of lactobacilli exhibited an inhibitory effect on the in vitro growth of H. pylori. The results suggested that lactobacilli are the dominant gastric microbiota of Mongolian gerbils and the three lactobacilli isolated from the gastric mucosa samples with an inhibitory effect on H. pylori might have an anti-infective effect against H. pylori.}, }
@article {pmid24161806, year = {2013}, author = {Magrí, A and Béline, F and Dabert, P}, title = {Feasibility and interest of the anammox process as treatment alternative for anaerobic digester supernatants in manure processing--an overview.}, journal = {Journal of environmental management}, volume = {131}, number = {}, pages = {170-184}, doi = {10.1016/j.jenvman.2013.09.021}, pmid = {24161806}, issn = {1095-8630}, mesh = {Anaerobiosis ; Bioreactors/microbiology ; Nitrogen/metabolism ; Waste Disposal, Fluid/*methods ; }, abstract = {Completely autotrophic nitrogen removal (ANR) is based on the combination of partial nitritation (PN) and anaerobic ammonium oxidation (anammox). It is a promising alternative for the subsequent treatment of biogas digester supernatants in livestock manure processing and nitrogen surplus scenarios. However, as no full-scale experiences in the treatment of manure digestates by ANR have been published to date, future field studies addressing treatment of this kind of effluent would be of great interest. Some topics to be considered in these studies would be coupling anaerobic digestion and ANR, analysis of the factors that affect the process, comparing reactor configurations, microbial ecology, gas emissions, and achieving robust performance. This paper provides an overview of published studies on ANR. Specific issues related to the applicability of the process for treating manure digestates are discussed. The energy requirements of ANR are compared with those of other technological alternatives aimed at recovering nitrogen from digester supernatants. The results of the assessment were shown to depend on the composition of the supernatant. In this regard, the PN-anammox process was shown to be more competitive than other alternatives particularly at concentrations of up to 2 kg NH4(+)-N m(-3).}, }
@article {pmid24159324, year = {2013}, author = {Hardoim, CC and Cox, CJ and Peixoto, RS and Rosado, AS and Costa, R and van Elsas, JD}, title = {Diversity of the candidate phylum Poribacteria in the marine sponge Aplysina fulva.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {44}, number = {1}, pages = {329-334}, pmid = {24159324}, issn = {1517-8382}, abstract = {Poribacterial clone libraries constructed for Aplysina fulva sponge specimens were analysed with respect to diversity and phylogeny. Results imply the coexistence of several, prevalently "intra-specific" poribacterial genotypes in a single sponge host, and suggest quantitative analysis as a desirable approach in studies of the diversity and distribution of poribacterial cohorts in marine sponges.}, }
@article {pmid24158690, year = {2014}, author = {Rehnstam-Holm, AS and Atnur, V and Godhe, A}, title = {Defining the niche of Vibrio parahaemolyticus during pre- and post-monsoon seasons in the coastal Arabian Sea.}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {57-65}, pmid = {24158690}, issn = {1432-184X}, mesh = {*Ecosystem ; Food Chain ; India ; Models, Biological ; Real-Time Polymerase Chain Reaction ; Salinity ; *Seasons ; Seawater/microbiology ; Temperature ; Vibrio parahaemolyticus/*growth &amp; development ; *Water Microbiology ; }, abstract = {The bacteria Vibrio parahaemolyticus is an important component of coastal ecosystems worldwide, and in recent years, V. parahaemolyticus has caused several cases of food-borne gastroenteritis. However, research investigating which parameters are important in regulating V. parahaemolyticus abundance in tropical areas with relatively stable temperatures and salinity are largely lacking. The objective here was to investigate which environmental forces are driving elevated abundances of V. parahaemolyticus in a tropical oligotrophic coastal area in the Arabian Sea. We analysed a large number of environmental parameters in parallel with cell densities of V. parahaemolyticus and Vibrio spp. Abundance data was obtained using real-time PCR, during two different sampling periods, representative for two distinct seasons. Water temperature and salinity were stable during and between sampling periods, but V. parahaemolyticus abundances were on average six times higher during the first sampling period in December, compared to the second period in February-March. V. parahaemolyticus abundance was found to be positively correlated to inorganic phosphate concentration and copepod abundance. We thus hypothesise that these are important factors regulating V. parahaemolyticus abundance in coastal tropical areas during these periods.}, }
@article {pmid24158689, year = {2014}, author = {Zaccone, R and Azzaro, M and Azzaro, F and Bergamasco, A and Caruso, G and Leonardi, M and La Ferla, R and Maimone, G and Mancuso, M and Monticelli, LS and Raffa, F and Crisafi, E}, title = {Seasonal dynamics of prokaryotic abundance and activities in relation to environmental parameters in a transitional aquatic ecosystem (Cape Peloro, Italy).}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {45-56}, pmid = {24158689}, issn = {1432-184X}, mesh = {Alkaline Phosphatase/metabolism ; Carbon/chemistry ; *Ecosystem ; *Heterotrophic Processes ; Italy ; Lakes/microbiology ; Leucyl Aminopeptidase/metabolism ; Nitrogen/chemistry ; Salinity ; *Seasons ; Temperature ; Vibrio/*growth &amp; development ; *Water Microbiology ; beta-Glucosidase/metabolism ; }, abstract = {This study examines the effects of temporal changes on microbial parameters in a brackish aquatic ecosystem. To this aim, the abundances of prokaryotes and vibrios together with the rates of enzymatic hydrolysis of proteins by leucine aminopeptidase (LAP), polysaccharides by β-glucosidase (GLU) and organic phosphates by alkaline phosphatase (AP), heterotrophic prokaryotic production (HPP), respiration (R), were seasonally investigated, during a 2-year period in the coastal area of Cape Peloro (Messina, Italy), constituted by two brackish lakes (Faro and Ganzirri). In addition, physical and chemical parameters (temperature, salinity, nutrients) and particulate organic carbon and nitrogen (POC, PN) were measured. The influence of multiple factors on prokaryotic abundances and activities was analysed. The results showed that Cape Peloro area is characterised by high seasonal variability of the microbial parameters that is higher than the spatial one. Combined changes in particulate matter and temperature (T), could explain the variability in vibrios abundance, GLU and R activities in both lakes, indicating a direct stimulation of the warm season on the heterotrophic prokaryotic metabolism. Positive correlations between T (from 13.3 to 29.6 °C) and HPP, LAP, AP, POC, PN are also observed in Ganzirri Lake. Moreover, the trophic status index and most of the microbial parameters show significant seasonal differences. This study demonstrates that vibrios abundance and microbial activities are responsive to the spatial and seasonal changes of examined area. The combined effects of temperature and trophic conditions on the microbial parameters lead us to suggest their use as potential indicators of the prokaryotic response to climate changes in temperate brackish areas.}, }
@article {pmid24158688, year = {2014}, author = {Cortés-Pérez, S and Rodríguez-Zaragoza, S and Mendoza-López, MR}, title = {Trophic structure of amoeba communities near roots of Medicago sativa after contamination with fuel oil no. 6.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {430-442}, pmid = {24158688}, issn = {1432-184X}, mesh = {Amoeba/growth &amp; development/*isolation &amp; purification ; Biodegradation, Environmental ; Environmental Pollution/analysis ; Fuel Oils/analysis ; Hydrocarbons/chemistry ; Medicago sativa/*microbiology ; Plant Roots/*microbiology ; Soil Pollutants/analysis ; }, abstract = {Root exudation increases microbial activity, selecting bacterial and fungal communities that metabolize organic matter such as hydrocarbons. However, a strong contamination pulse of hydrocarbons around plant roots may reorganize the soil's microbial trophic structure toward amoebae feeding on bacteria. We conducted a microcosm experiment to elucidate the effect of Medicago sativa on the trophic structure of naked amoebae after a strong pulse of pollution (50,000 ppm of fuel oil no. 6, which is a mixture of long chains ranging from C10 to C28). Plants were seeded 24 h after contamination and species of amoebae in the microcosms were identified at 1, 30, and 60 days after pollution. Several species from three trophic groups of naked amoeba were still alive 24 h after the hydrocarbon pulse. Non-planted microcosms harbored three trophic groups after 60 days, while planted ones nourished four groups. The bacterivore group was the most diverse in all microcosms, followed by protist-eaters and omnivores. The quantity of amoebae was significantly higher (3.4×10(3) organisms/g soil) in the planted pots than in the non-planted ones (1.3×10(3) organisms/g soil after 30 days of pollution (P ≤ 0.01). The shortest hydrocarbon chains (C10-C14) disappeared or diminished in all microcosms, and the longest ones increased in the planted ones. M. sativa thus exerted a positive effect on species richness, quantity, and the composition of amoebae trophic groups in contaminated soil. This indirect effect on bacterial predators is another key factor underlying hydrocarbon assimilation by living organisms during phytoremediation.}, }
@article {pmid24152720, year = {2014}, author = {Kinkel, LL and Schlatter, DC and Xiao, K and Baines, AD}, title = {Sympatric inhibition and niche differentiation suggest alternative coevolutionary trajectories among Streptomycetes.}, journal = {The ISME journal}, volume = {8}, number = {2}, pages = {249-256}, pmid = {24152720}, issn = {1751-7370}, mesh = {Anti-Bacterial Agents/pharmacology ; *Antibiosis ; *Biological Evolution ; *Ecosystem ; Phenotype ; *Soil Microbiology ; Streptomycetaceae/drug effects/*physiology ; }, abstract = {Soil bacteria produce a diverse array of antibiotics, yet our understanding of the specific roles of antibiotics in the ecological and evolutionary dynamics of microbial interactions in natural habitats remains limited. Here, we show a significant role for antibiotics in mediating antagonistic interactions and nutrient competition among locally coexisting Streptomycete populations from soil. We found that antibiotic inhibition is significantly more intense among sympatric than allopatric Streptomycete populations, indicating local selection for inhibitory phenotypes. For sympatric but not allopatric populations, antibiotic inhibition is significantly positively correlated with niche overlap, indicating that inhibition is targeted toward bacteria that pose the greatest competitive threat. Our results support the hypothesis that antibiotics serve as weapons in mediating local microbial interactions in soil and suggest that coevolutionary niche displacement may reduce the likelihood of an antibiotic arms race. Further insight into the diverse roles of antibiotics in microbial ecology and evolution has significant implications for understanding the persistence of antibiotic inhibitory and resistance phenotypes in environmental microbes, optimizing antibiotic drug discovery and developing strategies for managing microbial coevolutionary dynamics to enhance inhibitory phenotypes.}, }
@article {pmid24152321, year = {2014}, author = {Martinez, AJ and Weldon, SR and Oliver, KM}, title = {Effects of parasitism on aphid nutritional and protective symbioses.}, journal = {Molecular ecology}, volume = {23}, number = {6}, pages = {1594-1607}, doi = {10.1111/mec.12550}, pmid = {24152321}, issn = {1365-294X}, mesh = {Animals ; Aphids/genetics/*microbiology/*parasitology/physiology ; Bacterial Toxins/genetics ; Bacteriophages/physiology ; Buchnera/*physiology ; Enterobacteriaceae/*physiology/virology ; Genes, Bacterial ; Genotype ; Molecular Sequence Data ; *Symbiosis ; *Wasps ; }, abstract = {Insects often carry heritable symbionts that negotiate interactions with food plants or natural enemies. All pea aphids, Acyrthosiphon pisum, require infection with the nutritional symbiont Buchnera, and many are also infected with Hamiltonella, which protects against the parasitoid Aphidius ervi. Hamiltonella-based protection requires bacteriophages called APSEs with protection levels varying by strain and associated APSE. Endoparasitoids, including A. ervi, may benefit from protecting the nutritional symbiosis and suppressing the protective one, while the aphid and its heritable symbionts have aligned interests when attacked by the wasp. We investigated the effects of parasitism on the abundance of aphid nutritional and protective symbionts. First, we determined strength of protection associated with multiple symbiont strains and aphid genotypes as these likely impact symbiont responses. Unexpectedly, some A. pisum genotypes cured of facultative symbionts were resistant to parasitism and resistant aphid lines carried Hamiltonella strains that conferred no additional protection. Susceptible aphid clones carried protective strains. qPCR estimates show that parasitism significantly influenced both Buchnera and Hamiltonella titres, with multiple factors contributing to variation. In susceptible lines, parasitism led to increases in Buchnera near the time of larval wasp emergence consistent with parasite manipulation, but effects were variable in resistant lines. Parasitism also resulted in increases in APSE and subsequent decreases in Hamiltonella, and we discuss how this response may relate to the protective phenotype. In summary, we show that parasitism alters the within-host ecology of both nutritional and protective symbioses with effects likely significant for all players in this antagonistic interaction.}, }
@article {pmid24152143, year = {2013}, author = {Brzychczy-Wloch, M and Gorska, S and Brzozowska, E and Gamian, A and Heczko, PB and Bulanda, M}, title = {Identification of high immunoreactive proteins from Streptococcus agalactiae isolates recognized by human serum antibodies.}, journal = {FEMS microbiology letters}, volume = {349}, number = {1}, pages = {61-70}, doi = {10.1111/1574-6968.12292}, pmid = {24152143}, issn = {1574-6968}, mesh = {Antibodies, Bacterial/blood/*metabolism ; Antigens, Bacterial/genetics/*immunology ; Chromatography, Liquid ; Electrophoresis, Polyacrylamide Gel ; Humans ; Streptococcus agalactiae/genetics/*immunology ; Tandem Mass Spectrometry ; }, abstract = {The aim of the studies was to identify immunogenic proteins of Streptococcus agalactiae (group B streptococcus; GBS) isolates. Investigation of the immunoreactivity with human sera allowed us to determine major immunogenic proteins which might be potential candidates for the development of vaccine. For the study, we have selected 60 genetically different, well-characterized GBS clinical isolates. The proteins immunoreactivity with 24 human sera from patients with GBS infections, carriers, and control group without GBS was detected by SDS-PAGE and Western blotting. As a result, some major immunogenic proteins were identified, of which four proteins with molecular masses of about 45 to 50 kDa, which exhibited the highest immunoreactivity features, were analyzed by LC-MS/MS. The proteins were identified by comparative analysis of peptides masses using MASCOT and statistical analysis. The results showed known molecules such as enolase (47.4 kDa), aldehyde dehydrogenase (50.6 kDa), and ones not previously described such as trigger factor (47 kDa) and elongation factor Tu (44 kDa). The preliminary results indicated that some GBS proteins that elicit protective immunity hold promise not only as components in a vaccine as antigens but also as carriers or adjuvants in polysaccharide conjugate vaccines, but more studies are needed.}, }
@article {pmid24148100, year = {2014}, author = {Briggs, BR and Brodie, EL and Tom, LM and Dong, H and Jiang, H and Huang, Q and Wang, S and Hou, W and Wu, G and Huang, L and Hedlund, BP and Zhang, C and Dijkstra, P and Hungate, BA}, title = {Seasonal patterns in microbial communities inhabiting the hot springs of Tengchong, Yunnan Province, China.}, journal = {Environmental microbiology}, volume = {16}, number = {6}, pages = {1579-1591}, doi = {10.1111/1462-2920.12311}, pmid = {24148100}, issn = {1462-2920}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; China ; Genes, Archaeal ; Genes, Bacterial ; Geologic Sediments/microbiology ; Hot Springs/*microbiology ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; *Water Microbiology ; }, abstract = {Studies focusing on seasonal dynamics of microbial communities in terrestrial and marine environments are common; however, little is known about seasonal dynamics in high-temperature environments. Thus, our objective was to document the seasonal dynamics of both the physicochemical conditions and the microbial communities inhabiting hot springs in Tengchong County, Yunnan Province, China. The PhyloChip microarray detected 4882 operational taxonomic units (OTUs) within 79 bacterial phylum-level groups and 113 OTUs within 20 archaeal phylum-level groups, which are additional 54 bacterial phyla and 11 archaeal phyla to those that were previously described using pyrosequencing. Monsoon samples (June 2011) showed increased concentrations of potassium, total organic carbon, ammonium, calcium, sodium and total nitrogen, and decreased ferrous iron relative to the dry season (January 2011). At the same time, the highly ordered microbial communities present in January gave way to poorly ordered communities in June, characterized by higher richness of Bacteria, including microbes related to mesophiles. These seasonal changes in geochemistry and community structure are likely due to high rainfall influx during the monsoon season and indicate that seasonal dynamics occurs in high-temperature environments experiencing significant changes in seasonal recharge. Thus, geothermal environments are not isolated from the surrounding environment and seasonality affects microbial ecology.}, }
@article {pmid24147109, year = {2013}, author = {Carroll, IM and Ringel-Kulka, T and Ferrier, L and Wu, MC and Siddle, JP and Bueno, L and Ringel, Y}, title = {Fecal protease activity is associated with compositional alterations in the intestinal microbiota.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e78017}, pmid = {24147109}, issn = {1932-6203}, support = {DK084294/DK/NIDDK NIH HHS/United States ; K01 DK092330/DK/NIDDK NIH HHS/United States ; DK092330/DK/NIDDK NIH HHS/United States ; K23 DK075621/DK/NIDDK NIH HHS/United States ; DK075621/DK/NIDDK NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; R03 DK084294/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; DNA, Bacterial/genetics ; Feces/*enzymology/microbiology ; Female ; Humans ; Intestines/*microbiology ; Lactobacillales/genetics/physiology ; Male ; Peptide Hydrolases/*metabolism ; RNA, Ribosomal, 16S/genetics ; Streptococcaceae/genetics/physiology ; }, abstract = {OBJECTIVE: Intestinal proteases carry out a variety of functions in the gastrointestinal (GI) tract. Studies have reported that elevated enteric proteases in patients with GI disease can alter intestinal physiology, however the origin (human vs. microbial) of elevated proteases in patients with GI disease is unclear.<br><br>AIM: The aim of this study was to investigate the association between protease activity and the microbiota in human fecal samples.<br><br>DESIGN: In order to capture a wide range of fecal protease (FP) activity stool samples were collected from 30 IBS patients and 24 healthy controls. The intestinal microbiota was characterized using 454 high throughput pyro-sequencing of the 16S rRNA gene. The composition and diversity of microbial communities were determined and compared using the Quantitative Insights Into Microbial Ecology (QIIME) pipeline. FP activity levels were determined using an ELISA-based method. FP activity was ranked and top and bottom quartiles (n=13 per quartile) were identified as having high and low FP activity, respectively.<br><br>RESULTS: The overall diversity of the intestinal microbiota displayed significant clustering separation (p = 0.001) between samples with high vs. low FP activity. The Lactobacillales, Lachnospiraceae, and Streptococcaceae groups were positively associated with FP activity across the entire study population, whilst the Ruminococcaceae family and an unclassified Coriobacteriales family were negatively associated with FP activity.<br><br>CONCLUSIONS: These data demonstrate significant associations between specific intestinal bacterial groups and fecal protease activity and provide a basis for further causative studies investigating the role of enteric microbes and GI diseases.}, }
@article {pmid24141944, year = {2014}, author = {Meyer, A and Focks, A and Radl, V and Welzl, G and Schöning, I and Schloter, M}, title = {Influence of land use intensity on the diversity of ammonia oxidizing bacteria and archaea in soils from grassland ecosystems.}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {161-166}, pmid = {24141944}, issn = {1432-184X}, mesh = {Agriculture/methods ; Ammonia/*metabolism ; Archaea/*classification/metabolism ; Bacteria/*classification/metabolism ; Ecosystem ; Fertilizers ; Germany ; Nitrification ; Oxidoreductases/genetics ; *Phylogeny ; Poaceae ; Polymorphism, Restriction Fragment Length ; Seasons ; *Soil Microbiology ; }, abstract = {In the present study, the influence of the land use intensity on the diversity of ammonia oxidizing bacteria (AOB) and archaea (AOA) in soils from different grassland ecosystems has been investigated in spring and summer of the season (April and July). Diversity of AOA and AOB was studied by TRFLP fingerprinting of amoA amplicons. The diversity from AOB was low and dominated by a peak that could be assigned to Nitrosospira. The obtained profiles for AOB were very stable and neither influenced by the land use intensity nor by the time point of sampling. In contrast, the obtained patterns for AOA were more complex although one peak that could be assigned to Nitrosopumilus was dominating all profiles independent from the land use intensity and the sampling time point. Overall, the AOA profiles were much more dynamic than those of AOB and responded clearly to the land use intensity. An influence of the sampling time point was again not visible. Whereas AOB profiles were clearly linked to potential nitrification rates in soil, major TRFs from AOA were negatively correlated to DOC and ammonium availability and not related to potential nitrification rates.}, }
@article {pmid24141943, year = {2014}, author = {Kramarsky-Winter, E and Arotsker, L and Rasoulouniriana, D and Siboni, N and Loya, Y and Kushmaro, A}, title = {The possible role of cyanobacterial filaments in coral black band disease pathology.}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {177-185}, pmid = {24141943}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology/ultrastructure ; Cyanobacteria/classification/*pathogenicity ; DNA, Bacterial/genetics ; Indian Ocean ; Microscopy, Electron, Transmission ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Black band disease (BBD), characterized by a black mat or line that migrates across a coral colony leaving behind it a bare skeleton, is a persistent disease affecting massive corals worldwide. Previous microscopic and molecular examination of this disease in faviid corals from the Gulf of Eilat revealed a number of possible pathogens with the most prominent being a cyanobacterium identified as Pseudoscillatoria coralii. We examined diseased coral colonies using histopathological and molecular methods in order to further assess the possible role of this cyanobacterium, its mode of entry, and pathological effects on the coral host tissues. Affected areas of colonies with BBD were sampled for examination using both light and transmission electron microscopies. Results showed that this dominant cyanobacterium was found on the coral surface, at the coral-skeletal interface, and invading the polyp tissues and gastrovascular cavity. Although tissues surrounding the invasive cyanobacterial filaments did not show gross morphological alterations, microscopic examination revealed that the coral cells surrounding the lesion were dissociated, necrotic, and highly vacuolated. No amoebocytes were evident in the mesoglea of affected tissues suggesting a possible repression of the coral immune response. Morphological and molecular similarity of the previously isolated BBD-associated cyanobacterium P. coralii to the current samples strengthens the premise that this species is involved in the disease in this coral. These results indicate that the cyanobacteria may play a pivotal role in this disease and that the mode of entry may be via ingestion, penetrating the coral via the gastrodermis, as well as through the skeletal-tissue interface.}, }
@article {pmid24141942, year = {2014}, author = {Pérez, J and Galán, J and Descals, E and Pozo, J}, title = {Effects of fungal inocula and habitat conditions on alder and eucalyptus leaf litter decomposition in streams of northern Spain.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {245-255}, pmid = {24141942}, issn = {1432-184X}, mesh = {Alnus/*microbiology ; Biodiversity ; Ecosystem ; Eucalyptus/*microbiology ; Mitosporic Fungi/isolation &amp; purification/*metabolism ; Plant Leaves/microbiology ; Rivers/*microbiology ; Spain ; Spores, Fungal/metabolism ; Water/chemistry ; *Water Microbiology ; }, abstract = {We investigated how fungal decomposer (aquatic hyphomycetes) communities colonizing alder and eucalyptus leaf litter respond to changes in habitat characteristics (transplantation experiment). We examined the breakdown of leaf materials and the associated fungal communities at two contrasting sites, a headwater stream (H) and a midreach (M). Agroforestry increased from headwater to midreach. One month after the start of experiments at both sites, some leaf samples from the midreach site were transplanted to the headwater site (M-H treatment). Although both sites showed similar dissolved inorganic nutrient concentrations, eucalyptus leaves initially incubated at the midreach site (M, M-H) increased their breakdown rate compared to those incubated along the experiment at the headwater site (H). Alder breakdown rate was not enhanced, suggesting that their consumption was not limited by nutrient availability. Sporulation rates clearly differed between leaf types (alder > eucalyptus) and streams (H > M), but no transplantation effect was detected. When comparing conidial assemblages after transplantation, an inoculum effect (persistence of early colonizing species) was clear in both leaf species. Substrate preference and shifts in the relative importance of some fungal species along the process were also observed. Overall, our results support the determining role of the initial conditioning phase on the whole litter breakdown process, highlighting the importance of intrinsic leaf characteristics and those of the incubation habitat.}, }
@article {pmid24141941, year = {2014}, author = {Dickerson, TL and Williams, HN}, title = {Functional diversity of bacterioplankton in three North Florida freshwater lakes over an annual cycle.}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {34-44}, pmid = {24141941}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/growth &amp; development ; Denaturing Gradient Gel Electrophoresis ; Florida ; Fresh Water/*microbiology ; Lakes ; Metabolome ; *Phylogeny ; Plankton/*classification/genetics/growth &amp; development ; Seasons ; Water Microbiology ; }, abstract = {The phylogenetic diversity of freshwater bacterioplankton is widely known; however, there is minimal information on the functional diversity of the bacterial communities in these systems. Understanding the functional diversity of freshwater bacterial communities is important because heterotrophic bacteria can be impacted by anthropogenic perturbation, which in turn can alter biogeochemical cycling. The objective of this study was to use Biolog EcoPlates to acquire spatial and temporal community-level physiological profiles (CLPPs) for three freshwater lakes of different trophic levels and to assess the phylogenetic affiliation of the bacteria responsible for utilizing the various carbon guilds within them by denaturing gradient gel electrophoresis (DGGE). CLPP results showed that bacterial communities utilized the carbon guilds similarly between sites within the three lakes. However, when the metabolic profile of each lake was compared, Lake Bradford and Moore Lake were more similar to one another than to Lake Munson, the eutrophic lake. Additionally, although the bacteria that utilized the five carbon guilds included representatives from the classes α-, β-, γ-Proteobacteria, Flavobacteria and Sphingobacteria, Lake Munson had the largest number of Flavobacteria and γ-Proteobacteria in comparison to Moore Lake and Lake Bradford. Overall, Biolog analysis was useful in identifying differences in the functional diversity of bacterial communities between lakes of different trophic statuses and can be used as a tool to assess ecosystem health.}, }
@article {pmid24141940, year = {2014}, author = {Dojani, S and Kauff, F and Weber, B and Büdel, B}, title = {Genotypic and phenotypic diversity of cyanobacteria in biological soil crusts of the Succulent Karoo and Nama Karoo of southern Africa.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {286-301}, pmid = {24141940}, issn = {1432-184X}, mesh = {Africa, Southern ; Biodiversity ; Cloning, Molecular ; Cyanobacteria/*classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Ecosystem ; *Genotype ; *Phenotype ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Biological soil crusts (BSCs) are communities of cryptogamic organisms, occurring in arid and semiarid regions all over the world. Based on both morphological identification and genetic analyses, we established a first cyanobacterial inventory using the biphasic approach for BSCs within two major biomes of southern Africa. The samples were collected at two different sites in the Succulent Karoo and one in the Nama Karoo. After cultivation and morphological identification, the 16S rRNA gene was sequenced from the cyanobacterial cultures. From the soil samples, the DNA was extracted, and the 16S rRNA gene sequenced. All the sequences of the clone libraries from soil and cultures were compared with those of the public databases. Forty-five different species were morphologically identified in the samples of the Succulent Karoo (observatories of Soebatsfontein and Goedehoop). Based on the genetic analyses, 60 operational taxonomic units (OTUs) were identified for the Succulent Karoo and 43 for the Nama Karoo (based on 95% sequence similarity). The cloned sequences corresponded well with the morphologically described taxa in cultures and sequences in the public databases. Besides known species of typical crust-forming cyanobacterial genera (Microcoleus, Phormidium, Tolypothrix and Scytonema), we found sequences of so far undescribed species of the genera Leptolyngbya, Pseudanabaena, Phormidium, Oscillatoria, Schizothrix and Microcoleus. Most OTUs were restricted to distinct sites. Grazed soils showed lower taxa numbers than undisturbed soils, implying the presence of early successional crust types and reduced soil surface protection. Our combined approach of morphological identification and genetic analyses allowed both a taxa inventory and the analysis of species occurring under specific habitat conditions.}, }
@article {pmid24141939, year = {2014}, author = {Staley, C and Harwood, VJ}, title = {Differential expression of a sodium-phosphate cotransporter among Vibrio vulnificus strains.}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {24-33}, pmid = {24141939}, issn = {1432-184X}, mesh = {Bacterial Proteins/genetics/*metabolism ; Bacterial Typing Techniques ; Environment ; Genotype ; Hydrogen-Ion Concentration ; Phosphates/chemistry ; Reverse Transcriptase Polymerase Chain Reaction ; Salinity ; Seawater/chemistry ; Sequence Analysis, DNA ; Sodium-Phosphate Cotransporter Proteins/genetics/*metabolism ; Vibrio vulnificus/*genetics/growth &amp; development/metabolism ; }, abstract = {Vibrio vulnificus is an estuarine bacterium with pathogenic potential. Its three known biotypes differ in host distribution. We have found the nptA gene for a sodium-phosphate cotransporter, which is rare in bacteria, in each biotype. nptA transcript abundance differed significantly among biotypes, leading to the hypothesis that transcript levels differ under environmental conditions associated with estuarine and host environments. nptA transcript abundance was assessed in V. vulnificus biotypes 1 (C and E genotypes), 2 and 3 strains under varied salinity, phosphate concentration, and pH. Differences in transcript abundance separated strains into two groups. Type C and biotype 3 strains formed Group 1, while type E and biotype 2 strains formed Group 2. Group 2 strains had significantly greater nptA RNA transcript abundance than Group 1. Transcript abundance in the two groups also responded differently to pH and salinity, suggesting differential regulation of nptA in response to environmental conditions. Comparison of the deduced amino acid sequences of NptA among strains resulted in strain grouping similar to that based on transcript abundance. Variation in transcript abundance between groups may affect the ability of V. vulnificus strains to colonize hosts and/or to compete as free-living bacteria in various habitats.}, }
@article {pmid24141938, year = {2014}, author = {Luglia, M and Criquet, S and Sarrazin, M and Ziarelli, F and Guiral, D}, title = {Functional patterns of microbial communities of rhizospheric soils across the development stages of a young mangrove in French Guiana.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {302-317}, pmid = {24141938}, issn = {1432-184X}, mesh = {Avicennia/*growth &amp; development/*microbiology ; Carbon/analysis ; Chemical Phenomena ; DNA, Bacterial/genetics ; *Ecosystem ; French Guiana ; Hydrogen-Ion Concentration ; Linear Models ; Magnetic Resonance Spectroscopy ; Nitrogen/analysis ; Salinity ; *Soil Microbiology ; }, abstract = {The functional patterns of microbial communities (microbial respiration, enzyme activities, functional diversity) and the relevant physico-chemical characteristics of rhizospheric soils were studied during the process of mudflat colonization by mangrove. The study site is a fringe mangrove stand located in Montabo Bay at Cayenne (French Guiana). It is characterized by different vegetation development stages dominated by an assemblage of Avicennia germinans and Laguncularia racemosa. Rhizospheric and surface soils were collected from three stations based on successional stages of mangrove colonization: pioneer (P), coppice (C), and young forest (F). The microbial functional patterns showed significant progressive shifts along the mangrove vegetation profile. The P stages, those most influenced by tide currents, were macroscopically characterized by hydro-sedimentary instability and micro-phytobenthic colonization of mudflat. This stage, characterized by low total organic carbon (TOC) content and quality, showed the lowest extracellular enzymatic activities and the highest functional metabolic diversities. TOC quality analyses by (13)C CPMAS NMR provided evidence of progressive TOC enrichment and an increasing imprint of aboveground vegetation on C quality as succession occurs. These differences in the origin, amount, and quality of soil organic matter (SOM) of older stages exerted both a quantitative and qualitative control over microbial functional responses. This indicated the enhancement of aboveground-belowground functional linkages, leading to the expression of high decomposition activities and a functional loss and specialization of rhizospheric microbial communities.}, }
@article {pmid24140808, year = {2013}, author = {Tong Thi, AN and Noseda, B and Samapundo, S and Nguyen, BL and Broekaert, K and Rasschaert, G and Heyndrickx, M and Devlieghere, F}, title = {Microbial ecology of Vietnamese Tra fish (Pangasius hypophthalmus) fillets during processing.}, journal = {International journal of food microbiology}, volume = {167}, number = {2}, pages = {144-152}, doi = {10.1016/j.ijfoodmicro.2013.09.010}, pmid = {24140808}, issn = {1879-3460}, mesh = {Acinetobacter/genetics/isolation &amp; purification ; Aeromonas/genetics/isolation &amp; purification ; Animals ; Bacteria/genetics/*isolation &amp; purification ; Catfishes/microbiology ; Chlorine/chemistry ; Enterobacteriaceae/genetics/isolation &amp; purification ; Enterococcus/genetics/isolation &amp; purification ; Fish Products/*microbiology ; *Food Contamination ; Food Handling/*methods ; Freezing ; Lactococcus/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Temperature ; Vietnam ; Water ; }, abstract = {There are numerous factors that can have an impact on the microbial ecology and quality of frozen Pangasius hypophthalmus fillets during processing in Vietnam. The presence of spoilage bacteria along the processing line can shorten the shelf-life of thawed frozen fish products. Therefore, the spoilage microbiota throughout the processing chain of two companies (BC: large scale factory, chlorine-based process, BW: large scale factory, water-based process and SC: small scale factory, chlorine-based process) was identified by culture-dependent techniques and 16S rRNA gene sequencing. The microbiological counts were observed to be insignificantly different (p>0.05) between BC and BW. Surprisingly, chlorine treated fillets from the SC line were revealed to have significantly higher microbial counts than potable water treated fillets at BW line. This was determined to be a result of temperature abuse during processing at SC, with temperatures even greater than 10 °C being recorded from skinning onwards. On the contrary, the microbiota related to spoilage for BC and BW lines was determined by 16S rRNA gene sequencing to be more diverse than that on the SC line. A total of 174 isolates, 20 genera and 38 species were identified along the processing chains. The genera Aeromonas, Acinetobacter, Lactococcus and Enterococcus were prevalent at various processing steps on all the processing lines evaluated. A diverse range of isolates belonging to the Enterobacteriaceae such as Providencia, Shigella, Klebsiella, Enterobacter and Wautersiella were isolated from fillets sampled on the SC line whereas Serratia was only observed on fillets sampled on the BC and BW lines. The results can be used to improve Good Manufacturing Practices for processed Pangasius fillets and to select effective measures to prolong the shelf-life of thawed Vietnamese Pangasius fillets products.}, }
@article {pmid24140326, year = {2013}, author = {Oh, J and Hristov, AN and Lee, C and Cassidy, T and Heyler, K and Varga, GA and Pate, J and Walusimbi, S and Brzezicka, E and Toyokawa, K and Werner, J and Donkin, SS and Elias, R and Dowd, S and Bravo, D}, title = {Immune and production responses of dairy cows to postruminal supplementation with phytonutrients.}, journal = {Journal of dairy science}, volume = {96}, number = {12}, pages = {7830-7843}, doi = {10.3168/jds.2013-7089}, pmid = {24140326}, issn = {1525-3198}, mesh = {Abomasum/metabolism ; Animal Feed/*analysis ; Animal Nutritional Physiological Phenomena ; Animals ; *Capsicum ; Cattle/*immunology/physiology ; *Curcumin ; Diet/veterinary ; *Dietary Supplements ; Feces/chemistry ; Female ; Fermentation ; *Garlic ; Lactation/physiology ; Milk/chemistry ; Rumen/physiology ; }, abstract = {This study investigated the effect of phytonutrients (PN) supplied postruminally on nutrient utilization, gut microbial ecology, immune response, and productivity of lactating dairy cows. Eight ruminally cannulated Holstein cows were used in a replicated 4×4 Latin square. Experimental periods lasted 23 d, including 14-d washout and 9-d treatment periods. Treatments were control (no PN) and daily doses of 2g/cow of either curcuma oleoresin (curcumin), garlic extract (garlic), or capsicum oleoresin (capsicum). Phytonutrients were pulse-dosed into the abomasum of the cows, through the rumen cannula, 2 h after feeding during the last 9 d of each experimental period. Dry matter intake was not affected by PN, although it tended to be lower for the garlic treatment compared with the control. Milk yield was decreased (2.2 kg/d) by capsicum treatment compared with the control. Feed efficiency, milk composition, milk fat and protein yields, milk N efficiency, and 4.0% fat-corrected milk yield were not affected by treatment. Rumen fermentation variables, apparent total-tract digestibility of nutrients, N excretion with feces and urine, and diversity of fecal bacteria were also not affected by treatment. Phytonutrients had no effect on blood chemistry, but the relative proportion of lymphocytes was increased by the capsicum treatment compared with the control. All PN increased the proportion of total CD4(+) cells and total CD4(+) cells that co-expressed the activation status signal and CD25 in blood. The percentage of peripheral blood mononuclear cells (PBMC) that proliferated in response to concanavalin A and viability of PBMC were not affected by treatment. Cytokine production by PBMC was not different between control and PN. Expression of mRNA in liver for key enzymes in gluconeogenesis, fatty acid oxidation, and response to reactive oxygen species were not affected by treatment. No difference was observed due to treatment in the oxygen radical absorbance capacity of blood plasma but, compared with the control, garlic treatment increased 8-isoprostane levels. Overall, the PN used in this study had subtle or no effects on blood cells and blood chemistry, nutrient digestibility, and fecal bacterial diversity, but appeared to have an immune-stimulatory effect by activating and inducing the expansion of CD4 cells in dairy cows. Capsicum treatment decreased milk yield, but this and other effects observed in this study should be interpreted with caution because of the short duration of treatment.}, }
@article {pmid24137541, year = {2013}, author = {Metcalf, JL and Wegener Parfrey, L and Gonzalez, A and Lauber, CL and Knights, D and Ackermann, G and Humphrey, GC and Gebert, MJ and Van Treuren, W and Berg-Lyons, D and Keepers, K and Guo, Y and Bullard, J and Fierer, N and Carter, DO and Knight, R}, title = {A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system.}, journal = {eLife}, volume = {2}, number = {}, pages = {e01104}, pmid = {24137541}, issn = {2050-084X}, support = {P20 MD006084/MD/NIMHD NIH HHS/United States ; P20MD006084/MD/NIMHD NIH HHS/United States ; }, mesh = {Animals ; Forensic Sciences ; Mice ; *Microbiota ; *Models, Animal ; *Postmortem Changes ; }, abstract = {Establishing the time since death is critical in every death investigation, yet existing techniques are susceptible to a range of errors and biases. For example, forensic entomology is widely used to assess the postmortem interval (PMI), but errors can range from days to months. Microbes may provide a novel method for estimating PMI that avoids many of these limitations. Here we show that postmortem microbial community changes are dramatic, measurable, and repeatable in a mouse model system, allowing PMI to be estimated within approximately 3 days over 48 days. Our results provide a detailed understanding of bacterial and microbial eukaryotic ecology within a decomposing corpse system and suggest that microbial community data can be developed into a forensic tool for estimating PMI. DOI:http://dx.doi.org/10.7554/eLife.01104.001.}, }
@article {pmid24134811, year = {2013}, author = {Heinritz, SN and Mosenthin, R and Weiss, E}, title = {Use of pigs as a potential model for research into dietary modulation of the human gut microbiota.}, journal = {Nutrition research reviews}, volume = {26}, number = {2}, pages = {191-209}, doi = {10.1017/S0954422413000152}, pmid = {24134811}, issn = {1475-2700}, mesh = {Animals ; *Diet ; Humans ; Intestines/*microbiology ; *Microbiota ; *Models, Animal ; *Prebiotics ; *Probiotics ; Swine/*microbiology ; }, abstract = {The human intestinal microbial ecosystem plays an important role in maintaining health. A multitude of diseases including diarrhoea, gastrointestinal inflammatory disorders, such as necrotising enterocolitis (NEC) of neonates, and obesity are linked to microbial composition and metabolic activity. Therefore, research on possible dietary strategies influencing microbial composition and activity, both preventive and curative, is being accomplished. Interest has focused on pre- and probiotics that stimulate the intestinal production of beneficial bacterial metabolites such as butyrate, and beneficially affect microbial composition. The suitability of an animal model to study dietary linked diseases is of much concern. The physiological similarity between humans and pigs in terms of digestive and associated metabolic processes places the pig in a superior position over other non-primate models. Furthermore, the pig is a human-sized omnivorous animal with comparable nutritional requirements, and shows similarities to the human intestinal microbial ecosystem. Also, the pig has been used as a model to assess microbiota-health interactions, since pigs exhibit similar syndromes to humans, such as NEC and partly weanling diarrhoea. In contrast, when using rodent models to study diet-microbiota-health interactions, differences between rodents and humans have to be considered. For example, studies with mice and human subjects assessing possible relationships between the composition and metabolic activity of the gut microbiota and the development of obesity have shown inconsistencies in results between studies. The present review displays the similarities and differences in intestinal microbial ecology between humans and pigs, scrutinising the pig as a potential animal model, with regard to possible health effects.}, }
@article {pmid24130477, year = {2013}, author = {Defoirdt, T}, title = {Antivirulence therapy for animal production: filling an arsenal with novel weapons for sustainable disease control.}, journal = {PLoS pathogens}, volume = {9}, number = {10}, pages = {e1003603}, pmid = {24130477}, issn = {1553-7374}, mesh = {Animals ; Communicable Disease Control/*methods ; Gram-Negative Bacteria/metabolism/*pathogenicity ; Gram-Negative Bacterial Infections/*therapy/*veterinary ; Virulence Factors/*metabolism ; }, }
@article {pmid24128146, year = {2014}, author = {Bacci, G and Bazzicalupo, M and Benedetti, A and Mengoni, A}, title = {StreamingTrim 1.0: a Java software for dynamic trimming of 16S rRNA sequence data from metagenetic studies.}, journal = {Molecular ecology resources}, volume = {14}, number = {2}, pages = {426-434}, doi = {10.1111/1755-0998.12187}, pmid = {24128146}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Metagenomics/*methods ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {Next-generation sequencing technologies are extensively used in the field of molecular microbial ecology to describe taxonomic composition and to infer functionality of microbial communities. In particular, the so-called barcode or metagenetic applications that are based on PCR amplicon library sequencing are very popular at present. One of the problems, related to the utilization of the data of these libraries, is the analysis of reads quality and removal (trimming) of low-quality segments, while retaining sufficient information for subsequent analyses (e.g. taxonomic assignment). Here, we present StreamingTrim, a DNA reads trimming software, written in Java, with which researchers are able to analyse the quality of DNA sequences in fastq files and to search for low-quality zones in a very conservative way. This software has been developed with the aim to provide a tool capable of trimming amplicon library data, retaining as much as taxonomic information as possible. This software is equipped with a graphical user interface for a user-friendly usage. Moreover, from a computational point of view, StreamingTrim reads and analyses sequences one by one from an input fastq file, without keeping anything in memory, permitting to run the computation on a normal desktop PC or even a laptop. Trimmed sequences are saved in an output file, and a statistics summary is displayed that contains the mean and standard deviation of the length and quality of the whole sequence file. Compiled software, a manual and example data sets are available under the BSD-2-Clause License at the GitHub repository at https://github.com/GiBacci/StreamingTrim/.}, }
@article {pmid24124501, year = {2013}, author = {van der Wal, A and Tecon, R and Kreft, JU and Mooij, WM and Leveau, JH}, title = {Explaining bacterial dispersion on leaf surfaces with an individual-based model (PHYLLOSIM).}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e75633}, pmid = {24124501}, issn = {1932-6203}, support = {NC/K000683/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; }, mesh = {*Bacteria ; *Models, Theoretical ; Plant Leaves/*microbiology ; }, abstract = {We developed the individual-based model PHYLLOSIM to explain observed variation in the size of bacterial clusters on plant leaf surfaces (the phyllosphere). Specifically, we tested how different 'waterscapes' impacted the diffusion of nutrients from the leaf interior to the surface and the growth of individual bacteria on these nutrients. In the 'null' model or more complex 'patchy' models, the surface was covered with a continuous water film or with water drops of equal or different volumes, respectively. While these models predicted the growth of individual bacterial immigrants into clusters of variable sizes, they were unable to reproduce experimentally derived, previously published patterns of dispersion which were characterized by a much larger variation in cluster sizes and a disproportionate occurrence of clusters consisting of only one or two bacteria. The fit of model predictions to experimental data was about equally poor (<5%) regardless of whether the water films were continuous or patchy. Only by allowing individual bacteria to detach from developing clusters and re-attach elsewhere to start a new cluster, did PHYLLOSIM come much closer to reproducing experimental observations. The goodness of fit including detachment increased to about 70-80% for all waterscapes. Predictions of this 'detachment' model were further supported by the visualization and quantification of bacterial detachment and attachment events at an agarose-water interface. Thus, both model and experiment suggest that detachment of bacterial cells from clusters is an important mechanism underlying bacterial exploration of the phyllosphere.}, }
@article {pmid24124405, year = {2013}, author = {Kim, M and Lee, KH and Yoon, SW and Kim, BS and Chun, J and Yi, H}, title = {Analytical tools and databases for metagenomics in the next-generation sequencing era.}, journal = {Genomics &amp; informatics}, volume = {11}, number = {3}, pages = {102-113}, pmid = {24124405}, issn = {1598-866X}, abstract = {Metagenomics has become one of the indispensable tools in microbial ecology for the last few decades, and a new revolution in metagenomic studies is now about to begin, with the help of recent advances of sequencing techniques. The massive data production and substantial cost reduction in next-generation sequencing have led to the rapid growth of metagenomic research both quantitatively and qualitatively. It is evident that metagenomics will be a standard tool for studying the diversity and function of microbes in the near future, as fingerprinting methods did previously. As the speed of data accumulation is accelerating, bioinformatic tools and associated databases for handling those datasets have become more urgent and necessary. To facilitate the bioinformatics analysis of metagenomic data, we review some recent tools and databases that are used widely in this field and give insights into the current challenges and future of metagenomics from a bioinformatics perspective.}, }
@article {pmid24123200, year = {2014}, author = {Lee, HJ and Whang, KS}, title = {Streptomyces graminilatus sp. nov., isolated from bamboo litter.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {64}, number = {Pt 2}, pages = {528-532}, doi = {10.1099/ijs.0.049528-0}, pmid = {24123200}, issn = {1466-5034}, mesh = {Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Peptidoglycan/chemistry ; Phospholipids/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sasa/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; Streptomyces/*classification/genetics/isolation &amp; purification ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {A Gram-stain-positive, novel actinobacterium, designated strain JL-6(T), was isolated from the litter of a bamboo (Sasa borealis) forest in Damyang, Korea. Strain JL-6(T) had white-grey, smooth, cylindrical spores that were borne in straight, long spore-chains. The novel strain grew aerobically at 15-28 °C (optimum, 28 °C), pH 4.0-8.0 (optimum, pH 5.5) and with 0-1.5% (w/v) NaCl. The cell-wall peptidoglycan contained ll-diaminopimelic acid, glutamic acid, alanine and glycine. The predominant menaquinones were MK-9(H6) and MK-9(H8). Whole-cell hydrolysates mainly contained glucose and ribose. Phosphatidylinositol and phosphatidylcholine were the diagnostic phospholipids. The G+C content of the genomic DNA was 72.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JL-6(T) belonged to the genus Streptomyces with sequence similarities ranging from 97.3% to 98.3%. However, DNA-DNA hybridization between JL-6(T) and the closest related strain, Streptomyces turgidiscabies, ATCC 700248(T) and other closely related species in the genus Streptomyces showed <50% relatedness. Based on these observations, strain JL-6(T) is proposed to represent a novel species of the genus Streptomyces, for which the name Streptomyces graminilatus sp. nov. is proposed. The type strain is JL-6(T) (= KACC 16470(T) = NBRC 108882(T)).}, }
@article {pmid24122627, year = {2014}, author = {Hussain, A and Bruant, G and Mehta, P and Raghavan, V and Tartakovsky, B and Guiot, SR}, title = {Population analysis of mesophilic microbial fuel cells fed with carbon monoxide.}, journal = {Applied biochemistry and biotechnology}, volume = {172}, number = {2}, pages = {713-726}, doi = {10.1007/s12010-013-0556-9}, pmid = {24122627}, issn = {1559-0291}, mesh = {Acetates/pharmacology ; Archaea/classification ; Bacteria/classification ; Biodiversity ; Bioelectric Energy Sources/*microbiology ; Carbon Monoxide/*pharmacology ; Denaturing Gradient Gel Electrophoresis ; Electricity ; Geobacter/drug effects/growth &amp; development ; High-Throughput Nucleotide Sequencing ; Microbiota/drug effects ; Phylogeny ; Sewage/microbiology ; }, abstract = {Electricity generation in a microbial fuel cell (MFC) fed with carbon monoxide (CO) has been recently demonstrated; however, the microbial ecology of this system has not yet been described. In this work the diversity of the microbial community present at the anode of CO-fed MFCs was studied by performing denaturing gradient gel electrophoresis (DGGE) and high-throughput sequencing (HTS) analyses. HTS indicated a significant increase of the archaeal genus Methanobacterium and of the bacterial order Clostridiales, notably including Clostridium species, while in both MFCs DGGE identified members of the bacterial genera Geobacter, Desulfovibrio, and Clostridium, and of the archaeal genera Methanobacterium, Methanofollis, and Methanosaeta. In particular, the presence of Geobacter sulfurreducens was identified. Tolerance of G. sulfurreducens to CO was confirmed by growing G. sulfurreducens with acetate under a 100 % CO atmosphere. This observation, along with the identification of acetogens, supports the hypothesis of the two-step process in which CO is converted to acetate by the carboxidotrophic Bacteria and acetate is then oxidized by CO-tolerant electricigenic bacteria to produce electricity.}, }
@article {pmid24121801, year = {2014}, author = {Bottos, EM and Woo, AC and Zawar-Reza, P and Pointing, SB and Cary, SC}, title = {Airborne bacterial populations above desert soils of the McMurdo Dry Valleys, Antarctica.}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {120-128}, pmid = {24121801}, issn = {1432-184X}, mesh = {Actinobacteria/classification/isolation &amp; purification ; Aerosols ; *Air Microbiology ; Antarctic Regions ; Bacteria/classification/*isolation &amp; purification ; Climate ; DNA, Bacterial/genetics ; *Ecosystem ; Genes, rRNA ; Phylogeny ; Seasons ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Bacteria are assumed to disperse widely via aerosolized transport due to their small size and resilience. The question of microbial endemicity in isolated populations is directly related to the level of airborne exogenous inputs, yet this has proven hard to identify. The ice-free terrestrial ecosystem of Antarctica, a geographically and climatically isolated continent, was used to interrogate microbial bio-aerosols in relation to the surrounding ecology and climate. High-throughput sequencing of bacterial ribosomal RNA (rRNA) genes was combined with analyses of climate patterns during an austral summer. In general terms, the aerosols were dominated by Firmicutes, whereas surrounding soils supported Actinobacteria-dominated communities. The most abundant taxa were also common to aerosols from other continents, suggesting that a distinct bio-aerosol community is widely dispersed. No evidence for significant marine input to bioaerosols was found at this maritime valley site, instead local influence was largely from nearby volcanic sources. Back trajectory analysis revealed transport of incoming regional air masses across the Antarctic Plateau, and this is envisaged as a strong selective force. It is postulated that local soil microbial dispersal occurs largely via stochastic mobilization of mineral soil particulates.}, }
@article {pmid24121800, year = {2014}, author = {Ventura, IM and Costa, T and Klaczko, LB}, title = {Low temperature reveals genetic variability against male-killing Spiroplasma in Drosophila melanogaster natural populations.}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {229-235}, pmid = {24121800}, issn = {1432-184X}, mesh = {Animals ; Drosophila melanogaster/*microbiology/physiology ; Female ; Genetic Variation ; Male ; Phenotype ; Population Dynamics ; Sex Ratio ; Spiroplasma/*genetics ; Symbiosis ; *Temperature ; }, abstract = {Spiroplasma endosymbionts are maternally inherited microorganisms which infect many arthropod species. In some Drosophila species, it acts as a reproductive manipulator, spreading in populations by killing the sons of infected mothers. Distinct Drosophila melanogaster populations from Brazil exhibit variable male-killing Spiroplasma prevalences. In this study, we investigated the presence of variability for the male-killing phenotype among Drosophila and/or Spiroplasma strains and verified if it correlates with the endosymbiont prevalence in natural populations. For that, we analyzed the male-killing expression when Spiroplasma strains from different populations were transferred to a standard D. melanogaster line (Canton-S) and when a common Spiroplasma strain was transferred to different wild-caught D. melanogaster lines, both at optimal and challenging temperatures for the bacteria. No variation was observed in the male-killing phenotype induced by different Spiroplasma strains. No phenotypic variability among fly lines was detected at optimal temperature (23 °C), as well. Conversely, significant variation in the male-killing expression was revealed among D. melanogaster lines at 18.5 °C, probably caused by imperfect transmission of the endosymbiont. Distinct lines differed in their average sex ratios as well as in the pattern of male-killing expression as the infected females aged. Greater variation occurred among lines from one locality, although there was no clear correlation between the male-killing intensity and the endosymbiont prevalence in each population. Imperfect transmission or male killing may also occur in the field, thus helping to explain the low or intermediate prevalences reported in nature. We discuss the implications of our results for the dynamics of male-killing Spiroplasma in natural populations.}, }
@article {pmid24118804, year = {2014}, author = {Pester, M and Maixner, F and Berry, D and Rattei, T and Koch, H and Lücker, S and Nowka, B and Richter, A and Spieck, E and Lebedeva, E and Loy, A and Wagner, M and Daims, H}, title = {NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizing Nitrospira.}, journal = {Environmental microbiology}, volume = {16}, number = {10}, pages = {3055-3071}, doi = {10.1111/1462-2920.12300}, pmid = {24118804}, issn = {1462-2920}, support = {294343/ERC_/European Research Council/International ; P 20185/FWF_/Austrian Science Fund FWF/Austria ; P 25111/FWF_/Austrian Science Fund FWF/Austria ; P 25231/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; Genes, Bacterial ; Genetic Markers ; Molecular Sequence Data ; Nitrite Reductases/*genetics ; Nitrites/metabolism ; Oxidation-Reduction ; Phylogeny ; Protein Subunits/genetics ; Soil Microbiology ; }, abstract = {Nitrospira are the most widespread and diverse known nitrite-oxidizing bacteria and key nitrifiers in natural and engineered ecosystems. Nevertheless, their ecophysiology and environmental distribution are understudied because of the recalcitrance of Nitrospira to cultivation and the lack of a molecular functional marker, which would allow the detection of Nitrospira in the environment. Here we introduce nxrB, the gene encoding subunit beta of nitrite oxidoreductase, as a functional and phylogenetic marker for Nitrospira. Phylogenetic trees based on nxrB of Nitrospira were largely congruent to 16S ribosomal RNA-based phylogenies. By using new nxrB-selective polymerase chain reaction primers, we obtained almost full-length nxrB sequences from Nitrospira cultures, two activated sludge samples, and several geographically and climatically distinct soils. Amplicon pyrosequencing of nxrB fragments from 16 soils revealed a previously unrecognized diversity of terrestrial Nitrospira with 1801 detected species-level operational taxonomic units (OTUs) (using an inferred species threshold of 95% nxrB identity). Richness estimates ranged from 10 to 946 coexisting Nitrospira species per soil. Comparison with an archaeal amoA dataset obtained from the same soils [Environ. Microbiol. 14: 525-539 (2012)] uncovered that ammonia-oxidizing archaea and Nitrospira communities were highly correlated across the soil samples, possibly indicating shared habitat preferences or specific biological interactions among members of these nitrifier groups.}, }
@article {pmid24118011, year = {2014}, author = {Schmidt, H and Eickhorst, T}, title = {Detection and quantification of native microbial populations on soil-grown rice roots by catalyzed reporter deposition-fluorescence in situ hybridization.}, journal = {FEMS microbiology ecology}, volume = {87}, number = {2}, pages = {390-402}, doi = {10.1111/1574-6941.12232}, pmid = {24118011}, issn = {1574-6941}, mesh = {Archaea/genetics/isolation &amp; purification ; Bacteria/genetics/isolation &amp; purification ; Colony Count, Microbial ; In Situ Hybridization, Fluorescence ; Oryza/*microbiology ; Plant Roots/*microbiology ; Rhizosphere ; *Soil Microbiology ; Wetlands ; }, abstract = {Catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) was applied to detect microbial cells on the rhizoplane of wetland rice (Oryza sativa L.). Fluorescent signals of high intensity and specificity allowed for a reliable quantification of selected microbial phyla. Absolute cell numbers of archaea and bacteria were observed to be highest at flowering stage of rice plant development (P < 0.05) showing values of 1.32 and 6.26 × 10(4) cells mm(-2) rhizoplane, respectively. Highest colonization densities shifted from the root tip toward more mature regions with increasing plant age. Significant differences between cell numbers observed within a short distance (0-15 mm) indicated irregular distribution patterns of microbiota. Root tips, elongation zones, and openings at the base of lateral roots represented preferential areas for microbial colonization, which were often covered with iron coatings and densely colonized with potential iron-oxidizing Betaproteobacteria (59% of bacteria). Methanogenic archaea were abundant on the rhizoplane (up to 0.96 × 10(3) cells mm(-2) rhizoplane), and the decline of their relative abundance with plant age was also found in the associated rhizosphere soil. Cell numbers of methanotrophic bacteria significantly increased at flowering (6.38 × 10(3) cells mm(-2) rhizoplane; P < 0.05), indicating their stimulation by root-derived substrates which was less pronounced in the rhizosphere soil.}, }
@article {pmid24113822, year = {2014}, author = {Jiménez, DJ and Korenblum, E and van Elsas, JD}, title = {Novel multispecies microbial consortia involved in lignocellulose and 5-hydroxymethylfurfural bioconversion.}, journal = {Applied microbiology and biotechnology}, volume = {98}, number = {6}, pages = {2789-2803}, doi = {10.1007/s00253-013-5253-7}, pmid = {24113822}, issn = {1432-0614}, mesh = {Aerobiosis ; Bacteria/*classification/isolation &amp; purification/metabolism ; Bacterial Load ; Biodiversity ; Biotransformation ; Colony Count, Microbial ; Fungi/*classification/isolation &amp; purification/metabolism ; Furaldehyde/*analogs &amp; derivatives/metabolism ; Lignin/*metabolism ; *Microbial Consortia ; Molecular Sequence Data ; Plant Stems/metabolism ; Sequence Analysis, DNA ; Triticum/metabolism ; }, abstract = {To develop a targeted metagenomics approach for the analysis of novel multispecies microbial consortia involved in the bioconversion of lignocellulose and furanic compounds, we applied replicated sequential batch aerobic enrichment cultures with either pretreated or untreated wheat straw as the sources of carbon and energy. After each transfer, exponential growth of bacteria was detected using microscopic cell counts, indicating that the substrate was being utilized. In batch, the final bacterial abundances increased from an estimated 5 to 8.7-9.5 log 16S rRNA gene copy numbers/ml. The abundances of fungal propagules showed greater variation, i.e., between 5.4 and 8.0 log ITS1 copies/ml. Denaturing gradient gel electrophoresis analyses showed that the bacterial consortia in both treatments reached approximate structural stability after six transfers. Moreover, the structures of the fungal communities were strongly influenced by substrate treatment. A total of 124 bacterial strains were isolated from the two types of enrichment cultures. The most abundant strains were affiliated with the genera Raoultella/Klebsiella, Kluyvera, Citrobacter, Enterobacter, Pseudomonas, Acinetobacter, Flavobacterium and Arthrobacter. Totals of 43 and 11 strains obtained from the untreated and pretreated substrates, respectively, showed (hemi)cellulolytic activity (CMC-ase and xylanase), whereas 96 strains were capable of growth in 7.5 mM 5-hydroxymethylfurfural. About 50 % of the latter showed extracellular oxidoreductase activity as detected by a novel iodide oxidation method. Also, (hemi)cellulolytic fungal strains related to Coniochaeta, Plectosphaerella and Penicillium were isolated. One Trichosporon strain was isolated from pretreated wheat straw. The two novel bacterial-fungal consortia are starting points for lignocellulose degradation applications.}, }
@article {pmid24112537, year = {2013}, author = {Sato, Y and Willis, BL and Bourne, DG}, title = {Pyrosequencing-based profiling of archaeal and bacterial 16S rRNA genes identifies a novel archaeon associated with black band disease in corals.}, journal = {Environmental microbiology}, volume = {15}, number = {11}, pages = {2994-3007}, doi = {10.1111/1462-2920.12256}, pmid = {24112537}, issn = {1462-2920}, mesh = {Animals ; Anthozoa/*microbiology ; Base Sequence ; Cellular Microenvironment ; Cyanobacteria/*genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Euryarchaeota/*genetics ; Microbial Consortia/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Ribotyping ; Sequence Analysis, DNA ; }, abstract = {Black band disease (BBD) is a microbial consortium that creates anoxic, sulfide-rich microenvironments and kills underlying coral tissues as it rapidly migrates across colonies. Although bacterial communities associated with BBD have been studied extensively, the presence and roles of archaea are unexplored. Using amplicon-pyrosequencing of 16S ribosomal RNA genes, we investigated the community structure of both archaea and bacteria within microbial lesions of BBD and the less-virulent precursor stage, 'cyanobacterial patches' (CP), affecting the coral Montipora hispida. We detected characteristic shifts in microbial communities during the development of BBD from CP, reflecting microenvironmental changes within lesions. Archaeal profiles in CP suggested a diverse assemblage affiliated with the Thaumarchaeota and Euryarchaeota, similar to communities described for oxic marine environments. In contrast, a novel ribotype, distantly affiliated to the Euryarchaeota, dominated up to 94% of archaeal sequences retrieved from BBD. The physiological characteristics of this dominant archaeal ribotype are unknown because of the novelty of its 16S ribosomal RNA gene sequences; however, their prominent associations with BBD lesions suggest the ability to thrive in the organic- and sulfide-rich anoxic microenvironment characteristic of BBD lesions. Discovery of this novel archaeal ribotype provides new insights into the microbial ecology and aetiology of BBD.}, }
@article {pmid24107182, year = {2014}, author = {Anderson, OR}, title = {Bacterial and heterotrophic nanoflagellate densities and C-biomass estimates along an Alaskan tundra transect with prediction of respiratory CO2 efflux.}, journal = {The Journal of eukaryotic microbiology}, volume = {61}, number = {1}, pages = {11-16}, doi = {10.1111/jeu.12081}, pmid = {24107182}, issn = {1550-7408}, mesh = {Arctic Regions ; Bacteria/*growth &amp; development/*metabolism ; Bacterial Load ; Biomass ; Carbon Dioxide/*metabolism ; Cell Count ; Ciliophora/*growth &amp; development/*metabolism ; Soil/*parasitology ; *Soil Microbiology ; }, abstract = {Although tundra terrestrial ecology is significantly affected by global warming, we know relatively little about how eukaryotic microbial communities respond and how much microbial respiratory CO(2) may be released due to available organic nutrient sources in the permafrost melt. Prior research has shown a strong positive correlation between bacteria and fungi in some Arctic locales; this research focused on the relationships of terrestrial bacteria and heterotrophic nanoflagellates. The densities and estimated C-biomass of bacteria and heterotrophic nanoflagellates (a major occurring group of protozoa) were assessed in 14 samples obtained along a 10 km transect in northwest AK during the summer of 2012. Two samples were taken, one at the top and one near the base of seven hummocks along the transect. Densities (no./g soil) of bacteria varied from 2.7-16 × 10(9), and nanoflagellates 0.7-7.9 × 10(7). C-biomass (μg/g soil) of bacteria varied from 358 to 2,114, and nanoflagellates 12-37. Additionally, the rate of respiration was analyzed in the laboratory for each soil sample. A linear relationship between soil respiration and bacterial densities was obtained (20 °C): R(s) = 12.32 + 14.07 Bd (p ≪ 0.01); where R(s) is soil respiration (nmol/min/g soil) and B(d) = bacterial density (no. × 10(9) /g soil).}, }
@article {pmid24101916, year = {2013}, author = {Fish, JA and Chai, B and Wang, Q and Sun, Y and Brown, CT and Tiedje, JM and Cole, JR}, title = {FunGene: the functional gene pipeline and repository.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {291}, pmid = {24101916}, issn = {1664-302X}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; UH3 DK083993/DK/NIDDK NIH HHS/United States ; }, abstract = {Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer. While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/) offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.}, }
@article {pmid24098498, year = {2013}, author = {Fredriksson, NJ and Hermansson, M and Wilén, BM}, title = {The choice of PCR primers has great impact on assessments of bacterial community diversity and dynamics in a wastewater treatment plant.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e76431}, pmid = {24098498}, issn = {1932-6203}, mesh = {Bacteria/classification/*genetics ; Biodiversity ; DNA Primers/genetics ; Gene Library ; Humans ; *Metagenome ; Microbiota ; Polymerase Chain Reaction/*methods ; RNA, Bacterial ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; Sewage/microbiology ; Wastewater/*microbiology ; }, abstract = {Assessments of bacterial community diversity and dynamics are fundamental for the understanding of microbial ecology as well as biotechnological applications. We show that the choice of PCR primers has great impact on the results of analyses of diversity and dynamics using gene libraries and DNA fingerprinting. Two universal primer pairs targeting the 16S rRNA gene, 27F&amp;1492R and 63F&amp;M1387R, were compared and evaluated by analyzing the bacterial community in the activated sludge of a large-scale wastewater treatment plant. The two primer pairs targeted distinct parts of the bacterial community, none encompassing the other, both with similar richness. Had only one primer pair been used, very different conclusions had been drawn regarding dominant phylogenetic and putative functional groups. With 27F&amp;1492R, Betaproteobacteria would have been determined to be the dominating taxa while 63F&amp;M1387R would have described Alphaproteobacteria as the most common taxa. Microscopy and fluorescence in situ hybridization analysis showed that both Alphaproteobacteria and Betaproteobacteria were abundant in the activated sludge, confirming that the two primer pairs target two different fractions of the bacterial community. Furthermore, terminal restriction fragment polymorphism analyses of a series of four activated sludge samples showed that the two primer pairs would have resulted in different conclusions about community stability and the factors contributing to changes in community composition. In conclusion, different PCR primer pairs, although considered universal, target different ranges of bacteria and will thus show the diversity and dynamics of different fractions of the bacterial community in the analyzed sample. We also show that while a database search can serve as an indicator of how universal a primer pair is, an experimental assessment is necessary to evaluate the suitability for a specific environmental sample.}, }
@article {pmid24096886, year = {2014}, author = {Chung, CC and Huang, CY and Gong, GC and Lin, YC}, title = {Influence of the Changjiang River flood on Synechococcus ecology in the surface waters of the East China Sea.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {273-285}, pmid = {24096886}, issn = {1432-184X}, mesh = {Biodiversity ; China ; DNA, Bacterial/genetics ; Ecology ; Floods ; Oceans and Seas ; Phycocyanin/chemistry ; Phycoerythrin/chemistry ; Phylogeny ; Phylogeography ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Seasons ; Sequence Analysis, DNA ; Synechococcus/*classification/*isolation &amp; purification ; Water/chemistry ; *Water Microbiology ; }, abstract = {Synechococcus spp. have been suggested as the primary component of picophytoplankton in the East China Sea (ECS). However, the influences of sudden environmental changes on Synechococcus assemblage composition have not yet been investigated. In the summer of 2010, a disastrous flood occurred in the Changjiang River basin. To improve our understanding of how this flood affected the Synechococcus ecology on the ECS surface, their assemblages and distributions have been described using two-laser flow cytometry and phylogenetic analysis of the phycocyanin operon. During the nonflooding summer of 2009, phycoerythrin-rich (PE-rich) Synechococcus thrived near the outer boundary of the Changjiang River diluted water (CDW) coverage, while phycocyanin-rich (PC-rich) Synechococcus predominated inside the turbid CDW with a transparency of <80%. During the 2010 summer, flooding expanded the CDW coverage area to over half of the ECS. PE-rich cells showed a homogeneous distribution and a decline in abundance, while the spatial pattern of the PC-rich Synechococcus resembled the pattern from 2009. Based on the phycocyanin operon phylogeny, the Synechococcus in the ECS were categorized into five groups, ECS-1 to ECS-4 and ECS-PE, comprising a total of 19 operational taxonomic units. In the summer of 2009, ECS-2 dominated in the coast, and the ECS-3 and ECS-PE clades prevailed in the offshore waters. However, during the summer of 2010, ECS-4 and ECS-PE became the dominant strains. The injection of abundant anthropogenic pollutants and the enhancement of transparency within the CDW expansion area appear to be the factors needed to transiently alter the ecology of Synechococcus after flooding.}, }
@article {pmid24096885, year = {2014}, author = {Mulcahy, LR and Isabella, VM and Lewis, K}, title = {Pseudomonas aeruginosa biofilms in disease.}, journal = {Microbial ecology}, volume = {68}, number = {1}, pages = {1-12}, pmid = {24096885}, issn = {1432-184X}, support = {R01 AI085585/AI/NIAID NIH HHS/United States ; T-R01AI085585-01/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Biofilms/drug effects ; Cystic Fibrosis/microbiology ; Disease Models, Animal ; Drug Resistance, Bacterial ; Humans ; Immune System ; Pseudomonas aeruginosa/drug effects/genetics/*growth &amp; development/*pathogenicity ; Wounds and Injuries/microbiology ; }, abstract = {Pseudomonas aeruginosa is a ubiquitous organism that is the focus of intense research because of its prominent role in disease. Due to its relatively large genome and flexible metabolic capabilities, this organism exploits numerous environmental niches. It is an opportunistic pathogen that sets upon the human host when the normal immune defenses are disabled. Its deadliness is most apparent in cystic fibrosis patients, but it also is a major problem in burn wounds, chronic wounds, chronic obstructive pulmonary disorder, surface growth on implanted biomaterials, and within hospital surface and water supplies, where it poses a host of threats to vulnerable patients (Peleg and Hooper, N Engl J Med 362:1804-1813, 2010; Breathnach et al., J Hosp Infect 82:19-24, 2012). Once established in the patient, P. aeruginosa can be especially difficult to treat. The genome encodes a host of resistance genes, including multidrug efflux pumps (Poole, J Mol Microbiol Biotechnol 3:255-264, 2001) and enzymes conferring resistance to beta-lactam and aminoglycoside antibotics (Vahdani et al., Annal Burns Fire Disast 25:78-81, 2012), making therapy against this gram-negative pathogen particularly challenging due to the lack of novel antimicrobial therapeutics (Lewis, Nature 485: 439-440, 2012). This challenge is compounded by the ability of P. aeruginosa to grow in a biofilm, which may enhance its ability to cause infections by protecting bacteria from host defenses and chemotherapy. Here, we review recent studies of P. aeruginosa biofilms with a focus on how this unique mode of growth contributes to its ability to cause recalcitrant infections.}, }
@article {pmid24096427, year = {2013}, author = {Ercolini, D and Pontonio, E and De Filippis, F and Minervini, F and La Storia, A and Gobbetti, M and Di Cagno, R}, title = {Microbial ecology dynamics during rye and wheat sourdough preparation.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {24}, pages = {7827-7836}, pmid = {24096427}, issn = {1098-5336}, mesh = {Bacteria/*classification/genetics ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; *Food Microbiology ; Fungi/*classification/genetics ; Molecular Sequence Data ; Phylogeny ; Secale ; Sequence Analysis, DNA ; Time Factors ; Triticum ; }, abstract = {The bacterial ecology during rye and wheat sourdough preparation was described by 16S rRNA gene pyrosequencing. Viable plate counts of presumptive lactic acid bacteria, the ratio between lactic acid bacteria and yeasts, the rate of acidification, a permutation analysis based on biochemical and microbial features, the number of operational taxonomic units (OTUs), and diversity indices all together demonstrated the maturity of the sourdoughs during 5 to 7 days of propagation. Flours were mainly contaminated by metabolically active genera (Acinetobacter, Pantoea, Pseudomonas, Comamonas, Enterobacter, Erwinia, and Sphingomonas) belonging to the phylum Proteobacteria or Bacteroidetes (genus Chryseobacterium). Their relative abundances varied with the flour. Soon after 1 day of propagation, this population was almost completely inhibited except for the Enterobacteriaceae. Although members of the phylum Firmicutes were present at very low or intermediate relative abundances in the flours, they became dominant soon after 1 day of propagation. Lactic acid bacteria were almost exclusively representative of the Firmicutes by this time. Weissella spp. were already dominant in rye flour and stably persisted, though they were later flanked by the Lactobacillus sakei group. There was a succession of species during 10 days of propagation of wheat sourdoughs. The fluctuation between dominating and subdominating populations of L. sakei group, Leuconostoc spp., Weissella spp., and Lactococcus lactis was demonstrated. Other subdominant species such as Lactobacillus plantarum were detectable throughout propagation. As shown by PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analysis, Saccharomyces cerevisiae dominated throughout the sourdough propagation. Notwithstanding variations due to environmental and technology determinants, the results of this study represent a clear example of how the microbial ecology evolves during sourdough preparation.}, }
@article {pmid24096353, year = {2014}, author = {Whang, KS and Lee, JC and Lee, HR and Han, SI and Chung, SH}, title = {Terriglobus tenax sp. nov., an exopolysaccharide-producing acidobacterium isolated from rhizosphere soil of a medicinal plant.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {64}, number = {Pt 2}, pages = {431-437}, doi = {10.1099/ijs.0.053769-0}, pmid = {24096353}, issn = {1466-5034}, mesh = {Acidobacteria/*classification/genetics/isolation &amp; purification ; Angelica sinensis/*microbiology ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phosphatidylethanolamines/chemistry ; Phospholipids/chemistry ; *Phylogeny ; Plants, Medicinal/microbiology ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {An exopolysaccharide-producing bacterium, designated strain DRP 35(T), was isolated from the rhizosphere soil of a medicinal herb, Angelica sinensis, at Geumsan in Korea. Cells were Gram-staining-negative, non-motile, catalase-positive and oxidase-negative short rods. The isolate grew aerobically from 15 to 45 °C (optimum 30 °C), pH 3.5-7.0 (optimum pH 5.0) and in the presence of 0-1.0% (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain DRP 35(T) belongs to the genus Terriglobus in the phylum Acidobacteria with a sequence similarity of 97.2% and 97.0% to Terriglobus saanensis SP1PR4(T) and Terriglobus roseus KBS63(T), respectively. The genomic DNA G+C content was 62.1 mol%. DNA-DNA relatedness between strain DRP 35(T) and the type strains of the other species of the genus Terriglobus, T. saanensis SP1PR4(T) and T. roseus KBS63(T), were 24.6 and 17.2%, respectively. The predominant menaquinone was MK-8. Major fatty acids were iso-C(15 : 0), C(16 : 1)ω7c and C(16 : 0). The polar lipids were phosphatidylethanolamine, unidentified aminophospholipid and unknown phospholipids. On the basis of polyphasic analysis from this study, strain DRP 35(T) represents a novel species of the genus Terriglobus for which the name Terriglobus tenax sp. nov. is proposed. The type strain is DRP 35(T) (= KACC 16474(T) = NBRC 109677(T)).}, }
@article {pmid24096000, year = {2013}, author = {Doğan-Subaşı, E and Bastiaens, L and Boon, N and Dejonghe, W}, title = {Microbial dechlorination activity during and after chemical oxidant treatment.}, journal = {Journal of hazardous materials}, volume = {262}, number = {}, pages = {598-605}, doi = {10.1016/j.jhazmat.2013.09.003}, pmid = {24096000}, issn = {1873-3336}, mesh = {Chloroflexi/*drug effects/genetics/metabolism ; Gene Dosage ; Genes, Bacterial ; Hydrogen-Ion Concentration ; Oxidants/*pharmacology ; Oxidation-Reduction ; Potassium Permanganate/*pharmacology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sodium Compounds/*pharmacology ; Soil Pollutants/*metabolism ; Sulfates/*pharmacology ; Trichloroethylene/*metabolism ; }, abstract = {Potassium permanganate (PM) and sodium persulfate (PS) are used in soil remediation, however, their compatibility with a coinciding or subsequent biotreatment is poorly understood. In this study, different concentrations of PM (0.005-2g/L) and PS (0.01-4.52 g/L) were applied and their effects on the abundance, activity, and reactivation potential of a dechlorinating enrichment culture were investigated. Expression of the tceA, vcrA and 16S rRNA genes of Dehalococcoides spp. were detected at 0.005-0.01 g/L PM and 0.01-0.02 g/L PS. However, with 0.5-2g/L PM and 1.13-4.52 g/L PS no gene expression was recorded, neither were indicator molecules for total cell activity (Adenosine triphosphate, ATP) detected. Dilution did not promote the reactivation of the microbial cells when the redox potential was above -100 mV. Similarly, inoculated cells did not dechlorinate trichloroethene (TCE) above -100 mV. When the redox potential was decreased to -300 mV and the reactors were bioaugmented for a second time, dechlorination activity recovered, but only in the reactors with 1.13 and 2.26 g/L PS. In conclusion, our results show that chemical oxidants can be combined with a biotreatment at concentrations below 0.5 g/L PM and 1g/L PS.}, }
@article {pmid24092956, year = {2013}, author = {Michaelsen, A and Pinzari, F and Barbabietola, N and Piñar, G}, title = {Monitoring the effects of different conservation treatments on paper-infecting fungi.}, journal = {International biodeterioration &amp; biodegradation}, volume = {84}, number = {100}, pages = {333-341}, pmid = {24092956}, issn = {0964-8305}, support = {V 194/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Fungi are among the most degradative organisms inducing biodeterioration of paper-based items of cultural heritage. Appropriate conservation measures and restoration treatments to deal with fungal infections include mechanical, chemical, and biological methods, which entail effects on the paper itself and health hazards for humans. Three different conservation treatments, namely freeze-drying, gamma rays, and ethylene oxide fumigation, were compared and monitored to assess their short- (one month, T1) and long-term (one year, T2) effectiveness to inhibit fungal growth. After the inoculation with fungi possessing cellulose hydrolysis ability - Chaetomium globosum, Trichoderma viride, and Cladosporium cladosporioides - as single strains or as a mixture, different quality paper samples were treated and screened for fungal viability by culture-dependent and -independent techniques. Results derived from both strategies were contradictory. Both gamma irradiation and EtO fumigation showed full efficacy as disinfecting agents when evaluated with cultivation techniques. However, when using molecular analyses, the application of gamma rays showed a short-term reduction in DNA recovery and DNA fragmentation; the latter phenomenon was also observed in a minor degree in samples treated with freeze-drying. When RNA was used as an indicator of long-term fungal viability, differences in the RNA recovery from samples treated with freeze-drying or gamma rays could be observed in samples inoculated with the mixed culture. Only the treatment with ethylene oxide proved negative for both DNA and RNA recovery. Therefore, DNA fragmentation after an ethylene oxide treatment can hamper future paleogenetic and archaeological molecular studies on the objects.}, }
@article {pmid24091030, year = {2013}, author = {Antiabong, JF and Boardman, W and Adetutu, EM and Brown, MH and Ball, AS}, title = {Does anaerobic bacterial antibiosis decrease fungal diversity in oral necrobacillosis disease?.}, journal = {Research in veterinary science}, volume = {95}, number = {3}, pages = {1012-1020}, doi = {10.1016/j.rvsc.2013.09.008}, pmid = {24091030}, issn = {1532-2661}, mesh = {Anaerobiosis ; Animals ; *Antibiosis/genetics ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; Denaturing Gradient Gel Electrophoresis/veterinary ; Fungi/genetics ; Fusobacterium Infections/microbiology/*veterinary ; Fusobacterium necrophorum/genetics ; Macropodidae/*microbiology ; Male ; Mouth/microbiology ; Mycoses/microbiology/veterinary ; Periodontal Diseases/microbiology/*veterinary ; Polymerase Chain Reaction/veterinary ; }, abstract = {Oral necrobacillosis (ON) is a model polymicrobial disease that affects macropods in captivity and livestock. Several studies in humans and animals have focused mainly on the bacterial etiology of this disease with little or no information on the role/association of fungi with ON. Using a Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) assay and statistical analysis of the fungal community structure in healthy and disease groups, a reduction in the species diversity and drastic reduction (>1000 fold) in the fungal population in wallabies with ON was observed. Furthermore, an in vitro assay revealed a potential anaerobic-bacteria antibiosis mechanism in the observed decrease in fungal population in ON and a synergistic bacterial-fungal interaction in wallabies with healthy oral status. This study contributes to our knowledge of the fungal community structure associated with ON and forms the basis for an investigation at an epidemiological scale in order to exploit the clinical potentials of these findings.}, }
@article {pmid24089597, year = {2013}, author = {Bialek, K and Cysneiros, D and O'Flaherty, V}, title = {Low-temperature (10°C) anaerobic digestion of dilute dairy wastewater in an EGSB bioreactor: microbial community structure, population dynamics, and kinetics of methanogenic populations.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2013}, number = {}, pages = {346171}, pmid = {24089597}, issn = {1472-3654}, mesh = {Anaerobiosis ; Bacteroidetes/genetics/isolation &amp; purification ; Biomass ; Bioreactors/*microbiology ; Dairying ; Methane/*biosynthesis ; Methanobacteriales/*metabolism ; Methanomicrobiales/*metabolism ; Oxygen/chemistry ; Population Dynamics ; Proteobacteria/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Spirochaetales/genetics/isolation &amp; purification ; Wastewater/chemistry/*microbiology ; }, abstract = {The feasibility of anaerobic digestion of dairy wastewater at 10°C was investigated in a high height : diameter ratio EGSB reactor. Stable performance was observed at an applied organic loading rate (OLR) of 0.5-2 kg COD m(-3) d(-1) with chemical oxygen demand (COD) removal efficiencies above 85%. When applied OLR increased to values above 2 kg COD m(-3) d(-1), biotreatment efficiency deteriorated, with methanogenesis being the rate-limiting step. The bioreactor recovered quickly (3 days) after reduction of the OLR. qPCR results showed a reduction in the abundance of hydrogenotrophic methanogenic Methanomicrobiales and Methanobacteriales throughout the steady state period followed by a sharp increase in their numbers (111-fold) after the load shock. Specific methanogenic activity and maximum substrate utilising rate (A(max)) of the biomass at the end of trial indicated increased activity and preference towards hydrogenotrophic methanogenesis, which correlated well with the increased abundance of hydrogenotrophic methanogens. Acetoclastic Methanosaeta spp. remained at stable levels throughout the trial. However, increased apparent half-saturation constant (K(m)) at the end of the trial indicated a decrease in the specific substrate affinity for acetate of the sludge, suggesting that Methanosaeta spp., which have high substrate affinity, started to be outcompeted in the reactor.}, }
@article {pmid24088205, year = {2013}, author = {Murali Mohan, A and Hartsock, A and Bibby, KJ and Hammack, RW and Vidic, RD and Gregory, KB}, title = {Microbial community changes in hydraulic fracturing fluids and produced water from shale gas extraction.}, journal = {Environmental science &amp; technology}, volume = {47}, number = {22}, pages = {13141-13150}, doi = {10.1021/es402928b}, pmid = {24088205}, issn = {1520-5851}, mesh = {Bacteria/genetics/*growth &amp; development ; Base Sequence ; Biodiversity ; Geologic Sediments/*chemistry ; Molecular Sequence Data ; Natural Gas/*analysis ; Pennsylvania ; RNA, Ribosomal, 16S/genetics ; *Waste Disposal, Fluid ; *Water Microbiology ; }, abstract = {Microbial communities associated with produced water from hydraulic fracturing are not well understood, and their deleterious activity can lead to significant increases in production costs and adverse environmental impacts. In this study, we compared the microbial ecology in prefracturing fluids (fracturing source water and fracturing fluid) and produced water at multiple time points from a natural gas well in southwestern Pennsylvania using 16S rRNA gene-based clone libraries, pyrosequencing, and quantitative PCR. The majority of the bacterial community in prefracturing fluids constituted aerobic species affiliated with the class Alphaproteobacteria. However, their relative abundance decreased in produced water with an increase in halotolerant, anaerobic/facultative anaerobic species affiliated with the classes Clostridia, Bacilli, Gammaproteobacteria, Epsilonproteobacteria, Bacteroidia, and Fusobacteria. Produced water collected at the last time point (day 187) consisted almost entirely of sequences similar to Clostridia and showed a decrease in bacterial abundance by 3 orders of magnitude compared to the prefracturing fluids and produced water samplesfrom earlier time points. Geochemical analysis showed that produced water contained higher concentrations of salts and total radioactivity compared to prefracturing fluids. This study provides evidence of long-term subsurface selection of the microbial community introduced through hydraulic fracturing, which may include significant implications for disinfection as well as reuse of produced water in future fracturing operations.}, }
@article {pmid24083554, year = {2013}, author = {Montoya, L and Vizioli, C and Rodríguez, N and Rastoll, MJ and Amils, R and Marin, I}, title = {Microbial community composition of Tirez lagoon (Spain), a highly sulfated athalassohaline environment.}, journal = {Aquatic biosystems}, volume = {9}, number = {1}, pages = {19}, pmid = {24083554}, issn = {2046-9063}, abstract = {BACKGROUND: The aim was to study the seasonal microbial diversity variations of an athalassohaline environment with a high concentration of sulfates in Tirez lagoon (La Mancha, Spain). Despite the interest in these types of environments there is scarce information about their microbial ecology, especially on their anoxic sediments.<br><br>RESULTS: We report the seasonal microbial diversity of the water column and the sediments of a highly sulfated lagoon using both molecular and conventional microbiological methods. Algae and Cyanobacteria were the main photosynthetic primary producers detected in the ecosystem in the rainy season. Also dinoflagelates and filamentous fungi were identified in the brines. The highest phylotype abundance in water and sediments corresponded to members of the bacterial phylum Proteobacteria, mainly of the Gamma- and Alphaproteobacteria classes. Firmicutes and Actinobacteria were isolated and identified in Tirez brines and sediment samples. Halophilic sulfate reducing Deltaproteobacteria were also detected (Desulfohalobium).<br><br>CONCLUSIONS: Important differences have been found in the microbial diversity present in the Tirez water column and the sediments between the wet and dry seasons. Also the Tirez lagoon showed a high richness of the bacterial Alpha- and Deltaproteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and for the archaeal Euryarchaeota.}, }
@article {pmid24081282, year = {2014}, author = {Christaki, U and Kormas, KA and Genitsaris, S and Georges, C and Sime-Ngando, T and Viscogliosi, E and Monchy, S}, title = {Winter-summer succession of unicellular eukaryotes in a meso-eutrophic coastal system.}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {13-23}, pmid = {24081282}, issn = {1432-184X}, mesh = {Cercozoa/classification/growth &amp; development ; *Food Chain ; Fungi/classification/growth &amp; development ; Haptophyta/classification/growth &amp; development ; Plankton/classification/*growth &amp; development ; RNA, Ribosomal, 18S/genetics ; *Seasons ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The objective of this study was to explore the succession of planktonic unicellular eukaryotes by means of 18S rRNA gene tag pyrosequencing in the eastern English Channel (EEC) during the winter to summer transition. The 59 most representative (>0.1%, representing altogether 95% of total reads), unique operational taxonomic units (OTUs) from all samples belonged to 18 known high-level taxonomic groups and 1 unaffiliated clade. The five most abundant OTUs (69.2% of total reads) belonged to Dinophyceae, Cercozoa, Haptophyceae, marine alveolate group I, and Fungi. Cluster and network analysis between samples distinguished the winter, the pre-bloom, the Phaeocystis globosa bloom and the post-bloom early summer conditions. The OTUs-based network revealed that P. globosa showed a relatively low number of connections-most of them negative-with all other OTUs. Fungi were linked to all major taxonomic groups, except Dinophyceae. Cercozoa mostly co-occurred with the Fungi, the Bacillariophyceae and several of the miscellaneous OTUs. This study provided a more detailed exploration into the planktonic succession pattern of the EEC due to its increased depth of taxonomic sampling over previous efforts based on classical monitoring observations. Data analysis implied that the food web concept in a coastal system based on predator-prey (e.g. grazer-phytoplankton) relationships is just a part of the ecological picture; and those organisms exploiting a variety of strategies, such as saprotrophy and parasitism, are persistent and abundant members of the community.}, }
@article {pmid24077652, year = {2014}, author = {Andrus, JM and Porter, MD and Rodríguez, LF and Kuehlhorn, T and Cooke, RA and Zhang, Y and Kent, AD and Zilles, JL}, title = {Spatial variation in the bacterial and denitrifying bacterial community in a biofilter treating subsurface agricultural drainage.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {265-272}, pmid = {24077652}, issn = {1432-184X}, mesh = {Agriculture ; Bacteria/classification/*growth &amp; development ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; *Denitrification ; *Drainage, Sanitary ; Filtration ; *Microbial Consortia ; Polymorphism, Restriction Fragment Length ; Spatial Analysis ; *Waste Disposal, Fluid ; }, abstract = {Denitrifying biofilters can remove agricultural nitrates from subsurface drainage, reducing nitrate pollution that contributes to coastal hypoxic zones. The performance and reliability of natural and engineered systems dependent upon microbially mediated processes, such as the denitrifying biofilters, can be affected by the spatial structure of their microbial communities. Furthermore, our understanding of the relationship between microbial community composition and function is influenced by the spatial distribution of samples.In this study we characterized the spatial structure of bacterial communities in a denitrifying biofilter in central Illinois. Bacterial communities were assessed using automated ribosomal intergenic spacer analysis for bacteria and terminal restriction fragment length polymorphism of nosZ for denitrifying bacteria.Non-metric multidimensional scaling and analysis of similarity (ANOSIM) analyses indicated that bacteria showed statistically significant spatial structure by depth and transect,while denitrifying bacteria did not exhibit significant spatial structure. For determination of spatial patterns, we developed a package of automated functions for the R statistical environment that allows directional analysis of microbial community composition data using either ANOSIM or Mantel statistics.Applying this package to the biofilter data, the flow path correlation range for the bacterial community was 6.4 m at the shallower, periodically in undated depth and 10.7 m at the deeper, continually submerged depth. These spatial structures suggest a strong influence of hydrology on the microbial community composition in these denitrifying biofilters. Understanding such spatial structure can also guide optimal sample collection strategies for microbial community analyses.}, }
@article {pmid24077115, year = {2013}, author = {Kåhrström, CT}, title = {Microbial ecology: a bacterial decoy skews plant defences.}, journal = {Nature reviews. Microbiology}, volume = {11}, number = {11}, pages = {740}, pmid = {24077115}, issn = {1740-1534}, mesh = {Animals ; Bacteria/*immunology ; Coleoptera/*microbiology ; Herbivory/*physiology ; Solanum lycopersicum/*immunology/*microbiology ; Mouth/*microbiology ; *Plant Immunity ; }, }
@article {pmid24072077, year = {2014}, author = {Lin, YT and Tang, SL and Pai, CW and Whitman, WB and Coleman, DC and Chiu, CY}, title = {Changes in the soil bacterial communities in a cedar plantation invaded by moso bamboo.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {421-429}, pmid = {24072077}, issn = {1432-184X}, mesh = {Acidobacteria/genetics/*isolation &amp; purification ; Biodiversity ; Cloning, Molecular ; Cryptomeria/*microbiology ; DNA, Bacterial/genetics ; Gene Library ; Phylogeny ; Poaceae/*microbiology ; Proteobacteria/genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Moso bamboo is fast-growing and negatively allelopathic to neighboring plants. However, there is little information on the effects of its establishment and expansion to adjacent forest soil communities. To better understand the impacts of bamboo invasion on soil communities, the phylogenetic structure and diversity of the soil bacterial communities in moso bamboo forest, adjacent Japanese cedar plantation, and bamboo-invaded transition zone were examined using a combination of 16S rRNA gene clone libraries and bar-coded pyrosequencing techniques. Based on the number of operational taxonomic units (OTUs), Shannon diversity index, Chao1 estimator, and rarefaction analysis of both techniques, the bamboo soil bacterial community was the most diverse, followed by the transition zone, with the cedar plantation possessing the lowest diversity. The results from both techniques revealed that the Acidobacteria and Proteobacteria predominated in the three communities, though the relative abundance was different. The 250 most abundant OTUs represented about 70% of the total sequences found by pyrosequencing. Most of these OTUs were found in all three soil communities, demonstrating the overall similarity among the bacterial communities. Nonmetric multidimensional scaling analysis showed further that the bamboo and transition soil communities were more similar with each other than the cedar soils. These results suggest that bamboo invasion to the adjacent cedar plantation gradually increased the bacterial diversity and changed the soil community. In addition, while the 10 most abundant OTUs were distributed worldwide, related sequences were not abundant in soils from outside the forest studied here. This result may be an indication of the uniqueness of this region.}, }
@article {pmid24071779, year = {2013}, author = {Neef, A and Sanz, Y}, title = {Future for probiotic science in functional food and dietary supplement development.}, journal = {Current opinion in clinical nutrition and metabolic care}, volume = {16}, number = {6}, pages = {679-687}, doi = {10.1097/MCO.0b013e328365c258}, pmid = {24071779}, issn = {1473-6519}, mesh = {Diet ; *Dietary Supplements ; Functional Food/*analysis ; Gastrointestinal Tract ; Humans ; Microbiota ; Nutritional Status ; Probiotics/*administration &amp; dosage ; }, abstract = {PURPOSE OF REVIEW: The purpose of this study is to provide an update of probiotic science evolving from classical approaches to the development of next-generation probiotics, parallel to advances in the understanding of the complexity of the gut microbiome and its role in human health.<br><br>RECENT FINDINGS: The probiotic concept is based on the notion that the gut ecosystem contributes to human physiology and, consequently, its modulation may help to maintain health and reduce disease risk. The understanding of the complexity of the gut microbiota and the specific components associated with progression from health to disease is rapidly increasing, thanks to the use of high-throughput and next-generation sequencing techniques in progressively better controlled epidemiological studies. Evidence on microbiome-mediated effects by intervention with classical probiotics on humans is, however, limited. The new information is helping to set a rationale for selection of a next generation of probiotics. Candidates include Clostridia clusters IV, XIVa and XVIII, Faecalibacterium prausnitzii, Akkermansia muciniphila and Bacteroides uniformis, the effects of which have been evaluated in preclinical trials with promising results for inflammatory and diet-related disorders. Yet, the extent to which new probiotic formulations consisting of nonconventional indigenous gut bacteria will be effective on humans at a population level or in personalized nutrition strategies remains to be explored.<br><br>SUMMARY: Understanding the role that indigenous intestinal bacteria and their ecological interactions play in human health and disease based on epidemiological, intervention and mechanistic studies will provide a robust rationale for selection of probiotic strains and facilitate the optimization of integrated dietary strategies to efficiently modulate the human gut microbiome, leading to improvements in nutrition and clinical practice.}, }
@article {pmid24067258, year = {2014}, author = {Harter, J and Krause, HM and Schuettler, S and Ruser, R and Fromme, M and Scholten, T and Kappler, A and Behrens, S}, title = {Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community.}, journal = {The ISME journal}, volume = {8}, number = {3}, pages = {660-674}, pmid = {24067258}, issn = {1751-7370}, mesh = {Charcoal/chemistry/*metabolism ; Denitrification ; Fertilizers ; Nitrogen/chemistry ; Nitrous Oxide/*metabolism ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Nitrous oxide (N2O) contributes 8% to global greenhouse gas emissions. Agricultural sources represent about 60% of anthropogenic N2O emissions. Most agricultural N2O emissions are due to increased fertilizer application. A considerable fraction of nitrogen fertilizers are converted to N2O by microbiological processes (that is, nitrification and denitrification). Soil amended with biochar (charcoal created by pyrolysis of biomass) has been demonstrated to increase crop yield, improve soil quality and affect greenhouse gas emissions, for example, reduce N2O emissions. Despite several studies on variations in the general microbial community structure due to soil biochar amendment, hitherto the specific role of the nitrogen cycling microbial community in mitigating soil N2O emissions has not been subject of systematic investigation. We performed a microcosm study with a water-saturated soil amended with different amounts (0%, 2% and 10% (w/w)) of high-temperature biochar. By quantifying the abundance and activity of functional marker genes of microbial nitrogen fixation (nifH), nitrification (amoA) and denitrification (nirK, nirS and nosZ) using quantitative PCR we found that biochar addition enhanced microbial nitrous oxide reduction and increased the abundance of microorganisms capable of N2-fixation. Soil biochar amendment increased the relative gene and transcript copy numbers of the nosZ-encoded bacterial N2O reductase, suggesting a mechanistic link to the observed reduction in N2O emissions. Our findings contribute to a better understanding of the impact of biochar on the nitrogen cycling microbial community and the consequences of soil biochar amendment for microbial nitrogen transformation processes and N2O emissions from soil.}, }
@article {pmid24064954, year = {2013}, author = {Haruta, S}, title = {Rediscovery of the microbial world in microbial ecology.}, journal = {Microbes and environments}, volume = {28}, number = {3}, pages = {281-284}, pmid = {24064954}, issn = {1347-4405}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; *Ecosystem ; }, }
@article {pmid24062736, year = {2013}, author = {Penton, CR and Johnson, TA and Quensen, JF and Iwai, S and Cole, JR and Tiedje, JM}, title = {Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {279}, pmid = {24062736}, issn = {1664-302X}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, abstract = {Targeting sequencing to genes involved in key environmental processes, i.e., ecofunctional genes, provides an opportunity to sample nature's gene guilds to greater depth and help link community structure to process-level outcomes. Vastly different approaches have been implemented for sequence processing and, ultimately, for taxonomic placement of these gene reads. The overall quality of next generation sequence analysis of functional genes is dependent on multiple steps and assumptions of unknown diversity. To illustrate current issues surrounding amplicon read processing we provide examples for three ecofunctional gene groups. A combination of in silico, environmental and cultured strain sequences was used to test new primers targeting the dioxin and dibenzofuran degrading genes dxnA1, dbfA1, and carAa. The majority of obtained environmental sequences were classified into novel sequence clusters, illustrating the discovery value of the approach. For the nitrite reductase step in denitrification, the well-known nirK primers exhibited deficiencies in reference database coverage, illustrating the need to refine primer-binding sites and/or to design multiple primers, while nirS primers exhibited bias against five phyla. Amino acid-based OTU clustering of these two N-cycle genes from soil samples yielded only 114 unique nirK and 45 unique nirS genus-level groupings, likely a reflection of constricted primer coverage. Finally, supervised and non-supervised OTU analysis methods were compared using the nifH gene of nitrogen fixation, with generally similar outcomes, but the clustering (non-supervised) method yielded higher diversity estimates and stronger site-based differences. High throughput amplicon sequencing can provide inexpensive and rapid access to nature's related sequences by circumventing the culturing barrier, but each unique gene requires individual considerations in terms of primer design and sequence processing and classification.}, }
@article {pmid24061344, year = {2013}, author = {Ram, AS and Palesse, S and Colombet, J and Sabart, M and Perriere, F and Sime-Ngando, T}, title = {Variable viral and grazer control of prokaryotic growth efficiency in temperate freshwater lakes (French Massif Central).}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {906-916}, pmid = {24061344}, issn = {1432-184X}, mesh = {Carbon/metabolism ; *Ecosystem ; Eukaryota/*metabolism ; France ; Heterotrophic Processes ; Lakes/*microbiology/*virology ; Prokaryotic Cells/*physiology/*virology ; Virus Physiological Phenomena ; Viruses/growth &amp; development ; }, abstract = {The effects of viral lysis and heterotrophic nanoflagellate grazing (top down forces) on prokaryotic mortality and their subsequent impact on their metabolism were estimated in the upper euphotic and deeper aphotic depth of 11 freshwater lakes located in the French Massif Central. The standing stocks of viruses (VA) and heterotrophic nanoflagellate (HNF) varied significantly (p < 0.05) with sampled depth. VA was substantially (twofold on an average) and significantly higher (p < 0.03) at the aphotic compared to euphotic depth, whereas the reverse was true (p < 0.02) for HNF. Among the prokaryote subgroup, high nucleic acid content prokaryotes explained for significant variability in the total VA and served as principle host target for viral proliferation. Like standing stocks, flagellate grazing and viral infection rates also followed similar patterns. In the investigated lakes, the mechanism for regulating prokaryotic production varied with sampled depth from grazing control in the euphotic to control due to viral lysis in the aphotic. We also tested the hypothesis of top down control on prokaryotic growth efficiency (PGE, which we used as an index of prokaryotic physiological and energetic status at the community level) at both depths. Overall, among the studied lakes, PGE varied widely (4-51 %) with significantly (p < 0.05) lower values in the aphotic (mean = 18 ± 4 %) than euphotic depth (mean = 32 ± 9 %). Contrasting observations on the top down control of PGE between sampled depths were observed. The presence of grazers was found to stimulate PGE at the euphotic, whereas viruses through their lytic infection had a strong negative impact on PGE at the aphotic depth. Such observed differences in PGE and the mechanism controlling prokaryotic production with depth could eventually have strong implication on carbon and nutrient flux patterns in the studied lakes.}, }
@article {pmid24061343, year = {2013}, author = {Konopka, A and Plymale, AE and Carvajal, DA and Lin, X and McKinley, JP}, title = {Environmental controls on the activity of aquifer microbial communities in the 300 area of the Hanford site.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {889-896}, pmid = {24061343}, issn = {1432-184X}, mesh = {Bacteria/genetics/isolation &amp; purification/*metabolism ; *Ecosystem ; Geologic Sediments/chemistry/*microbiology ; Groundwater/chemistry/*microbiology ; Uranium/chemistry/metabolism ; Washington ; }, abstract = {Aquifer microbes in the 300 Area of the Hanford Site in southeastern Washington State, USA, are located in an oligotrophic environment and are periodically exposed to U(VI) concentrations that can range up to 10 μM in small sediment fractures. Assays of (3)H-leucine incorporation indicated that both sediment-associated and planktonic microbes were metabolically active, and that organic C was growth-limiting in the sediments. Although bacteria suspended in native groundwater retained high activity when exposed to 100 μM U(VI), they were inhibited by U(VI) <1 μM in synthetic groundwater that lacked added bicarbonate. Chemical speciation modeling suggested that positively charged species and particularly (UO2)3(OH)5 (+) rose in concentration as more U(VI) was added to synthetic groundwater, but that carbonate complexes dominated U(VI) speciation in natural groundwater. U toxicity was relieved when increasing amounts of bicarbonate were added to synthetic groundwater containing 4.5 μM U(VI). Pertechnetate, an oxyanion that is another contaminant of concern at the Hanford Site, was not toxic to groundwater microbes at concentrations up to 125 μM.}, }
@article {pmid24061342, year = {2013}, author = {Li, ZP and Liu, HL and Jin, CA and Cui, XZ and Jing, Y and Yang, FH and Li, GY and Wright, AD}, title = {Differences in the methanogen population exist in sika deer (Cervus nippon) fed different diets in China.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {879-888}, pmid = {24061342}, issn = {1432-184X}, mesh = {Animal Feed/*analysis ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; China ; Deer/metabolism/*microbiology ; Male ; Methane/*metabolism ; Molecular Sequence Data ; Phylogeny ; Rumen/*microbiology ; }, abstract = {Understanding the methanogen structure from sika deer (Cervus nippon) in China may be beneficial to methane mitigation. In the present preliminary study, we investigated the methanogen community in the rumen of domesticated sika deer fed either tannin-rich plants (oak leaf, OL group) or corn stalk (CS group) using 16S rRNA gene clone libraries. Overall, we obtained 197 clone sequences, revealing 146 unique phylotypes, which were assigned to 36 operational taxonomic units at the species level (98 % identity). Methanogens related to the genus Methanobrevibacter were the predominant phylotypes representing 83.9 % (OL library) and 85.9 % (CS library) of the clones. Methanobrevibacter millerae was the most abundant species in both libraries, but the proportion of M. millerae-related clones in the CS library was higher than in the OL library (69.5 and 51.4 %, respectively). Moreover, Methanobrevibacter wolinii-related clones (32.5 %) were predominant in the OL library. Methanobrevibacter smithii-related clones and Methanobrevibacter ruminantium-related clones accounted for 6.5 and 6.6 % in the CS library, respectively. However, these clones were absent from the OL library. The concentrations of butyrate and total short-chain fatty acids (SCFAs) were significantly higher in the OL group, but the concentrations of acetate, propionate, and valerate and the acetate to propionate ratio in the OL group were not significantly different between the two groups. Tannin-rich plants may have affected the distribution of genus Methanobrevibacter phylotypes at the species level and the concentration and composition of SCFAs.}, }
@article {pmid24061057, year = {2014}, author = {Jiang, Y and Xu, H and Warren, A}, title = {Insights into discriminating environmental quality status using taxonomic distinctness based on a small species pool of ciliated protozoa in marine ecosystems.}, journal = {The Science of the total environment}, volume = {468-469}, number = {}, pages = {663-670}, doi = {10.1016/j.scitotenv.2013.08.083}, pmid = {24061057}, issn = {1879-1026}, mesh = {Animal Nutritional Physiological Phenomena/*genetics ; Animals ; China ; Ciliophora/classification/*genetics ; Ecological Parameter Monitoring/*methods ; Environmental Monitoring/*methods ; *Genetic Variation ; Linear Models ; Marine Biology ; Oceans and Seas ; Population Density ; Population Dynamics ; Species Specificity ; Water Quality/*standards ; }, abstract = {The objective of this study was to determine the feasibility of developing a protocol for assessing marine water quality based on taxonomic relatedness within a small pool of planktonic ciliates. An annual dataset was compiled based on samples collected biweekly at five sites, with a gradient of environmental stress, during a 1-year cycle in Jiaozhou Bay, northern China. A total of 60 species, belonging to 17 genera 10 families, 5 orders and 2 classes of the phylum Ciliophora, were identified. Among five orders, Tintinnida showed a low variability mainly at species level whereas the other orders (especially Strombidiida and Choreotrichida, although with the exception of the genus Strombidium) represented a high variability at higher taxonomic ranks (e.g. family or order). Mantel analyses showed that spatial patterns of the ciliate assemblages, with tinitinnids and Strombidium spp. excluded, were significantly correlated with those of the total planktonic ciliate communities in terms of their response to environmental status. The average taxonomic distinctness (Δ(+)) based on the small species pool was significantly negatively correlated with the changes in concentrations of nutrients (P<0.05). Furthermore, the paired indices of Δ(+) and the variation in taxonomic distinctness (Λ(+)) showed a clear departure from the expected taxonomic pattern. These findings suggest that it is possible to assess the status of marine water quality using the taxonomic relatedness within a small pool of planktonic ciliates.}, }
@article {pmid24060131, year = {2013}, author = {Navas-Molina, JA and Peralta-Sánchez, JM and González, A and McMurdie, PJ and Vázquez-Baeza, Y and Xu, Z and Ursell, LK and Lauber, C and Zhou, H and Song, SJ and Huntley, J and Ackermann, GL and Berg-Lyons, D and Holmes, S and Caporaso, JG and Knight, R}, title = {Advancing our understanding of the human microbiome using QIIME.}, journal = {Methods in enzymology}, volume = {531}, number = {}, pages = {371-444}, pmid = {24060131}, issn = {1557-7988}, support = {R01 GM086884/GM/NIGMS NIH HHS/United States ; T32 GM008759/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; R01GM086884/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*genetics/pathogenicity ; Computational Biology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Mice ; Microbiota/*genetics ; Phylogeny ; Software ; }, abstract = {High-throughput DNA sequencing technologies, coupled with advanced bioinformatics tools, have enabled rapid advances in microbial ecology and our understanding of the human microbiome. QIIME (Quantitative Insights Into Microbial Ecology) is an open-source bioinformatics software package designed for microbial community analysis based on DNA sequence data, which provides a single analysis framework for analysis of raw sequence data through publication-quality statistical analyses and interactive visualizations. In this chapter, we demonstrate the use of the QIIME pipeline to analyze microbial communities obtained from several sites on the bodies of transgenic and wild-type mice, as assessed using 16S rRNA gene sequences generated on the Illumina MiSeq platform. We present our recommended pipeline for performing microbial community analysis and provide guidelines for making critical choices in the process. We present examples of some of the types of analyses that are enabled by QIIME and discuss how other tools, such as phyloseq and R, can be applied to expand upon these analyses.}, }
@article {pmid24060128, year = {2013}, author = {Hawley, AK and Kheirandish, S and Mueller, A and Leung, HT and Norbeck, AD and Brewer, HM and Pasa-Tolic, L and Hallam, SJ}, title = {Molecular tools for investigating microbial community structure and function in oxygen-deficient marine waters.}, journal = {Methods in enzymology}, volume = {531}, number = {}, pages = {305-329}, doi = {10.1016/B978-0-12-407863-5.00016-2}, pmid = {24060128}, issn = {1557-7988}, mesh = {Archaea/*genetics ; Biodiversity ; DNA, Bacterial/genetics ; Microbial Consortia/*genetics ; Oxygen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry ; }, abstract = {Water column oxygen (O2)-deficiency shapes food-web structure by progressively directing nutrients and energy away from higher trophic levels into microbial community metabolism resulting in fixed nitrogen loss and greenhouse gas production. Although respiratory O2 consumption during organic matter degradation is a natural outcome of a productive surface ocean, global-warming-induced stratification intensifies this process leading to oxygen minimum zone (OMZ) expansion. Here, we describe useful tools for detection and quantification of potential key microbial players and processes in OMZ community metabolism including quantitative polymerase chain reaction primers targeting Marine Group I Thaumarchaeota, SUP05, Arctic96BD-19, and SAR324 small-subunit ribosomal RNA genes and protein extraction methods from OMZ waters compatible with high-resolution mass spectrometry for profiling microbial community structure and functional dynamics.}, }
@article {pmid24060127, year = {2013}, author = {Mueller, RS and Pan, C}, title = {Sample handling and mass spectrometry for microbial metaproteomic analyses.}, journal = {Methods in enzymology}, volume = {531}, number = {}, pages = {289-303}, doi = {10.1016/B978-0-12-407863-5.00015-0}, pmid = {24060127}, issn = {1557-7988}, mesh = {Bacteria/genetics ; Chromatography, Liquid/*methods ; Mass Spectrometry/*methods ; *Metagenome ; Microbial Consortia/genetics ; Proteome/genetics ; *Specimen Handling ; }, abstract = {Metaproteomic studies of whole microbial communities from environmental samples (e.g., soil, sediments, freshwater, seawater, etc.) have rapidly increased in recent years due to many technological advances in mass spectrometry (MS). A single 24-h liquid chromatograph-tandem mass spectrometry (LC-MS/MS) measurement can potentially detect and quantify thousands of proteins from many dominant and subdominant naturally occurring microbial populations. Importantly, amino acid sequences and relative abundance information for detected peptides are determined, which allows for the characterization of expressed protein functions within communities and specific matches to be made to microbial lineages, with potential subspecies resolution. Continued optimization of protein extraction and fractionation protocols, development of quantification methods, and advances in mass spectrometry instrumentation are enabling more accurate and comprehensive peptide detection within samples, leading to wider research applicability, greater ease of use, and overall accessibility. This chapter provides a brief overview of metaproteomics experimental options, including a general protocol for sample handling and LC-MS/MS measurement.}, }
@article {pmid24060123, year = {2013}, author = {Roume, H and Heintz-Buschart, A and Muller, EE and Wilmes, P}, title = {Sequential isolation of metabolites, RNA, DNA, and proteins from the same unique sample.}, journal = {Methods in enzymology}, volume = {531}, number = {}, pages = {219-236}, doi = {10.1016/B978-0-12-407863-5.00011-3}, pmid = {24060123}, issn = {1557-7988}, mesh = {Bacteria/genetics/metabolism ; DNA/*isolation &amp; purification/metabolism ; Feces/microbiology ; Genome, Bacterial ; Humans ; *Metabolomics ; Plankton/genetics/metabolism ; Proteins/*isolation &amp; purification ; RNA/*isolation &amp; purification/metabolism ; Systems Biology ; }, abstract = {In microbial ecology, high-resolution molecular approaches are essential for characterizing the vast organismal and functional diversity and understanding the interaction of microbial communities with biotic and abiotic environmental factors. Integrated omics, comprising genomics, transcriptomics, proteomics, and metabolomics allows conclusive links to be drawn between genetic potential and function. However, this requires truly systematic measurements. In this chapter, we first assess the levels of heterogeneity within mixed microbial communities, thereby demonstrating the need for analyzing biomolecular fractions obtained from a single and undivided sample to facilitate multi-omic analysis and meaningful data integration. Further, we describe a methodological workflow for the reproducible isolation of concomitant metabolites, RNA (optionally split into large and small RNA fractions), DNA, and proteins. Depending on the nature of the sample, the methodology comprises different (pre)processing and preservation steps. If possible, extracellular polar and nonpolar metabolites may first be extracted from cell supernatants using organic solvents. Cells are homogenized by cryomilling before small molecules are extracted with organic solvents. After cell lysis, nucleic acids and protein fractions are sequentially isolated using chromatographic spin columns. To prove the broad applicability of the methodology, we applied it to microbial consortia of biotechnological (biological wastewater treatment biomass), environmental (freshwater planktonic communities), and biomedical (human fecal sample) research interest. The methodological framework should be applicable to other microbial communities as well as other biological samples with a minimum of tailoring and represents an important first step in standardization for the emerging field of Molecular Eco-Systems Biology.}, }
@article {pmid24060119, year = {2013}, author = {Martínez, A and Osburne, MS}, title = {Preparation of fosmid libraries and functional metagenomic analysis of microbial community DNA.}, journal = {Methods in enzymology}, volume = {531}, number = {}, pages = {123-142}, doi = {10.1016/B978-0-12-407863-5.00007-1}, pmid = {24060119}, issn = {1557-7988}, mesh = {DNA, Bacterial ; Genetic Vectors ; *Genomic Library ; Metagenomics/*methods ; Microbial Consortia/*genetics ; }, abstract = {One of the most important challenges in contemporary microbial ecology is to assign a functional role to the large number of novel genes discovered through large-scale sequencing of natural microbial communities that lack similarity to genes of known function. Functional screening of metagenomic libraries, that is, screening environmental DNA clones for the ability to confer an activity of interest to a heterologous bacterial host, is a promising approach for bridging the gap between metagenomic DNA sequencing and functional characterization. Here, we describe methods for isolating environmental DNA and constructing metagenomic fosmid libraries, as well as methods for designing and implementing successful functional screens of such libraries.}, }
@article {pmid24060115, year = {2013}, author = {Thompson, A and Bench, S and Carter, B and Zehr, J}, title = {Coupling FACS and genomic methods for the characterization of uncultivated symbionts.}, journal = {Methods in enzymology}, volume = {531}, number = {}, pages = {45-60}, doi = {10.1016/B978-0-12-407863-5.00003-4}, pmid = {24060115}, issn = {1557-7988}, mesh = {Ecology ; *Flow Cytometry ; Genome, Bacterial ; *High-Throughput Nucleotide Sequencing ; *Metagenomics ; Symbiosis/*genetics ; }, abstract = {Symbioses between microbes are likely widespread and functionally relevant in diverse biological systems; however, they are difficult to discover. Most microbes remain uncultivated, symbioses can be relatively rare or dynamic, and intercellular connections can be delicate. Thus, traditional methods such as microscopy are inadequate for efficient discovery and precise characterization of novel interactions, their metabolic basis, and the species involved. High-throughput metagenomic sequencing of entire microbial communities has revolutionized the field of microbial ecology; however, genomic signals from symbionts can get buried in sequences from abundant organisms and evidence for direct links between microbial species cannot be gained from bulk samples. Thus, a specialized approach to the characterization of symbioses between naturally occurring microbes is required. This chapter presents methods for combining fluorescence-activated cell sorting to isolate and separate uncultivated symbionts with molecular biology techniques for DNA amplification in order to characterize uncultivated symbionts through genomic and metagenomic techniques.}, }
@article {pmid24058885, year = {2013}, author = {McCoy, CO and Matsen, FA}, title = {Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth.}, journal = {PeerJ}, volume = {1}, number = {}, pages = {e157}, pmid = {24058885}, issn = {2167-8359}, support = {R37 AI038518/AI/NIAID NIH HHS/United States ; }, abstract = {In microbial ecology studies, the most commonly used ways of investigating alpha (within-sample) diversity are either to apply non-phylogenetic measures such as Simpson's index to Operational Taxonomic Unit (OTU) groupings, or to use classical phylogenetic diversity (PD), which is not abundance-weighted. Although alpha diversity measures that use abundance information in a phylogenetic framework do exist, they are not widely used within the microbial ecology community. The performance of abundance-weighted phylogenetic diversity measures compared to classical discrete measures has not been explored, and the behavior of these measures under rarefaction (sub-sampling) is not yet clear. In this paper we compare the ability of various alpha diversity measures to distinguish between different community states in the human microbiome for three different datasets. We also present and compare a novel one-parameter family of alpha diversity measures, BWPDθ, that interpolates between classical phylogenetic diversity (PD) and an abundance-weighted extension of PD. Additionally, we examine the sensitivity of these phylogenetic diversity measures to sampling, via computational experiments and by deriving a closed form solution for the expectation of phylogenetic quadratic entropy under re-sampling. On the three datasets, a phylogenetic measure always performed best, and two abundance-weighted phylogenetic diversity measures were the only measures ranking in the top four across all datasets. OTU-based measures, on the other hand, are less effective in distinguishing community types. In addition, abundance-weighted phylogenetic diversity measures are less sensitive to differing sampling intensity than their unweighted counterparts. Based on these results we encourage the use of abundance-weighted phylogenetic diversity measures, especially for cases such as microbial ecology where species delimitation is difficult.}, }
@article {pmid24058578, year = {2013}, author = {Pereira E Silva, MC and Schloter-Hai, B and Schloter, M and van Elsas, JD and Salles, JF}, title = {Temporal dynamics of abundance and composition of nitrogen-fixing communities across agricultural soils.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e74500}, pmid = {24058578}, issn = {1932-6203}, mesh = {*Agriculture ; Bacteria/genetics ; Base Sequence ; *Biodiversity ; Denaturing Gradient Gel Electrophoresis ; Genes, Bacterial/genetics ; Genetic Variation ; Netherlands ; *Nitrogen Fixation ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; Time Factors ; }, abstract = {BACKGROUND: Despite the fact that the fixation of nitrogen is one of the most significant nutrient processes in the terrestrial ecosystem, a thorough study of the spatial and temporal patterns in the abundance and distribution of N-fixing communities has been missing so far.<br><br>In order to understand the dynamics of diazotrophic communities and their resilience to external changes, we quantified the abundance and characterized the bacterial community structures based on the nifH gene, using real-time PCR, PCR-DGGE and 454-pyrosequencing, across four representative Dutch soils during one growing season. In general, higher nifH gene copy numbers were observed in soils with higher pH than in those with lower pH, but lower numbers were related to increased nitrate and ammonium levels. Results from nifH gene pyrosequencing confirmed the observed PCR-DGGE patterns, which indicated that the N fixers are highly dynamic across time, shifting around 60%. Forward selection on CCA analysis identified N availability as the main driver of these variations, as well as of the evenness of the communities, leading to very unequal communities. Moreover, deep sequencing of the nifH gene revealed that sandy soils (B and D) had the lowest percentage of shared OTUs across time, compared with clayey soils (G and K), indicating the presence of a community under constant change. Cosmopolitan nifH species (present throughout the season) were affiliated with Bradyrhizobium, Azospirillum and Methylocistis, whereas other species increased their abundances progressively over time, when appropriate conditions were met, as was notably the case for Paenibacilus and Burkholderia.<br><br>CONCLUSIONS: Our study provides the first in-depth pyrosequencing analysis of the N-fixing community at both spatial and temporal scales, providing insights into the cosmopolitan and specific portions of the nitrogen fixing bacterial communities in soil.}, }
@article {pmid24057323, year = {2014}, author = {Azúa, I and Goiriena, I and Baña, Z and Iriberri, J and Unanue, M}, title = {Release and consumption of D-amino acids during growth of marine prokaryotes.}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {1-12}, pmid = {24057323}, issn = {1432-184X}, mesh = {Alanine/metabolism ; Amino Acids/*metabolism ; Aspartic Acid/metabolism ; Axenic Culture ; Bays ; D-Aspartic Acid/metabolism ; Ecosystem ; Heterotrophic Processes ; Microbial Consortia ; Organic Chemicals/metabolism ; Seawater/*microbiology ; Vibrio/*metabolism ; }, abstract = {Analysis of the composition of the marine-dissolved organic matter has highlighted the importance of D-amino acids, whose origin is attributed mainly to the remains of bacterial peptidoglycan released as a result of grazing or viral lysis. However, very few studies have focused on the active release of D-amino acids by bacteria. With this purpose, we measured the concentration of dissolved amino acids in both enantiomeric forms with two levels of complexity: axenic cultures of Vibrio furnissii and Vibrio alginolyticus and microcosms created from marine microbial assemblages (Biscay Bay, Cantabrian Sea) with and without heterotrophic nanoflagellates (HNFs). Axenic cultures showed that only D-Ala was significantly released and accumulated in the medium up to a concentration of 120 nM, probably as a consequence of the rearrangement of peptidoglycan. The marine microbial assemblages showed that only two D-amino acids significantly accumulated in the environment, D-Ala and D-aspartic acid (Asp), in both the absence and presence of HNFs. The D/L ratio increased during the incubation and reached maximum values of 3.0 to 4.3 for Ala and 0.4 to 10.6 for Asp and correlated with prokaryotic and HNF abundance as well as the rate of prokaryotic thymidine and leucine incorporation. Prokaryotes preferentially consumed L-amino acids, but the relative uptake rates of D-Ala significantly increased in the growth phase. These results demonstrate that bacteria can release and consume D-amino acids at high rates during growth, even in the absence of viruses and grazers, highlighting the importance of bacteria as producers of dissolved organic matter (DOM) in the sea.}, }
@article {pmid24057322, year = {2014}, author = {Stauffert, M and Duran, R and Gassie, C and Cravo-Laureau, C}, title = {Response of archaeal communities to oil spill in bioturbated mudflat sediments.}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {108-119}, pmid = {24057322}, issn = {1432-184X}, mesh = {Animals ; Archaea/classification/*growth &amp; development/metabolism ; DNA, Archaeal/genetics ; *Ecosystem ; France ; Genes, Archaeal ; Geologic Sediments/*chemistry ; Hydrocarbons/metabolism ; *Microbial Consortia ; *Petroleum Pollution ; Phylogeny ; Polychaeta ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The response of archaeal community to oil spill with the combined effect of the bioturbation activity of the polychaetes Hediste diversicolor was determined in mudflat sediments from the Aber-Benoît basin (Brittany, French Atlantic coast), maintained in microcosms. The dynamics of the archaeal community was monitored by combining comparative terminal restriction fragment length polymorphism (T-RFLP) fingerprints and sequence library analyses based on 16S rRNA genes and 16S cDNA. Methanogens were also followed by targeting the mcrA gene. Crenarchaeota were always detected in all communities irrespective of the addition of H. diversicolor and/or oil. In the presence of oil, modifications of archaeal community structures were observed. These modifications were more pronounced when H. diversicolor was added resulting in a more diverse community especially for the Euryarchaeota and Thaumarchaeota. The analysis of mcrA transcripts showed a specific structure for each condition since the beginning of the experiment. Overall, oiled microcosms showed different communities irrespective of H. diversicolor addition, while similar hydrocarbon removal capacities were observed.}, }
@article {pmid24057273, year = {2014}, author = {Thelaus, J and Andersson, A and Broman, T and Bäckman, S and Granberg, M and Karlsson, L and Kuoppa, K and Larsson, E and Lundmark, E and Lundström, JO and Mathisen, P and Näslund, J and Schäfer, M and Wahab, T and Forsman, M}, title = {Francisella tularensis subspecies holarctica occurs in Swedish mosquitoes, persists through the developmental stages of laboratory-infected mosquitoes and is transmissible during blood feeding.}, journal = {Microbial ecology}, volume = {67}, number = {1}, pages = {96-107}, pmid = {24057273}, issn = {1432-184X}, mesh = {Animals ; Culicidae/*microbiology ; DNA, Bacterial/isolation &amp; purification ; Endemic Diseases ; Feeding Behavior ; Female ; *Francisella tularensis ; Insect Vectors/*microbiology ; Larva/microbiology ; Mice ; Mice, Inbred C57BL ; Sweden ; Tularemia/*transmission ; }, abstract = {In Sweden, mosquitoes are considered the major vectors of the bacterium Francisella tularensis subsp. holarctica, which causes tularaemia. The aim of this study was to investigate whether mosquitoes acquire the bacterium as aquatic larvae and transmit the disease as adults. Mosquitoes sampled in a Swedish area where tularaemia is endemic (Örebro) were positive for the presence of F. tularensis deoxyribonucleic acid throughout the summer. Presence of the clinically relevant F. tularensis subsp. holarctica was confirmed in 11 out of the 14 mosquito species sampled. Experiments performed using laboratory-reared Aedes aegypti confirmed that F. tularensis subsp. holarctica was transstadially maintained from orally infected larvae to adult mosquitoes and that 25% of the adults exposed as larvae were positive for the presence of F. tularensis-specific sequences for at least 2 weeks. In addition, we found that F. tularensis subsp. holarctica was transmitted to 58% of the adult mosquitoes feeding on diseased mice. In a small-scale in vivo transmission experiment with F. tularensis subsp. holarctica-positive adult mosquitoes and susceptible mice, none of the animals developed tularaemia. However, we confirmed that there was transmission of the bacterium to blood vials by mosquitoes that had been exposed to the bacterium in the larval stage. Taken together, these results provide evidence that mosquitoes play a role in disease transmission in part of Sweden where tularaemia recurs.}, }
@article {pmid24056930, year = {2013}, author = {Philippot, L and Raaijmakers, JM and Lemanceau, P and van der Putten, WH}, title = {Going back to the roots: the microbial ecology of the rhizosphere.}, journal = {Nature reviews. Microbiology}, volume = {11}, number = {11}, pages = {789-799}, pmid = {24056930}, issn = {1740-1534}, mesh = {Bacteria/classification ; Climate Change ; Conservation of Natural Resources ; Ecosystem ; Plant Roots/*microbiology ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {The rhizosphere is the interface between plant roots and soil where interactions among a myriad of microorganisms and invertebrates affect biogeochemical cycling, plant growth and tolerance to biotic and abiotic stress. The rhizosphere is intriguingly complex and dynamic, and understanding its ecology and evolution is key to enhancing plant productivity and ecosystem functioning. Novel insights into key factors and evolutionary processes shaping the rhizosphere microbiome will greatly benefit from integrating reductionist and systems-based approaches in both agricultural and natural ecosystems. Here, we discuss recent developments in rhizosphere research in relation to assessing the contribution of the micro- and macroflora to sustainable agriculture, nature conservation, the development of bio-energy crops and the mitigation of climate change.}, }
@article {pmid24055388, year = {2013}, author = {Brown Kav, A and Benhar, I and Mizrahi, I}, title = {A method for purifying high quality and high yield plasmid DNA for metagenomic and deep sequencing approaches.}, journal = {Journal of microbiological methods}, volume = {95}, number = {2}, pages = {272-279}, doi = {10.1016/j.mimet.2013.09.008}, pmid = {24055388}, issn = {1872-8359}, mesh = {Animals ; Cattle ; DNA, Bacterial/genetics/*isolation &amp; purification ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/*methods ; Plasmids/genetics/*isolation &amp; purification ; Polymerase Chain Reaction ; Rumen/microbiology ; Sequence Analysis, DNA/methods ; }, abstract = {Deep sequencing techniques used in metagenomic approaches have greatly advanced the study of microbial communities in various environments. However, one microbial segment that has remained largely unexplored is the natural plasmids residing within microbial environments. Plasmids are perceived as mobile genetic elements that exist extra-chromosomally and occasionally carry accessory genes that confer an advantage to their host in its ecological niche. They are thus thought to play an important evolutionary role in microbial communities by laterally introducing genes and traits into microbial genomes. Despite their importance, technical obstacles still limit the metagenomic study of natural plasmids using deep sequencing techniques. These include low copy number of the plasmids and heterogeneity of microbes in environmental samples, reflected in the low abundance of each individual plasmid. Furthermore, the extracted plasmids usually contain remnants of chromosomal DNA that can potentially interfere with the analysis of unique plasmid traits. We have recently studied the rumen metagenomic plasmid population using a newly developed procedure that successfully overcomes these obstacles. This procedure enables extraction of pure plasmid DNA suited for deep sequencing studies. Here we present a detailed description and characterization of this procedure which could potentially allow the study of plasmids in other environmental niches.}, }
@article {pmid24053940, year = {2013}, author = {Benner, J and Helbling, DE and Kohler, HP and Wittebol, J and Kaiser, E and Prasse, C and Ternes, TA and Albers, CN and Aamand, J and Horemans, B and Springael, D and Walravens, E and Boon, N}, title = {Is biological treatment a viable alternative for micropollutant removal in drinking water treatment processes?.}, journal = {Water research}, volume = {47}, number = {16}, pages = {5955-5976}, doi = {10.1016/j.watres.2013.07.015}, pmid = {24053940}, issn = {1879-2448}, mesh = {Environmental Monitoring ; Water Pollutants, Chemical/analysis ; Water Purification/*methods ; *Water Supply ; }, abstract = {In western societies, clean and safe drinking water is often taken for granted, but there are threats to drinking water resources that should not be underestimated. Contamination of drinking water sources by anthropogenic chemicals is one threat that is particularly widespread in industrialized nations. Recently, a significant amount of attention has been given to the occurrence of micropollutants in the urban water cycle. Micropollutants are bioactive and/or persistent chemicals originating from diverse sources that are frequently detected in water resources in the pg/L to μg/L range. The aim of this review is to critically evaluate the viability of biological treatment processes as a means to remove micropollutants from drinking water resources. We first place the micropollutant problem in context by providing a comprehensive summary of the reported occurrence of micropollutants in raw water used directly for drinking water production and in finished drinking water. We then present a critical discussion on conventional and advanced drinking water treatment processes and their contribution to micropollutant removal. Finally, we propose biological treatment and bioaugmentation as a potential targeted, cost-effective, and sustainable alternative to existing processes while critically examining the technical limitations and scientific challenges that need to be addressed prior to implementation. This review will serve as a valuable source of data and literature for water utilities, water researchers, policy makers, and environmental consultants. Meanwhile this review will open the door to meaningful discussion on the feasibility and application of biological treatment and bioaugmentation in drinking water treatment processes to protect the public from exposure to micropollutants.}, }
@article {pmid24046075, year = {2013}, author = {Zhang, XX and Gao, JS and Cao, YH and Ma, XT and He, JZ}, title = {Long-term rice and green manure rotation alters the endophytic bacterial communities of the rice root.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {917-926}, pmid = {24046075}, issn = {1432-184X}, mesh = {Agriculture ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Endophytes/classification/genetics/*isolation &amp; purification ; Manure/*analysis ; Molecular Sequence Data ; Oryza/growth &amp; development/*microbiology ; Phylogeny ; Plant Roots/*microbiology ; Time Factors ; }, abstract = {This study focuses on the effects of long-term rice rotated with milk vetch being as green manure on the composition of bacteria in rice roots. The endophytic bacterial communities in rice roots of the rice-rice-milk vetch (R-R-MV) and the rice-rice-winter fallow (R-R-WF) crop rotations with a 28-year research history were investigated using combined culture-dependent and culture-independent methods. It was found that the endophytic bacterial population in rice roots with the green manure was significantly higher than that of without it. There were 169 and 77 strains of endophytic bacteria that were isolated from rice roots of the R-R-MV and the R-R-WF, respectively. The 16S rRNA gene analysis shows that the 77 R-R-WF bacteria belong to 15 species of 14 genera while the other 169 R-R-MV bacteria belong to 21 species of 19 genera, in which Herbaspirillum and Cedecea were two mutually dominant populations and Burkholderia, Pseudomonas, Sphingomonas, and Pantoea accounted for large proportions of the endophytic bacteria in rice roots through R-R-MV rotation. The analysis of 16S rDNA clone libraries showed that the Shannon-Weaver diversity index of endophytic bacteria in R-R-MV approximates that in R-R-WF rotation, whereas the richness indexes of Chao 1 and ACE in R-R-MV rotation system were significantly higher than those in R-R-WF rotation. The diversity of endophytic bacteria was richer in R-R-MV. Both the culture-dependent and the culture-independent method revealed significant effect of long-term different tillage systems on the microbial community.}, }
@article {pmid24046074, year = {2013}, author = {Chiaramonte, JB and Roberto, Mdo C and Pagioro, TA}, title = {Seasonal dynamics and community structure of bacterioplankton in upper Paraná River floodplain.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {773-783}, pmid = {24046074}, issn = {1432-184X}, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; *Ecosystem ; Floods ; Rivers/chemistry/*microbiology ; Seasons ; }, abstract = {Knowing the bacterial community, as well as understanding how it changes during a hydrological pulse, is very important to understand nutrient cycles in floodplain systems. The bacterial community structure was analyzed in the 12 sites of upper Paraná River floodplain, and its changes during a flood pulse were described. In order to understand how high and low water phases change bacterial community by changing abiotical variables, the bacterial community distribution was determined in superficial water of 12 different sampling stations, every 3 months, from December 2010 to September 2011. The bacterial community structure and diversity was analyzed by fluorescent in situ hybridization, considering the main domains Bacteria and Archaea and the subdivisions of the phylum Proteobacteria (Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria) and the Cytophaga-Flavobacterium cluster. Smaller densities were observed on ebb and low water periods and the highest density was observed in March 2011. The high water period caused a decrease in diversity because of the lost of equitability. The highest values of Shannon-Wiener index were found on December 2010 and September 2011. The nutrients runoff to the aquatic environments of the floodplain promoted an increase in the total bacterial density during the high water phase as well as changes in bacterial community composition. The bacterial community presented both spatial and temporal differences. Yet, temporal changes in limnological characteristics of the floodplain were the most important predictor of bacterial community and also influenced its diversity.}, }
@article {pmid24046073, year = {2013}, author = {Singh, AK and Rai, GK and Singh, M and Dubey, SK}, title = {Bacterial community structure in the rhizosphere of a Cry1Ac Bt-brinjal crop and comparison to its non-transgenic counterpart in the tropical soil.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {927-939}, pmid = {24046073}, issn = {1432-184X}, mesh = {Bacillus thuringiensis Toxins ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Endotoxins/genetics/metabolism ; Hemolysin Proteins/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Plants, Genetically Modified/genetics/*microbiology ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; Solanum melongena/genetics/*microbiology ; }, abstract = {To elucidate whether the transgenic crop alters the rhizospheric bacterial community structure, a 2-year study was performed with Cry1Ac gene-inserted brinjal crop (Bt) and their near isogenic non-transformed trait (non-Bt). The event of Bt crop (VRBT-8) was screened using an insect bioassay and enzyme-linked immunosorbent assay. Soil moisture, NH4 (+)-N, NO3 (-)-N, and PO4 (-)-P level had non-significant variation. Quantitative polymerase chain reaction revealed that abundance of bacterial 16S rRNA gene copies were lower in soils associated with Bt brinjal. Microbial biomass carbon (MBC) showed slight reduction in Bt brinjal soils. Higher MBC values in the non-Bt crop soil may be attributed to increased root activity and availability of readily metabolizable carbon compounds. The restriction fragment length polymorphism of PCR-amplified rRNA gene fragments detected 13 different bacterial groups with the exclusive presence of β-Proteobacteria, Chloroflexus, Planctomycetes, and Fusobacteria in non-Bt, and Cyanobacteria and Bacteroidetes in Bt soils, respectively, reflecting minor changes in the community structure. Despite the detection of Cry1Ac protein in the rhizospheric soil, the overall impact of Cry1Ac expressing Bt brinjal was less compared to that due to seasonal changes.}, }
@article {pmid24045641, year = {2013}, author = {Wang, Q and Quensen, JF and Fish, JA and Lee, TK and Sun, Y and Tiedje, JM and Cole, JR}, title = {Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool.}, journal = {mBio}, volume = {4}, number = {5}, pages = {e00592-13}, pmid = {24045641}, issn = {2150-7511}, support = {UH3 DK083993/DK/NIDDK NIH HHS/United States ; UH3DK083993/DK/NIDDK NIH HHS/United States ; }, mesh = {Alaska ; Algorithms ; Amino Acid Sequence ; Bacteria/classification/*enzymology/genetics/isolation &amp; purification ; Bacterial Proteins/*genetics ; Ecosystem ; Florida ; Frameshift Mutation ; Hawaii ; Metagenomics/*instrumentation/methods ; Molecular Sequence Data ; Oxidoreductases/*genetics ; Phylogeny ; Soil Microbiology ; Utah ; }, abstract = {UNLABELLED: Biological nitrogen fixation is an important component of sustainable soil fertility and a key component of the nitrogen cycle. We used targeted metagenomics to study the nitrogen fixation-capable terrestrial bacterial community by targeting the gene for nitrogenase reductase (nifH). We obtained 1.1 million nifH 454 amplicon sequences from 222 soil samples collected from 4 National Ecological Observatory Network (NEON) sites in Alaska, Hawaii, Utah, and Florida. To accurately detect and correct frameshifts caused by indel sequencing errors, we developed FrameBot, a tool for frameshift correction and nearest-neighbor classification, and compared its accuracy to that of two other rapid frameshift correction tools. We found FrameBot was, in general, more accurate as long as a reference protein sequence with 80% or greater identity to a query was available, as was the case for virtually all nifH reads for the 4 NEON sites. Frameshifts were present in 12.7% of the reads. Those nifH sequences related to the Proteobacteria phylum were most abundant, followed by those for Cyanobacteria in the Alaska and Utah sites. Predominant genera with nifH sequences similar to reads included Azospirillum, Bradyrhizobium, and Rhizobium, the latter two without obvious plant hosts at the sites. Surprisingly, 80% of the sequences had greater than 95% amino acid identity to known nifH gene sequences. These samples were grouped by site and correlated with soil environmental factors, especially drainage, light intensity, mean annual temperature, and mean annual precipitation. FrameBot was tested successfully on three ecofunctional genes but should be applicable to any.<br><br>IMPORTANCE: High-throughput phylogenetic analysis of microbial communities using rRNA-targeted sequencing is now commonplace; however, such data often allow little inference with respect to either the presence or the diversity of genes involved in most important ecological processes. To study the gene pool for these processes, it is more straightforward to assess the genes directly responsible for the ecological function (ecofunctional genes). However, analyzing these genes involves technical challenges beyond those seen for rRNA. In particular, frameshift errors cause garbled downstream protein translations. Our FrameBot tool described here both corrects frameshift errors in query reads and determines their closest matching protein sequences in a set of reference sequences. We validated this new tool with sequences from defined communities and demonstrated the tool's utility on nifH gene fragments sequenced from soils in well-characterized and major terrestrial ecosystem types.}, }
@article {pmid24040342, year = {2013}, author = {Henderson, G and Cox, F and Kittelmann, S and Miri, VH and Zethof, M and Noel, SJ and Waghorn, GC and Janssen, PH}, title = {Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e74787}, pmid = {24040342}, issn = {1932-6203}, mesh = {Animals ; Cattle/microbiology ; DNA/*isolation &amp; purification ; Ecology ; Microbial Consortia ; Phylogeny ; Polymerase Chain Reaction ; Principal Component Analysis ; Rumen/*microbiology ; Sequence Analysis, DNA/*methods ; Sheep/microbiology ; }, abstract = {Molecular microbial ecology techniques are widely used to study the composition of the rumen microbiota and to increase understanding of the roles they play. Therefore, sampling and DNA extraction methods that result in adequate yields of microbial DNA that also accurately represents the microbial community are crucial. Fifteen different methods were used to extract DNA from cow and sheep rumen samples. The DNA yield and quality, and its suitability for downstream PCR amplifications varied considerably, depending on the DNA extraction method used. DNA extracts from nine extraction methods that passed these first quality criteria were evaluated further by quantitative PCR enumeration of microbial marker loci. Absolute microbial numbers, determined on the same rumen samples, differed by more than 100-fold, depending on the DNA extraction method used. The apparent compositions of the archaeal, bacterial, ciliate protozoal, and fungal communities in identical rumen samples were assessed using 454 Titanium pyrosequencing. Significant differences in microbial community composition were observed between extraction methods, for example in the relative abundances of members of the phyla Bacteroidetes and Firmicutes. Microbial communities in parallel samples collected from cows by oral stomach-tubing or through a rumen fistula, and in liquid and solid rumen digesta fractions, were compared using one of the DNA extraction methods. Community representations were generally similar, regardless of the rumen sampling technique used, but significant differences in the abundances of some microbial taxa such as the Clostridiales and the Methanobrevibacter ruminantium clade were observed. The apparent microbial community composition differed between rumen sample fractions, and Prevotellaceae were most abundant in the liquid fraction. DNA extraction methods that involved phenol-chloroform extraction and mechanical lysis steps tended to be more comparable. However, comparison of data from studies in which different sampling techniques, different rumen sample fractions or different DNA extraction methods were used should be avoided.}, }
@article {pmid24038691, year = {2013}, author = {Ho, A and Erens, H and Mujinya, BB and Boeckx, P and Baert, G and Schneider, B and Frenzel, P and Boon, N and Van Ranst, E}, title = {Termites facilitate methane oxidation and shape the methanotrophic community.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {23}, pages = {7234-7240}, pmid = {24038691}, issn = {1098-5336}, mesh = {Animals ; Bacteria/*classification/*metabolism ; Bacterial Load ; *Biodiversity ; Isoptera/*physiology ; Methane/*metabolism ; Microarray Analysis ; Oxidation-Reduction ; Polymerase Chain Reaction ; *Soil Microbiology ; }, abstract = {Termite-derived methane contributes 3 to 4% to the total methane budget globally. Termites are not known to harbor methane-oxidizing microorganisms (methanotrophs). However, a considerable fraction of the methane produced can be consumed by methanotrophs that inhabit the mound material, yet the methanotroph ecology in these environments is virtually unknown. The potential for methane oxidation was determined using slurry incubations under conditions with high (12%) and in situ (∼0.004%) methane concentrations through a vertical profile of a termite (Macrotermes falciger) mound and a reference soil. Interestingly, the mound material showed higher methanotrophic activity. The methanotroph community structure was determined by means of a pmoA-based diagnostic microarray. Although the methanotrophs in the mound were derived from populations in the reference soil, it appears that termite activity selected for a distinct community. Applying an indicator species analysis revealed that putative atmospheric methane oxidizers (high-indicator-value probes specific for the JR3 cluster) were indicative of the active nest area, whereas methanotrophs belonging to both type I and type II were indicative of the reference soil. We conclude that termites modify their environment, resulting in higher methane oxidation and selecting and/or enriching for a distinct methanotroph population.}, }
@article {pmid24034943, year = {2013}, author = {He, Y and Zhou, BJ and Deng, GH and Jiang, XT and Zhang, H and Zhou, HW}, title = {Comparison of microbial diversity determined with the same variable tag sequence extracted from two different PCR amplicons.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {208}, pmid = {24034943}, issn = {1471-2180}, mesh = {Animals ; *Biota ; DNA Primers/*genetics ; Feces/*microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenomics/*methods ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {BACKGROUND: Deep sequencing of the variable region of 16S rRNA genes has become the predominant tool for studying microbial ecology. As sequencing datasets have accumulated, meta-analysis of sequences obtained with different variable 16S rRNA gene targets and by different sequencing methods has become an intriguing prospect that remains to be evaluated experimentally.<br><br>RESULTS: We amplified a group of fecal samples using both V4F-V6R and V6F-V6R primer sets, excised the same V6 fragment from the two sets of Illumina sequencing data, and compared the resulting data in terms of the &#x3b1;-diversity, &#x3b2;-diversity, and community structure. Principal component analysis (PCA) comparing the microbial community structures of different datasets, including those with simulated sequencing errors, was very reliable. Procrustes analysis showed a high degree of concordance between the different datasets for both abundance-weighted and binary Jaccard distances (P&#x2009;<&#x2009;0.05), and a meta-analysis of individual datasets resulted in similar conclusions. The Shannon's diversity index was consistent as well, with comparable values obtained for the different datasets and for the meta-analysis of different datasets. In contrast, richness estimators (OTU and Chao) varied significantly, and the meta-analysis of richness estimators was also biased. The community structures of the two datasets were obviously different and led to significant changes in the biomarkers identified by the LEfSe statistical tool.<br><br>CONCLUSIONS: Our results suggest that beta-diversity analysis and Shannon's diversity are relatively reliable for meta-analysis, while community structures and biomarkers are less consistent. These results should be useful for future meta-analyses of microbiomes from different data sources.}, }
@article {pmid24033913, year = {2014}, author = {Puentes-Téllez, PE and Kovács, &#xc1;T and Kuipers, OP and van Elsas, JD}, title = {Comparative genomics and transcriptomics analysis of experimentally evolved Escherichia coli MC1000 in complex environments.}, journal = {Environmental microbiology}, volume = {16}, number = {3}, pages = {856-870}, doi = {10.1111/1462-2920.12239}, pmid = {24033913}, issn = {1462-2920}, mesh = {*Biological Evolution ; Environment ; *Environmental Microbiology ; Escherichia coli/classification/*genetics ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Genome, Bacterial/*genetics ; Genomics ; Metabolic Networks and Pathways/genetics ; Mutation ; Oxygen/metabolism ; Principal Component Analysis ; Transcriptome/*genetics ; }, abstract = {It has recently become feasible to study the basis and nature of evolutionary changes in bacteria in an experimental setting using defined media. However, assessment of adaptive changes in complex environments has been scarce. In an effort to describe the responses in such environments, we unravel, in a comparative approach, the transcriptional and genetic profiles of 19 Escherichia coli strains that evolved in Luria Bertani medium under three different oxygen regimes over 1000 generations. A positive relationship between upregulation of gene expression and the number of mutations was observed, suggesting that a number of metabolic pathways were activated. Phenotypic polymorphisms were observed in parallel cultures, of which some were related with mutations at the regulatory level. Non-parallel responses were observed at the intrapopulational level, which is indicative of diversifying selection. Parallel responses encompassed transcriptome diversity, and their effects were directly affected by differing genomic backgrounds. A fluctuating selective force produced higher phenotypic diversity compared with constant forces. This study demonstrates how phenotypic innovations may depend on the relationship between genomic changes and local ecological conditions. Using both comparative genomics and transcriptomics approaches, the results help elucidating various adaptive responses in cultures in unexplored complex environments.}, }
@article {pmid24033859, year = {2014}, author = {Varon-Lopez, M and Dias, AC and Fasanella, CC and Durrer, A and Melo, IS and Kuramae, EE and Andreote, FD}, title = {Sulphur-oxidizing and sulphate-reducing communities in Brazilian mangrove sediments.}, journal = {Environmental microbiology}, volume = {16}, number = {3}, pages = {845-855}, doi = {10.1111/1462-2920.12237}, pmid = {24033859}, issn = {1462-2920}, mesh = {Bacteria/classification/*genetics ; Brazil ; *Ecosystem ; *Environmental Microbiology ; Environmental Monitoring ; Genes, Bacterial/genetics ; Geologic Sediments/chemistry/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Soil Pollutants/analysis ; Sulfates/metabolism ; Sulfur/metabolism ; }, abstract = {Mangrove soils are anaerobic environments rich in sulphate and organic matter. Although the sulphur cycle is one of the major actors in this ecosystem, little is known regarding the sulphur bacteria communities in mangrove soils. We investigated the abundance, composition and diversity of sulphur-oxidizing (SOB) and sulphate-reducing (SRB) bacteria in sediments from three Brazilian mangrove communities: two contaminated, one with oil (OilMgv) and one with urban waste and sludge (AntMgv), and one pristine (PrsMgv). The community structures were assessed using quantitative real-time polymerase chain reaction (qPCR), polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and clone libraries, using genes for the enzymes adenosine-5'-phosphosulphate reductase (aprA) and sulphite reductase (Dsr) (dsrB). The abundance for qPCR showed the ratio dsrB/aprA to be variable among mangroves and higher according to the gradient observed for oil contamination in the OilMgv. The PCR-DGGE patterns analysed by Nonmetric Multidimensional Scaling revealed differences among the structures of the three mangrove communities. The clone libraries showed that Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria were the most abundant groups associated with sulphur cycling in mangrove sediments. We conclude that the microbial SOB and SRB communities in mangrove soils are different in each mangrove forest and that such microbial communities could possibly be used as a proxy for contamination in mangrove forests.}, }
@article {pmid24031949, year = {2012}, author = {Ghizelini, AM and Mendonça-Hagler, LC and Macrae, A}, title = {Microbial diversity in Brazilian mangrove sediments - a mini review.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {43}, number = {4}, pages = {1242-1254}, pmid = {24031949}, issn = {1517-8382}, abstract = {The importance and protection of mangrove ecosystems has been recognized in Brazilian Federal law since 1965. Being protected in law, however, has not always guaranteed their protection in practice. Mangroves are found in coastal and estuarine locations, which are prime real estate for the growth of cities, ports and other economic activities important for Brazilian development. In this mini-review we introduce what mangroves are and why they are so important. We give a brief overview of the microbial diversity found in mangrove sediments and then focus on diversity studies from Brazilian mangroves. We highlight the breadth and depth of knowledge about mangrove microbial communities gained from studying Brazilian mangroves. We report on the exciting findings of molecular microbial ecology methods that have been very successfully applied to study bacterial communities. We note that there have been fewer studies that focus on fungal communities and that fungal diversity studies deserve more attention. The review ends with a look at how a combination of new molecular biology methods and isolation studies are being developed to monitor and conserve mangrove ecosystems and their associated microbial communities. These recent studies are having a global impact and we hope they will help to protect and re-establish mangrove ecosystems.}, }
@article {pmid24030599, year = {2014}, author = {Ganesh, S and Parris, DJ and DeLong, EF and Stewart, FJ}, title = {Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone.}, journal = {The ISME journal}, volume = {8}, number = {1}, pages = {187-211}, pmid = {24030599}, issn = {1751-7370}, mesh = {Bacteria/classification/*genetics/metabolism ; *Biodiversity ; Chile ; *Metagenome ; Metagenomics ; Oxidation-Reduction ; Oxygen/analysis/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; }, abstract = {Marine oxygen minimum zones (OMZs) support diverse microbial communities with roles in major elemental cycles. It is unclear how the taxonomic composition and metabolism of OMZ microorganisms vary between particle-associated and free-living size fractions. We used amplicon (16S rRNA gene) and shotgun metagenome sequencing to compare microbial communities from large (>1.6 μm) and small (0.2-1.6 μm) filter size fractions along a depth gradient in the OMZ off Chile. Despite steep vertical redox gradients, size fraction was a significantly stronger predictor of community composition compared to depth. Phylogenetic diversity showed contrasting patterns, decreasing towards the anoxic OMZ core in the small size fraction, but exhibiting maximal values at these depths within the larger size fraction. Fraction-specific distributions were evident for key OMZ taxa, including anammox planctomycetes, whose coding sequences were enriched up to threefold in the 0.2-1.6 μm community. Functional gene composition also differed between fractions, with the >1.6 μm community significantly enriched in genes mediating social interactions, including motility, adhesion, cell-to-cell transfer, antibiotic resistance and mobile element activity. Prokaryotic transposase genes were three to six fold more abundant in this fraction, comprising up to 2% of protein-coding sequences, suggesting that particle surfaces may act as hotbeds for transposition-based genome changes in marine microbes. Genes for nitric and nitrous oxide reduction were also more abundant (three to seven fold) in the larger size fraction, suggesting microniche partitioning of key denitrification steps. These results highlight an important role for surface attachment in shaping community metabolic potential and genome content in OMZ microorganisms.}, }
@article {pmid24030595, year = {2014}, author = {Daniel, H and Gholami, AM and Berry, D and Desmarchelier, C and Hahne, H and Loh, G and Mondot, S and Lepage, P and Rothballer, M and Walker, A and Böhm, C and Wenning, M and Wagner, M and Blaut, M and Schmitt-Kopplin, P and Kuster, B and Haller, D and Clavel, T}, title = {High-fat diet alters gut microbiota physiology in mice.}, journal = {The ISME journal}, volume = {8}, number = {2}, pages = {295-308}, pmid = {24030595}, issn = {1751-7370}, support = {294343/ERC_/European Research Council/International ; }, mesh = {Animals ; Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; Biodiversity ; Cecum/microbiology ; *Diet, High-Fat ; Gastrointestinal Tract/*microbiology ; Male ; Metabolome ; Mice ; Mice, Inbred C57BL ; Microbiota/*physiology ; Obesity/microbiology ; Proteome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The intestinal microbiota is known to regulate host energy homeostasis and can be influenced by high-calorie diets. However, changes affecting the ecosystem at the functional level are still not well characterized. We measured shifts in cecal bacterial communities in mice fed a carbohydrate or high-fat (HF) diet for 12 weeks at the level of the following: (i) diversity and taxa distribution by high-throughput 16S ribosomal RNA gene sequencing; (ii) bulk and single-cell chemical composition by Fourier-transform infrared- (FT-IR) and Raman micro-spectroscopy and (iii) metaproteome and metabolome via high-resolution mass spectrometry. High-fat diet caused shifts in the diversity of dominant gut bacteria and altered the proportion of Ruminococcaceae (decrease) and Rikenellaceae (increase). FT-IR spectroscopy revealed that the impact of the diet on cecal chemical fingerprints is greater than the impact of microbiota composition. Diet-driven changes in biochemical fingerprints of members of the Bacteroidales and Lachnospiraceae were also observed at the level of single cells, indicating that there were distinct differences in cellular composition of dominant phylotypes under different diets. Metaproteome and metabolome analyses based on the occurrence of 1760 bacterial proteins and 86 annotated metabolites revealed distinct HF diet-specific profiles. Alteration of hormonal and anti-microbial networks, bile acid and bilirubin metabolism and shifts towards amino acid and simple sugars metabolism were observed. We conclude that a HF diet markedly affects the gut bacterial ecosystem at the functional level.}, }
@article {pmid24028202, year = {2013}, author = {Van den Abbeele, P and Venema, K and Van de Wiele, T and Verstraete, W and Possemiers, S}, title = {Different human gut models reveal the distinct fermentation patterns of Arabinoxylan versus inulin.}, journal = {Journal of agricultural and food chemistry}, volume = {61}, number = {41}, pages = {9819-9827}, doi = {10.1021/jf4021784}, pmid = {24028202}, issn = {1520-5118}, mesh = {Animals ; Bacteria/growth &amp; development/*metabolism ; Bifidobacterium/growth &amp; development/metabolism ; Dietary Fiber/analysis/metabolism/microbiology ; Fermentation ; Gastrointestinal Tract/*metabolism/microbiology ; Humans ; Inulin/*metabolism ; Microbiota ; Models, Biological ; Prebiotics/analysis/microbiology ; Rats ; Xylans/chemistry/*metabolism ; }, abstract = {Different in vitro models have been developed to assess how food compounds affect the human gut microbiota. Using two such models (SHIME(R) and TIM-2), we compared how long-chain arabinoxylan (LC-AX), a wheat-derived potentially prebiotic fiber, and inulin (IN), a well-established prebiotic compound, modulate SCFA production and bifidobacteria composition. While both the SHIME and TIM-2 differ in experimental design, they both demonstrated that LC-AX and IN specifically increased the health-promoting metabolites propionate and butyrate, respectively. Furthermore, LC-AX stimulated Bifidobacterium longum, while IN stimulated other bifidobacteria including Bifidobacterium adolescentis. The SHIME experiment also revealed that effects of LC-AX were more persistent during the 2-week wash-out period. These results confirm a recent in vivo study, during which humanized rats were treated with the same LC-AX/IN. In conclusion, results from different human gut models suggest that, besides IN, LC-AX are promising prebiotic candidates with high specificity toward Bifidobacterium longum and a selective propionate increase.}, }
@article {pmid24024954, year = {2013}, author = {Sixt, BS and Kostanjšek, R and Mustedanagic, A and Toenshoff, ER and Horn, M}, title = {Developmental cycle and host interaction of Rhabdochlamydia porcellionis, an intracellular parasite of terrestrial isopods.}, journal = {Environmental microbiology}, volume = {15}, number = {11}, pages = {2980-2993}, doi = {10.1111/1462-2920.12252}, pmid = {24024954}, issn = {1462-2920}, support = {281633/ERC_/European Research Council/International ; }, mesh = {Acanthamoeba/microbiology ; Animals ; Apoptosis/*physiology ; Cell Line ; Chlamydiales/*pathogenicity ; Cytoplasm ; Host-Pathogen Interactions/*physiology ; Humans ; Insecta/microbiology ; Isopoda/*microbiology ; }, abstract = {Environmental chlamydiae are a diverse group of obligate intracellular bacteria related to well-known pathogens of humans. To date, only very little is known about chlamydial species infecting arthropods. In this study, we used cocultivation with insect cells for recovery and maintenance of Rhabdochlamydia porcellionis, a parasite of the crustacean host Porcellio scaber. In vitro, the infection cycle of R. porcellionis was completed within 7 days, resulting in the release of infectious particles by host cell lysis. Lack of apoptosis induction during the entire course of infection, combined with a reduced sensitivity of infected cultures to experimentally induced programmed cell death, indicates that R. porcellionis like its human pathogenic relatives counteracts this host defence mechanism. Interestingly, the rod-shaped variant of R. porcellionis, proposed to represent their mature infective stage, was not detected in cell culture, suggesting that its development may require prolonged maturation or may be triggered by specific conditions encountered only in the animal host. This first cell culture-based system for the cultivation and investigation of an arthropod-associated chlamydial species will help to better understand the biology of a so far neglected group of chlamydiae and its recently suggested potential to cause disease in humans.}, }
@article {pmid24024645, year = {2014}, author = {Agulló-Barceló, M and Moss, JA and Green, J and Gillespie, S and Codony, F and Lucena, F and Nocker, A}, title = {Quantification of relative proportions of intact cells in microbiological samples using the example of Cryptosporidium parvum oocysts.}, journal = {Letters in applied microbiology}, volume = {58}, number = {1}, pages = {70-78}, doi = {10.1111/lam.12157}, pmid = {24024645}, issn = {1472-765X}, mesh = {*Azides ; Cryptosporidium parvum/genetics/*physiology ; DNA, Protozoan/analysis/genetics ; Hot Temperature ; Microbial Viability ; Oocysts/*physiology ; Polymerase Chain Reaction/*methods ; Propidium/*analogs &amp; derivatives ; Ultraviolet Rays ; }, abstract = {UNLABELLED: The fast analysis of relative proportions of live and dead cells can be of great value whether for comparing inactivation efficiencies of different biocidal treatments or for monitoring organisms of interest in environmental samples. We introduce here a straightforward method to determine the percentage of intact cells based on treatment of samples with the viability dye propidium monoazide (PMA). PMA selectively enters membrane-damaged cells and suppresses their PCR detection through modification of their DNA. The study was performed using Cryptosporidium parvum oocysts as a model although the principle should be applicable to other organisms. Validation was performed with defined mixtures of live and heat-killed oocysts and by exposing oocysts to a heat stress gradient. The method correctly indicated increasingly lower proportions of intact cells with increasing temperatures. When comparing the loss of membrane integrity of UV-killed (40 mJ cm(-2)) oocysts during storage in nonsterile tap water, results suggested that integrity declines slowly (over weeks) and at a rate comparable to non-UV-exposed oocysts. For all experiments, the amplification of longer DNA sequences was found beneficial. In the UV experiment, longer amplicons revealed not only higher sensitivity in excluding membrane-damaged oocysts, but also in excluding DNA with UV-induced damage.<br><br>Whether in the context of microbial ecology or in an industrial context, many questions in microbiology are linked to microbial viability. As cultivation of micro-organisms can be long or may not be possible, fast methods to assess the numbers of live cells are in great demand. We present here a straightforward strategy to determine the relative proportions of intact cells. The PCR-based rapid method is expected to be useful where relative information is sufficient (e.g. for comparing the effect of different antimicrobial treatments on known numbers of micro-organisms) or when the presence of PCR inhibitors does not allow absolute quantification.}, }
@article {pmid24024093, year = {2013}, author = {Panelli, S and Brambati, E and Bonacina, C and Feligini, M}, title = {Diversity of fungal flora in raw milk from the Italian Alps in relation to pasture altitude.}, journal = {SpringerPlus}, volume = {2}, number = {}, pages = {405}, pmid = {24024093}, issn = {2193-1801}, abstract = {The present paper explores the diversity of mycobiota inhabiting raw milk sampled at different altitudes (1400 m, 1800 m, 2200 m) from cows grazing Alpine pastures of Valle d'Aosta (North-Western Italian Alps). To this aim, multilocus sequencing was performed at barcodes commonly used for fungal identification (ITS1, D1/D2 domains of the 26S rRNA gene, and part of the β-tubulin gene). A total of 31 species were detected, most of them yeasts, followed by moulds and by 2 sequences of macroscopic fungi. Several yeasts and moulds were well-characterized inhabitants of the dairy environment, known to positively contribute to cheesemaking. Among these, Candida was the most represented genus with a tendency to cluster at the highest altitudes (6 over 8 observations at ≥ 1800 m), and Kluyveromyces marxianus the most abundant single species, retrieved at all altitudes. The environmental ascomycetous Atrotorquata lineata, never put in relation with food nor described outside North-America, was another species among those most frequently retrieved and was detected in 6 milks at 1400 and 1800 m. The remaining fungi, in general never reported in milk, were mostly environmental. Many of them resulted associated with plants as pathogens or symbionts. Finally, the highest sampled altitude yielded a significant fungal diversity (17 species). This work enlarges the knowledge of fungal consortia inhabiting raw milk and introduces microbial ecology among the altitude-dependent factors, in the composition of Alpine pastures, with the potential of shaping the properties of milks and cheeses, together with the already described physical, chemical and botanical variables.}, }
@article {pmid24020336, year = {2013}, author = {Hanzel, J and Myrold, D and Sessitsch, A and Smalla, K and Tebbe, CC and Totsche, KU}, title = {Microbial ecology of biogeochemical interfaces - diversity, structure, and function of microhabitats in soil.}, journal = {FEMS microbiology ecology}, volume = {86}, number = {1}, pages = {1-2}, doi = {10.1111/1574-6941.12194}, pmid = {24020336}, issn = {1574-6941}, mesh = {Ecosystem ; Soil/chemistry ; *Soil Microbiology ; }, }
@article {pmid24014534, year = {2013}, author = {Penton, CR and St Louis, D and Cole, JR and Luo, Y and Wu, L and Schuur, EA and Zhou, J and Tiedje, JM}, title = {Fungal diversity in permafrost and tallgrass prairie soils under experimental warming conditions.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {22}, pages = {7063-7072}, pmid = {24014534}, issn = {1098-5336}, mesh = {Alaska ; Ascomycota/*classification/genetics ; Basidiomycota/*classification/genetics ; Bayes Theorem ; *Biodiversity ; Chytridiomycota/*classification/genetics ; DNA, Fungal/genetics ; Genes, Fungal ; Molecular Sequence Data ; Mycological Typing Techniques ; Oklahoma ; Phylogeny ; Poaceae/*microbiology ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Soil fungi play a major role in terrestrial ecosystem functioning through interactions with soil structure, plants, micro- and mesofauna, and nutrient cycling through predation, pathogenesis, mutualistic, and saprotrophic roles. The diversity of soil fungi was assessed by sequencing their 28S rRNA gene in Alaskan permafrost and Oklahoma tallgrass prairie soils at experimental sites where the effect of climate warming is under investigation. A total of 226,695 reads were classified into 1,063 genera, covering 62% of the reference data set. Using the Bayesian Classifier offered by the Ribosomal Database Project (RDP) with 50% bootstrapping classification confidence, approximately 70% of sequences were returned as "unclassified" at the genus level, although the majority (∼65%) were classified at the class level, which provided insight into these lesser-known fungal lineages. Those unclassified at the genus level were subjected to BLAST analysis against the ARB-SILVA database, where ∼50% most closely matched nonfungal taxa. Compared to the more abundant sequences, a higher proportion of rare operational taxonomic units (OTU) were successfully classified to genera at 50% bootstrap confidence, indicating that the fungal rare biosphere in these sites is not composed of sequencing artifacts. There was no significant effect after 1 year of warming on the fungal community structure at both sites, except perhaps for a few minor members, but there was a significant effect of sample depth in the permafrost soils. Despite overall significant community structure differences driven by variations in OTU dominance, the prairie and permafrost soils shared 90% and 63% of all fungal sequences, respectively, indicating a fungal "seed bank" common between both sites.}, }
@article {pmid24013213, year = {2013}, author = {Barbosa, C and Venail, P and Holguin, AV and Vives, MJ}, title = {Co-evolutionary dynamics of the bacteria Vibrio sp. CV1 and phages V1G, V1P1, and V1P2: implications for phage therapy.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {897-905}, pmid = {24013213}, issn = {1432-184X}, mesh = {Animals ; Aquaculture ; Bacterial Infections/microbiology/therapy/*veterinary ; Bacteriophages/classification/genetics/*physiology ; *Biological Evolution ; Biological Therapy/*veterinary ; Humans ; Penaeidae/*microbiology ; Vibrio/*genetics/*virology ; }, abstract = {Bacterial infections are the second largest cause of mortality in shrimp hatcheries. Among them, bacteria from the genus Vibrio constitute a major threat. As the use of antibiotics may be ineffective and banned from the food sector, alternatives are required. Historically, phage therapy, which is the use of bacteriophages, is thought to be a promising option to fight against bacterial infections. However, as for antibiotics, resistance can be rapidly developed. Since the emergence of resistance is highly undesirable, a formal characterization of the dynamics of its acquisition is mandatory. Here, we explored the co-evolutionary dynamics of resistance between the bacteria Vibrio sp. CV1 and the phages V1G, V1P1, and V1P2. Single-phage treatments as well as a cocktail composed of the three phages were considered. We found that in the presence of a single phage, bacteria rapidly evolved resistance, and the phages decreased their infectivity, suggesting that monotherapy may be an inefficient treatment to fight against Vibrio infections in shrimp hatcheries. On the contrary, the use of a phage cocktail considerably delayed the evolution of resistance and sustained phage infectivity for periods in which shrimp larvae are most susceptible to bacterial infections, suggesting the simultaneous use of multiple phages as a serious strategy for the control of vibriosis. These findings are very promising in terms of their consequences to different industrial and medical scenarios where bacterial infections are present.}, }
@article {pmid24008514, year = {2013}, author = {Rout, ME and Southworth, D}, title = {The root microbiome influences scales from molecules to ecosystems: The unseen majority.}, journal = {American journal of botany}, volume = {100}, number = {9}, pages = {1689-1691}, doi = {10.3732/ajb.1300291}, pmid = {24008514}, issn = {1537-2197}, mesh = {Ecosystem ; Host-Pathogen Interactions ; Microbiota/*physiology ; Plant Roots/*microbiology ; Plants/*microbiology ; Rhizosphere ; Signal Transduction ; *Soil Microbiology ; Symbiosis ; }, abstract = {Plants are teeming with microbial organisms including those that colonize internal tissues as well as those that adhere to external surfaces. In the rhizosphere, the plant-associated microbiome is intricately involved in plant health and serves as a reservoir of additional genes that plants can access when needed. Microbiome regulation of plant trait expression affects plant performance, which in turn influences various ecosystem functions, such as primary productivity and soil health. Understanding these plant- and microbe-driven interactions requires a study of the nature and effects of the plant microbiome. Conceptualizing the microbiome requires a synthesis of microbial ecology, physiology, and bioinformatics, integrated with insight into host biology and ecology. Microbiome structure and function analyses are recognized as essential components to understand the genetic and functional capacity of the host (previously assigned solely to the host) and include vital aspects of metabolism and physiology. Here, as a special section, we present a set of papers that address the complex interactions between plants and root microbiomes in the rhizosphere. This unseen majority spans scales; with its microorganisms numerically dominant in terrestrial ecosystems, the root microbiome is also involved in plant genetics through integral roles in plant trait expression that can effect community composition and ecosystem functions, such as soil health.}, }
@article {pmid24006902, year = {2013}, author = {Possemiers, S and Pinheiro, I and Verhelst, A and Van den Abbeele, P and Maignien, L and Laukens, D and Reeves, SG and Robinson, LE and Raas, T and Schneider, YJ and Van de Wiele, T and Marzorati, M}, title = {A dried yeast fermentate selectively modulates both the luminal and mucosal gut microbiota and protects against inflammation, as studied in an integrated in vitro approach.}, journal = {Journal of agricultural and food chemistry}, volume = {61}, number = {39}, pages = {9380-9392}, doi = {10.1021/jf402137r}, pmid = {24006902}, issn = {1520-5118}, mesh = {Anti-Inflammatory Agents/*metabolism ; Bacterial Adhesion ; Bifidobacterium/growth &amp; development/immunology/metabolism ; Cell Line ; Clostridium/growth &amp; development/immunology/metabolism ; Coculture Techniques ; Cytokines/antagonists &amp; inhibitors/metabolism ; Enterobacteriaceae/growth &amp; development/immunology/*metabolism ; Enterocytes/immunology/*metabolism/microbiology ; Fermentation ; Humans ; Immunologic Factors/*metabolism ; Lactobacillaceae/growth &amp; development/immunology/metabolism ; Monocytes/immunology/*metabolism/microbiology ; Mucus/metabolism ; *Prebiotics ; Saccharomyces cerevisiae/*metabolism ; }, abstract = {EpiCor, derived from Saccharomyces cerevisiae, has been shown to have immunomodulating properties in human clinical trials and in vitro. However, the underlying mechanisms behind its immune protection via the gut remain largely unknown. Therefore, the aim of this study was to use an integrated in vitro approach to evaluate the metabolism of EpiCor by the intestinal microflora, its modulating effect on the gut microbiota, and its anti-inflammatory activity on human-derived cell lines. Using the SHIME model, in combination with a mucus adhesion assay, has shown that low doses of EpiCor have a prebiotic-like modulatory effect on the luminal- and mucosa-associated microbiota. These include gradual changes in general community structure, reduction of potential pathogens, quantitative increase in lactobacilli, and qualitative modulation of bifidobacteria. Moreover, by combination of the SHIME with Caco-2 cells and Caco-2/THP1 cocultures, a significant decrease in pro-inflammatory cytokines was observed at the end of the treatment period.}, }
@article {pmid24006482, year = {2014}, author = {Han, SI and Lee, HJ and Whang, KS}, title = {Chitinophaga polysaccharea sp. nov., an exopolysaccharide-producing bacterium isolated from the rhizoplane of Dioscorea japonica.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {64}, number = {Pt 1}, pages = {55-59}, doi = {10.1099/ijs.0.055228-0}, pmid = {24006482}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Bacteroidetes/*classification/genetics/isolation &amp; purification ; Base Composition ; DNA, Bacterial/genetics ; Dioscorea/*microbiology ; Fatty Acids/chemistry ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {A novel strain designated MRP-15(T), belonging to the class Sphingobacteriia (phylum Bacteroidetes), was isolated from the rhizoplane of Dioscorea japonica in South Korea and was characterized taxonomically using a polyphasic approach. The strain was found to comprise Gram-stain-negative, aerobic, non-motile, non-spore-forming rods. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belonged to the genus Chitinophaga but was clearly separated from established species of the genus Chitinophaga. 16S rRNA gene sequence similarities between strain MRP-15(T) and type strains of established species of the genus Chitinophaga ranged from 90.3 to 97.8 %. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; major fatty acids, iso-C15 : 0 and C16 : 1ω5c) supported the affiliation of strain MRP-15(T) with the genus Chitinophaga. Therefore strain MRP-15(T) represents a novel species of the genus Chitinophaga, for which the name Chitinophaga polysaccharea sp. nov. is proposed. The type strain is MRP-15(T) (= KACC 17184(T) = NCAIMB 02530(T)).}, }
@article {pmid23999276, year = {2013}, author = {Mosher, JJ and Bernberg, EL and Shevchenko, O and Kan, J and Kaplan, LA}, title = {Efficacy of a 3rd generation high-throughput sequencing platform for analyses of 16S rRNA genes from environmental samples.}, journal = {Journal of microbiological methods}, volume = {95}, number = {2}, pages = {175-181}, doi = {10.1016/j.mimet.2013.08.009}, pmid = {23999276}, issn = {1872-8359}, support = {2P20 RR016472-09/RR/NCRR NIH HHS/United States ; }, mesh = {Biofilms ; DNA, Bacterial/genetics/*isolation &amp; purification ; Ecosystem ; Geologic Sediments/microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics/*isolation &amp; purification ; Sequence Analysis, DNA/*methods ; Shewanella/genetics ; Soil Microbiology ; }, abstract = {Longer sequences of the bacterial 16S rRNA gene could provide greater phylogenetic and taxonomic resolutions and advance knowledge of population dynamics within complex natural communities. We assessed the accuracy of a Pacific Biosciences (PacBio) single molecule, real time (SMRT) sequencing based on DNA polymerization, a promising 3rd generation high-throughput technique, and compared this to the 2nd generation Roche 454 pyrosequencing platform. Amplicons of the 16S rRNA gene from a known isolate, Shewanella oneidensis MR1, and environmental samples from two streambed habitats, rocks and sediments, and a riparian zone soil, were analyzed. On the PacBio we analyzed ~500 bp amplicons that covered the V1-V3 regions and the full 1500 bp amplicons of the V1-V9 regions. On the Roche 454 we analyzed the ~500 bp amplicons. Error rates associated with the isolate were lowest with the Roche 454 method (2%), increased by more than 2-fold for the 500 bp amplicons with the PacBio SMRT chip (4-5%), and by more than 8-fold for the full gene with the PacBio SMRT chip (17-18%). Higher error rates with the PacBio SMRT chip artificially inflated estimates of richness and lowered estimates of coverage for environmental samples. The 3rd generation sequencing technology we evaluated does not provide greater phylogenetic and taxonomic resolutions for studies of microbial ecology.}, }
@article {pmid23999256, year = {2013}, author = {Jin, M and Bothfeld, W and Austin, S and Sato, TK and La Reau, A and Li, H and Foston, M and Gunawan, C and LeDuc, RD and Quensen, JF and Mcgee, M and Uppugundla, N and Higbee, A and Ranatunga, R and Donald, CW and Bone, G and Ragauskas, AJ and Tiedje, JM and Noguera, DR and Dale, BE and Zhang, Y and Balan, V}, title = {Effect of storage conditions on the stability and fermentability of enzymatic lignocellulosic hydrolysate.}, journal = {Bioresource technology}, volume = {147}, number = {}, pages = {212-220}, doi = {10.1016/j.biortech.2013.08.018}, pmid = {23999256}, issn = {1873-2976}, mesh = {Enzyme Stability ; *Fermentation ; Hydrogen-Ion Concentration ; Hydrolysis ; Lignin/*metabolism ; Magnetic Resonance Spectroscopy ; Saccharomyces cerevisiae/metabolism ; Temperature ; }, abstract = {To minimize the change of lignocellulosic hydrolysate composition during storage, the effects of storage conditions (temperature, pH and time) on the composition and fermentability of hydrolysate prepared from AFEX™ (Ammonia Fiber Expansion - a trademark of MBI, Lansing, MI) pretreated corn stover were investigated. Precipitates formed during hydrolysate storage increased with increasing storage pH and time. The precipitate amount was the least when hydrolysate was stored at 4 °C and pH 4.8, accounting for only 0.02% of the total hydrolysate weight after 3-month storage. No significant changes of NMR (Nuclear Magnetic Resonance) spectra and concentrations of sugars, minerals and heavy metals were observed after storage under this condition. When pH was adjusted higher before fermentation, precipitates also formed, consisting of mostly struvite (MgNH4PO4·6H2O) and brushite (CaHPO4·2H2O). Escherichia coli and Saccharomyces cerevisiae fermentation studies and yeast cell growth assays showed no significant difference in fermentability between fresh hydrolysate and stored hydrolysate.}, }
@article {pmid23996143, year = {2013}, author = {Xie, J and Strobel, GA and Mends, MT and Hilmer, J and Nigg, J and Geary, B}, title = {Collophora aceris, a novel antimycotic producing endophyte associated with Douglas Maple.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {784-795}, pmid = {23996143}, issn = {1432-184X}, mesh = {Acer/*microbiology ; Antifungal Agents/chemistry/*metabolism ; Ascomycota/classification/genetics/*isolation &amp; purification/*metabolism ; Endophytes/classification/genetics/*isolation &amp; purification/*metabolism ; Fungi/drug effects ; Molecular Sequence Data ; Phylogeny ; Plant Diseases/microbiology ; Spores, Fungal/genetics/growth &amp; development/isolation &amp; purification ; }, abstract = {A novel endophyte designated Collophora aceris, was obtained from stem tissues of Douglas Maple (Acer glabrum var. douglasii) in a Pacific Northwest temperate rainforest. Colonies were slow growing, white, creamy, moist, and translucent to opaque on potato dextrose agar and other media with few aerial hyphae. It also produced solid, dark sclerotia (200-400 μm) on oatmeal agar and no evidence of pseudopycnidia as per other Collophora spp. Conidia were rod-like in the size ranging from 2.2-8.4 × 0.8-1.8 μm and produced holoblastically on conidiogenous cells by budding with no collarette at the budding site. Phylogenetic analyses, based on 18S rDNA sequence data, showed that C. aceris possessed 99 % similarity to other Collophora spp. However, ITS-5.8S rDNA sequence data indicated that the organism was potentially related to Allantophomopsis spp. Finally, combined morphological, physiological, and molecular genetics data indicated that this organism is most like Collophora spp. but it is distinctly unique when compared to all other fungi in this group. It is to be noted that this is the first report of any member of this genus existing as an endophyte. This fungus makes a wide spectrum antimycotic agent (Collophorin) with biological activity against such pathogenic fungi as Pythium ultimum, Phytophthora cinnamomi, Phytophthora palmivora, and Rhizoctonia solani. Collophorin was purified to homogeneity and shown to have a unique mass of 120.0639, an empirical formula of C8H8O1, and UV absorption bands at 260 and 378 nm. This work also indicates that C. aceris possesses the biological potential to provide protection of its host against an array of common plant pathogens.}, }
@article {pmid23994646, year = {2013}, author = {McDonald, JA and Schroeter, K and Fuentes, S and Heikamp-Dejong, I and Khursigara, CM and de Vos, WM and Allen-Vercoe, E}, title = {Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model.}, journal = {Journal of microbiological methods}, volume = {95}, number = {2}, pages = {167-174}, doi = {10.1016/j.mimet.2013.08.008}, pmid = {23994646}, issn = {1872-8359}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Adult ; Bacillus/growth &amp; development/isolation &amp; purification ; Bacteroidetes/growth &amp; development/isolation &amp; purification ; Clostridium/growth &amp; development/isolation &amp; purification ; DNA, Bacterial/isolation &amp; purification ; Denaturing Gradient Gel Electrophoresis ; Ecosystem ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; *Microbiota ; *Models, Biological ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Reproducibility of Results ; }, abstract = {In vitro gut models provide several advantages over in vivo models for the study of the human gut microbiota. However, because communities developed in these models are inevitably simplified simulations of the in vivo environment, it is necessary to broadly define the differences between in vitro consortia and the communities from which they are derived. In this study we characterized microbial community development in a twin-vessel single-stage chemostat model of the human distal gut ecosystem using both gel (Denaturing Gradient Gel Electrophoresis) and phylogenetic microarray (Human Intestinal Tract Chip) based techniques. Five different sets of twin-vessels were inoculated with feces from three different healthy adult donors and allowed to reach steady state compositions. We found that twin-vessel single-stage chemostats could develop and maintain stable, diverse, and reproducible communities that reach steady state compositions in all five runs by at most 36 days post-inoculation. As noted in other in vitro studies, steady state communities were enriched in Bacteroidetes but not Clostridium cluster XIVa, Bacilli or other Firmicutes relative to the fecal inocula. Communities developed within this model had higher within-run reproducibility than between-run repeatability when using consecutive fecal donations. Both fecal inocula and steady state chemostat communities seeded with feces from different donors had distinct compositions. We conclude that twin-vessel single-stage chemostat models represent a valid simulation of the human distal gut environment and can support complex, representative microbial communities ideal for experimental manipulation.}, }
@article {pmid23994422, year = {2015}, author = {Hennebel, T and Boon, N and Maes, S and Lenz, M}, title = {Biotechnologies for critical raw material recovery from primary and secondary sources: R&amp;D priorities and future perspectives.}, journal = {New biotechnology}, volume = {32}, number = {1}, pages = {121-127}, doi = {10.1016/j.nbt.2013.08.004}, pmid = {23994422}, issn = {1876-4347}, mesh = {Biotechnology/*methods ; *Conservation of Natural Resources ; Electrochemistry ; Metallurgy ; *Research ; Wastewater/chemistry ; }, abstract = {Europe is confronted with an increasing supply risk of critical raw materials. These can be defined as materials of which the risks of supply shortage and their impacts on the economy are higher compared to most of other raw materials. Within the framework of the EU Innovation Partnership on raw materials Initiative, a list of 14 critical materials was defined, including some bulk metals, industrial minerals, the platinum group metals and rare earth elements. To tackle the supply risk challenge, innovation is required with respect to sustainable primary mining, substitution of critical metals, and urban mining. In these three categories, biometallurgy can play a crucial role. Indeed, microbe-metal interactions have been successfully applied on full scale to win materials from primary sources, but are not sufficiently explored for metal recovery or recycling. On the one hand, this article gives an overview of the microbial strategies that are currently applied on full scale for biomining; on the other hand it identifies technologies, currently developed in the laboratory, which have a perspective for large scale metal recovery and the needs and challenges on which bio-metallurgical research should focus to achieve this ambitious goal.}, }
@article {pmid23994204, year = {2013}, author = {Mao, SY and Zhang, RY and Wang, DS and Zhu, WY}, title = {Impact of subacute ruminal acidosis (SARA) adaptation on rumen microbiota in dairy cattle using pyrosequencing.}, journal = {Anaerobe}, volume = {24}, number = {}, pages = {12-19}, doi = {10.1016/j.anaerobe.2013.08.003}, pmid = {23994204}, issn = {1095-8274}, mesh = {*Acidosis ; Animals ; Biota/*drug effects ; Cattle ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The objective of this study was to evaluate the changes in bacterial populations in the rumen of dairy cattle following adaptation to subacute ruminal acidosis (SARA) using 16S rRNA gene pyrosequencing. Rumen contents were collected from four cattle adapted to either a 40% (control diet, COD) or 70% (SARA induction diet, SAID) concentrate feeds. DNA was extracted from each of the samples. Bacterial 16S rRNA genes of ruminal DNA extracts were PCR amplified with 2 bar coded primer sets and sequenced by 454 pyrosequencing. At a high taxonomic level, the percentage of Proteobacteria and Bacteroidetes were reduced by SAID feeding, whereas Firmicutes and Actinobacteria were more abundant in the SAID than in the COD group. At the genus level, as compared with the COD group, the abundances of Prevotella, Treponema, Anaeroplasma, Papillibacter, Acinetobacter and unclassified populations including unclassified Lentisphaerae, and unclassified bacteria were lower (P < 0.05), while the percentages of Ruminococcus, Atopobium, unclassified Clostridiales and Bifidobacterium were increased (P < 0.05) in the SAID group. Feeding of SAID reduced (P < 0.001) the diversity of the rumen microbial community. Taken together, our findings provide a comprehensive picture of current knowledge of the community structure of the rumen bacterial ecosystem during SARA, and enhance our understanding about the ruminal microbial ecology that may be useful in the prevention of ruminal acidosis.}, }
@article {pmid23991051, year = {2013}, author = {Vojvodic, S and Rehan, SM and Anderson, KE}, title = {Microbial gut diversity of Africanized and European honey bee larval instars.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e72106}, pmid = {23991051}, issn = {1932-6203}, support = {K12 GM000708/GM/NIGMS NIH HHS/United States ; }, mesh = {Acetobacteraceae/genetics/physiology ; Africa ; Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Bees/*microbiology ; *Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Bacterial/chemistry/genetics ; Europe ; Gastrointestinal Tract/*microbiology ; Genetic Variation ; Lactobacillus/genetics/physiology ; Larva/microbiology ; *Microbiota ; Molecular Sequence Data ; Neisseriaceae/genetics/physiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {The first step in understanding gut microbial ecology is determining the presence and potential niche breadth of associated microbes. While the core gut bacteria of adult honey bees is becoming increasingly apparent, there is very little and inconsistent information concerning symbiotic bacterial communities in honey bee larvae. The larval gut is the target of highly pathogenic bacteria and fungi, highlighting the need to understand interactions between typical larval gut flora, nutrition and disease progression. Here we show that the larval gut is colonized by a handful of bacterial groups previously described from guts of adult honey bees or other pollinators. First and second larval instars contained almost exclusively Alpha 2.2, a core Acetobacteraceae, while later instars were dominated by one of two very different Lactobacillus spp., depending on the sampled site. Royal jelly inhibition assays revealed that of seven bacteria occurring in larvae, only one Neisseriaceae and one Lactobacillus sp. were inhibited. We found both core and environmentally vectored bacteria with putatively beneficial functions. Our results suggest that early inoculation by Acetobacteraceae may be important for microbial succession in larvae. This assay is a starting point for more sophisticated in vitro models of nutrition and disease resistance in honey bee larvae.}, }
@article {pmid23990071, year = {2014}, author = {Bhattacharyya, PN and Tanti, B and Barman, P and Jha, DK}, title = {Culture-independent metagenomic approach to characterize the surface and subsurface soil bacterial community in the Brahmaputra valley, Assam, North-East India, an Indo-Burma mega-biodiversity hotspot.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {30}, number = {2}, pages = {519-528}, pmid = {23990071}, issn = {1573-0972}, mesh = {*Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; India ; Phylogeny ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Soil bacterial communities, which contain the highest level of prokaryotic diversity of any natural environment, are important for ecosystem functioning. A culture-independent metagenomic approach was employed in the present investigation to characterize the diversity of soil bacterial community composition in five geochemically and hydrologically different surface and subsurface soil habitats of Brahmaputra valley, Assam, North-East India, an Indo-Burma mega-biodiversity hotspot. The diversity of soil bacterial community was determined through sequence analysis of 16S-23S intergenic spacer regions (ISR). Polymerase chain reaction (PCR) universal primers, 1406F (5'-TGYACACACCGCCCGT-3') and 155r (5'-GGGTTBCATTCRG-3') were used for amplification of 16S-23S ribosomal DNA intergenic spacers of bacteria. Amplification resulted in an intense array of PCR products approximately ranging in size from 200 to 900 bp. Clear banding patterns were observed in analysed samples using the primer set in combination. A clear change in microbial ISR profile was observed on visual analysis of gel electrophoresis profiles. Fast alignment database searches of PCR amplicons of 16S-23S ISR sequence data revealed that the isolated sequences resembled five major phylogenetic groups of bacteria, namely α-, β- and γ-subdivisions of Proteobacteria, Acidobacterium and Comamonadaceae.}, }
@article {pmid23963224, year = {2013}, author = {Fernandes, I and Duarte, S and Cássio, F and Pascoal, C}, title = {Effects of riparian plant diversity loss on aquatic microbial decomposers become more pronounced with increasing time.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {763-772}, pmid = {23963224}, issn = {1432-184X}, mesh = {Alnus/metabolism/*microbiology ; Bacteria/genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; *Biodiversity ; Ecosystem ; Eucalyptus/metabolism/*microbiology ; Fresh Water/analysis/*microbiology ; Fungi/genetics/isolation &amp; purification/*metabolism ; Plant Leaves/microbiology ; Quercus/metabolism/*microbiology ; Steam/analysis ; Time Factors ; }, abstract = {We examined the potential long-term impacts of riparian plant diversity loss on diversity and activity of aquatic microbial decomposers. Microbial assemblages were obtained in a mixed-forest stream by immersion of mesh bags containing three leaf species (alder, oak and eucalyptus), commonly found in riparian corridors of Iberian streams. Simulation of species loss was done in microcosms by including a set of all leaf species, retrieved from the stream, and non-colonized leaves of three, two or one leaf species. Leaves were renewed every month throughout six months, and microbial inoculum was ensured by a set of colonized leaves from the previous month. Microbial diversity, leaf mass loss and fungal biomass were assessed at the second and sixth months after plant species loss. Molecular diversity of fungi and bacteria, as the total number of operational taxonomic units per leaf diversity treatment, decreased with leaf diversity loss. Fungal biomass tended to decrease linearly with leaf species loss on oak and eucalyptus, suggesting more pronounced effects of leaf diversity on lower quality leaves. Decomposition of alder and eucalyptus leaves was affected by leaf species identity, mainly after longer times following diversity loss. Leaf decomposition of alder decreased when mixed with eucalyptus, while decomposition of eucalyptus decreased in mixtures with oak. Results suggest that the effects of leaf diversity on microbial decomposers depended on leaf species number and also on which species were lost from the system, especially after longer times. This may have implications for the management of riparian forests to maintain stream ecosystem functioning.}, }
@article {pmid23963223, year = {2013}, author = {Fonte, ES and Amado, AM and Meirelles-Pereira, F and Esteves, FA and Rosado, AS and Farjalla, VF}, title = {The combination of different carbon sources enhances bacterial growth efficiency in aquatic ecosystems.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {871-878}, pmid = {23963223}, issn = {1432-184X}, mesh = {Bacteria/genetics/*growth &amp; development/isolation &amp; purification/*metabolism ; Carbon/analysis/*metabolism ; Ecosystem ; Fresh Water/analysis/*microbiology ; Organic Chemicals/analysis/metabolism ; Water Microbiology ; }, abstract = {The dissolved organic carbon (DOC) pool is composed of several organic carbon compounds from different carbon sources. Each of these sources may support different bacterial growth rates, but few studies have specifically analyzed the effects of the combination of different carbon sources on bacterial metabolism. In this study, we evaluated the response of several metabolic parameters, including bacterial biomass production (BP), bacterial respiration (BR), bacterial growth efficiency (BGE), and bacterial community structure, on the presence of three DOC sources alone and in combination. We hypothesized that the mixture of different DOC sources would increase the efficiency of carbon use by bacteria (BGE). We established a full-factorial substitutive design (seven treatments) in which the effects of the number and identity of DOC sources on bacterial metabolism were evaluated. We calculated the expected metabolic rates of the combined DOC treatments based on the single-DOC treatments and observed a positive interaction on BP, a negative interaction on BR, and, consequently, a positive interaction on BGE for the combinations. The bacterial community composition appeared to have a minor impact on differences in bacterial metabolism among the treatments. Our data indicate that mixtures of DOC sources result in a more efficient biological use of carbon. This study provides strong evidence that the mixture of different DOC sources is a key factor affecting the role of bacteria in the carbon flux of aquatic ecosystems.}, }
@article {pmid23963222, year = {2013}, author = {An, S and Couteau, C and Luo, F and Neveu, J and DuBow, MS}, title = {Bacterial diversity of surface sand samples from the Gobi and Taklamaken deserts.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {850-860}, pmid = {23963222}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; China ; Desert Climate ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Phylogeny ; Silicon Dioxide/analysis ; }, abstract = {Arid regions represent nearly 30 % of the Earth's terrestrial surface, but their microbial biodiversity is not yet well characterized. The surface sands of deserts, a subset of arid regions, are generally subjected to large temperature fluctuations plus high UV light exposure and are low in organic matter. We examined surface sand samples from the Taklamaken (China, three samples) and Gobi (Mongolia, two samples) deserts, using pyrosequencing of PCR-amplified 16S V1/V2 rDNA sequences from total extracted DNA in order to gain an assessment of the bacterial population diversity. In total, 4,088 OTUs (using ≥97 % sequence similarity levels), with Chao1 estimates varying from 1,172 to 2,425 OTUs per sample, were discernable. These could be grouped into 102 families belonging to 15 phyla, with OTUs belonging to the Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria phyla being the most abundant. The bacterial population composition was statistically different among the samples, though members from 30 genera were found to be common among the five samples. An increase in phylotype numbers with increasing C/N ratio was noted, suggesting a possible role in the bacterial richness of these desert sand environments. Our results imply an unexpectedly large bacterial diversity residing in the harsh environment of these two Asian deserts, worthy of further investigation.}, }
@article {pmid23963221, year = {2013}, author = {Li, J and Li, F and Yu, S and Qin, S and Wang, G}, title = {Impacts of mariculture on the diversity of bacterial communities within intertidal sediments in the Northeast of China.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {861-870}, pmid = {23963221}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; China ; Ecosystem ; Fisheries ; Geologic Sediments/analysis/*microbiology ; Molecular Sequence Data ; Phylogeny ; Silicon Dioxide/analysis ; }, abstract = {Mariculture is one of the major seafood supplies worldwide and has caused serious environmental concerns on the coastal zone. Its rapid development has been shown to disrupt the sediment ecosystems and thus influence the benthic bacterial communities. Bacterial diversity and community structure within both adjacent farms and non-cultured zones intertidal sediments along the coasts of Qinhuangdao and Dalian, China, were investigated using full-length 16S rRNA gene-based T-RFLP analyses and clone library construction. Richness and Shannon-Wiener index were significantly increased at sites adjacent the mariculture farm with mean values of 29 and 2.97 from peak profiles of T-RFLP result. Clustering analyses suggested that impacts of mariculture on bacterial diversity of sediment were significantly larger than those resulted from temporal and spatial scales. Upon comparisons of RFLP patterns from 602 clones from libraries of the selected five samples, 137 OTUs were retrieved. Members of γ- and δ-Proteobacteria, Bacilli, Flavobacteria, and Actinobacteria were recorded in all libraries. In addition, γ-Proteobacteria were dominant in all samples (21.7~45.0 %). Redundancy analysis revealed that the distribution of bacterial composition seemed to be determined by the variables of salinity, PO4 (3-)-P, NH4 (+)-N, and Chlorophyll a content. The phyla of γ-Proteobacteria, Clostridia, Flavobacteria, Bacilli, and Planctomycetes were principal components to contribute to the bacterial differences of clone libraries. Our finding demonstrated that these phyla could display variations of bacterial composition linked to environmental disturbance resulted from mariculture.}, }
@article {pmid23963220, year = {2013}, author = {Thompson, CC and Silva, GG and Vieira, NM and Edwards, R and Vicente, AC and Thompson, FL}, title = {Genomic taxonomy of the genus prochlorococcus.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {752-762}, pmid = {23963220}, issn = {1432-184X}, mesh = {Biodiversity ; *Genome, Bacterial ; Genomics ; Molecular Sequence Data ; *Phylogeny ; Prochlorococcus/*classification/*genetics ; Seawater/*microbiology ; }, abstract = {The genus Prochlorococcus is globally abundant and dominates the total phytoplankton biomass and production in the oligotrophic ocean. The single species, Prochlorococcus marinus, comprises six named ecotypes. Our aim was to analyze the taxonomic structure of the genus Prochlorococcus. We analyzed the complete genomes of 13 cultured P. marinus type and reference strains by means of several genomic taxonomy tools (i.e., multilocus sequence analysis, amino acid identity, Karlin genomic signature, and genome to genome distance). In addition, we estimated the diversity of Prochlorococcus species in over 100 marine metagenomes from all the major oceanic provinces. According to our careful taxonomic analysis, the 13 strains corresponded, in fact, to ten different Prochlorococcus species. This analysis establishes a new taxonomic framework for the genus Prochlorococcus. Further, the analysis of the metagenomic data suggests that, in total, there may only be 35 Prochlorococcus species in the world's oceans. We propose that the dearth of species observed in this study is driven by high selective pressures that limit diversification in the global ocean.}, }
@article {pmid23962186, year = {2013}, author = {Wang, H and Edwards, MA and Falkinham, JO and Pruden, A}, title = {Probiotic approach to pathogen control in premise plumbing systems? A review.}, journal = {Environmental science &amp; technology}, volume = {47}, number = {18}, pages = {10117-10128}, doi = {10.1021/es402455r}, pmid = {23962186}, issn = {1520-5851}, mesh = {Disinfection/methods ; Drinking Water/*microbiology ; *Probiotics ; Sanitary Engineering ; Water Microbiology ; Water Purification/*methods ; }, abstract = {Opportunistic pathogens occurring in premise (i.e., building) plumbing systems, including strains of Legionella, Mycobacterium, Acanthamoeba, and Pseudomonas, are now frequently cited agents of waterborne disease outbreaks. Unlike traditional fecal pathogens, opportunistic pathogens are part of the drinking water microbial ecology and therefore require new paradigms for their control. With the onset of the "microbiome era", notions of eradicating all microbes in drinking water have proven unrealistic, making a probiotic concept worthy of consideration. Research is needed to better understand how engineering controls may individually, or in combination, select for a desirable microbiome, and how the microbiome itself may mediate proliferation of opportunistic pathogens. Ecological interactions such as competition, antagonism, and obligate parasite-host relationships offer potential targets for probiotic control of opportunistic pathogens. A probiotic approach may be defined as intentional inoculation of beneficial microbes or choosing conditions that select for a desirable microbiome. This critical review synthesizes the state of the knowledge of the factors governing opportunistic pathogen control in premise plumbing and potential opportunities for and barriers to implementation of a probiotic approach. Future effort is recommended to demonstrate the feasibility of the probiotic concept; to develop effective, practical, and safe protocols; and to engage relevant stakeholders in evaluating options and assessing corresponding risks.}, }
@article {pmid23962113, year = {2013}, author = {Yao, F and Vik, U and Brysting, AK and Carlsen, T and Halvorsen, R and Kauserud, H}, title = {Substantial compositional turnover of fungal communities in an alpine ridge-to-snowbed gradient.}, journal = {Molecular ecology}, volume = {22}, number = {19}, pages = {5040-5052}, doi = {10.1111/mec.12437}, pmid = {23962113}, issn = {1365-294X}, mesh = {*Biodiversity ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Mycorrhizae/classification/*genetics ; Norway ; Plant Roots/*microbiology ; Polygonaceae/microbiology ; Sequence Analysis, DNA ; Snow/*microbiology ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The main gradient in vascular plant, bryophyte and lichen species composition in alpine areas, structured by the topographic gradient from wind-exposed ridges to snowbeds, has been extensively studied. Tolerance to environmental stress, resulting from wind abrasion and desiccation towards windswept ridges or reduced growing season due to prolonged snow cover towards snowbeds, is an important ecological mechanism in this gradient. The extent to which belowground fungal communities are structured by the same topographic gradient and the eventual mechanisms involved are less well known. In this study, we analysed variation in fungal diversity and community composition associated with roots of the ectomycorrhizal plant Bistorta vivipara along the ridge-to-snowbed gradient. We collected root samples from fifty B. vivipara plants in ten plots in an alpine area in central Norway. The fungal communities were analysed using 454 pyrosequencing analyses of tag-encoded ITS1 amplicons. A distinct gradient in the fungal community composition was found that coincided with variation from ridge to snowbeds. This gradient was paralleled by change in soil content of carbon, nitrogen and phosphorus. A large proportion (66%) of the detected 801 nonsingleton operational taxonomic units (OTUs) were ascomycetes, while basidiomycetes dominated quantitatively (i.e. with respect to number of reads). Numerous fungal OTUs, many with taxonomic affinity to Sebacinales, Cortinarius and Meliniomyces, showed distinct affinities either to ridge or to snowbed plots, indicating habitat specialization. The compositional turnover of fungal communities along the gradient was not paralleled by a gradient in species richness.}, }
@article {pmid23961233, year = {2013}, author = {Omri, I and Aouidi, F and Bouallagui, H and Godon, JJ and Hamdi, M}, title = {Performance study of biofilter developed to treat H2S from wastewater odour.}, journal = {Saudi journal of biological sciences}, volume = {20}, number = {2}, pages = {169-176}, pmid = {23961233}, issn = {1319-562X}, abstract = {Biofiltration is an efficient biotechnological process used for waste gas abatement in various industrial processes. It offers low operating and capital costs and produces minimal secondary waste streams. The objective of this study was to evaluate the performance of a pilot scale biofilter in terms of pollutants' removal efficiencies and the bacterial dynamics under different inlet concentrations of H2S. The treatment of odourous pollutants by biofiltration was investigated at a municipal wastewater treatment plant (WWTP) (Charguia, Tunis, Tunisia). Sampling and analyses were conducted for 150 days. Inlet H2S concentration recorded was between 200 and 1300 mg H2S.m(-3). Removal efficiencies reached 99% for the majority of the running time at an empty bed retention time (EBRT) of 60 s. Heterotrophic bacteria were found to be the dominant microorganisms in the biofilter. The bacteria were identified as the members of the genus Bacillus, Pseudomonas and xanthomonadacea bacterium. The polymerase chain reaction-single stranded conformation polymorphism (PCR-SSCP) method showed that bacterial community profiles changed with the H2S inlet concentration. Our results indicated that the biofilter system, containing peat as the packing material, was proved able to remove H2S from the WWTP odourous pollutants.}, }
@article {pmid23959831, year = {2013}, author = {Vandamme, P and De Brandt, E and Houf, K and Salles, JF and Dirk van Elsas, J and Spilker, T and LiPuma, JJ}, title = {Burkholderia humi sp. nov., Burkholderia choica sp. nov., Burkholderia telluris sp. nov., Burkholderia terrestris sp. nov. and Burkholderia udeis sp. nov.: Burkholderia glathei-like bacteria from soil and rhizosphere soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {63}, number = {Pt 12}, pages = {4707-4718}, doi = {10.1099/ijs.0.048900-0}, pmid = {23959831}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; Burkholderia/*classification/genetics/isolation &amp; purification ; China ; DNA Gyrase/genetics ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Humans ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; Wastewater/microbiology ; }, abstract = {Analysis of partial gyrB gene sequences revealed six taxa in a group of 17 Burkholderia glathei-like isolates which were further examined by (GTG)5-PCR fingerprinting, 16S rRNA gene sequence analysis, DNA-DNA hybridizations, determination of the DNA G+C content, whole-cell fatty acid analysis and an analysis of cell and colony morphology and more than 180 biochemical characteristics. The results demonstrated that one taxon consisting of three human clinical isolates represented Burkholderia zhejiangensis, a recently described methyl-parathion-degrading bacterium isolated from a wastewater-treatment system in China. The remaining taxa represented five novel species isolated from soil or rhizosphere soil samples, and could be distinguished by both genotypic and phenotypic characteristics. We therefore propose to formally classify these bacteria as Burkholderia humi sp. nov. (type strain, LMG 22934(T) = CCUG 63059(T)), Burkholderia choica sp. nov. (type strain, LMG 22940(T) = CCUG 63063(T)), Burkholderia telluris sp. nov. (type strain, LMG 22936(T) = CCUG 63060(T)), Burkholderia udeis sp. nov. (type strain, LMG 27134(T) = CCUG 63061(T)) and Burkholderia terrestris sp. nov. (type strain, LMG 22937(T) = CCUG 63062(T)).}, }
@article {pmid23959115, year = {2013}, author = {Schlatter, DC and DavelosBaines, AL and Xiao, K and Kinkel, LL}, title = {Resource use of soilborne Streptomyces varies with location, phylogeny, and nitrogen amendment.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {961-971}, pmid = {23959115}, issn = {1432-184X}, mesh = {Carbon/analysis/metabolism ; Molecular Sequence Data ; Nitrogen/analysis/*metabolism ; *Phylogeny ; Soil/chemistry ; *Soil Microbiology ; Streptomyces/*classification/genetics/isolation &amp; purification/*metabolism ; }, abstract = {In this study, we explore variation in resource use among Streptomyces in prairie soils. Resource use patterns were highly variable among Streptomyces isolates and were significantly related to location, phylogeny, and nitrogen (N) amendment history. Streptomyces populations from soils less than 1 m apart differed significantly in their ability to use resources, indicating that drivers of resource use phenotypes in soil are highly localized. Variation in resource use within Streptomyces genetic groups was significantly associated with the location from which Streptomyces were isolated, suggesting that resource use is adapted to local environments. Streptomyces from soils under long-term N amendment used fewer resources and grew less efficiently than those from non-amended soils, demonstrating that N amendment selects for Streptomyces with more limited catabolic capacities. Finally, resource use among Streptomyces populations was correlated with soil carbon content and Streptomyces population densities. We hypothesize that variation in resource use among Streptomyces reflects adaptation to local resource availability and competitive species interactions in soil and that N amendments alter selection for resource use phenotypes.}, }
@article {pmid23959114, year = {2013}, author = {Præsteng, KE and Pope, PB and Cann, IK and Mackie, RI and Mathiesen, SD and Folkow, LP and Eijsink, VG and Sundset, MA}, title = {Probiotic dosing of Ruminococcus flavefaciens affects rumen microbiome structure and function in reindeer.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {840-849}, pmid = {23959114}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Biodiversity ; Cellulose/metabolism ; Digestion ; Male ; *Microbiota ; Molecular Sequence Data ; Phylogeny ; Probiotics/*administration &amp; dosage ; Reindeer/metabolism/microbiology ; Rumen/metabolism/*microbiology ; Ruminococcus/*physiology ; }, abstract = {Highly cellulolytic bacterial species such as Ruminococcus flavefaciens are regarded essential for the microbial breakdown of cellulose in the rumen. We have investigated the effect of ruminal dosing of R. flavefaciens strain 8/94-32 during realimentation of starved reindeer (males, n = 3). Microbiome function measured as in situ digestion of cellulose and food pellets (percent DMD; dry matter disappearance) decreased after probiotic dosing. Microbial community analyses (>100,000 16S rDNA gene sequences for 27 samples) demonstrated that ruminal dosing influenced the microbiome structure; reflected by increased phylogenetic distances from background samples (unweighted UniFrac analysis) and reduced species diversity and evenness. Despite the inability to detect strain 8/94-32 post-dosing, the relative abundance of its affiliate family Ruminococcaceae remained consistent throughout the trial, whilst a dominant peak in the genus Prevotella and decline in uncharacterized Bacteroidetes (uBacNR) were observed in treatment samples. No clear relationships were observed between the relative abundance of Ruminococcaceae, Prevotella and uBacNR with cellulose DMD; however, Prevotella (negative) and uBacNR (positive) exhibited relationships with pellet DMD. These unexpected effects of ruminal dosing of a cellulolytic bacterium on digestibility are relevant for other studies on rumen manipulation.}, }
@article {pmid23958678, year = {2013}, author = {López Barreiro, D and Zamalloa, C and Boon, N and Vyverman, W and Ronsse, F and Brilman, W and Prins, W}, title = {Influence of strain-specific parameters on hydrothermal liquefaction of microalgae.}, journal = {Bioresource technology}, volume = {146}, number = {}, pages = {463-471}, doi = {10.1016/j.biortech.2013.07.123}, pmid = {23958678}, issn = {1873-2976}, mesh = {*Biofuels ; Biomass ; Chromatography, Gel ; Culture Media ; *Microalgae ; Nitrogen/chemistry ; *Photobioreactors ; Scenedesmus/metabolism ; Species Specificity ; Stramenopiles/metabolism ; *Temperature ; Time Factors ; }, abstract = {Algae are an interesting feedstock for producing biofuel via hydrothermal liquefaction (HTL), due to their high water content. In this study, algae slurries (5-7 wt% daf) from different species were liquefied at 250 and 375 °C in batch autoclaves during 5 min. The aim was to analyze the influence of strain-specific parameters (cell structure, biochemical composition and growth environment) on the HTL process. Results show big variations in the biocrude oil yield within species at 250 °C (from 17.6 to 44.8 wt%). At 375 °C, these differences become less significant (from 45.6 to 58.1 wt%). An appropriate characterization of feedstock appeared to be critical to interpret the results. If a high conversion of microalgae-to-biocrude is pursued, near critical conditions are required, with Scenedesmus almeriensis (freshwater) and Nannochloropsis gaditana (marine) leading to the biocrude oils with lower nitrogen content from each growth environment.}, }
@article {pmid23952148, year = {2013}, author = {Luo, G and Wang, W and Angelidaki, I}, title = {Anaerobic digestion for simultaneous sewage sludge treatment and CO biomethanation: process performance and microbial ecology.}, journal = {Environmental science &amp; technology}, volume = {47}, number = {18}, pages = {10685-10693}, doi = {10.1021/es401018d}, pmid = {23952148}, issn = {1520-5851}, mesh = {Anaerobiosis ; Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; *Bioreactors ; Carbon Monoxide/*metabolism ; Methane/*metabolism ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; Sewage ; }, abstract = {Syngas is produced by thermal gasification of both nonrenewable and renewable sources including biomass and coal, and it consists mainly of CO, CO2, and H2. In this paper we aim to bioconvert CO in the syngas to CH4. A novel technology for simultaneous sewage sludge treatment and CO biomethanation in an anaerobic reactor was presented. Batch experiments showed that CO was inhibitory to methanogens, but not to bacteria, at CO partial pressure between 0.25 and 1 atm under thermophilic conditions. During anaerobic digestion of sewage sludge supplemented with CO added through a hollow fiber membrane (HFM) module in continuous thermophilic reactors, CO did not inhibit the process even at a pressure as high as 1.58 atm inside the HFM, due to the low dissolved CO concentration in the liquid. Complete consumption of CO was achieved with CO gas retention time of 0.2 d. Results from high-throughput sequencing analysis showed clear differences of the microbial community structures between the samples from liquid and biofilm on the HFM in the reactor with CO addition. Species close to Methanosarcina barkeri and Methanothermobacter thermautotrophicus were the two main archaeal species involved in CO biomethanation. However, the two species were distributed differently in the liquid phase and in the biofilm. Although the carboxidotrophic activities test showed that CO was converted by both archaea and bacteria, the bacterial species responsible for CO conversion are unknown.}, }
@article {pmid23950955, year = {2013}, author = {Callewaert, C and Kerckhof, FM and Granitsiotis, MS and Van Gele, M and Van de Wiele, T and Boon, N}, title = {Characterization of Staphylococcus and Corynebacterium clusters in the human axillary region.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e70538}, pmid = {23950955}, issn = {1932-6203}, mesh = {Axilla/*microbiology ; Biodiversity ; Cluster Analysis ; Corynebacterium/*classification/genetics ; Denaturing Gradient Gel Electrophoresis ; Female ; Humans ; Male ; Microbiota ; Phylogeny ; Skin/microbiology ; Staphylococcus/*classification/genetics ; }, abstract = {The skin microbial community is regarded as essential for human health and well-being, but likewise plays an important role in the formation of body odor in, for instance, the axillae. Few molecular-based research was done on the axillary microbiome. This study typified the axillary microbiome of a group of 53 healthy subjects. A profound view was obtained of the interpersonal, intrapersonal and temporal diversity of the human axillary microbiota. Denaturing gradient gel electrophoresis (DGGE) and next generation sequencing on 16S rRNA gene region were combined and used as extent to each other. Two important clusters were characterized, where Staphylococcus and Corynebacterium species were the abundant species. Females predominantly clustered within the Staphylococcus cluster (87%, n = 17), whereas males clustered more in the Corynebacterium cluster (39%, n = 36). The axillary microbiota was unique to each individual. Left-right asymmetry occurred in about half of the human population. For the first time, an elaborate study was performed on the dynamics of the axillary microbiome. A relatively stable axillary microbiome was noticed, although a few subjects evolved towards another stable community. The deodorant usage had a proportional linear influence on the species diversity of the axillary microbiome.}, }
@article {pmid23950718, year = {2013}, author = {Sixt, BS and Siegl, A and Müller, C and Watzka, M and Wultsch, A and Tziotis, D and Montanaro, J and Richter, A and Schmitt-Kopplin, P and Horn, M}, title = {Metabolic features of Protochlamydia amoebophila elementary bodies--a link between activity and infectivity in Chlamydiae.}, journal = {PLoS pathogens}, volume = {9}, number = {8}, pages = {e1003553}, pmid = {23950718}, issn = {1553-7374}, support = {281633/ERC_/European Research Council/International ; I 291/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Acanthamoeba/metabolism/*microbiology/ultrastructure ; Chlamydia trachomatis/metabolism/pathogenicity/ultrastructure ; Chlamydiales/*metabolism/ultrastructure ; Citric Acid Cycle/*physiology ; Glucose/*metabolism ; HeLa Cells ; Humans ; Oxygen Consumption/*physiology ; Pentose Phosphate Pathway/*physiology ; Symbiosis/physiology ; }, abstract = {The Chlamydiae are a highly successful group of obligate intracellular bacteria, whose members are remarkably diverse, ranging from major pathogens of humans and animals to symbionts of ubiquitous protozoa. While their infective developmental stage, the elementary body (EB), has long been accepted to be completely metabolically inert, it has recently been shown to sustain some activities, including uptake of amino acids and protein biosynthesis. In the current study, we performed an in-depth characterization of the metabolic capabilities of EBs of the amoeba symbiont Protochlamydia amoebophila. A combined metabolomics approach, including fluorescence microscopy-based assays, isotope-ratio mass spectrometry (IRMS), ion cyclotron resonance Fourier transform mass spectrometry (ICR/FT-MS), and ultra-performance liquid chromatography mass spectrometry (UPLC-MS) was conducted, with a particular focus on the central carbon metabolism. In addition, the effect of nutrient deprivation on chlamydial infectivity was analyzed. Our investigations revealed that host-free P. amoebophila EBs maintain respiratory activity and metabolize D-glucose, including substrate uptake as well as host-free synthesis of labeled metabolites and release of labeled CO2 from (13)C-labeled D-glucose. The pentose phosphate pathway was identified as major route of D-glucose catabolism and host-independent activity of the tricarboxylic acid (TCA) cycle was observed. Our data strongly suggest anabolic reactions in P. amoebophila EBs and demonstrate that under the applied conditions D-glucose availability is essential to sustain metabolic activity. Replacement of this substrate by L-glucose, a non-metabolizable sugar, led to a rapid decline in the number of infectious particles. Likewise, infectivity of Chlamydia trachomatis, a major human pathogen, also declined more rapidly in the absence of nutrients. Collectively, these findings demonstrate that D-glucose is utilized by P. amoebophila EBs and provide evidence that metabolic activity in the extracellular stage of chlamydiae is of major biological relevance as it is a critical factor affecting maintenance of infectivity.}, }
@article {pmid23949950, year = {2013}, author = {Guesmi, A and Ettoumi, B and El Hidri, D and Essanaa, J and Cherif, H and Mapelli, F and Marasco, R and Rolli, E and Boudabous, A and Cherif, A}, title = {Uneven distribution of Halobacillus trueperi species in arid natural saline systems of Southern Tunisian Sahara.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {831-839}, pmid = {23949950}, issn = {1432-184X}, mesh = {Biodiversity ; Ecosystem ; Geologic Sediments/analysis/*microbiology ; Halobacillus/*classification/genetics/*isolation &amp; purification/metabolism ; Molecular Sequence Data ; Phylogeny ; Sodium Chloride/analysis/*metabolism ; Soil/chemistry ; *Soil Microbiology ; Tunisia ; }, abstract = {The genetic diversity of a collection of 336 spore-forming isolates recovered from five salt-saturated brines and soils (Chott and Sebkhas) mainly located in the hyper-arid regions of the southern Tunisian Sahara has been assessed. Requirements and abilities for growth at a wide range of salinities\ showed that 44.3 % of the isolates were extremely halotolerant, 23 % were moderate halotolerant, and 32.7 % were strict halophiles, indicating that they are adapted to thrive in these saline ecosystems. A wide genetic diversity was documented based on 16S-23S rRNA internal transcribed spacer fingerprinting profiles (ITS) and 16S rRNA gene sequences that clustered the strains into seven genera: Bacillus, Gracilibacillus, Halobacillus, Oceanobacillus, Paenibacillus, Pontibacillus, and Virgibacillus. Halobacillus trueperi was the most encountered species in all the sites and presented a large intraspecific diversity with a multiplicity of ITS types. The most frequent ITS type included 42 isolates that were chosen for assessing of the intraspecific diversity by BOX-PCR fingerprinting. A high intraspecific microdiversity was documented by 14 BOX-PCR genotypes whose distribution correlated with the strain geographic origin. Interestingly, H. trueperi isolates presented an uneven geographic distribution among sites with the highest frequency of isolation from the coastal sites, suggesting a marine rather than terrestrial origin of the strains. The high frequency and diversity of H. trueperi suggest that it is a major ecosystem-adapted microbial component of the Tunisian Sahara harsh saline systems of marine origin.}, }
@article {pmid23949662, year = {2014}, author = {Nyyssönen, M and Hultman, J and Ahonen, L and Kukkonen, I and Paulin, L and Laine, P and Itävaara, M and Auvinen, P}, title = {Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield.}, journal = {The ISME journal}, volume = {8}, number = {1}, pages = {126-138}, pmid = {23949662}, issn = {1751-7370}, mesh = {Adaptation, Physiological/genetics ; Archaea/classification/genetics/*physiology ; Bacteria/classification/genetics/virology ; *Bacterial Physiological Phenomena ; Bacteriophages/genetics ; *Biodiversity ; Carbon Cycle ; Finland ; Geology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Water/chemistry ; }, abstract = {Microbial life in the nutrient-limited and low-permeability continental crystalline crust is abundant but remains relatively unexplored. Using high-throughput sequencing to assess the 16S rRNA gene diversity, we found diverse bacterial and archaeal communities along a 2516-m-deep drill hole in continental crystalline crust in Outokumpu, Finland. These communities varied at different sampling depths in response to prevailing lithology and hydrogeochemistry. Further analysis by shotgun metagenomic sequencing revealed variable carbon and nutrient utilization strategies as well as specific functional and physiological adaptations uniquely associated with specific environmental conditions. Altogether, our results show that predominant geological and hydrogeochemical conditions, including the existence and connectivity of fracture systems and the low amounts of available energy, have a key role in controlling microbial ecology and evolution in the nutrient and energy-poor deep crustal biosphere.}, }
@article {pmid23949660, year = {2014}, author = {Lagkouvardos, I and Weinmaier, T and Lauro, FM and Cavicchioli, R and Rattei, T and Horn, M}, title = {Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae.}, journal = {The ISME journal}, volume = {8}, number = {1}, pages = {115-125}, pmid = {23949660}, issn = {1751-7370}, support = {281633/ERC_/European Research Council/International ; }, mesh = {Bacterial Proteins/genetics ; *Biodiversity ; Chlamydiaceae/*classification/*genetics ; Databases, Genetic ; Ecology ; Environmental Microbiology ; Metagenomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In the era of metagenomics and amplicon sequencing, comprehensive analyses of available sequence data remain a challenge. Here we describe an approach exploiting metagenomic and amplicon data sets from public databases to elucidate phylogenetic diversity of defined microbial taxa. We investigated the phylum Chlamydiae whose known members are obligate intracellular bacteria that represent important pathogens of humans and animals, as well as symbionts of protists. Despite their medical relevance, our knowledge about chlamydial diversity is still scarce. Most of the nine known families are represented by only a few isolates, while previous clone library-based surveys suggested the existence of yet uncharacterized members of this phylum. Here we identified more than 22,000 high quality, non-redundant chlamydial 16S rRNA gene sequences in diverse databases, as well as 1900 putative chlamydial protein-encoding genes. Even when applying the most conservative approach, clustering of chlamydial 16S rRNA gene sequences into operational taxonomic units revealed an unexpectedly high species, genus and family-level diversity within the Chlamydiae, including 181 putative families. These in silico findings were verified experimentally in one Antarctic sample, which contained a high diversity of novel Chlamydiae. In our analysis, the Rhabdochlamydiaceae, whose known members infect arthropods, represents the most diverse and species-rich chlamydial family, followed by the protist-associated Parachlamydiaceae, and a putative new family (PCF8) with unknown host specificity. Available information on the origin of metagenomic samples indicated that marine environments contain the majority of the newly discovered chlamydial lineages, highlighting this environment as an important chlamydial reservoir.}, }
@article {pmid23942794, year = {2013}, author = {Li, Q and Wang, X and Liu, X and Jiao, N and Wang, G}, title = {Abundance and novel lineages of thraustochytrids in Hawaiian waters.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {823-830}, pmid = {23942794}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Biodiversity ; Ecosystem ; Hawaii ; Molecular Sequence Data ; Phylogeny ; Seasons ; Seawater/*microbiology ; }, abstract = {Thraustochydrids has been known for their ubiquitous distribution in the ocean. However, a few efforts have been made to investigate their ecology. In this study, we have applied molecular method, acriflavine direct detection, and classical oceanographic methods to investigate the abundance and diversity of thraustochytrids in the North Pacific subtropical gyre. Our results revealed interesting temporal and spatial variations of their population. Out of three seasons (spring, summer, and fall), cruise Hawaii Ocean Time-series (HOT)-216 during November 2009 obtained the highest abundance of thraustochytrids ranging from 1,890 (Station S1C1, 45 m) to 630,000 (Station S2C12, 100 m) cells L(-1) of seawater, which accounted for a 0.79 to 281.0 % biomass ratio to that of bacteria in terms of gram carbon per liter. A patchy distribution of these organisms was widely observed in the water column and they were somehow related to the maximum chlorophyll layers. A total of 25 operational taxonomic units (OTUs) from cruise HOT-216 formed four phylogroups in the specific labyrinthulomycetes 18S rRNA-based phylogenetic tree, with the largest group of 20 OTUs fell into the Aplanochytrium cluster and the others aligned with uncultured clones or none, thus appeared to be undescribed. This study indicates the presence of new thraustochytrids lineages and their quantitative importance in the marine water column.}, }
@article {pmid23936439, year = {2013}, author = {Frans, I and Dierckens, K and Crauwels, S and Van Assche, A and Leisner, JJ and Larsen, MH and Michiels, CW and Willems, KA and Lievens, B and Bossier, P and Rediers, H}, title = {Does virulence assessment of Vibrio anguillarum using sea bass (Dicentrarchus labrax) larvae correspond with genotypic and phenotypic characterization?.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e70477}, pmid = {23936439}, issn = {1932-6203}, mesh = {Animals ; Bass/*microbiology ; DNA, Bacterial/genetics ; *Genotype ; Larva/microbiology ; *Phenotype ; Phylogeny ; Polymerase Chain Reaction ; Vibrio/classification/*genetics/*pathogenicity/physiology ; Virulence ; }, abstract = {BACKGROUND: Vibriosis is one of the most ubiquitous fish diseases caused by bacteria belonging to the genus Vibrio such as Vibrio (Listonella) anguillarum. Despite a lot of research efforts, the virulence factors and mechanism of V. anguillarum are still insufficiently known, in part because of the lack of standardized virulence assays.<br><br>We investigated and compared the virulence of 15 V. anguillarum strains obtained from different hosts or non-host niches using a standardized gnotobiotic bioassay with European sea bass (Dicentrarchus labrax L.) larvae as model hosts. In addition, to assess potential relationships between virulence and genotypic and phenotypic characteristics, the strains were characterized by random amplified polymorphic DNA (RAPD) and repetitive extragenic palindromic PCR (rep-PCR) analyses, as well as by phenotypic analyses using Biolog's Phenotype MicroArray&#x2122; technology and some virulence factor assays.<br><br>CONCLUSIONS/SIGNIFICANCE: Virulence testing revealed ten virulent and five avirulent strains. While some relation could be established between serotype, genotype and phenotype, no relation was found between virulence and genotypic or phenotypic characteristics, illustrating the complexity of V. anguillarum virulence. Moreover, the standardized gnotobiotic system used in this study has proven its strength as a model to assess and compare the virulence of different V. anguillarum strains in vivo. In this way, the bioassay contributes to the study of mechanisms underlying virulence in V. anguillarum.}, }
@article {pmid23933825, year = {2013}, author = {Rubin, JE and Harms, NJ and Fernando, C and Soos, C and Detmer, SE and Harding, JC and Hill, JE}, title = {Isolation and characterization of Brachyspira spp. including "Brachyspira hampsonii" from lesser snow geese (Chen caerulescens caerulescens) in the Canadian Arctic.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {813-822}, pmid = {23933825}, issn = {1432-184X}, mesh = {Animal Migration ; Animals ; Arctic Regions ; Brachyspira/classification/genetics/*isolation &amp; purification ; Canada ; Diarrhea/microbiology/*veterinary ; Disease Reservoirs/microbiology/*veterinary ; Geese/*microbiology/physiology ; Gram-Negative Bacterial Infections/microbiology/*veterinary ; Molecular Sequence Data ; Phylogeny ; Swine ; Swine Diseases/*microbiology ; }, abstract = {Brachyspira is associated with diarrhea and colitis in pigs, and control of these pathogens is complicated by their complex ecology. Identification of wildlife reservoirs of Brachyspira requires the discrimination of colonized animals and those simply contaminated through environmental exposure. Lesser snow geese (Chen caerulescens caerulescens) were sampled in the Canadian arctic during the summer of 2011, and cloacal swabs were cultured on selective media. Brachyspira isolates were obtained from 15/170 (8.8 %) samples, and 12/15 isolates were similar to isolates previously recovered from pigs, including "Brachyspira hampsonii", a recently characterized species associated with dysentery-like disease in pigs in North America. A pilot inoculation study with one strongly β-hemolytic B. hampsonii isolate resulted in fecal shedding of the isolate by inoculated pigs for up to 14 days post-inoculation, but no severe clinical disease. Results of this study indicate that lesser snow geese can be colonized by Brachyspira strains that can also colonize pigs. Millions of lesser snow geese (C. caerulescens caerulescens) travel through the major pork-producing areas of Canada and the USA during their annual migration, making them a potential factor in the continental distribution of these bacteria.}, }
@article {pmid23927408, year = {2013}, author = {Woodhams, DC and Brucker, RM}, title = {Disease defence through generations: leaf-cutter ants and their symbiotic bacteria.}, journal = {Molecular ecology}, volume = {22}, number = {16}, pages = {4141-4143}, doi = {10.1111/mec.12431}, pmid = {23927408}, issn = {1365-294X}, mesh = {Actinomycetales/*classification/*genetics ; Animals ; Ants/*microbiology ; *Genetic Variation ; *Symbiosis ; }, abstract = {Microbial ecology of animals is taking on significance in the modern dialogue for the biology of species. Similar to a nuclear genome, the entire bacterial assemblage maintains an ancestral signal of the host's evolution leading to cophylogeny between the host and the microbes they harbour (Brucker &amp; Bordenstein 2012b). The stability of such associations is of great interest as they provide a means for species to acquire new traits and genetic diversity that their own genomes lack (McFall-Ngai et al. 2013). The role of gut microbiota, for example, in host health and nutrition is widely recognized and a shared characteristic among animals. The role of bacteria colonizing the outside surfaces of animals is less well understood, but rather than random colonization, these microbes on skin, cuticles, scales and feathers in many cases provide benefits to the host. The symbiosis of leaf-cutter ants, their fungus gardens and their microbiota is a fascinating and complex system. Whether culture-independent bacterial diversity on the cuticle of leaf-cutter ants is high or highly constrained by subcuticular gland secretions is one prominent question. In this issue of Molecular Ecology, Andersen et al. (2013) show that leaf-cutting ants, Acromyrmex echinatior, maintain a dominant and colony-specific bacterium called Pseudonocardia on their cuticles (the laterocervical plates in particular). This bacterium is involved in protecting the ants and their fungal gardens from disease. Other fungus-gardening attine species as well as soil and vegetation can harbour Pseudonocardia. However, it was previously unknown how stable the bacterial strain-ant colony association was through the lifetime of the colony.}, }
@article {pmid23923328, year = {2013}, author = {Guidi, V and Lüthy, P and Tonolla, M}, title = {Comparison between diflubenzuron and a Bacillus thuringiensis israelensis- and Lysinibacillus sphaericus-based formulation for the control of mosquito larvae in urban catch basins in Switzerland.}, journal = {Journal of the American Mosquito Control Association}, volume = {29}, number = {2}, pages = {138-145}, doi = {10.2987/12-6301R.1}, pmid = {23923328}, issn = {8756-971X}, mesh = {Animals ; *Bacillaceae ; Bacillus thuringiensis ; Cities ; *Culicidae ; *Diflubenzuron ; *Insecticides ; Larva ; *Mosquito Control ; *Pest Control, Biological ; Switzerland ; }, abstract = {A field test was conducted to evaluate a commercial biolarvicide based on Bacillus thuringiensis var. israelensis and Lysinibacillus sphaericus to control mosquitoes breeding in catch basins in southern Switzerland. The efficacy and residual activity of the microbial mosquito larvicide applied at the recommended rate of 10 g per catch basin was compared to the currently used larvicide diflubenzuron. Both products provided a very good control activity (> 97% of reduction) of late instars (3rd and 4th instars) and pupae for 4 wk. However, only the microbial formulation controlled immature stages during the whole period of the trial, with > 98% of larval reduction. A single application of the microbial larvicide applied at 10 g per catch basin significantly reduced the number of immature mosquitoes for at least 70 days. The quantity of rainfall in the 48-h period before each sampling and the water temperature did not influence the efficacy of the treatments. Under the environmental conditions encountered in southern Switzerland, the larvicide tested may be a valid alternative to diflubenzuron to control mosquitoes in urban catch basins. The long-lasting control by the microbial larvicide further reduces the number of treatments required to keep the population of mosquitoes at low levels.}, }
@article {pmid23917147, year = {2013}, author = {Marzorati, M and Negroni, A and Fava, F and Verstraete, W and Boon, N}, title = {Application of a molecular based approach for the early detection of short term 3-chloroaniline shock loads on activated sludge bacterial community and functionality.}, journal = {New biotechnology}, volume = {30}, number = {6}, pages = {763-771}, doi = {10.1016/j.nbt.2013.07.004}, pmid = {23917147}, issn = {1876-4347}, mesh = {Aniline Compounds/*metabolism/pharmacology ; *Bacteria/classification/genetics/metabolism ; Bacterial Typing Techniques/*methods ; Bioreactors ; Microbial Consortia/*physiology ; Sequence Analysis, DNA/*methods ; Sequence Analysis, RNA/*methods ; Sewage/*microbiology ; Water Pollutants, Chemical/*metabolism/pharmacology ; Water Purification ; }, abstract = {Microbial processes are central elements in wastewater treatment plants (WWTPs) to mineralize the organic matter, to degrade pollutants and to decrease the amount of suspended solids. This activity can be disrupted by organic and inorganic pollutants present in wastewater streams. Hence, it is of primary importance to investigate and monitor the structure and functionality of the sludge-resident microbial communities. We simulated a 3-chloroaniline (3-CA) shock load in 3-CA adapted and non-adapted semi-continuous activated-sludge (SCAS) reactors to selectively stress the Ammonia Oxidizing Bacteria (AOB). Recently developed setting-independent theoretical interpretation of molecular DNA and RNA fingerprinting patterns were used to evaluate the responses of the microbial populations. Ammonium accumulation in treated reactors upon 3-CA addition confirmed the disruption of the functionality under stress conditions. Molecular analyses coupled to their interpretation highlighted that shock loaded reactors clustered separately from non-treated ones, especially when AOBs community was specifically targeted. Furthermore, the interpretation of RNA-based analyses, as compared to DNA-based ones, allowed to more promptly depicting shifts in a stressed community. We showed that the use of RNA-based molecular tools in combination with a new set of parameters is a powerful tool to link functional failures with microbial structure modifications in WWTPs, providing a potential tool for a rational optimization of the processes (Microbial Resource Management - MRM).}, }
@article {pmid23914185, year = {2013}, author = {Basiliko, N and Henry, K and Gupta, V and Moore, TR and Driscoll, BT and Dunfield, PF}, title = {Controls on bacterial and archaeal community structure and greenhouse gas production in natural, mined, and restored Canadian peatlands.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {215}, pmid = {23914185}, issn = {1664-302X}, abstract = {Northern peatlands are important global C reservoirs, largely because of their slow rates of microbial C mineralization. Particularly in sites that are heavily influenced by anthropogenic disturbances, there is scant information about microbial ecology and whether or not microbial community structure influences greenhouse gas production. This work characterized communities of bacteria and archaea using terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of 16S rRNA and functional genes across eight natural, mined, or restored peatlands in two locations in eastern Canada. Correlations were explored among chemical properties of peat, bacterial and archaeal community structure, and carbon dioxide (CO2) and methane (CH4) production rates under oxic and anoxic conditions. Bacteria and archaea similar to those found in other peat soil environments were detected. In contrast to other reports, methanogen diversity was low in our study, with only 2 groups of known or suspected methanogens. Although mining and restoration affected substrate availability and microbial activity, these land-uses did not consistently affect bacterial or archaeal community composition. In fact, larger differences were observed between the two locations and between oxic and anoxic peat samples than between natural, mined, and restored sites, with anoxic samples characterized by less detectable bacterial diversity and stronger dominance by members of the phylum Acidobacteria. There were also no apparent strong linkages between prokaryote community structure and CH4 or CO2 production, suggesting that different organisms exhibit functional redundancy and/or that the same taxa function at very different rates when exposed to different peat substrates. In contrast to other earlier work focusing on fungal communities across similar mined and restored peatlands, bacterial and archaeal communities appeared to be more resistant or resilient to peat substrate changes brought about by these land uses.}, }
@article {pmid23913198, year = {2013}, author = {Xu, J and Zhuang, L and Yang, G and Yuan, Y and Zhou, S}, title = {Extracellular quinones affecting methane production and methanogenic community in paddy soil.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {950-960}, pmid = {23913198}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Humic Substances/analysis ; Methane/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Quinones/chemistry/*metabolism ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {This study investigated the change of CH4 production and methanogenic community in response to the presence of humic substances (humics) analogue, anthraquinone-2,6-disulfonate (AQDS). Anaerobic experiments used a Chinese paddy soil, and three concentration levels of 0.5, 5, and 20 mM AQDS were conducted. Results suggested that the effect of AQDS on methanogenesis was time-dependent and concentration-dependent. Twenty millimolars of AQDS was toxic for methanogenic activity almost for the entire experimental period. Slight inhibition of methanogenesis by AQDS respiration in the 0.5- and 5-mM AQDS-supplemented treatments occurred within the early period, while CH4 accumulated throughout the later period was approximately five and ten times greater than that of the controls without AQDS, respectively. AQDS reduction coupling to acetate oxidization enriched Geobacter species, and the mcrA-targeted T-RFLP profiles revealed significant increase of Methanosarcina at the expense of Methanobacterium in the 0.5- and 5-mM AQDS treatments. The enriched syntrophic association between Geobacter and Methanosarcina was deduced to be an effective methanogenic pathway for converting acetate to CH4 via direct interspecies electron transfer. This study implied the ecological importance of syntrophic interaction between methanogens and microorganisms enriched by anaerobic respiration of non-methanogenic terminal electron acceptors in paddy soils.}, }
@article {pmid23913197, year = {2013}, author = {Correa, H and Haltli, B and Duque, C and Kerr, R}, title = {Bacterial communities of the gorgonian octocoral Pseudopterogorgia elisabethae.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {972-985}, pmid = {23913197}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Colombia ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Pseudopterogorgia elisabethae is a common inhabitant of Caribbean reefs and is a well-known source of diterpenes with diverse biological activities. Notably, this octocoral is the sole source of the pseudopterosin family of anti-inflammatory diterpenes and is harvested to supply commercial demand for these metabolites. We have characterized the composition of the bacterial community associated with P. elisabethae collected from Providencia Island, Colombia, using both culture-dependent and culture-independent approaches. Culture-independent analysis revealed that the bacterial communities were composed of eight phyla, of which Proteobacteria was the most abundant. At the class level, bacterial communities were dominated by Gammaproteobacteria (82-87 %). Additionally, operational taxonomic units related to Pseudomonas and Endozoicomonas species were the most abundant phylotypes consistently associated with P. elisabethae colonies. Culture-dependent analysis resulted in the identification of 40 distinct bacteria classified as Bacilli (15), Actinobacteria (12), Gammaproteobacteria (9), Alphaproteobacteria (3), and Betaproteobacteria (1). Only one of the 40 cultured bacteria was closely related to a dominant phylotype detected in the culture-independent study, suggesting that conventional culturing techniques failed to culture the majority of octocoral-associated bacterial diversity. To the best of our knowledge, this is the first characterization of the bacterial diversity associated with P. elisabethae.}, }
@article {pmid23912720, year = {2013}, author = {Han, SI and Lee, JC and Lee, HJ and Whang, KS}, title = {Planifilum composti sp. nov., a thermophile isolated from compost.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {63}, number = {Pt 12}, pages = {4557-4561}, doi = {10.1099/ijs.0.053199-0}, pmid = {23912720}, issn = {1466-5034}, mesh = {Bacillales/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Diaminopimelic Acid/chemistry ; Fatty Acids/chemistry ; Hot Temperature ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; *Soil Microbiology ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {Two thermophilic bacteria, designated strains P8(T) and P12, were isolated from compost in Korea. The isolates grew aerobically from 50 to 75 °C (optimum at 55 °C) and at pH 4.0-9.0 (optimum pH 6.5). Aerial mycelia were not observed. Single spores were produced along the substrate hypha. The predominant menaquinone was MK-7. Major fatty acids were iso-C17 : 0, iso-C15 : 0 and iso-C16 : 0. The cell wall contained meso-diaminopimelic acid and the polar lipids were phosphatidylethanolamine, an aminophospholipid and sphingoglycolipid. The DNA G+C contents were 55.9-56.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains P8(T) and P12 belonged to the genus Planifilum in the family Thermoactinomycetaceae with sequence similarities of 96.1-97.2 %. Levels of DNA-DNA relatedness between strain P8(T) and the type strains of recognized species of the genus Planifilum ranged from 28.9 to 38.2 %. On the basis of data from the present polyphasic study, strains P8(T) and P12 are considered to represent a novel species of the genus Planifilum, for which the name Planifilum composti sp. nov. is proposed. The type strain is P8(T) (= KACC 16581(T) = NBRC 108858(T)).}, }
@article {pmid23909466, year = {2014}, author = {Scott, KP and Martin, JC and Duncan, SH and Flint, HJ}, title = {Prebiotic stimulation of human colonic butyrate-producing bacteria and bifidobacteria, in vitro.}, journal = {FEMS microbiology ecology}, volume = {87}, number = {1}, pages = {30-40}, doi = {10.1111/1574-6941.12186}, pmid = {23909466}, issn = {1574-6941}, mesh = {Bifidobacterium/*growth &amp; development/*metabolism ; Butyrates/*metabolism ; Colon/metabolism/*microbiology ; Culture Media/metabolism ; Gastrointestinal Tract/metabolism/microbiology ; Gram-Positive Bacteria/classification/*growth &amp; development/*metabolism ; Humans ; Prebiotics/analysis/*microbiology ; }, abstract = {Dietary macronutrients affect the composition of the gut microbiota, and prebiotics are used to improve and maintain a healthy gut. The impact of prebiotics on dominant gut bacteria other than bifidobacteria, however, is under-researched. Here, we report carbohydrate utilisation patterns for representative butyrate-producing anaerobes, belonging to the Gram-positive Firmicutes families Lachnospiraceae and Ruminococcaceae, by comparison with selected Bacteroides and Bifidobacterium species. Growth assessments using anaerobic Hungate tubes and a new rapid microtitre plate assay were generally in good agreement. The Bacteroides strains tested showed some growth on basal medium with no added carbohydrates, utilising peptides in the growth medium. The butyrate-producing strains exhibited different growth profiles on the substrates, which included starch, inulin, fructooligosaccharides (FOS), galactooligosaccharides (GOS) and xylooligosaccharides (XOS). Eleven were able to grow on short-chain FOS, but this number decreased as the chain length of the fructan substrates increased. Long-chain inulin was utilised by Roseburia inulinivorans, but by none of the Bifidobacterium species examined here. XOS was a more selective growth substrate than FOS, with only six of the 11 Firmicutes strains able to use XOS for growth. These results illustrate the selectivity of different prebiotics and help to explain why some are butyrogenic.}, }
@article {pmid23906180, year = {2013}, author = {Börnigen, D and Morgan, XC and Franzosa, EA and Ren, B and Xavier, RJ and Garrett, WS and Huttenhower, C}, title = {Functional profiling of the gut microbiome in disease-associated inflammation.}, journal = {Genome medicine}, volume = {5}, number = {7}, pages = {65}, pmid = {23906180}, issn = {1756-994X}, support = {K08 AI078942/AI/NIAID NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 CA154426/CA/NCI NIH HHS/United States ; R01 DK092405/DK/NIDDK NIH HHS/United States ; }, abstract = {The microbial residents of the human gut are a major factor in the development and lifelong maintenance of health. The gut microbiota differs to a large degree from person to person and has an important influence on health and disease due to its interaction with the human immune system. Its overall composition and microbial ecology have been implicated in many autoimmune diseases, and it represents a particularly important area for translational research as a new target for diagnostics and therapeutics in complex inflammatory conditions. Determining the biomolecular mechanisms by which altered microbial communities contribute to human disease will be an important outcome of current functional studies of the human microbiome. In this review, we discuss functional profiling of the human microbiome using metagenomic and metatranscriptomic approaches, focusing on the implications for inflammatory conditions such as inflammatory bowel disease and rheumatoid arthritis. Common themes in gut microbial ecology have emerged among these diverse diseases, but they have not yet been linked to targetable mechanisms such as microbial gene and genome composition, pathway and transcript activity, and metabolism. Combining these microbial activities with host gene, transcript and metabolic information will be necessary to understand how and why these complex interacting systems are altered in disease-associated inflammation.}, }
@article {pmid23902518, year = {2013}, author = {Shah, F and Rineau, F and Canbäck, B and Johansson, T and Tunlid, A}, title = {The molecular components of the extracellular protein-degradation pathways of the ectomycorrhizal fungus Paxillus involutus.}, journal = {The New phytologist}, volume = {200}, number = {3}, pages = {875-887}, pmid = {23902518}, issn = {1469-8137}, mesh = {Ammonium Compounds/metabolism ; Basidiomycota/enzymology/genetics/*metabolism ; Endopeptidases/metabolism ; Exopeptidases/metabolism ; Fungal Proteins/genetics/*metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Fungal ; Hydrogen-Ion Concentration ; Metabolic Networks and Pathways ; Mycorrhizae/enzymology/genetics/*metabolism ; Nitrogen/*metabolism ; Polymers ; Proteins/*metabolism ; Proteolysis ; Soil/*chemistry ; Soil Microbiology ; Trees/metabolism ; }, abstract = {Proteins contribute to a major part of the organic nitrogen (N) in forest soils. This N is mobilized and becomes available to trees as a result of the depolymerizing activities of symbiotic ectomycorrhizal fungi. The mechanisms by which these fungi depolymerize proteins and assimilate the released N are poorly characterized. Biochemical analysis and transcriptome profiling were performed to examine the proteolytic machinery and the uptake system of the ectomycorrhizal basidiomycete Paxillus involutus during the assimilation of organic N from various protein sources and extracts of organic matter. All substrates induced secretion of peptidase activity with an acidic pH optimum, mostly contributed by aspartic peptidases. The peptidase activity was transiently repressed by ammonium. Transcriptional analysis revealed a large number of extracellular endo- and exopeptidases. The expression levels of these peptidases were regulated in parallel with transporters and enzymes involved in the assimilation and metabolism of the released peptides and amino acids. For the first time the molecular components of the protein degradation pathways of an ectomycorrhizal fungus are described. The data suggest that the transcripts encoding these components are regulated in response to the chemical properties and the availability of the protein substrates.}, }
@article {pmid23900649, year = {2014}, author = {Guo, X and Gong, J}, title = {Differential effects of abiotic factors and host plant traits on diversity and community composition of root-colonizing arbuscular mycorrhizal fungi in a salt-stressed ecosystem.}, journal = {Mycorrhiza}, volume = {24}, number = {2}, pages = {79-94}, pmid = {23900649}, issn = {1432-1890}, mesh = {*Biota ; China ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Ecosystem ; Genes, rRNA ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Mycorrhizae/classification/*drug effects ; *Osmotic Pressure ; Phylogeny ; Plant Roots/*microbiology ; RNA, Fungal/genetics ; RNA, Ribosomal, 18S/genetics ; Salts/*analysis ; Sequence Analysis, DNA ; Soil/*chemistry ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) were investigated in roots of 18 host plant species in a salinized south coastal plain of Laizhou Bay, China. From 18 clone libraries of 18S rRNA genes, all of the 22 AMF phylotypes were identified into Glomus, of which 18 and 4 were classified in group A and B in the phylogenetic tree, respectively. The phylotypes related to morphologically defined Glomus species occurred generally in soil with higher salinity. AMF phylotype richness, Shannon index, and evenness were not significantly different between root samples from halophytes vs. non-halophytes, invades vs. natives, or annuals vs. perennials. However, AMF diversity estimates frequently differed along the saline gradient or among locations, but not among pH gradients. Moreover, UniFrac tests showed that both plant traits (salt tolerance, life style or origin) and abiotic factors (salinity, pH, or location) significantly affected the community composition of AMF colonizers. Redundancy and variation partitioning analyses revealed that soil salinity and pH, which respectively explained 6.9 and 4.2 % of the variation, were the most influential abiotic variables in shaping the AMF community structure. The presented data indicate that salt tolerance, life style, and origin traits of host species may not significantly affect the AMF diversity in roots, but do influence the community composition in this salinized ecosystem. The findings also highlight the importance of soil salinity and pH in driving the distribution of AMF in plant and soil systems.}, }
@article {pmid23899369, year = {2013}, author = {Andersen, SB and Hansen, LH and Sapountzis, P and Sørensen, SJ and Boomsma, JJ}, title = {Specificity and stability of the Acromyrmex-Pseudonocardia symbiosis.}, journal = {Molecular ecology}, volume = {22}, number = {16}, pages = {4307-4321}, pmid = {23899369}, issn = {1365-294X}, mesh = {Actinomycetales/*classification/*genetics ; Animals ; Ants/genetics/*microbiology ; *Genetic Variation ; Panama ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Species Specificity ; *Symbiosis ; }, abstract = {The stability of mutualistic interactions is likely to be affected by the genetic diversity of symbionts that compete for the same functional niche. Fungus-growing (attine) ants have multiple complex symbioses and thus provide ample opportunities to address questions of symbiont specificity and diversity. Among the partners are Actinobacteria of the genus Pseudonocardia that are maintained on the ant cuticle to produce antibiotics, primarily against a fungal parasite of the mutualistic gardens. The symbiosis has been assumed to be a hallmark of evolutionary stability, but this notion has been challenged by culturing and sequencing data indicating an unpredictably high diversity. We used 454 pyrosequencing of 16S rRNA to estimate the diversity of the cuticular bacterial community of the leaf-cutting ant Acromyrmex echinatior and other fungus-growing ants from Gamboa, Panama. Both field and laboratory samples of the same colonies were collected, the latter after colonies had been kept under laboratory conditions for up to 10 years. We show that bacterial communities are highly colony-specific and stable over time. The majority of colonies (25/26) had a single dominant Pseudonocardia strain, and only two strains were found in the Gamboa population across 17 years, confirming an earlier study. The microbial community on newly hatched ants consisted almost exclusively of a single strain of Pseudonocardia while other Actinobacteria were identified on older, foraging ants in varying but usually much lower abundances. These findings are consistent with recent theory predicting that mixtures of antibiotic-producing bacteria can remain mutualistic when dominated by a single vertically transmitted and resource-demanding strain.}, }
@article {pmid23897832, year = {2013}, author = {Rousk, J and Smith, AR and Jones, DL}, title = {Investigating the long-term legacy of drought and warming on the soil microbial community across five European shrubland ecosystems.}, journal = {Global change biology}, volume = {19}, number = {12}, pages = {3872-3884}, doi = {10.1111/gcb.12338}, pmid = {23897832}, issn = {1365-2486}, mesh = {Acetic Acid/metabolism ; Bacteria/growth &amp; development ; *Climate Change ; *Droughts ; *Ecosystem ; Europe ; Fungi/growth &amp; development ; *Hot Temperature ; Leucine/metabolism ; Seasons ; *Soil Microbiology ; }, abstract = {We investigated how the legacy of warming and summer drought affected microbial communities in five different replicated long-term (>10 years) field experiments across Europe (EU-FP7 INCREASE infrastructure). To focus explicitly on legacy effects (i.e., indirect rather than direct effects of the environmental factors), we measured microbial variables under the same moisture and temperature in a brief screening, and following a pre-incubation at stable conditions. Specifically, we investigated the size and composition of the soil microbial community (PLFA) alongside measurements of bacterial (leucine incorporation) and fungal (acetate in ergosterol incorporation) growth rates, previously shown to be highly responsive to changes in environmental factors, and microbial respiration. We found no legacy effects on the microbial community size, composition, growth rates, or basal respiration rates at the effect sizes used in our experimental setup (0.6 °C, about 30% precipitation reduction). Our findings support previous reports from single short-term ecosystem studies thereby providing a clear evidence base to allow long-term, broad-scale generalizations to be made. The implication of our study is that warming and summer drought will not result in legacy effects on the microbial community and their processes within the effect sizes here studied. While legacy effects on microbial processes during perturbation cycles, such as drying-rewetting, and on tolerance to drought and warming remain to be studied, our results suggest that any effects on overall ecosystem processes will be rather limited. Thus, the legacies of warming and drought should not be prioritized factors to consider when modeling contemporary rates of biogeochemical processes in soil.}, }
@article {pmid23897211, year = {2013}, author = {Ma, B and Lv, X and Warren, A and Gong, J}, title = {Shifts in diversity and community structure of endophytic bacteria and archaea across root, stem and leaf tissues in the common reed, Phragmites australis, along a salinity gradient in a marine tidal wetland of northern China.}, journal = {Antonie van Leeuwenhoek}, volume = {104}, number = {5}, pages = {759-768}, doi = {10.1007/s10482-013-9984-3}, pmid = {23897211}, issn = {1572-9699}, mesh = {Archaea/classification/*isolation &amp; purification ; Bacteria/classification/*isolation &amp; purification ; *Biota ; China ; Endophytes/classification/*isolation &amp; purification ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Plant Stems/microbiology ; Poaceae/metabolism/*microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Salts/*metabolism ; Wetlands ; }, abstract = {The effects of salt stress on endophytic prokaryotic communities in plants are largely unknown, and the distribution patterns of bacterial and archaeal endophytes in different tissues of a plant species are rarely compared. We investigated the endophytic bacterial and archaeal communities in roots, stems and leaves of the common reed, Phragmites australis, collected from three tidal zones along a salinity gradient, using terminal restriction fragment (T-RF) length polymorphism analysis of the 16S rRNA genes. The results showed that the bacterial diversity in the roots was significantly higher than that in the leaves, whereas similar archaeal diversity was revealed for either plant tissues or tidal zones. Network analysis revealed that T-RFs were grouped largely by tissue, and the major groups were generally linked by a few common T-RFs. Unique T-RFs in roots were mainly present in plants growing in the supratidal zone, but unique T-RFs in stems and leaves were mainly present in those from the middle and high tidal zones. Non-metric multidimensional scaling ordination and analysis of similarity revealed that bacterial communities were significantly different among tissues (P < 0.05), but similar among tidal zones (P = 0.49). However, the archaeal communities differed among tidal zones (P < 0.05), but were similar among tissues (P = 0.89). This study indicates that: (1) the endophytic archaeal communities are influenced more significantly than the endophytic bacterial communities by soil salinity, and (2) the differential distribution patterns of bacterial and archaeal endophytes in plant tissues along a salinity gradient imply that these two groups play different roles in coastal hydrophytes.}, }
@article {pmid23895438, year = {2013}, author = {McTee, MR and Gibbons, SM and Feris, K and Gordon, NS and Gannon, JE and Ramsey, PW}, title = {Heavy metal tolerance genes alter cellular thermodynamics in Pseudomonas putida and river Pseudomonas spp. and influence amebal predation.}, journal = {FEMS microbiology letters}, volume = {347}, number = {2}, pages = {97-106}, doi = {10.1111/1574-6968.12226}, pmid = {23895438}, issn = {1574-6968}, support = {52005905//Howard Hughes Medical Institute/United States ; }, mesh = {Amoeba/microbiology ; Drug Resistance, Bacterial/*genetics ; *Food Chain ; Metals, Heavy ; Pseudomonas/genetics/metabolism ; Pseudomonas putida/genetics/metabolism ; Rivers/*microbiology/*parasitology ; *Thermodynamics ; *Water Microbiology ; }, abstract = {Predation rates were measured for two Acanthamoeba castellanii strains feeding on metal-tolerant and metal-sensitive strains of Pseudomonas putida and compared with cellular thermodynamic data. Predation rates by A. castellanii strain ATCC 30010 correlated with cell volume of the prey. To explore whether this observation could be environmentally relevant, pseudomonad species were isolated from a pristine and a metal-contaminated river and were paired based on phylogenetic and physiological relatedness. Then, cellular thermodynamics and predation rates were measured on the most similar pseudomonad pair. Under cadmium stress, the strain from contaminated river sediments, Pseudomonas sp. CF150, exited metabolic dormancy faster than its pair from pristine sediments, Pseudomonas sp. N9, but consumed available resources less efficiently (more energy was lost as heat). Predation rates by both strains of ameba were greater on Pseudomonas sp. CF150 than on Pseudomonas sp. N9 at the highest cadmium concentration.}, }
@article {pmid23893265, year = {2013}, author = {Saccà, ML and Fajardo, C and Nande, M and Martín, M}, title = {Effects of nano zero-valent iron on Klebsiella oxytoca and stress response.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {806-812}, pmid = {23893265}, issn = {1432-184X}, mesh = {Bacterial Proteins/genetics/metabolism ; Iron/*chemistry/*toxicity ; Klebsiella oxytoca/*drug effects/genetics/*metabolism ; Oxidation-Reduction ; Oxidative Stress/drug effects ; Proteomics ; Soil Microbiology ; }, abstract = {Nano zero-valent iron (NZVI) is a new option for contaminated soil and groundwater treatment, despite little is known on their impact on environmental microorganisms. Klebsiella oxytoca K5 strain, isolated from the NZVI-treated soil, was used to investigate the bacterial, phenotypical and molecular response to commercial NZVI exposure. Cytotoxicity assays at three NZVI concentrations (1, 5 and 10 mg mL(-1)) suggested a negligible bacteriostatic effect and the lack of bactericidal effect. Structural changes were analysed by electronic microscopy. Scanning electron microscopy revealed the presence of NZVI around some bacterial cells, but no apparent morphological changes were seen. NZVI attachment to the cell surface was confirmed by transmission electron microscopy, although most of them were not affected. A proteomic approach (two-dimensional electrophoresis, matrix-assisted laser desorption ionization time-of-flight mass spectrometry) was used to investigate NZVI impact. For the first time to our knowledge, results revealed that exposure of a soil bacterium to NZVI resulted in the overproduction of tryptophanase, associated with oxidative stress response. K5 may set up an adaptative stress response involving indole as a signal molecule to inform the bacterial population about environmental changes. These findings would improve knowledge on the molecular mechanisms underlying bacterial response to NZVI exposure.}, }
@article {pmid23884715, year = {2013}, author = {Yang, JK and Cheng, ZB and Li, J and Miao, LH}, title = {Community composition of nirS-type denitrifier in a shallow eutrophic lake.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {796-805}, pmid = {23884715}, issn = {1432-184X}, mesh = {Bacteria/classification/enzymology/genetics/*isolation &amp; purification ; Bacterial Proteins/genetics/*metabolism ; China ; Denitrification ; Ecosystem ; Eutrophication ; Geologic Sediments/microbiology ; Lakes/chemistry/*microbiology ; Molecular Sequence Data ; Nitrite Reductases/genetics/*metabolism ; Nitrites/metabolism ; Phylogeny ; Polymorphism, Restriction Fragment Length ; }, abstract = {Denitrification is a major biological process to reduce nitrate to molecular nitrogen (N2). In shallow eutrophic lakes, this process can remove the largest portion of fixed nitrogen and plays an important role in self-purification of this ecosystem. To understand the structure of denitrifying communities in a shallow eutrophic lake, denitrifier communities in four sub-lakes of East Lake in Wuhan, China, were explored by restriction fragment length polymorphisms (RFLP) analysis and sequencing of nirS gene clone libraries. nirS is a functional marker gene for denitrification encoding cytochrome cd 1-containing nitrite reductase, which catalyzes the reduction of nitrite to nitric oxide. Both RFLP fingerprints clustering analysis and phylogeny analysis based on the amino acid sequences of NirS revealed that NirS-type communities in East Lake sediment could be roughly divided into three clusters. Cluster I accounted for 74-82 % of clones from the moderately eutrophic sub-lakes Tuan, Tang Ling, and Guo Zheng. Cluster II accounted for 76 % of the communities in hypertrophic sub-lake Miao Lake and cluster III as a minor group (7 % of the total), mainly presented in Miao Lake. Phylogenetic analysis revealed that cluster I was related to the reference clones from a broad range of ecological environments, and clusters II and III were more phylogenetically related to the reference clones from entrophic environments. Canonical correspondence analysis indicated that total nitrogen, total phosphate, total organic carbon, and NH4-N and NO2-N were important environmental factors affecting the dispersion of NirS-type denitrifier in the sediments. Cluster I showed a weak relationship with the nutrient content, while cluster II and III were positively related with the nutrient content. Principal coordinates analysis indicated that NirS-type communities from Tuan Lake, Tang Ling Lake, and Guo Zheng Lake sediments were divergent from those found in river, estuary sediment, and forest soil but similar to communities in constructed wetland sediment despite large geographic distances. The communities from the hypertrophic sub-lake Miao Lake deviated from other sub-lakes and the reference communities and clustered independently. Our results support the argument that environmental factors regulate the composition and distribution of the functional bacterial groups.}, }
@article {pmid23880793, year = {2013}, author = {del Mar Fernández-Arjona, M and Bañares-España, E and García-Sánchez, MJ and Hernández-López, M and López-Rodas, V and Costas, E and Flores-Moya, A}, title = {Disentangling mechanisms involved in the adaptation of photosynthetic microorganisms to the extreme sulphureous water from Los Baños de Vilo (S Spain).}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {742-751}, pmid = {23880793}, issn = {1432-184X}, mesh = {Adaptation, Physiological ; Chlorophyta/genetics/*physiology ; Microcystis/genetics/*metabolism ; Mutation ; *Photosynthesis ; Selection, Genetic ; Spain ; Sulfides/analysis/*metabolism ; Water/analysis ; }, abstract = {Los Baños de Vilo (S Spain) is a natural spa characterized by extreme sulphureous waters; however, populations of chlorophyceans inhabit in the spa. The adaptation mechanisms allowing resistance by photosynthetic microorganisms to the extreme sulphureous waters were studied by using a modified Luria-Delbrück fluctuation analysis. For this purpose, the adaptation of the chlorophycean Dictyosphaerium chlorelloides and the cyanobacterium Microcystis aeruginosa (both isolated from non-sulphureous water) were analysed in order to distinguish between physiological adaptation (acclimation) and genetic adaptation by the selection of rare spontaneous mutations. Acclimation to the extreme water was achieved by D. chlorelloides; however, M. aeruginosa cells proliferated as a consequence of selection of favoured mutants (i.e. genetic adaptation). The resistant cells of M. aeruginosa appeared with a frequency of 7.1 × 10(-7) per cell per generation, and the frequency of the resistant allele, under non-selective conditions, was estimated to be 1.1 × 10(-6) per cells as a consequence of the balance mutation-selection. It could be hypothesized that the populations of eukaryotic algae living in the Los Baños de Vilo could be the descendants of chlorophyceans that arrived fortuitously at the spa in the past. On the other hand, cyanobacteria could quickly adapt by the selection of favoured mutants. The single mutation that allows resistance to sulphureous water from Baños de Vilo in M. aeruginosa represents a phenotypic burden impairing growth rate and photosynthetic performance. The resistant-variant cells of M. aeruginosa showed a lower acclimated growth rate and a decreased maximum quantum yield and photosynthetic efficiency, in comparison to the wild-type cells.}, }
@article {pmid23880792, year = {2013}, author = {Adams, RI and Amend, AS and Taylor, JW and Bruns, TD}, title = {A unique signal distorts the perception of species richness and composition in high-throughput sequencing surveys of microbial communities: a case study of fungi in indoor dust.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {735-741}, pmid = {23880792}, issn = {1432-184X}, mesh = {*Air Microbiology ; Air Pollution, Indoor/analysis ; *Biodiversity ; Dust/analysis ; Ecosystem ; Fungi/classification/*genetics/*isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Sequence-based surveys of microorganisms in varied environments have found extremely diverse assemblages. A standard practice in current high-throughput sequence (HTS) approaches in microbial ecology is to sequence the composition of many environmental samples at once by pooling amplicon libraries at a common concentration before processing on one run of a sequencing platform. Biomass of the target taxa, however, is not typically determined prior to HTS, and here, we show that when abundances of the samples differ to a large degree, this standard practice can lead to a perceived bias in community richness and composition. Fungal signal in settled dust of five university teaching laboratory classrooms, one of which was used for a mycology course, was surveyed. The fungal richness and composition in the dust of the nonmycology classrooms were remarkably similar to each other, while the mycology classroom was dominated by abundantly sporulating specimen fungi, particularly puffballs, and appeared to have a lower overall richness based on rarefaction curves and richness estimators. The fungal biomass was three to five times higher in the mycology classroom than the other classrooms, indicating that fungi added to the mycology classroom swamped the background fungi present in indoor air. Thus, the high abundance of a few taxa can skew the perception of richness and composition when samples are sequenced to an even depth. Next, we used in silico manipulations of the observed data to confirm that a unique signature can be identified with HTS approaches when the source is abundant, whether or not the taxon identity is distinct. Lastly, aerobiology of indoor fungi is discussed.}, }
@article {pmid23880418, year = {2013}, author = {Swanson, CA and Sliwinski, MK}, title = {One-dimensional TRFLP-SSCP is an effective DNA fingerprinting strategy for soil Archaea that is able to simultaneously differentiate broad taxonomic clades based on terminal fragment length polymorphisms and closely related sequences based on single stranded conformation polymorphisms.}, journal = {Journal of microbiological methods}, volume = {94}, number = {3}, pages = {317-324}, doi = {10.1016/j.mimet.2013.07.003}, pmid = {23880418}, issn = {1872-8359}, mesh = {*Archaea/classification/genetics/isolation &amp; purification ; DNA Fingerprinting/*methods ; Gene Library ; Genes, Archaeal/genetics ; Iowa ; Phylogeny ; Polymorphism, Restriction Fragment Length/*genetics ; Polymorphism, Single-Stranded Conformational/*genetics ; *Soil Microbiology ; }, abstract = {DNA fingerprinting methods provide a means to rapidly compare microbial assemblages from environmental samples without the need to first cultivate species in the laboratory. The profiles generated by these techniques are able to identify statistically significant temporal and spatial patterns, correlations to environmental gradients, and biological variability to estimate the number of replicates for clone libraries or next generation sequencing (NGS) surveys. Here we describe an improved DNA fingerprinting technique that combines terminal restriction fragment length polymorphisms (TRFLP) and single stranded conformation polymorphisms (SSCP) so that both can be used to profile a sample simultaneously rather than requiring two sequential steps as in traditional two-dimensional (2-D) gel electrophoresis. For the purpose of profiling Archaeal 16S rRNA genes from soil, the dynamic range of this combined 1-D TRFLP-SSCP approach was superior to TRFLP and SSCP. 1-D TRFLP-SSCP was able to distinguish broad taxonomic clades with genetic distances greater than 10%, such as Euryarchaeota and the Thaumarchaeal clades g_Ca. Nitrososphaera (formerly 1.1b) and o_NRP-J (formerly 1.1c) better than SSCP. In addition, 1-D TRFLP-SSCP was able to simultaneously distinguish closely related clades within a genus such as s_SCA1145 and s_SCA1170 better than TRFLP. We also tested the utility of 1-D TRFLP-SSCP fingerprinting of environmental assemblages by comparing this method to the generation of a 16S rRNA clone library of soil Archaea from a restored Tallgrass prairie. This study shows 1-D TRFLP-SSCP fingerprinting provides a rapid and phylogenetically informative screen of Archaeal 16S rRNA genes in soil samples.}, }
@article {pmid23879839, year = {2014}, author = {Hödl, I and Mari, L and Bertuzzo, E and Suweis, S and Besemer, K and Rinaldo, A and Battin, TJ}, title = {Biophysical controls on cluster dynamics and architectural differentiation of microbial biofilms in contrasting flow environments.}, journal = {Environmental microbiology}, volume = {16}, number = {3}, pages = {802-812}, pmid = {23879839}, issn = {1462-2920}, support = {Y 420/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; *Biofilms ; Biophysical Phenomena/*physiology ; Computer Simulation ; Environment ; Rivers/*microbiology ; *Water Microbiology ; *Water Movements ; }, abstract = {Ecology, with a traditional focus on plants and animals, seeks to understand the mechanisms underlying structure and dynamics of communities. In microbial ecology, the focus is changing from planktonic communities to attached biofilms that dominate microbial life in numerous systems. Therefore, interest in the structure and function of biofilms is on the rise. Biofilms can form reproducible physical structures (i.e. architecture) at the millimetre-scale, which are central to their functioning. However, the spatial dynamics of the clusters conferring physical structure to biofilms remains often elusive. By experimenting with complex microbial communities forming biofilms in contrasting hydrodynamic microenvironments in stream mesocosms, we show that morphogenesis results in 'ripple-like' and 'star-like' architectures--as they have also been reported from monospecies bacterial biofilms, for instance. To explore the potential contribution of demographic processes to these architectures, we propose a size-structured population model to simulate the dynamics of biofilm growth and cluster size distribution. Our findings establish that basic physical and demographic processes are key forces that shape apparently universal biofilm architectures as they occur in diverse microbial but also in single-species bacterial biofilms.}, }
@article {pmid23877581, year = {2013}, author = {Chaudhary, PP and Brablcová, L and Buriánková, I and Rulík, M}, title = {Molecular diversity and tools for deciphering the methanogen community structure and diversity in freshwater sediments.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {17}, pages = {7553-7562}, doi = {10.1007/s00253-013-5102-8}, pmid = {23877581}, issn = {1432-0614}, mesh = {Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; *Biodiversity ; Fresh Water/*microbiology ; *Genetic Techniques ; Genetic Variation ; Geologic Sediments/*microbiology ; Methane/*metabolism ; }, abstract = {Methanogenic archaeal communities existing in freshwater sediments are responsible for approximately 50 % of the total global emission of methane. This process contributes significantly to global warming and, hence, necessitates interventional control measures to limit its emission. Unfortunately, the diversity and functional interactions of methanogenic populations occurring in these habitats are yet to be fully characterized. Considering several disadvantages of conventional culture-based methodologies, in recent years, impetus is given to molecular biology approaches to determine the community structure of freshwater sedimentary methanogenic archaea. 16S rRNA and methyl coenzyme M reductase (mcrA) gene-based cloning techniques are the first choice for this purpose. In addition, electrophoresis-based (denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and terminal restriction fragment length polymorphism) and quantitative real-time polymerase chain reaction techniques have also found extensive applications. These techniques are highly sensitive, rapid, and reliable as compared to traditional culture-dependent approaches. Molecular diversity studies revealed the dominance of the orders Methanomicrobiales and Methanosarcinales of methanogens in freshwater sediments. The present review discusses in detail the status of the diversity of methanogens and the molecular approaches applied in this area of research.}, }
@article {pmid23875618, year = {2013}, author = {Murali Mohan, A and Hartsock, A and Hammack, RW and Vidic, RD and Gregory, KB}, title = {Microbial communities in flowback water impoundments from hydraulic fracturing for recovery of shale gas.}, journal = {FEMS microbiology ecology}, volume = {86}, number = {3}, pages = {567-580}, doi = {10.1111/1574-6941.12183}, pmid = {23875618}, issn = {1574-6941}, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; *Extraction and Processing Industry ; Geologic Sediments/microbiology ; *Natural Gas ; New York ; *Petroleum ; Proteobacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Wastewater/microbiology ; *Water Microbiology ; }, abstract = {Hydraulic fracturing for natural gas extraction from shale produces waste brine known as flowback that is impounded at the surface prior to reuse and/or disposal. During impoundment, microbial activity can alter the fate of metals including radionuclides, give rise to odorous compounds, and result in biocorrosion that complicates water and waste management and increases production costs. Here, we describe the microbial ecology at multiple depths of three flowback impoundments from the Marcellus shale that were managed differently. 16S rRNA gene clone libraries revealed that bacterial communities in the untreated and biocide-amended impoundments were depth dependent, diverse, and most similar to species within the taxa γ-proteobacteria, α-proteobacteria, δ-proteobacteria, Clostridia, Synergistetes, Thermotogae, Spirochetes, and Bacteroidetes. The bacterial community in the pretreated and aerated impoundment was uniform with depth, less diverse, and most similar to known iodide-oxidizing bacteria in the α-proteobacteria. Archaea were identified only in the untreated and biocide-amended impoundments and were affiliated to the Methanomicrobia class. This is the first study of microbial communities in flowback water impoundments from hydraulic fracturing. The findings expand our knowledge of microbial diversity of an emergent and unexplored environment and may guide the management of flowback impoundments.}, }
@article {pmid23875315, year = {2013}, author = {Arends, JB and Van Denhouwe, S and De Vrieze, J and Boon, N and Verstraete, W and Rabaey, K}, title = {Integration of wetland wastewater treatment with disinfection via bioelectrochemical H2O2 production.}, journal = {Communications in agricultural and applied biological sciences}, volume = {78}, number = {1}, pages = {173-177}, pmid = {23875315}, issn = {1379-1176}, mesh = {Biological Oxygen Demand Analysis ; Disinfection ; Electrochemical Techniques/instrumentation/*methods ; Filtration ; Hydrogen Peroxide/*chemistry ; Waste Disposal, Fluid/*methods ; Wastewater/chemistry/microbiology ; *Wetlands ; }, }
@article {pmid23875313, year = {2013}, author = {Geirnaert, A and Steyaert, A and Van den Abbeele, P and Eeckhaut, V and Van Immerseel, F and Boon, N and Van de Wiele, T}, title = {In vitro characterization of gastrointestinal behavior of Butyricicoccus pullicaecorum, a novel butyrate producing isolate with probiotic potential to counterbalance dysbiosis in inflammatory bowel disease.}, journal = {Communications in agricultural and applied biological sciences}, volume = {78}, number = {1}, pages = {157-163}, pmid = {23875313}, issn = {1379-1176}, mesh = {Acetates/metabolism ; Butyrates/*metabolism ; Chromatography, Gas ; Colon/metabolism/*microbiology ; Colony Count, Microbial ; Gram-Positive Endospore-Forming Rods/*growth &amp; development/*metabolism ; Humans ; Inflammatory Bowel Diseases/metabolism/microbiology ; Polymerase Chain Reaction ; Probiotics/*metabolism ; Upper Gastrointestinal Tract/metabolism/*microbiology ; }, }
@article {pmid23875310, year = {2013}, author = {Callewaert, C and De Maeseneire, E and Van de Wiele, T and Boon, N}, title = {Bacterial and odor profile of polyester and cotton clothes after a fitness session.}, journal = {Communications in agricultural and applied biological sciences}, volume = {78}, number = {1}, pages = {135-140}, pmid = {23875310}, issn = {1379-1176}, mesh = {Adult ; Bacteria/genetics/*isolation &amp; purification/metabolism ; *Bacterial Physiological Phenomena ; *Clothing ; Colony Count, Microbial ; Cotton Fiber ; DNA Fingerprinting ; Denaturing Gradient Gel Electrophoresis ; *Exercise ; Female ; Humans ; Male ; *Odorants ; Polyesters ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; Textiles ; }, }
@article {pmid23875299, year = {2013}, author = {Ganendra, G and De Muynck, W and Ho, A and Boon, N}, title = {Methane emission mitigation by methane-oxidizing bacteria immobilized on building materials.}, journal = {Communications in agricultural and applied biological sciences}, volume = {78}, number = {1}, pages = {61-67}, pmid = {23875299}, issn = {1379-1176}, mesh = {Bacteria/*metabolism ; Belgium ; Calcium Carbonate/chemistry ; Carbon Dioxide/*metabolism ; Colony Count, Microbial ; Construction Materials/analysis/*microbiology ; Flame Ionization ; Methane/*metabolism ; Oxidation-Reduction ; Oxygen/*metabolism ; }, }
@article {pmid23875012, year = {2013}, author = {Kuramae, EE and Verbruggen, E and Hillekens, R and de Hollander, M and Röling, WF and van der Heijden, MG and Kowalchuk, GA}, title = {Tracking fungal community responses to maize plants by DNA- and RNA-based pyrosequencing.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e69973}, pmid = {23875012}, issn = {1932-6203}, mesh = {DNA Primers/genetics ; DNA, Complementary/genetics ; Fungi/*genetics ; High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; Mycorrhizae/genetics ; RNA, Ribosomal, 18S/genetics ; *Soil Microbiology ; Species Specificity ; Zea mays/*growth &amp; development ; }, abstract = {We assessed soil fungal diversity and community structure at two sampling times (t1 = 47 days and t2 = 104 days of plant age) in pots associated with four maize cultivars, including two genetically modified (GM) cultivars by high-throughput pyrosequencing of the 18S rRNA gene using DNA and RNA templates. We detected no significant differences in soil fungal diversity and community structure associated with different plant cultivars. However, DNA-based analyses yielded lower fungal OTU richness as compared to RNA-based analyses. Clear differences in fungal community structure were also observed in relation to sampling time and the nucleic acid pool targeted (DNA versus RNA). The most abundant soil fungi, as recovered by DNA-based methods, did not necessary represent the most "active" fungi (as recovered via RNA). Interestingly, RNA-derived community compositions at t1 were highly similar to DNA-derived communities at t2, based on presence/absence measures of OTUs. We recovered large proportions of fungal sequences belonging to arbuscular mycorrhizal fungi and Basidiomycota, especially at the RNA level, suggesting that these important and potentially beneficial fungi are not affected by the plant cultivars nor by GM traits (Bt toxin production). Our results suggest that even though DNA- and RNA-derived soil fungal communities can be very different at a given time, RNA composition may have a predictive power of fungal community development through time.}, }
@article {pmid23874682, year = {2013}, author = {Poutahidis, T and Kleinewietfeld, M and Smillie, C and Levkovich, T and Perrotta, A and Bhela, S and Varian, BJ and Ibrahim, YM and Lakritz, JR and Kearney, SM and Chatzigiagkos, A and Hafler, DA and Alm, EJ and Erdman, SE}, title = {Microbial reprogramming inhibits Western diet-associated obesity.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e68596}, pmid = {23874682}, issn = {1932-6203}, support = {U01 CA164337/CA/NCI NIH HHS/United States ; U19 AI070352/AI/NIAID NIH HHS/United States ; R01 AI091568/AI/NIAID NIH HHS/United States ; P01 AI039671/AI/NIAID NIH HHS/United States ; R01 CA108854/CA/NCI NIH HHS/United States ; P01 AI045757/AI/NIAID NIH HHS/United States ; R01CA108854/CA/NCI NIH HHS/United States ; U19 AI046130/AI/NIAID NIH HHS/United States ; P01AI045757/AI/NIAID NIH HHS/United States ; P30-ES002109/ES/NIEHS NIH HHS/United States ; T32 GM087237/GM/NIGMS NIH HHS/United States ; P30 ES002109/ES/NIEHS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Animals ; Cells, Cultured ; Diet/*adverse effects ; Fast Foods/adverse effects ; Female ; Humans ; Intestines/immunology/microbiology ; Limosilactobacillus reuteri/*physiology ; Male ; Mice ; Mice, Inbred C57BL ; Microbiota/physiology ; Middle Aged ; Obesity/*diet therapy/*etiology/immunology/microbiology ; Probiotics/*therapeutic use ; T-Lymphocytes, Helper-Inducer/physiology ; Western World ; Yogurt ; Young Adult ; }, abstract = {A recent epidemiological study showed that eating 'fast food' items such as potato chips increased likelihood of obesity, whereas eating yogurt prevented age-associated weight gain in humans. It was demonstrated previously in animal models of obesity that the immune system plays a critical role in this process. Here we examined human subjects and mouse models consuming Westernized 'fast food' diet, and found CD4(+) T helper (Th)17-biased immunity and changes in microbial communities and abdominal fat with obesity after eating the Western chow. In striking contrast, eating probiotic yogurt together with Western chow inhibited age-associated weight gain. We went on to test whether a bacteria found in yogurt may serve to lessen fat pathology by using purified Lactobacillus reuteri ATCC 6475 in drinking water. Surprisingly, we discovered that oral L. reuteri therapy alone was sufficient to change the pro-inflammatory immune cell profile and prevent abdominal fat pathology and age-associated weight gain in mice regardless of their baseline diet. These beneficial microbe effects were transferable into naïve recipient animals by purified CD4(+) T cells alone. Specifically, bacterial effects depended upon active immune tolerance by induction of Foxp3(+) regulatory T cells (Treg) and interleukin (Il)-10, without significantly changing the gut microbial ecology or reducing ad libitum caloric intake. Our finding that microbial targeting restored CD4(+) T cell balance and yielded significantly leaner animals regardless of their dietary 'fast food' indiscretions suggests population-based approaches for weight management and enhancing public health in industrialized societies.}, }
@article {pmid23872930, year = {2013}, author = {Fan, Y and Wernegreen, JJ}, title = {Can't take the heat: high temperature depletes bacterial endosymbionts of ants.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {727-733}, pmid = {23872930}, issn = {1432-184X}, support = {R01 GM062626/GM/NIGMS NIH HHS/United States ; R01GM062626/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Ants/*microbiology ; Endophytes/chemistry/genetics/*physiology ; Enterobacteriaceae/chemistry/genetics/*physiology ; Hot Temperature ; Symbiosis ; }, abstract = {Members of the ant tribe Camponotini have coevolved with Blochmannia, an obligate intracellular bacterial mutualist. This endosymbiont lives within host bacteriocyte cells that line the ant midgut, undergoes maternal transmission from host queens to offspring, and contributes to host nutrition via nitrogen recycling and nutrient biosynthesis. While elevated temperature has been shown to disrupt obligate bacterial mutualists of some insects, its impact on the ant-Blochmannia partnership is less clear. Here, we test the effect of heat on the density of Blochmannia in two related Camponotus species in the lab. Transcriptionally active Blochmannia were quantified using RT-qPCR as the ratio of Blochmannia 16S rRNA to ant host elongation factor 1-α transcripts. Our results showed that 4 weeks of heat treatment depleted active Blochmannia by >99 % in minor workers and unmated queens. However, complete elimination of Blochmannia transcripts rarely occurred, even after 16 weeks of heat treatment. Possible mechanisms of observed thermal sensitivity may include extreme AT-richness and related features of Blochmannia genomes, as well as host stress responses. Broadly, the observed depletion of an essential microbial mutualist in heat-treated ants is analogous to the loss of zooanthellae during coral bleaching. While the ecological relevance of Blochmannia's thermal sensitivity is uncertain, our results argue that symbiont dynamics should be part of models predicting how ants and other animals will respond and adapt to a warming climate.}, }
@article {pmid23871297, year = {2013}, author = {Gubry-Rangin, C and Béna, G and Cleyet-Marel, JC and Brunel, B}, title = {Definition and evolution of a new symbiovar, sv. rigiduloides, among Ensifer meliloti efficiently nodulating Medicago species.}, journal = {Systematic and applied microbiology}, volume = {36}, number = {7}, pages = {490-496}, doi = {10.1016/j.syapm.2013.06.004}, pmid = {23871297}, issn = {1618-0984}, mesh = {Bacterial Proteins/genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; *Genetic Variation ; Genotype ; Medicago/*microbiology ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phylogeny ; Plant Root Nodulation ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; Sinorhizobium meliloti/*classification/genetics/*isolation &amp; purification/physiology ; }, abstract = {Understanding functional diversity is one of the main goals of microbial ecology, and definition of new bacterial ecotypes contributes significantly to this objective. Nitrogen-fixing bacteria provide a good system for investigation of ecotypes/biovars/symbiovars, as they present different specific associations with several host plants. This specific symbiosis is reflected both in the nodulation and fixation efficiency and in genetic characters of the bacteria, and several biovars have already been described in the bacterial species Ensifer meliloti. In the present study, the species affiliation of E. meliloti strains trapped from nodules sampled from Medicago rigiduloïdes roots was analyzed using housekeeping recA genes and DNA-DNA hybridization. The genetic diversity of these isolates was also investigated using several symbiotic markers: nodulation (nodA, nodB, nodC) and nitrogen fixation (nifH) genes, as well as the performance of phenotypic tests of nodulation capacity and nitrogen fixation efficiency. These analyses led to the proposal of a new bacterial symbiovar, E. meliloti sv. rigiduloides, that fixed nitrogen efficiently on M. rigiduloïdes, but not on Medicago truncatula. Using phylogenetic reconstructions, including the different described symbiovars, several hypotheses of lateral gene transfer and gene loss are proposed to explain the emergence of symbiovars within this species. The widespread geographical distribution of this symbiovar around the Mediterranean Basin, in contrast to restriction of M. rigiduloïdes to Eastern European countries, suggests that these isolates might also be associated with other plant species. The description of a new symbiovar within E. meliloti confirms the need for accurate bacterial ecological classification, especially for analysis of bacterial populations.}, }
@article {pmid23865888, year = {2013}, author = {Hardoim, PR and Nazir, R and Sessitsch, A and Elhottová, D and Korenblum, E and van Overbeek, LS and van Elsas, JD}, title = {The new species Enterobacter oryziphilus sp. nov. and Enterobacter oryzendophyticus sp. nov. are key inhabitants of the endosphere of rice.}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {164}, pmid = {23865888}, issn = {1471-2180}, mesh = {Bacterial Typing Techniques ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA-Directed RNA Polymerases/genetics/physiology ; Enterobacteriaceae/*classification/genetics/*isolation &amp; purification ; Fatty Acids/analysis ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Oryza/*microbiology ; Phylogeny ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Six independent Gram-negative, facultatively anaerobic, non-spore-forming, nitrogen-fixing rod-shaped isolates were obtained from the root endosphere of rice grown at the International Rice Research Institute (IRRI) and investigated in a polyphasic taxonomic study.<br><br>RESULTS: The strains produced fatty acid patterns typical for members of the family Enterobacteriaceae. Comparative sequence analyses of the 16S rRNA as well as rpoB genes allocated the strains to two well-defined groups within the genus Enterobacter, family Enterobacteriaceae. The analyses indicated Enterobacter radicincitans, Enterobacter arachidis and Enterobacter oryzae to be the closest related species. An RpoB (translated) protein comparison supported the placement in the genus Enterobacter and the relatedness of our isolates to the aforementioned species. Genomic DNA:DNA hybridization analyses and biochemical analyses provided further evidence that the novel strains belong to two new species within the genus Enterobacter. The two species can be differentiated from each other and from existing enteric species by acid production from L-rhamnose and D-melibiose, decarboxylation of ornithine and utilization of D-alanine, D-raffinose L-proline and L-aspartic acid, among other characteristics. Members of both species revealed capacities to colonise rice roots, including plant-growth-promoting capabilities such as an active supply of fixed nitrogen to the plant and solubilisation of inorganic phosphorus, next to traits allowing adaptation to the plant.<br><br>CONCLUSIONS: Two novel proposed enterobacterial species, denominated Enterobacter oryziphilus sp. nov. (type strain REICA_142(T)=LMG 26429(T)=NCCB 100393(T)) and Enterobacter oryzendophyticus sp. nov. (type strain REICA_082(T)=LMG 26432(T) =NCCB 100390(T)) were isolated from rice roots. Both species are capable of promoting rice growth by supplying nitrogen and phosphorus.}, }
@article {pmid23865748, year = {2013}, author = {Rodriguez-Lanetty, M and Granados-Cifuentes, C and Barberan, A and Bellantuono, AJ and Bastidas, C}, title = {Ecological Inferences from a deep screening of the Complex Bacterial Consortia associated with the coral, Porites astreoides.}, journal = {Molecular ecology}, volume = {22}, number = {16}, pages = {4349-4362}, doi = {10.1111/mec.12392}, pmid = {23865748}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Caribbean Region ; Coral Reefs ; Gammaproteobacteria/classification/genetics/*isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {The functional role of the bacterial organisms in the reef ecosystem and their contribution to the coral well-being remain largely unclear. The first step in addressing this gap of knowledge relies on in-depth characterization of the coral microbial community and its changes in diversity across coral species, space and time. In this study, we focused on the exploration of microbial community assemblages associated with an ecologically important Caribbean scleractinian coral, Porites astreoides, using Illumina high-throughput sequencing of the V5 fragment of 16S rRNA gene. We collected data from a large set of biological replicates, allowing us to detect patterns of geographical structure and resolve co-occurrence patterns using network analyses. The taxonomic analysis of the resolved diversity showed consistent and dominant presence of two OTUs affiliated with the order Oceanospirillales, which corroborates a specific pattern of bacterial association emerging for this coral species and for many other corals within the genus Porites. We argue that this specific association might indicate a symbiotic association with the adult coral partner. Furthermore, we identified a highly diverse rare bacterial 'biosphere' (725 OTUs) also living along with the dominant bacterial symbionts, but the assemblage of this biosphere is significantly structured along the geographical scale. We further discuss that some of these rare bacterial members show significant association with other members of the community reflecting the complexity of the networked consortia within the coral holobiont.}, }
@article {pmid23864569, year = {2013}, author = {Garcia, SL and Salka, I and Grossart, HP and Warnecke, F}, title = {Depth-discrete profiles of bacterial communities reveal pronounced spatio-temporal dynamics related to lake stratification.}, journal = {Environmental microbiology reports}, volume = {5}, number = {4}, pages = {549-555}, doi = {10.1111/1758-2229.12044}, pmid = {23864569}, issn = {1758-2229}, mesh = {Bacteria/*classification/*genetics ; *Biota ; Germany ; Lakes/chemistry/*microbiology ; Oxygen/analysis ; Time Factors ; }, abstract = {With this work we intend to stress the importance of considering discrete depth sampling for bacterial community analysis of stratified aquatic systems. Depth is a very important parameter to consider when sampling bacterial communities, as their abundance and composition can change within the distinct water layers. Stratified lakes are good model systems to study these connections since changes in environmental parameters can occur on a cm-scale at the thermo- and/or chemocline. Lake Grosse Fuchskuhle was sampled at discrete fine-scale depths at three time points covering a stage in which the lake was stratified and the beginning of winter mixing. In this paper we present the most abundant bacterial groups at the different depths sampled and also the most abundant operational taxonomic units (OTUs). Overall, oxygen was found to be an important factor shaping the microbial community composition.}, }
@article {pmid23857378, year = {2013}, author = {Kuznetsova, TA and Kam, M and Khokhlova, IS and Kostina, NV and Dobrovolskaya, TG and Umarov, MM and Degen, AA and Shenbrot, GI and Krasnov, BR}, title = {Desert gerbils affect bacterial composition of soil.}, journal = {Microbial ecology}, volume = {66}, number = {4}, pages = {940-949}, pmid = {23857378}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Denitrification ; Ecosystem ; Gastrointestinal Tract/microbiology ; Gerbillinae/classification/microbiology/*physiology ; Nitrogen/metabolism ; Nitrogen Fixation ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Rodents affect soil microbial communities by burrow architecture, diet composition, and foraging behavior. We examined the effect of desert rodents on nitrogen-fixing bacteria (NFB) communities by identifying bacteria colony-forming units (CFU) and measuring nitrogen fixation rates (ARA), denitrification (DA), and CO2 emission in soil from burrows of three gerbil species differing in diets. Psammomys obesus is folivorous, Meriones crassus is omnivorous, consuming green vegetation and seeds, and Dipodillus dasyurus is predominantly granivorous. We also identified NFB in the digestive tract of each rodent species and in Atriplex halimus and Anabasis articulata, dominant plants at the study site. ARA rates of soil from burrows of the rodent species were similar, and substantially lower than control soil, but rates of DA and CO2 emission differed significantly among burrows. Highest rates of DA and CO2 emission were measured in D. dasyurus burrows and lowest in P. obesus. CFU differed among bacteria isolates, which reflected dietary selection. Strains of cellulolytic representatives of the family Myxococcaceae and the genus Cytophaga dominated burrows of P. obesus, while enteric Bacteroides dominated burrows of D. dasyurus. Burrows of M. crassus contained both cellulolytic and enteric bacteria. Using discriminant function analysis, differences were revealed among burrow soils of all rodent species and control soil, and the two axes accounted for 91 % of the variance in bacterial occurrences. Differences in digestive tract bacterial occurrences were found among these rodent species. Bacterial colonies in P. obesus and M. crassus burrows were related to bacteria of A. articulata, the main plant consumed by both species. In contrast, bacteria colonies in the burrow soil of D. dasyurus were related to bacteria in its digestive tract. We concluded that gerbils play an important role as ecosystem engineers within their burrow environment and affect the microbial complex of the nitrogen-fixing organisms in soils.}, }
@article {pmid23857377, year = {2013}, author = {Fujimoto, M and Crossman, JA and Scribner, KT and Marsh, TL}, title = {Microbial community assembly and succession on lake sturgeon egg surfaces as a function of simulated spawning stream flow rate.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {500-511}, pmid = {23857377}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Ecosystem ; Fishes/growth &amp; development/*microbiology ; Lakes/chemistry ; Molecular Sequence Data ; Ovum/growth &amp; development/*microbiology ; Phylogeny ; *Water Movements ; }, abstract = {We investigated microbial succession on lake sturgeon (Acipenser fulvescens) egg surfaces over the course of their incubation period as a function of simulated stream flow rate. The primary objective was to characterize the microbial community assembly during succession and to examine how simulated stream flow rate affect the successional process. Sturgeon eggs were reared under three flow regimes; high (0.55 m/s), low (0.18 m/s), and variable (0.35 and 0.11 m/s alternating 12 h intervals). Eggs were collected from each flow regime at different egg developmental stages. Microbial community DNA was extracted from egg surface and the communities were examined using 16S rRNA gene-based terminal restriction fragment length polymorphism and 454 pyrosequencing. Analysis of these datasets using principal component analysis revealed that microbial communities were clustered by egg developmental stages (early, middle, and late) regardless of flow regimes. 454 pyrosequencing data suggested that 90-98 % of the microbial communities were composed of the phyla Proteobacteria and Bacteroidetes throughout succession. β-Protebacteria was more dominant in the early stage, Bacteroidetes became more dominant in the middle stage, and α-Proteobacteria became dominant in the late stage. A total of 360 genera and 5,826 OTUs at 97 % similarity cutoff were associated with the eggs. Midway through egg development, the egg-associated communities of the low flow regime had a higher diversity than those communities developed under high or variable flow regimes. Results show that microbial community turnover occurred during embryogenesis, and stream flow rate influenced the microbial succession processes on the sturgeon egg surfaces.}, }
@article {pmid23850847, year = {2013}, author = {Macías-Díaz, JE and Macías, S and Medina-Ramírez, IE}, title = {An efficient nonlinear finite-difference approach in the computational modeling of the dynamics of a nonlinear diffusion-reaction equation in microbial ecology.}, journal = {Computational biology and chemistry}, volume = {47}, number = {}, pages = {24-30}, doi = {10.1016/j.compbiolchem.2013.05.003}, pmid = {23850847}, issn = {1476-928X}, mesh = {Bacteria/classification/growth &amp; development/*metabolism ; Biofilms ; Computational Biology ; *Computer Simulation ; Diffusion ; *Ecosystem ; *Models, Biological ; *Nonlinear Dynamics ; }, abstract = {In this manuscript, we present a computational model to approximate the solutions of a partial differential equation which describes the growth dynamics of microbial films. The numerical technique reported in this work is an explicit, nonlinear finite-difference methodology which is computationally implemented using Newton's method. Our scheme is compared numerically against an implicit, linear finite-difference discretization of the same partial differential equation, whose computer coding requires an implementation of the stabilized bi-conjugate gradient method. Our numerical results evince that the nonlinear approach results in a more efficient approximation to the solutions of the biofilm model considered, and demands less computer memory. Moreover, the positivity of initial profiles is preserved in the practice by the nonlinear scheme proposed.}, }
@article {pmid23848238, year = {2014}, author = {Stoeck, T and Breiner, HW and Filker, S and Ostermaier, V and Kammerlander, B and Sonntag, B}, title = {A morphogenetic survey on ciliate plankton from a mountain lake pinpoints the necessity of lineage-specific barcode markers in microbial ecology.}, journal = {Environmental microbiology}, volume = {16}, number = {2}, pages = {430-444}, pmid = {23848238}, issn = {1462-2920}, mesh = {Austria ; Chlorophyll/analysis ; Chlorophyll A ; Ciliophora/classification/cytology/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Protozoan/genetics ; *Genes, rRNA ; Lakes/*microbiology ; Plankton/classification/cytology/genetics ; RNA, Ribosomal, 18S/genetics ; Water Microbiology ; }, abstract = {Analyses of high-throughput environmental sequencing data have become the 'gold-standard' to address fundamental questions of microbial diversity, ecology and biogeography. Findings that emerged from sequencing are, e.g. the discovery of the extensive 'rare microbial biosphere' and its potential function as a seed-bank. Even though applied since several years, results from high-throughput environmental sequencing have hardly been validated. We assessed how well pyrosequenced amplicons [the hypervariable eukaryotic V4 region of the small subunit ribosomal RNA (SSU rRNA) gene] reflected morphotype ciliate plankton. Moreover, we assessed if amplicon sequencing had the potential to detect the annual ciliate plankton stock. In both cases, we identified significant quantitative and qualitative differences. Our study makes evident that taxon abundance distributions inferred from amplicon data are highly biased and do not mirror actual morphotype abundances at all. Potential reasons included cell losses after fixation, cryptic morphotypes, resting stages, insufficient sequence data availability of morphologically described species and the unsatisfying resolution of the V4 SSU rRNA fragment for accurate taxonomic assignments. The latter two underline the necessity of barcoding initiatives for eukaryotic microbes to better and fully exploit environmental amplicon data sets, which then will also allow studying the potential of seed-bank taxa as a buffer for environmental changes.}, }
@article {pmid23847814, year = {2012}, author = {González-Zorn, B and Escudero, JA}, title = {Ecology of antimicrobial resistance: humans, animals, food and environment.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {15}, number = {3}, pages = {101-109}, doi = {10.2436/20.1501.01.163}, pmid = {23847814}, issn = {1139-6709}, mesh = {Animals ; Antimitotic Agents/*pharmacology ; Bacteria/*drug effects ; *Drug Resistance, Microbial ; *Ecology ; *Environment ; *Food Microbiology ; Humans ; }, abstract = {Antimicrobial resistance is a major health problem. After decades of research, numerous difficulties in tackling resistance have emerged, from the paucity of new antimicrobials to the inefficient contingency plans to reduce the use of antimicrobials; consequently, resistance to these drugs is out of control. Today we know that bacteria from the environment are often at the very origin of the acquired resistance determinants found in hospitals worldwide. Here we define the genetic components that flow from the environment to pathogenic bacteria and thereby confer a quantum increase in resistance levels, as resistance units (RU). Environmental bacteria as well as microbiomes from humans, animals, and food represent an infinite reservoir of RU, which are based on genes that have had, or not, a resistance function in their original bacterial hosts. This brief review presents our current knowledge of antimicrobial resistance and its consequences, with special focus on the importance of an ecologic perspective of antimicrobial resistance. This discipline encompasses the study of the relationships of entities and events in the framework of curing and preventing disease, a definition that takes into account both microbial ecology and antimicrobial resistance. Understanding the flux of RU throughout the diverse ecosystems is crucial to assess, prevent and eventually predict emerging scaffolds before they colonize health institutions. Collaborative horizontal research scenarios should be envisaged and involve all actors working with humans, animals, food and the environment.}, }
@article {pmid23846833, year = {2013}, author = {Asano, R and Nakai, Y and Kawada, W and Shimura, Y and Inamoto, T and Fukushima, J}, title = {Seawater inundation from the 2011 Tohoku tsunami continues to strongly affect soil bacterial communities 1 year later.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {639-646}, pmid = {23846833}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Ecosystem ; Japan ; Molecular Sequence Data ; Phylogeny ; Seawater/*analysis ; Soil/chemistry ; *Soil Microbiology ; Tsunamis ; }, abstract = {The effects of inundation caused by the 2011 Tohoku tsunami on soil bacterial communities in agricultural fields were evaluated. Bacterial communities were compared across three different types of soil, unflooded field (UF) soil, soil flooded for 2 weeks (short term (ST)), and soil flooded for 2 months (long term (LT)), using polymerase chain reaction-pyrosequencing of 16S rRNA genes. Acidobacteria were dominant in UF, with a relative abundance of approximately 35 %, and Proteobacteria dominated flooded soils (30-67 %). Hierarchical cluster analysis indicated that the community structure of soil bacteria in flooded soils (ST and LT) clearly differed from that in UF. Differences between LT and ST fields were rarely observed in terms of chemical properties and microbial community structure at the phylum level. However, sulfur-oxidizing bacteria (SOB) and nitrite-oxidizing bacteria (NOB) in LT tended to occur at high and low abundances, respectively. Halothiobacillus, a halotolerant SOB, was detected in all LT fields. Unexpectedly, a zeta-Proteobacteria, which had previously only been detected in marine environments, was detected in LT fields only. Our results demonstrate that the effects of the 2011 Tohoku tsunami on soil bacterial communities in agricultural fields may have lasted at least 1 year. Furthermore, SOB, NOB, and zeta-Proteobacteria may serve as indicators of the effects of seawater inundation on microorganisms.}, }
@article {pmid23844136, year = {2013}, author = {Dias, AC and Dini-Andreote, F and Hannula, SE and Andreote, FD and Pereira E Silva, Mde C and Salles, JF and de Boer, W and van Veen, J and van Elsas, JD}, title = {Different selective effects on rhizosphere bacteria exerted by genetically modified versus conventional potato lines.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e67948}, pmid = {23844136}, issn = {1932-6203}, mesh = {Bacteria/classification/*genetics/*metabolism ; Biodiversity ; Biomarkers/metabolism ; Fatty Acids/chemistry/metabolism ; Metagenome ; Microbiota ; Phenotype ; Phospholipids/chemistry/metabolism ; Phylogeny ; Plant Roots/microbiology ; Plants, Genetically Modified ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil Microbiology ; Solanum tuberosum/genetics/growth &amp; development/*microbiology ; }, abstract = {BACKGROUND: In this study, we assessed the actively metabolizing bacteria in the rhizosphere of potato using two potato cultivars, i.e. the genetically-modified (GM) cultivar Modena (having tubers with altered starch content) and the near-isogenic non-GM cultivar Karnico. To achieve our aims, we pulse-labelled plants at EC90 stage with (13)C-CO2 and analysed their rhizosphere microbial communities 24 h, 5 and 12 days following the pulse. In the analyses, phospholipid fatty acid/stable isotope probing (PLFA-SIP) as well as RNA-SIP followed by reverse transcription and PCR-DGGE and clone library analysis, were used to determine the bacterial groups that actively respond to the root-released (13)C labelled carbonaceous compounds.<br><br>The PLFA-SIP data revealed major roles of bacteria in the uptake of root-released (13)C carbon, which grossly increased with time. Gram-negative bacteria, including members of the genera Pseudomonas and Burkholderia, were strong accumulators of the (13)C-labeled compounds at the two cultivars, whereas Gram-positive bacteria were lesser responders. PCR-DGGE analysis of cDNA produced from the two cultivar types showed that these had selected different bacterial, alpha- and betaproteobacterial communities at all time points. Moreover, an effect of time was observed, indicating dynamism in the structure of the active bacterial communities. PCR-DGGE as well as clone library analyses revealed that the main bacterial responders at cultivar Karnico were taxonomically affiliated with the genus Pseudomonas, next to Gluconacetobacter and Paracoccus. Cultivar Modena mainly attracted Burkholderia, next to Moraxella-like (Moraxellaceae family) and Sphingomonas types.<br><br>CONCLUSIONS/SIGNIFICANCE: Based on the use of Pseudomonas and Burkholderia as proxies for differentially-selected bacterial genera, we conclude that the selective forces exerted by potato cultivar Modena on the active bacterial populations differed from those exerted by cultivar Karnico.}, }
@article {pmid23839799, year = {2013}, author = {Jassey, VE and Meyer, C and Dupuy, C and Bernard, N and Mitchell, EA and Toussaint, ML and Metian, M and Chatelain, AP and Gilbert, D}, title = {To what extent do food preferences explain the trophic position of heterotrophic and mixotrophic microbial consumers in a Sphagnum peatland?.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {571-580}, pmid = {23839799}, issn = {1432-184X}, mesh = {Amoeba/classification/*physiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Food Chain ; Food Preferences ; Heterotrophic Processes ; Population Dynamics ; Sphagnopsida/*microbiology/*parasitology ; }, abstract = {Although microorganisms are the primary drivers of biogeochemical cycles, the structure and functioning of microbial food webs are poorly studied. This is the case in Sphagnum peatlands, where microbial communities play a key role in the global carbon cycle. Here, we explored the structure of the microbial food web from a Sphagnum peatland by analyzing (1) the density and biomass of different microbial functional groups, (2) the natural stable isotope (δ(13)C and δ(15)N) signatures of key microbial consumers (testate amoebae), and (3) the digestive vacuole contents of Hyalosphenia papilio, the dominant testate amoeba species in our system. Our results showed that the feeding type of testate amoeba species (bacterivory, algivory, or both) translates into their trophic position as assessed by isotopic signatures. Our study further demonstrates, for H. papilio, the energetic benefits of mixotrophy when the density of its preferential prey is low. Overall, our results show that testate amoebae occupy different trophic levels within the microbial food web, depending on their feeding behavior, the density of their food resources, and their metabolism (i.e., mixotrophy vs. heterotrophy). Combined analyses of predation, community structure, and stable isotopes now allow the structure of microbial food webs to be more completely described, which should lead to improved models of microbial community function.}, }
@article {pmid23835180, year = {2013}, author = {Sánchez, E and Donat, E and Ribes-Koninckx, C and Fernández-Murga, ML and Sanz, Y}, title = {Duodenal-mucosal bacteria associated with celiac disease in children.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {18}, pages = {5472-5479}, pmid = {23835180}, issn = {1098-5336}, mesh = {Bacteria/*classification/*isolation &amp; purification ; Bacteriological Techniques ; *Biodiversity ; Biopsy ; Celiac Disease/*microbiology ; Child ; Child, Preschool ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Duodenum/*microbiology ; Humans ; Intestinal Mucosa/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Celiac disease (CD) is an immune-mediated enteropathy triggered by the ingestion of cereal gluten proteins. This disorder is associated with imbalances in the gut microbiota composition that could be involved in the pathogenesis of CD. The aim of this study was to characterize the composition and diversity of the cultivable duodenal mucosa-associated bacteria of CD patients and control children. Duodenal biopsy specimens from patients with active disease on a gluten-containing diet (n = 32), patients with nonactive disease after adherence to a gluten-free diet (n = 17), and controls (n = 8) were homogenized and plated on plate count agar, Wilkins-Chalgren agar, brain heart agar, or yeast, Casitone, and fatty acid agar. The isolates were identified by partial 16S rRNA gene sequencing. Renyi diversity profiles showed the highest diversity values for active CD patients, followed by nonactive CD patients and control individuals. Members of the phylum Proteobacteria were more abundant in patients with active CD than in the other child groups, while those of the phylum Firmicutes were less abundant. Members of the families Enterobacteriaceae and Staphylococcaceae, particularly the species Klebsiella oxytoca, Staphylococcus epidermidis, and Staphylococcus pasteuri, were more abundant in patients with active disease than in controls. In contrast, members of the family Streptococcaceae were less abundant in patients with active CD than in controls. Furthermore, isolates of the Streptococcus anginosus and Streptococcus mutans groups were more abundant in controls than in both CD patient groups, regardless of inflammatory status. The findings indicated that the disease is associated with the overgrowth of possible pathobionts that exclude symbionts or commensals that are characteristic of the healthy small intestinal microbiota.}, }
@article {pmid23831006, year = {2014}, author = {Moya-Pérez, A and Romo-Vaquero, M and Tomás-Barberán, F and Sanz, Y and García-Conesa, MT}, title = {Hepatic molecular responses to Bifidobacterium pseudocatenulatum CECT 7765 in a mouse model of diet-induced obesity.}, journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD}, volume = {24}, number = {1}, pages = {57-64}, doi = {10.1016/j.numecd.2013.04.011}, pmid = {23831006}, issn = {1590-3729}, mesh = {Animals ; *Bifidobacterium ; *Diet, High-Fat ; Dietary Supplements ; Disease Models, Animal ; Early Growth Response Protein 1/genetics/metabolism ; Fatty Acids/metabolism ; Insulin-Like Growth Factor Binding Protein 2/genetics/metabolism ; Lipase/metabolism ; Lipid Metabolism ; Liver/metabolism/microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Microarray Analysis ; Obesity/metabolism/*microbiology ; Probiotics/*administration &amp; dosage ; Protein Phosphatase 1/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Transcriptome ; Triglycerides/metabolism ; Weight Gain ; }, abstract = {BACKGROUND AND AIMS: Bifidobacterium pseudocatenulatum CECT 7765 moderates body weight gain and metabolic parameters in high-fat diet-(HFD)-fed mice but, the mechanisms of action are not yet understood. To further understand the effects of this bacterial strain, we have investigated the molecular changes in the liver of mice fed a HFD and supplemented with the bacteria.<br><br>METHODS AND RESULTS: Gene expression and protein levels were measured in the liver of C57BL/6 male mice following sub-chronic consumption of a HFD and B. pseudocatenulatum CECT 7765. Our results show that the consumption of this bacterial strain modulated the expression of key genes involved in the regulation of energy metabolism and transport of lipids that were affected by the HFD.B. pseudocatenulatum CECT 7765 significantly counteracted the effects caused by the HFD on the fatty acid transporter CD36, the transcription regulator of lipid biosynthesis EGR1 and the regulators of glucose metabolism, IGFBP2 and PPP1R3B, both at the mRNA and protein levels. The bacterial strain slightly induced the transcript levels of PNPLA2, a lipase that hydrolyses triglycerides in lipid droplets. In the standard diet (SD)-fed mice, the administration of B. pseudocatenulatum CECT 7765 donwregulated the expression of INSIG1 and HMGCR critically involved in the regulation of cholesterol levels.<br><br>CONCLUSION: B. pseudocatenulatum CECT 7765 modified the expression of key regulators of fatty acid and cholesterol metabolism and transport, lipid levels and glucose levels in the liver which supports the beneficial metabolic effects of this bacterial strain.}, }
@article {pmid23829083, year = {2013}, author = {Bodaszewska-Lubas, M and Brzychczy-Wloch, M and Adamski, P and Gosiewski, T and Strus, M and Heczko, PB}, title = {Adherence of group B streptococci to human rectal and vaginal epithelial cell lines in relation to capsular polysaccharides as well as alpha-like protein genes - pilot study.}, journal = {Polish journal of microbiology}, volume = {62}, number = {1}, pages = {85-90}, pmid = {23829083}, issn = {1733-1331}, mesh = {Bacterial Adhesion/*physiology ; Bacterial Capsules ; Bacterial Proteins/metabolism ; Cell Line ; Epithelial Cells/*microbiology ; Female ; Humans ; Pilot Projects ; Polysaccharides, Bacterial/*physiology ; Rectum/*chemistry ; Streptococcus agalactiae/*physiology ; Vagina/*chemistry ; }, abstract = {Streptococcus agalactiae (Group B Streptococci, GBS) constitutes a risk factor for infections of the newborns born by colonized mothers. The adherence of GBS to epithelial cells has been proved to be an important factor in the colonization of mucus membranes of both human rectum and vagina. The objective of the study was to assess the adhesion of the selected GBS strains to the human colon adenocarcinoma cell line (HT-29) and human epidermoid vulvo-vaginal cells (A-431) in relation to the capsular polysaccharides and alpha-like protein genes. GBS strains from the human sources belonging to Ia, Ib, II, III and V serotypes possessing different surface alpha-like protein genes such as the alp 2, alp 3, bca, epsilon and rib in the conventional adherence assay were examined. The adherence of GBS strains to the HT-29 cell line was considerably higher than to the A-431 cell line. For GBS serotype Ia and III, a significant difference between the adhesion to the HT-29 and A-431 cell lines was presented. The adhesion of GBS strains to the HT-29 cell line depended on alpha-like protein genes. The most adhesive ones were the GBS strains containing the rib and alp 2 genes. The adherence of GBS strains to the A-431 cell line depended on both their serotype and alpha-like protein genes. Serotype III adhered to the A-431 cells most tightly, particularly the strains containing the rib and alp 2 genes. GBS strains containing the rib gene adhered to the HT-29 and A-431 cell lines more firmly than GBS strains containing other alpha-like protein genes.}, }
@article {pmid23828521, year = {2013}, author = {Ramond, JB and Welz, PJ and Tuffin, MI and Burton, SG and Cowan, DA}, title = {Selection of diazotrophic bacterial communities in biological sand filter mesocosms used for the treatment of phenolic-laden wastewater.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {563-570}, pmid = {23828521}, issn = {1432-184X}, mesh = {Bacteria/classification/*isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Biodiversity ; Filtration ; Nitrogen/analysis/metabolism ; Phenols/*metabolism ; Phylogeny ; Silicon Dioxide/chemistry ; Wastewater/analysis/microbiology ; Water Pollutants, Chemical/*metabolism ; *Water Purification/instrumentation ; }, abstract = {Agri effluents such as winery or olive mill wastewaters are characterized by high phenolic concentrations. These compounds are highly toxic and generally refractory to biodegradation. Biological sand filters (BSFs) represent inexpensive, environmentally friendly, and sustainable wastewater treatment systems which rely vastly on microbial catabolic processes. Using denaturing gradient gel electrophoresis and terminal-restriction fragment length polymorphism, this study aimed to assess the impact of increasing concentrations of synthetic phenolic-rich wastewater, ranging from 96 mg L(-1) gallic acid and 138 mg L(-1) vanillin (i.e., a total chemical oxygen demand (COD) of 234 mg L(-1)) to 2,400 mg L(-1) gallic acid and 3,442 mg L(-1) vanillin (5,842 mg COD L(-1)), on bacterial communities and the specific functional diazotrophic community from BSF mesocosms. This amendment procedure instigated efficient BSF phenolic removal, significant modifications of the bacterial communities, and notably led to the selection of a phenolic-resistant and less diverse diazotrophic community. This suggests that bioavailable N is crucial in the functioning of biological treatment processes involving microbial communities, and thus that functional alterations in the bacterial communities in BSFs ensure provision of sufficient bioavailable nitrogen for the degradation of wastewater with a high C/N ratio.}, }
@article {pmid23828520, year = {2013}, author = {Pan, H and He, X and Lux, R and Luan, J and Shi, W}, title = {Killing of Escherichia coli by Myxococcus xanthus in aqueous environments requires exopolysaccharide-dependent physical contact.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {630-638}, pmid = {23828520}, issn = {1432-184X}, support = {R01 GM054666/GM/NIGMS NIH HHS/United States ; GM54666/GM/NIGMS NIH HHS/United States ; }, mesh = {*Antibiosis ; Escherichia coli/genetics/*physiology ; Lipopolysaccharides/metabolism ; Myxococcus xanthus/genetics/*physiology ; Polysaccharides, Bacterial/*metabolism ; }, abstract = {Nutrient or niche-based competition among bacteria is a widespread phenomenon in the natural environment. Such interspecies interactions are often mediated by secreted soluble factors and/or direct cell-cell contact. As ubiquitous soil bacteria, Myxococcus species are able to produce a variety of bioactive secondary metabolites to inhibit the growth of other competing bacterial species. Meanwhile, Myxococcus spp. also exhibit sophisticated predatory behavior, an extreme form of competition that is often stimulated by close contact with prey cells and largely depends on the availability of solid surfaces. Myxococcus spp. can also be isolated from aquatic environments. However, studies focusing on the interaction between Myxococcus and other bacteria in such environments are still limited. In this study, using the well-studied Myxococcus xanthus DK1622 and Escherichia coli as model interspecies interaction pair, we demonstrated that in an aqueous environment, M. xanthus was able to kill E. coli in a cell contact-dependent manner and that the observed contact-dependent killing required the formation of co-aggregates between M. xanthus and E. coli cells. Further analysis revealed that exopolysaccharide (EPS), type IV pilus, and lipopolysaccharide mutants of M. xanthus displayed various degrees of attenuation in E. coli killing, and it correlated well with the mutants' reduction in EPS production. In addition, M. xanthus showed differential binding ability to different bacteria, and bacterial strains unable to co-aggregate with M. xanthus can escape the killing, suggesting the specific nature of co-aggregation and the targeted killing of interacting bacteria. In conclusion, our results demonstrated EPS-mediated, contact-dependent killing of E. coli by M. xanthus, a strategy that might facilitate the survival of this ubiquitous bacterium in aquatic environments.}, }
@article {pmid23817604, year = {2013}, author = {Porporato, EM and Lo Giudice, A and Michaud, L and De Domenico, E and Spanò, N}, title = {Diversity and antibacterial activity of the bacterial communities associated with two Mediterranean sea pens, Pennatula phosphorea and Pteroeides spinosum (Anthozoa: Octocorallia).}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {701-714}, pmid = {23817604}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology ; Anti-Bacterial Agents/*metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; *Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Italy ; Molecular Sequence Data ; Phylogeny ; }, abstract = {A description of the bacterial communities associated with the Mediterranean pennatulids (sea pens) Pennatula phosphorea and Pteroeides spinosum from the Straits of Messina (Italy) is reported. The automated ribosomal intergenic spacer analysis showed a marked difference between coral (tissues and mucus) and non-coral (underlying sediment and surrounding water) habitats. The diversity of the coral-associated communities was more deeply analysed by sequencing the 16S rRNA genes of bacterial clones. P. phosphorea and P. spinosum harbour distinct bacterial communities, indicating the occurrence of species-specific coral-associated bacteria. In addition, only few phylotypes were shared between mucus and tissues of the same pennatulid species, suggesting that there might be a sort of microhabitat partitioning between the associated microbial communities. The predominance of Alphaproteobacteria was observed for the communities associated with both tissues and mucus of P. phosphorea (84 and 58.2 % of total sequences, respectively). Conversely, the bacterial community in the mucus layer of P. spinosum was dominated by Alphaproteobacteria (74.2 %) as opposed to the tissue library that was dominated by the Gammaproteobacteria and Mollicutes (40.6 and 35.4 %, respectively). The antibacterial activity of 78 bacterial isolates against indicator organisms was assayed. Active isolates (15.4 %), which predominantly affiliated to Vibrio spp., were mainly obtained from coral mucus. Results from the present study enlarge our knowledge on the composition and antibacterial activity of coral-associated bacterial communities.}, }
@article {pmid23812105, year = {2013}, author = {They, NH and Ferreira, LM and Marins, LF and Abreu, PC}, title = {Stability of bacterial composition and activity in different salinity waters in the dynamic Patos Lagoon estuary: evidence from a lagrangian-like approach.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {551-562}, pmid = {23812105}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Brazil ; Denaturing Gradient Gel Electrophoresis ; Ecosystem ; Estuaries ; Phylogeny ; Salinity ; Seawater/analysis/*microbiology ; }, abstract = {We employed a Lagrangian-like sampling design to evaluate bacterial community composition (BCC--using temporal temperature gel gradient electrophoresis), community-level physiological profiles (CLPP--using the EcoPlate™ assay), and influencing factors in different salinity waters in the highly dynamic Patos Lagoon estuary (southern Brazil) and adjacent coastal zone. Samples were collected monthly by following limnetic-oligohaline (0-1), mesohaline (14-16), and polyhaline (28-31) waters for 1 year. The BCC was specific for each salinity range, whereas the CLPPs were similar for mesohaline and polyhaline waters, and both were different from the limnetic-oligohaline samples. The limnetic-oligohaline waters displayed an oxidation capacity for almost all organic substrates tested, whereas the mesohaline and polyhaline waters presented lower numbers of oxidized substrates, suggesting that potential activities of bacteria increased from the polyhaline to oligohaline waters. However, the polyhaline samples showed a higher utilization of some simple carbohydrates, amino acids, and polymers, indicating a shortage of inorganic nutrients (especially nitrogen) and organic substrates in coastal saltwater. The hypothesis of bacterial nitrogen limitation was corroborated by the higher Nuse index (an EcoPlate™-based nitrogen limitation indicator) in the polyhaline waters and the importance of NO(2)(-), NO(3)(-), low-molecular-weight substances, and the low-molecular-weight:high-molecular-weight substances ratio, indicated by the canonical correspondence analyses (CCAs). Our results demonstrate the important stability of microbial community composition and potential metabolic activity in the different water salinity ranges, which are independent of the region and time of the year of sample collection in the estuary. This is a quite unexpected result for a dynamic environment such as the Patos Lagoon estuary.}, }
@article {pmid23812104, year = {2013}, author = {Mgbeahuruike, AC and Kohler, A and Asiegbu, FO}, title = {Expression analysis of the impact of culture filtrates from the biocontrol agent, Phlebiopsis gigantea on the conifer pathogen, Heterobasidion annosum s.s. Transcriptome.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {669-681}, pmid = {23812104}, issn = {1432-184X}, mesh = {Basidiomycota/drug effects/*genetics/metabolism ; Fungal Proteins/genetics/metabolism ; Fungicides, Industrial/metabolism/*pharmacology ; Gene Expression Regulation, Fungal/drug effects ; Plant Diseases/*microbiology/prevention &amp; control ; Polyporales/*chemistry/metabolism ; Tracheophyta/*microbiology ; Transcriptome/*drug effects ; }, abstract = {Phlebiopsis gigantea has been routinely used as the biological control agent for the conifer pathogen Heterobasidion annosum sensu lato, but the actual mechanism for the biocontrol process is not known. To investigate the effect of secreted molecules from culture filtrate produced by P. gigantea on the gene expression profile of H. annosum s.s., microarray analysis was used. Analysis of the differentially expressed genes led to the identification of genes with diverse functions. A major proportion of the up- and downregulated genes were either uncharacterized or genes whose functions were not known. A number of genes coding for proteins involved in metabolism, transport, and signal transduction were differentially downregulated; comparatively lower number of such genes were upregulated. Some genes involved in transport (polyamine transporters, 2573-fold, P = 0.002) and metabolism (endoglucanase, 622.5-fold, P = 0.002, cytochrome P450, 133.2-fold, P = 0.05) showed high transcript fold changes and were statistically significantly upregulated. Genes encoding defense-related proteins such as hydrophobins were either downregulated or expressed at relatively low levels. Further analysis of the effect of the culture filtrate on glucose metabolism showed downregulation of some key enzymes at the early stage of the glycolytic pathway while some genes were upregulated at the later stage of the pathway. A subset of the genes were selected and used to validate the micro-array result by quantitative real time polymerase chain reaction (qPCR) method. Generally, the high transcript levels of genes encoding several biochemically important genes (protein kinases, major facilitator superfamily polyamine transporters, endoglucanase, cytochrome P450, endoglucanase) suggests their potential functional relevance in signal perception, stress tolerance, cell defenses, and detoxification of toxic molecules during competitive interaction. These results have provided further insights into possible molecular and genetic factors underlying the response of H. annosum to metabolites from P. gigantea during interspecific interaction.}, }
@article {pmid23811512, year = {2013}, author = {Cretoiu, MS and Korthals, GW and Visser, JH and van Elsas, JD}, title = {Chitin amendment increases soil suppressiveness toward plant pathogens and modulates the actinobacterial and oxalobacteraceal communities in an experimental agricultural field.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {17}, pages = {5291-5301}, pmid = {23811512}, issn = {1098-5336}, mesh = {Animals ; *Antibiosis ; Bacteria/*growth &amp; development ; *Biodiversity ; Chitin/*metabolism ; DNA, Bacterial/chemistry/genetics ; Molecular Sequence Data ; Nematoda/*growth &amp; development ; Netherlands ; Sequence Analysis, DNA ; *Soil Microbiology ; Verticillium/*growth &amp; development ; }, abstract = {A long-term experiment on the effect of chitin addition to soil on the suppression of soilborne pathogens was set up and monitored for 8 years in an experimental field, Vredepeel, The Netherlands. Chitinous matter obtained from shrimps was added to soil top layers on two different occasions, and the suppressiveness of soil toward Verticillium dahliae, as well as plant-pathogenic nematodes, was assessed, in addition to analyses of the abundances and community structures of members of the soil microbiota. The data revealed that chitin amendment had raised the suppressiveness of soil, in particular toward Verticillium dahliae, 9 months after the (second) treatment, extending to 2 years following treatment. Moreover, major effects of the added chitin on the soil microbial communities were detected. First, shifts in both the abundances and structures of the chitin-treated soil microbial communities, both of total soil bacteria and fungi, were found. In addition, the abundances and structures of soil actinobacteria and the Oxalobacteraceae were affected by chitin. At the functional gene level, the abundance of specific (family-18 glycoside hydrolase) chitinase genes carried by the soil bacteria also revealed upshifts as a result of the added chitin. The effects of chitin noted for the Oxalobacteraceae were specifically related to significant upshifts in the abundances of the species Duganella violaceinigra and Massilia plicata. These effects of chitin persisted over the time of the experiment.}, }
@article {pmid23805131, year = {2013}, author = {Tully, BJ and Heidelberg, JF}, title = {Microbial communities associated with ferromanganese nodules and the surrounding sediments.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {161}, pmid = {23805131}, issn = {1664-302X}, abstract = {The formation and maintenance of deep-sea ferromanganese/polymetallic nodules still remains a mystery 140 years after their discovery. The wealth of rare metals concentrated in these nodules has spurred global interest in exploring the mining potential of these resources. The prevailing theory of abiotic formation has been called into question and the role of microbial metabolisms in nodule development is now an area of active research. To understand the community structure of microbes associated with nodules and their surrounding sediment, we performed targeted sequencing of the V4 hypervariable region of the 16S rRNA gene from three nodules collected from the central South Pacific. Results have shown that the microbial communities of the nodules are significantly distinct from the communities in the surrounding sediments, and that the interiors of the nodules harbor communities different from the exterior. This suggests not only differences in potential metabolisms between the nodule and sediment communities, but also differences in the dominant metabolisms of interior and exterior communities. We identified several operational taxonomic units (OTUs) unique to both the nodule and sediment environments. The identified OTUs were assigned putative taxonomic identifications, including two OTUs only found associated with the nodules, which were assigned to the α-Proteobacteria. Finally, we explored the diversity of the most assigned taxonomic group, the Thaumarchaea MG-1, which revealed novel OTUs compared to previous research from the region and suggests a potential role as a source of fixed carbon for ammonia oxidizing archaea in the environment.}, }
@article {pmid23804151, year = {2013}, author = {Gérard, E and Ménez, B and Couradeau, E and Moreira, D and Benzerara, K and Tavera, R and López-García, P}, title = {Specific carbonate-microbe interactions in the modern microbialites of Lake Alchichica (Mexico).}, journal = {The ISME journal}, volume = {7}, number = {10}, pages = {1997-2009}, pmid = {23804151}, issn = {1751-7370}, mesh = {Biofilms ; Carbonates/analysis/chemistry/*metabolism ; Cyanobacteria/classification/*metabolism/ultrastructure ; Lakes/*microbiology ; Mexico ; Microscopy, Confocal ; Phylogeny ; Pigments, Biological/chemistry ; Spectrum Analysis, Raman ; }, abstract = {The role of microorganisms in microbialite formation remains unresolved: do they induce mineral precipitation (microbes first) or do they colonize and/or entrap abiotic mineral precipitates (minerals first)? Does this role vary from one species to another? And what is the impact of mineral precipitation on microbial ecology? To explore potential biogenic carbonate precipitation, we studied cyanobacteria-carbonate assemblages in modern hydromagnesite-dominated microbialites from the alkaline Lake Alchichica (Mexico), by coupling three-dimensional imaging of molecular fluorescence emitted by microorganisms, using confocal laser scanning microscopy, and Raman scattering/spectrometry from the associated minerals at a microscale level. Both hydromagnesite and aragonite precipitate within a complex biofilm composed of photosynthetic and other microorganisms. Morphology and pigment-content analysis of dominant photosynthetic microorganisms revealed up to six different cyanobacterial morphotypes belonging to Oscillatoriales, Chroococcales, Nostocales and Pleurocapsales, as well as several diatoms and other eukaryotic microalgae. Interestingly, one of these morphotypes, Pleurocapsa-like, appeared specifically associated with aragonite minerals, the oldest parts of actively growing Pleurocapsa-like colonies being always aragonite-encrusted. We hypothesize that actively growing cells of Pleurocapsales modify local environmental conditions favoring aragonite precipitation at the expense of hydromagnesite, which precipitates at seemingly random locations within the biofilm. Therefore, at least part of the mineral precipitation in Alchichica microbialites is most likely biogenic and the type of biominerals formed depends on the nature of the phylogenetic lineage involved. This observation may provide clues to identify lineage-specific biosignatures in fossil stromatolites from modern to Precambrian times.}, }
@article {pmid23801761, year = {2013}, author = {Swan, BK and Tupper, B and Sczyrba, A and Lauro, FM and Martinez-Garcia, M and González, JM and Luo, H and Wright, JJ and Landry, ZC and Hanson, NW and Thompson, BP and Poulton, NJ and Schwientek, P and Acinas, SG and Giovannoni, SJ and Moran, MA and Hallam, SJ and Cavicchioli, R and Woyke, T and Stepanauskas, R}, title = {Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {28}, pages = {11463-11468}, pmid = {23801761}, issn = {1091-6490}, mesh = {Bacteria/*classification/genetics ; *Genome, Bacterial ; Geography ; *Marine Biology ; Oceans and Seas ; Plankton/*classification/genetics ; *Water Microbiology ; }, abstract = {Planktonic bacteria dominate surface ocean biomass and influence global biogeochemical processes, but remain poorly characterized owing to difficulties in cultivation. Using large-scale single cell genomics, we obtained insight into the genome content and biogeography of many bacterial lineages inhabiting the surface ocean. We found that, compared with existing cultures, natural bacterioplankton have smaller genomes, fewer gene duplications, and are depleted in guanine and cytosine, noncoding nucleotides, and genes encoding transcription, signal transduction, and noncytoplasmic proteins. These findings provide strong evidence that genome streamlining and oligotrophy are prevalent features among diverse, free-living bacterioplankton, whereas existing laboratory cultures consist primarily of copiotrophs. The apparent ubiquity of metabolic specialization and mixotrophy, as predicted from single cell genomes, also may contribute to the difficulty in bacterioplankton cultivation. Using metagenome fragment recruitment against single cell genomes, we show that the global distribution of surface ocean bacterioplankton correlates with temperature and latitude and is not limited by dispersal at the time scales required for nucleotide substitution to exceed the current operational definition of bacterial species. Single cell genomes with highly similar small subunit rRNA gene sequences exhibited significant genomic and biogeographic variability, highlighting challenges in the interpretation of individual gene surveys and metagenome assemblies in environmental microbiology. Our study demonstrates the utility of single cell genomics for gaining an improved understanding of the composition and dynamics of natural microbial assemblages.}, }
@article {pmid23798515, year = {2013}, author = {Zentek, J and Ferrara, F and Pieper, R and Tedin, L and Meyer, W and Vahjen, W}, title = {Effects of dietary combinations of organic acids and medium chain fatty acids on the gastrointestinal microbial ecology and bacterial metabolites in the digestive tract of weaning piglets.}, journal = {Journal of animal science}, volume = {91}, number = {7}, pages = {3200-3210}, doi = {10.2527/jas.2012-5673}, pmid = {23798515}, issn = {1525-3163}, mesh = {Animal Feed/analysis ; Animals ; Carboxylic Acids/administration &amp; dosage/*metabolism ; Chromatography, High Pressure Liquid/veterinary ; Diet/veterinary ; Dietary Supplements/analysis ; Fatty Acids/administration &amp; dosage/*metabolism ; Gastrointestinal Contents/chemistry/microbiology ; Gastrointestinal Tract/chemistry/*metabolism/*microbiology ; Hydrogen-Ion Concentration ; Male ; Real-Time Polymerase Chain Reaction/veterinary ; Sus scrofa/*microbiology/*physiology ; }, abstract = {Organic short and medium chain fatty acids are used in diets for piglets because they have an impact on the digestive processes and the intestinal microbiota. In this study, 48 pens (2 piglets/pen) were assigned randomly to 4 diets, without additive (control), with organic acids (OA; 0.416% fumaric and 0.328% lactic acid), with medium chain fatty acids (MCFA; 0.15% caprylic and capric acid), and a combination of OA and MCFA, to assess changes in the gastrointestinal microbiota with 12 pens per diet. Eight to nine piglets from each group were euthanized after 4 wk. Organic acids, MCFA, and pH in the digesta were determined and the intestinal microbiota was quantified by real-time PCR. The different diets had no effect on the growth performance. Concentration of added fumaric acid was below the detection limit in the upper small intestine whereas the concentration of lactic acid in the digesta was not affected by the treatments. The added MCFA was recovered in the MCFA treated groups in the stomach, but the concentrations declined in the upper small intestine. Concentration of short chain fatty acids was reduced in the colon digesta in piglets fed diets with OA compared with those fed unsupplemented diets (P = 0.029). The MCFA resulted in a pH reduction of the digesta, likely because of the effect on bacterial acid production. The addition of OA increased cell counts of Bacteroides-Porphyromonas-Prevotella group and clostridial clusters XIVa, I, and IV in the stomach, the clostridial cluster XIVa in the jejunum, and Bacteroides-Porphyromonas-Prevotella in the ileum and reduced counts of Streptococcus spp. in the colon (P < 0.05). The MCFA induced only minor changes in the gastrointestinal microbiota but increased cell counts for the Escherichia-Hafnia-Shigella group in the jejunum and the clostridial cluster XIVa in the colon digesta (P < 0.05). In the colon of piglets fed diets with organic OA, reduced mean cell counts of STb (est-II) positive Escherichia coli were found. In conclusion, OA and MCFA had effects on the intestinal microecology in piglets. The decrease of the intestinal pH and the reduction of E. coli virulence genes by OA could make the combination of short chain fatty acids and MCFA as interesting gut flora modifiers, which can eventually prevent postweaning diarrhea.}, }
@article {pmid23798442, year = {2013}, author = {Nguyen, DD and Wu, CH and Moree, WJ and Lamsa, A and Medema, MH and Zhao, X and Gavilan, RG and Aparicio, M and Atencio, L and Jackson, C and Ballesteros, J and Sanchez, J and Watrous, JD and Phelan, VV and van de Wiel, C and Kersten, RD and Mehnaz, S and De Mot, R and Shank, EA and Charusanti, P and Nagarajan, H and Duggan, BM and Moore, BS and Bandeira, N and Palsson, B&#xd8; and Pogliano, K and Gutiérrez, M and Dorrestein, PC}, title = {MS/MS networking guided analysis of molecule and gene cluster families.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {28}, pages = {E2611-20}, pmid = {23798442}, issn = {1091-6490}, support = {GM097509/GM/NIGMS NIH HHS/United States ; P41 GM103484/GM/NIGMS NIH HHS/United States ; R01 GM098105/GM/NIGMS NIH HHS/United States ; AI095125/AI/NIAID NIH HHS/United States ; R01 AI095125/AI/NIAID NIH HHS/United States ; GMS10RR029121/RR/NCRR NIH HHS/United States ; GM103809/GM/NIGMS NIH HHS/United States ; K01 GM103809/GM/NIGMS NIH HHS/United States ; TW006634/TW/FIC NIH HHS/United States ; S10 RR029121/RR/NCRR NIH HHS/United States ; R01 GM094802/GM/NIGMS NIH HHS/United States ; R01 GM097509/GM/NIGMS NIH HHS/United States ; P41 GM103485/GM/NIGMS NIH HHS/United States ; GM098105/GM/NIGMS NIH HHS/United States ; U01 TW006634/TW/FIC NIH HHS/United States ; GM094802/GM/NIGMS NIH HHS/United States ; R25 HG007153/HG/NHGRI NIH HHS/United States ; 8 P41 GM103485-05/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacillus/genetics ; Bacterial Proteins/chemistry/genetics ; Molecular Sequence Data ; *Multigene Family ; Peptides/chemistry/genetics ; Pseudomonas/genetics ; Tandem Mass Spectrometry/*methods ; }, abstract = {The ability to correlate the production of specialized metabolites to the genetic capacity of the organism that produces such molecules has become an invaluable tool in aiding the discovery of biotechnologically applicable molecules. Here, we accomplish this task by matching molecular families with gene cluster families, making these correlations to 60 microbes at one time instead of connecting one molecule to one organism at a time, such as how it is traditionally done. We can correlate these families through the use of nanospray desorption electrospray ionization MS/MS, an ambient pressure MS technique, in conjunction with MS/MS networking and peptidogenomics. We matched the molecular families of peptide natural products produced by 42 bacilli and 18 pseudomonads through the generation of amino acid sequence tags from MS/MS data of specific clusters found in the MS/MS network. These sequence tags were then linked to biosynthetic gene clusters in publicly accessible genomes, providing us with the ability to link particular molecules with the genes that produced them. As an example of its use, this approach was applied to two unsequenced Pseudoalteromonas species, leading to the discovery of the gene cluster for a molecular family, the bromoalterochromides, in the previously sequenced strain P. piscicida JCM 20779(T). The approach itself is not limited to 60 related strains, because spectral networking can be readily adopted to look at molecular family-gene cluster families of hundreds or more diverse organisms in one single MS/MS network.}, }
@article {pmid23797292, year = {2013}, author = {Menezes-Costa, A and Machado-Ferreira, E and Voloch, CM and Bonvicino, CR and Seuánez, HN and Leoncini, O and Soares, CA}, title = {Identification of bacterial infection in neotropical primates.}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {471-478}, pmid = {23797292}, issn = {1432-184X}, mesh = {Animals ; Animals, Wild/microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Infections/microbiology/*veterinary ; Haplorhini/classification/*microbiology ; Humans ; Molecular Sequence Data ; Phylogeny ; Primate Diseases/*microbiology ; }, abstract = {Emerging infectious diseases usually arise from wild animal populations. In the present work, we performed a screening for bacterial infection in natural populations of New World primates. The blood cell bulk DNAs from 181 individuals of four Platyrrhini genera were PCR screened for eubacterial 16S rRNA genes. Bacteria were detected and identified in 13 distinct individuals of Alouatta belzebul, Alouatta caraya, and Cebus apella monkeys from geographically distant regions in the states of Mato Grosso and Pará, Brazil. Sequence analyses showed that these Platyrrhini bacteria are closely related not only to human pathogens Pseudomonas spp. but also to Pseudomonas simiae and sheep-Acari infecting Pseudomonas spp. The identified Pseudomonas possibly represents a group of bacteria circulating in natural monkey populations.}, }
@article {pmid23797291, year = {2013}, author = {Shah, V and Zakrzewski, M and Wibberg, D and Eikmeyer, F and Schlüter, A and Madamwar, D}, title = {Taxonomic Profiling and Metagenome Analysis of a Microbial Community from a Habitat Contaminated with Industrial Discharges.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-013-0253-9}, pmid = {23797291}, issn = {1432-184X}, abstract = {Industrial units, manufacturing dyes, chemicals, solvents, and xenobiotic compounds, produce liquid and solid wastes, which upon conventional treatment are released in the nearby environment and thus are the major cause of pollution. Soil collected from contaminated Kharicut Canal bank (N 22°57.878'; E 072°38.478'), Ahmedabad, Gujarat, India was used for metagenomic DNA preparation to study the capabilities of intrinsic microbial community in dealing with xenobiotics. Sequencing of metagenomic DNA on the Genome Sequencer FLX System using titanium chemistry resulted in 409,782 reads accounting for 133,529,997 bases of sequence information. Taxonomic analyses and gene annotations were carried out using the bioinformatics platform Sequence Analysis and Management System for Metagenomic Datasets. Taxonomic profiling was carried out by three different complementary approaches: (a) 16S rDNA, (b) environmental gene tags, and (c) lowest common ancestor. The most abundant phylum and genus were found to be "Proteobacteria" and "Pseudomonas," respectively. Metagenome reads were mapped on sequenced microbial genomes and the highest numbers of reads were allocated to Pseudomonas stutzeri A1501. Assignment of obtained metagenome reads to Gene Ontology terms, Clusters of Orthologous Groups of protein categories, protein family numbers, and Kyoto Encyclopedia of Genes and Genomes hits revealed genomic potential of indigenous microbial community. In total, 157,024 reads corresponded to 37,028 different KEGG hits, and amongst them, 11,574 reads corresponded to 131 different enzymes potentially involved in xenobiotic biodegradation. These enzymes were mapped on biodegradation pathways of xenobiotics to elucidate their roles in possible catalytic reactions. Consequently, information obtained from the present study will act as a baseline which, subsequently along with other "-omic" studies, will help in designing future bioremediation strategies in effluent treatment plants and environmental clean-up projects.}, }
@article {pmid23793897, year = {2013}, author = {Douglas, AE}, title = {Microbial brokers of insect-plant interactions revisited.}, journal = {Journal of chemical ecology}, volume = {39}, number = {7}, pages = {952-961}, pmid = {23793897}, issn = {1573-1561}, support = {R01 GM095372/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biotransformation ; *Herbivory ; Insecta/*microbiology ; *Microbiota ; Pheromones/metabolism ; }, abstract = {Recent advances in sequencing methods have transformed the field of microbial ecology, making it possible to determine the composition and functional capabilities of uncultured microorganisms. These technologies have been instrumental in the recognition that resident microorganisms can have profound effects on the phenotype and fitness of their animal hosts by modulating the animal signaling networks that regulate growth, development, behavior, etc. Against this backdrop, this review assesses the impact of microorganisms on insect-plant interactions, in the context of the hypothesis that microorganisms are biochemical brokers of plant utilization by insects. There is now overwhelming evidence for a microbial role in insect utilization of certain plant diets with an extremely low or unbalanced nutrient content. Specifically, microorganisms enable insect utilization of plant sap by synthesizing essential amino acids. They also can broker insect utilization of plant products of extremely high lignocellulose content, by enzymatic breakdown of complex plant polysaccharides, nitrogen fixation, and sterol synthesis. However, the experimental evidence for microbial-mediated detoxification of plant allelochemicals is limited. The significance of microorganisms as brokers of plant utilization by insects is predicted to vary, possibly widely, as a result of potentially complex interactions between the composition of the microbiota and the diet and insect developmental age or genotype. For every insect species feeding on plant material, the role of resident microbiota as biochemical brokers of plant utilization is a testable hypothesis.}, }
@article {pmid23793624, year = {2013}, author = {Kozich, JJ and Westcott, SL and Baxter, NT and Highlander, SK and Schloss, PD}, title = {Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {17}, pages = {5112-5120}, pmid = {23793624}, issn = {1098-5336}, support = {R01 HG005975/HG/NHGRI NIH HHS/United States ; U54HG004973/HG/NHGRI NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; R01HG005975/HG/NHGRI NIH HHS/United States ; U54 HG004973/HG/NHGRI NIH HHS/United States ; 5R01GM099514/GM/NIGMS NIH HHS/United States ; P30DK034933/DK/NIDDK NIH HHS/United States ; R01 GM099514/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biota ; Computational Biology/*methods ; Feces/microbiology ; High-Throughput Nucleotide Sequencing/*methods/*standards ; Humans ; *Metagenome ; Mice ; Soil Microbiology ; }, abstract = {Rapid advances in sequencing technology have changed the experimental landscape of microbial ecology. In the last 10 years, the field has moved from sequencing hundreds of 16S rRNA gene fragments per study using clone libraries to the sequencing of millions of fragments per study using next-generation sequencing technologies from 454 and Illumina. As these technologies advance, it is critical to assess the strengths, weaknesses, and overall suitability of these platforms for the interrogation of microbial communities. Here, we present an improved method for sequencing variable regions within the 16S rRNA gene using Illumina's MiSeq platform, which is currently capable of producing paired 250-nucleotide reads. We evaluated three overlapping regions of the 16S rRNA gene that vary in length (i.e., V34, V4, and V45) by resequencing a mock community and natural samples from human feces, mouse feces, and soil. By titrating the concentration of 16S rRNA gene amplicons applied to the flow cell and using a quality score-based approach to correct discrepancies between reads used to construct contigs, we were able to reduce error rates by as much as two orders of magnitude. Finally, we reprocessed samples from a previous study to demonstrate that large numbers of samples could be multiplexed and sequenced in parallel with shotgun metagenomes. These analyses demonstrate that our approach can provide data that are at least as good as that generated by the 454 platform while providing considerably higher sequencing coverage for a fraction of the cost.}, }
@article {pmid23791362, year = {2013}, author = {Cocolin, L and Alessandria, V and Dolci, P and Gorra, R and Rantsiou, K}, title = {Culture independent methods to assess the diversity and dynamics of microbiota during food fermentation.}, journal = {International journal of food microbiology}, volume = {167}, number = {1}, pages = {29-43}, doi = {10.1016/j.ijfoodmicro.2013.05.008}, pmid = {23791362}, issn = {1879-3460}, mesh = {Bacterial Physiological Phenomena ; *Biodiversity ; *Denaturing Gradient Gel Electrophoresis ; *Fermentation ; Food Microbiology/*methods ; Fungi/physiology ; Humans ; Microbiota/*physiology ; }, abstract = {Culture independent methods first appeared in the food microbiology field at the end of the 90s and since then they have been applied extensively. These methods do not rely on cultivation and target nucleic acids (DNA and RNA) to identify and follow the changes that occur in the main populations present in a specific ecosystem. The method that has most often been used as a culture independent method in food microbiology is denaturing gradient gel electrophoresis (DGGE). The number of papers dealing with DGGE grew exponentially in the late nineties and, by analysing the studies available in the literature, it is possible to describe a trend in the subjects that have been investigated. DGGE was first used as a tool to monitor the ecology of fermented food, such as fermented sausage, cheese and sourdough, and later it also showed its potential in microbial spoilage process. In the last few years, the main application of DGGE has been to study fermented food from Asia, Africa and South America. The information collected using DGGE has made it possible to confirm the existing knowledge on food fermentation and spoilage. However, in some cases, new evidence that helps scientists to fully comprehend a specific microbial ecosystem has emerged. In this review, the roadmap of culture independent methods in food microbiology will be summarized, focusing on the DGGE technique. Examples of how this approach is useful to obtain a better understanding of microbial diversity are reported for several kinds of fermented food, such as fermented sausage, cheese and wine. The future of culture independent methods in food microbiology, with the increasing availability of next generation sequencing techniques, is also discussed.}, }
@article {pmid23788331, year = {2013}, author = {Bodelier, PL and Meima-Franke, M and Hordijk, CA and Steenbergh, AK and Hefting, MM and Bodrossy, L and von Bergen, M and Seifert, J}, title = {Microbial minorities modulate methane consumption through niche partitioning.}, journal = {The ISME journal}, volume = {7}, number = {11}, pages = {2214-2228}, pmid = {23788331}, issn = {1751-7370}, mesh = {Bacteria/genetics/*metabolism ; *Biodiversity ; Carbon Isotopes/analysis/metabolism ; Methane/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Soil/chemistry ; *Soil Microbiology ; *Wetlands ; }, abstract = {Microbes catalyze all major geochemical cycles on earth. However, the role of microbial traits and community composition in biogeochemical cycles is still poorly understood mainly due to the inability to assess the community members that are actually performing biogeochemical conversions in complex environmental samples. Here we applied a polyphasic approach to assess the role of microbial community composition in modulating methane emission from a riparian floodplain. We show that the dynamics and intensity of methane consumption in riparian wetlands coincide with relative abundance and activity of specific subgroups of methane-oxidizing bacteria (MOB), which can be considered as a minor component of the microbial community in this ecosystem. Microarray-based community composition analyses demonstrated linear relationships of MOB diversity parameters and in vitro methane consumption. Incubations using intact cores in combination with stable isotope labeling of lipids and proteins corroborated the correlative evidence from in vitro incubations demonstrating γ-proteobacterial MOB subgroups to be responsible for methane oxidation. The results obtained within the riparian flooding gradient collectively demonstrate that niche partitioning of MOB within a community comprised of a very limited amount of active species modulates methane consumption and emission from this wetland. The implications of the results obtained for biodiversity-ecosystem functioning are discussed with special reference to the role of spatial and temporal heterogeneity and functional redundancy.}, }
@article {pmid23784452, year = {2013}, author = {Kao-Kniffin, J and Zhu, B}, title = {A microbial link between elevated CO2 and methane emissions that is plant species-specific.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {621-629}, pmid = {23784452}, issn = {1432-184X}, mesh = {Air/*analysis ; Archaea/genetics/isolation &amp; purification/*metabolism ; Bacteria/genetics/isolation &amp; purification/*metabolism ; Carbon Dioxide/*analysis/metabolism ; Ecosystem ; Fatty Acids/metabolism ; Methane/*analysis/metabolism ; Plant Roots/metabolism/microbiology ; Poaceae/metabolism/*microbiology ; *Soil Microbiology ; Species Specificity ; }, abstract = {Rising atmospheric CO(2) levels alter the physiology of many plant species, but little is known of changes to root dynamics that may impact soil microbial mediation of greenhouse gas emissions from wetlands. We grew co-occurring wetland plant species that included an invasive reed canary grass (Phalaris arundinacea L.) and a native woolgrass (Scirpus cyperinus L.) in a controlled greenhouse facility under ambient (380 ppm) and elevated atmospheric CO(2) (700 ppm). We hypothesized that elevated atmospheric CO(2) would increase the abundance of both archaeal methanogen and bacterial methanotroph populations through stimulation of plant root and shoot biomass. We found that methane levels emitted from S. cyperinus shoots increased 1.5-fold under elevated CO(2), while no changes in methane levels were detected from P. arundincea. The increase in methane emissions was not explained by enhanced root or shoot growth of S. cyperinus. Principal components analysis of the total phospholipid fatty acid (PLFA) recovered from microbial cell membranes revealed that elevated CO(2) levels shifted the composition of the microbial community under S. cyperinus, while no changes were detected under P. arundinacea. More detailed analysis of microbial abundance showed no impact of elevated CO(2) on a fatty acid indicative of methanotrophic bacteria (18:2ω6c), and no changes were detected in the terminal restriction fragment length polymorphism (T-RFLP) relative abundance profiles of acetate-utilizing archaeal methanogens. Plant carbon depleted in (13)C was traced into the PLFAs of soil microorganisms as a measure of the plant contribution to microbial PLFA. The relative contribution of plant-derived carbon to PLFA carbon was larger in S. cyperinus compared with P. arundinacea in four PLFAs (i14:0, i15:0, a15:0, and 18:1ω9t). The δ(13)C isotopic values indicate that the contribution of plant-derived carbon to microbial lipids could differ in rhizospheres of CO(2)-responsive plant species, such as S. cyperinus in this study. The results from this study show that the CO(2)-methane link found in S. cyperinus can occur without a corresponding change in methanogen and methanotroph relative abundances, but PLFA analysis indicated shifts in the community profile of bacteria and fungi that were unique to rhizospheres under elevated CO(2).}, }
@article {pmid23782615, year = {2013}, author = {Zhang, Y and Sun, Y and Cole, JR}, title = {A Sensitive and Accurate protein domain cLassification Tool (SALT) for short reads.}, journal = {Bioinformatics (Oxford, England)}, volume = {29}, number = {17}, pages = {2103-2111}, doi = {10.1093/bioinformatics/btt357}, pmid = {23782615}, issn = {1367-4811}, mesh = {Algorithms ; Animals ; Arabidopsis Proteins/classification/genetics ; Contig Mapping ; Genome ; High-Throughput Nucleotide Sequencing ; Markov Chains ; Molecular Sequence Annotation ; *Protein Structure, Tertiary ; Proteins/classification/genetics ; *Sequence Analysis, RNA ; Snails/genetics ; *Software ; }, abstract = {MOTIVATION: Protein domain classification is an important step in functional annotation for next-generation sequencing data. For RNA-Seq data of non-model organisms that lack quality or complete reference genomes, existing protein domain analysis pipelines are applied to short reads directly or to contigs that are generated using de novo sequence assembly tools. However, these strategies do not provide satisfactory performance in classifying short reads into their native domain families.<br><br>RESULTS: We introduce SALT, a protein domain classification tool based on profile hidden Markov models and graph algorithms. SALT carefully incorporates the characteristics of reads that are sequenced from the domain regions and assembles them into contigs based on a supervised graph construction algorithm. We applied SALT to two RNA-Seq datasets of different read lengths and quantified its performance using the available protein domain annotations and the reference genomes. Compared with existing strategies, SALT showed better sensitivity and accuracy. In the third experiment, we applied SALT to a non-model organism. The experimental results demonstrated that it identified more transcribed protein domain families than other tested classifiers.<br><br>AVAILABILITY: The source code and supplementary data are available at https://sourceforge.net/projects/salt1/}, }
@article {pmid23781876, year = {2013}, author = {Livermore, JA and Jin, YO and Arnseth, RW and Lepuil, M and Mattes, TE}, title = {Microbial community dynamics during acetate biostimulation of RDX-contaminated groundwater.}, journal = {Environmental science &amp; technology}, volume = {47}, number = {14}, pages = {7672-7678}, doi = {10.1021/es4012788}, pmid = {23781876}, issn = {1520-5851}, support = {UL1RR024979/RR/NCRR NIH HHS/United States ; }, mesh = {Acetates/*metabolism ; Bacteria/classification/metabolism ; Groundwater/*chemistry ; *Water Microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Biostimulation of groundwater microbial communities (e.g., with carbon sources) is a common approach to achieving in situ bioremediation of organic pollutants (e.g., explosives). We monitored a field-scale approach to remediate the explosive RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) in an aquifer near the Iowa Army Ammunition Plant in Middletown, IA. The purpose of the study was to gain insight into the effect of biostimulation on the microbial community. Biostimulation with acetate led to the onset of RDX reduction at the site, which was most apparent in monitoring well MW309. Based on previous laboratory experiments, we hypothesized that RDX degradation and metabolite production would correspond to enrichment of one or more Fe(III)-reducing bacterial species. Community DNA from MW309 was analyzed with 454 pyrosequencing and terminal restriction fragment length polymorphism. Production of RDX metabolites corresponded to a microbial community shift from primarily Fe(III)-reducing Betaproteobacteria to a community dominated by Fe(III)-reducing Deltaproteobacteria (Geobacteraceae in particular) and Bacteroidetes taxa. This data provides a firsthand field-scale microbial ecology context to in situ RDX bioremediation using modern sequencing techniques that will inform future biostimulation applications.}, }
@article {pmid23771408, year = {2014}, author = {Guo, Q and Wan, R and Xie, S}, title = {Simazine degradation in bioaugmented soil: urea impact and response of ammonia-oxidizing bacteria and other soil bacterial communities.}, journal = {Environmental science and pollution research international}, volume = {21}, number = {1}, pages = {337-343}, pmid = {23771408}, issn = {1614-7499}, mesh = {Ammonia/metabolism ; Arthrobacter/classification/*metabolism ; Biodegradation, Environmental ; Fertilizers ; Herbicides/analysis/*metabolism ; Nitrogen/metabolism ; Polymorphism, Restriction Fragment Length ; Simazine/analysis/*metabolism ; Soil/chemistry ; *Soil Microbiology ; Urea/metabolism ; }, abstract = {The objective of this study was to investigate the impact of exogenous urea nitrogen on ammonia-oxidizing bacteria (AOB) and other soil bacterial communities in soil bioaugmented for simazine remediation. The previously isolated simazine-degrading Arthrobacter sp. strain SD1 was used to degrade the herbicide. The effect of urea on the simazine degradation capacity of the soil bioaugmented with Arthrobacter strain SD1 was assessed using quantitative PCR targeting the s-triazine-degrading trzN and atzC genes. Structures of bacterial and AOB communities were characterized using terminal restriction fragment length polymorphism. Urea fertilizer could affect simazine biodegradation and decreased the proportion of its trzN and atzC genes in soil augmented with Arthrobacter strain SD1. Bioaugmentation process could significantly alter the structures of both bacterial and AOB communities, which were strongly affected by urea amendment, depending on the dosage. This study could provide some new insights towards s-triazine bioremediation and microbial ecology in a bioaugmented system. However, further studies are necessary in order to elucidate the impact of different types and levels of nitrogen sources on s-triazine-degraders and bacterial and AOB communities in bioaugmented soil.}, }
@article {pmid23770896, year = {2013}, author = {Andersson, KM and Meerupati, T and Levander, F and Friman, E and Ahrén, D and Tunlid, A}, title = {Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {16}, pages = {4993-5004}, pmid = {23770896}, issn = {1098-5336}, mesh = {Amino Acid Sequence ; Animals ; Ascomycota/chemistry/*genetics/metabolism ; Chromatography, Liquid ; Electrophoresis, Polyacrylamide Gel ; Fungal Proteins/chemistry/*genetics/metabolism ; *Gene Expression Regulation, Fungal ; Hyphae/genetics/metabolism ; Mycelium/genetics/metabolism ; Nematoda/microbiology ; Phylogeny ; Proteome/chemistry/*genetics/metabolism ; Tandem Mass Spectrometry ; Transcriptome ; }, abstract = {Many nematophagous fungi use morphological structures called traps to capture nematodes by adhesion or mechanically. To better understand the cellular functions of adhesive traps, the trap cell proteome of the fungus Monacrosporium haptotylum was characterized. The trap of M. haptotylum consists of a unicellular structure called a knob that develops at the apex of a hypha. Proteins extracted from knobs and mycelia were analyzed using SDS-PAGE and liquid chromatography-tandem mass spectrometry (LC-MS-MS). The peptide sequences were matched against predicted gene models from the recently sequenced M. haptotylum genome. In total, 336 proteins were identified, with 54 expressed at significantly higher levels in the knobs than in the mycelia. The upregulated knob proteins included peptidases, small secreted proteins with unknown functions, and putative cell surface adhesins containing carbohydrate-binding domains, including the WSC domain. Phylogenetic analysis showed that all upregulated WSC domain proteins belonged to a large, expanded cluster of paralogs in M. haptotylum. Several peptidases and homologs of experimentally verified proteins in other pathogenic fungi were also upregulated in the knob proteome. Complementary profiling of gene expression at the transcriptome level showed poor correlation between the upregulation of knob proteins and their corresponding transcripts. We propose that the traps of M. haptotylum contain many of the proteins needed in the early stages of infection and that the trap cells can tightly control the translation and degradation of these proteins to minimize the cost of protein synthesis.}, }
@article {pmid23768552, year = {2013}, author = {Berry, D and Reinisch, W}, title = {Intestinal microbiota: a source of novel biomarkers in inflammatory bowel diseases?.}, journal = {Best practice &amp; research. Clinical gastroenterology}, volume = {27}, number = {1}, pages = {47-58}, doi = {10.1016/j.bpg.2013.03.005}, pmid = {23768552}, issn = {1532-1916}, mesh = {Bacterial Physiological Phenomena ; Biomarkers/*metabolism ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Inflammatory Bowel Diseases/*diagnosis/metabolism/*microbiology ; Metagenome/*physiology ; }, abstract = {The human intestine harbours a complex microbial ecosystem that performs manifold functions important to the nutrition and health of its host. Extensive study has revealed that the composition of the intestinal microbiota is altered in individuals with inflammatory bowel disease (IBD). The IBD associated intestinal microbiota generally has reduced species richness and diversity, lower temporal stability, and disruption of the secreted mucus layer structure. Multiple studies have identified certain bacterial taxa that are enriched or depleted in IBD including Enterobacteriaceae, Ruminococcus gnavus, and Desulfovibrio (enriched) and Faecalibacterium prausnitzii, Lachnospiraceae, and Akkermansia (depleted). Additionally, the relative abundance of some taxa appears to correlate with established markers of disease activity such as Enterobacteriaceae (enriched) and Lachnospiraceae (depleted). Signature shifts in fecal microbial community composition may therefore prove to be valuable as diagnostic biomarkers, particularly for longitudinal monitoring of disease activity and response to treatments.}, }
@article {pmid23765099, year = {2013}, author = {Makhalanyane, TP and Valverde, A and Birkeland, NK and Cary, SC and Tuffin, IM and Cowan, DA}, title = {Evidence for successional development in Antarctic hypolithic bacterial communities.}, journal = {The ISME journal}, volume = {7}, number = {11}, pages = {2080-2090}, pmid = {23765099}, issn = {1751-7370}, mesh = {Antarctic Regions ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; Models, Biological ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Time Factors ; }, abstract = {Hypoliths (cryptic microbial assemblages that develop on the undersides of translucent rocks) are significant contributors to regional C and N budgets in both hot and cold deserts. Previous studies in the Dry Valleys of Eastern Antarctica have reported three morphologically distinct hypolithic community types: cyanobacteria dominated (type I), fungus dominated (type II) and moss dominated (type III). Here we present terminal-restriction fragment length polymorphism analyses to elucidate the bacterial community structure in hypolithons and the surrounding soils. We show clear and robust distinction in bacterial composition between bulk surface soils and hypolithons. Moreover, the bacterial assemblages were similar in types II and III hypolithons and clearly distinct from those found in type I. Through 16S rRNA gene 454 pyrosequencing, we show that Proteobacteria dominated all three types of hypolithic communities. As expected, Cyanobacteria were more abundant in type I hypolithons, whereas Actinobacteria were relatively more abundant in types II and III hypolithons, and were the dominant group in soils. Using a probabilistic dissimilarity metric and random sampling, we demonstrate that deterministic processes are more important in shaping the structure of the bacterial community found in types II and III hypolithons. Most notably, the data presented in this study suggest that hypolithic bacterial communities establish via a successional model, with the type I hypolithons acting as the basal development state.}, }
@article {pmid23764733, year = {2013}, author = {Buse, HY and Donohue, MJ and Ashbolt, NJ}, title = {Hartmannella vermiformis inhibition of Legionella pneumophila cultivability.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {715-726}, pmid = {23764733}, issn = {1432-184X}, mesh = {Acanthamoeba/chemistry/metabolism/microbiology ; Anti-Bacterial Agents/chemistry/isolation &amp; purification/metabolism/*pharmacology ; Down-Regulation/*drug effects ; Hartmannella/*chemistry/metabolism/microbiology ; Legionella pneumophila/drug effects/*growth &amp; development ; Molecular Weight ; }, abstract = {Hartmannella vermiformis and Acanthamoeba polyphaga are frequently isolated from drinking water and permissive to Legionella pneumophila parasitization. In this study, extracellular factor(s) produced by H. vermiformis and A. polyphaga were assessed for their effects on cultivability of L. pneumophila. Page's amoeba saline (PAS) was used as an encystment medium for H. vermiformis and A. polyphaga monolayers, and the culture supernatants (HvS and ApS, respectively) were assessed against L. pneumophila growth. Compared to PAS and ApS, HvS significantly inhibited L. pneumophila strain Philadelphia-1 (Ph-1) cultivability by 3 log(10) colony forming unit (CFU) mL(-1) after 3 days of exposure compared to <0.5 log(10) CFU mL(-1) reduction of strain Lp02 (P < 0.001). Flow cytometric analysis revealed changes in the percentage and cultivability of three bacterial subpopulations: intact/slightly damaged membrane (ISM), undefined membrane status (UD), and mixed type (MT). After 3 days of HvS exposure, the MT subpopulation decreased significantly (31.6 vs 67.2 %, respectively, P < 0.001), while the ISM and UD subpopulations increased (+26.7 and +6.9 %, respectively) with the ISM subpopulation appearing as viable but nonculturable (VBNC) cells. HvS was separated into two fractions based on molecular weight, with more than 99 % of the L. pneumophila inhibition arising from the <5 kDa fraction (P < 0.001). Liquid chromatography indicated the inhibitory molecule(s) are likely polar and elute from a Novapak C18 column between 6 and 15 min. These results demonstrate that H. vermiformis is capable of extracellular modulation of L. pneumophila cultivability and probably promote the VBNC state for this bacterium.}, }
@article {pmid23764415, year = {2013}, author = {Hoyles, L and Clear, JA and McCartney, AL}, title = {Use of denaturing gradient gel electrophoresis to detect Actinobacteria associated with the human faecal microbiota.}, journal = {Anaerobe}, volume = {22}, number = {}, pages = {90-96}, doi = {10.1016/j.anaerobe.2013.06.001}, pmid = {23764415}, issn = {1095-8274}, mesh = {Actinobacteria/genetics/*isolation &amp; purification ; Adult ; Aged ; Denaturing Gradient Gel Electrophoresis ; Feces/*microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Infant ; Male ; *Microbiota ; Middle Aged ; Young Adult ; }, abstract = {With the exceptions of the bifidobacteria, propionibacteria and coriobacteria, the Actinobacteria associated with the human gastrointestinal tract have received little attention. This has been due to the seeming absence of these bacteria from most clone libraries. In addition, many of these bacteria have fastidious growth and atmospheric requirements. A recent cultivation-based study has shown that the Actinobacteria of the human gut may be more diverse than previously thought. The aim of this study was to develop a denaturing gradient gel electrophoresis (DGGE) approach for characterizing Actinobacteria present in faecal samples. Amount of DNA added to the Actinobacteria-specific PCR used to generate strong PCR products of equal intensity from faecal samples of five infants, nine adults and eight elderly adults was anti-correlated with counts of bacteria obtained using fluorescence in situ hybridization probe HGC69A. A nested PCR using Actinobacteria-specific and universal PCR-DGGE primers was used to generate profiles for the Actinobacteria. Cloning of sequences from the DGGE bands confirmed the specificity of the Actinobacteria-specific primers. In addition to members of the genus Bifidobacterium, species belonging to the genera Propionibacterium, Microbacterium, Brevibacterium, Actinomyces and Corynebacterium were found to be part of the faecal microbiota of healthy humans.}, }
@article {pmid23761788, year = {2013}, author = {Fernández-Suárez, R and Ramírez-Villatoro, G and Díaz-Ruiz, G and Eslava, C and Calderón, M and Navarro-Ocaña, A and Trejo-Márquez, A and Wacher, C}, title = {Effect of postharvest UV-C treatment on the bacterial diversity of Ataulfo mangoes by PCR-DGGE, survival of E. coli and antimicrobial activity.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {134}, pmid = {23761788}, issn = {1664-302X}, abstract = {Since Mexico is the second largest exporter of mangoes, its safety assurance is essential. Research in microbial ecology and knowledge of complex interactions among microbes must be better understood to achieve maximal control of pathogens. Therefore, we investigated the effect of UV-C treatments on bacterial diversity of the Ataulfo mangoes surface using PCR-DGGE analysis of variable region V3 of 16S rRNA genes, and the survival of E. coli, by plate counting. The UV-C irradiation reduced the microbial load on the surface of mangoes immediately after treatment and the structure of bacterial communities was modified during storage. We identified the key members of the bacterial communities on the surface of fruits, predominating Enterobacter genus. Genera as Lactococcus and Pantoea were only detected on the surface of non-treated (control) mangoes. This could indicate that these genera were affected by the UV-C treatment. On the other hand, the treatment did not have a significant effect on survival of E. coli. However, genera that have been recognized as antagonists against foodborne pathogens were identified in the bands patterns. Also, phenolic compounds were determined by HPLC and antimicrobial activity was assayed according to the agar diffusion method. The main phenolic compounds were chlorogenic, gallic, and caffeic acids. Mango peel methanol extracts (UV-C treated and control mangoes) showed antimicrobial activity against strains previously isolated from mango, detecting significant differences (P < 0.05) among treated and control mangoes after 4 and 12 days of storage. Ps. fluorescens and Ps. stutszeri were the most sensitive.}, }
@article {pmid23760828, year = {2012}, author = {Mela, F and Fritsche, K and de Boer, W and van den Berg, M and van Veen, JA and Maharaj, NN and Leveau, JH}, title = {Comparative genomics of bacteria from the genus Collimonas: linking (dis)similarities in gene content to phenotypic variation and conservation.}, journal = {Environmental microbiology reports}, volume = {4}, number = {4}, pages = {424-432}, doi = {10.1111/j.1758-2229.2012.00336.x}, pmid = {23760828}, issn = {1758-2229}, abstract = {Collimonas is a genus of soil bacteria comprising three recognized species: C. fungivorans, C. pratensis and C. arenae. Collimonads share the ability to degrade chitin (chitinolysis), feed on living fungal hyphae (mycophagy), and dissolve minerals (weathering), but vary in their inhibition of fungi (fungistasis). To better understand this phenotypic variability, we analysed the genomic content of four strains representing three Collimonas species (Ter14, Ter6, Ter91 and Ter10) by hybridization to a microarray based on reference strain C. fungivorans Ter331. The analysis revealed genes unique to strain Ter331 (e.g. those on the extrachromosomal element pTer331) and genes present in some but not all of the tested strains. Among the latter were several candidates that may contribute to fungistasis, including genes for the production and secretion of antifungals. We hypothesize that differential possession of these genes underlies the specialization of Collimonas strains towards different fungal hosts. We identified a set of 136 genes that were common in all tested Collimonas strains, but absent from the genomes of three other members of the family Oxalobacteraceae. Predicted products of these 'Collimonas core' genes include lytic, secreted enzymes such as chitinases, peptidases, nucleases and phosphatases with a putative role in mycophagy and weathering.}, }
@article {pmid23760464, year = {2013}, author = {Zhou, J and Jiang, YH and Deng, Y and Shi, Z and Zhou, BY and Xue, K and Wu, L and He, Z and Yang, Y}, title = {Random sampling process leads to overestimation of β-diversity of microbial communities.}, journal = {mBio}, volume = {4}, number = {3}, pages = {e00324-13}, pmid = {23760464}, issn = {2150-7511}, mesh = {*Biota ; *Environmental Microbiology ; Metagenomics/*methods ; Models, Theoretical ; Molecular Biology/*methods ; Reproducibility of Results ; Selection Bias ; }, abstract = {The site-to-site variability in species composition, known as β-diversity, is crucial to understanding spatiotemporal patterns of species diversity and the mechanisms controlling community composition and structure. However, quantifying β-diversity in microbial ecology using sequencing-based technologies is a great challenge because of a high number of sequencing errors, bias, and poor reproducibility and quantification. Herein, based on general sampling theory, a mathematical framework is first developed for simulating the effects of random sampling processes on quantifying β-diversity when the community size is known or unknown. Also, using an analogous ball example under Poisson sampling with limited sampling efforts, the developed mathematical framework can exactly predict the low reproducibility among technically replicate samples from the same community of a certain species abundance distribution, which provides explicit evidences of random sampling processes as the main factor causing high percentages of technical variations. In addition, the predicted values under Poisson random sampling were highly consistent with the observed low percentages of operational taxonomic unit (OTU) overlap (<30% and <20% for two and three tags, respectively, based on both Jaccard and Bray-Curtis dissimilarity indexes), further supporting the hypothesis that the poor reproducibility among technical replicates is due to the artifacts associated with random sampling processes. Finally, a mathematical framework was developed for predicting sampling efforts to achieve a desired overlap among replicate samples. Our modeling simulations predict that several orders of magnitude more sequencing efforts are needed to achieve desired high technical reproducibility. These results suggest that great caution needs to be taken in quantifying and interpreting β-diversity for microbial community analysis using next-generation sequencing technologies. IMPORTANCE Due to the vast diversity and uncultivated status of the majority of microorganisms, microbial detection, characterization, and quantitation are of great challenge. Although large-scale metagenome sequencing technology such as PCR-based amplicon sequencing has revolutionized the studies of microbial communities, it suffers from several inherent drawbacks, such as a high number of sequencing errors, biases, poor quantitation, and very high percentages of technical variations, which could greatly overestimate microbial biodiversity. Based on general sampling theory, this study provided the first explicit evidence to demonstrate the importance of random sampling processes in estimating microbial β-diversity, which has not been adequately recognized and addressed in microbial ecology. Since most ecological studies are involved in random sampling, the conclusions learned from this study should also be applicable to other ecological studies in general. In summary, the results presented in this study should have important implications for examining microbial biodiversity to address both basic theoretical and applied management questions.}, }
@article {pmid23757040, year = {2013}, author = {Delmont, TO and Simonet, P and Vogel, TM}, title = {Mastering methodological pitfalls for surviving the metagenomic jungle.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {35}, number = {8}, pages = {744-754}, doi = {10.1002/bies.201200155}, pmid = {23757040}, issn = {1521-1878}, mesh = {Biodiversity ; Biotechnology ; Computational Biology ; DNA/analysis ; Ecology ; Ecosystem ; Genes, Bacterial ; Genetic Variation ; Humans ; *Metagenome ; Microbiota/*genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {Metagenomics is a culture- and PCR-independent approach that is now widely exploited for directly studying microbial evolution, microbial ecology, and developing biotechnologies. Observations and discoveries are critically dependent on DNA extraction methods, sequencing technologies, and bioinformatics tools. The potential pitfalls need to be understood and, to some degree, mastered if the resulting data are to survive scrutiny. In particular, methodological variations appear to affect results from different ecosystems differently, thus increasing the risk of biological and ecological misinterpretation. Part of the difficulty is derived from the lack of knowledge concerning the true microbial diversity and because no approach can guarantee accessing microorganisms in the same proportion in which they exist in the environment. However, the variation between different approaches (e.g. DNA extraction techniques, sequence annotation systems) can be used to evaluate whether observations are meaningful. These methodological variations can be integrated into the error analysis before comparing microbial communities.}, }
@article {pmid23754719, year = {2013}, author = {Remus-Emsermann, MN and Kowalchuk, GA and Leveau, JH}, title = {Single-cell versus population-level reproductive success of bacterial immigrants to pre-colonized leaf surfaces.}, journal = {Environmental microbiology reports}, volume = {5}, number = {3}, pages = {387-392}, doi = {10.1111/1758-2229.12040}, pmid = {23754719}, issn = {1758-2229}, mesh = {Biomarkers/metabolism ; Clone Cells ; Colony Count, Microbial ; Genes, Reporter ; Genetic Fitness/*physiology ; Green Fluorescent Proteins ; Microbial Interactions/*physiology ; Pantoea/*physiology ; Phaseolus/*microbiology ; Plant Leaves/*microbiology ; Population Dynamics ; }, abstract = {We assessed how preemptive inoculation of plant leaves with bacteria affected the establishment of secondary colonizers. We quantified the latter in two ways: (i) at the population level, i.e. as counts of colony-forming units and (ii) at the level of single cells by tracking the reproductive success of individual bacteria. Both analyses showed that the ability of secondary immigrants to establish on the leaf was negatively correlated with the level of pre-population by primary colonizers. This effect was best described by an inverse dose-response curve with an apparent half-point inhibition efficacy of approximately 10(6) cells of primary colonizers per gram leaf. This efficacy was the same whether calculated from population- or average single-cell data. However, single-cell data revealed that even under conditions of heavy pre-population with primary colonizers, a small fraction of secondary immigrants still produced offspring, although the corresponding population measurement showed no increase in total population size. This observation has direct relevance for biocontrol strategies that are based on the principle of preemptive exclusion of foliar bacterial pathogens: even at seemingly saturating levels of primary inoculum, some secondary colonizers may still be able to reproduce and possibly reach a quorum to trigger behaviours that enhance survival or virulence.}, }
@article {pmid23754714, year = {2013}, author = {Ho, A and Kerckhof, FM and Luke, C and Reim, A and Krause, S and Boon, N and Bodelier, PL}, title = {Conceptualizing functional traits and ecological characteristics of methane-oxidizing bacteria as life strategies.}, journal = {Environmental microbiology reports}, volume = {5}, number = {3}, pages = {335-345}, doi = {10.1111/j.1758-2229.2012.00370.x}, pmid = {23754714}, issn = {1758-2229}, mesh = {Adaptation, Physiological ; *Bacterial Physiological Phenomena ; Climate ; Ecosystem ; *Gene Expression Regulation, Bacterial ; Methane/*metabolism ; Methylococcaceae/classification/*genetics/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/classification/*genetics ; Stress, Physiological ; }, abstract = {Methane-oxidizing bacteria (MOB) possess the ability to use methane for energy generation and growth, thereby, providing a key ecosystem service that is highly relevant to the regulation of the global climate. MOB subgroups have different responses to key environmental controls, reflecting on their functional traits. Their unique features (C1-metabolism, unique lipids and congruence between the 16S rRNA and pmoA gene phylogeny) have facilitated numerous environmental studies, which in combination with the availability of cultured representatives, yield the most comprehensive ecological picture of any known microbial functional guild. Here, we focus on the broad MOB subgroups (type I and type II MOB), and aim to conceptualize MOB functional traits and observational characteristics derived primarily from these environmental studies to be interpreted as microbial life strategies. We focus on the functional traits, and the conditions under which these traits will render different MOB subgroups a selective advantage. We hypothesize that type I and type II MOB generally have distinct life strategies, enabling them to predominate under different conditions and maintain functionality. The ecological characteristics implicated in their adopted life strategies are discussed, and incorporated into the Competitor-Stress tolerator-Ruderal functional classification framework as put forward for plant communities. In this context, type I MOB can broadly be classified as competitor-ruderal while type II MOB fit more within the stress tolerator categories. Finally, we provide an outlook on MOB applications by exemplifying two approaches where their inferred life strategies could be exploited thereby, putting MOB into the context of microbial resource management.}, }
@article {pmid23749062, year = {2013}, author = {del Campo, J and Balagué, V and Forn, I and Lekunberri, I and Massana, R}, title = {Culturing bias in marine heterotrophic flagellates analyzed through seawater enrichment incubations.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {489-499}, pmid = {23749062}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*growth &amp; development/isolation &amp; purification ; Biodiversity ; Eukaryota/classification/genetics/*growth &amp; development/metabolism ; Filtration ; Heterotrophic Processes ; Molecular Sequence Data ; Phylogeny ; Seawater/chemistry/*microbiology/*parasitology ; }, abstract = {The diversity of heterotrophic flagellates is generally based on cultivated strains, on which ultrastructural, physiological, and molecular studies have been performed. However, the relevance of these cultured strains as models of the dominant heterotrophic flagellates in the marine planktonic environment is unclear. In fact, molecular surveys typically recover novel eukaryotic lineages that have refused cultivation so far. This study was designed to directly address the culturing bias in planktonic marine heterotrophic flagellates. Several microcosms were established adding increasing amounts and sources of organic matter to a confined natural microbial community pre-filtered by 3 μm. Growth dynamics were followed by epifluorescence microscopy and showed the expected higher yield of bacteria and heterotrophic flagellates at increased organic matter additions. Moreover, protist diversity analyzed by molecular tools showed a clear substitution in the community, which differed more and more from the initial sample as the organic matter increased. Within this gradient, there was also an increase of sequences related to cultured organisms as well as a decrease in diversity. Culturing bias is partly explained by the use of organic matter in the isolation process, which drives a shift in the community to conditions closer to laboratory cultures. An intensive culturing effort using alternative isolation methods is necessary to allow the access to the missing heterotrophic flagellates that constitute the abundant and active taxa in marine systems.}, }
@article {pmid23748919, year = {2013}, author = {Lee, CW and Lim, JH and Heng, PL}, title = {Investigating the spatial distribution of phototrophic picoplankton in a tropical estuary.}, journal = {Environmental monitoring and assessment}, volume = {185}, number = {12}, pages = {9697-9704}, pmid = {23748919}, issn = {1573-2959}, mesh = {*Environmental Monitoring ; *Estuaries ; Fresh Water/analysis ; Plankton/*growth &amp; development ; Salinity ; Seawater/analysis ; Spatial Analysis ; Tropical Climate ; }, abstract = {We sampled extensively (29 stations) at the Klang estuarine system over a 3-day scientific expedition. We measured physical and chemical variables (temperature, salinity, dissolved oxygen, total suspended solids, dissolved inorganic nutrients) and related them to the spatial distribution of phototrophic picoplankton (Ppico). Multivariate analysis of variance of the physicochemical variables showed the heterogeneity of the Klang estuarine system where the stations at each transect were significantly different (Rao's F18, 36 = 8.401, p < 0.001). Correlation analyses also showed that variables related to Ppico abundance and growth were mutually exclusive. Distribution of Ppico was best explained by the physical mixing between freshwater and seawater whereas Ppico growth was correlated with temperature.}, }
@article {pmid23747590, year = {2013}, author = {Kim, J and Lim, J and Lee, C}, title = {Quantitative real-time PCR approaches for microbial community studies in wastewater treatment systems: applications and considerations.}, journal = {Biotechnology advances}, volume = {31}, number = {8}, pages = {1358-1373}, doi = {10.1016/j.biotechadv.2013.05.010}, pmid = {23747590}, issn = {1873-1899}, mesh = {*Bacteria/classification/genetics/isolation &amp; purification ; *DNA, Bacterial/analysis/genetics ; Microbial Consortia/*genetics ; Real-Time Polymerase Chain Reaction/*methods ; Wastewater/*microbiology ; }, abstract = {Quantitative real-time PCR (qPCR) has been widely used in recent environmental microbial ecology studies as a tool for detecting and quantifying microorganisms of interest, which aids in better understandings of the complexity of wastewater microbial communities. Although qPCR can be used to provide more specific and accurate quantification than other molecular techniques, it does have limitations that must be considered when applying it in practice. This article reviews the principle of qPCR quantification and its applications to microbial ecology studies in various wastewater treatment environments. Here we also address several limitations of qPCR-based approaches that can affect the validity of quantification data: template nucleic acid quality, nucleic acid extraction efficiency, specificity of group-specific primers and probes, amplification of nonviable DNA, gene copy number variation, and limited number of sequences in the database. Even with such limitations, qPCR is reportedly among the best methods for quantitatively investigating environmental microbial communities. The application of qPCR is and will continue to be increasingly common in studies of wastewater treatment systems. To obtain reliable analyses, however, the limitations that have often been overlooked must be carefully considered when interpreting the results.}, }
@article {pmid23741805, year = {2012}, author = {Savitha, N and Yamakanamardi, SM}, title = {Studies on abundance of zooplanktons in lakes of Mysore, India.}, journal = {Journal of environmental biology..}, volume = {33}, number = {6}, pages = {1079-1085}, pmid = {23741805}, issn = {0254-8704}, mesh = {Animals ; *Fresh Water ; India ; Population Dynamics ; Seasons ; *Zooplankton ; }, abstract = {This is the first comprehensive ecological study on the abundance of zooplankton in Kalale, Alanahalli and Dalvoy lakes of Mysore. The abundance of zooplankton as well as their relation with physico-chemical parameters was analyzed, every month in these lakes from June 2008-May 2010. The mean abundance of Rotifer (281 Org (l-1)), Cladocerans (27 Org l(-1)) and total abundance of zooplankton (343 Org l(-1)) were more and significantly different in Dalvoy lake; whereas, in Kalale lake the mean abundance of Rotifer (19 Org l(-1)), Cladocerans (3 Org l(-1)) and total abundance of zooplankton (79 Org l(-1)) and in Alanahalli lake the mean abundance of Rotifer (84 Org l(-1)), Cladocerans (9 Org l(-1)) and total abundance of zooplankton (149 Org l(-1)) were significantly less. However, the abundance of Copepods and Ostracods was similar in all the three lakes studied. The water bodies of Kalale lake were less polluted when compared toAlanahalli and Dalvoy lakes. The increases in conductivity, Chl a, turbidity, phosphate, carbon-di-oxide and total anions in Alanahalli and Dalvoy lakes may be attributed to the various anthropogenic activities in the catchment areas. Interrelationships between zooplankton variables and physico-chemical parameters were calculated using Pearson's correlation co-efficient (r) which revealed (25) significant (P < 0.05) relationships (More (11) in Dalvoy lake and moderate (7) in Alanahalli and Kalale lakes). The stepwise multiple regression analysis (r2) showed out of 21 physico-chemical parameters studied, as many as 12 were positively controlling the abundance of zooplankton, where as the phosphate and chloride were negatively controlling the total abundance of zooplankton and the abundance of ostracods respectively. The results obtained have been discussed in the light of the present literature available in the field of aquatic microbial ecology.}, }
@article {pmid23740199, year = {2013}, author = {Cennamo, P and Caputo, P and Giorgio, A and Moretti, A and Pasquino, N}, title = {Biofilms on tuff stones at historical sites: identification and removal by nonthermal effects of radiofrequencies.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {659-668}, pmid = {23740199}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/radiation effects ; *Bacterial Physiological Phenomena/radiation effects ; *Biofilms/radiation effects ; Geologic Sediments/*microbiology ; Radio Waves ; }, abstract = {A methodology aiming at identifying and removing biofilms from cultural heritage was applied to stones from tuff walls in historical sites. Identification of phototrophic encrusting microorganisms was carried out by optical and electron microscopy, as well as by molecular techniques (DNA analyses and denaturing gradient gel electrophoresis (DGGE)). In all sites, the examination of microbial components of biofilms resulted in the identification of 17 species belonging to Cyanobacteria, Rhodophyta, Bacillariophyta and Chlorophyta, with Cyanobacteria being the dominant components in all biofilms. In order to remove the biofilms, an innovative technique based on the use of nonthermal effects of radiofrequencies was adopted. The source of the electromagnetic fields was a signal generator connected to a horn antenna through an amplifier to provide the power boost required to generate the target field amplitude. Seven days after exposure to radiofrequency electromagnetic field, about 50 % reduction of biofilm was observed; after 14 days, biofilm extension was reduced by about 90 %. DGGE analyses performed after 14 days confirmed these visual inspections. Also, DGGE analyses carried out before and 14 days after treatments showed that 12 out of 17 identified species disappeared. A complete visual disappearance of biofilms was observed a month after the beginning of treatments. DGGE repeated at this time confirmed the total disappearance of biofilm-forming species. Treated stones, when transferred back to their original sites, did not show any microorganism re-growing after 6 months. No alteration in the color and structural consistency of tuff substrata was observed after radiofrequency treatments.}, }
@article {pmid23736813, year = {2013}, author = {Hirsch, J and Galidevara, S and Strohmeier, S and Devi, KU and Reineke, A}, title = {Effects on diversity of soil fungal community and fate of an artificially applied Beauveria bassiana strain assessed through 454 pyrosequencing.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {608-620}, pmid = {23736813}, issn = {1432-184X}, mesh = {Beauveria/genetics/isolation &amp; purification/*physiology ; *Biodiversity ; Fungi/classification/genetics/growth &amp; development/*isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; *Soil Microbiology ; }, abstract = {The entomopathogenic fungus Beauveria bassiana is widely used as a biological control agent (BCA) for insect pest control, with fungal propagules being either incorporated into the potting media or soil or sprayed directly onto the foliage or soil. To gain a better understanding of entomopathogenic fungal ecology when applied as a BCA to the soil environment, a case study using tag-encoded 454 pyrosequencing of fungal ITS sequences was performed to assess the fate and potential effect of an artificially applied B. bassiana strain on the diversity of soil fungal communities in an agricultural field in India. Results show that the overall fungal diversity was not influenced by application of B. bassiana during the 7 weeks of investigation. Strain-specific microsatellite markers indicated both an establishment of the applied B. bassiana strain in the treated plot and its spread to the neighboring nontreated control plot. These results might be important for proper risk assessment of entomopathogenic fungi-based BCAs.}, }
@article {pmid23736549, year = {2013}, author = {Zhang, N and Liu, W and Yang, H and Yu, X and Gutknecht, JL and Zhang, Z and Wan, S and Ma, K}, title = {Soil microbial responses to warming and increased precipitation and their implications for ecosystem C cycling.}, journal = {Oecologia}, volume = {173}, number = {3}, pages = {1125-1142}, pmid = {23736549}, issn = {1432-1939}, mesh = {Acclimatization/*physiology ; Analysis of Variance ; Bacteria/metabolism ; Carbon Cycle/*physiology ; China ; *Ecosystem ; *Global Warming ; *Rain ; *Soil Microbiology ; }, abstract = {A better understanding of soil microbial ecology is critical to gaining an understanding of terrestrial carbon (C) cycle-climate change feedbacks. However, current knowledge limits our ability to predict microbial community dynamics in the face of multiple global change drivers and their implications for respiratory loss of soil carbon. Whether microorganisms will acclimate to climate warming and ameliorate predicted respiratory C losses is still debated. It also remains unclear how precipitation, another important climate change driver, will interact with warming to affect microorganisms and their regulation of respiratory C loss. We explore the dynamics of microorganisms and their contributions to respiratory C loss using a 4-year (2006-2009) field experiment in a semi-arid grassland with increased temperature and precipitation in a full factorial design. We found no response of mass-specific (per unit microbial biomass C) heterotrophic respiration to warming, suggesting that respiratory C loss is directly from microbial growth rather than total physiological respiratory responses to warming. Increased precipitation did stimulate both microbial biomass and mass-specific respiration, both of which make large contributions to respiratory loss of soil carbon. Taken together, these results suggest that, in semi-arid grasslands, soil moisture and related substrate availability may inhibit physiological respiratory responses to warming (where soil moisture was significantly lower), while they are not inhibited under elevated precipitation. Although we found no total physiological response to warming, warming increased bacterial C utilization (measured by BIOLOG EcoPlates) and increased bacterial oxidation of carbohydrates and phenols. Non-metric multidimensional scaling analysis as well as ANOVA testing showed that warming or increased precipitation did not change microbial community structure, which could suggest that microbial communities in semi-arid grasslands are already adapted to fluctuating climatic conditions. In summary, our results support the idea that microbial responses to climate change are multifaceted and, even with no large shifts in community structure, microbial mediation of soil carbon loss could still occur under future climate scenarios.}, }
@article {pmid23733171, year = {2013}, author = {Scotta, C and Gomila, M and Mulet, M and Lalucat, J and García-Valdés, E}, title = {Whole-cell MALDI-TOF mass spectrometry and multilocus sequence analysis in the discrimination of Pseudomonas stutzeri populations: three novel genomovars.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {522-532}, pmid = {23733171}, issn = {1432-184X}, mesh = {Environmental Microbiology ; Genetic Variation ; Humans ; Molecular Sequence Data ; Multilocus Sequence Typing/*methods ; Phylogeny ; Pseudomonas Infections/*microbiology ; Pseudomonas stutzeri/*chemistry/classification/genetics/*isolation &amp; purification ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; }, abstract = {Pseudomonas stutzeri is a widely distributed species with very high genetic diversity and metabolic capacities, occupying many diverse ecological niches. A collection of 229 P. stutzeri strains isolated from different habitats and geographical locations has been previously characterised phylogenetically by rpoD gene sequencing analysis and in the present study 172 of them phenotypically by whole-cell MALDI-TOF mass spectrometry. Fifty-five strains were further analysed by multilocus sequencing analysis to determine the phylogenetic population structure. Both methods showed coherence in strain grouping; 226 strains were allocated in the 18 genomovars known presently. The remaining three strains are proposed as references for three novel genomovars in the species. The correlation and usefulness of sequence-based phylogenetic analysis and whole-cell MALDI-TOF mass spectrometry, which are essential for autoecological studies in microbial ecology, is discussed for the differentiation of P. stutzeri populations.}, }
@article {pmid23733170, year = {2013}, author = {Wu, N and Yang, X and Zhang, R and Li, J and Xiao, X and Hu, Y and Chen, Y and Yang, F and Lu, N and Wang, Z and Luan, C and Liu, Y and Wang, B and Xiang, C and Wang, Y and Zhao, F and Gao, GF and Wang, S and Li, L and Zhang, H and Zhu, B}, title = {Dysbiosis signature of fecal microbiota in colorectal cancer patients.}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {462-470}, pmid = {23733170}, issn = {1432-184X}, mesh = {Aged ; Bacteria/classification/genetics/*isolation &amp; purification ; Colonic Neoplasms/*microbiology ; Dysbiosis/*microbiology ; Feces/*microbiology ; Female ; Gastrointestinal Tract/microbiology ; Humans ; Male ; *Microbiota ; Middle Aged ; Molecular Sequence Data ; Phylogeny ; }, abstract = {The human gut microbiota is a complex system that is essential to the health of the host. Increasing evidence suggests that the gut microbiota may play an important role in the pathogenesis of colorectal cancer (CRC). In this study, we used pyrosequencing of the 16S rRNA gene V3 region to characterize the fecal microbiota of 19 patients with CRC and 20 healthy control subjects. The results revealed striking differences in fecal microbial population patterns between these two groups. Partial least-squares discriminant analysis showed that 17 phylotypes closely related to Bacteroides were enriched in the gut microbiota of CRC patients, whereas nine operational taxonomic units, represented by the butyrate-producing genera Faecalibacterium and Roseburia, were significantly less abundant. A positive correlation was observed between the abundance of Bacteroides species and CRC disease status (R = 0.462, P = 0.046 < 0.5). In addition, 16 genera were significantly more abundant in CRC samples than in controls, including potentially pathogenic Fusobacterium and Campylobacter species at genus level. The dysbiosis of fecal microbiota, characterized by the enrichment of potential pathogens and the decrease in butyrate-producing members, may therefore represent a specific microbial signature of CRC. A greater understanding of the dynamics of the fecal microbiota may assist in the development of novel fecal microbiome-related diagnostic tools for CRC.}, }
@article {pmid23732004, year = {2013}, author = {Tian, WD and Lopez-Vazquez, CM and Li, WG and Brdjanovic, D and van Loosdrecht, MC}, title = {Occurrence of PAOI in a low temperature EBPR system.}, journal = {Chemosphere}, volume = {92}, number = {10}, pages = {1314-1320}, doi = {10.1016/j.chemosphere.2013.05.009}, pmid = {23732004}, issn = {1879-1298}, mesh = {Betaproteobacteria/*metabolism ; Biodegradation, Environmental ; *Bioreactors ; Cold Temperature ; Glycogen/metabolism ; Phosphorus/*isolation &amp; purification/metabolism ; Waste Disposal, Fluid/methods ; Wastewater/*analysis ; }, abstract = {The occurrence of Accumulibacter Type I (a known phosphorus-accumulating organism, PAO) has received increased attention due to the potential operating benefits associated with their denitrifying activity in enhanced biological phosphorus removal (EBPR) wastewater treatment plants. In this study, after a shift from an enriched glycogen-accumulating organism (GAO) culture (competitors of PAO) to a PAO-enriched system, Accumulibacter Type I (PAO I) became dominant in an anaerobic-aerobic EBPR system fed with acetate and operated at 10°C with a net aerobic solids retention time (SRT) of 6 d. Since Accumulibacter Type II (PAO II) were not detected, the low temperature in combination with the net aerobic SRT applied appeared to have suppressed their growth as well. The stoichiometry of PAO I was in agreement with previous metabolic models, suggesting that it was the main PAO organisms present in previous studies operated under similar conditions. Moreover, under poly-P limiting conditions, PAO I were unable to switch to a GAO-like metabolism at low temperatures. These results contribute to increase the understanding of the physiology, microbial metabolism and microbial ecology of PAO I.}, }
@article {pmid23731353, year = {2013}, author = {Escalas, A and Bouvier, T and Mouchet, MA and Leprieur, F and Bouvier, C and Troussellier, M and Mouillot, D}, title = {A unifying quantitative framework for exploring the multiple facets of microbial biodiversity across diverse scales.}, journal = {Environmental microbiology}, volume = {15}, number = {10}, pages = {2642-2657}, doi = {10.1111/1462-2920.12156}, pmid = {23731353}, issn = {1462-2920}, mesh = {*Biodiversity ; Ecology/*methods ; *Environmental Microbiology ; Genetic Markers ; Genetic Techniques ; Models, Biological ; }, abstract = {Recent developments of molecular tools have revolutionized our knowledge of microbial biodiversity by allowing detailed exploration of its different facets and generating unprecedented amount of data. One key issue with such large datasets is the development of diversity measures that cope with different data outputs and allow comparison of biodiversity across different scales. Diversity has indeed three components: local (α), regional (γ) and the overall difference between local communities (β). Current measures of microbial diversity, derived from several approaches, provide complementary but different views. They only capture the β component of diversity, compare communities in a pairwise way, consider all species as equivalent or lack a mathematically explicit relationship among the α, β and γ components. We propose a unified quantitative framework based on the Rao quadratic entropy, to obtain an additive decomposition of diversity (γ = α + β), so the three components can be compared, and that integrate the relationship (phylogenetic or functional) among Microbial Diversity Units that compose a microbial community. We show how this framework is adapted to all types of molecular data, and we highlight crucial issues in microbial ecology that would benefit from this framework and propose ready-to-use R-functions to easily set up our approach.}, }
@article {pmid23728164, year = {2013}, author = {Shah, V and Zakrzewski, M and Wibberg, D and Eikmeyer, F and Schlüter, A and Madamwar, D}, title = {Taxonomic profiling and metagenome analysis of a microbial community from a habitat contaminated with industrial discharges.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {533-550}, pmid = {23728164}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; *Ecosystem ; India ; Industrial Waste/*analysis ; *Metagenome ; Phylogeny ; *Soil Microbiology ; Soil Pollutants/metabolism ; }, abstract = {Industrial units, manufacturing dyes, chemicals,solvents, and xenobiotic compounds, produce liquid and solid wastes, which upon conventional treatment are released in the nearby environment and thus are the major cause of pollution. Soil collected from contaminated Kharicut Canalbank (N 22°57.878′; E 072°38.478′), Ahmeda bad, Gujarat,India was used for metagenomic DNA preparation to study the capabilities of intrinsic microbial community in dealing with xenobiotics. Sequencing of metagenomic DNA on the Genome Sequencer FLX System using titanium chemistry resulted in 409,782 reads accounting for 133,529,997 bases of sequence information. Taxonomic analyses and gene annotations were carried out using the bioinformatics platform Sequence Analysis and Management System for Metagenomic Datasets. Taxonomic profiling was carried out by three different complementary approaches: (a) 16S rDNA, (b) environmental gene tags, and (c) lowest common ancestor. The most abundant phylum and genus were found to be “Proteobacteria”and “Pseudomonas,” respectively. Metagenome reads were mapped on sequenced microbial genomes and the highest numbers of reads were allocated to Pseudomonas stutzeri A1501. Assignment of obtained metagenome reads to Gene Ontology terms, Clusters of Orthologous Groups of protein categories, protein family numbers, and Kyoto Encyclopedia of Genes and Genomes hits revealed genomic potential of indigenous microbial community. In total, 157,024 reads corresponded to 37,028 different KEGG hits, and amongst them, 11,574 reads corresponded to 131 different enzymes potentially involved in xenobiotic biodegradation. These enzymes were mapped on biodegradation pathways of xenobiotics to elucidate their roles in possible catalytic reactions. Consequently, information obtained from the present study will act as a baseline which, subsequently along with other“-omic” studies, will help in designing future bioremediation strategies in effluent treatment plants and environmental cleanup projects.}, }
@article {pmid23727339, year = {2013}, author = {Daffonchio, D and Ferrer, M and Mapelli, F and Cherif, A and Lafraya, A and Malkawi, HI and Yakimov, MM and Abdel-Fattah, YR and Blaghen, M and Golyshin, PN and Kalogerakis, N and Boon, N and Magagnini, M and Fava, F}, title = {Bioremediation of Southern Mediterranean oil polluted sites comes of age.}, journal = {New biotechnology}, volume = {30}, number = {6}, pages = {743-748}, doi = {10.1016/j.nbt.2013.05.006}, pmid = {23727339}, issn = {1876-4347}, mesh = {Biodegradation, Environmental ; Mediterranean Region ; *Oceans and Seas ; Petroleum/*microbiology ; *Water Microbiology ; *Water Pollutants, Chemical ; }, abstract = {Mediterranean Sea is facing a very high risk of oil pollution due to the high number of oil extractive and refining sites along the basin coasts, and the intense maritime traffic of oil tankers. All the Mediterranean countries have adopted severe regulations for minimizing pollution events and bioremediation feasibility studies for the most urgent polluted sites are undergoing. However, the analysis of the scientific studies applying modern 'meta-omics' technologies that have been performed on marine oil pollution worldwide showed that the Southern Mediterranean side has been neglected by the international research. Most of the studies in the Mediterranean Sea have been done in polluted sites of the Northern side of the basin. Those of the Southern side are poorly studied, despite many of the Southern countries being major oil producers and exporters. The recently EU-funded research project ULIXES has as a major objective to increase the knowledge of the bioremediation potential of sites from the Southern Mediterranean countries. ULIXES is targeting four major polluted sites on the coastlines of Egypt, Jordan, Morocco and Tunisia, including seashore sands, lagoons, and oil refinery polluted sediments. The research is designed to unravel, categorize, catalogue, exploit and manage the diversity and ecology of microorganisms thriving in these polluted sites. Isolation of novel hydrocarbon degrading microbes and a series of state of the art 'meta-omics' technologies are the baseline tools for improving our knowledge on biodegradation capacities mediated by microbes under different environmental settings and for designing novel site-tailored bioremediation approaches. A network of twelve European and Southern Mediterranean partners is cooperating for plugging the existing gap of knowledge for the development of novel bioremediation processes targeting such poorly investigated polluted sites.}, }
@article {pmid23726710, year = {2013}, author = {De Vrieze, J and De Lathouwer, L and Verstraete, W and Boon, N}, title = {High-rate iron-rich activated sludge as stabilizing agent for the anaerobic digestion of kitchen waste.}, journal = {Water research}, volume = {47}, number = {11}, pages = {3732-3741}, doi = {10.1016/j.watres.2013.04.020}, pmid = {23726710}, issn = {1879-2448}, mesh = {Anaerobiosis ; Bioreactors ; Fatty Acids, Volatile/metabolism ; Ferrous Compounds/chemistry ; Food ; *Iron ; Methane/biosynthesis ; *Microbial Consortia ; Refuse Disposal/*methods ; Sewage/*microbiology ; Wastewater ; Water Purification/methods ; }, abstract = {Anaerobic digestion is a key technology in the bio-based economy and can be applied to convert a wide range of organic substrates into CH4 and CO2. Kitchen waste is a valuable substrate for anaerobic digestion, since it is an abundant source of organic matter. Yet, digestion of single kitchen waste often results in process failure. High-rate activated sludge or A-sludge is produced during the highly loaded first stage of the two-phase 'Adsorptions-Belebungsverfahren' or A/B activated sludge system for municipal wastewater treatment. In this specific case, the A-sludge was amended with FeSO4 to enhance phosphorous removal and coagulation during the water treatment step. This study therefore evaluated whether this Fe-rich A-sludge could be used to obtain stable methanation and higher methane production values during co-digestion with kitchen waste. It was revealed that Fe-rich A-sludge can be a suitable co-substrate for kitchen waste; i.e. methane production rate values of 1.15 ± 0.22 and 1.12 ± 0.28 L L(-1) d(-1) were obtained during mesophilic and thermophilic co-digestion respectively of a feed-mixture consisting of 15% KW and 85% A-sludge. The thermophilic process led to higher residual VFA concentrations, up to 2070 mg COD L(-1), and can therefore be considered less stable. Addition of micro- and macronutrients provided a more stable digestion of single kitchen waste, i.e. a methane production of 0.45 L L(-1) d(-1) was obtained in the micronutrient treatment compared to 0.30 L L(-1) d(-1) in the control treatment on day 61. Yet, methane production during single kitchen waste digestion still decreased toward the end of the experiment, despite the addition of micronutrients. Methane production rates were clearly influenced by the total numbers of archaea in the different reactors. This study showed that Fe-rich A-sludge and kitchen waste are suitable for co-digestion.}, }
@article {pmid23723056, year = {2013}, author = {Crespo, BG and Pommier, T and Fernández-Gómez, B and Pedrós-Alió, C}, title = {Taxonomic composition of the particle-attached and free-living bacterial assemblages in the Northwest Mediterranean Sea analyzed by pyrosequencing of the 16S rRNA.}, journal = {MicrobiologyOpen}, volume = {2}, number = {4}, pages = {541-552}, pmid = {23723056}, issn = {2045-8827}, mesh = {Bacteria/*classification/*genetics ; Bacterial Adhesion ; Bacterial Physiological Phenomena ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Mediterranean Sea ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Free-living (FL) and particle-attached (PA) bacterial assemblages in the Northwest Mediterranean Sea were studied using pyrosequencing data of the 16S rRNA. We have described and compared the richness, the distribution of Operational Taxonomic Units (OTUs) within the two fractions, the spatial distribution, and the taxonomic composition of FL and PA bacterial assemblages. The number of OTUs in the present work was two orders of magnitude higher than in previous studies. Only 25% of the total OTUs were common to both fractions, whereas 49% OTUs were exclusive to the PA fraction and 26% to the FL fraction. The OTUs exclusively present in PA or FL assemblages were very low in abundance (6% of total abundance). Detection of the rare OTUs revealed the larger richness of PA bacteria that was hidden in previous studies. Alpha-Proteobacteria dominated the FL bacterial assemblage and gamma-Proteobacteria dominated the PA fraction. Bacteroidetes were important in the PA fraction mainly at the coast. The high number of sequences in this study detected additional phyla from the PA fraction, such as Actinobacteria, Firmicutes, and Verrucomicrobia.}, }
@article {pmid23720032, year = {2013}, author = {Mishra, S and Upadhyay, RS and Nautiyal, CS}, title = {Unravelling the beneficial role of microbial contributors in reducing the allelopathic effects of weeds.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {13}, pages = {5659-5668}, doi = {10.1007/s00253-013-4885-y}, pmid = {23720032}, issn = {1432-0614}, mesh = {*Allelopathy ; Bacteria/growth &amp; development/*metabolism ; Biotransformation ; Fungi/growth &amp; development/*metabolism ; Pheromones/*metabolism ; Plant Weeds/growth &amp; development/metabolism/*physiology ; *Soil Microbiology ; }, abstract = {The field of allelopathy is one of the most fascinating but controversial processes in plant ecology that offers an exciting, interdisciplinary, complex, and challenging study. In spite of the established role of soil microbes in plant health, their role has also been consolidated in studies of allelopathy. Moreover, allelopathy can be better understood by incorporating soil microbial ecology that determines the relevance of allelopathy phenomenon. Therefore, while discussing the role of allelochemicals in plant-plant interactions, the dynamic nature of soil microbes should not be overlooked. The occurrence and toxicity of allelochemicals in soil depend on various factors, but the type of microflora in the surroundings plays a crucial role because it can interfere with its allelopathic nature. Such microbes could be of prime importance for biological control management of weeds reducing the cost and ill effects of chemical herbicides. Among microbes, our main focus is on bacteria--as they are dominant among other microbes and are being used for enhancing crop production for decades--and fungi. Hence, to refer to both bacteria and fungi, we have used the term microbes. This review discusses the beneficial role of microbes in reducing the allelopathic effects of weeds. The review is mainly focused on various functions of bacteria in (1) reducing allelopathic inhibition caused by weeds to reduce crop yield loss, (2) building inherent defense capacity in plants against allelopathic weed, and (3) deciphering beneficial rhizospheric process such as chemotaxis/biofilm, degradation of toxic allelochemicals, and induced gene expression.}, }
@article {pmid23717427, year = {2013}, author = {Vilar-Sanz, A and Puig, S and García-Lledó, A and Trias, R and Balaguer, MD and Colprim, J and Bañeras, L}, title = {Denitrifying bacterial communities affect current production and nitrous oxide accumulation in a microbial fuel cell.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e63460}, pmid = {23717427}, issn = {1932-6203}, mesh = {Bioelectric Energy Sources/*microbiology ; *Biofilms ; *Denitrification ; Electrodes ; Gene Dosage ; Genes, Bacterial ; Molecular Sequence Data ; Multilocus Sequence Typing ; Nitrous Oxide/*metabolism ; Proteobacteria/classification/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The biocathodic reduction of nitrate in Microbial Fuel Cells (MFCs) is an alternative to remove nitrogen in low carbon to nitrogen wastewater and relies entirely on microbial activity. In this paper the community composition of denitrifiers in the cathode of a MFC is analysed in relation to added electron acceptors (nitrate and nitrite) and organic matter in the cathode. Nitrate reducers and nitrite reducers were highly affected by the operational conditions and displayed high diversity. The number of retrieved species-level Operational Taxonomic Units (OTUs) for narG, napA, nirS and nirK genes was 11, 10, 31 and 22, respectively. In contrast, nitrous oxide reducers remained virtually unchanged at all conditions. About 90% of the retrieved nosZ sequences grouped in a single OTU with a high similarity with Oligotropha carboxidovorans nosZ gene. nirS-containing denitrifiers were dominant at all conditions and accounted for a significant amount of the total bacterial density. Current production decreased from 15.0 A · m(-3) NCC (Net Cathodic Compartment), when nitrate was used as an electron acceptor, to 14.1 A · m(-3) NCC in the case of nitrite. Contrarily, nitrous oxide (N2O) accumulation in the MFC was higher when nitrite was used as the main electron acceptor and accounted for 70% of gaseous nitrogen. Relative abundance of nitrite to nitrous oxide reducers, calculated as (qnirS+qnirK)/qnosZ, correlated positively with N2O emissions. Collectively, data indicate that bacteria catalysing the initial denitrification steps in a MFC are highly influenced by main electron acceptors and have a major influence on current production and N2O accumulation.}, }
@article {pmid23715804, year = {2013}, author = {Mercimek, HA and Dincer, S and Guzeldag, G and Ozsavli, A and Matyar, F}, title = {Aerobic biodegradation of 2,4,6-trinitrotoluene (TNT) by Bacillus cereus isolated from contaminated soil.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {512-521}, pmid = {23715804}, issn = {1432-184X}, mesh = {Aerobiosis ; Bacillus cereus/genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Nitrates/metabolism ; Nitrites/metabolism ; Soil Microbiology ; Soil Pollutants/analysis/*metabolism ; Trinitrotoluene/*metabolism ; }, abstract = {In this study, biological degradation of 2,4,6-trinitrotoluene (TNT) which is very highly toxic environmentally and an explosive in nitroaromatic character was researched in minimal medium by Bacillus cereus isolated from North Atlantic Treaty Organization (NATO) TNT-contaminated soils. In contrast to most previous studies, the capability of this bacteria to transform in liquid medium containing TNT was investigated. During degradation, treatment of TNT was followed by high-performance liquid chromatography (HPLC) and achievement of degradation was calculated as percentage. At an initial concentration of 50 and 75 mg L(-1), TNT was degraded respectively 68 % and 77 % in 96 h. It transformed into 2,4-dinitrotoluene and 4-aminodinitrotoluene derivates, which could be detected as intermediate metabolites by using thin-layer chromatography and gas chromatography-mass spectrometry analyses. Release of nitrite and nitrate ions were searched by spectrophotometric analyses. Depending upon Meisenheimer complex, while nitrite production was observed, nitrate was detected in none of the cultures. Results of our study propose which environmental pollutant can be removed by using microorganisms that are indigenous to the contaminated site.}, }
@article {pmid23708426, year = {2013}, author = {Verhagen, P and De Gelder, L and Boon, N}, title = {Inoculation with a mixed degrading culture improves the pesticide removal of an on-farm biopurification system.}, journal = {Current microbiology}, volume = {67}, number = {4}, pages = {466-471}, pmid = {23708426}, issn = {1432-0991}, mesh = {Agricultural Inoculants/classification/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; Biodegradation, Environmental ; Bioreactors/microbiology ; Environmental Restoration and Remediation/instrumentation/*methods ; Pesticides/*metabolism ; Water Pollutants, Chemical/*metabolism ; Water Purification/methods ; }, abstract = {To investigate whether the pesticide removal in on-farm biopurification systems (BPS) filled with two different types of substrata (biomix and plastic carriers) is affected by inoculation with a pesticide-degrading strain or mixed culture, lab-scale BPS used to treat chloropropham point source contaminations were bioaugmented with either a specialized chloropropham-degrading strain or a chloropropham-degrading enrichment culture. Application of both inoculum types leads to an accelerated degradation activity in the columns filled with plastic carriers. For both substratum types, inoculation with the mixed culture resulted in a lower breakthrough of the toxic intermediate 3-chloroaniline at high hydraulic loads, compared to inoculation with the pure isolate and no inoculation. This study suggests that the use of plastic carrier materials could be a proficient alternative to the use of a conventional biomix as a substratum in on-farm BPS and that inoculation with a mixed degrading culture can reduce the leaching of more mobile toxic intermediates.}, }
@article {pmid23706760, year = {2013}, author = {Daniel, DS and Ng, YK and Chua, EL and Arumugam, Y and Wong, WL and Kumaran, JV}, title = {Isolation and identification of gastrointestinal microbiota from the short-nosed fruit bat Cynopterus brachyotis brachyotis.}, journal = {Microbiological research}, volume = {168}, number = {8}, pages = {485-496}, doi = {10.1016/j.micres.2013.04.001}, pmid = {23706760}, issn = {1618-0623}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Bacterial Load ; Chiroptera/*microbiology ; Gastrointestinal Tract/*microbiology ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Studies on the microbial ecology of gut microbiota in bats are limited and such information is necessary in determining the ecological significance of these hosts. Short-nosed fruit bats (Cynopterus brachyotis brachyotis) are good candidates for microbiota studies given their close association with humans in urban areas. Thus, this study explores the gut microbiota of this species from Peninsular Malaysia by means of biochemical tests and 16S rRNA gene sequences analysis. The estimation of viable bacteria present in the stomach and intestine of C. b. brachyotis ranged from 3.06×10(10) to 1.36×10(15)CFU/ml for stomach fluid and 1.92×10(10) to 6.10×10(15)CFU/ml for intestinal fluid. A total of 34 isolates from the stomach and intestine of seven C. b. brachyotis were retrieved. A total of 16 species of bacteria from eight genera (Bacillus, Enterobacter, Enterococcus, Escherichia, Klebsiella, Pantoea, Pseudomonas and Serratia) were identified, Enterobacteriaceae being the most prevalent, contributing 12 out of 16 species isolated. Most isolates from the Family Enterobacteriaceae have been reported as pathogens to humans and wildlife. With the possibility of human wildlife transmission, the findings of this study focus on the importance of bats as reservoirs of potential bacterial pathogens.}, }
@article {pmid23705801, year = {2013}, author = {Ottesen, AR and González Peña, A and White, JR and Pettengill, JB and Li, C and Allard, S and Rideout, S and Allard, M and Hill, T and Evans, P and Strain, E and Musser, S and Knight, R and Brown, E}, title = {Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato).}, journal = {BMC microbiology}, volume = {13}, number = {}, pages = {114}, pmid = {23705801}, issn = {1471-2180}, mesh = {Bacteria/*classification/*genetics/isolation &amp; purification ; *Biota ; Fungi/*classification/*genetics/isolation &amp; purification ; Solanum lycopersicum/*microbiology ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Research to understand and control microbiological risks associated with the consumption of fresh fruits and vegetables has examined many environments in the farm to fork continuum. An important data gap however, that remains poorly studied is the baseline description of microflora that may be associated with plant anatomy either endemically or in response to environmental pressures. Specific anatomical niches of plants may contribute to persistence of human pathogens in agricultural environments in ways we have yet to describe. Tomatoes have been implicated in outbreaks of Salmonella at least 17 times during the years spanning 1990 to 2010. Our research seeks to provide a baseline description of the tomato microbiome and possibly identify whether or not there is something distinctive about tomatoes or their growing ecology that contributes to persistence of Salmonella in this important food crop.<br><br>RESULTS: DNA was recovered from washes of epiphytic surfaces of tomato anatomical organs; leaves, stems, roots, flowers and fruits of Solanum lycopersicum (BHN602), grown at a site in close proximity to commercial farms previously implicated in tomato-Salmonella outbreaks. DNA was amplified for targeted 16S and 18S rRNA genes and sheared for shotgun metagenomic sequencing. Amplicons and metagenomes were used to describe "native" bacterial microflora for diverse anatomical parts of Virginia-grown tomatoes.<br><br>CONCLUSIONS: Distinct groupings of microbial communities were associated with different tomato plant organs and a gradient of compositional similarity could be correlated to the distance of a given plant part from the soil. Unique bacterial phylotypes (at 95% identity) were associated with fruits and flowers of tomato plants. These include Microvirga, Pseudomonas, Sphingomonas, Brachybacterium, Rhizobiales, Paracocccus, Chryseomonas and Microbacterium. The most frequently observed bacterial taxa across aerial plant regions were Pseudomonas and Xanthomonas. Dominant fungal taxa that could be identified to genus with 18S amplicons included Hypocrea, Aureobasidium and Cryptococcus. No definitive presence of Salmonella could be confirmed in any of the plant samples, although 16S sequences suggested that closely related genera were present on leaves, fruits and roots.}, }
@article {pmid23702950, year = {2013}, author = {Raymond, B and Bonsall, MB}, title = {Cooperation and the evolutionary ecology of bacterial virulence: the Bacillus cereus group as a novel study system.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {35}, number = {8}, pages = {706-716}, doi = {10.1002/bies.201300028}, pmid = {23702950}, issn = {1521-1878}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacillus anthracis/genetics/pathogenicity ; Bacillus cereus/genetics/*pathogenicity ; Bacillus thuringiensis/genetics/*pathogenicity ; Bacteria/*pathogenicity ; Bacterial Proteins ; *Biological Evolution ; Depsipeptides/chemistry ; Ecosystem ; Host-Pathogen Interactions ; Humans ; Insect Proteins/physiology ; Phylogeny ; Quorum Sensing ; Receptors, Cell Surface/physiology ; Virulence/*genetics ; Virulence Factors ; }, abstract = {How significant is social evolution theory for the maintenance of virulence in natural populations? We assume that secreted, distantly acting virulence factors are highly likely to be cooperative public goods. Using this assumption, we discuss and critically assess the potential importance of social interactions for understanding the evolution, diversity and distribution of virulence in the Bacillus cereus group, a novel study system for microbial social biology. We conclude that dynamic equilibria in Cry toxin production, as well as strong spatial structure and population bottlenecks in hosts are the main ecological factors maintaining the cooperative secretion of virulence factors and argue that collective action has contributed to the evolution of narrow host range. Non-linearities in the benefits associated with public goods, as well as the lack of private secretion systems in the Firmicutes may also explain the prevalence and importance of distantly acting virulence factors in B. cereus and its relatives.}, }
@article {pmid23699253, year = {2013}, author = {Bokulich, NA and Bamforth, CW}, title = {The microbiology of malting and brewing.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {77}, number = {2}, pages = {157-172}, pmid = {23699253}, issn = {1098-5557}, mesh = {Beer/*microbiology ; Fermentation ; Genome, Fungal ; Hordeum/microbiology ; Phylogeny ; Saccharomyces/classification/genetics/metabolism ; }, abstract = {Brewing beer involves microbial activity at every stage, from raw material production and malting to stability in the package. Most of these activities are desirable, as beer is the result of a traditional food fermentation, but others represent threats to the quality of the final product and must be controlled actively through careful management, the daily task of maltsters and brewers globally. This review collates current knowledge relevant to the biology of brewing yeast, fermentation management, and the microbial ecology of beer and brewing.}, }
@article {pmid23689522, year = {2013}, author = {Hao, LY and Liu, X and Franchi, L}, title = {Inflammasomes in inflammatory bowel disease pathogenesis.}, journal = {Current opinion in gastroenterology}, volume = {29}, number = {4}, pages = {363-369}, doi = {10.1097/MOG.0b013e32836157a4}, pmid = {23689522}, issn = {1531-7056}, mesh = {Animals ; Bacteria/pathogenicity ; CARD Signaling Adaptor Proteins/immunology ; Colitis/immunology ; Disease Models, Animal ; Humans ; Immunity, Innate ; Inflammasomes/*immunology ; Inflammatory Bowel Diseases/*immunology/microbiology ; Microbiota/immunology ; }, abstract = {PURPOSE OF REVIEW: Inflammasomes are molecular platforms assembled in response to infection or danger signals, and they regulate the activation of caspase-1 and the maturation of the inflammatory cytokines IL-1β and IL-18. In this review, we will summarize the centrality of Nod-like receptor proteins that assemble inflammasomes and regulate intestinal homeostasis by controlling host defense responses, microbiota composition, intestinal inflammation and tissue damage.<br><br>RECENT FINDINGS: In the intestine, the innate immune system evolved to tolerate commensal microorganisms while maintaining the capacity to trigger host defense responses to invading pathogens. Recent findings suggest that inflammasomes play a critical role in the intricate interplay between the local microbial community and the mucosal immune system by sensing commensal bacteria, regulating microbial ecology, establishing the host defense response that discriminates pathogenic from commensal microbes and preventing the emergence of pathobionts. A model to reconcile the conflicting results in the literature on the role of inflammasomes in experimental colitis will be discussed.<br><br>SUMMARY: A better understanding of the relationship between inflammasome signaling and the intestinal microbiota might provide insight into the complex interaction of the innate immune system with the intestinal environment, and identify new approaches for the treatment of inflammatory bowel disease and gastrointestinal cancer.}, }
@article {pmid23686400, year = {2013}, author = {Gharsa, H and Ben Slama, K and Gómez-Sanz, E and Lozano, C and Klibi, N and Jouini, A and Messadi, L and Boudabous, A and Torres, C}, title = {Antimicrobial resistance, virulence genes, and genetic lineages of Staphylococcus pseudintermedius in healthy dogs in tunisia.}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {363-368}, pmid = {23686400}, issn = {1432-184X}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/*genetics ; Dogs/*microbiology ; *Drug Resistance, Bacterial ; Genetic Linkage ; Microbial Sensitivity Tests ; Staphylococcus/*drug effects/*genetics/isolation &amp; purification ; Tunisia ; Virulence Factors/*genetics ; }, abstract = {Nasal swabs of 100 healthy dogs were obtained in 2011 in Tunisia and tested for Staphylococcus pseudintermedius recovery. Antimicrobial resistance profile and virulence gene content were determined. Multilocus-sequence-typing (MLST) and SmaI-pulsed-field gel electrophoresis (PFGE) were investigated. S. pseudintermedius was recovered in 55 of the 100 tested samples (55 %), and one isolate per sample was further studied. All 55 S. pseudintermedius isolates were susceptible to methicillin (MSSP) but showed resistance to the following antimicrobials (% resistant isolates/resistance gene): penicillin (56.4/blaZ), tetracycline (40/tetM), trimethoprim-sulfamethoxazole (23.7), fusidic acid (9), kanamycin (3.7/aph(3´)-Ia), erythromycin-clindamycin (1.8/erm(B)), streptomycin (1.8/ant(6)-Ia), chloramphenicol (1.8) and ciprofloxacin (1.8). The following toxin genes were identified (% of isolates): lukS/F-I (98.2), expA (5.5), se-int (98.2), sec canine (1.8), siet (100), sea (5.5), seb (3.6), sec (10.9), sed (54.5), sei (5.5), sej (29.1), sek (3.6), ser (9.1), and hlg v (38.2). Ten different sequence-types were detected among 11 representative MSSP isolates: ST20, ST44, ST69, ST70, ST78, ST100, ST108, ST160, ST161, and ST162, the last three ones revealing novel alleles or allele combinations. Eleven different PFGE-patterns were identified in these isolates. The nares of healthy dogs could be a reservoir of antimicrobial resistant and virulent MSSP, highlighting the presence of the recently described exfoliating gene expA and several enterotoxin genes.}, }
@article {pmid23684992, year = {2013}, author = {Van Nevel, S and Koetzsch, S and Weilenmann, HU and Boon, N and Hammes, F}, title = {Routine bacterial analysis with automated flow cytometry.}, journal = {Journal of microbiological methods}, volume = {94}, number = {2}, pages = {73-76}, doi = {10.1016/j.mimet.2013.05.007}, pmid = {23684992}, issn = {1872-8359}, mesh = {Automation/instrumentation/*methods ; Bacteria/chemistry/*cytology ; Flow Cytometry/instrumentation/*methods ; Fluorescence ; }, abstract = {The impact of multi-well plate automation on bacterial flow cytometric analyses was investigated. Cell concentrations in up to 96 samples can be measured accurately, as long as a reproducible staining protocol and a total measurement time of below 80 min is used. Fluorescence distribution in the samples may, however, display some variability.}, }
@article {pmid23684037, year = {2013}, author = {Broadbent, JR and Brighton, C and McMahon, DJ and Farkye, NY and Johnson, ME and Steele, JL}, title = {Microbiology of Cheddar cheese made with different fat contents using a Lactococcus lactis single-strain starter.}, journal = {Journal of dairy science}, volume = {96}, number = {7}, pages = {4212-4222}, doi = {10.3168/jds.2012-6443}, pmid = {23684037}, issn = {1525-3198}, mesh = {Bacterial Load ; Cheese/analysis/*microbiology ; DNA, Bacterial/analysis ; Electrophoresis ; Fats/*analysis ; Fermentation ; Food Handling/methods ; Food Technology ; Lactobacillus/genetics/isolation &amp; purification ; Lactococcus lactis/genetics/isolation &amp; purification/*metabolism ; Lipids/analysis ; Taste ; }, abstract = {Flavor development in low-fat Cheddar cheese is typified by delayed or muted evolution of desirable flavor and aroma, and a propensity to acquire undesirable meaty-brothy or burnt-brothy off-flavor notes early in ripening. The biochemical basis for these flavor deficiencies is unclear, but flavor production in bacterial-ripened cheese is known to rely on microorganisms and enzymes present in the cheese matrix. Lipid removal fundamentally alters cheese composition, which can modify the cheese microenvironment in ways that may affect growth and enzymatic activity of starter or nonstarter lactic acid bacteria (NSLAB). Additionally, manufacture of low-fat cheeses often involves changes to processing protocols that may substantially alter cheese redox potential, salt-in-moisture content, acid content, water activity, or pH. However, the consequences of these changes on microbial ecology and metabolism remain obscure. The objective of this study was to investigate the influence of fat content on population dynamics of starter bacteria and NSLAB over 9 mo of aging. Duplicate vats of full fat, 50% reduced-fat, and low-fat (containing <6% fat) Cheddar cheeses were manufactured at 3 different locations with a single-strain Lactococcus lactis starter culture using standardized procedures. Cheeses were ripened at 8°C and sampled periodically for microbiological attributes. Microbiological counts indicated that initial populations of nonstarter bacteria were much lower in full-fat compared with low-fat cheeses made at all 3 sites, and starter viability also declined at a more rapid rate during ripening in full-fat compared with 50% reduced-fat and low-fat cheeses. Denaturing gradient gel electrophoresis of cheese bacteria showed that the NSLAB fraction of all cheeses was dominated by Lactobacillus curvatus, but a few other species of bacteria were sporadically detected. Thus, changes in fat level were correlated with populations of different bacteria, but did not appear to alter the predominant types of bacteria in the cheese.}, }
@article {pmid23681490, year = {2013}, author = {Kim, M and Heo, E and Kang, H and Adams, J}, title = {Changes in soil bacterial community structure with increasing disturbance frequency.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {171-181}, pmid = {23681490}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Ecosystem ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Little is known of the responsiveness of soil bacterial community structure to disturbance. In this study, we subjected a soil microcosm to physical disturbance, sterilizing 90 % of the soil volume each time, at a range of frequencies. We analysed the bacterial community structure using 454 pyrosequencing of the 16S rRNA gene. Bacterial diversity was found to decline with the increasing disturbance frequencies. Total bacterial abundance was, however, higher at intermediate and high disturbance frequencies, compared to low and no-disturbance treatments. Changing disturbance frequency also led to changes in community composition, with changes in overall species composition and some groups becoming abundant at the expense of others. Some phylogenetic groups were found to be relatively more disturbance-sensitive or tolerant than others. With increasing disturbance frequency, phylogenetic species variability (an index of community composition) itself became more variable from one sample to another, suggesting a greater role of chance in community composition. Compared to the tightly clustered community of the original undisturbed soil, in all the aged disturbed soils the lists of most abundant operational taxonomic units (OTUs) in each replicate were very different, suggesting a possible role of stochasticity in resource colonization and exploitation in the aged and disturbed soils. For example, colonization may be affected by whichever localized concentrations of bacterial populations happen to survive the last disturbance and be reincorporated in abundance into each pot. Overall, it appears that the soil bacterial community is very sensitive to physical disturbance, losing diversity, and that certain groups have identifiable 'high disturbance' vs. 'low disturbance' niches.}, }
@article {pmid23677009, year = {2013}, author = {von Bergen, M and Jehmlich, N and Taubert, M and Vogt, C and Bastida, F and Herbst, FA and Schmidt, F and Richnow, HH and Seifert, J}, title = {Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology.}, journal = {The ISME journal}, volume = {7}, number = {10}, pages = {1877-1885}, pmid = {23677009}, issn = {1751-7370}, mesh = {Animals ; Bacterial Proteins/*metabolism ; Carbon Isotopes/metabolism ; Ecology/*methods ; Humans ; Isotope Labeling ; Microbiota/genetics/*physiology ; Nitrogen Isotopes/metabolism ; *Proteomics ; }, abstract = {The recent development of metaproteomics has enabled the direct identification and quantification of expressed proteins from microbial communities in situ, without the need for microbial enrichment. This became possible by (1) significant increases in quality and quantity of metagenome data and by improvements of (2) accuracy and (3) sensitivity of modern mass spectrometers (MS). The identification of physiologically relevant enzymes can help to understand the role of specific species within a community or an ecological niche. Beside identification, relative and absolute quantitation is also crucial. We will review label-free and label-based methods of quantitation in MS-based proteome analysis and the contribution of quantitative proteome data to microbial ecology. Additionally, approaches of protein-based stable isotope probing (protein-SIP) for deciphering community structures are reviewed. Information on the species-specific metabolic activity can be obtained when substrates or nutrients are labeled with stable isotopes in a protein-SIP approach. The stable isotopes ((13)C, (15)N, (36)S) are incorporated into proteins and the rate of incorporation can be used for assessing the metabolic activity of the corresponding species. We will focus on the relevance of the metabolic and phylogenetic information retrieved with protein-SIP studies and for detecting and quantifying the carbon flux within microbial consortia. Furthermore, the combination of protein-SIP with established tools in microbial ecology such as other stable isotope probing techniques are discussed.}, }
@article {pmid23676925, year = {2013}, author = {Jasser, I and Królicka, A and Jakubiec, K and Chróst, RJ}, title = {Seasonal and spatial diversity of picocyanobacteria community in the Great Mazurian Lakes derived from DGGE analyses of ITS region of rDNA and cpcBAIGS [corrected] markers.}, journal = {Journal of microbiology and biotechnology}, volume = {23}, number = {6}, pages = {739-749}, doi = {10.4014/jmb.1208.08002}, pmid = {23676925}, issn = {1738-8872}, mesh = {*Biota ; Cyanobacteria/*genetics/*growth &amp; development ; DNA Fingerprinting/methods ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/*genetics ; *Genetic Variation ; Lakes/*microbiology ; *Phylogeography ; Poland ; Seasons ; }, abstract = {The seasonal and spatial diversity of picocyanobacteria (Pcy) in lakes of the Great Mazurian Lakes (GLM) system was examined by DGGE analysis of molecular markers derived from the 16S-23S internal transcribed spacer (ITS) of the ribosomal operon and the phycocyanin operon (cpcBA-IGS). The study of nine lakes, ranging from mesotrophy to hypereutrophy, demonstrated seasonal variance of Pcy. The richness and Shannon diversity index calculated on the basis of both markers were higher in spring and lower in early and late summer. No statistically significant relationships were found between the markers and trophic status of the studied lakes or Pcy abundance. There were, however, statistically significant relationships between the diversity indices and sampling time. The analysis pointed to a different distribution of the two markers. The ITS marker exhibited more unique sequences in time and space, whereas a greater role for common and ubiquitous sequences was indicated by the cpcBA-IGS data. Examination of the Pcy community structure demonstrated that communities were grouped in highly similar clusters according to sampling season/time rather than to the trophic status of the lake. Our results suggest that time is more important than trophic status in shaping the diversity and structure of Pcy communities. The seasonal changes in picocyanobacteria and differences in diversity and community structures are discussed in the context of well-established ecological hypotheses: the PEG model, intermediate disturbance hypothesis (IDH), and horizontal gene transfer (HGT).}, }
@article {pmid23673133, year = {2013}, author = {Han, Y and Ma, X and Zhao, W and Chang, Y and Zhang, X and Wang, X and Wang, J and Huang, Z}, title = {Sulfur-oxidizing bacteria dominate the microbial diversity shift during the pyrite and low-grade pyrolusite bioleaching process.}, journal = {Journal of bioscience and bioengineering}, volume = {116}, number = {4}, pages = {465-471}, doi = {10.1016/j.jbiosc.2013.04.012}, pmid = {23673133}, issn = {1347-4421}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; *Biotechnology ; Gene Library ; Hydrogen-Ion Concentration ; Iron/chemistry/*metabolism ; Manganese/chemistry/metabolism ; Manganese Compounds/chemistry/*metabolism ; Oxidation-Reduction ; Oxides/chemistry/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfides/chemistry/*metabolism ; Sulfur/*metabolism ; }, abstract = {The microbial ecology of the pyrite-pyrolusite bioleaching system and its interaction with ore has not been well-described. A 16S rRNA gene clone library was created to evaluate changes in the microbial community at different stages of the pyrite-pyrolusite bioleaching process in a shaken flask. The results revealed that the bacterial community was disturbed after 5 days of the reaction. Phylogenetic analysis of 16S rRNA sequences demonstrated that the predominant microorganisms were members of a genus of sulfur-oxidizing bacteria, Thiomonas sp., that subsequently remained dominant during the bioleaching process. Compared with iron-oxidizing bacteria, sulfur-oxidizing bacteria were more favorable to the pyrite-pyrolusite bioleaching system. Decreased pH due to microbial acid production was an important condition for bioleaching efficiency. Iron-oxidizing bacteria competed for pyrite reduction power with Mn(IV) in pyrolusite under specific conditions. These results extend our knowledge of microbial dynamics during pyrite-pyrolusite bioleaching, which is a key issue to improve commercial applications.}, }
@article {pmid23672341, year = {2013}, author = {Caron, DA}, title = {Towards a molecular taxonomy for protists: benefits, risks, and applications in plankton ecology.}, journal = {The Journal of eukaryotic microbiology}, volume = {60}, number = {4}, pages = {407-413}, doi = {10.1111/jeu.12044}, pmid = {23672341}, issn = {1550-7408}, mesh = {Ecology ; Eukaryota/classification/*genetics ; Genetic Variation/genetics ; Phylogeny ; Plankton/classification/*genetics ; }, abstract = {The increasing use of genetic information for the development of methods to study the diversity, distributions, and activities of protists in nature has spawned a new generation of powerful tools. For ecologists, one lure of these approaches lies in the potential for DNA sequences to provide the only immediately obvious means of normalizing the diverse criteria that presently exist for identifying and counting protists. A single, molecular taxonomy would allow studies of diversity across a broad range of species, as well as the detection and quantification of particular species of interest within complex, natural assemblages; goals that are not feasible using traditional methods. However, these advantages are not without their potential pitfalls and problems. Conflicts involving the species concept, disagreements over the true (physiological/ecological) meaning of genetic diversity, and a perceived threat by some that sequence information will displace knowledge regarding the morphologies, functions and physiologies of protistan taxa, have created debate and doubt regarding the efficacy and appropriateness of some genetic approaches. These concerns need continued discussion and eventual resolution as we move toward the irresistible attraction, and potentially enormous benefits, of the application of genetic approaches to protistan ecology.}, }
@article {pmid23670220, year = {2013}, author = {Blustein, J and Attina, T and Liu, M and Ryan, AM and Cox, LM and Blaser, MJ and Trasande, L}, title = {Association of caesarean delivery with child adiposity from age 6 weeks to 15 years.}, journal = {International journal of obesity (2005)}, volume = {37}, number = {7}, pages = {900-906}, pmid = {23670220}, issn = {1476-5497}, support = {UL1 RR029893/RR/NCRR NIH HHS/United States ; 1UL1RR029893/RR/NCRR NIH HHS/United States ; R01DK090989/DK/NIDDK NIH HHS/United States ; 092731/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; G9815508/MRC_/Medical Research Council/United Kingdom ; R01 DK090989/DK/NIDDK NIH HHS/United States ; }, mesh = {*Adiposity ; Adolescent ; Age of Onset ; Birth Weight ; Body Mass Index ; Breast Feeding ; Cesarean Section/*adverse effects/statistics &amp; numerical data ; Child ; Child, Preschool ; Decision Making ; Delivery, Obstetric ; Female ; Humans ; Infant ; Longitudinal Studies ; Male ; Microbiota ; Mothers ; Pediatric Obesity/*epidemiology/etiology ; Pregnancy ; Risk Factors ; Socioeconomic Factors ; United Kingdom/epidemiology ; }, abstract = {OBJECTIVES: o assess associations of caesarean section with body mass from birth through adolescence.<br><br>DESIGN: ongitudinal birth cohort study, following subjects up to 15 years of age.<br><br>SETTING AND PARTICIPANTS: Children born in 1991-1992 in Avon, UK who participated in the Avon Longitudinal Study of Parents and Children (ALSPAC) (n=10&#x2009;219).<br><br>PRIMARY OUTCOME: standardized measures of body mass (weight-for length z-scores at 6 weeks, 10 and 20 months; and body mass index (BMI) z-scores at 38 months, 7, 9, 11 and 15 years). Secondary outcome: categorical overweight or obese (BMI: 85th percentile) for age and gender, at 38 months, 7, 9, 11 and 15 years.<br><br>RESULTS: Of the 10&#x2009;219 children, 926 (9.06%) were delivered by caesarean section. Those born by caesarean had lower-birth weights than those born vaginally (-46.1&#x2009;g, 95% confidence interval(CI): 14.6-77.6&#x2009;g; P=0.004). In mixed multivariable models adjusting for birth weight, gender, parental body mass, family sociodemographics, gestational factors and infant feeding patterns, caesarean delivery was consistently associated with increased adiposity, starting at 6 weeks (+0.11&#x2009;s.d. units, 95% CI: 0.03-0.18; P=0.005), through age 15 (BMI z-score increment+0.10&#x2009;s.d. units, 95% CI: 0.001-0.198; P=0.042). By age 11 caesarean-delivered children had 1.83 times the odds of overweight or obesity (95% CI: 1.24-2.70; P=0.002). When the sample was stratified by maternal pre-pregnancy weight, the association among children born of overweight/obese mothers was strong and long-lasting. In contrast, evidence of an association among children born of normal-weight mothers was weak.<br><br>CONCLUSION: Cesarean delivery is associated with increased body mass in childhood and adolescence. Research is needed to further characterize the association in children of normal weight women. Additional work is also needed to understand the mechanism underlying the association, which may involve relatively enduring changes in the intestinal microbiome.}, }
@article {pmid23669449, year = {2013}, author = {Harish, A and Tunlid, A and Kurland, CG}, title = {Rooted phylogeny of the three superkingdoms.}, journal = {Biochimie}, volume = {95}, number = {8}, pages = {1593-1604}, doi = {10.1016/j.biochi.2013.04.016}, pmid = {23669449}, issn = {1638-6183}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Eukaryota/*classification/genetics ; Evolution, Molecular ; *Phylogeny ; }, abstract = {The traditional bacterial rooting of the three superkingdoms in sequence-based gene trees is inconsistent with new phylogenetic reconstructions based on genome content of compact protein domains. We find that protein domains at the level of the SCOP superfamily (SF) from sequenced genomes implement with maximum parsimony fully resolved rooted trees. Such genome content trees identify archaea and bacteria (akaryotes) as sister clades that diverge from an akaryote common ancestor, LACA. Several eukaryote sister clades diverge from a eukaryote common ancestor, LECA. LACA and LECA descend in parallel from the most recent universal common ancestor (MRUCA), which is not a bacterium. Rather, MRUCA presents 75% of the unique SFs encoded by extant genomes of the three superkingdoms, each encoding a proteome that partially overlaps all others. This alone implies that the common ancestor to the superkingdoms was very complex. Such ancestral complexity is confirmed by phylogenetic reconstructions. In addition, the divergence of proteomes from the complex ancestor in each superkingdom is both reductive in numbers of unique SFs as well as cumulative in the abundance of surviving SFs. These data suggest that the common ancestor was not the first cell lineage and that modern global phylogeny is the crown of a "recently" re-rooted tree. We suggest that a bottlenecked survivor of an environmental collapse, which preceded the flourishing of the modern crown, seeded the current phylogenetic tree.}, }
@article {pmid23667538, year = {2013}, author = {Wang, S and Hou, W and Dong, H and Jiang, H and Huang, L and Wu, G and Zhang, C and Song, Z and Zhang, Y and Ren, H and Zhang, J and Zhang, L}, title = {Control of temperature on microbial community structure in hot springs of the Tibetan Plateau.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e62901}, pmid = {23667538}, issn = {1932-6203}, mesh = {Biodiversity ; Chloroflexi/classification/genetics ; Cyanobacteria/classification/genetics ; Geologic Sediments/microbiology ; High-Throughput Nucleotide Sequencing ; Hot Springs/*microbiology ; Linear Models ; Soil Microbiology ; *Temperature ; Tibet ; }, abstract = {The Tibetan Plateau in Northwest China hosts a number of hot springs that represent a biodiversity hotspot for thermophiles, yet their diversity and relationship to environmental conditions are poorly explored in these habitats. In this study we investigated microbial diversity and community composition in 13 Tibetan hot springs with a wide range of temperatures (22.1-75°C) and other geochemical conditions by using the 16S rRNA gene pyrosequencing approach. Bacteria (10(8)-10(11) copy/g; 42 bacterial phyla) in Tibetan hot springs were more abundant and far more diverse than Archaea (10(7)-10(10) copy/g; 5 archaeal phyla). The dominant bacterial phyla systematically varied with temperature. Moderate temperatures (75-66°C) favored Aquificae, GAL35, and novel Bacteria, whereas low temperatures (60-22.1°C) selected for Deinococcus-Thermus, Cyanobacteria, and Chloroflexi. The relative abundance of Aquificae was correlated positively with temperature, but the abundances of Deinococcus-Thermus, Cyanobacteria, and Chloroflexi were negatively correlated with temperature. Cyanobacteria and Chloroflexi were abundant in Tibetan hot springs and their abundances were positively correlated at low temperatures (55-43°C) but negatively correlated at moderate temperatures (75-55°C). These correlation patterns suggest a complex physiological relationship between these two phyla. Most archaeal sequences were related to Crenarchaeota with only a few related to Euryarchaeota and Thaumarchaeota. Despite the fact that microbial composition in Tibetan hot springs was strongly shaped by temperature, microbial diversity (richness, evenness and Shannon diversity) was not significantly correlated with temperature change. The results of this study expand our current understanding of microbial ecology in Tibetan hot springs and provide a basis for a global comparison.}, }
@article {pmid23667421, year = {2013}, author = {Mitchell, JG and Seuront, L and Doubell, MJ and Losic, D and Voelcker, NH and Seymour, J and Lal, R}, title = {The role of diatom nanostructures in biasing diffusion to improve uptake in a patchy nutrient environment.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e59548}, pmid = {23667421}, issn = {1932-6203}, mesh = {Biological Transport ; Cell Membrane/metabolism ; Cell Wall/metabolism ; Diatoms/*cytology/*metabolism ; Diffusion ; *Environment ; Extracellular Space/metabolism ; *Nanostructures ; Phytoplankton/metabolism ; }, abstract = {BACKGROUND: Diatoms are important single-celled autotrophs that dominate most lit aquatic environments and are distinguished by surficial frustules with intricate designs of unknown function.<br><br>PRINCIPAL FINDINGS: We show that some frustule designs constrain diffusion to positively alter nutrient uptake. In nutrient gradients of 4 to 160 times over <5 cm, the screened-chambered morphology of Coscincodiscus sp. biases the nutrient diffusion towards the cell by at least 3.8 times the diffusion to the seawater. In contrast, the open-chambers of Thalassiosira eccentrica produce at least a 1.3 times diffusion advantage to the membrane over Coscincodiscus sp. when nutrients are homogeneous.<br><br>SIGNIFICANCE: Diffusion constraint explains the success of particular diatom species at given times and the overall success of diatoms. The results help answer the unresolved question of how adjacent microplankton compete. Furthermore, diffusion constraint by supramembrane nanostructures to alter molecular diffusion suggests that microbes compete via supramembrane topology, a competitive mechanism not considered by the standard smooth-surface equations used for nutrient uptake nor in microbial ecology and cell physiology.}, }
@article {pmid23666270, year = {2013}, author = {Aguilera, M and Vergara, P and Martínez, V}, title = {Environment-related adaptive changes of gut commensal microbiota do not alter colonic toll-like receptors but modulate the local expression of sensory-related systems in rats.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {232-243}, pmid = {23666270}, issn = {1432-184X}, mesh = {Adaptation, Physiological ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Cecum/microbiology/physiology ; Colon/microbiology/*physiology ; Ecosystem ; Gene Expression ; Humans ; Male ; *Microbiota ; Rats ; Rats, Sprague-Dawley ; Receptors, Pattern Recognition/*genetics/metabolism ; *Symbiosis ; Toll-Like Receptors/*genetics/metabolism ; }, abstract = {Pathogenic and protective roles have been attributed to gut commensal microbiota (GCM) in gastrointestinal inflammatory and functional disorders. We have shown that the adaptation to a new environment implies specific changes in the composition of GCM. Here we assessed if environment-related adaptive changes of GCM modulate the expression of colonic Toll-like receptors (TLRs) and sensory-related systems in rats. Adult male SD rats were maintained under different environmental conditions: barrier-breed-and-maintained, barrier-breed adapted to conventional conditions or conventional-breed-and-maintained. Fluorescent in situ hybridization and real-time quantitative PCR (qPCR) were used to characterize luminal ceco-colonic microbiota. Colonic expression of TLR2, TLR4, TLR5, and TLR7, cannabinoid receptors (CB1/CB2), μ-opioid receptor (MOR), transient receptor potential vanilloid (TRPV1, TRPV3, and TRPV4), protease-activated receptor 2 (PAR-2), and calcitonin gene-related peptide were quantified by RT-qPCR. CB1, CB2 and MOR expression, was evaluated also by immunohistochemistry. In rats, housing-related environmental conditions induce specific changes of GCM, without impact on the expression of TLR-dependent bacterial recognition systems. Expression of sensory-related markers (MOR, TRPV3, PAR-2, and CB2) decreased with the adaptation to a conventional environment, correlating with changes in Bacteroides spp., Lactobacillus spp., and Bifidobacterium spp. counts. This suggests an interaction between GCM and visceral sensory mechanisms, which might be part of the mechanisms underlying the beneficial effects of some bacterial groups on functional and inflammatory gastrointestinal disorders.}, }
@article {pmid23666241, year = {2013}, author = {Jolitz, RD and McKay, CP}, title = {Quantitative 3D model of light transmittance through translucent rocks applied to the hypolithic microbial community.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {112-119}, pmid = {23666241}, issn = {1432-184X}, mesh = {Bacteria/chemistry/*radiation effects ; Geologic Sediments/chemistry/*microbiology ; Light ; Models, Theoretical ; }, abstract = {In extreme desert environments, photosynthetic microorganisms often live on the buried undersides of translucent rocks. Computing the light level reaching these locations requires 3D modeling of a finite rock. We report on Monte Carlo calculations of skylight and sunlight transmission through a partially buried flat cylindrical rock using one billion photons per simulation. Transmitted light level drops inversely with increasing rock opacity, as expected for purely scattering media. For a half-buried rock with an extinction coefficient of 0.1 cm(-1) (opacity of 0.2), transmission at the bottom is 64 % for sunlight at a solar zenith angle of 60° and 82 % for skylight. Transmitted light level increases slowly with increasing scattering asymmetry factor of the rock independent of illumination or depth buried. Transmitted sunlight at zenith through a thick half-buried rock (opacity of 0.6) is six times brighter at the bottom than the subsurface sides. Skylight transmits equally to the subsurface sides and bottom. When the sun is not straight overhead, the sunward side of the rock is brighter than the underside of the rock. Compared to the sunlight transmitted to the bottom, transmitted sunlight inclined at 60° is 24 times brighter at the subsurface side towards the sun and 14 times brighter at the subsurface side 70° away from the sun. Transmitted sunlight emitted from zenith and skylight is uniformly bright at the bottom regardless of how deeply the rock is buried. Sunlight not at zenith transmits preferentially to the sunward bottom edge depending on the depth the rock is buried.}, }
@article {pmid23663004, year = {2013}, author = {Futai, K}, title = {Pine wood nematode, Bursaphelenchus xylophilus.}, journal = {Annual review of phytopathology}, volume = {51}, number = {}, pages = {61-83}, doi = {10.1146/annurev-phyto-081211-172910}, pmid = {23663004}, issn = {1545-2107}, mesh = {Animals ; Coleoptera/*parasitology ; Disease Resistance ; Helminth Proteins/metabolism ; Host-Parasite Interactions ; Insect Vectors/*parasitology ; Pinus/cytology/immunology/*parasitology/physiology ; Plant Diseases/immunology/*parasitology ; Trees ; Tylenchida/enzymology/growth &amp; development/pathogenicity/*physiology ; }, abstract = {After devastating vast areas of pine forests in Asian countries, the pine wilt disease spread into European forests in 1999 and is causing worldwide concern. This disease involves very complicated interactions between a pathogenic nematode, its vector beetle, host pine species, and fungi in dead hosts. Pathogenicity of the pine wood nematode is determined not only by its physical and chemical traits but also by its behavioral traits. Most life history traits of the pine wood nematode, such as its phoretic relationship with vector beetles, seem to be more effective in virulent than in avirulent isolates or species. As the pathogenicity determinants, secreted enzymes, and surface coat proteins are very important, they have therefore been studied intensively. The mechanism of quick death of a large pine tree as a result of infection by a tiny nematode could be ascribed to the dysfunction of the water-conducting system caused by the death of parenchyma cells, which must have originally evolved as an inherent resistant system.}, }
@article {pmid23662775, year = {2013}, author = {Stecher, B and Berry, D and Loy, A}, title = {Colonization resistance and microbial ecophysiology: using gnotobiotic mouse models and single-cell technology to explore the intestinal jungle.}, journal = {FEMS microbiology reviews}, volume = {37}, number = {5}, pages = {793-829}, doi = {10.1111/1574-6976.12024}, pmid = {23662775}, issn = {1574-6976}, mesh = {Animals ; Computational Biology ; *Germ-Free Life ; Intestines/*microbiology ; Isotope Labeling ; Mice ; *Microbiota ; *Models, Animal ; Single-Cell Analysis/*methods ; Symbiosis ; }, abstract = {The highly diverse intestinal microbiota forms a structured community engaged in constant communication with itself and its host and is characterized by extensive ecological interactions. A key benefit that the microbiota affords its host is its ability to protect against infections in a process termed colonization resistance (CR), which remains insufficiently understood. In this review, we connect basic concepts of CR with new insights from recent years and highlight key technological advances in the field of microbial ecology. We present a selection of statistical and bioinformatics tools used to generate hypotheses about synergistic and antagonistic interactions in microbial ecosystems from metagenomic datasets. We emphasize the importance of experimentally testing these hypotheses and discuss the value of gnotobiotic mouse models for investigating specific aspects related to microbiota-host-pathogen interactions in a well-defined experimental system. We further introduce new developments in the area of single-cell analysis using fluorescence in situ hybridization in combination with metabolic stable isotope labeling technologies for studying the in vivo activities of complex community members. These approaches promise to yield novel insights into the mechanisms of CR and intestinal ecophysiology in general, and give researchers the means to experimentally test hypotheses in vivo at varying levels of biological and ecological complexity.}, }
@article {pmid23658819, year = {2013}, author = {Li, J and Zheng, Y and Yan, J and Li, H and Wang, X and He, J and Ding, G}, title = {Effects of different regeneration scenarios and fertilizer treatments on soil microbial ecology in reclaimed opencast mining areas on the Loess Plateau, China.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e63275}, pmid = {23658819}, issn = {1932-6203}, mesh = {Biodiversity ; China ; *Ecological and Environmental Phenomena ; *Fertilizers ; *Mining ; Plants/classification ; Polymorphism, Restriction Fragment Length ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {The soil microbial community in reclaimed mining areas is fundamental to vegetative establishment. However, how this community responds to different regeneration scenarios and fertilizer treatments is poorly understood. This research evaluated plant and soil microbial communities from different regeneration scenarios and different fertilizer treatments. Regeneration scenarios significantly influenced soil bacterial, archaeal, and fungal rDNA abundance. The ratios of fungi to bacteria or archaea were increased with fertilizer application. The diversity of both plants and microbes was lowest in Lotus corniculatus grasslands. Regeneration scenario, fertilizer treatment, and their interaction influenced soil microbial richness, diversity and evenness indices. Labile carbon pool 2 was a significant factor affected plant and microbe communities in July, suggesting that plants and microbes may be competing for nutrients. The higher ratios of positive to negative association were found in soil bacteria and total microbe than in archaea and fungi. Stronger clustering of microbial communities from the same regeneration scenario indicated that the vegetative composition of regeneration site may have a greater influence on soil microbial communities than fertilizer treatment.}, }
@article {pmid23657544, year = {2013}, author = {Castellani, F and Ghidini, V and Tafi, MC and Boaretti, M and Lleo, MM}, title = {Fate of pathogenic bacteria in microcosms mimicking human body sites.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {224-231}, pmid = {23657544}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/pharmacology ; Ascitic Fluid/chemistry/*microbiology ; Bacterial Infections/*microbiology ; Enterococcus faecalis/drug effects/*physiology ; Escherichia coli/drug effects/*physiology ; Humans ; Microbial Viability ; Synovial Fluid/chemistry/*microbiology ; }, abstract = {During the infectious process, pathogens may reach anatomical sites where they are exposed to substances interfering with their growth. These substances can include molecules produced by the host, and his resident microbial population, as well as exogenous antibacterial drugs. Suboptimal concentrations of inhibitory molecules and stress conditions found in vivo (high or low temperatures, lack of oxygen, extreme pH) might induce in bacteria the activation of survival mechanisms blocking their division capability but allowing them to stay alive. These "dormant" bacteria can be reactivated in particular circumstances and would be able to express their virulence traits. In this study, it was evaluated the effect of some environmental conditions, such as optimal and suboptimal temperatures, direct light and antibiotic sub-inhibitory concentrations doses of antibiotic, on the human pathogens Escherichia coli and Enterococcus faecalis when incubated in fluids accumulated in the body of patients with different pathologies. It is shown that inoculation in a number of accumulated body fluids and the presence of gentamicin, reliable conditions encountered during pathological states, induce stress-responding strategies enabling bacteria to persist in microcosms mimicking the human body. Significant differences were detected in Gram-negative and Gram-positive species with E. faecalis surviving, as starved or viable but non-culturable forms, in any microcosm and condition tested and E. coli activating a viable but non-culturable state only in some clinical samples. The persistence of bacteria under these conditions, being non-culturable, might explain some recurrent infections without isolation of the causative agent after application of the standard microbiological methods.}, }
@article {pmid23657248, year = {2013}, author = {Carlisle, EM and Morowitz, MJ}, title = {The intestinal microbiome and necrotizing enterocolitis.}, journal = {Current opinion in pediatrics}, volume = {25}, number = {3}, pages = {382-387}, doi = {10.1097/MOP.0b013e3283600e91}, pmid = {23657248}, issn = {1531-698X}, mesh = {Child ; Enterocolitis, Necrotizing/*microbiology/therapy ; Feces/microbiology ; Host-Pathogen Interactions ; Humans ; Infant, Newborn ; Infant, Premature ; Infant, Premature, Diseases/*microbiology/therapy ; Intestines/*microbiology ; *Microbiota ; Probiotics/therapeutic use ; }, abstract = {PURPOSE OF REVIEW: Necrotizing enterocolitis (NEC) continues to be a major cause of morbidity and mortality in low birth weight infants. Although decades of research point to a role for gut bacteria in the pathogenesis of the disease, the exact relationship between microbes and NEC has not been elucidated. In this review, we describe recent advances in the use of molecular methods to compare gut bacteria in infants with and without NEC.<br><br>RECENT FINDINGS: Our understanding of how bacteria contribute to NEC pathogenesis has been limited by the use of traditional, culture-based investigations. Recent advances in microbial ecology and DNA sequencing have made it possible to comprehensively study gut bacterial populations and to understand their physiologic importance. Several studies have identified differences in the microbiota among infants with and without NEC, but the findings have often varied across studies.<br><br>SUMMARY: To date, no single change in the gut microbiota has definitively been identified as a risk factor or cause of NEC. The findings at present suggest that NEC does not result from growth of a single causative pathogen, but rather that the disease results from a generalized disturbance of normal colonization patterns in the developing gut.}, }
@article {pmid23656310, year = {2013}, author = {Van Nevel, S and De Roy, K and Boon, N}, title = {Bacterial invasion potential in water is determined by nutrient availability and the indigenous community.}, journal = {FEMS microbiology ecology}, volume = {85}, number = {3}, pages = {593-603}, doi = {10.1111/1574-6941.12145}, pmid = {23656310}, issn = {1574-6941}, mesh = {Acetates/metabolism ; Carbon/metabolism ; Drinking Water/*microbiology ; Microbial Interactions ; Microbial Viability ; Nitrogen/metabolism ; Phosphates/metabolism ; Pseudomonas putida/*growth &amp; development/metabolism ; *Water Microbiology ; Water Purification ; }, abstract = {In drinking water (DW) and the distribution systems, bacterial growth and biofilm formation have to be controlled both for limiting taste or odour development and preventing clogging or biocorrosion problems. After a contamination with undesired bacteria, factors like nutrient availability and temperature will influence the survival of these invaders. Understanding the conditions enabling invaders to proliferate is essential for a holistic approach towards microbial risk assessment in DW. Pseudomonas putida was used as a model invader because this easy-growing bacterium can use a wide range of substrates. Invasion experiments in oligo- to eutrophic waters showed the requirement of both a carbon and phosphate source for survival of P. putida in DW. Addition of C, N and P enabled P. putida to grow in DW from 5.80 × 10(4) to 1.84 × 10(8) cells mL(-1) and survive for at least 12 days. However, in surface water with similar nutrient concentrations, P. putida did not survive, indicating the concomitant importance of the present indigenous microbial community of the specific water sample. Either extensive carbon or phosphate limitation can be used in water treatment design in order to obtain a DW which is not susceptible for unwanted bacterial growth.}, }
@article {pmid23653046, year = {2013}, author = {Benito, D and Lozano, C and Gómez-Sanz, E and Zarazaga, M and Torres, C}, title = {Detection of methicillin-susceptible Staphylococcus aureus ST398 and ST133 strains in gut microbiota of healthy humans in Spain.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {105-111}, pmid = {23653046}, issn = {1432-184X}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Carrier State/microbiology ; Child ; Child, Preschool ; Feces/*microbiology ; Female ; Gastrointestinal Tract/microbiology ; Humans ; Male ; Methicillin-Resistant Staphylococcus aureus/classification/drug effects/genetics/*isolation &amp; purification ; Microbial Sensitivity Tests ; Middle Aged ; Multilocus Sequence Typing ; Spain ; Virulence Factors/genetics ; Young Adult ; }, abstract = {Fecal samples of 100 healthy humans were tested for Staphylococcus aureus recovery. Fifteen samples (15 %) contained S. aureus, all methicillin-susceptible (MSSA), being one isolate/sample further studied. These 15 isolates were characterized by spa and agr typing as well as multi-locus sequence typing. High diversity of spa types (n = 11) and sequences types (n = 8) was detected. Two S. aureus of lineages ST398 or ST133 were detected, and six isolates were ascribed to clonal complex 30 (CC30). Strains were susceptible to most of the 17 antimicrobial agents tested with exceptions: erythromycin/clindamycin (three strains, containing erm(C) and/or erm(A) + mph(C) genes) and tobramycin and mupirocin (one strain containing ant(4')-Ia + mup(A) genes). The presence of 18 staphylococcal enterotoxin genes was studied by PCR, and isolates were negative for lukF/lukS-PV genes, although strain ST133 harbored the lukD-lukE + lukM genes. Other virulence genes detected were (number of strains): tsst-1 (6), hla (15), hlb (9), hld (15), hlg (6), hlgv (9), cna (2), aur (14), and egc-like cluster (3). Analysis of immune evasion cluster genes showed six types, highlighting their absence in two strains of lineages ST133 and ST5. A high clonal diversity of MSSA strains was identified in the intestinal microbiota of healthy humans, being CC30 the most frequent one. This is the first report of MSSA ST133 and ST398 isolates in gut microbiota of healthy humans.}, }
@article {pmid23649297, year = {2013}, author = {Jiang, XT and Peng, X and Deng, GH and Sheng, HF and Wang, Y and Zhou, HW and Tam, NF}, title = {Illumina sequencing of 16S rRNA tag revealed spatial variations of bacterial communities in a mangrove wetland.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {96-104}, pmid = {23649297}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; DNA, Bacterial/*genetics ; Ecosystem ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Rhizosphere ; Wetlands ; }, abstract = {The microbial community plays an essential role in the high productivity in mangrove wetlands. A proper understanding of the spatial variations of microbial communities will provide clues about the underline mechanisms that structure microbial groups and the isolation of bacterial strains of interest. In the present study, the diversity and composition of the bacterial community in sediments collected from four locations, namely mudflat, edge, bulk, and rhizosphere, within the Mai Po Ramsar Wetland in Hong Kong, SAR, China were compared using the barcoded Illumina paired-end sequencing technique. Rarefaction results showed that the bulk sediment inside the mature mangrove forest had the highest bacterial α-diversity, while the mudflat sediment without vegetation had the lowest. The comparison of β-diversity using principal component analysis and principal coordinate analysis with UniFrac metrics both showed that the spatial effects on bacterial communities were significant. All sediment samples could be clustered into two major groups, inner (bulk and rhizosphere sediments collected inside the mangrove forest) and outer mangrove sediments (the sediments collected at the mudflat and the edge of the mangrove forest). With the linear discriminate analysis scores larger than 3, four phyla, namely Actinobacteria, Acidobacteria, Nitrospirae, and Verrucomicrobia, were enriched in the nutrient-rich inner mangrove sediments, while abundances of Proteobacteria and Deferribacterias were higher in outer mangrove sediments. The rhizosphere effect of mangrove plants was also significant, which had a lower α-diversity, a higher amount of Nitrospirae, and a lower abundance of Proteobacteria than the bulk sediment nearby.}, }
@article {pmid23645316, year = {2013}, author = {Walter, J and Martínez, I and Rose, DJ}, title = {Holobiont nutrition: considering the role of the gastrointestinal microbiota in the health benefits of whole grains.}, journal = {Gut microbes}, volume = {4}, number = {4}, pages = {340-346}, pmid = {23645316}, issn = {1949-0984}, mesh = {*Diet ; *Edible Grain ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; *Metagenome ; }, abstract = {Intake of whole grains and other food products high in dietary fiber have long been linked to the prevention of chronic diseases associated with inflammation. A contribution of the gastrointestinal microbiota to these effects has been suggested, but little is known on how whole grains interact with gut bacteria. We have recently published the first human trial that made use of next-generation sequencing to determine the effect of whole grains (whole grain barley, brown rice or a mixture of the two) on fecal microbiota structure and tested for associations between the gut microbiota and blood markers of inflammation, glucose and lipid metabolism. Our study revealed that whole grains impacted gut microbial ecology by increasing microbial diversity and inducing compositional alterations, some of which are considered to have beneficial effects on the host. Interestingly, whole grains, and in particular the combination of whole grain barley and brown rice, caused a reduction in plasma interleukin-6 (IL-6), which was linked to compositional features of the gut microbiota. Therefore, the study provided evidence that a short-term increased intake of whole grains led to compositional alterations of the gut microbiota that coincided with improvements in systemic inflammation. In this addendum, we summarize the findings of the study and provide a perspective on the importance of regarding humans as holobionts when considering the health effects of dietary strategies.}, }
@article {pmid23645201, year = {2013}, author = {Gunnigle, E and McCay, P and Fuszard, M and Botting, CH and Abram, F and O'Flaherty, V}, title = {A functional approach to uncover the low-temperature adaptation strategies of the archaeon Methanosarcina barkeri.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {14}, pages = {4210-4219}, pmid = {23645201}, issn = {1098-5336}, mesh = {Acetic Acid/metabolism ; Adaptation, Physiological ; Bacterial Proteins/*metabolism ; Bioreactors/microbiology ; Carbon Dioxide/metabolism ; Chromatography, Liquid ; Cold Temperature ; Cold-Shock Response ; Electrophoresis, Gel, Two-Dimensional ; Hydrogen/metabolism ; Methanol/metabolism ; Methanosarcina barkeri/growth &amp; development/*physiology ; Proteome/*metabolism ; Tandem Mass Spectrometry ; }, abstract = {Low-temperature anaerobic digestion (LTAD) technology is underpinned by a diverse microbial community. The methanogenic archaea represent a key functional group in these consortia, undertaking CO2 reduction as well as acetate and methylated C1 metabolism with subsequent biogas (40 to 60% CH4 and 30 to 50% CO2) formation. However, the cold adaptation strategies, which allow methanogens to function efficiently in LTAD, remain unclear. Here, a pure-culture proteomic approach was employed to study the functional characteristics of Methanosarcina barkeri (optimum growth temperature, 37°C), which has been detected in LTAD bioreactors. Two experimental approaches were undertaken. The first approach aimed to characterize a low-temperature shock response (LTSR) of M. barkeri DSMZ 800(T) grown at 37°C with a temperature drop to 15°C, while the second experimental approach aimed to examine the low-temperature adaptation strategies (LTAS) of the same strain when it was grown at 15°C. The latter experiment employed cell viability and growth measurements (optical density at 600 nm [OD600]), which directly compared M. barkeri cells grown at 15°C with those grown at 37°C. During the LTSR experiment, a total of 127 proteins were detected in 37°C and 15°C samples, with 20 proteins differentially expressed with respect to temperature, while in the LTAS experiment 39% of proteins identified were differentially expressed between phases of growth. Functional categories included methanogenesis, cellular information processing, and chaperones. By applying a polyphasic approach (proteomics and growth studies), insights into the low-temperature adaptation capacity of this mesophilically characterized methanogen were obtained which suggest that the metabolically diverse Methanosarcinaceae could be functionally relevant for LTAD systems.}, }
@article {pmid23640276, year = {2013}, author = {Li, YF and Wei, S and Yu, Z}, title = {Feedstocks affect the diversity and distribution of propionate CoA-transferase genes (pct) in anaerobic digesters.}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {351-362}, pmid = {23640276}, issn = {1432-184X}, mesh = {Amino Acid Sequence ; Anaerobiosis ; Bacteria/classification/enzymology/genetics/*isolation &amp; purification ; Bacterial Proteins/chemistry/*genetics ; *Biodiversity ; Bioreactors/*microbiology ; Coenzyme A-Transferases/chemistry/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sewage/*chemistry/microbiology ; }, abstract = {Anaerobic digestion (AD) is an attractive microbiological technology for both waste treatment and energy production. Syntrophic acetogenic bacteria are an important guild because they are essential for maintaining efficient and stable AD operation. However, this guild is poorly understood due to difficulties to culture them. In this study, we developed specific PCR assays targeting the propionate-CoA transferase genes (pct) to investigate their diversity and distribution in several mesophilic anaerobic digesters and a bench-scale temperature-phased AD (TPAD) system. Phylogenetic analysis of sequenced pct amplicons revealed the occurrence of Syntrophobacter fumaroxidans and six other clusters of putative pct genes. Principal coordinate analysis (PCoA) showed that pct diversity and abundance were largely correlated to the feedstocks of the digesters, while little difference was seen between the granular and the liquid fractions of each digester or between the two digesters of the TPAD system. Cluster-specific qPCR analysis revealed major impact of feedstocks and fractions on the abundance of pct genes. Readily fermentable substrates such as sugar- or starch-rich feedstocks selected for pct genes (Cluster I) related to Syntrophobacter, while manure feedstock selected for pct clusters related to pct of Clostridium spp. These results suggest that propionate metabolism can be affected by feedstocks and partition differently between solid and liquid phases in digesters. The PCR assays developed in this study may serve as a tool to investigate propionate-oxidizing bacteria in anaerobic digesters and other anaerobic environments.}, }
@article {pmid23640275, year = {2013}, author = {Rizoulis, A and Elliott, DR and Rolfe, SA and Thornton, SF and Banwart, SA and Pickup, RW and Scholes, JD}, title = {Diversity of planktonic and attached bacterial communities in a phenol-contaminated sandstone aquifer.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {84-95}, pmid = {23640275}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; *Biodiversity ; Ecosystem ; Fresh Water/analysis/microbiology ; Geologic Sediments/analysis/*microbiology ; Groundwater/analysis/*microbiology ; Molecular Sequence Data ; Phenol/analysis/*metabolism ; Phenols/*analysis/metabolism ; Phylogeny ; Plankton/classification/genetics/isolation &amp; purification/*metabolism ; Water Pollutants, Chemical/analysis/metabolism ; }, abstract = {Polluted aquifers contain indigenous microbial communities with the potential for in situ bioremediation. However, the effect of hydrogeochemical gradients on in situ microbial communities (especially at the plume fringe, where natural attenuation is higher) is still not clear. In this study, we used culture-independent techniques to investigate the diversity of in situ planktonic and attached bacterial communities in a phenol-contaminated sandstone aquifer. Within the upper and lower plume fringes, denaturing gradient gel electrophoresis profiles indicated that planktonic community structure was influenced by the steep hydrogeochemical gradient of the plume rather than the spatial location in the aquifer. Under the same hydrogeochemical conditions (in the lower plume fringe, 30 m below ground level), 16S rRNA gene cloning and sequencing showed that planktonic and attached bacterial communities differed markedly and that the attached community was more diverse. The 16S rRNA gene phylogeny also suggested that a phylogenetically diverse bacterial community operated at this depth (30 mbgl), with biodegradation of phenolic compounds by nitrate-reducing Azoarcus and Acidovorax strains potentially being an important process. The presence of acetogenic and sulphate-reducing bacteria only in the planktonic clone library indicates that some natural attenuation processes may occur preferentially in one of the two growth phases (attached or planktonic). Therefore, this study has provided a better understanding of the microbial ecology of this phenol-contaminated aquifer, and it highlights the need for investigating both planktonic and attached microbial communities when assessing the potential for natural attenuation in contaminated aquifers.}, }
@article {pmid23640274, year = {2013}, author = {Lalande, J and Villemur, R and Deschênes, L}, title = {A new framework to accurately quantify soil bacterial community diversity from DGGE.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {647-658}, pmid = {23640274}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Denaturing gradient gel electrophoresis (DGGE) has been and remains extensively used to assess and monitor the effects of various treatments on soil bacterial communities. Considering only abundant phylotypes, the diversity estimates produced by this technique have been proven to be uncorrelated to true community diversity. The aim of this paper was to develop a framework to estimate a community's true diversity from DGGE. Developed using in silico DGGE profiles generated from published pyrosequencing datasets, this framework elongates the rank-abundance distributions (RADs) drawn by band quantification using the peak-to-signal ratio (PSR) parameter, which was proven to be related to bacterial richness. The ability to compare DGGE-based diversity estimates to the true diversity of communities led to a unique opportunity to identify potential pitfalls when analyzing DGGE gels with commercial analysis software programs and gain insight into the process of DNA band clustering in the profiles. Bacterial diversity was compared through richness, Shannon, and Simpson's 1/D indices. Intermediate results demonstrated that, even though commercial gel analysis software programs were unable to produce consistent results throughout all samples, a newly developed Matlab-based framework unraveled the dominance profiles of communities from band quantification. Elongating these partial RADs using the PSRs extracted from the DGGE profiles chiefly made it possible to accurately estimate the true diversity of communities. For all the samples analyzed, the estimated Shannon and Simpson's 1/D were accurate at ±10 %. Richness estimations were less accurate, ranging from -11 to 31 % of the expected values. The framework showed great potential to study the structure and diversity of soil bacterial communities.}, }
@article {pmid23639548, year = {2013}, author = {Kiarie, E and Romero, LF and Nyachoti, CM}, title = {The role of added feed enzymes in promoting gut health in swine and poultry.}, journal = {Nutrition research reviews}, volume = {26}, number = {1}, pages = {71-88}, doi = {10.1017/S0954422413000048}, pmid = {23639548}, issn = {1475-2700}, mesh = {6-Phytase/administration &amp; dosage ; *Animal Feed ; Animals ; Bacteria ; Diet ; Digestion ; Energy Metabolism/physiology ; Enzymes/*administration &amp; dosage ; Gastrointestinal Tract/*microbiology ; Glycoside Hydrolases/administration &amp; dosage/metabolism ; *Health Promotion ; Microbiota/physiology ; Oligosaccharides/metabolism ; Peptide Hydrolases/administration &amp; dosage/metabolism ; Poultry/*physiology ; Poultry Diseases/microbiology/prevention &amp; control ; Prebiotics ; Swine/*physiology ; Swine Diseases/microbiology/prevention &amp; control ; }, abstract = {The value of added feed enzymes (FE) in promoting growth and efficiency of nutrient utilisation is well recognised in single-stomached animal production. However, the effects of FE on the microbiome of the gastrointestinal tract (GIT) are largely unrecognised. A critical role in host nutrition, health, performance and quality of the products produced is played by the intestinal microbiota. FE can make an impact on GIT microbial ecology by reducing undigested substrates and anti-nutritive factors and producing oligosaccharides in situ from dietary NSP with potential prebiotic effects. Investigations with molecular microbiology techniques have demonstrated FE-mediated responses on energy utilisation in broiler chickens that were associated with certain clusters of GIT bacteria. Furthermore, investigations using specific enteric pathogen challenge models have demonstrated the efficacy of FE in modulating gut health. Because FE probably change the substrate characteristics along the GIT, subsequent microbiota responses will vary according to the populations present at the time of administration and their reaction to such changes. Therefore, the microbiota responses to FE administration, rather than being absolute, are a continuum or a population of responses. However, recognition that FE can make an impact on the gut microbiota and thus gut health will probably stimulate development of FE capable of modulating gut microbiota to the benefit of host health under specific production conditions. The present review brings to light opportunities and challenges for the role of major FE (carbohydrases and phytase) on the gut health of poultry and swine species with a specific focus on the impact on GIT microbiota.}, }
@article {pmid23638391, year = {2013}, author = {Meadow, JF and Bateman, AC and Herkert, KM and O'Connor, TK and Green, JL}, title = {Significant changes in the skin microbiome mediated by the sport of roller derby.}, journal = {PeerJ}, volume = {1}, number = {}, pages = {e53}, pmid = {23638391}, issn = {2167-8359}, abstract = {Diverse bacterial communities live on and in human skin. These complex communities vary by skin location on the body, over time, between individuals, and between geographic regions. Culture-based studies have shown that human to human and human to surface contact mediates the dispersal of pathogens, yet little is currently known about the drivers of bacterial community assembly patterns on human skin. We hypothesized that participation in a sport involving skin to skin contact would result in detectable shifts in skin bacterial community composition. We conducted a study during a flat track roller derby tournament, and found that teammates shared distinct skin microbial communities before and after playing against another team, but that opposing teams' bacterial communities converged during the course of a roller derby bout. Our results are consistent with the hypothesis that the human skin microbiome shifts in composition during activities involving human to human contact, and that contact sports provide an ideal setting in which to evaluate dispersal of microorganisms between people.}, }
@article {pmid23636583, year = {2013}, author = {Marinho, MM and Souza, MB and Lürling, M}, title = {Light and phosphate competition between Cylindrospermopsis raciborskii and Microcystis aeruginosa is strain dependent.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {479-488}, pmid = {23636583}, issn = {1432-184X}, mesh = {Cylindrospermopsis/*metabolism/*radiation effects ; Fresh Water/microbiology ; Light ; Microcystis/*metabolism/*radiation effects ; Phosphates/*metabolism ; Species Specificity ; }, abstract = {The hypothesis that outcomes of phosphorus and light competition between Cylindrospermopsis raciborskii and Microcystis aeruginosa are strain dependent was tested experimentally. Critical requirements of phosphorus (P*) and of light (I*) of two strains of each species were determined through monoculture experiments, which indicated a trade-off between species and also between Microcystis strains. Competition experiments between species were performed using the weakest predicted competitors (with the highest values of P* and of I*) and with the strongest predicted competitors (with the lowest values of P* and of I*). Under light limitation, competition between the weakest competitors led C. raciborskii to dominate. Between the strongest competitors, the opposite was observed, M. aeruginosa displaced C. raciborskii, but both strains co-existed in equilibrium. Under phosphate limitation, competition between the weakest competitors led C. raciborskii to exclude M. aeruginosa, and between the strongest competitors, the opposite was observed, M. aeruginosa displaced C. raciborskii, but the system did not reach an equilibrium and both strains were washed out. Hence, outcomes of the competition depended on the pair of competing strains and not only on species or on type of limitation. We concluded that existence of different trade-offs among strains and between species underlie our results showing that C. raciborskii can either dominate or be displaced by M. aeruginosa when exposed to different conditions of light or phosphate limitation.}, }
@article {pmid23636582, year = {2013}, author = {Fernández, NV and Marchelli, P and Fontenla, SB}, title = {Ectomycorrhizas naturally established in Nothofagus nervosa seedlings under different cultivation practices in a forest nursery.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {581-592}, pmid = {23636582}, issn = {1432-184X}, mesh = {Forestry ; Fungi/classification/genetics/growth &amp; development/*isolation &amp; purification ; Magnoliopsida/growth &amp; development/*microbiology ; Molecular Sequence Data ; Mycorrhizae/classification/genetics/growth &amp; development/*isolation &amp; purification ; Phylogeny ; Plant Roots/growth &amp; development/microbiology ; Seedlings/*growth &amp; development/microbiology ; Trees/growth &amp; development/*microbiology ; }, abstract = {Mycorrhizas are mutualistic associations between soil fungi and plant roots which usually improve water and nutrient uptake, influencing plant fitness. Nothofagus nervosa (Raulí) is an ecologically and economically important species of South American temperate forests. Since this native tree species yields valuable timber, it was overexploited and its natural distribution area was critically reduced, so it is currently included in domestication and conservation programs. Among the factors that should be considered in these programs are the ectomycorrhizas (EcM), which would be important for the successful establishment and survival of outplanted seedlings. The aim of this work was to analyze the abundance and diversity of EcM in N. nervosa nursery-cultivated seedlings assessed by morphotyping, fungal isolation, and DNA sequencing. Arbuscular mycorrhiza (AM) occurrence was also studied. A 2-year trial was conducted following the cultivation conditions used for domestication programs. Seedlings were cultivated under two different cultivation practices (greenhouse and nursery soil) without artificial inoculation of mycorrhizal fungi. Seedlings' roots were examined at different times. It was observed that they developed EcM between 6 and 12 months after germination and AMs were not detected in any plant. The most abundant ectomycorrhizal fungi present in seedlings' roots were Tomentella ellisii (Basidiomycota) and an unidentified fungus named Ascomicetous EcM sp. 1. Abundance and diversity of EcM varied between the two cultivation techniques analyzed in this study, since seedlings that continued growing in the greenhouse had higher colonization values, but those transplanted to the nursery soil were colonized by a higher diversity of fungal taxa.}, }
@article {pmid23636494, year = {2013}, author = {Mao, S and Huo, W and Zhu, W}, title = {Use of pyrosequencing to characterize the microbiota in the ileum of goats fed with increasing proportion of dietary grain.}, journal = {Current microbiology}, volume = {67}, number = {3}, pages = {341-350}, pmid = {23636494}, issn = {1432-0991}, mesh = {*Animal Feed ; Animals ; Carboxylic Acids/analysis ; Diet/*methods ; *Edible Grain ; Goats ; Hydrogen-Ion Concentration ; Ileum/chemistry/*microbiology ; Male ; *Microbiota ; Rumen/chemistry/microbiology ; }, abstract = {This study evaluated the effects of an increasing proportion of dietary grain on changes in bacterial populations in the goat ileum. Nine ruminally fistulated, castrated male goats were assigned to three diets in a completely randomized design. Goats were fed three different dietary treatments containing different proportions of corn grain (0, 25, and 50 %). The pH of the ileal contents and rumen fluid (P = 0.015) linearly decreased (P < 0.001), and the acetate, propionate, butyrate, and total volatile fatty acid in ileal contents increased (P < 0.05) with increases in dietary corn, and similar results were also observed in rumen fluid. The barcoded DNA pyrosequencing method was used to reveal 8 phyla, 70 genera, and 1,693 16S operational taxonomic units (OTUs). At the genus level, the proportions of Acetitomaculum, Enterococcus, Atopobium, unclassified Coriobacteriaceae, and unclassified Planctomycetaceae were linearly decreased (P < 0.05) with increases in corn grain. At the species level, high grain feeding linearly decreased the percentage of OTU8686 (unclassified Bacteria) (P = 0.004). To the best of our knowledge, this is the first study using barcoded DNA pyrosequencing method to survey the ileal microbiome of goats and the results suggest that increasing levels of dietary corn change the composition of the ileal bacterial community. These findings provide previously unknown information about the ileal microbiota of goats and a new understanding of the ileal microbial ecology, which may be useful in modulating the gut microbiome.}, }
@article {pmid23631418, year = {2013}, author = {Anderson, OR}, title = {Naked amoebae in biofilms collected from a temperate freshwater pond.}, journal = {The Journal of eukaryotic microbiology}, volume = {60}, number = {4}, pages = {429-431}, doi = {10.1111/jeu.12042}, pmid = {23631418}, issn = {1550-7408}, mesh = {Amoeba/*growth &amp; development ; Biofilms/*growth &amp; development ; Biomass ; Fresh Water ; Ponds ; }, abstract = {Biofilms collected on Plexiglass substrates, from a freshwater pond in northern New York State, were examined microscopically for naked amoebae densities, sizes, diversity, and estimated C-biomass. Five samples were obtained during summer 2006 and 2007. The densities ranged from 109 to 136/cm(2) biofilm surface and 285 to 550/mg biofilm dry weight. Sizes ranged from 13 to 200 μm. Diversities ranged from 4.23 to 4.55. C-biomass ranged from 64 to 543 ng C/cm(2) and 125 to 1,700 μg C/g dry weight. Thirty morphospecies were identified among the five samples, including very large amoebae in the range of 100-200 μm. Large amoebae (≥ 50 μm) accounted for the largest proportion of the C-biomass.}, }
@article {pmid23625052, year = {2013}, author = {Barrett, M and Jahangir, MM and Lee, C and Smith, CJ and Bhreathnach, N and Collins, G and Richards, KG and O'Flaherty, V}, title = {Abundance of denitrification genes under different peizometer depths in four Irish agricultural groundwater sites.}, journal = {Environmental science and pollution research international}, volume = {20}, number = {9}, pages = {6646-6657}, pmid = {23625052}, issn = {1614-7499}, mesh = {*Agriculture ; Bacteria/classification/genetics/*metabolism ; *Genes, Bacterial ; Groundwater/*microbiology ; Ireland ; Nitrification ; *Water Microbiology ; }, abstract = {This study examined the relationship between the abundance of bacterial denitrifiers in groundwater at four sites, differing with respect to overlaying land management and peizometer depth. Groundwater was sourced from 36 multilevel piezometers, which were installed to target different groundwater zones: (1) subsoil, (2) subsoil to bedrock interface, and (3) bedrock. The gene copy concentrations (GCCs), as gene copies per liter, for bacterial 16S rRNA genes and the denitrifying functional genes, nirK, nirS, and nosZ, were determined using quantitative polymerase chain reaction assays. The results were related to gaseous nitrogen emissions and to the physicochemical properties of the four sites. Overall, nirK and nirS abundance appeared to show no significant correlation to N2O production (P = 0.9989; P = 0.3188); and no significant correlation was observed between nosZ and excess N2 concentrations (P = 0.0793). In the majority of piezometers investigated, the variation of nirK and nirS gene copy concentrations was considered significant (P < 0.0001). Dissolved organic carbon (DOC) decreased with aquifer depth and ranged from 1.0-4.0 mg l(-1), 0.9-2.4 mg l(-1), and 0.8-2.4 mg l(-1) within piezometers located in the subsoil, subsoil/bedrock interface, and bedrock depths, respectively. The availability of increasing DOC and the depth of the water table were positively correlated with increasing nir and nosZ GCCs (P = 0.0012). A significant temporal correlation was noted between nirS and piezometer depth (P < 0.001). Interestingly, the nirK, nirS, and nosZ GCCs varied between piezometer depths within specific sites, while GCCs remained relatively constant from site to site, thus indicating no direct impact of agricultural land management strategies investigated on denitrifier abundance.}, }
@article {pmid23624570, year = {2013}, author = {Sleator, RD}, title = {A beginner's guide to phylogenetics.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {1-4}, pmid = {23624570}, issn = {1432-184X}, mesh = {Bacteria/*classification/*genetics ; Biological Evolution ; Classification/*methods ; *Genetics ; Metagenomics ; *Phylogeny ; }, abstract = {Metagenomics and the development of high throughput next generation sequencing capabilities have forced significant development in the field of phylogenetics: the study of the evolutionary relatedness of the planet's inhabitants. Herein, I review the major tree-building strategies, challenges and opportunities which exist in this rapidly expanding field of evolutionary biology.}, }
@article {pmid23624541, year = {2013}, author = {Rampelotto, PH and de Siqueira Ferreira, A and Barboza, AD and Roesch, LF}, title = {Changes in diversity, abundance, and structure of soil bacterial communities in Brazilian Savanna under different land use systems.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {593-607}, pmid = {23624541}, issn = {1432-184X}, mesh = {Agriculture ; Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Brazil ; *Ecosystem ; Molecular Sequence Data ; Phylogeny ; *Soil Microbiology ; }, abstract = {The Brazilian Savanna, also known as "Cerrado", is the richest and most diverse savanna in the world and has been ranked as one of the main hotspots of biodiversity. The Cerrado is a representative biome in Central Brazil and the second largest biome in species diversity of South America. Nevertheless, large areas of native vegetation have been converted to agricultural land including grain production, livestock, and forestry. In this view, understanding how land use affects microbial communities is fundamental for the sustainable management of agricultural ecosystems. The aim of this work was to analyze and compare the soil bacterial communities from the Brazilian Cerrado associated with different land use systems using high throughput pyrosequencing of 16S rRNA genes. Relevant differences were observed in the abundance and structure of bacterial communities in soils under different land use systems. On the other hand, the diversity of bacterial communities was not relevantly changed among the sites studied. Land use systems had also an important impact on specific bacterial groups in soil, which might change the soil function and the ecological processes. Acidobacteria, Proteobacteria, and Actinobacteria were the most abundant groups in the Brazilian Cerrado. These findings suggest that more important than analyzing the general diversity is to analyze the composition of the communities. Since soil type was the same among the sites, we might assume that land use was the main factor defining the abundance and structure of bacterial communities.}, }
@article {pmid23624540, year = {2013}, author = {Kolařík, M and Jankowiak, R}, title = {Vector affinity and diversity of Geosmithia fungi living on subcortical insects inhabiting Pinaceae species in central and northeastern Europe.}, journal = {Microbial ecology}, volume = {66}, number = {3}, pages = {682-700}, pmid = {23624540}, issn = {1432-184X}, mesh = {Animals ; *Biodiversity ; Coleoptera/classification/*microbiology ; Europe ; Host Specificity ; Hypocreales/classification/genetics/*isolation &amp; purification/*physiology ; Insect Vectors/*microbiology ; Molecular Sequence Data ; Phylogeny ; Pinaceae/classification/*microbiology/parasitology ; Plant Diseases/*microbiology/parasitology ; }, abstract = {Fungi from the genus Geosmithia (Ascomycota: Hypocreales) are associated with bark beetles (Coleoptera: Scolytinae), though little is known about ecology, diversity, and distribution of these fungi across beetle and its host tree species. This study surveyed the diversity, distribution and vector affinity of Geosmithia isolated from subcortical insects that colonized trees from the family Pinaceae in Central and Northeastern Europe. Twelve Geosmithia species were isolated from 85 plant samples associated with 23 subcortical insect species (including 14 bark beetle species). Geosmithia community composition was similar across different localities and vector species; although the fungal communities associated with insects that colonized Pinus differed from that colonizing other tree species (Abies, Larix, and Picea). Ten Geosmithia species from four independent phylogenetic lineages were not reported previously from vectors feeding on other plant families and seem to be restricted to the vectors from Pinaceae only. We conclude that presence of such substrate specificity suggests a long and stable association between Geosmithia and bark beetles.}, }
@article {pmid23621863, year = {2013}, author = {Esteves, AI and Hardoim, CC and Xavier, JR and Gonçalves, JM and Costa, R}, title = {Molecular richness and biotechnological potential of bacteria cultured from Irciniidae sponges in the north-east Atlantic.}, journal = {FEMS microbiology ecology}, volume = {85}, number = {3}, pages = {519-536}, doi = {10.1111/1574-6941.12140}, pmid = {23621863}, issn = {1574-6941}, mesh = {Animals ; Antibiosis ; Atlantic Ocean ; Bacteria/*classification/genetics/isolation &amp; purification ; *Biodiversity ; Biotechnology ; Genotype ; Peptide Synthases/genetics ; Phylogeny ; Polyketide Synthases/genetics ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rhodobacteraceae/genetics/isolation &amp; purification ; }, abstract = {Several bioactive compounds originally isolated from marine sponges have been later ascribed or suggested to be synthesized by their symbionts. The cultivation of sponge-associated bacteria provides one possible route to the discovery of these metabolites. Here, we determine the bacterial richness cultured from two irciniid sponge species, Sarcotragus spinosulus and Ircinia variabilis, and ascertain their biotechnological potential. A total of 279 isolates were identified from 13 sponge specimens. These were classified into 17 genera - with Pseudovibrio, Ruegeria and Vibrio as the most dominant - and 3 to 10 putatively new bacterial species. While 16S rRNA gene sequencing identified 29 bacterial phylotypes at the 'species' level (97% sequence similarity), whole-genome BOX-PCR fingerprinting uncovered 155 genotypes, unveiling patterns of specimen-dependent occurrence of prevailing bacterial genomes across sponge individuals. Among the BOX-PCR genotypes recovered, 34% were active against clinically relevant strains, with Vibrio isolates producing the most active antagonistic effect. Several Pseudovibrio genotypes showed the presence of polyketide synthase (PKS) genes, and these were for the first time detected in isolates of the genus Aquimarina (Bacteroidetes). Our results highlight great biotechnological potential and interest for the Irciniidae sponge family and their diversified bacterial genomes.}, }
@article {pmid23621155, year = {2014}, author = {Meadow, JF and Altrichter, AE and Kembel, SW and Kline, J and Mhuireach, G and Moriyama, M and Northcutt, D and O'Connor, TK and Womack, AM and Brown, GZ and Green, JL and Bohannan, BJ}, title = {Indoor airborne bacterial communities are influenced by ventilation, occupancy, and outdoor air source.}, journal = {Indoor air}, volume = {24}, number = {1}, pages = {41-48}, pmid = {23621155}, issn = {1600-0668}, mesh = {Air Conditioning ; *Air Microbiology ; Air Pollution, Indoor/*prevention &amp; control ; Bacteria/genetics/*isolation &amp; purification ; DNA, Bacterial/chemistry/genetics ; Environmental Monitoring/*methods ; Humans ; Oregon ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry/genetics ; Time Factors ; Universities ; Ventilation ; }, abstract = {Architects and engineers are beginning to consider a new dimension of indoor air: the structure and composition of airborne microbial communities. A first step in this emerging field is to understand the forces that shape the diversity of bioaerosols across space and time within the built environment. In an effort to elucidate the relative influences of three likely drivers of indoor bioaerosol diversity - variation in outdoor bioaerosols, ventilation strategy, and occupancy load - we conducted an intensive temporal study of indoor airborne bacterial communities in a high-traffic university building with a hybrid HVAC (mechanically and naturally ventilated) system. Indoor air communities closely tracked outdoor air communities, but human-associated bacterial genera were more than twice as abundant in indoor air compared with outdoor air. Ventilation had a demonstrated effect on indoor airborne bacterial community composition; changes in outdoor air communities were detected inside following a time lag associated with differing ventilation strategies relevant to modern building design. Our results indicate that both occupancy patterns and ventilation strategies are important for understanding airborne microbial community dynamics in the built environment.}, }
@article {pmid23616466, year = {2013}, author = {Coelho, FJ and Rocha, RJ and Pires, AC and Ladeiro, B and Castanheira, JM and Costa, R and Almeida, A and Cunha, A and Lillebø, AI and Ribeiro, R and Pereira, R and Lopes, I and Marques, C and Moreira-Santos, M and Calado, R and Cleary, DF and Gomes, NC}, title = {Development and validation of an experimental life support system for assessing the effects of global climate change and environmental contamination on estuarine and coastal marine benthic communities.}, journal = {Global change biology}, volume = {19}, number = {8}, pages = {2584-2595}, doi = {10.1111/gcb.12227}, pmid = {23616466}, issn = {1354-1013}, mesh = {Animals ; Aquatic Organisms/physiology ; *Climate Change ; *Ecosystem ; Life Support Systems/economics/instrumentation ; Marine Biology/economics/instrumentation/*methods ; Seawater/chemistry/microbiology ; Water Pollutants/*toxicity ; }, abstract = {An experimental life support system (ELSS) was constructed to study the interactive effects of multiple stressors on coastal and estuarine benthic communities, specifically perturbations driven by global climate change and anthropogenic environmental contamination. The ELSS allows researchers to control salinity, pH, temperature, ultraviolet radiation (UVR), tidal rhythms and exposure to selected contaminants. Unlike most microcosms previously described, our system enables true independent replication (including randomization). In addition to this, it can be assembled using commercially available materials and equipment, thereby facilitating the replication of identical experimental setups in different geographical locations. Here, we validate the reproducibility and environmental quality of the system by comparing chemical and biological parameters recorded in our ELSS with those prevalent in the natural environment. Water, sediment microbial community and ragworm (the polychaete Hediste diversicolor) samples were obtained from four microcosms after 57 days of operation. In general, average concentrations of dissolved inorganic nutrients (NO3 (-) ; NH4 (+) and PO4 (-3)) in the water column of the ELSS experimental control units were within the range of concentrations recorded in the natural environment. While some shifts in bacterial community composition were observed between in situ and ELSS sediment samples, the relative abundance of most metabolically active bacterial taxa appeared to be stable. In addition, ELSS operation did not significantly affect survival, oxidative stress and neurological biomarkers of the model organism Hediste diversicolor. The validation data indicate that this system can be used to assess independent or interactive effects of climate change and environmental contamination on benthic communities. Researchers will be able to simulate the effects of these stressors on processes driven by microbial communities, sediment and seawater chemistry and to evaluate potential consequences to sediment toxicity using model organisms such as Hediste diversicolor.}, }
@article {pmid23615705, year = {2013}, author = {Singh, RK and Malik, N and Singh, S}, title = {Improved nutrient use efficiency increases plant growth of rice with the use of IAA-overproducing strains of endophytic Burkholderia cepacia strain RRE25.}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {375-384}, pmid = {23615705}, issn = {1432-184X}, mesh = {Burkholderia cepacia/genetics/isolation &amp; purification/*metabolism ; Endophytes/genetics/isolation &amp; purification/*metabolism ; Indoleacetic Acids/*metabolism ; Nitrogen/metabolism ; Oryza/*growth &amp; development/metabolism/*microbiology ; Phosphates/metabolism ; Potassium/metabolism ; }, abstract = {Effect of indole acetic acid (IAA)-overproducing mutants of Burkholderia cepacia (RRE25), a member of β-subclass of Proteobacteria and naturally occurring rice endophyte, was observed on the growth of rice (Oryza sativa L.) plants grown under greenhouse conditions. Nine mutants were characterized for altered biosynthesis of IAA after nitrous acid mutagenesis. These mutants were grouped into two classes: class I mutants have reduced production of IAA as compared to the wild type, while class II mutants showed overproduction of IAA. Mutants of both classes and RRE25, the parent (wild type), were inoculated on rice seedlings of two cultivars (Sarjoo-52 and NDR-97). Uptake of nitrogen, phosphorous, and potassium was estimated in these plants. Significant increase in the amount of uptake of all three elements was observed when inoculated with the IAA-overproducing mutants over control as well as in the plants inoculated with the wild type (RRE25). Effect of inoculation of IAA-overproducing mutants was more pronounced on the uptake of phosphorous in cultivar NDR-97 than Sarjoo-52, while it was opposite with respect to potassium uptake. Any significant difference was not observed in nitrogen uptake among the two cultivars. It shows that the host also plays an important role in the beneficial endophytic association. It was concluded from these results that one of the possible mechanisms of growth promotion of rice plants inoculated with bacterial endophytes is their effects on an increase in the capability of nutritional uptake possible through the effect of IAA production which results in proliferation of root system that could mine more nutrients from the soil.}, }
@article {pmid23613785, year = {2013}, author = {Le Roux, X and Schmid, B and Poly, F and Barnard, RL and Niklaus, PA and Guillaumaud, N and Habekost, M and Oelmann, Y and Philippot, L and Salles, JF and Schloter, M and Steinbeiss, S and Weigelt, A}, title = {Soil environmental conditions and microbial build-up mediate the effect of plant diversity on soil nitrifying and denitrifying enzyme activities in temperate grasslands.}, journal = {PloS one}, volume = {8}, number = {4}, pages = {e61069}, pmid = {23613785}, issn = {1932-6203}, mesh = {Analysis of Variance ; *Biodiversity ; *Denitrification ; *Ecosystem ; Enzymes/metabolism ; Fabaceae/microbiology ; *Nitrification ; Poaceae/*microbiology ; Regression Analysis ; *Soil Microbiology ; }, abstract = {Random reductions in plant diversity can affect ecosystem functioning, but it is still unclear which components of plant diversity (species number - namely richness, presence of particular plant functional groups, or particular combinations of these) and associated biotic and abiotic drivers explain the observed relationships, particularly for soil processes. We assembled grassland communities including 1 to 16 plant species with a factorial separation of the effects of richness and functional group composition to analyze how plant diversity components influence soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively), the abundance of nitrifiers (bacterial and archaeal amoA gene number) and denitrifiers (nirK, nirS and nosZ gene number), and key soil environmental conditions. Plant diversity effects were largely due to differences in functional group composition between communities of identical richness (number of sown species), though richness also had an effect per se. NEA was positively related to the percentage of legumes in terms of sown species number, the additional effect of richness at any given legume percentage being negative. DEA was higher in plots with legumes, decreased with increasing percentage of grasses, and increased with richness. No correlation was observed between DEA and denitrifier abundance. NEA increased with the abundance of ammonia oxidizing bacteria. The effect of richness on NEA was entirely due to the build-up of nitrifying organisms, while legume effect was partly linked to modified ammonium availability and nitrifier abundance. Richness effect on DEA was entirely due to changes in soil moisture, while the effects of legumes and grasses were partly due to modified nitrate availability, which influenced the specific activity of denitrifiers. These results suggest that plant diversity-induced changes in microbial specific activity are important for facultative activities such as denitrification, whereas changes in microbial abundance play a major role for non-facultative activities such as nitrification.}, }
@article {pmid23610649, year = {2013}, author = {Poisot, T and Péquin, B and Gravel, D}, title = {High-throughput sequencing: a roadmap toward community ecology.}, journal = {Ecology and evolution}, volume = {3}, number = {4}, pages = {1125-1139}, pmid = {23610649}, issn = {2045-7758}, abstract = {High-throughput sequencing is becoming increasingly important in microbial ecology, yet it is surprisingly under-used to generate or test biogeographic hypotheses. In this contribution, we highlight how adding these methods to the ecologist toolbox will allow the detection of new patterns, and will help our understanding of the structure and dynamics of diversity. Starting with a review of ecological questions that can be addressed, we move on to the technical and analytical issues that will benefit from an increased collaboration between different disciplines.}, }
@article {pmid23609130, year = {2013}, author = {Fernández-Martínez, MA and de Los Ríos, A and Sancho, LG and Pérez-Ortega, S}, title = {Diversity of endosymbiotic Nostoc in Gunnera magellanica from Tierra del Fuego, Chile [corrected].}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {335-350}, pmid = {23609130}, issn = {1432-184X}, mesh = {*Biodiversity ; Chile ; Magnoliopsida/*microbiology/physiology ; Molecular Sequence Data ; Nostoc/classification/genetics/*isolation &amp; purification/physiology ; Phylogeny ; *Symbiosis ; }, abstract = {Global warming is causing ice retreat in glaciers worldwide, most visibly over the last few decades in some areas of the planet. One of the most affected areas is the region of Tierra del Fuego (southern South America). Vascular plant recolonisation of recently deglaciated areas in this region is initiated by Gunnera magellanica, which forms symbiotic associations with the cyanobacterial genus Nostoc, a trait that likely confers advantages in this colonisation process. This symbiotic association in the genus Gunnera is notable as it represents the only known symbiotic relationship between angiosperms and cyanobacteria. The aim of this work was to study the genetic diversity of the Nostoc symbionts in Gunnera at three different, nested scale levels: specimen, population and region. Three different genomic regions were examined in the study: a fragment of the small subunit ribosomal RNA gene (16S), the RuBisCO large subunit gene coupled with its promoter sequence and a chaperon-like protein (rbcLX) and the ribosomal internal transcribed spacer (ITS) region. The identity of Nostoc as the symbiont was confirmed in all the infected rhizome tissue analysed. Strains isolated in the present study were closely related to strains known to form symbioses with other organisms, such as lichen-forming fungi or bryophytes. We found 12 unique haplotypes in the 16S rRNA (small subunit) region analysis, 19 unique haplotypes in the ITS region analysis and 57 in the RuBisCO proteins region (rbcLX). No genetic variability was found among Nostoc symbionts within a single host plant while Nostoc populations among different host plants within a given sampling site revealed major differences. Noteworthy, interpopulation variation was also shown between recently deglaciated soils and more ancient ones, between eastern and western sites and between northern and southern slopes of Cordillera Darwin. The cell structure of the symbiotic relationship was observed with low-temperature scanning electron microscopy, showing changes in morphology of both cyanobiont cells (differentiate more heterocysts) and plant cells (increased size). Developmental stages of the symbiosis, including cell walls and membranes and EPS matrix states, were also observed.}, }
@article {pmid23608631, year = {2013}, author = {Jover, LF and Cortez, MH and Weitz, JS}, title = {Mechanisms of multi-strain coexistence in host-phage systems with nested infection networks.}, journal = {Journal of theoretical biology}, volume = {332}, number = {}, pages = {65-77}, doi = {10.1016/j.jtbi.2013.04.011}, pmid = {23608631}, issn = {1095-8541}, mesh = {Bacteria/*virology ; Bacteriophages/*physiology ; Host-Pathogen Interactions/*physiology ; *Models, Biological ; }, abstract = {Bacteria and their viruses (bacteriophages) coexist in natural environments forming complex infection networks. Recent empirical findings suggest that phage-bacteria infection networks often possess a nested structure such that there is a hierarchical relationship among who can infect whom. Here we consider how nested infection networks may affect phage and bacteria dynamics using a multi-type Lotka-Volterra framework with cross-infection. Analysis of similar models has, in the past, assumed simpler interaction structures as a first step towards tractability. We solve the proposed model, finding trade-off conditions on the life-history traits of both bacteria and viruses that allow coexistence in communities with nested infection networks. First, we find that bacterial growth rate should decrease with increasing defense against infection. Second, we find that the efficiency of viral infection should decrease with host range. Next, we establish a relationship between relative densities and the curvature of life history trade-offs. We compare and contrast the current findings to the "Kill-the-Winner" model of multi-species phage-bacteria communities. Finally, we discuss a suite of testable hypotheses stemming from the current model concerning relationships between infection range, life history traits and coexistence in complex phage-bacteria communities.}, }
@article {pmid23606477, year = {2013}, author = {Davis, JJ and Xia, F and Overbeek, RA and Olsen, GJ}, title = {Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {63}, number = {Pt 7}, pages = {2727-2741}, pmid = {23606477}, issn = {1466-5034}, support = {HHSN272200900040C/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acyl-tRNA Synthetases/genetics ; Bacterial Proteins/genetics ; DNA, Bacterial/genetics ; *Genome, Bacterial ; Nucleic Acid Conformation ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Ribosomal Proteins/genetics ; Sequence Alignment ; Tenericutes/*classification/genetics ; }, abstract = {The tree of life is paramount for achieving an integrated understanding of microbial evolution and the relationships between physiology, genealogy and genomics. It provides the framework for interpreting environmental sequence data, whether applied to microbial ecology or to human health. However, there remain many instances where there is ambiguity in our understanding of the phylogeny of major lineages, and/or confounding nomenclature. Here we apply recent genomic sequence data to examine the evolutionary history of members of the classes Mollicutes (phylum Tenericutes) and Erysipelotrichia (phylum Firmicutes). Consistent with previous analyses, we find evidence of a specific relationship between them in molecular phylogenies and signatures of the 16S rRNA, 23S rRNA, ribosomal proteins and aminoacyl-tRNA synthetase proteins. Furthermore, by mapping functions over the phylogenetic tree we find that the erysipelotrichia lineages are involved in various stages of genomic reduction, having lost (often repeatedly) a variety of metabolic functions and the ability to form endospores. Although molecular phylogeny has driven numerous taxonomic revisions, we find it puzzling that the most recent taxonomic revision of the phyla Firmicutes and Tenericutes has further separated them into distinct phyla, rather than reflecting their common roots.}, }
@article {pmid23604403, year = {2013}, author = {Nelson, KE}, title = {Microbiomes.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {916-919}, pmid = {23604403}, issn = {1432-184X}, mesh = {Bacteria/chemistry/*genetics/isolation &amp; purification/metabolism ; *Metagenome ; *Metagenomics ; Seawater/*microbiology ; }, abstract = {During the past decade, there has been an explosion in the quantity of sequencing data that has come out of the studies of microbiomes. This has resulted primarily from new technological developments to interrogating any environment of choice. Additional downstream applications to interrogating these datasets include "omics" studies such as transcriptomics and proteomics, all leading to a deeper understanding of microbial diversity and the multitude of species that remain uncultured. Metagenomic studies are now being performed routinely on a wide range of environments including soils, oceans, air, plants, and various animal species. They are being used to identify novel microbial species, new pathways, and to elucidate the roles of viruses and phage in the environment. In this review, we get a perspective on where the science is headed and what we expect to learn as additional studies unfold.}, }
@article {pmid23594389, year = {2013}, author = {Van den Abbeele, P and Verstraete, W and El Aidy, S and Geirnaert, A and Van de Wiele, T}, title = {Prebiotics, faecal transplants and microbial network units to stimulate biodiversity of the human gut microbiome.}, journal = {Microbial biotechnology}, volume = {6}, number = {4}, pages = {335-340}, pmid = {23594389}, issn = {1751-7915}, mesh = {*Biodiversity ; Biological Therapy/*methods ; Diet/*methods ; Gastrointestinal Tract/*microbiology ; Humans ; *Microbiota ; *Prebiotics ; }, abstract = {Accumulating evidence demonstrates the intimate association between human hosts and the gut microbiome. Starting at birth, the sterile gut of the newborn acquires a diverse spectrum of microbes, needed for immunological priming. However, current practices (caesarean sections, use of formula milk) deprive newborns from being exposed to this broad spectrum of microbes. Unnecessary use of antibiotics and excessive hygienic precautions (e.g. natural versus chlorinated drinking water) together with the Western diet further contribute to a decreased microbial diversity in the adult gut. This has been correlated with recurrent Clostridium difficile infection, inflammatory bowel diseases and obesity, among others. A healthy gut microbiome is thus characterized by a diverse network of metabolically interacting microbial members. In this context, we review several existing and novel approaches to manage the gut microbiome. First, prebiotic compounds should be re-defined in the sense that they should enhance the ecological biodiversity rather than stimulating single species. Recent studies highlight that structurally different polysaccharides require specific primary degraders but also enhance a similar network of secondary degraders that benefit from cross-feeding. A faecal transplantation is a second approach to restore biodiversity when the microbiota is severely dysbiosed, with promising results regarding C. difficile-associated disease and obesity-related metabolic syndromes. A final strategy is the introduction of key microbial network units, i.e. pre-organized microbial associations, which strengthen the overall microbial network of the gut microbiome that supports human health.}, }
@article {pmid23592331, year = {2014}, author = {Lee, DG and Cho, KC and Chu, KH}, title = {Identification of triclosan-degrading bacteria in a triclosan enrichment culture using stable isotope probing.}, journal = {Biodegradation}, volume = {25}, number = {1}, pages = {55-65}, doi = {10.1007/s10532-013-9640-7}, pmid = {23592331}, issn = {1572-9729}, mesh = {Alphaproteobacteria/classification/genetics/*isolation &amp; purification/metabolism ; Anti-Infective Agents, Local/*metabolism ; Betaproteobacteria/classification/genetics/*isolation &amp; purification/metabolism ; Biodegradation, Environmental ; Carbon Isotopes ; Environmental Pollutants/*metabolism ; Gammaproteobacteria/classification/genetics/*isolation &amp; purification/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/classification/genetics ; Sewage/chemistry ; Triclosan/*metabolism ; }, abstract = {Triclosan, a widely used antimicrobial agent, is an emerging contaminant in the environment. Despite its antimicrobial character, biodegradation of triclosan has been observed in pure cultures, soils and activated sludge. However, little is known about the microorganisms responsible for the degradation in mixed cultures. In this study, active triclosan degraders in a triclosan-degrading enrichment culture were identified using stable isotope probing (SIP) with universally (13)C-labeled triclosan. Eleven clones contributed from active microorganisms capable of uptake the (13)C in triclosan were identified. None of these clones were similar to known triclosan-degraders/utilizers. These clones distributed among α-, β-, or γ-Proteobacteria: one belonging to Defluvibacter (α-Proteobacteria), seven belonging to Alicycliphilus (β-Proteobacteria), and three belonging to Stenotrophomonas (γ-Proteobacteria). Successive additions of triclosan caused a significant shift in the microbial community structure of the enrichment culture, with dominant ribotypes belonging to the genera Alicycliphilus and Defluvibacter. Application of SIP has successfully identified diverse uncultivable triclosan-degrading microorganisms in an activated sludge enrichment culture. The results of this study not only contributed to our understanding of the microbial ecology of triclosan biodegradation in wastewater, but also suggested that triclosan degraders are more phylogenetically diverse than previously reported.}, }
@article {pmid23588850, year = {2013}, author = {Martínez-Rodríguez, P and Hernández-Pérez, M and Bella, JL}, title = {Detection of Spiroplasma and Wolbachia in the bacterial gonad community of Chorthippus parallelus.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {211-223}, pmid = {23588850}, issn = {1432-184X}, mesh = {Animals ; Female ; Gonads/microbiology ; Grasshoppers/genetics/*microbiology/*physiology ; Male ; Molecular Sequence Data ; Phylogeny ; Reproduction ; Spiroplasma/classification/genetics/*isolation &amp; purification ; Wolbachia/classification/genetics/*isolation &amp; purification ; }, abstract = {We have recently detected the endosymbiont Wolbachia in multiple individuals and populations of the grasshopper Chorthippus parallelus (Orthoptera: acrididae). This bacterium induces reproductive anomalies, including cytoplasmic incompatibility. Such incompatibilities may help explain the maintenance of two distinct subspecies of this grasshopper, C. parallelus parallelus and C. parallelus erythropus, which are involved in a Pyrenean hybrid zone that has been extensively studied for the past 20 years, becoming a model system for the study of genetic divergence and speciation. To evaluate whether Wolbachia is the sole bacterial infection that might induce reproductive anomalies, the gonadal bacterial community of individuals from 13 distinct populations of C. parallelus was determined by denaturing gradient gel electrophoresis analysis of bacterial 16S rRNA gene fragments and sequencing. The study revealed low bacterial diversity in the gonads: a persistent bacterial trio consistent with Spiroplasma sp. and the two previously described supergroups of Wolbachia (B and F) dominated the gonad microbiota. A further evaluation of the composition of the gonad bacterial communities was carried out by whole cell hybridization. Our results confirm previous studies of the cytological distribution of Wolbachia in C. parallelus gonads and show a homogeneous infection by Spiroplasma. Spiroplasma and Wolbachia cooccurred in some individuals, but there was no significant association of Spiroplasma with a grasshopper's sex or with Wolbachia infection, although subtle trends might be detected with a larger sample size. This information, together with previous experimental crosses of this grasshopper, suggests that Spiroplasma is unlikely to contribute to sex-specific reproductive anomalies; instead, they implicate Wolbachia as the agent of the observed anomalies in C. parallelus.}, }
@article {pmid23588849, year = {2013}, author = {Berthrong, ST and Buckley, DH and Drinkwater, LE}, title = {Agricultural management and labile carbon additions affect soil microbial community structure and interact with carbon and nitrogen cycling.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {158-170}, pmid = {23588849}, issn = {1432-184X}, mesh = {Agriculture/*methods ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Carbon/*analysis/metabolism ; Carbon Cycle ; Ecosystem ; Nitrogen/*analysis/metabolism ; Nitrogen Cycle ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {We investigated how conversion from conventional agriculture to organic management affected the structure and biogeochemical function of soil microbial communities. We hypothesized the following. (1) Changing agricultural management practices will alter soil microbial community structure driven by increasing microbial diversity in organic management. (2) Organically managed soil microbial communities will mineralize more N and will also mineralize more N in response to substrate addition than conventionally managed soil communities. (3) Microbial communities under organic management will be more efficient and respire less added C. Soils from organically and conventionally managed agroecosystems were incubated with and without glucose ((13)C) additions at constant soil moisture. We extracted soil genomic DNA before and after incubation for TRFLP community fingerprinting of soil bacteria and fungi. We measured soil C and N pools before and after incubation, and we tracked total C respired and N mineralized at several points during the incubation. Twenty years of organic management altered soil bacterial and fungal community structure compared to continuous conventional management with the bacterial differences caused primarily by a large increase in diversity. Organically managed soils mineralized twice as much NO3 (-) as conventionally managed ones (44 vs. 23 μg N/g soil, respectively) and increased mineralization when labile C was added. There was no difference in respiration, but organically managed soils had larger pools of C suggesting greater efficiency in terms of respiration per unit soil C. These results indicate that the organic management induced a change in community composition resulting in a more diverse community with enhanced activity towards labile substrates and greater capacity to mineralize N.}, }
@article {pmid23587322, year = {2013}, author = {Lynch, MDj and Masella, AP and Hall, MW and Bartram, AK and Neufeld, JD}, title = {AXIOME: automated exploration of microbial diversity.}, journal = {GigaScience}, volume = {2}, number = {1}, pages = {3}, pmid = {23587322}, issn = {2047-217X}, abstract = {BACKGROUND: Although high-throughput sequencing of small subunit rRNA genes has revolutionized our understanding of microbial ecosystems, these technologies generate data at depths that benefit from automated analysis. Here we present AXIOME (Automation, eXtension, and Integration Of Microbial Ecology), a highly flexible and extensible management tool for popular microbial ecology analysis packages that promotes reproducibility and customization in microbial research.<br><br>FINDINGS: AXIOME streamlines and manages analysis of small subunit (SSU) rRNA marker data in QIIME and mothur. AXIOME also implements features including the PAired-eND Assembler for Illumina sequences (PANDAseq), non-negative matrix factorization (NMF), multi-response permutation procedures (MRPP), exploring and recovering phylogenetic novelty (SSUnique) and indicator species analysis. AXIOME has a companion graphical user interface (GUI) and is designed to be easily extended to facilitate customized research workflows.<br><br>CONCLUSIONS: AXIOME is an actively developed, open source project written in Vala and available from GitHub (http://neufeld.github.com/axiome) and as a Debian package. Axiometic, a GUI companion tool is also freely available (http://neufeld.github.com/axiometic). Given that data analysis has become an important bottleneck for microbial ecology studies, the development of user-friendly computational tools remains a high priority. AXIOME represents an important step in this direction by automating multi-step bioinformatic analyses and enabling the customization of procedures to suit the diverse research needs of the microbial ecology community.}, }
@article {pmid23584766, year = {2013}, author = {Brazelton, WJ and Morrill, PL and Szponar, N and Schrenk, MO}, title = {Bacterial communities associated with subsurface geochemical processes in continental serpentinite springs.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {13}, pages = {3906-3916}, pmid = {23584766}, issn = {1098-5336}, mesh = {Base Sequence ; Betaproteobacteria/*genetics ; *Biota ; DNA Fingerprinting ; Gram-Positive Bacteria/*genetics ; Hydrogen-Ion Concentration ; Iron/chemistry ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Natural Springs/*chemistry/*microbiology ; Newfoundland and Labrador ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Reactions associated with the geochemical process of serpentinization can generate copious quantities of hydrogen and low-molecular-weight organic carbon compounds, which may provide energy and nutrients to sustain subsurface microbial communities independently of the photosynthetically supported surface biosphere. Previous microbial ecology studies have tested this hypothesis in deep sea hydrothermal vents, such as the Lost City hydrothermal field. This study applied similar methods, including molecular fingerprinting and tag sequencing of the 16S rRNA gene, to ultrabasic continental springs emanating from serpentinizing ultramafic rocks. These molecular surveys were linked with geochemical measurements of the fluids in an interdisciplinary approach designed to distinguish potential subsurface organisms from those derived from surface habitats. The betaproteobacterial genus Hydrogenophaga was identified as a likely inhabitant of transition zones where hydrogen-enriched subsurface fluids mix with oxygenated surface water. The Firmicutes genus Erysipelothrix was most strongly correlated with geochemical factors indicative of subsurface fluids and was identified as the most likely inhabitant of a serpentinization-powered subsurface biosphere. Both of these taxa have been identified in multiple hydrogen-enriched subsurface habitats worldwide, and the results of this study contribute to an emerging biogeographic pattern in which Betaproteobacteria occur in near-surface mixing zones and Firmicutes are present in deeper, anoxic subsurface habitats.}, }
@article {pmid23577010, year = {2013}, author = {Bodelier, PL and Dedysh, SN}, title = {Microbiology of wetlands.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {79}, pmid = {23577010}, issn = {1664-302X}, }
@article {pmid23575374, year = {2013}, author = {Shade, A and Caporaso, JG and Handelsman, J and Knight, R and Fierer, N}, title = {A meta-analysis of changes in bacterial and archaeal communities with time.}, journal = {The ISME journal}, volume = {7}, number = {8}, pages = {1493-1506}, pmid = {23575374}, issn = {1751-7370}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Archaea/classification/genetics/*physiology ; Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; *Ecosystem ; *Environmental Microbiology ; Humans ; RNA, Ribosomal, 16S/genetics ; Time Factors ; }, abstract = {Ecologists have long studied the temporal dynamics of plant and animal communities with much less attention paid to the temporal dynamics exhibited by microbial communities. As a result, we do not know if overarching temporal trends exist for microbial communities or if changes in microbial communities are generally predictable with time. Using microbial time series assessed via high-throughput sequencing, we conducted a meta-analysis of temporal dynamics in microbial communities, including 76 sites representing air, aquatic, soil, brewery wastewater treatment, human- and plant-associated microbial biomes. We found that temporal variability in both within- and between-community diversity was consistent among microbial communities from similar environments. Community structure changed systematically with time in less than half of the cases, and the highest rates of change were observed within ranges of 1 day to 1 month for all communities examined. Microbial communities exhibited species-time relationships (STRs), which describe the accumulation of new taxa to a community, similar to those observed previously for plant and animal communities, suggesting that STRs are remarkably consistent across a broad range of taxa. These results highlight that a continued integration of microbial ecology into the broader field of ecology will provide new insight into the temporal patterns of microbial and 'macro'-bial communities alike.}, }
@article {pmid23575130, year = {2013}, author = {Corcoran, M and Morris, D and De Lappe, N and O'Connor, J and Lalor, P and Dockery, P and Cormican, M}, title = {Salmonella enterica biofilm formation and density in the Centers for Disease Control and Prevention's biofilm reactor model is related to serovar and substratum.}, journal = {Journal of food protection}, volume = {76}, number = {4}, pages = {662-667}, doi = {10.4315/0362-028X.JFP-12-303}, pmid = {23575130}, issn = {1944-9097}, mesh = {Bacterial Adhesion/physiology ; Biofilms/growth &amp; development ; Colony Count, Microbial ; Culture Media/*chemistry ; Food Microbiology ; *Models, Biological ; Salmonella enterica/*physiology ; }, abstract = {Foodborne pathogens can attach to, and survive on, food contact surfaces for long periods by forming a biofilm. Salmonella enterica is the second most common cause of foodborne illness in Ireland. The ability of S. enterica to form a biofilm could contribute to its persistence in food production areas, leading to cross-contamination of products and surfaces. Arising from a large foodborne outbreak of S. enterica serovar Agona associated with a food manufacturing environment, a hypothesis was formulated that the associated Salmonella Agona strain had an enhanced ability to form a biofilm relative to other S. enterica. To investigate this hypothesis, 12 strains of S. enterica, encompassing three S. enterica serovars, were assessed for the ability to form a biofilm on multiple food contact surfaces. All isolates formed a biofilm on the contact surfaces, and there was no consistent trend for the Salmonella Agona outbreak strain to produce a denser biofilm compared with other strains of Salmonella Agona or Salmonella Typhimurium. However, Salmonella Enteritidis biofilm was considerably less dense than Salmonella Typhimurium and Salmonella Agona biofilms. Biofilm density was greater on tile than on concrete, polycarbonate, stainless steel, or glass.}, }
@article {pmid23574466, year = {2013}, author = {Ebersole, JL and Dawson, DR and Morford, LA and Peyyala, R and Miller, CS and Gonzaléz, OA}, title = {Periodontal disease immunology: 'double indemnity' in protecting the host.}, journal = {Periodontology 2000}, volume = {62}, number = {1}, pages = {163-202}, pmid = {23574466}, issn = {1600-0757}, support = {P20 GM103538/GM/NIGMS NIH HHS/United States ; P20 RR020145/RR/NCRR NIH HHS/United States ; U01 DE017793/DE/NIDCR NIH HHS/United States ; }, mesh = {Adaptive Immunity/immunology ; Biofilms ; Cytokines/immunology ; Host-Pathogen Interactions/*immunology ; Humans ; Immunity, Innate/immunology ; Immunity, Mucosal/immunology ; Microbial Interactions/immunology ; Microbiota/immunology ; Periodontal Diseases/*immunology/microbiology ; }, abstract = {During the last two to three decades our understanding of the immunobiology of periodontal disease has increased exponentially, both with respect to the microbial agents triggering the disease process and the molecular mechanisms of the host engagement maintaining homeostasis or leading to collateral tissue damage. These foundational scientific findings have laid the groundwork for translating cell phenotype, receptor engagement, intracellular signaling pathways and effector functions into a 'picture' of the periodontium as the host responds to the 'danger signals' of the microbial ecology to maintain homeostasis or succumb to a disease process. These findings implicate the chronicity of the local response in attempting to manage the microbial challenge, creating a 'Double Indemnity' in some patients that does not 'insure' health for the periodontium. As importantly, in reflecting the title of this volume of Periodontology 2000, this review attempts to inform the community of how the science of periodontal immunology gestated, how continual probing of the biology of the disease has led to an evolution in our knowledge base and how more recent studies in the postgenomic era are revolutionizing our understanding of disease initiation, progression and resolution. Thus, there has been substantial progress in our understanding of the molecular mechanisms of host-bacteria interactions that result in the clinical presentation and outcomes of destructive periodontitis. The science has embarked from observations of variations in responses related to disease expression with a focus for utilization of the responses in diagnosis and therapeutic outcomes, to current investigations using cutting-edge fundamental biological processes to attempt to model the initiation and progression of soft- and hard-tissue destruction of the periodontium. As importantly, the next era in the immunobiology of periodontal disease will need to engage more sophisticated experimental designs for clinical studies to enable robust translation of basic biologic processes that are in action early in the transition from health to disease, those which stimulate microenvironmental changes that select for a more pathogenic microbial ecology and those that represent a rebalancing of the complex host responses and a resolution of inflammatory tissue destruction.}, }
@article {pmid23574465, year = {2013}, author = {Teles, R and Teles, F and Frias-Lopez, J and Paster, B and Haffajee, A}, title = {Lessons learned and unlearned in periodontal microbiology.}, journal = {Periodontology 2000}, volume = {62}, number = {1}, pages = {95-162}, pmid = {23574465}, issn = {1600-0757}, support = {DE-021553/DE/NIDCR NIH HHS/United States ; U01 DE021127/DE/NIDCR NIH HHS/United States ; DE-021565/DE/NIDCR NIH HHS/United States ; DE-017400/DE/NIDCR NIH HHS/United States ; DE-021742/DE/NIDCR NIH HHS/United States ; DE-021127/DE/NIDCR NIH HHS/United States ; }, mesh = {*Biofilms/classification/growth &amp; development ; Host-Pathogen Interactions/physiology ; Humans ; Microbial Interactions/physiology ; Microbiota/physiology ; Molecular Biology ; Periodontal Diseases/*microbiology/virology ; }, abstract = {Periodontal diseases are initiated by bacterial species living in polymicrobial biofilms at or below the gingival margin and progress largely as a result of the inflammation elicited by specific subgingival species. In the past few decades, efforts to understand the periodontal microbiota have led to an exponential increase in information about biofilms associated with periodontal health and disease. In fact, the oral microbiota is one of the best-characterized microbiomes that colonize the human body. Despite this increased knowledge, one has to ask if our fundamental concepts of the etiology and pathogenesis of periodontal diseases have really changed. In this article we will review how our comprehension of the structure and function of the subgingival microbiota has evolved over the years in search of lessons learned and unlearned in periodontal microbiology. More specifically, this review focuses on: (i) how the data obtained through molecular techniques have impacted our knowledge of the etiology of periodontal infections; (ii) the potential role of viruses in the etiopathogenesis of periodontal diseases; (iii) how concepts of microbial ecology have expanded our understanding of host-microbe interactions that might lead to periodontal diseases; (iv) the role of inflammation in the pathogenesis of periodontal diseases; and (v) the impact of these evolving concepts on therapeutic and preventive strategies to periodontal infections. We will conclude by reviewing how novel systems-biology approaches promise to unravel new details of the pathogenesis of periodontal diseases and hopefully lead to a better understanding of their mechanisms.}, }
@article {pmid23571665, year = {2013}, author = {Cai, HY and Yan, ZS and Wang, AJ and Krumholz, LR and Jiang, HL}, title = {Analysis of the attached microbial community on mucilaginous cyanobacterial aggregates in the eutrophic Lake Taihu reveals the importance of Planctomycetes.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {73-83}, pmid = {23571665}, issn = {1432-184X}, mesh = {Biodiversity ; China ; Cyanobacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Ecosystem ; Lakes/analysis/*microbiology ; Molecular Sequence Data ; Phylogeny ; Planctomycetales/classification/genetics/*isolation &amp; purification/metabolism ; }, abstract = {The phylogenetic diversity of the microbial community assemblage of the carpet-like mucilaginous cyanobacterial blooms in the eutrophic Lake Taihu was investigated. 16S ribosomal DNA clone libraries produced from the DNA of cyanobacterial assemblages that had been washed to remove unattached bacteria contained only cyanobacteria. However, a further treatment which included grinding the freeze-dried material to physically detach cells followed by the removal of larger cells by filtration allowed us to detect a large variety of bacteria within the cyanobacterial bloom community. Interestingly, the dominant members of the microbial community were Planctomycetes followed by Cytophaga-Flavobacterium-Bacteroides (CFB), Betaproteobacteria, and Gammaproteobacteria. The analysis of the 16S ribosomal DNA clone libraries made from enrichment culture revealed much higher phylogenetic diversity of bacteria. Dominant bacterial groups in the enrichment system were identified as members of the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria subdivisions, CFB group, and Planctomycetes. In addition, the clone libraries constructed from Planctomycetes-specific 16S ribosomal RNA primers also verified that the enrichment allowed a diversity of Planctomycetes to proliferate, although the community composition was altered after enrichment.}, }
@article {pmid23570991, year = {2014}, author = {Antiabong, JF and Boardman, W and Ball, AS}, title = {What can we learn from the microbial ecological interactions associated with polymicrobial diseases?.}, journal = {Veterinary immunology and immunopathology}, volume = {158}, number = {1-2}, pages = {30-36}, doi = {10.1016/j.vetimm.2013.03.009}, pmid = {23570991}, issn = {1873-2534}, mesh = {Animals ; Anti-Infective Agents/*therapeutic use ; Ecology/methods ; Humans ; Microbial Interactions/*immunology ; Periodontal Diseases/drug therapy/immunology/*microbiology ; }, abstract = {Periodontal diseases in humans and animals are model polymicrobial diseases which are associated with a shift in the microbial community structure and function; there is therefore a need to investigate these diseases from a microbial ecological perspective. This review highlights three important areas of microbial ecological investigation of polymicrobial diseases and the lessons that could be learnt: (1) identification of disease-associated microbes and the implications for choice of anti-infective treatment; (2) the implications associated with vaccine design and development and (3) application of the dynamics of microbial interaction in the discovery of novel anti-infective agents. This review emphasises the need to invigorate microbial ecological approaches to the study of periodontal diseases and other polymicrobial diseases for greater understanding of the ecological interactions between and within the biotic and abiotic factors of the environment.}, }
@article {pmid23563939, year = {2013}, author = {Lay, CY and Mykytczuk, NC and Yergeau, &#xc9; and Lamarche-Gagnon, G and Greer, CW and Whyte, LG}, title = {Defining the functional potential and active community members of a sediment microbial community in a high-arctic hypersaline subzero spring.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {12}, pages = {3637-3648}, pmid = {23563939}, issn = {1098-5336}, mesh = {Archaea/genetics ; Arctic Regions ; Bacteroidetes/genetics ; Base Sequence ; *Cold Temperature ; Cyanobacteria/genetics ; DNA Primers/genetics ; DNA, Complementary/genetics ; Geologic Sediments/*microbiology ; Metagenome/*genetics ; Molecular Sequence Data ; Natural Springs/*microbiology ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Sequence Analysis, DNA ; }, abstract = {The Lost Hammer (LH) Spring is the coldest and saltiest terrestrial spring discovered to date and is characterized by perennial discharges at subzero temperatures (-5°C), hypersalinity (salinity, 24%), and reducing (≈-165 mV), microoxic, and oligotrophic conditions. It is rich in sulfates (10.0%, wt/wt), dissolved H2S/sulfides (up to 25 ppm), ammonia (≈381 μM), and methane (11.1 g day(-1)). To determine its total functional and genetic potential and to identify its active microbial components, we performed metagenomic analyses of the LH Spring outlet microbial community and pyrosequencing analyses of the cDNA of its 16S rRNA genes. Reads related to Cyanobacteria (19.7%), Bacteroidetes (13.3%), and Proteobacteria (6.6%) represented the dominant phyla identified among the classified sequences. Reconstruction of the enzyme pathways responsible for bacterial nitrification/denitrification/ammonification and sulfate reduction appeared nearly complete in the metagenomic data set. In the cDNA profile of the LH Spring active community, ammonia oxidizers (Thaumarchaeota), denitrifiers (Pseudomonas spp.), sulfate reducers (Desulfobulbus spp.), and other sulfur oxidizers (Thermoprotei) were present, highlighting their involvement in nitrogen and sulfur cycling. Stress response genes for adapting to cold, osmotic stress, and oxidative stress were also abundant in the metagenome. Comparison of the composition of the functional community of the LH Spring to metagenomes from other saline/subzero environments revealed a close association between the LH Spring and another Canadian high-Arctic permafrost environment, particularly in genes related to sulfur metabolism and dormancy. Overall, this study provides insights into the metabolic potential and the active microbial populations that exist in this hypersaline cryoenvironment and contributes to our understanding of microbial ecology in extreme environments.}, }
@article {pmid23563743, year = {2013}, author = {Wang, B and Waters, AL and Sims, JW and Fullmer, A and Ellison, S and Hamann, MT}, title = {Complex marine natural products as potential epigenetic and production regulators of antibiotics from a marine Pseudomonas aeruginosa.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {1068-1075}, pmid = {23563743}, issn = {1432-184X}, support = {C06 RR014503/RR/NCRR NIH HHS/United States ; F32 AI083157/AI/NIAID NIH HHS/United States ; R01AT007318/AT/NCCIH NIH HHS/United States ; C06 RR-14503-01/RR/NCRR NIH HHS/United States ; F32AI083157/AI/NIAID NIH HHS/United States ; R01 AT007318/AT/NCCIH NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/analysis/*metabolism ; Biological Products/analysis/*metabolism ; Epigenomics ; Geologic Sediments/*microbiology ; Pseudomonas aeruginosa/*chemistry/classification/isolation &amp; purification/*metabolism ; Seawater/*microbiology ; }, abstract = {Marine microbes are capable of producing secondary metabolites for defense and competition. Factors exerting an impact on secondary metabolite production of microbial communities included bioactive natural products and co-culturing. These external influences may have practical applications such as increased yields or the generation of new metabolites from otherwise silent genes in addition to reducing or limiting the production of undesirable metabolites. In this paper, we discuss the metabolic profiles of a marine Pseudomonas aeruginosa in the presence of a number of potential chemical epigenetic regulators, adjusting carbon sources and co-culturing with other microbes to induce a competitive response. As a result of these stressors certain groups of antibiotics or antimalarial agents were increased most notably when treating P. aeruginosa with sceptrin and co-culturing with another Pseudomonas sp. An interesting cross-talking event between these two Pseudomonas species when cultured together and exposed to sceptrin was observed.}, }
@article {pmid23563708, year = {2013}, author = {Böer, SI and Heinemeyer, EA and Luden, K and Erler, R and Gerdts, G and Janssen, F and Brennholt, N}, title = {Temporal and spatial distribution patterns of potentially pathogenic Vibrio spp. at recreational beaches of the German north sea.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {1052-1067}, pmid = {23563708}, issn = {1432-184X}, mesh = {Germany ; North Sea ; Seasons ; Seawater/chemistry/*microbiology ; Temperature ; Vibrio/classification/genetics/*isolation &amp; purification ; }, abstract = {The number of reported Vibrio-related wound infections associated with recreational bathing in Northern Europe has increased within the last decades. In order to study the health risk from potentially pathogenic Vibrio spp. in the central Wadden Sea, the seasonal and spatial distribution of Vibrio vulnificus, Vibrio parahaemolyticus, Vibrio alginolyticus and Vibrio cholerae were investigated at ten recreational beaches in this area over a 2-year period. V. alginolyticus and V. parahaemolyticus were found to be omnipresent all year round in the study area, while V. vulnificus occurrence was restricted to summer months in the estuaries of the rivers Ems and Weser. Multiple linear regression models revealed that water temperature is the most important determinant of Vibrio spp. occurrence in the area. Differentiated regression models showed a species-specific response to water temperature and revealed a particularly strong effect of even minor temperature increases on the probability of detecting V. vulnificus in summer. In sediments, Vibrio spp. concentrations were up to three orders of magnitude higher than in water. Also, V. alginolyticus and V. parahaemolyticus were found to be less susceptible towards winter temperatures in the benthic environment than in the water, indicating an important role of sediments for Vibrio ecology. While only a very small percentage of tested V. parahaemolyticus proved to be potentially pathogenic, the presence of V. vulnificus during the summer months should be regarded with care.}, }
@article {pmid23563631, year = {2013}, author = {Navarro-Noya, YE and Suárez-Arriaga, MC and Rojas-Valdes, A and Montoya-Ciriaco, NM and Gómez-Acata, S and Fernández-Luqueño, F and Dendooven, L}, title = {Pyrosequencing analysis of the bacterial community in drinking water wells.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {19-29}, pmid = {23563631}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Groundwater/*microbiology ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Water Wells/*microbiology ; }, abstract = {Wells used for drinking water often have a large biomass and a high bacterial diversity. Current technologies are not always able to reduce the bacterial population, and the threat of pathogen proliferation in drinking water sources is omnipresent. The environmental conditions that shape the microbial communities in drinking water sources have to be elucidated, so that pathogen proliferation can be foreseen. In this work, the bacterial community in nine water wells of a groundwater aquifer in Northern Mexico were characterized and correlated to environmental characteristics that might control them. Although a large variation was observed between the water samples, temperature and iron concentration were the characteristics that affected the bacterial community structure and composition in groundwater wells. Small increases in the concentration of iron in water modified the bacterial communities and promoted the growth of the iron-oxidizing bacteria Acidovorax. The abundance of the genera Flavobacterium and Duganella was correlated positively with temperature and the Acidobacteria Gp4 and Gp1, and the genus Acidovorax with iron concentrations in the well water. Large percentages of Flavobacterium and Pseudomonas bacteria were found, and this is of special concern as bacteria belonging to both genera are often biofilm developers, where pathogens survival increases.}, }
@article {pmid23553590, year = {2014}, author = {Nayak, S and Porob, S and Fernandes, A and Meena, RM and Ramaiah, N}, title = {PCR detection of ansA from marine bacteria and its sequence characteristics from Bacillus tequilensis NIOS4.}, journal = {Journal of basic microbiology}, volume = {54}, number = {2}, pages = {162-168}, doi = {10.1002/jobm.201200355}, pmid = {23553590}, issn = {1521-4028}, mesh = {Amino Acid Sequence ; Aquatic Organisms ; Asparaginase/*genetics ; Bacillus/*genetics ; Bacterial Proteins/*genetics ; DNA, Bacterial/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {As many as 71 marine bacterial DNA extracts were PCR screened for L-asparaginase (ansA), a key gene in anti-cancer molecular-searches. Over 62% (44) of them were positive for ansA gene. The positive cultures were from genera Bacillus and Staphylococcus. The ansA gene cloned from isolate NIOS4 belonging to recently described Bacillus tequilensis is 1099 bp in length with a 990 bp ORF coding for 329 amino acids. BLASTx analysis revealed this sequence to be 98% similar to earlier reported ansA sequence from B. subtilis (Accession no. NP390239.1). By comparing its deduced amino acid sequence with other bacterial asparaginase sequences six substitutions at positions 305(Thr), 313(Lys), 314(Leu), 315(Asp), 318(Arg), and 320(Gln) are observed. Key residues like Thr(12), Thr(85), Asp(86), Lys(156), and Phe(165) taking part in active-site formation and imparting catalytic properties are conserved. The phylogenetic tree based of the ansA amino acid sequences revealed close relatedness of the NIOS4 ansA sequence with B. subtilis (Accession no. NP 390239.1). It's very close genetic resemblance to B. subtilis and conservation of certain key amino acid residues suggest it as a prospective candidate for evaluation and, production of L-asparaginases.}, }
@article {pmid23553002, year = {2013}, author = {McLean, TI}, title = {"Eco-omics": a review of the application of genomics, transcriptomics, and proteomics for the study of the ecology of harmful algae.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {901-915}, pmid = {23553002}, issn = {1432-184X}, mesh = {Ecology ; *Gene-Environment Interaction ; *Genomics ; *Harmful Algal Bloom ; Plants/*genetics ; *Proteomics ; Transcription, Genetic ; }, abstract = {The implementation of molecular techniques has been widely adopted throughout the life sciences except in the marine sciences. The latter trend is quickly being reversed as even more cutting-edge molecular platforms, referred to collectively as 'omics-related technologies, are being used in a number of laboratories that study various aspects of life in the marine environment. This review provides a brief overview of just a few representative studies that have used genomics, transcriptomics, or proteomics approaches to deepen our understanding, specifically, about the underlying molecular biology of harmful algae. The examples of the studies described here are particularly relevant in showing how the information gleaned from these technologies can uncover the genetic capacity of harmful algal bloom-forming species, can generate new hypotheses about mechanistic relationships that bridge gene-environment interactions, and can impinge on our understanding surrounding the ecology of these organisms.}, }
@article {pmid23553001, year = {2013}, author = {Plano, LR and Shibata, T and Garza, AC and Kish, J and Fleisher, JM and Sinigalliano, CD and Gidley, ML and Withum, K and Elmir, SM and Hower, S and Jackson, CR and Barrett, JB and Cleary, T and Davidson, M and Davis, J and Mukherjee, S and Fleming, LE and Solo-Gabriele, HM}, title = {Human-associated methicillin-resistant Staphylococcus aureus from a subtropical recreational marine beach.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {1039-1051}, pmid = {23553001}, issn = {1432-184X}, support = {P50 ES012736/ES/NIEHS NIH HHS/United States ; P50 ES12736/ES/NIEHS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Bacterial Toxins/genetics/metabolism ; Drug Resistance, Bacterial ; Exotoxins/genetics/metabolism ; Humans ; Leukocidins/genetics/metabolism ; Methicillin-Resistant Staphylococcus aureus/classification/genetics/*isolation &amp; purification ; Public Facilities ; Seawater/*microbiology ; Staphylococcal Infections/*microbiology ; }, abstract = {Reports of Staphylococcus aureus including methicillin-resistant S. aureus (MRSA) detected in marine environments have occurred since the early 1990 s. This investigation sought to isolate and characterize S. aureus from marine waters and sand at a subtropical recreational beach, with and without bathers present, in order to investigate possible sources and to identify the risks to bathers of exposure to these organisms. During 40 days over 17 months, 1,001 water and 36 intertidal sand samples were collected by either bathers or investigators at a subtropical recreational beach. Methicillin-sensitive S. aureus (MSSA) and MRSA were isolated and identified using selective growth media and an organism-specific molecular marker. Antimicrobial susceptibility, staphylococcal cassette chromosome mec (SCCmec) type, pulsed-field gel electrophoresis (PFGE) pattern, multi-locus sequence type (MLST), and staphylococcal protein A (spa) type were characterized for all MRSA. S. aureus was isolated from 248 (37 %) bather nearby water samples at a concentration range of <2-780 colony forming units per ml, 102 (31 %) ambient water samples at a concentration range of <2-260 colony forming units per ml, and 9 (25 %) sand samples. Within the sand environment, S. aureus was isolated more often from above the intertidal zone than from intermittently wet or inundated sand. A total of 1334 MSSA were isolated from 37 sampling days and 22 MRSA were isolated from ten sampling days. Seventeen of the 22 MRSA were identified by PFGE as the community-associated MRSA USA300. MRSA isolates were all SCCmec type IVa, encompassed five spa types (t008, t064, t622, t688, and t723), two MLST types (ST8 and ST5), and 21 of 22 isolates carried the genes for Panton-Valentine leukocidin. There was a correlation (r = 0.45; p = 0.05) between the daily average number of bathers and S. aureus in the water; however, no association between exposure to S. aureus in these waters and reported illness was found. This report supports the concept that humans are a potential direct source for S. aureus in marine waters.}, }
@article {pmid23550883, year = {2013}, author = {Vos, M and Wolf, AB and Jennings, SJ and Kowalchuk, GA}, title = {Micro-scale determinants of bacterial diversity in soil.}, journal = {FEMS microbiology reviews}, volume = {37}, number = {6}, pages = {936-954}, doi = {10.1111/1574-6976.12023}, pmid = {23550883}, issn = {1574-6976}, mesh = {Bacteria/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; *Biodiversity ; Microbial Interactions ; Phylogeography ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Soil habitats contain vast numbers of microorganisms and harbor a large portion of the planet's biological diversity. Although high-throughput sequencing technologies continue to advance our appreciation of this remarkable phylogenetic and functional diversity, we still have only a rudimentary understanding of the forces that allow diverse microbial populations to coexist in soils. This conspicuous knowledge gap may be partially due the human perspective from which we tend to examine soilborne microorganisms. This review focusses on the highly heterogeneous soil matrix from the vantage point of individual bacteria. Methods describing micro-scale soil habitats and their inhabitants based on sieving, dissecting, and visualizing individual soil aggregates are discussed, as are microcosm-based experiments allowing the manipulation of key soil parameters. We identify how the spatial heterogeneity of soil could influence a number of ecological interactions promoting the evolution and maintenance of bacterial diversity.}, }
@article {pmid23550823, year = {2013}, author = {Maurice, CF and Turnbaugh, PJ}, title = {Quantifying the metabolic activities of human-associated microbial communities across multiple ecological scales.}, journal = {FEMS microbiology reviews}, volume = {37}, number = {5}, pages = {830-848}, pmid = {23550823}, issn = {1574-6976}, support = {P50 GM068763/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Ecosystem ; Humans ; Metabolomics/*methods ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; Single-Cell Analysis/methods ; }, abstract = {Humans are home to complex microbial communities, whose aggregate genomes and their encoded metabolic activities are referred to as the human microbiome. Recently, researchers have begun to appreciate that different human body habitats and the activities of their resident microorganisms can be better understood in ecological terms, as a range of spatial scales encompassing single cells, guilds of microorganisms responsive to a similar substrate, microbial communities, body habitats, and host populations. However, the bulk of the work to date has focused on studies of culturable microorganisms in isolation or on DNA sequencing-based surveys of microbial diversity in small-to-moderate-sized cohorts of individuals. Here, we discuss recent work that highlights the potential for assessing the human microbiome at a range of spatial scales, and for developing novel techniques that bridge multiple levels: for example, through the combination of single-cell methods and metagenomic sequencing. These studies promise to not only provide a much-needed epidemiological and ecological context for mechanistic studies of culturable and genetically tractable microorganisms, but may also lead to the discovery of fundamental rules that govern the assembly and function of host-associated microbial communities.}, }
@article {pmid23548303, year = {2013}, author = {Turchi, B and Van Tassell, ML and Lee, A and Nuvoloni, R and Cerri, D and Miller, MJ}, title = {Short communication: phenotypic and genetic diversity of wild Lactococcus lactis isolated from traditional Pecorino cheeses of Tuscany.}, journal = {Journal of dairy science}, volume = {96}, number = {6}, pages = {3558-3563}, doi = {10.3168/jds.2012-6518}, pmid = {23548303}, issn = {1525-3198}, mesh = {Animals ; Cheese/*microbiology ; DNA, Bacterial/analysis/chemistry ; Ecology ; Fermentation ; *Genetic Variation ; Hydrogen-Ion Concentration ; Italy ; Lactococcus lactis/*classification/*genetics/physiology ; Milk/microbiology ; Peptide Hydrolases/metabolism ; Phenotype ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sheep ; }, abstract = {Wild Lactococcus lactis isolates from traditional Pecorino cheeses in 4 regions of Tuscany were isolated and characterized to evaluate the diversity of autochthonous lactococci. Sixty strains of Lactococcus were clustered by the results of carbohydrate utilization and diagnostic enzyme activity. Twenty-one unique strains were then chosen for characterization of salt and temperature tolerance, as well as acidification and proteolytic activity in milk. Genetic analysis of these strains was performed via 16S ribosomal DNA sequencing and multilocus sequence typing (MLST) to elucidate diversity relative to their location of origin. Phylogenetic analysis showed distinct clustering by region within organism subspecies, and phenotypic properties demonstrated concomitant trends. Multilocus sequence typing thus allowed for the regional distinction of isolates separate from those of previous works, supporting the concept that distinctive regional qualities of cheeses are strongly influenced by microbial ecology.}, }
@article {pmid23535981, year = {2013}, author = {Katyal, I and Chaban, B and Ng, B and Hill, JE}, title = {CRISPRs of Enterococcus faecalis and E. hirae isolates from pig feces have species-specific repeats but share some common spacer sequences.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {182-188}, pmid = {23535981}, issn = {1432-184X}, mesh = {Animals ; *Clustered Regularly Interspaced Short Palindromic Repeats ; DNA, Bacterial/*genetics ; DNA, Intergenic/*genetics ; Enterococcus/*genetics/*isolation &amp; purification ; Enterococcus faecalis/*genetics/*isolation &amp; purification ; Feces/*microbiology ; Species Specificity ; Sus scrofa ; }, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) are currently a topic of interest in microbiology due to their role as a prokaryotic immune system. Investigations of CRISPR distribution and characterization to date have focused on pathogenic bacteria, while less is known about CRISPR in commensal bacteria, where they may have a significant role in the ecology of the microbiota of humans and other animals, and act as a recorder of interactions between bacteria and viruses. A combination of PCR and sequencing was used to determine prevalence and distribution of CRISPR arrays in Enterococcus faecalis and Enterococcus hirae isolates from the feces of healthy pigs. Both type II CRISPR-Cas and Orphan CRISPR (without Cas genes) were detected in the 195 isolates examined. CRISPR-Cas was detected in 52 (46/88) and 42 % (45/107) E. faecalis and E. hirae isolates, respectively. The prevalence of Orphan CRISPR arrays was higher in E. faecalis isolates (95 %, 84/88) compared with E. hirae isolates (49 %, 53/107). Species-specific repeat sequences were identified in Orphan CRISPR arrays, and 42 unique spacer sequences were identified. Only two spacers matched previously characterized pig virome sequences, and many were apparently derived from chromosomal sequences of enterococci. Surprisingly, 17 (40 %) of the spacers were detected in both species. Shared spacer sequences are evidence of a lack of species specificity in the agents and mechanisms responsible for integration of spacers, and the abundance of spacer sequences corresponding to bacterial chromosomal sequences reflects interspecific interactions within the intestinal microbiota.}, }
@article {pmid23535917, year = {2013}, author = {Pantoja-Feliciano, IG and Clemente, JC and Costello, EK and Perez, ME and Blaser, MJ and Knight, R and Dominguez-Bello, MG}, title = {Biphasic assembly of the murine intestinal microbiota during early development.}, journal = {The ISME journal}, volume = {7}, number = {6}, pages = {1112-1115}, pmid = {23535917}, issn = {1751-7370}, support = {5R25GM061151/GM/NIGMS NIH HHS/United States ; S06GM08102/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; P20 RR16470/RR/NCRR NIH HHS/United States ; U54 NS039405/NS/NINDS NIH HHS/United States ; S06 GM008102/GM/NIGMS NIH HHS/United States ; U54 NS39405/NS/NINDS NIH HHS/United States ; R25 GM061151/GM/NIGMS NIH HHS/United States ; P20 RR016470/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Animals, Newborn/microbiology ; Bacteria/*classification/*growth &amp; development ; Bacteria, Anaerobic/classification/genetics/growth &amp; development ; Colon/*microbiology ; Female ; Lactobacillus/genetics/growth &amp; development ; Male ; Mice/*growth &amp; development/*microbiology ; *Microbiota ; Weaning ; }, abstract = {The birth canal provides mammals with a primary maternal inoculum, which develops into distinctive body site-specific microbial communities post-natally. We characterized the distal gut microbiota from birth to weaning in mice. One-day-old mice had colonic microbiota that resembled maternal vaginal communities, but at days 3 and 9 of age there was a substantial loss of intestinal bacterial diversity and dominance of Lactobacillus. By weaning (21 days), diverse intestinal bacteria had established, including strict anaerobes. Our results are consistent with vertical transmission of maternal microbiota and demonstrate a nonlinear ecological succession involving an early drop in bacterial diversity and shift in dominance from Streptococcus to Lactobacillus, followed by an increase in diversity of anaerobes, after the introduction of solid food. Mammalian newborns are born highly susceptible to colonization, and lactation may control microbiome assembly during early development.}, }
@article {pmid23533328, year = {2013}, author = {Vissers, EW and Anselmetti, FS and Bodelier, PL and Muyzer, G and Schleper, C and Tourna, M and Laanbroek, HJ}, title = {Temporal and spatial coexistence of archaeal and bacterial amoA genes and gene transcripts in Lake Lucerne.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2013}, number = {}, pages = {289478}, pmid = {23533328}, issn = {1472-3654}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biodiversity ; *Ecosystem ; Fresh Water/*microbiology ; Oxidoreductases/*genetics ; Seasons ; }, abstract = {Despite their crucial role in the nitrogen cycle, freshwater ecosystems are relatively rarely studied for active ammonia oxidizers (AO). This study of Lake Lucerne determined the abundance of both amoA genes and gene transcripts of ammonia-oxidizing archaea (AOA) and bacteria (AOB) over a period of 16 months, shedding more light on the role of both AO in a deep, alpine lake environment. At the surface, at 42 m water depth, and in the water layer immediately above the sediment, AOA generally outnumbered AOB. However, in the surface water during summer stratification, when both AO were low in abundance, AOB were more numerous than AOA. Temporal distribution patterns of AOA and AOB were comparable. Higher abundances of amoA gene transcripts were observed at the onset and end of summer stratification. In summer, archaeal amoA genes and transcripts correlated negatively with temperature and conductivity. Concentrations of ammonium and oxygen did not vary enough to explain the amoA gene and transcript dynamics. The observed herbivorous zooplankton may have caused a hidden flux of mineralized ammonium and a change in abundance of genes and transcripts. At the surface, AO might have been repressed during summer stratification due to nutrient limitation caused by active phytoplankton.}, }
@article {pmid23532503, year = {2013}, author = {Hajek, AE and Nielsen, C and Kepler, RM and Long, SJ and Castrillo, L}, title = {Fidelity among Sirex woodwasps and their fungal symbionts.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {753-762}, pmid = {23532503}, issn = {1432-184X}, mesh = {Animals ; Basidiomycota/genetics/isolation &amp; purification/*physiology ; Female ; Host Specificity ; Male ; Pinus/parasitology ; Species Specificity ; *Symbiosis ; Trees/parasitology ; United States ; Wasps/*microbiology/physiology ; }, abstract = {We report that associations between mutualistic fungi and their economically and ecologically important woodwasp hosts are not always specific as was previously assumed. Woodwasps in the genus Sirex engage in obligate nutritional ectosymbioses with two species of Amylostereum, a homobasid\iomycete genus of white rot fungi. In the present study, the Amylostereum species and genotypes associated with three species of Sirex native to eastern North America and one relatively recent invasive Sirex from Europe were investigated by comparing intergenic spacer regions (IGS). Sirex spp. were sampled over 6 years from 23 sites in six US states, ranging from Maine in the northeast to Louisiana in the southeast, to obtain samples of Amylostereum from mycangia of adult females. Two of the native Sirex species (Sirex nigricornis and Sirex nitidus) were associated with either Amylostereum chailletii or Amylostereum areolatum, refuting the hypothesis of strict species-specific relationships. However, the invasive Sirex noctilio and the native Sirex cyaneus were each collected with only A. areolatum or A. chailletii, respectively, although S. noctilio was associated with two different IGS genotypes of A. areolatum and S. cyaneus occurs sympatrically with the other native Sirex. In Pinus, the preferred host tree of S. nigricornis and S. noctilio, these species co-occurred in 25.9 % of trees sampled, and horizontal transmission of fungal strains from S. noctilio to S. nigricornis was documented, although only in one tree. The extent that further spread and establishment of S. noctilio will alter the composition of symbionts carried by native Sirex is unknown but will depend in part on the degree of flexibility in these host-symbiont associations.}, }
@article {pmid23529653, year = {2013}, author = {Huang, XF and Bakker, MG and Judd, TM and Reardon, KF and Vivanco, JM}, title = {Variations in diversity and richness of gut bacterial communities of termites (Reticulitermes flavipes) fed with grassy and woody plant substrates.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {531-536}, pmid = {23529653}, issn = {1432-184X}, mesh = {Animal Feed/*analysis ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/genetics ; Gastrointestinal Tract/metabolism/microbiology ; Isoptera/*metabolism/*microbiology ; Molecular Sequence Data ; Plants/*metabolism ; RNA, Ribosomal, 16S/genetics ; Wood/*metabolism ; }, abstract = {Diets shape the animal gut microbiota, although the relationships between diets and the structure of the gut microbial community are not yet well understood. The gut bacterial communities of Reticulitermes flavipes termites fed on four individual plant biomasses with different degrees of recalcitrance to biodegradation were investigated by 16S rRNA pyrosequencing analysis. The termite gut bacterial communities could be differentiated between grassy and woody diets, and among grassy diets (corn stover vs. sorghum). The majority of bacterial taxa were shared across all diets, but each diet significantly enriched some taxa. Interestingly, the diet of corn stover reduced gut bacterial richness and diversity compared to other diets, and this may be related to the lower recalcitrance of this biomass to degradation.}, }
@article {pmid23529652, year = {2013}, author = {Pita, L and López-Legentil, S and Erwin, PM}, title = {Biogeography and host fidelity of bacterial communities in Ircinia spp. from the Bahamas.}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {437-447}, pmid = {23529652}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; Bahamas ; Biodiversity ; *Host Specificity ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Porifera/classification/*microbiology/physiology ; Seawater/*microbiology ; Symbiosis ; }, abstract = {Research on sponge microbial assemblages has revealed different trends in the geographic variability and specificity of bacterial symbionts. Here, we combined replicated terminal-restriction fragment length polymorphism (T-RFLP) and clone library analyses of 16S rRNA gene sequences to investigate the biogeographic and host-specific structure of bacterial communities in two congeneric and sympatric sponges: Ircinia strobilina, two color morphs of Ircinia felix and ambient seawater. Samples were collected from five islands of the Bahamas separated by 80 to 400 km. T-RFLP profiles revealed significant differences in bacterial community structure among sponge hosts and ambient bacterioplankton. Pairwise statistical comparisons of clone libraries confirmed the specificity of the bacterial assemblages to each host species and differentiated symbiont communities between color morphs of I. felix. Overall, differences in bacterial communities within each host species and morph were unrelated to location. Our results show a high degree of symbiont fidelity to host sponge across a spatial scale of up to 400 km, suggesting that host-specific rather than biogeographic factors play a primary role in structuring and maintaining sponge-bacteria relationships in Ircinia species from the Bahamas.}, }
@article {pmid23529651, year = {2013}, author = {Weltzer, ML and Miller, SR}, title = {Division-specific differences in bacterial community assembly of two alkaline hot spring ecosystems from Yellowstone National Park.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {537-540}, pmid = {23529651}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; *Ecosystem ; Hot Springs/analysis/*microbiology ; United States ; }, abstract = {A fundamental issue in ecology is whether communities are random assemblages or, alternatively, whether there are rules that determine which combinations of taxa can co-occur. For microbial systems, in particular, the question of whether taxonomic groups exhibit differences in community organization remains unresolved but is critical for our understanding of community structure and function. Here, we used presence-absence matrices derived from bar-coded pyrosequencing data to evaluate the assembly patterns of eight bacterial divisions distributed along two Yellowstone National Park hot spring outflow channels. Four divisions (Cyanobacteria, Chloroflexi, Acidobacteria, and Cytophaga-Flavobacterium-Bacteroides) exhibited less co-occurrence than expected by chance, with phototrophic taxa showing the strongest evidence for nonrandom community structure. We propose that both differences in environmental tolerance and competitive interactions within divisions contribute to these nonrandom assembly patterns. The higher degree of nonrandom structure observed for phototrophic taxa compared with the other divisions may be due in part to greater overlap in resource usage, as has been previously proposed for plant communities.}, }
@article {pmid23525793, year = {2013}, author = {Karlińska-Batres, K and Wörheide, G}, title = {Phylogenetic diversity and community structure of the symbionts associated with the coralline sponge Astrosclera willeyana of the Great Barrier Reef.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {740-752}, pmid = {23525793}, issn = {1432-184X}, mesh = {Animals ; Archaea/*classification/genetics/*isolation &amp; purification/physiology ; Bacteria/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; Coral Reefs ; Microbial Consortia ; Molecular Sequence Data ; *Phylogeny ; Porifera/*microbiology/physiology ; Seawater/microbiology ; *Symbiosis ; }, abstract = {The coralline sponge Astrosclera willeyana, considered to be a living representative of the reef-building stromatoporoids of the Mesozoic and the Paleozoic periods, occurs widely throughout the Indo-Pacific oceans. We aimed to examine, for the first time, the phylogenetic diversity of the microbial symbionts associated with A. willeyana using molecular methods and to investigate the spatial variability in the sponge-derived microbial communities of A. willeyana from diverse sites along the Great Barrier Reef (GBR). Both denaturing gradient gel electrophoresis (DGGE) analyses of 12 Astrosclera specimens and sequencing of a 16S rRNA gene clone library, constructed using a specimen of A. willeyana from the Yonge Reef (380 clones), revealed the presence of a complex microbial community with high diversity. An assessment of the 16S rRNA gene sequences to the particular phylogenetic groups showed domination of the Chloroflexi (42 %), followed by the Gammaproteobacteria (14 %), Actinobacteria (11 %), Acidobacteria (8 %), and the Deferribacteres (7 %). Of the microbes that were identified, a further 15 % belonged to the Deltaproteobacteria, Alphaproteobacteria, and Nitrospirae genera. The minor phylogenetic groups Gemmatimonadetes, Spirochaetes, Cyanobacteria, Poribacteria, and the Archaea composed 3 % of the community. Over 94 % of the sequences obtained from A. willeyana grouped together with other sponge- or coral-derived sequences, and of these, 72 % formed, with nearest relatives, 46 sponge-specific or sponge-coral clusters, highlighting the uniqueness of the microbial consortia in sponges. The DGGE results showed clear divisions according to the geographical origin of the samples, indicating closer relationships between the microbial communities with respect to their geographic origin (northern vs. southern GBR).}, }
@article {pmid23525792, year = {2013}, author = {Morales-Jiménez, J and Vera-Ponce de León, A and García-Domínguez, A and Martínez-Romero, E and Zúñiga, G and Hernández-Rodríguez, C}, title = {Nitrogen-fixing and uricolytic bacteria associated with the gut of Dendroctonus rhizophagus and Dendroctonus valens (Curculionidae: Scolytinae).}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {200-210}, pmid = {23525792}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics ; Coleoptera/classification/growth &amp; development/*microbiology ; Female ; Gastrointestinal Tract/microbiology ; Larva/classification/growth &amp; development/microbiology ; Male ; Molecular Sequence Data ; Nitrogen/metabolism ; *Nitrogen Fixation ; Nitrogenase/genetics ; Phylogeny ; }, abstract = {The bark beetles of the genus Dendroctonus feed on phloem that is a nitrogen-limited source. Nitrogen fixation and nitrogen recycling may compensate or alleviate such a limitation, and beetle-associated bacteria capable of such processes were identified. Raoultella terrigena, a diazotrophic bacteria present in the gut of Dendroctonus rhizophagus and D. valens, exhibited high acetylene reduction activity in vitro with different carbon sources, and its nifH and nifD genes were sequenced. Bacteria able to recycle uric acid were Pseudomonas fluorescens DVL3A that used it as carbon and nitrogen source, Serratia proteomaculans 2A CDF and Rahnella aquatilis 6-DR that used uric acid as sole nitrogen source. Also, this is the first report about the uric acid content in whole eggs, larvae, and adults (male and female) samples of the red turpentine beetle (Dendroctonus valens). Our results suggest that the gut bacteria of these bark beetles could contribute to insect N balance.}, }
@article {pmid23524156, year = {2013}, author = {Callbeck, CM and Sherry, A and Hubert, CR and Gray, ND and Voordouw, G and Head, IM}, title = {Improving PCR efficiency for accurate quantification of 16S rRNA genes.}, journal = {Journal of microbiological methods}, volume = {93}, number = {2}, pages = {148-152}, doi = {10.1016/j.mimet.2013.03.010}, pmid = {23524156}, issn = {1872-8359}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Environmental Microbiology ; Microbiological Techniques/*methods ; RNA, Ribosomal, 16S/analysis/*genetics ; Real-Time Polymerase Chain Reaction/*methods ; }, abstract = {Quantitative real-time PCR is a valuable tool for microbial ecologists. To obtain accurate absolute quantification it is essential that PCR efficiency for pure standards is close to amplification efficiency for test samples. Counter to normal expectation that PCR efficiency might be lower in environmental DNA, due to the presence of PCR inhibitors, we report the counterintuitive observation that PCR efficiency of pure standards can be lower than for environmental DNA. This can lead to overestimation of gene abundances if not corrected. SYBR green-based qPCR assays of 16S rRNA genes targeting Bacteria, Syntrophus and Smithella spp., Marinobacter spp., Methanomicrobiales, Methanosarcinaceae, and Methanosaetaceae in samples from methanogenic crude oil biodegradation enrichments were tested. In five out of the six assays, PCR efficiency was lower with pure standards than with environmental DNA samples. We developed a solution to this problem based on amending pure clone standards with a background of non-target environmental 16S rRNA genes which significantly improved PCR efficiency of standards in the qPCR assays that exhibited this phenomenon. Overall this method of qPCR standard preparation achieved a more reliable and robust quantification of 16S rRNA genes. We believe this may be a potentially common issue in microbial ecology that often goes unreported, as intuitively one would not expect standards to have poorer PCR efficiency than samples.}, }
@article {pmid23512353, year = {2013}, author = {Pettersson, M and Bååth, E}, title = {Importance of inoculum properties on the structure and growth of bacterial communities during Recolonisation of humus soil with different pH.}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {416-426}, pmid = {23512353}, issn = {1432-184X}, mesh = {Agricultural Inoculants/genetics/*growth &amp; development/isolation &amp; purification ; Bacteria/genetics/*growth &amp; development/isolation &amp; purification ; *Biodiversity ; Calcium Compounds/analysis ; Ecosystem ; Hydrogen-Ion Concentration ; Oxides/analysis ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {The relationship between community structure and growth and pH tolerance of a soil bacterial community was studied after liming in a reciprocal inoculum study. An unlimed (UL) humus soil with a pH of 4.0 was fumigated with chloroform for 4 h, after which < 1 % of the initial bacterial activity remained. Half of the fumigated soil was experimentally limed (EL) to a pH of 7.6. Both the UL and the EL soil were then reciprocally inoculated with UL soil or field limed (FL) soil with a pH of 6.2. The FL soil was from a 15-year-old experiment. The structural changes were measured on both bacteria in soil and on bacteria able to grow on agar plates using phospholipids fatty acid (PLFA) and denaturing gradient gel electrophoresis (DGGE) analysis. The developing community pH tolerance and bacterial growth were also monitored over time using thymidine incorporation. The inoculum source had a significant impact on both growth and pH tolerance of the bacterial community in the EL soil. These differences between the EL soil inoculated with UL soil and FL soil were correlated to structural changes, as evidenced by both PLFA and DGGE analyses on the soil. Similar correlations were seen to the fraction of the community growing on agar plates. There were, however, no differences between the soil bacterial communities in the unlimed soils with different inocula. This study showed the connection between the development of function (growth), community properties (pH tolerance) and the structure of the bacterial community. It also highlighted the importance of both the initial properties of the community and the selection pressure after environmental changes in shaping the resulting microbial community.}, }
@article {pmid23508733, year = {2013}, author = {Hower, S and Phillips, MC and Brodsky, M and Dameron, A and Tamargo, MA and Salazar, NC and Jackson, CR and Barrett, JB and Davidson, M and Davis, J and Mukherjee, S and Ewing, RY and Gidley, ML and Sinigalliano, CD and Johns, L and Johnson, FE and Adebanjo, O and Plano, LR}, title = {Clonally related methicillin-resistant Staphylococcus aureus isolated from short-finned pilot whales (Globicephala macrorhynchus), human volunteers, and a bayfront cetacean rehabilitation facility.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {1024-1038}, pmid = {23508733}, issn = {1432-184X}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cetacea/*microbiology ; Fin Whale/*microbiology ; Florida ; Humans ; Methicillin-Resistant Staphylococcus aureus/classification/drug effects/genetics/*isolation &amp; purification ; Staphylococcal Infections/*microbiology/*veterinary ; Volunteers ; }, abstract = {In May of 2011, a live mass stranding of 26 short-finned pilot whales (Globicephala macrorhynchus) occurred in the lower Florida Keys. Five surviving whales were transferred from the original stranding site to a nearby marine mammal rehabilitation facility where they were constantly attended to by a team of volunteers. Bacteria cultured during the routine clinical care of the whales and necropsy of a deceased whale included methicillin-sensitive and methicillin-resistant Staphylococcus aureus (MSSA and MRSA). In order to investigate potential sources or reservoirs of MSSA and MRSA, samples were obtained from human volunteers, whales, seawater, and sand from multiple sites at the facility, nearby recreational beaches, and a canal. Samples were collected on 3 days. The second collection day was 2 weeks after the first, and the third collection day was 2 months after the last animal was removed from the facility. MRSA and MSSA were isolated on each day from the facility when animals and volunteers were present. MSSA was found at an adjacent beach on all three collection days. Isolates were characterized by utilizing a combination of quantitative real-time PCR to determine the presence of mecA and genes associated with virulence, staphylococcal protein A typing, staphylococcal cassette chromosome mec typing, multilocus sequence typing, and pulsed field gel electrophoresis (PFGE). Using these methods, clonally related MRSA were isolated from multiple environmental locations as well as from humans and animals. Non-identical but genetically similar MSSA and MRSA were also identified from distinct sources within this sample pool. PFGE indicated that the majority of MRSA isolates were clonally related to the prototype human strain USA300. These studies support the notion that S. aureus may be shed into an environment by humans or pilot whales and subsequently colonize or infect exposed new hosts.}, }
@article {pmid23504024, year = {2013}, author = {Lu, H and He, J and Wu, Z and Xu, W and Zhang, H and Ye, P and Yang, J and Zhen, S and Li, L}, title = {Assessment of microbiome variation during the perioperative period in liver transplant patients: a retrospective analysis.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {781-791}, pmid = {23504024}, issn = {1432-184X}, mesh = {Adult ; Bacteria/classification/genetics/*isolation &amp; purification ; Cross Infection/microbiology/*prevention &amp; control ; Feces/microbiology ; Humans ; Intestines/*microbiology ; *Liver Transplantation ; Male ; *Metagenome ; Perioperative Period ; Phylogeny ; Postoperative Complications/microbiology/*prevention &amp; control ; Retrospective Studies ; }, abstract = {Understanding the composition of the microbial populations in the intestines of liver transplant patients is important to preventing postoperative infection. We investigated the relationship between the risk of postoperative infection and variation in the predominant fecal microbial composition during the perioperative period. We prospectively analyzed the predominant intestinal microbiome of five asymptomatic adult carriers of hepatitis B virus (as controls without any antibiotics) at four weekly follow-up visits and 12 patients before operation and at three weekly postoperative follow-up visits within the first month. Analysis was by denaturing gradient gel electrophoresis (DGGE) and sequencing with digital processing of DGGE profiles using BioNumerics software. Our results showed that the predominant intestinal microbial diversity decreased substantially in eight patients during the perioperative period. Among these, five patients experienced infection with a postoperative hospital stay of more than 30 days. The rest of the four patients who experienced shorter postoperative hospital stays showed only slight variation in predominant intestinal bacterial composition and temporal stability similar to asymptomatic controls. Postoperative fecal DGGE profiles showed mostly bands assigned to Bacteroides and Firmicutes. We conclude that an empiric prophylaxis strategy that destructs gut microecological balance will not be effective in reducing the risk of postoperative infection. Instead, the destruction of intestinal microbiota might result in the appearance of opportunistic pathogens such as Bifidobacterium dentium which rarely appears in the intestinal DGGE profiles of normal humans. Cognizance of the variation of intestinal microbial profiles during the perioperative period is a critical aspect of caring for liver transplant recipients.}, }
@article {pmid23504023, year = {2013}, author = {Ruyters, S and Springael, D and Smolders, E}, title = {Recovery of soil ammonia oxidation after long-term zinc exposure is not related to the richness of the bacterial nitrifying community.}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {312-321}, pmid = {23504023}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; *Biodiversity ; Ecosystem ; Nitrification ; Oxidation-Reduction ; Soil/chemistry ; *Soil Microbiology ; Zinc/analysis/*metabolism ; }, abstract = {A soil sterilization-reinoculation approach was used to manipulate soil microbial diversity and to assess the effect of the diversity of the ammonia-oxidizing bacteria (AOB) on the recovery of the nitrifying community to metal stress (zinc). Gamma-irradiated soil was inoculated with 13 different combinations of up to 22 different soils collected worldwide to create varying degrees of AOB diversity. Two months after inoculation, AOB amoA DGGE based diversity (weighted richness) varied more than 10-fold among the 13 treatments, the largest value observed where the number of inocula had been largest. Subsequently, the 13 treatments were either or not amended with ZnCl2. Initially, Zn amendment completely inhibited nitrification. After 6 months of Zn exposure, recovery of the potential nitrification activity in the Zn amended soils ranged from <10 % to >100 % of the potential nitrification activity in the corresponding non-amended soils. This recovery was neither related to DGGE-based indices of AOB diversity nor to the AOB abundance assessed 2 months after inoculation (p > 0.05). However, recovery was significantly related (r = 0.75) to the potential nitrification rate before Zn amendment and only weakly to the number of soil inocula used in the treatments (r = 0.46). The lack of clear effects of AOB diversity on recovery may be related to an inherently sufficient diversity and functional redundancy of AOB communities in soil. Our data indicate that potential microbial activity can be a significant factor in recovery.}, }
@article {pmid23504022, year = {2013}, author = {Kanokratana, P and Mhuantong, W and Laothanachareon, T and Tangphatsornruang, S and Eurwilaichitr, L and Pootanakit, K and Champreda, V}, title = {Phylogenetic analysis and metabolic potential of microbial communities in an industrial bagasse collection site.}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {322-334}, pmid = {23504022}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification/metabolism ; Biodiversity ; Cellulose/*analysis ; Industrial Waste/*analysis ; Lignin/metabolism ; Molecular Sequence Data ; *Phylogeny ; }, abstract = {Industrial bagasse collection sites at sugar mills are an important resource for biomass-based industries and represent a unique ecological niche in lignocellulose degradation. In this study, microbial community structures at regions with varying microenvironmental conditions contained within a bagasse collection site were explored using tagged 16S rRNA gene pyrosequencing. Overall, remarkable differences in microbial community structures were found in aerobic surface and oxygen-limited interior regions of the pile. A variety of Alphaproteobacteria and Gammaproteobacteria represented the majority of bacteria in the aerobic upper-pile regions with the predominance of acetic acid bacteria towards the outer surface. Diverse Proteobacteria, Bacteroidetes, and Acidobacteria represented the predominant phyla at the exterior soil-contact pile base with an increasing abundance of anaerobic Spirochaetes with the increasing depth, where it shared similar community structures to that in the open-field soil from decomposed bagasse. Using complementary shotgun pyrosequencing, a variety of genes encoding various glycosyl hydrolases targeting cellulose and hemicellulose degradation were identified in the oxygen-limited interior pile base. Most were relevant to orders Clostridiales, Bacteroidales, Sphingobacteriales, and Cytophagales, suggesting their role in lignocellulose degradation in this region, as evidenced by the decrease in cellulose and respective increase in lignin fractions of the biomass. Partial carbon flux in the anoxic region was metabolized through mixed methanogenesis pathways as suggested by the annotated functional genes in methane synthesis. This study gives insights into native microbial community structures and functions in this unique lignocellulose degrading environment and provides the basis for controlling microbial processes important for utilization of bagasse in bio-industries.}, }
@article {pmid23503990, year = {2013}, author = {Yang, S and Sun, W and Tang, C and Jin, L and Zhang, F and Li, Z}, title = {Phylogenetic diversity of actinobacteria associated with soft coral Alcyonium gracllimum and stony coral Tubastraea coccinea in the East China Sea.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {189-199}, pmid = {23503990}, issn = {1432-184X}, mesh = {Actinobacteria/*classification/genetics/*isolation &amp; purification ; Animals ; Anthozoa/classification/*microbiology ; China ; *Genetic Variation ; Molecular Sequence Data ; Oceans and Seas ; *Phylogeny ; }, abstract = {Actinobacteria are widely distributed in the marine environment. To date, few studies have been performed to explore the coral-associated Actinobacteria, and little is known about the diversity of coral-associated Actinobacteria. In this study, the actinobacterial diversity associated with one soft coral Alcyonium gracllimum and one stony coral Tubastraea coccinea collected from the East China Sea was investigated using both culture-independent and culture-dependent approaches. A total of 19 actinobacterial genera were detected in these two corals, among which nine genera (Corynebacterium, Dietzia, Gordonia, Kocuria, Microbacterium, Micrococcus, Mycobacterium, Streptomyces, and Candidatus Microthrix) were common, three genera (Cellulomonas, Dermatophilus, and Janibacter) were unique to the soft coral, and seven genera (Brevibacterium, Dermacoccus, Leucobacter, Micromonospora, Nocardioides, Rhodococcus, and Serinicoccus) were unique to the stony coral. This finding suggested that highly diverse Actinobacteria were associated with different types of corals. In particular, five actinobacterial genera (Cellulomonas, Dermacoccus, Gordonia, Serinicoccus, and Candidatus Microthrix) were recovered from corals for the first time, extending the known diversity of coral-associated Actinobacteria. This study shows that soft and stony corals host diverse Actinobacteria and can serve as a new source of marine actinomycetes.}, }
@article {pmid23503989, year = {2013}, author = {Moore, MN and Depledge, MH and Fleming, L and Hess, P and Lees, D and Leonard, P and Madsen, L and Owen, R and Pirlet, H and Seys, J and Vasconcelos, V and Viarengo, A and , }, title = {Oceans and Human Health (OHH): a European perspective from the Marine Board of the European Science Foundation (Marine Board-ESF).}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {889-900}, pmid = {23503989}, issn = {1432-184X}, mesh = {*Ecosystem ; European Union/organization &amp; administration ; Humans ; *Public Health ; Seawater/*chemistry/microbiology ; *Water Pollution ; Workforce ; }, abstract = {The oceans and coastal seas provide mankind with many benefits including food for around a third of the global population, the air that we breathe and our climate system which enables habitation of much of the planet. However, the converse is that generation of natural events (such as hurricanes, severe storms and tsunamis) can have devastating impacts on coastal populations, while pollution of the seas by pathogens and toxic waste can cause illness and death in humans and animals. Harmful effects from biogenic toxins produced by algal blooms (HABs) and from the pathogens associated with microbial pollution are also a health hazard in seafood and from direct contact with water. The overall global burden of human disease caused by sewage pollution of coastal waters has been estimated at 4 million lost person-years annually. Finally, the impacts of all of these issues will be exacerbated by climate change. A holistic systems approach is needed. It must consider whole ecosystems, and their sustainability, such as integrated coastal zone management, is necessary to address the highly interconnected scientific challenges of increased human population pressure, pollution and over-exploitation of food (and other) resources as drivers of adverse ecological, social and economic impacts. There is also an urgent and critical requirement for effective and integrated public health solutions to be developed through the formulation of politically and environmentally meaningful policies. The research community required to address "Oceans &amp; Human Health" in Europe is currently very fragmented, and recognition by policy makers of some of the problems, outlined in the list of challenges above, is limited. Nevertheless, relevant key policy issues for governments worldwide include the reduction of the burden of disease (including the early detection of emerging pathogens and other threats) and improving the quality of the global environment. Failure to effectively address these issues will impact adversely on efforts to alleviate poverty, sustain the availability of environmental goods and services and improve health and social and economic stability; and thus, will impinge on many policy decisions, both nationally and internationally. Knowledge exchange (KE) will be a key element of any ensuing research. KE will facilitate the integration of biological, medical, epidemiological, social and economic disciplines, as well as the emergence of synergies between seemingly unconnected areas of science and socio-economic issues, and will help to leverage knowledge transfer across the European Union (EU) and beyond. An integrated interdisciplinary systems approach is an effective way to bring together the appropriate groups of scientists, social scientists, economists, industry and other stakeholders with the policy formulators in order to address the complexities of interfacial problems in the area of environment and human health. The Marine Board of the European Science Foundation Working Group on "Oceans and Human Health" has been charged with developing a position paper on this topic with a view to identifying the scientific, social and economic challenges and making recommendations to the EU on policy-relevant research and development activities in this arena. This paper includes the background to health-related issues linked to the coastal environment and highlights the main arguments for an ecosystem-based whole systems approach.}, }
@article {pmid23503746, year = {2013}, author = {Taubert, M and von Bergen, M and Seifert, J}, title = {Limitations in detection of 15N incorporation by mass spectrometry in protein-based stable isotope probing (protein-SIP).}, journal = {Analytical and bioanalytical chemistry}, volume = {405}, number = {12}, pages = {3989-3996}, doi = {10.1007/s00216-013-6828-y}, pmid = {23503746}, issn = {1618-2650}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*chemistry ; Isotope Labeling/*methods ; Molecular Sequence Data ; Nitrogen Isotopes/*analysis ; Peptides/*chemistry ; Pseudomonas fluorescens/*chemistry ; Tandem Mass Spectrometry/*methods ; }, abstract = {The method of protein-based stable isotope probing (protein-SIP) has previously been shown to allow the modeling of carbon fluxes in microbial communities, thus tackling one of the key questions in microbial ecology. The method allows the analysis of stable isotope distribution in peptides, revealing metabolic activities of the species present in an ecosystem. Besides carbon, an application of protein-SIP with nitrogen is of interest for resolving the nitrogen fluxes in microbial communities. Thus, the sensitivity and reliability of a protein-SIP approach employing (15)N was analyzed. For this, cultivations of Pseudomonas fluorescens ATCC 17483 with different ratios of (14)N/(15)N were performed, from 10 % down to 0.1 % (15)N. After incubation leading to complete labeling of biomass, proteins were extracted and separated by one-dimensional gel electrophoresis, followed by tryptic digest and UPLC Orbitrap MS/MS analysis. (15)N relative isotope abundance (RIA) was calculated based on isotopic patterns from identified peptides in mass spectra. Proteomics data have been deposited to ProteomeXchange with identifier PXD000127. The distribution of (15)N RIA values among peptides was analyzed in samples with different (15)N amount, and potential causes for variations within individual samples of either technical or biological origin were investigated. Using a number of 50 peptides, significant differences (p ≤ 0.05) in (15)N incorporation were found between samples of different (15)N RIA down to 0.1 %. The study demonstrates that protein-SIP using (15)N is sufficiently sensitive for quantitative investigation of microbial activity in nitrogen cycling processes.}, }
@article {pmid23497899, year = {2013}, author = {Bañeras, L and Trias, R and Godayol, A and Cerdán, L and Nawrath, T and Schulz, S and Anticó, E}, title = {Mass spectrometry identification of alkyl-substituted pyrazines produced by Pseudomonas spp. isolates obtained from wine corks.}, journal = {Food chemistry}, volume = {138}, number = {4}, pages = {2382-2389}, doi = {10.1016/j.foodchem.2012.12.030}, pmid = {23497899}, issn = {1873-7072}, mesh = {Food Packaging/*instrumentation ; Mass Spectrometry ; Odorants ; Pseudomonas/chemistry/genetics/isolation &amp; purification/*metabolism ; Pyrazines/chemistry/*metabolism ; Wine/analysis/*microbiology ; }, abstract = {We investigated the pyrazine production of 23 Pseudomonas isolates obtained from cork in order to assess their implications in off-flavour development. Off-flavour development in cork stoppers is a crucial process in maintaining the high quality of some wines. Pyrazine production was analyzed by headspace solid-phase-microextraction (HS-SPME) and gas chromatography coupled with mass spectrometry (GC-MS). Five out of the 23 isolates, i.e. Pseudomonas koreensis TCA20, Pseudomonas palleroniana TCA16, Pseudomonas putida TCA23 and N7, and Pseudomonas stutzeri TRA27a were able to produce branched alkyl-substituted pyrazines. For isolates N7 and TCA16, 14 compounds could be identified as pyrazines. The use of mineral media supplemented with different carbon and nitrogen sources resulted in changes in the pyrazine production capacity. In the two strains the amount of pyrazines produced was higher with glucose and decreased significantly with lactate. In all cases, 2,5-di(1-methylethyl)pyrazine was found to be dominant and independent of amino acid addition, suggesting a completely de novo synthesis. Aroma descriptions of most alkyl substituted pyrazines include mild vegetal aromas, not necessarily undesirable for the cork manufacturing industry. Methoxypyrazines, exhibiting earthy and musty aromas, could not be detected in any of the strains analysed.}, }
@article {pmid23494574, year = {2013}, author = {Xu, J and Jing, H and Kong, L and Sun, M and Harrison, PJ and Liu, H}, title = {Effect of seawater-sewage cross-transplants on bacterial metabolism and diversity.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {60-72}, pmid = {23494574}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; *Ecosystem ; Molecular Sequence Data ; Seawater/analysis/*microbiology ; Sewage/*microbiology ; }, abstract = {Bioassays experiments were conducted to determine the metabolic and community composition response of bacteria to transplants between relatively pristine coastal seawater and sewage-impacted seawater. There were four treatments: (1) pristine seawater bacteria + pristine seawater (Pb + Pw), (2) sewage-impacted bacteria + sewage-impacted water (Sb + Sw), (3) pristine seawater bacteria + sewage-impacted water (Pb + Sw), and (4) sewage-impacted bacteria + pristine seawater (Sb + Pw). Sewage-derived DOC was more labile and readily utilized by bacteria, which favored the growth of high nucleic acid (HNA) bacteria, resulting in high bacterial production (BP, 113 ± 4.92 to 130 ± 15.8 μg C l(-1) day(-1)) and low respiration rate (BR, <67 ± 11.3 μg C l(-1) day(-1)), as well as high bacterial growth efficiency (BGE, 0.68 ± 0.09 to 0.71 ± 0.05). In contrast, at the relatively pristine site, bacteria utilized natural marine-derived dissolved organic matter (DOM) at the expense of lowering their growth efficiency (BGE, <0.32 ± 0.02) with low BP (<62 ± 6.3 μg C l(-1) day(-1)) and high BR 133 ± 14.2 μg C l(-1) day(-1)). Sewage DOM input appeared to alter the partitioning of carbon between respiration and production of bacteria, resulting in a shift toward higher BGE, which would not enhance oxygen consumption. Taxonomic classification based on 454 pyrosequencing reads of the 16S rRNA gene amplicons revealed that changes in bacterial community structure occurred when seawater bacteria were transferred to the eutrophic sewage-impacted water. Sewage DOM fueled the growth of Gammma-proteobacteria and Epsilson-proteobacteria and reduced the bacterial richness, but the changes in the community were not apparent when sewage-impacted bacteria were transferred to pristine seawater.}, }
@article {pmid23494573, year = {2013}, author = {Griffitt, KJ and Grimes, DJ}, title = {Abundance and distribution of Vibrio cholerae, V. parahaemolyticus, and V. vulnificus following a major freshwater intrusion into the Mississippi Sound.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {578-583}, pmid = {23494573}, issn = {1432-184X}, mesh = {Ecosystem ; Rivers/chemistry/*microbiology ; Salinity ; Sodium Chloride/analysis/metabolism ; Vibrio cholerae/*growth &amp; development/isolation &amp; purification/metabolism ; Vibrio parahaemolyticus/growth &amp; development/isolation &amp; purification/metabolism ; Vibrio vulnificus/*growth &amp; development/isolation &amp; purification/metabolism ; }, abstract = {In response to a major influx of freshwater to the Mississippi Sound following the opening of the Bonnet Carre Spillway, water samples were collected from three sites along the Mississippi shoreline to assess the impact of altered salinity on three pathogenic Vibrio species. Salinity readings across the affected area during the 2011 sample period ranged from 1.4 to 12.9 ppt (mean = 7.0) and for the 2012 sample period from 14.1 to 23.6 ppt (mean = 19.8). Analyses of the data collected in 2011 showed a reduction in densities of Vibrio parahaemolyticus and Vibrio vulnificus with a concurrent increase of Vibrio cholerae numbers, with V. cholerae becoming the only Vibrio detected once salinity readings dropped to 6 ppt. Follow-up samples taken in 2012 after recovery of the salinity in the sound showed that the relative densities of the three pathogenic vibrios had reverted back to normal levels. This study shows that although the spillway was open but a few weeks and the effects were therefore time limited, the Mississippi River water had a profound, if temporary, effect on Vibrio ecology in the Mississippi Sound.}, }
@article {pmid23489554, year = {2013}, author = {Duncan, SH and Flint, HJ}, title = {Probiotics and prebiotics and health in ageing populations.}, journal = {Maturitas}, volume = {75}, number = {1}, pages = {44-50}, doi = {10.1016/j.maturitas.2013.02.004}, pmid = {23489554}, issn = {1873-4111}, mesh = {Aged ; *Aging ; Gastrointestinal Tract/*microbiology ; *Health Status ; Humans ; *Microbiota ; *Prebiotics ; *Probiotics ; }, abstract = {In healthy adults microbial communities that colonise different regions of the human colon contribute nutrients and energy to the host via the fermentation of non-digestible dietary components in the large intestine. A delicate balance of microbial species is required to maintain healthy metabolism and immune function. Disturbance in this microbial balance can have negative consequences for health resulting in elevated inflammation and infection, that are contributory factors in diabetes and cancer. There is a growing awareness that the microbial balance in the colon may become increasingly perturbed with aging and therefore hasten the onset of certain diseases. Societal and dietary factors influence microbial community composition both in the short and long term in the elderly (>65 years old) whilst immunosenescence may also be linked to a perturbed distal gut microbiota and frailty in the elderly. Significant progress has been made in defining some of the dominant members of the microbial community in the healthy large intestine and in identifying their roles in metabolism. There is therefore an urgent need for better awareness of the impact of diet, prebiotic and probiotic strategies in driving human colonic microbial composition in order to understand the possibilities for maintaining healthy gut function and well-being in an increasingly elderly population. Here we review gut microbial changes associated with aging and how diet, prebiotics and probiotics may modulate the gut microbiota to maintain health in the elderly.}, }
@article {pmid23487774, year = {2013}, author = {Berry, D and Stecher, B and Schintlmeister, A and Reichert, J and Brugiroux, S and Wild, B and Wanek, W and Richter, A and Rauch, I and Decker, T and Loy, A and Wagner, M}, title = {Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {12}, pages = {4720-4725}, pmid = {23487774}, issn = {1091-6490}, support = {294343/ERC_/European Research Council/International ; }, mesh = {Animals ; Bacteroides/*physiology ; *Ecosystem ; Humans ; Intestines/*microbiology ; Isotope Labeling ; Metagenome/*physiology ; Mice ; }, abstract = {The animal and human intestinal mucosa secretes an assortment of compounds to establish a physical barrier between the host tissue and intestinal contents, a separation that is vital for health. Some pathogenic microorganisms as well as members of the commensal intestinal microbiota have been shown to be able to break down these secreted compounds. Our understanding of host-compound degradation by the commensal microbiota has been limited to knowledge about simplified model systems because of the difficulty in studying the complex intestinal ecosystem in vivo. In this study, we introduce an approach that overcomes previous technical limitations and allows us to observe which microbial cells in the intestine use host-derived compounds. We added stable isotope-labeled threonine i.v. to mice and combined fluorescence in situ hybridization with high-resolution secondary ion mass spectrometry imaging to characterize utilization of host proteins by individual bacterial cells. We show that two bacterial species, Bacteroides acidifaciens and Akkermansia muciniphila, are important host-protein foragers in vivo. Using gnotobiotic mice we show that microbiota composition determines the magnitude and pattern of foraging by these organisms, demonstrating that a complex microbiota is necessary in order for this niche to be fully exploited. These results underscore the importance of in vivo studies of intestinal microbiota, and the approach presented in this study will be a powerful tool to address many other key questions in animal and human microbiome research.}, }
@article {pmid23486979, year = {2013}, author = {Zeng, H and Liu, J and Jackson, MI and Zhao, FQ and Yan, L and Combs, GF}, title = {Fatty liver accompanies an increase in lactobacillus species in the hind gut of C57BL/6 mice fed a high-fat diet.}, journal = {The Journal of nutrition}, volume = {143}, number = {5}, pages = {627-631}, pmid = {23486979}, issn = {1541-6100}, support = {R01 DK089178/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bile Acids and Salts ; Body Weight/*drug effects ; DNA, Bacterial ; Diet, High-Fat/*adverse effects ; Dietary Fats/*adverse effects/metabolism ; Energy Intake ; Fatty Liver/*etiology/metabolism/microbiology ; Feces/microbiology ; Inflammation/etiology ; Intestine, Large/drug effects/*microbiology ; *Lactobacillus ; Leptin/blood ; Liver/*drug effects/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Nitric Oxide Synthase Type II/metabolism ; Polymerase Chain Reaction ; Tumor Necrosis Factor-alpha/blood ; }, abstract = {High-fat (HF) diets can produce obesity and have been linked to the development of nonalcoholic fatty liver disease and changes in the gut microbiome. To test the hypothesis that HF feeding increases certain predominant hind gut bacteria and development of steatohepatitis, C57BL/6 mice were fed an HF (45% energy) or low-fat (LF) (10% energy) diet for 10 wk. At the end of the feeding period, body weights in the HF group were 34% greater than those in the LF group (P < 0.05). These changes were associated with dramatic increases in lipid droplet number and size, inflammatory cell infiltration, and inducible nitric oxide (NO) synthase protein concentration in the livers of mice fed the HF diet. Consistent with the fatty liver phenotype, plasma leptin and tumor necrosis factor-α concentrations were also elevated in mice fed the HF diet, indicative of chronic inflammation. Eight of 12 pairs of polymerase chain reaction (PCR) primers for bacterial species that typically predominate hind gut microbial ecology generated specific PCR products from the fecal DNA samples. The amount of DNA from Lactobacillus gasseri and/or Lactobacillus taiwanensis in the HF group was 6900-fold greater than that in the LF group. Many of these bacteria are bile acid resistant and are capable of bile acid deconjugation. Because bile acids are regulators of hepatic lipid metabolism, the marked increase of gut L. gasseri and/or L. taiwanensis species bacteria with HF feeding may play a role in development of steatohepatitis in this model.}, }
@article {pmid23486246, year = {2013}, author = {Wilhelm, L and Singer, GA and Fasching, C and Battin, TJ and Besemer, K}, title = {Microbial biodiversity in glacier-fed streams.}, journal = {The ISME journal}, volume = {7}, number = {8}, pages = {1651-1660}, pmid = {23486246}, issn = {1751-7370}, support = {Y 420/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; Biofilms ; Environment ; *Ice Cover ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; *Water Microbiology ; }, abstract = {While glaciers become increasingly recognised as a habitat for diverse and active microbial communities, effects of their climate change-induced retreat on the microbial ecology of glacier-fed streams remain elusive. Understanding the effect of climate change on microorganisms in these ecosystems is crucial given that microbial biofilms control numerous stream ecosystem processes with potential implications for downstream biodiversity and biogeochemistry. Here, using a space-for-time substitution approach across 26 Alpine glaciers, we show how microbial community composition and diversity, based on 454-pyrosequencing of the 16S rRNA gene, in biofilms of glacier-fed streams may change as glaciers recede. Variations in streamwater geochemistry correlated with biofilm community composition, even at the phylum level. The most dominant phyla detected in glacial habitats were Proteobacteria, Bacteroidetes, Actinobacteria and Cyanobacteria/chloroplasts. Microorganisms from ice had the lowest α diversity and contributed marginally to biofilm and streamwater community composition. Rather, streamwater apparently collected microorganisms from various glacial and non-glacial sources forming the upstream metacommunity, thereby achieving the highest α diversity. Biofilms in the glacier-fed streams had intermediate α diversity and species sorting by local environmental conditions likely shaped their community composition. α diversity of streamwater and biofilm communities decreased with elevation, possibly reflecting less diverse sources of microorganisms upstream in the catchment. In contrast, β diversity of biofilms decreased with increasing streamwater temperature, suggesting that glacier retreat may contribute to the homogenisation of microbial communities among glacier-fed streams.}, }
@article {pmid23483981, year = {2013}, author = {Larsen, P and Gilbert, J}, title = {Microbial bebop: creating music from complex dynamics in microbial ecology.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e58119}, pmid = {23483981}, issn = {1932-6203}, mesh = {Bacteria/*metabolism ; *Ecosystem ; Environmental Microbiology ; *Music ; }, abstract = {In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm.) from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.}, }
@article {pmid23483075, year = {2013}, author = {McDonald, D and Vázquez-Baeza, Y and Walters, WA and Caporaso, JG and Knight, R}, title = {From molecules to dynamic biological communities.}, journal = {Biology &amp; philosophy}, volume = {28}, number = {2}, pages = {241-259}, pmid = {23483075}, issn = {0169-3867}, support = {T32 GM008759/GM/NIGMS NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; }, abstract = {Microbial ecology is flourishing, and in the process, is making contributions to how the ecology and biology of large organisms is understood. Ongoing advances in sequencing technology and computational methods have enabled the collection and analysis of vast amounts of molecular data from diverse biological communities. While early studies focused on cataloguing microbial biodiversity in environments ranging from simple marine ecosystems to complex soil ecologies, more recent research is concerned with community functions and their dynamics over time. Models and concepts from traditional ecology have been used to generate new insight into microbial communities, and novel system-level models developed to explain and predict microbial interactions. The process of moving from molecular inventories to functional understanding is complex and challenging, and never more so than when many thousands of dynamic interactions are the phenomena of interest. We outline the process of how epistemic transitions are made from producing catalogues of molecules to achieving functional and predictive insight, and show how those insights not only revolutionize what is known about biological systems but also about how to do biology itself. Examples will be drawn primarily from analyses of different human microbiota, which are the microbial consortia found in and on areas of the human body, and their associated microbiomes (the genes of those communities). Molecular knowledge of these microbiomes is transforming microbiological knowledge, as well as broader aspects of human biology, health and disease.}, }
@article {pmid23482824, year = {2013}, author = {Zarraonaindia, I and Smith, DP and Gilbert, JA}, title = {Beyond the genome: community-level analysis of the microbial world.}, journal = {Biology &amp; philosophy}, volume = {28}, number = {2}, pages = {261-282}, pmid = {23482824}, issn = {0169-3867}, support = {//PHS HHS/United States ; }, abstract = {The development of culture-independent strategies to study microbial diversity and function has led to a revolution in microbial ecology, enabling us to address fundamental questions about the distribution of microbes and their influence on Earth's biogeochemical cycles. This article discusses some of the progress that scientists have made with the use of so-called "omic" techniques (metagenomics, metatranscriptomics, and metaproteomics) and the limitations and major challenges these approaches are currently facing. These 'omic methods have been used to describe the taxonomic structure of microbial communities in different environments and to discover new genes and enzymes of industrial and medical interest. However, microbial community structure varies in different spatial and temporal scales and none of the 'omic techniques are individually able to elucidate the complex aspects of microbial communities and ecosystems. In this article we highlight the importance of a spatiotemporal sampling design, together with a multilevel 'omic approach and a community analysis strategy (association networks and modeling) to examine and predict interacting microbial communities and their impact on the environment.}, }
@article {pmid23482585, year = {2013}, author = {Carney-Hinkle, EE and Tran, H and Bundy, JW and Moreno, R and Miller, PS and Burkey, TE}, title = {Effect of dam parity on litter performance, transfer of passive immunity, and progeny microbial ecology.}, journal = {Journal of animal science}, volume = {91}, number = {6}, pages = {2885-2893}, doi = {10.2527/jas.2011-4874}, pmid = {23482585}, issn = {1525-3163}, mesh = {Animals ; Bacteria/genetics/*isolation &amp; purification/metabolism ; Colostrum/chemistry ; Denaturing Gradient Gel Electrophoresis/veterinary ; Enzyme-Linked Immunosorbent Assay/veterinary ; Feces/microbiology ; Female ; *Immunity, Maternally-Acquired ; Immunoglobulin A/blood/metabolism ; Immunoglobulin G/blood/metabolism ; *Litter Size ; Male ; Milk/chemistry ; *Parity ; Polymerase Chain Reaction/veterinary ; Sus scrofa/immunology/microbiology/*physiology ; }, abstract = {Litter performance and progeny health status may be decreased in progeny derived from primiparous sows but improve with increasing parity. The objective was to evaluate litter performance, the production and passive transfer of Ig, and fecal microbial populations in progeny derived from first parity (P1) compared with fourth parity (P4) dams. Litter performance was recorded for P1 (n = 19) and P4 (n = 24) dams including number of pigs/litter (total born, born live, stillbirths, mummified fetuses, prewean mortality, and pigs weaned) and average litter and piglet BW at birth (d 0), d 7, d 14, and at weaning (average d 19). Blood samples were collected from all dams on d 90 and 114 of gestation and d 0 of lactation. Colostrum and milk samples were collected from each dam on d 0, 7, and 14 of lactation for quantification of IgG and IgA. Blood and fecal samples were collected from each litter (n = 6 pigs/litter) on d 1, 7, and 14 after parturition. Circulating IgG and IgA concentrations were quantified in all blood samples. Denaturing gradient gel electrophoresis (DGGE) was used to characterize similarity and diversity of fecal microbes among progeny. Progeny of P1 dams had decreased average litter BW at d 7 (25.7 vs. 30.0 kg; P < 0.03) and decreased average piglet BW throughout the experiment (d 0, 7, 14, and 19; P < 0.001) compared with P4 progeny. No parity × day interactions were observed with respect to immunoglobulin or microbial analyses. Concentrations of IgA tended to be greater (P = 0.09) in samples of colostrum and milk obtained from P4 compared with P1 dams. Serum IgG concentrations were greater (P < 0.02) in P4 progeny compared with P1 progeny. Results of DGGE revealed that P1 progeny had increased (P < 0.001) microbial similarity on d 7 and decreased (P < 0.03) microbial similarity on d 14 compared with P4 progeny. Progeny of P1 dams tended (P = 0.07) to have a greater Shannon's diversity index compared with P4 progeny on d 1, and P1 progeny had a greater (P < 0.03) Shannon's diversity index compared with P4 progeny on d 7. Litter performance, passive transfer of immunity, and progeny microbial ecology were affected by dam parity.}, }
@article {pmid23475615, year = {2013}, author = {Ercolini, D}, title = {High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {10}, pages = {3148-3155}, pmid = {23475615}, issn = {1098-5336}, mesh = {Bacteria/genetics/growth &amp; development ; Biota ; Ecosystem ; Fermentation ; Food Contamination/*analysis ; *Food Microbiology ; *Genes, Bacterial ; *High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Microbiota ; RNA, Bacterial/analysis ; Sequence Analysis, RNA ; }, abstract = {Following recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in food can now be achieved by using high-throughput sequencing (HTS) approaches after direct nucleic acid extraction from the sample to be studied. In this review, the workflow of applying culture-independent HTS to food matrices is described. The current scenario and future perspectives of HTS uses to study food microbiota are presented, and the decision-making process leading to the best choice of working conditions to fulfill the specific needs of food research is described.}, }
@article {pmid23475306, year = {2013}, author = {Newton, RJ and Bootsma, MJ and Morrison, HG and Sogin, ML and McLellan, SL}, title = {A microbial signature approach to identify fecal pollution in the waters off an urbanized coast of Lake Michigan.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {1011-1023}, pmid = {23475306}, issn = {1432-184X}, support = {R01 AI091829/AI/NIAID NIH HHS/United States ; 1R01AI091829-01A1/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Ecosystem ; Environmental Monitoring ; Feces/*chemistry ; Humans ; Lakes/*microbiology ; Michigan ; RNA, Ribosomal, 16S/genetics ; Sewage/analysis/microbiology ; Urbanization ; Water Pollution/*analysis ; }, abstract = {Urban coasts receive watershed drainage from ecosystems that include highly developed lands with sewer and stormwater infrastructure. In these complex ecosystems, coastal waters are often contaminated with fecal pollution, where multiple delivery mechanisms that often contain multiple fecal sources make it difficult to mitigate the pollution. Here, we exploit bacterial community sequencing of the V6 and V6V4 hypervariable regions of the bacterial 16S rRNA gene to identify bacterial distributions that signal the presence of sewer, fecal, and human fecal pollution. The sequences classified to three sewer infrastructure-associated bacterial genera, Acinetobacter, Arcobacter, and Trichococcus, and five fecal-associated bacterial families, Bacteroidaceae, Porphyromonadaceae, Clostridiaceae, Lachnospiraceae, and Ruminococcaceae, served as signatures of sewer and fecal contamination, respectively. The human fecal signature was determined with the Bayesian source estimation program SourceTracker, which we applied to a set of 40 sewage influent samples collected in Milwaukee, WI, USA to identify operational taxonomic units (≥ 97 % identity) that were most likely of human fecal origin. During periods of dry weather, the magnitudes of all three signatures were relatively low in Milwaukee's urban rivers and harbor and nearly zero in Lake Michigan. However, the relative contribution of the sewer and fecal signature frequently increased to > 2 % of the measured surface water communities following sewer overflows. Also during combined sewer overflows, the ratio of the human fecal pollution signature to the fecal pollution signature in surface waters was generally close to that of sewage, but this ratio decreased dramatically during dry weather and rain events, suggesting that nonhuman fecal pollution was the dominant source during these weather-driven scenarios. The qPCR detection of two human fecal indicators, human Bacteroides and Lachno2, confirmed the urban fecal footprint in this ecosystem extends to at least 8 km offshore.}, }
@article {pmid23472227, year = {2013}, author = {Remus-Emsermann, MN and Kim, EB and Marco, ML and Tecon, R and Leveau, JH}, title = {Draft Genome Sequence of the Phyllosphere Model Bacterium Pantoea agglomerans 299R.}, journal = {Genome announcements}, volume = {1}, number = {1}, pages = {}, pmid = {23472227}, issn = {2169-8287}, abstract = {Bacteria belonging to the genus Pantoea are common colonizers of plant leaf surfaces. Here, we present the draft genome sequence of Pantoea agglomerans 299R, a phyllosphere isolate that has become a model strain for studying the ecology of plant leaf-associated bacterial commensals.}, }
@article {pmid23466701, year = {2013}, author = {von Rosenvinge, EC and Song, Y and White, JR and Maddox, C and Blanchard, T and Fricke, WF}, title = {Immune status, antibiotic medication and pH are associated with changes in the stomach fluid microbiota.}, journal = {The ISME journal}, volume = {7}, number = {7}, pages = {1354-1366}, pmid = {23466701}, issn = {1751-7370}, support = {R01 DK046461/DK/NIDDK NIH HHS/United States ; RC2 HG005597/HG/NHGRI NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/genetics/immunology/isolation &amp; purification ; *Bacterial Physiological Phenomena ; *Biodiversity ; DNA, Ribosomal Spacer/genetics ; Fungi/drug effects/genetics/*physiology ; Gastrointestinal Contents/*chemistry/*microbiology ; HIV Infections/microbiology ; Humans ; Hydrogen-Ion Concentration ; Immunocompromised Host ; Microbiota/*drug effects/genetics/immunology/*physiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The stomach acts as a barrier to ingested microbes, thereby influencing the microbial ecology of the entire gastrointestinal (GI) tract. The stomach microbiota and the role of human host and environmental factors, such as health status or medications, in shaping its composition remain largely unknown. We sought to characterize the bacterial and fungal microbiota in the stomach fluid in order to gain insights into the role of the stomach in GI homeostasis. Gastric fluid was collected from 25 patients undergoing clinically indicated upper endoscopy. DNA isolates were used for PCR amplification of bacterial 16S ribosomal RNA (rRNA) genes and fungal internal transcribed spacers (ITS). RNA isolates were used for 16S rRNA cDNA generation and subsequent PCR amplification. While all stomach fluid samples are dominated by the phyla Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Fusobacteria (>99% of sequence reads), the transcriptionally active microbiota shows significant reduction in Actinobacteria (34%) and increase in Campylobacter (444%) (P<0.003), specifically the oral commensal and suspected intestinal pathogen Campylobacter concisus. Bacterial but not fungal diversity is reduced by antibiotic treatment (28%; P<0.02), immunosuppression in transplant recipients and HIV/AIDS patients (42%; P<0.001) and gastric fluid pH >4 (70%; P<0.05). Immunosuppression correlates with decreased abundance of Prevotella (24%), Fusobacterium (2%) and Leptotrichia (6%) and increased abundance of Lactobacillus (3844%) (P<0.003). We have generated the first in-depth characterization of the human gastric fluid microbiota, using bacterial 16S rRNA gene and transcript, and fungal ITS amplicon sequencing and provide evidence for a significant impact of the host immune status on its composition with likely consequences for human health.}, }
@article {pmid23463183, year = {2013}, author = {Pineiro, S and Chauhan, A and Berhane, TK and Athar, R and Zheng, G and Wang, C and Dickerson, T and Liang, X and Lymperopoulou, DS and Chen, H and Christman, M and Louime, C and Babiker, W and Stine, OC and Williams, HN}, title = {Niche partition of Bacteriovorax operational taxonomic units along salinity and temporal gradients in the Chesapeake Bay reveals distinct estuarine strains.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {652-660}, pmid = {23463183}, issn = {1432-184X}, mesh = {Bays/chemistry/*microbiology ; Deltaproteobacteria/*classification/genetics/*isolation &amp; purification/metabolism ; Maryland ; Molecular Sequence Data ; Phylogeny ; Salinity ; Seawater/chemistry/*microbiology ; Sodium Chloride/analysis/metabolism ; }, abstract = {The predatory Bacteriovorax are Gram-negative bacteria ubiquitous in saltwater systems that prey upon other Gram-negative bacteria in a similar manner to the related genus Bdellovibrio. Among the phylogenetically defined clusters of Bacteriovorax, cluster V has only been isolated from estuaries suggesting that it may be a distinct estuarine phylotype. To assess this hypothesis, the spatial and temporal distribution of cluster V and other Bacteriovorax phylogenetic assemblages along the salinity gradient of Chesapeake Bay were determined. Cluster V was expected to be found in significantly greater numbers in low to moderate salinity waters compared to high salinity areas. The analyses of water and sediment samples from sites in the bay revealed cluster V to be present at the lower salinity and not high salinity sites, consistent with it being an estuarine phylotype. Cluster IV had a similar distribution pattern and may also be specifically adapted to estuaries. While the distribution of clusters V and IV were similar for salinity, they were distinct on temperature gradients, being found in cooler and in warmer temperatures, respectively. The differentiation of phylotype populations along the salinity and temporal gradients in Chesapeake Bay revealed distinct niches inhabited by different phylotypes of Bacteriovorax and unique estuarine phylotypes.}, }
@article {pmid23461285, year = {2013}, author = {Mußmann, M and Ribot, M and von Schiller, D and Merbt, SN and Augspurger, C and Karwautz, C and Winkel, M and Battin, TJ and Martí, E and Daims, H}, title = {Colonization of freshwater biofilms by nitrifying bacteria from activated sludge.}, journal = {FEMS microbiology ecology}, volume = {85}, number = {1}, pages = {104-115}, doi = {10.1111/1574-6941.12103}, pmid = {23461285}, issn = {1574-6941}, mesh = {Ammonia/metabolism ; Bacteria/*classification/isolation &amp; purification/metabolism ; *Biofilms ; Fresh Water/*microbiology ; In Situ Hybridization, Fluorescence ; *Nitrification ; Nitrites/metabolism ; Nitrosomonas/genetics/isolation &amp; purification ; Oxidation-Reduction ; Oxidoreductases/genetics ; Sewage/*microbiology ; }, abstract = {Effluents from wastewater treatment plants (WWTPs) containing micro-organisms and residual nitrogen can stimulate nitrification in freshwater streams. We hypothesized that different ammonia-oxidizing (AOB) and nitrite-oxidizing (NOB) bacteria present in WWTP effluents differ in their potential to colonize biofilms in the receiving streams. In an experimental approach, we monitored biofilm colonization by nitrifiers in ammonium- or nitrite-fed microcosm flumes after inoculation with activated sludge. In a field study, we compared the nitrifier communities in a full-scale WWTP and in epilithic biofilms downstream of the WWTP outlet. Despite substantially different ammonia concentrations in the microcosms and the stream, the same nitrifiers were detected by fluorescence in situ hybridization in all biofilms. Of the diverse nitrifiers present in the WWTPs, only AOB of the Nitrosomonas oligotropha/ureae lineage and NOB of Nitrospira sublineage I colonized the natural biofilms. Analysis of the amoA gene encoding the alpha subunit of ammonia monooxygenase of AOB revealed seven identical amoA sequence types. Six of these affiliated with the N. oligotropha/ureae lineage and were shared between the WWTP and the stream biofilms, but the other shared sequence type grouped with the N. europaea/eutropha and N. communis lineage. Measured nitrification activities were high in the microcosms and the stream. Our results show that nitrifiers from WWTPs can colonize freshwater biofilms and confirm that WWTP-affected streams are hot spots of nitrification.}, }
@article {pmid23460521, year = {2013}, author = {Fine, DH and Toruner, GA and Velliyagounder, K and Sampathkumar, V and Godboley, D and Furgang, D}, title = {A lactotransferrin single nucleotide polymorphism demonstrates biological activity that can reduce susceptibility to caries.}, journal = {Infection and immunity}, volume = {81}, number = {5}, pages = {1596-1605}, pmid = {23460521}, issn = {1098-5522}, support = {R01 DE017968/DE/NIDCR NIH HHS/United States ; R21 DE016474/DE/NIDCR NIH HHS/United States ; DE-017968/DE/NIDCR NIH HHS/United States ; DE-016474/DE/NIDCR NIH HHS/United States ; }, mesh = {Analysis of Variance ; Anti-Infective Agents/*pharmacology ; Dental Caries/*genetics ; Dental Caries Susceptibility/*genetics ; *Genetic Predisposition to Disease ; Genotype ; Humans ; Lactoferrin/*genetics/pharmacology ; Lysine ; *Polymorphism, Single Nucleotide ; Saliva/metabolism/microbiology ; Streptococcus mutans/*drug effects ; }, abstract = {Streptococcus mutans is prominently linked to dental caries. Saliva's influence on caries is incompletely understood. Our goal was to identify a salivary protein with anti-S. mutans activity, characterize its genotype, and determine genotypic variants associated with S. mutans activity and reduced caries. An S. mutans affinity column was used to isolate active moieties from saliva obtained from a subject with minimal caries. The bound and eluted protein was identified as lactotransferrin (LTF) by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) analysis and confirmed by Western blotting with LTF antibody. A single nucleotide polymorphism (SNP) that produced a shift from arginine (R) to lysine (K) at amino acid position 47 in the LTF antimicrobial region (rs: 1126478) killed S. mutans in vitro. Saliva from a subject with moderate caries and with the LTF "wild-type" R form at position 47 had no such activity. A pilot genetic study (n = 30) showed that KK subjects were more likely to have anti-S. mutans activity than RR subjects (P = 0.001; relative risk = 3.6; 95% confidence interval [95% CI] = 1.5 to 11.13). Pretreatment of KK saliva with antibody to LTF reduced S. mutans killing in a dose-dependent manner (P = 0.02). KK subjects were less likely to have caries (P = 0.02). A synthetic 11-mer LTF/K peptide killed S. mutans and other caries-related bacteria, while the LTF/R peptide had no effect (P = 0.01). Our results provide functional evidence that the LTF/K variant results in both anti-S. mutans activity and reduced decay. We suggest that the LTF/K variant can influence oral microbial ecology in general and caries-provoking microbes specifically.}, }
@article {pmid23455433, year = {2013}, author = {Bärlocher, F and Kebede, YK and Gonçalves, AL and Canhoto, C}, title = {Incubation temperature and substrate quality modulate sporulation by aquatic hyphomycetes.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {30-39}, pmid = {23455433}, issn = {1432-184X}, mesh = {Alnus/chemistry/microbiology ; *Ecosystem ; Mitosporic Fungi/classification/*growth &amp; development/metabolism ; Plant Leaves/*chemistry/microbiology ; Quercus/chemistry/microbiology ; Rivers/*microbiology ; Spores, Fungal/classification/growth &amp; development/metabolism ; Temperature ; }, abstract = {Frequency and amplitude of temperature oscillations can profoundly affect structure and function of ecosystems. Unless the rate of a biological process changes linearly within the range of these fluctuations, the cumulative effect of temperature differs from the effect measured at the average temperature (Jensen's inequality). Here, we measured numbers and types of spores released by aquatic hyphomycetes from oak and alder leaves that had been exposed in a Portuguese stream for between 7 and 94 days. Recovered leaves were incubated at four temperatures between 5 and 20 °C. Over this range, the sporulation response to temperature was decelerating, with an estimated optimum around 12.5 °C. Assuming a linear response, therefore, overestimates spore release from decaying leaves. The calculated discrepancy was more pronounced with recalcitrant oak leaves (greater toughness, phenolics concentration, lower N and P concentration than alder), and reached 26.6 % when temperature was assumed to oscillate between 1 and 9 °C, rather than remaining constant at 5 °C. The maximum fluctuation of water temperature over 48 h during the field experiment was approximately 3 °C, which would result in a discrepancy of up to 6 %. The composition of the fungal community (assessed by species identification of released spores) was significantly influenced by the state of decomposition, but not by leaf species or temperature. When quantifying the potential impact of global change on aquatic fungal communities, the average increase as well as fluctuations of the temperature have to be considered.}, }
@article {pmid23455432, year = {2013}, author = {Powell, A and Baker-Austin, C and Wagley, S and Bayley, A and Hartnell, R}, title = {Isolation of pandemic Vibrio parahaemolyticus from UK water and shellfish produce.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {924-927}, pmid = {23455432}, issn = {1432-184X}, mesh = {Animals ; Food Contamination/analysis ; Foodborne Diseases/epidemiology/microbiology ; Humans ; Ostreidae/*microbiology ; Pandemics ; Seawater/*microbiology ; Shellfish/*microbiology ; United Kingdom/epidemiology ; Vibrio parahaemolyticus/classification/genetics/*isolation &amp; purification ; }, abstract = {Vibrio parahaemolyticus is a Gram-negative, halophilic bacterium found commonly in temperate and warm estuarine waters worldwide. V. parahaemolyticus is considered an emerging bacterial pathogen in Europe and has been responsible for several recent seafood-associated outbreaks. During ad hoc testing of raw shellfish produce in May 2012, pandemic group (O3:K6) V. parahaemolyticus was isolated from Pacific oysters (Crassostrea gigas), harvested in Southern England. Follow-on testing of water and shellfish, encompassing a small number geographically diverse sites, also retrieved pandemic group isolates. These strains are amongst the most northerly pandemic strains described to date and represent the first instance of pandemic V. parahaemolyticus isolated in the UK, highlighting the expanding geographical distribution of these foodborne pathogens in the environment.}, }
@article {pmid23455431, year = {2013}, author = {Uroz, S and Courty, PE and Pierrat, JC and Peter, M and Buée, M and Turpault, MP and Garbaye, J and Frey-Klett, P}, title = {Functional profiling and distribution of the forest soil bacterial communities along the soil mycorrhizosphere continuum.}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {404-415}, pmid = {23455431}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Fungi/classification/genetics/*isolation &amp; purification ; Molecular Sequence Data ; Mycorrhizae/classification/genetics/*isolation &amp; purification ; Phylogeny ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {An ectomycorrhiza is a multitrophic association between a tree root, an ectomycorrhizal fungus, free-living fungi and the associated bacterial communities. Enzymatic activities of ectomycorrhizal root tips are therefore result of the contribution from different partners of the symbiotic organ. However, the functional potential of the fungus-associated bacterial communities remains unknown. In this study, a collection of 80 bacterial strains randomly selected and isolated from a soil-ectomycorrhiza continuum (oak-Scleroderma citrinum ectomycorrhizas, the ectomycorrhizosphere and the surrounding bulk soil) were characterized. All the bacterial isolates were identified by partial 16S rRNA gene sequences as members of the genera Burkholderia, Collimonas, Dyella, Mesorhizobium, Pseudomonas, Rhizobium and Sphingomonas. The bacterial strains were then assayed for β-xylosidase, β-glucosidase, N-acetyl-hexosaminidase, β-glucuronidase, cellobiohydrolase, phosphomonoesterase, leucine-aminopeptidase and laccase activities, chitin solubilization and auxin production. Using these bioassays, we demonstrated significant differences in the functional distribution of the bacterial communities living in the different compartments of the soil-ectomycorrhiza continuum. The surrounding bulk soil was significantly enriched in bacterial isolates capable of hydrolysing cellobiose and N-acetylglucosamine. In contrast, the ectomycorrhizosphere appeared significantly enriched in bacterial isolates capable of hydrolysing glucopyranoside and chitin. Notably, chitinase and laccase activities were found only in bacterial isolates belonging to the Collimonas and Pseudomonas genera. Overall, the results suggest that the ectomycorrhizal fungi favour specific bacterial communities with contrasting functional characteristics from the surrounding soil.}, }
@article {pmid23455430, year = {2013}, author = {Caesar-Tonthat, TC and Espeland, E and Caesar, AJ and Sainju, UM and Lartey, RT and Gaskin, JF}, title = {Effects of Agaricus lilaceps fairy rings on soil aggregation and microbial community structure in relation to growth stimulation of western wheatgrass (Pascopyrum smithii) in Eastern Montana rangeland.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {120-131}, pmid = {23455430}, issn = {1432-184X}, mesh = {Agaricus/classification/genetics/isolation &amp; purification/*physiology ; Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Molecular Sequence Data ; Montana ; Phylogeny ; Poaceae/*growth &amp; development/*microbiology ; *Rhizosphere ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Stimulation of plant productivity caused by Agaricus fairy rings has been reported, but little is known about the effects of these fungi on soil aggregation and the microbial community structure, particularly the communities that can bind soil particles. We studied three concentric zones of Agaricus lilaceps fairy rings in Eastern Montana that stimulate western wheatgrass (Pascopyrum smithii): outside the ring (OUT), inside the ring (IN), and stimulated zone adjacent to the fungal fruiting bodies (SZ) to determine (1) soil aggregate proportion and stability, (2) the microbial community composition and the N-acetyl-β-D-glucosaminidase activity associated with bulk soil at 0-15 cm depth, (3) the predominant culturable bacterial communities that can bind to soil adhering to wheatgrass roots, and (4) the stimulation of wheatgrass production. In bulk soil, macroaggregates (4.75-2.00 and 2.00-0.25 mm) and aggregate stability increased in SZ compared to IN and OUT. The high ratio of fungal to bacteria (fatty acid methyl ester) and N-acetyl-β-D-glucosaminidase activity in SZ compared to IN and OUT suggest high fungal biomass. A soil sedimentation assay performed on the predominant isolates from root-adhering soil indicated more soil-binding bacteria in SZ than IN and OUT; Pseudomonas fluorescens and Stenotrophomonas maltophilia isolates predominated in SZ, whereas Bacillus spp. isolates predominated in IN and OUT. This study suggests that growth stimulation of wheatgrass in A. lilaceps fairy rings may be attributed to the activity of the fungus by enhancing soil aggregation of bulk soil at 0-15 cm depth and influencing the amount and functionality of specific predominant microbial communities in the wheatgrass root-adhering soil.}, }
@article {pmid23452227, year = {2013}, author = {Bletz, MC and Loudon, AH and Becker, MH and Bell, SC and Woodhams, DC and Minbiole, KP and Harris, RN}, title = {Mitigating amphibian chytridiomycosis with bioaugmentation: characteristics of effective probiotics and strategies for their selection and use.}, journal = {Ecology letters}, volume = {16}, number = {6}, pages = {807-820}, doi = {10.1111/ele.12099}, pmid = {23452227}, issn = {1461-0248}, mesh = {Amphibians/immunology/*microbiology ; Animals ; Biological Evolution ; Chytridiomycota/drug effects/*pathogenicity ; Ecosystem ; *Host-Pathogen Interactions/immunology ; Models, Biological ; Mycoses/drug therapy/*veterinary ; Probiotics/*pharmacology ; Skin/microbiology ; }, abstract = {Probiotic therapy through bioaugmentation is a feasible disease mitigation strategy based on growing evidence that microbes contribute to host defences of plants and animals. Amphibians are currently threatened by the rapid global spread of the pathogen, Batrachochytrium dendrobatidis (Bd), which causes the disease chytridiomycosis. Bioaugmentation of locally occurring protective bacteria on amphibians has mitigated this disease effectively in laboratory trials and one recent field trial. Areas still naïve to Bd provide an opportunity for conservationists to proactively implement probiotic strategies to prevent further amphibian declines. In areas where Bd is endemic, bioaugmentation can facilitate repatriation of susceptible amphibians currently maintained in assurance colonies. Here, we synthesise the current research in amphibian microbial ecology and bioaugmentation to identify characteristics of effective probiotics in relation to their interactions with Bd, their host, other resident microbes and the environment. To target at-risk species and amphibian communities, we develop sampling strategies and filtering protocols that result in probiotics that inhibit Bd under ecologically relevant conditions and persist on susceptible amphibians. This filtering tool can be used proactively to guide amphibian disease mitigation and can be extended to other taxa threatened by emerging infectious diseases.}, }
@article {pmid23450659, year = {2013}, author = {Willner, D and Hugenholtz, P}, title = {From deep sequencing to viral tagging: recent advances in viral metagenomics.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {35}, number = {5}, pages = {436-442}, doi = {10.1002/bies.201200174}, pmid = {23450659}, issn = {1521-1878}, mesh = {Bacteria/virology ; Computational Biology ; DNA, Viral/chemistry/*genetics ; *Genome, Viral ; High-Throughput Nucleotide Sequencing/instrumentation/*methods ; Host-Pathogen Interactions ; *Metagenomics ; Staining and Labeling/instrumentation/methods ; Viruses/*genetics ; }, abstract = {Culture-independent high-throughput sequencing has provided unprecedented insights into microbial ecology, particularly for Earth's most ubiquitous and diverse inhabitants - the viruses. A plethora of methods now exist for amplifying the vanishingly small amounts of nucleic acids in natural viral communities in order to sequence them, and sequencing depth is now so great that viral genomes can be detected and assembled even amid large concentrations of non-viral DNA. Complementing these advances in amplification and sequencing is the ability to physically link fluorescently labeled viruses to their host cells via high-throughput flow sorting. Sequencing of such isolated virus-host pairs facilitates cultivation-independent exploration of the natural host range of viruses. Within the next decade, as these technologies become widespread, we can expect to see a systematic expansion of our knowledge of viruses and their hosts.}, }
@article {pmid23443903, year = {2013}, author = {Fernandes, MF and Saxena, J and Dick, RP}, title = {Comparison of whole-cell fatty acid (MIDI) or phospholipid fatty acid (PLFA) extractants as biomarkers to profile soil microbial communities.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {145-157}, pmid = {23443903}, issn = {1432-184X}, mesh = {Bacteria/*chemistry ; Biomarkers/chemistry ; Fatty Acids/*chemistry ; Gas Chromatography-Mass Spectrometry ; Phospholipids/*chemistry ; Plants/chemistry ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {The whole-cell lipid extraction to profile microbial communities on soils using fatty acid (FA) biomarkers is commonly done with the two extractants associated with the phospholipid fatty acid (PLFA) or Microbial IDentification Inc. (MIDI) methods. These extractants have very different chemistry and lipid separation procedures, but often shown a similar ability to discriminate soils from various management and vegetation systems. However, the mechanism and the chemistry of the exact suite of FAs extracted by these two methods are poorly understood. Therefore, the objective was to qualitatively and quantitatively compare the MIDI and PLFA microbial profiling methods for detecting microbial community shifts due to soil type or management. Twenty-nine soil samples were collected from a wide range of soil types across Oregon and extracted FAs by each method were analyzed by gas chromatography (GC) and GC-mass spectrometry. Unlike PLFA profiles, which were highly related to microbial FAs, the overall MIDI-FA profiles were highly related to the plant-derived FAs. Plant-associated compounds were quantitatively related to particulate organic matter (POM) and qualitatively related to the standing vegetation at sampling. These FAs were negatively correlated to respiration rate normalized to POM (RespPOM), which increased in systems under more intensive management. A strong negative correlation was found between MIDI-FA to PLFA ratios and total organic carbon (TOC). When the reagents used in MIDI procedure were tested for the limited recovery of MIDI-FAs from soil with high organic matter, the recovery of MIDI-FA microbial signatures sharply decreased with increasing ratios of soil to extractant. Hence, the MIDI method should be used with great caution for interpreting changes in FA profiles due to shifts in microbial communities.}, }
@article {pmid23439773, year = {2013}, author = {Lücker, S and Nowka, B and Rattei, T and Spieck, E and Daims, H}, title = {The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {27}, pmid = {23439773}, issn = {1664-302X}, abstract = {In marine systems, nitrate is the major reservoir of inorganic fixed nitrogen. The only known biological nitrate-forming reaction is nitrite oxidation, but despite its importance, our knowledge of the organisms catalyzing this key process in the marine N-cycle is very limited. The most frequently encountered marine NOB are related to Nitrospina gracilis, an aerobic chemolithoautotrophic bacterium isolated from ocean surface waters. To date, limited physiological and genomic data for this organism were available and its phylogenetic affiliation was uncertain. In this study, the draft genome sequence of N. gracilis strain 3/211 was obtained. Unexpectedly for an aerobic organism, N. gracilis lacks classical reactive oxygen defense mechanisms and uses the reductive tricarboxylic acid cycle for carbon fixation. These features indicate microaerophilic ancestry and are consistent with the presence of Nitrospina in marine oxygen minimum zones. Fixed carbon is stored intracellularly as glycogen, but genes for utilizing external organic carbon sources were not identified. N. gracilis also contains a full gene set for oxidative phosphorylation with oxygen as terminal electron acceptor and for reverse electron transport from nitrite to NADH. A novel variation of complex I may catalyze the required reverse electron flow to low-potential ferredoxin. Interestingly, comparative genomics indicated a strong evolutionary link between Nitrospina, the nitrite-oxidizing genus Nitrospira, and anaerobic ammonium oxidizers, apparently including the horizontal transfer of a periplasmically oriented nitrite oxidoreductase and other key genes for nitrite oxidation at an early evolutionary stage. Further, detailed phylogenetic analyses using concatenated marker genes provided evidence that Nitrospina forms a novel bacterial phylum, for which we propose the name Nitrospinae.}, }
@article {pmid23435827, year = {2013}, author = {Han, M and Li, Z and Zhang, F}, title = {The ammonia oxidizing and denitrifying prokaryotes associated with sponges from different sea areas.}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {427-436}, pmid = {23435827}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Biodiversity ; China ; Denitrification ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Porifera/*microbiology ; Seawater/*microbiology ; }, abstract = {Marine sponges have been suggested to play an important role in the marine nitrogen cycling. However, the role of sponge microbes in the nitrogen transformation remains limited, especially on the bacterial ammonia oxidization and denitrification. Hence, in the present study, using functional genes (amoA, nirS, nirK, and nxrA) involved in ammonia oxidization and denitrification and 16S rRNA genes for specific bacterial groups as markers, phylogenetically diverse prokaryotes including bacteria and archaea, which may be involved in the ammonia oxidization and denitrification processes in sponges, were revealed in seven sponge species. Ammonia oxidizers were found in all species, whereas three sponges (Placospongia sp., Acanthella sp., and Pericharax heteroraphis) harbor only ammonia-oxidizing bacteria (AOB), two sponges (Spirastrellidae diplastrella and Mycale fibrexilis) host only ammonia-oxidizing archaea (AOA), while the remaining two sponges (Haliclona sp. and Lamellomorpha sp.) harbor both AOB and AOA. S. diplastrella and Lamellomorpha sp. also harbor denitrifying bacteria. Nitrite reductase gene nirK was detected only in Lamellomorpha sp. with higher phylogenetic diversity than nirS gene observed only in S. diplastrella. The detected functional genes related to the ammonia oxidization and nitrite reduction in deep-sea and shallow-water sponges highlighted the potential ecological roles of prokaryotes in sponge-related nitrogen transformation.}, }
@article {pmid23435826, year = {2013}, author = {Sandifer, PA and Trtanj, JM and Collier, TK}, title = {A perspective on the history and evolution of an Oceans and Human Health "metadiscipline" in the USA.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {880-888}, pmid = {23435826}, issn = {1432-184X}, mesh = {*Biological Evolution ; History, 20th Century ; History, 21st Century ; Humans ; Marine Biology/education/*history/organization &amp; administration ; Public Health/education/*history ; Public Health Administration/*history ; Seawater/*microbiology ; United States ; Workforce ; }, abstract = {We review recent history and evolution of Oceans and Human Health programs and related activities in the USA from a perspective within the Federal government. As a result of about a decade of support by the US Congress and through a few Federal agencies, notably the National Science Foundation, National Institute of Environmental Health Sciences, and National Ocean and Atmospheric Administration, robust Oceans and Human Health (OHH) research and application activities are now relatively widespread, although still small, in a number of agencies and academic institutions. OHH themes and issues have been incorporated into comprehensive federal ocean research plans and are reflected in the new National Ocean Policy enunciated by Executive Order 13547. In just a decade, OHH has matured into a recognized "metadiscipline," with development of a small, but robust and diverse community of science and practice, incorporation into academic educational programs, regular participation in ocean and coastal science and public health societies, and active engagement with public health decision makers. In addition to substantial increases in scientific information, the OHH community has demonstrated ability to respond rapidly and effectively to emergency situations such as those associated with extreme weather events (e.g., hurricanes, floods) and human-caused disasters (e.g., the Deep Water Horizon oil spill). Among many other things, next steps include development and implementation of agency health strategies and provision of specific services, such as ecological forecasts to provide routine early warnings for ocean health threats and opportunities for prevention and mitigation of these risks.}, }
@article {pmid23435248, year = {2013}, author = {Kim, SJ and Ahn, JH and Lee, TH and Weon, HY and Hong, SB and Seok, SJ and Whang, KS and Kwon, SW}, title = {Reyranella soli sp. nov., isolated from forest soil, and emended description of the genus Reyranella Pagnier et al. 2011.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {63}, number = {Pt 9}, pages = {3164-3167}, doi = {10.1099/ijs.0.045922-0}, pmid = {23435248}, issn = {1466-5034}, mesh = {Alphaproteobacteria/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; *Soil Microbiology ; Trees/microbiology ; Ubiquinone/analysis ; }, abstract = {A Gram-stain-negative, non-motile, rod-shaped bacterial strain, designated KIS14-15(T), was isolated from forest soil of Baengnyeong Island in the Yellow Sea in Korea and its taxonomic position was investigated by using a polyphasic study. Strain KIS14-15(T) grew optimally at 30 °C, at pH 6.0-7.0 and without NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain KIS14-15(T) formed a cluster with the strains of Reyranella massiliensis with a bootstrap resampling value of 100%. Strain KIS14-15(T) exhibited 16S rRNA gene sequence similarity values of 98.0% to R. massiliensis 521(T) and of less than 89% to the type strains of other taxa. The mean level of DNA-DNA relatedness between strain KIS14-15(T) and R. massiliensis KACC 16548(T) was 21% (reciprocal, 24%). The predominant ubiquinone found in strain KIS14-15(T) and R. massiliensis KACC 16548(T) was ubiquinone-10 (Q-10). The predominant fatty acids of strain KIS14-15(T) and R. massiliensis KACC 16548(T) were C(18:1)ω7c, C(18:1) 2-OH and 11-methyl C(18:1)ω7c. Total polar lipids of strain KIS14-15(T) were phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unknown aminolipid and one unknown lipid. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, demonstrated that strain KIS14-15(T) is distinguishable from R. massiliensis. On the basis of the data presented, strain KIS14-15(T) is considered to represent a novel species of the genus Reyranella, for which the name Reyranella soli sp. nov. is proposed. The type strain is KIS14-15(T) (= KACC 13034(T) =NBRC 108950(T)).}, }
@article {pmid23429887, year = {2013}, author = {Zhang, YK and Zhang, KJ and Sun, JT and Yang, XM and Ge, C and Hong, XY}, title = {Diversity of Wolbachia in natural populations of spider mites (genus Tetranychus): evidence for complex infection history and disequilibrium distribution.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {731-739}, pmid = {23429887}, issn = {1432-184X}, mesh = {Animals ; *Biodiversity ; China ; Endophytes/classification/genetics/isolation &amp; purification/*physiology ; Female ; Host Specificity ; Male ; Molecular Sequence Data ; Phylogeny ; Tetranychidae/classification/genetics/*microbiology ; Wolbachia/classification/genetics/isolation &amp; purification/*physiology ; }, abstract = {Wolbachia are endosymbiotic bacteria that commonly infect arthropods and cause reproductive disorders in host. Within several Tetranychus species, Wolbachia have been detected and shown to affect their reproduction. However, little is known about their transmission and distribution patterns in natural populations of Tetranychus species. Here, we used multilocus sequence typing to confirm Wolbachia infection status and examined the relationship between Wolbachia infection status and host phylogeny, mitochondrial diversity, and geographical range in five Tetranychus species (Tetranychus truncatus, Tetranychus urticae, Tetranychus pueraricola, Tetranychus phaselus, and Tetranychus kanzawai) from 21 populations in China. The prevalence of Wolbachia within the five Tetranychus species ranged from 31.4 to 100 %, and the strains were remarkably diverse. Together, these observations indicate that Wolbachia was introduced to these populations on multiple separate occasions. As in other arthropods, the same Tetranychus species can accommodate very different strains, and identical Wolbachia occasionally infect different species. These observations suggest that Wolbachia are transmitted both vertically and horizontally. Horizontally, transmission is probably mediated by the host plants. The distribution patterns of Wolbachia were quite different among populations of the same species, suggesting that the dynamics of Wolbachia in nature may be affected by ecological and other factors.}, }
@article {pmid23426009, year = {2013}, author = {Dolan, JR and Landry, MR and Ritchie, ME}, title = {The species-rich assemblages of tintinnids (marine planktonic protists) are structured by mouth size.}, journal = {The ISME journal}, volume = {7}, number = {6}, pages = {1237-1243}, pmid = {23426009}, issn = {1751-7370}, mesh = {Biodiversity ; California ; Ciliophora/*classification/cytology ; Ecology ; Mediterranean Sea ; Plankton/*classification/cytology ; *Seawater ; }, abstract = {Many microbial taxa in the marine plankton appear super-saturated in species richness. Here, we provide a partial explanation by analyzing how species are organized, species packing, in terms of both taxonomy and morphology. We focused on a well-studied group, tintinnid ciliates of the microzooplankton, in which feeding ecology is closely linked to morphology. Populations in three distinct systems were examined: an Eastern Mediterranean Gyre, a Western Mediterranean Gyre and the California Current. We found that species abundance distributions exhibited the long-tailed, log distributions typical of most natural assemblages of microbial and other organisms. In contrast, grouping in oral size-classes, which corresponds with prey-size exploited, revealed a geometric distribution consistent with a dominant role of a single resource in structuring an assemblage. The number of species found in a particular oral size-class increases with the numerical importance of the size-class in the overall population. We suggest that high species diversity reflects the fact that accompanying each dominant species are many ecologically similar species, presumably able to replace the dominant species, at least with regard to the size of prey exploited. Such redundancy suggests that species diversity greatly exceeds ecological diversity in the plankton.}, }
@article {pmid23423262, year = {2013}, author = {Alonso, C and Piccini, C and Unrein, F and Bertoglio, F and Conde, D and Pernthaler, J}, title = {Environmental dynamics as a structuring factor for microbial carbon utilization in a subtropical coastal lagoon.}, journal = {Frontiers in microbiology}, volume = {4}, number = {}, pages = {14}, pmid = {23423262}, issn = {1664-302X}, abstract = {Laguna de Rocha belongs to a series of shallow coastal lagoons located along South America. It is periodically connected to the sea through a sand bar, exhibiting a hydrological cycle where physicochemical and biological gradients are rapidly established and destroyed. Its most frequent state is the separation of a Northern zone with low salinity, high turbidity and nutrient load, and extensive macrophyte growth, and a Southern zone with higher salinity and light penetration, and low nutrient content and macrophyte biomass. This zonation is reflected in microbial assemblages with contrasting abundance, activity, and community composition. The physicochemical conditions exerted a strong influence on community composition, and transplanted assemblages rapidly transformed to resembling the community of the recipient environment. Moreover, the major bacterial groups responded differently to their passage between the zones, being either stimulated or inhibited by the environmental changes, and exhibiting contrasting sensitivities to gradients. Addition of allochthonous carbon sources induced pronounced shifts in the bacterial communities, which in turn affected the microbial trophic web by stimulating heterotrophic flagellates and virus production. By contrast, addition of organic and inorganic nutrient sources (P or N) did not have significant effects. Altogether, our results suggest that (i) the planktonic microbial assemblage of this lagoon is predominantly carbon-limited, (ii) different bacterial groups cope differently with this constraint, and (iii) the hydrological cycle of the lagoon plays a key role for the alleviation or aggravation of bacterial carbon limitation. Based on these findings we propose a model of how hydrology affects the composition of bacterioplankton and of carbon processing in Laguna de Rocha. This might serve as a starting hypothesis for further studies about the microbial ecology of this lagoon, and of comparable transitional systems.}, }
@article {pmid23420267, year = {2013}, author = {De Clippeleir, H and Vlaeminck, SE and De Wilde, F and Daeninck, K and Mosquera, M and Boeckx, P and Verstraete, W and Boon, N}, title = {One-stage partial nitritation/anammox at 15 °C on pretreated sewage: feasibility demonstration at lab-scale.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {23}, pages = {10199-10210}, doi = {10.1007/s00253-013-4744-x}, pmid = {23420267}, issn = {1432-0614}, mesh = {Ammonia/*chemistry ; Bacteria/genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Biological Oxygen Demand Analysis ; Bioreactors/microbiology ; Nitrification ; Nitrites/*chemistry ; Sewage/*chemistry ; Temperature ; Water Purification/instrumentation/*methods ; }, abstract = {Energy-positive sewage treatment can be achieved by implementation of oxygen-limited autotrophic nitrification/denitrification (OLAND) in the main water line, as the latter does not require organic carbon and therefore allows maximum energy recovery through anaerobic digestion of organics. To test the feasibility of mainstream OLAND, the effect of a gradual temperature decrease from 29 to 15 °C and a chemical oxygen demand (COD)/N increase from 0 to 2 was tested in an OLAND rotating biological contactor operating at 55-60 mg NH4(+)-N L(-1) and a hydraulic retention time of 1 h. Moreover, the effect of the operational conditions and feeding strategies on the reactor cycle balances, including NO and N2O emissions were studied in detail. This study showed for the first time that total nitrogen removal rates of 0.5 g N L(-1) day(-1) can be maintained when decreasing the temperature from 29 to 15 °C and when low nitrogen concentration and moderate COD levels are treated. Nitrite accumulation together with elevated NO and N2O emissions (5% of N load) were needed to favor anammox compared with nitratation at low free ammonia (<0.25 mg N L(-1)), low free nitrous acid (<0.9 μg N L(-1)), and higher DO levels (3-4 mg O2 L(-1)). Although the total nitrogen removal rates showed potential, the accumulation of nitrite and nitrate resulted in lower nitrogen removal efficiencies (around 40%), which should be improved in the future. Moreover, a balance should be found in the future between the increased NO and N2O emissions and a decreased energy consumption to justify OLAND mainstream treatment.}, }
@article {pmid23420205, year = {2013}, author = {Anand, R and Grayston, S and Chanway, C}, title = {N2-fixation and seedling growth promotion of lodgepole pine by endophytic Paenibacillus polymyxa.}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {369-374}, pmid = {23420205}, issn = {1432-184X}, mesh = {Endophytes/isolation &amp; purification/*metabolism ; Nitrogen/metabolism ; *Nitrogen Fixation ; Paenibacillus/isolation &amp; purification/*metabolism ; Pinus/growth &amp; development/metabolism/*microbiology ; Seedlings/*growth &amp; development/microbiology ; Trees/growth &amp; development/metabolism/microbiology ; }, abstract = {We inoculated lodgepole pine (Pinus contorta var. latifolia (Dougl.) Engelm.) with Paenibacillus polymyxa P2b-2R, a diazotrophic bacterium previously isolated from internal stem tissue of a naturally regenerating pine seedling to evaluate biological nitrogen fixation and seedling growth promotion by this microorganism. Seedlings generated from pine seed inoculated with strain P2b-2R were grown for up to 13 months in a N-limited soil mix containing 0.7 mM available N labeled as Ca((15)NO3)2 to facilitate detection of N2-fixation. Strain P2b-2R developed a persistent endophytic population comprising 10(2)-10(6) cfu g(-1) plant tissue inside pine roots, stems, and needles during the experiment. At the end of the growth period, P2b-2R had reduced seedling mortality by 14 % and (15)N foliar N abundance 79 % and doubled foliar N concentration and seedling biomass compared to controls. Our results suggest that N2-fixation by P. polymyxa enhanced growth of pine seedlings and support the hypothesis that plant-associated diazotrophs capable of endophytic colonization can satisfy a significant proportion of the N required by tree seedlings growing under N-limited conditions.}, }
@article {pmid23420204, year = {2013}, author = {Burge, CA and Kim, CJ and Lyles, JM and Harvell, CD}, title = {Special issue Oceans and Humans Health: the ecology of marine opportunists.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {869-879}, pmid = {23420204}, issn = {1432-184X}, mesh = {Animals ; *Bacterial Physiological Phenomena ; *Ecosystem ; Health ; *Host-Pathogen Interactions ; Humans ; Oceans and Seas ; Seawater/*microbiology ; }, abstract = {Opportunistic marine pathogens, like opportunistic terrestrial pathogens, are ubiquitous in the environment (waters, sediments, and organisms) and only cause disease in immune-compromised or stressed hosts. In this review, we discuss four host-pathogen interactions within the marine environment that are typically considered opportunistic: sea fan coral-fungus, eelgrass-Labyrinthula zosterae, sea fan-Labyrinthulomycetes, and hard clam-Quahog Parasite Unknown with particular focus on disease ecology, parasite pathology, host response, and known associated environmental conditions. Disease is a natural part of all ecosystems; however, in some cases, a shift in the balance between the host, pathogen, and the environment may lead to epizootics in natural or cultured populations. In marine systems, host-microbe interactions are less understood than their terrestrial counterparts. The biological and physical changes to the world's oceans, coupled with other anthropogenic influences, will likely lead to more opportunistic diseases in the marine environment.}, }
@article {pmid23419826, year = {2013}, author = {Kesberg, AI and Schleheck, D}, title = {Improved protocol for recovery of bacterial DNA from water filters: Sonication and backflushing of commercial syringe filters.}, journal = {Journal of microbiological methods}, volume = {93}, number = {1}, pages = {55-57}, doi = {10.1016/j.mimet.2013.02.001}, pmid = {23419826}, issn = {1872-8359}, mesh = {DNA, Bacterial/*isolation &amp; purification ; Filtration ; Magnetics ; Micropore Filters ; Microspheres ; Sonication ; Specimen Handling/*methods ; Syringes ; *Water Microbiology ; }, abstract = {Extraction of bacterial DNA from water filters is frequently used in aquatic microbial ecology, e.g., for sequencing-based diversity studies. Here, we describe an improved size-class filtration and bacterial DNA extraction protocol using commercial "syringe filters", involving sonication- and backflushing-steps and DNA-binding magnetic beads. Importantly, the sonication-step improved DNA recovery up to 10-fold. The DNA extraction-turnaround time is 4h, with a hands-on time of about 2h.}, }
@article {pmid23418126, year = {2013}, author = {Cano, PG and Santacruz, A and Trejo, FM and Sanz, Y}, title = {Bifidobacterium CECT 7765 improves metabolic and immunological alterations associated with obesity in high-fat diet-fed mice.}, journal = {Obesity (Silver Spring, Md.)}, volume = {21}, number = {11}, pages = {2310-2321}, doi = {10.1002/oby.20330}, pmid = {23418126}, issn = {1930-739X}, mesh = {Animals ; Bifidobacterium/*physiology ; Cytokines/metabolism ; *Diet, High-Fat ; Fatty Liver/prevention &amp; control ; Immunity, Cellular/physiology ; Insulin Resistance ; Lactobacillus/physiology ; Macrophages/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Obesity/etiology/*immunology/*metabolism ; Probiotics ; }, abstract = {OBJECTIVES: To evaluate the effects of administration of Bifidobacterium pseudocatenulatum CECT 7765 on metabolic and immune alterations in obese mice.<br><br>DESIGN AND METHODS: Adult male wild-type C57BL-6 mice were fed a standard diet or high-fat diet (HFD), supplemented or not with B. pseudocatenulatum CECT 7765 for 7 weeks. The assessments included biochemical and immunological parameters, insulin resistance, glucose tolerance, histology of liver, white-adipose and intestinal tissues, immunocompetent cell functions, and microbiota-related features.<br><br>RESULTS: B. pseudocatenulatum CECT 7765 reduced serum cholesterol, triglyceride, and glucose levels and decreased insulin resistance and improved glucose tolerance in obese mice. This strain reduced serum levels of leptin, interleukin (IL)-6 and monocyte chemotactic protein-1, while increased those of IL-4 in HFD-fed mice. B. pseudocatenulatum CECT7765 reduced liver steatosis and the number of larger adipocytes and number of fat micelles in enterocytes of obese mice. The strain also improved the function of macrophages and dendritic cells in relation to phagocytosis, cytokine production, and induction of T-lymphocyte proliferation. The strain administration increased bifidobacteria and reduced enterobacteria and the inflammatory properties of the gut content in HFD-fed mice.<br><br>CONCLUSION: B. pseudocatenulatum CECT 7765 was shown to ameliorate both metabolic and immunological dysfunctions related to obesity in HFD-fed mice.}, }
@article {pmid23417005, year = {2013}, author = {Ho, A and Vlaeminck, SE and Ettwig, KF and Schneider, B and Frenzel, P and Boon, N}, title = {Revisiting methanotrophic communities in sewage treatment plants.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {8}, pages = {2841-2846}, pmid = {23417005}, issn = {1098-5336}, mesh = {Alphaproteobacteria/genetics/*metabolism ; Bioreactors ; Gammaproteobacteria/genetics/*metabolism ; Methane/*metabolism ; Molecular Sequence Data ; Sewage/*microbiology ; Water Purification ; }, abstract = {The methanotrophic potential in sewage treatment sludge was investigated. We detected a diverse aerobic methanotrophic community that potentially plays a significant role in mitigating methane emission in this environment. The results suggest that community structure was determined by conditions specific to the processes in a sewage treatment plant.}, }
@article {pmid23411852, year = {2013}, author = {Schiwon, K and Arends, K and Rogowski, KM and Fürch, S and Prescha, K and Sakinc, T and Van Houdt, R and Werner, G and Grohmann, E}, title = {Comparison of antibiotic resistance, biofilm formation and conjugative transfer of Staphylococcus and Enterococcus isolates from International Space Station and Antarctic Research Station Concordia.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {638-651}, pmid = {23411852}, issn = {1432-184X}, mesh = {*Air Microbiology ; Antarctic Regions ; Anti-Bacterial Agents/*pharmacology ; *Biofilms ; *Conjugation, Genetic ; *Drug Resistance, Bacterial ; Ecosystem ; Enterococcus/drug effects/*genetics/isolation &amp; purification/physiology ; Hand/*microbiology ; Humans ; Microbial Sensitivity Tests ; Space Flight ; Staphylococcus/drug effects/*genetics/isolation &amp; purification/physiology ; }, abstract = {The International Space Station (ISS) and the Antarctic Research Station Concordia are confined and isolated habitats in extreme and hostile environments. The human and habitat microflora can alter due to the special environmental conditions resulting in microbial contamination and health risk for the crew. In this study, 29 isolates from the ISS and 55 from the Antarctic Research Station Concordia belonging to the genera Staphylococcus and Enterococcus were investigated. Resistance to one or more antibiotics was detected in 75.8 % of the ISS and in 43.6 % of the Concordia strains. The corresponding resistance genes were identified by polymerase chain reaction in 86 % of the resistant ISS strains and in 18.2 % of the resistant Concordia strains. Plasmids are present in 86.2 % of the ISS and in 78.2 % of the Concordia strains. Eight Enterococcus faecalis strains (ISS) harbor plasmids of about 130 kb. Relaxase and/or transfer genes encoded on plasmids from gram-positive bacteria like pIP501, pRE25, pSK41, pGO1 and pT181 were detected in 86.2 % of the ISS and in 52.7 % of the Concordia strains. Most pSK41-homologous transfer genes were detected in ISS isolates belonging to coagulase-negative staphylococci. We demonstrated through mating experiments that Staphylococcus haemolyticus F2 (ISS) and the Concordia strain Staphylococcus hominis subsp. hominis G2 can transfer resistance genes to E. faecalis and Staphylococcus aureus, respectively. Biofilm formation was observed in 83 % of the ISS and in 92.7 % of the Concordia strains. In conclusion, the ISS isolates were shown to encode more resistance genes and possess a higher gene transfer capacity due to the presence of three vir signature genes, virB1, virB4 and virD4 than the Concordia isolates.}, }
@article {pmid23410993, year = {2013}, author = {Rist, VT and Weiss, E and Eklund, M and Mosenthin, R}, title = {Impact of dietary protein on microbiota composition and activity in the gastrointestinal tract of piglets in relation to gut health: a review.}, journal = {Animal : an international journal of animal bioscience}, volume = {7}, number = {7}, pages = {1067-1078}, doi = {10.1017/S1751731113000062}, pmid = {23410993}, issn = {1751-732X}, mesh = {*Animal Husbandry ; Animals ; Bacteria/metabolism ; Dietary Carbohydrates/metabolism ; Dietary Proteins/*metabolism ; *Fermentation ; Gastrointestinal Tract/*metabolism/*microbiology ; Metagenome ; Sus scrofa/*metabolism/*microbiology ; }, abstract = {In pigs, the microbial ecosystem of the gastrointestinal tract (GIT) is influenced by various factors; however, variations in diet composition have been identified as one of the most important determinants. Marked changes in fermentation activities and microbial ecology may occur when altering the diet, for example, from milk to solid feed during weaning. In that way, access of pathogens to the disturbed ecosystem is alleviated, leading to infectious diseases and diarrhea. Thus, there is increasing interest in improving intestinal health by use of dietary ingredients suitable to beneficially affect the microbial composition and activity. For example, fermentable carbohydrates have been shown to promote growth of beneficial Lactobacillus species and bifidobacteria, thereby enhancing colonization resistance against potential pathogens or production of short-chain fatty acids, which can be used as energy source for epithelial cells. On the other hand, fermentation of protein results in the production of various potentially toxic products, such as amines and NH3, and is often associated with growth of potential pathogens. In that way, excessive protein intake has been shown to stimulate the growth of potentially pathogenic species such as Clostridium perfringens, and to reduce fecal counts of beneficial bifidobacteria. Therefore, it seems to be a promising approach to support growth and metabolic activity of the beneficial microbiota by developing suitable feeding strategies. For example, a reduction of dietary CP content and, at the same time, dietary supplementation with fermentable carbohydrates have proven to successfully suppress protein fermentation. In addition, the intestinal microbiota seems to be sensible to variations in dietary protein source, such as the use of highly digestible protein sources may reduce growth of protein-fermenting and potentially pathogenic species. The objective of the present review is to assess the impact of dietary protein on microbiota composition and activity in the GIT of piglets. Attention will be given to studies designed to determine the effect of variations in total protein supply, protein source and supplementation of fermentable carbohydrates to the diet on composition and metabolic activity of the intestinal microbiota.}, }
@article {pmid23405248, year = {2013}, author = {Miller, CS and Handley, KM and Wrighton, KC and Frischkorn, KR and Thomas, BC and Banfield, JF}, title = {Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e56018}, pmid = {23405248}, issn = {1932-6203}, mesh = {Bacteria/*classification/genetics ; *Biodiversity ; DNA, Bacterial/*genetics ; *Genetic Variation ; Geologic Sediments/*microbiology ; Groundwater/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {In microbial ecology, a fundamental question relates to how community diversity and composition change in response to perturbation. Most studies have had limited ability to deeply sample community structure (e.g. Sanger-sequenced 16S rRNA libraries), or have had limited taxonomic resolution (e.g. studies based on 16S rRNA hypervariable region sequencing). Here, we combine the higher taxonomic resolution of near-full-length 16S rRNA gene amplicons with the economics and sensitivity of short-read sequencing to assay the abundance and identity of organisms that represent as little as 0.01% of sediment bacterial communities. We used a new version of EMIRGE optimized for large data size to reconstruct near-full-length 16S rRNA genes from amplicons sheared and sequenced with Illumina technology. The approach allowed us to differentiate the community composition among samples acquired before perturbation, after acetate amendment shifted the predominant metabolism to iron reduction, and once sulfate reduction began. Results were highly reproducible across technical replicates, and identified specific taxa that responded to the perturbation. All samples contain very high alpha diversity and abundant organisms from phyla without cultivated representatives. Surprisingly, at the time points measured, there was no strong loss of evenness, despite the selective pressure of acetate amendment and change in the terminal electron accepting process. However, community membership was altered significantly. The method allows for sensitive, accurate profiling of the "long tail" of low abundance organisms that exist in many microbial communities, and can resolve population dynamics in response to environmental change.}, }
@article {pmid23404990, year = {2013}, author = {Krause, DO and Nagaraja, TG and Wright, AD and Callaway, TR}, title = {Board-invited review: Rumen microbiology: leading the way in microbial ecology.}, journal = {Journal of animal science}, volume = {91}, number = {1}, pages = {331-341}, doi = {10.2527/jas.2012-5567}, pmid = {23404990}, issn = {1525-3163}, mesh = {Animals ; Archaea/metabolism ; Bacteria, Anaerobic/physiology ; Cattle ; Fungi/metabolism ; Rumen/*microbiology/physiology ; }, abstract = {Robert Hungate, considered the father of rumen microbiology, was the first to initiate a systematic exploration of the microbial ecosystem of the rumen, but he was not alone. The techniques he developed to isolate and identify cellulose-digesting bacteria from the rumen have had a major impact not only in delineating the complex ecosystem of the rumen but also in clinical microbiology and in the exploration of a number of other anaerobic ecosystems, including the human hindgut. Rumen microbiology has pioneered our understanding of much of microbial ecology and has broadened our knowledge of ecology in general, as well as improved the ability to feed ruminants more efficiently. The discovery of anaerobic fungi as a component of the ruminal flora disproved the central dogma in microbiology that all fungi are aerobic organisms. Further novel interactions between bacterial species such as nutrient cross feeding and interspecies H2 transfer were first described in ruminal microorganisms. The complexity and diversity present in the rumen make it an ideal testing ground for microbial theories (e.g., the effects of nutrient limitation and excess) and techniques (such as 16S rRNA), which have rewarded the investigators that have used this easily accessed ecosystem to understand larger truths. Our understanding of characteristics of the ruminal microbial population has opened new avenues of microbial ecology, such as the existence of hyperammonia-producing bacteria and how they can be used to improve N efficiency in ruminants. In this review, we examine some of the contributions to science that were first made in the rumen, which have not been recognized in a broader sense.}, }
@article {pmid23403217, year = {2013}, author = {Zamalloa, C and Arends, JB and Boon, N and Verstraete, W}, title = {Performance of a lab-scale bio-electrochemical assisted septic tank for the anaerobic treatment of black water.}, journal = {New biotechnology}, volume = {30}, number = {5}, pages = {573-580}, doi = {10.1016/j.nbt.2013.01.009}, pmid = {23403217}, issn = {1876-4347}, mesh = {*Biofuels ; *Electrochemical Techniques ; Humans ; Sewage/*microbiology ; *Water Microbiology ; Water Purification/*methods ; }, abstract = {Septic tanks are used for the removal of organic particulates in wastewaters by physical accumulation instead of through the biological production of biogas. Improved biogas production in septic tanks is crucial to increase the potential of this system for both energy generation and organic matter removal. In this study, the effect on the biogas production and biogas quality of coupling a 20 L lab-scale septic tank with a microbial electrolysis cell (MEC) was investigated and compared with a standard septic tank. Both reactors were operated at a volumetric organic loading rate of 0.5gCOD/Ld and a hydraulic retention time between 20 and 40 days using black water as an input under mesophilic conditions for a period of 3 months. The MEC-septic tank was operated at an applied voltage of 2.0±0.1V and the current experienced ranged from 40 mA (0.9A/m(2) projected electrode area) to 180 mA (5A/m(2) projected electrode area). The COD removal was of the order of 85% and the concentration of residual COD was not different between both reactors. Yet, the total phosphorous in the output was on average 39% lower in the MEC-septic tank. Moreover, the biogas production rate in the MEC-septic tank was a factor of 5 higher than in the control reactor and the H2S concentration in the biogas was a factor of 2.5 lower. The extra electricity supplied to the MEC-septic tank was recovered as extra biogas produced. Overall, it appears that the combination of MEC and a septic tank offers perspectives in terms of lower discharge of phosphorus and H2S, nutrient recuperation and a more reliable supply of biogas.}, }
@article {pmid23400224, year = {2013}, author = {Douglas-Escobar, M and Elliott, E and Neu, J}, title = {Effect of intestinal microbial ecology on the developing brain.}, journal = {JAMA pediatrics}, volume = {167}, number = {4}, pages = {374-379}, doi = {10.1001/jamapediatrics.2013.497}, pmid = {23400224}, issn = {2168-6211}, support = {R01 HD 059143/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Brain/growth &amp; development/*physiology ; Child ; Child Development Disorders, Pervasive/epidemiology/microbiology ; Comorbidity ; Enteric Nervous System/physiology ; Gastrointestinal Diseases/epidemiology ; Humans ; Infant, Newborn ; Infant, Premature/physiology ; Intestines/immunology/*microbiology/*physiology ; Metagenome/immunology/*physiology ; Toll-Like Receptors/physiology ; }, abstract = {The mammalian gastrointestinal tract harbors a highly diverse microbial population that plays a major role in nutrition, metabolism, protection against pathogens, and development of the immune system. It is estimated that at least 1000 different bacterial species cohabit the human intestinal tract. Most recently, the Human Microbiome Project, using new genomic technologies, has started a catalog of specific microbiome composition and its correlation with health and specific diseases. Herein we provide a brief review of the intestinal microbiome, with a focus on new studies showing that there is an important link between the microbes that inhabit the intestinal tract and the developing brain. With future research, an understanding of this link may help us to treat various neurobehavioral problems such as autism, schizophrenia, and anxiety.}, }
@article {pmid23398612, year = {2013}, author = {Ren, L and He, D and Zeng, J and Wu, QL}, title = {Bacterioplankton communities turn unstable and become small under increased temperature and nutrient-enriched conditions.}, journal = {FEMS microbiology ecology}, volume = {84}, number = {3}, pages = {614-624}, doi = {10.1111/1574-6941.12089}, pmid = {23398612}, issn = {1574-6941}, mesh = {Actinobacteria/classification/genetics/*physiology ; *Bacterial Physiological Phenomena ; Betaproteobacteria/classification/genetics/*physiology ; Denaturing Gradient Gel Electrophoresis ; Ecosystem ; Environment ; Fresh Water/chemistry/*microbiology ; Genes, rRNA ; Nitrogen/analysis ; Phosphorus/analysis ; Phylogeny ; Plankton/classification/genetics/*physiology ; RNA, Ribosomal, 16S/genetics ; Temperature ; }, abstract = {The stability of microbial community composition under different environmental conditions is an important part of microbial ecology, but has not been investigated in such depth before. In this study, we investigated the composition of the bacterioplankton community composition (BCC) and its stability under different temperatures (15, 25 and 35 °C, respectively) and nutrient conditions (control vs. nitrogen- and phosphorus-enriched) in aquatic microcosms. The BCC was analysed using denaturing gradient gel electrophoresis of the bacterial 16S rRNA gene, followed by cloning and sequence analysis. BCC in the microcosms significantly changed under different temperature and nutrient conditions. Based on the results from clone libraries, ecological diversification were observed within two ubiquitous and dominant genera, Methylophilus and Polynucleobacter, under different temperature and nutrient conditions. Putative ultramicrobacteria, which included Actinobacteria, Polynucleobacter sp., LD12 and LD28 clusters and bacteria affiliated with subcluster I of Methylophilus, were found to dominate in bacterioplankton communities at higher temperatures (25 and 35 °C), regardless of nutrient conditions. We also observed that the rate of BCC change increased at higher temperatures and this increase was more pronounced in nutrient-enriched microcosms. These results indicated that bacterioplankton communities become unstable and decrease in size with increased temperature and in nutrient-enriched conditions.}, }
@article {pmid23397906, year = {2013}, author = {Krause, S and Meima-Franke, M and Hefting, MM and Bodelier, PL}, title = {Spatial patterns of methanotrophic communities along a hydrological gradient in a riparian wetland.}, journal = {FEMS microbiology ecology}, volume = {86}, number = {1}, pages = {59-70}, doi = {10.1111/1574-6941.12091}, pmid = {23397906}, issn = {1574-6941}, mesh = {Methane/*metabolism ; Methylococcaceae/*classification/genetics/isolation &amp; purification ; Oxidation-Reduction ; Soil/chemistry ; *Soil Microbiology ; *Wetlands ; }, abstract = {Microbial communities display a variety of biogeographical patterns mainly driven by large-scale environmental gradients. Here, we analysed the spatial distribution of methane-oxidizing bacteria (MOB) and methane oxidation in a strongly fluctuating environment. We investigated whether the spatial variability of the MOB community can be explained by an environmental gradient and whether this changes with different plot sizes. We applied a pmoA-specific microarray to detect MOB, measured methane oxidation, methane emissions and soil properties. All variables were measured in a 10 × 10 m, 1 × 1 m and 20 × 20 cm plot and interpreted using a geostatistical approach. Methane oxidation as well as MOB displayed spatial patterns reflected in the underlying flooding gradient. Overlapping and contrasting spatial patterns for type I and type II MOB suggested different ecological life strategies. With smaller plot size, the environmental gradient could not explain the variability in the data and local factors became more important. In conclusion, environmental gradients can generally explain variability in microbial spatial patterns; however, we think that this does not contribute to a mechanistic explanation for microbial diversity because the relevant scales for microorganisms are much smaller than those normally measured.}, }
@article {pmid23368516, year = {2013}, author = {Durno, WE and Hanson, NW and Konwar, KM and Hallam, SJ}, title = {Expanding the boundaries of local similarity analysis.}, journal = {BMC genomics}, volume = {14 Suppl 1}, number = {Suppl 1}, pages = {S3}, pmid = {23368516}, issn = {1471-2164}, mesh = {Algorithms ; Computational Biology ; Female ; Humans ; Internet ; Intestines/microbiology ; Male ; Metagenome ; Mouth/microbiology ; Saccharomyces cerevisiae/genetics ; Skin/microbiology ; *Software ; User-Computer Interface ; }, abstract = {BACKGROUND: Pairwise comparison of time series data for both local and time-lagged relationships is a computationally challenging problem relevant to many fields of inquiry. The Local Similarity Analysis (LSA) statistic identifies the existence of local and lagged relationships, but determining significance through a p-value has been algorithmically cumbersome due to an intensive permutation test, shuffling rows and columns and repeatedly calculating the statistic. Furthermore, this p-value is calculated with the assumption of normality -- a statistical luxury dissociated from most real world datasets.<br><br>RESULTS: To improve the performance of LSA on big datasets, an asymptotic upper bound on the p-value calculation was derived without the assumption of normality. This change in the bound calculation markedly improved computational speed from O(pm&#xb2;n) to O(m&#xb2;n), where p is the number of permutations in a permutation test, m is the number of time series, and n is the length of each time series. The bounding process is implemented as a computationally efficient software package, FASTLSA, written in C and optimized for threading on multi-core computers, improving its practical computation time. We computationally compare our approach to previous implementations of LSA, demonstrate broad applicability by analyzing time series data from public health, microbial ecology, and social media, and visualize resulting networks using the Cytoscape software.<br><br>CONCLUSIONS: The FASTLSA software package expands the boundaries of LSA allowing analysis on datasets with millions of co-varying time series. Mapping metadata onto force-directed graphs derived from FASTLSA allows investigators to view correlated cliques and explore previously unrecognized network relationships. The software is freely available for download at: http://www.cmde.science.ubc.ca/hallam/fastLSA/.}, }
@article {pmid23365276, year = {2012}, author = {Pieper, R and Neumann, K and Kröger, S and Richter, JF and Wang, J and Martin, L and Bindelle, J and Htoo, JK and Vahjen, V and Van Kessel, AG and Zentek, J}, title = {Influence of fermentable carbohydrates or protein on large intestinal and urinary metabolomic profiles in piglets.}, journal = {Journal of animal science}, volume = {90 Suppl 4}, number = {}, pages = {34-36}, doi = {10.2527/jas.53918}, pmid = {23365276}, issn = {1525-3163}, mesh = {Animal Feed ; Animal Nutritional Physiological Phenomena ; Animals ; Carbohydrates/*chemistry ; Diet/veterinary ; Dietary Carbohydrates/*pharmacology ; Dietary Proteins/*pharmacology ; Fermentation ; Gastrointestinal Contents/chemistry ; Intestine, Large/*metabolism ; Metabolome ; Swine/*physiology/*urine ; }, abstract = {It was recently shown that variations in the ratio of dietary fermentable carbohydrates (fCHO) and fermentable protein (fCP) differentially affect large intestinal microbial ecology and the mucosal response. Here we investigated the use of mass spectrometry to profile changes in metabolite composition in colon and urine associated with variation in dietary fCHO and fCP composition and mucosal physiology. Thirty-two weaned piglets were fed 4 diets in a 2 × 2 factorial design with low fCP and low fCHO, low fCP and high fCHO, high fCP and low fCHO, and high fCP and high fCHO. After 21 to 23 d, all pigs were euthanized and colon digesta and urine metabolite profiles were obtained by mass spectrometry. Analysis of mass spectra by partial least squares approach indicated a clustering of both colonic and urinary profiles for each pig by feeding group. Metabolite identification and annotation using the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed increased abundance of metabolites associated with arachidonic acid metabolism in colon of pigs fed a high concentration of fCP irrespective of dietary fCHO. Urinary metabolites did not show as clear patterns. Mass spectrometry can effectively differentiate metabolite profiles in colon contents and urine associated with changes in dietary composition. Whether metabolite profiling is an effective tool to identify specific metabolites (biomarkers) or metabolite profiles associated with gut function and integrity needs further elucidation.}, }
@article {pmid23360883, year = {2013}, author = {Olivares, M and Laparra, JM and Sanz, Y}, title = {Host genotype, intestinal microbiota and inflammatory disorders.}, journal = {The British journal of nutrition}, volume = {109 Suppl 2}, number = {}, pages = {S76-80}, doi = {10.1017/S0007114512005521}, pmid = {23360883}, issn = {1475-2662}, mesh = {Animals ; Celiac Disease/genetics/immunology/metabolism/microbiology ; Enterocolitis/*genetics/immunology/metabolism/*microbiology ; *Genetic Predisposition to Disease ; Genotype ; HLA-DQ Antigens/genetics/metabolism ; *Host-Parasite Interactions ; Host-Pathogen Interactions ; Humans ; Inflammatory Bowel Diseases/genetics/immunology/metabolism/microbiology ; Intestinal Diseases/*genetics/immunology/metabolism/*microbiology ; Intestinal Mucosa/immunology/metabolism/*microbiology ; Nod2 Signaling Adaptor Protein/genetics/metabolism ; }, abstract = {Intestinal microbiota may influence human physiology and disease risk due to the role it plays in mediating appropriate immune responses to harmful and innocuous antigens. Colonisation of the intestine in early life seems particularly important as it is the main environmental stimulus for immune system maturation. This is a dynamic process, which depends on both environmental and genetic factors. The pathogenesis of inflammatory bowel disease, such as Crohn's disease, involves genetic polymorphisms (e.g. CARD15/nucleotide-binding oligomerisation domain 2) related to an excessive inflammatory response to commensal microbiota and to its unbalanced composition. Atopic diseases have also been linked to imbalances in microbiota and to related genetic factors (e.g. TLR4 and CD14 genes), although these associations are still controversial. Research into the relationship between the genetic risk of developing celiac disease (human leukocyte antigen (HLA)-DQ2/DQ8) and the early colonisation process in infants at family risk of the disease has also reported that the HLA-DQ genotype could influence staphylococcal colonisation. Future observational studies considering both host genetics and microbiota could be critical in defining the complex host-microbe interactions and the respective role each plays in inflammatory disorders.}, }
@article {pmid23397369, year = {2013}, author = {Delgado, S and Cabrera-Rubio, R and Mira, A and Suárez, A and Mayo, B}, title = {Microbiological survey of the human gastric ecosystem using culturing and pyrosequencing methods.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {763-772}, pmid = {23397369}, issn = {1432-184X}, mesh = {Adult ; Aged ; Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; *Biodiversity ; Colony Count, Microbial/*methods ; Ecosystem ; Female ; Gastric Juice/*microbiology ; Humans ; Male ; Metagenome ; Middle Aged ; Phylogeny ; Sequence Analysis, DNA/*methods ; Stomach/*microbiology ; }, abstract = {Stomach mucosa biopsies and gastric juices samples of 12 healthy persons were analysed by culturing in selective- and non-selective-rich media. Microbial DNA from four mucosal samples was also amplified by nested PCR using universal bacterial primers, and the 16S rDNA amplicons pyrosequenced. The total number of cultivable microorganisms recovered from the samples ranged from 10(2) to 10(4) cfu/g or ml. The isolates were identified at the species level by PCR amplification and sequencing of the 16S rDNA. Isolates belonged mainly to four genera; Propionibacterium, Lactobacillus, Streptococcus and Staphylococcus. A total of 15,622 high-quality 16S rDNA sequence reads were obtained by pyrosequencing from the four mucosal samples. Sequence analysis grouped the reads into 59 families and 69 genera, revealing wide bacterial diversity. Considerable differences in the composition of the gastric microbiota were observed among the subjects, although in all samples the most abundant operational taxonomic units belonged to Streptococcus, Propionibacterium and Lactobacillus. Comparison of the stomach microbiota with that present in other parts of the human gastrointestinal tract revealed distinctive microbial communities. This is the first study in which a combination of culture and culture-independent techniques has been used to explore the bacterial diversity of the human stomach.}, }
@article {pmid23392641, year = {2013}, author = {Hughes, SN and Greig, DJ and Miller, WA and Byrne, BA and Gulland, FM and Harvey, JT}, title = {Dynamics of Vibrio with virulence genes detected in Pacific harbor seals (Phoca vitulina richardii) off California: implications for marine mammal health.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {982-994}, pmid = {23392641}, issn = {1432-184X}, mesh = {Animals ; Animals, Wild/microbiology ; Bacterial Proteins/*genetics/metabolism ; California ; Humans ; Mammals/microbiology ; Phoca/*microbiology ; Vibrio/classification/genetics/*isolation &amp; purification ; Vibrio Infections/microbiology/*veterinary ; Virulence Factors/*genetics/metabolism ; }, abstract = {Given their coastal site fidelity and opportunistic foraging behavior, harbor seals (Phoca vitulina) may serve as sentinels for coastal ecosystem health. Seals using urbanized coastal habitat can acquire enteric bacteria, including Vibrio that may affect their health. To understand Vibrio dynamics in seals, demographic and environmental factors were tested for predicting potentially virulent Vibrio in free-ranging and stranded Pacific harbor seals (Phoca vitulina richardii) off California. Vibrio prevalence did not vary with season and was greater in free-ranging seals (29 %, n = 319) compared with stranded seals (17 %, n = 189). Of the factors tested, location, turbidity, and/or salinity best predicted Vibrio prevalence in free-ranging seals. The relationship of environmental factors with Vibrio prevalence differed by location and may be related to oceanographic or terrestrial contributions to water quality. Vibrio parahaemolyticus, Vibrio alginolyticus, and Vibrio cholerae were observed in seals, with V. cholerae found almost exclusively in stranded pups and yearlings. Additionally, virulence genes (trh and tdh) were detected in V. parahaemolyticus isolates. Vibrio cholerae isolates lacked targeted virulence genes, but were hemolytic. Three out of four stranded pups with V. parahaemolyticus (trh+ and/or tdh+) died in rehabilitation, but the role of Vibrio in causing mortality is unclear, and Vibrio expression of virulence genes should be investigated. Considering that humans share the environment and food resources with seals, potentially virulent Vibrio observed in seals also may be of concern to human health.}, }
@article {pmid23390547, year = {2013}, author = {Guidi, V and Lehner, A and Lüthy, P and Tonolla, M}, title = {Dynamics of Bacillus thuringiensis var. israelensis and Lysinibacillus sphaericus spores in urban catch basins after simultaneous application against mosquito larvae.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e55658}, pmid = {23390547}, issn = {1932-6203}, mesh = {Animals ; Bacillaceae/classification/*genetics ; Bacillus thuringiensis/classification/*genetics ; Bacillus thuringiensis Toxins ; Bacterial Load ; Bacterial Proteins/genetics/isolation &amp; purification ; Bacterial Toxins/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Culex/microbiology ; Electrophoresis, Gel, Pulsed-Field ; Endotoxins/genetics/isolation &amp; purification ; Hemolysin Proteins/genetics/isolation &amp; purification ; Larva/microbiology ; Pest Control, Biological/*methods ; RNA, Ribosomal, 16S/*genetics/isolation &amp; purification ; Real-Time Polymerase Chain Reaction ; Sewage/microbiology ; Spores, Bacterial/classification/*genetics ; }, abstract = {Bacillus thuringiensis var. israelensis (Bti) and Lysinibacillus sphaericus (Lsph) are extensively used in mosquito control programs. These biocides are the active ingredients of a commercial larvicide. Quantitative data on the fate of both Bti and Lsph applied together for the control of mosquitoes in urban drainage structures such as catch basins are lacking. We evaluated the dynamics and persistence of Bti and Lsph spores released through their concomitant application in urban catch basins in southern Switzerland. Detection and quantification of spores over time in water and sludge samples from catch basins were carried out using quantitative real-time PCR targeting both cry4A and cry4B toxin genes for Bti and the binA gene for Lsph. After treatment, Bti and Lsph spores attained concentrations of 3.76 (± 0.08) and 4.13 (± 0.09) log ml(-1) in water, then decreased progressively over time, reaching baseline values. For both Bti and Lsph, spore levels in the order of 10(5) g(-1) were observed in the bottom sludge two days after the treatment and remained constant for the whole test period (275 days). Indigenous Lsph strains were isolated from previously untreated catch basins. A selection of those was genotyped using pulsed field gel electrophoresis of SmaI-digested chromosomal DNA, revealing that a subset of isolates were members of the clonal population of strain 2362. No safety issues related to the use of this biopesticide in the environment have been observed during this study, because no significant increase in the number of spores was seen during the long observation period. The isolation of native Lysinibacillus sphaericus strains belonging to the same clonal population as strain 2362 from catch basins never treated with Lsph-based products indicates that the use of a combination of Bti and Lsph for the control of mosquitoes does not introduce non-indigenous microorganisms in this area.}, }
@article {pmid23389251, year = {2013}, author = {Lan, S and Wu, L and Zhang, D and Hu, C}, title = {Assessing level of development and successional stages in biological soil crusts with biological indicators.}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {394-403}, pmid = {23389251}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Bryophyta/metabolism/*microbiology ; *Ecosystem ; Fungi/classification/genetics/*isolation &amp; purification ; Lichens/metabolism/*microbiology ; Photosynthesis ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Biological soil crusts (BSCs) perform vital ecosystem services, but the difference in biological components or developmental level still affects the rate and type of these services. In order to differentiate crust successional stages in quantity and analyze the relationship between crust developmental level and successional stages, this work determined several biological indicators in a series of different developmental BSCs in the Shapotou region of China. The results showed that crust developmental level (level of development index) can be well indicated by crust biological indicators. Photosynthetic biomass was the most appropriate to differentiate crust successional stages, although both photosynthetic biomass and respiration intensity increased with the development and succession of BSCs. Based on of the different biological compositions, BSCs were quantificationally categorized into different successional stages including cyanobacterial crusts (lichen and moss coverages <20 %), lichen crusts (lichen coverage >20 % but moss coverage <20 %), semi-moss crusts (moss coverage >20 % but <75 %), and moss crusts (moss coverage >75 %). In addition, it was found that cyanobacterial and microalgal biomass first increased as cyanobacterial crusts formed, then decreased when lots of mosses emerged on the crust surface; however nitrogen-fixing cyanobacteria and heterotrophic microbes increased in the later developmental BSCs. The structural adjustment of biological components in the different developmental BSCs may reflect the requirement of crust survival and material transition.}, }
@article {pmid23387867, year = {2013}, author = {Shakya, M and Quince, C and Campbell, JH and Yang, ZK and Schadt, CW and Podar, M}, title = {Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities.}, journal = {Environmental microbiology}, volume = {15}, number = {6}, pages = {1882-1899}, pmid = {23387867}, issn = {1462-2920}, support = {R01 HG004857/HG/NHGRI NIH HHS/United States ; 1R01HG004857-01A1/HG/NHGRI NIH HHS/United States ; }, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; *Biodiversity ; DNA Primers/genetics ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Microbiological Techniques/*standards ; Phylogeny ; RNA, Ribosomal/genetics ; Reproducibility of Results ; }, abstract = {Next-generation sequencing has dramatically changed the landscape of microbial ecology, large-scale and in-depth diversity studies being now widely accessible. However, determining the accuracy of taxonomic and quantitative inferences and comparing results obtained with different approaches are complicated by incongruence of experimental and computational data types and also by lack of knowledge of the true ecological diversity. Here we used highly diverse bacterial and archaeal synthetic communities assembled from pure genomic DNAs to compare inferences from metagenomic and SSU rRNA amplicon sequencing. Both Illumina and 454 metagenomic data outperformed amplicon sequencing in quantifying the community composition, but the outcome was dependent on analysis parameters and platform. New approaches in processing and classifying amplicons can reconstruct the taxonomic composition of the community with high reproducibility within primer sets, but all tested primers sets lead to significant taxon-specific biases. Controlled synthetic communities assembled to broadly mimic the phylogenetic richness in target environments can provide important validation for fine-tuning experimental and computational parameters used to characterize natural communities.}, }
@article {pmid23383036, year = {2013}, author = {Aistleitner, K and Heinz, C and Hörmann, A and Heinz, E and Montanaro, J and Schulz, F and Maier, E and Pichler, P and Benz, R and Horn, M}, title = {Identification and characterization of a novel porin family highlights a major difference in the outer membrane of chlamydial symbionts and pathogens.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e55010}, pmid = {23383036}, issn = {1932-6203}, mesh = {Amoeba/microbiology ; Bacterial Proteins/genetics/*metabolism ; Cell Membrane/*metabolism ; Chlamydiaceae/*cytology/genetics/*metabolism/physiology ; Escherichia coli/genetics ; Lipid Bilayers/metabolism ; Porins/genetics/*metabolism ; Protein Transport ; *Symbiosis ; Transcription, Genetic ; }, abstract = {The Chlamydiae constitute an evolutionary well separated group of intracellular bacteria comprising important pathogens of humans as well as symbionts of protozoa. The amoeba symbiont Protochlamydia amoebophila lacks a homologue of the most abundant outer membrane protein of the Chlamydiaceae, the major outer membrane protein MOMP, highlighting a major difference between environmental chlamydiae and their pathogenic counterparts. We recently identified a novel family of putative porins encoded in the genome of P. amoebophila by in silico analysis. Two of these Protochlamydiaouter membrane proteins, PomS (pc1489) and PomT (pc1077), are highly abundant in outer membrane preparations of this organism. Here we show that all four members of this putative porin family are toxic when expressed in the heterologous host Escherichia coli. Immunofluorescence analysis using antibodies against heterologously expressed PomT and PomS purified directly from elementary bodies, respectively, demonstrated the location of both proteins in the outer membrane of P. amoebophila. The location of the most abundant protein PomS was further confirmed by immuno-transmission electron microscopy. We could show that pomS is transcribed, and the corresponding protein is present in the outer membrane throughout the complete developmental cycle, suggesting an essential role for P. amoebophila. Lipid bilayer measurements demonstrated that PomS functions as a porin with anion-selectivity and a pore size similar to the Chlamydiaceae MOMP. Taken together, our results suggest that PomS, possibly in concert with PomT and other members of this porin family, is the functional equivalent of MOMP in P. amoebophila. This work contributes to our understanding of the adaptations of symbiotic and pathogenic chlamydiae to their different eukaryotic hosts.}, }
@article {pmid23378558, year = {2013}, author = {Van Meervenne, E and Boon, N and Verstraete, K and Devlieghere, F and De Reu, K and Herman, L and Buvens, G and Piérard, D and Van Coillie, E}, title = {Integron characterization and typing of Shiga toxin-producing Escherichia coli isolates in Belgium.}, journal = {Journal of medical microbiology}, volume = {62}, number = {Pt 5}, pages = {712-719}, doi = {10.1099/jmm.0.048934-0}, pmid = {23378558}, issn = {1473-5644}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Belgium/epidemiology ; Drug Resistance, Bacterial ; Escherichia coli Infections/epidemiology/*microbiology ; Food Microbiology ; Gene Expression Regulation, Bacterial/*physiology ; Humans ; Integrons/genetics/*physiology ; Multigene Family ; Shiga-Toxigenic Escherichia coli/drug effects/*genetics/isolation &amp; purification/pathogenicity ; Transcriptome ; Virulence ; }, abstract = {The presence of integrons and the antibiotic susceptibility profiles of STEC strains isolated in Belgium were analysed. The collection contained 306 strains, of which 225 were human isolates and 81 originated from different food or animal sources. Integrons were detected by PCR in 7.5% of the tested isolates and all were class 1 integrons. The integron-positive strains all belonged to the human collection. By RFLP, five different types (A, B, C, D, E) were distinguished. The antibiotic-resistance gene cassettes were identified by sequencing representatives of the five different types. Two types of gene cassettes were found in different combinations, one encoding resistance to streptomycin/spectinomycin and the other encoding resistance to trimethoprim. One of the gene cassettes present was the rarely detected aadA23, which was now apparently for the first time reported in Western Europe. Susceptibility profiling of the strains for 11 antibiotics was done by standard disc diffusion assays. Among the 23 integron-positive strains, 17 different antibiotic susceptibility profiles were found. In the 283 integron-negative strains, 24 different antibiotic susceptibility profiles were observed. The majority of these strains were susceptible to all tested antibiotics (n=218, 77.0%). The integron-positive strains were significantly more resistant to eight of the eleven tested antibiotics compared to the integron-negative strains (P<0.05). PFGE profiles of integron-positive strains within selected serogroups did not cluster together.}, }
@article {pmid23375967, year = {2013}, author = {Halmemies-Beauchet-Filleau, A and Kairenius, P and Ahvenjärvi, S and Crosley, LK and Muetzel, S and Huhtanen, P and Vanhatalo, A and Toivonen, V and Wallace, RJ and Shingfield, KJ}, title = {Effect of forage conservation method on ruminal lipid metabolism and microbial ecology in lactating cows fed diets containing a 60:40 forage-to-concentrate ratio.}, journal = {Journal of dairy science}, volume = {96}, number = {4}, pages = {2428-2447}, doi = {10.3168/jds.2012-6043}, pmid = {23375967}, issn = {1525-3198}, mesh = {Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Bacterial Load ; Butyrivibrio ; Cattle/*metabolism/microbiology ; Diet/*veterinary ; Digestion ; Fatty Acids ; Fatty Acids, Volatile/analysis ; Female ; Fermentation ; Hydrogen-Ion Concentration ; Lactation ; *Lipid Metabolism ; Lipolysis ; Poaceae ; Rumen/chemistry/*microbiology/parasitology ; Silage ; }, abstract = {The effect of forage conservation method on ruminal lipid metabolism and microbial ecology was examined in 2 complementary experiments in cows. Treatments comprised fresh chopped grass, barn-dried hay, or untreated (UTS) or formic acid-treated silage (FAS) prepared from the same grass sward. Preparation of conserved forages coincided with the collection of samples from cows offered fresh grass. In the first experiment, 5 multiparous Finnish Ayrshire cows (229 d in milk) were used to compare the effects of feeding diets based on grass followed by hay during 2 consecutive 14-d periods separated by a 5-d transition during which extensively wilted grass was fed. In the second experiment, 5 multiparous Finnish Ayrshire cows (53 d in milk) were assigned to 1 of 2 blocks and allocated treatments according to a replicated 3×3 Latin square design with 14-d periods to compare the effects of hay, UTS, and FAS. Cows received 7 or 9 kg/d of the same concentrate in experiments 1 and 2, respectively. Conservation of grass by drying, but not ensiling, decreased forage fatty acid content primarily due to losses of 18:2n-6 and 18:3n-3. Compared with grass, feeding hay had no effect on dry matter intake (DMI), rumen pH, or fermentation characteristics, other than increasing ammonia content, but lowered whole-tract organic matter and fiber digestibility (experiment 1). Relative to hay, silage increased DMI, rumen volatile fatty acid (VFA) concentrations, and molar proportions of butyrate, and decreased molar acetate proportions (experiment 2). Compared with UTS, FAS increased DMI, had no effect on rumen ammonia or VFA concentrations, but tended to lower rumen pH and the molar ratio of lipogenic to glucogenic VFA. Conservation method had no substantial effect on ruminal or whole-tract digestibility coefficients. Compared with fresh grass and silages, hay decreased lipolysis and biohydrogenation (BH) of dietary unsaturates in the rumen, resulting in similar flows of 18:2n-6 and 18:3n-3, but lower amounts of trans-11 18:1 and Δ11,13 18:2 at the omasum. The extent of silage fermentation had minimal influence on ruminal lipid metabolism. Treatments were not associated with changes in the relative abundance of specific bacteria known to be capable of BH or rumen protozoal numbers. In conclusion, conservation method altered forage lipids, the extent of lipolysis and BH in the rumen, and the flow of fatty acids at the omasum, in the absence of substantial changes in ruminal Butyrivibrio populations.}, }
@article {pmid23370726, year = {2013}, author = {Yang, J and Wang, C and Shu, C and Liu, L and Geng, J and Hu, S and Feng, J}, title = {Marine sediment bacteria harbor antibiotic resistance genes highly similar to those found in human pathogens.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {975-981}, pmid = {23370726}, issn = {1432-184X}, mesh = {Bacteria/classification/drug effects/*genetics/*isolation &amp; purification ; Bacterial Infections/*microbiology ; Bacterial Proteins/*genetics/metabolism ; *Drug Resistance, Bacterial ; Geologic Sediments/*microbiology ; Humans ; Metagenomics ; Seawater/microbiology ; }, abstract = {The ocean is a natural habitat for antibiotic-producing bacteria, and marine aquaculture introduces antibiotics into the ocean to treat infections and improve aquaculture production. Studies have shown that the ocean is an important reservoir of antibiotic resistance genes. However, there is a lack of understanding and knowledge about the clinical importance of the ocean resistome. We investigated the relationship between the ocean bacterial resistome and pathogenic resistome. We applied high-throughput sequencing and metagenomic analyses to explore the resistance genes in bacterial plasmids from marine sediments. Numerous putative resistance determinants were detected among the resistance genes in the sediment bacteria. We also found that several contigs shared high identity with transposons or plasmids from human pathogens, indicating that the sediment bacteria recently contributed or acquired resistance genes from pathogens. Marine sediment bacteria could play an important role in the global exchange of antibiotic resistance.}, }
@article {pmid23369466, year = {2013}, author = {Ludden, C and Cormican, M and Austin, B and Morris, D}, title = {Rapid environmental contamination of a new nursing home with antimicrobial-resistant organisms preceding occupation by residents.}, journal = {The Journal of hospital infection}, volume = {83}, number = {4}, pages = {327-329}, doi = {10.1016/j.jhin.2012.11.023}, pmid = {23369466}, issn = {1532-2939}, mesh = {Drug Resistance, Bacterial ; Enterobacteriaceae/*isolation &amp; purification ; Enterococcus/*isolation &amp; purification ; *Environmental Microbiology ; Humans ; Methicillin-Resistant Staphylococcus aureus/*isolation &amp; purification ; *Nursing Homes ; }, abstract = {Nursing homes are reservoirs for antimicrobial-resistant organisms (AROs). This study examined the time to environmental contamination with AROs in a new-build nursing home. Environmental sites in an occupied nursing home (N = 18) and a newly built replacement nursing home (N = 21) were monitored during an 11-week period before and after residents transferred between buildings. Meticillin-resistant Staphylococcus aureus was detected during commissioning in the new building and was a frequent finding throughout the building after residents had moved in. Extended-spectrum beta-lactamase-producing E. coli O25b:ST131 was detected once.}, }
@article {pmid23361528, year = {2013}, author = {Dobbs, FC and Goodrich, AL and Thomson, FK and Hynes, W}, title = {Pandemic serotypes of Vibrio cholerae isolated from ships' ballast tanks and coastal waters: assessment of antibiotic resistance and virulence genes (tcpA and ctxA).}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {969-974}, pmid = {23361528}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/pharmacology ; Cholera/epidemiology/*microbiology ; *Drug Resistance, Bacterial ; Fimbriae Proteins/genetics/*metabolism ; Humans ; Pandemics ; Seawater/*microbiology ; Serotyping ; Ships ; Vibrio cholerae/classification/drug effects/genetics/*isolation &amp; purification ; Virulence Factors/genetics/*metabolism ; }, abstract = {There is concern that ships' ballasting operations may disseminate Vibrio cholerae to ports throughout the world. Given evidence that the bacterium is indeed transported by ships, we isolated pandemic serotypes O1 and O139 from ballast tanks and characterized them with respect to antibiotic resistance and virulence genes ctxA and tcpA. We carried out concurrent studies with V. cholerae isolated from coastal waters. Of 284 isolates, 30 were serotype O1 and 59 were serotype O139. These serotypes were overrepresented in ballast tanks relative to the coastal waters sampled. All locations, whether coastal waters or ballast tanks, yielded samples from which serotype O1, O139, or both were isolated. There were three groups among the 62 isolates for which antibiotic characterization was conclusive: those exhibiting β-lactamase activity and resistance to at least one of the 12 antibiotics tested; those negative for β-lactamase but having antibiotic resistance; those negative for β-lactamase and registering no antibiotic resistance. When present, antibiotic resistance in nearly all cases was to ampicillin; resistance to multiple antibiotics was uncommon. PCR assays revealed that none of the isolates contained the ctxA gene and only two isolates, one O139 and one O1, contained the tcpA gene; both isolates originated from ballast water. These results support the bacteriological regulations proposed by the International Maritime Association for discharged ballast water.}, }
@article {pmid23360493, year = {2013}, author = {Kuramae, EE and Hillekens, RH and de Hollander, M and van der Heijden, MG and van den Berg, M and van Straalen, NM and Kowalchuk, GA}, title = {Structural and functional variation in soil fungal communities associated with litter bags containing maize leaf.}, journal = {FEMS microbiology ecology}, volume = {84}, number = {3}, pages = {519-531}, doi = {10.1111/1574-6941.12080}, pmid = {23360493}, issn = {1574-6941}, mesh = {Ascomycota/classification/genetics/metabolism ; Base Sequence ; Basidiomycota/classification/genetics/metabolism ; *Ecosystem ; Fungi/*classification/genetics/*metabolism ; Genes, Fungal ; Genes, rRNA ; High-Throughput Nucleotide Sequencing ; Metagenome ; *Plant Leaves/metabolism ; Soil ; *Soil Microbiology ; Transcriptome ; *Zea mays ; }, abstract = {Soil fungi are key players in the degradation of recalcitrant organic matter in terrestrial ecosystems. To examine the organisms and genes responsible for complex organic matter degradation in soil, we tracked changes in fungal community composition and expressed genes in soil adjacent to mesh bags containing maize leaves undergoing decomposition. Using high-throughput sequencing approaches, changes in fungal community composition were determined by targeting 18S rRNA gene sequences, whereas community gene expression was examined via a metatranscriptomic approach. The majority of the 93 000 partial 18S rRNA gene sequences generated, were affiliated with the Ascomycota and Basidiomycota. Fungal diversity was at least 224 operational taxonomic units at the 97% similarity cutoff level. During litter degradation, the relative proportion of Basidiomycota increased, with a decrease in Ascomycota : Basidiomycota ratios over time. The most commonly detected decomposition-associated fungi included Agaricomycetes and Tremellales as well as unclassified Mucoromycotina. The majority of protein families found in the metatranscriptomic data were affiliated to fungal groups described to degrade plant-derived cellulose, such as Mucoraceae, Chaetomiaceae, Sordariaceae, Sebacinaceae, Tremellaceae, Psathyrellaceae and Schizophyllaceae. The combination of high-throughput rRNA gene-based and metatranscriptomic approaches provided perspectives into the organisms and genes involved in complex organic matter in soil.}, }
@article {pmid23356954, year = {2013}, author = {Dolan, JR}, title = {Doing a protist book.}, journal = {Protist}, volume = {164}, number = {2}, pages = {154-159}, doi = {10.1016/j.protis.2012.12.001}, pmid = {23356954}, issn = {1618-0941}, mesh = {*Books ; Eukaryota/*pathogenicity/*physiology ; Humans ; *Publishing ; }, }
@article {pmid23355506, year = {2013}, author = {Scheublin, TR and Leveau, JH}, title = {Isolation of Arthrobacter species from the phyllosphere and demonstration of their epiphytic fitness.}, journal = {MicrobiologyOpen}, volume = {2}, number = {1}, pages = {205-213}, pmid = {23355506}, issn = {2045-8827}, mesh = {Arthrobacter/*classification/growth &amp; development/*isolation &amp; purification/metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Malus/*microbiology ; Molecular Sequence Data ; Pantoea ; Phylogeny ; Plant Leaves/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Bacteria of the genus Arthrobacter are common inhabitants of the soil environment, but can also be recovered from leaf surfaces (the phyllosphere). Using enrichment cultures on 4-chlorophenol, we succeeded in specifically isolating Arthrobacter bacteria from ground cover vegetation in an apple orchard. Based on 16S rRNA gene sequencing, the isolates were found to belong to at least three different species of Arthrobacter. Compared to the model bacterial epiphyte Pantoea agglomerans, the Arthrobacter isolates performed as well or even better in a standardized laboratory test of phyllosphere fitness. A similar performance was observed with the well-characterized soil isolate Arthrobacter chlorophenolicus A6. These findings suggest that the frequently reported presence of Arthrobacter strains on plant foliage can be explained by the capacity to multiply and persist in the phyllosphere environment. As bacteria from the genus Arthrobacter are known for their ability to degrade a wide variety of organic pollutants, their high phyllosphere competency marks them as a promising group for future studies on phyllosphere-based bioremediation, for example, as foliar bioaugmentation on ground cover or buffer-zone vegetation to prevent pesticides from reaching soil, surface-, or groundwater.}, }
@article {pmid23354293, year = {2013}, author = {Ziemer, CJ}, title = {Broad diversity and newly cultured bacterial isolates from enrichment of pig feces on complex polysaccharides.}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {448-461}, pmid = {23354293}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*growth &amp; development/*isolation &amp; purification ; *Biodiversity ; Culture Media/chemistry/*metabolism ; Feces/*microbiology ; Molecular Sequence Data ; Phylogeny ; Polysaccharides/*metabolism ; Swine ; }, abstract = {One of the fascinating functions of mammalian intestinal microbiota is fermentation of plant cell wall components. Eight-week continuous culture enrichments of pig feces with cellulose and xylan/pectin were used to isolate bacteria from this community. A total of 575 bacterial isolates were classified phylogenetically using 16S rRNA gene sequencing. Six phyla were represented in the bacterial isolates: Firmicutes (242), Bacteroidetes (185), Proteobacteria (65), Fusobacteria (55), Actinobacteria (23), and Synergistetes (5). The majority of the bacterial isolates had ≥ 97 % similarity to cultured bacteria with sequences in the RDP, but 179 isolates represent new species and/or genera. Within the Firmicutes isolates, most were classified in the families of Lachnospiraceae, Enterococcaceae, Staphylococcaceae, and Clostridiaceae I. The majority of the Bacteroidetes were most closely related to Bacteroides thetaiotaomicron, Bacteroides ovatus, and B. xylanisolvens. Many of the Firmicutes and Bacteroidetes isolates were identified as species that possess enzymes that ferment plant cell wall components, and the rest likely support these bacteria. The microbial communities that arose in these enrichment cultures had broad bacterial diversity. With over 30 % of the isolates not represented in culture, there are new opportunities to study genomic and metabolic capacities of these members of the complex intestinal microbiota.}, }
@article {pmid23354292, year = {2013}, author = {Oueriaghli, N and Béjar, V and Quesada, E and Martínez-Checa, F}, title = {Molecular ecology techniques reveal both spatial and temporal variations in the diversity of archaeal communities within the athalassohaline environment of Rambla Salada, Spain.}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {297-311}, pmid = {23354292}, issn = {1432-184X}, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Denaturing Gradient Gel Electrophoresis ; *Ecosystem ; Geologic Sediments/chemistry/microbiology ; Molecular Sequence Data ; Phylogeny ; Salinity ; Seasons ; Soil/chemistry ; Soil Microbiology ; Spain ; }, abstract = {We have studied the distribution of the archaeal communities in Rambla Salada (Murcia, Spain) over three different seasons and observed the influence upon them of the environmental variables, salinity, pH, oxygen and temperature. Samples were collected from three representative sites in order to gain an insight into the archaeal population of the rambla as a whole. Denaturing gradient gel electrophoresis patterns and diversity indexes indicate that the diversity of the archaeal community in Rambla Salada changed mainly according to the season. We found no significant differences between the types of sample studied: watery sediments and soils. The upwelling zone showed most diversity in its archaeal community. The overall archaeal community was composed mainly of Halobacteriales and Thermoplasmatales, accounting for 72.6 and 12.1 % of the total, respectively. Haloarcula was the most abundant genus, being present at all three sites during all three seasons. Some few Crenarchaeota were always found, mainly at low-salinity levels. Ordination canonical correspondence analysis demonstrated that salinity affected the structure of the community significantly, whilst pH, oxygen and temperature did so to a lesser extent. Most Halobacteriales correlated positively with salinity and pH, whilst Thermoplasmatales correlated negatively with both salinity and pH and positively with temperature and oxygen. The archaeal community with the highest diversity was sampled during June 2006, the season with the highest salt concentration. Catalyzed reporter deposition-fluorescence in situ hybridization showed that the percentage of archaea in Rambla Salada compared to the total number of microorganisms (as measured by DAPI) ranged from 11.1 to 16.7 %. Our research group had isolated the most abundant taxon, Haloarcula, previously in Rambla Salada using classical culture techniques, but on this occasion, using culture-independent methods, we were also able to identify some phylotypes, Halorubrum, Methanolobus, Natronomonas, Halomicrobium, Halobacterium, Halosimplex, uncultured Thermoplasmatales and uncultured Crenarchaeota, that had remained undetected during our earlier studies in this habitat.}, }
@article {pmid23354291, year = {2013}, author = {Li, M and Hong, Y and Cao, H and Gu, JD}, title = {Community structures and distribution of anaerobic ammonium oxidizing and nirS-encoding nitrite-reducing bacteria in surface sediments of the South China Sea.}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {281-296}, pmid = {23354291}, issn = {1432-184X}, mesh = {Ammonium Compounds/*metabolism ; Anaerobiosis ; Bacteria/classification/*enzymology/genetics/*isolation &amp; purification ; Bacterial Proteins/*genetics ; Biodiversity ; Ecosystem ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Nitrite Reductases/*genetics ; Nitrites/*metabolism ; Oceans and Seas ; Oxidation-Reduction ; Phylogeny ; Seawater/*microbiology ; }, abstract = {Anaerobic ammonium oxidation (anammox) and denitrification are two important processes responsible for nitrogen loss; monitoring of microbial communities carrying out these two processes offers a unique opportunity to understand the microbial nitrogen cycle. The aim of the current study was to characterize community structures and distribution of anammox and nirS-encoding nitrite-reducing bacteria in surface sediments of the northern South China Sea (SCS). The consistent phylogenetic results of three biomarkers of anammox bacteria, including 16S rRNA, hzo, and Scalindua-nirS genes, showed that Scalindua-like bacteria were the only anammox group presenting in surface sediments of the SCS. However, a relatively high micro-diversity was found within this group, including several SCS habitat-specific phylotypes, Candidatus "Scalindua zhenghei". Comparing to 16S rRNA gene, hzo and Scalindua-nirS genes provided a relatively higher resolution to elucidate anammox bacteria. For the nirS-encoding nitrite-reducing bacteria, the detected nirS gene sequences were closely related to various marine nirS denitrifiers, especially those which originated from coastal and estuarine sediments with a much higher diversity than anammox bacteria. Anammox bacterial communities shifted along with the seawater depth, while nirS-encoding nitrite-reducing bacteria did not. Although nirS-encoding nitrite-reducing bacteria have a much higher abundance and diversity than anammox bacteria, they showed similar abundance variation patterns in research sites, suggesting the two microbial groups might be affected by the similar environmental factors. The significant correlations among the abundance of the two microbial groups with the molar ratio of NH4 (+) to (NO2 (-) + NO3 (-)), pH, and organic matters of sediments strongly supported this hypothesis.}, }
@article {pmid23354181, year = {2013}, author = {Erken, M and Lutz, C and McDougald, D}, title = {The rise of pathogens: predation as a factor driving the evolution of human pathogens in the environment.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {860-868}, pmid = {23354181}, issn = {1432-184X}, mesh = {Animals ; Bacteria/*genetics/metabolism/pathogenicity ; Bacterial Infections/*microbiology ; *Biological Evolution ; *Ecosystem ; Humans ; Seawater/*microbiology ; Virulence Factors/*genetics/metabolism ; }, abstract = {Bacteria in the environment must survive predation from bacteriophage, heterotrophic protists, and predatory bacteria. This selective pressure has resulted in the evolution of a variety of defense mechanisms, which can also function as virulence factors. Here we discuss the potential dual function of some of the mechanisms, which protect against heterotrophic protists, and how predation pressure leads to the evolution of pathogenicity. This is in accordance with the coincidental evolution hypothesis, which suggests that virulence factors arose as a response to other selective pressures, for example, predation rather than for virulence per se. In this review we discuss some of those environmental factors that may be associated with the rise of pathogens in the marine environment. In particular, we will discuss the role of heterotrophic protists in the evolution of virulence factors in marine bacteria. Finally, we will discuss the implications for expansion of current pathogens and emergence of new pathogens.}, }
@article {pmid23354180, year = {2013}, author = {Powell, SM and Chapman, CC and Bermudes, M and Tamplin, ML}, title = {Dynamics of seawater bacterial communities in a shellfish hatchery.}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {245-256}, pmid = {23354180}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Molecular Sequence Data ; Ostreidae/*microbiology ; Seasons ; Seawater/*microbiology ; Shellfish/*microbiology ; }, abstract = {Bacterial disease is a significant issue for larviculture of several species of shellfish, including oysters. One source of bacteria is the seawater used throughout the hatchery. In this study carried out at a commercial oyster hatchery in Tasmania, Australia, the diversity of the bacterial community and its relationship with larval production outcomes were studied over a 2-year period using terminal restriction fragment length polymorphism and tag-encoded pyrosequencing. The bacterial communities were very diverse, dominated by the Alphaproteobacteria, Gammaproteobacteria, Flavobacteria and Cyanobacteria. The communities were highly variable on scales of days, weeks and seasons. The difference between the intake seawater and treated clean seawater used in the hatchery was smaller than the observed temporal differences in the seawater throughout the year. No clear correlation was observed between production outcomes and the overall bacterial community structure. However, one group of Cyanobacterial sequences was more abundant when mass mortality events occurred than when healthy spat were produced although they were always present.}, }
@article {pmid23354179, year = {2013}, author = {Meuser, JE and Baxter, BK and Spear, JR and Peters, JW and Posewitz, MC and Boyd, ES}, title = {Contrasting patterns of community assembly in the stratified water column of Great Salt Lake, Utah.}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {268-280}, pmid = {23354179}, issn = {1432-184X}, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Ecosystem ; Eukaryota/classification/genetics/*isolation &amp; purification ; Lakes/*chemistry/parasitology ; Molecular Sequence Data ; Phylogeny ; Utah ; }, abstract = {Phylogenetic examinations of communities sampled along geochemical gradients provide a framework for inferring the relative importance of niche-based ecological interactions (competition, environmental filtering) and neutral-based evolutionary interactions in structuring biodiversity. Great Salt Lake (GSL) in Utah exhibits strong spatial gradients due to both seasonal variation in freshwater input into the watershed and restricted fluid flow within North America's largest saline terminal lake ecosystem. Here, we examine the phylogenetic structure and composition of archaeal, bacterial, and eukaryal small subunit (SSU) rRNA genes sampled along a stratified water column (DWR3) in the south arm of GSL in order to infer the underlying mechanism of community assembly. Communities sampled from the DWR3 epilimnion were phylogenetically clustered (i.e., coexistence of close relatives due to environmental filtering) whereas those sampled from the DWR3 hypolimnion were phylogenetically overdispersed (i.e., coexistence of distant relatives due to competitive interactions), with minimal evidence for a role for neutral processes in structuring any assemblage. The shift from phylogenetically clustered to overdispersed assemblages was associated with an increase in salinity and a decrease in dissolved O2 (DO) concentration. Likewise, the phylogenetic diversity and phylogenetic similarity of assemblages was strongly associated with salinity or DO gradients. Thus, salinity and/or DO appeared to influence the mechanism of community assembly as well as the phylogenetic diversity and composition of communities. It is proposed that the observed patterns in the phylogenetic composition and structure of DWR3 assemblages are attributable to the meromictic nature of GSL, which prevents significant mixing between the epilimnion and the hypolimnion. This leads to strong physicochemical gradients at the halocline, which are capable of supporting a greater diversity. However, concomitant shifts in nutrient availability (e.g., DO) at and below the halocline drive competitive interactions leading to hypolimnion assemblages with minimal niche overlap.}, }
@article {pmid23354178, year = {2013}, author = {Russo, CD}, title = {The GRS/GRC from the perspective of a graduate student and first time attendee.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {922-923}, doi = {10.1007/s00248-013-0179-2}, pmid = {23354178}, issn = {1432-184X}, mesh = {Congresses as Topic ; Group Processes ; Humans ; Marine Biology/*education/organization &amp; administration ; Oceans and Seas ; Science/education/*organization &amp; administration ; Students/psychology ; }, abstract = {The networking and collaborative opportunities afforded to the attendees of the Ocean and Human Health Gordon Research Seminar (GRS) and the Gordon Research Conference (GRC) are vast and great. The GRS/GRC, in particular, has the capability of facilitating interlaboratory and interdisciplinary collaborations. The following article highlights the benefits associated with attending the GRS/GRC as a graduate student and first time attendee.}, }
@article {pmid23344252, year = {2013}, author = {Jeffery, IB and O'Toole, PW}, title = {Diet-microbiota interactions and their implications for healthy living.}, journal = {Nutrients}, volume = {5}, number = {1}, pages = {234-252}, pmid = {23344252}, issn = {2072-6643}, mesh = {Adult ; Aging/*physiology ; Animals ; Child ; Diabetes Mellitus/metabolism/microbiology ; *Diet ; Feces/microbiology ; Gastrointestinal Tract/metabolism/*microbiology ; Humans ; Inflammatory Bowel Diseases/metabolism/microbiology ; *Metagenome ; Mice ; Nutritional Requirements ; Obesity/metabolism/microbiology ; }, abstract = {It is well established that diet influences the health of an individual and that a diet rich in plant-based foods has many advantages in relation to the health and well-being of an individual. What has been unclear until recently is the large contribution of the gut microbiota to this effect. As well as providing basic nutritional requirements, the long-term diet of an animal modifies its gut microbiota. In adults, diets that have a high proportion of fruit and vegetables and a low consumption of meat are associated with a highly diverse microbiota and are defined by a greater abundance of Prevotella compared to Bacteroides, while the reverse is associated with a diet that contains a low proportion of plant-based foods. Furthermore, it is becoming increasingly clear that the effect of the microbial ecology of the gut goes beyond the local gut immune system and is implicated in immune-related disorders, such as IBS, diabetes and inflamm-ageing. In this review, we investigate the evidence that a balanced diet leads to a balanced, diverse microbiota with significant consequences for healthy ageing by focusing on conditions of interest.}, }
@article {pmid23340500, year = {2013}, author = {Konno, U and Kouduka, M and Komatsu, DD and Ishii, K and Fukuda, A and Tsunogai, U and Ito, K and Suzuki, Y}, title = {Novel microbial populations in deep granitic groundwater from Grimsel Test Site, Switzerland.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {626-637}, pmid = {23340500}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; Ecosystem ; Groundwater/analysis/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Switzerland ; }, abstract = {Freshwater aquifers in granitic rocks are widespread microbial habitats in the terrestrial subsurface. Microbial populations in deep granitic groundwater from two recently drilled (1 and 2 years) and two old boreholes (14 and 25 years) were compared. The 16S rRNA gene sequences related to "Candidatus Magnetobacterium bavaricum", Thermodesulfovibrio spp. of Nitrospirae (90.5-93.1 % similarity) and a novel candidate division with <90 % similarity to known cultivated species were dominant in all boreholes. Most of the environmental clones closely related to the novel lineages in Nitrospirae, which have been detected exclusively in deep groundwater samples. In contrast, betaproteobacterial sequences related to the family Rhodocyclaceae were obtained only from the recently drilled boreholes, which had higher total cell numbers. Catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) analysis supported the result from clone library analysis; betaproteobacterial cells were dominantly detected in recently drilled boreholes. These results suggest that while indigenous microbial populations represented by the novel phylotypes persisted in the boreholes for 25 years, betaproteobacterial species disappeared after 2 years owing to the change of substrate availability.}, }
@article {pmid23340423, year = {2013}, author = {De Roy, K and Marzorati, M and Negroni, A and Thas, O and Balloi, A and Fava, F and Verstraete, W and Daffonchio, D and Boon, N}, title = {Environmental conditions and community evenness determine the outcome of biological invasion.}, journal = {Nature communications}, volume = {4}, number = {}, pages = {1383}, pmid = {23340423}, issn = {2041-1723}, mesh = {Bacteria/drug effects ; Carbon/pharmacology ; *Ecosystem ; *Introduced Species ; Models, Biological ; Salinity ; Stress, Physiological/drug effects ; }, abstract = {Biological invasion is widely studied, however, conclusions on the outcome of this process mainly originate from observations in systems that leave a large number of experimental variables uncontrolled. Here using a fully controlled system consisting of assembled bacterial communities, we evaluate the degree of invasion and the effect on the community functionality in relation to the initial community evenness under specific environmental stressors. We show that evenness influences the level of invasion and that the introduced species can promote functionality under stress. The evenness-invasibility relationship is negative in the absence and neutral in the presence of stress. Under these conditions, the introduced species is able to maintain the functionality of uneven communities. These results indicate that communities, initially having the same genetic background, in the presence of the same invader, react in a different way with respect to invasibility and functionality depending on specific environmental conditions and community evenness.}, }
@article {pmid23336065, year = {2012}, author = {Erb-Downward, JR and Sadighi Akha, AA and Wang, J and Shen, N and He, B and Martinez, FJ and Gyetko, MR and Curtis, JL and Huffnagle, GB}, title = {Use of direct gradient analysis to uncover biological hypotheses in 16s survey data and beyond.}, journal = {Scientific reports}, volume = {2}, number = {}, pages = {774}, pmid = {23336065}, issn = {2045-2322}, support = {R01 HL082480/HL/NHLBI NIH HHS/United States ; U01 HL098961/HL/NHLBI NIH HHS/United States ; U19 AI090871/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; Cecum/microbiology ; Humans ; Lung/microbiology ; Metagenome ; Mice ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics/*metabolism ; }, abstract = {This study investigated the use of direct gradient analysis of bacterial 16S pyrosequencing surveys to identify relevant bacterial community signals in the midst of a "noisy" background, and to facilitate hypothesis-testing both within and beyond the realm of ecological surveys. The results, utilizing 3 different real world data sets, demonstrate the utility of adding direct gradient analysis to any analysis that draws conclusions from indirect methods such as Principal Component Analysis (PCA) and Principal Coordinates Analysis (PCoA). Direct gradient analysis produces testable models, and can identify significant patterns in the midst of noisy data. Additionally, we demonstrate that direct gradient analysis can be used with other kinds of multivariate data sets, such as flow cytometric data, to identify differentially expressed populations. The results of this study demonstrate the utility of direct gradient analysis in microbial ecology and in other areas of research where large multivariate data sets are involved.}, }
@article {pmid23335755, year = {2013}, author = {Dolinšek, J and Lagkouvardos, I and Wanek, W and Wagner, M and Daims, H}, title = {Interactions of nitrifying bacteria and heterotrophs: identification of a Micavibrio-like putative predator of Nitrospira spp.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {6}, pages = {2027-2037}, pmid = {23335755}, issn = {1098-5336}, mesh = {Bacteria/*metabolism ; Bicarbonates/metabolism ; Carbon Isotopes/metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Heterotrophic Processes ; In Situ Hybridization, Fluorescence ; Isotope Labeling ; *Microbial Interactions ; Microscopy, Confocal ; Molecular Sequence Data ; *Nitrification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; }, abstract = {Chemolithoautotrophic nitrifying bacteria release soluble organic compounds, which can be substrates for heterotrophic microorganisms. The identities of these heterotrophs and the specificities of their interactions with nitrifiers are largely unknown. In this study, we incubated nitrifying activated sludge with (13)C-labeled bicarbonate and used stable isotope probing of 16S rRNA to monitor the flow of carbon from uncultured nitrifiers to heterotrophs. To facilitate the identification of heterotrophs, the abundant 16S rRNA molecules from nitrifiers were depleted by catalytic oligonucleotides containing locked nucleic acids (LNAzymes), which specifically cut the 16S rRNA of defined target organisms. Among the (13)C-labeled heterotrophs were organisms remotely related to Micavibrio, a microbial predator of Gram-negative bacteria. Fluorescence in situ hybridization revealed a close spatial association of these organisms with microcolonies of nitrite-oxidizing sublineage I Nitrospira in sludge flocs. The high specificity of this interaction was confirmed by confocal microscopy and a novel image analysis method to quantify the localization patterns of biofilm microorganisms in three-dimensional (3-D) space. Other isotope-labeled bacteria, which were affiliated with Thermomonas, colocalized less frequently with nitrifiers and thus were commensals or saprophytes rather than specific symbionts or predators. These results suggest that Nitrospira spp. are subject to bacterial predation, which may influence the abundance and diversity of these nitrite oxidizers and the stability of nitrification in engineered and natural ecosystems. In silico screening of published next-generation sequencing data sets revealed a broad environmental distribution of the uncultured Micavibrio-like lineage.}, }
@article {pmid23325466, year = {2013}, author = {Sørensen, N and Daugbjerg, N and Richardson, K}, title = {Choice of pore size can introduce artefacts when filtering picoeukaryotes for molecular biodiversity studies.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {964-968}, pmid = {23325466}, issn = {1432-184X}, mesh = {Artifacts ; *Biodiversity ; Eukaryota/classification/genetics/*isolation &amp; purification ; Filtration/*instrumentation/standards ; Molecular Sequence Data ; Phylogeny ; Seawater/chemistry/*parasitology ; }, abstract = {Published results of studies based on samples size fractionated by sequential filtration (e.g. 0.2-3 μm) indicate that many ciliate, dinoflagellate and rhizarian phylotypes are found among marine picoeukaryotes. This is somewhat surprising as these protists are typically known as being large organisms (often >10 μm) and no picoplanktonic species have so far been identified. Here, the abundances of ciliate and dinoflagellate phylotypes in published molecular studies of picoeukaryotes are shown to correlate negatively with the pore size chosen for the end filter in the sequential filtrations (i.e. the filter used to collect the microbial biomass). This suggests that extracellular DNA adhering to small particles may be the source of ciliate and dinoflagellate phylotypes in picoplanktonic size fractions. This hypothesis was confirmed using real-time qPCR, which revealed significantly less dinoflagellate 18S rDNA in a 0.8-3-μm size fraction compared to 0.2-3 μm. On average, the abundance of putative extracellular phylotypes decreased by 84-89 % when a 0.8- μm end filter was used rather than a 0.2-μm end filter. A 0.8-μm filter is, however, not sufficient to retain all picoeukaryotic cells. Thus, selection of filter pore size involves a trade-off between avoiding artefacts generated by extracellular DNA and sampling the entire picoeukaryotic community. In contrast to ciliate and dinoflagellate phylotypes, rhizarian phylotypes in the picoplankton size range do not display a pattern consistent with an extracellular origin. This is likely due to the documented existence of picoplanktonic swarmer cells within this group.}, }
@article {pmid23325465, year = {2013}, author = {Depledge, MH and Harvey, AJ and Brownlee, C and Frost, M and Moore, MN and Fleming, LE}, title = {Changing views of the interconnections between the oceans and human health in Europe.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {852-859}, pmid = {23325465}, issn = {1432-184X}, mesh = {Animals ; *Ecosystem ; Health ; *Human Activities ; Humans ; Oceans and Seas ; Seawater/*chemistry ; }, abstract = {Early steps in the emergence of the discipline of "Oceans and Human Health" are charted in the USA and discussed in relation to past and present marine environment and human health research activities in Europe. Differences in terminology are considered, as well as differences in circumstances related to the various seas of Europe and the intensity of human coastal activity and impact. Opportunities to progress interdisciplinary research are described, and the value of horizon scanning for the early identification of emerging issues is highlighted. The challenges facing researchers and policymakers addressing oceans and human health issues are outlined and some suggestions offered regarding how further progress in research and training into both the risks and benefits of Oceans and Human Health might be made on both sides of the Atlantic.}, }
@article {pmid23318746, year = {2012}, author = {Twetman, S}, title = {Are we ready for caries prevention through bacteriotherapy?.}, journal = {Brazilian oral research}, volume = {26 Suppl 1}, number = {}, pages = {64-70}, doi = {10.1590/s1806-83242012000700010}, pmid = {23318746}, issn = {1807-3107}, mesh = {Antibiosis/physiology ; Bacteria/immunology ; Biofilms ; Dental Caries/*prevention &amp; control ; Humans ; Mouth/microbiology ; Probiotics/*therapeutic use ; }, abstract = {Recent insights in medical science indicate that human biofilms play an important role in health and well-being, and have put microbiota modulation through bacteriotherapy into focus. In dentistry, bacterial interference with probiotic bacteria to support the stability and diversity of oral biofilms has gained similar interest. Investigations in vitro into metabolic activity, co-aggregation, growth inhibition, bacteriocin production, and adhesion have collectively suggested a potential role for probiotic lactobacilli and bifidobacteria to modulate the oral microbial ecology. Likewise, short-term clinical studies with intermediate microbial endpoints indicate that interference with caries-associated bacteria seems possible through probiotic dairy products, tablets, lozenges and chewing gum in various dose regimens. Few randomized controlled clinical trials with caries outcomes are available, but three studies with preschool children and the elderly have demonstrated preventive fractions between 21% and 75%, following regular intake of milk supplemented with probiotic lactobacilli. However, further large-scale trials with orally derived anti-caries candidates are needed before we can say that we are ready for bacteriotherapy as an adjunct to complement the existing evidence-based methods for preventing and controlling caries in daily practice.}, }
@article {pmid23321084, year = {2012}, author = {Clark, EL and Daniell, TJ and Wishart, J and Hubbard, SF and Karley, AJ}, title = {How conserved are the bacterial communities associated with aphids? A detailed assessment of the Brevicoryne brassicae (Hemiptera: Aphididae) using 16S rDNA.}, journal = {Environmental entomology}, volume = {41}, number = {6}, pages = {1386-1397}, doi = {10.1603/EN12152}, pmid = {23321084}, issn = {1938-2936}, mesh = {Animals ; Aphids/*microbiology ; Biodiversity ; DNA, Bacterial/chemistry ; DNA, Ribosomal/chemistry ; Enterobacteriaceae/*classification/genetics/isolation &amp; purification ; Likelihood Functions ; Phylogeny ; Pseudomonas/*classification/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; }, abstract = {Aphids harbor a community of bacteria that include obligate and facultative endosymbionts belonging to the Enterobacteriaceae along with opportunistic, commensal, or pathogenic bacteria. This study represents the first detailed analysis of the identity and diversity of the bacterial community associated with the cabbage aphid, Brevicoryne brassicae (L.). 16S rDNA sequence analysis revealed that the community of bacteria associated with B. brassicae was diverse, with at least four different bacterial community types detected among aphid lines, collected from widely dispersed sites in Northern Britain. The bacterial sequence types isolated from B. brassicae showed little similarity to any bacterial endosymbionts characterized in insects; instead, they were closely related to free-living extracellular bacterial species that have been isolated from the aphid gut or that are known to be present in the environment, suggesting that they are opportunistic bacteria transmitted between the aphid gut and the environment. To quantify variation in bacterial community between aphid lines, which was driven largely by differences in the proportions of two dominant bacterial orders, the Pseudomonales and the Enterobacteriales, we developed a novel real-time (Taqman) qPCR assay. By improving our knowledge of aphid microbial ecology, and providing novel molecular tools to examine the presence and function of the microbial community, this study forms the basis of further research to explore the influence of the extracellular bacterial community on aphid fitness, pest status, and susceptibility to control by natural enemies.}, }
@article {pmid23314124, year = {2013}, author = {Garcia, GD and Gregoracci, GB and Santos, Ede O and Meirelles, PM and Silva, GG and Edwards, R and Sawabe, T and Gotoh, K and Nakamura, S and Iida, T and de Moura, RL and Thompson, FL}, title = {Metagenomic analysis of healthy and white plague-affected Mussismilia braziliensis corals.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {1076-1086}, pmid = {23314124}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology/*parasitology ; Bacteria/classification/genetics/*isolation &amp; purification ; Brazil ; Eukaryota/classification/genetics/*isolation &amp; purification ; *Metagenomics ; }, abstract = {Coral health is under threat throughout the world due to regional and global stressors. White plague disease (WP) is one of the most important threats affecting the major reef builder of the Abrolhos Bank in Brazil, the endemic coral Mussismilia braziliensis. We performed a metagenomic analysis of healthy and WP-affected M. braziliensis in order to determine the types of microbes associated with this coral species. We also optimized a protocol for DNA extraction from coral tissues. Our taxonomic analysis revealed Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, and Actinomycetes as the main groups in all healthy and WP-affected corals. Vibrionales, members of the Cytophaga-Flavobacterium-Bacteroides complex, Rickettsiales, and Neisseriales were more abundant in the WP-affected corals. Diseased corals also had more eukaryotic metagenomic sequences identified as Alveolata and Apicomplexa. Our results suggest that WP disease in M. braziliensis is caused by a polymicrobial consortium.}, }
@article {pmid23314097, year = {2013}, author = {Kostanjšek, R and Pašić, L and Daims, H and Sket, B}, title = {Structure and community composition of sprout-like bacterial aggregates in a Dinaric Karst subterranean stream.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {5-18}, pmid = {23314097}, issn = {1432-184X}, mesh = {Bacteria/*chemistry/classification/genetics/*isolation &amp; purification ; Biodiversity ; Caves/*microbiology ; DNA, Bacterial/genetics ; Ecosystem ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; }, abstract = {The Vjetrenica cave in the Dinaric Karst hosts a worldwide extraordinarily high cave biodiversity. Beside a diverse and specialized cave fauna, sprout-like formations attached to the bed of the cave stream were observed and described, but not further characterized, almost a century ago. Here we investigated these sprout-like microbial aggregates by the rRNA approach and detailed microscopy. Based on fluorescence in situ hybridization and ultrastructural analysis, the sprout-like formations are morphologically highly organized, and their core consists of a member of a novel deep-branching lineage in the bacterial phylum Nitrospirae. This organism displays an interesting cellular ultrastructure with different kinds of cytoplasmic inclusions and is embedded in a thick extracellular matrix, which contributes to the stability and shape of the aggregates. This novel bacterium has been provisionally classified as "Candidatus Troglogloea absoloni." The surface of the sprout-like aggregates is more diverse than the core. It is colonized by a bacterial biofilm consisting primarily of filamentous Betaproteobacteria, whereas other microbial populations present in the crust include members of the Bacteriodetes, Gammaproteobacteria, Actinombacteria, Alphaproteobacteria, and Planctomycetes, which are intermingled with mineral inclusions. This study represents the first thorough molecular and ultrastructural characterization of the elusive sprout-like bacterial aggregates, which are also found in other cave systems of the Dinaric Karst. The discovery of Ca. Troglogloea absoloni contributes to the known biodiversity of subterranean ecosystems and especially of macroscopic structures formed in caves by microorganisms, whose composition and ecological function often remain enigmatic.}, }
@article {pmid23314096, year = {2013}, author = {Paerl, HW and Otten, TG}, title = {Harmful cyanobacterial blooms: causes, consequences, and controls.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {995-1010}, pmid = {23314096}, issn = {1432-184X}, mesh = {Biomass ; Climate Change ; Cyanobacteria/classification/*growth &amp; development ; *Ecosystem ; Environmental Monitoring ; Eutrophication ; Water Microbiology ; Water Pollution/*prevention &amp; control ; }, abstract = {Cyanobacteria are the Earth's oldest oxygenic photoautotrophs and have had major impacts on shaping its biosphere. Their long evolutionary history (≈ 3.5 by) has enabled them to adapt to geochemical and climatic changes, and more recently anthropogenic modifications of aquatic environments, including nutrient over-enrichment (eutrophication), water diversions, withdrawals, and salinization. Many cyanobacterial genera exhibit optimal growth rates and bloom potentials at relatively high water temperatures; hence global warming plays a key role in their expansion and persistence. Bloom-forming cyanobacterial taxa can be harmful from environmental, organismal, and human health perspectives by outcompeting beneficial phytoplankton, depleting oxygen upon bloom senescence, and producing a variety of toxic secondary metabolites (e.g., cyanotoxins). How environmental factors impact cyanotoxin production is the subject of ongoing research, but nutrient (N, P and trace metals) supply rates, light, temperature, oxidative stressors, interactions with other biota (bacteria, viruses and animal grazers), and most likely, the combined effects of these factors are all involved. Accordingly, strategies aimed at controlling and mitigating harmful blooms have focused on manipulating these dynamic factors. The applicability and feasibility of various controls and management approaches is discussed for natural waters and drinking water supplies. Strategies based on physical, chemical, and biological manipulations of specific factors show promise; however, a key underlying approach that should be considered in almost all instances is nutrient (both N and P) input reductions; which have been shown to effectively reduce cyanobacterial biomass, and therefore limit health risks and frequencies of hypoxic events.}, }
@article {pmid23314095, year = {2013}, author = {Vishnivetskaya, TA and Fisher, LS and Brodie, GA and Phelps, TJ}, title = {Microbial communities involved in biological ammonium removal from coal combustion wastewaters.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {49-59}, pmid = {23314095}, issn = {1432-184X}, mesh = {Ammonium Compounds/*metabolism ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Coal/analysis ; Molecular Sequence Data ; Nitrification ; Oxidation-Reduction ; Phylogeny ; Wastewater/analysis/*microbiology ; }, abstract = {The efficiency of a novel integrated treatment system for biological removal of ammonium, nitrite, nitrate, and heavy metals from fossil power plant effluent was evaluated. Microbial communities were analyzed using bacterial and archaeal 16S rRNA gene clone libraries (Sanger sequences) and 454 pyrosequencing technology. While seasonal changes in microbial community composition were observed, the significant (P = 0.001) changes in bacterial and archaeal communities were consistent with variations in ammonium concentration. Phylogenetic analysis of 16S rRNA gene sequences revealed an increase of potential ammonium-oxidizing bacteria (AOB), Nitrosomonas, Nitrosococcus, Planctomycetes, and OD1, in samples with elevated ammonium concentration. Other bacteria, such as Nitrospira, Nitrococcus, Nitrobacter, Thiobacillus, ε-Proteobacteria, Firmicutes, and Acidobacteria, which play roles in nitrification and denitrification, were also detected. The AOB oxidized 56 % of the ammonium with the concomitant increase in nitrite and ultimately nitrate in the trickling filters at the beginning of the treatment system. Thermoprotei within the phylum Crenarchaeota thrived in the splitter box and especially in zero-valent iron extraction trenches, where an additional 25 % of the ammonium was removed. The potential ammonium-oxidizing Archaea (AOA) (Candidatus Nitrosocaldus) were detected towards the downstream end of the treatment system. The design of an integrated treatment system consisting of trickling filters, zero-valent iron reaction cells, settling pond, and anaerobic wetlands was efficient for the biological removal of ammonium and several other contaminants from wastewater generated at a coal burning power plant equipped with selective catalytic reducers for nitrogen oxide removal.}, }
@article {pmid23314094, year = {2013}, author = {Damare, VS and Damare, S and Ramanujam, P and Meena, RM and Raghukumar, S}, title = {Preliminary studies on the association between zooplankton and the stramenopilan fungi, aplanochytrids.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {955-963}, pmid = {23314094}, issn = {1432-184X}, mesh = {Animals ; Eukaryota/classification/genetics/isolation &amp; purification/*physiology ; Fungi/classification/genetics/*isolation &amp; purification/physiology ; Molecular Sequence Data ; Phylogeny ; Predatory Behavior ; Zooplankton/classification/genetics/*microbiology/physiology ; }, abstract = {The relationship of the marine heterokont stramenopilan protists, the aplanochytrids, with the zooplankton was studied in coastal waters. The aplanochytrids were fed to the zooplankton specimens and observed for grazing by two different approaches: [1] using fluorescently-labeled prey approach and [2] using internal transcribed spacer-based molecular probe and in situ hybridization approach. The aplanochytrid cells were detected in the guts as well as fecal pellets of the zooplankton, thus serving as prey to them. Aplanochytrids were consistently isolated from zooplankton specimens. The isolates did not produce a wide array of enzymes, implicating that they may not play a major role in degradation of zooplankton exoskeleton. They were found to produce only protease considerably and sometimes lipase too. The amplified rDNA restriction analysis showed similar patterns, suggesting that most of the isolates might be same strains of Aplanochytrium spp. The existence of aplanochytrids with the zooplankton in marine waters points towards their probable association either as predator-prey or as commensalistic rather than saprophytic type of association.}, }
@article {pmid23313091, year = {2013}, author = {Neilson, JW and Jordan, FL and Maier, RM}, title = {Analysis of artifacts suggests DGGE should not be used for quantitative diversity analysis.}, journal = {Journal of microbiological methods}, volume = {92}, number = {3}, pages = {256-263}, pmid = {23313091}, issn = {1872-8359}, support = {P42 ES004940/ES/NIEHS NIH HHS/United States ; 2 P42ES04940/ES/NIEHS NIH HHS/United States ; }, mesh = {*Artifacts ; Bacteria/*classification/*genetics ; *Biodiversity ; Denaturing Gradient Gel Electrophoresis/*methods ; Reproducibility of Results ; }, abstract = {PCR-denaturing gradient gel electrophoresis (PCR-DGGE) is widely used in microbial ecology for the analysis of comparative community structure. However, artifacts generated during PCR-DGGE of mixed template communities impede the application of this technique to quantitative analysis of community diversity. The objective of the current study was to employ an artificial bacterial community to document and analyze artifacts associated with multiband signatures and preferential template amplification and to highlight their impacts on the use of this technique for quantitative diversity analysis. Six bacterial species (three Betaproteobacteria, two Alphaproteobacteria, and one Firmicutes) were amplified individually and in combinations with primers targeting the V7/V8 region of the 16S rRNA gene. Two of the six isolates produced multiband profiles demonstrating that band number does not correlate directly with α-diversity. Analysis of the multiple bands from one of these isolates confirmed that both bands had identical sequences which lead to the hypothesis that the multiband pattern resulted from two distinct structural conformations of the same amplicon. In addition, consistent preferential amplification was demonstrated following pairwise amplifications of the six isolates. DGGE and real time PCR analysis identified primer mismatch and PCR inhibition due to 16S rDNA secondary structure as the most probable causes of preferential amplification patterns. Reproducible DGGE community profiles generated in this study confirm that PCR-DGGE provides an excellent high-throughput tool for comparative community structure analysis, but that method-specific artifacts preclude its use for accurate comparative diversity analysis.}, }
@article {pmid23306394, year = {2013}, author = {Johnson, CN}, title = {Fitness factors in vibrios: a mini-review.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {826-851}, pmid = {23306394}, issn = {1432-184X}, mesh = {Animals ; Bacterial Proteins/genetics/*metabolism ; Humans ; Rabbits ; Vibrio/genetics/*metabolism/pathogenicity ; Vibrio Infections/*microbiology/*veterinary ; Virulence Factors/genetics/*metabolism ; }, abstract = {Vibrios are Gram-negative curved bacilli that occur naturally in marine, estuarine, and freshwater systems. Some species include human and animal pathogens, and some vibrios are necessary for natural systems, including the carbon cycle and osmoregulation. Countless in vivo and in vitro studies have examined the interactions between vibrios and their environment, including molecules, cells, whole animals, and abiotic substrates. Many studies have characterized virulence factors, attachment factors, regulatory factors, and antimicrobial resistance factors, and most of these factors impact the organism's fitness regardless of its external environment. This review aims to identify common attributes among factors that increase fitness in various environments, regardless of whether the environment is an oyster, a rabbit, a flask of immortalized mammalian cells, or a planktonic chitin particle. This review aims to summarize findings published thus far to encapsulate some of the basic similarities among the many vibrio fitness factors and how they frame our understanding of vibrio ecology. Factors representing these similarities include hemolysins, capsular polysaccharides, flagella, proteases, attachment factors, type III secretion systems, chitin binding proteins, iron acquisition systems, and colonization factors.}, }
@article {pmid23306393, year = {2013}, author = {Zheng, C and Wang, G and Liu, J and Song, C and Gao, H and Liu, X}, title = {Characterization of the major capsid genes (g23) of T4-type bacteriophages in the wetlands of northeast China.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {616-625}, pmid = {23306393}, issn = {1432-184X}, mesh = {Bacteriophage T4/classification/*genetics/*isolation &amp; purification ; Capsid Proteins/*genetics ; China ; Fresh Water/*microbiology ; Molecular Sequence Data ; Phylogeny ; *Soil Microbiology ; Wetlands ; }, abstract = {To obtain genetic information and to evaluate the composition of T4-type bacteriophage (phage) communities in wetlands, environmental soil and water DNAs were obtained from two natural wetlands dominated by Carex lasiocarpa and Deyeuxia angustifolia plant species, and a neighboring paddy field in Sanjiang plain of northeast China. The biomarker gene of g23, which encodes the major capsid protein of T4-type phages, was amplified with primers MZIA1bis and MZIA6, and the PCR products were cloned and sequenced. In total, 96 and 50 different g23 clones were obtained from natural wetlands and a paddy field, respectively. A larger number of clones with low levels of identity to known sequences were found in water than in soil both in the natural wetlands and the paddy field, suggesting that many of T4-type phages in wetland water and paddy floodwater in Sanjiang plain are uncharacterized. Phylogenetic analyses showed that the g23 clones in natural wetlands, irrespective of water and soil, were distinctly different from those in marine waters, lake waters, and upland black soils, but were similar to those in paddy fields. The UniFrac analysis of g23 assemblages indicated that T4-type phage community compositions were different between soils and waters, and also were different between the natural wetlands and the paddy field. In general, the global analysis of g23 clone assemblages demonstrated that T4-type phage community compositions were different among natural wetlands, marines, lakes, paddy fields, and upland black soils.}, }
@article {pmid23306392, year = {2013}, author = {Zeleke, J and Lu, SL and Wang, JG and Huang, JX and Li, B and Ogram, AV and Quan, ZX}, title = {Methyl coenzyme M reductase A (mcrA) gene-based investigation of methanogens in the mudflat sediments of Yangtze River estuary, China.}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {257-267}, pmid = {23306392}, issn = {1432-184X}, mesh = {Bacteria/classification/*enzymology/genetics/*isolation &amp; purification ; Bacterial Proteins/*genetics/metabolism ; China ; Ecosystem ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; Rivers/*microbiology ; }, abstract = {Methanogen populations of an intertidal mudflat in the Yangtze River estuary of China were investigated based on the methyl coenzyme M reductase A (mcrA) gene using 454-pyrosequencing and quantitative real-time polymerase chain reaction (qPCR). Samples were collected at six depths from three locations. In the qPCR analyses, a mean depth-wise change of mcrA gene abundance was observed from (1.23 ± 0.13) × 10(7) to (1.16 ± 0.29) × 10(8) per g dried soil, which was inversely correlated with the depletion of sulfate (R(2) = 0.74; α = 0.05) and salinity (R (2) = 0.66; α = 0.05). The copy numbers of mcrA was at least 1 order of magnitude higher than dissimilatory sulfate reductase B (dsrB) genes, likely indicating the importance of methanogenesis at the mudflat. Sequences related to the orders Methanomicrobiales, Methanosarcinales, Methanobacteriales, Methanococcales and the uncultured methanogens; Rice Cluster I (RC-I), Zoige cluster I (ZC-I) and anaerobic methane oxidizing archaeal lineage-1 (ANME-1) were detected. Methanomicrobiales and Methanosarcinales dominated the entire sediment layers, but detectable changes of proportions were observed with depth. The hydrogenotrophic methanogens Methanomicrobiales slightly increased with depth while Methanosarcinales showed the reverse. Chao1 and ACE richness estimators revealed higher diversity of methanogens near the surface (0-10 cm) when compared with the bottom sediments. The near-surface sediments were mainly dominated by the family Methanosarcinaceae (45 %), which has members that can utilize substrates that cannot be used by sulfate-reducing bacteria. Overall, current data indicate that Methanosarcinales and Methanomicrobiales are the most dominant methanogens within the entire depth profile down to 100 cm, with higher abundance and diversity of methanogens in the deeper and upper sediment layers, respectively.}, }
@article {pmid23306376, year = {2013}, author = {Brzychczy-Wloch, M and Wojkowska-Mach, J and Helwich, E and Heczko, PB}, title = {Incidence of maternal GBS colonization and neonatal GBS disease among very low birth weight Polish neonates.}, journal = {Medical science monitor : international medical journal of experimental and clinical research}, volume = {19}, number = {}, pages = {34-39}, pmid = {23306376}, issn = {1643-3750}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Antibiotic Prophylaxis ; Colony Count, Microbial ; Female ; Genitalia, Female/microbiology ; Humans ; Incidence ; Infant, Newborn ; Infant, Newborn, Diseases/drug therapy/*epidemiology/microbiology ; *Infant, Very Low Birth Weight ; Male ; Poland/epidemiology ; Pregnancy ; Pregnancy Complications, Infectious/drug therapy/*epidemiology/microbiology ; Streptococcal Infections/drug therapy/*epidemiology/microbiology ; Streptococcus agalactiae/drug effects/*growth &amp; development ; }, abstract = {BACKGROUND: In 2008, the Polish Gynecological Society issued recommendations to screen pregnant women for GBS colonization and offer antibiotic prophylaxis at delivery. The goal of this study was to assess compliance with these recommendations among women delivering very low birth weight infants (VLBW) in Poland.<br><br>MATERIAL/METHODS: The 6 Polish Perinatological Institutions managing infections in the framework of the Polish Perinatological Network were subjected to the analysis. A retrospective case-cohort study for 2009 was conducted using the standard protocols and definitions. The collected data pertained to 812 pregnant women who gave birth to 910 babies with VLBW.<br><br>RESULTS: The statistical variation across the 6 studied centers associated with GBS prevention of infections was noted. Bacteriological examinations of samples taken from the vagina were performed only in 273 (34%) of the women, ranging between 2% and 93%, depending on the center. GBS carriage was proven in 19% of these women, ranging between 8% and 27%. The culture method was inadequate because of highly variable results. It was found that the rate of GBS determination is statistically connected with the number of women's screenings performed in the study centers. The intrapartum antibiotic prophylaxis (IAP) was used only in the half of GBS-positive women (47%). Six cases of early-onset GBS infections (5 blood stream infections and 1 pneumonia) were registered in the studied newborns, of which 4 neonates were born to women who received IAP against GBS. The incidence rate of GBS infection in VLBW neonates was 6.6 per 1000 live births, with a high death rate (up to 33%).<br><br>CONCLUSIONS: Poor compliance with GBS screening and antibiotic prevention were observed among women delivering very low birth weight infants. GBS infection was noted in a significant proportion of VLBW neonates; we believe a uniform policy should be put in place to manage these high-risk women and babies.}, }
@article {pmid23306123, year = {2013}, author = {Zamalloa, C and Boon, N and Verstraete, W}, title = {Decentralized two-stage sewage treatment by chemical-biological flocculation combined with microalgae biofilm for nutrient immobilization in a roof installed parallel plate reactor.}, journal = {Bioresource technology}, volume = {130}, number = {}, pages = {152-160}, doi = {10.1016/j.biortech.2012.11.128}, pmid = {23306123}, issn = {1873-2976}, mesh = {Adsorption ; Biofilms ; *Bioreactors ; Flocculation ; Microalgae/*metabolism ; Microscopy, Electron, Scanning ; Photosynthesis ; Sewage ; Temperature ; Wastewater/analysis ; Water Purification/economics/*instrumentation/methods ; }, abstract = {In this lab-scale study, domestic wastewater is subjected to a chemical biological adsorption (A-stage), followed by treatment in an innovative roof installed parallel plate microalgae biofilm reactor for nutrient immobilization (I-stage). The A-stage process was operated at a hydraulic retention time (HRT) of 1h and a solid retention time of 1day (FeSO(4) as flocculant). The I-stage, which consequently received the effluent of the A-stage process, was operated at an HRT of 1day and exposed to natural light. The overall system removed on average 74% of the total chemical oxygen demand, 82% of the total suspended solids, 67% of the total nitrogen and 96% of the total phosphorous in the wastewater. The design involves a relatively low capital and operating cost which is in the order of 0.5€/m(3) wastewater treated. These aspects suggest that the A/I process can be used as a decentralized domestic wastewater treatment system.}, }
@article {pmid23302421, year = {2013}, author = {De Vrieze, J and Verstraete, W and Boon, N}, title = {Repeated pulse feeding induces functional stability in anaerobic digestion.}, journal = {Microbial biotechnology}, volume = {6}, number = {4}, pages = {414-424}, pmid = {23302421}, issn = {1751-7915}, mesh = {Bacteria, Anaerobic/growth &amp; development/*metabolism ; Biofuels/*microbiology ; Bioreactors/*microbiology ; Biota ; *Environmental Microbiology ; Organic Chemicals/metabolism ; }, abstract = {Anaerobic digestion is an environmental key technology in the future bio-based economy. To achieve functional stability, a minimal microbial community diversity is required. This microbial community should also have a certain 'elasticity', i.e. the ability to rapidly adapt to suboptimal conditions or stress. In this study it was evaluated whether a higher degree of functional stability could be achieved by changing the feeding pattern, which can change the evenness, dynamics and richness of the bacterial community. The first reactor (CSTR stable) was fed on daily basis, whereas the second reactor (CSTR dynamic) was fed every 2 days. Average biogas production was 0.30 l CH4 l(-1) day(-1) in both reactors, although daily variation was up to four times higher in the CSTR dynamic compared with the CSTR stable during the first 50 days. Bacterial analysis revealed that this CSTR dynamic had a two times higher degree of bacterial community dynamics. The CSTR dynamic also appeared to be more tolerant to an organic shock load of 8 g COD l(-1) and ammonium levels up to 8000 mg TAN l(-1). These results suggest that the regular application of a limited pulse of organic material and/or a variation in the substrate composition might promote higher functional stability in anaerobic digestion.}, }
@article {pmid23300853, year = {2012}, author = {Hardoim, CC and Esteves, AI and Pires, FR and Gonçalves, JM and Cox, CJ and Xavier, JR and Costa, R}, title = {Phylogenetically and spatially close marine sponges harbour divergent bacterial communities.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e53029}, pmid = {23300853}, issn = {1932-6203}, mesh = {Animal Distribution ; Animals ; Bacteria/*classification/genetics ; Biodiversity ; Molecular Sequence Data ; Phylogeny ; Porifera/*microbiology ; Seawater/*microbiology ; }, abstract = {Recent studies have unravelled the diversity of sponge-associated bacteria that may play essential roles in sponge health and metabolism. Nevertheless, our understanding of this microbiota remains limited to a few host species found in restricted geographical localities, and the extent to which the sponge host determines the composition of its own microbiome remains a matter of debate. We address bacterial abundance and diversity of two temperate marine sponges belonging to the Irciniidae family--Sarcotragus spinosulus and Ircinia variabilis--in the Northeast Atlantic. Epifluorescence microscopy revealed that S. spinosulus hosted significantly more prokaryotic cells than I. variabilis and that prokaryotic abundance in both species was about 4 orders of magnitude higher than in seawater. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) profiles of S. spinosulus and I. variabilis differed markedly from each other--with higher number of ribotypes observed in S. spinosulus--and from those of seawater. Four PCR-DGGE bands, two specific to S. spinosulus, one specific to I. variabilis, and one present in both sponge species, affiliated with an uncultured sponge-specific phylogenetic cluster in the order Acidimicrobiales (Actinobacteria). Two PCR-DGGE bands present exclusively in S. spinosulus fingerprints affiliated with one sponge-specific phylogenetic cluster in the phylum Chloroflexi and with sponge-derived sequences in the order Chromatiales (Gammaproteobacteria), respectively. One Alphaproteobacteria band specific to S. spinosulus was placed in an uncultured sponge-specific phylogenetic cluster with a close relationship to the genus Rhodovulum. Our results confirm the hypothesized host-specific composition of bacterial communities between phylogenetically and spatially close sponge species in the Irciniidae family, with S. spinosulus displaying higher bacterial community diversity and distinctiveness than I. variabilis. These findings suggest a pivotal host-driven effect on the shape of the marine sponge microbiome, bearing implications to our current understanding of the distribution of microbial genetic resources in the marine realm.}, }
@article {pmid23299348, year = {2013}, author = {Li, H and Colica, G and Wu, PP and Li, D and Rossi, F and De Philippis, R and Liu, Y}, title = {Shifting species interaction in soil microbial community and its influence on ecosystem functions modulating.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {700-708}, pmid = {23299348}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; *Biodiversity ; *Ecosystem ; Molecular Sequence Data ; Phylogeny ; *Soil Microbiology ; }, abstract = {The supportive and negative evidence for the stress gradient hypothesis (SGH) led to an ongoing debate among ecologists and called for new empirical and theoretical work. In this study, we took various biological soil crust (BSCs) samples along a spatial gradient with four environmental stress levels to examine the fitness of SGH in microbial interactions and evaluate its influence on biodiversity-function relationships in BSCs. A new assessment method of species interactions within hard-cultured invisible soil community was employed, directly based on denaturing gradient gel electrophoresis fingerprint images. The results showed that biotic interactions in soil phototroph community dramatically shifted from facilitation to dominant competition with the improvement of microhabitats. It offered new evidence, which presented a different perspective on the hypothesis that the relative importance of facilitation and competition varies inversely along the gradient of abiotic stress. The path analysis indicated that influence of biotic interactions (r = 0.19, p < 0.05) on ecosystem functions is lower than other community properties (r = 0.62, p < 0.001), including soil moisture, crust coverage, and biodiversity. Furthermore, the correlation between species interactions and community properties was non-significant with low negative influence (r = -0.27, p > 0.05). We demonstrate that the inversion of biotic interaction as a response to the gradient of abiotic stresses existed not only in the visible plant community but also in the soil microbial community.}, }
@article {pmid23299347, year = {2013}, author = {Li, K and Liu, R and Zhang, H and Yun, J}, title = {The diversity and abundance of bacteria and oxygenic phototrophs in saline biological desert crusts in Xinjiang, northwest China.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {40-48}, pmid = {23299347}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Biodiversity ; China ; Desert Climate ; Ecosystem ; Geologic Sediments/analysis/microbiology ; Molecular Sequence Data ; Oxygen/*metabolism ; Phylogeny ; Sodium Chloride/*metabolism ; *Soil Microbiology ; }, abstract = {Although microorganisms, particularly oxygenic phototrophs, are known as the major players in the biogeochemical cycles of elements in desert soil ecosystems and have received extensive attention, still little is known about the effects of salinity on the composition and abundances of microbial community in desert soils. In this study, the diversity and abundance of bacteria and oxygenic phototrophs in biological desert crusts from Xinjiang province, which were under different salinity conditions, were investigated by using clone library and quantitative PCR (qPCR). The 16S rRNA gene phylogenetic analysis showed that cyanobacteria, mainly Microcoleus vagnitus of the order Oscillatoriales, were predominant in the low saline crusts, while other phototrophs, such as diatom, were the main microorganism group responsible for the oxygenic photosynthesis in the high saline crusts. Furthermore, the higher salt content in crusts may stimulate the growth of other bacteria, including Deinococcus-Thermus, Bacteroidetes, and some subdivisions of Proteobacteria (β-, γ-, and δ-Proteobacteria). The cpcBA-IGS gene analysis revealed the existence of novel M. vagnitus strains in this area. The qPCR results showed that the abundance of oxygenic phototrophs was significantly higher under lower saline condition than that in the higher saline crusts, suggesting that the higher salinity in desert crusts could suppress the numbers of total bacteria and phototrophic bacteria but did highly improve the diversity of salt-tolerant bacteria.}, }
@article {pmid23299346, year = {2013}, author = {Zhang, W and Long, X and Huo, X and Chen, Y and Lou, K}, title = {16S rRNA-based PCR-DGGE analysis of actinomycete communities in fields with continuous cotton cropping in Xinjiang, China.}, journal = {Microbial ecology}, volume = {66}, number = {2}, pages = {385-393}, pmid = {23299346}, issn = {1432-184X}, mesh = {Actinobacteria/classification/genetics/*isolation &amp; purification ; Bacterial Typing Techniques ; China ; DNA, Bacterial/*genetics ; Ecosystem ; Electrophoresis, Polyacrylamide Gel ; Gossypium/growth &amp; development/*microbiology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; *Soil Microbiology ; }, abstract = {The purpose of this study was to examine the variations in the microbial community structure of soil actinomycetes in fields with continuous cropping of cotton in Xinjiang Autonomous Region, China. Soil samples were collected from four depths in fields with 7-year continuous cotton cropping. The community structure of soil actinomycetes was examined using the 16S rRNA-based polymerase chain reaction-density gradient gel electrophoresis (PCR-DGGE) techniques. The microbial diversity indices of the soil samples from different depths generally decreased along with the period of continuous cotton cropping. When the period of continuous cropping of cotton reached 5 years, the diversity indices rose again and gradually stabilized at a level slightly lower than that of soils with original ecology (i.e., 0-year cotton cropping). Cluster analysis showed that at the 1-20-cm depth, the actinomycete community structure of the soil subjected to 1-year cotton cropping was similar to that of soil subjected to 0-year cotton cropping, whereas that of soils after 3-year continuous cotton cropping showed high similarity. At the 21-40-cm depth, the actinomycete community structure showed various changes but generally recovered to its original pattern after repeated fluctuations. Principal component analysis showed that at the 1-30-cm depth, the actinomycete community structure varied similarly regardless of the period of continuous cotton cropping. In contrast, there were no clear actinomycete community structure variation trends at the 31-40-cm soil depth. Homology comparison of sequences recovered from the DGGE bands showed that the obtained sequences shared similarities >88 %. Alignment with the known homologous sequences indicated a lack of microorganisms related to soil-borne cotton diseases. Continuous cotton cropping exerted significant influences on the community structure of soil actinomycetes in Xinjiang Autonomous Region, which were largely determined by the soil depth and the period of continuous cotton cropping. The microbial diversity of soil actinomycete communities gradually recovered after 5-year continuous cropping. Thereafter, a new actinomycete community structure that was beneficial for continuous cropping of cotton was formed and stabilized each year.}, }
@article {pmid23296446, year = {2013}, author = {Boscaro, V and Petroni, G and Ristori, A and Verni, F and Vannini, C}, title = {"Candidatus Defluviella procrastinata" and "Candidatus Cyrtobacter zanobii", two novel ciliate endosymbionts belonging to the "Midichloria clade".}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {302-310}, pmid = {23296446}, issn = {1432-184X}, mesh = {Alphaproteobacteria/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Euplotes/*microbiology ; In Situ Hybridization, Fluorescence ; Paramecium/*microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {The "Midichloria clade" is a recently discovered but well-established evolutionary lineage clustering inside the order Rickettsiales (Alphaproteobacteria). Not much is known about the biology of these organisms. The best characterized ones are endocellular symbionts of very different eukaryotic hosts, ranging from arthropods to protists. "Candidatus Midichloria mitochondrii", the most studied organism of the group, is an interesting object of study because of its unique capability to infect metazoans' mitochondria and the presence of flagellar genes in its genome. With this work, we aim at increasing the knowledge on the biodiversity and phylogeny of the "Midichloria group". We characterized according to the "full cycle rRNA approach" two novel endosymbionts of ciliated protozoa, i.e. Paramecium nephridiatum and Euplotes aediculatus. According to the nomenclatural rules for uncultivated prokaryotes, we established the novel taxa "Candidatus Defluviella procrastinata" and "Candidatus Cyrtobacter zanobii" for the two bacterial symbionts. Our phylogenetic analysis based on 16S rRNA gene sequences confirms that the evolutionary histories of "Midichloria clade" representatives and of their hosts are very different. This suggests that the symbiotic processes arose many times independently, perhaps through ways of transmission still not described in Rickettsiales.}, }
@article {pmid23291898, year = {2013}, author = {Lee, HR and Han, SI and Rhee, KH and Whang, KS}, title = {Mucilaginibacter herbaticus sp. nov., isolated from the rhizosphere of the medicinal plant Angelica sinensis.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {63}, number = {Pt 8}, pages = {2787-2793}, doi = {10.1099/ijs.0.038398-0}, pmid = {23291898}, issn = {1466-5034}, mesh = {Angelica sinensis/*microbiology ; Bacterial Typing Techniques ; Bacteroidetes/*classification/genetics/isolation &amp; purification ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Phylogeny ; Plants, Medicinal/microbiology ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; Sphingolipids/analysis ; Vitamin K 2/analogs &amp; derivatives/analysis ; }, abstract = {A strictly aerobic, Gram-staining-negative, non-motile and rod-shaped bacterial strain, DR-9(T), was isolated from rhizosphere soil of the medicinal herb Angelica sinensis. Strain DR-9(T) grew at 20-40 °C, at pH 4.0-9.0 and in the presence of 0-1 % (w/v) NaCl. The major fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c and/or iso-C15 : 0 2-OH), MK-7 was the major isoprenoid quinone, and phosphatidylethanolamine and an unidentified aminophospholipid were the major polar lipids. A phylogenetic tree based on 16S rRNA gene sequences showed that strain DR-9(T) formed a lineage within the genus Mucilaginibacter and was closely related to Mucilaginibacter polysacchareus DRP28(T) (96.1 % sequence similarity), Mucilaginibacter myungsuensis HMD1056(T) (95.9 % sequence similarity), Mucilaginibacter ximonensis XM-003(T) (95.8 %) and Mucilaginibacter boryungensis BDR-9(T) (95.1 %). The status of strain DR-9(T) as a representative of a separate species was confirmed by DNA hybridization, with 38.6, 36.3 and 29.9 % DNA-DNA relatedness with M. polysacchareus DRP28(T), M. ximonensis XM-003(T) and M. boryungensis BDR-9(T), respectively. The genomic DNA G+C content of strain DR-9(T) was 49.8 %. These data suggest that strain DR-9(T) should be considered as a representative of a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter herbaticus sp. nov. is proposed. The type strain is DR-9(T) (= KACC 16469(T) = NBRC 108839(T)).}, }
@article {pmid23284712, year = {2012}, author = {Pereira e Silva, MC and Dias, AC and van Elsas, JD and Salles, JF}, title = {Spatial and temporal variation of archaeal, bacterial and fungal communities in agricultural soils.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e51554}, pmid = {23284712}, issn = {1932-6203}, mesh = {*Agriculture ; Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; *Biodiversity ; DNA, Ribosomal/analysis/genetics ; Fungi/*classification/genetics/isolation &amp; purification ; Real-Time Polymerase Chain Reaction ; *Soil Microbiology ; }, abstract = {BACKGROUND: Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time.<br><br>In this study, we explored the temporal and spatial responses of soil bacterial, archaeal and fungal &#x3b2;-diversities to abiotic parameters. Taking into account data from a 3-year sampling period, we analyzed the abundances and community structures of Archaea, Bacteria and Fungi along with key soil chemical parameters. We questioned how these abiotic variables influence the turnover of bacterial, archaeal and fungal communities and how they impact the long-term patterns of changes of the aforementioned soil communities. Interestingly, we found that the bacterial and fungal &#x3b2;-diversities are quite stable over time, whereas archaeal diversity showed significantly higher fluctuations. These fluctuations were reflected in temporal turnover caused by soil management through addition of N-fertilizers.<br><br>CONCLUSIONS: Our study showed that management practices applied to agricultural soils might not significantly affect the bacterial and fungal communities, but cause slow and long-term changes in the abundance and structure of the archaeal community. Moreover, the results suggest that, to different extents, abiotic and biotic factors determine the community assembly of archaeal, bacterial and fungal communities.}, }
@article {pmid23284709, year = {2012}, author = {Abell, GC and Robert, SS and Frampton, DM and Volkman, JK and Rizwi, F and Csontos, J and Bodrossy, L}, title = {High-throughput analysis of ammonia oxidiser community composition via a novel, amoA-based functional gene array.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e51542}, pmid = {23284709}, issn = {1932-6203}, mesh = {Ammonia/*metabolism ; Archaea/classification/*genetics/isolation &amp; purification ; Archaeal Proteins/*genetics ; Autotrophic Processes/*physiology ; Bacteria/classification/*genetics/isolation &amp; purification ; Bacterial Proteins/*genetics ; Biomarkers/metabolism ; Environmental Monitoring ; Gene Expression Profiling ; High-Throughput Screening Assays ; Nitrification ; Nitrites/metabolism ; Oligonucleotide Array Sequence Analysis ; Oxidation-Reduction ; Oxidoreductases/*genetics/metabolism ; Soil Microbiology ; }, abstract = {Advances in microbial ecology research are more often than not limited by the capabilities of available methodologies. Aerobic autotrophic nitrification is one of the most important and well studied microbiological processes in terrestrial and aquatic ecosystems. We have developed and validated a microbial diagnostic microarray based on the ammonia-monooxygenase subunit A (amoA) gene, enabling the in-depth analysis of the community structure of bacterial and archaeal ammonia oxidisers. The amoA microarray has been successfully applied to analyse nitrifier diversity in marine, estuarine, soil and wastewater treatment plant environments. The microarray has moderate costs for labour and consumables and enables the analysis of hundreds of environmental DNA or RNA samples per week per person. The array has been thoroughly validated with a range of individual and complex targets (amoA clones and environmental samples, respectively), combined with parallel analysis using traditional sequencing methods. The moderate cost and high throughput of the microarray makes it possible to adequately address broader questions of the ecology of microbial ammonia oxidation requiring high sample numbers and high resolution of the community composition.}, }
@article {pmid23280498, year = {2013}, author = {Vezzulli, L and Colwell, RR and Pruzzo, C}, title = {Ocean warming and spread of pathogenic vibrios in the aquatic environment.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {817-825}, pmid = {23280498}, issn = {1432-184X}, support = {2R01A1039129-11A2//PHS HHS/United States ; }, mesh = {Animals ; *Climate Change ; *Ecosystem ; Humans ; Seawater/chemistry/*microbiology ; Vibrio/isolation &amp; purification/pathogenicity/*physiology ; Vibrio Infections/*microbiology ; }, abstract = {Vibrios are among the most common bacteria that inhabit surface waters throughout the world and are responsible for a number of severe infections both in humans and animals. Several reports recently showed that human Vibrio illnesses are increasing worldwide including fatal acute diarrheal diseases, such as cholera, gastroenteritis, wound infections, and septicemia. Many scientists believe this increase may be associated with global warming and rise in sea surface temperature (SST), although not enough evidence is available to support a causal link between emergence of Vibrio infections and climate warming. The effect of increased SST in promoting spread of vibrios in coastal and brackish waters is considered a causal factor explaining this trend. Field and laboratory studies carried out over the past 40 years supported this hypothesis, clearly showing temperature promotes Vibrio growth and persistence in the aquatic environment. Most recently, a long-term retrospective microbiological study carried out in the coastal waters of the southern North Sea provided the first experimental evidence for a positive and significant relationship between SST and Vibrio occurrence over a multidecadal time scale. As a future challenge, macroecological studies of the effects of ocean warming on Vibrio persistence and spread in the aquatic environment over large spatial and temporal scales would conclusively support evidence acquired to date combined with studies of the impact of global warming on epidemiologically relevant variables, such as host susceptibility and exposure. Assessing a causal link between ongoing climate change and enhanced growth and spread of vibrios and related illness is expected to improve forecast and mitigate future outbreaks associated with these pathogens.}, }
@article {pmid23280497, year = {2013}, author = {Froelich, B and Oliver, JD}, title = {The interactions of Vibrio vulnificus and the oyster Crassostrea virginica.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {807-816}, pmid = {23280497}, issn = {1432-184X}, mesh = {Animals ; Humans ; Ostreidae/*microbiology/physiology ; Shellfish/*microbiology ; Shellfish Poisoning/*microbiology ; Sodium Chloride ; Temperature ; Vibrio Infections/*microbiology ; Vibrio vulnificus/genetics/isolation &amp; purification/*physiology ; }, abstract = {The human bacterial pathogen, Vibrio vulnificus, is found in brackish waters and is concentrated by filter-feeding molluscan shellfish, especially oysters, which inhabit those waters. Ingestion of raw or undercooked oysters containing virulent strains of V. vulnificus can result in rapid septicemia and death in 50 % of victims. This review summarizes the current knowledge of the environmental interactions between these two organisms, including the effects of salinity and temperature on colonization, uptake, and depuration rates of various phenotypes and genotypes of the bacterium, and host-microbe immunological interactions.}, }
@article {pmid23280496, year = {2013}, author = {Basu, S and Deobagkar, DD and Matondkar, SG and Furtado, I}, title = {Culturable bacterial flora associated with the dinoflagellate green Noctiluca miliaris during active and declining bloom phases in the Northern Arabian Sea.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {934-954}, pmid = {23280496}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Dinoflagellida/growth &amp; development/*microbiology ; Molecular Sequence Data ; Nitrogen/analysis ; Oceans and Seas ; Phylogeny ; Seawater/analysis/*microbiology/parasitology ; }, abstract = {A massive algal bloom of the dinoflagellate Noctiluca miliaris (green) was located in the Northern Arabian Sea by IRS-P4-2 (OCM-II) for microbiological studies, during two consecutive cruises of February-March 2009. Culturable bacterial load during bloom were ≈ 2-3-fold higher in comparison to non-bloom waters and ranged from 3.20 × 10(5) to 6.84 × 10(5) cfu ml(-1). An analysis of the dominant heterotrophs associated with Noctiluca bloom resulted in phylogenetic and a detailed metabolic characterization of 70 bacterial isolates from an overlapping active and declining bloom phase location near north-central Arabian Sea. The active phase flora was dominated by Gram-positive forms (70.59 %), a majority of which belonged to Bacillus (35.29 %) of Firmicutes. As the bloom declined, Gram-negative forms (61.11 %) emerged dominant, and these belonged to a diverse γ-proteobacterial population consisting of Shewanella (16.67 %) and equal fractions of a Cobetia-Pseudomonas-Psychrobacter-Halomonas population (36.11 %). A Unifrac-based principal coordinate analysis of partial 16S rDNA sequences showed significant differences among the active and declining phase flora and also with reported endocytic flora of Noctiluca (red). A nonparametric multidimensional scaling (NMDS) of antibiogram helped differentiation among closely related strains. The organic matter synthesized by N. miliaris appears to be quickly utilized and remineralized as seen from the high efficiency of isolates to metabolize various complex and simple C/N substrates such as carbohydrates, proteins/amino acids, lipids, sulfide production from organic matter, and solubilize phosphates. The ability of a large fraction of these strains (50-41.67 %) to further aerobically denitrify indicates their potential for nitrogen removal from these high-organic microniches of the Noctiluca bloom in the Arabian Sea, also known for high denitrification activity. The results indicate that culturable euphotic bacterial associates of Noctiluca are likely to play a critical role in the biogeochemical ramifications of these unique seasonally emerging tropical open-water blooms of the Northern Arabian Sea.}, }
@article {pmid23277394, year = {2013}, author = {Bhatt, VD and Dande, SS and Patil, NV and Joshi, CG}, title = {Molecular analysis of the bacterial microbiome in the forestomach fluid from the dromedary camel (Camelus dromedarius).}, journal = {Molecular biology reports}, volume = {40}, number = {4}, pages = {3363-3371}, pmid = {23277394}, issn = {1573-4978}, mesh = {Animals ; Bacteria/classification/*genetics/isolation &amp; purification ; Body Fluids/*microbiology ; Camelus/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenome/genetics ; Rumen/*microbiology ; }, abstract = {Rumen microorganisms play an important role in ruminant digestion and absorption of nutrients and have great potential applications in the field of rumen adjusting, food fermentation and biomass utilization etc. In order to investigate the composition of microorganisms in the rumen of camel (Camelus dromedarius), this study delves in the microbial diversity by culture-independent approach. It includes comparison of rumen samples investigated in the present study to other currently available metagenomes to reveal potential differences in rumen microbial systems. Pyrosequencing based metagenomics was applied to analyze phylogenetic and metabolic profiles by MG-RAST, a web based tool. Pyrosequencing of camel rumen sample yielded 8,979,755 nucleotides assembled to 41,905 sequence reads with an average read length of 214 nucleotides. Taxonomic analysis of metagenomic reads indicated Bacteroidetes (55.5 %), Firmicutes (22.7 %) and Proteobacteria (9.2 %) phyla as predominant camel rumen taxa. At a finer phylogenetic resolution, Bacteroides species dominated the camel rumen metagenome. Functional analysis revealed that clustering-based subsystem and carbohydrate metabolism were the most abundant SEED subsystem representing 17 and 13 % of camel metagenome, respectively. A high taxonomic and functional similarity of camel rumen was found with the cow metagenome which is not surprising given the fact that both are mammalian herbivores with similar digestive tract structures and functions. Combined pyrosequencing approach and subsystems-based annotations available in the SEED database allowed us access to understand the metabolic potential of these microbiomes. Altogether, these data suggest that agricultural and animal husbandry practices can impose significant selective pressures on the rumen microbiota regardless of rumen type. The present study provides a baseline for understanding the complexity of camel rumen microbial ecology while also highlighting striking similarities and differences when compared to other animal gastrointestinal environments.}, }
@article {pmid23274881, year = {2013}, author = {Gerwick, WH and Fenner, AM}, title = {Drug discovery from marine microbes.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {800-806}, pmid = {23274881}, issn = {1432-184X}, support = {R01 CA100851/CA/NCI NIH HHS/United States ; CA100851/CA/NCI NIH HHS/United States ; TW006634/TW/FIC NIH HHS/United States ; D43 TW009343/TW/FIC NIH HHS/United States ; NS053398/NS/NINDS NIH HHS/United States ; U01 TW006634/TW/FIC NIH HHS/United States ; R01 CA108874/CA/NCI NIH HHS/United States ; CA108874/CA/NCI NIH HHS/United States ; R01 NS053398/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Aquatic Organisms/*chemistry/microbiology/physiology ; Bacteria/*metabolism ; Biological Products/*chemistry/metabolism ; *Drug Discovery ; Invertebrates/*chemistry/microbiology/physiology ; Seawater/microbiology ; Symbiosis ; }, abstract = {The marine environment has been a source of more than 20,000 inspirational natural products discovered over the past 50 years. From these efforts, 9 approved drugs and 12 current clinical trial agents have been discovered, either as natural products or as molecules inspired from the natural product structure. To a significant degree, these have come from collections of marine invertebrates largely obtained from shallow-water tropical ecosystems. However, there is a growing recognition that marine invertebrates are oftentimes populated with enormous quantities of "associated" or symbiotic microorganisms and that microorganisms are the true metabolic sources of these most valuable of marine natural products. Also, because of the inherently multidisciplinary nature of this field, a high degree of innovation is characteristic of marine natural product drug discovery efforts.}, }
@article {pmid23274880, year = {2013}, author = {Rohini-Kumar, M and Osborne, JW and Saravanan, VS}, title = {Comparison of soil bacterial communities of Pinus patula of Nilgiris, western ghats with other biogeographically distant pine forest clone libraries.}, journal = {Microbial ecology}, volume = {66}, number = {1}, pages = {132-144}, pmid = {23274880}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Gene Library ; India ; Phylogeny ; Pinus/*microbiology ; *Soil Microbiology ; Trees/*microbiology ; }, abstract = {The bacterial community structure of the rhizosphere and non-rhizosphere soil of Pinus patula, found in the Nilgiris region of Western Ghats, was studied by constructing 16S rRNA gene clone libraries. In the rhizosphere and non-rhizosphere soil clone libraries constructed, 13 and 15 bacterial phyla were identified, respectively. The clone libraries showed the predominance of members of culturally underrepresented phyla like Acidobacteria and Verrucomicrobia. The Alphaproteobacteria and Acidobacteria clones were predominant in rhizosphere and non-rhizosphere soil samples, respectively. In rhizosphere, amongst Alphaproteobacteria members, Bradyrhizobium formed the significant proportion, whereas in non-rhizosphere, members of subdivision-6 of phylum Acidobacteria were abundant. The diversity analysis of P. patula soil libraries showed that the phylotypes (16S rRNA gene similarity cutoff, ≥97 %) of Acidobacteria and Bacteroidetes were relatively predominant and diverse followed by Alphaproteobacteria and Verrucomicrobia. The diversity indices estimated higher richness and abundance of bacteria in P. patula soil clone libraries than the pine forest clone libraries retrieved from previous studies. The tools like principal co-ordinate analysis and Jackknife cluster analysis, which were under UniFrac analysis indicated that variations in soil bacterial communities were attributed to their respective geographical locations due to the phylogenetic divergence amongst the clone libraries. Overall, the P. patula rhizosphere and non-rhizosphere clone libraries were found significantly unique in composition, evenly distributed and highly rich in phylotypes, amongst the biogeographically distant clone libraries. It was finally hypothesised that the phylogenetic divergence amongst the bacterial phylotypes and natural selection plays a pivotal role in the variations of bacterial communities across the geographical distance.}, }
@article {pmid23271454, year = {2013}, author = {Savage, D and Barbetti, MJ and MacLeod, WJ and Salam, MU and Renton, M}, title = {Temporal patterns of ascospore release in Leptosphaeria maculans vary depending on geographic region and time of observation.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {584-592}, pmid = {23271454}, issn = {1432-184X}, mesh = {Ascomycota/*growth &amp; development ; Australia ; Climate ; Geography ; Seasons ; Spores, Fungal/*growth &amp; development ; Temperature ; Time Factors ; }, abstract = {Diurnal patterns of spore release have been observed in a number of fungal pathogens that undergo wind-assisted dispersal. The mechanisms that drive these patterns, while not well understood, are thought to relate to the ability of dispersing spores to survive their journey and infect new hosts. In this paper, we characterise the diurnal pattern of ascospore release by a Western Australian population of Leptosphaeria maculans. Although L. maculans has been previously shown to exhibit diurnal patterns of ascospore release, these patterns appear to vary from region to region. In order to characterise the pattern of release in the Mediterranean climate of Western Australia, we analysed historical data describing the bi-hourly count of airborne ascospores at Mt Barker, Western Australia. Results of this analysis showed diurnal patterns that differ from those previously observed in other countries, with ascospore release in our study most likely to occur in the afternoon. Furthermore, we found that the time of peak release can shift from month to month within any one season, and from year to year. In explaining the hourly pattern of spore release over an entire season, time since rainfall, time since last release, temperature, hour and month were all shown to be significant variables.}, }
@article {pmid23270314, year = {2012}, author = {Weissbrodt, DG and Shani, N and Sinclair, L and Lefebvre, G and Rossi, P and Maillard, J and Rougemont, J and Holliger, C}, title = {PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {306}, pmid = {23270314}, issn = {1471-2180}, mesh = {*Biota ; Computational Biology/*methods ; DNA, Ribosomal/chemistry/*genetics ; Groundwater/microbiology ; *Phylogeny ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Wastewater/microbiology ; }, abstract = {BACKGROUND: In molecular microbial ecology, massive sequencing is gradually replacing classical fingerprinting techniques such as terminal-restriction fragment length polymorphism (T-RFLP) combined with cloning-sequencing for the characterization of microbiomes. Here, a bioinformatics methodology for pyrosequencing-based T-RF identification (PyroTRF-ID) was developed to combine pyrosequencing and T-RFLP approaches for the description of microbial communities. The strength of this methodology relies on the identification of T-RFs by comparison of experimental and digital T-RFLP profiles obtained from the same samples. DNA extracts were subjected to amplification of the 16S rRNA gene pool, T-RFLP with the HaeIII restriction enzyme, 454 tag encoded FLX amplicon pyrosequencing, and PyroTRF-ID analysis. Digital T-RFLP profiles were generated from the denoised full pyrosequencing datasets, and the sequences contributing to each digital T-RF were classified to taxonomic bins using the Greengenes reference database. The method was tested both on bacterial communities found in chloroethene-contaminated groundwater samples and in aerobic granular sludge biofilms originating from wastewater treatment systems.<br><br>RESULTS: PyroTRF-ID was efficient for high-throughput mapping and digital T-RFLP profiling of pyrosequencing datasets. After denoising, a dataset comprising ca. 10'000 reads of 300 to 500 bp was typically processed within ca. 20 minutes on a high-performance computing cluster, running on a Linux-related CentOS 5.5 operating system, enabling parallel processing of multiple samples. Both digital and experimental T-RFLP profiles were aligned with maximum cross-correlation coefficients of 0.71 and 0.92 for high- and low-complexity environments, respectively. On average, 63&#xb1;18% of all experimental T-RFs (30 to 93 peaks per sample) were affiliated to phylotypes.<br><br>CONCLUSIONS: PyroTRF-ID profits from complementary advantages of pyrosequencing and T-RFLP and is particularly adapted for optimizing laboratory and computational efforts to describe microbial communities and their dynamics in any biological system. The high resolution of the microbial community composition is provided by pyrosequencing, which can be performed on a restricted set of selected samples, whereas T-RFLP enables simultaneous fingerprinting of numerous samples at relatively low cost and is especially adapted for routine analysis and follow-up of microbial communities on the long run.}, }
@article {pmid23269847, year = {2013}, author = {Gehring, AU and Kind, J and Charilaou, M and García-Rubio, I}, title = {S-band ferromagnetic resonance spectroscopy and the detection of magnetofossils.}, journal = {Journal of the Royal Society, Interface}, volume = {10}, number = {80}, pages = {20120790}, pmid = {23269847}, issn = {1742-5662}, mesh = {*Bacteria ; Ferrosoferric Oxide/*chemistry ; *Fossils ; Magnetic Resonance Spectroscopy/*methods ; }, abstract = {We report the use of S-band ferromagnetic resonance (FMR) spectroscopy to compare the anisotropic properties of magnetite particles in chains of cultured intact magnetotactic bacteria (MTB) between 300 and 15 K with those of sediment samples of Holocene age in order to infer the presence of magnetofossils and their preservation in a geological time frame. The spectrum of intact MTB at 300 K exhibits distinct uniaxial anisotropy because of the chain alignment of the cellular magnetite particles and their easy axes. This anisotropy becomes less pronounced upon cooling and below the Verwey transition (T(V)) it is nearly vanished mainly owing to the change of direction of the easy axes. In a natural sample, magnetofossils were detected by uniaxial anisotropy traits similar to those obtained from cultured MTB above T(V). Our comparative study emphasizes that indispensable information can be obtained from S-band FMR spectra, which offers even a better resolution than X-band FMR for discovering magnetofossils, and this in turn can contribute towards strengthening our relatively sparse database for deciphering the microbial ecology during the Earth's history.}, }
@article {pmid23269552, year = {2013}, author = {Yang, C and Ji, Y and Wang, X and Yang, C and Yu, DW}, title = {Testing three pipelines for 18S rDNA-based metabarcoding of soil faunal diversity.}, journal = {Science China. Life sciences}, volume = {56}, number = {1}, pages = {73-81}, doi = {10.1007/s11427-012-4423-7}, pmid = {23269552}, issn = {1869-1889}, mesh = {Animals ; Annelida/classification/genetics/growth &amp; development ; Arthropods/classification/genetics/growth &amp; development ; *Biodiversity ; Computational Biology/*methods ; DNA Barcoding, Taxonomic ; DNA, Ribosomal/chemistry/genetics ; Eukaryota/classification/genetics/growth &amp; development ; *Genetic Variation ; Nematoda/classification/genetics/growth &amp; development ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA ; Soil/*parasitology ; }, abstract = {A number of basic and applied questions in ecology and environmental management require the characterization of soil and leaf litter faunal diversity. Recent advances in high-throughput sequencing of barcode-gene amplicons ('metabarcoding') have made it possible to survey biodiversity in a robust and efficient way. However, one obstacle to the widespread adoption of this technique is the need to choose amongst many candidates for bioinformatic processing of the raw sequencing data. We compare three candidate pipelines for the processing of 18S small subunit rDNA metabarcode data from solid substrates: (i) USEARCH/CROP, (ii) Denoiser/UCLUST, and (iii) OCTUPUS. The three pipelines produced reassuringly similar and highly correlated assessments of community composition that are dominated by taxa known to characterize the sampled environments. However, OCTUPUS appears to inflate phylogenetic diversity, because of higher sequence noise. We therefore recommend either the USEARCH/CROP or Denoiser/UCLUST pipelines, both of which can be run within the QIIME (Quantitative Insights Into Microbial Ecology) environment.}, }
@article {pmid23269456, year = {2013}, author = {Bae, HS and Hou, A}, title = {23S rRNA gene-based enterococci community signatures in Lake Pontchartrain, Louisiana, USA, following urban runoff inputs after Hurricane Katrina.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {289-301}, pmid = {23269456}, issn = {1432-184X}, mesh = {*Cyclonic Storms ; DNA, Bacterial/genetics ; *Disasters ; Enterococcus/classification/genetics/*isolation &amp; purification ; *Environmental Monitoring ; Feces/microbiology ; Floods ; Gene Library ; Lakes/*microbiology ; Louisiana ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 23S/genetics ; Water Movements ; Water Pollution/*analysis ; Water Quality ; }, abstract = {Little is known about the impacts of fecal polluted urban runoff inputs on the structure of enterococci communities in estuarine waters. This study employed a 23S rRNA gene-based polymerase chain reaction (PCR) assay with newly designed genus-specific primers, Ent127F-Ent907R, to determine the possible impacts of Hurricane Katrina floodwaters via the 17th Street Canal discharge on the community structure of enterococci in Lake Pontchartrain. A total of 94 phylotypes were identified through the restriction fragment length polymorphism (RFLP) screening of 494 clones while only 8 phylotypes occurred among 88 cultivated isolates. Sequence analyses of representative phylotypes and their temporal and spatial distribution in the lake and the canal indicated the Katrina floodwater input introduced a large portion of Enterococcus flavescens, Enterococcus casseliflavus, and Enterococcus dispar into the lake; typical fecal groups Enterococcus faecium, Enterococcus durans, Enterococcus hirae, and Enterococcus mundtii were detected primarily in the floodwater-impacted waters. This study provides a global picture of enterococci in estuarine waters impacted by Hurricane Katrina-derived urban runoff. It also demonstrates the culture-independent PCR approach using 23S rRNA gene as a molecular marker could be a good alternative in ecological studies of enterococci in natural environments to overcome the limitation of conventional cultivation methods.}, }
@article {pmid23269455, year = {2013}, author = {López-Pérez, M and Gonzaga, A and Martin-Cuadrado, AB and López-García, P and Rodriguez-Valera, F and Kimes, NE}, title = {Intra- and intergenomic variation of ribosomal RNA operons in concurrent Alteromonas macleodii strains.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {720-730}, pmid = {23269455}, issn = {1432-184X}, mesh = {Alteromonas/chemistry/classification/*genetics/isolation &amp; purification ; Base Sequence ; Biodiversity ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/*genetics ; *Genetic Variation ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Operon ; Phylogeny ; RNA, Ribosomal/chemistry/*genetics ; Seawater/*microbiology ; }, abstract = {Biodiversity estimates based on ribosomal operon sequence diversity rely on the premise that a sequence is characteristic of a single specific taxon or operational taxonomic unit (OTU). Here, we have studied the sequence diversity of 14 ribosomal RNA operons (rrn) contained in the genomes of two isolates (five operons in each genome) and four metagenomic fosmids, all from the same seawater sample. Complete sequencing of the isolate genomes and the fosmids establish that they represent strains of the same species, Alteromonas macleodii, with average nucleotide identity (ANI) values >97 %. Nonetheless, we observed high levels of intragenomic heterogeneity (i.e., variability between operons of a single genome) affecting multiple regions of the 16S and 23S rRNA genes as well as the internally transcribed spacer 1 (ITS-1) region. Furthermore, the ribosomal operons exhibited intergenomic heterogeneity (i.e., variability between operons located in separate genomes) in each of these regions, compounding the variability. Our data reveal the extensive heterogeneity observed in natural populations of A. macleodii at a single point in time and support the idea that distinct lineages of A. macleodii exist in the deep Mediterranean. These findings highlight the potential of rRNA fingerprinting methods to misrepresent species diversity while simultaneously failing to recognize the ecological significance of individual strains.}, }
@article {pmid23269454, year = {2013}, author = {Guidolin, AS and Cônsoli, FL}, title = {Molecular characterization of Wolbachia strains associated with the invasive Asian citrus psyllid Diaphorina citri in Brazil.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {475-486}, pmid = {23269454}, issn = {1432-184X}, mesh = {Animals ; Bacterial Typing Techniques ; Brazil ; Citrus ; DNA, Bacterial/genetics ; DNA, Mitochondrial/genetics ; Genotype ; Haplotypes ; Hemiptera/genetics/*microbiology ; Host Specificity ; Insect Vectors/genetics/*microbiology ; Introduced Species ; Multilocus Sequence Typing ; Phylogeny ; Sequence Analysis, DNA ; Symbiosis ; Wolbachia/*classification/genetics ; }, abstract = {Wolbachia is a symbiont intensively studied due to its ability to interfere with their host's reproduction, and it has been recently proposed as an alternative tool to control insect pests or vectors of diseases. The Asian citrus psyllid Diaphorina citri is an important pest of citrus since it vectors the bacterium that causes the "Huanglongbing" disease in citrus. The frequency and diversity of Wolbachia associated with D. citri is unknown, limiting the utilization of Wolbachia as an alternative strategy for insect management. Thus, we aimed to determine the natural rate of infection, to characterize the Wolbachia strains associated with this psyllid by "multilocus sequencing typing" (MLST) and wsp analysis, and to verify the association of the symbiont to particular genotypes of the host. Analysis indicated Wolbachia infects 100 % of all specimens tested from all 15 sampled populations. MLST revealed the occurrence of five new sequence types (STs) of Wolbachia, while analysis based on the wsp sequences indicated only four different types of Wolbachia. ST-173 was predominant, while the remaining STs were population specific. Analysis of the host-symbiont relationship did not reveal any particular association of Wolbachia and haplotypes or a decrease in nucleotide diversity of D. citri in populations in which more than one ST was recorded. The consequences of the diversity of STs reported are still unknown, but the fact that Wolbachia infection is fixed and that there is one ST with a broad distribution highlights the use of this symbiont as an alternative strategy to control D. citri.}, }
@article {pmid23267382, year = {2012}, author = {Hosseini, E and Poursina, F and de Wiele, TV and Safaei, HG and Adibi, P}, title = {Helicobacter pylori in Iran: A systematic review on the association of genotypes and gastroduodenal diseases.}, journal = {Journal of research in medical sciences : the official journal of Isfahan University of Medical Sciences}, volume = {17}, number = {3}, pages = {280-292}, pmid = {23267382}, issn = {1735-1995}, abstract = {BACKGROUND: Helicobacter pylori (H. pylori) infection is known as a major etiologic factor for a variety of gastroduodenal diseases. In Iran, with a high rate of H. pylori infection close to 90%, numerous studies have revealed many aspects of interaction between the bacterium, mucosal surface and induction of disease outcome. The organism is genetically diverse and several virulence factors are attributed to the more virulent strains. The well-characterized virulence factors of H. pylori are cytotoxin associated gene A and vacuolating cytotoxin gene A. The distribution pattern of H. pylori genotypes and its association with disease status varies geographically. The present review focused on the virulence factors and genotyping of H. pylori in relation to gastroduodenal disorders in different regions of Iran.<br><br>METHODS: In total, 398 studies were reported on different aspects related to H. pylori in our electronic search from 1995-2011. H. pylori infection and its virulence factors in association with disease status were investigated in 159 reports. Looking specifically at the gastrointestinal tract disorders, the most relevant reports including 37 papers were selected.<br><br>RESULTS: We found no correlation of cagA genotype and disease status in the majority of studies, whereas vacA was demonstrated as a useful marker in predicting the disease outcome. The results of reports on other virulence factors of H. pylori such as blood group antigen-binding adhesion gene A, the induced by contact with epithelium gene A, the outer inflammatory protein A, the duodenal ulcer promoting gene A, and Helicobacter outer membrane gene and their relation with disease status were contradictory.<br><br>CONCLUSIONS: Although different markers of H. pylori were emphasized as useful when predicting disease outcomes in some studies, the inconsistent researches and the scarcity of data made any conclusion or even comparison impossible. Considering the gap of information observed during our search relating to genotyping and other aspects of H. pylori infection, further investigations are suggested.}, }
@article {pmid23267351, year = {2012}, author = {Shade, A and Peter, H and Allison, SD and Baho, DL and Berga, M and Bürgmann, H and Huber, DH and Langenheder, S and Lennon, JT and Martiny, JB and Matulich, KL and Schmidt, TM and Handelsman, J}, title = {Fundamentals of microbial community resistance and resilience.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {417}, pmid = {23267351}, issn = {1664-302X}, support = {RC1 DK086831/DK/NIDDK NIH HHS/United States ; }, abstract = {Microbial communities are at the heart of all ecosystems, and yet microbial community behavior in disturbed environments remains difficult to measure and predict. Understanding the drivers of microbial community stability, including resistance (insensitivity to disturbance) and resilience (the rate of recovery after disturbance) is important for predicting community response to disturbance. Here, we provide an overview of the concepts of stability that are relevant for microbial communities. First, we highlight insights from ecology that are useful for defining and measuring stability. To determine whether general disturbance responses exist for microbial communities, we next examine representative studies from the literature that investigated community responses to press (long-term) and pulse (short-term) disturbances in a variety of habitats. Then we discuss the biological features of individual microorganisms, of microbial populations, and of microbial communities that may govern overall community stability. We conclude with thoughts about the unique insights that systems perspectives - informed by meta-omics data - may provide about microbial community stability.}, }
@article {pmid23266188, year = {2013}, author = {Foesel, BU and Rohde, M and Overmann, J}, title = {Blastocatella fastidiosa gen. nov., sp. nov., isolated from semiarid savanna soil - the first described species of Acidobacteria subdivision 4.}, journal = {Systematic and applied microbiology}, volume = {36}, number = {2}, pages = {82-89}, doi = {10.1016/j.syapm.2012.11.002}, pmid = {23266188}, issn = {1618-0984}, mesh = {Acidobacteria/*classification/genetics/*isolation &amp; purification/physiology ; Bacterial Typing Techniques ; Base Composition ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Desert Climate ; Fatty Acids/analysis ; Heterotrophic Processes ; Locomotion ; Microscopy ; Molecular Sequence Data ; Organic Chemicals/metabolism ; Phylogeny ; Pigments, Biological/metabolism ; Quinones/analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Acidobacteria represent abundant members of soil microbial communities but only few representatives could be isolated and validly described so far. Currently, eighteen species of subdivision 1, one species of subdivision 3, three species of subdivision 8, and one species of subdivision 10 are recognized. In contrast, Acidobacteria of subdivision 4 have largely escaped cultivation although they belong to the most abundant and diverse acidobacterial groups in soils. A member of subdivision 4, strain A2-16(T), was isolated from a semiarid savanna soil. Cells were motile spheres to rods with a tendency to form chains and larger aggregates. Cultures were orange to pink colored, neutrophilic mesophiles, and showed aerobic chemoorganoheterotrophic growth on very few complex substrates and protocatechuate, and weak growth on chitin, cellulose and starch. While protein substrates such as casamino acids or peptone were utilized, individual amino acids did not promote growth. Also, growth on alternative electron acceptors or fermentative growth could not be observed. Major fatty acids were summed features 1 (15:1 iso H/13:0 3-OH) and 3 (16:1ω7c/15:0 iso 2-OH). The major quinone was MK-8. The DNA G+C content was 46.5mol%. Phylogenetic analysis placed A2-16(T) amidst uncultured members of Acidobacteria subdivision 4. The most closely related environmental 16S rRNA gene sequences (96-97% nucleotide identity) were several clone sequences from terrestrial environments. Based on these characteristics, the isolated strain is proposed as a new species of a novel genus, Blastocatella fastidiosa gen. nov., sp. nov. The type strain of B. fastidiosa is A2-16(T) (=DSM 25172(T)=LMG26944(T)).}, }
@article {pmid23263968, year = {2013}, author = {Dolinsek, J and Dorninger, C and Lagkouvardos, I and Wagner, M and Daims, H}, title = {Depletion of unwanted nucleic acid templates by selective cleavage: LNAzymes, catalytically active oligonucleotides containing locked nucleic acids, open a new window for detecting rare microbial community members.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {5}, pages = {1534-1544}, pmid = {23263968}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics/*methods ; Molecular Sequence Data ; Oligonucleotides/genetics/*metabolism ; RNA/*metabolism ; RNA Stability ; Ribonucleases/*metabolism ; Sensitivity and Specificity ; Sequence Analysis, DNA ; }, abstract = {Many studies of molecular microbial ecology rely on the characterization of microbial communities by PCR amplification, cloning, sequencing, and phylogenetic analysis of genes encoding rRNAs or functional marker enzymes. However, if the established clone libraries are dominated by one or a few sequence types, the cloned diversity is difficult to analyze by random clone sequencing. Here we present a novel approach to deplete unwanted sequence types from complex nucleic acid mixtures prior to cloning and downstream analyses. It employs catalytically active oligonucleotides containing locked nucleic acids (LNAzymes) for the specific cleavage of selected RNA targets. When combined with in vitro transcription and reverse transcriptase PCR, this LNAzyme-based technique can be used with DNA or RNA extracts from microbial communities. The simultaneous application of more than one specific LNAzyme allows the concurrent depletion of different sequence types from the same nucleic acid preparation. This new method was evaluated with defined mixtures of cloned 16S rRNA genes and then used to identify accompanying bacteria in an enrichment culture dominated by the nitrite oxidizer "Candidatus Nitrospira defluvii." In silico analysis revealed that the majority of publicly deposited rRNA-targeted oligonucleotide probes may be used as specific LNAzymes with no or only minor sequence modifications. This efficient and cost-effective approach will greatly facilitate tasks such as the identification of microbial symbionts in nucleic acid preparations dominated by plastid or mitochondrial rRNA genes from eukaryotic hosts, the detection of contaminants in microbial cultures, and the analysis of rare organisms in microbial communities of highly uneven composition.}, }
@article {pmid23263237, year = {2013}, author = {Al-Bader, D and Eliyas, M and Rayan, R and Radwan, S}, title = {Subsurface associations of Acaryochloris-related picocyanobacteria with oil-utilizing bacteria in the Arabian Gulf water body: promising consortia in oil sediment bioremediation.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {555-565}, pmid = {23263237}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Cyanobacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Geologic Sediments/*microbiology ; Hydrocarbons/metabolism ; Molecular Sequence Data ; Petroleum/*metabolism ; Phylogeny ; Seawater/*microbiology ; }, abstract = {Two picocyanobacterial strains related to Acaryochloris were isolated from the Arabian Gulf, 3 m below the water surface, one from the north shore and the other from the south shore of Kuwait. Both strains were morphologically, ultrastructurally, and albeit to a less extend, phylogenetically similar to Acaryochloris. However, both isolates lacked chlorophyll d and produced instead chlorophyll a, as the major photosynthetic pigment. Both picocyanobacterial isolates were associated with oil-utilizing bacteria in the magnitude of 10(5) cells g(-1). According to their 16S rRNA gene sequences, bacteria associated with the isolate from the north were affiliated to Paenibacillus sp., Bacillus pumilus, and Marinobacter aquaeolei, but those associated with the isolate from the south were affiliated to Bacillus asahii and Alcanivorax jadensis. These bacterial differences were probably due to environmental variations. In batch cultures, the bacterial consortia in the nonaxenic biomass as well as the pure bacterial isolates effectively consumed crude oil and pure aliphatic and aromatic hydrocarbons, including very high-molecular-weight compounds. Water and diethylether extracts from the phototrophic biomass enhanced growth of individual bacterial isolates and their hydrocarbon-consumption potential in batch cultures. It was concluded that these consortia could be promising in bioremediation of hydrocarbon pollutants, especially heavy sediments in the marine ecosystem.}, }
@article {pmid23263236, year = {2013}, author = {Sylvander, P and Häubner, N and Snoeijs, P}, title = {The thiamine content of phytoplankton cells is affected by abiotic stress and growth rate.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {566-577}, pmid = {23263236}, issn = {1432-184X}, mesh = {Chlorophyta/chemistry/growth &amp; development/*metabolism ; Cyanobacteria/chemistry/growth &amp; development/*metabolism ; Diatoms/chemistry/growth &amp; development/*metabolism ; Dinoflagellida/chemistry/growth &amp; development/*metabolism ; Ecosystem ; Kinetics ; Phytoplankton/chemistry/growth &amp; development/*metabolism ; Thiamine/*metabolism ; }, abstract = {Thiamine (vitamin B1) is produced by many plants, algae and bacteria, but by higher trophic levels, it must be acquired through the diet. We experimentally investigated how the thiamine content of six phytoplankton species belonging to five different phyla is affected by abiotic stress caused by changes in temperature, salinity and photon flux density. Correlations between growth rate and thiamine content per cell were negative for the five eukaryotic species, but not for the cyanobacterium Nodularia spumigena. We demonstrate a high variability in thiamine content among phytoplankton species, with the highest content in N. spumigena. Salinity was the factor with the strongest effect, followed by temperature and photon flux density, although the responses varied between the investigated phytoplankton species. Our results suggest that regime shifts in phytoplankton community composition through large-scale environmental changes has the potential to alter the thiamine availability for higher trophic levels. A decreased access to this essential vitamin may have serious consequences for aquatic food webs.}, }
@article {pmid23263235, year = {2013}, author = {Gloeckner, V and Lindquist, N and Schmitt, S and Hentschel, U}, title = {Ectyoplasia ferox, an experimentally tractable model for vertical microbial transmission in marine sponges.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {462-474}, pmid = {23263235}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Gene Library ; Larva/microbiology/physiology ; Phylogeny ; Porifera/*microbiology/physiology ; RNA, Ribosomal, 16S/genetics ; Reproduction ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {The oviparous sponge Ectyoplasia ferox is commonly found in Florida and the Bahamas. Every year in August and/or September about 6 days after a full moon, E. ferox will shed embryo-containing spawning material into the seawater from which hundreds to thousands of larvae will hatch per host individual. In order to investigate vertical microbial transmission in E. ferox, 16S rRNA gene library construction and denaturing gradient gel electrophoresis was employed. Microbial symbionts from six phyla and the unknown lineage SAUL were shown to be vertically transmitted. The identification of 21 VT clusters, of which 19 were situated within sponge-specific or sponge-coral-specific clusters, indicated that a large fraction of the symbiotic microbial consortium was present in the sexual reproductive stages. Spawning led to a 50 % reduction of microbial numbers in the adult sponge mesohyl. We furthermore provide the first evidence that the symbiotic microbial consortia of E. ferox were generally metabolically active within the reproductive stages. Finally, we propose E. ferox as a model system for vertical transmission owing to the ease of experimental access to all sexual reproductive stages, and to experimental tractability in the laboratory including the possibility of rearing symbiont-free juvenile sponges.}, }
@article {pmid23263234, year = {2013}, author = {Oliver, JD}, title = {Vibrio vulnificus: death on the half shell. A personal journey with the pathogen and its ecology.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {793-799}, pmid = {23263234}, issn = {1432-184X}, mesh = {Animals ; Female ; Humans ; Male ; Ostreidae/*microbiology ; Shellfish/*microbiology ; Shellfish Poisoning/*microbiology/mortality ; Vibrio Infections/*microbiology/mortality ; Vibrio vulnificus/genetics/isolation &amp; purification/metabolism/*pathogenicity ; }, abstract = {Vibrio vulnificus is an estuarine bacterium which occurs in high numbers in filter-feeding molluscan shellfish, such as oysters. In individuals with certain underlying diseases, ingestion of the bacterium, e.g., in raw or undercooked oysters, can lead to a rapid and extremely fatal infection. Indeed, this one bacterium is responsible for 95 % of all seafood-borne deaths. In addition, the bacterium is capable of entering a preexisting lesion or cut obtained during coastal recreational activities, resulting in potentially fatal wound infections. This brief review, which comprised a presentation made at the Gordon Research Conference on "Oceans and Human Health," reflects over 35 years of research on this bacterium in the author's laboratory. It describes some of the known virulence factors and why males account for ca 85 % of all V. vulnificus cases. It notes the two genotypes now known to exist and how this pathogen enters a dormant, "viable but nonculturable" state during the winter months. Finally, the review discusses how global warming may be causing worldwide increases in the frequency and geographical extent of Vibrio infections.}, }
@article {pmid23259483, year = {2012}, author = {Oehler, D and Poehlein, A and Leimbach, A and Müller, N and Daniel, R and Gottschalk, G and Schink, B}, title = {Genome-guided analysis of physiological and morphological traits of the fermentative acetate oxidizer Thermacetogenium phaeum.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {723}, pmid = {23259483}, issn = {1471-2164}, mesh = {Acetates/*metabolism ; Bacteria, Anaerobic/cytology/*genetics/metabolism ; Base Composition ; Base Sequence ; DNA Primers/genetics ; Fermentation ; Genome, Bacterial/*genetics ; Genomics/*methods ; Gram-Positive Endospore-Forming Rods/cytology/*genetics/metabolism ; Microscopy, Electron ; Molecular Sequence Data ; Oxidation-Reduction ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Thermacetogenium phaeum is a thermophilic strictly anaerobic bacterium oxidizing acetate to CO(2) in syntrophic association with a methanogenic partner. It can also grow in pure culture, e.g., by fermentation of methanol to acetate. The key enzymes of homoacetate fermentation (Wood-Ljungdahl pathway) are used both in acetate oxidation and acetate formation. The obvious reversibility of this pathway in this organism is of specific interest since syntrophic acetate oxidation operates close to the energetic limitations of microbial life.<br><br>RESULTS: The genome of Th. phaeum is organized on a single circular chromosome and has a total size of 2,939,057 bp. It comprises 3.215 open reading frames of which 75% could be assigned to a gene function. The G+C content is 53.88 mol%. Many CRISPR sequences were found, indicating heavy phage attack in the past. A complete gene set for a phage was found in the genome, and indications of phage action could also be observed in culture. The genome contained all genes required for CO(2) reduction through the Wood-Ljungdahl pathway, including two formyl tetrahydrofolate ligases, three carbon monoxide dehydrogenases, one formate hydrogenlyase complex, three further formate dehydrogenases, and three further hydrogenases. The bacterium contains a menaquinone MQ-7. No indications of cytochromes or Rnf complexes could be found in the genome.<br><br>CONCLUSIONS: The information obtained from the genome sequence indicates that Th. phaeum differs basically from the three homoacetogenic bacteria sequenced so far, i.e., the sodium ion-dependent Acetobacterium woodii, the ethanol-producing Clostridium ljungdahlii, and the cytochrome-containing Moorella thermoacetica. The specific enzyme outfit of Th. phaeum obviously allows ATP formation both in acetate formation and acetate oxidation.}, }
@article {pmid23259452, year = {2013}, author = {Li, M and Huang, WE and Gibson, CM and Fowler, PW and Jousset, A}, title = {Stable isotope probing and Raman spectroscopy for monitoring carbon flow in a food chain and revealing metabolic pathway.}, journal = {Analytical chemistry}, volume = {85}, number = {3}, pages = {1642-1649}, doi = {10.1021/ac302910x}, pmid = {23259452}, issn = {1520-6882}, mesh = {Animals ; CHO Cells ; Caenorhabditis elegans/metabolism ; Carbon/*metabolism ; Carbon Isotopes/metabolism ; Cricetinae ; Cricetulus ; Escherichia coli/metabolism ; *Food Chain ; Humans ; Isotope Labeling/*methods ; Metabolic Networks and Pathways/*physiology ; Spectrum Analysis, Raman/*methods ; }, abstract = {Accurately measuring carbon flows is a challenge for understanding processes such as diverse intracellular metabolic pathways and predator-prey interactions. Combined with stable isotope probing (SIP), single-cell Raman spectroscopy was demonstrated for the first time to link the food chain from carbon substrate to bacterial prey up to predators at the single-cell level in a quantitative and nondestructive manner. Escherichia coli OP50 with different (13)C content, which were grown in a mixture of (12)C- and fully carbon-labeled (13)C-glucose (99%) as a sole carbon source, were fed to the nematode. The (13)C signal in Caenorhabditis elegans was proportional to the (13)C content in E. coli. Two Raman spectral biomarkers (Raman bands for phenylalanine at 1001 cm(-1) and thymine at 747 cm(-1) Raman bands), were used to quantify the (13)C content in E. coli and C. elegans over a range of 1.1-99%. The phenylalanine Raman band was a suitable biomarker for prokaryotic cells and thymine Raman band for eukaryotic cells. A biochemical mechanism accounting for the Raman red shifts of phenylalanine and thymine in response to (13)C-labeling is proposed in this study and is supported by quantum chemical calculation. This study offers new insights of carbon flow via the food chain and provides a research tool for microbial ecology and investigation of biochemical pathways.}, }
@article {pmid23251134, year = {2012}, author = {Theroux, S and Huang, Y and Amaral-Zettler, L}, title = {Comparative molecular microbial ecology of the spring haptophyte bloom in a greenland arctic oligosaline lake.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {415}, pmid = {23251134}, issn = {1664-302X}, abstract = {The Arctic is highly sensitive to increasing global temperatures and is projected to experience dramatic ecological shifts in the next few decades. Oligosaline lakes are common in arctic regions where evaporation surpasses precipitation, however these extreme microbial communities are poorly characterized. Many oligosaline lakes, in contrast to freshwater ones, experience annual blooms of haptophyte algae that generate valuable alkenone biomarker records that can be used for paleoclimate reconstruction. These haptophyte algae are globally important, and globally distributed, aquatic phototrophs yet their presence in microbial molecular surveys is scarce. To target haptophytes in a molecular survey, we compared microbial community structure during two haptophyte bloom events in an arctic oligosaline lake, Lake BrayaSø in southwestern Greenland, using high-throughput pyrotag sequencing. Our comparison of two annual bloom events yielded surprisingly low taxon overlap, only 13% for bacterial and 26% for eukaryotic communities, which indicates significant annual variation in the underlying microbial populations. Both the bacterial and eukaryotic communities strongly resembled high-altitude and high latitude freshwater environments. In spite of high alkenone concentrations in the water column, and corresponding high haptophyte rRNA gene copy numbers, haptophyte pyrotag sequences were not the most abundant eukaryotic tag, suggesting that sequencing biases obscured relative abundance data. With over 170 haptophyte tag sequences, we observed only one haptophyte algal Operational Taxonomic Unit, a prerequisite for accurate paleoclimate reconstruction from the lake sediments. Our study is the first to examine microbial diversity in a Greenland lake using next generation sequencing and the first to target an extreme haptophyte bloom event. Our results provide a context for future explorations of aquatic ecology in the warming arctic.}, }
@article {pmid23250116, year = {2013}, author = {Ling, Z and Liu, X and Chen, W and Luo, Y and Yuan, L and Xia, Y and Nelson, KE and Huang, S and Zhang, S and Wang, Y and Yuan, J and Li, L and Xiang, C}, title = {The restoration of the vaginal microbiota after treatment for bacterial vaginosis with metronidazole or probiotics.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {773-780}, pmid = {23250116}, issn = {1432-184X}, mesh = {Administration, Intravaginal ; Bacteria/classification/genetics/growth &amp; development/isolation &amp; purification ; Cohort Studies ; Female ; Humans ; Lactobacillus/genetics/isolation &amp; purification/physiology ; Metagenome/*drug effects ; Metronidazole/*administration &amp; dosage ; Molecular Sequence Data ; Phylogeny ; Probiotics/*administration &amp; dosage ; Treatment Outcome ; Vagina/*microbiology ; Vaginosis, Bacterial/*drug therapy/microbiology ; }, abstract = {Whether or not treatment with antibiotics or probiotics for bacterial vaginosis (BV) is associated with a change in the diversity of vaginal microbiota in women was investigated. One hundred fifteen women, consisting of 30 healthy subjects, 30 BV-positive control subjects, 30 subjects with BV treated with a 7-day metronidazole regimen, and 25 subjects with BV treated with a 10-day probiotics regimen, were analyzed to determine the efficacy and disparity of diversity and richness of vaginal microbiota using 454 pyrosequencing. Follow-up visits at days 5 and 30 showed a greater BV cure rate in the probiotics-treated subjects (88.0 and 96 %, respectively) compared to the metronidazole-treated subjects (83.3 and 70 %, respectively [p = 0.625 at day 5 and p = 0.013 at day 30]). Treatment with metronidazole reduced the taxa diversity and eradicated most of the BV-associated phylotypes, while probiotics only suppressed the overgrowth and re-established vaginal homeostasis gradually and steadily. Despite significant interindividual variation, the microbiota of the actively treated groups or participants constituted a unique profile. Along with the decrease in pathogenic bacteria, such as Gardnerella, Atopobium, Prevotella, Megasphaera, Coriobacteriaceae, Lachnospiraceae, Mycoplasma, and Sneathia, a Lactobacillus-dominated vaginal microbiota was recovered. Acting as vaginal sentinels and biomarkers, the relative abundance of Lactobacillus and pathogenic bacteria determined the consistency of the BV clinical and microbiologic cure rates, as well as recurrent BV. Both 7-day intravaginal metronidazole and 10-day intravaginal probiotics have good efficacy against BV, while probiotics maintained normal vaginal microbiota longer due to effective and steady vaginal microbiota restoration, which provide new insights into BV treatment.}, }
@article {pmid23250115, year = {2013}, author = {Worchel, ER and Giauque, HE and Kivlin, SN}, title = {Fungal symbionts alter plant drought response.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {671-678}, pmid = {23250115}, issn = {1432-184X}, mesh = {Biomass ; Climate Change ; Droughts ; Endophytes/classification/genetics/physiology ; Fungi/classification/genetics/*physiology ; Photosynthesis ; Poaceae/growth &amp; development/*microbiology/*physiology ; *Symbiosis ; Water/metabolism ; }, abstract = {Grassland productivity is often primarily limited by water availability, and therefore, grasslands may be especially sensitive to climate change. Fungal symbionts can mediate plant drought response by enhancing drought tolerance and avoidance, but these effects have not been quantified across grass species. We performed a factorial meta-analysis of previously published studies to determine how arbuscular mycorrhizal (AM) fungi and endophytic fungal symbionts affect growth of grasses under drought. We then examined how the effect of fungal symbionts on plant growth was influenced by biotic (plant photosynthetic pathway) and abiotic (level of drought) factors. We also measured the phylogenetic signal of fungal symbionts on grass growth under control and drought conditions. Under drought conditions, grasses colonized by AM fungi grew larger than those without mycorrhizal symbionts. The increased growth of grasses conferred from fungal symbionts was greatest at the lowest soil moisture levels. Furthermore, under both drought and control conditions, C3 grasses colonized by AM fungi grew larger than C3 grasses without symbionts, but the biomass of C4 grasses was not affected by AM fungi. Endophytes did not increase plant biomass overall under any treatment. However, there was a phylogenetically conserved increase in plant biomass in grasses colonized by endophytes. Grasses and their fungal symbionts seem to interact within a context-dependent symbiosis, varying with biotic and abiotic conditions. Because plant-fungal symbioses significantly alter plant drought response, including these responses could improve our ability to predict grassland functioning under global change.}, }
@article {pmid23250114, year = {2013}, author = {Shapiro, K and Miller, WA and Silver, MW and Odagiri, M and Largier, JL and Conrad, PA and Mazet, JA}, title = {Research commentary: Association of zoonotic pathogens with fresh, estuarine, and marine macroaggregates.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {928-933}, pmid = {23250114}, issn = {1432-184X}, mesh = {Animals ; Bacteria/genetics/*isolation &amp; purification ; Bacteriophages/genetics/*isolation &amp; purification ; Ecosystem ; Fresh Water/microbiology/*parasitology/virology ; Giardia/genetics/*isolation &amp; purification ; Seawater/microbiology/*parasitology/virology ; *Water Microbiology ; Zoonoses/microbiology/*parasitology/transmission/virology ; }, abstract = {Aquatic macroaggregates (flocs ≥ 0.5 mm) provide an important mechanism for vertical flux of nutrients and organic matter in aquatic ecosystems, yet their role in the transport and fate of zoonotic pathogens is largely unknown. Terrestrial pathogens that enter coastal waters through contaminated freshwater runoff may be especially prone to flocculation due to fluid dynamics and electrochemical changes that occur where fresh and marine waters mix. In this study, laboratory experiments were conducted to evaluate whether zoonotic pathogens (Cryptosporidium, Giardia, Salmonella) and a virus surrogate (PP7) are associated with aquatic macroaggregates and whether pathogen aggregation is enhanced in saline waters. Targeted microorganisms showed increased association with macroaggregates in estuarine and marine waters, as compared with an ultrapure water control and natural freshwater. Enrichment factor estimations demonstrated that pathogens are 2-4 orders of magnitude more concentrated in aggregates than in the estuarine and marine water surrounding the aggregates. Pathogen incorporation into aquatic macroaggregates may influence their transmission to susceptible hosts through settling and subsequent accumulation in zones where aggregation is greatest, as well as via enhanced uptake by invertebrates that serve as prey for marine animals or as seafood for humans.}, }
@article {pmid23242136, year = {2013}, author = {Brock, AK and Berger, B and Mewis, I and Ruppel, S}, title = {Impact of the PGPB Enterobacter radicincitans DSM 16656 on growth, glucosinolate profile, and immune responses of Arabidopsis thaliana.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {661-670}, pmid = {23242136}, issn = {1432-184X}, mesh = {Arabidopsis/genetics/*growth &amp; development/immunology/*microbiology ; Arabidopsis Proteins/genetics/immunology ; Cyclopentanes/immunology ; Endophytes/*physiology ; Enterobacter/*physiology ; Ethylenes/immunology ; Gene Expression Regulation, Plant ; Glucosinolates/*immunology ; Oxylipins/immunology ; Plant Growth Regulators/immunology ; Salicylic Acid/immunology ; }, abstract = {Plant growth-promoting bacteria (PGPB) affect plant cellular processes in various ways. The endophytic bacterial strain Enterobacter radicincitans DSM 16656 has been shown to improve plant growth and yield in various agricultural and vegetable crops. Besides its ability to fix atmospheric nitrogen, produce phytohormones, and solubilize phosphate compounds, the strain is highly competitive against native endophytic organisms and colonizes the endorhizosphere in high numbers. Here, we show that E. radicincitans inoculation of the noncrop plant Arabidopsis thaliana promotes plant growth. Furthermore, high performance liquid chromatography (HPLC) analysis revealed that bacterial inoculation slightly decreased amounts of aliphatic glucosinolates in plant leaves in a fast-growing stage but increased these compounds in an older phase where growth is mostly completed. This effect seems to correlate with developmental stage and depends on the nitrogen requirement. Additionally, nitrogen deficiency studies with seedlings grown on medium containing different nitrogen concentrations suggest that plant nitrogen demand can influence the intensity of plant growth enhancement by E. radicincitans. This endophyte seems not to activate stress-inducible mitogen-activated protein kinases (MAPKs). Analyzing transcription of the defense-related genes PR1, PR2, PR5, and PDF1.2 by quantitative real time polymerase chain reaction (qPCR) revealed that E. radicincitans DSM 16656 is able to induce priming via salicylic acid (SA) or jasmonate (JA)/ethylene (ET) signaling pathways to protect plants against potential pathogen attack.}, }
@article {pmid23240815, year = {2013}, author = {Lawley, TD and Walker, AW}, title = {Intestinal colonization resistance.}, journal = {Immunology}, volume = {138}, number = {1}, pages = {1-11}, pmid = {23240815}, issn = {1365-2567}, support = {/WT_/Wellcome Trust/United Kingdom ; 93614/MRC_/Medical Research Council/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; 076964/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Gastrointestinal Tract/*immunology/metabolism/*microbiology ; Humans ; Microbial Interactions ; }, abstract = {Dense, complex microbial communities, collectively termed the microbiota, occupy a diverse array of niches along the length of the mammalian intestinal tract. During health and in the absence of antibiotic exposure the microbiota can effectively inhibit colonization and overgrowth by invading microbes such as pathogens. This phenomenon is called 'colonization resistance' and is associated with a stable and diverse microbiota in tandem with a controlled lack of inflammation, and involves specific interactions between the mucosal immune system and the microbiota. Here we overview the microbial ecology of the healthy mammalian intestinal tract and highlight the microbe-microbe and microbe-host interactions that promote colonization resistance. Emerging themes highlight immunological (T helper type 17/regulatory T-cell balance), microbiota (diverse and abundant) and metabolic (short-chain fatty acid) signatures of intestinal health and colonization resistance. Intestinal pathogens use specific virulence factors or exploit antibiotic use to subvert colonization resistance for their own benefit by triggering inflammation to disrupt the harmony of the intestinal ecosystem. A holistic view that incorporates immunological and microbiological facets of the intestinal ecosystem should facilitate the development of immunomodulatory and microbe-modulatory therapies that promote intestinal homeostasis and colonization resistance.}, }
@article {pmid23236009, year = {2013}, author = {Pérez-Cobas, AE and Gosalbes, MJ and Friedrichs, A and Knecht, H and Artacho, A and Eismann, K and Otto, W and Rojo, D and Bargiela, R and von Bergen, M and Neulinger, SC and Däumer, C and Heinsen, FA and Latorre, A and Barbas, C and Seifert, J and dos Santos, VM and Ott, SJ and Ferrer, M and Moya, A}, title = {Gut microbiota disturbance during antibiotic therapy: a multi-omic approach.}, journal = {Gut}, volume = {62}, number = {11}, pages = {1591-1601}, pmid = {23236009}, issn = {1468-3288}, mesh = {Aged ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/isolation &amp; purification ; Bacterial Typing Techniques/methods ; Biodiversity ; DNA, Bacterial/analysis ; Feces/microbiology ; Gastrointestinal Tract/metabolism/*microbiology ; Gene Expression Profiling/methods ; Gene Expression Regulation/drug effects ; Humans ; Male ; Metabolome/drug effects ; Microbiota/*drug effects ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; beta-Lactams/*pharmacology ; }, abstract = {OBJECTIVE: Antibiotic (AB) usage strongly affects microbial intestinal metabolism and thereby impacts human health. Understanding this process and the underlying mechanisms remains a major research goal. Accordingly, we conducted the first comparative omic investigation of gut microbial communities in faecal samples taken at multiple time points from an individual subjected to β-lactam therapy.<br><br>METHODS: The total (16S rDNA) and active (16S rRNA) microbiota, metagenome, metatranscriptome (mRNAs), metametabolome (high-performance liquid chromatography coupled to electrospray ionisation and quadrupole time-of-flight mass spectrometry) and metaproteome (ultra high performing liquid chromatography coupled to an Orbitrap MS(2) instrument [UPLC-LTQ Orbitrap-MS/MS]) of a patient undergoing AB therapy for 14 days were evaluated.<br><br>RESULTS: Apparently oscillatory population dynamics were observed, with an early reduction in Gram-negative organisms (day 6) and an overall collapse in diversity and possible further colonisation by 'presumptive' naturally resistant bacteria (day 11), followed by the re-growth of Gram-positive species (day 14). During this process, the maximum imbalance in the active microbial fraction occurred later (day 14) than the greatest change in the total microbial fraction, which reached a minimum biodiversity and richness on day 11; additionally, major metabolic changes occurred at day 6. Gut bacteria respond to ABs early by activating systems to avoid the antimicrobial effects of the drugs, while 'presumptively' attenuating their overall energetic metabolic status and the capacity to transport and metabolise bile acid, cholesterol, hormones and vitamins; host-microbial interactions significantly improved after treatment cessation.<br><br>CONCLUSIONS: This proof-of-concept study provides an extensive description of gut microbiota responses to follow-up &#x3b2;-lactam therapy. The results demonstrate that ABs targeting specific pathogenic infections and diseases may alter gut microbial ecology and interactions with host metabolism at a much higher level than previously assumed.}, }
@article {pmid23235287, year = {2013}, author = {Van den Abbeele, P and Belzer, C and Goossens, M and Kleerebezem, M and De Vos, WM and Thas, O and De Weirdt, R and Kerckhof, FM and Van de Wiele, T}, title = {Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model.}, journal = {The ISME journal}, volume = {7}, number = {5}, pages = {949-961}, pmid = {23235287}, issn = {1751-7370}, mesh = {Acyl Coenzyme A/metabolism ; Adult ; Butyrates/metabolism ; Clostridium/classification/genetics/*isolation &amp; purification/*physiology ; Colon/chemistry/*microbiology ; Ecosystem ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Intestinal Mucosa/microbiology ; Male ; *Models, Biological ; Monte Carlo Method ; Mucins/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The human gut is colonized by a complex microbiota with multiple benefits. Although the surface-attached, mucosal microbiota has a unique composition and potential to influence human health, it remains difficult to study in vivo. Therefore, we performed an in-depth microbial characterization (human intestinal tract chip (HITChip)) of a recently developed dynamic in vitro gut model, which simulates both luminal and mucosal gut microbes (mucosal-simulator of human intestinal microbial ecosystem (M-SHIME)). Inter-individual differences among human subjects were confirmed and microbial patterns unique for each individual were preserved in vitro. Furthermore, in correspondence with in vivo studies, Bacteroidetes and Proteobacteria were enriched in the luminal content while Firmicutes rather colonized the mucin layer, with Clostridium cluster XIVa accounting for almost 60% of the mucin-adhered microbiota. Of the many acetate and/or lactate-converting butyrate producers within this cluster, Roseburia intestinalis and Eubacterium rectale most specifically colonized mucins. These 16S rRNA gene-based results were confirmed at a functional level as butyryl-CoA:acetate-CoA transferase gene sequences belonged to different species in the luminal as opposed to the mucin-adhered microbiota, with Roseburia species governing the mucosal butyrate production. Correspondingly, the simulated mucosal environment induced a shift from acetate towards butyrate. As not only inter-individual differences were preserved but also because compared with conventional models, washout of relevant mucin-adhered microbes was avoided, simulating the mucosal gut microbiota represents a breakthrough in modeling and mechanistically studying the human intestinal microbiome in health and disease. Finally, as mucosal butyrate producers produce butyrate close to the epithelium, they may enhance butyrate bioavailability, which could be useful in treating diseases, such as inflammatory bowel disease.}, }
@article {pmid23233090, year = {2013}, author = {Patin, NV and Kunin, V and Lidström, U and Ashby, MN}, title = {Effects of OTU clustering and PCR artifacts on microbial diversity estimates.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {709-719}, pmid = {23233090}, issn = {1432-184X}, mesh = {Actinomycetales/classification/*genetics/isolation &amp; purification ; *Biodiversity ; DNA Primers/genetics ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction/methods/*standards ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Next-generation sequencing has increased the coverage of microbial diversity surveys by orders of magnitude, but differentiating artifacts from rare environmental sequences remains a challenge. Clustering 16S rRNA sequences into operational taxonomic units (OTUs) organizes sequence data into groups of 97 % identity, helping to reduce data volumes and avoid analyzing sequencing artifacts by grouping them with real sequences. Here, we analyze sequence abundance distributions across environmental samples and show that 16S rRNA sequences of >99 % identity can represent functionally distinct microorganisms, rendering OTU clustering problematic when the goal is an accurate analysis of organism distribution. Strict postsequencing quality control (QC) filters eliminated the most prevalent artifacts without clustering. Further experiments proved that DNA polymerase errors in polymerase chain reaction (PCR) generate a significant number of substitution errors, most of which pass QC filters. Based on our findings, we recommend minimizing the number of PCR cycles in DNA library preparation and applying strict postsequencing QC filters to reduce the most prevalent artifacts while maintaining a high level of accuracy in diversity estimates. We further recommend correlating rare and abundant sequences across environmental samples, rather than clustering into OTUs, to identify remaining sequence artifacts without losing the resolution afforded by high-throughput sequencing.}, }
@article {pmid23229414, year = {2013}, author = {Mahanty, B and Kim, S and Kim, CG}, title = {Assessment of a biostimulated or bioaugmented calcification system with Bacillus pasteurii in a simulated soil environment.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {679-688}, pmid = {23229414}, issn = {1432-184X}, mesh = {Bacillus/*metabolism ; Calcium/metabolism ; Calcium Carbonate/*metabolism ; Soil/analysis ; *Soil Microbiology ; }, abstract = {To evaluate how native soil microorganism and nutrients interact in a bioaugmented or biostimulated calcification process, batch experiments were conducted in saturated soil extract either amended with Bacillus pasteurii and/or NB-NH4Cl media (nutrient broth, 3.0 g/L; NH4Cl, 10.0 g/L; NaHCO3, 2.12 g/L). The NB-NH4Cl medium was chosen out of three potential candidates, where B. pasteurii precipitated the maximum amount of calcium (>95 %) as calcite in 12 h of incubation. The addition of B. pasteurii into saturated soil extract marginally improved the calcification to 4.26 % compared to the unamended control (3.2 %). Calcification with B. pasteurii in autoclaved soil extract was even better (18.75 %). However, the addition of the NB-NH4Cl medium into the soil extract could significantly improve the calcification irrespective of whether B. pasteurii was added (88.46 %) or not (77.04 %). It suggests that soil microbial activity was not limiting even though soil nutrient was inadequate. It also indicates a possible negative interaction between soil microorganisms and B. pasteurii under nutrient-limited conditions.}, }
@article {pmid23227894, year = {2013}, author = {Berleman, J and Auer, M}, title = {The role of bacterial outer membrane vesicles for intra- and interspecies delivery.}, journal = {Environmental microbiology}, volume = {15}, number = {2}, pages = {347-354}, doi = {10.1111/1462-2920.12048}, pmid = {23227894}, issn = {1462-2920}, mesh = {Bacterial Outer Membrane Proteins/*metabolism ; Bacterial Proteins/metabolism ; Biological Transport ; DNA, Bacterial/genetics ; Drug Delivery Systems ; Gram-Negative Bacteria/metabolism/pathogenicity/*physiology ; }, abstract = {An increasing number of Gram-negative bacteria have been observed to secrete outer membrane vesicles (OMVs). Many mysteries remain with respect to OMV formation, the regulation of OMV content and mode of targeting and fusion. Bacterial OMVs appear to serve a variety of purposes in intra- and interspecies microbial extracellular activities. OMVs have been shown to mediate cell-to-cell exchange of DNA, protein and small signalling molecules. The impact of such material exchanges on microbial communities and pathogenic processes, including the delivery of toxins at high concentration through OMVs, is discussed. This rather recent aspect of microbial ecology is likely to remain an important area of research as an in-depth understanding of OMVs may allow new approaches for combating bacterial infections and provide new routes for selective drug delivery.}, }
@article {pmid23227825, year = {2013}, author = {Steenbergh, AK and Bodelier, PL and Heldal, M and Slomp, CP and Laanbroek, HJ}, title = {Does microbial stoichiometry modulate eutrophication of aquatic ecosystems?.}, journal = {Environmental microbiology}, volume = {15}, number = {5}, pages = {1572-1579}, doi = {10.1111/1462-2920.12042}, pmid = {23227825}, issn = {1462-2920}, mesh = {Archaea/*metabolism ; Bacteria/*metabolism ; Baltic States ; Carbon/metabolism ; *Ecosystem ; *Eutrophication ; Geologic Sediments/microbiology ; Nitrogen/metabolism ; Oceans and Seas ; Phosphorus/metabolism ; }, abstract = {The stoichiometry of prokaryotes (Bacteria and Archaea) can control benthic phosphorus (P) fluxes relative to carbon (C) and nitrogen (N) during organic matter remineralization. This paper presents the first experimental data on benthic microbial stoichiometry. We used X-ray microanalysis to determine C : N : P ratios of individual prokaryotes from C-limited Baltic Sea sediments incubated under oxic or anoxic conditions. At approximately 400:1, C : P ratios of prokaryotes from both oxic and anoxic incubations were higher than the Redfield ratio for marine organic matter (106:1), whereas prokaryotic C : N ratios (6.4:1) were close to the Redfield ratio. We conclude that high microbial C : P ratios contribute to the enhanced remineralization of P from organic matter relative to C and N observed in many low oxygen marine settings.}, }
@article {pmid23226495, year = {2012}, author = {Bass, D and Yabuki, A and Santini, S and Romac, S and Berney, C}, title = {Reticulamoeba is a long-branched Granofilosean (Cercozoa) that is missing from sequence databases.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e49090}, pmid = {23226495}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Cercozoa/classification/*genetics ; DNA Primers ; *Databases, Genetic ; Information Storage and Retrieval ; Likelihood Functions ; Phylogeny ; }, abstract = {We sequenced the 18S ribosomal RNA gene of seven isolates of the enigmatic marine amoeboflagellate Reticulamoeba Grell, which resolved into four genetically distinct Reticulamoeba lineages, two of which correspond to R. gemmipara Grell and R. minor Grell, another with a relatively large cell body forming lacunae, and another that has similarities to both R. minor and R. gemmipara but with a greater propensity to form cell clusters. These lineages together form a long-branched clade that branches within the cercozoan class Granofilosea (phylum Cercozoa), showing phylogenetic affinities with the genus Mesofila. The basic morphology of Reticulamoeba is a roundish or ovoid cell with a more or less irregular outline. Long and branched reticulopodia radiate from the cell. The reticulopodia bear granules that are bidirectionally motile. There is also a biflagellate dispersal stage. Reticulamoeba is frequently observed in coastal marine environmental samples. PCR primers specific to the Reticulamoeba clade confirm that it is a frequent member of benthic marine microbial communities, and is also found in brackish water sediments and freshwater biofilm. However, so far it has not been found in large molecular datasets such as the nucleotide database in NCBI GenBank, metagenomic datasets in Camera, and the marine microbial eukaryote sampling and sequencing consortium BioMarKs, although closely related lineages can be found in some of these datasets using a highly targeted approach. Therefore, although such datasets are very powerful tools in microbial ecology, they may, for several methodological reasons, fail to detect ecologically and evolutionary key lineages.}, }
@article {pmid23224253, year = {2013}, author = {Ortiz, M and Neilson, JW and Nelson, WM and Legatzki, A and Byrne, A and Yu, Y and Wing, RA and Soderlund, CA and Pryor, BM and Pierson, LS and Maier, RM}, title = {Profiling bacterial diversity and taxonomic composition on speleothem surfaces in Kartchner Caverns, AZ.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {371-383}, pmid = {23224253}, issn = {1432-184X}, mesh = {Arizona ; Bacteria/*classification/genetics/isolation &amp; purification ; *Biodiversity ; Caves/*microbiology ; DNA, Bacterial/genetics ; Gene Library ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Caves are relatively accessible subterranean habitats ideal for the study of subsurface microbial dynamics and metabolisms under oligotrophic, non-photosynthetic conditions. A 454-pyrotag analysis of the V6 region of the 16S rRNA gene was used to systematically evaluate the bacterial diversity of ten cave surfaces within Kartchner Caverns, a limestone cave. Results showed an average of 1,994 operational taxonomic units (97 % cutoff) per speleothem and a broad taxonomic diversity that included 21 phyla and 12 candidate phyla. Comparative analysis of speleothems within a single room of the cave revealed three distinct bacterial taxonomic profiles dominated by either Actinobacteria, Proteobacteria, or Acidobacteria. A gradient in observed species richness along the sampling transect revealed that the communities with lower diversity corresponded to those dominated by Actinobacteria while the more diverse communities were those dominated by Proteobacteria. A 16S rRNA gene clone library from one of the Actinobacteria-dominated speleothems identified clones with 99 % identity to chemoautotrophs and previously characterized oligotrophs, providing insights into potential energy dynamics supporting these communities. The robust analysis conducted for this study demonstrated a rich bacterial diversity on speleothem surfaces. Further, it was shown that seemingly comparable speleothems supported divergent phylogenetic profiles suggesting that these communities are very sensitive to subtle variations in nutritional inputs and environmental factors typifying speleothem surfaces in Kartchner Caverns.}, }
@article {pmid23224222, year = {2013}, author = {Gori, K and Ryssel, M and Arneborg, N and Jespersen, L}, title = {Isolation and identification of the microbiota of Danish farmhouse and industrially produced surface-ripened cheeses.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {602-615}, pmid = {23224222}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Biodiversity ; Cattle ; Cheese/analysis/*microbiology ; Denmark ; *Metagenome ; Milk/*microbiology ; Molecular Sequence Data ; Phylogeny ; Yeasts/classification/genetics/*isolation &amp; purification/metabolism ; }, abstract = {For studying the microbiota of four Danish surface-ripened cheeses produced at three farmhouses and one industrial dairy, both a culture-dependent and culture-independent approach were used. After dereplication of the initial set of 433 isolates by (GTG)5-PCR fingerprinting, 217 bacterial and 25 yeast isolates were identified by sequencing of the 16S rRNA gene or the D1/D2 domain of the 26S rRNA gene, respectively. At the end of ripening, the cheese core microbiota of the farmhouse cheeses consisted of the mesophilic lactic acid bacteria (LAB) starter cultures Lactococcus lactis subsp. lactis and Leuconostoc mesenteorides as well as non-starter LAB including different Lactobacillus spp. The cheese from the industrial dairy was almost exclusively dominated by Lb. paracasei. The surface bacterial microbiota of all four cheeses were dominated by Corynebacterium spp. and/or Brachybacterium spp. Brevibacterium spp. was found to be subdominant compared to other bacteria on the farmhouse cheeses, and no Brevibacterium spp. was found on the cheese from the industrial dairy, even though B. linens was used as surface-ripening culture. Moreover, Gram-negative bacteria identified as Alcalignes faecalis and Proteus vulgaris were found on one of the farmhouse cheeses. The surface yeast microbiota consisted primarily of one dominating species for each cheese. For the farmhouse cheeses, the dominant yeast species were Yarrowia lipolytica, Geotrichum spp. and Debaryomyces hansenii, respectively, and for the cheese from the industrial dairy, D. hansenii was the dominant yeast species. Additionally, denaturing gradient gel electrophoresis (DGGE) analysis revealed that Streptococcus thermophilus was present in the farmhouse raw milk cheese analysed in this study. Furthermore, DGGE bands corresponding to Vagococcus carniphilus, Psychrobacter spp. and Lb. curvatus on the cheese surfaces indicated that these bacterial species may play a role in cheese ripening.}, }
@article {pmid23220956, year = {2013}, author = {Inceoglu, &#xd6; and van Overbeek, LS and Falcão Salles, J and van Elsas, JD}, title = {Normal operating range of bacterial communities in soil used for potato cropping.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {4}, pages = {1160-1170}, pmid = {23220956}, issn = {1098-5336}, mesh = {*Biota ; DNA, Bacterial/chemistry/genetics ; *Metagenome ; Molecular Sequence Data ; Polymerase Chain Reaction ; Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; Solanum tuberosum/*growth &amp; development ; }, abstract = {In this study, the impacts of six potato (Solanum tuberosum) cultivars with different tuber starch allocations (including one genetically modified [GM] line) on the bacterial communities in field soil were investigated across two growth seasons interspersed with 1 year of barley cultivation, using quantitative PCR, clone library, and PCR-denaturing gradient gel electrophoresis (DGGE) analyses. It was hypothesized that the modifications in the tuber starch contents of these plants, yielding changed root growth rates and exudation patterns, might have elicited altered bacterial communities in the soil. The data showed that bacterial abundances in the bulk soil varied over about 2 orders of magnitude across the 3 years. As expected, across all cultivars, positive potato rhizosphere effects on bacterial abundances were noted in the two potato years. The bulk soil bacterial community structures revealed progressive shifts across time, and moving-window analysis revealed a 60% change over the total experiment. Consistent with previous findings, the community structures in the potato rhizosphere compartments were mainly affected by the growth stage of the plants and, to a lesser extent, by plant cultivar type. The data from the soil under the non-GM potato lines were then taken to define the normal operating range (NOR) of the microbiota under potatoes. Interestingly, the bacterial communities under the GM potato line remained within this NOR. In regard to the bacterial community compositions, particular bacterial species in the soil appeared to be specific to (i) the plant species under investigation (barley versus potato) or, with respect to potatoes, (ii) the plant growth stage. Members of the genera Arthrobacter, Streptomyces, Rhodanobacter, and Dokdonella were consistently found only at the flowering potato plants in both seasons, whereas Rhodoplanes and Sporosarcina were observed only in the soil planted to barley.}, }
@article {pmid23216542, year = {2012}, author = {Lwin, KO and Kondo, M and Ban-Tokuda, T and Lapitan, RM and Del-Barrio, AN and Fujihara, T and Matsui, H}, title = {Ruminal fermentation and microbial ecology of buffaloes and cattle fed the same diet.}, journal = {Animal science journal = Nihon chikusan Gakkaiho}, volume = {83}, number = {12}, pages = {767-776}, doi = {10.1111/j.1740-0929.2012.01031.x}, pmid = {23216542}, issn = {1740-0929}, mesh = {Animal Feed ; Animals ; Buffaloes/*microbiology ; Cattle/*microbiology ; *Fermentation ; Fibrobacter/*genetics/isolation &amp; purification ; Fungi ; Gene Library ; Genetic Variation ; Hybridization, Genetic ; Methane/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rumen/metabolism/*microbiology ; }, abstract = {Although buffaloes and cattle are ruminants, their digestive capabilities and rumen microbial compositions are considered to be different. The purpose of this study was to compare the rumen microbial ecology of crossbred water buffaloes and cattle that were fed the same diet. Cattle exhibited a higher fermentation rate than buffaloes. Methane production and methanogen density were lower in buffaloes. Phylogenetic analysis of Fibrobacter succinogenes-specific 16S ribosomal RNA gene clone library showed that the diversity of groups within a species was significantly different (P < 0.05) between buffalo and cattle and most of the clones were affiliated with group 2 of the species. Population densities of F.succinogenes, Ruminococcus albus and R. flavefaciens were higher until 6 h post-feeding in cattle; however, buffaloes exhibited different traits. The population of anaerobic fungi decreased at 3 h in cattle compared to buffaloes and was similar at 0 h and 6 h. The diversity profiles of bacteria and fungi were similar in the two species. The present study showed that the profiles of the fermentation process, microbial population and diversity were similar in crossbred water buffaloes and crossbred cattle.}, }
@article {pmid23212654, year = {2013}, author = {Wang, X and Liu, X and Kono, S and Wang, G}, title = {The ecological perspective of microbial communities in two pairs of competitive Hawaiian native and invasive macroalgae.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {361-370}, pmid = {23212654}, issn = {1432-184X}, mesh = {Bacteria/classification/*isolation &amp; purification ; *Biodiversity ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Gene Library ; Gracilaria/microbiology ; Hawaii ; Introduced Species ; Laurencia/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhodophyta/*microbiology ; Seawater/microbiology ; Seaweed/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Marine macroalgae are known to harbor large populations of microbial symbionts, and yet, microbe symbiosis in invasive macroalgae remains largely unknown. In this study, we applied molecular methods to study microbial communities associated with two invasive algae Acanthophora spicifera and Gracilaria salicornia and the two native algae Gracilaria coronopifolia and Laurencia nidifica at spatial and temporal scales in Hawaiian coral reef ecosystems. Bacterial communities of both the invasive and native macroalgae displayed little spatial and temporal variations, suggesting consistent and stable bacterial associations with these macroalgae. Results of this study identified three types of bacterial populations: nonspecific (present in both algal and water samples); algae-specific (found in all algal species); and species-specific (only found in individual species). The bacterial diversity of invasive algae was lower than that of their native counterparts at phylum and species levels. Notably, the vast majority (71 %) of bacterial communities associated with the invasive algae G. salicornia were representatives of Cyanobacteria, suggesting a potential ecological significance of symbiotic Cyanobacteria.}, }
@article {pmid23212653, year = {2013}, author = {Mijnendonckx, K and Provoost, A and Ott, CM and Venkateswaran, K and Mahillon, J and Leys, N and Van Houdt, R}, title = {Characterization of the survival ability of Cupriavidus metallidurans and Ralstonia pickettii from space-related environments.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {347-360}, pmid = {23212653}, issn = {1432-184X}, mesh = {Biofilms/growth &amp; development ; Cupriavidus/drug effects/genetics/*growth &amp; development/isolation &amp; purification/radiation effects ; DNA, Bacterial/genetics ; Disinfection ; Drinking Water/microbiology ; Drug Resistance, Multiple, Bacterial ; *Environment, Controlled ; Genes, Bacterial ; Phylogeny ; Plasmids/genetics ; RNA, Ribosomal, 16S/genetics ; Ralstonia pickettii/drug effects/genetics/*growth &amp; development/isolation &amp; purification/radiation effects ; Silver/pharmacology ; *Spacecraft ; Sterilization ; Ultraviolet Rays ; }, abstract = {Four Cupriavidus metallidurans and eight Ralstonia pickettii isolates from the space industry and the International Space Station (ISS) were characterized in detail. Nine of the 12 isolates were able to form a biofilm on plastics and all were resistant to several antibiotics. R. pickettii isolates from the surface of the Mars Orbiter prior to flight were 2.5 times more resistant to UV-C(254nm) radiation compared to the R. pickettii type strain. All isolates showed moderate to high tolerance against at least seven different metal ions. They were tolerant to medium to high silver concentrations (0.5-4 μM), which are higher than the ionic silver disinfectant concentrations measured regularly in the drinking water aboard the ISS. Furthermore, all isolates survived a 23-month exposure to 2 μM AgNO(3) in drinking water. These resistance properties are putatively encoded by their endogenous megaplasmids. This study demonstrated that extreme resistance is not required to withstand the disinfection and sterilization procedures implemented in the ISS and space industry. All isolates acquired moderate to high tolerance against several stressors and can grow in oligotrophic conditions, enabling them to persist in these environments.}, }
@article {pmid23204426, year = {2013}, author = {Puentes-Téllez, PE and Hansen, MA and Sørensen, SJ and van Elsas, JD}, title = {Adaptation and heterogeneity of Escherichia coli MC1000 growing in complex environments.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {3}, pages = {1008-1017}, pmid = {23204426}, issn = {1098-5336}, mesh = {*Adaptation, Biological ; Culture Media/chemistry ; DNA, Bacterial/chemistry/genetics ; *Environmental Microbiology ; Escherichia coli/*genetics/*growth &amp; development ; *Genetic Variation ; Genome, Bacterial ; Genotype ; Longitudinal Studies ; Oxygen/metabolism ; Phenotype ; Sequence Analysis, DNA ; }, abstract = {In a study aiming to assess bacterial evolution in complex growth media, we evaluated the long-term adaptive response of Escherichia coli MC1000 in Luria-Bertani (LB) medium. Seven parallel populations were founded and followed over 150 days in sequential batch cultures under three different oxygen conditions (defined environments), and 19 evolved forms were isolated. The emergence of forms with enhanced fitness was evident in competition experiments of all evolved forms versus the ancestral strain. The evolved forms were then subjected to phenotypic and genomic analyses relative to the ancestor. Profound changes were found in their phenotypes as well as whole-genome sequences. Interestingly, considerable heterogeneity was found at the intrapopulational level. However, consistently occurring parallel adaptive responses were found across all populations. The evolved forms all contained a mutation in galR, a repressor of the galactose operon. Concomitantly, the new forms revealed enhanced growth on galactose as well as galactose-containing disaccharides. This response was likely driven by the LB medium.}, }
@article {pmid23204362, year = {2012}, author = {Byappanahalli, MN and Nevers, MB and Korajkic, A and Staley, ZR and Harwood, VJ}, title = {Enterococci in the environment.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {76}, number = {4}, pages = {685-706}, pmid = {23204362}, issn = {1098-5557}, mesh = {Animals ; Drinking Water/microbiology ; Ecosystem ; *Enterococcaceae/classification/isolation &amp; purification/pathogenicity/physiology ; *Environmental Microbiology ; Environmental Monitoring ; Feces/*microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Soil Microbiology ; *Water Microbiology ; *Water Pollution ; }, abstract = {Enterococci are common, commensal members of gut communities in mammals and birds, yet they are also opportunistic pathogens that cause millions of human and animal infections annually. Because they are shed in human and animal feces, are readily culturable, and predict human health risks from exposure to polluted recreational waters, they are used as surrogates for waterborne pathogens and as fecal indicator bacteria (FIB) in research and in water quality testing throughout the world. Evidence from several decades of research demonstrates, however, that enterococci may be present in high densities in the absence of obvious fecal sources and that environmental reservoirs of these FIB are important sources and sinks, with the potential to impact water quality. This review focuses on the distribution and microbial ecology of enterococci in environmental (secondary) habitats, including the effect of environmental stressors; an outline of their known and apparent sources, sinks, and fluxes; and an overview of the use of enterococci as FIB. Finally, the significance of emerging methodologies, such as microbial source tracking (MST) and empirical predictive models, as tools in water quality monitoring is addressed. The mounting evidence for widespread extraenteric sources and reservoirs of enterococci demonstrates the versatility of the genus Enterococcus and argues for the necessity of a better understanding of their ecology in natural environments, as well as their roles as opportunistic pathogens and indicators of human pathogens.}, }
@article {pmid23202435, year = {2013}, author = {Bokulich, NA and Subramanian, S and Faith, JJ and Gevers, D and Gordon, JI and Knight, R and Mills, DA and Caporaso, JG}, title = {Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.}, journal = {Nature methods}, volume = {10}, number = {1}, pages = {57-59}, pmid = {23202435}, issn = {1548-7105}, support = {U54HG004969/HG/NHGRI NIH HHS/United States ; P01 DK078669/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01HD059127/HD/NICHD NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; U54 HG004969/HG/NHGRI NIH HHS/United States ; R01 HD059127/HD/NICHD NIH HHS/United States ; DK78669/DK/NIDDK NIH HHS/United States ; }, mesh = {*Biodiversity ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; *Quality Control ; Sequence Analysis, DNA/*methods ; }, abstract = {High-throughput sequencing has revolutionized microbial ecology, but read quality remains a considerable barrier to accurate taxonomy assignment and α-diversity assessment for microbial communities. We demonstrate that high-quality read length and abundance are the primary factors differentiating correct from erroneous reads produced by Illumina GAIIx, HiSeq and MiSeq instruments. We present guidelines for user-defined quality-filtering strategies, enabling efficient extraction of high-quality data and facilitating interpretation of Illumina sequencing results.}, }
@article {pmid23201093, year = {2013}, author = {Noval Rivas, M and Burton, OT and Wise, P and Zhang, YQ and Hobson, SA and Garcia Lloret, M and Chehoud, C and Kuczynski, J and DeSantis, T and Warrington, J and Hyde, ER and Petrosino, JF and Gerber, GK and Bry, L and Oettgen, HC and Mazmanian, SK and Chatila, TA}, title = {A microbiota signature associated with experimental food allergy promotes allergic sensitization and anaphylaxis.}, journal = {The Journal of allergy and clinical immunology}, volume = {131}, number = {1}, pages = {201-212}, pmid = {23201093}, issn = {1097-6825}, support = {R56 AI100889/AI/NIAID NIH HHS/United States ; T32 HL007627/HL/NHLBI NIH HHS/United States ; AI007512/AI/NIAID NIH HHS/United States ; R21 AI080002/AI/NIAID NIH HHS/United States ; R01 AI085090/AI/NIAID NIH HHS/United States ; AI100889/AI/NIAID NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; AI 080002/AI/NIAID NIH HHS/United States ; DK034854/DK/NIDDK NIH HHS/United States ; T32 AI007512/AI/NIAID NIH HHS/United States ; HL07627/HL/NHLBI NIH HHS/United States ; DK078938/DK/NIDDK NIH HHS/United States ; R01 DK078938/DK/NIDDK NIH HHS/United States ; R56 DK078938/DK/NIDDK NIH HHS/United States ; }, mesh = {Administration, Oral ; Allergens/administration &amp; dosage/immunology ; Anaphylaxis/immunology/microbiology ; Animals ; Disease Susceptibility/immunology ; Female ; Food/adverse effects ; Food Hypersensitivity/*immunology/*microbiology/therapy ; *Food Microbiology ; Immune Tolerance/immunology ; Immunotherapy, Adoptive ; Intestinal Mucosa/immunology/microbiology ; Male ; Metagenome/genetics/*immunology ; Mice ; Mice, Transgenic ; Phylogeny ; T-Lymphocytes, Regulatory/cytology/immunology ; }, abstract = {BACKGROUND: Commensal microbiota play a critical role in maintaining oral tolerance. The effect of food allergy on the gut microbial ecology remains unknown.<br><br>OBJECTIVE: We sought to establish the composition of the gut microbiota in experimental food allergy and its role in disease pathogenesis.<br><br>METHODS: Food allergy-prone mice with a gain-of-function mutation in the IL-4 receptor &#x3b1; chain (Il4raF709) and wild-type (WT) control animals were subjected to oral sensitization with chicken egg ovalbumin (OVA). Enforced tolerance was achieved by using allergen-specific regulatory T (Treg) cells. Community structure analysis of gut microbiota was performed by using a high-density 16S rDNA oligonucleotide microarrays (PhyloChip) and massively parallel pyrosequencing of 16S rDNA amplicons.<br><br>RESULTS: OVA-sensitized Il4raF709 mice exhibited a specific microbiota signature characterized by coordinate changes in the abundance of taxa of several bacterial families, including the Lachnospiraceae, Lactobacillaceae, Rikenellaceae, and Porphyromonadaceae. This signature was not shared by similarly sensitized WT mice, which did not exhibit an OVA-induced allergic response. Treatment of OVA-sensitized Il4raF709 mice with OVA-specific Treg cells led to a distinct tolerance-associated signature coincident with the suppression of the allergic response. The microbiota of allergen-sensitized Il4raF709 mice differentially promoted OVA-specific IgE responses and anaphylaxis when reconstituted in WT germ-free mice.<br><br>CONCLUSION: Mice with food allergy exhibit a specific gut microbiota signature capable of transmitting disease susceptibility and subject to reprogramming by enforced tolerance. Disease-associated microbiota may thus play a pathogenic role in food allergy.}, }
@article {pmid23197942, year = {2012}, author = {Siggins, A and Enright, AM and Abram, F and Botting, C and O'Flaherty, V}, title = {Impact of trichloroethylene exposure on the microbial diversity and protein expression in anaerobic granular biomass at 37°C and 15°C.}, journal = {Archaea (Vancouver, B.C.)}, volume = {2012}, number = {}, pages = {940159}, pmid = {23197942}, issn = {1472-3654}, mesh = {Anaerobiosis ; Biomass ; Bioreactors/*microbiology ; *Biota ; Cluster Analysis ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Metagenome ; Molecular Sequence Data ; Phylogeny ; Proteins/*metabolism ; Proteobacteria/*classification/genetics/metabolism ; Proteome ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Temperature ; Trichloroethylene/*toxicity ; *Water Microbiology ; }, abstract = {Granular biomass from a laboratory-scale anaerobic bioreactor trial was analysed to identify changes in microbial community structure and function in response to temperature and trichloroethylene (TCE). Two bioreactors were operated at 37°C, while two were operated at 15°C. At the time of sampling, one of each temperature pair of bioreactors was exposed to process failure-inducing concentrations of TCE (60 mg L(-1)) while the other served as a TCE-free control. Bacterial community structure was investigated using denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone library analysis. Temperature was identified as an important factor for bacterial community composition, while minor differences were associated with trichloroethylene supplementation. Proteobacteria was the dominant phylum in all bioreactors, while clone library analysis revealed a higher proportion of Bacteroidetes-, Chloroflexi-, and Firmicutes-like clones at 15°C than at 37°C. Comparative metaproteomics in the presence and absence of TCE was carried out by two-dimensional gel electrophoresis (2-DGE), and 28 protein spots were identified, with putative functions related to cellular processes, including methanogenesis, glycolysis, the glyoxylate cycle, and the methyl malonyl pathway. A good agreement between metaproteomic species assignment and phylogenetic information was observed, with 10 of the identified proteins associated with members of the phylum Proteobacteria.}, }
@article {pmid23192699, year = {2013}, author = {Saul-Tcherkas, V and Unc, A and Steinberger, Y}, title = {Soil microbial diversity in the vicinity of desert shrubs.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {689-699}, pmid = {23192699}, issn = {1432-184X}, mesh = {Amaranthaceae/*microbiology ; Artemisia/*microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Desert Climate ; Ecosystem ; Phylogeny ; *Soil Microbiology ; Trees/microbiology ; }, abstract = {Water and nutrient availability are the major limiting factors of biological activity in arid and semiarid ecosystems. Therefore, perennial plants have developed different ecophysiological adaptations to cope with harsh conditions. The chemical profile of the root exudates varies among plant species and this can induce variability in associated microbial populations. We examined the influence of two shrubs species, Artemisia sieberi and Noaea mucronata, on soil microbial diversity. Soil samples were collected monthly, from December 2006 to November 2007, near canopies of both shrubs (0-10-cm depth). Samples were used for abiotic tests and determination of soil bacterial diversity. No significant differences were found in the abiotic variables (soil moisture, total organic matter, and total soluble nitrogen (TSN)) between soil samples collected from under the two shrubs during the study period. No obvious differences in the Shannon-Weaver index, evenness values, or total phylogenetic distances were found for the soil microbial communities. However, detailed denaturing gradient gel electrophoresis (DGGE) clustering as well as taxonomic diversity analyses indicated clear shifts in the soil microbial community composition. These shifts were governed by seasonal variability in water availability and, significantly, by plant species type.}, }
@article {pmid23186036, year = {2012}, author = {van der Ha, D and Nachtergaele, L and Kerckhof, FM and Rameiyanti, D and Bossier, P and Verstraete, W and Boon, N}, title = {Conversion of biogas to bioproducts by algae and methane oxidizing bacteria.}, journal = {Environmental science &amp; technology}, volume = {46}, number = {24}, pages = {13425-13431}, doi = {10.1021/es303929s}, pmid = {23186036}, issn = {1520-5851}, mesh = {Biofuels/*microbiology ; Carbon/analysis ; Carbon Dioxide/pharmacology ; Esters/analysis ; Flocculation/drug effects ; Lipids/*chemistry ; Methylococcaceae/drug effects/growth &amp; development/*metabolism ; Nitrogen/pharmacology ; Polyesters/*metabolism ; Scenedesmus/drug effects/growth &amp; development/*metabolism ; }, abstract = {Biogas produced by anaerobic digestion is typically converted into electricity and low value heat. In this study, biogas is microbially transformed into valuable bioproducts. As proof of principle, the production of feed additives, i.e. lipids and polyhydroxybutyrate, out of biogas was evaluated. In a first stage, the CO2 in a synthetic biogas was photosynthetically fixed by an algae Scenedesmus sp. culture at an average rate of 192 ± 9 mg CO2 L[-1] liquid d[-1], resulting in concomitant O2 production. After N-depletion, more than 30% of the 220 ± 7 mg lipids g[-1] total organic carbon were unsaturated. In a second stage, the theoretical resulting gas mixture of 60% CH4 and 40% O2 was treated by a methane oxidizing Methylocystis parvus culture, with oxidation rates up to 452 ± 7 mg[-1] CH4-C L[-1] liquid d[-1]. By repeated N-limitation, concentrations of 295 ± 50 mg intracellular polyhydroxybutyrate g[-1] cell dry weight were achieved. Finally, a one-stage approach with controlled coculturing of both microbial groups resulted in harvestable bioflocs. This is the first time that a total microbial conversion of both greenhouse gases into biomass was achieved without external O2 provision. Based on these results, a biotechnological approach is discussed whereby all kinds of biogas can be transformed into valuable bioproducts.}, }
@article {pmid23184592, year = {2012}, author = {Kuczynski, J and Stombaugh, J and Walters, WA and González, A and Caporaso, JG and Knight, R}, title = {Using QIIME to analyze 16S rRNA gene sequences from microbial communities.}, journal = {Current protocols in microbiology}, volume = {Chapter 1}, number = {}, pages = {Unit 1E.5.}, pmid = {23184592}, issn = {1934-8533}, support = {HG4872/HG/NHGRI NIH HHS/United States ; T32 GM008759/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; U01 HG004866/HG/NHGRI NIH HHS/United States ; GM65103/GM/NIGMS NIH HHS/United States ; R01 HG004872/HG/NHGRI NIH HHS/United States ; GM8759/GM/NIGMS NIH HHS/United States ; HG4866/HG/NHGRI NIH HHS/United States ; LM9451/LM/NLM NIH HHS/United States ; DK83981/DK/NIDDK NIH HHS/United States ; UH2 DK083981/DK/NIDDK NIH HHS/United States ; P01 DK078669/DK/NIDDK NIH HHS/United States ; UH3 DK083981/DK/NIDDK NIH HHS/United States ; T15 LM009451/LM/NLM NIH HHS/United States ; DK78669/DK/NIDDK NIH HHS/United States ; T32 GM065103/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Biodiversity ; Computational Biology/instrumentation/*methods ; DNA, Bacterial/genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/instrumentation/*methods ; *Software ; }, abstract = {QIIME (canonically pronounced "chime") is a software application that performs microbial community analysis. It is an acronym for Quantitative Insights Into Microbial Ecology, and has been used to analyze and interpret nucleic acid sequence data from fungal, viral, bacterial, and archaeal communities. The following protocols describe how to install QIIME on a single computer and use it to analyze microbial 16S sequence data from nine distinct microbial communities.}, }
@article {pmid23184157, year = {2013}, author = {Otálora, MA and Salvador, C and Martínez, I and Aragón, G}, title = {Does the reproductive strategy affect the transmission and genetic diversity of bionts in cyanolichens? A case study using two closely related species.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {517-530}, pmid = {23184157}, issn = {1432-184X}, mesh = {Cyanobacteria/*genetics ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fungi/*genetics ; *Genetic Variation ; Genetics, Population ; Haplotypes ; Lichens/*genetics ; Phylogeny ; Reproduction ; Sequence Analysis, DNA ; Spain ; Symbiosis ; }, abstract = {Observed levels of population genetic diversity are often associated with differences in species dispersal and reproductive strategies. In symbiotic organisms, the genetic diversity level of each biont should also be highly influenced by biont transmission. In this study, we evaluated the influence of the reproductive strategies of cyanolichen species on the current levels of population genetic diversity of bionts. To eliminate any phylogenetic noise, we selected two closely related species within the genus Degelia, which only differ in their reproductive systems. We sampled all known populations of both species in central Spain and genotyped the fungal and cyanobacterial components of lichen samples using DNA sequences as molecular markers. We applied population genetics approaches to evaluate the genetic diversity and population genetic structure of the symbiotic components of both lichen species. Our results indicate that fungal and cyanobiont genetic diversity is highly influenced by the reproductive systems of lichen fungus. We detected higher bionts genetic diversity values in the sexual species Degelia plumbea. By contrast, the levels of fungal and cyanobiont genetic diversity in the asexual species Degelia atlantica were extremely low (almost clonal), and the species shows a high specificity towards its cyanobiont. Our results indicate that reproduction by vegetative propagules, in species of the genus Degelia, favors vertical transmission and clonality, which affects the species' capacity for resources and competition, thereby limiting the species to restricted niches.}, }
@article {pmid23184156, year = {2013}, author = {Mendes-Soares, H and Velicer, GJ}, title = {Decomposing predation: testing for parameters that correlate with predatory performance by a social bacterium.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {415-423}, pmid = {23184156}, issn = {1432-184X}, support = {R01 GM079690/GM/NIGMS NIH HHS/United States ; }, mesh = {*Food Chain ; Myxococcus xanthus/*growth &amp; development/physiology ; *Soil Microbiology ; }, abstract = {Predator-prey interactions presumably play major roles in shaping the composition and dynamics of microbial communities. However, little is understood about the population biology of such interactions or how predation-related parameters vary or correlate across prey environments. Myxococcus xanthus is a motile soil bacterium that feeds on a broad range of other soil microbes that vary greatly in the degree to which they support M. xanthus growth. In order to decompose predator-prey interactions at the population level, we quantified five predation-related parameters during M. xanthus growth on nine phylogenetically diverse bacterial prey species. The horizontal expansion rate of swarming predator colonies fueled by prey lawns served as our measure of overall predatory performance, as it incorporates both the searching (motility) and handling (killing and consumption of prey) components of predation. Four other parameters-predator population growth rate, maximum predator yield, maximum prey kill, and overall rate of prey death-were measured from homogeneously mixed predator-prey lawns from which predator populations were not allowed to expand horizontally by swarming motility. All prey species fueled predator population growth. For some prey, predator-specific prey death was detected contemporaneously with predator population growth, whereas killing of other prey species was detected only after cessation of predator growth. All four of the alternative parameters were found to correlate significantly with predator swarm expansion rate to varying degrees, suggesting causal interrelationships among these diverse predation measures. More broadly, our results highlight the importance of examining multiple parameters for thoroughly understanding the population biology of microbial predation.}, }
@article {pmid23184155, year = {2013}, author = {Birri, DJ and Brede, DA and Tessema, GT and Nes, IF}, title = {Bacteriocin production, antibiotic susceptibility and prevalence of haemolytic and gelatinase activity in faecal lactic acid bacteria isolated from healthy Ethiopian infants.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {504-516}, pmid = {23184155}, issn = {1432-184X}, mesh = {Bacteriocins/*biosynthesis ; Cytotoxins/biosynthesis ; DNA, Bacterial/genetics ; *Drug Resistance, Bacterial ; Enterococcus/drug effects/genetics/isolation &amp; purification/metabolism ; Ethiopia ; Feces/*microbiology ; Female ; Gelatinases/metabolism ; Hemolysis ; Humans ; Infant ; Infant, Newborn ; Lactic Acid/metabolism ; Lactobacillus/drug effects/genetics/isolation &amp; purification/metabolism ; Male ; Microbial Sensitivity Tests ; RNA, Ribosomal, 16S/genetics ; Streptococcus/drug effects/genetics/isolation &amp; purification/metabolism ; Virulence Factors/analysis ; }, abstract = {The objective of this study was to characterise lactic acid bacteria (LAB) isolated from faecal samples of healthy Ethiopian infants, with emphasis on bacteriocin production and antibiotic susceptibility. One hundred fifty LAB were obtained from 28 healthy Ethiopian infants. The isolates belonged to Lactobacillus (81/150), Enterococcus (54/150) and Streptococcus (15/150) genera. Lactobacillus species were more abundant in the breast-fed infants while Enterococcus dominated the mixed-fed population. Bacteriocin-producing LAB species were isolated from eight of the infants. Many different bacteriocins were identified, including one new bacteriocin from Streptococcus salivarius, avicin A (class IIa) from Enterococcus avium, one class IIa bacteriocin from Enterococcus faecalis strains, one unknown bacteriocin from E. faecalis and two unknown bacteriocins from Lactobacillus fermentum strains and the two-peptide gassericin T from Lactobacillus gasseri isolate. Susceptibility tests performed for nine antibiotics suggest that some lactobacilli might have acquired resistance to erythromycin (3 %) and tetracycline (4 %) only. The streptococci were generally antibiotic sensitive except for penicillin, to which they showed intermediate resistance. All enterococci were susceptible to ampicillin while 13 % showed penicillin resistance. Only one E. faecalis isolate was vancomycin-resistant. Tetracycline (51 %) and erythromycin (26 %) resistance was prevalent among the enterococci, but multidrug resistance was confined to E. faecalis (47 %) and Enterococcus faecium (33 %). Screening of enterococcal virulence traits revealed that 2 % were β-haemolytic. The structural genes of cytolysin were detected in 28 % of the isolates in five enterococcal species, the majority being E. faecalis and Enterococcus raffinosus. This study shows that bacteriocin production and antibiotic resistance is a common trait of faecal LAB of Ethiopian infants while virulence factors occur at low levels.}, }
@article {pmid23183250, year = {2013}, author = {Hazen, TC and Rocha, AM and Techtmann, SM}, title = {Advances in monitoring environmental microbes.}, journal = {Current opinion in biotechnology}, volume = {24}, number = {3}, pages = {526-533}, doi = {10.1016/j.copbio.2012.10.020}, pmid = {23183250}, issn = {1879-0429}, mesh = {DNA/genetics/isolation &amp; purification ; Ecology/*methods ; *Environmental Microbiology ; Environmental Monitoring/*methods ; Metagenomics/methods ; Sample Size ; Sequence Analysis ; }, abstract = {Culture-independent approaches, such as next-generation sequencing and microarray-based tools, provide insight into the identity and functional diversity of microbial communities. Although these approaches are potentially powerful tools in understanding microbial structure and function, there are a number of limitations that may bias conclusions. In order to mitigate these biases, an understanding of potential biases within each stage of the experimental process is necessary. This review focuses on the biases associated with sample collection, nucleic acid extraction, processing, sequencing analyses, and Chip technologies used in microbial ecology studies.}, }
@article {pmid23182864, year = {2013}, author = {Singh, S and Eldin, C and Kowalczewska, M and Raoult, D}, title = {Axenic culture of fastidious and intracellular bacteria.}, journal = {Trends in microbiology}, volume = {21}, number = {2}, pages = {92-99}, doi = {10.1016/j.tim.2012.10.007}, pmid = {23182864}, issn = {1878-4380}, mesh = {*Axenic Culture ; Bacteria/*growth &amp; development ; }, abstract = {The culture of microorganisms has been the basis of microbiology. However, revolutionary tools such as metagenomics have made it possible to describe uncultivated bacteria, but several breakthroughs have occurred in culture leading to a revival of these techniques. In this review we focus on new applications that have successfully cultivated previously uncultivated bacteria. We also review the axenic cultivation of intracellular bacteria such as Tropheryma whipplei and Coxiella burnetii. These successes provide new tools for the design of axenic media for intracellular bacteria, such as Rickettsiae and Chlamydiae, or historically uncultivable pathogens, such as Mycobacterium leprae and Treponema pallidum. The future axenic culture of these microorganisms will facilitate antibiotic susceptibility testing and will provide insight into their microbial ecology and pathogenicity.}, }
@article {pmid23178724, year = {2013}, author = {Kim, SJ and Weon, HY and Ahn, JH and Hong, SB and Seok, SJ and Whang, KS and Kwon, SW}, title = {Roseomonas aerophila sp. nov., isolated from air.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {63}, number = {Pt 6}, pages = {2334-2337}, doi = {10.1099/ijs.0.046482-0}, pmid = {23178724}, issn = {1466-5034}, mesh = {*Air Microbiology ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Methylobacteriaceae/*classification/genetics/isolation &amp; purification ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sequence Analysis, DNA ; Ubiquinone/analysis ; }, abstract = {An aerobic, Gram-stain-negative, motile, mesophilic bacterium, designated strain 7515T-07(T), was isolated from an air sample in the Taean region, Republic of Korea. The strain grew at 4-40 °C (optimum, 30 °C) and pH 5.0-9.0 (optimum, pH 7.0). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 7515T-07(T) was related to members of the genus Roseomonas and had highest 16S rRNA gene sequence similarity with Roseomonas ludipueritiae 170/96(T) (96.7%). 16S RNA gene sequence similarity between strain 7515T-07(T) and Roseomonas gilardii ATCC 49956(T) (the type species of the genus Roseomonas) was 93.4%. Strain 7515T-07(T) contained Q-10 as the ubiquinone and C18:1ω7c and C19:0 cyclo ω8c as the dominant fatty acids (>10%). The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and two unidentified aminolipids. The DNA G+C content was 73.0 mol%. Combined data from phenotypic, phylogenetic and chemotaxonomic studies demonstrated that strain 7515T-07(T) is a representative of a novel species of the genus Roseomonas, for which the name Roseomonas aerophila sp. nov. is proposed. The type strain is 7515T-07(T) (=KACC 16529(T)=NBRC 108923(T)).}, }
@article {pmid23176460, year = {2012}, author = {Desloover, J and Arends, JB and Hennebel, T and Rabaey, K}, title = {Operational and technical considerations for microbial electrosynthesis.}, journal = {Biochemical Society transactions}, volume = {40}, number = {6}, pages = {1233-1238}, doi = {10.1042/BST20120111}, pmid = {23176460}, issn = {1470-8752}, mesh = {*Bioelectric Energy Sources ; Biofilms ; Carbon Dioxide/chemistry/metabolism ; Electrodes ; Electron Transport ; Hydrogen-Ion Concentration ; Oxidation-Reduction ; Proteobacteria/*metabolism/physiology ; }, abstract = {Extracellular electron transfer has, in one decade, emerged from an environmental phenomenon to an industrial process driver. On the one hand, electron transfer towards anodes leads to production of power or chemicals such as hydrogen, caustic soda and hydrogen peroxide. On the other hand, electron transfer from cathodes enables bioremediation and bioproduction. Although the microbiology of extracellular electron transfer is increasingly being understood, bringing the processes to application requires a number of considerations that are both operational and technical. In the present paper, we investigate the key applied aspects related to electricity-driven bioproduction, including biofilm development, reactor and electrode design, substrate fluxes, surface chemistry, hydrodynamics and electrochemistry, and finally end-product removal/toxicity. Each of these aspects will be critical for the full exploitation of the intriguing physiological feat that extracellular electron transfer is today.}, }
@article {pmid23175332, year = {2012}, author = {Bodaszewska-Lubas, M and Brzychczy-Wloch, M and Gosiewski, T and Heczko, PB}, title = {Antibacterial activity of selected standard strains of lactic acid bacteria producing bacteriocins--pilot study.}, journal = {Postepy higieny i medycyny doswiadczalnej (Online)}, volume = {66}, number = {}, pages = {787-794}, doi = {10.5604/17322693.1015531}, pmid = {23175332}, issn = {1732-2693}, mesh = {Adult ; Antibiosis/*immunology ; Bacteriocins/*biosynthesis ; Female ; Humans ; Infant, Newborn ; Lactic Acid ; Lactobacillus/classification/*immunology/*metabolism ; Lactobacillus plantarum/immunology ; Pilot Projects ; Pregnancy ; Species Specificity ; Streptococcal Infections/immunology/microbiology ; Streptococcus/*immunology ; Vaginitis/immunology/microbiology ; }, abstract = {INTRODUCTION: In this paper, an attempt was made to evaluate the antibacterial potential of standard strains of lactic acid bacteria (LAB) producing bacteriocins of various classes, thus demonstrating various mechanisms of cell membrane damages against the Streptococcus agalactiae strains (Group B Streptococcus, GBS), depending on surface polysaccharides and surface alpha-like protein genes.<br><br>MATERIALS/METHODS: Antimicrobial property of the strains of L. plantarum C 11, L. sakei DSMZ 6333, and L. lactis ATCC 11454 producing bacteriocins: JK and EF plantaricins, sakacin and nisin, respectively, against the GBS strains was evaluated. The chosen to the study GBS strains were represented by serotypes Ia, Ib, II, III, V and they had bca, epsilon, rib, alp2 or alp3 alpha-like protein genes. The experiment was conducted by means of suspension culture and the bacteria count was determined using the serial dilution method.<br><br>RESULTS: A great ability of L. plantarum C 11 strain was proven to inhibit the GBS growth. The strain of L. sakei DSMZ 6333 did not demonstrate any ability to inhibit the growth of GBS, whereas L. lactis ATCC 11454 inhibited the growth of S. agalactiae indicator strains to a minor extent. Statistically significant differences were demonstrated between the GBS strains representing various serotypes against the antimicrobial activity of model LAB strains. The least sensitive to the activity of bacteriocins were the strains representing serotypes Ib and III, whereas the strains representing serotype II were the most sensitive. The sensitivity of the GBS strains to the antimicrobial activity of LAB was not dependent on alpha-like protein genes.<br><br>DISCUSSION: Among the LAB standard strains producing bacteriocins, the strongest antimicrobial property was observed in the strain of L. plantarum C 11. Because of the generally known and verified strong antagonistic property of the strains of L. plantarum species against indicator bacteria, it is necessary to further pursue the research presented in this paper.}, }
@article {pmid23147032, year = {2013}, author = {Sanz, Y and Rastmanesh, R and Agostoni, C}, title = {Understanding the role of gut microbes and probiotics in obesity: how far are we?.}, journal = {Pharmacological research}, volume = {69}, number = {1}, pages = {144-155}, doi = {10.1016/j.phrs.2012.10.021}, pmid = {23147032}, issn = {1096-1186}, mesh = {Animals ; Bacteria/genetics/metabolism ; Gastrointestinal Tract/*metabolism/*microbiology ; Humans ; Metagenome/genetics/physiology ; Obesity/*etiology/metabolism/*microbiology ; Probiotics/*pharmacology ; }, abstract = {Obesity has been associated with structural alterations in the gut microbiota, suggesting potential causality between specific microbial taxa and this disorder. Studies in animal models have also provided evidence for plausible gut microbiota mechanisms of action underlying body weight regulation. Yet evidence identifying which specific microbes contribute to or predict obesity is not completely consistent across studies. More recently, diet has also been shown to be primarily involved in regulating the microbiota structure initially related to obesity, suggesting that the role of microbes in energy balance is under the influence of diet. Controversy over the role of components of the gut microbiota in obesity has extended to bacteria, which although weakly related to body weight in observational and human intervention studies, are of interest due to their use as probiotics. This review focuses exclusively on human observational studies and probiotic intervention trials, excluding animal studies and studies in infants at early developmental stages, since such results cannot be extrapolated to human obesity at later stages in life. In this context, evidence for relationships between the gut microbiota composition and obesity and the possible role of probiotics is reviewed, discussing the strengths and weaknesses of the studies conducted to date.}, }
@article {pmid23145833, year = {2013}, author = {Cray, JA and Russell, JT and Timson, DJ and Singhal, RS and Hallsworth, JE}, title = {A universal measure of chaotropicity and kosmotropicity.}, journal = {Environmental microbiology}, volume = {15}, number = {1}, pages = {287-296}, doi = {10.1111/1462-2920.12018}, pmid = {23145833}, issn = {1462-2920}, support = {BB/F003471/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/F00347/11/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Agar/chemistry ; Hydrophobic and Hydrophilic Interactions ; Linear Models ; Macromolecular Substances/*chemistry/metabolism ; Pressure ; Solutions ; Spectrophotometry ; Temperature ; Water/chemistry ; }, abstract = {Diverse parameters, including chaotropicity, can limit the function of cellular systems and thereby determine the extent of Earth's biosphere. Whereas parameters such as temperature, hydrophobicity, pressure, pH, Hofmeister effects, and water activity can be quantified via standard scales of measurement, the chao-/kosmotropic activities of environmentally ubiquitous substances have no widely accepted, universal scale. We developed an assay to determine and quantify chao-/kosmotropicity for 97 chemically diverse substances that can be universally applied to all solutes. This scale is numerically continuous for the solutes assayed (from +361 kJ kg(-1) mol(-1) for chaotropes to -659 kJ kg(-1) mol(-1) for kosmotropes) but there are key points that delineate (i) chaotropic from kosmotropic substances (i.e. chaotropes ≥ +4; kosmotropes ≤ -4 kJ kg(-1) mol(-1)); and (ii) chaotropic solutes that are readily water-soluble (log P < 1.9) from hydrophobic substances that exert their chaotropic activity, by proxy, from within the hydrophobic domains of macromolecular systems (log P > 1.9). Examples of chao-/kosmotropicity values are, for chaotropes: phenol +143, CaCl(2) +92.2, MgCl(2) +54.0, butanol +37.4, guanidine hydrochloride +31.9, urea +16.6, glycerol [> 6.5 M] +6.34, ethanol +5.93, fructose +4.56; for kosmotropes: proline -5.76, sucrose -6.92, dimethylsulphoxide (DMSO) -9.72, mannitol -6.69, trehalose -10.6, NaCl -11.0, glycine -14.2, ammonium sulfate -66.9, polyethylene glycol- (PEG-)1000 -126; and for relatively neutral solutes: methanol, +3.12, ethylene glycol +1.66, glucose +1.19, glycerol [< 5 M] +1.06, maltose -1.43 (kJ kg(-1) mol(-1)). The data obtained correlate with solute interactions with, and structure-function changes in, enzymes and membranes. We discuss the implications for diverse fields including microbial ecology, biotechnology and astrobiology.}, }
@article {pmid23139734, year = {2012}, author = {Hampton, J and Lladser, ME}, title = {Estimation of distribution overlap of urn models.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e42368}, pmid = {23139734}, issn = {1932-6203}, support = {R01 HG004872/HG/NHGRI NIH HHS/United States ; HG4872/HG/NHGRI NIH HHS/United States ; }, mesh = {Databases as Topic ; Humans ; Metagenome/genetics ; Models, Biological ; *Models, Statistical ; *Probability ; }, abstract = {A classical problem in statistics is estimating the expected coverage of a sample, which has had applications in gene expression, microbial ecology, optimization, and even numismatics. Here we consider a related extension of this problem to random samples of two discrete distributions. Specifically, we estimate what we call the dissimilarity probability of a sample, i.e., the probability of a draw from one distribution not being observed in [Formula: see text] draws from another distribution. We show our estimator of dissimilarity to be a [Formula: see text]-statistic and a uniformly minimum variance unbiased estimator of dissimilarity over the largest appropriate range of [Formula: see text]. Furthermore, despite the non-Markovian nature of our estimator when applied sequentially over [Formula: see text], we show it converges uniformly in probability to the dissimilarity parameter, and we present criteria when it is approximately normally distributed and admits a consistent jackknife estimator of its variance. As proof of concept, we analyze V35 16S rRNA data to discern between various microbial environments. Other potential applications concern any situation where dissimilarity of two discrete distributions may be of interest. For instance, in SELEX experiments, each urn could represent a random RNA pool and each draw a possible solution to a particular binding site problem over that pool. The dissimilarity of these pools is then related to the probability of finding binding site solutions in one pool that are absent in the other.}, }
@article {pmid23138712, year = {2013}, author = {Prakash, O and Shouche, Y and Jangid, K and Kostka, JE}, title = {Microbial cultivation and the role of microbial resource centers in the omics era.}, journal = {Applied microbiology and biotechnology}, volume = {97}, number = {1}, pages = {51-62}, doi = {10.1007/s00253-012-4533-y}, pmid = {23138712}, issn = {1432-0614}, mesh = {Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; *Biodiversity ; *Environmental Microbiology ; Fungi/classification/genetics/growth &amp; development/*isolation &amp; purification ; Metagenomics/*methods ; Microbiological Techniques/*methods ; }, abstract = {Despite tremendous advances in microbial ecology over the past two decades, traditional cultivation methods have failed to grow ecologically more relevant microorganisms in the laboratory, leading to a predominance of weed-like species in the world's culture collections. In this review, we highlight the gap between culture-based and culture-independent methods of microbial diversity analysis, especially in investigations of slow growers, oligotrophs, and fastidious and recalcitrant microorganisms. Furthermore, we emphasize the importance of microbial cultivation and the acquisition of the cultivation-based phenotypic data for the testing of hypotheses arising from genomics and proteomics approaches. Technical difficulties in cultivating novel microorganisms and how modern approaches have helped to overcome these limitations are highlighted. After cultivation, adequate preservation without changes in genotypic and phenotypic features of these microorganisms is necessary for future research and training. Hence, the contribution of microbial resource centers in the handling, preservation, and distribution of this novel diversity is discussed. Finally, we explore the concept of microbial patenting and requisite guidelines of the "Budapest Treaty" for establishment of an International Depositary Authority.}, }
@article {pmid23133394, year = {2012}, author = {Penz, T and Schmitz-Esser, S and Kelly, SE and Cass, BN and Müller, A and Woyke, T and Malfatti, SA and Hunter, MS and Horn, M}, title = {Comparative genomics suggests an independent origin of cytoplasmic incompatibility in Cardinium hertigii.}, journal = {PLoS genetics}, volume = {8}, number = {10}, pages = {e1003012}, pmid = {23133394}, issn = {1553-7404}, support = {P 22703/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Arthropods/microbiology ; Bacterial Proteins/genetics/metabolism ; Bacteroidetes/*genetics/metabolism ; Biological Evolution ; Biosynthetic Pathways ; Cytoplasm/metabolism ; Gene Order ; *Genome, Bacterial ; *Genomics ; Host-Pathogen Interactions ; Symbiosis/genetics ; }, abstract = {Terrestrial arthropods are commonly infected with maternally inherited bacterial symbionts that cause cytoplasmic incompatibility (CI). In CI, the outcome of crosses between symbiont-infected males and uninfected females is reproductive failure, increasing the relative fitness of infected females and leading to spread of the symbiont in the host population. CI symbionts have profound impacts on host genetic structure and ecology and may lead to speciation and the rapid evolution of sex determination systems. Cardinium hertigii, a member of the Bacteroidetes and symbiont of the parasitic wasp Encarsia pergandiella, is the only known bacterium other than the Alphaproteobacteria Wolbachia to cause CI. Here we report the genome sequence of Cardinium hertigii cEper1. Comparison with the genomes of CI-inducing Wolbachia pipientis strains wMel, wRi, and wPip provides a unique opportunity to pinpoint shared proteins mediating host cell interaction, including some candidate proteins for CI that have not previously been investigated. The genome of Cardinium lacks all major biosynthetic pathways but harbors a complete biotin biosynthesis pathway, suggesting a potential role for Cardinium in host nutrition. Cardinium lacks known protein secretion systems but encodes a putative phage-derived secretion system distantly related to the antifeeding prophage of the entomopathogen Serratia entomophila. Lastly, while Cardinium and Wolbachia genomes show only a functional overlap of proteins, they show no evidence of laterally transferred elements that would suggest common ancestry of CI in both lineages. Instead, comparative genomics suggests an independent evolution of CI in Cardinium and Wolbachia and provides a novel context for understanding the mechanistic basis of CI.}, }
@article {pmid23133348, year = {2012}, author = {Kembel, SW and Wu, M and Eisen, JA and Green, JL}, title = {Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance.}, journal = {PLoS computational biology}, volume = {8}, number = {10}, pages = {e1002743}, pmid = {23133348}, issn = {1553-7358}, mesh = {Bacteria/*genetics ; *Biodiversity ; Cluster Analysis ; Computer Simulation ; Databases, Genetic ; *Gene Dosage ; Humans ; Microbial Consortia ; Models, Biological ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Skin/microbiology ; Water Microbiology ; }, abstract = {The abundance of different SSU rRNA ("16S") gene sequences in environmental samples is widely used in studies of microbial ecology as a measure of microbial community structure and diversity. However, the genomic copy number of the 16S gene varies greatly - from one in many species to up to 15 in some bacteria and to hundreds in some microbial eukaryotes. As a result of this variation the relative abundance of 16S genes in environmental samples can be attributed both to variation in the relative abundance of different organisms, and to variation in genomic 16S copy number among those organisms. Despite this fact, many studies assume that the abundance of 16S gene sequences is a surrogate measure of the relative abundance of the organisms containing those sequences. Here we present a method that uses data on sequences and genomic copy number of 16S genes along with phylogenetic placement and ancestral state estimation to estimate organismal abundances from environmental DNA sequence data. We use theory and simulations to demonstrate that 16S genomic copy number can be accurately estimated from the short reads typically obtained from high-throughput environmental sequencing of the 16S gene, and that organismal abundances in microbial communities are more strongly correlated with estimated abundances obtained from our method than with gene abundances. We re-analyze several published empirical data sets and demonstrate that the use of gene abundance versus estimated organismal abundance can lead to different inferences about community diversity and structure and the identity of the dominant taxa in microbial communities. Our approach will allow microbial ecologists to make more accurate inferences about microbial diversity and abundance based on 16S sequence data.}, }
@article {pmid23129136, year = {2013}, author = {Brablcová, L and Buriánková, I and Badurová, P and Rulík, M}, title = {The phylogenetic structure of microbial biofilms and free-living bacteria in a small stream.}, journal = {Folia microbiologica}, volume = {58}, number = {3}, pages = {235-243}, pmid = {23129136}, issn = {1874-9356}, mesh = {Archaea/classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; *Biofilms ; Biomass ; Chemical Phenomena ; Czech Republic ; Geologic Sediments/microbiology ; In Situ Hybridization, Fluorescence ; *Phylogeny ; Rivers/*microbiology ; }, abstract = {The phylogenetic composition, bacterial biomass, and biovolume of both planktonic and biofilm communities were studied in a low-order Bystřice stream near Olomouc City, in the Czech Republic. The aim of the study was to compare the microbial communities colonizing different biofilm substrata (stream aggregates, stream sediment, underwater tree roots, stream stones, and aquatic macrophytes) to those of free-living bacteria. The phylogenetic composition was analyzed using fluorescence in situ hybridization for main phylogenetic groups. All phylogenetic groups studied were detected in all sample types. The stream stone was the substratum where nearly all phylogenetic groups were the most abundant, while the lowest proportion to the DAPI-stained cells was found for free-living bacteria. The probe specific for the domain Bacteria detected 20.6 to 45.8 % of DAPI-stained cells while the probe specific for the domain Archaea detected 4.3 to 17.9 %. The most abundant group of Proteobacteria was Alphaproteobacteria with a mean of 14.2 %, and the least abundant was Betaproteobacteria with a mean of 11.4 %. The average value of the Cytophaga-Flavobacteria group was 10.5 %. Total cell numbers and bacterial biomass were highest in sediment and root biofilm. The value of cell biovolume was highest in stone biofilm and lowest in sediment. Overall, this study revealed relevant differences in phylogenetic composition, bacterial biomass, and biovolume between different stream biofilms and free-living bacteria.}, }
@article {pmid23121623, year = {2013}, author = {Koo, OK and Mertz, AW and Akins, EL and Sirsat, SA and Neal, JA and Morawicki, R and Crandall, PG and Ricke, SC}, title = {Analysis of microbial diversity on deli slicers using polymerase chain reaction and denaturing gradient gel electrophoresis technologies.}, journal = {Letters in applied microbiology}, volume = {56}, number = {2}, pages = {111-119}, doi = {10.1111/lam.12021}, pmid = {23121623}, issn = {1472-765X}, mesh = {Bacteria/classification/*isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/isolation &amp; purification ; Denaturing Gradient Gel Electrophoresis ; Food Contamination/prevention &amp; control ; Food Handling/*instrumentation ; *Food Microbiology ; Polymerase Chain Reaction ; Restaurants ; Sanitation ; }, abstract = {Cross-contamination of pathogenic and spoilage bacteria from food-contact surfaces to food products is a serious public health issue. Bacteria may survive and attach to food-contact surfaces by residual food components and/or background bacteria which may subsequently transfer to other food products. Deli slicers, generally used for slicing ready-to-eat products, can serve as potential sources for considerable bacterial transfer. The objective of this study was to assess the extent and distribution of microbial diversity of deli slicers by identification of pathogenic and background bacteria. Slicer-swab samples were collected from restaurants in Arkansas and Texas in the United States. Ten surface areas for each slicer were swabbed using sterile sponges. Denaturing gradient gel electrophoresis (DGGE) was applied to investigate the fingerprint of samples, and each band was further identified by sequence analysis. Pseudomonads were identified as the dominant bacteria followed by Enterobacteriaceae family, and lactic acid bacteria such as Lactococcus lactis and Streptococcus thermophilus were also found. Bacterial distribution was similar for all surface areas, while the blade guard exhibited the greatest diversity. This study provides a profile of the microbial ecology of slicers using DGGE to develop more specific sanitation practices and to reduce cross-contamination during slicing.}, }
@article {pmid23115974, year = {2012}, author = {Guo, Y and Wu, Y and Lin, X and Zhong, W and Ding, W and Zhu, J and Jia, Z}, title = {[Three successive extractions reduce quantification bias of microbial communities associated with incomplete DNA recovery in soil].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {52}, number = {7}, pages = {894-901}, pmid = {23115974}, issn = {0001-6209}, mesh = {Chemical Fractionation/*methods ; DNA, Archaeal/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics/*isolation &amp; purification ; Desiccation ; Polymerase Chain Reaction ; *Soil Microbiology ; }, abstract = {OBJECTIVE: To assess the quantification bias associated with incomplete extractions of soil microbial DNA and the feasibility of air-dried soil for microbial ecology study.<br><br>METHODS: The flooded rice soil and upland wheat soil were used, and multiple extractions of soil microbial DNA was performed by lysing a single sample for 5 successive times. The copy number of 16S rRNA and amoA genes of Archaea and Bacteria was quantified in each DNA extraction by real-time. PCR.<br><br>RESULTS: Cumulative DNA yields in 3 successive extractions accounted for more than 76% of microbial DNA in soils, and more than 77.5% of gene copies could be recovered. Air-drying decreased the abundance of bacterial 16S rRNA gene and archaeal 16S rRNA gene by 90.3% and 12.5%, and the abundance of bacterial and archaeal amoA genes showed a decline by 81.2% and 84.3%, respectively. The decline showed similar trend in two soils, suggesting air-dried soil could be of choice for biogeographic survey of microbial communities.<br><br>CONCLUSION: Three successive extractions of microbial DNA in soil could be of choice for microbial ecology study in order to reduce quantification bias associated with incomplete DNA recovery. Air-dried soil could be employed under certain circumstances, and further investigation is warranted for the underlying mechanism by which microbial communities manage to survive the desiccation of soil.}, }
@article {pmid23107967, year = {2013}, author = {De Corte, S and Bechstein, S and Lokanathan, AR and Kjems, J and Boon, N and Meyer, RL}, title = {Comparison of bacterial cells and amine-functionalized abiotic surfaces as support for Pd nanoparticle synthesis.}, journal = {Colloids and surfaces. B, Biointerfaces}, volume = {102}, number = {}, pages = {898-904}, doi = {10.1016/j.colsurfb.2012.08.045}, pmid = {23107967}, issn = {1873-4367}, mesh = {Biotechnology/methods ; Chitosan/chemistry ; Nanoparticles/*chemistry ; Nitrophenols/chemistry ; Palladium/*chemistry ; }, abstract = {An increasing demand for catalytic Pd nanoparticles has motivated the search for sustainable production methods. An innovative approach uses bacterial cells as support material for synthesizing Pd nanoparticles by reduction of Pd(II) with e.g. hydrogen or formate. Nevertheless, drawbacks of microbially supported Pd catalysts are the low catalytic activity compared to conventional Pd nanocatalysts and the possible poisoning of the catalyst surface by sulfur originating from bacterial proteins. A recent study showed that amine groups were a key component in surface-supported synthesis of Pd nanoparticles, and that abiotic surfaces could support the Pd particle synthesis as efficiently as bacteria. In this study, we explore the possibility of replacing bacteria with amine-functionalized materials, and we compare different functionalization strategies. Pd nanoparticles formed on the support materials were visualized by transmission electron microscopy, and their activity was evaluated by catalysis of p-nitrophenol reduction. Surfaces functionalized with 3-aminopropyltriethoxysilane and chitosan were interesting alternatives to bacterial cells, as the catalytic activity of Pd particles formed on these surfaces was higher than for Pd particles formed on Shewanella oneidensis cells. Smaller Pd nanoparticles generally have better catalytic properties, and previous studies have shown that the particle size can be lowered by increasing the amount of support material used during Pd particle formation. However, increasing the concentration of S. oneidensis cells beyond a certain threshold lead to deactivation of the Pd catalyst. This was not observed for the sulfur-free support materials, implying that such amine-rich materials can provide an excellent support for environmentally friendly synthesis of surface-immobilized Pd nanoparticles.}, }
@article {pmid23107503, year = {2012}, author = {Sekwati-Monang, B and Valcheva, R and Gänzle, MG}, title = {Microbial ecology of sorghum sourdoughs: effect of substrate supply and phenolic compounds on composition of fermentation microbiota.}, journal = {International journal of food microbiology}, volume = {159}, number = {3}, pages = {240-246}, doi = {10.1016/j.ijfoodmicro.2012.09.013}, pmid = {23107503}, issn = {1879-3460}, mesh = {Bacterial Load ; *Fermentation ; *Food Microbiology ; Glycerol/analysis/metabolism ; Lactobacillus/growth &amp; development/metabolism/*physiology ; *Metagenome ; Polymerase Chain Reaction ; Sorghum/metabolism/microbiology ; Triticum/microbiology ; }, abstract = {The choice of the cereal substrate determines sourdough microbiota, however, the substrate-associated ecological factors for this phenomenon have not been elucidated. This study investigated the competitiveness of Lactobacillus sanfranciscensis LTH 2590, a wheat sourdough isolate, and four isolates from sorghum sourdoughs (ting), Lactobacillus casei FUA3166, Lactobacillus harbinensis FUA3199, Lactobacillus parabuchneri FUA3169, and Lactobacillus coryniformis FUA3307, in sorghum sourdoughs, sorghum sourdoughs supplemented with maltose, or wheat sourdoughs. Fermentations were characterised by determination of cell counts, pH, and quantification of metabolites. Maltose was the main carbon source in wheat sourdoughs whereas glucose was the major carbon source in sorghum. L. coryniformis and L. parabuchneri produced 1,3- and 1,2-propanediol from glycerol and lactate, respectively, metabolites that were previously not observed in sourdough. To determine the competitiveness of strains, wheat and sorghum slurries were inoculated with equal cells counts of L. sanfranciscensis, L. parabuchneri, and L. casei fermented at 28°C or 34°C and propagated by back-slopping every 24h. Lactobacilli in sourdough were quantified by plating and species-specific quantitative PCR (qPCR). Generally, sorghum and wheat sourdoughs inoculated with isolates from ting gave no appreciable differences in the metabolites produced during the fermentation process. L. sanfranciscensis grew in wheat but not in sorghum sourdoughs, or sorghum sourdoughs supplemented with 2% maltose, 1% tryptone, 0.1% l-cysteine and 2% sucrose. Furthermore, L.sanfranciscensis decreased progressively during propagation of sorghum sourdoughs but ting isolates were overgrown by L. sanfranciscensis after three propagations in wheat sourdoughs independent of the incubation temperature. The anti-microbial activity of four different types of sorghum extracts was tested against L. sanfranciscensis, L. parabuchneri, and L. casei to correlate the resistance to phenolic compounds to growth in wheat or sorghum sourdoughs. L. sanfranciscensis was inhibited by phenolic extracts from sorghum flours whereas ting isolates were resistant. In conclusion, microbiota of sorghum sourdough differ from wheat and rye because sorghum contains active concentrations of antimicrobial phenolic compounds, and offers glucose as major carbon source.}, }
@article {pmid23105050, year = {2012}, author = {Pester, M and Brambilla, E and Alazard, D and Rattei, T and Weinmaier, T and Han, J and Lucas, S and Lapidus, A and Cheng, JF and Goodwin, L and Pitluck, S and Peters, L and Ovchinnikova, G and Teshima, H and Detter, JC and Han, CS and Tapia, R and Land, ML and Hauser, L and Kyrpides, NC and Ivanova, NN and Pagani, I and Huntmann, M and Wei, CL and Davenport, KW and Daligault, H and Chain, PS and Chen, A and Mavromatis, K and Markowitz, V and Szeto, E and Mikhailova, N and Pati, A and Wagner, M and Woyke, T and Ollivier, B and Klenk, HP and Spring, S and Loy, A}, title = {Complete genome sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and Desulfosporosinus acidiphilus DSM22704T.}, journal = {Journal of bacteriology}, volume = {194}, number = {22}, pages = {6300-6301}, pmid = {23105050}, issn = {1098-5530}, support = {P 20185/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {DNA, Bacterial/genetics ; *Genome, Bacterial ; Molecular Sequence Data ; Peptococcaceae/*classification/*genetics ; Species Specificity ; }, abstract = {Desulfosporosinus species are sulfate-reducing bacteria belonging to the Firmicutes. Their genomes will give insights into the genetic repertoire and evolution of sulfate reducers typically thriving in terrestrial environments and able to degrade toluene (Desulfosporosinus youngiae), to reduce Fe(III) (Desulfosporosinus meridiei, Desulfosporosinus orientis), and to grow under acidic conditions (Desulfosporosinus acidiphilus).}, }
@article {pmid23104407, year = {2013}, author = {Kielak, AM and Cretoiu, MS and Semenov, AV and Sørensen, SJ and van Elsas, JD}, title = {Bacterial chitinolytic communities respond to chitin and pH alteration in soil.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {1}, pages = {263-272}, pmid = {23104407}, issn = {1098-5336}, mesh = {*Biota ; Chitin/*metabolism ; Chitinases/genetics ; Denaturing Gradient Gel Electrophoresis ; Genetic Variation ; Hydrogen-Ion Concentration ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Chitin amendment is a promising soil management strategy that may enhance the suppressiveness of soil toward plant pathogens. However, we understand very little of the effects of added chitin, including the putative successions that take place in the degradative process. We performed an experiment in moderately acid soil in which the level of chitin, next to the pH, was altered. Examination of chitinase activities revealed fast responses to the added crude chitin, with peaks of enzymatic activity occurring on day 7. PCR-denaturing gradient gel electrophoresis (DGGE)-based analyses of 16S rRNA and chiA genes showed structural changes of the phylogenetically and functionally based bacterial communities following chitin addition and pH alteration. Pyrosequencing analysis indicated (i) that the diversity of chiA gene types in soil is enormous and (i) that different chiA gene types are selected by the addition of chitin at different prevailing soil pH values. Interestingly, a major role of Gram-negative bacteria versus a minor one of Actinobacteria in the immediate response to the added chitin (based on 16S rRNA gene abundance and chiA gene types) was indicated. The results of this study enhance our understanding of the response of the soil bacterial communities to chitin and are of use for both the understanding of soil suppressiveness and the possible mining of soil for novel enzymes.}, }
@article {pmid23104073, year = {2013}, author = {van der Ha, D and Vanwonterghem, I and Hoefman, S and De Vos, P and Boon, N}, title = {Selection of associated heterotrophs by methane-oxidizing bacteria at different copper concentrations.}, journal = {Antonie van Leeuwenhoek}, volume = {103}, number = {3}, pages = {527-537}, doi = {10.1007/s10482-012-9835-7}, pmid = {23104073}, issn = {1572-9699}, mesh = {*Biota ; Copper/*metabolism ; Denaturing Gradient Gel Electrophoresis ; *Heterotrophic Processes ; Methylococcaceae/*growth &amp; development/*metabolism ; }, abstract = {Due to the increasing atmospheric concentration of the greenhouse gas methane, more knowledge is needed on the management of methanotrophic communities. While most studies have focused on the characteristics of the methane-oxidizing bacteria (MOB), less is known about their interactions with the associated heterotrophs. Interpretative tools based on denaturing gradient gel electrophoresis allowed to evaluate the influence of copper-an important enzymatic regulator for MOB-on the activity and composition of the bacterial community. Over 30 days, enrichments with 0.1, 1.0 and 10 μM Cu(2+) respectively, showed comparable methane oxidation activities. The different copper concentrations did not create major shifts in the methanotrophic communities, as a Methylomonas sp. was able to establish dominance at all different copper concentrations by switching between both known methane monooxygenases. The associated heterotrophic communities showed continuous shifts, but over time all cultures evolved to a comparable composition, independent of the copper concentration. This indicates that the MOB selected for certain heterotrophs, possibly fulfilling vital processes such as removal of toxic compounds. The presence of a large heterotrophic food web indirectly depending on methane as sole carbon and energy source was confirmed by a clone library wherein MOB only formed a minority of the identified species.}, }
@article {pmid23097129, year = {2013}, author = {Kotay, SM and Mansell, BL and Hogsett, M and Pei, H and Goel, R}, title = {Anaerobic ammonia oxidation (ANAMMOX) for side-stream treatment of anaerobic digester filtrate process performance and microbiology.}, journal = {Biotechnology and bioengineering}, volume = {110}, number = {4}, pages = {1180-1192}, doi = {10.1002/bit.24767}, pmid = {23097129}, issn = {1097-0290}, mesh = {Anaerobiosis ; Bacteria, Anaerobic/genetics/*metabolism ; Base Sequence ; *Bioreactors ; DNA Primers ; DNA, Bacterial/isolation &amp; purification ; Filtration ; Fungi/genetics/*metabolism ; In Situ Hybridization, Fluorescence ; Oxidation-Reduction ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {A laboratory scale semi-batch fed anaerobic ammonia oxidation (ANAMMOX) reactor was operated in the lab under two different feeding operations. In the first scenario, termed as phase I, the reactor was seeded and operated with NO(2) -N added externally with the filtrate to the reactor in the ratio needed for the successful ANAMMOX. A second reactor was also initiated shortly after the start-up of the ANAMMOX to accomplish partial nitrification (nitritation reactor) to generate NO(2) -N. In phase II, the operation of the ANAMMOX reactor was switched to the mode in which case the partially nitrified effluent from the nitritation reactor was fed to the ANAMMOX reactor. In both phases, real filtrate from a local wastewater treatment plant was used as the feed. The ANAMMOX reactor sustained a loading rate (average 0.33 ± 0.03 with a max of 0.4 g N (L day)(-1)) which is comparable with many other fed-batch reactors in the literature. Consistent total N removal (average of 82 ± 4%) could be sustained in the ANAMMOX reactor during both phases. The nitritation reactor also consistently enabled a NO(2) -N to NH(3) -N ratio of 1.2:1 which was needed for the successful operation of the ANAMMOX reactor in phase II. Sequence analysis and FISH showed that Kuenenia stuttgartiensis dominated the enriched ANAMMOX community along with several unidentified, but seemingly enriched, potential ANAMMOX strains. Microbial ecology analysis for nitritation reactor showed the dominance of Nitrosomonas europaea. In summary, this manuscript provides important information on the start-up and operation of anammox reactor with detailed investigation on microbial ecology in this reactor.}, }
@article {pmid23091469, year = {2012}, author = {Sime-Ngando, T}, title = {Phytoplankton chytridiomycosis: fungal parasites of phytoplankton and their imprints on the food web dynamics.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {361}, pmid = {23091469}, issn = {1664-302X}, abstract = {Parasitism is one of the earlier and common ecological interactions in the nature, occurring in almost all environments. Microbial parasites typically are characterized by their small size, short generation time, and high rates of reproduction, with simple life cycle occurring generally within a single host. They are diverse and ubiquitous in aquatic ecosystems, comprising viruses, prokaryotes, and eukaryotes. Recently, environmental 18S rDNA surveys of microbial eukaryotes have unveiled major infecting agents in pelagic systems, consisting primarily of the fungal order of Chytridiales (chytrids). Chytrids are considered the earlier branch of the Eumycetes and produce motile, flagellated zoospores, characterized by a small size (2-6 μm), and a single, posterior flagellum. The existence of these dispersal propagules includes chytrids within the so-called group of zoosporic fungi, which are particularly adapted to the plankton lifestyle where they infect a wide variety of hosts, including fishes, eggs, zooplankton, algae, and other aquatic fungi but primarily freshwater phytoplankton. Related ecological implications are huge because chytrids can killed their hosts, release substrates for microbial processes, and provide nutrient-rich particles as zoospores and short fragments of filamentous inedible hosts for the grazer food chain. Furthermore, based on the observation that phytoplankton chytridiomycosis preferentially impacts the larger size species, blooms of such species (e.g., filamentous cyanobacteria) may not totally represent trophic bottlenecks. Besides, chytrid epidemics represent an important driving factor in phytoplankton seasonal successions. In this review, I summarize the knowledge on the diversity, community structure, quantitative importance, and functional roles of fungal chytrids, primarily those who are parasites of phytoplankton, and infer the ecological implications and potentials for the food web dynamics and properties. I reach the conclusion that phytoplankton chytridiomycosis represents an important but as yet overlooked ecological driving force in aquatic food web dynamics and network organization.}, }
@article {pmid23083746, year = {2013}, author = {Keshri, J and Mishra, A and Jha, B}, title = {Microbial population index and community structure in saline-alkaline soil using gene targeted metagenomics.}, journal = {Microbiological research}, volume = {168}, number = {3}, pages = {165-173}, doi = {10.1016/j.micres.2012.09.005}, pmid = {23083746}, issn = {1618-0623}, mesh = {Archaea/*classification/genetics ; Archaeal Proteins/genetics ; Bacteria/*classification/genetics ; Bacterial Proteins/genetics ; *Biota ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Hydrogen-Ion Concentration ; *Metagenomics ; Molecular Sequence Data ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Population indices of bacteria and archaea were investigated from saline-alkaline soil and a possible microbe-environment pattern was established using gene targeted metagenomics. Clone libraries were constructed using 16S rRNA and functional gene(s) involved in carbon fixation (cbbL), nitrogen fixation (nifH), ammonia oxidation (amoA) and sulfur metabolism (apsA). Molecular phylogeny revealed the dominance of Actinobacteria, Firmicutes and Proteobacteria along with archaeal members of Halobacteraceae. The library consisted of novel bacterial (20%) and archaeal (38%) genera showing ≤95% similarity to previously retrieved sequences. Phylogenetic analysis indicated ability of inhabitant to survive in stress condition. The 16S rRNA gene libraries contained novel gene sequences and were distantly homologous with cultured bacteria. Functional gene libraries were found unique and most of the clones were distantly related to Proteobacteria, while clones of nifH gene library also showed homology with Cyanobacteria and Firmicutes. Quantitative real-time PCR exhibited that bacterial abundance was two orders of magnitude higher than archaeal. The gene(s) quantification indicated the size of the functional guilds harboring relevant key genes. The study provides insights on microbial ecology and different metabolic interactions occurring in saline-alkaline soil, possessing phylogenetically diverse groups of bacteria and archaea, which may be explored further for gene cataloging and metabolic profiling.}, }
@article {pmid23080246, year = {2012}, author = {Ellis, JT and Sims, RC and Miller, CD}, title = {Monitoring microbial diversity of bioreactors using metagenomic approaches.}, journal = {Sub-cellular biochemistry}, volume = {64}, number = {}, pages = {73-94}, doi = {10.1007/978-94-007-5055-5_4}, pmid = {23080246}, issn = {0306-0225}, mesh = {Biological Products/metabolism ; Bioreactors/*microbiology/standards ; Biota/genetics ; Ecological Parameter Monitoring/*methods/standards ; Ecosystem ; *Genetic Variation ; Industrial Microbiology/methods/standards ; Metagenomics/*methods/standards ; Microbial Interactions/genetics ; }, abstract = {With the rapid development of molecular techniques, particularly 'omics' technologies, the field of microbial ecology is growing rapidly. The applications of next generation sequencing have allowed researchers to produce massive amounts of genetic data on individual microbes, providing information about microbial communities and their interactions through in situ and in vitro measurements. The ability to identify novel microbes, functions, and enzymes, along with developing an understanding of microbial interactions and functions, is necessary for efficient production of useful and high value products in bioreactors. The ability to optimize bioreactors fully and understand microbial interactions and functions within these systems will establish highly efficient industrial processes for the production of bioproducts. This chapter will provide an overview of bioreactors and metagenomic technologies to help the reader understand microbial communities, interactions, and functions in bioreactors.}, }
@article {pmid23072625, year = {2012}, author = {Rosendale, DI and Blatchford, PA and Sims, IM and Parkar, SG and Carnachan, SM and Hedderley, D and Ansell, J}, title = {Characterizing kiwifruit carbohydrate utilization in vitro and its consequences for human faecal microbiota.}, journal = {Journal of proteome research}, volume = {11}, number = {12}, pages = {5863-5875}, doi = {10.1021/pr300646m}, pmid = {23072625}, issn = {1535-3907}, mesh = {Actinidia/*metabolism ; Bacteria/genetics/growth &amp; development/metabolism ; Bacterial Proteins/metabolism ; Biota ; *Carbohydrate Metabolism ; Cellulose/metabolism ; Culture Media/metabolism ; Dietary Carbohydrates/metabolism ; Enzyme Activation ; Enzyme Assays ; Feces/*microbiology ; Fermentation ; Fruit/*metabolism ; Gastrointestinal Tract/metabolism/microbiology ; Genes, rRNA ; Humans ; *Metagenome ; Polysaccharides/metabolism ; RNA, Ribosomal, 16S/metabolism ; Solubility ; }, abstract = {It is well accepted that our gut bacteria have coevolved with us in relation to our genetics, diet and lifestyle and are integrated metabolically with us to affect our gut health adversely or beneficially. "Who is there" may vary quite widely between individuals, as might "how they do it", but "what they make" may be less variable. Many different individual species of bacteria can perform the same saccharolytic functions and so the availability of substrate (host or diet-derived) along with the degradative enzymes they possess may be key drivers of gut ecology. In this case study, we discuss detailed microbial ecology and metabolism analysis for three individuals following 48 h of in vitro faecal fermentation, using green kiwifruit as the substrate. In parallel, we have analyzed the chemical changes to the kiwifruit carbohydrates present in the fermenta to close the circle on substrate usage/degradative enzymes possessed/microbes present/microbial byproducts produced. In the absence of host carbohydrate, we see that kiwifruit carbohydrates were differentially utilized to drive microbial diversity, yet resulted in similar byproduct production. The starting ecology of each individual influenced the quantitative and qualitative microbial changes; but not necessarily the metabolic byproduct production. Thus, we propose that it is the consistent functional changes that are relevant for assessment of gut health benefits of any food. We recommend that in this era of large scale genotype/-omics studies that hypothesis-driven, bottom-up research is best placed to interpret metagenomic data in parallel with functional, phenotypic data.}, }
@article {pmid23071673, year = {2012}, author = {Carroll, IM and Ringel-Kulka, T and Siddle, JP and Klaenhammer, TR and Ringel, Y}, title = {Characterization of the fecal microbiota using high-throughput sequencing reveals a stable microbial community during storage.}, journal = {PloS one}, volume = {7}, number = {10}, pages = {e46953}, pmid = {23071673}, issn = {1932-6203}, support = {K01 DK092330/DK/NIDDK NIH HHS/United States ; UL1 RR025747/RR/NCRR NIH HHS/United States ; UL1RR025747/RR/NCRR NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/growth &amp; development ; Biodiversity ; DNA, Bacterial/chemistry/genetics ; Feces/*microbiology ; Freezing ; Genetic Variation ; Humans ; Intestines/microbiology ; Irritable Bowel Syndrome/microbiology ; Metagenome/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; Specimen Handling/*methods ; Time Factors ; }, abstract = {The handling and treatment of biological samples is critical when characterizing the composition of the intestinal microbiota between different ecological niches or diseases. Specifically, exposure of fecal samples to room temperature or long term storage in deep freezing conditions may alter the composition of the microbiota. Thus, we stored fecal samples at room temperature and monitored the stability of the microbiota over twenty four hours. We also investigated the stability of the microbiota in fecal samples during a six month storage period at -80°C. As the stability of the fecal microbiota may be affected by intestinal disease, we analyzed two healthy controls and two patients with irritable bowel syndrome (IBS). We used high-throughput pyrosequencing of the 16S rRNA gene to characterize the microbiota in fecal samples stored at room temperature or -80°C at six and seven time points, respectively. The composition of microbial communities in IBS patients and healthy controls were determined and compared using the Quantitative Insights Into Microbial Ecology (QIIME) pipeline. The composition of the microbiota in fecal samples stored for different lengths of time at room temperature or -80°C clustered strongly based on the host each sample originated from. Our data demonstrates that fecal samples exposed to room or deep freezing temperatures for up to twenty four hours and six months, respectively, exhibit a microbial composition and diversity that shares more identity with its host of origin than any other sample.}, }
@article {pmid23070552, year = {2012}, author = {Wootton, L}, title = {Microbial ecology: non-coding RNAs make E. coli unpalatable.}, journal = {Nature reviews. Microbiology}, volume = {10}, number = {11}, pages = {732}, pmid = {23070552}, issn = {1740-1534}, }
@article {pmid23070318, year = {2012}, author = {Estrela, S and Trisos, CH and Brown, SP}, title = {From metabolism to ecology: cross-feeding interactions shape the balance between polymicrobial conflict and mutualism.}, journal = {The American naturalist}, volume = {180}, number = {5}, pages = {566-576}, pmid = {23070318}, issn = {1537-5323}, support = {082273/WT_/Wellcome Trust/United Kingdom ; 082273/Z/07/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*metabolism ; Ecology ; Humans ; Microbial Interactions/*physiology ; *Models, Biological ; *Symbiosis ; }, abstract = {Polymicrobial interactions are widespread in nature and play a major role in maintaining human health and ecosystems. Whenever one organism uses metabolites produced by another organism as energy or nutrient sources, it is called cross-feeding. The ecological outcomes of cross-feeding interactions are poorly understood and potentially diverse: mutualism, competition, exploitation, or commensalism. A major reason for this uncertainty is the lack of theoretical approaches linking microbial metabolism to microbial ecology. To address this issue, we explore the dynamics of a one-way interspecific cross-feeding interaction in which food can be traded for a service (detoxification). Our results show that diverse ecological interactions (competition, mutualism, exploitation) can emerge from this simple cross-feeding interaction and can be predicted by the metabolic, demographic, and environmental parameters that govern the balance of the costs and benefits of association. In particular, our model predicts stronger mutualism for intermediate by-product toxicity because the resource-service exchange is constrained to the service being neither too vital (high toxicity impairs resource provision) nor dispensable (low toxicity reduces need for service). These results support the idea that bridging microbial ecology and metabolism is a critical step toward a better understanding of the factors governing the emergence and dynamics of polymicrobial interactions.}, }
@article {pmid23064947, year = {2013}, author = {de Campos, SB and Youn, JW and Farina, R and Jaenicke, S and Jünemann, S and Szczepanowski, R and Beneduzi, A and Vargas, LK and Goesmann, A and Wendisch, VF and Passaglia, LM}, title = {Changes in root bacterial communities associated to two different development stages of canola (Brassica napus L. var oleifera) evaluated through next-generation sequencing technology.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {593-601}, pmid = {23064947}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Typing Techniques ; Biodiversity ; Brassica napus/*growth &amp; development/microbiology ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Data ; Phylogeny ; Plant Roots/growth &amp; development/*microbiology ; *Soil Microbiology ; }, abstract = {Crop production may benefit from plant growth-promoting bacteria. The knowledge on bacterial communities is indispensable in agricultural systems that intend to apply beneficial bacteria to improve plant health and production of crops such as canola. In this work, the diversity of root bacterial communities associated to two different developmental phases of canola (Brassica napus L.) plants was assessed through the application of new generation sequencing technology. Total bacterial DNA was extracted from root samples from two different growth states of canola (rosette and flowering). It could be shown how bacterial communities inside the roots changed with the growing stage of the canola plants. There were differences in the abundance of the genera, family, and even the phyla identified for each sample. While in both root samples Proteobacteria was the most common phylum, at the rosette stage, the most common bacteria belonged to the family Pseudomonadaceae and the genus Pseudomonas, and in the flowering stage, the Xanthomonadaceae family and the genus Xanthomonas dominated the community. This implies in a switch in the predominant bacteria in the different developmental stages of the plant, suggesting that the plant itself interferes with the associated microbial community.}, }
@article {pmid23064335, year = {2013}, author = {Youngblut, ND and Shade, A and Read, JS and McMahon, KD and Whitaker, RJ}, title = {Lineage-specific responses of microbial communities to environmental change.}, journal = {Applied and environmental microbiology}, volume = {79}, number = {1}, pages = {39-47}, pmid = {23064335}, issn = {1098-5336}, mesh = {*Biota ; Cluster Analysis ; Electron Transport Complex IV/genetics ; *Environmental Microbiology ; Genetic Variation ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {A great challenge facing microbial ecology is how to define ecologically relevant taxonomic units. To address this challenge, we investigated how changing the definition of operational taxonomic units (OTUs) influences the perception of ecological patterns in microbial communities as they respond to a dramatic environmental change. We used pyrosequenced tags of the bacterial V2 16S rRNA region, as well as clone libraries constructed from the cytochrome oxidase C gene ccoN, to provide additional taxonomic resolution for the common freshwater genus Polynucleobacter. At the most highly resolved taxonomic scale, we show that distinct genotypes associated with the abundant Polynucleobacter lineages exhibit divergent spatial patterns and dramatic changes over time, while the also abundant Actinobacteria OTUs are highly coherent. This clearly demonstrates that different bacterial lineages demand different taxonomic definitions to capture ecological patterns. Based on the temporal distribution of highly resolved taxa in the hypolimnion, we demonstrate that change in the population structure of a single genotype can provide additional insight into the mechanisms of community-level responses. These results highlight the importance and feasibility of examining ecological change in microbial communities across taxonomic scales while also providing valuable insight into the ecological characteristics of ecologically coherent groups in this system.}, }
@article {pmid23063222, year = {2012}, author = {Saber, MH and Schwarzberg, K and Alonaizan, FA and Kelley, ST and Sedghizadeh, PP and Furlan, M and Levy, TA and Simon, JH and Slots, J}, title = {Bacterial flora of dental periradicular lesions analyzed by the 454-pyrosequencing technology.}, journal = {Journal of endodontics}, volume = {38}, number = {11}, pages = {1484-1488}, doi = {10.1016/j.joen.2012.06.037}, pmid = {23063222}, issn = {1878-3554}, mesh = {DNA, Bacterial/*genetics ; Dental Pulp Cavity/*microbiology ; Humans ; Metagenome ; Periapical Periodontitis/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {INTRODUCTION: Symptomatic teeth with periradicular lesions of infectious origin remain a significant challenge in dentistry, and the reason for the acute perturbation is incompletely understood. The present study used pyrosequencing of bacterial 16S ribosomal RNA (rRNA) genes to characterize the microbiota of periradicular lesions.<br><br>METHODS: Thirteen periradicular lesions from 11 symptomatic and 2 asymptomatic teeth were sampled during apical surgery. Samples were subjected to DNA extraction and 16S rRNA polymerase chain reaction (PCR) amplification. PCR amplicons were then sequenced by using the Roche 454 GS FLX platform. Data were analyzed with the Quantitative Insights into Microbial Ecology (QIIME) software package.<br><br>RESULTS: Seven of the 13 periradicular lesions (53.8%) yielded PCR amplicons, which generated 35,731 high-quality DNA sequences belonging to 10 bacterial phyla and 73 bacterial genera. All 7 lesions were associated with symptoms. The phyla with most bacterial taxa were Proteobacteria (proportion of total bacterial taxa, 33.3%), Firmicutes (30.9%), Actinobacteria (12.2%), and Bacteroidetes (11.4%). The most abundant genera were Fusobacterium (average of total sequences, 21.0%), Streptococcus (8.0%), Prevotella (7.5%), Corynebacterium (7.2%), Porphyromonas (6.0%). and Actinomyces (5.8%).<br><br>CONCLUSIONS: This study demonstrated that the microbiota of symptomatic periapical lesions is predominated by anaerobic bacteria but also contains substantial levels of streptococci, actinomyces, and bacteria not previously identified in the oral cavity. The etiopathogenic role and therapeutic implication of periradicular bacteria need to be determined.}, }
@article {pmid23060870, year = {2012}, author = {Daebeler, A and Abell, GC and Bodelier, PL and Bodrossy, L and Frampton, DM and Hefting, MM and Laanbroek, HJ}, title = {Archaeal dominated ammonia-oxidizing communities in Icelandic grassland soils are moderately affected by long-term N fertilization and geothermal heating.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {352}, pmid = {23060870}, issn = {1664-302X}, abstract = {The contribution of ammonia-oxidizing bacteria and archaea (AOB and AOA, respectively) to the net oxidation of ammonia varies greatly between terrestrial environments. To better understand, predict and possibly manage terrestrial nitrogen turnover, we need to develop a conceptual understanding of ammonia oxidation as a function of environmental conditions including the ecophysiology of associated organisms. We examined the discrete and combined effects of mineral nitrogen deposition and geothermal heating on ammonia-oxidizing communities by sampling soils from a long-term fertilization site along a temperature gradient in Icelandic grasslands. Microarray, clone library and quantitative PCR analyses of the ammonia monooxygenase subunit A (amoA) gene accompanied by physico-chemical measurements of the soil properties were conducted. In contrast to most other terrestrial environments, the ammonia-oxidizing communities consisted almost exclusively of archaea. Their bacterial counterparts proved to be undetectable by quantitative polymerase chain reaction suggesting AOB are only of minor relevance for ammonia oxidation in these soils. Our results show that fertilization and local, geothermal warming affected detectable ammonia-oxidizing communities, but not soil chemistry: only a subset of the detected AOA phylotypes was present in higher temperature soils and AOA abundance was increased in the fertilized soils, while soil physio-chemical properties remained unchanged. Differences in distribution and structure of AOA communities were best explained by soil pH and clay content irrespective of temperature or fertilizer treatment in these grassland soils, suggesting that these factors have a greater potential for ecological niche-differentiation of AOA in soil than temperature and N fertilization.}, }
@article {pmid23056217, year = {2012}, author = {Maughan, H and Wang, PW and Diaz Caballero, J and Fung, P and Gong, Y and Donaldson, SL and Yuan, L and Keshavjee, S and Zhang, Y and Yau, YC and Waters, VJ and Tullis, DE and Hwang, DM and Guttman, DS}, title = {Analysis of the cystic fibrosis lung microbiota via serial Illumina sequencing of bacterial 16S rRNA hypervariable regions.}, journal = {PloS one}, volume = {7}, number = {10}, pages = {e45791}, pmid = {23056217}, issn = {1932-6203}, mesh = {Bacteria/classification/*genetics ; Computer Simulation ; Cystic Fibrosis/*microbiology ; DNA, Bacterial/chemistry/genetics ; Genetic Variation ; Humans ; Lung/microbiology/pathology ; Metagenome/*genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Sputum/microbiology ; }, abstract = {The characterization of bacterial communities using DNA sequencing has revolutionized our ability to study microbes in nature and discover the ways in which microbial communities affect ecosystem functioning and human health. Here we describe Serial Illumina Sequencing (SI-Seq): a method for deep sequencing of the bacterial 16S rRNA gene using next-generation sequencing technology. SI-Seq serially sequences portions of the V5, V6 and V7 hypervariable regions from barcoded 16S rRNA amplicons using an Illumina short-read genome analyzer. SI-Seq obtains taxonomic resolution similar to 454 pyrosequencing for a fraction of the cost, and can produce hundreds of thousands of reads per sample even with very high multiplexing. We validated SI-Seq using single species and mock community controls, and via a comparison to cystic fibrosis lung microbiota sequenced using 454 FLX Titanium. Our control runs show that SI-Seq has a dynamic range of at least five orders of magnitude, can classify >96% of sequences to the genus level, and performs just as well as 454 and paired-end Illumina methods in estimation of standard microbial ecology diversity measurements. We illustrate the utility of SI-Seq in a pilot sample of central airway secretion samples from cystic fibrosis patients.}, }
@article {pmid23055998, year = {2012}, author = {Schimel, JP and Schaeffer, SM}, title = {Microbial control over carbon cycling in soil.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {348}, pmid = {23055998}, issn = {1664-302X}, abstract = {A major thrust of terrestrial microbial ecology is focused on understanding when and how the composition of the microbial community affects the functioning of biogeochemical processes at the ecosystem scale (meters-to-kilometers and days-to-years). While research has demonstrated these linkages for physiologically and phylogenetically "narrow" processes such as trace gas emissions and nitrification, there is less conclusive evidence that microbial community composition influences the "broad" processes of decomposition and organic matter (OM) turnover in soil. In this paper, we consider how soil microbial community structure influences C cycling. We consider the phylogenetic level at which microbes form meaningful guilds, based on overall life history strategies, and suggest that these are associated with deep evolutionary divergences, while much of the species-level diversity probably reflects functional redundancy. We then consider under what conditions it is possible for differences among microbes to affect process dynamics, and argue that while microbial community structure may be important in the rate of OM breakdown in the rhizosphere and in detritus, it is likely not important in the mineral soil. In mineral soil, physical access to occluded or sorbed substrates is the rate-limiting process. Microbial community influences on OM turnover in mineral soils are based on how organisms allocate the C they take up - not only do the fates of the molecules differ, but they can affect the soil system differently as well. For example, extracellular enzymes and extracellular polysaccharides can be key controls on soil structure and function. How microbes allocate C may also be particularly important for understanding the long-term fate of C in soil - is it sequestered or not?}, }
@article {pmid23053695, year = {2013}, author = {Marzorati, M and Maignien, L and Verhelst, A and Luta, G and Sinnott, R and Kerckhof, FM and Boon, N and Van de Wiele, T and Possemiers, S}, title = {Barcoded pyrosequencing analysis of the microbial community in a simulator of the human gastrointestinal tract showed a colon region-specific microbiota modulation for two plant-derived polysaccharide blends.}, journal = {Antonie van Leeuwenhoek}, volume = {103}, number = {2}, pages = {409-420}, doi = {10.1007/s10482-012-9821-0}, pmid = {23053695}, issn = {1572-9699}, mesh = {Aloe/*chemistry ; Bacteria/*metabolism ; *Biota ; Colon/*microbiology ; DNA Barcoding, Taxonomic ; Denaturing Gradient Gel Electrophoresis ; Humans ; *Models, Theoretical ; Polymerase Chain Reaction ; Polysaccharides/isolation &amp; purification/*metabolism ; Sequence Analysis, DNA ; }, abstract = {The combination of a Simulator of the Human Intestinal Microbial Ecosystem with ad hoc molecular techniques (i.e. pyrosequencing, denaturing gradient gel electrophoresis and quantitative PCR) allowed an evaluation of the extent to which two plant polysaccharide supplements could modify a complex gut microbial community. The presence of Aloe vera gel powder and algae extract in product B as compared to the standard blend (product A) improved its fermentation along the entire simulated colon. The potential extended effect of product B in the simulated distal colon, as compared to product A, was confirmed by: (i) the separate clustering of the samples before and after the treatment in the phylogenetic-based dendrogram and OTU-based PCoA plot only for product B; (ii) a higher richness estimator (+33 vs. -36 % of product A); and (iii) a higher dynamic parameter (21 vs. 13 %). These data show that the combination of well designed in vitro simulators with barcoded pyrosequencing is a powerful tool for characterizing changes occurring in the gut microbiota following a treatment. However, for the quantification of low-abundance species-of interest because of their relationship to potential positive health effects (i.e. bifidobacteria or lactobacilli)-conventional molecular ecological approaches, such as PCR-DGGE and qPCR, still remain a very useful complementary tool.}, }
@article {pmid23053048, year = {2012}, author = {Cerezuela, R and Fumanal, M and Tapia-Paniagua, ST and Meseguer, J and Moriñigo, MA and Esteban, MA}, title = {Histological alterations and microbial ecology of the intestine in gilthead seabream (Sparus aurata L.) fed dietary probiotics and microalgae.}, journal = {Cell and tissue research}, volume = {350}, number = {3}, pages = {477-489}, doi = {10.1007/s00441-012-1495-4}, pmid = {23053048}, issn = {1432-0878}, mesh = {Animals ; Diet ; Intestines/immunology/*microbiology ; *Microalgae ; Models, Animal ; Probiotics/*administration &amp; dosage ; Sea Bream/immunology/*microbiology ; }, abstract = {The effects on histology and microbial ecology in gilthead seabream (Sparus aurata) intestine caused by dietary probiotic and microalgae were studied. Fish were fed non-supplemented (C, control) or supplemented diets with Tetraselmis chuii, Phaeodactylum tricornutum and Bacillus subtilis single or combined (diets T, P, B, BT and BP) for 4 weeks. Curiously, fish fed the experimental diets showed similar morphological alterations when studied by light and electron microscopy and significant signs of intestinal damage were detected. No effect of microalgae or B. subtilis on the intestinal absorptive area was observed, whereas the number of goblet cells and IELs were significantly lower in fish fed the T, P, B and BT diets and T, BT and BP diets, respectively. Interestingly, only the diets containing B. subtilis resulted in a significant reduction of microvilli height. Alterations such as wide intercellular spaces and large vacuoles in enterocytes were observed in fish fed T, B, BT, BT and P in lesser degrees. These observations demonstrate that fish fed experimental diets presented different signs of oedema and inflammation that could compromise their body homeostasis. Moreover, the experimental diets cause important alterations in the intestinal microbiota by a significant decrease in bacterial diversity, as demonstrated by the fall in specific richness, Shannon and range-weighted richness indices. To our knowledge, this is the first in vivo study regarding the implications of the use of probiotics in combination with immunostimulants on fish intestinal morphology and microbiota. More morphofunctional studies are needed in order to correlate the nutritional and immune aspects of fish gut.}, }
@article {pmid23052928, year = {2013}, author = {Doyle, JJ}, title = {What distinguishes the Gordon Research Conference on Oceans and Human Health? A retrospective 2008-2012.}, journal = {Microbial ecology}, volume = {65}, number = {4}, pages = {920-921}, doi = {10.1007/s00248-012-0131-x}, pmid = {23052928}, issn = {1432-184X}, mesh = {Congresses as Topic ; Group Processes ; Humans ; Marine Biology/*education ; Oceans and Seas ; *Public Health/education ; Science/education/*organization &amp; administration ; }, abstract = {This piece is being submitted as a short commentary for the special edition on Oceans and Human Health (OHH). It is written from the perspective of a student who has attended all three biennial Gordon Research Conferences and Seminars on OHH beginning in 2008.}, }
@article {pmid23052927, year = {2013}, author = {Arellano, SM and Lee, OO and Lafi, FF and Yang, J and Wang, Y and Young, CM and Qian, PY}, title = {Deep sequencing of Myxilla (Ectyomyxilla) methanophila, an epibiotic sponge on cold-seep tubeworms, reveals methylotrophic, thiotrophic, and putative hydrocarbon-degrading microbial associations.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {450-461}, pmid = {23052927}, issn = {1432-184X}, mesh = {Animals ; Bacteria/*classification/genetics ; Biofilms ; DNA, Bacterial/genetics ; Gene Library ; Gulf of Mexico ; High-Throughput Nucleotide Sequencing ; Polycyclic Aromatic Hydrocarbons/metabolism ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Symbiosis ; Water Microbiology ; }, abstract = {The encrusting sponge Myxilla (Ectyomyxilla) methanophila (Poecilosclerida: Myxillidae) is an epibiont on vestimentiferan tubeworms at hydrocarbon seeps on the upper Louisiana slope of the Gulf of Mexico. It has long been suggested that this sponge harbors methylotrophic bacteria due to its low δ(13)C value and high methanol dehydrogenase activity, yet the full community of microbial associations in M. methanophila remained uncharacterized. In this study, we sequenced 16S rRNA genes representing the microbial community in M. methanophila collected from two hydrocarbon-seep sites (GC234 and Bush Hill) using both Sanger sequencing and next-generation 454 pyrosequencing technologies. Additionally, we compared the microbial community in M. methanophila to that of the biofilm collected from the associated tubeworm. Our results revealed that the microbial diversity in the sponges from both sites was low but the community structure was largely similar, showing a high proportion of methylotrophic bacteria of the genus Methylohalomonas and polycyclic aromatic hydrocarbon (PAH)-degrading bacteria of the genera Cycloclasticus and Neptunomonas. Furthermore, the sponge microbial clone library revealed the dominance of thioautotrophic gammaproteobacterial symbionts in M. methanophila. In contrast, the biofilm communities on the tubeworms were more diverse and dominated by the chemoorganotrophic Moritella at GC234 and methylotrophic Methylomonas and Methylohalomonas at Bush Hill. Overall, our study provides evidence to support previous suggestion that M. methanophila harbors methylotrophic symbionts and also reveals the association of PAH-degrading and thioautotrophic microbes in the sponge.}, }
@article {pmid23052926, year = {2013}, author = {Giaveno, MA and Urbieta, MS and Ulloa, JR and Toril, EG and Donati, ER}, title = {Physiologic versatility and growth flexibility as the main characteristics of a novel thermoacidophilic Acidianus strain isolated from Copahue geothermal area in Argentina.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {336-346}, pmid = {23052926}, issn = {1432-184X}, mesh = {Acidianus/classification/genetics/*growth &amp; development/isolation &amp; purification/*physiology ; Aerobiosis ; Anaerobiosis ; Argentina ; Base Composition ; DNA, Archaeal/genetics ; Hot Springs/*microbiology ; Iron/metabolism ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfur/metabolism ; }, abstract = {A novel thermoacidophilic archaeal strain has been isolated from three geothermal acidic hot springs in Copahue, Argentina. One of the most striking characteristic of ALE1 isolate is its metabolic versatility. It grows on sulphur, tetrathionate, iron (II) and sucrose under aerobic conditions, but it can also develop under anaerobic conditions using iron (III) or sulphur as electron acceptors and sulphur or hydrogen as electron donors autotrophically. A temperature of 75 °C and a pH between 2.5 and 3.0 are strain ALE1 optimal growth conditions, but it is able to oxidise iron (II) even at pH 1.0. Cells are irregular cocci surrounded by a regularly arrayed glycoprotein layer (S-layer). Phylogenetic analysis shows that strain ALE1 belongs to the family Sulfolobaceae in the class Thermoprotei, within the phylum Crenarchaeota. Based on 16S rRNA gene sequence similarity on NCBI database, ALE1 does not have closely related relatives, neither in culture nor uncultured, which is more surprising. Its closest related species are strains of Acidianus hospitalis (91 % of sequence similarity), Acidianus infernus (90 %), Acidianus ambivalens (90 %) and Acidianus manzanensis (90 %). Its DNA base composition of 34.5 % mol C + G is higher than that reported for other Acidianus species. Considering physiological and phylogenetic characteristics of strain ALE1, we considered it to represent a novel species of the genus Acidianus (candidatus "Acidianus copahuensis"). The aim of this study is to physiologically characterise this novel archaea in order to understand its role in iron and sulphur geochemical cycles in the Copahue geothermal area and to evaluate its potential applications in bioleaching and biooxidation.}, }
@article {pmid23052925, year = {2013}, author = {Raftery, TD and Lindler, H and McNealy, TL}, title = {Altered host cell-bacteria interaction due to nanoparticle interaction with a bacterial biofilm.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {496-503}, pmid = {23052925}, issn = {1432-184X}, mesh = {Acanthamoeba/*microbiology/physiology ; Biofilms/*drug effects ; Gold/*pharmacology ; Legionella pneumophila/*drug effects/growth &amp; development ; *Nanoparticles ; }, abstract = {Nanoparticle (NP) use in everyday applications creates the potential for NPs to enter the environment where, in aquatic systems, they are likely to settle on substrates and interact with microbial communities. Legionella pneumophila biofilms are found as part of microbial communities in both natural and man-made environments, especially in man-made cooling systems. The bacterium is the causative agent of Legionnaires' disease. Legionella requires a host cell for replication in the environment, and amoebae commonly serve as this host cell. Our previous work demonstrated significant changes in Legionella biofilm morphology after exposure to 0.7 μg/L gold NPs (AuNPs). Here, we investigate how these morphology changes alter host-bacteria interactions using Acanthamoeba polyphaga as a model. Host-bacteria-NP interactions are affected by NP characteristics. Biofilms exposed to 4- and 18-nm, citrate-capped, spherical AuNPs significantly altered the grazing ability of A. polyphaga, which was not observed in biofilms exposed to 24-nm polystyrene beads. Uptake and replication of NP-exposed planktonic L. pneumophila within A. polyphaga were not altered regardless of NP size or core chemistry. Nanomaterial effects on the interaction of benthic organisms and bacteria may be directly or, as shown here, indirectly dependent on bacterial morphology. NP contamination therefore may alter interactions in a normal ecosystem function.}, }
@article {pmid23051694, year = {2013}, author = {Wang, G and Or, D}, title = {Hydration dynamics promote bacterial coexistence on rough surfaces.}, journal = {The ISME journal}, volume = {7}, number = {2}, pages = {395-404}, pmid = {23051694}, issn = {1751-7370}, mesh = {Bacteria/*growth &amp; development ; *Models, Theoretical ; Soil/analysis ; *Soil Microbiology ; Surface Properties ; Water/*analysis ; }, abstract = {Identification of mechanisms that promote and maintain the immense microbial diversity found in soil is a central challenge for contemporary microbial ecology. Quantitative tools for systematic integration of complex biophysical and trophic processes at spatial scales, relevant for individual cell interactions, are essential for making progress. We report a modeling study of competing bacterial populations cohabiting soil surfaces subjected to highly dynamic hydration conditions. The model explicitly tracks growth, motion and life histories of individual bacterial cells on surfaces spanning dynamic aqueous networks that shape heterogeneous nutrient fields. The range of hydration conditions that confer physical advantages for rapidly growing species and support competitive exclusion is surprisingly narrow. The rapid fragmentation of soil aqueous phase under most natural conditions suppresses bacterial growth and cell dispersion, thereby balancing conditions experienced by competing populations with diverse physiological traits. In addition, hydration fluctuations intensify localized interactions that promote coexistence through disproportional effects within densely populated regions during dry periods. Consequently, bacterial population dynamics is affected well beyond responses predicted from equivalent and uniform hydration conditions. New insights on hydration dynamics could be considered in future designs of soil bioremediation activities, affect longevity of dry food products, and advance basic understanding of bacterial diversity dynamics and its role in global biogeochemical cycles.}, }
@article {pmid23050591, year = {2012}, author = {Desloover, J and Woldeyohannis, AA and Verstraete, W and Boon, N and Rabaey, K}, title = {Electrochemical resource recovery from digestate to prevent ammonia toxicity during anaerobic digestion.}, journal = {Environmental science &amp; technology}, volume = {46}, number = {21}, pages = {12209-12216}, doi = {10.1021/es3028154}, pmid = {23050591}, issn = {1520-5851}, mesh = {Ammonia/*chemistry ; Anaerobiosis ; Bioreactors ; Electrochemical Techniques ; Electrodes ; Hydrogen-Ion Concentration ; Osmolar Concentration ; Quaternary Ammonium Compounds/*chemistry ; Waste Disposal, Fluid/*methods ; Wastewater ; }, abstract = {Ammonia inhibition during anaerobic digestion limits the substrate loading rate and endangers process stability. Furthermore, digestates are interesting feedstocks for nutrient recovery. In this lab-scale study, an electrochemical cell was used to investigate the NH(4)(+) flux from anode to cathode. Under optimal conditions with synthetic wastewater, an NH(4)(+) charge transfer efficiency of 96% and NH(4)(+) flux of 120 g N m(-2) d(-1) could be obtained at a concomitant electricity input of 5 kWh kg(-1) N removed. A more selective NH(4)(+) transfer could be established by maintaining a high concentration of other cations in the cathode compartment. Comparable NH(4)(+) fluxes could be obtained with digestate at an electrical power input of 13 kWh kg(-1) N removed and 41% current efficiency. The ammonium level in the digestate could be lowered from 2.1 to 0.8 - 1.2 g N L(-1). Interestingly, also potassium fluxes of up to 241 g K(+) m(-2) d(-1) could be obtained at 23% current efficiency. As the cathode can be operated at high pH without the need for chemical addition, stripping and absorption of dissolved ammonia could reach 100% efficiency. By valorization of the generated side products, this technology shows economic potential for practical application.}, }
@article {pmid23049526, year = {2012}, author = {Nostrand, JD and He, Z and Zhou, J}, title = {Use of functional gene arrays for elucidating in situ biodegradation.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {339}, pmid = {23049526}, issn = {1664-302X}, abstract = {Microarrays have revolutionized the study of microbiology by providing a high-throughput method for examining thousands of genes with a single test and overcome the limitations of many culture-independent approaches. Functional gene arrays (FGA) probe a wide range of genes involved in a variety of functions of interest to microbial ecology (e.g., carbon degradation, N fixation, metal resistance) from many different microorganisms, cultured and uncultured. The most comprehensive FGA to date is the GeoChip array, which targets tens of thousands of genes involved in the geochemical cycling of carbon, nitrogen, phosphorus, and sulfur, metal resistance and reduction, energy processing, antibiotic resistance and contaminant degradation as well as phylogenetic information (gyrB). Since the development of GeoChips, many studies have been performed using this FGA and have shown it to be a powerful tool for rapid, sensitive, and specific examination of microbial communities in a high-throughput manner. As such, the GeoChip is well-suited for linking geochemical processes with microbial community function and structure. This technology has been used successfully to examine microbial communities before, during, and after in situ bioremediation at a variety of contaminated sites. These studies have expanded our understanding of biodegradation and bioremediation processes and the associated microorganisms and environmental conditions responsible. This review provides an overview of FGA development with a focus on the GeoChip and highlights specific GeoChip studies involving in situ bioremediation.}, }
@article {pmid23041495, year = {2012}, author = {Zimmerman, CE and Stamper, PD and Bryant, L and Farley, J and Golova, J and Holmberg, R and Howard, T and Linger, Y and Meyers, K and Perov, A and Rudy, GB and Carroll, KC and Chandler, DP}, title = {Development of a simple, low-density array to detect methicillin-resistant Staphylococcus aureus and mecA dropouts in nasal swabs.}, journal = {Journal of microbiological methods}, volume = {91}, number = {3}, pages = {366-376}, doi = {10.1016/j.mimet.2012.09.010}, pmid = {23041495}, issn = {1872-8359}, mesh = {Bacterial Proteins/*genetics ; Humans ; Methicillin-Resistant Staphylococcus aureus/classification/genetics/*isolation &amp; purification/metabolism ; Mucus/metabolism/microbiology ; Nasal Mucosa/metabolism/*microbiology ; Oligonucleotide Array Sequence Analysis/*methods ; Penicillin-Binding Proteins ; Retrospective Studies ; Sensitivity and Specificity ; Staphylococcal Infections/*microbiology ; }, abstract = {Detection of methicillin-resistant Staphylococcus aureus (MRSA) is important for prevention and control of MRSA infections, but the discovery of mecA dropouts and SCCmec junction sequences with homology to coagulase-negative staphylococci (CoNS) has challenged several real-time PCR tests. The objective of this study was to develop a user-friendly, gel element microarray test for MRSA detection, to estimate the analytical performance characteristics of the test on bacterial isolates, and to perform an initial evaluation of the test on nasopharyngeal swabs from patients known to have a high prevalence of S. aureus containing mecA dropouts. The assay limit of detection for the test was 250 fg (or less) of genomic DNA per amplification reaction (approximately 80 cell equivalents) and MRSA was consistently detected at a ratio of 1:12,000 in a non-target background. Of 87 bacterial isolates, the test accurately classified 86 (98.8%) overall, and correctly identified 14 mecA dropout specimens that were falsely positive in the BD GeneOhm MRSA test or BD GeneOhm StaphSR test. A retrospective analysis of 246 nasal swab samples acquired from a high-risk patient population (overall prevalence=10.8% by culture) resulted in 80.5% sensitivity (95% CI=68.4%, 92.6%) and 96.6% specificity. Of these 246 samples, 174 (71%) were positive for mecA, 86 (35%) were positive for S. aureus tufA and 46 (19%) were positive for a SCCmec junction sequence. To estimate method repeatability, 48 samples representing the full range of phenotypes, genotypes and microarray probe SNR values were tested in triplicate, with three discordant results for a concordance rate of 97.9% (141/144 tests). These data demonstrate that a very simple microarray test can identify mecA dropouts with high specificity in either cultured isolates or nasal swabs from a high-prevalence, high-risk patient population. However, the clinical sensitivity of the test will likely depend on local microbial ecology and the prevalence of mecA positive CoNS in any given patient population.}, }
@article {pmid23039919, year = {2012}, author = {Ozaktas, T and Taskin, B and Gozen, AG}, title = {High level multiple antibiotic resistance among fish surface associated bacterial populations in non-aquaculture freshwater environment.}, journal = {Water research}, volume = {46}, number = {19}, pages = {6382-6390}, doi = {10.1016/j.watres.2012.09.010}, pmid = {23039919}, issn = {1879-2448}, mesh = {Ampicillin/pharmacology ; Animals ; Aquaculture ; Bacteria/classification/*genetics ; Chloramphenicol Resistance ; Cyprinidae/*microbiology ; *Drug Resistance, Bacterial/genetics ; Fresh Water ; Kanamycin Resistance ; Lakes ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Mucus/microbiology ; Plasmids/genetics ; RNA, Ribosomal, 16S ; Streptomycin/pharmacology ; Turkey ; }, abstract = {Freshwater fish, Alburnus alburnus (bleak), were captured from Lake Mogan, situated in Ankara, during spring. The surface mucus of the fish was collected and associated bacteria were cultured and isolated. By sequencing PCR-amplified 16S RNA encoding genes, the isolates were identified as members of 12 different genera: Acinetobacter, Aeromonas, Bacillus, Brevundimonas, Gordonia, Kocuria, Microbacterium, Mycobacterium, Pseudomonas, Rhodococcus, and Staphylococcus, in addition to one strain that was unidentified. The mucus-dwelling bacterial isolates were tested for resistance against ampicillin, kanamycin, streptomycin and chloramphenicol. About 95% of the isolates were found to be resistant to ampicillin, 93% to chloramphenicol, and 88% to kanamycin and streptomycin. A Microbacterium oxydans and the unidentified environmental isolate were resistant to all four antibiotics tested at very high levels (>1600 μg/ml ampicillin and streptomycin; >1120 μg/ml kanamycin; >960 μg/ml chloramphenicol). Only a Kocuria sp. was sensitive to all four antibiotics at the lowest concentrations tested (3.10 μg/ml ampicillin and streptomycin; 2.15 μg/ml kanamycin; 1.85 μg/ml chloramphenicol). The rest of the isolates showed different resistance levels. Plasmid isolations were carried out to determine if the multiple antibiotic resistance could be attributed to the presence of plasmids. However, no plasmid was detected in any of the isolates. The resistance appeared to be mediated by chromosome-associated functions. This study indicated that multiple antibiotic resistance at moderate to high levels is common among the current phenotypes of the fish mucus-dwelling bacterial populations in this temperate, shallow lake which has not been subjected to any aquaculturing so far but under anthropogenic effect being in a recreational area.}, }
@article {pmid23039094, year = {2012}, author = {Dolan, JR and Pierce, RW and Yang, EJ and Kim, SY}, title = {Southern ocean biogeography of tintinnid ciliates of the marine plankton.}, journal = {The Journal of eukaryotic microbiology}, volume = {59}, number = {6}, pages = {511-519}, doi = {10.1111/j.1550-7408.2012.00646.x}, pmid = {23039094}, issn = {1550-7408}, mesh = {*Biodiversity ; Ciliophora/*classification/*isolation &amp; purification ; Oceans and Seas ; *Phylogeography ; Plankton/*parasitology ; Seawater/*parasitology ; }, abstract = {Ciliate microzooplankton are important grazers in most pelagic ecosystems and among them, tintinnids, with their largely species-specific loricas, allow relatively easy assessment of questions of diversity and distributions. Herein, we present the results of a survey of species records of tintinnids from the Southern Ocean (locations below 40°S) reported in 56 publications yielding 2,047 species records (synonyms included) from 402 locations. The 192 species reported can be parsed into two main groups: 32 endemic Southern Ocean species, known only from 40°S and further south, and a second group of 181 widespread species, forms with extensive geographic ranges extending into the Southern Ocean. Widespread species reported from the Southern Ocean can be further divided into a group of 81 species, each recorded multiple times in the Southern Ocean waters and 70 apparent "stray" species which have only been found but once. The endemic and widespread species of the Southern Ocean show both distinct distributional patterns and morphological differences. The assemblage of Southern Ocean endemics is found mostly within the Antarctic zone delimited by the average location of the Polar Front and contains a relatively large portion of wide-mouthed forms. We give suggestions for future study.}, }
@article {pmid23038174, year = {2013}, author = {Martínez, I and Lattimer, JM and Hubach, KL and Case, JA and Yang, J and Weber, CG and Louk, JA and Rose, DJ and Kyureghian, G and Peterson, DA and Haub, MD and Walter, J}, title = {Gut microbiome composition is linked to whole grain-induced immunological improvements.}, journal = {The ISME journal}, volume = {7}, number = {2}, pages = {269-280}, pmid = {23038174}, issn = {1751-7370}, mesh = {Adult ; Bacteroidetes/growth &amp; development ; Bifidobacterium/growth &amp; development ; Biodiversity ; Biomarkers/blood ; Blood Glucose/analysis ; Cross-Over Studies ; *Diet ; *Edible Grain ; Eubacterium/growth &amp; development ; Feces/microbiology ; Female ; Gastrointestinal Tract/immunology/metabolism/*microbiology ; Hordeum ; Humans ; Inflammation/blood ; Insulin/blood ; Interleukin-6/blood ; Male ; *Metagenome ; Oryza ; Young Adult ; }, abstract = {The involvement of the gut microbiota in metabolic disorders, and the ability of whole grains to affect both host metabolism and gut microbial ecology, suggest that some benefits of whole grains are mediated through their effects on the gut microbiome. Nutritional studies that assess the effect of whole grains on both the gut microbiome and human physiology are needed. We conducted a randomized cross-over trial with four-week treatments in which 28 healthy humans consumed a daily dose of 60 g of whole-grain barley (WGB), brown rice (BR), or an equal mixture of the two (BR+WGB), and characterized their impact on fecal microbial ecology and blood markers of inflammation, glucose and lipid metabolism. All treatments increased microbial diversity, the Firmicutes/Bacteroidetes ratio, and the abundance of the genus Blautia in fecal samples. The inclusion of WGB enriched the genera Roseburia, Bifidobacterium and Dialister, and the species Eubacterium rectale, Roseburia faecis and Roseburia intestinalis. Whole grains, and especially the BR+WGB treatment, reduced plasma interleukin-6 (IL-6) and peak postprandial glucose. Shifts in the abundance of Eubacterium rectale were associated with changes in the glucose and insulin postprandial response. Interestingly, subjects with greater improvements in IL-6 levels harbored significantly higher proportions of Dialister and lower abundance of Coriobacteriaceae. In conclusion, this study revealed that a short-term intake of whole grains induced compositional alterations of the gut microbiota that coincided with improvements in host physiological measures related to metabolic dysfunctions in humans.}, }
@article {pmid23034184, year = {2012}, author = {Ceuppens, S and Uyttendaele, M and Hamelink, S and Boon, N and Van de Wiele, T}, title = {Inactivation of Bacillus cereus vegetative cells by gastric acid and bile during in vitro gastrointestinal transit.}, journal = {Gut pathogens}, volume = {4}, number = {1}, pages = {11}, pmid = {23034184}, issn = {1757-4749}, abstract = {BACKGROUND: The foodborne pathogen Bacillus cereus can cause diarrhoeal food poisoning by production of enterotoxins in the small intestine. The prerequisite for diarrhoeal disease is thus survival during gastrointestinal passage.<br><br>METHODS: Vegetative cells of 3 different B. cereus strains were cultivated in a real composite food matrix, lasagne verde, and their survival during subsequent simulation of gastrointestinal passage was assessed using in vitro experiments simulating transit through the human upper gastrointestinal tract (from mouth to small intestine).<br><br>RESULTS: No survival of vegetative cells was observed, despite the high inoculum levels of 7.0 to 8.0 log CFU/g and the presence of various potentially protective food components. Significant fractions (approx. 10% of the consumed inoculum) of B. cereus vegetative cells survived gastric passage, but they were subsequently inactivated by bile exposure in weakly acidic intestinal medium (pH 5.0). In contrast, the low numbers of spores present (up to 4.0 log spores/g) showed excellent survival and remained viable spores throughout the gastrointestinal passage simulation.<br><br>CONCLUSION: Vegetative cells are inactivated by gastric acid and bile during gastrointestinal passage, while spores are resistant and survive. Therefore, the physiological form (vegetative cells or spores) of the B. cereus consumed determines the subsequent gastrointestinal survival and thus the infective dose, which is expected to be much lower for spores than vegetative cells. No significant differences in gastrointestinal survival ability was found among the different strains. However, considerable strain variability was observed in sporulation tendency during growth in laboratory medium and food, which has important implications for the gastrointestinal survival potential of the different B. cereus strains.}, }
@article {pmid23019655, year = {2012}, author = {Blainey, PC and Milla, CE and Cornfield, DN and Quake, SR}, title = {Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis.}, journal = {Science translational medicine}, volume = {4}, number = {153}, pages = {153ra130}, pmid = {23019655}, issn = {1946-6242}, support = {DP1 OD000251/OD/NIH HHS/United States ; R01 HG004863/HG/NHGRI NIH HHS/United States ; R01 HL070628/HL/NHLBI NIH HHS/United States ; 5R01HG004863-02/HG/NHGRI NIH HHS/United States ; }, mesh = {Adult ; Bacteria/*genetics/*isolation &amp; purification ; Base Sequence ; Case-Control Studies ; Cystic Fibrosis/*microbiology/*pathology/physiopathology ; Female ; Forced Expiratory Volume ; Humans ; Lung/*microbiology/*pathology/physiopathology ; Male ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Vital Capacity ; }, abstract = {Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the gene encoding the CF transmembrane conductance regulator. Disruption of electrolyte homeostasis at mucosal surfaces leads to severe lung, pancreatic, intestinal, hepatic, and reproductive abnormalities. Loss of lung function as a result of chronic lung disease is the primary cause of death from CF. Using high-throughput sequencing to survey microbes in the sputum of 16 CF patients and 9 control individuals, we identified diverse microbial communities in the healthy samples, contravening conventional wisdom that healthy airways are not significantly colonized. Comparing these communities with those from the CF patients revealed significant differences in microbial ecology, including differential representation of uncultivated phylotypes. Despite patient-specific differences, our analysis revealed a focal microbial profile characteristic of CF. The profile differentiated case and control groups even when classically recognized CF pathogens were excluded. As a control, lung explant tissues were also processed from a group of patients with pulmonary disease. The findings in lung tissue corroborated the presence of taxa identified in the sputum samples. Comparing the sequencing results with clinical data indicated that diminished microbial diversity is associated with severity of pulmonary inflammation within our adult CF cohort.}, }
@article {pmid23017185, year = {2012}, author = {Rehman, T}, title = {Role of the gut microbiota in age-related chronic inflammation.}, journal = {Endocrine, metabolic &amp; immune disorders drug targets}, volume = {12}, number = {4}, pages = {361-367}, doi = {10.2174/187153012803832620}, pmid = {23017185}, issn = {2212-3873}, mesh = {Aging/physiology ; Animals ; Bacterial Load ; Chronic Disease ; Gastrointestinal Tract/*microbiology ; Humans ; Inflammation/*microbiology/*physiopathology ; Metagenome/*physiology ; Phylogeny ; Prebiotics ; Probiotics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Changing demographics have made aging and age-related chronic diseases an enormous and growing biomedical and societal challenge. The biological processes of aging may involve a role for the gut microbiota. Aspects of host physiology such as immune homeostasis and energy balance are profoundly influenced by the microbiota. Immune dysregulation characterizes old age and constitutes a major pathomechanism underlying frailty and age-associated chronic diseases. A growing body of literature implicates age-related perturbations in the gut microbial ecology as contributing to a global inflammatory state in the elderly. A better understanding of the nature and determinants of the host-microbe relationship in old age has the potential to translate into strategies that promote healthy aging and extend life span. This review summarizes our current understanding of the configuration of the age-related gut microbiota and its likely role in determining the immune phenotype in the elderly. It also highlights the specific components of the microbiota that can be targeted to modulate the age-related chronic inflammation.}, }
@article {pmid23015014, year = {2013}, author = {Baltar, F and Arístegui, J and Gasol, JM and Yokokawa, T and Herndl, GJ}, title = {Bacterial versus archaeal origin of extracellular enzymatic activity in the Northeast Atlantic deep waters.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {277-288}, pmid = {23015014}, issn = {1432-184X}, support = {I 486/FWF_/Austrian Science Fund FWF/Austria ; P 23234/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Archaea/*enzymology ; Atlantic Ocean ; Bacteria/*enzymology ; Erythromycin ; Leucyl Aminopeptidase/analysis ; Seawater/chemistry/*microbiology ; alpha-Glucosidases/analysis ; beta-Glucosidase/analysis ; }, abstract = {We determined the total and dissolved extracellular enzymatic activity (EEA) of α-glucosidase and β-glucosidase (AGase and BGase), alkaline phosphatase (APase) and leucine aminopeptidase (LAPase) activities in the epi-, meso- and bathypelagic waters of the subtropical Northeast Atlantic. EEA was also determined in treatments in which bacterial EEA was inhibited by erythromycin. Additionally, EEA decay experiments were performed with surface and deep waters to determine EEA lifetimes in both water masses. The proportion of dissolved to total EEA (66-89 %, 44-88 %, 57-82 % and 86-100 % for AGase, BGase, APase and LAPase, respectively) was generally higher than the cell-associated (i.e., particulate) EEA. The percentage of dissolved to total EEA was inversely proportional to the percentage of erythromycin-inhibited to total EEA. Since erythromycin-inhibited plus dissolved EEA equaled total EEA, this tentatively suggests that cell-associated EEA in the open oceanic water column is almost exclusively of bacterial origin. The decay constants of dissolved EEA were in the range of 0.002-0.048 h(-1) depending on the type of extracellular enzyme, temperature and depth in the water column. Although dissolved EEA can have different origins, the major contribution of Bacteria to cell-associated EEA and the long life-time of dissolved EEA suggest that Bacteria-and not mesophilic Archaea-are essentially the main producers of EEA in the open subtropical Northeast Atlantic down to bathypelagic layers.}, }
@article {pmid23011286, year = {2013}, author = {Meron, D and Buia, MC and Fine, M and Banin, E}, title = {Changes in microbial communities associated with the sea anemone Anemonia viridis in a natural pH gradient.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {269-276}, pmid = {23011286}, issn = {1432-184X}, mesh = {Animals ; Bacteria/genetics/*isolation &amp; purification ; *Biota ; Carbon Dioxide/analysis ; Chlorophyll/analysis ; DNA, Bacterial/genetics ; Dinoflagellida/isolation &amp; purification ; *Hydrogen-Ion Concentration ; Italy ; Mediterranean Sea ; Proton-Motive Force ; Sea Anemones/*microbiology ; Seawater/chemistry ; }, abstract = {Ocean acidification, resulting from rising atmospheric carbon dioxide concentrations, is a pervasive stressor that can affect many marine organisms and their symbionts. Studies which examine the host physiology and microbial communities have shown a variety of responses to the ocean acidification process. Recently, several studies were conducted based on field experiments, which take place in natural CO(2) vents, exposing the host to natural environmental conditions of varying pH. This study examines the sea anemone Anemonia viridis which is found naturally along the pH gradient in Ischia, Italy, with an aim to characterize whether exposure to pH impacts the holobiont. The physiological parameters of A. viridis (Symbiodinium density, protein, and chlorophyll a+c concentration) and its microbial community were monitored. Although reduction in pH was seen to have had an impact on composition and diversity of associated microbial communities, no significant changes were observed in A. viridis physiology, and no microbial stress indicators (i.e., pathogens, antibacterial activity, etc.) were detected. In light of these results, it appears that elevated CO(2) does not have a negative influence on A. viridis that live naturally in the site. This suggests that natural long-term exposure and dynamic diverse microbial communities may contribute to the acclimation process of the host in a changing pH environment.}, }
@article {pmid23001596, year = {2013}, author = {Paulino-Lima, IG and Azua-Bustos, A and Vicuña, R and González-Silva, C and Salas, L and Teixeira, L and Rosado, A and Leitao, AA and Lage, C}, title = {Isolation of UVC-tolerant bacteria from the hyperarid Atacama Desert, Chile.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {325-335}, pmid = {23001596}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*radiation effects ; Biodiversity ; Chile ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; *Desert Climate ; Exobiology ; RNA, Ribosomal, 16S/genetics ; Radiation Tolerance ; *Soil Microbiology ; Ultraviolet Rays ; }, abstract = {Martian surface microbial inhabitants would be challenged by a constant and unimpeded flux of UV radiation, and the study of analog model terrestrial environments may be of help to understand how such life forms could survive under this stressful condition. One of these environments is the Atacama Desert (Chile), a well-known Mars analog due to its extreme dryness and intense solar UV radiation. Here, we report the microbial diversity at five locations across this desert and the isolation of UVC-tolerant microbial strains found in these sites. Denaturing gradient gel electrophoresis (DGGE) of 16S rDNA sequences obtained from these sites showed banding patterns that suggest distinct and complex microbial communities. Analysis of 16S rDNA sequences obtained from UV-tolerant strains isolated from these sites revealed species related to the Bacillus and Pseudomonas genera. Vegetative cells of one of these isolates, Bacillus S3.300-2, showed the highest UV tolerance profile (LD(10) = 318 J m(2)), tenfold higher than a wild-type strain of Escherichia coli. Thus, our results show that the Atacama Desert harbors a noteworthy microbial community that may be considered for future astrobiological-related research in terms of UV tolerance.}, }
@article {pmid22996271, year = {2012}, author = {Liu, YL and Nascimento, M and Burne, RA}, title = {Progress toward understanding the contribution of alkali generation in dental biofilms to inhibition of dental caries.}, journal = {International journal of oral science}, volume = {4}, number = {3}, pages = {135-140}, pmid = {22996271}, issn = {1674-2818}, support = {R01 DE010362/DE/NIDCR NIH HHS/United States ; R90 DE022530/DE/NIDCR NIH HHS/United States ; T90 DE021990/DE/NIDCR NIH HHS/United States ; DE10362/DE/NIDCR NIH HHS/United States ; }, mesh = {Agmatine/metabolism ; Alkalies/*metabolism ; Arginine/metabolism ; Dental Caries/*prevention &amp; control ; Dental Plaque/enzymology/*metabolism/*microbiology ; Humans ; Hydrogen-Ion Concentration ; Hydrolases/metabolism ; Urease/metabolism ; }, abstract = {Alkali production by oral bacteria is believed to have a major impact on oral microbial ecology and to be inhibitory to the initiation and progression of dental caries. A substantial body of evidence is beginning to accumulate that indicates the modulation of the alkalinogenic potential of dental biofilms may be a promising strategy for caries control. This brief review highlights recent progress toward understanding molecular genetic and physiologic aspects of important alkali-generating pathways in oral bacteria, and the role of alkali production in the ecology of dental biofilms in health and disease.}, }
@article {pmid22990462, year = {2013}, author = {Sun, J and Hu, XL and Le, GW and Shi, YH}, title = {Inhibition of Fe-induced colon oxidative stress by lactobacilli in mice.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {29}, number = {2}, pages = {209-216}, pmid = {22990462}, issn = {1573-0972}, mesh = {Animals ; Antioxidants/metabolism ; Bacteria/growth &amp; development/metabolism ; Colon/*metabolism/*microbiology ; Down-Regulation ; Humans ; Hydrogen Peroxide/*metabolism ; Hydroxyl Radical/metabolism ; Iron, Dietary/*metabolism ; Lactobacillus/growth &amp; development/*metabolism ; Male ; Malondialdehyde/metabolism ; Mice ; *Oxidative Stress ; }, abstract = {Iron (Fe) can promote hydrogen peroxide (H(2)O(2)) and hydroxyl radical generation in the colonic surface and promote growth of Fe-dependent bacteria. Some Lactobacillus strains are resistant to oxygen free-radicals, allowing them to survive in a Fe-modulated mucosal environment and influence colon microbial ecology and redox state. Here, we investigated the capacity of lactobacilli with different antioxidant abilities to modify the bacterial profile and prevent oxidative stress in the colon of Fe-overloaded mice. Survival time of Lactobacillus rhamnosus LGG (LGG) in the presence of H(2)O(2) and hydroxyl radical was significantly longer compared with the mid- and non-antioxidative strains, Lactobacillus paracasei Fn032 and Lactobacillus plantarum Fn001, respectively. Different Lactobacillus strains are specific in free-radical scavenging activities of their cell-free extracts, which increased to varying extent depending on strains when bacteria were exposed to simulated gastric and pancreatic juice. Fe-overloaded mice showed increased colonic luminal ferrous Fe content, Enterococcus and Escherichia coli concentrations, mucosal malondialdehyde and free-radicals, and decreased mucosal total antioxidative capacity and oxidative enzymatic activity. Translocation of endotoxin to the liver was also significantly increased (P < 0.05). Lactobacilli inhibited ferrous Fe accumulation, especially in LGG and Fn032. LGG significantly inhibited the increase of colonic mucosal free-radicals and malondialdehyde content (P < 0.05). Fn032 only inhibited malondialdehyde (P < 0.05). LGG and Fn032 significantly inhibited increases in colonic Enterococcus (P < 0.05). Fn001 showed no significant antioxidative ability in vivo. The difference of these effects in vivo were well agreed with scavenging activities against reactive oxygen species (ROS) of simulated gastrointestinals fluid pretreated cells in vitro. In conclusion, ROS scavenging activities was essential for Lactobacillus to prevent oxidative stress in vivo and inhibition of ROS-producing bacterial growth and mucosal barrier injury.}, }
@article {pmid22986821, year = {2012}, author = {Zhang, L and Peng, Y and Wu, S and Sun, L and Huang, E and Huang, T and Xu, L and Wu, C and Gelbič, I and Guan, X}, title = {Microbial ecology and association of Bacillus thuringiensis in chicken feces originating from feed.}, journal = {Current microbiology}, volume = {65}, number = {6}, pages = {784-791}, pmid = {22986821}, issn = {1432-0991}, mesh = {Animal Feed/*microbiology ; Animals ; Bacillus thuringiensis/genetics/growth &amp; development/*isolation &amp; purification ; Chickens/*microbiology ; Duodenum/microbiology ; *Ecosystem ; Feces/*microbiology ; Green Fluorescent Proteins/genetics/metabolism ; Polymerase Chain Reaction/methods ; }, abstract = {To explain the association of Bacillus thuringiensis (Bt) with animal feces, an ecological analysis in chickens was conducted by introducing a cry(-) strain marked by production of green fluorescent protein (GFP). After feeding with the tagged Bt strains, the feces of the tested chickens were collected at different times, isolated, and the morphology of Bt was observed. It was shown that Bt strain HD-73GFP in spore form could be isolated from feces of chickens for a period of 13 d, and then it disappeared thereafter. Bt could be detected only up to day 4 (but not thereafter), when chickens were fed with vegetative cells of HD-73GFP. To confirm the source of newly isolated strains, the gfp gene was examined by polymerase chain reaction (PCR), which showed that all the isolated strains harbored the marker gene. Recent data from isolation and PCR had suggested that fecal Bt strains had originated from food. Chicken tissues were thus dissected to isolate Bt strains and to investigate whether Bt could be located in vivo. Bt was located within the duodenum in spore form. Compared to the morphology of the isolated strains at different growth times, the growth rates of all the tested Bt had little changes when passing through the digestive system to the feces. Dissection of the chickens confirmed that Bt was safe for the tested animal.}, }
@article {pmid22984895, year = {2013}, author = {Vissers, EW and Blaga, CI and Bodelier, PL and Muyzer, G and Schleper, C and Sinninghe Damsté, JS and Tourna, M and Laanbroek, HJ}, title = {Seasonal and vertical distribution of putative ammonia-oxidizing thaumarchaeotal communities in an oligotrophic lake.}, journal = {FEMS microbiology ecology}, volume = {83}, number = {2}, pages = {515-526}, doi = {10.1111/1574-6941.12013}, pmid = {22984895}, issn = {1574-6941}, mesh = {Ammonia ; Archaea/*classification/genetics/isolation &amp; purification ; Lakes/*microbiology ; Lipids/analysis ; Oxidoreductases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Seasons ; Switzerland ; }, abstract = {The discovery of Archaea carrying an amoA gene coding for the A-subunit of ammonia monooxygenase gave a boost to studies aimed at detecting this gene under diverse conditions. Despite numerous studies describing the archaeal amoA gene abundance and richness in different habitats, the understanding of the freshwater ecology of potentially archaeal ammonia oxidizers, recently positioned in the phylum Thaumarchaeota, is still lacking. In a seasonal and vertical study of deep oligotrophic Lake Lucerne, Switzerland, with high Thaumarchaeota-specific crenarchaeol concentrations, we showed that all archaeal 16S rRNA genes found belong to the thaumarchaeotal phylum. The abundances of archaeal 16S rRNA and amoA genes remained in the same order of magnitude (average 6 × mL(-1)) and displayed matching seasonal dynamics within 16 monthly collected samples at three different water depths (r(2) = 0.80, slope of 1.06). The Thaumarchaeota in this lake form a distinct cluster in both the 16S rRNA and amoA gene phylogenies, are affiliated to other thaumarchaeotal freshwater sequences within group 1.1a Archaea, and fall in the low saline cluster of the amoA phylogeny. In accordance with temperature and conductivity, the Thaumarchaeota in the surface water showed a significantly different seasonality and lower abundance than their counterparts in the deeper waters. This study indicates that the ecology of Thaumarchaeota, with their potential in nitrogen cycling, may differ per water depth in deep freshwater ecosystems.}, }
@article {pmid22983497, year = {2013}, author = {Lee, SH and Jang, I and Chae, N and Choi, T and Kang, H}, title = {Organic layer serves as a hotspot of microbial activity and abundance in Arctic tundra soils.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {405-414}, pmid = {22983497}, issn = {1432-184X}, mesh = {Archaea/genetics ; Arctic Regions ; Bacteria/genetics ; *Biodiversity ; Carbon/analysis ; DNA, Archaeal/analysis ; DNA, Bacterial/analysis ; DNA, Fungal/analysis ; *Ecosystem ; Fungi/genetics ; Multivariate Analysis ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Soil/analysis ; *Soil Microbiology ; Svalbard ; }, abstract = {Tundra ecosystem is of importance for its high accumulation of organic carbon and vulnerability to future climate change. Microorganisms play a key role in carbon dynamics of the tundra ecosystem by mineralizing organic carbon. We assessed both ecosystem process rates and community structure of Bacteria, Archaea, and Fungi in different soil layers (surface organic layer and subsurface mineral soil) in an Arctic soil ecosystem located at Spitsbergen, Svalbard during the summer of 2008 by using biochemical and molecular analyses, such as enzymatic assay, terminal restriction fragment length polymorphism (T-RFLP), quantitative polymerase chain reaction (qPCR), and pyrosequencing. Activity of hydrolytic enzymes showed difference according to soil type. For all three microbial communities, the average gene copy number did not significantly differ between soil types. However, archaeal diversities appeared to differ according to soil type, whereas bacterial and fungal diversity indices did not show any variation. Correlation analysis between biogeochemical and microbial parameters exhibited a discriminating pattern according to microbial or soil types. Analysis of the microbial community structure showed that bacterial and archaeal communities have different profiles with unique phylotypes in terms of soil types. Water content and hydrolytic enzymes were found to be related with the structure of bacterial and archaeal communities, whereas soil organic matter (SOM) and total organic carbon (TOC) were related with bacterial communities. The overall results of this study indicate that microbial enzyme activity were generally higher in the organic layer than in mineral soils and that bacterial and archaeal communities differed between the organic layer and mineral soils in the Arctic region. Compared to mineral soil, peat-covered organic layer may represent a hotspot for secondary productivity and nutrient cycling in this ecosystem.}, }
@article {pmid22978352, year = {2013}, author = {van der Wal, A and Geydan, TD and Kuyper, TW and de Boer, W}, title = {A thready affair: linking fungal diversity and community dynamics to terrestrial decomposition processes.}, journal = {FEMS microbiology reviews}, volume = {37}, number = {4}, pages = {477-494}, doi = {10.1111/1574-6976.12001}, pmid = {22978352}, issn = {1574-6976}, mesh = {Carbon Cycle ; *Ecosystem ; Fungi/*growth &amp; development ; Global Warming ; *Soil Microbiology ; }, abstract = {Filamentous fungi are critical to the decomposition of terrestrial organic matter and, consequently, in the global carbon cycle. In particular, their contribution to degradation of recalcitrant lignocellulose complexes has been widely studied. In this review, we focus on the functioning of terrestrial fungal decomposers and examine the factors that affect their activities and community dynamics. In relation to this, impacts of global warming and increased N deposition are discussed. We also address the contribution of fungal decomposer studies to the development of general community ecological concepts such as diversity-functioning relationships, succession, priority effects and home-field advantage. Finally, we indicate several research directions that will lead to a more complete understanding of the ecological roles of terrestrial decomposer fungi such as their importance in turnover of rhizodeposits, the consequences of interactions with other organisms and niche differentiation.}, }
@article {pmid22977615, year = {2011}, author = {Zhang, SM and Tian, F and Huang, QF and Zhao, YF and Guo, XK and Zhang, FQ}, title = {Bacterial diversity of subgingival plaque in 6 healthy Chinese individuals.}, journal = {Experimental and therapeutic medicine}, volume = {2}, number = {5}, pages = {1023-1029}, pmid = {22977615}, issn = {1792-0981}, abstract = {The subgingival microbial ecology is complex, and little is known regarding its bacteria species composition in healthy Chinese individuals. This study aimed to identify the subgingival microbiota from 6 healthy Chinese subjects. Subgingival samples from 6 volunteers were collected, the 16S rRNA gene was amplified using broad-range bacterial primers, and clone libraries were constructed. For the initial 2,439 sequences analyzed, 383 species-level operational taxonomic units (SLOTUs) belonging to seven phyla were identified, estimated as 51% [95% confidence interval (CI) 44-55] of the SLOTUs in this ecosystem. Most (85%) of the bacterial sequences, falling into 228 types of species, corresponded to known and cultivated species. However, 146 (6%) sequences, comprising 104 phylotypes, had <97% similarity to prior database sequences. Ten bacterial genera were conserved among all 6 individuals, comprising 2,000 (82%) of the 2,439 clones analyzed. Ten species were noted in all of the 6 subjects, comprising 1,435 (58.8%) of the 2,439 clones. Streptococcus infantis was the species most frequently cloned. Furthermore, certain species which may participate in the pathogenesis of periodontal disease were present in the 6 subjects. Although the initial subgingival plaque community of each subject was unique in terms of diversity and composition, 10 common key species were found in the 6 Chinese individuals. These ten species of bacteria in the human subgingival plaque in the 6 healthy individuals may be key species which, to some extent, affect periodontal health. Destruction of these key species in subgingival bacteria may break the microbiota balance and may easily lead to over-breeding conditions resulting in pathogenic oral disease.}, }
@article {pmid22976340, year = {2013}, author = {Besaury, L and Marty, F and Buquet, S and Mesnage, V and Muyzer, G and Quillet, L}, title = {Culture-dependent and independent studies of microbial diversity in highly copper-contaminated Chilean marine sediments.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {311-324}, pmid = {22976340}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Chile ; Copper/*analysis ; Gene Library ; Genes, Bacterial ; Geologic Sediments/chemistry/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/microbiology ; Sulfur-Reducing Bacteria/classification/genetics/isolation &amp; purification ; Water Microbiology ; Water Pollutants/*analysis ; }, abstract = {Cultivation and molecular-based approaches were used to study microbial diversity in two Chilean marine sediments contaminated with high (835 ppm) and very high concentrations of copper (1,533 ppm). The diversity of cultivable bacteria resistant to copper was studied at oxic and anoxic conditions, focusing on sulfate-, thiosulfate-, and iron-reducing bacteria. For both sediments, the cultivable bacteria isolated at oxic conditions were mostly affiliated to the genus Bacillus, while at anoxic conditions the majority of the cultivable bacteria found were closely related to members of the genera Desulfovibrio, Sphingomonas, and Virgibacillus. Copper resistance was between 100 and 400 ppm, with the exception of a strain affiliated to members of the genus Desulfuromonas, which was resistant up to 1,000 ppm of copper. In parallel, cloning and sequencing of 16S rRNA was performed to study the total bacterial diversity in the sediments. A weak correlation was observed between the isolated strains and the 16S rRNA operational taxonomic units detected. The presence of copper resistance genes (copA, cusA, and pcoA) was tested for all the strains isolated; only copA was detected in a few isolates, suggesting that other copper resistance mechanisms could be used by the bacteria in those highly copper-contaminated sediments.}, }
@article {pmid22976339, year = {2013}, author = {Kaewkla, O and Franco, CM}, title = {Rational approaches to improving the isolation of endophytic actinobacteria from Australian native trees.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {384-393}, pmid = {22976339}, issn = {1432-184X}, mesh = {Actinobacteria/classification/genetics/*isolation &amp; purification ; Australia ; Bacteriological Techniques/*methods ; Biodiversity ; Culture Media ; Cupressaceae/microbiology ; DNA, Bacterial/genetics ; Eucalyptus/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rosales/microbiology ; Sequence Analysis, DNA ; Trees/*microbiology ; }, abstract = {In recent years, new actinobacterial species have been isolated as endophytes of plants and shrubs and are sought after both for their role as potential producers of new drug candidates for the pharmaceutical industry and as biocontrol inoculants for sustainable agriculture. Molecular-based approaches to the study of microbial ecology generally reveal a broader microbial diversity than can be obtained by cultivation methods. This study aimed to improve the success of isolating individual members of the actinobacterial population as pure cultures as well as improving the ability to characterise the large numbers obtained in pure culture. To achieve this objective, our study successfully employed rational and holistic approaches including the use of isolation media with low concentrations of nutrients normally available to the microorganism in the plant, plating larger quantities of plant sample, incubating isolation plates for up to 16 weeks, excising colonies when they are visible and choosing Australian endemic trees as the source of the actinobacteria. A hierarchy of polyphasic methods based on culture morphology, amplified 16S rRNA gene restriction analysis and limited sequencing was used to classify all 576 actinobacterial isolates from leaf, stem and root samples of two eucalypts: a Grey Box and Red Gum, a native apricot tree and a native pine tree. The classification revealed that, in addition to 413 Streptomyces spp., isolates belonged to 16 other actinobacterial genera: Actinomadura (two strains), Actinomycetospora (six), Actinopolymorpha (two), Amycolatopsis (six), Gordonia (one), Kribbella (25), Micromonospora (six), Nocardia (ten), Nocardioides (11), Nocardiopsis (one), Nonomuraea (one), Polymorphospora (two), Promicromonospora (51), Pseudonocardia (36), Williamsia (two) and a novel genus Flindersiella (one). In order to prove novelty, 12 strains were characterised fully to the species level based on polyphasic taxonomy. One strain represented a novel genus in the family Nocardioides, and the other 11 strains were accepted as novel species. In summary, the holistic isolation strategies were successful in obtaining significant culturable actinobacterial diversity within Australian native trees that includes rare and novel species.}, }
@article {pmid22975124, year = {2012}, author = {Hassan, SH and Kim, YS and Oh, SE}, title = {Power generation from cellulose using mixed and pure cultures of cellulose-degrading bacteria in a microbial fuel cell.}, journal = {Enzyme and microbial technology}, volume = {51}, number = {5}, pages = {269-273}, doi = {10.1016/j.enzmictec.2012.07.008}, pmid = {22975124}, issn = {1879-0909}, mesh = {Actinomycetales/growth &amp; development/*metabolism ; Bioelectric Energy Sources/*microbiology ; Biotechnology/*methods ; Cellulose/*metabolism ; Culture Media ; *Electricity ; Streptomyces/growth &amp; development/*metabolism ; }, abstract = {Microbial fuel cells (MFCs) have been used to generate electricity from various organic compounds such as acetate, glucose, and lactate. We demonstrate here that electricity can be produced in an MFC using cellulose as the electron donor source. Tests were conducted using two-chambered MFCs, the anode medium was inoculated with mixed or pure culture of cellulose-degrading bacteria Nocardiopsis sp. KNU (S strain) or Streptomyces enissocaesilis KNU (K strain), and the catholyte in the cathode compartment was 50mM ferricyanide as catholyte. The power density for the mixed culture was 0.188 mW (188 mW/m(2)) at a current of 0.5mA when 1g/L cellulose was used. However, the power density decreased as the cellulose concentration in the anode compartment decreased. The columbic efficiencies (CEs) ranged from 41.5 to 33.4%, corresponding to an initial cellulose concentration of 0.1-1.0 g/L. For the pure culture, cellobioase enzyme was added to increase the conversion of cellulose to simple sugars, since electricity production is very low. The power densities for S and K strain pure cultures with cellobioase were 162 mW/m(2) and 145 mW/m(2), respectively. Cyclic voltammetry (CV) experiments showed the presence of peaks at 380, 500, and 720 mV vs. Ag/AgCl for the mixed bacterial culture, indicating its electrochemical activity without an external mediator. Furthermore, this MFC system employs a unique microbial ecology in which both the electron donor (cellulose) and the electron acceptor (carbon paper) are insoluble.}, }
@article {pmid22974422, year = {2013}, author = {Zened, A and Combes, S and Cauquil, L and Mariette, J and Klopp, C and Bouchez, O and Troegeler-Meynadier, A and Enjalbert, F}, title = {Microbial ecology of the rumen evaluated by 454 GS FLX pyrosequencing is affected by starch and oil supplementation of diets.}, journal = {FEMS microbiology ecology}, volume = {83}, number = {2}, pages = {504-514}, doi = {10.1111/1574-6941.12011}, pmid = {22974422}, issn = {1574-6941}, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Cattle ; *Dietary Supplements ; Female ; Plant Oils/administration &amp; dosage/*pharmacology ; Rumen/*microbiology ; Sequence Analysis, DNA ; Silage ; Starch/administration &amp; dosage/*pharmacology ; Sunflower Oil ; Zea mays ; }, abstract = {To provide a comprehensive examination of the bacterial diversity in the rumen content of cows fed different diets, high-throughput 16S rRNA gene-based pyrosequencing was used. Four rumen fistulated nonlactating Holstein cows received 12 kg of dry matter per day of four diets based on maize silage during four periods: the low-starch diet (22% starch, 3% fat); the high-starch diet, supplemented with wheat plus barley (35% starch, 3% fat); the low-starch plus oil diet, supplemented with 5% of sunflower oil (20% starch, 7.6% fat) and the high-starch plus oil diet (33% starch, 7.3% fat). Samples were taken after 12 days of adaptation, 5 h postfeeding. Whatever the diet, bacterial community of sieved rumen contents was dominated by Firmicutes and Bacteroidetes. Lachnospiraceae, Ruminococcaceae, Prevotellaceae, and Rikenellaceae families were highly present and were clearly affected by cow diet. The highest abundance of Prevotellaceae and the lowest abundance of Ruminococcaceae and Rikenellaceae were found with the high-starch plus oil diet. Dietary starch increased the relative abundance of only three genera: Barnesiella, Oribacterium and Olsenella, but decreased the relative abundances of several genera, with very significant effects for Rikenellaceae_RC9 and Butyrivibrio-Pseudobutyrivibrio. Oil alone had a limited effect, but interestingly, starch plus oil addition differently affected the bacterial populations compared to starch addition without oil.}, }
@article {pmid22971047, year = {2012}, author = {Pickles, BJ and Genney, DR and Anderson, IC and Alexander, IJ}, title = {Spatial analysis of ectomycorrhizal fungi reveals that root tip communities are structured by competitive interactions.}, journal = {Molecular ecology}, volume = {21}, number = {20}, pages = {5110-5123}, doi = {10.1111/j.1365-294X.2012.05739.x}, pmid = {22971047}, issn = {1365-294X}, mesh = {*Biodiversity ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Databases, Nucleic Acid ; Meristem/*microbiology ; Mycorrhizae/*genetics/physiology ; Pinus/microbiology ; Polymorphism, Restriction Fragment Length ; Soil Microbiology ; Spatial Analysis ; Stochastic Processes ; }, abstract = {Microbial ecology has made large advances over the last decade, mostly because of improvements in molecular analysis techniques that have enabled the detection and identification of progressively larger numbers of microbial species. However, determining the ecological patterns and processes taking place in communities of microbes remains a significant challenge. Are communities randomly assembled through dispersal and priority effects, or do species interact with each other leading to positive and negative associations? For mycorrhizal fungi, evidence is accumulating that stochastic and competitive interactions between species may both have a role in shaping community structure. Could the methodological approach, which is often incidence based, impact the outcomes detected? Here, we applied an incidence-based Terminal Restriction Fragment Length Polymorphism (T-RFLP) database approach to examine species diversity and ecological interactions within a community of ectomycorrhizal (ECM) fungi. Co-occurrence analysis revealed that the ECM community colonizing root tips was strongly structured by competitive interactions, or ecological processes generating a similar spatial pattern, rather than neutral processes. Analysis of β-diversity indicated that community structure was significantly more similar (spatially autocorrelated) at distances equal to or <3.41 m. The eight most frequently encountered species in the root tip community of ECM fungi displayed significant competitive interactions with at least one other species, showing that the incidence-based approach was capable of detecting this sort of ecological information.}, }
@article {pmid22970184, year = {2012}, author = {Lee, CK and Herbold, CW and Polson, SW and Wommack, KE and Williamson, SJ and McDonald, IR and Cary, SC}, title = {Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e44224}, pmid = {22970184}, issn = {1932-6203}, mesh = {Algorithms ; Bacteria/*genetics ; Base Sequence ; *Bias ; *Biota ; DNA Primers/metabolism ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; Statistics, Nonparametric ; *Temperature ; }, abstract = {Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure.}, }
@article {pmid22968328, year = {2013}, author = {Ling, Z and Liu, X and Wang, Y and Li, L and Xiang, C}, title = {Pyrosequencing analysis of the salivary microbiota of healthy Chinese children and adults.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {487-495}, pmid = {22968328}, issn = {1432-184X}, mesh = {Asian People ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Child ; Child, Preschool ; DNA, Bacterial/genetics ; Female ; Humans ; Male ; *Metagenome ; Saliva/*microbiology ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Describing the biogeography of bacterial communities within the human body is critical for establishing healthy baselines from which to detect differences associated with diseases. Little is known, however, about the baseline of normal salivary microbiota from healthy Chinese children and adults. With parallel barcoded 454 pyrosequencing, the bacterial diversity and richness of saliva were thoroughly investigated from ten healthy Chinese children and adults. The overall taxonomic distribution of our metagenomic data demonstrated that the diversity of salivary microbiota from children was more complex than adults, while the composition and richness of salivary microbiota were similar in children and adults, especially for predominant bacteria. A large number of bacterial phylotypes were shared by healthy children and adults, indicating the existence of a core salivary microbiome. In children and adults, the vast majority of sequences in salivary microbiota belonged to Streptococcus, Prevotella, Neisseria, Haemophilus, Porphyromonas, Gemella, Rothia, Granulicatella, Fusobacterium, Actinomyces, Veillonella, and Aggregatibacter, which constituted the major components of normal salivary microbiota. With the exception of Actinomyces, the other seven non-predominant bacteria including Moraxella, Leptotrichia, Peptostreptococcus, Eubacterium, and members of Neisseriaceae, Flavobacteriaceae, and SR1 showed significant differences between children and adults (p < 0.05). We first established the framework of normal salivary microbiota from healthy Chinese children and adults. Our data represent a critical step for determining the diversity of healthy microbiota in Chinese children and adults, and our data established a platform for additional large-scale studies focusing on the interactions between health and diseases in the future.}, }
@article {pmid22968327, year = {2013}, author = {Patterson, RT and Lamoureux, ED and Neville, LA and Macumber, AL}, title = {Arcellacea (testate lobose amoebae) as pH indicators in a pyrite mine-acidified lake, Northeastern Ontario, Canada.}, journal = {Microbial ecology}, volume = {65}, number = {3}, pages = {541-554}, pmid = {22968327}, issn = {1432-184X}, mesh = {Acids/metabolism ; Amoebida/classification/genetics/*isolation &amp; purification/metabolism ; Ecosystem ; Environmental Monitoring/*methods ; Hydrogen-Ion Concentration ; Iron/*analysis ; Lakes/*chemistry/parasitology ; Ontario ; Phylogeny ; Sulfides/*analysis ; }, abstract = {Arcellacea (testate lobose amoebae) were examined in 24 sediment-water interface samples collected over two late August field seasons in 2010 and 2011, from James and Granite lakes, Temagami Region, Northeastern Ontario. The work was carried out to quantitatively test species-environment relationships in a lake system known to be characterized by a significant pH gradient, partially the result of contamination from the early twentieth century Northland Pyrite Mine Co., located on the shoreline in the southern basin of James Lake. Redundancy analysis confirmed that arcellacean assemblage structure was most strongly controlled by pH, explaining 14.06 % (p < 0.002) of the total variance. Q- and R-mode cluster analysis supported by detrended correspondence analysis yielded two major faunal assemblages. The Oligotrophic Assemblage (1) had a Shannon Diversity Index (SDI) ranging up to 2.45, typical of healthy boreal lakes. This assemblage characterized samples collected from higher pH stations within James and Granite lakes away from the immediate area of the mine site, while the Low pH Assemblage 2010 (2a) and Low pH Assemblage 2011 (2b) groupings were from the very low pH environments of James Lake adjacent to the former mine site. Both low diversity assemblages (SDI ranging from 0.62 to 1.22) were characterized by Arcella vulgaris, a species known to thrive in hostile lacustrine environments. Differing depositional conditions during August 2010, a probable result of different prevailing wind patterns that summer, led to allochthonous specimens of the seasonally planktic Cucurbitella tricuspis dominating the Low pH Assemblage 2010 (2a) fauna.}, }
@article {pmid22967509, year = {2012}, author = {Ulloa, O and Canfield, DE and DeLong, EF and Letelier, RM and Stewart, FJ}, title = {Microbial oceanography of anoxic oxygen minimum zones.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {40}, pages = {15996-16003}, pmid = {22967509}, issn = {1091-6490}, mesh = {Anaerobiosis ; *Biota ; Environmental Monitoring/*statistics &amp; numerical data ; Metagenome/*genetics ; Oceanography ; Oceans and Seas ; Oxygen/*analysis/chemistry ; Seawater/*chemistry ; *Water Microbiology ; }, abstract = {Vast expanses of oxygen-deficient and nitrite-rich water define the major oxygen minimum zones (OMZs) of the global ocean. They support diverse microbial communities that influence the nitrogen economy of the oceans, contributing to major losses of fixed nitrogen as dinitrogen (N(2)) and nitrous oxide (N(2)O) gases. Anaerobic microbial processes, including the two pathways of N(2) production, denitrification and anaerobic ammonium oxidation, are oxygen-sensitive, with some occurring only under strictly anoxic conditions. The detection limit of the usual method (Winkler titrations) for measuring dissolved oxygen in seawater, however, is much too high to distinguish low oxygen conditions from true anoxia. However, new analytical technologies are revealing vanishingly low oxygen concentrations in nitrite-rich OMZs, indicating that these OMZs are essentially anoxic marine zones (AMZs). Autonomous monitoring platforms also reveal previously unrecognized episodic intrusions of oxygen into the AMZ core, which could periodically support aerobic metabolisms in a typically anoxic environment. Although nitrogen cycling is considered to dominate the microbial ecology and biogeochemistry of AMZs, recent environmental genomics and geochemical studies show the presence of other relevant processes, particularly those associated with the sulfur and carbon cycles. AMZs correspond to an intermediate state between two "end points" represented by fully oxic systems and fully sulfidic systems. Modern and ancient AMZs and sulfidic basins are chemically and functionally related. Global change is affecting the magnitude of biogeochemical fluxes and ocean chemical inventories, leading to shifts in AMZ chemistry and biology that are likely to continue well into the future.}, }
@article {pmid22967313, year = {2012}, author = {Bialek, K and Kumar, A and Mahony, T and Lens, PN and O'Flaherty, V}, title = {Microbial community structure and dynamics in anaerobic fluidized-bed and granular sludge-bed reactors: influence of operational temperature and reactor configuration.}, journal = {Microbial biotechnology}, volume = {5}, number = {6}, pages = {738-752}, pmid = {22967313}, issn = {1751-7915}, mesh = {Bacteria/*classification/*genetics ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Dairy Products ; Denaturing Gradient Gel Electrophoresis ; Food Industry ; Methane/metabolism ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sewage/*microbiology ; Temperature ; Wastewater/*microbiology ; Water Purification ; }, abstract = {Methanogenic community structure and dynamics were investigated in two different, replicated anaerobic wastewater treatment reactor configurations [inverted fluidized bed (IFB) and expanded granular sludge bed (EGSB)] treating synthetic dairy wastewater, during operating temperature transitions from 37°C to 25°C, and from 25°C to 15°C, over a 430-day trial. Non-metric multidimensional scaling (NMS) and moving-window analyses, based on quantitative real-time PCR data, along with denaturing gradient gel electrophoresis (DGGE) profiling, demonstrated that the methanogenic communities developed in a different manner in these reactor configurations. A comparable level of performance was recorded for both systems at 37°C and 25°C, but a more dynamic and diverse microbial community in the IFB reactors supported better stability and adaptative capacity towards low temperature operation. The emergence and maintenance of particular bacterial genotypes (phylum Firmicutes and Bacteroidetes) was associated with efficient protein hydrolysis in the IFB, while protein hydrolysis was inefficient in the EGSB. A significant community shift from a Methanobacteriales and Methanosaetaceae towards a Methanomicrobiales-predominated community was demonstrated during operation at 15°C in both reactor configurations.}, }
@article {pmid22965804, year = {2013}, author = {Carrillo-Benítez, MG and Guzmán-Franco, AW and Alatorre-Rosas, R and Enríquez-Vara, JN}, title = {Diversity and genetic population structure of fungal pathogens infecting white grub larvae in agricultural soils.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {437-449}, pmid = {22965804}, issn = {1432-184X}, mesh = {Agriculture ; Animals ; Beauveria/*genetics/physiology ; Coleoptera/*microbiology ; DNA, Fungal/analysis ; Genotype ; Larva/microbiology ; Metarhizium/*genetics/physiology ; Microsatellite Repeats ; Pest Control, Biological ; Phylogeny ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {White grub larvae are important soil-dwelling pests in many regions of Mexico as they attack many important crops such as maize. The use of synthetic chemicals is currently the main control strategy, but they are not always effective; thus, other alternatives are needed. Microbial control using entomopathogenic fungi represents an important alternative strategy, and species within the genera Beauveria and Metarhizium are considered amongst the most promising candidates. Seventeen Beauveria spp. and two Metarhizium spp. isolates were obtained in surveys of white grub larvae from different regions of Guanajuato, Mexico. All isolates were capable of infecting healthy larvae of the white grub Phyllophaga polyphilla in laboratory assays, but mortality never exceeded 50 %. Isolates were identified using morphological and molecular methods. Based on elongation factor1-α and ITS partial gene sequence data, all Beauveria isolates were identified as Beauveria pseudobassiana. Elongation factor1-α and β-tubulin sequence data identified the Metarhizium isolates to be Metarhizium pingshaense. In contrast, three additional Metarhizium isolates obtained the previous year in the same region were identified as M. pingshaense, Metarhizium anisopliae and Metarhizium robertsii. Microsatellite genotyping showed that all B. pseudobassiana isolates were the same haplotype. Enterobacterial Repetitive Intergenic Consensus fingerprinting information confirmed no significant variation amongst the B. pseudobassiana isolates. The ecological role of these isolates and their impact on white grub larvae populations are discussed.}, }
@article {pmid22965803, year = {2013}, author = {Coelho-Souza, SA and Miranda, MR and Salgado, LT and Coutinho, R and Guimaraes, JR}, title = {Adaptation of the 3H-leucine incorporation technique to measure heterotrophic activity associated with biofilm on the blades of the seaweed Sargassum spp.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {424-436}, pmid = {22965803}, issn = {1432-184X}, mesh = {Bacteria/*metabolism/radiation effects ; *Biofilms ; *Heterotrophic Processes ; Leucine/metabolism ; Light ; Microscopy, Electron, Scanning ; Sargassum/*microbiology ; Seaweed/microbiology ; *Water Microbiology ; }, abstract = {The ecological interaction between microorganisms and seaweeds depends on the production of secondary compounds that can influence microbial diversity in the water column and the composition of reef environments. We adapted the (3)H-leucine incorporation technique to measure bacterial activity in biofilms associated with the blades of the macroalgae Sargassum spp. We evaluated (1) if the epiphytic bacteria on the blades were more active in detritus or in the biofilm, (2) substrate saturation and linearity of (3)H-leucine incorporation, (3) the influence of specific metabolic inhibitors during (3)H-leucine incorporation under the presence or absence of natural and artificial light, and (4) the efficiency of radiolabeled protein extraction. Scanning electron microscopy showed heterogeneous distribution of bacteria, diatoms, and polymeric extracellular secretions. Active bacteria were present in both biofilm and detritus on the blades. The highest (3)H-leucine incorporation was obtained when incubating blades not colonized by macroepibionts. Incubations done under field conditions reported higher (3)H-leucine incorporation than in the laboratory. Light quality and sampling manipulation seemed to be the main factors behind this difference. The use of specific metabolic inhibitors confirmed that bacteria are the main group incorporating (3)H-leucine but their association with primary production suggested a symbiotic relationship between bacteria, diatoms, and the seaweed.}, }
@article {pmid22961365, year = {2013}, author = {Kelly, JJ and Peterson, E and Winkelman, J and Walter, TJ and Rier, ST and Tuchman, NC}, title = {Elevated atmospheric CO2 impacts abundance and diversity of nitrogen cycling functional genes in soil.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {394-404}, pmid = {22961365}, issn = {1432-184X}, mesh = {Archaea/enzymology/genetics/*growth &amp; development ; Atmosphere ; Bacteria/enzymology/genetics/*growth &amp; development ; Carbon Dioxide/*analysis ; Climate Change ; DNA, Archaeal/analysis ; DNA, Bacterial/analysis ; Gene Library ; Genes, Archaeal ; Genes, Bacterial ; Nitrite Reductases/analysis ; *Nitrogen Cycle ; Oxidoreductases/analysis ; Populus/*microbiology ; *Soil Microbiology ; }, abstract = {The concentration of CO(2) in the Earth's atmosphere has increased over the last century. Although this increase is unlikely to have direct effects on soil microbial communities, increased atmospheric CO(2) may impact soil ecosystems indirectly through plant responses. This study tested the hypothesis that exposure of plants to elevated CO(2) would impact soil microorganisms responsible for key nitrogen cycling processes, specifically denitrification and nitrification. We grew trembling aspen (Populus tremuloides) trees in outdoor chambers under ambient (360 ppm) or elevated (720 ppm) levels of CO(2) for 5 years and analyzed the microbial communities in the soils below the trees using quantitative polymerase chain reaction and clone library sequencing targeting the nitrite reductase (nirK) and ammonia monooxygenase (amoA) genes. We observed a more than twofold increase in copy numbers of nirK and a decrease in nirK diversity with CO(2) enrichment, with an increased predominance of Bradyrhizobia-like nirK sequences. We suggest that this dramatic increase in nirK-containing bacteria may have contributed to the significant loss of soil N in the CO(2)-treated chambers. Elevated CO(2) also resulted in a significant decrease in copy numbers of bacterial amoA, but no change in archaeal amoA copy numbers. The decrease in abundance of bacterial amoA was likely a result of the loss of soil N in the CO(2)-treated chambers, while the lack of response for archaeal amoA supports the hypothesis that physiological differences in these two groups of ammonia oxidizers may enable them to occupy distinct ecological niches and respond differently to environmental change.}, }
@article {pmid22961364, year = {2013}, author = {Vainio, EJ and Piri, T and Hantula, J}, title = {Virus community dynamics in the conifer pathogenic fungus Heterobasidion parviporum following an artificial introduction of a partitivirus.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {28-38}, pmid = {22961364}, issn = {1432-184X}, mesh = {Basidiomycota/genetics/pathogenicity/*virology ; Genotype ; Mycelium/virology ; Picea/*microbiology ; RNA Virus Infections/transmission ; RNA Viruses/*physiology ; RNA, Viral/isolation &amp; purification ; }, abstract = {Viruses infecting the conifer pathogenic fungus Heterobasidion annosum sensu lato are intracellular and spread via anastomosis contacts. In the laboratory, these viruses transmit readily even between somatically incompatible isolates, but their dispersal capacity in natural conditions has not been previously studied. We introduced a mycovirus to a heavily diseased forest site by inoculating Norway spruce stumps with heartrot decay using a mycelial suspension of Heterobasidion parviporum strain RT3.49C hosting the partitivirus strain HetRV4-pa1. The Heterobasidion population at the sample plot was screened for mycoviruses prior to and after the inoculation. Based on sequence analysis, the resident H. parviporum strains harbored six different strains of the virus species Heterobasidion RNA virus 6 (HetRV6) and one strain of HetRV4 prior to the inoculation. After three growth seasons, the inoculated H. parviporum host strain was not detected, but the introduced virus had infected two resident H. parviporum genets. The presence of a preexisting HetRV6 infection did not hinder spread of the introduced partitivirus but resulted in coinfections instead. The resident HetRV6 virus population seemed to be highly stable during the incubation period, while the single indigenous HetRV4 infection was not detected after the inoculation. In laboratory infection experiments, the introduced virus could be transmitted successfully into all of the resident H. parviporum genets. This study shows for the first time transmission of a Heterobasidion virus between somatically incompatible hosts in natural conditions.}, }
@article {pmid22961363, year = {2013}, author = {Faulwetter, JL and Burr, MD and Parker, AE and Stein, OR and Camper, AK}, title = {Influence of season and plant species on the abundance and diversity of sulfate reducing bacteria and ammonia oxidizing bacteria in constructed wetland microcosms.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {111-127}, pmid = {22961363}, issn = {1432-184X}, mesh = {Ammonia/metabolism ; DNA, Bacterial/isolation &amp; purification ; Genes, Bacterial ; Hydrogensulfite Reductase/genetics ; Oxidoreductases/genetics ; Poaceae/*growth &amp; development ; *Seasons ; Sulfates/metabolism ; Sulfur-Reducing Bacteria/classification/*growth &amp; development ; Waste Disposal, Fluid ; Wastewater/microbiology ; *Water Microbiology ; *Wetlands ; }, abstract = {Constructed wetlands offer an effective means for treatment of wastewater from a variety of sources. An understanding of the microbial ecology controlling nitrogen, carbon and sulfur cycles in constructed wetlands has been identified as the greatest gap for optimizing performance of these promising treatment systems. It is suspected that operational factors such as plant types and hydraulic operation influence the subsurface wetland environment, especially redox, and that the observed variation in effluent quality is due to shifts in the microbial populations and/or their activity. This study investigated the biofilm associated sulfate reducing bacteria and ammonia oxidizing bacteria (using the dsrB and amoA genes, respectively) by examining a variety of surfaces within a model wetland (gravel, thick roots, fine roots, effluent), and the changes in activity (gene abundance) of these functional groups as influenced by plant species and season. Molecular techniques were used including quantitative PCR and denaturing gradient gel electrophoresis (DGGE), both with and without propidium monoazide (PMA) treatment. PMA treatment is a method for excluding from further analysis those cells with compromised membranes. Rigorous statistical analysis showed an interaction between the abundance of these two functional groups with the type of plant and season (p < 0.05). The richness of the sulfate reducing bacterial community, as indicated by DGGE profiles, increased in planted vs. unplanted microcosms. For ammonia oxidizing bacteria, season had the greatest impact on gene abundance and diversity (higher in summer than in winter). Overall, the primary influence of plant presence is believed to be related to root oxygen loss and its effect on rhizosphere redox.}, }
@article {pmid22958530, year = {2012}, author = {Sweet, MJ and Scriven, LA and Singleton, I}, title = {Microsatellites for microbiologists.}, journal = {Advances in applied microbiology}, volume = {81}, number = {}, pages = {169-207}, doi = {10.1016/B978-0-12-394382-8.00005-8}, pmid = {22958530}, issn = {0065-2164}, mesh = {Bacteria/genetics ; DNA ; *DNA Primers ; Fungi/genetics ; Genetic Markers ; *Microsatellite Repeats ; Sequence Analysis, DNA ; }, abstract = {Microsatellites are repeating sequences of 2-6base pairs of DNA. Currently, they are used as molecular markers in many organisms, specifically in genetic studies analyzing kinship and population structure. In addition, they can be used to study gene duplication and/or deletion. Although they are used in studies on microorganisms including fungi, bacteria, protists, and archaea, it appears that these genetic markers are not being utilized to their full microbiological potential. Microsatellites have many advantages over other genetic markers currently in use as they are in general species specific, and therefore, cross-contamination by nontarget organisms is rare. Furthermore, microsatellites are suitable for use with fast and cheap DNA extraction methods, with ancient DNA or DNA from hair and fecal samples used in noninvasive sampling, making them widely available as a genetic marker. Microsatellites have already proven to be a useful tool for evolutionary studies of pathogenic microorganisms such as Candida albicans and Helicobacter pylori, and the onset of new sequencing techniques (such as 454, PACBIO, and mini-ion sequencing) means the ability to detect such markers will become less time consuming and cheaper, thus further expanding their potential to answer important microbial ecology questions.}, }
@article {pmid22956212, year = {2013}, author = {Tsyganov, AN and Keuper, F and Aerts, R and Beyens, L}, title = {Flourish or flush: effects of simulated extreme rainfall events on Sphagnum-dwelling testate amoebae in a subarctic bog (Abisko, Sweden).}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {101-110}, pmid = {22956212}, issn = {1432-184X}, mesh = {Amoeba/*physiology ; Biodiversity ; *Rain ; *Sphagnopsida ; Sweden ; *Wetlands ; }, abstract = {Extreme precipitation events are recognised as important drivers of ecosystem responses to climate change and can considerably affect high-latitude ombrotrophic bogs. Therefore, understanding the relationships between increased rainfall and the biotic components of these ecosystems is necessary for an estimation of climate change impacts. We studied overall effects of increased magnitude, intensity and frequency of rainfall on assemblages of Sphagnum-dwelling testate amoebae in a field climate manipulation experiment located in a relatively dry subarctic bog (Abisko, Sweden). The effects of the treatment were estimated using abundance, species diversity and structure of living and empty shell assemblages of testate amoebae in living and decaying layers of Sphagnum. Our results show that increased rainfall reduced the mean abundance and species richness of living testate amoebae. Besides, the treatment affected species structure of both living and empty shell assemblages, reducing proportions of hydrophilous species. The effects are counterintuitive as increased precipitation-related substrate moisture was expected to have opposite effects on testate amoeba assemblages in relatively dry biotopes. Therefore, we conclude that other rainfall-related factors such as increased infiltration rates and frequency of environmental disturbances can also affect testate amoeba assemblages in Sphagnum and that hydrophilous species are particularly sensitive to variation in these environmental variables.}, }
@article {pmid22956211, year = {2013}, author = {Ikeda, AC and Bassani, LL and Adamoski, D and Stringari, D and Cordeiro, VK and Glienke, C and Steffens, MB and Hungria, M and Galli-Terasawa, LV}, title = {Morphological and genetic characterization of endophytic bacteria isolated from roots of different maize genotypes.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {154-160}, pmid = {22956211}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Endophytes/classification/*genetics/isolation &amp; purification ; Genotype ; Phylogeny ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Zea mays/genetics/*microbiology ; }, abstract = {Maize is one of the most important crops worldwide, and in Brazil, the state of Paraná stands as its largest producer. The crop demands high inputs of N fertilizers, therefore all strategies aiming to optimize the grain production with lower inputs are very relevant. Endophytic bacteria have a high potential to increment maize grain yield by means of input via biological nitrogen fixation and/or plant growth promotion, in this last case increasing the absorption of water and nutrients by the plants. In this study, we established a collection of 217 endophytic bacteria, isolated from roots of four lineages and three hybrid genotypes of maize, and isolated in four different N-free culture media. Biochemical-comprising growth in different carbon sources, intrinsic tolerance to antibiotics, and biochemical tests for catalase, nitrate reductase, urease, and growth in N-free media in vitro-and genetic characterization by BOX-PCR revealed great variability among the isolates. Both commercial hybrids and homozygous lineages were broadly colonized by endophytes, and sequencing of the 16S rRNA gene revealed the presence of bacteria belonging to the genera Pantoea, Bacillus, Burkholderia, and Klebsiella. Qualitative differences in endophytic colonization were detected between lineages and hybrid genotypes.}, }
@article {pmid22952367, year = {2012}, author = {Hristov, AN and Callaway, TR and Lee, C and Dowd, SE}, title = {Rumen bacterial, archaeal, and fungal diversity of dairy cows in response to ingestion of lauric or myristic acid.}, journal = {Journal of animal science}, volume = {90}, number = {12}, pages = {4449-4457}, doi = {10.2527/jas.2011-4624}, pmid = {22952367}, issn = {1525-3163}, mesh = {Animal Feed ; Animal Nutritional Physiological Phenomena ; Animals ; Archaea/classification/*drug effects/genetics ; Bacteria/classification/*drug effects/genetics ; Base Sequence/genetics ; Cattle/*microbiology/physiology ; Dairying ; Diet/veterinary ; Female ; Fungi/classification/drug effects/genetics ; Gastrointestinal Contents/microbiology ; Lauric Acids/*pharmacology ; Myristic Acid/*pharmacology ; Rumen/*microbiology ; }, abstract = {The objective of this experiment, part of a larger study, was to investigate changes in rumen bacterial, archaeal, and fungal diversity in cows fed medium-chain saturated fatty acids. In the main study, 6 lactating dairy cows were dosed intraruminally with 240 g/(cow · d) of stearic (SA, control), lauric (LA), or myristic (MA) acid in a replicated 3 × 3 Latin square design trial. Experimental periods were 28 d, and cows were transfaunated between periods. Lauric acid decreased protozoal counts in the rumen by 96% compared with SA and MA (compared with SA, MA had no effect on ruminal protozoa). Whole ruminal contents samples were collected 2, 4, 6, 8, 10, 14, 18, and 24 h after the morning feeding on d 23 of each experimental period, stored frozen, and later composited by cow and period for microbial profile analyses, which involved tag-encoded flexible (FLX) amplicon pyrosequencing to provide diversity analyses of gastrointestinal bacterial, archaeal, and fungal populations of the cattle. The LA treatment, either directly or through its effect on protozoa, had a profound effect on the microbial ecology of the rumen. Ruminal populations of Prevotella, Bacteroides, and Enterorhabdus were decreased (P = 0.04 to P < 0.001) by more than 2-fold in LA treatments compared with SA, and Clostridium populations were decreased (P = 0.01) in LA- compared with MA-treated cows. The proportion of Ruminococcus was not affected by treatment, although the LA treatment had the least proportion of Ruminococcus. Proportions of Eubacterium, Butyrivibrio, Olsenella, and Lactobacillus genera were increased (P = 0.03 to 0.01) by LA compared with MA or SA. The LA treatment, possibly through its effect on protozoa physically associated with archaea, resulted in an increase (P = 0.01) in the archaeal methanogenic genus Methanosphaera and a decrease (P = 0.01) in Methanobrevibacter. Few changes in fungal populations caused by treatment were detected. Collectively, results indicate that LA, either through antiprotozoal or direct antimicrobial effects, altered bacterial and archaeal populations in the rumen of dairy cows, but effects on fungal populations were not clear.}, }
@article {pmid22950026, year = {2012}, author = {Baltar, F and Lindh, MV and Parparov, A and Berman, T and Pinhassi, J}, title = {Prokaryotic community structure and respiration during long-term incubations.}, journal = {MicrobiologyOpen}, volume = {1}, number = {2}, pages = {214-224}, pmid = {22950026}, issn = {2045-8827}, abstract = {Despite the importance of incubation assays for studies in microbial ecology that frequently require long confinement times, few reports are available in which changes in the assemblage structure of aquatic prokaryotes were monitored during long-term incubations. We measured rates of dissolved organic carbon degradation and microbial respiration by consumption of dissolved oxygen (DO) in four experiments with Lake Kinneret near-surface water and, concomitantly, we analyzed the variability in prokaryotic community structure during long-term dark bottle incubations. During the first 24 h, there were only minor changes in bacterial community composition. Thereafter there were marked changes in the prokaryotic community structure during the incubations. In contrast, oxygen consumption rates (a proxy for both respiration and dissolved organic carbon degradation rates) remained stable for up to 10-23 days. This study is one of the first to examine closely the phylo-genetic changes that occur in the microbial community of untreated freshwater during long-term (days) incubations in dark, sealed containers. Novel information on the diversity of the main bacterial phylotypes that may be involved in dissolved organic matter degradation in lake Kinneret is also provided. Our results suggest that, under certain ecological settings, constant community metabolic rates can be maintained as a result of shifts in community composition.}, }
@article {pmid22950016, year = {2012}, author = {Zirnstein, I and Arnold, T and Krawczyk-Bärsch, E and Jenk, U and Bernhard, G and Röske, I}, title = {Eukaryotic life in biofilms formed in a uranium mine.}, journal = {MicrobiologyOpen}, volume = {1}, number = {2}, pages = {83-94}, pmid = {22950016}, issn = {2045-8827}, abstract = {The underground uranium mine Königstein (Saxony, Germany), currently in the process of remediation, represents an underground acid mine drainage (AMD) environment, that is, low pH conditions and high concentrations of heavy metals including uranium, in which eye-catching biofilm formations were observed. During active uranium mining from 1984 to 1990, technical leaching with sulphuric acid was applied underground on-site resulting in a change of the underground mine environment and initiated the formation of AMD and also the growth of AMD-related copious biofilms. Biofilms grow underground in the mine galleries in a depth of 250 m (50 m above sea level) either as stalactite-like slime communities or as acid streamers in the drainage channels. The eukaryotic diversity of these biofilms was analyzed by microscopic investigations and by molecular methods, that is, 18S rDNA PCR, cloning, and sequencing. The biofilm communities of the Königstein environment showed a low eukaryotic biodiversity and consisted of a variety of groups belonging to nine major taxa: ciliates, flagellates, amoebae, heterolobosea, fungi, apicomplexa, stramenopiles, rotifers and arthropoda, and a large number of uncultured eukaryotes, denoted as acidotolerant eukaryotic cluster (AEC). In Königstein, the flagellates Bodo saltans, the stramenopiles Diplophrys archeri, and the phylum of rotifers, class Bdelloidea, were detected for the first time in an AMD environment characterized by high concentrations of uranium. This study shows that not only bacteria and archaea may live in radioactive contaminated environments, but also species of eukaryotes, clearly indicating their potential influence on carbon cycling and metal immobilization within AMD-affected environment.}, }
@article {pmid22949246, year = {2012}, author = {Ranasinghe, PD and Satoh, H and Oshiki, M and Oshima, K and Suda, W and Hattori, M and Mino, T}, title = {Revealing microbial community structures in large- and small-scale activated sludge systems by barcoded pyrosequencing of 16S rRNA gene.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {66}, number = {10}, pages = {2155-2161}, doi = {10.2166/wst.2012.428}, pmid = {22949246}, issn = {0273-1223}, mesh = {Bacteria/*classification/*genetics ; *Bioreactors ; DNA Barcoding, Taxonomic ; Gene Expression Regulation, Bacterial ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sewage ; Transcriptome ; Waste Disposal, Fluid/*methods ; }, abstract = {The diversity of bacterial groups in activated sludge from large- and small-scale wastewater treatment plants was explored by barcoded pyrosequencing of 16S rRNA gene. Activated sludge samples (three small and 17 large scale) were collected from 12 wastewater treatment plants to clarify precise taxonomy and relative abundances. DNA was extracted, and amplified by 4 base barcoded 27f/519r primer set. The 454 Titanium (Roche) pyrosequences were obtained and analyses performed by Quantitative Insight Into Microbial Ecology (QIIME) with around 100,000 reads. Sequence statistics were computed, while constructing a phylogenetic tree and heatmap. Computed results explained total microbial diversity at phylum and class level and resolution was further extended to Operational Taxonomic Unit (OTU) based taxonomic assignment for investigating community distribution based on individual sample. Composition of sequence reads were compared and microbial community structures for large- and small-scale treatment plants were identified as major phyla (Proteobacteria and Bacteroidetes) and classes (Betaproteobacteria and Bacteroidetes). Also, family level breakdowns were explained and differences in family Nitrospiraceae and phylum Actinobacteria found at their species level were also illustrated. Thus, the pyrosequencing method provides high resolution insight into microbial community structures in activated sludge that might have been unnoticed with conventional approaches.}, }
@article {pmid22945233, year = {2013}, author = {Grieco, MA and Cavalcante, JJ and Cardoso, AM and Vieira, RP and Machado, EA and Clementino, MM and Medeiros, MN and Albano, RM and Garcia, ES and de Souza, W and Constantino, R and Martins, OB}, title = {Microbial community diversity in the gut of the South American termite Cornitermes cumulans (Isoptera: Termitidae).}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {197-204}, pmid = {22945233}, issn = {1432-184X}, mesh = {Animals ; Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Gastrointestinal Tract/*microbiology ; Isoptera/*microbiology ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Termites inhabit tropical and subtropical areas where they contribute to structure and composition of soils by efficiently degrading biomass with aid of resident gut microbiota. In this study, culture-independent molecular analysis was performed based on bacterial and archaeal 16S rRNA clone libraries to describe the gut microbial communities within Cornitermes cumulans, a South American litter-feeding termite. Our data reveal extensive bacterial diversity, mainly composed of organisms from the phyla Spirochaetes, Bacteroidetes, Firmicutes, Actinobacteria, and Fibrobacteres. In contrast, a low diversity of archaeal 16S rRNA sequences was found, comprising mainly members of the Crenarchaeota phylum. The diversity of archaeal methanogens was further analyzed by sequencing clones from a library for the mcrA gene, which encodes the enzyme methyl coenzyme reductase, responsible for catalyzing the last step in methane production, methane being an important greenhouse gas. The mcrA sequences were diverse and divided phylogenetically into three clades related to uncultured environmental archaea and methanogens found in different termite species. C. cumulans is a litter-feeding, mound-building termite considered a keystone species in natural ecosystems and also a pest in agriculture. Here, we describe the archaeal and bacterial communities within this termite, revealing for the first time its intriguing microbiota.}, }
@article {pmid22945232, year = {2013}, author = {Meinersmann, RJ and Berrang, ME and Little, E}, title = {Campylobacter spp. recovered from the Upper Oconee River Watershed, Georgia in a 4-year study.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {22-27}, pmid = {22945232}, issn = {1432-184X}, mesh = {Bacterial Typing Techniques ; Campylobacter/classification/*isolation &amp; purification ; Campylobacter coli/classification/isolation &amp; purification ; Campylobacter jejuni/classification/isolation &amp; purification ; Georgia ; Multilocus Sequence Typing ; Phylogeny ; Rivers/*microbiology ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Waterways should be considered in the migration routes of Campylobacter, and the genus has been isolated from several water sources. Inferences on migration routes can be made from tracking genetic types in populations found in specific habitats and testing how they are linked to other types. Water samples were taken over a 4-year period from waterways in the Upper Oconee River Watershed, Georgia, to recover isolates of thermophilic Campylobacter. The isolates were typed by multilocus sequence typing (MLST) and analyzed to determine the overall diversity of Campylobacter in that environment. Forty-seven independent isolates were recovered from 560 samples (8.4 %). Two (~4 %) isolates were Campylobacter coli, three (~6 %) isolates were putatively identified as Campylobacter lari, and the remaining 42 (~90 %) were Campylobacter jejuni. The C. jejuni and C. coli isolates were typed by the Oxford MLST scheme. Thirty sequence types (STs) were identified including 13 STs that were not found before in the MLST database, including 24 novel alleles. Of the 17 previously described STs, 10 have been isolated from humans, 6 from environmental water, and 6 from wild birds (five types from multiple sources). Seven sites had multiple positive samples, and on two occasions, the same ST was isolated at the same site. The most common type was STST61 with four isolates, and the most common clonal complex was CC179 with nine isolates. CC179 has been commonly associated with environmental water. Although some Campylobacter STs that were found in the Oconee River engage in widespread migration, most are tightly associated with or unique to environmental water sources.}, }
@article {pmid22940734, year = {2013}, author = {Bengtsson, G and Törneman, N and De Lipthay, JR and Sørensen, SJ}, title = {Microbial diversity and PAH catabolic genes tracking spatial heterogeneity of PAH concentrations.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {91-100}, pmid = {22940734}, issn = {1432-184X}, mesh = {Biodegradation, Environmental ; *Biodiversity ; Creosote ; DNA, Bacterial/genetics ; Dioxygenases/*genetics ; *Genes, Bacterial ; Genotype ; Polycyclic Aromatic Hydrocarbons/*analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Soil Pollutants/*analysis ; Sweden ; }, abstract = {We analyzed the within-site spatial heterogeneity of microbial community diversity, polyaromatic hydrocarbon (PAH) catabolic genotypes, and physiochemical soil properties at a creosote contaminated site. Genetic diversity and community structure were evaluated from an analysis of denaturant gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified sequences of 16S rRNA gene. The potential PAH degradation capability was determined from PCR amplification of a suit of aromatic dioxygenase genes. Microbial diversity, evenness, and PAH genotypes were patchily distributed, and hot and cold spots of their distribution coincided with hot and cold spots of the PAH distribution. The analyses revealed a positive covariation between microbial diversity, biomass, evenness, and PAH concentration, implying that the creosote contamination at this site promotes diversity and abundance. Three patchily distributed PAH-degrading genotypes, NAH, phnA, and pdo1, were identified, and their abundances were positively correlated with the PAH concentration and the fraction of soil organic carbon. The covariation of the PAH concentration with the number and spatial distribution of catabolic genotypes suggests that a field site capacity to degrade PAHs may vary with the extent of contamination.}, }
@article {pmid22940733, year = {2013}, author = {Ritchie, RJ}, title = {The ammonia transport, retention and futile cycling problem in cyanobacteria.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {180-196}, pmid = {22940733}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Biological Transport ; Cell Membrane Permeability ; Hydrogen-Ion Concentration ; Membrane Potentials ; Methylamines/metabolism ; *Models, Biological ; *Substrate Cycling ; Synechococcus/*metabolism ; }, abstract = {Ammonia is the preferred nitrogen source for many algae including the cyanobacterium Synechococcus elongatis (Synechococcus R-2; PCC 7942). Modelling ammonia uptake by cells is not straightforward because it exists in solution as NH(3) and NH (4) (+) . NH(3) is readily diffusible not only via the lipid bilayer but also through aquaporins and other more specific porins. On the other hand, NH (4) (+) requires cationic transporters to cross a membrane. Significant intracellular ammonia pools (≈1-10 mol m(-3)) are essential for the synthesis of amino acids from ammonia. The most common model envisaged for how cells take up ammonia and use it as a nitrogen source is the "pump-leak model" where uptake occurs through a simple diffusion of NH(3) or through an energy-driven NH (4) (+) pump balancing a leak of NH(3) out of the cell. The flaw in such models is that cells maintain intracellular pools of ammonia much higher than predicted by such models. With caution, [(14)C]-methylamine can be used as an analogue tracer for ammonia and has been used to test various models of ammonia transport and metabolism. In this study, simple "proton trapping" accumulation by the diffusion of uncharged CH(3)NH(2) has been compared to systems where CH(3)NH (3) (+) is taken up through channels, driven by the membrane potential (ΔU (i,o)) or the electrochemical potential for Na(+) (ΔμNa (i,o) (+)). No model can be reconciled with experimental data unless the permeability of CH(3)NH(2) across the cell membrane is asymmetric: permeability into the cell is very high through gated porins, whereas permeability out of the cell is very low (≈40 nm s(-1)) and independent of the extracellular pH. The best model is a Na (in) (+) /CH(3)NH (3) (+) (in) co-porter driven by ΔμNa (i,o) (+) balancing synthesis of methylglutamine and a slow leak governed by Ficks law, and so there is significant futile cycling of methylamine across the cell membrane to maintain intracellular methylamine pools high enough for fixation by glutamine synthetase. The modified pump-leak model with asymmetric permeability of the uncharged form is a viable model for understanding ammonia uptake and retention in plants, free-living microbes and organisms in symbiotic relationships.}, }
@article {pmid22940732, year = {2013}, author = {Boscaro, V and Fokin, SI and Schrallhammer, M and Schweikert, M and Petroni, G}, title = {Revised systematics of Holospora-like bacteria and characterization of "Candidatus Gortzia infectiva", a novel macronuclear symbiont of Paramecium jenningsi.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {255-267}, pmid = {22940732}, issn = {1432-184X}, mesh = {DNA, Bacterial/genetics ; Holosporaceae/*classification/genetics ; In Situ Hybridization, Fluorescence ; Paramecium/*microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {The genus Holospora (Rickettsiales) includes highly infectious nuclear symbionts of the ciliate Paramecium with unique morphology and life cycle. To date, nine species have been described, but a molecular characterization is lacking for most of them. In this study, we have characterized a novel Holospora-like bacterium (HLB) living in the macronuclei of a Paramecium jenningsi population. This bacterium was morphologically and ultrastructurally investigated in detail, and its life cycle and infection capabilities were described. We also obtained its 16S rRNA gene sequence and developed a specific probe for fluorescence in situ hybridization experiments. A new taxon, "Candidatus Gortzia infectiva", was established for this HLB according to its unique characteristics and the relatively low DNA sequence similarities shared with other bacteria. The phylogeny of the order Rickettsiales based on 16S rRNA gene sequences has been inferred, adding to the available data the sequence of the novel bacterium and those of two Holospora species (Holospora obtusa and Holospora undulata) characterized for the purpose. Our phylogenetic analysis provided molecular support for the monophyly of HLBs and showed a possible pattern of evolution for some of their features. We suggested to classify inside the family Holosporaceae only HLBs, excluding other more distantly related and phenotypically different Paramecium endosymbionts.}, }
@article {pmid22936765, year = {2012}, author = {Kowalchuk, GA}, title = {Ecology. Bad news for soil carbon sequestration?.}, journal = {Science (New York, N.Y.)}, volume = {337}, number = {6098}, pages = {1049-1050}, doi = {10.1126/science.1227303}, pmid = {22936765}, issn = {1095-9203}, mesh = {Carbon/*metabolism ; Carbon Dioxide/*metabolism ; Mycorrhizae/*metabolism ; *Soil Microbiology ; }, }
@article {pmid22928928, year = {2013}, author = {Anderson, RE and Beltrán, MT and Hallam, SJ and Baross, JA}, title = {Microbial community structure across fluid gradients in the Juan de Fuca Ridge hydrothermal system.}, journal = {FEMS microbiology ecology}, volume = {83}, number = {2}, pages = {324-339}, doi = {10.1111/j.1574-6941.2012.01478.x}, pmid = {22928928}, issn = {1574-6941}, mesh = {Archaea/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Ecosystem ; Hydrothermal Vents/*microbiology ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; }, abstract = {Physical and chemical gradients are dominant factors in shaping hydrothermal vent microbial ecology, where archaeal and bacterial habitats encompass a range between hot, reduced hydrothermal fluid and cold, oxidized seawater. To determine the impact of these fluid gradients on microbial communities inhabiting these systems, we surveyed bacterial and archaeal community structure among and between hydrothermal plumes, diffuse flow fluids, and background seawater in several hydrothermal vent sites on the Juan de Fuca Ridge using 16S rRNA gene diversity screening (clone libraries and terminal restriction length polymorphisms) and quantitative polymerase chain reaction methods. Community structure was similar between hydrothermal plumes and background seawater, where a number of taxa usually associated with low-oxygen zones were observed, whereas high-temperature diffuse fluids exhibited a distinct phylogenetic profile. SUP05 and Arctic96BD-19 sulfur-oxidizing bacteria were prevalent in all three mixing regimes where they exhibited overlapping but not identical abundance patterns. Taken together, these results indicate conserved patterns of redox-driven niche partitioning between hydrothermal mixing regimes and microbial communities associated with sinking particles and oxygen-deficient waters. Moreover, the prevalence of SUP05 and Arctic96BD-19 in plume and diffuse flow fluids indicates a more cosmopolitan role for these groups in the ecology and biogeochemistry of the dark ocean.}, }
@article {pmid22926501, year = {2013}, author = {Meadow, JF and Zabinski, CA}, title = {Prokaryotic communities differ along a geothermal soil photic gradient.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {171-179}, pmid = {22926501}, issn = {1432-184X}, mesh = {Cyanobacteria/genetics/isolation &amp; purification ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; Diatomaceous Earth ; *Ecosystem ; Hot Springs/microbiology ; *Metagenome ; Phylogeny ; Planctomycetales/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Soil/*analysis ; *Soil Microbiology ; Verrucomicrobia/genetics/isolation &amp; purification ; Wyoming ; }, abstract = {Geothermal influenced soils exert unique physical and chemical limitations on resident microbial communities but have received little attention in microbial ecology research. These environments offer a model system in which to investigate microbial community heterogeneity and a range of soil ecological concepts. We conducted a 16S bar-coded pyrosequencing survey of the prokaryotic communities in a diatomaceous geothermal soil system and compared communities across soil types and along a conspicuous photic depth gradient. We found significant differences between the communities of the two different soils and also predictable differences between samples taken at different depths. Additionally, we targeted three ecologically relevant bacterial phyla, Cyanobacteria, Planctomycetes, and Verrucomicrobia, for clade-wise comparisons with these variables and found strong differences in their abundances, consistent with the autecology of these groups.}, }
@article {pmid22920558, year = {2012}, author = {Hadar, Y and Papadopoulou, KK}, title = {Suppressive composts: microbial ecology links between abiotic environments and healthy plants.}, journal = {Annual review of phytopathology}, volume = {50}, number = {}, pages = {133-153}, doi = {10.1146/annurev-phyto-081211-172914}, pmid = {22920558}, issn = {1545-2107}, mesh = {Antibiosis ; Biodiversity ; Ecology ; Ecosystem ; *Microbial Consortia ; Plant Diseases/*microbiology ; Plants/*microbiology ; Soil ; *Soil Microbiology ; }, abstract = {Suppressive compost provides an environment in which plant disease development is reduced, even in the presence of a pathogen and a susceptible host. Despite the numerous positive reports, its practical application is still limited. The main reason for this is the lack of reliable prediction and quality control tools for evaluation of the level and specificity of the suppression effect. Plant disease suppression is the direct result of the activity of consortia of antagonistic microorganisms that naturally recolonize the compost during the cooling phase of the process. Thus, it is imperative to increase the level of understanding of compost microbial ecology and population dynamics. This may lead to the development of an ecological theory for complex ecosystems as well as favor the establishment of hypothesis-driven studies.}, }
@article {pmid22920514, year = {2012}, author = {Souza, V and Siefert, JL and Escalante, AE and Elser, JJ and Eguiarte, LE}, title = {The Cuatro Ciénegas Basin in Coahuila, Mexico: an astrobiological Precambrian Park.}, journal = {Astrobiology}, volume = {12}, number = {7}, pages = {641-647}, pmid = {22920514}, issn = {1557-8070}, mesh = {Biological Evolution ; *Ecosystem ; *Exobiology/methods ; Mexico ; Models, Biological ; Time Factors ; *Wilderness ; }, abstract = {The Cuatro Ciénegas Basin (CCB) is a rare oasis in the Chihuahuan Desert in the state of Coahuila, Mexico. It has a biological endemism similar to that of the Galapagos Islands, and its spring-fed ecosystems have very low nutrient content (nitrogen or phosphorous) and are dominated by diverse microbialites. Thus, it has proven to be a distinctive opportunity for the field of astrobiology, as the CCB can be seen as a proxy for an earlier time in Earth's history, in particular the late Precambrian, the biological frontier when prokaryotic life yielded at least partial dominance to eukaryotes and multicellular life. It is a kind of ecological time machine that provides abundant opportunities for collaborative investigations by geochemists, geologists, ecologists, and population biologists in the study of the evolutionary processes that structured Earth-based life, especially in the microbial realm. The CCB is an object of investigation for the identification of biosignatures of past and present biota that can be used in our search for extraterrestrial life. In this review, we summarize CCB research efforts that began with microbial ecology and population biology projects and have since been expanded into broader efforts that involve biogeochemistry, comparative genomics, and assessments of biosignatures. We also propose that, in the future, the CCB is sanctioned as a "Precambrian Park" for astrobiology.}, }
@article {pmid22920513, year = {2012}, author = {Souza, V and Eguiarte, LE and Travisano, M and Elser, JJ and Rooks, C and Siefert, JL}, title = {Travel, sex, and food: what's speciation got to do with it?.}, journal = {Astrobiology}, volume = {12}, number = {7}, pages = {634-640}, pmid = {22920513}, issn = {1557-8070}, mesh = {Bacteria/*genetics/*metabolism ; Gene Flow/*genetics ; Gene Transfer, Horizontal/*genetics ; *Genetic Speciation ; Mexico ; }, abstract = {We discuss the potential interactions among travel (dispersal and gene flow), bacterial "sex" (mainly as horizontal gene transfer), and food (metabolic plasticity and responses to nutrient availability) in shaping microbial communities. With regard to our work at a unique desert oasis, the Cuatro Ciénegas Basin in Coahuila, Mexico, we propose that diversification and low phosphorus availability, in combination with mechanisms for nutrient recycling and community cohesion, result in enhanced speciation through reproductive as well as geographic isolation. We also discuss these mechanisms in the broader sense of ecology and evolution. Of special relevance to astrobiology and central to evolutionary biology, we ask why there are so many species on Earth and provide a working hypothesis and a conceptual framework within which to consider the question. Key Words: Microbial ecology-Microbial mats-Evolution-Horizontal gene transfer-Metabolism.}, }
@article {pmid22919612, year = {2012}, author = {Gaynor, EC and Szymanski, CM}, title = {The 30th anniversary of Campylobacter, Helicobacter, and Related Organisms workshops-what have we learned in three decades?.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {20}, doi = {10.3389/fcimb.2012.00020}, pmid = {22919612}, issn = {2235-2988}, mesh = {Biomedical Research/trends ; Campylobacter/*pathogenicity ; Campylobacter Infections/*epidemiology/*microbiology ; Education/*history ; Helicobacter Infections/*epidemiology/*microbiology ; Helicobacter pylori/*pathogenicity ; History, 20th Century ; History, 21st Century ; Humans ; }, abstract = {As we commemorate the 30(th) anniversary of the Campylobacter, Helicobacter, and Related Organisms (CHRO) workshops with this special Frontiers edition, we look back upon three decades of research and provide some highlights from the 16(th) International CHRO meeting. Although Theodor Escherich himself provided drawings of campylobacters back in the 1880s, Campylobacter jejuni was not identified until the 1950s. Helicobacter pylori was first described to be the causative agent of stomach ulcers at a CHRO meeting by Barry Marshall and Robin Warren-who later received the Nobel Prize for their findings that bacteria could cause diseases previously believed to be caused by human factors. Now, several genome sequences for campylobacters, helicobacters, and related organisms are available and we have moved into an era examining the intersection between host microbial ecology and pathogen infection. Both pioneers and new investigators in the CHRO research field continue to obtain "unexpected results" demonstrating that campylobacters and helicobacters do not follow classic paradigms of other well-characterized gastrointestinal pathogens and we are learning that there is a plethora of interesting related organisms beyond C. jejuni and H. pylori. This review summarizes recent discoveries in CHRO research and the exciting directions ahead.}, }
@article {pmid22915156, year = {2013}, author = {Cirés, S and Wörmer, L and Wiedner, C and Quesada, A}, title = {Temperature-dependent dispersal strategies of Aphanizomenon ovalisporum (Nostocales, Cyanobacteria): implications for the annual life cycle.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {12-21}, pmid = {22915156}, issn = {1432-184X}, mesh = {Aphanizomenon/cytology/growth &amp; development/*physiology ; Linear Models ; Ponds/*microbiology ; Seasons ; *Temperature ; }, abstract = {Aphanizomenon ovalisporum is a planktonic nostocalean cyanobacterium with increasing research interest due to its ability to produce the potent cytotoxin cylindrospermopsin and its potential invasiveness under the global warming scenario. The present study provides novel data on the potential dispersal strategies of A. ovalisporum by analyzing the influence of temperature (10-40 °C) on akinete differentiation and cell morphometry in cultures of A. ovalisporum UAM 290 isolated from a Spanish pond. Our results confirmed a temperature-dependent akinete differentiation, with the maximum akinete production reached at 20 °C (15 % of the cells), a low basal production at 25-30 °C (<0.4 % of the cells) and no detectable production at 35 °C. Furthermore, we reported the fragmentation of A. ovalisporum filaments at temperatures of 25 °C and above. Additionally, we observed that the morphology of vegetative cells varied under different temperature scenarios. Indeed, a strong negative correlation was found between temperature and the width, length and biovolume of vegetative cells, whereas akinete dimensions remained stable along the temperature gradient. Therefore, linear regressions between temperature and the cell size parameters are herein presented aiming to facilitate the identification of A. ovalisporum in the field throughout the course of the year. This is the first study evidencing that akinete production is triggered by temperatures between 20 and 25 °C in A. ovalisporum and reporting the existence of filament fragmentation as a potential dispersal strategy of this species. The importance of these findings for understanding the annual life cycle and invasive potential of A. ovalisporum is further discussed herein.}, }
@article {pmid22915155, year = {2013}, author = {Nazir, R and Warmink, JA and Voordes, DC and van de Bovenkamp, HH and van Elsas, JD}, title = {Inhibition of mushroom formation and induction of glycerol release-ecological strategies of Burkholderia terrae BS001 to create a hospitable niche at the fungus Lyophyllum sp. strain Karsten.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {245-254}, pmid = {22915155}, issn = {1432-184X}, mesh = {Agaricales/metabolism/*physiology ; Biofilms ; Burkholderia/*growth &amp; development/metabolism ; Glycerol/*metabolism ; Hyphae/growth &amp; development/metabolism ; *Microbial Interactions ; *Soil Microbiology ; }, abstract = {We investigated the ecological strategies exerted by the soil bacterium Burkholderia terrae BS001 at the hyphae of the soil saprotrophic fungus Lyophyllum sp. strain Karsten. Recently, this bacterium has been reported to form biofilms around, and to comigrate with, growing hyphae of Lyophyllum sp. strain Karsten. In addition, it was found to be able to utilize fungal metabolites. Here, we extend this work to shed some light on the interactions between the bacterial and fungal partner which allow ecological success for the former. In standing liquid microcosms inoculated with Lyophyllum sp. strain Karsten, we detected, upon prolonged incubation, the formation of a mycelial mat at the liquid-air interface. From this mat, primordia were formed after 4-6 weeks, which eventually resulted in mushrooms. However, upon addition of strain BS001 to the bulk liquid, mushroom formation from the fungal mat was clearly inhibited, as evidenced by (1) the formation of significantly lower numbers of primordia and (2) a delay of the onset of primordia formation. Moreover and importantly, the presence of strain BS001 caused the fungus to secrete large amounts of exudates at the mycelial mat, whereas such exudation was absent from control (uninoculated) or Escherichia coli K12- or Variovorax paradoxus BS64-inoculated microcosms. In the exudates, glycerol was the main carbonaceous component, and this compound could be easily utilized by strain BS001. Thus, in different experimental set-ups with the fungal partner, strain BS001 was shown to grow in the fungal exudates on the mat. The two fungal-interactive phenotypes were specific for B. terrae strain BS001, as the other bacteria used in our study, i.e. E. coli K12 and V. paradoxus BS64, did not exhibit any of these phenomena.}, }
@article {pmid22913313, year = {2012}, author = {Piper, GL and Kaplan, LJ}, title = {Antibiotic heterogeneity optimizes antimicrobial prescription and enables resistant pathogen control in the intensive care unit.}, journal = {Surgical infections}, volume = {13}, number = {4}, pages = {194-202}, doi = {10.1089/sur.2012.121}, pmid = {22913313}, issn = {1557-8674}, mesh = {Anti-Bacterial Agents/*administration &amp; dosage ; Bacteria/drug effects ; Bacterial Infections/drug therapy/prevention &amp; control/*therapy ; Cross Infection/drug therapy/prevention &amp; control/*therapy ; Drug Resistance, Multiple, Bacterial ; Humans ; Infection Control/*methods ; Intensive Care Units ; }, abstract = {BACKGROUND: Multi-drug-resistant organisms (MDRO) complicate care increasingly on the general ward and in the emergency department, operating room, and intensive care unit (ICU). Whereas barrier precautions are important in limiting transmission of MDRO between patients, few tactics have been defined that reduce the genesis of MDRO.<br><br>METHOD: Review of pertinent English-language literature.<br><br>RESULTS: Antibiotic heterogeneity practices, as part of an overall antimicrobial drug stewardship program, offer one readily deployable means to reduce selection pressure for MDRO development in the ICU. The data underpinning this approach and data derived from its use indicate that, especially in surgical ICUs, heterogeneity of antibiotic prescribing can preserve or restore microbial ecology, reduce the prevalence of MDRO and the incidence of infections caused thereby, and facilitate the implementation and effectiveness of other antibiotic-sparing tactics, such as de-escalation.<br><br>CONCLUSION: Heterogeneity of antibiotic prescribing is effective in preventing the dissemination of MDRO pathogens.}, }
@article {pmid22909141, year = {2012}, author = {Miceli, JF and Parameswaran, P and Kang, DW and Krajmalnik-Brown, R and Torres, CI}, title = {Enrichment and analysis of anode-respiring bacteria from diverse anaerobic inocula.}, journal = {Environmental science &amp; technology}, volume = {46}, number = {18}, pages = {10349-10355}, doi = {10.1021/es301902h}, pmid = {22909141}, issn = {1520-5851}, mesh = {Bioelectric Energy Sources/*microbiology ; *Biofilms/growth &amp; development ; Electricity ; Electrodes/*microbiology ; Electrons ; Geobacter/*physiology ; }, abstract = {One of the limitations currently faced by microbial electrochemical cell (MXC) technologies lies in the shortage of different organisms capable of forming a biofilm and channeling electrons from substrates to the anode at high current densities. Using a poised anode (-0.30 V vs Ag/AgCl) and acetate as the electron donor in a MXC, we demonstrated the presence of highly efficient anode-respiring bacteria (ARB) able to produce high current densities (>1.5 A/m(2) anode) in seven out of thirteen environmental samples. These included marshes, lake sediments, saline microbial mats, and anaerobic soils obtained from geographically diverse locations. Our microbial ecology analysis, using pyrosequencing, shows that bacteria related to the genus Geobacter, a known and commonly found ARB, dominate only two of the biofilm communities producing high current; other biofilm communities contained different known and/or novel ARB. The presence of ARB in geographically diverse locations indicates that ARB thrive in a wide range of ecosystems. Studying ARB from different environmental conditions will allow us to better understand the ubiquity of anode respiration, compare the capabilities of different ARB consortia, and find ARB with useful metabolic capacities for future applications.}, }
@article {pmid22904213, year = {2013}, author = {Álvarez-Pérez, S and Lievens, B and Jacquemyn, H and Herrera, CM}, title = {Acinetobacter nectaris sp. nov. and Acinetobacter boissieri sp. nov., isolated from floral nectar of wild Mediterranean insect-pollinated plants.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {63}, number = {Pt 4}, pages = {1532-1539}, doi = {10.1099/ijs.0.043489-0}, pmid = {22904213}, issn = {1466-5034}, mesh = {Acinetobacter/*classification/genetics/isolation &amp; purification ; Animals ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Flowers/microbiology ; Insecta ; Mediterranean Region ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Phylogeny ; Plant Nectar/*analysis ; Pollination ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The taxonomic status of 14 strains of members of the genus Acinetobacter isolated from floral nectar of wild Mediterranean insect-pollinated plants, which did not belong to any previously described species within this genus, was investigated following a polyphasic approach. Confirmation that these strains formed two separate lineages within the genus Acinetobacter was obtained from comparative analysis of the partial sequences of the 16S rRNA gene and the gene encoding the β-subunit of RNA polymerase (rpoB), DNA-DNA reassociation data, determination of the DNA G+C content and physiological tests. The names Acinetobacter nectaris sp. nov. and Acinetobacter boissieri sp. nov. are proposed. The type strain of A. nectaris sp. nov. is SAP 763.2(T) (= LMG 26958(T) = CECT 8127(T)) and that of A. boissieri sp. nov. is SAP 284.1(T) (= LMG 26959(T) = CECT 8128(T)).}, }
@article {pmid22904051, year = {2012}, author = {Katharios-Lanwermeyer, S and Rakic-Martinez, M and Elhanafi, D and Ratani, S and Tiedje, JM and Kathariou, S}, title = {Coselection of cadmium and benzalkonium chloride resistance in conjugative transfers from nonpathogenic Listeria spp. to other Listeriae.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {21}, pages = {7549-7556}, pmid = {22904051}, issn = {1098-5336}, mesh = {Anti-Infective Agents, Local/pharmacology ; Bacterial Proteins/genetics ; Benzalkonium Compounds/*pharmacology ; Cadmium/*pharmacology ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Food Handling ; Gene Transfer, Horizontal ; Listeria/*drug effects/*genetics/pathogenicity ; Temperature ; }, abstract = {Resistance to the quaternary ammonium disinfectant benzalkonium chloride (BC) may be an important contributor to the ability of Listeria spp. to persist in the processing plant environment. Although a plasmid-borne disinfectant resistance cassette (bcrABC) has been identified in Listeria monocytogenes, horizontal transfer of these genes has not been characterized. Nonpathogenic Listeria spp. such as L. innocua and L. welshimeri are more common than L. monocytogenes in food processing environments and may contribute to the dissemination of disinfectant resistance genes in listeriae, including L. monocytogenes. In this study, we investigated conjugative transfer of resistance to BC and to cadmium from nonpathogenic Listeria spp. to other nonpathogenic listeriae, as well as to L. monocytogenes. BC-resistant L. welshimeri and L. innocua harboring bcrABC, along with the cadmium resistance determinant cadA2, were able to transfer resistance to other nonpathogenic listeriae as well as to L. monocytogenes of diverse serotypes, including strains from the 2011 cantaloupe outbreak. Transfer among nonpathogenic Listeria spp. was noticeably higher at 25°C than at 37°C, whereas acquisition of resistance by L. monocytogenes was equally efficient at 25 and 37°C. When the nonpathogenic donors were resistant to both BC and cadmium, acquisition of cadmium resistance was an effective surrogate for transfer of resistance to BC, suggesting coselection between these resistance attributes. The results suggest that nonpathogenic Listeria spp. may behave as reservoirs for disinfectant and heavy metal resistance genes for other listeriae, including the pathogenic species L. monocytogenes.}, }
@article {pmid22903164, year = {2013}, author = {Clivot, H and Danger, M and Pagnout, C and Wagner, P and Rousselle, P and Poupin, P and Guérold, F}, title = {Impaired leaf litter processing in acidified streams : learning from microbial enzyme activities.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {1-11}, pmid = {22903164}, issn = {1432-184X}, mesh = {Acids/*chemistry ; Aluminum/chemistry ; Biodegradation, Environmental ; Biomass ; Carbon/analysis ; Enzymes/metabolism ; France ; Fungi/enzymology/*metabolism ; Hydrogen-Ion Concentration ; Nitrogen/analysis ; Phosphorus/analysis ; Plant Leaves/*metabolism/microbiology ; Rivers/*chemistry/*microbiology ; *Water Microbiology ; }, abstract = {Anthropogenic acidification in headwater streams is known to affect microbial assemblages involved in leaf litter breakdown. Far less is known about its potential effects on microbial enzyme activities. To assess the effects of acidification on microbial activities associated with decaying leaves, a 70-day litter bag experiment was conducted in headwater streams at six sites across an acidification gradient. The results revealed that microbial leaf decomposition was strongly and negatively correlated with total Al concentrations (r = -0.99, p < 0.001) and positively correlated with Ca(2+) concentrations (r = 0.94, p = 0.005) and pH (r = 0.93, p = 0.008). Denaturing gradient gel electrophoresis analyses showed that microbial assemblages differed between non-impacted and impacted sites, whereas fungal biomass associated with decaying leaves was unaffected. The nutrient content of leaf detritus and ecoenzymatic activities of carbon (C), nitrogen (N) and phosphorus (P) acquisition revealed that N acquisition was unaltered, while P acquisition was significantly reduced across the acidification gradient. The P content of leaf litter was negatively correlated with total Al concentrations (r = -0.94, p < 0.01) and positively correlated with decomposition rates (r = 0.95, p < 0.01). This potential P limitation of microbial decomposers in impacted sites was confirmed by the particularly high turnover activity for phosphatase and imbalanced ratios between the ecoenzymatic activities of C and P acquisition. The toxic form of Al has well-known direct effects on aquatic biota under acidic conditions, but in this study, Al was found to also potentially affect microbially mediated leaf processing by interfering with the P cycle. These effects may in turn have repercussions on higher trophic levels and whole ecosystem functioning.}, }
@article {pmid22903163, year = {2013}, author = {Koczura, R and Mokracka, J and Barczak, A and Krysiak, N and Kaznowski, A}, title = {Association between the presence of class 1 integrons, virulence genes, and phylogenetic groups of Escherichia coli isolates from river water.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {84-90}, pmid = {22903163}, issn = {1432-184X}, mesh = {DNA, Bacterial/genetics ; Escherichia coli/*genetics/*pathogenicity ; Integrons/*genetics ; *Phylogeny ; Poland ; Rivers/*microbiology ; Virulence/*genetics ; Virulence Factors/genetics ; Water Microbiology ; }, abstract = {Ninety-six class 1 integron-positive and 96 integron-negative Escherichia coli isolates cultured from the water of the Warta River, Poland, were characterized for their phylogenetic group affiliation and for the presence of genes associated with virulence. Most strains belonged to phylogenetic group A, but phylogenetic group affiliation was not related with the presence of integrons. The occurrence of heat-stable toxin gene of enterotoxigenic E. coli, S fimbriae subunit gene sfaS, and siderophore receptor genes, fyuA and iutA, was associated with the presence of class 1 integrons. Moreover, virulence factor score (the total number of virulence-associated genes) was associated with the presence of integrons in groups. The results bring new insight into relations between the presence of integrons in E. coli, virulence traits, as well as phylogenetic group affiliation.}, }
@article {pmid22903090, year = {2012}, author = {Perumbakkam, S and Craig, AM}, title = {Anaerobic transformation of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) by ovine rumen microorganisms.}, journal = {Research in microbiology}, volume = {163}, number = {8}, pages = {567-575}, doi = {10.1016/j.resmic.2012.08.001}, pmid = {22903090}, issn = {1769-7123}, mesh = {Anaerobiosis ; Animals ; Azocines/*metabolism ; Bacteria/classification/genetics/*metabolism ; Biota ; Biotransformation ; Chromatography, Liquid ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Rumen/*metabolism/*microbiology ; Sequence Analysis, DNA ; Sheep ; Tandem Mass Spectrometry ; }, abstract = {Explosives such as octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) provide a challenge in terms of bioremediation. In the present study, sheep rumen was studied for its potential to detoxify HMX using analytical chemistry and molecular microbial ecology tools. Results indicated significant loss (p < 0.05) of HMX at 8 h post-incubation and complete disappearance of the parent molecule after 16 h. Qualitative LC-MS/MS analysis provided evidence for the formation of 1-NO-HMX and MEDINA metabolites. A total of 1006 16S rRNA-V3 clones were sequenced and the Classifier tool of the RDPII database was used to sort the sequences at their phylum level. Most sequences were associated with either the phylum Bacteroidetes or Firmicutes. Significant differences at the phylum level (p < 0.001) were found between 0 h and 8 h HMX treatments. Using LibCompare analysis, 8 h HMX treatment showed enrichment of clones (p < 0.01) belonging to the genus Prevotella. From these results, it could be concluded that members of the genus Prevotella are enriched in the rumen and are capable of detoxifying HMX.}, }
@article {pmid22903087, year = {2013}, author = {Pichrtová, M and Remias, D and Lewis, LA and Holzinger, A}, title = {Changes in phenolic compounds and cellular ultrastructure of arctic and antarctic strains of Zygnema (Zygnematophyceae, Streptophyta) after exposure to experimentally enhanced UV to PAR ratio.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {68-83}, pmid = {22903087}, issn = {1432-184X}, support = {P 24242/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Antarctic Regions ; Arctic Regions ; Chlorophyll/analysis ; Chlorophyll A ; Chromatography, High Pressure Liquid ; DNA, Plant/genetics ; Microscopy, Electron, Transmission ; Phenols/*analysis ; Photosynthesis/radiation effects ; Photosystem II Protein Complex/radiation effects ; Phylogeny ; Streptophyta/chemistry/*radiation effects/*ultrastructure ; *Ultraviolet Rays ; Xanthophylls/analysis ; }, abstract = {Ultraviolet (UV) radiation has become an important stress factor in polar regions due to anthropogenically induced ozone depletion. Although extensive research has been conducted on adaptations of polar organisms to this stress factor, few studies have focused on semi-terrestrial algae so far, in spite of their apparent vulnerability. This study investigates the effect of UV on two semi-terrestrial arctic strains (B, G) and one Antarctic strain (E) of the green alga Zygnema, isolated from Arctic and Antarctic habitats. Isolates of Zygnema were exposed to experimentally enhanced UV A and B (predominant UV A) to photosynthetic active radiation (PAR) ratio. The pigment content, photosynthetic performance and ultrastructure were studied by means of high-performance liquid chromatography (HPLC), chlorophyll a fluorescence and transmission electron microscopy (TEM). In addition, phylogenetic relationships of the investigated strains were characterised using rbcL sequences, which determined that the Antarctic isolate (E) and one of the Arctic isolates (B) were closely related, while G is a distinct lineage. The production of protective phenolic compounds was confirmed in all of the tested strains by HPLC analysis for both controls and UV-exposed samples. Moreover, in strain E, the content of phenolics increased significantly (p = 0.001) after UV treatment. Simultaneously, the maximum quantum yield of photosystem II photochemistry significantly decreased in UV-exposed strains E and G (p < 0.001), showing a clear stress response. The phenolics were most probably stored at the cell periphery in vacuoles and cytoplasmic bodies that appear as electron-dense particles when observed by TEM after high-pressure freeze fixation. While two strains reacted moderately on UV exposure in their ultrastructure, in strain G, damage was found in chloroplasts and mitochondria. Plastidal pigments and xanthophyll cycle pigments were investigated by HPLC analysis; UV A- and UV B-exposed samples had a higher deepoxidation state as controls, particularly evident in strain B. The results indicate that phenolics are involved in UV protection of Zygnema and also revealed different responses to UV stress across the three strains, suggesting that other protection mechanisms may be involved in these organisms.}, }
@article {pmid22903086, year = {2013}, author = {Costa, R and Keller-Costa, T and Gomes, NC and da Rocha, UN and van Overbeek, L and van Elsas, JD}, title = {Evidence for selective bacterial community structuring in the freshwater sponge Ephydatia fluviatilis.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {232-244}, pmid = {22903086}, issn = {1432-184X}, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; Fresh Water/microbiology ; *Metagenome ; Netherlands ; *Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {To understand the functioning of sponges, knowledge of the structure of their associated microbial communities is necessary. However, our perception of sponge-associated microbiomes remains mainly restricted to marine ecosystems. Here, we report on the molecular diversity and composition of bacteria in the freshwater sponge Ephydatia fluviatilis inhabiting the artificial lake Vinkeveense Plassen, Utrecht, The Netherlands. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprints revealed that the apparent diversities within the domain Bacteria and the phylum Actinobacteria were lower in E. fluviatilis than in bulk water. Enrichment of specific PCR-DGGE bands in E. fluviatilis was detected. Furthermore, sponge- and bulk water-derived bacterial clone libraries differed with respect to bacterial community composition at the phylum level. E. fluviatilis-derived sequences were affiliated with six recognized phyla, i.e., Proteobacteria, Planctomycetes, Actinobacteria, Bacteroidetes, Chlamydiae and Verrucomicrobia, in order of relative abundance; next to the uncultured candidate phylum TM7 and one deeply rooted bacterial lineage of undefined taxonomy (BLUT). Actinobacteria, Proteobacteria, and Bacteroidetes were the dominant bacterial phyla in the freshwater clone library whereas sequences affiliated with Planctomycetes, Verrucomicrobia, Acidobacteria and Armatimonadetes were found at lower frequencies. Fine-tuned phylogenetic inference showed no or negligible overlaps between the E. fluviatilis and water-derived phylotypes within bacterial taxa such as Alphaproteobacteria, Bacteroidetes and Actinobacteria. We also ascertained the status of two alphaproteobacterial lineages as freshwater sponge-specific phylogenetic clusters, and report on high distinctiveness of other E. fluviatilis specific phylotypes, especially within the Bacteroidetes, Planctomycetes and Chlamydia taxa. This study supports the contention that the composition and diversity of bacteria in E. fluviatilis is partially driven by the host organism.}, }
@article {pmid22898652, year = {2012}, author = {Nekrutenko, A and Taylor, J}, title = {Next-generation sequencing data interpretation: enhancing reproducibility and accessibility.}, journal = {Nature reviews. Genetics}, volume = {13}, number = {9}, pages = {667-672}, pmid = {22898652}, issn = {1471-0064}, support = {U41 HG006620/HG/NHGRI NIH HHS/United States ; HG005133/HG/NHGRI NIH HHS/United States ; HG006620/HG/NHGRI NIH HHS/United States ; HG004909/HG/NHGRI NIH HHS/United States ; }, mesh = {Access to Information ; Base Sequence ; Data Interpretation, Statistical ; Genetic Privacy ; High-Throughput Nucleotide Sequencing/*methods/*trends ; Humans ; Molecular Sequence Data ; Reproducibility of Results ; Sequence Analysis, DNA/*methods/*trends ; }, abstract = {Areas of life sciences research that were previously distant from each other in ideology, analysis practices and toolkits, such as microbial ecology and personalized medicine, have all embraced techniques that rely on next-generation sequencing instruments. Yet the capacity to generate the data greatly outpaces our ability to analyse it. Existing sequencing technologies are more mature and accessible than the methodologies that are available for individual researchers to move, store, analyse and present data in a fashion that is transparent and reproducible. Here we discuss currently pressing issues with analysis, interpretation, reproducibility and accessibility of these data, and we present promising solutions and venture into potential future developments.}, }
@article {pmid22895828, year = {2013}, author = {Ceh, J and van Keulen, M and Bourne, DG}, title = {Intergenerational transfer of specific bacteria in corals and possible implications for offspring fitness.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {227-231}, pmid = {22895828}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; Germ Cells/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Diverse and abundant bacterial populations play important functional roles in the multi-partite association of the coral holobiont. The specificity of coral-associated assemblages remains unclear, and little is known about the inheritance of specific bacteria from the parent colony to their offspring. This study investigated if broadcast spawning and brooding corals release specific and potentially beneficial bacteria with their offspring to secure maintenance across generations. Two coral species, Acropora tenuis and Pocillopora damicornis, were maintained in 0.2 μm filtered seawater during the release of their gametes and planulae, respectively. Water samples, excluding gametes and planulae, were subsequently collected, and bacterial diversity was assessed through a pyrosequencing approach amplifying a 470-bp region of the 16S rRNA gene including the variable regions 1-3. Compared to the high bacterial diversity harboured by corals, only a few taxa of bacteria were released by adult corals. Both A. tenuis and P. damicornis released similar bacteria, and the genera Alteromonas and Roseobacter were abundant in large proportions in the seawater of both species after reproduction. This study suggests that adult corals may release bacteria with their offspring to benefit the fitness in early coral life stages.}, }
@article {pmid22890730, year = {2013}, author = {Brígido, C and Oliveira, S}, title = {Most acid-tolerant chickpea mesorhizobia show induction of major chaperone genes upon acid shock.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {145-153}, pmid = {22890730}, issn = {1432-184X}, mesh = {*Acids ; Chaperonin 60/genetics ; Cicer/*microbiology ; Gene Expression Profiling ; Genes, Bacterial ; Hydrogen-Ion Concentration ; Mesorhizobium/*genetics/physiology ; Molecular Chaperones/*genetics ; Soil/chemistry ; *Soil Microbiology ; Stress, Physiological ; }, abstract = {Our goals were to evaluate the tolerance of mesorhizobia to acid and alkaline conditions as well as to investigate whether acid tolerance is related to the species or the origin site of the isolates. In addition, to investigate the molecular basis of acid tolerance, the expression of chaperone genes groEL and dnaKJ was analyzed using acid-tolerant and sensitive mesorhizobia. Tolerance to pH 5 and 9 was evaluated in liquid medium for 98 Portuguese chickpea mesorhizobia belonging to four species clusters. All isolates showed high sensitivity to pH 9. In contrast, mesorhizobia revealed high diversity in terms of tolerance to acid stress: 35 % of the isolates were acid sensitive and 45 % were highly tolerant to pH 5 or moderately acidophilic. An association between mesorhizobia tolerance to acid conditions and the origin soil pH was found. Furthermore, significant differences between species clusters regarding tolerance to acidity were obtained. Ten isolates were used to investigate the expression levels of the chaperone genes by northern hybridization. Interestingly, most acid-tolerant isolates displayed induction of the dnaK and groESL genes upon acid shock while the sensitive ones showed repression. This study suggests that acid tolerance in mesorhizobia is related to the pH of the origin soil and to the species cluster of the isolates. Additionally, the transcriptional analysis suggests a relationship between induction of major chaperone genes and higher tolerance to acid pH in mesorhizobia. This is the first report on transcriptional analysis of the major chaperones genes in mesorhizobia under acidity, contributing to a better understanding of the molecular mechanisms of rhizobia acidity tolerance.}, }
@article {pmid22890729, year = {2013}, author = {Sha, Q and Vattem, DA and Forstner, MR and Hahn, D}, title = {Quantifying Salmonella population dynamics in water and biofilms.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {60-67}, pmid = {22890729}, issn = {1432-184X}, mesh = {Animals ; *Biofilms ; Caenorhabditis elegans/microbiology ; Salmonella/growth &amp; development/*isolation &amp; purification/pathogenicity ; *Water Microbiology ; }, abstract = {Members of the bacterial genus Salmonella are recognized worldwide as major zoonotic pathogens often found to persist in non-enteric environments including heterogeneous aquatic biofilms. In this study, Salmonella isolates that had been detected repeatedly over time in aquatic biofilms at different sites in Spring Lake, San Marcos, Texas, were identified as serovars Give, Thompson, Newport and -:z10:z39. Pathogenicity results from feeding studies with the nematode Caenorhabditis elegans as host confirmed that these strains were pathogenic, with Salmonella-fed C. elegans dying faster (mean survival time between 3 and 4 days) than controls, i.e., Escherichia coli-fed C. elegans (mean survival time of 9.5 days). Cells of these isolates inoculated into water at a density of up to 10(6) ml(-1) water declined numerically by 3 orders of magnitude within 2 days, reaching the detection limit of our quantitative polymerase chain reaction (qPCR)-based quantification technique (i.e., 10(3) cells ml(-1)). Similar patterns were obtained for cells in heterogeneous aquatic biofilms developed on tiles and originally free of Salmonella that were kept in the inoculated water. Cell numbers increased during the first days to more than 10(7) cells cm(-2), and then declined over time. Ten-fold higher cell numbers of Salmonella inoculated into water or into biofilm resulted in similar patterns of population dynamics, though cells in biofilms remained detectable with numbers around 10(4) cells cm(-2) after 4 weeks. Independent of detectability by qPCR, samples of all treatments harbored viable salmonellae that resembled the inoculated isolates after 4 weeks of incubation. These results demonstrate that pathogenic salmonellae were isolated from heterogeneous aquatic biofilms and that they could persist and stay viable in such biofilms in high numbers for some time.}, }
@article {pmid22886507, year = {2013}, author = {Demirci, O and Hamamcı, DA}, title = {Antioxidant responses in Phanerochaete chrysosporium exposed to Astrazone Red FBL textile dye.}, journal = {Cell biochemistry and function}, volume = {31}, number = {1}, pages = {86-90}, doi = {10.1002/cbf.2865}, pmid = {22886507}, issn = {1099-0844}, mesh = {Azo Compounds/administration &amp; dosage/*toxicity ; Biodegradation, Environmental ; Catalase/metabolism ; Coloring Agents/administration &amp; dosage/*toxicity ; Dose-Response Relationship, Drug ; Fungal Proteins/metabolism ; Glutathione/metabolism ; Glutathione Reductase/metabolism ; Glutathione Transferase/metabolism ; Oxidation-Reduction ; Oxidative Stress/drug effects ; Phanerochaete/*drug effects/enzymology/growth &amp; development ; Water Pollutants, Chemical/administration &amp; dosage/*toxicity ; }, abstract = {Interest in environmental-pollutant-induced oxidative stress and knowledge of the interactions between reactive oxygen species and cellular systems have increased in toxicology and microbial ecology considerably in recent decades. These reactive oxidants are produced by a variety of environmental sources: ionizing radiations, ultraviolet light, redox cycling drugs, hyperoxia, ischemia and redox-active xenobiotics or during metabolism of environmental pollutants, such as heavy metals in mining industries, dyes in wastewater of textile industries, pesticides and polycyclic hydrocarbons, i.e. foreign materials. In this study, the effect of dye on the antioxidative defence system of Phanerochaete chrysosporium was investigated, and we showed the ability of Phanerochaete chrysosporium to antioxidative response and defence system exposed to Astrazone Red FBL. Catalase, glutathione reductase, glutathione s-transferase activities and level of glutathione decreased, depending on the period of growth in each exposure to low and high concentration group (20 and 50 ppm) compared with the control group.}, }
@article {pmid22885637, year = {2013}, author = {Guerrero-Ferreira, R and Gorman, C and Chavez, AA and Willie, S and Nishiguchi, MK}, title = {Characterization of the bacterial diversity in Indo-West Pacific loliginid and sepiolid squid light organs.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {214-226}, pmid = {22885637}, issn = {1432-184X}, support = {R25 GM061222/GM/NIGMS NIH HHS/United States ; T34 GM007667/GM/NIGMS NIH HHS/United States ; 1SC1AI081659/AI/NIAID NIH HHS/United States ; R25 GM048998/GM/NIGMS NIH HHS/United States ; S06 GM008136/GM/NIGMS NIH HHS/United States ; GM-61222-01/GM/NIGMS NIH HHS/United States ; R25 GM48998/GM/NIGMS NIH HHS/United States ; SC1 AI081659/AI/NIAID NIH HHS/United States ; SO6 GM008136-32 S2/GM/NIGMS NIH HHS/United States ; }, mesh = {Animal Structures/*microbiology ; Animals ; Australia ; Bacteriological Techniques ; DNA, Bacterial/genetics ; Decapodiformes/*microbiology ; Luminescence ; Metagenome ; Photobacterium/*classification/genetics/isolation &amp; purification ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; Thailand ; Vibrio/*classification/genetics/isolation &amp; purification ; }, abstract = {Loliginid and sepiolid squid light organs are known to host a variety of bacterial species from the family Vibrionaceae, yet little is known about the species diversity and characteristics among different host squids. Here we present a broad-ranging molecular and physiological analysis of the bacteria colonizing light organs in loliginid and sepiolid squids from various field locations of the Indo-West Pacific (Australia and Thailand). Our PCR-RFLP analysis, physiological characterization, carbon utilization profiling, and electron microscopy data indicate that loliginid squid in the Indo-West Pacific carry a consortium of bacterial species from the families Vibrionaceae and Photobacteriaceae. This research also confirms our previous report of the presence of Vibrio harveyi as a member of the bacterial population colonizing light organs in loliginid squid. pyrH sequence data were used to confirm isolate identity, and indicates that Vibrio and Photobacterium comprise most of the light organ colonizers of squids from Australia, confirming previous reports for Australian loliginid and sepiolid squids. In addition, combined phylogenetic analysis of PCR-RFLP and 16S rDNA data from Australian and Thai isolates associated both Photobacterium and Vibrio clades with both loliginid and sepiolid strains, providing support that geographical origin does not correlate with their relatedness. These results indicate that both loliginid and sepiolid squids demonstrate symbiont specificity (Vibrionaceae), but their distribution is more likely due to environmental factors that are present during the infection process. This study adds significantly to the growing evidence for complex and dynamic associations in nature and highlights the importance of exploring symbiotic relationships in which non-virulent strains of pathogenic Vibrio species could establish associations with marine invertebrates.}, }
@article {pmid22882187, year = {2013}, author = {Maignien, L and Parkes, RJ and Cragg, B and Niemann, H and Knittel, K and Coulon, S and Akhmetzhanov, A and Boon, N}, title = {Anaerobic oxidation of methane in hypersaline cold seep sediments.}, journal = {FEMS microbiology ecology}, volume = {83}, number = {1}, pages = {214-231}, doi = {10.1111/j.1574-6941.2012.01466.x}, pmid = {22882187}, issn = {1574-6941}, mesh = {Anaerobiosis ; Archaea/classification/isolation &amp; purification/metabolism ; Bacteria/classification/isolation &amp; purification/metabolism ; DNA, Archaeal/genetics/isolation &amp; purification ; DNA, Bacterial/genetics/isolation &amp; purification ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; Seawater/chemistry/*microbiology ; Sulfates/metabolism ; *Water Microbiology ; }, abstract = {Life in hypersaline environments is typically limited by bioenergetic constraints. Microbial activity at the thermodynamic edge, such as the anaerobic oxidation of methane (AOM) coupled to sulphate reduction (SR), is thus unlikely to thrive in these environments. In this study, carbon and sulphur cycling was investigated in the extremely hypersaline cold seep sediments of Mercator mud volcano. AOM activity was partially inhibited but still present at salinity levels of 292 g L(-1) (c. eightfold sea water concentration) with rates of 2.3 nmol cm(-3) day(-1) and was even detectable under saturated conditions. Methane and evaporite-derived sulphate comigrated in the ascending geofluids, which, in combination with a partial activity inhibition, resulted in AOM activity being spread over unusually wide depth intervals. Up to 79% of total cells in the AOM zone were identified by fluorescence in situ hybridization (FISH) as anaerobic methanotrophs of the ANME-1. Most ANME-1 cells formed monospecific chains without any attached partner. At all sites, AOM activity co-occurred with SR activity and sometimes significantly exceeded it. Possible causes of these unexpected results are discussed. This study demonstrates that in spite of a very low energy yield of AOM, microorganisms carrying this reaction can thrive in salinity up to halite saturation.}, }
@article {pmid22878248, year = {2012}, author = {Creatsas, G and Deligeoroglou, E}, title = {Microbial ecology of the lower genital tract in women with sexually transmitted diseases.}, journal = {Journal of medical microbiology}, volume = {61}, number = {Pt 10}, pages = {1347-1351}, doi = {10.1099/jmm.0.042507-0}, pmid = {22878248}, issn = {1473-5644}, mesh = {Bacteria/classification/*isolation &amp; purification ; Candida albicans/*isolation &amp; purification ; Female ; Humans ; Sexually Transmitted Diseases/*microbiology/*virology ; Viruses/*classification ; }, abstract = {Sexually transmitted diseases (STDs) in women are of great concern to all health-care providers since many of them are preventable and/or treatable conditions which, if left untreated, could have serious sequelae such as pelvic inflammatory disease, infertility, cervical cancer, systemic disease, etc. They may also become a major public health problem when dealing with diseases such as hepatitis, etc., or in people with human immunodeficiency virus. We present here a comprehensive review of the common causes of STDs and their treatment.}, }
@article {pmid22878238, year = {2012}, author = {Dutton, RJ and Turnbaugh, PJ}, title = {Taking a metagenomic view of human nutrition.}, journal = {Current opinion in clinical nutrition and metabolic care}, volume = {15}, number = {5}, pages = {448-454}, doi = {10.1097/MCO.0b013e3283561133}, pmid = {22878238}, issn = {1473-6519}, support = {P50 GM068763/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Diet ; *Digestion ; *Food Microbiology ; Gastrointestinal Tract/metabolism/*microbiology ; Humans ; *Metagenome ; *Metagenomics ; }, abstract = {PURPOSE OF REVIEW: Humans harbor microbial communities throughout the gastrointestinal tract that both respond to and modify orally ingested macronutrients, bioactive compounds, and xenobiotics; for example, the metabolism of polyphenols, heterocyclic amines, and phosphatidylcholine. However, the composition and physiological impact of our diet is also linked to the methods of food production, preparation, and consumption, which are altered by environmental and food-borne microbial communities. Metagenomic analyses spanning these various steps in human nutrition will be critical for a more comprehensive view.<br><br>RECENT FINDINGS: Studies in humans and animal models have highlighted the key role that diet plays in shaping gut microbial ecology, and how the trillions of microbes in the gut (microbiota) enable the digestion of substrates inaccessible to our own human enzymes. These transformations have been implicated in a variety of diseases and disorders, ranging from obesity, inflammatory bowel disease, heart disease, to cancer.<br><br>SUMMARY: In order to move towards personalized nutrition and medicine, it is important to take into account both our host and microbial genomes. The resulting metagenomic view of human nutrition, ranging from the initial biotransformations of food to digestion and the end result on human physiology, could have wide-ranging implications for food science, human evolutionary biology, and microbial ecology.}, }
@article {pmid22864854, year = {2013}, author = {Paramasivam, N and Ben-Dov, E and Arotsker, L and Kramarsky-Winter, E and Zvuloni, A and Loya, Y and Kushmaro, A}, title = {Bacterial consortium of Millepora dichotoma exhibiting unusual multifocal lesion event in the Gulf of Eilat, Red Sea.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {50-59}, pmid = {22864854}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology/ultrastructure ; Bacteria/classification/isolation &amp; purification/*pathogenicity ; DNA, Bacterial/genetics ; Indian Ocean ; *Metagenome ; Microscopy, Electron, Transmission ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Colonies of the hydrocoral Millepora dichotoma along the Gulf of Eilat are exhibiting unusual tissue lesions in the form of white spots. The emergence and rapid establishment of these multifocal tissue lesions was the first of its kind reported in this region. A characterization of this morphological anomaly revealed bleached tissues with a significant presence of bacteria in the tissue lesion area. To ascertain possible differences in microbial biota between the lesion area and non-affected tissues, we characterized the bacterial diversity in the two areas of these hydrocorals. Both culture-independent (molecular) and culture-dependent assays showed a shift in bacterial community structure between the healthy and affected tissues. Several 16S rRNA gene sequences retrieved from the affected tissues matched sequences of bacterial clones belonging to Alphaproteobacteria and Bacteroidetes members previously associated with various diseases in scleractinian corals.}, }
@article {pmid22864853, year = {2013}, author = {Lins-de-Barros, MM and Cardoso, AM and Silveira, CB and Lima, JL and Clementino, MM and Martins, OB and Albano, RM and Vieira, RP}, title = {Microbial community compositional shifts in bleached colonies of the Brazilian reef-building coral Siderastrea stellata.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {205-213}, pmid = {22864853}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Brazil ; Chlorophyta/classification/*genetics ; DNA Barcoding, Taxonomic ; DNA, Algal/genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Diatoms/classification/genetics ; Ecosystem ; Gene Library ; Phylogeny ; Plastids/genetics ; RNA, Ribosomal, 16S/genetics ; Rhodophyta/*classification/genetics ; Symbiosis ; }, abstract = {The association of metazoan, protist, and microbial communities with Scleractinian corals forms the basis of the coral holobiont. Coral bleaching events have been occurring around the world, introducing changes in the delicate balance of the holobiont symbiotic interactions. In this study, Archaea, bacteria, and eukaryotic phototrophic plastids of bleached colonies of the Brazilian coral Siderastrea stellata were analyzed for the first time, using 16S rRNA gene libraries. Prokaryotic communities were slightly more diverse in healthy than in bleached corals. However, the eukaryotic phototrophic plastids community was more diverse in bleached corals. Archaea phylogenetic analyses revealed a high percentage of Crenarchaeota sequences, mainly related to Nitrosopumilus maritimus and Cenarchaeum symbiosum. Dramatic changes in bacterial community composition were observed in this bleaching episode. The dominant bacterial group was Alphaproteobacteria followed by Gammaproteobacteria in bleached and Betaproteobacteria in healthy samples. Plastid operational taxonomic units (OTUs) from both coral samples were mainly related to red algae chloroplasts (Florideophycea), but we also observed some OTUs related to green algae chloroplasts (Chlorophyta). There seems to be a strong relationship between the Bacillariophyta phylum and our bleached coral samples as clones related to members of the diatom genera Amphora and Nitzschia were detected. The present study reveals information from a poorly investigated coral species and improves the knowledge of coral microbial community shifts that could occur during bleaching episodes.}, }
@article {pmid22864852, year = {2013}, author = {Chen, Y and Ren, CG and Yang, B and Peng, Y and Dai, CC}, title = {Priming effects of the endophytic fungus Phomopsis liquidambari on soil mineral N transformations.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {161-170}, pmid = {22864852}, issn = {1432-184X}, mesh = {Ascomycota/*metabolism ; Bacteria/*metabolism ; Endophytes/*metabolism ; Nitrates/metabolism ; *Nitrification ; Nitrogen/*metabolism ; Plant Leaves ; Quaternary Ammonium Compounds/metabolism ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Nitrogen (N) is a crucial nutrient for soil biota, and its cycling is determined by the organic carbon decomposing process. Some endophytic fungi are latent saprotrophs that trigger their saprotrophic metabolism to promote litter organic matter cycling as soon as the host tissue senesces or dies. However, the effects of endophytic fungi on litter and soil N dynamics in vitro have rarely been investigated. In this study, we investigated N dynamics (total and mineral N) in both litter and soil in incubations of a pure culture of an endophytic fungus Phomopsis liquidambari with litter and following soil burial of the litter. Soil enzymes and microbial communities participating in the N transformations were also investigated. A pure culture of P. liquidambari released litter NH (4) (+) -N in the initial stages (10 days) of the incubation. However, following soil burial, the presence of both P. liquidambari and soil ammonia-oxidizing bacteria (AOB) resulted in an increase in soil NO (3) (-) -N. These results indicate that the endophytic fungus P. liquidambari in vitro stimulates organic mineralization and promote NH (4) (+) -N release. Such effects triggered soil AOB-driven nitrification process.}, }
@article {pmid22864851, year = {2013}, author = {Sercu, B and Jones, AD and Wu, CH and Escobar, MH and Serlin, CL and Knapp, TA and Andersen, GL and Holden, PA}, title = {The influence of in situ chemical oxidation on microbial community composition in groundwater contaminated with chlorinated solvents.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {39-49}, pmid = {22864851}, issn = {1432-184X}, mesh = {Bacteria/*classification/growth &amp; development/metabolism ; Biodegradation, Environmental ; Biofilms ; Biomass ; DNA, Bacterial/genetics ; Groundwater/chemistry/*microbiology ; Oligonucleotide Array Sequence Analysis ; Oxidation-Reduction ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sodium Compounds/chemistry ; Solvents/chemistry ; Trichloroethylene/*chemistry ; *Water Microbiology ; Water Pollutants, Chemical/*chemistry ; }, abstract = {In situ chemical oxidation with permanganate has become an accepted remedial treatment for groundwater contaminated with chlorinated solvents. This study focuses on the immediate and short-term effects of sodium permanganate (NaMnO(4)) on the indigenous subsurface microbial community composition in groundwater impacted by trichloroethylene (TCE). Planktonic and biofilm microbial communities were studied using groundwater grab samples and reticulated vitreous carbon passive samplers, respectively. Microbial community composition was analyzed by terminal restriction fragment length polymorphism and a high-density phylogenetic microarray (PhyloChip). Significant reductions in microbial diversity and biomass were shown during NaMnO(4) exposure, followed by recovery within several weeks after the oxidant concentrations decreased to <1 mg/L. Bray-Curtis similarities and nonmetric multidimensional scaling showed that microbial community composition before and after NaMnO(4) was similar, when taking into account the natural variation of the microbial communities. Also, 16S rRNA genes of two reductive dechlorinators (Desulfuromonas spp. and Sulfurospirillum spp.) and diverse taxa capable of cometabolic TCE oxidation were detected in similar quantities by PhyloChip across all monitoring wells, irrespective of NaMnO(4) exposure and TCE concentrations. However, minimal biodegradation of TCE was observed in this study, based on oxidized conditions, concentration patterns of chlorinated and nonchlorinated hydrocarbons, geochemistry, and spatiotemporal distribution of TCE-degrading bacteria.}, }
@article {pmid22864803, year = {2013}, author = {Sene, G and Thiao, M and Samba-Mbaye, R and Khasa, D and Kane, A and Mbaye, MS and Beaulieu, M&#xc8; and Manga, A and Sylla, SN}, title = {The abundance and diversity of legume-nodulating rhizobia in 28-year-old plantations of tropical, subtropical, and exotic tree species: a case study from the Forest Reserve of Bandia, Senegal.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {128-144}, pmid = {22864803}, issn = {1432-184X}, mesh = {Acacia/*microbiology ; Agriculture ; Biodiversity ; Bradyrhizobium/*classification/genetics/isolation &amp; purification ; Mesorhizobium/*classification/genetics/isolation &amp; purification ; Phylogeny ; *Plant Root Nodulation ; Root Nodules, Plant/microbiology ; Seasons ; Senegal ; Sinorhizobium/*classification/genetics/isolation &amp; purification ; Soil Microbiology ; Symbiosis ; Trees/microbiology ; }, abstract = {Several fast-growing and multipurpose tree species have been widely used in West Africa to both reverse the tendency of land degradation and restore soil productivity. Although beneficial effects have been reported on soil stabilization, there still remains a lack of information about their impact on soil microorganisms. Our investigation has been carried out in exotic and native tree plantations of 28 years and aimed to survey and compare the abundance and genetic diversity of natural legume-nodulating rhizobia (LNR). The study of LNR is supported by the phylogenetic analysis which clustered the isolates into three genera: Bradyrhizobium, Mesorhizobium, and Sinorhizobium. The results showed close positive correlations between the sizes of LNR populations estimated both in the dry and rainy seasons and the presence of legume tree hosts. There were significant increases in Rhizobium spp. population densities in response to planting with Acacia spp., and high genetic diversities and richness of genotypes were fittest in these tree plantations. This suggests that enrichment of soil Rhizobium spp. populations is host specific. The results indicated also that species of genera Mesorhizobium and Sinorhizobium were lacking in plantations of non-host species. By contrast, there was a widespread distribution of Bradyrhizobium spp. strains across the tree plantations, with no evident specialization in regard to plantation type. Finally, the study provides information about the LNR communities associated with a range of old tree plantations and some aspects of their relationships to soil factors, which may facilitate the management of man-made forest systems that target ecosystem rehabilitation and preservation of soil biota.}, }
@article {pmid22860008, year = {2012}, author = {McGhee, GC and Sundin, GW}, title = {Erwinia amylovora CRISPR elements provide new tools for evaluating strain diversity and for microbial source tracking.}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e41706}, pmid = {22860008}, issn = {1932-6203}, mesh = {Bacteriophages/genetics ; Base Sequence ; Chromosome Mapping ; Cluster Analysis ; Conserved Sequence ; Erwinia amylovora/*genetics/isolation &amp; purification/virology ; Genes, Bacterial ; Genetic Loci ; Genetic Variation ; Genotype ; Malus/microbiology ; Molecular Sequence Annotation ; Phylogeny ; Plant Diseases/microbiology ; Plasmids ; *Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; }, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPRs) comprise a family of short DNA repeat sequences that are separated by non repetitive spacer sequences and, in combination with a suite of Cas proteins, are thought to function as an adaptive immune system against invading DNA. The number of CRISPR arrays in a bacterial chromosome is variable, and the content of each array can differ in both repeat number and in the presence or absence of specific spacers. We utilized a comparative sequence analysis of CRISPR arrays of the plant pathogen Erwinia amylovora to uncover previously unknown genetic diversity in this species. A total of 85 E. amylovora strains varying in geographic isolation (North America, Europe, New Zealand, and the Middle East), host range, plasmid content, and streptomycin sensitivity/resistance were evaluated for CRISPR array number and spacer variability. From these strains, 588 unique spacers were identified in the three CRISPR arrays present in E. amylovora, and these arrays could be categorized into 20, 17, and 2 patterns types, respectively. Analysis of the relatedness of spacer content differentiated most apple and pear strains isolated in the eastern U.S. from western U.S. strains. In addition, we identified North American strains that shared CRISPR genotypes with strains isolated on other continents. E. amylovora strains from Rubus and Indian hawthorn contained mostly unique spacers compared to apple and pear strains, while strains from loquat shared 79% of spacers with apple and pear strains. Approximately 23% of the spacers matched known sequences, with 16% targeting plasmids and 5% targeting bacteriophage. The plasmid pEU30, isolated in E. amylovora strains from the western U.S., was targeted by 55 spacers. Lastly, we used spacer patterns and content to determine that streptomycin-resistant strains of E. amylovora from Michigan were low in diversity and matched corresponding streptomycin-sensitive strains from the background population.}, }
@article {pmid22855211, year = {2013}, author = {Parks, DH and Beiko, RG}, title = {Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities.}, journal = {The ISME journal}, volume = {7}, number = {1}, pages = {173-183}, pmid = {22855211}, issn = {1751-7370}, mesh = {Bacteria/*classification/genetics ; Ecology/*methods ; *Environmental Microbiology ; Humans ; *Metagenome ; *Models, Biological ; *Phylogeny ; Software ; }, abstract = {High-throughput sequencing techniques have made large-scale spatial and temporal surveys of microbial communities routine. Gaining insight into microbial diversity requires methods for effectively analyzing and visualizing these extensive data sets. Phylogenetic β-diversity measures address this challenge by allowing the relationship between large numbers of environmental samples to be explored using standard multivariate analysis techniques. Despite the success and widespread use of phylogenetic β-diversity measures, an extensive comparative analysis of these measures has not been performed. Here, we compare 39 measures of phylogenetic β diversity in order to establish the relative similarity of these measures along with key properties and performance characteristics. While many measures are highly correlated, those commonly used within microbial ecology were found to be distinct from those popular within classical ecology, and from the recently recommended Gower and Canberra measures. Many of the measures are surprisingly robust to different rootings of the gene tree, the choice of similarity threshold used to define operational taxonomic units, and the presence of outlying basal lineages. Measures differ considerably in their sensitivity to rare organisms, and the effectiveness of measures can vary substantially under alternative models of differentiation. Consequently, the depth of sequencing required to reveal underlying patterns of relationships between environmental samples depends on the selected measure. Our results demonstrate that using complementary measures of phylogenetic β diversity can further our understanding of how communities are phylogenetically differentiated. Open-source software implementing the phylogenetic β-diversity measures evaluated in this manuscript is available at http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity.}, }
@article {pmid22852704, year = {2012}, author = {Julou, T and Desprat, N and Bensimon, D and Croquette, V}, title = {Monitoring microbial population dynamics at low densities.}, journal = {The Review of scientific instruments}, volume = {83}, number = {7}, pages = {074301}, doi = {10.1063/1.4729796}, pmid = {22852704}, issn = {1089-7623}, mesh = {Cell Count ; Colony Count, Microbial/*instrumentation ; Equipment Design ; Equipment Failure Analysis ; *Lasers ; Lighting/*instrumentation ; Photometry/*instrumentation ; Spectrum Analysis/*instrumentation ; }, abstract = {We propose a new and simple method for the measurement of microbial concentrations in highly diluted cultures. This method is based on an analysis of the intensity fluctuations of light scattered by microbial cells under laser illumination. Two possible measurement strategies are identified and compared using simulations and measurements of the concentration of gold nanoparticles. Based on this comparison, we show that the concentration of Escherichia coli and Saccharomyces cerevisiae cultures can be easily measured in situ across a concentration range that spans five orders of magnitude. The lowest measurable concentration is three orders of magnitude (1000×) smaller than in current optical density measurements. We show further that this method can also be used to measure the concentration of fluorescent microbial cells. In practice, this new method is well suited to monitor the dynamics of population growth at early colonization of a liquid culture medium. The dynamic data thus obtained are particularly relevant for microbial ecology studies.}, }
@article {pmid22850272, year = {2012}, author = {Singh, KM and Jakhesara, SJ and Koringa, PG and Rank, DN and Joshi, CG}, title = {Metagenomic analysis of virulence-associated and antibiotic resistance genes of microbes in rumen of Indian buffalo (Bubalus bubalis).}, journal = {Gene}, volume = {507}, number = {2}, pages = {146-151}, doi = {10.1016/j.gene.2012.07.037}, pmid = {22850272}, issn = {1879-0038}, mesh = {Animals ; Bacteria/drug effects/genetics/isolation &amp; purification ; Base Sequence ; Buffaloes/*microbiology ; Cattle ; DNA, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; India ; *Metagenome ; Metagenomics ; Rumen/microbiology ; Virulence/genetics ; }, abstract = {A major research goal in rumen microbial ecology is to understand the relationship between community composition and its function, particularly involved in fermentation process is of a potential interest. The buffalo rumen microbiota impacts human food safety as well as animal health. Although the bacteria of bovine rumen have been well characterized, techniques have been lacking to correlate total community structure with gene function. We applied 454 next generations sequencing technology to characterize general microbial diversity present in buffalo rumen metagenome and also identified the repertoire of microbial genes present, including genes associated with antibiotic resistance and bacterial virulence. Results suggest that over six percent (6.44%) of the sequences from our buffalo rumen pool sample could be categorized as virulence genes and genes associated with resistance to antibiotic and toxic compounds (RATC), which is a higher proportion of virulence genes reported from metagenome samples of chicken cecum (5.39%), cow rumen (4.43%) and Sargasso sea (2.95%). However, it was lower than the proportion found in cow milk (11.33%) cattle faeces (8.4%), Antarctic marine derived lake (8.45%), human fecal (7.7%) and farm soil (7.79%). The dynamic nature of metagenomic data, together with the large number of RATC classes observed in samples from widely different ecologies indicates that metagenomic data can be used to track potential targets and relative amounts of antibiotic resistance genes in individual animals. In addition, these data can be also used to generate antibiotic resistance gene profiles to facilitate an understanding of the ecology of the microbial communities in each habitat as well as the epidemiology of antibiotic resistant gene transport between and among habitats.}, }
@article {pmid22849830, year = {2012}, author = {Whiteley, AS and Jenkins, S and Waite, I and Kresoje, N and Payne, H and Mullan, B and Allcock, R and O'Donnell, A}, title = {Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform.}, journal = {Journal of microbiological methods}, volume = {91}, number = {1}, pages = {80-88}, doi = {10.1016/j.mimet.2012.07.008}, pmid = {22849830}, issn = {1872-8359}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; *Biota ; DNA Barcoding, Taxonomic/economics/methods ; Metagenomics/economics/*methods ; Polymerase Chain Reaction/economics/methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/economics/methods ; Wastewater/microbiology ; }, abstract = {Here we demonstrate a cost effective and scalable microbial ecology sequencing platform using the Ion Torrent Personal Genome Machine (PGM). We assessed both PCR amplified 16S rRNA and shotgun metagenomic approaches and generated 100,000+ to 1,000,000+ reads using 'post-light' based sequencing technology within different sized semi-conductor chips. Further development of Golay barcoded Ion Tags allowed multiplex analyses of microbial communities with substantially reduced costs compared with platforms such as 454/GS-FLX. Using these protocols we assessed the bacterial and archaeal dynamics within covered anaerobic digesters used to treat piggery wastes. Analysis of these sequence data showed that these novel methanogenic waste treatment systems are dominated by bacterial taxa, in particular Clostridium, Synergistia and Bacteroides that were maintained as a stable community over extended time periods. Archaeal community dynamics were more stochastic with the key methanogenic taxa more difficult to resolve, principally due to the poor congruence seen between community structures generated either by nested PCR or metagenomic approaches for archaeal analyses. Our results show that for microbial community structure and function analyses, the PGM platform provides a low cost, scalable and high throughput solution for both Tag sequencing and metagenomic analyses.}, }
@article {pmid22847270, year = {2012}, author = {Bañeras, L and Ruiz-Rueda, O and López-Flores, R and Quintana, XD and Hallin, S}, title = {The role of plant type and salinity in the selection for the denitrifying community structure in the rhizosphere of wetland vegetation.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {15}, number = {2}, pages = {89-99}, doi = {10.2436/20.1501.01.162}, pmid = {22847270}, issn = {1618-1905}, mesh = {Bacteria/enzymology/genetics/*growth &amp; development ; DNA, Bacterial/chemistry/genetics ; Denitrification/*genetics/physiology ; *Ecosystem ; Nitrite Reductases/genetics/metabolism ; Oxidoreductases/genetics/metabolism ; Plants/*microbiology ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; *Rhizosphere ; Salinity ; *Soil Microbiology ; Spain ; Statistics, Nonparametric ; Wetlands ; }, abstract = {Coastal wetlands, as transient links from terrestrial to marine environments, are important for nitrogen removal by denitrification. Denitrification strongly depends on both the presence of emergent plants and the denitrifier communities selected by different plant species. In this study, the effects of vegetation and habitat heterogeneity on the community of denitrifying bacteria were investigated in nine coastal wetlands in two preserved areas of Spain. Sampling locations were selected to cover a range of salinity (0.81 to 31.3 mS/cm) and nitrate concentrations (0.1 to 303 μM NO3-), allowing the evaluation of environmental variables that select for denitrifier communities in the rhizosphere of Phragmites sp., Ruppia sp., and Paspalum sp. Potential nitrate reduction rates were found to be dependent on the sampling time and plant species and related to the denitrifier community structure, which was assessed by terminal restriction fragment length polymorphism analysis of the functional genes nirS, nirK and nosZ. The results showed that denitrifier community structure was also governed by plant species and salinity, with significant influences of other variables, such as sampling time and location. Ruppia sp. and Phragmites sp. selected for certain communities, whereas this was not the case for Paspalum sp. The plant species effect was strongest on nirK-type denitrifiers, whereas water carbon content was a significant factor defining the structure of the nosZ-harboring community. The differences recognized using the three functional gene markers indicated that different drivers act on denitrifying populations capable of complete denitrification, compared to the overall denitrifier community. This finding may have implications for emissions of the greenhouse gas nitrous oxide.}, }
@article {pmid22844426, year = {2012}, author = {Gauffin Cano, P and Santacruz, A and Moya, &#xc1; and Sanz, Y}, title = {Bacteroides uniformis CECT 7771 ameliorates metabolic and immunological dysfunction in mice with high-fat-diet induced obesity.}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e41079}, pmid = {22844426}, issn = {1932-6203}, mesh = {Absorption ; Adipocytes/microbiology/pathology ; Adipose Tissue/metabolism/microbiology ; Animals ; Bacteroides/*physiology ; Body Weight ; Cell Size ; Cytokines/biosynthesis ; Dendritic Cells/immunology/microbiology ; Diet, High-Fat/*adverse effects ; Enterocytes/metabolism/microbiology ; Fatty Liver/immunology/microbiology ; Macrophages, Peritoneal/metabolism/microbiology ; Male ; Metagenome ; Mice ; Mice, Inbred C57BL ; Obesity/etiology/*immunology/*metabolism/microbiology ; Species Specificity ; }, abstract = {BACKGROUND: Associations have been made between obesity and reduced intestinal numbers of members of the phylum Bacteroidetes, but there is no direct evidence of the role these bacteria play in obesity. Herein, the effects of Bacteroides uniformis CECT 7771 on obesity-related metabolic and immune alterations have been evaluated.<br><br>METHODS AND FINDINGS: Adult (6-8 week) male wild-type C57BL-6 mice were fed a standard diet or a high-fat-diet HFD to induce obesity, supplemented or not with B. uniformis CECT 7771 for seven weeks. Animal weight was monitored and histologic, biochemical, immunocompetent cell functions, and features of the faecal microbiota were analysed after intervention. The oral administration of B. uniformis CECT 7771 reduced body weight gain, liver steatosis and liver cholesterol and triglyceride concentrations and increased small adipocyte numbers in HFD-fed mice. The strain also reduced serum cholesterol, triglyceride, glucose, insulin and leptin levels, and improved oral tolerance to glucose in HFD fed mice. The bacterial strain also reduced dietary fat absorption, as indicated by the reduced number of fat micelles detected in enterocytes. Moreover, B. uniformis CECT 7771 improved immune defence mechanisms, impaired in obesity. HFD-induced obesity led to a decrease in TNF-&#x3b1; production by peritoneal macrophages stimulated with LPS, conversely, the administration of B. uniformis CECT 7771 increased TNF-&#x3b1; production and phagocytosis. Administering this strain also increased TNF-&#x3b1; production by dendritic cells (DCs) in response to LPS stimulation, which was significantly reduced by HFD. B. uniformis CECT 7771 also restored the capacity of DCs to induce a T-cell proliferation response, which was impaired in obese mice. HFD induced marked changes in gut microbiota composition, which were partially restored by the intervention.<br><br>CONCLUSIONS: Altogether, the findings indicate that administration of B. uniformis CECT 7771 ameliorates HFD-induced metabolic and immune dysfunction associated with intestinal dysbiosis in obese mice.}, }
@article {pmid22843604, year = {2012}, author = {Nazir, R and Hansen, MA and Sørensen, S and van Elsas, JD}, title = {Draft genome sequence of the soil bacterium Burkholderia terrae strain BS001, which interacts with fungal surface structures.}, journal = {Journal of bacteriology}, volume = {194}, number = {16}, pages = {4480-4481}, pmid = {22843604}, issn = {1098-5530}, mesh = {Burkholderia/*genetics/isolation &amp; purification/physiology ; DNA, Bacterial/*chemistry/*genetics ; *Genome, Bacterial ; Laccaria/physiology ; Microbial Interactions ; Molecular Sequence Data ; *Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {Burkholderia terrae BS001 is a soil bacterium which was originally isolated from the mycosphere of the ectomycorrhizal fungus Laccaria proxima. It exhibits a range of fungus-interacting traits which reveal its propensity to actively interact at fungal interfaces. Here, we present the approximately 11.5-Mb (G+C content, 61.52%) draft genome sequence of B. terrae BS001 with the aim of providing insight into the genomic basis of its ecological success in fungus-affected soil settings.}, }
@article {pmid22837150, year = {2012}, author = {García-Maldonado, JQ and Bebout, BM and Celis, LB and López-Cortés, A}, title = {Phylogenetic diversity of methyl-coenzyme M reductase (mcrA) gene and methanogenesis from trimethylamine in hypersaline environments.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {15}, number = {1}, pages = {33-41}, doi = {10.2436/20.1501.01.156}, pmid = {22837150}, issn = {1618-1905}, mesh = {Amino Acid Sequence ; *Ecosystem ; Genetic Variation ; Methane/*biosynthesis ; Methanosarcinaceae/classification/*enzymology/*genetics ; Methylamines/*metabolism ; Oxidoreductases/chemistry/*genetics ; Phylogeny ; *Salinity ; }, abstract = {Methanogens have been reported in complex microbial communities from hypersaline environments, but little is known about their phylogenetic diversity. In this work, methane concentrations in environmental gas samples were determined while methane production rates were measured in microcosm experiments with competitive and non-competitive substrates. In addition, the phylogenetic diversity of methanogens in microbial mats from two geographical locations was analyzed: the well studied Guerrero Negro hypersaline ecosystem, and a site not previously investigated, namely Laguna San Ignacio, Baja California Sur, Mexico. Methanogenesis in these microbial mats was suspected based on the detection of methane (in the range of 0.00086 to 3.204 %) in environmental gas samples. Microcosm experiments confirmed methane production by the mats and demonstrated that it was promoted only by non-competitive substrates (trimethylamine and methanol), suggesting that methylotrophy is the main characteristic process by which these hypersaline microbial mats produce methane. Phylogenetic analysis of amino acid sequences of the methyl coenzyme-M reductase (mcrA) gene from natural and manipulated samples revealed various methylotrophic methanogens belonging exclusively to the family Methanosarcinaceae. Moderately halophilic microorganisms of the genus Methanohalophilus were predominant (>60 % of mcrA sequences retrieved). Slightly halophilic and marine microorganisms of the genera Methanococcoides and Methanolobus, respectively, were also identified, but in lower abundances.}, }
@article {pmid22837003, year = {2012}, author = {Hashimoto, T and Perlot, T and Rehman, A and Trichereau, J and Ishiguro, H and Paolino, M and Sigl, V and Hanada, T and Hanada, R and Lipinski, S and Wild, B and Camargo, SM and Singer, D and Richter, A and Kuba, K and Fukamizu, A and Schreiber, S and Clevers, H and Verrey, F and Rosenstiel, P and Penninger, JM}, title = {ACE2 links amino acid malnutrition to microbial ecology and intestinal inflammation.}, journal = {Nature}, volume = {487}, number = {7408}, pages = {477-481}, pmid = {22837003}, issn = {1476-4687}, mesh = {Angiotensin-Converting Enzyme 2 ; Animals ; Biocatalysis ; Colitis/drug therapy/*etiology/*microbiology/pathology ; Dextran Sulfate ; Diarrhea/complications ; Dietary Proteins/metabolism/pharmacology ; Female ; Gene Deletion ; Genetic Predisposition to Disease ; Germ-Free Life ; Homeostasis ; Immunity, Innate ; Intestines/*microbiology/pathology ; Male ; Malnutrition/*complications/metabolism ; *Metagenome ; Mice ; Models, Biological ; Niacinamide/metabolism/pharmacology/therapeutic use ; Peptidyl-Dipeptidase A/deficiency/genetics/*metabolism ; Renin-Angiotensin System/physiology ; TOR Serine-Threonine Kinases/metabolism ; Trinitrobenzenesulfonic Acid ; Tryptophan/*metabolism/pharmacology/therapeutic use ; }, abstract = {Malnutrition affects up to one billion people in the world and is a major cause of mortality. In many cases, malnutrition is associated with diarrhoea and intestinal inflammation, further contributing to morbidity and death. The mechanisms by which unbalanced dietary nutrients affect intestinal homeostasis are largely unknown. Here we report that deficiency in murine angiotensin I converting enzyme (peptidyl-dipeptidase A) 2 (Ace2), which encodes a key regulatory enzyme of the renin-angiotensin system (RAS), results in highly increased susceptibility to intestinal inflammation induced by epithelial damage. The RAS is known to be involved in acute lung failure, cardiovascular functions and SARS infections. Mechanistically, ACE2 has a RAS-independent function, regulating intestinal amino acid homeostasis, expression of antimicrobial peptides, and the ecology of the gut microbiome. Transplantation of the altered microbiota from Ace2 mutant mice into germ-free wild-type hosts was able to transmit the increased propensity to develop severe colitis. ACE2-dependent changes in epithelial immunity and the gut microbiota can be directly regulated by the dietary amino acid tryptophan. Our results identify ACE2 as a key regulator of dietary amino acid homeostasis, innate immunity, gut microbial ecology, and transmissible susceptibility to colitis. These results provide a molecular explanation for how amino acid malnutrition can cause intestinal inflammation and diarrhoea.}, }
@article {pmid22832920, year = {2012}, author = {Bellinger, BJ and Hagerthey, SE and Newman, S and Cook, MI}, title = {Detrital floc and surface soil microbial biomarker responses to active management of the nutrient impacted Florida everglades.}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {893-908}, pmid = {22832920}, issn = {1432-184X}, mesh = {Biomass ; Eutrophication ; Fatty Acids/analysis ; Florida ; Phospholipids/analysis ; Phosphorus/analysis/chemistry/*metabolism ; Soil/analysis/*chemistry ; *Soil Microbiology ; Typhaceae/*growth &amp; development ; Wetlands ; }, abstract = {Alterations in microbial community composition, biomass, and function in the Florida Everglades impacted by cultural eutrophication reflect a new physicochemical environment associated with monotypic stands of Typha domingensis. Phospholipid fatty acid (PLFA) biomarkers were used to quantify microbial responses in detritus and surface soils in an active management experiment in the eutrophic Everglades. Creation of open plots through removal of Typha altered the physical and chemical characteristics of the region. Mass of PLFA biomarkers increased in open plots, but magnitude of changes differed among microbial groups. Biomarkers indicative of Gram-negative bacteria and fungi were significantly greater in open plots, reflective of the improved oxic environment. Reduction in the proportion of cyclopropyl lipids and the ratio of Gram-positive to Gram-negative bacteria in open plots further suggested an altered oxygen environment and conditions for the rapid growth of Gram-negative bacteria. Changes in the PLFA composition were greater in floc relative to soils, reflective of rapid inputs of new organic matter and direct interaction with the new physicochemical environment. Created open plot microbial mass and composition were significantly different from the oligotrophic Everglades due to differences in phosphorus availability, plant community structure, and a shift to organic peat from marl-peat soils. PLFA analysis also captured the dynamic inter-annual hydrologic variability, notably in PLFA concentrations, but to a lesser degree content. Recently, use of concentration has been advocated over content in studies of soil biogeochemistry, and our results highlight the differential response of these two quantitative measures to similar pressures.}, }
@article {pmid22832919, year = {2012}, author = {Batzer, JC and Sisson, AJ and Harrington, TC and Mayfield, DA and Gleason, ML}, title = {Temporal patterns in appearance of sooty blotch and flyspeck fungi on apples.}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {928-941}, pmid = {22832919}, issn = {1432-184X}, mesh = {Ascomycota/classification/genetics/isolation &amp; purification ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; Fruit/*microbiology ; Fungi/*classification/genetics/isolation &amp; purification ; Iowa ; Malus/growth &amp; development/*microbiology ; Plant Diseases/*microbiology ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Species Specificity ; }, abstract = {Sooty blotch and flyspeck (SBFS) is a complex of about 80 fungal species that blemish the surface of apple fruit in humid regions worldwide. The dark colonies become visible in mid- to late summer, reducing the value of fresh fruit. Although many SBFS species can co-occur in the same orchard and even on the same apple, little is known about temporal patterns of these species, including the timing of colony appearance. To test the hypothesis that colonies of SBFS species appear on apples at characteristic times during the growing season, 50 apples were monitored weekly at three Iowa orchards in 2006 and six orchards in 2007 and 2008. However, a mean of 24.3 apples per orchard was assessed at harvest because of apple drop throughout the season. Colonies were marked with colored pens as they appeared. After harvest and after storage of apples at 2 °C for 3 months, SBFS colonies on each fruit were counted and classified by morphology, and a representative subset of colonies was excised from the fruit and preserved on dried peels for species identification using rDNA. Seventeen species were identified. Stomiopeltis spp. RS1 and RS2 appeared on apples 10 to 14 days before other SBFS taxa. Dissoconium aciculare was generally the last species to appear on apple fruit, and it continued to appear during postharvest storage. The most prevalent taxa in Iowa orchards were also the most abundant. Diversity of SBFS fungi in an orchard was positively correlated with cumulative hours of surface wetness hours due to rainfall or dew, which is believed to favor growth of SBFS fungi. Species-specific information about temporal patterns of appearance on apple fruit may lead to improved SBFS management strategies.}, }
@article {pmid22831972, year = {2012}, author = {Bokulich, NA and Mills, DA}, title = {Next-generation approaches to the microbial ecology of food fermentations.}, journal = {BMB reports}, volume = {45}, number = {7}, pages = {377-389}, doi = {10.5483/bmbrep.2012.45.7.148}, pmid = {22831972}, issn = {1976-670X}, mesh = {Electrophoresis, Polyacrylamide Gel ; *Fermentation ; *Food Microbiology ; Polymerase Chain Reaction ; }, abstract = {Food fermentations have enhanced human health since the dawn of time and remain a prevalent means of food processing and preservation. Due to their cultural and nutritional importance, many of these foods have been studied in detail using molecular tools, leading to enhancements in quality and safety. Furthermore, recent advances in high-throughput sequencing technology are revolutionizing the study of food microbial ecology, deepening insight into complex fermentation systems. This review provides insight into novel applications of select molecular techniques, particularly next-generation sequencing technology, for analysis of microbial communities in fermented foods. We present a guideline for integrated molecular analysis of food microbial ecology and a starting point for implementing next-generation analysis of food systems.}, }
@article {pmid22828897, year = {2012}, author = {Kalscheur, KN and Rojas, M and Peterson, CG and Kelly, JJ and Gray, KA}, title = {Algal exudates and stream organic matter influence the structure and function of denitrifying bacterial communities.}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {881-892}, pmid = {22828897}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; Biofilms ; Carbon/analysis ; DNA, Bacterial/analysis/genetics ; *Denitrification ; *Ecosystem ; Gas Chromatography-Mass Spectrometry/methods ; Human Activities ; Microalgae/*chemistry/metabolism ; Organic Chemicals/*analysis ; RNA, Ribosomal, 16S/genetics ; Rivers/*chemistry/microbiology ; Sequence Analysis, DNA ; }, abstract = {Within aquatic ecosystems, periphytic biofilms can be hot spots of denitrification, and previous work has suggested that algal taxa within periphyton can influence the species composition and activity of resident denitrifying bacteria. This study tested the hypothesis that algal species composition within biofilms influences the structure and function of associated denitrifying bacterial communities through the composition of organic exudates. A mixed population of bacteria was incubated with organic carbon isolated from one of seven algal species or from one of two streams that differed in anthropogenic inputs. Pyrolysis-gas chromatography-mass spectrometry (Py-GC/MS) revealed differences in the organic composition of algal exudates and stream waters, which, in turn, selected for distinct bacterial communities. Organic carbon source had a significant effect on potential denitrification rates (DNP) of the communities, with organics isolated from a stream with high anthropogenic inputs resulting in a bacterial community with the highest DNP. There was no correlation between DNP and numbers of denitrifiers (based on nirS copy numbers), but there was a strong relationship between the species composition of denitrifier communities (as indicated by tag pyrosequencing of nosZ genes) and DNP. Specifically, the relative abundance of Pseudomonas stutzeri-like nosZ sequences across treatments correlated significantly with DNP, and bacterial communities incubated with organic carbon from the stream with high anthropogenic inputs had the highest relative abundance of P. stutzeri-like nosZ sequences. These results demonstrate a significant relationship between bacterial community composition and function and provide evidence of the potential impacts of anthropogenic inputs on the structure and function of stream microbial communities.}, }
@article {pmid22827861, year = {2012}, author = {Peterkova-Koci, K and Robles-Murguia, M and Ramalho-Ortigao, M and Zurek, L}, title = {Significance of bacteria in oviposition and larval development of the sand fly Lutzomyia longipalpis.}, journal = {Parasites &amp; vectors}, volume = {5}, number = {}, pages = {145}, pmid = {22827861}, issn = {1756-3305}, support = {P20-RR017686/RR/NCRR NIH HHS/United States ; R01 AI074691/AI/NIAID NIH HHS/United States ; R21 AI088051-01/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics ; Behavior, Animal ; Feces/microbiology ; Female ; Gastrointestinal Tract/microbiology ; Larva/microbiology ; Oviposition ; Psychodidae/*microbiology/*physiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rabbits ; }, abstract = {BACKGROUND: Microbial ecology of phlebotomine sand flies is not well understood although bacteria likely play an important role in the sand fly biology and vector capacity for Leishmania parasites. In this study, we assessed the significance of the microbial community of rabbit feces in oviposition and larval development of Lutzomyia longipalpis as well as bacterial colonization of the gut of freshly emerged flies.<br><br>METHODS: Sterile (by autoclaving) and non-sterile (control) rabbit feces were used in the two-choice assay to determine their oviposition attractiveness to sand fly females. Bacteria were identified by amplification and sequencing of the 16S rRNA gene with universal eubacterial primers. Sterile, control (non-sterile), and sterilized and inoculated rabbit feces were used to assess the significance of bacteria in L. longipalpis development. Newly emerged adult flies were surface-sterilized and screened for the bacterial population size and diversity by the culturing approach. The digestive tract of L4 sterile and control larvae was incubated with Phalloidin to visualize muscle tissues and DAPI to visualize nuclei.<br><br>RESULTS: Two-choice behavioural assays revealed a great preference of L. longipalpis to lay eggs on rabbit feces with an active complex bacterial community (control) (85.8&#x2009;% of eggs) in comparison to that of sterile (autoclaved) rabbit feces (14.2&#x2009;%). Bioassays demonstrated that L. longipalpis larvae can develop in sterile rabbit feces although development time to adult stage was greatly extended (47&#x2009;days) and survival of larvae was significantly lower (77.8&#x2009;%) compared to that of larvae developing in the control rabbit feces (32&#x2009;days and 91.7&#x2009;%). Larval survival on sterilized rabbit feces inoculated with the individual bacterial isolates originating from this substrate varied greatly depending on a bacterial strain. Rhizobium radiobacter supported larval development to adult stage into the greatest extent (39&#x2009;days, 88.0&#x2009;%) in contrast to that of Bacillus spp. (76&#x2009;days, 36.0&#x2009;%). From the complex natural bacterial community of rabbit feces, R. radiobacter survived pupation and colonized the newly emerged females most successfully (82.6&#x2009;% of all bacteria cultured); however, only 25&#x2009;% of females were positive for bacteria in the digestive tract upon emergence. Immunohistochemistry did not reveal any obvious differences in anatomy of the digestive tract between control and axenic larvae.<br><br>CONCLUSIONS: The bacterial community in the sand fly larval habitat affects oviposition and larval development although bacteria are not essential for successful development of L. longipalpis. Different bacteria contribute to larval development to various degrees and some, e.g. Rhizobium radiobacter, survive pupation and colonize the digestive tract of newly emerged females. With the establishment of the axenic rearing system, this study opens new venues to study the effect of bacteria on the gut epithelial immunity and vector competence of sand flies for Leishmania parasites with a goal to develop paratransgenic approaches for Leishmania control.}, }
@article {pmid22826803, year = {2012}, author = {Yamaguchi, N and Ichijo, T and Sakotani, A and Baba, T and Nasu, M}, title = {Global dispersion of bacterial cells on Asian dust.}, journal = {Scientific reports}, volume = {2}, number = {}, pages = {525}, pmid = {22826803}, issn = {2045-2322}, mesh = {*Air Microbiology ; Asia ; *Bacteria/classification/genetics/growth &amp; development ; Biodiversity ; *Dust ; Ecosystem ; Environmental Monitoring ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The atmospheric dispersion of bacteria over long distances is an important facet of microbial ecology. Certain groups of dispersed bacteria can adapt to their new location and affect established ecosystems. Aeolian dust particles are known to be carriers of microbes but further research is needed to expand our understanding of this field of microbiology. Here we showed the potential of aeolian dust to global migration of bacterial cells. We demonstrated the presence of microbial cells on dust particles directly by bio-imaging. Bacterial abundance on dust particles declined from 10(5) to less than 10(3) cells/m3 as the dust event subsided. Taxonomically diverse bacteria were identified by 16S rRNA gene sequencing and some of these bacteria retained growth potential. Our results confirm that bacteria can attach to aeolian dust particles and they have the potential to migrate globally during dust events and thus can contribute to the diversity of downwind ecosystems.}, }
@article {pmid22822369, year = {2012}, author = {Hunt, LR and Smith, SM and Downum, KR and Mydlarz, LD}, title = {Microbial regulation in gorgonian corals.}, journal = {Marine drugs}, volume = {10}, number = {6}, pages = {1225-1243}, pmid = {22822369}, issn = {1660-3397}, mesh = {Animals ; Anthozoa/*chemistry/*microbiology ; Anti-Bacterial Agents/*chemistry/*pharmacology ; Bacteria/*drug effects ; Cell Communication/drug effects ; Florida ; Puerto Rico ; Quorum Sensing/*drug effects ; }, abstract = {Gorgonian corals possess many novel natural products that could potentially mediate coral-bacterial interactions. Since many bacteria use quorum sensing (QS) signals to facilitate colonization of host organisms, regulation of prokaryotic cell-to-cell communication may represent an important bacterial control mechanism. In the present study, we examined extracts of twelve species of Caribbean gorgonian corals, for mechanisms that regulate microbial colonization, such as antibacterial activity and QS regulatory activity. Ethanol extracts of gorgonians collected from Puerto Rico and the Florida Keys showed a range of both antibacterial and QS activities using a specific Pseudomonas aeruginosa QS reporter, sensitive to long chain AHLs and a short chain N-acylhomoserine lactones (AHL) biosensor, Chromobacterium violaceium. Overall, the gorgonian corals had higher antimicrobial activity against non-marine strains when compared to marine strains. Pseudopterogorgia americana, Pseusopterogorgia acerosa, and Pseudoplexuara flexuosa had the highest QS inhibitory effect. Interestingly, Pseudoplexuara porosa extracts stimulated QS activity with a striking 17-fold increase in signal. The stimulation of QS by P. porosa or other elements of the holobiont may encourage colonization or recruitment of specific microbial species. Overall, these results suggest the presence of novel stimulatory QS, inhibitory QS and bactericidal compounds in gorgonian corals. A better understanding of these compounds may reveal insight into coral-microbial ecology and whether a therapeutic potential exists.}, }
@article {pmid22821465, year = {2012}, author = {Levy, R and Borenstein, E}, title = {Reverse Ecology: from systems to environments and back.}, journal = {Advances in experimental medicine and biology}, volume = {751}, number = {}, pages = {329-345}, doi = {10.1007/978-1-4614-3567-9_15}, pmid = {22821465}, issn = {0065-2598}, mesh = {Adaptation, Physiological/genetics ; Algorithms ; Biological Evolution ; Biotechnology ; Ecology/*methods ; Environment ; *Genome ; Genomics ; Microbial Consortia/*genetics ; Models, Genetic ; Systems Biology/*methods ; }, abstract = {The structure of complex biological systems reflects not only their function but also the environments in which they evolved and are adapted to. Reverse Ecology-an emerging new frontier in Evolutionary Systems Biology-aims to extract this information and to obtain novel insights into an organism's ecology. The Reverse Ecology framework facilitates the translation of high-throughput genomic data into large-scale ecological data, and has the potential to transform ecology into a high-throughput field. In this chapter, we describe some of the pioneering work in Reverse Ecology, demonstrating how system-level analysis of complex biological networks can be used to predict the natural habitats of poorly characterized microbial species, their interactions with other species, and universal patterns governing the adaptation of organisms to their environments. We further present several studies that applied Reverse Ecology to elucidate various aspects of microbial ecology, and lay out exciting future directions and potential future applications in biotechnology, biomedicine, and ecological engineering.}, }
@article {pmid22815440, year = {2012}, author = {Garbeva, P and van Elsas, JD and de Boer, W}, title = {Draft genome sequence of the antagonistic rhizosphere bacterium Serratia plymuthica strain PRI-2C.}, journal = {Journal of bacteriology}, volume = {194}, number = {15}, pages = {4119-4120}, pmid = {22815440}, issn = {1098-5530}, mesh = {Antibiosis ; Base Composition ; DNA, Bacterial/*chemistry/*genetics ; *Genome, Bacterial ; Molecular Sequence Data ; Rhizosphere ; *Sequence Analysis, DNA ; Serratia/*genetics/isolation &amp; purification/physiology ; Soil Microbiology ; }, abstract = {Serratia plymuthica strain PRI-2C is a rhizosphere bacterial strain with antagonistic activity against different plant pathogens. Here we present the 5.39-Mb (G+C content, 55.67%) draft genome sequence of S. plymuthica strain PRI-2C with the aim of providing insight into the genomic basis of its antagonistic activity.}, }
@article {pmid22810059, year = {2013}, author = {Garcia, SL and McMahon, KD and Martinez-Garcia, M and Srivastava, A and Sczyrba, A and Stepanauskas, R and Grossart, HP and Woyke, T and Warnecke, F}, title = {Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton.}, journal = {The ISME journal}, volume = {7}, number = {1}, pages = {137-147}, pmid = {22810059}, issn = {1751-7370}, mesh = {Actinobacteria/genetics/*metabolism ; DNA, Bacterial/genetics ; Ecosystem ; Fresh Water/*microbiology ; *Genome, Bacterial ; Membrane Transport Proteins/genetics/metabolism ; Phylogeny ; Plankton/genetics/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Actinobacteria within the acI lineage are often numerically dominating in freshwater ecosystems, where they can account for >50% of total bacteria in the surface water. However, they remain uncultured to date. We thus set out to use single-cell genomics to gain insights into their genetic make-up, with the aim of learning about their physiology and ecological niche. A representative from the highly abundant acI-B1 group was selected for shotgun genomic sequencing. We obtained a draft genomic sequence in 75 larger contigs (sum=1.16 Mb), with an unusually low genomic G+C mol% (∼42%). Actinobacteria core gene analysis suggests an almost complete genome recovery. We found that the acI-B1 cell had a small genome, with a rather low percentage of genes having no predicted functions (∼15%) as compared with other cultured and genome-sequenced microbial species. Our metabolic reconstruction hints at a facultative aerobe microorganism with many transporters and enzymes for pentoses utilization (for example, xylose). We also found an actinorhodopsin gene that may contribute to energy conservation under unfavorable conditions. This project reveals the metabolic potential of a member of the global abundant freshwater Actinobacteria.}, }
@article {pmid22808103, year = {2012}, author = {Ofek, M and Hadar, Y and Minz, D}, title = {Ecology of root colonizing Massilia (Oxalobacteraceae).}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e40117}, pmid = {22808103}, issn = {1932-6203}, mesh = {Agrobacterium tumefaciens/genetics ; Colony Count, Microbial ; Cucumis sativus/*microbiology ; *Ecological and Environmental Phenomena ; Oxalobacteraceae/*growth &amp; development ; Phylogeny ; Plant Roots/*microbiology ; Pythium/microbiology ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Seedlings/microbiology ; Seeds/microbiology ; Soil Microbiology ; }, abstract = {BACKGROUND: Ecologically meaningful classification of bacterial populations is essential for understanding the structure and function of bacterial communities. As in soils, the ecological strategy of the majority of root-colonizing bacteria is mostly unknown. Among those are Massilia (Oxalobacteraceae), a major group of rhizosphere and root colonizing bacteria of many plant species.<br><br>The ecology of Massilia was explored in cucumber root and seed, and compared to that of Agrobacterium population, using culture-independent tools, including DNA-based pyrosequencing, fluorescence in situ hybridization and quantitative real-time PCR. Seed- and root-colonizing Massilia were primarily affiliated with other members of the genus described in soil and rhizosphere. Massilia colonized and proliferated on the seed coat, radicle, roots, and also on hyphae of phytopathogenic Pythium aphanidermatum infecting seeds. High variation in Massilia abundance was found in relation to plant developmental stage, along with sensitivity to plant growth medium modification (amendment with organic matter) and potential competitors. Massilia absolute abundance and relative abundance (dominance) were positively related, and peaked (up to 85%) at early stages of succession of the root microbiome. In comparison, variation in abundance of Agrobacterium was moderate and their dominance increased at later stages of succession.<br><br>CONCLUSIONS: In accordance with contemporary models for microbial ecology classification, copiotrophic and competition-sensitive root colonization by Massilia is suggested. These bacteria exploit, in a transient way, a window of opportunity within the succession of communities within this niche.}, }
@article {pmid22807668, year = {2012}, author = {Faust, K and Sathirapongsasuti, JF and Izard, J and Segata, N and Gevers, D and Raes, J and Huttenhower, C}, title = {Microbial co-occurrence relationships in the human microbiome.}, journal = {PLoS computational biology}, volume = {8}, number = {7}, pages = {e1002606}, pmid = {22807668}, issn = {1553-7358}, support = {U54HG004969/HG/NHGRI NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 HG005969/HG/NHGRI NIH HHS/United States ; U54 HG004969/HG/NHGRI NIH HHS/United States ; CA139193/CA/NCI NIH HHS/United States ; R21 CA139193/CA/NCI NIH HHS/United States ; 1R01HG005969/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacteria/*classification ; *Bacterial Physiological Phenomena ; Computational Biology ; DNA, Bacterial/chemistry ; Ecosystem ; Female ; Gastrointestinal Tract/microbiology ; Genes, rRNA/genetics ; Humans ; Linear Models ; Male ; Metagenome/*physiology ; Microbial Interactions/physiology ; Nasal Cavity/microbiology ; Phylogeny ; Skin/microbiology ; Vagina/microbiology ; }, abstract = {The healthy microbiota show remarkable variability within and among individuals. In addition to external exposures, ecological relationships (both oppositional and symbiotic) between microbial inhabitants are important contributors to this variation. It is thus of interest to assess what relationships might exist among microbes and determine their underlying reasons. The initial Human Microbiome Project (HMP) cohort, comprising 239 individuals and 18 different microbial habitats, provides an unprecedented resource to detect, catalog, and analyze such relationships. Here, we applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs) to taxonomic marker (16S rRNA gene) profiles of this cohort, resulting in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome. This network revealed strong niche specialization, with most microbial associations occurring within body sites and a number of accompanying inter-body site relationships. Microbial communities within the oropharynx grouped into three distinct habitats, which themselves showed no direct influence on the composition of the gut microbiota. Conversely, niches such as the vagina demonstrated little to no decomposition into region-specific interactions. Diverse mechanisms underlay individual interactions, with some such as the co-exclusion of Porphyromonaceae family members and Streptococcus in the subgingival plaque supported by known biochemical dependencies. These differences varied among broad phylogenetic groups as well, with the Bacilli and Fusobacteria, for example, both enriched for exclusion of taxa from other clades. Comparing phylogenetic versus functional similarities among bacteria, we show that dominant commensal taxa (such as Prevotellaceae and Bacteroides in the gut) often compete, while potential pathogens (e.g. Treponema and Prevotella in the dental plaque) are more likely to co-occur in complementary niches. This approach thus serves to open new opportunities for future targeted mechanistic studies of the microbial ecology of the human microbiome.}, }
@article {pmid22806816, year = {2012}, author = {Liu, Y and Zuo, S and Zou, Y and Wang, J and Song, W}, title = {Investigation on diversity and population succession dynamics of indigenous bacteria of the maize spermosphere.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {28}, number = {1}, pages = {391-396}, pmid = {22806816}, issn = {1573-0972}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Base Sequence ; Biodiversity ; Ecosystem ; Endophytes/classification/genetics/*isolation &amp; purification ; *Food Microbiology ; Genes, Bacterial ; Germination ; Metagenome ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Seeds/microbiology ; Zea mays/growth &amp; development/*microbiology ; }, abstract = {The spermosphere, an important habitat to the plant micro-ecosystem, has a unique significance to seed microbial ecology, but has been poorly researched. In this study, the mature seeds of reciprocal cross maize (Zea mays L., Nongda108) were collected to investigate the diversity and population succession dynamics of indigenous spermosphere bacteria at 12, 24 and 36 h into seed germination using 16S rDNA library construction. In the spermosphere of Nongda108A (Huang C × 178), the dominant bacteria genera identified were Pseudomonas and Burkholderia. The proportion of Pseudomonas increased from 59.60 to 75.00% then 82.61%; while Burkholderia decreased from 39.39 to 25.00% then 15.22% at 12, 24 and 36 h, respectively. Bacillus, Paenibacillus and Stenotrophomonas were the dominant genera in Nongda108B. The proportion of Paenibacillus after 12, 24 and 36 h into germination decreased from 68.00 to 46.15 to 13.27%, respectively. The proportion of non-Paenibacillus genera increased from 32.00 (Stenotrophomonas) to 53.85 (Bacillus) to 77.55% (Burkholderia) from 12 h to 24 h to 36 h, respectively. Some dominant bacteria genera identified from maize spermosphere have been identified as common PGPR.}, }
@article {pmid22806042, year = {2012}, author = {Soares, FL and Melo, IS and Dias, AC and Andreote, FD}, title = {Cellulolytic bacteria from soils in harsh environments.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {28}, number = {5}, pages = {2195-2203}, pmid = {22806042}, issn = {1573-0972}, mesh = {Antarctic Regions ; Bacteria/classification/*enzymology/isolation &amp; purification/*metabolism ; Brazil ; Cellulases/*metabolism ; Cellulose/*metabolism ; Cluster Analysis ; Culture Media/chemistry ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Desert Climate ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Temperature ; }, abstract = {It is believed that the exposure of organisms to harsh climate conditions may select for differential enzymatic activities, making the surviving organisms a very promising source for bioprospecting. Soil bacteria play an important role in degradation of organic matter, which is mostly due to their ability to decompose cellulose-based materials. This work focuses on the isolation and identification of cellulolytic bacteria from soil found in two environments with stressful climate conditions (Antarctica and the Brazilian semi-arid caatinga). Cellulolytic bacteria were selected using enrichments at high and low temperatures (4 or 60°C) in liquid media (trypic soy broth-TSB and minimum salt medium-MM) supplemented with cellulose (1%). Many of the isolates (119 out of 254-46.9%) displayed the ability to degrade carboxymethyl-cellulose, indicating the presence of endoglucolytic activity, while only a minority of these isolates (23 out of 254-9.1%) showed exoglucolytic activity (degradation of avicel). The obtained isolates revealed a preferential endoglucolytic activity according to the temperature of enrichments. Also, the identification of some isolates by partial sequencing of the 16S rRNA gene indicated that the Bacteroidetes (e.g., Pedobacter, Chryseobacterium and Flavobacterium) were the main phylum of cellulolytic bacteria isolated from soil in Antarctica; the Firmicutes (e.g., Bacillus) were more commonly isolated from samples from the caatinga; and Actinobacteria were found in both types of soil (e.g., Microbacterium and Arthrobacter). In conclusion, this work reports the isolation of bacteria able to degrade cellulose-based material from soil at very low or very high temperatures, a finding that should be further explored in the search for cellulolytic enzymes to be used in the bioenergy industry.}, }
@article {pmid22805914, year = {2012}, author = {Bhattacharyya, PN and Jha, DK}, title = {Plant growth-promoting rhizobacteria (PGPR): emergence in agriculture.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {28}, number = {4}, pages = {1327-1350}, pmid = {22805914}, issn = {1573-0972}, mesh = {Agriculture/*methods ; Bacteria/*metabolism ; *Plant Development ; *Soil Microbiology ; }, abstract = {Plant growth-promoting rhizobacteria (PGPR) are the rhizosphere bacteria that can enhance plant growth by a wide variety of mechanisms like phosphate solubilization, siderophore production, biological nitrogen fixation, rhizosphere engineering, production of 1-Aminocyclopropane-1-carboxylate deaminase (ACC), quorum sensing (QS) signal interference and inhibition of biofilm formation, phytohormone production, exhibiting antifungal activity, production of volatile organic compounds (VOCs), induction of systemic resistance, promoting beneficial plant-microbe symbioses, interference with pathogen toxin production etc. The potentiality of PGPR in agriculture is steadily increased as it offers an attractive way to replace the use of chemical fertilizers, pesticides and other supplements. Growth promoting substances are likely to be produced in large quantities by these rhizosphere microorganisms that influence indirectly on the overall morphology of the plants. Recent progress in our understanding on the diversity of PGPR in the rhizosphere along with their colonization ability and mechanism of action should facilitate their application as a reliable component in the management of sustainable agricultural system. The progress to date in using the rhizosphere bacteria in a variety of applications related to agricultural improvement along with their mechanism of action with special reference to plant growth-promoting traits are summarized and discussed in this review.}, }
@article {pmid22805741, year = {2012}, author = {Díez-Vives, C and Gasol, JM and Acinas, SG}, title = {Evaluation of marine bacteroidetes-specific primers for microbial diversity and dynamics studies.}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {1047-1055}, pmid = {22805741}, issn = {1432-184X}, mesh = {Bacteroidetes/classification/*genetics ; *DNA Primers ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal/analysis/genetics ; Denaturing Gradient Gel Electrophoresis/*methods ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S ; Seawater/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Assumptions on the matching specificity of group-specific bacterial primers may bias the interpretation of environmental microbial studies. As available sequence data continue growing, the performance of primers and probes needs to be reevaluated. Here, we present an evaluation of several commonly used and one newly designed Bacteroidetes-specific primer (CF418). First, we revised the in silico primer coverage and specificity with the current SILVA and RDP databases. We found minor differences with previous studies, which could be explained by the chosen databases, taxonomies, and matching criteria. We selected eight commonly used Bacteroidetes primers and tested them with a collection of assorted marine bacterial isolates. We also used the denaturing gradient gel electrophoresis (DGGE) approach in environmental samples to evaluate their ability to yield clear and diverse band patterns corresponding to Bacteroidetes phylotypes. Among the primers tested, CF968R did not provide satisfactory results in DGGE, although it exhibited the highest in silico coverage for Flavobacteria. Primers CFB560 and CFB555 presented undesirable features, such as requiring nested protocols or presence of degeneracies. Finally, the new primer CF418 and primer CF319a were used to explore the Bacteroidetes dynamics throughout a 1-year cycle in Mediterranean coastal waters (Blanes Bay Microbial Observatory). Both primers provided clear and diverse banding patterns, but the low specificity of CF319a was evidenced by 83.3 % of the bands sequenced corresponding to nontarget taxa. The satisfactory DGGE banding patterns and the wide diversity of sequences retrieved from DGGE bands with primer CF418 prove it to be a valuable alternative for the study of Bacteroidetes communities, recovering a wide range of phylotypes within the group.}, }
@article {pmid22805003, year = {2012}, author = {Giotis, ES and Loeffler, A and Knight-Jones, T and Lloyd, DH}, title = {Development of a skin colonization model in gnotobiotic piglets for the study of the microbial ecology of meticillin-resistant Staphylococcus aureus ST398.}, journal = {Journal of applied microbiology}, volume = {113}, number = {4}, pages = {992-1000}, doi = {10.1111/j.1365-2672.2012.05397.x}, pmid = {22805003}, issn = {1365-2672}, mesh = {Animals ; Bacterial Load ; *Disease Models, Animal ; Germ-Free Life ; Methicillin-Resistant Staphylococcus aureus/*pathogenicity ; Skin Diseases, Bacterial/*microbiology ; Staphylococcal Infections/*microbiology ; Sus scrofa/*microbiology ; }, abstract = {AIMS: Meticillin-resistant Staphylococcus aureus (MRSA) ST398 continues to spread amongst pigs and other domestic animals and man. This highlights the need for models to examine MRSA colonization and investigate control strategies. This study aimed to develop a gnotobiotic pig model and assess the potential of bacterial interference from selected coagulase-negative staphylococci (CNS) against MRSA ST398.<br><br>METHODS AND RESULTS: Groups of 2-week-old piglets were atraumatically inoculated either with MRSA and/or CNS. Skin and mucosae were swabbed, and bacterial counts compared over a period of 21&#xa0;days. Piglets developed healthily, and bacterial populations increased similarly for both MRSA and CNS until day 32. On day 37, MRSA counts in groups with CNS reduced significantly compared with MRSA alone (P&#xa0;=&#xa0;0&#xb7;03).<br><br>CONCLUSIONS: The results showed that inoculation of piglet skin with MRSA resulted in spontaneous colonization and that MRSA ST398 has a low pathogenic potential in gnotobiotic piglets. Quantitative bacteriology indicated that initial MRSA colonization was unaffected by concurrent CNS colonization but that interference may occur over a longer period.<br><br>Gnotobiotic piglets provide a reproducible model suitable for bacterial interference studies, which should be further explored as an alternative to antimicrobials in the control of MRSA.}, }
@article {pmid22804726, year = {2013}, author = {Cahenzli, J and Balmer, ML and McCoy, KD}, title = {Microbial-immune cross-talk and regulation of the immune system.}, journal = {Immunology}, volume = {138}, number = {1}, pages = {12-22}, pmid = {22804726}, issn = {1365-2567}, mesh = {Animals ; Epithelial Cells/immunology/microbiology ; Humans ; Immune System/*immunology/*microbiology ; Intestines/cytology/immunology/microbiology ; }, abstract = {We are all born germ-free. Following birth we enter into a lifelong relationship with microbes residing on our body's surfaces. The lower intestine is home to the highest microbial density in our body, which is also the highest microbial density known on Earth (up to 10(12) /g of luminal contents). With our indigenous microbial cells outnumbering our human cells by an order of magnitude our body is more microbial than human. Numerous immune adaptations confine these microbes within the mucosa, enabling most of us to live in peaceful homeostasis with our intestinal symbionts. Intestinal epithelial cells not only form a physical barrier between the bacteria-laden lumen and the rest of the body but also function as multi-tasking immune cells that sense the prevailing microbial (apical) and immune (basolateral) milieus, instruct the underlying immune cells, and adapt functionally. In the constant effort to ensure intestinal homeostasis, the immune system becomes educated to respond appropriately and in turn immune status can shape the microbial consortia. Here we review how the dynamic immune-microbial dialogue underlies maturation and regulation of the immune system and discuss recent findings on the impact of diet on both microbial ecology and immune function.}, }
@article {pmid22799264, year = {2012}, author = {De Clippeleir, H and Courtens, E and Mosquera, M and Vlaeminck, SE and Smets, BF and Boon, N and Verstraete, W}, title = {Efficient total nitrogen removal in an ammonia gas biofilter through high-rate OLAND.}, journal = {Environmental science &amp; technology}, volume = {46}, number = {16}, pages = {8826-8833}, doi = {10.1021/es301717b}, pmid = {22799264}, issn = {1520-5851}, mesh = {Ammonia/*isolation &amp; purification ; Base Sequence ; DNA Primers ; Filtration/*instrumentation ; Nitrification ; Nitrogen/*isolation &amp; purification ; Oxygen/chemistry ; Real-Time Polymerase Chain Reaction ; }, abstract = {Ammonia gas is conventionally treated in nitrifying biofilters; however, addition of organic carbon to perform post-denitrification is required to obtain total nitrogen removal. Oxygen-limited autotrophic nitrification/denitrification (OLAND), applied in full-scale for wastewater treatment, can offer a cost-effective alternative for gas treatment. In this study, the OLAND application thus was broadened toward ammonia loaded gaseous streams. A down flow, oxygen-saturated biofilter (height of 1.5 m; diameter of 0.11 m) was fed with an ammonia gas stream (248 ± 10 ppmv) at a loading rate of 0.86 ± 0.04 kg N m(-3) biofilter d(-1) and an empty bed residence time of 14 s. After 45 days of operation a stable nitrogen removal rate of 0.67 ± 0.06 kg N m(-3) biofilter d(-1), an ammonia removal efficiency of 99%, a removal of 75-80% of the total nitrogen, and negligible NO/N(2)O productions were obtained at water flow rates of 1.3 ± 0.4 m(3) m(-2) biofilter section d(-1). Profile measurements revealed that 91% of the total nitrogen activity was taking place in the top 36% of the filter. This study demonstrated for the first time highly effective and sustainable autotrophic ammonia removal in a gas biofilter and therefore shows the appealing potential of the OLAND process to treat ammonia containing gaseous streams.}, }
@article {pmid22799205, year = {2012}, author = {Zhang, L and He, J}, title = {[A novel archaeal phylum: thaumarchaeota--a review].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {52}, number = {4}, pages = {411-421}, pmid = {22799205}, issn = {0001-6209}, mesh = {Ammonia/metabolism ; Archaea/*classification/genetics/metabolism ; DNA, Ribosomal ; Phylogeny ; }, abstract = {Based on the archaeal 16S rRNA gene phylogenetic tree, the archaeal domain is divided into two major phyla, Euryarchaeota and Crenarchaeota. During the past 20 years, diverse groups of archaea have been found to be widely distributed in moderate environments with the rapid development and application of molecular techniques in microbial ecology. Increasing evidence demonstrated that these archaea, especially ammonia-oxidizing archaea, play a major role in biogeochemical cycles of nitrogen and carbon elements. These mesophilic archaea were placed initially as a sister group of the Crenarchaeota and named as "non-thermophilic Crenarchaeota". More recently, phylogenetic analyses based on more SSU and SLU rDNA sequences suggested that the non-thermophilic Crenarchaeota constituted a separate phylum of the Archaea that branched off before the separation of Crenarchaeota and Euryarchaeota. The Thaumarchaeota (the Greek "Thaumas", meaning wonder) was therefore proposed for a novel phylum, as the third archaeal phylum. More studies based on r-proteins and comparative genomics confirm that the Thaumarchaeota are distinct from Crenarchaeota. In this paper, we gave a translated Chinese name for Thaumarchaeota and reviewed the recent progress on the phylogeny position, genetics, ecology and physiology of the Thaumarchaeota.}, }
@article {pmid22796811, year = {2012}, author = {Fiocchi, C}, title = {Towards a 'cure' for IBD.}, journal = {Digestive diseases (Basel, Switzerland)}, volume = {30}, number = {4}, pages = {428-433}, doi = {10.1159/000338148}, pmid = {22796811}, issn = {1421-9875}, mesh = {Disease Progression ; Environment ; Gastrointestinal Tract/microbiology/pathology ; Humans ; Immune System/immunology ; Inflammatory Bowel Diseases/genetics/immunology/microbiology/*therapy ; Metagenome ; }, abstract = {To discuss a cure for IBD, one should first define the concept 'a cure'. If it is intended as the general restoration of health, this is already possible, as many current therapies do a good job in inducing long periods of remission in Crohn's disease, and colectomy can technically cure ulcerative colitis. If it is more strictly defined as the complete and permanent elimination of the cause, predisposing and permissive factors, reinstatement of normal microbial ecology and restoration of mucosal immune homeostasis, then a cure for IBD is out of reach, at least for now. Regardless of the definition, major strides have been made in attempting to cure IBD by addressing the key components of its pathogenesis: the environment (exposome), the genetic makeup (genome), the gut microbiota (microbiome) and the immune system (immunome). However, the isolated modulation of each component is insufficient to provide a cure, and different requirements may be needed depending on the stage of the disease and each patient subset. To achieve a cure, one key approach is currently missing: the integration of knowledge from all the pathogenic components. We continue to learn more and more about each component using traditional 'canonical' systems, which allow the accumulation of data without taking into consideration the other components. We are still not studying the 'omes' of IBD, we should be using 'omics' technologies that can generate a more global vision of IBD pathogenesis on which to base novel, multiple pathway-integrated therapies.}, }
@article {pmid22796724, year = {2012}, author = {Epelde, L and Martín-Sánchez, I and González-Oreja, JA and Anza, M and Gómez-Sagasti, MT and Garbisu, C}, title = {Impact of sources of environmental degradation on microbial community dynamics in non-polluted and metal-polluted soils.}, journal = {The Science of the total environment}, volume = {433}, number = {}, pages = {264-272}, doi = {10.1016/j.scitotenv.2012.06.049}, pmid = {22796724}, issn = {1879-1026}, mesh = {*Biodegradation, Environmental ; Biodiversity ; Climate Change ; Electrophoresis, Polyacrylamide Gel ; Metals/*metabolism ; Polymerase Chain Reaction ; *Soil ; *Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {Soils are currently being degraded at an alarming rate due to increasing pressure from different sources of environmental degradation. Consequently, we carried out a 4-month microcosm experiment to measure the impact of different sources of environmental degradation (biodiversity loss, nitrogen deposition and climate change) on soil health in a non-polluted (non-degraded) and a heavily metal-polluted (degraded) soil, and to compare their responses. To this aim, we determined a variety of soil microbial properties with potential as bioindicators of soil health: basal respiration; β-glucosaminidase and protease activities; abundance (Q-PCR) of bacterial, fungal and chitinase genes; richness (PCR-DGGE) of fungal and chitinase genes. Non-polluted and metal-polluted soils showed different response microbial dynamics when subjected to sources of environmental degradation. The non-polluted soil appeared resilient to "biodiversity loss" and "climate change" treatments. The metal-polluted soil was probably already too severely affected by the presence of high levels of toxic metals to respond to other sources of stress. Our data together suggests that soil microbial activity and biomass parameters are more sensitive to the applied sources of environmental degradation, showing immediate responses of greater magnitude, while soil microbial diversity parameters do not show such variations.}, }
@article {pmid22791963, year = {2012}, author = {Van Meervenne, E and Van Coillie, E and Kerckhof, FM and Devlieghere, F and Herman, L and De Gelder, LS and Top, EM and Boon, N}, title = {Strain-specific transfer of antibiotic resistance from an environmental plasmid to foodborne pathogens.}, journal = {Journal of biomedicine &amp; biotechnology}, volume = {2012}, number = {}, pages = {834598}, pmid = {22791963}, issn = {1110-7251}, support = {R01 AI084918/AI/NIAID NIH HHS/United States ; R01AI084918/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/*genetics ; Escherichia coli Infections/microbiology ; Escherichia coli O157/drug effects/*genetics ; Flow Cytometry ; Foodborne Diseases/microbiology ; *Gene Transfer, Horizontal ; Humans ; Phenotype ; Plasmids/*genetics ; Polymerase Chain Reaction ; Salmonella/drug effects/*genetics ; Salmonella Infections/microbiology ; }, abstract = {Pathogens resistant to multiple antibiotics are rapidly emerging, entailing important consequences for human health. This study investigated if the broad-host-range multiresistance plasmid pB10, isolated from a wastewater treatment plant, harbouring amoxicillin, streptomycin, sulfonamide, and tetracycline resistance genes, was transferable to the foodborne pathogens Salmonella spp. or E. coli O157:H7 and how this transfer alters the phenotype of the recipients. The transfer ratio was determined by both plating and flow cytometry. Antibiotic resistance profiles were determined for both recipients and transconjugants using the disk diffusion method. For 14 of the 15 recipient strains, transconjugants were detected. Based on plating, transfer ratios were between 6.8 × 10[-9] and 3.0 × 10[-2] while using flow cytometry, transfer ratios were between <1.0 × 10[-5] and 1.9 × 10[-2]. With a few exceptions, the transconjugants showed phenotypically increased resistance, indicating that most of the transferred resistance genes were expressed. In summary, we showed that an environmental plasmid can be transferred into foodborne pathogenic bacteria at high transfer ratios. However, the transfer ratio seemed to be recipient strain dependent. Moreover, the newly acquired resistance genes could turn antibiotic susceptible strains into resistant ones, paving the way to compromise human health.}, }
@article {pmid22783248, year = {2012}, author = {Botta, C and Cocolin, L}, title = {Microbial dynamics and biodiversity in table olive fermentation: culture-dependent and -independent approaches.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {245}, pmid = {22783248}, issn = {1664-302X}, abstract = {The microbial ecology of the table olive fermentation process is a complex set of dynamics in which the roles of the lactic acid bacteria (LAB) and yeast populations are closely related, and this synergism is of fundamental importance to obtain high quality products. Several studies on the ecology of table olives, both in spontaneous fermentations and in inoculated ones, have focused on the identification and characterization of yeasts, as they play a key role in the definition of the final organoleptic profiles through the production of volatile compounds. Moreover, these are able to promote the growth of LAB, which is responsible for the stabilization of the final product through the acidification activity and the inhibition of the growth of pathogenic bacteria. The current empirical production process of table olives could be improved through the development of mixed starter cultures. These can only be developed after a deep study of the population dynamics of yeasts and LAB by means of molecular methods. Until now, most studies have exploited culture-dependent approaches to define the natural microbiota of brine and olives. These approaches have identified two main species of LAB, namely Lactobacillus plantarum and L. pentosus, while, as far as yeasts are concerned, the most frequently isolated genera are Candida, Pichia, and Saccharomyces. However, there are a few studies in literature in which a culture-independent approach has been employed. This review summarizes the state of the art of the microbial ecology of table olive fermentations and it focuses on the different approaches and molecular methods that have been applied.}, }
@article {pmid22768065, year = {2012}, author = {Papa, E and Docktor, M and Smillie, C and Weber, S and Preheim, SP and Gevers, D and Giannoukos, G and Ciulla, D and Tabbaa, D and Ingram, J and Schauer, DB and Ward, DV and Korzenik, JR and Xavier, RJ and Bousvaros, A and Alm, EJ}, title = {Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease.}, journal = {PloS one}, volume = {7}, number = {6}, pages = {e39242}, pmid = {22768065}, issn = {1932-6203}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 DK092405/DK/NIDDK NIH HHS/United States ; T32 GM087237/GM/NIGMS NIH HHS/United States ; 1-R21-A1084032-01A1//PHS HHS/United States ; }, mesh = {Adolescent ; Adult ; Anti-Bacterial Agents/therapeutic use ; Biodiversity ; Child ; Child, Preschool ; Cohort Studies ; Colitis, Ulcerative/diagnosis/microbiology/pathology ; Crohn Disease/diagnosis/microbiology/pathology ; Demography ; Diagnosis, Differential ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology/*pathology ; Humans ; Inflammatory Bowel Diseases/classification/*diagnosis/drug therapy/*microbiology ; Leukocyte L1 Antigen Complex/metabolism ; Male ; *Metagenome/genetics ; Remission Induction ; Reproducibility of Results ; Severity of Illness Index ; Software ; Young Adult ; }, abstract = {BACKGROUND: Pediatric inflammatory bowel disease (IBD) is challenging to diagnose because of the non-specificity of symptoms; an unequivocal diagnosis can only be made using colonoscopy, which clinicians are reluctant to recommend for children. Diagnosis of pediatric IBD is therefore frequently delayed, leading to inappropriate treatment plans and poor outcomes. We investigated the use of 16S rRNA sequencing of fecal samples and new analytical methods to assess differences in the microbiota of children with IBD and other gastrointestinal disorders.<br><br>We applied synthetic learning in microbial ecology (SLiME) analysis to 16S sequencing data obtained from i) published surveys of microbiota diversity in IBD and ii) fecal samples from 91 children and young adults who were treated in the gastroenterology program of Children's Hospital (Boston, USA). The developed method accurately distinguished control samples from those of patients with IBD; the area under the receiver-operating-characteristic curve (AUC) value was 0.83 (corresponding to 80.3% sensitivity and 69.7% specificity at a set threshold). The accuracy was maintained among data sets collected by different sampling and sequencing methods. The method identified taxa associated with disease states and distinguished patients with Crohn's disease from those with ulcerative colitis with reasonable accuracy. The findings were validated using samples from an additional group of 68 patients; the validation test identified patients with IBD with an AUC value of 0.84 (e.g. 92% sensitivity, 58.5% specificity).<br><br>CONCLUSIONS/SIGNIFICANCE: Microbiome-based diagnostics can distinguish pediatric patients with IBD from patients with similar symptoms. Although this test can not replace endoscopy and histological examination as diagnostic tools, classification based on microbial diversity is an effective complementary technique for IBD detection in pediatric patients.}, }
@article {pmid22767125, year = {2012}, author = {Shnit-Orland, M and Sivan, A and Kushmaro, A}, title = {Antibacterial activity of Pseudoalteromonas in the coral holobiont.}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {851-859}, pmid = {22767125}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology ; *Antibiosis ; DNA, Bacterial/analysis/genetics ; *Ecosystem ; Gram-Negative Bacteria/genetics/growth &amp; development/isolation &amp; purification ; Gram-Positive Bacteria/genetics/*growth &amp; development/isolation &amp; purification ; Indian Ocean ; Israel ; Microbial Sensitivity Tests/methods ; Microbial Viability ; Phylogeny ; Pseudoalteromonas/classification/genetics/growth &amp; development/*isolation &amp; purification ; Sequence Analysis, DNA ; Staphylococcus aureus/genetics/growth &amp; development ; Symbiosis ; }, abstract = {Corals harbor diverse and abundant prokaryotic populations. Bacterial communities residing in the coral mucus layer may be either pathogenic or symbiotic. Some species may produce antibiotics as a method of controlling populations of competing microbial species. The present study characterizes cultivable Pseudoalteromonas sp. isolated from the mucus layer of different coral species from the northern Gulf of Eilat, Red Sea, Israel. Six mucus-associated Pseudoalteromonas spp. obtained from different coral species were screened for antibacterial activity against 23 tester strains. Five of the six Pseudoalteromonas strains demonstrated extracellular antibacterial activity against Gram-positive-but not Gram-negative-tester strains. Active substances secreted into the cell-free supernatant are heat-tolerant and inhibit growth of Bacillus cereus, Staphylococcus aureus, and of ten endogenous Gram-positive marine bacteria isolated from corals. The Pseudoalteromonas spp. isolated from Red sea corals aligned in a phylogenetic tree with previously isolated Pseudoalteromonas spp. of marine origin that demonstrated antimicrobial activity. These results suggest that coral mucus-associated Pseudoalteromonas may play a protective role in the coral holobiont's defense against potential Gram-positive coral pathogens.}, }
@article {pmid22767124, year = {2012}, author = {McGinty, ES and Pieczonka, J and Mydlarz, LD}, title = {Variations in reactive oxygen release and antioxidant activity in multiple Symbiodinium types in response to elevated temperature.}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {1000-1007}, pmid = {22767124}, issn = {1432-184X}, mesh = {Animals ; Antioxidants/*metabolism ; Catalase/metabolism ; Dinoflagellida/classification/genetics/metabolism/*physiology ; *Heat-Shock Response ; *Hot Temperature ; Reactive Oxygen Species/*metabolism ; Superoxide Dismutase/metabolism ; }, abstract = {As ocean temperatures rise, investigations into what the physiological effects will be on the symbiotic microalga Symbiodinium, and how these may play into the cnidarian bleaching response, have highlighted the contribution of reactive oxygen species (ROS). Previous studies have laid this groundwork using a limited number of Symbiodinium phylotypes, and so this study aims to expand this understanding by exploring the effects of sub-lethal elevated temperatures on the physiological response of seven genetically distinct types of Symbiodinium, including A1, B1, B2, C1, D, E1, and F2. The production of ROS (at 26 °C, 29 °C, 30 °C, and 31 °C) and activity of the antioxidants catalase (CAT) and superoxide dismutase (SOD) (at 26 °C and 31 °C) were measured as indicators of sensitivity or tolerance to heat stress. Symbiodinium types B1 and C1 were the most thermally sensitive, with C1 producing the highest amount of ROS at elevated temperatures. Types A1 and F2 were tolerant, having no increase in ROS production, and were the only types to increase both CAT and SOD activity with temperature stress. Type B2 had decreased ROS production and elevation of CAT activity, while type E1 had decreased levels of ROS production at elevated temperatures. Type D was the only Symbiodinium type to remain unaffected by elevated temperatures. These results are consistent with previous findings of relative sensitivity or tolerance to elevated temperatures, specifically with regards to types A1, B1, and F2. The inclusion of types B2, C1, D, and E1 provides further new evidence of how types differ in their thermal responses, suggesting differing mechanisms exist in the Symbiodnium response to higher temperature and highlighting the importance of establishing symbiont identity when exploring the response of intact associations to this type of stress.}, }
@article {pmid22767123, year = {2012}, author = {Guo, R and Zheng, N and Lu, H and Yin, H and Yao, J and Chen, Y}, title = {Increased diversity of fungal flora in the vagina of patients with recurrent vaginal candidiasis and allergic rhinitis.}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {918-927}, pmid = {22767123}, issn = {1432-184X}, mesh = {Adolescent ; Adult ; Candida/classification/genetics/isolation &amp; purification ; Candida albicans/classification/genetics/isolation &amp; purification ; Candidiasis, Vulvovaginal/*complications/*microbiology ; DNA, Fungal/analysis/isolation &amp; purification ; Female ; Fungi/*classification/*genetics/isolation &amp; purification ; Humans ; Middle Aged ; Molecular Sequence Data ; RNA, Ribosomal, 18S/genetics ; Rhinitis, Allergic ; Rhinitis, Allergic, Perennial/*complications/*microbiology ; Sequence Analysis, DNA ; Vagina/*microbiology ; Young Adult ; }, abstract = {Recurrent vaginal candidiasis (RVC) is considered to be a hypersensitivity disorder that is associated with allergic rhinitis (AR) in immune deficiencies; however, whether or not the composition of the vaginal fungal flora in patients with AR and RVC is altered and if such alterations in patients with AR are associated with the development of RVC remain unclear. In the present study, a cultivation-independent method with the 18S rRNA gene clone library was used to analyze the diversity and composition of the vaginal fungal flora in patients with AR and RVC and to explore the association. Three fungal phyla (Ascomycotae, 22 out of 28; Basidiomycetes, 5 out of 28; and Oomycetes, 1 out of 28) were identified from groups of healthy volunteers, patients with AR, patients with RVC, and patients with RVC complicated by AR, including 28 phylotypes of fungal flora (10, 15, 17, and 21 phylotypes for each group, respectively). The predominant genera of fungi identified in the vagina included Candida, uncultured fungi, and Dothideomycetes. An increased proportion of Candida albicans accompanied with decreased proportions of Saccharomyces cerevisiae and uncultured fungi was observed in patients with AR or RVC (P < 0.05). Candida glabrata, Eladia saccula, Trichosporon jirovecii, and Phytophthora spp. occurred simultaneously in the three patient groups. The composition of the fungal communities in the four groups was statistically different (P < 0.001). The vaginal fungal diversity in patients with AR or RVC was significantly higher compared with healthy volunteers (P < 0.05). The data revealed an increased diversity and varied composition of the vaginal fungal flora in patients with AR and RVC and indicated that disturbed vaginal fungal flora in patients with AR might be correlated with disease progression in patients with RVC.}, }
@article {pmid22767122, year = {2012}, author = {Oh, YM and Kim, M and Lee-Cruz, L and Lai-Hoe, A and Go, R and Ainuddin, N and Rahim, RA and Shukor, N and Adams, JM}, title = {Distinctive bacterial communities in the rhizoplane of four tropical tree species.}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {1018-1027}, pmid = {22767122}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/*isolation &amp; purification ; Bacteroidetes/classification/genetics/isolation &amp; purification ; Betaproteobacteria/classification/genetics/isolation &amp; purification ; DNA, Bacterial/analysis/genetics ; *Ecosystem ; Genes, rRNA ; Malaysia ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Sequence Analysis, DNA/methods ; Species Specificity ; Streptophyta/growth &amp; development/*microbiology ; Tracheophyta/growth &amp; development/*microbiology ; Trees/microbiology ; *Tropical Climate ; }, abstract = {It is known that the microbial community of the rhizosphere is not only influenced by factors such as root exudates, phenology, and nutrient uptake but also by the plant species. However, studies of bacterial communities associated with tropical rainforest tree root surfaces, or rhizoplane, are lacking. Here, we analyzed the bacterial community of root surfaces of four species of native trees, Agathis borneensis, Dipterocarpus kerrii, Dyera costulata, and Gnetum gnemon, and nearby bulk soils, in a rainforest arboretum in Malaysia, using 454 pyrosequencing of the 16S rRNA gene. The rhizoplane bacterial communities for each of the four tree species sampled clustered separately from one another on an ordination, suggesting that these assemblages are linked to chemical and biological characteristics of the host or possibly to the mycorrhizal fungi present. Bacterial communities of the rhizoplane had various similarities to surrounding bulk soils. Acidobacteria, Alphaproteobacteria, and Betaproteobacteria were dominant in rhizoplane communities and in bulk soils from the same depth (0-10 cm). In contrast, the relative abundance of certain bacterial lineages on the rhizoplane was different from that in bulk soils: Bacteroidetes and Betaproteobacteria, which are known as copiotrophs, were much more abundant in the rhizoplane in comparison to bulk soil. At the genus level, Burkholderia, Acidobacterium, Dyella, and Edaphobacter were more abundant in the rhizoplane. Burkholderia, which are known as both pathogens and mutualists of plants, were especially abundant on the rhizoplane of all tree species sampled. The Burkholderia species present included known mutualists of tropical crops and also known N fixers. The host-specific character of tropical tree rhizoplane bacterial communities may have implications for understanding nutrient cycling, recruitment, and structuring of tree species diversity in tropical forests. Such understanding may prove to be useful in both tropical forestry and conservation.}, }
@article {pmid22760734, year = {2012}, author = {Smith, DJ and Jaffe, DA and Birmele, MN and Griffin, DW and Schuerger, AC and Hee, J and Roberts, MS}, title = {Free tropospheric transport of microorganisms from Asia to North America.}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {973-985}, pmid = {22760734}, issn = {1432-184X}, mesh = {*Air Microbiology ; *Air Movements ; Air Pollutants/*analysis ; Alternaria/classification/genetics/isolation &amp; purification ; Asia ; Atmosphere/*chemistry ; Bacteria/classification/genetics/*isolation &amp; purification ; Carbon Monoxide/analysis ; Chaetomium/classification/genetics/isolation &amp; purification ; DNA, Bacterial/analysis/isolation &amp; purification ; DNA, Fungal/analysis/isolation &amp; purification ; Environmental Monitoring/methods ; Fungi/classification/genetics/*isolation &amp; purification ; Microbial Viability ; North America ; Ozone/analysis ; Plant Diseases/microbiology ; Polymerase Chain Reaction/methods ; }, abstract = {Microorganisms are abundant in the troposphere and can be transported vast distances on prevailing winds. This study measures the abundance and diversity of airborne bacteria and fungi sampled at the Mt. Bachelor Observatory (located 2.7 km above sea level in North America) where incoming free tropospheric air routinely arrives from distant sources across the Pacific Ocean, including Asia. Overall deoxyribonucleic acid (DNA) concentrations for microorganisms in the free troposphere, derived from quantitative polymerase chain reaction assays, averaged 4.94 × 10(-5) ng DNA m(-3) for bacteria and 4.77 × 10(-3) ng DNA m(-3) for fungi. Aerosols occasionally corresponded with microbial abundance, most often in the springtime. Viable cells were recovered from 27.4 % of bacterial and 47.6 % of fungal samples (N = 124), with 49 different species identified by ribosomal DNA gene sequencing. The number of microbial isolates rose significantly above baseline values on 22-23 April 2011 and 13-15 May 2011. Both events were analyzed in detail, revealing distinct free tropospheric chemistries (e.g., low water vapor, high aerosols, carbon monoxide, and ozone) useful for ruling out boundary layer contamination. Kinematic back trajectory modeling suggested air from these events probably originated near China or Japan. Even after traveling for 10 days across the Pacific Ocean in the free troposphere, diverse and viable microbial populations, including presumptive plant pathogens Alternaria infectoria and Chaetomium globosum, were detected in Asian air samples. Establishing a connection between the intercontinental transport of microorganisms and specific diseases in North America will require follow-up investigations on both sides of the Pacific Ocean.}, }
@article {pmid22760733, year = {2012}, author = {Wang, X and Sun, M and Wang, J and Yang, L and Luo, L and Li, P and Kong, F}, title = {Microcystis genotype succession and related environmental factors in Lake Taihu during cyanobacterial blooms.}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {986-999}, pmid = {22760733}, issn = {1432-184X}, mesh = {Biomass ; China ; Denaturing Gradient Gel Electrophoresis ; Ecosystem ; Environmental Monitoring/methods ; Genotype ; Hydrogen-Ion Concentration ; *Lakes/chemistry/microbiology ; Microcystins/biosynthesis ; Microcystis/classification/*genetics/*growth &amp; development ; Nitrates/metabolism ; Polymerase Chain Reaction ; Seasons ; }, abstract = {From spring to autumn, heavy Microcystis blooms always occur in Lake Taihu, although environmental conditions vary markedly. We speculated that Microcystis genotype succession could play an important role in adaptation to environmental changes and long-term maintenance of the high Microcystis biomass. In this study, we investigated Microcystis genotype succession pattern and the related environmental variables in Lake Taihu during cyanobacterial blooms. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction -amplified the genus-specific cpcBA and mcyJ gene fragments was used to monitor the variations of Microcystis genotype and potential microcystin (MC)-producing Microcystis genotype compositions during blooms biweekly in three sites (Meiliang Bay, lake center, and Gonghu Bay) and CANOCO 4.5 for Windows were used for the multivariate statistical analysis of their relationships to environmental variables. DGGE patterns indicated that the number of dominant cpcBA genotype per sample increased from spring to autumn. Principal component analysis ordination plots of DGGE profiles showed clear temporal distribution pattern, but not spatial distribution pattern based on both cpcBA and mcyJ genotype compositions. These results indicated there were relatively gradual successions of Microcystis cpcBA and mcyJ genotype compositions in each site, and no distinct spatial difference among the three sites. Redundancy analyses of the gel patterns showed that, in all the three sites, three environmental factors (nitrate, pH, and chemical oxygen demand) were correlated significantly to successions of both cpcBA and mcyJ genotypes except for mcyJ genotype in the lake center. Spearman's correlations indicated that the three environmental variables were also strongly correlated with chl a and MC concentrations. These results suggested that the environmental factors affecting succession of Microcystis community composition might also influence the growth of Microcystis and MC production.}, }
@article {pmid22752177, year = {2012}, author = {White, CP and Debry, RW and Lytle, DA}, title = {Microbial survey of a full-scale, biologically active filter for treatment of drinking water.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {17}, pages = {6390-6394}, pmid = {22752177}, issn = {1098-5336}, mesh = {Archaea/classification/genetics ; Bacteria/*classification/genetics ; *Biota ; DNA, Bacterial/chemistry/genetics ; Drinking Water ; *Environmental Microbiology ; Filtration/*methods ; Molecular Sequence Data ; Sequence Analysis, DNA ; Water Purification/*methods ; }, abstract = {The microbial community of a full-scale, biologically active drinking water filter was surveyed using molecular techniques. Nitrosomonas, Nitrospira, Sphingomonadales, and Rhizobiales dominated the clone libraries. The results elucidate the microbial ecology of biological filters and demonstrate that biological treatment of drinking water should be considered a viable alternative to physicochemical methods.}, }
@article {pmid22744760, year = {2012}, author = {Morris, D and Boyle, F and Morris, C and Condon, I and Delannoy-Vieillard, AS and Power, L and Khan, A and Morris-Downes, M and Finnegan, C and Powell, J and Monahan, R and Burns, K and O'Connell, N and Boyle, L and O'Gorman, A and Humphreys, H and Brisse, S and Turton, J and Woodford, N and Cormican, M}, title = {Inter-hospital outbreak of Klebsiella pneumoniae producing KPC-2 carbapenemase in Ireland.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {67}, number = {10}, pages = {2367-2372}, doi = {10.1093/jac/dks239}, pmid = {22744760}, issn = {1460-2091}, mesh = {*Disease Outbreaks ; Ertapenem ; Genes, Bacterial ; Hospitals ; Humans ; Imipenem/pharmacology ; Ireland/epidemiology ; Klebsiella Infections/*epidemiology/*microbiology ; Klebsiella pneumoniae/*enzymology/isolation &amp; purification ; Meropenem ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Molecular Typing ; Polymerase Chain Reaction ; Thienamycins/pharmacology ; beta-Lactamases/*metabolism ; beta-Lactams/pharmacology ; }, abstract = {OBJECTIVES: To describe an outbreak of KPC-2-producing Klebsiella pneumoniae with inter-hospital spread and measures taken to control transmission.<br><br>METHODS: Between January and March 2011, 13 K. pneumoniae isolates were collected from nine patients at hospital A and two patients at hospital B. Meropenem, imipenem and ertapenem MICs were determined by Etest, carbapenemase production was confirmed by the modified Hodge method and by a disc synergy test, and confirmed carbapenemase producers were tested for the presence of carbapenemase-encoding genes by PCR. PFGE, plasmid analysis, multilocus variable-number tandem-repeat analysis (MLVA) and multilocus sequence typing (MLST) analysis were performed on all or a subset of isolates.<br><br>RESULTS: Meropenem, imipenem and ertapenem MICs were 4 to >32, 8-32 and >16 mg/L, respectively. PCR and sequencing confirmed the presence of bla(KPC-2). PFGE identified four distinguishable (&#x2265;88%) pulsed-field profiles (PFPs). Isolates distinguishable by PFGE had identical MLVA profiles, and MLST analysis indicated all isolates belonged to the ST258 clone. Stringent infection prevention and control measures were implemented. Over a period of almost 8 months no further carbapenemase-producing Enterobacteriaceae (CPE) were isolated. However, KPC-2-producing K. pneumoniae was detected in two further patients in hospital A in August (PFP indistinguishable from previous isolates) and October 2011 (PFP similar to but distinguishable from previous isolates).<br><br>CONCLUSIONS: Stringent infection prevention and control measures help contain CPE in the healthcare setting; however, in the case of hospital A, where CPE appears to be established in the population served, it may be virtually impossible to achieve eradication or avoid reintroduction into the hospital.}, }
@article {pmid22743759, year = {2012}, author = {Collado, MC and Cernada, M and Baüerl, C and Vento, M and Pérez-Martínez, G}, title = {Microbial ecology and host-microbiota interactions during early life stages.}, journal = {Gut microbes}, volume = {3}, number = {4}, pages = {352-365}, pmid = {22743759}, issn = {1949-0984}, mesh = {*Biota ; Gastrointestinal Tract/*microbiology ; Humans ; Immune System/*physiology ; Infant, Newborn ; *Metagenome ; }, abstract = {The role of human microbiota has been redefined during recent years and its physiological role is now much more important than earlier understood. Intestinal microbial colonization is essential for the maturation of immune system and for the developmental regulation of the intestinal physiology. Alterations in this process of colonization have been shown to predispose and increase the risk to disease later in life. The first contact of neonates with microbes is provided by the maternal microbiota. Moreover, mode of delivery, type of infant feeding and other perinatal factors can influence the establishment of the infant microbiota. Taken into consideration all the available information it could be concluded that the exposure to the adequate microbes early in gestation and neonatal period seems to have a relevant role in health. Maternal microbial environment affects maternal and fetal immune physiology and, of relevance, this interaction with microbes at the fetal-maternal interface could be modulated by specific microbes administered to the pregnant mother. Indeed, probiotic interventions aiming to reduce the risk of immune-mediated diseases may appear effective during early life.}, }
@article {pmid22739491, year = {2012}, author = {Bowen, JL and Morrison, HG and Hobbie, JE and Sogin, ML}, title = {Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates.}, journal = {The ISME journal}, volume = {6}, number = {11}, pages = {2014-2023}, pmid = {22739491}, issn = {1751-7370}, support = {P50 ES012742/ES/NIEHS NIH HHS/United States ; 1 P50 ES012742-01/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics ; *Biodiversity ; High-Throughput Nucleotide Sequencing ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sequence Analysis, DNA ; *Soil Microbiology ; *Wetlands ; }, abstract = {Much of the phylogenetic diversity in microbial systems arises from rare taxa that comprise the long tail of taxon rank distribution curves. This vast diversity presents a challenge to testing hypotheses about the effects of perturbations on microbial community composition because variability of rare taxa among environmental replicates may be sufficiently large that it would require a prohibitive degree of sequencing to discern differences between samples. In this study we used pyrosequencing of 16S rRNA tags to examine the diversity and within-site variability of salt marsh sediment bacteria. Our goal was to determine whether pyrosequencing could produce similar patterns in community composition among replicate environmental samples from the same location. We hypothesized that repeated sampling from the same location would produce different snapshots of the rare community due to incomplete sequencing of the taxonomically rich rare biosphere. We demonstrate that the salt marsh sediments we sampled contain a remarkably diverse array of bacterial taxa and, in contrast to our hypothesis, repeated sampling from within the same site produces reliably similar patterns in bacterial community composition, even among rare organisms. These results demonstrate that deep sequencing of 16s tags is well suited to distinguish site-specific similarities and differences among rare taxa and is a valuable tool for hypothesis testing in microbial ecology.}, }
@article {pmid22735936, year = {2012}, author = {Khadempour, L and LeMay, V and Jack, D and Bohlmann, J and Breuil, C}, title = {The relative abundance of mountain pine beetle fungal associates through the beetle life cycle in pine trees.}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {909-917}, pmid = {22735936}, issn = {1432-184X}, mesh = {Animals ; Coleoptera/*growth &amp; development/*microbiology ; DNA, Fungal/analysis/genetics/isolation &amp; purification ; *Life Cycle Stages ; Ophiostoma/classification/genetics/isolation &amp; purification ; Ophiostomatales/*classification/genetics/isolation &amp; purification ; Pinus/*microbiology/*parasitology ; Plant Bark/microbiology/parasitology ; Polymerase Chain Reaction/methods ; Symbiosis ; }, abstract = {The mountain pine beetle (MPB) is a native bark beetle of western North America that attacks pine tree species, particularly lodgepole pine. It is closely associated with the ophiostomatoid ascomycetes Grosmannia clavigera, Leptographium longiclavatum, Ophiostoma montium, and Ceratocystiopsis sp.1, with which it is symbiotically associated. To develop a better understanding of interactions between beetles, fungi, and host trees, we used target-specific DNA primers with qPCR to assess the changes in fungal associate abundance over the stages of the MPB life cycle that occur in galleries under the bark of pine trees. Multivariate analysis of covariance identified statistically significant changes in the relative abundance of the fungi over the life cycle of the MPB. Univariate analysis of covariance identified a statistically significant increase in the abundance of Ceratocystiopsis sp.1 through the beetle life cycle, and pair-wise analysis showed that this increase occurs after the larval stage. In contrast, the abundance of O. montium and Leptographium species (G. clavigera, L. longiclavatum) did not change significantly through the MPB life cycle. From these results, the only fungus showing a significant increase in relative abundance has not been formally described and has been largely ignored by other MPB studies. Although our results were from only one site, in previous studies we have shown that the fungi described were all present in at least ten sites in British Columbia. We suggest that the role of Ceratocystiopsis sp.1 in the MPB system should be explored, particularly its potential as a source of nutrients for teneral adults.}, }
@article {pmid22735212, year = {2012}, author = {Hang, I and Rinttila, T and Zentek, J and Kettunen, A and Alaja, S and Apajalahti, J and Harmoinen, J and de Vos, WM and Spillmann, T}, title = {Effect of high contents of dietary animal-derived protein or carbohydrates on canine faecal microbiota.}, journal = {BMC veterinary research}, volume = {8}, number = {}, pages = {90}, pmid = {22735212}, issn = {1746-6148}, mesh = {Animals ; Bacteria/*classification/genetics ; Diet/*veterinary ; Dietary Carbohydrates/administration &amp; dosage/*pharmacology ; Dietary Proteins/administration &amp; dosage/*pharmacology ; *Dogs ; Feces/*microbiology ; Phylogeny ; RNA, Bacterial ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Considerable evidence suggests that food impacts both the gastro-intestinal (GI) function and the microbial ecology of the canine GI tract. The aim of this study was to evaluate the influence of high-carbohydrate (HC), high-protein (HP) and dry commercial (DC) diets on the canine colonic microbiota in Beagle dogs. Diets were allocated according to the Graeco-Latin square design. For this purpose, microbial DNA was isolated from faecal samples and separated by density gradient centrifugation, resulting in specific profiling based on the guanine-cytosine content (%G+C). In addition, 16 S rRNA gene amplicons were obtained from the most abundant %G + C peaks and analysed by sequence analysis, producing a total of 720 non-redundant sequences (240 sequences per diet).<br><br>RESULTS: The DC diet sample showed high abundance of representatives of the orders Clostridiales, Lactobacillales, Coriobacteriales and Bacteroidales. Sequence diversity was highest for DC diet samples and included representatives of the orders Lactobacillales and Bacteroidales, which were not detected in samples from the HP and HC diets. These latter two diets also had reduced levels of representatives of the family Lachnospiraceae, specifically Clostridial cluster XIVa. The HC diet favoured representatives of the order Erysipelotrichales, more specifically the Clostridial cluster XVIII, while the HP diet favoured representatives of the order Fusobacteriales.<br><br>CONCLUSIONS: This study detected Coriobacteriales in dog faeces, possibly due to the non-selective nature of the %G&#x2009;+&#x2009;C profiling method used in combination with sequencing. Moreover, our work demonstrates that the effect of diet on faecal microbiota can be explained based on the metabolic properties of the detected microbial taxa.}, }
@article {pmid22729545, year = {2012}, author = {Gomez-Alvarez, V and Revetta, RP and Santo Domingo, JW}, title = {Metagenomic analyses of drinking water receiving different disinfection treatments.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {17}, pages = {6095-6102}, pmid = {22729545}, issn = {1098-5336}, mesh = {Archaea/classification/drug effects/genetics ; Bacteria/classification/drug effects/genetics ; *Biodiversity ; Chlorine/*pharmacology ; Disinfectants/*pharmacology ; Disinfection/*methods ; Drinking Water/*microbiology ; Eukaryota/classification/drug effects/genetics ; *Metagenome ; Sequence Analysis, DNA ; Viruses/classification/drug effects/genetics ; Water Purification/*methods ; }, abstract = {A metagenome-based approach was used to assess the taxonomic affiliation and function potential of microbial populations in free-chlorine-treated (CHL) and monochloramine-treated (CHM) drinking water (DW). In all, 362,640 (averaging 544 bp) and 155,593 (averaging 554 bp) pyrosequencing reads were analyzed for the CHL and CHM samples, respectively. Most annotated proteins were found to be of bacterial origin, although eukaryotic, archaeal, and viral proteins were also identified. Differences in community structure and function were noted. Most notably, Legionella-like genes were more abundant in the CHL samples while mycobacterial genes were more abundant in CHM samples. Genes associated with multiple disinfectant mechanisms were identified in both communities. Moreover, sequences linked to virulence factors, such as antibiotic resistance mechanisms, were observed in both microbial communities. This study provides new insights into the genetic network and potential biological processes associated with the molecular microbial ecology of DW microbial communities.}, }
@article {pmid22729142, year = {2012}, author = {Friedman, CS and Crosson, LM}, title = {Putative phage hyperparasite in the rickettsial pathogen of abalone, "Candidatus Xenohaliotis californiensis".}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {1064-1072}, pmid = {22729142}, issn = {1432-184X}, mesh = {Anaplasmataceae/genetics/*isolation &amp; purification/ultrastructure/*virology ; Animals ; Bacteriophages/*isolation &amp; purification/pathogenicity/ultrastructure ; California ; DNA, Bacterial/analysis/genetics ; Gastropoda/*microbiology ; *Host-Parasite Interactions ; In Situ Hybridization ; Microscopy, Electron, Transmission ; Sequence Analysis, DNA ; }, abstract = {Studies on the ecology of microbial parasites and their hosts are predicated on understanding the assemblage of and relationship among the species present. Changes in organismal morphology and physiology can have profound effects on host-parasite interactions and associated microbial community structure. The marine rickettsial organism, "Candidatus Xenohaliotis californiensis" (WS-RLO), that causes withering syndrome of abalones has had a consistent morphology based on light and electron microscopy. However, a morphological variant of the WS-RLO has recently been observed infecting red abalone from California. We used light and electron microscopy, in situ hybridization and16S rDNA sequence analysis to compare the WS-RLO and the morphologically distinct RLO variant (RLOv). The WS-RLO forms oblong inclusions within the abalone posterior esophagus (PE) and digestive gland (DG) tissues that contain small rod-shaped bacteria; individual bacteria within the light purple inclusions upon hematoxylin and eosin staining cannot be discerned by light microscopy. Like the WS-RLO, the RLOv forms oblong inclusions in the PE and DG but contain large, pleomorphic bacteria that stain dark navy blue with hematoxylin and eosin. Transmission electron microscopy (TEM) examination revealed that the large pleomorphic bacteria within RLOv inclusions were infected with a spherical to icosahedral-shaped putative phage hyperparasite. TEM also revealed the presence of rod-shaped bacteria along the periphery of the RLOv inclusions that were morphologically indistinguishable from the WS-RLO. Binding of the WS-RLO-specific in situ hybridization probe to the RLOv inclusions demonstrated sequence similarity between these RLOs. In addition, sequence analysis revealed 98.9-99.4 % similarity between 16S rDNA sequences of the WS-RLO and RLOv. Collectively, these data suggest that both of these RLOs infecting California abalone are "Candidatus Xenohaliotis californiensis," and that the novel variant is infected by a putative phage hyperparasite that induced morphological variation of its RLO host.}, }
@article {pmid22729017, year = {2012}, author = {Martinson, EO and Herre, EA and Machado, CA and Arnold, AE}, title = {Culture-free survey reveals diverse and distinctive fungal communities associated with developing figs (Ficus spp.) in Panama.}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {1073-1084}, pmid = {22729017}, issn = {1432-184X}, mesh = {Animals ; *Ecosystem ; Ficus/*growth &amp; development/*microbiology ; Flowers/*microbiology ; Fungi/*classification/*genetics/growth &amp; development ; Molecular Sequence Data ; Panama ; Phylogeny ; Pollination ; Seeds/*microbiology ; Sequence Analysis, DNA ; Wasps/*microbiology ; }, abstract = {The ancient association of figs (Ficus spp.) and their pollinating wasps (fig wasps; Chalcidoidea, Hymenoptera) is one of the most interdependent plant-insect mutualisms known. In addition to pollinating wasps, a diverse community of organisms develops within the microcosm of the fig inflorescence and fruit. To better understand the multipartite context of the fig-fig wasp association, we used a culture-free approach to examine fungal communities associated with syconia of six species of Ficus and their pollinating wasps in lowland Panama. Diverse fungi were recovered from surface-sterilized flowers of all Ficus species, including gall- and seed flowers at four developmental stages. Fungal communities in syconia and on pollinating wasps were similar, dominated by diverse and previously unknown Saccharomycotina, and distinct from leaf- and stem endophyte communities in the same region. Before pollination, fungal communities were similar between gall- and seed flowers and among Ficus species. However, fungal communities differed significantly in flowers after pollination vs. before pollination, and between anciently diverged lineages of Ficus with active vs. passive pollination syndromes. Within groups of relatively closely related figs, there was little evidence for strict-sense host specificity between figs and particular fungal species. Instead, mixing of fungal communities among related figs, coupled with evidence for possible transfer by pollinating wasps, is consistent with recent suggestions of pollinator mixing within syconia. In turn, changes in fungal communities during fig development and ripening suggest an unexplored role of yeasts in the context of the fig-pollinator wasp mutualism.}, }
@article {pmid22726612, year = {2012}, author = {Marks, CR and Stevenson, BS and Rudd, S and Lawson, PA}, title = {Nitrospira-dominated biofilm within a thermal artesian spring: a case for nitrification-driven primary production in a geothermal setting.}, journal = {Geobiology}, volume = {10}, number = {5}, pages = {457-466}, doi = {10.1111/j.1472-4669.2012.00335.x}, pmid = {22726612}, issn = {1472-4669}, mesh = {Archaea/classification/*isolation &amp; purification/metabolism ; Arkansas ; Bacteria/classification/*isolation &amp; purification/metabolism ; Biofilms/*growth &amp; development ; *Biota ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Hot Springs/*microbiology ; Molecular Sequence Data ; *Nitrification ; Oxidoreductases/genetics ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Water chemistry, energetic modeling, and molecular analyses were combined to investigate the microbial ecology of a biofilm growing in a thermal artesian spring within Hot Springs National Park, AR. This unique fresh water spring has a low dissolved chemical load and is isolated from both light and direct terrestrial carbon input - resulting in an oligotrophic ecosystem limited for fixed carbon and electron donors. Evaluation of energy yields of lithotrophic reactions putatively linked to autotrophy identified the aerobic oxidation of methane, hydrogen, sulfide, ammonia, and nitrite as the most exergonic. Small subunit (SSU) rRNA gene libraries from biofilm revealed a low-diversity microbial assemblage populated by bacteria and archaea at a gene copy ratio of 45:1. Members of the bacterial family 'Nitrospiraceae', known for their autotrophic nitrite oxidation, dominated the bacterial SSU rRNA gene library (approximately 45%). Members of the Thaumarchaeota ThAOA/HWCGIII (>96%) and Thaumarchaeota Group I.1b (2.5%), which both contain confirmed autotrophic ammonia oxidizers, dominated the archaeal SSU rRNA library. Archaea appear to dominate among the ammonia oxidizers, as only ammonia monooxygenase subunit A (amoA) genes belonging to members of the Thaumarchaeota were detected. The geochemical, phylogenetic, and genetic data support a model that describes a novel thermophilic biofilm built largely by an autotrophic nitrifying microbial assemblage. This is also the first observation of 'Nitrospiraceae' as the dominant organisms within a geothermal environment.}, }
@article {pmid22723796, year = {2012}, author = {Ahlgren, NA and Rocap, G}, title = {Diversity and Distribution of Marine Synechococcus: Multiple Gene Phylogenies for Consensus Classification and Development of qPCR Assays for Sensitive Measurement of Clades in the Ocean.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {213}, pmid = {22723796}, issn = {1664-302X}, abstract = {Marine Synechococcus is a globally significant genus of cyanobacteria that is comprised of multiple genetic lineages or clades. These clades are thought to represent ecologically distinct units, or ecotypes. Because multiple clades often co-occur together in the oceans, Synechococcus are ideal microbes to explore how closely related bacterial taxa within the same functional guild of organisms co-exist and partition marine habitats. Here we sequenced multiple gene loci from cultured strains to confirm the congruency of clade classifications between the 16S-23S rDNA internally transcribed spacer (ITS), 16S rDNA, narB, ntcA, and rpoC1 loci commonly used in Synechococcus diversity studies. We designed quantitative PCR (qPCR) assays that target the ITS for 10 Synechococcus clades, including four clades, XV, XVI, CRD1, and CRD2, not covered by previous assays employing other loci. Our new qPCR assays are very sensitive and specific, detecting down to tens of cells per ml. Application of these qPCR assays to field samples from the northwest Atlantic showed clear shifts in Synechococcus community composition across a coastal to open-ocean transect. Consistent with previous studies, clades I and IV dominated cold, coastal Synechococcus communities. Clades II and X were abundant at the two warmer, off-shore stations, and at all stations multiple Synechococcus clades co-occurred. qPCR assays developed here provide valuable tools to further explore the dynamics of microbial community structure and the mechanisms of co-existence.}, }
@article {pmid22719852, year = {2012}, author = {Srinivasan, S and Hoffman, NG and Morgan, MT and Matsen, FA and Fiedler, TL and Hall, RW and Ross, FJ and McCoy, CO and Bumgarner, R and Marrazzo, JM and Fredricks, DN}, title = {Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria.}, journal = {PloS one}, volume = {7}, number = {6}, pages = {e37818}, pmid = {22719852}, issn = {1932-6203}, support = {P30 CA015704/CA/NCI NIH HHS/United States ; R01 AI061628/AI/NIAID NIH HHS/United States ; R01 HG005966/HG/NHGRI NIH HHS/United States ; R01 HG005966-01/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics ; Base Sequence ; DNA Primers ; Female ; Humans ; Metagenome ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Vagina/*microbiology ; Vaginosis, Bacterial/*microbiology ; }, abstract = {BACKGROUND: Bacterial vaginosis (BV) is a common condition that is associated with numerous adverse health outcomes and is characterized by poorly understood changes in the vaginal microbiota. We sought to describe the composition and diversity of the vaginal bacterial biota in women with BV using deep sequencing of the 16S rRNA gene coupled with species-level taxonomic identification. We investigated the associations between the presence of individual bacterial species and clinical diagnostic characteristics of BV.<br><br>Broad-range 16S rRNA gene PCR and pyrosequencing were performed on vaginal swabs from 220 women with and without BV. BV was assessed by Amsel's clinical criteria and confirmed by Gram stain. Taxonomic classification was performed using phylogenetic placement tools that assigned 99% of query sequence reads to the species level. Women with BV had heterogeneous vaginal bacterial communities that were usually not dominated by a single taxon. In the absence of BV, vaginal bacterial communities were dominated by either Lactobacillus crispatus or Lactobacillus iners. Leptotrichia amnionii and Eggerthella sp. were the only two BV-associated bacteria (BVABs) significantly associated with each of the four Amsel's criteria. Co-occurrence analysis revealed the presence of several sub-groups of BVABs suggesting metabolic co-dependencies. Greater abundance of several BVABs was observed in Black women without BV.<br><br>CONCLUSIONS/SIGNIFICANCE: The human vaginal bacterial biota is heterogeneous and marked by greater species richness and diversity in women with BV; no species is universally present. Different bacterial species have different associations with the four clinical criteria, which may account for discrepancies often observed between Amsel and Nugent (Gram stain) diagnostic criteria. Several BVABs exhibited race-dependent prevalence when analyzed in separate groups by BV status which may contribute to increased incidence of BV in Black women. Tools developed in this project can be used to study microbial ecology in diverse settings at high resolution.}, }
@article {pmid22712445, year = {2013}, author = {Bengtson, P and Bastviken, D and Oberg, G}, title = {Possible roles of reactive chlorine II: assessing biotic chlorination as a way for organisms to handle oxygen stress.}, journal = {Environmental microbiology}, volume = {15}, number = {4}, pages = {991-1000}, doi = {10.1111/j.1462-2920.2012.02807.x}, pmid = {22712445}, issn = {1462-2920}, mesh = {Bacteria/*enzymology ; Catalysis ; Chloride Peroxidase/genetics/*metabolism ; Chlorine/chemistry/*metabolism ; *Environmental Microbiology ; Fungi/*metabolism ; Gene Expression Regulation, Enzymologic ; Halogenation ; Hydrocarbons, Chlorinated/chemistry/metabolism ; Oxidative Stress/*physiology ; Oxygen/chemistry/*metabolism ; Plants/microbiology ; Reactive Oxygen Species/metabolism ; Vanadium/metabolism ; }, abstract = {Natural formation of organically bound chlorine is extensive in many environments. The enzymes associated with the formation of chlorinated organic matter are produced by a large variety of organisms. Little is known about the ecological role of the process, the key question being: why do microorganisms promote chlorination of organic matter? In a recent paper we discuss whether organic matter chlorination may be a result of antagonistic interactions among microorganisms. In the present paper we evaluate whether extracellular microbial formation of reactive chlorine may be used as a defence against oxygen stress, and we discuss whether this process is likely to contribute to the formation of chlorinated organic matter. Our analysis suggests that periodic exposure to elevated concentrations of reactive oxygen species is a common denominator among the multitude of organisms that are able to enzymatically catalyse formation of reactive chlorine. There is also some evidence suggesting that the production of such enzymes in algae and bacteria is induced by oxygen stress. The relative contribution from this process to the extensive formation of chlorinated organic matter in natural environments remains to be empirically assessed.}, }
@article {pmid22711422, year = {2012}, author = {Valverde, A and Tuffin, M and Cowan, DA}, title = {Biogeography of bacterial communities in hot springs: a focus on the actinobacteria.}, journal = {Extremophiles : life under extreme conditions}, volume = {16}, number = {4}, pages = {669-679}, pmid = {22711422}, issn = {1433-4909}, mesh = {*Actinobacteria/cytology/genetics/growth &amp; development ; *Biodiversity ; Hot Springs/*microbiology ; Hot Temperature ; Hydrogen-Ion Concentration ; Phylogeography/methods ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; }, abstract = {Actinobacteria are ubiquitous in soil, freshwater and marine ecosystems. Although various studies have focused on the microbial ecology of this phylum, data are scant on the ecology of actinobacteria endemic to hot springs. Here, we have investigated the molecular diversity of eubacteria, with specific focus on the actinobacteria in hot springs in Zambia, China, New Zealand and Kenya. Temperature and pH values at sampling sites ranged between 44.5 and 86.5 °C and 5-10, respectively. Non-metric multidimensional scaling analysis of 16S rRNA gene T-RFLP patterns showed that samples could be separated by geographical location. Multivariate analysis showed that actinobacterial community composition was best predicted by changes in pH and temperature, whereas temperature alone was the most important variable explaining differences in bacterial community structure. Using 16S rRNA gene libraries, 28 major actinobacterial OTUs were found. Both molecular techniques indicated that many of the actinobacterial phylotypes were unique and exclusive to the respective sample. Collectively, these results support the view that both actinobacterial diversity and endemism are high in hot spring ecosystems.}, }
@article {pmid22706066, year = {2012}, author = {Trias, R and Ruiz-Rueda, O and García-Lledó, A and Vilar-Sanz, A and López-Flores, R and Quintana, XD and Hallin, S and Bañeras, L}, title = {Emergent macrophytes act selectively on ammonia-oxidizing bacteria and archaea.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {17}, pages = {6352-6356}, pmid = {22706066}, issn = {1098-5336}, mesh = {Ammonia/*metabolism ; Archaea/*classification/*genetics/metabolism ; Bacteria/*classification/*genetics/metabolism ; Biodiversity ; Hydrogen-Ion Concentration ; Metagenome ; Oxidation-Reduction ; Plant Roots/*microbiology ; Wetlands ; }, abstract = {Ammonia-oxidizing bacteria (AOB) and archaea (AOA) were quantified in the sediments and roots of dominant macrophytes in eight neutral to alkaline coastal wetlands. The AOA dominated in most samples, but the bacterial-to-archaeal amoA gene ratios increased with increasing ammonium levels and pH in the sediments. For all plant species, the ratios increased on the root surface relative to the adjacent bulk sediment. This suggests that root surfaces in these environments provide conditions favoring enrichment of AOB.}, }
@article {pmid22706045, year = {2012}, author = {Bengtson, P and Sterngren, AE and Rousk, J}, title = {Archaeal abundance across a pH gradient in an arable soil and its relationship to bacterial and fungal growth rates.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {16}, pages = {5906-5911}, pmid = {22706045}, issn = {1098-5336}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Archaea/*growth &amp; development/*isolation &amp; purification ; Bacteria/*growth &amp; development ; Fungi/*growth &amp; development ; Genes, rRNA ; Hydrogen-Ion Concentration ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Soil pH is one of the most influential factors for the composition of bacterial and fungal communities, but the influence of soil pH on the distribution and composition of soil archaeal communities has yet to be systematically addressed. The primary aim of this study was to determine how total archaeal abundance (quantitative PCR [qPCR]-based estimates of 16S rRNA gene copy numbers) is related to soil pH across a pH gradient (pH 4.0 to 8.3). Secondarily, we wanted to assess how archaeal abundance related to bacterial and fungal growth rates across the same pH gradient. We identified two distinct and opposite effects of pH on the archaeal abundance. In the lowest pH range (pH 4.0 to 4.7), the abundance of archaea did not seem to correspond to pH. Above this pH range, there was a sharp, almost 4-fold decrease in archaeal abundance, reaching a minimum at pH 5.1 to 5.2. The low abundance of archaeal 16S rRNA gene copy numbers at this pH range then sharply increased almost 150-fold with pH, resulting in an increase in the ratio between archaeal and bacterial copy numbers from a minimum of 0.002 to more than 0.07 at pH 8. The nonuniform archaeal response to pH could reflect variation in the archaeal community composition along the gradient, with some archaea adapted to acidic conditions and others to neutral to slightly alkaline conditions. This suggestion is reinforced by observations of contrasting outcomes of the (competitive) interactions between archaea, bacteria, and fungi toward the lower and higher ends of the examined pH gradient.}, }
@article {pmid22703282, year = {2012}, author = {Pinto, AJ and Love, NG}, title = {Bioreactor function under perturbation scenarios is affected by interactions between bacteria and protozoa.}, journal = {Environmental science &amp; technology}, volume = {46}, number = {14}, pages = {7558-7566}, doi = {10.1021/es301220f}, pmid = {22703282}, issn = {1520-5851}, mesh = {Ammonia/metabolism ; Bacteria/*drug effects/*metabolism ; Biomass ; Bioreactors/*microbiology ; Cadmium/*toxicity ; Eukaryota/*drug effects/*metabolism ; Gene Dosage/genetics ; Microbial Interactions ; Nitrification/drug effects ; Oxidation-Reduction/drug effects ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; Stress, Physiological/drug effects/genetics ; }, abstract = {This study investigated the impact of transient cadmium perturbations on the structure and function of the microbial community in an activated sludge system. The impact of cadmium perturbation on the bioreactor performance, bacterial activity, bacterial community structure, and bacteria-protozoa interactions was examined. The bacterial community exhibited a short-term inhibition following a pulse perturbation of cadmium. Process recovery was associated with an increase in bacterial abundance above the unperturbed control reactor, followed by high biomass activity after the washout of cadmium. This trend was seen for multiple experiments at both laboratory- and pilot-scale. The increase in biomass activity could not be explained by changes in bacterial community structure. Independent experiments showed that the increase in bacterial abundance, and by association biomass activity, was caused by the decrease in the protozoal grazing due to the higher inhibition of ciliated protozoa as compared to bacteria when exposed to cadmium. This paper highlights the importance of expanding the investigative boundaries of the microbial ecology of bioengineered systems to include protozoal grazing, especially under perturbation scenarios.}, }
@article {pmid22693569, year = {2012}, author = {De Weirdt, R and Crabbé, A and Roos, S and Vollenweider, S and Lacroix, C and van Pijkeren, JP and Britton, RA and Sarker, S and Van de Wiele, T and Nickerson, CA}, title = {Glycerol supplementation enhances L. reuteri's protective effect against S. Typhimurium colonization in a 3-D model of colonic epithelium.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e37116}, pmid = {22693569}, issn = {1932-6203}, support = {U19 AI090872/AI/NIAID NIH HHS/United States ; }, mesh = {Cell Survival/drug effects ; Colon/*cytology ; Culture Media, Conditioned/metabolism ; *Dietary Supplements ; Fermentation/drug effects ; Glyceraldehyde/analogs &amp; derivatives/metabolism ; Glycerol/metabolism/*pharmacology ; HT29 Cells ; Humans ; Intestinal Mucosa/cytology/*drug effects/*microbiology ; Limosilactobacillus reuteri/drug effects/metabolism/*physiology ; Models, Molecular ; Propane/metabolism ; Salmonella typhimurium/*growth &amp; development/physiology ; }, abstract = {The probiotic effects of Lactobacillus reuteri have been speculated to partly depend on its capacity to produce the antimicrobial substance reuterin during the reduction of glycerol in the gut. In this study, the potential of this process to protect human intestinal epithelial cells against infection with Salmonella enterica serovar Typhimurium was investigated. We used a three-dimensional (3-D) organotypic model of human colonic epithelium that was previously validated and applied to study interactions between S. Typhimurium and the intestinal epithelium that lead to enteric salmonellosis. Using this model system, we show that L. reuteri protects the intestinal cells against the early stages of Salmonella infection and that this effect is significantly increased when L. reuteri is stimulated to produce reuterin from glycerol. More specifically, the reuterin-containing ferment of L. reuteri caused a reduction in Salmonella adherence and invasion (1 log unit), and intracellular survival (2 log units). In contrast, the L. reuteri ferment without reuterin stimulated growth of the intracellular Salmonella population with 1 log unit. The short-term exposure to reuterin or the reuterin-containing ferment had no observed negative impact on intestinal epithelial cell health. However, long-term exposure (24 h) induced a complete loss of cell-cell contact within the epithelial aggregates and compromised cell viability. Collectively, these results shed light on a potential role for reuterin in inhibiting Salmonella-induced intestinal infections and may support the combined application of glycerol and L. reuteri. While future in vitro and in vivo studies of reuterin on intestinal health should fine-tune our understanding of the mechanistic effects, in particular in the presence of a complex gut microbiota, this the first report of a reuterin effect on the enteric infection process in any mammalian cell type.}, }
@article {pmid22688860, year = {2012}, author = {Vasileiadis, S and Coppolecchia, D and Puglisi, E and Balloi, A and Mapelli, F and Hamon, RE and Daffonchio, D and Trevisan, M}, title = {Response of ammonia oxidizing bacteria and archaea to acute zinc stress and different moisture regimes in soil.}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {1028-1037}, pmid = {22688860}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Archaea/classification/genetics/metabolism/*physiology ; Bacteria/classification/genetics/*metabolism ; Bacterial Physiological Phenomena ; DNA, Archaeal/analysis/genetics ; DNA, Bacterial/analysis/genetics ; Ecosystem ; *Heat-Shock Response ; Nitrification ; Oxidation-Reduction ; Oxidoreductases/genetics ; Polymerase Chain Reaction ; Soil/chemistry ; *Soil Microbiology ; *Water ; Zinc/analysis/*pharmacology ; }, abstract = {Ammonia oxidation has been intensively studied for its sensitivity to environmental shifts and stresses. However, acute stress effects on the occurrence and composition of ammonia oxidizing bacteria (AOB) and archaea (AOA) based on expression of related molecular markers in complex soil environments have been to an extent overlooked, particularly concerning transient but commonly occurring environmental changes like soil moisture shifts. The present study investigates the responses of AOB and AOA to moisture shifts and high Zn soil content. AmoA gene copies and transcripts of AOB and AOA along with potential nitrification activity were measured in a soil microcosm approach for investigating the referred environmental shifts. Moisture change from 87 to 50 % of the water holding capacity caused a ~99 % reduction of AOB but not of AOA amoA transcripts that did not change significantly. Increasing applied zinc concentrations resulted in a reduction of potential nitrification rates and negatively affected studied gene expressions of both AOB and AOA, with AOB being more responsive. Both 16 S rRNA and amoA transcripts of AOB had an inverse relation to the applied zinc, indicating a gradual loss in total cell activity. Our results suggest the existence of pronounced differences between AOB and AOA concerning ammonia oxidation activity.}, }
@article {pmid22688859, year = {2012}, author = {Ollivier, J and Wanat, N and Austruy, A and Hitmi, A and Joussein, E and Welzl, G and Munch, JC and Schloter, M}, title = {Abundance and diversity of ammonia-oxidizing prokaryotes in the root-rhizosphere complex of Miscanthus × giganteus grown in heavy metal-contaminated soils.}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {1038-1046}, pmid = {22688859}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Archaea/classification/enzymology/genetics/*isolation &amp; purification ; Arsenic/metabolism ; Bacteria/classification/enzymology/genetics/*isolation &amp; purification ; Lead/metabolism ; Metals, Heavy/*metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Phylogeny ; Plant Roots/microbiology ; *Poaceae/growth &amp; development/microbiology ; Polymerase Chain Reaction/methods ; Polymorphism, Restriction Fragment Length ; *Rhizosphere ; Soil Pollutants/*metabolism ; }, abstract = {Mine wastes have been considered as a source of heavy metal (HM) contamination in the environment and negatively impact many important ecosystem services provided by soils. Plants like Miscanthus, which tolerate high HM concentrations in soil, are often used for phytoremediation and provide the possibility to use these soils at least for the production of energy crops. However, it is not clear if plant growth at these sites is limited by the availability of nutrients, mainly nitrogen, as microbes in soil might be affected by the contaminant. Therefore, in this study, we investigated in a greenhouse experiment the response of ammonia-oxidizing microbes in the root-rhizosphere complex of Miscanthus × giganteus grown in soils with different levels of long-term arsenic (As) and lead (Pb) contamination. Quantitative PCR of the ammonia monooxigenease gene (amoA) was performed to assess the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) at two different points of plant growth. Furthermore, bulk soil samples before planting were analyzed. In addition, terminal restriction fragment length polymorphism (T-RFLP) analysis was used to investigate the diversity of archaeal amoA amplicons. Whereas high concentrations of As and Pb in soil (83 and 15 g/kg, respectively) resulted independent from plant growth in a clear reduction of AOA and AOB compared to the control soils with lower HM contents, in soils with contamination levels of 10 g/kg As and 0.2 g/kg Pb, only AOB were negatively affected in bulk soil samples. Diversity analysis of archaeal amoA genes revealed clear differences in T-RFLP patterns in response to the degree of HM contamination. Therefore, our results could clearly prove the different response patterns of AOA and AOB in HM-contaminated soils and the development of archaeal amoA phylotypes which are more tolerant towards HMs in soil samples from the areas that were impacted the most by mining waste, which could contribute to functional redundancy of ammonia-oxidizing microbes in soils and stability of nitrification pattern.}, }
@article {pmid22677953, year = {2012}, author = {Chapman, WK and Paul, L}, title = {Evidence that northern pioneering pines with tuberculate mycorrhizae are unaffected by varying soil nitrogen levels.}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {964-972}, pmid = {22677953}, issn = {1432-184X}, mesh = {British Columbia ; Mycorrhizae/*metabolism ; Nitrates/analysis ; Nitrogen/*analysis ; Nitrogen Isotopes/analysis ; Pinus/*growth &amp; development/metabolism/microbiology ; Plant Roots/metabolism/microbiology ; Quaternary Ammonium Compounds/analysis ; Soil/*chemistry ; }, abstract = {Tuberculate mycorrhizae on Pinus contorta (lodgepole pine) have previously been shown to reduce acetylene, but an outstanding question has been to what degree these structures could meet the nitrogen requirements of the tree. We compared the growth, tissue nitrogen contents, and stable nitrogen isotope ratios of P. contorta growing in gravel pits to the same species growing on adjacent intact soil. Trees growing in severely nitrogen deficient gravel pits had virtually identical growth rates and tissue nitrogen contents to those growing on intact soil that had nitrogen levels typical for the area. δ(15)N values for trees in the gravel pits were substantially lower than δ(15)N values for trees on intact soil, and isotope ratios in vegetation were lower than the isotope ratios of the soil. The form of soil nitrogen in the gravel pits was almost exclusively nitrate, while ammonium predominated in the intact soil. Discrimination against (15)N during plant uptake of soil nitrate in the highly N-deficient soil should be weak or nonexistent. Therefore, the low δ(15)N in the gravel pit trees suggests that trees growing in gravel pits were using another nitrogen source in addition to the soil. Precipitation-borne nitrogen in the study area is extremely low. In conjunction with our other work, these findings strongly suggests that P. contorta and its microbial symbionts or associates fix nitrogen in sufficient amounts to sustain vigorous tree growth on the most nitrogen-deficient soils.}, }
@article {pmid22675653, year = {2012}, author = {Pylro, VS and Vespoli, Lde S and Duarte, GF and Yotoko, KS}, title = {Detection of horizontal gene transfers from phylogenetic comparisons.}, journal = {International journal of evolutionary biology}, volume = {2012}, number = {}, pages = {813015}, pmid = {22675653}, issn = {2090-052X}, abstract = {Bacterial phylogenies have become one of the most important challenges for microbial ecology. This field started in the mid-1970s with the aim of using the sequence of the small subunit ribosomal RNA (16S) tool to infer bacterial phylogenies. Phylogenetic hypotheses based on other sequences usually give conflicting topologies that reveal different evolutionary histories, which in some cases may be the result of horizontal gene transfer events. Currently, one of the major goals of molecular biology is to understand the role that horizontal gene transfer plays in species adaptation and evolution. In this work, we compared the phylogenetic tree based on 16S with the tree based on dszC, a gene involved in the cleavage of carbon-sulfur bonds. Bacteria of several genera perform this survival task when living in environments lacking free mineral sulfur. The biochemical pathway of the desulphurization process was extensively studied due to its economic importance, since this step is expensive and indispensable in fuel production. Our results clearly show that horizontal gene transfer events could be detected using common phylogenetic methods with gene sequences obtained from public sequence databases.}, }
@article {pmid22675605, year = {2012}, author = {Gilbert, JA and Catlett, C and Desai, N and Knight, R and White, O and Robbins, R and Sankaran, R and Sansone, SA and Field, D and Meyer, F}, title = {Conceptualizing a Genomics Software Institute (GSI).}, journal = {Standards in genomic sciences}, volume = {6}, number = {1}, pages = {136-144}, pmid = {22675605}, issn = {1944-3277}, abstract = {Microbial ecology has been enhanced greatly by the ongoing 'omics revolution, bringing half the world's biomass and most of its biodiversity into analytical view for the first time; indeed, it feels almost like the invention of the microscope and the discovery of the new world at the same time. With major microbial ecology research efforts accumulating prodigious quantities of sequence, protein, and metabolite data, we are now poised to address environmental microbial research at macro scales, and to begin to characterize and understand the dimensions of microbial biodiversity on the planet. What is currently impeding progress is the need for a framework within which the research community can develop, exchange and discuss predictive ecosystem models that describe the biodiversity and functional interactions. Such a framework must encompass data and metadata transparency and interoperation; data and results validation, curation, and search; application programming interfaces for modeling and analysis tools; and human and technical processes and services necessary to ensure broad adoption. Here we discuss the need for focused community interaction to augment and deepen established community efforts, beginning with the Genomic Standards Consortium (GSC), to create a science-driven strategic plan for a Genomic Software Institute (GSI).}, }
@article {pmid22674555, year = {2012}, author = {Lemon, KP and Armitage, GC and Relman, DA and Fischbach, MA}, title = {Microbiota-targeted therapies: an ecological perspective.}, journal = {Science translational medicine}, volume = {4}, number = {137}, pages = {137rv5}, pmid = {22674555}, issn = {1946-6242}, support = {DP2 OD007290/OD/NIH HHS/United States ; DP1 OD000964/OD/NIH HHS/United States ; DE020751/DE/NIDCR NIH HHS/United States ; DP1OD000964/OD/NIH HHS/United States ; P30 DE020751/DE/NIDCR NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; Humans ; Metagenome/drug effects/*physiology ; Probiotics/therapeutic use ; }, abstract = {The connection between disease and the disruption of homeostatic interactions between the host and its microbiota is now well established. Drug developers and clinicians are starting to rely more heavily on therapies that directly target the microbiota and on the ecology of the microbiota to understand the outcomes of these treatments. The effects of those microbiota-targeted therapies that alter community composition range in scale from eliminating individual strains of a single species (for example, with antibacterial conjugate vaccines) to replacing the entire community with a new intact microbiota (for example, by fecal transplantation). Secondary infections linked to antibiotic use provide a cautionary tale of the unintended consequences of perturbing a microbial species network and highlight the need for new narrow-spectrum antibiotics with rapid companion diagnostics. Insights into microbial ecology will also benefit the development of probiotics, whose therapeutic prospects will depend on rigorous clinical testing. Future probiotics may take the form of a consortium of long-term community residents: "a fecal transplant in a capsule." The efficacy of microbiota-targeted therapies will need to be assessed using new diagnostic tools that measure community function rather than composition, including the temporal response of a microbial community to a defined perturbation such as an antibiotic or probiotic.}, }
@article {pmid22674445, year = {2012}, author = {Sintubin, L and Verstraete, W and Boon, N}, title = {Biologically produced nanosilver: current state and future perspectives.}, journal = {Biotechnology and bioengineering}, volume = {109}, number = {10}, pages = {2422-2436}, doi = {10.1002/bit.24570}, pmid = {22674445}, issn = {1097-0290}, mesh = {Bacteria/metabolism ; Biotechnology/*methods ; Fungi/metabolism ; Metabolic Networks and Pathways ; *Nanoparticles ; Plants/metabolism ; Silver/*metabolism ; }, abstract = {Silver nanoparticles are one of the most commercialized nanomaterials. They are widely applied as biocides for their strong antimicrobial activity, but also their conductive, optic and catalytic properties make them wanted in many applications. The chemical and physical processes which are used to synthesize silver nanoparticles generally have many disadvantages and are not eco-friendly. In this review, we will discuss biological alternatives that have been developed using microorganisms or plants to produce biogenic silver. Until now, only their antimicrobial activity has been studied more into detail. In contrast, a wide range of practical applications as biocide, biosensor, and catalyst are still unexplored. The shape, size, and functionalization of the nanoparticles is defined by the biological system used to produce the nanoparticles, hence for every application a specific biological production process needs to be chosen. On the other hand, biogenic silver needs to compete with chemically produced nanosilver on the market. Large scale production generating inexpensive nanoparticles is needed. This can only be achieved when the biological production system is chosen in function of the yield. Hence, the true challenge for biogenic silver is finding the balance between scalability, price, and applicability.}, }
@article {pmid22672512, year = {2012}, author = {De Fine Licht, HH and Biedermann, PH}, title = {Patterns of functional enzyme activity in fungus farming ambrosia beetles.}, journal = {Frontiers in zoology}, volume = {9}, number = {1}, pages = {13}, pmid = {22672512}, issn = {1742-9994}, abstract = {INTRODUCTION: In wood-dwelling fungus-farming weevils, the so-called ambrosia beetles (Curculionidae: Scolytinae and Platypodinae), wood in the excavated tunnels is used as a medium for cultivating fungi by the combined action of digging larvae (which create more space for the fungi to grow) and of adults sowing and pruning the fungus. The beetles are obligately dependent on the fungus that provides essential vitamins, amino acids and sterols. However, to what extent microbial enzymes support fungus farming in ambrosia beetles is unknown. Here we measure (i) 13 plant cell-wall degrading enzymes in the fungus garden microbial consortium of the ambrosia beetle Xyleborinus saxesenii, including its primary fungal symbionts, in three compartments of laboratory maintained nests, at different time points after gallery foundation and (ii) four specific enzymes that may be either insect or microbially derived in X. saxesenii adult and larval individuals.<br><br>RESULTS: We discovered that the activity of cellulases in ambrosia fungus gardens is relatively small compared to the activities of other cellulolytic enzymes. Enzyme activity in all compartments of the garden was mainly directed towards hemicellulose carbohydrates such as xylan, glucomannan and callose. Hemicellulolytic enzyme activity within the brood chamber increased with gallery age, whereas irrespective of the age of the gallery, the highest overall enzyme activity were detected in the gallery dump material expelled by the beetles. Interestingly endo-&#x3b2;-1,3(4)-glucanase activity capable of callose degradation was identified in whole-body extracts of both larvae and adult X. saxesenii, whereas endo-&#x3b2;-1,4-xylanase activity was exclusively detected in larvae.<br><br>CONCLUSION: Similar to closely related fungi associated with bark beetles in phloem, the microbial symbionts of ambrosia beetles hardly degrade cellulose. Instead, their enzyme activity is directed mainly towards comparatively more easily accessible hemicellulose components of the ray-parenchyma cells in the wood xylem. Furthermore, the detection of xylanolytic enzymes exclusively in larvae (which feed on fungus colonized wood) and not in adults (which feed only on fungi) indicates that only larvae (pre-) digest plant cell wall structures. This implies that in X. saxesenii and likely also in many other ambrosia beetles, adults and larvae do not compete for the same food within their nests - in contrast, larvae increase colony fitness by facilitating enzymatic wood degradation and fungus cultivation.}, }
@article {pmid22672413, year = {2012}, author = {Candela, M and Rampelli, S and Turroni, S and Severgnini, M and Consolandi, C and De Bellis, G and Masetti, R and Ricci, G and Pession, A and Brigidi, P}, title = {Unbalance of intestinal microbiota in atopic children.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {95}, pmid = {22672413}, issn = {1471-2180}, mesh = {Adolescent ; *Biota ; Child ; Child, Preschool ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Hypersensitivity/*microbiology ; Male ; *Metagenome ; Microarray Analysis ; }, abstract = {BACKGROUND: Playing a strategic role in the host immune function, the intestinal microbiota has been recently hypothesized to be involved in the etiology of atopy. In order to investigate the gastrointestinal microbial ecology of atopic disease, here we performed a pilot comparative molecular analysis of the faecal microbiota in atopic children and healthy controls.<br><br>RESULTS: Nineteen atopic children and 12 healthy controls aged 4-14&#x2009;years were enrolled. Stools were collected and the faecal microbiota was characterized by means of the already developed phylogenetic microarray platform, HTF-Microbi.Array, and quantitative PCR. The intestinal microbiota of atopic children showed a significant depletion in members of the Clostridium cluster IV, Faecalibacterium prausnitzii, Akkermansia muciniphila and a corresponding increase of the relative abundance of Enterobacteriaceae.<br><br>CONCLUSION: Depleted in key immunomodulatory symbionts, the atopy-associated microbiota can represent an inflammogenic microbial consortium which can contribute to the severity of the disease. Our data open the way to the therapeutic manipulation of the intestinal microbiota in the treatment of atopy by means of pharmaceutical probiotics.}, }
@article {pmid22658762, year = {2012}, author = {Lijek, RS and Weiser, JN}, title = {Co-infection subverts mucosal immunity in the upper respiratory tract.}, journal = {Current opinion in immunology}, volume = {24}, number = {4}, pages = {417-423}, pmid = {22658762}, issn = {1879-0372}, support = {R37 AI038446/AI/NIAID NIH HHS/United States ; R01 AI078538/AI/NIAID NIH HHS/United States ; AI-055400/AI/NIAID NIH HHS/United States ; T32 AI055400/AI/NIAID NIH HHS/United States ; R01 AI038446/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Coinfection ; Haemophilus Infections/*immunology ; Host-Pathogen Interactions ; Humans ; Immunity, Mucosal/*physiology ; Influenza, Human/*immunology ; Pneumococcal Infections/*immunology ; Respiratory Tract Infections/*microbiology ; Staphylococcal Infections/*immunology ; }, abstract = {Polymicrobial interactions on mucosal surfaces can influence inflammation, immunity, and disease outcome. Here, we review how host responses to colonization in the upper respiratory tract with the bacterial pathogen Streptococcus pneumoniae can be altered by co-infection. Recent advances provide a mechanistic understanding of how mucosal immunity can be subverted at distinct immunological time-points during pneumococcal colonization by other pathogens such as Haemophilus influenzae, influenza type A and Staphylococcus aureus. These examples use animal models of co-infection to highlight how otherwise effective host responses can be rendered ineffective by co-infection, and vice versa. The complex microbial ecology of mucosal sites must be considered to fully understand how immune responses in a natural setting influence the outcome of host-pathogen interactions.}, }
@article {pmid22655057, year = {2012}, author = {Schillinger, C and Petrich, A and Lux, R and Riep, B and Kikhney, J and Friedmann, A and Wolinsky, LE and Göbel, UB and Daims, H and Moter, A}, title = {Co-localized or randomly distributed? Pair cross correlation of in vivo grown subgingival biofilm bacteria quantified by digital image analysis.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e37583}, pmid = {22655057}, issn = {1932-6203}, support = {R03 DE018424/DE/NIDCR NIH HHS/United States ; 1R03DE018424-01A1/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteroides/*growth &amp; development ; Biofilms/*growth &amp; development ; Colony Count, Microbial ; Female ; Fusobacterium nucleatum/*growth &amp; development ; Humans ; Image Processing, Computer-Assisted ; Male ; Periodontal Diseases/*microbiology ; Periodontal Pocket/microbiology ; Porphyromonas gingivalis/*growth &amp; development ; Prevotella intermedia/*growth &amp; development ; Software ; }, abstract = {The polymicrobial nature of periodontal diseases is reflected by the diversity of phylotypes detected in subgingival plaque and the finding that consortia of suspected pathogens rather than single species are associated with disease development. A number of these microorganisms have been demonstrated in vitro to interact and enhance biofilm integration, survival or even pathogenic features. To examine the in vivo relevance of these proposed interactions, we extended the spatial arrangement analysis tool of the software daime (digital image analysis in microbial ecology). This modification enabled the quantitative analysis of microbial co-localization in images of subgingival biofilm species, where the biomass was confined to fractions of the whole-image area, a situation common for medical samples. Selected representatives of the disease-associated red and orange complexes that were previously suggested to interact with each other in vitro (Tannerella forsythia with Fusobacterium nucleatum and Porphyromonas gingivalis with Prevotella intermedia) were chosen for analysis and labeled with specific fluorescent probes via fluorescence in situ hybridization. Pair cross-correlation analysis of in vivo grown biofilms revealed tight clustering of F. nucleatum/periodonticum and T. forsythia at short distances (up to 6 µm) with a pronounced peak at 1.5 µm. While these results confirmed previous in vitro observations for F. nucleatum and T. forsythia, random spatial distribution was detected between P. gingivalis and P. intermedia in the in vivo samples. In conclusion, we successfully employed spatial arrangement analysis on the single cell level in clinically relevant medical samples and demonstrated the utility of this approach for the in vivo validation of in vitro observations by analyzing statistically relevant numbers of different patients. More importantly, the culture-independent nature of this approach enables similar quantitative analyses for "as-yet-uncultured" phylotypes which cannot be characterized in vitro.}, }
@article {pmid22646978, year = {2012}, author = {Deng, Y and Jiang, YH and Yang, Y and He, Z and Luo, F and Zhou, J}, title = {Molecular ecological network analyses.}, journal = {BMC bioinformatics}, volume = {13}, number = {}, pages = {113}, pmid = {22646978}, issn = {1471-2105}, mesh = {Computational Biology/*methods ; Ecology/*methods ; Ecosystem ; Genes, rRNA ; Metagenomics/*methods ; RNA, Ribosomal, 16S/genetics ; Software ; Soil/analysis ; Soil Microbiology ; Temperature ; }, abstract = {BACKGROUND: Understanding the interaction among different species within a community and their responses to environmental changes is a central goal in ecology. However, defining the network structure in a microbial community is very challenging due to their extremely high diversity and as-yet uncultivated status. Although recent advance of metagenomic technologies, such as high throughout sequencing and functional gene arrays, provide revolutionary tools for analyzing microbial community structure, it is still difficult to examine network interactions in a microbial community based on high-throughput metagenomics data.<br><br>RESULTS: Here, we describe a novel mathematical and bioinformatics framework to construct ecological association networks named molecular ecological networks (MENs) through Random Matrix Theory (RMT)-based methods. Compared to other network construction methods, this approach is remarkable in that the network is automatically defined and robust to noise, thus providing excellent solutions to several common issues associated with high-throughput metagenomics data. We applied it to determine the network structure of microbial communities subjected to long-term experimental warming based on pyrosequencing data of 16 S rRNA genes. We showed that the constructed MENs under both warming and unwarming conditions exhibited topological features of scale free, small world and modularity, which were consistent with previously described molecular ecological networks. Eigengene analysis indicated that the eigengenes represented the module profiles relatively well. In consistency with many other studies, several major environmental traits including temperature and soil pH were found to be important in determining network interactions in the microbial communities examined. To facilitate its application by the scientific community, all these methods and statistical tools have been integrated into a comprehensive Molecular Ecological Network Analysis Pipeline (MENAP), which is open-accessible now (http://ieg2.ou.edu/MENA).<br><br>CONCLUSIONS: The RMT-based molecular ecological network analysis provides powerful tools to elucidate network interactions in microbial communities and their responses to environmental changes, which are fundamentally important for research in microbial ecology and environmental microbiology.}, }
@article {pmid22644483, year = {2012}, author = {Mosier, AC and Lund, MB and Francis, CA}, title = {Ecophysiology of an ammonia-oxidizing archaeon adapted to low-salinity habitats.}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {955-963}, pmid = {22644483}, issn = {1432-184X}, mesh = {*Adaptation, Physiological ; Ammonia/*metabolism ; Archaea/classification/genetics/*physiology/ultrastructure ; Culture Media ; *Ecosystem ; Geologic Sediments/microbiology ; Microscopy, Electron, Transmission ; Oxidation-Reduction ; San Francisco ; Seawater/microbiology ; Sodium Chloride/*pharmacology ; }, abstract = {Ammonia oxidation in marine and terrestrial ecosystems plays a pivotal role in the cycling of nitrogen and carbon. Recent discoveries have shown that ammonia-oxidizing archaea (AOA) are both abundant and diverse in these systems, yet very little is known about their physiology. Here we report a physiological analysis of a novel low-salinity-type AOA enriched from the San Francisco Bay estuary, Candidatus Nitrosoarchaeum limnia strain SFB1. N. limnia has a slower growth rate than Nitrosopumilus maritimus and Nitrososphaera viennensis EN76, the only pure AOA isolates described to date, but the growth rate is comparable to the growth of marine AOA enrichment cultures. The growth rate only slightly decreased when N. limnia was grown under lower-oxygen conditions (5.5 % oxygen in the headspace). Although N. limnia was capable of growth at 75 % of seawater salinity, there was a longer lag time, incomplete oxidation of ammonia to nitrite, and slower overall growth rate. Allylthiourea (ATU) only partially inhibited growth and ammonia oxidation by N. limnia at concentrations known to completely inhibit bacterial ammonia oxidation. Using electron microscopy, we confirmed the presence of flagella as suggested by various flagellar biosynthesis genes in the N. limnia genome. We demonstrate that N. limnia is representative of a low-salinity estuarine AOA ecotype and that more than 85 % of its proteins have highest identity to other coastal and estuarine metagenomic sequences. Our findings further highlight the physiology of N. limnia and help explain its ecological adaptation to low-salinity niches.}, }
@article {pmid22644482, year = {2012}, author = {Davis, TS and Boundy-Mills, K and Landolt, PJ}, title = {Volatile emissions from an epiphytic fungus are semiochemicals for eusocial wasps.}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {1056-1063}, pmid = {22644482}, issn = {1432-184X}, mesh = {Animals ; Ascomycota/chemistry/*metabolism ; Fungi/chemistry ; Odorants ; Pheromones/chemistry/*physiology ; *Symbiosis ; Volatile Organic Compounds/chemistry/*metabolism ; Wasps/*physiology ; }, abstract = {Microbes are ubiquitous on plant surfaces. However, interactions between epiphytic microbes and arthropods are rarely considered as a factor that affects arthropod behaviors. Here, volatile emissions from an epiphytic fungus were investigated as semiochemical attractants for two eusocial wasps. The fungus Aureobasidium pullulans was isolated from apples, and the volatile compounds emitted by fungal colonies were quantified. The attractiveness of fungal colonies and fungal volatiles to social wasps (Vespula spp.) were experimentally tested in the field. Three important findings emerged: (1) traps baited with A. pullulans caught 2750 % more wasps on average than unbaited control traps; (2) the major headspace volatiles emitted by A. pullulans were 2-methyl-1-butanol, 3-methyl-1-butanol, and 2-phenylethyl alcohol; and (3) a synthetic blend of fungal volatiles attracted 4,933 % more wasps on average than unbaited controls. Wasps were most attracted to 2-methyl-1-butanol. The primary wasp species attracted to fungal volatiles were the western yellowjacket (Vespula pensylvanica) and the German yellowjacket (V. germanica), and both species externally vectored A. pullulans. This is the first study to link microbial volatile emissions with eusocial wasp behaviors, and these experiments indicate that volatile compounds emitted by an epiphytic fungus can be responsible for wasp attraction. This work implicates epiphytic microbes as important components in the community ecology of some eusocial hymenopterans, and fungal emissions may signal suitable nutrient sources to foraging wasps. Our experiments are suggestive of a potential symbiosis, but additional studies are needed to determine if eusocial wasp-fungal associations are widespread, and whether these associations are incidental, facultative, or obligate.}, }
@article {pmid22641923, year = {2012}, author = {Czerwiński, J and Højberg, O and Smulikowska, S and Engberg, RM and Mieczkowska, A}, title = {Effects of sodium butyrate and salinomycin upon intestinal microbiota, mucosal morphology and performance of broiler chickens.}, journal = {Archives of animal nutrition}, volume = {66}, number = {2}, pages = {102-116}, doi = {10.1080/1745039x.2012.663668}, pmid = {22641923}, issn = {1745-039X}, mesh = {Animal Feed ; Animals ; Butyrates/administration &amp; dosage/*pharmacology ; Chickens/*growth &amp; development ; Coccidiostats/administration &amp; dosage/pharmacology ; Drug Therapy, Combination ; Female ; Intestinal Mucosa/*drug effects ; Intestines/*drug effects/*microbiology ; Pyrans/administration &amp; dosage/*pharmacology ; }, abstract = {The effect of dietary sodium butyrate (SB) or salinomycin (SAL) or both additives on performance, small intestinal morphology and microbial ecology of broiler chickens was studied. A growth trial was conducted with 96 Ross 308 female broilers from 1 to 30 days of age. Four treatment groups were fed with a non-supplemented control diet or three experimental diets supplemented with i) 300 mg SB (Adimix 30 coated) per kg, ii) 60 mg SAL (Sacox) per kg or iii) both additives in combination. Feed intake and body-weight gain decreased and gain-to-feed ratio increased due to SAL supplementation, while addition of SB did not affect performance in comparison with the control diet but positively affected feed intake and body-weight gain in comparison with birds fed the SAL-supplemented diet. Villus height in jejunum decreased, while crypt depth increased due to SAL supplementation. Addition of SB increased crypt depth in jejunum. No significant effect of either additive was observed in ileum morphology. Total short-chain organic acids concentration in ileal digesta decreased with SAL supplementation, mainly due to lower lactic acid concentration, but no effects were observed in the caeca. The SAL supplementation was accompanied by a pH increase in ileum and a pH decrease in caecum. No significant effect of SB addition was observed for these parameters. Total bacterial numbers and Lactobacillus [lactic acid bacteria (LAB)] counts in ileal and caecal contents were lower in birds fed with SAL-supplemented diet in comparison with birds fed with control or SB diet. DNA fingerprints revealed SAL supplementation to affect the microbial population by suppressing dominating LAB, potentially L. aviarius. The presented results show that dietary SAL, supplemented alone or in combination with SB, suppressed the microbial activity and altered the microbial community structure mainly in ileum. SAL alone negatively affected feed intake and body-weight gain; however, the effect was ameliorated by SB supplementation.}, }
@article {pmid22639220, year = {2012}, author = {Pett-Ridge, J and Weber, PK}, title = {NanoSIP: NanoSIMS applications for microbial biology.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {881}, number = {}, pages = {375-408}, doi = {10.1007/978-1-61779-827-6_13}, pmid = {22639220}, issn = {1940-6029}, mesh = {In Situ Hybridization ; Isotope Labeling ; Microbiological Techniques/*methods ; Spectrometry, Mass, Secondary Ion/*methods ; }, abstract = {Recent advances in high-resolution imaging secondary ion mass spectrometry (SIMS) (J Biol 5: 20, 2006) have made isotopic tracing at the single-cell level a standard technique for microbial ecology and systems biology; elemental and metal cofactor analyses are also showing significant promise. For example, with the NanoSIMS, metabolic activities of single microbial cells can be tracked by imaging natural isotopic/elemental composition or isotope distribution after stable isotope probing. When linked to molecular visualization methods, such as in situ hybridization and antibody labeling, these techniques enable in situ function to be linked to microbial identity and gene expression. We broadly call this combination of methods nanoSIP, for nanometer-scale stable isotope probing. Here we present the primary materials and methods used for nanoSIP, with an emphasis on key steps and potential pitfalls. Applications to pure cultures, cocultures, and complex communities are discussed.}, }
@article {pmid22639075, year = {2012}, author = {Jorquera, MA and Shaharoona, B and Nadeem, SM and de la Luz Mora, M and Crowley, DE}, title = {Plant growth-promoting rhizobacteria associated with ancient clones of creosote bush (Larrea tridentata).}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {1008-1017}, pmid = {22639075}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Bacteroidetes/classification/genetics/growth &amp; development/isolation &amp; purification ; Carbon-Carbon Lyases/genetics/metabolism ; Cucumis sativus/growth &amp; development/microbiology ; *Desert Climate ; Larrea/genetics/*growth &amp; development/metabolism/*microbiology ; Molecular Sequence Data ; *Plant Development ; Plant Roots/growth &amp; development/microbiology ; Proteobacteria/classification/genetics/growth &amp; development/isolation &amp; purification ; *Rhizosphere ; Sequence Analysis, DNA ; Soil Microbiology ; Symbiosis ; }, abstract = {Plant growth-promoting rhizobacteria (PGPR) are common components of the rhizosphere, but their role in adaptation of plants to extreme environments is not yet understood. Here, we examined rhizobacteria associated with ancient clones of Larrea tridentata in the Mohave desert, including the 11,700-year-old King Clone, which is oldest known specimen of this species. Analysis of unculturable and culturable bacterial community by PCR-DGGE revealed taxa that have previously been described on agricultural plants. These taxa included species of Proteobacteria, Bacteroidetes, and Firmicutes that commonly carry traits associated with plant growth promotion, including genes encoding aminocyclopropane carboxylate deaminase and β-propeller phytase. The PGPR activities of three representative isolates from L. tridentata were further confirmed using cucumber plants to screen for plant growth promotion. This study provides an intriguing first view of the mutualistic bacteria that are associated with some of the world's oldest living plants and suggests that PGPR likely contribute to the adaptation of L. tridentata and other plant species to harsh environmental conditions in desert habitats.}, }
@article {pmid22624389, year = {2012}, author = {Qian, Y and Quan, XC and Pei, YS and Ma, JY and Tao, K}, title = {[Microbial ecology analysis of the biofilm from two biological contact oxidation processes with different performance].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {33}, number = {3}, pages = {922-931}, pmid = {22624389}, issn = {0250-3301}, mesh = {Aerobiosis ; Anaerobiosis ; Biofilms ; Bioreactors/*microbiology ; Ecosystem ; Nitrobacter/*metabolism ; Nitrogen/isolation &amp; purification/metabolism ; Oxidation-Reduction ; Quaternary Ammonium Compounds/isolation &amp; purification/metabolism ; Rivers ; Sewage/chemistry/*microbiology ; Water Pollutants, Chemical/*isolation &amp; purification/metabolism ; }, abstract = {This study investigated the performance of one-step aerobic biological oxidation process and anoxic/aerobic two-step biological oxidation process treating modeled river water containing low carbon and rich ammonia. Biofilm microbial ecology was analyzed with multiple molecular technologies including PCR-DGGE, FISH/CLSM and FISH/FCM to investigate the succession of bacteria community and space distribution along with abundance of the main functional bacteria, and to research the micro-influential factors and the mechanism of different biological contact oxidation processes for their performance. Results showed that two-step contact oxidation process achieved higher removal percentage than that of the one-step process, with COD and NH4(+) -N removal enhanced about 10% and 32%-59%, respectively. A much thicker biofilm was obtained by the one-step process compared to the two-step process, and nitrobacterium was mainly distributed in the depth of 180-200 microm and 105-125 microm, respectively. PCR-DGGE results found that the two-step process demonstrated less microbial diversity than that of the one-step process, FISH/FCM results showed that ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) abundance increased in the two-step process with the increase of operation time, while that of the one-step process declined. Experiment results demonstrate that functional partitioning of the anoxic-aerobic two-step biological contact oxidation process could be in favor for harvesting nitrobacteria and other special bacteria in different reactor spaces, which can improve removal efficiency for organics and ammonia finally.}, }
@article {pmid22622766, year = {2012}, author = {Davis, JP and Struchtemeyer, CG and Elshahed, MS}, title = {Bacterial communities associated with production facilities of two newly drilled thermogenic natural gas wells in the Barnett Shale (Texas, USA).}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {942-954}, pmid = {22622766}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/analysis/genetics/isolation &amp; purification ; Extraction and Processing Industry/*methods ; *Hot Temperature ; *Microbial Consortia ; Molecular Sequence Data ; *Natural Gas ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Texas ; Water/chemistry ; *Water Microbiology ; }, abstract = {We monitored the bacterial communities in the gas-water separator and water storage tank of two newly drilled natural gas wells in the Barnett Shale in north central Texas, using a 16S rRNA gene pyrosequencing approach over a period of 6 months. Overall, the communities were composed mainly of moderately halophilic and halotolerant members of the phyla Firmicutes and Proteobacteria (classes Βeta-, Gamma-, and Epsilonproteobacteria) in both wells at all sampling times and locations. Many of the observed lineages were encountered in prior investigations of microbial communities from various fossil fluid formations and production facilities. In all of the samples, multiple H(2)S-producing lineages were encountered; belonging to the sulfate- and sulfur-reducing class Deltaproteobacteria, order Clostridiales, and phylum Synergistetes, as well as the thiosulfate-reducing order Halanaerobiales. The bacterial communities from the separator and tank samples bore little resemblance to the bacterial communities in the drilling mud and hydraulic-fracture waters that were used to drill these wells, suggesting the in situ development of the unique bacterial communities in such well components was in response to the prevalent geochemical conditions present. Conversely, comparison of the bacterial communities on temporal and spatial scales suggested the establishment of a core microbial community in each sampled location. The results provide the first overview of bacterial dynamics and colonization patterns in newly drilled, thermogenic natural gas wells and highlights patterns of spatial and temporal variability observed in bacterial communities in natural gas production facilities.}, }
@article {pmid22622765, year = {2012}, author = {Bartrons, M and Catalan, J and Casamayor, EO}, title = {High bacterial diversity in epilithic biofilms of oligotrophic mountain lakes.}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {860-869}, pmid = {22622765}, issn = {1432-184X}, mesh = {Altitude ; Bacteria, Aerobic/*classification/genetics/growth &amp; development ; Bacteria, Anaerobic/*classification/genetics/growth &amp; development ; Biofilms/*growth &amp; development ; DNA, Bacterial/analysis/genetics/isolation &amp; purification ; DNA, Ribosomal/genetics ; Ecosystem ; Genes, rRNA ; Lakes/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spain ; }, abstract = {Benthic microbial biofilms attached to rocks (epilithic) are major sites of carbon cycling and can dominate ecosystem primary production in oligotrophic lakes. We studied the bacterial community composition of littoral epilithic biofilms in five connected oligotrophic high mountain lakes located at different altitudes by genetic fingerprinting and clone libraries of the 16S rRNA gene. Different intra-lake samples were analyzed, and consistent changes in community structure (chlorophyll a and organic matter contents, and bacterial community composition) were observed along the altitudinal gradient, particularly related with the location of the lake above or below the treeline. Epilithic biofilm genetic fingerprints were both more diverse among lakes than within lakes and significantly different between montane (below the tree line) and alpine lakes (above the tree line). The genetic richness in the epilithic biofilm was much higher than in the plankton of the same lacustrine area studied in previous works, with significantly idiosyncratic phylogenetic composition (specifically distinct from lake plankton or mountain soils). Data suggest the coexistence of aerobic, anaerobic, phototrophic, and chemotrophic microorganisms in the biofilm, Bacteroidetes and Cyanobacteria being the most important bacterial taxa, followed by Alpha-, Beta-, Gamma-, and Deltaproteobacteria, Chlorobi, Planctomycetes, and Verrucomicrobia. The degree of novelty was especially high for epilithic Bacteroidetes, and up to 50 % of the sequences formed monophyletic clusters distantly related to any previously reported sequence. More than 35 % of the total sequences matched at <95 % identity to any previously reported 16S rRNA gene, indicating that alpine epilithic biofilms are unexplored habitats that contain a substantial degree of novelty within a short geographical distance. Further research is needed to determine whether these communities are involved in more biogeochemical pathways than previously thought.}, }
@article {pmid22622764, year = {2012}, author = {Kirkup, BC and Craft, DW and Palys, T and Black, C and Heitkamp, R and Li, C and Lu, Y and Matlock, N and McQueary, C and Michels, A and Peck, G and Si, Y and Summers, AM and Thompson, M and Zurawski, DV}, title = {Traumatic wound microbiome workshop.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {837-850}, pmid = {22622764}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics ; Biomedical Research ; Humans ; *Metagenome ; Wound Infection/*diagnosis/*microbiology ; *Wounds and Injuries ; }, abstract = {On May 9-10, 2011, the Walter Reed Army Institute of Research, as the Army Center of Excellence for Infectious Disease, assembled over a dozen leaders in areas related to research into the communities of microorganisms which colonize and infect traumatic wounds. The objectives of the workshop were to obtain guidance for government researchers, to spur research community involvement in the field of traumatic wound research informed by a microbiome perspective, and to spark collaborative efforts serving the Wounded Warriors and similarly wounded civilians. During the discussions, it was made clear that the complexity of these infections will only be met by developing a new art of clinical practice that engages the numerous microbes and their ecology. It requires the support of dedicated laboratories and technologists who advance research methods such as community sequencing, as well as the kinds of data analysis expertise and facilities. These strategies already appear to be bearing fruit in the clinical management of chronic wounds. There are now funding announcements and programs supporting this area of research open to extramural collaborators.}, }
@article {pmid22622763, year = {2012}, author = {Edberg, F and Andersson, AF and Holmström, SJ}, title = {Bacterial community composition in the water column of a lake formed by a former uranium open pit mine.}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {870-880}, pmid = {22622763}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/analysis/genetics ; *Ecosystem ; Ferric Compounds/analysis/metabolism ; Genes, rRNA ; Lakes/*chemistry/*microbiology ; *Mining ; Proteobacteria/classification/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Sulfur/analysis/metabolism ; *Uranium ; Water Pollutants, Chemical/analysis/metabolism ; }, abstract = {Mining of pyrite minerals is a major environmental issue involving both biological and geochemical processes. Here we present a study of an artificial lake of a former uranium open pit mine with the aim to connect the chemistry and bacterial community composition (454-pyrosequencing of 16S rRNA genes) in the stratified water column. A shift in the water chemistry from oxic conditions in the epilimnion to anoxic, alkaline, and metal and sulfide-rich conditions in the hypolimnion was corresponded by a strong shift in the bacterial community, with few shared operational taxonomic units (OTU) between the water layers. The epilimnetic bacterial community of the lake (~20 years old) showed similarities to other temperate freshwater lakes, while the hypolimnetic bacterial community showed similarity to extreme chemical environments. The epilimnetic bacterial community had dominance of Actinobacteria and Betaproteobacteria. The hypolimnion displayed a higher bacterial diversity and was dominated by the phototrophic green sulphur bacterium of the genus Chlorobium (ca. 40 % of the total community). Deltaproteobacteria were only represented in the hypolimnion and the most abundant OTUs were affiliated with ferric iron and sulfate reducers of the genus Geobacter and Desulfobulbus, respectively. The chemistry is clearly controlling, especially the hypolimnetic, bacterial community but the community composition also indicates that the bacteria are involved in metal cycling in the lake.}, }
@article {pmid22622335, year = {2012}, author = {Chen, Y and Oba, M and Guan, LL}, title = {Variation of bacterial communities and expression of Toll-like receptor genes in the rumen of steers differing in susceptibility to subacute ruminal acidosis.}, journal = {Veterinary microbiology}, volume = {159}, number = {3-4}, pages = {451-459}, doi = {10.1016/j.vetmic.2012.04.032}, pmid = {22622335}, issn = {1873-2542}, mesh = {Acidosis/*genetics/immunology/metabolism/*veterinary ; Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Cattle ; Cattle Diseases/*immunology/*microbiology ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Male ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Rumen/metabolism/*microbiology ; Toll-Like Receptor 2/*genetics ; Toll-Like Receptor 4/*genetics ; }, abstract = {In order to determine differences in the ruminal bacterial community and host Toll-like receptor (TLR) gene expression of beef cattle with different susceptibility to acidosis, rumen papillae and content were collected from acidosis-susceptible (AS, n=3) and acidosis-resistant (AR, n=3) steers. The ruminal bacterial community was characterized using PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative real time PCR (qRT-PCR) analysis. Global R analysis of bacterial profile similarity revealed that bacterial diversity was significantly different between AR and AS groups for both rumen content (P=0.001) and epithelial (P=0.002) communities. The copy number of total bacterial 16S rRNA genes in content of AS steers was 10-fold higher than that of AR steers, and the copy number of total 16S rRNA genes of epimural bacteria in AR steers was positively correlated with ruminal pH (r=0.59, P=0.04), and negatively correlated with total VFA concentration (r=-0.59, P=0.05). The expressions of host TLR2 and 4 genes were significantly higher in AR steers compared to those in AS steers. These findings enhance our understanding about the ruminal microbial ecology and host gene expression changes that may be useful in the prevention of ruminal acidosis.}, }
@article {pmid22615123, year = {2012}, author = {Erable, B and Féron, D and Bergel, A}, title = {Microbial catalysis of the oxygen reduction reaction for microbial fuel cells: a review.}, journal = {ChemSusChem}, volume = {5}, number = {6}, pages = {975-987}, doi = {10.1002/cssc.201100836}, pmid = {22615123}, issn = {1864-564X}, mesh = {Bacteria/metabolism ; *Bioelectric Energy Sources ; Catalysis ; Oxidation-Reduction ; Oxygen/metabolism ; }, abstract = {The slow kinetics of the electrochemical oxygen reduction reaction (ORR) is a crucial bottleneck in the development of microbial fuel cells (MFCs). This article firstly gives an overview of the particular constraints imposed on ORR by MFC operating conditions: neutral pH, slow oxygen mass transfer, sensitivity to reactive oxygen species, fouling and biofouling. A review of the literature is then proposed to assess how microbial catalysis could afford suitable solutions. Actually, microbial catalysis of ORR occurs spontaneously on the surface of metallic materials and is an effective motor of microbial corrosion. In this framework, several mechanisms have been proposed, which are reviewed in the second part of the article. The last part describes the efforts made in the domain of MFCs to determine the microbial ecology of electroactive biofilms and define efficient protocols for the formation of microbial oxygen-reducing cathodes. Although no clear mechanism has been established yet, several promising solutions have been recently proposed.}, }
@article {pmid22614997, year = {2012}, author = {Malvankar, NS and Lovley, DR}, title = {Microbial nanowires: a new paradigm for biological electron transfer and bioelectronics.}, journal = {ChemSusChem}, volume = {5}, number = {6}, pages = {1039-1046}, doi = {10.1002/cssc.201100733}, pmid = {22614997}, issn = {1864-564X}, mesh = {Bacterial Physiological Phenomena ; *Biofilms ; Biotechnology ; Electric Conductivity ; Ferric Compounds/chemistry ; Fimbriae Proteins/metabolism ; Fimbriae, Bacterial/metabolism ; *Nanostructures ; Oxidation-Reduction ; }, abstract = {The discovery that Geobacter sulfurreducens can produce protein filaments with metallic-like conductivity, known as microbial nanowires, that facilitate long-range electron transport is a paradigm shift in biological electron transfer and has important implications for biogeochemistry, microbial ecology, and the emerging field of bioelectronics. Although filaments in a wide diversity of microorganisms have been called microbial nanowires, the type IV pili of G. sulfurreducens and G. metallireducens are the only filaments that have been shown to be required for extracellular electron transport to extracellular electron acceptors or for conduction of electrons through biofilms. Studies of G. sulfurreducens pili preparations and intact biofilms under physiologically relevant conditions have provided multiple lines of evidence for metallic-like conduction along the length of pili and for the possibility of pili networks to confer high conductivity within biofilms. This mechanism of electron conduction contrasts with the previously known mechanism for biological electron transfer via electron tunneling or hopping between closely associated molecules, a strategy unlikely to be well adapted for long-range electron transport outside the cell. In addition to promoting electron exchange with abiotic electron acceptors, microbial nanowires have recently been shown to be involved in direct interspecies electron transfer between syntrophic partners. An improved understanding of the mechanisms for metallic-like conductivity in microbial nanowires, as well as engineering microorganisms with desirable catalytic abilities with nanowires, could lead to new applications in microbial electrosynthesis and bioelectronics.}, }
@article {pmid22614940, year = {2012}, author = {Vajna, B and Szili, D and Nagy, A and Márialigeti, K}, title = {An improved sequence-aided T-RFLP analysis of bacterial succession during oyster mushroom substrate preparation.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {702-713}, pmid = {22614940}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/growth &amp; development ; DNA, Bacterial/analysis/genetics ; Ecosystem ; Molecular Sequence Data ; Phylogeny ; *Pleurotus/growth &amp; development/metabolism ; *Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA/*methods ; *Soil Microbiology ; }, abstract = {While oyster mushroom (Pleurotus spp.) is one of the most popular cultivated edible mushrooms, there is scanty information about the microbial community taking part in mushroom substrate production. In this study, an improved sequence-aided terminal restriction fragment length polymorphism (T-RFLP) was used to identify and (semi-)quantify the dominant bacteria of oyster mushroom substrate preparation. The main features of the improved T-RFLP data analysis were the alignment of chromatograms with variable clustering thresholds, the visualization of data matrix with principal component analysis ordination superimposed with cluster analysis, and the search for stage-specific peaks (bacterial taxa) with similarity percentage (analysis of similarity) analysis, followed by identification with clone libraries. By applying this method, the dominance of the following bacterial genera was revealed during oyster mushroom substrate preparation: Pseudomonas and Sphingomonas at startup, Bacillus, Geobacillus, Ureibacillus, Pseudoxanthomonas, and Thermobispora at the end of partial composting, and finally several genera of Actinobacteria, Thermus, Bacillus, Geobacillus, Thermobacillus, and Ureibacillus in the mature substrate. As the proportion of uncultured bacteria increased during the process, it is worth establishing strain collections from partial composting and from mature substrate for searching new species.}, }
@article {pmid22614939, year = {2012}, author = {Dittmer, J and Lesobre, J and Raimond, R and Zimmer, M and Bouchon, D}, title = {Influence of changing plant food sources on the gut microbiota of saltmarsh detritivores.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {814-825}, pmid = {22614939}, issn = {1432-184X}, mesh = {Amphipoda/microbiology/*physiology ; Animals ; Arthropods/microbiology/*physiology ; Bacteria/classification/*genetics/isolation &amp; purification ; Bacteroides/genetics/isolation &amp; purification ; Behavior, Animal ; Ecosystem ; *Feeding Behavior ; Gammaproteobacteria/genetics/isolation &amp; purification ; Gastrointestinal Tract/*microbiology ; Metagenome ; Molecular Sequence Data ; Poaceae/*classification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vibrio/genetics/isolation &amp; purification ; *Wetlands ; }, abstract = {Changes in agricultural land-use of saltmarshes along the German North Sea coast have favoured the succession of the marsh grass Elytrigia atherica over the long-established Spartina anglica. Consequently, E. atherica represents a potential food source of increasing importance for plant-feeding soil detritivores. Considering the importance of this ecological guild for decomposition processes and nutrient cycling, we focussed on two sympatric saltmarsh soil macrodetritivores and their associated gut microbiota to investigate how the digestive processes of these species may be affected by changing plant food sources. Using genetic fingerprints of partial 16S rRNA gene sequences, we analysed composition and diversity of the bacterial gut community in a diplopod and an amphipod crustacean in relation to different feeding regimes representing the natural vegetation changes. Effects of syntopy on the host-specific gut microbiota were also taken into account by feeding the two detritivore species either independently or on the same plant sample. Bacterial community composition was influenced by both the host species and the available plant food sources, but the latter had a stronger effect on microbial community structure. Furthermore, bacterial diversity was highest after feeding on a mixture of both plant species, regardless of the host species. The gut microbiota of these two detritivores can thus be expected to change along with the on-going succession at the plant community level in this environment. Cloning and sequencing of bacterial 16S rRNA gene fragments further indicated a host-related effect since the two detritivores differed in terms of predominant bacterial taxa: diplopods harboured mainly representatives of the phyla Bacteroidetes and Gammaproteobacteria. In contrast, the genus Vibrio was found for the amphipod host across all feeding conditions.}, }
@article {pmid22614100, year = {2012}, author = {Perumbakkam, S and Craig, AM}, title = {Biochemical and microbial analysis of ovine rumen fluid incubated with 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX).}, journal = {Current microbiology}, volume = {65}, number = {2}, pages = {195-201}, pmid = {22614100}, issn = {1432-0991}, mesh = {Animals ; Bacteroidetes/classification/isolation &amp; purification/*metabolism ; *Biota ; Biotransformation ; Gastric Juice/*microbiology ; Gram-Positive Bacteria/classification/isolation &amp; purification/metabolism ; Rumen/*microbiology ; Sheep ; Time Factors ; Triazines/*metabolism ; }, abstract = {In this study, the rumen was assessed for its potential to detoxify RDX using molecular microbial ecology as well as analytical chemistry techniques. Results indicated significant loss (P < 0.05) of RDX in <8-h post incubation, and qualitative LC-MS/MS analysis showed evidence for the formation of 1-NO-RDX (M-O + HCOO) and methylenedinitramine metabolites. A total of 1106 16S rRNA-V3 clones were sequenced, and most sequences associated with either the phyla Bacteroidetes or Firmicutes. A LibCompare analysis for the RDX treatment showed an enrichment (P < 0.01) of the genus Prevotella. From these results, it can be concluded that the rumen is capable of detoxifying RDX, and the members of the genus Prevotella are linked to this detoxification.}, }
@article {pmid22611550, year = {2012}, author = {Karlsson, AE and Johansson, T and Bengtson, P}, title = {Archaeal abundance in relation to root and fungal exudation rates.}, journal = {FEMS microbiology ecology}, volume = {80}, number = {2}, pages = {305-311}, doi = {10.1111/j.1574-6941.2012.01298.x}, pmid = {22611550}, issn = {1574-6941}, mesh = {Archaea/classification/genetics/*growth &amp; development ; Bacteria/classification/genetics ; Biodiversity ; DNA, Archaeal ; DNA, Bacterial/genetics ; Exudates and Transudates/metabolism ; Fungi/*physiology ; Molecular Sequence Data ; Phylogeny ; Picea/microbiology ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; Trees/microbiology ; }, abstract = {Archaea are ubiquitous in forest soils, but little is known about the factors regulating their abundance and distribution. Low molecular weight organic compounds represent an important energy source for archaea in marine environments, and it is reasonable to suspect that archaeal abundance is dependent on such compounds in soils as well, represented by, for example, plant and fungal exudates. To test this hypothesis, we designed a microcosm experiment in which we grew ponderosa pine, sitka spruce, and western hemlock in forest soil. Root and mycorrhizal exudation rates were estimated in a 13C pulse-chase experiment, and the number of archaeal and bacterial 16S rRNA genes was determined by qPCR. Archaeal abundance differed among plant species, and the number of archaeal 16S rRNA genes was generally lower in soil receiving high concentration of exudates. The mycorrhizal fungi of ponderosa pine seemed to favor archaea, while no such effect was found for mycorrhized sitka spruce or western hemlock. The low abundance of archaea in the proximity of roots and mycorrhiza may be a result of slow growth rates and poor competitive ability of archaea vs. bacteria and does not necessarily reflect a lack of heterotrophic abilities of the archaeal community.}, }
@article {pmid22611351, year = {2012}, author = {Tong, J and Trapido-Rosenthal, H and Wang, J and Wang, Y and Li, QX and Lu, Y}, title = {Antiviral activities and putative identification of compounds in microbial extracts from the Hawaiian coastal waters.}, journal = {Marine drugs}, volume = {10}, number = {3}, pages = {521-538}, pmid = {22611351}, issn = {1660-3397}, support = {P50 ES012740/ES/NIEHS NIH HHS/United States ; P50ES012740/ES/NIEHS NIH HHS/United States ; P20 MD006084/MD/NIMHD NIH HHS/United States ; G12RR003061/RR/NCRR NIH HHS/United States ; G12 RR003061/RR/NCRR NIH HHS/United States ; }, mesh = {Analysis of Variance ; Animals ; Antiviral Agents/chemistry/*pharmacology ; Aquatic Organisms ; Bacteria/chemistry ; Cell Survival/drug effects ; Chlorocebus aethiops ; Chromatography, Gas ; Hawaii ; Herpesvirus 1, Human/drug effects ; Humans ; Mass Spectrometry ; Pacific Ocean ; Porifera/chemistry ; Seawater/*microbiology ; Vero Cells ; Viral Plaque Assay ; Virus Replication/drug effects ; }, abstract = {Marine environments are a rich source of significant bioactive compounds. The Hawaiian archipelago, located in the middle of the Pacific Ocean, hosts diverse microorganisms, including many endemic species. Thirty-eight microbial extracts from Hawaiian coastal waters were evaluated for their antiviral activity against four mammalian viruses including herpes simplex virus type one (HSV-1), vesicular stomatitis virus (VSV), vaccinia virus and poliovirus type one (poliovirus-1) using in vitro cell culture assay. Nine of the 38 microbial crude extracts showed antiviral potencies and three of these nine microbial extracts exhibited significant activity against the enveloped viruses. A secosteroid, 5α(H),17α(H),(20R)-beta-acetoxyergost-8(14)-ene was putatively identified and confirmed to be the active compound in these marine microbial extracts. These results warrant future in-depth tests on the isolation of these active elements in order to explore and validate their antiviral potential as important therapeutic remedies.}, }
@article {pmid22595093, year = {2012}, author = {Whang, LM and Wu, YJ and Lee, YC and Chen, HW and Fukushima, T and Chang, MY and Cheng, SS and Hsu, SF and Chang, CH and Shen, W and Huang, CK and Fu, R and Chang, B}, title = {Nitrification performance and microbial ecology of nitrifying bacteria in a full-scale membrane bioreactor treating TFT-LCD wastewater.}, journal = {Bioresource technology}, volume = {122}, number = {}, pages = {70-77}, doi = {10.1016/j.biortech.2012.04.092}, pmid = {22595093}, issn = {1873-2976}, mesh = {Aerobiosis ; Bacteria/*metabolism ; Biodegradation, Environmental ; Biological Oxygen Demand Analysis ; Bioreactors/*microbiology ; Liquid Crystals/*microbiology ; *Membranes, Artificial ; Nitrates/analysis ; *Nitrification ; Nitrogen/analysis ; Oxidation-Reduction ; Polymorphism, Restriction Fragment Length ; Quaternary Ammonium Compounds/analysis ; Real-Time Polymerase Chain Reaction ; Sewage/microbiology ; Transistors, Electronic/*microbiology ; Waste Disposal, Fluid ; Wastewater/microbiology ; Water Purification/*instrumentation ; }, abstract = {This study investigated nitrification performance and nitrifying community in one full-scale membrane bioreactor (MBR) treating TFT-LCD wastewater. For the A/O MBR system treating monoethanolamine (MEA) and dimethyl sulfoxide (DMSO), no nitrification was observed, due presumably to high organic loading, high colloidal COD, low DO, and low hydraulic retention time (HRT) conditions. By including additional A/O or O/A tanks, the A/O/A/O MBR and the O/A/O MBR were able to perform successful nitrification. The real-time PCR results for quantification of nitrifying populations showed a high correlation to nitrification performance, and can be a good indicator of stable nitrification. Terminal restriction fragment length polymorphism (T-RFLP) results of functional gene, amoA, suggest that Nitrosomonas oligotropha-like AOB seemed to be important to a good nitrification in the MBR system. In the MBR system, Nitrobacter- and Nitrospira-like NOB were both abundant, but the low nitrite environment is likely to promote the growth of Nitrospira-like NOB.}, }
@article {pmid22587947, year = {2012}, author = {Thomas, T and Gilbert, J and Meyer, F}, title = {Metagenomics - a guide from sampling to data analysis.}, journal = {Microbial informatics and experimentation}, volume = {2}, number = {1}, pages = {3}, pmid = {22587947}, issn = {2042-5783}, abstract = {Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content of entire communities of organisms. The field of metagenomics has been responsible for substantial advances in microbial ecology, evolution, and diversity over the past 5 to 10 years, and many research laboratories are actively engaged in it now. With the growing numbers of activities also comes a plethora of methodological knowledge and expertise that should guide future developments in the field. This review summarizes the current opinions in metagenomics, and provides practical guidance and advice on sample processing, sequencing technology, assembly, binning, annotation, experimental design, statistical analysis, data storage, and data sharing. As more metagenomic datasets are generated, the availability of standardized procedures and shared data storage and analysis becomes increasingly important to ensure that output of individual projects can be assessed and compared.}, }
@article {pmid22584298, year = {2012}, author = {Puglisi, E and Vasileiadis, S and Demiris, K and Bassi, D and Karpouzas, DG and Capri, E and Cocconcelli, PS and Trevisan, M}, title = {Impact of fungicides on the diversity and function of non-target ammonia-oxidizing microorganisms residing in a litter soil cover.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {692-701}, pmid = {22584298}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Antifungal Agents/*pharmacology ; Archaea/*drug effects/genetics/growth &amp; development/metabolism ; Betaproteobacteria/*drug effects/genetics/growth &amp; development/metabolism ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; Ecosystem ; Nitrification ; Nitrogen Cycle ; Oxidation-Reduction ; Polymerase Chain Reaction/methods ; Pyrimidines/*pharmacology ; RNA, Archaeal/chemistry/genetics ; RNA, Bacterial/chemistry/genetics ; Soil/analysis ; *Soil Microbiology ; Triazoles/*pharmacology ; }, abstract = {Litter soil cover constitutes an important micro-ecosystem in sustainable viticulture having a key role in nutrient cycling and serving as a habitat of complex microbial communities. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are known to regulate nitrification in soil while little is known regarding their function and diversity in litter. We investigated the effects of two fungicides, penconazole and cyprodinil, commonly used in vineyards, on the function and diversity of total and active AOB and AOA in a microcosm study. Functional changes measured via potential nitrification and structural changes assessed via denaturating gradient gel electrophoresis (DGGE) at the DNA and RNA levels were contrasted with pesticide dissipation in the litter layer. The latter was inversely correlated with potential nitrification, which was temporarily inhibited at the initial sampling dates (0 to 21 days) when nearly 100 % of the applied pesticide amounts was still present in the litter. Fungicides induced changes in AOB and AOA communities with RNA-DGGE analysis showing a higher sensitivity. AOA were more responsive to pesticide application compared to AOB. Potential nitrification was less sensitive to the fungicides and was restored faster than structural changes, which persisted. These results support the theory of microbial redundancy for nitrification in a stressed litter environment.}, }
@article {pmid22584297, year = {2012}, author = {Pratt, B and Riesen, R and Johnston, CG}, title = {PLFA analyses of microbial communities associated with PAH-contaminated riverbank sediment.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {680-691}, pmid = {22584297}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Ecosystem ; Fatty Acids/*analysis ; Geologic Sediments/*chemistry/microbiology ; Phospholipids/*analysis ; Polycyclic Aromatic Hydrocarbons/*analysis ; Rivers/*chemistry/microbiology ; Soil Pollutants/analysis ; Water Pollutants, Chemical/analysis ; }, abstract = {Sediment contaminated with polycyclic aromatic hydrocarbons (PAHs) is widely distributed in aquatic ecosystems. The microbial community structure of riverbank PAH-contaminated sediments was investigated using phospholipid-derived fatty acid (PLFA) analysis. Surface and subsurface riverbank sediment was collected from a highly contaminated site and from an uncontaminated site along the Mahoning River, OH. PAH concentrations, physical sediment characteristics, and other microbial community parameters (biomass as phospholipid phosphate (PLP) and activity) were also measured. PAHs were detected in all samples but were only quantifiable in the contaminated (250 μg/g g(-1)) subsurface sediment. Subsurface samples from both locations showed very similar PLP values and distribution of PLFAs, with 27-37 % of the microbial community structure being composed of sulfate reducing and other anaerobic bacteria. Principal components analysis indicated no correlation between PAH contamination and PLFA diversity. Although PLP and phospholipid fatty acid measurements of bacterial communities did not reflect the environmental differences among sites, the highly PAH-contaminated sediment showed the highest measured microbial activity (reduction of 1,200 nmol INT g(-1) h(-1)), likely from a population adapted to environmental pollutants, rates that are much higher than measured in many uncontaminated soil and sediment systems. These data warrant further investigation into community structure at the genetic level and indicate potential for bioremediation by indigenous microbes.}, }
@article {pmid22582069, year = {2012}, author = {Behnam, F and Vilcinskas, A and Wagner, M and Stoecker, K}, title = {A straightforward DOPE (double labeling of oligonucleotide probes)-FISH (fluorescence in situ hybridization) method for simultaneous multicolor detection of six microbial populations.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {15}, pages = {5138-5142}, pmid = {22582069}, issn = {1098-5336}, mesh = {Colony Count, Microbial/*methods ; In Situ Hybridization, Fluorescence/*methods ; Oligonucleotide Probes/*chemistry/genetics ; RNA, Ribosomal/genetics ; Species Specificity ; Staining and Labeling/*methods ; }, abstract = {Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes is an essential tool for the cultivation-independent identification of microbes within environmental and clinical samples. However, one of the major constraints of conventional FISH is the very limited number of different target organisms that can be detected simultaneously with standard epifluorescence or confocal laser scanning microscopy. Recently, this limitation has been overcome via an elegant approach termed combinatorial labeling and spectral imaging FISH (CLASI-FISH) (23). This technique, however, suffers compared to conventional FISH from an inherent loss in sensitivity and potential probe binding biases caused by the competition of two differentially labeled oligonucleotide probes for the same target site. Here we demonstrate that the application of multicolored, double-labeled oligonucleotide probes enables the simultaneous detection of up to six microbial target populations in a straightforward and robust manner with higher sensitivity and less bias. Thus, this newly developed technique should be an attractive option for all researchers interested in applying conventional FISH methods for the study of microbial communities.}, }
@article {pmid22580956, year = {2012}, author = {Guibert, LM and Loviso, CL and Marcos, MS and Commendatore, MG and Dionisi, HM and Lozada, M}, title = {Alkane biodegradation genes from chronically polluted subantarctic coastal sediments and their shifts in response to oil exposure.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {605-616}, pmid = {22580956}, issn = {1432-184X}, mesh = {Alkanes/*metabolism ; Antarctic Regions ; Biodegradation, Environmental ; Cytochrome P-450 CYP4A/*genetics ; DNA, Bacterial/genetics/metabolism ; Environmental Pollutants/*metabolism ; Gammaproteobacteria/*genetics/isolation &amp; purification/metabolism ; Geologic Sediments/*microbiology ; Hydrocarbons/metabolism ; Molecular Sequence Data ; Petroleum/*metabolism ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Although sediments are the natural hydrocarbon sink in the marine environment, the ecology of hydrocarbon-degrading bacteria in sediments is poorly understood, especially in cold regions. We studied the diversity of alkane-degrading bacterial populations and their response to oil exposure in sediments of a chronically polluted Subantarctic coastal environment, by analyzing alkane monooxygenase (alkB) gene libraries. Sequences from the sediment clone libraries were affiliated with genes described in Proteobacteria and Actinobacteria, with 67 % amino acid identity in average to sequences from isolated microorganisms. The majority of the sequences were most closely related to uncultured microorganisms from cold marine sediments or soils from high latitude regions, highlighting the role of temperature in the structuring of this bacterial guild. The distribution of alkB sequences among samples of different sites and years, and selection after experimental oil exposure allowed us to identify ecologically relevant alkB genes in Subantarctic sediments, which could be used as biomarkers for alkane biodegradation in this environment. 16 S rRNA amplicon pyrosequencing indicated the abundance of several genera for which no alkB genes have yet been described (Oleispira, Thalassospira) or that have not been previously associated with oil biodegradation (Spongiibacter-formerly Melitea-, Maribius, Robiginitomaculum, Bizionia and Gillisia). These genera constitute candidates for future work involving identification of hydrocarbon biodegradation pathway genes.}, }
@article {pmid22580367, year = {2012}, author = {Wright, JJ and Konwar, KM and Hallam, SJ}, title = {Microbial ecology of expanding oxygen minimum zones.}, journal = {Nature reviews. Microbiology}, volume = {10}, number = {6}, pages = {381-394}, pmid = {22580367}, issn = {1740-1534}, mesh = {*Biota ; *Energy Metabolism ; Greenhouse Effect ; Methane/metabolism ; Nitrous Oxide/metabolism ; Oxygen/*metabolism ; Seawater/*microbiology ; }, abstract = {Dissolved oxygen concentration is a crucial organizing principle in marine ecosystems. As oxygen levels decline, energy is increasingly diverted away from higher trophic levels into microbial metabolism, leading to loss of fixed nitrogen and to production of greenhouse gases, including nitrous oxide and methane. In this Review, we describe current efforts to explore the fundamental factors that control the ecological and microbial biodiversity in oxygen-starved regions of the ocean, termed oxygen minimum zones. We also discuss how recent advances in microbial ecology have provided information about the potential interactions in distributed co-occurrence and metabolic networks in oxygen minimum zones, and we provide new insights into coupled biogeochemical processes in the ocean.}, }
@article {pmid22578996, year = {2012}, author = {Hsieh, HH and Wang, SY and Chen, TL and Huang, YL and Chen, MJ}, title = {Effects of cow's and goat's milk as fermentation media on the microbial ecology of sugary kefir grains.}, journal = {International journal of food microbiology}, volume = {157}, number = {1}, pages = {73-81}, doi = {10.1016/j.ijfoodmicro.2012.04.014}, pmid = {22578996}, issn = {1879-3460}, mesh = {Animals ; Carbon/metabolism ; Cattle ; Cultured Milk Products/chemistry/*microbiology ; Edible Grain/metabolism ; Female ; *Fermentation ; Goats ; Lactobacillus/growth &amp; development ; Lactococcus lactis ; Leuconostoc/growth &amp; development/isolation &amp; purification ; Milk/chemistry/microbiology ; }, abstract = {In the present study, we have investigated the importance of fermentation media on grain formation and the microbial characteristics of sugary kefir. The sugary kefir grains were fermented in brown sugar, cow's milk or goat's milk. Using culture-dependent and culture-independent methods, we identified the microorganisms present in both the grains and filtrate and then evaluated their distribution. The structure of the grains was also observed by scanning electronic microscopy (SEM). The identification results indicated that there were remarkable changes in microbial ecological profiles of the sugary kefir grains and their filtrates when brown sugar and milk were compared as fermentation media. Three lactic acid bacteria (LAB) species (Leuconostoc mesenteroides, Lactobacillus mali and Lactobacillus hordei) were found in the grains fermented using brown sugar. However, four species, named Leu. mesenteroides, Lactococcus lactis, Bifidobacterium psychraerophilum and Enterococcus faecalis, were identified in the grains fermented using either cow's or goat's milk. The size and structure of the kefir grains were also significantly influenced by the culture medium. We hypothesize that the grains originally may contain many different microorganisms and the identified changes are an adaption to each specific medium during grain formation and growth. The distribution of strains thus may vary depending on the carbon and energy sources available for grain fermentation and these microbial changes will further affect the granulation and growth of the grains. This study is important to our understanding of the mechanism of kefir grain formation and growth because it explores the relationship between fermentation media and kefir microorganisms.}, }
@article {pmid22576821, year = {2012}, author = {Ghirardi, S and Dessaint, F and Mazurier, S and Corberand, T and Raaijmakers, JM and Meyer, JM and Dessaux, Y and Lemanceau, P}, title = {Identification of traits shared by rhizosphere-competent strains of fluorescent pseudomonads.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {725-737}, pmid = {22576821}, issn = {1432-184X}, mesh = {4-Butyrolactone/analogs &amp; derivatives/metabolism ; Anti-Bacterial Agents/biosynthesis ; Solanum lycopersicum/*microbiology ; Phenazines/metabolism ; Phenotype ; Plant Roots/*microbiology ; Pseudomonas/*classification/genetics/growth &amp; development/metabolism ; Pseudomonas fluorescens/*classification/genetics/growth &amp; development/metabolism ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Rhizosphere competence of fluorescent pseudomonads is a prerequisite for the expression of their beneficial effects on plant growth and health. To date, knowledge on bacterial traits involved in rhizosphere competence is fragmented and derived mostly from studies with model strains. Here, a population approach was taken by investigating a representative collection of 23 Pseudomonas species and strains from different origins for their ability to colonize the rhizosphere of tomato plants grown in natural soil. Rhizosphere competence of these strains was related to phenotypic traits including: (1) their carbon and energetic metabolism represented by the ability to use a wide range of organic compounds, as electron donors, and iron and nitrogen oxides, as electron acceptors, and (2) their ability to produce antibiotic compounds and N-acylhomoserine lactones (N-AHSL). All these data including origin of the strains (soil/rhizosphere), taxonomic identification, phenotypic cluster based on catabolic profiles, nitrogen dissimilating ability, siderovars, susceptibility to iron starvation, antibiotic and N-AHSL production, and rhizosphere competence were submitted to multiple correspondence analyses. Colonization assays revealed a significant diversity in rhizosphere competence with survival rates ranging from approximately 0.1 % to 61 %. Multiple correspondence analyses indicated that rhizosphere competence was associated with siderophore-mediated iron acquisition, substrate utilization, and denitrification. However, the catabolic profile of one rhizosphere-competent strain differed from the others and its competence was associated with its ability to produce antibiotics phenazines and N-AHSL. Taken together, these data suggest that competitive strains have developed two types of strategies to survive in the rhizosphere.}, }
@article {pmid22574130, year = {2012}, author = {Miller-Coleman, RL and Dodsworth, JA and Ross, CA and Shock, EL and Williams, AJ and Hartnett, HE and McDonald, AI and Havig, JR and Hedlund, BP}, title = {Korarchaeota diversity, biogeography, and abundance in Yellowstone and Great Basin hot springs and ecological niche modeling based on machine learning.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e35964}, pmid = {22574130}, issn = {1932-6203}, support = {P20 RR016464/RR/NCRR NIH HHS/United States ; }, mesh = {*Artificial Intelligence ; *Biodiversity ; *Ecological and Environmental Phenomena ; Ecosystem ; *Hot Springs/chemistry ; Hydrogen-Ion Concentration ; Korarchaeota/*classification/genetics ; *Phylogeography ; Temperature ; Water/chemistry ; }, abstract = {Over 100 hot spring sediment samples were collected from 28 sites in 12 areas/regions, while recording as many coincident geochemical properties as feasible (>60 analytes). PCR was used to screen samples for Korarchaeota 16S rRNA genes. Over 500 Korarchaeota 16S rRNA genes were screened by RFLP analysis and 90 were sequenced, resulting in identification of novel Korarchaeota phylotypes and exclusive geographical variants. Korarchaeota diversity was low, as in other terrestrial geothermal systems, suggesting a marine origin for Korarchaeota with subsequent niche-invasion into terrestrial systems. Korarchaeota endemism is consistent with endemism of other terrestrial thermophiles and supports the existence of dispersal barriers. Korarchaeota were found predominantly in >55°C springs at pH 4.7-8.5 at concentrations up to 6.6×10(6) 16S rRNA gene copies g(-1) wet sediment. In Yellowstone National Park (YNP), Korarchaeota were most abundant in springs with a pH range of 5.7 to 7.0. High sulfate concentrations suggest these fluids are influenced by contributions from hydrothermal vapors that may be neutralized to some extent by mixing with water from deep geothermal sources or meteoric water. In the Great Basin (GB), Korarchaeota were most abundant at spring sources of pH<7.2 with high particulate C content and high alkalinity, which are likely to be buffered by the carbonic acid system. It is therefore likely that at least two different geological mechanisms in YNP and GB springs create the neutral to mildly acidic pH that is optimal for Korarchaeota. A classification support vector machine (C-SVM) trained on single analytes, two analyte combinations, or vectors from non-metric multidimensional scaling models was able to predict springs as Korarchaeota-optimal or sub-optimal habitats with accuracies up to 95%. To our knowledge, this is the most extensive analysis of the geochemical habitat of any high-level microbial taxon and the first application of a C-SVM to microbial ecology.}, }
@article {pmid22573240, year = {2012}, author = {Stabili, L and Cardone, F and Alifano, P and Tredici, SM and Piraino, S and Corriero, G and Gaino, E}, title = {Epidemic mortality of the sponge Ircinia variabilis (Schmidt, 1862) associated to proliferation of a Vibrio bacterium.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {802-813}, pmid = {22573240}, issn = {1432-184X}, mesh = {Animals ; DNA, Bacterial/analysis ; DNA, Ribosomal/genetics ; Italy ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Phylogeny ; Porifera/*microbiology/ultrastructure ; RNA, Ribosomal, 16S/genetics ; Seawater ; Sequence Analysis, DNA ; Temperature ; Vibrio/classification/genetics/*isolation &amp; purification/*pathogenicity ; }, abstract = {In recent years, several episodes of mass mortality of sessile epibenthic invertebrates, including sponges, have been recorded worldwide. In the present study, we report a disease event on Ircinia variabilis recorded in September 2009 along the southern Adriatic and Ionian seas (Apulian coast), with the aim to quantify the mortality incidence on the sponge population, to investigate the effect of the disease on the sponge tissues and to assess whether the disease is associated with vibrios proliferation. The injured sponges showed wide necrotic areas on the surface or disruption of the body in several portions. Necrotic areas were whitish and often were covered with a thin mucous coat formed by bacteria. In the most affected specimens, sponge organisation resulted partial or complete loss, with the final exposure of the dense skeletal network of spongine fibres to the environment. The results of microbiological cultural analysis using in parallel Marine Agar 2216 and thiosulphate/citrate/bile salts/sucrose agar demonstrated that, in affected specimens, vibrios represented 15.8 % of the total I. variabilis surface culturable bacteria. Moreover, all the isolated vibrios, grown from the wide whitish areas that characterize the surface of the diseased sponges, were identified, and their assignment to the Vibrio rotiferianus was consistent with phylogenetic analysis and data of morphological, cultural and biochemical tests. Studies on V. rotiferianus have shown that its pathogenicity, with respect to various aquatic organisms, is higher than that of Vibrio harveyi. The factors triggering the disease outbreak in Ircinia variabilis populations remain unclear. At present, we can hypothesize the involvement in the disease of a synergetic mechanism that, under stressful physiological conditions (high temperature, elevated nutrients and reduced water flow), induces sponge pathogens, in our case V. rotiferanius, to become virulent, making sponges unable to control their proliferation. Additional studies are needed to understand the etiological processes as well as the factors involved in sponges recovering from this epidemic event allowing them to face mass mortality. A drastic reduction of sponge-specific representatives could have marked a negative impact on the environmental health on account of their role in the sea remediation processes as filter-feeding organisms.}, }
@article {pmid22573239, year = {2012}, author = {Maciá-Vicente, JG and Ferraro, V and Burruano, S and Lopez-Llorca, LV}, title = {Fungal assemblages associated with roots of halophytic and non-halophytic plant species vary differentially along a salinity gradient.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {668-679}, pmid = {22573239}, issn = {1432-184X}, mesh = {Ascomycota/classification/genetics/isolation &amp; purification ; Basidiomycota/classification/genetics/isolation &amp; purification ; DNA, Fungal ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; Endophytes/classification/genetics/isolation &amp; purification ; Fungi/classification/genetics/*isolation &amp; purification ; Phylogeny ; Plant Roots/*microbiology ; Plants/drug effects/*microbiology ; *Salinity ; Salt-Tolerant Plants/drug effects/growth &amp; development/*microbiology ; Sequence Analysis, DNA ; Sodium Chloride/pharmacology ; Soil/analysis ; *Soil Microbiology ; Species Specificity ; }, abstract = {Structure of fungal communities is known to be influenced by host plants and environmental conditions. However, in most cases, the dynamics of these variation patterns are poorly understood. In this work, we compared richness, diversity, and composition between assemblages of endophytic and rhizospheric fungi associated to roots of two plants with different lifestyles: the halophyte Inula crithmoides and the non-halophyte I. viscosa (syn. Dittrichia viscosa L.), along a spatially short salinity gradient. Roots and rhizospheric soil from these plants were collected at three points between a salt marsh and a sand dune, and fungi were isolated and characterized by ITS rDNA sequencing. Isolates were classified in a total of 90 operational taxonomic units (OTUs), belonging to 17 fungal orders within Ascomycota and Basidiomycota. Species composition of endophytic and soil communities significantly differed across samples. Endophyte communities of I. crithmoides and I. viscosa were only similar in the intermediate zone between the salt marsh and the dune, and while the latter displayed a single, generalist association of endophytes, I. crithmoides harbored different assemblages along the gradient, adapted to the specific soil conditions. In the lower salt marsh, root assemblages were strongly dominated by a single dark septate sterile fungus, also prevalent in other neighboring salt marshes. Interestingly, although its occurrence was positively correlated to soil salinity, in vitro assays revealed a strong inhibition of its growth by salts. Our results suggest that host lifestyle and soil characteristics have a strong effect on endophytic fungi and that environmental stress may entail tight plant-fungus relationships for adaptation to unfavorable conditions.}, }
@article {pmid22572638, year = {2012}, author = {Berry, D and Schwab, C and Milinovich, G and Reichert, J and Ben Mahfoudh, K and Decker, T and Engel, M and Hai, B and Hainzl, E and Heider, S and Kenner, L and Müller, M and Rauch, I and Strobl, B and Wagner, M and Schleper, C and Urich, T and Loy, A}, title = {Phylotype-level 16S rRNA analysis reveals new bacterial indicators of health state in acute murine colitis.}, journal = {The ISME journal}, volume = {6}, number = {11}, pages = {2091-2106}, pmid = {22572638}, issn = {1751-7370}, mesh = {Animals ; Bacteria/*classification/genetics/*isolation &amp; purification ; Colitis/chemically induced/metabolism/*microbiology ; Dextran Sulfate ; Disease Models, Animal ; Humans ; In Situ Hybridization, Fluorescence ; Inflammatory Bowel Diseases/complications/genetics/*microbiology ; Intestinal Mucosa/metabolism ; Intestines/microbiology ; *Metagenome ; Mice ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Human inflammatory bowel disease and experimental colitis models in mice are associated with shifts in intestinal microbiota composition, but it is unclear at what taxonomic/phylogenetic level such microbiota dynamics can be indicative for health or disease. Here, we report that dextran sodium sulfate (DSS)-induced colitis is accompanied by major shifts in the composition and function of the intestinal microbiota of STAT1(-/-) and wild-type mice, as determined by 454 pyrosequencing of bacterial 16S rRNA (gene) amplicons, metatranscriptomics and quantitative fluorescence in situ hybridization of selected phylotypes. The bacterial families Ruminococcaceae, Bacteroidaceae, Enterobacteriaceae, Deferribacteraceae and Verrucomicrobiaceae increased in relative abundance in DSS-treated mice. Comparative 16S rRNA sequence analysis at maximum possible phylogenetic resolution identified several indicator phylotypes for DSS treatment, including the putative mucin degraders Akkermansia and Mucispirillum. The analysis additionally revealed strongly contrasting abundance changes among phylotypes of the same family, particularly within the Lachnospiraceae. These extensive phylotype-level dynamics were hidden when reads were grouped at higher taxonomic levels. Metatranscriptomic analysis provided insights into functional shifts in the murine intestinal microbiota, with increased transcription of genes associated with regulation and cell signaling, carbohydrate metabolism and respiration and decreased transcription of flagellin genes during inflammation. These findings (i) establish the first in-depth inventory of the mouse gut microbiota and its metatranscriptome in the DSS colitis model, (ii) reveal that family-level microbial community analyses are insufficient to reveal important colitis-associated microbiota shifts and (iii) support a scenario of shifting intra-family structure and function in the phylotype-rich and phylogenetically diverse Lachnospiraceae in DSS-treated mice.}, }
@article {pmid22570120, year = {2012}, author = {Ylla, I and Romaní, AM and Sabater, S}, title = {Labile and recalcitrant organic matter utilization by river biofilm under increasing water temperature.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {593-604}, pmid = {22570120}, issn = {1432-184X}, mesh = {Biofilms/*growth &amp; development ; Carbon/*metabolism ; Cellobiose/metabolism ; Dipeptides/metabolism ; *Hot Temperature ; Humic Substances ; Organic Chemicals/*metabolism ; Oxygen Consumption ; Rivers/chemistry/*microbiology ; }, abstract = {Microbial biofilms in rivers contribute to the decomposition of the available organic matter which typically shows changes in composition and bioavailability due to their origin, seasonality, and watershed characteristics. In the context of global warming, enhanced biofilm organic matter decomposition would be expected but this effect could be specific when either a labile or a recalcitrant organic matter source would be available. A laboratory experiment was performed to mimic the effect of the predicted increase in river water temperature (+4 °C above an ambient temperature) on the microbial biofilm under differential organic matter sources. The biofilm microbial community responded to higher water temperature by increasing bacterial cell number, respiratory activity (electron transport system) and microbial extracellular enzymes (extracellular enzyme activity). At higher temperature, the phenol oxidase enzyme explained a large fraction of respiratory activity variation suggesting an enhanced microbial use of degradation products from humic substances. The decomposition of hemicellulose (β-xylosidase activity) seemed to be also favored by warmer conditions. However, at ambient temperature, the enzymes highly responsible for respiration activity variation were β-glucosidase and leu-aminopeptidase, suggesting an enhanced microbial use of polysaccharides and peptides degradation products. The addition of labile dissolved organic carbon (DOC; dipeptide plus cellobiose) caused a further augmentation of heterotrophic biomass and respiratory activity. The changes in the fluorescence index and the ratio Abs(250)/total DOC indicated that higher temperature accelerated the rates of DOC degradation. The experiment showed that the more bioavailable organic matter was rapidly cycled irrespective of higher temperature while degradation of recalcitrant substances was enhanced by warming. Thus, pulses of carbon at higher water temperature might have consequences for DOC processing.}, }
@article {pmid22570119, year = {2012}, author = {Mulec, J and Vaupotič, J and Walochnik, J}, title = {Prokaryotic and eukaryotic airborne microorganisms as tracers of microclimatic changes in the underground (Postojna Cave, Slovenia).}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {654-667}, pmid = {22570119}, issn = {1432-184X}, mesh = {*Air Microbiology ; Amoeba/classification/genetics/*isolation &amp; purification ; Bacteria/genetics/*isolation &amp; purification ; Caves/*microbiology ; *Climate Change ; Culture Media ; Fungi/genetics/*isolation &amp; purification ; *Microclimate ; Radiation Dosage ; Radiation Monitoring/methods ; Radon/analysis ; Seasons ; Slovenia ; Stem Cells ; }, abstract = {Bioaerosols in cave air can serve as natural tracers and, together with physical parameters, give a detailed view of conditions in the cave atmosphere and responses to climatic changes. Airborne microbes in the Postojna Cave system indicated very dynamic atmospheric conditions, especially in the transitory seasonal periods between winter and summer. Physical parameters of cave atmosphere explained the highest variance in structure of microbial community in the winter and in the summer. The airborne microbial community is composed of different microbial groups with generally low abundances. At sites with elevated organic input, occasional high concentrations of bacteria and fungi can be expected of up to 1,000 colony-forming units/m(3) per individual group. The most abundant group of airborne amoebozoans were the mycetozoans. Along with movements of air masses, airborne algae also travel deep underground. In a cave passage with elevated radon concentration (up to 60 kBq/m(3)) airborne biota were less abundant; however, the concentration of DNA in the air was comparable to that in other parts of the cave. Due to seasonal natural air inflow, high concentrations of biological and inanimate particles are introduced underground. Sedimentation of airborne allochthonous material might represent an important and continuous source of organic material for cave fauna.}, }
@article {pmid22570118, year = {2012}, author = {Araujo, JF and de Castro, AP and Costa, MM and Togawa, RC and Júnior, GJ and Quirino, BF and Bustamante, MM and Williamson, L and Handelsman, J and Krüger, RH}, title = {Characterization of soil bacterial assemblies in Brazilian savanna-like vegetation reveals acidobacteria dominance.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {760-770}, pmid = {22570118}, issn = {1432-184X}, mesh = {Acidobacteria/classification/*genetics/isolation &amp; purification ; Bacteria/classification/*genetics/isolation &amp; purification ; Brazil ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal Spacer/analysis/genetics ; *Ecosystem ; Molecular Sequence Data ; Poaceae ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Proteobacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; Trees ; }, abstract = {The Brazilian Cerrado is the second largest biome in Brazil and is considered a biodiversity hotspot. In this work, we compared the bacterial communities in Cerrado soil associated with four types of native vegetation (Cerrado Denso, Cerrado sensu stricto, Campo Sujo, and Mata de Galeria) by ribosomal RNA intergenic spacer analysis, terminal fragment restriction length polymorphism and pyrosequencing. The fingerprinting results were very similar. The bacterial communities of Cerrado Denso and Cerrado sensu stricto grouped together and were distinct from those in Campo Sujo and Mata de Galeria. Pyrosequencing generated approximately 40,000 16S rRNA gene sequences per sample and allowed the identification of 17 phyla in soil samples under Cerrado vegetation. Acidobacteria were dominant in all areas studied with a relative frequency of 40-47 %, followed closely by Proteobacteria accounting for 34-40 % of the sequences. Results from all molecular techniques used suggested that the bacterial communities of Cerrado sensu stricto and Cerrado Denso are very similar to each other, while Campo Sujo forms a separate group, and Mata de Galeria is the most distinct with higher species richness. This is the first extensive study of native Cerrado soil microbiota, an important but endangered biome.}, }
@article {pmid22562107, year = {2012}, author = {Antunes, JT and Leão, PN and Vasconcelos, VM}, title = {Influence of biotic and abiotic factors on the allelopathic activity of the cyanobacterium Cylindrospermopsis raciborskii strain LEGE 99043.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {584-592}, pmid = {22562107}, issn = {1432-184X}, mesh = {*Biofilms/growth &amp; development ; *Chlorophyta/growth &amp; development/physiology ; Cyanobacteria/growth &amp; development/physiology ; *Cylindrospermopsis/growth &amp; development/physiology ; Ecosystem ; Hydrogen-Ion Concentration ; *Light ; Phosphates/metabolism ; Rivers/*chemistry/microbiology ; *Temperature ; }, abstract = {Allelopathy is considered to be one of the factors underlying the global expansion of the toxic cyanobacterium Cylindrospermopsis raciborskii. Although the production and release of allelopathic compounds by cyanobacteria is acknowledged to be influenced by environmental parameters, the response of C. raciborskii remains generally unrecognized. Here, the growth and allelopathic potential of C. raciborskii strain LEGE 99043 towards the ubiquitous microalga Ankistrodesmus falcatus were analyzed under different biotic and abiotic conditions. Filtrates from C. raciborskii cultures growing at different cell densities displayed broad inhibitory activity. Moreover, higher temperature, higher light intensity as well phosphate limitation further enhanced this activity. The distinct and comprehensive patterns of inhibition verified during the growth phase, and under the tested parameters, suggest the action of several, still unidentified allelopathic compounds. It is expectable that the observed increase in allelopathic activity can result in distinct ecological advantages to C. raciborskii.}, }
@article {pmid22562106, year = {2012}, author = {Ventura, IM and Martins, AB and Lyra, ML and Andrade, CA and Carvalho, KA and Klaczko, LB}, title = {Spiroplasma in Drosophila melanogaster populations: prevalence, male-killing, molecular identification, and no association with Wolbachia.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {794-801}, pmid = {22562106}, issn = {1432-184X}, mesh = {Animals ; Brazil ; DNA, Bacterial/genetics/isolation &amp; purification ; Drosophila melanogaster/*microbiology ; Female ; Male ; Phylogeny ; Polymerase Chain Reaction ; Prevalence ; Sex Factors ; Sex Ratio ; Species Specificity ; Spiroplasma/classification/*genetics/isolation &amp; purification/*physiology ; Symbiosis ; Wolbachia/genetics/isolation &amp; purification/*physiology ; }, abstract = {Spiroplasma endosymbionts are maternally transmitted bacteria that may kill infected sons resulting in the production of female-biased broods. The prevalence of male killers varies considerably both between and within species. Here, we evaluate the spatial and temporal status of male-killing and non-male-killing Spiroplasma infection in three Brazilian populations of Drosophila melanogaster, nearly a decade after the first occurrence report for this species. The incidence of the male-killing Spiroplasma ranged from close to 0 to 17.7 % (so far the highest estimate for a Drosophila species) with a suggestion of temporal decline in a population. We also found non-male-killing Spiroplasma coexisting in one population at lower prevalence (3-5 %), and we did not detect it in the other two. This may be taken as a suggestion of a spreading advantage conferred by the male-killing strategy. Sequencing two loci, we identified the phylogenetic position of Spiroplasma strains from the three localities, showing that all strains group closely in the poulsonii clade. Due to intensive sampling effort, we were able to test the association between Spiroplasma infections and another widespread endosymbiont, Wolbachia, whose prevalence ranged from 81.8 to 100 %. The prevalence of Wolbachia did not differ between Spiroplasma-infected and uninfected strains in our largest sample nor were the prevalences of the two endosymbionts associated across localities.}, }
@article {pmid22562105, year = {2012}, author = {Ceballos, I and Mosquera, S and Angulo, M and Mira, JJ and Argel, LE and Uribe-Velez, D and Romero-Tabarez, M and Orduz-Peralta, S and Villegas, V}, title = {Cultivable bacteria populations associated with leaves of banana and plantain plants and their antagonistic activity against Mycosphaerella fijiensis.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {641-653}, pmid = {22562105}, issn = {1432-184X}, mesh = {*Antibiosis ; Ascomycota/growth &amp; development/*pathogenicity ; Bacillus/classification/genetics/*growth &amp; development/*isolation &amp; purification ; Bacteria/classification/genetics/growth &amp; development/isolation &amp; purification ; Colony Count, Microbial ; Culture Media ; DNA, Bacterial/analysis/genetics ; Musa/*microbiology ; Plant Diseases/microbiology ; Plant Leaves/*microbiology ; Plantago/*microbiology ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; Spores, Bacterial/growth &amp; development ; }, abstract = {Mycosphaerella fijiensis is the etiological agent of Black Sigatoka, a fungal disease that affects production of banana and plantain crops in tropical regions. The sizes of cultivable epiphytic and endophytic bacterial populations, aerobic endospore forming bacteria (AEFB), and antagonist bacteria against M. fijiensis isolated from three Musa spp. cultivars from Urabá (Colombia) were studied, in order to find a suitable screening strategy to isolate antagonistic bacteria. Most of the variability found in the epiphytic and endophytic bacterial community sizes among fruit trees was explained by the cultivar differences. We found population sizes ranging from 1.25 × 10(3) to 9.64 × 10(5) CFU/g of fresh leaf and found that 44 % of total cultivable bacteria belong to the AEFB group. We isolated 648 AEFB from three different cultivars and assessed their antagonistic activity against M. fijiensis using the cell-free supernatant obtained from bacterial liquid cultures in three different in vitro assays. Five percent of those bacteria showed higher percent inhibition than the positive control Bacillus subtilis UA321 has (percent inhibition = 84 ± 5) in the screening phase. Therefore, they were selected as antagonistic bacteria against the pathogen. The strains with the highest percentage of antagonism were found in older leaves for the three cultivars, given support to recommend this group of leaves for future samplings. Some of these isolated bacteria affected the mycelium and ascospores morphology of the fungus. They also presented in vitro characteristics related to a successful colonization of the phylloplane such as indolic compounds, surfactant production, and biofilm formation, which makes them possible, potential candidates as biological control agents.}, }
@article {pmid22559069, year = {2012}, author = {Mazzola, M and Manici, LM}, title = {Apple replant disease: role of microbial ecology in cause and control.}, journal = {Annual review of phytopathology}, volume = {50}, number = {}, pages = {45-65}, doi = {10.1146/annurev-phyto-081211-173005}, pmid = {22559069}, issn = {1545-2107}, mesh = {Agriculture/methods ; Ecology ; Fumigation ; Malus/*microbiology/*parasitology ; Plant Diseases/microbiology/parasitology/*prevention &amp; control ; Soil ; *Soil Microbiology ; Trees ; }, abstract = {Replant disease of apple is common to all major apple growing regions of the world. Difficulties in defining disease etiology, which can be exacerbated by abiotic factors, have limited progress toward developing alternatives to soil fumigation for disease control. However, the preponderance of data derived from studies of orchard soil biology employing multidisciplinary approaches has defined a complex of pathogens/parasites as causal agents of the disease. Approaches to manipulate microbial resources endemic to the orchard soil system have been proposed to induce a state of general soil suppressiveness to replant disease. Such a long-term strategy may benefit the existing orchard through extending the period of economic viability and reduce overall disease pressure to which young trees are exposed during establishment of successive plantings on the site. Alternatively, more near-term methods have been devised to achieve specific quantitative and qualitative changes in soil biology during the period of orchard renovation that may lead to effective disease suppression.}, }
@article {pmid22558795, year = {2012}, author = {Zekker, I and Vlaeminck, SE and Bagchi, S and Courtens, E and De Clippeleir, H and Kerckhof, FM and Boon, N}, title = {Selecting nitrifying inocula on different ammonium concentrations.}, journal = {Communications in agricultural and applied biological sciences}, volume = {77}, number = {1}, pages = {275-279}, pmid = {22558795}, issn = {1379-1176}, mesh = {Bacteria/*classification/*metabolism ; Biomass ; Bioreactors/microbiology ; Dose-Response Relationship, Drug ; Quaternary Ammonium Compounds/*metabolism ; Waste Disposal, Fluid/methods ; Water Pollutants, Chemical/*metabolism ; }, }
@article {pmid22558780, year = {2012}, author = {Geirnaert, A and Debruyne, B and Eeckhaut, V and Van Immerseel, F and Boon, N and Van de Wiele, T}, title = {In vitro evaluation of the upper gastrointestinal passage of a novel butyrate producing isolate to counterbalance dysbiosis in inflammatory bowel disease.}, journal = {Communications in agricultural and applied biological sciences}, volume = {77}, number = {1}, pages = {195-199}, pmid = {22558780}, issn = {1379-1176}, mesh = {Animals ; Butyrates/*metabolism ; Gastrointestinal Tract/*physiology ; Gram-Positive Endospore-Forming Rods/*physiology ; Humans ; Hydrogen-Ion Concentration ; Inflammatory Bowel Diseases/*therapy ; Oxygen/chemistry/pharmacology ; Probiotics/*therapeutic use ; Time Factors ; }, }
@article {pmid22558777, year = {2012}, author = {Courtens, E and De Clippeleir, H and Berckmoes, K and Verstraete, W and Boon, N and Vlaeminck, SE}, title = {Simple strategies to control the oxygen budget of an OLAND rotating biological contactor.}, journal = {Communications in agricultural and applied biological sciences}, volume = {77}, number = {1}, pages = {177-181}, pmid = {22558777}, issn = {1379-1176}, mesh = {*Bioreactors ; Nitrates/chemistry/metabolism ; Nitrogen/chemistry/metabolism ; Oxygen/*metabolism ; Quaternary Ammonium Compounds/*chemistry/*metabolism ; Time Factors ; Waste Disposal, Fluid/methods ; Water Pollutants, Chemical/chemistry/metabolism ; }, }
@article {pmid22558776, year = {2012}, author = {Callewaert, C and Kerckhof, FM and Granitsiotis, M and Van de Wiele, T and Boon, N}, title = {The bacterial fingerprint of the armpit and its variation in time.}, journal = {Communications in agricultural and applied biological sciences}, volume = {77}, number = {1}, pages = {171-175}, pmid = {22558776}, issn = {1379-1176}, mesh = {Adult ; Axilla/*microbiology ; Bacteria/*classification/*genetics ; *DNA Fingerprinting ; Female ; Humans ; Male ; Skin/*microbiology ; Time Factors ; }, }
@article {pmid22558774, year = {2012}, author = {De Clippeleir, H and Courtens, E and Vlaeminck, SE and Boon, N and Verstraete, W}, title = {A high-rate ammonia gas biofilter based on partial nitritation/anammox removes total nitrogen at high efficiency.}, journal = {Communications in agricultural and applied biological sciences}, volume = {77}, number = {1}, pages = {157-161}, pmid = {22558774}, issn = {1379-1176}, mesh = {Air Pollutants/chemistry ; Ammonia/*chemistry ; Biodegradation, Environmental ; Bioreactors ; Filtration/*methods ; Gases/*chemistry ; Nitrates/*chemistry ; Nitrites/*chemistry ; Nitrogen/*chemistry ; Time Factors ; }, }
@article {pmid22558772, year = {2012}, author = {Zamalloa, C and Boon, N and Verstraete, W}, title = {Combination of chemical biological flocculation and microalgae biofilm growth for decentralized sewage treatment.}, journal = {Communications in agricultural and applied biological sciences}, volume = {77}, number = {1}, pages = {145-149}, pmid = {22558772}, issn = {1379-1176}, mesh = {*Biofilms ; Bioreactors ; Flocculation ; Microalgae/*metabolism ; Sewage/*chemistry ; Waste Disposal, Fluid/*methods ; Water Pollutants, Chemical ; }, }
@article {pmid22558754, year = {2012}, author = {Geirnaert, A and Debruyne, B and Eeckhaut, V and Van Immerseel, F and Booni, N and Van de Wiele, T}, title = {In vitro evaluation of the upper gastrointestinal passage of a novel butyrate producing isolate to counterbalance dysbiosis in inflammatory bowel disease.}, journal = {Communications in agricultural and applied biological sciences}, volume = {77}, number = {1}, pages = {45-49}, pmid = {22558754}, issn = {1379-1176}, mesh = {Bacteriological Techniques ; Butyrates/*metabolism ; Gram-Positive Endospore-Forming Rods/*metabolism ; Humans ; Hydrogen-Ion Concentration ; Inflammatory Bowel Diseases/*microbiology ; Oxygen ; Probiotics ; Time Factors ; }, }
@article {pmid22554901, year = {2012}, author = {Cernat, RC and Scott, KP}, title = {Evaluation of novel assays to assess the influence of different iron sources on the growth of Clostridium difficile.}, journal = {Anaerobe}, volume = {18}, number = {3}, pages = {298-304}, doi = {10.1016/j.anaerobe.2012.04.007}, pmid = {22554901}, issn = {1095-8274}, mesh = {2,2'-Dipyridyl/pharmacology ; Anti-Bacterial Agents/pharmacology ; Clostridioides difficile/drug effects/*growth &amp; development/metabolism ; Culture Media ; Culture Techniques ; Ferrous Compounds/*metabolism ; Iron Chelating Agents/pharmacology ; Iron-Binding Proteins/*metabolism ; Microbial Sensitivity Tests ; }, abstract = {The ability of four Clostridium difficile strains to utilize various exogenous organic and inorganic iron sources for growth under iron-depleted (250 μM DPP) and iron-limited (75 μM DPP) conditions was analyzed in liquid broth cultures grown in tubes and in microtiter plates, and data compared with results from a bioassay developed on solid media. The growth profile of C. difficile varied depending on the iron source and availability. Addition of FeSO(4), FeCl(3), Fe citrate and ferritin allowed growth in an iron-depleted environment whereas glycoproteins (iron-saturated and low-iron lactoferrin, apo- and holo-transferrin) and heme proteins (hemoglobin, hematin and hemin) did not. All iron sources, except lactoferrin, were able to restore bacterial growth under iron-limited conditions to varying extents. The results demonstrated that the broth microtiter assay developed here was reproducible, reliable and convenient for high-throughput analysis of the growth of C. difficile compared to alternative traditional methods.}, }
@article {pmid22546962, year = {2012}, author = {Hulcr, J and Rountree, NR and Diamond, SE and Stelinski, LL and Fierer, N and Dunn, RR}, title = {Mycangia of ambrosia beetles host communities of bacteria.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {784-793}, pmid = {22546962}, issn = {1432-184X}, mesh = {Ambrosia ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Coleoptera/classification/*microbiology/*ultrastructure ; DNA, Bacterial/analysis ; DNA, Ribosomal ; Ecosystem ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; }, abstract = {The research field of animal and plant symbioses is advancing from studying interactions between two species to whole communities of associates. High-throughput sequencing of microbial communities supports multiplexed sampling for statistically robust tests of hypotheses about symbiotic associations. We focus on ambrosia beetles, the increasingly damaging insects primarily associated with fungal symbionts, which have also been reported to support bacteria. To analyze the diversity, composition, and specificity of the beetles' prokaryotic associates, we combine global sampling, insect anatomy, 454 sequencing of bacterial rDNA, and multivariate statistics to analyze prokaryotic communities in ambrosia beetle mycangia, organs mostly known for transporting symbiotic fungi. We analyze six beetle species that represent three types of mycangia and include several globally distributed species, some with major economic importance (Dendroctonus frontalis, Xyleborus affinis, Xyleborus bispinatus-ferrugineus, Xyleborus glabratus, Xylosandrus crassiusculus, and Xylosandrus germanus). Ninety-six beetle mycangia yielded 1,546 bacterial phylotypes. Several phylotypes appear to form the core microbiome of the mycangium. Three Mycoplasma (originally thought restricted to vertebrates), two Burkholderiales, and two Pseudomonadales are repeatedly present worldwide in multiple beetle species. However, no bacterial phylotypes were universally present, suggesting that ambrosia beetles are not obligately dependent on bacterial symbionts. The composition of bacterial communities is structured by the host beetle species more than by the locality of origin, which suggests that more bacteria are vertically transmitted than acquired from the environment. The invasive X. glabratus and the globally distributed X. crassiusculus have unique sets of bacteria, different from species native to North America. We conclude that the mycangium hosts in multiple vertically transmitted bacteria such as Mycoplasma, most of which are likely facultative commensals or parasites.}, }
@article {pmid22545126, year = {2012}, author = {Bodilis, J and Nsigue-Meilo, S and Besaury, L and Quillet, L}, title = {Variable copy number, intra-genomic heterogeneities and lateral transfers of the 16S rRNA gene in Pseudomonas.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e35647}, pmid = {22545126}, issn = {1932-6203}, mesh = {Gene Dosage ; Genes, Bacterial ; Genes, rRNA ; Genetic Heterogeneity ; Phylogeny ; Pseudomonas/*genetics ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; rRNA Operon ; }, abstract = {Even though the 16S rRNA gene is the most commonly used taxonomic marker in microbial ecology, its poor resolution is still not fully understood at the intra-genus level. In this work, the number of rRNA gene operons, intra-genomic heterogeneities and lateral transfers were investigated at a fine-scale resolution, throughout the Pseudomonas genus. In addition to nineteen sequenced Pseudomonas strains, we determined the 16S rRNA copy number in four other Pseudomonas strains by Southern hybridization and Pulsed-Field Gel Electrophoresis, and studied the intra-genomic heterogeneities by Denaturing Gradient Gel Electrophoresis and sequencing. Although the variable copy number (from four to seven) seems to be correlated with the evolutionary distance, some close strains in the P. fluorescens lineage showed a different number of 16S rRNA genes, whereas all the strains in the P. aeruginosa lineage displayed the same number of genes (four copies). Further study of the intra-genomic heterogeneities revealed that most of the Pseudomonas strains (15 out of 19 strains) had at least two different 16S rRNA alleles. A great difference (5 or 19 nucleotides, essentially grouped near the V1 hypervariable region) was observed only in two sequenced strains. In one of our strains studied (MFY30 strain), we found a difference of 12 nucleotides (grouped in the V3 hypervariable region) between copies of the 16S rRNA gene. Finally, occurrence of partial lateral transfers of the 16S rRNA gene was further investigated in 1803 full-length sequences of Pseudomonas available in the databases. Remarkably, we found that the two most variable regions (the V1 and V3 hypervariable regions) had probably been laterally transferred from another evolutionary distant Pseudomonas strain for at least 48.3 and 41.6% of the 16S rRNA sequences, respectively. In conclusion, we strongly recommend removing these regions of the 16S rRNA gene during the intra-genus diversity studies.}, }
@article {pmid22544346, year = {2012}, author = {Chauhan, A and Pathak, A and Ogram, A}, title = {Composition of methane-oxidizing bacterial communities as a function of nutrient loading in the Florida everglades.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {750-759}, pmid = {22544346}, issn = {1432-184X}, mesh = {*Ecosystem ; Florida ; Methane/*metabolism ; Methylococcaceae/classification/*genetics/growth &amp; development ; Methylocystaceae/classification/*genetics/growth &amp; development ; Molecular Sequence Data ; Oxygenases/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; *Wetlands ; }, abstract = {Agricultural runoff of phosphorus (P) in the northern Florida Everglades has resulted in several ecosystem level changes, including shifts in the microbial ecology of carbon cycling, with significantly higher methane being produced in the nutrient-enriched soils. Little is, however, known of the structure and activities of methane-oxidizing bacteria (MOB) in these environments. To address this, 0 to 10 cm plant-associated soil cores were collected from nutrient-impacted (F1), transition (F4), and unimpacted (U3) areas, sectioned in 2-cm increments, and methane oxidation rates were measured. F1 soils consumed approximately two-fold higher methane than U3 soils; additionally, most probable numbers of methanotrophs were 4-log higher in F1 than U3 soils. Metabolically active MOB containing pmoA sequences were characterized by stable-isotope probing using 10 % (v/v) (13)CH(4). pmoA sequences, encoding the alpha subunit of methane monooxygenase and related to type I methanotrophs, were identified from both impacted and unimpacted soils. Additionally, impacted soils also harbored type II methanotrophs, which have been shown to exhibit preferences for high methane concentrations. Additionally, across all soils, novel pmoA-type sequences were also detected, indicating presence of MOB specific to the Everglades. Multivariate statistical analyses confirmed that eutrophic soils consisted of metabolically distinct MOB community that is likely driven by nutrient enrichment. This study enhances our understanding on the biological fate of methane being produced in productive wetland soils of the Florida Everglades and how nutrient-enrichment affects the composition of methanotroph bacterial communities.}, }
@article {pmid22544345, year = {2012}, author = {Vokou, D and Vareli, K and Zarali, E and Karamanoli, K and Constantinidou, HI and Monokrousos, N and Halley, JM and Sainis, I}, title = {Exploring biodiversity in the bacterial community of the Mediterranean phyllosphere and its relationship with airborne bacteria.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {714-724}, pmid = {22544345}, issn = {1432-184X}, mesh = {*Air Microbiology ; Bacteria/classification/*genetics/growth &amp; development/isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/analysis/genetics ; *Ecosystem ; Greece ; Magnoliopsida/classification/*microbiology ; Molecular Sequence Data ; Plant Leaves/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; }, abstract = {We studied the structure and diversity of the phyllosphere bacterial community of a Mediterranean ecosystem, in summer, the most stressful season in this environment. To this aim, we selected nine dominant perennial species, namely Arbutus unedo, Cistus incanus, Lavandula stoechas, Myrtus communis, Phillyrea latifolia, Pistacia lentiscus, Quercus coccifera (woody), Calamintha nepeta, and Melissa officinalis (herbaceous). We also examined the extent to which airborne bacteria resemble the epiphytic ones. Genotype composition of the leaf and airborne bacteria was analysed by using denaturing gradient gel electrophoresis profiling of a 16S rDNA gene fragment; 75 bands were cloned and sequenced corresponding to 28 taxa. Of these, two were found both in the air and the phyllosphere, eight only in the air, and the remaining 18 only in the phyllosphere. Only four taxa were found on leaves of all nine plant species. Cluster analysis showed highest similarity for the five evergreen sclerophyllous species. Aromatic plants were not grouped all together: the representatives of Lamiaceae, bearing both glandular and non-glandular trichomes, formed a separate group, whereas the aromatic and evergreen sclerophyllous M. communis was grouped with the other species of the same habit. The epiphytic communities that were the richest in bacterial taxa were those of C. nepeta and M. officinalis (Lamiaceae). Our results highlight the remarkable presence of lactic acid bacteria in the phyllosphere under the harsh conditions of the Mediterranean summer, the profound dissimilarity in the structure of bacterial communities in phyllosphere and air, and the remarkable differences of leaf microbial communities on neighbouring plants subjected to similar microbial inocula; they also point to the importance of the leaf glandular trichome in determining colonization patterns.}, }
@article {pmid22538976, year = {2012}, author = {Corrigan, A and Horgan, K and Clipson, N and Murphy, RA}, title = {Effect of dietary prebiotic (mannan oligosaccharide) supplementation on the caecal bacterial community structure of turkeys.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {826-836}, pmid = {22538976}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/drug effects/*genetics ; Cecum/drug effects/*microbiology ; DNA, Ribosomal Spacer/analysis ; *Dietary Supplements ; Ecosystem ; Mannans/pharmacology ; Molecular Sequence Data ; Oligosaccharides/chemistry/*pharmacology ; Phylogeny ; *Prebiotics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Sequence Analysis, DNA ; Turkeys/*microbiology ; }, abstract = {The identification of specific bacterial species influenced by mannan oligosaccharide (MOS) supplementation may assist in the formulation of new and improved diets that promote intestinal health and improve bird performance, offering suitable alternatives to antimicrobials in feed for sustainable poultry production. This study has been conducted to evaluate the use of a MOS compound derived from the yeast cell wall of Saccharomyces cerevisiae on turkey performance, bacterial community structure and their phylogenetic associations. A 42-day turkey trial was carried out on birds fed control and MOS-supplemented diets. Bird performance data (weight gains, feed consumption and feed efficiency ratios) were collected, and caecal contents were extracted from randomly caught poults on days 28, 35 and 42 posthatch. Bird performance data showed no improvements as a result of dietary supplementation. Automated ribosomal intergenic spacer analysis (ARISA) revealed the bacterial community structure to be significantly altered on days 28 and 35 posthatch but not day 42 as a result of dietary supplementation. This technique was coupled with 16S rRNA gene sequence analysis to elucidate phylogenetic identities of bacteria. The dominant bacteria of the caecum on all days in both treatment groups were members of phylum Firmicutes, followed by the Bacteroidetes and Proteobacteria phyla, respectively. Statistical analysis of the 16S rRNA gene libraries showed that the composition of the MOS clone library differed significantly to the control on day 35 posthatch. It can be concluded that MOS alters the bacterial community structure in the turkey caecum.}, }
@article {pmid22538644, year = {2012}, author = {Lee, JH and Yi, H and Jeon, YS and Won, S and Chun, J}, title = {TBC: a clustering algorithm based on prokaryotic taxonomy.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {50}, number = {2}, pages = {181-185}, pmid = {22538644}, issn = {1976-3794}, mesh = {*Algorithms ; Bacteria/chemistry/*classification/genetics ; Phylogeny ; Prokaryotic Cells/chemistry/*classification ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; }, abstract = {High-throughput DNA sequencing technologies have revolutionized the study of microbial ecology. Massive sequencing of PCR amplicons of the 16S rRNA gene has been widely used to understand the microbial community structure of a variety of environmental samples. The resulting sequencing reads are clustered into operational taxonomic units that are then used to calculate various statistical indices that represent the degree of species diversity in a given sample. Several algorithms have been developed to perform this task, but they tend to produce different outcomes. Herein, we propose a novel sequence clustering algorithm, namely Taxonomy-Based Clustering (TBC). This algorithm incorporates the basic concept of prokaryotic taxonomy in which only comparisons to the type strain are made and used to form species while omitting full-scale multiple sequence alignment. The clustering quality of the proposed method was compared with those of MOTHUR, BLASTClust, ESPRIT-Tree, CD-HIT, and UCLUST. A comprehensive comparison using three different experimental datasets produced by pyrosequencing demonstrated that the clustering obtained using TBC is comparable to those obtained using MOTHUR and ESPRIT-Tree and is computationally efficient. The program was written in JAVA and is available from http://sw.ezbiocloud.net/tbc.}, }
@article {pmid22537844, year = {2012}, author = {Van Nevel, S and Hennebel, T and De Beuf, K and Du Laing, G and Verstraete, W and Boon, N}, title = {Transparent exopolymer particle removal in different drinking water production centers.}, journal = {Water research}, volume = {46}, number = {11}, pages = {3603-3611}, doi = {10.1016/j.watres.2012.04.002}, pmid = {22537844}, issn = {1879-2448}, mesh = {Belgium ; Biological Oxygen Demand Analysis ; Biopolymers/chemistry/*isolation &amp; purification ; Colloids ; *Drinking Water ; Filtration/methods ; Groundwater ; Polysaccharides/chemistry/isolation &amp; purification ; Water Purification/*methods ; Water Quality ; }, abstract = {Transparent exopolymer particles (TEP) have recently gained interest in relation to membrane fouling. These sticky, gel-like particles consist of acidic polysaccharides excreted by bacteria and algae. The concentrations, expressed as xanthan gum equivalents L[-1] (μg X(eq) L[-1]), usually reach hundred up to thousands μg X(eq) L[-1] in natural waters. However, very few research was performed on the occurrence and fate of TEP in drinking water, this far. This study examined three different drinking water production centers, taking in effluent of a sewage treatment plant (STP), surface water and groundwater, respectively. Each treatment step was evaluated on TEP removal and on 13 other chemical and biological parameters. An assessment on TEP removal efficiency of a diverse range of water treatment methods and on correlations between TEP and other parameters was performed. Significant correlations between particulate TEP (>0.4 μm) and viable cell concentrations were found, as well as between colloidal TEP (0.05-0.4 μm) and total COD, TOC, total cell or viable cell concentrations. TEP concentrations were very dependent on the raw water source; no TEP was detected in groundwater but the STP effluent contained 1572 μg X(eq) L[-1] and the surface water 699 μg X(eq) L[-1]. Over 94% of total TEP in both plants was colloidal TEP, a fraction neglected in nearly every other TEP study. The combination of coagulation and sand filtration was effective to decrease the TEP levels by 67%, while the combination of ultrafiltration and reverse osmosis provided a total TEP removal. Finally, in none of the installations TEP reached the final drinking water distribution system at significant concentrations. Overall, this study described the presence and removal of TEP in drinking water systems.}, }
@article {pmid22536201, year = {2012}, author = {Laanbroek, HJ and Keijzer, RM and Verhoeven, JT and Whigham, DF}, title = {The Distribution of Ammonia-Oxidizing Betaproteobacteria in Stands of Black Mangroves (Avicennia germinans).}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {153}, pmid = {22536201}, issn = {1664-302X}, abstract = {The distribution of species of aerobic chemolitho-autotrophic microorganisms such as ammonia-oxidizing bacteria are governed by pH, salinity, and temperature as well as the availability of oxygen, ammonium, carbon dioxide, and other inorganic elements required for growth. Impounded mangrove forests in the Indian River Lagoon, a coastal estuary on the east coast of Florida, are dominated by mangroves, especially stands of Black mangrove (Avicennia germinans) that differ in the size and density of individual plants. In March 2009, the management of one impoundment was changed to a regime of pumping estuarine water into the impoundment at critical times of the year to eliminate breeding sites for noxious insects. We collected soil samples in three different Black mangrove habitats before and after the change in management to determine the impacts of the altered hydrologic regimes on the distribution of 16s rRNA genes belonging to ammonia-oxidizing betaproteobacteria (β-AOB). We also sampled soils in an adjacent impoundment in which there had not been any hydrologic alteration. At the level of 97% mutual similarity in the 16s rRNA gene, 13 different operational taxonomic units were identified; the majority related to the lineages of Nitrosomonas marina (45% of the total clones), Nitrosomonas sp. Nm143 (23%), and Nitrosospira cluster 1 (19%). Long-term summer flooding of the impoundment in 2009, after initiation of the pumping regime, reduced the percentage of N. marina by half between 2008 and 2010 in favor of the two other major lineages and the potential ammonia-oxidizing activity decreased by an average of 73%. Higher interstitial salinities, probably due to a prolonged winter drought, had a significant effect on the composition of the β-AOB in March 2009 compared to March 2008: Nitrosomonas sp. Nm143 was replaced by Nitrosospira cluster 1 as the second most important lineage. There were small, but significant differences in the bacterial communities between the flooded and non-flooded impoundments. There were also differences in the community composition of the bacteria in the three Black mangrove habitats. N. marina was most dominant in all three habitats, but was partly replaced by Nitrosospira cluster 1 in sites dominated by sparsely distributed trees and by Nitrosomonas sp. Nm143 in sites characterized by taller, more densely distributed Black mangrove trees.}, }
@article {pmid22535662, year = {2012}, author = {Eriguchi, Y and Takashima, S and Oka, H and Shimoji, S and Nakamura, K and Uryu, H and Shimoda, S and Iwasaki, H and Shimono, N and Ayabe, T and Akashi, K and Teshima, T}, title = {Graft-versus-host disease disrupts intestinal microbial ecology by inhibiting Paneth cell production of α-defensins.}, journal = {Blood}, volume = {120}, number = {1}, pages = {223-231}, doi = {10.1182/blood-2011-12-401166}, pmid = {22535662}, issn = {1528-0020}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Translocation/immunology ; Bone Marrow Transplantation/adverse effects ; Escherichia coli/growth &amp; development ; Escherichia coli Infections/drug therapy/immunology/metabolism ; Female ; Graft vs Host Disease/*immunology/*microbiology ; Gram-Negative Bacterial Infections/drug therapy/*immunology/metabolism ; Intestines/immunology/*microbiology ; Major Histocompatibility Complex/immunology ; Mice ; Mice, Inbred C3H ; Mice, Inbred C57BL ; Paneth Cells/*immunology/metabolism/microbiology ; Severity of Illness Index ; alpha-Defensins/*metabolism ; }, abstract = {Allogeneic hematopoietic stem cell transplantation (SCT) is a curative therapy for various hematologic disorders. Graft-versus-host disease (GVHD) and infections are the major complications of SCT, and their close relationship has been suggested. In this study, we evaluated a link between 2 complications in mouse models. The intestinal microbial communities are actively regulated by Paneth cells through their secretion of antimicrobial peptides, α-defensins. We discovered that Paneth cells are targeted by GVHD, resulting in marked reduction in the expression of α-defensins, which selectively kill noncommensals, while preserving commensals. Molecular profiling of intestinal microbial communities showed loss of physiologic diversity among the microflora and the overwhelming expansion of otherwise rare bacteria Escherichia coli, which caused septicemia. These changes occurred only in mice with GVHD, independently on conditioning-induced intestinal injury, and there was a significant correlation between alteration in the intestinal microbiota and GVHD severity. Oral administration of polymyxin B inhibited outgrowth of E coli and ameliorated GVHD. These results reveal the novel mechanism responsible for shift in the gut flora from commensals toward the widespread prevalence of pathogens and the previously unrecognized association between GVHD and infection after allogeneic SCT.}, }
@article {pmid22530737, year = {2012}, author = {Wittekamp, BH and Bonten, MJ}, title = {Antibiotic prophylaxis in the era of multidrug-resistant bacteria.}, journal = {Expert opinion on investigational drugs}, volume = {21}, number = {6}, pages = {767-772}, doi = {10.1517/13543784.2012.681642}, pmid = {22530737}, issn = {1744-7658}, mesh = {Animals ; Anti-Bacterial Agents/economics/*therapeutic use ; Antibiotic Prophylaxis/economics/*methods ; Clinical Trials as Topic ; Cost-Benefit Analysis ; Decontamination/methods ; *Drug Resistance, Multiple, Bacterial ; Gastrointestinal Tract/microbiology ; Humans ; Intensive Care Units ; Oropharynx/microbiology ; }, abstract = {The prophylactic use of antibiotics can only be justified when clinical benefits on relevant patient outcomes, such as morbidity or mortality, cost-effectiveness, and absence of immediate emergence of antibiotic resistance have been unequivocally demonstrated. In some intensive care unit (ICU) patients, antibiotic prophylaxis is used as part of selective digestive tract decontamination (SDD) and selective oropharyngeal decontamination (SOD). Recent trials in ICUs with low levels of antibiotic resistance strongly suggest that both regimens reduce the incidence of ICU-acquired infections and improve patient survival. Naturally, the unique microbial ecology of such settings reduce generalizability of results. Therefore, the routine use of SOD and SDD remains highly controversial, especially in ICUs with higher levels of antibiotic resistance. Moreover, convincing evidence is still missing on several important aspects related to efficacy and safety. Despite numerous trials, effects of SDD and SOD on antibiotic resistance during and after decolonization treatment have still been insufficiently investigated, and existing results are contradicting. Furthermore, the effects of both regimens on the non-culturable part of the intestinal flora remain unknown. Finally, cost-effectiveness has not been thoroughly investigated, and prices of the antimicrobial agents that have been used have increased dramatically in recent years. In this review, important knowledge gaps that so far prevent the widespread use of SDD and SOD will be addressed.}, }
@article {pmid22529898, year = {2012}, author = {Hannula, SE and de Boer, W and van Veen, J}, title = {A 3-year study reveals that plant growth stage, season and field site affect soil fungal communities while cultivar and GM-trait have minor effects.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e33819}, pmid = {22529898}, issn = {1932-6203}, mesh = {Biodiversity ; Biomass ; Ecosystem ; Fungi/enzymology/growth &amp; development ; *Plants, Genetically Modified ; Rhizosphere ; *Seasons ; *Soil ; *Soil Microbiology ; Solanum tuberosum/genetics/*growth &amp; development/*microbiology ; Time Factors ; }, abstract = {In this three year field study the impact of different potato (Solanum tuberosum L.) cultivars including a genetically modified (GM) amylopectin-accumulating potato line on rhizosphere fungal communities are investigated using molecular microbiological methods. The effects of growth stage of a plant, soil type and year on the rhizosphere fungi were included in this study. To compare the effects, one GM cultivar, the parental isoline, and four non-related cultivars were planted in the fields and analysed using T-RFLP on the basis of fungal phylum specific primers combined with multivariate statistical methods. Additionally, fungal biomass and some extracellular fungal enzymes (laccases, Mn-peroxidases and cellulases) were quantified in order to gain insight into the function of the fungal communities. Plant growth stage and year (and agricultural management) had the strongest effect on both diversity and function of the fungal communities while the GM-trait studied was the least explanatory factor. The impact of cultivar and soil type was intermediate. Occasional differences between cultivars, the amylopectin-accumulating potato line, and its parental variety were detected, but these differences were mostly transient in nature and detected either only in one soil, one growth stage or one year.}, }
@article {pmid22526805, year = {2012}, author = {Cretoiu, MS and Kielak, AM and Abu Al-Soud, W and Sørensen, SJ and van Elsas, JD}, title = {Mining of unexplored habitats for novel chitinases--chiA as a helper gene proxy in metagenomics.}, journal = {Applied microbiology and biotechnology}, volume = {94}, number = {5}, pages = {1347-1358}, pmid = {22526805}, issn = {1432-0614}, mesh = {Animals ; Chitinases/*genetics/isolation &amp; purification/*metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; Ecosystem ; *Environmental Microbiology ; Genes, Bacterial ; Genetic Variation ; *Metagenome ; Metagenomics/*methods ; Polygonaceae/microbiology ; Polymerase Chain Reaction ; Porifera/microbiology ; Sequence Analysis, DNA ; }, abstract = {The main objective of this study was to assess the abundance and diversity of chitin-degrading microbial communities in ten terrestrial and aquatic habitats in order to provide guidance to the subsequent exploration of such environments for novel chitinolytic enzymes. A combined protocol which encompassed (1) classical overall enzymatic assays, (2) chiA gene abundance measurement by qPCR, (3) chiA gene pyrosequencing, and (4) chiA gene-based PCR-DGGE was used. The chiA gene pyrosequencing is unprecedented, as it is the first massive parallel sequencing of this gene. The data obtained showed the existence across habitats of core bacterial communities responsible for chitin assimilation irrespective of ecosystem origin. Conversely, there were habitat-specific differences. In addition, a suite of sequences were obtained that are as yet unregistered in the chitinase database. In terms of chiA gene abundance and diversity, typical low-abundance/diversity versus high-abundance/diversity habitats was distinguished. From the combined data, we selected chitin-amended agricultural soil, the rhizosphere of the Arctic plant Oxyria digyna and the freshwater sponge Ephydatia fluviatilis as the most promising habitats for subsequent bioexploration. Thus, the screening strategy used is proposed as a guide for further metagenomics-based exploration of the selected habitats.}, }
@article {pmid22526402, year = {2012}, author = {Zhang, XY and Bao, J and Wang, GH and He, F and Xu, XY and Qi, SH}, title = {Diversity and antimicrobial activity of culturable fungi isolated from six species of the South China Sea gorgonians.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {617-627}, pmid = {22526402}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/classification/*microbiology ; Anti-Infective Agents/*metabolism/pharmacology ; *Antibiosis ; Bacteria/drug effects/*growth &amp; development ; Biodiversity ; China ; Culture Media ; DNA, Fungal/analysis/genetics ; DNA, Ribosomal Spacer/analysis/genetics ; Fungi/*classification/genetics/*growth &amp; development/isolation &amp; purification ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Oceans and Seas ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Fungi in gorgonians are now known to cause gorgonian diseases, but little attention has been paid to the nature of fungal communities associated with gorgonians. The diversity of culturable fungi associated with six species of healthy South China Sea gorgonians were investigated using a culture-dependent method followed by analysis of fungal internal transcribed spacer sequences. A total of 121 fungal isolates were recovered and identified using the Basic Local Alignment Search Tool search program. These belonged to 41 fungal species from 20 genera. Of these, 30 species and 12 genera are new reports for gorgonians, and the genera Aspergillus and Penicillium were the most diverse and common in the six gorgonian species. Comparison of the fungal communities in the six gorgonian species, together with results from previous relevant studies, indicated that different gorgonian species and the same gorgonian species living in different geographic locations had different fungal communities. The gorgonian Dichotella gemmacea harbored the most fungal species and isolates, while Echinogorgia aurantiaca had the least fungal diversity. Among the six media used for fungal isolation, potato glucose agar yielded the highest isolates (27 isolates), while glucose peptone starch agar had the best recoverability of fungal species (15 species). The antimicrobial activity of the 121 fungal isolates was tested against three marine bacteria and two marine gorgonian pathogenic fungi. A relatively high proportion (38 %) of fungal isolates displayed distinct antibacterial and antifungal activity, suggesting that the gorgonian-associated fungi may aid their hosts in protection against pathogens. This is the first report comparing the diversity of fungal communities among the South China Sea gorgonians. It contributes to our knowledge of gorgonian-associated fungi and further increases the pool of fungi available for natural bioactive product screening.}, }
@article {pmid22526401, year = {2012}, author = {Rösel, S and Allgaier, M and Grossart, HP}, title = {Long-term characterization of free-living and particle-associated bacterial communities in Lake Tiefwaren reveals distinct seasonal patterns.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {571-583}, pmid = {22526401}, issn = {1432-184X}, mesh = {Actinobacteria/classification/genetics/growth &amp; development ; Animals ; Bacteria/*classification/genetics/growth &amp; development ; Biodiversity ; Cyanobacteria/classification/genetics/growth &amp; development ; DNA, Bacterial/analysis/genetics/isolation &amp; purification ; Denaturing Gradient Gel Electrophoresis ; Ecosystem ; Germany ; Lakes/*microbiology ; Molecular Sequence Data ; Phylogeny ; Phytoplankton/classification/genetics/*microbiology ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; Zooplankton/classification/genetics/*microbiology ; }, abstract = {Seasonal changes in environmental conditions have a strong impact on microbial community structure and dynamics in aquatic habitats. To better elucidate the response of bacterial communities to environmental changes, we have measured a large variety of limnetic variables and investigated bacterial community composition (BCC) and dynamics over seven consecutive years between 2003 and 2009 in mesotrophic Lake Tiefwaren (NE Germany). We separated between free-living (FL, >0.2, <5.0 μm) and particle-associated (PA, >5.0 μm) bacteria to account for different bacterial lifestyles and to obtain a higher resolution of the microbial diversity. Changes in BCC were studied by DGGE based on PCR-amplified 16S rRNA gene fragments. Sequencing of DGGE bands revealed that ca. 70 % of all FL bacteria belonged to the Actinobacteria, whereas PA bacteria were dominated by Cyanobacteria (43 %). FL communities were generally less diverse and rather stable over time compared to their PA counterpart. Annual changes in reoccurring seasonal patterns of dominant freshwater bacteria were supported by statistical analyses, which revealed several significant correlations between DGGE profiles and various environmental variables, e.g. temperature and nutrients. Overall, FL bacteria were generally less affected by environmental changes than members of the PA fraction. Close association of PA bacteria with phytoplankton and zooplankton suggests a tight coupling of PA bacteria to organisms of higher trophic levels. Our results indicate substantial differences in bacterial lifestyle of pelagic freshwater bacteria, which are reflected by contrasting seasonal dynamics and relationships to a number of environmental variables.}, }
@article {pmid22526400, year = {2012}, author = {Erwin, PM and López-Legentil, S and Turon, X}, title = {Ultrastructure, molecular phylogenetics, and chlorophyll a content of novel cyanobacterial symbionts in temperate sponges.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {771-783}, pmid = {22526400}, issn = {1432-184X}, mesh = {Animals ; Chlorophyll/*metabolism ; Chlorophyll A ; Climate ; Cyanobacteria/*genetics/metabolism/*ultrastructure ; DNA, Ribosomal Spacer/analysis/genetics ; *Genetic Variation ; Microscopy, Electron, Transmission ; Photosynthesis ; *Phylogeny ; Porifera/classification/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; Synechococcus/classification/genetics/metabolism/ultrastructure ; }, abstract = {Marine sponges often harbor photosynthetic symbionts that may enhance host metabolism and ecological success, yet little is known about the factors that structure the diversity, specificity, and nature of these relationships. Here, we characterized the cyanobacterial symbionts in two congeneric and sympatric host sponges that exhibit distinct habitat preferences correlated with irradiance: Ircinia fasciculata (higher irradiance) and Ircinia variabilis (lower irradiance). Symbiont composition was similar among hosts and dominated by the sponge-specific cyanobacterium Synechococcus spongiarum. Phylogenetic analyses of 16S-23S rRNA internal transcribed spacer (ITS) gene sequences revealed that Mediterranean Ircinia spp. host a specific, novel symbiont clade ("M") within the S. spongiarum species complex. A second, rare cyanobacterium related to the ascidian symbiont Synechocystis trididemni was observed in low abundance in I. fasciculata and likewise corresponded to a new symbiont clade. Symbiont communities in I. fasciculata exhibited nearly twice the chlorophyll a concentrations of I. variabilis. Further, S. spongiarum clade M symbionts in I. fasciculata exhibited dense intracellular aggregations of glycogen granules, a storage product of photosynthetic carbon assimilation rarely observed in I. variabilis symbionts. In both host sponges, S. spongiarum cells were observed interacting with host archeocytes, although the lower photosynthetic activity of Cyanobacteria in I. variabilis suggests less symbiont-derived nutritional benefit. The observed differences in clade M symbionts among sponge hosts suggest that ambient irradiance conditions dictate symbiont photosynthetic activity and consequently may mediate the nature of host-symbiont relationships. In addition, the plasticity exhibited by clade M symbionts may be an adaptive attribute that allows for flexibility in host-symbiont interactions across the seasonal fluctuations in light and temperature characteristic of temperate environments.}, }
@article {pmid22504588, year = {2012}, author = {Larsen, PE and Field, D and Gilbert, JA}, title = {Predicting bacterial community assemblages using an artificial neural network approach.}, journal = {Nature methods}, volume = {9}, number = {6}, pages = {621-625}, pmid = {22504588}, issn = {1548-7105}, mesh = {Actinomycetales/physiology ; Bacteria/*genetics ; Deltaproteobacteria/physiology ; Ecology ; *Ecosystem ; Gammaproteobacteria/physiology ; Metagenome ; *Microbial Interactions ; Models, Biological ; Neural Networks, Computer ; Seawater/microbiology ; }, abstract = {Understanding the interactions between the Earth's microbiome and the physical, chemical and biological environment is a fundamental goal of microbial ecology. We describe a bioclimatic modeling approach that leverages artificial neural networks to predict microbial community structure as a function of environmental parameters and microbial interactions. This method was better at predicting observed community structure than were any of several single-species models that do not incorporate biotic interactions. The model was used to interpolate and extrapolate community structure over time with an average Bray-Curtis similarity of 89.7. Additionally, community structure was extrapolated geographically to create the first microbial map derived from single-point observations. This method can be generalized to the many microbial ecosystems for which detailed taxonomic data are currently being generated, providing an observation-based modeling technique for predicting microbial taxonomic structure in ecological studies.}, }
@article {pmid22502862, year = {2012}, author = {Alonso, C}, title = {Tips and tricks for high quality MAR-FISH preparations: focus on bacterioplankton analysis.}, journal = {Systematic and applied microbiology}, volume = {35}, number = {8}, pages = {503-512}, doi = {10.1016/j.syapm.2012.02.005}, pmid = {22502862}, issn = {1618-0984}, mesh = {Autoradiography/*methods ; Bacteria/*classification/*genetics ; In Situ Hybridization, Fluorescence/*methods ; Plankton/*microbiology ; *Water Microbiology ; }, abstract = {The combination of microautoradiography and fluorescence in situ hybridization (MAR-FISH) is a powerful technique for tracking the incorporation of radiolabelled compounds by specific bacterial populations at a single cell resolution. It has been widely applied in aquatic microbial ecology as a tool to unveil key ecophysiological features, shedding light on relevant ecological issues such as bacterial biomass production, the role of different bacterioplankton groups in the global carbon and sulphur cycle, and, at the same time, providing insights into the life styles and niche differentiation of cosmopolitan members of the aquatic microbial communities. Despite its great potential, its application has remained restricted to a few laboratories around the world, in part due to its reputation as a "difficult technique". Therefore, the objective of this minireview is to highlight the impact of MAR-FISH application on aquatic microbial ecology, and also to provide basic concepts, as well as practical tips, for processing MAR-FISH preparations, thus aiming to contribute to a more widespread application of this powerful method.}, }
@article {pmid22500928, year = {2012}, author = {Wang, G and Post, WM}, title = {A theoretical reassessment of microbial maintenance and implications for microbial ecology modeling.}, journal = {FEMS microbiology ecology}, volume = {81}, number = {3}, pages = {610-617}, doi = {10.1111/j.1574-6941.2012.01389.x}, pmid = {22500928}, issn = {1574-6941}, mesh = {Bacteria/*growth &amp; development/*metabolism ; Biomass ; Ecology/*methods ; Energy Metabolism ; *Models, Biological ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {We attempted to reconcile three microbial maintenance models (Herbert, Pirt, and Compromise) through a theoretical reassessment. We provided a rigorous proof that the true growth yield coefficient (Y(G)) is the ratio of the specific maintenance rate (a in Herbert) to the maintenance coefficient (m in Pirt). Other findings from this study include: (1) the Compromise model is identical to the Herbert for computing microbial growth and substrate consumption, but it expresses the dependence of maintenance on both microbial biomass and substrate; (2) the maximum specific growth rate in the Herbert (μ(max,H)) is higher than those in the other two models (μ(max,P) and μ(max,C)), and the difference is the physiological maintenance factor (m(q) = a); and (3) the overall maintenance coefficient (m(T)) is more sensitive to m(q) than to the specific growth rate (μ(G)) and Y(G). Our critical reassessment of microbial maintenance provides a new approach for quantifying some important components in soil microbial ecology models.}, }
@article {pmid22485111, year = {2012}, author = {Mills, HJ and Reese, BK and Shepard, AK and Riedinger, N and Dowd, SE and Morono, Y and Inagaki, F}, title = {Characterization of Metabolically Active Bacterial Populations in Subseafloor Nankai Trough Sediments above, within, and below the Sulfate-Methane Transition Zone.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {113}, pmid = {22485111}, issn = {1664-302X}, abstract = {A remarkable number of microbial cells have been enumerated within subseafloor sediments, suggesting a biological impact on geochemical processes in the subseafloor habitat. However, the metabolically active fraction of these populations is largely uncharacterized. In this study, an RNA-based molecular approach was used to determine the diversity and community structure of metabolically active bacterial populations in the upper sedimentary formation of the Nankai Trough seismogenic zone. Samples used in this study were collected from the slope apron sediment overlying the accretionary prism at Site C0004 during the Integrated Ocean Drilling Program Expedition 316. The sediments represented microbial habitats above, within, and below the sulfate-methane transition zone (SMTZ), which was observed approximately 20 m below the seafloor (mbsf). Small subunit ribosomal RNA were extracted, quantified, amplified, and sequenced using high-throughput 454 pyrosequencing, indicating the occurrence of metabolically active bacterial populations to a depth of 57 mbsf. Transcript abundance and bacterial diversity decreased with increasing depth. The two communities below the SMTZ were similar at the phylum level, however only a 24% overlap was observed at the genus level. Active bacterial community composition was not confined to geochemically predicted redox stratification despite the deepest sample being more than 50 m below the oxic/anoxic interface. Genus-level classification suggested that the metabolically active subseafloor bacterial populations had similarities to previously cultured organisms. This allowed predictions of physiological potential, expanding understanding of the subseafloor microbial ecosystem. Unique community structures suggest very diverse active populations compared to previous DNA-based diversity estimates, providing more support for enhancing community characterizations using more advanced sequencing techniques.}, }
@article {pmid22476815, year = {2012}, author = {Bowen De León, K and Ramsay, BD and Fields, MW}, title = {Quality-score refinement of SSU rRNA gene pyrosequencing differs across gene region for environmental samples.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {499-508}, pmid = {22476815}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics ; Ecosystem ; Genes, rRNA/*genetics ; Hot Springs/*microbiology ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/methods/*standards ; *Soil Microbiology ; Species Specificity ; }, abstract = {Due to potential sequencing errors in pyrosequencing data, species richness and diversity indices of microbial systems can be miscalculated. The "traditional" sequence refinement method is not sufficient to account for overestimations (e.g., length, primer errors, ambiguous nucleotides). Recent in silico and single-organism studies have revealed the importance of sequence quality scores in the estimation of ecological indices; however, this is the first study to compare quality-score stringencies across four regions of the SSU rRNA gene sequence (V1V2, V3, V4, and V6) with actual environmental samples compared directly to corresponding clone libraries produced from the same primer sets. The nucleic acid sequences determined via pyrosequencing were subjected to varying quality-score cutoffs that ranged from 25 to 32, and at each quality-score cutoff, either 10 or 15 % of the nucleotides were allowed to be below the cutoff. When species richness estimates were compared for the tested samples, the cutoff values of Q27(15%), Q30(10%), and Q32(15%) for V1V2, V4, and V6, respectively, estimated similar values as obtained with clone libraries and Sanger sequencing. The most stringent Q tested (Q32(10%)) was not enough to account for species richness inflation of the V3 region pyrosequence data. Results indicated that quality-score assessment greatly improved estimates of ecological indices for environmental samples (species richness and α-diversity) and that the effect of quality-score filtering was region-dependent.}, }
@article {pmid22476759, year = {2012}, author = {Salaün, S and La Barre, S and Dos Santos-Goncalvez, M and Potin, P and Haras, D and Bazire, A}, title = {Influence of exudates of the kelp Laminaria digitata on biofilm formation of associated and exogenous bacterial epiphytes.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {359-369}, pmid = {22476759}, issn = {1432-184X}, mesh = {Bacteria/classification/*drug effects/growth &amp; development/isolation &amp; purification ; Bacterial Adhesion/*drug effects/physiology ; Biofilms/*drug effects/growth &amp; development ; Kelp/metabolism/microbiology ; Laminaria/*metabolism/*microbiology ; Mannitol/metabolism/pharmacology ; Plant Exudates/chemistry/*pharmacology ; Seawater/microbiology ; }, abstract = {Wild populations of brown marine algae (Phaeophyta) provide extensive surfaces to bacteria and epiphytic eukaryotes for colonization. On one hand, various strategies allow kelps prevent frond surface fouling which would retard growth by reducing photosynthesis and increasing pathogenesis. On the other hand, production and release of organic exudates of high energy value, sometimes in association with more or less selective control of settlement of epiphytic strains, allow bacteria to establish surface consortia not leading to macrofouling. Here, we present the analysis of adhesion and biofilm formation of bacterial isolates from the kelp Laminaria digitata and of characterized and referenced marine isolates. When they were grown in flow cell under standard nutrient regimes, all used bacteria, except one, were able to adhere on glass and then develop as biofilms, with different architecture. Then, we evaluated the effect of extracts from undisturbed young Laminaria thalli and from young thalli subjected to oxidative stress elicitation; this latter condition induced the production of defense molecules. We observed increasing or decreasing adhesion depending on the referenced strains, but no effects were observed against strains isolated from L. digitata. Such effects were less observed on biofilms. Our results suggested that L. digitata is able to modulate its bacterial colonization. Finally, mannitol, a regular surface active component of Laminaria exudates was tested individually, and it showed a pronounced increased on one biofilm strain. Results of these experiments are original and can be usefully linked to what we already know on the oxidative halogen metabolism peculiar to Laminaria. Hopefully, we will be able to understand more about the unique relationship that bacteria have been sharing with Laminaria for an estimated one billion years.}, }
@article {pmid22469289, year = {2012}, author = {Rineau, F and Roth, D and Shah, F and Smits, M and Johansson, T and Canbäck, B and Olsen, PB and Persson, P and Grell, MN and Lindquist, E and Grigoriev, IV and Lange, L and Tunlid, A}, title = {The ectomycorrhizal fungus Paxillus involutus converts organic matter in plant litter using a trimmed brown-rot mechanism involving Fenton chemistry.}, journal = {Environmental microbiology}, volume = {14}, number = {6}, pages = {1477-1487}, pmid = {22469289}, issn = {1462-2920}, mesh = {Agaricales/growth &amp; development/metabolism/*physiology ; Biodegradation, Environmental ; Carbon/metabolism ; Ecosystem ; Hydrogen Peroxide/*metabolism ; Iron/*metabolism ; Mycorrhizae/chemistry/growth &amp; development/metabolism/physiology ; Nitrogen/metabolism ; Plant Roots/metabolism/microbiology ; Plants/metabolism/microbiology ; *Soil Microbiology ; Symbiosis ; Trees/metabolism/microbiology ; Wood/*metabolism ; }, abstract = {Soils in boreal forests contain large stocks of carbon. Plants are the main source of this carbon through tissue residues and root exudates. A major part of the exudates are allocated to symbiotic ectomycorrhizal fungi. In return, the plant receives nutrients, in particular nitrogen from the mycorrhizal fungi. To capture the nitrogen, the fungi must at least partly disrupt the recalcitrant organic matter-protein complexes within which the nitrogen is embedded. This disruption process is poorly characterized. We used spectroscopic analyses and transcriptome profiling to examine the mechanism by which the ectomycorrhizal fungus Paxillus involutus degrades organic matter when acquiring nitrogen from plant litter. The fungus partially degraded polysaccharides and modified the structure of polyphenols. The observed chemical changes were consistent with a hydroxyl radical attack, involving Fenton chemistry similar to that of brown-rot fungi. The set of enzymes expressed by Pa. involutus during the degradation of the organic matter was similar to the set of enzymes involved in the oxidative degradation of wood by brown-rot fungi. However, Pa. involutus lacked transcripts encoding extracellular enzymes needed for metabolizing the released carbon. The saprotrophic activity has been reduced to a radical-based biodegradation system that can efficiently disrupt the organic matter-protein complexes and thereby mobilize the entrapped nutrients. We suggest that the released carbon then becomes available for further degradation and assimilation by commensal microbes, and that these activities have been lost in ectomycorrhizal fungi as an adaptation to symbiotic growth on host photosynthate. The interdependence of ectomycorrhizal symbionts and saprophytic microbes would provide a key link in the turnover of nutrients and carbon in forest ecosystems.}, }
@article {pmid22465599, year = {2012}, author = {Larsen, P and Hamada, Y and Gilbert, J}, title = {Modeling microbial communities: current, developing, and future technologies for predicting microbial community interaction.}, journal = {Journal of biotechnology}, volume = {160}, number = {1-2}, pages = {17-24}, doi = {10.1016/j.jbiotec.2012.03.009}, pmid = {22465599}, issn = {1873-4863}, mesh = {Biotechnology ; *Ecosystem ; *Environmental Microbiology ; *Metagenome ; *Microbial Interactions ; *Models, Biological ; }, abstract = {Never has there been a greater opportunity for investigating microbial communities. Not only are the profound effects of microbial ecology on every aspect of Earth's geochemical cycles beginning to be understood, but also the analytical and computational tools for investigating microbial Earth are undergoing a rapid revolution. This environmental microbial interactome, the system of interactions between the microbiome and the environment, has shaped the planet's past and will undoubtedly continue to do so in the future. We review recent approaches for modeling microbial community structures and the interactions of microbial populations with their environments. Different modeling approaches consider the environmental microbial interactome from different aspects, and each provides insights to different facets of microbial ecology. We discuss the challenges and opportunities for the future of microbial modeling and describe recent advances in microbial community modeling that are extending current descriptive technologies into a predictive science.}, }
@article {pmid22462789, year = {2012}, author = {Grootaert, C and Van de Wiele, T and Verstraete, W and Bracke, M and Vanhoecke, B}, title = {Angiopoietin-like protein 4: health effects, modulating agents and structure-function relationships.}, journal = {Expert review of proteomics}, volume = {9}, number = {2}, pages = {181-199}, doi = {10.1586/epr.12.12}, pmid = {22462789}, issn = {1744-8387}, mesh = {Angiopoietin-Like Protein 4 ; Angiopoietins/genetics/metabolism/*physiology ; Animals ; Cardiovascular Diseases/metabolism ; Energy Metabolism ; Gastrointestinal Tract/metabolism/microbiology ; Humans ; Lipid Metabolism ; Liver/metabolism ; Metabolic Diseases ; Neoplasms/metabolism ; Organ Specificity ; Peroxisome Proliferator-Activated Receptors/agonists/metabolism ; Protein Isoforms/metabolism/physiology ; }, abstract = {Angiopoietin-like protein 4 (ANGPTL4) has been identified as a multifunctional signal protein. It is produced by a variety of tissues, and is secreted into the bloodstream in glycosylated, oligomerized, native and cleaved isoforms to modulate physiological events such as angiogenesis, cell differentiation and the crosstalk between liver, brain, adipose and muscle tissue in lipid and glucose metabolism. In addition, the expression and isoform appearance of ANGPTL4 are modified by the intestinal microbiota. With an eye on an effective strategy to improve health using ANGPTL4, we will focus on: health issues associated with ANGPTL4 expression, including obesity, Type 2 diabetes, cardiovascular diseases and cancer; several modulators of ANGPTL4 of chemical, microbiological, food and host origin; and the correlation of the specific ANGPTL4 isoforms with these modulators and their health effects.}, }
@article {pmid24031878, year = {2012}, author = {Etto, RM and Cruz, LM and Jesus, EC and Galvão, CW and Galvão, F and Souza, EM and Pedrosa, FO and Steffens, MB}, title = {Prokaryotic communities of acidic peatlands from the southern Brazilian Atlantic Forest.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {43}, number = {2}, pages = {661-674}, pmid = {24031878}, issn = {1517-8382}, abstract = {The acidic peatlands of southern Brazil are ecosystems essential for the maintenance of the Atlantic Forest, one of the 25 hot-spots of biodiversity in the world. In this work, we investigated the composition of prokaryotic communities in four histosols of three acidic peatland regions by constructing small-subunit (SSU) rRNA gene libraries and sequencing. SSU rRNA gene sequence analysis showed the prevalence of Acidobacteria (38.8%) and Proteobacteria (27.4%) of the Bacteria domain and Miscellaneous (58%) and Terrestrial (24%) groups of Crenarchaeota of the Archaea domain. As observed in other ecosystems, archaeal communities showed lower richness than bacterial communities. We also found a limited number of Euryarchaeota and of known methanotrophic bacteria in the clone libraries.}, }
@article {pmid23757274, year = {2012}, author = {Krause, S and Lüke, C and Frenzel, P}, title = {Methane source strength and energy flow shape methanotrophic communities in oxygen-methane counter-gradients.}, journal = {Environmental microbiology reports}, volume = {4}, number = {2}, pages = {203-208}, doi = {10.1111/j.1758-2229.2011.00322.x}, pmid = {23757274}, issn = {1758-2229}, abstract = {The role of microbial diversity for ecosystem functioning has become an important subject in microbial ecology. Recent work indicates that microbial communities and microbial processes can be very sensitive to anthropogenic disturbances. However, to what extent microbial communities may change upon, resist to, or overcome disturbances might differ depending on substrate availability. We used soil from an Italian rice field in gradient microcosms, and analysed the response of methanotrophic communities to an NH4 (+) pulse as a potential disturbance under two different CH4 source strengths. We found a significant influence of source strength, i.e. the energy flow through the methanotrophic community, while NH4 (+) had no effect. Our data suggest that historical contingencies, i.e. nitrogen fertilization, led to an ammonium-tolerant MOB community. Methanotrophs were able to oxidize virtually all CH4 diffusing into the oxic-anoxic boundary layer regardless of NH4 (+) addition. Total and active methanotrophic communities were assessed by a pmoA-specific microarray. From the reservoir of dormant methanotrophs, different species became active with Methylobacter and an environmental cluster affiliated with paddy soils being indicative for high CH4 source strength. Thus, a microbial seed bank is an important prerequisite to maintain functioning in a fluctuating environment.}, }
@article {pmid23757271, year = {2012}, author = {Ben-Dov, E and Shapiro, OH and Kushmaro, A}, title = {'Next-base' effect on PCR amplification.}, journal = {Environmental microbiology reports}, volume = {4}, number = {2}, pages = {183-188}, doi = {10.1111/j.1758-2229.2011.00318.x}, pmid = {23757271}, issn = {1758-2229}, abstract = {The base adjacent to the 3' end of universal PCR primers targeting the 16S rRNA gene is often variable and apparently biases the microbial community composition as represented by PCR-based surveys. To test this hypothesis, four templates of 44 bases each and two complementary primers (21 bases) were designed to differ only in the bases adjacent to the primers, and their amplification efficiencies were evaluated using quantitative PCR. For extension temperatures of 72°C, 73°C and 74°C, improvement in initial amplification efficiency was observed for templates with guanine or cytosine at the position contiguous to the primers. However, no clear preference was observed when extension temperature was lowered to 70°C. Shortening the primers by one base, so that the variable position was located two base pairs downstream from the primer, attenuated but did not eliminate this bias. A conformational change of the quaternary polymerase - primer - template - dNTP complex upon commencing of polymerization is thought to be a rate-limiting step. A possible explanation for the observed bias is the stabilization of this complex by the adjacent guanine or cytosine. Reducing PCR extension temperature to 70°C minimizes amplification biases caused by variable template-contiguous bases to the 3' end of universal PCR primers. Next-base nucleotide composition should be taken in consideration in designing primers targeting 16S rRNA or other functional genes used in microbial ecology studies.}, }
@article {pmid22460792, year = {2012}, author = {Benezra, A and DeStefano, J and Gordon, JI}, title = {Anthropology of microbes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {17}, pages = {6378-6381}, pmid = {22460792}, issn = {1091-6490}, mesh = {Humans ; *Microbiology ; }, abstract = {We describe the need to further integrate the fields of human microbial ecology and anthropology and outline some of the potential goals and benefits of this collaborative work.}, }
@article {pmid22460437, year = {2012}, author = {Pajares, S and Bonilla-Rosso, G and Travisano, M and Eguiarte, LE and Souza, V}, title = {Mesocosms of aquatic bacterial communities from the Cuatro Cienegas Basin (Mexico): a tool to test bacterial community response to environmental stress.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {346-358}, pmid = {22460437}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*radiation effects ; Cloning, Molecular ; DNA, Bacterial/analysis/genetics/isolation &amp; purification ; Ecosystem ; Fresh Water/*microbiology ; Gene Library ; Mexico ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Temperature ; *Ultraviolet Rays ; }, abstract = {Microbial communities are responsible for important ecosystem processes, and their activities are regulated by environmental factors such as temperature and solar ultraviolet radiation. Here we investigate changes in aquatic microbial community structure, diversity, and evenness in response to changes in temperature and UV radiation. For this purpose, 15 mesocosms were seeded with both microbial mat communities and plankton from natural pools within the Cuatro Cienegas Basin (Mexico). Clone libraries (16S rRNA) were obtained from water samples at the beginning and at the end of the experiment (40 days). Phylogenetic analysis indicated substantial changes in aquatic community composition and structure in response to temperature and UV radiation. Extreme treatments with elevation in temperature or UV radiation reduced diversity in relation to the Control treatments, causing a reduction in richness and increase in dominance, with a proliferation of a few resistant operational taxonomic units. Each phylum was affected differentially by the new conditions, which translates in a differential modification of ecosystem functioning. This suggests that the impact of environmental stress, at least at short term, will reshape the aquatic bacterial communities of this unique ecosystem. This work also demonstrates the possibility of designing manageable synthetic microbial community ecosystems where controlled environmental variables can be manipulated. Therefore, microbial model systems offer a complementary approach to field and laboratory studies of global research problems associated with the environment.}, }
@article {pmid22452819, year = {2012}, author = {Vlaeminck, SE and De Clippeleir, H and Verstraete, W}, title = {Microbial resource management of one-stage partial nitritation/anammox.}, journal = {Microbial biotechnology}, volume = {5}, number = {3}, pages = {433-448}, pmid = {22452819}, issn = {1751-7915}, mesh = {Bacteria/growth &amp; development/*metabolism ; Bioreactors/*microbiology ; Biotechnology/*methods ; Nitrification ; Quaternary Ammonium Compounds/*metabolism ; Sewage/chemistry/microbiology ; }, abstract = {About 30 full-scale partial nitritation/anammox plants are established, treating mostly sewage sludge reject water, landfill leachate or food processing digestate. Although two-stage and one-stage processes each have their advantages, the one-stage configuration is mostly applied, termed here as oxygen-limited autotrophic nitrification/denitrification (OLAND), and is the focus of this review. The OLAND application domain is gradually expanding, with technical-scale plants on source-separated domestic wastewater, pre-treated manure and sewage, and liquors from organic waste bioenergy plants. A 'microbial resource management' (MRM) OLAND framework was elaborated, showing how the OLAND engineer/operator (1: input) can design/steer the microbial community (2: biocatalyst) to obtain optimal functionality (3: output). In the physicochemical toolbox (1), design guidelines are provided, as well as advantages of different reactor technologies. Particularly the desirable aeration regime, feeding regime and shear forces are not clear yet. The development of OLAND trickling filters, membrane bioreactors and systems with immobilized biomass is awaited. The biocatalyst box (2) considers 'Who': biodiversity and its dynamic patterns, 'What': physiology, and 'Where': architecture creating substrate gradients. Particularly community dynamics and extracellular polymeric substances (EPS) still require insights. Performant OLAND (3) comprises fast start-up (storage possibility; fast growth of anammox bacteria), process stability (endured biomass retention; stress resilience), reasonable overall costs, high nitrogen removal efficiency and a low environmental footprint. Three important OLAND challenges are elaborated in detailed frameworks, demonstrating how to maximize nitrogen removal efficiency, minimize NO and N(2)O emissions and obtain through OLAND a plant-wide net energy gain from sewage treatment.}, }
@article {pmid22451218, year = {2012}, author = {Berner, C and Johansson, T and Wallander, H}, title = {Long-term effect of apatite on ectomycorrhizal growth and community structure.}, journal = {Mycorrhiza}, volume = {22}, number = {8}, pages = {615-621}, pmid = {22451218}, issn = {1432-1890}, mesh = {Apatites/metabolism/*pharmacology ; Basidiomycota/*drug effects/genetics/growth &amp; development/isolation &amp; purification ; Biodiversity ; Biological Transport ; Biomass ; Carbon/metabolism ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Ergosterol/analysis ; Mycelium ; Mycorrhizae/*drug effects/genetics/growth &amp; development/isolation &amp; purification ; Phosphorus/*metabolism ; Picea/drug effects/growth &amp; development/*microbiology ; Plant Roots/growth &amp; development/microbiology ; Sequence Analysis, DNA ; Soil/chemistry ; Sweden ; Symbiosis ; Time ; Trees ; }, abstract = {Ectomycorrhizal (ECM) fungi are efficient at taking up phosphorus (P) from mineral sources, such as apatite, which are not easily available to the host trees. Since ECM fungal species differ in P uptake rates, it can be expected that the composition of the ECM fungal community will change upon exposure to apatite, provided that the P transfer is rewarded by more carbon being transferred to the fungal symbiont. Control and apatite-amended mesh bags were buried in pairs in the humus layer of a P-poor Norway spruce forest. The ECM fungal community that colonized these bags was analyzed by DNA extraction, PCR amplification of the internal transcribed spacer (ITS) region, cloning, and random sequencing. Fungal biomass was estimated by ergosterol analysis. No change in the ECM fungal community structure was seen after 5 years of apatite exposure, although the fungal biomass increased threefold upon apatite amendment. Our results indicate that host trees enhance carbon allocation to ECM fungi colonizing P sources in P-poor forests but the lack of change in the composition of the ECM fungal community suggests that P transfer rates were similar among the species. Alternatively, higher P transfer among certain species was not rewarded with higher carbon transfer from the host.}, }
@article {pmid22450512, year = {2012}, author = {Watanabe, M and Tagami, Y and Miura, K and Kageyama, D and Stouthamer, R}, title = {Distribution patterns of Wolbachia endosymbionts in the closely related flower bugs of the genus Orius: implications for coevolution and horizontal transfer.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {537-545}, pmid = {22450512}, issn = {1432-184X}, mesh = {Animals ; *Biological Evolution ; Cloning, Molecular ; Flowers/*parasitology ; *Gene Transfer, Horizontal ; Heteroptera/classification/*microbiology ; Japan ; Molecular Sequence Data ; Multilocus Sequence Typing ; Phylogeny ; Recombination, Genetic ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; Wolbachia/classification/*genetics/physiology ; }, abstract = {Vertical transmission is the primary route of the endosymbiont Wolbachia for its own spread among invertebrate hosts, but horizontal transmission between different hosts is believed to have occurred multiple times. However, it is not well known how Wolbachia commonly spread among closely related hosts. We focused on the closely related species of the minute pirate bugs belonging to the genus Orius, which are important biological control agents in agricultural crops because they are the most useful natural enemy of various tiny pests, such as thrips. Here, we examined five Orius species (Orius sauteri, Orius nagaii, Orius minutus, Orius strigicollis, and Orius tantillus) from eight geographic localities in Japan for Wolbachia infection. Two distinct strains, wOus1 and wOus2, were detected based on Wolbachia surface protein (wsp) gene sequencing. Furthermore, multilocus sequence typing revealed that each of the strains comprised two variants that differed in a single nucleotide. The overall distribution patterns of the two Wolbachia strains were found to differ among host species: prevalent double infection with wOus1 and wOus2 in O. strigicollis; fixation of single infection with wOus2 in O. nagaii; occurrence of single infection with wOus1 in O. sauteri; prevalence of single infection with wOus1 in O. minutus with an exception in a single population; and lack of Wolbachia infection in O. tantillus. Such differences in the distribution patterns of Wolbachia may reflect the evolutionary history of Wolbachia infection among Orius species and/or ecological and physiological differences among the Orius species that determine the invasiveness and maintenance of the two Wolbachia strains.}, }
@article {pmid22450511, year = {2012}, author = {Fontes, ML and Abreu, PC}, title = {A vigorous specialized microbial food web in the suboxic waters of a shallow subtropical coastal lagoon.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {334-345}, pmid = {22450511}, issn = {1432-184X}, mesh = {Anaerobiosis ; Animals ; Bacteriochlorophyll A/metabolism ; Biomass ; Brazil ; Chromatiaceae/*metabolism ; Ciliophora/*metabolism ; Ecosystem ; *Food Chain ; Fresh Water/chemistry/*microbiology ; Oxygen/metabolism/*pharmacology ; Oxygen Consumption ; Photosynthesis ; Seasons ; Zooplankton/*metabolism ; }, abstract = {To examine the extent of the microbial food web in suboxic waters of a shallow subtropical coastal lagoon, the density and biomass of bacteria and protozooplankton were quantified under different dissolved oxygen (DO) levels. In addition, bottom waters of a stratified site were compared with bottom waters of a homogeneous site under periods of high and low biological oxygen production/consumption in the lagoon. At the stratified site, microbial biomass decreased with oxygen decline, from oxia to suboxia, with a recovery of the initial total biomass after a 20-day period of persistent suboxia. A peak in density and biomass of purple sulfur bacteria (PSB) (90 μg C L(-1)) occurred in the suboxic waters 20 days prior to the peak in biomass of ciliates >50 μm (Loxophyllum sp. of 150 μm) (160 μg C L(-1)), demonstrating a top down biomass control. Ciliates >50 μm were positively correlated with PSB and bacteriochlorophyll a (photosynthetic pigment of PSB). Total protozoan biomass reached 430 μg C L(-1) in the suboxic waters of the stratified site, with ciliates >50 μm accounting for 90% of the total ciliate biomass and of 55 % of biomass of protozoa. At the homogeneous site, total protozoan biomass was only 66 μg C L(-1), where flagellates and ciliates <25 μm were the dominant microorganisms. Therefore, as light is available for primary producers in the bottom waters of shallow stratified coastal lagoons or estuaries, one can expect that high primary production of PSB may favor a specialized microbial food web composed by larger microorganisms, accessible to zooplankton that tolerate low DO levels.}, }
@article {pmid22450510, year = {2012}, author = {Trabal, N and Mazón-Suástegui, JM and Vázquez-Juárez, R and Asencio-Valle, F and Morales-Bojórquez, E and Romero, J}, title = {Molecular analysis of bacterial microbiota associated with oysters (Crassostrea gigas and Crassostrea corteziensis) in different growth phases at two cultivation sites.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {555-569}, pmid = {22450510}, issn = {1432-184X}, mesh = {Animals ; Aquaculture ; Bacteria/classification/*genetics/isolation &amp; purification ; Burkholderia cepacia/classification/genetics/isolation &amp; purification ; Crassostrea/*growth &amp; development/*microbiology ; DNA, Bacterial/analysis/genetics ; Denaturing Gradient Gel Electrophoresis ; *Metagenome ; Molecular Sequence Data ; Polymerase Chain Reaction/methods ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {Microbiota presumably plays an essential role in inhibiting pathogen colonization and in the maintenance of health in oysters, but limited data exist concerning their different growth phases and conditions. We analyzed the bacterial microbiota composition of two commercial oysters: Crassostrea gigas and Crassostrea corteziensis. Differences in microbiota were assayed in three growth phases: post-larvae at the hatchery, juvenile, and adult at two grow-out cultivation sites. Variations in the microbiota were assessed by PCR analysis of the 16S rRNA gene in DNA extracted from depurated oysters. Restriction fragment length polymorphism (RFLP) profiles were studied using Dice's similarity coefficient (Cs) and statistical principal component analysis (PCA). The microbiota composition was determined by sequencing temperature gradient gel electrophoresis (TGGE) bands. The RFLP analysis of post-larvae revealed homology in the microbiota of both oyster species (Cs > 88 %). Dice and PCA analyses of C. corteziensis but not C. gigas showed differences in the microbiota according to the cultivation sites. The sequencing analysis revealed low bacterial diversity (primarily β-Proteobacteria, Firmicutes, and Spirochaetes), with Burkholderia cepacia being the most abundant bacteria in both oyster species. This study provides the first description of the microbiota in C. corteziensis, which was shown to be influenced by cultivation site conditions. During early growth, we observed that B. cepacia colonized and remained strongly associated with the two oysters, probably in a symbiotic host-bacteria relationship. This association was maintained in the three growth phases and was not altered by environmental conditions or the management of the oysters at the grow-out site.}, }
@article {pmid22441572, year = {2012}, author = {Lee, SH and Kim, SY and Kang, H}, title = {Effects of elevated CO2 on communities of denitrifying bacteria and methanogens in a temperate marsh microcosm.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {485-498}, pmid = {22441572}, issn = {1432-184X}, mesh = {Bacteria/*drug effects/*enzymology/genetics/growth &amp; development ; Carbon Dioxide/*pharmacology ; *Denitrification ; *Ecosystem ; Methane/*metabolism ; Molecular Sequence Data ; Nitrite Reductases/genetics ; Oxidoreductases/genetics ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; Typhaceae/growth &amp; development ; *Wetlands ; }, abstract = {The effects of elevated CO(2) on soil bacterial community with upland vegetation have been widely studied, but limited information is available regarding responses of denitrifier and methanogen communities to elevated CO(2) in wetland ecosystems. Using restriction fragment length polymorphism (RFLP), terminal RFLP analysis, and real-time quantitative PCR, we compared communities of denitrifiers and methanogens in a laboratory-scale wetland system planted with one of three macrophytes, Typha latifolia, Scirpus lacustris, or Juncus effusus, after 110 days of incubation. Our study showed that elevated CO(2) could affect community structures of both denitrifiers and methanogens, each of which had a unique response pattern. In particular, elevated CO(2) shifted nirS-containing community with a unique structure irrespective of vegetation type. mcrA-containing community appeared to shift to community with unique types of hydrogenotrophs under elevated CO(2) conditions. The change of dissolved organic carbon driven by elevated CO(2) appeared to be related with the shift of both denitrifiers and methanogens. Overall, this study indicates that elevated CO(2) could change the community structure of denitrifiers and methanogens temporarily. These results also suggest a presence of stable dominant populations that were not substantially affected by changes in CO(2) concentration.}, }
@article {pmid22438040, year = {2012}, author = {Barata, A and Santos, SC and Malfeito-Ferreira, M and Loureiro, V}, title = {New insights into the ecological interaction between grape berry microorganisms and Drosophila flies during the development of sour rot.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {416-430}, pmid = {22438040}, issn = {1432-184X}, mesh = {Acetic Acid/metabolism ; Animals ; Ascomycota/classification/genetics/*growth &amp; development/metabolism ; Bacteria/classification/genetics/*growth &amp; development/metabolism ; Basidiomycota/classification/genetics/*growth &amp; development/metabolism ; Drosophila/*growth &amp; development/microbiology ; *Ecosystem ; Fermentation ; Fruit/microbiology ; Molecular Sequence Data ; Plant Diseases/*microbiology ; Sequence Analysis, DNA ; Vitis/*microbiology ; }, abstract = {In this work, we studied the ecological interactions between grape berry microorganisms and Drosophila sp. flies involved in sour rot disease during grape ripening. After veráison the total microbial counts of grape berries affected by sour rot increased from about 2 log CFU/g of berries to more than 7 log CFU/g. Berry damage provoked a clear shift in yeast diversity from basidiomycetes to ascomycetous fermentative species. The latter were mostly Pichia terricola, Hanseniaspora uvarum, Candida zemplinina, and Zygoascus hellenicus. However, these species were not able to produce the metabolites characteristic of sour rot (gluconic and acetic acids) in inoculated berries. On the contrary, the acetic acid bacteria Gluconacetobacter saccharivorans produced high levels of these acids, mainly when berries were incubated in the presence of the insect Drosophila sp. Sour rot was not observed when grape bunches were physically separated from insects, even when berries were artificially injured. The wounds made in berry skin healed in the absence of insects, thus preventing the development of sour rot. Therefore, in the vineyard, the induction of sour rot depends on the contamination of wounded berries by a microbial consortium--yeasts and acetic acid bacteria--transported by drosophilid insects which disseminate sour rot among damaged berries. In the absence of these insects, plant defense mechanisms are effective and lead to skin healing, preventing disease spread. Thus, we showed that Drosophila sp. act as a vector for microorganisms associated with grape sour rot disease.}, }
@article {pmid22438039, year = {2012}, author = {Llewellyn, CA and White, DA and Martinez-Vincente, V and Tarran, G and Smyth, TJ}, title = {Distribution of mycosporine-like amino acids along a surface water meridional transect of the Atlantic.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {320-333}, pmid = {22438039}, issn = {1432-184X}, support = {BB/E018998/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acids/*analysis/metabolism ; Atlantic Ocean ; Cyanobacteria/*metabolism ; Cyclohexanols/analysis/metabolism ; Cyclohexanones/analysis/metabolism ; Cyclohexylamines/analysis/metabolism ; Glycine/analogs &amp; derivatives/analysis/metabolism ; Nitrogen Fixation ; Phytoplankton/*metabolism ; Prochlorococcus/*metabolism ; Seawater/*chemistry/microbiology ; Species Specificity ; }, abstract = {The composition and abundance of mycosporine-like amino acids (MAAs) were investigated in the surface waters along a 13,000-km meridional transect (52° N to 45° S) in the Atlantic Ocean (Atlantic Meridional Transect programme: Cruise AMT 18: 4/10/2008-10/11/2008). MAAs were ubiquitous along the transect, although the composition of the MAAs was variable. Highest concentrations were in the far south (below 40° S; MAA >1 μg L(-1)) and in north subtropical equatorial region (NER: 0-25° N; MAA up to 0.8 μg L(-1)). Highest MAA relative to chlorophyll-a occurred in the NER (MAA/chl-a ratio between 2 and 5). MAA/chl-a significantly correlated with the preceding month's mean daily UV dose and with UV-B/UV-A. In the far south, high MAA concentrations coincided with high phytoplankton biomass, high nutrients and a deep mixed layer associated with the austral spring. Here, the phytoplankton community was dominated by micro- and nano-eukaryotes. At the NER, the high MAA/chl-a coincided with low nutrient concentrations, a shallow mixed layer depth (20-70 m) and to a lesser extent to a shallow nitracline (40-90 m). Here, the phytoplankton consisted primarily of picophytoplankton (0-0.2 μm), dominated by the pico-cyanobacteria Synechococcus sp. and Prochlorococcus sp. and by the nitrogen fixing filamentous cyanobacterium Trichodesmium. The low nitrate concentrations (<0.1 μmol L(-1)) at the NER suggest that nitrogen fixation was required for MAA production. Specific MAAs could not easily be assigned to particular groups of phytoplankton and we could not rule out the possibility that MAAs were associated with symbiotic cyanobacteria contained within heterotrophic dinoflagellates or diatoms.}, }
@article {pmid22434885, year = {2012}, author = {Gans, JD and Dunbar, J and Eichorst, SA and Gallegos-Graves, LV and Wolinsky, M and Kuske, CR}, title = {A robust PCR primer design platform applied to the detection of Acidobacteria Group 1 in soil.}, journal = {Nucleic acids research}, volume = {40}, number = {12}, pages = {e96}, pmid = {22434885}, issn = {1362-4962}, mesh = {Acidobacteria/genetics/*isolation &amp; purification ; Algorithms ; DNA Primers/*chemistry ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Software ; *Soil Microbiology ; }, abstract = {Environmental biosurveillance and microbial ecology studies use PCR-based assays to detect and quantify microbial taxa and gene sequences within a complex background of microorganisms. However, the fragmentary nature and growing quantity of DNA-sequence data make group-specific assay design challenging. We solved this problem by developing a software platform that enables PCR-assay design at an unprecedented scale. As a demonstration, we developed quantitative PCR assays for a globally widespread, ecologically important bacterial group in soil, Acidobacteria Group 1. A total of 33,684 Acidobacteria 16S rRNA gene sequences were used for assay design. Following 1 week of computation on a 376-core cluster, 83 assays were obtained. We validated the specificity of the top three assays, collectively predicted to detect 42% of the Acidobacteria Group 1 sequences, by PCR amplification and sequencing of DNA from soil. Based on previous analyses of 16S rRNA gene sequencing, Acidobacteria Group 1 species were expected to decrease in response to elevated atmospheric CO(2). Quantitative PCR results, using the Acidobacteria Group 1-specific PCR assays, confirmed the expected decrease and provided higher statistical confidence than the 16S rRNA gene-sequencing data. These results demonstrate a powerful capacity to address previously intractable assay design challenges.}, }
@article {pmid22430508, year = {2012}, author = {Miller, KI and Qing, C and Sze, DM and Roufogalis, BD and Neilan, BA}, title = {Culturable endophytes of medicinal plants and the genetic basis for their bioactivity.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {431-449}, pmid = {22430508}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/metabolism ; Antifungal Agents/metabolism ; Bacteria/classification/genetics/*growth &amp; development/isolation &amp; purification ; China ; Culture Media ; Endophytes/enzymology/genetics/*growth &amp; development/isolation &amp; purification ; Fungi/classification/genetics/*growth &amp; development/isolation &amp; purification ; Genes, rRNA ; Molecular Sequence Data ; Peptide Synthases/*genetics ; Phylogeny ; Plants, Medicinal/*microbiology ; Polyketide Synthases/*genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {The bioactive compounds of medicinal plants are products of the plant itself or of endophytes living inside the plant. Endophytes isolated from eight different anticancer plants collected in Yunnan, China, were characterized by diverse 16S and 18S rRNA gene phylogenies. A functional gene-based molecular screening strategy was used to target nonribosomal peptide synthetase (NRPS) and type I polyketide synthase (PKS) genes in endophytes. Bioinformatic analysis of these biosynthetic pathways facilitated inference of the potential bioactivity of endophyte natural products, suggesting that the isolated endophytes are capable of producing a plethora of secondary metabolites. All of the endophyte culture broth extracts demonstrated antiproliferative effects in at least one test assay, either cytotoxic, antibacterial or antifungal. From the perspective of natural product discovery, this study confirms the potential for endophytes from medicinal plants to produce anticancer, antibacterial and antifungal compounds. In addition, PKS and NRPS gene screening is a valuable method for screening isolates of biosynthetic potential.}, }
@article {pmid22430507, year = {2012}, author = {Sherman, C and Steinberger, Y}, title = {Microbial functional diversity associated with plant litter decomposition along a climatic gradient.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {399-415}, pmid = {22430507}, issn = {1432-184X}, mesh = {Bacteria/growth &amp; development/*metabolism ; *Biodegradation, Environmental ; Biodiversity ; Biomass ; Carbon Dioxide/metabolism ; *Climate ; Colony Count, Microbial ; Desert Climate ; *Ecosystem ; Israel ; Mediterranean Region ; Plants/*metabolism/*microbiology ; Rain ; Seasons ; Temperature ; }, abstract = {Predicted changes in climate associated with increased greenhouse gas emissions can cause increases in global mean temperature and changes in precipitation regimes. These changes may affect key soil processes, e.g., microbial CO(2) evolution and biomass, mineralization rates, primary productivity, biodiversity, and litter decomposition, which play an important role in carbon and nutrient cycling in terrestrial ecosystems. Our study examined the changes in litter microbial communities and decomposition along a climatic gradient, ranging from arid desert to humid Mediterranean regions in Israel. Wheat straw litter bags were placed in arid, semi-arid, Mediterranean, and humid Mediterranean sites. Samples were collected seasonally over a 2-year period in order to evaluate mass loss, litter moisture, C/N ratio, bacterial colony-forming units (CFUs), microbial CO(2) evolution and biomass, microbial functional diversity, and catabolic profile. Decomposition rate was the highest during the first year of the study at the Mediterranean and arid sites. Community-level physiological profile and microbial biomass were the highest in summer, while bacterial CFUs were the highest in winter. Microbial functional diversity was found to be highest at the humid Mediterranean site, whereas substrate utilization increased at the arid site. Our results support the assumption that climatic factors control litter degradation and regulate microbial activity.}, }
@article {pmid22430506, year = {2012}, author = {Mouton, M and Postma, F and Wilsenach, J and Botha, A}, title = {Diversity and characterization of culturable fungi from marine sediment collected from St. Helena Bay, South Africa.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {311-319}, pmid = {22430506}, issn = {1432-184X}, mesh = {Anaerobiosis ; Biodiversity ; Culture Media ; Fungi/*classification/genetics/*growth &amp; development/physiology ; Geologic Sediments/chemistry/*microbiology ; Mycological Typing Techniques ; Nitrogen/metabolism ; Nitrogen Cycle ; Polymerase Chain Reaction ; Seawater/chemistry/microbiology ; Sequence Analysis, DNA ; South Africa ; }, abstract = {Marine fungi are known to originate from a wide variety of habitats within the marine environment. Marine sediment represents one environmental niche, with most fungi occurring in these sediments being facultative marine fungi with terrestrial origins. It has not been proven whether these fungi merely survive the harsh environmental conditions presented by the ocean sediment, as opposed to playing an active role in this ecological niche. During this study, marine sediment was collected from St. Helena Bay, on the west coast of the Western Cape, South Africa. Using dilution, enrichment, and repetitive culturing techniques, 59 fungal isolates were obtained from marine sediments and identified to at least genus level using morphological and molecular methods. Moreover, a series of tests were performed to characterize the physical and physicochemical attributes of the isolates. Results showed that the isolates not only survived but also had the potential to grow in the natural conditions present in this environment. Extracellular cellulase was produced by the filamentous fungal isolates indicating their probable role in detrital decay processes and therefore the carbon cycle on the ocean bed. Also, denitrification patterns were observed when isolates were grown in liquid media amended with NaNO(2), NaNO(3), and (NH(4))SO(4), implicating that these fungi have the potential to play an active role in denitrification, co-denitrification, and ammonification phases of nitrogen cycles occurring in the marine sediments.}, }
@article {pmid22430505, year = {2012}, author = {Bhattarai, S and Ross, KA and Schmid, M and Anselmetti, FS and Bürgmann, H}, title = {Local conditions structure unique archaeal communities in the anoxic sediments of meromictic Lake Kivu.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {291-310}, pmid = {22430505}, issn = {1432-184X}, mesh = {Anaerobiosis ; Archaea/classification/*genetics/growth &amp; development/metabolism ; Cloning, Molecular ; Crenarchaeota/classification/genetics/growth &amp; development/metabolism ; DNA, Archaeal/analysis/chemistry/genetics ; DNA, Ribosomal/analysis ; *Ecosystem ; Euryarchaeota/classification/genetics/growth &amp; development/metabolism ; Gene Library ; Genes, rRNA ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; Methane/metabolism ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Meromictic Lake Kivu is renowned for its enormous quantity of methane dissolved in the hypolimnion. The methane is primarily of biological origin, and its concentration has been increasing in the past half-century. Insight into the origin of methane production in Lake Kivu has become relevant with the recent commercial extraction of methane from the hypolimnion. This study provides the first culture-independent approach to identifying the archaeal communities present in Lake Kivu sediments at the sediment-water interface. Terminal restriction fragment length polymorphism analysis suggests considerable heterogeneity in the archaeal community composition at varying sample locations. This diversity reflects changes in the geochemical conditions in the sediment and the overlying water, which are an effect of local groundwater inflows. A more in-depth look at the archaeal community composition by clone library analysis revealed diverse phylogenies of Euryarchaeota and Crenarachaeota. Many of the sequences in the clone libraries belonged to globally distributed archaeal clades such as the rice cluster V and Lake Dagow sediment environmental clusters. Several of the determined clades were previously thought to be rare among freshwater sediment Archaea (e.g., sequences related to the SAGMEG-1 clade). Surprisingly, there was no observed relation of clones to known hydrogentrophic methanogens and less than 2 % of clones were related to acetoclastic methanogens. The local variability, diversity, and novelty of the archaeal community structure in Lake Kivu should be considered when making assumptions on the biogeochemical functioning of its sediments.}, }
@article {pmid22430504, year = {2012}, author = {Xie, Y and Luo, Z and Li, Z and Deng, M and Liu, H and Zhu, B and Ruan, B and Li, L}, title = {Structural shifts of fecal microbial communities in rats with acute rejection after liver transplantation.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {546-554}, pmid = {22430504}, issn = {1432-184X}, mesh = {Animals ; Bacteria/*classification/*genetics/growth &amp; development ; Bacteroides/genetics/growth &amp; development ; Bifidobacterium/genetics ; Denaturing Gradient Gel Electrophoresis/methods ; Feces/*microbiology ; *Graft Rejection ; Intestinal Mucosa/microbiology ; Liver/metabolism/pathology ; *Liver Transplantation ; Male ; Metagenome ; Polymerase Chain Reaction/methods ; Rats ; Rats, Inbred Lew ; Reverse Transcriptase Polymerase Chain Reaction/methods ; Ruminococcus/genetics/growth &amp; development ; }, abstract = {Bacterial translocation and the development of sepsis after orthotopic liver transplantation (OLT) may be promoted by immunological damage to the intestinal mucosa or by quantitative and qualitative changes in intestinal microbiota. This study monitored structural shifts of gut microbiota in rats with OLT using PCR-denaturing gradient gel electrophoresis (DGGE) and real-time quantitative PCR (RT-qPCR). RT-qPCR targets six major microorganisms (Domain Bacteria, Bacteroides, Bifidobacteria, Enterobacteriaceae, Lactobacillus and Clostridium leptum subgroup). Isograft, Allograft and Sham model were studied. Bacterial translocation to host organs and plasma endotoxin were determined. Alteration in gut microbiota was associated with the elevation of plasma endotoxin and a higher rate of bacterial translocation (BT) to liver in rats with acute rejection. Dynamic analysis of DGGE fingerprints showed that the gut microbiota structure of animals in the three groups was similar before the operation. But significant alterations in the composition of fecal microbiota in Allograft group were observed at 1 and 2 weeks after the OLT. The acute rejection was accompanied by the shifts of gut microbiota towards members of Bacteroides and Ruminococcus. Results from RT-qPCR indicated that Bacteroides significantly increased at 2 weeks after the OLT, whereas numbers of Bifidobacterium spp. decreased at 1 week and recovered at 2 weeks after the OLT. In summary, our data showed that rats with acute rejection after OLT exhibited significant structure shifts in the gut microbiota which dominant by overgrowth of Bacteroides and Ruminococcus, and these were associated with elevation of plasma endotoxin and higher rate of BT.}, }
@article {pmid22430503, year = {2012}, author = {Mishra, A and Gond, SK and Kumar, A and Sharma, VK and Verma, SK and Kharwar, RN and Sieber, TN}, title = {Season and tissue type affect fungal endophyte communities of the Indian medicinal plant Tinospora cordifolia more strongly than geographic location.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {388-398}, pmid = {22430503}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/pharmacology ; Ascomycota/classification/genetics/*isolation &amp; purification ; Ecosystem ; Endophytes/classification/genetics/*isolation &amp; purification ; Fungi ; Humans ; India ; Microbial Sensitivity Tests ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Plant Stems/microbiology ; Plants, Medicinal/*microbiology ; *Seasons ; Species Specificity ; Spores, Bacterial/drug effects ; Tinospora/*microbiology ; }, abstract = {A total of 1,151 endophytic fungal isolates representing 29 taxa were isolated from symptom-less, surface-sterilized segments of stem, leaf, petiole, and root of Tinospora cordifolia which had been collected at three locations differing in air pollution in India (Ramnagar, Banaras Hindu University, Maruadih) during three seasons (summer, monsoon, winter). Endophytes were most abundant in leaf tissues (29.38% of all isolates), followed by stem (18.16%), petiole (10.11%), and root segments (6.27%). The frequency of colonization (CF) varied more strongly among tissue type and season than location. CF was maximal during monsoon followed by winter and minimal during summer. A species each of Guignardia and Acremonium could only be isolated from leaves, whereas all other species occurred in at least two tissue types. Penicillium spp. were dominant (12.62% of all isolates), followed by Colletotrichum spp. (11.8%), Cladosporium spp. (8.9%), Chaetomium globosum (8.1%), Curvularia spp. (7.6%), and Alternaria alternata (6.8%). Species richness, evenness, and the Shannon-Wiener diversity index followed the same pattern as the CF with the tissue type and the season having the greatest effect on these indices, suggesting that tissue type and season are more influential than geography. Dissimilarity of endophyte communities in regards to species composition was highest among seasons. Colletotrichum linicola occurred almost exclusively in winter, Fusarium oxysporum only in winter and summer but never during monsoon and Curvularia lunata only in winter and during monsoon but never in summer. Emissions of NO(2), SO(2), and suspended particulate matter were negatively correlated with the CF. Ozone did not have any effect. The frequency of most species declined with increasing pollution, but some showed an opposite trend (e.g., Aspergillus flavus). Five unnamed taxa (sterile mycelia) were identified as Aspergillus tubingensis, Colletotrichum crassipes, Botryosphaeria rhodina, Aspergillus sydowii, and Pseudofusicoccum violaceum, using molecular tools. Fifteen of the 29 endophyte taxa exhibited antibacterial activity. B. rhodina (JQ031157) and C. globosum showed activity against all bacterial human pathogens tested, with the former showing higher activity than the latter.}, }
@article {pmid22428117, year = {2012}, author = {Wakahama, T and Okuyama, H and Maoka, T and Takaichi, S}, title = {Unique carotenoid lactoside, P457, in Symbiodinium sp. of dinoflagellate.}, journal = {Acta biochimica Polonica}, volume = {59}, number = {1}, pages = {155-157}, pmid = {22428117}, issn = {1734-154X}, mesh = {Carotenoids/*chemistry ; Dinoflagellida/*chemistry ; Lactose/*analogs &amp; derivatives/chemistry ; Molecular Structure ; }, abstract = {The dinoflagellates are a large group of unicellular alge in marine and fresh water. Some are an endosymbiont of marine animals. Photosynthetic dinoflagellates have peridinin, a light-harvesting carotenoid. In addition, a unique carotenoid, P457, was found from Amphinidium. The presence of P457 in Symbiodinium derived from marine animals has not been reported. We reconfirmed the molecular structure of P457, a neoxanthin-like carotenoid with an aldehyde group and a lactoside, from Symbiodinium sp. NBRC 104787 isolated from a sea anemone. In addition, we investigated the distribution of P457 and peridinin in various Symbiodinium and scleractinian coral species, and possible biosynthetic pathways of these carotenoids are proposed.}, }
@article {pmid22427865, year = {2012}, author = {Toenshoff, ER and Kvellestad, A and Mitchell, SO and Steinum, T and Falk, K and Colquhoun, DJ and Horn, M}, title = {A novel betaproteobacterial agent of gill epitheliocystis in seawater farmed Atlantic salmon (Salmo salar).}, journal = {PloS one}, volume = {7}, number = {3}, pages = {e32696}, pmid = {22427865}, issn = {1932-6203}, mesh = {Animals ; Aquaculture ; Bacterial Infections/genetics/*veterinary ; *Betaproteobacteria ; Epithelium/*microbiology/pathology ; Fish Diseases/*microbiology ; Gills/*microbiology/pathology ; In Situ Hybridization, Fluorescence/veterinary ; Norway ; RNA, Ribosomal, 16S/genetics ; *Salmo salar ; Species Specificity ; }, abstract = {Epitheliocystis, a disease characterised by cytoplasmic bacterial inclusions (cysts) in the gill and less commonly skin epithelial cells, has been reported in many marine and freshwater fish species and may be associated with mortality. Previously, molecular and ultrastructural analyses have exclusively associated members of the Chlamydiae with such inclusions. Here we investigated a population of farmed Atlantic salmon from the west coast of Norway displaying gill epitheliocystis. Although 'Candidatus Piscichlamydia salmonis', previously reported to be present in such cysts, was detected by PCR in most of the gill samples analysed, this bacterium was found to be a rare member of the gill microbiota, and not associated with the observed cysts as demonstrated by fluorescence in situ hybridization assays. The application of a broad range 16 S rRNA targeted PCR assay instead identified a novel betaproteobacterium as an abundant member of the gill microbiota. Fluorescence in situ hybridization demonstrated that this bacterium, tentatively classified as 'Candidatus Branchiomonas cysticola', was the cyst-forming agent in these samples. While histology and ultrastructure of 'Ca. B. cysticola' cysts revealed forms similar to the reticulate and intermediate bodies described in earlier reports from salmon in seawater, no elementary bodies typical of the chlamydial developmental cycle were observed. In conclusion, this study identified a novel agent of epitheliocystis in sea-farmed Atlantic salmon and demonstrated that these cysts can be caused by bacteria phylogenetically distinct from the Chlamydiae.}, }
@article {pmid22419104, year = {2012}, author = {Paziewska, A and Siński, E and Harris, PD}, title = {Recombination, diversity and allele sharing of infectivity proteins between Bartonella species from rodents.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {525-536}, pmid = {22419104}, issn = {1432-184X}, mesh = {*Alleles ; Animals ; Arvicolinae ; Bacterial Proteins/genetics ; Bartonella/classification/*genetics/pathogenicity ; Bartonella Infections/microbiology/*veterinary ; *Genetic Variation ; Murinae ; Poland ; *Recombination, Genetic ; Rodent Diseases/*microbiology ; Species Specificity ; Virulence Factors/*genetics ; }, abstract = {The alpha-Proteobacterium Bartonella is a common parasite of voles and mice, giving rise to short-lived (4 weeks to 2 months) infections. Here, we report high sequence diversity in genes of the VirB/VirD type IV secretion system (T4SS), amongst Bartonella from natural rodent populations in NE Poland. The VirB5 protein is predicted to consist of three conserved alpha helices separated by loops of variable length which include numerous indels. The C-terminal domain includes repeat stretches of KEK residues, reflecting underlying homopolymeric stretches of adenine residues. A total of 16 variants of VirB5, associated with host identity, but not bacterial taxon, were identified from 22 Bartonella isolates. One was clearly a recombinant from two others, another included an insertion of two KEK repeats. The virB5 gene appears to evolve via both mutation and recombination, as well as slippage mediated insertion/deletion events. The recombinational units are thought to be relatively short, as there was no evidence of linkage disequilibrium between virB5 and the bepA locus only 5.5 kb distant. The diversity of virB5 is assumed to be related to immunological role of this protein in Bartonella infections; diversity of virB5 may assist persistence of Bartonella in the rodent population, despite the relatively short (3-4 weeks) duration of individual infections. It is clear from the distribution of virB5 and bepA alleles that recombination within and between clades is widespread, and frequently crosses the boundaries of conventionally recognised Bartonella species.}, }
@article {pmid22419103, year = {2012}, author = {Chaudhry, V and Rehman, A and Mishra, A and Chauhan, PS and Nautiyal, CS}, title = {Changes in bacterial community structure of agricultural land due to long-term organic and chemical amendments.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {450-460}, pmid = {22419103}, issn = {1432-184X}, mesh = {Agriculture/*methods ; Bacteria/classification/*genetics/*growth &amp; development ; *Ecosystem ; Environmental Monitoring ; Fertilizers ; Genes, rRNA ; Manure ; Phylogeny ; Poaceae/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Community level physiological profiling and pyrosequencing-based analysis of the V1-V2 16S rRNA gene region were used to characterize and compare microbial community structure, diversity, and bacterial phylogeny from soils of chemically cultivated land (CCL), organically cultivated land (OCL), and fallow grass land (FGL) for 16 years and were under three different land use types. The entire dataset comprised of 16,608 good-quality sequences (CCL, 6,379; OCL, 4,835; FGL, 5,394); among them 12,606 sequences could be classified in 15 known phylum. The most abundant phylum were Proteobacteria (29.8%), Acidobacteria (22.6%), Actinobacteria (11.1%), and Bacteroidetes (4.7%), while 24.3% of the sequences were from bacterial domain but could not be further classified to any known phylum. Proteobacteria, Bacteroidetes, and Gemmatimonadetes were found to be significantly abundant in OCL soil. On the contrary, Actinobacteria and Acidobacteria were significantly abundant in CCL and FGL, respectively. Our findings supported the view that organic compost amendment (OCL) activates diverse group of microorganisms as compared with conventionally used synthetic chemical fertilizers. Functional diversity and evenness based on carbon source utilization pattern was significantly higher in OCL as compared to CCL and FGL, suggesting an improvement in soil quality. This abundance of microbes possibly leads to the enhanced level of soil organic carbon, soil organic nitrogen, and microbial biomass in OCL and FGL soils as collated with CCL. This work increases our current understanding on the effect of long-term organic and chemical amendment applications on abundance, diversity, and composition of bacterial community inhabiting the soil for the prospects of agricultural yield and quantity of soil.}, }
@article {pmid22419056, year = {2012}, author = {Vermeiren, J and Hindryckx, P and Van Nieuwenhuyse, G and Laukens, D and De Vos, M and Boon, N and Van de Wiele, T}, title = {Intrarectal nitric oxide administration prevents cellular infiltration but not colonic injury during dextran sodium sulfate colitis.}, journal = {Digestive diseases and sciences}, volume = {57}, number = {7}, pages = {1832-1837}, pmid = {22419056}, issn = {1573-2568}, mesh = {Administration, Rectal ; Animals ; Cell Membrane Permeability/drug effects ; Colitis/chemically induced/*pathology/*prevention &amp; control ; Colon/drug effects/metabolism/*pathology ; Dextran Sulfate/adverse effects ; Disease Models, Animal ; Dose-Response Relationship, Drug ; Mice ; Mice, Inbred Strains ; Nitric Oxide/*administration &amp; dosage/metabolism/*pharmacology ; Peroxidase/metabolism ; Severity of Illness Index ; }, abstract = {BACKGROUND: During inflammation in the gastrointestinal tract, the production of nitric oxide (NO) is mediated by the mucosal conversion of L-arginine. Recently, it was shown that the gut microbiota can also produce NO.<br><br>AIMS: The effect of gut luminal NO on inflammatory processes of an experimental colitis mice model was investigated by administrating NO directly to the colon, mimicking microbial NO production.<br><br>METHODS: Twenty-four mice received daily intrarectal treatment with a NO donor in 2 doses and 8 mice were treated with placebo. Starting 1 day later, 18 of these mice were fed ad libitum with 4% of dextran sodium sulfate (DSS) in their drinking water to induce colitis. At day 6, histopathology (both the inflammation and damage score), myeloperoxidase (MPO)-activity, colon length and colonic permeability were evaluated.<br><br>RESULTS: Co-administration of NO during DSS exposure inhibited the induction of an increasing colonic MPO-activity. This protective effect of NO was confirmed by the histological inflammation score showing a similar trend. The colonic permeability was restored when very low levels of NO were administered to the DSS-mice. On the other hand, the colon length of the NO-treated DSS-mice was negatively correlated with the NO dose and the histological damage score was not improved.<br><br>CONCLUSIONS: Our results indicate that intrarectal administration of NO has clear anti-inflammatory effects in experimental colitis, but does not prevent colonic damage. Therefore, NO-producing microorganisms in the gut lumen should be accounted as a modulating process during colitis.}, }
@article {pmid22418081, year = {2012}, author = {De Vrieze, J and Hennebel, T and Boon, N and Verstraete, W}, title = {Methanosarcina: the rediscovered methanogen for heavy duty biomethanation.}, journal = {Bioresource technology}, volume = {112}, number = {}, pages = {1-9}, doi = {10.1016/j.biortech.2012.02.079}, pmid = {22418081}, issn = {1873-2976}, mesh = {Anaerobiosis ; Biodegradation, Environmental ; Bioreactors/microbiology ; Methane/*metabolism ; Methanosarcina/*metabolism ; }, abstract = {Anaerobic digestion is an important technology in the framework of renewable energy production. The anaerobic digestion system is susceptible to perturbations due to the sensitivity of the methanogens towards environmental factors. Currently, technology is evolving from conventional waste treatment, i.e. the removal of pollutants, to very intensive biogas production from concentrated wastes, in the framework of bio-energy production. In the latter configuration Methanosarcina species appear to be of crucial importance. Methanosarcina sp. are, compared to other methanogens, quite robust towards different impairments. They are reported to be tolerant to total ammonium concentrations up to 7000 mg L(-1), salt concentrations up to 18,000 mg Na(+)L(-1), a pH shock of 0.8-1.0 units and acetate concentrations up to 15,000 mg CODL(-1). The possibilities of Methanosarcina sp. as key organisms in specific types of anaerobic digestion systems are demonstrated in this review.}, }
@article {pmid22417507, year = {2011}, author = {Rodríguez-Lerma, GK and Gutiérrez-Moreno, K and Cárdenas-Manríquez, M and Botello-Álvarez, E and Jiménez-Islas, H and Rico-Martínez, R and Navarrete-Bolaños, JL}, title = {Microbial ecology studies of spontaneous fermentation: starter culture selection for prickly pear wine production.}, journal = {Journal of food science}, volume = {76}, number = {6}, pages = {M346-52}, doi = {10.1111/j.1750-3841.2011.02208.x}, pmid = {22417507}, issn = {1750-3841}, mesh = {Beverages/analysis/*microbiology ; Databases, Factual ; Diet/ethnology ; Ethanol/analysis ; Fermentation ; Flame Ionization ; Fruit/chemistry/*microbiology ; Gas Chromatography-Mass Spectrometry ; Kinetics ; Mexico ; Molecular Typing ; Mycological Typing Techniques ; Opuntia/chemistry/*microbiology ; Pichia/classification/isolation &amp; purification/*metabolism ; Quality Control ; Rural Population ; Saccharomyces cerevisiae/classification/isolation &amp; purification/*metabolism ; Species Specificity ; Volatile Organic Compounds/analysis/chemistry ; Wine/*analysis/*microbiology ; }, abstract = {A procedure for designing starter cultures for fermentation is illustrated for prickly pear wine production. The illustration includes kinetic studies on inoculated and spontaneous fermentation, microorganism identification studies based on molecular biology tools, and microbial ecology studies, which led to the selection of strains that are capable of synthesizing alcohol and desirable volatile compounds. Results show that a mixed starter inoculum containing Pichia fermentans and Saccharomyces cerevisiae leads to a fermented product that contains 8.37% alcohol (v/v). The gas chromatography and mass spectrometry (GC-MS) analysis shows the presence of 9 major volatile compounds (Isobutanol, Isopentanol, Ethyl acetate, Isoamyl acetate, Ethyl octanoate, Ethyl decanoate, Ethyl 9-decanoate, β-Phenylethyl acetate, and Phenylethyl alcohol) that have ethereal, fruity, aromatic notes that are considered to be essential for a fine wine flavor. These compounds harmonically synergize with the alcohol to produce a fermented product with a unique flavor and taste. Several assays using the mixed culture show that the process is stable, predictable, controllable, and reproducible. Moreover, the results show that a mixed culture leads to a broader range of aromatic products than that produced by a single, pure culture. Therefore, we conclude that combinations of Saccharomyces strains and non-Saccharomyces strains can be used to obtain high-quality fermented beverages from prickly pear juice.}, }
@article {pmid22409443, year = {2012}, author = {Behrens, S and Kappler, A and Obst, M}, title = {Linking environmental processes to the in situ functioning of microorganisms by high-resolution secondary ion mass spectrometry (NanoSIMS) and scanning transmission X-ray microscopy (STXM).}, journal = {Environmental microbiology}, volume = {14}, number = {11}, pages = {2851-2869}, doi = {10.1111/j.1462-2920.2012.02724.x}, pmid = {22409443}, issn = {1462-2920}, mesh = {*Environmental Microbiology ; *Microscopy, Electron, Scanning Transmission ; Nitrogen Fixation ; *Spectrometry, Mass, Secondary Ion ; X-Rays ; }, abstract = {Environmental microbiology research increasingly focuses on the single microbial cell as the defining entity that drives environmental processes. The interactions of individual microbial cells with each other, the environment and with higher organisms shape microbial communities and control the functioning of whole ecosystems. A single-cell view of microorganisms in their natural environment requires analytical tools that measure both cell function and chemical speciation at the submicrometre scale. Here we review the technical capabilities and limitations of high-resolution secondary ion mass spectrometry (NanoSIMS) and scanning transmission (soft) X-ray microscopy (STXM) and give examples of their applications. Whereas NanoSIMS can be combined with isotope-labelling, thereby localizing the distribution of cellular activities (e.g. carbon/nitrogen fixation/turnover), STXM provides information on the location and chemical speciation of metabolites and products of redox reactions. We propose the combined use of both techniques and discuss the technical challenges of their joint application. Both techniques have the potential to enhance our understanding of cellular mechanisms and activities that contribute to microbially mediated processes, such as the biogeochemical cycling of elements, the transformation of contaminants and the precipitation of mineral phases.}, }
@article {pmid22408730, year = {2012}, author = {Bodelier, PL and Bär-Gilissen, MJ and Meima-Franke, M and Hordijk, K}, title = {Structural and functional response of methane-consuming microbial communities to different flooding regimes in riparian soils.}, journal = {Ecology and evolution}, volume = {2}, number = {1}, pages = {106-127}, pmid = {22408730}, issn = {2045-7758}, abstract = {Climate change will lead to more extreme precipitation and associated increase of flooding events of soils. This can turn these soils from a sink into a source of atmospheric methane. The latter will depend on the balance of microbial methane production and oxidation. In the present study, the structural and functional response of methane oxidizing microbial communities was investigated in a riparian flooding gradient. Four sites differing in flooding frequency were sampled and soil-physico-chemistry as well as methane oxidizing activities, numbers and community composition were assessed. Next to this, the active community members were determined by stable isotope probing of lipids. Methane consumption as well as population size distinctly increased with flooding frequency. All methane consumption parameters (activity, numbers, lipids) correlated with soil moisture, organic matter content, and conductivity. Methane oxidizing bacteria were present and activated quickly even in seldom flooded soils. However, the active species comprised only a few representatives belonging to the genera Methylobacter, Methylosarcina, and Methylocystis, the latter being active only in permanently or regularly flooded soils.This study demonstrates that soils exposed to irregular flooding harbor a very responsive methane oxidizing community that has the potential to mitigate methane produced in these soils. The number of active species is limited and dominated by one methane oxidizing lineage. Knowledge on the characteristics of these microbes is necessary to assess the effects of flooding of soils and subsequent methane cycling therein.}, }
@article {pmid22406286, year = {2012}, author = {De Corte, S and Sabbe, T and Hennebel, T and Vanhaecke, L and De Gusseme, B and Verstraete, W and Boon, N}, title = {Doping of biogenic Pd catalysts with Au enables dechlorination of diclofenac at environmental conditions.}, journal = {Water research}, volume = {46}, number = {8}, pages = {2718-2726}, doi = {10.1016/j.watres.2012.02.036}, pmid = {22406286}, issn = {1879-2448}, mesh = {Biodegradation, Environmental ; Carbamazepine/isolation &amp; purification ; Catalysis ; Chromatography, Liquid ; Diatrizoate/isolation &amp; purification ; Diclofenac/chemistry/*isolation &amp; purification ; Gold/*metabolism ; *Halogenation ; Hospitals ; Kinetics ; Mass Spectrometry ; Medical Waste/analysis ; Palladium/*metabolism ; Shewanella/*metabolism ; Time Factors ; Waste Disposal, Fluid ; Water Purification ; }, abstract = {By using the metal reducing capacities of bacteria, Pd nanoparticles can be produced in a sustainable way ('bio-Pd'). These bio-Pd nanoparticles can be used as a catalyst in, for example, dehalogenation reactions. However, some halogenated compounds are not efficiently degraded using a bio-Pd catalyst. This study shows that the activity of bio-Pd can be improved by doping with Au(0) ('bio-Pd/Au'). In contrast with bio-Pd, bio-Pd/Au could perform the removal of the model pharmaceutical compound diclofenac from an aqueous medium in batch experiments at neutral pH and with H(2) as the hydrogen donor (first order decay constant of 0.078 ± 0.009 h(-1)). Dehalogenation was for both catalysts the only observed reaction. For bio-Pd/Au, a disproportional increase of catalytic activity was observed with increasing Pd-content of the catalyst. In contrast, when varying the Au-content of the catalyst, a Pd/Au mass ratio of 50/1 showed the highest catalytic activity (first order decay value of 0.52 ± 0.02 h(-1)). The removal of 6.40 μg L(-1) diclofenac from a wastewater treatment plant effluent using bio-Pd was not possible even after prolonged reaction time. However, by using the most active bio-Pd/Au catalyst, 43.8 ± 0.5% of the initially present diclofenac could be removed after 24 h. This study shows that doping of bio-Pd nanoparticles with Au(0) can be a promising approach for the reductive treatment of wastewaters containing halogenated contaminants.}, }
@article {pmid22404962, year = {2012}, author = {Zargar, K and Conrad, A and Bernick, DL and Lowe, TM and Stolc, V and Hoeft, S and Oremland, RS and Stolz, J and Saltikov, CW}, title = {ArxA, a new clade of arsenite oxidase within the DMSO reductase family of molybdenum oxidoreductases.}, journal = {Environmental microbiology}, volume = {14}, number = {7}, pages = {1635-1645}, doi = {10.1111/j.1462-2920.2012.02722.x}, pmid = {22404962}, issn = {1462-2920}, mesh = {Arsenate Reductases/genetics ; Arsenic/*metabolism ; Autotrophic Processes ; California ; Ectothiorhodospira/*enzymology/genetics ; Genes, Bacterial ; Hot Springs/microbiology ; Iron-Sulfur Proteins ; Metagenome ; Operon ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Arsenotrophy, growth coupled to autotrophic arsenite oxidation or arsenate respiratory reduction, occurs only in the prokaryotic domain of life. The enzymes responsible for arsenotrophy belong to distinct clades within the DMSO reductase family of molybdenum-containing oxidoreductases: specifically arsenate respiratory reductase, ArrA, and arsenite oxidase, AioA (formerly referred to as AroA and AoxB). A new arsenite oxidase clade, ArxA, represented by the haloalkaliphilic bacterium Alkalilimnicola ehrlichii strain MLHE-1 was also identified in the photosynthetic purple sulfur bacterium Ectothiorhodospira sp. strain PHS-1. A draft genome sequence of PHS-1 was completed and an arx operon similar to MLHE-1 was identified. Gene expression studies showed that arxA was strongly induced with arsenite. Microbial ecology investigation led to the identification of additional arxA-like sequences in Mono Lake and Hot Creek sediments, both arsenic-rich environments in California. Phylogenetic analyses placed these sequences as distinct members of the ArxA clade of arsenite oxidases. ArxA-like sequences were also identified in metagenome sequences of several alkaline microbial mat environments of Yellowstone National Park hot springs. These results suggest that ArxA-type arsenite oxidases appear to be widely distributed in the environment presenting an opportunity for further investigations of the contribution of Arx-dependent arsenotrophy to the arsenic biogeochemical cycle.}, }
@article {pmid22403578, year = {2012}, author = {Pereira E Silva, MC and Poly, F and Guillaumaud, N and van Elsas, JD and Salles, JF}, title = {Fluctuations in Ammonia Oxidizing Communities Across Agricultural Soils are Driven by Soil Structure and pH.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {77}, pmid = {22403578}, issn = {1664-302X}, abstract = {The milieu in soil in which microorganisms dwell is never constant. Conditions such as temperature, water availability, pH and nutrients frequently change, impacting the overall functioning of the soil system. To understand the effects of such factors on soil functioning, proxies (indicators) of soil function are needed that, in a sensitive manner, reveal normal amplitude of variation. Thus, the so-called normal operating range (NOR) of soil can be defined. In this study we determined different components of nitrification by analyzing, in eight agricultural soils, how the community structures and sizes of ammonia oxidizing bacteria and archaea (AOB and AOA, respectively), and their activity, fluctuate over spatial and temporal scales. The results indicated that soil pH and soil type are the main factors that influence the size and structure of the AOA and AOB, as well as their function. The nitrification rates varied between 0.11 ± 0.03 μgN h(-1) gdw(-1) and 1.68 ± 0.11 μgN h(-1) gdw(-1), being higher in soils with higher clay content (1.09 ± 0.12 μgN h(-1) gdw(-1)) and lower in soils with lower clay percentages (0.27 ± 0.04 μgN h(-1) gdw(-1)). Nitrifying activity was driven by soil pH, mostly related to its effect on AOA but not on AOB abundance. Regarding the influence of soil parameters, clay content was the main soil factor shaping the structure of both the AOA and AOB communities. Overall, the potential nitrifying activities were higher and more variable over time in the clayey than in the sandy soils. Whereas the structure of AOB fluctuated more (62.7 ± 2.10%) the structure of AOA communities showed lower amplitude of variation (53.65 ± 3.37%). Similar trends were observed for the sizes of these communities. The present work represents a first step toward defining a NOR for soil nitrification. The sensitivity of the process and organisms to impacts from the milieu support their use as proxies in the NOR of agricultural soils. Moreover, the clear effect of soil texture established here suggests that the NOR should be defined in a soil type-specific manner.}, }
@article {pmid22403575, year = {2012}, author = {Pester, M and Knorr, KH and Friedrich, MW and Wagner, M and Loy, A}, title = {Sulfate-reducing microorganisms in wetlands - fameless actors in carbon cycling and climate change.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {72}, pmid = {22403575}, issn = {1664-302X}, support = {P 18836/FWF_/Austrian Science Fund FWF/Austria ; P 20185/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Freshwater wetlands are a major source of the greenhouse gas methane but at the same time can function as carbon sink. Their response to global warming and environmental pollution is one of the largest unknowns in the upcoming decades to centuries. In this review, we highlight the role of sulfate-reducing microorganisms (SRM) in the intertwined element cycles of wetlands. Although regarded primarily as methanogenic environments, biogeochemical studies have revealed a previously hidden sulfur cycle in wetlands that can sustain rapid renewal of the small standing pools of sulfate. Thus, dissimilatory sulfate reduction, which frequently occurs at rates comparable to marine surface sediments, can contribute up to 36-50% to anaerobic carbon mineralization in these ecosystems. Since sulfate reduction is thermodynamically favored relative to fermentative processes and methanogenesis, it effectively decreases gross methane production thereby mitigating the flux of methane to the atmosphere. However, very little is known about wetland SRM. Molecular analyses using dsrAB [encoding subunit A and B of the dissimilatory (bi)sulfite reductase] as marker genes demonstrated that members of novel phylogenetic lineages, which are unrelated to recognized SRM, dominate dsrAB richness and, if tested, are also abundant among the dsrAB-containing wetland microbiota. These discoveries point toward the existence of so far unknown SRM that are an important part of the autochthonous wetland microbiota. In addition to these numerically dominant microorganisms, a recent stable isotope probing study of SRM in a German peatland indicated that rare biosphere members might be highly active in situ and have a considerable stake in wetland sulfate reduction. The hidden sulfur cycle in wetlands and the fact that wetland SRM are not well represented by described SRM species explains their so far neglected role as important actors in carbon cycling and climate change.}, }
@article {pmid22397093, year = {2012}, author = {Zentek, J and Buchheit-Renko, S and Männer, K and Pieper, R and Vahjen, W}, title = {Intestinal concentrations of free and encapsulated dietary medium-chain fatty acids and effects on gastric microbial ecology and bacterial metabolic products in the digestive tract of piglets.}, journal = {Archives of animal nutrition}, volume = {66}, number = {1}, pages = {14-26}, doi = {10.1080/1745039x.2011.644916}, pmid = {22397093}, issn = {1745-039X}, mesh = {Animal Feed/*analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Bacteria/isolation &amp; purification/*metabolism ; Caprylates/chemistry/*pharmacology ; Decanoic Acids/chemistry/*pharmacology ; Diet/veterinary ; Gastrointestinal Tract/chemistry/*microbiology ; Male ; Swine/*metabolism ; }, abstract = {The influence of low dietary levels of free and encapsulated medium-chain fatty acids on their concentrations in the digesta, the gastric microbial ecology and bacterial metabolic products in the gastrointestinal tract (GIT) in weaned piglets was studied. Starting after weaning, 36 piglets were fed a diet without (Control) or with medium-chain fatty acids uncoated (MCFA) or coated with vegetable fat and lecithin (MCFAc). After 4 weeks, the animals were killed, and digesta from the stomach and different sections of the GIT were collected. The concentrations of caprylic (p < 0.001) and capric (p = 0.001) acids were higher in the stomachs of piglets fed diets MCFA and MCFAc compared to the Control group. The concentrations dropped rapidly along the GIT, regardless of encapsulation, and tended to be higher in groups MCFA and MCFAc compared to the Control. Compared to the Control group, ingestion of diet MCFAc led to an increase in the number of eubacteria (p = 0.001), enterobacteriaceae (p < 0.001), clostridial clusters I (p = 0.001) and IV (p = 0.019), Lactobacillus johnsonii (p < 0.001) and Lactobacillus amylovorus (p = 0.001) in gastric contents. A similar trend was seen with diet MCFA. Relative concentrations of short-chain fatty acids were characterised by lower propionic acid levels (p = 0.045), numerically (p < 0.1) higher acetic, lower n-butyric and i-valeric acid concentrations in the small intestine. Lactic acid concentrations were not significantly changed in the GIT, but ammonia concentrations increased (p < 0.001) in the distal small intestine in the MCFA and MCFAc groups. In conclusion, medium-chain fatty acids affected microbial ecology parameters in the gastric contents and bacterial metabolites in the small intestine. At low dietary levels, medium-chain fatty acids may be regarded as modulators of the gastric microbiota in weaned piglets.}, }
@article {pmid22395784, year = {2012}, author = {Tripathi, BM and Kim, M and Singh, D and Lee-Cruz, L and Lai-Hoe, A and Ainuddin, AN and Go, R and Rahim, RA and Husni, MH and Chun, J and Adams, JM}, title = {Tropical soil bacterial communities in Malaysia: pH dominates in the equatorial tropics too.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {474-484}, pmid = {22395784}, issn = {1432-184X}, mesh = {Actinobacteria/classification/*genetics/isolation &amp; purification ; Agriculture ; Biodiversity ; Carbon/analysis ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Forestry ; Genes, rRNA ; Gram-Negative Bacteria/classification/*genetics/isolation &amp; purification ; Hydrogen-Ion Concentration ; Malaysia ; Molecular Sequence Data ; Nitrogen/analysis ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA/methods ; Soil/*analysis/chemistry ; *Soil Microbiology ; *Tropical Climate ; }, abstract = {The dominant factors controlling soil bacterial community variation within the tropics are poorly known. We sampled soils across a range of land use types--primary (unlogged) and logged forests and crop and pasture lands in Malaysia. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1-V3 region was pyrosequenced using the 454 Roche machine. We found that land use in itself has a weak but significant effect on the bacterial community composition. However, bacterial community composition and diversity was strongly correlated with soil properties, especially soil pH, total carbon, and C/N ratio. Soil pH was the best predictor of bacterial community composition and diversity across the various land use types, with the highest diversity close to neutral pH values. In addition, variation in phylogenetic structure of dominant lineages (Alphaproteobacteria, Beta/Gammaproteobacteria, Acidobacteria, and Actinobacteria) is also significantly correlated with soil pH. Together, these results confirm the importance of soil pH in structuring soil bacterial communities in Southeast Asia. Our results also suggest that unlike the general diversity pattern found for larger organisms, primary tropical forest is no richer in operational taxonomic units of soil bacteria than logged forest, and agricultural land (crop and pasture) is actually richer than primary forest, partly due to selection of more fertile soils that have higher pH for agriculture and the effects of soil liming raising pH.}, }
@article {pmid22395783, year = {2012}, author = {Dini-Andreote, F and Andreote, FD and Araújo, WL and Trevors, JT and van Elsas, JD}, title = {Bacterial genomes: habitat specificity and uncharted organisms.}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {1-7}, pmid = {22395783}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/*genetics/isolation &amp; purification ; *Ecosystem ; Environmental Microbiology ; *Genome, Bacterial ; Humans ; Phylogeny ; }, abstract = {The capability and speed in generating genomic data have increased profoundly since the release of the draft human genome in 2000. Additionally, sequencing costs have continued to plummet as the next generation of highly efficient sequencing technologies (next-generation sequencing) became available and commercial facilities promote market competition. However, new challenges have emerged as researchers attempt to efficiently process the massive amounts of sequence data being generated. First, the described genome sequences are unequally distributed among the branches of bacterial life and, second, bacterial pan-genomes are often not considered when setting aims for sequencing projects. Here, we propose that scientists should be concerned with attaining an improved equal representation of most of the bacterial tree of life organisms, at the genomic level. Moreover, they should take into account the natural variation that is often observed within bacterial species and the role of the often changing surrounding environment and natural selection pressures, which is central to bacterial speciation and genome evolution. Not only will such efforts contribute to our overall understanding of the microbial diversity extant in ecosystems as well as the structuring of the extant genomes, but they will also facilitate the development of better methods for (meta)genome annotation.}, }
@article {pmid22391799, year = {2012}, author = {Colombet, J and Sime-Ngando, T}, title = {Seasonal depth-related gradients in virioplankton: lytic activity and comparison with protistan grazing potential in Lake Pavin (France).}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {67-78}, pmid = {22391799}, issn = {1432-184X}, mesh = {*Bacterial Physiological Phenomena ; *Ecosystem ; Eukaryota/*physiology ; Lakes/*chemistry/microbiology/parasitology/virology ; Plankton/*physiology ; Seasons ; *Virus Physiological Phenomena ; Viruses/isolation &amp; purification ; }, abstract = {This study presents an original depth-related survey of virioplankton lytic activity in relation to prokaryotic production and potential protistan bacterivory in the deep (Z(max) = 92 m) meromictic volcanic Lake Pavin (Massif Central, France). The sampling strategy was designed to be representative of the physico-chemical gradients of the water column of the lake, and of the seasonal variability as well, i.e. 12 different depths sampled in triplicates from April to December 2005. In the space, viral lytic activity estimated from the frequency of visibly infected prokaryotic cells and from burst size over the study period generally decreased with depth. This was viewed as a paradox compared to the abundances of viruses and prokaryotes and to the prokaryotic production which increased with depth. The seasonal variability in viral lytic activity was correlated with prokaryotic variables (abundance and production) in the deepest waters, i.e. from the hypolimnion downwards. Compared to previous studies known from the mixolimnion, we conclude that the deep waters in Lake Pavin represent an exclusive environment for heterotrophic prokaryotes whose seasonal activity offers an optimal and unique resource for thriving viral communities, some of which may be typical, endemic to the ambient dark, cold and stable deep water masses. Overall, the main findings in the present study get well around a previous statement that the ecology of the deepest waters of Lake Pavin is essentially driven by the dark viral loop (dissolved organic matter-prokaryotes-viruses) processes, which can sequester organic matters and nutrients for a long-lived turnover time. This is in agreement with recent demonstrations from marine systems that meso- and bathypelagic waters are optimal environments for viral survival and proliferation.}, }
@article {pmid22391798, year = {2012}, author = {Rotaru, C and Woodard, TL and Choi, S and Nevin, KP}, title = {Spatial heterogeneity of bacterial communities in sediments from an infiltration basin receiving highway runoff.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {461-473}, pmid = {22391798}, issn = {1432-184X}, mesh = {Acetates/analysis/*pharmacology ; Bacteria/classification/drug effects/*genetics ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis/genetics ; *Ecosystem ; Ferrous Compounds/metabolism ; Geologic Sediments/*microbiology ; Groundwater/chemistry/*microbiology ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Water Pollutants/analysis/*pharmacology ; }, abstract = {The bacterial community diversity of highway runoff-contaminated sediment that had undergone 19 years of acetate-based de-icing agents addition followed by three years of acetate-free de-icing agents was investigated. Analysis of 26 sediment samples from two drilled soil cores by means of 16S rDNA PCR generated 3,402 clones, indicating an overall high bacterial diversity, with no prominent members within the communities. Sequence analyses provided evidences that each sediment sample displayed a specific structure bacterial community. Proteobacteria-affiliated clones (58% and 43% for the two boreholes) predominated in all samples, followed by Actinobacteria (12% and 16%), Firmicutes (7% and 12%) and Chloroflexi (7% and 11%). The subsurface geochemistry complemented the molecular methods to further distinguish ambient and contaminant plume zones. Principal component analysis revealed that the levels of Fe(II) and dissolved oxygen were strongly correlated with bacterial communities. At elevated Fe(II) levels, sequences associated with anaerobic bacteria were detected in high levels. As iron levels declined and oxygen levels increased below the plume bottom, there was a gradual shift in the community structure toward the increase of aerobic bacteria.}, }
@article {pmid22391797, year = {2012}, author = {Lewis, DE and Chauhan, A and White, JR and Overholt, W and Green, SJ and Jasrotia, P and Wafula, D and Jagoe, C}, title = {Microbial and geochemical assessment of bauxitic un-mined and post-mined chronosequence soils from Mocho Mountains, Jamaica.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {738-749}, pmid = {22391797}, issn = {1432-184X}, mesh = {*Aluminum Oxide ; Bacteria/classification/*genetics/isolation &amp; purification ; Biodiversity ; Ecosystem ; Genes, rRNA/*genetics ; Jamaica ; *Mining ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; Soil/*analysis ; *Soil Microbiology ; }, abstract = {Microorganisms are very sensitive to environmental change and can be used to gauge anthropogenic impacts and even predict restoration success of degraded environments. Here, we report assessment of bauxite mining activities on soil biogeochemistry and microbial community structure using un-mined and three post-mined sites in Jamaica. The post-mined soils represent a chronosequence, undergoing restoration since 1987, 1997, and 2007. Soils were collected during dry and wet seasons and analyzed for pH, organic matter (OM), total carbon (TC), nitrogen (TN), and phosphorus. The microbial community structure was assessed through quantitative PCR and massively parallel bacterial ribosomal RNA (rRNA) gene sequencing. Edaphic factors and microbial community composition were analyzed using multivariate statistical approaches and revealed a significant, negative impact of mining on soil that persisted even after greater than 20 years of restoration. Seasonal fluctuations contributed to variation in measured soil properties and community composition, but they were minor in comparison to long-term effects of mining. In both seasons, post-mined soils were higher in pH but OM, TC, and TN decreased. Bacterial rRNA gene analyses demonstrated a general decrease in diversity in post-mined soils and up to a 3-log decrease in rRNA gene abundance. Community composition analyses demonstrated that bacteria from the Proteobacteria (α, β, γ, δ), Acidobacteria, and Firmicutes were abundant in all soils. The abundance of Firmicutes was elevated in newer post-mined soils relative to the un-mined soil, and this contrasted a decrease, relative to un-mined soils, in proteobacterial and acidobacterial rRNA gene abundances. Our study indicates long-lasting impacts of mining activities to soil biogeochemical and microbial properties with impending loss in soil productivity.}, }
@article {pmid22386929, year = {2012}, author = {Barcón, T and Alonso-Gutiérrez, J and Omil, F}, title = {Molecular and physiological approaches to understand the ecology of methanol degradation during the biofiltration of air streams.}, journal = {Chemosphere}, volume = {87}, number = {10}, pages = {1179-1185}, doi = {10.1016/j.chemosphere.2011.12.039}, pmid = {22386929}, issn = {1879-1298}, mesh = {Air Pollutants/*chemistry/metabolism ; Air Pollution/prevention &amp; control ; Ascomycota/genetics/isolation &amp; purification ; Bacteria/isolation &amp; purification ; Biofilms ; Bioreactors/microbiology ; Candida/*genetics/isolation &amp; purification ; Filtration/*methods ; Fungi/genetics/isolation &amp; purification ; Hydrogen-Ion Concentration ; In Situ Hybridization, Fluorescence ; Methanol/*chemistry/metabolism ; Molecular Sequence Data ; Odorants/analysis ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/genetics ; Waste Disposal, Fluid ; }, abstract = {A 13.4 L biofilter treating an off-gas stream supplemented with methanol under two different situations was studied in terms of MeOH removal efficiency, microbial ecology and odor removal. During Period 1 (P1) the reactor was packed with wood bark chips with no pH control, treating an off-gas resulting from the aerobic chamber of a membrane biological reactor treating sewage and located outdoor, whereas during Period 2 (P2) a compressed air stream fed with MeOH was treated using PVC rings and maintaining pH at neutral values. Both systems operated at 96 g MeOH m(-3) h(-1) achieving removal efficiencies of around 90% during P1 and 99.9% during P2. The relative activity of biomass developed in both systems was assessed using respirometric analysis with samples obtained from both biofilms. Higher biomass activity was obtained during P2 (0.25-0.35 kg MeOH kg(-1) VSS d(-1)) whereas 1.1 kg MeOH kg(-1) VSS d(-1) was obtained in the case of P1. The application of molecular and microscopic techniques showed that the eukaryotes were predominant during P1, being the yeast Candida boidinii the most abundant microorganism. A specific Fluorescence in situ hybridization probe was designed for C. boidinii and tested successfully. As a result of the neutral pH, a clear predominance of prokaryotes was detected during P2. Interestingly, some anaerobic bacteria were detected such as Desulfovibrio, Desulfobacteraceae species and also some archaea such as Methanosarcina.}, }
@article {pmid22385317, year = {2012}, author = {García-Moyano, A and González-Toril, E and Aguilera, &#xc1; and Amils, R}, title = {Comparative microbial ecology study of the sediments and the water column of the Río Tinto, an extreme acidic environment.}, journal = {FEMS microbiology ecology}, volume = {81}, number = {2}, pages = {303-314}, doi = {10.1111/j.1574-6941.2012.01346.x}, pmid = {22385317}, issn = {1574-6941}, mesh = {Bacteria/*genetics/isolation &amp; purification ; DNA, Bacterial/isolation &amp; purification ; Ferric Compounds/chemistry ; Gene Library ; Geologic Sediments/chemistry/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rivers/*chemistry/*microbiology ; Spain ; Sulfur/chemistry ; Water/chemistry ; *Water Microbiology ; }, abstract = {Due to its highly metalliferous waters and low pH, the Rio Tinto has shown its potential for modelling both acid mine drainage systems and biohydrometallurgical operations. Most geomicrobiological studies of these systems have focused on the oxic water column. A sequence-based approach in combination with in situ detection techniques enabled us to examine the composition and structure of the microbial communities associated with the suboxic and anoxic sediments along the river course and to compare them with the planktonic communities inhabiting the water column. The results obtained with the different approaches were consistent and revealed some major patterns: higher cell density and higher richness (75 vs. 48 operational taxonomic units) in the sediments than in the water column. The microbial communities were related but the river sediments appear to be enriched in certain populations, some of which have not previously been reported in the Rio Tinto basin. The differences detected between sampling stations along the river correlate with certain environmental parameters (e.g. iron concentration gradient). The biological and geochemical data show the importance of the sediments as representing a phase of particular high diversity, probably related to key metabolic processes within both the iron and the sulfur cycles.}, }
@article {pmid22369237, year = {2011}, author = {Mohammed, MH and Ghosh, TS and Reddy, RM and Reddy, CV and Singh, NK and Mande, SS}, title = {INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences.}, journal = {BMC genomics}, volume = {12 Suppl 3}, number = {Suppl 3}, pages = {S4}, pmid = {22369237}, issn = {1471-2164}, mesh = {Algorithms ; Classification/*methods ; *Databases, Factual ; Genome ; Internet ; *Metagenomics ; User-Computer Interface ; }, abstract = {BACKGROUND: Taxonomic classification of metagenomic sequences is the first step in metagenomic analysis. Existing taxonomic classification approaches are of two types, similarity-based and composition-based. Similarity-based approaches, though accurate and specific, are extremely slow. Since, metagenomic projects generate millions of sequences, adopting similarity-based approaches becomes virtually infeasible for research groups having modest computational resources. In this study, we present INDUS - a composition-based approach that incorporates the following novel features. First, INDUS discards the 'one genome-one composition' model adopted by existing compositional approaches. Second, INDUS uses 'compositional distance' information for identifying appropriate assignment levels. Third, INDUS incorporates steps that attempt to reduce biases due to database representation.<br><br>RESULTS: INDUS is able to rapidly classify sequences in both simulated and real metagenomic sequence data sets with classification efficiency significantly higher than existing composition-based approaches. Although the classification efficiency of INDUS is observed to be comparable to those by similarity-based approaches, the binning time (as compared to alignment based approaches) is 23-33 times lower.<br><br>CONCLUSION: Given it's rapid execution time, and high levels of classification efficiency, INDUS is expected to be of immense interest to researchers working in metagenomics and microbial ecology.<br><br>AVAILABILITY: A web-server for the INDUS algorithm is available at http://metagenomics.atc.tcs.com/INDUS/}, }
@article {pmid22383122, year = {2012}, author = {Jackson, CR and Furtula, V and Farrell, EG and Barrett, JB and Hiott, LM and Chambers, P}, title = {A comparison of BOX-PCR and pulsed-field gel electrophoresis to determine genetic relatedness of enterococci from different environments.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {378-387}, pmid = {22383122}, issn = {1432-184X}, mesh = {Animal Husbandry ; Animals ; Bacterial Typing Techniques ; British Columbia ; Cluster Analysis ; Electrophoresis, Gel, Pulsed-Field/*methods ; Enterococcus/*classification/genetics/isolation &amp; purification ; Enterococcus faecalis/classification/genetics/isolation &amp; purification ; Enterococcus faecium/classification/genetics/isolation &amp; purification ; Environmental Monitoring/methods ; Feces/*microbiology ; Fresh Water/*microbiology ; Genetic Variation ; Polymerase Chain Reaction/*methods ; *Poultry ; Reproducibility of Results ; Sensitivity and Specificity ; }, abstract = {Genetic relatedness of enterococci from poultry litter to enterococci from nearby surface water and groundwater in the Lower Fraser Valley regions of British Columbia, Canada was determined. A new automated BOX-PCR and Pulsed-Field Gel Electrophoresis (PFGE) were used to subtype enterococcal isolates from broiler and layer litter and surface and groundwater. All surface water samples (n = 12) were positive for enterococci, as were 11% (3/28) of groundwater samples. Enterococcus faecium (n = 90) was isolated from all sources, while Enterococcus faecalis (n = 59) was isolated from all sources except layer litter. The majority of E. faecalis originated from broiler litter (28/59; 47.5%) while the majority of E. faecium were isolated from layer litter (29/90; 32.2%). E. faecalis grouped primarily by source using BOX-PCR. Isolates from water samples were dispersed more frequently among PFGE groups containing isolates from poultry litter. E. faecium strains were genetically diverse as overall clustering was independent of source by both molecular methods. Subgroups of E. faecium isolates based upon source (layer litter) were present in BOX-PCR groups. Three individual E. faecalis groups and two individual E. faecium groups were 100% similar using BOX-PCR; only one instance of 100% similarity among isolates using PFGE was observed. Although enterococci from litter and water sources were grouped together using BOX-PCR and PFGE, isolates originating from water could not be definitively identified as originating from poultry litter. Automation of BOX-PCR amplicon separation and visualization increased the reproducibility and standardization of subtyping using this procedure.}, }
@article {pmid22383121, year = {2012}, author = {Gagen, EJ and Mosoni, P and Denman, SE and Al Jassim, R and McSweeney, CS and Forano, E}, title = {Methanogen colonisation does not significantly alter acetogen diversity in lambs isolated 17 h after birth and raised aseptically.}, journal = {Microbial ecology}, volume = {64}, number = {3}, pages = {628-640}, pmid = {22383121}, issn = {1432-184X}, mesh = {Acetic Acid/*metabolism ; Animals ; Animals, Newborn/*growth &amp; development/microbiology ; Asepsis ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Cellulose/metabolism ; Ecosystem ; Methane/*metabolism ; Methanobrevibacter/growth &amp; development ; Molecular Sequence Data ; Rumen/*microbiology ; Sequence Analysis, DNA ; Sheep, Domestic/*growth &amp; development/microbiology ; Time Factors ; }, abstract = {Reductive acetogenesis is not competitive with methanogenesis in adult ruminants, whereas acetogenic bacteria are the dominant hydrogenotrophs in the early rumen microbiota. The ecology of hydrogenotrophs in the developing rumen was investigated using young lambs, raised in sterile isolators, and conventional adult sheep. Two lambs were born naturally, left with their dams for 17 h and then placed into a sterile isolator and reared aseptically. They were inoculated with cellulolytic bacteria and later with Methanobrevibacter sp. 87.7 to investigate the effect of methanogen establishment on the rumen acetogen population since they lacked cultivable representatives of methanogens. Putative acetogens were investigated by acetyl-CoA synthase and formyltetrahydrofolate synthetase gene analysis and methanogens by methyl coenzyme reductase A gene analysis. Unexpectedly, a low abundant but diverse population of methanogens (predominantly Methanobrevibacter spp.) was identified in isolated lambs pre-inoculation with Mbb. sp 87.7, which was similar to the community structure in conventional sheep. In contrast, potential acetogen diversity in isolated lambs and conventional sheep was different. Potential acetogens affiliated between the Lachnospiraceae and Clostridiaceae in conventional sheep and with the Blautia genus and the Lachnospiraceae in isolated lambs. The establishment of Mbb. sp. 87.7 (1,000-fold increase in methanogens) did not substantially affect acetogen diversity.}, }
@article {pmid22383120, year = {2012}, author = {Aagesen, AM and Häse, CC}, title = {Sequence analyses of type IV pili from Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {509-524}, pmid = {22383120}, issn = {1432-184X}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; Fimbriae Proteins/chemistry/*genetics ; Fimbriae, Bacterial/chemistry/*genetics ; Genetic Variation ; Humans ; Mannose-Binding Lectin/chemistry/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; Vibrio cholerae/*genetics ; Vibrio parahaemolyticus/genetics ; Vibrio vulnificus/*genetics ; }, abstract = {Bacterial surface structures called pili have been studied extensively for their role as possible colonization factors. Most sequenced Vibrio genomes predict a variety of pili genes in these organisms, including several types of type IV pili. In particular, the mannose-sensitive hemagglutinin (MSHA) and the PilA pili, also known as the chitin-regulated pilus (ChiRP), are type IVa pili commonly found in Vibrio genomes and have been shown to play a role in the colonization of Vibrio species in the environment and/or host tissue. Here, we report sequence comparisons of two type IVa pilin subunit genes, mshA and pilA, and their corresponding amino acid sequences, for several strains from the three main human pathogenic Vibrio species, V. cholerae, V. parahaemolyticus, and V. vulnificus. We identified specific groupings of these two genes in V. cholerae, whereas V. parahaemolyticus and V. vulnificus strains had no apparent allelic clusters, and these genes were strikingly divergent. These results were compared with other genes from the MSHA and PilA operons as well as another Vibrio pili from the type IVb group, the toxin co-regulated pilus (TCP) from V. cholerae. Our data suggest that a selective pressure exists to cause these strains to vary their MSHA and PilA pilin subunits. Interestingly, V. cholerae strains possessing TCP have the same allele for both mshA and pilA. In contrast, V. cholerae isolates without TCP have polymorphisms in their mshA and pilA sequences similar to what was observed for both V. parahaemolyticus and V. vulnificus. This data suggests a possible linkage between host interactions and maintaining a highly conserved type IV pili sequence in V. cholerae. Although the mechanism underlying this intriguing diversity has yet to be elucidated, our analyses are an important first step towards gaining insights into the various aspects of Vibrio ecology.}, }
@article {pmid22383119, year = {2012}, author = {Parejko, JA and Mavrodi, DV and Mavrodi, OV and Weller, DM and Thomashow, LS}, title = {Population structure and diversity of phenazine-1-carboxylic acid producing fluorescent Pseudomonas spp. from dryland cereal fields of central Washington State (USA).}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {226-241}, pmid = {22383119}, issn = {1432-184X}, support = {T32GM083864/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biodiversity ; Edible Grain/*growth &amp; development/microbiology ; Molecular Sequence Data ; Phenazines/metabolism ; Phylogeny ; Pseudomonas fluorescens/classification/genetics/*isolation &amp; purification/metabolism ; Rhizosphere ; *Soil Microbiology ; Washington ; }, abstract = {Certain strains of the rhizosphere bacterium Pseudomonas fluorescens contain the phenazine biosynthesis operon (phzABCDEFG) and produce redox-active phenazine antibiotics that suppress a wide variety of soilborne plant pathogens. In 2007 and 2008, we isolated 412 phenazine-producing (Phz(+)) fluorescent Pseudomonas strains from roots of dryland wheat and barley grown in the low-precipitation region (<350 mm annual precipitation) of central Washington State. Based on results of BOX-PCR genomic fingerprinting analysis, these isolates, as well as the model biocontrol Phz(+) strain P. fluorescens 2-79, were assigned to 31 distinct genotypes separated into four clusters. All of the isolates exhibited high 16S rDNA sequence similarity to members of the P. fluorescens species complex including Pseudomonas orientalis, Pseudomonas gessardii, Pseudomonas libanensis, and Pseudomonas synxantha. Further recA-based sequence analyses revealed that the majority of new Phz(+) isolates (386 of 413) form a clade distinctly separated from P. fluorescens 2-79. Analysis of phzF alleles, however, revealed that the majority of those isolates (280 of 386) carried phenazine biosynthesis genes similar to those of P. fluorescens 2-79. phzF-based analyses also revealed that phenazine genes were under purifying selection and showed evidence of intracluster recombination. Phenotypic analyses using Biolog substrate utilization and observations of phenazine-1-carboxylic acid production showed considerable variability amongst members of all four clusters. Biodiversity indices indicated significant differences in diversity and evenness between the sampled sites. In summary, this study revealed a genotypically and phenotypically diverse group of phenazine producers with a population structure not seen before in indigenous rhizosphere-inhabiting Phz(+) Pseudomonas spp.}, }
@article {pmid22375139, year = {2012}, author = {Wang, J and Krause, S and Muyzer, G and Meima-Franke, M and Laanbroek, HJ and Bodelier, PL}, title = {Spatial patterns of iron- and methane-oxidizing bacterial communities in an irregularly flooded, riparian wetland.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {64}, pmid = {22375139}, issn = {1664-302X}, abstract = {Iron- and methane-cycling are important processes in wetlands with one connected to plant growth and the other to greenhouse gas emission, respectively. In contrast to acidic habitats, there is scarce information on the ecology of microbes oxidizing ferrous iron at circumneutral pH. The latter is mainly due to the lack of isolated representatives and molecular detection techniques. Recently, we developed PCR-DGGE and qPCR assays to detect and enumerate Gallionella-related neutrophilic iron-oxidizers (Ga-FeOB) enabling the assessment of controlling physical as well as biological factors in various ecosystems. In this study, we investigated the spatial distribution of Ga-FeOB in co-occurrence with methane-oxidizing bacteria (MOB) in a riparian wetland. Soil samples were collected at different spatial scales (ranging from meters to centimeters) representing a hydrological gradient. The diversity of Ga-FeOB was assessed using PCR-DGGE and the abundance of both Ga-FeOB and MOB by qPCR. Geostatistical methods were applied to visualize the spatial distribution of both groups. Spatial distribution as well as abundance of Ga-FeOB and MOB was clearly correlated to the hydrological gradient as expressed in moisture content of the soil. Ga-FeOB outnumbered the MOB subgroups suggesting their competitiveness or the prevalence of Fe(2+) over CH(4) oxidation in this floodplain.}, }
@article {pmid22370877, year = {2012}, author = {Duodu, S and Larsson, P and Sjödin, A and Forsman, M and Colquhoun, DJ}, title = {The distribution of Francisella-like bacteria associated with coastal waters in Norway.}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {370-377}, pmid = {22370877}, issn = {1432-184X}, mesh = {DNA, Bacterial/analysis/genetics/isolation &amp; purification ; DNA, Ribosomal/analysis ; Francisella/*classification/*genetics/isolation &amp; purification ; Fresh Water/*microbiology ; Molecular Sequence Data ; Norway ; Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {We report the diversity and distribution of Francisella species in Norwegian coastal and fresh waters following a nationwide survey in which water and sediment samples were collected from locations spanning almost the entire Norwegian coastline. In total, samples were obtained from 149 and 64 seawater and freshwater sites, respectively. DNA extracts from these environmental samples were initially screened by polymerase chain reaction (PCR) using Francisella genus-specific 16S rDNA primers. Positive samples were then amplified with genus-specific primers targeting Francisella succinate dehydrogenase A gene and Francisella philomiragia group-specific sequences for the SAICAR synthetase/phosphoribosylamine-glycine ligase gene. Francisella-related bacteria were identified in approximately 30% of seawater sampled sites, mainly in southern Norway, although a single positive sample was identified in the far north of the country. No PCR positives were identified from the freshwater sources. Sequences related to recognised species, both pathogenic and environmental, were identified, with the majority closely associated with F. philomiragia. However, a number of identified sequences probably represent previously undescribed species. Our data provide evidence of a significant background of Francisella spp. in geographical areas associated with outbreaks of fish francisellosis in Norway.}, }
@article {pmid22370876, year = {2012}, author = {Mota, CR and So, MJ and de los Reyes, FL}, title = {Identification of nitrite-reducing bacteria using sequential mRNA fluorescence in situ hybridization and fluorescence-assisted cell sorting.}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {256-267}, pmid = {22370876}, issn = {1432-184X}, mesh = {Bacteria/enzymology/genetics/*isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Flow Cytometry/*methods ; In Situ Hybridization, Fluorescence/*methods ; Nitrite Reductases/genetics/metabolism ; Nitrites/*metabolism ; Oxidation-Reduction ; Pseudomonas stutzeri/genetics/isolation &amp; purification/metabolism ; Sewage/chemistry/*microbiology ; }, abstract = {Sequential mRNA fluorescence in situ hybridization (mRNA FISH) and fluorescence-assisted cell sorting (SmRFF) was used for the identification of nitrite-reducing bacteria in mixed microbial communities. An oligonucleotide probe labeled with horseradish peroxidase (HRP) was used to target mRNA of nirS, the gene that encodes nitrite reductase, the enzyme responsible for the dissimilatory reduction of nitrite to nitric oxide. Clones for nirS expression were constructed and used to provide proof of concept for the SmRFF method. In addition, cells from pure cultures of Pseudomonas stutzeri and denitrifying activated sludge were hybridized with the HRP probe, and tyramide signal amplification was performed, conferring a strongly fluorescent signal to cells containing nirS mRNA. Flow cytometry-assisted cell sorting was used to detect and physically separate two subgroups from a mixed microbial community: non-fluorescent cells and an enrichment of fluorescent, nitrite-reducing cells. Denaturing gradient gel electrophoresis (DGGE) and subsequent sequencing of 16S ribosomal RNA (rRNA) genes were used to compare the fragments amplified from the two sorted subgroups. Sequences from bands isolated from DGGE profiles suggested that the dominant, active nitrite reducers were closely related to Acidovorax BSB421. Furthermore, following mRNA FISH detection of nitrite-reducing bacteria, 16S rRNA FISH was used to detect ammonia-oxidizing and nitrite-oxidizing bacteria on the same activated sludge sample. We believe that the molecular approach described can be useful as a tool to help address the longstanding challenge of linking function to identity in natural and engineered habitats.}, }
@article {pmid22367081, year = {2012}, author = {Monnet, C and Back, A and Irlinger, F}, title = {Growth of aerobic ripening bacteria at the cheese surface is limited by the availability of iron.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {9}, pages = {3185-3192}, pmid = {22367081}, issn = {1098-5336}, mesh = {Arthrobacter/*growth &amp; development/metabolism ; Bacteria, Aerobic/*growth &amp; development/metabolism ; Biosynthetic Pathways/genetics ; Brevibacterium/*growth &amp; development/metabolism ; Cheese/*microbiology ; Corynebacterium/*growth &amp; development/metabolism ; Deferoxamine/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Iron/*metabolism ; Membrane Transport Proteins/biosynthesis ; Real-Time Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Transcription, Genetic ; }, abstract = {The microflora on the surface of smear-ripened cheeses is composed of various species of bacteria and yeasts that contribute to the production of the desired organoleptic properties. The objective of the present study was to show that iron availability is a limiting factor in the growth of typical aerobic ripening bacteria in cheese. For that purpose, we investigated the effect of iron or siderophore addition in model cheeses that were coinoculated with a yeast and a ripening bacterium. Both iron and the siderophore desferrioxamine B stimulated the growth of ripening bacteria belonging to the genera Arthrobacter, Corynebacterium, and Brevibacterium. The extent of stimulation was strain dependent, and generally, the effect of desferrioxamine B was greater than that of iron. Measurements of the expression of genes related to the metabolism of iron by Arthrobacter arilaitensis Re117 by real-time reverse transcription-PCR showed that these genes were transcribed during growth in cheese. The addition of desferrioxamine B increased the expression of two genes encoding iron-siderophore ABC transport binding proteins. The addition of iron decreased the expression of siderophore biosynthesis genes and of part of the genes encoding iron-siderophore ABC transport components. It was concluded that iron availability is a limiting factor in the growth of typical cheese surface bacteria. The selection of strains with efficient iron acquisition systems may be useful for the development of defined-strain surface cultures. Furthermore, the importance of iron metabolism in the microbial ecology of cheeses should be investigated since it may result in positive or negative microbial interactions.}, }
@article {pmid22364368, year = {2012}, author = {Tecon, R and Leveau, JH}, title = {The mechanics of bacterial cluster formation on plant leaf surfaces as revealed by bioreporter technology.}, journal = {Environmental microbiology}, volume = {14}, number = {5}, pages = {1325-1332}, doi = {10.1111/j.1462-2920.2012.02715.x}, pmid = {22364368}, issn = {1462-2920}, mesh = {Biomarkers/metabolism ; Fabaceae/*microbiology ; Green Fluorescent Proteins/metabolism ; Pantoea/genetics/metabolism/*physiology ; Plant Leaves/*microbiology ; }, abstract = {Bacteria that colonize the leaves of terrestrial plants often occur in clusters whose size varies from a few to thousands of cells. For the formation of such bacterial clusters, two non-mutually exclusive but very different mechanisms may be proposed: aggregation of multiple cells or clonal reproduction of a single cell. Here we assessed the contribution of both mechanisms on the leaves of bean plants that were colonized by the bacterium Pantoea agglomerans. In one approach, we used a mixture of green and red fluorescent P. agglomerans cells to populate bean leaves. We observed that this resulted in clusters made up of only one colour as well as two-colour clusters, thus providing evidence for both mechanisms. Another P. agglomerans bioreporter, designed to quantify the reproductive success of bacterial colonizers by proxy to the rate at which green fluorescent protein is diluted from dividing cells, revealed that during the first hours on the leaf surface, many bacteria were dividing, but not staying together and forming clusters, which is suggestive of bacterial relocation. Together, these findings support a dynamic model of leaf surface colonization, where both aggregative and reproductive mechanisms take place. The bioreporter-based approach we employed here should be broadly applicable towards a more quantitative and mechanistic understanding of bacterial colonization of surfaces in general.}, }
@article {pmid22364314, year = {2012}, author = {Toenshoff, ER and Gruber, D and Horn, M}, title = {Co-evolution and symbiont replacement shaped the symbiosis between adelgids (Hemiptera: Adelgidae) and their bacterial symbionts.}, journal = {Environmental microbiology}, volume = {14}, number = {5}, pages = {1284-1295}, doi = {10.1111/j.1462-2920.2012.02712.x}, pmid = {22364314}, issn = {1462-2920}, support = {P 22533/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Betaproteobacteria/*classification/genetics/*physiology/ultrastructure ; Female ; Gammaproteobacteria/*classification/genetics/*physiology/ultrastructure ; Hemiptera/genetics/*microbiology/ultrastructure ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Symbiosis/genetics ; }, abstract = {The Adelgidae (Insecta: Hemiptera), a small group of insects, are known as severe pests on various conifers of the northern hemisphere. Despite of this, little is known about their bacteriocyte-associated endosymbionts, which are generally important for the biology and ecology of plant sap-sucking insects. Here, we investigated the adelgid species complexes Adelges laricis/tardus, Adelges abietis/viridis and Adelges cooleyi/coweni, identified based on their coI and ef1alpha genes. Each of these insect groups harboured two phylogenetically different bacteriocyte-associated symbionts belonging to the Betaproteobacteria and the Gammaproteobacteria, respectively, as inferred from phylogenetic analyses of 16S rRNA gene sequences and demonstrated by fluorescence in situ hybridization. The betaproteobacterial symbionts of all three adelgid complexes ('Candidatus Vallotia tarda', 'Candidatus Vallotia virida' and 'Candidatus Vallotia cooleyia') share a common ancestor and show a phylogeny congruent with that of their respective hosts. Similarly, there is evidence for co-evolution between the gammaproteobacterial symbionts ('Candidatus Profftia tarda', 'Candidatus Profftia virida') and A. laricis/tardus and A. abietis/viridis. In contrast, the gammaproteobacterial symbiont of A. cooleyi/coweni ('Candidatus Gillettellia cooleyia') is different from that of the other two adelgids but shows a moderate relationship to the symbiont 'Candidatus Ecksteinia adelgidicola' of A. nordmannianae/piceae. All symbionts were present in all adelgid populations and life stages analysed, suggesting vertical transmission from mother to offspring. In sharp contrast to their sister group, the aphids, adelgids do not consistently contain a single obligate (primary) symbiont but have acquired phylogenetically different bacterial symbionts during their evolution, which included multiple infections and symbiont replacement.}, }
@article {pmid22363520, year = {2012}, author = {Toulza, E and Tagliabue, A and Blain, S and Piganeau, G}, title = {Analysis of the global ocean sampling (GOS) project for trends in iron uptake by surface ocean microbes.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e30931}, pmid = {22363520}, issn = {1932-6203}, mesh = {Adaptation, Physiological/drug effects/genetics ; Bacteria/classification/drug effects/genetics ; Biomarkers/metabolism ; Databases as Topic ; Ecosystem ; Genes, Bacterial/genetics ; Geography ; *Internationality ; Iron/*metabolism/pharmacology ; Metabolic Networks and Pathways/drug effects ; Oceanography/*methods ; Oceans and Seas ; Seawater/*microbiology ; Surface Properties/drug effects ; }, abstract = {Microbial metagenomes are DNA samples of the most abundant, and therefore most successful organisms at the sampling time and location for a given cell size range. The study of microbial communities via their DNA content has revolutionized our understanding of microbial ecology and evolution. Iron availability is a critical resource that limits microbial communities' growth in many oceanic areas. Here, we built a database of 2319 sequences, corresponding to 140 gene families of iron metabolism with a large phylogenetic spread, to explore the microbial strategies of iron acquisition in the ocean's bacterial community. We estimate iron metabolism strategies from metagenome gene content and investigate whether their prevalence varies with dissolved iron concentrations obtained from a biogeochemical model. We show significant quantitative and qualitative variations in iron metabolism pathways, with a higher proportion of iron metabolism genes in low iron environments. We found a striking difference between coastal and open ocean sites regarding Fe(2+) versus Fe(3+) uptake gene prevalence. We also show that non-specific siderophore uptake increases in low iron open ocean environments, suggesting bacteria may acquire iron from natural siderophore-like organic complexes. Despite the lack of knowledge of iron uptake mechanisms in most marine microorganisms, our approach provides insights into how the iron metabolic pathways of microbial communities may vary with seawater iron concentrations.}, }
@article {pmid22363438, year = {2012}, author = {Hardoim, PR and Hardoim, CC and van Overbeek, LS and van Elsas, JD}, title = {Dynamics of seed-borne rice endophytes on early plant growth stages.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e30438}, pmid = {22363438}, issn = {1932-6203}, mesh = {Bacteria/growth &amp; development/isolation &amp; purification ; Base Sequence ; Denaturing Gradient Gel Electrophoresis ; Endophytes/*physiology ; Molecular Sequence Data ; Oryza/*growth &amp; development/*microbiology ; Plant Shoots/microbiology ; Polymerase Chain Reaction ; Rhizosphere ; Seeds/*microbiology ; Soil Microbiology ; }, abstract = {Bacterial endophytes are ubiquitous to virtually all terrestrial plants. With the increasing appreciation of studies that unravel the mutualistic interactions between plant and microbes, we increasingly value the beneficial functions of endophytes that improve plant growth and development. However, still little is known on the source of established endophytes as well as on how plants select specific microbial communities to establish associations. Here, we used cultivation-dependent and -independent approaches to assess the endophytic bacterrial community of surface-sterilized rice seeds, encompassing two consecutive rice generations. We isolated members of nine bacterial genera. In particular, organisms affiliated with Stenotrophomonas maltophilia and Ochrobactrum spp. were isolated from both seed generations. PCR-based denaturing gradient gel electrophoresis (PCR-DGGE) of seed-extracted DNA revealed that approximately 45% of the bacterial community from the first seed generation was found in the second generation as well. In addition, we set up a greenhouse experiment to investigate abiotic and biotic factors influencing the endophytic bacterial community structure. PCR-DGGE profiles performed with DNA extracted from different plant parts showed that soil type is a major effector of the bacterial endophytes. Rice plants cultivated in neutral-pH soil favoured the growth of seed-borne Pseudomonas oryzihabitans and Rhizobium radiobacter, whereas Enterobacter-like and Dyella ginsengisoli were dominant in plants cultivated in low-pH soil. The seed-borne Stenotrophomonas maltophilia was the only conspicuous bacterial endophyte found in plants cultivated in both soils. Several members of the endophytic community originating from seeds were observed in the rhizosphere and surrounding soils. Their impact on the soil community is further discussed.}, }
@article {pmid22363327, year = {2012}, author = {Mills, HJ and Reese, BK and Peter, CS}, title = {Characterization of Microbial Population Shifts during Sample Storage.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {49}, pmid = {22363327}, issn = {1664-302X}, abstract = {The objective of this study was to determine shifts in the microbial community structure and potential function based on standard Integrated Ocean Drilling Program (IODP) storage procedures for sediment cores. Standard long-term storage protocols maintain sediment temperature at 4°C for mineralogy, geochemical, and/or geotechnical analysis whereas standard microbiological sampling immediately preserves sediments at -80°C. Storage at 4°C does not take into account populations may remain active over geologic time scales at temperatures similar to storage conditions. Identification of active populations within the stored core would suggest geochemical and geophysical conditions within the core change over time. To test this potential, the metabolically active fraction of the total microbial community was characterized from IODP Expedition 325 Great Barrier Reef sediment cores prior to and following a 3-month storage period. Total RNA was extracted from complementary 2, 20, and 40 m below sea floor sediment samples, reverse transcribed to complementary DNA and then sequenced using 454 FLX sequencing technology, yielding over 14,800 sequences from the six samples. Interestingly, 97.3% of the sequences detected were associated with lineages that changed in detection frequency during the storage period including key biogeochemically relevant lineages associated with nitrogen, iron, and sulfur cycling. These lineages have the potential to permanently alter the physical and chemical characteristics of the sediment promoting misleading conclusions about the in situ biogeochemical environment. In addition, the detection of new lineages after storage increases the potential for a wider range of viable lineages within the subsurface that may be underestimated during standard community characterizations.}, }
@article {pmid22357743, year = {2012}, author = {Pieper, R and Kröger, S and Richter, JF and Wang, J and Martin, L and Bindelle, J and Htoo, JK and von Smolinski, D and Vahjen, W and Zentek, J and Van Kessel, AG}, title = {Fermentable fiber ameliorates fermentable protein-induced changes in microbial ecology, but not the mucosal response, in the colon of piglets.}, journal = {The Journal of nutrition}, volume = {142}, number = {4}, pages = {661-667}, doi = {10.3945/jn.111.156190}, pmid = {22357743}, issn = {1541-6100}, mesh = {Animal Feed/economics ; Animals ; Clostridium/*growth &amp; development/isolation &amp; purification ; Colon/immunology/*microbiology ; Crosses, Genetic ; Dietary Fiber/*administration &amp; dosage/metabolism ; Dietary Proteins/*adverse effects/metabolism ; Fatty Acids, Volatile/metabolism ; Female ; Fermentation ; Food-Processing Industry/economics ; Gene Expression Regulation ; Immunity, Mucosal ; Industrial Waste/adverse effects/analysis/economics ; Inflammation Mediators/metabolism ; Intestinal Mucosa/immunology/*microbiology ; Male ; Mucins/genetics/metabolism ; *Oxidative Stress ; Soybean Proteins/adverse effects/metabolism ; Sus scrofa/growth &amp; development/immunology/*microbiology ; Weaning ; }, abstract = {Dietary inclusion of fermentable carbohydrates (fCHO) is reported to reduce large intestinal formation of putatively toxic metabolites derived from fermentable proteins (fCP). However, the influence of diets high in fCP concentration on epithelial response and interaction with fCHO is still unclear. Thirty-two weaned piglets were fed 4 diets in a 2 × 2 factorial design with low fCP/low fCHO [14.5% crude protein (CP)/14.5% total dietary fiber (TDF)]; low fCP/high fCHO (14.8% CP/16.6% TDF); high fCP low fCHO (19.8% CP/14.5% TDF); and high fCP/high fCHO (20.1% CP/18.0% TDF) as dietary treatments. After 21-23 d, pigs were killed and colon digesta and tissue samples analyzed for indices of microbial ecology, tissue expression of genes for cell turnover, cytokines, mucus genes (MUC), and oxidative stress indices. Pig performance was unaffected by diet. fCP increased (P < 0.05) cell counts of clostridia in the Clostridium leptum group and total short and branched chain fatty acids, ammonia, putrescine, histamine, and spermidine concentrations, whereas high fCHO increased (P < 0.05) cell counts of clostridia in the C. leptum and C. coccoides groups, shifted the acetate to propionate ratio toward acetate (P < 0.05), and reduced ammonia and putrescine (P < 0.05). High dietary fCP increased (P < 0.05) expression of PCNA, IL1β, IL10, TGFβ, MUC1, MUC2, and MUC20, irrespective of fCHO concentration. The ratio of glutathione:glutathione disulfide was reduced (P < 0.05) by fCP and the expression of glutathione transferase was reduced by fCHO (P < 0.05). In conclusion, fermentable fiber ameliorates fermentable protein-induced changes in most measures of luminal microbial ecology but not the mucosal response in the large intestine of pigs.}, }
@article {pmid22355318, year = {2012}, author = {Vos, M and Quince, C and Pijl, AS and de Hollander, M and Kowalchuk, GA}, title = {A comparison of rpoB and 16S rRNA as markers in pyrosequencing studies of bacterial diversity.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e30600}, pmid = {22355318}, issn = {1932-6203}, mesh = {DNA, Bacterial/*genetics ; *Genetic Markers ; *Genetic Variation ; Phylogeny ; Proteobacteria/*classification/*genetics ; RNA Polymerase II/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The 16S rRNA gene is the gold standard in molecular surveys of bacterial and archaeal diversity, but it has the disadvantages that it is often multiple-copy, has little resolution below the species level and cannot be readily interpreted in an evolutionary framework. We compared the 16S rRNA marker with the single-copy, protein-coding rpoB marker by amplifying and sequencing both from a single soil sample. Because the higher genetic resolution of the rpoB gene prohibits its use as a universal marker, we employed consensus-degenerate primers targeting the Proteobacteria.<br><br>Pyrosequencing can be problematic because of the poor resolution of homopolymer runs. As these erroneous runs disrupt the reading frame of protein-coding sequences, removal of sequences containing nonsense mutations was found to be a valuable filter in addition to flowgram-based denoising. Although both markers gave similar estimates of total diversity, the rpoB marker revealed more species, requiring an order of magnitude fewer reads to obtain 90% of the true diversity. The application of population genetic methods was demonstrated on a particularly abundant sequence cluster.<br><br>CONCLUSIONS/SIGNIFICANCE: The rpoB marker can be a complement to the 16S rRNA marker for high throughput microbial diversity studies focusing on specific taxonomic groups. Additional error filtering is possible and tests for recombination or selection can be employed.}, }
@article {pmid22355147, year = {2012}, author = {Doostmohammadi, A and Stocker, R and Ardekani, AM}, title = {Low-Reynolds-number swimming at pycnoclines.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {10}, pages = {3856-3861}, pmid = {22355147}, issn = {1091-6490}, mesh = {Algorithms ; Bacterial Physiological Phenomena ; Computer Simulation ; Diffusion ; Ecology ; Ecosystem ; Lakes ; Models, Biological ; Models, Statistical ; *Movement ; Oceans and Seas ; Oscillometry/methods ; Salts ; Temperature ; Viscosity ; Water/chemistry ; *Water Microbiology ; }, abstract = {Microorganisms play pivotal functions in the trophic dynamics and biogeochemistry of aquatic ecosystems. Their concentrations and activities often peak at localized hotspots, an important example of which are pycnoclines, where water density increases sharply with depth due to gradients in temperature or salinity. At pycnoclines organisms are exposed to different environmental conditions compared to the bulk water column, including reduced turbulence, slow mass transfer, and high particle and predator concentrations. Here we show that, at an even more fundamental level, the density stratification itself can affect microbial ecology at pycnoclines, by quenching the flow signature, increasing the energetic expenditure, and stifling the nutrient uptake of motile organisms. We demonstrate this through numerical simulations of an archetypal low-Reynolds-number swimmer, the "squirmer." We identify the Richardson number--the ratio of buoyancy forces to viscous forces--as the fundamental parameter that quantifies the effects of stratification. These results demonstrate an unexpected effect of buoyancy on low-Reynolds-number swimming, potentially affecting a broad range of abundant organisms living at pycnoclines in oceans and lakes.}, }
@article {pmid22354313, year = {2012}, author = {Pérez, J and Descals, E and Pozo, J}, title = {Aquatic hyphomycete communities associated with decomposing alder leaf litter in reference headwater streams of the Basque Country (northern Spain).}, journal = {Microbial ecology}, volume = {64}, number = {2}, pages = {279-290}, pmid = {22354313}, issn = {1432-184X}, mesh = {Alnus/*microbiology ; *Biodegradation, Environmental ; *Ecosystem ; Mitosporic Fungi/classification/genetics/isolation &amp; purification/*physiology ; Plant Leaves/*metabolism/microbiology ; Rivers/chemistry/*microbiology ; Spain ; Spores, Fungal/physiology ; }, abstract = {The community of aquatic hyphomycetes associated with decomposing alder leaf litter was studied during autumn-winter in nine headwater reference streams of the Basque Country (northern Spain). In order to study the spatial variability in composition and community structure, three streams from each of three different river basins were compared. The colonization dynamics and community changes throughout the decomposition process were also followed in three of the rivers (one per basin). The taxonomic richness and community structure of these fungi varied among rivers, including similar streams of a given watershed. However, neither species diversity nor total abundance was statistically related to environmental variables. Only the conidial production of two of the species, Flagellospora curvula and Lunulospora curvula appeared to be enhanced by nitrate availability in the water. The taxonomic richness and the reproductive activity (sporulation rate) were positively related to the leaf litter decomposition rate. The changes in conidial production along the process were similar for all the streams and helped explain leaf litter quality dynamics.}, }
@article {pmid22349935, year = {2012}, author = {Zaccone, R and Boldrin, A and Caruso, G and La Ferla, R and Maimone, G and Santinelli, C and Turchetto, M}, title = {Enzymatic activities and prokaryotic abundance in relation to organic matter along a West-East Mediterranean transect (TRANSMED cruise).}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {54-66}, pmid = {22349935}, issn = {1432-184X}, mesh = {Bacteria/chemistry/*enzymology/growth &amp; development/metabolism ; Bacterial Proteins/analysis/*metabolism ; Carbon/analysis/metabolism ; Kinetics ; Mediterranean Sea ; Nitrogen/analysis/metabolism ; Organic Chemicals/analysis/metabolism ; Phosphorus/analysis/metabolism ; Seawater/chemistry/*microbiology ; }, abstract = {The distribution of extracellular enzymatic activities (EEA) [leucine aminopeptidase (LAP), ß-glucosidase (GLU), alkaline phosphatase (AP)], as well as that of prokaryotic abundance (PA) and biomass (PB), dissolved organic carbon (DOC), particulate organic carbon and particulate total nitrogen (POC, PTN), was determined in the epi-, meso-, and bathypelagic waters of the Mediterranean Sea along a West-East transect and at one Atlantic station located outside the Strait of Gibraltar. This study represents a synoptical evaluation of the microbial metabolism during early summer. Decreasing trends with depth were observed for most of the parameters (PA, PB, AP, DOC, POC, PTN). Significant differences between the western and eastern basins of the Mediterranean Sea were found, displaying higher rates of LAP and GLU and lower C/N ratios more in the eastern than in the western areas. Conversely, in the epipelagic layer, PA and PB were found to be higher in the western than in the eastern basins. PB was significantly related to DOC concentration (all data, n = 145, r = 0.53, P < 0.01), while significant correlations of EEA with POC and PTN were found in the epipelagic layer, indicating an active response of microbial metabolism to organic substrates. Specific enzyme activities normalized to cell abundance pointed out high values of LAP and GLU in the bathypelagic layer, especially in the eastern basin, while cell-specific AP was high in the epi- and bathypelagic zone of the eastern basin indicating a rapid regeneration of inorganic P for both prokaryotes and phytoplankton needs. Low activity and abundance characterized the Atlantic station, while opposite trends of these parameters were observed along the Mediterranean transect, showing the uncoupling between abundance and activity data. In the east Mediterranean Sea, decomposition processes increased probably in response to mesoscale structures which lead to organic matter downwelling.}, }
@article {pmid22349905, year = {2012}, author = {Gorra, R and Webster, G and Martin, M and Celi, L and Mapelli, F and Weightman, AJ}, title = {Dynamic microbial community associated with iron-arsenic co-precipitation products from a groundwater storage system in Bangladesh.}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {171-186}, pmid = {22349905}, issn = {1432-184X}, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Arsenic/*chemistry/metabolism ; Bacteria/classification/genetics/*isolation &amp; purification ; Bangladesh ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Groundwater/chemistry/*microbiology ; Iron/*chemistry/metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The prokaryotic community in Fe-As co-precipitation product from a groundwater storage tank in Bangladesh was investigated over a 5-year period to assess the diversity of the community and to infer biogeochemical mechanisms that may contribute to the formation and stabilisation of co-precipitation products and to Fe and As redox cycling. Partial 16S rRNA gene sequences from Bacteria and Archaea, functional markers (mcrA and dsrB) and iron-oxidising Gallionella-related 16S rRNA gene sequences were determined using denaturing gradient gel electrophoresis (DGGE). Additionally, a bacterial 16S rRNA gene library was also constructed from one representative sample. Biogeochemical characterization demonstrated that co-precipitation products consist of a mixture of inorganic minerals, mainly hydrous ferric oxides, intimately associated with organic matter of microbial origin that contribute to the chemical and physical stabilisation of a poorly ordered structure. DGGE analysis and polymerase chain reaction-cloning revealed that the diverse bacterial community structure in the co-precipitation product progressively stabilised with time resulting in a prevalence of methylotrophic Betaproteobacteria, while the archaeal community was less diverse and was dominated by members of the Euryarchaeota. Results show that Fe-As co-precipitation products provide a habitat characterised by anoxic/oxic niches that supports a phylogenetically and metabolically diverse group of prokaryotes involved in metal, sulphur and carbon cycling, supported by the presence of Gallionella-like iron-oxidizers, methanogens, methylotrophs, and sulphate reducers. However, no phylotypes known to be directly involved in As(V) respiration or As(III) oxidation were found.}, }
@article {pmid22343308, year = {2012}, author = {Ze, X and Duncan, SH and Louis, P and Flint, HJ}, title = {Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon.}, journal = {The ISME journal}, volume = {6}, number = {8}, pages = {1535-1543}, pmid = {22343308}, issn = {1751-7370}, mesh = {Bacteria/genetics/growth &amp; development/*metabolism ; Coculture Techniques ; Colon/metabolism/*microbiology ; Feces/microbiology ; Fermentation ; Humans ; Ruminococcus/*metabolism ; Species Specificity ; Starch/*metabolism ; Time Factors ; }, abstract = {The release of energy from particulate substrates such as dietary fiber and resistant starch (RS) in the human colon may depend on the presence of specialist primary degraders (or 'keystone species') within the microbial community. We have explored the roles of four dominant amylolytic bacteria found in the human colon in the degradation and utilization of resistant starches. Eubacterium rectale and Bacteroides thetaiotaomicron showed limited ability to utilize RS2- and RS3-resistant starches by comparison with Bifidobacterium adolescentis and Ruminococcus bromii. In co-culture, however, R. bromii proved unique in stimulating RS2 and RS3 utilization by the other three bacterial species, even in a medium that does not permit growth of R. bromii itself. Having previously demonstrated low RS3 fermentation in vivo in two individuals with undetectable populations of R. bromii-related bacteria, we show here that supplementation of mixed fecal bacteria from one of these volunteers with R. bromii, but not with the other three species, greatly enhanced the extent of RS3 fermentation in vitro. This argues strongly that R. bromii has a pivotal role in fermentation of RS3 in the human large intestine, and that variation in the occurrence of this species and its close relatives may be a primary cause of variable energy recovery from this important component of the diet. This work also indicates that R. bromii possesses an exceptional ability to colonize and degrade starch particles when compared with previously studied amylolytic bacteria from the human colon.}, }
@article {pmid22342514, year = {2012}, author = {Sibley, CD and Peirano, G and Church, DL}, title = {Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {12}, number = {3}, pages = {505-521}, pmid = {22342514}, issn = {1567-7257}, mesh = {Bacteria/genetics/isolation &amp; purification/pathogenicity ; Communicable Diseases/*diagnosis/epidemiology/microbiology ; Computational Biology ; Fungi/genetics/isolation &amp; purification/pathogenicity ; *Genome, Bacterial ; *Genome, Fungal ; Genotyping Techniques ; Humans ; Microarray Analysis/methods ; Microbiological Techniques/*methods/standards ; Molecular Typing/*methods ; Polymerase Chain Reaction/methods ; Polymorphism, Restriction Fragment Length ; Reagent Kits, Diagnostic ; }, abstract = {Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections.}, }
@article {pmid22341463, year = {2012}, author = {Wei, X and Yang, Z and Rey, FE and Ridaura, VK and Davidson, NO and Gordon, JI and Semenkovich, CF}, title = {Fatty acid synthase modulates intestinal barrier function through palmitoylation of mucin 2.}, journal = {Cell host &amp; microbe}, volume = {11}, number = {2}, pages = {140-152}, pmid = {22341463}, issn = {1934-6069}, support = {DK20579/DK/NIDDK NIH HHS/United States ; R01 HL038180/HL/NHLBI NIH HHS/United States ; DK088083/DK/NIDDK NIH HHS/United States ; DK52574/DK/NIDDK NIH HHS/United States ; R01 DK076729/DK/NIDDK NIH HHS/United States ; DK70977/DK/NIDDK NIH HHS/United States ; P60 DK020579/DK/NIDDK NIH HHS/United States ; R01 DK088083/DK/NIDDK NIH HHS/United States ; DK56260/DK/NIDDK NIH HHS/United States ; DK56341/DK/NIDDK NIH HHS/United States ; R01 DK070977/DK/NIDDK NIH HHS/United States ; DK076729/DK/NIDDK NIH HHS/United States ; P30 DK056341/DK/NIDDK NIH HHS/United States ; HL38180/HL/NHLBI NIH HHS/United States ; R37 HL038180/HL/NHLBI NIH HHS/United States ; P30 DK020579/DK/NIDDK NIH HHS/United States ; R01 DK056260/DK/NIDDK NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacterial Infections/immunology/pathology ; Body Weight ; Colon/*immunology/*metabolism/pathology ; Fatty Acid Synthases/*metabolism ; Intestinal Mucosa/immunology/metabolism/pathology ; Lipoylation ; Mice ; Mucin-2/*metabolism ; Survival Analysis ; }, abstract = {The intestinal mucus barrier prevents pathogen invasion and maintains host-microbiota homeostasis. We show that fatty acid synthase (FAS), an insulin-responsive enzyme essential for de novo lipogenesis, helps maintain the mucus barrier by regulating Mucin 2, the dominant mucin in the colon and a central component of mucus. Inducible Cre recombinase-directed inactivation of the FAS gene in the colonic epithelium of mice is associated with disruptions in the intestinal mucus barrier as well as increased intestinal permeability, colitis, systemic inflammation, and changes in gut microbial ecology. FAS deficiency blocked the generation of palmitoylated Mucin 2, which must be S-palmitoylated at its N terminus for proper secretion and function. Furthermore, a diabetic mouse model exhibited lower FAS levels and a decreased mucus layer, which could be restored with insulin treatment. Thus, the role of FAS in maintaining intestinal barrier function may explain the pathogenesis of intestinal inflammation in diabetes and other disorders.}, }
@article {pmid22339879, year = {2012}, author = {Carroll, IM and Ringel-Kulka, T and Siddle, JP and Ringel, Y}, title = {Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome.}, journal = {Neurogastroenterology and motility}, volume = {24}, number = {6}, pages = {521-30, e248}, pmid = {22339879}, issn = {1365-2982}, support = {DK084294/DK/NIDDK NIH HHS/United States ; R03 DK084294/DK/NIDDK NIH HHS/United States ; K01 DK092330/DK/NIDDK NIH HHS/United States ; K23 DK075621/DK/NIDDK NIH HHS/United States ; DK075621/DK/NIDDK NIH HHS/United States ; UL1RR025747/RR/NCRR NIH HHS/United States ; UL1 RR025747/RR/NCRR NIH HHS/United States ; }, mesh = {Adult ; Aged ; DNA, Bacterial/analysis/genetics ; Diarrhea/genetics/*microbiology ; Feces/chemistry/*microbiology ; Female ; Humans ; Intestines/chemistry/*microbiology ; Irritable Bowel Syndrome/genetics/*microbiology ; Male ; Metagenome/*genetics ; Middle Aged ; }, abstract = {BACKGROUND: The intestinal microbiota has been implicated in the pathophysiology of irritable bowel syndrome (IBS). Due to the variable resolutions of techniques used to characterize the intestinal microbiota, and the heterogeneity of IBS, the defined alterations of the IBS intestinal microbiota are inconsistent. We analyzed the composition of the intestinal microbiota in a defined subgroup of IBS patients (diarrhea-predominant IBS, D-IBS) using a technique that provides the deepest characterization available for complex microbial communities.<br><br>METHODS: Fecal DNA was isolated from 23 D-IBS patients and 23 healthy controls (HC). Variable regions V1-V3 and V6 of the 16S rRNA gene were amplified from all samples. PCR products were sequenced using 454 high throughput sequencing. The composition, diversity and richness of microbial communities were determined and compared between D-IBS and HC using the quantitative insights into microbial ecology pipeline.<br><br>KEY RESULTS: The contribution of bacterial groups to the composition of the intestinal microbiota differed between D-IBS and HC. D-IBS patients had significantly higher levels of Enterobacteriaceae (P = 0.03), and lower levels of Fecalibacterium genera (P = 0.04) compared to HC. &#x3b2;-Diversity values demonstrated significantly lower levels of UniFrac distances in HC compared to D-IBS patients. The richness of 16S rRNA sequences was significantly decreased in D-IBS patients (P < 0.04).<br><br>CONCLUSIONS &amp; INFERENCES: Our 16S rRNA sequence data demonstrates a community-level dysbiosis in D-IBS. The altered composition of the intestinal microbiota in D-IBS is associated with significant increases in detrimental and decreases in beneficial bacterial groups, and a reduction in microbial richness.}, }
@article {pmid22335102, year = {2011}, author = {Gonzalez, BC and Spinola, AL and Lamon, AW and Araujo, JC and Campos, JR}, title = {The use of microsensors to study the role of the loading rate and surface velocity on the growth and the composition of nitrifying biofilms.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {64}, number = {8}, pages = {1607-1613}, doi = {10.2166/wst.2011.716}, pmid = {22335102}, issn = {0273-1223}, mesh = {Bacteria/metabolism ; *Biofilms ; Bioreactors ; In Situ Hybridization, Fluorescence ; Nitrogen/chemistry/metabolism ; Oxidation-Reduction ; Oxygen ; Waste Disposal, Fluid/*methods ; }, abstract = {The good composition and activity of biofilms are very important for successful operation and control of fixed-film biological reactors employed in liquid effluents treatment. During the last decade, microsensors have been applied to study microbial ecology. These sensors could provide information regarding the microbial activity concerning nitrification and denitrification that occur inside biofilms. Other techniques of molecular biology, such as fluorescence in situ hybridization (FISH), have also contributed to this matter because their application aids in the identification of the bacterial populations that compose the biofilms. The focus of this paper was to study the loading rate and surface velocity to promote the development of nitrifying biofilms in three distinct flow cells that were employed in the post treatment of a synthetic wastewater simulating the effluent from a UASB (Upflow Anaerobic Sludge Blanket) reactor. Using the FISH technique, it was found that the population of ammonia-oxidizing-bacteria was greater than that of nitrite-oxidizing-bacteria; this was also supported by the lower production of nitrate determined by physicochemical and microsensor analyses. It was verified that the loading rate and surface velocity that promoted the greatest nitrogen removal were 0.25 g N-amon m(-2)biofilm day(-1) and 1 m h(-1), respectively.}, }
@article {pmid22329626, year = {2012}, author = {Direito, SO and Marees, A and Röling, WF}, title = {Sensitive life detection strategies for low-biomass environments: optimizing extraction of nucleic acids adsorbing to terrestrial and Mars analogue minerals.}, journal = {FEMS microbiology ecology}, volume = {81}, number = {1}, pages = {111-123}, doi = {10.1111/j.1574-6941.2012.01325.x}, pmid = {22329626}, issn = {1574-6941}, mesh = {Adsorption ; Aluminum Silicates ; Biomass ; Clay ; DNA/*isolation &amp; purification ; DNA, Bacterial/isolation &amp; purification ; Earth, Planet ; Groundwater ; *Mars ; *Minerals/chemistry ; Silicates/analysis ; }, abstract = {The adsorption of nucleic acids to mineral matrixes can result in low extraction yields and negatively influences molecular microbial ecology studies, in particular for low-biomass environments on Earth and Mars. We determined the recovery of nucleic acids from a range of minerals relevant to Earth and Mars. Clay minerals, but also other silicates and nonsilicates, showed very low recovery (< 1%). Consequently, optimization of DNA extraction was directed towards clays. The high temperatures and acidic conditions used in some methods to dissolve mineral matrices proved to destruct DNA. The most efficient method comprised a high phosphate solution (P/EtOH; 1 M phosphate, 15% ethanol buffer at pH 8) introduced at the cell-lysing step in DNA extraction, to promote chemical competition with DNA for adsorption sites. This solution increased DNA yield from clay samples spiked with known quantities of cells up to nearly 100-fold. DNA recovery was also enhanced from several mineral samples retrieved from an aquifer, while maintaining reproducible DGGE profiles. DGGE profiles were obtained for a clay sample for which no profile could be generated with the standard DNA isolation protocol. Mineralogy influenced microbial community composition. The method also proved suitable for the recovery of low molecular weight DNA (< 1.5 kb).}, }
@article {pmid22327336, year = {2012}, author = {Kaplan, JL and Walker, WA}, title = {Early gut colonization and subsequent obesity risk.}, journal = {Current opinion in clinical nutrition and metabolic care}, volume = {15}, number = {3}, pages = {278-284}, doi = {10.1097/MCO.0b013e32835133cb}, pmid = {22327336}, issn = {1473-6519}, support = {P30 DK040561/DK/NIDDK NIH HHS/United States ; R01 HD012437/HD/NICHD NIH HHS/United States ; P01 DK033506/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Disease Models, Animal ; Gastrointestinal Tract/metabolism/*microbiology ; Humans ; *Metagenome ; Obesity/*physiopathology/prevention &amp; control ; Prebiotics ; Probiotics ; Risk Factors ; }, abstract = {PURPOSE OF REVIEW: Early microbial colonization patterns of the human gastrointestinal tract are increasingly implicated in the pathogenesis of human disease. Recently, large-scale shifts in gut microbiota have been demonstrated in both animal and human models of obesity. This review examines the latest research into the gut dysbiosis associated with an obese phenotype and considers the evidence that may link early microbial colonization patterns with subsequent obesity risk.<br><br>RECENT FINDINGS: Studies that link microbiome modifying early life events to subsequent obesity risk provide some indirect evidence to support a causal role for gut microbiota in the pathogenesis of obesity. However, more direct evidence proving causation is currently lacking and there is no existing support for the role of specific early gut colonization patterns in later risk of obesity.<br><br>SUMMARY: Although an obesity-associated dysbiosis is well supported by the current literature, cause and effect remain difficult to discern. Longitudinal, prospective studies that evaluate changes in gut microbial ecology over time are needed to better discern the role of specific microbial patterns in the pathogenesis of obesity. Better understanding of this relationship may lead to exciting new obesity treatment and prevention strategies in the future.}, }
@article {pmid22327271, year = {2012}, author = {Staniewski, MA and Short, CM and Short, SM}, title = {Contrasting community versus population-based estimates of grazing and virus-induced mortality of phytoplankton.}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {25-38}, pmid = {22327271}, issn = {1432-184X}, mesh = {Chlorophyta/genetics/*physiology/virology ; Cyanobacteria/genetics/*physiology/virology ; *Ecosystem ; Food Chain ; Haptophyta/genetics/*physiology/virology ; Phytoplankton/genetics/*physiology/virology ; Ponds/*virology ; Population Dynamics ; *Virus Physiological Phenomena ; Viruses/isolation &amp; purification ; }, abstract = {In this study, grazing and virus-induced mortality of phytoplankton was investigated in a freshwater pond at the University of Toronto Mississauga, Canada, during September 2009. The modified dilution assay, which partitions phytoplankton mortality into virus and grazing-induced fractions, was used along with newly designed, taxon-specific quantitative polymerase chain reaction (qPCR) assays that target psbA gene fragments to estimate growth and mortality rates for both the entire phytoplankton community and four distinct phytoplankton populations. Community mortality was estimated via fluorometric determination of chlorophyll a (Chl a) concentrations, whereas the relative mortality of individual phytoplankton populations was estimated via qPCR. The sources and amounts of mortality for individual phytoplankton populations differed from those of the whole community, as well as from each other. Grazing was found to be the only significant source of mortality for the community (0.32 day(-1)), and the Prymnesiales (1.65 day(-1)) and Chroococcales (2.79 day(-1)) populations studied. On the other hand, the Chlamydomonadales population examined experienced both significant grazing (1.01 day(-1)) and viral lysis (0.96 day(-1)), while the Chlorellales population only experienced significant mortality as a result of viral lysis (1.38 day(-1)). Our results demonstrate that the combination of qPCR and the modified dilution method can be used to estimate both viral lysis and grazing pressure on several individual phytoplankton populations within a community simultaneously. Further, previously noted limitations of the modified dilution method associated with the dilution of specific phytoplankton populations at low abundances can be overcome with the qPCR-based approach. Most importantly, this study demonstrates that when used alone, whole community-based methods of assessing mortality can overlook valuable information about carbon flow in aquatic microbial food webs.}, }
@article {pmid22327270, year = {2012}, author = {Palijan, G}, title = {Abundance and biomass responses of microbial food web components to hydrology and environmental gradients within a floodplain of the River Danube.}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {39-53}, pmid = {22327270}, issn = {1432-184X}, mesh = {Bacteria/*growth &amp; development/isolation &amp; purification ; Biomass ; Ecosystem ; Floods ; *Food Chain ; Phytoplankton/*growth &amp; development/isolation &amp; purification ; Rivers/chemistry/*microbiology ; Seasons ; }, abstract = {This study investigated the relationships of time-dependent hydrological variability and selected microbial food web components. Samples were collected monthly from the Kopački Rit floodplain in Croatia, over a period of 19 months, for analysis of bacterioplankton abundance, cell size and biomass; abundance of heterotrophic nanoflagellates and nanophytoplankton; and concentration of chlorophyll a. Similar hydrological variability at different times of the year enabled partition of seasonal effects from hydrological changes on microbial community properties. The results suggested that, unlike some other studies investigating sites with different connectivity, bacterioplankton abundance, and phytoplankton abundance and biomass increased during lentic conditions. At increasing water level, nanophytoplankton showed lower sensitivity to disturbance in comparison with total phytoplankton biomass: this could prolong autotrophic conditions within the floodplain. Bacterioplankton biomass, unlike phytoplankton, was not impacted by hydrology. The bacterial biomass less affected by hydrological changes can be an important additional food component for the floodplain food web. The results also suggested a mechanism controlling bacterial cell size independent of hydrology, as bacterial cell size was significantly decreased as nanoflagellate abundance increased. Hydrology, regardless of seasonal sucession, has the potential to structure microbial food webs, supporting microbial development during lentic conditions. Conversely, other components appear unaffected by hydrology or may be more strongly controlled by biotic interactions. This research, therefore, adds to understanding on microbial food web interactions in the context of flood and flow pulses in river-floodplain ecosystems.}, }
@article {pmid22327269, year = {2012}, author = {Ross, KA and Feazel, LM and Robertson, CE and Fathepure, BZ and Wright, KE and Turk-Macleod, RM and Chan, MM and Held, NL and Spear, JR and Pace, NR}, title = {Phototrophic phylotypes dominate mesothermal microbial mats associated with hot springs in Yellowstone National Park.}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {162-170}, pmid = {22327269}, issn = {1432-184X}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Colorado ; DNA, Bacterial/genetics ; Hot Springs/*microbiology ; Molecular Sequence Data ; Phototrophic Processes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The mesothermal outflow zones (50-65°C) of geothermal springs often support an extensive zone of green and orange laminated microbial mats. In order to identify and compare the microbial inhabitants of morphologically similar green-orange mats from chemically and geographically distinct springs, we generated and analyzed small-subunit ribosomal RNA (rRNA) gene amplicons from six mesothermal mats (four previously unexamined) in Yellowstone National Park. Between three and six bacterial phyla dominated each mat. While many sequences bear the highest identity to previously isolated phototrophic genera belonging to the Cyanobacteria, Chloroflexi, and Chlorobi phyla, there is also frequent representation of uncultured, unclassified members of these groups. Some genus-level representatives of these dominant phyla were found in all mats, while others were unique to a single mat. Other groups detected at high frequencies include candidate divisions (such as the OP candidate clades) with no cultured representatives or complete genomes available. In addition, rRNA genes related to the recently isolated and characterized photosynthetic acidobacterium "Candidatus Chloracidobacterium thermophilum" were detected in most mats. In contrast to microbial mats from well-studied hypersaline environments, the mesothermal mats in this study accrue less biomass and are substantially less diverse, but have a higher proportion of known phototrophic organisms. This study provides sequences appropriate for accurate phylogenetic classification and expands the molecular phylogenetic survey of Yellowstone microbial mats.}, }
@article {pmid22324372, year = {2012}, author = {Rekecki, A and Gunasekara, RA and Dierckens, K and Laureau, S and Boon, N and Favoreel, H and Cornelissen, M and Sorgeloos, P and Ducatelle, R and Bossier, P and Van den Broeck, W}, title = {Bacterial host interaction of GFP-labelled Vibrio anguillarum HI-610 with gnotobiotic sea bass, Dicentrarchus labrax (L.), larvae.}, journal = {Journal of fish diseases}, volume = {35}, number = {4}, pages = {265-273}, doi = {10.1111/j.1365-2761.2011.01342.x}, pmid = {22324372}, issn = {1365-2761}, mesh = {Air Sacs/microbiology ; Animals ; Bass/*microbiology ; Enterocytes/microbiology ; Esophagus/microbiology ; Fish Diseases/*microbiology ; *Germ-Free Life ; Green Fluorescent Proteins ; *Host-Pathogen Interactions ; Larva/microbiology ; Vibrio/pathogenicity/*physiology ; Vibrio Infections/microbiology/*veterinary ; }, abstract = {The location and cell damage caused by Vibrio anguillarum, the causative agent of classical vibriosis, within the developing gut of the newly hatched sea bass, Dicentrarchus labrax (L.), is unknown. A gnotobiotic sea bass model was used to investigate the early interactions of V. anguillarum with sea bass larvae. In the present study, germ-free sea bass larvae were orally exposed to a V. anguillarum HI-610 pathogen labelled with the green fluorescent protein (GFP-HI-610) and sampled at regular intervals. Pathogenic colonization of gut enterocytes was observed 2 h post-exposure (p.e.) and onwards, whereas bacteria within the swim bladder were visualized 48 h p.e and onwards. Ultrastructural findings demonstrated direct bacterial contact with the host cell in the oesophageal mucosa and putative attachment to microvilli of mid- and hindgut enterocytes. The present findings form a starting point for studies assessing the impact of potential candidates (probiotics, prebiotics, antimicrobial peptides) to mitigate bacterial virulence.}, }
@article {pmid22321940, year = {2012}, author = {Hennebel, T and De Corte, S and Verstraete, W and Boon, N}, title = {Microbial production and environmental applications of Pd nanoparticles for treatment of halogenated compounds.}, journal = {Current opinion in biotechnology}, volume = {23}, number = {4}, pages = {555-561}, doi = {10.1016/j.copbio.2012.01.007}, pmid = {22321940}, issn = {1879-0429}, mesh = {Bacteria/classification/*metabolism ; *Biodegradation, Environmental ; Catalysis ; Halogens/*metabolism ; Humans ; Kinetics ; *Nanoparticles ; *Palladium ; Wastewater/*chemistry ; *Water Purification/methods ; }, abstract = {New biological inspired methods were recently developed to recover precious metals from waste streams and to concomitantly produce palladium nanoparticles on bacteria, that is, bio-Pd. This technology offers a variety of opportunities, as the process can considered to be green, tunable, affordable and scalable. The nanoparticle formation and the specific role of the bacteria in the reclamation process are highlighted. The effective performance of bio-Pd as catalyst in dehalogenation reactions, as well as in hydrogenation, reduction and CC coupling reactions has been extensively described in literature. Especially dehalogenation of environmental contaminants represents a promising market for application of bio-Pd. Therefore, several treatment technologies based on bio-Pd in the different environmental compartments are considered and domains, in which bio-Pd can be used at full scale are described. Finally, the perspectives for implementation of the bio-Pd technology in the future are set forward.}, }
@article {pmid22319868, year = {2011}, author = {Joseph, B and Yamakanamardi, SM}, title = {Monthly changes in the abundance and biomass of zooplankton and water quality parameters in Kukkarahalli Lake of Mysore, India.}, journal = {Journal of environmental biology..}, volume = {32}, number = {5}, pages = {551-557}, pmid = {22319868}, issn = {0254-8704}, mesh = {Animals ; *Biomass ; *Ecosystem ; India ; Lakes/*chemistry ; Population Dynamics ; Time Factors ; *Water Pollutants ; Zooplankton/*physiology ; }, abstract = {Zooplankton abundance and distribution are of ecological importance, as they are very sensitive to change, therefore zooplankton make ideal indicators of aquatic ecosystem. This study carried out on the abundance of rotifer, cladoceran, cyclopoid-copepod and ostracod zooplankton groups and biomass of total zooplankton were studied every month for one year. It is interesting and noteworthy to note that Calanoid and Harpacticoid zooplankton groups and free carbon dioxide were completely absent in all the four sampling sites throughout the study year. About 53% of the variation in the abundance of Cladoceran, 55% of variation in the Cyclopoid-copepod, 39% of variation in the ostracod and 53% of variation in the abundance of total zooplankton were mainly due to pH. Interestingly, negative relationship was found between the total zooplankton and concentration of phosphate as in this lake 67% decrease in wet biomass was mainly because of phosphate, where as 47% of dry biomass of total zooplankton was positively correlated with conductivity.}, }
@article {pmid22318873, year = {2012}, author = {Wang, R and Kaplan, A and Guo, L and Shi, W and Zhou, X and Lux, R and He, X}, title = {The influence of iron availability on human salivary microbial community composition.}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {152-161}, pmid = {22318873}, issn = {1432-184X}, support = {R01 DE020102/DE/NIDCR NIH HHS/United States ; R01 DE021108/DE/NIDCR NIH HHS/United States ; DE021108/DE/NIDCR NIH HHS/United States ; DE020102/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Female ; Humans ; Iron/analysis/*metabolism ; Male ; Metagenome ; Phylogeny ; Saliva/chemistry/*microbiology ; }, abstract = {It is a well-recognized fact that the composition of human salivary microbial community is greatly affected by its nutritional environment. However, most studies are currently focused on major carbon or nitrogen sources with limited attention to trace elements like essential mineral ions. In this study, we examined the effect of iron availability on the bacterial profiles of an in vitro human salivary microbial community as iron is an essential trace element for the survival and proliferation of virtually all microorganisms. Analysis via a combination of PCR with denaturing gradient gel electrophoresis demonstrated a drastic change in species composition of an in vitro human salivary microbiota when iron was scavenged from the culture medium by addition of the iron chelator 2,2'-bipyridyl. This shift in community profile was prevented by the presence of excessive ferrous iron (Fe(2+)). Most interestingly, under iron deficiency, the in vitro grown salivary microbial community became dominated by several hemolytic bacterial species, including Streptococcus spp., Gemella spp., and Granulicatella spp. all of which have been implicated in infective endocarditis. These data provide evidence that iron availability can modulate host-associated oral microbial communities, resulting in a microbiota with potential clinical impact.}, }
@article {pmid22316246, year = {2012}, author = {Kim, SH and Harzman, C and Davis, JK and Hutcheson, R and Broderick, JB and Marsh, TL and Tiedje, JM}, title = {Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {21}, pmid = {22316246}, issn = {1471-2180}, mesh = {Carbon Dioxide/metabolism ; DNA, Bacterial/*chemistry/*genetics ; Desulfitobacterium/*genetics/metabolism ; Genes, Bacterial ; *Genome, Bacterial ; Halogens/metabolism ; Metabolic Networks and Pathways/genetics ; Metals/metabolism ; Molecular Sequence Data ; Nitrogen Fixation ; Organic Chemicals/metabolism ; Oxidation-Reduction ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The genome of the Gram-positive, metal-reducing, dehalorespiring Desulfitobacterium hafniense DCB-2 was sequenced in order to gain insights into its metabolic capacities, adaptive physiology, and regulatory machineries, and to compare with that of Desulfitobacterium hafniense Y51, the phylogenetically closest strain among the species with a sequenced genome.<br><br>RESULTS: The genome of Desulfitobacterium hafniense DCB-2 is composed of a 5,279,134-bp circular chromosome with 5,042 predicted genes. Genome content and parallel physiological studies support the cell's ability to fix N2 and CO2, form spores and biofilms, reduce metals, and use a variety of electron acceptors in respiration, including halogenated organic compounds. The genome contained seven reductive dehalogenase genes and four nitrogenase gene homologs but lacked the Nar respiratory nitrate reductase system. The D. hafniense DCB-2 genome contained genes for 43 RNA polymerase sigma factors including 27 sigma-24 subunits, 59 two-component signal transduction systems, and about 730 transporter proteins. In addition, it contained genes for 53 molybdopterin-binding oxidoreductases, 19 flavoprotein paralogs of the fumarate reductase, and many other FAD/FMN-binding oxidoreductases, proving the cell's versatility in both adaptive and reductive capacities. Together with the ability to form spores, the presence of the CO2-fixing Wood-Ljungdahl pathway and the genes associated with oxygen tolerance add flexibility to the cell's options for survival under stress.<br><br>CONCLUSIONS: D. hafniense DCB-2's genome contains genes consistent with its abilities for dehalogenation, metal reduction, N2 and CO2 fixation, anaerobic respiration, oxygen tolerance, spore formation, and biofilm formation which make this organism a potential candidate for bioremediation at contaminated sites.}, }
@article {pmid22314388, year = {2012}, author = {Yoshida, S and Ohba, A and Liang, YM and Koitabashi, M and Tsushima, S}, title = {Specificity of Pseudomonas isolates on healthy and Fusarium head blight-infected spikelets of wheat heads.}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {214-225}, pmid = {22314388}, issn = {1432-184X}, mesh = {Antibiosis ; Biofilms ; Flowers/growth &amp; development/microbiology ; Fusarium/*physiology ; Molecular Sequence Data ; Pest Control, Biological ; Phylogeny ; Plant Diseases/*microbiology/prevention &amp; control ; Pseudomonas/classification/genetics/*isolation &amp; purification/physiology ; Species Specificity ; Triticum/growth &amp; development/*microbiology ; }, abstract = {The specificity of culturable bacteria on healthy and Fusarium head blight (FHB)-infected spikelets of wheat heads was investigated to find a candidate of biocontrol agents against FHB. The bacterial genus Pseudomonas was commonly isolated from the tissues, and phylogenetic analysis using 16S ribosomal RNA gene sequences of isolates of the genera revealed that particular phylogenetic groups in the genus specifically inhabited either healthy or infected spikelet tissues. The specificity of each group was suggested to be due to differences in the ability to form biofilms and colonize spikelet tissues; isolates originated from healthy spikelets formed biofilms on polyvinyl chloride microplate wells and highly colonized the spikelet tissues. Other bacterial groups obtained from FHB-infected spikelets less formed biofilms and attached with low densities on the spikelet tissues. Their colonization on the tissues, however, was promoted when co-inoculated with the causal pathogenic fungus, Fusarium graminearum, and several isolates were observed to smash the mycelia in vivo. Moreover, based on results of in vitro mycelial growth inhibition activity, the diseased tissue-originated isolates were verified to have a negative effect on the fungal growth. These results suggest that Pseudomonas isolates obtained from infected spikelet tissues were highly associated with the FHB pathogen and have potential as candidates for biological control against FHB.}, }
@article {pmid22307290, year = {2012}, author = {Ritchie, AE and Johnson, ZI}, title = {Abundance and genetic diversity of aerobic anoxygenic phototrophic bacteria of coastal regions of the pacific ocean.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {8}, pages = {2858-2866}, pmid = {22307290}, issn = {1098-5336}, mesh = {Aerobiosis ; Bacteria, Aerobic/*classification/*isolation &amp; purification/metabolism/physiology ; Bacterial Proteins/genetics ; *Biodiversity ; *Genetic Variation ; Molecular Sequence Data ; Pacific Ocean ; Photosynthetic Reaction Center Complex Proteins/genetics ; *Phototrophic Processes ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophic microbes that are found in a broad range of aquatic environments. Although potentially significant to the microbial ecology and biogeochemistry of marine ecosystems, their abundance and genetic diversity and the environmental variables that regulate these properties are poorly understood. Using samples along nearshore/offshore transects from five disparate islands in the Pacific Ocean (Oahu, Molokai, Futuna, Aniwa, and Lord Howe) and off California, we show that AAP bacteria, as quantified by the pufM gene biomarker, are most abundant near shore and in areas with high chlorophyll or Synechococcus abundance. These AAP bacterial populations are genetically diverse, with most members belonging to the alpha- or gammaproteobacterial groups and with subclades that are associated with specific environmental variables. The genetic diversity of AAP bacteria is structured along the nearshore/offshore transects in relation to environmental variables, and uncultured pufM gene libraries suggest that nearshore communities are distinct from those offshore. AAP bacterial communities are also genetically distinct between islands, such that the stations that are most distantly separated are the most genetically distinct. Together, these results demonstrate that environmental variables regulate both the abundance and diversity of AAP bacteria but that endemism may also be a contributing factor in structuring these communities.}, }
@article {pmid22297401, year = {2012}, author = {Acosta-Mercado, D and Cancel-Morales, N and Chinea, JD and Santos-Flores, CJ and De Jesús, IS}, title = {Could the canopy structure of bryophytes serve as an indicator of microbial biodiversity? A test for testate amoebae and microcrustaceans from a subtropical cloud forest in Dominican Republic.}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {200-213}, pmid = {22297401}, issn = {1432-184X}, mesh = {Amoebida/classification/*growth &amp; development/isolation &amp; purification ; Animals ; *Biodiversity ; Biomass ; Bryophyta/*growth &amp; development ; Crustacea/classification/*growth &amp; development ; Dominican Republic ; Ecosystem ; Plant Leaves/growth &amp; development ; }, abstract = {The mechanisms that ultimately regulate the diversity of microbial eukaryotic communities in bryophyte ecosystems remain a contentious topic in microbial ecology. Although there is robust consensus that abiotic factors, such as water chemistry of the bryophyte and pH, explain a significant proportion of protist and microcrustacean diversity, there is no systematic assessment of the role of bryophyte habitat complexity on such prominent microbial groups. Water-holding capacity is correlated with bryophyte morphology and canopy structure. Similarly, canopy structure explains biodiversity dynamics of the macrobiota suggesting that canopy structure may also be a potential parameter for understanding microbial diversity. Canopy roughness of the dominant bryophyte species within the Bahoruco Cloud Forest, Cachote, Dominican Republic, concomitant with their associated diversity of testate amoebae and microcrustaceans was estimated to determine whether canopy structure could be added to the list of factors explaining microbial biodiversity in bryophytes. We hypothesized that smooth (with high moisture content) canopies will have higher species richness, density, and biomass of testate amoebae and higher richness and density of microcrustaceans than rough (desiccation-prone) canopies. For testate amoebae, we found 83 morphospecies with relative low abundances. Species richness and density differed among bryophytes with different bryophyte canopy structures and based on non-metric multidimensional scaling, canopy roughness explained 25% of the variation in species composition although not as predicted. Acroporium pungens (low roughness, LR) had the lowest species richness (2 ± 0.61 SD per gram dry weight bryophyte), and density (2.1 ± 0.61 SD individual per gram of dry weight bryophyte); whereas Thuidium urceolatum (high roughness) had the highest richness (24 ± 10.82 SD) and density (94 ± 64.30 SD). The fact that the bryophyte with the highest roughness had the highest levels of diversity for testate amoebae suggests that moisture levels at the level of the bryophyte canopy may not represent a biodiversity driver in a cloud forest with high relative humidity; however, high roughness could generate a dynamic and fluctuating moisture environment with concomitant alternating microbial communities. A total of 26 microcrustacean morphospecies were found across 11 bryophytes; however, no bryophyte canopy effect was detected on their richness and density. Microcrustacean mean density was low ranging from less than one individual per 50 cm2 of bryophyte in Leucobryum (LR) to a maximum of 6 ± 3.37 SD individuals/50 cm2 in Monoclea (LR). This lack of pattern suggests that possible explanatory variables may be related to larger scale processes than those examined in this study.}, }
@article {pmid23757234, year = {2012}, author = {Lima, N and Rogers, T and Acevedo-Whitehouse, K and Brown, MV}, title = {Temporal stability and species specificity in bacteria associated with the bottlenose dolphins respiratory system.}, journal = {Environmental microbiology reports}, volume = {4}, number = {1}, pages = {89-96}, doi = {10.1111/j.1758-2229.2011.00306.x}, pmid = {23757234}, issn = {1758-2229}, abstract = {We demonstrate that the exhaled breath condensate, or 'blow', from marine mammals can be used to examine respiratory associated microbial communities using non-invasive sampling methods. Blow samples from two species of bottlenose dolphin, Tursiops truncatus and T. aduncus, along with hybrid offspring, were examined using molecular microbial ecology methods. A temporal analysis revealed that microbial community structure of each individual remained distinct from other individuals over a two-month period, indicting strong host specificity. The taxonomic composition of samples, based on pyrosequencing of the V1-V3 regions of the 16S rRNA gene, from 24 healthy individuals was dominated by the Cardiobacteraceae lineage of Gammaproteobacteria, comprising on average 52% of sequences in all samples. Sequences in this taxa were associated with novel clades that contain only sequences from dolphin respiratory tracts. Other genera that likely form part of the core biota include the Saccharospirillaceae (Gammaproteobacteria), Arcobacter (Epsilonproteobacteria), Hydrogenimonaceae (Epsilonproteobacteria), Halotalea (Gammaproteobacteria), Aquimarina (Flavobacteria) and Helococcus (Clostridia). Significant differences between samples from different species were observed only at the species/ strain level, driven by the relative contributions of strains from the most common phylogenetic lineages. Analysis of communities associated with hybrid animals provides tentative evidence for a paternal role in community assembly. Clear overlap was observed with data collected by capture and swabbing of bottlenose dolphins blowholes, indicating this method provides a novel non-invasive alternative to monitoring marine mammal population health.}, }
@article {pmid23757228, year = {2012}, author = {Igisu, M and Takai, K and Ueno, Y and Nishizawa, M and Nunoura, T and Hirai, M and Kaneko, M and Naraoka, H and Shimojima, M and Hori, K and Nakashima, S and Ohta, H and Maruyama, S and Isozaki, Y}, title = {Domain-level identification and quantification of relative prokaryotic cell abundance in microbial communities by Micro-FTIR spectroscopy.}, journal = {Environmental microbiology reports}, volume = {4}, number = {1}, pages = {42-49}, doi = {10.1111/j.1758-2229.2011.00277.x}, pmid = {23757228}, issn = {1758-2229}, abstract = {Domain-level identification of microbial cells or cell-like structures is crucial for investigating natural microbial communities and their ecological significance. By using micro-Fourier transform infrared (micro-FTIR) spectroscopy, we established a technical basis for the domain-level diagnosis and quantification of prokaryotic cell abundance in natural microbial communities. Various prokaryotic cultures (12 species of bacteria and 10 of archaea) were examined using micro-FTIR spectroscopic analysis. The aliphatic CH3 /CH2 absorbance ratios (R3/2) showed domain-specific signatures, possibly reflecting distinctive cellular lipid compositions. The signatures were preserved even after chemical cell fixation (formaldehyde) and nucleic acid staining (DAPI) processes - techniques that are essential in studying microbial ecology. The micro-FTIR technique was successfully applied for quantification of the bacteria/archaea abundance ratio in an active microbial mat community in a subsurface hot aquifer stream. We conclude that the micro-FTIR R3/2 measurement is both fast and effective for domain-level diagnosis and quantification of first-order prokaryotic community structures.}, }
@article {pmid22286498, year = {2012}, author = {Islas-Espinoza, M and Reid, BJ and Wexler, M and Bond, PL}, title = {Soil bacterial consortia and previous exposure enhance the biodegradation of sulfonamides from pig manure.}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {140-151}, pmid = {22286498}, issn = {1432-184X}, mesh = {Animals ; Anti-Bacterial Agents/analysis/*metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; DNA, Bacterial/genetics ; Manure/analysis/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Sulfamethazine/analysis/*metabolism ; Swine ; Veterinary Drugs/analysis/metabolism ; }, abstract = {Persistence or degradation of synthetic antibiotics in soil is crucial in assessing their environmental risks. Microbial catabolic activity in a sandy loamy soil with pig manure using 12C- and 14C-labelled sulfamethazine (SMZ) respirometry showed that SMZ was not readily degradable. But after 100 days, degradation in sulfadiazine-exposed manure was 9.2%, far greater than soil and organic manure (0.5% and 0.11%, respectively, p < 0.05). Abiotic degradation was not detected suggesting microbial catabolism as main degradation mechanism. Terminal restriction fragment length polymorphism showed biodiversity increases within 1 day of SMZ spiking and especially after 200 days, although some species plummeted. A clone library from the treatment with highest degradation showed that most bacteria belonged to α, β and γ classes of Proteobacteria, Firmicutes, Bacteroidetes and Acidobacteria. Proteobacteria (α, β and γ), Firmicutes and Bacteroidetes which were the most abundant classes on day 1 also decreased most following prolonged exposure. From the matrix showing the highest degradation rate, 17 SMZ-resistant isolates biodegraded low levels of 14C-labelled SMZ when each species was incubated separately (0.2-1.5%) but biodegradation was enhanced when the four isolates with the highest biodegradation were incubated in a consortium (Bacillus licheniformis, Pseudomonas putida, Alcaligenes sp. and Aquamicrobium defluvium as per 16S rRNA gene sequencing), removing up to 7.8% of SMZ after 20 days. One of these species (B. licheniformis) was a known livestock and occasional human pathogen. Despite an environmental role of these species in sulfonamide bioremediation, the possibility of horizontal transfer of pathogenicity and resistance genes should caution against an indiscriminate use of these species as sulfonamide degraders.}, }
@article {pmid22286497, year = {2012}, author = {Siboni, N and Ben-Dov, E and Sivan, A and Kushmaro, A}, title = {Geographic specific coral-associated ammonia-oxidizing archaea in the northern Gulf of Eilat (Red Sea).}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {18-24}, pmid = {22286497}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Animals ; Anthozoa/*microbiology ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Archaeal Proteins/genetics ; Biodiversity ; Geography ; Indian Ocean ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; }, abstract = {Coral holobionts are densely populated with microorganisms that are essential for their well-being. Here we compared the diversity of the archaeal ammonia monooxygenase alpha subunit (amoA) gene from three coral genera, Acanthastrea sp., Favia sp., and Fungia granulosa, from the Gulf of Eilat, Red Sea. At 99% similarity, archaeal amoA from the three coral genera shared 71% of their cloned sequences, while the Favia and Acanthastrea presented a few genus-specific clones. In addition, the sequences retrieved in our samples displayed lower similarity to amoA sequences previously found in association with other coral species from different geographic regions. This finding suggests that the populations of ammonia-oxidizing archaea are less host-specific and more geographically dependent.}, }
@article {pmid23990811, year = {2012}, author = {Shenderov, BA}, title = {Gut indigenous microbiota and epigenetics.}, journal = {Microbial ecology in health and disease}, volume = {23}, number = {}, pages = {}, pmid = {23990811}, issn = {0891-060X}, abstract = {This review introduces and discusses data regarding fundamental and applied investigations in mammalian epigenomics and gut microbiota received over the last 10 years. Analysis of these data enabled us first to come to the conclusion that the multiple low-molecular-weight substances of indigenous gut microbiota origin should be considered one of the main endogenous factors actively participating in epigenomic mechanisms that are responsible for the mammalian genome reprograming and post-translated modifications. Gut microecological imbalance caused by various biogenic and abiogenic agents and factors can produce different epigenetic abnormalities and the onset and progression of metabolic diseases associated. The authors substantiate the necessity to create an international project 'Human Gut Microbiota and Epigenomics' that facilitates interdisciplinary collaborations among scientists and clinicians engaged in host microbial ecology, nutrition, metagenomics, epigenomics, and metabolomics investigations as well as in disease prevention and treatment. Some priority scientific and applied directions in the current omic technologies coupled with gnotobiological approaches are suggested that can open a new era in characterizing the role of the symbiotic microbiota small metabolic and signal molecules in the host epigenomics. Although the discussed subject is only at an early stage its validation can open novel approaches in drug discovery studies.}, }
@article {pmid23914612, year = {2012}, author = {Kiewra, D and Lonc, E}, title = {Epidemiological consequences of host specificity of ticks (Ixodida).}, journal = {Annals of parasitology}, volume = {58}, number = {4}, pages = {181-187}, pmid = {23914612}, issn = {2299-0631}, mesh = {Animals ; Host-Parasite Interactions ; Species Specificity ; Tick Infestations/*epidemiology/*parasitology ; *Ticks ; }, abstract = {Arthropod-borne diseases still pose a serious health problem worldwide. Epidemiological consequences result from various environmental connections and interaction between parasites and their host, including host specificity of parasites and transmitted pathogens. The ixodid ticks (Ixodida) occupy a prominent position within the group of parasites as being vectors on the northern hemisphere in temperate climate zone. They are blood-feeding ectoparasites with different host specificity and capacity to transmit various pathogens. Feeding on many mammals (including humans), birds, reptiles and amphibians they present a great medical problem. For example, Ixodes ricinus can infest several hundred species of animals. It is a vector of pathogenic viral, bacterial and protozoal organisms, including Borrelia burgdorferi sensu lato complex which is the etiological agent of Lyme borreliosis. The competent reservoir hosts of Borrelia include many common species of small and medium-sized rodents as well as several bird species. Epidemiological consequences are complicated by the fact that specific Borrelia genospecies are associated with particular reservoir hosts. Thus, detailed analysis of epidemiological consequences requires a comprehensive knowledge of the biology and ecology of vectors, pathogens and their reservoirs including host specificity of ticks. Spatial modelling tick-borne risk in time and space is made possible by the use of remote sensing and techniques of geographical information system (GIS).}, }
@article {pmid23761354, year = {2011}, author = {Dolan, JR and Stoeck, T}, title = {Repeated sampling reveals differential variability in measures of species richness and community composition in planktonic protists.}, journal = {Environmental microbiology reports}, volume = {3}, number = {6}, pages = {661-666}, doi = {10.1111/j.1758-2229.2011.00250.x}, pmid = {23761354}, issn = {1758-2229}, abstract = {Diversity metrics and descriptors of protistan community structure were calculated from 12 samples of 10 l each collected from the Bay of Villefranche in the NW Mediterranean Sea. Variability of the sampling was on scales of minutes and meters. The individual samples were compared with each other and compared with a pooled data set from the total volume of 120 l, considered as the 'true' community. We focused on a single group of planktonic protists, tintinnids, a coherent functional and phylogenetic group in which morpho-species identifications by light microscopy are unambiguous. Tintinnid abundance in the samples ranged from 217 to 321 cells of 16-21 species with the number of rare species in a sample (< 1% of abundance) positively related to species richness of the sample. Rarefaction estimates of total species richness in the 12 samples ranged from 21 ± 3.5 to 37 ± 3.6 compared with the 34 species of the pooled data set. The measures of similarity reflected the differences between samples in both the numbers and identities of the least abundant or rare species. The species abundance distribution using pooled data was best fit by a log-series or geometric distribution; eight species accounted for about 90% of total cells and most species, the remaining 22 out of 34, were 'rare' (concentration < 1% of total cells). Among the samples, 5 were best fit by a geometric model, 1 by a log-series distribution, 2 by a log-normal or log-series model, and 4 could not be clearly assigned a particular distribution. Our results suggest that single sample estimates of species richness are relatively robust compared with measures of taxonomic similarity and species abundance distribution. When measuring differences among populations sample variability should be considered.}, }
@article {pmid23761304, year = {2011}, author = {Antunes, A and Ngugi, DK and Stingl, U}, title = {Microbiology of the Red Sea (and other) deep-sea anoxic brine lakes.}, journal = {Environmental microbiology reports}, volume = {3}, number = {4}, pages = {416-433}, doi = {10.1111/j.1758-2229.2011.00264.x}, pmid = {23761304}, issn = {1758-2229}, abstract = {The Red Sea harbours approximately 25 deep-sea anoxic brine pools. They constitute extremely unique and complex habitats with the conjugation of several extreme physicochemical parameters rendering them some of the most inhospitable environments on Earth. After 50 years of research mostly driven by chemists, geophysicists and geologists, the microbiology of the brines has been receiving increased interest in the last decade. Recent molecular and cultivation-based studies have provided us with a first glimpse on the enormous biodiversity of the local microbial communities, the identification of several new taxonomic groups, and the isolation of novel extremophiles that thrive in these environments. This review presents a general overview of these unusual biotopes and compares them with other similar environments in the Mediterranean Sea and the Gulf of Mexico, with a focus on their microbial ecology.}, }
@article {pmid24031681, year = {2011}, author = {Magalhães, KT and de Melo Pereira, GV and Campos, CR and Dragone, G and Schwan, RF}, title = {Brazilian kefir: structure, microbial communities and chemical composition.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {42}, number = {2}, pages = {693-702}, pmid = {24031681}, issn = {1517-8382}, abstract = {Microbial ecology and chemical composition of Brazilian kefir beverage was performed. The microorganisms associated with Brazilian kefir were investigated using a combination of phenotypic and genotypic methods. A total of 359 microbial isolates were identified. Lactic acid bacteria (60.5%) were the major isolated group identified, followed by yeasts (30.6%) and acetic acid bacteria (8.9%). Lactobacillus paracasei (89 isolates), Lactobacillus parabuchneri (41 isolates), Lactobacillus casei (32 isolates), Lactobacillus kefiri (31 isolates), Lactococcus lactis (24 isolates), Acetobacter lovaniensis (32 isolates), Kluyveromyces lactis (31 isolates), Kazachstania aerobia (23 isolates), Saccharomyces cerevisiae (41 isolates) and Lachancea meyersii (15 isolates) were the microbial species isolated. Scanning electron microscopy showed that the microbiota was dominated by bacilli (short and curved long) cells growing in close association with lemon-shaped yeasts cells. During the 24 h of fermentation, the protein content increased, while lactose and fat content decreased. The concentration of lactic acid ranged from 1.4 to 17.4 mg/ml, and that of acetic acid increased from 2.1 to 2.73 mg/ml. The production of ethanol was limited, reaching a final mean value of 0.5 mg/ml.}, }
@article {pmid23761255, year = {2011}, author = {Shapiro, OH and Hatzenpichler, R and Buckley, DH and Zinder, SH and Orphan, VJ}, title = {Multicellular photo-magnetotactic bacteria.}, journal = {Environmental microbiology reports}, volume = {3}, number = {2}, pages = {233-238}, doi = {10.1111/j.1758-2229.2010.00215.x}, pmid = {23761255}, issn = {1758-2229}, abstract = {Multicellular magnetotactic bacteria (MMB) are unique microorganisms typically comprised of 10-40 bacterial cells arranged around a central acellular compartment. Their life cycle has no known unicellular stage and division occurs by separation of a single MMB aggregate into two identical offspring. In this study, South-seeking multicellular magnetotactic bacteria (ssMMB) were enriched from a New England salt marsh. When exposed to light, ssMMB reversed their magnetotactic behaviour to become North-seeking. The exposure time needed to generate the reversal response varied with light wavelength and intensity. Extensive exposure to light appeared to be lethal. This is the first report of a Northern hemisphere MMB displaying South-seeking behaviour and the first time a MMB is found to exhibit photo-magnetotaxis. We suggest that this mechanism enables ssMMB to optimize their location with regard to chemical gradients and light intensities, and propose a model to explain the peculiar balance between photo- and magnetotaxis.}, }
@article {pmid22587876, year = {2011}, author = {Squartini, A}, title = {Where the bugs are: analyzing distributions of bacterial phyla by descriptor keyword search in the nucleotide database.}, journal = {Microbial informatics and experimentation}, volume = {1}, number = {1}, pages = {7}, pmid = {22587876}, issn = {2042-5783}, abstract = {BACKGROUND: The associations between bacteria and environment underlie their preferential interactions with given physical or chemical conditions. Microbial ecology aims at extracting conserved patterns of occurrence of bacterial taxa in relation to defined habitats and contexts.<br><br>RESULTS: In the present report the NCBI nucleotide sequence database is used as dataset to extract information relative to the distribution of each of the 24 phyla of the bacteria superkingdom and of the Archaea. Over two and a half million records are filtered in their cross-association with each of 48 sets of keywords, defined to cover natural or artificial habitats, interactions with plant, animal or human hosts, and physical-chemical conditions. The results are processed showing: (a) how the different descriptors enrich or deplete the proportions at which the phyla occur in the total database; (b) in which order of abundance do the different keywords score for each phylum (preferred habitats or conditions), and to which extent are phyla clustered to few descriptors (specific) or spread across many (cosmopolitan); (c) which keywords individuate the communities ranking highest for diversity and evenness.<br><br>CONCLUSIONS: A number of cues emerge from the results, contributing to sharpen the picture on the functional systematic diversity of prokaryotes. Suggestions are given for a future automated service dedicated to refining and updating such kind of analyses via public bioinformatic engines.}, }
@article {pmid22587826, year = {2011}, author = {Gilbert, JA and O'Dor, R and King, N and Vogel, TM}, title = {The importance of metagenomic surveys to microbial ecology: or why Darwin would have been a metagenomic scientist.}, journal = {Microbial informatics and experimentation}, volume = {1}, number = {1}, pages = {5}, pmid = {22587826}, issn = {2042-5783}, abstract = {Scientific discovery is incremental. The Merriam-Webster definition of 'Scientific Method' is "principles and procedures for the systematic pursuit of knowledge involving the recognition and formulation of a problem, the collection of data through observation and experiment, and the formulation and testing of hypotheses". Scientists are taught to be excellent observers, as observations create questions, which in turn generate hypotheses. After centuries of science we tend to assume that we have enough observations to drive science, and enable the small steps and giant leaps which lead to theories and subsequent testable hypotheses. One excellent example of this is Charles Darwin's Voyage of the Beagle, which was essentially an opportunistic survey of biodiversity. Today, obtaining funding for even small-scale surveys of life on Earth is difficult; but few argue the importance of the theory that was generated by Darwin from his observations made during this epic journey. However, these observations, even combined with the parallel work of Alfred Russell Wallace at around the same time have still not generated an indisputable 'law of biology'. The fact that evolution remains a 'theory', at least to the general public, suggests that surveys for new data need to be taken to a new level.}, }
@article {pmid23766277, year = {2010}, author = {Lavin, P and González, B and Santibáñez, JF and Scanlan, DJ and Ulloa, O}, title = {Novel lineages of Prochlorococcus thrive within the oxygen minimum zone of the eastern tropical South Pacific.}, journal = {Environmental microbiology reports}, volume = {2}, number = {6}, pages = {728-738}, doi = {10.1111/j.1758-2229.2010.00167.x}, pmid = {23766277}, issn = {1758-2229}, abstract = {The eastern tropical Pacific Ocean holds two of the main oceanic oxygen minimum zones of the global ocean. The presence of an oxygen-depleted layer at intermediate depths, which also impinges on the seafloor and in some cases the euphotic zone, plays a significant role in structuring both pelagic and benthic communities, and also in the vertical partitioning of microbial assemblages. Here, we assessed the genetic diversity and distribution of natural populations of the cyanobacteria Prochlorococcus and Synechococcus within oxic and suboxic waters of the eastern tropical Pacific using cloning and sequencing, and terminal restriction fragment length polymorphism (T-RFLP) analyses applied to the 16S-23S rRNA internal transcribed spacer region. With the T-RFLP approach we could discriminate 19 cyanobacterial clades, of which 18 were present in the study region. Synechococcus was more abundant in the surface oxic waters of the eastern South Pacific, while Prochlorococcus dominated the subsurface low-oxygen waters. Two of the dominant clades in the oxygen-deficient waters belong to novel and yet uncultivated lineages of low-light adapted Prochlorococcus.}, }
@article {pmid23766274, year = {2010}, author = {Grossart, HP}, title = {Ecological consequences of bacterioplankton lifestyles: changes in concepts are needed.}, journal = {Environmental microbiology reports}, volume = {2}, number = {6}, pages = {706-714}, doi = {10.1111/j.1758-2229.2010.00179.x}, pmid = {23766274}, issn = {1758-2229}, abstract = {In recent years, microbial ecology has developed from a peripheral discipline into a central field of microbiology. This change in state and perception is mainly driven by a rapid development of methods applied in the manifold fields related to microbial ecology. In biogeochemistry, for example, the use of high-resolution techniques such as FT-ICR-MS (Fourier transform ion cyclotron mass spectroscopy) has uncovered an enormous diversity and complexity of natural organic matter produced or degraded microbially either in dissolved or particulate forms. On the other hand, the introduction of high-throughput sequencing methods, such as 454 pyrosequencing, in combination with advances in bioinformatics allows for studying the bacterial diversity in natural samples circumventing cultivation dependent approaches. These new molecular tools enable in depth studies on single-cell genomes, distinct populations or even metacommunities. In combination with metatranscriptome and proteome studies it is for the first time possible to simultaneously unravel the structure and function of complex communities in situ. These technique-derived findings have, on the one hand, dramatically increased our knowledge on the vast diversity and complexity of bacterial habitats and, on the other hand, on phylogentic diversity and physiological responses of natural bacterial communities to their environment. However, until now microbial ecology is lacking an ecologically relevant species definition and useful tools for the identification of ecologically coherent taxa. Studies on intra- and interspecies interactions even with higher organisms demonstrate that bacteria can rapidly adapt to temporal and spatial changes in their environment. Aquatic bacteria have optimized and dramatically expanded their living space by efficient exploitation of organic matter point sources such as particles/aggregates and higher organisms. Although it is evident that particles/aggregates and organisms such as phytoplankton are 'hotspots' for microbial growth and transformation processes, it has not affected sampling strategies of aquatic microbial ecologists, who often focus solely on the free-living bacterial fractions and a priori exclude higher organisms by non-representative water sampling. Therefore, aquatic microbial ecologists have largely overlooked the fact that many aquatic bacteria may possess a complex lifestyle and frequently alternate between a free-living and a surface-associated stage. Here, I propose that modern concepts in aquatic microbial ecology should take into account the high chemical diversity and spatio-temporal variability of the bacterial environment. Interactions of aquatic bacteria with surfaces including living organisms are the key to understanding their physiological adaptations and population dynamics, as well as their contribution to biogeochemical cycles. New sampling strategies and theoretical concepts are needed in aquatic microbial ecology to access the whole spectrum of bacterial lifestyles and their ecological and evolutionary consequences.}, }
@article {pmid22815576, year = {2010}, author = {Tayung, K and Jha, DK}, title = {Antimicrobial endophytic fungal assemblages inhabiting bark of Taxus baccata L. of Indo-Burma mega biodiversity hotspot.}, journal = {Indian journal of microbiology}, volume = {50}, number = {Suppl 1}, pages = {74-81}, pmid = {22815576}, issn = {0973-7715}, abstract = {Fungal endophytes were isolated from inner bark of Taxus baccata L., an important source of potent anticancer drug taxol. Bark samples were collected from two locations of Arunachal Pradesh, India, part of the Indo-Burma mega biodiversity hotspot, during two seasons i.e. monsoon and winter. Altogether 77 fungal strains representing 18 genera were isolated from T. baccata bark during the present investigation. The colonizing frequency was recorded as 38.5% and the fungal community comprised of 78% of Hyphomycetes, 5.2% of Coelomycetes, 2.6% of Zygomycetes and Ascomycetes and 9.1% of sterile mycelia. Most common and frequently isolated genera were Fusarium, Penicillium and Aspergillus. Simpson and Shannon diversity indices indicated higher species diversity during monsoon than during winter seasons irrespective of the locations. The two locations harbored 5 to 37 endophyte species and the similarity index was low during winter and high during monsoon. Ethyl acetate extract of fermentation cultures of these fungi were tested for their antimicrobial activity against a panel of human pathogenic Gram-positive and Gram-negative bacteria and fungi. Fifteen fungal isolates out of the isolated strains displayed antimicrobial activity. An endophytic fungus, identified as Fusarium sp. displayed significant antimicrobial activity against all the test pathogens.}, }
@article {pmid22444606, year = {2010}, author = {Lourenço, M and Ramos-Morales, E and Wallace, RJ}, title = {The role of microbes in rumen lipolysis and biohydrogenation and their manipulation.}, journal = {Animal : an international journal of animal bioscience}, volume = {4}, number = {7}, pages = {1008-1023}, doi = {10.1017/S175173111000042X}, pmid = {22444606}, issn = {1751-732X}, abstract = {Despite the fact that the ruminant diet is rich in polyunsaturated fatty acids (PUFA), ruminant products - meat, milk and dairy - contain mainly saturated fatty acids (SFA) because of bacterial lipolysis and subsequent biohydrogenation of ingested PUFA in the rumen. The link between SFA consumption by man and coronary heart disease is well established. In contrast, ruminant products also contain fatty acids that are known to be beneficial to human health, namely conjugated linoleic acids (CLAs). The aims of research in this field have been to understand the microbial ecology of lipolysis and biohydrogenation and to find ways of manipulating ruminal microbes to increase the flow of PUFA and CLA from the rumen into meat and milk. This review describes our present understanding of the microbial ecology of ruminal lipid metabolism, including some apparently anomalous and paradoxical observations, and the status of how the metabolism may be manipulated and the possible consequential effects on other aspects of ruminal digestion. Intuitively, it may appear that inhibiting the ruminal lipase would cause more dietary PUFA to reach the mammary gland. However, lipolysis releases the non-esterified fatty acids that form the substrates for biohydrogenation, but which can, if they accumulate, inhibit the whole process. Thus, increasing lipase activity could be beneficial if the increased release of non-esterified PUFA inhibited the metabolism of CLA. Rumen ciliate protozoa do not carry out biohydrogenation, yet protozoal lipids are much more highly enriched in CLA than bacterial lipids. How could this happen if protozoa do not metabolise PUFA? The answer seems to lie in the ingestion of plant organelles, particularly chloroplasts, and the partial metabolism of the fatty acids by contaminating bacteria. Bacteria related to Butyrivibrio fibrisolvens are by far the most active and numerous biohydrogenating bacteria isolated from the rumen. But do we misunderstand the role of different bacterial species in biohydrogenation because there are uncultivated species that we need to understand and include in the analysis? Manipulation methods include dietary vegetable and fish oils and plant-derived chemicals. Their usefulness, efficacy and possible effects on fatty acid metabolism and on ruminal microorganisms and other areas of their metabolism are described, and areas of opportunity identified.}, }
@article {pmid23765997, year = {2010}, author = {Defoirdt, T and Darshanee Ruwandeepika, HA and Karunasagar, I and Boon, N and Bossier, P}, title = {Quorum sensing negatively regulates chitinase in Vibrio harveyi.}, journal = {Environmental microbiology reports}, volume = {2}, number = {1}, pages = {44-49}, doi = {10.1111/j.1758-2229.2009.00043.x}, pmid = {23765997}, issn = {1758-2229}, abstract = {Quorum sensing, bacterial cell-to-cell communication, regulates the virulence of Vibrio harveyi towards different hosts. Chitinase can be considered as a virulence factor because it helps pathogenic bacteria to attach to the host and to penetrate its tissues (e.g. in case of shrimp). Here, we show that quorum sensing negatively regulates chitinase in V. harveyi. Chitinolytic activity towards natural chitin from crab shells, the synthetic chitin derivative chitin azure, and fluorogenic chitin oligomers was significantly higher in a mutant in which the quorum-sensing system is completely inactivated when compared with a mutant in which the system is maximally active. Furthermore, the addition of signal molecule containing cell-free culture fluids decreased chitinase activity in a Harveyi Autoinducer 1 and Autoinducer 2-deficient double mutant. Finally, chitinase A mRNA levels were fivefold lower in the mutant in which the quorum-sensing system is maximally active when compared with the mutant in which the system is completely inactivated. [Correction added on 25 September 2009, after first online publication: the preceding sentence was corrected from 'Finally, chitinase A mRNA levels were fivefold lower in the mutant in which the quorum-sensing system is completely inactivated when compared with the mutant in which the system is maximally active.'] We argue that this regulation might help the vibrios to switch between host-associated and free-living life styles.}, }
@article {pmid23765851, year = {2009}, author = {Van Essche, M and Sliepen, I and Loozen, G and Van Eldere, J and Quirynen, M and Davidov, Y and Jurkevitch, E and Boon, N and Teughels, W}, title = {Development and performance of a quantitative PCR for the enumeration of Bdellovibrionaceae.}, journal = {Environmental microbiology reports}, volume = {1}, number = {4}, pages = {228-233}, doi = {10.1111/j.1758-2229.2009.00034.x}, pmid = {23765851}, issn = {1758-2229}, abstract = {Quantification of Bdellovibrio-and-like organisms (BALOs) by microbial culturing has a number of substantial drawbacks. Therefore a quantitative PCR (qPCR) assay was designed for the culture-independent enumeration of the Bdellovibrionaceae. After optimization, the dynamic range of the qPCR assay was assessed, the specificity was evaluated and a comparison with quantitative microbial culturing was made. To evaluate the suitability of the qPCR assay for analysing environmental samples, fresh water samples were investigated by microbial culturing and by the qPCR assay. The results revealed a substantial difference between the two techniques and indicate that most Bdellovibrionaceae cells are left undetected in environmental samples when only current microbial culturing techniques are used. The application of this new technique is therefore likely to confirm the hitherto underestimated sizes and roles of predatory bacterial populations in nature.}, }
@article {pmid24031382, year = {2009}, author = {Andreote, FD and Azevedo, JL and Araújo, WL}, title = {Assessing the diversity of bacterial communities associated with plants.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {40}, number = {3}, pages = {417-432}, pmid = {24031382}, issn = {1517-8382}, abstract = {Plant-bacteria interactions result from reciprocal recognition between both species. These interactions are responsible for essential biological processes in plant development and health status. Here, we present a review of the methodologies applied to investigate shifts in bacterial communities associated with plants. A description of techniques is made from initial isolations to culture-independent approaches focusing on quantitative Polymerase Chain Reaction in real time (qPCR), Denaturing Gradient Gel Electrophoresis (DGGE), clone library construction and analysis, the application of multivariate analyses to microbial ecology data and the upcoming high throughput methodologies such as microarrays and pyrosequencing. This review supplies information about the development of traditional methods and a general overview about the new insights into bacterial communities associated with plants.}, }
@article {pmid23765740, year = {2009}, author = {Possemiers, S and Verstraete, W}, title = {Oestrogenicity of prenylflavonoids from hops: activation of pro-oestrogens by intestinal bacteria.}, journal = {Environmental microbiology reports}, volume = {1}, number = {2}, pages = {100-109}, doi = {10.1111/j.1758-2229.2009.00011.x}, pmid = {23765740}, issn = {1758-2229}, abstract = {For many centuries, hops (Humulus lupulus L.) have been used as essential ingredient in beers, providing the typical bitterness and hoppy flavour. However, the last few years the plant has gained increasing attention as a source of prenylflavonoids and in 1999, 8-prenylnaringenin (8-PN) was identified as the most potent phyto-oestrogen known so far. Hop extracts are therefore now marketed to reduce menopausal complaints. However, 8-PN concentrations in hops are very low, and variable efficiency of these extracts was observed. Yet, hops also contain isoxanthohumol (IX) in much higher amounts (IX/8-PN ratio in hop extracts is typically 10-20). This article reviews our recent findings on how the human intestinal microbiota may activate IX. Depending on inter-individual differences in the intestinal transformation potential, this conversion could easily increase the 8-PN exposure 10-fold. The variability in efficacy of hop extracts may therefore be explained by variable intestinal metabolism. Based on this scientific knowledge, an innovative strategy was developed to decrease this variability. First, Eubacterium limosum, capable of rapidly metabolizing all IX into 8-PN, was isolated from the complex intestinal ecosystem. This bacterium was then used to develop a new generation of hop products with increased reliability in effect. This strategy involves the use of the bacterium as probiotic, in which the bacterium is administered in combination with the original hop extract. This leads to efficient intestinal 8-PN production, also in individuals who originally did not harbour the appropriate bacteria. The findings presented in this review can therefore be considered as a typical example that good insight in the specific metabolic potential of complex microbial communities and individual bacterial species may offer important opportunities for the management and modulation of the microbial organization towards a certain metabolic function.}, }
@article {pmid23765724, year = {2009}, author = {Bañeras, L and Gich, F and Martinez-Medina, M and Miller, M and Abella, CA and Borrego, CM}, title = {New phylotypes of mesophilic filamentous anoxygenic phototrophic bacteria enriched from sulfide-containing environments.}, journal = {Environmental microbiology reports}, volume = {1}, number = {1}, pages = {86-93}, doi = {10.1111/j.1758-2229.2008.00009.x}, pmid = {23765724}, issn = {1758-2229}, abstract = {Agar-based solid media with increasing concentrations of organic matter were used to isolate new members of the Chloroflexaceae (phylum Chloroflexi) from mesophilic environments containing sulfide. Inorganic media yielded less than 10% positive enrichments, which were not able to be maintained after repetitive inoculations in fresh medium. The use of casaminoacids and complex organic acid mixtures increased the number of positive enrichments (up to 45%) from both water and sediment samples. Two different green filamentous bacteria, SisoF2 and SalF, could be stably maintained as co-cultures for long periods and their phylogeny inferred from the analysis of complete sequences of the 16S rRNA gene. Ribotype SalF showed a high homology (95-98%) to previously isolated Oscillochloris trichoides strains. The 16S rRNA gene sequence retrieved from culture SisoF2 was largely divergent (< 92% similarity) from any sequence derived from either cultured representatives or environmental samples, suggesting that ribotype SisoF2 may constitute a new genus within the phylum. The presence of the new morphotypes in the environment from where they were enriched was analysed by high-resolution phylogenetic fingerprinting.}, }
@article {pmid23765719, year = {2009}, author = {Huang, WE and Ward, AD and Whiteley, AS}, title = {Raman tweezers sorting of single microbial cells.}, journal = {Environmental microbiology reports}, volume = {1}, number = {1}, pages = {44-49}, doi = {10.1111/j.1758-2229.2008.00002.x}, pmid = {23765719}, issn = {1758-2229}, abstract = {We have selectively isolated microbial cells by identifying and then manipulating cells using a combination of Raman microspectroscopy and optical trapping. The criterion for cell discrimination is based on spectral peak shifts within the Raman spectrum of individual cells. A specific shift in the phenylalanine peak position from 1001 rel. cm(-1) to 965 rel. cm(-1) is utilized to indicate the uptake of (13) C within the cell that utilized (13) C-substrate. Cells were captured and manipulated using an infrared (1064 nm) laser while Raman spectra were acquired over shorter timescales (30 s) using a co-aligned 514.5 nm laser beam. Selected cells were manoeuvred to a clean part of a capillary tube and the tubes were cleaved to physically separate the cells. The technique was tested for cell viability and cross-contamination effects using 70 single yeast cells (Saccharomyces cerevisia). Following these tests, 58 single bacterial cells (Escherichia coli DH5α, and Pseudomonas fluorescens SBW25::Km-RFP) that exhibited (13) C uptake were sorted from bacterial populations. Among those isolated cells, 11 out of 18 yeast cells and 7 out of 18 single SBW25::Km-RFP cells were recovered by incubation; 2 out of 7 sorted yeast cells and 3 out of 8 sorted bacterial cells (single SBW25::Km-RFP) were genome amplified correctly. We show that the Raman tweezers approach has the potential to open a new frontier to study unculturable microorganisms, which account for more than 99% microbes in natural environment.}, }
@article {pmid22443591, year = {2008}, author = {John Wallace, R}, title = {Gut microbiology - broad genetic diversity, yet specific metabolic niches.}, journal = {Animal : an international journal of animal bioscience}, volume = {2}, number = {5}, pages = {661-668}, doi = {10.1017/S1751731108001687}, pmid = {22443591}, issn = {1751-7311}, abstract = {Analysis of 16S ribosomal RNA (rRNA)-encoding gene sequences from gut microbial ecosystems reveals bewildering genetic diversity. Some metabolic functions, such as glucose utilisation, are fairly widespread throughout the genetic spectrum. Others, however, are not. Despite so many phylotypes being present, single species or perhaps only two or three species often carry out key functions. Among ruminal bacteria, only three species can break down highly structured cellulose, despite the prevalence and importance of cellulose in ruminant diets, and one of those species, Fibrobacter succinogenes, is distantly related to the most abundant ruminal species. Fatty acid biohydrogenation in the rumen, particularly the final step of biohydrogenation of C18 fatty acids, stearate formation, is achieved only by a small sub-group of bacteria related to Butyrivibrio fibrisolvens. Individuals who lack Oxalobacter formigenes fail to metabolise oxalate and suffer kidney stones composed of calcium oxalate. Perhaps the most celebrated example of the difference a single species can make is the 'mimosine story' in ruminants. Mimosine is a toxic amino acid found in the leguminous plant, Leucaena leucocephala. Mimosine can cause thyroid problems by being converted to the goitrogen, 3-hydroxy-4(1H)-pyridone, in the rumen. Observations that mimosine-containing plants were toxic to ruminants in some countries but not others led to the discovery of Synergistes jonesii, which metabolises 3-hydroxy-4(1H)-pyridone and protects animals from toxicity. Thus, despite the complexities indicated by molecular microbial ecology and genomics, it should never be forgotten that gut communities contain important metabolic niches inhabited by species with highly specific metabolic capability.}, }
@article {pmid24185744, year = {1996}, author = {Balczon, JM and Pratt, JR}, title = {The functional responses of two benthic algivorous ciliated protozoa with differing feeding strategies.}, journal = {Microbial ecology}, volume = {31}, number = {2}, pages = {209-224}, pmid = {24185744}, issn = {0095-3628}, abstract = {Surface-associated algivorous ciliated protozoa are common in the benthos of streams, but little is known about the feeding ecology of these organisms. We compared the functional responses of two algivorous ciliated protozoa, Oxytricha fallax (a filter feeder) and Trithigmostoma cucullulus (an encounter feeder). The ciliates were fed (14)C-labeled Navicula cryptocephala in laboratory feeding experiments to determine their potential to consume significant amounts of algal prey. Logistic regression, and plots of the proportion of N. cryptocephala ingested vs. the total number offered, indicated functional responses of a typical rectangular hyperbolic (type II) form for both ciliates. Ingestion rates were estimated from regressions of the number of (14)C-labeled N. cryptocephala cells ingested per ciliate vs. time. Maximum feeding rates and half-saturation concentrations were estimated by fitting the observed ingestion rates and experimental algal densities to a function of the Michaelis-Menten enzyme kinetics form using nonlinear regression. For O. fallax, the maximum feeding rate was estimated to be 1.07 N. cryptocephala cells per minute, and the half-saturation concentration was 3.9 × 102 N. cryptocephala per square centimeter. For T. cucullulus the maximum feeding rate was estimated to be 0.2 N. cryptocephala per minute, and the half-saturation concentration was 5.4 × 10(3) N. cryptocephala per square centimeter. The data were also fitted using only the number of cells ingested at 60 and 120 min, by converting the endpoint consumption to rates. For O. fallax, the estimated maximum feeding rates were 1.3 and 1.0 N. cryptocephala per minute for 60 and 120 min, respectively, and estimated half-saturation concentrations were 5.1 × 10(2) and 3.5 × 10(2) N. cryptocephala per square centimeter. For T. cucullulus, estimated maximum feeding rates were 0.6 and 0.4 N. cryptocephala per minute for 60 and 120 min, respectively, and estimated half-saturation concentrations were 1.5 × 10(4) and 1.1 × 104 N. cryptocephala per square centimeter. These results suggest that kinetic methods for estimating ingestion rates are more accurate than endpoint determinations. Based on field observations of periphyton densities, these ciliates potentially are consuming 4.8% of the total available standing crop of diatom biomass per day and this could represent up to 16% of total available daily primary production.}, }
@article {pmid24185743, year = {1996}, author = {Mazzafera, P and Olsson, O and Sandberg, G}, title = {Degradation of caffeine and related methylxanthines bySerratia marcescens isolated from soil under coffee cultivation.}, journal = {Microbial ecology}, volume = {31}, number = {2}, pages = {199-207}, pmid = {24185743}, issn = {0095-3628}, abstract = {A strain of Serratia marcescens showing the ability to degrade caffeine and other methylxanthines was isolated from soil under coffee cultivation. Growth was observed only with xanthines methylated at the 7 position (caffeine, 1,3,7-dimethylxanthine; paraxanthine, 1,7-dimethylxanthine; theobromine, 3,7-dimethylxanthine and 7-methylxanthine). Paraxanthine and theobromine were released in liquid medium when caffeine was used as the sole source of carbon and nitrogen. When paraxanthine or theobromine were used, 3-methylxanthine, 7-methylxanthine, and xanthine were detected in the liquid medium. Serratia marcescens did not grow with theophylline (1,3-dimethylxanthine), 1-methylxanthine, and 3-methylxanthine, and poor growth was observed with xanthine. Methyluric acid formation from methylxanthines was tested in cell-free extracts by measuring dehydrogenase reduction of tetrazolium salt in native-polyacrylamide gel electrophoresis gel. Activity was observed for all methylxanthines, even those with which no bacterial growth was observed. Our results suggest that in this strain of S. marcescens caffeine is degraded to theobromine (3,7-dimethylxanthine) and/or paraxanthine (1,7-dimethylxanthine), and subsequently to 7-methylxanthine and xanthine. Methyluric acid formation could not be confirmed.}, }
@article {pmid24185742, year = {1996}, author = {Pérez-Uz, B}, title = {Bacterial preferences and growth kinetic variation inUronema marinum andUronema nigricans (Ciliophora: Scuticociliatida).}, journal = {Microbial ecology}, volume = {31}, number = {2}, pages = {189-198}, pmid = {24185742}, issn = {0095-3628}, abstract = {The growth kinetics of two species of the genus Uronema, the marine U. marinum and the freshwater U. nigricans, have been studied under equivalent culture conditions. Ciliates were fed on three bacterial strains at three different concentrations (10(6), 10(7), and 10(8) bacteria ml(-1)). Growth rates in U. marinum were between 10 and 70% higher than those observed for the freshwater clone of U. nigricans, while net stationary phase populations were 1-60 times higher in U. marinum than in U. nigricans. The half-saturation constants (KS) for each bacterial strain showed that U. nigricans reached its [Formula: see text] μmax at one to three times lower concentration than that observed for U. marinum. Despite the close morphological similarity of these species, U. marinum and U. nigricans exhibited sustained distinct growth behavior that might reflect the survival strategies followed in their specific environments.}, }
@article {pmid24185741, year = {1996}, author = {Wynn-Williams, DD}, title = {Response of pioneer soil microalgal colonists to environmental change in Antarctica.}, journal = {Microbial ecology}, volume = {31}, number = {2}, pages = {177-188}, pmid = {24185741}, issn = {0095-3628}, abstract = {There is increasing evidence of climate change in Antarctica, especially elevated temperature and ultraviolet B (UVB) flux within the ozone "hole." Its origins are debatable, but the effects on ice recession, water availability, and summer growth conditions are demonstrable. Light-dependent, temperature-sensitive, fast-growing organisms respond to these physical and biogeographical changes. Microalgae (cyanobacteria and eukaryotic algae), which are pioneer colonists of Antarctic mineral fellfield soils, are therefore highly suitable biological indicators of such changes. In frost-heaved soil polygons containing naturally sorted fine mineral particles, microalgal growth is restricted to a shallow zone of light penetration. By virtue of this light requirement, microalgae are exposed to extreme seasonal fluctuations in temperature (air and black-body radiation), photosynthetically active radiation, UV radiation, and desiccation. Dominance of conspicuous autofluorescent indicator species with distinctive morphology allowed quantification of responses using epifluorescence microscopy, and image analysis of undisturbed, unstained communities. However, the physical changes in climate, although significant in the long term, are gradual. The changes were therefore amplified experimentally by enclosing the communities at a fellfield site on Signy Island, maritime Antarctica, in cloches (small greenhouses). These were made of polystyrene of either UV transparent or UV opaque acrylic plastic, with or without walls. During a 6-year period, statistically significant changes were observed in microalgal colonization of the soil surface and in the morphology of filamentous populations. Evidence of community succession correlated with measured changes in local environment was found. Results from Signy Island and at continental sites on Alexander Island suggested that rates of microalgal colonization and community development might change significantly during current climate changes in Antarctica.}, }
@article {pmid24185740, year = {1996}, author = {McCarthy, SA}, title = {Effects of temperature and salinity on survival of toxigenicVibrio cholerae O1 in seawater.}, journal = {Microbial ecology}, volume = {31}, number = {2}, pages = {167-175}, pmid = {24185740}, issn = {0095-3628}, abstract = {In 1991 and 1992, the Latin American epidemic strain of Vibrio cholerae O1 was isolated from ballast water, bilge water, and sewage taken from cargo ships docked in Mobile Bay, Alabama. The findings raised questions regarding the organism's ability to survive long-term aboard ships and to withstand the exchange of ballast at sea. The effects of temperature (6, 18, and 30°C) and salinity (8, 16, and 32 ppt) on survival of V. cholerae O1 strains C6706 and C6707 and a ballast water isolate in sterile seawater were determined. The ballast water isolate, which had a D-value (number of days required to produce a 1 log10 reduction in colony-forming units per milliliter) of 240 days at 18°C, 32 ppt salinity, had the longest survival time. The range of D-values was 36-240 days at 18°C, 60-120 days at 30°C, and 5-20 days at 6°C. In sterile seawater short-term survival was temperature dependent, whereas long-term survival was salinity dependent. In raw seawater, survival time of the ballast water isolate was reduced to 12-27 days, implying the existence of biological influences. As also shown in our previous work, the organism appeared to be able to survive for several months under relatively stable conditions in ballast water aboard ships; however, viability may be reduced to only a few weeks after the organism is introduced into estuarine or marine environments.}, }
@article {pmid24185739, year = {1996}, author = {Bååth, E}, title = {Thymidine incorporation of bacteria sequentially extracted from soil using repeated homogenization-centrifugation.}, journal = {Microbial ecology}, volume = {31}, number = {2}, pages = {153-166}, pmid = {24185739}, issn = {0095-3628}, abstract = {Bacteria were sequentially extracted from soil into a water suspension after shaking soil with water or mixing it in a blender followed by a low-speed centrifugation. Bacteria, which were released only after several cycles of homogenization-centrifugation, had higher growth rates as judged from thymidine and leucine incorporation, whereas bacteria that were more readily released by a gentle shaking procedure had the lowest growth rate. This indicated that bacteria more tightly bound to soil particles were growing faster than those that were more easily released into the water suspension. The same pattern was found both in an agricultural and a forest soil, with contrasting pH and organic matter content, and irrespective of whether the bacteria were labeled before or after the centrifugation steps. The different growth rates of the bacteria could not be explained by different partitioning of label between different macromolecules, different cell size, different viability of the bacteria, or different dilution of the added radioactive substrate in the different homogenization-centrifugation fractions. The total amount of phospholipid fatty acids per bacterial cell was also similar in the different fractions. Different composition of the bacterial communities in the different homogenization-centrifugation fractions was indicated by a gradually altered phospholipid fatty acid pattern of the extracted bacteria, and an increased hydrophobicity of the bacteria released only after several homogenization-centrifugation treatments.}, }
@article {pmid24185738, year = {1996}, author = {Maranger, R and Bird, DF}, title = {High concentrations of viruses in the sediments of Lac Gilbert, Québec.}, journal = {Microbial ecology}, volume = {31}, number = {2}, pages = {141-151}, pmid = {24185738}, issn = {0095-3628}, abstract = {Viruses were found to be very abundant in the top layer of the sediments of Lac Gilbert, Québec. Viruses were extracted from the sediments using pyrophosphate buffer, and viruses from the diluted extracts were pelleted onto grids and enumerated using transmission electron microscopy. Viral abundance in the sediments ranged from 6.5 × 10(8) to 1.83 × 10(10) ml(-1), which is 10- to 1,000-fold greater than the number observed in the water column. This increase corresponds well with the 100- to 1,000-fold increase in bacterial abundance in the sediments. Viral abundance differed significantly among the surface sediment samples taken at different bottom depths and among samples taken at different depths of the water column. Viral abundance also varied significantly between the oxic and anoxic zones of the water column and the sediments. The virus-to-bacteria ratio varied greatly among the different sediment sites but not among depths in the water column. Viral abundance in the water column was related to bacterial abundance and chlorophyll concentration, whereas viruses in the sediments were most abundant in sediments with high organic matter content. Elevated viral abundance and their erratic distribution in the sediments suggest that viruses might play an important role in sediment microbial dynamics.}, }
@article {pmid24185737, year = {1996}, author = {Smit, E and Wolters, AC and Lee, H and Trevors, JT and van Elsas, JD}, title = {Interactions between a genetically markedPseudomonas fluorescens strain and bacteriophage ΦR2f in soil: Effects of nutrients, alginate encapsulation, and the wheat rhizosphere.}, journal = {Microbial ecology}, volume = {31}, number = {2}, pages = {125-140}, pmid = {24185737}, issn = {0095-3628}, abstract = {The introduction of bacteriophages could potentially be used as a control method to limit the population size of engineered bacteria that have been introduced into soil. Hence, the ability of a species-specific phage, ΦR2f, to infect and lyse its host, a Pseudomonas fluorescens R2f transposon Tn5 derivative, in soil, was studied. Control experiments in liquid media revealed that productive lysis of host cells by phage ϕR2f occurred when cells were freely suspended, whereas cells present in alginate beads resisted lysis. The presence of nutrients enhanced the degree of lysis as well as the production of phage progeny, both with the suspended cells and with cells escaped from the alginate beads. Experiments in which host cells and phage ΦR2f were introduced into two soils of different texture revealed that host cells were primarily lysed in the presence of added nutrients, and phage reached highest titres in these nutrient-amended soils. Encapsulation of the host cells in alginate beads inhibited lysis by the phage in soil. Populations of free host cells introduced into soil that colonized the rhizosphere of wheat were not substantially lysed by phage ΦR2f. However, P. fluorescens R2f populations colonizing the rhizosphere after introduction in alginate beads were reduced in size by a factor of 1,000. Cells migrating from the alginate beads towards the roots may have been in a state of enhanced metabolic activity, allowing for phage ΦR2f infection and cell lysis.}, }
@article {pmid24185736, year = {1996}, author = {Mikell, AT and Smith, CL and Richardson, JC}, title = {Evaluation of media and techniques to enumerate heterotrophic microbes from karst and sand aquifer springs.}, journal = {Microbial ecology}, volume = {31}, number = {2}, pages = {115-124}, pmid = {24185736}, issn = {0095-3628}, abstract = {Several media and techniques were compared for their efficiency to enumerate viable heterotrophs from both a karst and sand aquifer spring. A medium designed to enumerate bacteria from nutrient-poor waters (HCFU) as well as R2A medium proved superior to tryptic soy agar; however, the difference was always less than one order of magnitude. Membrane filtration resulted in lower counts of microbes than the spread plate, multitube turbidity, or drop plate methods from samples of both sand and karst springs. The drop plate technique yielded higher viable counts from the sand spring and basin of the karst spring, with a precision of 21% (coefficient of variation) and a maximum plating efficiency of 3.4% (viable count/direct count × 100). Subsequently, 63% of isolates from drop plates were recovered on HCFU. Microcolonies were visible by epifluorescence microscopy, acridine orange staining, and subsequent examination of excised agar sections containing drops.}, }
@article {pmid24185640, year = {1996}, author = {Jin, X and Nalewajko, C and Kushner, DJ}, title = {Comparative study of nickel toxicity to growth and photosynthesis in nickel-resistant and -sensitive strains of Scenedesmus acutus f. alternans (Chlorophyceae).}, journal = {Microbial ecology}, volume = {31}, number = {1}, pages = {103-114}, pmid = {24185640}, issn = {0095-3628}, abstract = {Nickel (Ni) toxicity to growth and photosynthesis was studied in four strains of Scenedesmus acutus f. alternans. Effects of Ni dosage and duration of exposure on growth and photosynthesis were strain specific. Large differences in responses of both growth and photosynthesis to Ni were detected between three resistant strains (B4, Cu-Tol, and Ni-Tol) and one sensitive strain (UTEX 72). Growth of UTEX 72 was ≥ 18 times more sensitive to Ni than those of the three resistant strains. The order of Ni dosages (fmol Ni/pg cell dry weight) causing 50% inhibition (D150) of growth rates in the four strains was Ni-Tol (10.5) > B4 (8.19) > Cu-Tol (4.60) > UTEX 72 (0.25). The effect of Ni dosage on photosynthetic rate as percentage of control corresponded to a saturation curve and was a strong function of duration of exposure. The DI50s of photosynthetic rates were ≥3.5 times lower in UTEX 72 than in the three resistant strains, and in all four strains they decreased sharply with the increase in duration of exposure. The order of the four strains in DI50s of photosynthetic rate was B4 (58.2) > Cu-Tol (38.0) > Ni-Tol (28.9) > UTEX 72 (8.24) for 6-h exposure and Ni-Tol (2.88) > Cu-Tol (1.30) > B4 (1.01) > UTEX 72 (0.15) for 24-h exposure. The DI50s of photosynthetic rate for 6-h exposure were higher than those of growth rate in all four strains, and for 24-h exposure they were lower, except in UTEX 72. Thus, the relative Ni sensitivity of growth and photosynthesis of the four strains depends on the duration of exposure. The results of factorial analysis of variance suggested that Ni toxicity to photosynthesis is a consequence of a strong interaction among strain, Ni dosage, and duration of exposure.}, }
@article {pmid24185639, year = {1996}, author = {Menon, P and Becquevort, S and Billen, G and Servais, P}, title = {Kinetics of flagellate grazing in the presence of two types of bacterial prey.}, journal = {Microbial ecology}, volume = {31}, number = {1}, pages = {89-101}, pmid = {24185639}, issn = {0095-3628}, abstract = {Grazing rates of mixed cultures of freshwater, heterotrophic nanoflagellates on two populations of bacterial prey present together at varying concentrations were measured by using fluorescently labeled bacteria. The effect of one population on the ingestion kinetics of the other was consistent with a theory based on competitive inhibition of enzymatic reactions. However, allochthonous bacteria, when present in low concentrations within a much larger population of small autochthonous bacteria, may be preferentially grazed, which is due to their large size.}, }
@article {pmid24185638, year = {1996}, author = {Insam, H and Amor, K and Renner, M and Crepaz, C}, title = {Changes in functional abilities of the microbial community during composting of manure.}, journal = {Microbial ecology}, volume = {31}, number = {1}, pages = {77-87}, pmid = {24185638}, issn = {0095-3628}, abstract = {The objective of this study was (a) to detect changes of the functional abilities of the microflora during composting of manure as a result of windrow turning frequency and (b) to detect differences between distinct zones within the windrows. Biolog GN microtiter plates containing 95 different carbon sources were inoculated with diluted suspensions of compost material containing 15,000 microorganisms per well (120 μl). We found a dramatic shift in functional microbial community structure during the 8-week composting process. The shift was more rapid when the compost windrows were turned. The substrate use pattern in the outer, well-aerated zone of the unturned windrow was similar to that of the turned windrows. Microbial biomass and respiration decreased more rapidly in the turned than in the unturned windrows, indicating a different pace of compost maturation. The data suggest that the Biolog assay may be a suitable approach to determine compost maturity.}, }
@article {pmid24185637, year = {1996}, author = {Aa, K and Olsen, RA}, title = {The use of various substrates and substrate concentrations by a Hyphomicrobium sp. isolated from soil: Effect on growth rate and growth yield.}, journal = {Microbial ecology}, volume = {31}, number = {1}, pages = {67-76}, pmid = {24185637}, issn = {0095-3628}, abstract = {The content of Hyphomicrobium sp. was estimated from a clay loam soil using the most probable number technique with methanol as the sole carbon source. The method enumerated Hyphomicrobia as 0.2% of the total bacteria determined by acridine orange direct counts. Hyphomicrobium sp. was not able to use C-C compounds such as glucose or acetate for growth. Maximal growth yield and growth rate were obtained when the concentration of methanol was in the range of 0.5-5 mg C/liter. Substrate affinity measurements revealed Ks values of 0.8 μM and 5.8 μM when the methanol concentration was 0.5-2.5 μM and 5-200 μM, respectively. Hyphomicrobium sp. had the ability to assimilate volatile organic compounds from air for growth. A growth yield of 0.7 mg/liter cell carbon was obtained in a mineral medium that contained no additions of organic compounds but had been stored for 4 weeks in flasks, allowing volatile compounds from the air to dissolve in the medium. When air was pumped into the culture during cultivating, the growth yield was proportional to the flow rate of air into the culture.}, }
@article {pmid24185636, year = {1996}, author = {Benstead, J and Lloyd, D}, title = {Spatial and temporal variations of dissolved gases (CH4, CO 2, and O 2) in peat cores.}, journal = {Microbial ecology}, volume = {31}, number = {1}, pages = {57-66}, pmid = {24185636}, issn = {0095-3628}, abstract = {Spatial and temporal variations in the concentrations of dissolved gases (CH4, CO2, and O2) in peat cores were studied using membrane inlet mass spectrometry (MIMS). Variations in vertical gas profiles were observed between random peat cores taken from hollows on the same peat bog. Methane concentrations in profiles (0-30 cm) generally increased with depth and reached maximum values in the range of 200-450 μM CH4 below about 13-cm depth. In some profiles, a peak of dissolved methane was observed at 7-cm depth. Oxygen penetrated to approximately 2-cm depth in the hollows. The sampling probe was used to continuously monitor CH4, CO2, and O2 concentrations at fixed depths in peat cores over periods of several days. The concentration of dissolved CO2 and O2 at 1-cm depth oscillated over a 24-h period with the maximum of CO2 concentration corresponding with the minimum of 02. Diurnal variations in CO2 but not CH4 were measured at 15-cm depth; dissolved CO2 levels decreased during daylight hours to a constant minimum concentration of 4.85 mm. This report also describes the application of MIMS for the measurement of gaseous diffusion rates in peat using an inert gas (argon); the value of D, the diffusion coefficient, was 2.07 × 10(-8) m(2) s(-1).}, }
@article {pmid24185635, year = {1996}, author = {Hanisch, K and Schweitzer, B and Simon, M}, title = {Use of dissolved carbohydrates by planktonic bacteria in a mesotrophic lake.}, journal = {Microbial ecology}, volume = {31}, number = {1}, pages = {41-55}, pmid = {24185635}, issn = {0095-3628}, abstract = {Dissolved carbohydrates comprise one of the largest pools of labile organic matter readily available for bacterial use in pelagic ecosystems. Despite this fact, very little is known about use of dissolved carbohydrates by planktonic bacteria. We studied use of total dissolved carbohydrates (TDCHO) by planktonic bacteria in mesotrophic Lake Constance, Germany, from April until August 1992. We examined the decrease of TDCHO over time together with the increase of bacterial numbers in 1-μm filtered lake water incubated at in situ temperature in the dark. TDCHO analyses were done after hydrolysis by sulfuric acid as free monosaccharides and oxidation by periodate to formaldehyde with 3-methyl-2-benzothiazolinone-hydrazon-hypochloride (MBTH). Preliminary tests showed that hydrolysis by sulfuric acid gave higher yields than hydrolysis by HCl. Our results show that TDCHO are readily used by bacteria and compose substantial fractions of the C requirements for their growth. Concentrations of TDCHO varied between 1.7 and 5.5 μM (glucose equivalents), and use rates varied between 0.47 and 3.43 μg C liter(-1) h(-1). Highest rates of TDCHO use occurred during the phytoplankton spring bloom, during the clear-water phase in June, and during a phytoplankton bloom in August. Ratios of use of TDCHO/bacterial biomass production varied between 0.17 and 3.05. During the spring bloom, TDCHO and total dissolved amino acids (TDAA) were used in equal amounts. During the clear-water phase at chlorophyll a concentrations <3 μg liter(-1), however, bacteria only consumed TDCHO and excreted amino acids. The growth efficiency based on the consumption of TDCHO and TDAA varied between 16 and 21% during the phytoplankton spring bloom and was 35% during the clear-water phase.}, }
@article {pmid24185634, year = {1996}, author = {Shang, C and Caldwell, DE and Stewart, JW and Tiessen, H and Huang, PM}, title = {Bioavailability of organic and inorganic phosphates adsorbed on short-range ordered aluminum precipitate.}, journal = {Microbial ecology}, volume = {31}, number = {1}, pages = {29-39}, pmid = {24185634}, issn = {0095-3628}, abstract = {A nonreductive community-level study of P availability was conducted using various forms of adsorbed P. Orthophosphate (Pi), inositol hexaphosphate (IHP), and glucose 6-phosphate (G6P) were adsorbed to a short-range ordered Al precipitate. These bound phosphates provided a P source sufficient to support the growth of microbial communities from acidic Brazilian soils (oxisols). Adsorbed IHP, the most abundant form of organic phosphate in most soils, had the lowest bioavailability among the three phosphates studied. Adsorbed G6P and Pi were almost equally available. The amount of adsorbed Pi (1 cmol P kg(-1)) required to support microbial growth was at least 30 times less than that of IHP (30 cmol P kg(-1)). With increased surface coverage, adsorbed IHP became more bioavailable. This availability was attributed to a change in the structure of surface complexes and presumably resulted from the decreased number of high-affinity surface sites remaining at high levels of coverage. It thus appears that the bioavailability of various forms of adsorbed phosphate was determined primarily by the stability of the phosphate-surface complexes that they formed, rather than by the total amount of phosphate adsorbed. IHP, having the potential to form stable multiple-ring complexes, had the highest surface affinity and the lowest bioavailability. Bioaggregates consisting of bacteria and Al precipitate were observed and may be necessary for effective release of adsorbed P. Bacteria in the genera Enterobacter and Pseudomonas were the predominate organisms selected during these P-limited enrichments.}, }
@article {pmid24185633, year = {1996}, author = {Felip, M and Pace, ML and Cole, JJ}, title = {Regulation of planktonic bacterial growth rates: The effects of temperature and resources.}, journal = {Microbial ecology}, volume = {31}, number = {1}, pages = {15-28}, pmid = {24185633}, issn = {0095-3628}, abstract = {We examined the potential limitation of bacterial growth by temperature and nutrients in a eutrophic lake. Dilution cultures from winter and summer were incubated at both high (>20°C) and low (4°C) temperatures and enriched with various combinations of organic carbon (C), inorganic nitrogen (N), and inorganic phosphorus (P). Bacterial abundance, (3)H-thymidine incorporation, and (3)H-leucine incorporation were measured over the growth cycle. For both winter and summer assemblages, low temperature limited growth even when resources (C, N, and P) were added. When temperature was adequate, bacterial growth in dilution cultures was co-limited by C, N, and P Additions of either C, P, or N and P alone provide little or only modest stimulation of growth, suggesting that under in situ conditions both nutrients and organic carbon limit bacterial growth. Our results provide little evidence of seasonal adaptation to low temperatures for bacterial communities in temperate lakes. Instead, bacterial growth appears to be temperature limited during winter and resource limited during summer. We propose that, in general, bacterial growth rates are temperature dependent up to a threshold, but that the patterns of change across temperature gradients are resource dependent, such that temperature has little effect on growth in resource-rich environments but a strong effect in resource-poor environments.}, }
@article {pmid24185632, year = {1996}, author = {Glazebrook, PW and Moriarty, G and Hayward, AC and Macrae, IC}, title = {Seasonal changes in numbers and the location of a particular bacterial strain of Alteromonas sp. in seagrass sediments.}, journal = {Microbial ecology}, volume = {31}, number = {1}, pages = {1-13}, pmid = {24185632}, issn = {0095-3628}, abstract = {Many variables must be considered in seeking to describe differences in population sizes for native aquatic bacterial populations. In this study of seagrass- and nearby plant-free sediments, seasonal effects on total bacterial counts were found to be highly significant, outweighing the significance of factors such as geographic variability, but on populations of a chosen Alteromonas sp., they were not significant at the 5% level. Summer counts for both populations were higher than those for winter; this result is likely to reflect the higher productivity of the host Zostera capricomi in summer months, resulting in the exudation of increased amounts of organic nutrients. The Alteromonas sp. occurred in greatest abundance (1.8% of the total population) at the seagrass sediment site from which it was originally isolated and formed up to 1.5% of the population in adjacent plant-free sediments. In fluorescent microscopy studies with labeled antibodies, the Alteromonas sp. was found to be ubiquitous in seagrass and plant-free sediments but was found closely associated in much higher numbers with seagrass root-rhizome tissue, suggesting a possible nutritional relationship between plant and bacterium. In associated trials of sediment preservation techniques, bacterial counts of replicate sediments preserved with glutaraldehyde (3% v/v) were higher than those obtained using Lugol's iodine or freezing.}, }
@article {pmid24185568, year = {1995}, author = {Andlid, T and Juárez, RV and Gustafsson, L}, title = {Yeast colonizing the intestine of rainbow trout (Salmo gairdneri) and turbot (Scophtalmus maximus).}, journal = {Microbial ecology}, volume = {30}, number = {3}, pages = {321-334}, pmid = {24185568}, issn = {0095-3628}, abstract = {Yeast were isolated from the intestine of farmed rainbow trout (Salmo gairdneri), turbot (Scophtalmus maximus), and free-living flat-fish (Pleuronectes platessa and P. flesus). The average number of viable yeasts recovered from farmed rainbow trout was 3.0 × 10(3) and 0.5 × 10(2) cells per gram homogenized intestine for white and red-pigmented yeasts, respectively. The dominant species were Debaryomyces hansenii, Saccharomyces cerevisiae, Rhodotorula rubra, and R. glutinis. In 5 of 10 free-lving marine fish, > 100 viable yeast cells per gram intestinal mucus were recovered. Red-pigmented yeasts dominated and composed >90% of the isolates. Colonization experiments were performed by inoculating rainbow trout and turbot with fish-specific, isolated yeast strains and by examining the microbial intestinal colonization at intervals. Inoculation of experimental fish with pure cultures of R. glutinis and D. hansenii HF1 yielded colonization at a level several orders of magnitude higher than before the inoculation. Up to 3.8 × 10(4), 3.1 × 10(6), and 2.3 × 10(9) viable yeast cells per gram intestine or feces were recovered in three separate colonization experiments. The high level of colonizing yeasts persisted for several weeks. The concentrations of yeasts in the tank water never exceeded 10(3) viable cells per milliliter. No traces of fish sickness as a result of high yeast colonization were recorded during any of the colonization experiments. For periods of the experiments, the concentration of aerobic bacteria in the fish intestine was lower than the intestinal yeast concentration. Scanning electron microscopy studies demonstrated a close association of the yeasts with the intestinal mucosa. The mucosal colonization was further demonstrated by separating intestinal content, mucus, and tissue. All compartments were colonized by >10(3) viable yeast cells per gram. No bacteria were detected on the micrographs, indicating that their affinity for the intestinal mucosa was less than that of the yeasts.}, }
@article {pmid24185567, year = {1995}, author = {Vishniac, HS}, title = {Simulated in situ competitive ability and survival of a representative soil yeast, Cryptococcus albidus.}, journal = {Microbial ecology}, volume = {30}, number = {3}, pages = {309-320}, pmid = {24185567}, issn = {0095-3628}, abstract = {Microcosms containing an air-dried autoclaved loamy sand (Eufala A) with low salt and organic content were inoculated with a representative (obligately aerobic, encapsulated) soil yeast, Cryptococcus albidus var. albidus (T) ATCC 10666, singly (for growth rate and survival determinations) and together with the bacterial biota native to Eufala A. The yeast competed successfully with the more rapidly growing bacteria in the presence of added water from 1% (5.7% of field capacity) to 14% (80% of field capacity) but grew for shorter times than when grown alone; times correlated with the lag phase of the bacterial biota. When well-watered (10 and 14%) competition cultures were allowed to dry and used as inoculum for subcultures, the yeast made significant growth only at 1% added water but survived at the higher moisture concentrations. The competitive ability of Cr. albidus confirms the previously reported advantages of the cryptococcal capsule in hydration and desiccation and, together with lengthy survival, suggests that the importance of such yeasts in the biogeochemistry of arid soils has been seriously underestimated.}, }
@article {pmid24185566, year = {1995}, author = {Long, SC and Aelion, CM and Dobbins, DC and Pfaender, FK}, title = {A comparison of microbial community characteristics among petroleum-contaminated and uncontaminated subsurface soil samples.}, journal = {Microbial ecology}, volume = {30}, number = {3}, pages = {297-307}, pmid = {24185566}, issn = {0095-3628}, abstract = {Measurements of microbial community size, including total cell counts and specific degrader enumerations, were conducted on subsurface soil samples from both petroleum-contaminated and pristine aquifers. Samples were collected from both uncontaminated and contaminated areas of the petroleum-contaminated sites. In pristine and uncontaminated samples, total cell counts (acridine orange direct counts) were related to depth. The deeper samples contained smaller total microbial populations. However, indices of microbial activity varied considerably from sample to sample and probably reflect soil and site heterogeneity. Exposure to petroleum contamination apparently altered the microbial community structure. In samples exposed to low levels of contaminants as vapors and/or dissolved phases (ppb concentrations), and not free product, the toluene-specific degrader populations were larger at greater depths, and the numbers of amino acid-specific degraders were highly correlated to the numbers of decane-specific degraders, indicating that petroleum-adapted microbial communities were present in the contaminated samples. In highly contaminated samples, total microbial population densities decreased with increasing depth; however, microbial activity tended to increase with depth. These results indicate that petroleum contaminants exert toxic effects on the active microbial community at high exposures and enrich specific degraders at ppb levels of dissolved contaminants.}, }
@article {pmid24185565, year = {1995}, author = {Becker, PM and Dott, W}, title = {Functional analysis of communities of aerobic heterotrophic bacteria from hydrocarbon-contaminated sites.}, journal = {Microbial ecology}, volume = {30}, number = {3}, pages = {285-296}, pmid = {24185565}, issn = {0095-3628}, abstract = {Microbial communities from soil and groundwater of oil-contaminated sites (Beelitzhof in Berlin-Nikolassee and the former Pintsch site in Hanau, both in Germany) were characterized by description of the physiological potential of arbitrary samples of 48 aerobic heterotrophic bacterial isolates. It was demonstrated that the sum of metabolic abilities, presented as a percentage of substrate-degrading microorganisms in a sample, is both site specific and reproducible. The percentage of hydrocarbon-degrading microorganisms in the communities was most strongly influenced by the diversity and amount of carbon supply (whereas after addition of mineral salts, total cell counts increased). For example, in groundwater of the waste oil-contaminated Pintsch site, only the accessible short-chain alkanes up to dodecane could be metabolized. After dosing with hydrogen peroxide, long-chain alkane-degrading bacteria were found in significant amounts among the predominant microorganisms, which was apparently due to a solubilization effect that brought the longer alkanes (and their degraders) into the groundwater. Because the addition of precultured organisms to a soil-composting windrow had no effect on the degradation pattern of its microbiota, the carbon sources available probably determined whether allochthonous bacteria would become indigenous. Although the physiological potentials of the individual bacteria complemented each other and thus determined the distinctive profile characteristic of the microbial community, the individual members could differ in their metabolic abilities, as was shown by the distribution of positive test results in different samples, and they could also differ in their taxonomic status. Evidently, the taxonomic status of the bacteria did not determine their activities: Strains of the same species showed different degradation abilities for hydrocarbon substrates. However, the taxonomic status of isolates seemed to be highly dependent on the physicochemical factors of a site (soil structure, water capacity, etc.).}, }
@article {pmid24185564, year = {1995}, author = {Chen, DL and Chalk, PM and Freney, JR and Smith, CJ and Luo, QX}, title = {Estimation of nitrification rates in flooded soils.}, journal = {Microbial ecology}, volume = {30}, number = {3}, pages = {269-284}, pmid = {24185564}, issn = {0095-3628}, abstract = {Three techniques for estimating nitrification rates in flooded soils were evaluated in short-term incubation experiments using three soils. The techniques were based on inhibition of either ammonium or nitrite oxidation and (13)N isotope dilution. Of four inhibitors of ammonium oxidation evaluated, one (allylthiourea) was ineffective and two (2-ethynylpyridine or phenyl acetylene dissolved in ethanol) promoted immobilization of ammonium. Emulsified 2-ethynylpyridine and acetylene were equally effective inhibitors of ammonium oxidation and had little or no effect on gross rates of N mineralization and immobilization. Four inhibitors of nitrite oxidation were evaluated, but this approach was compromised by the nonspecificity of three of the compounds-potassium cyanide, 2-ethylamino-4-isopropylamino-6-methylthio-s-triazine (ametryne) and 3-(3,4-dichlorophenyl)-1-methylurea (DMU)-and by the partial effectiveness of another (potassium chlorate). Two methods based on isotope dilution gave similar estimates of nitrification rates. These rates were similar to those estimated by inhibition of ammonium oxidation in one soil but were lower in the other two soils. In the latter two soils, nitrification of labeled ammonium derived from dissimilatory nitrate reduction resulted in underestimation of nitrification rates by isotope dilution.}, }
@article {pmid24185563, year = {1995}, author = {Hallbeck, L and Pedersen, K}, title = {Benefits associated with the stalk of Gallionella ferruginea, evaluated by comparison of a stalk-forming and a non-stalk-forming strain and biofilm studies in situ.}, journal = {Microbial ecology}, volume = {30}, number = {3}, pages = {257-268}, pmid = {24185563}, issn = {0095-3628}, abstract = {Factors that regulate and induce stalk formation by the iron-oxidizing and stalk-forming bacterium Gallionella ferruginea were studied in laboratory cultures and in situ. A stalk-forming strain, Sta(+), and a non-stalk-forming strain, Sta(-), were used for comparative studies of the benefits associated with the stalk. Two different growth media were used: a ferrous sulfide medium (FS-medium), with slow oxidation of iron giving high concentrations of toxic oxygen radicals and a ferrous carbonate medium (FC-medium), with fast iron oxidation giving low concentration of the toxic oxygen radicals. It was found that Sta(+) cells grown in the FS-medium survived 3 weeks longer than Sta(-) cells grown in the FS-medium. When each strain was grown in the FC-medium, the Sta(-) cells had an advantage and survived 8 weeks longer than the Sta(+) cells. No difference in survival was found for Sta(+) cells grown in FS-medium compared to growth in FC-medium. In laboratory cultures, the average stalk length per cell values were 7-2.5 times higher (92 h and 150-300 h growth, respectively) in a medium with 620 μM iron than in a medium with 290 μM iron. Gallionella ferruginea Sta(+) outcompeted Sta(-) cells when inoculated as mixed populations in FC-medium. It has previously been suggested that stalk formation in vitro is induced by oxygen. To confirm this observation, biofilm development in natural waters was studied in two wells, one with trace amounts of oxygen (LH) and one without (TH). A dense biofilm developed on surfaces exposed to flowing well LH water, but no biofilm developed in well TH. Stalks were formed in water samples from both wells when allowed to make contact with air. This work demonstrates for the first time that the stalk has a protecting function against the toxic oxygen radicals formed during the chemical iron oxidation. It also shows that it is the oxidation rate of the ferrous iron and not its concentration that is harmful to the cells. The stalk gives G. ferruginea a unique possibility to colonize and survive in habitats with high contents of iron, inaccessible for bacteria without a defense system against the oxidation of iron.}, }
@article {pmid24185562, year = {1995}, author = {Shiah, FK and Ducklow, HW}, title = {Regulation of bacterial abundance and production by substrate supply and bacterivory: A mesocosm study.}, journal = {Microbial ecology}, volume = {30}, number = {3}, pages = {239-255}, pmid = {24185562}, issn = {0095-3628}, abstract = {Daily bacterial abundance and production, heterotrophic nanoflagellates (HNAN) abundance, chlorophyll, and NH4 (+) concentrations were measured in four indoor 400-liter tanks over 13 days to study the role of heterotrophic bacterioplankton in NH4 (-) cycling and to identify the succession of top-down and bottom-up processes in regulating bacterial biomass and production. Ammonium (NH4 (+)) was added to these four tanks daily whenever its concentration in tanks was < 4 μM. Tanks 3 and 4 (treatment tanks) also received 4 μM of glucose daily till the end of experiment. Lower NH4 (-) concentrations and higher bacterial specific growth rate and production observed in the treatment tanks indicated that bacteria might take up NH4+ with the addition of labile organic carbon. Bacterial biomass was controlled by substrate supply and HNAN grazing from day 7 to day 13, when phytoplankton declined. Bacterial size distribution patterns were determined primarily by substrate supply, with HNAN grazing playing a less important role. Certain variabilities existed between the control (and the treatment) tanks. These inconsistencies could be due to differences in time of expression of given variables. However, the total amounts of bacterial biomass accumulated in the four tanks were very similar. The inconsistency in timing of expression of variables was probably due to different initial conditions in each tank. The ecological meanings of the inconsistency in timing and overall consistency were discussed.}, }
@article {pmid24185561, year = {1995}, author = {Neely, RK and Wetzel, RG}, title = {Simultaneous use of (14)C and (3)H to determine autotrophic production and bacterial protein production in periphyton.}, journal = {Microbial ecology}, volume = {30}, number = {3}, pages = {227-237}, pmid = {24185561}, issn = {0095-3628}, abstract = {A method of simultaneously quantifying photoautotrophic (algae and cyanobacteria) and bacterial production in periphyton communities by (14)C-bicarbonate and (3)H-leucine incorporation was investigated and applied to communities subjected to specific intensities of photosynthetically active radiation (400-700 nm). Maximum photosynthetic output (2.23 ± 0.29 (SE) μg C cm(-2) h(-1)) and bacterial production (0.07 ± 0.006 μg C cm(-2) h(-1)) occurred at the highest photon flux density (400 μmol m(-2) s(-1)). Over a photon flux density range of 20-400 μmol m(-2) s(-1), bacterial and autotroph productivity were significantly and positively correlated (r = 0.89). Furthermore, application of 3-(3,4-dichlorophenyl)-1,1-dimethyl urea, a photosystem 11 inhibitor, to periphyton films reduced bacterial production by 46%, but it had no such effect on bacteria-only cultures. Therefore, the magnitude of bacterial production in periphyton was coupled to the photosynthesis/metabolism of algae and/or cyanobacteria.}, }
@article {pmid24185487, year = {1995}, author = {Coulombe, C and Lavoie, MC}, title = {Evolution of resident oral bacterial biota in BALB/c mice during pregnancy and lactation.}, journal = {Microbial ecology}, volume = {30}, number = {2}, pages = {219-225}, pmid = {24185487}, issn = {0095-3628}, abstract = {To assess the influence of pregnancy and lactation on the oral microbial ecology of BALB/c mice, we followed the distribution of the predominant oral bacteria of four groups of these mice during these two periods. Compared with nonpregnant control female mice of the same age maintained under the same conditions, the distribution of the resident oral bacterial species differed significantly only during the lactation period (8-16 days after parturition). This difference could possibly be attributed to hormonal influences and/or grooming habits.}, }
@article {pmid24185486, year = {1995}, author = {Kersters, I and Van Vooren, L and Huys, G and Janssen, P and Kersters, K and Verstraet, W}, title = {Influence of temperature and process technology on the occurrence of Aeromonas species and hygienic indicator organisms in drinking water production plants.}, journal = {Microbial ecology}, volume = {30}, number = {2}, pages = {203-218}, pmid = {24185486}, issn = {0095-3628}, abstract = {The occurrence of Aeromonas spp. and hygienic indicator organisms in raw and treated waters of five drinking water production plants in Flanders (Belgium) was surveyed over a period of 17 months. Aeromonads were isolated on ampicillin-dextrin agar (ADA) and further identified by gas-liquid chromatographic analysis of their cellular fatty acid methyl ester (FAME) content. ADA medium was found to be highly specific for the enumeration of Aeromonas spp. In general, Aeromonas counts were very low in untreated groundwater but numbered 10(4)-10(6) colony-forming units per liter in open storage reservoirs for surface water. Aeromonas spp. were seasonally distributed with maximal densities occurring during the summer. The ecology of Aeromonas in the different waters was studied in relation to the physical, chemical, and microbiological water characteristics. Strongly positive correlations were observed between Aeromonas densities and heterotrophic plate counts, whereas a clearly negative relationship was found with dissolved oxygen. On average, 99.7% of the aeromonads were removed by flocculation-decantation followed by breakpoint chlorination, whereas 98.9% were removed by slow sand filtration. Flocculation-decantation without breakpoint chlorination did not reduce the microbial numbers. At three of four drinking water production plants tested, rapid sand filtration decreased the number of aeromonads and hygienic indicator organisms. At one plant, however, the numbers of Aeromonas and hygienic indicator organisms were high in the sand filter effluents. Increased numbers of aeromonads were also counted in the effluent of the activated carbon filters. Hence, inactivation of Aeromonas spp. by the current process technology appears not sufficient to exclude postchlorination. The survival of aeromonads in certain filter systems may be due to the growth of these bacteria on biodegradable organic material, provided by the decomposition from bacteria, algae, or other sources.}, }
@article {pmid24185485, year = {1995}, author = {Sawabe, T and Oda, Y and Shiomi, Y and Ezura, Y}, title = {Alginate degradation by bacteria isolated from the gut of sea urchins and abalones.}, journal = {Microbial ecology}, volume = {30}, number = {2}, pages = {193-202}, pmid = {24185485}, issn = {0095-3628}, abstract = {Degradation of alginate and its constituents, polymannuronate (polyM) and polyguluronate (polyG), by gut bacteria isolated from sea urchins and abalones in the northern part of Japan, were investigated. Bacterial counts in the guts of sea urchin S. intermedius, were 10(5) to 10(8) CFU/g, and in abalone H. discus hannai, counts ranged from 10(6) to 10(9) CFU/g. More than 80% of total 600 isolates were found to have alginolytic activity. The alginolytic bacteria were predominantly fermentative, but some differences were observed in their substrate specificity as well as between the flora in the gut of sea urchins and the abalones. Seventy percent of the alginolytic bacteria from the sea urchins showed no degrading preference for polyM or polyG blocks, and were able to degrade both the substrates simultaneously. Most of the alginolytic bacteria (96.6%) from sea urchins belonged to the genus Vibrio. The majority of alginolytic bacteria (68.0% on average) from abalones only degraded polyG and they were predominantly non-motile fermenters. From these results, it appeared that a different type of association exists between alginolytic gut microflora and the marine algal feeders with respect to the level of contribution by bacteria to the host's digestion of alginate.}, }
@article {pmid24185484, year = {1995}, author = {Effendi, I and Austin, B}, title = {Dormant/unculturable cells of the fish pathogen Aeromonas salmonicida.}, journal = {Microbial ecology}, volume = {30}, number = {2}, pages = {183-192}, pmid = {24185484}, issn = {0095-3628}, abstract = {Viable cells of Aeromonas salmonicida remained in experimental marine systems after plate counts indicated an absence of culturable cells. These so-called viable but nonculturable (VBNC) cells were coccoid and smaller than their normal culturable counterparts. There was no reduction in lipopolysaccharide of the VBNC cells. There was an alteration in protein composition, however, with a decline in some (15, 70, 30, 22, and 17 kDa), but an increase in another protein (49 kDa). A significant loss of DNA occurred. The VBNC cells responded to fluorescent antibodies prepared against A. salmonicida by developing enlarged and bizarre shapes in the presence of yeast extract and nalidixic acid (the direct viable count technique), and they demonstrated respiratory activity. It was concluded that A. salmonicida survived in seawater, but major morphological changes occurred with cells retaining some viability but losing pathogenicity to Atlantic salmon (Salmo salar).}, }
@article {pmid24185483, year = {1995}, author = {Ghoul, M and Minet, J and Bernard, T and Dupray, E and Cormier, M}, title = {Marine macroalgae as a source for osmoprotection for Escherichia coli.}, journal = {Microbial ecology}, volume = {30}, number = {2}, pages = {171-181}, pmid = {24185483}, issn = {0095-3628}, abstract = {At elevated osmolarity of the mineral medium M63, marine macroalgae constitute important osmoprotectants and nutrients sources for Escherichia coli. Growth of bacterial population (16 strains) was improved by supplementing M63 salts medium with either aqueous or ethanolic algal extracts obtained from Ascophyllum nodosum, Fucus serratus, Enteromorpha ramulosa, Ulva lactuca, and Palmaria palmata. In their presence, growth was still observed even at 1.02 M NaCl. Furthermore, the E. coli ZB400 growth in presence of whole macroalgae thalli in M63/0.85 M NaCI reached its maximum within 24 h (5 × 10(7) - 5 × 10(8) colony-forming units [CFU] per milliliter). In the presence of A. nodosum, bacterial growth was inhibited. In the same experimental conditions, ethanolic extracts improved E. coli growth significantly, because the yield reached 10(11) CFU per milliliter. Ulva lactuca and P. palmata allowed the better growth. The Dragendorff-positive compounds extracted from bacterial cells growing on each ethanolic extract exhibited an osmoprotective effect as proved by a disk-diffusion assay. On the other hand, the -onium compounds (quaternary ammonium [betaines] and tertiary sulphonium) and total free amino acid contents of U. lactuca ethanolic extracts were higher than in others. Fucaceae extracts demonstrated especially high protein content. Algal extracts constitute not only an appreciable osmoprotection source for E. coli but also nutrient sources.}, }
@article {pmid24185482, year = {1995}, author = {Zubkov, MV and Sleigh, MA}, title = {Ingestion and assimilation by marine protists fed on bacteria labeled with radioactive thymidine and leucine estimated without separating predator and prey.}, journal = {Microbial ecology}, volume = {30}, number = {2}, pages = {157-170}, pmid = {24185482}, issn = {0095-3628}, abstract = {A procedure has been developed for preparing living bacteria, quantitatively labeled with (3)H-thymidine and (14)C-leucine, for short-term grazing experiments. The negligible rate of accumulation in protozoan macromolecules of moieties of bacterial macromolecules labeled with (3)H compared with moieties labeled with (14)C permits estimation of the consumption, digestion, and assimilation of prey biomass in protists without separating them from bacteria. The principles of this method are described, and the results of its application in examples of grazing by the ciliates Euplotes and Uronema and the flagellate Pteridomonas on the bacterium Vibrio are outlined.}, }
@article {pmid24185481, year = {1995}, author = {Kamer, M and Rassoulzadegan, F}, title = {Extracellular enzyme activity: Indications for high short-term variability in a coastal marine ecosystem.}, journal = {Microbial ecology}, volume = {30}, number = {2}, pages = {143-156}, pmid = {24185481}, issn = {0095-3628}, abstract = {Extracellular α-glucosidase, β-glucosidase, and aminopeptidase activity variations (measured by use of fluorogenic substrate analogs) at a coastal station in the Mediterranean Sea were investigated over a 1-year period. A 27-h cycle and daily measurements were made in a summer situation. We observed strong relative diurnal variations, compared to seasonal variations, in α- and β-glucosidase. Within 24 h, 0-100% of both α- and β-glucosidase were found in the dissolved phase. The aminopeptidase activities did not show a strong diurnal variation, but day to day variations were similar in magnitude to seasonal changes. Consistently, high proportions of all three enzymes were found in the dissolved phase on a seasonal scale. Seasonal measurements at 50- and 100-m depths showed a weak negative dependency on depth for extracellular enzyme activity. The potential importance of both hourly and daily changes in extracellular enzyme activity and of free enzymes is considered.}, }
@article {pmid24185480, year = {1995}, author = {Sinsabaugh, RL and Findlay, S}, title = {Microbial production, enzyme activity, and carbon turnover in surface sediments of the Hudson River estuary.}, journal = {Microbial ecology}, volume = {30}, number = {2}, pages = {127-141}, pmid = {24185480}, issn = {0095-3628}, abstract = {The detrital food web is a major nexus of energy flow in nearly all aquatic ecosystems. Energy enters this nexus by microbial assimilation of detrital carbon. To link microbiological variables with ecosystem process, it is necessary to understand the regulatory hierarchy that controls the distribution of microbial biomass and activity. Toward that goal, we investigated variability in microbial abundance and activities within the tidal freshwater estuary of the Hudson River. Surface sediments were collected from four contrasting sites: a mid-channel shoal, two types of wetlands, and a tributary confluence. These samples, collected in June to August 1992, were sorted into two to four size fractions, depending on the particle size distribution at each site. Each fraction was analyzed for bacterial biomass (by acridine orange direct counting), bacterial production (by (3)H-thymidine incorporation into DNA), fungal biomass (by ergosterol extraction), fungal production (by biomass accrual), and the potential activities of seven extracellular enzymes involved in the degradation of detrital structural molecules. Decomposition rates for particulate organic carbon (POC) were estimated from a statistical model relating mass loss rates to endocellulase activity. Within samples, bacterial biomass and productivity were negatively correlated with particle size: Standing stocks and rates in the <63-μm class were roughly twofold greater than in the >4-mm class. Conversely, fungal biomass was positively correlated with particle size, with standing stocks in the largest size class more than 1OX greater than in the smallest. Extracellular enzyme activities also differed significantly among size classes, with high carbohydrase activities associated with the largest particles, while oxidative activities predominated in the smallest size classes. Among sites, the mid-channel sediments had the lowest POC standing stock (2% of sediment dry mass) and longest turnover time (approximately 1.7 years), with bacterial productivity approximately equal to fungal (56 vs. 46 μg C per gram POC per day, respectively). In the Typha wetland, POC standing stock was high (10%); turnover time was about 0.3 years; and 90% of the microbial productivity was fungal (670 vs. 84 μg C per gram POC per day). The other two sites, a Trapa wetland and a tributary confluence, showed intermediate values for microbial productivity and POC turnover. Differences among sites were described by regression models that related the distribution of microbial biomass (r (2) = 0.98) and productivity (r (2) = 0.81) to particle size and carbon quality. These factors also determined POC decomposition rates. Net microbial production efficiency (production rate/decomposition rate) averaged 10.6%, suggesting that the sediments were exporting large quantities of unassimilated dissolved organic carbon into the water column. Our results suggest that studies of carbon processing in large systems, like the Hudson River estuary, can be facilitated by regression models that relate microbial dynamics to more readily measured parameters.}, }
@article {pmid24185479, year = {1995}, author = {Stehr, G and Zörner, S and Böttcher, B and Koops, HP}, title = {Exopolymers: An ecological characteristic of a floc-attached, ammonia-oxidizing bacterium.}, journal = {Microbial ecology}, volume = {30}, number = {2}, pages = {115-126}, pmid = {24185479}, issn = {0095-3628}, abstract = {A lithotrophic ammonia-oxidizing bacterium of the Nitrosomonas type was isolated from the lower River Elbe. Enrichment was attained from suspended particulate matter (SPM) of a water sample. At its natural environment, this species almost exclusively occurred attached to flocs, as demonstrated with the immunofluorescence technique. On the species level, the isolate was not related to any of the described Nitrosomonas species. The strain was characterized by strong production of exopolymeric substances (EPS) and was observed to occur self-flocculating in pure cultures. Low ammonia concentrations stimulated EPS production. The EPS revealed an extensive capacity for binding particulate and dissolved materials, as well as cells of other bacterial species. This capacity was affected by changing pH values or salt concentrations of the medium. The EPS appeared to function as a buffer against toxic compounds and against changing environmental conditions. Another Nitrosomonas strain isolated from the Elbe estuary, but lacking recognizable EPS production, was used for comparison.}, }
@article {pmid24185416, year = {1995}, author = {Beller, HR and Reinhard, M}, title = {The role of iron in enhancing anaerobic toluene degradation in sulfate-reducing enrichment cultures.}, journal = {Microbial ecology}, volume = {30}, number = {1}, pages = {105-114}, pmid = {24185416}, issn = {0095-3628}, abstract = {Ferrous iron enhanced the toluene degradation rate of sulfidogenic enrichment cultures inoculated with contaminated subsurface soil from an aviation fuel storage facility near the Patuxent River (Md.). Ferrous iron had an analogous effect on the degradation rate of benzoic acid, a transient metabolite of anaerobic toluene degradation in these cultures, when benzoic acid was used as a sole carbon and energy source. Two hypotheses were proposed to explain iron's effect: (a) Iron may have prevented sulfide toxicity via precipitation of sulfide as FeS, and (b) iron might have been a limiting nutrient required for degradation (i.e., amendments of iron could have compensated for iron removed from solution by precipitation as FeS). To test these hypotheses, substrate degradation rates were compared in the presence of FeSO4 (a sulfate source that both precipitates sulfide species and precludes iron limitation) versus ZnSO4 (a sulfate source that precipitates sulfide species but does not preclude iron limitation) versus MgSO4 (a sulfate source that neither precipitates sulfide nor precludes iron limitation). For both toluene and benzoic acid, FeSO4 and ZnSO4 were comparable in their enhancement of substrate degradation rates and were superior to MgSO4 in that respect. Thus, iron appears to ameliorate sulfide toxicity, not nutritional iron limitation, in these cultures. The observation that ethylenediaminetetraacetic acid, a chelating agent capable of retaining iron in solution in the presence of sulfide, did not stimulate the cultures is consistent with this conclusion. The implications of these results for bioremediation of fuel-contaminated aquifers that contain sulfate-reducing bacteria are discussed.}, }
@article {pmid24185415, year = {1995}, author = {Schweitzer, B and Simon, M}, title = {Growth limitation of planktonic bacteria in a large mesotrophic lake.}, journal = {Microbial ecology}, volume = {30}, number = {1}, pages = {89-104}, pmid = {24185415}, issn = {0095-3628}, abstract = {We studied nutrient-limitation of bacterioplankton growth in Lake Constance, a mesotrophic lake, between February and August in 1992. We amended 1-μm filtrates with a single nutrient or nutrient combinations at 5 or 10 μm final concentration, and the limiting nutrient or nutrient combination was inferred from the assay in which bacterial growth was most stimulated. The following nutrients were added individually or in combination: glucose, amino acids, peptone, and ammonium as C and N sources, and inorganic phosphate. From January until the beginning of the phytoplankton spring bloom in mid-April, C alone was growth-limiting. During the spring bloom a complex growth-limitation pattern occurred; first P was limiting, then for only 1 week C + N together, and thereafter P + C. During the clear-water phase with very low chlorophyll concentrations, P + C together limited bacterial growth again, interrupted by a period when C + N + P shortage caused a triple limitation. Later in the season, P + C were growth-limiting again. The growth efficiency (bacterial biomass produced/substrates used) on the basis of amino acid and carbohydrate used varied between 17 and 35%. The addition of various C and N sources indicated that the growth efficiency strongly depended on the quality of the substrates and the adaptation of the bacterial assemblages, for example, whether C and N originated from amino acids or glucose and ammonium.}, }
@article {pmid24185414, year = {1995}, author = {Kusch, J}, title = {Adaptation of inducible defense in Euplotes daidaleos (Ciliophora) to predation risks by various predators.}, journal = {Microbial ecology}, volume = {30}, number = {1}, pages = {79-88}, pmid = {24185414}, issn = {0095-3628}, abstract = {The extent of induced morphological defense in Euplotes daidaleos correlates to this ciliate's predation risk from the defense-inducing predator species. Euplotes daidaleos responded by morphological transformation only to organisms that are able to feed on typically formed Euplotes cells (63 ± 5 μm cell width in E. daidaleos). Three of those potential predator species caused defensive changes to various degrees (Student's t-test, P < 0.1 to P < 0.0001): Lembadion bullinum (Ciliata) induced 82 ± 6 μm cell width in E. daidaleos; Chaetogaster diastrophus (Oligochaeta) induced 85 = 6 μm width; and Stenostomum sphagnetorum (Turbellaria) induced 89 ± 8 μm width (at a density of 10 predators per milliliter, respectively). At higher predator densities (50 or 100 organisms per milliliter), Euplotes developed a correspondingly larger width (to a maximum of 103 ± 10 μm in the presence of S. sphagnetorum). Euplotes did not respond to organisms (e.g., Blepharisma japonicum, Colpidium campylum, Didinium nasutum, Paramecium caudatum, Spirostomum ambiguum, Stentor coeruleus) that cannot feed on this ciliate species. Daphnia longispina and Bursaria truncatella predators, which can feed on large prey of ≥125, or ≥200 μm in diameter, respectively, also had no effect on the morphology of Euplotes. The extent of defense in Euplotes that was induced by 10 predators per milliliter during 24 h decreased the predation risk from those predators to 67% in the presence of S. sphagnetorum, to 50% with L. bullinum, and to 15% with C. diastrophus, compared to the typical form of Euplotes. In a natural population, the defensive form of E. daidaleos was found with average cell widths of 88 ± 8 μm. The results indicate that predator-induced defense in natural Euplotes populations is beneficial to this prey and that it is adapted to the predation abilities of Euplotes predators, whereby energetical costs related to defensive changes may be saved.}, }
@article {pmid24185413, year = {1995}, author = {Christoffersen, K and Ahl, T and Nybroe, O}, title = {Grazing of nonindigenous bacteria by nano-sized protozoa in a natural coastal system.}, journal = {Microbial ecology}, volume = {30}, number = {1}, pages = {67-78}, pmid = {24185413}, issn = {0095-3628}, abstract = {Mesocosms (∼4.5 m(3)) situated in a closed bay area were used to investigate the effect of protozoan predation on nonindigenous bacteria. Pseudomonas fluorescens strain Agl was released into mesocosms as a single inoculum of 1 × 10(5) cells ml(-1) (final concentration) or as four inocula (same concentration each) at intervals of 3 days. Mesocosms that had received growth media corresponding to the inoculum served as controls. Numbers of P. fluorescens Ag1 decreased rapidly whether released as single or multiple inocula. Direct estimation of protozoan predation using fluorescently labeled P. fluorescens from log phase and starved cultures, respectively, revealed that natural populations of heterotrophic nanoflagellates consumed substantial amounts of the nonindigenous bacterial strain. The volume of fluorescently labeled cells prepared from starved cells was 68% of log phase cell volume, but the individual clearance of the small cells was five to seven times higher than that of the log phase bacteria. The natural populations of nanoflagellates consumed 34-62% of P. fluorescens Ag1 daily if starved bacteria were offered as food, and 3-13% if the cells were in the logarithmic growth phase. This suggests that the effect of protozoan predation on nonindigenous bacterial strains is substantial because cultured bacteria are likely to starve in natural environments. The addition of P. fluorescens Ag1 and the growth medium enhanced the abundance of natural bacteria, chlorophyll a, heterotrophic nanoflagellates, and ciliates, but it did not improve the growth conditions for the released strain. The effects on the indigenous populations were more pronounced after addition of fresh medium than following inoculation with cells, which possibly was due to the lower nutrient content of spent medium. However, these results, based on direct estimation of protozoan predation on log phase and starved nonindigenous bacteria, point to the conclusion that mortality induced by bacterivorous predators is the key factor determining removal of nonindigenous bacteria introduced in natural aquatic systems.}, }
@article {pmid24185412, year = {1995}, author = {Hadas, O and Pinkas, R}, title = {Sulfate reduction processes in sediments at different sites in Lake Kinneret, Israel.}, journal = {Microbial ecology}, volume = {30}, number = {1}, pages = {55-66}, pmid = {24185412}, issn = {0095-3628}, abstract = {Lake Kinneret, Israel, is a warm (13-30°C) monomictic lake that stratifies in April and turns over in December. Between January and June each year, a heavy bloom (up to 250 g wet weight n(-2) 2) of the dinoflagellate Peridinium gatunense dominates the phytoplankton biomass. In early summer, the bloom collapses, and the sinking Peridinium biomass serves as a trigger for intense sulfate-reduction activity throughout the hypolimnion and within the sediments. The availability of organic matter and sulfate was high shortly after the bloom crash and the beginning of stratification and was lowest in December before overturn. Sulfate-reduction rates at three different sites in the lake were studied. In the sediments, the rates varied seasonally and among stations from 5 to 1600 nmol SO4 (-2) reduced cm(-3) day(-1), with respect to the distance from the Jordan River, depth, organic content, and stratification period. During years of low lake water levels, intense sulfate reduction occurred in the hypolimnion, resulting in anoxia and high concentrations of H2S (>400 μM). In years with high water levels, early bloom, and delayed stratification, higher rates of sulfate reduction were recorded in the sediments, probably as a result of a greater fraction of the primary production (organic matter) reaching the bottom.}, }
@article {pmid24185411, year = {1995}, author = {Deng, MY and Cliver, DO}, title = {Antiviral effects of bacteria isolated from manure.}, journal = {Microbial ecology}, volume = {30}, number = {1}, pages = {43-54}, pmid = {24185411}, issn = {0095-3628}, abstract = {The objectives of this study were to determine the role of microbial activity in inactivation of hepatitis A virus (HAV) and to learn how the virus is inactivated. Of 31 bacterial strains isolated from animal manure, 10 efficiently inactivated HAV in fluid thioglycollate medium, with D10 values (time, in days, required for a 90% reduction of virus titer) of ≤ 10 at 30°C. The D10 value of the control suspension without bacteria was 35.1. Most of the 10 strains raised the pH of the medium during growth; comparisons suggested that alkalinity was not a principal antiviral property of these cultures. Cell-free filtrates of nine of these strains caused net 90% inactivation of HAV within 6 days at 37°C; the other did not. The inactivation capacity of four of the nine culture filtrates was significantly reduced by incubation with selected protease inhibitors before the virus was added. These protease inhibitors did not affect the activities of the other five culture filtrates. Fractions prepared by ultrafiltration (nominal molecular weights <1,000) from two of these cultures inactivated HAV suggesting that their mode of action was not enzymatic.}, }
@article {pmid24185410, year = {1995}, author = {Weinbauer, MG and Fuks, D and Puskaric, S and Peduzzi, P}, title = {Diel, seasonal, and depth-related variability of viruses and dissolved DNA in the northern Adriatic Sea.}, journal = {Microbial ecology}, volume = {30}, number = {1}, pages = {25-41}, pmid = {24185410}, issn = {0095-3628}, abstract = {The depth-dependent, seasonal, and diel variability of virus numbers, dissolved DNA (D-DNA), and other microbial parameters was investigated in the northern Adriatic Sea. During periods of water stratification, we found higher virus abundances and virus/bacterium ratios (VBRs) as well as a larger variability of D-DNA concentrations at the thermocline, probably as a result of higher microbial biomass. At the two investigated stations, virus densities were highest in summer and autumn (up to 9.5 × 10(10) 1(-1)) and lowest in winter (< 10(9) 1(-1)); D-DNA concentrations were highest in summer and lowest in winter. The VBR as well as an estimated proportion of viral DNA on total D-DNA showed a strong seasonal variability. VBR averaged 15.0 (range, 0.9-89.1), and the percentage of viral DNA in total D-DNA averaged 18.3% (range, 0.1-96.1%). An estimation of the percentage of bacteria lysed by viruses, based on 2-h sample intervals in situ, ranged from 39.6 to 212.2% d(-1) in 5 m and from 19.9 to 157.2% d(-1) in 22 m. The estimated contribution of virus-mediated bacterial DNA release to the D-DNA pool ranged from 32.9 to 161% d(-1) in 5 m and from 10.3 to 74.2% d(-1) in 22 m. Multiple regression analysis and the diel dynamics of microbial parameters indicate that viral lysis occasionally could be more important in regulating bacterial abundances than grazing by heterotrophic nanoflagellates.}, }
@article {pmid24185409, year = {1995}, author = {Tonso, NL and Matheson, VG and Holben, WE}, title = {Polyphasic characterization of a suite of bacterial isolates capable of degrading 2,4-D.}, journal = {Microbial ecology}, volume = {30}, number = {1}, pages = {3-24}, pmid = {24185409}, issn = {0095-3628}, abstract = {To develop a better understanding of the ecological aspects of microbial biodegradation, it is important to assess the phenotypic and biochemical diversity of xenobiotic degrading organisms. Forty-six bacterial isolates capable of degrading 2,4-dichlorophenoxyacetic acid (2,4-D) and representing several geographically distinct locations were characterized and placed into taxonomic groups based on the results of several independent analyses. The isolates were characterized based on Gram's reaction, colony morphology, cell morphology, fatty acid methyl ester (FAME) fingerprints, carbon substrate oxidation patterns (BIOLOG), DNA homology to whole-plasmid probes and repetitive extragenic palindromic (REP) fingerprints. Attempts to group organisms taxonomically based on colony morphology and cell morphology were largely unsuccessful. Both FAME and BIOLOG analyses were generally unable to provide reliable genus or species identifications of these environmental isolates by comparison of fingerprints or substrate use patterns to existing data bases. Modification of the standard protocols for these analyses, however, allowed taxonomic grouping of the isolates and the construction of new data bases, comprised solely of 2,4-D-degrading organisms, against which future novel isolates can be compared. Independent cluster analysis of the FAME and BIOLOG data shows that the isolates can be segregated into five taxonomic classes. The collection of 2,4-D-degrading isolates was also separated into five classes based on DNA homology to whole-plasmid probes obtained from individual isolates. REP analysis allowed isolates that likely represent the same (or very similar) organism(s) to be identified and grouped. Each of the analyses used represents a mechanistically different means of classifying organisms, yet the taxonomic groupings obtained by several of the methods (FAME, BIOLOG, DNA homology, and to some degree, REP analysis) were in good agreement. This indicates that the features discriminated by these different methods represent fundamental characteristics that determine phylogenetic groups of bacteria.}, }
@article {pmid24185408, year = {1995}, author = {Fletcher, M and Fredrickson, JK}, title = {Joint editorial: To mark a change in editorship of microbial ecology.}, journal = {Microbial ecology}, volume = {30}, number = {1}, pages = {1-2}, doi = {10.1007/BF00184509}, pmid = {24185408}, issn = {0095-3628}, }
@article {pmid24185349, year = {1995}, author = {Fuller, ME and Mu, DY and Scow, KM}, title = {Biodegradation of trichloroethylene and toluene by indigenous microbial populations in vadose sediments.}, journal = {Microbial ecology}, volume = {29}, number = {3}, pages = {311-325}, pmid = {24185349}, issn = {0095-3628}, abstract = {The unsaturated subsurface (vadose zone) receives significant amounts of hazardous chemicals, yet little is known about its microbial communities and their capacity to biodegrade pollutants. Trichloroethylene (TCE) biodegradation occurs readily in surface soils; however, the process usually requires enzyme induction by aromatic compounds, methane, or other cosubstrates. The aerobic biodegradation of toluene and TCE by indigenous microbial populations was measured in samples collected from the vadose zone at unpolluted and gasoline-contaminated sites. Incubation at field moisture levels showed little activity on either TCE or toluene, so samples were tested in soil suspensions. No degradation occurred in samples suspended in water or phosphate buffer solution; however, both toluene and TCE were degraded in samples suspended in mineral salts medium. TCE degradation depended on toluene degradation, and little loss occurred under sterile conditions. Studies with specific nutrients showed that addition of ammonium sulfate was essential for degradation, and addition of other mineral nutrients further enhanced the rate. Additional studies with vadose sediments amended with nutrients showed similar trends to those observed in sediment suspensions. Initial rates of biodegradation in suspensions were faster in uncontaminated samples than in gasolinecontaminated samples, but the same percentages of chemicals were degraded. Biodegradation was slower and less extensive in shallower samples than deeper samples from the uncontaminated site. Two toluene-degrading organisms isolated from a gasoline-contaminated sample were identified as Corynebacterium variabilis SVB74 and Acinetobacter radioresistens SVB65. Inoculation with 10(6) cells of C. variabilis ml(-1) of soil solution did not enhance the rate of degradation above that of the indigenous population. These results indicate that mineral nutrients limited the rate of TCE and toluene degradation by indigenous populations and that no additional benefit was derived from inoculation with a toluene-degrading bacterial strain.}, }
@article {pmid24185348, year = {1995}, author = {Tiano, P and Accolla, P and Tomaselli, L}, title = {Phototrophic biodeteriogens on lithoid surfaces: An ecological study.}, journal = {Microbial ecology}, volume = {29}, number = {3}, pages = {299-309}, doi = {10.1007/BF00164892}, pmid = {24185348}, issn = {0095-3628}, abstract = {For two strains, the green alga Pleurococcus CVB4 and the cyanobacterium Lyngbya CCB2, isolated from the pioneering algal biocoenosis present on a marble statue, we determined the optimum range of growth in selective cultural media in relation to pH, light intensity, and temperature, together with the ability of these organisms to colonize stone surfaces that differed either in the structure-texture or in the physico-chemical composition of the various lithotypes. The results showed a higher capacity of the green alga to withstand environmental factor changes. For both organisms the preferential colonization of the stone surface was correlated primarily, together with the environmental factors (pH, temperature, irradiance), to the physical characteristics (roughness and porosity) and secondarily to the chemical composition of the assayed lithotypes.}, }
@article {pmid24185347, year = {1995}, author = {Kinkel, LL and Wilson, M and Lindow, SE}, title = {Effect of sampling scale on the assessment of epiphytic bacterial populations.}, journal = {Microbial ecology}, volume = {29}, number = {3}, pages = {283-297}, pmid = {24185347}, issn = {0095-3628}, abstract = {Bacterial populations on above-ground plant surfaces were estimated at three different biological scales, including leaflet disks, entire leaflets, and whole plants. The influence of sample scale on the estimation of mean bacterial population size per unit and per gram and on the variability among sampling units was quantified at each scale. Populations were highly variable among sampling units at every scale examined, suggesting that there is no optimal scale at which sample variance is reduced. The distribution of population sizes among sample units was sometimes, but not consistently, described by the lognormal. Regardless of the sampling scale, expression of population sizes on a per gram basis may not reduce variance, because population size was not generally a function of sample unit weight within any single sampling scale. In addition, the data show that scaling populations on a per gram basis does not provide a useful means of comparing population estimates from samples taken at different scales. The implications of these results for designing sampling strategies to address specific issues in microbial ecology are discussed.}, }
@article {pmid24185346, year = {1995}, author = {Bashan, Y and Holguin, G}, title = {Inter-root movement of Azospirillum brasilense and subsequent root colonization of crop and weed seedlings growing in soil.}, journal = {Microbial ecology}, volume = {29}, number = {3}, pages = {269-281}, pmid = {24185346}, issn = {0095-3628}, abstract = {Inter-root movement and dispersion of the beneficial bacterium Azospirillum brasilense were monitored in root systems of wheat seedlings growing in the field and in growth chamber soil trays. Two strains were used, a motile wild-type strain (Cd, mot(+)) and a motility deficient strain (mot(-)), which was derived from the Cd strain. Root colonization by two wild-type strains (Cd and Sp-245) was studied in 64 plant species growing in pots in the greenhouse. The two wild-type strains of A. brasilense were capable of colonizing all tested plant species. In soil trays and in the field, mot(+) cells moved from inoculated roots to non-inoculated roots of either wheat plants or weeds growing in the same field plot, but the mot(-) strain did not move toward non-inoculated roots of either plant species. In the field, both mot(+) and mot(-) strains of A. brasilense survived well in the rhizosphere of wheat for 30 days, but only mot(+) moved between different weeds, regardless of the species, botanical family, or whether they were annuals or perennials. In plant-free, water-saturated soils, either in columns or in the field, both strains remained at the inoculation site and did not move.It is proposed (a) that A. brasilense is not a plant-specific bacterium and that (b) colonization of the entire root system in soil is an active process determined by bacterial motility; it is not plant specific, but depends on the presence of plants.}, }
@article {pmid24185345, year = {1995}, author = {Hänninen, ML and Salmi, S and Siitonen, A}, title = {Maximum growth temperature ranges of Aeromonas Spp. isolated from clinical or environmental sources.}, journal = {Microbial ecology}, volume = {29}, number = {3}, pages = {259-267}, pmid = {24185345}, issn = {0095-3628}, abstract = {Only a limited number of phenotypic tests are available for the differentiation of all 13 known hybridization groups (HG) of Aeromonas spp. These organisms have a wide spectrum of warm-blooded and cold-blooded hosts. In the present study, the maximum growth temperatures (tmax) of the most common HGs of Aeromonas spp. originating from human fecal samples, food, water, and healthy and diseased fish were determined with a plate-type continuous temperature-gradient incubator. We observed that determination of the tmax can be applied for differentiation of HG 1 from HG 2 and 3 (phenospecies A. hydrophila); HG 6 from HG 4, 5A, and 5B (phenospecies A. caviae); HG 7 from HG 8/10 (phenospecies A. sobria); and HG 11 from HG 8/10 (phenospecies A. veronii). HG 1, 4, 8/10, and 13 strains occurring also in human clinical samples had a high tmax, about 40°C or higher. Hybridization group 2, 3, 5A, and 5B strains, which in most cases originated from water or food, had tmax values in the range of about 36-39°C, while HG 6, 7, and 11 had tmax values in the range of about 33-37°C. Fish pathogenic strains of A. salmonicida subsp. salmonicida and subsp. achromogenes had the lowest tmax values from about 30 to 35°C.}, }
@article {pmid24185344, year = {1995}, author = {Jensen, PR and Fenical, W}, title = {The relative abundance and seawater requirements of gram-positive bacteria in near-shore tropical marine samples.}, journal = {Microbial ecology}, volume = {29}, number = {3}, pages = {249-257}, pmid = {24185344}, issn = {0095-3628}, abstract = {The relative abundance of gram-positive bacteria in a variety of near-shore marine samples was determined using the KOH method. Gram-positive bacteria accounted for 14%, 25%, 31 %, and 12%, respectively, of the colony-forming bacteria obtained from seawater, sediments, and the surfaces of algae and invertebrates. A total of 481 gram-positive strains were isolated representing a wide range of morphological groups including regular and irregular rods, cocci, and actinomycetes. Seventy-seven percent of the strains characterized did not form spores and were aerobic, catalase-positive rods with regular to irregular cell morphologies. Eighty-two percent of the strains tested showed an obligate requirement of seawater for growth. None of the cocci tested required seawater or sodium for growth. This is the first report documenting that gram-positive bacteria can compose a large percentage of the culturable, heterotrophic bacteria associated with the surfaces of tropical marine algae.}, }
@article {pmid24185343, year = {1995}, author = {Middelboe, M and Søndergaard, M and Letarte, Y and Borch, NH}, title = {Attached and free-living bacteria: Production and polymer hydrolysis during a diatom bloom.}, journal = {Microbial ecology}, volume = {29}, number = {3}, pages = {231-248}, pmid = {24185343}, issn = {0095-3628}, abstract = {Abundance, production and extracellular enzymatic activity of free-living and attached bacteria were measured during the development and collapse of a spring bloom in a eutrophic lake. Free-living bacteria accounted for most of the total bacterial production during the first part of the bloom. Their production had a significant positive correlation to chlorophyll (P < .01) and polysaccharide concentration (P < .02) and to potential β-glucosidase and aminopeptidase activity (P < .05), suggesting that algal release of dissolved polymeric compounds provided an important carbon source for bacterial production. As the bloom collapsed, we observed a change in the activity and structure of the microbial community. The mean contribution of attached bacteria to total bacterial production increased from 12% during the first part of the bloom to 26% at the end. Also, the extracellular enzymatic activity of attached bacteria increased as the bloom collapsed and constituted up to 75% of the total hydrolytic activity. An estimated disparity between hydrolytic activity and the corresponding carbon demand of attached bacteria suggested a net release of dissolved organic compounds from organic particles via polymer hydrolysis by attached bacteria.}, }
@article {pmid24185342, year = {1995}, author = {Chrzanowski, TH and Sterner, RW and Elser, JJ}, title = {Nutrient enrichment and nutrient regeneration stimulate bacterioplankton growth.}, journal = {Microbial ecology}, volume = {29}, number = {3}, pages = {221-230}, pmid = {24185342}, issn = {0095-3628}, abstract = {Bacterial abundance results from predatory losses of individuals and replacement of losses through growth. Growth depends on sustained input of organic substrates and mineral nutrients. In this work we tested the hypothesis that bacterial growth in two oligotrophic Canadian shield lakes was limited by nitrogen (N) or phosphorus (P). We also determined whether consumer-regenerated resources contributed substantially to net bacterial growth. Two types of dilution assays were conducted to determine the response of bacteria to nutrient enrichment: diluted whole water (DWW, 1:9 whole/filtered with 0.2 μm of filtered lake water) and diluted fractionated water (DFW, 1.0 μm prefiltered then diluted as above). Replicate bottles in each dilution assay received either N (50 μM), P (10 μM), or both N and P enrichments. Controls received no nutrients. Resource-saturated growth rates and grazing rates were estimated from a standard dilution-growth approach. Bacterial growth was stimulated by addition of P alone and in combination with N. Consumers regenerated sufficient resources to support up to half the bacterial growth rate, but the benefit derived from consumers was minor when compared to mortality.}, }
@article {pmid24186724, year = {1995}, author = {Heuer, H and Dwyer, DF and Timmis, KN and Wagner-Döbler, I}, title = {Efficacy in aquatic microcosms of a genetically engineered pseudomonad applicable for bioremediation.}, journal = {Microbial ecology}, volume = {29}, number = {2}, pages = {203-220}, pmid = {24186724}, issn = {0095-3628}, abstract = {A genetically engineered microorganism (GEM), Pseudomonas sp. B13 FRI (pFRC20P) (abbreviated FR120), has previously been engineered to simultaneously mineralize mixtures of methylated and chlorinated benzoic acids and phenols through a modified ortho cleavage pathway. In this study, its performance was investigated both in different types of aquatic microcosms and in pure culture to determine (1) if under simulated in situ conditions the genetically engineered pathway effectively removes mixtures of model pollutants simultaneously, quickly, and completely; (2) where the optimum pollutant concentration range for this activity lies; and (3) how physical, chemical, and biological factors in the microcosms influence degradation rates. Growth and degradation parameters of FR 120 in pure culture were determined with 3-chlorobenzoate (3CB), 4-methylbenzoate (4MB), and equimolar mixtures of both as carbon sources. These substrates were degraded simultaneously, albeit with different degradation velocities, by FR120. The optimum growth concentrations for 3CB and 4MB were 3.0 mm and 2.1 mM, respectively, and the inhibition constants (Ki) were 11 mm (3CB) and 6 mm (4MB). The pathway was induced at low concentrations of substrate (> 1 [μM). The first order degradation constants (kl) were determined with respect to substrate concentration, cell density, and temperature. In aquatic microcosms inoculated with FR120, first order degradation constants and half lives of target chemicals were calculated based on the total amount of aromatics recovered. Half lives ranged from 1.3 days to 3.0 days, depending on the target chemical and the type of microcosm. Degradation constants determined in pure culture were extrapolated to the densities of FR120, substrate concentrations, and temperature occurring in the microcosm experiments, and used to calculate theoretical half lives. In water microcosms, theoretical and observed half lives corresponded well, indicating that FR120 functioned optimally in this environment. In whole core sediment microcosms, and especially at low cell densities, the observed degradation activity was in some cases considerably higher than expected from pure culture degradation rates. This suggests that environmental conditions in the sediment were more favorable to the degradation of substituted aromatics than those in pure culture. The physiological characteristics of FR120 and its performance in aquatic microcosms make it a good candidate for bioremediation at sites contamninated with mixtures of chlorinated and methylated aromatics.}, }
@article {pmid24186723, year = {1995}, author = {Leser, TD}, title = {Validation of microbial community structure and ecological functional parameters in an aquatic microcosm designed for testing genetically engineered microorganisms.}, journal = {Microbial ecology}, volume = {29}, number = {2}, pages = {183-201}, pmid = {24186723}, issn = {0095-3628}, abstract = {Microcosms were designed to facilitate studies of the fate, functioning, and ecological effects of microorganisms released into the aquatic environment. The microcosms were three-phase systems (sediment/water/air) with three compartments (a primary producer component, a herbivore grazer component, and intact sediment cores). The microcosms were validated by comparing gross ecological parameters and microbial community structure between the microcosms and the eutrophic Lake Bagsværd, which was simulated in the model. The photosynthetic potential and chlorophyll a concentrations were significantly lower in the microcosms than in the lake, which apparently was due to inorganic nutrient limitation. In the microcosms, total bacterial numbers and metabolic activity by [(3)H]thymidine incorporation were unaffected by the reduced algal biomass and primary production, simulating field conditions closely, with a strong dependence on temperature. Two days after filling the microcosms, the percentage of similarity of the microbial communities in the microcosm and Lake Bagsværd was 40%, measured by hybridizations of total microbial DNA. The similarity increased during the 10-day experimental period to 63-76%. In two experiments, Alcaligenes eutrophus AEO106(pRO101) was released into the microcosms. The release reduced the similarity between microcosms and lake to 2% and 27%, depending on the number of introduced cells. Concomitant to a decline in the A. eutrophus AEO106(pRO101) population, the similarity gradually recovered. It is concluded that the microcosms can simulate a freshwater lake ecosystem, but care has to be taken when extrapolating microcosm results to the source ecosystem because of the possible different selective conditions in the microcosm.}, }
@article {pmid24186722, year = {1995}, author = {Bak, RP and van Duyl, FC and Nieuwland, G}, title = {Organic sedimentation and macrofauna as forcing factors in marine benthic nanofagellate communities.}, journal = {Microbial ecology}, volume = {29}, number = {2}, pages = {173-182}, pmid = {24186722}, issn = {0095-3628}, abstract = {We investigated how benthic nanoflagellate communities in marine sediments respond to sedimentation of organic material and to the presence of macrofaunal organisms in controlled boxcosms. An input of 24 g C m(-2) resulted in a sharp increase in densities, from 93 to 477 × 10(3) flagellates cm(-3) within 11 days. At the onset, this increase was paralleled by enhanced bacterial production and bacterial numbers. When bacterial production collapsed, flagellate ingestion rates, varying from 17 to 67 bact flag(-1) h(-1), were sufficient to control bacterial abundance. The presence of macrofauna accelerated the burst in flagellate densities. With macrofauna the same maximum densities were reached, but later densities dropped to relatively low levels. Macrofaunal bioturbation resulted in higher flagellate densities deeper in the sediment (up to 1200% at 3 cm and up to 460% at 6 cm deep).}, }
@article {pmid24186721, year = {1995}, author = {Burke, CM}, title = {Benthic microbial production of oxygen supersaturates the bottom water of a stratified hypersaline lake.}, journal = {Microbial ecology}, volume = {29}, number = {2}, pages = {163-171}, pmid = {24186721}, issn = {0095-3628}, abstract = {Lake Hayward is a hypersaline lake that stratifies seasonally and maintains oxygen supersaturation in its bottom water for about 6 months each year. This phenomenon was found to be the result of photosynthesis by the benthic microbial communities, composed primarily of the cyanobacteria Cyanothece spp., Spirulina sp., and Oscillatoria sp. When these communities were present and the lake was stratified, the bottom water was supersaturated with oxygen (up to 370%). During illumination, the benthic microbial communities rapidly developed very high concentrations (e.g., >500 μM) of oxygen, which then diffused into the overlying water. However, while the overlying water became supersaturated, the concentration in the water was lower than in the benthic microbial communities because (1) transport across the sediment-water interface was limited by diffusion, and (2) turbulence rapidly mixed the oxygen throughout the much larger volume of the bottom water (approximately 1.5 m deep). Thus, import of oxygen by the benthic microbial communities at night proceeded more slowly than daytime export, allowing supersaturation of the bottom water to develop.}, }
@article {pmid24186720, year = {1995}, author = {Elser, JJ and Chrzanowski, TH and Sterner, RW and Schampel, JH and Foster, DK}, title = {Elemental ratios and the uptake and release of nutrients by phytoplankton and bacteria in three lakes of the Canadian shield.}, journal = {Microbial ecology}, volume = {29}, number = {2}, pages = {145-162}, pmid = {24186720}, issn = {0095-3628}, abstract = {The dynamics of carbon (C), nitrogen (N), and phosphorus (P), elemental ratios, and dark uptake/release of N and P in bacterial and phytoplankton size fractions were studied during summer 1992 in three lakes of contrasting food web structure and trophic status (L240, L110, L227). We wished to determine if phytoplankton and bacteria differed in their elemental characteristics and to evaluate whether the functional role of bacteria in nutrient cycling (i.e., as sink or source) depended on bacterial elemental characteristics. Bacterial contributions to total suspended particulate material and to fluxes of nutrients in the dark were substantial and varied for different elements. This indicated that some techniques for assaying phytoplankton physiological condition are compromised by bacterial contributions. C/N ratios were generally less variable than C/P and N/P ratios. Both elemental ratios and biomass-normalized N and P flux indicated that phytoplankton growth in each lake was predominantly P-limited, although in L227 these data reflect the dominance of N-fixing cyanobacteria, and N was likely limiting early in the sampling season. In L227, phytoplankton N/P ratio and biomass-normalized N flux were negatively correlated, indicating that flux data were likely a reasonable measure of the N status of the phytoplankton. However, for L227 phytoplankton, P-flux per unit biomass was a hyperbolic function of N/P, suggesting that the dominant L227 cyanobacteria have a limited uptake and storage capacity and that P-flux per unit biomass may not be a good gauge of the P-limitation status of phytoplankton in this situation. Examination of N-flux data in the bacterial size fraction relative to the N/P ratio of the bacteria revealed a threshold N/P ratio (∼22:1 N/P, by atoms), below which, bacteria took up and sequestered added N, and above which, N was released. Thus, the functional role of bacteria in N cycling in these ecosystems depended on their N/P stoichiometry.}, }
@article {pmid24186719, year = {1995}, author = {Kairesalo, T and Tuominen, L and Hartikainen, H and Rankinen, K}, title = {The role of bacteria in the nutrient exchange between sediment and water in a flow-through system.}, journal = {Microbial ecology}, volume = {29}, number = {2}, pages = {129-144}, pmid = {24186719}, issn = {0095-3628}, abstract = {The contribution of bacteria to phosphorus (P) and nitrogen (N) release from, or retention in, sediment was studied in a flow-through system. "Live" and formaldehyde-"killed" sediment communities were incubated in 25-liter bottles with a continuous flow of P- or P + N-enriched water. Sediment bacteria in the killed communities were inhibited by adding formaldehyde (final concentration 0.04% v/v) to the sediment before the start of the experiment. Bacterial activity in the live sediments measured with [(3)H]thymidine and [(14)C]leucine incorporation techniques did not change essentially during the experiment period (7-8 days). Chemical mechanisms were found to be of principal importance in PO4-P retention in the sediment. In the live samples, the net retention of PO4-P was lower than in the killed samples, which was likely due to the reduced O2 conditions in the sediment as a consequence of bacterial mineralization. In total P exchange, however, bacteria increased the retention rate by recycling dissolved organic P in the sediment. In the live communities the retention of N was very efficient, and all the introduced NH4 -N and NO3-N was immobilized by sediment bacteria. Nitrogen enrichment, however, did not alter the P exchange rates. The gradual emergence of bacterial activity (and grazing) in the killed communities, subsequent to the dilution of formaldehyde concentration, enhanced the release of PO4-P and NH4-N from sediment.}, }
@article {pmid24186718, year = {1995}, author = {Servais, P}, title = {Measurement of the incorporation rates of four amino acids into proteins for estimating bacterial production.}, journal = {Microbial ecology}, volume = {29}, number = {2}, pages = {115-128}, pmid = {24186718}, issn = {0095-3628}, abstract = {In aquatic ecosystems, [(3)H]thymidine incorporation into bacterial DNA and [(3)H]leucine incorporation into proteins are usually used to estimate bacterial production. The incorporation rates of four amino acids (leucine, tyrosine, lysine, alanine) into proteins of bacteria were measured in parallel on natural freshwater samples from the basin of the river Meuse (Belgium). Comparison of the incorporation into proteins and into the total macromolecular fraction showed that these different amino acids were incorporated at more than 90% into proteins. From incorporation measurements at four subsaturated concentrations (range, 2-77 nm), the maximum incorporation rates were determined. Strong correlations (r > 0.91 for all the calculated correlations) were found between the maximum incorporation rates of the different tested amino acids over a range of two orders of magnitude of bacterial activity. Bacterial production estimates were calculated using theoretical and experimental conversion factors. The productions calculated from the incorporation rates of the four amino acids were in good concordance, especially when the experimental conversion factors were used (slope range, 0.91-1.11, and r > 0.91). This study suggests that the incorporation of various amino acids into proteins can be used to estimate bacterial production.}, }
@article {pmid24186642, year = {1995}, author = {Barkovskii, A and Bouillant, ML and Monrozier, LJ and Balandreau, J}, title = {Azospirillum strains use phenolic compounds as intermediates for electron transfer under oxygen-limiting conditions.}, journal = {Microbial ecology}, volume = {29}, number = {1}, pages = {99-114}, pmid = {24186642}, issn = {0095-3628}, abstract = {The effects of catechol, vanillic, caffeic (CAF), 2-hydroxyphenylacetic, 4-hydroxy- and 3,4-dihydroxybenzoic (3,4-DHBA) acids on the growth of a common rice rhizosphere inhabitant, Azospirillum lipoferum were studied. Two strains of this nonfermenting nitrogen-fixing bacterium were used: a motile strain (4B), and a nonmotile strain (4T). Under atmospheric conditions (pO2 = 21 kPa), the growth of strain 4T was inhibited by catechol (0.1 mM) only. None of these compounds affected the growth of strain 413. Under 5 kPa O2, no effect was observed on strain 413, whereas three of the six tested phenolics stimulated the growth of strain 4T; maximum effects were observed for 3,4-DHBA and CAF. As revealed by TLC and HPLC, under low oxygen, more new lipophilic compounds were formed from CAF by strain 4T, differing from CAF autooxydation products and from the products obtained under 21 kPa O2. It was hypothesized that strain 4T had the ability to use an oxidized derivative of CAF as a terminal electron acceptor. This hypothesis was tested in experiments under nitrogen-fixing conditions, in the absence of oxygen, and in the presence of N2O as a reoxidizing agent for CAF. Acetylene was used both as a substrate to measure nitrogenase activity (ARA) and to inhibit the biological transfer of electrons to N2O. The addition of CAF in the presence of N2O had the same effect on ARA rates as an addition of oxygen. It is concluded that the strain 4T of Azospirillum lipoferum is able to sustain some of its activities (e.g., N2 fixation) using phenolics as alternative electron acceptors under low oxygen conditions.}, }
@article {pmid24186641, year = {1995}, author = {Vandenabeele, J and Vande Woestyne, M and Houwen, F and Germonpré, R and Vandesande, D and Verstraete, W}, title = {Role of autotrophic nitrifiers in biological manganese removal from groundwater containing manganese and ammonium.}, journal = {Microbial ecology}, volume = {29}, number = {1}, pages = {83-98}, pmid = {24186641}, issn = {0095-3628}, abstract = {Upon start-up of a rapid sand filter fed with groundwater containing Mn(2+) and NH(4+), the first to be removed was NH(4+), which was oxidized to NO2 (-). After both NH(4+) and NO2 (-). were completely oxidized to NO3 (-), the removal of Mn(2+) commenced. Batch experiments showed that the addition of Nitrosomonas europaea and Nitrobacter winogradskyi stimulated the Mn(2+) removal by sandfilter microbial consortia. NO2 (-). was found to have a marked inhibitory effect on the removal of Mn(2+) and could reduce the removal rate by half. In this respect, NO2 (-)-mediated chemical reduction of manganese oxide was demonstrated at slightly acidic pH values. In pure cultures of Nitrosomonas europaea and Nitrobacter winogradskyi, no Mn(2+) oxidation occurred, but reduction of MnO2 to Mn(2+) was found when NO2 (-). accumulated. These results indicate that the development of NO2/(-). oxidizers is critical in the removal of Mn(2+) in rapid sand filters. By oxidizing NO2 (-). NO2 (-). oxidizers eliminate the negative effect of NO2 (-). on the biological oxidation of Mn(2+).}, }
@article {pmid24186640, year = {1995}, author = {Robertson, BK and Dreyfus, B and Alexander, M}, title = {Ecology of stem-nodulating Rhizobium and Azorhizobium in four vegetation zones of Senegal.}, journal = {Microbial ecology}, volume = {29}, number = {1}, pages = {71-81}, pmid = {24186640}, issn = {0095-3628}, abstract = {The occurrence and distribution of Azorhizobium and Rhizobium strains that induce stem nodulation of Sesbania rostrata were determined in four vegetation zones in Senegal. Based on tests with 16 Rhizobium and 10 Azorhizobium strains nodulating S. rostrata, a method was devised to distinguish among the strains. In all vegetation zones, members of both genera were more abundant in rhizosphere than nonrhizosphere soil under S. rostrata, Cassia obtusifolia, Acacia senegal, and Hystic suaveolens, and Rhizobium was present at higher densities than Azorhizobium. Azorhizobium was more abundant on the leaves and stems than Rhizobium in three of the vegetation zones, and the density of Azorhizobium but not Rhizobium was far greater on the leaves of S. rostrata than the three nonhost species in all four zones. Approximately 90% of the stem nodules and 39-48% of the root nodules on S. rostrata in all four zones were formed by Azorhizobium.}, }
@article {pmid24186639, year = {1995}, author = {Thomaz, SM and Wetzel, RG}, title = {[(3)H]Leucine incorporation methodology to estimate epiphytic bacterial biomass production.}, journal = {Microbial ecology}, volume = {29}, number = {1}, pages = {63-70}, pmid = {24186639}, issn = {0095-3628}, abstract = {[(3)H]leucine incorporation into protein, as a method of measuring bacterial biomass production (BBP), was adapted to epiphytic bacteria. Incorporation of the isotope was saturated at concentrations higher than 400 nM. Disruption of thicker biofilms by sonication resulted in higher values of BBP and ratios of BBP/biomass when compared to those of intact biofilm. Thin biofilms formed early in the decomposition process did not show this phenomenon. These results support to evidence that more internally located cells of the matrices either have greatly reduced access to the leucine from the overlying medium or that fast recycling of leucine occurs in the biofilm.}, }
@article {pmid24186638, year = {1995}, author = {Christensen, H and Olsen, RA and Bakken, LR}, title = {Flow cytometric measurements of cell volumes and DNA contents during culture of indigenous soil bacteria.}, journal = {Microbial ecology}, volume = {29}, number = {1}, pages = {49-62}, pmid = {24186638}, issn = {0095-3628}, abstract = {Indigenous soil bacteria were released from a clay loam soil by repeated washing and centrifugation followed by density gradient centrifugation to remove enough soil particles to allow a flow cytometric (FC) study of cell numbers, cell sizes, and DNA content in single cells. The bacteria were suspended in liquid soil extract medium and incubated at 15°C for 60 h, during which direct fluorescence microscopic counts (acridine orange direct counts, AODC) were done along with the FC measurements. Cells of Escherichia coli with a known number of whole genomes per cell (rifampicin treated) were used as a calibration standard both for the DNA measurements (mitramycin-ethidium bromide stain) and cell volumes (light scatter). In response to the nutrients in the soil extract medium, the indigenous soil bacteria increased in numbers and respiration rate after a lag period of about 17 h. The onset of growth was seen first as an increase in respiration rate, numbers of large cells, and the amounts of DNA per cell in the large cells. Respiration and direct microscopical determination of biovolume was used to calculate the average growth yield on the basis of cell carbon, which was found to be 20-30% during the period of active growth. For separate volume groups of the indigenous cells, the DNA content ranged from 1.5 to 15 fg DNA per cell, the majority being below 4 fg DNA. During growth in soil extract medium, the numbers of large cells (volume > 0.18 μm(3)) increased, and the frequency of cells with high DNA contents increased as well for this group. For the smallest sized cells (volumes < 0.065 μm(3)) it was not possible to detect any increase in numbers during the 60-h incubation, and the DNA contents of these cells remained virtually unchanged. Compared with cell volumes based on microscopy (AODC), the FC-light scatter data grossly overestimated the volume for indigenous cells but apparently not for the newly formed cells during growth in the suspension. This probably reflects differences in light scatter properties due to adsorbed materials on the indigenous cells. The FC-DNA measurements confirmed earlier findings in that the average DNA content per cell was low (around 2 fg DNA per cell), but demonstrated a positive relationship between cell size and DNA content for indigenous cells.}, }
@article {pmid24186637, year = {1995}, author = {Williams, HN and Schoeffield, AJ and Guether, D and Kelley, J and Shah, D and Falkler, WA}, title = {Recovery of bdellovibrios from submerged surfaces and other aquatic habitats.}, journal = {Microbial ecology}, volume = {29}, number = {1}, pages = {39-48}, pmid = {24186637}, issn = {0095-3628}, abstract = {The distribution of bdellovibrios was investigated over a wide geographical area of the Chesapeake Bay including some tributaries and subestuaries. Bdellovibrios were recovered from five aquatic habitats; water, sediment, oyster shell surface biofilm, zooplankton, and plants over a wide range of temperature and salinity measurements. Consistently, the greatest number of the predators was recovered from samples of biofilm irrespective of temperature and salinity. A decrease in the numbers and frequency of predators recovered from all habitats was observed at temperatures below 10°C. Only the shell surface biofilm samples yielded bdellovibrios 100% of the time. The organisms were recovered from 79% of water samples and 44% of sediment samples. The results reveal that bdellovibrios are surface-associated organisms and that this association appears to provide some protection for the predators at low temperatures.}, }
@article {pmid24186636, year = {1995}, author = {Pinckney, J and Paerl, HW and Reid, RP and Bebout, B}, title = {Ecophysiology of stromatolitic microbial mats, Stocking Island, exuma cays, Bahamas.}, journal = {Microbial ecology}, volume = {29}, number = {1}, pages = {19-37}, pmid = {24186636}, issn = {0095-3628}, abstract = {Intertidal stromatolites, covered by cyanobacterial mats, were recently discovered at Stocking Island, Exuma Cays, Bahamas. Ecophysiological responses (CO2 fixation, N2 fixation, and photoacclimation) of these cyanobacterial mats to experimental manipulations were examined to identify potential environmental variables controlling community structure and function. The mats exhibit horizontal zonation that shifts from soft to crusty to hard in a seaward direction. Cluster analysis of chemotaxonomic photopigments (chlorophylls and carotenoids) revealed that visually distinct mat types are composed of distinct phototrophic assemblages. Under reduced irradiance, diatoms within the mats photoacclimated by increasing accessory photopigments (diadinoxanthin, fucoxanthin, and chlorophyll c 1 c 2) and cyanobacteria reduced the photoprotective carotenoid echinenone. In a 4-day nutrient addition bioassay experiment, nitrate, phosphate, dissolved organic carbon, and trace metal enrichments did not enhance CO2 fixation, but phosphate enrichments tripled N2 fixation rates. The addition of DCMU increased N2 fixation rates relative to nonamended light and dark rates, indicating light (photosystem I) enhanced nitrogenase activity. Soft mats appear to represent the early stages of colonization and stabilization of mat communities. Active growth following stabilization results in the formation of partially-lithified crusty mats, which eventually become highly-lithified and form hard mats. Collectively, our results suggest that Stocking Island stromatolitic mats have low growth rates and consequently exhibit slow responses to increased nutrient availability and changes in ambient irradiance. In general, intertidal stromatolitic mats at Stocking Island appear to exhibit low rates of CO2 and N2 fixation relative to nonlithifying temperate cyanobacteral mats. Although production is low, respiration is likewise low, leading to the suggestion that high production to respiration ratios (P:R) may be necessary for lithification of intertidal stromatolitic mats.}, }
@article {pmid24186635, year = {1995}, author = {Chappell, KR and Goulder, R}, title = {A between-river comparison of extracellular-enzyme activity.}, journal = {Microbial ecology}, volume = {29}, number = {1}, pages = {1-17}, pmid = {24186635}, issn = {0095-3628}, abstract = {River-water extracellular-enzyme activity in the lowland Rivers Ouse and Derwent, northeast England, had much in common. In both rivers, the mean enzyme activities over 15 months differed in the following order: leucine aminopeptidase > phosphatase > β-D-glucosidase > β-D-galactosi-idase and β-D-xylosidase. None of the five enzymes assayed had significant between-river difference in activity, and there was significant between-river correlation of β-D-glucosidase, phosphatase, and leucine-aminopeptidase activity. The common enzyme regimes were probably more due to between-river similarity of planktonic microbiota than to similar physico-chemical conditions. The potential for glucose uptake by bacterioplankton closely followed β-D-glucosidase activity in magnitude and periodicity. The potential for leucine uptake, however, was much less than leucine-aminopeptidase activity; hence rate of leucine release probably did not limit leucine uptake. There was an appreciable and highly variable proportion of free (<0.2 μm) enzyme activity in river water; ranges were β-D-glucosidase 10-30%, phosphatase 53% to apparently 104%, and leucine aminopeptidase 22-98%. These free enzymes did not necessarily originate from planktonic microbiota and may explain the fairly loose coupling between whole-water enzyme activity and microbial variables. Marked downstream increase in enzyme activity, along about 104 km of the River Derwent, was found on only one of three sampling days; hence the single site used for regular sampling was reasonably representative of most of the river.}, }
@article {pmid24186462, year = {1994}, author = {Wetzel, RL}, title = {Modeling the microbial loop: An estuarine modeler's perspective.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {331-334}, pmid = {24186462}, issn = {0095-3628}, abstract = {Contemporary models of the microbial loop should be critically evaluated relative to their compartmental structures, flow networks, and treatment of upper ocean physics (vertical and horizontal boundary conditions). The development of new models that include better representation of the autotrophic components and mixotrophy/competitive interactions is warranted. The mathematical structures should reflect contemporary knowledge of controls (e.g., multiple resource limitation), thresholds and limits, and be based on testable assumptions. Stochastic processes must at some point be included to evaluate known patterns of spatial and temporal variability.}, }
@article {pmid24186461, year = {1994}, author = {Christian, RR}, title = {Aggregation and disaggregation of microbial food webs.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {327-329}, pmid = {24186461}, issn = {0095-3628}, abstract = {Models of the microbial food web have generally used compartments aggregated by general body size and gross taxonomy. It has been assumed that these also reflect guilds or holons. Generally, results of simulation or analysis based on this structure have been reasonably well validated. Herein I summarize why the aggregations may be justified and what may be learned from disaggregation.}, }
@article {pmid24186460, year = {1994}, author = {Hopkinson, CS and Vallino, JJ}, title = {Toward the development of generally applicable models of the microbial loop in aquatic ecosystems.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {321-326}, pmid = {24186460}, issn = {0095-3628}, abstract = {Simulation modeling has been an integral, albeit ad hoc, component of the field of aquatic microbial ecology for the past two decades. One of the most critical steps in simulation modeling is the initial formulation of a clear set of questions and goals. It is doubtful that a single generic model could be constructed to address adequately all questions of interest concerning the microbial loop because of the tremendous range in time scales that define these questions. Progress in the field of aquatic microbial ecology will benefit from an integrated research program including experimental and modeling approaches. A submodel of bacterial utilization of various qualities of organic matter that we have under construction is presented. This submodel will be a component of a larger model to evaluate the effects of quality and quantity of organic matter and inorganic nutrient inputs on estuarine food web structure and efficiency. The overall model will be general enough in its structure that it should be applicable to a wide range of questions concerning the microbial loop, with time scales ranging from hours to days.}, }
@article {pmid24186459, year = {1994}, author = {Ducklow, HW}, title = {Modeling the microbial food web.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {303-319}, pmid = {24186459}, issn = {0095-3628}, abstract = {Models of the microbial food web have their origin in the debate over the importance of bacteria as an energetic subsidy for higher trophic levels leading to harvestable fisheries. Conceptualization of the microbial food web preceded numerical models by 10-15 years. Pomeroy's work was central to both efforts. Elements necessary for informative and comprehensive models of microbial loops in plankton communities include coupled carbon and nitrogen flows utilizing a size-based approach to structuring and parameterizing the food web. Realistic formulation of nitrogen flows requires recognition that both nitrogenous and nonnitrogenous organic matter are important substrates for bacteria. Nitrogen regeneration driven by simple mass-specific excretion constants seems to overestimate the role of bacteria in the regeneration process. Quantitative assessment of the link-sink question, in which the original loop models are grounded, requires sophisticated analysis of size-based trophic structures. The effects of recycling complicate calculation of the link between bacteria or dissolved organic matter and mesozooplankton, and indirect effects show that the link might be much stronger than simple analyses have suggested. Examples drawn from a series of oceanic mixed layer plankton models are used to illustrate some of these points. Single-size class models related to traditional P-Z-N approaches are incapable of simulating bacterial biomass cycles in some locations (e.g., Bermuda) but appear to be adequate for more strongly seasonal regimes at higher latitudes.}, }
@article {pmid24186458, year = {1994}, author = {Revsbech, NP}, title = {Limitation of primary production by heterotrophic assimilation and transformation of inorganic nutrients.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {299-301}, pmid = {24186458}, issn = {0095-3628}, abstract = {The planktonic environment is usually characterized by non-steady state conditions with events of phytoplankton blooms and sedimentation. Inorganic nutrients are stripped from the water column by sedimentation and end up in the sediments where they may be permanently deposited, or nitrogen may be liberated as nitrogen gas by denitrification. A major part of the denitrification activity is a coupled process of nitrification and denitrification which is dependent on a good supply of oxygen to the sediment. Urea may constitute a major part of the total outflux of dissolved N compounds from the sediment.}, }
@article {pmid24186457, year = {1994}, author = {Caron, DA}, title = {Inorganic nutrients, bacteria, and the microbial loop.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {295-298}, pmid = {24186457}, issn = {0095-3628}, abstract = {The realization that natural assemblages of planktonic bacteria may acquire a significant fraction of their nitrogen and phosphorus via the uptake of dissolved inorganic nutrients has modified our traditional view of these microorganisms as nutrient remineralizers in plankton communities. Bacterial uptake of inorganic nitrogen and phosphorus may place bacteria and phytoplankton in competition for growth-limiting nutrients, rather than in their traditional roles as the respective "source" and "sink" for these nutrients in the plankton. Bacterial nutrient uptake also implies that bacterivorous protozoa may play a pivotal role in the remineralization of these elements in the microbial loop. The overall contribution of bacterial utilization of inorganic nutrients to total nutrient uptake in the ocean is still poorly understood, but some generalizations are emerging with respect to the geographical areas and community physiological conditions that might elicit this behavior.}, }
@article {pmid24186456, year = {1994}, author = {Morita, RY}, title = {Complications in the determination of the nutrient status of the marine environment.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {291-294}, pmid = {24186456}, issn = {0095-3628}, abstract = {How much of the organic matter in the oceans is truly bioavailable under in situ conditions? This bioavailability may be altered by perturbation, priming, bottle (surface or confinement) effects, and air contaminants. Measured free organic matter may not be free in situ but may depend on method of analysis. We have yet to determine the threshold energy for growth of microbes and their energy of maintenance under in situ conditions.}, }
@article {pmid24186455, year = {1994}, author = {Turley, C}, title = {Controls of the microbial loop: Nutrient limitation and enzyme production, location and control.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {287-289}, pmid = {24186455}, issn = {0095-3628}, abstract = {A major controlling factor for bacterial growth is their ability to hydrolyze high molecular weight molecules too complex to be transported directly across the cell's membrane. The utility of such an extracellular enzyme hydrolysis system, location of the enzymes (free or attached), environmental controls of enzyme production, and implications of multiple hydrolysis-uptake systems are explored in relation to free-living oceanic bacteria and bacteria attached to rapidly sinking aggregates.}, }
@article {pmid24186454, year = {1994}, author = {Button, DK}, title = {The physical base of marine bacterial ecology.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {273-285}, pmid = {24186454}, issn = {0095-3628}, abstract = {Specific affinity theory is compared with traditional ways of understanding the nutrient concentration dependency of microbial growth. It is demonstrated that the Michaelis constant increases with the ratio of metabolic enzyme to membrane permease content of bacteria so that small values can reflect specialization for nutrient collection. When compared to the specific affinity, Kt gives a measure of oligotrophic capacity. Specific affinity, on the other hand, reflects nutrient collection ability directly, and increases with the number of permeases. It can be estimated, along with the other kinetic constant, Vmax, by use of isotopes in natural samples. Because of systematic errors in estimating Vmax, specific affinity is the preferred measure of substrate accumulation ability. The advantage of simultaneous collection of multiple substrates in dilute solution is demonstrated. The structural basis of this advantage is computed from collision frequency and recollision probability, computations that further show that multisubstrate usage is essential for bacterial growth under low-nutrient conditions. Computed growth rates from specific affinities require that several substrates be used simultaneously for growth at measured concentrations. Formulations anticipate that the surface of oligobacteria should be occupied by a diversity of transporter types, that each type of transporter should occupy only a small portion of the cell surface, and the number of cytoplasmic enzymes can be small, allowing small cell size to give a large surface-to-volume ratio for high specific affinity. The large number of substrate types that may be accumulated by a single oligobacterial species is consistent with extensive species diversity.}, }
@article {pmid24186453, year = {1994}, author = {Kirchman, DL}, title = {The uptake of inorganic nutrients by heterotrophic bacteria.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {255-271}, pmid = {24186453}, issn = {0095-3628}, abstract = {It is now well known that heterotrophic bacteria account for a large portion of total uptake of both phosphate (60% median) and ammonium (30% median) in freshwaters and marine environments. Less clear are the factors controlling relative uptake by bacteria, and the consequences of this uptake on the plankton community and biogeochemical processes, e.g., new production. Some of the variation in reported inorganic nutrient uptake by bacteria is undoubtedly due to methodological problems, but even so, uptake would be expected to vary because of variation in several parameters, perhaps the most interesting being dissolved organic matter. Uptake of ammonium by bacteria is very low whereas uptake of dissolved free amino acids (DFAA) is high in eutrophic estuaries (the Delaware Bay and Chesapeake Bay). The concentrations and turnover of DFAA are insufficient, however, in oligotrophic oceans where bacteria turn to ammonium and nitrate, although the latter only as a last resort. I argue here that high uptake of dissolved organic carbon, which has been questioned, is necessary to balance the measured uptake of dissolved inorganic nitrogen (DIN) in seawater culture experiments. What is problematic is that this DIN uptake exceeds bacterial biomass production. One possibility is that bacteria excrete dissolved organic nitrogen (DON). A recent study offers some support for this hypothesis. Lysis by viruses would also release DON.While ammonium uptake by heterotrophic bacteria has been hypothesized to affect phytoplankton community structure, other impacts on the phytoplankton and biomass production (both total and new) are less clear and need further work. Also, even though bacteria account for a very large fraction of phosphate uptake, how this helps to structure the plankton community has not been examined. What is clear is that the interactions between bacterial and phytoplankton uptake of inorganic nutrients are more complicated than simple competition.}, }
@article {pmid24186452, year = {1994}, author = {Berman, T and Stone, L}, title = {Musings on the microbial loop: Twenty years after.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {251-253}, doi = {10.1007/BF00166815}, pmid = {24186452}, issn = {0095-3628}, }
@article {pmid24186451, year = {1994}, author = {Coleman, DC}, title = {The microbial loop concept as used in terrestrial soil ecology studies.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {245-250}, pmid = {24186451}, issn = {0095-3628}, abstract = {Components and processes in the aquatic microbial loop are compared with the composition and functioning of the soil microbial loop. Relative to their bacterial and/or fungal food sources, many of the soil water-film fauna (e.g., protozoa, nematodes) are conspicuous by low biomasses and high turnover rates of carbon and mineral nutrients. Comparisons with production and turnover rates of aerial (pore-inhabiting) fauna are made, and the highly patchy nature of soil microhabitats is shown to be similar to that of aquatic (marine) habitats.}, }
@article {pmid24186450, year = {1994}, author = {Suttle, CA}, title = {The significance of viruses to mortality in aquatic microbial communities.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {237-243}, pmid = {24186450}, issn = {0095-3628}, abstract = {A variety of approaches including enumeration of visibly infected microbes, removal of viral particles, decay of viral infectivity, and measurements of viral production rates have been used to infer the impact of viruses on microbial mortality. The results are surprisingly consistent and suggest that, on average, about 20% of marine heterotrophic bacteria are infected by viruses and 10-20% of the bacterial community is lysed daily by viruses. The effect of viruses on phytoplankton is less certain, but ca. 3% of Synechococcus biomass may be lysed daily. The fraction of primary productivity this represents depends upon the relative biomass and growth rate of Synechococcus. Virus enrichment experiments suggest that the productivity of eukaryotic phytoplankton would be ca. 2% higher in the absence of viruses. Overall, probably about 2-3% of primary productivity is lost to viral lysis. There is considerable variation about these estimates; however, they represent a starting point for incorporating viral-mediated processes into aquatic ecosystem models.}, }
@article {pmid24186449, year = {1994}, author = {Sherr, EB and Sherr, BF}, title = {Bacterivory and herbivory: Key roles of phagotrophic protists in pelagic food webs.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {223-235}, pmid = {24186449}, issn = {0095-3628}, abstract = {Research on "microbial loop" organisms, heterotrophic bacteria and phagotrophic protists, has been stimulated in large measure by Pomeroy's seminal paper published in BioScience in 1974. We now know that a significant fate of bacterioplankton production is grazing by < 20-µm-sized flagellates. By selectively grazing larger, more rapidly growing and dividing cells in the bacterioplankton assemblage, bacterivores may be directly cropping bacterial production rather than simply the standing stock of bacterial cells. Protistan herbivory, however, is likely to be a more significant pathway of carbon flow in pelagic food webs than is bacterivory. Herbivores include both < 20-µm flagellates as well as > 20-µm ciliates and heterotrophic dinoflagellates in the microzooplankton. Protists can grow as fast as, or faster than their phytoplankton prey. Phototrophic cells grazed by protists range from bacterial-sized prochlorophytes to large diatom chains (which are preyed upon by extracellularly-feeding dinoflagellates). Recent estimates of microzooplankton herbivory in various parts of the sea suggest that protists routinely consume from 25 to 100% of daily phytoplankton production, even in diatom-dominated upwelling blooms. Phagotrophic protists should be viewed as a dominant biotic control of both bacteria and of phytoplankton in the sea.}, }
@article {pmid24186448, year = {1994}, author = {Bratbak, G and Thingstad, F and Heldal, M}, title = {Viruses and the microbial loop.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {209-221}, pmid = {24186448}, issn = {0095-3628}, abstract = {The abundance of viral-like particles in marine ecosystems ranges from <104 ml(-1) to >10(8) ml(-1). Their distribution in time and space parallels that of other biological parameters such as bacterial abundance and chlorophyll a. There is a lack of consensus between methods used to assess viral activity, i.e., rate of change in viral abundance (increase or decrease). The highest rates, 10-100 days(-1), are observed in experiments with short sampling intervals (0.2-2 h), while lower rates, on the order of 1 day(-1), are observed in experiments with longer sampling intervals (days). Few studies have been carried out, but viruses appear, at least in some cases, to have a significant impact on carbon and nutrient flow in microbial food webs. Viruses have also been demonstrated to exert a species specific control of both bacteria and phytoplankton populations in natural waters.}, }
@article {pmid24186447, year = {1994}, author = {Velimirov, B}, title = {Carbon fluxes in the microbial loop: Comments.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {205-207}, pmid = {24186447}, issn = {0095-3628}, abstract = {The heterotrophic bacterial community of oceanic aggregates which mediates particle solubilization, displays features (low carbon demand and low turnover) that are difficult to reconcile with the observed high enzyme activities and cell numbers. Hypotheses are proposed to explain this discrepancy. Furthermore, production of both free and attached bacteria may have been underestimated by neglecting the ultramicrobacteria (UMB). Production of UMB may represent up to 28% of the total bacterial production.}, }
@article {pmid24186446, year = {1994}, author = {Pedrós-Alió, C}, title = {The problem of species aggregation in food webs.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {201-203}, pmid = {24186446}, issn = {0095-3628}, }
@article {pmid24186445, year = {1994}, author = {Meyer, JL}, title = {The microbial loop in flowing waters.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {195-199}, pmid = {24186445}, issn = {0095-3628}, abstract = {The microbial loop in flowing waters is dependent on allochthonous sources of carbon, which vary in quality. The proportion of dissolved organic carbon (DOC) that can be degraded ranges from <1 to over 50%, and the bioavailability of DOC (micrograms bacterial biomass produced per milligram DOC present) ranges over two orders of magnitude. Bioavailability of DOC is predictable from the ratio of H/C and O/C of the DOC, but further work is needed to develop simple predictors of bioavailability of DOC in a range of environments. Consumers of bacteria in streams range in size from protists to insect larvae, with highest rates of bacterial consumption found among the meiofauna and certain filter feeders and grazers. Because there appear to be fewer trophic transfers in the lotic microbial loop, it functions more as a link in flowing waters than it appears to do in the marine plankton.}, }
@article {pmid24186444, year = {1994}, author = {Pace, ML and Cole, JJ}, title = {Comparative and experimental approaches to top-down and bottom-up regulation of bacteria.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {181-193}, pmid = {24186444}, issn = {0095-3628}, abstract = {The regulation of bacterial community biomass and productivity by resources and predators is a central concern in the study of microbial food webs. Resource or bottom-up regulation refers to the limitation of bacteria by carbon and nutrients derived from allocthonous inputs, primary production, and heterotrophic production. Predatory or top-down regulation refers to the limitation of bacteria below levels supportable by resources alone. Large scale comparative studies demonstrate strong correlations between bacterial productivity and biomass, suggesting significant resource regulation. Comparisons of the abundances of heterotrophic flagellates and bacteria, however, imply that in some cases there may be top-down regulation of bacteria in eutrophic environments. Experimental studies in lakes support the importance of resource regulation and reveal little top-down control from protozoans. Increases in bacterial abundance and production with nutrient enrichment were limited in enclosure experiments with high abundances of the cladoceran, Daphnia. Regulation of bacteria by Daphnia may occur in many lakes seasonally and prevail in some lakes throughout the year where these animals sustain dense populations. In most situations, however, bacteria appear to be limited primarily by resources.}, }
@article {pmid24186443, year = {1994}, author = {Azam, F and Smith, DC and Steward, GF and Hagström, A}, title = {Bacteria-organic matter coupling and its significance for oceanic carbon cycling.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {167-179}, pmid = {24186443}, issn = {0095-3628}, abstract = {This paper synthesizes current ideas on the role of the microbial loop in carbon fluxes in the ocean and proposes some directions for future research. Organic matter flux into bacteria is highly variable, which can significantly influence the pathways of carbon flow in the ocean. A goal for future research is to elucidate the mechanistic bases of bacteria-organic matter coupling. This research should take into consideration the micrometer-scale distribution of bacteria and the composition, structure, and dynamics of the organic matter field in the bacterium's microhabitat. The ideas on the interactions of bacteria with the particulate organic phase need to be revised in view of recent findings of highly abundant, previously unknown particles ranging in size from nanometers to hundreds of micrometers. The "hot-spots" in the distribution of organic matter and remineralized nutrients can influence the rates as well as the direction of biogeochemical fluxes. Slow-to-degrade dissolved organic matter (DOM) may be produced because of loose bacteria-organic matter coupling resulting in DOM storage. Its use at a later time and place has profound implications for carbon fluxes and food web dynamics. A fundamental research need for the future is to understand the ecological interactions among the members of the microbial loop in an appropriate microhabitat context. While this goal was previously intractable, new molecular and optical techniques should make it possible to understand the biogeochemical activities of the microbial loop in terms of the ecology and evolution of pelagic microbial communities.}, }
@article {pmid24186442, year = {1994}, author = {White, DC}, title = {Is there anything else you need to understand about the microbiota that cannot be derived from analysis of nucleic acids?.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {163-166}, pmid = {24186442}, issn = {0095-3628}, }
@article {pmid24186441, year = {1994}, author = {Kemp, PF}, title = {A philosophy of methods development: The assimilation of new methods and information into aquatic microbial ecology.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {159-162}, doi = {10.1007/BF00166804}, pmid = {24186441}, issn = {0095-3628}, abstract = {Emerging methodologies can be used to provide a strong basic understanding of the diversity of microbial behavior and interactions. However, these new methods should be thoroughly and rigorously validated under controlled conditions before being extended to uncontrolled field conditions. Data based on novel approaches are likely to provide insights that are not easily related to existing information based on conventional methodologies. As an example, measurements of the ribosomal RNA (rRNA) content of bacteria show similar spatial patterns as measurements of thymidine incorporation into DNA and leucine incorporation into protein. However, the spatial patterns are not identical, and these parameters are not equally intercorrelated nor equally predictable from basic oceanographic data. Therefore, rRNA content measurements provide a new dimension of information that can be used to explore the relationship of bacteria to their environment, complementing the information obtained from conventional methods.}, }
@article {pmid24186440, year = {1994}, author = {Newell, SY}, title = {Ecomethodology for organoosmotrophs: Prokaryotic unicellular versus eukaryotic mycelial.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {151-157}, pmid = {24186440}, issn = {0095-3628}, abstract = {Although they are very unlikely to play large direct roles in water-column microbial loops, eukaryotic mycelial decomposers (the mycelial true fungi, eumycotes, and zoosporic "fungi," oomycotes) have the potential to be important secondary producers in decaying plant material in shallow aquatic systems. Their secondary productivity may lead to important exchanges of material with microbial loops: output of ascospores, conidia, zoosporic flagellates, leaked lysates, and particles of decayed plants containing mycelium; input of dissolved organics and inorganic nutrients. Development of methods for ecological study of the aquatic mycelial eukaryotic decomposers has not advanced as rapidly as that for the prokaryotes of microbial loops, probably because (1) there are fewer aquatic microbial ecologists with mycological training and inclination than with prokaryotic leanings; and (2) the mycelial decomposers are difficult to work with, because they produce their mycelial mass virtually entirely within opaque solid substrates. Direct microscopic methods have emerged as prime tools for the measurement of prokaryotic mass, whereas an index-chemical assay (ergosterol) is currently the most efficient way to measure the mass of eumycotes. For measuring productivity of prokaryotes of microbial loops, microbial ecologists may choose from several (>10) published and field-tested methods, involving direct microscopy or monitoring of radiotracers. Extensive reviews of distribution and dynamics of aquatic bacterial mass and productivity have appeared. For measuring productivity of eukaryotic mycelial decomposers, one has only two published methods from which to choose, a direct-microscopic and a radiotracer method, neither of which has had adequate field testing. We are, furthermore, much less well equipped to obtain mass and productivity information for the poorly known mycelial oomycotes than we are for the eumycotes. Application of productivity techniques and nucleic-acid technology, may within the next decade allow knowledge of ecology of aquatic eukaryotic mycelial decomposers to advance to levels approaching that for the prokaryotes of microbial loops.}, }
@article {pmid24186439, year = {1994}, author = {Karl, DM}, title = {Accurate estimation of microbial loop processes and rates.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {147-150}, doi = {10.1007/BF00166802}, pmid = {24186439}, issn = {0095-3628}, abstract = {Our conceptual models of microbial food webs in aquatic ecosystems provide a unifying hypothesis for the design and conduct of field studies. Our ability to provide a rigorous test of these hypotheses, however, relies to a large extent on the availability of precise and accurate methods. Although considerable progress has been made over the past two decades, unambiguous resolution of in situ microbial rates and processes will probably require improved or novel methodologies.}, }
@article {pmid24186438, year = {1994}, author = {Fuhrman, JA and Lee, SH and Masuchi, Y and Davis, AA and Wilcox, RM}, title = {Characterization of marine prokaryotic communities via DNA and RNA.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {133-145}, pmid = {24186438}, issn = {0095-3628}, abstract = {We know very little about species distributions in prokaryotic marine plankton. Such information is very interesting in its own right, and ignorance of it is also beginning to hamper process studies, such as those on viral infection. New DNA- and RNA-based approaches avoid many prior limitations. Here we discuss four such applications: (1) cloning and sequencing of 16S rRNA genes to produce lists of what types of organisms are present; (2) quantification of these individual types in marine samples by nucleic acid hybridization, including single cell fluorescence; (3) quantitative comparison by DNA-DNA hybridization of entire microbial communities in terms of shared common types, without knowledge of community components; and (4) finding cultures that are representative of native communities. Several previously uncharacterized types of bacteria and archaea (probably including novel phyla) are present in marine plankton. Evidence from both the Atlantic and Pacific suggests that as-of-yet uncultivated archaea may dominate the deep sea, and thus may be the most abundant group of organisms on Earth. Such archaea are in surface waters as well, and can be visualized with fluorescent probes and enriched at room temperature with addition of organic nutrients. Community hybridization shows that variability of microbial community compositions in time and space is high. Although most native bacteria do not grow in culture, some proteobacterial cultures appear by genomic hybridization to be representative of certain communities. These and other results indicate the utility of DNA- and RNA-based methods.}, }
@article {pmid24186437, year = {1994}, author = {Hollibaugh, JT}, title = {Relationship between thymidine metabolism, bacterioplankton community metabolic capabilities, and sources of organic matter.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {117-131}, pmid = {24186437}, issn = {0095-3628}, abstract = {Numerous investigations have been directed at verifying and calibrating methods for measuring bacterioplankton production, particularly methods based on the incorporation of thymidine (TdR) into DNA. Careful examination of these data can provide insights into other aspects of the ecology of aerobic heterotrophic microbial communities. Once method-specific biases are eliminated, these measurements indicate that there are broad-scale patterns in the metabolic fate of TdR, differences that seem to reflect broad differences in community metabolic capabilities. Based on work conducted primarily in San Francisco and Tomales Bays, California, I suggest that the metabolic fate of TdR in a given environment may reflect the relative importance to bacterioplankton nutrition of detritus versus fresh phytoplankton carbon. This is probably due to differences in community composition that result from growth on qualitatively different carbon sources. If true, the metabolic fate of TdR may provide a broadly applicable, but simple, index that can be used to assess the relative importance of these general sources of organic matter. Such an index could be very useful in characterizing lacustrine, estuarine, and nearshore environments.}, }
@article {pmid24186436, year = {1994}, author = {Hobbie, JE}, title = {The state of the microbes: A summary of a symposium honoring Lawrence Pomeroy.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {113-116}, doi = {10.1007/BF00166799}, pmid = {24186436}, issn = {0095-3628}, }
@article {pmid24186435, year = {1994}, author = {Wiebe, WJ and Moran, MA and Hodson, RE}, title = {Preface.}, journal = {Microbial ecology}, volume = {28}, number = {2}, pages = {111-112}, doi = {10.1007/BF00166798}, pmid = {24186435}, issn = {0095-3628}, }
@article {pmid24190397, year = {1994}, author = {Michereff, SJ and Silveira, NS and Reis, A and Mariano, RL}, title = {Epiphytic bacteria antagonistic to Curvularia leaf spot of yam.}, journal = {Microbial ecology}, volume = {28}, number = {1}, pages = {101-110}, pmid = {24190397}, issn = {0095-3628}, abstract = {Curvularia eragrostidis yam leaf spot is a serious concern among the northeast Brazilian yam growing areas. In order to study its biocontrol, bacterial isolates from the yam phylloplane were tested against the pathogen. They were evaluated with respect to the following parameters: (1) inhibition of C. eragrostidis mycelial growth by using paired culture and cellophane membrane methods, (2) inhibition of conidium germination by using a paired suspension test, (3) reduction of disease severity and, (4) persistence of antagonistic action, on plants under greenhouse conditions. From a total of 162 bacterial isolates, 39 showed antagonism to the pathogen in paired culture. The bacteria produced extracellular, nonvolatile, and diffusible metabolites in the membrane cellophane test. Seventeen isolates resulted in more than 75% inhibition of C. eragrostidis mycelial growth. Among them, IF-26 showed the greatest antagonism. The isolates IF-82, IF-88, and IF-109 inhibited pathogen conidial germination, with average inhibition levels of 99.2, 98.2 and 96.2%, respectively. Under greenhouse conditions the antagonists were applied at three different time intervals relative to C. eragrostidis inoculation: 3 days before, at the same time, and 3 days after. IF-82 and IF-88 applied at the same time as pathogen inoculation both reduced disease severity 75%. IF-82 showed the best persistence of antagonistic action, with an average of 96.3%. IF-82, identified as Bacillus subtilis, was the best biocontrol agent for the yam leaf spot disease in this study.}, }
@article {pmid24190396, year = {1994}, author = {Rusterholtz, KJ and Mallory, LM}, title = {Density, activity, and diversity of bacteria indigenous to a karstic aquifer.}, journal = {Microbial ecology}, volume = {28}, number = {1}, pages = {79-99}, pmid = {24190396}, issn = {0095-3628}, abstract = {The microbial ecology of karstic ground water is largely unknown. The density, activity, and diversity of bacteria indigenous to subsurface karstic material in Mammoth Cave National Park, Mammoth Cave, Kentucky were studied using minimally disruptive, on-site procedures. Two sites, located 100 m below the surface and consisting of saturated fine to coarse sand in pooled water, were examined. Samples were taken aseptically using modified, sterile 60-cc syringes. Total cell and total respiring cell densities were determined using an acridine orange/p-iodonitrotetrazolium violet (AO/INT) staining procedure. Cells in selected cores were stained with INT and incubated in the cave for 4 h prior to fixing with glutaraldehyde and subsequent transport to the laboratory. Cells were stained with AO in the laboratory. Low- and high-nutrient media were used to determine viable cell counts. Plates were incubated in the cave for 1 day at ambient temperature prior to transportation to the laboratory in an insulated cooler. Viable cell counts ranged from 1.0 × 106 to 8.1 × 106 cells wet g(-1) of sediment. Total direct counts were 3.9 × 106 and 1.4 × 107 cells wet g(-1) for the Olivia's Dome and the Catherine's Dome sites, respectively. Viable cell counts were highly similar to respiring cell counts at both sites. At the Olivia's Dome site, viable cell counts represented 26-31% of the direct cell counts, while 58% of the total cell count were actively respiring. At the Catherine's Dome site, viable cell counts represented 11-58% of the direct counts, while 53% of the cells were actively respiring. A total of 237 strains recovered from low- and high-nutrient media at both Olivia's and Catherine's Domes, and 10 reference strains were examined for 117 morphological, biochemical, and physiological characteristics. Results were coded in a binary fashion and analyzed using numerical taxonomic techniques. Similarity values were calculated using a simple matching coefficient. Fifty-two clusters, ranging in size from 2 to 13 members, were defined at the 80-85% similarity level with the weighted pair-group mathematical average algorithm (WPGMA). The matrix was examined using the Jaccard coefficient and WPGMA clustering to control for distortion due to negative matches and varying group size. Presumptively identified genera include, Arthrobacter, Brevibacterium, Bacillus, Cornyebacterium, Actinomyces, Aureobacterium, Chromobacterium, and Mycobacterium. Pseudomonas spp. were not recovered. Fifty percent of the clustered operational taxonomic units (OTUs) were not identified. Thirty percent of the clustered OTUs were irregular, asporogenous, Gram-positive rods. The bacterial communities varied between sites, and isolation medium had a strong influence on the strains recovered. The bacterial community in the karstic sediments sampled exhibits a high degree of diversity having no dominant strain or strains.}, }
@article {pmid24190395, year = {1994}, author = {Mort, SL and Dean-Ross, D}, title = {Biodegradation of phenolic compounds by sulfate-reducing bacteria from contaminated sediments.}, journal = {Microbial ecology}, volume = {28}, number = {1}, pages = {67-77}, pmid = {24190395}, issn = {0095-3628}, abstract = {The biodegradation of phenolic compounds under sulfate-reducing conditions was studied in sediments from northern Indiana. Phenol, p-cresol and 4-chlorophenol were selected as test substrates and added to sediment suspensions from four sites at an initial concentration of 10 mg/liter. Degradative abilities of the sediment microorganisms from the four sites could be related to previous exposure to phenolic pollution. Time to onset of biodegradation of p-cresol and phenol in sediment suspensions from a nonindustrialized site was approximately 70 and 100 days, respectively, in unacclimated cultures. In sediment slurries from three sites with a history of wastewater discharges containing phenolics, time to onset of biodegradation was 50-70 days for p-cresol and 50-70 days for phenol in unacclimated cultures. In acclimated cultures from all four sites, the length of the lag phase was reduced to 14-35 days for p-cresol and 25-60 days for phenol. Length of the biodegradative phase varied from 25 to 40 days for phenol and 10 to 50 days for p-cresol and was not markedly affected by acclimation. Substrate mineralization by sulfate-reducing bacteria was confirmed with radiotracer techniques using an acclimated sediment culture from one site. Addition of molybdate, a specific inhibitor of sulfate reduction, and bacterial cell inactivation inhibited sulfate reduction and substrate utilization. None of the sites exhibited the ability to degrade 4-chlorophenol, nor were acclimated phenol and p-cresol degrading cultures from a particular site able to cometabolize 4-chlorophenol.}, }
@article {pmid24190394, year = {1994}, author = {Lang, E and Viedt, H}, title = {Degradation by and toxicity to bacteria of chlorinated phenols and benzenes, and hexachlorocyclohexane isomers.}, journal = {Microbial ecology}, volume = {28}, number = {1}, pages = {53-65}, pmid = {24190394}, issn = {0095-3628}, abstract = {Mixed cultures degrading chlorinated benzenes, chlorinated phenols, or hexachlorocyclohexane (HCH) as the sole source of carbon and energy were obtained by enrichment from contaminated soil samples. Cultures which metabolized 3-chlorophenol (3-CP), 2,3-dichlorophenol (2,3-DCP), or 2,6-dichlorophenol (2,6-DCP) were able to utilize several other chlorinated compounds as substrates, whereas cultures enriched with 1,2,4,5-tetrachlorobenzene (1,2,4,5-TeCB), α-HCH, or γ-HCH did not metabolize most of the other chlorinated congeners tested. Chloride release and growth rates with all four chlorinated phenols decreased with increasing initial substrate concentrations within the range of 30-250 μmol liter(-1). Maximum chloride release was 3.8 mg liter(-1) corresponding to 35 μmol liter(-1) trichlorophenol within 7 weeks. In contrast, the rate of metabolism of the nonphenolic compounds 1,2,4,5-TeCB, α-HCH, or γ-HCH increased with increasing substrate concentrations. Initial concentrations of 750 μmol liter(-1) α-HCH or 1,2,4,5-TeCB were completely dechlorinated within 2 weeks. Because aqueous solubility and bioavailability of the chlorophenolic compounds is much higher than that of the nonphenolic compounds, it is suggested that the high bioavailability of the chlorophenolic compounds is the reason for the high toxicity of these substrates to the degrading cultures. In contrast, the low aqueous solubilities of the chlorinated benzenes and HCH-isomers caused consistently low concentrations in the medium, which were high enough to induce degradation but too low to damage the bacterial cells.}, }
@article {pmid24190393, year = {1994}, author = {Keller, MD and Shapiro, LP and Haugen, EM and Cucci, TL and Sherr, EB and Sherr, BF}, title = {Phagotrophy of fluorescently labeled bacteria by an oceanic phytoplankter.}, journal = {Microbial ecology}, volume = {28}, number = {1}, pages = {39-52}, pmid = {24190393}, issn = {0095-3628}, abstract = {Using fluorescently-labeled bacteria and detection by flow cytometry and epifluorescence microscopy, we demonstrate inducible mixotrophy in a marine photosynthetic flagellate, Ochromonas sp. (class Chrysophyceae). Phagotrophic uptake of bacteria increases under conditions of low or limiting light and nutrients, but deceases in periods of prolonged darkness; sustained phagotrophy may require light. In addition, this alga appears to discriminate between and preferentially ingest different types of bacteria. Although this clone is primarily photosynthetic, phagotrophy contributes to its nutrition, especially when light or nutrients limit photosynthesis.}, }
@article {pmid24190392, year = {1994}, author = {Kazumi, J and Capone, DG}, title = {Heterotrophic microbial activity in shallow aquifer sediments of Long Island, New York.}, journal = {Microbial ecology}, volume = {28}, number = {1}, pages = {19-37}, pmid = {24190392}, issn = {0095-3628}, abstract = {Bacterial numbers and activities (as estimated by glucose uptake and total thymidine incorporation) were investigated at two sites in Long Island, New York aquifer sediments. In general, bacterial activities were higher in shallow (1.5-4.5 m below the water table or BWT), oxic sediments than in deep (10-18 m BWT), anoxic sediments. The average total glucose uptake rates were 0.18 ± 0.10 ng gdw(-1) h(-1) in shallow sediments and 0.09 ± 0.11 ng gdw(-1) h(-1) in deep sediments; total thymidine incorporation rates were 0.10 ± 0.13 pmol gdw(-1) h(-1) and 0.03 ± 0.03 pmol gdw(-1) h(-1) in shallow and deep sediments, respectively. Incorporation of glucose was highly efficient, as only about 10% of added label was recovered as CO2. Bacterial abundance (estimated from acridine orange direct counts) was 2.5 ± 2.0 × 10(7) cells gdw(-1) and 2.0 ± 1.3 × 10(7) cells gdw(-1) in shallow and deep sediments, respectively. These bacterial activity and abundance estimates are similar to values found in other aquifer environments, but are 10- to 1000-fold lower than values in soil or surface sediment of marine and estuarine systems. In general, cell specific microbial activities were lower in sites from Connetquot Park, a relatively pristine site, when compared to activities found in sites from Jamesport, which has had a history of aldicarb (a pesticide) contamination. To our knowledge, this is the first report of bacterial activity measurements in the shallow, sandy aquifers of Long Island, New York.}, }
@article {pmid24190391, year = {1994}, author = {Grossmann, S}, title = {Bacterial activity in sea ice and open water of the Weddell Sea, Antarctica: A microautoradiographic study.}, journal = {Microbial ecology}, volume = {28}, number = {1}, pages = {1-18}, pmid = {24190391}, issn = {0095-3628}, abstract = {Metabolic activity of bacteria was investigated in open water, newly forming sea ice, and successive stages of pack ice in the Weddell Sea. Microautoradiography, using [(3)H]leucine as substrate, was compared with incorporation rates of [(3)H]leucine into proteins. Relation of [(3)H]leucine incorporation to the biomass of active bacteria provides information about changes of specific metabolic activity of cells. During a phytoplankton bloom in an ice-free, stratified water column, total numbers of bacteria in the euphotic zone averaged 2.3 × 10(5) ml(-1), but only about 13% showed activity via leucine uptake. Growth rate of the active bacteria was estimated as 0.3-0.4 days(-1). Total cell concentration of bacteria in 400 m depth was 6.6 × 10(4) ml(-1). Nearly 50% of these cells were active, although biomass production and specific growth rate were only about one-tenth that of the surface populations. When sea ice was forming in high concentrations of phytoplankton, bacterial biomass in the newly formed ice was 49.1 ng C ml(-1), exceeding that in open water by about one order of magnitude. Attachment of large bacteria to algal cells seems to cause their enrichment in the new ice, since specific bacterial activity was reduced during ice formation, and enrichment of bacteria was not observed when ice formed at low algal concentration. During growth of pack ice, biomass of bacteria increased within the brine channel system. Specific activity was still reduced at these later stages of ice development, and percentages of active cells were as low as 3-5%. In old, thick pack ice, bacterial activity was high and about 30% of cells were active. However, biomass-specific activity of bacteria remained significantly lower than that in open water. It is concluded that bacterial assemblages different to those of open water developed within the ice and were dominated by bacteria with lower average metabolic activity than those of ice-free water.}, }
@article {pmid24190342, year = {1994}, author = {Srikanth, S and Berk, SG}, title = {Adaptation of amoebae to cooling tower biocides.}, journal = {Microbial ecology}, volume = {27}, number = {3}, pages = {293-301}, pmid = {24190342}, issn = {0095-3628}, abstract = {Adaptation of amoebae to four cooling tower Biocides, which included a thiocarbamate compound, tributyltin neodecanoate mixed with quaternary ammonium compounds (TBT/QAC), another QAC alone, and an isothiazolin derivative, was studied. Previously we found that amoebae isolated from waters of cooling towers were more resistant to cooling tower biocides than amoebae from other habitats. Acanthamoeba hatchetti and Cochliopodium bilimbosum, obtained from American Type Culture Collection and used in the previous studies, were tested to determine whether they could adapt to cooling tower Biocides. A. hatchetti was preexposed to subinhibitory concentrations of the four Biocides for 72h, after which they were tested for their resistance to the same and other biocides. C. bilimbosum was exposed to only two biocides, as exposure to the other two was lethal after 72 h. Preexposure to the subinhibitory concentrations of the Biocides increased the resistance of the amoebae, as indicated by a significant increase in the minimum inhibitory concentration (up to 30-fold). In addition, cross-resistance was also observed, i.e., exposure to one biocide caused resistance to other biocides. These results show that amoebae can adapt to biocides in a short time. The phenomenon of cross-resistance indicates that regularly alternating biocides, as is done to control microbial growth in cooling towers, may not be effective in keeping amoeba populations in check. On the contrary, exposure to one biocide may boost the amoebae's resistance to a second biocide before the second biocide is used in the cooling tower. Since amoebae may harbor Legionella, or alone cause human diseases, these results may be important in designing effective strategies for controlling pathogens in cooling towers.}, }
@article {pmid24190341, year = {1994}, author = {Wolfaardt, GM and Lawrence, JR and Headley, JV and Robarts, RD and Caldwell, DE}, title = {Microbial exopolymers provide a mechanism for bioaccumulation of contaminants.}, journal = {Microbial ecology}, volume = {27}, number = {3}, pages = {279-291}, pmid = {24190341}, issn = {0095-3628}, abstract = {Scanning confocal laser microscopy was used to directly visualize accumulation of the herbicide diclofop methyl and its breakdown products by a degradative biofilm community, cultivated in continuous-flow cell cultures. Some bacterial cells accumulated these compounds. However, most accumulation occurred in cell capsules and certain regions of the exopolymer matrix. Mass spectroscopic analysis of the biofilm material confirmed accumulation of the parent compound and its breakdown products in the biofilms. Lower molecular weight degradation products were found in the effluent, indicating mineralization of diclofop by the flow cell cultures. Grazing protozoa feeding on the biofilms nonselectively ingested cell capsules and exopolymers, suggesting direct transfer and accumulation of the contaminants in protozoa. These findings demonstrated that microbial exopolymers can play an important role in the bioaccumulation of contaminants in natural systems.}, }
@article {pmid24190340, year = {1994}, author = {Bååth, E}, title = {Thymidine and leucine incorporation in soil bacteria with different cell size.}, journal = {Microbial ecology}, volume = {27}, number = {3}, pages = {267-278}, pmid = {24190340}, issn = {0095-3628}, abstract = {Thymidine and leucine incorporation into macromolecules of soil bacteria extracted by homogenization-centrifugation were measured after size-fractionation of the bacterial suspension through different sized filters (1.0, 0.8, 0.6, 0.4 μm). The specific thymidine incorporation rate was highest for the unfiltered and 1.0 μm filtered suspensions (approximately 10 × 10(-21) mol thymidine bacteria(-1) h(-1)), but decreased to 1.39 × 10(-21) mol bacteria(-1) h(-1) for bacteria passing the 0.4 μm filter. The proportion of culturable bacteria (percent colony forming units/acridine orange direct counts) also decreased with bacterial cell size from 5.0% for the unfiltered bacterial suspension to 0.8% in the 0.4 µm filtrate. A strong linear correlation (r (2) = 0.995) was found between the specific thymidine incorporation rate and the proportion of culturable bacteria. Leucine incorporation gave similar results to the thymidine incorporation. No effects of cell size on the degree of isotope dilution or unspecific labeling of other macromolecules were found either for the thymidine or the leucine incorporation technique. These data indicate that small bacteria, although more numerous than larger ones, not only constitute a smaller proportion of the soil bacterial biomass than larger bacteria, but also contribute to a lesser degree to carbon transformations in soil.}, }
@article {pmid24190339, year = {1994}, author = {Sundh, I and Nilsson, M and Granberg, G and Svensson, BH}, title = {Depth distribution of microbial production and oxidation of methane in northern boreal peatlands.}, journal = {Microbial ecology}, volume = {27}, number = {3}, pages = {253-265}, pmid = {24190339}, issn = {0095-3628}, abstract = {The depth distributions of anaerobic microbial methane production and potential aerobic microbial methane oxidation were assessed at several sites in both Sphagnum- and sedge-dominated boreal peatlands in Sweden, and compared with net methane emissions from the same sites. Production and oxidation of methane were measured in peat slurries, and emissions were measured with the closed-chamber technique. Over all eleven sites sampled, production was, on average, highest 12 cm below the depth of the average water table. On the other hand, highest potential oxidation of methane coincided with the depth of the average water table. The integrated production rate in the 0-60 cm interval ranged between 0.05 and 1.7 g CH4 m (-2) day(-) and was negatively correlated with the depth of the average water table (linear regression: r (2) = 0.50, P = 0.015). The depth-integrated potential CH4-oxidation rate ranged between 3.0 and 22.1 g CH4 m(-2) day(-1) and was unrelated to the depth of the average water table. A larger fraction of the methane was oxidized at sites with low average water tables; hence, our results show that low net emission rates in these environments are caused not only by lower methane production rates, but also by conditions more favorable for the development of CH4-oxidizing bacteria in these environments.}, }
@article {pmid24190338, year = {1994}, author = {Vandevivere, P and Welch, SA and Ullman, WJ and Kirchman, DL}, title = {Enhanced dissolution of silicate minerals by bacteria at near-neutral pH.}, journal = {Microbial ecology}, volume = {27}, number = {3}, pages = {241-251}, pmid = {24190338}, issn = {0095-3628}, abstract = {Previous studies have shown that various microorganisms can enhance the dissolution of silicate minerals at low (<5) or high (>8) pH. However, it was not known if they can have an effect at near-neutral pH. Almost half of 17 isolates examined in this study stimulated bytownite dissolution at near-neutral pH while in a resting state in buffered glucose. Most of the isolates found to stimulate dissolution also oxidized glucose to gluconic acid. More detailed analysis with one of these isolates suggested that this partial oxidation was the predominant, if not sole, mechanism of enhanced dissolution. Enhanced dissolution did not require direct contact between the dissolving mineral and the bacteria. Gluconate-promoted dissolution was also observed with other silicate minerals such as albite, quartz, and kaolinite.}, }
@article {pmid24190337, year = {1994}, author = {Wallace, WH and Fleming, JT and White, DC and Sayler, GS}, title = {An algD-bioluminescent reporter plasmid to monitor alginate production in biofilms.}, journal = {Microbial ecology}, volume = {27}, number = {3}, pages = {225-239}, pmid = {24190337}, issn = {0095-3628}, abstract = {A broad-host range algD-lux bioluminescent reporter plasmid was developed to examine the role of exopolymer production in biofilm function. The algD-lux reporter plasmid will allow rapid on-line in situ detection of environmental factors that induce alginate biosynthesis. The algD promoter was stimulated by factors previously reported to induce alginate production, including ethanol and NaCl, and differences were observed with different nitrogen sources. With growth on minimal media with either glucose or succinate as a carbon source, succinate had a greater inductive effect on the algD promoter. An increase in light output of 1.3-fold and 1.7-fold was seen with cultures amended with 50 and 150 mM NaCI, respectively, compared to cultures with succinate alone. NaCl induction of the algD promoter was confirmed by algD RNA slot blots. Light output increased 2.0-fold and 1.7-fold with 0.25% and 0.5% ethanol, respectively, compared with controls grown with succinate only. While the rate of algD promoter response was initially similar when either NH4 or NO3 was used as a nitrogen source, NH4-grown cultures maintained a higher light output during late log phase compared to NO3-grown cultures.}, }
@article {pmid24190336, year = {1994}, author = {Wallace, WH and Rice, JF and White, DC and Sayler, GS}, title = {Distribution of alginate genes in bacterial isolates from corroded metal surfaces.}, journal = {Microbial ecology}, volume = {27}, number = {3}, pages = {213-223}, pmid = {24190336}, issn = {0095-3628}, abstract = {The distribution of alginate genes encoding biosynthesis of alginate was examined for bacterial isolates associated with corrosive biofilms recovered from source water, cooling lines, and reactor surfaces of a nuclear power plant. A total of 120 diverse Gram-positive and -negative isolates were obtained. Using DNA:DNA hybridization, 11 isolates were shown to contain sequences homologous to structural (algD, algG, alg-76) and/or regulatory (albB) alginate biosynthetic genes derived from an alginate-producing cystic fibrosis isolate of Pseudomonas aeruginosa (FRD1). Identification of isolates was accomplished by fatty acids methyl esters (FAME) analysis and the Biolog identification system. Nine of the twelve isolates were identified as various Pseudomonas spp., and two additional Gram-negative isolates were tentatively identified as Aeromonas veronii and Stenotrophomonas maltophilia. The remaining isolate was identified as a Gram-positive Bacillus pumilus. The results of the investigation extend current knowledge on the distribution of alginate biosynthetic genes in environmental isolates and permits the development of a more environmentally realistic model system to investigate the role of exopolymer production in biofilm formation and biocorrosion processes.}, }
@article {pmid24190335, year = {1994}, author = {Kerkhof, L}, title = {A species-specific probe and a PCR assay for the marine bacterium, Pseudomonas stutzeri strain Zobell.}, journal = {Microbial ecology}, volume = {27}, number = {3}, pages = {201-212}, pmid = {24190335}, issn = {0095-3628}, abstract = {The cloning, sequencing, and analysis of a Pseudomonas stutzeri Zobell 23S rRNA gene is described. Three variable regions were identified, and oligonucleotides homologous to portions of these regions were synthesized. The oligonucleotides were used as probes to screen DNA from various cultured bacteria to identify a species-specific probe. All probes were found to hybridize strongly with P. stutzeri Zobell DNA under stringent conditions and did not hybridize with other Pseudomonas species. One probe showed slight cross-reactivity with DNA from four other bacteria under the hybridization conditions used. Finally, PCR conditions were optimized for detection of P. stutzeri Zobell in mixed culture with a detection limit of 400 cells. The assay detected P. stutzeri Zobell rDNA in coastal seawater samples sampled over a 20-month period. In the future, these probes could be used to quantify the 23S rRNA and rDNA from P. stutzeri Zobell in mixed culture and in environmental samples.}, }
@article {pmid24190275, year = {1994}, author = {Gilbert, JJ}, title = {Jumping behavior in the oligotrich ciliates Strobilidium velox and Halteria grandinella, and its significance as a defense against rotifer predators.}, journal = {Microbial ecology}, volume = {27}, number = {2}, pages = {189-200}, pmid = {24190275}, issn = {0095-3628}, abstract = {The jumping behavior of Strobilidium velox and Halteria grandinella was analyzed videographically. On average, undisturbed cells of these species jumped 1.7-3.6 and 8 times per minute and spent 0.8 and 1.0% of their time jumping, respectively. Both ciliate species initiated jumps after encounters with rotifer predators. S. velox jumped on contact with Asplanchna girodi, traveling a mean distance of 1.5 mm (33 body lengths) at a mean velocity of 7 mm/s (154 body lengths/s) at 17°C. H. grandinella jumped on contact or near contact with Synchaeta pectinata, traveling a mean distance of 0.37 mm (18 body lengths) at a mean velocity of 2.76 mm/s (131 body lengths/s) at 20°C. The maximum velocity recorded during these escape jumps was 16.07 mm/s for S. velox and 3.70 mm/s for H. grandinella. In S. velox, swimming velocity during jumps was not significantly correlated either with swimming velocity just before jumping (mean = 0.15 mm/s) or with distance traveled. In H. grandinella, jumping velocity and distance also were not significantly correlated. Jumping in S. velox and H. grandinella was calculated to require approximately 149% and 41 % of total metabolic rate, respectively. Jumping seemed to be an effective defense against rotifer predation. Only 3% of 93 S. velox cells contacted by A. girodi were captured, and only 12% of 92 H. grandinella cells contacted or closely approached by S. pectinata were captured; all other cells jumped away. A predation experiment showed that A. girodi was about twice as, and significantly more, likely to ingest Paramecium tetraurelia as S. velox in a mixture of equal numbers of these ciliates. The swimming velocity of S. velox during jumps is the highest one so far reported for an oligotrich, and equals the highest one reported for any ciliate (Mesodinium rubrum).}, }
@article {pmid24190274, year = {1994}, author = {de la Torre, MA and Gomez-Alarcon, G}, title = {Manganese and iron oxidation by fungi isolated from building stone.}, journal = {Microbial ecology}, volume = {27}, number = {2}, pages = {177-188}, pmid = {24190274}, issn = {0095-3628}, abstract = {Acid and nonacid generating fungal strains isolated from weathered sandstone, limestone, and granite of Spanish cathedrals were assayed for their ability to oxidize iron and manganese. In general, the concentration of the different cations present in the mineral salt media directly affected Mn(IV) oxide formation, although in some cases, the addition of glucose and nitrate to the culture media was necessary. Mn(II) oxidation in acidogenic strains was greater in a medium containing the highest concentrations of glucose, nitrate, and manganese. High concentrations of Fe(II), glucose, and mineral salts were optimal for iron oxidation. Mn(IV) precipitated as oxides or hydroxides adhered to the mycelium. Most of the Fe(III) remained in solution by chelation with organic acids excreted by acidogenic strains. Other metabolites acted as Fe(III) chelators in nonacidogenic strains, although Fe(III) deposits around the mycelium were also detected. Both iron and manganese oxidation were shown to involve extracellular, hydrosoluble enzymes, with maximum specific activities during exponential growth. Strains able to oxidize manganese were also able to oxidize iron. It is concluded that iron and manganese oxidation reported in this work were biologically induced by filamentous fungi mainly by direct (enzymatic) mechanisms.}, }
@article {pmid24190273, year = {1994}, author = {Hashemi, F and Leppard, GG and Kushnert, DJ}, title = {Copper resistance in Anabaena variabilis: Effects of phosphate nutrition and polyphosphate bodies.}, journal = {Microbial ecology}, volume = {27}, number = {2}, pages = {159-176}, pmid = {24190273}, issn = {0095-3628}, abstract = {A copper-resistant Anabaena variabilis strain was obtained after repeated culturing in progressively higher concentrations of Cu(NO3)2. This strain maintained its resistance even after a year of repeated subculturing in copper-free medium. The resistant strain differed from the sensitive parent strain with respect to filament length, cell shape and size, and control of heterocyst formation. The resistant strain was also more resistant to cadmium, zinc, and nickel. Copper distribution studies conducted with atomic absorption spectroscopy revealed that at low copper levels the sensitive strain bound significantly more metal than the resistant strain. At higher copper levels, however, the resistant strain bound large amounts of the metal. Phosphate-loaded resistant cells could grow in higher copper concentrations than phosphate-starved resistant cells. Toluidine blue staining showed that the resistant strain contained more polyphosphate bodies than the sensitive strain; the resistant cells also had higher internal phosphate levels. X-ray microanalysis, however, did not show a direct localization of copper on polyphosphate bodies. More than one mechanism of resistance may exist in this A. variabilis strain.}, }
@article {pmid24190272, year = {1994}, author = {Van Wambeke, F}, title = {Influence of phytoplankton lysis or grazing on bacterial metabolism and trophic relationships.}, journal = {Microbial ecology}, volume = {27}, number = {2}, pages = {143-158}, pmid = {24190272}, issn = {0095-3628}, abstract = {Experimental microcosms were used to study the dynamics of heterotrophic bacterial populations with respect to phytoplankton loss. In a two-stage linked culture system, we artificially separated production and loss processes of a diatom Phaeodactylum tricornutum. In the first (productive) stage, the algae developed axenically and continuously. The outflow was fluxed in two degradation stages, where phytoplankton-derived detritus resulted respectively from: (1) excretion and by-products of phagotrophic organisms (protozoans), and (2) bacterial degradation through bacterial attachment and lysis. According to the phytoplankton decay mode, i.e., lysis or grazing, bacterial adaptations were different. The study of bacterial productivity and aminopeptidase activity showed specific bacterial evolution during the succession of different prey-predator relationships. The occurrence of aggregates allowed nanoflagellates to develop an alternative diet; they fed not only on bacteria, but also on partially degraded phytoplankton detritus, inducing a strong short-cut in the food chain. Sources and controls of extracellular proteolytic activity are discussed. Such experimental approaches are interesting because they separate bacterial lysis and protozoan grazing of phytoplankton, as well as the fates of their corresponding phytoplankton detritus in the microbial food web.}, }
@article {pmid24190271, year = {1994}, author = {Roy, R and Legendre, P and Knowles, R and Charlton, MN}, title = {Denitrification and methane production in sediment of Hamilton Harbour (Canada).}, journal = {Microbial ecology}, volume = {27}, number = {2}, pages = {123-141}, pmid = {24190271}, issn = {0095-3628}, abstract = {Systematic sampling of 21 sites covering Hamilton Harbour (Lake Ontario, Canada) was carried out during the summer in 1990 and 1991 in order to study how well environmental factors, such as O2, NO 3 (-) , and organic carbon, and the spatial structure can explain observed variation of potential denitrification, CH4 and CO2 production, as well as N2 fixation in sediment slurries. Using canonical redundancy analysis and an extension of this method to partial out the variance into spatial and environmental components, we found that most of the explained fraction of potential microbial activities (70-90%) was accounted for by the significant environmental variables (NH 4 (+) , particulate carbon, dissolved organic carbon, dissolved O2, depth, and temperature) and not much by the spatial polynomial trend surface. We found significant path coefficients (0.53 and 0.57 in 1990 and 1991) between CO2 production and potential denitrification, which suggests that denitrifiers are dependent upon a heterotrophic bacterial population for directly assimilable carbon sources. We also found significant path coefficients between particulate carbon and both CH4 production (0.67 and 0.33) and CO2 production (0.50 and 0.38), while significant path coefficients were also found between dissolved organic carbon and CO2 production (0.34 and 0.47). We conclude that beside well-known abiotic factors such as O2, NO 3 (-) , and organic carbon, a biotic factor involved in carbon metabolism may be important in explaining the spatial variation of denitrification capacity in the sediment of Hamilton Harbour.}, }
@article {pmid24190270, year = {1994}, author = {Brettar, I and Ramos-Gonzalez, MI and Ramos, JL and Höfle, MG}, title = {Fate of Pseudomonas putida after release into lake water mesocosms: Different survival mechanisms in response to environmental conditions.}, journal = {Microbial ecology}, volume = {27}, number = {2}, pages = {99-122}, pmid = {24190270}, issn = {0095-3628}, abstract = {To study the fate of Pseudomonas putida DSM 3931 in an aquatic environment, cultures of the strain were released into lake water mesocosms. P. putida, bearing the TOL-plasmid, was released as a representative xenobiotic-degrading microorganism. The release was carried out in mesocosms with unamended lake water and in lake water with added culture medium to compare the survival of the strain due to the influence of different organic load. As a comparison, the survival of P. putida was followed in microcosms with sterile lake water. Survival and fate of the strain were determined by means of immunofluorescence with highly specific monoclonal antibodies and growth on selective agar medium for up to ten weeks after release. Addition of medium had a pronounced influence on survival in mesocosms. In mesocosms without added medium, the number of P. putida cells decreased within ten days by over 2 orders of magnitude. In mesocosms with medium, cell numbers increased in the first two days by an order of magnitude and were, after ten days, in the same range as at the time of introduction. Over time, cell numbers decreased but remained detectable in both types of mesocosms for up to ten weeks after release. In mesocosms with unamended lake water, the major fraction of the cells was attached to particles after two days. In mesocosms with medium, large aggregates of P. putida cells formed which included algae. The observed decrease in cell numbers in mesocosms was attributed mainly to grazing. Sedimentation was an additional factor contributing to loss of cells out of the water column, which especially affected aggregate-forming cells in mesocosms with medium in the long run (beyond two weeks). These studies demonstrate that experimental tools on a mesoscale are crucial in order to understand the complex processes microorganisms are subjected to after release into a natural environment, and that single cell detection, such as immunofluorescence, is essential to understand mechanisms of survival and elimination.}, }
@article {pmid24190170, year = {1994}, author = {De Leij, FA and Whipps, JM and Lynch, JM}, title = {The use of colony development for the characterization of bacterial communities in soil and on roots.}, journal = {Microbial ecology}, volume = {27}, number = {1}, pages = {81-97}, pmid = {24190170}, issn = {0095-3628}, abstract = {A simple agar plating method for the description of microbial communities is described. This method is based on the quantification of the numbers of bacterial colonies in 6-7 age-based classes as they appear on agar media over a period of 6-10 days. The method can be used to quantify microbial communities in different habitats (roots and soil) and can be related to the ecophysiology of the microbial communities present. Significant differences in distribution patterns were found in time and depth on the roots. In general, as roots matured, the microbial communities changed from one dominated by r-strategists to one that was more distributed towards K-strategists. The soil had the greatest percentage of organisms that could be characterized as K-strategists. The method was also used to compare microbial communities on wheat roots and in soil in both the field and in microcosms in the glasshouse. In general, the method enabled differentiation between r- and K-strategists in environmental samples, something that could not be done using an ecophysiological index (a modification of the Shannon diversity index) or total bacterial numbers alone.}, }
@article {pmid24190169, year = {1994}, author = {Tibbles, BJ and Rawlings, DE}, title = {Characterization of nitrogen-fixing bacteria from a temperate saltmarsh lagoon, including isolates that produce ethane from acetylene.}, journal = {Microbial ecology}, volume = {27}, number = {1}, pages = {65-80}, pmid = {24190169}, issn = {0095-3628}, abstract = {Nitrogen-fixing bacteria were isolated from sediments and water of a saltmarsh lagoon on the west coast of South Africa, and characterized according to factors that regulate nitrogen fixation in the marine environment. The majority of isolates were assigned to the Photobacterium or Vibrio genera on the basis of physiological and biochemical characteristics. One isolate was further assigned to the species Vibrio diazotrophicus. Carbohydrate utilization by each diazotrophic isolate was examined. Abilities of the isolates to utilize a range of mono-, di-, and polysaccharides largely reflected the predicted availability of organic carbon and energy in the lagoon, except that chitin was not utilized. Biochemical tests on the utilization of combined nitrogen showed that one isolate could utilize nitrate, and that this strain was susceptible to full repression of nitrogenase activity by 10mM nitrate. Urease activity was not detected in any of the isolates. In the absence of molybdenum two of the isolates, a Photobacterium spp. and V. diazotrophicus, reduced acetylene to ethylene and ethane, a property frequently associated with the activity of alternative nitrogenases. Addition of 25µM molybdenum inhibited ethane production by V. diazotrophicus, but stimulated ethylene and ethane production by the Photobacterium isolate. Addition of 28µM vanadium did not appear to regulate ethane production by either strain. Assays of nitrogenase activity in sediments from which some isolates were obtained indicated that molybdenum was not limiting nitrogenase activity at naturally-occurring concentrations. Southern hybridizations of the chromosomes of these strains with the anfH and vnfH genes of Azotobacter vinelandii and the nifH gene of Klebsiella pneumoniae indicated the presence of only one nitrogenase in these isolates.}, }
@article {pmid24190168, year = {1994}, author = {Munro, PM and Clement, RL and Flatau, GN and Gauthier, MJ}, title = {Effect of thermal, oxidative, acidic, osmotic, or nutritional stresses on subsequent culturability of Escherichia coli in seawater.}, journal = {Microbial ecology}, volume = {27}, number = {1}, pages = {57-63}, pmid = {24190168}, issn = {0095-3628}, abstract = {Survival of stressed Escherichia coli with or without the rpoS gene was assessed after 2 and 6 days in sterile seawater. Cells were submitted to thermal (48°C), acidic (pH 5.1), oxidative (H2O2 1mM), nutritional (C, N, P starvation), or osmotic (NaCl 0.5M) stresses for periods ranging from 0 to 4 h. We found a stress-mediated cross protection against seawater relative to controls. Viability was higher when cells were acid, oxidatively, nutritionally or osmotically stressed. Survival increased in cells stressed at 37°C as compared with 20°C. With the exception of osmotic stress, we found that this stress-induced cross protection was rpoS dependent.}, }
@article {pmid24190167, year = {1994}, author = {Ohtonen, R}, title = {Accumulation of organic matter along a pollution gradient: Application of odum's theory of ecosystem energetics.}, journal = {Microbial ecology}, volume = {27}, number = {1}, pages = {43-55}, pmid = {24190167}, issn = {0095-3628}, abstract = {Forest soil biology in Scots pine forests of the Empetrum-Vaccinium type was studied around the industrialized city of Oulu, northern Finland since 1987. The forest sites lie along a sulphur and nitrogen concentration gradient in the mor humus ranging from 1.6 to 3.9 mg S g(-1) organic matter (OM) and from 14 to 23 mg N g(-1) OM. A number of biological parameters have earlier been found to vary along this gradient, thus indicating that the ecosystems are subjected to a pollution stress. Total microbial biomass and various activity parameters were studied in 1991. The different methods are discussed and the results interpreted within the light of Odum's theory of the energetic stabilization of ecosystems. Microbial biomass C determined by the fumigation-extraction (FE) technique varied from 5 to 10 mg g(-)OM, N from 0.5 to 1.0 mg g(-1)OM, and basal respiration rate from 0.040 to 0.097 mg CO2 h(-1) g(-1)OM. All decreased along the pollution gradient. Substrate induced respiration values (SIR) varied from 0.025 to 0.085 mg CO2-C h(-1) g(-1)dw. SIR correlated well with the biomass values determined by the FE technique. The lag time of the microbial community after glucose addition (varying from 13 to 22 h) was shortened and the specific respiration increment of the microbial community in response to glucose addition increased along the gradient. The metabolic quotient (respiration/biomass) of the microflora strongly depended on the technique and equation used in calculating the microbial biomass. The results show a reduced biomass, but a more intensive regeneration and intensified activity per biomass unit of microorganisms in polluted forest soil. This in turn denotes an alteration in the microbial community in favor of a higher proportion of r-strategists under the disturbed conditions. In contrast, K-strategists may be more dominant under less polluted conditions. This interpretation is presented with some reservations concerning methodology. There is a need for the calibration of each method for determining microbial biomass in different types of soil.}, }
@article {pmid24190166, year = {1994}, author = {Jürgens, K and Arndt, H and Rothhaupt, KO}, title = {Zooplankton-mediated changes of bacterial community structure.}, journal = {Microbial ecology}, volume = {27}, number = {1}, pages = {27-42}, pmid = {24190166}, issn = {0095-3628}, abstract = {Enclosure experiments in the mesotrophic Schöhsee in northern Germany were designed to study the impact of metazooplankton on components of the microbial food web (bacteria, flagellates, ciliates). Zooplankton was manipulated in 500-liter epilimnetic mesocosms so that either Daphnia or copepods were dominating, or metazooplankton was virtually absent. The bacterial community responded immediately to changes in zooplankton composition. Biomass, productivity, and especially the morphology of the bacteria changed drastically in the different treatments. Cascading predation effects on the bacterioplankton were transmitted mainly by phagotrophic protozoans which had changed in species composition and biomass. When Daphnia dominated, protozoans were largely suppressed and the original morphological structure of the bacteria (mainly small rods and cocci) remained throughout the experiment. Dominance of copepods or the absence of metazoan predators resulted in a mass appearance of bacterivorous protists (flagellates and ciliates). They promoted a fast decline of bacterial abundance and a shift to the predominance of morphologically inedible forms, mainly long filaments. After 3 days they formed 80-90% of the bacterial biomass. The results indicate that metazooplankton predation on phagotrophic protozoans is a key mechanism for the regulation of bacterioplankton density and community structure.}, }
@article {pmid24190165, year = {1994}, author = {Purcell, AH and Suslow, KG and Klein, M}, title = {Transmission via plants of an insect pathogenic bacterium that does not multiply or move in plants.}, journal = {Microbial ecology}, volume = {27}, number = {1}, pages = {19-26}, pmid = {24190165}, issn = {0095-3628}, abstract = {A bacterial parasite (designated as BEV) of the leafhopper Euscelidius variegatus, which is passed transovarially to offspring, was transmitted from insect to insect via feeding of the insects in plants. The rate of bacterial infection of leafhoppers fed upon plants that had previously been exposed to BEV-infected leafhoppers declined with an increase in the time that infected leafhoppers had been off rye grass. Transmission of BEV also occurred on sugar beet and barley but not celery. The bacterium was also transmitted to and acquired from membrane-encased artificial diets. There was no evidence that the bacterium was transmitted via plant surfaces, but transmission and direct culture assays from plants indicated that the bacterium did not multiply or move within plants. This parasite-host relationship may represent a primitive stage in either the evolution of intracellular symbiosis with its insect host or to alternative parasitization of plant and insect hosts via insect transmission, as is the case for insect-vectored plant pathogens.}, }
@article {pmid24190164, year = {1994}, author = {Wehr, JD and Le, J and Campbell, L}, title = {Does microbial biomass affect pelagic ecosystem efficiency? An experimental study.}, journal = {Microbial ecology}, volume = {27}, number = {1}, pages = {1-17}, pmid = {24190164}, issn = {0095-3628}, abstract = {Bacteria and other microorganisms in the pelagic zone participate in the recycling of organic matter and nutrients within the water column. The microbial loop is thought to enhance ecosystem efficiency through rapid recycling and reduced sinking rates, thus reducing the loss of nutrients contained in organisms remaining within the photic zone. We conducted experiments with lake communities in 5400-liter mesocosms, and measured the flux of materials and nutrients out of the water column. A factorial design manipulated 8 nutrient treatments: 4 phosphorus levels × 2 nitrogen levels. Total sedimentation rates were greatest in high-N mesocosms; within N-surplus communities, [Symbol: see text]1 µM P resulted in 50% increase in total particulate losses. P additions without added N had small effects on nutrient losses from the photic zone; +2 µM P tanks received 334 mg P per tank, yet after 14 days lost only 69 mg more particulate-P than did control communities. Nutrient treatments resulted in marked differences in phytoplankton biomass (twofold N effect, fivefold P effect in +N mesocosms only), bacterioplankton densities (twofold N-effect, twofold P effects in -N and +N mesocosms), and the relative importance of autotrophic picoplankton (maximum in high NY mesocosms). Multiple regression analysis found that of 8 plankton and water chemistry variables, the ratio of autotrophic picoplankton to total phytoplankton (measured as chlorophyll α) explained the largest portion of the total variation in sedimentation loss rates (65% of P-flux, 57% of N-flux, 26% of total flux). In each case, systems with greater relative importance of autotrophic picoplankton had significantly reduced loss rates. In contrast, greater numbers of planktonic bacteria were associated with increased sedimentation rates and lower system efficiency. We suggest that different microbial components may have contrasting effects on the presumed enhanced efficiency provided by the microbial loop.}, }
@article {pmid24186556, year = {1994}, author = {Powell, JL and Loutit, MW}, title = {The detection of fish pathogenVibrio anguillarum in water and fish using a species-specific DNA probe combined with membrane filtration.}, journal = {Microbial ecology}, volume = {28}, number = {3}, pages = {375-383}, pmid = {24186556}, issn = {0095-3628}, abstract = {The marine bacteriumVibrio anguillarum causes disease in fish worldwide and is particularly devastating in aquaculture. Little is known about the ecology ofV. anguillarum in the environment and how this may relate to the pathogenicity of this organism. Combining membrane filtration and a species-specific DNA probe, culturableV. anguillarum cells were detected in water from three habitats and in chinook salmon (Onchorynchus tshawytscha) tissue samples. Results show that different marine habitats have a marked effect on cell numbers and that water temperature may play a role in the culturability and distribution ofV. anguillarum. Vibrio anguillarum was detected from the gills of salmon within 24 h of transfer of fingerlings from freshwater to seawater, with cell numbers reaching a concentration of 1.9 × 10(2) cells g(-1) tissue 28 days post transfer.Vibrio anguillarum cell numbers were low in the colon throughout the study, andV. anguillarum was not detected in healthy kidney samples. The methodology reported in this paper allows the accurate quantification of culturableV. anguillarum cells and has allowed a preliminary study of the ecology of this species.}, }
@article {pmid24186555, year = {1994}, author = {Powell, JL and Loutit, MW}, title = {Development of a DNA probe using differential hybridization to detect the fish pathogenVibrio anguillarum.}, journal = {Microbial ecology}, volume = {28}, number = {3}, pages = {365-373}, pmid = {24186555}, issn = {0095-3628}, abstract = {The fish pathogenVibrio anguillarum causes significant economic losses in commercially cultured fish species worldwide. At present, identification ofV. anguillarum requires conventional isolation and culturing techniques. Using differential hybridization, a 310 base pairV. anguillarum-specific DNA fragment was isolated for use as a probe. In specificity studies against 19 different bacterial species, including twoVibrio sp. and fish pathogens, and 223 marine bacterial isolates, the probe hybridized exclusively toV. anguillarum strains. The probe also strongly hybridizes to 7 of 9 serotypes tested, with serotype 09 giving a weak probe reaction and serotype O7 negative. The probe allows rapid and accurate detection of both pathogenic and environmental strains ofV. anguillarum.}, }
@article {pmid24186554, year = {1994}, author = {Phelps, TJ and Pfiffner, SM and Sargent, KA and White, DC}, title = {Factors influencing the abundance and metabolic capacities of microorganisms in Eastern Coastal Plain sediments.}, journal = {Microbial ecology}, volume = {28}, number = {3}, pages = {351-364}, pmid = {24186554}, issn = {0095-3628}, abstract = {The abundance and metabolic capacities of microorganisms residing in 49 sediment samples from 4 boreholes in Atlantic Coastal Plain sediments were examined. Radiolabeled time-course experiments assessing in situ mirobial capacities were initiated within 30 min of core recovery. Acetate (1-(14)C- and(3)H-) incorporation into lipids, microbial colony forming units, and nutrient limitations were examined in aliquots of subsurface sediments. Water-saturated sands exhibited activity and numbers of viable microorganisms that were orders of magnitude greater than those of the low permeability dense clays. Increased radioisotope utilization rates were observed after 6-24-h incubation times when sediments were amended with additional water and/or nutrients. Supplements of water, phosphate, nitrate, sulfate, glucose, or minerals resulted in the stimulation of microbial activities, as evidenced by the rate of acetate incorporation into microbial lipids. Additions of water or phosphate resulted in the greatest stimulation of microbial activities. Regardless of depth, sediments that contained >20% clay particles exhibited lower activities and biomass densities, and greater stimulation with abundant water supplementation than did sediments containing >66% sands and hydraulic conductivities > 200 μm sec.(-1).}, }
@article {pmid24186553, year = {1994}, author = {Phelps, TJ and Murphy, EM and Pfiffner, SM and White, DC}, title = {Comparison between geochemical and biological estimates of subsurface microbial activities.}, journal = {Microbial ecology}, volume = {28}, number = {3}, pages = {335-349}, pmid = {24186553}, issn = {0095-3628}, abstract = {Geochemical and biological estimates of in situ microbial activities were compared from the aerobic and microaerophilic sediments of the Atlantic Coastal Plain. Radioisotope time-course experiments suggested oxidation rates greater than millimolar quantities per year for acetate and glucose. Geochemical analyses assessing oxygen consumption, soluble organic carbon utilization, sulfate reduction, and carbon dioxide production suggested organic oxidation rates of nano- to micromolar quantities per year. Radiotracer timecourse experiments appeared to overestimate rates of organic carbon oxidation, sulfate reduction, and biomass production by a factor of 10(3)-10(6) greater than estimates calculated from groundwater analyses. Based on the geochemical evidence, in situ microbial metabolism was estimated to be in the nano- to micromolar range per year, and the average doubling time for the microbial community was estimated to be centuries.}, }
@article {pmid24190096, year = {1993}, author = {Ousley, MA and Lynch, JM and Whipps, JM}, title = {Effect of Trichoderma on plant growth: A balance between inhibition and growth promotion.}, journal = {Microbial ecology}, volume = {26}, number = {3}, pages = {277-285}, doi = {10.1007/BF00176959}, pmid = {24190096}, issn = {0095-3628}, abstract = {The effect of lettuce (Latuca sativa L.) germination and growth in nonsterilized potting compost of 0.1% and 1.0% w/w incorporation of fermenter biomass inocula of six strains of Trichoderma was investigated. Except for strains WT and T35 at 0.1 % w/w, all inocula inhibited germination. Biomass of strains WT, T35, 20, and 47 at 1.0% promoted shoot fresh weight, whereas strains TH1 and 8MF2 were inhibitory. In contrast, when biomass of strains WT, TH1, and 8MF2 was autoclaved and incorporated at 1%, shoot fresh weight was promoted, but the biomass of T35 was inhibitory. None of the strains incorporated at 0.1 % w/w increased shoot fresh weight, and autoclaved biomass of TH1, T35, and 20 incorporated at 0.1% w/w resulted in lower shoot fresh weights in comparison with uninoculated controls. The shoot dry weight of lettuce seedlings could be enhanced by germinating seeds in uninoculated compost and after five days' growth transferring them into WT-inoculated compost. Inoculum of strain TH1 when applied using this method was very inhibitory. With WT the degree of increase in shoot fresh weight and germination rate declined as the fermentation time to produce inocula was increased.}, }
@article {pmid24190095, year = {1993}, author = {Rodrigue, L and Barras, MJ and Marcotte, H and Lavoie, MC}, title = {Bacterial colonization of the oral cavity of the BALB/c mouse.}, journal = {Microbial ecology}, volume = {26}, number = {3}, pages = {267-275}, pmid = {24190095}, issn = {0095-3628}, abstract = {The acquisition of the human oral bacterial flora follows a relatively well known sequence of succession that can be influenced by various host factors. These factors have not been studied in the mouse. In the present work, we followed the bacterial colonization of the oral cavity of mice from birth, and tested our mouse model for its suitability in studying the influence of weaning and puberty on the indigenous oral bacterial flora. We observed that the first colonizers were staphylococci, followed by lactobacilli. The proportions of these two predominant bacteria fluctuated for a period of 30-50 days, but evolved towards the proportions previously observed among the indigenous bacterial species of 6-8 week-old BALB/c male mice (predominantly Lactobacillus murinus and Staphylococcus aureus). The weaning period significantly altered the equilibrium among the oral bacterial flora. This equilibrium was not significantly modified during puberty.}, }
@article {pmid24190094, year = {1993}, author = {Plante, C and Jumars, P}, title = {Immunofluorescence assay for effects on field abundance of a naturally occurring pseudomonad during passage through the gut of a marine deposit feeder, Abarenicola pacifica.}, journal = {Microbial ecology}, volume = {26}, number = {3}, pages = {247-266}, pmid = {24190094}, issn = {0095-3628}, abstract = {In a seasonal study we used immunofluorescence to follow a specific bacterial population, as well as total numbers, through the fore-, mid-, and hindgut of a deposit feeder, Abarenicola pacifica. We chose a pseudomonad because of its high ambient abundance. On five dates, we collected A. pacifica gut contents, with concurrent measurements of sedimentary food quality (chlorophyll a, protein, bacterial abundance), animal egestion rates (inversely proportional to gut residence time), and temperature. Increasing bacterial numbers from ingested sediment to foregut contents, and decreases from foregut to midgut indicate significant selection and digestion, respectively, of both the pseudomonad and the total bacterial community. Inverse correlations between egestion rate and digestive removal of bacteria offer some support for the prediction that digestion of bacteria is proportional to time spent exposed to digestive enzymes, although the significance of the associated statistical tests is marginal. No hindgut growth of the pseudomonad was observed, likely due to the short gut residence time of A. pacifica. The pseudomonad showed variation of less than a factor of 3 in its ambient sedimentary abundance over the year.}, }
@article {pmid24190093, year = {1993}, author = {Jolly, JM and Lappin-Scott, HM and Anderson, JM and Clegg, CD}, title = {Scanning electron microscopy of the gut microflora of two earthworms: Lumbricus terrestris and Octolasion cyaneum.}, journal = {Microbial ecology}, volume = {26}, number = {3}, pages = {235-245}, pmid = {24190093}, issn = {0095-3628}, abstract = {Scanning electron microscopy was used to investigate the presence of microorganisms, probably bacteria, on the gut surface of earthworms. The washed surfaces of the intestines of two earthworms, Lumbricus terrestris and Octolasion cyaneum, were examined. Numerous organisms resembling bacteria were observed throughout the gut, some in situations suggesting attachment. Compared with similar investigations in other invertebrates, there were fewer bacteria, showing less morphological diversity, on the earthworm gut surface. The majority of organisms viewed were coccoid, some were filamentous, and a few rod-shaped cells were observed. Cocci, often in chains, were seen in the foregut of both species. Although cocci were also numerous in the midgut region, particularly in the typhlosole, in O. cyaneum tufts of segmented, filamentous organisms were also seen with some segments resembling spores. Fewer organisms were found in the hindgut, but in L. terrestris there were segmented, filamentous organisms, attached to the epithelium by way of a "socket-like" structure, similar to that by which segmented, filamentous bacteria (SFBs) are attached to the ileum of rats and mice. Transmission electron microscopy of the hindgut of L. terrestris was undertaken to explore the structure and attachment of SFBs to the gut epithelium. However, although a few rod-shaped bacteria were observed, no SFBs were located. The observations reported here provide evidence that earthworms have an attached gut microflora of filamentous microorganisms which are probably indigenous, and as far as we are aware this is the first published report of such findings in these invertebrates.}, }
@article {pmid24190092, year = {1993}, author = {Helander, ML and Neuvonen, S and Sieber, T and Petrini, O}, title = {Simulated acid rain affects birch leaf endophyte populations.}, journal = {Microbial ecology}, volume = {26}, number = {3}, pages = {227-234}, pmid = {24190092}, issn = {0095-3628}, abstract = {Endophytes were frequently isolated from mountain birch (Betula pubescens var. tortuosa (Ledeb.) Nyman) leaves at a subarctic site where natural air pollution is low. We tested whether simulated acid rain had any influence on the occurrence of endophytes. Dry controls with only ambient rain and irrigated controls treated with spring water of pH 6 were compared with acid treatments at pH 3 and pH 4, prepared by adding both sulphuric and nitric acids. Treatments began in 1985 and leaf samples were taken twice during the summer of 1992. Leaves were surface sterilized, five leaf disks from each leaf placed on malt extract agar, and growing colonies were counted and identified. The most frequently isolated endophyte from birch leaves was a Fusicladium anamorph of Venturia sp. (88% of all the isolates in July and 75% of all the isolates in August), followed by a sterile mycelium and Melanconium sp. The number of endophytes isolated and the species number increased from July to August. Endophytes were most frequently isolated from the basal part of the midrib. The percentage of colonization by endophytes was similar in short and long shoots. More endophytes were isolated from leaves of branches taken at 1 m height than at 2 m height. The stronger acid rain treatment (pH 3) reduced by approximately 25% the number of isolated endophytes in August. Treatments did not have any effect on species composition of endophyte assemblages in birch leaves.}, }
@article {pmid24190091, year = {1993}, author = {Lee, MH and Hwang, MO and Choi, SY and Min, KH}, title = {n-Alkane dissimilation by Rhodopseudomonas sphaeroides transferred OCT plasmid.}, journal = {Microbial ecology}, volume = {26}, number = {3}, pages = {219-226}, pmid = {24190091}, issn = {0095-3628}, abstract = {The OCT plasmid from Pseudomonas maltophilia N246-1 was transferred to Rhodopseudomonas sphaeroides M1 with very low frequency (1.4-1.9 × 10(-5) per recipient cell at pH 7-8 for a 3-hour reaction time). P. maltophilia N246-1 was able to utilize C8-C14 of n-alkanes, whereas R. gas-liquid chromatography determined that the broad range of carbon numbers of n-alkanes in crude oil was remarkably degraded by the transconjugant, R. sphaeroides M1-C1, compared with donor strain N246-1. The fact that donor and transconjugant strains simultaneously lost the capacity to utilize n-alkanes on L-broth medium suggests that the OCT plasmids are unstable. It was found that the OCT plasmid of P. maltophilia N246 was incompatible with the IncP-2 group of P. aeruginosa KCTC 11245.}, }
@article {pmid24190090, year = {1993}, author = {Tulonen, T}, title = {Bacterial production in a mesohumic lake estimated from [(14)C]leucine incorporation rate.}, journal = {Microbial ecology}, volume = {26}, number = {3}, pages = {201-217}, pmid = {24190090}, issn = {0095-3628}, abstract = {Incorporation of [(14)C]leucine into proteins of bacteria was studied in a temperate mesohumic lake. The maximum incorporation of [(14)C] leucine was reached at a concentration of 30 nM determined in dilution cultures. Growth experiments were used to estimate factors for converting leucine incorporation to bacterial cell numbers or biomass. The initially high conversion factors calculated by the derivative method decreased to lower values after the bacteria started to grow. Average conversion factors were 7.09 × 10(16) cells mol(-1) and 7.71 × 10(15) μm(3) mol(-1), if the high initial values were excluded. Using the cumulative method, the average conversion factor was 5.38 × 10(15) μm(-3) mol(-1) I . The empirically measured factor converting bacterial biomass to carbon was 0.36 pg C μm(-3) or 33.1 fg C cell(-1). Bacterial production was highest during the growing season, ranging between 1.8 and 13.2 μg C liter(-1) day(-1), and lowest in winter, at 0.2-2.9 μg C liter(-1) day(-1). Bacterial production showed clear response to changes in the phytoplankton production, which indicates that photosynthetically produced dissolved compounds were used by bacteria. In the epilimnion bacterial production was, on average, 19-33% of primary production. Assuming 50% growth efficiency for bacteria, the allochthonous organic carbon could have also been an additional energy and carbon source for bacteria, especially in autumn and winter. In winter, a strong relationship was found between temperature and bacterial production. The measuring of [(14)C]leucine incorporation proved to be a simple and useful method for estimating bacterial production in humic water. However, an appropriate amount of [(14)C]leucine has to be used to ensure the maximum uptake of label and to minimize isotope dilution.}, }
@article {pmid24190089, year = {1993}, author = {Lambert, DL and Taylor, PN and Goulder, R}, title = {Between-site comparison of freshwater bacterioplankton by DNA hybridization.}, journal = {Microbial ecology}, volume = {26}, number = {3}, pages = {189-200}, pmid = {24190089}, issn = {0095-3628}, abstract = {Natural assemblages of freshwater bacterioplankton in enriched lowland rivers had greater cell-specific metabolic activity than those in gravel-pit ponds. Similarly, cell-specific activity and mean cell Size in calcareous headstreams tended to be greater than in intermittently-acid headstreams on millstone grit. DNA was extracted and purified from bacterioplankton assemblages, and between-site comparisons were made in terms of percentage similarity as indicated by DNA hybridization. Cluster analysis, using percentage-similarity matrices, placed bacterioplankton assemblages from different site types into distinct groups. This suggested that between-site physiological differences were related to intrinsically different bacterial composition rather than to different physiological response to different environmental conditions by essentially similar bacterial assemblages.}, }
@article {pmid24190011, year = {1993}, author = {Kämpfer, P and Steiof, M and Becker, PM and Dott, W}, title = {Characterization of chemoheterotrophic bacteria associated with the in situ bioremediation of a waste-oil contaminated site.}, journal = {Microbial ecology}, volume = {26}, number = {2}, pages = {161-188}, pmid = {24190011}, issn = {0095-3628}, abstract = {In the course of an in situ bioremediation, different hydrologically controllable test plots were installed on the ground of a waste-oil contaminated site, and continuously injected with nutrient solution and the electron acceptors NO3 (-), O2, and H2O2. In a two-year period, groundwater samples obtained from different recovery wells within these field plots, in addition to subsoil samples, were monitored for several chemical and microbiological parameters. The removal of hydrocarbons observed in the water samples could not unambiguously be attributed to biodegradation, and was probably caused by groundwater treatment measures. However, chemical (gaschromatographic) and microbiological data from the subsoil samples indicated a biological degradation of pollutants. Analysis of the groundwater samples of the different test plots revealed only minor quantitative differences. With time, only a slight increase in bacterial numbers on different media, including hydrocarbon-agar, was observed. In general, chemical and microbiological analyses of groundwater samples cannot replace analyses of subsoil samples for a sufficient documentation of in situ remediation processes in subsoil. From the groundwater and subsoil samples, 3,446 pure cultures, obtained from R2A agar, were characterized morphologically and physiologically, and identified in order to study the culturable bacterial communities. Several qualitative differences in composition and diversity of the bacterial communities among the test plots were observed. More than 70 different species or taxonomic groups (most of them known as hydrocarbon degrading taxa) could be identified from the groundwater samples; these were mainly the Gram-negative genera Acinetobacter, Alcaligenes, Comamonas, Hydrogenophaga, Pseudomonas, Flavobacterium/Flexibacter/Cytophaga, and others. A high proportion of Gram-positive organisms (42.5%), belonging to Bacillus and the various genera of coryneform and nocardioform organisms, were isolated from the subsoil samples.}, }
@article {pmid24190010, year = {1993}, author = {Haldeman, DL and Amy, PS and Ringelberg, D and White, DC}, title = {Characterization of the microbiology within a 21 m(3)section of rock from the deep subsurface.}, journal = {Microbial ecology}, volume = {26}, number = {2}, pages = {145-159}, pmid = {24190010}, issn = {0095-3628}, abstract = {The distribution of aerobic chemoheterotrophic microorganisms within a 21 m3 section of deep subsurface rock was determined. Nineteen samples for microbiological analysis were aseptically taken by hand from the walls of a 400 m deep subsurface tunnel after an alpine miner created fresh rock faces 0.76, 1.52, 2.28, and 3.04 m into the tunnel wall. The direct counts were several orders of magnitude greater than viable counts in all samples. One of each morphologically distinct bacterial type from each sample was purified and analyzed for fatty acid methyl esters (FAME) using the Microbial Identification System (MIDI). Numbers of bacterial types, diversity, and equitability of recoverable microbial communities were the same or similar using either morphotype or FAME analyses as the basis for distinguishing between bacterial types. Twenty-nine genera (Euclidean distance of [Symbol: see text]25) were found within the rock section, while 28 of the 210 bacterial types isolated were nonculturable under the growth regime required for cluster analysis. Most isolates clustered at the genus level with Arthrobacter, Gordona, and Acinetobacter. Two genera, containing 16 isolates, were unmatched to known organisms within the MIDI data base and clustered with other isolates at a Euclidean distance greater than 50. While some species (Euclidean distance [Symbol: see text]10) were recovered from multiple sites within the rock section, most were found at 1-3 sites and usually without a definitive pattern of distribution.}, }
@article {pmid24190009, year = {1993}, author = {Inglis, GD and Sigler, L and Goette, MS}, title = {Aerobic microorganisms associated with alfalfa leafcutter bees (megachile rotundata).}, journal = {Microbial ecology}, volume = {26}, number = {2}, pages = {125-143}, pmid = {24190009}, issn = {0095-3628}, abstract = {Characterization of microorganisms associated with alfalfa leaf-cutter bee (Megachile rotundata) nectar, pollen, provisions, larval guts, and frass (excreta) in Alberta demonstrated a varied aerobic microflora. Yeasts were isolated frequently from nectar, pollen, and provisions but rarely from guts or frass. The most prevalent yeast taxa were: Candida bombicola, Cryptococcus albidus, Metschnikowia reukaufii, and Rhodotorula glutinis. Although few filamentous fungi were found in nectar, they were frequently isolated from pollen and provisions; the predominant taxa were Alternaria alternata, Cladosporium cladosporioides, C. herbarum, Epicoccum nigrum, and Penicillium chrysogenum. Bacteria, including species of Bacillus, Corynebacterium, Micrococcus, and the actinomycete Streptomyces, also were prevalent in provisions and/or on pollen. In general, the diversity of microorganisms isolated from alimentary canals and frass was lower than from nectar, pollen, and provisions. Bacillus firmus, B. licheniformis, B. megaterium, B. pumilus, and Streptomyces spp. were the most frequently isolated bacteria, whereas Trichosporonoides megachiliensis was the most common filamentous fungus isolated from larval guts and/or frass. These taxa may be part of the resident microflora of the alimentary canal. Populations of bacteria and filamentous fungi, but not yeasts, were larger from Ascosphaera aggregata-infected larvae than from healthy larvae. However, with the exception of Aspergillus niger and T. megachiliensis in frass from healthy larvae, no taxon of filamentous fungi was conspicuously present or absent in infected larvae, healthy larvae, or their frass.}, }
@article {pmid24190008, year = {1993}, author = {Iriberri, J and Ayo, B and Unanue, M and Barcina, I and Egea, L}, title = {Channeling of bacterioplanktonic production toward phagotrophic flagellates and ciliates under different seasonal conditions in a river.}, journal = {Microbial ecology}, volume = {26}, number = {2}, pages = {111-124}, pmid = {24190008}, issn = {0095-3628}, abstract = {The objective of this study was to analyze the flux of biomass through the communities of bacteria and phagotrophic protists in the cold and warm conditions occurring seasonally in Butrón River. Bacterial and heterotrophic protistan (flagellate and ciliate) abundance was determined by epifluorescence direct counts; protistan grazing on planktonic bacteria was measured from fluorescently labeled bacteria uptake rates; and the estimate of bacterial secondary production was obtained from [(3)H]thymidine incorporation rates. The abundance of bacterial, flagellate, and ciliate communities was similar during cold and warm situations. However, we observed that estimates of dynamic parameters, i.e., secondary bacterial production and protistan grazing, in both situations were noticeably different. In the warm situation, grazing rates of flagellates and ciliates (bacteria per protist per hour) were, respectively, 7 times and 18 times higher than those determined in the cold situation, and the grazing rates of the protistan communities (bacteria per protists present in 1 ml of water per hour) increased up to 5 times in the case of flagellates and 42 times in the case of ciliates. Estimates of bacterial secondary production were also higher during the warm situation, showing a ninefold increase. The percentage of bacterial production preyed upon by flagellates or ciliates was not significantly different between the two conditions. These results showed that in the different conditions of a system, the flux of biomass between the trophic levels may be quite different although this process may not be reflected in the abundance of each community of bacteria, flagellates, and ciliates.}, }
@article {pmid24190007, year = {1993}, author = {Pentecost, A}, title = {Field relationships between scytonemin density, growth, and irradiance in cyanobacteria occurring in low illumination regimes.}, journal = {Microbial ecology}, volume = {26}, number = {2}, pages = {101-110}, pmid = {24190007}, issn = {0095-3628}, abstract = {In situ measurements of ultraviolet (UV) irradiance, carbon fixation, and scytonemin pigmentation were made on Scytonema populations from contrasting localities in England. Significant negative correlations were obtained between the following variate pairs: pigmentation and UV irradiance; pigmentation and carbon fixation rate. A significant positive correlation was found between pigmentation and sheath thickness.The negative correlation between pigmentation and UV irradiance was unexpected and appeared contrary to the results of previous studies, which indicated a positive correlation between the variates and the recognition of scytonemin as a radiation shield. However, by considering how radiation damage is related to cell division and the water relations of the sites investigated, it was shown that scytonemin is still functioning as a radiation shield, even in shaded sites. Rivularia colonies produced scytonemin only upon their upper, sun-exposed surfaces and were positively correlated with UV irradiance. This paper also describes the successful use of some new and inexpensive techniques to measure pigments in cyanobacterium sheaths, and integrated in situ UV-irradiance.}, }
@article {pmid24190006, year = {1993}, author = {Sander, BC and Kalff, J}, title = {Factors controlling bacterial production in marine and freshwater sediments.}, journal = {Microbial ecology}, volume = {26}, number = {2}, pages = {79-99}, pmid = {24190006}, issn = {0095-3628}, abstract = {We collected benthic bacterial production data measured by (3)H thymidine incorporation (TTI) (25 studies), frequency of dividing cells (FDC) (3 studies), dark-C02 assimilation (1 study) and (3)H-adenine uptake (2 studies) from the literature, which included 18 marine, 6 river, and 2 lake studies. In all of the studies that used the TTI method, (3)H-DNA was isolated and incubations were carried out at in situ temperatures. Most of the researchers also determined (3)H-DNA extraction efficiencies and isotope dilution, thus interpretable estimates of bacterial production were used in the analysis. In marine sediments, bacterial production rates were linked to bacterial biomass, bacterial abundance, sediment organic matter, temperature, and sediment chlorophyll a, with these variables explaining between 40% and 68% of the variation in production rates. Simple relationships between production and bacterial biomass or bacterial abundance, or between production and sediment organic matter, were improved by also including temperature in the analysis of marine sediments. Sediment organic matter explained an appreciable fraction (58%) of the observed production in freshwater sediments. Temperature was the most powerful predictor of the observed variability in specific growth rates (r (2) = 0.48 and r (2) = 0.58) in marine and freshwater sediments, respectively. Thus, bacterial production and specific growth rates are most closely linked to substrate supply and temperature in marine and freshwater sediments.}, }
@article {pmid24189989, year = {1993}, author = {Kieft, TL and Amy, PS and Brockman, FJ and Fredrickson, JK and Bjornstad, BN and Rosacker, LL}, title = {Microbial abundance and activities in relation to water potential in the vadose zones of arid and semiarid sites.}, journal = {Microbial ecology}, volume = {26}, number = {1}, pages = {59-78}, pmid = {24189989}, issn = {0095-3628}, abstract = {Numbers and activities of microorganisms were measured in the vadose zones of three arid and semiarid areas of the western United States, and the influence of water availability was determined. These low-moisture environments have vadose zones that are commonly hundreds of meters thick. The specific sampling locations chosen were on or near U.S. Department of Energy facilities: the Nevada Test Site (NTS), the Idaho National Engineering Laboratory (INEL), and the Hanford Site (HS) in southcentral Washington State. Most of the sampling locations were uncontaminated, but geologically representative of nearby locations with storage and/or leakage of waste compounds in the vadose zone. Lithologies of samples included volcanic tuff, basalt, glaciofluvial and fluvial sediments, and paleosols (buried soils). Samples were collected aseptically, either by drilling bore-holes (INEL and HS), or by excavation within tunnels (NTS) and outcrop faces (paleosols near the HS). Total numbers of microorganisms were counted using direct microscopy, and numbers of culturable microorganisms were determined using plate-count methods. Desiccation-tolerant microorganisms were quantified by plate counts performed after 24 h desiccation of the samples. Mineralization of (14)C-labeled glucose and acetate was quantified in samples at their ambient moisture contents, in dried samples, and in moistened samples, to test the hypothesis that water limits microbial activities in vadose zones. Total numbers of microorganisms ranged from log 4.5 to 7.1 cells g(-1) dry wt. Culturable counts ranged from log <2 to 6.7 CFU g(-1) dry wt, with the highest densities occurring in paleosol (buried soil) samples. Culturable cells appeared to be desiccation-tolerant in nearly all samples that had detectable viable heterotrophs. Water limited mineralization in some, but not all samples, suggesting that an inorganic nutrient or other factor may limit microbial activities in some vadose zone environments.}, }
@article {pmid24189988, year = {1993}, author = {Mariano, RL and McCarter, SM}, title = {Epiphytic survival of Pseudomonas viridiflava on tomato and selected weed species.}, journal = {Microbial ecology}, volume = {26}, number = {1}, pages = {47-58}, pmid = {24189988}, issn = {0095-3628}, abstract = {A rifampicin-nalidixic acid mutant of Pseudomonas viridiflava (PV) was studied in the field and greenhouse with respect to its epiphytic survival on the roots and foliage of a susceptible (FM 6203) and resistant (Ontario 7710) tomato cultivar and 16 weed species. In the field, populations varied between years, which was attributed to differences in environmental conditions. Hot, dry conditions caused rapid decline or elimination of populations. Some hosts were more conducive than others in promoting epiphytic growth, and generally, roots were better survival sites than foliage. Some hosts such as johnsongrass, lambsquarters, pigweed, prickly sida, and red sorrel had no detectable populations of PV on foliage 2 weeks after inoculation. (Plants had been misted with a 10(8) cfu/ml suspension until run off occurred.) PV was recovered at week 4 on the foliage of the two tomato cultivars, beggarweed, jimsonweed, morning glory, smooth vetch, and wild mustard, and was recovered until week 16 on roots of buckhorn plantain in the field and for the same period on the ground cherry in the field and greenhouse. In scanning electron microscopy studies, PV was observed to survive as microcolonies in depressions between epidermal cells, around trichomes, along veins, and sometimes around stomates of tomato and beggarweed. Bacterial cells sometimes were held together and to the leaf surface by fibril-like strands. These studies show that PV does have an epiphytic stage on both tomato and certain weed species. However, the epidemiological significance of the epiphytic stage is probably dependent on environmental conditions.}, }
@article {pmid24189987, year = {1993}, author = {Mansfield, SD and Bärlocher, F}, title = {Seasonal variation of fungal biomass in the sediment of a salt marsh in New Brunswick.}, journal = {Microbial ecology}, volume = {26}, number = {1}, pages = {37-45}, pmid = {24189987}, issn = {0095-3628}, abstract = {In a marsh in New Brunswick, Canada, belowground biomass of Spartina alterniflora consistently exceeded aboveground biomass by a factor of approximately 9. Both values peaked in July. Redox potential of the sediment was negative at all levels tested (2, 6, and 11 cm below surface), and was negatively correlated with depth. Concentrations of ergosterol, a sterol typical of higher fungi, were negatively correlated with redox potential and were highest in roots and rhizomes in July and August, 1-3 cm below the surface. These maxima corresponded to a fungal content of approximately 0.6% per ash-free dry mass of Spartina material. Balsa wood panels buried in anaerobic salt marsh sediment were colonized by fungi within 12 weeks. Eight fungal species isolated from S. alterniflora roots did not grow in the absence of oxygen, but were able to grow downward into an anaerobic medium.}, }
@article {pmid24189986, year = {1993}, author = {Gauthier, MJ and Flatau, GN and Clément, RL and Munro, PM}, title = {The loss of culturability by Escherichia coli cells in seawater depends on availability of phosphate ions and phosphate transport systems.}, journal = {Microbial ecology}, volume = {26}, number = {1}, pages = {29-35}, pmid = {24189986}, issn = {0095-3628}, abstract = {Using strains with or without the PhoE porin or different components of the phosphate regulon, we determined that maintenance of the culturability of Escherichia coli in seawater depended significantly on the presence of structures allowing access of phosphate ions to the periplasm, then to the cytoplasm of cells. Cells totally deprived of the two main phosphate transport systems (Pit, Pst) exhibited the highest loss of culturability. Most of this effect resulted from the loss of the high-affinity Pst system, and more specifically that of the periplasmic phosphate-binding protein PhoS. Survival was enhanced in seawater supplemented with phosphate (0.5 mM), whether or not these structures were present. From an ecological point of view, it is assumed that the presence of phosphate ions, even at low concentrations, can influence the behavior of E. coli cells in seawater.}, }
@article {pmid24189985, year = {1993}, author = {Feliatra, F and Bianchi, M}, title = {Rates of nitrification and carbon uptake in the Rhône River plume (northwestern Mediterranean Sea).}, journal = {Microbial ecology}, volume = {26}, number = {1}, pages = {21-28}, pmid = {24189985}, issn = {0095-3628}, abstract = {Nitrification rates were measured along a salinity gradient in the Rhône River estuary, using specific inhibitors (allylthiourea and chlorate) coupled with the measurement of change in nitrite concentration and inorganic carbon uptake by nitrifiers. Rates of ammonium and nitrite oxidation were similar up to 15 practical salinity units (from 1 to 2 μmol N oxidized liter(-1) day(-1)). For higher salinities, nitrite and ammonium oxidation rates were 0.14 and 0.23 μmol N oxidized liter(-1) day(-1), respectively. Ammonium oxidizers assimilated 19-150 × 10-3 μmol C liter(-1) day(-1), while nitrite oxidizers fixed 4.8-72.6 × 10-3 μmol C liter(-1) day(-1). The amounts of nitrogen oxidized and C incorporated demonstrated a linear correlation (r (2) > 0.99). The ratio of N oxidized to C incorporated ranged between 14.3 to 12.3 for ammonium oxidizers, and between 31.6 and 29 for nitrite oxidizers, the lower values being measured in seawater.}, }
@article {pmid24189984, year = {1993}, author = {Tumber, VP and Robarts, RD and Arts, MT and Evans, MS and Caldwell, DE}, title = {The influence of environmental factors on seasonal changes in bacterial cell volume in two prairie saline lakes.}, journal = {Microbial ecology}, volume = {26}, number = {1}, pages = {9-20}, pmid = {24189984}, issn = {0095-3628}, abstract = {Bacterial biovolumes of hypertrophic Humboldt Lake (total dissolved solids = 3.3 g liter(-1); 6 m deep) and oligotrophic Redberry Lake (total dissolved solids = 20.9 g liter(-1); 17 m deep), Saskatchewan, were measured concurrently with a variety of environmental variables to identify the major factors correlated with volume changes. There was no difference (P > 0.05) in mean bacterial volume between Redberry Lake (0.084 ± 0.034 μm(3) SD) and Humboldt Lake (0.083 ± 0.021 μm(3) SD). Statistical analyses suggested there were marked differences in the factors associated with the pronounced seasonality of bacterial cell volumes in these two lakes. Variance in bacterial volume in the epilimnion of Redberry Lake was best explained by a multivariate regression model which included ciliate abundance and chlorophyll concentration (r (2) = 0.96). The model accounting for changes in hypolimnetic bacterial volume included ciliate numbers and primary production (r (2) = 0.94), of the measured variables. Bacterial volume in Humboldt Lake was most highly correlated with primary production (r (2) = 0.59). Bacterial production (estimated as the rate of thymidine incorporation into DNA) and growth (thymidine incorporation rate normalized to cell numbers) were not correlated to cell volume, with the exception of cocci volume in Humboldt Lake.}, }
@article {pmid24189983, year = {1993}, author = {Berman, T and Kaplan, B and Chava, S and Parparova, R and Nishri, A}, title = {Effects of iron and chelation on Lake Kinneret bacteria.}, journal = {Microbial ecology}, volume = {26}, number = {1}, pages = {1-8}, pmid = {24189983}, issn = {0095-3628}, abstract = {The response of natural populations of bacteria (prepared by passing Lake Kinneret water through 1 μm filters) to additions of Fe(2+) and/or the chelator ethylenediaminetetraacetic acid (EDTA) was followed by measuring the incorporation of (3)H-thymidine into >0.2 μm particulates, and also by determining the increments in cell numbers after 24 h. In most cases, a stimulation of (3)H-thymidine incorporation was observed in supplemented samples relative to untreated controls after 3 and 24 h incubation. The increase in bacterial numbers was also enhanced by these supplements. Generally, EDTA alone evoked a greater stimulation than Fe(2+); combined supplements gave no further increase. This response pattern appeared consistently throughout the year in samples taken from near-surface lake waters. These results suggest that the availability of iron or chelators may play an important role in regulating bacterial metabolism and growth even in aquatic ecosystems like Lake Kinneret where ambient concentrations of total Fe are relatively high.}, }
@article {pmid24189925, year = {1993}, author = {Johnston, CG and Vestal, JR}, title = {Biogeochemistry of oxalate in the antarctic cryptoendolithic lichen-dominated community.}, journal = {Microbial ecology}, volume = {25}, number = {3}, pages = {305-319}, pmid = {24189925}, issn = {0095-3628}, abstract = {Cryptoendolithic (hidden in rock) lichen-dominated microbial communities from the Ross Desert of Antarctica were shown to produce oxalate (oxalic acid). Oxalate increased mineral dissolution, which provides nutrients, creates characteristic weathering patterns, and may ultimately influence the biological residence time of the community. Oxalate was the only organic acid detectable by HPLC, and its presence was verified by GC/MS. Community photosynthetic metabolism was involved in oxalate production since rates of (14)C-oxalate production from (14)C02 were higher in light than in dark incubations. Flaking of the sandstone at the level of the lichen-dominated zone a few millimeters beneath the rock surface can be explained by dissolution of the sandstone cement, which was enhanced by Si, Fe, and Al oxalate complex formation. Added oxalate was observed to increase the solubility of Si, Fe, Al, P, and K. Oxalate's ability to form soluble trivalent metal-oxalate complexes correlated with the observed order of metal oxide depletion from the lichen-dominated zone (Mn > Fe > Al). Thermodynamic calculations predict that Fe oxalate complex formation mobilizes amorphous Fe oxides (ferrihydrite) in the lichen-dominated zone, and where oxalate is depleted, ferrihydrite should precipitate. Hematite, a more crystalline Fe oxide, should remain solid at in situ oxalate concentrations. Oxalate was not a carbon source for the indigenous heterotrophs, but the microbiota were involved in oxalate mineralization to CO2, since oxalate mineralization was reduced in poisoned incubations. Photooxidation of oxalate to C02 coupled with photoreduction of Fe(Ill) may be responsible for oxalate removal in situ, since rates of (14)C-oxalate mineralization in dark incubations were at least 50% lower than those in the light. Removal of oxalate from Si, Fe, and Al complexes should allow free dissolved Si, Fe, and Al to precipitate as amorphous silicates and metal oxides. This may explain increased siliceous crust (rock varnish or desert varnish) formation near the surface of colonized rocks were light intensity is greatest.}, }
@article {pmid24189924, year = {1993}, author = {Scheu, S and Wirth, S and Eberhardt, U}, title = {Decomposition of (14)C-labeled cellulose substrates in litter and soil from a beechwood on limestone.}, journal = {Microbial ecology}, volume = {25}, number = {3}, pages = {287-304}, pmid = {24189924}, issn = {0095-3628}, abstract = {The decomposition of three different (14)C-labeled cellulose substrates (plant holocellulose, plant cellulose prepared from (14)C-labeled beech wood (Fagus sylvatica) and bacterial cellulose produced by Acetobacter xylinum) in samples from the litter and mineral soil layer of a beechwood on limestone was studied. In a long-term (154 day) experiment, mineralization of cellulose materials, production of (14)C-labeled water-soluble compounds, and incorporation of (14)C in microbial biomass was in the order Acetobacter cellulose > holocellulose > plant cellulose in both litter and soil. In general, mineralization of cellulose, production of (14)C-labeled water-soluble compounds, and incorporation of (14)C in microbial biomass were more pronounced, but microbial biomass (14)C declined more rapidly in litter than in soil. In short-term (14 day) incubations, mineralization of cellulose substrates generally corresponded with cellulase and xylanase activities in litter and soil. Pre-incubation with trace amounts of unlabeled holocellulose significantly increased the decomposition of (14)C-labeled cellulose substrates and increased cellulase activity later in the experiment but did not affect xylanase activity. The sum of (14)CO2 production, (14)C in microbial biomass, and (14)C in water-soluble compounds is considered to be a sensitive parameter by which to measure cellulolytic activity in soil and litter samples in short-term incubations. Shorter periods than 14 days are preferable in assays using Acetobacter cellulose, because the decomposition of this substrate is more variable than that of holocellulose and plant cellulose.}, }
@article {pmid24189923, year = {1993}, author = {Pahm, MA and Alexander, M}, title = {Selecting inocula for the biodegradation of organic compounds at low concentrations.}, journal = {Microbial ecology}, volume = {25}, number = {3}, pages = {275-286}, pmid = {24189923}, issn = {0095-3628}, abstract = {The inability of many organisms to degrade pollutants at low concentrations is a problem when selecting inocula for bioremediation of sites with these low concentrations. Thus, a study was conducted to determine the effect of low concentrations of p-nitrophenol (PNP) on growth of four PNP-degrading bacteria and their abilities to metabolize low concentrations of the compound in culture and samples from an oligotrophic lake. PNP did not increase the growth rates of Flavobacterium sp. M4, Pseudomonas sp. K, Flavobacterium sp. M1, and Pseudomonas sp. SP3 at concentrations of less than 2, 4, 10, and 100 ng/ml, respectively, when it was the sole added carbon source in culture, but it stimulated multiplication at higher concentrations. In liquid culture with the nitro compound as sole added carbon source, the four bacteria extensively mineralized PNP at 50 and 100 ng/ml, and three of the four degraded much of the substrate at 25 ng/ml. Pseudomonas sp. SP3 mineralized more than 20% but the two Flavobacterium strains converted less than 10% of the substrate to C02 at 10 ng/ml, and none of the three mineralized more than 5% at 1 and 5 ng PNP/ml. Under conditions where more than 99% of the radioactivity from (14)C-PNP added at 1 ng/ml remained in solution, two of the isolates formed organic products. Pseudomonas sp. K had no activity at 1, 5, and 10 ng/ml. In contrast, when each of the bacteria was separately inoculated into samples of water from an oligotrophic lake and from a well in which PNP was not biodegraded, the bacteria were able to mineralize as little as 1 ng PNP/ml. The addition to a salts solution of 10 ng of glucose per ml resulted in mineralization of PNP at concentrations too low to be mineralized when the nitro compound was the sole source of added carbon. Bacteria may thus be able to mineralize substrates in natural waters at concentrations below those suggested by tests conducted in culture media, possibly because of the availability of other carbon sources for the bacteria.}, }
@article {pmid24189922, year = {1993}, author = {Delille, D and Siron, R}, title = {Effect of dispersed oil on heterotrophic bacterial communities in cold marine waters.}, journal = {Microbial ecology}, volume = {25}, number = {3}, pages = {263-273}, pmid = {24189922}, issn = {0095-3628}, abstract = {Mesocosm studies were conducted to evaluate the effect of dispersed oil on total and heterotrophic bacterial communities of under-ice seawater from the St. Lawrence Estuary. A regular survey of bacterial changes in the oil-contaminated seawater was performed during a two week period. The bacterial community structure was investigated by carrying out 27 morphological and biochemical tests on 168 isolated strains. The results show a detectable but transient response of the bacterial community to crude oil addition. While total bacterial counts were approximately constant during the experiment, dispersed oil induced an increase in heterotrophic bacterial microflora (from 10(4) to 10(5) bacteria ml(-1) after two weeks of contamination). The dispersed oil appeared to have an inhibitory effect on some components of the bacterial community. A decrease of most probable number values was observed just after addition of crude oil in the most polluted tanks and one day later in the less polluted tank. However, except for the most polluted tank, this adverse effect disappeared rapidly. While the dispersed oil induced a total disappearance of some components of the bacterial community in the most polluted tank, the structure of the bacterial community in the less polluted tank appeared relatively unchanged after 14 days of contamination.}, }
@article {pmid24189921, year = {1993}, author = {Gasol, JM}, title = {Benthic flagellates and ciliates in fine freshwater sediments: Calibration of a live counting procedure and estimation of their abundances.}, journal = {Microbial ecology}, volume = {25}, number = {3}, pages = {247-262}, pmid = {24189921}, issn = {0095-3628}, abstract = {Despite the recognized importance of protozoans (flagellates and ciliates) as predators of bacteria, there are very few estimates of their abundance in fine sediments of freshwater lakes. This is due, in part, to the lack of a standard methodology. Because of the low concentration of protists in relation to particles, epifluorescence counts can not always be used. Instead, dilution followed by live counting was used to solve the masking by sediment particles. One to twenty μ1 sample aliquots were diluted with filtered lake water in a Palmer-Maloney counting slide. Four to eight replicates were sufficient to minimize the counting error, while minimizing effort. The method is highly replicable and could potentially be calibrated for different sediment types because sediment masking depends on the mean particle size of the sediment. When this method was applied in a survey of benthic sites in Quebec lakes, flagellate abundances were found to range from 100 to 180,000 cells ml(-1), while ciliate numbers ranged from 26 to 11,000 cells ml(-1). Bacteria are 105 to 10(7) times more abundant than protists and, thus, the impact of these protists on sediment bacterial dynamics is likely to be minimal.}, }
@article {pmid24189920, year = {1993}, author = {Ward, BB and Cockcroft, AR}, title = {Immunofluorescence detection of the denitrifying strain Pseudomonas stutzeri (ATCC 14405) in seawater and intertidal sediment environments.}, journal = {Microbial ecology}, volume = {25}, number = {3}, pages = {233-246}, pmid = {24189920}, issn = {0095-3628}, abstract = {A strain-specific immunofluorescence assay for enumeration of a marine denitrifying bacterium was developed and applied in the marine environment. The polyclonal antiserum for Pseudomonas stutzeri (ATCC 14405) did not react with other pseudomonads, other heterotrophs, or autotrophic nitrifying strains. The abundance of P. stutzeri in the shallow water column of Monterey Bay was less than 0.1% of the total bacterial abundance and decreased with depth, whereas the total bacterial abundance was variable and nearly constant with depth. P. stutzeri was also detected in the sediments of a microbial mat from Tomales Bay. The relatively low contribution of P. stutzeri to the total bacterial abundance in both environments implies that it is not a major component of the heterotrophic assemblage. This conclusion appears to hold for most other strains for which specific assays have been applied in the marine environment. The isolation of several different denitrifying strains from local marine environments implies that the culturable population is quite diverse, even in the absence of different selective enrichment media. Thus, strain specific immunofluorescence is of limited use in quantifying functional groups of bacteria. Conversely, they provide specific information on the diversity of natural populations and their relation to culturable strains.}, }
@article {pmid24189919, year = {1993}, author = {Harris, JM}, title = {The presence, nature, and role of gut microflora in aquatic invertebrates: A synthesis.}, journal = {Microbial ecology}, volume = {25}, number = {3}, pages = {195-231}, pmid = {24189919}, issn = {0095-3628}, abstract = {This review of the literature concerns the gut microbiota of aquatic invertebrates and highlights the questions and processes that merit attention if an understanding of the role of gut microbes in the physiology of host invertebrates and nutrient dynamics of aquatic systems is to be gained. A substantial number of studies report the presence of gut microbes in aquatic invertebrates. Crustacea, Mollusca, and Echinodermata have received the most attention, with few studies involving other invertebrate groups. Different types of associations (e.g., ingestion, contribution of exoenzymes, incubation, parasitism) are reported to occur between gut microbes and aquatic invertebrates, and it is clear that gut bacterial communities cannot be treated as single functional entities, but that individual populations require examination. In addition, gut microbes may be either ingested transients or residents, the presence of which have different implications for the invertebrate. The most commonly reported genera of gut bacteria are Vibrio, Pseudomonas, Flavobacterium, Micrococcus, and Aeromonas. Quite a number of authors report the physiological properties of gut microbes (including enzyme activities and attributes such as nitrogen fixation), while less attention has been given to consideration of the colonization sites within the digestive tract, the density and turnover of gut bacteria, and the factors affecting the presence and nature of gut microflora. In addition, although a few studies have demonstrated a positive relationship between invertebrates and their gut microbiota, particularly with regard to nutrient gain by the invertebrate, very little conclusive evidence exists as to the role of bacteria in the physiology of host invertebrates. This has resulted from a lack of process-oriented studies. The findings for aquatic gut microbes are compared to those of gut bacteria associated with terrestrial invertebrates, where gut microbes contribute significantly to nutrient gain by the host in some environments.}, }
@article {pmid24189814, year = {1993}, author = {Haldeman, DL and Amy, PS}, title = {Bacterial heterogeneity in deep subsurface tunnels at Rainier Mesa, Nevada test site.}, journal = {Microbial ecology}, volume = {25}, number = {2}, pages = {183-194}, pmid = {24189814}, issn = {0095-3628}, abstract = {To characterize the deep subsurface environment of Rainier Mesa, Nevada Test Site, rock samples were taken from tunnels U 12b, U12g, U12p, and U 12n, which varied in depth from 50 m to 450 m and in gravimetric moisture content from 4% to 27%. Values for total count, viable count, biomass, Simpson diversity, equitability, similarity coefficient, and number of distinct colony types indicated microbiological variability between samples. Viable counts ranged from less than 1 × 10(1) to 2.4 × 10(5) CFU g dry wt(-1) of rock. Direct counts and enumeration based on phospholipid determination indicated larger numbers of cells g dry wt-1 of rock than viable counts. Simpson diversity indices, equitability, and numbers of distinct colony types varied from 3.00 to 8.05, 0.21 to 0.89, and 7 to 19, respectively, and indicated heterogeneity between samples. Each distinct morphotype was purified and characterized. Gram reaction, morphology, metal and antibiotic resistances, and metabolic activities of each isolate confirmed spatial variability among microbiota isolated from different locations. Most probable numbers of nitrifying, sulfur oxidizing, and sulfur-reducing bacteria were below the limit of detection in all samples, while the numbers of nitrogen fixing bacteria ranged from below the level of detection to 7.8 × 10(2) cells g dry wt(-1) of rock sample, and the numbers of dentrifying bacteria ranged from below the level of detection to greater than 1.6 × 10(3) cells g dry wt(-1) of rock sample.}, }
@article {pmid24189813, year = {1993}, author = {Proctor, LM and Okubo, A and Fuhrman, JA}, title = {Calibrating estimates of phage-induced mortality in marine bacteria: Ultrastructural studies of marine bacteriophage development from one-step growth experiments.}, journal = {Microbial ecology}, volume = {25}, number = {2}, pages = {161-182}, pmid = {24189813}, issn = {0095-3628}, abstract = {The timing of lytic phage development and the relationship between host generation times and latent periods were investigated by electron microscopy of one-step growth experiments in two strains of marine Vibrio species. Results were used in a correction factor developed to interpret field studies of phage-infected marine bacteria. Both the number of mature phage per average cell section and the percentage of cells with mature phage increased exponentially by 73-86% into the latent periods. Assuming that bacterial infection and lysis take place continually in the ocean, conversion factors for relating the percentage of visibly infected bacteria to the total percentage of the bacterial community that are phage-infected were calculated as 3.70-7.14. When this range of factors was applied to previously-collected field data [Proctor LM, Fuhrman JA (1990) Nature (Lond) 343:60-62; Proctor LM, Fuhrman JA (1991) Mar Ecol Prog Ser 69:133-142] from 3 to 31% of the free-living bacteria and 3 to 26% of particulate-associated bacteria appeared to be phage-infected at any given time. Based upon a steady-state model in which half the daughter cells survive to divide again, the percent of total mortality would be twice the total percentage of phage-infected cells. From 6 to 62% and from 6 to 52% of mortality for the free-living and particulate-associated bacterial community, respectively, may be due to viruses.}, }
@article {pmid24189812, year = {1993}, author = {Wiebe, WJ and Sheldon, WM and Pomeroy, LR}, title = {Evidence for an enhanced substrate requirement by marine mesophilic bacterial isolates at minimal growth temperatures.}, journal = {Microbial ecology}, volume = {25}, number = {2}, pages = {151-159}, pmid = {24189812}, issn = {0095-3628}, abstract = {Bacterial isolates from the subtropical southeastern continental shelf were cultured in a matrix of temperature and substrate concentrations encompassing a range of temperature and substrate concentrations equal to and exceeding natural ones. At the annual minimum temperature, marine heterotrophic bacterial isolates required higher concentrations of dissolved substrates for active growth than are usually found in seawater. We show this to result from a nonlinear interaction of the combined effects of temperature and substrate concentration on bacterial growth and respiratory rate. As a result, bacterial and protozoan utilization of phytoplankton production during winter and early spring is low, permitting greater energy flow to zooplankton and benthic animals, while in late spring, summer, and fall, the microbial loop dominates energy flux and organic carbon utilization. Escherichia coli shows a similar nonlinear response to temperature at minimal substrate concentrations, albeit at a higher range of concentrations than were utilized by the marine isolates. Thus, bacteria from subtropical regions are shown to have a differential growth response near the minimum temperature for growth, depending on the concentration of available substrates.}, }
@article {pmid24189811, year = {1993}, author = {Chróst, RJ and Rai, H}, title = {Ectoenzyme activity and bacterial secondary production in nutrient-impoverished and nutrient-enriched freshwater mesocosms.}, journal = {Microbial ecology}, volume = {25}, number = {2}, pages = {131-150}, pmid = {24189811}, issn = {0095-3628}, abstract = {This report presents results on relationships between the kinetics (Vmax and Km) of β-glucosidase (GLCase) and aminopeptidase (AMPase) activity, and dissolved organic carbon (DOC) and bacterial secondary production in freshwater mesocosms of differing degrees of eutrophication. These relationships varied in different mesocosms and depended on the trophic status of water and the exudation rates of organic carbon (EOC) by phytoplankton. Close coupling of bacterial production to Vmax of GLCase activity was observed only in nutrient-enriched mesocosms. The relationship between GLCase and DOC content was also significant in enriched water. There was no correlation between the Vmax, of GLCase and DOC and bacterial production in nutrient-impoverished and control (mesotrophic) enclosures. However, the Vmax of AMPase correlated well to DOC and bacterial production in these mesocosms. AMPase activity did not correlate with DOC and bacterial production in nutrient-impoverished mesocosms. There was no relationship between bacterial biomass and enzyme activity in all studied mesocosms. Comparison of the rates of phytoplankton production of EOC and rates of the bacterial organic carbon demand (BOCD) in nutrient-impoverished mesocosms showed that EOC flux constituted, on average, 90% of BOCD. However, in nutrient-enriched mesocosms EOC contributed only, on average, 27% to the BOCD; thus, in these mesocosms, bacteria were probably organic-carbon limited. It is hypothesized that to bypass substrate limitation, bacteria produced GLCase and AMPase. These enzymes had a high specific activity and high affinity to their substrates and efficiently hydrolyzed polysaccharides and proteins, thereby supplying microorganisms with readily utilizable products of enzyme catalysis.}, }
@article {pmid24189810, year = {1993}, author = {Chrzanowski, TH and Simek, K and Sada, RH and Williams, S}, title = {Estimates of bacterial growth rate constants from thymidine incorporation and variable conversion factors.}, journal = {Microbial ecology}, volume = {25}, number = {2}, pages = {121-130}, pmid = {24189810}, issn = {0095-3628}, abstract = {Thymidine incorporation into DNA is widely used to estimate rates of bacterial growth and secondary production in aquatic systems. The procedure requires the use of several conversion factors and assumptions to convert rates of thymidine uptake to rates of carbon production. Perhaps the most controversial of the conversion factors is that which converts rates of incorporation to the rate of cell production. During a year-long study in Lake Arlington, Texas, we empirically determined conversion factors from bacterial growth in filtered (1.0 μm porosity) and diluted (1:9) lake water. Bacterial growth rate constants determined from changes in cell abundance were compared to growth rate constants estimated from empirically derived (both instantaneous and annually averaged), theoretical, and modeled conversion factors. Single value conversion factors (i.e., theoretical, or average of 19 empirically determined conversion factors) did not yield estimates of bacterial growth rate constants that compared favorably to growth estimates from changes in bacterial abundance. Conversion factors, determined from a regression model based on empirically determined conversion factors, gave annual growth estimates that were similar to those obtained from changes in cell abundance.}, }
@article {pmid24189809, year = {1993}, author = {Mitchell, JG and Weller, R and Beconi, M and Sell, J and Holland, J}, title = {A practical optical trap for manipulating and isolating bacteria from complex microbial communities.}, journal = {Microbial ecology}, volume = {25}, number = {2}, pages = {113-119}, pmid = {24189809}, issn = {0095-3628}, abstract = {A wide variety of naturally occurring bacteria cannot be isolated by classical microbiological methods, hindering study of microbial communities. To partially remove this limitation, a method using optical trapping was developed. It allows for one-step isolation of bacteria from a complex community to a pure culture. The method transfers a single bacterium to sterile culture medium using a non-destructive laser beam. The ease with which a previously unculturable cell was cultured by trapping suggests that competition may limit growth in some natural communities of bacteria.}, }
@article {pmid24189708, year = {1993}, author = {Caron, DA and Sanders, RW and Lim, EL and Marrasé, C and Amaral, LA and Whitney, S and Aoki, RB and Porters, KG}, title = {Light-dependent phagotrophy in the freshwater mixotrophic chrysophyte Dinobryon cylindricum.}, journal = {Microbial ecology}, volume = {25}, number = {1}, pages = {93-111}, pmid = {24189708}, issn = {0095-3628}, abstract = {The mixotrophic (bacterivorous), freshwater chrysophyte Dinobryon cylindricum was cultured under a variety of light regimes and in bacterized and axenic cultures to investigate the role of phototrophy and phagotrophy for the growth of this alga. D. cylindricum was found to be an obligate phototroph. The alga was unable to survive in continuous darkness even when cultures were supplemented with high concentrations of bacteria, and bacterivory ceased in cultures placed in the dark for a period longer than one day. Axenic growth of the alga was poor even in an optimal light regime. Live bacteria were required for sustained, vigorous growth of the alga in the light. Carbon (C), nitrogen (N), and phosphorus (P) budgets determined for the alga during growth in bacterized cultures indicated that bacterial biomass ingested by the alga may have contributed up to 25% of the organic carbon budget of the alga. Photosynthesis was the source of most ([Symbol: see text]75%) of the organic carbon of the alga. D. cylindricum populations survived but did not grow when cultured in a continuous low light intensity (30 μE m(-2) sec(-1)), or in a light intensity of 150 μE m(-2) sec(-1) for only two hours each day. Net efficiency of incorporation of bacterial C, N, and P into algal biomass under these two conditions was zero (i.e., no net algal population growth). We conclude that the primary function of bacterivorous behavior in D. cylindricum may be to provide essential growth factor(s) or major nutrients for photosynthetic growth, or to allow for the survival of individuals during periods of very low light intensity or short photoperiod.}, }
@article {pmid24189707, year = {1993}, author = {Fritze, H and Bååth, E}, title = {Microfungal species composition and fungal biomass in a coniferous forest soil polluted by alkaline deposition.}, journal = {Microbial ecology}, volume = {25}, number = {1}, pages = {83-92}, pmid = {24189707}, issn = {0095-3628}, abstract = {Isolations of soil microfungi from the humus (F/H-layer) of a coniferous forest soil which was either unpolluted (pH 4.1) or polluted (pH 6.6) for 25 years by deposition of alkaline dust, were made by soil washing and spore plating. Both techniques revealed similar changes in species composition. Alkaline dust exposure caused a reduction in overall species numbers, but led to higher relative isolation frequencies of Mortierella alpina, Oidiodendron tenuissimum, Penicillium montanese, Sagenomella verticillata, and Trichosporiella sporotrichioides. The incidence of M. isabellina, O. cf. clamydosporium, P. spinulosum, Penicillium sp. 1, P. sclerotiorum, Trichoderma viride, and Verticillium bulbillosum was reduced on polluted sites. The amount of the mainly fungal-derived phospholipid fatty acid 18 : 2ω6 decreased by 23%, while the amount of ergosterol increased by 9% in the polluted soil.}, }
@article {pmid24189706, year = {1993}, author = {Garnham, GW and Codd, GA and Gadd, GM}, title = {Uptake of cobalt and cesium by microalgal- and cyanobacterial-clay mixtures.}, journal = {Microbial ecology}, volume = {25}, number = {1}, pages = {71-82}, pmid = {24189706}, issn = {0095-3628}, abstract = {Accumulation of cobalt and cesium by the microalga Scenedesmus obliquus and the cyanobacterium Synechocystis PCC 6803 has been characterized at metal concentrations ranging from 1-100 µM in the presence of three clay minerals, montmorillonite, illite, and kaolinite. The majority of metal uptake over a 4 h period consisted of rapid binding to the clay mineral-cell aggregates, and was unaffected by incubation in the dark or by the presence of the metabolic inhibitor carbonyl cyanide-3-chlorophenyl hydrazone (CCCP). This was followed by a slower, energy-dependent uptake of metal by the cell components of the mixtures, which was inhibited by incubation in the dark or in the presence of CCCP. The initial phase of uptake by the clay mineral-cell mixtures and mixture components alone conformed to a Freundlich adsorption isotherm, the order of uptake for both cobalt and cesium being montmorillonite-cells > illite-cells > kaolinite-cells. S. obliquus-clay mineral mixtures accumulated more cobalt and cesium than Synechocystis PCC 6803-clay mineral mixtures. On a dry weight basis, clay minerals alone accumulated greater amounts of metals than clay mineral-cell mixtures, which accumulated more than the cells alone. However, when the same data was expressed as amount of metal adsorbed per unit surface area, S. obliquus, in most cases, adsorbed greater amounts of cobalt and cesium than the clay minerals or Synechocystis PCC 6803. As the proportion of clay in a cell-clay mineral mixture was increased, the amount of metal accumulated also increased. Reduced accumulation of cobalt and cesium by cell-clay mineral mixtures, exhibited by equal amounts of the individual components added together, indicated that the formation of clay-cell aggregates had masked some of the binding sites normally available to metal ions. Accumulation of cobalt and cesium by all clay mineral-cell mixtures was dependent on the external pH and NaCl concentration, and decreased with decreasing pH and increasing external NaCl concentration.}, }
@article {pmid24189705, year = {1993}, author = {Stevens, TO and McKinley, JP and Fredrickson, JK}, title = {Bacteria associated with deep, alkaline, anaerobic groundwaters in Southeast Washington.}, journal = {Microbial ecology}, volume = {25}, number = {1}, pages = {35-50}, pmid = {24189705}, issn = {0095-3628}, abstract = {The microbial diversity in two deep, confined aquifers, the Grande Ronde (1270 m) and the Priest Rapids (316 m), Hanford Reservation, Washington, USA, was investigated by sampling from artesian wells. These basaltic aquifers were alkaline (pH 8.5 to 10.5) and anaerobic (Eh -200 to -450 mV). The wells were allowed to free-flow until pH and Eh stabilized, then the microflora was sampled with water filtration and flow-through sandtrap methods. Direct microscopic counts showed 7.6 × 10(5) and 3.6 × 10(3) bacteria ml(-1) in water from the Grande Ronde and Priest Rapids aquifers, respectively. The sand filter method yielded 5.7 × 10(8) and 1.1 × 10(5) cells g(-1) wet weight of sand. The numbers of bacteria did not decrease as increasing volumes of water were flushed out. The heterotrophic diversity of these bacterial populations was assessed using enrichments for 20 functional groups. These groups were defined by their ability to grow in a matrix of five different electron acceptors (O2, Fe(III), NO3 (-), SO4 (2-), HCO3 (-)) and four groups of electron donors (fermentation products, monomers, polymers, aromatics) in a mineral salts medium at pH 9.5. Growth was assessed by protein production. Culture media were subsequently analyzed to determine substrate utilization patterns. Substrate utilization patterns proved to be more reliable indicators of the presence of a particular physiological group than was protein production. The sand-trap method obtained a greater diversity of bacteria than did water filtration, presumably by enriching the proportion of normally sessile bacteria relative to planktonic bacteria. Substrate utilization patterns were different for microflora from the two aquifers and corresponded to their different geochemistries. Activities in the filtered water enrichments more closely matched those predicted by aquifer geochemistry than did the sand-trap enrichments. The greatest activities were found in Fe(III)-reducing enrichments from both wells, SO4-reducing enrichments from the Grande Ronde aquifer, and methanogenic enrichments from the Priest Rapids aquifer. Organisms from these aquifers may be useful for high-pH bioremediation applications as well as production of biotechnological products. These organisms may also be useful for modeling potential reactions near buried concrete, as might be found in subsurface waste depositories.}, }
@article {pmid24189704, year = {1993}, author = {Servais, P and Garnier, J}, title = {Contribution of heterotrophic bacterial production to the carbon budget of the river Seine (France).}, journal = {Microbial ecology}, volume = {25}, number = {1}, pages = {19-33}, pmid = {24189704}, issn = {0095-3628}, abstract = {Bacterial activity was measured in the river Seine by two methods, (3)H-thymidine incorporation into DNA and (3)H-leucine incorporation into proteins. Both incorporation rates are characterized by low values upstream of Paris, a large increase just downstream of the outfall of the Achères treatment plant effluents, and then decreasing values further downstream. The covariation of both activities is demonstrated by the constancy of the molar ratio (leucine to thymidine incorporation rate) in the range of 6 to 8 for all the samples, except in the perturbed area where it is higher (15 to 35). These high values of molar ratio are linked to the introduction into the river of large sized bacteria ([Symbol: see text]1 µm) with higher incorporation rates per cell or biomass unit than the small autochthonous bacteria (< 1 µm). Growth rates of large bacteria were on average 3.7 times higher than those of small bacteria. Bacterial production was calculated with experimentally determined conversion factors (0.5 × 10(18) cells per mole of thymidine incorporated and 900 gC per mole of leucine incorporated) and by taking into account the activity of both size classes of bacteria measured through fractionation experiments (post-incubation filtration). Production estimated in the perturbed area downstream of Ach6res was very high, up to 60 µgC liter(-1)h(-1) in the summer. Carbon consumption by bacteria in the area perturbed by the Ach6res effluents was calculated assuming a growth yield of 0.2 and compared to the load of biodegradable organic matter discharged by the treatment plant. In summer, an additional supply of organic matter is required to account for the intense bacterial activity, suggesting the importance of phytoplankton production in the carbon budget.}, }
@article {pmid24189703, year = {1993}, author = {Graham, DW and Chaudhary, JA and Hanson, RS and Arnold, RG}, title = {Factors affecting competition between type I and type II methanotrophs in two-organism, continuous-flow reactors.}, journal = {Microbial ecology}, volume = {25}, number = {1}, pages = {1-17}, pmid = {24189703}, issn = {0095-3628}, abstract = {Competition experiments were performed in a continuous-flow reactor using Methylosinus trichosporium OB3b, a type II methanotroph, and Methylomonas albus BG8, a type I methanotroph. The experiments were designed to establish conditions under which type II methanotrophs, which have significant cometabolic potential, prevail over type I strains. The primary determinants of species selection were dissolved methane, copper, and nitrate concentrations. Dissolved oxygen and methanol concentrations played secondary roles. M. trichosporium OB3b proved dominant under copper and nitratelimited conditions. The ratio of M. trichosporium to M. albus in the reactor increased ten-fold in less than 100 hours following the removal of copper from the reactor feed. Numbers of M. albus declined to levels that were below detection limits (<106/ml) under nitrogen-limited conditions. In the latter experiment, the competitive success of M. trichosporiumdepended on the maintenance of an ambient dissolved oxygen level below about 7.5 × 10(-5) M, or 30% of saturation with air. The ability of M. trichosporium to express soluble methane monooxygenase under copper limitation and nitrogenase under nitrate limitation was very significant. M. albus predominated under methane-limited conditions, especially when low levels of methanol were simultaneously added with methane to the reactor. The results imply that nitrogen limitation can be used to select for type II strains such as M. trichosporium OB3b.}, }
@article {pmid24192826, year = {1992}, author = {Both, GJ and Gerards, S and Laanbroek, HJ}, title = {The occurrence of chemolitho-autotrophic nitrifiers in water-saturated grassland soils.}, journal = {Microbial ecology}, volume = {23}, number = {1}, pages = {15-26}, pmid = {24192826}, issn = {0095-3628}, abstract = {Relatively high most probable number (MPN) counts of chemolithotrophic nitrite oxidizers were present in water-saturated soils compared with MPNs and activity of ammonia oxidizers. These high numbers of nitrite oxidizers were confirmed by fluorescent antibody counts and potential activity measurements. Application of different nitrite concentrations in the MPN procedure discriminated within the community of nitrite oxidizers and revealed a large number of nitrite-sensitive nitrite oxidizers and a subcommunity of nitrite-insensitive nitrite oxidizers. The size of this subcommunity was small but corresponded with the low numbers of ammonium oxidizers. Numbers of nitrite-sensitive nitrite oxidizers outnumbered the ammonia oxidizing bacteria by 2-4 orders of magnitude in these soils. The possibility is discussed that the fraction of the nitrite-insensitive cells was active as aerobic nitrite oxidizers, whereas the nitrite-sensitive cells represented an inactive group of nitrite oxidizers growing as heterotrophs or as anaerobes reducing nitrite. In this situation, both MPN enumerations at a low nitrite concentration and activity measurements could give false information about the size of the in situ nitrite-oxidizing community.}, }
@article {pmid24192825, year = {1992}, author = {Pedersen, K and Ekendahl, S}, title = {Assimilation of CO2 and introduced organic compounds by bacterial communities in groundwater from southeastern Sweden deep crystalline bedrock.}, journal = {Microbial ecology}, volume = {23}, number = {1}, pages = {1-14}, pmid = {24192825}, issn = {0095-3628}, abstract = {The nutritional responses of unattached and attached bacterial communities were studied in groundwater from 3 sampling depths, i.e., 830-841 m, 910-921 m, and 999-1,078 m, of the subvertical borehole KLX01 at the Laxemar study area in SE Sweden. The salinity profile of the groundwater in this borehole is homogeneous. There were negative redox potentials (Eh) in the waters (-220 to -270 mV) and they contained sulfide, hydrogen, and methane. Biofilm reactors with hydrophilic glass surfaces were connected to the flowing groundwaters from each of the 3 depths with flow rates of approximately 3 x 10(-3) m sec(-1) over 19 days. There were 0.15 to 0.68 × 10(5) unattached bacteria ml(-1) groundwater and 0.94 to 1.2 × 10(5) attached bacteria cm(-2) on the surfaces. The assimilations of (14)CO2, (14)C-formate, 1,2,3-(3)H-acetate, U-(14)C-lactate, U-(14)C-glucose, and L-4,5-(3)H-leucine by the communities were demonstrated with microautoradiographic and liquid scintillation counting techniques. There were significant assimilations of CO2 by all communities, except for the unattached bacteria at the 910-921 m depth, indicating in situ production of organic carbon from carbonate. Assimilation of formate was detected in two communities, indicating the presence of bacteria able to substitute CO2 with formate. Acetate, lactate, and glucose assimilations demonstrated the presence of heterotrophic bacteria. The assimilation of lactate by the attached bacteria dominated over acetate and glucose at all depths. Leucine was assimilated by 20 to 98% of the communities, which showed that major portions of the communities studied were viable. The results indicate that the attached communities at the 830-841 m and 910-921 m depths were in more metabolically active states than the unattached bacteria. Incubation in air compared with N2 indicated that portions of the studied communities were obligate anaerobes, as their ability to assimilate the added compounds was sensitive to oxygen. The results show that the use of several different compounds reduces the risk for false conclusions about the viability and the metabolic activity of the deep groundwater communities.}, }
@article {pmid22286379, year = {2012}, author = {Franzolin, R and St-Pierre, B and Northwood, K and Wright, AD}, title = {Analysis of rumen methanogen diversity in water buffaloes (Bubalus bubalis) under three different diets.}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {131-139}, pmid = {22286379}, issn = {1432-184X}, mesh = {Animal Feed/*analysis ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; *Biodiversity ; Buffaloes/genetics/*metabolism/*microbiology ; Diet ; Metagenome ; Methane/*metabolism ; Molecular Sequence Data ; Phylogeny ; Rumen/metabolism/*microbiology ; }, abstract = {The water buffalo (Bubalus bubalis) is a prominent livestock species for the production of milk and meat in many countries. We investigated the diversity of rumen methanogens in Mediterranean water buffaloes maintained in Brazil under different diets: corn silage, grazing pasture, or sugar cane. A total of 467 clones were isolated from three methanogen 16S rRNA gene clone libraries that each represented a distinct feed type. The 467 clones were assigned to 19 species-level operational taxonomic units (OTUs). Four OTUs were represented in all three libraries, eight OTUs were library-specific, six OTUs were found in only the corn silage and pasture grazing libraries, and one OTU was shared only between pasture grazing and sugar cane libraries. We found that Methanobrevibacter-related sequences were the most abundant in the water buffaloes sampled for our analysis, in contrast to previously reported studies showing that Methanomicrobium mobile-like methanogens were the most abundant methanogens in water buffaloes of Murrah and Surti breeds sampled in India. Considering the worldwide distribution of water buffaloes and the likely wide variety of diets provided, our results combined with studies from other groups support that larger scope analyses of microbiomes for this livestock species would provide great insight into the contribution of geographical location, breed, and diet in determining the population structure of rumen microorganisms.}, }
@article {pmid22286378, year = {2012}, author = {Pontarp, M and Canbäck, B and Tunlid, A and Lundberg, P}, title = {Phylogenetic analysis suggests that habitat filtering is structuring marine bacterial communities across the globe.}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {8-17}, pmid = {22286378}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; *Ecosystem ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; }, abstract = {The phylogenetic structure and community composition were analysed in an existing data set of marine bacterioplankton communities to elucidate the evolutionary and ecological processes dictating the assembly. The communities were sampled from coastal waters at nine locations distributed worldwide and were examined through the use of comprehensive clone libraries of 16S ribosomal RNA genes. The analyses show that the local communities are phylogenetically different from each other and that a majority of them are phylogenetically clustered, i.e. the species (operational taxonomic units) were more related to each other than expected by chance. Accordingly, the local communities were assembled non-randomly from the global pool of available bacterioplankton. Further, the phylogenetic structures of the communities were related to the water temperature at the locations. In agreement with similar studies, including both macroorganisms and bacteria, these results suggest that marine bacterial communities are structured by “habitat filtering”, i.e. through non-random colonization and invasion determined by environmental characteristics. Different bacterial types seem to have different ecological niches that dictate their survival in different habitats. Other eco-evolutionary processes that may contribute to the observed phylogenetic patterns are discussed. The results also imply a mapping between phenotype and phylogenetic relatedness which facilitates the use of community phylogenetic structure analysis to infer ecological and evolutionary assembly processes.}, }
@article {pmid22286377, year = {2012}, author = {Burdíková, Z and Čapek, M and Švindrych, Z and Gryndler, M and Kubínová, L and Holcová, K}, title = {Ecology of testate amoebae in the Komořany ponds in the Vltava Basin.}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {117-130}, pmid = {22286377}, issn = {1432-184X}, mesh = {Amoeba/classification/*isolation &amp; purification ; Biodiversity ; Czech Republic ; *Ecosystem ; Phylogeny ; Ponds/chemistry/*parasitology ; Seasons ; }, abstract = {Testate amoeba (TA) assemblages were collected in 2005 from four ponds in Komořany (Prague, Czech Republic). An analysis of seasonal taxonomic variability of TA populations and its correlation with the limnological characteristics of the area (temperature, pH, total organic carbon, nitrogen, phosphorus, heavy metals, etc.) was performed. The predominant genera were Difflugia, Arcella, and Centropyxis. The most significant changes in the TA community occurred between March and July. Arcella genus dominated in March and April; in May, Arcella and Centropyxis genera were present in the same amount; in June, Arcella genus disappeared, and Difflugia genus started to dominate the community. A multivariate redundancy analysis showed statistically significant correlations between the environmental parameters and the composition of the TA community. The results indicate a negative correlation between TA quantities and Ni, Cd, PAH, Mn, As, and Pb. TA were also affected by concentrations of NH4(+), NO3(-), and P, as well as by temperature variations. The observed correlations between the species composition and environmental parameters can be used in paleoecological interpretations of fossil TA communities. Our results also prove the suitability of TA as water quality indicators in urban areas.}, }
@article {pmid22281804, year = {2012}, author = {Jackson, SA and Kennedy, J and Morrissey, JP and O'Gara, F and Dobson, AD}, title = {Pyrosequencing reveals diverse and distinct sponge-specific microbial communities in sponges from a single geographical location in Irish waters.}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {105-116}, pmid = {22281804}, issn = {1432-184X}, mesh = {Animals ; Bacteria/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; DNA, Bacterial ; DNA, Ribosomal/genetics ; Ireland ; Molecular Sequence Data ; Phylogeny ; Porifera/classification/*microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA/*methods ; Species Specificity ; }, abstract = {Marine sponges are host to numerically vast and phylogenetically diverse bacterial communities, with 26 major phyla to date having been found in close association with sponge species worldwide. Analyses of these microbial communities have revealed many sponge-specific novel genera and species. These endosymbiotic microbes are believed to play significant roles in sponge physiology including the production of an array of bioactive secondary metabolites. Here, we report on the use of culture-based and culture-independent (pyrosequencing) techniques to elucidate the bacterial community profiles associated with the marine sponges Raspailia ramosa and Stelligera stuposa sampled from a single geographical location in Irish waters and with ambient seawater. To date, little is known about the microbial ecology of sponges of these genera. Culture isolation grossly underestimated sponge-associated bacterial diversity. Four bacterial phyla (Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria) were represented amongst ~200 isolates, compared with ten phyla found using pyrosequencing. Long average read lengths of ~430 bp (V1-V3 region of 16S rRNA gene) allowed for robust resolution of sequences to genus level. Bacterial OTUs (2,109 total), at 95% sequence similarity, from ten bacterial phyla were recovered from R. ramosa, 349 OTUs were identified in S. stuposa representing eight phyla, while 533 OTUs from six phyla were found in surrounding seawater. Bacterial communities differed significantly between sponge species and the seawater. Analysis of the data for sponge-specific taxa revealed that 2.8% of classified reads from the sponge R. ramosa can be defined as sponge-specific, while 26% of S. stuposa sequences represent sponge-specific bacteria. Novel sponge-specific clusters were identified, whereas the majority of previously reported sponge-specific clusters (e.g. Poribacteria) were absent from these sponge species. This deep and robust analysis provides further evidence that the microbial communities associated with marine sponge species are highly diverse and divergent from one another and appear to be host-selected through as yet unknown processes.}, }
@article {pmid22278669, year = {2012}, author = {Staubach, F and Künzel, S and Baines, AC and Yee, A and McGee, BM and Bäckhed, F and Baines, JF and Johnsen, JM}, title = {Expression of the blood-group-related glycosyltransferase B4galnt2 influences the intestinal microbiota in mice.}, journal = {The ISME journal}, volume = {6}, number = {7}, pages = {1345-1355}, pmid = {22278669}, issn = {1751-7370}, support = {R01 HL039693/HL/NHLBI NIH HHS/United States ; R01-HL039693/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification/genetics ; Female ; Intestines/*microbiology ; Male ; *Metagenome ; Mice ; Mice, Inbred C57BL ; N-Acetylgalactosaminyltransferases/genetics/*metabolism ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Selection, Genetic ; Specific Pathogen-Free Organisms ; }, abstract = {Glycans on mucosal surfaces have an important role in host-microbe interactions. The locus encoding the blood-group-related glycosyltransferase β-1,4-N-acetylgalactosaminyltransferase 2 (B4galnt2) is subject to strong selective forces in natural house-mouse populations that contain a common allelic variant that confers loss of B4galnt2 gene expression in the gastrointestinal (GI) tract. We reasoned that altered glycan-dependent intestinal host-microbe interactions may underlie these signatures of selection. To determine whether B4galnt2 influences the intestinal microbial ecology, we profiled the microbiota of wild-type and B4galnt2-deficient siblings throughout the GI tract using 16S rRNA gene pyrosequencing. This revealed both distinct communities at different anatomic sites and significant changes in composition with respect to genotype, indicating a previously unappreciated role of B4galnt2 in host-microbial homeostasis. Among the numerous B4galnt2-dependent differences identified in the abundance of specific bacterial taxa, we unexpectedly detected a difference in the pathogenic genus, Helicobacter, suggesting Helicobacter spp. also interact with B4galnt2 glycans. In contrast to other glycosyltransferases, we found that the host intestinal B4galnt2 expression is not dependent on presence of the microbiota. Given the long-term maintenance of alleles influencing B4galnt2 expression by natural selection and the GI phenotypes presented here, we suggest that variation in B4galnt2 GI expression may alter susceptibility to GI diseases such as infectious gastroenteritis.}, }
@article {pmid22262670, year = {2012}, author = {Clevenger, KD and Fast, W}, title = {"Clicking" on the lights to reveal bacterial social networking.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {13}, number = {4}, pages = {508-510}, doi = {10.1002/cbic.201100767}, pmid = {22262670}, issn = {1439-7633}, mesh = {Bacteria/*cytology/*metabolism ; *Click Chemistry ; Dendrimers ; Fluorescence ; *Quorum Sensing ; }, abstract = {"No man is an island." With apologies to John Donne, the same could be said for a bacterium. The discovery of bacterial quorum sensing and its relevance to microbial ecology and pathogenesis have fueled the increasing scrutiny of the molecular mechanisms responsible for the apparent group behavior of microbes. A number of chemically diverse small molecules act as diffusible signaling molecules that regulate gene expression in a population-dependent manner. Some of these signals, such as the N-acyl-L-homoserine lactones, are produced and sensed by others in the same or closely related species, and other chemical classes of signals are used more broadly for interspecies and even interkingdom communication. As a field, the study of these microbial social networks has been termed "sociomicrobiology".}, }
@article {pmid22258099, year = {2012}, author = {Remus-Emsermann, MN and Tecon, R and Kowalchuk, GA and Leveau, JH}, title = {Variation in local carrying capacity and the individual fate of bacterial colonizers in the phyllosphere.}, journal = {The ISME journal}, volume = {6}, number = {4}, pages = {756-765}, pmid = {22258099}, issn = {1751-7370}, mesh = {*Ecosystem ; Fabaceae/*microbiology ; Models, Biological ; Pantoea/*growth &amp; development ; Plant Leaves/*microbiology ; }, abstract = {Using a phyllosphere model system, we demonstrated that the term 'carrying capacity', as it is commonly used in microbial ecology, needs to be understood as the sum of many 'local carrying capacities' in order to better explain and predict the course and outcome of bacterial colonization of an environment. Using a green fluorescent protein-based bioreporter system for the quantification of reproductive success (RS) in individual Erwinia herbicola cells, we were able to reconstruct the contribution of individual immigrants to bacterial population sizes on leaves. Our analysis revealed that plant foliage represents to bacteria an environment where individual fate is determined by the local carrying capacity of the site where an immigrant cell lands. With increasing inoculation densities, the RS of most immigrants declined, suggesting that local carrying capacity under the tested conditions was linked to local nutrient availability. Fitting the observed experimental data to an adapted model of phyllosphere colonization indicated that there might exist three types of sites on leaves, which differ in their frequency of occurrence and local carrying capacity. Specifically, our data were consistent with a leaf environment that is characterized by few sites where individual immigrants can produce high numbers of offspring, whereas the remainder of the leaf offered an equal number of sites with low and medium RS. Our findings contribute to a bottom-up understanding of bacterial colonization of leaf surfaces, which includes a quantifiable role of chance in the experience at the individual level and in the outcome at the population level.}, }
@article {pmid22253735, year = {2012}, author = {Sixt, BS and Hiess, B and König, L and Horn, M}, title = {Lack of effective anti-apoptotic activities restricts growth of Parachlamydiaceae in insect cells.}, journal = {PloS one}, volume = {7}, number = {1}, pages = {e29565}, pmid = {22253735}, issn = {1932-6203}, mesh = {Amoeba/drug effects/microbiology ; Animals ; *Apoptosis/drug effects ; Caspase Inhibitors ; Caspases/metabolism ; Cell Line ; Cell Nucleus/drug effects/metabolism ; Chlamydia Infections/microbiology ; Chlamydiales/drug effects/*growth &amp; development ; DNA Fragmentation/drug effects ; Drosophila melanogaster/*cytology/drug effects/*microbiology ; Protease Inhibitors/pharmacology ; Symbiosis/drug effects ; Time Factors ; }, abstract = {The fundamental role of programmed cell death in host defense is highlighted by the multitude of anti-apoptotic strategies evolved by various microbes, including the well-known obligate intracellular bacterial pathogens Chlamydia trachomatis and Chlamydia (Chlamydophila) pneumoniae. As inhibition of apoptosis is assumed to be essential for a successful infection of humans by these chlamydiae, we analyzed the anti-apoptotic capacity of close relatives that occur as symbionts of amoebae and might represent emerging pathogens. While Simkania negevensis was able to efficiently replicate within insect cells, which served as model for metazoan-derived host cells, the Parachlamydiaceae (Parachlamydia acanthamoebae and Protochlamydia amoebophila) displayed limited intracellular growth, yet these bacteria induced typical features of apoptotic cell death, including formation of apoptotic bodies, nuclear condensation, internucleosomal DNA fragmentation, and effector caspase activity. Induction of apoptosis was dependent on bacterial activity, but not bacterial de novo protein synthesis, and was detectable already at very early stages of infection. Experimental inhibition of host cell death greatly enhanced parachlamydial replication, suggesting that lack of potent anti-apoptotic activities in Parachlamydiaceae may represent an important factor compromising their ability to successfully infect non-protozoan hosts. These findings highlight the importance of the evolution of anti-apoptotic traits for the success of chlamydiae as pathogens of humans and animals.}, }
@article {pmid22252223, year = {2012}, author = {Zhao, JY and Dang, H}, title = {Coastal seawater bacteria harbor a large reservoir of plasmid-mediated quinolone resistance determinants in Jiaozhou Bay, China.}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {187-199}, pmid = {22252223}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/drug effects/genetics/*isolation &amp; purification ; Bacterial Proteins/genetics ; Bays/*microbiology ; China ; *Drug Resistance, Bacterial ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Phylogeny ; Plasmids/*genetics/metabolism ; Quinolones/*pharmacology ; Seawater/*microbiology ; }, abstract = {Diversity and prevalence of plasmid-mediated quinolone resistance determinants were investigated in environmental bacteria isolated from surface seawater of Jiaozhou Bay, China. Five qnr gene alleles were identified in 34 isolates by PCR amplification, including qnrA3 gene in a Shewanella algae isolate, qnrB9 gene in a Citrobacter freundii isolate, qnrD gene in 22 Proteus vulgaris isolates, qnrS1 gene in 1 Enterobacter sp. and 4 Klebsiella spp. isolates, and qnrS2 gene in 1 Pseudomonas sp. and 4 Pseudoalteromonas sp. isolates. The qnrC, aac(6')-Ib-cr, and qepA genes could not be detected in this study. The 22 qnrD-positive Proteus vulgaris isolates could be differentiated into four genotypes based on ERIC-PCR assay. The qnrS1 and qnrD genes could be transferred to Escherichia coli J53 Azi(R) or E. coli TOP10 recipient strains using conjugation or transformation methods. Among the 34 qnr-positive isolates, 30 had a single point mutation in the QRDRs of GyrA protein (Ala67Ser, Ser83Ile, or Ser83Thr), indicating that cooperation of chromosome- and plasmid-mediated resistance contributed to the spread and evolution of quinolone resistance in this coastal bay. Eighty-five percent of the isolates were also found to be resistant to ampicillin, and bla(CMY), bla(OXY), bla(SHV), and bla(TEM) genes were detected in five isolates that also harbored the qnrB9 or qnrS1 gene. Our current study is the first identification of qnrS2 gene in Pseudoalteromonas and Pseudomonas strains, and qnrD gene in Proteus vulgaris strains. High prevalence of diverse qnr genes in Jiaozhou Bay indicates that coastal seawater may serve as an important reservoir, natural source, and dissemination vehicle of quinolone resistance determinants.}, }
@article {pmid22251411, year = {2012}, author = {Ozok, AR and Persoon, IF and Huse, SM and Keijser, BJ and Wesselink, PR and Crielaard, W and Zaura, E}, title = {Ecology of the microbiome of the infected root canal system: a comparison between apical and coronal root segments.}, journal = {International endodontic journal}, volume = {45}, number = {6}, pages = {530-541}, pmid = {22251411}, issn = {1365-2591}, support = {UH2 DK083993/DK/NIDDK NIH HHS/United States ; 1UH2DK083993-01/DK/NIDDK NIH HHS/United States ; }, mesh = {Actinobacteria/classification ; Archaea/classification ; Bacteria/*classification ; Bacteria, Anaerobic/classification ; Biodiversity ; DNA, Ribosomal/classification ; Dental Pulp Cavity/*microbiology ; Dentin/microbiology ; Ecosystem ; Gram-Negative Bacteria/classification ; Gram-Positive Bacteria/classification ; Humans ; Metagenome/*physiology ; Periapical Periodontitis/*microbiology ; Proteobacteria/classification ; RNA, Bacterial/classification ; RNA, Ribosomal, 16S/classification ; Sequence Analysis, DNA ; Tooth Apex/*microbiology ; }, abstract = {AIM: To evaluate the microbial ecology of the coronal and apical segments of infected root canal systems using a complete sampling technique and next-generation sequencing.<br><br>METHODOLOGY: The roots of 23 extracted teeth with apical periodontitis were sectioned in half, horizontally, and cryo-pulverized. Bacterial communities were profiled using tagged 454 pyrosequencing of the 16S rDNA hypervariable V5-V6 region.<br><br>RESULTS: The sequences were classified into 606 taxa (species or higher taxon), representing 24 bacterial phyla or candidate divisions and one archaeal phylum. Proteobacteria were more abundant in the apical samples (P&#x2003;<&#x2003;0.05), whilst Actinobacteria were in significantly higher proportions in the coronal samples. The apical samples harboured statistically significantly more taxa than the coronal samples (P&#x2003;=&#x2003;0.01) and showed a higher microbial diversity. Several taxa belonging to fastidious obligate anaerobes were significantly more abundant in the apical segments of the roots compared with their coronal counterparts.<br><br>CONCLUSIONS: Endodontic infections are more complex than reported previously. The apical part of the root canal system drives the selection of a more diverse and more anaerobic community than the coronal part. The presence of a distinct ecological niche in the apical region explains the difficulty of eradication of the infection and emphasizes the need for new treatment approaches to be developed.}, }
@article {pmid22244791, year = {2012}, author = {Desloover, J and Vlaeminck, SE and Clauwaert, P and Verstraete, W and Boon, N}, title = {Strategies to mitigate N2O emissions from biological nitrogen removal systems.}, journal = {Current opinion in biotechnology}, volume = {23}, number = {3}, pages = {474-482}, doi = {10.1016/j.copbio.2011.12.030}, pmid = {22244791}, issn = {1879-0429}, mesh = {Air Pollutants/*metabolism ; Biodegradation, Environmental ; Environmental Restoration and Remediation/economics/*methods ; Manure/microbiology ; Nitrous Oxide/*metabolism/toxicity ; *Refuse Disposal ; Sewage/microbiology ; }, abstract = {N2O emissions from the biological treatment of sewage, manure, landfill leachates and industrial effluents have gained considerable interest among policy makers and environmental scientists. Estimated global emission rates from these sources can contribute up to 10% of the anthropogenic N2O emissions. Particularly at the level of a treatment plant, the N2O impact can be very significant and reach up to 80% of the operational CO2 footprint. Imperfect nitritation by an imbalance in the two-step nitritation metabolism of ammonia-oxidizing bacteria is considered as the main contributor to N2O production with hydroxylamine and particularly nitrite as key precursors. Monitoring of these compounds is warranted to understand and abate N2O emissions. Mitigation strategies should also comprise optimizations of the process parameters as well as bio-augmentative approaches empowered to restore the functional capacity and to deal with unwanted accumulation of intermediates. These strategies require validation for their effectiveness and costs at full-scale.}, }
@article {pmid22234511, year = {2012}, author = {Morales-Jiménez, J and Zúñiga, G and Ramírez-Saad, HC and Hernández-Rodríguez, C}, title = {Gut-associated bacteria throughout the life cycle of the bark beetle Dendroctonus rhizophagus Thomas and Bright (Curculionidae: Scolytinae) and their cellulolytic activities.}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {268-278}, pmid = {22234511}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Cellulose/metabolism ; Gastrointestinal Tract/growth &amp; development/*microbiology ; Larva/growth &amp; development/microbiology ; *Life Cycle Stages ; Mexico ; Molecular Sequence Data ; Phylogeny ; Weevils/*growth &amp; development/*microbiology ; }, abstract = {Dendroctonus rhizophagus Thomas and Bright (Curculionidae: Scolytinae) is an endemic economically important insect of the Sierra Madre Occidental in Mexico. This bark beetle has an atypical behavior within the genus because just one beetle couple colonizes and kills seedlings and young trees of 11 pine species. In this work, the bacteria associated with the Dendroctonus rhizophagus gut were analyzed by culture-dependent and culture-independent methods. Analysis of 16S rRNA sequences amplified directly from isolates of gut bacteria suggests that the bacterial community associated with Dendroctonus rhizophagus, like that of other Dendroctonus spp. and Ips pini, is limited in number. Nine bacterial genera of γ-Proteobacteria and Actinobacteria classes were detected in the gut of Dendroctonus rhizophagus. Stenotrophomonas and Rahnella genera were the most frequently found bacteria from Dendroctonus rhizophagus gut throughout their life cycle. Stenotrophomonas maltophilia, Ponticoccus gilvus, and Kocuria marina showed cellulolytic activity in vitro. Stenotrophomonas maltophilia, Rahnella aquatilis, Raoultella terrigena, Ponticoccus gilvus, and Kocuria marina associated with larvae or adults of Dendroctonus rhizophagus could be implicated in nitrogen fixation and cellulose breakdown, important roles associated to insect development and fitness, especially under the particularly difficult life conditions of this beetle.}, }
@article {pmid22234510, year = {2012}, author = {Kuhnert, R and Oberkofler, I and Peintner, U}, title = {Fungal growth and biomass development is boosted by plants in snow-covered soil.}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {79-90}, pmid = {22234510}, issn = {1432-184X}, mesh = {Biomass ; *Ecosystem ; Fungi/classification/genetics/*growth &amp; development/*isolation &amp; purification ; Molecular Sequence Data ; Seasons ; Soil/chemistry ; *Soil Microbiology ; Temperature ; }, abstract = {Soil microbial communities follow distinct seasonal cycles which result in drastic changes in processes involving soil nutrient availability. The biomass of fungi has been reported to be highest during winter, but is fungal growth really occurring in frozen soil? And what is the effect of plant cover on biomass formation and on the composition of fungal communities? To answer these questions, we monitored microbial biomass N, ergosterol, and the amount of fungal hyphae during summer and winter in vegetated and unvegetated soils of an alpine primary successional habitat. The winter fungal communities were identified by rDNA ITS clone libraries. Winter soil temperatures ranged between -0.6°C and -0.1°C in snow-covered soil. We found distinct seasonal patterns for all biomass parameters, with highest biomass concentrations during winter in snow-covered soil. The presence of plant cover had a significant positive effect on the amount of biomass in the soil, but the type of plant cover (plant species) was not a significant factor. A mean hyphal ingrowth of 5.6 m g(-1) soil was detected in snow-covered soil during winter, thus clearly proving fungal growth during winter in snow-covered soil. Winter fungal communities had a typical species composition: saprobial fungi were dominating, among them many basidiomycete yeasts. Plant cover had no influence on the composition of winter fungal communities.}, }
@article {pmid22233905, year = {2012}, author = {Vavilin, VA}, title = {Estimating evolution of δ(13)CH(4) during methanization of municipal solid waste based on chemical reactions, isotope accumulation in products and microbial ecology.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {65}, number = {2}, pages = {270-276}, doi = {10.2166/wst.2012.791}, pmid = {22233905}, issn = {0273-1223}, mesh = {Carbon Isotopes ; Carboxylic Acids/metabolism ; Hydrolysis ; Methane/*biosynthesis ; Methanosarcinales/metabolism ; *Models, Biological ; *Refuse Disposal ; }, abstract = {Natural isotopic composition in substrate may be used to reveal the metabolic pathways of substrate transformation by microbial community. In this paper, a change in δ(13)CH(4) during methanization of reconstituted municipal solid waste was described using a mathematical model based on stoichiometric chemical reactions, equation for the (13)C isotope accumulation in products at the low natural C(13)/C(12) ratio and microbial ecology. A set of experimental data used in the model was taken from Qu et al. (2009a). According to the model, during mesophilic municipal solid waste methanization initially hydrogenotrophic and further aceticlastic methanogenesis dominated. At the final stage hydrogenotrophic methanogenesis followed by acetate oxidation dominated again. In spite of rather high measured values of δ(13)C for CO(2) above -21‰, a sharp decrease in δ(13)CH(4) from -20‰ to -60‰ at the final stage was explained by a larger fractionation against (13)C during methanogenesis from H(2)/H(2)CO(3) due to a kinetic isotope effect when hydrogenotrophic methanogens preferentially take down light (12)C. The model also confirmed that in thermophilic conditions a comparatively stable value of δ(13)CH(4) about -60‰ measured earlier (Qu et al. 2009b) was due to a dominance of hydrogenotrophic methanogenesis during all methanization process of cardboard waste.}, }
@article {pmid22233808, year = {2012}, author = {Valentine, DL and Mezić, I and Maćešić, S and Črnjarić-Žic, N and Ivić, S and Hogan, PJ and Fonoberov, VA and Loire, S}, title = {Dynamic autoinoculation and the microbial ecology of a deep water hydrocarbon irruption.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {50}, pages = {20286-20291}, pmid = {22233808}, issn = {1091-6490}, mesh = {Bacteria/growth &amp; development/metabolism ; Biodegradation, Environmental ; Ecosystem ; Gulf of Mexico ; Hydrocarbons/*metabolism/toxicity ; Models, Biological ; Petroleum Pollution/*adverse effects ; *Water Microbiology ; Water Pollutants, Chemical/metabolism/toxicity ; }, abstract = {The irruption of gas and oil into the Gulf of Mexico during the Deepwater Horizon event fed a deep sea bacterial bloom that consumed hydrocarbons in the affected waters, formed a regional oxygen anomaly, and altered the microbiology of the region. In this work, we develop a coupled physical-metabolic model to assess the impact of mixing processes on these deep ocean bacterial communities and their capacity for hydrocarbon and oxygen use. We find that observed biodegradation patterns are well-described by exponential growth of bacteria from seed populations present at low abundance and that current oscillation and mixing processes played a critical role in distributing hydrocarbons and associated bacterial blooms within the northeast Gulf of Mexico. Mixing processes also accelerated hydrocarbon degradation through an autoinoculation effect, where water masses, in which the hydrocarbon irruption had caused blooms, later returned to the spill site with hydrocarbon-degrading bacteria persisting at elevated abundance. Interestingly, although the initial irruption of hydrocarbons fed successive blooms of different bacterial types, subsequent irruptions promoted consistency in the structure of the bacterial community. These results highlight an impact of mixing and circulation processes on biodegradation activity of bacteria during the Deepwater Horizon event and suggest an important role for mixing processes in the microbial ecology of deep ocean environments.}, }
@article {pmid22232669, year = {2012}, author = {van Elsas, JD and Chiurazzi, M and Mallon, CA and Elhottova, D and Kristufek, V and Salles, JF}, title = {Microbial diversity determines the invasion of soil by a bacterial pathogen.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {4}, pages = {1159-1164}, pmid = {22232669}, issn = {1091-6490}, mesh = {*Biodiversity ; Colony Count, Microbial ; Escherichia coli O157/*growth &amp; development ; *Introduced Species ; Netherlands ; *Soil Microbiology ; Survival Analysis ; Time Factors ; }, abstract = {Natural ecosystems show variable resistance to invasion by alien species, and this resistance can relate to the species diversity in the system. In soil, microorganisms are key components that determine life support functions, but the functional redundancy in the microbiota of most soils has long been thought to overwhelm microbial diversity-function relationships. We here show an inverse relationship between soil microbial diversity and survival of the invading species Escherichia coli O157:H7, assessed by using the marked derivative strain T. The invader's fate in soil was determined in the presence of (i) differentially constructed culturable bacterial communities, and (ii) microbial communities established using a dilution-to-extinction approach. Both approaches revealed a negative correlation between the diversity of the soil microbiota and survival of the invader. The relationship could be explained by a decrease in the competitive ability of the invader in species-rich vs. species-poor bacterial communities, reflected in the amount of resources used and the rate of their consumption. Soil microbial diversity is a key factor that controls the extent to which bacterial invaders can establish.}, }
@article {pmid22225785, year = {2012}, author = {McDonald, JE and Houghton, JN and Rooks, DJ and Allison, HE and McCarthy, AJ}, title = {The microbial ecology of anaerobic cellulose degradation in municipal waste landfill sites: evidence of a role for fibrobacters.}, journal = {Environmental microbiology}, volume = {14}, number = {4}, pages = {1077-1087}, doi = {10.1111/j.1462-2920.2011.02688.x}, pmid = {22225785}, issn = {1462-2920}, mesh = {Bacteria, Anaerobic/genetics/metabolism ; Biodegradation, Environmental ; Cellulose/analysis/*metabolism ; Clostridium/genetics/metabolism ; DNA Primers/genetics/metabolism ; Ecology ; Fibrobacter/genetics/metabolism/*physiology ; Fungi/metabolism ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; *Refuse Disposal ; Waste Products/statistics &amp; numerical data ; }, abstract = {Cellulose is reputedly the most abundant organic polymer in the biosphere, yet despite the fundamental role of cellulolytic microorganisms in global carbon cycling and as potential sources of novel enzymes for biotechnology, their identity and ecology is not well established. Cellulose is a major component of landfill waste and its degradation is therefore a key feature of the anaerobic microbial decomposition process. Here, we targeted a number of taxa containing known cellulolytic anaerobes (members of the bacterial genus Fibrobacter, lineages of Clostridium clusters I, III, IV and XIV, and anaerobic fungi of the Neocallimastigales) in landfill leachate and colonized cellulose 'baits' via PCR and quantitative PCR (qPCR). Fibrobacter spp. and Clostridium clusters III, IV and XIV were detected in almost all leachate samples and cluster III and XIV clostridia were the most abundant (1-6% and 1-17% of total bacterial 16S rRNA gene copies respectively). Two landfill leachate microcosms were constructed to specifically assess those microbial communities that colonize and degrade cellulose substrates in situ. Scanning electron microscopy (SEM) of colonized cotton revealed extensive cellulose degradation in one microcosm, and Fibrobacter spp. and Clostridium cluster III represented 29% and 17%, respectively, of total bacterial 16S rRNA gene copies in the biofilm. Visible cellulose degradation was not observed in the second microcosm, and this correlated with negligible relative abundances of Clostridium cluster III and Fibrobacter spp. (≤ 0.1%), providing the first evidence that the novel fibrobacters recently detected in landfill sites and other non-gut environments colonize and degrade cellulose substrates in situ.}, }
@article {pmid22225547, year = {2012}, author = {Siggins, A and Gunnigle, E and Abram, F}, title = {Exploring mixed microbial community functioning: recent advances in metaproteomics.}, journal = {FEMS microbiology ecology}, volume = {80}, number = {2}, pages = {265-280}, pmid = {22225547}, issn = {1574-6941}, mesh = {Bioengineering ; *Ecosystem ; Environment ; *Environmental Microbiology ; Humans ; Metagenome ; Metagenomics ; Proteome/metabolism ; Proteomics/*trends ; }, abstract = {System approaches to elucidate ecosystem functioning constitute an emerging area of research within microbial ecology. Such approaches aim at investigating all levels of biological information (DNA, RNA, proteins and metabolites) to capture the functional interactions occurring in a given ecosystem and track down characteristics that could not be accessed by the study of isolated components. In this context, the study of the proteins collectively expressed by all the microorganisms present within an ecosystem (metaproteomics) is not only crucial but can also provide insights into microbial functionality. Overall, the success of metaproteomics is closely linked to metagenomics, and with the exponential increase in the availability of metagenome sequences, this field of research is starting to experience generation of an overwhelming amount of data, which requires systematic analysis. Metaproteomics has been employed in very diverse environments, and this review discusses the recent advances achieved in the context of human biology, soil, marine and freshwater environments as well as natural and bioengineered systems.}, }
@article {pmid22224928, year = {2012}, author = {Pozuelo, MJ and Agis-Torres, A and Hervert-Hernández, D and Elvira López-Oliva, M and Muñoz-Martínez, E and Rotger, R and Goñi, I}, title = {Grape antioxidant dietary fiber stimulates Lactobacillus growth in rat cecum.}, journal = {Journal of food science}, volume = {77}, number = {2}, pages = {H59-62}, doi = {10.1111/j.1750-3841.2011.02520.x}, pmid = {22224928}, issn = {1750-3841}, mesh = {Animals ; Antioxidants/*pharmacology ; Bifidobacterium/growth &amp; development ; Cecum/drug effects/*microbiology ; Diet ; Dietary Fiber/*administration &amp; dosage ; *Dietary Supplements ; Lactobacillus/*drug effects/growth &amp; development ; Male ; Plant Extracts/pharmacology ; Polyphenols/pharmacology ; Rats ; Rats, Wistar ; Real-Time Polymerase Chain Reaction/methods ; Vitis/*chemistry ; }, abstract = {UNLABELLED: The digesta is a highly active biological system where epithelial cells, microbiota, nondigestible dietary components, and a large number of metabolic products interact. The gut microbiota can be modulated by both endogenous and exogenous substrates. Undigested dietary residues are substrates for colonic microbiota and may influence gut microbial ecology. The objective of this work was to study the capacity of grape antioxidant dietary fiber (GADF), which is rich in polyphenols, to modify the bacterial profile in the cecum of rats. Male adult Wistar rats were fed for 4 wk with diets containing either cellulose or GADF as dietary fiber. The effect of GADF on bacterial growth was evaluated in vitro and on the cecal microbiota of rats using quantitative real time polymerase chain reaction (RT-PCR). The results showed that GADF intake stimulates proliferation of Lactobacillus and slightly affects the composition of Bifidobacterium species. GADF was also found to have a stimulative effect on Lactobacillus reuteri and Lactobacillus acidophilus in vitro. These findings suggest that the consumption of a diet rich in plant foods with high dietary fiber and polyphenol content may enhance the gastrointestinal health of the host through microbiota modulation.<br><br>PRACTICAL APPLICATION: Grape antioxidant fiber combines nutritional and physiological properties of dietary fiber and natural antioxidants from grapes. Grape antioxidant fiber could be used as an ingredient for functional foods and as a dietary supplement to increase the intake of dietary fiber and bioactive compounds.}, }
@article {pmid22224476, year = {2012}, author = {Fernández, NV and Mestre, MC and Marchelli, P and Fontenla, SB}, title = {Yeast and yeast-like fungi associated with dry indehiscent fruits of Nothofagus nervosa in Patagonia, Argentina.}, journal = {FEMS microbiology ecology}, volume = {80}, number = {1}, pages = {179-192}, doi = {10.1111/j.1574-6941.2011.01287.x}, pmid = {22224476}, issn = {1574-6941}, mesh = {Argentina ; Base Sequence ; Fruit/microbiology ; Fungi/*classification/genetics/growth &amp; development/isolation &amp; purification ; Magnoliopsida/*microbiology ; Molecular Sequence Data ; Seeds/microbiology ; Yeasts/*classification/genetics/growth &amp; development/isolation &amp; purification ; }, abstract = {Nothofagus nervosa (Raulí) is a native tree species that yields valuable timber. It was overexploited in the past and is currently included in domestication and conservation programs. Several research programs have focused on the characterization of epiphytic microorganisms because it has been demonstrated that they can affect plant-pathogen interactions and/or promote plant growth. Although the microbial ecology of leaves has been well studied, less is known about microorganisms occurring on seeds and noncommercial fruits. In this work, we analyzed the yeast and yeast-like fungi present on N. nervosa fruits destined for the propagation of this species, as well as the effects of fruit preservation and seed dormancy-breaking processes on fungal diversity. Morphological and molecular methods were used, and differences between fungal communities were analyzed using a similarity index. A total of 171 isolates corresponding to 17 species were recovered, most of which belong to the phylum Ascomycota. The majority of the species develop mycelia, produce pigments and mycosporines, and these adaptation strategies are discussed. It was observed that the preservation process considerably reduced yeast and yeast-like fungal diversity. This is the first study concerning microbial communities associated with this ecologically and economically important species, and the information presented is relevant to domestication programs.}, }
@article {pmid22221490, year = {2012}, author = {De Gusseme, B and Soetaert, M and Hennebel, T and Vanhaecke, L and Boon, N and Verstraete, W}, title = {Catalytic dechlorination of diclofenac by biogenic palladium in a microbial electrolysis cell.}, journal = {Microbial biotechnology}, volume = {5}, number = {3}, pages = {396-402}, pmid = {22221490}, issn = {1751-7915}, mesh = {Bacteria/chemistry/*metabolism ; Biodegradation, Environmental ; Bioelectric Energy Sources/*microbiology ; Bioreactors/microbiology ; Catalysis ; Diclofenac/*metabolism ; Electrodes ; Electrolysis ; Palladium/*metabolism ; }, abstract = {Diclofenac is one of the most commonly detected pharmaceuticals in wastewater treatment plant (WWTP) effluents and the receiving water bodies. In this study, biogenic Pd nanoparticles ('bio-Pd') were successfully applied in a microbial electrolysis cell (MEC) for the catalytic reduction of diclofenac. Hydrogen gas was produced in the cathodic compartment, and consumed as a hydrogen donor by the bio-Pd on the graphite electrodes. In this way, complete dechlorination of 1 mg diclofenac l(-1) was achieved during batch recirculation experiments, whereas no significant removal was observed in the absence of the biocatalyst. The complete dechlorination of diclofenac was demonstrated by the concomitant production of 2-anilinophenylacetate (APA). Through the addition of -0.8 V to the circuit, continuous and complete removal of diclofenac was achieved in synthetic medium at a minimal HRT of 2 h. Continuous treatment of hospital WWTP effluent containing 1.28 µg diclofenac l(-1) resulted in a lower removal efficiency of 57%, which can probably be attributed to the affinity of other environmental constituents for the bio-Pd catalyst. Nevertheless, reductive catalysis coupled to sustainable hydrogen production in a MEC offers potential to lower the release of micropollutants from point-sources such as hospital WWTPs.}, }
@article {pmid22221449, year = {2012}, author = {Meerburg, F and Hennebel, T and Vanhaecke, L and Verstraete, W and Boon, N}, title = {Diclofenac and 2-anilinophenylacetate degradation by combined activity of biogenic manganese oxides and silver.}, journal = {Microbial biotechnology}, volume = {5}, number = {3}, pages = {388-395}, pmid = {22221449}, issn = {1751-7915}, mesh = {Aniline Compounds ; Biodegradation, Environmental ; Diclofenac/*metabolism ; Manganese Compounds/*metabolism ; Oxidation-Reduction ; Oxides/*metabolism ; Phenylacetates ; Pseudomonas putida/*metabolism ; Silver/*metabolism ; Water Pollutants, Chemical/*metabolism ; Water Purification/*methods ; }, abstract = {The occurrence of a range of recalcitrant organic micropollutants in our aquatic environment has led to the development of various tertiary wastewater treatment methods. In this study, biogenic manganese oxides (Bio-MnOx), biogenic silver nanoparticles (Bio-Ag(0)) and ionic silver were used for the oxidative removal of the frequently encountered drug diclofenac and its dechlorinated form, 2-anilinophenylacetate (APA). Diclofenac was rapidly degraded during ongoing manganese oxidation by Pseudomonas putida MnB6. Furthermore, whereas preoxidized Bio-MnOx, Bio-Ag(0) and Ag(+) separately did not show any removal capacity for diclofenac, an enhanced removal occurred when Bio-MnOx and silver species were combined. Similar results were obtained for APA. Finally, a slow removal of diclofenac but more rapid APA degradation was observed when silver was added to manganese-free P. putida biomass. Combining these results, three mechanisms of diclofenac and APA removal could be distinguished: (i) a co-metabolic removal during active Mn(2+) oxidation by P. putida; (ii) a synergistic interaction between preoxidized Bio-MnOx and silver species; and (iii) a (bio)chemical process by biomass enriched with silver catalysts. This paper demonstrates the use of P. putida for water treatment purposes and is the first report of the application of silver combined with biogenic manganese for the removal of organic water contaminants.}, }
@article {pmid22214994, year = {2012}, author = {Urbieta, MS and González Toril, E and Aguilera, A and Giaveno, MA and Donati, E}, title = {First prokaryotic biodiversity assessment using molecular techniques of an acidic river in Neuquén, Argentina.}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {91-104}, pmid = {22214994}, issn = {1432-184X}, mesh = {Archaea/*classification/genetics/*isolation &amp; purification/metabolism ; Argentina ; Bacteria/*classification/genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Molecular Typing/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers/chemistry/*microbiology ; }, abstract = {Two acidic hot springs close to the crater of Copahue Volcano (Neuquén, Argentina) are the source of the Río Agrio. The river runs several kilometres before flowing into Caviahue Lake. Along the river, temperature, iron, other metal and proton concentrations decrease gradually with distance downstream. From the source to the lake and depending on the season, pH can rise from 1.0 (or even less) to about 4.0, while temperature values decrease from 70°C to 15°C. Water samples were taken from different stations on the river selected according to their physicochemical parameters. In order to assess prokaryotic biodiversity throughout the water column, different and complementary molecular biology techniques were used, mainly in situ hybridisation and 16S rRNA gene cloning and sequencing. All microorganisms found are typical of acidic environments. Sulphur-oxidizing bacteria like Acidithiobacillus thiooxidans and Acidithiobacillus albertensis were detected in every station. Moderately thermophile iron- and sulphur-oxidizing bacteria like members of Alicyclobacillus and Sulfobacillus genera were also ubiquitous. Strict iron-oxidizing bacteria like Leptospirillum and Ferrimicrobium were present at the source of the river, but disappeared downstream where iron concentrations were much lower. Iron-oxidizing, mesophilic Ferroplasma spp. were the main archaea found. The data presented in this work represent the first molecular assessment of this rare natural acidic environment.}, }
@article {pmid22214077, year = {2011}, author = {Vankerckhoven, E and Verbessem, B and Crauwels, S and Declerck, P and Muylaert, K and Willems, KA and Rediers, H}, title = {Exploring the potential synergistic effects of chemical disinfectants and UV on the inactivation of free-living bacteria and treatment of biofilms in a pilot-scale system.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {64}, number = {6}, pages = {1247-1253}, doi = {10.2166/wst.2011.718}, pmid = {22214077}, issn = {0273-1223}, mesh = {Bacteria/*drug effects ; Biofilms/*drug effects ; Disinfectants/*pharmacology ; Hydrogen Peroxide/pharmacology ; Peracetic Acid/pharmacology ; *Ultraviolet Rays ; }, abstract = {The main objective of this study is to explore possible synergistic or additive effects of combinations of chemical disinfectants (sodium hypochlorite, peracetic acid, hydrogen peroxide, chlorine dioxide) and UV in their efficacy in inactivating free-living bacteria and removing biofilms. In contrast to most studies, this study examines disinfection of municipal water in a pilot-scale system using a mixed bacterial suspension, which enables a better simulation of the conditions encountered in actual industrial environments. It was shown that the combination of either hypochlorite, hydrogen peroxide, peracetic acid, or chlorine dioxide with UV yielded additive effects on the inactivation of free-living bacteria. Actual synergy was observed for the combination of UV and 5 ppm hydrogen peroxide. Regarding biofilm treatment, additive effects were observed using the combination of hydrogen peroxide and UV. The promising results obtained in this study indicate that the combination of UV and chemical disinfectants can considerably reduce the amount of chemicals required for the effective disinfection and treatment of biofilms.}, }
@article {pmid22213355, year = {2012}, author = {Comolli, LR and Duarte, R and Baum, D and Luef, B and Downing, KH and Larson, DM and Csencsits, R and Banfield, JF}, title = {A portable cryo-plunger for on-site intact cryogenic microscopy sample preparation in natural environments.}, journal = {Microscopy research and technique}, volume = {75}, number = {6}, pages = {829-836}, pmid = {22213355}, issn = {1097-0029}, support = {P01 GM051487/GM/NIGMS NIH HHS/United States ; }, mesh = {Cryoelectron Microscopy/*methods ; Environmental Microbiology ; *Freezing ; *Point-of-Care Systems ; Specimen Handling/*methods ; }, abstract = {We present a modern, light portable device specifically designed for environmental samples for cryogenic transmission-electron microscopy (cryo-TEM) by on-site cryo-plunging. The power of cryo-TEM comes from preparation of artifact-free samples. However, in many studies, the samples must be collected at remote field locations, and the time involved in transporting samples back to the laboratory for cryogenic preservation can lead to severe degradation artifacts. Thus, going back to the basics, we developed a simple mechanical device that is light and easy to transport on foot yet effective. With the system design presented here we are able to obtain cryo-samples of microbes and microbial communities not possible to culture, in their near-intact environmental conditions as well as in routine laboratory work, and in real time. This methodology thus enables us to bring the power of cryo-TEM to microbial ecology.}, }
@article {pmid22213055, year = {2012}, author = {Ransom-Jones, E and Jones, DL and McCarthy, AJ and McDonald, JE}, title = {The Fibrobacteres: an important phylum of cellulose-degrading bacteria.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {267-281}, pmid = {22213055}, issn = {1432-184X}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; DNA, Bacterial/*genetics ; *Environmental Microbiology ; Fibrobacter/classification/genetics/isolation &amp; purification/*physiology ; Fibrobacteres/*classification/genetics/isolation &amp; purification ; Gastrointestinal Tract/metabolism/*microbiology ; Isoptera/metabolism/microbiology ; Lakes ; Mammals/metabolism/microbiology ; Phylogeny ; Refuse Disposal ; }, abstract = {The phylum Fibrobacteres currently comprises one formal genus, Fibrobacter, and two cultured species, Fibrobacter succinogenes and Fibrobacter intestinalis, that are recognised as major bacterial degraders of lignocellulosic material in the herbivore gut. Historically, members of the genus Fibrobacter were thought to only occupy mammalian intestinal tracts. However, recent 16S rRNA gene-targeted molecular approaches have demonstrated that novel centres of variation within the genus Fibrobacter are present in landfill sites and freshwater lakes, and their relative abundance suggests a potential role for fibrobacters in cellulose degradation beyond the herbivore gut. Furthermore, a novel subphylum within the Fibrobacteres has been detected in the gut of wood-feeding termites, and proteomic analyses have confirmed their involvement in cellulose hydrolysis. The genome sequence of F. succinogenes rumen strain S85 has recently suggested that within this group of organisms a "third" way of attacking the most abundant form of organic carbon in the biosphere, cellulose, has evolved. This observation not only has evolutionary significance, but the superior efficiency of anaerobic cellulose hydrolysis by Fibrobacter spp., in comparison to other cellulolytic rumen bacteria that typically utilise membrane-bound enzyme complexes (cellulosomes), may be explained by this novel cellulase system. There are few bacterial phyla with potential functional importance for which there is such a paucity of phenotypic and functional data. In this review, we highlight current knowledge of the Fibrobacteres phylum, its taxonomy, phylogeny, ecology and potential as a source of novel glycosyl hydrolases of biotechnological importance.}, }
@article {pmid22202889, year = {2012}, author = {Goberna, M and García, C and Insam, H and Hernández, MT and Verdú, M}, title = {Burning fire-prone Mediterranean shrublands: immediate changes in soil microbial community structure and ecosystem functions.}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {242-255}, pmid = {22202889}, issn = {1432-184X}, mesh = {Archaea/genetics/growth &amp; development/*isolation &amp; purification ; Bacteria/genetics/growth &amp; development/*isolation &amp; purification ; *Ecosystem ; Fires ; Fungi/genetics/growth &amp; development/*isolation &amp; purification ; Mediterranean Region ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Wildfires subject soil microbes to extreme temperatures and modify their physical and chemical habitat. This might immediately alter their community structure and ecosystem functions. We burned a fire-prone shrubland under controlled conditions to investigate (1) the fire-induced changes in the community structure of soil archaea, bacteria and fungi by analysing 16S or 18S rRNA gene amplicons separated through denaturing gradient gel electrophoresis; (2) the physical and chemical variables determining the immediate shifts in the microbial community structure; and (3) the microbial drivers of the change in ecosystem functions related to biogeochemical cycling. Prokaryotes and eukaryotes were structured by the local environment in pre-fire soils. Fire caused a significant shift in the microbial community structure, biomass C, respiration and soil hydrolases. One-day changes in bacterial and fungal community structure correlated to the rise in total organic C and NO(3)(-)-N caused by the combustion of plant residues. In the following week, bacterial communities shifted further forced by desiccation and increasing concentrations of macronutrients. Shifts in archaeal community structure were unrelated to any of the 18 environmental variables measured. Fire-induced changes in the community structure of bacteria, rather than archaea or fungi, were correlated to the enhanced microbial biomass, CO(2) production and hydrolysis of C and P organics. This is the first report on the combined effects of fire on the three biological domains in soils. We concluded that immediately after fire the biogeochemical cycling in Mediterranean shrublands becomes less conservative through the increased microbial biomass, activity and changes in the bacterial community structure.}, }
@article {pmid22202888, year = {2012}, author = {Murdock, JN and Wetzel, DL}, title = {Macromolecular response of individual algal cells to nutrient and atrazine mixtures within biofilms.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {761-772}, pmid = {22202888}, issn = {1432-184X}, mesh = {Atrazine/*pharmacology ; Biofilms/drug effects ; Chlorophyll/metabolism ; Chlorophyll A ; Chlorophyta/*drug effects/metabolism ; Cyanobacteria/drug effects/*metabolism ; Diatoms/drug effects/metabolism ; Herbicides/*pharmacology ; Quaternary Ammonium Compounds/metabolism ; Spectrophotometry, Infrared/methods ; Water Pollutants, Chemical/*pharmacology ; }, abstract = {Pollutant effects on biofilm physiology are difficult to assess due to differential susceptibility of species and difficulty separating individual species for analysis. Also, measuring whole assemblage responses such as metabolism can mask species-specific responses, as some species may decrease and others increase metabolic activity. Physiological responses can add information to compositional data, and may be a more sensitive indicator of effect. It is difficult, however, to separate individual species for biochemical analyses. Agricultural runoff often contains multiple pollutants that may alter algal assemblages in receiving waters. It is unclear how mixtures containing potential algal growth stimulators and inhibitors (e.g., nutrients and herbicides) alter algal assemblage structure and function. In research presented here, algal biofilms were exposed to nutrients, atrazine, and their mixtures, and assemblage-level structural and functional changes were measured. Synchrotron infrared microspectroscopy (IMS) was used to isolate the biochemical changes within individual cells from a dominant species of a green alga (Mougeotia sp.), a diatom (Navicula sp.), and a cyanobacterium (Hapalosiphon sp.). At the assemblage level, mixtures generally increased algal biovolume, decreased chlorophyll a, and had no effect on metabolism or ammonium uptake. Navicula had a strong negative response to atrazine initially, but later was more affected by nutrients. Hapalosiphon responded positively to both atrazine and nutrients, and Mougeotia did not exhibit any biochemical trends. Generally, biochemical changes in each species were similar to cells experiencing low stress conditions, with increased relative protein and decreased relative lipid. IMS provided direct evidence that individual species in a natural biofilm can have unique responses to atrazine, nutrients, and mixtures. Results suggest that the initial benthic community composition should have a strong influence on the overall impact of agricultural pollutants.}, }
@article {pmid22202887, year = {2012}, author = {Oberbeckmann, S and Fuchs, BM and Meiners, M and Wichels, A and Wiltshire, KH and Gerdts, G}, title = {Seasonal dynamics and modeling of a Vibrio community in coastal waters of the North Sea.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {543-551}, pmid = {22202887}, issn = {1432-184X}, mesh = {Models, Biological ; North Sea ; Seasons ; Seawater/chemistry/*microbiology ; Vibrio/classification/genetics/*isolation &amp; purification ; }, abstract = {Vibrio species are ubiquitously distributed in marine waters all over the world. High genome plasticity due to frequent mutation, recombination, and lateral gene transfer enables Vibrio to adapt rapidly to environmental changes. The genus Vibrio comprises several human pathogens, which commonly cause outbreaks of severe diarrhea in tropical regions. In recent years, pathogenic Vibrio emerged also in coastal European waters. Little is known about factors driving the proliferation of Vibrio spp. in temperate waters such as the North Sea. In this study a quantification of Vibrio in the North Sea and their response to biotic and abiotic parameters were assessed. Between January and December 2009, Vibrio at Helgoland Roads (North Sea, Germany) were quantified using fluorescence in situ hybridization. Vibrio numbers up to 3.4 × 10(4) cells × mL(-1) (2.2% of total microbial counts) were determined in summer, but their abundance was significantly lower in winter (5 × 10(2) cells × mL(-1)). Correlations between Vibrio and nutrients (SiO(2), PO(4) (3-), DIN), Secchi depth, temperature, salinity, and chlorophyll a were calculated using Spearman rank analysis. Multiple stepwise regression analysis was carried out to analyze the additive influence of multiple factors on Vibrio. Based on these calculations, we found that high water temperature and low salinity best explained the increase of Vibrio cell numbers. Other environmental parameters, especially nutrients and chlorophyll a, also had an influence. All variables were shown to be subject to the overall seasonal dynamics at Helgoland Roads. Multiple regression models could represent an efficient and reliable tool to predict Vibrio abundances in response to the climate change in European waters.}, }
@article {pmid22202886, year = {2012}, author = {He, X and Hu, W and Kaplan, CW and Guo, L and Shi, W and Lux, R}, title = {Adherence to streptococci facilitates Fusobacterium nucleatum integration into an oral microbial community.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {532-542}, pmid = {22202886}, issn = {1432-184X}, support = {R01 DE020102/DE/NIDCR NIH HHS/United States ; R01 DE021108/DE/NIDCR NIH HHS/United States ; DE021108/DE/NIDCR NIH HHS/United States ; DE020102/DE/NIDCR NIH HHS/United States ; }, mesh = {Adult ; Animals ; *Bacterial Adhesion ; Female ; Fusobacterium nucleatum/*physiology ; Humans ; Hydrogen Peroxide/metabolism ; Male ; Mice ; Mouth Diseases/*microbiology ; Saliva/microbiology ; Streptococcus sanguis/*physiology ; }, abstract = {The development of multispecies oral microbial communities involves complex intra- and interspecies interactions at various levels. The ability to adhere to the resident bacteria or the biofilm matrix and overcome community resistance are among the key factors that determine whether a bacterium can integrate into a community. Fusobacterium nucleatum is a prevalent Gram-negative oral bacterial species that is able to adhere to a variety of oral microbes and has been implicated in playing an important role in the establishment of multispecies oral microbial community. However, the majority of experiments thus far has focused on the physical adherence between two species as measured by in vitro co-aggregation assays, while the community-based effects on the integration of F. nucleatum into multispecies microbial community remains to be investigated. In this study, we focus on community integration of F. nucleatum. We demonstrated using an established in vitro mice oral microbiota (O-mix) that the viability of F. nucleatum was significantly reduced upon addition to the O-mix due to cell contact-dependent induction of hydrogen peroxide (H(2)O(2)) production by oral community. Interestingly, this inhibitory effect was significantly alleviated when F. nucleatum was allowed to adhere to its known interacting partner species (such as Streptococcus sanguinis) prior to addition. Furthermore, this aggregate formation-dependent protection was absent in the F. nucleatum mutant strain ΔFn1526 that is unable to bind to a number of Gram-positive species. More importantly, this protective effect was also observed during integration of F. nucleatum into a human salivary microbial community (S-mix). These results suggest that by adhering to other oral microbes, F. nucleatum is able to mask the surface components that are recognized by H(2)O(2) producing oral community members. This evasion strategy prevents detection by antagonistic oral bacteria and allows integration into the developing oral microbial community.}, }
@article {pmid22199217, year = {2012}, author = {Lee, HJ and Han, SI and Whang, KS}, title = {Catenulispora graminis sp. nov., a rhizobacterium from bamboo (Phyllostachys nigro var. henonis) rhizosphere soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {62}, number = {Pt 11}, pages = {2589-2592}, doi = {10.1099/ijs.0.035501-0}, pmid = {22199217}, issn = {1466-5034}, mesh = {Actinomycetales/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Bambusa/*microbiology ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Phylogeny ; Quinones/analysis ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {A novel actinobacterium, designated strain BR-34(T), was isolated from rhizosphere soil of bamboo (Phyllostachys nigro var. henonis) sampled in Damyang, Korea. The strain was found to have morphological and chemotaxonomic characteristics typical of the genus Catenulispora. The strain contained iso-C(16 : 0) as the major fatty acid and MK-9(H(4)), MK-9(H(6)) and MK-9(H(8)) as major isoprenoid quinones. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BR-34(T) formed a cluster separate from members of the genus Catenulispora and was related most closely to Catenulispora acidiphila ID139908(T) (97.4% similarity), Catenulispora rubra Aac-30(T) (97.3%), Catenulispora yoronensis TT N02-20(T) (97.3%) and Catenulispora subtropica TT 99-48(T) (97%). However, the level of DNA-DNA relatedness between strain BR-34(T) and C. acidiphila ID139908(T) was only 45.32%. Based on DNA-DNA relatedness, morphological and phenotypic data, strain BR-34(T) could be distinguished from the type strains of phylogenetically related species. It is therefore considered to represent a novel species of the genus Catenulispora, for which the name Catenulispora graminis sp. nov. is proposed. The type strain is BR-34(T) (=KACC 15070(T)=NBRC 107755(T)).}, }
@article {pmid22198685, year = {2012}, author = {Goudar, CT}, title = {An explicit solution for progress curve analysis in systems characterized by endogenous substrate production.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {898-904}, pmid = {22198685}, issn = {1432-184X}, mesh = {Algorithms ; Animals ; Geologic Sediments/*chemistry ; Hydrogen/*metabolism ; Kinetics ; *Models, Biological ; Nonlinear Dynamics ; Rumen/chemistry/*metabolism ; Sewage/*chemistry ; Substrate Specificity ; }, abstract = {The Lambert W function was used to explicitly relate substrate concentration S, to time t, and the kinetic parameters V (m), K (m), and R in the modified Michaelis-Menten equation that accounts for endogenous substrate production. The applicability of this explicit formulation for kinetic parameter estimation by progress curve analysis was demonstrated using a combination of synthetic and experimental substrate depletion data. Synthetic substrate depletion data were generated using S (0) values of 1, 2, and 3 μM and V (m), K (m), and R values of 1.0 μM h(-1), 1.0 μM, and 0.1 μM h(-1), respectively, and contained 5% normally distributed error. Experimental data were obtained from two previously published studies on hydrogen depletion in four experimental systems. In all instances, experimental data were well described by the explicit solution presented in this study. Differential equation solution and iterative S estimation are eliminated with the explicit solution approach, thereby simplifying progress curve analysis in systems characterized by endogenous substrate production.}, }
@article {pmid22197171, year = {2012}, author = {Nielsen, PH and Saunders, AM and Hansen, AA and Larsen, P and Nielsen, JL}, title = {Microbial communities involved in enhanced biological phosphorus removal from wastewater--a model system in environmental biotechnology.}, journal = {Current opinion in biotechnology}, volume = {23}, number = {3}, pages = {452-459}, doi = {10.1016/j.copbio.2011.11.027}, pmid = {22197171}, issn = {1879-0429}, mesh = {Biotechnology/methods ; Ecosystem ; *Metagenome ; Models, Biological ; *Phosphorus ; Wastewater/*chemistry/*microbiology ; *Water Purification ; }, abstract = {Enhanced biological phosphorus removal (EBPR) is one of the most advanced and complicated wastewater treatment processes applied today, and it is becoming increasingly popular worldwide as a sustainable way to remove and potentially reuse P. It is carried out by complex microbial communities consisting primarily of uncultured microorganisms. The EBPR process is a well-studied system with clearly defined boundaries which makes it very suitable as a model ecosystem in microbial ecology. Of particular importance are the transformations of C, N, and P, the solid-liquid separation properties and the functional and structural stability. A range of modern molecular methods has been used to study these communities in great detail including single cell microbiology, various -omics methods, flux analyses, and modeling making this one of the best studied microbial ecosystems so far. Recently, an EBPR core microbiome has been described and we present in this article some highlights and show how this complex microbial community can be used as model ecosystem in environmental biotechnology.}, }
@article {pmid22194981, year = {2011}, author = {Ran-Ressler, RR and Khailova, L and Arganbright, KM and Adkins-Rieck, CK and Jouni, ZE and Koren, O and Ley, RE and Brenna, JT and Dvorak, B}, title = {Branched chain fatty acids reduce the incidence of necrotizing enterocolitis and alter gastrointestinal microbial ecology in a neonatal rat model.}, journal = {PloS one}, volume = {6}, number = {12}, pages = {e29032}, pmid = {22194981}, issn = {1932-6203}, support = {R01 HD039657/HD/NICHD NIH HHS/United States ; R21 HD064604/HD/NICHD NIH HHS/United States ; HD039657/HD/NICHD NIH HHS/United States ; HD064604/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Animals, Newborn ; Bacteria/*drug effects/genetics ; Chromatography, Gas ; Diet ; Disease Models, Animal ; Enterocolitis, Necrotizing/*drug therapy/genetics/*microbiology ; Fatty Acids/blood/chemistry/*pharmacology/*therapeutic use ; Gastrointestinal Tract/*drug effects/metabolism/*microbiology/pathology ; Gene Expression Regulation/drug effects ; Genetic Variation/drug effects ; Health ; Ileum/drug effects/metabolism/pathology ; Immunohistochemistry ; Incidence ; Interleukin-10/genetics/metabolism ; Liver/drug effects/metabolism ; Mucins/genetics/metabolism ; Neuropeptides/genetics/metabolism ; Peptides/metabolism ; Phospholipids/metabolism ; RNA, Messenger/genetics/metabolism ; Rats ; Rats, Sprague-Dawley ; Trefoil Factor-3 ; }, abstract = {INTRODUCTION: Branched chain fatty acids (BCFA) are found in the normal term human newborn's gut, deposited as major components of vernix caseosa ingested during late fetal life. We tested the hypothesis that premature infants' lack of exposure to gastrointestinal (GI) BCFA is associated with their microbiota and risk for necrotizing enterocolitis (NEC) using a neonatal rat model.<br><br>METHODS: Pups were collected one day before scheduled birth. The pups were exposed to asphyxia and cold stress to induce NEC. Pups were assigned to one of three experimental treatments. DF (dam-fed); Control, hand-fed rat milk substitute; BCFA, hand-fed rat milk substitute with 20%w/w BCFA. Total fat was equivalent (11%wt) for both the Control and BCFA groups. Cecal microbiota were characterized by 16S rRNA gene pyrosequencing, and intestinal injury, ileal cytokine and mucin gene expression, interleukin-10 (IL-10) peptide immunohistochemistry, and BCFA uptake in ileum phospholipids, serum and liver were assessed.<br><br>RESULTS: NEC incidence was reduced by over 50% in the BCFA group compared to the Control group as assessed in ileal tissue; microbiota differed among all groups. BCFA-fed pups harbored greater levels of BCFA-associated Bacillus subtilis and Pseudomonas aeruginosa compared to Controls. Bacillus subtilis levels were five-fold greater in healthy pups compared to pups with NEC. BCFA were selectively incorporated into ileal phospholipids, serum and liver tissue. IL-10 expression increased three-fold in the BCFA group versus Controls and no other inflammatory or mucosal mRNA markers changed.<br><br>CONCLUSION: At constant dietary fat level, BCFA reduce NEC incidence and alter microbiota composition. BCFA are also incorporated into pup ileum where they are associated with enhanced IL-10 and may exert other specific effects.}, }
@article {pmid22194284, year = {2012}, author = {Ernebjerg, M and Kishony, R}, title = {Distinct growth strategies of soil bacteria as revealed by large-scale colony tracking.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {5}, pages = {1345-1352}, pmid = {22194284}, issn = {1098-5336}, support = {P50 GM068763/GM/NIGMS NIH HHS/United States ; R01 GM081617/GM/NIGMS NIH HHS/United States ; 5P50 GM068763-07/GM/NIGMS NIH HHS/United States ; }, mesh = {Automation ; Bacteria/*growth &amp; development ; Bacteriological Techniques ; Colony Count, Microbial ; High-Throughput Screening Assays ; Image Processing, Computer-Assisted ; *Soil Microbiology ; }, abstract = {Our understanding of microbial ecology has been significantly furthered in recent years by advances in sequencing techniques, but comprehensive surveys of the phenotypic characteristics of environmental bacteria remain rare. Such phenotypic data are crucial for understanding the microbial strategies for growth and the diversity of microbial ecosystems. Here, we describe a high-throughput measurement of the growth of thousands of bacterial colonies using an array of flat-bed scanners coupled with automated image analysis. We used this system to investigate the growth properties of members of a microbial community from untreated soil. The system provides high-quality measurements of the number of CFU, colony growth rates, and appearance times, allowing us to directly study the distribution of these properties in mixed environmental samples. We find that soil bacteria display a wide range of growth strategies which can be grouped into several clusters that cannot be reduced to any of the classical dichotomous divisions of soil bacteria, e.g., into copiotophs and oligotrophs. We also find that, at early times, cells are most likely to form colonies when other, nearby colonies are present but not too dense. This maximization of culturability at intermediate plating densities suggests that the previously observed tendency for high density to lead to fewer colonies is partly offset by the induction of colony formation caused by interactions between microbes. These results suggest new types of growth classification of soil bacteria and potential effects of species interactions on colony growth.}, }
@article {pmid22193925, year = {2012}, author = {Resat, H and Bailey, V and McCue, LA and Konopka, A}, title = {Modeling microbial dynamics in heterogeneous environments: growth on soil carbon sources.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {883-897}, pmid = {22193925}, issn = {1432-184X}, mesh = {Bacteria/*growth &amp; development/*metabolism ; Carbon/chemistry/*metabolism ; Cellulose/metabolism ; Hydrolases/metabolism ; Hydrolysis ; Kinetics ; *Models, Biological ; Soil/*chemistry ; *Soil Microbiology ; Substrate Specificity ; }, abstract = {We have developed a new kinetic model to study how microbial dynamics are affected by the heterogeneity in the physical structure of the environment and by different strategies for hydrolysis of polymeric carbon. The hybrid model represented the dynamics of substrates and enzymes using a continuum representation and the dynamics of the cells were modeled individually. Individual-based biological model allowed us to explicitly simulate microbial diversity, and to model cell physiology as regulated via optimal allocation of cellular resources to enzyme synthesis, control of growth rate by protein synthesis capacity, and shifts to dormancy. This model was developed to study how microbial community functioning is influenced by local environmental conditions in heterogeneous media such as soil and by the functional attributes of individual microbes. Microbial community dynamics were simulated at two spatial scales: micro-pores that resemble 6-20-μm size portions of the soil physical structure and in 111-μm size soil aggregates with a random pore structure. Different strategies for acquisition of carbon from polymeric cellulose were investigated. Bacteria that express membrane-associated hydrolase had different growth and survival dynamics in soil pores than bacteria that release extracellular hydrolases. The kinetic differences suggested different functional niches for these two microbe types in cellulose utilization. Our model predicted an emergent behavior in which co-existence of membrane-associated hydrolase and extracellular hydrolases releasing organisms led to higher cellulose utilization efficiency and reduced stochasticity. Our analysis indicated that their co-existence mutually benefits these organisms, where basal cellulose degradation activity by membrane-associated hydrolase-expressing cells shortened the soluble hydrolase buildup time and, when enzyme buildup allowed for cellulose degradation to be fast enough to sustain exponential growth, all the organisms in the community shared the soluble carbon product and grew together. Although pore geometry affected the kinetics of cellulose degradation, the patterns observed for the bacterial community dynamics in the 6-20 μm-sized micro-pores were relevant to the dynamics in the more complex 111-μm-sized porous soil aggregates, implying that micro-scale studies can be useful approximations to aggregate scale studies when local effects on microbial dynamics are studied. As shown with examples in this study, various functional niches of the bacterial communities can be investigated using complex predictive mathematical models where the role of key environmental aspects such as the heterogeneous three-dimensional structure, functional niches of the community members, and environmental biochemical processes are directly connected to microbial metabolism and maintenance in an integrated model.}, }
@article {pmid22192760, year = {2012}, author = {De Roy, K and Clement, L and Thas, O and Wang, Y and Boon, N}, title = {Flow cytometry for fast microbial community fingerprinting.}, journal = {Water research}, volume = {46}, number = {3}, pages = {907-919}, doi = {10.1016/j.watres.2011.11.076}, pmid = {22192760}, issn = {1879-2448}, mesh = {Bacteria/*genetics/*isolation &amp; purification ; Cluster Analysis ; DNA Fingerprinting/*methods ; Denaturing Gradient Gel Electrophoresis ; Discriminant Analysis ; Drinking Water/*microbiology ; Flow Cytometry/*methods ; Temperature ; Water Microbiology ; }, abstract = {Characterizing the microbial community of water is important in different domains, ranging from food and beverage production to wastewater treatment. Conventional methods, such as heterotrophic plate count, selective plating and molecular techniques, are time consuming and labor intensive. A flow cytometry based approach was developed for a fast and objective comparison of microbial communities based on the distribution of cellular features from single cells within these communities. The method consists of two main parts, firstly the generation of fingerprint data by flow cytometry and secondly a novel statistical pipeline for the analysis of flow cytometric data. The combined method was shown to be useful for the discrimination and classification of different brands of drinking water. It was also successfully applied to detect changes in microbial community composition of drinking water caused by changing environmental factors. Generally, the method can be used as a fast fingerprinting method of microbial communities in aquatic samples and as a tool to detect shifts within these communities.}, }
@article {pmid22191449, year = {2012}, author = {Angelakis, E and Armougom, F and Million, M and Raoult, D}, title = {The relationship between gut microbiota and weight gain in humans.}, journal = {Future microbiology}, volume = {7}, number = {1}, pages = {91-109}, doi = {10.2217/fmb.11.142}, pmid = {22191449}, issn = {1746-0921}, mesh = {Animals ; Bacteria/*genetics/isolation &amp; purification/metabolism ; Gastrointestinal Tract/metabolism/*microbiology ; Humans ; *Metagenome ; Mice ; Obesity/etiology/metabolism/*microbiology/physiopathology ; *Weight Gain ; }, abstract = {The human gut microbiota is a metabolic organ that is determined by a dynamic process of selection and competition. Age, dietary habits and geographical origin of people have an important impact on the intestinal microbiota. The role of the microbiota is still largely unknown, but the bacteria of the gut flora do contribute enzymes that are absent in humans and play an essential role in the catabolism of dietary fibers. Germ-free mice provide a complementary approach for characterizing the properties of the human gut microbiota. Recently, microbial changes in the human gut were proposed to be one of the possible causes of obesity. This review summarizes the latest research on the association between microbial ecology and host weight.}, }
@article {pmid22189864, year = {2012}, author = {Ekkers, DM and Cretoiu, MS and Kielak, AM and Elsas, JD}, title = {The great screen anomaly--a new frontier in product discovery through functional metagenomics.}, journal = {Applied microbiology and biotechnology}, volume = {93}, number = {3}, pages = {1005-1020}, pmid = {22189864}, issn = {1432-0614}, mesh = {Biological Factors/genetics/*metabolism ; Biotechnology/*methods ; Computational Biology/methods ; Ecosystem ; *Environmental Microbiology ; Gene Library ; *Genes ; Metagenomics/*methods ; }, abstract = {Functional metagenomics, the study of the collective genome of a microbial community by expressing it in a foreign host, is an emerging field in biotechnology. Over the past years, the possibility of novel product discovery through metagenomics has developed rapidly. Thus, metagenomics has been heralded as a promising mining strategy of resources for the biotechnological and pharmaceutical industry. However, in spite of innovative work in the field of functional genomics in recent years, yields from function-based metagenomics studies still fall short of producing significant amounts of new products that are valuable for biotechnological processes. Thus, a new set of strategies is required with respect to fostering gene expression in comparison to the traditional work. These new strategies should address a major issue, that is, how to successfully express a set of unknown genes of unknown origin in a foreign host in high throughput. This article is an opinionating review of functional metagenomic screening of natural microbial communities, with a focus on the optimization of new product discovery. It first summarizes current major bottlenecks in functional metagenomics and then provides an overview of the general metagenomic assessment strategies, with a focus on the challenges that are met in the screening for, and selection of, target genes in metagenomic libraries. To identify possible screening limitations, strategies to achieve optimal gene expression are reviewed, examining the molecular events all the way from the transcription level through to the secretion of the target gene product.}, }
@article {pmid22189863, year = {2012}, author = {Su, C and Lei, L and Duan, Y and Zhang, KQ and Yang, J}, title = {Culture-independent methods for studying environmental microorganisms: methods, application, and perspective.}, journal = {Applied microbiology and biotechnology}, volume = {93}, number = {3}, pages = {993-1003}, doi = {10.1007/s00253-011-3800-7}, pmid = {22189863}, issn = {1432-0614}, mesh = {Animals ; Bacteria/classification/*genetics ; *Ecosystem ; Electrophoresis/methods ; *Environmental Microbiology ; *Genetic Techniques ; Humans ; Polymorphism, Restriction Fragment Length/genetics ; Polymorphism, Single-Stranded Conformational ; RNA, Ribosomal/genetics ; }, abstract = {Since the application of molecular methods, culture-independent methods (CIMs) have been developed to study microbial communities from various environments. In the past 20 years, several methods based on the direct amplification and analyses of the small subunit ribosomal RNA gene have been developed to directly study environmental microorganisms. These methods include denaturing/temperature gradient gel electrophoresis, single-strand-conformation polymorphism, restriction fragment length polymorphism, terminal restriction fragment length polymorphism, and quantitative polymerase chain reaction (PCR). Similarly, non-PCR-based molecular techniques, such as microarray and fluorescence in situ hybridization have also been adopted. In recent years, several novel fields of investigation such as metagenomics, metatranscriptomics, metaproteomics, and single-cell genomics were developed, largely propelled by the innovation and application of next-generation sequencing methods. Several single-cell-based technologies such as Raman microspectroscopy and nano-scale secondary ion mass spectrometry are also increasingly used in the fields of microbial ecology and environmental microbiology. The application of these methods has revolutionized microbiology by allowing scientists to directly analyze natural microbial communities in situ, including their genes, transcripts, proteins, and metabolites and how their interactions impact their distribution patterns. In this review, we present an up-to-date review on different CIMs and their applications, our focuses are on the comparison of different CIMs and their application in the analyses of microbial diversities and communities.}, }
@article {pmid22189021, year = {2012}, author = {Barata, A and Malfeito-Ferreira, M and Loureiro, V}, title = {The microbial ecology of wine grape berries.}, journal = {International journal of food microbiology}, volume = {153}, number = {3}, pages = {243-259}, doi = {10.1016/j.ijfoodmicro.2011.11.025}, pmid = {22189021}, issn = {1879-3460}, mesh = {Agriculture ; Aspergillus/metabolism ; Bacteria/*isolation &amp; purification/metabolism ; Candida/metabolism ; Ecology ; Fermentation ; Food Microbiology ; Fruit/metabolism ; Fungi/*isolation &amp; purification/metabolism ; Ochratoxins/biosynthesis/metabolism ; Vitis/metabolism/*microbiology ; Wine/microbiology ; Yeasts/classification/isolation &amp; purification/metabolism ; Zygosaccharomyces/isolation &amp; purification/metabolism ; }, abstract = {Grapes have a complex microbial ecology including filamentous fungi, yeasts and bacteria with different physiological characteristics and effects upon wine production. Some species are only found in grapes, such as parasitic fungi and environmental bacteria, while others have the ability to survive and grow in wines, constituting the wine microbial consortium. This consortium covers yeast species, lactic acid bacteria and acetic acid bacteria. The proportion of these microorganisms depends on the grape ripening stage and on the availability of nutrients. Grape berries are susceptible to fungal parasites until véraison after which the microbiota of truly intact berries is similar to that of plant leaves, which is dominated by basidiomycetous yeasts (e.g. Cryptococcus spp., Rhodotorula spp. Sporobolomyces spp.) and the yeast-like fungus Aureobasidium pullulans. The cuticle of visually intact berries may bear microfissures and softens with ripening, increasing nutrient availability and explaining the possible dominance by the oxidative or weakly fermentative ascomycetous populations (e.g. Candida spp., Hanseniaspora spp., Metschnikowia spp., Pichia spp.) approaching harvest time. When grape skin is clearly damaged, the availability of high sugar concentrations on the berry surface favours the increase of ascomycetes with higher fermentative activity like Pichia spp. and Zygoascus hellenicus, including dangerous wine spoilage yeasts (e.g. Zygosaccharomyces spp., Torulaspora spp.), and of acetic acid bacteria (e.g. Gluconobacter spp., Acetobacter spp.). The sugar fermenting species Saccharomyces cerevisiae is rarely found on unblemished berries, being favoured by grape damage. Lactic acid bacteria are minor partners of grape microbiota and while being the typical agent of malolactic fermentation, Oenococcus oeni has been seldom isolated from grapes in the vineyard. Environmental ubiquitous bacteria of the genus Enterobacter spp., Enterococcus spp., Bacillus spp., Burkholderia spp., Serratia spp., Staphylococcus spp., among others, have been isolated from grapes but do not have the ability to grow in wines. Saprophytic moulds, like Botrytis cinerea, causing grey rot, or Aspergillus spp., possibly producing ochratoxin, are only active in the vineyard, although their metabolites may affect wine quality during grape processing. The impact of damaged grapes in yeast ecology has been underestimated mostly because of inaccurate grape sampling. Injured berries hidden in apparently sound bunches explain the recovery of a higher number of species when whole bunches are picked. Grape health status is the main factor affecting the microbial ecology of grapes, increasing both microbial numbers and species diversity. Therefore, the influence of abiotic (e.g. climate, rain, hail), biotic (e.g. insects, birds, phytopathogenic and saprophytic moulds) and viticultural (e.g. fungicides) factors is dependent on their primary damaging effect.}, }
@article {pmid22183673, year = {2012}, author = {Lievens, B and Justé, A and Willems, KA}, title = {Fungal plant pathogen detection in plant and soil samples using DNA macroarrays.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {835}, number = {}, pages = {491-507}, doi = {10.1007/978-1-61779-501-5_30}, pmid = {22183673}, issn = {1940-6029}, mesh = {DNA, Fungal/genetics/isolation &amp; purification ; Fungi/*genetics/*isolation &amp; purification ; Luminescent Measurements ; Nucleic Acid Hybridization/methods ; Oligonucleotide Array Sequence Analysis/*methods ; Plant Diseases/*microbiology ; Plants/*microbiology ; Polymerase Chain Reaction/methods ; *Soil Microbiology ; }, abstract = {PCR-based DNA array technology is one of the most suitable techniques to detect and identify multiple pathogens in a single assay. Out of the different array platforms that currently exist, membrane-based DNA macroarrays are the most convenient for plant disease diagnosis because of low costs, great sensitivity, and modest equipment requirements. Here we describe a protocol for routine detection of plant pathogens using DNA macroarrays, i.e., from sampling to analysis of hybridization results. Diagnosis can be completed within 36 h after sample collection.}, }
@article {pmid22183047, year = {2012}, author = {Carbonero, F and Oakley, BB and Hawkins, RJ and Purdy, KJ}, title = {Genotypic distribution of a specialist model microorganism, Methanosaeta, along an estuarine gradient: does metabolic restriction limit niche differentiation potential?.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {856-864}, pmid = {22183047}, issn = {1432-184X}, mesh = {Cloning, Molecular ; DNA, Archaeal/analysis ; Deltaproteobacteria/genetics/metabolism ; Denaturing Gradient Gel Electrophoresis ; *Ecosystem ; *Estuaries ; Gene Library ; Genotype ; Methanosarcinales/classification/*genetics/isolation &amp; purification/*metabolism ; Molecular Sequence Data ; RNA, Archaeal/analysis ; Sequence Analysis, DNA ; }, abstract = {A reductionist ecological approach of using a model genus was adopted in order to understand how microbial community structure is driven by metabolic properties. The distribution along an estuarine gradient of the highly specialised genus Methanosaeta was investigated and compared to the previously determined distribution of the more metabolically flexible Desulfobulbus. Methanosaeta genotypic distribution along the Colne estuary (Essex, UK) was determined by DNA- and RNA-based denaturing gradient gel electrophoresis and 16S rRNA gene sequence analyses. Methanosaeta distribution was monotonic, with a consistently diverse community and no apparent niche partitioning either in DNA or RNA analyses. This distribution pattern contrasts markedly with the previously described niche partitioning and sympatric differentiation of the model generalist, Desulfobulbus. To explain this difference, it is hypothesised that Methanosaeta's strict metabolic needs limit its adaptation potential, thus populations do not partition into spatially distinct groups and so do not appear to be constrained by gross environmental factors such as salinity. Thus, at least for these two model genera, it appears that metabolic flexibility may be an important factor in spatial distribution and this may be applicable to other microbes.}, }
@article {pmid22183046, year = {2012}, author = {Goodenough, AE and Stallwood, B}, title = {Differences in culturable microbial communities in bird nestboxes according to orientation and influences on offspring quality in great tits (Parus major).}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {986-995}, pmid = {22183046}, issn = {1432-184X}, mesh = {Animals ; Bacteria/genetics/*growth &amp; development/isolation &amp; purification ; *Bacterial Load ; Clutch Size ; *Ecosystem ; Fungi/genetics/*growth &amp; development/isolation &amp; purification ; *Nesting Behavior ; Passeriformes/*physiology ; Species Specificity ; }, abstract = {Although bird-microbial interactions have become a topic of increasing research, the influence of nest-site characteristics, such as cavity orientation, on nest microbial communities in free-living passerines has not, to our knowledge, been investigated. This is despite the possibility of microbial differences explaining non-random patterns in nest-site selection and offspring quality, such as those exhibited by great tits (Parus major). We swabbed great tit nestboxes that faced either south-southwest (180-269°) or north-northeast (0-89°). Overall, 28 bacterial species and 11 fungal species were isolated, but the culturable microbial community differed substantially between different orientations-indeed nestboxes could be classified to their orientation group with high accuracy using microbial data. Nestboxes facing south-southwest had a significantly higher fungal load (typically double) than those facing north-northeast due to a higher abundance of two species, Epicoccum purpurascens and Cladosporium cladosporioides. There was no relationship between total bacterial load and orientation, although the abundance of one species, Pseudomonas veronii, was significantly lower in south-southwest boxes. The abundance of the allergen E. purpurascens explained almost 20% of the variation in offspring quality, being significantly and inversely related to chick size (high loads associated with small, poor quality, chicks). Our results provide empirical evidence for a correlation between nestbox orientation and culturable microbial load and a further correlation between abundance of one species, E. purpurascens, and offspring quality. Thus, microbial load, which is itself influenced by nest cavity parameters, could be the proximate factor that influences nest-site choice through its effect on offspring quality (and thus, overall fecundity).}, }
@article {pmid22180822, year = {2011}, author = {O'Brien, SL and Glass, EM and Brulc, JM and Gilbert, JA and Antonopoulos, DA and Meyer, F}, title = {Meeting report: the 2 annual argonne soils workshop, argonne national laboratory, chicago illinois, USA, october 6-8, 2010.}, journal = {Standards in genomic sciences}, volume = {5}, number = {2}, pages = {198-202}, pmid = {22180822}, issn = {1944-3277}, abstract = {This report summarizes the proceedings of the 2(nd) Annual Argonne Soils Workshop held at Argonne National Laboratory October 6-8, 2010. The workshop assembled a diverse group of soil ecologists, microbiologists, molecular biologists, and computational scientists to discuss the challenges and opportunities related to implementation of metagenomics approaches in soil microbial ecology. The overarching theme of the workshop was "designing ecologically meaningful soil metagenomics research", which encouraged presentations on both ecological and computational topics. The workshop fostered valuable cross-discipline communication and delivered the message that soil metagenomics research must be based on an iterative process between biological inquiry and bioinformatics tools.}, }
@article {pmid22179207, year = {2011}, author = {Maccaferri, S and Biagi, E and Brigidi, P}, title = {Metagenomics: key to human gut microbiota.}, journal = {Digestive diseases (Basel, Switzerland)}, volume = {29}, number = {6}, pages = {525-530}, doi = {10.1159/000332966}, pmid = {22179207}, issn = {1421-9875}, mesh = {Gastrointestinal Tract/*metabolism/*microbiology ; Gene Expression Profiling ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The human gastrointestinal tract harbors the most complex human microbial ecosystem (intestinal microbiota). The comprehensive genome of these microbial populations (intestinal microbiome) is estimated to have a far greater genetic potential than the human genome itself. Correlations between changes in composition and activity of the gut microbiota and common disorders, such as inflammatory bowel diseases, obesity, diabetes, and atopic diseases, have been proposed, increasing the interest of the scientific community in this research field. In this perspective, a comprehensive and detailed view of the human gut microbiota, in terms of phylogenetic composition as well as genetic and metabolic potential, is essential to understand the dynamics and possible mechanisms of the cause/effect relationships between gut microbiota and pathology. Metagenomics has emerged as one of the most powerful sequence-driven approaches to study the composition and the genetic potential of this complex ecosystem, and efforts in this direction have been smoothed by the implementation of next generation sequencing platforms. Here, we highlight the potential of the newest high-throughput, culture-independent approaches for the characterization of the human gut microbiome in health and disease. Recent and promising results in this field are presented, underlining the perspectives and future research direction of human gut microbial ecology.}, }
@article {pmid22176749, year = {2012}, author = {McKeown, RM and Hughes, D and Collins, G and Mahony, T and O'Flaherty, V}, title = {Low-temperature anaerobic digestion for wastewater treatment.}, journal = {Current opinion in biotechnology}, volume = {23}, number = {3}, pages = {444-451}, doi = {10.1016/j.copbio.2011.11.025}, pmid = {22176749}, issn = {1879-0429}, mesh = {Anaerobiosis ; Biofuels ; *Bioreactors ; Biotechnology ; Cold Temperature ; Methane/*metabolism ; Sewage/chemistry ; Wastewater/*microbiology ; Water Purification/*methods ; }, abstract = {Methanogenesis is an important biogeochemical process for the degradation of organic matter within cold environments, and is associated with the release of the potent greenhouse gas, methane. Cold methanogenesis has been harnessed, in engineered systems, as low-temperature anaerobic digestion (LTAD) for wastewater treatment and bioenergy generation. LTAD represents a nascent wastewater treatment biotechnology, which offers an attractive alternative to conventional aerobic and anaerobic processes. Successful, high-rate, LTAD of sewage and industrial wastewaters (e.g. from the brewery, food-processing and pharmaceutical sectors), with concomitant biogas generation, has been demonstrated at laboratory-scale and pilot-scale. A holistic, polyphasic approach, which integrates bioprocess, physiological and molecular biological datasets has been critical to the development of the LTAD concept.}, }
@article {pmid22174803, year = {2011}, author = {Hammer, EC and Rillig, MC}, title = {The influence of different stresses on glomalin levels in an arbuscular mycorrhizal fungus--salinity increases glomalin content.}, journal = {PloS one}, volume = {6}, number = {12}, pages = {e28426}, pmid = {22174803}, issn = {1932-6203}, mesh = {Biomass ; Computer Simulation ; Fungal Proteins/*metabolism ; Glycoproteins/*metabolism ; Mycelium/drug effects ; Mycorrhizae/drug effects/growth &amp; development/*metabolism/*physiology ; Osmolar Concentration ; Osmosis/drug effects ; *Salinity ; Sodium Chloride/pharmacology ; *Stress, Physiological/drug effects ; }, abstract = {Glomalin is a glycoprotein produced by arbuscular mycorrhizal (AM) fungi, and the soil fraction containing glomalin is correlated with soil aggregation. Thus, factors potentially influencing glomalin production could be of relevance for this ecosystem process and for understanding AM fungal physiology. Previous work indicated that glomalin production in AM fungi may be a stress response, or related to suboptimal mycelium growth. We show here that environmental stress can enhance glomalin production in the mycelium of the AM fungus Glomus intraradices. We applied NaCl and glycerol in different intensities to the medium in which the fungus was grown in vitro, causing salinity stress and osmotic stress, respectively. As a third stress type, we simulated grazing on the extraradical hyphae of the fungus by mechanically injuring the mycelium by clipping. NaCl caused a strong increase, while the clipping treatment led to a marginally significant increase in glomalin production. Even though salinity stress includes osmotic stress, we found substantially different responses in glomalin production due to the NaCl and the glycerol treatment, as glycerol addition did not cause any response. Thus, our results indicate that glomalin is involved in inducible stress responses in AM fungi for salinity, and possibly grazing stress.}, }
@article {pmid22173371, year = {2012}, author = {Visser, AA and Nobre, T and Currie, CR and Aanen, DK and Poulsen, M}, title = {Exploring the potential for actinobacteria as defensive symbionts in fungus-growing termites.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {975-985}, pmid = {22173371}, issn = {1432-184X}, mesh = {Actinobacteria/genetics/*growth &amp; development/metabolism ; Animals ; Anti-Bacterial Agents/biosynthesis/pharmacology ; *Antibiosis ; Biological Assay ; DNA, Bacterial/analysis/genetics/isolation &amp; purification ; Fungi/classification/drug effects/genetics/*growth &amp; development ; Isoptera/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {In fungus-growing termites, fungi of the subgenus Pseudoxylaria threaten colony health through substrate competition with the termite fungus (Termitomyces). The potential mechanisms with which termites suppress Pseudoxylaria have remained unknown. Here we explore if Actinobacteria potentially play a role as defensive symbionts against Pseudoxylaria in fungus-growing termites. We sampled for Actinobacteria from 30 fungus-growing termite colonies, spanning the three main termite genera and two geographically distant sites. Our isolations yielded 360 Actinobacteria, from which we selected subsets for morphological (288 isolates, grouped in 44 morphotypes) and for 16S rRNA (35 isolates, spanning the majority of morphotypes) characterisation. Actinobacteria were found throughout all sampled nests and colony parts and, phylogenetically, they are interspersed with Actinobacteria from origins other than fungus-growing termites, indicating lack of specificity. Antibiotic-activity screening of 288 isolates against the fungal cultivar and competitor revealed that most of the Actinobacteria-produced molecules with antifungal activity. A more detailed bioassay on 53 isolates, to test the specificity of antibiotics, showed that many Actinobacteria inhibit both Pseudoxylaria and Termitomyces, and that the cultivar fungus generally is more susceptible to inhibition than the competitor. This suggests that either defensive symbionts are not present in the system or that they, if present, represent a subset of the community isolated. If so, the antibiotics must be used in a targeted fashion, being applied to specific areas by the termites. We describe the first discovery of an assembly of antibiotic-producing Actinobacteria occurring in fungus-growing termite nests. However, due to the diversity found, and the lack of both phylogenetic and bioactivity specificity, further work is necessary for a better understanding of the putative role of antibiotic-producing bacteria in the fungus-growing termite mutualistic system.}, }
@article {pmid22170424, year = {2012}, author = {Lee, CK and Barbier, BA and Bottos, EM and McDonald, IR and Cary, SC}, title = {The Inter-Valley Soil Comparative Survey: the ecology of Dry Valley edaphic microbial communities.}, journal = {The ISME journal}, volume = {6}, number = {5}, pages = {1046-1057}, pmid = {22170424}, issn = {1751-7370}, mesh = {Antarctic Regions ; Bacteria/*classification/genetics/growth &amp; development ; DNA, Bacterial/analysis/genetics ; Desiccation ; *Ecosystem ; Ice ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/analysis/genetics ; Sequence Analysis, DNA ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Recent applications of molecular genetics to edaphic microbial communities of the McMurdo Dry Valleys and elsewhere have rejected a long-held belief that Antarctic soils contain extremely limited microbial diversity. The Inter-Valley Soil Comparative Survey aims to elucidate the factors shaping these unique microbial communities and their biogeography by integrating molecular genetic approaches with biogeochemical analyses. Although the microbial communities of Dry Valley soils may be complex, there is little doubt that the ecosystem's food web is relatively simple, and evidence suggests that physicochemical conditions may have the dominant role in shaping microbial communities. To examine this hypothesis, bacterial communities from representative soil samples collected in four geographically disparate Dry Valleys were analyzed using molecular genetic tools, including pyrosequencing of 16S rRNA gene PCR amplicons. Results show that the four communities are structurally and phylogenetically distinct, and possess significantly different levels of diversity. Strikingly, only 2 of 214 phylotypes were found in all four valleys, challenging a widespread assumption that the microbiota of the Dry Valleys is composed of a few cosmopolitan species. Analysis of soil geochemical properties indicated that salt content, alongside altitude and Cu(2+), was significantly correlated with differences in microbial communities. Our results indicate that the microbial ecology of Dry Valley soils is highly localized and that physicochemical factors potentially have major roles in shaping the microbiology of ice-free areas of Antarctica. These findings hint at links between Dry Valley glacial geomorphology and microbial ecology, and raise previously unrecognized issues related to environmental management of this unique ecosystem.}, }
@article {pmid22167078, year = {2012}, author = {Zimmermann, J and Portillo, MC and Serrano, L and Ludwig, W and Gonzalez, JM}, title = {Acidobacteria in freshwater ponds at Doñana National Park, Spain.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {844-855}, pmid = {22167078}, issn = {1432-184X}, mesh = {Acidobacteria/classification/*genetics/growth &amp; development/isolation &amp; purification ; DNA Primers ; Ecosystem ; In Situ Hybridization, Fluorescence ; Phylogeny ; Ponds/*microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Spain ; }, abstract = {The Acidobacteria show a widespread distribution in natural ecosystems. In this study, we analyzed the presence of Acidobacteria in freshwater ponds at Doñana National Park (southwestern Spain). Nucleic acid sequence analysis, quantitative, real-time RT-PCR, and fluorescence in situ hybridization (FISH) were carried out. Acidobacteria in these aquatic environments were investigated using their 16S and 23S rDNA sequences and acidobacterial specific primer pairs through phylogenetic approaches. The presence of up to five subdivisions of Acidobacteria was detected during this study. The analyzed ponds exhibited distinctive patterns of acidobacterial clades. In order to detect their role in ecosystem functions, metabolically active Acidobacteria were detected based upon rRNA analyses. Quantitative, real-time RT-PCR showed a low percentage of metabolically active Acidobacteria at suboxic zones within the water column covered by surface Fe-rich films. Oxygen-saturated areas showed around 4% of total bacterial RNA belonging to Acidobacteria both in the water column and the sediment surface. The morphology of the most abundant Acidobacteria was revealed by FISH as cocci generally in pairs or chains. Enrichment cultures were also obtained and indicated a putative metabolism based on aerobic and heterotrophic characteristics likely taking advantage of the abundant organic matter present at the investigated sites. These results represent a significant contribution toward understanding the distribution and ecological role of the phylum Acidobacteria in natural ecosystems, specifically at Doñana National Park freshwater ponds.}, }
@article {pmid22161565, year = {2011}, author = {Kuczynski, J and Stombaugh, J and Walters, WA and González, A and Caporaso, JG and Knight, R}, title = {Using QIIME to analyze 16S rRNA gene sequences from microbial communities.}, journal = {Current protocols in bioinformatics}, volume = {Chapter 10}, number = {}, pages = {10.7.1-10.7.20}, pmid = {22161565}, issn = {1934-340X}, support = {DK83981/DK/NIDDK NIH HHS/United States ; HG4872/HG/NHGRI NIH HHS/United States ; T32 GM008759/GM/NIGMS NIH HHS/United States ; U01 HG004866/HG/NHGRI NIH HHS/United States ; GM65103/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 HG004872/HG/NHGRI NIH HHS/United States ; GM8759/GM/NIGMS NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; HG4866/HG/NHGRI NIH HHS/United States ; LM9451/LM/NLM NIH HHS/United States ; DK78669/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics ; Biodiversity ; DNA, Bacterial/chemistry ; *Genes, rRNA ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA/*methods ; *Software ; }, abstract = {QIIME (canonically pronounced "chime") is a software application that performs microbial community analysis. It is an acronym for Quantitative Insights Into Microbial Ecology, and has been used to analyze and interpret nucleic acid sequence data from fungal, viral, bacterial, and archaeal communities. The following protocols describe how to install QIIME on a single computer and use it to analyze microbial 16S sequence data from nine distinct microbial communities.}, }
@article {pmid22159526, year = {2012}, author = {Zumsteg, A and Luster, J and Göransson, H and Smittenberg, RH and Brunner, I and Bernasconi, SM and Zeyer, J and Frey, B}, title = {Bacterial, archaeal and fungal succession in the forefield of a receding glacier.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {552-564}, pmid = {22159526}, issn = {1432-184X}, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Ecosystem ; Fungi/classification/genetics/*isolation &amp; purification ; Ice Cover/chemistry/*microbiology ; Molecular Sequence Data ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; Switzerland ; }, abstract = {Glacier forefield chronosequences, initially composed of barren substrate after glacier retreat, are ideal locations to study primary microbial colonization and succession in a natural environment. We characterized the structure and composition of bacterial, archaeal and fungal communities in exposed rock substrates along the Damma glacier forefield in central Switzerland. Soil samples were taken along the forefield from sites ranging from fine granite sand devoid of vegetation near the glacier terminus to well-developed soils covered with vegetation. The microbial communities were studied with genetic profiling (T-RFLP) and sequencing of clone libraries. According to the T-RFLP profiles, bacteria showed a high Shannon diversity index (H) (ranging from 2.3 to 3.4) with no trend along the forefield. The major bacterial lineages were Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Cyanobacteria. An interesting finding was that Euryarchaeota were predominantly colonizing young soils and Crenarchaeota mainly mature soils. Fungi shifted from an Ascomycota-dominated community in young soils to a more Basidiomycota-dominated community in old soils. Redundancy analysis indicated that base saturation, pH, soil C and N contents and plant coverage, all related to soil age, correlated with the microbial succession along the forefield.}, }
@article {pmid22159498, year = {2012}, author = {Liliensiek, AK and Thakuria, D and Clipson, N}, title = {Influences of plant species composition, fertilisation and Lolium perenne ingression on soil microbial community structure in three Irish grasslands.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {509-521}, pmid = {22159498}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Ecosystem ; Fertilizers/*analysis ; Fungi/classification/genetics/*isolation &amp; purification ; Hydrogen-Ion Concentration ; Lolium/*growth &amp; development ; Poaceae/*chemistry/classification ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Semi-natural grassland soils are frequently fertilised for agricultural improvement. This practice often comes at a loss of the indigenous flora while fast-growing nitrogen-responsive species, such as Lolium perenne, take over. Since soil microbial communities depend on plant root exudates for carbon and nitrogen sources, this shift in vegetation is thought to influence soil microbial community structure. In this study, we investigated the influence of different plant species, fertilisation and L. perenne ingression on microbial communities in soils from three semi-natural Irish grasslands. Bacterial and fungal community compositions were determined by automated ribosomal intergenic spacer analysis, and community changes were linked to environmental factors by multivariate statistical analysis. Soil type had a strong effect on bacterial and fungal communities, mainly correlated to soil pH, as well as soil carbon and nitrogen status. Within each soil type, plant species composition was the main influencing factor followed by nitrogen fertilisation and finally Lolium ingression in the acidic upland and mesotrophic grassland. In the alkaline grassland, however, Lolium ingression had a stronger effect than fertilisation. Our results suggest that a change in plant species diversity strongly influences the microbial community structure, which may subsequently lead to significant changes in ecosystem functioning.}, }
@article {pmid22159497, year = {2012}, author = {Yun, J and Zhuang, G and Ma, A and Guo, H and Wang, Y and Zhang, H}, title = {Community structure, abundance, and activity of methanotrophs in the Zoige wetland of the Tibetan Plateau.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {835-843}, pmid = {22159497}, issn = {1432-184X}, mesh = {China ; Methane/*metabolism ; Methylococcaceae/enzymology/genetics/*growth &amp; development/isolation &amp; purification ; Methylocystaceae/enzymology/genetics/*growth &amp; development/isolation &amp; purification ; Molecular Sequence Data ; Oxygenases/genetics ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; *Wetlands ; }, abstract = {The Zoige wetland of the Tibetan Plateau is a high-altitude tundra wetland and one of the biggest methane emission centers in China. In this study, methanotrophs with respect to community structure, abundance, and activity were investigated in peat soils collected in the vicinity of different marshland plants that dominate different regions of the wetland, including Polygonum amphibium, Carex muliensis, and Eleocharis valleculosa (EV). 16S rRNA gene and particulate methane monooxygenase gene (pmoA) clone library sequence data indicated the presence of methanotrophs with two genera, Methylobacter and Methylocystis. Methylococcus, like pmoA gene sequences, were also retrieved and showed low similarity to those from Methylococcus spp. and thus indicates the existence of novel methanotrophs in the Zoige wetland. Quantitative polymerase chain reaction (qPCR) assays were used to measure the abundance of methantrophs and detected 10(7) to 10(8) of total pmoA gene copies per gram dry weight of soil in the three marshes. Group-specific qPCR and reverse transcriptase qPCR results found that the Methylobacter genus dominates the wetland, and Methylocystis methanotrophs were less abundant, although this group of methanotrophs was estimated to be more active according to mRNA/DNA ratio. Furthermore, EV marsh demonstrated the highest methanotrophs abundance and activity among the three marshes investigated. Our study suggests that both type I and type II methanotrophs contribute to the methane oxidation in the Zoige wetland.}, }
@article {pmid22158360, year = {2011}, author = {Kothamasi, D and Spurlock, M and Kiers, ET}, title = {Agricultural microbial resources: private property or global commons?.}, journal = {Nature biotechnology}, volume = {29}, number = {12}, pages = {1091-1093}, pmid = {22158360}, issn = {1546-1696}, mesh = {Agriculture/economics/*legislation &amp; jurisprudence ; European Union ; Humans ; Industrial Microbiology/economics/*legislation &amp; jurisprudence ; Patents as Topic ; Pesticides/economics ; United Nations ; United States ; }, }
@article {pmid22153908, year = {2012}, author = {Gillan, DC and Baeyens, W and Bechara, R and Billon, G and Denis, K and Grosjean, P and Leermakers, M and Lesven, L and Pede, A and Sabbe, K and Gao, Y}, title = {Links between bacterial communities in marine sediments and trace metal geochemistry as measured by in situ DET/DGT approaches.}, journal = {Marine pollution bulletin}, volume = {64}, number = {2}, pages = {353-362}, doi = {10.1016/j.marpolbul.2011.11.001}, pmid = {22153908}, issn = {1879-3363}, mesh = {*Biodiversity ; *Biomass ; Chemistry Techniques, Analytical ; Environmental Monitoring/*methods ; Geologic Sediments/*chemistry/*microbiology ; Metals/*analysis ; Water Pollutants, Chemical/*analysis ; }, abstract = {Our current view about the relationship between metals and bacteria in marine sediments might be biased because most studies only use ex situ approaches to quantify metals. The aim of the present research was to compare ex situ and in situ methods of metal measurement (DET and DGT--diffusive equilibration or diffusive gradients in thin-films) and relate the results with two commonly used microbiological variables (bacterial biomass and bacterial diversity as revealed by DGGE). No previous studies have used such in situ approaches in microbial ecology. For biomass and most of the investigated trace metals (Ag, Cd, Sn, Cr, Ni, Cu, Pb, and Al) no significant correlations were found. The exceptions were Fe, Mn, Co, and As which behave like micronutrients. For bacterial diversity, no relevant relationships were found. We conclude that in situ methods are more adapted tools for microbial ecologists but that ex situ approaches are still necessary.}, }
@article {pmid22150269, year = {2012}, author = {Kiersztyn, B and Siuda, W and Chróst, RJ}, title = {Persistence of bacterial proteolytic enzymes in lake ecosystems.}, journal = {FEMS microbiology ecology}, volume = {80}, number = {1}, pages = {124-134}, doi = {10.1111/j.1574-6941.2011.01276.x}, pmid = {22150269}, issn = {1574-6941}, mesh = {Amino Acids/metabolism ; Bacteria/*enzymology/genetics/growth &amp; development ; Bacterial Proteins/analysis/*metabolism ; Ecosystem ; Lakes/chemistry/*microbiology ; Leucyl Aminopeptidase/analysis/metabolism ; Peptide Hydrolases/analysis/*metabolism ; Proteolysis ; }, abstract = {This study analyzes proteolytic enzyme persistence and the role of dead (or metabolically inactive) aquatic bacteria in organic matter cycling. Samples from four lakes of different trophic status were used. Irrespective of the trophic status of the examined lakes, bacterial aminopeptidases remained active even 72 h after the death of the bacteria that produced them. The total pool of proteolytic enzymes in natural lake water samples was also stable. We found that the rates of amino acid enzymatic release from proteinaceous matter added to preserved lake water sample were constant for at least 96 h (r(2) = 0.99, n = 17, P ≤ 0.0001, V(max) = 84.6 nM h(-1)). We also observed that proteases built into bacterial cell debris fragments remained active for a long time, even after the total destruction of cells. Moreover, during 24 h of incubation time, about 20% of these enzymatically active fragments adsorbed onto natural seston particles, becoming a part of the 'attached enzymes system' that is regarded as the 'hot-spot' of protein degradation in aquatic ecosystems.}, }
@article {pmid22146690, year = {2011}, author = {Grootaert, C and Marzorati, M and Van den Abbeele, P and Van de Wiele, T and Possemiers, S}, title = {Prebiotics to manage the microbial control of energy homeostasis.}, journal = {Beneficial microbes}, volume = {2}, number = {4}, pages = {305-318}, doi = {10.3920/BM2011.0020}, pmid = {22146690}, issn = {1876-2891}, mesh = {*Energy Metabolism ; Epithelial Cells/microbiology/physiology ; *Homeostasis ; Humans ; Intestinal Mucosa/*microbiology/*physiology ; Metagenome/*drug effects ; *Prebiotics ; }, abstract = {The prevalence of obesity is continuously growing and has reached epidemic proportions. It is clear that current methods to combat obesity are not effective enough to reduce the problem. Therefore, further investigation is needed to develop new strategies. Recent research pointed out a potential role of the microbial community associated to the human host in controlling and influencing the energy homeostasis. According to the concept of Gastrointestinal Resource Management, this microbiota and its metabolic potential can be steered with the aim of improving host health. This review therefore focuses on the modulation of the intestinal microbiota through prebiotics with the aim to control several aspects of metabolic homeostasis. In a first part, the importance of host-microbe cross-talk at the intestinal epithelium is discussed. Yet, energy metabolism, which includes both lipid and glucose metabolism, is also regulated by several key organs including the adipose tissue, brain, liver, muscles, pancreas and gut. Therefore, in a second part, we will discuss the microbial factors that are involved in the communication between these different tissues, and their potential management. Finally, we will give some future prospects of the use of prebiotics in an individualised treatment of metabolic disorders.}, }
@article {pmid22145990, year = {2012}, author = {Ke, X and Lu, Y}, title = {Adaptation of ammonia-oxidizing microorganisms to environment shift of paddy field soil.}, journal = {FEMS microbiology ecology}, volume = {80}, number = {1}, pages = {87-97}, doi = {10.1111/j.1574-6941.2011.01271.x}, pmid = {22145990}, issn = {1574-6941}, mesh = {*Adaptation, Physiological ; Agriculture ; Ammonia/analysis/*metabolism ; Archaea/*physiology ; Bacteria/genetics/growth &amp; development/*metabolism ; Base Sequence ; China ; Molecular Sequence Data ; Nitrogen/analysis/metabolism ; Oryza ; Oxidation-Reduction ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/analysis/*metabolism ; }, abstract = {Adaptation of microorganisms to the environment is a central theme in microbial ecology. The objective of this study was to investigate the response of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) to a soil medium shift. We employed two rice field soils collected from Beijing and Hangzhou, China. These soils contained distinct AOB communities dominated by Nitrosomonas in Beijing rice soil and Nitrosospira in Hangzhou rice soil. Three mixtures were generated by mixing equal quantities of Beijing soil and Hangzhou soil (BH), Beijing soil with sterilized Hangzhou soil (BSH), and Hangzhou soil with sterilized Beijing soil (HSB). Pure and mixed soils were permanently flooded, and the surface-layer soil where ammonia oxidation occurred was collected to determine the response of AOB and AOA to the soil medium shift. AOB populations increased during the incubation, and the rates were initially faster in Beijing soil than in Hangzhou soil. Nitrosospira (cluster 3a) and Nitrosomonas (communis cluster) increased with time in correspondence with ammonia oxidation in the Hangzhou and Beijing soils, respectively. The 'BH' mixture exhibited a shift from Nitrosomonas at day 0 to Nitrosospira at days 21 and 60 when ammonia oxidation became most active. In 'HSB' and 'BSH' mixtures, Nitrosospira showed greater stimulation than Nitrosomonas, both with and without N amendment. These results suggest that Nitrosospira spp. were better adapted to soil environment shifts than Nitrosomonas. Analysis of the AOA community revealed that the composition of AOA community was not responsive to the soil environment shifts or to nitrogen amendment.}, }
@article {pmid22144147, year = {2012}, author = {Williamson, SJ and Yooseph, S}, title = {From bacterial to microbial ecosystems (metagenomics).}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {804}, number = {}, pages = {35-55}, doi = {10.1007/978-1-61779-361-5_3}, pmid = {22144147}, issn = {1940-6029}, mesh = {Computational Biology/*methods ; DNA, Bacterial/*isolation &amp; purification ; *Ecosystem ; Gene Library ; Metagenome/*genetics ; Metagenomics/*methods ; Sequence Analysis, DNA/*methods ; Specimen Handling/*methods ; }, abstract = {Metagenomics is revolutionizing the field of microbial ecology through techniques that eliminate the prerequisite of culturing. Metagenomic studies of microbial populations in different environments reveal the incredible diversity and adaptive capabilities of these organisms. With the advent of cheaper, high-throughput sequencing technologies, these studies are also producing vast amounts of sequence data. Here, we discuss the different components of a metagenomic study including sample collection, DNA extraction, sequencing, and informatics. We highlight their issues and challenges, and review the solutions that are currently in use. We conclude with examples of metagenomic studies conducted on environments of varying complexities.}, }
@article {pmid22141924, year = {2012}, author = {Pester, M and Rattei, T and Flechl, S and Gröngröft, A and Richter, A and Overmann, J and Reinhold-Hurek, B and Loy, A and Wagner, M}, title = {amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions.}, journal = {Environmental microbiology}, volume = {14}, number = {2}, pages = {525-539}, pmid = {22141924}, issn = {1462-2920}, support = {P 18836/FWF_/Austrian Science Fund FWF/Austria ; P 20185/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Ammonia/*metabolism ; Archaea/classification/*genetics ; Austria ; Biodiversity ; Costa Rica ; *Genes, Archaeal ; Greenland ; High-Throughput Nucleotide Sequencing ; Namibia ; Nitrification ; Phylogeny ; Soil ; *Soil Microbiology ; }, abstract = {Ammonia-oxidizing archaea (AOA) play an important role in nitrification and many studies exploit their amoA genes as marker for their diversity and abundance. We present an archaeal amoA consensus phylogeny based on all publicly available sequences (status June 2010) and provide evidence for the diversification of AOA into four previously recognized clusters and one newly identified major cluster. These clusters, for which we suggest a new nomenclature, harboured 83 AOA species-level OTU (using an inferred species threshold of 85% amoA identity). 454 pyrosequencing of amoA amplicons from 16 soils sampled in Austria, Costa Rica, Greenland and Namibia revealed that only 2% of retrieved sequences had no database representative on the species-level and represented 30-37 additional species-level OTUs. With the exception of an acidic soil from which mostly amoA amplicons of the Nitrosotalea cluster were retrieved, all soils were dominated by amoA amplicons from the Nitrososphaera cluster (also called group I.1b), indicating that the previously reported AOA from the Nitrosopumilus cluster (also called group I.1a) are absent or represent minor populations in soils. AOA richness estimates on the species level ranged from 8-83 co-existing AOAs per soil. Presence/absence of amoA OTUs (97% identity level) correlated with geographic location, indicating that besides contemporary environmental conditions also dispersal limitation across different continents and/or historical environmental conditions might influence AOA biogeography in soils.}, }
@article {pmid22138964, year = {2012}, author = {Arakawa, Y and Akiyama, Y and Furukawa, H and Suda, W and Amachi, S}, title = {Growth stimulation of iodide-oxidizing α-Proteobacteria in iodide-rich environments.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {522-531}, pmid = {22138964}, issn = {1432-184X}, mesh = {Alphaproteobacteria/genetics/*growth &amp; development/isolation &amp; purification/metabolism ; Iodides/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Seawater/chemistry/*microbiology ; }, abstract = {α-Proteobacteria that can oxidize iodide (I(-)) to molecular iodine (I(2)) have only been isolated from iodide-rich natural and artificial environments, i.e., natural gas brine waters and seawaters supplemented with iodide, respectively. To understand the growth characteristics of such iodide-oxidizing bacteria (IOB) under iodide-rich environments, microcosms comprising natural seawater and 1 mM iodide were prepared, and the succession of microbial communities was monitored by culture-independent techniques. PCR-denaturing gradient gel electrophoresis and 16S rRNA gene sequence analysis showed that bacteria closely related with known IOB were predominant in the microcosms after several weeks of incubation. Quantitative PCR analysis targeting specific 16S rRNA gene regions of IOB showed that the relative abundance of IOB in the microcosms was 6-76% of the total bacterial population, whereas that in natural seawater was less than 1%. When 10(3) cells mL(-1) of IOB were inoculated into natural seawater supplemented with 0.1-1 mM iodide, significant growth (cell densities, 10(5)-10(6) cells mL(-1)) and I(2) production (6-32 μM) were observed. Interestingly, similar growth stimulation occurred when 12-44 μM of I(2) was added to seawater, instead of iodide. IOB were found to be more I(2) tolerant than the other heterotrophic bacteria in seawater. These results suggest that I(2) plays a key role in the growth stimulation of IOB in seawater. IOB could potentially attack other bacteria with I(2) to occupy their ecological niche in iodide-rich environments.}, }
@article {pmid22134648, year = {2012}, author = {Bernhard, JM and Edgcomb, VP and Casciotti, KL and McIlvin, MR and Beaudoin, DJ}, title = {Denitrification likely catalyzed by endobionts in an allogromiid foraminifer.}, journal = {The ISME journal}, volume = {6}, number = {5}, pages = {951-960}, pmid = {22134648}, issn = {1751-7370}, mesh = {Bacteria/classification/*metabolism ; DNA, Bacterial/genetics ; *Denitrification ; Foraminifera/*microbiology ; Geologic Sediments/microbiology ; In Situ Hybridization, Fluorescence ; Nitrates/*metabolism ; Nitrogen Isotopes/metabolism ; Phylogeny ; Symbiosis ; }, abstract = {Nitrogen can be a limiting macronutrient for carbon uptake by the marine biosphere. The process of denitrification (conversion of nitrate to gaseous compounds, including N(2) (nitrogen gas)) removes bioavailable nitrogen, particularly in marine sediments, making it a key factor in the marine nitrogen budget. Benthic foraminifera reportedly perform complete denitrification, a process previously considered nearly exclusively performed by bacteria and archaea. If the ability to denitrify is widespread among these diverse and abundant protists, a paradigm shift is required for biogeochemistry and marine microbial ecology. However, to date, the mechanisms of foraminiferal denitrification are unclear, and it is possible that the ability to perform complete denitrification is because of the symbiont metabolism in some foraminiferal species. Using sequence analysis and GeneFISH, we show that for a symbiont-bearing foraminifer, the potential for denitrification resides in the endobionts. Results also identify the endobionts as denitrifying pseudomonads and show that the allogromiid accumulates nitrate intracellularly, presumably for use in denitrification. Endobionts have been observed within many foraminiferal species, and in the case of associations with denitrifying bacteria, may provide fitness for survival in anoxic conditions. These associations may have been a driving force for early foraminiferal diversification, which is thought to have occurred in the Neoproterozoic era when anoxia was widespread.}, }
@article {pmid22134599, year = {2012}, author = {Evans, TN and Seviour, RJ}, title = {Estimating biodiversity of fungi in activated sludge communities using culture-independent methods.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {773-786}, pmid = {22134599}, issn = {1432-184X}, mesh = {*Biodiversity ; Biomass ; Culture Media ; DNA, Fungal/analysis/isolation &amp; purification ; Denaturing Gradient Gel Electrophoresis/*methods ; Ecosystem ; Fungi/*classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA/methods ; Sewage/*microbiology ; Waste Disposal, Fluid/methods ; }, abstract = {Fungal diversity of communities in several activated sludge plants treating different influent wastes was determined by comparative sequence analyses of their 18S rRNA genes. Methods for DNA extraction and choice of primers for PCR amplification were both optimised using denaturing gradient gel electrophoresis profile patterns. Phylogenetic analysis revealed that the levels of fungal biodiversity in some communities, like those treating paper pulp wastes, were low, and most of the fungi detected in all communities examined were novel uncultured representatives of the major fungal subdivisions, in particular, the newly described clade Cryptomycota. The fungal populations in activated sludge revealed by these culture-independent methods were markedly different to those based on culture-dependent data. Members of the genera Penicillium, Cladosporium, Aspergillus and Mucor, which have been commonly identified in mixed liquor, were not identified in any of these plant communities. Non-fungal eukaryotic 18S rRNA genes were also amplified with the primer sets used. This is the first report where culture-independent methods have been applied to flocculated activated sludge biomass samples to estimate fungal community composition and, as expected, the data obtained gave a markedly different view of their population biodiversity compared to that based on culture-dependent methods.}, }
@article {pmid22129449, year = {2012}, author = {Vermeiren, J and Van de Wiele, T and Van Nieuwenhuyse, G and Boeckx, P and Verstraete, W and Boon, N}, title = {Sulfide- and nitrite-dependent nitric oxide production in the intestinal tract.}, journal = {Microbial biotechnology}, volume = {5}, number = {3}, pages = {379-387}, pmid = {22129449}, issn = {1751-7915}, mesh = {Adult ; Bacteria/*metabolism ; Humans ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Male ; Models, Biological ; Nitric Oxide/*metabolism ; Nitrites/*metabolism ; Sulfides/*metabolism ; }, abstract = {In the gut ecosystem, nitric oxide (NO) has been described to have damaging effects on the energy metabolism of colonocytes. Described mechanisms of NO production are microbial reduction of nitrate via nitrite to NO and conversion of l-arginine by NO synthase. The aim of this study was to investigate whether dietary compounds can stimulate the production of NO by representative cultures of the human intestinal microbiota and whether this correlates to other processes in the intestinal tract. We have found that the addition of a reduced sulfur compound, i.e. cysteine, contributed to NO formation. This increase was ascribed to higher sulfide concentrations generated from cysteine that in turn promoted the chemical conversion of nitrite to NO. The NO release from nitrite was of the order of 4‰ at most. Overall, it was shown that two independent biological processes contribute to the chemical formation of NO in the intestinal tract: (i) the production of sulfide by fermentation of sulfur containing amino acids or reduction of sulfate by sulfate reducing bacteria, and (ii) the reduction of nitrate to nitrite. Our results indicate that dietary thiol compounds in combination with nitrate may contribute to colonocytes damaging processes by promoting NO formation.}, }
@article {pmid22129404, year = {2011}, author = {Rydzanicz, K and Kącki, Z and Jawień, P}, title = {Environmental factors associated with the distribution of floodwater mosquito eggs in irrigated fields in Wrocław, Poland.}, journal = {Journal of vector ecology : journal of the Society for Vector Ecology}, volume = {36}, number = {2}, pages = {332-342}, doi = {10.1111/j.1948-7134.2011.00173.x}, pmid = {22129404}, issn = {1948-7134}, mesh = {*Aedes ; Agricultural Irrigation ; Altitude ; Animals ; Environment ; *Floods ; Fresh Water ; Larva ; Mosquito Control/methods ; Oviposition ; *Ovum ; Phalaris ; Plants ; Poland ; Population Density ; Soil ; }, abstract = {A survey of distribution patterns of floodwater mosquito eggs related to environmental conditions such as moisture and plant associations was conducted by using soil samples from irrigated fields in Wrocław, Poland. Mosquito egg distribution was determined by repeatedly flooding the soil samples with aerated water at a temperature of 25° C. Under laboratory conditions, hatching in installments of Aedes caspius (Pallas) and Aedes vexans (Meigen) were commonly observed. The results show that ∼75% of the larvae of Ae. caspius and Ae. vexans hatched after the first flooding under summer-like conditions, whereas, following the second and third flooding, the numbers of hatched larvae were significantly lower. In our study, within one intermediate flooded field, a total of 66 plant species was identified and classified into six communities. All vegetation types were associated by varied egg densities and showed differences both in richness and Shannon-Wiener diversity index as well as in ecological indices for moisture, soil reaction, and nutrient level. Small changes in elevation along the slope within the study area showed a large difference in the distribution of mosquito eggs. The highest average egg density was observed in zones with high occurrence of Phalaris arundinacea, usually prevalent in intermediate flooded and fertile areas. Knowledge of the indicators for the distribution of floodwater mosquito eggs in temporary breeding sites may be essential for organizing a successful, integrated mosquito control program with special regard to microbial control agents.}, }
@article {pmid22128350, year = {2011}, author = {Allen, HK and Looft, T and Bayles, DO and Humphrey, S and Levine, UY and Alt, D and Stanton, TB}, title = {Antibiotics in feed induce prophages in swine fecal microbiomes.}, journal = {mBio}, volume = {2}, number = {6}, pages = {}, pmid = {22128350}, issn = {2150-7511}, mesh = {Animal Feed ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/*drug effects/genetics/*virology ; Biota ; Carbadox/pharmacology ; Chlortetracycline/pharmacology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Drug Combinations ; Gastrointestinal Tract/*microbiology/*virology ; Metagenome ; Penicillin G/pharmacology ; Prophages/classification/*drug effects/genetics/*growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfamethazine/pharmacology ; Swine ; }, abstract = {UNLABELLED: Antibiotics are a cost-effective tool for improving feed efficiency and preventing disease in agricultural animals, but the full scope of their collateral effects is not understood. Antibiotics have been shown to mediate gene transfer by inducing prophages in certain bacterial strains; therefore, one collateral effect could be prophage induction in the gut microbiome at large. Here we used metagenomics to evaluate the effect of two antibiotics in feed (carbadox and ASP250 [chlortetracycline, sulfamethazine, and penicillin]) on swine intestinal phage metagenomes (viromes). We also monitored the bacterial communities using 16S rRNA gene sequencing. ASP250, but not carbadox, caused significant population shifts in both the phage and bacterial communities. Antibiotic resistance genes, such as multidrug resistance efflux pumps, were identified in the viromes, but in-feed antibiotics caused no significant changes in their abundance. The abundance of phage integrase-encoding genes was significantly increased in the viromes of medicated swine over that in the viromes of nonmedicated swine, demonstrating the induction of prophages with antibiotic treatment. Phage-bacterium population dynamics were also examined. We observed a decrease in the relative abundance of Streptococcus bacteria (prey) when Streptococcus phages (predators) were abundant, supporting the "kill-the-winner" ecological model of population dynamics in the swine fecal microbiome. The data show that gut ecosystem dynamics are influenced by phages and that prophage induction is a collateral effect of in-feed antibiotics.<br><br>IMPORTANCE: This study advances our knowledge of the collateral effects of in-feed antibiotics at a time in which the widespread use of "growth-promoting" antibiotics in agriculture is under scrutiny. Using comparative metagenomics, we show that prophages are induced by in-feed antibiotics in swine fecal microbiomes and that antibiotic resistance genes were detected in most viromes. This suggests that in-feed antibiotics are contributing to phage-mediated gene transfer, potentially of antibiotic resistance genes, in the swine gut. Additionally, the so-called "kill-the-winner" model of phage-bacterium population dynamics has been shown in aquatic ecosystems but met with conflicting evidence in gut ecosystems. The data support the idea that swine fecal Streptococcus bacteria and their phages follow the kill-the-winner model. Understanding the role of phages in gut microbial ecology is an essential component of the antibiotic resistance problem and of developing potential mitigation strategies.}, }
@article {pmid22127192, year = {2012}, author = {Guillén, MD and Abascal, B}, title = {Nature and distribution of the volatile components in the different regions of an artisanal ripened sheep cheese.}, journal = {The Journal of dairy research}, volume = {79}, number = {1}, pages = {102-109}, doi = {10.1017/S0022029911000781}, pmid = {22127192}, issn = {1469-7629}, mesh = {Animals ; Cheese/*analysis/*standards ; Food Analysis ; Gas Chromatography-Mass Spectrometry ; *Sheep ; Solid Phase Microextraction ; Volatile Organic Compounds/*chemistry ; }, abstract = {The distribution of the volatile components in four regions, Rind, Exterior, Intermediate, and Interior, of hand-made Idiazabal cheese which had been ripened for two months was studied in detail. It is proved that the headspace of this ripened sheep cheese is non-homogeneous in the different cheese regions. The Rind is the richest region in volatile compounds, followed by the Exterior region. A large number of compounds with different functional groups have their greatest abundances in the Rind with negative abundance gradients towards the interior regions. Many of these are undetectable in the Intermediate and Interior regions. Other compounds such as aldehydes having a great number of carbon atoms, and most of the acids have their greatest abundances in the Exterior region. Alcohols, ketones and esters of small size have their greatest abundances in the Intermediate region. And finally, a reduced number of compounds are distributed homogeneously in all cheese regions. The origin of the compounds, the conditions that favour their formation, their functional groups, size, shape and reactivity could be factors involved in their distribution in the cheese, which in turn is associated with the microbial ecology, chemical reactions and physical effects.}, }
@article {pmid22124571, year = {2012}, author = {Sereda, JM and Vandergucht, DM and Hudson, JJ}, title = {In situ UVA exposure modulates change in the uptake of radiophosphate in size-fractionated plankton assemblages following UVR exposure.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {751-760}, pmid = {22124571}, issn = {1432-184X}, mesh = {Ecosystem ; *Lakes ; Phosphorus Radioisotopes/*metabolism ; Phytoplankton/growth &amp; development/*metabolism/*radiation effects ; Saskatchewan ; *Ultraviolet Rays ; }, abstract = {We investigated the effect of ultraviolet radiation (UVR) on the uptake and partitioning of radiophosphate ((33)PO (4) (3-)) in size-fractionated plankton assemblages (0.2-0.8, 0.8-2.0 and >2.0 μm) collected from nine freshwater lakes located in Saskatchewan, Canada. A significant (p < 0.05) reduction in (33)PO (4) (3-) uptake by plankton was observed in seven of the nine lakes. Plankton >2.0 μm were generally unaffected by UVR, whereas the 0.2-0.8 μm size fraction exhibited severe photoinhibition. The effect of UVR on the 0.8-2.0 μm size fraction was variable, ranging from significant reductions to significant increases in (33)PO (4) (3-) uptake. The >2.0 μm size fraction was composed of a diversity of phytoplankton genera, suggesting that P uptake mechanisms for a range of phytoplankton are resistant to UVR. Our ability to detect a UVR effect on specific plankton size fractions was confounded by the resolution of the analysis. That is, only examining the <2.0 and >2.0 μm size fractions concealed the effect of UVR on plankton <0.8 μm. The magnitude of decrease in P uptake by plankton <0.8 μm was significantly and negatively correlated with in situ UVA exposure. Our results underscore the need for studies to consider both the size resolution of their analysis (i.e., the size of target organisms) and the ambient light conditions under which organisms may have acclimated before generalizing results across limnetic systems.}, }
@article {pmid22124570, year = {2012}, author = {Burgess, EA and Unrine, JM and Mills, GL and Romanek, CS and Wiegel, J}, title = {Comparative geochemical and microbiological characterization of two thermal pools in the Uzon Caldera, Kamchatka, Russia.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {471-489}, pmid = {22124570}, issn = {1432-184X}, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Hot Springs/chemistry/*microbiology ; Molecular Sequence Data ; Phylogeny ; Russia ; Sequence Analysis, DNA ; }, abstract = {Arkashin Schurf (Arkashin) and Zavarzin Spring (Zavarzin), two active thermal pools in the Uzon Caldera, Kamchatka, Russia, were studied for geochemical and microbiological characterization. Arkashin, the smaller of the two pools, had broader temperature and pH ranges, and the sediments had higher concentrations of total As (4,250 mg/kg) relative to Zavarzin (48.9 mg/kg). Glycerol dialkyl glycerol tetraether profiles represented distinct archaeal communities in each pool and agreed well with previous studies of these pools. Although no archaeal 16S rRNA sequences were recovered from Arkashin, sequences recovered from Zavarzin were mostly representatives of the Crenarchaeota and "Korarchaeota," and 13% of the sequences were unclassifiable. The bacterial community in Arkashin was dominated by uncultured "Bacteroidetes," Hydrogenobaculum of the Aquificales and Variovorax of the Betaproteobacteria, and 19% of the sequences remained unclassified. These results were consistent with other studies of As-rich features. The most abundant members of the Zavarzin bacterial community included the Chloroflexi, as well as members of the classes Deltaproteobacteria and Clostridia. In addition, 24% of the sequences were unclassified and at least 5% of those represent new groups among the established Bacterial phyla. Ecological structure in each pool was inferred from taxonomic classifications and bulk stable isotope δ values of C, N, and S. Hydrogenobaculum was responsible for primary production in Arkashin. However, in Zavarzin, the carbon source appeared to be allochthonous to the identified bacterial community members. Additionally, sequences related to organisms expected to participate in N and S cycles were identified from both pools.}, }
@article {pmid22115825, year = {2012}, author = {Larsson, E and Tremaroli, V and Lee, YS and Koren, O and Nookaew, I and Fricker, A and Nielsen, J and Ley, RE and Bäckhed, F}, title = {Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88.}, journal = {Gut}, volume = {61}, number = {8}, pages = {1124-1131}, pmid = {22115825}, issn = {1468-3288}, mesh = {Animals ; Bacteria/*isolation &amp; purification ; Disease Models, Animal ; Gastrointestinal Tract/immunology/metabolism/*microbiology ; *Gene Expression ; Immunity, Cellular/genetics ; Intestinal Mucosa/immunology/*metabolism/microbiology ; Male ; *Metagenome ; Mice ; Mice, Inbred C57BL ; Microarray Analysis ; Myeloid Differentiation Factor 88/biosynthesis/*genetics ; Polymerase Chain Reaction ; RNA/*genetics ; }, abstract = {BACKGROUND: The gut microbiota has profound effects on host physiology but local host-microbial interactions in the gut are only poorly characterised and are likely to vary from the sparsely colonised duodenum to the densely colonised colon. Microorganisms are recognised by pattern recognition receptors such as Toll-like receptors, which signal through the adaptor molecule MyD88.<br><br>METHODS: To identify host responses induced by gut microbiota along the length of the gut and whether these required MyD88, transcriptional profiles of duodenum, jejunum, ileum and colon were compared from germ-free and conventionally raised wild-type and Myd88-/- mice. The gut microbial ecology was assessed by 454-based pyrosequencing and viruses were analysed by PCR.<br><br>RESULTS: The gut microbiota modulated the expression of a large set of genes in the small intestine and fewer genes in the colon but surprisingly few microbiota-regulated genes required MyD88 signalling. However, MyD88 was essential for microbiota-induced colonic expression of the antimicrobial genes Reg3&#x3b2; and Reg3&#x3b3; in the epithelium, and Myd88 deficiency was associated with both a shift in bacterial diversity and a greater proportion of segmented filamentous bacteria in the small intestine. In addition, conventionally raised Myd88-/- mice had increased expression of antiviral genes in the colon, which correlated with norovirus infection in the colonic epithelium.<br><br>CONCLUSION: This study provides a detailed description of tissue-specific host transcriptional responses to the normal gut microbiota along the length of the gut and demonstrates that the absence of MyD88 alters gut microbial ecology.}, }
@article {pmid22115444, year = {2011}, author = {Korres, AM and Buss, DS and Ventura, JA and Fernandes, PM}, title = {Candida krusei and Kloeckera apis inhibit the causal agent of pineapple fusariosis, Fusarium guttiforme.}, journal = {Fungal biology}, volume = {115}, number = {12}, pages = {1251-1258}, doi = {10.1016/j.funbio.2011.09.001}, pmid = {22115444}, issn = {1878-6146}, mesh = {Ananas/microbiology/*physiology ; *Antibiosis ; Candida/isolation &amp; purification/*physiology ; Fusarium/*growth &amp; development/physiology ; Kloeckera/isolation &amp; purification/*physiology ; Plant Diseases/*microbiology ; }, abstract = {Studies based on microbial ecology and antagonistic interactions play an important role in the development of new alternative strategies in controlling plant pathogens and are relevant to further biotechnological applications. Antagonistic interactions between the yeasts Candida krusei and Kloeckera apis isolated from rotten pineapple fruits, and two isolates of the pathogenic filamentous fungus Fusarium guttiforme (Syn.: Fusarium subglutinans f. sp. ananas) resistant and susceptible to fungicide benzimidazole were studied in broth culture, and on plate assays. The yeasts significantly reduced Fusarium conidial germination after 24h of cocultivation in broth culture, and also mycelial growth on plate assays. Slide coculture appeared to show attachment of yeasts to the hyphal surface and also slight morphological abnormalities caused by C. krusei. Filtrates of cocultures of fungi and yeasts inhibited fungal growth, but filtrates of the yeast cultures alone did not, suggesting that the antagonistic action of the yeasts is inducible. The F. guttiforme isolate sensitive to benzimidazole was most affected by both yeasts in pineapple juice, reaching a maximum of 36.5 % germ tube inhibition. This isolate was also inhibited by yeasts in mycocinogenic plate assay. These results demonstrated that C. krusei and K. apis are effective in inhibiting F. guttiforme growth and that the mode of action is associated with hyperparasitism and mycocinogenic activity.}, }
@article {pmid22114656, year = {2011}, author = {Hori, R and Nishida, T and Okuyama, H}, title = {Hydrophilic and Hydrophobic Compounds Antithetically Affect the Growth of Eicosapentaenoic Acid-Synthesizing Escherichia coli Recombinants.}, journal = {The open microbiology journal}, volume = {5}, number = {}, pages = {114-118}, pmid = {22114656}, issn = {1874-2858}, abstract = {The growth of Escherichia coli DH5α recombinants producing eicosapentaenoic acid (EPA) (DH5αEPA+) and those not producing EPA (DH5αEPA-) was compared in the presence of hydrophilic or hydrophobic growth inhibitors. The minimal inhibitory concentrations of hydrophilic inhibitors such as reactive oxygen species and antibiotics were higher for DH5αEPA+ than for DH5αEPA-, and vice versa for hydrophobic inhibitors such as protonophores and radical generators. E. coli DH5α with higher levels of EPA became more resistant to ethanol. The cell surface hydrophobicity of DH5αEPA+ was higher than that of DH5αEPA-, suggesting that EPA may operate as a structural constituent in the cell membrane to affect the entry and efflux of hydrophilic and hydrophobic inhibitors.}, }
@article {pmid22113373, year = {2012}, author = {Oakley, BB and Carbonero, F and Dowd, SE and Hawkins, RJ and Purdy, KJ}, title = {Contrasting patterns of niche partitioning between two anaerobic terminal oxidizers of organic matter.}, journal = {The ISME journal}, volume = {6}, number = {5}, pages = {905-914}, pmid = {22113373}, issn = {1751-7370}, mesh = {Anaerobiosis ; Bacteria, Anaerobic/genetics/physiology ; Cluster Analysis ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Deltaproteobacteria/genetics/*physiology ; *Ecosystem ; Genotype ; Methane/metabolism ; Methanosarcinales/genetics/*physiology ; Phylogeny ; Seawater/microbiology ; Sequence Analysis, DNA ; Sulfates/metabolism ; Water Microbiology ; }, abstract = {Understanding the ecological principles underlying the structure and function of microbial communities remains an important goal for microbial ecology. We examined two biogeochemically important taxa, the sulfate-reducing bacterial genus, Desulfobulbus, and the methanogenic archaeal genus, Methanosaeta, to compare and contrast niche partitioning by these two taxa that are ecologically linked as anaerobic terminal oxidizers of organic material. An observational approach utilizing functional gene pyrosequencing was combined with a community-based reciprocal incubation experiment and characterization of a novel Desulfobulbus isolate. To analyze the pyrosequencing data, we constructed a data analysis pipeline, which we validated with several control data sets. For both taxa, particular genotypes were clearly associated with certain portions of an estuarine gradient, consistent with habitat or niche partitioning. Methanosaeta genotypes were generally divided between those found almost exclusively in the marine habitat (∼30% of operational taxonomic units (OTUs)), and those which were ubiquitously distributed across all or most of the estuary (∼70% of OTUs). In contrast to this relatively monotonic distribution, for Desulfobulbus, there were many more genotypes, and their distributions represented a wide range of inferred niche widths from specialist genotypes found only at a single site, to ubiquitous or generalist genotypes found in all 10 sites examined along the full estuarine gradient. Incubation experiments clearly showed that, for both taxa, communities from opposite ends of the estuary did not come to resemble one another, regardless of the chemical environment. Growth of a Desulfobulbus isolated into pure culture indicated that the potential niche of this organism is significantly larger than the realized niche. We concluded that niche partitioning can be an important force structuring microbial populations, with biotic and abiotic components having very different effects depending on the physiology and ecology of each taxon.}, }
@article {pmid22110622, year = {2011}, author = {Garbeva, P and Tyc, O and Remus-Emsermann, MN and van der Wal, A and Vos, M and Silby, M and de Boer, W}, title = {No apparent costs for facultative antibiotic production by the soil bacterium Pseudomonas fluorescens Pf0-1.}, journal = {PloS one}, volume = {6}, number = {11}, pages = {e27266}, pmid = {22110622}, issn = {1932-6203}, mesh = {Agar/pharmacology ; Anti-Bacterial Agents/*biosynthesis ; Culture Techniques ; Gene Expression Regulation, Bacterial ; Mutation ; Pseudomonas fluorescens/drug effects/genetics/growth &amp; development/*metabolism ; *Soil Microbiology ; }, abstract = {BACKGROUND: Many soil-inhabiting bacteria are known to produce secondary metabolites that can suppress microorganisms competing for the same resources. The production of antimicrobial compounds is expected to incur fitness costs for the producing bacteria. Such costs form the basis for models on the co-existence of antibiotic-producing and non-antibiotic producing strains. However, so far studies quantifying the costs of antibiotic production by bacteria are scarce. The current study reports on possible costs, for antibiotic production by Pseudomonas fluorescens Pf0-1, a soil bacterium that is induced to produce a broad-spectrum antibiotic when it is confronted with non-related bacterial competitors or supernatants of their cultures.<br><br>We measured the possible cost of antibiotic production for Pseudomonas fluorescens Pf0-1 by monitoring changes in growth rate with and without induction of antibiotic production by supernatant of a bacterial competitor, namely Pedobacter sp.. Experiments were performed in liquid as well as on semi-solid media under nutrient-limited conditions that are expected to most clearly reveal fitness costs. Our results did not reveal any significant costs for production of antibiotics by Pseudomonas fluorescens Pf0-1. Comparison of growth rates of the antibiotic-producing wild-type cells with those of non-antibiotic producing mutants did not reveal costs of antibiotic production either.<br><br>SIGNIFICANCE: Based on our findings we propose that the facultative production of antibiotics might not be selected to mitigate metabolic costs, but instead might be advantageous because it limits the risk of competitors evolving resistance, or even the risk of competitors feeding on the compounds produced.}, }
@article {pmid22109097, year = {2012}, author = {Fujii, M and Kojima, H and Iwata, T and Urabe, J and Fukui, M}, title = {Dissolved organic carbon as major environmental factor affecting bacterioplankton communities in mountain lakes of eastern Japan.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {496-508}, pmid = {22109097}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Carbon/*metabolism ; Ecosystem ; Japan ; Lakes/chemistry/*microbiology ; Molecular Sequence Data ; Phylogeny ; Plankton/classification/genetics/*isolation &amp; purification/*metabolism ; Water Microbiology ; }, abstract = {Relationships between environmental factors and bacterial communities were investigated in 41 freshwater lakes located in mountainous regions of eastern Japan. Bacterioplankton community composition (BCC) was determined by polymerase chain reaction-denaturing gradient gel electrophoresis of the 16S rRNA gene and then evaluated on the basis of physicochemical and biological variables of the lakes. Canonical correspondence analysis revealed that BCC of oligotrophic lakes was significantly influenced by dissolved organic carbon (DOC) content, but its effect was not apparent in the analysis covering all lakes including mesotrophic and eutrophic ones. The generalized linear model showed the negative association of DOC on the taxon richness of bacterioplankton communities. DOC was positively correlated with the catchment area per lake volume, suggesting that a large fraction of DOC supplied to the lake was derived from terrestrial sources. These results suggest that allochthonous DOC has a significant effect on bacterioplankton communities especially in oligotrophic lakes. The genus Polynucleobacter was detected most frequently. The occurrence of Polynucleobacter species was positively associated with DOC and negatively associated with total phosphorus (TP) levels. In addition, TP had a stronger effect than DOC, suggesting that oligotrophy is the most important factor on the occurrence of this genus.}, }
@article {pmid22109096, year = {2012}, author = {Tommonaro, G and Abbamondi, GR and Iodice, C and Tait, K and De Rosa, S}, title = {Diketopiperazines produced by the halophilic archaeon, Haloterrigena hispanica, activate AHL bioreporters.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {490-495}, pmid = {22109096}, issn = {1432-184X}, mesh = {Acyl-Butyrolactones/*metabolism ; Diketopiperazines/chemistry/*metabolism ; Escherichia coli/genetics/metabolism ; Genes, Reporter ; Halobacteriaceae/chemistry/*metabolism ; Molecular Structure ; *Signal Transduction ; Sodium Chloride/*metabolism ; }, abstract = {The generic term "quorum sensing" has been adopted to describe the bacterial cell-to-cell communication mechanism which coordinates gene expression when the population has reached a high cell density. Quorum sensing depends on the synthesis of small molecules that diffuse in and out of bacterial cells. There are few reports about this mechanism in Archaea. We report the isolation and chemical characterization of small molecules belonging to class of diketopiperazines (DKPs) in Haloterrigena hispanica, an extremely halophilic archaeon. One of the DKPs isolated, the compound cyclo-(L-prolyl-L-valine) activated N-acyl homoserine lactone (AHL) bioreporters, indicating that Archaea may have the ability to interact with AHL-producing bacteria within mixed communities.}, }
@article {pmid22109095, year = {2012}, author = {Ormeño-Orrillo, E and Rogel-Hernández, MA and Lloret, L and López-López, A and Martínez, J and Barois, I and Martínez-Romero, E}, title = {Change in land use alters the diversity and composition of Bradyrhizobium communities and led to the introduction of Rhizobium etli into the tropical rain forest of Los Tuxtlas (Mexico).}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {822-834}, pmid = {22109095}, issn = {1432-184X}, mesh = {Agriculture ; Bacterial Proteins/genetics ; Bradyrhizobium/classification/*genetics/*growth &amp; development/isolation &amp; purification ; DNA, Ribosomal/genetics ; *Ecosystem ; Forestry ; Mexico ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Rain ; Rhizobium etli/classification/genetics/*growth &amp; development/isolation &amp; purification ; Sequence Analysis, DNA ; *Soil Microbiology ; Symbiosis ; *Trees ; *Tropical Climate ; }, abstract = {Nitrogen-fixing bacteria of the Bradyrhizobium genus are major symbionts of legume plants in American tropical forests, but little is known about the effects of deforestation and change in land use on their diversity and community structure. Forest clearing is followed by cropping of bean (Phaseolus vulgaris) and maize as intercropped plants in Los Tuxtlas tropical forest of Mexico. The identity of bean-nodulating rhizobia in this area is not known. Using promiscuous trap plants, bradyrhizobia were isolated from soil samples collected in Los Tuxtlas undisturbed forest, and in areas where forest was cleared and land was used as crop fields or as pastures, or where secondary forests were established. Rhizobia were also trapped by using bean plants. Bradyrhizobium strains were classified into genospecies by dnaK sequence analysis supported by recA, glnII and 16S-23S rDNA IGS loci analyses. A total of 29 genospecies were identified, 24 of which did not correspond to any described taxa. A reduction in Bradyrhizobium diversity was observed when forest was turned to crop fields or pastures. Diversity seemed to recover to primary forest levels in secondary forests that derived from abandoned crop fields or pastures. The shifts in diversity were not related to soil characteristics but seemingly to the density of nodulating legumes present at each land use system (LUS). Bradyrhizobium community composition in soils was dependent on land use; however, similarities were observed between crop fields and pastures but not among forest and secondary forest. Most Bradyrhizobium genospecies present in forest were not recovered or become rare in the other LUS. Rhizobium etli was found as the dominant bean-nodulating rhizobia present in crop fields and pastures, and evidence was found that this species was introduced in Los Tuxtlas forest.}, }
@article {pmid22105517, year = {2012}, author = {Chaudhary, HJ and Peng, G and Hu, M and He, Y and Yang, L and Luo, Y and Tan, Z}, title = {Genetic diversity of endophytic diazotrophs of the wild rice, Oryza alta and identification of the new diazotroph, Acinetobacter oryzae sp. nov.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {813-821}, pmid = {22105517}, issn = {1432-184X}, mesh = {Acinetobacter/classification/*genetics/metabolism ; Bacteria/classification/*genetics/isolation &amp; purification ; DNA Fingerprinting ; DNA, Bacterial/analysis ; DNA, Ribosomal ; Electrophoresis, Polyacrylamide Gel ; Endophytes/classification/*genetics/isolation &amp; purification ; Genes, rRNA ; *Genetic Variation ; Molecular Sequence Data ; *Nitrogen Fixation ; Oryza/*microbiology ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Plant Stems/microbiology ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Thirty-three endophytic diazotrophs were isolated from surface-sterilized leaves, stem, and roots of wild rice Oryza alta. The SDS-PAGE profile of total protein and insertion sequence-based polymerase chain reaction (IS-PCR) fingerprinting grouped the isolates into four clusters (I-IV). The 16S rRNA gene sequence homology of the representative strains B21, B31, B1, and B23 of clusters I, II, III, and IV were assigned to Pseudomonas oleovorans (99.2% similarity), Burkholderia fungorum (99.4% similarity), Enterobacter cloacae (98.9% similarity), and Acinetobacter johnsonii (98.4% similarity), respectively. The results showed wide genetic diversity of the putative diazotrophic strains of the wild rice, O. alta, and the strains of cluster IV are the first report of nitrogen-fixing Acinetobacter species. The cell size, phenotypic characters, total protein profile, genomic DNA fingerprinting, DNA-DNA hybridization, and antibiotic resistance differentiated strain B23(T) from its closest relatives A. johnsonii LMG999(T) and Acinetobacter haemolyticus LMG996(T). The DNA-DNA hybridization also distinguished the strain B23(T) from the closely related Acinetobacter species. Based on these data, a novel species, Acinetobacter oryzae sp. nov., and strain B23(T) (=LMG25575(T) = CGMCC1.10689(T)) as the type strain were proposed.}, }
@article {pmid22105516, year = {2012}, author = {Lapanje, A and Wimmersberger, C and Furrer, G and Brunner, I and Frey, B}, title = {Pattern of elemental release during the granite dissolution can be changed by aerobic heterotrophic bacterial strains isolated from Damma Glacier (central Alps) deglaciated granite sand.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {865-882}, pmid = {22105516}, issn = {1432-184X}, mesh = {Bacteria, Aerobic/genetics/growth &amp; development/*isolation &amp; purification/metabolism ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal/genetics ; Genes, rRNA ; *Heterotrophic Processes ; Ice Cover/*microbiology ; Minerals/chemistry/*metabolism ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Silicon Dioxide/chemistry ; *Soil Microbiology ; }, abstract = {Colonisation and weathering of freshly deglaciated granite are key processes in initial soil formation and development. We have obtained 438 isolates from granite sand covering glacial toe, 284 isolates at 22°C and 154 at 4°C incubation temperatures, respectively, to obtain cultures for the investigation of their weathering capabilities under laboratory conditions. The isolation of bacteria from granite sand was performed on rich-, intermediate- and low-nutrient-content solid media. Isolates were identified by 16S rRNA gene sequencing. According to the genera-associated weathering capabilities described in the literature and according to their abundance in our culture collection, we selected eight strains to analyse their effects on the weathering dynamics of granite sand during the batch culture experiment. Analysis of culturable bacteria showed higher species richness among isolates from 22°C than from 4°C incubations. In the R2A and 1/100 Ravan media, we observed the highest species richness of isolates obtained at 22°C and 4°C incubation temperatures, respectively. The obtained 16S rRNA sequences revealed the presence of alpha-, beta- and gamma-proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. The most numerous group of isolates was distantly related to Collimonas representatives, and according to the sequences of the 16S rRNA genes, they can form a new genus. Isolates from this group had the capability of causing increased dissolution rates for Fe, W, Ni and Rb. In general, at each sampling during the 30-day experiment, every strain showed a unique weathering profile resulting from differential rates of the dissolution and the precipitation of different minerals in the batch culture. Consequently, the presence of different strains, their growth stage and changes in proportions of strains in the bacterial community can affect further soil development and the successive colonisation by plants.}, }
@article {pmid22103313, year = {2012}, author = {Tashiro, Y and Uchiyama, H and Nomura, N}, title = {Multifunctional membrane vesicles in Pseudomonas aeruginosa.}, journal = {Environmental microbiology}, volume = {14}, number = {6}, pages = {1349-1362}, doi = {10.1111/j.1462-2920.2011.02632.x}, pmid = {22103313}, issn = {1462-2920}, mesh = {Biofilms/growth &amp; development ; Biological Transport ; Gram-Negative Bacteria/pathogenicity/physiology/ultrastructure ; Pseudomonas aeruginosa/pathogenicity/*physiology/ultrastructure ; Transport Vesicles/*physiology ; }, abstract = {Gram-negative bacteria secrete small particles called membrane vesicles (MVs) into the extracellular milieu. While MVs have important roles in delivering toxins from pathogenic bacteria to eukaryotic cells, these vesicles also play ecological roles necessary for survival in various environmental conditions. Pseudomonas aeruginosa, which lives in soil, ocean, plant, animal and human environments, has become a model organism for studying these small extracellular particles. Such studies have increased our understanding of the function and biogenesis of bacterial MVs. Pseudomonas aeruginosa MVs possess versatile components and chemical substances with unique structures. These characteristics allow MVs to play their multifunctional biological roles, including microbial interaction, maintenance of biofilm structure and host infection. This review summarizes the comprehensive biochemical and physiochemical properties of MVs derived from P. aeruginosa. These studies will help us understand their biological roles of MVs not only in pathogenicity but also in microbial ecology. Also, the mechanisms of MV production, as currently understood, are discussed.}, }
@article {pmid22099187, year = {2012}, author = {Fast, W and Tipton, PA}, title = {The enzymes of bacterial census and censorship.}, journal = {Trends in biochemical sciences}, volume = {37}, number = {1}, pages = {7-14}, pmid = {22099187}, issn = {0968-0004}, support = {R01 GM059653/GM/NIGMS NIH HHS/United States ; GM59653/GM/NIGMS NIH HHS/United States ; }, mesh = {4-Butyrolactone/analogs &amp; derivatives/biosynthesis/chemistry/metabolism ; Carboxylic Ester Hydrolases/chemistry/genetics/*metabolism ; Crystallography, X-Ray ; Gram-Negative Bacteria/*enzymology/metabolism ; Ligases/chemistry/genetics/*metabolism ; Models, Molecular ; }, abstract = {N-Acyl-L-homoserine lactones (AHLs) are a major class of quorum-sensing signals used by Gram-negative bacteria to regulate gene expression in a population-dependent manner, thereby enabling group behavior. Enzymes capable of generating and catabolizing AHL signals are of significant interest for the study of microbial ecology and quorum-sensing pathways, for understanding the systems that bacteria have evolved to interact with small-molecule signals, and for their possible use in therapeutic and industrial applications. The recent structural and functional studies reviewed here provide a detailed insight into the chemistry and enzymology of bacterial communication.}, }
@article {pmid22097058, year = {2011}, author = {Lu, Y and Slater, FR and Mohd-Zaki, Z and Pratt, S and Batstone, DJ}, title = {Impact of operating history on mixed culture fermentation microbial ecology and product mixture.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {64}, number = {3}, pages = {760-765}, doi = {10.2166/wst.2011.699}, pmid = {22097058}, issn = {0273-1223}, mesh = {Bacteria/classification/genetics/*metabolism ; *Biofuels ; Ecology ; *Fermentation ; Hydrogen-Ion Concentration ; Phylogeny ; Polymorphism, Restriction Fragment Length ; }, abstract = {Mixed culture fermentation is an alternative to pure culture fermentation for production of biofuels and valuable products. A glucose-fed, continuous reactor was operated cyclically to a central pH of 5.5 from a number of precedent pHs, from 4.5 to 7.5. At each pH, stable chemical production was reached after 2 retention times and was held for least 2 further retention times prior to the next change. Bacterial groups were identified by phylogenetic analysis of 16S rRNA gene clones. Bacterial community dynamics were monitored by terminal-restriction fragment length polymorphism. More ethanol was produced at high pH, and more butyrate at lower pH. At pH 5.5, the product spectrum was not measurably influenced by precedent pH but showed seemingly random changes. The impact of precedent pH on community structure was more systematic, with clear indications that when the pH was returned to 5.5, the bacterial group that was dominant at the precedent pH remained at high abundance. This result is important, since it indicates a decoupling between microbial function (as indicated by product spectrum), and community structure. More work is needed to determine the longevity of this hysteresis effect. There was evidence that groups retained their ability to re-emerge even after times of low abundance.}, }
@article {pmid22092917, year = {2012}, author = {Vermeiren, J and Van den Abbeele, P and Laukens, D and Vigsnaes, LK and De Vos, M and Boon, N and Van de Wiele, T}, title = {Decreased colonization of fecal Clostridium coccoides/Eubacterium rectale species from ulcerative colitis patients in an in vitro dynamic gut model with mucin environment.}, journal = {FEMS microbiology ecology}, volume = {79}, number = {3}, pages = {685-696}, doi = {10.1111/j.1574-6941.2011.01252.x}, pmid = {22092917}, issn = {1574-6941}, mesh = {Acyl Coenzyme A/genetics/metabolism ; Adult ; Aged ; Butyrates/metabolism ; Clostridium/growth &amp; development/*physiology ; Coenzyme A-Transferases/genetics/metabolism ; Colitis, Ulcerative/metabolism/*microbiology ; Eubacterium/growth &amp; development/*physiology ; Fatty Acids, Volatile/metabolism ; Female ; Gastrointestinal Tract/microbiology ; Humans ; Intestinal Mucosa/microbiology ; Male ; Middle Aged ; Models, Biological ; Mucins/*metabolism ; }, abstract = {The mucus layer in the colon, acting as a barrier to prevent invasion of pathogens, is thinner and discontinuous in patients with ulcerative colitis (UC). A recent developed in vitro dynamic gut model, the M-SHIME, was used to compare long-term colonization of the mucin layer by the microbiota from six healthy volunteers (HV) and six UC patients and thus distinguish the mucin adhered from the luminal microbiota. Although under the same nutritional conditions, short-chain fatty acid production by the luminal communities from UC patients showed a tendency toward a lower butyrate production. A more in-depth community analysis of those microbial groups known to produce butyrate revealed that the diversity of the Clostridium coccoides/Eubacterium rectale and Clostridium leptum group, and counts of Faecalibacterium prausnitzii were lower in the luminal fractions of the UC samples. Counts of Roseburia spp. were lower in the mucosal fractions of the UC samples. qPCR analysis for butyryl-CoA:acetate CoA transferase, responsible for butyrate production, displayed a lower abundance in both the luminal and mucosal fractions of the UC samples. The M-SHIME model revealed depletion in butyrate producing microbial communities not restricted to the luminal but also in the mucosal samples from UC patients compared to HV.}, }
@article {pmid22092289, year = {2012}, author = {Dworkin, M}, title = {Sergei Winogradsky: a founder of modern microbiology and the first microbial ecologist.}, journal = {FEMS microbiology reviews}, volume = {36}, number = {2}, pages = {364-379}, doi = {10.1111/j.1574-6976.2011.00299.x}, pmid = {22092289}, issn = {1574-6976}, mesh = {Bacteria/genetics/isolation &amp; purification/metabolism ; Ecology/*history ; History, 19th Century ; History, 20th Century ; Humans ; Male ; Microbiology/*history ; Russia ; }, abstract = {Sergei Winogradsky, was born in Russia in 1856 and was to become a founder of modern microbiology. After his Master's degree work on the nutrition and growth physiology of the yeast Mycoderma vini at the University of St. Petersburg, he joined the laboratory of Anton DeBary in Strassburg. There he carried out his studies on the sulfur-oxidizing bacterium Beggiatoa which resulted in his formulation of the theory of chemolithotrophy. He then joined the Swiss Polytechnic Institute in Zurich where he did his monumental work on bacterial nitrification. He isolated the first pure cultures of the nitrifying bacteria and confirmed that they carried out the separate steps of the conversion of ammonia to nitrite and of nitrite to nitrate. This led directly to the concept of the cycles of sulfur and nitrogen in Nature. He returned to Russia and there was the first to isolate a free-living dinitrogen-fixing bacterium. In the flush of success, he retired from science and spent 15 years on his familial estate in the Ukraine. The Russian revolution forced him to flee Russia. He joined the Pasteur Institute in Paris where he spent his remaining 24 years initiating and developing the field of microbial ecology. He died in 1953.}, }
@article {pmid22091783, year = {2012}, author = {Lee, PK and Warnecke, F and Brodie, EL and Macbeth, TW and Conrad, ME and Andersen, GL and Alvarez-Cohen, L}, title = {Phylogenetic microarray analysis of a microbial community performing reductive dechlorination at a TCE-contaminated site.}, journal = {Environmental science &amp; technology}, volume = {46}, number = {2}, pages = {1044-1054}, pmid = {22091783}, issn = {1520-5851}, support = {P42 ES004705/ES/NIEHS NIH HHS/United States ; ES04705-19/ES/NIEHS NIH HHS/United States ; }, mesh = {Archaea/genetics/metabolism ; Bacteria/*genetics/*metabolism ; Cluster Analysis ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; *Oligonucleotide Array Sequence Analysis ; *Phylogeny ; RNA, Bacterial ; RNA, Ribosomal, 16S/genetics ; Trichloroethylene/*chemistry ; Water Pollutants, Chemical/chemistry/*metabolism ; }, abstract = {A high-density phylogenetic microarray (PhyloChip) was applied to track bacterial and archaeal populations through different phases of remediation at Ft. Lewis, WA, a trichloroethene (TCE)-contaminated groundwater site. Biostimulation with whey, and bioaugmentation with a Dehalococcoides-containing enrichment culture were strategies implemented to enhance dechlorination. As a measure of species richness, over 1300 operational taxonomic units (OTUs) were detected in DNA from groundwater samples extracted during different stages of treatment and in the bioaugmentation culture. In order to determine active members within the community, 16S rRNA from samples were analyzed by microarray and ∼600 OTUs identified. A cDNA clone library of the expressed 16S rRNA corroborated the observed diversity and activity of some of the phyla. Principle component analysis of the treatment plot samples revealed that the microbial populations were constantly changing during the course of the study. Dynamic analysis of the archaeal population showed significant increases in methanogens at the later stages of treatment that correlated with increases in methane concentrations of over 2 orders of magnitude. Overall, the PhyloChip analyses in this study have provided insights into the microbial ecology and population dynamics at the TCE-contaminated field site useful for understanding the in situ reductive dechlorination processes.}, }
@article {pmid22089131, year = {2011}, author = {Chang, HC and Paek, J and Kim, DH}, title = {Natural polymorphisms in C. elegans HECW-1 E3 ligase affect pathogen avoidance behaviour.}, journal = {Nature}, volume = {480}, number = {7378}, pages = {525-529}, pmid = {22089131}, issn = {1476-4687}, support = {R01 GM084477/GM/NIGMS NIH HHS/United States ; GM084477/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Behavior, Animal ; *Caenorhabditis elegans/enzymology/genetics/microbiology ; Caenorhabditis elegans Proteins/*genetics/*metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Enzymologic ; *Polymorphism, Genetic ; Pseudomonas aeruginosa/*physiology ; Receptors, Neuropeptide Y/metabolism ; Sensory Receptor Cells/enzymology ; Ubiquitin-Protein Ligases/*genetics/*metabolism ; }, abstract = {Heritable variation in behavioural traits generally has a complex genetic basis, and thus naturally occurring polymorphisms that influence behaviour have been defined only in rare instances. The isolation of wild strains of Caenorhabditis elegans has facilitated the study of natural genetic variation in this species and provided insights into its diverse microbial ecology. C. elegans responds to bacterial infection with conserved innate immune responses and, although lacking the immunological memory of vertebrate adaptive immunity, shows an aversive learning response to pathogenic bacteria. Here, we report the molecular characterization of naturally occurring coding polymorphisms in a C. elegans gene encoding a conserved HECT domain-containing E3 ubiquitin ligase, HECW-1. We show that two distinct polymorphisms in neighbouring residues of HECW-1 each affect C. elegans behavioural avoidance of a lawn of Pseudomonas aeruginosa. Neuron-specific rescue and ablation experiments and genetic interaction analysis indicate that HECW-1 functions in a pair of sensory neurons to inhibit P. aeruginosa lawn avoidance behaviour through inhibition of the neuropeptide receptor NPR-1 (ref. 10), which we have previously shown promotes P. aeruginosa lawn avoidance behaviour. Our data establish a molecular basis for natural variation in a C. elegans behaviour that may undergo adaptive changes in response to microbial pathogens.}, }
@article {pmid22085912, year = {2012}, author = {Kellogg, CA and Piceno, YM and Tom, LM and DeSantis, TZ and Zawada, DG and Andersen, GL}, title = {PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology.}, journal = {Journal of microbiological methods}, volume = {88}, number = {1}, pages = {103-109}, doi = {10.1016/j.mimet.2011.10.019}, pmid = {22085912}, issn = {1872-8359}, mesh = {Analytic Sample Preparation Methods/*methods ; Animals ; Anthozoa/*microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; Ecosystem ; Oligonucleotide Array Sequence Analysis ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; }, abstract = {Interest in coral microbial ecology has been increasing steadily over the last decade, yet standardized methods of sample collection still have not been defined. Two methods were compared for their ability to sample coral-associated microbial communities: tissue punches and foam swabs, the latter being less invasive and preferred by reef managers. Four colonies of star coral, Montastraea annularis, were sampled in the Dry Tortugas National Park (two healthy and two with white plague disease). The PhyloChip™ G3 microarray was used to assess microbial community structure of amplified 16S rRNA gene sequences. Samples clustered based on methodology rather than coral colony. Punch samples from healthy and diseased corals were distinct. All swab samples clustered closely together with the seawater control and did not group according to the health state of the corals. Although more microbial taxa were detected by the swab method, there is a much larger overlap between the water control and swab samples than punch samples, suggesting some of the additional diversity is due to contamination from water absorbed by the swab. While swabs are useful for noninvasive studies of the coral surface mucus layer, these results show that they are not optimal for studies of coral disease.}, }
@article {pmid22084639, year = {2011}, author = {Anderson, RE and Brazelton, WJ and Baross, JA}, title = {Is the genetic landscape of the deep subsurface biosphere affected by viruses?.}, journal = {Frontiers in microbiology}, volume = {2}, number = {}, pages = {219}, pmid = {22084639}, issn = {1664-302X}, abstract = {Viruses are powerful manipulators of microbial diversity, biogeochemistry, and evolution in the marine environment. Viruses can directly influence the genetic capabilities and the fitness of their hosts through the use of fitness factors and through horizontal gene transfer. However, the impact of viruses on microbial ecology and evolution is often overlooked in studies of the deep subsurface biosphere. Subsurface habitats connected to hydrothermal vent systems are characterized by constant fluid flux, dynamic environmental variability, and high microbial diversity. In such conditions, high adaptability would be an evolutionary asset, and the potential for frequent host-virus interactions would be high, increasing the likelihood that cellular hosts could acquire novel functions. Here, we review evidence supporting this hypothesis, including data indicating that microbial communities in subsurface hydrothermal fluids are exposed to a high rate of viral infection, as well as viral metagenomic data suggesting that the vent viral assemblage is particularly enriched in genes that facilitate horizontal gene transfer and host adaptability. Therefore, viruses are likely to play a crucial role in facilitating adaptability to the extreme conditions of these regions of the deep subsurface biosphere. We also discuss how these results might apply to other regions of the deep subsurface, where the nature of virus-host interactions would be altered, but possibly no less important, compared to more energetic hydrothermal systems.}, }
@article {pmid22083250, year = {2012}, author = {García-Amado, MA and Godoy-Vitorino, F and Piceno, YM and Tom, LM and Andersen, GL and Herrera, EA and Domínguez-Bello, MG}, title = {Bacterial diversity in the cecum of the world's largest living rodent (Hydrochoerus hydrochaeris).}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {719-725}, pmid = {22083250}, issn = {1432-184X}, mesh = {Animals ; Animals, Wild/microbiology ; Bacteria/classification/*genetics/isolation &amp; purification ; Cecum/*microbiology ; DNA, Bacterial/analysis/genetics/isolation &amp; purification ; Female ; Male ; *Metagenome ; Oligonucleotide Array Sequence Analysis ; RNA, Ribosomal, 16S/genetics ; Rodentia/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The capybara (Hydrochoerus hydrochaeris) is the world's largest living rodent. Native to South America, this hindgut fermenter is herbivorous and coprophagous and uses its enlarged cecum to digest dietary plant material. The microbiota of specialized hindgut fermenters has remained largely unexplored. The aim of this work was to describe the composition of the bacterial community in the fermenting cecum of wild capybaras. The analysis of bacterial communities in the capybara cecum is a first step towards the functional characterization of microbial fermentation in this model of hindgut fermentation. We sampled cecal contents from five wild adult capybaras (three males and two females) in the Venezuelan plains. DNA from cecal contents was extracted, the 16S rDNA was amplified, and the amplicons were hybridized onto a DNA microarray (G2 PhyloChip). We found 933 bacterial operational taxonomic units (OTUs) from 182 families in 21 bacterial phyla in the capybara cecum. The core bacterial microbiota (present in at least four animals) was represented by 575 OTUs. About 86% of the cecal bacterial OTUs belong to only five phyla, namely, Firmicutes (322 OTUs), Proteobacteria (301 OTUs), Bacteroidetes (76 OTUs), Actinobacteria (69 OTUs), and Sphirochaetes (37 OTUs). The capybara harbors a diverse bacterial community that includes lineages involved in fiber degradation and nitrogen fixation in other herbivorous animals.}, }
@article {pmid22081571, year = {2012}, author = {Trias, R and García-Lledó, A and Sánchez, N and López-Jurado, JL and Hallin, S and Bañeras, L}, title = {Abundance and composition of epiphytic bacterial and archaeal ammonia oxidizers of marine red and brown macroalgae.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {2}, pages = {318-325}, pmid = {22081571}, issn = {1098-5336}, mesh = {Ammonia/*metabolism ; Archaea/*classification/genetics/metabolism ; Bacteria/*classification/genetics/metabolism ; *Biodiversity ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Laminaria/*microbiology ; Mediterranean Sea ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Rhodophyta/*microbiology ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are important for nitrogen cycling in marine ecosystems. Little is known about the diversity and abundance of these organisms on the surface of marine macroalgae, despite the algae's potential importance to create surfaces and local oxygen-rich environments supporting ammonia oxidation at depths with low dissolved oxygen levels. We determined the abundance and composition of the epiphytic bacterial and archaeal ammonia-oxidizing communities on three species of macroalgae, Osmundaria volubilis, Phyllophora crispa, and Laminaria rodriguezii, from the Balearic Islands (western Mediterranean Sea). Quantitative PCR of bacterial and archaeal 16S rRNA and amoA genes was performed. In contrast to what has been shown for most other marine environments, the macroalgae's surfaces were dominated by bacterial amoA genes rather than those from the archaeal counterpart. On the basis of the sequences retrieved from AOB and AOA amoA gene clone libraries from each algal species, the bacterial ammonia-oxidizing communities were related to Nitrosospira spp. and to Nitrosomonas europaea and only 6 out of 15 operational taxonomic units (OTUs) were specific for the host species. Conversely, the AOA diversity was higher (43 OTUs) and algal species specific, with 17 OTUs specific for L. rodriguezii, 3 for O. volubilis, and 9 for P. crispa. Altogether, the results suggest that marine macroalgae may exert an ecological niche for AOB in marine environments, potentially through specific microbe-host interactions.}, }
@article {pmid22080257, year = {2012}, author = {Belisle, M and Peay, KG and Fukami, T}, title = {Flowers as islands: spatial distribution of nectar-inhabiting microfungi among plants of Mimulus aurantiacus, a hummingbird-pollinated shrub.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {711-718}, pmid = {22080257}, issn = {1432-184X}, support = {T32 GM007276/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Birds ; California ; *Ecosystem ; Flowers/*microbiology ; Fungi/classification/genetics/*isolation &amp; purification ; Mimulus/*microbiology ; Plant Nectar ; *Pollination ; Polymerase Chain Reaction ; Saccharomycetales/classification/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; }, abstract = {Microfungi that inhabit floral nectar offer unique opportunities for the study of microbial distribution and the role that dispersal limitation may play in generating distribution patterns. Flowers are well-replicated habitat islands, among which the microbes disperse via pollinators. This metapopulation system allows for investigation of microbial distribution at multiple spatial scales. We examined the distribution of the yeast, Metschnikowia reukaufii, and other fungal species found in the floral nectar of the sticky monkey flower, Mimulus aurantiacus, a hummingbird-pollinated shrub, at a California site. We found that the frequency of nectar-inhabiting microfungi on a given host plant was not significantly correlated with light availability, nectar volume, or the percent cover of M. aurantiacus around the plant, but was significantly correlated with the location of the host plant and loosely correlated with the density of flowers on the plant. These results suggest that dispersal limitation caused by spatially nonrandom foraging by pollinators may be a primary factor driving the observed distribution pattern.}, }
@article {pmid22080256, year = {2012}, author = {McGuire, KL and Fierer, N and Bateman, C and Treseder, KK and Turner, BL}, title = {Fungal community composition in neotropical rain forests: the influence of tree diversity and precipitation.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {804-812}, pmid = {22080256}, issn = {1432-184X}, mesh = {DNA, Fungal/analysis/genetics/isolation &amp; purification ; *Ecosystem ; Fungi/classification/genetics/*growth &amp; development/isolation &amp; purification ; Plant Leaves/metabolism/microbiology ; *Rain ; Soil/*chemistry ; *Soil Microbiology ; Trees/*classification/microbiology ; *Tropical Climate ; }, abstract = {Plant diversity is considered one factor structuring soil fungal communities because the diversity of compounds in leaf litter might determine the extent of resource heterogeneity for decomposer communities. Lowland tropical rain forests have the highest plant diversity per area of any biome. Since fungi are responsible for much of the decomposition occurring in forest soils, understanding the factors that structure fungi in tropical forests may provide valuable insight for predicting changes in global carbon and nitrogen fluxes. To test the role of plant diversity in shaping fungal community structure and function, soil (0-20 cm) and leaf litter (O horizons) were collected from six established 1-ha forest census plots across a natural plant diversity gradient on the Isthmus of Panama. We used 454 pyrosequencing and phospholipid fatty acid analysis to evaluate correlations between microbial community composition, precipitation, soil nutrients, and plant richness. In soil, the number of fungal taxa increased significantly with increasing mean annual precipitation, but not with plant richness. There were no correlations between fungal communities in leaf litter and plant diversity or precipitation, and fungal communities were found to be compositionally distinct between soil and leaf litter. To directly test for effects of plant species richness on fungal diversity and function, we experimentally re-created litter diversity gradients in litter bags with 1, 25, and 50 species of litter. After 6 months, we found a significant effect of litter diversity on decomposition rate between one and 25 species of leaf litter. However, fungal richness did not track plant species richness. Although studies in a broader range of sites is required, these results suggest that precipitation may be a more important factor than plant diversity or soil nutrient status in structuring tropical forest soil fungal communities.}, }
@article {pmid22079351, year = {2012}, author = {Wagner, M and Haider, S}, title = {New trends in fluorescence in situ hybridization for identification and functional analyses of microbes.}, journal = {Current opinion in biotechnology}, volume = {23}, number = {1}, pages = {96-102}, doi = {10.1016/j.copbio.2011.10.010}, pmid = {22079351}, issn = {1879-0429}, mesh = {Archaea/genetics ; Bacteria/genetics ; DNA Primers/genetics ; In Situ Hybridization, Fluorescence/*methods/trends ; Oligonucleotide Probes/genetics ; RNA Probes/genetics ; }, abstract = {Fluorescence in situ hybridization (FISH) has become an indispensable tool for rapid and direct single-cell identification of microbes by detecting signature regions in their rRNA molecules. Recent advances in this field include new web-based tools for assisting probe design and optimization of experimental conditions, easy-to-implement signal amplification strategies, innovative multiplexing approaches, and the combination of FISH with transmission electron microscopy or extracellular staining techniques. Further emerging developments focus on sorting FISH-identified cells for subsequent single-cell genomics and on the direct detection of specific genes within single microbial cells by advanced FISH techniques employing various strategies for massive signal amplification.}, }
@article {pmid22076694, year = {2012}, author = {Fernández, DA and Roldán, A and Azcón, R and Caravaca, F and Bååth, E}, title = {Effects of water stress, organic amendment and mycorrhizal inoculation on soil microbial community structure and activity during the establishment of two heavy metal-tolerant native plant species.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {794-803}, pmid = {22076694}, issn = {1432-184X}, mesh = {Apiaceae/drug effects/*growth &amp; development/microbiology ; Beta vulgaris/chemistry ; Cupressaceae/drug effects/*growth &amp; development/microbiology ; Dehydration ; Droughts ; Glomeromycota/*growth &amp; development ; Metals, Heavy/*pharmacology ; Mycorrhizae/*growth &amp; development ; Plant Roots/growth &amp; development/microbiology ; *Soil Microbiology ; Soil Pollutants/pharmacology ; }, abstract = {Our aim was to examine the effect of water stress on plant growth and development of two native plant species (Tetraclinis articulata and Crithmum maritimum) and on microbial community composition and activity in the rhizosphere soil, following the addition of an organic amendment, namely sugar beet residue (SBR), and/or the inoculation with an arbuscular mycorrhizal (AM) fungus, namely Glomus mosseae, in a non-sterile heavy metal-polluted soil. The AM inoculation did not have any significant effect on plant growth of both species. In T. articulata, SBR increased shoot growth, foliar P, total phospholipid fatty acids (PLFA), fungi-related PLFA, AM fungi-related neutral lipid fatty acid, bacterial gram-positive/gram-negative PLFA ratio and the β-glucosidase and dehydrogenase activities. SBR and AM inoculation increased phosphatase activity in T. articulata plants grown under drought conditions. In both plants, there was a synergistic effect between AM inoculation and SBR on mycorrhizal colonisation under drought conditions. In C. maritimum, the increase produced by the SBR on total amounts of PLFA, bacterial gram-positive-related PLFA and bacterial gram-negative-related PLFA was considerably higher under drought conditions. Our results suggest that the effectiveness of the amendment with regard to stimulating microbial communities and plant growth was largely limited by drought, particularly for plant species with a low degree of mycorrhizal colonisation.}, }
@article {pmid22075624, year = {2012}, author = {Hwang, C and Ling, F and Andersen, GL and LeChevallier, MW and Liu, WT}, title = {Evaluation of methods for the extraction of DNA from drinking water distribution system biofilms.}, journal = {Microbes and environments}, volume = {27}, number = {1}, pages = {9-18}, pmid = {22075624}, issn = {1347-4405}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; *Biofilms ; Chemistry Techniques, Analytical/*methods ; DNA, Bacterial/genetics/*isolation &amp; purification ; Drinking Water/*microbiology ; }, abstract = {While drinking water biofilms have been characterized in various drinking water distribution systems (DWDS), little is known about the impact of different DNA extraction methods on the subsequent analysis of microbial communities in drinking water biofilms. Since different DNA extraction methods have been shown to affect the outcome of microbial community analysis in other environments, it is necessary to select a DNA extraction method prior to the application of molecular tools to characterize the complex microbial ecology of the DWDS. This study compared the quantity and quality of DNA yields from selected DWDS bacteria with different cell wall properties using five widely used DNA extraction methods. These were further selected and evaluated for their efficiency and reproducibility of DNA extraction from DWDS samples. Terminal restriction fragment length analysis and the 454 pyrosequencing technique were used to interpret the differences in microbial community structure and composition, respectively, from extracted DNA. Such assessments serve as a concrete step towards the determination of an optimal DNA extraction method for drinking water biofilms, which can then provide a reliable comparison of the meta-analysis results obtained in different laboratories.}, }
@article {pmid22074255, year = {2011}, author = {Case, RJ and Boucher, Y}, title = {Molecular musings in microbial ecology and evolution.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {58}, pmid = {22074255}, issn = {1745-6150}, mesh = {Archaea/classification/genetics ; Bacteria/classification/*genetics ; Biota ; *Ecology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Archaeal ; *Genes, Bacterial ; Genes, rRNA ; Genetic Markers ; Genetic Variation ; Microbiological Phenomena ; Phylogeny ; Ribosomes/genetics ; }, abstract = {A few major discoveries have influenced how ecologists and evolutionists study microbes. Here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in these two branches of microbiology, and how they have impacted on both scientific thinking and methodology.The first question is "What has been the influence of the 'Universal Tree of Life' based on molecular markers?" For evolutionists, the tree was a tool to understand the past of known (cultured) organisms, mapping the invention of various physiologies on the evolutionary history of microbes. For ecologists the tree was a guide to discover the current diversity of unknown (uncultured) organisms, without much knowledge of their physiology.The second question we ask is "What was the impact of discovering frequent lateral gene transfer among microbes?" In evolutionary microbiology, frequent lateral gene transfer (LGT) made a simple description of relationships between organisms impossible, and for microbial ecologists, functions could not be easily linked to specific genotypes. Both fields initially resisted LGT, but methods or topics of inquiry were eventually changed in one to incorporate LGT in its theoretical models (evolution) and in the other to achieve its goals despite that phenomenon (ecology).The third and last question we ask is "What are the implications of the unexpected extent of diversity?" The variation in the extent of diversity between organisms invalidated the universality of species definitions based on molecular criteria, a major obstacle to the adaptation of models developed for the study of macroscopic eukaryotes to evolutionary microbiology. This issue has not overtly affected microbial ecology, as it had already abandoned species in favor of the more flexible operational taxonomic units. This field is nonetheless moving away from traditional methods to measure diversity, as they do not provide enough resolution to uncover what lies below the species level.The answers of the evolutionary microbiologist and microbial ecologist to these three questions illustrate differences in their theoretical frameworks. These differences mean that both fields can react quite distinctly to the same discovery, incorporating it with more or less difficulty in their scientific practice.}, }
@article {pmid22073014, year = {2011}, author = {Leyton, Y and Borquez, J and Darias, J and Cueto, M and Díaz-Marrero, AR and Riquelme, C}, title = {Oleic acid produced by a marine Vibrio spp. acts as an anti-Vibrio parahaemolyticus agent.}, journal = {Marine drugs}, volume = {9}, number = {10}, pages = {2155-2163}, pmid = {22073014}, issn = {1660-3397}, mesh = {Anti-Infective Agents/isolation &amp; purification/*pharmacology ; Chromatography, Gas ; Chromatography, High Pressure Liquid ; Chromatography, Reverse-Phase ; Microbial Sensitivity Tests ; Oleic Acid/isolation &amp; purification/*pharmacology/physiology ; Vibrio/chemistry/*physiology ; Vibrio parahaemolyticus/*drug effects ; }, abstract = {It is known that some strains of Vibrio parahaemolyticus are responsible for gastroenteric diseases caused by the ingestion of marine organisms contaminated with these bacterial strains. Organic products that show inhibitory activity on the growth of the pathogenic V. parahaemolyticus were extracted from a Vibrio native in the north of Chile. The inhibitory organic products were isolated by reverse phase chromatography and permeation by Sephadex LH20, and were characterized by spectroscopic and spectrometric techniques. The results showed that the prevailing active product is oleic acid, which was compared with standards by gas chromatography and high-performance liquid chromatography (HPLC). These active products might be useful for controlling the proliferation of pathogenic clones of V. parahaemolyticus.}, }
@article {pmid22072124, year = {2012}, author = {Oishi, R and Tada, C and Asano, R and Yamamoto, N and Suyama, Y and Nakai, Y}, title = {Growth of ammonia-oxidizing archaea and bacteria in cattle manure compost under various temperatures and ammonia concentrations.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {787-793}, pmid = {22072124}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Animals ; Archaea/classification/enzymology/genetics/*growth &amp; development ; Bacteria/classification/enzymology/genetics/*growth &amp; development ; Cattle ; Culture Media ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Manure/*microbiology ; Nitrosomonas/classification/enzymology/genetics/growth &amp; development ; Oxidation-Reduction ; Oxidoreductases/*genetics/metabolism ; Polymerase Chain Reaction/methods ; Soil/analysis ; *Temperature ; }, abstract = {A recent study showed that ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) coexist in the process of cattle manure composting. To investigate their physiological characteristics, liquid cultures seeded with fermenting cattle manure compost were incubated at various temperatures (37°C, 46°C, or 60°C) and ammonium concentrations (0.5, 1, 4, or 10 mM NH (4) (+) -N). The growth rates of the AOB and AOA were monitored using real-time polymerase chain reaction analysis targeting the bacterial and archaeal ammonia monooxygenase subunit A genes. AOB grew at 37°C and 4 or 10 mM NH (4) (+) -N, whereas AOA grew at 46°C and 10 mM NH (4) (+) -N. Incubation with allylthiourea indicated that the AOB and AOA grew by oxidizing ammonia. Denaturing gradient gel electrophoresis and subsequent sequencing analyses revealed that a bacterium related to Nitrosomonas halophila and an archaeon related to Candidatus Nitrososphaera gargensis were the predominant AOB and AOA, respectively, in the seed compost and in cultures after incubation. This is the first report to demonstrate that the predominant AOA in cattle manure compost can grow and can probably oxidize ammonia under moderately thermophilic conditions.}, }
@article {pmid22070656, year = {2011}, author = {Desloover, J and Puig, S and Virdis, B and Clauwaert, P and Boeckx, P and Verstraete, W and Boon, N}, title = {Biocathodic nitrous oxide removal in bioelectrochemical systems.}, journal = {Environmental science &amp; technology}, volume = {45}, number = {24}, pages = {10557-10566}, doi = {10.1021/es202047x}, pmid = {22070656}, issn = {1520-5851}, mesh = {Air Pollutants/analysis/*chemistry ; Air Pollution/prevention &amp; control ; Electrodes ; Global Warming ; Greenhouse Effect ; Nitrous Oxide/analysis/*chemistry ; Refuse Disposal/methods ; }, abstract = {Anthropogenic nitrous oxide (N(2)O) emissions represent up to 40% of the global N(2)O emission and are constantly increasing. Mitigation of these emissions is warranted since N(2)O is a strong greenhouse gas and important ozone-depleting compound. Until now, only physicochemical technologies have been applied to mitigate point sources of N(2)O, and no biological treatment technology has been developed so far. In this study, a bioelectrochemical system (BES) with an autotrophic denitrifying biocathode was considered for the removal of N(2)O. The high N(2)O removal rates obtained ranged between 0.76 and 1.83 kg N m(-3) net cathodic compartment (NCC) d(-1) and were proportional to the current production, resulting in cathodic coulombic efficiencies near 100%. Furthermore, our experiments suggested the active involvement of microorganisms as the catalyst for the reduction of N(2)O to N(2), and the optimal cathode potential ranged from -200 to 0 mV vs standard hydrogen electrode (SHE) in order to obtain high conversion rates. Successful operation of the system for more than 115 days with N(2)O as the sole cathodic electron acceptor strongly indicated that N(2)O respiration yielded enough energy to maintain the biological process. To our knowledge, this study provides for the first time proof of concept of biocathodic N(2)O removal at long-term without the need for high temperatures and expensive catalysts.}, }
@article {pmid22068488, year = {2011}, author = {Na, H and Kim, OS and Yoon, SH and Kim, Y and Chun, J}, title = {Comparative approach to capture bacterial diversity of coastal waters.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {49}, number = {5}, pages = {729-740}, pmid = {22068488}, issn = {1976-3794}, mesh = {Bacteria/*classification/genetics/growth &amp; development/*isolation &amp; purification ; Bacteriological Techniques/*methods ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Metagenomics/*methods ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Despite the revolutionary advancements in DNA sequencing technology and cultivation techniques, few studies have been done to directly compare these methods. In this study, a 16S rRNA gene-based, integrative approach combining culture-independent techniques with culture-dependent methods was taken to investigate the bacterial community structure of coastal seawater collected from the Yellow Sea, Korea. For culture-independent studies, we used the latest model pyrosequencer, Roche/454 Genome Sequencer FLX Titanium. Pyrosequencing captured a total of 52 phyla including 27 candidate divisions from the water column, whereas the traditional cloning approach captured only 15 phyla including 2 candidate divisions. In addition, of 878 genera retrieved, 92.1 % of the sequences were unique to pyrosequencing. For culture-dependent analysis, plate culturing, plate washing, enrichment, and high-throughput culturing (HTC) methods were applied. Phylogenetic analysis showed that the plate-washing clones formed a cluster devoid of any previously cultured representatives within the family Rhodobacteraceae. One HTC isolate (SF293) fell into the OM182 clade, which was not recovered by other culturing methods described here. By directly comparing the sequences obtained from cultures with those from culture-independent work, we found that only 33% of the culture sequences were identical to those from clone libraries and pyrosequences. This study presents a detailed comparison of common molecular and cultivation techniques available in microbial ecology. As different methods yielded different coverage, we suggest choosing the approach after carefully examining the scientific questions being asked.}, }
@article {pmid22067077, year = {2011}, author = {Liao, L and Xu, XW and Jiang, XW and Wang, CS and Zhang, DS and Ni, JY and Wu, M}, title = {Microbial diversity in deep-sea sediment from the cobalt-rich crust deposit region in the Pacific Ocean.}, journal = {FEMS microbiology ecology}, volume = {78}, number = {3}, pages = {565-585}, doi = {10.1111/j.1574-6941.2011.01186.x}, pmid = {22067077}, issn = {1574-6941}, mesh = {Acidobacteria/classification/genetics/isolation &amp; purification ; Archaea/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Cobalt/*chemistry ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Gene Library ; Geologic Sediments/chemistry/*microbiology ; Metals/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Pacific Ocean ; *Phylogeny ; Planctomycetales/classification/genetics/isolation &amp; purification ; Proteobacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Sulfur/metabolism ; }, abstract = {Cobalt-rich crusts are important metallic mineral resources with great economic potential, usually distributed on seamounts located in the Pacific Ocean. Microorganisms are believed to play a role in the formation of crusts as well as in metal cycling. To explore the microbial diversity related to cobalt-rich crusts, 16S ribosomal RNA gene clone libraries were constructed from three consecutive sediment layers. In total, 417 bacterial clones were obtained from three bacterial clone libraries, representing 17 distinct phylogenetic groups. Proteobacteria dominated in the bacterial communities, followed by Acidobacteria and Planctomycetes. Compared with high bacterial diversity, archaea showed a remarkably low diversity, with all 137 clones belonging to marine archaeal group I except one novel euryarchaeotal clone. The microbial communities were potentially involved in sulfur, nitrogen and metal cycling in the area of cobalt-rich crusts. Sulfur oxidation and metal oxidation were potentially major sources of energy for this ecosystem. This is the first reported investigation of microbial diversity in sediments associated with cobalt-rich crusts, and it casts fresh light on the microbial ecology of these important ecosystems.}, }
@article {pmid22066695, year = {2012}, author = {Kuramae, EE and Yergeau, E and Wong, LC and Pijl, AS and van Veen, JA and Kowalchuk, GA}, title = {Soil characteristics more strongly influence soil bacterial communities than land-use type.}, journal = {FEMS microbiology ecology}, volume = {79}, number = {1}, pages = {12-24}, doi = {10.1111/j.1574-6941.2011.01192.x}, pmid = {22066695}, issn = {1574-6941}, mesh = {Alphaproteobacteria/classification/genetics/growth &amp; development ; Bacteria/*classification/genetics/growth &amp; development ; Biodiversity ; DNA, Bacterial/analysis ; Denaturing Gradient Gel Electrophoresis ; Gammaproteobacteria/classification/genetics/growth &amp; development ; Netherlands ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {To gain insight into the factors driving the structure of bacterial communities in soil, we applied real-time PCR, PCR-denaturing gradient gel electrophoreses, and phylogenetic microarray approaches targeting the 16S rRNA gene across a range of different land usages in the Netherlands. We observed that the main differences in the bacterial communities were not related to land-use type, but rather to soil factors. An exception was the bacterial community of pine forest soils (PFS), which was clearly different from all other sites. PFS had lowest bacterial abundance, lowest numbers of operational taxonomic units (OTUs), lowest soil pH, and highest C : N ratios. C : N ratio strongly influenced bacterial community structure and was the main factor separating PFS from other fields. For the sites other than PFS, phosphate was the most important factor explaining the differences in bacterial communities across fields. Firmicutes were the most dominant group in almost all fields, except in PFS and deciduous forest soils (DFS). In PFS, Alphaproteobacteria was most represented, while in DFS, Firmicutes and Gammaproteobacteria were both highly represented. Interestingly, Bacillii and Clostridium OTUs correlated with pH and phosphate, which might explain their high abundance across many of the Dutch soils. Numerous bacterial groups were highly correlated with specific soil factors, suggesting that they might be useful as indicators of soil status.}, }
@article {pmid22066474, year = {2011}, author = {Mikkonen, A and Lappi, K and Wallenius, K and Lindström, K and Suominen, L}, title = {Ecological inference on bacterial succession using curve-based community fingerprint data analysis, demonstrated with rhizoremediation experiment.}, journal = {FEMS microbiology ecology}, volume = {78}, number = {3}, pages = {604-616}, doi = {10.1111/j.1574-6941.2011.01187.x}, pmid = {22066474}, issn = {1574-6941}, mesh = {Alphaproteobacteria/*genetics/growth &amp; development ; Betaproteobacteria/*genetics/growth &amp; development/metabolism ; Biodegradation, Environmental ; Biomass ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Ecology/methods ; *Fuel Oils ; Galega/growth &amp; development ; Polymerase Chain Reaction ; *Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {Nucleic acid-based community fingerprinting methods are valuable tools in microbial ecology, as they offer rapid and robust means to compare large series of replicates and references. To avoid the time-consuming and potentially subjective procedures of peak-based examination, we assessed the possibility to apply direct curve-based data analysis on community fingerprints produced with bacterial length heterogeneity PCR (LH-PCR). The dataset comprised 180 profiles from a 21-week rhizoremediation greenhouse experiment with three treatments and 10 sampling times. Curve-based analysis quantified the progressive effect of the plant (Galega orientalis) and the reversible effect of the contaminant (fuel oil) on bacterial succession. The major observed community shifts were assigned to changes in plant biomass and contamination level by canonical correlation analysis. A novel method to extract relative abundance data from the fingerprint curves for Shannon diversity index revealed contamination to reversibly decrease community complexity. By cloning and sequencing the fragment lengths, recognized to change in time in the averaged LH-PCR profiles, we identified Aquabacterium (Betaproteobacteria) as the putative r-strategic fuel oil degrader, and K-strategic Alphaproteobacteria growing in abundance later in succession. Curve-based community fingerprint analysis can be used for rapid data prescreening or as a robust alternative for the more heavily parameterized peak-based analysis.}, }
@article {pmid22057471, year = {2012}, author = {Mohlin, M and Roleda, MY and Pattanaik, B and Tenne, SJ and Wulff, A}, title = {Interspecific resource competition-combined effects of radiation and nutrient limitation on two diazotrophic filamentous cyanobacteria.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {736-750}, pmid = {22057471}, issn = {1432-184X}, mesh = {*Aphanizomenon/growth &amp; development/metabolism/radiation effects ; Baltic States ; Cyanobacteria/classification/growth &amp; development/metabolism/radiation effects ; Nitrates/*metabolism/pharmacology ; *Nitrogen Fixation ; *Nodularia/growth &amp; development/metabolism/radiation effects ; Oceans and Seas ; Phosphates/*metabolism/pharmacology ; Photosynthesis ; Seasons ; Seawater/*microbiology ; Species Specificity ; Ultraviolet Rays ; }, abstract = {The cyanobacterial blooms in the Baltic Sea are dominated by diazotrophic cyanobacteria, the potentially toxic species Aphanizomenon sp. and the toxic species Nodularia spumigena. The seasonal succession with peaks of Aphanizomenon sp., followed by peaks of N. spumigena, has been explained by the species-specific niches of the two species. In a three-factorial outdoor experiment, we tested if nutrient and radiation conditions may impact physiological and biochemical responses of N. spumigena and Aphanizomenon sp. in the presence or absence of the other species. The two nutrient treatments were f/2 medium without NO (3) (-) (-N) and f/2 medium without PO (4) (3-) (-P), and the two ambient radiation treatments were photosynthetic active radiation >395 nm (PAR) and PAR + UV-A + UV-B >295 nm. The study showed that Aphanizomenon sp. was not negatively affected by the presence of N. spumigena and that N. spumigena was better adapted to both N and P limitation in interaction with ultraviolet radiation (UVR, 280-400 nm). In the Baltic Sea, these physical conditions are likely to prevail in the surface water during summer. Interestingly, the specific growth rate of N. spumigena was stimulated by the presence of Aphanizomenon sp. We suggest that the seasonal succession, with peaks of Aphanizomenon sp. followed by peaks of N. spumigena, is a result from species-specific preferences of environmental conditions and/or stimulation by Aphanizomenon sp. rather than an allelopathic effect of N. spumigena. The results from our study, together with a predicted stronger stratification due to effects of climate change in the Baltic Sea with increased temperature and increased precipitation and increased UV-B due to ozone losses, reflect a scenario with a continuing future dominance of the toxic N. spumigena.}, }
@article {pmid22057398, year = {2012}, author = {Hubert, J and Kopecký, J and Perotti, MA and Nesvorná, M and Braig, HR and Ságová-Marečková, M and Macovei, L and Zurek, L}, title = {Detection and identification of species-specific bacteria associated with synanthropic mites.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {919-928}, pmid = {22057398}, issn = {1432-184X}, mesh = {Acari/classification/genetics/*microbiology ; Animals ; Bacteria/classification/*genetics/*isolation &amp; purification ; Cloning, Molecular ; Dermatophagoides farinae/microbiology ; In Situ Hybridization, Fluorescence ; Mites/microbiology ; Molecular Sequence Data ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Internal bacterial communities of synanthropic mites Acarus siro, Dermatophagoides farinae, Lepidoglyphus destructor, and Tyrophagus putrescentiae (Acari: Astigmata) were analyzed by culturing and culture-independent approaches from specimens obtained from laboratory colonies. Homogenates of surface-sterilized mites were used for cultivation on non-selective agar and DNA extraction. Isolated bacteria were identified by sequencing of the 16S rRNA gene. PCR amplified 16S rRNA genes were analyzed by terminal restriction fragment length polymorphism analysis (T-RFLP) and cloning sequencing. Fluorescence in situ hybridization using universal bacterial probes was used for direct bacterial localization. T-RFLP analysis of 16S rRNA gene revealed distinct species-specific bacterial communities. The results were further confirmed by cloning and sequencing (284 clones). L. destructor and D. farinae showed more diverse communities then A. siro and T. putrescentiae. In the cultivated part of the community, the mean CFUs from four mite species ranged from 5.2 × 10(2) to 1.4 × 10(3) per mite. D. farinae had significantly higher CFUs than the other species. Bacteria were located in the digestive and reproductive tract, parenchymatical tissue, and in bacteriocytes. Among the clones, Bartonella-like bacteria occurring in A. siro and T. putresecentiae represented a distinct group related to Bartonellaceae and to Bartonella-like symbionts of ants. The clones of high similarity to Xenorhabdus cabanillasii were found in L. destructor and D. farinae, and one clone related to Photorhabdus temperata in A. siro. Members of Sphingobacteriales cloned from D. farinae and A. siro clustered with the sequences of "Candidatus Cardinium hertigii" and as a separate novel cluster.}, }
@article {pmid22052370, year = {2012}, author = {Nyberg, KA and Enwall, K and Schnürer, A and Sundh, I and Hallin, S}, title = {Response of induced perturbation on replicating β-proteobacterial ammonia-oxidizing populations in soil.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {701-709}, pmid = {22052370}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Betaproteobacteria/classification/genetics/isolation &amp; purification/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; *Soil Microbiology ; }, abstract = {The short-term response of induced perturbation by 4-ethylphenol on β-proteobacterial ammonia oxidizers (β-AOB) was investigated in two soils with initial differences in community structure. The hypotheses were that short-term effects of a disturbance of the AOB community is best monitored by specifically looking at the active populations and that soils with dissimilar active AOB populations would display different degree of resistance or resilience. Two soils from a previously characterized long-term field study fertilized with manure or sewage sludge was used. Soil microcosms were incubated in the laboratory over 15 days. The substrate-induced ammonia oxidation was measured, and the composition of β-AOB communities was determined by PCR-DGGE of specific β-AOB 16S rRNA gene fragments. Actively replicating members of the β-AOB were distinguished by the use of bromodeoxyuridine (BrdU) immunocapture. This approach demonstrated that only a minor fraction of the total AOB community was active. Exposure to 4-ethylphenol resulted in approximately 90% lowered substrate-induced ammonia oxidation rates in both soils. This activity inhibition was not accompanied by shifts in β-AOB community structure when total β-AOB DNA was studied. By contrast, changes were seen in the DGGE banding pattern of the BrdU-labeled community DNA after 4-ethylphenol addition in the manure-fertilized soil. In the sewage sludge fertilized soil, the banding pattern of the BrdU-labeled β-AOB remained unchanged, but bands were weaker after the disturbance. In conclusion, it was shown that BrdU immunocapture was applicable to detect shifts in community composition among replicating β-AOB populations in soil. However, this was not reflected by the soils' ammonia oxidation capacity to resist to or recover from the induced perturbation suggesting that rapid population shifts may not influence soil functioning in a short-term perspective.}, }
@article {pmid22046287, year = {2011}, author = {Bhadury, P and Bik, H and Lambshead, JD and Austen, MC and Smerdon, GR and Rogers, AD}, title = {Molecular diversity of fungal phylotypes co-amplified alongside nematodes from coastal and deep-sea marine environments.}, journal = {PloS one}, volume = {6}, number = {10}, pages = {e26445}, pmid = {22046287}, issn = {1932-6203}, mesh = {Animals ; Classification ; Ecosystem ; Fungi/classification/genetics/*isolation &amp; purification ; Marine Biology/*methods ; Molecular Sequence Data ; Nematoda/*isolation &amp; purification ; Oceans and Seas ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Nematodes and fungi are both ubiquitous in marine environments, yet few studies have investigated relationships between these two groups. Microbial species share many well-documented interactions with both free-living and parasitic nematode species, and limited data from previous studies have suggested ecological associations between fungi and nematodes in benthic marine habitats. This study aimed to further document the taxonomy and distribution of fungal taxa often co-amplified from nematode specimens. A total of 15 fungal 18S rRNA phylotypes were isolated from nematode specimens representing both deep-sea and shallow water habitats; all fungal isolates displayed high pairwise sequence identities with published data in Genbank (99-100%) and unpublished high-throughput 454 environmental datasets (>95%). BLAST matches indicate marine fungal sequences amplified in this study broadly represent taxa within the phyla Ascomycota and Basidiomycota, and several phylotypes showed robust groupings with known taxa in phylogenetic topologies. In addition, some fungal phylotypes appeared to be present in disparate geographic habitats, suggesting cosmopolitan distributions or closely related species complexes in at least some marine fungi. The present study was only able to isolate fungal DNA from a restricted set of nematode taxa; further work is needed to fully investigate the taxonomic scope and function of nematode-fungal interactions.}, }
@article {pmid22046169, year = {2011}, author = {Remus-Emsermann, MN and de Oliveira, S and Schreiber, L and Leveau, JH}, title = {Quantification of lateral heterogeneity in carbohydrate permeability of isolated plant leaf cuticles.}, journal = {Frontiers in microbiology}, volume = {2}, number = {}, pages = {197}, pmid = {22046169}, issn = {1664-302X}, abstract = {In phyllosphere microbiology, the distribution of resources available to bacterial colonizers of leaf surfaces is generally understood to be very heterogeneous. However, there is little quantitative understanding of the mechanisms that underlie this heterogeneity. Here, we tested the hypothesis that different parts of the cuticle vary in the degree to which they allow diffusion of the leaf sugar fructose to the surface. To this end, individual, isolated cuticles of poplar leaves were each analyzed for two properties: (1) the permeability for fructose, which involved measurement of diffused fructose by gas chromatography and flame ionization detection (GC-FID), and (2) the number and size of fructose-permeable sites on the cuticle, which was achieved using a green-fluorescent protein (GFP)-based bacterial bioreporter for fructose. Bulk flux measurements revealed an average permeance P of 3.39 × 10(-9) ms(-1), while the bioreporter showed that most of the leaching fructose was clustered to sites around the base of shed trichomes, which accounted for only 0.37% of the surface of the cuticles under study. Combined, the GC-FID and GFP measurements allowed us to calculate an apparent rate of fructose diffusion at these preferential leaching sites of 9.15 × 10(-7) ms(-1). To the best of our knowledge, this study represents the first successful attempt to quantify cuticle permeability at a resolution that is most relevant to bacterial colonizers of plant leaves. The estimates for P at different spatial scales will be useful for future models that aim to explain and predict temporal and spatial patterns of bacterial colonization of plant foliage based on lateral heterogeneity in sugar permeability of the leaf cuticle.}, }
@article {pmid22041546, year = {2012}, author = {Hoyles, L and Honda, H and Logan, NA and Halket, G and La Ragione, RM and McCartney, AL}, title = {Recognition of greater diversity of Bacillus species and related bacteria in human faeces.}, journal = {Research in microbiology}, volume = {163}, number = {1}, pages = {3-13}, doi = {10.1016/j.resmic.2011.10.004}, pmid = {22041546}, issn = {1769-7123}, mesh = {Adult ; Bacillus/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Feces/*microbiology ; Female ; Humans ; Male ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In a study looking at culturable aerobic Actinobacteria associated with the human gastrointestinal tract, the vast majority of isolates obtained from dried human faeces belonged to the genus Bacillus and related bacteria. A total of 124 isolates were recovered from the faeces of 10 healthy adult donors. 16S rRNA gene sequence analyses showed the majority belonged to the families Bacillaceae (n=81) and Paenibacillaceae (n=3), with Bacillus species isolated from all donors. Isolates tentatively identified as Bacillus clausii (n=32) and Bacillus licheniformis (n=28) were recovered most frequently, with the genera Lysinibacillus, Ureibacillus, Oceanobacillus, Ornithinibacillus and Virgibacillus represented in some donors. Phenotypic data confirmed the identities of isolates belonging to well-characterized species. Representatives of the phylum Actinobacteria were recovered in much lower numbers (n=11). Many of the bacilli exhibited antimicrobial activity against one or more strains of Clostridium difficile, Clostridium perfringens, Listeria monocytogenes and Staphylococcus aureus, with some (n=12) found to have no detectable cytopathic effect on HEp-2 cells. This study has revealed greater diversity within gut-associated aerobic spore-formers than previous studies, and suggests that bacilli with potential as probiotics could be isolated from the human gut.}, }
@article {pmid22040283, year = {2012}, author = {Ferrer, M and Werner, J and Chernikova, TN and Bargiela, R and Fernández, L and La Cono, V and Waldmann, J and Teeling, H and Golyshina, OV and Glöckner, FO and Yakimov, MM and Golyshin, PN and , }, title = {Unveiling microbial life in the new deep-sea hypersaline Lake Thetis. Part II: a metagenomic study.}, journal = {Environmental microbiology}, volume = {14}, number = {1}, pages = {268-281}, doi = {10.1111/j.1462-2920.2011.02634.x}, pmid = {22040283}, issn = {1462-2920}, mesh = {Archaea/*genetics ; Autotrophic Processes ; Bacteria/*genetics ; Carbon Dioxide/metabolism ; Computational Biology ; Mediterranean Sea ; *Metagenome ; Metagenomics ; Oxidation-Reduction ; Phylogeny ; Ribulose-Bisphosphate Carboxylase/genetics ; Seawater/*chemistry/*microbiology ; Sequence Analysis, DNA ; Sulfur Compounds/metabolism ; Water Microbiology ; }, abstract = {So far only little is known about the microbial ecology of Mediterranean deep-sea hypersaline anoxic lakes (DHALs). These brine lakes were formed by evaporite dissolution/brine seeps and are important model environments to provide insights into possible metabolisms and distributions of microorganisms on the early Earth. Our study on the Lake Thetis, a new thalassohaline DHAL located South-East of the Medriff Corridor, has revealed microbial communities of contrasting compositions with a high number of novel prokaryotic candidate divisions. The major finding of our present work is co-occurrence of at least three autotrophic carbon dioxide fixation pathways in the brine-seawater interface that are likely fuelled by an active ramified sulphur cycle. Genes for the reductive acetyl-CoA and reductive TCA pathways were also found in the brine suggesting that these pathways are operational even at extremely elevated salinities and that autotrophy is more important in hypersaline environments than previously assumed. Surprisingly, genes coding for RuBisCo were found in the highly reduced brine. Three types of sulphide oxidation pathways were found in the interface. The first involves a multienzyme Sox complex catalysing the complete oxidation of reduced sulphur compounds to sulphate, the second type recruits SQR sulphide:quinone reductase for oxidation of sulphide to elemental sulphur, which, in the presence of sulphide, could further be reduced by polysulphide reductases in the third pathway. The presence of the latter two allows a maximal energy yield from the oxidation of sulphide and at the same time prevents the acidification and the accumulation of S(0) deposits. Amino acid composition analysis of deduced proteins revealed a significant overrepresentation of acidic residues in the brine compared with the interface. This trait is typical for halophilic organisms as an adaptation to the brine's extreme hypersalinity. This work presents the first metagenomic survey of the microbial communities of the recently discovered Lake Thetis whose brine constitutes one of saltiest water bodies ever reported.}, }
@article {pmid22038036, year = {2012}, author = {Becklin, KM and Hertweck, KL and Jumpponen, A}, title = {Host identity impacts rhizosphere fungal communities associated with three alpine plant species.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {682-693}, pmid = {22038036}, issn = {1432-184X}, mesh = {Fungi/classification/genetics/*isolation &amp; purification/*physiology ; Host Specificity ; Magnoliopsida/*microbiology ; Molecular Sequence Data ; Mycorrhizae/classification/genetics/*isolation &amp; purification/*physiology ; Phylogeny ; Plant Roots/microbiology ; *Rhizosphere ; Soil Microbiology ; Taraxacum/*microbiology ; }, abstract = {Fungal diversity and composition are still relatively unknown in many ecosystems; however, host identity and environmental conditions are hypothesized to influence fungal community assembly. To test these hypotheses, we characterized the richness, diversity, and composition of rhizosphere fungi colonizing three alpine plant species, Taraxacum ceratophorum, Taraxacum officinale, and Polemonium viscosum. Roots were collected from open meadow and willow understory habitats at treeline on Pennsylvania Mountain, Colorado, USA. Fungal small subunit ribosomal DNA was sequenced using fungal-specific primers, sample-specific DNA tags, and 454 pyrosequencing. We classified operational taxonomic units (OTUs) as arbuscular mycorrhizal (AMF) or non-arbuscular mycorrhizal (non-AMF) fungi and then tested whether habitat or host identity influenced these fungal communities. Approximately 14% of the sequences represented AMF taxa (44 OTUs) with the majority belonging to Glomus groups A and B. Non-AMF sequences represented 186 OTUs belonging to Ascomycota (58%), Basidiomycota (26%), Zygomycota (14%), and Chytridiomycota (2%) phyla. Total AMF and non-AMF richness were similar between habitats but varied among host species. AMF richness and diversity per root sample also varied among host species and were highest in T. ceratophorum compared with T. officinale and P. viscosum. In contrast, non-AMF richness and diversity per root sample were similar among host species except in the willow understory where diversity was reduced in T. officinale. Fungal community composition was influenced by host identity but not habitat. Specifically, T. officinale hosted a different AMF community than T. ceratophorum and P. viscosum while P. viscosum hosted a different non-AMF community than T. ceratophorum and T. officinale. Our results suggest that host identity has a stronger effect on rhizosphere fungi than habitat. Furthermore, although host identity influenced both AMF and non-AMF, this effect was stronger for the mutualistic AMF community.}, }
@article {pmid22038035, year = {2012}, author = {Neave, MJ and Streten-Joyce, C and Glasby, CJ and McGuinness, KA and Parry, DL and Gibb, KS}, title = {The bacterial community associated with the marine polychaete Ophelina sp.1 (Annelida: Opheliidae) is altered by copper and zinc contamination in sediments.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {639-650}, pmid = {22038035}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Copper/*analysis/metabolism ; Geologic Sediments/*analysis ; Phylogeny ; Polychaeta/*microbiology ; Seawater/analysis/*microbiology ; Water Pollutants, Chemical/*analysis/metabolism ; Water Pollution, Chemical ; Zinc/*analysis/metabolism ; }, abstract = {Tolerant species of polychaete worms can survive in polluted environments using various resistance mechanisms. One aspect of resistance not often studied in polychaetes is their association with symbiotic bacteria, some of which have resistance to metals and may help the organism to survive. We used "next generation" 454 sequencing of bacterial 16S rRNA sequences associated with polychaetes from a copper- and zinc-polluted harbor and from a reference site to determine bacterial community structure. We found changes in the bacteria at the polluted site, including increases in the abundance of bacteria from the order Alteromonadales. These changes in the bacteria associated with polychaetes may be relatively easy to detect and could be a useful indicator of metal pollution.}, }
@article {pmid22038034, year = {2012}, author = {Bachar, A and Soares, MI and Gillor, O}, title = {The effect of resource islands on abundance and diversity of bacteria in arid soils.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {694-700}, pmid = {22038034}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Ecosystem ; Israel ; Molecular Sequence Data ; Phylogeny ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Bacteria and nutrients were determined in upper soil samples collected underneath and between canopies of the dominant perennial in each of three sites along a steep precipitation gradient ranging from the Negev desert in the south of Israel to a Mediterranean forest in the north. Bacterial abundance, monitored by phospholipid fatty acid analysis, was significantly higher under the shrub canopy (compared to barren soils) in the arid and semi-arid sites but not in the Mediterranean soils. Bacterial community composition, determined using terminal restriction fragment length polymorphism and clone libraries, differed according to the sample's origin. Closer examination revealed that in the arid and semi-arid sites, α-Proteobacteria are more abundant under the shrub canopy, while barren soils are characterized by a higher abundance of Actinobacteria. The bacterial communities in the Mediterranean soils were similar in both patch types. These results correspond to the hypothesis of "resource islands", suggesting that shrub canopies provide a resource haven in low-resource landscapes. Yet, a survey of the physicochemical parameters of inter- and under-shrub soils could not attribute the changes in bacterial diversity to soil moisture, organic matter, or essential macronutrients. We suggest that in the nutrient-poor soils of the arid and semi-arid sites, bacteria occupying the soil under the shrub canopy may have longer growth periods under favorable conditions, resulting in their increased biomass and altered community composition.}, }
@article {pmid22036930, year = {2011}, author = {Girardi, C and Greve, J and Lamshöft, M and Fetzer, I and Miltner, A and Schäffer, A and Kästner, M}, title = {Biodegradation of ciprofloxacin in water and soil and its effects on the microbial communities.}, journal = {Journal of hazardous materials}, volume = {198}, number = {}, pages = {22-30}, doi = {10.1016/j.jhazmat.2011.10.004}, pmid = {22036930}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents/*metabolism ; *Biodegradation, Environmental ; Ciprofloxacin/*metabolism ; *Soil Microbiology ; Soil Pollutants/*metabolism ; *Water Microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {While antibiotics are frequently found in the environment, their biodegradability and ecotoxicological effects are not well understood. Ciprofloxacin inhibits active and growing microorganisms and therefore can represent an important risk for the environment, especially for soil microbial ecology and microbial ecosystem services. We investigated the biodegradation of (14)C-ciprofloxacin in water and soil following OECD tests (301B, 307) to compare its fate in both systems. Ciprofloxacin is recalcitrant to biodegradation and transformation in the aqueous system. However, some mineralisation was observed in soil. The lower bioavailability of ciprofloxacin seems to reduce the compound's toxicity against microorganisms and allows its biodegradation. Moreover, ciprofloxacin strongly inhibits the microbial activities in both systems. Higher inhibition was observed in water than in soil and although its antimicrobial potency is reduced by sorption and aging in soil, ciprofloxacin remains biologically active over time. Therefore sorption does not completely eliminate the effects of this compound.}, }
@article {pmid21726221, year = {2011}, author = {Peterson, SN and Snesrud, E and Schork, NJ and Bretz, WA}, title = {Dental caries pathogenicity: a genomic and metagenomic perspective.}, journal = {International dental journal}, volume = {61 Suppl 1}, number = {Suppl 1}, pages = {11-22}, pmid = {21726221}, issn = {0020-6539}, support = {R01 DE015351/DE/NIDCR NIH HHS/United States ; }, mesh = {Animals ; *Biofilms ; Dental Caries/*genetics/*microbiology ; Dental Plaque/genetics/microbiology ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; *Genomics ; Glycolysis ; Humans ; Metagenome ; Microbial Interactions ; Streptococcus mutans/genetics/metabolism ; }, abstract = {In this review we address the subject of dental caries pathogenicity from a genomic and metagenomic perspective. The application of genomic technologies is certain to yield novel insights into the relationship between the bacterial flora, dental health and disease. Three primary attributes of bacterial species are thought to have direct impact on caries development, these include: adherence on tooth surfaces (biofilm formation), acid production and acid tolerance. Attempts to define the specific aetiological agents of dental caries have proven to be elusive, supporting the notion that caries aetiology is perhaps complex and multi-faceted. The recently introduced Human Microbiome Project (HMP) that endeavors to characterise the micro-organisms living in and on the human body is likely to shed new light on these questions and improve our understanding of polymicrobial disease, microbial ecology in the oral cavity and provide new avenues for therapeutic and molecular diagnostics developments.}, }
@article {pmid22031452, year = {2012}, author = {Lukjancenko, O and Ussery, DW and Wassenaar, TM}, title = {Comparative genomics of Bifidobacterium, Lactobacillus and related probiotic genera.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {651-673}, pmid = {22031452}, issn = {1432-184X}, mesh = {Bifidobacterium/classification/*genetics/isolation &amp; purification ; *Genome, Bacterial ; *Genomics ; Humans ; Lactobacillus/classification/*genetics/isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; Probiotics/chemistry/*classification/isolation &amp; purification ; }, abstract = {Six bacterial genera containing species commonly used as probiotics for human consumption or starter cultures for food fermentation were compared and contrasted, based on publicly available complete genome sequences. The analysis included 19 Bifidobacterium genomes, 21 Lactobacillus genomes, 4 Lactococcus and 3 Leuconostoc genomes, as well as a selection of Enterococcus (11) and Streptococcus (23) genomes. The latter two genera included genomes from probiotic or commensal as well as pathogenic organisms to investigate if their non-pathogenic members shared more genes with the other probiotic genomes than their pathogenic members. The pan- and core genome of each genus was defined. Pairwise BLASTP genome comparison was performed within and between genera. It turned out that pathogenic Streptococcus and Enterococcus shared more gene families than did the non-pathogenic genomes. In silico multilocus sequence typing was carried out for all genomes per genus, and the variable gene content of genomes was compared within the genera. Informative BLAST Atlases were constructed to visualize genomic variation within genera. The clusters of orthologous groups (COG) classes of all genes in the pan- and core genome of each genus were compared. In addition, it was investigated whether pathogenic genomes contain different COG classes compared to the probiotic or fermentative organisms, again comparing their pan- and core genomes. The obtained results were compared with published data from the literature. This study illustrates how over 80 genomes can be broadly compared using simple bioinformatic tools, leading to both confirmation of known information as well as novel observations.}, }
@article {pmid22029695, year = {2012}, author = {Golby, S and Ceri, H and Gieg, LM and Chatterjee, I and Marques, LL and Turner, RJ}, title = {Evaluation of microbial biofilm communities from an Alberta oil sands tailings pond.}, journal = {FEMS microbiology ecology}, volume = {79}, number = {1}, pages = {240-250}, doi = {10.1111/j.1574-6941.2011.01212.x}, pmid = {22029695}, issn = {1574-6941}, mesh = {Alberta ; Bacteria/classification/genetics/growth &amp; development ; Biodegradation, Environmental ; Biofilms/*growth &amp; development ; Hydrocarbons ; Industrial Waste ; *Petroleum Pollution ; Ponds ; Silicon Dioxide ; *Water Microbiology ; }, abstract = {Bitumen extraction from the oil sands of Alberta has resulted in millions of cubic meters of waste stored on-site in tailings ponds. Unique microbial ecology is expected in these ponds, which may be key to their bioremediation potential. We considered that direct culturing of microbes from a tailings sample as biofilms could lead to the recovery of microbial communities that provide good representation of the ecology of the tailings. Culturing of mixed species biofilms in vitro using the Calgary Biofilm Device (CBD) under aerobic, microaerobic, and anaerobic growth conditions was successful both with and without the addition of various growth nutrients. Denaturant gradient gel electrophoresis and 16S rRNA gene pyrotag sequencing revealed that unique mixed biofilm communities were recovered under each incubation condition, with the dominant species belonging to Pseudomonas, Thauera, Hydrogenophaga, Rhodoferax, and Acidovorax. This work used an approach that allowed organisms to grow as a biofilm directly from a sample collected of their environment, and the biofilms cultivated in vitro were representative of the endogenous environmental community. For the first time, representative environmental mixed species biofilms have been isolated and grown under laboratory conditions from an oil sands tailings pond environment and a description of their composition is provided.}, }
@article {pmid22015684, year = {2012}, author = {Kobune, S and Kajimura, H and Masuya, H and Kubono, T}, title = {Symbiotic fungal flora in leaf galls induced by Illiciomyia yukawai (Diptera: Cecidomyiidae) and in its mycangia.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {619-627}, pmid = {22015684}, issn = {1432-184X}, mesh = {Animals ; Diptera/growth &amp; development/*microbiology/*physiology ; Female ; Fungi/*physiology ; Male ; Plant Leaves/microbiology/*parasitology ; Plant Tumors/microbiology/*parasitology ; *Symbiosis ; }, abstract = {We investigated the association between a gall midge, Illiciomyia yukawai, and its symbiotic fungi on Japanese star anise, Illicium anisatum. The number of fungal species isolated from the galls increased with development of the galls, whereas those from the leaves showed a different trend. Botryosphaeria dothidea was dominant in the galls from June to October, and after that Phomopsis sp. 1, Colletotrichum sp., and Pestalotiopsis sp. became dominant. Although B. dothidea was not isolated from the leaves, it was detected from mycangia (abdominal sternite VII) of egg-laying adults at a high isolation frequency (>90%). However, B. dothidea was not isolated from mycangia of adults emerging from galls that were enclosed by plastic bags. This indicates that I. yukawai is closely associated with B. dothidea and that its newly emerged adults do not take the fungus into mycangia directly from the galls where they had developed. Also, the fungus from the fungal layers of ambrosia galls has less ability to propagate on artificial media despite the presence of its mycelial mass in mature galls.}, }
@article {pmid22015683, year = {2012}, author = {Renault, D and Vallance, J and Déniel, F and Wery, N and Godon, JJ and Barbier, G and Rey, P}, title = {Diversity of bacterial communities that colonize the filter units used for controlling plant pathogens in soilless cultures.}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {170-187}, pmid = {22015683}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/*growth &amp; development ; Base Sequence ; *Biofilms ; DNA, Bacterial/genetics ; Filtration/instrumentation ; Genetic Variation ; *Hydroponics ; *Microbial Consortia/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In recent years, increasing the level of suppressiveness by the addition of antagonistic bacteria in slow filters has become a promising strategy to control plant pathogens in the recycled solutions used in soilless cultures. However, knowledge about the microflora that colonize the filtering columns is still limited. In order to get information on this issue, the present study was carried out over a 4-year period and includes filters inoculated or not with suppressive bacteria at the start of the filtering process (two or three filters were used each year). After 9 months of filtration, polymerase chain reaction (PCR)-single strand conformation polymorphism analyses point out that, for the same year of experiment, the bacterial communities from control filters were relatively similar but that they were significantly different between the bacteria-amended and control filters. To characterize the changes in bacterial communities within the filters, this microflora was studied by quantitative PCR, community-level physiological profiles, and sequencing 16SrRNA clone libraries (filters used in year 1). Quantitative PCR evidenced a denser bacterial colonization of the P-filter (amended with Pseudomonas putida strains) than control and B-filter (amended with Bacillus cereus strains). Functional analysis focused on the cultivable bacterial communities pointed out that bacteria from the control filter metabolized more carbohydrates than those from the amended filters whose trophic behaviors were more targeted towards carboxylic acids and amino acids. The bacterial communities in P- and B-filters both exhibited significantly more phylotype diversity and markedly distinct phylogenetic compositions than those in the C-filter. Although there were far fewer Proteobacteria in B- and P-filters than in the C-filter (22% and 22% rather than 69% of sequences, respectively), the percentages of Firmicutes was much higher (44% and 55% against 9%, respectively). Many Pseudomonas species were also found in the bacterial communities of the control filter. The persistence of the amended suppressive-bacteria in the filters is discussed with regards to the management of suppressive microflora in soilless culture.}, }
@article {pmid22014373, year = {2012}, author = {Zhao, Z and Qin, Y and Lai, Z and Peng, L and Cai, X and Wang, L and Guo, X and Yang, H}, title = {Microbial ecology of swine farms and PRRS vaccine vaccination strategies.}, journal = {Veterinary microbiology}, volume = {155}, number = {2-4}, pages = {247-256}, doi = {10.1016/j.vetmic.2011.09.028}, pmid = {22014373}, issn = {1873-2542}, mesh = {Animals ; Circovirus/isolation &amp; purification ; Herpesvirus 1, Suid/isolation &amp; purification ; Male ; Porcine Reproductive and Respiratory Syndrome/diagnosis/*prevention &amp; control/*virology ; Porcine respiratory and reproductive syndrome virus/*immunology/isolation &amp; purification ; Swine ; Vaccination/veterinary ; Vaccines, Attenuated/immunology ; *Viral Vaccines/immunology ; }, abstract = {The present study investigated the microbial ecology and vaccination strategies against porcine reproductive and respiratory syndrome (PRRS) in field condition. Four representative farms with a history of PRRS were included in this study. Over the almost 3-year period, the average detection rate was 68.9%, making PRRSV the first most frequently detected virus, followed by porcine circovirus type 2 (PCV2) (64.2%), pseudorabies virus (PRV) (11.03%) and classical swine fever virus (CSFV) (4.41%). Streptococcus suis (77.92%), Haemophilus parasuis (51.25%) and Escherichia coli (52.39%), Pasteurella multocida (26.77%) were isolated most frequently in association with PRRSV. Under the present microbial ecology, production performances of sows their offspring after mass vaccination with a PRRS attenuated vaccine were evaluated. In addition, large scale PRRS vaccines usage and efficacy were further performed. The results indicated that mass vaccination following our immunization program can improve health status and production performances of both sows (2ml/i.m. booster after 4 weeks, and then immunized quarterly) and their offsprings (1ml/i.m. on 14-18 days of age).}, }
@article {pmid22006549, year = {2012}, author = {Auclair, J and Parent, S and Villemur, R}, title = {Functional diversity in the denitrifying biofilm of the methanol-fed marine denitrification system at the Montreal Biodome.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {726-735}, pmid = {22006549}, issn = {1432-184X}, mesh = {Bacterial Proteins/genetics/*metabolism ; *Biofilms ; *Denitrification ; Hyphomicrobiaceae/genetics/*metabolism ; Methanol/*metabolism ; Nitrates/metabolism ; Nitrites/metabolism ; Piscirickettsiaceae/genetics/isolation &amp; purification/*metabolism ; Polymerase Chain Reaction/methods ; Quebec ; Seawater/*microbiology ; }, abstract = {Nitrate is a serious problem in closed-circuit public aquariums because its accumulation rapidly becomes toxic to many lifeforms. A moving bed biofilm denitrification reactor was installed at the Montreal Biodome to treat its 3,250-m(3) seawater system. Naturally occurring microorganisms from the seawater affluent colonized the reactor carriers to form a denitrifying biofilm. Here, we investigated the functional diversity of this biofilm by retrieving gene sequences related to narG, napA, nirK, nirS, cnorB, and nosZ. A total of 25 sequences related to these genes were retrieved from the biofilm. Among them, the corresponding napA1, nirK1, cnorB9, and nosZ3 sequences were identical to the corresponding genes found in Hyphomicrobium sp. NL23 while the narG1 and narG2 sequences were identical to the two corresponding narG genes found in Methylophaga sp. JAM1. These two bacterial strains were previously isolated from the denitrifying biofilm. To assess the abundance of denitrifiers and nitrate respirers in the biofilm, the gene copy number of all the narG, napA, nirS, and nirK sequences found in biofilm was determined by quantitative PCR. napA1, nirK1, narG1, and narG2, which were all associated with either Methylophaga sp. JAM1 or Hyphomicrobium sp. NL23, were the most abundant genes. The other genes were 10 to 10,000 times less abundant. nirK, cnorB, and nosZ but not napA transcripts from Hyphomicrobium sp. NL23 were detected in the biofilm, and only the narG1 transcripts from Methylophaga sp. JAM1 were detected in the biofilm. Among the 19 other genes, the transcripts of only two genes were detected in the biofilm. Our results show the predominance of Methylophaga sp. JAM1 and Hyphomicrobium sp. NL23 among the denitrifiers detected in the biofilm. The results suggest that Hyphomicrobium sp. NL23 could use the nitrite present in the biofilm generated by nitrate respirers such as Methylophaga sp. JAM1.}, }
@article {pmid22005739, year = {2012}, author = {Zamalloa, C and De Vrieze, J and Boon, N and Verstraete, W}, title = {Anaerobic digestibility of marine microalgae Phaeodactylum tricornutum in a lab-scale anaerobic membrane bioreactor.}, journal = {Applied microbiology and biotechnology}, volume = {93}, number = {2}, pages = {859-869}, doi = {10.1007/s00253-011-3624-5}, pmid = {22005739}, issn = {1432-0614}, mesh = {Anaerobiosis ; Archaea/classification/*growth &amp; development/metabolism ; Bacteria/classification/*growth &amp; development/metabolism ; Biofuels ; Biomass ; Bioreactors/*microbiology ; Biota ; Cluster Analysis ; Culture Media/chemistry ; DNA Fingerprinting ; Denaturing Gradient Gel Electrophoresis ; Diatoms/*metabolism ; Membranes/microbiology ; Methane/*metabolism ; }, abstract = {The biomass of industrially grown Phaeodactylum tricornutum was subjected in a novel way to bio-methanation at 33°C, i.e., in an anaerobic membrane bioreactor (AnMBR) at a hydraulic retention time of 2.5 days, at solid retention times of 20 to 10 days and at loading rates in the range of 2.6-5.9 g biomass-COD L(-1) day(-1) with membrane fluxes ranging from 1 to 0.8 L m(-2) h(-1). The total COD recovered as biogas was in the order of 52%. The input suspension was converted to a clear effluent rich in total ammonium nitrogen (546 mg TAN L(-1)) and phosphate (141 mg PO(4)-P L(-1)) usable as liquid fertilizer. The microbial community richness, dynamics, and organization in the reactor were interpreted using the microbial resource management approach. The AnMBR communities were found to be moderate in species richness and low in dynamics and community organization relative to UASB and conventional CSTR sludges. Quantitative polymerase chain reaction analysis revealed that Methanosaeta sp. was the dominant acetoclastic methanogen species followed by Methanosarcina sp. This work demonstrated that the use of AnMBR for the digestion of algal biomass is possible. The fact that some 50% of the organic matter is not liquefied means that the algal particulates in the digestate constitute a considerable fraction which should be valorized properly, for instance as slow release organic fertilizer. Overall, 1 kg of algae dry matter (DM) could be valorized in the form of biogas (euro 2.07), N and P in the effluent (euro 0.02) and N and P in the digestate (euro 0.04), thus totaling about euro 2.13 per kilogram algae DM.}, }
@article {pmid22004828, year = {2011}, author = {Boulares, M and Mejri, L and Hassouna, M}, title = {Study of the microbial ecology of wild and aquacultured Tunisian fresh fish.}, journal = {Journal of food protection}, volume = {74}, number = {10}, pages = {1762-1768}, doi = {10.4315/0362-028X.JFP-11-057}, pmid = {22004828}, issn = {1944-9097}, mesh = {Animals ; Animals, Wild/microbiology ; Aquaculture/*standards ; Bacteria/*isolation &amp; purification ; Colony Count, Microbial ; Consumer Product Safety ; Fishes/*microbiology ; Food Contamination/*analysis ; Food Microbiology ; Food Preservation ; Seafood/*microbiology ; Tunisia ; }, abstract = {Eighty samples of fresh fish were collected in Tunisia and analyzed for microbial load. Quality and hygienic safety of the meat and intestines of wild and aquacultured fresh fish were determined. The mesophilic aerobic plate count and populations of psychrotrophic lactic acid bacteria (LAB) and other psychrotrophic bacteria ranged from 5.67 to 7.29, 4.51 to 6, and 5.07 to 6.21 log CFU/g, respectively. For all microbiological determinations, bacterial counts were lower in meat than in the intestines of fresh fish. For all samples lower microbial populations were found in most of the wild fish than in the aquacultured fish. No isolates of the pathogenic genera Salmonella and Listeria were detected in any sample. Among the 160 strains of biopreservative psychrotrophic LAB and the 150 strains of spoilage psychrotrophic gram-negative bacteria identified by biochemical and molecular methods, Lactobacillus (six species) and Pseudomonas (six species) predominated. Lactococcus, Leuconostoc, Carnobacterium (C. piscicola and C. divergens), Aeromonas, and Photobacterium were the most common genera, and Lactococcus lactis, Lactobacillus plantarum, Pseudomonas fluorescens, and Aeromonas hydrophila were the most common species. These findings indicate that the microbiological quality of fresh fish in Tunisia can be preserved by controlling pathogenic and psychrotrophic bacteria.}, }
@article {pmid22001998, year = {2012}, author = {Pierre, G and Graber, M and Rafiliposon, BA and Dupuy, C and Orvain, F and De Crignis, M and Maugard, T}, title = {Biochemical composition and changes of extracellular polysaccharides (ECPS) produced during microphytobenthic biofilm development (Marennes-Oléron, France).}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {157-169}, pmid = {22001998}, issn = {1432-184X}, mesh = {Atlantic Ocean ; Bacteria/*growth &amp; development/metabolism ; Bays/*microbiology ; Biofilms/*growth &amp; development ; Biomass ; France ; Geologic Sediments/*microbiology ; Polysaccharides/*chemistry/isolation &amp; purification ; Polysaccharides, Bacterial/chemistry ; }, abstract = {The main goal of this work was to study the dynamics and biochemical composition of extracellular polysaccharides (ECPS), a fraction of the extracellular polymeric substances (EPS) produced during the development of a microphytobenthic biofilm in a European intertidal mudflat (Marennes-Oléron Bay, France) during winter. Microphytobenthic biomass was surveyed during four consecutive emersion periods to confirm the biofilm growth. Bacteria abundance was also checked considering the importance of heterotrophic bacteria observed by various authors in the dynamics of EPS. Various colorimetric assays, coupled to biochemical chromatographic analysis, were used to characterize the three main fractions of extracted EPS: colloidal, bound, and residual. The monosaccharide distribution of colloidal ECPS highlighted their role of carbon source for bacteria (>50% of glucose) even if no increase of colloidal carbohydrate amounts was observed during the tidal exposure. Bound ECPS were composed of deoxy or specific sugars (30% rhamnose) and uronic acids (18% galacturonic acid). Their levels and dynamics could be correlated to the development of the microphytobenthic biofilm, enhancing the stabilization of the sediment or increasing binding forces accordingly. Residual fractions, containing refractory bound ECPS and other internal polymeric substances, were composed of various carbohydrates. The high ratio of glucose in these fractions (18% to 43%) was interesting, as it was once attributed to colloidal sugars due to poor extraction procedures. Finally, the presence of inositol (15%) was significant since no author has highlighted it before, knowing that inositol is a major growth factor for heterotrophic bacteria.}, }
@article {pmid22001997, year = {2012}, author = {Labreuche, Y and Pallandre, L and Ansquer, D and Herlin, J and Wapotro, B and Le Roux, F}, title = {Pathotyping of Vibrio isolates by multiplex PCR reveals a risk of virulent strain spreading in New Caledonian shrimp farms.}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {127-138}, pmid = {22001997}, issn = {1432-184X}, mesh = {Adhesins, Bacterial/genetics ; Animals ; *Aquaculture ; DNA Gyrase/genetics ; DNA, Bacterial/genetics ; *Multiplex Polymerase Chain Reaction ; New Caledonia ; Penaeidae/*microbiology ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Shellfish/*microbiology ; Vibrio/classification/genetics/*isolation &amp; purification/*pathogenicity ; }, abstract = {Two recurring syndromes threaten the viability of the shrimp industry in New Caledonia, which represents the second largest export business. The "Syndrome 93" is a cold season disease due to Vibrio penaeicida affecting all shrimp farms, while the "Summer Syndrome" is a geographically restricted vibriosis caused by a virulent lineage of Vibrio nigripulchritudo. Microbiological procedures for diagnosis of these diseases are time-consuming and do not have the ability to discriminate the range of virulence potentials of V. nigripulchritudo. In this study, we developed a multiplex PCR method to simultaneously detect these two bacterial species and allow for pathotype discrimination. The detection limits of this assay, that includes an internal amplification control to eliminate any false-negative results, were determined at 10 pg purified DNA and 200 cfu/ml. After confirming the effectiveness of our method using experimentally infected animals, its accuracy was compared to standard biochemical methods during a field survey using 94 samples collected over 3 years from shrimp farms encountering mortality events. The multiplex PCR showed very high specificity for the detection of V. penaeicida and V. nigripulchritudo (inclusivity and exclusivity 100%) and allowed us to detect the spreading of highly pathogenic isolates of V. nigripulchritudo to a farm adjoining the "Summer Syndrome area." This assay represents a simple, rapid, and cost-effective diagnostic tool for implementing timely risk management decisions but also understanding the seasonal and geographical distribution of these pathogens.}, }
@article {pmid21997543, year = {2012}, author = {Pakpour, S and Jabaji, S and Chénier, MR}, title = {Frequency of antibiotic resistance in a swine facility 2.5 years after a ban on antibiotics.}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {41-50}, pmid = {21997543}, issn = {1432-184X}, mesh = {Animal Feed ; Animal Husbandry/*standards ; Animals ; Anti-Bacterial Agents/*administration &amp; dosage/pharmacology ; Bacteria/*drug effects/genetics ; Canada ; Chlortetracycline/*pharmacology ; Drug Resistance, Multiple, Bacterial/*genetics ; Feces/microbiology ; Female ; Male ; Microbial Sensitivity Tests ; RNA, Ribosomal, 16S/genetics ; Swine/*microbiology ; Tetracycline Resistance/genetics ; Time Factors ; Tylosin/*pharmacology ; }, abstract = {The addition of antibiotics to livestock feed has contributed to the selection of antibiotic-resistant bacteria in concentrated animal feeding operations and agricultural ecosystems. The objective of this study was to assess the occurrence of resistance to chlortetracycline and tylosin among bacterial populations at the Swine Complex of McGill University (Province of Quebec, Canada) in the absence of antibiotic administration to pigs for 2.5 years prior to the beginning of this study. Feces from ten pigs born from the same sow and provided feed without antibiotic were sampled during suckling (n = 6 for enumerations, n = 10 for PCR), weanling (n = 10 both for PCR and enumerations), growing (n = 10 both for PCR and enumerations), and finishing (n = 10 both for PCR and enumerations). The percentage of chlortetracycline-resistant anaerobic bacterial populations (Tet(R)) was higher than that of tylosin-resistant anaerobic bacterial populations (Tyl(R)) at weanling, growing, and finishing. Prior to the transportation of animals to the slaughterhouse, resistant populations varied between 6.5 and 9.4 Log colony-forming units g humid feces(-1). In all pigs, tet(L), tet(O), and erm(B) were detected at suckling and weanling, whereas only tet(O) was detected at growing and finishing. The abundance of tet(O) was similar between males and females at weanling and growing and reached 5.1 × 10(5) and 5.6 × 10(5) copies of tet(O)/ng of total DNA in males and females, respectively, at finishing. Results showed high abundances and proportions of Tet(R) and Tyl(R) anaerobic bacterial populations, as well as the occurrence of tet and erm resistance genes within these populations despite the absence of antibiotic administration to pigs at this swine production facility since January 2007, i.e., 2.5 years prior to the beginning of this study. This work showed that the occurrence of bacterial resistance to chlortetracycline and tylosin is high at the Swine Complex of McGill University.}, }
@article {pmid21994035, year = {2012}, author = {Downing, S and van de Venter, M and Downing, TG}, title = {The effect of exogenous β-N-methylamino-L: -alanine on the growth of Synechocystis PCC6803.}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {149-156}, pmid = {21994035}, issn = {1432-184X}, mesh = {Amino Acids, Diamino/metabolism/*pharmacology ; Cyanobacteria/chemistry ; Cyanobacteria Toxins ; Synechocystis/*drug effects/growth &amp; development/metabolism ; }, abstract = {β-N-Methylamino-L: -alanine (BMAA), a non-proteinogenic amino acid, has been detected in a range of cyanobacteria, including terrestrial, aquatic, free living and endosymbiotic species. The widespread occurrence of cyanobacteria in the environment raises concerns regarding the ecological and toxicological impact of BMAA, and consequently, studies have focussed extensively on the toxicity and environmental impact of BMAA, while no research has addressed the ecophysiological or metabolic role of the compound in cyanobacteria. In this study, both the uptake of exogenous BMAA by and the effect of exogenous BMAA on the growth of Synechocystis PCC6803 were investigated. BMAA was rapidly taken up by the non-diazotrophic cyanobacterium Synechocystis PCC6803 in a concentration dependent manner. The presence of exogenous BMAA resulted in a substantial and concentration-dependent decrease in cell growth and the substantial loss of photosynthetic pigmentation. Similar effects were seen in the presence of the non-proteinogenic amino acid, 2,4-diaminobutyric acid but to a lesser degree than that of BMAA. The effects were reversed when light was decreased from 16 to 10 μmol m(-2) s(-1). Control cultures grown in the presence of L: -arginine, L: -asparagine, L: -glutamate and glycine showed normal or slightly increased growth with no change in pigmentation. The decrease in growth rate coupled to bleaching indicates that BMAA may induce chlorosis in the presence of adequate photosynthetic radiation suggesting a connection between BMAA and the induction of conditions, such as nitrogen or sulphur depletion, that result in growth arrest and the induction of chlorosis.}, }
@article {pmid21994034, year = {2012}, author = {Oliveira, I and Pereira, JA and Lino-Neto, T and Bento, A and Baptista, P}, title = {Fungal diversity associated to the olive moth, Prays Oleae bernard: a survey for potential entomopathogenic fungi.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {964-974}, pmid = {21994034}, issn = {1432-184X}, mesh = {Agriculture ; Animals ; Beauveria/genetics/isolation &amp; purification ; Fungi/classification/*genetics/isolation &amp; purification ; Larva/microbiology ; Moths/*microbiology ; Olea/growth &amp; development/*parasitology ; *Pest Control, Biological ; Portugal ; Pupa/microbiology ; }, abstract = {Olive production is one of the main agricultural activities in Portugal. In the region of Trás-os-Montes, this crop has been considerably affected by Prays oleae. In order to evaluate the diversity of fungi on Prays oleae population of Trás-os-Montes olive orchards, larvae and pupae of the three annual generations (phyllophagous, antophagous and carpophagous) were collected and evaluated for fungal growth on their surface. From the 3,828 larvae and pupae, a high percentage of individuals exhibited growth of a fungal agent (40.6%), particularly those from the phyllophagous generation. From all the moth generations, a total of 43 species from 24 genera were identified, but the diversity and abundance of fungal species differed between the three generations. Higher diversity was found in the carpophagous generation, followed by the antophagous and phyllophagous generations. The presence of fungi displaying entomopathogenic features was highest in the phyllophagous larvae and pupae, with Beauveria bassiana as the most abundant taxa. The first report of Beauveria bassiana presence on Prays oleae could open new strategies for the biocontrol of this major pest in olive groves since the use of an already adapted species increases the guarantee of success of a biocontrol approach. The identification of antagonistic fungi able to control agents that cause major olive diseases, such as Verticillium dahliae, will benefit future biological control approaches for limiting this increasingly spreading pathogen.}, }
@article {pmid21994033, year = {2012}, author = {Hill, PG and Heywood, JL and Holland, RJ and Purdie, DA and Fuchs, BM and Zubkov, MV}, title = {Internal and external influences on near-surface microbial community structure in the vicinity of the Cape Verde Islands.}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {139-148}, pmid = {21994033}, issn = {1432-184X}, mesh = {Alphaproteobacteria/genetics/isolation &amp; purification ; Aquatic Organisms/classification ; Atlantic Ocean ; Bacteria/genetics/*isolation &amp; purification ; Bacteroidetes/genetics/isolation &amp; purification ; Cabo Verde ; Cyanobacteria/genetics/isolation &amp; purification ; Gammaproteobacteria/genetics/isolation &amp; purification ; *Microbial Consortia ; Plankton/microbiology ; Seawater/*microbiology ; }, abstract = {Microbial community structure in the subtropical north-east Atlantic Ocean was compared between 2 years and variation attributed to environmental variables. Surface seawater communities were analysed by flow cytometry and fluorescence in situ hybridisation. Probes specific to Alphaproteobacteria, Cyanobacteria, Gammaproteobacteria and Bacteroidetes identified 67-100% of cells. Due to natural variation in the study region due to the occurrence of major currents and islands, data could not be pooled but were instead divided between distinct water masses. Community structure did not differ greatly around the Cape Verde Islands between sampling periods but varied substantially in the open ocean, suggesting different environmental perturbations favour specific bacterial groups. Wind speed varied significantly between years, with moderate to strong breeze in winter 2008 and gales in winter 2006 (8.9 ± 0.2 ms(-1) and 16.0 ± 0.4 ms(-1), respectively). Enhanced wind-driven turbulence was associated with domination by the SAR11 clade of Alphaproteobacteria, which were present at 2.4-fold in the abundance of Prochlorococcus (41.8 ± 1.6% cells, compared to 17.7 ± 7.1%). Conversely, the calmer conditions of 2008 seemed to favour Prochlorococcus (40.0 ± 1.2% cells). Prochlorococcus high-light adapted clade HLI were only numerous during wind-driven turbulence, whereas oligotrophic-adapted clade HLII dominated under calm conditions. Bacteroidetes were most prominent in turbulent conditions (9.5 ± 1.3% cells as opposed to 4.7 ± 0.3%), as were Synechococcus. In 2008, a considerable dust deposition event occurred in the region, which may have led to the substantial Gammaproteobacteria population (22.5 ± 4.0% cells compared to 4.6 ± 0.6% in 2006). Wind-driven turbulence may have a significant impact on microbial community structure in the surface ocean. Therefore, community change following dust storm events may be linked to associated wind in addition to dust-derived nutrients.}, }
@article {pmid21990016, year = {2012}, author = {Crotty, FV and Adl, SM and Blackshaw, RP and Murray, PJ}, title = {Protozoan pulses unveil their pivotal position within the soil food web.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {905-918}, pmid = {21990016}, issn = {1432-184X}, support = {BBS/E/C/00005740/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/C/00005741/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Arthropods/physiology ; Ciliophora/*physiology ; Ecosystem ; Eukaryota/*physiology ; *Food Chain ; Insecta/*physiology ; Nematoda/*physiology ; Oligochaeta/physiology ; Soil/*parasitology ; }, abstract = {Protozoa are one of the most abundant groups of bacterivores within the soil and are responsible for mineralisation of bacterial biomass, having a large impact on C and N cycling. Little is known of their contribution to soil nutrient transfers or the identity of their consumers. Here, for the first time indigenous flagellates and ciliates, enriched to 83 atom% for (13)C and 10 atom% for (15)N, were introduced to soil cores from two different land managements, grassland and woodland with the same soil type, to trace the flow of protozoan C and N through the soil food web. Nematodes, Collembola, earthworms and insect larvae obtained the greatest amounts of C and N of protozoan origin, either through direct consumption or uptake of biomass post-cell death. Our results show that changes in management, affect the functioning of the soil food web and the utilisation of protozoa as a food source.}, }
@article {pmid21990015, year = {2012}, author = {Kim, M and Singh, D and Lai-Hoe, A and Go, R and Abdul Rahim, R and Ainuddin, AN and Chun, J and Adams, JM}, title = {Distinctive phyllosphere bacterial communities in tropical trees.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {674-681}, pmid = {21990015}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Molecular Sequence Data ; Plant Leaves/*microbiology ; Trees/*microbiology ; Tropical Climate ; }, abstract = {Recent work has suggested that in temperate and subtropical trees, leaf surface bacterial communities are distinctive to each individual tree species and dominated by Alpha- and Gammaproteobacteria. In order to understand how general this pattern is, we studied the phyllosphere bacterial community on leaves of six species of tropical trees at a rainforest arboretum in Malaysia. This represents the first detailed study of 'true' tropical lowland tree phyllosphere communities. Leaf surface DNA was extracted and pyrosequenced targeting the V1-V3 region of 16S rRNA gene. As was previously found in temperate and subtropical trees, each tree species had a distinctive bacterial community on its leaves, clustering separately from other tree species in an ordination analysis. Bacterial communities in the phyllosphere were unique to plant leaves in that very few operational taxonomic units (0.5%) co-occurred in the surrounding soil environment. A novel and distinctive aspect of tropical phyllosphere communities is that Acidobacteria were one of the most abundant phyla across all samples (on average, 17%), a pattern not previously recognized. Sequences belonging to Acidobacteria were classified into subgroups 1-6 among known 24 subdivisions, and subgroup 1 (84%) was the most abundant group, followed by subgroup 3 (15%). The high abundance of Acidobacteria on leaves of tropical trees indicates that there is a strong relationship between host plants and Acidobacteria in tropical rain forest, which needs to be investigated further. The similarity of phyllosphere bacterial communities amongst the tree species sampled shows a significant tendency to follow host plant phylogeny, with more similar communities on more closely related hosts.}, }
@article {pmid21989255, year = {2012}, author = {Van den Abbeele, P and Roos, S and Eeckhaut, V and MacKenzie, DA and Derde, M and Verstraete, W and Marzorati, M and Possemiers, S and Vanhoecke, B and Van Immerseel, F and Van de Wiele, T}, title = {Incorporating a mucosal environment in a dynamic gut model results in a more representative colonization by lactobacilli.}, journal = {Microbial biotechnology}, volume = {5}, number = {1}, pages = {106-115}, pmid = {21989255}, issn = {1751-7915}, support = {BBS/E/F/00044452/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; Intestinal Mucosa/*microbiology ; Lactobacillus/classification/genetics/*growth &amp; development/isolation &amp; purification ; Models, Biological ; Phylogeny ; }, abstract = {To avoid detrimental interactions with intestinal microbes, the human epithelium is covered with a protective mucus layer that traps host defence molecules. Microbial properties such as adhesion to mucus further result in a unique mucosal microbiota with a great potential to interact with the host. As mucosal microbes are difficult to study in vivo, we incorporated mucin-covered microcosms in a dynamic in vitro gut model, the simulator of the human intestinal microbial ecosystem (SHIME). We assessed the importance of the mucosal environment in this M-SHIME (mucosal-SHIME) for the colonization of lactobacilli, a group for which the mucus binding domain was recently discovered. Whereas the two dominant resident Lactobacilli, Lactobacillus mucosae and Pediococcus acidilactici, were both present in the lumen, L. mucosae was strongly enriched in mucus. As a possible explanation, the gene encoding a mucus binding (mub) protein was detected by PCR in L. mucosae. Also the strongly adherent Lactobacillus rhamnosus GG (LGG) specifically colonized mucus upon inoculation. Short-term assays confirmed the strong mucin-binding of both L. mucosae and LGG compared with P.acidilactici. The mucosal environment also increased long-term colonization of L. mucosae and enhanced its stability upon antibiotic treatment (tetracycline, amoxicillin and ciprofloxacin). Incorporating a mucosal environment thus allowed colonization of specific microbes such as L. mucosae and LGG, in correspondence with the in vivo situation. This may lead to more in vivo-like microbial communities in such dynamic, long-term in vitro simulations and allow the study of the unique mucosal microbiota in health and disease.}, }
@article {pmid21988358, year = {2011}, author = {Lievens, B and Frans, I and Heusdens, C and Justé, A and Jonstrup, SP and Lieffrig, F and Willems, KA}, title = {Rapid detection and identification of viral and bacterial fish pathogens using a DNA array-based multiplex assay.}, journal = {Journal of fish diseases}, volume = {34}, number = {11}, pages = {861-875}, doi = {10.1111/j.1365-2761.2011.01304.x}, pmid = {21988358}, issn = {1365-2761}, mesh = {Animals ; Bacterial Infections/diagnosis/*veterinary ; Carps ; DNA Helicases/genetics ; DNA-Directed DNA Polymerase/genetics ; Fish Diseases/*diagnosis ; Fisheries/*methods ; Flavobacteriaceae Infections/diagnosis/*veterinary ; Flavobacterium/genetics ; Herpesviridae/genetics ; Herpesviridae Infections/diagnosis/*veterinary ; Multiplex Polymerase Chain Reaction/*veterinary ; Oligonucleotide Array Sequence Analysis/*veterinary ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sensitivity and Specificity ; }, abstract = {Fish diseases can be caused by a variety of diverse organisms, including bacteria, fungi, viruses and protozoa, and pose a universal threat to the ornamental fish industry and aquaculture. The lack of rapid, accurate and reliable means by which fish pathogens can be detected and identified has been one of the main limitations in fish pathogen diagnosis and fish disease management and has consequently stimulated the search for alternative diagnostic techniques. Here, we describe a method based on multiplex and broad-range PCR amplification combined with DNA array hybridization for the simultaneous detection and identification of all cyprinid herpesviruses (CyHV-1, CyHV-2 and CyHV-3) and some of the most important fish pathogenic Flavobacterium species, including F. branchiophilum, F. columnare and F. psychrophilum. For virus identification, the DNA polymerase and helicase genes were targeted. For bacterial identification, the ribosomal RNA gene was used. The developed methodology permitted 100% specificity for the identification of the target species. Detection sensitivity was equivalent to 10 viral genomes or less than a picogram of bacterial DNA. The utility and power of the array for sensitive pathogen detection and identification in complex samples such as infected tissue is demonstrated in this study.}, }
@article {pmid21984348, year = {2012}, author = {Jaiswal, SK and Anand, A and Dhar, B and Vaishampayan, A}, title = {Genotypic characterization of phage-typed indigenous soybean bradyrhizobia and their host range symbiotic effectiveness.}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {116-126}, pmid = {21984348}, issn = {1432-184X}, mesh = {*Bacteriophage Typing ; Base Sequence ; Bradyrhizobium/genetics/isolation &amp; purification/*physiology/virology ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; Genetic Variation ; Genotype ; *Host Specificity ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizobium/genetics/isolation &amp; purification/physiology ; Root Nodules, Plant/*microbiology ; Sequence Analysis, RNA ; Glycine max/*microbiology ; *Symbiosis ; }, abstract = {Analysis of genetic diversity among indigenous rhizobia and its symbiotic effectiveness with soybean cultivar is important for development of knowledge about rhizobial ecology. In India, little is known about the genetic resources and diversity of rhizobia nodulating soybean. Indigenous bradyrhizobia isolated from root nodules of soybean plants, collected from traditional cultivating regions of two states (Madhya Pradesh and Uttar Pradesh) of India, were screened for bacteriophage sensitivity to identify successful broad host range symbiotic effectivity. Of 172 rhizobial isolates, 91 showed sensitivities to eight lytic phages and form ten groups on the basis of sensitivity patterns. The genetic diversity of 23 isolates belonging to different phage groups was assessed along with that of strains USDA123 and USDA94 by the restriction fragment length polymorphism (RFLP) analysis of 16S rDNA, intergenic spacer (IGS) (16S-23S rDNA), and DnaK regions. RFLP analysis of 16S rDNA formed 5 groups, whereas 19 and 9 groups were revealed by IGS and the DnaK genes, respectively. The IGS regions showed many amplified polymorphic bands. Nine isolates which revealed high RFLP polymorphism in the abovementioned regions (16S rRNA, IGS, DnaK) were used for 16S rRNA sequence analyses. The results indicate that taxonomically, all isolates were related to Rhizobium etli, Bradyrhizobium spp., and Bradyrhizobium yuanmingense. The doubling time of isolates varied from 9 h (MPSR155) to 16.2 h (MPSR068) in YM broth. Five isolates which did not show cross infectivity with isolated phage strains were studied for symbiotic efficiency. All isolates showed broad host range symbiotic effectiveness forming effective nodules on Vigna mungo, Vigna radiata, Vigna unguiculata, and Cajanus cajan. The present study provides information on genetic diversity and host range symbiosis of indigenous soybean rhizobia typed by different phages.}, }
@article {pmid21984347, year = {2012}, author = {Kvennefors, EC and Sampayo, E and Kerr, C and Vieira, G and Roff, G and Barnes, AC}, title = {Regulation of bacterial communities through antimicrobial activity by the coral holobiont.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {605-618}, pmid = {21984347}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/chemistry/*metabolism/*microbiology/physiology ; Anti-Bacterial Agents/*metabolism ; Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Bacterial Physiological Phenomena ; *Biodiversity ; Mucus/chemistry/metabolism ; Phylogeny ; }, abstract = {Interactions between corals and associated bacteria and amongst these bacterial groups are likely to play a key role in coral health. However, the complexity of these interactions is poorly understood. We investigated the functional role of specific coral-associated bacteria in maintaining microbial communities on the coral Acropora millepora (Ehrenberg 1834) and the ability of coral mucus to support or inhibit bacterial growth. Culture-independent techniques were used to assess bacterial community structures whilst bacterial culture was employed to assess intra- and inter-specific antimicrobial activities of bacteria. Members of Pseudoalteromonas and ribotypes closely related to Vibrio coralliilyticus displayed potent antimicrobial activity against a range of other cultured isolates and grew readily on detached coral mucus. Although such bacterial ribotypes would be expected to have a competitive advantage, they were rare or absent on intact and healthy coral colonies growing in situ (analysed using denaturing gradient gel electrophoresis and 16S rRNA gene sequencing). The most abundant bacterial ribotypes found on healthy corals were Gammaproteobacteria, previously defined as type A coral associates. Our results indicate that this group of bacteria and specific members of the Alphaproteobacteria described here as 'type B associates' may be important functional groups for coral health. We suggest that bacterial communities on coral are kept in check by a combination of host-derived and microbial interactions and that the type A associates in particular may play a key role in maintaining stability of microbial communities on healthy coral colonies.}, }
@article {pmid21983641, year = {2012}, author = {Meyer, KM and Leveau, JH}, title = {Microbiology of the phyllosphere: a playground for testing ecological concepts.}, journal = {Oecologia}, volume = {168}, number = {3}, pages = {621-629}, pmid = {21983641}, issn = {1432-1939}, mesh = {Biodiversity ; Ecology/methods ; Models, Theoretical ; Phylogeography ; Plant Leaves/*microbiology ; }, abstract = {Many concepts and theories in ecology are highly debated, because it is often difficult to design decisive tests with sufficient replicates. Examples include biodiversity theories, succession concepts, invasion theories, coexistence theories, and concepts of life history strategies. Microbiological tests of ecological concepts are rapidly accumulating, but have yet to tap into their full potential to complement traditional macroecological theories. Taking the example of microbial communities on leaf surfaces (i.e. the phyllosphere), we show that most explorations of ecological concepts in this field of microbiology focus on autecology and population ecology, while community ecology remains understudied. Notable exceptions are first tests of the island biogeography theory and of biodiversity theories. Here, the phyllosphere provides the unique opportunity to set up replicated experiments, potentially moving fields such as biogeography, macroecology, and landscape ecology beyond theoretical and observational evidence. Future approaches should take advantage of the great range of spatial scales offered by the leaf surface by iteratively linking laboratory experiments with spatial simulation models.}, }
@article {pmid21982679, year = {2011}, author = {Boon, N and Pycke, BF and Marzorati, M and Hammes, F}, title = {Nutrient gradients in a granular activated carbon biofilter drives bacterial community organization and dynamics.}, journal = {Water research}, volume = {45}, number = {19}, pages = {6355-6361}, doi = {10.1016/j.watres.2011.09.016}, pmid = {21982679}, issn = {1879-2448}, mesh = {Bacteria/*growth &amp; development ; Bioreactors/microbiology ; Carbon/analysis ; Charcoal/*chemistry ; Drinking Water/*microbiology ; Filtration/*instrumentation ; Humic Substances/analysis ; Water Pollutants, Chemical/isolation &amp; purification ; Water Purification/*instrumentation ; }, abstract = {The quality of drinking water is ensured by hygienic barriers and filtration steps, such as ozonation and granular activated carbon (GAC) filtration. Apart from adsorption, GAC filtration involves microbial processes that remove biodegradable organic carbon from the ozonated ground or surface water and ensures biological stability of the treated water. In this study, microbial community dynamics in were monitored during the start-up and maturation of an undisturbed pilot-scale GAC filter at 4 depths (10, 45, 80 and 115 cm) over a period of 6 months. New ecological tools, based on 16S rRNA gene-DGGE, were correlated to filter performance and microbial activity and showed that the microbial gradients developing in the filter was of importance. At 10 cm from the top, receiving the freshly ozonated water with the highest concentration of nutrients, the microbial community dynamics were minimal and the species richness remained low. However, the GAC samples at 80-115 cm showed a 2-3 times higher species richness than the 10-45 cm samples. The highest biomass densities were observed at 45-80 cm, which corresponded with maximum removal of dissolved and assimilable organic carbon. Furthermore, the start-up period was clearly distinguishable using the Lorenz analysis, as after 80 days, the microbial community shifted to an apparent steady-state condition with increased evenness. This study showed that GAC biofilter performance is not necessarily correlated to biomass concentration, but rather that an elevated functionality can be the result of increased microbial community richness, evenness and dynamics.}, }
@article {pmid21978625, year = {2011}, author = {Song, J and An, D and Ren, N and Zhang, Y and Chen, Y}, title = {Effects of pH and ORP on microbial ecology and kinetics for hydrogen production in continuously dark fermentation.}, journal = {Bioresource technology}, volume = {102}, number = {23}, pages = {10875-10880}, doi = {10.1016/j.biortech.2011.09.024}, pmid = {21978625}, issn = {1873-2976}, mesh = {Biomass ; *Bioreactors ; Biotechnology/*methods ; Butyrates/chemistry ; Butyric Acid ; Carbon/chemistry ; Clostridium/*genetics/*metabolism ; Ethanol/chemistry ; Fermentation ; Hydrogen/chemistry ; Hydrogen-Ion Concentration ; In Situ Hybridization, Fluorescence/methods ; Kinetics ; Oxygen/chemistry ; Sewage/chemistry ; Time Factors ; Waste Disposal, Fluid/methods ; }, abstract = {The microbial structure and kinetic characteristics of the hydrogen producing strains in two fermentative continuous stirred-tank reactors (CSTRs) were studied by controlling pH and oxidation and reduction potential (ORP). The fluorescence in situ hybridization (FISH) tests were conducted to investigate the fermentative performance of Clostridium histolyticum (C. histolyticum), Clostridium lituseburense (C. lituseburense) and Enterobacteriaceae. The experimental results showed that in ethanol-type reactor 1#, the relative abundance of the strains was 48%, 30% and 22%. Comparatively, the relative abundance in butyric acid-type reactor 2# was 24%, 55% and 19% with butyric acids and hydrogen as the main products. The kinetic results indicated that the hydrogen yield coefficients YP/X in both reactors were 8.357 and 5.951 l-H2/g, while the coefficients of the cellular yield were 0.0268 and 0.0350 g-Cell/g, respectively. At the same biomass, the hydrogen yield in ethanol-type reactors was more than that in butyric acid reactors. However, the cellular synthesis rate in ethanol-type reactors was low when the same carbon source was used.}, }
@article {pmid21977665, year = {2011}, author = {Tsekova, K and Ganeva, S and Hristov, A and Todorova, D and Beschkov, V}, title = {Simultaneous copper, cobalt and phenol removal from aqueous solutions by alternating biosorption and biodegradation.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {63}, number = {10}, pages = {2388-2394}, doi = {10.2166/wst.2011.464}, pmid = {21977665}, issn = {0273-1223}, mesh = {Biodegradation, Environmental ; Biomass ; Candida/*metabolism ; Cobalt/chemistry ; Copper/chemistry ; Metals, Heavy/*isolation &amp; purification ; Phenol/chemistry/*metabolism ; Rhizopus/*chemistry ; Waste Disposal, Fluid/*methods ; }, abstract = {A strategy for removal of heavy metals and phenol from wastewaters is proposed. It involves consecutive cation biosorption by fungi, phenol biodegradation by the yeast association Candida sp. 2326 + Candida sp. 2327 and regeneration. Copper and cobalt removal from aqueous solutions containing 80-120 mg/L phenol by biosorption, using Rhizopus archizus cells immobilized onto poly (vinyl alcohol), was investigated by conducting a series of batch experiments. The removal efficiencies were 81% for Cu and 5% for Co. The residual concentrations of Cu (1.9 mg/L) and of Co (9.5 mg/L) did not change the biodegradation dynamics of phenol. A quantitative biodegradation of 120 mg/L phenol proceeded within 22 h. After biodegradation of phenol, the removal efficiencies achieved by biosorption after regeneration were 90% for Cu and 44% for Co. It was found that copper and cobalt form positively charged complexes with phenol. This complex formation hinders the retention of Cu and Co by the biosorbent and reduces the uptake of their cations.}, }
@article {pmid21968611, year = {2012}, author = {Savage, D and Barbetti, MJ and MacLeod, WJ and Salam, MU and Renton, M}, title = {Seasonal and diurnal patterns of spore release can significantly affect the proportion of spores expected to undergo long-distance dispersal.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {578-585}, pmid = {21968611}, issn = {1432-184X}, mesh = {*Ecosystem ; Fungi/*physiology ; *Models, Biological ; Seasons ; Spores, Fungal/*physiology ; Wind ; }, abstract = {Many of the fungal pathogens that threaten agricultural and natural systems undergo wind-assisted dispersal. During turbulent wind conditions, long-distance dispersal can occur, and airborne spores are carried over distances greater than the mean. The occurrence of long-distance dispersal is an important ecological process, as it can drastically increase the extent to which pathogen epidemics spread across a landscape, result in rapid transmission of disease to previously uninfected areas, and influence the spatial structure of pathogen populations in fragmented landscapes. Since the timing of spore release determines the wind conditions that prevail over a dispersal event, this timing is likely to affect the probability of long-distance dispersal occurring. Using a Lagrangian stochastic model, we test the effect of seasonal and diurnal variation in the release of spores on wind-assisted dispersal. Spores released during the hottest part of the day are shown to be more likely to undergo long-distance dispersal than those released at other times. Furthermore, interactions are shown to occur between seasonal and diurnal patterns of release. These results have important consequences for further modelling of wind-assisted dispersal and the use of models to predict the spread of fungal pathogens and resulting population and epidemic dynamics.}, }
@article {pmid21966473, year = {2011}, author = {Tamaki, H and Wright, CL and Li, X and Lin, Q and Hwang, C and Wang, S and Thimmapuram, J and Kamagata, Y and Liu, WT}, title = {Analysis of 16S rRNA amplicon sequencing options on the Roche/454 next-generation titanium sequencing platform.}, journal = {PloS one}, volume = {6}, number = {9}, pages = {e25263}, pmid = {21966473}, issn = {1932-6203}, mesh = {Environmental Microbiology ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis/*instrumentation/*methods ; }, abstract = {BACKGROUND: 16S rRNA gene pyrosequencing approach has revolutionized studies in microbial ecology. While primer selection and short read length can affect the resulting microbial community profile, little is known about the influence of pyrosequencing methods on the sequencing throughput and the outcome of microbial community analyses. The aim of this study is to compare differences in output, ease, and cost among three different amplicon pyrosequencing methods for the Roche/454 Titanium platform<br><br>The following three pyrosequencing methods for 16S rRNA genes were selected in this study: Method-1 (standard method) is the recommended method for bi-directional sequencing using the LIB-A kit; Method-2 is a new option designed in this study for unidirectional sequencing with the LIB-A kit; and Method-3 uses the LIB-L kit for unidirectional sequencing. In our comparison among these three methods using 10 different environmental samples, Method-2 and Method-3 produced 1.5-1.6 times more useable reads than the standard method (Method-1), after quality-based trimming, and did not compromise the outcome of microbial community analyses. Specifically, Method-3 is the most cost-effective unidirectional amplicon sequencing method as it provided the most reads and required the least effort in consumables management.<br><br>CONCLUSIONS: Our findings clearly demonstrated that alternative pyrosequencing methods for 16S rRNA genes could drastically affect sequencing output (e.g. number of reads before and after trimming) but have little effect on the outcomes of microbial community analysis. This finding is important for both researchers and sequencing facilities utilizing 16S rRNA gene pyrosequencing for microbial ecological studies.}, }
@article {pmid21965156, year = {2012}, author = {Wu, ZW and Lu, HF and Wu, J and Zuo, J and Chen, P and Sheng, JF and Zheng, SS and Li, LJ}, title = {Assessment of the fecal lactobacilli population in patients with hepatitis B virus-related decompensated cirrhosis and hepatitis B cirrhosis treated with liver transplant.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {929-937}, pmid = {21965156}, issn = {1432-184X}, mesh = {DNA, Bacterial/analysis/genetics/isolation &amp; purification ; Feces/*microbiology ; Hepatitis B/*complications/virology ; Hepatitis B virus ; Humans ; Lactobacillus/classification/genetics/*isolation &amp; purification ; Liver Cirrhosis/*therapy/virology ; *Liver Transplantation ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {This study aims to provide an overview of the diversity of intestinal Lactobacillus among Chinese patients with hepatitis B virus (HBV)-related decompensated cirrhosis and who received liver transplant for hepatitis B cirrhosis. Fecal samples were collected from 38 healthy volunteers, 61 patients with HBV-related decompensated cirrhosis (group LC) and 74 patients who had liver transplant for hepatitis B cirrhosis (group LT). Quantitative polymerase chain reaction technology with species-specific primers was applied to investigate lactobacilli 16S rDNA in crude DNA, extracted from fecal samples. Software package Statistical Package for the Social Sciences and Palaeontological Statistics for Windows was used to analyze the data. Lactobacilli population of the two patient groups was different from the healthy control subjects, principal differences being marked decrease in the population of Lactobacillus rhamnosus (p < 0.001 for both patient groups) and reduction in the frequency of Lactobacillus fermentus (p < 0.001 for group LC and p < 0.01 for group LT). Our findings on the frequency of lactobacilli population suggested decreased diversity in groups LC and LT (compared with the healthy controls (p < 0.001 and p < 0.01, respectively)). Patients tended to have less complex fecal lactobacilli composition than the healthy controls, especially in the group LC.}, }
@article {pmid21960435, year = {2011}, author = {Kojima, Y and Toki, T and Morimoto, T and Yoshiyama, M and Kimura, K and Kadowaki, T}, title = {Infestation of Japanese native honey bees by tracheal mite and virus from non-native European honey bees in Japan.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {895-906}, pmid = {21960435}, issn = {1432-184X}, mesh = {Animals ; Beekeeping ; Bees/*parasitology/*virology ; Insect Viruses/genetics/*isolation &amp; purification ; Introduced Species ; Japan/epidemiology ; Mite Infestations/*epidemiology/transmission ; Phylogeny ; Varroidae/*pathogenicity ; Virus Diseases/*epidemiology/transmission ; }, abstract = {Invasion of alien species has been shown to cause detrimental effects on habitats of native species. Insect pollinators represent such examples; the introduction of commercial bumble bee species for crop pollination has resulted in competition for an ecological niche with native species, genetic disturbance caused by mating with native species, and pathogen spillover to native species. The European honey bee, Apis mellifera, was first introduced into Japan for apiculture in 1877, and queen bees have been imported from several countries for many years. However, its effects on Japanese native honey bee, Apis cerana japonica, have never been addressed. We thus conducted the survey of honey bee viruses and Acarapis mites using both A. mellifera and A. c. japonica colonies to examine their infestation in native and non-native honey bee species in Japan. Honey bee viruses, Deformed wing virus (DWV), Black queen cell virus (BQCV), Israeli acute paralysis virus (IAPV), and Sacbrood virus (SBV), were found in both A. mellifera and A. c. japonica colonies; however, the infection frequency of viruses in A. c. japonica was lower than that in A. mellifera colonies. Based on the phylogenies of DWV, BQCV, and SBV isolates from A. mellifera and A. c. japonica, DWV and BQCV may infect both honey bee species; meanwhile, SBV has a clear species barrier. For the first time in Japan, tracheal mite (Acarapis woodi) was specifically found in the dead honey bees from collapsing A. c. japonica colonies. This paper thus provides further evidence that tracheal-mite-infested honey bee colonies can die during cool winters with no other disease present. These results demonstrate the infestation of native honey bees by parasite and pathogens of non-native honey bees that are traded globally.}, }
@article {pmid21955796, year = {2012}, author = {Garren, M and Azam, F}, title = {New directions in coral reef microbial ecology.}, journal = {Environmental microbiology}, volume = {14}, number = {4}, pages = {833-844}, doi = {10.1111/j.1462-2920.2011.02597.x}, pmid = {21955796}, issn = {1462-2920}, mesh = {Animals ; Anthozoa/microbiology/physiology ; Climate Change ; Conservation of Natural Resources ; *Coral Reefs ; Ecology/*trends ; Geologic Sediments/microbiology ; Oceans and Seas ; *Water Microbiology ; }, abstract = {Microbial processes largely control the health and resilience of coral reef ecosystems, and new technologies have led to an exciting wave of discovery regarding the mechanisms by which microbial communities support the functioning of these incredibly diverse and valuable systems. There are three questions at the forefront of discovery: What mechanisms underlie coral reef health and resilience? How do environmental and anthropogenic pressures affect ecosystem function? What is the ecology of microbial diseases of corals? The goal is to understand the functioning of coral reefs as integrated systems from microbes and molecules to regional and ocean-basin scale ecosystems to enable accurate predictions of resilience and responses to perturbations such as climate change and eutrophication. This review outlines recent discoveries regarding the microbial ecology of different microenvironments within coral ecosystems, and highlights research directions that take advantage of new technologies to build a quantitative and mechanistic understanding of how coral health is connected through microbial processes to its surrounding environment. The time is ripe for natural resource managers and microbial ecologists to work together to create an integrated understanding of coral reef functioning. In the context of long-term survival and conservation of reefs, the need for this work is immediate.}, }
@article {pmid21947462, year = {2012}, author = {Ul Haq, I and Chaudhry, WN and Andleeb, S and Qadri, I}, title = {Isolation and partial characterization of a virulent bacteriophage IHQ1 specific for Aeromonas punctata from stream water.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {954-963}, pmid = {21947462}, issn = {1432-184X}, mesh = {Adsorption ; Aeromonas/classification/*virology ; Bacteriophages/genetics/*isolation &amp; purification/*physiology/ultrastructure ; Host Specificity ; Hydrogen-Ion Concentration ; Microscopy, Electron, Transmission ; Pakistan ; Proteomics ; Rivers/*microbiology ; Species Specificity ; Viral Proteins/genetics ; }, abstract = {Aeromonas punctata is the causative agent of septicemia, diarrhea, wound infections, meningitis, peritonitis, and infections of the joints, bones and eyes. Bacteriophages are often considered alternative agents for controlling bacterial infection and contamination. In this study, we described the isolation and preliminary characterization of bacteriophage IHQ1 (family Myoviridae) active against the Gram-negative bacterial strain A. punctata. This virulent bacteriophage was isolated from stream water sample. Genome analysis indicated that phage IHQ1 was a double-stranded DNA virus with an approximate genome size of 25-28 kb. The initial characterization of this newly isolated phage showed that it has a narrow host range and infects only A. punctata as it failed to infect seven other clinically isolated pathogenic strains, i.e., methicillin-resistant Staphylococcus aureus 6403, MRSA 17644, Acinetobacter 33408, Acinetobacter 1172, Pseudomonas aeruginosa 22250, P. aeruginosa 11219, and Escherichia coli. Proteomic pattern of phage IHQ1, generated by SDS-PAGE using purified phage particles, showed three major and three minor protein bands with molecular weights ranging from 25 to 70 kDa. The adsorption rate of phage IHQ1 to the host bacterium was also determined, which was significantly enhanced by the addition of 10 mM CaCl(2). From the single-step growth experiment, it was inferred that the latent time period of phage IHQ1 was 24 min and a burst size of 626 phages per cell. Moreover, the pH and thermal stability of phage IHQ1 were also investigated. The maximum stability of the phage was observed at optimal pH 7.0, and it was totally unstable at extreme acidic pH 3; however, it was comparatively stable at alkaline pH 11.0. At 37°C the phage showed maximum number of plaques, and the viability was almost 100%. The existence of Aeromonas bacteriophage is very promising for the eradication of this opportunistic pathogen and also for future applications such as the design of new detection and phage typing (diagnosis) methods. The specificity of the bacteriophage for A. punctata makes it an attractive candidate for phage therapy of A. punctata infections.}, }
@article {pmid21947461, year = {2012}, author = {Bohorquez, LC and Delgado-Serrano, L and López, G and Osorio-Forero, C and Klepac-Ceraj, V and Kolter, R and Junca, H and Baena, S and Zambrano, MM}, title = {In-depth characterization via complementing culture-independent approaches of the microbial community in an acidic hot spring of the Colombian Andes.}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {103-115}, pmid = {21947461}, issn = {1432-184X}, mesh = {Actinobacteria/genetics/isolation &amp; purification ; Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; Colombia ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Genes, rRNA ; Hot Springs/*microbiology ; *Microbial Consortia ; Molecular Sequence Data ; Phylogeny ; Proteobacteria/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The microbial community of a Colombian high mountain hot spring, El Coquito, was analyzed using three different culture-independent assessments of 16S ribosomal RNA genes: clone libraries, pyrosequencing of the V5-V6 hypervariable region, and microarray. This acidic spring had a diverse community composed mainly of Bacteria that shared characteristics with those from other hot springs and extreme acidic environments. The microbial community was dominated by Proteobacteria, Firmicutes, and Planctomycetes and contained chemotrophic bacteria potentially involved in cycling of ferrous and sulfur-containing minerals and phototrophic organisms, most of which were eukaryotic micro-algae. Despite the presence of a large proportion of novel, unclassified sequences, the taxonomic profiles obtained with each strategy showed similarities at higher taxonomic levels. However, some groups, such as Spirochaetes and Aquificae, were identified using only one methodology, and more taxa were detected with the gene array, which also shared more groups with the pyrosequencing data. Overall, the combined use of different approaches provided a broader view of the microbial community in this acidic hot spring.}, }
@article {pmid21947430, year = {2012}, author = {Fürnkranz, M and Lukesch, B and Müller, H and Huss, H and Grube, M and Berg, G}, title = {Microbial diversity inside pumpkins: microhabitat-specific communities display a high antagonistic potential against phytopathogens.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {418-428}, pmid = {21947430}, issn = {1432-184X}, mesh = {Austria ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; *Biological Control Agents ; Cucurbita/growth &amp; development/*microbiology ; DNA, Bacterial/analysis/genetics ; DNA, Fungal/analysis/genetics ; Endophytes ; Environment ; Flowers/microbiology ; Fruit/microbiology ; Fungi/classification/genetics/*isolation &amp; purification/physiology ; Microbiological Techniques ; Molecular Sequence Data ; Plant Diseases/*microbiology ; Plant Roots/microbiology ; Polymorphism, Single-Stranded Conformational ; RNA, Ribosomal, 16S/analysis/genetics ; Species Specificity ; }, abstract = {Recent and substantial yield losses of Styrian oil pumpkin (Cucurbita pepo L. subsp. pepo var. styriaca Greb.) are primarily caused by the ascomycetous fungus Didymella bryoniae but bacterial pathogens are frequently involved as well. The diversity of endophytic microbial communities from seeds (spermosphere), roots (endorhiza), flowers (anthosphere), and fruits (carposphere) of three different pumpkin cultivars was studied to develop a biocontrol strategy. A multiphasic approach combining molecular, microscopic, and cultivation techniques was applied to select a consortium of endophytes for biocontrol. Specific community structures for Pseudomonas and Bacillus, two important plant-associated genera, were found for each microenvironment by fingerprinting of 16S ribosomal RNA genes. All microenvironments were dominated by bacteria; fungi were less abundant. Of the 2,320 microbial isolates analyzed in dual culture assays, 165 (7%) were tested positively for in vitro antagonism against D. bryoniae. Out of these, 43 isolates inhibited the growth of bacterial pumpkin pathogens (Pectobacterium carotovorum, Pseudomonas viridiflava, Xanthomonas cucurbitae); here only bacteria were selected. Microenvironment-specific antagonists were found, and the spermosphere and anthosphere were revealed as underexplored reservoirs for antagonists. In the latter, a potential role of pollen grains as bacterial vectors between flowers was recognized. Six broad spectrum antagonists selected according to their activity, genotypic diversity, and occurrence were evaluated under greenhouse conditions. Disease severity on pumpkins of D. bryoniae was significantly reduced by Pseudomonas chlororaphis treatment and by a combined treatment of strains (Lysobacter gummosus, P. chlororaphis, Paenibacillus polymyxa, and Serratia plymuthica). This result provides a promising prospect to biologically control pumpkin diseases.}, }
@article {pmid21947429, year = {2012}, author = {Leão, PN and Ramos, V and Vale, M and Machado, JP and Vasconcelos, VM}, title = {Microbial community changes elicited by exposure to cyanobacterial allelochemicals.}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {85-95}, pmid = {21947429}, issn = {1432-184X}, mesh = {Genes, rRNA ; Genotype ; Lakes/*microbiology ; Microbial Consortia/*drug effects ; Microcystis/*drug effects/genetics/growth &amp; development/isolation &amp; purification ; Molecular Sequence Data ; Oscillatoria/*metabolism ; Pheromones/*pharmacology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {An increasing body of evidence points out that allelopathy may be an important process shaping microbial communities in aquatic ecosystems. Cyanobacteria have well-documented allelopathic properties, mainly derived from the evaluation of the activity of allelopathic extracts or pure compounds towards monocultures of selected target microorganisms. Consequently, little is known regarding the community dynamics of microorganisms associated with allelopathic interactions. In this laboratory-based study, a Microcystis spp.-dominated microbial community from a freshwater lake was exposed, for 15 days, to exudates from the cyanobacterium Oscillatoria sp. strain LEGE 05292 in laboratory conditions. This cyanobacterium is known to produce the allelochemicals portoamides, which were among the exuded compounds. The community composition was followed (by means of polymerase chain reaction followed by denaturing gradient gel electrophoresis and microscopic analyses) and compared to that of a non-exposed situation. Following exposure, clear differences in the community structure were observed, in particular for cyanobacteria and unicellular eukaryotic taxa. Interestingly, distinct Microcystis genotypes present in the community were differentially impacted by the exposure, highlighting the fine-scale dynamics elicited by the exudates. These results support a role for cyanobacterial allelochemicals in the structuring of aquatic microbial communities.}, }
@article {pmid21943072, year = {2011}, author = {Schmitz-Esser, S and Penz, T and Spang, A and Horn, M}, title = {A bacterial genome in transition--an exceptional enrichment of IS elements but lack of evidence for recent transposition in the symbiont Amoebophilus asiaticus.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {270}, pmid = {21943072}, issn = {1471-2148}, support = {P 22703/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteroidetes/*genetics ; Base Composition/genetics ; Base Sequence ; Blotting, Southern ; DNA Transposable Elements/*genetics ; *Evolution, Molecular ; *Genetic Variation ; Genome, Bacterial/*genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Transcription, Genetic/genetics ; }, abstract = {BACKGROUND: Insertion sequence (IS) elements are important mediators of genome plasticity and are widespread among bacterial and archaeal genomes. The 1.88 Mbp genome of the obligate intracellular amoeba symbiont Amoebophilus asiaticus contains an unusually large number of transposase genes (n = 354; 23% of all genes).<br><br>RESULTS: The transposase genes in the A. asiaticus genome can be assigned to 16 different IS elements termed ISCaa1 to ISCaa16, which are represented by 2 to 24 full-length copies, respectively. Despite this high IS element load, the A. asiaticus genome displays a GC skew pattern typical for most bacterial genomes, indicating that no major rearrangements have occurred recently. Additionally, the high sequence divergence of some IS elements, the high number of truncated IS element copies (n = 143), as well as the absence of direct repeats in most IS elements suggest that the IS elements of A. asiaticus are transpositionally inactive. Although we could show transcription of 13 IS elements, we did not find experimental evidence for transpositional activity, corroborating our results from sequence analyses. However, we detected contiguous transcripts between IS elements and their downstream genes at nine loci in the A. asiaticus genome, indicating that some IS elements influence the transcription of downstream genes, some of which might be important for host cell interaction.<br><br>CONCLUSIONS: Taken together, the IS elements in the A. asiaticus genome are currently in the process of degradation and largely represent reflections of the evolutionary past of A. asiaticus in which its genome was shaped by their activity.}, }
@article {pmid21938508, year = {2012}, author = {Rojas, JD and Sette, LD and de Araujo, WL and Lopes, MS and da Silva, LF and Furlan, RL and Padilla, G}, title = {The diversity of polyketide synthase genes from sugarcane-derived fungi.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {565-577}, pmid = {21938508}, issn = {1432-184X}, mesh = {Amino Acid Sequence ; Fungal Proteins/chemistry/*genetics/metabolism ; Fungi/classification/*enzymology/genetics/isolation &amp; purification ; *Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Polyketide Synthases/chemistry/*genetics/metabolism ; Saccharum/*microbiology ; Sequence Alignment ; }, abstract = {The chemical ecology and biotechnological potential of metabolites from endophytic and rhizosphere fungi are receiving much attention. A collection of 17 sugarcane-derived fungi were identified and assessed by PCR for the presence of polyketide synthase (PKS) genes. The fungi were all various genera of ascomycetes, the genomes of which encoded 36 putative PKS sequences, 26 shared sequence homology with β-ketoacyl synthase domains, while 10 sequences showed homology to known fungal C-methyltransferase domains. A neighbour-joining phylogenetic analysis of the translated sequences could group the domains into previously established chemistry-based clades that represented non-reducing, partially reducing and highly reducing fungal PKSs. We observed that, in many cases, the membership of each clade also reflected the taxonomy of the fungal isolates. The functional assignment of the domains was further confirmed by in silico secondary and tertiary protein structure predictions. This genome mining study reveals, for the first time, the genetic potential of specific taxonomic groups of sugarcane-derived fungi to produce specific types of polyketides. Future work will focus on isolating these compounds with a view to understanding their chemical ecology and likely biotechnological potential.}, }
@article {pmid21938020, year = {2012}, author = {Yergeau, E and Bokhorst, S and Kang, S and Zhou, J and Greer, CW and Aerts, R and Kowalchuk, GA}, title = {Shifts in soil microorganisms in response to warming are consistent across a range of Antarctic environments.}, journal = {The ISME journal}, volume = {6}, number = {3}, pages = {692-702}, pmid = {21938020}, issn = {1751-7370}, mesh = {Antarctic Regions ; Bacteria/classification/genetics/*growth &amp; development ; *Biota ; *Climate Change ; Fungi/classification/genetics/*growth &amp; development ; Microarray Analysis ; Nitrogen Cycle ; RNA, Ribosomal, 16S/genetics ; Soil/analysis ; *Soil Microbiology ; Temperature ; }, abstract = {Because of severe abiotic limitations, Antarctic soils represent simplified systems, where microorganisms are the principal drivers of nutrient cycling. This relative simplicity makes these ecosystems particularly vulnerable to perturbations, like global warming, and the Antarctic Peninsula is among the most rapidly warming regions on the planet. However, the consequences of the ongoing warming of Antarctica on microorganisms and the processes they mediate are unknown. Here, using 16S rRNA gene pyrosequencing and qPCR, we report highly consistent responses in microbial communities across disparate sub-Antarctic and Antarctic environments in response to 3 years of experimental field warming (+0.5 to 2 °C). Specifically, we found significant increases in the abundance of fungi and bacteria and in the Alphaproteobacteria-to-Acidobacteria ratio, which could result in an increase in soil respiration. Furthermore, shifts toward generalist bacterial communities following warming weakened the linkage between the bacterial taxonomic and functional richness. GeoChip microarray analyses also revealed significant warming effects on functional communities, specifically in the N-cycling microorganisms. Our results demonstrate that soil microorganisms across a range of sub-Antarctic and Antarctic environments can respond consistently and rapidly to increasing temperatures.}, }
@article {pmid21935610, year = {2012}, author = {Burge, CA and Friedman, CS}, title = {Quantifying Ostreid herpesvirus (OsHV-1) genome copies and expression during transmission.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {596-604}, pmid = {21935610}, issn = {1432-184X}, mesh = {Animals ; *Gene Dosage ; *Genome, Viral ; Herpesviridae/classification/*genetics/isolation &amp; purification ; Ostreidae/physiology/*virology ; }, abstract = {Understanding the pathogenic potential of a new pathogen strain or a known pathogen in a new locale is crucial for management of disease in both wild and farmed animals. The Ostreid herpesvirus-1 (OsHV-1), a known pathogen of early-life-stage Pacific oysters, Crassostrea gigas, has been associated with mortalities of juvenile oysters in many locations around the world including Tomales Bay, California. In two trials, the California OsHV-1 strain was transmitted from infected juvenile C. gigas to naïve C. gigas larvae. Survival of control larvae was high throughout both trials (97-100%) and low among those exposed to OsHV-1. No OsHV-1-exposed larvae survived to day 9 in trial 1, while trial 2 was terminated at day 7 when survival was 36.90 ± 8.66%. To assess the amount of OsHV-1 DNA present, we employed quantitative polymerase chain reaction (qPCR) assays based on the A fragment and OsHV-1 catalytic subunit of a DNA polymerase δ (DNA pol) gene. Viral genome copy numbers based on qPCR assays peaked between 3 and 5 days. To measure the presence of viable and actively transcribing virus, the DNA pol gene qPCR assay was optimized for RNA analysis after being reverse transcribed (RT-qPCR). A decline in virus gene expression was measured using RT-qPCR: relative to earlier experimental time points copy numbers were significantly lower on day 9, trial 1 (p < 0.05) and day 7, trial 2 (p < 0.05). Peaks in copies of active virus per genome occurred during two periods in trial 1 (days 1 and 5/7, p < 0.05) and one period in trial 2 (day 1, p < 0.05). Transmission electron microscopy confirmed OsHV-1 infection; herpesvirus-like nucleocapsids, capsids, and extracellular particles were visualized. We demonstrated the ability to transmit OsHV-1 from infected juvenile oysters to naïve larvae, which indicates the spread of OsHV-1 between infected hosts in the field and between commercial farms is possible. We also developed an important tool (OsHV-1-specific RT-qPCR for an active virus gene) for use in monitoring for active virus in the field and in laboratory based transmission experiments.}, }
@article {pmid21935609, year = {2012}, author = {Ballor, NR and Leadbetter, JR}, title = {Analysis of extensive [FeFe] hydrogenase gene diversity within the gut microbiota of insects representing five families of Dictyoptera.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {586-595}, pmid = {21935609}, issn = {1432-184X}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/chemistry/*enzymology/genetics/isolation &amp; purification ; Bacterial Proteins/chemistry/*genetics/metabolism ; Cockroaches/classification/*microbiology ; Gastrointestinal Tract/microbiology ; Genetic Variation ; Hydrogenase/chemistry/*genetics/metabolism ; Isoptera/classification/*microbiology ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; }, abstract = {We have designed and utilized degenerate primers in the phylogenetic analysis of [FeFe] hydrogenase gene diversity in the gut ecosystems of roaches and lower termites. H(2) is an important free intermediate in the breakdown of wood by termite gut microbial communities, reaching concentrations in some species exceeding those measured for any other biological system. The primers designed target with specificity the largest group of enzymatic H domain proteins previously identified in a termite gut metagenome. "Family 3" hydrogenase sequences were amplified from the guts of lower termites, Incisitermes minor, Zootermopsis nevadensis, and Reticulitermes hesperus, and two roaches, Cryptocercus punctulatus and Periplaneta americana. Subsequent analyses revealed that all termite and Cryptocercus sequences were phylogenetically distinct from non-termite-associated hydrogenases available from public databases. The abundance of unique sequence operational taxonomic units (as many as 21 from each species) underscores the previously demonstrated physiological importance of H(2) to the gut ecosystems of these wood-feeding insects. The diversity of sequences observed might be reflective of multiple niches that the enzymes have been evolved to accommodate. Sequences cloned from Cryptocercus and the lower termite samples, all of which are wood feeding insects, clustered closely with one another in phylogenetic analyses to the exclusion of alleles from P. americana, an omnivorous cockroach, also cloned during this study. We present primers targeting a family of termite gut [FeFe] hydrogenases and provide results that are consistent with a pivotal role for hydrogen in the termite gut ecosystem and point toward unique evolutionary adaptations to the gut ecosystem.}, }
@article {pmid21930919, year = {2011}, author = {Mussmann, M and Brito, I and Pitcher, A and Sinninghe Damsté, JS and Hatzenpichler, R and Richter, A and Nielsen, JL and Nielsen, PH and Müller, A and Daims, H and Wagner, M and Head, IM}, title = {Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {40}, pages = {16771-16776}, pmid = {21930919}, issn = {1091-6490}, support = {I 44/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Ammonia/*metabolism ; Archaea/*enzymology ; Autoradiography ; Base Sequence ; Cluster Analysis ; DNA Primers/genetics ; Europe ; *Extraction and Processing Industry ; Glyceryl Ethers/metabolism ; In Situ Hybridization, Fluorescence ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/*genetics/*metabolism ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Waste Products/*analysis ; *Water Purification ; }, abstract = {Nitrification is a core process in the global nitrogen cycle that is essential for the functioning of many ecosystems. The discovery of autotrophic ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota has changed our perception of the microbiology of nitrification, in particular since their numerical dominance over ammonia-oxidizing bacteria (AOB) in many environments has been revealed. These and other data have led to a widely held assumption that all amoA-encoding members of the Thaumarchaeota (AEA) are autotrophic nitrifiers. In this study, 52 municipal and industrial wastewater treatment plants were screened for the presence of AEA and AOB. Thaumarchaeota carrying amoA were detected in high abundance only in four industrial plants. In one plant, thaumarchaeotes closely related to soil group I.1b outnumbered AOB up to 10,000-fold, and their numbers, which can only be explained by active growth in this continuous culture system, were two to three orders of magnitude higher than could be sustained by autotrophic ammonia oxidation. Consistently, (14)CO(2) fixation could only be detected in AOB but not in AEA in actively nitrifying sludge from this plant via FISH combined with microautoradiography. Furthermore, in situ transcription of archaeal amoA, and very weak in situ labeling of crenarchaeol after addition of (13)CO(2), was independent of the addition of ammonium. These data demonstrate that some amoA-carrying group I.1b Thaumarchaeota are not obligate chemolithoautotrophs.}, }
@article {pmid21923700, year = {2012}, author = {Gihring, TM and Green, SJ and Schadt, CW}, title = {Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes.}, journal = {Environmental microbiology}, volume = {14}, number = {2}, pages = {285-290}, doi = {10.1111/j.1462-2920.2011.02550.x}, pmid = {21923700}, issn = {1462-2920}, mesh = {*Biodiversity ; *Gene Library ; Genes, rRNA ; Humans ; Sequence Analysis, RNA/*methods ; }, abstract = {Technologies for massively parallel sequencing are revolutionizing microbial ecology and are vastly increasing the scale of ribosomal RNA (rRNA) gene studies. Although pyrosequencing has increased the breadth and depth of possible rRNA gene sampling, one drawback is that the number of reads obtained per sample is difficult to control. Pyrosequencing libraries typically vary widely in the number of sequences per sample, even within individual studies, and there is a need to revisit the behaviour of richness estimators and diversity indices with variable gene sequence library sizes. Multiple reports and review papers have demonstrated the bias in non-parametric richness estimators (e.g. Chao1 and ACE) and diversity indices when using clone libraries. However, we found that biased community comparisons are accumulating in the literature. Here we demonstrate the effects of sample size on Chao1, ACE, CatchAll, Shannon, Chao-Shen and Simpson's estimations specifically using pyrosequencing libraries. The need to equalize the number of reads being compared across libraries is reiterated, and investigators are directed towards available tools for making unbiased diversity comparisons.}, }
@article {pmid21921930, year = {2011}, author = {van Ooij, C}, title = {Microbial ecology: first come, first served?.}, journal = {Nature reviews. Microbiology}, volume = {9}, number = {10}, pages = {698-699}, pmid = {21921930}, issn = {1740-1534}, }
@article {pmid21920580, year = {2011}, author = {García-Lledó, A and Vilar-Sanz, A and Trias, R and Hallin, S and Bañeras, L}, title = {Genetic potential for N2O emissions from the sediment of a free water surface constructed wetland.}, journal = {Water research}, volume = {45}, number = {17}, pages = {5621-5632}, doi = {10.1016/j.watres.2011.08.025}, pmid = {21920580}, issn = {1879-2448}, mesh = {Bacteria/genetics ; Biological Oxygen Demand Analysis ; Denitrification/genetics ; Gene Dosage/genetics ; Geography ; Geologic Sediments/*chemistry ; Linear Models ; Nitrous Oxide/*analysis ; Poaceae/*genetics ; RNA, Ribosomal, 16S/genetics ; Spain ; Statistics, Nonparametric ; Surface Properties ; Time Factors ; Typhaceae/*genetics ; Waste Disposal, Fluid ; Water/*chemistry ; *Wetlands ; }, abstract = {Removal of nitrogen is a key aspect in the functioning of constructed wetlands. However, incomplete denitrification may result in the net emission of the greenhouse gas nitrous oxide (N(2)O) resulting in an undesired effect of a system supposed to provide an ecosystem service. In this work we evaluated the genetic potential for N(2)O emissions in relation to the presence or absence of Phragmites and Typha in a free water surface constructed wetland (FWS-CW), since vegetation, through the increase in organic matter due to litter degradation, may significantly affect the denitrification capacity in planted areas. Quantitative real-time PCR analyses of genes in the denitrification pathway indicating capacity to produce or reduce N(2)O were conducted at periods of different water discharge. Genetic potential for N(2)O emissions was estimated from the relative abundances of all denitrification genes and nitrous oxide reductase encoding genes (nosZ). nosZ abundance was invariably lower than the other denitrifying genes (down to 100 fold), and differences increased significantly during periods of high nitrate loads in the CW suggesting a higher genetic potential for N(2)O emissions. This situation coincided with lower nitrogen removal efficiencies in the treatment cell. The presence and the type of vegetation, mainly due to changes in the sediment carbon and nitrogen content, correlated negatively to the ratio between nitrate and nitrite reducers and positively to the ratio between nitrite and nitrous oxide reducers. These results suggest that the potential for nitrous oxide emissions is higher in vegetated sediments.}, }
@article {pmid21915632, year = {2012}, author = {Chaiyapechara, S and Rungrassamee, W and Suriyachay, I and Kuncharin, Y and Klanchui, A and Karoonuthaisiri, N and Jiravanichpaisal, P}, title = {Bacterial community associated with the intestinal tract of P. monodon in commercial farms.}, journal = {Microbial ecology}, volume = {63}, number = {4}, pages = {938-953}, pmid = {21915632}, issn = {1432-184X}, mesh = {Animals ; *Aquaculture ; Bacteria/*classification/*genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Denaturing Gradient Gel Electrophoresis ; *Ecosystem ; Gammaproteobacteria/classification/genetics/isolation &amp; purification ; Intestines/*microbiology ; Molecular Sequence Data ; Penaeidae/growth &amp; development/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Thailand ; }, abstract = {The potentially important roles of intestinal bacteria on immune response, disease resistance, and nutrition for the black tiger shrimp Penaeus monodon have been increasingly investigated. However, so far, little is known about the intestinal bacterial community of the shrimp in the commercial aquaculture settings. In this study, the intestinal bacterial communities of juvenile P. monodon (70 individuals) from eight commercial farms in Thailand were examined using 16S rDNA PCR-DGGE, and seven 16S rDNA clone libraries from representative DGGE profiles were constructed. Bacteria in the γ-Proteobacteria class were the only common bacteria group found in the intestinal tracts of shrimp from all farms. The dominant bacterial genera in the intestinal population of each shrimp varied among different farms, and these genera were Vibrio, Photobacterium, Aeromonas, or Propionigenium (phylum Fusobacteria). Other commonly found genera included Actinomyces, Anaerobaculum, Halospirulina, Pseudomonas, Mycoplasma, and Shewanella. Twelve phyla of bacteria including Proteobacteria, Firmicutes, Fusobacteria, Actinobacteria, Cyanobacteria, Tenericutes, Deinococcus-Thermus, Planctomycetes, Spirochaetes, Synergistetes, Thermotogae, and Verrucomicrobia were represented in the sequences. Additionally, strictly anaerobic bacteria such as Propionigenium and Fusibacter were found. These intestinal bacterial communities varied significantly among different commercial farms and were distinct from their rearing water. The results provide descriptive structures of the intestinal bacterial communities of P. monodon in commercial farms, which can further be applied to areas of research on the immunity, disease resistance, and nutrition of shrimp to improve aquaculture of the black tiger shrimp.}, }
@article {pmid21915631, year = {2012}, author = {Olapade, OA}, title = {Diel fluctuations in the abundance and community diversity of coastal bacterioplankton assemblages over a tidal cycle.}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {96-102}, pmid = {21915631}, issn = {1432-184X}, mesh = {Bacteria/genetics/*isolation &amp; purification ; Bacterial Typing Techniques ; Bacteroidetes/genetics/isolation &amp; purification ; Bays/*microbiology ; California ; Cyanobacteria/genetics/isolation &amp; purification ; Cytophaga/genetics/isolation &amp; purification ; DNA, Bacterial/analysis/genetics ; Flavobacterium/genetics/isolation &amp; purification ; Genetic Variation ; *Microbial Consortia ; Molecular Sequence Data ; Pacific Ocean ; Plankton/*physiology ; Proteobacteria/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; *Tidal Waves ; }, abstract = {The diel change in abundance and community diversity of the bacterioplankton assemblages within the Pacific Ocean at a fixed location in Monterey Bay, California (USA) were examined with several culture-independent (i.e., nucleic acid staining, fluorescence in situ hybridization {FISH}, and 16S ribosomal RNA gene libraries) approaches over a tidal cycle. FISH analyses revealed the quantitative predominance of bacterial members belonging to the Cytophaga-Flavobacterium cluster as well as two Proteobacteria (α- and γ-) subclasses within the bacterioplankton assemblages, especially during high tide (HT) and outgoing tide (OT) than the other tidal events. While the clone libraries showed that majority of the sequences were similar to the 16S rRNA gene sequences of unknown bacteria (32% to 73%), however, the operational taxonomic units from members of the α-Proteobacteria, Bacteroidetes, Firmicutes, and Cyanobacteria were also well represented during the four tidal events examined. Comparatively, sequence diversity was highest in OT, lowest in low tide, and very similar between HT and incoming tide. The results indicate that the dynamics of bacterial occurrence and diversity appeared to be more pronounced during HT and OT, further indicative of the ecological importance of several environmental variables including temperature, light intensity, and nutrient availability that are also concurrently fluctuating during these tidal events in marine systems.}, }
@article {pmid21910024, year = {2012}, author = {Qiu, M and Chen, X and Deng, D and Guo, J and Sun, G and Mai, B and Xu, M}, title = {Effects of electron donors on anaerobic microbial debromination of polybrominated diphenyl ethers (PBDEs).}, journal = {Biodegradation}, volume = {23}, number = {3}, pages = {351-361}, doi = {10.1007/s10532-011-9514-9}, pmid = {21910024}, issn = {1572-9729}, mesh = {Anaerobiosis ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Electron Transport ; Geologic Sediments/*microbiology ; Halogenated Diphenyl Ethers/*metabolism ; Halogenation ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Polybrominated diphenyl ethers (PBDEs) are a class of widely used flame retardants that have been highly accumulated in sediments. It is reported that microorganisms play an important role in the reductive debromination of PBDEs in anaerobic sediments. However, little is known about the effects of electron donors on the microbial community structure and their debromination capacity in PBDE transformation. In this study, alternate carbon substrates were used as electron donors to enrich the PBDE-debrominating microbial consortia to evaluate the effects of electron donors on PBDE microbial debromination. Decabromodiphenyl ether (BDE-209) was found to be the dominant (more than 50%) PBDEs congener in all consortia, and the percentage of BDE-209 was deceased by 12% (methanol), 11% (ethanol), 8% (acetate), 9% (lactate), 5% (pyruvate), and 11% (no electron donors), while the relative abundances of most lesser-brominated PBDEs increased after 90-day incubation compared to the initial profile of PBDEs. Substantial shifts in the microbial community structure among different amendments were observed based on denaturing gradient gel electrophoresis results. Pseudomonas spp. were identified to be the predominant organisms and the abundances of Band R, which was associated with Pseudomonas sp. SCSWA09, was well correlated with the biodegradation rate of BDE-209. Finally, the microbial community structure was highly correlated with the concentration of deca-BDE, octa-BDE and total nitrogen. These results provide insights into in situ bioremediation of environments contaminated by PBDEs and our understanding of microbial ecology associated with PBDE-debromination.}, }
@article {pmid21906041, year = {2011}, author = {Henneberger, R and Birch, D and Bergquist, P and Walter, M and Anitori, RP}, title = {The fluorescent dyes TO-PRO-3 and TOTO-3 iodide allow detection of microbial cells in soil samples without interference from background fluorescence.}, journal = {BioTechniques}, volume = {51}, number = {3}, pages = {190-192}, doi = {10.2144/000113736}, pmid = {21906041}, issn = {1940-9818}, mesh = {Bacteria/*isolation &amp; purification ; Carbocyanines/*analysis/chemistry ; Fluorescent Dyes/*analysis/chemistry ; In Situ Hybridization, Fluorescence/*methods ; Quinolines/*analysis/chemistry ; *Soil Microbiology ; Thiazoles/*analysis/chemistry ; }, abstract = {Visualization of microorganisms in soils and sediments using fluorescent dyes is a common method in microbial ecology studies, but is often hampered by strong nonspecific background fluorescence that can mask genuine cellular signals. The cyanine nucleic acid binding dyes TO-PRO-3 and TOTO-3 iodide enabled a clear detection of microbial cells in a mineral soil, while nonspecific background was greatly reduced compared with commonly used dyes. When used as counterstains for fluorescence in situ hybridization (FISH), both cyanine dyes allowed identification of microbial cells despite strong background from nonspecifically bound probes. TO-PRO-3 and TOTO-3 are easy to use and represent superior alternatives for detecting microorganisms in soil environments.}, }
@article {pmid21904954, year = {2012}, author = {Di Giuseppe, G and Cervia, D and Vallesi, A}, title = {Divergences in the response to ultraviolet radiation between polar and non-polar ciliated protozoa: UV radiation effects in Euplotes.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {334-338}, pmid = {21904954}, issn = {1432-184X}, mesh = {Ecosystem ; Euplotes/classification/growth &amp; development/*radiation effects ; Phylogeny ; Species Specificity ; Time Factors ; *Ultraviolet Rays ; }, abstract = {Ultraviolet (UV) radiation has detrimental effects on marine ecosystems, in particular in the polar regions where stratospheric ozone reduction causes higher levels of solar radiation. We analyzed two polar species of Euplotes, Euplotes focardii and Euplotes nobilii, for the sensitivity to UV radiation in comparison with two akin species from mid-latitude and tropical waters. Results showed that they face UV radiation much more efficiently than the non-polar species by adopting alternative strategies that most likely reflect different times of colonization of the polar waters. While E. focardii, which is endemic to the Antarctic, survives for longer exposed to UV radiation, E. nobilii, which inhabits both the Antarctic and Arctic, recovers faster from UV-induced damage.}, }
@article {pmid21901521, year = {2012}, author = {Procópio, L and Alvarez, VM and Jurelevicius, DA and Hansen, L and Sørensen, SJ and Cardoso, JS and Pádula, M and Leitão, AC and Seldin, L and van Elsas, JD}, title = {Insight from the draft genome of Dietzia cinnamea P4 reveals mechanisms of survival in complex tropical soil habitats and biotechnology potential.}, journal = {Antonie van Leeuwenhoek}, volume = {101}, number = {2}, pages = {289-302}, pmid = {21901521}, issn = {1572-9699}, mesh = {Actinomycetales/classification/enzymology/*genetics/growth &amp; development/isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; Biotechnology ; Ecosystem ; *Genome, Bacterial ; Microbial Viability ; Molecular Sequence Data ; Phylogeny ; *Soil Microbiology ; }, abstract = {The draft genome of Dietzia cinnamea strain P4 was determined using pyrosequencing. In total, 428 supercontigs were obtained and analyzed. We here describe and interpret the main features of the draft genome. The genome contained a total of 3,555,295 bp, arranged in a single replicon with an average G+C percentage of 70.9%. It revealed the presence of complete pathways for basically all central metabolic routes. Also present were complete sets of genes for the glyoxalate and reductive carboxylate cycles. Autotrophic growth was suggested to occur by the presence of genes for aerobic CO oxidation, formate/formaldehyde oxidation, the reverse tricarboxylic acid cycle and the 3-hydropropionate cycle for CO(2) fixation. Secondary metabolism was evidenced by the presence of genes for the biosynthesis of terpene compounds, frenolicin, nanaomycin and avilamycin A antibiotics. Furthermore, a probable role in azinomycin B synthesis, an important product with antitumor activity, was indicated. The complete alk operon for the degradation of n-alkanes was found to be present, as were clusters of genes for biphenyl ring dihydroxylation. This study brings new insights in the genetics and physiology of D. cinnamea P4, which is useful in biotechnology and bioremediation.}, }
@article {pmid21898103, year = {2012}, author = {İnceoğlu, &#xd6; and Falcão Salles, J and van Elsas, JD}, title = {Soil and cultivar type shape the bacterial community in the potato rhizosphere.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {460-470}, pmid = {21898103}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification/metabolism ; Biodiversity ; DNA Fingerprinting ; DNA, Bacterial/analysis/genetics ; Denaturing Gradient Gel Electrophoresis ; Phylogeny ; Plant Roots/chemistry/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/analysis/genetics ; Rhizosphere ; Soil/*analysis ; Solanum tuberosum/genetics/*microbiology ; }, abstract = {The rhizospheres of five different potato cultivars (including a genetically modified cultivar) obtained from a loamy sand soil and two from a sandy peat soil, next to corresponding bulk soils, were studied with respect to their community structures and potential function. For the former analyses, we performed bacterial 16S ribosomal RNA gene-based PCR denaturing gradient gel electrophoresis (PCR-DGGE) on the basis of soil DNA; for the latter, we extracted microbial communities and subjected these to analyses in phenotype arrays (PM1, PM2, and PM4, Biolog), with a focus on the use of different carbon, sulfur and phosphorus sources. In addition, we performed bacterial PCR-DGGE on selected wells to assess the structures of these substrate-responsive communities. Effects of soil type, the rhizosphere, and cultivar on the microbial community structures were clearly observed. Soil type was the most determinative parameter shaping the functional communities, whereas the rhizosphere and cultivar type also exerted an influence. However, no genetically modified plant effect was observed. The effects were imminent based on general community analysis and also single-compound analysis. Utilization of some of the carbon and sulfur sources was specific per cultivar, and different microbial communities were found as defined by cultivar. Thus, both soil and cultivar type shaped the potato root-associated bacterial communities that were responsive to some of the substrates in phenotype arrays.}, }
@article {pmid21898102, year = {2012}, author = {Stibal, M and Telling, J and Cook, J and Mak, KM and Hodson, A and Anesio, AM}, title = {Environmental controls on microbial abundance and activity on the greenland ice sheet: a multivariate analysis approach.}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {74-84}, pmid = {21898102}, issn = {1432-184X}, mesh = {Autotrophic Processes ; Bacteria/*growth &amp; development ; Bacterial Typing Techniques ; Cyanobacteria/growth &amp; development ; Ecosystem ; Greenland ; Heterotrophic Processes ; Ice Cover/*microbiology ; Multivariate Analysis ; Phototrophic Processes ; Viridiplantae/*growth &amp; development ; Viruses/growth &amp; development ; }, abstract = {Microbes in supraglacial ecosystems have been proposed to be significant contributors to regional and possibly global carbon cycling, and quantifying the biogeochemical cycling of carbon in glacial ecosystems is of great significance for global carbon flow estimations. Here we present data on microbial abundance and productivity, collected along a transect across the ablation zone of the Greenland ice sheet (GrIS) in summer 2010. We analyse the relationships between the physical, chemical and biological variables using multivariate statistical analysis. Concentrations of debris-bound nutrients increased with distance from the ice sheet margin, as did both cell numbers and activity rates before reaching a peak (photosynthesis) or a plateau (respiration, abundance) between 10 and 20 km from the margin. The results of productivity measurements suggest an overall net autotrophy on the GrIS and support the proposed role of ice sheet ecosystems in carbon cycling as regional sinks of CO(2) and places of production of organic matter that can be a potential source of nutrients for downstream ecosystems. Principal component analysis based on chemical and biological data revealed three clusters of sites, corresponding to three 'glacier ecological zones', confirmed by a redundancy analysis (RDA) using physical data as predictors. RDA using data from the largest 'bare ice zone' showed that glacier surface slope, a proxy for melt water flow, accounted for most of the variation in the data. Variation in the chemical data was fully explainable by the determined physical variables. Abundance of phototrophic microbes and their proportion in the community were identified as significant controls of the carbon cycling-related microbial processes.}, }
@article {pmid21892672, year = {2012}, author = {Bressan, A and Terlizzi, F and Credi, R}, title = {Independent origins of vectored plant pathogenic bacteria from arthropod-associated Arsenophonus endosymbionts.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {628-638}, pmid = {21892672}, issn = {1432-184X}, mesh = {Animals ; Beta vulgaris/*microbiology ; Enterobacteriaceae/classification/genetics/*isolation &amp; purification/*physiology ; Female ; Fragaria/*microbiology ; Hemiptera/*microbiology/physiology ; Male ; Molecular Sequence Data ; Phylogeny ; Plant Diseases/*microbiology ; *Symbiosis ; }, abstract = {The genus Arsenophonus (Gammaproteobacteria) is comprised of intracellular symbiotic bacteria that are widespread across the arthropods. These bacteria can significantly influence the ecology and life history of their hosts. For instance, Arsenophonus nasoniae causes an excess of females in the progeny of parasitoid wasps by selectively killing the male embryos. Other Arsenophonus bacteria have been suspected to protect insect hosts from parasitoid wasps or to expand the host plant range of phytophagous sap-sucking insects. In addition, a few reports have also documented some Arsenophonus bacteria as plant pathogens. The adaptation to a plant pathogenic lifestyle seems to be promoted by the infection of sap-sucking insects in the family Cixiidae, which then transmit these bacteria to plants during the feeding process. In this study, we define the specific localization of an Arsenophonus bacterium pathogenic to sugar beet and strawberry plants within the plant hosts and the insect vector, Pentastiridius leporinus (Hemiptera: Cixiidae), using fluorescence in situ hybridization assays. Phylogenetic analysis on 16S rRNA and nucleotide coding sequences, using both maximum likelihood and Bayesian criteria, revealed that this bacterium is not a sister taxon to "Candidatus Phlomobacter fragariae," a previously characterized Arsenophonus bacterium pathogenic to strawberry plants in France and Japan. Ancestral state reconstruction analysis indicated that the adaptation to a plant pathogenic lifestyle likely evolved from an arthropod-associated lifestyle and showed that within the genus Arsenophonus, the plant pathogenic lifestyle arose independently at least twice. We also propose a novel Candidatus status, "Candidatus Arsenophonus phytopathogenicus" novel species, for the bacterium associated with sugar beet and strawberry diseases and transmitted by the planthopper P. leporinus.}, }
@article {pmid21890669, year = {2011}, author = {Berry, D and Ben Mahfoudh, K and Wagner, M and Loy, A}, title = {Barcoded primers used in multiplex amplicon pyrosequencing bias amplification.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {21}, pages = {7846-7849}, pmid = {21890669}, issn = {1098-5336}, support = {P 20185/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {DNA Primers/*genetics ; *Diagnostic Errors ; Polymerase Chain Reaction/*methods ; Polymorphism, Restriction Fragment Length ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; }, abstract = {"Barcode-tagged" PCR primers used for multiplex amplicon sequencing generate a thus-far-overlooked amplification bias that produces variable terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing data from the same environmental DNA template. We propose a simple two-step PCR approach that increases reproducibility and consistently recovers higher genetic diversity in pyrosequencing libraries.}, }
@article {pmid21887519, year = {2012}, author = {Laghdass, M and Catala, P and Caparros, J and Oriol, L and Lebaron, P and Obernosterer, I}, title = {High contribution of SAR11 to microbial activity in the north west Mediterranean Sea.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {324-333}, pmid = {21887519}, issn = {1432-184X}, mesh = {Adenosine Triphosphate/metabolism ; Alphaproteobacteria/*growth &amp; development/*metabolism ; Amino Acids/metabolism ; Autoradiography ; Carbon/metabolism ; Ecosystem ; France ; Glucose/metabolism ; In Situ Hybridization, Fluorescence ; Indoles/chemistry ; Leucine/metabolism ; Mediterranean Sea ; Nitrogen/metabolism ; Phosphorus/metabolism ; Seasons ; Seawater/*microbiology ; }, abstract = {We investigated the abundance and activity of SAR11 on a monthly time scale between January 2008 and October 2008 in the oligotrophic NW Mediterranean Sea. Applying MICRO-CARD-FISH, we observed that SAR11 had a large contribution to bulk abundance (37 ± 6% of DAPI-stained cells) and to bulk bacterial heterotrophic production (BHP), as estimated from leucine incorporation (55 ± 15% of DAPI-cells assimilating leucine) in surface waters (5 m) throughout the study period. SAR11 contributed also substantially to the assimilation of glucose, ATP, and a combination of amino acids (44 ± 17%, 37 ± 14%, and 43 ± 12% of DAPI cells assimilating these compounds, respectively), organic compounds that provide either single or combined sources of C, P, and N. Temporal changes in the abundance of SAR11 cells that assimilated leucine, glucose, amino acids, and ATP revealed a pattern consistent with that of substrate-active DAPI cells, suggesting that the activity of SAR11 can explain to a large extent the variability in total cells contributing to the utilization of these compounds. Short-term nutrient enrichment experiments performed on each sampling date revealed a strong co-limitation of at least two of the three elements analyzed (C, N, P), in particular, during summer and early autumn. The in situ abundance of SAR11 cells assimilating leucine appeared to increase with P limitation as determined in the nutrient enrichment experiments (r = 0.81, p = 0.015). Our results demonstrate that SAR11 is an important component of the active bacterial community in the NW Mediterranean Sea. Our observations further indicate that the activity of the bulk bacterial community is linked to the activity of SAR11, possibly due to its adaptation to nutrient limitation.}, }
@article {pmid21886785, year = {2011}, author = {Inceoğlu, &#xd6; and Al-Soud, WA and Salles, JF and Semenov, AV and van Elsas, JD}, title = {Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing.}, journal = {PloS one}, volume = {6}, number = {8}, pages = {e23321}, pmid = {21886785}, issn = {1932-6203}, mesh = {*Agriculture ; Bacteria/classification/*genetics ; Cluster Analysis ; Flowers/physiology ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Seasons ; Sequence Analysis, DNA/*methods ; Soil Microbiology ; Solanum tuberosum/growth &amp; development/*microbiology ; *Temperature ; }, abstract = {BACKGROUND: Plants selectively attract particular soil microorganisms, in particular consumers of root-excreted compounds. It is unclear to what extent cultivar type and/or growth stage affect this process.<br><br>DNA-based pyrosequencing was used to characterize the structure of bacterial communities in a field cropped with potato. The rhizospheres of six cultivars denoted Aveka, Aventra, Karnico, Modena, Premiere and Desiree, at three growth stages (young, flowering and senescence) were examined, in addition to corresponding bulk soils. Around 350,000 sequences were obtained (5,700 to 38,000 per sample). Across all samples, rank abundance distributions best fitted the power law model, which indicates a community composed of a few highly dominant species next to numerous rare species. Grouping of the sequences showed that members of the Actinobacteria, Alphaproteobacteria, next to as-yet-unclassified bacteria, dominated. Other groups that were consistently found, albeit at lower abundance, were Beta-, Gamma- and Deltaproteobacteria and Acidobacteria. Principal components analyses revealed that rhizosphere samples were significantly different from corresponding bulk soil in each growth stage. Furthermore, cultivar effects were found in the young plant stage, whereas these became insignificant in the flowering and senescence stages. Besides, an effect of time of season was observed for both rhizosphere and bulk soils. The analyzed rhizosphere samples of the potato cultivars were grouped into two groups, in accordance with the allocation of carbon to starch in their tubers, i.e. Aveka, Aventra and Karnico (high) versus Premiere and Desiree (low) and thus replicates per group were established.<br><br>CONCLUSIONS: Across all potato cultivars, the young plant stages revealed cultivar-dependent bacterial community structures, which disappeared in the flowering and senescence stages. Furthermore, Pseudomonas, Beta-, Alpha- and Deltaproteobacteria flourished under different ecological conditions than the Acidobacteria.}, }
@article {pmid21883787, year = {2011}, author = {Van den Abbeele, P and Gérard, P and Rabot, S and Bruneau, A and El Aidy, S and Derrien, M and Kleerebezem, M and Zoetendal, EG and Smidt, H and Verstraete, W and Van de Wiele, T and Possemiers, S}, title = {Arabinoxylans and inulin differentially modulate the mucosal and luminal gut microbiota and mucin-degradation in humanized rats.}, journal = {Environmental microbiology}, volume = {13}, number = {10}, pages = {2667-2680}, doi = {10.1111/j.1462-2920.2011.02533.x}, pmid = {21883787}, issn = {1462-2920}, mesh = {Animals ; Bacteria/drug effects/genetics/metabolism ; Cecum/*microbiology ; Colon/*microbiology ; Feces/microbiology ; Fermentation ; Humans ; Inulin/*pharmacology ; Male ; Metagenome/*drug effects ; Mucins/*metabolism ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Prebiotics ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Inbred F344 ; Xylans/*pharmacology ; Young Adult ; }, abstract = {The endogenous gut microbiota affects the host in many ways. Prebiotics should favour beneficial intestinal microbes and thus improve host health. In this study, we investigated how a novel class of potential prebiotic long-chain arabinoxylans (LC-AX) and the well-established prebiotic inulin (IN) modulate the gut microbiota of humanized rats. Six weeks after axenic rats were inoculated with a human faecal microbiota, their colonic microbiota was similar to this inoculum (∼ 70%), whereas their caecal microbiota was enriched with Verrucomicrobia and Firmicutes concomitant with lower abundance of Bacteroidetes. Moreover, different Bifidobacterium species colonized the lumen (B. adolescentis) and mucus (B. longum and B. bifidum). Both LC-AX and IN increased SCFA levels and induced a shift from acetate towards health-promoting propionate and butyrate respectively. By applying a high-resolution phylogenetic micro-array (HITChip) at the site of fermentation (caecum), IN and LC-AX were shown to stimulate bacterial groups with known butyrate-producers (Roseburia intestinalis, Eubacterium rectale, Anaerostipes caccae) and bifidobacteria (B. longum) respectively. Prebiotic administration also resulted in lower caecal abundances of the mucin-degrading Akkermansia muciniphila and potentially more mucin production by the host. Both factors might explain the increased caecal mucin levels for LC-AX (threefold) and IN (sixfold). These mucins were degraded along the colon, resulting in high faecal abundances of Akkermansia muciniphila for LC-AX and especially IN-treated rats. Finally, the microbial changes caused an adaptation period for the host with less weight gain, after which the host fine-tuned the interaction with this altered microbiota. Our results demonstrate that next to IN, LC-AX are promising prebiotic compounds by stimulating production of health-promoting metabolites by specific microbes in the proximal regions. Further, prebiotic supplementation shifted mucin degradation to distal regions, where mucin-degraders may produce beneficial metabolites (e.g. propionate by Akkermansia muciniphila), so that prebiotics may potentially improve gut health along the entire length of the intestine.}, }
@article {pmid21882071, year = {2011}, author = {Pollock, JL and Kogan, LA and Thorpe, AS and Holben, WE}, title = {(±)-catechin, a root exudate of the invasive centaurea stoebe lam. (Spotted knapweed) exhibits bacteriostatic activity against multiple soil bacterial populations.}, journal = {Journal of chemical ecology}, volume = {37}, number = {9}, pages = {1044-1053}, pmid = {21882071}, issn = {1573-1561}, mesh = {Bacteria/growth &amp; development ; Catechin/*metabolism ; Centaurea/*metabolism ; Plant Roots/*metabolism ; *Soil Microbiology ; }, abstract = {Understanding the effects of allelopathic plant chemicals on soil microorganisms is critical to understanding their ecological roles and importance in exotic plant invasion. Centaurea stoebe Lam. (spotted knapweed), an aggressive invasive weed in North America, secretes a racemic mixture of (±)-catechin as a root exudate. This enantiomeric, polyphenolic compound has been reported to have allelopathic effects on surrounding flora and microflora. To better understand how catechin affects microbial communities in the root zone of spotted knapweed, we assessed its impact on the total culturable bacterial component and numerous individual bacterial populations from Romanian (native range) and Montana (invaded range) soils. Catechin suppressed total culturable count numbers from the bacterial community and inhibited growth of some, but not all, soil bacterial populations tested. The native soil bacterial community was significantly more resistant to inhibitory effects of catechin than either the invaded or non-invaded soils. We further show that the inhibitory effect of catechin on nine different soil bacterial strains from seven genera was reversible, demonstrating that it acts via a bacteriostatic rather than bactericidal mechanism. These findings suggest that catechin might affect bacterial community composition and activity in the root zone.}, }
@article {pmid21881944, year = {2012}, author = {Chaban, B and Links, MG and Hill, JE}, title = {A molecular enrichment strategy based on cpn60 for detection of epsilon-proteobacteria in the dog fecal microbiome.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {348-357}, pmid = {21881944}, issn = {1432-184X}, mesh = {Animals ; Bacterial Proteins/*genetics ; Bacteriological Techniques/methods ; Chaperonin 60/*genetics ; Diarrhea/microbiology/*veterinary ; Dog Diseases/*microbiology ; Dogs/*microbiology ; Epsilonproteobacteria/*classification/genetics/*isolation &amp; purification ; Feces/*microbiology ; Metagenome ; Sequence Analysis, DNA ; }, abstract = {Members of the rare microbiome can be important components of complex microbial communities. For example, pet dog ownership is a known risk factor for human campylobacteriosis, and Campylobacter is commonly detected in dog feces by targeted assays. However, these organisms have not been detected by metagenomic methods. The goal of this study was to characterize fecal microbiota from healthy and diarrheic pet dogs using two different levels of molecular detection. PCR amplification and pyrosequencing of the universal cpn60 gene target was used to obtain microbial profiles from each dog. To investigate the relatively rare epsilon-proteobacteria component of the microbiome, a molecular enrichment was carried out using a PCR that first amplified the cpn10-cpn60 region from epsilon-proteobacteria, followed by universal cpn60 target amplification and pyrosequencing. From the non-enriched survey, the major finding was a significantly higher proportion of Bacteroidetes, notably Bacteroides vulgatus, in healthy dogs compared to diarrheic dogs. Epsilon-proteobacteria from the genera Helicobacter and Campylobacter were also detected at a low level in the non-enriched profiles of some dogs. Molecular enrichment increased the proportion of epsilon-proteobacteria sequences detected from each dog, as well as identified novel, presumably rare sequences not seen in the non-enriched profiles. Enriched profiles contained known species of Arcobacter, Campylobacter, Flexispira, and Helicobacter and identified two possibly novel species. These findings add to our understanding of the canine fecal microbiome in general, the epsilon-proteobacteria component specifically, and present a novel modification to traditional metagenomic approaches for study of the rare microbiome.}, }
@article {pmid21881943, year = {2012}, author = {Soto, E and Revan, F}, title = {Culturability and persistence of Francisella noatunensis subsp. orientalis (syn. Francisella asiatica) in sea- and freshwater microcosms.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {398-404}, pmid = {21881943}, issn = {1432-184X}, mesh = {Animals ; *Cichlids ; Colony Count, Microbial ; Fish Diseases/*microbiology/mortality ; Francisella/growth &amp; development/*isolation &amp; purification/pathogenicity ; Fresh Water/microbiology ; Gram-Negative Bacterial Infections/microbiology/mortality/*veterinary ; Hot Temperature ; Real-Time Polymerase Chain Reaction ; Salinity ; Seawater/microbiology ; Time Factors ; }, abstract = {Francisella noatunensis subsp. orientalis (syn. Francisella asiatica), the causative agent of franciselliosis in warm-water fish, is a Gram-negative facultative intracellular bacterium. Although it has been characterized as one of the most pathogenic bacteria in fish, the water conditions that allow for its survival and infectious capacities outside the fish host are not known. Data obtained in this project indicate that both temperature and salinity are important factors in the culturability and persistence of F. noatunensis subsp. orientalis in both sea- and freshwater microcosms. These results indicate that culturable F. noatunensis subsp. orientalis persist for longer periods of time and at higher numbers in seawater, and its persistence is inversely related to water temperature. Moreover, the pathogenic properties of the bacteria suspended in water microcosms appear to decrease after only 24 h and become non-infective after 2 days in the absence of the fish host.}, }
@article {pmid21880051, year = {2011}, author = {Jin, YO and Mattes, TE}, title = {Assessment and modification of degenerate qPCR primers that amplify functional genes from etheneotrophs and vinyl chloride-assimilators.}, journal = {Letters in applied microbiology}, volume = {53}, number = {5}, pages = {576-580}, doi = {10.1111/j.1472-765X.2011.03144.x}, pmid = {21880051}, issn = {1472-765X}, mesh = {Bacteria/*genetics ; Biodegradation, Environmental ; DNA Primers/genetics ; Ethylenes/*metabolism ; Genes, Bacterial/genetics ; Groundwater/microbiology ; Polymerase Chain Reaction/methods ; Vinyl Chloride/*metabolism ; }, abstract = {AIMS: Degenerate qPCR primer sets that target the functional genes etnC and etnE in etheneotrophs and vinyl chloride-assimilating bacteria were assessed and modified in an effort to improve performance.<br><br>METHODS AND RESULTS: Functional gene abundance in four pure cultures was estimated by qPCR using novel (MRTC and MRTE) and existing (RTC and RTE) degenerate primer sets and compared to abundances estimated with nondegenerate gene-specific primers (GSPs). Functional gene abundance in groundwater DNA extracted from several contaminated sites was also estimated with MRTC and MRTE primers.<br><br>CONCLUSIONS: MRTC primers displayed significantly improved etnC quantification in both pure cultures and environmental samples.<br><br>Application of MRTC and MRTE primer sets will enhance microbial ecology studies involving etheneotrophs and qPCR analyses that support vinyl chloride bioremediation strategies.}, }
@article {pmid21877727, year = {2011}, author = {De Corte, S and Hennebel, T and Fitts, JP and Sabbe, T and Bliznuk, V and Verschuere, S and van der Lelie, D and Verstraete, W and Boon, N}, title = {Biosupported bimetallic Pd-Au nanocatalysts for dechlorination of environmental contaminants.}, journal = {Environmental science &amp; technology}, volume = {45}, number = {19}, pages = {8506-8513}, doi = {10.1021/es2019324}, pmid = {21877727}, issn = {1520-5851}, mesh = {Biodegradation, Environmental ; Catalysis ; Chemical Precipitation ; Diclofenac/isolation &amp; purification ; Environmental Pollutants/*isolation &amp; purification ; Gold/*chemistry ; *Halogenation ; Hydrogen-Ion Concentration ; Kinetics ; Metals/*chemistry ; Nanoparticles/*chemistry/ultrastructure ; Palladium/*chemistry ; Shewanella/*metabolism/ultrastructure ; Time Factors ; Trichloroethylene/isolation &amp; purification ; X-Ray Diffraction ; }, abstract = {Biologically produced monometallic palladium nanoparticles (bio-Pd) have been shown to catalyze the dehalogenation of environmental contaminants, but fail to efficiently catalyze the degradation of other important recalcitrant halogenated compounds. This study represents the first report of biologically produced bimetallic Pd/Au nanoparticle catalysts. The obtained catalysts were tested for the dechlorination of diclofenac and trichlorethylene. When aqueous bivalent Pd(II) and trivalent Au(III) ions were both added to concentrations of 50 mg L(-1) and reduced simultaneously by Shewanella oneidensis in the presence of H(2), the resulting cell-associated bimetallic nanoparticles (bio-Pd/Au) were able to dehalogenate 78% of the initially added diclofenac after 24 h; in comparison, no dehalogenation was observed using monometallic bio-Pd or bio-Au. Other catalyst-synthesis strategies did not show improved dehalogenation of TCE and diclofenac compared with bio-Pd. Synchrotron-based X-ray diffraction, (scanning) transmission electron microscopy and energy dispersive X-ray spectroscopy indicated that the simultaneous reduction of Pd and Au supported on cells of S. oneidensis resulted in the formation of a unique bimetallic crystalline structure. This study demonstrates that the catalytic activity and functionality of possibly environmentally more benign biosupported Pd-catalysts can be improved by coprecipitation with Au.}, }
@article {pmid21873232, year = {2011}, author = {Libkind, D and Hittinger, CT and Valério, E and Gonçalves, C and Dover, J and Johnston, M and Gonçalves, P and Sampaio, JP}, title = {Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {35}, pages = {14539-14544}, pmid = {21873232}, issn = {1091-6490}, support = {R01 GM032540/GM/NIGMS NIH HHS/United States ; GM032540/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Classification ; Ecology ; Molecular Sequence Data ; Saccharomyces cerevisiae/classification/*genetics ; }, abstract = {Domestication of plants and animals promoted humanity's transition from nomadic to sedentary lifestyles, demographic expansion, and the emergence of civilizations. In contrast to the well-documented successes of crop and livestock breeding, processes of microbe domestication remain obscure, despite the importance of microbes to the production of food, beverages, and biofuels. Lager-beer, first brewed in the 15th century, employs an allotetraploid hybrid yeast, Saccharomyces pastorianus (syn. Saccharomyces carlsbergensis), a domesticated species created by the fusion of a Saccharomyces cerevisiae ale-yeast with an unknown cryotolerant Saccharomyces species. We report the isolation of that species and designate it Saccharomyces eubayanus sp. nov. because of its resemblance to Saccharomyces bayanus (a complex hybrid of S. eubayanus, Saccharomyces uvarum, and S. cerevisiae found only in the brewing environment). Individuals from populations of S. eubayanus and its sister species, S. uvarum, exist in apparent sympatry in Nothofagus (Southern beech) forests in Patagonia, but are isolated genetically through intrinsic postzygotic barriers, and ecologically through host-preference. The draft genome sequence of S. eubayanus is 99.5% identical to the non-S. cerevisiae portion of the S. pastorianus genome sequence and suggests specific changes in sugar and sulfite metabolism that were crucial for domestication in the lager-brewing environment. This study shows that combining microbial ecology with comparative genomics facilitates the discovery and preservation of wild genetic stocks of domesticated microbes to trace their history, identify genetic changes, and suggest paths to further industrial improvement.}, }
@article {pmid21873204, year = {2011}, author = {Sul, WJ and Cole, JR and Jesus, Eda C and Wang, Q and Farris, RJ and Fish, JA and Tiedje, JM}, title = {Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {35}, pages = {14637-14642}, pmid = {21873204}, issn = {1091-6490}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics ; *Cluster Analysis ; RNA, Ribosomal, 16S/genetics ; *Sequence Alignment ; }, abstract = {High-throughput sequencing of 16S rRNA genes has increased our understanding of microbial community structure, but now even higher-throughput methods to the Illumina scale allow the creation of much larger datasets with more samples and orders-of-magnitude more sequences that swamp current analytic methods. We developed a method capable of handling these larger datasets on the basis of assignment of sequences into an existing taxonomy using a supervised learning approach (taxonomy-supervised analysis). We compared this method with a commonly used clustering approach based on sequence similarity (taxonomy-unsupervised analysis). We sampled 211 different bacterial communities from various habitats and obtained ∼1.3 million 16S rRNA sequences spanning the V4 hypervariable region by pyrosequencing. Both methodologies gave similar ecological conclusions in that β-diversity measures calculated by using these two types of matrices were significantly correlated to each other, as were the ordination configurations and hierarchical clustering dendrograms. In addition, our taxonomy-supervised analyses were also highly correlated with phylogenetic methods, such as UniFrac. The taxonomy-supervised analysis has the advantages that it is not limited by the exhaustive computation required for the alignment and clustering necessary for the taxonomy-unsupervised analysis, is more tolerant of sequencing errors, and allows comparisons when sequences are from different regions of the 16S rRNA gene. With the tremendous expansion in 16S rRNA data acquisition underway, the taxonomy-supervised approach offers the potential to provide more rapid and extensive community comparisons across habitats and samples.}, }
@article {pmid21865034, year = {2011}, author = {Garcia-Peña, EI and Parameswaran, P and Kang, DW and Canul-Chan, M and Krajmalnik-Brown, R}, title = {Anaerobic digestion and co-digestion processes of vegetable and fruit residues: process and microbial ecology.}, journal = {Bioresource technology}, volume = {102}, number = {20}, pages = {9447-9455}, doi = {10.1016/j.biortech.2011.07.068}, pmid = {21865034}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Ecology ; Fruit/*metabolism ; Hydrogen-Ion Concentration ; Mexico ; Polymerase Chain Reaction ; Vegetables/*metabolism ; }, abstract = {This study evaluated the feasibility of methane production from fruit and vegetable waste (FVW) obtained from the central food distribution market in Mexico City using an anaerobic digestion (AD) process. Batch systems showed that pH control and nitrogen addition had significant effects on biogas production, methane yield, and volatile solids (VS) removal from the FVW (0.42 m(biogas)(3)/kg VS, 50%, and 80%, respectively). Co-digestion of the FVW with meat residues (MR) enhanced the process performance and was also evaluated in a 30 L AD system. When the system reached stable operation, its methane yield was 0.25 (m(3)/kg TS), and the removal of the organic matter measured as the total chemical demand (tCOD) was 65%. The microbial population (general Bacteria and Archaea) in the 30 L system was also determined and characterized and was closely correlated with its potential function in the AD system.}, }
@article {pmid21864878, year = {2011}, author = {Serrano, D and Suárez, S and Lema, JM and Omil, F}, title = {Removal of persistent pharmaceutical micropollutants from sewage by addition of PAC in a sequential membrane bioreactor.}, journal = {Water research}, volume = {45}, number = {16}, pages = {5323-5333}, doi = {10.1016/j.watres.2011.07.037}, pmid = {21864878}, issn = {1879-2448}, mesh = {Base Sequence ; *Bioreactors ; DNA Primers ; In Situ Hybridization, Fluorescence ; *Membranes, Artificial ; Pharmaceutical Preparations/*isolation &amp; purification ; Sewage/*chemistry ; Water Pollutants, Chemical/*isolation &amp; purification ; }, abstract = {The performance of a membrane bioreactor operating in a sequential mode (SMBR) using an external flat-plate membrane was investigated. After 200 days of operation, a single addition of 1 g L(-1) Powdered Activated Carbon (PAC) was added directly into the mixed liquor in order to enhance the simultaneous removal of nutrients and pharmaceutical micropollutants from synthetic urban wastewater. Throughout the entire operation (288 days), Chemical Oxygen Demand (COD) removal efficiencies were up to 95%, ammonium nitrogen removal was maintained over 70-80%, whereas phosphorus removal achieved only high values (around 80%) after PAC addition. During the operation of the SMBR without PAC addition, micropollutants which exerted a more recalcitrant behaviour were carbamazepine, diazepam, diclofenac and trimethoprim, with no significant removal. On the other hand, moderate removals (42-64%) were observed for naproxen and erythromycin, whereas ibuprofen, roxithromycin and fluoxetine were removed in the range of 71-97%. The addition of PAC into the aeration tank was a successful tool to improve the removal of the more recalcitrant compounds up to 85%. The highest removal with PAC was observed for carbamazepine, trimethoprim as well as for roxithromycin, erythromycin and fluoxetine. The latter four compounds have amine groups and pKa in the range 6.7-10.1, thus the interaction between PAC and the positively charged amino groups might be the cause of their comparatively better results. Microbial ecology present in the biomass showed a higher abundance of Accumulibacter phosphatis as well as the ammonium oxidizing bacteria belonging to the genus Nitrosomonas after PAC addition.}, }
@article {pmid21858215, year = {2011}, author = {Steger, D and Berry, D and Haider, S and Horn, M and Wagner, M and Stocker, R and Loy, A}, title = {Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion.}, journal = {PloS one}, volume = {6}, number = {8}, pages = {e23727}, pmid = {21858215}, issn = {1932-6203}, support = {P 18836/FWF_/Austrian Science Fund FWF/Austria ; P 20185/FWF_/Austrian Science Fund FWF/Austria ; R21 EB008844/EB/NIBIB NIH HHS/United States ; 1-R21-EB008844/EB/NIBIB NIH HHS/United States ; }, mesh = {Algorithms ; Diffusion ; Models, Chemical ; Models, Genetic ; Nucleic Acid Hybridization/*methods ; Nucleic Acid Probes/chemistry/*genetics ; Nucleic Acids/chemistry/*genetics ; Oligonucleotide Array Sequence Analysis/*methods ; Reproducibility of Results ; Surface Properties ; }, abstract = {BACKGROUND: The hybridization of nucleic acid targets with surface-immobilized probes is a widely used assay for the parallel detection of multiple targets in medical and biological research. Despite its widespread application, DNA microarray technology still suffers from several biases and lack of reproducibility, stemming in part from an incomplete understanding of the processes governing surface hybridization. In particular, non-random spatial variations within individual microarray hybridizations are often observed, but the mechanisms underpinning this positional bias remain incompletely explained.<br><br>This study identifies and rationalizes a systematic spatial bias in the intensity of surface hybridization, characterized by markedly increased signal intensity of spots located at the boundaries of the spotted areas of the microarray slide. Combining observations from a simplified single-probe block array format with predictions from a mathematical model, the mechanism responsible for this bias is found to be a position-dependent variation in lateral diffusion of target molecules. Numerical simulations reveal a strong influence of microarray well geometry on the spatial bias.<br><br>CONCLUSIONS: Reciprocal adjustment of the size of the microarray hybridization chamber to the area of surface-bound probes is a simple and effective measure to minimize or eliminate the diffusion-based bias, resulting in increased uniformity and accuracy of quantitative DNA microarray hybridization.}, }
@article {pmid21858036, year = {2011}, author = {Sannasiddappa, TH and Costabile, A and Gibson, GR and Clarke, SR}, title = {The influence of Staphylococcus aureus on gut microbial ecology in an in vitro continuous culture human colonic model system.}, journal = {PloS one}, volume = {6}, number = {8}, pages = {e23227}, pmid = {21858036}, issn = {1932-6203}, mesh = {Bacteria/genetics/*growth &amp; development/metabolism ; Butyric Acid/metabolism ; Colon/*microbiology ; *Ecosystem ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Tract/*microbiology ; Humans ; In Situ Hybridization, Fluorescence ; Metagenome/genetics ; Models, Biological ; Staphylococcal Infections/microbiology ; Staphylococcus aureus/genetics/*growth &amp; development/metabolism ; Time Factors ; Tissue Culture Techniques/instrumentation/methods ; }, abstract = {An anaerobic three-stage continuous culture model of the human colon (gut model), which represent different anatomical areas of the large intestine, was used to study the effect of S. aureus infection of the gut on the resident faecal microbiota. Studies on the development of the microbiota in the three vessels were performed and bacteria identified by culture independent fluorescence in situ hybridization (FISH). Furthermore, short chain fatty acids (SCFA), as principal end products of gut bacterial metabolism, were measured along with a quantitative assessment of the predominant microbiota. During steady state conditions, numbers of S. aureus cells stabilised until they were washed out, but populations of indigenous bacteria were transiently altered; thus S. aureus was able to compromise colonisation resistance by the colonic microbiota. Furthermore, the concentration of butyric acid in the vessel representing the proximal colon was significantly decreased by infection. Thus infection by S. aureus appears to be able to alter the overall structure of the human colonic microbiota and the microbial metabolic profiles. This work provides an initial in vitro model to analyse interactions with pathogens.}, }
@article {pmid21857972, year = {2011}, author = {Coll-Lladó, M and Acinas, SG and Pujades, C and Pedrós-Alió, C}, title = {Transcriptome fingerprinting analysis: an approach to explore gene expression patterns in marine microbial communities.}, journal = {PloS one}, volume = {6}, number = {8}, pages = {e22950}, pmid = {21857972}, issn = {1932-6203}, mesh = {Base Sequence ; Chlorophyta/classification/genetics ; DNA Fingerprinting/*methods ; DNA Primers/genetics ; *Ecosystem ; Gene Expression Profiling/*methods ; Metagenomics/methods ; RNA, Messenger/genetics/metabolism ; Reproducibility of Results ; Reverse Transcriptase Polymerase Chain Reaction ; Seawater/*microbiology ; *Transcriptome ; }, abstract = {Microbial transcriptomics are providing new insights into the functional processes of microbial communities. However, analysis of each sample is still expensive and time consuming. A rapid and low cost method that would allow the identification of the most interesting samples for posterior in-depth metatranscriptomics analysis would be extremely useful. Here we present Transcriptome Fingerprinting Analysis (TFA) as an approach to fulfill this objective in microbial ecology studies. We have adapted the differential display technique for mRNA fingerprinting based on the PCR amplification of expressed transcripts to interrogate natural microbial eukaryotic communities. Unlike other techniques, TFA does not require prior knowledge of the mRNA sequences to be detected. We have used a set of arbitrary primers coupled with a fluorescence labeled primer targeting the poly(A) tail of the eukaryotic mRNA, with further detection of the resulting labeled cDNA products in an automated genetic analyzer. The output represented by electropherogram peak patterns allowed the comparison of a set of genes expressed at the time of sampling. TFA has been optimized by testing the sensitivity of the method for different initial RNA amounts, and the repeatability of the gene expression patterns with increasing time after sampling both with cultures and environmental samples. Results show that TFA is a promising approach to explore the dynamics of gene expression patterns in microbial communities.}, }
@article {pmid21850447, year = {2012}, author = {Chen, H and Fu, L and Luo, L and Lu, J and White, WL and Hu, Z}, title = {Induction and resuscitation of the viable but nonculturable state in a cyanobacteria-lysing bacterium isolated from cyanobacterial bloom.}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {64-73}, pmid = {21850447}, issn = {1432-184X}, mesh = {Actinomycetales/classification/isolation &amp; purification/metabolism/*physiology ; Antibiosis ; Aquatic Organisms ; Cyanobacteria/growth &amp; development/*metabolism ; DNA, Bacterial/analysis ; DNA, Ribosomal/genetics ; Lakes/*microbiology ; *Microbial Viability ; Microcystis/growth &amp; development/*metabolism ; RNA, Ribosomal, 16S/genetics ; Rhodobacteraceae/classification/isolation &amp; purification/metabolism/*physiology ; Sequence Analysis, DNA ; Staphylococcus/classification/isolation &amp; purification/metabolism/*physiology ; }, abstract = {The viable but nonculturable (VBNC) state has been found to be a growth strategy used by many aquatic pathogens; however, few studies have focused on VBNC state on other aquatic bacterial groups. The purpose of this study was to explore the VBNC state of cyanobacteria-lysing bacteria and the conditions that regulate their VBNC state transformation. Three cyanobacteria-lysing heterotrophic bacterial strains (F1, F2 and F3) were isolated with liquid infection method from a lake that has experienced a cyanobacterial bloom. According to their morphological, physiological and biochemical characteristics and results of 16SrDNA sequence analysis, F1, F2 and F3 were identified as strains of Staphylococcus sp., Stappia sp. and Microbacterium sp., respectively. After being co-cultured with the axenic cyanobacterium, Microcystis aeruginosa 905, for 7 days, strains F1, F2 and F3 exhibited an inhibition effect on cyanobacterial growth, which was expressed as a reduction in chlorophyll concentration of 96.0%, 94.9% and 84.8%, respectively. Both autoclaved and filtered bacterial cultures still showed lytic effects on cyanobacterial cells while centrifuged pellets were less efficient than other fractions. This indicated that lytic factors were extracelluar and heat-resistant. The environmental conditions that could induce the VBNC state of strain F1 were also studied. Under low temperature (4°C), distilled deionized water (DDW) induced almost 100% of F1 cells to the VBNC state after 6 days while different salinities (1%, 3% and 5% of NaCl solution) and lake water required 18 days. A solution of the cyanobacterial toxin microcystin-LR (MC-LR) crude extract also induced F1 to the VBNC state, and the effect was stronger than DDW. Even the lowest MC-LR concentration (10 μg L(-1)) could induce 69.7% of F1 cells into VBNC state after 24 h. On the other hand, addition of Microcystis aeruginosa cells caused resuscitation of VBNC state F1 cells within 1 day, expressed as an increase of viable cell number and a decrease of VBNC ratio. Both VBNC state and culturable state F1 cells showed lytic effects on cyanobacteria, with their VBNC ratio varying during co-culturing with cyanobacteria. The findings indicated that VBNC state transformation of cyanobacteria-lysing bacteria could be regulated by cyanobacterial cells or their toxin, and the transformation may play an important role in cyanobacterial termination.}, }
@article {pmid21850446, year = {2012}, author = {Suárez-Moreno, ZR and Caballero-Mellado, J and Coutinho, BG and Mendonça-Previato, L and James, EK and Venturi, V}, title = {Common features of environmental and potentially beneficial plant-associated Burkholderia.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {249-266}, pmid = {21850446}, issn = {1432-184X}, mesh = {Burkholderia/*classification/genetics/*physiology ; Fungi/physiology ; Magnoliopsida/*microbiology/physiology ; Phylogeny ; Species Specificity ; *Symbiosis ; }, abstract = {The genus Burkholderia comprises more than 60 species isolated from a wide range of niches. Although they have been shown to be diverse and ubiquitously distributed, most studies have thus far focused on the pathogenic species due to their clinical importance. However, the increasing number of recently described Burkholderia species associated with plants or with the environment has highlighted the division of the genus into two main clusters, as suggested by phylogenetical analyses. The first cluster includes human, animal, and plant pathogens, such as Burkholderia glumae, Burkholderia pseudomallei, and Burkholderia mallei, as well as the 17 defined species of the Burkholderia cepacia complex, while the other, more recently established cluster comprises more than 30 non-pathogenic species, which in most cases have been found to be associated with plants, and thus might be considered to be potentially beneficial. Several species from the latter group share characteristics that are of use when associating with plants, such as a quorum sensing system, the presence of nitrogen fixation and/or nodulation genes, and the ability to degrade aromatic compounds. This review examines the commonalities in this growing subgroup of Burkholderia species and discusses their prospective biotechnological applications.}, }
@article {pmid21845446, year = {2012}, author = {Kahlisch, L and Henne, K and Gröbe, L and Brettar, I and Höfle, MG}, title = {Assessing the viability of bacterial species in drinking water by combined cellular and molecular analyses.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {383-397}, pmid = {21845446}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/*isolation &amp; purification ; Colony Count, Microbial ; DNA Fingerprinting/*methods ; DNA, Bacterial/genetics ; Drinking Water/*microbiology ; Flow Cytometry ; Microbial Viability ; Molecular Sequence Data ; Organic Chemicals/chemistry ; Polymerase Chain Reaction ; Polymorphism, Single-Stranded Conformational ; Propidium/chemistry ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The question which bacterial species are present in water and if they are viable is essential for drinking water safety but also of general relevance in aquatic ecology. To approach this question we combined propidium iodide/SYTO9 staining ("live/dead staining" indicating membrane integrity), fluorescence-activated cell sorting (FACS) and community fingerprinting for the analysis of a set of tap water samples. Live/dead staining revealed that about half of the bacteria in the tap water had intact membranes. Molecular analysis using 16S rRNA and 16S rRNA gene-based single-strand conformation polymorphism (SSCP) fingerprints and sequencing of drinking water bacteria before and after FACS sorting revealed: (1) the DNA- and RNA-based overall community structure differed substantially, (2) the community retrieved from RNA and DNA reflected different bacterial species, classified as 53 phylotypes (with only two common phylotypes), (3) the percentage of phylotypes with intact membranes or damaged cells were comparable for RNA- and DNA-based analyses, and (4) the retrieved species were primarily of aquatic origin. The pronounced difference between phylotypes obtained from DNA extracts (dominated by Betaproteobacteria, Bacteroidetes, and Actinobacteria) and from RNA extracts (dominated by Alpha-, Beta-, Gammaproteobacteria, Bacteroidetes, and Cyanobacteria) demonstrate the relevance of concomitant RNA and DNA analyses for drinking water studies. Unexpected was that a comparable fraction (about 21%) of phylotypes with membrane-injured cells was observed for DNA- and RNA-based analyses, contradicting the current understanding that RNA-based analyses represent the actively growing fraction of the bacterial community. Overall, we think that this combined approach provides an interesting tool for a concomitant phylogenetic and viability analysis of bacterial species of drinking water.}, }
@article {pmid21838709, year = {2011}, author = {Frans, I and Michiels, CW and Bossier, P and Willems, KA and Lievens, B and Rediers, H}, title = {Vibrio anguillarum as a fish pathogen: virulence factors, diagnosis and prevention.}, journal = {Journal of fish diseases}, volume = {34}, number = {9}, pages = {643-661}, doi = {10.1111/j.1365-2761.2011.01279.x}, pmid = {21838709}, issn = {1365-2761}, mesh = {Animals ; Fish Diseases/*diagnosis/*microbiology/*prevention &amp; control ; Gene Expression Regulation, Bacterial/*physiology ; Iron/metabolism ; Lipopolysaccharides ; Microscopy, Electron ; Quorum Sensing/*physiology ; Siderophores/metabolism ; Vibrio/*pathogenicity/ultrastructure ; Vibrio Infections/diagnosis/prevention &amp; control/*veterinary ; Virulence Factors/metabolism ; }, abstract = {Vibrio anguillarum, also known as Listonella anguillarum, is the causative agent of vibriosis, a deadly haemorrhagic septicaemic disease affecting various marine and fresh/brackish water fish, bivalves and crustaceans. In both aquaculture and larviculture, this disease is responsible for severe economic losses worldwide. Because of its high morbidity and mortality rates, substantial research has been carried out to elucidate the virulence mechanisms of this pathogen and to develop rapid detection techniques and effective disease-prevention strategies. This review summarizes the current state of knowledge pertaining to V. anguillarum, focusing on pathogenesis, known virulence factors, diagnosis, prevention and treatment.}, }
@article {pmid21837472, year = {2012}, author = {de Melo Pereira, GV and Magalhães, KT and Lorenzetii, ER and Souza, TP and Schwan, RF}, title = {A multiphasic approach for the identification of endophytic bacterial in strawberry fruit and their potential for plant growth promotion.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {405-417}, pmid = {21837472}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/*isolation &amp; purification/metabolism ; Colony Count, Microbial ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Endophytes/classification/genetics/isolation &amp; purification/metabolism ; Fragaria/*growth &amp; development/*microbiology ; Indoleacetic Acids/metabolism ; Molecular Sequence Data ; Nitrogen Fixation ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Siderophores/metabolism ; }, abstract = {This study used a multiphasic approach, characterized by the simultaneous use of culture-dependent and culture-independent methods, to investigate endophytic bacterial communities in strawberry (Fragaria ananassa) fruit. A total of 92 bacterial endophytes were isolated and initially grouped by their repetitive extragenic palindromic (rep)-PCR banding pattern and biochemical features. Phylogenetic analysis of the 16S rRNA gene sequences of 45 representatives showed that the isolates belonged to the species Bacillus subtilis (eight isolates), Bacillus sp. (seven isolates), Enterobacter sp. (seven isolates), Enterobacter ludwigii (six isolates), Lactobacillus plantarum (six isolates), Pseudomonas sp. (five isolates), Pantoea punctata (three isolates), and Curtobacterium citreum (three isolates). Nucleic acids were extracted from the strawberry fruit and subjected to 16S rRNA gene directed polymerase chain reaction denaturing gradient gel electrophoresis (16S rRNA PCR-DGGE). The species B. subtilis, Enterobacter sp., and Pseudomonas sp. were detected both by isolation and DGGE. The DGGE fingerprints of total bacterial DNA did not exhibit bands corresponding to several of the representative species isolated in the extinction dilution (L. plantarum, C. citreum, and P. punctata). In contrast, bands in the DGGE profile that were identified as relatives of Arthrobacter sp. and one uncultivable Erythrobacter sp. were not recovered by cultivation techniques. After isolation, the nitrogen fixation ability and the in vitro production of indole-3-acetic acid (IAA) equivalents and siderophores were evaluated. A high percentage of isolates were found to possess the ability to produce siderophores and IAA equivalents; however, only a few isolates belonging to the genera Pseudomonas and Enterobacter showed the ability to fix nitrogen. Plant growth promotion was evaluated under greenhouse conditions and revealed the ability of the Bacillus strains to enhance the number of leaves, shoot length, root dry weight, and shoot dry weight. The activity of the bacterial isolate identified as B. subtilis NA-108 exerted the greatest influence on strawberry growth and showed a 42.8% increase in number of leaves, 15.26% for high shoot, 43.5% increase in root dry weight, and a 77% increase in shoot dry weight when compared with untreated controls.}, }
@article {pmid21833540, year = {2012}, author = {Yurkov, A and Krüger, D and Begerow, D and Arnold, N and Tarkka, MT}, title = {Basidiomycetous yeasts from boletales fruiting bodies and their interactions with the mycoparasite Sepedonium chrysospermum and the host fungus Paxillus.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {295-303}, pmid = {21833540}, issn = {1432-184X}, mesh = {Ascomycota/classification/genetics/isolation &amp; purification/physiology ; Basidiomycota/classification/genetics/isolation &amp; purification/*physiology ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Ecosystem ; Fruiting Bodies, Fungal/classification/genetics/physiology ; Germany ; Hypocreales/*growth &amp; development/physiology ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal, 28S/genetics ; Species Specificity ; Yeasts/classification/*genetics/*isolation &amp; purification/physiology ; }, abstract = {Interactions between mushrooms, yeasts, and parasitic fungi are probably common in nature, but are rarely described. Bolete fruiting bodies are associated with a broad spectrum of microorganisms including yeasts, and they are commonly infected with filamentous mycoparasites of the genus Sepedonium (teleomorph Hypomyces). We report the isolation of 17 yeast strains from Paxillus and Xerocomus, 16 of which were obtained from the surface tissue, the primary site of Sepedonium infection. Phylogenetic analyses with the D1/D2 region of the 28S ribosomal gene and the internal transcribed spacers placed the yeasts as Rhodotorula, Rhodosporidium, and Mastigobasidium from the Pucciniomycotina, Cryptococcus, Cystofilobasidium, Holtermanniella, and Trichosporon from the Agaricomycotina, and Kluyveromyces from the Saccharomycotina including the first isolation of Rhodotorula graminis from Europe. To investigate the influence of the yeast strains on the mycoparasite and the host fungus, in vitro assays were conducted with Sepedonium chrysospermum and Paxillus involutus. Both S. chrysospermum growth inhibitory and stimulating yeast strains were detected among the isolates. The number of S. chrysospermum inhibitory yeast strains increased and the number of S. chrysospermum stimulatory yeast strains decreased in the presence of P. involutus in co-cultures. Low nutrient levels in the culture medium also led to an increased number of S. chrysospermum inhibitory yeast strains and ten yeasts inhibited the mycoparasite in spatial separation by a crosswall. Six yeast strains inhibited P. involutus in dual culture, and the inhibitory P. involutus yeast interactions increased to nine in the presence of S. chrysospermum. Our results suggest that the bolete-associated yeasts influence the growth of the mycoparasitic fungus, which may affect the health of the fruiting bodies.}, }
@article {pmid21833539, year = {2012}, author = {Chochlakis, D and Ioannou, I and Sandalakis, V and Dimitriou, T and Kassinis, N and Papadopoulos, B and Tselentis, Y and Psaroulaki, A}, title = {Spotted fever group Rickettsiae in ticks in Cyprus.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {314-323}, pmid = {21833539}, issn = {1432-184X}, mesh = {Animals ; Antigens, Bacterial/genetics ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Proteins/genetics ; Canidae ; Citrate (si)-Synthase/genetics ; Cyprus ; Hares ; Ixodidae/*microbiology ; Molecular Sequence Data ; Polymerase Chain Reaction ; Rickettsia/*classification/genetics/*isolation &amp; purification ; Rickettsia Infections/epidemiology/microbiology/parasitology/veterinary ; Ruminants ; Seasons ; Sequence Analysis, DNA ; Species Specificity ; Tick-Borne Diseases/epidemiology/microbiology/parasitology/veterinary ; }, abstract = {In two surveys conducted from March 1999 to March 2001 and from January 2004 to December 2006, a total of 3,950 ticks (belonging to ten different species) were collected from seven domestic and wild animals (goat, sheep, cattle, dog, fox, hare, and mouflon) from different localities throughout Cyprus. In order to establish their infection rate with Spotted Fever Rickettsiae (SFG), ticks were pooled and tested by polymerase chain reaction targeting gltA and ompA genes, followed by sequencing analysis. When tick pools tested positive, individual ticks were then tested one by one, and of the 3,950 ticks screened, rickettsial DNA was identified in 315 ticks (infection rate, 8%). Five SFG Rickettsiae were identified: Rickettsia aeschlimannii in Hyalomma marginatum marginatum, Rickettsia massiliae in Rhipicephalus turanicus and Rhipicephalus sanguineus, Rickettsia sibirica mongolotimonae in Hyalomma anatolicum excavatum, and a Rickettsia endosymbiont of Haemaphysalis sulcata (later described as Rickettsia hoogstraalii) in Haemaphysalis punctata. Two additional genes, 17 kDa and ompB, were targeted to characterize a new genotype of "Candidatus Rickettsia barbariae" genotype in R. turanicus, designated here as "Candidatus Rickettsia barbariae" Cretocypriensis. These results confirm the presence of a spectrum of SFG Rickettsiae on the island. Further studies are necessary to gain better knowledge on the epidemiology of SFG Rickettsiae in Cyprus.}, }
@article {pmid21833037, year = {2012}, author = {Toenshoff, ER and Penz, T and Narzt, T and Collingro, A and Schmitz-Esser, S and Pfeiffer, S and Klepal, W and Wagner, M and Weinmaier, T and Rattei, T and Horn, M}, title = {Bacteriocyte-associated gammaproteobacterial symbionts of the Adelges nordmannianae/piceae complex (Hemiptera: Adelgidae).}, journal = {The ISME journal}, volume = {6}, number = {2}, pages = {384-396}, pmid = {21833037}, issn = {1751-7370}, support = {P 22533/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Gammaproteobacteria/*classification/genetics/*physiology/ultrastructure ; Hemiptera/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; *Symbiosis ; }, abstract = {Adelgids (Insecta: Hemiptera: Adelgidae) are known as severe pests of various conifers in North America, Canada, Europe and Asia. Here, we present the first molecular identification of bacteriocyte-associated symbionts in these plant sap-sucking insects. Three geographically distant populations of members of the Adelges nordmannianae/piceae complex, identified based on coI and ef1alpha gene sequences, were investigated. Electron and light microscopy revealed two morphologically different endosymbionts, coccoid or polymorphic, which are located in distinct bacteriocytes. Phylogenetic analyses of their 16S and 23S rRNA gene sequences assigned both symbionts to novel lineages within the Gammaproteobacteria sharing <92% 16S rRNA sequence similarity with each other and showing no close relationship with known symbionts of insects. Their identity and intracellular location were confirmed by fluorescence in situ hybridization, and the names 'Candidatus Steffania adelgidicola' and 'Candidatus Ecksteinia adelgidicola' are proposed for tentative classification. Both symbionts were present in all individuals of all investigated populations and in different adelgid life stages including eggs, suggesting vertical transmission from mother to offspring. An 85 kb genome fragment of 'Candidatus S. adelgidicola' was reconstructed based on a metagenomic library created from purified symbionts. Genomic features including the frequency of pseudogenes, the average length of intergenic regions and the presence of several genes which are absent in other long-term obligate symbionts, suggested that 'Candidatus S. adelgidicola' is an evolutionarily young bacteriocyte-associated symbiont, which has been acquired after diversification of adelgids from their aphid sister group.}, }
@article {pmid21829326, year = {2011}, author = {Arslan, BK and Boyd, ES and Dolci, WW and Dodson, KE and Boldt, MS and Pilcher, CB}, title = {Workshops Without Walls: broadening access to science around the world.}, journal = {PLoS biology}, volume = {9}, number = {8}, pages = {e1001118}, pmid = {21829326}, issn = {1545-7885}, mesh = {Access to Information ; *Education, Distance/economics ; Exobiology/education ; International Cooperation ; Science/*education ; Social Media ; United States ; United States National Aeronautics and Space Administration ; Videoconferencing ; }, abstract = {The National Aeronautics and Space Administration (NASA) Astrobiology Institute (NAI) conducted two "Workshops Without Walls" during 2010 that enabled global scientific exchange--with no travel required. The second of these was on the topic "Molecular Paleontology and Resurrection: Rewinding the Tape of Life." Scientists from diverse disciplines and locations around the world were joined through an integrated suite of collaborative technologies to exchange information on the latest developments in this area of origin of life research. Through social media outlets and popular science blogs, participation in the workshop was broadened to include educators, science writers, and members of the general public. In total, over 560 people from 31 US states and 30 other nations were registered. Among the scientific disciplines represented were geochemistry, biochemistry, molecular biology and evolution, and microbial ecology. We present this workshop as a case study in how interdisciplinary collaborative research may be fostered, with substantial public engagement, without sustaining the deleterious environmental and economic impacts of travel.}, }
@article {pmid21826491, year = {2012}, author = {Caburlotto, G and Bianchi, F and Gennari, M and Ghidini, V and Socal, G and Aubry, FB and Bastianini, M and Tafi, M and Lleo, MM}, title = {Integrated evaluation of environmental parameters influencing Vibrio occurrence in the coastal Northern Adriatic Sea (Italy) facing the Venetian lagoon.}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {20-31}, pmid = {21826491}, issn = {1432-184X}, mesh = {Aquatic Organisms/*isolation &amp; purification ; Climate ; Geologic Sediments/*microbiology ; Italy ; Plankton/microbiology ; Salinity ; Seawater/*microbiology ; Vibrio/*classification/*isolation &amp; purification ; Water Microbiology ; }, abstract = {In the marine environment, the persistence and abundance of Vibrio are related to a number of environmental parameters. The influence of the different environmental variables in determining the Vibrio occurrence could be different in the specific geographic areas around the world. Moreover, oceanographic parameters are generally interdependent and should not be considered separately when their influence on bacterial presence and concentration is tested. In this study, an integrated approach was used to identify key parameters determining the abundance of Vibrio spp in marine samples from the Venetian Lagoon in Italy, which is an important area for fish farming and tourism. Multivariate techniques have been adopted to analyze the dataset: using PCA, it was shown that a relatively high proportion of the total variance in this area was mainly due to two independent variables, namely salinity and temperature. Using cluster analysis, it was possible to categorize different groups with homogeneous features as regards space ("stations") and time ("seasons") distribution, as well as to quantify the values of environmental variables and the Vibrio abundances in each category. Furthermore, integrating key environmental factors and bacterial concentration values, it was possible to identify levels of salinity and sea surface temperature which were optimal for Vibrio concentration in water, plankton, and sediment samples. The identification of key environmental variables conditioning Vibrio occurrence should facilitate ocean monitoring, making it possible to predict unexpected variations in marine microflora which determine possible public health risks in coastal areas.}, }
@article {pmid21826490, year = {2012}, author = {Banitz, T and Johst, K and Wick, LY and Fetzer, I and Harms, H and Frank, K}, title = {The relevance of conditional dispersal for bacterial colony growth and biodegradation.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {339-347}, pmid = {21826490}, issn = {1432-184X}, mesh = {Bacteria/*growth &amp; development/*metabolism ; Biodegradation, Environmental ; Environment ; Models, Biological ; Pseudomonas putida/*growth &amp; development/*metabolism ; Soil Pollutants/metabolism ; }, abstract = {Bacterial degradation is an ecosystem service that offers a promising method for the remediation of contaminated soils. To assess the dynamics and efficiency of bacterial degradation, reliable microbial simulation models, along with the relevant processes, are required. We present an approach aimed at improving reliability by studying the relevance and implications of an important concept from theoretical ecology in the context of a bacterial system: conditional dispersal denoting that the dispersal strategy depends on environmental conditions. Different dispersal strategies, which either incorporate or neglect this concept, are implemented in a bacterial model and results are compared to data obtained from laboratory experiments with Pseudomonas putida colonies growing on glucose agar. Our results show that, with respect to the condition of resource uptake, the model's correspondence to experimental data is significantly higher for conditional than for unconditional bacterial dispersal. In particular, these results support the hypothesis that bacteria disperse less when resources are abundant. We also show that the dispersal strategy has a considerable impact on model predictions for bacterial degradation of resources: disregarding conditional bacterial dispersal can lead to overestimations when assessing the performance of this ecosystem service.}, }
@article {pmid21825123, year = {2011}, author = {Burke, C and Steinberg, P and Rusch, D and Kjelleberg, S and Thomas, T}, title = {Bacterial community assembly based on functional genes rather than species.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {34}, pages = {14288-14293}, pmid = {21825123}, issn = {1091-6490}, mesh = {Bacteria/classification/*genetics/*growth &amp; development ; *Biota ; Colony Count, Microbial ; Genes, Bacterial/*genetics ; Molecular Sequence Annotation ; Species Specificity ; Ulva/*microbiology ; }, abstract = {The principles underlying the assembly and structure of complex microbial communities are an issue of long-standing concern to the field of microbial ecology. We previously analyzed the community membership of bacterial communities associated with the green macroalga Ulva australis, and proposed a competitive lottery model for colonization of the algal surface in an attempt to explain the surprising lack of similarity in species composition across different algal samples. Here we extend the previous study by investigating the link between community structure and function in these communities, using metagenomic sequence analysis. Despite the high phylogenetic variability in microbial species composition on different U. australis (only 15% similarity between samples), similarity in functional composition was high (70%), and a core of functional genes present across all algal-associated communities was identified that were consistent with the ecology of surface- and host-associated bacteria. These functions were distributed widely across a variety of taxa or phylogenetic groups. This observation of similarity in habitat (niche) use with respect to functional genes, but not species, together with the relative ease with which bacteria share genetic material, suggests that the key level at which to address the assembly and structure of bacterial communities may not be "species" (by means of rRNA taxonomy), but rather the more functional level of genes.}, }
@article {pmid21822970, year = {2011}, author = {Taubert, M and Baumann, S and von Bergen, M and Seifert, J}, title = {Exploring the limits of robust detection of incorporation of 13C by mass spectrometry in protein-based stable isotope probing (protein-SIP).}, journal = {Analytical and bioanalytical chemistry}, volume = {401}, number = {6}, pages = {1975-1982}, doi = {10.1007/s00216-011-5289-4}, pmid = {21822970}, issn = {1618-2650}, mesh = {Bacterial Proteins/*metabolism ; Carbon Isotopes/*metabolism ; Isotope Labeling/*methods ; Proteomics/methods ; Pseudomonas fluorescens/*metabolism ; Sensitivity and Specificity ; Tandem Mass Spectrometry/*methods ; }, abstract = {One of the features of protein-based stable isotope probing is the parallel identification of differentially labeled peptide forms and the accurate calculation of their relative isotope abundances. The level of incorporation is informative of the metabolic activity of the species that synthesized the said protein and peptide. To model the carbon flux in a microbial community, an accurate assessment is crucial. Since the initial processes in carbon consumption are one of the most interesting objectives in microbial ecology, the methodology to detect low amounts of incorporation was tuned, and the limits of robust detection were analyzed. For this, Pseudomonas fluorescens DSM 50090T was grown on galactose using different ratios of (12)C/(13)C galactose from 10% down to 0.1% labeled galactose. After prolonged cultivation to ensure complete labeling, protein samples were separated by one-dimensional gel electrophoresis, subsequently tryptically digested and analyzed by ultra-performance liquid chromatography (UPLC) Orbitrap tandem mass spectrometry (MS/MS) measurements. The isotopic patterns from identified peptides in the mass spectra were used to calculate the (13)C relative isotope abundance (RIA) in the respective peptides. The statistic distribution of the RIA values in dependence of the number of analyzed peptides was compared between the different ratios of unlabeled/labeled substrate. The acquired data showed that the applied method is capable of detecting a difference in (13)C incorporation of ±0.1% RIA based on at least 20 peptides. This sensitivity makes protein-stable isotope probing a valuable method for quantitative assessment of species specific metabolic activity in metaproteomics.}, }
@article {pmid21822905, year = {2011}, author = {Ivey, ML and Phister, TG}, title = {Detection and identification of microorganisms in wine: a review of molecular techniques.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {38}, number = {10}, pages = {1619-1634}, pmid = {21822905}, issn = {1476-5535}, mesh = {Bacteria/genetics/*isolation &amp; purification ; Flow Cytometry ; Nucleic Acid Hybridization/methods ; Real-Time Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Wine/*microbiology ; Yeasts/genetics/*isolation &amp; purification ; }, abstract = {The microbial ecology of wine is complex. Microbes can play both positive and negative roles in the quality of the final product. Due to this impact, the microbial ecology of wine has been well studied. Traditional indirect methods, such as plating, have largely been replaced by a number of molecular methods. These methods are typically either indirect methods used for identification of cultured organisms, or direct methods used to profile whole populations or identify specific microbes in a mixed population. These molecular methods offer a number of advantages over traditional methods including speed and precision. This review will examine both direct and indirect molecular methods, provide examples of their impact on the study of the microbial ecology of wine, and also discuss their strengths and limitations.}, }
@article {pmid21821067, year = {2011}, author = {Cole, M and Wrubel, J and Henegan, P and Janzen, C and Holt, J and Tobin, T}, title = {Development of a small-scale bioreactor method to monitor the molecular diversity and environmental impacts of bacterial biofilm communities from an acid mine drainage impacted creek.}, journal = {Journal of microbiological methods}, volume = {87}, number = {1}, pages = {96-104}, doi = {10.1016/j.mimet.2011.07.015}, pmid = {21821067}, issn = {1872-8359}, mesh = {Biofilms/*growth &amp; development ; *Bioreactors ; Coal Mining ; Gram-Negative Bacteria/genetics/*physiology ; Gram-Positive Bacteria/genetics/*physiology ; Hydrogen-Ion Concentration ; Metals/analysis ; Models, Biological ; Oxidation-Reduction ; Pennsylvania ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Sulfur/analysis ; Water/analysis ; Water Pollution, Chemical ; }, abstract = {Shamokin Creek is a tributary of the Susquehanna River in central Pennsylvania that is heavily impacted by the acid mine drainage (AMD) caused by the oxidation of pyrite from the region's extensive anthracite coal mining industry. Recent studies have begun to characterize the microbial communities present in this and other AMD-impacted waters, but varying environmental conditions have complicated attempts to determine the ecological impacts of individual bacterial species within these communities. This study developed a small-scale biofilm reactor protocol that allowed us to simultaneously monitor the development of bacterial biofilm communities in AMD-impacted creek collected water using terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes, while assessing the impacts that the developing biofilms were having on water quality. Our analysis confirmed that the diversity and composition of these small in situ biofilm communities could be monitored using molecular methods, and indicated the possible presence of many taxa frequently found in AMD environments, including Sulfobacillus, Nitrospira, Desulfovibrio, Geobacter, and Leptothrix species. A significant increase in the total sulfate was observed in the bioreactor, and as most likely due to the accumulation of sulfur-oxidizing bacteria such as Sulfobacillus in the biofilms. This system will allow us to study the microbial ecology of Shamokin Creek through controlled experiments that will ultimately integrate microscopic, molecular, physiological and chemical analyses, and that can be utilized to develop more effective and cost-efficient environmental remediation techniques for AMD-impacted areas.}, }
@article {pmid21814872, year = {2012}, author = {Xu, M and Wang, B and Fu, Y and Chen, Y and Yang, F and Lu, H and Chen, Y and Xu, J and Li, L}, title = {Changes of fecal Bifidobacterium species in adult patients with hepatitis B virus-induced chronic liver disease.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {304-313}, pmid = {21814872}, issn = {1432-184X}, mesh = {Adult ; Bifidobacterium/*classification/genetics/isolation &amp; purification ; China ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Feces/microbiology ; Female ; Hepatitis B virus/physiology ; Hepatitis B, Chronic/*microbiology/virology ; Humans ; Intestines/*microbiology ; Liver Cirrhosis/microbiology/virology ; Male ; Middle Aged ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Probiotics/administration &amp; dosage ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The beneficial effects of Bifidobacteria on health have been widely accepted. Patients with chronic liver disease have varying degrees of intestinal microflora imbalance with a decrease of total Bifidobacterial counts. Since different properties have been attributed to different Bifidobacterium species and there is no information available for the detailed changes in the genus Bifidobacterium in patients with chronic liver disease heretofore, it is meaningful to investigate the structure of this bacterium at the species level in these patients. The aim of this study was to characterize the composition of intestinal Bifidobacterium in patients with hepatitis B virus-induced chronic liver disease. Nested-PCR-based denaturing gradient gel electrophoresis (PCR-DGGE), clone library, and real-time quantitative PCR were performed on the fecal samples of 16 patients with chronic hepatitis B (CHB patients), 16 patients with hepatitis B virus-related cirrhosis (HBV cirrhotics), and 15 healthy subjects (Controls). Though there was no significant difference in the diversity among the three groups (P = 0.196), Bifidobacterium dentium seems to be specifically enhanced in patients as the PCR-DGGE profiles showed, which was further validated by clone library and real-time quantitative PCR. In contrast to the B. dentium, Bifidobacterium catenulatum/Bifidobacterium pseudocatenulatum were detected less frequently in the predominant profile and by quantitative PCR in HBV cirrhotics than in the controls, and the level of this species was also significantly different between these two groups (P = 0.023). Although having no quantitative difference among the three groups, Bifidobacterium longum was less commonly detected in HBV cirrhotics than in CHB patients and Controls by quantitative PCR (P = 0.011). Thus, the composition of intestinal Bifidobacterium was deeply altered in CHB and HBV cirrhotic patients with a shift from beneficial species to opportunistic pathogens. The results provide further insights into the dysbiosis of the intestinal microbiota in patients with hepatitis B virus-induced chronic liver disease and might potentially serve as guidance for the probiotics interventions of these diseases.}, }
@article {pmid21811796, year = {2012}, author = {Chen, Z and Liu, J and Wu, M and Xie, X and Wu, J and Wei, W}, title = {Differentiated response of denitrifying communities to fertilization regime in paddy soil.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {446-459}, pmid = {21811796}, issn = {1432-184X}, mesh = {Bacteria/classification/*enzymology/genetics/*isolation &amp; purification ; Bacterial Proteins/*genetics ; China ; Denitrification ; Fertilizers/analysis ; Gene Dosage ; Molecular Sequence Data ; Nitrite Reductases/*genetics ; Oryza ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Real-Time Polymerase Chain Reaction ; Soil/analysis ; *Soil Microbiology ; }, abstract = {The impact of fertilization regimes on sequential denitrifying communities was investigated in a rice paddy field with 17 years continuous fertilization, located in Taoyuan Agro-ecosystem Research Station (110°72″ E, 28°52″ N), China. The diversity, community composition, and size of denitrifying genes of narG, qnorB, and nosZ were determined using molecular tools including terminal restriction fragment length polymorphism, quantitative polymerase chain reaction (qPCR), cloning, and sequencing analysis. Soil samples were collected from the plots with no fertilizer (NF), urea (UR), balanced mineral fertilizers (BM), and BM combined with rice straw (BMR). UR and BM caused marked increase in the community size of the denitrifying genes; however, BMR resulted in the highest abundance. The community size of narG was the most affected by the fertilization regimes, while qnorB was the least. Fertilization also induced some shifts in the composition of denitrifying genes, but the responses of different genes varied. However, fertilization regimes caused no significant changes to the diversity of the denitrifying genes. Potential denitrification activity (PDA) was significantly correlated with the abundance of narG and nosZ rather than qnorB, but there were no such correlations between PDA and the composition and diversity of denitrifying communities. Conclusively, long-term fertilization significantly affected denitrifying community size and composition, but not diversity. Among the sequential denitrifying genes, narG was the most, while qnorB was the least sensitive communities to fertilization regimes.}, }
@article {pmid21811795, year = {2012}, author = {Özen, AI and Ussery, DW}, title = {Defining the Pseudomonas genus: where do we draw the line with Azotobacter?.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {239-248}, pmid = {21811795}, issn = {1432-184X}, mesh = {Azotobacter vinelandii/*classification/*genetics ; Cellvibrio/classification/genetics ; Evolution, Molecular ; Gammaproteobacteria/classification/genetics ; *Genome, Bacterial ; *Phylogeny ; Pseudomonas/*classification/*genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {The genus Pseudomonas has gone through many taxonomic revisions over the past 100 years, going from a very large and diverse group of bacteria to a smaller, more refined and ordered list having specific properties. The relationship of the Pseudomonas genus to Azotobacter vinelandii is examined using three genomic sequence-based methods. First, using 16S rRNA trees, it is shown that A. vinelandii groups within the Pseudomonas close to Pseudomonas aeruginosa. Genomes from other related organisms (Acinetobacter, Psychrobacter, and Cellvibrio) are outside the Pseudomonas cluster. Second, pan genome family trees based on conserved gene families also show A. vinelandii to be more closely related to Pseudomonas than other related organisms. Third, exhaustive BLAST comparisons demonstrate that the fraction of shared genes between A. vinelandii and Pseudomonas genomes is similar to that of Pseudomonas species with each other. The results of these different methods point to a high similarity between A. vinelandii and the Pseudomonas genus, suggesting that Azotobacter might actually be a Pseudomonas.}, }
@article {pmid21811794, year = {2012}, author = {Wang, P and Shen, H and Xie, P}, title = {Can hydrodynamics change phosphorus strategies of diatoms?-Nutrient levels and diatom blooms in lotic and lentic ecosystems.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {369-382}, pmid = {21811794}, issn = {1432-184X}, mesh = {Alkaline Phosphatase/metabolism ; China ; Chlorophyll/analysis/metabolism ; Chlorophyll A ; Diatoms/growth &amp; development/isolation &amp; purification/*metabolism ; *Eutrophication ; Fresh Water/*chemistry ; *Hydrodynamics ; Phosphorus/analysis/*metabolism ; Photosynthesis ; Species Specificity ; }, abstract = {Diatom blooms occur in many water bodies worldwide, causing significant ecological and social concerns. In order to understand the mechanisms of diatom blooms formation, the effects of varying phosphorus (P) concentration and hydrodynamics on the growth of diatoms were studied by combining results from field observations and laboratory experiments. The field investigation showed that spring diatom blooms (Cyclotella meneghiniana and Stephanodiscus hantzschii) occurred in Lake Taihu and Hanjiang River with similar environmental factors such as water temperature, pH, and dissolved oxygen in 2008. Concentrations of total phosphorus (TP), total nitrogen, and ammonia nitrogen (NH(4)-N) in Lake Taihu were significantly higher than the concentrations in the Hanjiang River. Laboratory experiments were conducted to evaluate growth and physiological responses of four lotic diatoms (Cyclotella atomus, Fragilaria crotonensis, Nitzschia palea, and S. hantzschii, isolated from the Hanjiang River) and three lentic diatoms (C. meneghiniana, Melosira varians, and Stephanodiscus minutulus, isolated from Lake Taihu, Lake Donghu, and Guanqiao Pond, respectively) to various P concentrations under small-scale turbulent and standing conditions. Our results showed that, with turbulence, lotic diatoms C. atomus, F. crotonensis, N. palea, and S. hantzschii demonstrated a significant increase in affinity for P compared with lentic diatoms C. meneghiniana, M. varians, and S. minutulus. Moreover, lotic diatoms C. atomus, F. crotonensis, and N. palea had higher growth rates and photosynthetic efficiencies with small-scale turbulence than with standing conditions both in P-limited and P-replete conditions. Lotic species S. hantzschii and three lentic diatoms (C. meneghiniana, M. varians, and S. minutulus) grew well under standing conditions. Our results may explain our field observation that the occurrence of diatom blooms in lakes is often associated with higher TP concentrations whereas in rivers, diatom blooms occur at a wide range of TP concentrations under flows. Therefore, different hydrodynamics and nutrient concentrations determined the dominant diatom species, according to their habitat-dependent physiological characteristics.}, }
@article {pmid21811793, year = {2012}, author = {Wang, L and Oda, Y and Grewal, S and Morrison, M and Michel, FC and Yu, Z}, title = {Persistence of resistance to erythromycin and tetracycline in swine manure during simulated composting and lagoon treatments.}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {32-40}, pmid = {21811793}, issn = {1432-184X}, mesh = {Animal Husbandry ; Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Typing Techniques ; Drug Resistance, Multiple, Bacterial/*genetics ; Erythromycin/*pharmacology ; Escherichia coli/drug effects/genetics ; Feces/*microbiology ; Livestock/microbiology ; Microbial Sensitivity Tests ; RNA, Ribosomal, 16S/analysis ; Soil ; Swine ; Tetracycline Resistance/genetics ; Tetracyclines/*pharmacology ; }, abstract = {The use of antimicrobials in food animal production leads to the development of antimicrobial resistance (AMR), and animal manure constitutes the largest reservoir of such AMR. In previous studies, composted swine manure was found to contain substantially lower abundance of AMR genes that encode resistance to tetracyclines (tet genes) and macrolide-lincosamide-streptogramin B (MLS(B)) superfamily (erm genes), than manures that were treated by lagoons or biofilters. In this study, temporal changes in AMR carried by both cultivated and uncultivated bacteria present in swine manure during simulated composting and lagoon storage were analyzed. Treatments were designed to simulate the environmental conditions of composting (55°C with modest aeration) and lagoon storage (ambient temperature with modest aeration). As determined by selective plate counting, over a 48-day period, cultivated aerobic heterotrophic erythromycin-resistant bacteria and tetracycline-resistant bacteria decreased by more than 4 and 7 logs, respectively, in the simulated composting treatment while only 1 to 2 logs for both resistant bacterial groups in the simulated lagoon treatment. Among six classes each of erm and tet genes quantified by class-specific real-time PCR assays, the abundance of erm(A), erm(C), erm(F), erm(T), erm(X), tet(G), tet(M), tet(O), tet(T), and tet(W) declined marginally during the first 17 days, but dramatically thereafter within 31 days of the composting treatment. No appreciable reduction of any of the erm or tet genes analyzed was observed during the simulated lagoon treatment. Correlation analysis showed that most of the AMR gene classes had similar persistence pattern over the course of the treatments, though not all AMR genes were destructed at the same rate during the treatments.}, }
@article {pmid21811792, year = {2012}, author = {Ballor, NR and Paulsen, I and Leadbetter, JR}, title = {Genomic analysis reveals multiple [FeFe] hydrogenases and hydrogen sensors encoded by treponemes from the H(2)-rich termite gut.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {282-294}, pmid = {21811792}, issn = {1432-184X}, mesh = {Animals ; Bacterial Proteins/*genetics ; Formate Dehydrogenases/genetics/metabolism ; Gastrointestinal Tract/metabolism/microbiology ; Hydrogen/metabolism ; Hydrogenase/*genetics ; Isoptera/metabolism/*microbiology ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Treponema/classification/enzymology/*genetics/metabolism ; }, abstract = {We have completed a bioinformatic analysis of the hydrogenases encoded in the genomes of three termite gut treponeme isolates: hydrogenotrophic, homoacetogenic Treponema primitia strains ZAS-1 and ZAS-2, and the hydrogen-producing, sugar-fermenting Treponema azotonutricium ZAS-9. H(2) is an important free intermediate in the breakdown of wood by termite gut microbial communities, reaching concentrations in some species exceeding those measured for any other biological system. The spirochetes encoded 4, 8, and 5 [FeFe] hydrogenase-like proteins, identified by their H domains, respectively, but no other recognizable hydrogenases. The [FeFe] hydrogenases represented many sequence families previously proposed in an analysis of termite gut metagenomic data. Each strain encoded both putative [FeFe] hydrogenase enzymes and evolutionarily related hydrogen sensor/transducer proteins likely involved in phosphorelay or methylation pathways, and possibly even chemotaxis. A new family of [FeFe] hydrogenases (FDH-Linked) is proposed that may form a multimeric complex with formate dehydrogenase to provide reducing equivalents for reductive acetogenesis in T. primitia. The many and diverse [FeFe] hydrogenase-like proteins encoded within the sequenced genomes of the termite gut treponemes has enabled the discovery of a putative new class of [FeFe] hydrogenase proteins potentially involved in acetogenesis and furthered present understanding of many families, including sensory, of H domain proteins beyond what was possible through the use of fragmentary termite gut metagenome sequence data alone, from which they were initially defined.}, }
@article {pmid21811791, year = {2012}, author = {Karsten, U and Holzinger, A}, title = {Light, temperature, and desiccation effects on photosynthetic activity, and drought-induced ultrastructural changes in the green alga Klebsormidium dissectum (Streptophyta) from a high alpine soil crust.}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {51-63}, pmid = {21811791}, issn = {1432-184X}, mesh = {*Adaptation, Physiological ; Dehydration ; Droughts ; Light ; *Photosynthesis ; Soil ; Streptophyta/*metabolism/*ultrastructure ; Temperature ; }, abstract = {Members of the cosmopolitan green algal genus Klebsormidium (Klebsormidiales, Streptophyta) are typical components of terrestrial microbiotic communities such as biological soil crusts, which have many important ecological functions. In the present study, Klebsormidium dissectum (Gay) Ettl &amp; Gärtner was isolated from a high alpine soil crust in the Tyrolean Alps, Austria. Physiological performance in terms of growth and photosynthesis was investigated under different controlled abiotic conditions and compared with ultrastructural changes under the treatments applied. K. dissectum showed very low light requirements as reflected in growth patterns and photosynthetic efficiency. Increasing temperatures from 5°C to 40°C led to different effects on respiratory oxygen consumption and photosynthetic oxygen evolution. While at low temperatures (5-10°C), respiration was not detectable or on a very low level, photosynthesis was relatively high, Reversely, at the highest temperature, respiration was unaffected, and photosynthesis strongly inhibited pointing to strong differences in temperature sensitivity between both physiological processes. Although photosynthetic performance of K. dissectum was strongly affected under short-term desiccation and recovered only partly after rehydration, this species was capable to survive even 3 weeks at 5% relative air humidity. K. dissectum cells have a cell width of 5.6 ± 0.3 μm and a cell length of 8.4 ± 2.0 μm. Desiccated cells showed a strongly reduced cell width (46% of control) and cell length (65% of control). In addition, in desiccated cells, fewer mitochondria were stained by DIOC(6), and damaged plasma membranes were detected by FM 1-43 staining. High-pressure freeze fixation as well as chemical fixation allowed visualizing ultrastructural changes caused by desiccation. In such cells, the nucleus and chloroplast were still visibly intact, but the extremely thin cell walls (75-180 nm) were substantially deformed. The cytoplasm appeared electron dense and mitochondria were altered. Although K. dissectum can be characterized as euryoecious species, all ecophysiological and ultrastructural data indicate susceptibility to desiccation. However, the steadily occurring fragmentation of filaments into smaller units leads to improved self protection and thus may represent a life strategy to better survive longer periods of drought in exposed alpine soil crusts.}, }
@article {pmid21805083, year = {2012}, author = {Kagami, M and Amano, Y and Ishii, N}, title = {Community structure of planktonic fungi and the impact of parasitic chytrids on phytoplankton in Lake Inba, Japan.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {358-368}, pmid = {21805083}, issn = {1432-184X}, mesh = {Benzenesulfonates/chemistry ; Biota ; Chytridiomycota/classification/genetics/isolation &amp; purification/physiology ; DNA, Fungal/*analysis ; Denaturing Gradient Gel Electrophoresis ; Diatoms/*microbiology ; Fungi/classification/genetics/*isolation &amp; purification/*physiology ; Japan ; Lakes/microbiology ; Molecular Sequence Data ; Phylogeny ; Phytoplankton/microbiology ; Plankton/classification/genetics/*isolation &amp; purification/*physiology ; Polymerase Chain Reaction ; Seasons ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Freshwater fungi have received little attention by scientific research in recent years, especially fungi of the pelagic zone. Recently, parasitic fungi, termed chytrids, have been found to play important roles in aquatic food webs. Yet, the diversity and community structure of planktonic fungi including chytrids are not well studied. In this study, we examined the temporal fluctuations of freshwater fungi, including chytrids, in Lake Inba by using molecular techniques of denaturing gradient gel electrophoresis (DGGE). DGGE profiles, and associated sequence analysis, indicated that chytrids were present on all sampling dates from May to October (n = 12). In addition, analysis showed that a large proportion of the sequences belonged to chytrids of both parasitic and saprotrophic species. This finding was supported by microscopic observations using Calcofluor white to stain chytrids infecting various phytoplankton species. The percentages of infection by chytrids on two dominant diatom species, Aulacoseira granulata and Aulacoseira ambigua, showed a similar seasonal pattern in the DGGE band profiles. From the phylogenetic analysis and microscopic identification, the chytrids infecting the two diatoms are likely to be affiliated to Chytriomyces sp. and Zygorhizidium sp.. This is the first study to show that DGGE is a useful preliminary approach for examining the diversity of planktonic fungi including chytrids. Our results indicate both parasitic and saprotrophic chytrids are a significant component of freshwater fungi inhabiting the pelagic zone of Lake Inba, Japan. Further modification of DGGE, together with new molecular techniques and microscopic observation, would reveal the hidden diversity and ecological significance of planktonic fungi in aquatic ecosystems.}, }
@article {pmid21800088, year = {2011}, author = {Nemoto, F and Kojima, H and Fukui, M}, title = {Diversity of freshwater Thioploca species and their specific association with filamentous bacteria of the phylum Chloroflexi.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {753-764}, pmid = {21800088}, issn = {1432-184X}, mesh = {Chloroflexi/*physiology ; DNA, Bacterial/genetics ; Fresh Water/*microbiology ; Japan ; Lakes ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Sequence Analysis, DNA ; Thiotrichaceae/classification/*genetics/physiology ; Water Microbiology ; }, abstract = {Phylogenetic diversity among filamentous sulfur-oxidizing bacteria of the genus Thioploca inhabiting freshwater/brackish environments was analyzed in detail. The 16S rRNA gene sequence of Thioploca found in a freshwater lake in Japan, Lake Okotanpe, was identical to that of Thioploca from Lake Ogawara, a brackish lake. The samples of the two lakes could be differentiated by the sequences of their 23S rRNA genes and 16S-23S rRNA internal transcribed spacer (ITS) regions. The 23S rRNA-based phylogenetic relationships between Thioploca samples from four lakes (Lake Okotanpe, Lake Ogawara, Lake Biwa, and Lake Constance) were similar to those based on the 16S rRNA gene sequences. In addition, multiple types of the ITS sequences were obtained from Thioploca inhabiting Lake Okotanpe and Lake Constance. Variations within respective Thioploca populations were also observed in the analysis of the soxB gene, involved in sulfur oxidation. As major members of the sheath-associated microbial community, bacteria of the phylum Chloroflexi were consistently detected in the samples from different lakes. Fluorescence in situ hybridization revealed that they were filamentous and abundantly distributed within the sheaths of Thioploca.}, }
@article {pmid21796360, year = {2012}, author = {Jimenez, M and Chaidez, C}, title = {Improving Salmonella determination in Sinaloa rivers with ultrafiltration and most probable number methods.}, journal = {Environmental monitoring and assessment}, volume = {184}, number = {7}, pages = {4271-4277}, pmid = {21796360}, issn = {1573-2959}, mesh = {Colony Count, Microbial ; Environmental Monitoring/instrumentation/*methods ; Mexico ; Rivers/*microbiology ; Salmonella/*isolation &amp; purification ; *Ultrafiltration ; *Water Microbiology ; }, abstract = {Monitoring of waterborne pathogens is improved by using concentration methods prior to detection; however, direct microbial enumeration is desired to study microbial ecology and human health risks. The aim of this work was to determine Salmonella presence in river water with an ultrafiltration system coupled with the ISO 6579:1993 isolation standard method (UFS-ISO). Most probable number (MPN) method was used directly in water samples to estimate Salmonella populations. Additionally, the effect between Salmonella determination and water turbidity was evaluated. Ten liters or three tenfold dilutions (1, 0.1, and 0.01 mL) of water were processed for Salmonella detection and estimation by the UFS-ISO and MPN methods, respectively. A total of 84 water samples were tested, and Salmonella was confirmed in 64/84 (76%) and 38/84 (44%) when UFS-ISO and MPN were used, respectively. Salmonella populations were less than 5 × 10(3) MPN/L in 73/84 of samples evaluated (87%), and only three (3.5%) showed contamination with numbers greater than 4.5 × 10(4) MPN/L. Water turbidity did not affect Salmonella determination regardless of the performed method. These findings suggest that Salmonella abundance in Sinaloa rivers is not a health risk for human infections in spite of its persistence. Thus, choosing the appropriate strategy to study Salmonella in river water samples is necessary to clarify its behavior and transport in the environment.}, }
@article {pmid21791581, year = {2011}, author = {Zhou, J and Deng, Y and Luo, F and He, Z and Yang, Y}, title = {Phylogenetic molecular ecological network of soil microbial communities in response to elevated CO2.}, journal = {mBio}, volume = {2}, number = {4}, pages = {}, pmid = {21791581}, issn = {2150-7511}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biodiversity ; Carbon/analysis ; Carbon Dioxide/*metabolism ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Ecosystem ; Genes, rRNA ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Minnesota ; Nitrogen/analysis ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Homology, Nucleic Acid ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {UNLABELLED: Understanding the interactions among different species and their responses to environmental changes, such as elevated atmospheric concentrations of CO(2), is a central goal in ecology but is poorly understood in microbial ecology. Here we describe a novel random matrix theory (RMT)-based conceptual framework to discern phylogenetic molecular ecological networks using metagenomic sequencing data of 16S rRNA genes from grassland soil microbial communities, which were sampled from a long-term free-air CO(2) enrichment experimental facility at the Cedar Creek Ecosystem Science Reserve in Minnesota. Our experimental results demonstrated that an RMT-based network approach is very useful in delineating phylogenetic molecular ecological networks of microbial communities based on high-throughput metagenomic sequencing data. The structure of the identified networks under ambient and elevated CO(2) levels was substantially different in terms of overall network topology, network composition, node overlap, module preservation, module-based higher-order organization, topological roles of individual nodes, and network hubs, suggesting that the network interactions among different phylogenetic groups/populations were markedly changed. Also, the changes in network structure were significantly correlated with soil carbon and nitrogen contents, indicating the potential importance of network interactions in ecosystem functioning. In addition, based on network topology, microbial populations potentially most important to community structure and ecosystem functioning can be discerned. The novel approach described in this study is important not only for research on biodiversity, microbial ecology, and systems microbiology but also for microbial community studies in human health, global change, and environmental management.<br><br>IMPORTANCE: The interactions among different microbial populations in a community play critical roles in determining ecosystem functioning, but very little is known about the network interactions in a microbial community, owing to the lack of appropriate experimental data and computational analytic tools. High-throughput metagenomic technologies can rapidly produce a massive amount of data, but one of the greatest difficulties is deciding how to extract, analyze, synthesize, and transform such a vast amount of information into biological knowledge. This study provides a novel conceptual framework to identify microbial interactions and key populations based on high-throughput metagenomic sequencing data. This study is among the first to document that the network interactions among different phylogenetic populations in soil microbial communities were substantially changed by a global change such as an elevated CO(2) level. The framework developed will allow microbiologists to address research questions which could not be approached previously, and hence, it could represent a new direction in microbial ecology research.}, }
@article {pmid21787875, year = {2011}, author = {Mikelsaar, M}, title = {Human microbial ecology: lactobacilli, probiotics, selective decontamination.}, journal = {Anaerobe}, volume = {17}, number = {6}, pages = {463-467}, doi = {10.1016/j.anaerobe.2011.07.005}, pmid = {21787875}, issn = {1095-8274}, mesh = {Anti-Infective Agents/administration &amp; dosage/*pharmacology ; Bacteria/*drug effects/*growth &amp; development ; *Biota ; Decontamination/*methods ; Gastrointestinal Tract/*microbiology ; Humans ; *Probiotics ; }, abstract = {Health care-associated infections are closely associated with different medical interventions which interrupt the balance of human microbiota. The occasional predominance of opportunistic pathogens may lead to their translocation into the lymph nodes and bloodstream, causing endogenous (primary or secondary) hospital infections. The question is raised as to if there is a possibility for prevention of the imbalance of GI microbiota during medical interventions in critically ill patients. Prophylactic selective decontamination of the digestive tract (SDD) simultaneously applies three to four different antimicrobials for the suppression of enteric aerobic microbes, which are potentially pathogenic microorganisms. However, there is no convincing evidence that the indigenous beneficial intestinal microbiota are preserved, resulting in reduced mortality of high-risk patients. In this overview, we have evaluated the antimicrobial treatment guidelines of the Infectious Diseases Society of America (IDSA) for intra-abdominal infections in adults and seniors according to their safety for different Lactobacillus spp. The data from our group and in the literature have shown that all tested lactobacilli strains (nearly one hundred) were insusceptible to metronidazole while different species of lactobacilli of the three fermentation groups expressed particular antibiotic susceptibility to vancomycin, cefoxitin, ciprofloxacin and some new tetracyclines. We have relied on microbial ecology data showing that the GI tracts of adults and the elderly are simultaneously colonised at least with several (four to a maximum of 12) Lactobacillus species expressing variable intrinsic insusceptibility to the aforementioned antimicrobials, according to the provided data in table. This finding offers the possibility of preserving the colonisation of the intestine with some beneficial lactobacilli during antimicrobial treatment in critically ill patients with health care-associated infections. Several probiotic Lactobacillus spp. strains are intrinsically resistant to antimicrobials and can be used during antibacterial therapy, however, their application as an additive to antimicrobial treatment in critically ill patients needs to be investigated in well-designed clinical trials.}, }
@article {pmid21785985, year = {2012}, author = {Fan, LF and Tang, SL and Chen, CP and Hsieh, HL}, title = {Diversity and composition of sulfate- and sulfite-reducing prokaryotes as affected by marine-freshwater gradient and sulfate availability.}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {224-237}, pmid = {21785985}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/*metabolism ; DNA, Bacterial/genetics ; Fresh Water/*microbiology ; Geologic Sediments/microbiology ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; Seawater/*microbiology ; Sequence Analysis, DNA ; Sulfates/*metabolism ; Sulfite Reductase (NADPH)/genetics/metabolism ; Sulfites/*metabolism ; Taiwan ; }, abstract = {Sulfate- and sulfite-reducing prokaryotes (SSRP) communities play a key role in both sulfur and carbon cycles. In estuarine ecosystems, sulfate concentrations change with tides and could be limited in tidal freshwater reach or deep sediments. In a subtropical estuary of northern Taiwan in December 2007, we examined the compositional changes of SSRP communities. We examined three sites: from the lower estuarine brackish-water reach (site GR and mangrove vegetation site, GM) to the upper estuarine tidal freshwater reach (site HR), as well as from surface to a 50-cm depth. The partial sequence of sulfite reductase (dsrB) genes was used as a molecular marker of SSRP, linked to polymerase chain reaction and denaturing gradient gel electrophoresis (DGGE) techniques. SSRP communities of the DGGE profiles varied with sites according to one-way analyses of similarities (Global R = 0.69, P = 0.001). Using cluster analysis, the DGGE profile was found to show site-specific clusters and a distinct depth zonation (five, six, and two SSRP communities at the GM, GR, and HR sites, respectively). SSRP composition was highly correlated to the combination of salinity, reduced sulfur, and total organic carbon contents (BIO-ENV analysis, r (s) = 0.56). After analyzing a total of 35 dsrB sequences in the DGGE gel, six groups with 15 phylotypes were found, which were closely related to marine-freshwater gradient. Moreover, sequences neighboring sulfite-reducing prokaryotes were observed, in addition to those affiliated to sulfate-reducing prokaryotes. Four phylotypes harvested in HR resembled the genus Desulfitobacterium, a sulfite-reducing prokaryote, which failed to use sulfate as an electron acceptor and were active in freshwater and sulfate-limited habitat. The other five phylotypes in the HR reach belonged to the sulfate-reducing prokaryotes of the genera Desulfatiferula, Desulfosarcina, Desulfovibrio, and Desulfotomaculum, which appeared to tolerate low salinity and low sulfate supply. SSRP phylotypes at the mangrove-vegetated GM site (five phylotypes in two groups) were phylogenetically less diverse, when compared with those at the non-mangrove-vegetated GR site (three phylotypes in three groups) and the tidally influenced freshwater HR site (nine phylotypes in five groups). Phylotypes found at GR and GM were all affiliated to marine sulfate-reducing prokaryote strains of the genera Desulfofaba, Desulfobotulus, Desulfatiferula, Desulfosarcina, and Desulfotomaculum. Notably, a phylotype recorded in the surface sediment at GR resembled the genus Desulfobulbus, which was recorded from freshwater environment consisting of the freshwater input at GR during ebb tides.}, }
@article {pmid21779812, year = {2012}, author = {González-Arenzana, L and López, R and Santamaría, P and Tenorio, C and López-Alfaro, I}, title = {Dynamics of indigenous lactic acid bacteria populations in wine fermentations from La Rioja (Spain) during three vintages.}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {12-19}, pmid = {21779812}, issn = {1432-184X}, mesh = {Alcohols/metabolism ; Bacterial Typing Techniques ; DNA, Bacterial/analysis ; Fermentation ; Food Microbiology ; Genotype ; Lactic Acid/*metabolism ; Levilactobacillus brevis/genetics/isolation &amp; purification/metabolism ; Lactobacillus plantarum/genetics/isolation &amp; purification/metabolism ; Oenococcus/genetics/isolation &amp; purification/*metabolism ; RNA, Ribosomal, 16S/analysis ; Sequence Alignment ; Spain ; Wine/*microbiology ; }, abstract = {Diversity of lactic acid bacteria (LAB) species has been analyzed for three consecutive years (2006, 2007, and 2008) during alcoholic and malolactic fermentations of Tempranillo wine in a winery at La Rioja. The results showed differences in malolactic fermentation duration, and in both diversity of LAB species and diversity of Oenococcus oeni genotypes. O. oeni was shown to be the predominant species (73% of total isolates). Monitoring the different strains of O. oeni using pulsed-field gel electrophoresis of chromosomal DNA digested with SfiI and ApaI allowed detection of a total of 37 distinct genotypes, most of them comprised at least two isolates. Six appeared in more than one vintage, one of them being present in the three studied years. Moreover, four genotypes were indistinct of the strains isolated from the air of this same winery in 2007 vintage. The frequency of participation of each genotype varied from year to year, thus dominant genotypes at one year were minority or not present at another year. This suggests that distinct indigenous O. oeni strains are better adapted to the different winery conditions every year. Predominant genotypes that appeared in more than one vintage and lead to quality wines with low histamine contents could be considered as interesting for selecting of new malolactic starter cultures.}, }
@article {pmid21772835, year = {2011}, author = {Young, VB and Kahn, SA and Schmidt, TM and Chang, EB}, title = {Studying the Enteric Microbiome in Inflammatory Bowel Diseases: Getting through the Growing Pains and Moving Forward.}, journal = {Frontiers in microbiology}, volume = {2}, number = {}, pages = {144}, pmid = {21772835}, issn = {1664-302X}, support = {UH3 DK083993/DK/NIDDK NIH HHS/United States ; }, abstract = {In this commentary, we will review some of the early efforts aimed at understanding the role of the enteric microbiota in the causality of inflammatory bowel diseases. By examining these studies and drawing on our own experiences bridging clinical gastroenterology and microbial ecology as part of the NIH-funded Human Microbiome Project (Turnbaugh et al., 2007), we hope to help define some of the "growing pains" that have hampered these initial efforts. It is our sincere hope that this discussion will help advance future efforts in this area by identifying current challenges and limitations and by suggesting strategies to overcome these obstacles.}, }
@article {pmid21766218, year = {2012}, author = {Postec, A and Tapia, N and Bernadac, A and Joseph, M and Davidson, S and Wu, LF and Ollivier, B and Pradel, N}, title = {Magnetotactic bacteria in microcosms originating from the French Mediterranean Coast subjected to oil industry activities.}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {1-11}, pmid = {21766218}, issn = {1432-184X}, mesh = {Alphaproteobacteria/genetics/isolation &amp; purification/*metabolism ; Aquatic Organisms/metabolism ; DNA, Bacterial/analysis/chemistry/genetics ; Ferrosoferric Oxide/*metabolism ; France ; Genetic Variation ; Geologic Sediments/microbiology ; Industrial Oils ; Iron/*metabolism ; Magnetosomes/physiology ; Mediterranean Region ; Molecular Sequence Data ; Oil and Gas Fields/microbiology ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfides/*metabolism ; Sulfur Compounds ; }, abstract = {Magnetotactic bacteria (MTB) mineralize nanosized magnetite or greigite crystals within cells and thus play an important role in the biogeochemical process. Despite decades of research, knowledge of MTB distribution and ecology, notably in areas subjected to oil industry activities, is still limited. In the present study, we investigated the presence of MTB in the Gulf of Fos, French Mediterranean coast, which is subjected to intensive oil industry activities. Microcosms containing sediments/water (1:2, v/v) from several sampling sites were monitored over several weeks. The presence of MTB was revealed in five of eight sites. Diverse and numerous MTB were revealed particularly from one site (named CAR), whilst temporal variations of a homogenous magnetotactic cocci population was shown within the LAV site microcosm over a 4-month period. Phylogenetic analysis revealed that they belonged to Alphaproteobacteria, and a novel genus from the LAV site was evidenced. Among the physicochemical parameters measured, a correlation was shown between the variation of MTB abundance in microcosms and the redox state of sulphur compounds.}, }
@article {pmid21755290, year = {2011}, author = {Graças, DA and Miranda, PR and Baraúna, RA and McCulloch, JA and Ghilardi, R and Schneider, MP and Silva, A}, title = {Microbial diversity of an anoxic zone of a hydroelectric power station reservoir in Brazilian Amazonia.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {853-861}, pmid = {21755290}, issn = {1432-184X}, mesh = {Archaea/*classification/genetics ; *Biodiversity ; Brazil ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Gene Library ; Geologic Sediments/microbiology ; Phylogeny ; *Power Plants ; Proteobacteria/*classification/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Microbial diversity was evaluated in an anoxic zone of Tucuruí Hydroelectric Power Station reservoir in Brazilian Amazonia using a culture-independent approach by amplifying and sequencing fragments of the 16S rRNA gene using metagenomic DNA as a template. Samples obtained from the photic, aphotic (40 m) and sediment (60 m) layers were used to construct six 16S rDNA libraries containing a total of 1,152 clones. The sediment, aphotic and photic layers presented 64, 33 and 35 unique archaeal operational taxonomic units (OTUs). The estimated richness of these layers was evaluated to be 153, 106 and 79 archaeal OTUs, respectively, using the abundance-based coverage estimator (ACE) and 114, 83 and 77 OTUs using the Chao1 estimator. For bacterial sequences, 114, 69 and 57 OTUs were found in the sediment, aphotic and photic layers, which presented estimated richnesses of 1,414, 522 and 197 OTUs (ACE) and 1,059, 1,014 and 148 OTUs (Chao1), respectively. Phylogenetic analyses of the sequences obtained revealed a high richness of microorganisms which participate in the carbon cycle, namely, methanogenic archaea and methanotrophic proteobacteria. Most sequences obtained belong to non-culturable prokaryotes. The present study offers the first glimpse of the huge microbial diversity of an anoxic area of a man-made lacustrine environment in the tropics.}, }
@article {pmid21748268, year = {2011}, author = {Cao, H and Hong, Y and Li, M and Gu, JD}, title = {Phylogenetic diversity and ecological pattern of ammonia-oxidizing archaea in the surface sediments of the western Pacific.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {813-823}, pmid = {21748268}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Archaea/*classification/enzymology/genetics ; *Biodiversity ; Cluster Analysis ; DNA, Archaeal/genetics ; Genes, Archaeal ; Geologic Sediments/*microbiology ; Oxidoreductases/genetics ; Pacific Ocean ; *Phylogeny ; Seawater/microbiology ; Sequence Analysis, DNA ; }, abstract = {The phylogenetic diversity of ammonia-oxidizing archaea (AOA) was surveyed in the surface sediments from the northern part of the South China Sea (SCS). The distribution pattern of AOA in the western Pacific was discussed through comparing the SCS with other areas in the western Pacific including Changjiang Estuary and the adjacent East China Sea where high input of anthropogenic nitrogen was evident, the tropical West Pacific Continental Margins close to the Philippines, the deep-sea methane seep sediments in the Okhotsk Sea, the cold deep sea of Northeastern Japan Sea, and the hydrothermal field in the Southern Okinawa Trough. These various environments provide a wide spectrum of physical and chemical conditions for a better understanding of the distribution pattern and diversities of AOA in the western Pacific. Under these different conditions, the distinct community composition between shallow and deep-sea sediments was clearly delineated based on the UniFrac PCoA and Jackknife Environmental Cluster analyses. Phylogenetic analyses showed that a few ammonia-oxidizing archaeal subclades in the marine water column/sediment clade and endemic lineages were indicative phylotypes for some environments. Higher phylogenetic diversity was observed in the Philippines while lower diversity in the hydrothermal vent habitat. Water depth and possibly with other environmental factors could be the main driving forces to shape the phylogenetic diversity of AOA observed, not only in the SCS but also in the whole western Pacific. The multivariate regression tree analysis also supported this observation consistently. Moreover, the functions of current and other climate factors were also discussed in comparison of phylogenetic diversity. The information collectively provides important insights into the ecophysiological requirements of uncultured ammonia-oxidizing archaeal lineages in the western Pacific Ocean.}, }
@article {pmid21748267, year = {2012}, author = {Lo Giudice, A and Caruso, C and Mangano, S and Bruni, V and De Domenico, M and Michaud, L}, title = {Marine bacterioplankton diversity and community composition in an antarctic coastal environment.}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {210-223}, pmid = {21748267}, issn = {1432-184X}, mesh = {Antarctic Regions ; Aquatic Organisms ; Bacteria/genetics/*growth &amp; development/*isolation &amp; purification ; Base Sequence ; Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; *Ecosystem ; In Situ Hybridization, Fluorescence ; *Microbial Consortia ; Molecular Sequence Data ; Plankton/genetics/*growth &amp; development/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The bacterial community inhabiting the water column at Terra Nova Bay (Ross Sea, Antarctica) was examined by the fluorescent in situ hybridization (FISH) technique and the genotypic and phenotypic characterization of 606 bacterial isolates. Overall, the FISH analysis revealed a bacterioplankton composition that was typical of Antarctic marine environments with the Cytophaga/Flavobacter (CF) group of Bacteroidetes that was equally dominant with the Actinobacteria and Gammaproteobacteria. As sampling was performed during the decay of sea-ice, it is plausible to assume the origin of Bacteroidetes from the sea-ice compartment where they probably thrive in high concentration of DOM which is efficiently remineralized to inorganic nutrients. This finding was supported by the isolation of Gelidibacter, Polaribacter, and Psychroflexus members (generally well represented in Antarctic sea-ice) which showed the ability to hydrolyze macromolecules, probably through the production of extracellular enzymes. A consistently pronounced abundance of the Gammaproteobacteria (67.8%) was also detected within the cultivable fraction. Altogether, the genera Psychromonas and Pseudoalteromonas accounted for 65.4% of total isolates and were ubiquitous, thus suggesting that they may play a key role within the analyzed bacterioplankton community. In particular, Pseudoalteromonas isolates possessed nitrate reductase and were able to hydrolyze substrates for protease, esterase, and β-galactosidase, thus indicating their involvement in the carbon and nitrogen cycling. Finally, the obtained results highlight the ability of the Actinobacteria to survive and proliferate in the Terra Nova Bay seawater as they generally showed a wide range of salt tolerance and appeared to be particularly competitive with strictly marine bacteria by better utilizing supplied carbon sources.}, }
@article {pmid21747797, year = {2011}, author = {Bodelier, PL}, title = {Toward understanding, managing, and protecting microbial ecosystems.}, journal = {Frontiers in microbiology}, volume = {2}, number = {}, pages = {80}, pmid = {21747797}, issn = {1664-302X}, abstract = {Microbial communities are at the very basis of life on earth, catalyzing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity-conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper identifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology.}, }
@article {pmid21744159, year = {2011}, author = {Polizzi, V and Fazzini, L and Adams, A and Picco, AM and De Saeger, S and Van Peteghem, C and De Kimpe, N}, title = {Autoregulatory properties of (+)-thujopsene and influence of environmental conditions on its production by Penicillium decumbens.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {838-852}, pmid = {21744159}, issn = {1432-184X}, mesh = {Air Pollution, Indoor/analysis ; Antifungal Agents/metabolism/pharmacology ; *Environment ; Gas Chromatography-Mass Spectrometry ; Humidity ; Mycelium/drug effects/growth &amp; development ; Penicillium/*chemistry/growth &amp; development ; Sesquiterpenes/*metabolism ; Solid Phase Microextraction ; Spores, Fungal/metabolism ; Temperature ; Volatile Organic Compounds/metabolism ; }, abstract = {A Penicillium decumbens strain was collected from a water-damaged building, and the production of microbial volatile organic compounds (MVOCs) was investigated by means of headspace solid-phase microextraction, followed by GC-MS analysis. The strain was characterized by a high production of (+)-thujopsene. The influence of various temperatures, relative humidity (RH) values, substrates, and inoculum concentrations on fungal growth and (+)-thujopsene production was studied. The optimal temperature and relative humidity for P. decumbens growth were 30°C and 100% RH, respectively. In general, the more favourable the incubation parameters were for growth, the faster maximum (+)-thujopsene production was reached. Moreover, the antifungal activity of thujopsene was tested against 16 fungal strains. The growth of five of these fungal strains was negatively affected both by thujopsene alone and when grown in contact with the MVOCs produced by P. decumbens. Following these results and since growth of P. decumbens itself was also inhibited by thujopsene, an autoregulatory function for this compound was proposed. Few data are present in the literature about chemical communication between fungi. The present research could, therefore, contribute to understanding fungal metabolism and behaviour in indoor environments.}, }
@article {pmid21740150, year = {2011}, author = {Stevens, EW and Sumner, DY and Harwood, CL and Crutchfield, JP and Hamann, B and Kreylos, O and Puckett, E and Senge, P}, title = {Understanding microbialite morphology using a comprehensive suite of three-dimensional analysis tools.}, journal = {Astrobiology}, volume = {11}, number = {6}, pages = {509-518}, doi = {10.1089/ast.2010.0560}, pmid = {21740150}, issn = {1557-8070}, mesh = {*Environmental Microbiology ; *Fossils ; Imaging, Three-Dimensional ; South Africa ; }, abstract = {Microbialites can have complex morphologies that preserve clues to ancient microbial ecology. However, extracting and interpreting these clues is challenging due to both the complexity of microbial structures and the difficulties of connecting morphology to microbial processes. Fenestrate microbialites from the 2521±3 Ma Gamohaan Formation, South Africa, have intricate structures composed of three distinct microbial structures: steeply dipping supports (surfaces defined by organic inclusions), more shallowly dipping supports with diffuse organic inclusions below them, and draping laminae. In polished slabs, shallowly dipping supports with diffuse organic inclusions show apparent dips from 27° to 60°, and supports without associated zones of diffuse inclusions dip 75° to 88°, which suggests a distinction between support types based on orientation. However, dips exposed in polished slabs are apparent dips, and three-dimensional analysis is required for analysis of true dips. Through the Keck Center for Active Visualization in Earth Sciences (KeckCAVES), we used locally developed software that controls a three-dimensional environment with head and hand tracking (an "immersive environment") to visualize and interpret virtual microbialite data sets. Immersive environments have not penetrated into standard scientific work processes ("workflows") due to their high costs, steep learning curves, and low productivity for users. By contrast, our suite of software tools allowed us to develop a personalized scientific workflow that provides a complete path from initial ideas to characterization of fenestrate microbialites' features. Results of three-dimensional analysis of fenestrate microbialites show that supports with inclusions dip 65° to 75°, whereas supports without inclusions dip 85° to 90°. These results demonstrate that all supports have very steep dips, and a 10° dip gap exists between supports with and without inclusions, which suggests they grew in fundamentally different ways. Results also emphasize how valuable three-dimensional analysis is when combined with a comprehensive workflow for understanding intricate structures such as fenestrate microbialites.}, }
@article {pmid21735154, year = {2012}, author = {Singh, D and Takahashi, K and Kim, M and Chun, J and Adams, JM}, title = {A hump-backed trend in bacterial diversity with elevation on Mount Fuji, Japan.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {429-437}, pmid = {21735154}, issn = {1432-184X}, mesh = {*Altitude ; Bacteria/*classification/genetics ; Japan ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; }, abstract = {Little is known of how bacterial diversity in soils varies with elevation. One previous study found a decline with elevation, whereas another found no trend. We chose Mount Fuji of Japan as a geologically and topographically simple mountain system. Samples were taken at elevational intervals, between the base of the mountain at 1,000 m and its summit at 3,700 m. Polymerase chain reaction-amplified soil DNA for the bacterial 16S gene targeting V1-V3 region was pyrosequenced using the 454 Roche machine, and taxonomically classified with reference to a bioinformatic database. There was a significant "peak" in total bacterial diversity at around 2,500 m above the tree line with a decline towards the highest elevations around 3,700 m near the summit. Individual bacterial phyla show distinct trends-increase, decrease, or a mid-elevational "bulge" in diversity. Bacterial diversity does not parallel woody plant or herbaceous plant diversity. We suggest that beyond the tree and vegetation line, the more extreme temperature fluctuations, stronger UV, lack of nutrients, and more frequent disturbance of the loose substrate of these slopes allows less competition and greater bacterial species diversity due to "lottery" recruitment. However, at the highest elevations, the physiological challenges are so extreme that fewer bacterial species are capable of surviving.}, }
@article {pmid21735153, year = {2011}, author = {Ferrer, M and Guazzaroni, ME and Richter, M and García-Salamanca, A and Yarza, P and Suárez-Suárez, A and Solano, J and Alcaide, M and van Dillewijn, P and Molina-Henares, MA and López-Cortés, N and Al-Ramahi, Y and Guerrero, C and Acosta, A and de Eugenio, LI and Martínez, V and Marques, S and Rojo, F and Santero, E and Genilloud, O and Pérez-Pérez, J and Rosselló-Móra, R and Ramos, JL}, title = {Taxonomic and functional metagenomic profiling of the microbial community in the anoxic sediment of a sub-saline shallow lake (Laguna de Carrizo, Central Spain).}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {824-837}, pmid = {21735153}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Euryarchaeota/classification/*genetics ; Gene Library ; Geologic Sediments/*microbiology ; Lakes/microbiology ; *Metagenome ; Molecular Sequence Data ; Nitrogen/metabolism ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spain ; Sulfur/metabolism ; }, abstract = {The phylogenetic and functional structure of the microbial community residing in a Ca(2+)-rich anoxic sediment of a sub-saline shallow lake (Laguna de Carrizo, initially operated as a gypsum (CaSO(4) × 2 H(2)O) mine) was estimated by analyzing the diversity of 16S rRNA amplicons and a 3.1 Mb of consensus metagenome sequence. The lake has about half the salinity of seawater and possesses an unusual relative concentration of ions, with Ca(2+) and SO (4) (2-) being dominant. The 16S rRNA sequences revealed a diverse community with about 22% of the bacterial rRNAs being less than 94.5% similar to any rRNA currently deposited in GenBank. In addition to this, about 79% of the archaeal rRNA genes were mostly related to uncultured Euryarchaeota of the CCA47 group, which are often associated with marine and oxygen-depleted sites. Sequence analysis of assembled genes revealed that 23% of the open reading frames of the metagenome library had no hits in the database. Among annotated genes, functions related to (thio) sulfate and (thio) sulfonate-reduction and iron-oxidation, sulfur-oxidation, denitrification, synthrophism, and phototrophic sulfur metabolism were found as predominant. Phylogenetic and biochemical analyses indicate that the inherent physical-chemical characteristics of this habitat coupled with adaptation to anthropogenic activities have resulted in a highly efficient community for the assimilation of polysulfides, sulfoxides, and organosulfonates together with nitro-, nitrile-, and cyanide-substituted compounds. We discuss that the relevant microbial composition and metabolic capacities at Laguna de Carrizo, likely developed as an adaptation to thrive in the presence of moderate salinity conditions and potential toxic bio-molecules, in contrast with the properties of previously known anoxic sediments of shallow lakes.}, }
@article {pmid21732020, year = {2011}, author = {Ficová, M and Betáková, T and Pančík, P and Václav, R and Prokop, P and Halásová, Z and Kúdelová, M}, title = {Molecular detection of murine herpesvirus 68 in ticks feeding on free-living reptiles.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {862-867}, pmid = {21732020}, issn = {1432-184X}, mesh = {Animals ; DNA, Viral/isolation &amp; purification ; Disease Vectors ; Herpesviridae Infections/transmission ; Ixodes/*virology ; Lizards/*parasitology ; Rhadinovirus/*isolation &amp; purification ; Slovakia ; }, abstract = {The MHV-68 (designed as Murid herpesvirus 4 (MuHV 4) strain 68) isolated from two rodents, Myodes glareolus and Apodemus flavicollis, is considered as a natural pathogen of free-living murid rodents. Recently, the detection of MHV antibodies in the blood of animals living in the same biotope as MHV-infected mice has suggested that ticks may have a role in the transmission of this pathogen. Ixodes ricinus is one the most abundant tick species in Europe known to transmit multiple pathogens causing human and animal diseases. In this study, nymphs and larvae feeding on 116 individuals of a temperate lizard species-the green lizard Lacerta viridis captured in the Slovak Karst National Park, were examined for MHV-68. The specific sequence of virion glycoprotein 150 was amplified in DNA individually isolated from I. ricinus ticks using single-copy sensitive nested polymerase chain reaction. MHV-68 was detected in ten of 649 nymphs and in five of 150 larvae, respectively. We found that 9.6% of green lizards fed at least one MHV-68-infected immature tick. Occurrence of MHV-68 within all ticks tested was 1.8%. This study is first to show that immature I. ricinus ticks feeding on free-living lizards in a Central European region could be infected with gammaherpesvirus (MHV-68), naturally infecting free-living murid rodents. Our results provide evidence supporting the hypothesis that ticks may play a mediating role in circulation of MHV-68 in nature.}, }
@article {pmid21731976, year = {2011}, author = {Erijman, L and Figuerola, EL and Guerrero, LD and Ayarza, JM}, title = {[Impact of the recent advances in the analysis of microbial communities on the control of the wastewater treatment process].}, journal = {Revista Argentina de microbiologia}, volume = {43}, number = {2}, pages = {127-135}, doi = {10.1590/S0325-75412011000200011}, pmid = {21731976}, issn = {0325-7541}, mesh = {Aerobiosis ; Biodiversity ; Biomass ; Ecosystem ; *Environmental Microbiology ; Forecasting ; Metagenomics ; *Microbial Consortia ; Sewage/*microbiology ; Soil Microbiology ; Waste Disposal, Fluid/*methods/standards ; Water Microbiology ; Water Purification/*methods ; }, abstract = {One of the main functions of environmental biotechnology is to address the study of microbial communities that provide essential services to society. Beyond the similarities with industrial and agricultural microbiology, the unique features exhibited by environmental biotechnology, such as process objectives, biomass characteristics and type and mode of feeding (substrates), allow a clear distinction from the other related disciplines. Recent advances in microbial ecology, ecophysiology, genomics and process engineering are herein reviewed to illustrate how the integration of the new knowledge can help overcome the shortcomings of classic microbiological analyses to understand, predict and optimize the performance of wastewater treatment.}, }
@article {pmid21728039, year = {2011}, author = {Lelong, A and Haberkorn, H and Le Goïc, N and Hégaret, H and Soudant, P}, title = {A new insight into allelopathic effects of Alexandrium minutum on photosynthesis and respiration of the diatom Chaetoceros neogracile revealed by photosynthetic-performance analysis and flow cytometry.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {919-930}, pmid = {21728039}, issn = {1432-184X}, mesh = {Cell Count ; Cell Respiration/drug effects ; Diatoms/*drug effects/metabolism ; Dinoflagellida/*chemistry ; Flow Cytometry ; Marine Toxins/*chemistry ; Photosynthesis/*drug effects ; Time Factors ; }, abstract = {The allelopathic effects of Alexandrium minutum, a toxic dinoflagellate, on the diatom Chaetoceros neogracile were evaluated using unialgal cultures evaluated by flow cytometry (FCM) and photosynthetic-performance analysis. Using FCM, we demonstrated that red chlorophyll fluorescence, relative cell size (Forward scatter of blue laser light, FSC) and cell complexity (Side scatter, 90°-angle scatter of blue laser light, SSC) significantly and rapidly decreased in C. neogracile cells exposed to A. minutum. Cells of C. neogracile exposed to A. minutum had fewer active photosynthetic reaction centers and sharply decreased photosynthetic efficiency. These effects were intensified with advancing A. minutum batch culture age and cell density. The supernatant of A. minutum contained the majority of the putative allelopathic compounds, and the biological activity of these compounds remained active less than 9 h after release. This paper describes for the first time specific effects of allelochemicals produced by A. minutum on the photosynthetic apparatus of microalgal target cells. The biochemical composition of A. minutum allelopathic agents, however, remains unknown and still needs to be investigated.}, }
@article {pmid21728038, year = {2011}, author = {Li, CQ and Liu, WC and Zhu, P and Yang, JL and Cheng, KD}, title = {Phylogenetic diversity of bacteria associated with the marine sponge Gelliodes carnosa collected from the Hainan Island coastal waters of the South China Sea.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {800-812}, pmid = {21728038}, issn = {1432-184X}, mesh = {Actinobacteria/classification/*genetics/isolation &amp; purification ; Animals ; Antibiosis ; *Biodiversity ; DNA, Bacterial/genetics ; Gene Library ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; Porifera/*microbiology ; Proteobacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Seawater ; Sequence Analysis, DNA ; }, abstract = {Several molecular techniques were employed to document the bacterial diversity associated with the marine sponge Gelliodes carnosa. Cultivation-dependent and cultivation-independent methods were used to obtain the 16S rRNA gene sequences of the bacteria. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the bacterial community structure was highly diverse with representatives of the high G + C Gram-positive bacteria, cyanobacteria, low G + C Gram-positive bacteria, and proteobacteria (α-, β-, and γ-), most of which were also found in other marine environments, including in association with other sponges. Overall, 300 bacterial isolates were cultivated, and a total of 62 operational taxonomic units (OTUs) were identified from these isolates by restriction fragment length polymorphism (RFLP) analysis and DNA sequencing of the 16S rRNA genes. Approximately 1,000 16S rRNA gene clones were obtained by the cultivation-independent method. A total of 310 clones were randomly selected for RFLP analysis, from which 33 OTUs were acquired by further DNA sequencing and chimera checking. A total of 12 cultured OTUs (19.4% of the total cultured OTUs) and 13 uncultured OTUs (39.4% of the total uncultured OTUs) had low sequence identity (≤97%) with their closest matches in GenBank and were probably new species. Our data provide strong evidence for the presence of a diverse variety of unidentified bacteria in the marine sponge G. carnosa. A relatively high proportion of the isolates exhibited antimicrobial activity, and the deferred antagonism assay showed that over half of the active isolates exhibited a much stronger bioactivity when grown on medium containing seawater. In addition to demonstrating that the sponge-associated bacteria could be a rich source of new biologically active natural products, the results may have ecological implications. This study expands our knowledge of the diversity of sponge-associated bacteria and contributes to the growing database of the bacterial communities within sponges.}, }
@article {pmid21728037, year = {2012}, author = {Gupta, V and Smemo, KA and Yavitt, JB and Basiliko, N}, title = {Active methanotrophs in two contrasting North American peatland ecosystems revealed using DNA-SIP.}, journal = {Microbial ecology}, volume = {63}, number = {2}, pages = {438-445}, pmid = {21728037}, issn = {1432-184X}, mesh = {Alphaproteobacteria/*classification/*genetics/isolation &amp; purification ; Archaea/classification/genetics/isolation &amp; purification ; DNA, Bacterial/analysis/genetics ; Denaturing Gradient Gel Electrophoresis ; Ecosystem ; Gammaproteobacteria/*classification/*genetics/isolation &amp; purification ; Hydrogen-Ion Concentration ; Methane/*metabolism ; Molecular Sequence Data ; New York ; Oxidation-Reduction ; Oxygenases/analysis/genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/analysis/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; Wetlands ; }, abstract = {The active methanotroph community was investigated in two contrasting North American peatlands, a nutrient-rich sedge fen and nutrient-poor Sphagnum bog using in vitro incubations and (13)C-DNA stable-isotope probing (SIP) to measure methane (CH(4)) oxidation rates and label active microbes followed by fingerprinting and sequencing of bacterial and archaeal 16S rDNA and methane monooxygenase (pmoA and mmoX) genes. Rates of CH(4) oxidation were slightly, but significantly, faster in the bog and methanotrophs belonged to the class Alphaproteobacteria and were similar to other methanotrophs of the genera Methylocystis, Methylosinus, and Methylocapsa or Methylocella detected in, or isolated from, European bogs. The fen had a greater phylogenetic diversity of organisms that had assimilated (13)C, including methanotrophs from both the Alpha- and Gammaproteobacteria classes and other potentially non-methanotrophic organisms that were similar to bacteria detected in a UK and Finnish fen. Based on similarities between bacteria in our sites and those in Europe, including Russia, we conclude that site physicochemical characteristics rather than biogeography controlled the phylogenetic diversity of active methanotrophs and that differences in phylogenetic diversity between the bog and fen did not relate to measured CH(4) oxidation rates. A single crenarchaeon in the bog site appeared to be assimilating (13)C in 16S rDNA; however, its phylogenetic similarity to other CO(2)-utilizing archaea probably indicates that this organism is not directly involved in CH(4) oxidation in peat.}, }
@article {pmid21720829, year = {2012}, author = {Harke, MJ and Berry, DL and Ammerman, JW and Gobler, CJ}, title = {Molecular response of the bloom-forming cyanobacterium, Microcystis aeruginosa, to phosphorus limitation.}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {188-198}, pmid = {21720829}, issn = {1432-184X}, mesh = {Alkaline Phosphatase/biosynthesis/metabolism ; Bacterial Proteins/genetics ; Base Sequence ; Biological Transport, Active/genetics ; Genes, Bacterial ; Microcystis/*genetics/growth &amp; development/*metabolism ; Phosphate-Binding Proteins/*genetics ; Phosphorus/*metabolism ; Phytoplankton/growth &amp; development ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Cyanobacteria blooms caused by species such as Microcystis have become commonplace in many freshwater ecosystems. Although phosphorus (P) typically limits the growth of freshwater phytoplankton populations, little is known regarding the molecular response of Microcystis to variation in P concentrations and sources. For this study, we examined genes involved in P acquisition in Microcystis including two high-affinity phosphate-binding proteins (pstS and sphX) and a putative alkaline phosphatase (phoX). Sequence analyses among ten clones of Microcystis aeruginosa and one clone of Microcystis wesenbergii indicates that these genes are present and conserved within the species, but perhaps not the genus, as phoX was not identified in M. wesenbergii. Experiments with clones of M. aeruginosa indicated that expression of these three genes was strongly upregulated (50- to 400-fold) under low inorganic P conditions and that the expression of phoX was correlated with alkaline phosphatase activity (p < 0.005). In contrast, cultures grown exclusively on high levels of organic phosphorus sources (adenosine 5'-monophosphate, β-glycerol phosphate, and D: -glucose-6-phosphate) or under nitrogen-limited conditions displayed neither high levels of gene expression nor alkaline phosphatase activity. Since Microcystis dominates phytoplankton assemblages in summer when levels of inorganic P (P(i)) are often low and/or dominate lakes with low P(i) and high organic P, our findings suggest this cyanobacterium may rely on pstS, sphX, and phoX to efficiently transport P(i) and exploit organic sources of P to form blooms.}, }
@article {pmid21720688, year = {2011}, author = {Bavestrello F, L and Cabello M, A}, title = {[Community antibiotic consumption in Chile, 2000-2008].}, journal = {Revista chilena de infectologia : organo oficial de la Sociedad Chilena de Infectologia}, volume = {28}, number = {2}, pages = {107-112}, pmid = {21720688}, issn = {0716-1018}, mesh = {*Anti-Bacterial Agents/supply &amp; distribution ; Chile ; Drug Utilization/legislation &amp; jurisprudence/statistics &amp; numerical data ; Humans ; *Legislation, Drug ; Pharmacies/legislation &amp; jurisprudence/*statistics &amp; numerical data ; Retrospective Studies ; }, abstract = {BACKGROUND: The Chilean Ministry of Health has implemented regulatory rules for the consumption of anti-biotics since September 1999, with sales restriction limited only with medical prescription.<br><br>AIM: To analyze the impact of established regulatory measures from 2000 to 2008.<br><br>MATERIAL AND METHODS: A retrospective analysis of antibiotics sales in pharmacies from 2000 to 2008 was performed. The information was obtained from the International Marketing System (IMS Health), an auditing system of pharmacy sales. The consumption unit used was the Defined Daily Dose per 1000 inhabitants/day (DDD).<br><br>RESULTS: From 2000 to 2002 the regulatory rules had a great impact, but since 2002 the antibiotic consumption increased, especially amoxicillin, returning to similar lev&#xe9;is observed in 1998.<br><br>CONCLUSIONS: The regulatory measures had an initial impact, but there was not reinforcement in the time and there was no further control. It is necessary to assume a permanent task and support of the authorities of health to ed&#xfa;cate the population about the implications of the inadequate use of antimicrobials and his effect on the microbial ecology.}, }
@article {pmid21716647, year = {2011}, author = {Teplitski, M and Leitão, JH and Sela, S}, title = {Microbial ecology and global health.}, journal = {International journal of microbiology}, volume = {2011}, number = {}, pages = {564701}, doi = {10.1155/2011/564701}, pmid = {21716647}, issn = {1687-9198}, }
@article {pmid21715158, year = {2011}, author = {Siggins, A and Enright, AM and O'Flaherty, V}, title = {Temperature dependent (37-15°C) anaerobic digestion of a trichloroethylene-contaminated wastewater.}, journal = {Bioresource technology}, volume = {102}, number = {17}, pages = {7645-7656}, doi = {10.1016/j.biortech.2011.05.055}, pmid = {21715158}, issn = {1873-2976}, mesh = {*Anaerobiosis ; Archaea/genetics/metabolism ; Base Sequence ; Biomass ; Bioreactors ; DNA Primers ; Electrophoresis, Polyacrylamide Gel ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Temperature ; Trichloroethylene/*metabolism ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The impact of a trichloroethylene (TCE) contaminated wastewater on the microbial community structure of an anaerobic granular biomass at 15°C compared to 37°C was investigated. Four expanded granular sludge bed (EGSB) bioreactors (R1-R4) were employed in pairs at 37 and 15°C. The influents of one of each pair were supplemented with increasing concentrations of TCE (max. 60 mgl(-1)). At 37°C, stable operation was maintained with 88% COD removal and >99% TCE removal at maximum influent TCE concentrations. R3 performance decreased at influent TCE concentration of 60 mgl(-1), although TCE removal rates of >97% were recorded. Archaeal community analysis via clone library and quantitative polymerase chain reaction (qPCR) analysis, and bacterial community analysis via denaturing gradient gel electrophoresis (DGGE), indicated that temperature resulted in a greater change in community structure than the presence of TCE, and clones related to cold adaptation of biomass were identified at 15°C.}, }
@article {pmid21713435, year = {2011}, author = {Wang, Y and Boyd, E and Crane, S and Lu-Irving, P and Krabbenhoft, D and King, S and Dighton, J and Geesey, G and Barkay, T}, title = {Environmental conditions constrain the distribution and diversity of archaeal merA in Yellowstone National Park, Wyoming, U.S.A.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {739-752}, pmid = {21713435}, issn = {1432-184X}, mesh = {Archaea/enzymology/*genetics ; DNA Primers/genetics ; DNA, Archaeal/genetics ; *Genes, Archaeal ; Hot Springs/*microbiology ; Linear Models ; Models, Genetic ; Oxidoreductases/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Water Microbiology ; Wyoming ; }, abstract = {The distribution and phylogeny of extant protein-encoding genes recovered from geochemically diverse environments can provide insight into the physical and chemical parameters that led to the origin and which constrained the evolution of a functional process. Mercuric reductase (MerA) plays an integral role in mercury (Hg) biogeochemistry by catalyzing the transformation of Hg(II) to Hg(0). Putative merA sequences were amplified from DNA extracts of microbial communities associated with mats and sulfur precipitates from physicochemically diverse Hg-containing springs in Yellowstone National Park, Wyoming, using four PCR primer sets that were designed to capture the known diversity of merA. The recovery of novel and deeply rooted MerA lineages from these habitats supports previous evidence that indicates merA originated in a thermophilic environment. Generalized linear models indicate that the distribution of putative archaeal merA lineages was constrained by a combination of pH, dissolved organic carbon, dissolved total mercury and sulfide. The models failed to identify statistically well supported trends for the distribution of putative bacterial merA lineages as a function of these or other measured environmental variables, suggesting that these lineages were either influenced by environmental parameters not considered in the present study, or the bacterial primer sets were designed to target too broad of a class of genes which may have responded differently to environmental stimuli. The widespread occurrence of merA in the geothermal environments implies a prominent role for Hg detoxification in these environments. Moreover, the differences in the distribution of the merA genes amplified with the four merA primer sets suggests that the organisms putatively engaged in this activity have evolved to occupy different ecological niches within the geothermal gradient.}, }
@article {pmid21713434, year = {2011}, author = {Fan, F and Yang, Q and Li, Z and Wei, D and Cui, X and Liang, Y}, title = {Impacts of organic and inorganic fertilizers on nitrification in a cold climate soil are linked to the bacterial ammonia oxidizer community.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {982-990}, pmid = {21713434}, issn = {1432-184X}, mesh = {Ammonia/metabolism ; Archaea/genetics/*growth &amp; development/metabolism ; Bacteria/genetics/*growth &amp; development/metabolism ; China ; *Cold Climate ; DNA, Archaeal/genetics/isolation &amp; purification ; DNA, Bacterial/genetics/isolation &amp; purification ; *Fertilizers ; Genes, Archaeal ; Genes, Bacterial ; *Nitrification ; Oxidoreductases/genetics ; Soil/analysis ; *Soil Microbiology ; }, abstract = {The microbiology underpinning soil nitrogen cycling in northeast China remains poorly understood. These agricultural systems are typified by widely contrasting temperature, ranging from -40 to 38°C. In a long-term site in this region, the impacts of mineral and organic fertilizer amendments on potential nitrification rate (PNR) were determined. PNR was found to be suppressed by long-term mineral fertilizer treatment but enhanced by manure treatment. The abundance and structure of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities were assessed using quantitative polymerase chain reaction and denaturing gradient gel electrophoresis techniques. The abundance of AOA was reduced by all fertilizer treatments, while the opposite response was measured for AOB, leading to a six- to 60-fold reduction in AOA/AOB ratio. The community structure of AOA exhibited little variation across fertilization treatments, whereas the structure of the AOB community was highly responsive. PNR was correlated with community structure of AOB rather than that of AOA. Variation in the community structure of AOB was linked to soil pH, total carbon, and nitrogen contents induced by different long-term fertilization regimes. The results suggest that manure amendment establishes conditions which select for an AOB community type which recovers mineral fertilizer-suppressed soil nitrification.}, }
@article {pmid21710225, year = {2012}, author = {Krüger, T and Hölzel, N and Luckas, B}, title = {Influence of cultivation parameters on growth and microcystin production of Microcystis aeruginosa (Cyanophyceae) isolated from Lake Chao (China).}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {199-209}, pmid = {21710225}, issn = {1432-184X}, mesh = {Bacterial Toxins/*biosynthesis ; China ; Cryopreservation ; Culture Media, Conditioned ; Hydrogen-Ion Concentration ; Lakes/*microbiology ; Microcystins/*biosynthesis ; Microcystis/*growth &amp; development/isolation &amp; purification/*metabolism ; Nitrates/metabolism ; Nitrogen/metabolism ; Phosphates/metabolism ; Synechocystis ; }, abstract = {Microcystis aeruginosa isolated in 2005 from the shallow eutrophic Lake Chao (Anhui, China) was investigated in terms of growth parameters and microcystin production under varying nutrient concentrations (P, N) and pH values (abiotic factors) as well as under the influence of spent medium of the non-toxic cyanobacterium Synechocystis sp. (biotic factors). Stimulating effects on growth were observed at the alkaline pH value (10.5), whereas toxin production was significantly increased under phosphate-P limitation (0.6 mg L(-1) medium). Within a broad range of nitrate-N concentrations (41.2-247.2 mg L(-1) medium), no significant influence on cell growth and microcystin production was observed; however, N-starvation resulted in a typical decrease of growth and toxicity. In addition, cryopreservation of M. aeruginosa evidenced the decrease of toxin production by time-dependent exposure with the cryoprotectant dimethyl sulfoxide under thawing conditions without affecting the growth of the cyanobacterial cells.}, }
@article {pmid21709214, year = {2011}, author = {Winget, DM and Helton, RR and Williamson, KE and Bench, SR and Williamson, SJ and Wommack, KE}, title = {Repeating patterns of virioplankton production within an estuarine ecosystem.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {28}, pages = {11506-11511}, pmid = {21709214}, issn = {1091-6490}, mesh = {Bacteria/virology ; Biodiversity ; Carbon Cycle ; Delaware ; *Ecosystem ; Fresh Water/microbiology/virology ; Plankton/*virology ; Seasons ; Seawater/microbiology/virology ; }, abstract = {The Chesapeake Bay, a seasonally variable temperate estuary, provides a natural laboratory for examining the fluctuations and impacts of viral lysis on aquatic microorganisms. Viral abundance (VA) and viral production (VP) were monitored in the Chesapeake Bay over 4 1/2 annual cycles, producing a unique, long-term, interannual study of virioplankton production. High and dynamic VP rates, averaging 7.9 × 10(6) viruses per mL per h, indicate that viral lysis impacts a significant fraction of microorganisms in the Chesapeake. Viral-mediated bacterial mortality, VA, VP, and organic carbon release all displayed similar interannual and seasonal trends with higher values in 2003 and 2006 than in 2004 and 2005 and peaks in early spring and summer. Surprisingly, higher rates of viral lysis occurred in winter, resulting in a magnified effect of viral lysis on bacterioplankton during times of reduced productivity. Viral lysis directly impacted the organic carbon pool, contributing on average 76 μg of C per L per d, an amount capable of sustaining ∼55% of Chesapeake Bay bacterial production. The observed repeating interannual patterns of VP and lysis are likely interlinked with seasonal cycles of host abundance and diversity, which are in turn driven by annual cycles in environmental conditions, emphasizing the complex interplay of seasonality and microbial ecology in the Chesapeake Bay.}, }
@article {pmid21707958, year = {2012}, author = {Canbäck, B and André, C and Galindo, J and Johannesson, K and Johansson, T and Panova, M and Tunlid, A and Butlin, R}, title = {The Littorina sequence database (LSD)--an online resource for genomic data.}, journal = {Molecular ecology resources}, volume = {12}, number = {1}, pages = {142-148}, doi = {10.1111/j.1755-0998.2011.03042.x}, pmid = {21707958}, issn = {1755-0998}, mesh = {Animals ; *Databases, Genetic ; Gastropoda/*genetics ; Genetic Markers ; Genomics/*instrumentation ; Internet ; Online Systems ; User-Computer Interface ; }, abstract = {We present an interactive, searchable expressed sequence tag database for the periwinkle snail Littorina saxatilis, an upcoming model species in evolutionary biology. The database is the result of a hybrid assembly between Sanger and 454 sequences, 1290 and 147,491 sequences respectively. Normalized and non-normalized cDNA was obtained from different ecotypes of L. saxatilis collected in the UK and Sweden. The Littorina sequence database (LSD) contains 26,537 different contigs, of which 2453 showed similarity with annotated proteins in UniProt. Querying the LSD permits the selection of the taxonomic origin of blast hits for each contig, and the search can be restricted to particular taxonomic groups. The database allows access to UniProt annotations, blast output, protein family domains (PFAM) and Gene Ontology. The database will allow users to search for genetic markers and identifying candidate genes or genes for expression analyses. It is open for additional deposition of sequence information for L. saxatilis and other species of the genus Littorina. The LSD is available at http://mbio-serv2.mbioekol.lu.se/Littorina/.}, }
@article {pmid21706196, year = {2011}, author = {Kayee, P and Sonthiphand, P and Rongsayamanont, C and Limpiyakorn, T}, title = {Archaeal amoA genes outnumber bacterial amoA genes in municipal wastewater treatment plants in Bangkok.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {776-788}, pmid = {21706196}, issn = {1432-184X}, mesh = {Ammonia ; Archaea/enzymology/*genetics ; Betaproteobacteria/enzymology/*genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; *Genes, Archaeal ; *Genes, Bacterial ; Oxidoreductases/genetics ; Phylogeny ; Sequence Analysis, DNA ; Sewage/*microbiology ; Thailand ; Water Microbiology ; }, abstract = {The contribution of ammonia-oxidizing archaea (AOA) to nitrogen removal in wastewater treatment plants (WWTPs) remains unknown. This study investigated the abundance of archaeal (AOA) and bacterial (ammonia-oxidizing bacteria (AOB)) amoA genes in eight of Bangkok's municipal WWTPs. AOA amoA genes (3.28 × 10(7) ± 1.74 × 10(7)-2.23 × 10(11) ± 1.92 × 10(11) copies l(-1) sludge) outnumbered AOB amoA genes in most of the WWTPs even though the plants' treatment processes, influent and effluent characteristics, removal efficiencies, and operation varied. An estimation of the ammonia-oxidizing activity of AOA and AOB suggests that AOA involved in autotrophic ammonia oxidation in the WWTPs. Statistical analysis shows that the numbers of AOA amoA genes correlated negatively to the ammonium levels in effluent wastewater, while no correlation was found between the AOA amoA gene numbers and the oxygen concentrations in aeration tanks. An analysis of the AOB sequences shows that AOB found in the WWTPs limited to only two AOB clusters which exhibit high or moderate affinity to ammonia. In contrast to AOB, AOA sequences of various clusters were retrieved, and they were previously recovered from a variety of environments, such as thermal and marine environments.}, }
@article {pmid21701871, year = {2011}, author = {Cao, S and Wang, J and Chen, D}, title = {Influence of illumination on settlement of diatom Navicula sp.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {931-940}, pmid = {21701871}, issn = {1432-184X}, mesh = {*Biofouling ; Diatoms/*radiation effects ; *Light ; Lighting ; }, abstract = {Diatoms are responsible for biofouling, which causes many problems in various marine industries. This study examined the effects of different light conditions (intensity, incident direction, time of illumination) on the settling behavior of the marine diatom Navicula sp. on glass surfaces. The density of this diatom's settlement on glass was strongly influenced by light conditions. Moreover, very weak light emitted on the bottom of the culture dish could also rapidly inhibit diatom settlement. These phenomena were explained by spatial interference between chloroplast and holdfast-like structures inside the thecae. The holdfast-like structure is observed to be responsible for diatom locomotion and hence the settlement behavior. It was proposed that the interrelation of illumination and attachment of diatoms allowed them to better adapt to the habitat with higher efficiency of attachment and successive reproduction.}, }
@article {pmid21698403, year = {2011}, author = {Boucher, D and Laffaire, JB and Jaziri, F and David, C and Biderre-Petit, C and Duquenne, P and Peyretaillade, E and Peyret, P}, title = {Bacterial community composition of biological degreasing systems and health risk assessment for workers.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {868-881}, pmid = {21698403}, issn = {1432-184X}, mesh = {Bacteria/genetics/*isolation &amp; purification ; Colony Count, Microbial ; *Industrial Microbiology ; *Occupational Exposure ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Risk Assessment ; Waste Disposal, Fluid/methods ; }, abstract = {Biological degreasing system is a new technology based on the degradation capabilities of microorganisms to remove oil, grease, or lubricants from metal parts. No data is available about the potential biological health hazards in such system. Thus, a health risk assessment linked to the bacterial populations present in this new degreasing technology is, therefore, necessary for workers. We performed both cultural and molecular approaches in several biological degreasing systems for various industrial contexts to investigate the composition and dynamics of bacterial populations. These biological degreasing systems did not work with the original bacterial populations. Indeed, they were colonized by a defined and restricted group of bacteria. This group replaced the indigenous bacterial populations known for degrading complex substrates. Klebsiella pneumoniae, Klebsiella oxytoca, Pseudomonas aeruginosa, and Pantoea agglomerans were important members of the microflora found in most of the biological degreasing systems. These bacteria might represent a potential health hazard for workers.}, }
@article {pmid21698402, year = {2011}, author = {Gao, W and Shi, X and Wu, J and Jin, Y and Zhang, W and Meldrum, DR}, title = {Phylogenetic and gene expression analysis of cyanobacteria and diatoms in the twilight waters of the temperate northeast Pacific Ocean.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {765-775}, pmid = {21698402}, issn = {1432-184X}, mesh = {Autotrophic Processes ; Cyanobacteria/*genetics ; DNA, Bacterial/genetics ; Diatoms/*genetics ; Gene Expression Profiling ; Gene Library ; Pacific Ocean ; Photosynthesis ; *Phylogeny ; Plastids/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Seawater/*microbiology ; Water Microbiology ; }, abstract = {In this study, to explore the microbial community structure and its functionality in the deep-sea environments, we initially performed a 16S ribosomal RNA (rRNA)-based community structure analyses for microbial communities in the sea water collected from sites of 765-790 m in depth in the Pacific Ocean. Interestingly, in the clone library we detected the presence of both photoautotrophic bacteria such as cyanobacteria and photoheterotrophic bacteria, such as Chloroflexus sp. To further explore the existence and diversity of possible light-utilizing microorganisms, we then constructed and analyzed a 23S rRNA plastid gene cloning library. The results showed that the majority of this cloning library was occupied by oxygenic photoautotrophic organisms, such as diatoms Thalassiosira spp. and cyanobacterium Synechococcus sp. In addition, the diversity of these oxygenic photoautotrophic organisms was very limited. Moreover, both reverse-transcription PCR and quantitative reverse-transcription PCR approaches had been employed to detect expression of the genes involved in protein synthesis and photosynthesis of photoautotrophic organisms, and the positive results were obtained. The possible mechanisms underlying the existence of very limited diversity of photosynthetic organisms at this depth of ocean, as well as the positive detection of rRNA and mRNA of diatom and cyanobacteria, were discussed.}, }
@article {pmid21698401, year = {2011}, author = {Feng, Y and Lin, X and Yu, Y and Zhu, J}, title = {Elevated ground-level O(3) changes the diversity of anoxygenic purple phototrophic bacteria in paddy field.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {789-799}, pmid = {21698401}, issn = {1432-184X}, mesh = {DNA Fingerprinting ; DNA, Bacterial/genetics ; Ecosystem ; Genes, Bacterial ; Genetic Variation ; Genotyping Techniques ; Oryza/*microbiology ; Ozone/*analysis ; *Phylogeny ; Proteobacteria/genetics/*growth &amp; development ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The knowledge of the impact of elevated ground-level O(3) below ground the agro-ecosystem is limited. A field experiment in China Ozone Free-Air Concentration Enrichment (FACE-O(3)) facility on a rice-wheat rotation system was carried out to investigate responses of anoxygenic phototrophic purple bacteria (AnPPB) to elevated ground-level O(3). AnPPB community structures and sizes in paddy soil were monitored by molecular approaches including PCR-DGGE and real-time quantitative PCR based upon the pufM gene on three typical rice growth stages. Repetitive sequence-based PCR (rep-PCR) in combination with culture-reliant method was conducted to reveal changes in genotypic diversity. Elevated ground-level O(3) statistically reduce AnPPB abundance and percentage in total bacterial community in flooded rice soil via decreasing their genotypic diversity and metabolic versatility. Concomitantly, their community composition changed after rice anthesis stage under elevated ground-level O(3). Our results from AnPPB potential responses imply that continuously elevated ground-level O(3) in the future would eventually harm the health of paddy ecosystem through negative effect on soil microorganisms.}, }
@article {pmid21697960, year = {2012}, author = {Brettar, I and Christen, R and Höfle, MG}, title = {Analysis of bacterial core communities in the central Baltic by comparative RNA-DNA-based fingerprinting provides links to structure-function relationships.}, journal = {The ISME journal}, volume = {6}, number = {1}, pages = {195-212}, pmid = {21697960}, issn = {1751-7370}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Baltic States ; DNA Fingerprinting/*methods ; DNA, Bacterial/*analysis/genetics ; *Genes, rRNA ; Oceans and Seas ; Phylogeny ; Plankton/*classification/genetics/isolation &amp; purification ; Polymorphism, Single-Stranded Conformational ; RNA, Ribosomal, 16S/*analysis/genetics ; Seawater/*microbiology ; }, abstract = {Understanding structure-function links of microbial communities is a central theme of microbial ecology since its beginning. To this end, we studied the spatial variability of the bacterioplankton community structure and composition across the central Baltic Sea at four stations, which were up to 450 km apart and at a depth profile representative for the central part (Gotland Deep, 235 m). Bacterial community structure was followed by 16S ribosomal RNA (rRNA)- and 16S rRNA gene-based fingerprints using single-strand conformation polymorphism (SSCP) electrophoresis. Species composition was determined by sequence analysis of SSCP bands. High similarities of the bacterioplankton communities across several hundred kilometers were observed in the surface water using RNA- and DNA-based fingerprints. In these surface communities, the RNA- and DNA-based fingerprints resulted in very different pattern, presumably indicating large difference between the active members of the community as represented by RNA-based fingerprints and the present members represented by the DNA-based fingerprints. This large discrepancy changed gradually over depth, resulting in highly similar RNA- and DNA-based fingerprints in the anoxic part of the water column below 130 m depth. A conceivable mechanism explaining this high similarity could be the reduced oxidative stress in the anoxic zone. The stable communities on the surface and in the anoxic zone indicate the strong influence of the hydrography on the bacterioplankton community structure. Comparative analysis of RNA- and DNA-based community structure provided criteria for the identification of the core community, its key members and their links to biogeochemical functions.}, }
@article {pmid21694499, year = {2011}, author = {Nava, GM and Stappenbeck, TS}, title = {Diversity of the autochthonous colonic microbiota.}, journal = {Gut microbes}, volume = {2}, number = {2}, pages = {99-104}, pmid = {21694499}, issn = {1949-0984}, support = {P30 DK052574/DK/NIDDK NIH HHS/United States ; R01 AI084887/AI/NIAID NIH HHS/United States ; DK52574/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Biodiversity ; Cluster Analysis ; Colon/*microbiology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Humans ; *Metagenome ; Mice ; Mucous Membrane/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {A longstanding hypothesis in intestinal microbial ecology is that autochthonous microbes (resident) play a role that is distinct from allochthonous microbes (transient microbes in the fecal stream). A challenge has been to identify this pool of microbes. We used laser capture microdissection to collect microbes from the mouse ascending colon. This area contains transverse folds that mimic human intestinal folds and contains a distinct population of intestinal microbes that is associated with the mucosa. Our analysis of bacterial 16S rRNA genes showed that this area was enriched for Lachnospiraceae and Ruminococcaceae. In this addendum, we further compare this community to studies of mucosa-associated microbes in humans. This analysis reveals common phylogenetic groups of bacteria that are present in both mouse and human. However, we found microorganisms at the genus and species levels including Faecalibacterium prausnitzii which appears to be specific for humans. We propose that that examination of the mucosa-associated microbes in wild type and genetically modified mice will be a valuable component to define host microbial interactions that are essential for homeostasis.}, }
@article {pmid21690563, year = {2011}, author = {Collingro, A and Tischler, P and Weinmaier, T and Penz, T and Heinz, E and Brunham, RC and Read, TD and Bavoil, PM and Sachse, K and Kahane, S and Friedman, MG and Rattei, T and Myers, GS and Horn, M}, title = {Unity in variety--the pan-genome of the Chlamydiae.}, journal = {Molecular biology and evolution}, volume = {28}, number = {12}, pages = {3253-3270}, pmid = {21690563}, issn = {1537-1719}, support = {R01 AI051472/AI/NIAID NIH HHS/United States ; 1R01AI051472/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Outer Membrane Proteins/chemistry/genetics ; Bacterial Proteins/chemistry/genetics ; Bacterial Secretion Systems/genetics ; Base Sequence ; Cell Membrane ; Chlamydia/classification/*genetics/pathogenicity ; Chlamydiales/classification/*genetics/pathogenicity ; DNA, Bacterial/analysis/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Bacterial ; Host-Pathogen Interactions ; Molecular Sequence Data ; Phylogeny ; Plasmids ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Chlamydiae are evolutionarily well-separated bacteria that live exclusively within eukaryotic host cells. They include important human pathogens such as Chlamydia trachomatis as well as symbionts of protozoa. As these bacteria are experimentally challenging and genetically intractable, our knowledge about them is still limited. In this study, we obtained the genome sequences of Simkania negevensis Z, Waddlia chondrophila 2032/99, and Parachlamydia acanthamoebae UV-7. This enabled us to perform the first comprehensive comparative and phylogenomic analysis of representative members of four major families of the Chlamydiae, including the Chlamydiaceae. We identified a surprisingly large core gene set present in all genomes and a high number of diverse accessory genes in those Chlamydiae that do not primarily infect humans or animals, including a chemosensory system in P. acanthamoebae and a type IV secretion system. In S. negevensis, the type IV secretion system is encoded on a large conjugative plasmid (pSn, 132 kb). Phylogenetic analyses suggested that a plasmid similar to the S. negevensis plasmid was originally acquired by the last common ancestor of all four families and that it was subsequently reduced, integrated into the chromosome, or lost during diversification, ultimately giving rise to the extant virulence-associated plasmid of pathogenic chlamydiae. Other virulence factors, including a type III secretion system, are conserved among the Chlamydiae to variable degrees and together with differences in the composition of the cell wall reflect adaptation to different host cells including convergent evolution among the four chlamydial families. Phylogenomic analysis focusing on chlamydial proteins with homology to plant proteins provided evidence for the acquisition of 53 chlamydial genes by a plant progenitor, lending further support for the hypothesis of an early interaction between a chlamydial ancestor and the primary photosynthetic eukaryote.}, }
@article {pmid21690380, year = {2011}, author = {Mitri, S and Xavier, JB and Foster, KR}, title = {Social evolution in multispecies biofilms.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108 Suppl 2}, number = {Suppl 2}, pages = {10839-10846}, pmid = {21690380}, issn = {1091-6490}, support = {242670/ERC_/European Research Council/International ; }, mesh = {Bacteria/growth &amp; development ; Biofilms/*growth &amp; development ; *Biological Evolution ; Computer Simulation ; Ecology ; *Environment ; Genome, Bacterial ; Species Specificity ; }, abstract = {Microbial ecology is revealing the vast diversity of strains and species that coexist in many environments, ranging from free-living communities to the symbionts that compose the human microbiome. In parallel, there is growing evidence of the importance of cooperative phenotypes for the growth and behavior of microbial groups. Here we ask: How does the presence of multiple species affect the evolution of cooperative secretions? We use a computer simulation of spatially structured cellular groups that captures key features of their biology and physical environment. When nutrient competition is strong, we find that the addition of new species can inhibit cooperation by eradicating secreting strains before they can become established. When nutrients are abundant and many species mix in one environment, however, our model predicts that secretor strains of any one species will be surrounded by other species. This "social insulation" protects secretors from competition with nonsecretors of the same species and can improve the prospects of within-species cooperation. We also observe constraints on the evolution of mutualistic interactions among species, because it is difficult to find conditions that simultaneously favor both within- and among-species cooperation. Although relatively simple, our model reveals the richness of interactions between the ecology and social evolution of multispecies microbial groups, which can be critical for the evolution of cooperation.}, }
@article {pmid21682840, year = {2011}, author = {Meyer, KM and Macalady, JL and Fulton, JM and Kump, LR and Schaperdoth, I and Freeman, KH}, title = {Carotenoid biomarkers as an imperfect reflection of the anoxygenic phototrophic community in meromictic Fayetteville Green Lake.}, journal = {Geobiology}, volume = {9}, number = {4}, pages = {321-329}, doi = {10.1111/j.1472-4669.2011.00285.x}, pmid = {21682840}, issn = {1472-4669}, mesh = {Biomarkers/analysis ; Carotenoids/*analysis ; Fresh Water/*analysis ; Geologic Sediments/*analysis ; New York ; Phototrophic Processes ; Phytoplankton/*chemistry/genetics ; RNA, Ribosomal, 16S/*chemistry ; }, abstract = {Organic biomarkers in marine sedimentary rocks hold important clues about the early history of Earth's surface environment. The chemical relicts of carotenoids from anoxygenic sulfur bacteria are of particular interest to geoscientists because of their potential to signal episodes of marine photic-zone euxinia such as those proposed for extended periods in the Proterozoic as well as brief intervals during the Phanerozoic. It is therefore critical to constrain the environmental and physiological factors that influence carotenoid production and preservation in modern environments. Here, we present the results of coupled pigment and nucleic acid clone library analyses from planktonic and benthic samples collected from a microbially dominated meromictic lake, Fayetteville Green Lake (New York). Purple sulfur bacteria (PSB) are abundant and diverse both in the water column at the chemocline and in benthic mats below oxygenated shallow waters, with different PSB species inhabiting the two environments. Okenone (from PSB) is an abundant carotenoid in both the chemocline waters and in benthic mats. Green sulfur bacteria and their primary pigment Bchl e are also represented in and below the chemocline. However, the water column and sediments are devoid of the green sulfur bacteria carotenoid isorenieratene. The unexpected absence of isorenieratene and apparent benthic production of okenone provide strong rationale for continued exploration of the microbial ecology of biomarker production in modern euxinic environments.}, }
@article {pmid21682098, year = {2011}, author = {Plewa, K and Lone, E}, title = {Seasonal biodiversity of pathogenic fungi in farming air area. Case study.}, journal = {Wiadomosci parazytologiczne}, volume = {57}, number = {2}, pages = {118-122}, pmid = {21682098}, issn = {0043-5163}, mesh = {*Agriculture ; *Air Microbiology ; Air Pollutants/*isolation &amp; purification ; Animal Husbandry ; Animals ; *Biodiversity ; *Environmental Monitoring ; Fungi/classification/*isolation &amp; purification ; Poland ; Poultry ; *Seasons ; Species Specificity ; }, abstract = {Poultry production proved to be a significant source of bioaerosols. The exposure to high concentration of microorganisms in the air can cause primarily irritations, infections, allergies, and toxic effects. The aim of the present study was to investigate the seasonal biodiversity of airborne fungi in the poultry house, in the surrounding area, as well as to estimate health risk. Seasonal investigations were conducted in the spring, summer, autumn and winter 2010 in the poultry house located near Wrocław in Lower Silesia (Poland). The air samples were collected with the use of a Merck MAS-100 onto nutrient Sabouraud agar and were incubated for 5 days at 26 degrees C. Subsequently the colony-forming units (CFU) were determined. The identification of the isolated fungi was made in accordance with the standard procedures. In the summer and autumn when the weather conditions are most friendly for the spread and the development of numerous microorganisms, fungi were more abundant in the surrounding area than in early spring and winter, when both humidity and temperature were lower. The total of 26 species were analysed (10 in the poultry house and 17 in the surrounding areas). Among 12 fungal genera: Aspergillus, Penicilium, Alternaria, Exophiala, Mycelia sterilla, Fusarium, Cladosporium, Scopulariopsis, Chaetomium, Acremonium, Candida and Rhodotorula nearly everything occurred to be the potential respiratory allergens.}, }
@article {pmid21671962, year = {2011}, author = {de Menezes, AB and Lewis, E and O'Donovan, M and O'Neill, BF and Clipson, N and Doyle, EM}, title = {Microbiome analysis of dairy cows fed pasture or total mixed ration diets.}, journal = {FEMS microbiology ecology}, volume = {78}, number = {2}, pages = {256-265}, doi = {10.1111/j.1574-6941.2011.01151.x}, pmid = {21671962}, issn = {1574-6941}, mesh = {Animal Husbandry/methods ; Animals ; Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Biodiversity ; Cattle ; Dairying/*methods ; Diet/methods/*veterinary ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Genome, Protozoan/genetics ; *Metagenome ; Methane/analysis/metabolism ; Rumen/microbiology/parasitology ; }, abstract = {Understanding rumen microbial ecology is essential for the development of feed systems designed to improve livestock productivity, health and for methane mitigation strategies from cattle. Although rumen microbial communities have been studied previously, few studies have applied next-generation sequencing technologies to that ecosystem. The aim of this study was to characterize changes in microbial community structure arising from feeding dairy cows two widely used diets: pasture and total mixed ration (TMR). Bacterial, archaeal and protozoal communities were characterized by terminal restriction fragment length polymorphism of the amplified SSU rRNA gene and statistical analysis showed that bacterial and archaeal communities were significantly affected by diet, whereas no effect was observed for the protozoal community. Deep amplicon sequencing of the 16S rRNA gene revealed significant differences in the bacterial communities between the diets and between rumen solid and liquid content. At the family level, some important groups of rumen bacteria were clearly associated with specific diets, including the higher abundance of the Fibrobacteraceae in TMR solid samples and members of the propionate-producing Veillonelaceae in pasture samples. This study will be relevant to the study of rumen microbial ecology and livestock feed management.}, }
@article {pmid21669296, year = {2011}, author = {Vavias, S and Alexopoulos, A and Plessas, S and Stefanis, C and Voidarou, C and Stavropoulou, E and Bezirtzoglou, E}, title = {Microbial ecology of the watery ecosystems of Evros river in North Eastern Greece and its influence upon the cultivated soil ecosystem.}, journal = {Anaerobe}, volume = {17}, number = {6}, pages = {325-329}, doi = {10.1016/j.anaerobe.2011.05.005}, pmid = {21669296}, issn = {1095-8274}, mesh = {Agriculture ; *Biota ; *Ecosystem ; Greece ; Human Activities ; Humans ; Industry ; Rivers/*microbiology ; *Soil Microbiology ; *Water Microbiology ; Water Pollution ; }, abstract = {The aim of the present study was to evaluate the microbial ecosystem of cultivated soils along the Evros river in NE Greece. Evros river together with its derivative rivers constitute the capital source of life and sustainable development of the area. Along this riverside watery ecosystem systematic agro-cultures were developed such as wheat, corn and vegetable cultures. The evaluation of the ecosystem microbial charge was conducted in both axes which are the watery ecosystem and the riverside cultivated soil area. Considerable discrimination of water quality was observed when considering chemical and microbiological parameters of the Evros river ecosystem. Ardas river possesses a better water quality than Evros and Erythropotamos, which is mainly due to the higher quantities that these two rivers accumulate from industrial, farming and urban residues leading to higher degree of pollution. An increased microbial pollution was recorded in two of the three rivers monitored and a direct relation in microbial and chemical charging between water and cultivated-soil ecosystems was observed. The protection of these ecosystems with appropriate cultivated practices and control of human and animal activities will define the homeostasis of the environmental area.}, }
@article {pmid21667196, year = {2011}, author = {Otten, TG and Paerl, HW}, title = {Phylogenetic inference of colony isolates comprising seasonal Microcystis blooms in Lake Taihu, China.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {907-918}, pmid = {21667196}, issn = {1432-184X}, mesh = {China ; Chlorophyll/analysis ; Chlorophyll A ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Fresh Water/*microbiology ; *Harmful Algal Bloom ; Lakes/microbiology ; Microcystins/genetics ; Microcystis/classification/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; *Seasons ; Sequence Analysis, DNA ; Temperature ; Wind ; }, abstract = {Blooms of the toxin-producing cyanobacterium, Microcystis spp., are an increasingly prevalent water quality problem and health hazard worldwide. China's third largest lake, Lake Taihu, has been experiencing progressively more severe Microcystis blooms over the past three decades. In 2009 and 2010, individual Microcystis colonies, consisting of four different morphospecies, were isolated and genotyped using a whole-cell multiplex PCR assay. The 16S-23S rDNA-ITS sequences were aligned based on Bayesian inference and indicated that one morphospecies was genetically unique (Microcystis wesenbergii) and three were indistinguishable (Microcystis aeruginosa, Microcystis flos-aquae, and Microcystis ichthyoblabe). Microcystin (mcyB) genes were detected intermittently in two of the morphospecies while the other two morphospecies lacked the mcyB gene in all samples. Water temperature was found to influence bloom formation and morphotype prevalence, and chlorophyll a and temperature were positively and significantly correlated with microcystin concentration. Cooler water temperatures promoted toxigenic strains of Microcystis. Wind appeared to influence the distribution of morphotypes across the lake, with M. aeruginosa and M. ichthyoblabe being more susceptible to wind stress than M. wesenbergii and M. flos-aquae. The results of this study indicated that the blooms were composed of a variety of Microcystis morphospecies, with more genotypes observed than can be attributed to individual morphotypes. We conclude that morphology is not a reliable indicator of toxigenicity in Lake Taihu, and caution should be exercised when the M. aeruginosa morphotype is present because it is capable of producing MC-LR, the most toxic microcystin isoform.}, }
@article {pmid21667195, year = {2011}, author = {Freese, HM and Schink, B}, title = {Composition and stability of the microbial community inside the digestive tract of the aquatic crustacean Daphnia magna.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {882-894}, pmid = {21667195}, issn = {1432-184X}, mesh = {Animals ; Bacteria/*classification/genetics ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Daphnia/*microbiology ; Fresh Water/microbiology ; Gastrointestinal Tract/*microbiology ; Gene Library ; *Metagenome ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Small filter-feeding zooplankton organisms like the cladoceran Daphnia spp. are key members of freshwater food webs. Although several interactions between Daphnia and bacteria have been investigated, the importance of the microbial communities inside Daphnia guts has been studied only poorly so far. In the present study, we characterised the bacterial community composition inside the digestive tract of a laboratory-reared clonal culture of Daphnia magna using 16S rRNA gene libraries and terminal-restriction length polymorphism fingerprint analyses. In addition, the diversity and stability of the intestinal microbial community were investigated over time, with different food sources as well as under starvation stress and death, and were compared to the community in the cultivation water. The diversity of the Daphnia gut microbiota was low. The bacterial community consisted mainly of Betaproteobacteria (e.g. Limnohabitans sp.), few Gammaproteobacteria (e.g. Pseudomonas sp.) and Bacteroidetes that were related to facultatively anaerobic bacteria, but did not contain typical fermentative or obligately anaerobic gut bacteria. Rather, the microbiota was constantly dominated by Limnohabitans sp. which belongs to the Lhab-A1 tribe (previously called R-BT065 cluster) that is abundant in various freshwaters. Other bacterial groups varied distinctly even under constant cultivation conditions. Overall, the intestinal microbial community did not reflect the community in the surrounding cultivation water and clustered separately when analysed via the Additive Main Effects and Multiplicative Interaction model. In addition, the microbiota proved to be stable also when Daphnia were exposed to bacteria associated with a different food alga. After starvation, the community in the digestive tract was reduced to stable members. After death of the host animals, the community composition in the gut changed distinctly, and formerly undetected bacteria were activated. Our results suggest that the Daphnia microbiota consists mainly of an aerobic resident bacterial community which is indigenous to this habitat.}, }
@article {pmid21664638, year = {2011}, author = {Siggins, A and Enright, AM and O'Flaherty, V}, title = {Low-temperature (7 °C) anaerobic treatment of a trichloroethylene-contaminated wastewater: microbial community development.}, journal = {Water research}, volume = {45}, number = {13}, pages = {4035-4046}, doi = {10.1016/j.watres.2011.05.013}, pmid = {21664638}, issn = {1879-2448}, mesh = {Anaerobiosis ; Bioreactors/microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Temperature ; Trichloroethylene/*metabolism ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The feasibility of low-temperature (7 °C) anaerobic digestion for the treatment of a trichloroethylene (TCE) contaminated wastewater was investigated. Two expanded granular sludge bed (EGSB) bioreactors (R1 and R2) were employed for the mineralisation of a synthetic volatile fatty acid based wastewater at an initial organic loading rate (OLR) of 3 kg COD m(-3) d(-1), and an operating temperature of 15 °C. Successive reductions in OLR to 0.75 kg COD m(-3) d(-1), and operational temperature to 7 °C, resulted in stable bioreactor operation by day 417, with COD removal efficiency and biogas CH(4) content ≥ 74%, for both bioreactors. Subsequently, the influent to R1 was supplemented with increasing concentrations (10, 20, 30 mg l(-1)) of TCE, while R2 acted as a control. At an influent TCE concentration of 30 mg l(-1), although phase average TCE removal rates of 79% were recorded, a sustained decrease in R1 performance was observed, with COD removal of 6%, and % biogas CH(4) of 3% recorded on days 595 and 607, respectively. Specific methanogenic activity (SMA) assays identified a general shift from acetate- to hydrogen-mediated methanogenesis in both R1 and R2 biomass, while toxicity assays confirmed an increased sensitivity of the acetoclastic community in R1 to TCE and dichloroethylene (DCE), which contributed to acetate accumulation. Quantitative Polymerase Chain Reaction (qPCR) analysis of the methanogenic community confirmed the dominance of hydrogenotrophic methanogens in both R1 and R2, representing 71-89% of the total methanogenic population, however acetoclastic Methanosaeta were the dominant organisms, based on 16S rRNA gene clone library analysis of reactor biomass. The greatest change in the bacterial community, as demonstrated by UPGMA analysis of DGGE banding profiles, was observed in R1 biomass between days 417 and 609, although 88% similarity was retained between these sampling points.}, }
@article {pmid21663047, year = {2011}, author = {De Gusseme, B and Hennebel, T and Vanhaecke, L and Soetaert, M and Desloover, J and Wille, K and Verbeken, K and Verstraete, W and Boon, N}, title = {Biogenic palladium enhances diatrizoate removal from hospital wastewater in a microbial electrolysis cell.}, journal = {Environmental science &amp; technology}, volume = {45}, number = {13}, pages = {5737-5745}, doi = {10.1021/es200702m}, pmid = {21663047}, issn = {1520-5851}, mesh = {Bacteria/metabolism ; Catalysis ; Diatrizoate/analysis/*metabolism ; Electrolysis/methods ; Graphite ; *Hospitals ; Hydrogen ; Nanoparticles/*chemistry ; Palladium/chemistry/*metabolism ; Spectrum Analysis ; Thermal Conductivity ; Waste Disposal, Fluid/*methods ; Water Pollutants, Chemical/analysis/*metabolism ; Water Purification/*methods ; }, abstract = {To decrease the load of pharmaceuticals to the environment, decentralized wastewater treatment has been proposed for important point-sources such as hospitals. In this study, a microbial electrolysis cell (MEC) was used for the dehalogenation of the iodinated X-ray contrast medium diatrizoate. The presence of biogenic palladium nanoparticles (bio-Pd) in the cathode significantly enhanced diatrizoate removal by direct electrochemical reduction and by reductive catalysis using the H(2) gas produced at the cathode of the MEC. Complete deiodination of 3.3 μM (2 mg L(-1)) diatrizoate from a synthetic medium was achieved after 24 h of recirculation at an applied voltage of -0.4 V. An equimolar amount of the deiodinated metabolite 3,5-diacetamidobenzoate (DAB) was detected. Higher cell voltages increased the dehalogenation rates, resulting in a complete removal after 2 h at -0.8 V. At this cell voltage, the MEC was also able to remove 85% of diatrizoate from hospital effluent containing 0.5 μM (292 μg L(-1)), after 24 h of recirculation. Complete removal was obtained when the effluent was continuously fed at a volumetric loading rate of 204 mg diatrizoate m(-3) total cathodic compartment (TCC) day(-1) to the MEC with a hydraulic retention time of 8 h. At -0.8 V, the MEC system could also eliminate 54% of diatrizoate from spiked urine during a 24 h recirculation experiment. The final product DAB was demonstrated to be removable by nitrifying biomass, which suggests that the combination of a MEC and bio-Pd in its cathode offers potential to dehalogenate pharmaceuticals, and to significantly lower the environmental burden of hospital waste streams.}, }
@article {pmid21661577, year = {2011}, author = {Dingemans, BJ and Bakker, ES and Bodelier, PL}, title = {Aquatic herbivores facilitate the emission of methane from wetlands.}, journal = {Ecology}, volume = {92}, number = {5}, pages = {1166-1173}, doi = {10.1890/10-1297.1}, pmid = {21661577}, issn = {0012-9658}, mesh = {Animals ; Environmental Monitoring ; Feeding Behavior/*physiology ; *Fresh Water ; Geese/*physiology ; Methane/*chemistry/metabolism ; Poaceae/*metabolism ; *Wetlands ; }, abstract = {Wetlands are significant sources of atmospheric methane. Methane produced by microbes enters roots and escapes to the atmosphere through the shoots of emergent wetland plants. Herbivorous birds graze on helophytes, but their effect on methane emission remains unknown. We hypothesized that grazing on shoots of wetland plants can modulate methane emission from wetlands. Diffusive methane emission was monitored inside and outside bird exclosures, using static flux chambers placed over whole vegetation and over single shoots. Both methods showed significantly higher methane release from grazed vegetation. Surface-based diffusive methane emission from grazed plots was up to five times higher compared to exclosures. The absence of an effect on methane-cycling microbial processes indicated that this modulating effect acts on the gas transport by the plants. Modulation of methane emission by animal-plant-microbe interactions deserves further attention considering the increasing bird populations and changes in wetland vegetation as a consequence of changing land use and climate change.}, }
@article {pmid21655235, year = {2011}, author = {Wu, L and Wang, H and Zhang, Z and Lin, R and Zhang, Z and Lin, W}, title = {Comparative metaproteomic analysis on consecutively Rehmannia glutinosa-monocultured rhizosphere soil.}, journal = {PloS one}, volume = {6}, number = {5}, pages = {e20611}, pmid = {21655235}, issn = {1932-6203}, mesh = {Proteomics/*methods ; Rehmannia/*metabolism ; *Rhizosphere ; Soil/*chemistry ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {BACKGROUND: The consecutive monoculture for most of medicinal plants, such as Rehmannia glutinosa, results in a significant reduction in the yield and quality. There is an urgent need to study for the sustainable development of Chinese herbaceous medicine.<br><br>Comparative metaproteomics of rhizosphere soil was developed and used to analyze the underlying mechanism of the consecutive monoculture problems of R. glutinosa. The 2D-gel patterns of protein spots for the soil samples showed a strong matrix dependency. Among the spots, 103 spots with high resolution and repeatability were randomly selected and successfully identified by MALDI TOF-TOF MS for a rhizosphere soil metaproteomic profile analysis. These proteins originating from plants and microorganisms play important roles in nutrient cycles and energy flow in rhizospheric soil ecosystem. They function in protein, nucleotide and secondary metabolisms, signal transduction and resistance. Comparative metaproteomics analysis revealed 33 differentially expressed protein spots in rhizosphere soil in response to increasing years of monoculture. Among them, plant proteins related to carbon and nitrogen metabolism and stress response, were mostly up-regulated except a down-regulated protein (glutathione S-transferase) involving detoxification. The phenylalanine ammonia-lyase was believed to participate in the phenylpropanoid metabolism as shown with a considerable increase in total phenolic acid content with increasing years of monoculture. Microbial proteins related to protein metabolism and cell wall biosynthesis, were up-regulated except a down-regulated protein (geranylgeranyl pyrophosphate synthase) functioning in diterpenoid synthesis. The results suggest that the consecutive monoculture of R. glutinosa changes the soil microbial ecology due to the exudates accumulation, as a result, the nutrient cycles are affected, leading to the retardation of plant growth and development.<br><br>CONCLUSIONS/SIGNIFICANCE: Our results demonstrated the interactions among plant, soil and microflora in the proteomic level are crucial for the productivity and quality of R. glutinosa in consecutive monoculture system.}, }
@article {pmid21647696, year = {2011}, author = {Rokni-Zadeh, H and Mangas-Losada, A and De Mot, R}, title = {PCR detection of novel non-ribosomal peptide synthetase genes in lipopeptide-producing Pseudomonas.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {941-947}, pmid = {21647696}, issn = {1432-184X}, mesh = {Bacterial Proteins/genetics/*metabolism ; DNA, Bacterial/genetics ; Lipopeptides/*biosynthesis ; Peptide Synthases/genetics/*metabolism ; Peptides, Cyclic/biosynthesis ; Phylogeny ; Polymerase Chain Reaction/methods ; Pseudomonas/enzymology/*genetics ; Sequence Analysis, DNA ; }, abstract = {Bacterial lipopeptides (LPs) are a diverse group of secondary metabolites synthesized through one or more non-ribosomal peptide synthetases (NRPSs). In certain genera, such as Pseudomonas and Bacillus, these enzyme systems are often involved in synthesizing biosurfactants or antimicrobial compounds. Several different types of LPs have been reported for non-pathogenic plant-associated Pseudomonas. Focusing on this group of bacteria, we devised and validated a PCR method to detect novel LP-synthesizing NRPS genes by targeting their lipoinitiation and tandem thioesterase domains, thus avoiding amplification of genes for non-LP metabolites, such as the pyoverdine siderophores present in all fluorescent Pseudomonas. This approach enabled detection of as yet unknown NRPS genes in strains producing viscosin, viscosinamide, WLIP, or lokisin. Furthermore, it proved valuable to identify novel candidate LP producers among Pseudomonas rhizosphere isolates. By phylogenetic analysis of these amplicons, several of the corresponding NRPS genes can be tentatively assigned to the viscosin, amphisin, or entolysin biosynthetic groups, while some others may represent novel NRPS systems.}, }
@article {pmid21647227, year = {2011}, author = {Marchesi, JR and Dutilh, BE and Hall, N and Peters, WH and Roelofs, R and Boleij, A and Tjalsma, H}, title = {Towards the human colorectal cancer microbiome.}, journal = {PloS one}, volume = {6}, number = {5}, pages = {e20447}, pmid = {21647227}, issn = {1932-6203}, mesh = {Aged ; Bacterial Adhesion ; Colorectal Neoplasms/*microbiology/pathology ; DNA Fingerprinting ; DNA, Intergenic/genetics ; Denaturing Gradient Gel Electrophoresis ; Female ; Humans ; Intestinal Mucosa/microbiology/pathology ; Male ; *Metagenome ; Middle Aged ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Ribosomes/genetics ; Sequence Analysis, RNA ; }, abstract = {Multiple factors drive the progression from healthy mucosa towards sporadic colorectal carcinomas and accumulating evidence associates intestinal bacteria with disease initiation and progression. Therefore, the aim of this study was to provide a first high-resolution map of colonic dysbiosis that is associated with human colorectal cancer (CRC). To this purpose, the microbiomes colonizing colon tumor tissue and adjacent non-malignant mucosa were compared by deep rRNA sequencing. The results revealed striking differences in microbial colonization patterns between these two sites. Although inter-individual colonization in CRC patients was variable, tumors consistently formed a niche for Coriobacteria and other proposed probiotic bacterial species, while potentially pathogenic Enterobacteria were underrepresented in tumor tissue. As the intestinal microbiota is generally stable during adult life, these findings suggest that CRC-associated physiological and metabolic changes recruit tumor-foraging commensal-like bacteria. These microbes thus have an apparent competitive advantage in the tumor microenvironment and thereby seem to replace pathogenic bacteria that may be implicated in CRC etiology. This first glimpse of the CRC microbiome provides an important step towards full understanding of the dynamic interplay between intestinal microbial ecology and sporadic CRC, which may provide important leads towards novel microbiome-related diagnostic tools and therapeutic interventions.}, }
@article {pmid21646433, year = {2011}, author = {Orcutt, BN and Sylvan, JB and Knab, NJ and Edwards, KJ}, title = {Microbial ecology of the dark ocean above, at, and below the seafloor.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {75}, number = {2}, pages = {361-422}, pmid = {21646433}, issn = {1098-5557}, mesh = {Archaea/classification/*isolation &amp; purification/metabolism ; Bacteria/classification/*isolation &amp; purification/metabolism ; Biodiversity ; Darkness ; Eukaryota/classification/*isolation &amp; purification/metabolism ; Geologic Sediments/*microbiology ; Hot Springs/microbiology ; Seawater/*microbiology ; }, abstract = {The majority of life on Earth--notably, microbial life--occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean-the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.-has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats.}, }
@article {pmid21643700, year = {2011}, author = {Reháková, K and Chlumská, Z and Doležal, J}, title = {Soil cyanobacterial and microalgal diversity in dry mountains of Ladakh, NW Himalaya, as related to site, altitude, and vegetation.}, journal = {Microbial ecology}, volume = {62}, number = {2}, pages = {337-346}, pmid = {21643700}, issn = {1432-184X}, mesh = {*Altitude ; Biota ; Chlorophyll/analysis ; Cyanobacteria/*growth &amp; development ; Microalgae/*growth &amp; development ; Microscopy, Fluorescence/methods ; Multivariate Analysis ; Phototrophic Processes ; Soil/chemistry ; *Soil Microbiology ; Tibet ; }, abstract = {Although phototrophic microbial communities are important components of soils in arid and semi-arid ecosystems around the world, the knowledge of their taxonomic composition and dependency on soil chemistry and vegetation is still fragmentary. We studied the abundance and the diversity of cyanobacteria and eukaryotic microalgae along altitudinal gradients (3,700-5,970 m) at four sites in the dry mountains of Ladakh (Little Tibet, Zanskar Mountains, and Eastern Karakoram), using epifluorescence. The effects of environmental factors (altitude, mountain range, and vegetation type) on soil physico-chemical parameters (pH; texture; organic matter, nitrogen, ammonia, and phosphorus contents; and concentration of chlorophylls and carotenoids) and on the composition and biovolume of phototrophs were tested by multivariate redundancy analysis and variance partitioning. Phototrophs were identified in all collected samples, and phototroph biovolume ranged from 0.08 to 0.32 mm(3) g(-1) dry weight. The dominant component was cyanobacteria, which represented 70.9% to 98.6% of the biovolume. Cyanobacterial species richness was low in that only 28 morphotypes were detected. The biovolume of Oscillatoriales consisted mainly of Phormidium spp. and Microcoleus vaginatus. The environmental factors accounted for 43.8% of the total variability in microbial and soil data, 20.6% of which was explained solely by mountain range, 7.0% by altitude, and 8.4% by vegetation type. Oscillatoriales prevailed in alpine meadows (which had relatively high organic matter and fine soil texture), while Nostocales dominated in the subnival zone and screes. Eukaryotic microalgae together with cyanobacteria in the order Chroococcales were mostly present in the subnival zone. We conclude that the high elevation, semiarid, and arid soils in Ladakh are suitable habitats for microbial phototrophic communities and that the differences in these communities are associated with site, altitude, and vegetation type.}, }
@article {pmid21643699, year = {2011}, author = {Jacobsen, A and Hendriksen, RS and Aaresturp, FM and Ussery, DW and Friis, C}, title = {The Salmonella enterica pan-genome.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {487-504}, pmid = {21643699}, issn = {1432-184X}, mesh = {Comparative Genomic Hybridization ; DNA Transposable Elements ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; *Genome, Bacterial ; Genomic Islands ; Multigene Family ; Plasmids/genetics ; RNA, Ribosomal, 16S/genetics ; Salmonella enterica/*genetics ; Sequence Analysis, DNA ; }, abstract = {Salmonella enterica is divided into four subspecies containing a large number of different serovars, several of which are important zoonotic pathogens and some show a high degree of host specificity or host preference. We compare 45 sequenced S. enterica genomes that are publicly available (22 complete and 23 draft genome sequences). Of these, 35 were found to be of sufficiently good quality to allow a detailed analysis, along with two Escherichia coli strains (K-12 substr. DH10B and the avian pathogenic E. coli (APEC O1) strain). All genomes were subjected to standardized gene finding, and the core and pan-genome of Salmonella were estimated to be around 2,800 and 10,000 gene families, respectively. The constructed pan-genomic dendrograms suggest that gene content is often, but not uniformly correlated to serotype. Any given Salmonella strain has a large stable core, whilst there is an abundance of accessory genes, including the Salmonella pathogenicity islands (SPIs), transposable elements, phages, and plasmid DNA. We visualize conservation in the genomes in relation to chromosomal location and DNA structural features and find that variation in gene content is localized in a selection of variable genomic regions or islands. These include the SPIs but also encompass phage insertion sites and transposable elements. The islands were typically well conserved in several, but not all, isolates--a difference which may have implications in, e.g., host specificity.}, }
@article {pmid21640949, year = {2011}, author = {Maron, PA and Mougel, C and Ranjard, L}, title = {Soil microbial diversity: Methodological strategy, spatial overview and functional interest.}, journal = {Comptes rendus biologies}, volume = {334}, number = {5-6}, pages = {403-411}, doi = {10.1016/j.crvi.2010.12.003}, pmid = {21640949}, issn = {1768-3238}, mesh = {Agriculture ; Bacteria/classification/genetics ; *Biodiversity ; Ecosystem ; Environment ; France ; Microbiology ; *Soil Microbiology ; }, abstract = {Since the development of industrialization, urbanization and agriculture, soils have been subjected to numerous variations in environmental conditions, which have resulted in modifications of the taxonomic diversity and functioning of the indigenous microbial communities. As a consequence, the functional significance of these losses/modifications of biodiversity, in terms of the capacity of ecosystems to maintain the functions and services on which humanity depends, is now of pivotal importance. In this context, one of the main challenges in soil microbial ecology is to better understand and predict the processes that drive soil microbial diversity and the link between diversity and ecosystem process. This review describes past, present and ongoing conceptual and methodological strategies employed to better assess and understand the distribution and evolution of soil microbial diversity with the aim of increasing our capacity to translate such diversity into soil biological functioning and, more widely, into ecosystem services.}, }
@article {pmid21629788, year = {2011}, author = {Wagner, BD and Robertson, CE and Harris, JK}, title = {Application of two-part statistics for comparison of sequence variant counts.}, journal = {PloS one}, volume = {6}, number = {5}, pages = {e20296}, pmid = {21629788}, issn = {1932-6203}, support = {U01 HL081335/HL/NHLBI NIH HHS/United States ; 1U01HL081335-01/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Models, Statistical ; Sequence Analysis/*methods ; }, abstract = {Investigation of microbial communities, particularly human associated communities, is significantly enhanced by the vast amounts of sequence data produced by high throughput sequencing technologies. However, these data create high-dimensional complex data sets that consist of a large proportion of zeros, non-negative skewed counts, and frequently, limited number of samples. These features distinguish sequence data from other forms of high-dimensional data, and are not adequately addressed by statistical approaches in common use. Ultimately, medical studies may identify targeted interventions or treatments, but lack of analytic tools for feature selection and identification of taxa responsible for differences between groups, is hindering advancement. The objective of this paper is to examine the application of a two-part statistic to identify taxa that differ between two groups. The advantages of the two-part statistic over common statistical tests applied to sequence count datasets are discussed. Results from the t-test, the Wilcoxon test, and the two-part test are compared using sequence counts from microbial ecology studies in cystic fibrosis and from cenote samples. We show superior performance of the two-part statistic for analysis of sequence data. The improved performance in microbial ecology studies was independent of study type and sequence technology used.}, }
@article {pmid21625973, year = {2011}, author = {Sullivan, ME and Booth, RK}, title = {The potential influence of short-term environmental variability on the composition of testate amoeba communities in Sphagnum peatlands.}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {80-93}, pmid = {21625973}, issn = {1432-184X}, mesh = {Amoeba/*classification/isolation &amp; purification ; Biodiversity ; *Ecosystem ; Environment ; Sphagnopsida/*parasitology ; Wetlands ; }, abstract = {Testate amoebae are a group of moisture-sensitive, shell-producing protozoa that have been widely used as indicators of changes in mean water-table depth within oligotrophic peatlands. However, short-term environmental variability (i.e., sub-annual) also probably influences community composition. The objective of this study was to assess the potential influence of short-term environmental variability on the composition of testate amoeba communities in Sphagnum-dominated peatlands. Testate amoebae and environmental conditions, including hourly measurements of relative humidity within the upper centimeter of the peatland surface, were examined throughout the 2008 growing season at 72 microsites within 11 peatlands of Pennsylvania and Wisconsin, USA. Relationships among testate amoeba communities, vegetation, depth to water table, pH, and an index of short-term environmental variability (EVI), were examined using nonmetric multidimensional scaling and correlation analysis. Results suggest that EVI influences testate amoeba communities, with some taxa more abundant under highly variable conditions (e.g., Arcella discoides, Difflugia pulex, and Hyalosphenia subflava) and others more abundant when environmental conditions at the peatland surface were relatively stable (e.g., Archerella flavum and Bullinularia indica). The magnitude of environmental variability experienced at the peatland surface appears to be primarily controlled by vegetation composition and density. In particular, sites with dense Sphagnum cover had lower EVI values than sites with loose-growing Sphagnum or vegetation dominated by vascular plants and/or non-Sphagnum bryophytes. Our results suggest that more environmental information may be inferred from testate amoebae than previously recognized. Knowledge of relationships between testate amoebae and short-term environmental variability should lead to more detailed and refined environmental inferences.}, }
@article {pmid21625972, year = {2011}, author = {Hook, SE and Steele, MA and Northwood, KS and Wright, AD and McBride, BW}, title = {Impact of high-concentrate feeding and low ruminal pH on methanogens and protozoa in the rumen of dairy cows.}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {94-105}, pmid = {21625972}, issn = {1432-184X}, mesh = {Animal Feed/*analysis ; Animals ; Cattle/microbiology/parasitology/*physiology ; Eating ; Female ; Hydrogen-Ion Concentration ; Lactation ; Methanobrevibacter/classification/genetics/*isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; Rumen/chemistry/metabolism/*microbiology/*parasitology ; Trichostomatida/classification/genetics/*isolation &amp; purification ; }, abstract = {Non-lactating dairy cattle were transitioned to a high-concentrate diet to investigate the effect of ruminal pH suppression, commonly found in dairy cattle, on the density, diversity, and community structure of rumen methanogens, as well as the density of rumen protozoa. Four ruminally cannulated cows were fed a hay diet and transitioned to a 65% grain and 35% hay diet. The cattle were maintained on an high-concentrate diet for 3 weeks before the transition back to an hay diet, which was fed for an additional 3 weeks. Rumen fluid and solids and fecal samples were obtained prior to feeding during weeks 0 (hay), 1, and 3 (high-concentrate), and 4 and 6 (hay). Subacute ruminal acidosis was induced during week 1. During week 3 of the experiment, there was a significant increase in the number of protozoa present in the rumen fluid (P=0.049) and rumen solids (P=0.004), and a significant reduction in protozoa in the rumen fluid in week 6 (P=0.003). No significant effect of diet on density of rumen methanogens was found in any samples, as determined by real-time PCR. Clone libraries were constructed for weeks 0, 3, and 6, and the methanogen diversity of week 3 was found to differ from week 6. Week 3 was also found to have a significantly altered methanogen community structure, compared to the other weeks. Twenty-two unique 16S rRNA phylotypes were identified, three of which were found only during high-concentrate feeding, three were found during both phases of hay feeding, and seven were found in all three clone libraries. The genus Methanobrevibacter comprised 99% of the clones present. The rumen fluid at weeks 0, 3, and 6 of all the animals was found to contain a type A protozoal population. Ultimately, high-concentrate feeding did not significantly affect the density of rumen methanogens, but did alter methanogen diversity and community structure, as well as protozoal density within the rumen of nonlactating dairy cattle. Therefore, it may be necessary to monitor the rumen methanogen and protozoal communities of dairy cattle susceptible to depressed pH when methane abatement strategies are being investigated.}, }
@article {pmid21625971, year = {2011}, author = {Compant, S and Mitter, B and Colli-Mull, JG and Gangl, H and Sessitsch, A}, title = {Endophytes of grapevine flowers, berries, and seeds: identification of cultivable bacteria, comparison with other plant parts, and visualization of niches of colonization.}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {188-197}, pmid = {21625971}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*growth &amp; development/*isolation &amp; purification ; Flowers/microbiology ; Fruit/microbiology ; Molecular Sequence Data ; Phylogeny ; Seeds/microbiology ; Vitis/*microbiology ; }, abstract = {Endophytic bacteria can colonize various plants and organs. However, endophytes colonizing plant reproductive organs have been rarely analyzed. In this study, endophytes colonizing flowers as well as berries and seeds of grapevine plants grown under natural conditions were investigated by cultivation as well as by fluorescence in situ hybridization. For comparison, bacteria were additionally isolated from other plant parts and the rhizosphere and characterized. Flowers, fruits, and seeds hosted various endophytic bacteria. Some taxa were specifically isolated from plant reproductive organs, whereas others were also detected in the rhizosphere, endorhiza or grape inflo/infructescence stalk at the flowering or berry harvest stage. Microscopic analysis by fluorescence in situ hybridization of resin-embedded samples confirmed the presence of the isolated taxa in plant reproductive organs and enabled us to localize them within the plant. Gammaproteobacteria (including Pseudomonas spp.) and Firmicutes (including Bacillus spp.) were visualized inside the epidermis and xylem of ovary and/or inside flower ovules. Firmicutes, mainly Bacillus spp. were additionally visualized inside berries, in the intercellular spaces of pulp cells and/or xylem of pulp, but also along some cell walls inside parts of seeds. Analysis of cultivable bacteria as well as microscopic results indicated that certain endophytic bacteria can colonize flowers, berries, or seeds. Our results also indicated that some specific taxa may not only derive from the root environment but also from other sources such as the anthosphere.}, }
@article {pmid21625245, year = {2011}, author = {Sanchez, C}, title = {Microbial ecology: Bacteria reinforce plant defences.}, journal = {Nature reviews. Microbiology}, volume = {9}, number = {7}, pages = {483}, pmid = {21625245}, issn = {1740-1534}, }
@article {pmid21624126, year = {2011}, author = {Caporaso, JG and Lauber, CL and Costello, EK and Berg-Lyons, D and Gonzalez, A and Stombaugh, J and Knights, D and Gajer, P and Ravel, J and Fierer, N and Gordon, JI and Knight, R}, title = {Moving pictures of the human microbiome.}, journal = {Genome biology}, volume = {12}, number = {5}, pages = {R50}, pmid = {21624126}, issn = {1474-760X}, support = {AI083264/AI/NIAID NIH HHS/United States ; HG004872-02S1/HG/NHGRI NIH HHS/United States ; AI070921/AI/NIAID NIH HHS/United States ; DK078669/DK/NIDDK NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; HG004872/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics ; Computer Simulation ; Gastrointestinal Tract/*microbiology ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; Inflammatory Bowel Diseases/microbiology ; Metagenome/*genetics ; Obesity/microbiology ; Organ Specificity ; RNA, Ribosomal, 16S/genetics ; Seasons ; Time Factors ; }, abstract = {BACKGROUND: Understanding the normal temporal variation in the human microbiome is critical to developing treatments for putative microbiome-related afflictions such as obesity, Crohn’s disease, inflammatory bowel disease and malnutrition. Sequencing and computational technologies, however, have been a limiting factor in performing dense time series analysis of the human microbiome. Here, we present the largest human microbiota time series analysis to date, covering two individuals at four body sites over 396 timepoints.<br><br>RESULTS: We find that despite stable differences between body sites and individuals, there is pronounced variability in an individual&#x2019;s microbiota across months, weeks and even days. Additionally, only a small fraction of the total taxa found within a single body site appear to be present across all time points, suggesting that no core temporal microbiome exists at high abundance (although some microbes may be present but drop below the detection threshold). Many more taxa appear to be persistent but non-permanent community members.<br><br>CONCLUSIONS: DNA sequencing and computational advances described here provide the ability to go beyond infrequent snapshots of our human-associated microbial ecology to high-resolution assessments of temporal variations over protracted periods, within and between body habitats and individuals. This capacity will allow us to define normal variation and pathologic states, and assess responses to therapeutic interventions.}, }
@article {pmid21622836, year = {2012}, author = {Lee, HJ and Han, SI and Whang, KS}, title = {Streptomyces gramineus sp. nov., an antibiotic-producing actinobacterium isolated from bamboo (Sasa borealis) rhizosphere soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {62}, number = {Pt 4}, pages = {856-859}, doi = {10.1099/ijs.0.030163-0}, pmid = {21622836}, issn = {1466-5034}, mesh = {Antibiosis ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Phylogeny ; Pigmentation ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Sasa/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; Streptomyces/*classification/genetics/isolation &amp; purification ; Vitamin K 2/analogs &amp; derivatives/chemistry ; }, abstract = {Two actinobacterial strains, JR-43T and JR-4, were isolated from bamboo (Sasa borealis) rhizosphere soil. The isolates produced grey aerial mycelium and a yellow soluble pigment on ISP 4. Microscopic observation revealed that strains JR-43T and JR-4 produced rectiflexibiles spore chains with spiny surfaces. Both isolates had antibacterial activity against plant-pathogenic bacteria, such as Xanthomonas campestris LMG 568T and Xanthomonas axonopodis pv. vesicatoria LMG 905. The isolates contained iso-C14:0, iso-C15:0, anteiso-C15:0 and iso-C16:0 as the major fatty acids and MK-9(H6) and MK-9(H8) as the major isoprenoid quinones. Phylogenetic analysis of the 16S rRNA gene sequences of strains JR-43T and JR-4 showed that they grouped within Streptomyces cluster II and had highest sequence similarity to Streptomyces seoulensis NBRC 16668T and Streptomyces recifensis NBRC 12813T (both 98.2 % 16S rRNA gene sequence similarity). DNA-DNA relatedness between strain JR-43T and S. seoulensis NBRC 16668T and S. recifensis NBRC 12813T ranged from 31.42 to 42.92 %. Based on DNA-DNA relatedness and morphological and phenotypic data, strains JR-43T and JR-4 could be distinguished from the type strains of phylogenetically related species. They are therefore considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces gramineus sp. nov. is proposed. The type strain is JR-43T (=KACC 15079T=NBRC 107863T). Strain JR-4 (=KACC 15078= NBRC 107864) is a reference strain [corrected].}, }
@article {pmid21617896, year = {2011}, author = {Sercu, B and Van De Werfhorst, LC and Murray, JL and Holden, PA}, title = {Terrestrial sources homogenize bacterial water quality during rainfall in two urbanized watersheds in Santa Barbara, CA.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {574-583}, pmid = {21617896}, issn = {1432-184X}, mesh = {Bacteria/genetics/*isolation &amp; purification ; California ; *Cities ; Colony Count, Microbial ; Feces/microbiology ; Fresh Water/microbiology ; Genetic Markers ; Humans ; Methanobrevibacter/genetics/isolation &amp; purification ; Polymorphism, Restriction Fragment Length ; Rain/microbiology ; *Water Microbiology ; Water Movements ; Water Pollution/analysis ; *Water Quality ; }, abstract = {Microbiological contamination from runoff is a human health concern in urbanized coastal environments, but the contamination sources are often unknown. This study quantified fecal indicator bacteria and compared the distributions of human-specific genetic markers and bacterial community composition during dry and wet weather in urban creeks draining two neighboring watersheds in Santa Barbara, CA. In a prior study conducted during exclusively dry weather, the creeks were contaminated with human waste as indicated by elevated numbers of the human-specific Bacteroidales marker HF183 (Sercu et al. in Environ Sci Technol 43:293-298, 2009). During the storm, fecal indicator bacterial numbers and loads increased orders of magnitude above dry weather conditions. Moreover, bacterial community composition drastically changed during rainfall and differed from dry weather flow by (1) increased bacterial diversity, (2) reduced spatial heterogeneity within and between watersheds, and (3) clone library sequences more related to terrestrial than freshwater taxa. Finally, the spatial patterns of human-associated genetic markers (HF183 and Methanobrevibacter smithii nifH gene) changed during wet weather, and the contribution of surface soils to M. smithii nifH gene detection was suspected. The increased fecal indicator bacteria numbers during wet weather were likely associated with terrestrial sources, instead of human waste sources that dominated during dry weather flow.}, }
@article {pmid21617895, year = {2011}, author = {Passy, SI and Larson, CA}, title = {Succession in stream biofilms is an environmentally driven gradient of stress tolerance.}, journal = {Microbial ecology}, volume = {62}, number = {2}, pages = {414-424}, pmid = {21617895}, issn = {1432-184X}, mesh = {Adaptation, Physiological ; *Biofilms ; *Biota ; Culture Media/chemistry/pharmacology ; Culture Techniques/methods ; Cyanobacteria/drug effects/*growth &amp; development ; Diatoms/drug effects/*growth &amp; development ; Food ; Microbial Interactions ; Nitrogen/pharmacology ; Phosphorus/pharmacology ; *Stress, Physiological ; *Water Movements ; }, abstract = {The century-long research on succession has bestowed us with a number of theories, but little agreement on what causes species replacements through time. The majority of studies has explored the temporal trends of individual species in plant and much less so in microbial communities, arguing that interspecific interactions, especially competition, play a key role in community organization throughout succession. In this experimental investigation of periphytic succession in re-circulating laboratory streams, we examined the density and the relative abundance of diatoms and soft algae for 35 days across gradients of low to high nutrient supply (nitrogen + phosphorus) and low to intermediate current velocity (10 vs. 30 cm·s(-1)). All algal species were classified into trophic groups and morphological guilds, both of which responded more strongly to nutrient than current velocity manipulations, as shown by regression analyses. We concluded that within the manipulated environmental ranges: (1) Succession was a gradient of stress tolerance, driven primarily by nutrient supply and secondarily, by current velocity. Nutrient supply had a qualitative effect in determining whether the contribution of species tolerant vs. sensitive to nutrient limitation would increase through time, while current velocity had a quantitative influence and affected only the rate of this increase. (2) The mechanism of algal succession at a functional level was a neutral coexistence, whereby the tolerant low profile guild maintained high density when overgrown by sensitive species, while sensitive species, constituting mostly the motile and high profile guilds, were neither facilitated nor inhibited by tolerant species but controlled by the environment. It is suggested that the mechanism of succession may depend on the level of biological organization with interspecific interactions giving way to neutral coexistence along the hierarchy from species to functional groups. Considering that the functional makeup is strictly environmentally defined, while species composition reflects local and regional species pools that may exhibit substantial geographic variability, succession is deterministic at a functional level but stochastic at a species level.}, }
@article {pmid21614460, year = {2011}, author = {Villa, F and Pitts, B and Stewart, PS and Giussani, B and Roncoroni, S and Albanese, D and Giordano, C and Tunesi, M and Cappitelli, F}, title = {Efficacy of zosteric acid sodium salt on the yeast biofilm model Candida albicans.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {584-598}, pmid = {21614460}, issn = {1432-184X}, mesh = {Animals ; Antifungal Agents/*pharmacology ; Biofilms/*drug effects ; Candida albicans/*drug effects/growth &amp; development ; Cell Adhesion ; Cell Line ; Chlorhexidine/pharmacology ; Chlorine/pharmacology ; Cinnamates/*pharmacology ; Fatty Acids, Monounsaturated/pharmacology ; Humans ; Hydrogen Peroxide/pharmacology ; Mice ; Sulfuric Acid Esters/*pharmacology ; }, abstract = {Candida albicans is the most notorious and the most widely studied yeast biofilm former. Design of experiments (DoE) showed that 10 mg/L zosteric acid sodium salt reduced C. albicans adhesion and the subsequent biofilm formation by at least 70%, on both hydrophilic and hydrophobic surfaces of 96-well plates. Indeed, biofilm imaging revealed the dramatic impact of zosteric acid sodium salt on biofilm thickness and morphology, due to the inability of the cells to form filamentous structures while remaining metabolically active. In the same way, 10 mg/L zosteric acid sodium salt inhibited C. albicans biofilm formation when added after the adhesion phase. Contrary to zosteric acid sodium salt, methyl zosterate did not affect yeast biofilm. In addition, zosteric acid sodium salt enhanced sensitivity to chlorhexidine, chlorine, hydrogen peroxide, and cis-2-decenoic acid, with a reduction of 0.5 to 8 log units. Preliminary in vitro studies using suitable primary cell based models revealed that zosteric acid sodium salt did not compromise the cellular activity, adhesion, proliferation or morphology of either the murine fibroblast line L929 or the human osteosarcoma line MG-63. Thus the use of zosteric acid sodium salt could provide a suitable, innovative, preventive, and integrative approach to preventing yeast biofilm formation.}, }
@article {pmid21614459, year = {2011}, author = {Gutierrez-Zamora, ML and Zemb, O and Manefield, M}, title = {Direct rRNA fingerprinting, a novel method to profile low diversity microbial communities.}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {177-187}, pmid = {21614459}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Typing Techniques/*methods ; *Biodiversity ; DNA Fingerprinting/*methods ; DNA, Bacterial/genetics ; Ecosystem ; Fresh Water/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {In the past decade, an increasing number of methods in microbial ecology have been developed that address the questions of which microbes exist in the environment, what their roles are and, to some extent, what their abundance is. In the present paper, we propose and describe the proof of principle of a novel method for analysing shifts in microbial community composition that uses small RNA fragments directly derived from 16S rRNA. Community fingerprints are generated on the basis of sequence-dependent conformational differences of rRNA fragments. We applied this method to profile artificial and natural communities and to detect changes in community structure in enrichment cultures. This method constitutes a PCR-free alternative to microbial community characterisation and can provide information on the relative abundance of rRNA from individual phylotypes in low diversity samples.}, }
@article {pmid21614084, year = {2011}, author = {Mela, F and Fritsche, K and de Boer, W and van Veen, JA and de Graaff, LH and van den Berg, M and Leveau, JH}, title = {Dual transcriptional profiling of a bacterial/fungal confrontation: Collimonas fungivorans versus Aspergillus niger.}, journal = {The ISME journal}, volume = {5}, number = {9}, pages = {1494-1504}, pmid = {21614084}, issn = {1751-7370}, mesh = {Animals ; *Antibiosis ; Aspergillus niger/genetics/*physiology ; *Gene Expression Profiling ; Hyphae/physiology ; Nitrogen/metabolism ; Oxalobacteraceae/genetics/*physiology ; Spores, Fungal/physiology ; Stress, Physiological ; }, abstract = {Interactions between bacteria and fungi cover a wide range of incentives, mechanisms and outcomes. The genus Collimonas consists of soil bacteria that are known for their antifungal activity and ability to grow at the expense of living fungi. In non-contact confrontation assays with the fungus Aspergillus niger, Collimonas fungivorans showed accumulation of biomass concomitant with inhibition of hyphal spread. Through microarray analysis of bacterial and fungal mRNA from the confrontation arena, we gained new insights into the mechanisms underlying the fungistatic effect and mycophagous phenotype of collimonads. Collimonas responded to the fungus by activating genes for the utilization of fungal-derived compounds and for production of a putative antifungal compound. In A. niger, differentially expressed genes included those involved in lipid and cell wall metabolism and cell defense, which correlated well with the hyphal deformations that were observed microscopically. Transcriptional profiles revealed distress in both partners: downregulation of ribosomal proteins and upregulation of mobile genetic elements in the bacteria and expression of endoplasmic reticulum stress and conidia-related genes in the fungus. Both partners experienced nitrogen shortage in each other's presence. Overall, our results indicate that the Collimonas/Aspergillus interaction is a complex interplay between trophism, antibiosis and competition for nutrients.}, }
@article {pmid21611689, year = {2011}, author = {Machado-Ferreira, E and Dietrich, G and Hojgaard, A and Levin, M and Piesman, J and Zeidner, NS and Soares, CA}, title = {Coxiella symbionts in the Cayenne tick Amblyomma cajennense.}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {134-142}, pmid = {21611689}, issn = {1432-184X}, mesh = {Animals ; Coxiella/classification/genetics/*isolation &amp; purification/*physiology ; Female ; Ixodidae/*microbiology/physiology ; Molecular Sequence Data ; Phylogeny ; *Symbiosis ; }, abstract = {Members of the Coxiella genus are intracellular bacteria that can infect a variety of animals including humans. A symbiotic Coxiella was recently described in Amblyomma americanum ticks in the Northern Hemisphere with no further investigations of other Amblyomma species in other geographic regions. These ixodid ticks represent a group of important vectors for human infectious agents. In the present work, we have demonstrated that symbiotic Coxiella (SCox) are widespread, occurring in South America and infecting 100% of all life stages and eggs of the Cayenne ticks Amblyomma cajennense from Brazil and the USA. Using light microscopy, in situ hybridization, and PCR, we demonstrated SCox in salivary glands, ovaries, and the intestines of A. cajennense. These symbionts are vertically and transtadially transmitted in laboratory reared A. cajennense, and quantitative PCR analyses indicate that SCox are more abundant in adult female ticks, reaching values corresponding to an 11×, 38×, and 200× increase in SCox 16S rRNA gene copy number in unfed females, compared to unfed nymphs, larvae, and eggs, respectively. Phylogenetic analyses showed distinct SCox subpopulations in the USA and Brazil and demonstrated that SCox bacteria do not group with pathogenic Coxiella burnetii.}, }
@article {pmid21611688, year = {2011}, author = {Tiquia, SM}, title = {Extracellular hydrolytic enzyme activities of the heterotrophic microbial communities of the Rouge River: an approach to evaluate ecosystem response to urbanization.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {679-689}, pmid = {21611688}, issn = {1432-184X}, mesh = {Aminopeptidases/analysis ; Bacteria/*enzymology ; Carbon/analysis ; Chlorophyll/analysis ; Colony Count, Microbial ; *Ecosystem ; Esterases/analysis ; Groundwater/chemistry/microbiology ; Heterotrophic Processes ; Michigan ; Phosphoric Monoester Hydrolases/analysis ; Rivers/chemistry/*microbiology ; *Urbanization ; *Water Microbiology ; }, abstract = {The potential effects of urbanization on the bioavailability of dissolved organic carbon (DOC) were tested by determining the extracellular enzyme activities of the heterotrophic microbial communities of the Rouge River. The activities of 19 enzymes were monitored across two water samples (river water and groundwater) at different spatial and temporal scales. High phosphatase, esterase, and aminopeptidase activities was observed in site 9 (site most exposed to anthropogenic sources) showed higher concentrations of DOC compared to sites 1 and 8 (sites exposed to less anthropogenic sources), where moderate activities of diverse range of enzymes were observed. High relative contributions of phosphatase, esterase, and aminopeptidase activities to the overall enzyme activity as observed in site 9 stressed the increased importance of peptides as C source for heterotrophic communities and high in-stream carbon processing, which account for high nonspecific extracellular enzyme activities. In contrast, high contribution of glycosyl hydrolases occurred consistently across all sites, which highlights the significance of microbial detrital and plant biomass as carbon sources. Majority of the enzymes showed evidence of activity at various extents during spring and summer. However, higher activities of leucine aminopeptidase, valine aminopeptidase, β-glucosidase, and α-mannosidase were observed in the summer; and alkaline phosphatase and α-glucosidase in the spring. The results presented here suggest a shift in organic carbon bioavailability across all sites of contrasting urbanization, despite similarities in DOC concentrations. Hence, API ZYM technique can be used as an effective indicator of river water and groundwater system health across an urban gradient.}, }
@article {pmid21611687, year = {2011}, author = {Xiao, Y and Zeng, GM and Yang, ZH and Ma, YH and Huang, C and Shi, WJ and Xu, ZY and Huang, J and Fan, CZ}, title = {Effects of continuous thermophilic composting (CTC) on bacterial community in the active composting process.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {599-608}, pmid = {21611687}, issn = {1432-184X}, mesh = {Bacillus/genetics/*growth &amp; development ; Biomass ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; *Hot Temperature ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Refuse Disposal/*methods ; *Soil ; *Soil Microbiology ; }, abstract = {The method of continuous thermophilic composting (CTC) remarkably shortened the active composting cycle and enhanced the compost stability. Effects of CTC on the quantities of bacteria, with a comparison to the traditional composting (TC) method, were explored by plate count with incubation at 30, 40 and 50°C, respectively, and by quantitative PCR targeting the universal bacterial 16S rRNA genes and the Bacillus 16S rRNA genes. The comparison of cultivatable or uncultivatable bacterial numbers indicated that CTC might have increased the biomass of bacteria, especially Bacillus spp., during the composting. Denaturing gradient gel electrophoresis (DGGE) analysis was employed to investigate the effects of CTC on bacterial diversity, and a community dominated by fewer species was detected in a typical CTC run. The analysis of sequence and phylogeny based on DGGE indicated that the continuously high temperature had changed the structure of bacterial community and strengthened the mainstay role of the thermophilic and spore-forming Bacillus spp. in CTC run.}, }
@article {pmid21607876, year = {2011}, author = {Pelz-Stelinski, K and Kaufman, MG and Walker, ED}, title = {Beetle (Coleoptera: Scirtidae) facilitation of larval mosquito growth in tree hole habitats is linked to multitrophic microbial interactions.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {690-703}, pmid = {21607876}, issn = {1432-184X}, support = {R01 AI021884/AI/NIAID NIH HHS/United States ; R37 AI021884/AI/NIAID NIH HHS/United States ; R56 AI021884/AI/NIAID NIH HHS/United States ; AI21884/AI/NIAID NIH HHS/United States ; }, mesh = {Aedes/*growth &amp; development ; Animals ; Bacteria/genetics/growth &amp; development ; Biomass ; Coleoptera/*growth &amp; development ; *Ecosystem ; Fungi/genetics/growth &amp; development ; Larva/growth &amp; development ; Plant Leaves/*microbiology ; Polymorphism, Restriction Fragment Length ; Trees ; *Water Microbiology ; }, abstract = {Container-breeding mosquitoes, such as Aedes triseriatus, ingest biofilms and filter water column microorganisms directly to obtain the bulk of their nutrition. Scirtid beetles often co-occur with A. triseriatus and may facilitate the production of mosquito adults under low-resource conditions. Using molecular genetic techniques and quantitative assays, we observed changes in the dynamics and composition of bacterial and fungal communities present on leaf detritus and in the water column when scirtid beetles co-occur with A. triseriatus. Data from terminal restriction fragment polymorphism analysis indicated scirtid presence alters the structure of fungal communities in the water column but not leaf-associated fungal communities. Similar changes in leaf and water bacterial communities occurred in response to mosquito presence. In addition, we observed increased processing of leaf detritus, higher leaf-associated enzyme activity, higher bacterial productivity, and higher leaf-associated fungal biomass when scirtid beetles were present. Such shifts suggest beetle feeding facilitates mosquito production indirectly through the microbial community rather than directly through an increase in available fine particulate organic matter.}, }
@article {pmid21607550, year = {2011}, author = {Tobler, DJ and Benning, LG}, title = {Bacterial diversity in five Icelandic geothermal waters: temperature and sinter growth rate effects.}, journal = {Extremophiles : life under extreme conditions}, volume = {15}, number = {4}, pages = {473-485}, pmid = {21607550}, issn = {1433-4909}, mesh = {Bacteria/genetics/*growth &amp; development ; *Biodiversity ; Hot Springs/*microbiology ; Iceland ; *Water Microbiology ; }, abstract = {The microbial ecology associated with siliceous sinters was studied in five geochemically diverse Icelandic geothermal systems. Bacterial 16S rRNA clone libraries were constructed from water-saturated precipitates from each site resulting in a total of 342 bacterial clone sequences and 43 species level phylotypes. In near-neutral, saline (2.6-4.7% salinity) geothermal waters where sinter growth varied between 10 and ~300 kg year(-1) m(-2), 16S rRNA gene analyses revealed very low (no OTUs could be detected) to medium (9 OTUs) microbial activity. The most dominant phylotypes found in these waters belong to marine genera of the Proteobacteria. In contrast, in alkaline (pH = 9-10), meteoric geothermal waters with temperature = 66-96°C and <1-20 kg year(-1)m(-2) sinter growth, extensive biofilms (a total of 34 OTUs) were observed within the waters and these were dominated by members of the class Aquificae (mostly related to Thermocrinis), Deinococci (Thermus species) as well as Proteobacteria. The observed phylogenetic diversity (i.e., number and composition of detected OTUs) is argued to be related to the physico-chemical regime prevalent in the studied geothermal waters; alkaliphilic thermophilic microbial communities with phylotypes related to heterotrophic and autotrophic microorganisms developed in alkaline high temperature waters, whereas halophilic mesophilic communities dominated coastal geothermal waters.}, }
@article {pmid21606447, year = {2011}, author = {Weedman, SM and Rostagno, MH and Patterson, JA and Yoon, I and Fitzner, G and Eicher, SD}, title = {Yeast culture supplement during nursing and transport affects immunity and intestinal microbial ecology of weanling pigs.}, journal = {Journal of animal science}, volume = {89}, number = {6}, pages = {1908-1921}, doi = {10.2527/jas.2009-2539}, pmid = {21606447}, issn = {1525-3163}, mesh = {Animals ; Animals, Suckling ; Dietary Supplements ; Female ; Gene Expression Regulation ; Immunity, Innate/*drug effects ; Intestines/*microbiology ; Leukocytes/drug effects/physiology ; Maternal Nutritional Physiological Phenomena ; RNA/genetics/metabolism ; Saccharomyces cerevisiae/*physiology ; Swine/growth &amp; development/*immunology/*microbiology ; Toll-Like Receptors/genetics/metabolism ; Transportation ; Weaning ; }, abstract = {The objectives of this study were to determine the influence of a Saccharomyces cerevisiae fermentation product on innate immunity and intestinal microbial ecology after weaning and transport stress. In a randomized complete block design, before weaning and in a split-plot analysis of a 2 × 2 factorial arrangement of yeast culture (YY) and transport (TT) after weaning, 3-d-old pigs (n = 108) were randomly assigned within litter (block) to either a control (NY, milk only) or yeast culture diet (YY; delivered in milk to provide 0.1 g of yeast culture product/kg of BW) from d 4 to 21. At weaning (d 21), randomly, one-half of the NY and YY pigs were assigned to a 6-h transport (NY-TT and YY-TT) before being moved to nursery housing, and the other one-half were moved directly to nursery housing (NY-NT and YY-NT, where NT is no transport). The yeast treatment was a 0.2% S. cerevisiae fermentation product and the control treatment was a 0.2% grain blank in feed for 2 wk. On d 1 before transport and on d 1, 4, 7, and 14 after transport, blood was collected for leukocyte assays, and mesenteric lymph node, jejunal, and ileal tissue, and jejunal, ileal, and cecal contents were collected for Toll-like receptor expression (TLR); enumeration of Escherichia coli, total coliforms, and lactobacilli; detection of Salmonella; and microbial analysis. After weaning, a yeast × transport interaction for ADG was seen (P = 0.05). Transport affected (P = 0.09) ADFI after weaning. Yeast treatment decreased hematocrit (P = 0.04). A yeast × transport interaction was found for counts of white blood cells (P = 0.01) and neutrophils (P = 0.02) and for the neutrophil-to-lymphocyte ratio (P = 0.02). Monocyte counts revealed a transport (P = 0.01) effect. Interactions of yeast × transport (P = 0.001) and yeast × transport × day (P = 0.09) for TLR2 and yeast × transport (P = 0.08) for TLR4 expression in the mesenteric lymph node were detected. Day affected lactobacilli, total coliform, and E. coli counts. More pigs were positive for Salmonella on d 7 and 14 than on d 4, and more YY-TT pigs were positive (P = 0.07) on d 4. The number of bands for microbial amplicons in the ileum was greater for pigs in the control treatment than in the yeast treatment on d 0, and this number tended to decrease (P = 0.066) between d 1 and 14 for all pigs. Similarity coefficients for jejunal contents were greater (P = 0.03) for pigs fed NY than for those fed YY, but pigs fed YY had greater similarity coefficients for ileal (P = 0.001) and cecal (P = 0.058) contents. The number of yeast × transport × day interactions demonstrates the complexity of the stress and dietary relationship.}, }
@article {pmid21602394, year = {2011}, author = {Verhagen, P and De Gelder, L and Hoefman, S and De Vos, P and Boon, N}, title = {Planktonic versus biofilm catabolic communities: importance of the biofilm for species selection and pesticide degradation.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {14}, pages = {4728-4735}, pmid = {21602394}, issn = {1098-5336}, mesh = {Adaptation, Physiological/*drug effects ; Aniline Compounds ; Bacteria/*drug effects/isolation &amp; purification/metabolism ; Biodegradation, Environmental ; Biofilms/*drug effects ; Chlorpropham/analysis/chemistry/metabolism ; Culture Media ; Peptide Mapping ; Pesticides/*metabolism/pharmacology ; Plankton/*drug effects/metabolism ; RNA, Ribosomal, 16S/metabolism ; Sewage/microbiology ; Soil ; Soil Microbiology ; }, abstract = {Chloropropham-degrading cultures were obtained from sludge and soil samples by using two different enrichment techniques: (i) planktonic enrichments in shaken liquid medium and (ii) biofilm enrichments on two types of solid matrixes (plastic chips and gravel). Denaturing gradient gel electrophoresis fingerprinting showed that planktonic and biofilm cultures had a different community composition depending on the presence and type of added solid matrix during enrichment. This was reflected in the unique chloropropham-degrading species that could be isolated from the different cultures. Planktonic and biofilm cultures also differed in chloropropham-degrading activity. With biofilm cultures, slower chloropropham removal was observed, but with less build-up of the toxic intermediate 3-chloroaniline. Disruption of the biofilm architecture resulted in degradation characteristics shifting toward those of the free suspensions, indicating the importance of a well-established biofilm structure for good performance. These results show that biofilm-mediated enrichment techniques can be used to select for pollutant-degrading microorganisms that like to proliferate in a biofilm and that cannot be isolated using conventional shaken-liquid procedures. Furthermore, the influence of the biofilm architecture on the pesticide degradation characteristics suggests that for bioaugmentation the use of biofilm catabolic communities might be a proficient alternative to using planktonic freely suspended cultures.}, }
@article {pmid21602363, year = {2012}, author = {Han, SI and Lee, HJ and Lee, HR and Kim, KK and Whang, KS}, title = {Mucilaginibacter polysacchareus sp. nov., an exopolysaccharide-producing bacterial species isolated from the rhizoplane of the herb Angelica sinensis.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {62}, number = {Pt 3}, pages = {632-637}, doi = {10.1099/ijs.0.029793-0}, pmid = {21602363}, issn = {1466-5034}, mesh = {Angelica sinensis/growth &amp; development ; Bacterial Typing Techniques ; Bacteroidetes/*classification/genetics/*isolation &amp; purification/metabolism ; Base Composition ; Benzoquinones/analysis ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fatty Acids/analysis ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phylogeny ; Pigments, Biological/metabolism ; Polyenes/metabolism ; Polysaccharides, Bacterial/*metabolism ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Three exopolysaccharide-producing bacteria, designated strains DRP28(T), DRP29 and DRP31, were isolated from the rhizoplane of Angelica sinensis from the Geumsan, Republic of Korea. Cells were straight rods, Gram reaction-negative, aerobic, non-motile, and catalase- and oxidase- positive. Flexirubin-type pigments were absent. Phylogenetic analysis of the 16S rRNA gene indicated that these bacteria belong to the genus Mucilaginibacter in the phylum Bacteroidetes. 16S rRNA gene sequence similarities to strains of recognized species of the genus Mucilaginibacter were 93.8-97.4%. The major fatty acids were iso-C(15:0) and summed feature 3 (C(16:1)ω7c and/or iso-C(15:0) 2-OH). The strains contained MK-7 as the major isoprenoid quinone. Strains DRP28(T), DRP29 and DRP31 formed a single, distinct genomospecies with DNA G+C contents of 41.9-42.7 mol% and DNA hybridization values of 82.6-86.8%; the strains exhibited DNA-DNA hybridization values of only 20.4-41.3% with related species of the genus Mucilaginibacter. On the basis of evidence presented in this study, strains DRP28(T), DRP29 and DRP31 were considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter polysacchareus sp. nov. is proposed. The type strain is DRP28(T) (=KACC 15075(T) =NBRC 107757(T)).}, }
@article {pmid21597940, year = {2011}, author = {Hu, A and Jiao, N and Zhang, CL}, title = {Community structure and function of planktonic Crenarchaeota: changes with depth in the South China Sea.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {549-563}, pmid = {21597940}, issn = {1432-184X}, mesh = {China ; Crenarchaeota/classification/genetics/*growth &amp; development ; DNA, Archaeal/genetics ; *Ecosystem ; *Genes, Archaeal ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {Marine Crenarchaeota represent a widespread and abundant microbial group in marine ecosystems. Here, we investigated the abundance, diversity, and distribution of planktonic Crenarchaeota in the epi-, meso-, and bathypelagic zones at three stations in the South China Sea (SCS) by analysis of crenarchaeal 16S rRNA gene, ammonia monooxygenase gene amoA involved in ammonia oxidation, and biotin carboxylase gene accA putatively involved in archaeal CO(2) fixation. Quantitative PCR analyses indicated that crenarchaeal amoA and accA gene abundances varied similarly with archaeal and crenarchaeal 16S rRNA gene abundances at all stations, except that crenarchaeal accA genes were almost absent in the epipelagic zone. Ratios of the crenarchaeal amoA gene to 16S rRNA gene abundances decreased ~2.6 times from the epi- to bathypelagic zones, whereas the ratios of crenarchaeal accA gene to marine group I crenarchaeal 16S rRNA gene or to crenarchaeal amoA gene abundances increased with depth, suggesting that the metabolism of Crenarchaeota may change from the epi- to meso- or bathypelagic zones. Denaturing gradient gel electrophoresis profiling of the 16S rRNA genes revealed depth partitioning in archaeal community structures. Clone libraries of crenarchaeal amoA and accA genes showed two clusters: the "shallow" cluster was exclusively derived from epipelagic water and the "deep" cluster was from meso- and/or bathypelagic waters, suggesting that niche partitioning may take place between the shallow and deep marine Crenarchaeota. Overall, our results show strong depth partitioning of crenarchaeal populations in the SCS and suggest a shift in their community structure and ecological function with increasing depth.}, }
@article {pmid21594594, year = {2011}, author = {Pieja, AJ and Rostkowski, KH and Criddle, CS}, title = {Distribution and selection of poly-3-hydroxybutyrate production capacity in methanotrophic proteobacteria.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {564-573}, pmid = {21594594}, issn = {1432-184X}, mesh = {Acyltransferases/genetics/metabolism ; Copper/metabolism ; Culture Media/chemistry ; Hydroxybutyrates/*metabolism ; Nitrogen/*metabolism ; Polyesters/*metabolism ; Proteobacteria/genetics/*metabolism ; Sewage ; }, abstract = {Methanotrophs are known to produce poly-3-hydroxybutyrate (PHB), but there is conflicting evidence in the literature as to which genera produce the polymer. We screened type I and II proteobacterial methanotrophs that use the ribulose monophosphate and serine pathways for carbon assimilation, respectively, for both phaC, which encodes for PHB synthase, and the ability to produce PHB under nitrogen-limited conditions. Twelve strains from six different genera were evaluated. All type I strains tested negative for phaC and PHB production; all Type II strains tested positive for phaC and PHB production. In order to identify conditions that favor PHB production, we also evaluated a range of selection conditions using a diverse activated sludge inoculum. Use of medium typically recommended for methanotroph enrichment led to enrichments dominated by type I methanotrophs. Conditions that were selected for enrichments dominated by PHB-producing Type II methanotrophs were: (1) use of nitrogen gas as the sole nitrogen source in the absence of copper, (2) use of a dilute mineral salts media in the absence of copper, and (3) use of media prepared at pH values of 4-5.}, }
@article {pmid21593798, year = {2011}, author = {Delmont, TO and Malandain, C and Prestat, E and Larose, C and Monier, JM and Simonet, P and Vogel, TM}, title = {Metagenomic mining for microbiologists.}, journal = {The ISME journal}, volume = {5}, number = {12}, pages = {1837-1843}, pmid = {21593798}, issn = {1751-7370}, mesh = {Climate Change ; Ecosystem ; *Environmental Microbiology ; Metagenomics/*methods ; }, abstract = {Microbial ecologists can now start digging into the accumulating mountains of metagenomic data to uncover the occurrence of functional genes and their correlations to microbial community members. Limitations and biases in DNA extraction and sequencing technologies impact sequence distributions, and therefore, have to be considered. However, when comparing metagenomes from widely differing environments, these fluctuations have a relatively minor role in microbial community discrimination. As a consequence, any functional gene or species distribution pattern can be compared among metagenomes originating from various environments and projects. In particular, global comparisons would help to define ecosystem specificities, such as involvement and response to climate change (for example, carbon and nitrogen cycle), human health risks (eg, presence of pathogen species, toxin genes and viruses) and biodegradation capacities. Although not all scientists have easy access to high-throughput sequencing technologies, they do have access to the sequences that have been deposited in databases, and therefore, can begin to intensively mine these metagenomic data to generate hypotheses that can be validated experimentally. Information about metabolic functions and microbial species compositions can already be compared among metagenomes from different ecosystems. These comparisons add to our understanding about microbial adaptation and the role of specific microbes in different ecosystems. Concurrent with the rapid growth of sequencing technologies, we have entered a new age of microbial ecology, which will enable researchers to experimentally confirm putative relationships between microbial functions and community structures.}, }
@article {pmid21590300, year = {2011}, author = {van Heerden, A and van Zyl, WH and Cruywagen, CW and Mouton, M and Botha, A}, title = {The lignicolous fungus Coniochaeta pulveracea and its interactions with syntrophic yeasts from the woody phylloplane.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {609-619}, pmid = {21590300}, issn = {1432-184X}, mesh = {Ascomycota/enzymology/genetics/*growth &amp; development ; Biodegradation, Environmental ; Carboxymethylcellulose Sodium/metabolism ; Culture Media ; *Microbial Interactions ; Phylogeny ; Wood/*microbiology ; Xylans/metabolism ; Xylose/metabolism ; Yeasts/*growth &amp; development ; }, abstract = {The yeast-like fungus Coniochaeta pulveracea was studied with regard to its novel lignocellulolytic activities and the possible effect thereof on yeasts from the woody phylloplane. An enrichment procedure was used to isolate C. pulveracea from a decaying Acacia tree, and the identity of the isolate was confirmed using morphology, as well as molecular and phylogenetic techniques. This isolate, as well as strains representing C. pulveracea from different geographical regions, were compared with regard to optimum growth temperature and enzyme activity to representatives of closely related species. These include strains of Coniochaeta boothii, Coniochaeta rhopalochaeta, and Coniochaeta subcorticalis. Plate assays for cellulase and xylanase activity indicated that all representatives of the above-mentioned species were able to produce extracellular hydrolytic enzymes and were also able to degrade birchwood toothpicks during a 50-day incubation period at 30°C. To test the ability of these fungi and their enzymes to release simple sugars from complex cellulosic substrates, filtrates obtained from liquid cultures of Coniochaeta, cultivated on carboxymethyl cellulose (CMC) as sole carbon source, were analyzed using high-performance liquid chromatography analysis. Consequently, the presence of mono- and disaccharides such as glucose and cellobiose was confirmed in these culture filtrates. Two subsequent experiments were conducted to determine whether these simple sugars released from woody material by Coniochaeta may enhance growth of phylloplane yeasts. In the first experiment, representatives of Coniochaeta were co-cultured with selected yeasts suspended in agar plates containing birchwood toothpicks, followed by examination of plates for colony formation. Results indicated that Coniochaeta growth on the toothpicks enhanced growth of nearby yeast colonies in the agar plates. In the second experiment, representatives of selected yeasts and Coniochaeta species were co-cultured on CMC and xylan-containing plates where after yeast colony formation was recorded on the plates. Saccharomyces cerevisiae strains, engineered to utilize specific wood degradation products, i.e., cellobiose or xylose, as sole carbon source were used as positive controls. While it was found that cellobiose released from CMC was assimilated by the yeasts, no evidence could be obtained that xylose released from xylan was used as carbon source by the yeasts. These ambiguous results could be ascribed to secretion of nutritious metabolic end products, other than the products of fungal xylanases.}, }
@article {pmid21590286, year = {2011}, author = {Hennebel, T and Van Nevel, S and Verschuere, S and De Corte, S and De Gusseme, B and Cuvelier, C and Fitts, JP and van der Lelie, D and Boon, N and Verstraete, W}, title = {Palladium nanoparticles produced by fermentatively cultivated bacteria as catalyst for diatrizoate removal with biogenic hydrogen.}, journal = {Applied microbiology and biotechnology}, volume = {91}, number = {5}, pages = {1435-1445}, doi = {10.1007/s00253-011-3329-9}, pmid = {21590286}, issn = {1432-0614}, mesh = {Bacteria/chemistry/*metabolism ; Biodegradation, Environmental ; Bioreactors/microbiology ; Catalysis ; Diatrizoate/*metabolism ; Environmental Restoration and Remediation/instrumentation/*methods ; Fermentation ; Hydrogen/*metabolism ; Kinetics ; Metal Nanoparticles/*chemistry/microbiology ; Oxidation-Reduction ; Palladium/*chemistry/metabolism ; Water Pollutants, Chemical/*metabolism ; }, abstract = {A new biological inspired method to produce nanopalladium is the precipitation of Pd on a bacterium, i.e., bio-Pd. This bio-Pd can be applied as catalyst in dehalogenation reactions. However, large amounts of hydrogen are required as electron donor in these reactions resulting in considerable costs. This study demonstrates how bacteria, cultivated under fermentative conditions, can be used to reductively precipitate bio-Pd catalysts and generate the electron donor hydrogen. In this way, one could avoid the costs coupled to hydrogen supply. The catalytic activities of Pd(0) nanoparticles produced by different strains of bacteria (bio-Pd) cultivated under fermentative conditions were compared in terms of their ability to dehalogenate the recalcitrant aqueous pollutants diatrizoate and trichloroethylene. While all of the fermentative bio-Pd preparations followed first order kinetics in the dehalogenation of diatrizoate, the catalytic activity differed systematically according to hydrogen production and starting Pd(II) concentration in solution. Batch reactors with nanoparticles formed by Citrobacter braakii showed the highest diatrizoate dehalogenation activity with first order constants of 0.45 ± 0.02 h[-1] and 5.58 ± 0.6 h[-1] in batches with initial concentrations of 10 and 50 mg L[-1] Pd, respectively. Nanoparticles on C. braakii, used in a membrane bioreactor treating influent containing 20 mg L[-1] diatrizoate, were capable of dehalogenating 22 mg diatrizoate mg[-1] Pd over a period of 19 days before bio-Pd catalytic activity was exhausted. This study demonstrates the possibility to use the combination of Pd(II), a carbon source and bacteria under fermentative conditions for the abatement of environmental halogenated contaminants.}, }
@article {pmid21589876, year = {2011}, author = {Zinger, L and Lejon, DP and Baptist, F and Bouasria, A and Aubert, S and Geremia, RA and Choler, P}, title = {Contrasting diversity patterns of crenarchaeal, bacterial and fungal soil communities in an alpine landscape.}, journal = {PloS one}, volume = {6}, number = {5}, pages = {e19950}, pmid = {21589876}, issn = {1932-6203}, mesh = {*Biodiversity ; Ecosystem ; Fungi/*classification ; *Soil Microbiology ; }, abstract = {BACKGROUND: The advent of molecular techniques in microbial ecology has aroused interest in gaining an understanding about the spatial distribution of regional pools of soil microbes and the main drivers responsible of these spatial patterns. Here, we assessed the distribution of crenarcheal, bacterial and fungal communities in an alpine landscape displaying high turnover in plant species over short distances. Our aim is to determine the relative contribution of plant species composition, environmental conditions, and geographic isolation on microbial community distribution.<br><br>Eleven types of habitats that best represent the landscape heterogeneity were investigated. Crenarchaeal, bacterial and fungal communities were described by means of Single Strand Conformation Polymorphism. Relationships between microbial beta diversity patterns were examined by using Bray-Curtis dissimilarities and Principal Coordinate Analyses. Distance-based redundancy analyses and variation partitioning were used to estimate the relative contributions of different drivers on microbial beta diversity. Microbial communities tended to be habitat-specific and did not display significant spatial autocorrelation. Microbial beta diversity correlated with soil pH. Fungal beta-diversity was mainly related to soil organic matter. Though the effect of plant species composition was significant for all microbial groups, it was much stronger for Fungi. In contrast, geographic distances did not have any effect on microbial beta diversity.<br><br>CONCLUSIONS/SIGNIFICANCE: Microbial communities exhibit non-random spatial patterns of diversity in alpine landscapes. Crenarcheal, bacterial and fungal community turnover is high and associated with plant species composition through different set of soil variables, but is not caused by geographical isolation.}, }
@article {pmid21584756, year = {2011}, author = {Kelly, LC and Cockell, CS and Herrera-Belaroussi, A and Piceno, Y and Andersen, G and DeSantis, T and Brodie, E and Thorsteinsson, T and Marteinsson, V and Poly, F and LeRoux, X}, title = {Bacterial diversity of terrestrial crystalline volcanic rocks, Iceland.}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {69-79}, pmid = {21584756}, issn = {1432-184X}, support = {G0900740/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Geologic Sediments/chemistry/*microbiology ; Iceland ; Molecular Sequence Data ; Phylogeny ; Volcanic Eruptions/*analysis ; }, abstract = {Bacteria inhabiting crystalline rocks from two terrestrial Icelandic volcanic lava flows of similar age and from the same geographical region, but differing in porosity and mineralogy, were characterised. Microarray (PhyloChip) and clone library analysis of 16S rRNA genes revealed the presence of a diverse assemblage of bacteria in each lava flow. Both methods suggested a more diverse community at the Dómadalshraun site (rhyolitic/andesitic lava flow) than that present at the Hnausahraun site (basaltic lava flow). Proteobacteria dominated the clone library at the Dómadalshraun site, while Acidobacteria was the most abundant phylum in the Hnausahraun site. Although analysis of similarities of denaturing gradient gel electrophoresis profiles suggested a strong correlation of community structure with mineralogy, rock porosity may also play an important role in shaping the bacterial community in crystalline volcanic rocks. Clone sequences were most similar to uncultured microorganisms, mainly from soil environments. Of these, Antarctic soils and temperate rhizosphere soils were prominent, as were clones retrieved from Hawaiian and Andean volcanic soils. The novel diversity of these Icelandic microbial communities was supported by the finding that up to 46% of clones displayed <85% sequence identities to sequences currently deposited in the RDP database.}, }
@article {pmid21584755, year = {2011}, author = {Meisterhans, G and Raymond, N and Lebreton, S and Salin, F and Bourasseau, L and de Montaudouin, X and Garabetian, F and Jude-Lemeilleur, F}, title = {Dynamics of bacterial communities in cockles (Cerastoderma edule) with respect to trematode parasite (Bucephalus minimus) infestation.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {620-631}, pmid = {21584755}, issn = {1432-184X}, mesh = {Animals ; Bacteria/genetics/*isolation &amp; purification ; *Biodiversity ; Cardiidae/*microbiology/*parasitology ; Colony Count, Microbial ; DNA Fingerprinting ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Host-Parasite Interactions ; Trematoda/*pathogenicity ; }, abstract = {The bacterial communities associated with the cockle (Cerastoderma edule) were investigated at the individual level through a 10-month monitoring programme. Temporal changes and those changes associated with a common parasite of the cockle, Bucephalus minimus, were investigated by monthly sampling of individuals, selected based on their shell length (cohort monitoring). Cockle bacterial community abundance (CBCA) and diversity (CBCD) were estimated by epifluorescence microscopy counts and automated ribosomal intergenic spacer analysis, respectively. CBCA showed a temporal pattern peaking at 30 × 10(6) cells per gram of cockle flesh and intervalval liquid in October and a significant 1.8-fold increase linked with B. minimus occurrence. CBCD was characterized by 112 ± 26 intergenic transcribed spacer (ITS) per individual and showed a relative homology between individuals (52 ± 6%, Jaccard similarity) in spite of more than 30% of rare ITS. Consistent with an undisturbed evolution of the condition index of the studied cohort individuals as an estimate of their physiological state, neither temporal nor parasite-induced change in CBCA has been related to marked changes in CBCD.}, }
@article {pmid21584754, year = {2011}, author = {Elifantz, H and Kautsky, L and Mor-Yosef, M and Tarchitzky, J and Bar-Tal, A and Chen, Y and Minz, D}, title = {Microbial activity and organic matter dynamics during 4 years of irrigation with treated wastewater.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {973-981}, pmid = {21584754}, issn = {1432-184X}, mesh = {*Agricultural Irrigation ; Agriculture ; Carbon/analysis ; Diospyros/growth &amp; development ; Fresh Water/analysis ; Hydrolysis ; Israel ; Organic Chemicals/*analysis ; Seasons ; Soil/analysis ; *Soil Microbiology ; *Waste Disposal, Fluid ; }, abstract = {The global changes in rainfall frequency and quantity have subjected arid and semi-arid regions to long periods of drought. As this phenomenon corresponds to increasing trend of water shortage, the use of treated wastewater (TWW) has been suggested as an alternative for irrigation of agricultural crops in these areas. The aim of the study was to investigate the short- and middle-term effects of TWW irrigation on the soil microbial activities and organic carbon content. The microbial community activity was measured every 1-3 months for 4 years in a persimmon (Diospyros kaki) orchard. These activities were used here as an indicator for the soil health. The hydrolysis activity (detected by fluorescein diacetate hydrolysis (FDA) assay) increased during the irrigation season and was significantly higher in soils irrigated with TWW compared to those irrigated with freshwater (FW). This activity was also negatively correlated with dissolved organic carbon (DOC) concentrations during the irrigation season, suggesting that the community degraded the DOC in the soils regardless of its origin. The irrigation season was also characterized by an increase in nitrification potential in both TWW- and FW-irrigated soils, which coincided with high concentrations of nitrate (50 mg kg(-1) soil). Overall, there was an increase in all measured activities during the irrigation season, and they were higher in the TWW soils. However, it appears that after each irrigation season, the potential activity of the community returned to levels similar to or even slightly lower than those of FW-irrigated soil during the wet season, suggesting that the periodic irrigation did not significantly change the soil microbial activity.}, }
@article {pmid21576336, year = {2011}, author = {Liang, X and Chen, YY and Ruiz, T and Wu, H}, title = {New cell surface protein involved in biofilm formation by Streptococcus parasanguinis.}, journal = {Infection and immunity}, volume = {79}, number = {8}, pages = {3239-3248}, pmid = {21576336}, issn = {1098-5522}, support = {R01 DE017474/DE/NIDCR NIH HHS/United States ; R01 DE017954/DE/NIDCR NIH HHS/United States ; R01DE017954/DE/NIDCR NIH HHS/United States ; }, mesh = {Adhesins, Bacterial/genetics/*metabolism ; *Bacterial Adhesion ; Bacterial Proteins/genetics/*metabolism ; Binding Sites ; Biofilms/*growth &amp; development ; DNA, Bacterial/chemistry/genetics ; Fimbriae Proteins/genetics/metabolism ; Gene Deletion ; Humans ; Membrane Proteins/genetics/*metabolism ; Molecular Sequence Data ; Protein Binding ; Protein Interaction Mapping ; Protein Multimerization ; Protein Structure, Tertiary ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Streptococcus/genetics/growth &amp; development/metabolism/*physiology ; }, abstract = {Dental biofilm formation is critical for maintaining the healthy microbial ecology of the oral cavity. Streptococci are predominant bacterial species in the oral cavity and play important roles in the initiation of plaque formation. In this study, we identified a new cell surface protein, BapA1, from Streptococcus parasanguinis FW213 and determined that BapA1 is critical for biofilm formation. Sequence analysis revealed that BapA1 possesses a typical cell wall-sorting signal for cell surface-anchored proteins from Gram-positive bacteria. No functional orthologue was reported in other streptococci. BapA1 possesses nine putative pilin isopeptide linker domains which are crucial for pilus assembly in a number of Gram-positive bacteria. Deletion of the 3' portion of bapA1 generated a mutant that lacks surface-anchored BapA1 and abolishes formation of short fibrils on the cell surface. The mutant failed to form biofilms and exhibited reduced adherence to an in vitro tooth model. The BapA1 deficiency also inhibited bacterial autoaggregation. The N-terminal muramidase-released-protein-like domain mediated BapA1-BapA1 interactions, suggesting that BapA1-mediated cell-cell interactions are important for bacterial autoaggregation and biofilm formation. Furthermore, the BapA1-mediated bacterial adhesion and biofilm formation are independent of a fimbria-associated serine-rich repeat adhesin, Fap1, demonstrating that BapA1 is a new streptococcal adhesin.}, }
@article {pmid21573760, year = {2011}, author = {Danevčič, T and Stopar, D}, title = {Asymmetric response of carbon metabolism at high and low salt stress in Vibrio sp. DSM14379.}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {198-204}, pmid = {21573760}, issn = {1432-184X}, mesh = {Bacterial Proteins/genetics/metabolism ; Carbon/*metabolism ; Metabolic Networks and Pathways ; Seawater/microbiology ; Sodium Chloride/*metabolism ; Vibrio/genetics/isolation &amp; purification/*metabolism ; }, abstract = {Energy redistribution between growth and maintenance in salt-stressed cells is especially important for bacteria living in estuarine environments. In this study, Gram-negative bacterium Vibrio sp. DSM14379, isolated from the estuarine waters of the northern Adriatic Sea, was grown aerobically in a peptone-yeast extract medium with different salt concentrations (ranging from 0.3% to 10% (w/v) NaCl). Carbon flux through the central metabolic pathways was determined at low and high salt concentrations. At low salt concentrations, total endogenous respiration, dehydrogenase activity, and net intracellular adenosine triphosphate (ATP) concentration significantly increased, the phosphofructokinase and pyruvate kinase activity decreased, whereas glucose-6-phosphate dehydrogenase activity remained unchanged. The carrying capacity of bacterial culture decreased dramatically, indicating a severe metabolic imbalance at low salt concentrations. At high salt concentrations, carrying capacity decreased gradually. There was a large increase in glucose-6-phosphate dehydrogenase activity, which correlated with a 10-fold increase in concentration of osmoprotectant L-proline. There was no significant change of net intracellular ATP concentration, phosphofructokinase, or pyruvate kinase activity. The results indicate that Vibrio sp. DSM14379 central metabolic pathways respond to low and high salt concentrations asymmetrically; cells are better adapted to high salt concentrations. In addition, cells in the stationary phase can tolerate induced salt stress without a significant change in dehydrogenase activity or endogenous respiration for at least 1 h, but need to alter their macromolecular composition and carbon flux distribution for long-term survival.}, }
@article {pmid21567188, year = {2011}, author = {Pérez-de-Mora, A and Engel, M and Schloter, M}, title = {Abundance and diversity of n-alkane-degrading bacteria in a forest soil co-contaminated with hydrocarbons and metals: a molecular study on alkB homologous genes.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {959-972}, pmid = {21567188}, issn = {1432-184X}, mesh = {Alkanes/*metabolism ; Bacteria/enzymology/*genetics ; Biodegradation, Environmental ; Biomass ; Cluster Analysis ; Cytochrome P-450 CYP4A/genetics/metabolism ; DNA Fingerprinting ; DNA, Bacterial/genetics/isolation &amp; purification ; Genes, Bacterial ; Genotype ; Germany ; Hydrocarbons/metabolism ; Metals/metabolism ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Soil/analysis ; *Soil Microbiology ; Soil Pollutants/*metabolism ; Trees/microbiology ; }, abstract = {Unraveling functional genes related to biodegradation of organic compounds has profoundly improved our understanding of biological remediation processes, yet the ecology of such genes is only poorly understood. We used a culture-independent approach to assess the abundance and diversity of bacteria catalyzing the degradation of n-alkanes with a chain length between C(5) and C(16) at a forest site co-contaminated with mineral oil hydrocarbons and metals for nearly 60 years. The alkB gene coding for a rubredoxin-dependent alkane monooxygenase enzyme involved in the initial activation step of aerobic aliphatic hydrocarbon metabolism was used as biomarker. Within the area of study, four different zones were evaluated: one highly contaminated, two intermediately contaminated, and a noncontaminated zone. Contaminant concentrations, hydrocarbon profiles, and soil microbial respiration and biomass were studied. Abundance of n-alkane-degrading bacteria was quantified via real-time PCR of alkB, whereas genetic diversity was examined using molecular fingerprints (T-RFLP) and clone libraries. Along the contamination plume, hydrocarbon profiles and increased respiration rates suggested on-going natural attenuation at the site. Gene copy numbers of alkB were similar in contaminated and control areas. However, T-RFLP-based fingerprints suggested lower diversity and evenness of the n-alkane-degrading bacterial community in the highly contaminated zone compared to the other areas; both diversity and evenness were negatively correlated with metal and hydrocarbon concentrations. Phylogenetic analysis of alkB denoted a shift of the hydrocarbon-degrading bacterial community from Gram-positive bacteria in the control zone (most similar to Mycobacterium and Nocardia types) to Gram-negative genotypes in the contaminated zones (Acinetobacter and alkB sequences with little similarity to those of known bacteria). Our results underscore a qualitative rather than a quantitative response of hydrocarbon-degrading bacteria to the contamination at the molecular level.}, }
@article {pmid21565393, year = {2011}, author = {Elinav, E and Strowig, T and Kau, AL and Henao-Mejia, J and Thaiss, CA and Booth, CJ and Peaper, DR and Bertin, J and Eisenbarth, SC and Gordon, JI and Flavell, RA}, title = {NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis.}, journal = {Cell}, volume = {145}, number = {5}, pages = {745-757}, pmid = {21565393}, issn = {1097-4172}, support = {/HHMI/Howard Hughes Medical Institute/United States ; T32 HL007974/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification ; Bacteroidetes ; Chemokine CCL5/metabolism ; Colitis/chemically induced/*immunology/*microbiology/physiopathology ; Colon/immunology/*microbiology ; Dextran Sulfate ; Disease Susceptibility ; Inflammasomes/*immunology ; Interleukin-18/immunology ; Mice ; Mice, 129 Strain ; Mice, Inbred C57BL ; Receptors, Cell Surface/genetics/*metabolism ; }, abstract = {Inflammasomes are multiprotein complexes that function as sensors of endogenous or exogenous damage-associated molecular patterns. Here, we show that deficiency of NLRP6 in mouse colonic epithelial cells results in reduced IL-18 levels and altered fecal microbiota characterized by expanded representation of the bacterial phyla Bacteroidetes (Prevotellaceae) and TM7. NLRP6 inflammasome-deficient mice were characterized by spontaneous intestinal hyperplasia, inflammatory cell recruitment, and exacerbation of chemical colitis induced by exposure to dextran sodium sulfate (DSS). Cross-fostering and cohousing experiments revealed that the colitogenic activity of this microbiota is transferable to neonatal or adult wild-type mice, leading to exacerbation of DSS colitis via induction of the cytokine, CCL5. Antibiotic treatment and electron microscopy studies further supported the role of Prevotellaceae as a key representative of this microbiota-associated phenotype. Altogether, perturbations in this inflammasome pathway, including NLRP6, ASC, caspase-1, and IL-18, may constitute a predisposing or initiating event in some cases of human IBD.}, }
@article {pmid21564459, year = {2011}, author = {Jones, MD and Crandell, DW and Singleton, DR and Aitken, MD}, title = {Stable-isotope probing of the polycyclic aromatic hydrocarbon-degrading bacterial guild in a contaminated soil.}, journal = {Environmental microbiology}, volume = {13}, number = {10}, pages = {2623-2632}, pmid = {21564459}, issn = {1462-2920}, support = {P42 ES005948/ES/NIEHS NIH HHS/United States ; 5 P42 ES005948/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics/*metabolism ; Benz(a)Anthracenes/metabolism ; Biodegradation, Environmental ; Carbon Isotopes/analysis ; DNA, Bacterial/chemistry/genetics ; Fluorenes/metabolism ; Gene Library ; Molecular Sequence Data ; Naphthalenes/metabolism ; Phenanthrenes/metabolism ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Pyrenes/metabolism ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {The bacteria responsible for the degradation of naphthalene, phenanthrene, pyrene, fluoranthene or benz[a]anthracene in a polycyclic aromatic hydrocarbon (PAH)-contaminated soil were investigated by DNA-based stable-isotope probing (SIP). Clone libraries of 16S rRNA genes were generated from the (13) C-enriched ('heavy') DNA recovered from each SIP experiment, and quantitative PCR primers targeting the 16S rRNA gene were developed to measure the abundances of many of the SIP-identified sequences. Clone libraries from the SIP experiments with naphthalene, phenanthrene and fluoranthene primarily contained sequences related to bacteria previously associated with the degradation of those compounds. However, Pigmentiphaga-related sequences were newly associated with naphthalene and phenanthrene degradation, and sequences from a group of uncultivated γ-Proteobacteria known as Pyrene Group 2 were newly associated with fluoranthene and benz[a]anthracene degradation. Pyrene Group 2-related sequences were the only sequences recovered from the clone library generated from SIP with pyrene, and they were 82% of the sequences recovered from the clone library generated from SIP with benz[a]anthracene. In time-course experiments with each substrate in unlabelled form, the abundance of each of the measured groups increased in response to the corresponding substrate. These results provide a comprehensive description of the microbial ecology of a PAH-contaminated soil as it relates to the biodegradation of PAHs from two to four rings, and they underscore that bacteria in Pyrene Group 2 are well-suited for the degradation of four-ring PAHs.}, }
@article {pmid21556885, year = {2011}, author = {Koch, H and Schmid-Hempel, P}, title = {Bacterial communities in central European bumblebees: low diversity and high specificity.}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {121-133}, pmid = {21556885}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Bees/*microbiology ; *Genetic Variation ; Germany ; *Host Specificity ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Switzerland ; }, abstract = {Recent studies on the microbial flora of the honeybee gut have revealed an apparently highly specific community of resident bacteria that might play a role in immune defence and food preservation for their hosts. However, at present, very little is known about the diversity and ecology of bacteria occurring in non-domesticated bees like bumblebees, which are of similar importance as honeybees for the pollination of agricultural and wild flowers. To fill this gap in knowledge, we examined six of the most common bumblebee species in Central Europe from three locations in Germany and Switzerland for their bacterial communities. We used a culture-independent molecular approach based on sequencing the 16S rRNA gene from a selection of individuals and examining a larger number of samples by terminal restriction fragment length polymorphism profiles. The gut flora was dominated by very few and mostly undescribed groups of bacteria belonging to the Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria. This core set of bacteria was present in all of the examined bumblebee species. These bacteria are similar to, but distinct from, bacteria previously described from the honeybee gut. Significant differences were observed between the communities of bacteria in the different bumblebee species; the effect of sampling location was less strong. A novel group of Betaproteobacteria additionally shows evidence for host species-specific genotypes. The gut flora of bumblebees therefore is apparently composed of relatively few highly specialized bacteria, indicating a strong interaction and possibly important functions with their hosts.}, }
@article {pmid21556884, year = {2011}, author = {Park, SJ and Park, BJ and Jung, MY and Kim, SJ and Chae, JC and Roh, Y and Forwick, M and Yoon, HI and Rhee, SK}, title = {Influence of deglaciation on microbial communities in marine sediments off the coast of Svalbard, Arctic Circle.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {537-548}, pmid = {21556884}, issn = {1432-184X}, mesh = {Adaptation, Physiological ; Bacteria/genetics ; *Climate Change ; Crenarchaeota/genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; *Ecosystem ; Geologic Sediments/*microbiology ; *Ice Cover ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Svalbard ; *Water Microbiology ; }, abstract = {Increases in global temperatures have been shown to enhance glacier melting in the Arctic region. Here, we have evaluated the effects of meltwater runoff on the microbial communities of coastal marine sediment located along a transect of Temelfjorden, in Svalbard. As close to the glacier front, the sediment properties were clearly influenced by deglaciation. Denaturing gradient gel electrophoresis profiles showed that the sediment microbial communities of the stations of glacier front (stations 188-178) were distinguishable from that of outer fjord region (station 176). Canonical correspondence analysis indicated that total carbon and calcium carbonate in sediment and chlorophyll a in bottom water were key factors driving the change of microbial communities. Analysis of 16S rRNA gene clone libraries suggested that microbial diversity was higher within the glacier-proximal zone (station 188) directly affected by the runoffs than in the outer fjord region. While the crenarchaeotal group I.1a dominated at station 176 (62%), Marine Benthic Group-B and other Crenarchaeota groups were proportionally abundant. With regard to the bacterial community, alpha-Proteobacteria and Flavobacteria lineages prevailed (60%) at station 188, whereas delta-Proteobacteria (largely sulfate-reducers) predominated (32%) at station 176. Considering no clone sequences related to sulfate-reducers, station 188 may be more oxic compared to station 176. The distance-wise compositional variation in the microbial communities is attributable to their adaptations to the sediment environments which are differentially affected by melting glaciers.}, }
@article {pmid21556883, year = {2011}, author = {Bouvier, T and Maurice, CF}, title = {A single-cell analysis of virioplankton adsorption, infection, and intracellular abundance in different bacterioplankton physiologic categories.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {669-678}, pmid = {21556883}, issn = {1432-184X}, mesh = {Adsorption ; Bacteria/cytology/ultrastructure/*virology ; Bacteriophages/*physiology ; Cell Membrane/ultrastructure ; Fresh Water/microbiology/virology ; Nucleic Acids/analysis ; Seawater/microbiology/virology ; Virion/physiology ; Virus Attachment ; *Water Microbiology ; }, abstract = {Culture studies of phage-host systems have shown that phage proliferation strongly depends on the physiological state of the host, but it is still unclear to what extent this holds true within aquatic ecosystems. We used a combination of flow sorting and electron microscopy to explore how the frequency of bacterial cells with attached viruses (FCAV), of visibly infected cells, and the number of intracellular viruses are distributed within five physiologic categories: cells with high (HNA) and low (LNA) nucleic acid content, with a compromised membrane, in division, and with an intact-looking morphology. FCAV was not different between the cellular physiologic categories, suggesting low influence of host physiology on viral adsorption. Infected cells were found within all the physiologic categories, besides the dividing cells, but showed different levels of new virion production, with the abundance of intracellular viruses ranked as follows: HNA > intact-looking cells > LNA > compromised membrane cells. These results favor the physiological control hypothesis of viral progeny production. The calculation of viral production rate of the HNA and LNA cells show that viral infection of HNA cells likely accounts for the majority of viral production. It also show that cells considered as less active can still act as resources for phages, although they contain much less intracellular phage particles.}, }
@article {pmid21556882, year = {2011}, author = {Papadopoulou, ES and Karpouzas, DG and Menkissoglu-Spiroudi, U}, title = {Extraction parameters significantly influence the quantity and the profile of PLFAs extracted from soils.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {704-714}, pmid = {21556882}, issn = {1432-184X}, mesh = {Chemical Fractionation ; Chromatography, Gas ; Fatty Acids/*analysis ; Phospholipids/*analysis ; Soil/*chemistry ; *Soil Microbiology ; Solvents ; }, abstract = {Phospholipid fatty acid (PLFA) analysis is a robust method for characterizing soil microbial communities. We determined the effects of extraction solvent (chloroform vs dichloromethane) and buffer (phosphate vs citrate) on the yield and the profile of PLFAs extracted from an acidic (pH 5.5) and an alkaline (pH 8.6) soil following two 2-h sequential extractions. The yield and the profile of the PLFAs obtained separately by the first and the second 2-h extraction were compared to identify the impact of sequential extractions on the PLFA extraction efficiency. Chloroform-citrate and a 2 × 2-h extraction maximized PLFA yields in both soils. Multivariate analysis of the data showed that the choice of the extraction mixture did not significantly influence the profile of the PLFAs obtained by the first 2-h extraction, whereas it had a profound effect on the profile of the PLFAs obtained by the second 2-h extraction. Most PLFAs were extracted during the first extraction except 18:2ω6,9 and 22:0 which were almost equally extracted by the two sequential extractions. The choice of organic solvent significantly influenced the profile of the PLFAs extracted; their yield increased with chloroform with the exception of 18:2ω6,9 and 22:0 which were favored by dichloromethane. Overall, a 2 × 2-h extraction with chloroform/methanol/citrate is expected to provide maximum PLFA yields.}, }
@article {pmid21554561, year = {2012}, author = {De Corte, S and Hennebel, T and De Gusseme, B and Verstraete, W and Boon, N}, title = {Bio-palladium: from metal recovery to catalytic applications.}, journal = {Microbial biotechnology}, volume = {5}, number = {1}, pages = {5-17}, pmid = {21554561}, issn = {1751-7915}, mesh = {Bacteria/chemistry/*metabolism ; Biodegradation, Environmental ; Catalysis ; Nanoparticles/chemistry/microbiology ; Oxidation-Reduction ; Palladium/chemistry/*metabolism ; Recycling ; }, abstract = {While precious metals are available to a very limited extent, there is an increasing demand to use them as catalyst. This is also true for palladium (Pd) catalysts and their sustainable recycling and production are required. Since Pd catalysts exist nowadays mostly under the form of nanoparticles, these particles need to be produced in an environment-friendly way. Biological synthesis of Pd nanoparticles ('bio-Pd') is an innovative method for both metal recovery and nanocatalyst synthesis. This review will discuss the different bio-Pd precipitating microorganisms, the applications of the catalyst (both for environmental purposes and in organic chemistry) and the state of the art of the reactors based on the bio-Pd concept. In addition, some main challenges are discussed, which need to be overcome in order to create a sustainable nanocatalyst. Finally, some outlooks for bio-Pd in environmental technology are presented.}, }
@article {pmid21554380, year = {2011}, author = {Thomas, MC and Thomas, DK and Selinger, LB and Inglis, GD}, title = {spyder, a new method for in silico design and assessment of 16S rRNA gene primers for molecular microbial ecology.}, journal = {FEMS microbiology letters}, volume = {320}, number = {2}, pages = {152-159}, doi = {10.1111/j.1574-6968.2011.02302.x}, pmid = {21554380}, issn = {1574-6968}, mesh = {Algorithms ; Amino Acid Sequence ; Base Sequence ; Computational Biology/*methods ; Computer-Aided Design ; *DNA Primers ; Databases, Nucleic Acid ; *Environmental Microbiology ; Escherichia coli/genetics ; *Genes, Bacterial ; Molecular Sequence Data ; RNA, Ribosomal, 16S/*genetics ; Sequence Alignment ; *Software ; }, abstract = {Molecular microbial ecology studies are heavily reliant on 'Universal' 16S rRNA gene primers for elucidating microbial community structure and composition, and yet primer design and optimization is often overlooked. Primers that exhibit minor biases due to primer-template mismatches can substantially alter the pool of amplicons from a community DNA sample, resulting in inaccurate conclusions. As a result, it is important that primers are critically evaluated against the most comprehensive data sets available before commencing molecular microbial community studies. We present a user-friendly, multi-platform (e.g. Windows, Linux, Mac) method named spyder for the in silico design and assessment of 16S rRNA gene primers. The method utilizes the Ribosomal Database Project's Probe Match feature coupled with a compact program (available at http://people.uleth.ca/~selibl/Spyder/Spyder.html) that aligns and identifies mismatches between primers and templates. To demonstrate the value of spyder, we assessed commonly used 'Universal' and phyla-specific primers and identified primer modifications that improved the coverage of target organisms by 5-42% as well as removed excessive degeneracies.}, }
@article {pmid21553058, year = {2011}, author = {Pradhan, A and Seena, S and Pascoal, C and Cássio, F}, title = {Can metal nanoparticles be a threat to microbial decomposers of plant litter in streams?.}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {58-68}, pmid = {21553058}, issn = {1432-184X}, mesh = {Alnus/chemistry/microbiology ; Bacteria/*drug effects/genetics/isolation &amp; purification/metabolism ; Copper/*pharmacology ; Fungi/*drug effects/genetics/isolation &amp; purification/metabolism ; Nanoparticles/analysis ; Plant Leaves/chemistry/*microbiology ; Rivers/*microbiology ; Silver/*pharmacology ; Water Pollutants, Chemical/*pharmacology ; }, abstract = {The extensive use of nanometal-based products increases the chance of their release into aquatic environments, raising the question whether they can pose a risk to aquatic biota and the associated ecological processes. Aquatic microbes, namely fungi and bacteria, play a key role in forested streams by decomposing plant litter from terrestrial vegetation. Here, we investigated the effects of nanocopper oxide and nanosilver on leaf litter decomposition by aquatic microbes, and the results were compared with the impacts of their ionic precursors. Alder leaves were immersed in a stream of Northwest Portugal to allow microbial colonization before being exposed in microcosms to increased nominal concentrations of nanometals (CuO, 100, 200 and 500 ppm; Ag, 100 and 300 ppm) and ionic metals (Cu(2+) in CuCl(2), 10, 20 and 30 ppm; Ag(+) in AgNO(3), 5 and 20 ppm) for 21 days. Results showed that rates of leaf decomposition decreased with exposure to nano- and ionic metals. Nano- and ionic metals inhibited bacterial biomass (from 68.6% to 96.5% of control) more than fungal biomass (from 28.5% to 82.9% of control). The exposure to increased concentrations of nano- and ionic metals decreased fungal sporulation rates from 91.0% to 99.4%. These effects were accompanied by shifts in the structure of fungal and bacterial communities based on DNA fingerprints and fungal spore morphology. The impacts of metal nanoparticles on leaf decomposition by aquatic microbes were less pronounced compared to their ionic forms, despite metal ions were applied at one order of magnitude lower concentrations. Overall, results indicate that the increased release of nanometals to the environment may affect aquatic microbial communities with impacts on organic matter decomposition in streams.}, }
@article {pmid21547449, year = {2011}, author = {Borić, M and Danevčič, T and Stopar, D}, title = {Prodigiosin from Vibrio sp. DSM 14379; a new UV-protective pigment.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {528-536}, pmid = {21547449}, issn = {1432-184X}, mesh = {Coculture Techniques ; Pigments, Biological/biosynthesis ; Prodigiosin/*biosynthesis/isolation &amp; purification ; Ultraviolet Rays ; Vibrio/*metabolism/radiation effects ; }, abstract = {Pigments such as melanin, scytonemin and carotenoids protect microbial cells against the harmful effects of ultraviolet (UV) radiation. The role in UV protection has never been assigned to the prodigiosin pigment. In this work, we demonstrate that prodigiosin provides a significant level of protection against UV stress in Vibrio sp. DSM 14379. In the absence of pigment production, Vibrio sp. was significantly more susceptible to UV stress, and there was no difference in UV survival between the wild-type strain and non-pigmented mutant. The pigment's protective role was more important at higher doses of UV irradiation and correlated with pigment concentration in the cell. Pigmented cells survived high UV exposure (324 J/m(2)) around 1,000-fold more successfully compared to the non-pigmented mutant cells. Resistance to UV stress was conferred to the non-pigmented mutant by addition of exogenous pigment extract to the growth medium. A level of UV protection equivalent to that exhibited by the wild-type strain was attained by the non-pigmented mutant once the prodigiosin concentration had reached comparable levels to those found in the wild-type strain. In co-culture experiments, prodigiosin acted as a UV screen, protecting both the wild-type and non-pigmented mutants. Our results suggest a new ecophysiological role for prodigiosin.}, }
@article {pmid21546306, year = {2011}, author = {Pester, M and Schleper, C and Wagner, M}, title = {The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology.}, journal = {Current opinion in microbiology}, volume = {14}, number = {3}, pages = {300-306}, pmid = {21546306}, issn = {1879-0364}, mesh = {Ammonia/metabolism ; Archaea/*classification/genetics/*physiology ; Cluster Analysis ; *Ecosystem ; *Environmental Microbiology ; Oxidation-Reduction ; *Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Thaumarchaeota range among the most abundant archaea on Earth. Initially classified as 'mesophilic Crenarchaeota', comparative genomics has recently revealed that they form a separate and deep-branching phylum within the Archaea. This novel phylum comprises in 16S rRNA gene trees not only all known archaeal ammonia oxidizers but also several clusters of environmental sequences representing microorganisms with unknown energy metabolism. Ecophysiological studies of ammonia-oxidizing Thaumarchaeota suggest adaptation to low ammonia concentrations and an autotrophic or possibly mixotrophic lifestyle. Extrapolating from the wide substrate range of copper-containing membrane-bound monooxygenases, to which the thaumarchaeal ammonia monooxygenases belong, the use of substrates other than ammonia for generating energy by some members of the Thaumarchaeota seems likely.}, }
@article {pmid21539240, year = {2011}, author = {Verhagen, P and De Gelder, L and Boon, N}, title = {Biofilm based bioremediation strategies for the treatment of pesticide waste streams.}, journal = {Communications in agricultural and applied biological sciences}, volume = {76}, number = {1}, pages = {239-243}, pmid = {21539240}, issn = {1379-1176}, mesh = {Bacteria/*metabolism ; Biodegradation, Environmental ; *Biofilms ; Environmental Restoration and Remediation/instrumentation/*methods ; Pesticides/*metabolism ; Sewage/microbiology ; Soil Microbiology ; Water Pollutants/*metabolism ; Water Pollutants, Chemical ; }, }
@article {pmid21539227, year = {2011}, author = {Van Nevel, S and Hennebel, T and Verschuere, S and De Corte, S and Boon, N and Verstraete, W}, title = {Palladium nanoparticles produced by fermentatively grown bacteria as catalyst for diatrizoate removal with biogenic hydrogen.}, journal = {Communications in agricultural and applied biological sciences}, volume = {76}, number = {1}, pages = {185-188}, pmid = {21539227}, issn = {1379-1176}, mesh = {Biodegradation, Environmental ; Catalysis ; Citrobacter/chemistry/growth &amp; development/*metabolism ; Clostridium butyricum/chemistry/growth &amp; development/*metabolism ; Diatrizoate/*metabolism ; Fermentation ; Hydrogen/*metabolism ; Nanoparticles/chemistry ; Oxidation-Reduction ; Palladium/*chemistry/metabolism ; }, }
@article {pmid21539223, year = {2011}, author = {De Corte, S and Hennebel, T and Benner, J and De Gusseme, B and Verstraete, W and Boon, N}, title = {Dehalogenation of trichloroethylene in microbial electrolysis cells with biogenic palladium nanoparticles.}, journal = {Communications in agricultural and applied biological sciences}, volume = {76}, number = {1}, pages = {167-170}, pmid = {21539223}, issn = {1379-1176}, mesh = {Biodegradation, Environmental ; Bioelectric Energy Sources/*microbiology ; Electrolysis ; Halogenation ; Nanoparticles/*chemistry ; Oxidation-Reduction ; Palladium/*chemistry ; Shewanella/chemistry/*metabolism ; Trichloroethylene/*metabolism ; Water Pollutants, Chemical/*metabolism ; }, }
@article {pmid21539222, year = {2011}, author = {De Clippeleir, H and Yan, X and Verstraete, W and Vlaeminck, SE}, title = {Oland is feasible to treat sewage-like nitrogen concentrations at low hydraulic residence time.}, journal = {Communications in agricultural and applied biological sciences}, volume = {76}, number = {1}, pages = {163-166}, pmid = {21539222}, issn = {1379-1176}, mesh = {Bacteria/metabolism ; Biodegradation, Environmental ; Nitrogen/*analysis ; Sewage/*analysis/microbiology ; Waste Disposal, Fluid/*methods ; Water Pollutants, Chemical/analysis/metabolism ; }, }
@article {pmid21539221, year = {2011}, author = {Desloover, J and De Clippeleir, H and Boeckx, P and Du Laing, G and Colsen, J and Verstraete, W and Vlaeminck, SE}, title = {Performance and greenhouse gas emissions from an industrial nitrogen removal plant: trade-off between water and air quality?.}, journal = {Communications in agricultural and applied biological sciences}, volume = {76}, number = {1}, pages = {159-162}, pmid = {21539221}, issn = {1379-1176}, mesh = {Air Pollutants/*analysis ; Gases/*analysis ; *Greenhouse Effect ; Methane/analysis ; Nitrogen/*analysis ; Nitrous Oxide/analysis ; Sewage/*analysis ; Waste Management/*methods ; Water/*analysis ; }, }
@article {pmid21539219, year = {2011}, author = {Van Der Ha, D and Leyre, G and Bundervoet, B and Verstraete, W and Boon, N}, title = {Sustainable carbon neutral methane oxidation in anaerobic effluents through a partnership of methane oxidizing communities and microalgae.}, journal = {Communications in agricultural and applied biological sciences}, volume = {76}, number = {1}, pages = {151-154}, pmid = {21539219}, issn = {1379-1176}, mesh = {Anaerobiosis ; Carbon/*metabolism ; Light ; Methane/*metabolism ; Microalgae/*metabolism/radiation effects ; Oxidation-Reduction ; }, }
@article {pmid21539208, year = {2011}, author = {Grootaert, C and Van De Wiele, T and Van Roosbroeck, I and Posse-Miers, S and Vercoutter-Edouart, AS and Verstraete, W and Bracke, M and Vanhoecke, B}, title = {Bacterial modulation of the fasting induced adipose factor (FIAF) in an intestinal cell line model: a potential host-microbe crosstalk related to obesity.}, journal = {Communications in agricultural and applied biological sciences}, volume = {76}, number = {1}, pages = {101-105}, pmid = {21539208}, issn = {1379-1176}, mesh = {Angiopoietin-Like Protein 4 ; Angiopoietins/genetics/*metabolism ; Bacteria/metabolism ; Caco-2 Cells ; Humans ; Hydrogen Peroxide/metabolism ; Intestinal Mucosa/*metabolism ; Intestines/*microbiology ; Models, Biological ; Obesity/genetics/*metabolism/microbiology ; }, }
@article {pmid21539202, year = {2011}, author = {Sintubin, L and De Gusseme, B and Van Der Meeren, P and Pycke, BF and Verstraete, W and Boon, N}, title = {Antibacterial properties of biogenic silver stabilised on lactobacillus cell walls.}, journal = {Communications in agricultural and applied biological sciences}, volume = {76}, number = {1}, pages = {77-80}, pmid = {21539202}, issn = {1379-1176}, mesh = {Anti-Bacterial Agents/*pharmacology ; Cell Wall/*drug effects ; Disinfection ; Lactobacillus/*drug effects ; Silver/*pharmacology ; }, }
@article {pmid21539201, year = {2011}, author = {De Gusseme, B and Sintubin, L and Baert, L and Thibo, E and Hennebel, T and Vermeulen, G and Uyttrendaele, M and Verstraete, W and Boon, N}, title = {Biogenic silver nanoparticles for disinfection of viral contaminated water.}, journal = {Communications in agricultural and applied biological sciences}, volume = {76}, number = {1}, pages = {73-76}, pmid = {21539201}, issn = {1379-1176}, mesh = {Disinfectants/*toxicity ; Disinfection/instrumentation/*methods ; Fresh Water/*virology ; Nanoparticles/toxicity ; Silver/*pharmacology ; Viruses/*drug effects/growth &amp; development ; Water Pollution/analysis ; }, }
@article {pmid21539198, year = {2011}, author = {Zhang, Y and Boon, N}, title = {Anaerobic oxidation of methane in a simulated cold seep ecosystem.}, journal = {Communications in agricultural and applied biological sciences}, volume = {76}, number = {1}, pages = {61-64}, pmid = {21539198}, issn = {1379-1176}, mesh = {Anaerobiosis ; Bacteria/classification/genetics/*metabolism ; Bioreactors/microbiology ; Cold Temperature ; Ecosystem ; Geologic Sediments/microbiology ; Methane/*metabolism ; Oxidation-Reduction ; }, }
@article {pmid21539195, year = {2011}, author = {Vermeiren, J and Van De Wiele, T and Eeckhaut, V and Van Immerseel, F and De Vos, M and Laukens, D and Boon, N}, title = {Detrimental shifts in microbial communities from inflammatory bowel disease patients upon selective pressures.}, journal = {Communications in agricultural and applied biological sciences}, volume = {76}, number = {1}, pages = {49-52}, pmid = {21539195}, issn = {1379-1176}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics/*isolation &amp; purification/metabolism ; Bacterial Proteins/genetics/metabolism ; Feces/microbiology ; Humans ; Inflammatory Bowel Diseases/drug therapy/*microbiology ; }, }
@article {pmid21538105, year = {2011}, author = {Pachiadaki, MG and Kallionaki, A and Dählmann, A and De Lange, GJ and Kormas, KA}, title = {Diversity and spatial distribution of prokaryotic communities along a sediment vertical profile of a deep-sea mud volcano.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {655-668}, pmid = {21538105}, issn = {1432-184X}, mesh = {Archaea/genetics/growth &amp; development/*isolation &amp; purification ; Bacteria/genetics/growth &amp; development/*isolation &amp; purification ; *Biodiversity ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Geologic Sediments/chemistry/*microbiology ; Mediterranean Sea ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/microbiology ; Sequence Analysis, DNA ; Water Microbiology ; }, abstract = {We investigated the top 30-cm sediment prokaryotic community structure in 5-cm spatial resolution, at an active site of the Amsterdam mud volcano, East Mediterranean Sea, based on the 16S rRNA gene diversity. A total of 339 and 526 sequences were retrieved, corresponding to 25 and 213 unique (≥98% similarity) phylotypes of Archaea and Bacteria, respectively, in all depths. The Shannon-Wiener diversity index H was higher for Bacteria (1.92-4.03) than for Archaea (0.99-1.91) and varied differently between the two groups. Archaea were dominated by anaerobic methanotrophs ANME-1, -2 and -3 groups and were related to phylotypes involved in anaerobic oxidation of methane from similar habitats. The much more complex Bacteria community consisted of 20 phylogenetic groups at the phylum/candidate division level. Proteobacteria, in particular δ-Proteobacteria, was the dominant group. In most sediment layers, the dominant phylotypes of both the Archaea and Bacteria communities were found in neighbouring layers, suggesting some overlap in species richness. The similarity of certain prokaryotic communities was also depicted by using four different similarity indices. The direct comparison of the retrieved phylotypes with those from the Kazan mud volcano of the same field revealed that 40.0% of the Archaea and 16.9% of the Bacteria phylotypes are common between the two systems. The majority of these phylotypes are closely related to phylotypes originating from other mud volcanoes, implying a degree of endemicity in these systems.}, }
@article {pmid21534258, year = {2010}, author = {}, title = {Marine genomics: at the interface of marine microbial ecology and biotechnological applications. Proceedings of a CIESM-NSF/EC Workshop. October 12-14, 2008. Monaco.}, journal = {Microbial biotechnology}, volume = {3}, number = {5}, pages = {489-621}, pmid = {21534258}, issn = {1751-7915}, mesh = {Aquatic Organisms/*genetics ; Biodiversity ; *Biotechnology ; *Genomics ; *Marine Biology ; Seawater/*microbiology ; }, }
@article {pmid21531609, year = {2011}, author = {Wilson, DB}, title = {Microbial diversity of cellulose hydrolysis.}, journal = {Current opinion in microbiology}, volume = {14}, number = {3}, pages = {259-263}, doi = {10.1016/j.mib.2011.04.004}, pmid = {21531609}, issn = {1879-0364}, mesh = {Bacteria/*enzymology/*metabolism ; *Biodiversity ; Cellulose/*metabolism ; Fungi/*enzymology/*metabolism ; Hydrolysis ; }, abstract = {Enzymatic hydrolysis of cellulose by microorganisms is a key step in the global carbon cycle. Despite its abundance only a small percentage of microorganisms can degrade cellulose, probably because it is present in recalcitrant cell walls. There are at least five distinct mechanisms used by different microorganisms to degrade cellulose all of which involve cellulases. Cellulolytic organisms and cellulases are extremely diverse possibly because their natural substrates, plant cell walls, are very diverse. At this time the microbial ecology of cellulose degradation in any environment is still not clearly understood even though there is a great deal of information available about the bovine rumen. Two major problems that limit our understanding of this area are the vast diversity of organisms present in most cellulose degrading environments and the inability to culture most of them.}, }
@article {pmid21523464, year = {2011}, author = {Golberg, K and Eltzov, E and Shnit-Orland, M and Marks, RS and Kushmaro, A}, title = {Characterization of quorum sensing signals in coral-associated bacteria.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {783-792}, pmid = {21523464}, issn = {1432-184X}, mesh = {4-Butyrolactone/analogs &amp; derivatives/metabolism ; Animals ; Anthozoa/*microbiology ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Molecular Sequence Data ; Phylogeny ; *Quorum Sensing ; Signal Transduction ; }, abstract = {Marine environment habitats, such as the coral mucus layer, are abundant in nutrients and rich with diverse populations of microorganisms. Since interactions among microorganisms found in coral mucus can be either mutualistic or competitive, understanding quorum sensing-based acyl homoserine lactone (AHL) language may shed light on the interaction between coral-associated microbial communities in the native host. More than 100 bacterial isolates obtained from different coral species were screened for their ability to produce AHL. When screening the isolated coral bacteria for AHL induction activity using the reporter strains Escherichia coli K802NR-pSB1075 and Agrobacterium tumefaciens KYC55, we found that approximately 30% of the isolates tested positive. Thin layer chromatography separation of supernatant extracts revealed different AHL profiles, with detection of at least one active compound in the supernatant of those bacterial extracts being able to induce AHL activity in the two different bioreporter strains. The active extract of bacterial isolate 3AT 1-10-4 was subjected to further analysis by preparative thin layer chromatography and liquid chromatography tandem mass spectrometry. One of the compounds was found to correspond with N-(3-hydroxydecanoyl)-L-homoserine lactone. 16S rRNA gene sequencing of the isolates with positive AHL activity affiliated them with the Vibrio genus. Understanding the ecological role of AHL in the coral environment and its regulatory circuits in the coral holobiont-associated microbial community will further expand our knowledge of such interactions.}, }
@article {pmid21521227, year = {2011}, author = {Hosseini, E and Grootaert, C and Verstraete, W and Van de Wiele, T}, title = {Propionate as a health-promoting microbial metabolite in the human gut.}, journal = {Nutrition reviews}, volume = {69}, number = {5}, pages = {245-258}, doi = {10.1111/j.1753-4887.2011.00388.x}, pmid = {21521227}, issn = {1753-4887}, mesh = {Bacteria/*metabolism ; Carbohydrate Metabolism ; Diet ; *Fermentation ; Gastrointestinal Tract/*microbiology ; Humans ; *Prebiotics ; Propionates/*metabolism/pharmacology ; }, abstract = {Propionate is a major microbial fermentation metabolite in the human gut with putative health effects that extend beyond the gut epithelium. Propionate is thought to lower lipogenesis, serum cholesterol levels, and carcinogenesis in other tissues. Steering microbial propionate production through diet could therefore be a potent strategy to increase health effects from microbial carbohydrate fermentation. The present review first discusses the two main propionate-production pathways and provides an extended gene-based list of microorganisms with the potential to produce propionate. Second, it evaluates the promising potential of arabinoxylan, polydextrose, and L-rhamnose to act as substrates to increase microbial propionate. Third, given the complexity of the gut microbiota, propionate production is approached from a microbial-ecological perspective that includes interaction processes such as cross-feeding mechanisms. Finally, it introduces the development of functional gene-based analytical tools to detect and characterize propionate-producing microorganisms in a complex community. The information in this review may be helpful for designing functional food strategies that aim to promote propionate-associated health benefits.}, }
@article {pmid21519913, year = {2011}, author = {Zhou, K and Zhang, X and Zhang, F and Li, Z}, title = {Phylogenetically diverse cultivable fungal community and polyketide synthase (PKS), non-ribosomal peptide synthase (NRPS) genes associated with the South China Sea sponges.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {644-654}, pmid = {21519913}, issn = {1432-184X}, mesh = {Animals ; China ; DNA, Fungal/genetics ; Fungi/enzymology/*genetics/isolation &amp; purification ; Oceans and Seas ; Peptide Synthases/*genetics ; *Phylogeny ; Polyketide Synthases/*genetics ; Polymorphism, Restriction Fragment Length ; Porifera/*microbiology ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {Compared with sponge-associated bacteria, the phylogenetic diversity of fungi in sponge and the association of sponge fungi remain largely unknown. Meanwhile, no detection of polyketide synthase (PKS) or non-ribosomal peptide synthase (NRPS) genes in sponge-associated fungi has been attempted. In this study, diverse and novel cultivable fungi including 10 genera (Aspergillus, Ascomycete, Fusarium, Isaria, Penicillium, Plectosphaerella, Pseudonectria, Simplicillium, Trichoderma, and Volutella) in four orders (Eurotiales, Hypocreales, Microascales, and Phyllachorales) of phylum Ascomycota were isolated from 10 species marine sponges in the South China Sea. Eurotiales and Hypocreales fungi were suggested as sponge generalists. The predominant isolates were Penicillium and Aspergillus in Eurotiales followed by Volutella in Hypocreales. Based on the conserved Beta-ketosynthase of PKS and A domain of NRPS, 15 polyketide synthases, and four non-ribosomal peptides synthesis genes, including non-reducing and reducing PKSs and hybrid PKS-NRPS, were detected in these fungal isolates. A lateral gene transfer event was indicated in the comparison between the phylogenetic diversity of 18S rRNA genes and β-ketoacyl synthase domain sequences. Some fungi, especially those with PKS or NRPS genes, showed antimicrobial activity against P. fluorescens, S. aureus and B. subtilis. It was the first time to investigate PKS and NRPS genes in sponge-associated fungi. Based on the detected antibiotics biosynthesis-related PKS and NRPS genes and antimicrobial activity, the potential ecological role of sponge-associated fungi in the chemical defense for sponge host was suggested. This study extended our knowledge of sponge-associated fungal phylogenetic diversity and their potential roles in the chemical defense.}, }
@article {pmid21518214, year = {2011}, author = {Grootaert, C and Van de Wiele, T and Van Roosbroeck, I and Possemiers, S and Vercoutter-Edouart, AS and Verstraete, W and Bracke, M and Vanhoecke, B}, title = {Bacterial monocultures, propionate, butyrate and H2O2 modulate the expression, secretion and structure of the fasting-induced adipose factor in gut epithelial cell lines.}, journal = {Environmental microbiology}, volume = {13}, number = {7}, pages = {1778-1789}, doi = {10.1111/j.1462-2920.2011.02482.x}, pmid = {21518214}, issn = {1462-2920}, mesh = {Angiopoietin-Like Protein 4 ; Angiopoietins/*metabolism ; Bacteria/*metabolism ; Bacterial Adhesion ; Butyrates/*metabolism ; Caco-2 Cells ; Epithelial Cells/*metabolism ; Fasting ; Glycosylation ; HCT116 Cells ; Humans ; Hydrogen Peroxide/*metabolism ; Propionates/*metabolism ; Protein Isoforms/metabolism ; }, abstract = {Previous research showed that an intestinal microbial community represses the fasting-induced adipose factor (FIAF) in the gut epithelium, thereby increasing fat storage in the host. This study was designed to investigate the overall effect of different bacterial species and metabolites on FIAF in intestinal (Caco-2, HT-29 and HCT-116) and hepatic (HepG2) cancer cell lines. First, we showed that FIAF was present in different isoforms, and secreted as N-glycosylated proteins, exclusively at the basal side of the cell monolayer. Second, co-incubation of cell lines with bacterial monocultures and metabolites altered both FIAF production and isoform appearance. Propionate and/or butyrate treatment increased FIAF expression and cleavage in all tested cell lines. In contrast, different bacteria induced cell line-specific FIAF modulation. Clostridium perfringens induced FIAF isoform changes in Caco-2 cells. Enterococcus faecalis and Bacteroides thetaiotaomicron treatment resulted in cell line-specific FIAF increases, whereas Escherichia coli significantly decreased FIAF expression in HCT-116 cells. Treatment with H(2) O(2) and peroxide-producing E. faecalis strains induced FIAF isoform changes in Caco-2 cells. Since bacteria and bacterial metabolites alter both FIAF production and isoform appearance, further investigation may reveal an important role for bacteria in FIAF-regulated physiological processes, such as cell differentiation and fat metabolism.}, }
@article {pmid21517915, year = {2011}, author = {Llirós, M and Alonso-Sáez, L and Gich, F and Plasencia, A and Auguet, O and Casamayor, EO and Borrego, CM}, title = {Active bacteria and archaea cells fixing bicarbonate in the dark along the water column of a stratified eutrophic lagoon.}, journal = {FEMS microbiology ecology}, volume = {77}, number = {2}, pages = {370-384}, doi = {10.1111/j.1574-6941.2011.01117.x}, pmid = {21517915}, issn = {1574-6941}, mesh = {Acetyl-CoA Carboxylase/genetics ; Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; Bicarbonates/*metabolism ; *Carbon Cycle ; Carbon Dioxide/metabolism ; Carbon Isotopes/analysis ; *Darkness ; Denaturing Gradient Gel Electrophoresis ; Fresh Water/chemistry/microbiology ; Gene Library ; Genes, Archaeal ; Genes, Bacterial ; In Situ Hybridization, Fluorescence ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; }, abstract = {We studied the carbon dioxide fixation activity in a stratified hypereutrophic karstic lagoon using a combination of fingerprinting techniques targeting bacterial and archaeal 16S rRNA genes, functional gene cloning [the acetyl-CoA carboxylase (accC)], and isotopic labelling ((14)C-bicarbonate) coupled to single-cell analyses [microautoradiography combined with catalyzed reported deposition-FISH (MAR-CARD-FISH)]. The microbial planktonic community was dominated by bacteria with maximal abundances of archaea just below the oxic/anoxic transition zone (7% of total cells). In situ incubations with radiolabelled bicarbonate showed maximal photoassimilation activity in the oxic epilimnion, whereas dark CO(2) fixation was consistently observed throughout the water column, with a maximum at the oxic/anoxic interface (8.6 mg C m(-3) h(-1)). The contributions of light and dark carbon fixation activities in the whole water column were 69% and 31% of the total C incorporated, respectively. MAR-CARD-FISH incubations corroborated these results and revealed that the highest fraction of bacterial and archaeal cells actively uptaking bicarbonate in the light was found at the surface. The bacterial community was mainly composed of green sulfur bacteria (Chlorobi) and members of the Betaproteobacteria and the Bacteroidetes. The archaeal assemblage was composed of phylotypes of the Miscellaneous Crenarchaeotic Group and a few methanogens. Clone libraries of the accC gene showed an absolute dominance of bacterial carboxylases. Our results suggest that the dark carbon fixation activity measured was mainly related to CO(2) incorporation by heterotrophs rather than to the activity of true chemoautotrophs.}, }
@article {pmid21514469, year = {2011}, author = {Chain, PS and Xie, G and Starkenburg, SR and Scholz, MB and Beckloff, N and Lo, CC and Davenport, KW and Reitenga, KG and Daligault, HE and Detter, JC and Freitas, TA and Gleasner, CD and Green, LD and Han, CS and McMurry, KK and Meincke, LJ and Shen, X and Zeytun, A}, title = {Genomics for key players in the N cycle from guinea pigs to the next frontier.}, journal = {Methods in enzymology}, volume = {496}, number = {}, pages = {289-318}, doi = {10.1016/B978-0-12-386489-5.00012-9}, pmid = {21514469}, issn = {1557-7988}, support = {Y1-DE-6006-02/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/*genetics/metabolism ; *Genome, Bacterial ; Genomics/*methods ; Molecular Sequence Annotation/*methods ; Nitrification/*genetics ; Nitrogen Cycle/*genetics ; Nitrosomonas europaea/genetics/metabolism ; Sequence Analysis, DNA/*methods ; }, abstract = {While sequencing methods were available in the late 1970s, it was not until the human genome project and a significant influx of funds for such research that this technology became high throughput. The fields of microbiology and microbial ecology, among many others, have been tremendously impacted over the years, to such an extent that the determination of complete microbial genome sequences is now commonplace. Given the lower costs of next-generation sequencing platforms, even small laboratories from around the world will be able to generate millions of base pairs of data, equivalent to entire genomes worth of sequence information. With this prospect just around the corner, it is timely to provide an overview of the genomics process: from sample preparation to some of the analytical methods used to gain functional knowledge from sequence information.}, }
@article {pmid21514465, year = {2011}, author = {Daims, H and Wagner, M}, title = {In situ techniques and digital image analysis methods for quantifying spatial localization patterns of nitrifiers and other microorganisms in biofilm and flocs.}, journal = {Methods in enzymology}, volume = {496}, number = {}, pages = {185-215}, doi = {10.1016/B978-0-12-386489-5.00008-7}, pmid = {21514465}, issn = {1557-7988}, support = {I 44/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/genetics/growth &amp; development/*isolation &amp; purification ; Biofilms/*growth &amp; development ; Flocculation ; In Situ Hybridization, Fluorescence/*methods ; Microscopy, Confocal/methods ; *Nitrification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The spatial localization patterns of microorganisms in multispecies biofilms reflect numerous phenomena that influence sessile microbial life, such as substrate concentration gradients within the biofilm and biological interactions with other biofilm populations. Quantitative and population-specific in situ analyses of spatial patterns have a high potential to provide novel insights into the biology of biofilm organisms, including yet uncultured microbes, but such approaches have been developed and used in a few studies only. Here, we outline digital image analysis methods to quantify the coaggregation, mutual avoidance, or random distribution of microbial populations in biofilm and flocs. A protocol is provided for fluorescence in situ hybridization with rRNA-targeted probes, which preserves the three-dimensional biofilm architecture for confocal microscopy and image analysis, and the combined use of these approaches is demonstrated by spatial analyses of nitrifying bacteria in complex biofilm samples.}, }
@article {pmid21509607, year = {2011}, author = {Hewson, I and Brown, JM and Gitlin, SA and Doud, DF}, title = {Nucleopolyhedrovirus detection and distribution in terrestrial, freshwater, and marine habitats of Appledore Island, Gulf of Maine.}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {48-57}, pmid = {21509607}, issn = {1432-184X}, mesh = {Animals ; *Ecosystem ; Fresh Water/*virology ; Maine ; Molecular Sequence Data ; Moths/virology ; Nucleopolyhedroviruses/classification/genetics/*isolation &amp; purification ; Phylogeny ; Plankton/virology ; Seawater/*virology ; *Soil Microbiology ; Viral Proteins/genetics ; }, abstract = {Viruses in aquatic ecosystems comprise those produced by both autochthonous and allochthonous host taxa. However, there is little information on the diversity and abundance of viruses of allochthonous origin, particularly from non-anthropogenic sources, in freshwater and marine ecosystems. We investigated the presence of nucleopolyhedroviruses (NPV) (Baculovirus), which commonly infect terrestrial lepidopteran taxa, across the landscape of Appledore Island, Gulf of Maine. PCR and qPCR primers were developed around a 294-bp fragment of the polyhedrin (polH) gene, which is the major constituent protein of NPV multivirion polyhedral occlusion bodies. polH was successfully amplified from several aquatic habitats, and recovered polH sequences were most similar to known lepidopteran NPV. Using quantitative PCR designed around a cluster of detected sequences, we detected polH in Appledore Island soils, supratidal freshwater ponds, nearshore sediments, near- and offshore plankton, and in floatsam. This diverse set of locations suggests that NPVs are widely dispersed along the terrestrial--marine continuum and that free polyhedra may be washed into ponds and eventually to sea. The putative hosts of detected NPVs were webworms (Hyphantria sp.) which form dense nests in late summer on the dominant Appledore Island vegetation (Prunus virginiana). Our data indicate that viruses of terrestrial origin (i.e., allochthonous viruses) may be dispersed widely in coastal marine habitats. The dispersal of NPV polH and detection within offshore net plankton (>64 μm) demonstrates that terrestrial viruses may interact with larger particles and plankton of coastal marine ecosystem, which further suggests that viral genomic information may be transported between biomes.}, }
@article {pmid21503776, year = {2011}, author = {Remold, SK and Brown, CK and Farris, JE and Hundley, TC and Perpich, JA and Purdy, ME}, title = {Differential habitat use and niche partitioning by Pseudomonas species in human homes.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {505-517}, pmid = {21503776}, issn = {1432-184X}, mesh = {Biodiversity ; *Ecosystem ; *Environmental Microbiology ; *Housing ; Humans ; Kentucky ; Phylogeny ; Pseudomonas/classification/growth &amp; development/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Many species of Pseudomonas have the ability to use a variety of resources and habitats, and as a result Pseudomonas are often characterized as having broad fundamental niches. We questioned whether actual habitat use by Pseudomonas species is equally broad. To do this, we sampled extensively to describe the biogeography of Pseudomonas within the human home, which presents a wide variety of habitats for microbes that live in close proximity to humans but are not part of the human flora, and for microbes that are opportunistic pathogens, such as Pseudomonas aeruginosa. From 960 samples taken in 20 homes, we obtained 163 Pseudomonas isolates. The most prevalent based on identification using the SepsiTest BLAST analysis of 16S rRNA (http://www.sepsitest-blast.de) were Pseudomonas monteilii (42 isolates), Pseudomonas plecoglossicida, Pseudomonas fulva, and P. aeruginosa (approximately 25 each). Of these, all but P. fulva differed in recovery rates among evaluated habitat types (drains, soils, water, internal vertebrate sites, vertebrate skin, inanimate surfaces, and garbage/compost) and all four species also differed in recovery rates among subcategories of habitat types (e.g., types of soils or drains). We also found that at both levels of habitat resolution, each of these six most common species (the four above plus Pseudomonas putida and Pseudomonas oryzihabitans) were over- or under-represented in some habitats relative to their contributions to the total Pseudomonas collected across all habitats. This pattern is consistent with niche partitioning. These results suggest that, whereas Pseudomonas are often characterized as generalists with broad fundamental niches, these species in fact have more restricted realized niches. Furthermore, niche partitioning driven by competition among Pseudomonas species may be contributing to the observed variability in habitat use by Pseudomonas in this system.}, }
@article {pmid21503775, year = {2011}, author = {Mandal, SK and Singh, RP and Patel, V}, title = {Isolation and characterization of exopolysaccharide secreted by a toxic dinoflagellate, Amphidinium carterae Hulburt 1957 and its probable role in harmful algal blooms (HABs).}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {518-527}, pmid = {21503775}, issn = {1432-184X}, mesh = {Bacillus/physiology ; Dinoflagellida/growth &amp; development/*metabolism ; *Harmful Algal Bloom ; Magnetic Resonance Spectroscopy ; Microscopy, Atomic Force ; Molecular Weight ; Polysaccharides/*isolation &amp; purification ; Species Specificity ; Spectrometry, X-Ray Emission ; Spectroscopy, Fourier Transform Infrared ; }, abstract = {Extracellular polymeric substances (EPS) produced by a toxic dinoflagellate Amphidinium carterae Hulburt 1957 was isolated and characterized. Molecular masses of the EPS were about 233 and 1,354 kDa. Spectral analyses by (1)H nuclear magnetic resonance and Fourier Transformed-Infrared Spectroscopy revealed the characteristic of the functional groups viz. primary amine, carboxyl, halide, and sulfate groups present in the EPS. However, five elements (C, O, Na, S, and Ca) were detected by scanning electron microscopy - energy dispersive X-ray spectroscopy (SEM-EDX) analysis. X-ray diffraction and differential scanning calorimetric analysis confirmed the amorphous nature of EPS, which was comprised of an average particle size of 13.969 μm (d 0.5) with 181 nm average roughness. Two monosaccharide constituents, galactose (73.13%) and glucose (26.87%) were detected by gas chromatography-mass spectroscopy analysis. Thermal gravimetric analysis revealed that degradation of EPS obtained from A. carterae takes place in three steps. The EPS produced by A. carterae was found to be beneficial for the growth of both A. carterae and Bacillus pumilus. The potential heterogeneous properties of EPS may play an important role in harmful algal bloom.}, }
@article {pmid21500343, year = {2011}, author = {Sixt, BS and Heinz, C and Pichler, P and Heinz, E and Montanaro, J and Op den Camp, HJ and Ammerer, G and Mechtler, K and Wagner, M and Horn, M}, title = {Proteomic analysis reveals a virtually complete set of proteins for translation and energy generation in elementary bodies of the amoeba symbiont Protochlamydia amoebophila.}, journal = {Proteomics}, volume = {11}, number = {10}, pages = {1868-1892}, doi = {10.1002/pmic.201000510}, pmid = {21500343}, issn = {1615-9861}, mesh = {Acanthamoeba/*microbiology ; Bacterial Proteins/genetics/*metabolism ; Chlamydiales/genetics/*metabolism/physiology ; Electrophoresis, Gel, Two-Dimensional ; Energy Metabolism ; Metabolic Networks and Pathways ; Microscopy, Electron, Transmission ; Peptide Mapping ; Protein Biosynthesis ; Proteome/*chemistry ; Proteomics ; Symbiosis/physiology ; Transcription, Genetic ; }, abstract = {Chlamydiae belong to the most successful intracellular bacterial pathogens. They display a complex developmental cycle and an extremely broad host spectrum ranging from vertebrates to protozoa. The family Chlamydiaceae comprises exclusively well-known pathogens of humans and animals, whereas the members of its sister group, the Parachlamydiaceae, naturally occur as symbionts of free-living amoebae. Comparative analysis of these two groups provides valuable insights into chlamydial evolution and mechanisms for microbe-host interaction. Based on the complete genome sequence of the Acanthamoeba spp. symbiont Protochlamydia amoebophila UWE25, we performed the first detailed proteome analysis of the infectious stage of a symbiotic chlamydia. A 2-D reference proteome map was established and the analysis was extensively complemented by shotgun proteomics. In total, 472 proteins were identified, which represent 23.2% of all encoded proteins. These cover a wide range of functional categories, including typical house-keeping proteins, but also putative virulence-associated proteins. A number of proteins that are not encoded in genomes of Chlamydiaceae were observed and the expression of 162 proteins classified as hypothetical or unknown proteins could be demonstrated. Our findings indicate that P. amoebophila exploits its additional genetic repertoire (compared with the Chlamydiaceae), and that its elementary bodies are remarkably well equipped with proteins involved in transcription, translation, and energy generation.}, }
@article {pmid21498766, year = {2011}, author = {Iwai, S and Johnson, TA and Chai, B and Hashsham, SA and Tiedje, JM}, title = {Comparison of the specificities and efficacies of primers for aromatic dioxygenase gene analysis of environmental samples.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {11}, pages = {3551-3557}, pmid = {21498766}, issn = {1098-5336}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; P42 ES004911-20/ES/NIEHS NIH HHS/United States ; }, mesh = {Computational Biology ; DNA Primers/*genetics ; Dioxygenases/*genetics/metabolism ; *Environmental Microbiology ; Genetic Variation ; Hydrocarbons, Aromatic/metabolism ; *Metagenomics ; Polymerase Chain Reaction/*methods ; }, abstract = {Aromatic dioxygenase genes have long been of interest for bioremediation and aromatic carbon cycling studies. To date, 115 primers and probes have been designed and used to analyze dioxygenase gene diversities in environmental samples. Here we analyze those primers' specificities, coverages, and PCR product lengths compared to known aromatic dioxygenase genes based on in silico analysis as well as summarize their differing advantages or effectiveness from over 50 reported experimental studies. We also provide some guidance for primer use in future studies.}, }
@article {pmid21497663, year = {2011}, author = {Plessas, S and Alexopoulos, A and Voidarou, C and Stavropoulou, E and Bezirtzoglou, E}, title = {Microbial ecology and quality assurance in food fermentation systems. The case of kefir grains application.}, journal = {Anaerobe}, volume = {17}, number = {6}, pages = {483-485}, doi = {10.1016/j.anaerobe.2011.03.014}, pmid = {21497663}, issn = {1095-8274}, mesh = {*Biota ; Cultured Milk Products/*microbiology ; Fermentation ; Food Industry/*methods ; Quality Control ; }, abstract = {Fermentation technology has become a modern method for food production the last decades as a process for enhancing product stability, safety and sensory standards. The main reason for this development is the increasing consumers' demand for safe and high quality food products. The above has led the scientific community to the thorough study for the appropriate selection of specific microorganisms with desirable properties such as bacteriocin production, and probiotic properties. The main food products produced through fermentation activity are bread, wine, beer cheese and other dairy products. The microorganisms conducting the above processes are mainly yeasts and lactic acid bacteria. The end products of carbohydrate catabolism by these microorganisms contribute not only to preservation as it was believed years ago, but also to the flavour, aroma and texture and to the increase of the nutritional quality by thereby helping determine unique product characteristics. Thus, controlling the function of specific microorganisms or the succession of microorganisms that dominate the microflora is therefore advantageous, because it can increase product quality, functionality and value. Throughout the process of the discovery of microbiological diversity in various fermented food systems, the development of starter culture technology has gained more scientific attention, and it could be used for the control of the manufacturing operation, and management of product quality. In the frame of this review the presentation of the quality enhancement of most consumed fermented food products around the world is attempted and the new trends in production of fermented food products, such as bread is discussed. The review is focused in kefir grains application in bread production.}, }
@article {pmid21491206, year = {2011}, author = {Read, S and Marzorati, M and Guimarães, BC and Boon, N}, title = {Microbial Resource Management revisited: successful parameters and new concepts.}, journal = {Applied microbiology and biotechnology}, volume = {90}, number = {3}, pages = {861-871}, doi = {10.1007/s00253-011-3223-5}, pmid = {21491206}, issn = {1432-0614}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Genetic Techniques ; *Microbiological Techniques ; *Research Design ; }, abstract = {In the twenty-first century, scientists will want to steer the microbial black box in (engineered) ecosystems, rather than only study and describe them. This strategy led to a new way of thinking: Microbial Resource Management (MRM). For the last few years, MRM has been utilized to consolidate and communicate our acquired knowledge of the microbiome to many areas of the scientific community. This shared knowledge has brought us closer to formulating a plan toward the analysis, and at a later stage, the management of our varied microbial communities and to look at ways of harnessing their unique abilities for future practices. We require this acquired knowledge for a more sustainable solution to our ongoing global challenges such as our diminishing energy and water supply. Like any successful concept, MRM must be updated to adapt to new molecular technologies, and thus, in this review, MRM has been reengineered to encompass these changes. This review reports how MRM has been used successfully over the last few years within various environments and how we can broaden its capabilities to increase its compliance in the face of state of the art ever changing technologies. Not only have we reengineered and improved MRM, but also we have discussed how newly formed relationships between technologies can provide the full picture of these complex microbial communities and their interactions for future opportunities.}, }
@article {pmid21491114, year = {2011}, author = {Hong, YG and Li, M and Cao, H and Gu, JD}, title = {Residence of habitat-specific anammox bacteria in the deep-sea subsurface sediments of the South China Sea: analyses of marker gene abundance with physical chemical parameters.}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {36-47}, pmid = {21491114}, issn = {1432-184X}, mesh = {Bacteria, Anaerobic/classification/*genetics/*isolation &amp; purification/metabolism ; Bacterial Proteins/genetics ; Biodiversity ; China ; *Ecosystem ; Genetic Markers ; Geologic Sediments/chemistry/*microbiology ; Molecular Sequence Data ; Oceans and Seas ; Phylogeny ; Quaternary Ammonium Compounds/*metabolism ; Seawater/chemistry/*microbiology ; Species Specificity ; }, abstract = {Anaerobic ammonium oxidation (anammox) has been recognized as an important process for the global nitrogen cycle. In this study, the occurrence and diversity of anammox bacteria in the deep-sea subsurface sediments of the South China Sea (SCS) were investigated. Results indicated that the anammox bacterial sequences recovered from this habitat by amplifying both 16S rRNA gene and hydrazine oxidoreductase encoding hzo gene were all closely related to the Candidatus Scalindua genus. A total of 96 16S rRNA gene sequences from 346 clones were grouped into five subclusters: two subclusters affiliated with the brodae and arabica species, while three new subclusters named zhenghei-I, -II, and -III showed ≤ 97.4% nucleic acid sequence identity with other known Candidatus Scalindua species. Meanwhile, 88 hzo gene sequences from the sediments also formed five distant subclusters within hzo cluster 1c. Through fluorescent real-time PCR analysis, the abundance of anammox bacteria in deep-sea subsurface sediment was quantified by hzo genes, which ranged from 1.19 × 10(4) to 7.17 × 10(4) copies per gram of dry sediments. Combining all the information from this study, diverse Candidatus Scalindua anammox bacteria were found in the deep-sea subsurface sediments of the SCS, and they could be involved in the nitrogen loss from the fixed inventory in the habitat.}, }
@article {pmid21489340, year = {2012}, author = {Brzychczy-Włoch, M and Gosiewski, T and Bodaszewska-Lubas, M and Adamski, P and Heczko, PB}, title = {Molecular characterization of capsular polysaccharides and surface protein genes in relation to genetic similarity of group B streptococci isolated from Polish pregnant women.}, journal = {Epidemiology and infection}, volume = {140}, number = {2}, pages = {329-336}, doi = {10.1017/S0950268811000616}, pmid = {21489340}, issn = {1469-4409}, mesh = {Adult ; Bacterial Capsules/*genetics ; Bacterial Proteins/*genetics ; Carrier State/microbiology ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field/*methods ; Female ; Genetic Variation ; Genotype ; Humans ; Membrane Proteins/*genetics ; Phylogeny ; Poland ; Polymerase Chain Reaction ; Pregnancy ; Rectum/microbiology ; Serotyping ; Streptococcus agalactiae/*classification/*genetics/isolation &amp; purification ; Vagina/microbiology ; }, abstract = {Serotyping, subtyping and genotyping are important tools for epidemiological studies of group B streptococci (GBS). We investigated the genotype distribution of 353 GBS isolates originating from vaginal or rectal carriage to identify capsular serotypes and subtypes based on the surface protein genes of the alpha-like protein (Alp) family. GBS were recovered from 30% of 1176 pregnant women during the period 2007-2009, with a predominance of capsular genotypes III (35%), Ia (20%), V (17%), II (15%), Ib (8%) and IV (5%). The most common Alp gene was epsilon (26%), followed by rib (22%), alp2 (21%), bca (17%) and alp3 (14%). Several protein genes were significantly associated (G(2)=249·635, P<0·0001) with particular serotypes: epsilon with Ia, Ib, IV; bca with Ib, II; rib with II, III; alp3 with V; alp2 with III. High genetic diversity within GBS strains was observed using DNA macrorestriction. Serotypes Ib, II and III demonstrated the greatest genetic heterogeneity and serotype V the lowest heterogeneity (relative frequency coefficient ≥0·03 vs. -0·46, respectively). Macrolide-resistant strains with serotype V and alp3 gene, showed higher uniformity in genetic profile. The distribution of serotypes and surface proteins of GBS strains are necessary data to inform the design and formulation of new GBS vaccines for use in Poland and other countries.}, }
@article {pmid21488909, year = {2011}, author = {Kuramae, E and Gamper, H and van Veen, J and Kowalchuk, G}, title = {Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with a neutral pH.}, journal = {FEMS microbiology ecology}, volume = {77}, number = {2}, pages = {285-294}, doi = {10.1111/j.1574-6941.2011.01110.x}, pmid = {21488909}, issn = {1574-6941}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biota ; Calcium Carbonate ; Cluster Analysis ; Hydrogen-Ion Concentration ; Netherlands ; Phylogeny ; *Plant Development ; Poaceae/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; Time Factors ; }, abstract = {Although soil pH has been shown to be an important factor driving microbial communities, relatively little is known about the other potentially important factors that shape soil-borne microbial community structure. This study examined plant and microbial communities across a series of neutral pH fields (pH=7.0-7.5) representing a chronosequence of secondary succession after former arable fields were taken out of production. These fields ranged from 17 to >66 years since the time of abandonment, and an adjacent arable field was included as a reference. Hierarchical clustering analysis, nonmetric multidimensional scaling and analysis of similarity of 52 different plant species showed that the plant community composition was significantly different in the different chronosequences, and that plant species richness and diversity increased with time since abandonment. The microbial community structure, as analyzed by phylogenetic microarrays (PhyloChips), was significantly different in arable field and the early succession stage, but no distinct microbial communities were observed for the intermediate and the late succession stages. The most determinant factors in shaping the soil-borne microbial communities were phosphorous and NH(4)(+). Plant community composition and diversity did not have a significant effect on the belowground microbial community structure or diversity.}, }
@article {pmid21484497, year = {2011}, author = {Ayuso, SV and Guerrero, Mdel C and Montes, C and López-Archilla, AI}, title = {Regulation and spatiotemporal patterns of extracellular enzyme activities in a coastal, sandy aquifer system (Doñana, SW Spain).}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {162-176}, pmid = {21484497}, issn = {1432-184X}, mesh = {Alkaline Phosphatase/analysis/metabolism ; Bacteria/chemistry/*enzymology ; Bacterial Proteins/*analysis/metabolism ; Ecosystem ; Extracellular Space/chemistry/*enzymology ; Fresh Water/*chemistry/*microbiology ; Leucyl Aminopeptidase/analysis/metabolism ; Seasons ; Spain ; beta-Glucosidase/analysis/metabolism ; }, abstract = {A seasonal study of extracellular enzyme activities (EEA) was conducted in the coastal, sandy aquifer system located in the greater fluvial-littoral ecosystem of Doñana (SW, Spain). Glucosidase, leucine aminopeptidase, alkaline phosphatase, and phenol oxidase activities were determined over a 2-year period in 30 piezometers spread in an area of approximately 100 km(2). Taking into account all enzymes, piezometers, and seasons, EEA ranged over several orders of magnitude, from 1.01 × 10(-5) ± 2.92 × 10(-6) to 1.37 ± 0.13 nmol (methylumbelliferyl, amido-4-methylcoumarin, or dihydroxyphenylalanine) mL(-1) h(-1). The quality, much more than the quantity, of organic matter and nutrients seemed to be the major variables that controlled the spatiotemporal patterns showed by EEA. EEA patterns obtained in this study agree with several functional models of microbial communities, such as optimal resource allocation and nutrient co-limitation. This study probably represents the first one in which these functional models have been tested in subsurface systems. Results obtained in this study seem to suggest that microbial communities inhabiting groundwaters in Doñana are not dead or compromised cells. By contrast, these communities play relevant roles in carbon and nutrient cycling, continue with the decomposition process that begins in the sediments of the shallow lakes located in the area, provide remineralized carbon and nutrients to producers of these surface aquatic systems, and close energy and matter cycles. This study proposes that groundwater systems should be considered dynamic systems, comparable in functional complexity to surface systems.}, }
@article {pmid21480792, year = {2011}, author = {Schulze-Makuch, D and Haque, S and de Sousa Antonio, MR and Ali, D and Hosein, R and Song, YC and Yang, J and Zaikova, E and Beckles, DM and Guinan, E and Lehto, HJ and Hallam, SJ}, title = {Microbial life in a liquid asphalt desert.}, journal = {Astrobiology}, volume = {11}, number = {3}, pages = {241-258}, doi = {10.1089/ast.2010.0488}, pmid = {21480792}, issn = {1557-8070}, mesh = {Cluster Analysis ; *Ecosystem ; *Environmental Microbiology ; Genes, Archaeal ; Genes, Bacterial ; Genes, rRNA ; *Hydrocarbons/chemistry ; Molecular Sequence Data ; Trinidad and Tobago ; }, abstract = {Pitch Lake in Trinidad and Tobago is a natural asphalt reservoir nourished by pitch seepage, a form of petroleum that consists of mostly asphaltines, from the surrounding oil-rich region. During upward seepage, pitch mixes with mud and gases under high pressure, and the lighter portion evaporates or is volatilized, which produces a liquid asphalt residue characterized by low water activity, recalcitrant carbon substrates, and noxious chemical compounds. An active microbial community of archaea and bacteria, many of them novel strains (particularly from the new Tar ARC groups), totaling a biomass of up to 10(7) cells per gram, was found to inhabit the liquid hydrocarbon matrix of Pitch Lake. Geochemical and molecular taxonomic approaches revealed diverse, novel, and deeply branching microbial lineages with the potential to mediate anaerobic hydrocarbon degradation processes in different parts of the asphalt column. In addition, we found markers for archaeal methane metabolism and specific gene sequences affiliated with facultative and obligate anaerobic sulfur- and nitrite-oxidizing bacteria. The microbial diversity at Pitch Lake was found to be unique when compared to microbial communities analyzed at other hydrocarbon-rich environments, which included Rancho Le Brea, a natural asphalt environment in California, USA, and an oil well and a mud volcano in Trinidad and Tobago, among other sites. These results open a window into the microbial ecology and biogeochemistry of recalcitrant hydrocarbon matrices and establish the site as a terrestrial analogue for modeling the biotic potential of hydrocarbon lakes such as those found on Saturn's largest moon Titan.}, }
@article {pmid21475991, year = {2011}, author = {Kernaghan, G and Patriquin, G}, title = {Host associations between fungal root endophytes and boreal trees.}, journal = {Microbial ecology}, volume = {62}, number = {2}, pages = {460-473}, pmid = {21475991}, issn = {1432-184X}, mesh = {Abies/microbiology ; Ascomycota/classification/*genetics/growth &amp; development/isolation &amp; purification ; Betula/microbiology ; DNA, Ribosomal Spacer/genetics ; Endophytes/classification/genetics/*growth &amp; development/isolation &amp; purification ; Multivariate Analysis ; Mycorrhizae/growth &amp; development ; Nova Scotia ; Phylogeny ; Picea/microbiology ; Plant Roots/*microbiology ; Polymorphism, Restriction Fragment Length ; Quebec ; Sequence Analysis, DNA ; Trees/*microbiology ; }, abstract = {Fungal root endophytes colonize root tissue concomitantly with mycorrhizal fungi, but their identities and host preferences are largely unknown. We cultured fungal endophytes from surface-sterilized Cenococcum geophilum ectomycorrhizae of Betula papyrifera, Abies balsamea, and Picea glauca from two boreal sites in eastern Canada. Isolates were initially grouped on the basis of cultural morphology and then identified by internal transcribed spacer ribosomal DNA sequencing or by PCR restriction fragment length polymorphism. Phylogenetic analysis of the sequence data revealed 31 distinct phylotypes among the isolates, comprising mainly members of the ascomycete families Helotiaceae, Dermateaceae, Myxotrichaceae, and Hyaloscyphaceae, although other fungi were also isolated. Multivariate analyses indicate a clear separation among the endophyte communities colonizing each host tree species. Some phylotypes were evenly distributed across the roots of all three host species, some were found preferentially on particular hosts, and others were isolated from single hosts only. The results indicate that fungal root endophytes of boreal trees are not randomly distributed, but instead form relatively distinct assemblages on different host tree species.}, }
@article {pmid21472015, year = {2011}, author = {Yilmaz, P and Gilbert, JA and Knight, R and Amaral-Zettler, L and Karsch-Mizrachi, I and Cochrane, G and Nakamura, Y and Sansone, SA and Glöckner, FO and Field, D}, title = {The genomic standards consortium: bringing standards to life for microbial ecology.}, journal = {The ISME journal}, volume = {5}, number = {10}, pages = {1565-1567}, pmid = {21472015}, issn = {1751-7370}, support = {BB/E025080/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/I000771/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Ecology/methods/standards ; Genome ; Genomics/*standards ; High-Throughput Nucleotide Sequencing ; Microbiological Techniques ; Microbiology/standards ; }, }
@article {pmid21470255, year = {2011}, author = {Rousk, J and Bååth, E}, title = {Growth of saprotrophic fungi and bacteria in soil.}, journal = {FEMS microbiology ecology}, volume = {78}, number = {1}, pages = {17-30}, doi = {10.1111/j.1574-6941.2011.01106.x}, pmid = {21470255}, issn = {1574-6941}, mesh = {Acetates/analysis/metabolism ; Bacteria/*growth &amp; development/metabolism ; Biomass ; Desiccation ; Ecosystem ; Ergosterol/analysis/metabolism ; Fungi/*growth &amp; development/metabolism ; Leucine/analysis/metabolism ; Soil/chemistry ; *Soil Microbiology ; Thymidine/analysis/metabolism ; }, abstract = {Bacterial and fungal growth rate measurements are sensitive variables to detect changes in environmental conditions. However, while considerable progress has been made in methods to assess the species composition and biomass of fungi and bacteria, information about growth rates remains surprisingly rudimentary. We review the recent history of approaches to assess bacterial and fungal growth rates, leading up to current methods, especially focusing on leucine/thymidine incorporation to estimate bacterial growth and acetate incorporation into ergosterol to estimate fungal growth. We present the underlying assumptions for these methods, compare estimates of turnover times for fungi and bacteria based on them, and discuss issues, including for example elusive conversion factors. We review what the application of fungal and bacterial growth rate methods has revealed regarding the influence of the environmental factors of temperature, moisture (including drying/rewetting), pH, as well as the influence of substrate additions, the presence of plants and toxins. We highlight experiments exploring the competitive and facilitative interaction between bacteria and fungi enabled using growth rate methods. Finally, we predict that growth methods will be an important complement to molecular approaches to elucidate fungal and bacterial ecology, and we identify methodological concerns and how they should be addressed.}, }
@article {pmid21468709, year = {2011}, author = {Sintubin, L and De Gusseme, B and Van der Meeren, P and Pycke, BF and Verstraete, W and Boon, N}, title = {The antibacterial activity of biogenic silver and its mode of action.}, journal = {Applied microbiology and biotechnology}, volume = {91}, number = {1}, pages = {153-162}, doi = {10.1007/s00253-011-3225-3}, pmid = {21468709}, issn = {1432-0614}, mesh = {Anti-Bacterial Agents/*metabolism/*pharmacology ; Bacteria/drug effects ; Limosilactobacillus fermentum/*metabolism ; Nanoparticles/chemistry ; Silver/*metabolism/*pharmacology ; }, abstract = {In a previous study, biogenic silver nanoparticles were produced by Lactobacillus fermentum which served as a matrix preventing aggregation. In this study the antibacterial activity of this biogenic silver was compared to ionic silver and chemically produced nanosilver. The minimal inhibitory concentration (MIC) was tested on Gram-positive and Gram-negative bacteria and was comparable for biogenic silver and ionic silver ranging from 12.5 to 50 mg/L. In contrast, chemically produced nanosilver had a much higher MIC of at least 500 mg/L, due to aggregation upon application. The minimal bactericidal concentration (MBC) in drinking water varied from 0.1 to 0.5 mg/L for biogenic silver and ionic silver, but for chemically produced nanosilver concentrations, up to 12.5 mg/L was needed. The presence of salts and organic matter decreased the antimicrobial activity of all types of silver resulting in a higher MBC and a slower inactivation of the bacteria. The mode of action of biogenic silver was mainly attributed to the release of silver ions due to the high concentration of free silver ions measured and the resemblance in performance between biogenic silver and ionic silver. Radical formation by biogenic silver and direct contact were found to contribute little to the antibacterial activity. In conclusion, biogenic nanosilver exhibited equal antimicrobial activity compared to ionic silver and can be a valuable alternative for chemically produced nanosilver.}, }
@article {pmid21468661, year = {2011}, author = {Roe, AD and James, PM and Rice, AV and Cooke, JE and Sperling, FA}, title = {Spatial community structure of mountain pine beetle fungal symbionts across a latitudinal gradient.}, journal = {Microbial ecology}, volume = {62}, number = {2}, pages = {347-360}, pmid = {21468661}, issn = {1432-184X}, mesh = {Alberta ; Altitude ; Animals ; *Biota ; British Columbia ; Coleoptera/*microbiology ; Multilocus Sequence Typing ; Mycological Typing Techniques ; Ophiostomatales/classification/genetics/*growth &amp; development ; Pinus/parasitology ; Principal Component Analysis ; Regression Analysis ; *Symbiosis ; }, abstract = {Symbiont redundancy in obligate insect-fungal systems is thought to buffer the insect host against symbiont loss and to extend the environmental conditions under which the insect can persist. The mountain pine beetle is associated with at least three well-known and putatively obligate ophiostomatoid fungal symbionts that vary in their environmental tolerances. To better understand the spatial variation in beetle-fungal symbiotic associations, we examined the community composition of ophiostomatoid fungi associated with the mountain pine beetle as a function of latitude and elevation. The region investigated represents the leading edge of a recent outbreak of mountain pine beetle in western Canada. Using regression and principal components analysis, we identified significant spatial patterns in fungal species abundances that indicate symmetrical replacement between two of the three fungi along a latitudinal gradient and little variation in response to elevation. We also identified significant variation in the prevalence of pair-wise species combinations that occur within beetle galleries. Frequencies of pair-wise combinations were significantly different from what was expected given overall species abundances. These results suggest that complex processes of competitive exclusion and coexistence help determine fungal community composition and that the consequences of these processes vary spatially. The presence of three fungal symbionts in different proportions and combinations across a wide range of environmental conditions may help explain the success of mountain pine beetle attacks across a broad geographic range.}, }
@article {pmid21465304, year = {2011}, author = {De Clippeleir, H and Yan, X and Verstraete, W and Vlaeminck, SE}, title = {OLAND is feasible to treat sewage-like nitrogen concentrations at low hydraulic residence times.}, journal = {Applied microbiology and biotechnology}, volume = {90}, number = {4}, pages = {1537-1545}, doi = {10.1007/s00253-011-3222-6}, pmid = {21465304}, issn = {1432-0614}, mesh = {Bacteria/*metabolism ; Denitrification ; Nitrification ; Nitrogen/*metabolism ; Oxygen/*metabolism ; Quaternary Ammonium Compounds/metabolism ; Sewage/chemistry/*microbiology ; Waste Disposal, Fluid/*methods ; Water Purification/*methods ; }, abstract = {Energy-positive sewage treatment can, in principle, be obtained by maximizing energy recovery from concentrated organics and by minimizing energy consumption for concentration and residual nitrogen removal in the main stream. To test the feasibility of the latter, sewage-like nitrogen influent concentrations were treated with oxygen-limited autotrophic nitrification/denitrification (OLAND) in a lab-scale rotating biological contactor at 25°C. At influent ammonium concentrations of 66 and 29 mg N L(-1) and a volumetric loading rate of 840 mg N L(-1) day(-1) yielding hydraulic residence times (HRT) of 2.0 and 1.0 h, respectively, relatively high nitrogen removal rates of 444 and 383 mg N L(-1) day(-1) were obtained, respectively. At low nitrogen levels, adapted nitritation and anammox communities were established. The decrease in nitrogen removal was due to decreased anammox and increased nitratation, with Nitrospira representing 6% of the biofilm. The latter likely occurred given the absence of dissolved oxygen (DO) control, since decreasing the DO concentration from 1.4 to 1.2 mg O(2) L(-1) decreased nitratation by 35% and increased anammox by 32%. Provided a sufficient suppression of nitratation, this study showed the feasibility of OLAND to treat low nitrogen levels at low HRT, a prerequisite to energy-positive sewage treatment.}, }
@article {pmid21451564, year = {2011}, author = {van Ooij, C}, title = {Microbial ecology: Strong fences make good neighbours.}, journal = {Nature reviews. Microbiology}, volume = {9}, number = {3}, pages = {150}, pmid = {21451564}, issn = {1740-1534}, }
@article {pmid21450087, year = {2011}, author = {Cruz-García, C and Murray, AE and Rodrigues, JL and Gralnick, JA and McCue, LA and Romine, MF and Löffler, FE and Tiedje, JM}, title = {Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1.}, journal = {BMC microbiology}, volume = {11}, number = {}, pages = {64}, pmid = {21450087}, issn = {1471-2180}, mesh = {Anaerobiosis ; Bacterial Proteins/genetics/*metabolism ; *Energy Metabolism ; Gene Deletion ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Metabolic Networks and Pathways/*genetics ; Nitrates/metabolism ; Sequence Analysis, DNA ; Shewanella/genetics/growth &amp; development/metabolism/*physiology ; Transcription Factors/genetics/*metabolism ; }, abstract = {BACKGROUND: EtrA in Shewanella oneidensis MR-1, a model organism for study of adaptation to varied redox niches, shares 73.6% and 50.8% amino acid sequence identity with the oxygen-sensing regulators Fnr in E. coli and Anr in Pseudomonas aeruginosa, respectively; however, its regulatory role of anaerobic metabolism in Shewanella spp. is complex and not well understood.<br><br>RESULTS: The expression of the nap genes, nrfA, cymA and hcp was significantly reduced in etrA deletion mutant EtrA7-1; however, limited anaerobic growth and nitrate reduction occurred, suggesting that multiple regulators control nitrate reduction in this strain. Dimethyl sulfoxide (DMSO) and fumarate reductase gene expression was down-regulated at least 2-fold in the mutant, which, showed lower or no reduction of these electron acceptors when compared to the wild type, suggesting both respiratory pathways are under EtrA control. Transcript analysis further suggested a role of EtrA in prophage activation and down-regulation of genes implicated in aerobic metabolism.<br><br>CONCLUSION: In contrast to previous studies that attributed a minor regulatory role to EtrA in Shewanella spp., this study demonstrates that EtrA acts as a global transcriptional regulator and, in conjunction with other regulators, fine-tunes the expression of genes involved in anaerobic metabolism in S. oneidensis strain MR-1. Transcriptomic and sequence analyses of the genes differentially expressed showed that those mostly affected by the mutation belonged to the "Energy metabolism" category, while stress-related genes were indirectly regulated in the mutant possibly as a result of a secondary perturbation (e.g. oxidative stress, starvation). We also conclude based on sequence, physiological and expression analyses that this regulator is more appropriately termed Fnr and recommend this descriptor be used in future publications.}, }
@article {pmid21448673, year = {2011}, author = {Postma, J and Schilder, MT and van Hoof, RA}, title = {Indigenous populations of three closely related Lysobacter spp. in agricultural soils using real-time PCR.}, journal = {Microbial ecology}, volume = {62}, number = {4}, pages = {948-958}, pmid = {21448673}, issn = {1432-184X}, mesh = {Agriculture/methods ; Base Sequence ; DNA Primers/*genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; Lysobacter/classification/genetics/*growth &amp; development/isolation &amp; purification ; Molecular Sequence Data ; Netherlands ; Real-Time Polymerase Chain Reaction ; Soil/analysis ; *Soil Microbiology ; Species Specificity ; }, abstract = {Previous research had shown that three closely related species of Lysobacter, i.e., Lysobacter antibioticus, Lysobacter capsici, and Lysobacter gummosus, were present in different Rhizoctonia-suppressive soils. However, the population dynamics of these three Lysobacter spp. in different habitats remains unknown. Therefore, a specific primer-probe combination was designed for the combined quantification of these three Lysobacter spp. using TaqMan. Strains of the three target species were efficiently detected with TaqMan, whereas related non-target strains of Lysobacter enzymogenes and Xanthomonas campestris were not or only weakly amplified. Indigenous Lysobacter populations were analyzed in soils of 10 organic farms in the Netherlands during three subsequent years with TaqMan. These soils differed in soil characteristics and crop rotation. Additionally, Lysobacter populations in rhizosphere and bulk soil of different crops on one of these farms were studied. In acid sandy soils low Lysobacter populations were present, whereas pH neutral clay soils contained high populations (respectively, <4.0-5.87 and 6.22-6.95 log gene copy numbers g(-1) soil). Clay content, pH and C/N ratio, but not organic matter content in soil, correlated with higher Lysobacter populations. Unexpectedly, different crops did not significantly influence population size of the three Lysobacter spp. and their populations were barely higher in rhizosphere than in bulk soil.}, }
@article {pmid21447011, year = {2011}, author = {Abram, F and Enright, AM and O'Reilly, J and Botting, CH and Collins, G and O'Flaherty, V}, title = {A metaproteomic approach gives functional insights into anaerobic digestion.}, journal = {Journal of applied microbiology}, volume = {110}, number = {6}, pages = {1550-1560}, doi = {10.1111/j.1365-2672.2011.05011.x}, pmid = {21447011}, issn = {1365-2672}, mesh = {Anaerobiosis ; Archaea/classification/genetics/*metabolism ; Archaeal Proteins/genetics/metabolism ; Bacteria/classification/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Bioreactors/*microbiology ; Chromatography, Liquid ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Two-Dimensional ; Phylogeny ; Proteome/*analysis ; Proteomics/*methods ; RNA, Ribosomal, 16S/genetics ; Tandem Mass Spectrometry ; Temperature ; Waste Disposal, Fluid ; }, abstract = {AIMS: The objective of this work was to provide functional evidence of key metabolic pathways important for anaerobic digestion processes through the identification of highly expressed proteins in a mixed anaerobic microbial consortium.<br><br>METHODS AND RESULTS: The microbial communities from an anaerobic industrial-like wastewater treatment bioreactor were characterized using phylogenetic analyses and metaproteomics. Clone libraries indicated that the bacterial community in the bioreactor was diverse while the archaeal population was mainly composed of Methanocorpusculum-like (76%) micro-organisms. Three hundred and eighty-eight reproducible protein spots were obtained on 2-D gels, of which 70 were excised and 33 were identified. The putative functions of the proteins detected in the anaerobic bioreactor were related to cellular processes, including methanogenesis from CO(2) and acetate, glycolysis and the pentose phosphate pathway. Metaproteomics also indicated, by protein assignment, the presence of specific micro-organisms in the bioreactor. However, only a limited overlap was observed between the phylogenetic and metaproteomic analyses.<br><br>CONCLUSIONS: This study provides some direct evidence of the microbial activities taking place during anaerobic digestion.<br><br>This study demonstrates metaproteomics as a useful tool to uncover key biochemical pathways underpinning specific anaerobic bioprocesses.}, }
@article {pmid21443910, year = {2011}, author = {Grootaert, C and Boon, N and Zeka, F and Vanhoecke, B and Bracke, M and Verstraete, W and Van de Wiele, T}, title = {Adherence and viability of intestinal bacteria to differentiated Caco-2 cells quantified by flow cytometry.}, journal = {Journal of microbiological methods}, volume = {86}, number = {1}, pages = {33-41}, doi = {10.1016/j.mimet.2011.03.011}, pmid = {21443910}, issn = {1872-8359}, mesh = {Bacteria/*cytology/growth &amp; development ; *Bacterial Adhesion ; Caco-2 Cells ; Flow Cytometry/*methods ; Humans ; Intestines/*microbiology ; *Microbial Viability ; Models, Biological ; }, abstract = {Recent developments in host-microbe research give rise to a growing demand for rapid and accurate methods to quantify bacterial adhesion to epithelial cells. Here, we describe a new flow cytometric method to determine the amount and viability of gut bacteria, adhered to a monolayer of differentiated cells. The latter is a more relevant epithelium model than the suspended eukaryotic cells currently used in flow cytometric protocols. During the development of the method, we monitored the adhesion potential of six bacterial species and an intestinal microbial community to Caco-2 cells. The combination of SYBR Green I/propidium iodide was more efficient than carboxyfluorescein diacetate to stain the bacterial cells. In addition, a better separation between the Caco-2 background signal and viable and dead bacteria was obtained. A precise amount of Triton X-100 was used to detach adhered bacteria from Caco-2 cells and cell debris. Yet, a limited decrease in viability was observed for the intestinal microbial community treated with Triton X-100. The flow cytometric lower detection limit for pure bacterial cultures was 3.0-4.0log/mL, whereas a 5.0-5.5log/mL detection limit was obtained in the presence of Caco-2 cell background. The latter was sufficient to quantify adhered bacteria. To the best of our knowledge, this is the first description of a flow cytometric protocol that quantifies adhesion of both pure and mixed gut microbial cultures to a differentiated monolayer of Caco-2 cells and that allows to distinguish between viable and dead adhered bacteria.}, }
@article {pmid21442252, year = {2011}, author = {Yu, J and Steinberger, Y}, title = {Vertical distribution of microbial community functionality under the canopies of Zygophyllum dumosum and Hammada scoparia in the Negev Desert, Israel.}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {218-227}, pmid = {21442252}, issn = {1432-184X}, mesh = {Amaranthaceae/*microbiology ; Bacteria/growth &amp; development/isolation &amp; purification/*metabolism ; Biomass ; Carbon/metabolism ; Desert Climate ; *Ecosystem ; Israel ; Plant Roots/microbiology ; Soil/*analysis ; *Soil Microbiology ; Zygophyllum/*microbiology ; }, abstract = {Patchy desert shrubs magnify the horizontal heterogeneities of carbon source and nutrient availability in an arid ecosystem, significantly affecting the abundance and activity of the soil microbial community. Since each shrub species develops special ecophysiological adaptations to the extreme harsh desert environments, previous studies elucidated that the effects of perennial shrubs on microbial diversity are unequal. The aim of the present study, conducted in the Negev Desert, Israel, was to illustrate the vertical changes of soil microbial community functionality in the root zone of perennial shrubs. Soil samples were collected from the 0-50 cm depth at 10-cm intervals under the canopy of Zygophyllum dumosum, Hammada scoparia, and from the open spaces between them, in the wet and dry seasons. Soil moisture and organic matter exhibited a significant (P<0.001) plant and depth dependence. The mean basal respiration rates and microbial biomass in soils collected beneath perennial shrubs were relatively higher than the control during the wet season, however, a contrasting trend was observed at some soil depths during the dry season. Relatively high abundance and activity of aromatic and carboxylic acid utilizers were observed in the vicinity of perennial shrubs, and the values recorded during the dry season were generally higher than the corresponding values during the wet season. In addition, a "mirror effect" in vertical changes of the community-level physiological profile was observed between Z. dumosum and H. scoparia. This study demonstrated the stratification of the functional aspects in soils under the canopy of perennial shrubs, thus indicating that the scattered distribution of vegetation not only causes horizontal heterogeneities of the microbial community in an arid system, but also that the ecophysiological adaptations developed by xerophytes regulate the abundance and saprotrophic functionality of microorganisms in the root zone.}, }
@article {pmid21440283, year = {2011}, author = {van der Ha, D and Bundervoet, B and Verstraete, W and Boon, N}, title = {A sustainable, carbon neutral methane oxidation by a partnership of methane oxidizing communities and microalgae.}, journal = {Water research}, volume = {45}, number = {9}, pages = {2845-2854}, doi = {10.1016/j.watres.2011.03.005}, pmid = {21440283}, issn = {1879-2448}, mesh = {Air Pollutants/analysis/*metabolism ; Bacteria/growth &amp; development/*metabolism ; Biological Oxygen Demand Analysis ; Carbon/metabolism ; Carbon Footprint ; Conservation of Natural Resources ; Methane/analysis/*metabolism ; Microalgae/growth &amp; development/*metabolism ; Oxidation-Reduction ; Oxygen/metabolism ; Waste Disposal, Fluid/*methods ; }, abstract = {Effluents of anaerobic wastewater treatment plants are saturated with methane, an effective greenhouse gas. We propose a novel approach to treat such effluents using a coculture of methane oxidizing communities and microalgae, further indicated as methalgae, which would allow microbial methane oxidation with minimal CO(2) emissions. Coculturing a methane oxidizing community with microalgae in sequence batch reactors under continuous lightning yielded a factor of about 1.6 more biomass relative to the control without microalgae. Moreover, 55% less external oxygen supply was needed to maintain the methane oxidation, as oxygen was produced in situ by the microalgae. An overall methane oxidation rate of 171±27 mg CH(4) L(-1) liquid phase d(-1) was accomplished in a semi-batch setup, while the excess CO(2) production was lower than 1mg CO(2) L(-1) d(-1). Both nitrate and ammonium were feasible nitrogen sources for the methalgae. These results show that a coculture of microalgae and methane oxidizing communities can be used to oxidize dissolved methane under O(2)-limiting conditions, which could lead to a novel treatment for dissolved methane in anaerobic effluents.}, }
@article {pmid21440280, year = {2011}, author = {Desloover, J and De Clippeleir, H and Boeckx, P and Du Laing, G and Colsen, J and Verstraete, W and Vlaeminck, SE}, title = {Floc-based sequential partial nitritation and anammox at full scale with contrasting N2O emissions.}, journal = {Water research}, volume = {45}, number = {9}, pages = {2811-2821}, doi = {10.1016/j.watres.2011.02.028}, pmid = {21440280}, issn = {1879-2448}, mesh = {Air Pollutants/*analysis/chemistry/metabolism ; Ammonia/analysis/metabolism ; Biodegradation, Environmental ; Bioreactors/microbiology ; Flocculation ; *Nitrogen Cycle ; Nitrogen Dioxide/*analysis/chemistry/metabolism ; Oxidation-Reduction ; Waste Disposal, Fluid/*methods ; }, abstract = {New Activated Sludge (NAS(®)) is a hybrid, floc-based nitrogen removal process without carbon addition, based on the control of sludge retention times (SRT) and dissolved oxygen (DO) levels. The aim of this study was to examine the performance of a retrofitted four-stage NAS(®) plant, including on-line measurements of greenhouse gas emissions (N(2)O and CH(4)). The plant treated anaerobically digested industrial wastewater, containing 264 mg N L(-1), 1154 mg chemical oxygen demand (COD) L(-1) and an inorganic carbon alkalinity of 34 meq L(-1). The batch-fed partial nitritation step received an overall nitrogen loading rate of 0.18-0.22 kg N m(-3) d(-1), thereby oxidized nitrogen to nitrite (45-47%) and some nitrate (13-15%), but also to N(2)O (5.1-6.6%). This was achieved at a SRT of 1.7 d and DO around 1.0 mg O(2) L(-1). Subsequently, anammox, denitrification and nitrification compartments were followed by a final settler, at an overall SRT of 46 d. None of the latter three reactors emitted N(2)O. In the anammox step, 0.26 kg N m(-3) d(-1) was removed, with an estimated contribution of 71% by the genus Kuenenia, which constituted 3.1% of the biomass. Overall, a nitrogen removal efficiency of 95% was obtained, yielding a dischargeable effluent. Retrofitting floc-based nitrification/denitrification with carbon addition to NAS(®) allowed to save 40% of the operational wastewater treatment costs. Yet, a decrease of the N(2)O emissions by about 50% is necessary in order to obtain a CO(2) neutral footprint. The impact of emitted CH(4) was 20 times lower.}, }
@article {pmid21436882, year = {2011}, author = {Allen, LZ and Ishoey, T and Novotny, MA and McLean, JS and Lasken, RS and Williamson, SJ}, title = {Single virus genomics: a new tool for virus discovery.}, journal = {PloS one}, volume = {6}, number = {3}, pages = {e17722}, pmid = {21436882}, issn = {1932-6203}, mesh = {Bacteriophage T4/*genetics/*isolation &amp; purification ; Bacteriophage lambda/*genetics/*isolation &amp; purification ; Flow Cytometry ; Genetic Loci/genetics ; Genome, Viral/genetics ; Genomics/*methods ; Microscopy, Confocal ; Polymerase Chain Reaction ; Reference Standards ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {Whole genome amplification and sequencing of single microbial cells has significantly influenced genomics and microbial ecology by facilitating direct recovery of reference genome data. However, viral genomics continues to suffer due to difficulties related to the isolation and characterization of uncultivated viruses. We report here on a new approach called 'Single Virus Genomics', which enabled the isolation and complete genome sequencing of the first single virus particle. A mixed assemblage comprised of two known viruses; E. coli bacteriophages lambda and T4, were sorted using flow cytometric methods and subsequently immobilized in an agarose matrix. Genome amplification was then achieved in situ via multiple displacement amplification (MDA). The complete lambda phage genome was recovered with an average depth of coverage of approximately 437X. The isolation and genome sequencing of uncultivated viruses using Single Virus Genomics approaches will enable researchers to address questions about viral diversity, evolution, adaptation and ecology that were previously unattainable.}, }
@article {pmid21431934, year = {2011}, author = {Badin, AL and Monier, A and Volatier, L and Geremia, RA and Delolme, C and Bedell, JP}, title = {Structural stability, microbial biomass and community composition of sediments affected by the hydric dynamics of an urban stormwater infiltration basin. Dynamics of physical and microbial characteristics of stormwater sediment.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {885-897}, pmid = {21431934}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biomass ; Environmental Monitoring ; Fungi/classification/genetics/*isolation &amp; purification ; Geologic Sediments/*chemistry/*microbiology ; Rain/chemistry ; Urban Renewal ; *Water Microbiology ; }, abstract = {The sedimentary layer deposited at the surface of stormwater infiltration basins is highly organic and multicontaminated. It undergoes considerable moisture content fluctuations due to the drying and inundation cycles (called hydric dynamics) of these basins. Little is known about the microflora of the sediments and its dynamics; hence, the purpose of this study is to describe the physicochemical and biological characteristics of the sediments at different hydric statuses of the infiltration basin. Sediments were sampled at five time points following rain events and dry periods. They were characterized by physical (aggregation), chemical (nutrients and heavy metals), and biological (total, bacterial and fungal biomasses, and genotypic fingerprints of total bacterial and fungal communities) parameters. Data were processed using statistical analyses which indicated that heavy metal (1,841 μg/g dry weight (DW)) and organic matter (11%) remained stable through time. By contrast, aggregation, nutrient content (NH4[+], 53-717 μg/g DW), pH (6.9-7.4), and biological parameters were shown to vary with sediment water content and sediment biomass, and were higher consecutive to stormwater flows into the basin (up to 7 mg C/g DW) than during dry periods (0.6 mg C/g DW). Coinertia analysis revealed that the structure of the bacterial communities is driven by the hydric dynamics of the infiltration basin, although no such trend was found for fungal communities. Hydric dynamics more than rain events appear to be more relevant for explaining variations of aggregation, microbial biomass, and shift in the microbial community composition. We concluded that the hydric dynamics of stormwater infiltration basins greatly affects the structural stability of the sedimentary layer, the biomass of the microbial community living in it and its dynamics. The decrease in aggregation consecutive to rewetting probably enhances access to organic matter (OM), explaining the consecutive release of NH4[+], the bloom of the microbial biomass, and the change in structure of the bacterial community. These results open new perspectives for basin management since the risk of OM and pollutant transfer to the aquifer is greatly affected by alternating dry and flood periods.}, }
@article {pmid21431933, year = {2011}, author = {Koopman, MM and Carstens, BC}, title = {The microbial Phyllogeography of the carnivorous plant Sarracenia alata.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {750-758}, pmid = {21431933}, issn = {1432-184X}, mesh = {Bacteria/*classification/*genetics/isolation &amp; purification ; Biodiversity ; Ecosystem ; Louisiana ; Molecular Sequence Data ; Phylogeography ; Sarraceniaceae/classification/genetics/*microbiology ; }, abstract = {Carnivorous pitcher plants host diverse microbial communities. This plant-microbe association provides a unique opportunity to investigate the evolutionary processes that influence the spatial diversity of microbial communities. Using next-generation sequencing of environmental samples, we surveyed microbial communities from 29 pitcher plants (Sarracenia alata) and compare community composition with plant genetic diversity in order to explore the influence of historical processes on the population structure of each lineage. Analyses reveal that there is a core S. alata microbiome, and that it is similar in composition to animal gut microfaunas. The spatial structure of community composition in S. alata (phyllogeography) is congruent at the deepest level with the dominant features of the landscape, including the Mississippi river and the discrete habitat boundaries that the plants occupy. Intriguingly, the microbial community structure reflects the phylogeographic structure of the host plant, suggesting that the phylogenetic structure of bacterial communities and population genetic structure of their host plant are influenced by similar historical processes.}, }
@article {pmid21431767, year = {2011}, author = {Sun, Y and Wolcott, RD and Dowd, SE}, title = {Tag-encoded FLX amplicon pyrosequencing for the elucidation of microbial and functional gene diversity in any environment.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {733}, number = {}, pages = {129-141}, doi = {10.1007/978-1-61779-089-8_9}, pmid = {21431767}, issn = {1940-6029}, mesh = {Animals ; Bacteria/*genetics/isolation &amp; purification ; Biodiversity ; DNA Primers/genetics ; DNA, Bacterial/*genetics/isolation &amp; purification ; DNA, Ribosomal/genetics/isolation &amp; purification ; *Genetic Variation ; Metagenome/genetics ; Microspheres ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; }, abstract = {Comprehensive evaluation of microbial diversity in almost any environment is now possible. Questions such as "Does the addition of fiber to the diet of humans change the gastrointestinal microbiota?" can now be answered easily and inexpensively. Tag-encoded FLX-amplicon pyrosequencing (TEFAP) has been utilized to evaluate bacterial, archaeal, fungal, algal, as well as functional genes. Using the new tag-encoded FLX amplicon pyrosequencing (bTEFAP) approach, we have evaluated the microbial diversity using a more cost-effective and largely reproducible method that would allow us to sequence the ribosomal RNA genes of microorganisms (hereafter focused on bacteria), without the need for the inherent bias of culture methods. These developments have ushered in a new age of microbial ecology studies, and we have utilized this technology to evaluate the microbiome in a wide range of systems in almost any conceivable environment.}, }
@article {pmid21431766, year = {2011}, author = {Zhang, H and Parameswaran, P and Badalamenti, J and Rittmann, BE and Krajmalnik-Brown, R}, title = {Integrating high-throughput pyrosequencing and quantitative real-time PCR to analyze complex microbial communities.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {733}, number = {}, pages = {107-128}, doi = {10.1007/978-1-61779-089-8_8}, pmid = {21431766}, issn = {1940-6029}, mesh = {Bacteria/*genetics ; DNA, Archaeal/genetics/isolation &amp; purification ; DNA, Bacterial/genetics/isolation &amp; purification ; Electrolysis ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Methanomicrobiaceae/*genetics ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; Sewage/microbiology ; *Systems Integration ; Time Factors ; }, abstract = {New high-throughput technologies continue to emerge for studying complex microbial communities. In particular, massively parallel pyrosequencing enables very high numbers of sequences, providing a more complete view of community structures and a more accurate inference of the functions than has been possible just a few years ago. In parallel, quantitative real-time PCR (QPCR) allows quantitative monitoring of specific community members over time, space, or different environmental conditions. In this review, we discuss the principles of these two methods and their complementary applications in studying microbial ecology in bioenvironmental systems. We explain parallel sequencing of amplicon libraries and using bar codes to differentiate multiple samples in a pyrosequencing run. We also describe best procedures and chemistries for QPCR amplifications and address advantages of applying automation to increase accuracy. We provide three examples in which we used pyrosequencing and QPCR together to define and quantify members of microbial communities: in the human large intestine, in a methanogenic digester whose sludge was made more bioavailable by a high-voltage pretreatment, and on the biofilm anode of a microbial electrolytic cell. We highlight our key findings in these systems and how both methods were used in concert to achieve those findings. Finally, we supply detailed methods for generating PCR amplicon libraries for pyrosequencing, pyrosequencing data analysis, QPCR methodology, instrumentation, and automation.}, }
@article {pmid21429065, year = {2011}, author = {Yang, L and Jelsbak, L and Molin, S}, title = {Microbial ecology and adaptation in cystic fibrosis airways.}, journal = {Environmental microbiology}, volume = {13}, number = {7}, pages = {1682-1689}, doi = {10.1111/j.1462-2920.2011.02459.x}, pmid = {21429065}, issn = {1462-2920}, mesh = {*Adaptation, Physiological ; Cystic Fibrosis/complications/immunology/*microbiology ; Drug Resistance, Bacterial ; Humans ; Microbial Interactions ; Mutation ; Opportunistic Infections/complications/immunology/microbiology ; Pseudomonas Infections/complications/immunology/*microbiology ; Pseudomonas aeruginosa/drug effects/genetics/*physiology ; Respiratory Tract Infections/complications/immunology/*microbiology ; }, abstract = {Chronic infections in the respiratory tracts of cystic fibrosis (CF) patients are important to investigate, both from medical and from fundamental ecological points of view. Cystic fibrosis respiratory tracts can be described as natural environments harbouring persisting microbial communities with Pseudomonas aeruginosa as a dominant pathogen. Various factors contribute to the complexity of this ecosystem, including community composition, dynamics and interactions, as well as heterogeneous distribution and fluctuation of components of the immune system, antibiotics and nutrients. All these elements constitute the selective forces that drive the evolution of the microbes after they migrate from the outer environment to human airways. Pseudomonas aeruginosa adapts to the new environment through genetic changes and exhibits a special lifestyle in chronic CF airways. Understanding the persistent colonization of microbial pathogens in CF patients in the context of ecology and evolution will expand our knowledge of the pathogenesis of chronic infections and improve therapeutic strategies.}, }
@article {pmid21426365, year = {2011}, author = {Caliz, J and Vila, X and Martí, E and Sierra, J and Cruañas, R and Garau, MA and Montserrat, G}, title = {Impact of chlorophenols on microbiota of an unpolluted acidic soil: microbial resistance and biodegradation.}, journal = {FEMS microbiology ecology}, volume = {78}, number = {1}, pages = {150-164}, doi = {10.1111/j.1574-6941.2011.01093.x}, pmid = {21426365}, issn = {1574-6941}, mesh = {Bacteria/genetics/growth &amp; development/metabolism ; Base Sequence ; Biodegradation, Environmental ; Chlorophenols/metabolism/*toxicity ; Fungi/physiology ; Metagenome/physiology ; Molecular Sequence Data ; Pentachlorophenol/metabolism/toxicity ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; Soil Pollutants/metabolism/*toxicity ; Trees/microbiology ; }, abstract = {The impact of 2-monochlorophenol (MCP), 2,4,6-trichlorophenol (TCP) and pentachlorophenol (PCP) on the microbial community of an acidic forest soil was studied under controlled laboratory conditions by spiking microcosms with the pollutants at concentrations ranging from 0.1 to 5000 mg kg(-1). A decrease in the cumulative respirometric values and changes in the bacterial and fungal community composition were detected at 1000 mg MCP kg(-1), 100 mg TCP kg(-1) and 100 and 1000 mg PCP kg(-1). However, drastic effects on the microbial community were revealed only at higher concentrations of MCP and TCP, although the toxicity of PCP was expected to be stronger. The acidic condition of the soil presumably reduces bioavailability of PCP, leading to less pronounced effects than the other pollutants. This finding highlights the consideration of pollutant bioavailability in each environment to adequately assess contamination effects. Twenty-two different chlorophenol-resistant and potentially degrading microorganisms were isolated from highly polluted microcosms. The most resistant isolates were related to Burkholderia arboris, Bacillus circulans, Paenibacillus taichungensis, Luteibacter rhizovicina and Janibacter melonis. These isolates also showed the capacity to reduce the concentration of TCP or PCP between 15% and 35% after 5 days of incubation (initial concentration of 50 mg L(-1)). The isolate related to B. circulans is an atypical case of a member of the Firmicutes group for which chlorophenol-degrading capacities have been described.}, }
@article {pmid21426364, year = {2011}, author = {Hardoim, PR and Andreote, FD and Reinhold-Hurek, B and Sessitsch, A and van Overbeek, LS and van Elsas, JD}, title = {Rice root-associated bacteria: insights into community structures across 10 cultivars.}, journal = {FEMS microbiology ecology}, volume = {77}, number = {1}, pages = {154-164}, pmid = {21426364}, issn = {1574-6941}, support = {P 21261/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/classification/*genetics ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Genotype ; Oryza/genetics/*microbiology ; Plant Roots/genetics/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Soil/analysis ; *Soil Microbiology ; }, abstract = {In this study, the effects of plant genotype, soil type and nutrient use efficiency on the composition of different bacterial communities associated with rice roots were investigated. Thus, total bacteria, Alpha- and Betaproteobacteria, Pseudomonas and Actinobacteria were studied using PCR, followed by denaturing gradient gel electrophoresis (PCR-DGGE). Rice genotype determined, to a large extent, the composition of the different bacterial communities across cultivars. Several cultivars belonging to Oryza sativa ssp. indica tended to select similar bacterial communities, whereas those belonging to subspecies japonica and aromatica selected ones with divergent community structures. An effect of soil type was pronounced for the Actinobacteria communities, while a small effect of 'improved' and 'traditional' plants was noted for all communities analyzed. A few dominant bands in PCR-DGGE, affiliated with Rhizobium radiobacter, Dickeya zeae, Mycobacterium bolletii and with members of the Rhizobiales, Rhodospirillaceae and Paenibacillaceae, were spread across cultivars. In contrast, a majority of bands (e.g. affiliated with Enterobacter cloacae or Burkholderia kururiensis) was only present in particular cultivars or was erratically distributed among rice replicates. These findings suggested that both bacterial adaptation and plant genotype contribute to the shaping of the dynamic bacterial communities associated with roots of rice plants.}, }
@article {pmid21424823, year = {2011}, author = {Aranda, S and Montes-Borrego, M and Landa, BB}, title = {Purple-pigmented violacein-producing Duganella spp. inhabit the rhizosphere of wild and cultivated olives in southern Spain.}, journal = {Microbial ecology}, volume = {62}, number = {2}, pages = {446-459}, pmid = {21424823}, issn = {1432-184X}, mesh = {Anti-Infective Agents/chemistry ; Bacterial Typing Techniques ; Cluster Analysis ; Color ; DNA Gyrase/genetics ; Genes, Bacterial ; Genes, rRNA ; Indoles/*metabolism ; Olea/*microbiology ; Oxalobacteraceae/genetics/growth &amp; development/*isolation &amp; purification/metabolism ; Phylogeny ; Pigments, Biological/*metabolism ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Spain ; }, abstract = {Bacteria have evolved mechanisms that allow them to grow and survive in highly competitive environments like soil and the rhizosphere. Using classical microbiological, physiological, and genetic analyses, we isolated and identified for the first time Duganella spp. associated with the rhizosphere of woody plants in Mediterranean environments that are able to produce violacein, a blue-purple secondary metabolite of considerable biotechnological interest. Based on physiological and biochemical characterization and phylogenetic analysis of different genes including 16S rRNA, gyrB, and vioA (implicated in the synthesis of violacein), the seven Duganella spp. strains isolated and studied were differentiated according to their host of origin (wild versus cultivated olives) and potentially might belong to new species. All the Duganella spp. strains produced violacein in vitro, with natural production levels significantly higher than that previously reported for other violacein-producing bacteria without optimizing growing conditions. The important biological, medical, and industrial applications of violacein make these bacteria good candidates for their biotechnological exploitation because low violacein yields are considered as one of the main limitations of using wild-type strains for extensive exploitation and pigment production. Independent of violacein production, purple-pigmented strains from olives showed proteolytic and lipolytic activities and a weak siderophore production. No in vitro inhibitory activity was demonstrated for bacteria or crude violacein filtrates against plant-pathogenic Gram-negative bacteria and fungi, but they did inhibit Gram-positive bacteria.}, }
@article {pmid21424822, year = {2011}, author = {Peeters, K and Hodgson, DA and Convey, P and Willems, A}, title = {Culturable diversity of heterotrophic bacteria in Forlidas Pond (Pensacola Mountains) and Lundström Lake (Shackleton Range), Antarctica.}, journal = {Microbial ecology}, volume = {62}, number = {2}, pages = {399-413}, pmid = {21424822}, issn = {1432-184X}, mesh = {Antarctic Regions ; Bacteria/classification/genetics/*growth &amp; development/isolation &amp; purification ; Bacterial Typing Techniques ; Colony Count, Microbial ; Culture Media/chemistry ; Genes, rRNA ; *Genetic Variation ; Heterotrophic Processes ; Lakes/*microbiology ; Phylogeny ; Ponds/*microbiology ; RNA, Ribosomal, 16S/*genetics ; Water Microbiology ; }, abstract = {Cultivation techniques were used to study the heterotrophic bacterial diversity in two microbial mat samples originating from the littoral zone of two continental Antarctic lakes (Forlidas Pond and Lundström Lake) in the Dufek Massif (within the Pensacola Mountains group of the Transantarctic Mountains) and Shackleton Range, respectively. Nearly 800 isolates were picked after incubation on several growth media at different temperatures. They were grouped using a whole-genome fingerprinting technique, repetitive element palindromic PCR and partial 16S rRNA gene sequencing. Phylogenetic analysis of the complete 16S rRNA gene sequences of 82 representatives showed that the isolates belonged to four major phylogenetic groups: Actinobacteria, Bacteroidetes, Proteobacteria and Firmicutes. A relatively large difference between the samples was apparent. Forlidas Pond is a completely frozen water body underlain by hypersaline brine, with summer thaw forming a slightly saline littoral moat. This was reflected in the bacterial diversity with a dominance of isolates belonging to Firmicutes, whereas isolates from the freshwater Lundström Lake revealed a dominance of Actinobacteria. A total of 42 different genera were recovered, including first records from Antarctica for Albidiferax, Bosea, Curvibacter, Luteimonas, Ornithinibacillus, Pseudoxanthomonas, Sphingopyxis and Spirosoma. Additionally, a considerable number of potential new species and new genera were recovered distributed over different phylogenetic groups. For several species where previously only the type strain was available in cultivation, we report additional strains. Comparison with public databases showed that overall, 72% of the phylotypes are cosmopolitan whereas 23% are currently only known from Antarctica. However, for the Bacteroidetes, the majority of the phylotypes recovered are at present known only from Antarctica and many of these represent previously unknown species.}, }
@article {pmid21424821, year = {2011}, author = {Aguilar, M and Spiegel, FW and Lado, C}, title = {Microhabitat and climatic preferences of protosteloid amoebae in a region with a Mediterranean climate.}, journal = {Microbial ecology}, volume = {62}, number = {2}, pages = {361-373}, pmid = {21424821}, issn = {1432-184X}, mesh = {Amoebozoa/*growth &amp; development/isolation &amp; purification ; *Biota ; *Climate ; Culture Techniques ; Regression Analysis ; Spain ; Species Specificity ; Temperature ; }, abstract = {The role of microhabitat and climate variation in structuring protosteloid amoebae communities has been investigated for the first time in the Mediterranean Basin, a biodiversity hotspot for plants and animals and the largest of the world's five areas with a Mediterranean climate. Abundance data were obtained from natural substrates collected in 13 localities from central Spain, and a total of 1,504 colonies and 18 species were recorded. For this new area, it has been carried out an optimization of the culturing effort based on rarefaction analyses, thus making possible to adapt the protocol to the objectives in future research. Canonical correspondence analysis and generalized linear models showed that microhabitat type was the most important factor for differentiating the niches of the species studied, but climatic variables, especially minimum temperature of the coldest month, precipitation seasonality, and temperature range, had secondary but also important effects. Bark inhabitants tend to be more abundant in localities with high temperature range and low annual precipitation. Aerial litter was the microhabitat with the highest species richness, abundance, and evenness. Species typical of this microhabitat are more abundant when there is high precipitation, low temperature of the warmest month, and low minimum temperature of the coldest month.}, }
@article {pmid21424795, year = {2011}, author = {Cabrol, L and Malhautier, L}, title = {Integrating microbial ecology in bioprocess understanding: the case of gas biofiltration.}, journal = {Applied microbiology and biotechnology}, volume = {90}, number = {3}, pages = {837-849}, doi = {10.1007/s00253-011-3191-9}, pmid = {21424795}, issn = {1432-0614}, mesh = {Bacteria/genetics/isolation &amp; purification/*metabolism ; *Biodiversity ; Bioreactors/*microbiology ; Filtration/*instrumentation ; Gases/*metabolism ; }, abstract = {Biofilters are packed-bed bioreactors where contaminants, once transferred from the gas phase to the biofilm, are oxidized by diverse and complex communities of attached microorganisms. Over the last decade, more and more studies aimed at opening the back box of biofiltration by unraveling the biodiversity-ecosystem function relationship. In this review, we report the insights provided by the microbial ecology approach in biofilters and we emphasize the parallels existing with other engineered ecosystems used for wastewater treatment, as they all constitute relevant model ecosystems to explore ecological issues. We considered three characteristic ecological indicators: the density, the diversity, and the structure of the microbial community. Special attention was paid to the temporal and spatial dynamics of each indicator, insofar as it can disclose the potential relationship, or absence of relation, with any operating or functional parameter. We also focused on the impact of disturbance regime on the microbial community structure, in terms of resistance, resilience, and memory. This literature review led to mitigated conclusions in terms of biodiversity-ecosystem function relationship. Depending on the environmental system itself and the way it is investigated, the spatial and temporal dynamics of the microbial community can be either correlated (e.g., spatial stratification) or uncoupled (e.g., temporal instability) to the ecosystem function. This lack of generality shows the limits of current 16S approach in complex ecosystems, where a functional approach may be more suitable.}, }
@article {pmid21424277, year = {2011}, author = {van Overbeek, LS and Franke, AC and Nijhuis, EH and Groeneveld, RM and da Rocha, UN and Lotz, LA}, title = {Bacterial communities associated with Chenopodium album and Stellaria media seeds from arable soils.}, journal = {Microbial ecology}, volume = {62}, number = {2}, pages = {257-264}, pmid = {21424277}, issn = {1432-184X}, mesh = {Bacterial Typing Techniques ; Biota ; Chenopodium album/*microbiology ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis/methods ; Lysobacter/classification/genetics/*growth &amp; development ; Polymerase Chain Reaction ; Principal Component Analysis ; Seeds/*microbiology ; *Soil Microbiology ; Stellaria/*microbiology ; }, abstract = {The bacterial community compositions in Chenopodium album and Stellaria media seeds recovered from soil (soil weed seedbank), from bulk soil, and from seeds harvested from plants grown in the same soils were compared. It was hypothesized that bacterial communities in soil weed seedbanks are distinct from the ones present in bulk soils. For that purpose, bacterial polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) fingerprints, made from DNA extracts of different soils and seed fractions, were analyzed by principal component analysis. Bacterial fingerprints from C. album and S. media seeds differed from each other and from soil. Further, it revealed that bacterial fingerprints from soil-recovered and plant-harvested seeds from the same species clustered together. Hence, it was concluded that microbial communities associated with seeds in soil mostly originated from the mother plant and not from soil. In addition, the results indicated that the presence of a weed seedbank in arable soils can increase soil microbial diversity. Thus, a change in species composition or size of the soil weed seedbank, for instance, as a result of a change in crop management, could affect soil microbial diversity. The consequence of increased diversity is yet unknown, but by virtue of identification of dominant bands in PCR-DGGE fingerprints as Lysobacter oryzae (among four other species), it became clear that bacteria potentially antagonizing phytopathogens dominate in C. album seeds in soil. The role of these potential antagonists on weed and crop plant growth was discussed.}, }
@article {pmid21421306, year = {2011}, author = {Li, SL and Lin, JS and Wang, YH and Lee, ZK and Kuo, SC and Tseng, IC and Cheng, SS}, title = {Strategy of controlling the volumetric loading rate to promote hydrogen-production performance in a mesophilic-kitchen-waste fermentor and the microbial ecology analyses.}, journal = {Bioresource technology}, volume = {102}, number = {18}, pages = {8682-8687}, doi = {10.1016/j.biortech.2011.02.067}, pmid = {21421306}, issn = {1873-2976}, mesh = {Bacteria/genetics/*metabolism ; Base Sequence ; Biofuels ; Bioreactors/microbiology ; Biotechnology/*instrumentation/*methods ; DNA, Ribosomal/genetics ; Ecosystem ; Fermentation/*physiology ; Hydrogen/*metabolism ; Hydrogenation ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; *Temperature ; Time Factors ; Waste Disposal, Fluid ; Waste Products/*analysis ; }, abstract = {The kitchen waste was chosen as a high solid (42 gL(-1) of volatile suspended solid, VSS) and high organic (107 gL(-1) of chemical oxygen demand) feedstock for operating a 3-L mesophilic fermentor. The greatest specific hydrogen production rate (r(H2) was observed in Stage 3 as 3.4 L-H2 L(-1) day(-1) with a volumetric loading rate (VLR) of 100 g-CODL(-1) day(-1); the highest hydrogen yield was observed in Stage 2 as 96 mL-H2 g(-1) of influent VSS with a VLR of 46 g-COD L(-1) day(-1). In Stages 1 (with a VLR of 27 g-COD L(-1)) and 2, the sum of Butyrivibrio fibrisolvens and Clostridium proteoclasticum is dominant, but in Stage 3, Olsenella genomosp, became dominant and constituted 44% of the entire population. The dependence of VLR and r(H2)could be regressed as a linear equation of r(H2) = (2.83 VLR + 40.5) x 10(-2) .}, }
@article {pmid21421068, year = {2011}, author = {Alexopoulos, A and Plessas, S and Voidarou, C and Noussias, H and Stavropoulou, E and Mantzourani, I and Tzora, A and Skoufos, I and Bezirtzoglou, E}, title = {Microbial ecology of fish species ongrowing in Greek sea farms and their watery environment.}, journal = {Anaerobe}, volume = {17}, number = {6}, pages = {264-266}, doi = {10.1016/j.anaerobe.2011.03.003}, pmid = {21421068}, issn = {1095-8274}, mesh = {Animals ; *Aquaculture ; Bacteria/*classification/*isolation &amp; purification ; Bass/*microbiology ; *Biota ; Feces/microbiology ; Greece ; Sea Bream/*microbiology ; *Water Microbiology ; }, abstract = {The present study focuses on the bacteriological profile of both watery ecosystem and fishes from different North and Central West Greek fish-farms ongrowing euryhaline fish species. The natural microflora of the fish and the water of their ongrowing units in selected farms were studied for a period of 20 months. The analyzed samples were mainly sea bream (Sparus aurata) 61.3% and sea bass (Dicentrarchus labrax) 24%. In most of the watery ecosystems coming from the different sampling areas, total and fecal coliforms as well as total and fecal streptococci were abundant in all water samples. Enterococcus, Escherichia coli and Pseudomonas were present at a level of 3 logs cfu/100 ml. The anaerobic Clostridium perfringens was found in vegetative (21.3%) and spore forms (13.3%). It is of interest to note that pathogens as Pasteurella piscicida and Vibrio anguillarum were isolated only in a small number of samples. Staphylococcus aureus was detected in 4% of the samples, other Staphylococcus sp. in 29.3%, E. coli in 30.7%, Salmonella sp. in 1.3%, Pseudomonas sp. in 13.3%, Clostridia lec(-) in 49.3%, Bacillus sp. in 38.7%, Vibrio sp. in 18.7%, Lactobacillus and Lactococcus sp. in 36% και 29.3% respectively. Vegetative forms of C. perfringens were detected in 22.7%. Although, our results showed no significant correlations between the sea water and fish microflora, more focus on this bipolar interacting system should be necessary in order to avoid any possible disturbance in the balance of the healthy farming ecosystem with the host organisms.}, }
@article {pmid21409345, year = {2011}, author = {Colinon-Dupuich, C and Février, L and Ranjard, L and Coppin, F and Cournoyer, B and Nazaret, S}, title = {Radioecological risk assessment of low selenium concentrations through genetic fingerprints and metabolic profiling of soil bacterial communities.}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {14-24}, pmid = {21409345}, issn = {1432-184X}, mesh = {Bacteria/*genetics/isolation &amp; purification/*metabolism ; DNA Fingerprinting ; Metabolome ; Radioactive Waste/analysis ; Selenium Radioisotopes/*metabolism ; Soil/*analysis ; *Soil Microbiology ; Soil Pollutants, Radioactive/*metabolism ; }, abstract = {In a context of environmental risk assessment of nuclear (79)Se radionuclide, the impact of low Se-selenite concentrations (0.008 and 8 mg kg(-1)) on bacterial communities of two soils, a silty clay loam and a sandy soil, was investigated over a 6-month incubation time. This Se-selenite was partially labelled with (75)Se. The state of the Se-impacted bacterial communities was analyzed through total bacterial counts, DNA fingerprints (ARISA profiles) and metabolic profiling (carbon substrate utilization patterns). Furthermore, the genetic diversity of bacterial populations involved in Se volatilization was evaluated by tpm (thiopurine methyltransferase gene) profiling. Emissions of (75)Se and CaCl(2)-extractable (75)Se were measured by γ-spectrometry and scintillation analysis. Se-selenite inputs changed transiently the substrate utilization patterns of bacterial communities but did not affect the other indicators. Se volatilization was at its highest level just after adding Se-selenite and for about 1 week. This volatilization was proportional to the added Se-selenite concentrations. It was 100-fold higher in silty clay loam, even though Se bioavailability was reduced in this soil. The soils were amended with crushed grass 3 months after the addition of Se-selenite. This organic amendment affected the organization of bacterial communities and increased the Se-volatilizing activities of both soils. Original soil organic carbon and bacterial diversity and activities seemed responsible for the different levels of Se emissions observed in soils. tpm lineages, encoding Se methyltransferases, were detected in both soils, confirming the broad distribution of tpm-harbouring bacteria and their probable role in the emissions of volatile Se. Five distinct groups of tpm were recorded per soil, with tpmI lineage being detected throughout the incubation period. This study demonstrates the ability of bacterial communities at volatilizing Se concentrations inferior to geochemical backgrounds and suggests that a probable transfer of nuclear Se will occur through volatilization after an environmental spill.}, }
@article {pmid21409344, year = {2011}, author = {Kim, YH and Kim, IS and Moon, EY and Park, JS and Kim, SJ and Lim, JH and Park, BT and Lee, EJ}, title = {High abundance and role of antifungal bacteria in compost-treated soils in a wildfire area.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {725-737}, pmid = {21409344}, issn = {1432-184X}, mesh = {*Antibiosis ; Bacteria/*isolation &amp; purification ; Colony Count, Microbial ; *Fires ; Fungi/*isolation &amp; purification ; Republic of Korea ; Soil/analysis ; *Soil Microbiology ; Trees/*microbiology ; }, abstract = {Compost has been widely used in order to promote vegetation growth in post-harvested and burned soils. The effects on soil microorganisms were scarcely known, so we performed the microbial analyses in a wildfire area of the Taebaek Mountains, Korea, during field surveys from May to September 2007. Using culture-dependent and -independent methods, we found that compost used in burned soils influenced a greater impact on soil fungi than bacteria. Compost-treated soils contained higher levels of antifungal strains in the genera Bacillus and Burkholderia than non-treated soils. When the antifungal activity of Burkholderia sp. strain O1a_RA002, which had been isolated from a compost-treated soil, was tested for the growth inhibition of bacteria and fungi isolated from burned soils, the membrane-filtered culture supernatant inhibited 19/37 fungal strains including soil fungi, Eupenicillium spp. and Devriesia americana; plant pathogens, Polyschema larviformis and Massaria platani; an animal pathogen, Mortierella verticillata; and an unidentified Ascomycota. However, this organism only inhibited 11/151 bacterial strains tested. These patterns were compatible with the culture-independent DGGE results, suggesting that the compost used in burned soils had a greater impact on soil fungi than bacteria through the promotion of the growth of antifungal bacteria. Our findings indicate that compost used in burned soils is effective in restoring soil conditions to a state closer to those of nearby unburned forest soils at the early stage of secondary succession.}, }
@article {pmid21407210, year = {2011}, author = {Raes, J and Letunic, I and Yamada, T and Jensen, LJ and Bork, P}, title = {Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data.}, journal = {Molecular systems biology}, volume = {7}, number = {}, pages = {473}, pmid = {21407210}, issn = {1744-4292}, mesh = {Adaptation, Physiological ; Algorithms ; Biodiversity ; *Climate ; Data Interpretation, Statistical ; *Ecology ; *Ecosystem ; Genetic Loci/*genetics ; Geography ; Metabolic Networks and Pathways ; *Metagenomics ; Molecular Sequence Annotation ; Oceans and Seas ; Regression Analysis ; Seawater/*microbiology ; Species Specificity ; }, abstract = {Using metagenomic 'parts lists' to infer global patterns on microbial ecology remains a significant challenge. To deduce important ecological indicators such as environmental adaptation, molecular trait dispersal, diversity variation and primary production from the gene pool of an ecosystem, we integrated 25 ocean metagenomes with geographical, meteorological and geophysicochemical data. We find that climatic factors (temperature, sunlight) are the major determinants of the biomolecular repertoire of each sample and the main limiting factor on functional trait dispersal (absence of biogeographic provincialism). Molecular functional richness and diversity show a distinct latitudinal gradient peaking at 20° N and correlate with primary production. The latter can also be predicted from the molecular functional composition of an environmental sample. Together, our results show that the functional community composition derived from metagenomes is an important quantitative readout for molecular trait-based biogeography and ecology.}, }
@article {pmid21404936, year = {2011}, author = {Hennebel, T and De Gusseme, B and Soetaert, M and De Corte, S and De Sloover, J and Verstraete, W and Boon, N}, title = {Dehalogenation of trichloroethylene in microbial electrolysis cells with biogenic palladium nanoparticles.}, journal = {Communications in agricultural and applied biological sciences}, volume = {76}, number = {2}, pages = {59-61}, pmid = {21404936}, issn = {1379-1176}, mesh = {Bacteria/*metabolism ; Electrochemistry ; Electrodes ; Electrolysis ; Graphite ; Hydrogen/chemistry ; Metal Nanoparticles/*chemistry ; Palladium/*chemistry ; Trichloroethylene/*chemistry/*metabolism ; Water Pollutants, Chemical/chemistry ; Water Purification/methods ; }, }
@article {pmid21404934, year = {2011}, author = {Desloover, J and Puig, S and Verstraete, W and Boon, N}, title = {Autotrophic nitrous oxide removal in bioelectrochemical systems.}, journal = {Communications in agricultural and applied biological sciences}, volume = {76}, number = {2}, pages = {51-53}, pmid = {21404934}, issn = {1379-1176}, mesh = {*Autotrophic Processes ; Bacteria/*metabolism ; *Bioelectric Energy Sources ; *Electrochemistry ; Nitrous Oxide/chemistry/*metabolism ; }, }
@article {pmid21404933, year = {2011}, author = {Arends, JB and Blondeel, E and Tennison, S and Boon, N and Verstraete, W}, title = {Anode materials for sediment microbial fuel cells.}, journal = {Communications in agricultural and applied biological sciences}, volume = {76}, number = {2}, pages = {47-50}, pmid = {21404933}, issn = {1379-1176}, mesh = {Bacteria/*metabolism ; *Bioelectric Energy Sources ; Electric Impedance ; Electrodes ; Geologic Sediments/*microbiology ; Soil ; Time Factors ; }, }
@article {pmid21404932, year = {2011}, author = {Arends, JB and D'Haese, A and Boon, N and Verstraete, W}, title = {Cathodes for sediment microbial fuel cells.}, journal = {Communications in agricultural and applied biological sciences}, volume = {76}, number = {2}, pages = {43-46}, pmid = {21404932}, issn = {1379-1176}, mesh = {Bacteria/*metabolism ; *Bioelectric Energy Sources ; Electric Impedance ; Electrodes ; Geologic Sediments/*microbiology ; Oxygen/metabolism ; }, }
@article {pmid21404930, year = {2011}, author = {Vanwonterghem, I and Read, S and Van der Ha, D and Verstraete, W and Boon, N}, title = {Methanotrophic microbiome.}, journal = {Communications in agricultural and applied biological sciences}, volume = {76}, number = {2}, pages = {33-36}, pmid = {21404930}, issn = {1379-1176}, mesh = {Agriculture ; *Air Pollutants ; Bacteria/*classification/*metabolism ; *Bioelectric Energy Sources ; Global Warming ; Methane/chemistry/*metabolism ; Oxidation-Reduction ; Time Factors ; }, }
@article {pmid21404927, year = {2011}, author = {Friedrich, MW}, title = {The microbial ecology of electrigenic microorganisms in plant-rhizosphere based microbial fuel cells.}, journal = {Communications in agricultural and applied biological sciences}, volume = {76}, number = {2}, pages = {25-26}, pmid = {21404927}, issn = {1379-1176}, mesh = {Bacteria/*metabolism ; *Bioelectric Energy Sources ; Electrochemistry ; Plant Roots/*growth &amp; development ; Plants/*metabolism ; Soil Microbiology ; }, }
@article {pmid21399677, year = {2011}, author = {dos Santos, HF and Cury, JC and do Carmo, FL and dos Santos, AL and Tiedje, J and van Elsas, JD and Rosado, AS and Peixoto, RS}, title = {Mangrove bacterial diversity and the impact of oil contamination revealed by pyrosequencing: bacterial proxies for oil pollution.}, journal = {PloS one}, volume = {6}, number = {3}, pages = {e16943}, pmid = {21399677}, issn = {1932-6203}, mesh = {Bacteria/*drug effects/*genetics/isolation &amp; purification ; *Biodiversity ; Environmental Pollution/*adverse effects/analysis ; Hydrocarbons/analysis ; Molecular Sequence Data ; Oils/*adverse effects/analysis ; Petroleum/analysis ; RNA, Ribosomal, 16S/genetics ; Rhizophoraceae/*microbiology ; Sequence Analysis, DNA/*methods ; *Temperature ; }, abstract = {BACKGROUND: Mangroves are transitional coastal ecosystems in tropical and sub-tropical regions and represent biologically important and productive ecosystems. Despite their great ecological and economic importance, mangroves are often situated in areas of high anthropogenic influence, being exposed to pollutants, such as those released by oil spills.<br><br>A microcosm experiment was conducted, which simulated an oil spill in previously pristine mangrove sediment. The effect of the oil spill on the extant microbial community was studied using direct pyrosequencing. Extensive bacterial diversity was observed in the pristine mangrove sediment, even after oil contamination. The number of different OTUs only detected in contaminated samples was significantly higher than the number of OTUs only detected in non-contaminated samples. The phylum Proteobacteria, in particular the classes Gammaproteobacteria and Deltaproteobacteria, were prevalent before and after the simulated oil spill. On the other hand, the order Chromatiales and the genus Haliea decreased upon exposure to 2 and 5% oil, these are proposed as sensitive indicators of oil contamination. Three other genera, Marinobacterium, Marinobacter and Cycloclasticus increased their prevalence when confronted with oil. These groups are possible targets for the biomonitoring of the impact of oil in mangrove settings.<br><br>CONCLUSIONS/SIGNIFICANCE: We suggest the use of sequences of the selected genera as proxies for oil pollution, using qPCR assessments. The quantification of these genera in distinct mangrove systems in relation to the local oil levels would permit the evaluation of the level of perturbance of mangroves, being useful in field monitoring. Considering the importance of mangroves to many other environments and the susceptibility of such areas to oil spills this manuscript will be of broad interest.}, }
@article {pmid21396675, year = {2011}, author = {Siggins, A and Enright, AM and O'Flaherty, V}, title = {Methanogenic community development in anaerobic granular bioreactors treating trichloroethylene (TCE)-contaminated wastewater at 37 °C and 15 °C.}, journal = {Water research}, volume = {45}, number = {8}, pages = {2452-2462}, doi = {10.1016/j.watres.2011.01.030}, pmid = {21396675}, issn = {1879-2448}, mesh = {Anaerobiosis ; Biodiversity ; Bioreactors/*microbiology ; Methane/metabolism ; Methanobacteriales/classification/genetics/*metabolism ; Temperature ; Trichloroethylene/analysis/chemistry/*metabolism ; Waste Disposal, Fluid/*methods ; Water Pollutants, Chemical/analysis/chemistry/*metabolism ; }, abstract = {Four expanded granular sludge bed (EGSB) bioreactors were seeded with a mesophilically-grown granular sludge and operated in duplicate for mesophilic (37 °C; R1 &amp; R2) and low- (15°; R3 &amp; R4) temperature treatment of a synthetic volatile fatty acid (VFA) based wastewater (3 kg COD m(-3) d(-1)) with one of each pair (R1 &amp; R3) supplemented with increasing concentrations of trichloroethylene (TCE; 10, 20, 40, 60 mg l(-1)) and one acting as a control. Bioreactor performance was evaluated by % COD removal efficiency and % biogas methane (CH(4)) content. Quantitative Polymerase Chain Reaction (qPCR) was used to investigate the methanogenic community composition and dynamics in the bioreactors during the trial, while specific methanogenic activity (SMA) and toxicity assays were utilized to investigate the activity and TCE/dichloroethylene (DCE) toxicity thresholds of key trophic groups, respectively. At both 37 °C and 15 °C, TCE levels of 60 mg l(-1) resulted in the decline of % COD removal efficiencies to 29% (Day 235) and 37% (Day 238), respectively, and in % biogas CH(4) to 54% (Day 235) and 5% (Day 238), respectively. Despite the inhibitory effect of TCE on the anaerobic digestion process, the main drivers influencing methanogenic community development, as determined by qPCR and Non-metric multidimensional scaling analysis, were (i) wastewater composition and (ii) operating temperature. At the apical TCE concentration both SMA and qPCR of methanogenic archaea suggested that acetoclastic methanogens were somewhat inhibited by the presence of TCE and/or its degradation derivatives, while competition by dechlorinating organisms may have limited the availability of H(2) for hydrogenotrophic methanogenesis. In addition, there appeared to be an inverse correlation between SMA levels and TCE tolerance, a finding that was supported by the analysis of the inhibitory effect of TCE on two additional biomass sources. The results indicate that low-temperature anaerobic digestion is a feasible approach for the treatment of TCE-containing wastewater.}, }
@article {pmid21394608, year = {2011}, author = {Minter, EJ and Fenton, A and Cooper, J and Montagnes, DJ}, title = {Prey-dependent mortality rate: a critical parameter in microbial models.}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {155-161}, pmid = {21394608}, issn = {1432-184X}, mesh = {Ciliophora/*physiology ; *Ecosystem ; Models, Biological ; Population Dynamics ; }, abstract = {Protozoa are key components of a wide range of ecosystems, but ecological models that incorporate these microbes often suffer from poor parameterisation, specifically of top-level predator loss rates. We (1) suggest that top-level predator mortality is prey-dependent, (2) provide a novel approach to assess this response, and (3) illustrate the ecological relevance of these findings. Ciliates, Paramecium caudatum (prey) and Didinium nasutum (predator), were used to evaluate predator mortality at varying prey levels. To assess mortality, multiple (>100) predators were individually examined (in 2-ml wells), daily (for 3 days), between 0 and 120 preys ml(-1). Data were used to determine non-linear mortality and growth responses over a range of prey abundances. The responses, plus literature data were then used to parameterise a predator-prey model, based on the Rosenzweig-MacArthur structure. The model assessed the impact of variable and three levels of constant (high, average and low) mortality rates on P. caudatum-D. nasutum population dynamics. Our method to determine variable mortality rate revealed a strong concave decline in mortality with increasing prey abundance. The model indicated: (1) high- and low-constant mortality rates yielded dynamics that deviate substantially from those obtained from a variable rate; (2) average mortality rate superficially produced dynamics similar to the variable rate, but there were differences in the period of predator-prey cycles, and the lowest abundance of prey and predators (by ~2 orders of magnitude). The differences between incorporating variable and constant mortality rate indicate that including a variable rate could substantially improve microbial-based ecological models.}, }
@article {pmid21394607, year = {2011}, author = {Bomberg, M and Münster, U and Pumpanen, J and Ilvesniemi, H and Heinonsalo, J}, title = {Archaeal communities in boreal forest tree rhizospheres respond to changing soil temperatures.}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {205-217}, pmid = {21394607}, issn = {1432-184X}, mesh = {Archaea/*classification/genetics/*isolation &amp; purification ; Betula/*microbiology ; Molecular Sequence Data ; Picea/*microbiology ; Pinus/*microbiology ; *Rhizosphere ; Soil/*chemistry ; Soil Microbiology ; Temperature ; Trees/microbiology ; }, abstract = {Temperature has generally great effects on both the activity and composition of microbial communities in different soils. We tested the impact of soil temperature and three different boreal forest tree species on the archaeal populations in the bulk soil, rhizosphere, and mycorrhizosphere. Scots pine, silver birch, and Norway spruce seedlings were grown in forest humus microcosms at three different temperatures, 7-11.5°C (night-day temperature), 12-16°C, and 16-22°C, of which 12-16°C represents the typical mid-summer soil temperature in Finnish forests. RNA and DNA were extracted from indigenous ectomycorrhiza, non-mycorrhizal long roots, and boreal forest humus and tested for the presence of archaea by nested PCR of the archaeal 16S rRNA gene followed by denaturing gradient gel electrophoresis (DGGE) profiling and sequencing. Methanogenic Euryarchaeota belonging to Methanolobus sp. and Methanosaeta sp. were detected on the roots and mycorrhiza. The most commonly detected archaeal 16S rRNA gene sequences belonged to group I.1c Crenarchaeota, which are typically found in boreal and alpine forest soils. Interestingly, also one sequence belonging to group I.1b Crenarchaeota was detected from Scots pine mycorrhiza although sequences of this group are usually found in agricultural and forest soils in temperate areas. Tree- and temperature-related shifts in the archaeal population structure were observed. A clear decrease in crenarchaeotal DGGE band number was seen with increasing temperature, and correspondingly, the number of euryarchaeotal DGGE bands, mostly methanogens, increased. The greatest diversity of archaeal DGGE bands was detected in Scots pine roots and mycorrhizas. No archaea were detected from humus samples from microcosms without tree seedling, indicating that the archaea found in the mycorrhizosphere and root systems were dependent on the plant host. The detection of archaeal 16S rRNA gene sequences from both RNA and DNA extractions show that the archaeal populations were living and that they may have significant contribution to the methane cycle in boreal forest soil, especially when soil temperatures rise.}, }
@article {pmid21394529, year = {2011}, author = {Canganella, F and Wiegel, J}, title = {Extremophiles: from abyssal to terrestrial ecosystems and possibly beyond.}, journal = {Die Naturwissenschaften}, volume = {98}, number = {4}, pages = {253-279}, pmid = {21394529}, issn = {1432-1904}, mesh = {Autotrophic Processes ; Desiccation ; *Ecosystem ; Exobiology ; Hydrogen-Ion Concentration ; Hydrostatic Pressure ; Phototrophic Processes ; Prokaryotic Cells/cytology/*physiology ; Radiation ; Salinity ; Solvents ; Temperature ; }, abstract = {The anthropocentric term "extremophile" was introduced more than 30 years ago to describe any organism capable of living and growing under extreme conditions-i.e., particularly hostile to human and to the majority of the known microorganisms as far as temperature, pH, and salinity parameters are concerned. With the further development of studies on microbial ecology and taxonomy, more "extreme" environments were found and more extremophiles were described. Today, many different extremophiles have been isolated from habitats characterized by hydrostatic pressure, aridity, radiations, elevated temperatures, extreme pH values, high salt concentrations, and high solvent/metal concentrations, and it is well documented that these microorganisms are capable of thriving under extreme conditions better than any other organism living on Earth. Extremophiles have also been investigated as far as the search for life in other planets is concerned and even to evaluate the hypothesis that life on Earth came originally from space. Extremophiles are interesting for basic and applied sciences. Particularly fascinating are their structural and physiological features allowing them to stand extremely selective environmental conditions. These properties are often due to specific biomolecules (DNA, lipids, enzymes, osmolites, etc.) that have been studied for years as novel sources for biotechnological applications. In some cases (DNA polymerase, thermostable enzymes), the search was successful and the final application was achieved, but certainly further exploitations are next to come.}, }
@article {pmid21391286, year = {2011}, author = {Nagalingam, NA and Kao, JY and Young, VB}, title = {Microbial ecology of the murine gut associated with the development of dextran sodium sulfate-induced colitis.}, journal = {Inflammatory bowel diseases}, volume = {17}, number = {4}, pages = {917-926}, pmid = {21391286}, issn = {1536-4844}, support = {R01 DK070875/DK/NIDDK NIH HHS/United States ; DK070875/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Colitis/chemically induced/*microbiology/*pathology ; Dextran Sulfate/*toxicity ; Disease Models, Animal ; Gastrointestinal Tract/immunology/*microbiology ; *Gene Expression Profiling ; Humans ; Mice ; Mice, Inbred C57BL ; RNA, Messenger/genetics ; RNA, Ribosomal, 16S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {BACKGROUND: Dextran sodium sulfate (DSS) is used to induce murine colitis. Although the exact mechanism by which DSS administration causes disease is unknown, evidence suggests that the resident bacteria play a role in the development of murine DSS colitis, analogous to their role in human inflammatory bowel diseases.<br><br>METHODS: C57BL/6 mice received 5% DSS in the drinking water and were euthanized 3 days and 14 days after the initiation of DSS treatment. Culture-independent methods were used to follow changes in the community structure of the gut's microbiota following DSS treatment. Histologic evidence of disease and changes in host gene expression were assessed.<br><br>RESULTS: Histologic colitis was minimal in DSS-treated animals at 3 days, but severe after 14 days. Analysis of 16S rRNA-encoding gene clone libraries demonstrated that the microbial communities in the ceca of DSS-treated mice were distinct from those in control mice. The microbiota in the cecum of DSS-treated animals was characterized by an overall decrease in microbial richness, an increase in members of the phylum Verrucomicrobia, and decrease in Tenericutes. Changes in the host's inflammatory response and microbial communities occurred before the histologic appearance of severe disease in the colon, but were seen concurrently in the cecum.<br><br>CONCLUSIONS: DSS administration is associated with reproducible changes in the gut microbial diversity of mice. Microbial and immunological changes appeared before the development of severe inflammation in the colon. This indicates that these changes in microbial community may play role in the potentiation of the abnormal inflammatory response seen in DSS-treated animals.}, }
@article {pmid21390532, year = {2011}, author = {Kolukirik, M and Ince, O and Ince, BK}, title = {Increment in anaerobic hydrocarbon degradation activity of Halic Bay sediments via nutrient amendment.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {871-884}, pmid = {21390532}, issn = {1432-184X}, mesh = {Anaerobiosis ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Geologic Sediments/chemistry/*microbiology ; Hydrocarbons/*metabolism ; Seawater/*microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {In this study, hydrocarbon (HC) degradation activity of a HC-rich marine sediment was assessed in anaerobic microcosms during a 224 days incubation period. Natural TOC/N/P ratio of the sediment porewater (1,000/5/1) was gradually decreased to 1,000/40/6 which resulted in approximately ninefold increase in gas production (CH(4)+CO(2)) and HC removal. Addition of external HCs to the microcosms was also resulted in approximately twofold higher gas production and HC removal. A high proportion (92%) of aromatic HCs and all n-alkanes were removed from the microcosms under unlimited nutrient supply conditions without external HC addition. The microorganisms of the sediment degraded a wide range of aliphatic (n-C(9-31) alkanes and acyclic isoprenoids) and aromatic (18 different one- to five-ring aromatics) HCs. Monitoring functional gene and transcript abundances revealed that methanogenesis and dissimilatory sulfate reduction took place simultaneously during the first 126 days, afterwards, only the syntrophic methanogenic consortium was active. Genes and transcripts related to initial activation of HCs were highly abundant throughout the incubation period showing that fumarate addition was the main pathway of anaerobic HC degradation. In conclusion, biostimulation of highly polluted anoxic marine sediments via nutrient amendment is effective and may constitute a suitable and cost-effective field-scale bioremediation strategy.}, }
@article {pmid21390531, year = {2011}, author = {Bettarel, Y and Bouvier, T and Agis, M and Bouvier, C and Chu, TV and Combe, M and Mari, X and Nghiem, MN and Nguyen, TT and Pham, TT and Pringault, O and Rochelle-Newall, E and Torréton, JP and Tran, HQ}, title = {Viral distribution and life strategies in the Bach Dang Estuary, Vietnam.}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {143-154}, pmid = {21390531}, issn = {1432-184X}, mesh = {Fresh Water/analysis/*virology ; Molecular Sequence Data ; Phylogeny ; Seawater/analysis/*virology ; Sodium Chloride/analysis ; Vietnam ; Virus Latency ; *Virus Physiological Phenomena ; Viruses/classification/genetics/*isolation &amp; purification ; }, abstract = {Although the structure and dynamics of planktonic viruses in freshwater and seawater environments are relatively well documented, little is known about the occurrence and activity of these viruses in estuaries, especially in the tropics. Viral abundance, life strategies, and morphotype distribution were examined in the Bach Dang Estuary (Vietnam) during the dry season in 2009. The abundance of both viruses and their prokaryotic hosts decreased significantly from upstream to downstream, probably as the result of nutrient dilution and osmotic stress faced by the freshwater communities. The antibiotic mitomycin-C revealed that the fraction of lysogenic cells was substantially higher in the lower seawater part of the estuary (max 27.1%) than in the upper freshwater area where no inducible lysogens were observed. The question of whether there is a massive, continuous induction of marine lysogens caused by the mixing with freshwater is considered. Conversely, the production of lytic viruses declined as salinity increased, indicating a spatial succession of viral life strategies in this tropical estuary. Icosahedral tailless viruses with capsids smaller than 60 nm dominated the viral assemblage throughout the estuary (63.0% to 72.1% of the total viral counts), and their distribution was positively correlated with that of viral lytic production. Interestingly, the gamma-proteobacteria explained a significant portion of the variance in the <60 nm and 60 to 90 nm tailless viruses (92% and 80%, respectively), and in the Myoviridae (73%). Also, 60% of the variance of the tailless larger viruses (>90 nm) was explained by the beta-proteobacteria. Overall, these results support the view that the environment, through selection mechanisms, probably shapes the structure of the prokaryotic community. This might be in turn a source of selection for the virioplankton community via specific affiliation favoring particular morphotypes and life strategies.}, }
@article {pmid21388173, year = {2011}, author = {Ahn, JH and Kwan, T and Chandran, K}, title = {Comparison of partial and full nitrification processes applied for treating high-strength nitrogen wastewaters: microbial ecology through nitrous oxide production.}, journal = {Environmental science &amp; technology}, volume = {45}, number = {7}, pages = {2734-2740}, doi = {10.1021/es103534g}, pmid = {21388173}, issn = {1520-5851}, mesh = {Ammonia/metabolism ; Bacteria/classification/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Base Sequence ; Bioreactors/microbiology ; Ecology ; Molecular Sequence Data ; *Nitrification ; Nitrous Oxide/*metabolism ; Water Microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The goal of this study was to compare the microbial ecology, gene expression, biokinetics, and N2O emissions from a lab-scale bioreactor operated sequentially in full-nitrification and partial-nitrification modes. Based on sequencing of 16S rRNA and ammonia monooxygenase subunit A (amoA) genes, ammonia oxidizing bacteria (AOB) populations during full- and partial-nitrification modes were distinct from one another. The concentrations of AOB (XAOB) and their respiration rates during full- and partial-nitrification modes were statistically similar, whereas the concentrations of nitrite oxidizing bacteria (XNOB) and their respiration rates declined significantly after the switch from full- to partial-nitrification. The transition from full-nitrification to partial nitrification resulted in a protracted transient spike of nitrous oxide (N2O) and nitric oxide (NO) emissions, which later stabilized. The trends in N2O and NO emissions correlated well with trends in the expression of nirK and norB genes that code for the production of these gases in AOB. Both the transient and stabilized N2O and NO emissions during partial nitrification were statistically higher than those during steady-state full-nitrification. Based on these results, partial nitrification strategies for biological nitrogen removal, although attractive for their reduced operating costs and energy demand, may need to be optimized against the higher carbon foot-print attributed to their N2O emissions.}, }
@article {pmid21387098, year = {2011}, author = {Geiger, A and Fardeau, ML and Njiokou, F and Joseph, M and Asonganyi, T and Ollivier, B and Cuny, G}, title = {Bacterial diversity associated with populations of Glossina spp. from Cameroon and distribution within the Campo sleeping sickness focus.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {632-643}, pmid = {21387098}, issn = {1432-184X}, mesh = {Animals ; Bacteria/genetics/growth &amp; development/*isolation &amp; purification ; Biodiversity ; Cameroon ; DNA, Bacterial/genetics ; Gastrointestinal Tract/microbiology ; Insect Vectors/*microbiology ; Likelihood Functions ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Tsetse Flies/*microbiology ; }, abstract = {Tsetse flies were sampled in three villages of the Campo sleeping sickness focus in South Cameroon. The aim of this study was to investigate the flies' gut bacterial composition using culture-dependent techniques. Out of the 32 flies analyzed (27 Glossina palpalis palpalis, two Glossina pallicera, one Glossina nigrofusca, and two Glossina caliginea), 17 were shown to be inhabited by diverse bacteria belonging to the Proteobacteria, the Firmicutes, or the Bacteroidetes phyla. Phylogenetic analysis based on 16S rRNA gene sequences indicated the presence of 16 bacteria belonging to the genera Acinetobacter (4), Enterobacter (4), Enterococcus (2), Providencia (1), Sphingobacterium (1), Chryseobacterium (1), Lactococcus (1), Staphylococcus (1), and Pseudomonas (1). Using identical bacterial isolation and identification processes, the diversity of the inhabiting bacteria analyzed in tsetse flies sampled in Cameroon was much higher than the diversity found previously in flies collected in Angola. Furthermore, bacterial infection rates differed greatly between the flies from the three sampling areas (Akak, Campo Beach/Ipono, and Mabiogo). Last, the geographic distribution of the different bacteria was highly uneven; two of them identified as Sphingobacterium spp. and Chryseobacterium spp. were only found in Mabiogo. Among the bacteria identified, several are known for their capability to affect the survival of their insect hosts and/or insect vector competence. In some cases, bacteria belonging to a given genus were shown to cluster separately in phylogenetic trees; they could be novel species within their corresponding genus. Therefore, such investigations deserve to be pursued in expanded sampling areas within and outside Cameroon to provide greater insight into the diverse bacteria able to infect tsetse flies given the severe human and animal sickness they transmit.}, }
@article {pmid21385188, year = {2011}, author = {Pereira e Silva, MC and Semenov, AV and van Elsas, JD and Salles, JF}, title = {Seasonal variations in the diversity and abundance of diazotrophic communities across soils.}, journal = {FEMS microbiology ecology}, volume = {77}, number = {1}, pages = {57-68}, doi = {10.1111/j.1574-6941.2011.01081.x}, pmid = {21385188}, issn = {1574-6941}, mesh = {Agriculture ; Bacteria/genetics/*isolation &amp; purification ; *Biodiversity ; DNA Primers ; DNA, Bacterial/analysis ; Denaturing Gradient Gel Electrophoresis ; Denitrification ; Environment ; Gene Library ; Netherlands ; *Nitrogen Fixation ; Oxidoreductases/genetics ; Phylogeny ; *Seasons ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; }, abstract = {The nitrogen (N)-fixing community is a key functional community in soil, as it replenishes the pool of biologically available N that is lost to the atmosphere via anaerobic ammonium oxidation and denitrification. We characterized the structure and dynamic changes in diazotrophic communities, based on the nifH gene, across eight different representative Dutch soils during one complete growing season, to evaluate the amplitude of the natural variation in abundance and diversity, and identify possible relationships with abiotic factors. Overall, our results indicate that soil type is the main factor influencing the N-fixing communities, which were more abundant and diverse in the clay soils (n=4) than in the sandy soils (n=4). On average, the amplitude of variation in community size as well as the range-weighted richness were also found to be higher in the clay soils. These results indicate that N-fixing communities associated with sandy and clay soil show a distinct amplitude of variation under field conditions, and suggest that the diazotrophic communities associated with clay soil might be more sensitive to fluctuations associated with the season and agricultural practices. Moreover, soil characteristics such as ammonium content, pH and texture most strongly correlated with the variations observed in the diversity, size and structure of N-fixing communities, whose relative importance was determined across a temporal and spatial scale.}, }
@article {pmid21384215, year = {2011}, author = {Perryman, SE and Rees, GN and Walsh, CJ and Grace, MR}, title = {Urban stormwater runoff drives denitrifying community composition through changes in sediment texture and carbon content.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {932-940}, pmid = {21384215}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Carbon/*analysis/metabolism ; Denitrification ; Fresh Water/*chemistry/microbiology ; Geologic Sediments/*chemistry/*microbiology ; Molecular Sequence Data ; Phylogeny ; Urban Renewal ; }, abstract = {The export of nitrogen from urban catchments is a global problem, and denitrifying bacteria in stream ecosystems are critical for reducing in-stream N. However, the environmental factors that control the composition of denitrifying communities in streams are not well understood. We determined whether denitrifying community composition in sediments of nine streams on the eastern fringe of Melbourne, Australia was correlated with two measures of catchment urban impact: effective imperviousness (EI, the proportion of a catchment covered by impervious surfaces with direct connection to streams) or septic tank density (which affects stream water chemistry, particularly stream N concentrations). Denitrifying community structure was examined by comparing terminal restriction fragment length polymorphisms of nosZ genes in the sediments, as the nosZ gene codes for nitrous oxide reductase, the last step in the denitrification pathway. We also determined the chemical and physical characteristics of the streams that were best correlated with denitrifying community composition. EI was strongly correlated with community composition and sediment physical and chemical properties, while septic tank density was not. Sites with high EI were sandier, with less fine sediment and lower organic carbon content, higher sediment cations (calcium, sodium and magnesium) and water filterable reactive phosphorus concentrations. These were also the best small-scale environmental variables that explained denitrifying community composition. Among our study streams, which differed in the degree of urban stormwater impact, sediment grain size and carbon content are the most likely drivers of change in community composition. Denitrifying community composition is another in a long list of ecological indicators that suggest the profound degradation of streams is caused by urban stormwater runoff. While the relationships between denitrifying community composition and denitrification rates are yet to be unequivocally established, landscape-scale indices of environmental impact such as EI may prove to be useful indicators of change in microbial communities.}, }
@article {pmid21384214, year = {2011}, author = {Endoh, R and Suzuki, M and Okada, G and Takeuchi, Y and Futai, K}, title = {Fungus symbionts colonizing the galleries of the ambrosia beetle Platypus quercivorus.}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {106-120}, pmid = {21384214}, issn = {1432-184X}, mesh = {Ambrosia/*parasitology ; Animals ; Fungi/classification/genetics/*isolation &amp; purification/*physiology ; Molecular Sequence Data ; Phylogeny ; Plant Diseases/*parasitology ; *Symbiosis ; Weevils/*microbiology ; }, abstract = {Isolations were made to determine the fungal symbionts colonizing Platypus quercivorus beetle galleries of dead or dying Quercus laurifolia, Castanopsis cuspidata, Quercus serrata, Quercus crispula, and Quercus robur. For these studies, logs from oak wilt-killed trees were collected from Kyoto Prefecture, Japan. Fungi were isolated from the: (1) entrances of beetle galleries, (2) vertical galleries, (3) lateral galleries, and (4) the larval cradle of P. quercivorus in each host tree. Among the fungus colonies which appeared on YM agar plates, 1,219 were isolated as the representative isolates for fungus species inhabiting in the galleries based on their cultural characteristics. The validity of the visual classification of the fungus colonies was checked and if necessary properly corrected using microsatellite-primed PCR fingerprints. The nucleotide sequence of the D1/D2 region of the large subunit nuclear rRNA gene detected 38 fungus species (104 strains) of which three species, i.e., Candida sp. 3, Candida kashinagacola (both yeasts), and the filamentous fungus Raffaelea quercivora were isolated from all the tree species. The two yeasts were most prevalent in the interior of galleries, regardless of host tree species, suggesting their close association with the beetle. A culture-independent method, terminal restriction fragment length polymorphism (T-RFLP) analysis was also used to characterize the fungus flora of beetle galleries. T-RFLP patterns showed that yeast species belonging to the genus Ambrosiozyma frequently occurred on the gallery walls along with the two Candida species. Ours is the first report showing the specific fungi inhabiting the galleries of a platypodid ambrosia beetle.}, }
@article {pmid21377821, year = {2011}, author = {Hayes, D and Izzard, L and Seviour, R}, title = {Microbial ecology of autothermal thermophilic aerobic digester (ATAD) systems for treating waste activated sludge.}, journal = {Systematic and applied microbiology}, volume = {34}, number = {2}, pages = {127-138}, doi = {10.1016/j.syapm.2010.11.017}, pmid = {21377821}, issn = {1618-0984}, mesh = {Actinobacteria/genetics ; *Biodegradation, Environmental ; *Biota ; Clostridium/genetics ; Denaturing Gradient Gel Electrophoresis ; Geobacillus/genetics/isolation &amp; purification ; Hot Temperature ; Humans ; In Situ Hybridization, Fluorescence ; Microbial Consortia/*genetics ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Thermus thermophilus/genetics/isolation &amp; purification ; }, abstract = {Despite their widespread use, our understanding of the microbial ecology of the autothermal thermophilic aerobic digesters (ATAD) used to dispose of sludge from wastewater treatment plants is poor. Applying both culture-dependent and molecular methods to two ATAD systems in Victoria, Australia treating different wastewaters revealed that their communities were highly specialized. Denaturing gradient gel electrophoresis (DGGE) profiling suggested differences in their population compositions and both changed over time. However, both showed low level biodiversity, and contained several novel bacterial populations. 16S rRNA clone library data and FISH analyses showed that Thermus thermophilus dominated both communities and that of a third ATAD plant in NSW (more than 90% of the total bacterial biovolume in repeated samples taken from each of the three ATAD plants). Culture-dependent methods also showed Geobacillus spp. were present in both Victorian communities. Nevertheless, the ecophysiology of these populations and their putative roles in sludge digestion remain unclear. FISH/microautoradiographic studies did not provide conclusive data elucidating which substrate/s T. thermophilus might utilize in the ATAD reactors.}, }
@article {pmid21373815, year = {2011}, author = {Kim, DY and Countway, PD and Gast, RJ and Caron, DA}, title = {Rapid shifts in the structure and composition of a protistan assemblage during bottle incubations affect estimates of total protistan species richness.}, journal = {Microbial ecology}, volume = {62}, number = {2}, pages = {383-398}, pmid = {21373815}, issn = {1432-184X}, mesh = {Base Sequence ; *Biota ; Chlorophyll/analysis ; Chlorophyll A ; Culture Techniques/methods ; DNA, Protozoan/genetics ; Eukaryota/classification/drug effects/genetics/*growth &amp; development ; Genes, rRNA ; Iron/pharmacology ; Molecular Sequence Data ; Nitrogen/pharmacology ; Phosphorus/pharmacology ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Seawater ; Sequence Analysis, DNA ; }, abstract = {Changes in the structure and composition of a protistan community were characterized through the analysis of small-subunit ribosomal RNA gene (18S) sequences for a 3-day bottle incubation using a single sample collected in the western North Atlantic. Cloning and sequencing was used to investigate changes in perceived species richness and diversity as a consequence of environmental perturbation. The treatments included a control (unamended seawater), inorganic nutrient enrichment, and enrichment with a complex organic mixture. Five clone libraries were constructed and analyzed at the time of collection (t-0 h) and after 24 (t-24 h) and 72 (t-72 h) h for the control, and at t-72 h for the inorganic and organic enrichments, resulting in an analysis of 1,626 partial 18S rDNA sequences that clustered into 238 operational taxonomic units (OTUs). Analysis of the clone libraries revealed that protistan assemblages were highly dynamic and changed substantially at both the OTU level and higher taxonomic classifications during time frames consistent with many oceanographic methods used for measuring biological rates. Changes were most dramatic in enrichments, which yielded community compositions that were strongly dominated by one or a few taxa. Changes in community structure during incubation dramatically influenced estimates of species richness, which were substantially lower with longer incubation and especially with amendment, even though all incubated samples originated from the same aliquot of seawater. Containment and enrichment of the seawater sample led to the detection of otherwise undetected protistan taxa, suggesting that characterization of protistan diversity in a sample only at the time of collection could lead to an underrepresentation of unique taxa. Additionally, the rapid increase in the relative abundance of some members of the "rare biosphere" in our results implies an ecological importance of at least some of the taxa comprising the "rare biosphere."}, }
@article {pmid21373814, year = {2011}, author = {Santos-González, JC and Nallanchakravarthula, S and Alström, S and Finlay, RD}, title = {Soil, but not cultivar, shapes the structure of arbuscular mycorrhizal fungal assemblages associated with strawberry.}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {25-35}, pmid = {21373814}, issn = {1432-184X}, mesh = {Fragaria/*microbiology ; Fungi/*classification/genetics/growth &amp; development/isolation &amp; purification ; Molecular Sequence Data ; Mycorrhizae/*classification/genetics/growth &amp; development/isolation &amp; purification ; *Phylogeny ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Arbuscular mycorrhizal fungi are widespread plant symbionts occurring in most agricultural crops, where they can play key roles in the growth and health of their plant hosts. Plant benefits can depend on the identity of the associated arbuscular mycorrhizal fungi (AMF), but little is known about the identity of the fungal partners in most agricultural systems. In this study, we describe the AMF assemblages associated with four cultivars of strawberry in an outdoor experiment using two field soils with different origin and management history. Assemblages were characterised by clone library sequencing of 18S rRNA gene fragments. Soil dramatically influenced the degree of mycorrhizal colonisation and AMF assemblage structure in the roots. No differences were observed between cultivars. Fungi belonging to the genus Acaulospora dominated the AMF assemblages in one soil, but they were not detected in the other. These results suggest that physicochemical soil characteristics and management can play a role in determining the identity and structure of microbial communities associated with particular hosts in agricultural systems.}, }
@article {pmid21368115, year = {2011}, author = {Werner, JJ and Knights, D and Garcia, ML and Scalfone, NB and Smith, S and Yarasheski, K and Cummings, TA and Beers, AR and Knight, R and Angenent, LT}, title = {Bacterial community structures are unique and resilient in full-scale bioenergy systems.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {10}, pages = {4158-4163}, pmid = {21368115}, issn = {1091-6490}, support = {NIDDK05634//PHS HHS/United States ; NCRR000954//PHS HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; NIDDK020579//PHS HHS/United States ; P41 RR000954/RR/NCRR NIH HHS/United States ; }, mesh = {Energy Metabolism ; *Microbiology ; Phylogeny ; }, abstract = {Anaerobic digestion is the most successful bioenergy technology worldwide with, at its core, undefined microbial communities that have poorly understood dynamics. Here, we investigated the relationships of bacterial community structure (>400,000 16S rRNA gene sequences for 112 samples) with function (i.e., bioreactor performance) and environment (i.e., operating conditions) in a yearlong monthly time series of nine full-scale bioreactor facilities treating brewery wastewater (>20,000 measurements). Each of the nine facilities had a unique community structure with an unprecedented level of stability. Using machine learning, we identified a small subset of operational taxonomic units (OTUs; 145 out of 4,962), which predicted the location of the facility of origin for almost every sample (96.4% accuracy). Of these 145 OTUs, syntrophic bacteria were systematically overrepresented, demonstrating that syntrophs rebounded following disturbances. This indicates that resilience, rather than dynamic competition, played an important role in maintaining the necessary syntrophic populations. In addition, we explained the observed phylogenetic differences between all samples on the basis of a subset of environmental gradients (using constrained ordination) and found stronger relationships between community structure and its function rather than its environment. These relationships were strongest for two performance variables--methanogenic activity and substrate removal efficiency--both of which were also affected by microbial ecology because these variables were correlated with community evenness (at any given time) and variability in phylogenetic structure (over time), respectively. Thus, we quantified relationships between community structure and function, which opens the door to engineer communities with superior functions.}, }
@article {pmid21366818, year = {2012}, author = {Suenaga, H}, title = {Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities.}, journal = {Environmental microbiology}, volume = {14}, number = {1}, pages = {13-22}, doi = {10.1111/j.1462-2920.2011.02438.x}, pmid = {21366818}, issn = {1462-2920}, mesh = {Ecology/methods ; *Ecosystem ; Environment ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/*methods ; Microbiological Techniques/*methods ; *Multigene Family ; Sequence Analysis, DNA/methods ; }, abstract = {A major research goal in microbial ecology is to understand the relationship between gene organization and function involved in environmental processes of potential interest. Given that more than an estimated 99% of microorganisms in most environments are not amenable to culturing, methods for culture-independent studies of genes of interest have been developed. The wealth of metagenomic approaches allows environmental microbiologists to directly explore the enormous genetic diversity of microbial communities. However, it is extremely difficult to obtain the appropriate sequencing depth of any particular gene that can entirely represent the complexity of microbial metagenomes and be able to draw meaningful conclusions about these communities. This review presents a summary of the metagenomic approaches that have been useful for collecting more information about specific genes. Specific subsets of metagenomes that focus on sequence analysis were selected in each metagenomic studies. This 'targeted metagenomics' approach will provide extensive insight into the functional, ecological and evolutionary patterns of important genes found in microorganisms from various ecosystems.}, }
@article {pmid21365233, year = {2011}, author = {Cuong, ND and Nicolaisen, MH and Sørensen, J and Olsson, S}, title = {Hyphae-colonizing Burkholderia sp.--a new source of biological control agents against sheath blight disease (Rhizoctonia solani AG1-IA) in rice.}, journal = {Microbial ecology}, volume = {62}, number = {2}, pages = {425-434}, pmid = {21365233}, issn = {1432-184X}, mesh = {Antibiosis ; Bacillus/genetics/growth &amp; development/isolation &amp; purification/metabolism ; *Biological Control Agents ; Burkholderia/classification/genetics/*growth &amp; development/isolation &amp; purification ; Colony Count, Microbial ; Crops, Agricultural/microbiology ; Genes, rRNA ; Hyphae/physiology ; Oryza/*microbiology ; Phylogeny ; Plant Diseases/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizoctonia/*growth &amp; development/isolation &amp; purification ; Soil Microbiology ; Water/chemistry ; }, abstract = {Sheath blight infection of rice by Rhizoctonia solani Kühn AG1-IA often results in serious yield losses in intensive rice cultivation. Biological control agents (BCAs) have previously been isolated but poor efficiency is often observed when applied under field conditions. This study compares a traditional dual-culture plate assay and a new water-surface microcosm assay for isolation of antagonistic soil bacteria. In the water-surface microcosm assay, floating pathogen mycelium is used as a source for isolation of hyphae-colonizing soil bacteria (HCSB), which are subsequently screened for antagonism. Ten antagonistic soil bacteria (ASB) isolated from a variety of Vietnamese rice soils using dual-culture plates were found to be affiliated with Bacillus based on 16S rRNA gene sequencing. However, all the ASB isolates grew poorly and showed no antagonism in the water-surface microcosm assay. In contrast, 11 (out of 13) HCSB isolates affiliated with Burkholderia sp. all grew well by colonizing the hyphae in the microcosms. Two of the Burkholderia sp. isolates, assigned to B. vietnamiensis based on recA gene sequencing, strongly inhibited fungal growth in both the dual-culture and water-surface microcosm assays; HCSB isolates affiliated to other species or species groups showed limited or no inhibition of R. solani in the microcosms. Our results suggest that HCSB obtained from floating pathogen hyphae can be a new source for isolation of efficient BCAs against R. solani, as the isolation assay mimics the natural habitat for fungal-bacterial interaction in the fields.}, }
@article {pmid21365232, year = {2011}, author = {Hamilton, TL and Boyd, ES and Peters, JW}, title = {Environmental constraints underpin the distribution and phylogenetic diversity of nifH in the Yellowstone geothermal complex.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {860-870}, pmid = {21365232}, issn = {1432-184X}, mesh = {Bacteria/*classification/enzymology/genetics/*isolation &amp; purification ; Bacterial Proteins/*genetics ; *Genetic Variation ; Hot Springs/*microbiology ; Molecular Sequence Data ; Oxidoreductases/*genetics ; *Phylogeny ; Temperature ; Wyoming ; }, abstract = {Biological nitrogen fixation is a keystone process in many ecosystems, providing bioavailable forms of fixed nitrogen for members of the community. In the present study, degenerate primers targeting the nitrogenase iron protein-encoding gene (nifH) were designed and employed to investigate the physical and chemical parameters that underpin the distribution and diversity of nifH as a proxy for nitrogen-fixing organisms in the geothermal springs of Yellowstone National Park (YNP), Wyoming. nifH was detected in 57 of the 64 YNP springs examined, which varied in pH from 1.90 to 9.78 and temperature from 16°C to 89°C. This suggested that the distribution of nifH in YNP is widespread and is not constrained by pH and temperature alone. Phylogenetic and statistical analysis of nifH recovered from 13 different geothermal spring environments indicated that the phylogeny exhibits evidence for both geographical and ecological structure. Model selection indicated that the phylogenetic relatedness of nifH assemblages could be best explained by the geographic distance between sampling sites. This suggests that nifH assemblages are dispersal limited with respect to the fragmented nature of the YNP geothermal spring environment. The second highest ranking explanatory variable for predicting the phylogenetic relatedness of nifH assemblages was spring water conductivity (a proxy for salinity), suggesting that salinity may constrain the distribution of nifH lineages in geographically isolated YNP spring ecosystems. In summary, these results indicate a widespread distribution of nifH in YNP springs, and suggest a role for geographical and ecological factors in constraining the distribution of nifH lineages in the YNP geothermal complex.}, }
@article {pmid21365231, year = {2011}, author = {Blazewicz, SJ and Schwartz, E}, title = {Dynamics of [18]O incorporation from H2 [18]O into soil microbial DNA.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {911-916}, pmid = {21365231}, issn = {1432-184X}, mesh = {Bacteria/chemistry/genetics/isolation &amp; purification/*metabolism ; DNA, Bacterial/analysis/genetics/*metabolism ; Oxygen Isotopes/analysis/*metabolism ; Soil/analysis ; Soil Microbiology ; Water/*analysis/metabolism ; }, abstract = {Heavy water (H(2)(18)O) has been used to label DNA of soil microorganisms in stable isotope probing experiments, yet no measurements have been reported for the (18)O content of DNA from soil incubated with heavy water. Here we present the first measurements of atom% (18)O for DNA extracted from soil incubated with the addition of H(2)(18)O. Four experiments were conducted to test how the atom% (18)O of DNA, extracted from Ponderosa Pine forest soil incubated with heavy water, was affected by the following variables: (1) time, (2) nutrients, (3) soil moisture, and (4) atom% (18)O of added H(2)O. In the time series experiment, the atom% (18)O of DNA increased linearly (R(2) = 0.994, p < 0.01) over the first 72 h of incubation. In the nutrient addition experiment, there was a positive correlation (R(2) = 0.991, p = 0.006) between the log(10) of the amount of tryptic soy broth, a complex nutrient broth, added to soil and the log(10) of the atom% (18)O of DNA. For the experiment where soil moisture was manipulated, the atom% (18)O of DNA increased with higher soil moisture until soil moisture reached 30%, above which (18)O enrichment of DNA declined as soils became more saturated. When the atom% (18)O for H(2)O added was varied, there was a positive linear relationship between the atom% (18)O of the added water and the atom% (18)O of the DNA. Results indicate that quantification of (18)O incorporated into DNA from H(2)(18)O has potential to be used as a proxy for microbial growth in soil.}, }
@article {pmid21361997, year = {2011}, author = {Van den Abbeele, P and Van de Wiele, T and Verstraete, W and Possemiers, S}, title = {The host selects mucosal and luminal associations of coevolved gut microorganisms: a novel concept.}, journal = {FEMS microbiology reviews}, volume = {35}, number = {4}, pages = {681-704}, doi = {10.1111/j.1574-6976.2011.00270.x}, pmid = {21361997}, issn = {1574-6976}, mesh = {Animals ; Asthma/immunology/microbiology ; Biological Evolution ; Gastrointestinal Tract/immunology/*microbiology ; Host-Pathogen Interactions ; Humans ; Hypersensitivity/immunology/microbiology ; Immunity, Innate/immunology ; Immunity, Mucosal/immunology ; Inflammatory Bowel Diseases/immunology/microbiology ; Intestinal Mucosa/immunology/microbiology ; Models, Biological ; Obesity/immunology/microbiology ; *Symbiosis ; Vertebrates/immunology/*microbiology ; }, abstract = {Along the human gastrointestinal tract, microorganisms are confronted with multiple barriers. Besides selective physical conditions, the epithelium is regularly replaced and covered with a protective mucus layer trapping immune molecules. Recent insights into host defense strategies show that the host selects the intestinal microbiota, particularly the mucosa-associated microbial community. In this context, humans coevolved with thousands of intestinal microbial species that have adapted to provide host benefits, while avoiding pathogenic behavior that might destabilize their host interaction. While mucosal microorganisms would be crucial for immunological priming, luminal microorganisms would be important for nutrient digestion. Further, we propose that the intestinal microorganisms also coevolved with each other, leading to coherently organized, resilient microbial associations. During disturbances, functionally redundant members become more abundant and are crucial for preserving community functionality. The outside of the mucus layer, where host defense molecules are more diluted, could serve as an environment where microorganisms are protected from disturbances in the lumen and from where they can recolonize the lumen after perturbations. This might explain the remarkable temporal stability of microbial communities. Finally, commensals that become renegade or a decreased exposure to essential coevolved microorganisms may cause particular health problems such as inflammatory bowel diseases, obesity or allergies.}, }
@article {pmid21360147, year = {2011}, author = {De Clippeleir, H and Defoirdt, T and Vanhaecke, L and Vlaeminck, SE and Carballa, M and Verstraete, W and Boon, N}, title = {Long-chain acylhomoserine lactones increase the anoxic ammonium oxidation rate in an OLAND biofilm.}, journal = {Applied microbiology and biotechnology}, volume = {90}, number = {4}, pages = {1511-1519}, doi = {10.1007/s00253-011-3177-7}, pmid = {21360147}, issn = {1432-0614}, mesh = {Acyl-Butyrolactones/chemistry/*metabolism ; Bacteria/chemistry/*metabolism ; *Biofilms ; Bioreactors/microbiology ; Denitrification ; Kinetics ; Nitrification ; Oxygen/*metabolism ; Quaternary Ammonium Compounds/chemistry/*metabolism ; }, abstract = {The oxygen-limited autotrophic nitrification/denitrification (OLAND) process comprises one-stage partial nitritation and anammox, catalyzed by aerobic and anoxic ammonium-oxidizing bacteria (AerAOB and AnAOB), respectively. The goal of this study was to investigate whether quorum sensing influences anoxic ammonium oxidation in an OLAND biofilm, with AnAOB colonizing 13% of the biofilm, as determined with fluorescent in situ hybridization (FISH). At high biomass concentrations, the specific anoxic ammonium oxidation rate of the OLAND biofilm significantly increased with a factor of 1.5 ± 0.2 compared to low biomass concentrations. Supernatant obtained from the biofilm showed no ammonium-oxidizing activity on itself, but its addition to low OLAND biomass concentrations resulted in a significant activity increase of the biomass. In the biofilm supernatant, the presence of long-chain acylhomoserine lactones (AHLs) was shown using the reporter strain Chromobacterium violaceum CV026, and one specific AHL, N-dodecanoyl homoserine lactone (C(12)-HSL), was identified via LC-MS/MS. Furthermore, C(12)-HSL was detected in an AnAOB-enriched community, but not in an AerAOB-enriched community. Addition of C(12)-HSL to low OLAND biomass concentrations resulted in a significantly higher ammonium oxidation rate (p < 0.05). To our knowledge, this is the first report demonstrating that AHLs enhance the anoxic ammonium oxidation process. Future work should confirm which species are responsible for the in situ production of C(12)-HSL in AnAOB-based applications.}, }
@article {pmid21360141, year = {2011}, author = {Landesman, WJ and Dighton, J}, title = {Shifts in microbial biomass and the bacteria: fungi ratio occur under field conditions within 3 h after rainfall.}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {228-236}, pmid = {21360141}, issn = {1432-184X}, mesh = {Bacteria/*growth &amp; development ; Biomass ; Climate Change ; Droughts ; *Ecosystem ; Fungi/*growth &amp; development ; Rain ; Seasons ; Soil/analysis ; *Soil Microbiology ; Water/analysis ; }, abstract = {Increases in the frequency of soil drying and extreme precipitation projected by climate models may have important consequences for soil microbial community composition. However, the microbial response may occur over short time scales not captured by traditional sampling methods. Following a 2-year rainfall exclusion experiment in a pine forest ecosystem, we used phospholipid fatty acid profiling to measure the hourly, daily, and weekly-scale response of soil microbial biomass and the bacteria/fungi ratio to a precipitation event. We compared this response to the rewetting of un-manipulated plots. Within 3 h of watering, we detected increases in fungal and bacterial biomass of 125% and 66%, respectively, in un-manipulated plots, but only small increases in biomass within drought plots. We detected a decrease in the bacteria/fungi ratio in un-manipulated plots and an increase in this ratio in the drought plots. This surprising result was likely caused by root mortality (resulting from the previous 2-year rain exclusion) and an increase in ammonium pools in the drought plots, both of which could have suppressed fungal growth. Whereas past research suggests that soil microbes are resistant to drying-rewetting stress and to changes in annual precipitation patterns, here we show that microbes are sensitive to soil drying, but highly resilient, recovering within hours or days of a rain event. We propose that more emphasis be placed on hourly-scale field measurements of soil microbial community structure in future climate change studies.}, }
@article {pmid21360140, year = {2011}, author = {Neidig, N and Paul, RJ and Scheu, S and Jousset, A}, title = {Secondary metabolites of Pseudomonas fluorescens CHA0 drive complex non-trophic interactions with bacterivorous nematodes.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {853-859}, pmid = {21360140}, issn = {1432-184X}, mesh = {Animals ; Antinematodal Agents/*metabolism/pharmacology ; Caenorhabditis elegans/drug effects/microbiology/*physiology ; Predatory Behavior ; Pseudomonas fluorescens/chemistry/*metabolism ; Soil Microbiology ; }, abstract = {Non-trophic interactions are increasingly recognised as a key parameter of predator-prey interactions. In soil, predation by bacterivorous nematodes is a major selective pressure shaping soil bacterial communities, and many bacteria have evolved defence mechanisms such as toxicity. In this study, we show that extracellular secondary metabolites produced by the model soil bacterium Pseudomonas fluorescens CHA0 function as a complex defence strategy against bacterivorous nematodes. Using a collection of functional mutants lacking genes for the biosynthesis of one or several extracellular metabolites, we evaluated the impact of bacterial secondary metabolites on the survival and chemotactic behaviour of the nematode Caenorhabditis elegans. Additionally, we followed up the stress status of the nematodes by measuring the activation of the abnormal DAuer Formation (DAF) stress cascade. All studied secondary metabolites contributed to the toxicity of the bacteria, with hydrogen cyanide efficiently repelling the nematodes, and both hydrogen cyanide and 2,4-DAPG functioning as nematicides. Moreover, these metabolites elicited the DAF stress response cascade of C. elegans, showing that they affect nematode physiology already at sublethal concentrations. The results suggest that bacterial secondary metabolites responsible for the suppression of plant pathogens strongly inhibit bacterivorous nematodes and thus likely contribute to the resistance of bacteria against predators in soil.}, }
@article {pmid21360139, year = {2011}, author = {Trivedi, P and Spann, T and Wang, N}, title = {Isolation and characterization of beneficial bacteria associated with citrus roots in Florida.}, journal = {Microbial ecology}, volume = {62}, number = {2}, pages = {324-336}, pmid = {21360139}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/metabolism ; Azides/chemistry ; Bacteria/genetics/growth &amp; development/*isolation &amp; purification/metabolism ; Bacterial Proteins/metabolism ; Biological Control Agents ; Chitinases/biosynthesis ; Citrus sinensis/growth &amp; development/*microbiology ; Crops, Agricultural/growth &amp; development/microbiology ; Florida ; Indoleacetic Acids/metabolism ; Nitrogen Fixation ; Plant Diseases/microbiology ; Plant Roots/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Siderophores/biosynthesis ; *Soil Microbiology ; }, abstract = {Cultivable diversity of bacteria associated with citrus was investigated as part of a larger study to understand the roles of beneficial bacteria and utilize them to increase the productive capacity and sustainability of agro-ecosystems. Citrus roots from Huanglongbing (HLB) diseased symptomatic and asymptomatic citrus were used in this study. A total of 227 and 125 morphologically distinct colonies were isolated and characterized from HLB asymptomatic and symptomatic trees, respectively. We observed that the frequency of bacterial isolates possessing various plant beneficial properties was significantly higher in the asymptomatic samples. A total of 39 bacterial isolates showing a minimum of five beneficial traits related to mineral nutrition [phosphate (P) solubilization, siderophore production, nitrogen (N) fixation], development [indole acetic acid (IAA) synthesis], health [production of antibiotic and lytic enzymes (chitinase)], induction of systemic resistance [salicylic acid (SA) production], stress relief [production of 1-amino-cyclopropane-1-carboxylate deaminase] and production of quorum sensing [N-acyl homoserine lactones] signals were characterized. A bioassay using ethidium monoazide (EMA)-qPCR was developed to select bacteria antagonistic to Candidatus Liberibacter asiaticus. Using the modified EMA-qPCR assay, we found six bacterial isolates showing maximum similarity to Paenibacillus validus, Lysinibacillus fusiformis, Bacillus licheniformis, Pseudomonas putida, Microbacterium oleivorans, and Serratia plymutica could significantly reduce the population of viable Ca. L. asiaticus in HLB symptomatic leaf samples. In conclusion, we have isolated and characterized multiple beneficial bacterial strains from citrus roots which have the potential to enhance plant growth and suppress diseases.}, }
@article {pmid21360138, year = {2011}, author = {Wu, L and Lan, S and Zhang, D and Hu, C}, title = {Small-scale vertical distribution of algae and structure of lichen soil crusts.}, journal = {Microbial ecology}, volume = {62}, number = {3}, pages = {715-724}, pmid = {21360138}, issn = {1432-184X}, mesh = {*Biomass ; Chlorophyll/analysis ; Chlorophyta/growth &amp; development ; Cyanobacteria/growth &amp; development ; Diatoms/growth &amp; development ; Lichens/*growth &amp; development ; Polysaccharides/analysis ; Soil/*analysis ; *Soil Microbiology ; }, abstract = {Although many studies have been conducted on the ecological functions and ecophysiological characteristics of lichen soil crusts (LSCs), no explanation of these results has been provided based on crust structures. Using algae soil crusts (ASCs) as comparison, this work studied the small-scale vertical distribution of algal biomass and stratification in two types of LSCs, by combining the binocular stereomicroscope observations, microscope observations, plate cultures, chlorophyll analysis, and polysaccharides analysis. The results showed an obvious difference in the proportion but not the composition of the algae species between the ASCs and the two LSCs. Approximately 60% and 80% of the total algal biomass were concentrated in the top 1 mm of the soil profile and thalli in the ASCs and LSCs, respectively. This implies that symbiotic algae are the dominant species and primary organic carbon producers in LSCs, and the algal biomass decreased with the depth in both the ASCs and LSCs. The small-scale vertical distributions of the crustal algal biomass and polysaccharides were characterized by obvious successional stage, whereas these were unrelated to the crust type within the successional stage. Additionally, a large amount of fungi, which were always piercing the entire crusts, were observed in the LSCs, but only occasionally in the ASCs. These special structures are purported to cause the LSCs to achieve specific ecological functions, such as higher carbon fixation and greater compressive strength. High biomass, large living space, and advantageous resource utilization privilege suggest that the lichen association is mutualistic and the direction from ASCs to LSCs is developmental.}, }
@article {pmid21359558, year = {2011}, author = {Cámara, B and De los Ríos, A and Urizal, M and de Buergo, MA and Varas, MJ and Fort, R and Ascaso, C}, title = {Characterizing the microbial colonization of a dolostone quarry: implications for stone biodeterioration and response to biocide treatments.}, journal = {Microbial ecology}, volume = {62}, number = {2}, pages = {299-313}, pmid = {21359558}, issn = {1432-184X}, mesh = {Biota ; *Biotransformation ; Calcium Carbonate/*chemistry ; Colorimetry ; Construction Materials/*microbiology ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Denaturing Gradient Gel Electrophoresis ; Disinfectants/*pharmacology ; Genes, rRNA ; Lichens/drug effects/*growth &amp; development/isolation &amp; purification ; Magnesium/*chemistry ; Microscopy, Electron, Scanning ; Porosity ; Spain ; }, abstract = {This study examines the microbial colonization of three fronts of an abandoned dolostone quarry (Redueña, Madrid, Spain) exposed to atmospheric conditions for different time periods since Roman times to the present. Through scanning electron microscopy in backscattered electron mode (SEM-BSE), endolithic colonization was predominantly detected in the most recently exposed front, while in the longer exposed quarry fronts, epilithic forms of growth were most often observed. These observations were confirmed by denaturing gradient gel electrophoresis (DGGE) analysis. Based on the distribution pattern of microbial colonization in the different quarry fronts, we then established a sequence of colonization events that took place over this long time frame. Bioalteration processes related to this sequential colonization were also identified. Characterizing these sequential processes can be useful for interpreting biodeterioration processes in historic dolostone monuments, especially those affecting constructions in the area of the Redueña stone quarry. In a second experimental stage, different biocide treatments were tested on this quarry rock to find the best way to avoid the microbial colonization effects identified. Through combined SEM-BSE/DGGE analysis, the efficacy of several biocides against the microorganisms inhabiting the dolostones was assessed after 4 and 16 months treatment. In general, all treatments were effective at reducing around 80% of the lichen cover, although effects on endolithic lithobiontic communities were dependent on how well the rock surface had been mechanically cleaned prior to treatment and gradually disappeared over time.}, }
@article {pmid21357458, year = {2012}, author = {Justé, A and Van Trappen, S and Verreth, C and Cleenwerck, I and De Vos, P and Lievens, B and Willems, KA}, title = {Characterization of Tetragenococcus strains from sugar thick juice reveals a novel species, Tetragenococcus osmophilus sp. nov., and divides Tetragenococcus halophilus into two subspecies, T. halophilus subsp. halophilus subsp. nov. and T. halophilus subsp. flandriensis subsp. nov.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {62}, number = {Pt 1}, pages = {129-137}, doi = {10.1099/ijs.0.029157-0}, pmid = {21357458}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; Belgium ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Enterococcaceae/*classification/genetics/*isolation &amp; purification/physiology ; *Food Microbiology ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Most bacteria recovered so far from sugar thick juice during storage represent strains of the species Tetragenococcus halophilus. Recently, several Gram-positive, non-motile, non-spore-forming cocci with other physiological and genetic traits were isolated from sugar thick juice samples from different origins. In this study, representative isolates were investigated using a polyphasic taxonomic approach. The 16S rRNA gene sequence similarity between these isolates and their closest relative, Tetragenococcus muriaticus, was 97.4%. The level of DNA-DNA relatedness between isolate T1(T), representing the newly found Tetragenococcus isolates, and T. muriaticus was 57%. Isolate T1(T) had a DNA G+C content of 36.7 mol%. Phylogenetic data and genomic and phenotypic features demonstrated that the isolates represent a novel species, for which the name Tetragenococcus osmophilus sp. nov. is proposed with T1(T) as the type strain (=LMG 26041(T) =DSM 23765(T)). Additionally, T. halophilus isolates from high-salt and high-sugar environments showed clear differences in several physiological and genetic characteristics like RAPD fingerprints and 16S rRNA gene sequences. DNA-DNA hybridizations, however, showed 79 to 80% relatedness between osmophilic and halophilic T. halophilus isolates, demonstrating that the different strains belong to the same species. Based on the phenotypic and genotypic differences observed, as well as the different origins of the strains and the industrial relevance of thick juice degradation, two subspecies of T. halophilus are described in this manuscript: T. halophilus subsp. halophilus subsp. nov. for the strains isolated from salt media and T. halophilus subsp. flandriensis subsp. nov. for the strains isolated from sugar-rich environments, which were first isolated in Flanders, Belgium. The type strains for the subspecies are IAM 1676(T) (=LMG 11490(T) =DSM 20339(T)) and T5(T) (=LMG 26042(T) =DSM 23766(T)), respectively.}, }
@article {pmid21354780, year = {2011}, author = {Shapiro, OH and Kushmaro, A}, title = {Bacteriophage ecology in environmental biotechnology processes.}, journal = {Current opinion in biotechnology}, volume = {22}, number = {3}, pages = {449-455}, doi = {10.1016/j.copbio.2011.01.012}, pmid = {21354780}, issn = {1879-0429}, mesh = {Bacteria/growth &amp; development/*virology ; Bacteriophages/genetics/*pathogenicity ; Biodiversity ; Biotechnology ; Ecology ; Ecosystem ; Food Chain ; Waste Disposal, Fluid ; Water Microbiology ; }, abstract = {Heterotrophic bacteria are an integral part of any environmental biotechnology process (EBP). Therefore, factors controlling bacterial abundance, activity, and community composition are central to the understanding of such processes. Among these factors, top-down control by bacteriophage predation has so far received very limited attention. With over 10(8) particles per ml, phage appear to be the most numerous biological entities in EBP. Phage populations in EBP appear to be highly dynamic and to correlate with the population dynamics of their hosts and genomic evidence suggests bacteria evolve to avoid phage predation. Clearly, there is much to learn regarding bacteriophage in EBP before we can truly understand the microbial ecology of these globally important systems.}, }
@article {pmid21351251, year = {2011}, author = {Vogel, RF and Hammes, WP and Habermeyer, M and Engel, KH and Knorr, D and Eisenbrand, G and , }, title = {Microbial food cultures--opinion of the Senate Commission on Food Safety (SKLM) of the German Research Foundation (DFG).}, journal = {Molecular nutrition &amp; food research}, volume = {55}, number = {4}, pages = {654-662}, doi = {10.1002/mnfr.201100010}, pmid = {21351251}, issn = {1613-4133}, mesh = {Cell Culture Techniques/standards ; Drug Resistance, Microbial ; Fermentation ; Food Handling/standards ; Food Microbiology/legislation &amp; jurisprudence/methods/*standards ; Food Safety ; Foodborne Diseases/*prevention &amp; control ; Fungi/growth &amp; development/metabolism/pathogenicity ; Germany ; Gram-Positive Bacteria/growth &amp; development/metabolism/pathogenicity ; Microbiological Techniques/standards ; Probiotics/adverse effects/standards ; Terminology as Topic ; }, abstract = {In the EU, there are no specific legal regulations regarding microbial food cultures. However, at European and national level, there are regulations that require microbial cultures to be checked in terms of their compliance with legal requirements. Due to the lack of definitions for microbial food cultures with various applications, there are uncertainties regarding how they are to be assessed. The increased elaboration of microbial ecology and modern taxonomy has allowed the description of numerous new species that are attractive for use in food cultures or are already in use, on which, however, only limited experience is available. In view of these developments, the SKLM has prepared this statement, focusing on definitions, gaps in knowledge and further research needs. It aims to support the producers and users of microbial cultures as well as authorities responsible for consumer health protection with respect to safety assessment and to contribute to consumer information. The scientific status concerning these cultures in food technology, the traditional roots of their application and their potential for sustaining and/or furthering food variety and quality have not been adequately described up to now. This is the subject of the present SKLM statement. In addition, definitions are proposed for cultures used in food technology that may also be useful for the assessment in a legal context. The opinion was released in German on 29 March 2010, the English version was agreed on 15 November 2010.}, }
@article {pmid21347721, year = {2011}, author = {Prieto, P and Schilirò, E and Maldonado-González, MM and Valderrama, R and Barroso-Albarracín, JB and Mercado-Blanco, J}, title = {Root hairs play a key role in the endophytic colonization of olive roots by Pseudomonas spp. with biocontrol activity.}, journal = {Microbial ecology}, volume = {62}, number = {2}, pages = {435-445}, pmid = {21347721}, issn = {1432-184X}, mesh = {Agricultural Inoculants/*growth &amp; development ; *Biological Control Agents ; Endophytes/*growth &amp; development ; Luminescent Proteins/metabolism ; Microscopy, Confocal ; Olea/growth &amp; development/*microbiology ; Plant Roots/*microbiology ; Pseudomonas/*growth &amp; development/isolation &amp; purification ; }, abstract = {The use of indigenous bacterial root endophytes with biocontrol activity against soil-borne phytopathogens is an environmentally-friendly and ecologically-efficient action within an integrated disease management framework. The earliest steps of olive root colonization by Pseudomonas fluorescens PICF7 and Pseudomonas putida PICP2, effective biocontrol agents (BCAs) against Verticillium wilt of olive (Olea europaea L.) caused by the fungus Verticillium dahliae Kleb., are here described. A gnotobiotic study system using in vitro propagated olive plants, differential fluorescent-protein tagging of bacteria, and confocal laser scanning microscopy analysis have been successfully used to examine olive roots-Pseudomonas spp. interactions at the single-cell level. In vivo simultaneous visualization of PICF7 and PICP2 cells on/in root tissues enabled to discard competition between the two bacterial strains during root colonization. Results demonstrated that both BCAs are able to endophytically colonized olive root tissues. Moreover, results suggest a pivotal role of root hairs in root colonization by both biocontrol Pseudomonas spp. However, colonization of root hairs appeared to be a highly specific event, and only a very low number of root hairs were effectively colonized by introduced bacteria. Strains PICF7 and PICP2 can simultaneously colonize the same root hair, demonstrating that early colonization of a given root hair by one strain did not hinder subsequent attachment and penetration by the other. Since many environmental factors can affect the number, anatomy, development, and physiology of root hairs, colonization competence and biocontrol effectiveness of BCAs may be greatly influenced by root hair's fitness. Finally, the in vitro study system here reported has shown to be a suitable tool to investigate colonization processes of woody plant roots by microorganisms with biocontrol potential.}, }
@article {pmid21340737, year = {2011}, author = {Eaton, HL and De Lorme, M and Chaney, RL and Craig, AM}, title = {Ovine ruminal microbes are capable of biotransforming hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX).}, journal = {Microbial ecology}, volume = {62}, number = {2}, pages = {274-286}, pmid = {21340737}, issn = {1432-184X}, mesh = {Animals ; Archaea/genetics/growth &amp; development/isolation &amp; purification/metabolism ; Bacteria/genetics/growth &amp; development/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Chromatography, High Pressure Liquid ; Culture Media/chemistry ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Genes, rRNA ; Genetic Variation ; Male ; Microbial Consortia ; Nitrogen/metabolism ; Phylogeny ; Rumen/*microbiology ; Sequence Homology, Nucleic Acid ; Sheep/microbiology ; Time Factors ; Triazines/*metabolism ; }, abstract = {Bioremediation is of great interest in the detoxification of soil contaminated with residues from explosives such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Although there are numerous forms of in situ and ex situ bioremediation, ruminants would provide the option of an in situ bioreactor that could be transported to the site of contamination. Bovine rumen fluid has been previously shown to transform 2,4,6-trinitrotoluene (TNT), a similar compound, in 4 h. In this study, RDX incubated in whole ovine rumen fluid was nearly eliminated within 4 h. Whole ovine rumen fluid was then inoculated into five different types of media to select for archaeal and bacterial organisms capable of RDX biotransformation. Cultures containing 30 μg mL(-1) RDX were transferred each time the RDX concentration decreased to 5 μg mL(-1) or less. Time point samples were analyzed for RDX biotransformation by HPLC. The two fastest transforming enrichments were in methanogenic and low nitrogen basal media. After 21 days, DNA was extracted from all enrichments able to partially or completely transform RDX in 7 days or less. To understand microbial diversity, 16S rRNA-gene-targeted denaturing gradient gel electrophoresis (DGGE) fingerprinting was conducted. Cloning and sequencing of partial 16S rRNA fragments were performed on both low nitrogen basal and methanogenic media enrichments. Phylogenetic analysis revealed similar homologies to eight different bacterial and one archaeal genera classified under the phyla Firmicutes, Actinobacteria, and Euryarchaeota. After continuing enrichment for RDX degraders for 1 year, two consortia remained: one that transformed RDX in 4 days and one which had slowed after 2 months of transfers without RDX. DGGE comparison of the slower transforming consortium to the faster one showed identical banding patterns except one band. Homology matches to clones from the two consortia identified the same uncultured Clostridia genus in both; Sporanaerobacter acetigenes was identified only in the consortia able to completely transform RDX. This is the first study to examine the rumen as a potential bioremediation tool for soils contaminated with RDX, as well as to discover S. acetigenes in the rumen and its potential ability to metabolize this energetic compound.}, }
@article {pmid21340736, year = {2011}, author = {Van Puyvelde, S and Cloots, L and Engelen, K and Das, F and Marchal, K and Vanderleyden, J and Spaepen, S}, title = {Transcriptome analysis of the rhizosphere bacterium Azospirillum brasilense reveals an extensive auxin response.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {723-728}, pmid = {21340736}, issn = {1432-184X}, mesh = {Azospirillum brasilense/*genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; *Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Indoleacetic Acids/*metabolism ; Molecular Sequence Data ; *Rhizosphere ; }, abstract = {The rhizosphere bacterium Azospirillum brasilense produces the auxin indole-3-acetic acid (IAA) through the indole-3-pyruvate pathway. As we previously demonstrated that transcription of the indole-3-pyruvate decarboxylase (ipdC) gene is positively regulated by IAA, produced by A. brasilense itself or added exogenously, we performed a microarray analysis to study the overall effects of IAA on the transcriptome of A. brasilense. The transcriptomes of A. brasilense wild-type and the ipdC knockout mutant, both cultured in the absence and presence of exogenously added IAA, were compared.Interfering with the IAA biosynthesis/homeostasis in A. brasilense through inactivation of the ipdC gene or IAA addition results in much broader transcriptional changes than anticipated. Based on the multitude of changes observed by comparing the different transcriptomes, we can conclude that IAA is a signaling molecule in A. brasilense. It appears that the bacterium, when exposed to IAA, adapts itself to the plant rhizosphere, by changing its arsenal of transport proteins and cell surface proteins. A striking example of adaptation to IAA exposure, as happens in the rhizosphere, is the upregulation of a type VI secretion system (T6SS) in the presence of IAA. The T6SS is described as specifically involved in bacterium-eukaryotic host interactions. Additionally, many transcription factors show an altered regulation as well, indicating that the regulatory machinery of the bacterium is changing.}, }
@article {pmid21340735, year = {2011}, author = {Li, QQ and Wang, ET and Zhang, YZ and Zhang, YM and Tian, CF and Sui, XH and Chen, WF and Chen, WX}, title = {Diversity and biogeography of rhizobia isolated from root nodules of Glycine max grown in Hebei Province, China.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {917-931}, pmid = {21340735}, issn = {1432-184X}, mesh = {Bradyrhizobium/classification/genetics/*isolation &amp; purification/physiology ; China ; *Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Rhizobiaceae/classification/genetics/*isolation &amp; purification/physiology ; Root Nodules, Plant/*microbiology ; Glycine max/growth &amp; development/*microbiology/physiology ; Symbiosis ; }, abstract = {A total of 215 rhizobial strains were isolated and analyzed with 16S rRNA gene, 16S-23S intergenic spacer, housekeeping genes atpD, recA, and glnII, and symbiotic genes nifH and nodC to understand the genetic diversity of soybean rhizobia in Hebei province, China. All the strains except one were symbiotic bacteria classified into nine genospecies in the genera of Bradyrhizobium and Sinorhizobium. Surveys on the distribution of these rhizobia in different regions showed that Bradyrhizobium japonicum and Bradyrhizobium elkanii strains were found only in neutral to slightly alkaline soils whereas Bradyrhizobium yuanmingense, Bradyrhizobium liaoningense-related strains and strains of five Sinorhizobium genospecies were found in alkaline-saline soils. Correspondence and canonical correspondence analyses on the relationship of rhizobial distribution and their soil characteristics reveal that high soil pH, electrical conductivity, and potassium content favor distribution of the B. yuanmingense and the five Sinorhizobium species but inhibit B. japonicum and B. elkanii. High contents of available phosphorus and organic matters benefit Sinorhizobium fredii and B. liaoningense-related strains and inhibit the others groups mentioned above. The symbiotic gene (nifH and nodC) lineages among B. elkanii, B. japonicum, B. yuanmingense, and Sinorhizobium spp. were observed in the strains, signifying that vertical gene transfer was the main mechanism to maintain these genes in the soybean rhizobia. However, lateral transfer of symbiotic genes commonly in Sinorhizobium spp. and rarely in Bradyrhizobium spp. was also detected. These results showed the genetic diversity, the biogeography, and the soil determinant factors of soybean rhizobia in Hebei province of China.}, }
@article {pmid21336683, year = {2011}, author = {Tarbe, AL and Unrein, F and Stenuite, S and Pirlot, S and Sarmento, H and Sinyinza, D and Descy, JP}, title = {Protist herbivory: a key pathway in the pelagic food web of Lake Tanganyika.}, journal = {Microbial ecology}, volume = {62}, number = {2}, pages = {314-323}, pmid = {21336683}, issn = {1432-184X}, mesh = {Africa ; Bacterial Load ; Carbon/metabolism ; Cyanobacteria/growth &amp; development ; Eukaryota/growth &amp; development/*physiology ; *Food Chain ; Herbivory/*physiology ; *Lakes ; Microscopy, Fluorescence ; Phytoplankton/growth &amp; development ; Seasons ; Synechococcus/growth &amp; development ; *Water Microbiology ; }, abstract = {Herbivory and bacterivory by phagotrophic protists were estimated in the southern basin of the oligotrophic Lake Tanganyika at different seasons (in the rainy season in February-March 2007 and in the dry season in July-August 2006 and September 2007), using two independent methods: the selective inhibitor technique for assessing community grazing on picocyanobacteria (PCya) and fluorescently labelled bacteria (FLB) and Synechococcus (FLA) to estimate bacterivory and herbivory by phagotrophic nanoflagellates (NF) and ciliates. Protistan grazing impact on both heterotrophic bacteria and PCya was mainly due to NF, which contributed up to 96% of the microbial grazing. There was a clear selection of FLA by protists. PCya represented the main carbon source for both flagellates and ciliates in the mixolimnion, accounting for an average of 83% of the total carbon obtained from the ingestion of picoplanktonic organisms. Protists were the main consumers of particulate primary production (46-74% depending on season). Significant seasonal variation of grazing rates (0.011-0.041 h(-1)) was found, chiefly following variation of PCya production and biomass. Assuming a growth efficiency of 0.4, total protozoan production varied seasonally (189-313 g C m(-2) day(-1)) and was roughly half of particulate phytoplankton production. This study provides evidence that NF and PCya were tightly coupled in Lake Tanganyika and that herbivory by protists may be one of the reasons why this great lake has high productivity. Our results bring support to the idea that microbial herbivory is a major process in oligotrophic freshwater systems.}, }
@article {pmid21335340, year = {2011}, author = {Chan, YW and Mohr, R and Millard, AD and Holmes, AB and Larkum, AW and Whitworth, AL and Mann, NH and Scanlan, DJ and Hess, WR and Clokie, MR}, title = {Discovery of cyanophage genomes which contain mitochondrial DNA polymerase.}, journal = {Molecular biology and evolution}, volume = {28}, number = {8}, pages = {2269-2274}, doi = {10.1093/molbev/msr041}, pmid = {21335340}, issn = {1537-1719}, mesh = {Bacteriophages/classification/*enzymology/*genetics ; Cyanobacteria/virology ; DNA, Mitochondrial/*genetics ; DNA-Directed DNA Polymerase/*genetics/metabolism ; Evolution, Molecular ; Gene Expression Regulation, Viral ; Genome, Viral ; Phylogeny ; }, abstract = {DNA polymerase γ is a family A DNA polymerase responsible for the replication of mitochondrial DNA in eukaryotes. The origins of DNA polymerase γ have remained elusive because it is not present in any known bacterium, though it has been hypothesized that mitochondria may have inherited the enzyme by phage-mediated nonorthologous displacement. Here, we present an analysis of two full-length homologues of this gene, which were found in the genomes of two bacteriophages, which infect the chlorophyll-d containing cyanobacterium Acaryochloris marina. Phylogenetic analyses of these phage DNA polymerase γ proteins show that they branch deeply within the DNA polymerase γ clade and therefore share a common origin with their eukaryotic homologues. We also found homologues of these phage polymerases in the environmental Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA) database, which fell in the same clade. An analysis of the CAMERA assemblies containing the environmental homologues together with the filter fraction metadata indicated some of these assemblies may be of bacterial origin. We also show that the phage-encoded DNA polymerase γ is highly transcribed as the phage genomes are replicated. These findings provide data that may assist in reconstructing the evolution of mitochondria.}, }
@article {pmid21333271, year = {2011}, author = {Huang, CB and Alimova, Y and Myers, TM and Ebersole, JL}, title = {Short- and medium-chain fatty acids exhibit antimicrobial activity for oral microorganisms.}, journal = {Archives of oral biology}, volume = {56}, number = {7}, pages = {650-654}, pmid = {21333271}, issn = {1879-1506}, support = {R41 DE017265/DE/NIDCR NIH HHS/United States ; R41DE17265-01/DE/NIDCR NIH HHS/United States ; }, mesh = {Acetic Acid/pharmacology ; Aggregatibacter actinomycetemcomitans/drug effects ; Anti-Infective Agents/*pharmacology ; Biofilms/drug effects ; Butyric Acid/pharmacology ; Candida albicans/drug effects ; Caproates/pharmacology ; Caprylates/pharmacology ; Decanoic Acids/pharmacology ; Fatty Acids/*pharmacology ; Fatty Acids, Volatile/*pharmacology ; Formates/pharmacology ; Fusobacterium nucleatum/drug effects ; Hemiterpenes ; Humans ; Isobutyrates/pharmacology ; Lauric Acids/pharmacology ; Materials Testing ; Microbial Interactions/drug effects ; Mouth/*microbiology ; Myristic Acid/pharmacology ; Palmitic Acid/pharmacology ; Pentanoic Acids/pharmacology ; Porphyromonas gingivalis/drug effects ; Propionates/pharmacology ; Streptococcus gordonii/drug effects ; Streptococcus mutans/drug effects ; Streptococcus sanguis/drug effects ; }, abstract = {OBJECTIVES: This study assessed the antibacterial activity of short-, medium-, and long-chain fatty acids against various oral microorganisms.<br><br>METHODS: The short-chain fatty acids [formic acid (C1), acetic acid (C2), propionic acid (C3), butyric acid (C4), isobutyric acid (C4), isovaleric acid (C5), hexanoic acid (C6)], medium-chain fatty acids [octanoic acid (C8), capric acid (C10), lauric acid (12)], and long-chain fatty acids [myristic acid (C14), palmitic acid (C16)], were investigated for antimicrobial activity against Streptococcus mutans, Streptococcus gordonii, Streptococcus sanguis, Candida albicans, Aggregatibacter actinomycetemcomitans, Fusobacterium nucleatum, and Porphyromonas gingivalis.<br><br>RESULTS: The data demonstrated that the fatty acids exhibited patterns of inhibition against oral bacteria with some specificity that appeared related more to the bacterial species that the general structural characteristics of the microorganism. As a group the fatty acids were much less effective against C. albicans than the oral bacteria, with effectiveness limited to hexanoic, octanoic, and lauric acids. Formic acid, capric, and lauric acids were broadly inhibitory for the bacteria. Interestingly, fatty acids that are produced at metabolic end-products by a number of these bacteria, were specifically inactive against the producing species, whilst substantially inhibiting the growth of other oral microorganisms.<br><br>CONCLUSIONS: The results indicate that the antimicrobial activity of short-chain fatty acids (SCFAs), medium-chain fatty acids (MCFAs), long-chain fatty acids (LCFAs) could influence the microbial ecology in the oral cavity via at least 2 potential pathways. First, the agents delivered exogenously as therapeutic adjuncts could be packaged to enhance a microbial-regulatory environment in the subgingival sulcus. Second, it would be the intrinsic nature of these fatty acid inhibitors in contributing to the characteristics of the microbial biofilms, their evolution, and emergence of species within the biofilms. Further studies on these functions are required to better understand the nature of these potential microbial interactions in the biofilms.}, }
@article {pmid21331609, year = {2011}, author = {Rastogi, G and Barua, S and Sani, RK and Peyton, BM}, title = {Investigation of microbial populations in the extremely metal-contaminated Coeur d'Alene River sediments.}, journal = {Microbial ecology}, volume = {62}, number = {1}, pages = {1-13}, pmid = {21331609}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification/metabolism ; Bacterial Proteins/genetics ; Geologic Sediments/chemistry/*microbiology ; Metals, Heavy/analysis/*metabolism ; Mining ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers/chemistry/*microbiology ; Water Pollutants, Chemical/analysis/*metabolism ; Water Pollution, Chemical ; }, abstract = {The deposition of mine tailings generated from 125 years of sulfidic ore mining resulted in the enrichment of Coeur d'Alene River (CdAR) sediments with significant amounts of toxic heavy metals. A review of literature suggests that microbial populations play a pivotal role in the biogeochemical cycling of elements in such mining-impacted sedimentary environments. To assess the indigenous microbial communities associated with metal-enriched sediments of the CdAR, high-density 16S microarray (PhyloChip) and clone libraries specific to bacteria (16S rRNA), ammonia oxidizers (amoA), and methanogens (mcrA) were analyzed. PhyloChip analysis provided a comprehensive assessment of bacterial populations and detected the largest number of phylotypes in Proteobacteria followed by Firmicutes and Actinobacteria. Furthermore, PhyloChip and clone libraries displayed considerable metabolic diversity in indigenous microbial populations by capturing several chemolithotrophic groups such as ammonia oxidizers, iron-reducers and -oxidizers, methanogens, and sulfate-reducers in the CdAR sediments. Twenty-two phylotypes detected on PhyloChip could not be classified even at phylum level thus suggesting the presence of novel microbial populations in the CdAR sediments. Clone libraries demonstrated very limited diversity of ammonia oxidizers and methanogens in the CdAR sediments as evidenced by the fact that only Nitrosospira- and Methanosarcina-related phylotypes were retrieved in amoA and mcrA clone libraries, respectively.}, }
@article {pmid21331608, year = {2011}, author = {Singh, SK and Strobel, GA and Knighton, B and Geary, B and Sears, J and Ezra, D}, title = {An endophytic Phomopsis sp. possessing bioactivity and fuel potential with its volatile organic compounds.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {729-739}, pmid = {21331608}, issn = {1432-184X}, mesh = {Antifungal Agents/*metabolism/pharmacology ; Ascomycota/classification/genetics/isolation &amp; purification/*metabolism ; Fungi/drug effects ; Molecular Sequence Data ; Orchidaceae/*microbiology ; Phylogeny ; Plant Diseases/microbiology ; Volatile Organic Compounds/*metabolism/pharmacology ; }, abstract = {An unusual Phomopsis sp. was isolated as endophyte of Odontoglossum sp. (Orchidaceae), associated with a cloud forest in Northern Ecuador. This fungus produces a unique mixture of volatile organic compounds (VOCs) including sabinene (a monoterpene with a peppery odor) only previously known from higher plants. In addition, some of the other more abundant VOCs recorded by GC/MS in this organism were 1-butanol, 3-methyl; benzeneethanol; 1-propanol, 2-methyl and 2-propanone. The gases of Phomopsis sp. possess antifungal properties and an artificial mixture of the VOCs mimicked the antibiotic effects of this organism with the greatest bioactivity against a wide range of plant pathogenic test fungi including: Pythium, Phytophthora, Sclerotinia, Rhizoctonia, Fusarium, Botrytis, Verticillium, and Colletotrichum. The IC(50) values for the artificial gas mixture of Phomopsis sp. varied between 8 and 25.65 μl/mL. Proton transfer reaction-mass spectrometry monitored the concentration of VOCs emitted by Phomopsis sp. and yielded a total VOC concentration of ca. 18 ppmv in the head space at the seventh day of incubation at 23°C on PDA. As with many VOC-producing endophytes, this Phomopsis sp. did survive and grow in the presence of the inhibitory gases of Muscodor albus. A discussion is presented on the possible involvement of VOC production by the fungus and its role in the biology/ecology of the fungus/plant/environmental relationship.}, }
@article {pmid21331222, year = {2010}, author = {Grossart, HP and Tang, KW}, title = {www.aquaticmicrobial.net.}, journal = {Communicative &amp; integrative biology}, volume = {3}, number = {6}, pages = {491-494}, pmid = {21331222}, issn = {1942-0889}, abstract = {Despite recent advances and new applications of molecular and biogeochemical methodology in aquatic microbial ecology, our perception of the aquatic microbial world remains one dominated by "free-living" bacteria that account for most of the microbial activities in the pelagic zone. Recent research has, however, shown that there exist vast and hidden "microbial networks" within the water column, connected via various microhabitats such as aggregates, fecal pellets and higher organisms. Bacterial abundance within these networks may rival or exceed that of the "free-living" bacteria. Hence, what we have learned in traditional aquatic microbial ecology represents merely a fraction of the microbial world. Within these networks a bacterium can travel long distances, communicate and closely interact with other bacteria and efficiently exchange genetic information with one another. The presence of microbial networks within the water column demands better sampling strategies and a new way to understand bacterial ecology, evolution and functions within the broader context of systems biology.}, }
@article {pmid21330726, year = {2011}, author = {Pycke, BF and Etchebehere, C and Van de Caveye, P and Negroni, A and Verstraete, W and Boon, N}, title = {A time-course analysis of four full-scale anaerobic digesters in relation to the dynamics of change of their microbial communities.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {63}, number = {4}, pages = {769-775}, doi = {10.2166/wst.2011.307}, pmid = {21330726}, issn = {0273-1223}, mesh = {Anaerobiosis ; Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; Biodegradation, Environmental ; Bioreactors/microbiology ; Cluster Analysis ; Methane/metabolism ; Polymorphism, Restriction Fragment Length ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; Time Factors ; }, abstract = {This study describes the microbial community richness, -dynamics, and -organization of four full-scale anaerobic digesters during a time-course study of 45 days. The microbial community was analyzed using a Bacteria- and Archaea-targeting 16S rRNA gene-based Terminal-Restriction Fragment Length Polymorphism approach. Clustering analysis separated meso- and thermophilic reactors for both archaeal and bacterial communities. Regardless of the operating temperature, each installation possessed a distinct community profile. For both microbial domains, about 8 dominant terminal-restriction fragments could be observed, with a minimum of 4 and a maximum of 14. The bacterial community organization (a coefficient which describes the specific degree of evenness) showed a factor 2 more variation in the mesophilic reactors, compared with the thermophilic ones. The archaeal community structure of the mesophilic UASB reactor was found to be more stable. The community composition was highly dynamic for Bacteria and Archaea, with a rate of change between 20-50% per 15 days. This study illustrated that microbial communities in full-scale anaerobic digesters are unique to the installation and that community properties are dynamic. Converging complex microbial processes such as anaerobic digestion which rely on a multitude of microbial teams apparently can be highly dynamic.}, }
@article {pmid21329217, year = {2011}, author = {Kujawinski, EB}, title = {The impact of microbial metabolism on marine dissolved organic matter.}, journal = {Annual review of marine science}, volume = {3}, number = {}, pages = {567-599}, doi = {10.1146/annurev-marine-120308-081003}, pmid = {21329217}, issn = {1941-1405}, mesh = {Bacteria/*metabolism ; *Biodegradation, Environmental ; *Ecosystem ; Oceans and Seas ; }, abstract = {Microbes mediate global biogeochemical cycles through their metabolism, and all metabolic processes begin with the interaction between the microbial cell wall or membrane and the external environment. For all heterotrophs and many autotrophs, critical growth substrates and factors are present within the dilute and heterogeneous mixture of compounds that constitutes dissolved organic matter (DOM). In short, the microbe-molecule interaction is one of the fundamental reactions within the global carbon cycle. Here, I summarize recent findings from studies that examine DOM-microbe interactions from either the DOM perspective (organic geochemistry) or the microbe perspective (microbial ecology). Gaps in our knowledge are highlighted and future integrative research directions are proposed.}, }
@article {pmid21329209, year = {2011}, author = {Gilbert, JA and Dupont, CL}, title = {Microbial metagenomics: beyond the genome.}, journal = {Annual review of marine science}, volume = {3}, number = {}, pages = {347-371}, doi = {10.1146/annurev-marine-120709-142811}, pmid = {21329209}, issn = {1941-1405}, mesh = {Bacteria/*genetics ; Evolution, Molecular ; Genetic Variation ; *Metagenomics ; Oceans and Seas ; }, abstract = {Metagenomics literally means "beyond the genome." Marine microbial metagenomic databases presently comprise approximately 400 billion base pairs of DNA, only approximately 3% of that found in 1 ml of seawater. Very soon a trillion-base-pair sequence run will be feasible, so it is time to reflect on what we have learned from metagenomics. We review the impact of metagenomics on our understanding of marine microbial communities. We consider the studies facilitated by data generated through the Global Ocean Sampling expedition, as well as the revolution wrought at the individual laboratory level through next generation sequencing technologies. We review recent studies and discoveries since 2008, provide a discussion of bioinformatic analyses, including conceptual pipelines and sequence annotation and predict the future of metagenomics, with suggestions of collaborative community studies tailored toward answering some of the fundamental questions in marine microbial ecology.}, }
@article {pmid21327032, year = {2010}, author = {Derrien, M and van Passel, MW and van de Bovenkamp, JH and Schipper, RG and de Vos, WM and Dekker, J}, title = {Mucin-bacterial interactions in the human oral cavity and digestive tract.}, journal = {Gut microbes}, volume = {1}, number = {4}, pages = {254-268}, pmid = {21327032}, issn = {1949-0984}, abstract = {Mucins are a family of heavily glycosylated proteins that are the major organic components of the mucus layer, the protective layer covering the epithelial cells in many human and animal organs, including the entire gastro-intestinal tract. Microbes that can associate with mucins benefit from this interaction since they can get available nutrients, experience physico-chemical protection and adhere, resulting in increased residence time. Mucin-degrading microorganisms, which often are found in consortia, have not been extensively characterized as mucins are high molecular weight glycoproteins that are hard to study because of their size, complexity and heterogeneity. The purpose of this review is to discuss how advances in mucus and mucin research, and insight in the microbial ecology promoted our understanding of mucin degradation. Recent insight is presented in mucin structure and organization, the microorganisms known to use mucin as growth substrate, with a specific attention on Akkermansia muciniphila, and the molecular basis of microbial mucin degradation owing to availability of genome sequences.}, }
@article {pmid21325835, year = {2011}, author = {Elsner, P}, title = {Anatomical and physiological basis of topical therapy of the mucosa.}, journal = {Current problems in dermatology}, volume = {40}, number = {}, pages = {1-8}, doi = {10.1159/000321038}, pmid = {21325835}, issn = {1662-2944}, mesh = {Administration, Topical ; Anal Canal/anatomy &amp; histology ; Dermatologic Agents/administration &amp; dosage ; Female ; Humans ; Hydrogen-Ion Concentration ; Irritants/adverse effects ; Male ; Mucous Membrane/*anatomy &amp; histology/drug effects/*physiology ; Permeability ; Skin/drug effects/microbiology ; Skin Diseases/drug therapy/pathology/physiopathology ; Skin Physiological Phenomena ; Vulva/anatomy &amp; histology/physiology ; }, abstract = {The mucosa as a nonkeratinized epithelium covering body surfaces has widely differing anatomical and physiological properties depending on the organ system involved (gastrointestinal, respiratory, urinary, genital, ocular). In general, the mucosae close to the skin are more permeable to exogenous substances, more prone to irritant reactivity, and they have a unique microbial ecology which is qualitatively and quantitatively different from that of the adjacent keratinized epithelium. Clinical presentations of exogenous dermatoses in mucosae appear different from those of the skin. These specific properties of mucosae have to be considered in the development and application of topical agents, cosmetics and consumer products.}, }
@article {pmid21318282, year = {2011}, author = {Bruneel, O and Volant, A and Gallien, S and Chaumande, B and Casiot, C and Carapito, C and Bardil, A and Morin, G and Brown, GE and Personné, CJ and Le Paslier, D and Schaeffer, C and Van Dorsselaer, A and Bertin, PN and Elbaz-Poulichet, F and Arsène-Ploetze, F}, title = {Characterization of the active bacterial community involved in natural attenuation processes in arsenic-rich creek sediments.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {793-810}, pmid = {21318282}, issn = {1432-184X}, mesh = {Arsenic/analysis/*metabolism ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Geologic Sediments/chemistry/*microbiology ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Acid mine drainage of the Carnoulès mine (France) is characterized by acid waters containing high concentrations of arsenic and iron. In the first 30 m along the Reigous, a small creek draining the site, more than 38% of the dissolved arsenic was removed by co-precipitation with Fe(III), in agreement with previous studies, which suggest a role of microbial activities in the co-precipitation of As(III) and As(V) with Fe(III) and sulfate. To investigate how this particular ecosystem functions, the bacterial community was characterized in water and sediments by 16S rRNA encoding gene library analysis. Based on the results obtained using a metaproteomic approach on sediments combined with high-sensitivity HPLC-chip spectrometry, several GroEL orthologs expressed by the community were characterized, and the active members of the prokaryotic community inhabiting the creek sediments were identified. Many of these bacteria are β-proteobacteria such as Gallionella and Thiomonas, but γ-proteobacteria such as Acidithiobacillus ferrooxidans and α-proteobacteria such as Acidiphilium, Actinobacteria, and Firmicutes were also detected.}, }
@article {pmid21317256, year = {2011}, author = {Wang, J and Vollrath, S and Behrends, T and Bodelier, PL and Muyzer, G and Meima-Franke, M and Den Oudsten, F and Van Cappellen, P and Laanbroek, HJ}, title = {Distribution and diversity of Gallionella-like neutrophilic iron oxidizers in a tidal freshwater marsh.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {7}, pages = {2337-2344}, pmid = {21317256}, issn = {1098-5336}, mesh = {Denaturing Gradient Gel Electrophoresis ; Fresh Water/*microbiology ; Gallionellaceae/*classification/*genetics ; *Genetic Variation ; Iron/*metabolism ; *Metagenome ; Oxidation-Reduction ; Polymerase Chain Reaction ; Seasons ; *Wetlands ; }, abstract = {Microbial iron oxidation is an integral part of the iron redox cycle in wetlands. Nonetheless, relatively little is known about the composition and ecology of iron-oxidizing communities in the soils and sediments of wetlands. In this study, sediment cores were collected across a freshwater tidal marsh in order to characterize the iron-oxidizing bacteria (FeOB) and to link their distributions to the geochemical properties of the sediments. We applied recently designed 16S rRNA primers targeting Gallionella-related FeOB by using a nested PCR-denaturing gradient gel electrophoresis (DGGE) approach combined with a novel quantitative PCR (qPCR) assay. Gallionella-related FeOB were detected in most of the samples. The diversity and abundance of the putative FeOB were generally higher in the upper 5 to 12 cm of sediment than in deeper sediment and higher in samples collected in April than in those collected in July and October. Oxygen supply by macrofauna appears to be a major force in controlling the spatial and temporal variations in FeOB communities. The higher abundance of Gallionella-related FeOB in April coincided with elevated concentrations of extractable Fe(III) in the sediments. Despite this coincidence, the distributions of FeOB did not exhibit a simple relationship to the redox zonation inferred from the geochemical depth profiles.}, }
@article {pmid21315985, year = {2011}, author = {Dommel, MK and Lücking, G and Scherer, S and Ehling-Schulz, M}, title = {Transcriptional kinetic analyses of cereulide synthetase genes with respect to growth, sporulation and emetic toxin production in Bacillus cereus.}, journal = {Food microbiology}, volume = {28}, number = {2}, pages = {284-290}, doi = {10.1016/j.fm.2010.07.001}, pmid = {21315985}, issn = {1095-9998}, mesh = {Bacillus cereus/genetics/*metabolism ; Bacterial Toxins/*biosynthesis/genetics ; Depsipeptides/genetics/metabolism ; *Food Microbiology ; Humans ; Ligases/genetics/metabolism ; Promoter Regions, Genetic ; Reverse Transcriptase Polymerase Chain Reaction ; Spores, Bacterial/genetics/metabolism ; Transcription Factors/genetics/metabolism ; }, abstract = {In light of the increasing number of serious food borne outbreaks caused by emetic Bacillus cereus, a better understanding of the cereulide synthetase (ces) gene expression and toxin synthesis is required. Here, the relative expression levels of three ces genes (cesP, cesA and cesB) were investigated using quantitative real-time reverse transcription PCR in relation to growth, degree of sporulation and toxin production of the emetic reference strain B. cereus F4810/72 and the weakly emetic strain IH41385. The strict co-transcription of all three genes confirmed the operon structure of the ces gene cluster responsible for cereulide formation. ces transcription turned out to be highly temporal and tightly regulated; ces mRNA was only detectable during mid to late exponential growth in both strains. The low toxigenic potential of the weakly emetic strain IH41385 correlated well with its respective ces transcripts, showing reduced activity at a transcriptional level. Two non-sporulating mutants (F4810/72Δspo0A and F4810/72INsigH) demonstrated that cereulide synthesis is part of the Spo0A regulon but independent of later sporulation processes. Besides strain specific intrinsic factors, ces transcription was found to be significantly influenced by the cellular growth state as well as by extrinsic abiotic factors, like salt. An increase of sodium chloride in the media resulted in lower ces transcription and coincided with lower cereulide toxin levels. Interestingly, at 25 gl(-1) NaCl, toxin levels were already reduced without strongly affecting the growth of B. cereus, indicating an inhibitory effect of NaCl on cereulide biosynthesis independent of growth. This illustrates that ces gene expression and toxicity cannot be predicted solely from growth rates or cell numbers, but is influenced by complex interactions of various intrinsic as well as extrinsic factors, which remain to be clarified in detail.}, }
@article {pmid21304727, year = {2010}, author = {Gilbert, JA and Meyer, F and Antonopoulos, D and Balaji, P and Brown, CT and Brown, CT and Desai, N and Eisen, JA and Evers, D and Field, D and Feng, W and Huson, D and Jansson, J and Knight, R and Knight, J and Kolker, E and Konstantindis, K and Kostka, J and Kyrpides, N and Mackelprang, R and McHardy, A and Quince, C and Raes, J and Sczyrba, A and Shade, A and Stevens, R}, title = {Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project.}, journal = {Standards in genomic sciences}, volume = {3}, number = {3}, pages = {243-248}, pmid = {21304727}, issn = {1944-3277}, abstract = {Between July 18(th) and 24(th) 2010, 26 leading microbial ecology, computation, bioinformatics and statistics researchers came together in Snowbird, Utah (USA) to discuss the challenge of how to best characterize the microbial world using next-generation sequencing technologies. The meeting was entitled "Terabase Metagenomics" and was sponsored by the Institute for Computing in Science (ICiS) summer 2010 workshop program. The aim of the workshop was to explore the fundamental questions relating to microbial ecology that could be addressed using advances in sequencing potential. Technological advances in next-generation sequencing platforms such as the Illumina HiSeq 2000 can generate in excess of 250 billion base pairs of genetic information in 8 days. Thus, the generation of a trillion base pairs of genetic information is becoming a routine matter. The main outcome from this meeting was the birth of a concept and practical approach to exploring microbial life on earth, the Earth Microbiome Project (EMP). Here we briefly describe the highlights of this meeting and provide an overview of the EMP concept and how it can be applied to exploration of the microbiome of each ecosystem on this planet.}, }
@article {pmid21304725, year = {2010}, author = {Gilbert, JA and Meyer, F and Knight, R and Field, D and Kyrpides, N and Yilmaz, P and Wooley, J}, title = {Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22-27, 2010.}, journal = {Standards in genomic sciences}, volume = {3}, number = {3}, pages = {235-239}, pmid = {21304725}, issn = {1944-3277}, abstract = {This report summarizes the proceedings of the Metagenomics, Metadata, Metaanalysis, Models and Metainfrastructure (M5) Roundtable at the 13th International Society for Microbial Ecology Meeting in Seattle, WA, USA August 22-27, 2010. The Genomic Standards Consortium (GSC) hosted this meeting as a community engagement exercise to describe the GSC to the microbial ecology community during this important international meeting. The roundtable included five talks given by members of the GSC, and was followed by audience participation in the form of a roundtable discussion. This report summarizes this event. Further information on the GSC and its range of activities can be found at http://www.gensc.org.}, }
@article {pmid21304582, year = {2011}, author = {Cury, JC and Araujo, FV and Coelho-Souza, SA and Peixoto, RS and Oliveira, JA and Santos, HF and Dávila, AM and Rosado, AS}, title = {Microbial diversity of a Brazilian coastal region influenced by an upwelling system and anthropogenic activity.}, journal = {PloS one}, volume = {6}, number = {1}, pages = {e16553}, pmid = {21304582}, issn = {1932-6203}, mesh = {*Biodiversity ; *Biomass ; Brazil ; *Ecosystem ; Food Chain ; RNA, Ribosomal/analysis ; Seawater/*microbiology ; Water Pollution/*adverse effects ; }, abstract = {BACKGROUND: Upwelling systems are characterised by an intense primary biomass production in the surface (warmest) water after the outcrop of the bottom (coldest) water, which is rich in nutrients. Although it is known that the microbial assemblage plays an important role in the food chain of marine systems and that the upwelling systems that occur in southwest Brazil drive the complex dynamics of the food chain, little is known about the microbial composition present in this region.<br><br>We carried out a molecular survey based on SSU rRNA gene from the three domains of the phylogenetic tree of life present in a tropical upwelling region (Arraial do Cabo, Rio de Janeiro, Brazil). The aim was to analyse the horizontal and vertical variations of the microbial composition in two geographically close areas influenced by anthropogenic activity (sewage disposal/port activity) and upwelling phenomena, respectively. A lower estimated diversity of microorganisms of the three domains of the phylogenetic tree of life was found in the water of the area influenced by anthropogenic activity compared to the area influenced by upwelling phenomena. We observed a heterogenic distribution of the relative abundance of taxonomic groups, especially in the Archaea and Eukarya domains. The bacterial community was dominated by Proteobacteria, Cyanobacteria and Bacteroidetes phyla, whereas the microeukaryotic community was dominated by Metazoa, Fungi, Alveolata and Stramenopile. The estimated archaeal diversity was the lowest of the three domains and was dominated by uncharacterised marine Crenarchaeota that were most closely related to Marine Group I.<br><br>CONCLUSIONS/SIGNIFICANCE: The variety of conditions and the presence of different microbial assemblages indicated that the area of Arraial do Cabo can be used as a model for detailed studies that contemplate the correlation between pollution-indicating parameters and the depletion of microbial diversity in areas close to anthropogenic activity; functional roles and geochemical processes; phylogeny of the uncharacterised diversity; and seasonal variations of the microbial assemblages.}, }
@article {pmid21300771, year = {2011}, author = {Zhu, J and Yin, X and Yu, H and Zhao, L and Sabour, P and Gong, J}, title = {Involvement of quorum sensing and heat-stable enterotoxin a in cell damage caused by a porcine enterotoxigenic Escherichia coli strain.}, journal = {Infection and immunity}, volume = {79}, number = {4}, pages = {1688-1695}, pmid = {21300771}, issn = {1098-5522}, mesh = {Animals ; Bacterial Proteins/genetics ; Carbon-Sulfur Lyases/genetics ; Enterotoxigenic Escherichia coli/genetics/*metabolism/*pathogenicity ; Enterotoxins/*genetics/metabolism ; Escherichia coli Infections/genetics/metabolism ; Gene Expression ; Gene Expression Regulation, Bacterial/genetics ; Homoserine/*analogs &amp; derivatives/genetics/metabolism ; Lactones/*metabolism ; Quorum Sensing ; Reverse Transcriptase Polymerase Chain Reaction ; Swine ; Virulence Factors/genetics/metabolism ; }, abstract = {Enterotoxigenic Escherichia coli (ETEC) strains with K88 fimbriae are often associated with the outbreaks of diarrhea in newborn and weaned piglets worldwide. In the present study, we observed that 10[8] CFU/ml of K88(+) ETEC strain JG280 caused more death of pig intestinal IPEC-J2 cells than did 10[9] CFU/ml, suggesting that ETEC-induced cell death was cell density dependent and that quorum sensing (QS) may play a role in pathogenesis. Subsequent investigations demonstrated a positive correlation between autoinducer 2 (AI-2) activity of JG280 and death of IPEC-J2 cells during the infection for up to 3 h. However, there was a negative correlation between AI-2 activity and expression of the JG280 enterotoxin genes estA and estB when IPEC-J2 cells were exposed to the pathogen at 10[8] CFU/ml. We therefore cloned the luxS gene (responsible for AI-2 production) from JG280 and overexpressed it in E. coli DH5α, because deletion of the luxS gene was retarded by the lack of suitable antibiotic selection markers and the resistance of this pathogen to a wide range of antibiotics. The addition of culture fluid from E. coli DH5α with the overexpressed luxS reduced cell death of IPEC-J2 cells by 10[8] CFU/ml JG280. The addition also reduced the estA expression by JG280. Nonpathogenic K88(+) strain JFF4, which lacks the enterotoxin genes, caused no death of IPEC-J2 cells, although it produced AI-2 activity comparable to that produced by JG280. These results suggest the involvement of AI-2-mediated quorum sensing in K88(+) ETEC pathogenesis, possibly through a negative regulation of STa production.}, }
@article {pmid21298263, year = {2011}, author = {Sun, B and Dong, ZX and Zhang, XX and Li, Y and Cao, H and Cui, ZL}, title = {Rice to vegetables: short- versus long-term impact of land-use change on the indigenous soil microbial community.}, journal = {Microbial ecology}, volume = {62}, number = {2}, pages = {474-485}, pmid = {21298263}, issn = {1432-184X}, mesh = {Agriculture/*methods ; Bacteria/classification/*genetics/isolation &amp; purification/metabolism ; Bacterial Typing Techniques ; Biomass ; *Biota ; Carbon/metabolism ; Fungi/growth &amp; development/isolation &amp; purification ; Genes, rRNA ; Microscopy, Electron, Scanning ; Nitrogen/metabolism ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Land-use change is known to have a significant effect on the indigenous soil microbial community, but it is unknown if there are any general trends regarding how this effect varies over time. Here, we describe a comparative analysis of microbial communities from three adjacent agricultural fields: one-century-old paddy field (OP) and two vegetable fields (new vegetable field (NV) and old vegetable field (OV)) that were established on traditional paddy fields 10 and 100 years ago, respectively. Soil chemical and physical analysis showed that both vegetable fields were more nutrient rich than the paddy field in terms of organic C, total N, total P, and available K. The vegetable fields possessed relatively higher abundance of culturable bacteria, fungi, and specific groups of bacteria (Actinomyces, nitrifying bacteria, and cellulose-decomposing bacteria) but lower levels of microbial biomass C and N. Notably, the decrease of biomass was further confirmed by analysis of seven additional soils in chronosequence sampled from the same area. Next we examined the metabolic diversity of the microbial community using the EcoPlate(TM) system from Biolog Inc. (Hayward, CA, USA). The utilization patterns of 31 unique C substrates (i.e., community-level physiological profile) showed that microorganisms in vegetable soil and paddy soil prefer to use different C substrates (polymeric compounds for NV and OV soils, phenolic acids for OP soil). Principal component analysis and the average well color development data showed that the NV is metabolically more distinct from the OV and OP. The effect was likely attributable to the elevated soil pH in NV soil. Furthermore, we assessed the diversity of soil bacterial populations using the cultivation-independent technology of amplified ribosomal DNA restriction analysis (ARDRA). Results showed that levels of bacterial diversity in OP and NV soils were similar (Shannon's diversity index H = 4.83 and 4.79, respectively), whereas bacteria in OV soil have the lowest score of diversity (H = 3.48). The low level of bacterial diversity in OV soil was supported by sequencing of ten randomly selected 16S rDNA clones from each of the three rDNA libraries. Phylogenetic analysis showed that all the ten OV clones belonged to Proteobacteria with eight in the gamma-subdivision and two in the alpha-subdivision. In contrast, the ten clones from NV and OP soils were classified into four and eight bacterial classes or unclassified groups, respectively. Taken together, our data suggest that land-use change from rice to vegetables resulted in a decrease of bacterial diversity and soil biomass despite an increase in the abundance of culturable microorganisms and, moreover, the decrease of bacterial diversity occurred during long-term rather than short-term vegetable cultivation.}, }
@article {pmid21295817, year = {2011}, author = {Caliz, J and Vila, X and Martí, E and Sierra, J and Nordgren, J and Lindgren, PE and Bañeras, L and Montserrat, G}, title = {The microbiota of an unpolluted calcareous soil faces up chlorophenols: Evidences of resistant strains with potential for bioremediation.}, journal = {Chemosphere}, volume = {83}, number = {2}, pages = {104-116}, doi = {10.1016/j.chemosphere.2011.01.016}, pmid = {21295817}, issn = {1879-1298}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; Biodegradation, Environmental ; Calcium Carbonate/analysis ; Chlorophenols/analysis/*toxicity ; Drug Tolerance/*genetics ; Phylogeny ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants/analysis/*toxicity ; }, abstract = {To highlight the effects of a variety of chlorophenols (CP) in relation to the response of an indigenous bacterial community, an agricultural Mediterranean calcareous soil has been studied in microcosms incubated under controlled laboratory conditions. Soil samples were artificially polluted with 2-monochlorophenol (MCP), 2,4,6-trichlorophenol (TCP) and pentachlorophenol (PCP), at concentrations ranging from 0.1 up to 5000 mg kg(-1). Both activity and composition of the microbial community were assessed during several weeks, respectively, by respirometric methods and PCR-DGGE analysis of extracted DNA and RNA. Significant decreases in soil respirometric values and changes in the bacterial community composition were observed at concentrations above 1000 mg kg(-1) MCP and TCP, and above 100 mg kg(-1) PCP. However, the persistence of several active bacterial populations in soil microcosms contaminated with high concentration of CP, as indicated by DGGE fingerprints, suggested the capacity of these native bacteria to survive in the presence of the pollutants, even without a previous adaptation or contact with them. The isolation of potential CP degraders was attempted by culture plating from microcosms incubated with high CP concentrations. Twenty-three different isolates were screened for their resistance to TCP and PCP. The most resistant isolates were identified as Kocuria palustris, Lysobacter gummosus, Bacillus sp. and Pseudomonas putida, according to 16S rRNA gene homology. In addition, these four isolates also showed the capacity to reduce the concentration of TCP and PCP from 15% to 30% after 5d of incubation in laboratory assays (initial pollutant concentration of 50 mg L(-1)). Isolate ITP29, which could be a novel species of Bacillus, has been revealed as the first known member in this bacterial group with potential for CP bioremediation applications, usually wide-spread in the soil natural communities, which has not been reported to date as a CP degrader.}, }
@article {pmid21290465, year = {2010}, author = {van Dijk, MA and Gregori, G and Hoogveld, HL and Rijkeboer, M and Denis, M and Malkassian, A and Gons, HJ}, title = {Optimizing the setup of a flow cytometric cell sorter for efficient quantitative sorting of long filamentous cyanobacteria.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {77}, number = {10}, pages = {911-924}, doi = {10.1002/cyto.a.20946}, pmid = {21290465}, issn = {1552-4930}, mesh = {Cell Adhesion ; Cell Movement ; Cell Separation/*methods ; Cell Survival ; Cells, Cultured ; Cyanobacteria/*cytology/metabolism ; Flow Cytometry/*instrumentation/methods ; }, abstract = {Heterogeneity within natural phytoplankton communities makes it very difficult to analyze parameters at the single-cell level. Flow cytometric sorting is therefore a useful tool in aquatic sciences, as it provides material for post-sort analysis and culturing. Sorting subpopulations from natural communities, however, often requires handling morphologically diverse and complex particles with various abundances. Long particles, such as filament-forming cyanobacteria (>100-μm long), prove very difficult to handle. These potentially toxic organisms are widespread in eutrophic systems and have important ecological consequences. Being able to sort filamentous cyanobacteria efficiently and as viable cells is therefore highly desirable when studying factors associated with their toxicity and occurrence. This unconventional sorting requires extensive user experience and special instrument setup. We have investigated the effect of hydrodynamic and electromechanical components of a flow cytometer, and sorting protocol on the quantitative sorting efficiency of these long particles using two filamentous cyanobacterial strains with average lengths of ∼100 and ∼300 μm. Sorting efficiency ranged from 9.4 to 96.0% and was significantly affected by filament length, sorting envelope, drop delay (dd), and for the long species also by tip size, but not by cycle time. Filaments survived sorting and were not damaged. The optimal settings found for the modular MoFlo® cell-sorter to sort the filaments were a 100-μm flow tip at 30 psi (207 kPa) with a three-droplet envelope in Enrich mode while using an extended analysis time of 17.6 μs and an intermediate plate charge and deflection percentage combination of 3,000 V/60%, combined with a dd 0 for the cultures with 100-μm filaments and dd +1 for the culture with 300-μm filaments. To the best of our knowledge, the filaments up to 1063.5 μm sorted in this study are the longest ever sorted.}, }
@article {pmid21287346, year = {2011}, author = {Martins, J and Peixe, L and Vasconcelos, VM}, title = {Unraveling cyanobacteria ecology in wastewater treatment plants (WWTP).}, journal = {Microbial ecology}, volume = {62}, number = {2}, pages = {241-256}, pmid = {21287346}, issn = {1432-184X}, mesh = {Bacterial Toxins/classification/*metabolism ; Biodegradation, Environmental ; *Biota ; Ciliophora/growth &amp; development/metabolism ; Cyanobacteria/classification/growth &amp; development/*metabolism ; Cyanobacteria Toxins ; Geography ; Marine Toxins/classification/*metabolism ; Microcystins/classification/*metabolism ; Molecular Structure ; Phytoplankton/growth &amp; development/metabolism ; Seasons ; Waste Disposal, Fluid/*methods ; Water Microbiology ; Water Purification/methods ; }, abstract = {Cyanobacteria may be important components of wastewater treatment plants' (WWTP) biological treatment, reaching levels of 100% of the total phytoplankton density in some systems. The occurrence of cyanobacteria and their associated toxins in these systems present a risk to the aquatic environments and to public health, changing drastically the ecology of microbial communities and associated organisms. Many studies reveal that cyanotoxins, namely microcystins may not act as antibacterial compounds but they might have negative impacts on protozoans, inhibiting their growing and respiration rates and leading to changes in cellular morphology, decreasing consequently the treatment efficacy in WWTP. On the other side, flagellates and ciliates may ingest some cyanobacteria species while the formation of colonies by these prokaryotes may be seen as a defense mechanism against predation. Problems regarding the occurrence of cyanobacteria in WWTP are not limited to toxin production. Other cyanobacterial secondary metabolites may act as antibacterial compounds leading to the disruption of bacterial communities that biologically convert organic materials in WWTP being fundamental to the efficacy of the process. Studies reveal that the potential antibacterial capacity differs according to cyanobacteria specie and it seems to be more effective in Gram (+) bacteria. Thus, to understand the effects of cyanobacterial communities in the efficiency of the waste water treatment it will be necessary to unravel the complex interactions between cyanobacterial populations, bacteria, and protozoa in WWTP in situ studies.}, }
@article {pmid21287345, year = {2011}, author = {Ling, Z and Liu, X and Chen, X and Zhu, H and Nelson, KE and Xia, Y and Li, L and Xiang, C}, title = {Diversity of cervicovaginal microbiota associated with female lower genital tract infections.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {704-714}, pmid = {21287345}, issn = {1432-184X}, mesh = {Bacteria/genetics/*isolation &amp; purification ; Case-Control Studies ; Cervix Uteri/*microbiology ; China ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Female ; Humans ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Uterine Cervicitis/*microbiology ; Vagina/*microbiology ; Vaginosis, Bacterial/*microbiology ; }, abstract = {The female genital tract (FGT) harbors very large numbers of bacterial species that are known to play an important role on vaginal health. Previous studies have focused on bacterial diversity in the vagina, but little is known about the ectocervical microbiota associated with FGT infections. In our study, vaginal swabs and ectocervical swabs were collected from 100 participants in China, including 30 women with bacterial vaginosis (BV; BV group), 22 women with cervicitis (Cer group), 18 women with BV in combination with cervicitis (BC group) and 30 healthy control women (CN group). The diversity and richness of cervicovaginal microbiota were investigated with culture-independent polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) targeting 11 microorganisms that have been associated with FGT infections. Despite significant interpersonal variations, the PCR-DGGE profiles revealed that vaginal microbiota and ectocervical microbiota were clearly much more complex in the BV group, while the ectocervical microbiota showed no significant difference between healthy and diseased participants. Using species-specific qPCR, BV and cervicitis were significantly associated with a dramatic decrease in Lactobacillus species (p < 0.05), and potential pathogenic species such as Gardnerella, Atopobium, Eggerthella, Leptotrichia/Sneathia, and Prevotella were more common and in higher copy numbers in BV than in CN samples (p values ranged from 0.000 to 0.021). No significant differences were observed between healthy and cervicitis samples (p > 0.05) in ectocervical microbiota. The total numbers of bacteria were significantly lower in the ectocervix as compared in the vagina (p < 0.05). Intriguingly, vaginal microbiota from participants with BV in combination with cervicitis was quite different from that of participants with BV or cervicitis alone. Our study demonstrated that the cervicovaginal microbiota was actively involved in the process of FGT infections. The predominant bacteria of the cervicovaginal communities were clearly associated with BV; however, there was not sufficient evidence that the ectocervical microbiota is directly involved in the development of cervicitis.}, }
@article {pmid21286786, year = {2011}, author = {Di Lorenzo, M and Stork, M and Crosa, JH}, title = {Genetic and biochemical analyses of chromosome and plasmid gene homologues encoding ICL and ArCP domains in Vibrio anguillarum strain 775.}, journal = {Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine}, volume = {24}, number = {4}, pages = {629-643}, pmid = {21286786}, issn = {1572-8773}, support = {R01 AI019018/AI/NIAID NIH HHS/United States ; R01 GM064600/GM/NIGMS NIH HHS/United States ; GM64600/GM/NIGMS NIH HHS/United States ; AI19018/AI/NIAID NIH HHS/United States ; }, mesh = {Carrier Proteins/genetics/*metabolism ; Catalytic Domain ; Chromosomes, Bacterial/*genetics ; Escherichia coli/enzymology/genetics/metabolism ; Hydroxybenzoates/*metabolism ; Mutagenesis, Site-Directed ; Oxo-Acid-Lyases/genetics/*metabolism ; Phenotype ; Plasmids/*genetics ; Vibrio/classification/enzymology/*genetics/metabolism ; }, abstract = {Anguibactin, the siderophore produced by Vibrio anguillarum 775 is synthesized from 2,3-dihydroxybenzoic acid (DHBA), cysteine and hydroxyhistamine via a nonribosomal peptide synthetase (NRPS) mechanism. Most of the genes encoding anguibactin biosynthetic proteins are harbored by the pJM1 plasmid. In this work we report the identification of a homologue of the plasmid-encoded angB on the chromosome of strain 775. The product of both genes harbor an isochorismate lyase (ICL) domain that converts isochorismic acid to 2,3-dihydro-2,3-dihydroxybenzoic acid, one of the steps of DHBA synthesis. We show in this work that both ICL domains are functional in the production of DHBA in V. anguillarum as well as in E. coli. Substitution by alanine of the aspartic acid residue in the active site of both ICL domains completely abolishes their isochorismate lyase activity in vivo. The two proteins also carry an aryl carrier protein (ArCP) domain. In contrast with the ICL domains only the plasmid encoded ArCP can participate in anguibactin production as determined by complementation analyses and site-directed mutagenesis in the active site of the plasmid encoded protein, S248A. The site-directed mutants, D37A in the ICL domain and S248A in the ArCP domain of the plasmid encoded AngB were also tested in vitro and clearly show the importance of each residue for the domain function and that each domain operates independently.}, }
@article {pmid21286703, year = {2011}, author = {Lu, H and Wu, Z and Xu, W and Yang, J and Chen, Y and Li, L}, title = {Intestinal microbiota was assessed in cirrhotic patients with hepatitis B virus infection. Intestinal microbiota of HBV cirrhotic patients.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {693-703}, pmid = {21286703}, issn = {1432-184X}, mesh = {Adult ; Bacteria/classification/*genetics ; Case-Control Studies ; China ; DNA, Bacterial/genetics ; Feces/microbiology ; Female ; Genes, Bacterial ; Hepatitis B, Chronic/*microbiology ; Humans ; Immunoglobulin A/metabolism ; Intestines/*microbiology ; Liver Cirrhosis/microbiology/virology ; Male ; *Metagenome ; Middle Aged ; Operon ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Tumor Necrosis Factor-alpha/metabolism ; Virulence Factors/genetics ; }, abstract = {To unravel the profile of intestinal microecological parameters in Chinese patients with asymptomatic carriage of hepatitis B virus (HBV), chronic hepatitis B, decompensated HBV cirrhosis, and health controls and to establish their correlation with liver disease progression, we performed quantitative PCR and immunological techniques to investigate fecal parameters, including population of fecal predominant bacteria and the abundance of some virulence genes derived from Escherichia coli, Bacteroides fragilis, Clostridium difficile, and Clostridium perfringens in fecal crude DNA and some immunological parameters in extracts of all fecal samples. Data analysis indicated that 16S rRNA gene copy numbers for Faecalibacterium prausnitzii, Enterococcus faecalis, Enterobacteriaceae, bifidobacteria, and lactic acid bacteria (Lactobacillus, Pediococcus, Leuconostoc, and Weissella) showed marked variation in the intestine of HBV cirrhotic patients. The Bifidobacteria/Enterobacteriaceae (B/E) ratio, which may indicate microbial colonization resistance of the bowel, was decreased significantly in turn from 1.15 ± 0.11 in healthy controls, 0.99 ± 0.09 in asymptomatic carriers, and 0.76 ± 0.08 in patients with chronic hepatitis B to 0.64 ± 0.09 in patients with decompensated HBV cirrhosis (for all, P < 0.01). This suggests that B/E ratio is useful for following the level of intestinal microecological disorder in the course of liver disease progression. The data for virulence gene abundance suggested increased diversity of virulence factors during liver disease progression. Fecal secretory IgA and tumor necrosis factor-α in decompensated HBV cirrhotic patients were present at higher levels than in other groups, which indicates that a complicated autoregulatory system tries to achieve a new intestinal microecological balance.}, }
@article {pmid21286702, year = {2011}, author = {Fortunato, CS and Crump, BC}, title = {Bacterioplankton community variation across river to ocean environmental gradients.}, journal = {Microbial ecology}, volume = {62}, number = {2}, pages = {374-382}, pmid = {21286702}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*growth &amp; development/isolation &amp; purification ; Bacterial Typing Techniques ; *Biota ; Chlorophyll/analysis ; Chlorophyll A ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Environment ; Genes, rRNA ; Oceans and Seas ; Oregon ; Rivers/*microbiology ; Salinity ; Temperature ; Washington ; *Water Microbiology ; }, abstract = {Coastal zones encompass a complex spectrum of environmental gradients that each impact the composition of bacterioplankton communities. Few studies have attempted to address these gradients comprehensively. We generated a synoptic, 16S rRNA gene-based bacterioplankton community profile of a coastal zone by applying the fingerprinting technique denaturing gradient gel electrophoresis to water samples collected from the Columbia River, estuary, and plume, and along coastal transects covering 360 km of the Oregon and Washington coasts and extending to the deep ocean (>2,000 m). Communities were found to cluster into five distinct groups based on location in the system (ANOSIM, p < 0.003): estuary, plume, epipelagic, shelf bottom (depth < 150 m), and slope bottom (depth > 650 m). Across all environments, abiotic factors (salinity, temperature, depth) explained most of the community variability (ρ = 0.734). But within each coastal environment, biotic factors explained most of the variability. Thus, structuring physical factors in coastal zones, such as salinity and temperature, define the boundaries of many distinct microbial habitats, but within these habitats variability in microbial communities is explained by biological gradients in primary and secondary productivity.}, }
@article {pmid21286701, year = {2011}, author = {Giacomucci, L and Bertoncello, R and Salvadori, O and Martini, I and Favaro, M and Villa, F and Sorlini, C and Cappitelli, F}, title = {Microbial deterioration of artistic tiles from the façade of the Grande Albergo Ausonia &amp; Hungaria (Venice, Italy).}, journal = {Microbial ecology}, volume = {62}, number = {2}, pages = {287-298}, pmid = {21286701}, issn = {1432-184X}, mesh = {Art ; *Biotransformation ; Ceramics/*chemistry ; Color ; Construction Materials/*microbiology ; Cyanobacteria/genetics/*growth &amp; development/isolation &amp; purification/metabolism ; DNA, Ribosomal Spacer/genetics ; Denaturing Gradient Gel Electrophoresis ; Environmental Microbiology ; Fungi/genetics/*growth &amp; development/isolation &amp; purification/metabolism ; Genes, rRNA ; Hydrogen-Ion Concentration ; Italy ; Microbiological Techniques ; Microscopy ; }, abstract = {The Grande Albergo Ausonia &amp; Hungaria (Venice Lido, Italy) has an Art Nouveau polychrome ceramic coating on its façade, which was restored in 2007. Soon after the conservation treatment, many tiles of the façade decoration showed coloured alterations putatively attributed to the presence of microbial communities. To confirm the presence of the biological deposit and the stratigraphy of the Hungaria tiles, stereomicroscope, optical and environmental scanning electron microscope observations were made. The characterisation of the microbial community was performed using a PCR-DGGE approach. This study reported the first use of a culture-independent approach to identify the total community present in biodeteriorated artistic tiles. The case study examined here reveals that the coloured alterations on the tiles were mainly due to the presence of cryptoendolithic cyanobacteria. In addition, we proved that the microflora present on the tiles was generally greatly influenced by the environment of the Hungaria hotel. We found several microorganisms related to the alkaline environment, which is in the range of the tile pH, and related to the aquatic environment, the presence of the acrylic resin Paraloid B72® used during the 2007 treatment and the pollutants of the Venice lagoon.}, }
@article {pmid21274525, year = {2011}, author = {Jiménez, M and Martínez-Urtaza, J and Chaidez, C}, title = {Geographical and temporal dissemination of salmonellae isolated from domestic animal hosts in the Culiacan Valley, Mexico.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {811-820}, pmid = {21274525}, issn = {1432-184X}, mesh = {Animals ; *Animals, Domestic/microbiology ; Cattle ; Chickens ; Feces ; Mexico ; Molecular Sequence Data ; Phylogeny ; Salmonella/classification/genetics/*isolation &amp; purification ; Salmonella Infections, Animal/*microbiology/*transmission ; Sheep ; }, abstract = {The prevalence and diversity of salmonellae from domestic animal hosts were investigated in the Culiacan Valley, Mexico. A total of 240 farm animal feces (cows, chicken, and sheep) were evaluated for Salmonella spp. presence from July 2008 to June 2009. Salmonella enterica subsp. enterica strains were isolated from 76 samples (31.7%), and 20 serotypes were identified being Salmonella Oranienburg (25%), Salmonella Give (14%), Salmonella Saintpaul (12%), and Salmonella Minnesota (11%) the most frequent isolates. Twenty-four percent (18/76) of the isolates were resistant to ampicillin. Salmonella Oranienburg, Salmonella Minnesota, Salmonella Give, Salmonella Agona, Salmonella Weltevreden, and Salmonella Newport serotypes showed multiple pulsed-field electrophoresis patterns. Salmonella Oranienburg was the dominant serotype in the Culiacan Valley; however, no specific distribution patterns were detected in animal sources or sampling sites. The genetic diversity of salmonellae could be an evidence of the continuous animal exposition to the bacteria. Also, Salmonella adaptation in asymptomatic animals could be justified by the development of natural host immunity. This study provides novel information about Salmonella population distribution in domestic animals living at tropical areas. The presence of asymptomatic carriers may be critical to understand the routes of transmission of Salmonella in areas of high disease prevalence.}, }
@article {pmid21271245, year = {2011}, author = {Sridhar, KR and Sudheep, NM}, title = {The spatial distribution of fungi on decomposing woody litter in a freshwater stream, Western Ghats, India.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {635-645}, pmid = {21271245}, issn = {1432-184X}, mesh = {Biodegradation, Environmental ; Biodiversity ; Fungi/*growth &amp; development ; India ; Rivers/chemistry/*microbiology ; Spores, Fungal/growth &amp; development ; *Water Microbiology ; Wood/*microbiology ; }, abstract = {We mapped filamentous fungal association with mechanically "hard" and "soft" woody litter naturally deposited in a stream of the Western Ghats of India. Using a durometer (rubber hardness tester), the toughness of surface of wood collected from stream was determined by considering durometer reading from 60-72 to 30-37 as hardwood and softwood, respectively. From each wood (1.5 cm diameter), two segments each of 3 cm length were excised and vertically cut into nine sections comprising eight marginal and one central section. From three stream locations, hardwood and softwood sections were assessed for the occurrence of lignicolous and Ingoldian fungi. A first set of wood sections was incubated in damp chambers up to 4 months with periodical screening (every 2 weeks) for lignicolous fungi. Another set was incubated in bubble chambers up to 72 h to ascertain colonization of Ingoldian fungi. In hardwood sections, 17 lignicolous fungi (ascomycetes, four; mitosporic fungi, 13; mean, 6.8; range, 6-8/section) and ten Ingoldian fungi (mean, 2; range, 0-4/section) comprising nine lignicolous (11.1-40.7%) and three Ingoldian (11.1-14.8%) fungi as core-group taxa were recovered. In softwood, ten lignicolous fungi (ascomycetes, 0; mitosporic fungi, ten; mean, 3.8; range, 2-5/section) and 26 Ingoldian fungi (mean, 8.1; range, 5-10/section) comprising six lignicolous (11.1-85.2%) and 12 Ingoldian (11.1-88.9%) fungi as core-group taxa were recovered. The ratio of lignicolous fungi/Ingoldian fungi was higher in hardwood than softwood (1.7 vs. 0.4). The spore output of Ingoldian fungi was higher in softwood (mean, 901 g(-1); range, 80-2546 g(-1)) than hardwood (mean, 21 g(-1); range, 0-140 g(-1)). The Shannon diversity of lignicolous fungi was higher in hardwood than softwood (3.604 vs. 2.665), whereas it was opposite for Ingoldian fungi (3.116 vs. 3.918). The overall fungal diversity was higher in softwood than hardwood (4.413 vs. 4.219). The range of Jaccard's index of similarity among wood sections was higher in lignicolous fungi (8-71% and 13-75%) than Ingoldian fungi (0-50% and 8-55%) in hardwood and softwood. The rarefaction indices of expected number of taxa against hardwood sections revealed higher and persistent lignicolous fungi than the Ingoldian fungi, while the Ingoldian fungi were persistent in softwood sections, although they were lower than lignicolous fungi. Our study demonstrated the dominance of lignicolous fungi and Ingoldian fungi in hardwood and softwood, respectively.}, }
@article {pmid21271244, year = {2011}, author = {Rouco, M and López-Rodas, V and Flores-Moya, A and Costas, E}, title = {Evolutionary changes in growth rate and toxin production in the cyanobacterium Microcystis aeruginosa under a scenario of eutrophication and temperature increase.}, journal = {Microbial ecology}, volume = {62}, number = {2}, pages = {265-273}, pmid = {21271244}, issn = {1432-184X}, mesh = {Acclimatization ; *Biological Evolution ; *Eutrophication ; Harmful Algal Bloom ; Microcystins/*biosynthesis ; Microcystis/chemistry/genetics/*growth &amp; development ; Mutation ; Nitrates/metabolism ; Selection, Genetic ; *Temperature ; }, abstract = {Toxic blooms of the cyanobacterium Microcystis aeruginosa affect humans and animals in inland water systems worldwide, and it has been hypothesized that the development of these blooms will increase under the future scenario of global change, considering eutrophication and temperature increase as two important consequences. The importance of genetic adaptation, chance and history on evolution of growth rate, and toxin production of M. aeruginosa was studied under these new conditions. The experiment followed the idea of "replaying life's tape" by means of the simultaneous propagation of 15 independent isolates of three M. aeruginosa strains, which were grown under doubled nutrient concentration and temperature during c. 87 generations. Adaptation by new mutations that resulted in the enhancement of growth rate arose during propagation of derived cultures under the new environmental conditions was the main component of evolution; however, chance also contributed in a lesser extension to evolution of growth rate. Mutations were selected, displacing the wild-type ancestral genotypes. In contrast, the effect of selection on mutations affecting microcystin production was neutral. Chance and history were the pacemakers in evolution of toxin production. Although this study might be considered an oversimplification of the reality, it suggest that a future scenario of global change might lead to an increase in M. aeruginosa bloom frequency, but no predictions about the frequency of toxicity can be made.}, }
@article {pmid21269466, year = {2011}, author = {Ahmad, A and Ghosh, A and Schal, C and Zurek, L}, title = {Insects in confined swine operations carry a large antibiotic resistant and potentially virulent enterococcal community.}, journal = {BMC microbiology}, volume = {11}, number = {1}, pages = {23}, pmid = {21269466}, issn = {1471-2180}, mesh = {Animals ; Cockroaches/*microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus/*drug effects/genetics/*pathogenicity ; Enterococcus faecalis/drug effects/genetics/pathogenicity ; Genotype ; Houseflies/*microbiology ; Phenotype ; Swine ; Virulence/genetics ; }, abstract = {BACKGROUND: Extensive use of antibiotics as growth promoters in the livestock industry constitutes strong selection pressure for evolution and selection of antibiotic resistant bacterial strains. Unfortunately, the microbial ecology and spread of these bacteria in the agricultural, urban, and suburban environments are poorly understood. Insects such as house flies (Musca domestica) and German cockroaches (Blattella germanica) can move freely between animal waste and food and may play a significant role in the dissemination of antibiotic resistant bacteria within and between animal production farms and from farms to residential settings.<br><br>RESULTS: Enterococci from the digestive tract of house flies (n = 162), and feces of German cockroaches (n = 83) and pigs (n = 119), collected from two commercial swine farms were isolated, quantified, identified, and screened for antibiotic resistance and virulence. The majority of samples (93.7%) were positive for enterococci with concentrations 4.2 &#xb1; 0.7 &#xd7; 10&#x2074; CFU/house fly, 5.5 &#xb1; 1.1 &#xd7; 10&#x2076; CFU/g of cockroach feces, and 3.2 &#xb1; 0.8 &#xd7; 10&#x2075; CFU/g of pig feces. Among all the identified isolates (n = 639) Enterococcus faecalis was the most common (55.5%), followed by E. hirae (24.9%), E. faecium (12.8%), and E. casseliflavus (6.7%). E. faecalis was most prevalent in house flies and cockroaches, and E. hirae was most common in pig feces. Our data showed that multi-drug (mainly tetracycline and erythromycin) resistant enterococci were common from all three sources and frequently carried antibiotic resistance genes including tet(M) and erm(B) and Tn916/1545 transposon family. E. faecalis frequently harbored virulence factors gelE, esp, and asa1. PFGE analysis of selected E. faecalis and E. faecium isolates demonstrated that cockroaches and house flies shared some of the same enterococcal clones that were detected in the swine manure indicating that insects acquired enterococci from swine manure.<br><br>CONCLUSIONS: This study shows that house flies and German cockroaches in the confined swine production environment likely serve as vectors and/or reservoirs of antibiotic resistant and potentially virulent enterococci and consequently may play an important role in animal and public health.}, }
@article {pmid21262359, year = {2011}, author = {Carraro, L and Maifreni, M and Bartolomeoli, I and Martino, ME and Novelli, E and Frigo, F and Marino, M and Cardazzo, B}, title = {Comparison of culture-dependent and -independent methods for bacterial community monitoring during Montasio cheese manufacturing.}, journal = {Research in microbiology}, volume = {162}, number = {3}, pages = {231-239}, doi = {10.1016/j.resmic.2011.01.002}, pmid = {21262359}, issn = {1769-7123}, mesh = {Bacteria/*classification/genetics/growth &amp; development/*isolation &amp; purification ; Bacterial Typing Techniques ; Bacteriological Techniques/*methods ; *Biodiversity ; Cheese/*microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The microbial community in milk is of great importance in the manufacture of traditional cheeses produced using raw milk and natural cultures. During milk curdling and cheese ripening, complex interactions occur in the microbial community, and accurate identification of the microorganisms involved provides essential information for understanding their role in these processes and in flavor production. Recent improvements in molecular biological methods have led to their application to food matrices, and thereby opened new perspectives for the study of microbial communities in fermented foods. In this study, a description of microbial community composition during the manufacture and ripening of Montasio cheese was provided. A combined approach using culture-dependent and -independent methods was applied. Culture-dependent identification was compared with 16S clone libraries sequencing data obtained from both DNA and reverse-transcribed RNA (cDNA) amplification and real-time quantitative PCR (qPCR) assays developed to detect and quantify specific bacterial species/genera (Streptococcus thermophilus, Lactobacillus casei, Pediococcus pentosaceus, Enterococcus spp., Pseudomonas spp.). S. thermophilus was the predominant LAB species throughout the entire ripening period of Montasio cheese. The culture-independent method demonstrates the relevant presence of Pseudomonas spp. and Lactococcus piscium at the beginning of ripening. The culture-dependent approach and the two culture-independent approaches produced complementary information, together generating a general view of cheese microbial ecology.}, }
@article {pmid21258788, year = {2011}, author = {Notomista, E and Pennacchio, F and Cafaro, V and Smaldone, G and Izzo, V and Troncone, L and Varcamonti, M and Di Donato, A}, title = {The marine isolate Novosphingobium sp. PP1Y shows specific adaptation to use the aromatic fraction of fuels as the sole carbon and energy source.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {582-594}, pmid = {21258788}, issn = {1432-184X}, mesh = {*Adaptation, Biological ; Biodegradation, Environmental ; Carbon/*metabolism ; DNA, Bacterial/genetics ; Gasoline/*microbiology ; Hydrocarbons, Aromatic/*metabolism ; Italy ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sphingomonadaceae/genetics/growth &amp; development/isolation &amp; purification/*metabolism ; }, abstract = {Novosphingobium sp. PP1Y, isolated from a surface seawater sample collected from a closed bay in the harbour of Pozzuoli (Naples, Italy), uses fuels as its sole carbon and energy source. Like some other Sphingomonads, this strain can grow as either planktonic free cells or sessile-aggregated flocks. In addition, this strain was found to grow as biofilm on several types of solid and liquid hydrophobic surfaces including polystyrene, polypropylene and diesel oil. Strain PP1Y is not able to grow on pure alkanes or alkane mixtures but is able to grow on a surprisingly wide range of aromatic compounds including mono, bi, tri and tetracyclic aromatic hydrocarbons and heterocyclic compounds. During growth on diesel oil, the organic layer is emulsified resulting in the formation of small biofilm-coated drops, whereas during growth on aromatic hydrocarbons dissolved in paraffin the oil layer is emulsified but the drops are coated only if the mixtures contain selected aromatic compounds, like pyrene, propylbenzene, tetrahydronaphthalene and heterocyclic compounds. These peculiar characteristics suggest strain PP1Y has adapted to efficiently grow at the water/fuel interface using the aromatic fraction of fuels as the sole carbon and energy source.}, }
@article {pmid21258787, year = {2011}, author = {Reininger, V and Grünig, CR and Sieber, TN}, title = {Microsatellite-based quantification method to estimate biomass of endophytic Phialocephala species in strain mixtures.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {676-683}, pmid = {21258787}, issn = {1432-184X}, mesh = {Ascomycota/genetics/*growth &amp; development ; *Biomass ; DNA, Fungal/genetics/isolation &amp; purification ; *Microsatellite Repeats ; Mycelium/genetics/*growth &amp; development ; Mycology/*methods ; Picea/microbiology ; Plant Roots/microbiology ; Polymerase Chain Reaction ; Regression Analysis ; }, abstract = {Fungi of the Phialocephala fortinii sensu lato-Acephala applanata species complex (PAC) are ubiquitous endophytic colonizers of tree roots in which they form genotypically diverse communities. Measurement of the colonization density of each of the fungal colonizers is a prerequisite to study the ecology of these communities. Up to now, there is no method readily available for the quantification of PAC strains co-colonizing the same root. The new DNA quantification method presented here is based on the amplification of microsatellites by competitive polymerase chain reaction (PCR). The method proved to be suitable to detect and quantify at least two strains within one single sample by the addition of a known amount of mycelium of a reference strain before DNA extraction. The method exploits the correlation between the reference/target ratio of light emitted during microsatellite detection (peak ratio) and the reference/target ratio of mycelial weights to determine the biomass of the target strain. Hence, calibration curves were obtained by linear regression of the peak ratios on the weight ratios for different mixtures of reference and target strains. The slopes of the calibration curves and the coefficients of determination were close to 1, indicating that peak ratios are good predictors of weight ratios. Estimates of fungal biomass in mycelial test mixtures of known composition laid within the 95% prediction interval and deviated on average by 16% (maximally 50%) from the true biomass. On average, 3-6% of the root biomass of Norway spruce seedlings consisted of mycelial biomass of either one of two inoculated PAC strains. Biomass estimates obtained by real-time quantitative PCR were correlated with the estimates obtained by the microsatellite-based method, but variation between the two estimates from the same root was high in some samples. The microsatellite-based DNA quantification method described here is currently the best method for strainwise estimation of endophytic biomass of PAC fungi in small root samples.}, }
@article {pmid21257304, year = {2011}, author = {Voordouw, G}, title = {Production-related petroleum microbiology: progress and prospects.}, journal = {Current opinion in biotechnology}, volume = {22}, number = {3}, pages = {401-405}, doi = {10.1016/j.copbio.2010.12.005}, pmid = {21257304}, issn = {1879-0429}, mesh = {Bacteria/*metabolism ; Corrosion ; Extraction and Processing Industry ; Fermentation ; Methane/metabolism ; Microbial Consortia ; Nitrates/metabolism ; Petroleum/economics/metabolism/*microbiology ; Sulfates/metabolism ; Sulfides/metabolism ; Sulfur-Reducing Bacteria/metabolism ; }, abstract = {Microbial activity in oil reservoirs is common. Methanogenic consortia hydrolyze low molecular weight components to methane and CO2, transforming light oil to heavy oil to bitumen. The presence of sulfate in injection water causes sulfate-reducing bacteria to produce sulfide. This souring can be reversed by nitrate, stimulating nitrate-reducing bacteria. Removing biogenic sulfide is important, because it contributes to pitting corrosion and resulting pipeline failures. Increased water production eventually makes oil production uneconomic. Microbial fermentation products can lower oil viscosity or interfacial tension and produced biomass can block undesired flow paths to produce more oil. These biotechnologies benefit from increased understanding of reservoir microbial ecology through new sequence technologies and help to decrease the environmental impact of oil production.}, }
@article {pmid21257031, year = {2011}, author = {Wang, SY and Chen, HC and Dai, TY and Huang, IN and Liu, JR and Chen, MJ}, title = {Identification of lactic acid bacteria in Taiwanese ropy fermented milk and evaluation of their microbial ecology in bovine and caprine milk.}, journal = {Journal of dairy science}, volume = {94}, number = {2}, pages = {623-635}, doi = {10.3168/jds.2010-3503}, pmid = {21257031}, issn = {1525-3198}, mesh = {Animals ; Cattle ; *Fermentation ; *Food Microbiology ; Goats ; Lactic Acid ; Lactococcus lactis/classification/*isolation &amp; purification ; Leuconostoc/classification/*isolation &amp; purification ; Milk/*microbiology ; Polymerase Chain Reaction/methods/veterinary ; Taiwan ; }, abstract = {The purpose of this study was to identify species of lactic acid bacteria in Taiwanese ropy fermented milk and to study their microbial dynamics during the fermentation process through conventional microbiological cultivation and PCR-denaturing gradient gel electrophoresis. Identification results indicated that Lactococcus lactis ssp. cremoris and Leuconostoc mesenteroides ssp. mesenteroides were the major lactic acid bacteria in Taiwanese ropy fermented milk. Interestingly, 3 groups were identified as Lc. lactis ssp. cremoris using 16S rDNA sequencing, but they showed different denaturing gradient gel electrophoresis patterns and assimilation of carbohydrates. In addition, the microbial dynamics study in different fermentation stages demonstrated that Lc. lactis ssp. cremoris was the most dominant bacterial species in the samples, followed by Leu. mesenteroides ssp. mesenteroides with no differences among the fermentation stages. Finally, the microbial distribution profiles showed that the microbial ecology was different in bovine, caprine, and reconstituted milk, which might further affect the characteristics of the product.}, }
@article {pmid21251973, year = {2011}, author = {Zhang, Y and Arends, JB and Van de Wiele, T and Boon, N}, title = {Bioreactor technology in marine microbiology: from design to future application.}, journal = {Biotechnology advances}, volume = {29}, number = {3}, pages = {312-321}, doi = {10.1016/j.biotechadv.2011.01.004}, pmid = {21251973}, issn = {1873-1899}, mesh = {*Bioreactors ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {Marine micro-organisms have been playing highly diverse roles over evolutionary time: they have defined the chemistry of the oceans and atmosphere. During the last decades, the bioreactors with novel designs have become an important tool to study marine microbiology and ecology in terms of: marine microorganism cultivation and deep-sea bioprocess characterization; unique bio-chemical product formation and intensification; marine waste treatment and clean energy generation. In this review we briefly summarize the current status of the bioreactor technology applied in marine microbiology and the critical parameters to take into account during the reactor design. Furthermore, when we look at the growing population, as well as, the pollution in the coastal areas of the world, it is urgent to find sustainable practices that beneficially stimulate both the economy and the natural environment. Here we outlook a few possibilities where innovative bioreactor technology can be applied to enhance energy generation and food production without harming the local marine ecosystem.}, }
@article {pmid21249353, year = {2011}, author = {Hagerberg, D and Manique, N and Brandt, KK and Larsen, J and Nybroe, O and Olsson, S}, title = {Low concentration of copper inhibits colonization of soil by the arbuscular mycorrhizal fungus Glomus intraradices and changes the microbial community structure.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {844-852}, pmid = {21249353}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Copper/*metabolism ; Glomeromycota/classification/genetics/*growth &amp; development/metabolism ; Mycorrhizae/classification/genetics/*growth &amp; development/metabolism ; Soil/analysis ; *Soil Microbiology ; Zea mays/growth &amp; development/*microbiology ; }, abstract = {Common agricultural practices result in accumulation of copper in agricultural soils worldwide. The effect of bioavailable copper ([Cu](bio)) on colonization of soil by the AM fungus Glomus intraradices and other soil microorganisms was investigated in microcosms containing copper-amended soil. To avoid indirect effects through the plant, copper was only added to root-free microcosm compartments. [Cu](bio) was measured using a Pseudomonas fluorescens biosensor strain. In the range of 0-1.5 μg g(-1) [Cu](bio), a log-log linear relationship between added copper and [Cu](bio) was found. Microbial colonization of the root-free compartment was evaluated by whole-cell fatty acid analysis (WCFA) and amplified rDNA restriction analysis (ARDRA). The WCFA analysis showed that the AM fungus soil colonization was severely inhibited by Cu with a 50% reduction of mycorrhizal growth at 0.26 μg g(-1) [Cu](bio). The growth of other main microbial groups was not significantly affected by copper. However, ARDRA analysis showed a very strong effect of copper on the bacterial community composition probably caused by an increased proportion of Cu-resistant bacteria. Our results suggest that problems with plant yield may arise when converting slightly copper-contaminated soils to land uses such as low-input and sustainable agriculture that are dependent on AM fungal symbiosis.}, }
@article {pmid21249352, year = {2011}, author = {Hulcr, J and Adams, AS and Raffa, K and Hofstetter, RW and Klepzig, KD and Currie, CR}, title = {Presence and diversity of Streptomyces in Dendroctonus and sympatric bark beetle galleries across North America.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {759-768}, pmid = {21249352}, issn = {1432-184X}, mesh = {Animals ; *Biodiversity ; Coleoptera/*microbiology ; Molecular Sequence Data ; North America ; Phylogeny ; Streptomyces/classification/genetics/*isolation &amp; purification ; }, abstract = {Recent studies have revealed several examples of intimate associations between insects and Actinobacteria, including the Southern Pine Beetle Dendroctonus frontalis and the Spruce Beetle Dendroctonus rufipennis. Here, we surveyed Streptomyces Actinobacteria co-occurring with 10 species of Dendroctonus bark beetles across the United States, using both phylogenetic and community ecology approaches. From these 10 species, and 19 other scolytine beetles that occur in the same trees, we obtained 154 Streptomyces-like isolates and generated 16S sequences from 134 of those. Confirmed 16S sequences of Streptomyces were binned into 36 distinct strains using a threshold of 0.2% sequence divergence. The 16S rDNA phylogeny of all isolates does not correlate with the distribution of strains among beetle species, localities, or parts of the beetles or their galleries. However, we identified three Streptomyces strains occurring repeatedly on Dendroctonus beetles and in their galleries. Identity of these isolates was corroborated using a house-keeping gene sequence (efTu). These strains are not confined to a certain species of beetle, locality, or part of the beetle or their galleries. However, their role as residents in the woodboring insect niche is supported by the repeated association of their 16S and efTu from across the continent, and also having been reported in studies of other subcortical insects.}, }
@article {pmid21246195, year = {2011}, author = {Kebli, H and Drouin, P and Brais, S and Kernaghan, G}, title = {Species composition of saproxylic fungal communities on decaying logs in the boreal forest.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {898-910}, pmid = {21246195}, issn = {1432-184X}, mesh = {Biodiversity ; Fungi/classification/genetics/*isolation &amp; purification/metabolism ; Molecular Sequence Data ; Phylogeny ; Trees/chemistry/metabolism/*microbiology ; Wood/chemistry/metabolism/*microbiology ; }, abstract = {Coarse woody debris supports large numbers of saproxylic fungal species. However, most of the current knowledge comes from Scandinavia and studies relating the effect of stand or log characteristics on the diversity and composition of decomposer fungi have not been conducted in Northeastern Canada. Logs from five tree species were sampled along a decomposition gradient in nine stands representing three successional stages of the boreal mixed forest of Northwestern Quebec, Canada. Using a molecular fingerprinting technique, we assessed fungal community Shannon-Weaver diversity index, richness, and composition. We used linear mixed models and multivariate analyses to link changes in fungal communities to log and stand characteristics. We found a total of 33 operational taxonomic units (OTUs) including an indicator species for balsam fir (similar to Athelia sp.) and one found only in aspen stands (similar to Calocera cornea). Spruce logs supported the highest fungal Shannon-Weaver diversity index and OTU number. Our results support the hypothesis that log species influences fungal richness and diversity. However, log decay class does not. Stand composition, volume of coarse woody debris, and log chemical composition were all involved in structuring fungal communities. Maintaining the diversity of wood-decomposing communities therefore requires the presence of dead wood from diverse log species.}, }
@article {pmid21246194, year = {2011}, author = {Gerçe, B and Schwartz, T and Syldatk, C and Hausmann, R}, title = {Differences between bacterial communities associated with the surface or tissue of Mediterranean sponge species.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {769-782}, pmid = {21246194}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Mediterranean Sea ; Molecular Sequence Data ; Phylogeny ; Porifera/*microbiology ; Seawater/microbiology ; }, abstract = {Bacterial communities associated with the surfaces of several Mediterranean sponge species (Agelas oroides, Chondrosia reniformis, Petrosia ficiformis, Geodia sp., Tethya sp., Axinella polypoides, Dysidea avara, and Oscarella lobularis) were compared to those associated with the mesohyl of sponges and other animate or inanimate reference surfaces as well as with those from bulk seawater. Denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified bacterial 16S ribosomal RNA genes obtained from the surfaces and tissues of these sponges demonstrated that the bacterial communities were generally different from each other. The bacterial communities from sponges were different from those on reference surfaces or from bulk seawater. Additionally, clear distinctions in 16S rDNA fingerprint patterns between the bacterial communities from mesohyl samples of "high-microbial abundance (HMA) sponges" and "low-microbial abundance sponges" were revealed by DGGE and cluster analysis. A dominant occurrence of particularly GC-rich 16S ribosomal DNA (rDNA) fragments was found only in the DGGE banding pattern obtained from the mesohyl of HMA sponges. Furthermore, sequencing analysis of 16S rDNA fragments obtained from mesohyl samples of HMA sponges revealed a dominant occurrence of sponge-associated bacteria. The bacterial communities within the mesohyl of HMA sponges showed a close relationship to each other and seem to be sponge-specific.}, }
@article {pmid21244598, year = {2011}, author = {De Schryver, P and Dierckens, K and Thi, QQ and Amalia, R and Marzorati, M and Bossier, P and Boon, N and Verstraete, W}, title = {Convergent dynamics of the juvenile European sea bass gut microbiota induced by poly-β-hydroxybutyrate.}, journal = {Environmental microbiology}, volume = {13}, number = {4}, pages = {1042-1051}, doi = {10.1111/j.1462-2920.2010.02410.x}, pmid = {21244598}, issn = {1462-2920}, mesh = {Animals ; Aquaculture ; Bacteria/genetics/*growth &amp; development/metabolism ; Bass/growth &amp; development/*microbiology ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Ecosystem ; Feces/microbiology ; Hydroxybutyrates/*metabolism ; Intestines/*microbiology ; *Metagenome ; Polyesters/*metabolism ; }, abstract = {Poly-β-hydroxybutyrate (PHB) is a bacterial energy and carbon storage compound which exhibits a controlling effect on the gastrointestinal microbiota. Its beneficial activities for aquaculture have already been shown in terms of increased disease resistance and growth performance in a number of studies. However, the action of PHB on the intestinal microbial community in the treated animals has not yet been studied in depth. In this research, the effects of PHB on the microbiota composition in the intestinal tract of juvenile sea bass were examined. It was found that fish cohabiting in the same tank were on average 87% similar regarding the intestinal microbiota. When subjected to the same treatment and environmental conditions but reared in different tanks, the compositions of the enteric communities diverged. The provision of PHB overruled this tank effect by sustaining a microbial core community in the gut that represented 60% of the total bacterial diversity at the highest PHB level of 10%. The microbial community compositions converged between replicate tanks upon supplementation of PHB and were characterized by high dynamics and increased evenness. The results are discussed in the framework of hypotheses that try to relate the intestinal microbial community composition to the health status of the host organisms.}, }
@article {pmid21243351, year = {2011}, author = {Ishak, HD and Plowes, R and Sen, R and Kellner, K and Meyer, E and Estrada, DA and Dowd, SE and Mueller, UG}, title = {Bacterial diversity in Solenopsis invicta and Solenopsis geminata ant colonies characterized by 16S amplicon 454 pyrosequencing.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {821-831}, pmid = {21243351}, issn = {1432-184X}, mesh = {Animals ; Ants/*microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Social insects harbor diverse assemblages of bacterial microbes, which may play a crucial role in the success or failure of biological invasions. The invasive fire ant Solenopsis invicta (Formicidae, Hymenoptera) is a model system for understanding the dynamics of invasive social insects and their biological control. However, little is known about microbes as biotic factors influencing the success or failure of ant invasions. This pilot study is the first attempt to characterize and compare microbial communities associated with the introduced S. invicta and the native Solenopsis geminata in the USA. Using 16S amplicon 454 pyrosequencing, bacterial communities of workers, brood, and soil from nest walls were compared between neighboring S. invicta and S. geminata colonies at Brackenridge Field Laboratory, Austin, Texas, with the aim of identifying potential pathogenic, commensal, or mutualistic microbial associates. Two samples of S. geminata workers showed high counts of Spiroplasma bacteria, a known pathogen or mutualist of other insects. A subsequent analysis using PCR and sequencing confirmed the presence of Spiroplasma in additional colonies of both Solenopsis species. Wolbachia was found in one alate sample of S. geminata, while one brood sample of S. invicta had a high count of Lactococcus. As expected, ant samples from both species showed much lower microbial diversity than the surrounding soil. Both ant species had similar overall bacterial diversities, although little overlap in specific microbes. To properly characterize a single bacterial community associated with a Solenopsis ant sample, rarefaction analyses indicate that it is necessary to obtain 5,000-10,000 sequences. Overall, 16S amplicon 454 pyrosequencing appears to be a cost-effective approach to screen whole microbial diversity associated with invasive ant species.}, }
@article {pmid21240482, year = {2011}, author = {Akuzawa, M and Hori, T and Haruta, S and Ueno, Y and Ishii, M and Igarashi, Y}, title = {Distinctive responses of metabolically active microbiota to acidification in a thermophilic anaerobic digester.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {595-605}, pmid = {21240482}, issn = {1432-184X}, mesh = {Acids/*metabolism ; Anaerobiosis ; Bioreactors/*microbiology ; Chloroflexi/genetics/*metabolism ; DNA, Bacterial/genetics ; Fatty Acids, Volatile/*biosynthesis ; Formate-Tetrahydrofolate Ligase/genetics ; Gene Expression Profiling ; Gene Library ; Genes, Bacterial ; Hydrogen-Ion Concentration ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Waste Disposal, Fluid/methods ; }, abstract = {Acidification is one of the most common and serious problems inducing process failure in anaerobic digesters. The production of volatile fatty acids (VFAs) mainly triggers acidic shock. However, little is known about the bacteria involved in the processes of acidogenic metabolism, such as fermentation and reductive acetogenesis. Here, the metabolic responses of a methanogenic community to the acidification and resulting process deterioration were investigated using transcriptional profiling of both the 16S rRNA and formyltetrahydrofolate synthetase (FTHFS) genes. The 16S rRNA-based analyses demonstrated that the dynamic shift of bacterial populations was closely correlated with reactor performance, especially with VFA accumulation levels. The pH drop accompanied by an increase in VFAs stimulated the metabolic activation of an uncultured Chloroflexi subphylum I bacterium. The subphylum has been characterized as a fermentative carbohydrate degrader using culture- and molecular-based ecophysiological assays. At the beginning of VFA accumulation, FTHFS genes were expressed; the transcripts were derived from phylogenetically predicted homoacetogens, suggesting that reductive acetogenesis was operated by hitherto unidentified bacteria. When acetate concentrations were high, the FTHFS expression ceased and Thermoanaerobacterium aciditolerans proliferated selectively. This thermoacidophilic bacterium would play a decisive role in acetate production via fermentative metabolism. The results of this study reveal for the first time that an uncultured Chloroflexi, T. aciditolerans, and novel homoacetogens were metabolically associated with acidic shock and subsequent VFA accumulation in an anaerobic digester.}, }
@article {pmid21234753, year = {2011}, author = {Saag, P and Tilgar, V and Mänd, R and Kilgas, P and Mägi, M}, title = {Plumage bacterial assemblages in a breeding wild passerine: relationships with ecological factors and body condition.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {740-749}, pmid = {21234753}, issn = {1432-184X}, mesh = {Animals ; Animals, Wild/growth &amp; development/microbiology ; Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Breeding ; *Ecosystem ; Feathers/*microbiology ; Female ; Male ; Passeriformes/*growth &amp; development/*microbiology ; }, abstract = {Microorganisms have been shown to play an important role in shaping the life histories of animals, and it has recently been suggested that feather-degrading bacteria influence the trade-off between parental effort and self-preening behavior in birds. We studied a wild breeding population of great tits (Parus major) to explore habitat-, seasonal-, and sex-related variation in feather-degrading and free-living bacteria inhabiting the birds' yellow ventral feathers and to investigate associations with body condition. The density and species richness of bacterial assemblages was studied using flow cytometry and ribosomal intergenic spacer analysis. The density of studied bacteria declined between the nest-building period and the first brood. The number of bacterial phylotypes per bird was higher in coniferous habitat, while bacterial densities were higher in deciduous habitat. Free-living bacterial density was positively correlated with female mass; conversely, there was a negative correlation between attached bacterial density and female mass during the period of peak reproductive effort. Bacterial species richness was sex dependent, with more diverse bacterial assemblages present on males than females. Thus, this study revealed that bacterial assemblages on the feathers of breeding birds are affected both by life history and ecological factors and are related to body condition.}, }
@article {pmid21234752, year = {2011}, author = {Tabata, J and Hattori, Y and Sakamoto, H and Yukuhiro, F and Fujii, T and Kugimiya, S and Mochizuki, A and Ishikawa, Y and Kageyama, D}, title = {Male killing and incomplete inheritance of a novel spiroplasma in the moth Ostrinia zaguliaevi.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {254-263}, pmid = {21234752}, issn = {1432-184X}, mesh = {Animals ; Female ; Genes, Bacterial ; *Inheritance Patterns ; Male ; Moths/*microbiology ; Ovary/microbiology/ultrastructure ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Sex Ratio ; Spiroplasma/classification/genetics/*pathogenicity ; }, abstract = {Bacteria of the genus Spiroplasma are widely found in plants and arthropods. Some of the maternally transmitted Spiroplasma endosymbionts in arthropods are known to kill young male hosts (male killing). Here, we describe a new case of Spiroplasma-induced male killing in a moth, Ostrinia zaguliaevi. The all-female trait caused by Spiroplasma was maternally inherited for more than 11 generations but was spontaneously lost in several lineages. Antibiotic treatment eliminated the Spiroplasma infection and restored the 1:1 sex ratio. The survival rates and presence/absence of the W chromosome in the embryonic and larval stages of O. zaguliaevi showed that males were selectively killed, exclusively during late embryogenesis in all-female broods. Based on phylogenetic analyses of 16S rRNA, dnaA and rpoB gene sequences, the causative bacteria were identified as Spiroplasma belonging to the tick symbiont Spiroplasma ixodetis clade. Electron microscopy confirmed bacterial structures in the follicle cells and follicular sheath of adult females. Although many congeneric Ostrinia moths harbor another sex ratio-distorting bacterium (Wolbachia), only O. zaguliaevi harbors Spiroplasma.}, }
@article {pmid21223336, year = {2011}, author = {Hammer, EC and Pallon, J and Wallander, H and Olsson, PA}, title = {Tit for tat? A mycorrhizal fungus accumulates phosphorus under low plant carbon availability.}, journal = {FEMS microbiology ecology}, volume = {76}, number = {2}, pages = {236-244}, doi = {10.1111/j.1574-6941.2011.01043.x}, pmid = {21223336}, issn = {1574-6941}, mesh = {Carbon/*metabolism ; Culture Media/chemistry ; Glomeromycota/metabolism/physiology ; Mycelium/metabolism/physiology ; Mycorrhizae/*metabolism/physiology ; Phosphates/metabolism ; Phosphorus/*metabolism ; Plant Roots/*microbiology ; Symbiosis/*physiology ; }, abstract = {The exchange of carbohydrates and mineral nutrients in the arbuscular mycorrhizal (AM) symbiosis must be controlled by both partners in order to sustain an evolutionarily stable mutualism. Plants downregulate their carbon (C) flow to the fungus when nutrient levels are sufficient, while the mechanism controlling fungal nutrient transfer is unknown. Here, we show that the fungus accumulates nutrients when connected to a host that is of less benefit to the fungus, indicating a potential of the fungus to control the transfer of nutrients. We used a monoxenic in vitro model of root organ cultures associated with Glomus intraradices, in which we manipulated the C availability to the plant. We found that G. intraradices accumulated up to seven times more nutrients in its spores, and up to nine times more in its hyphae, when the C pool available to the associated roots was halved. The strongest effect was found for phosphorus (P), considered to be the most important nutrient in the AM symbiosis. Other elements such as potassium and chorine were also accumulated, but to a lesser extent, while no accumulation of iron or manganese was found. Our results suggest a functional linkage between C and P exchange.}, }
@article {pmid21223327, year = {2011}, author = {Gray, MA and Stone, RP and McLaughlin, MR and Kellogg, CA}, title = {Microbial consortia of gorgonian corals from the Aleutian islands.}, journal = {FEMS microbiology ecology}, volume = {76}, number = {1}, pages = {109-120}, doi = {10.1111/j.1574-6941.2010.01033.x}, pmid = {21223327}, issn = {1574-6941}, mesh = {Alaska ; Animals ; Anthozoa/*microbiology ; Bacteria/*classification/genetics/isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/genetics ; Gene Library ; Genes, Bacterial ; *Microbial Consortia ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Gorgonians make up the majority of corals in the Aleutian archipelago and provide critical fish habitat in areas of economically important fisheries. The microbial ecology of the deep-sea gorgonian corals Paragorgea arborea, Plumarella superba, and Cryogorgia koolsae was examined with culture-based and 16S rRNA gene-based techniques. Six coral colonies (two per species) were collected. Samples from all corals were cultured, and clone libraries were constructed from P. superba and C. koolsae. Cultured bacteria were dominated by the Gammaproteobacteria, especially Vibrionaceae, with other phyla comprising <6% of the isolates. The clone libraries showed dramatically different bacterial communities between corals of the same species collected at different sites, with no clear pattern of conserved bacterial consortia. Two of the clone libraries (one from each coral species) were dominated by Tenericutes, with Alphaproteobacteria dominating the remaining sequences. The other libraries were more diverse and had a more even distribution of bacterial phyla, showing more similarity between genera than within coral species. Here we report the first microbiological characterization of P. arborea, P. superba, and C. koolsae.}, }
@article {pmid21223326, year = {2011}, author = {Rousk, J and Brookes, PC and Bååth, E}, title = {Fungal and bacterial growth responses to N fertilization and pH in the 150-year 'Park Grass' UK grassland experiment.}, journal = {FEMS microbiology ecology}, volume = {76}, number = {1}, pages = {89-99}, doi = {10.1111/j.1574-6941.2010.01032.x}, pmid = {21223326}, issn = {1574-6941}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/*growth &amp; development ; Biomass ; Carbon Dioxide/analysis ; Fatty Acids/analysis ; Fertilizers ; Fungi/*growth &amp; development ; Hydrogen-Ion Concentration ; Nitrogen/*metabolism ; Phospholipids/analysis ; Poaceae/microbiology ; Soil/chemistry ; *Soil Microbiology ; United Kingdom ; }, abstract = {The effects of nitrogen (N) fertilization (0-150 kg N ha[-1] year[-1] since 1865) and pH (3.3-7.4) on fungal and bacterial growth, biomass and phospholipid fatty acid (PLFA) composition were investigated in grassland soils from the 'Park Grass Experiment', Rothamsted Research, UK. Bacterial growth decreased and fungal growth increased with lower pH, resulting in a 50-fold increase in the relative importance of fungi between pH 7.4 and 3.3. The PLFA-based fungal:bacterial biomass ratio was unchanged between pH 4.5 and 7.4, and decreased only below pH 4.5. Respiration and substrate-induced respiration biomass both decreased three- to fourfold with lower pH, but biomass concentrations estimated using PLFAs were unaffected by pH. N fertilization did not affect bacterial growth and marginally affected fungal growth while PLFA biomass marker concentrations were all reduced by higher N additions. Respiration decreased with higher N application, suggesting a reduced quality of the soil organic carbon. The PLFA composition was strongly affected by both pH and N. A comparison with a pH gradient in arable soil allowed us to generalize the pH effect between systems. There are 30-50-fold increases in the relative importance of fungi between high (7.4-8.3) and low (3.3-4.5) pH with concomitant reductions of respiration by 30-70%.}, }
@article {pmid21222211, year = {2011}, author = {Karlsson, FH and Ussery, DW and Nielsen, J and Nookaew, I}, title = {A closer look at bacteroides: phylogenetic relationship and genomic implications of a life in the human gut.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {473-485}, pmid = {21222211}, issn = {1432-184X}, mesh = {Bacteroidetes/*classification/genetics ; Chlorobi/*classification/genetics ; Comparative Genomic Hybridization ; Computational Biology ; DNA, Bacterial/genetics ; Gastrointestinal Tract/*microbiology ; Genome, Bacterial ; Humans ; *Metagenome ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The human gut is extremely densely inhabited by bacteria mainly from two phyla, Bacteroidetes and Firmicutes, and there is a great interest in analyzing whole-genome sequences for these species because of their relation to human health and disease. Here, we do whole-genome comparison of 105 Bacteroidetes/Chlorobi genomes to elucidate their phylogenetic relationship and to gain insight into what is separating the gut living Bacteroides and Parabacteroides genera from other Bacteroidetes/Chlorobi species. A comprehensive analysis shows that Bacteroides species have a higher number of extracytoplasmic function σ factors (ECF σ factors) and two component systems for extracellular signal transduction compared to other Bacteroidetes/Chlorobi species. A whole-genome phylogenetic analysis shows a very little difference between the Parabacteroides and Bacteroides genera. Further analysis shows that Bacteroides and Parabacteroides species share a large common core of 1,085 protein families. Genome atlases illustrate that there are few and only small unique areas on the chromosomes of four Bacteroides/Parabacteroides genomes. Functional classification to clusters of othologus groups show that Bacteroides species are enriched in carbohydrate transport and metabolism proteins. Classification of proteins in KEGG metabolic pathways gives a detailed view of the genome's metabolic capabilities that can be linked to its habitat. Bacteroides pectinophilus and Bacteroides capillosus do not cluster together with other Bacteroides species, based on analysis of 16S rRNA sequence, whole-genome protein families and functional content, 16S rRNA sequences of the two species suggest that they belong to the Firmicutes phylum. We have presented a more detailed and precise description of the phylogenetic relationships of members of the Bacteroidetes/Chlorobi phylum by whole genome comparison. Gut living Bacteroides have an enriched set of glycan, vitamin, and cofactor enzymes important for diet digestion.}, }
@article {pmid21221569, year = {2011}, author = {Butinar, L and Strmole, T and Gunde-Cimerman, N}, title = {Relative incidence of ascomycetous yeasts in arctic coastal environments.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {832-843}, pmid = {21221569}, issn = {1432-184X}, mesh = {Arctic Regions ; Ascomycota/classification/genetics/*isolation &amp; purification ; Cold Temperature ; Ice Cover/*microbiology ; Molecular Sequence Data ; Phylogeny ; Seawater/*microbiology ; Yeasts/classification/genetics/*isolation &amp; purification ; }, abstract = {Previous studies of fungi in polar environments have revealed a prevalence of basidiomycetous yeasts in soil and in subglacial environments of polythermal glaciers. Ascomycetous yeasts have rarely been reported from extremely cold natural environments, even though they are known contaminants of frozen foods. Using media with low water activity, we have isolated various yeast species from the subglacial ice of four glaciers from the coastal Arctic environment of Kongsfjorden, Spitzbergen, including Debaryomyces hansenii and Pichia guillermondii, with counts reaching 10(4) CFU L(-1). Together with the basidiomycetes Cryptococcus liquefaciens and Rhodotorula mucilaginosa, these yeasts represent the stable core of the subglacial yeast communities. Other glacial ascomycetous species isolated included Candida parapsilosis and a putative new species that resembles Candida pseudorugosa. The archiascomycete Protomyces inouyei has seldom been detected anywhere in the world but was here recovered from ice in a glacier cave. The glacier meltwater contained only D. hansenii, whereas the seawater contained D. hansenii, Debaryomyces maramus, Pichia guilliermondii, what appears to represent a novel species resembling Candida galli and Metschnikowia bicuspidata. Only P. guilliermondii was isolated from sea ice, while snow/ice in the fjord tidal zone included C. parapsilosis, D. hansenii, P. guilliermondii and Metschnikowia zobellii. All of these isolated strains were characterized as psychrotolerant and xero/halotolerant, with the exception of P. inouyei.}, }
@article {pmid21219415, year = {2011}, author = {Lecomte, J and St-Arnaud, M and Hijri, M}, title = {Isolation and identification of soil bacteria growing at the expense of arbuscular mycorrhizal fungi.}, journal = {FEMS microbiology letters}, volume = {317}, number = {1}, pages = {43-51}, doi = {10.1111/j.1574-6968.2011.02209.x}, pmid = {21219415}, issn = {1574-6968}, mesh = {Agrostis/microbiology ; Bacteria/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Glomeromycota/*growth &amp; development ; *Microbial Interactions ; Molecular Sequence Data ; Mycorrhizae/*growth &amp; development ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Soil-microorganism symbioses are of fundamental importance for plant adaptation to the environment. Research in microbial ecology has revealed that some soil bacteria are associated with arbuscular mycorrhizal fungi (AMF). However, these interactions may be much more complex than originally thought. To assess the type of bacteria associated with AMF, we initially isolated spores of Glomus irregulare from an Agrostis stolonifera rhizosphere. The spores were washed with sterile water and plated onto G. irregulare mycelium growing in vitro in a root-free compartment of bicompartmented Petri dishes. We hypothesized that this system should select for bacteria closely associated with the fungus because the only nutrients available to the bacteria were those derived from the hyphae. Twenty-nine bacterial colonies growing on the AMF hyphae were subcultured and identified using 16S rRNA gene sequences. All bacterial isolates showed high sequence identity to Bacillus cereus, Bacillus megaterium, Bacillus simplex, Kocuria rhizophila, Microbacterium ginsengisoli, Sphingomonas sp. and Variovorax paradoxus. We also assessed bacterial diversity on the surface of spores by PCR-denaturating gradient gel electrophoresis. Finally, we used live cellular imaging to show that the bacteria isolated can grow on the surface of hyphae with different growing patterns in contrast to Escherichia coli as a control.}, }
@article {pmid21216981, year = {2011}, author = {Kanakupt, K and Vester Boler, BM and Dunsford, BR and Fahey, GC}, title = {Effects of short-chain fructooligosaccharides and galactooligosaccharides, individually and in combination, on nutrient digestibility, fecal fermentative metabolite concentrations, and large bowel microbial ecology of healthy adults cats.}, journal = {Journal of animal science}, volume = {89}, number = {5}, pages = {1376-1384}, doi = {10.2527/jas.2010-3201}, pmid = {21216981}, issn = {1525-3163}, mesh = {Ammonia/analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Bifidobacterium/isolation &amp; purification ; Blood Cell Count/veterinary ; Cats/*metabolism ; Colony Count, Microbial/veterinary ; DNA, Bacterial/chemistry/genetics ; Dietary Proteins/*metabolism ; Digestion/*physiology ; Fatty Acids, Nonesterified/analysis ; Feces/chemistry/microbiology ; Intestine, Large/*metabolism/microbiology ; Male ; Oligosaccharides/*administration &amp; dosage/metabolism ; Polymerase Chain Reaction/veterinary ; Prebiotics ; }, abstract = {Short-chain fructooligosaccharides (scFOS) and galactooligosaccharides (GOS) are nondigestible oligosaccharides that result in a prebiotic effect in some animal species; however, the cat has not been well studied in this regard. This experiment evaluated scFOS and GOS supplementation on nutrient digestibility, fermentative end product production, and fecal microbial ecology of cats. Eight healthy adult cats were fed diets containing no prebiotic, 0.5% scFOS, 0.5% GOS, or 0.5% scFOS + 0.5% GOS (scFOS + GOS) in a replicated 4 × 4 Latin square design. Apparent total tract CP digestibility was decreased (P < 0.05) when cats were fed a diet containing scFOS + GOS compared with the other treatments. Dry matter, OM, acid hydrolyzed fat, and GE digestibilities were not different (P > 0.05) among treatments. Cats fed scFOS-, GOS-, and scFOS + GOS-supplemented diets had greater (P < 0.05) fecal Bifidobacterium spp. populations compared with cats fed the control diet. Fecal pH was less (P < 0.05) for cats fed the scFOS + GOS-supplemented diet compared with the control. Butyrate (P = 0.05) and valerate (P < 0.05) concentrations were greater when cats consumed the scFOS + GOS diet. Acetate tended (P = 0.10) to be greater when cats were fed the scFOS + GOS diet. Total short-chain fatty acid (P = 0.06) and total branched-chain fatty acid (P = 0.06) concentrations also tended to be greater when cats consumed the scFOS + GOS treatment. Fecal protein catabolites, including ammonia, 4-methylphenol, indole, and biogenic amines, blood lymphocytes, neutrophils, total white blood cell counts, or fecal DM concentration and output did not differ (P > 0.05) among treatments. Low level supplementation of scFOS, GOS, and their combination exert positive effects on select indices of gut health in cats.}, }
@article {pmid21207019, year = {2011}, author = {Reinoso, R and Blanco, S and Torres-Villamizar, LA and Bécares, E}, title = {Mechanisms for parasites removal in a waste stabilisation pond.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {684-692}, pmid = {21207019}, issn = {1432-184X}, mesh = {Animals ; Bacteria/isolation &amp; purification ; Coliphages/isolation &amp; purification ; Cryptosporidium/isolation &amp; purification ; Geologic Sediments/microbiology/parasitology/virology ; Giardia/isolation &amp; purification ; Helminths/isolation &amp; purification ; Oocysts ; Parasite Egg Count ; Seasons ; Sewage/*microbiology/*parasitology ; Water/*parasitology ; *Water Microbiology ; Water Purification/*methods ; }, abstract = {A waste stabilisation pond (WSP) system formed by two anaerobic ponds, a facultative pond and a maturation pond was studied from December 2003 to September 2004 in north-western Spain in order to evaluate its efficiency in the removal of faecal indicator bacteria (total coliforms, Escherichia coli, faecal streptococci), coliphages, helminth eggs and protozoan (oo)cysts (Cryptosporidium and Giardia). Furthermore, sediment samples were collected from the bottom of the ponds to assess the settling rates and thus determine the main pathogen removal mechanisms in the WSPs system. The overall removal ranged from 1.4 log units for coliphages in the cold period to 5.0 log units for E. coli in the hot period. Cryptosporidium oocysts were reduced by an average of 96%, Giardia cysts by 98% and helminth eggs by 100%. The anaerobic ponds showed significantly higher surface removal rates (4.6, 5.2 and 3.7 log (oo)cysts/eggs removed m(-2) day(-1), respectively) than facultative and maturation ponds. Sunlight and water physicochemical conditions were the main factors influencing C. parvum oocysts removal both in the anaerobic and maturation ponds, whereas other factors like predation or natural mortality were more important in the facultative pond. Sedimentation, the most commonly proposed mechanism for cyst removal had, therefore, a negligible influence in the studied ponds.}, }
@article {pmid21188377, year = {2011}, author = {Vohník, M and Burdíková, Z and Vyhnal, A and Koukol, O}, title = {Interactions between testate amoebae and saprotrophic microfungi in a Scots pine litter microcosm.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {660-668}, pmid = {21188377}, issn = {1432-184X}, mesh = {Ascomycota/*physiology ; Lobosea/microbiology/*physiology ; *Microbial Interactions ; Mycelium/physiology ; Pinus sylvestris/*microbiology ; *Soil Microbiology ; }, abstract = {In all terrestrial ecosystems, testate amoebae (TA) encounter fungi. There are strong indications that both groups engage in multiple interactions, including mycophagy and decomposition of TA shells, processes which might be fundamental in nutrient cycling in certain ecosystems. Here, we present the results of an experiment focusing on interactions between TA and saprotrophic microfungi colonizing Scots pine (Pinus sylvestris L.) litter needles. The needles were collected from a temperate pine forest and cultivated in damp chambers. Over a few weeks, melanized mycelium of Anavirga laxa Sutton started to grow out of some needles; simultaneously, the common forest-soil TA Phryganella acropodia (Hertwig and Lesser) Hopkinson reproduced and spread around the mycelium. We investigated whether a potential relationship between TA and saprotrophic microfungi exists by comparing the composition of TA communities on and around the needles and testing the spatial relationship between the A. laxa mycelium and P. acropodia shells in the experimental microcosm. Additionally, we asked whether P. acropodia utilized the A. laxa mycelium as a nutrient source and screened whether P. acropodia shells were colonized by the microfungi inhabiting the experimental microcosm. Our results indicate that saprotrophic microfungi may affect the composition of TA communities and their mycelium may affect distribution of TA individuals in pine litter. Our observations suggest that P. acropodia did not graze directly on A. laxa mycelium, but rather fed on its exudates or bacteria associated with the exudates. The fungus Pochonia bulbillosa (Gams &amp; Malla) Zare &amp; Gams was often found parasitising encysted shells or decomposing already dead individuals of P. acropodia. TA and pine litter microfungi engage in various direct and indirect interactions which are still poorly understood and deserve further investigation. Their elucidation will improve our knowledge on fundamental processes influencing coexistence of soil microflora and microfauna.}, }
@article {pmid21188376, year = {2011}, author = {Azúa-Bustos, A and González-Silva, C and Mancilla, RA and Salas, L and Gómez-Silva, B and McKay, CP and Vicuña, R}, title = {Hypolithic cyanobacteria supported mainly by fog in the coastal range of the Atacama Desert.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {568-581}, pmid = {21188376}, issn = {1432-184X}, mesh = {Biodiversity ; Chile ; Cyanobacteria/classification/genetics/*growth &amp; development ; *Desert Climate ; *Humidity ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Photosynthesis ; Quartz ; RNA, Ribosomal, 16S/genetics ; Rain ; *Soil Microbiology ; Temperature ; Water/physiology ; *Weather ; }, abstract = {The Atacama Desert is one of the driest places on Earth, with an arid core highly adverse to the development of hypolithic cyanobacteria. Previous work has shown that when rain levels fall below ~1 mm per year, colonization of suitable quartz stones falls to virtually zero. Here, we report that along the coast in these arid regions, complex associations of cyanobacteria, archaea, and heterotrophic bacteria inhabit the undersides of translucent quartz stones. Colonization rates in these areas, which receive virtually no rain but mainly fog, are significantly higher than those reported inland in the hyperarid zone at the same latitude. Here, hypolithic colonization rates can be up to 80%, with all quartz rocks over 20 g being colonized. This finding strongly suggests that hypolithic microbial communities thriving in the seaward face of the Coastal Range can survive with fog as the main regular source of moisture. A model is advanced where the development of the hypolithic communities under quartz stones relies on a positive feedback between fog availability and the higher thermal conductivity of the quartz rocks, which results in lower daytime temperatures at the quartz-soil interface microenvironment.}, }
@article {pmid21183198, year = {2011}, author = {De Gusseme, B and Hennebel, T and Christiaens, E and Saveyn, H and Verbeken, K and Fitts, JP and Boon, N and Verstraete, W}, title = {Virus disinfection in water by biogenic silver immobilized in polyvinylidene fluoride membranes.}, journal = {Water research}, volume = {45}, number = {4}, pages = {1856-1864}, doi = {10.1016/j.watres.2010.11.046}, pmid = {21183198}, issn = {1879-2448}, mesh = {Bacteriophages/drug effects/*isolation &amp; purification ; Biodegradation, Environmental/drug effects ; Bioreactors/microbiology ; Disinfection/*methods ; Filtration ; Hydrophobic and Hydrophilic Interactions/drug effects ; Lactobacillus/*metabolism ; *Membranes, Artificial ; Microscopy, Electron, Scanning ; Polyvinyls/*chemistry ; Silver/*pharmacology ; Static Electricity ; Virus Inactivation/drug effects ; Waste Disposal, Fluid ; Water Purification/*methods ; }, abstract = {The development of innovative water disinfection strategies is of utmost importance to prevent outbreaks of waterborne diseases related to poor treatment of (drinking) water. Recently, the association of silver nanoparticles with the bacterial cell surface of Lactobacillus fermentum (referred to as biogenic silver or bio-Ag(0)) has been reported to exhibit antiviral properties. The microscale bacterial carrier matrix serves as a scaffold for Ag(0) particles, preventing aggregation during encapsulation. In this study, bio-Ag(0) was immobilized in different microporous PVDF membranes using two different pre-treatments of bio-Ag(0) and the immersion-precipitation method. Inactivation of UZ1 bacteriophages using these membranes was successfully demonstrated and was most probably related to the slow release of Ag(+) from the membranes. At least a 3.4 log decrease of viruses was achieved by application of a membrane containing 2500 mg bio-Ag(0)(powder) m(-2) in a submerged plate membrane reactor operated at a flux of 3.1 L m(-2) h(-1). Upon startup, the silver concentration in the effluent initially increased to 271 μg L(-1) but after filtration of 31 L m(-2), the concentration approached the drinking water limit (= 100 μg L(-1)). A virus decline of more than 3 log was achieved at a membrane flux of 75 L m(-2) h(-1), showing the potential of this membrane technology for water disinfection on small scale.}, }
@article {pmid21181142, year = {2011}, author = {Kovacs, A and Ben-Jacob, N and Tayem, H and Halperin, E and Iraqi, FA and Gophna, U}, title = {Genotype is a stronger determinant than sex of the mouse gut microbiota.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {423-428}, pmid = {21181142}, issn = {1432-184X}, mesh = {Animals ; DNA Fingerprinting ; DNA, Ribosomal Spacer/genetics ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; *Genotype ; Male ; *Metagenome ; Mice ; Mice, Inbred Strains ; Polymorphism, Genetic ; Sex Factors ; }, abstract = {The mammalian gut microbiota is considered to be determined mostly by diet, while the effect of genotype is still controversial. Here, we examined the effect of genotype on the gut microbiota in normal populations, exhibiting only natural polymorphisms, and evaluated this effect in comparison to the effect of sex. DNA fingerprinting approaches were used to profile the gut microbiota of eight different recombinant inbred mouse lines of the collaborative cross consortium, whose level of genetic diversity mimics that of a natural human population. Analyses based on automated ribosomal internal transcribed spacer analysis demonstrated significant higher similarity of the gut microbiota composition within mouse lines than between them or within same-gender groups. Thus, genetic background significantly impacts the microbiota composition and is a stronger determinant than gender. These findings imply that genetic polymorphisms help shape the intestinal microbiota of mammals and consequently could affect host susceptibility to diseases.}, }
@article {pmid21178499, year = {2010}, author = {Penz, T and Horn, M and Schmitz-Esser, S}, title = {The genome of the amoeba symbiont "Candidatus Amoebophilus asiaticus" encodes an afp-like prophage possibly used for protein secretion.}, journal = {Virulence}, volume = {1}, number = {6}, pages = {541-545}, doi = {10.4161/viru.1.6.13800}, pmid = {21178499}, issn = {2150-5608}, support = {P 22703/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Amoeba/*microbiology ; Bacterial Adhesion ; Bacterial Proteins/*genetics/metabolism ; Bacterial Secretion Systems/*genetics ; Bacteroidetes/*genetics/metabolism ; DNA, Bacterial/genetics ; *Genome, Bacterial ; Prophages/*genetics ; Symbiosis ; }, abstract = {The recently sequenced genome of the obligate intracellular amoeba symbiont 'Candidatus Amoebophilus asiaticus' is unique among prokaryotic genomes due to its extremely large fraction of genes encoding proteins harboring eukaryotic domains such as ankyrin-repeats, TPR/SEL1 repeats, leucine-rich repeats, as well as F- and U-box domains, most of which likely serve in the interaction with the amoeba host. Here we provide evidence for the presence of additional proteins which are presumably presented extracellularly and should thus also be important for host cell interaction. Surprisingly, we did not find homologues of any of the well-known protein secretion systems required to translocate effector proteins into the host cell in the A. asiaticus genome, and the type six secretion systems seems to be incomplete. Here we describe the presence of a putative prophage in the A. asiaticus genome, which shows similarity to the antifeeding prophage from the insect pathogen Serratia entomophila. In S. entomophila this system is used to deliver toxins into insect hosts. This putative antifeeding-like prophage might thus represent the missing protein secretion apparatus in A. asiaticus.}, }
@article {pmid21177100, year = {2011}, author = {Bchir, FS and Gannoun, H and El Herry, S and Hamdi, M}, title = {Optimization of Spongiochloris sp. biomass production in the abattoir digestate.}, journal = {Bioresource technology}, volume = {102}, number = {4}, pages = {3869-3876}, doi = {10.1016/j.biortech.2010.11.036}, pmid = {21177100}, issn = {1873-2976}, mesh = {Abattoirs ; Animals ; Biodegradation, Environmental ; *Biomass ; Biotechnology/methods ; Chlorophyll/chemistry ; Chlorophyll A ; Chlorophyta/*metabolism ; Culture Media ; Industrial Waste ; Iron/chemistry ; Kinetics ; Models, Statistical ; Sewage ; Sulfates/chemistry ; }, abstract = {In the present study, the abattoir digestate was used as a culture medium for Spongiochloris sp. growth with added mineral components under optimized conditions in batch culture. Firstly, an Hadamard matrix was used to investigate the impact of certain influencing factors on the Spongiochloris sp. growth. Then, a fractional factorial design 2(7-4) was successfully employed to optimize the concentration of different added components to abattoir digestate for increased Spongiochloris sp. biomass production. The major influencing factors were NaHCO(3) and FeSO(4) at a level of 2000 mg/L and 5mg/L, respectively. A high biomass production of 5.29 × 10(6) cell/mL and an important content of chlorophyll a of 65.32 mg/L were obtained after 42 days of culture of Spongiochloris sp. on the defined abattoir medium at static conditions.}, }
@article {pmid21174086, year = {2011}, author = {Goffredi, SK and Kantor, AH and Woodside, WT}, title = {Aquatic microbial habitats within a neotropical rainforest: bromeliads and pH-associated trends in bacterial diversity and composition.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {529-542}, pmid = {21174086}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics ; *Biodiversity ; Bromeliaceae/chemistry/*microbiology ; Carbon/analysis ; Costa Rica ; DNA, Bacterial/genetics ; Hydrogen-Ion Concentration ; Nitrogen/analysis ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/analysis ; Trees/*microbiology ; Tropical Climate ; }, abstract = {Tank-forming bromeliads, suspended in the rainforest canopy, possess foliage arranged in compact rosettes capable of long-term retention of rainwater. This large and unique aquatic habitat is inhabited by microorganisms involved in the important decomposition of impounded material. Moreover, these communities are likely influenced by environmental factors such as pH, oxygen, and light. Bacterial community composition and diversity was determined for the tanks of several bromeliad species (Aechmea and Werauhia) from northern Costa Rica, which span a range of parameters, including tank morphology and pH. These were compared with a nearby forest soil sample, an artificial tank (amber bottle), and a commercially available species (Aechmea). Bacterial community diversity, as measured by 16S rRNA analysis and tRFLP, showed a significant positive correlation with tank pH. A majority of 16S rRNA bacterial phylotypes found in association with acidic bromeliad tanks of pH < 5.1 were affiliated with the Alphaproteobacteria, Acidobacteria, Planctomycetes, and Bacteroidetes, and were similar to those found in acidic peat bogs, yet distinct from the underlying soil community. In contrast, bromeliads with tank pH > 5.3, including the commercial bromeliad with the highest pH (6.7), were dominated by Betaproteobacteria, Firmicutes, and Bacteroidetes. To empirically determine the effect of pH on bacterial community, the tank pH of a specimen of Aechmea was depressed, in the field, from 6.5 to 4.5, for 62 days. The resulting community changed predictably with decreased abundance of Betaproteobacteria and Firmicutes and a concomitant increase in Alphaproteobacteria and Acidobacteria. Collectively, these results suggest that bromeliad tanks provide important habitats for a diverse microbial community, distinct from the surrounding environment, which are influenced greatly by acid-base conditions. Additionally, total organic carbon (∼46%) and nitrogen (∼2%) of bromeliad-impounded sediment was elevated relative to soil and gene surveys confirmed the presence of both chitinases and nitrogenases, suggesting that bromeliad tanks may provide important habitats for microbes involved in the biological cycling of carbon and nitrogen in tropical forests.}, }
@article {pmid21169452, year = {2011}, author = {Steger, D and Wentrup, C and Braunegger, C and Deevong, P and Hofer, M and Richter, A and Baranyi, C and Pester, M and Wagner, M and Loy, A}, title = {Microorganisms with novel dissimilatory (bi)sulfite reductase genes are widespread and part of the core microbiota in low-sulfate peatlands.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {4}, pages = {1231-1242}, pmid = {21169452}, issn = {1098-5336}, support = {P 18836/FWF_/Austrian Science Fund FWF/Austria ; P 20185/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Alkanesulfonates/metabolism ; Bacteria/enzymology/*genetics ; DNA, Bacterial/chemistry/genetics ; Denaturing Gradient Gel Electrophoresis ; Environment ; Gene Library ; Genetic Variation ; Geologic Sediments ; Germany ; Hydrogensulfite Reductase/*genetics/metabolism ; Metagenome/*genetics ; Microarray Analysis ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Soil ; *Soil Microbiology ; Sulfates/metabolism ; Sulfites/metabolism ; Sulfur-Reducing Bacteria/enzymology/*genetics ; *Wetlands ; }, abstract = {Peatlands of the Lehstenbach catchment (Germany) house as-yet-unidentified microorganisms with phylogenetically novel variants of the dissimilatory (bi)sulfite reductase genes dsrAB. These genes are characteristic of microorganisms that reduce sulfate, sulfite, or some organosulfonates for energy conservation but can also be present in anaerobic syntrophs. However, nothing is currently known regarding the abundance, community dynamics, and biogeography of these dsrAB-carrying microorganisms in peatlands. To tackle these issues, soils from a Lehstenbach catchment site (Schlöppnerbrunnen II fen) from different depths were sampled at three time points over a 6-year period to analyze the diversity and distribution of dsrAB-containing microorganisms by a newly developed functional gene microarray and quantitative PCR assays. Members of novel, uncultivated dsrAB lineages (approximately representing species-level groups) (i) dominated a temporally stable but spatially structured dsrAB community and (ii) represented "core" members (up to 1% to 1.7% relative abundance) of the autochthonous microbial community in this fen. In addition, denaturing gradient gel electrophoresis (DGGE)- and clone library-based comparisons of the dsrAB diversity in soils from a wet meadow, three bogs, and five fens of various geographic locations (distance of ∼1 to 400 km) identified that one Syntrophobacter-related and nine novel dsrAB lineages are widespread in low-sulfate peatlands. Signatures of biogeography in dsrB-based DGGE data were not correlated with geographic distance but could be explained largely by soil pH and wetland type, implying that the distribution of dsrAB-carrying microorganisms in wetlands on the scale of a few hundred kilometers is not limited by dispersal but determined by local environmental conditions.}, }
@article {pmid21169440, year = {2011}, author = {Frenzel, E and Letzel, T and Scherer, S and Ehling-Schulz, M}, title = {Inhibition of cereulide toxin synthesis by emetic Bacillus cereus via long-chain polyphosphates.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {4}, pages = {1475-1482}, pmid = {21169440}, issn = {1098-5336}, mesh = {Bacillus cereus/drug effects/*genetics/growth &amp; development/*metabolism ; Bacterial Toxins/*biosynthesis ; Chromatography, High Pressure Liquid ; Depsipeptides/*biosynthesis/genetics/metabolism ; Down-Regulation/drug effects ; Food Industry/methods ; Food Microbiology/methods ; Peptide Biosynthesis, Nucleic Acid-Independent/drug effects ; Peptide Synthases/genetics/*metabolism ; Polymerase Chain Reaction ; Polyphosphates/*pharmacology ; Promoter Regions, Genetic ; Spectrometry, Mass, Electrospray Ionization ; }, abstract = {Severe intoxications caused by the Bacillus cereus emetic toxin cereulide can hardly be prevented due to the ubiquitous distribution and heat resistance of spores and the extreme thermal and chemical stability of cereulide. It would therefore be desirable to inhibit cereulide synthesis during food manufacturing processes or in prepared foods, which are stored under time-temperature abuse conditions. Toward this end, the impacts of three long-chain polyphosphate (polyP) formulations on growth and cereulide production were examined. The inhibition was dependent on the concentration and the type of the polyP blend, indicating that polyPs and not the orthophosphates were effective. Quantitative PCR (qPCR) monitoring at sublethal concentrations revealed that polyPs reduced the transcription of ces nonribosomal peptide synthetase (NRPS) genes by 3- to 4-fold along with a significantly reduced toxin production level. At lower concentrations, toxin synthesis was decreased, although the growth rate was not affected. These data indicate a differential effect on toxin synthesis independent of growth inhibition. The inhibition of toxin synthesis in food was also observed. Despite the growth of B. cereus, toxin synthesis was reduced by 70 to 100% in two model food systems (reconstituted infant food and oat milk), which were analyzed with HEp-2 cell culture assays and high-performance liquid chromatography (HPLC)/electrospray ionization-time of flight mass spectrometry (ESI-TOF-MS). Accordingly, ces promoter activity was strongly downregulated, as visualized by using a lux-based reporter strain. These data illustrate the potential of polyphosphate formulations to reduce the risk of cereulide synthesis in food and may contribute to targeted hurdle concepts.}, }
@article {pmid21167545, year = {2011}, author = {De Gusseme, B and Vanhaecke, L and Verstraete, W and Boon, N}, title = {Degradation of acetaminophen by Delftia tsuruhatensis and Pseudomonas aeruginosa in a membrane bioreactor.}, journal = {Water research}, volume = {45}, number = {4}, pages = {1829-1837}, doi = {10.1016/j.watres.2010.11.040}, pmid = {21167545}, issn = {1879-2448}, mesh = {Acetaminophen/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Biomass ; Bioreactors/*microbiology ; Chromatography, High Pressure Liquid ; Delftia/isolation &amp; purification/*metabolism ; *Membranes, Artificial ; Nitrification ; Pseudomonas aeruginosa/isolation &amp; purification/*metabolism ; Reference Standards ; Time Factors ; Ultraviolet Rays ; Water Purification/*instrumentation/*methods ; }, abstract = {The incidence and fate of pharmaceuticals in the water cycle impose a growing concern for the future reuse of treated water. Because of the recurrent global use of drugs such as Acetaminophen (APAP), an analgesic and antipyretic drug, they are often detected in wastewater treatment plant (WWTP) effluents, receiving surface waters and drinking water resources. In this study, the removal of APAP has been demonstrated in a membrane bioreactor (MBR) fed with APAP as the sole carbon source. After 16 days of operation, at a hydraulic retention time (HRT) of 5 days, more than 99.9% removal was obtained when supplying a synthetic WWTP effluent with 100 μg APAP L(-1). Batch experiments indicated no sorption of APAP to the biomass, no influence of the WWTP effluent matrix, and the capability of the microbial consortium to remove APAP at environmentally relevant concentrations (8.3 μg APAP L(-1)). Incubation with allylthiourea, an ammonia monooxygenase inhibitor, demonstrated that the APAP removal was mainly associated with heterotrophic bacteria and not with the ammonia-oxidizing bacteria. Two APAP degrading strains were isolated from the MBR biomass and identified as Delftia tsuruhatensis and Pseudomonas aeruginosa. During incubation of the isolates, hydroquinone - a potentially toxic transformation product - was temporarily formed but further degraded and/or metabolized. These results suggest that the specific enrichment of a microbial consortium in an MBR operated at a high sludge age might be a promising strategy for post-treatment of WWTP effluents containing pharmaceuticals.}, }
@article {pmid21163512, year = {2011}, author = {Forrez, I and Carballa, M and Fink, G and Wick, A and Hennebel, T and Vanhaecke, L and Ternes, T and Boon, N and Verstraete, W}, title = {Biogenic metals for the oxidative and reductive removal of pharmaceuticals, biocides and iodinated contrast media in a polishing membrane bioreactor.}, journal = {Water research}, volume = {45}, number = {4}, pages = {1763-1773}, doi = {10.1016/j.watres.2010.11.031}, pmid = {21163512}, issn = {1879-2448}, mesh = {Biodegradation, Environmental ; *Bioreactors ; Catalysis ; Contrast Media/*isolation &amp; purification ; Disinfectants/*isolation &amp; purification ; Halogenation ; Iodine Compounds/isolation &amp; purification ; Manganese Compounds/*chemistry ; Membranes, Artificial ; Oxidation-Reduction ; Oxides/*chemistry ; Palladium/*chemistry ; Pharmaceutical Preparations/*isolation &amp; purification ; Water Purification/*instrumentation ; }, abstract = {Pharmaceutical and personal care products, biocides and iodinated contrast media (ICM) are persistent compounds, which appear in ng to μg L(-1) in secondary effluents of sewage treatment plants (STPs). In this work, biogenic metals manganese oxides (BioMnOx) and bio-palladium (Bio-Pd) were applied in lab-scale membrane bioreactors (MBR) as oxidative and reductive technologies, respectively, to remove micropollutants from STP-effluent. From the 29 substances detected in the STP-effluent, 14 were eliminated in the BioMnOx-MBR: ibuprofen (>95%), naproxen (>95%), diuron (>94%), codeine (>93%), N-acetyl-sulfamethoxazole (92%), chlorophene (>89%), diclofenac (86%), mecoprop (81%), triclosan (>78%), clarithromycin, (75%), iohexol (72%), iopromide (68%), iomeprol (63%) and sulfamethoxazole (52%). The putative removal mechanisms were the chemical oxidation by BioMnOx and/or the biological removal by Pseudomonas putida and associated bacteria in the enriched biofilm. Yet, the removal rates (highest value: 2.6 μg diclofenac L(-1) d(-1)) need to improve by a factor 10 in order to be competitive with ozonation. ICM, persistent towards oxidative techniques, were successfully dehalogenated with a novel reductive technique using Bio-Pd as a nanosized catalyst in an MBR. Iomeprol, iopromide and iohexol were removed for >97% and the more recalcitrant diatrizoate for 90%. The conditions favorable for microbial H(2)-production enabling the charging of the Pd catalyst, were shown to be important for the removal of ICM. Overall, the results indicate that Mn oxide and Pd coupled to microbial catalysis offer novel potential for advanced water treatment.}, }
@article {pmid21161332, year = {2011}, author = {Singh, NS and Singh, DK}, title = {Biodegradation of endosulfan and endosulfan sulfate by Achromobacter xylosoxidans strain C8B in broth medium.}, journal = {Biodegradation}, volume = {22}, number = {5}, pages = {845-857}, doi = {10.1007/s10532-010-9442-0}, pmid = {21161332}, issn = {1572-9729}, mesh = {Achromobacter denitrificans/classification/genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Culture Media/metabolism ; Endosulfan/*analogs &amp; derivatives/*metabolism ; Insecticides/*metabolism ; Molecular Sequence Data ; Soil Microbiology ; }, abstract = {Endosulfan is one of the most widely used wide spectrum cyclodiene organochlorine insecticide. In environment, endosulfan can undergo either oxidation or hydrolysis reaction to form endosulfan sulfate and endosulfan diol respectively. Endosulfan sulfate is as toxic and as persistent as its parent isomers. In the present study, endosulfan degrading bacteria were isolated from soil through selective enrichment technique using sulfur free medium with endosulfan as sole sulfur source. Out of the 8 isolated bacterial strains, strain C8B was found to be the most efficient endosulfan degrader, degrading 94.12% α-endosulfan and 84.52% β-endosulfan. The bacterial strain was identified as Achromobacter xylosoxidans strain C8B on the basis of 16S rDNA sequence similarity. Achromobacter xylosoxidans strain C8B was also found to degrade 80.10% endosulfan sulfate using it as sulfur source. No known metabolites were found to be formed in the culture media during the entire course of degradation. Besides, the bacterial strain was found to degrade all the known endosulfan metabolites. There was marked increase in the quantity of released CO(2) from the culture media with endosulfan as sulfur source as compared to MgSO(4) suggesting that the bacterial strain, Achromobacter xylosoxidans strain C8B probably degraded endosulfan completely through the formation of endosulfan ether.}, }
@article {pmid21161207, year = {2011}, author = {Bauermeister, A and Moeller, R and Reitz, G and Sommer, S and Rettberg, P}, title = {Effect of relative humidity on Deinococcus radiodurans' resistance to prolonged desiccation, heat, ionizing, germicidal, and environmentally relevant UV radiation.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {715-722}, pmid = {21161207}, issn = {1432-184X}, mesh = {Deinococcus/physiology/*radiation effects ; *Desiccation ; *Gamma Rays ; *Hot Temperature ; *Humidity ; Microbial Viability ; *Radiation Tolerance ; Stress, Physiological ; *Ultraviolet Rays ; Water/physiology ; }, abstract = {To test the effect of humidity on the radiation resistance of Deinococcus radiodurans, air-dried cells were irradiated with germicidal 254 nm UV, and simulated environmental UV or γ-radiation and survival was compared to cells in suspension. It was observed that desiccated cells exhibited higher levels of resistance than cells in suspension toward UV or γ-radiation as well as after 85°C heat shock. It was also shown that low relative humidity improves survival during long-term storage of desiccated D. radiodurans cells. It can be concluded that periods or environments in which cells exist in a dehydrated state are beneficial for D. radiodurans' survival exposed to various other stresses.}, }
@article {pmid21160538, year = {2011}, author = {Weber, M and Teeling, H and Huang, S and Waldmann, J and Kassabgy, M and Fuchs, BM and Klindworth, A and Klockow, C and Wichels, A and Gerdts, G and Amann, R and Glöckner, FO}, title = {Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics.}, journal = {The ISME journal}, volume = {5}, number = {5}, pages = {918-928}, pmid = {21160538}, issn = {1751-7370}, mesh = {Algorithms ; *Biodiversity ; Cluster Analysis ; *Internet ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sensitivity and Specificity ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {Next-generation sequencing (NGS) technologies have enabled the application of broad-scale sequencing in microbial biodiversity and metagenome studies. Biodiversity is usually targeted by classifying 16S ribosomal RNA genes, while metagenomic approaches target metabolic genes. However, both approaches remain isolated, as long as the taxonomic and functional information cannot be interrelated. Techniques like self-organizing maps (SOMs) have been applied to cluster metagenomes into taxon-specific bins in order to link biodiversity with functions, but have not been applied to broad-scale NGS-based metagenomics yet. Here, we provide a novel implementation, demonstrate its potential and practicability, and provide a web-based service for public usage. Evaluation with published data sets mimicking varyingly complex habitats resulted into classification specificities and sensitivities of close to 100% to above 90% from phylum to genus level for assemblies exceeding 8 kb for low and medium complexity data. When applied to five real-world metagenomes of medium complexity from direct pyrosequencing of marine subsurface waters, classifications of assemblies above 2.5 kb were in good agreement with fluorescence in situ hybridizations, indicating that biodiversity was mostly retained within the metagenomes, and confirming high classification specificities. This was validated by two protein-based classifications (PBCs) methods. SOMs were able to retrieve the relevant taxa down to the genus level, while surpassing PBCs in resolution. In order to make the approach accessible to a broad audience, we implemented a feature-rich web-based SOM application named TaxSOM, which is freely available at http://www.megx.net/toolbox/taxsom. TaxSOM can classify reads or assemblies exceeding 2.5 kb with high accuracy and thus assists in linking biodiversity and functions in metagenome studies, which is a precondition to study microbial ecology in a holistic fashion.}, }
@article {pmid21153808, year = {2011}, author = {Saikaly, PE and Oerther, DB}, title = {Diversity of dominant bacterial taxa in activated sludge promotes functional resistance following toxic shock loading.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {557-567}, pmid = {21153808}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/*metabolism ; *Biodiversity ; Bioreactors/microbiology ; Chlorophenols/metabolism ; Copper Sulfate/metabolism ; DNA, Bacterial/genetics ; Nitrophenols/metabolism ; Oxygen/metabolism ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; }, abstract = {Examining the relationship between biodiversity and functional stability (resistance and resilience) of activated sludge bacterial communities following disturbance is an important first step towards developing strategies for the design of robust biological wastewater treatment systems. This study investigates the relationship between functional resistance and biodiversity of dominant bacterial taxa by subjecting activated sludge samples, with different levels of biodiversity, to toxic shock loading with cupric sulfate (Cu[II]), 3,5-dichlorophenol (3,5-DCP), or 4-nitrophenol (4-NP). Respirometric batch experiments were performed to determine the functional resistance of activated sludge bacterial community to the three toxicants. Functional resistance was estimated as the 30 min IC(50) or the concentration of toxicant that results in a 50% reduction in oxygen utilization rate compared to a referential state represented by a control receiving no toxicant. Biodiversity of dominant bacterial taxa was assessed using polymerase chain reaction-terminal restriction fragment length polymorphism (PCR-T-RFLP) targeting the 16S ribosomal RNA (16S rRNA) gene. Statistical analysis of 30 min IC(50) values and PCR-T-RFLP data showed a significant positive correlation (P < 0.05) between functional resistance and microbial diversity for each of the three toxicants tested. To our knowledge, this is the first study showing a positive correlation between biodiversity of dominant bacterial taxa in activated sludge and functional resistance. In this system, activated sludge bacterial communities with higher biodiversity are functionally more resistant to disturbance caused by toxic shock loading.}, }
@article {pmid21153634, year = {2011}, author = {Ó Cuív, P and Aguirre de Cárcer, D and Jones, M and Klaassens, ES and Worthley, DL and Whitehall, VL and Kang, S and McSweeney, CS and Leggett, BA and Morrison, M}, title = {The effects from DNA extraction methods on the evaluation of microbial diversity associated with human colonic tissue.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {353-362}, pmid = {21153634}, issn = {1432-184X}, mesh = {Aged ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Colon/*microbiology ; DNA Probes/genetics ; DNA, Archaeal/*isolation &amp; purification ; DNA, Bacterial/*isolation &amp; purification ; Humans ; Male ; *Metagenome ; Oligonucleotide Array Sequence Analysis/methods ; Phylogeny ; Polymerase Chain Reaction/methods ; }, abstract = {Potentially valuable sources of DNA have been extracted from human colonic tissues and are retained in biobanks throughout the world, and might be re-examined to better understand host-microbe interactions in health and disease. However, the published protocols for DNA extraction typically used by gastroenterologists have not been systematically compared in terms of their recovery of the microbial fraction associated with colonic tissue. For this reason, we examined how three different tissue DNA extraction methods (the QIAGEN AllPrep DNA/RNA kit, salting out and high molecular weight (HMW) methods of DNA extraction) employed in past clinical trials, and the repeated bead beating and column (RBB+C) method might impact the recovery of microbial DNA from colonic tissue, using a custom designed phylogenetic microarray for gut bacteria and archaea. All four methods produced very similar profiles of the microbial diversity, but there were some differences in probe signal intensities, with the HMW method producing stronger probe intensities for a subset of the Firmicutes probes including Clostridium and Streptococcus spp. Real-time PCR analysis revealed that the HMW and RBB+C extracted DNA contained significantly more DNA of Firmicutes origin and that the different DNA extraction methods also gave variable results in terms of host DNA recovery. All of the methods tested recovered DNA from the archaeal community although there were some differences in probe signal intensity. Based on these findings, we conclude that while all four methods are efficacious at releasing microbial DNA from biopsy tissue samples, the HMW and RBB+C methods of DNA extraction may release more DNA from some of the Firmicutes bacteria associated with colonic tissue. Thus, DNA archived in biobanks could be suitable for retrospective profiling analyses, provided the caveats with respect to the DNA extraction method(s) used are taken into account.}, }
@article {pmid21153024, year = {2011}, author = {Zeglin, LH and Dahm, CN and Barrett, JE and Gooseff, MN and Fitpatrick, SK and Takacs-Vesbach, CD}, title = {Bacterial community structure along moisture gradients in the parafluvial sediments of two ephemeral desert streams.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {543-556}, pmid = {21153024}, issn = {1432-184X}, mesh = {Antarctic Regions ; Bacteria/*classification/genetics/growth &amp; development ; Biodiversity ; DNA, Bacterial/genetics ; *Desert Climate ; Geologic Sediments/chemistry/*microbiology ; New Mexico ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Sequence Analysis, DNA ; Water/analysis ; *Water Microbiology ; }, abstract = {Microorganisms inhabiting stream sediments mediate biogeochemical processes of importance to both aquatic and terrestrial ecosystems. In deserts, the lateral margins of ephemeral stream channels (parafluvial sediments) are dried and rewetted, creating periodically wet conditions that typically enhance microbial activity. However, the influence of water content on microbial community composition and diversity in desert stream sediments is unclear. We sampled stream margins along gradients of wet to dry sediments, measuring geochemistry and bacterial 16S rRNA gene composition, at streams in both a cold (McMurdo Dry Valleys, Antarctica) and hot (Chihuahuan Desert, New Mexico, USA) desert. Across the gradients, sediment water content spanned a wide range (1.6-37.9% w/w), and conductivity was highly variable (12.3-1,380 μS cm(-2)). Bacterial diversity (at 97% sequence similarity) was high and variable, but did not differ significantly between the hot and cold desert and was not correlated with sediment water content. Instead, conductivity was most strongly related to diversity. Water content was strongly related to bacterial 16S rRNA gene community composition, though samples were distributed in wet and dry clusters rather than as assemblages shifting along a gradient. Phylogenetic analyses showed that many taxa from wet sediments at the hot and cold desert site were related to, respectively, halotolerant Gammaproteobacteria, and one family within the Sphingobacteriales (Bacteroidetes), while dry sediments at both sites contained a high proportion of taxa related to the Acidobacteria. These results suggest that bacterial diversity and composition in desert stream sediments is more strongly affected by hydrology and conductivity than temperature.}, }
@article {pmid21148775, year = {2011}, author = {Kiarie, E and Bhandari, S and Scott, M and Krause, DO and Nyachoti, CM}, title = {Growth performance and gastrointestinal microbial ecology responses of piglets receiving Saccharomyces cerevisiae fermentation products after an oral challenge with Escherichia coli (K88).}, journal = {Journal of animal science}, volume = {89}, number = {4}, pages = {1062-1078}, doi = {10.2527/jas.2010-3424}, pmid = {21148775}, issn = {1525-3163}, mesh = {Animal Feed ; Animal Nutritional Physiological Phenomena ; Animals ; Anti-Bacterial Agents/*administration &amp; dosage/pharmacology ; Carbadox/administration &amp; dosage/pharmacology ; Diarrhea/microbiology/prevention &amp; control/veterinary ; Diet/veterinary ; Enterotoxigenic Escherichia coli/isolation &amp; purification/*physiology ; Escherichia coli Infections/drug therapy/microbiology/prevention &amp; control/*veterinary ; Fermentation ; Gastrointestinal Tract/microbiology ; Hematocrit/veterinary ; Liver/microbiology ; Saccharomyces cerevisiae/*metabolism ; Spleen/microbiology ; *Sus scrofa ; Swine Diseases/microbiology/*prevention &amp; control ; Weaning ; }, abstract = {The effects of Saccharomyces cerevisiae fermentation products (YFP) on growth performance and gastrointestinal (GIT) microbial ecology in 90 weanling pigs orally challenged with Escherichia coli K88(+) (ETEC) were investigated. The YFP were an original YFP product (XPC) and a water-suspendable yeast fermentation prototype (WSYFP) from a commercial company. Treatments consisted of a negative control (NC, no in-feed or in-water additive), carbadox (AB, 55 mg of carbadox/kg of feed), XPC (in feed, 0.2%), and WSYFP (in water, 0.5, 1, or 2 g/pig per day), and each was allotted to 5 pens (3 pigs/pen). The diets met the 1998 NRC specifications. Pigs were acclimated to treatments for a 7-d period before an ETEC challenge. On d 8, blood was collected from pigs to determine the baseline packed cell volume (PCV) measurement, and pigs were orally challenged with ETEC. At various time points postchallenge, blood samples were taken, performance measures and fecal consistency scores were recorded, and gut digesta and tissue samples were taken to evaluate GIT morphology, microbial ecology, and metabolites. Preplanned contrasts were used for comparison. Pigs receiving YFP had greater ADFI than NC pigs on d 3 (424 vs. 378 g/d; P = 0.01) and d 7 (506 vs. 458 g/d; P = 0.03) postchallenge. This effect of YFP on ADFI was similar to that of AB on d 3, but pigs receiving AB ate more (576 vs. 506 g/d; P = 0.03) at d 7 than pigs receiving YFP. Pigs exhibited reduced (P < 0.001) PCV upon ETEC challenge; however, pigs receiving additives sustained a greater (P < 0.05) PCV at 72 h compared with the NC group. Compared with the NC pigs, pigs receiving YFP showed a smaller (P < 0.05) number of ileal mucosa adherent ETEC and prevalence of the order Enterobacteriales in the ileal digesta, which corresponded to less (5.09 vs. 6.97 mg/dL; P = 0.03) colonic ammonia on d 7 postchallenge. Most of the indices for ileal digesta bacterial richness and diversity were greater (P < 0.01) for YFP pigs compared with NC pigs. However, results also indicated that the influence of YFP on the piglet intestinal microenvironment might differ when given in feed or water during ETEC challenge. In conclusion, pigs receiving YFP showed a better appetite in the presence of ETEC, which, together with the greater ileal digesta bacteria richness and diversity and decreased ETEC adhering to the mucosa and reduced colonic ammonia, indicates a healthier GIT environment.}, }
@article {pmid21146980, year = {2011}, author = {Beristain-Cardoso, R and Gómez, J and Méndez-Pampín, R}, title = {Sulfide and ammonium oxidation, acetate mineralization by denitrification in a multipurpose UASB reactor.}, journal = {Bioresource technology}, volume = {102}, number = {3}, pages = {2549-2554}, doi = {10.1016/j.biortech.2010.11.084}, pmid = {21146980}, issn = {1873-2976}, mesh = {Acetates/*metabolism ; Bioreactors/*microbiology ; Minerals/*metabolism ; Nitrification/physiology ; Oxidation-Reduction ; Quaternary Ammonium Compounds/*metabolism ; Sewage/*microbiology ; Sulfides/*metabolism ; Water Pollutants/*metabolism ; }, abstract = {The physiological and kinetic behavior of a denitrifying granular sludge exposed to different sulfide loading rates (55-295 mg/L d) were evaluated in a UASB reactor fed with acetate, ammonium and nitrate. At any sulfide loading rates, the consumption efficiencies of sulfide, acetate and ammonium were above 95%, while nitrate consumption efficiencies were around 62-72%. At the highest sulfide loading rate the ammonium was used as electron donor for N(2) production. The increase of sulfide loading rate also affected the fate of sulfide oxidation, since elemental sulfur was the main end product instead of sulfate. However, the lithotrophic denitrifying kinetic was not affected. FISH oligonucleotide probes for Thiobacillus denitrificans, Thiomiscropira denitrificans, genus Paracoccus and Pseudomonas spp. were used to follow the microbial ecology. The results of this work have shown that four pollutants could simultaneously be removed, namely, sulfide, ammonium, acetate and nitrate under well defined denitrifying conditions.}, }
@article {pmid21146847, year = {2011}, author = {Lee, CW and Ng, AY and Bong, CW and Narayanan, K and Sim, EU and Ng, CC}, title = {Investigating the decay rates of Escherichia coli relative to Vibrio parahemolyticus and Salmonella Typhi in tropical coastal waters.}, journal = {Water research}, volume = {45}, number = {4}, pages = {1561-1570}, doi = {10.1016/j.watres.2010.11.025}, pmid = {21146847}, issn = {1879-2448}, mesh = {Chemical Fractionation ; Colony Count, Microbial ; Environmental Monitoring ; Escherichia coli/growth &amp; development/*isolation &amp; purification ; Malaysia ; Particle Size ; Salmonella typhi/growth &amp; development/*isolation &amp; purification ; Seawater/*microbiology/*virology ; *Tropical Climate ; Vibrio parahaemolyticus/*isolation &amp; purification ; }, abstract = {Using the size fractionation method, we measured the decay rates of Escherichia coli, Salmonella Typhi and Vibrio parahaemolyticus in the coastal waters of Peninsular Malaysia. The size fractions were total or unfiltered, <250 μm, <20 μm, <2 μm, <0.7 μm, <0.2 μm and <0.02 μm. We also carried out abiotic (inorganic nutrients) and biotic (bacterial abundance, production and protistan bacterivory) measurements at Port Dickson, Klang and Kuantan. Klang had highest nutrient concentrations whereas both bacterial production and protistan bacterivory rates were highest at Kuantan. We observed signs of protist-bacteria coupling via the following correlations: Protistan bacterivory-Bacterial Production: r = 0.773, df = 11, p < 0.01; Protist-Bacteria: r = 0.586, df = 12, p < 0.05. However none of the bacterial decay rates were correlated with the biotic variables measured. E. coli and Salmonella decay rates were generally higher in the larger fraction (>0.7 μm) than in the smaller fraction (<0.7 μm) suggesting the more important role played by protists. E. coli and Salmonella also decreased in the <0.02 μm fraction and suggested that these non-halophilic bacteria did not survive well in seawater. In contrast, Vibrio grew well in seawater. There was usually an increase in Vibrio after one day incubation. Our results confirmed that decay or loss rates of E. coli did not match that of Vibrio, and also did not correlate with Salmonella decay rates. However E. coli showed persistence where its decay rates were generally lower than Salmonella.}, }
@article {pmid21144106, year = {2011}, author = {Wu, WT and Cheng, HC and Chen, HL}, title = {Ameliorative effects of konjac glucomannan on human faecal β-glucuronidase activity, secondary bile acid levels and faecal water toxicity towards Caco-2 cells.}, journal = {The British journal of nutrition}, volume = {105}, number = {4}, pages = {593-600}, doi = {10.1017/S0007114510004009}, pmid = {21144106}, issn = {1475-2662}, mesh = {Adult ; Bile Acids and Salts/*metabolism ; Caco-2 Cells ; DNA Damage ; Feces/microbiology ; Female ; Glucuronidase/*metabolism ; Humans ; Male ; Mannans/*therapeutic use ; Middle Aged ; Placebos ; Water/metabolism ; Zea mays/metabolism ; }, abstract = {Konjac glucomannan (KGM) has been shown to increase human colon microbial ecology and reduce faecal toxicity in mice. The main goal of the present study was to assess the effects of a KGM supplement into a low-fibre diet on precancerous markers of colon cancer in a double-blind, placebo- and diet-controlled study. Adult volunteers consumed defined diets supplemented with konjac (4·5 g/d) or placebo (maize starch) for 4 weeks. Stools collected before and at the end of the supplementation were analysed for β-glucosidase, β-galactosidase and β-glucuronidase activities, microflora and bile acids. Faecal water was co-incubated with Caco-2 cells, a model of human colonocytes, to determine the cytotoxicity and DNA-damaging effect as assessed by the comet assay. The results indicated that the KGM supplement significantly decreased faecal β-glucuronidase activity by 25·6 (se 7·8) % and faecal secondary bile acid level by 42·4 (se 11·8) %. In contrast, consuming the defined diet supplemented with placebo for 4 weeks did not improve these determinants. The KGM-supplemented diet, but not the placebo diet, significantly increased the survival rate (%) of Caco-2 cells co-incubated with faecal water for 1 and 3 h, respectively. In addition, KGM significantly reduced the DNA damage induced by the faecal water alone or in combination with H2O2. The faecal bifidobacteria and lactobacilli levels increased only with the KGM-supplemented diet. Therefore, we conclude that supplementation of KGM into a low-fibre diet improved the faecal microbial ecology and metabolites, which may contribute to the reduced toxicity of faecal water and precancerous risk factors of human colon cancer.}, }
@article {pmid21141666, year = {2010}, author = {Schrenk, MO and Huber, JA and Edwards, KJ}, title = {Microbial provinces in the subseafloor.}, journal = {Annual review of marine science}, volume = {2}, number = {}, pages = {279-304}, doi = {10.1146/annurev-marine-120308-081000}, pmid = {21141666}, issn = {1941-1405}, mesh = {*Ecosystem ; Environmental Monitoring ; Geologic Sediments/*microbiology ; Oceans and Seas ; }, abstract = {The rocks and sediments of the oceanic subsurface represent a diverse mosaic of environments potentially inhabited by microorganisms. Understanding microbial ecosystems in subseafloor environments confounds standard ecological descriptions in part because we have difficulty elucidating and describing the scale of relevant processes. Habitat characteristics impact microbial activities and growth, which in turn affect microbial diversity, net production, and global biogeochemical cycles. Herein we provide descriptions of subseafloor microbial provinces, broadly defined as geologically and geographically coherent regions of the subseafloor that may serve as potential microbial habitats. The purpose of this review is to summarize and refine criteria for the definition and delineation of distinct subseafloor microbial habitats to aid in their exploration. This review and the criteria we outline aim to develop a unified framework to improve our understanding of subseafloor microbial ecology, enable quantification of geomicrobial processes, and facilitate their accurate assimilation into biogeochemical models.}, }
@article {pmid21141481, year = {2010}, author = {Qi, J and Zhao, X and Zhou, L and Sun, P and Zhang, X and Li, X}, title = {[Soil microbial community composition and diversity in Panax quinquefolius rhizosphere].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {35}, number = {18}, pages = {2378-2382}, pmid = {21141481}, issn = {1001-5302}, mesh = {*Biodiversity ; Panax/*microbiology ; Plant Diseases/microbiology ; *Rhizosphere ; Soil/*analysis ; *Soil Microbiology ; }, abstract = {The objective of this work was to analyze the soil microbial community diversity and structure in Panax quinquefolius rhizosphere and elucidated the rules of the ecology shift. Two community-based microbiological measurements, community level physiological profiling (CLPP) using Biolog sole C source utilization tests and phospholipid ester-linked fatty acid (PLFA) profiles, were used to evaluate soil microbial community function and composition of different Panax quinquefolius cropping soils. The properties, pH, N, P, K and organic matter were analyzed also. There were many differences in soil properties such as lower pH (5.82) in Jilin soil but higher pH (8.27) in Beijing soil and there were significant higher content of organic matter, available N, P, K in Jilin soil than those in Beijing soil. The analysis of soil microbial ecology showed a similar result in AWCD, Biolog and PLFA pattern. According to the PC1 score in principal analysis of Biolog and PLFA, the soils in 2, 3 and 4 years cultivated P. quinquefolius rhizophere were distinguished from the control and 1 year soils. The result indicated that the metabolism function reduced and the structure shifted in rhizophere soil microbial community after P. quinquefolius cropping. These may be the primary reason of the disease occur severely in P. quinquefolius field.}, }
@article {pmid21136591, year = {2010}, author = {Heinz, E and Pichler, P and Heinz, C and Op den Camp, HJ and Toenshoff, ER and Ammerer, G and Mechtler, K and Wagner, M and Horn, M}, title = {Proteomic analysis of the outer membrane of Protochlamydia amoebophila elementary bodies.}, journal = {Proteomics}, volume = {10}, number = {24}, pages = {4363-4376}, doi = {10.1002/pmic.201000302}, pmid = {21136591}, issn = {1615-9861}, mesh = {Acanthamoeba/microbiology ; Amino Acid Sequence ; Animals ; Bacterial Outer Membrane Proteins/*chemistry/classification ; Chlamydiales/*chemistry/ultrastructure ; Life Cycle Stages ; Molecular Sequence Data ; Proteome/*chemistry ; }, abstract = {Chlamydiae are obligate intracellular bacteria, comprising some of the most important bacterial pathogens of animals and humans. During their unique developmental cycle they have to attach to and enter their eukaryotic host cells, a process mediated by proteins in the chlamydial outer membrane. So far the only experimental data for chlamydial outer membrane proteins are available from members of the Chlamydiaceae, a family comprising exclusively human and animal pathogens. To get further insights into the evolution of the protein composition of the chlamydial outer membrane and into host-dependent differences, we performed an extensive experimental analysis of outer membrane fractions of Protochlamydia amoebophila elementary bodies, which constitute the infectious form of this non-pathogenic member of the Chlamydiae that thrives as a symbiont in Acanthamoeba spp. We used 1-D and 2-DE in combination with MALDI-TOF, MALDI-TOF/TOF and nanoLC-ESI-MS/MS, and compared our experimental results with a previously published in silico analysis of chlamydial outer membrane proteins. This resulted in the identification of 38 proteins supported by both studies and therefore very likely to be located in the P. amoebophila outer membrane. The obtained experimental data provide the first comprehensive overview of outer membrane proteins of a chlamydial organism outside the Chlamydiaceae. They reveal both fundamental differences and convergent evolution between pathogenic and symbiotic chlamydiae.}, }
@article {pmid21132427, year = {2011}, author = {Jägevall, S and Rabe, L and Pedersen, K}, title = {Abundance and diversity of biofilms in natural and artificial aquifers of the Äspö Hard Rock Laboratory, Sweden.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {410-422}, pmid = {21132427}, issn = {1432-184X}, mesh = {*Biodiversity ; *Biofilms ; DNA, Bacterial/genetics ; Gene Dosage ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Sulfur-Reducing Bacteria/*classification/growth &amp; development ; Sweden ; Water/chemistry ; *Water Microbiology ; }, abstract = {Six cores were drilled and retrieved from 186-m depth in the Äspö Hard Rock Laboratory (HRL) tunnel to investigate whether indigenous biofilms develop on fracture surfaces in groundwater-conducting aquifers in granitic rock. A clone library was constructed from fracture surface material (FSM), for community composition analysis. Quantitative polymerase chain reaction (qPCR) was applied to quantify gene copies using the 16S rRNA gene for domain Bacteria and the adenosine-phosphosulfate reductase gene (apsA) for sulfate-reducing bacteria (SRB). Results were compared with three groundwater systems with biofilms in laminar flow reactors (LFRs) at 450-m depth in the Äspö HRL. The total number of cells, counted microscopically, was approximately 2 × 10(5) cells cm(-2) in the LFR systems, consistent with the obtained qPCR 16S rRNA gene copies. qPCR analysis reported ∼1 × 10(2) up to ∼1 × 10(4) gene copies cm(-2) on the FSM from the drill cores. In the FSM biofilms, 33% of the sequenced clones were related to the iron-reducing bacterium Stenotrophomonas maltophilia, while in the LFR biofilms, 41% of the sequenced clones were affiliated with the genera Desulfovibrio, Desulforhopalus, Desulfomicrobium, and Desulfobulbus. The community composition of the FSM biofilms differed from the drill water community, excluding drill water contamination. This work reports significant numbers of microorganisms on natural hard rock aquifer fracture surfaces with site-specific community compositions. The probability that biofilms are generally present in groundwater-conducting aquifers in deep granitic rock is consequently great.}, }
@article {pmid21128072, year = {2011}, author = {Lee, SH and Kim, CG and Kang, H}, title = {Temporal dynamics of bacterial and fungal communities in a genetically modified (GM) rice ecosystem.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {646-659}, pmid = {21128072}, issn = {1432-184X}, mesh = {Bacteria/genetics/*growth &amp; development ; Biodiversity ; Carbon/metabolism ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fungi/genetics/*growth &amp; development ; Gene Dosage ; Genotype ; Multivariate Analysis ; Oryza/genetics/*microbiology ; Phylogeny ; Plants, Genetically Modified/*microbiology ; Polymorphism, Restriction Fragment Length ; Quaternary Ammonium Compounds/metabolism ; RNA, Ribosomal, 16S/genetics ; *Seasons ; Soil/chemistry ; Soil Microbiology ; Water/metabolism ; }, abstract = {We assessed the temporal dynamics of bacterial and fungal communities in a soil ecosystem supporting genetically modified (GM) rice (Oryza sativa L., ABC-TPSP; fusion of trehalose-6-phosphate synthase and phosphatase). Using terminal restriction fragment length polymorphism analysis and real-time quantitative PCR, we compared bacterial and fungal communities in the soils underlying GM rice (ABC-TPSP), and its host cultivar (Nakdong) during growing seasons and non-growing seasons. Overall, the soils supporting GM and non-GM rice did not differ significantly in diversity indices, including ribotype numbers, for either bacteria or fungi. The diversity index (H) in both the bacterial and fungal communities was correlated with water content, dissolved organic carbon (DOC), and ammonium nitrogen, and the correlation was stronger in fungi than in bacteria. Multivariate analysis showed no differences in microbial community structures between the two crop genotypes, but such differences did appear in time, with significant changes observed after harvest. Gene copy number was estimated as 10(8)~10(11) and 10(5)~10(7) per gram of soil for bacteria and fungi, respectively. As observed for community structure, the rice genotypes did not differ significantly in either bacterial- or fungal-specific gene copy numbers, although we observed a seasonal change in number. We summarize the results of this study as follows. (1) GM rice did not influence soil bacterial and fungal community structures as compared to non-GM rice in our system, (2) both bacterial and fungal communities changed with the growth stage of either rice genotype, (3) fungal communities were less variable than bacterial communities, and (4) although several environmental factors, including ammonium nitrogen and DOC correlated with shifts in microbial community structure, no single factor stood out.}, }
@article {pmid21128071, year = {2011}, author = {Loaces, I and Ferrando, L and Scavino, AF}, title = {Dynamics, diversity and function of endophytic siderophore-producing bacteria in rice.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {606-618}, pmid = {21128071}, issn = {1432-184X}, mesh = {Antibiosis ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Fungi/growth &amp; development ; Gram-Negative Bacteria/*classification/genetics/isolation &amp; purification ; Oryza/*microbiology ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Seeds/microbiology ; Sequence Analysis, DNA ; Siderophores/*biosynthesis ; *Soil Microbiology ; }, abstract = {Siderophore production confers to bacteria competitive advantages to colonize plant tissues and to exclude other microorganisms from the same ecological niche. This work shows that the community of endophytic siderophore-producing bacteria (SPB) associated to Oryza sativa cultivated in Uruguayan soils is dynamic and diverse. These bacteria were present in grains, roots, and leaves, and their density fluctuated between log(10) 3.44 and log(10) 5.52 cfu g(-1) fresh weight (fw) during the plant growth. Less than 10% of the heterotrophic bacteria produced siderophores in roots and leaves of young plants, but most of the heterotrophic bacteria were siderophore-producers in mature plants. According to their amplified restriction DNA ribosomal analysis (ARDRA) pattern, 54 of the 109 endophytic SPB isolated from different plant tissues or growth stages from replicate plots, were unique. Bacteria belonging to the genera Sphingomonas, Pseudomonas, Burkholderia, and Enterobacter alternated during plant growth, but the genus Pantoea was predominant in roots at tillering and in leaves at subsequent stages. Pantoea ananatis was the SPB permanently associated to any of the plant tissues, but the genetic diversity within this species-revealed by BOX-PCR fingerprinting- showed that different strains were randomly distributed along time and plant tissue, suggesting that a common trait of the species P. ananatis determined the interaction with the rice plant. Several isolates were stronger IAA producers than Azospirillum brasilense or Herbaspirillum seropedicae. In vitro inhibition assays showed that SPB of the genus Burkholderia were good antagonists of pathogenic fungi and that only one SPB isolate of the genus Pseudomonas was able to inhibit A. brasilense and H. seropedicae. These results denoted that SPB were selected into the rice plant. P. ananatis was the permanent and dominant associated species which was unable to inhibit two of the relevant plant growth-promoting bacteria.}, }
@article {pmid21124952, year = {2010}, author = {Klitgord, N and Segrè, D}, title = {Environments that induce synthetic microbial ecosystems.}, journal = {PLoS computational biology}, volume = {6}, number = {11}, pages = {e1001002}, pmid = {21124952}, issn = {1553-7358}, mesh = {Algorithms ; Culture Media/chemistry/metabolism ; Desulfovibrio vulgaris/metabolism ; *Ecosystem ; Escherichia coli/metabolism ; Methanococcus/metabolism ; *Microbial Interactions ; *Models, Biological ; Saccharomyces cerevisiae/metabolism ; Synthetic Biology/*methods ; Systems Biology/*methods ; }, abstract = {Interactions between microbial species are sometimes mediated by the exchange of small molecules, secreted by one species and metabolized by another. Both one-way (commensal) and two-way (mutualistic) interactions may contribute to complex networks of interdependencies. Understanding these interactions constitutes an open challenge in microbial ecology, with applications ranging from the human microbiome to environmental sustainability. In parallel to natural communities, it is possible to explore interactions in artificial microbial ecosystems, e.g. pairs of genetically engineered mutualistic strains. Here we computationally generate artificial microbial ecosystems without re-engineering the microbes themselves, but rather by predicting their growth on appropriately designed media. We use genome-scale stoichiometric models of metabolism to identify media that can sustain growth for a pair of species, but fail to do so for one or both individual species, thereby inducing putative symbiotic interactions. We first tested our approach on two previously studied mutualistic pairs, and on a pair of highly curated model organisms, showing that our algorithms successfully recapitulate known interactions, robustly predict new ones, and provide novel insight on exchanged molecules. We then applied our method to all possible pairs of seven microbial species, and found that it is always possible to identify putative media that induce commensalism or mutualism. Our analysis also suggests that symbiotic interactions may arise more readily through environmental fluctuations than genetic modifications. We envision that our approach will help generate microbe-microbe interaction maps useful for understanding microbial consortia dynamics and evolution, and for exploring the full potential of natural metabolic pathways for metabolic engineering applications.}, }
@article {pmid21121040, year = {2011}, author = {Bunge, J}, title = {Estimating the number of species with CatchAll.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {}, number = {}, pages = {121-130}, doi = {10.1142/9789814335058_0014}, pmid = {21121040}, issn = {2335-6936}, mesh = {Algorithms ; *Biodiversity ; Computational Biology ; Databases, Factual/statistics &amp; numerical data ; Ecosystem ; Finite Element Analysis ; Likelihood Functions ; Models, Statistical ; Seawater/microbiology ; *Software ; Species Specificity ; Statistics, Nonparametric ; }, abstract = {In many situations we are faced with the need to estimate the number of classes in a population from observed count data: this arises not only in biology, where we are interested in the number of taxa such as species, but also in many other fields such as public health, criminal justice, software engineering, etc. This problem has a rich history in theoretical statistics, dating back at least to 1943, and many approaches have been proposed and studied. However, to date only one approach has been implemented in readily available software, namely a relatively simple nonparametric method which, while straightforward to program, is not flexible and can be prone to information loss. Here we present CatchAll, a new, platform-independent, user-friendly, computationally optimized software package which calculates a powerful and flexible suite of parametric models (based on current statistical research) in addition to all existing nonparametric procedures. We briefly describe the software and its mathematical underpinnings (which are treated in depth elsewhere), and we work through an applied example from microbial ecology in detail.}, }
@article {pmid21120654, year = {2011}, author = {Franco-Vidal, L and Morán, XA}, title = {Relationships between coastal bacterioplankton growth rates and biomass production: comparison of leucine and thymidine uptake with single-cell physiological characteristics.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {328-341}, pmid = {21120654}, issn = {1432-184X}, mesh = {Bacteria/growth &amp; development/*metabolism ; Biomass ; Carbon Cycle ; Ecosystem ; Heterotrophic Processes ; Leucine/*metabolism ; Plankton/growth &amp; development/*metabolism ; Seasons ; Seawater/*microbiology ; Spain ; Thymidine/*metabolism ; Water Microbiology ; }, abstract = {Specific growth rates of heterotrophic bacterioplankton have been frequently estimated from in situ bacterial production (BP) to biomass (BB) ratios, using a series of assumptions that may result in serious discrepancies with values obtained from predator-free cultures. Here, we used both types of approaches together with a comprehensive assessment of single-cell physiological characteristics (membrane integrity, nucleic acid content, and active respiration) of coastal bacterioplankton during a complete annual cycle (February 2007-January 2008) in the southern Bay of Biscay off Xixón, Spain. Both leucine and thymidine incorporation rates were used in conjunction with empirical tracer to carbon or cells conversion factors (eCFs) to accurately derive BP. Leu and TdR incorporation rates covaried year-round, as did the corresponding eCFs at 0 and 50 m depth. eCFs peaked in autumn, with mean annual values close to the theoretical ones (3.4 kg C mol Leu(-1) and 2.0 × 10(18) cells mol TdR(-1)). Bacterial abundance (0.2-1.5 × 10(6) cells L(-1)) showed a bimodal distribution with maxima in May and October and minima in March. Live (membrane-intact) cells dominated year-round (79-97%), with high nucleic acid cells (42-88%) and actively respiring bacteria (CTC+, 1-16%) showing distinct surface maxima in April and July, respectively. BB (557-1,558 mg C m(-2)) and BP (7-139 mg C m(-2) day(-1)) presented two distinct peaks in spring and autumn, both of similar size due to a strong upwelling event observed in September. Specific growth rates (0.35-3.8 day(-1)) were one order of magnitude higher in predator-free incubations than bacterial turnover rates derived from integrated BP:BB ratios (0.01-0.16 and 0.01-0.09 day(-1), for Leu and TdR, respectively) and were not correlated, probably due to a significant contribution of low activity cells to total standing stocks. The Leu:TdR molar ratio averaged for the water column (6.6-25.5) decreased significantly with higher integrated BB, indicating that low standing stocks tend to present unbalanced growth. Discrepancies about the true magnitude of specific growth rates must be solved before fully appreciating the role of bacteria in the ocean carbon cycle.}, }
@article {pmid21113710, year = {2011}, author = {Navel, S and Mermillod-Blondin, F and Montuelle, B and Chauvet, E and Simon, L and Marmonier, P}, title = {Water-sediment exchanges control microbial processes associated with leaf litter degradation in the hyporheic zone: a microcosm study.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {968-979}, pmid = {21113710}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; *Ecosystem ; Fresh Water/chemistry/*microbiology ; Geologic Sediments/chemistry/*microbiology ; Nitrates/metabolism ; Oxygen/metabolism ; Plant Leaves/chemistry/*microbiology ; Water ; }, abstract = {The present study aimed to experimentally quantify the influence of a reduction of surface sediment permeability on microbial characteristics and ecological processes (respiration and leaf litter decomposition) occurring in the hyporheic zone (i.e. the sedimentary interface between surface water and groundwater). The physical structure of the water-sediment interface was manipulated by adding a 2-cm layer of coarse sand (unclogged systems) or fine sand (clogged systems) at the sediment surface of slow filtration columns filled with a heterogeneous gravel/sand sedimentary matrix. The influence of clogging was quantified through measurements of hydraulic conductivity, water chemistry, microbial abundances and activities and associated processes (decomposition of alder leaf litter inserted at a depth of 9 cm in sediments, oxygen and nitrate consumption by microorganisms). Fine sand deposits drastically reduced hydraulic conductivity (by around 8-fold in comparison with unclogged systems topped by coarse sand) and associated water flow, leading to a sharp decrease in oxygen (reaching less than 1 mg L(-1) at 3 cm depth) and nitrate concentrations with depth in sediments. The shift from aerobic to anaerobic conditions in clogged systems favoured the establishment of denitrifying bacteria living on sediments. Analyses performed on buried leaf litter showed a reduction by 30% of organic matter decomposition in clogged systems in comparison with unclogged systems. This reduction was linked to a negative influence of clogging on the activities and abundances of leaf-associated microorganisms. Finally, our study clearly demonstrated that microbial processes involved in organic matter decomposition were dependent on hydraulic conductivity and oxygen availability in the hyporheic zone.}, }
@article {pmid21113709, year = {2011}, author = {Zhu, D and Vaishampayan, PA and Venkateswaran, K and Fox, GE}, title = {STITCH: algorithm to splice, trim, identify, track, and capture the uniqueness of 16S rRNAs sequence pairs using public or in-house database.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {669-675}, pmid = {21113709}, issn = {1432-184X}, mesh = {*Algorithms ; Bacteria/classification/genetics ; Computational Biology/*methods ; *Databases, Nucleic Acid ; RNA Splicing ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA/*methods ; Software ; User-Computer Interface ; }, abstract = {A comparison of variable regions within the 16S rRNA gene is widely used to characterize relationships between bacteria and to identify phylogenetic affiliation of unknown bacteria. In environmental studies, polymerase chain reaction amplification of 16S rRNA followed by cloning and sequencing of numerous individual clones is an extensively used molecular method for elucidating microbial diversity. The sequencing process typically utilizes a forward and reverse primer pair to produce two partial reads (~700 to 800 base pairs each) that overlap and in total cover a large region of the full 16S rRNA sequence (~1.5 k base). In a typical application, this approach rapidly generates very large numbers of 16S rRNA datasets that can overwhelm manual processing efforts leading to both delays and errors. In particular, the approach presents two computational challenges: (1) the assembly of a composite sequence from the two partial reads and (2) the subsequent appropriate identification of the organism represented by the newly sequenced clones. Herein, we describe a software package, search, trim, identify, track, and capture the uniqueness of 16S rRNAs using public and in-house database (STITCH), which offers automated sequence pair splicing and genetic identification, thus simplifying the computationally intensive analysis of large sequencing libraries. The STITCH software is freely accessible over the Internet at: http://prion.bchs.uh.edu/stitch/.}, }
@article {pmid21110016, year = {2011}, author = {Schrallhammer, M and Schweikert, M and Vallesi, A and Verni, F and Petroni, G}, title = {Detection of a novel subspecies of Francisella noatunensis as endosymbiont of the ciliate Euplotes raikovi.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {455-464}, pmid = {21110016}, issn = {1432-184X}, mesh = {DNA, Bacterial/genetics ; Euplotes/*microbiology/ultrastructure ; Francisella/*classification/genetics/isolation &amp; purification ; *Phylogeny ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Francisella are facultative intracellular bacteria causing severe disease in a broad range of animals. Two species are notable: Francisella tularensis, the causative organism of tularemia and a putative warfare agent, and Francisella noatunensis, an emerging fish pathogen causing significant losses in wild and farmed fish. Although various aspects of Francisella biology have been intensively studied, their natural reservoir in periods between massive outbreaks remains mysterious. Protists have been suspected to serve as a disguised vector of Francisella and co-culturing attempts demonstrate that some species are able to survive and multiply within protozoan cells. Here, we report the first finding of a natural occurrence of Francisella sp. as a protist endosymbiont. By molecular and morphological approaches, we identified intracellular bacteria localized in a strain of the marine ciliate Euplotes raikovi, isolated from the coast of Adriatic Sea. Phylogenetic analysis placed these endosymbionts within the genus Francisella, in close but distinct association with F. noatunensis. We suggest the establishment of a novel subspecies within F. noatunensis and propose the cytoplasmatic endosymbiont of E. raikovi as "Candidatus F. noatunensis subsp. endociliophora" subsp. nov.}, }
@article {pmid21107833, year = {2011}, author = {Biderre-Petit, C and Boucher, D and Kuever, J and Alberic, P and Jézéquel, D and Chebance, B and Borrel, G and Fonty, G and Peyret, P}, title = {Identification of sulfur-cycle prokaryotes in a low-sulfate lake (Lake Pavin) using aprA and 16S rRNA gene markers.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {313-327}, pmid = {21107833}, issn = {1432-184X}, mesh = {Amino Acid Sequence ; DNA Primers/genetics ; DNA, Bacterial/genetics ; Epsilonproteobacteria/classification/enzymology/genetics ; France ; Fresh Water/chemistry/*microbiology ; Geologic Sediments/chemistry/microbiology ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfates/*metabolism ; Sulfur-Reducing Bacteria/*classification/enzymology/genetics ; *Water Microbiology ; }, abstract = {Geochemical researches at Lake Pavin, a low-sulfate-containing freshwater lake, suggest that the dominant biogeochemical processes are iron and sulfate reduction, and methanogenesis. Although the sulfur cycle is one of the main active element cycles in this lake, little is known about the sulfate-reducer and sulfur-oxidizing bacteria. The aim of this study was to assess the vertical distribution of these microbes and their diversities and to test the hypothesis suggesting that only few SRP populations are involved in dissimilatory sulfate reduction and that Epsilonproteobacteria are the likely key players in the oxidative phase of sulfur cycle by using a PCR aprA gene-based approach in comparison with a 16S rRNA gene-based analysis. The results support this hypothesis. Finally, this preliminary work points strongly the likelihood of novel metabolic processes upon the availability of sulfate and other electron acceptors.}, }
@article {pmid21107832, year = {2011}, author = {Barberán, A and Casamayor, EO}, title = {Euxinic freshwater hypolimnia promote bacterial endemicity in continental areas.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {465-472}, pmid = {21107832}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics ; *Biota ; DNA, Bacterial/genetics ; Fresh Water/chemistry/*microbiology ; *Phylogeny ; Plankton/classification/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Bacteria and archaea represent the vast majority of biodiversity on Earth. The ways that dynamic ecological and evolutionary processes interact in the microbial world are, however, poorly known. Here, we have explored community patterns of planktonic freshwater bacteria inhabiting stratified lakes with oxic/anoxic interfaces and euxinic (anoxic and sulfurous) water masses. The interface separates a well-oxygenated upper water mass (epilimnion) from a lower anoxic water compartment (hypolimnion). We assessed whether or not the vertical zonation of lakes promoted endemism in deeper layers by analyzing bacterial 16S rRNA gene sequences from the water column of worldwide distributed stratified lakes and applying a community ecology approach. Community similarity based on the phylogenetic relatedness showed that bacterial assemblages from the same water layer were more similar across lakes than to communities from different layer within lakes and that anoxic hypolimnia presented greater β-diversity than oxic epilimnia. Higher β-diversity values are attributable to low dispersal and small connectivity between community patches. In addition, surface waters had significant spatial but non-significant environmental components controlling phylogenetic β-diversity patterns, respectively. Conversely, the bottom layers were significantly correlated with environment but not with geographic distance. Thus, we observed different ecological mechanisms simultaneously acting on the same water body. Overall, bacterial endemicity is probably more common than previously thought, particularly in isolated and environmentally heterogeneous freshwater habitats. We argue for a microbial diversity conservation perspective still lacking in the global and local biodiversity preservation policies.}, }
@article {pmid21104154, year = {2011}, author = {Yan, Q and Yu, Y}, title = {Metagenome-based analysis: a promising direction for plankton ecological studies.}, journal = {Science China. Life sciences}, volume = {54}, number = {1}, pages = {75-81}, doi = {10.1007/s11427-010-4103-4}, pmid = {21104154}, issn = {1869-1889}, mesh = {*Ecology ; *Ecosystem ; Marine Biology ; *Metagenome ; Plankton/*genetics ; Seawater ; }, abstract = {The plankton community plays an especially important role in the functioning of aquatic ecosystems and also in biogeochemical cycles. Since the beginning of marine research expeditions in the 1870 s, an enormous number of planktonic organisms have been described and studied. Plankton investigation has become one of the most important areas of aquatic ecological study, as well as a crucial component of aquatic environmental evaluation. Nonetheless, traditional investigations have mainly focused on morphospecies composition, abundances and dynamics, which primarily depend on morphological identification and counting under microscopes. However, for many species/groups, with few readily observable characteristics, morphological identification and counting have historically been a difficult task. Over the past decades, microbiologists have endeavored to apply and extend molecular techniques to address questions in microbial ecology. These culture-independent studies have generated new insights into microbial ecology. One such strategy, metagenome-based analysis, has also proved to be a powerful tool for plankton research. This mini-review presents a brief history of plankton research using morphological and metagenome-based approaches and the potential applications and further directions of metagenomic analyses in plankton ecological studies are discussed. The use of metagenome-based approaches for plankton ecological study in aquatic ecosystems is encouraged.}, }
@article {pmid21102323, year = {2011}, author = {Cotter, PD}, title = {Small intestine and microbiota.}, journal = {Current opinion in gastroenterology}, volume = {27}, number = {2}, pages = {99-105}, doi = {10.1097/MOG.0b013e328341dc67}, pmid = {21102323}, issn = {1531-7056}, mesh = {Celiac Disease/*microbiology ; Humans ; Ileostomy ; Inflammatory Bowel Diseases/*microbiology ; Intestine, Small/*microbiology ; Irritable Bowel Syndrome/*microbiology ; Pouchitis/*microbiology ; }, abstract = {PURPOSE OF REVIEW: To highlight the recent studies which have enhanced our appreciation of the composition of the microbiota in the human small intestine and its relevance to the health of the host.<br><br>RECENT FINDINGS: In the past number of years, the composition of the microorganisms present in our small intestines has been the subject of greater scrutiny than ever before. These investigations have been possible as a consequence of the development and utilization of new molecular tools which have revolutionized the field of microbial ecology and have focused predominantly on the small intestinal microbiota associated with pediatric celiac disease, inflammatory bowel disease, irritable bowel syndrome and pouchitis. The impact of invasive procedures, such as small bowel transplant, ileostomy and ileal pouch anal anastomosis, on the ileal microbiota has also been investigated.<br><br>SUMMARY: The ever greater appreciation of the link between the small intestinal microbiota and the health status of the host has the potential to lead to the development of new strategies to alter this microbiota in a targeted way to prevent or treat specific disorders.}, }
@article {pmid21097583, year = {2011}, author = {Howard, EC and Sun, S and Reisch, CR and del Valle, DA and Bürgmann, H and Kiene, RP and Moran, MA}, title = {Changes in dimethylsulfoniopropionate demethylase gene assemblages in response to an induced phytoplankton bloom.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {2}, pages = {524-531}, pmid = {21097583}, issn = {1098-5336}, mesh = {Bacteria/classification/*enzymology/*genetics ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Metagenome ; Mexico ; Molecular Sequence Data ; Phylogeny ; Phytoplankton/*genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Sulfonium Compounds/*metabolism ; Sulfur/metabolism ; }, abstract = {Over half of the bacterioplankton cells in ocean surface waters are capable of carrying out a demethylation of the phytoplankton metabolite dimethylsulfoniopropionate (DMSP) that routes the sulfur moiety away from the climatically active gas dimethylsulfide (DMS). In this study, we tracked changes in dmdA, the gene responsible for DMSP demethylation, over the course of an induced phytoplankton bloom in Gulf of Mexico seawater microcosms. Analysis of >91,000 amplicon sequences indicated 578 different dmdA sequence clusters at a conservative clustering criterion of ≥90% nucleotide sequence identity over the 6-day study. The representation of the major clades of dmdA, several of which are linked to specific taxa through genomes of cultured marine bacterioplankton, remained fairly constant. However, the representation of clusters within these major clades shifted significantly in response to the bloom, including two Roseobacter-like clusters and a SAR11-like cluster, and the best correlate with shifts of the dominant dmdA clades was chlorophyll a concentration. Concurrent 16S rRNA amplification and sequencing indicated the presence of Roseobacter, SAR11, OM60, and marine Rhodospirillales populations, all of which are known to harbor dmdA genes, although the largest taxonomic change was an increase in Flavobacteriaceae, a group not yet demonstrated to have DMSP-demethylating capabilities. Sequence heterogeneity in dmdA and other functional gene populations is becoming increasingly evident with the advent of high-throughput sequencing technologies, and understanding the ecological implications of this heterogeneity is a major challenge for marine microbial ecology.}, }
@article {pmid21093087, year = {2011}, author = {Nieminen, TT and Vihavainen, E and Paloranta, A and Lehto, J and Paulin, L and Auvinen, P and Solismaa, M and Björkroth, KJ}, title = {Characterization of psychrotrophic bacterial communities in modified atmosphere-packed meat with terminal restriction fragment length polymorphism.}, journal = {International journal of food microbiology}, volume = {144}, number = {3}, pages = {360-366}, doi = {10.1016/j.ijfoodmicro.2010.10.018}, pmid = {21093087}, issn = {1879-3460}, mesh = {Bacteria/*genetics/*isolation &amp; purification ; Colony Count, Microbial ; Food Microbiology/*methods ; *Food Packaging ; Meat/*microbiology ; *Polymorphism, Restriction Fragment Length ; }, abstract = {Characterization of psychrotrophic lactic acid bacteria (LAB) and Brochothrix thermosphacta communities is needed to understand the microbial ecology of spoilage of modified atmosphere-packed (MAP) meats. To overcome the limitations of the currently used methods for the characterization of psychrotrophic bacterial communities in meat, we developed a culture-independent, 16S rRNA gene-targeted terminal restriction fragment length polymorphism (T-RFLP) method. An identification library consisting of 100 Gram-positive and 30 Gram-negative meat-associated bacterial strains was set up to identify the terminal restriction fragments derived from the communities. The taxonomic resolution level of the T-RFLP method was in between genus and species within the investigated LAB strains and within family and genus within the investigated Gram-negative strains. The established library was applied to identify the members of bacterial communities in MAP minced meat at the end of the shelf life. The T-RFLP results and plate counts on Man-Rogosa-Sharpe, Violet Red Bile Glucose, and Streptomycin sulfate thallium acetate actidione agars indicated that LAB and B. thermosphacta predominated in meat. The bacterial taxa associated with the T-RFLP results were compared to those identified among plate-grown LAB isolates by numerical ribopattern analysis. Both methods agreed that Leuconostoc spp. and Carnobacterium spp. prevailed in the LAB community in minced meat followed by Lactobacillus algidus, Lactococcus spp. and Weissella spp. Colony identification revealed that Leuconostoc gasicomitatum, L. gelidum, Carnobacterium divergens and C. maltaromaticum were the predominant LAB species. The T-RFLP results were shown to correlate with viable counts of Leuconostoc spp. and B. thermosphacta. The T-RFLP method was found to be a useful tool enabling rapid and high-throughput characterization of psychrotrophic bacteria prevailing in MAP meat.}, }
@article {pmid21093011, year = {2011}, author = {Bialek, K and Kim, J and Lee, C and Collins, G and Mahony, T and O'Flaherty, V}, title = {Quantitative and qualitative analyses of methanogenic community development in high-rate anaerobic bioreactors.}, journal = {Water research}, volume = {45}, number = {3}, pages = {1298-1308}, doi = {10.1016/j.watres.2010.10.010}, pmid = {21093011}, issn = {1879-2448}, mesh = {Anaerobiosis ; Bioreactors/*microbiology ; Denaturing Gradient Gel Electrophoresis ; Euryarchaeota/growth &amp; development/*metabolism ; Methane/*metabolism ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Methanogenic community structure and population dynamics were investigated in two anaerobic reactors treating a dairy wastewater, an Inverted Fluidized Bed (IFB) and Expanded Granular Sludge Bed (EGSB). A combination of real-time PCR, denaturing gradient gel electrophoresis and statistical techniques was employed. Distinct methanogenic communities developed in the IFB and EGSB reactors reflecting step-wise reductions in the applied hydraulic retention time from 72 to 12 h during the 200-day trial. The aceticlastic family Methanosarcinaceae was only detected in the IFB and the order Methanomicrobiales was also much more abundant in this reactor, while the aceticlastic family Methanosaetaceae was more abundant in the EGSB. The hydrogenotrophic order, Methanobacteriales, predominated in both reactors under all applied operational conditions. Non-metric multidimensional scaling (NMS) and moving-window analyses, based on absolute and relative abundance quantification data, demonstrated that the methanogenic communities developed in a different manner in the IFB, compared to the EGSB reactor. In our study, relative abundance-based quantification by NMS and moving-window analysis appeared to be a valuable molecular approach that was more applicable to reflect the changes in the anaerobic digestion process than approaches based either on qualitative analysis, or solely on absolute quantification of the various methanogenic groups. The overall results and findings provided a comparative, quantitative and qualitative insight into anaerobic digestion processes, which could be helpful for better future reactor design and process control.}, }
@article {pmid21091864, year = {2011}, author = {van der Wal, A and Leveau, JH}, title = {Modelling sugar diffusion across plant leaf cuticles: the effect of free water on substrate availability to phyllosphere bacteria.}, journal = {Environmental microbiology}, volume = {13}, number = {3}, pages = {792-797}, doi = {10.1111/j.1462-2920.2010.02382.x}, pmid = {21091864}, issn = {1462-2920}, mesh = {Bacteria/*growth &amp; development/metabolism ; Carbohydrate Metabolism ; Carbohydrates/*chemistry ; Diffusion ; Ecosystem ; Juglans/microbiology ; Light ; *Models, Biological ; Permeability ; Plant Leaves/*microbiology ; Water/*chemistry ; }, abstract = {We present a continuous model for the diffusion of sugars across intact plant leaf cuticles. It is based on the flow of sugars from a source, representing the leaf apoplast, to a sink, in the shape of a hemispherical drop of water on the outside of the cuticle. Flow is a function of the difference between sugar concentrations C(Source) and C(Sink) , permeability P of the cuticle, volume V(Sink) of the water drop, as well as its contact angle α with the cuticle surface. Using a bacterial bioreporter for fructose, and a two-compartment experimental set-up consisting of isolated cuticles of walnut (Juglans regia) carrying water droplets while floating on solutions with increasing concentrations of fructose, we determined a value of 1 × 10[-6] m h[-1] for P. Using this value, we explored different scenarios for the leaching of sugars across plant leaf cuticles to reveal in quantitative terms how diffusion takes longer when V(Sink) increases, P decreases or α increases. Bacterial growth was modelled as a function of changes in P, α and V(Sink) and was consistent with observations or suggestions from the literature in relation to the availability of free water on leaves. These results are discussed in the light of bacteria as ecosystem engineers, i.e. with the ability to modify the plant leaf surface environment in favour of their own survival, e.g. by increasing cuticle leakage or leaf wetness. Our model represents a first step towards a more comprehensive model which will enhance our quantitative understanding of the factors that play a role in nutrient availability to bacterial colonizers of the phyllosphere, or plant leaf surface.}, }
@article {pmid21090508, year = {2010}, author = {Kang, YJ and Cheng, J and Mei, LJ and Hu, J and Piao, Z and Yin, SX}, title = {Multiple copies of 16s rRNA gene affect the restriction patterns and DGGE profile as revealed by analysis of genome database.}, journal = {Mikrobiologiia}, volume = {79}, number = {5}, pages = {664-671}, pmid = {21090508}, issn = {0026-3656}, mesh = {Bacteria/*genetics/isolation &amp; purification ; Databases, Genetic ; *Denaturing Gradient Gel Electrophoresis ; *Gene Dosage ; *Genes, rRNA ; Genome, Bacterial ; *Polymorphism, Restriction Fragment Length ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; Sensitivity and Specificity ; }, abstract = {The use of 16S rRNA gene has been a "golden" method to determine the diversity of microbial communities in environmental samples, phylogenetic relationships of prokaryotes and taxonomic position of newly isolated organisms. However due to the presence of multiple heterogeneous 16S rRNA gene copies in many strains, the interpretation of microbial ecology via 16S rRNA sequences is complicated. Purpose of present paper is to demonstrate the extent to which the multiple heterogeneous 16S rRNA gene copies affect RFLP patterns and DGG E profiles by using the genome database. In present genome database, there are 782 bacterial strains in total whose genomes have been completely sequenced and annotated. Among the total strains, 639 strains (82%) possess multiple 16S rRNA gene copies, 415 strains (53%) whose multiple copies are heterogeneous in sequences as revealed by alignment, 236 strains (30%) whose multiple copies show different restrict patterns by CSP61 + Hinfl, MspI + Rsal or HhaI as analyzed in silico. Polymorphisms of the multiple copies in certain strains were further characterized by G + C% and phylogentic distances based on the sequences of V3 region, which are linked to DGGE patters. Polymorphisms of a few strains were shown as examples. Using artificial communities, it is demonstrated that the presence of multiple heterogeneous 16S rRNA gene copies potentially leads to over-estimation of the diversity of a community. It is suggested that care must be taken when interpreting 16S rRNA-based RFLP and DGGE data and profiling an environmental community.}, }
@article {pmid21087444, year = {2011}, author = {Kverka, M and Zakostelska, Z and Klimesova, K and Sokol, D and Hudcovic, T and Hrncir, T and Rossmann, P and Mrazek, J and Kopecny, J and Verdu, EF and Tlaskalova-Hogenova, H}, title = {Oral administration of Parabacteroides distasonis antigens attenuates experimental murine colitis through modulation of immunity and microbiota composition.}, journal = {Clinical and experimental immunology}, volume = {163}, number = {2}, pages = {250-259}, pmid = {21087444}, issn = {1365-2249}, mesh = {Acute Disease ; Administration, Oral ; Animals ; Antibodies, Bacterial/blood/immunology ; Antigens, Bacterial/*administration &amp; dosage/immunology ; Bacteroides/*immunology ; Chronic Disease ; Colitis/*therapy ; Cytokines/blood/immunology ; Female ; Intestinal Mucosa/immunology ; Metagenome/*immunology ; Mice ; Mice, Inbred BALB C ; Mice, SCID ; }, abstract = {Commensal bacteria have been shown to modulate the host mucosal immune system. Here, we report that oral treatment of BALB/c mice with components from the commensal, Parabacteroides distasonis, significantly reduces the severity of intestinal inflammation in murine models of acute and chronic colitis induced by dextran sulphate sodium (DSS). The membranous fraction of P. distasonis (mPd) prevented DSS-induced increases in several proinflammatory cytokines, increased mPd-specific serum antibodies and stabilized the intestinal microbial ecology. The anti-colitic effect of oral mPd was not observed in severe combined immunodeficient mice and probably involved induction of specific antibody responses and stabilization of the intestinal microbiota. Our results suggest that specific bacterial components derived from the commensal bacterium, P. distasonis, may be useful in the development of new therapeutic strategies for chronic inflammatory disorders such as inflammatory bowel disease.}, }
@article {pmid21086104, year = {2010}, author = {Gabriel, J}, title = {Development of soil microbiology methods: from respirometry to molecular approaches.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {37}, number = {12}, pages = {1289-1297}, pmid = {21086104}, issn = {1476-5535}, mesh = {Bacteria/genetics/*growth &amp; development/metabolism ; Bacteriological Techniques/instrumentation/methods ; Biomarkers ; Fermentation ; Soil/analysis ; *Soil Microbiology ; }, abstract = {This review deals with techniques and methods used in the study of the function and development of microorganisms occurring in soil with emphasis on the contributions of Czech Academician Ivan Málek and his coworkers or fellows (Jiří Macura, František Kunc) to the development of basic techniques used in soil microbiology. Early studies, including batch cultivation and respirometric techniques, as well as later developments of percolation and continuous-flow methods of cultivation of soil microorganisms are discussed. Recent developments in the application of analytical chemistry (HPLC or GC) and of molecular biological techniques to ecological questions that have revolutionized concepts in soil microbiology and microbial ecology are also briefly mentioned, including denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), phospholipid fatty acid analysis (PLFA) and others. The shift of soil microbiology from the study of individual microorganisms to entire microbial communities, including nonculturable species, is briefly discussed.}, }
@article {pmid21085946, year = {2011}, author = {Davis, TS and Hofstetter, RW and Foster, JT and Foote, NE and Keim, P}, title = {Interactions between the yeast Ogataea pini and filamentous fungi associated with the western pine beetle.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {626-634}, pmid = {21085946}, issn = {1432-184X}, mesh = {Animals ; Arizona ; Coleoptera/*microbiology ; Fungi/*growth &amp; development/isolation &amp; purification/metabolism ; Gas Chromatography-Mass Spectrometry ; Saccharomycetales/*growth &amp; development/isolation &amp; purification/metabolism ; *Symbiosis ; Volatile Organic Compounds/*metabolism ; }, abstract = {Ecologically important microbes other than filamentous fungi can be housed within the fungal-transport structures (mycangia) of Dendroctonus bark beetles. The yeast Ogataea pini (Saccharomycetales: Saccharomycetaceae) was isolated from the mycangia of western pine beetle (Dendroctonus brevicomis) populations in northern Arizona (USA) with a frequency of 56%. We performed a series of in vitro assays to test whether volatile organic compounds produced by O. pini affected radial growth rates of mutualistic and antagonistic species of filamentous fungi that are commonly found in association with the beetle including Entomocorticium sp. B, Ophiostoma minus, Beauvaria bassiana, and an Aspergillus sp. We determined the compounds O. pini produced when grown on 2% malt extract agar using a gas chromatography/mass spectrometry (GC/MS) analysis of headspace volatiles. Volatiles produced by O. pini on artificial media significantly enhanced the growth of the mutualistic Entomocorticium sp. B, and inhibited growth of the entomopathogenic fungus B. bassiana. GC/MS revealed that O. pini produced ethanol, carbon disulfide (CS(2)), and Δ-3-carene in headspace. The results of these studies implicate O. pini as an important component in D. brevicomis community ecology, and we introduce multiple hypotheses for future tests of the effects of yeasts in the symbiont assemblages associated with Dendroctonus bark beetles.}, }
@article {pmid21085051, year = {2011}, author = {Chiu, CH and Michelow, IC and Cronin, J and Ringer, SA and Ferris, TG and Puopolo, KM}, title = {Effectiveness of a guideline to reduce vancomycin use in the neonatal intensive care unit.}, journal = {The Pediatric infectious disease journal}, volume = {30}, number = {4}, pages = {273-278}, doi = {10.1097/INF.0b013e3182011d12}, pmid = {21085051}, issn = {1532-0987}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Bacterial Infections/*drug therapy ; Drug Utilization/*standards ; Guideline Adherence/*statistics &amp; numerical data ; *Health Services Research ; Humans ; Infant, Newborn ; Intensive Care, Neonatal/methods ; Massachusetts ; Organizational Policy ; Vancomycin/*therapeutic use ; }, abstract = {BACKGROUND: The Centers for Disease Control and Prevention recommend hospitals develop guidelines for the appropriate use of vancomycin as part of comprehensive antimicrobial stewardship. The objective of this study was to evaluate the effectiveness and safety of a guideline to restrict vancomycin use in the neonatal intensive care unit (NICU).<br><br>METHODS: A vancomycin use guideline was introduced in 2 tertiary care NICUs with low incidences of methicillin-resistant Staphylococcus aureus infections. We compared all infants >72 hours of age who were evaluated for late-onset infection before and after implementation of this guideline.<br><br>RESULTS: Vancomycin start rates were reduced from 6.9 to 4.5 per 1000 patient-days (35% reduction; P = 0.01) at Brigham and Women's Hospital, and from 17 to 6.4 per 1000 patient-days (62% reduction; P < 0.0001) at Massachusetts General Hospital. The number of infants exposed to vancomycin decreased from 5.2 to 3.1 per 1000 patient-days (40% reduction; P = 0.008) at Brigham and Women's Hospital, and 10.8 to 5.5 per 1000 patient-days (49% reduction; P = 0.009) at Massachusetts General Hospital. Causes of infection, duration of bacteremia, and incidence of complications or deaths attributable to late-onset infection did not change significantly at either institution.<br><br>CONCLUSIONS: Implementation of a NICU vancomycin use guideline significantly reduced exposure of newborns to vancomycin without adversely affecting short-term patient safety. Further studies are required to evaluate the long-term effect of vancomycin restriction on NICU patient safety and microbial ecology, particularly among institutions with higher rates of methicillin-resistant Staphylococcus aureus infections.}, }
@article {pmid21082178, year = {2011}, author = {Berdjeb, L and Ghiglione, JF and Domaizon, I and Jacquet, S}, title = {A 2-year assessment of the main environmental factors driving the free-living bacterial community structure in Lake Bourget (France).}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {941-954}, pmid = {21082178}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Denaturing Gradient Gel Electrophoresis ; *Ecosystem ; Environment ; France ; Fresh Water/chemistry/*microbiology ; Seasons ; }, abstract = {Despite the considerable attention that has been paid to bacterioplankton over recent decades, the dynamic of aquatic bacterial community structure is still poorly understood, and long-term studies are particularly lacking. Moreover, how the environment governs diversity patterns remains a key issue in aquatic microbial ecology. In this study, we used denaturing gradient gel electrophoresis of PCR-amplified partial 16S rRNA gene fragments and multivariable statistical approaches to explore the patterns of change in the free-living bacterial community in the mesotrophic and mono-meromictic Lake Bourget (France). A monthly sampling was conducted over two consecutive years (2007 and 2008) and at two different depths characterizing the epi- and hypolimnion of the lake (2 and 50 m, respectively). Temporal shifts in the bacterial community structure followed different patterns according to depth, and no seasonal reproducibility was recorded from 1 year to the next. Our results showed that the bacterial community structure displayed lower diversity at 2 m (22 bands) compared to 50 m (32 bands) and that bacterial community structure dynamics followed dissimilar trends between the two depths. At 2 m, five shifts in the bacterial community structure occurred, with the temporal scale varying between 2 and 8 months whereas, at 50 m, four shifts in the bacterial community structure took place at 50 m, with the temporal scale fluctuating between 3 and 13 months. More than 60% of the bacterial community structure variance was explained by seven variables at 2 m against eight at 50 m. Nutrients (PO(4)-P, NH(4)-N and NO(3)-N) and temperature were responsible for 49.6% of the variance at 2 m whereas these nutrients, with dissolved oxygen and chlorophyll a accounting for 59.6% of the variance at 50 m. Grazing by ciliates played also a critical role on the bacterial community structure at both depths. Our results suggest that the free-living bacterial community structure in the epi- and hypolimnion of Lake Bourget is mainly driven by combined, but differently weighted, top-down and bottom-up factors at 2 and 50 m.}, }
@article {pmid21080161, year = {2011}, author = {Velimirov, B and Milosevic, N and Kavka, GG and Farnleitner, AH and Kirschner, AK}, title = {Development of the bacterial compartment along the Danube River: a continuum despite local influences.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {955-967}, pmid = {21080161}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Ecosystem ; Rivers/chemistry/*microbiology ; }, abstract = {Microbial food webs dominate heterotrophic food webs in large rivers with bacterial metabolism being a key component of carbon processing. Thus, analysis of bacterial population dynamics is critical to understanding patterns and mechanisms of material cycling and energy fluxes in large rivers. Within the frame of the Joint Danube Survey (JDS) 2007, the longitudinal development of the natural bacterial community in the Danube in terms of bacterial numbers, morphotype composition, and heterotrophic production of the suspended and particle-attached fractions was followed at a fine spatial resolution of approximately 30 km for the first time in such a large river along a 2,600-km stretch. Twenty-one major tributaries and branches were also included. This allowed us to investigate whether bacterial standing stock and production undergo continuous, linear changes or whether discontinuities and local processes like the merging of tributaries or the potential impact of sewage input drive the bacterial population in the Danube. The presented investigation revealed surprising continuous patterns of changes of bacterial parameters along the Danube River. Despite the presence of impoundments or hydropower plants, large municipalities, and the discharge of large tributaries, most bacterial parameters (standing stock, morphotype succession, and attached bacterial production) developed gradually, indicating that mainly broad-scale drivers and not local conditions shape and control the bacterial community in the midstream of this large river. As most important broad-scale drivers, nutrients (inorganic and organic) and changes in particle concentrations were identified. These data are also in remarkable accordance with the patterns of changes of the genetic bacterial community composition, observed during the first JDS (2001) 6 years before. In contrast, bacterial activity did not follow a continuous trend and was mainly controlled by the input of sewage from large cities in the middle section, leading to a bloom of phytoplankton. The observed patterns and the comparison between the Danube, its tributaries and other large rivers worldwide indicate that the bacterial community in rivers has a powerful indicator function for estimating the ecological status of large river ecosystems once enough information has been collected at various temporal and spatial scales.}, }
@article {pmid21074033, year = {2010}, author = {Black, CE and Costerton, JW}, title = {Current concepts regarding the effect of wound microbial ecology and biofilms on wound healing.}, journal = {The Surgical clinics of North America}, volume = {90}, number = {6}, pages = {1147-1160}, doi = {10.1016/j.suc.2010.08.009}, pmid = {21074033}, issn = {1558-3171}, mesh = {Administration, Topical ; Anti-Infective Agents/therapeutic use ; Bandages ; Biofilms/*drug effects ; Debridement/methods ; Ecology ; Female ; Humans ; Male ; *Occlusive Dressings ; Risk Assessment ; Treatment Outcome ; Wound Healing/*physiology ; Wound Infection/*drug therapy ; Wounds and Injuries/*microbiology/physiopathology/*therapy ; }, abstract = {Biofilms are a collection of microbes that adhere to surfaces by manufacturing a matrix that shields them from environmental elements. Wound biofilms are difficult to evaluate clinically, and standard culture methods are inadequate for capturing the true bioburden present in the biofilm. New molecular techniques provide the means for rapid detection and evaluation of wound biofilms, and may prove to be useful in the clinical setting. Studies have shown that many commercial topical agents and wound dressings in use are ineffective against the biofilm matrix. At this stage, mechanical debridement appears to be essential in the eradication of a wound biofilm. Topical antimicrobial agents and antibiotics may be effective in the treatment of the wound bed after debridement in the prevention of biofilm reformation.}, }
@article {pmid21072830, year = {2011}, author = {de Lorenzo, V}, title = {Genes that move the window of viability of life: lessons from bacteria thriving at the cold extreme: mesophiles can be turned into extremophiles by substituting essential genes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {33}, number = {1}, pages = {38-42}, doi = {10.1002/bies.201000101}, pmid = {21072830}, issn = {1521-1878}, mesh = {Bacterial Vaccines/immunology ; Cold Temperature ; Escherichia coli/*genetics ; *Gene Expression Regulation, Bacterial/physiology ; Genes, Essential/physiology ; Genetic Engineering ; *Microbial Viability ; Microbiology/trends ; Mutagenesis, Insertional/*physiology ; }, abstract = {Whether occurrence of life at the physicochemical extremes results from the entire adaptation of organisms to such settings or it originates from the action of a few genes has been debated for a long time. Recent evidence suggests that a limited number of functions suffice to change the predilection of microorganisms for radically different environmental scenarios. For instance, expression of a few genes from cold-loving bacteria in mesophilic hosts allows them to grow at much lower temperatures and become heat-sensitive. This has been exploited not only for constructing Escherichia coli strains able to grow at 5-10 °C (and thus optimised as hosts for heterologous gene expression) but also for designing vaccines based on temperature-sensitive pathogens. Occurrence of genes/functions that reframe the windows of viability may also ask for a revision of some concepts in microbial ecology and may provide new tools for engineering bacteria with a superior biotechnological performance.}, }
@article {pmid21072585, year = {2011}, author = {Kim, K and Yoo, K and Ki, D and Son, IS and Oh, KJ and Park, J}, title = {Decision-Tree-based data mining and rule induction for predicting and mapping soil bacterial diversity.}, journal = {Environmental monitoring and assessment}, volume = {178}, number = {1-4}, pages = {595-610}, pmid = {21072585}, issn = {1573-2959}, mesh = {Bacteria/*classification ; *Biodiversity ; Data Mining/*methods ; *Decision Trees ; Geographic Information Systems ; Geography ; Models, Biological ; *Soil Microbiology ; }, abstract = {Soilmicrobial ecology plays a significant role in global ecosystems. Nevertheless, methods of model prediction and mapping have yet to be established for soil microbial ecology. The present study was undertaken to develop an artificial-intelligence- and geographical information system (GIS)-integrated framework for predicting and mapping soil bacterial diversity using pre-existing environmental geospatial database information, and to further evaluate the applicability of soil bacterial diversity mapping for planning construction of eco-friendly roads. Using a stratified random sampling, soil bacterial diversity was measured in 196 soil samples in a forest area where construction of an eco-friendly road was planned. Model accuracy, coherence analyses, and tree analysis were systematically performed, and four-class discretized decision tree (DT) with ordinary pair-wise partitioning (OPP) was selected as the optimal model among tested five DT model variants. GIS-based simulations of the optimal DT model with varying weights assigned to soil ecological quality showed that the inclusion of soil ecology in environmental components, which are considered in environmental impact assessment, significantly affects the spatial distributions of overall environmental quality values as well as the determination of an environmentally optimized road route. This work suggests a guideline to use systematic accuracy, coherence, and tree analyses in selecting an optimal DT model from multiple candidate model variants, and demonstrates the applicability of the OPP-improved DT integrated with GIS in rule induction for mapping bacterial diversity. These findings also provide implication on the significance of soil microbial ecology in environmental impact assessment and eco-friendly construction planning.}, }
@article {pmid21071631, year = {2010}, author = {Canfield, DE and Stewart, FJ and Thamdrup, B and De Brabandere, L and Dalsgaard, T and Delong, EF and Revsbech, NP and Ulloa, O}, title = {A cryptic sulfur cycle in oxygen-minimum-zone waters off the Chilean coast.}, journal = {Science (New York, N.Y.)}, volume = {330}, number = {6009}, pages = {1375-1378}, doi = {10.1126/science.1196889}, pmid = {21071631}, issn = {1095-9203}, mesh = {Anaerobiosis ; Bacteria/classification/genetics/*metabolism ; Chile ; Deltaproteobacteria/classification/genetics/metabolism ; Denitrification ; *Ecosystem ; Gammaproteobacteria/classification/genetics/metabolism ; Genes, Bacterial ; Metagenome ; Nitrates/metabolism ; Nitrites/metabolism ; Nitrogen Cycle ; Oxidation-Reduction ; Oxygen/*analysis ; Pacific Ocean ; Quaternary Ammonium Compounds/metabolism ; Seawater/chemistry/*microbiology ; Sequence Analysis, DNA ; Sulfates/metabolism ; Sulfides/metabolism ; Sulfur/*metabolism ; }, abstract = {Nitrogen cycling is normally thought to dominate the biogeochemistry and microbial ecology of oxygen-minimum zones in marine environments. Through a combination of molecular techniques and process rate measurements, we showed that both sulfate reduction and sulfide oxidation contribute to energy flux and elemental cycling in oxygen-free waters off the coast of northern Chile. These processes may have been overlooked because in nature, the sulfide produced by sulfate reduction immediately oxidizes back to sulfate. This cryptic sulfur cycle is linked to anammox and other nitrogen cycling processes, suggesting that it may influence biogeochemical cycling in the global ocean.}, }
@article {pmid21071496, year = {2011}, author = {De Maeyer, K and D'aes, J and Hua, GKH and Perneel, M and Vanhaecke, L and Noppe, H and Höfte, M}, title = {N-Acylhomoserine lactone quorum-sensing signalling in antagonistic phenazine-producing Pseudomonas isolates from the red cocoyam rhizosphere.}, journal = {Microbiology (Reading, England)}, volume = {157}, number = {Pt 2}, pages = {459-472}, doi = {10.1099/mic.0.043125-0}, pmid = {21071496}, issn = {1465-2080}, mesh = {Acyl-Butyrolactones/*metabolism ; Antibiosis ; Colocasia/*microbiology ; DNA, Bacterial/genetics ; Genes, Bacterial ; Mutation ; Operon ; Phenazines/*metabolism ; Plant Roots/microbiology ; Pseudomonas/genetics/*metabolism ; *Quorum Sensing ; *Rhizosphere ; Signal Transduction ; Tandem Mass Spectrometry ; }, abstract = {Forty fluorescent Pseudomonas strains isolated from white and red cocoyam roots were tested for their ability to synthesize N-acyl-l-homoserine lactones (acyl-HSLs). Remarkably, only isolates from the red cocoyam rhizosphere that were antagonistic against the cocoyam root rot pathogen Pythium myriotylum and synthesized phenazine antibiotics produced acyl-HSLs. This supports the assumption that acyl-HSL production is related to the antagonistic activity of the strains. After detection, the signal molecules were identified through TLC-overlay and liquid chromatography-multiple MS (LC-MS/MS) analysis. In our representative strain, Pseudomonas CMR12a, production of the signal molecules could be assigned to two quorum-sensing (QS) systems. The first one is the QS system for phenazine production, PhzI/PhzR, which seemed to be well conserved, since it was genetically organized in the same way as in the well-described phenazine-producing Pseudomonas strains Pseudomonas fluorescens 2-79, Pseudomonas chlororaphis PCL1391 and Pseudomonas aureofaciens 30-84. The newly characterized genes cmrI and cmrR make up the second QS system of CMR12a, under the control of the uncommon N-3-hydroxy-dodecanoyl-homoserine lactone (3-OH-C12-HSL) and with low similarity to other Pseudomonas QS systems. No clear function could yet be assigned to the CmrI/CmrR system, although it contributes to the biocontrol capability of CMR12a. Both the PhzI/PhzR and CmrI/CmrR systems are controlled by the GacS/GacA two-component regulatory system.}, }
@article {pmid21071229, year = {2011}, author = {Vos, M}, title = {A species concept for bacteria based on adaptive divergence.}, journal = {Trends in microbiology}, volume = {19}, number = {1}, pages = {1-7}, doi = {10.1016/j.tim.2010.10.003}, pmid = {21071229}, issn = {1878-4380}, mesh = {Bacteria/*classification/*genetics ; Biological Evolution ; Classification/*methods ; *Genetic Speciation ; Multilocus Sequence Typing ; Phylogeny ; }, abstract = {Bacterial strains are currently grouped into species based on overall genomic similarity and sharing of phenotypes deemed ecologically important. Many believe this polyphasic taxonomy is in need of revision because it lacks grounding in evolutionary theory, and boundaries between species are arbitrary. Recent taxonomy efforts using multilocus sequence typing (MLST) data are based on the identification of distinct phylogenetic clusters. However, these approaches face the problem of deciding the phylogenetic level at which clusters are representative of evolutionary or taxonomically distinct units. In this review, I propose classifying two phylogenetic clusters as separate species only when they have statistically significantly diverged as a result of adaptive evolution. More than a method for classification, the concept of adaptive divergence can be used in a 'reverse ecology' approach to identify lineages that are in the process of speciation or genes involved in initial adaptive divergence.}, }
@article {pmid21063870, year = {2011}, author = {Xia, X and Lie, TK and Qian, X and Zheng, Z and Huang, Y and Shen, Y}, title = {Species diversity, distribution, and genetic structure of endophytic and epiphytic Trichoderma associated with banana roots.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {619-625}, pmid = {21063870}, issn = {1432-184X}, mesh = {Amplified Fragment Length Polymorphism Analysis ; DNA, Fungal/genetics ; Genetic Variation ; Musa/*microbiology ; *Phylogeny ; Plant Roots/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; Trichoderma/*genetics/growth &amp; development/isolation &amp; purification ; }, abstract = {Selective isolation, molecular identification and AFLP were used to investigate the distribution of the various species of endophytic and epiphytic Trichoderma associated with banana roots and to compare and contrast their genetic structure. Three specific groups of Trichoderma were observed in the roots of banana. Group one, which made up the largest population, comprised T. asperellum, T. virens, and Hypocrea lixii, which were isolated from both inside and on the surface of the banana roots, while group two, made up of T. atroviride and T. koningiopsis, existed on the surface only. Group three, comprising only T. brevicompactum was isolated from the inside of the roots. The AFLP analysis revealed Nei's diversity indices of 0.15 and 0.26 for epiphytic T. asperellum and T. virens, respectively. The index values of 0.11 and 0.11 were obtained for endophytic T. asperellum and T. virens, respectively. The genetic diversity within endophytic T. asperellum and T. virens was lower than that within the epiphytes. This suggests that endophytic Trichoderma has a higher genetic conservation and is compatible with the relatively stable microenvironments inside roots.}, }
@article {pmid21062328, year = {2011}, author = {Jasser, I and Królicka, A and Karnkowska-Ishikawa, A}, title = {A novel phylogenetic clade of picocyanobacteria from the Mazurian lakes (Poland) reflects the early ontogeny of glacial lakes.}, journal = {FEMS microbiology ecology}, volume = {75}, number = {1}, pages = {89-98}, doi = {10.1111/j.1574-6941.2010.00990.x}, pmid = {21062328}, issn = {1574-6941}, mesh = {Cyanobacteria/classification/*genetics ; Fresh Water/microbiology ; Gene Transfer, Horizontal ; *Genetic Variation ; Operon ; Phycocyanin/genetics ; Phycoerythrin/genetics ; *Phylogeny ; Poland ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {The community of picocyanobacteria inhabiting the Great Mazurian Lakes system (comprising lakes ranging from mesotrophic to hypertrophic) is dominated by phycoerythrin-rich cells, which outnumber phycocyanin-rich cells, even in hypertrophic lakes. The genetic diversity and phylogeny of 43 strains of picocyanobacteria isolated from four Mazurian lakes were studied by analyzing the nucleotide sequences of the 16S rRNA gene and cpcBA-IGS operon. Phylogenetic analyses assigned some of the strains to several previously described clusters (Groups A, B, C, E and I) and revealed the existence of a novel clade, Group M (Mazurian), which exhibited a low level of similarity to the other clusters. Both phycocyanin and phycoerythrin picocyanobacteria were assigned to this clade based on an analysis of the 16S rRNA gene. The cpcBA sequence analysis assigned only phycocyanin strains to Group M, whereas the phycoerythrin strains from the M ribogroup were assigned to Groups B and E. We hypothesize that Group M originally contained only phycocyanin picocyanobacteria. The phycoerythrin found in strains belonging to ribogroup M seems to have been acquired through horizontal gene transfer as an adaptation to the changing environment early in the ontogeny of these glacial lakes.}, }
@article {pmid21057784, year = {2011}, author = {Singh, P and Raghukumar, C and Verma, P and Shouche, Y}, title = {Fungal community analysis in the deep-sea sediments of the Central Indian Basin by culture-independent approach.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {507-517}, pmid = {21057784}, issn = {1432-184X}, mesh = {*Biodiversity ; DNA Primers ; DNA, Fungal/genetics ; Fungi/*classification/genetics/isolation &amp; purification ; Gene Library ; Geologic Sediments/*microbiology ; Indian Ocean ; Phylogeny ; Seawater/microbiology ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Few studies have addressed the occurrence of fungi in deep-sea sediments, characterized by elevated hydrostatic pressure, low temperature, and fluctuating nutrient conditions. We evaluated the diversity of fungi at three locations of the Central Indian Basin (CIB) at a depth of ~5,000 m using culture-independent approach. Community DNA isolated from these sediments was amplified using universal and fungal-specific internal transcribed spacers and universal 18S rDNA primer pairs. A total of 39 fungal operational taxonomic units, with 32 distinct fungal taxa were recovered from 768 clones generated from 16 environmental clone libraries. The application of multiple primers enabled the recovery of eight sequences that appeared to be new. The majority of the recovered sequences belonged to diverse phylotypes of Ascomycota and Basidiomycota. Our results suggested the existence of cosmopolitan marine fungi in the sediments of CIB. This study further demonstrated that diversity of fungi varied spatially in the CIB. Individual primer set appeared to amplify different fungal taxa occasionally. This is the first report on culture-independent diversity of fungi from the Indian Ocean.}, }
@article {pmid21057783, year = {2011}, author = {Kanokratana, P and Uengwetwanit, T and Rattanachomsri, U and Bunterngsook, B and Nimchua, T and Tangphatsornruang, S and Plengvidhya, V and Champreda, V and Eurwilaichitr, L}, title = {Insights into the phylogeny and metabolic potential of a primary tropical peat swamp forest microbial community by metagenomic analysis.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {518-528}, pmid = {21057783}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/metabolism ; Biodegradation, Environmental ; Biodiversity ; Biomass ; DNA, Bacterial/genetics ; Gene Library ; *Metabolome ; Metagenome ; *Metagenomics ; Molecular Sequence Annotation ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Thailand ; *Wetlands ; }, abstract = {A primary tropical peat swamp forest is a unique ecosystem characterized by long-term accumulation of plant biomass under high humidity and acidic water-logged conditions, and is regarded as an important terrestrial carbon sink in the biosphere. In this study, the microbial community in the surface peat layer in Pru Toh Daeng, a primary tropical peat swamp forest, was studied for its phylogenetic diversity and metabolic potential using direct shotgun pyrosequencing of environmental DNA, together with analysis of 16S rRNA gene library and key metabolic genes. The community was dominated by aerobic microbes together with a significant number of facultative and anaerobic microbial taxa. Acidobacteria and diverse Proteobacteria (mainly Alphaproteobacteria) constituted the major phylogenetic groups, with minor representation of archaea and eukaryotic microbes. Based on comparative pyrosequencing dataset analysis, the microbial community showed high metabolic versatility of plant polysaccharide decomposition. A variety of glycosyl hydrolases targeting lignocellulosic and starch-based polysaccharides from diverse bacterial phyla were annotated, originating mostly from Proteobacteria, and Acidobacteria together with Firmicutes, Bacteroidetes, Chlamydiae/Verrucomicrobia, and Actinobacteria, suggesting the key role of these microbes in plant biomass degradation. Pyrosequencing dataset annotation and direct mcrA gene analysis indicated the presence of methanogenic archaea clustering in the order Methanomicrobiales, suggesting the potential on partial carbon flux from biomass degradation through methanogenesis. The insights on the peat swamp microbial assemblage thus provide a valuable approach for further study on biogeochemical processes in this unique ecosystem.}, }
@article {pmid21057015, year = {2011}, author = {Gibbons, SM and Feris, K and McGuirl, MA and Morales, SE and Hynninen, A and Ramsey, PW and Gannon, JE}, title = {Use of microcalorimetry to determine the costs and benefits to Pseudomonas putida strain KT2440 of harboring cadmium efflux genes.}, journal = {Applied and environmental microbiology}, volume = {77}, number = {1}, pages = {108-113}, pmid = {21057015}, issn = {1098-5336}, support = {G0601943/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Cadmium/*metabolism/*toxicity ; Calorimetry/*methods ; Environmental Pollutants/*metabolism/*toxicity ; Gene Deletion ; Genes, Bacterial ; Membrane Transport Proteins/genetics ; Pseudomonas putida/*drug effects/*growth &amp; development ; }, abstract = {A novel microcalorimetric approach was used to analyze the responses of a metal-tolerant soil bacterium (Pseudomonas putida strain KT2440) to metal resistance gene deletions in cadmium-amended media. As hypothesized, under cadmium stress, the wild-type strain benefited from the resistance genes by entering the exponential growth phase earlier than two knockout strains. In the absence of cadmium, strain KT1, carrying a deletion in the main component (czcA1) of a Cd/Zn chemiosmotic efflux transporter (CzcCBA1), grew more efficiently than the wild type and released ∼700 kJ (per mole of biomass carbon) less heat than the wild-type strain, showing the energetic cost of maintaining CzcCBA1 in the absence of cadmium. A second mutant strain (KT4) carrying a different gene deletion, ΔcadA2, which encodes the main Cd/Pb efflux transporter (a P-type ATPase), did not survive beyond moderate cadmium concentrations and exhibited a decreased growth yield in the absence of cadmium. Therefore, CadA2 plays an essential role in cadmium resistance and perhaps serves an additional function. The results of this study provide direct evidence that heavy metal cation efflux mechanisms facilitate shorter lag phases in the presence of metals and that the maintenance and expression of tolerance genes carry quantifiable energetic costs and benefits.}, }
@article {pmid21053955, year = {2010}, author = {Lu, H and Chandran, K}, title = {Diagnosis and quantification of glycerol assimilating denitrifying bacteria in an integrated fixed-film activated sludge reactor via 13C DNA stable-isotope probing.}, journal = {Environmental science &amp; technology}, volume = {44}, number = {23}, pages = {8943-8949}, doi = {10.1021/es102124f}, pmid = {21053955}, issn = {1520-5851}, mesh = {Bacteria/classification/genetics/*metabolism ; Base Sequence ; Biofilms ; Bioreactors/microbiology ; Carbon Radioisotopes/chemistry ; DNA Probes/chemistry ; DNA, Bacterial/chemistry ; Denitrification ; Ecology ; Glycerol/*metabolism ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Glycerol, a byproduct of biodiesel and oleo-chemical manufacturing operations, represents an attractive alternate to methanol as a carbon and electron donor for enhanced denitrification. However, unlike methanol, little is known about the diversity and activity of glycerol assimilating bacteria in activated sludge. In this study, the microbial ecology of glycerol assimilating denitrifying bacteria in a sequencing batch integrated fixed film activated sludge (SB-IFAS) reactor was investigated using (13)C-DNA stable isotope probing (SIP). During steady state SB-IFAS reactor operation, near complete nitrate removal (92.7 ± 5.8%) was achieved. Based on (13)C DNA clone libraries obtained after 360 days of SB-IFAS reactor operation, bacteria related to Comamonas spp. and Diaphorobacter spp. dominated in the suspended phase communities. (13)C assimilating members in the biofilm community were phylogenetically more diverse and were related to Comamonas spp., Bradyrhizobium spp., and Tessaracoccus spp. Possibly owing to greater substrate availability in the suspended phase, the glycerol-assimilating denitrifying populations (quantified by real-time PCR) were more abundant therein than in the biofilm phase. The biomass in the suspended phase also had a higher specific denitrification rate than the biofilm phase (p = 4.33e-4), and contributed to 69.7 ± 4.5% of the overall N-removal on a mass basis. The kinetics of glycerol based denitrification by suspended phase biomass were approximately 3 times higher than with methanol. Previously identified methanol assimilating denitrifying bacteria were not associated with glycerol assimilation, thereby suggesting limited cross-utilization of these two substrates for denitrification in the system tested.}, }
@article {pmid21052657, year = {2011}, author = {Saul-Tcherkas, V and Steinberger, Y}, title = {Soil microbial diversity in the vicinity of a Negev Desert shrub--Reaumuria negevensis.}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {64-81}, pmid = {21052657}, issn = {1432-184X}, mesh = {Analysis of Variance ; Bacteria/classification/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; *Biodiversity ; Desert Climate ; Microbial Viability ; Nitrogen/analysis ; Seasons ; Soil/analysis ; *Soil Microbiology ; Tamaricaceae/*microbiology ; Water/analysis ; }, abstract = {The Negev Desert is characterized by low soil-water availability and organic matter content, as well as important factors significantly influencing soil biological activity. In order to overcome the xeric environment, plant and soil biota have evolutionarily developed, over time, ecophysiological abilities that help them fulfill their biological role and function. Microorganisms are known as a major part of the ecosystem's total biomass and play an important role in decomposition processes and the nutrient cycle. Perennial shrubs have been found to play an important role as organic matter suppliers and as a physical barrier prolonging biological activity of microbial communities. Soil samples were collected monthly, from November 2006 to November 2007, from a 0 to 10-cm depth under the canopies of Reaumuria negevensis and from open areas (control) in order to evaluate abiotic components and microbial variables on a temporal basis. H' values, evenness, and β diversity (Sørensen's similarity) were determined by a molecular method based on sequencing. Water availability, organic matter content, and total soluble nitrogen were higher in soil samples collected in the vicinity of R. negevensis than in samples collected in open areas. Our study also indicated that, in spite of the similarity between H' values of soil samples collected in the vicinity of R. negevensis and the open area, a low percentage of similarity was found between the soil bacterial populations. These results support the hypothesis that distribution of resources in the environment under R. negevensis shrubs varies in space and time and also influences soil microbial diversity and the abiotic environmental role.}, }
@article {pmid21049271, year = {2011}, author = {Kirschner, AK and Schauer, S and Steinberger, B and Wilhartitz, I and Grim, CJ and Huq, A and Colwell, RR and Herzig, A and Sommer, R}, title = {Interaction of Vibrio cholerae non-O1/non-O139 with copepods, cladocerans and competing bacteria in the large alkaline lake Neusiedler See, Austria.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {496-506}, pmid = {21049271}, issn = {1432-184X}, mesh = {Animals ; Austria ; Cladocera/*microbiology ; Colony Count, Microbial ; Copepoda/*microbiology ; In Situ Hybridization, Fluorescence ; Temperature ; Vibrio cholerae non-O1/*growth &amp; development ; *Water Microbiology ; Zooplankton/microbiology ; }, abstract = {Vibrio cholerae is a human pathogen and natural inhabitant of aquatic environments. Serogroups O1/O139 have been associated with epidemic cholera, while non-O1/non-O139 serogroups usually cause human disease other than classical cholera. V. cholerae non-O1/non-O139 from the Neusiedler See, a large Central European lake, have caused ear and wound infections, including one case of fatal septicaemia. Recent investigations demonstrated rapid planktonic growth of V. cholerae non-O1/non-O139 and correlation with zooplankton biomass. The aim of this study was to elucidate the interaction of autochthonous V. cholerae with two dominant crustacean zooplankton species in the lake and investigate the influence of the natural bacterial community on this interaction. An existing data set was evaluated for statistical relationships between zooplankton species and V. cholerae and co-culture experiments were performed in the laboratory. A new fluorescence in situ hybridisation protocol was applied for quantification of V. cholerae non-O1/non-O139 cells, which significantly reduced analysis time. The experiments clearly demonstrated a significant relationship of autochthonous V. cholerae non-O1/non-O139 with cladocerans by promoting growth of V. cholerae non-O1/non-O139 in the water and on the surfaces of the cladocerans. In contrast, copepods had a negative effect on the growth of V. cholerae non-O1/non-O139 via competing bacteria from their surfaces. Thus, beside other known factors, biofilm formation by V. cholerae on crustacean zooplankton appears to be zooplankton taxon specific and may be controlled by the natural bacterial community.}, }
@article {pmid21048761, year = {2010}, author = {Yooseph, S and Nealson, KH and Rusch, DB and McCrow, JP and Dupont, CL and Kim, M and Johnson, J and Montgomery, R and Ferriera, S and Beeson, K and Williamson, SJ and Tovchigrechko, A and Allen, AE and Zeigler, LA and Sutton, G and Eisenstadt, E and Rogers, YH and Friedman, R and Frazier, M and Venter, JC}, title = {Genomic and functional adaptation in surface ocean planktonic prokaryotes.}, journal = {Nature}, volume = {468}, number = {7320}, pages = {60-66}, pmid = {21048761}, issn = {1476-4687}, mesh = {Aquatic Organisms/classification/*genetics/isolation &amp; purification/virology ; Biodiversity ; Biomass ; Databases, Protein ; Genome, Bacterial/genetics ; *Genomics ; *Metagenome ; Models, Biological ; Oceans and Seas ; Phylogeny ; Plankton/*genetics/growth &amp; development/isolation &amp; purification/metabolism ; Prokaryotic Cells/classification/*metabolism/virology ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; }, abstract = {The understanding of marine microbial ecology and metabolism has been hampered by the paucity of sequenced reference genomes. To this end, we report the sequencing of 137 diverse marine isolates collected from around the world. We analysed these sequences, along with previously published marine prokaryotic genomes, in the context of marine metagenomic data, to gain insights into the ecology of the surface ocean prokaryotic picoplankton (0.1-3.0 μm size range). The results suggest that the sequenced genomes define two microbial groups: one composed of only a few taxa that are nearly always abundant in picoplanktonic communities, and the other consisting of many microbial taxa that are rarely abundant. The genomic content of the second group suggests that these microbes are capable of slow growth and survival in energy-limited environments, and rapid growth in energy-rich environments. By contrast, the abundant and cosmopolitan picoplanktonic prokaryotes for which there is genomic representation have smaller genomes, are probably capable of only slow growth and seem to be relatively unable to sense or rapidly acclimate to energy-rich conditions. Their genomic features also lead us to propose that one method used to avoid predation by viruses and/or bacterivores is by means of slow growth and the maintenance of low biomass.}, }
@article {pmid21045216, year = {2010}, author = {Flint, HJ and O'Toole, PW and Walker, AW}, title = {Special issue: The Human Intestinal Microbiota.}, journal = {Microbiology (Reading, England)}, volume = {156}, number = {Pt 11}, pages = {3203-3204}, doi = {10.1099/mic.0.045443-0}, pmid = {21045216}, issn = {1465-2080}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/growth &amp; development ; Bacterial Proteins/metabolism ; Genomics ; Humans ; Intestines/*microbiology ; Irritable Bowel Syndrome/microbiology ; *Metagenome ; Prebiotics ; Probiotics ; }, }
@article {pmid21045053, year = {2011}, author = {Sun, S and Chen, J and Li, W and Altintas, I and Lin, A and Peltier, S and Stocks, K and Allen, EE and Ellisman, M and Grethe, J and Wooley, J}, title = {Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource.}, journal = {Nucleic acids research}, volume = {39}, number = {Database issue}, pages = {D546-51}, pmid = {21045053}, issn = {1362-4962}, support = {R01 RR025030/RR/NCRR NIH HHS/United States ; R01RR025030/RR/NCRR NIH HHS/United States ; }, mesh = {*Databases, Genetic ; Environment ; *Metagenome ; Metagenomics ; Software ; }, abstract = {The Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA, http://camera.calit2.net/) is a database and associated computational infrastructure that provides a single system for depositing, locating, analyzing, visualizing and sharing data about microbial biology through an advanced web-based analysis portal. CAMERA collects and links metadata relevant to environmental metagenome data sets with annotation in a semantically-aware environment allowing users to write expressive semantic queries against the database. To meet the needs of the research community, users are able to query metadata categories such as habitat, sample type, time, location and other environmental physicochemical parameters. CAMERA is compliant with the standards promulgated by the Genomic Standards Consortium (GSC), and sustains a role within the GSC in extending standards for content and format of the metagenomic data and metadata and its submission to the CAMERA repository. To ensure wide, ready access to data and annotation, CAMERA also provides data submission tools to allow researchers to share and forward data to other metagenomics sites and community data archives such as GenBank. It has multiple interfaces for easy submission of large or complex data sets, and supports pre-registration of samples for sequencing. CAMERA integrates a growing list of tools and viewers for querying, analyzing, annotating and comparing metagenome and genome data.}, }
@article {pmid21040354, year = {2011}, author = {Vlaeminck, SE and Hay, AG and Maignien, L and Verstraete, W}, title = {In quest of the nitrogen oxidizing prokaryotes of the early Earth.}, journal = {Environmental microbiology}, volume = {13}, number = {2}, pages = {283-295}, doi = {10.1111/j.1462-2920.2010.02345.x}, pmid = {21040354}, issn = {1462-2920}, mesh = {Ammonia/metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; Biological Evolution ; Nitrates/metabolism ; Nitric Oxide/metabolism ; Nitrites/metabolism ; Nitrogen/metabolism ; *Nitrogen Cycle ; Oxidation-Reduction ; }, abstract = {The introduction of nitrite and nitrate to the relatively reduced environment of the early Earth provided impetus for a tremendous diversification of microbial pathways. However, little is known about the first organisms to produce these valuable resources. In this review, the latest microbial discoveries are integrated in the evolution of the nitrogen cycle according to the great 'NO-ON' time debate, as we call it. This debate hypothesizes the first oxidation of nitrogen as abiotic and anoxic ('NO') versus biological and aerobic ('ON'). Confronting ancient biogeochemical niches with extant prokaryotic phylogenetics, physiology and morphology, pointed out that the well-described ammonia and nitrite oxidizing Proteobacteria likely did not play a pioneering role in microbial nitrogen oxidation. Instead, we hypothesize ancestral and primordial roles of methanotrophic NC10 bacteria and ammonia oxidizing archaea, respectively, for early nitrite production, and of anammox performing Planctomycetes followed by Nitrospira for early nitrate production. Additional genomic and structural information on the prokaryotic protagonists but also on their phages, together with the continued search for novel key players and processes, should further elucidate nitrogen cycle evolution. Through the ramifications between the biogeochemical cycles, this will improve our understanding on the evolution of terrestrial and perhaps extraterrestrial life.}, }
@article {pmid21036345, year = {2010}, author = {Rineau, F and Rose, C and Le Thiec, D and Garbaye, J}, title = {Liming in a beech forest results in more mineral elements stored in the mantle of Lactarius subdulcis ectomycorrhizas.}, journal = {Fungal biology}, volume = {114}, number = {11-12}, pages = {1007-1014}, doi = {10.1016/j.funbio.2010.09.011}, pmid = {21036345}, issn = {1878-6146}, mesh = {Basidiomycota/chemistry/*metabolism ; Calcium Compounds/analysis ; Fagus/growth &amp; development/*microbiology ; Minerals/analysis/*metabolism ; Mycorrhizae/chemistry/*metabolism ; Oxides/analysis ; Soil/analysis ; Trees/growth &amp; development/*microbiology ; }, abstract = {Liming is a forest practice used to counteract forest decline induced by soil acidification. It consists of direct Ca and Mg input in forest soil and restores tree mineral nutrition, but also causes drastic changes in nutrient availability in soil. Ectomycorrhizal (ECM) fungi significantly contribute in nutrient uptake by trees, and can recover them through organic acid secretion or through enzymatic degradation of organic matter. The symbiotic fungi use their extraradical mycelium for nutrient uptake, and then store them into the ECM mantle. In this study we measured how liming influences element contents in the mantle of Lactarius subdulcis ECMs, an abundant and particularly active in oxalate and laccase secretion in beech stands. For this purpose we used SEM observation coupled with energy- (EDX) and wavelength-dispersive-X-ray microanalyses (WDX). Results showed that ECM mantles of this species presented significantly higher Ca, Mg, Mn, K, Si, Al and Fe contents in limed plots. The nutrient amounts of L. subdulcis ECMs were significantly different between individuals for all the elements, showing a differential storage ability between individuals. The storage role of the ECM mantle can be interpreted in two different ways: i) a detoxification role for Al or heavy metals and ii) an increased potential nutrient resource by the fungus, which can benefit the tree.}, }
@article {pmid21035246, year = {2011}, author = {Semenov, AV and van Overbeek, L and Termorshuizen, AJ and van Bruggen, AH}, title = {Influence of aerobic and anaerobic conditions on survival of Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium in Luria-Bertani broth, farm-yard manure and slurry.}, journal = {Journal of environmental management}, volume = {92}, number = {3}, pages = {780-787}, doi = {10.1016/j.jenvman.2010.10.031}, pmid = {21035246}, issn = {1095-8630}, mesh = {Aerobiosis ; Anaerobiosis ; Animals ; Cattle ; Escherichia coli O157/*physiology ; Manure/*microbiology ; Salmonella enterica/*physiology ; }, abstract = {The influence of aerobic and anaerobic conditions on the survival of the enteropathogens Escherichia coli O157:H7 and Salmonella serovar Typhimurium was investigated in microcosms with broth, cattle manure or slurry. These substrates were inoculated with a green fluorescent protein transformed strain of the enteropathogens at 10(7) cells g(-1) dry weight. Survival data was fitted to the Weibull model. The survival curves in aerobic conditions generally showed a concave curvature, while the curvature was convex in anaerobic conditions. The estimated survival times showed that E. coli O157:H7 survived significantly longer under anaerobic than under aerobic conditions. Survival ranged from approximately. 2 weeks for aerobic manure and slurry to more than six months for anaerobic manure at 16 °C. On average, in 56.3% of the samplings, the number of recovered E. coli O157:H7 cells by anaerobic incubation of Petri plates was significantly (p < 0.05) higher in comparison with aerobic incubation. Survival of Salmonella serovar Typhimurium was not different between aerobic and anaerobic storage of LB broth or manure as well as between aerobic and anaerobic incubation of Petri dishes. The importance of changes in microbial community and chemical composition of manure and slurry was distinguished for the survival of E. coli O157:H7 in different oxygen conditions.}, }
@article {pmid21033659, year = {2010}, author = {Jin, YO and Mattes, TE}, title = {A quantitative PCR assay for aerobic, vinyl chloride- and ethene-assimilating microorganisms in groundwater.}, journal = {Environmental science &amp; technology}, volume = {44}, number = {23}, pages = {9036-9041}, doi = {10.1021/es102232m}, pmid = {21033659}, issn = {1520-5851}, mesh = {Bacteria, Aerobic/*genetics/isolation &amp; purification/metabolism ; Biodegradation, Environmental ; Biological Assay ; Carcinogens, Environmental/metabolism ; Environmental Monitoring/methods ; Ethylenes/*metabolism ; Fresh Water/microbiology ; *Polymerase Chain Reaction ; Vinyl Chloride/*metabolism ; Water Microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Vinyl chloride (VC) is a known human carcinogen that is primarily formed in groundwater via incomplete anaerobic dechlorination of chloroethenes. Aerobic, ethene-degrading bacteria (etheneotrophs), which are capable of both fortuitous and growth-linked VC oxidation, could be important in natural attenuation of VC plumes that escape anaerobic treatment. In this work, we developed a quantitative, real-time PCR (qPCR) assay for etheneotrophs in groundwater. We designed and tested degenerate qPCR primers for two functional genes involved in aerobic, growth-coupled VC- and ethene-oxidation (etnC and etnE). Primer specificity to these target genes was tested by comparison to nucleotide sequence databases, PCR analysis of template DNA extracted from isolates and environmental samples, and sequencing of qPCR products obtained from VC-contaminated groundwater. The assay was made quantitative by constructing standard curves (threshold cycle vs log gene copy number) with DNA amplified from Mycobacterium strain JS60, an etheneotrophic isolate. Analysis of groundwater samples from three different VC-contaminated sites revealed that etnC abundance ranged from 1.6 × 10(3) - 1.0 × 10(5) copies/L groundwater while etnE abundance ranged from 4.3 × 10(3) - 6.3 × 10(5) copies/L groundwater. Our data suggest this novel environmental measurement method will be useful for supporting VC bioremediation strategies, assisting in site closure, and conducting microbial ecology studies involving etheneotrophs.}, }
@article {pmid21033056, year = {2010}, author = {Rydzanicz, K and DeChant, P and Becker, N}, title = {Field efficacy of granular formulations of Bacillus thuringiensis Israelensis--strain AM65-52 against floodwater mosquitoes in Poland and Germany.}, journal = {Journal of the American Mosquito Control Association}, volume = {26}, number = {3}, pages = {295-301}, doi = {10.2987/09-5980.1}, pmid = {21033056}, issn = {8756-971X}, mesh = {Animals ; Bacillus thuringiensis/*metabolism ; Culicidae/*microbiology ; Germany ; Mosquito Control/*methods ; Pest Control, Biological/*methods ; Poland ; Time Factors ; Water ; }, abstract = {This paper presents results of studies evaluating the efficacy of various granular formulations of VectoBac (Bacillus thuringiensis israelensis de Barjac [Bti] H-14 strain AM65-52) against immature mosquitoes in 2 distinct habitats in Poland and Germany. Meadows intermittently flooded with sewage water in the city of Wroclaw, Poland, provide ideal habitats for immature stages of Aedes caspius, Ae. vexans, and Culex pipiens pipiens. Helicopter applications of VectoBac G and VectoBac TP sand granules (VectoBac TP-SG) at rates of 5 and 10 kg/ha to the meadows resulted in between 70.9% and 97.4% larval mortality. In Germany, some swampy woodlands in the upper Rhine Valley provide ideal habitats for snowmelt mosquitoes, Aedes cantans, Ae. punctor, Ae. rusticus, and Ae. communis. Ground applications of VectoBac G, VectoBac TP-SG, and VectoBac WG IcyPearls (VectoBac WG-IP) were made to these habitats when the water temperature was approximately 7 degrees C. Larval mortality at 7-day post-application ranged from 90.9% (VectoBac TP-SG: 10 kg/ha) to 98.0% (VectoBac WG-IP: 15 kg/ha). In a separate microcosm trial within the same habitat, all 3 granule formulations controlled larvae of Ae. cantans for 3 wk.}, }
@article {pmid20972562, year = {2011}, author = {Wu, L and Feinstein, LM and Valverde-Barrantes, O and Kershner, MW and Leff, LG and Blackwood, CB}, title = {Placing the effects of leaf litter diversity on saprotrophic microorganisms in the context of leaf type and habitat.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {399-409}, pmid = {20972562}, issn = {1432-184X}, mesh = {Bacteria/genetics/*growth &amp; development ; Biodegradation, Environmental ; Biomass ; Carbon/analysis ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; *Ecosystem ; Fungi/genetics/*growth &amp; development ; Nitrogen/analysis ; Plant Leaves/*microbiology ; Polymorphism, Restriction Fragment Length ; *Soil Microbiology ; }, abstract = {Because of conflicting results in previous studies, it is unclear whether litter diversity has a predictable impact on microbial communities or ecosystem processes. We examined whether effects of litter diversity depend on factors that could confound comparisons among previous studies, including leaf type, habitat type, identity of other leaves in the mixture, and spatial covariance at two scales within habitats. We also examined how litter diversity affects the saprotrophic microbial community using terminal restriction fragment length polymorphism to profile bacterial and fungal community composition, direct microscopy to quantify bacterial biomass, and ergosterol extraction to quantify fungal biomass. We found that leaf mixture diversity was rarely significant as a main effect (only for fungal biomass), but was often significant as an interaction with leaf type (for ash-free dry mass recovered, carbon-to-nitrogen ratio, fungal biomass, and bacterial community composition). Leaf type and habitat were significant as main effects for all response variables. The majority of variance in leaf ash-free dry mass and C/N ratio was explained after accounting for treatment effects and spatial covariation at the meter (block) and centimeter (litterbag) scales. However, a substantial amount of variability in microbial communities was left unexplained and must be driven by factors at other spatial scales or more complex spatiotemporal dynamics. We conclude that litter diversity effects are primarily dependent on leaf type, rather than habitat type or identity of surrounding leaves, which can guide the search for mechanisms underlying effects of litter diversity on ecosystem processes.}, }
@article {pmid20972561, year = {2011}, author = {Ayarza, JM and Erijman, L}, title = {Balance of neutral and deterministic components in the dynamics of activated sludge floc assembly.}, journal = {Microbial ecology}, volume = {61}, number = {3}, pages = {486-495}, pmid = {20972561}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*growth &amp; development ; Bioreactors/*microbiology ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Flocculation ; RNA, Ribosomal, 16S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sewage/*microbiology ; Stochastic Processes ; Time Factors ; }, abstract = {Understanding the processes that generate patterns of community structure is a central focus of ecological research. With that aim, we manipulated the structure of bacterial activated sludge to test the influence of the species richness and composition of bacterial communities on the dynamics of activated sludge floc assembly in lab-scale bioreactors. Bacterial community structure was analyzed using denaturing gradient gel electrophoresis of RT-PCR amplified 16S rRNA. Fingerprinting of four parallel reactors, started with the same source communities added in different proportions, converged to patterns that were more similar than expected by chance, suggesting a deterministic selection in floc development. Evidence for neutral dynamics was suggested by the dependence of the rate of replacement of species (bacterial taxa-time relationships) on the number of available species in the source community. Further indication of stochastic dynamics was obtained by the application of the Sloan neutral model for prokaryotes. The fitting of the observed data to the model predictions revealed that the importance of the stochastic component increased with the size of the reservoir of species richness from which the community is drawn. Taken together, the results illustrate how both neutral and deterministic dynamics operate simultaneously in the assembly of the bacterial floc and show that the balance of the two depends on the richness of the source community.}, }
@article {pmid20972239, year = {2010}, author = {Sánchez, E and Donat, E and Ribes-Koninckx, C and Calabuig, M and Sanz, Y}, title = {Intestinal Bacteroides species associated with coeliac disease.}, journal = {Journal of clinical pathology}, volume = {63}, number = {12}, pages = {1105-1111}, doi = {10.1136/jcp.2010.076950}, pmid = {20972239}, issn = {1472-4146}, mesh = {Bacteroides/*classification/isolation &amp; purification ; Bifidobacterium/classification/isolation &amp; purification ; Biodiversity ; Biopsy ; Case-Control Studies ; Celiac Disease/diet therapy/*microbiology/pathology ; Child ; Child, Preschool ; Denaturing Gradient Gel Electrophoresis/methods ; Duodenum/*microbiology/pathology ; Female ; Humans ; Infant ; Male ; Polymerase Chain Reaction/methods ; }, abstract = {AIMS: To characterise the predominant species of bacterial populations associated with duodenal biopsies of paediatric patients with active and treated coeliac disease.<br><br>METHODS: 20 biopsy specimens from patients with active coeliac disease, 12 from patients with treated coeliac disease, and eight from age-matched controls were evaluated for comparative purposes. Bacteroides, Bifidobacterium and lactic acid bacteria (LAB) populations were analysed by PCR-denaturing gradient gel electrophoresis using group-specific primers.<br><br>RESULTS: Bacteroides diversity was higher in biopsy specimens from controls than in those from patients with active and treated coeliac disease. Bacteroides distasonis, Bacteroides fragilis/Bacteroides thetaiotaomicron, Bacteroides uniformis and Bacteroides ovatus were more abundant in controls than in patients with coeliac disease (p<0.05). Bacteroides vulgatus was more frequently detected in controls than in patients with treated coeliac disease (p<0.01). Bacteroides dorei was more common in patients with active coeliac disease than in those with treated coeliac disease and control children (p<0.01). Bifidobacterium diversity was higher in patients with coeliac disease than in controls. Bifidobacterium adolescentis and Bifidobacterium animalis subsp lactis were more prevalent in patients with active coeliac disease than in patients with treated coeliac disease and control children. A higher LAB diversity was found in patients with treated coeliac disease and controls than in patients with active coeliac disease. Weissella spp and Lactobacillus fermentum were more frequently detected in patients with treated coeliac disease than in controls and patients with active coeliac disease.<br><br>CONCLUSIONS: Bacteroides, Bifidobacterium and LAB populations in the duodenum of Spanish children with typical coeliac disease (active and treated) and controls differ in diversity and species composition; this could contribute to features of the disease.}, }
@article {pmid20971898, year = {2011}, author = {Knab, S and Mushak, TM and Schmitz-Esser, S and Horn, M and Haferkamp, I}, title = {Nucleotide parasitism by Simkania negevensis (Chlamydiae).}, journal = {Journal of bacteriology}, volume = {193}, number = {1}, pages = {225-235}, pmid = {20971898}, issn = {1098-5530}, support = {P 19252/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Adaptation, Physiological ; Bacterial Proteins/genetics/*metabolism ; Chlamydiales/*genetics ; Energy Metabolism ; Gene Expression Regulation, Bacterial/physiology ; Genome, Bacterial ; Nucleotide Transport Proteins/genetics/*metabolism ; Nucleotides/metabolism ; Substrate Specificity ; }, abstract = {Intracellular bacteria live in an environment rich in most essential metabolites but need special mechanisms to access these substrates. Nucleotide transport proteins (NTTs) catalyze the import of ATP and other nucleotides from the eukaryotic host into the bacterial cell and render de novo synthesis of these compounds dispensable. The draft genome sequence of Simkania negevensis strain Z, a chlamydial organism considered a newly emerging pathogen, revealed four genes encoding putative nucleotide transport proteins (SnNTT1 to SnNTT4), all of which are transcribed during growth of S. negevensis in Acanthamoeba host cells, as confirmed by reverse transcription-PCR. Using heterologous expression in Escherichia coli, we could show that SnNTT1 functions as an ATP/ADP antiporter, SnNTT2 as a guanine nucleotide/ATP/H(+) symporter driven by the membrane potential, and SnNTT3 as a nucleotide triphosphate antiporter. In addition, SnNTT3 is able to transport dCTP, which has not been shown for a prokaryotic transport protein before. No substrate could be identified for SnNTT4. Taking these data together, S. negevensis employs a set of nucleotide transport proteins to efficiently tap its host's energy and nucleotide pools. Although similar to other chlamydiae, these transporters show distinct and unique adaptations with respect to substrate specificities and mode of transport.}, }
@article {pmid20963583, year = {2011}, author = {Davis, DA and Gamble, MD and Bagwell, CE and Bergholz, PW and Lovell, CR}, title = {Responses of salt marsh plant rhizosphere diazotroph assemblages to changes in marsh elevation, edaphic conditions and plant host species.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {386-398}, pmid = {20963583}, issn = {1432-184X}, mesh = {Chlorobi/enzymology/genetics/*growth &amp; development ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Geologic Sediments/chemistry/microbiology ; Magnoliopsida/*microbiology ; *Nitrogen Fixation ; Oxidoreductases/genetics ; Phylogeny ; Proteobacteria/enzymology/genetics/*growth &amp; development ; *Rhizosphere ; Seasons ; Seawater/chemistry/microbiology ; Sequence Analysis, DNA ; South Carolina ; Water Microbiology ; *Wetlands ; }, abstract = {An important source of new nitrogen in salt marsh ecosystems is microbial diazotrophy (nitrogen fixation). The diazotroph assemblages associated with the rhizospheres (sediment directly affected by the roots) of salt marsh plants are highly diverse, somewhat stable, and consist mainly of novel organisms. In Crab Haul Creek Basin, North Inlet, SC, the distribution of plant types into discrete zones is dictated by relatively minor differences in marsh elevation and it was hypothesized that the biotic and abiotic properties of the plant zones would also dictate the composition of the rhizosphere diazotroph assemblages. Over a period of 1 year, rhizosphere sediments were collected from monotypic stands of the black needlerush, Juncus roemerianus, the common pickleweed, Salicornia virginica, the short and tall growth forms of the smooth cordgrass Spartina alterniflora, and a mixed zone of co-occurring S. virginica and short form, S. alterniflora. DNA was extracted, purified and nifH sequences PCR amplified for denaturing gradient gel electrophoresis (DGGE) analysis to determine the composition of the diazotroph assemblages. The diazotroph assemblages were strongly influenced by season, abiotic environmental parameters and plant host. Sediment chemistry and nitrogen fixation activity were also significantly influenced by seasonal changes. DGGE bands that significantly affected seasonal and zone specific clustering were identified and most of these sequences were from novel diazotrophs, unaffiliated with any previously described organisms. At least one third of the recovered nifH sequences were from a diverse assemblage of Chlorobia, and γ-, α-, β- and δ-Proteobacteria. Diazotrophs that occurred throughout the growing season and among all zones (frequently detected) were also mostly novel. These significant sequences indicated that diazotrophs driving the structure of the assemblages were diverse, versatile, and some were ubiquitous while others were seasonally responsive. Several ubiquitous sequences were closely related to sequences of actively N(2) fixing diazotrophs previously recovered from this system. These sequences from ubiquitous and versatile organisms likely indicate the diazotrophs in these rhizosphere assemblages that significantly contribute to ecosystem function.}, }
@article {pmid20962877, year = {2011}, author = {Zhou, HW and Li, DF and Tam, NF and Jiang, XT and Zhang, H and Sheng, HF and Qin, J and Liu, X and Zou, F}, title = {BIPES, a cost-effective high-throughput method for assessing microbial diversity.}, journal = {The ISME journal}, volume = {5}, number = {4}, pages = {741-749}, pmid = {20962877}, issn = {1751-7370}, mesh = {Biodiversity ; DNA Barcoding, Taxonomic/economics/*methods ; DNA Primers ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing/economics/*methods ; Metagenome ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Pyrosequencing of 16S rRNA (16S) variable tags has become the most popular method for assessing microbial diversity, but the method remains costly for the evaluation of large numbers of environmental samples with high sequencing depths. We developed a barcoded Illumina paired-end (PE) sequencing (BIPES) method that sequences each 16S V6 tag from both ends on the Illumina HiSeq 2000, and the PE reads are then overlapped to obtain the V6 tag. The average accuracy of Illumina single-end (SE) reads was only 97.9%, which decreased from ∼99.9% at the start of the read to less than 85% at the end of the read; nevertheless, overlapping of the PE reads significantly increased the sequencing accuracy to 99.65% by verifying the 3' end of each SE in which the sequencing quality was degraded. After the removal of tags with two or more mismatches within the medial 40-70 bases of the reads and of tags with any primer errors, the overall base sequencing accuracy of the BIPES reads was further increased to 99.93%. The BIPES reads reflected the amounts of the various tags in the initial template, but long tags and high GC tags were underestimated. The BIPES method yields 20-50 times more 16S V6 tags than does pyrosequencing in a single-flow cell run, and each of the BIPES reads costs less than 1/40 of a pyrosequencing read. As a laborsaving and cost-effective method, BIPES can be routinely used to analyze the microbial ecology of both environmental and human microbiomes.}, }
@article {pmid20953951, year = {2010}, author = {Tomsheck, AR and Strobel, GA and Booth, E and Geary, B and Spakowicz, D and Knighton, B and Floerchinger, C and Sears, J and Liarzi, O and Ezra, D}, title = {Hypoxylon sp., an endophyte of Persea indica, producing 1,8-cineole and other bioactive volatiles with fuel potential.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {903-914}, pmid = {20953951}, issn = {1432-184X}, mesh = {Biofuels/analysis ; Cyclohexanols/analysis/*metabolism ; Eucalyptol ; *Industrial Microbiology ; Molecular Sequence Data ; Monoterpenes/analysis/*metabolism ; Persea/*microbiology/physiology ; Phylogeny ; Symbiosis ; Volatile Organic Compounds/analysis/*metabolism ; Xylariales/classification/genetics/*isolation &amp; purification/*physiology ; }, abstract = {An endophytic fungus of Persea indica was identified, on the basis of its anamorphic stage, as Nodulosporium sp. by SEM. Partial sequence analysis of ITS rDNA revealed the identity of the teleomorphic stage of the fungus as Hypoxylon sp. It produces an impressive spectrum of volatile organic compounds (VOCs), most notably 1,8-cineole, 1-methyl-1,4-cyclohexadiene, and tentatively identified (+)-.alpha.-methylene-.alpha.-fenchocamphorone, among many others, most of which are unidentified. Six-day-old cultures of Hypoxylon sp. displayed maximal VOC-antimicrobial activity against Botrytis cinerea, Phytophthora cinnamomi, Cercospora beticola, and Sclerotinia sclerotiorum suggesting that the VOCs may play some role in the biology of the fungus and its survival in its host plant. Media containing starch- or sugar-related substrates best supported VOC production by the fungus. Direct on-line quantification of VOCs was measured by proton transfer mass spectrometry covering a continuous range with optimum VOC production occurred at 6 days at 145 ppmv with a rate of production of 7.65 ppmv/h. This report unequivocally demonstrates that 1,8-cineole (a monoterpene) is produced by a microorganism, which represents a novel and important source of this compound. This monoterpene is an octane derivative and has potential use as a fuel additive as do the other VOCs of this organism. Thus, fungal sourcing of this compound and other VOCs as produced by Hypoxylon sp. greatly expands their potential applications in medicine, industry, and energy production.}, }
@article {pmid20953598, year = {2011}, author = {Mapelli, F and Marasco, R and Rizzi, A and Baldi, F and Ventura, S and Daffonchio, D and Borin, S}, title = {Bacterial communities involved in soil formation and plant establishment triggered by pyrite bioweathering on arctic moraines.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {438-447}, pmid = {20953598}, issn = {1432-184X}, mesh = {Arctic Regions ; Bacteria/*classification/genetics/growth &amp; development ; *Biodiversity ; DNA, Bacterial/genetics ; Gene Library ; Ice Cover/*microbiology ; Iron/metabolism ; Oxidation-Reduction ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; Sulfides/metabolism ; }, abstract = {In arctic glacier moraines, bioweathering primed by microbial iron oxidizers creates fertility gradients that accelerate soil development and plant establishment. With the aim of investigating the change of bacterial diversity in a pyrite-weathered gradient, we analyzed the composition of the bacterial communities involved in the process by sequencing 16S rRNA gene libraries from different biological soil crusts (BSC). Bacterial communities in three BSC of different morphology, located within 1 m distance downstream a pyritic conglomerate rock, were significantly diverse. The glacier moraine surrounding the weathered site showed wide phylogenetic diversity and high evenness with 15 represented bacterial classes, dominated by Alphaproteobacteria and pioneer Cyanobacteria colonizers. The bioweathered area showed the lowest diversity indexes and only nine bacterial families, largely dominated by Acidobacteriaceae and Acetobacteraceae typical of acidic environments, in accordance with the low pH of the BSC. In the weathered BSC, iron-oxidizing bacteria were cultivated, with counts decreasing along with the increase of distance from the rock, and nutrient release from the rock was revealed by environmental scanning electron microscopy-energy dispersive X-ray analyses. The vegetated area showed the presence of Actinomycetales, Verrucomicrobiales, Gemmatimonadales, Burkholderiales, and Rhizobiales, denoting a bacterial community typical of developed soils and indicating that the lithoid substrate of the bare moraine was here subjected to an accelerated colonization, driven by iron-oxidizing activity.}, }
@article {pmid20953417, year = {2010}, author = {Heidelberg, KB and Gilbert, JA and Joint, I}, title = {Marine genomics: at the interface of marine microbial ecology and biodiscovery.}, journal = {Microbial biotechnology}, volume = {3}, number = {5}, pages = {531-543}, pmid = {20953417}, issn = {1751-7915}, mesh = {Aquatic Organisms/classification/*genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; Biotechnology/trends ; *Genomics/history ; History, 20th Century ; History, 21st Century ; *Marine Biology/history ; Seawater/microbiology/virology ; }, abstract = {The composition and activities of microbes from diverse habitats have been the focus of intense research during the past decade with this research being spurred on largely by advances in molecular biology and genomic technologies. In recent years environmental microbiology has entered very firmly into the age of the 'omics' – (meta)genomics, proteomics, metabolomics, transcriptomics – with probably others on the rise. Microbes are essential participants in all biogeochemical processes on our planet, and the practical applications of what we are learning from the use of molecular approaches has altered how we view biological systems. In addition, there is considerable potential to use information about uncultured microbes in biodiscovery research as microbes provide a rich source of discovery for novel genes, enzymes and metabolic pathways. This review explores the brief history of genomic and metagenomic approaches to study environmental microbial assemblages and describes some of the future challenges involved in broadening our approaches – leading to new insights for understanding environmental problems and enabling biodiscovery research.}, }
@article {pmid20946352, year = {2010}, author = {De Weirdt, R and Possemiers, S and Vermeulen, G and Moerdijk-Poortvliet, TC and Boschker, HT and Verstraete, W and Van de Wiele, T}, title = {Human faecal microbiota display variable patterns of glycerol metabolism.}, journal = {FEMS microbiology ecology}, volume = {74}, number = {3}, pages = {601-611}, doi = {10.1111/j.1574-6941.2010.00974.x}, pmid = {20946352}, issn = {1574-6941}, mesh = {Adult ; Bacteria/metabolism ; Colon/*microbiology ; Feces/*microbiology ; Female ; Glycerol/*metabolism ; Humans ; Male ; *Metagenome ; Propylene Glycols/*metabolism ; Young Adult ; }, abstract = {Significant amounts of glycerol reach the colon microbiota daily through the diet and/or by in situ microbial production or release from desquamated epithelial cells. Some gut microorganisms may anaerobically reduce glycerol to 1,3-propanediol (1,3-PDO), with 3-hydroxypropanal as an intermediate. Accumulation of the latter intermediate may result in the formation of reuterin, which is known for its biological activity (e.g. antimicrobial properties). To date, glycerol metabolism in mixed cultures from the human colon has received little attention. Using in vitro batch incubations of faeces from 10 human individuals, we demonstrated that glycerol addition (140 mM) significantly affects the metabolism and composition of the microbial community. About a third of the samples exhibited rapid glycerol conversion, yielding proportionally higher levels of acetate and 1,3-PDO. In contrast, a slower glycerol metabolism resulted in higher levels of propionate. Furthermore, rapid glycerol metabolism correlated with significant shifts in the Lactobacillus-Enterococcus community, which were not observed in slower glycerol-metabolizing samples. As the conversion of glycerol to 1,3-PDO is a highly reducing process, we infer that the glycerol metabolism may act as an effective hydrogen sink. Given the importance of hydrogen-consuming processes in the gut, this work suggests that glycerol may have potential as a tool for modulating fermentation kinetics and profiles in the gastrointestinal tract.}, }
@article {pmid20941329, year = {2010}, author = {Zhou, J and Deng, Y and Luo, F and He, Z and Tu, Q and Zhi, X}, title = {Functional molecular ecological networks.}, journal = {mBio}, volume = {1}, number = {4}, pages = {}, pmid = {20941329}, issn = {2150-7511}, mesh = {Bacteria/*genetics/metabolism ; Carbon Dioxide/metabolism ; *Ecosystem ; *Gene Regulatory Networks ; *Soil Microbiology ; }, abstract = {Biodiversity and its responses to environmental changes are central issues in ecology and for society. Almost all microbial biodiversity research focuses on "species" richness and abundance but not on their interactions. Although a network approach is powerful in describing ecological interactions among species, defining the network structure in a microbial community is a great challenge. Also, although the stimulating effects of elevated CO(2) (eCO(2)) on plant growth and primary productivity are well established, its influences on belowground microbial communities, especially microbial interactions, are poorly understood. Here, a random matrix theory (RMT)-based conceptual framework for identifying functional molecular ecological networks was developed with the high-throughput functional gene array hybridization data of soil microbial communities in a long-term grassland FACE (free air, CO(2) enrichment) experiment. Our results indicate that RMT is powerful in identifying functional molecular ecological networks in microbial communities. Both functional molecular ecological networks under eCO(2) and ambient CO(2) (aCO(2)) possessed the general characteristics of complex systems such as scale free, small world, modular, and hierarchical. However, the topological structures of the functional molecular ecological networks are distinctly different between eCO(2) and aCO(2), at the levels of the entire communities, individual functional gene categories/groups, and functional genes/sequences, suggesting that eCO(2) dramatically altered the network interactions among different microbial functional genes/populations. Such a shift in network structure is also significantly correlated with soil geochemical variables. In short, elucidating network interactions in microbial communities and their responses to environmental changes is fundamentally important for research in microbial ecology, systems microbiology, and global change.}, }
@article {pmid20938840, year = {2011}, author = {Loy, A and Pester, M and Steger, D}, title = {Phylogenetic microarrays for cultivation-independent identification and metabolic characterization of microorganisms in complex samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {688}, number = {}, pages = {187-206}, doi = {10.1007/978-1-60761-947-5_13}, pmid = {20938840}, issn = {1940-6029}, mesh = {Archaea/genetics/growth &amp; development/*isolation &amp; purification/*metabolism ; Bacteria/genetics/growth &amp; development/*isolation &amp; purification/*metabolism ; DNA, Archaeal/genetics/metabolism ; DNA, Bacterial/genetics/metabolism ; Deoxyribonuclease I/metabolism ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis/*methods ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; Statistics as Topic ; Transcription, Genetic ; Zinc/chemistry/metabolism ; }, abstract = {High-throughput sequencing and hybridization technologies promise new insights into the natural diversity and dynamics of microorganisms. Among these new technologies are phylogenetic oligonucleotide microarrays (phylochips) that depend on the standard molecules for taxonomic and environmental studies of microorganisms: the ribosomal RNAs and their encoding genes. The beauty of phylochip hybridization is that a sample can be analyzed with hundreds to thousands of rRNA (gene)-targeted probes simultaneously, lending itself to the efficient diagnosis of many target organisms in many samples. An emerging application of phylochips is the highly parallel analysis of structure-function relationships of microbial community members by employing in vivo substrate-mediated isotope labeling of rRNA (via the isotope array approach). This chapter provides an introduction to phylochip and isotope array analysis and detailed wet-lab protocols for preparation, labeling, and hybridization of target nucleic acids.}, }
@article {pmid20938656, year = {2011}, author = {Jassey, VE and Chiapusio, G and Mitchell, EA and Binet, P and Toussaint, ML and Gilbert, D}, title = {Fine-scale horizontal and vertical micro-distribution patterns of testate amoebae along a narrow Fen/Bog gradient.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {374-385}, pmid = {20938656}, issn = {1432-184X}, mesh = {Amoeba/*growth &amp; development ; *Biodiversity ; Ecology/methods ; France ; Phenols/analysis ; Population Dynamics ; Sphagnopsida/chemistry/*microbiology ; Temperature ; Water/chemistry ; *Wetlands ; }, abstract = {The ecology of peatland testate amoebae is well studied along broad gradient from very wet (pool) to dry (hummock) micro-sites where testate amoebae are often found to respond primarily to the depth to water table (DWT). Much less is known on their responses to finer-scale gradients, and nothing is known of their possible response to phenolic compounds, which play a key role in carbon storage in peatlands. We studied the vertical (0-3, 3-6, and 6-9 cm sampling depths) micro-distribution patterns of testate amoebae in the same microhabitat (Sphagnum fallax lawn) along a narrow ecological gradient between a poor fen with an almost flat and homogeneous Sphagnum carpet (fen) and a "young bog" (bog) with more marked micro-topography and mosaic of poor fen and bog vegetation. We analyzed the relationships between the testate amoeba data and three sets of variables (1) "chemical" (pH, Eh potential, and conductivity), (2) "physical" (water temperature, altitude, i.e., Sphagnum mat micro-topography, and DWT), and (3) phenolic compounds in/from Sphagnum (water-soluble and primarily bound phenolics) as well as the habitat (fen/bog) and the sampling depth. Testate amoeba Shannon H' diversity, equitability J of communities, and total density peaked in lower parts of Sphagnum, but the patterns differed between the fen and bog micro-sites. Redundancy analyses revealed that testate amoeba communities differed significantly in relation to Eh, conductivity, water temperature, altitude, water-soluble phenolics, habitat, and sampling depth, but not to DWT, pH, or primarily bound phenolics. The sensitivity of testate amoebae to weak environmental gradients makes them particularly good integrators of micro-environmental variations and has implications for their use in paleoecology and environmental monitoring. The correlation between testate amoeba communities and the concentration of water-soluble phenolic suggests direct (e.g., physiological) and/or indirect (e.g., through impact on prey organisms) effects on testate amoebae, which requires further research.}, }
@article {pmid20936406, year = {2011}, author = {Philippot, L and Tscherko, D and Bru, D and Kandeler, E}, title = {Distribution of high bacterial taxa across the chronosequence of two alpine glacier forelands.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {303-312}, pmid = {20936406}, issn = {1432-184X}, mesh = {Austria ; Bacteria/*classification/genetics ; *Biota ; DNA, Bacterial/genetics ; Gene Dosage ; Genes, Bacterial ; Ice Cover/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Little is known about the changes in abundance of microbial taxa in relation to the chronosequence of receding glaciers. This study investigated how the abundances of ten bacterial phyla or classes varied along successional gradients in two glaciers, Ödenwinkelkees and Rotmoosferner, in the central Alps. Quantitative PCR was used to estimate the abundance of the different bacterial taxa in extended glacier chronosequences, including 10- to 160-year-old successional stages, the surface of the glacier, and a fully established soil. Actinobacteria (15-30%) was the dominant group within the chronosequences. Several taxa showed significant differences in the number of taxa-specific 16S rRNA gene copies per nanogram of DNA and/or in the ratio of taxa-specific to the total bacterial 16S rRNA gene copies (i.e., the relative abundance of the different taxa within the bacterial community) between the established soils or the glacier surface and the 10- to 160-year-old successional stages. A significantly higher proportion of Βetaproteobacteria (20%) was observed on the surface of both glaciers. However, no differences were observed between the 10- to 160-year-old successional stages in the number of taxa-specific 16S rRNA gene copies per nanogram of DNA or in the ratio of taxa-specific to the total bacterial 16S rRNA gene copies for the different taxa. Nevertheless, when the relative abundance data from all the studied taxa were combined and analyzed altogether, most of the sites could be distinguished from one other. This indicates that the overall composition of the bacterial community was more affected than the abundance of the targeted taxa by changes in environmental conditions along the chronosequences.}, }
@article {pmid20936405, year = {2011}, author = {Leflaive, J and Ten-Hage, L}, title = {Effects of 2E,4E-decadienal on motility and aggregation of diatoms and on biofilm formation.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {363-373}, pmid = {20936405}, issn = {1432-184X}, mesh = {Aldehydes/*pharmacology ; Biofilms/*drug effects ; Diatoms/*drug effects/*physiology ; Nitric Oxide/biosynthesis ; Species Specificity ; }, abstract = {Phototrophic biofilm formation and dynamics result from the interaction between several parameters, including chemical interactions. Some of the secondary metabolites released by microalgae can influence the composition of benthic communities. We determined the effects of decadienal (DD), a polyunsaturated aldehyde produced by diatoms, on a benthic diatom, Fistulifera saprophila. At 5 μg ml(-1), DD reduced cell motility by 88% and cell adhesion to the substrate by 91%. The effects occurred in less than 30 min. Using a fluorescent probe, we showed that DD could induce nitric oxide (NO) accumulation in F. saprophila cells. Cells exposed to a NO donor presented reduced adhesion and motility, which suggests the involvement of this cellular messenger in the mode of action of DD. Short-term experiments in microcosms showed that the presence of DD on a substrate strongly inhibited biofilm formation. Moreover, when the biofilm was bispecific, DD modified the proportion of the two species present. This indicates that the presence of DD-producing diatoms in a biofilm may favor the presence of certain microalgae at the expense of others. In addition to the effects on adhesion and motility, DD induced the formation of aggregates of F. saprophila cells. Aggregation was independent of NO production. Complementary experiments were performed with two other benthic diatoms, Nitzschia palea and Mayamea atomus. They showed that the effects of DD on adhesion and aggregation were species-dependent.}, }
@article {pmid20935136, year = {2011}, author = {Frank, DN}, title = {Growth and Development Symposium: promoting healthier humans through healthier livestock: animal agriculture enters the metagenomics era.}, journal = {Journal of animal science}, volume = {89}, number = {3}, pages = {835-844}, doi = {10.2527/jas.2010-3392}, pmid = {20935136}, issn = {1525-3163}, support = {1UH2DK083994-01/DK/NIDDK NIH HHS/United States ; }, mesh = {Agriculture/*trends ; Animals ; Ecosystem ; Environment ; Food/*standards ; Food Safety ; Humans ; Livestock/*genetics ; Nutritive Value ; *Public Health ; }, abstract = {The priorities of public health and agricultural sciences intersect through a shared objective to foster better human health. Enhancements in food quality and reductions in the environmental effects of modern agriculture represent 2 distinct paths through which animal sciences can contribute to the cause of public health. Recent developments in the study of human-associated microbial communities (microbiotas), notably in association with disease, indicate that better understanding of the microbial ecology of livestock can contribute to achieving the goals of better foods and a cleaner environment. Culture-independent microbiological technologies now permit comprehensive study of complex microbial communities in their natural environments. Microbiotas associated with both humans and animals provide myriad beneficial services to their hosts that, if lost or diminished, could compromise host health. Dysfunctional microbial communities have been noted in several human conditions, including inflammatory bowel disease, obesity, and antibiotic-associated diarrhea. Examination of the mechanisms by which the human microbiota influences health and disease susceptibility can inform similar studies of host-microbe function in the animal sciences. Insights gained from human studies indicate strategies to raise not only healthier livestock, through selective manipulation of microbial communities, but also healthier humans.}, }
@article {pmid20933389, year = {2011}, author = {Zamalloa, C and Vulsteke, E and Albrecht, J and Verstraete, W}, title = {The techno-economic potential of renewable energy through the anaerobic digestion of microalgae.}, journal = {Bioresource technology}, volume = {102}, number = {2}, pages = {1149-1158}, doi = {10.1016/j.biortech.2010.09.017}, pmid = {20933389}, issn = {1873-2976}, mesh = {Anaerobiosis ; Biofuels/analysis ; Conservation of Energy Resources/*economics/*methods ; Energy-Generating Resources/*economics ; Fermentation ; Microalgae/*metabolism ; Time Factors ; Volatilization ; }, abstract = {The potential of microalgae as feedstock for methane production is evaluated from a process technical and economic point of view. Production of mixed culture algae in raceway ponds on non-agricultural sites, such as landfills, was identified as a preferred approach. The potential of straightforward bio-methanation, which includes pre-concentration of microalgae and utilization of a high rate anaerobic reactor was examined based on the premises of achievable up-concentration from 0.2-0.6 kg m(-3) to 20-60 kg dry matter (DM) m(-3) and an effective bio-methanation of the concentrate at a loading rate of 20 kg DM m(-3) d(-1). The costs of biomass available for bio-methanation under such conditions were calculated to be in the range of €86-€124 ton(-1) DM. The levelized cost of energy by means of the process line "algae biomass--biogas--total energy module" would be in the order of €0.170-0.087 kWh(-1), taking into account a carbon credit of about €30 ton(-1) CO2(eq).}, }
@article {pmid20927511, year = {2011}, author = {Jiang, W and Jiang, Y and Li, C and Liang, J}, title = {Investigation of supragingival plaque microbiota in different caries status of Chinese preschool children by denaturing gradient gel electrophoresis.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {342-352}, pmid = {20927511}, issn = {1432-184X}, mesh = {Bacteria/*genetics ; Child, Preschool ; DNA Primers/genetics ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Dental Caries/*microbiology ; Dental Plaque/*microbiology ; Female ; Humans ; Male ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {This study aimed to detect differences in the richness of total supragingival plaque microbiota as well as the species composition of oral streptococci involved in the different stages of dental caries. Forty-five plaque samples were collected from caries-moderate (CM, 4 ≤ dmfs ≤ 6), caries-susceptible (CS, dmfs ≥ 10), and age-matched caries-free children separately. Total DNA was isolated directly from each sample, and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analyses using universal and primers specific for oral streptococci were carried out. Using 16S rDNA PCR-DGGE, 34 different species of bacteria were identified in a culture-independent manner and classified into 11 genera according to phylogenetic analysis. Among them, Mitis group streptococci and Campylobacter, which were present in health status, no longer appeared in caries-susceptible samples. In addition, Capnocytophaga, Burkholderia, and Prevotella were found significantly less frequently in the CS group samples (P < 0.05), while there were no significant differences among the prevalence of Neisseria, Leptotrichia, Haemophilus, Mutans group streptococci, Corynebacterium, and Actinomyces in the three groups. Further DGGE analysis of rnpB gene amplicons obtained with oral streptococci species-specific primers showed that a total of 23 species of oral streptococci were identified. Streptococcus sanguinis, Streptococcus mitis, and Streptococcus oralis showed a significantly higher prevalence in healthy children (P < 0.05), while that of Streptococcus mutans and Streptococcus sobrinus did not vary among the three groups. Overall, these results suggest that supragingival plaque microbiota as a whole undergoes a more complicated shift in the caries process.}, }
@article {pmid20924760, year = {2011}, author = {Hill, P and Krištůfek, V and Dijkhuizen, L and Boddy, C and Kroetsch, D and van Elsas, JD}, title = {Land use intensity controls actinobacterial community structure.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {286-302}, pmid = {20924760}, issn = {1432-184X}, mesh = {Actinobacteria/*classification/genetics/isolation &amp; purification ; Agriculture/methods ; *Biota ; Cluster Analysis ; DNA Primers/genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; Monte Carlo Method ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Actinobacteria are major producers of secondary metabolites; however, it is unclear how they are distributed in the environment. DNA was extracted from forest, pasture and cultivated soils, street sediments (dust and material in place), and sediments affected by animal activity (e.g. guano, vermicompost) and characterised with two actinobacterial and a bacterial-specific 16S rDNA primer set. Amplicons (140/156) generated with the two actinobacterial-specific and amplicons (471) generated with bacterial-specific primers were analysed. Amplicons from actinobacterial-specific primer were disproportionately actinomycetal from animal-affected (soil) samples and street sediments and either verrucomicrobial (i.e. non-actinobacterial) and from a novel non-actinomycetal actinobacterial group for soils. Actinobacterial amplified ribosomal DNA restriction analysis and terminal restriction fragment length polymorphism fingerprints clustered by land use, with cultivated soils clustering apart from uncultivated soils. Actinobacterial amplicons generated with eubacterial primers were overwhelmingly from (116/126) street sediments; acidobacterial amplicons from soils (74/75). In two street samples, >90% of clones were actinomycetal. Actinomycetes are selected in terrestrial soils and sediments by cultivation, urbanisation and animal activity.}, }
@article {pmid20890834, year = {2010}, author = {Kolter, R}, title = {Biofilms in lab and nature: a molecular geneticist's voyage to microbial ecology.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {13}, number = {1}, pages = {1-7}, doi = {10.2436/20.1501.01.105}, pmid = {20890834}, issn = {1618-1905}, support = {R01 GM058213/GM/NIGMS NIH HHS/United States ; }, mesh = {Antifungal Agents/metabolism ; Bacteria/*growth &amp; development/metabolism ; *Bacterial Physiological Phenomena ; *Biodiversity ; Biofilms/growth &amp; development ; *Ecosystem ; Lipopeptides/metabolism ; Lung/microbiology ; Nystatin/metabolism ; Peptides, Cyclic/metabolism ; Sarraceniaceae/microbiology ; Signal Transduction ; Surface-Active Agents/metabolism ; }, abstract = {This article reviews the latest findings on how extracellular signaling controls cell fate determination during the process of biofilm formation by Bacillus subtilis in the artificial setting of the laboratory. To complement molecular genetic approaches, surface-associated communities in settings as diverse as the pitcher plant Sarracenia purpurea and the human lung were investigated. The study of the pitcher plant revealed that the presence or absence of a mosquito larva in the pitcher plant controlled bacterial diversity in the ecosystem inside the pitcher plant. Through the analysis of the respiratory tract microbiota of humans suffering from cystic fibrosis (CF) a correlation between lung function and bacterial community diversity was found. Those that had lungs in good condition had also more diverse communities, whereas patients harboring Pseudomonas aeruginosa-the predominant CF pathogen-in their lungs had less diverse communities. Further studies focused on interspecies and intraspecies relationships at the molecular level in search for signaling molecules that would promote biofilm formation. Two molecules were found that induced biofilm formation in B. subtilis: nystatin-released by other species-and surfactin-released by B. subtilis itself. This is a role not previously known for two molecules that were known for other activities-nystatin as an antifungal and surfactin as a surfactant. In addition, surfactin was found to also trigger cannibalism under starvation. This could be a strategy to maintain the population because the cells destroyed serve as nutrients for the rest. The path that led the author to the study of microbial biofilms is also described.}, }
@article {pmid20888954, year = {2010}, author = {Nielsen, PH and van Loosdrecht, MC}, title = {Microbial ecology of drinking water and waste water treatment processes. Editorial.}, journal = {Water research}, volume = {44}, number = {17}, pages = {4825}, doi = {10.1016/j.watres.2010.09.011}, pmid = {20888954}, issn = {1879-2448}, mesh = {*Ecological and Environmental Phenomena ; *Water Microbiology ; Water Purification/*methods ; }, }
@article {pmid20886337, year = {2010}, author = {Wang, P and Li, T and Hu, A and Wei, Y and Guo, W and Jiao, N and Zhang, C}, title = {Community structure of archaea from deep-sea sediments of the South China Sea.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {796-806}, pmid = {20886337}, issn = {1432-184X}, mesh = {Archaea/*classification/genetics/*isolation &amp; purification ; Biodiversity ; China ; DNA, Archaeal/genetics ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; }, abstract = {Using the archaeal 16S rRNA gene, we determined the community structures of archaea of subseafloor sediments (∼9-11 m below seafloor) from two geographically distant cores (MD05-2896, south, water depth 1,657 m; MD05-2902, north, water depth 3,697 m) in the South China Sea. Euryarchaeota accounted for 61.4% of total archaeal clone libraries at MD05-2896 and 56.2% at MD05-2902. At both locations, the Euryarchaeota-related sequences were dominated by Marine Benthic Group D, Terrestrial Miscellaneous Eryarchaeotal Group, and South African GoldMine Euryarchaeotal Group; the Crenarchaeota-related sequences were dominated by Marine Benthic Group B, Marine Group I, pSL12, and C3. The community structure showed no significant difference with depth at each location, suggesting the lack of stratification of archaeal populations in the deep-sea marine sediments in the South China Sea. On the other hand, the community structure is significantly different between the two sites, which may be related to geographical difference in the South China Sea.}, }
@article {pmid20886336, year = {2010}, author = {Bruce, T and Martinez, IB and Maia Neto, O and Vicente, AC and Kruger, RH and Thompson, FL}, title = {Bacterial community diversity in the Brazilian Atlantic forest soils.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {840-849}, pmid = {20886336}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; Brazil ; DNA, Bacterial/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/analysis ; *Soil Microbiology ; Trees/microbiology ; }, abstract = {The aim of this study was to characterize the bacterial community diversity of the Brazilian Atlantic forest soil by means of both cultivation and 16S rRNA clone libraries. A collection of 86 representative isolates, obtained from six samples of Atlantic forest soils from the National Park of Serra dos Órgãos (PARNASO), belonged to the genera Arthrobacter, Bacillus, Burkholderia, Leifsonia, Paenibacillus, Pseudomonas, Ralstonia, Serratia, and Streptomyces according to the 16S rRNA sequences. Representative isolates from the different genera degraded cellulose and lignin. The culture-independent analysis based on 894 partial 16S rRNA gene sequences revealed that the most frequently retrieved groups belonged to the phyla Acidobacteria (29-54%), Proteobacteria (16-38%), and Verrucomicrobia (0.6-14%). The majority of the sequences (82.6%) were unidentified singletons and doubletons, indicating a high diversity of rare unique sequences. Chao1 estimator disclosed a high number of phyla (41-152) and species (263-446). This is the first survey on the Atlantic Forest soils using a combination of cultivation and culture-independent approaches. We conclude that the Brazilian Atlantic Forest soil represents a vast source of novel bacteria.}, }
@article {pmid20883730, year = {2010}, author = {Roux-Michollet, DD and Schimel, JP and Holden, PA}, title = {Pushing the limits for amplifying BrdU-labeled DNA encoding 16S rRNA: DNA polymerase as the determining factor.}, journal = {Journal of microbiological methods}, volume = {83}, number = {3}, pages = {312-316}, doi = {10.1016/j.mimet.2010.09.016}, pmid = {20883730}, issn = {1872-8359}, mesh = {Bacteria/genetics/isolation &amp; purification/metabolism ; Bromodeoxyuridine/analysis/metabolism ; DNA, Bacterial/genetics ; DNA-Directed DNA Polymerase/*metabolism ; Polymerase Chain Reaction/instrumentation/*methods ; RNA, Ribosomal, 16S/chemistry/*genetics ; Soil/analysis ; *Soil Microbiology ; Staining and Labeling/instrumentation/*methods ; }, abstract = {Identifying microorganisms that are active under specific conditions in ecosystems is a challenge in microbial ecology. Recently, the bromodeoxyuridine (BrdU) technique was developed to label actively growing cells. BrdU, a thymidine analog, is incorporated into newly synthesized DNA, and the BrdU-labeled DNA is then isolated from total extractable DNA by immunocapture using a BrdU-specific antibody. Analyzing the BrdU-labeled DNA allows for assessing the actively growing community, which can then be compared to the unlabeled DNA that represents the total community. However, applying the BrdU approach to study soils has been problematic due to low DNA amounts and soil contaminants. To address these challenges, we developed a protocol, optimizing specificity and reproducibility, to amplify BrdU-labeled gene fragments encoding 16S rRNA. We found that the determining factor was the DNA polymerase: among the 13 different polymerases we tested, only 3 provided adequate yields with minimal contamination, and only two of those three produced similar amplification patterns of community DNA.}, }
@article {pmid20878522, year = {2011}, author = {Lin, YT and Jangid, K and Whitman, WB and Coleman, DC and Chiu, CY}, title = {Change in bacterial community structure in response to disturbance of natural hardwood and secondary coniferous forest soils in central taiwan.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {429-437}, pmid = {20878522}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics ; *Biota ; DNA, Bacterial/genetics ; *Ecosystem ; Gene Library ; Genes, rRNA ; Phylogeny ; Sequence Analysis, DNA ; *Soil Microbiology ; Taiwan ; Tracheophyta/microbiology ; Trees/*microbiology ; }, abstract = {Forest management often results in changes in the soil and its microbial communities. In the present study, differences in the soil bacterial community caused by forest management practices were characterized using small subunit (SSU) ribosomal RNA (rRNA) gene clone libraries. The communities were from a native hardwood forest (HWD) and two adjacent conifer plantations in a low-elevation montane, subtropical experimental forest at the Lienhuachi Experimental Forest (LHCEF) in central Taiwan. At this locality, the elevation ranges from 600 to 950 m, the mean annual precipitation is 2,200 mm, the mean annual temperature is 20.8 °C, and the soil pH is 4. The conifer forests included a Cunninghamia konishii Hay (CNH) plantation of 40 years and an old growth Calocedrus formosana (Florin) Florin (CLC) forest of 80 years. A total of 476 clones were sequenced and assigned into 12 phylogenetic groups. Proteobacteria-affiliated clones (53%) predominated in the library from HWD soils. In contrast, Acidobacteria was the most abundant phylum and comprised 39% and 57% in the CLC and CNH libraries, respectively. Similarly, the most abundant OTUs in HWD soils were greatly reduced or absent in the CLC and CNH soils. Based on several diversity indices, the numbers of abundant OTUs and singletons, and rarefaction curves, the diversity of the HWD community (0.95 in evenness and Shannon diversity indices) was somewhat less than that in the CNH soils (0.97 in evenness and Shannon diversity indices). The diversity of the community in CLC soils was intermediate. The differences in diversity among the three communities may also reflect changes in abundances of a few OTUs. The CNH forest soil community may be still in a successional phase that is only partially stabilized after 40 years. Analysis of molecular variance also revealed that the bacterial community composition of HWD soils was significantly different from CLC and CNH soils (p = 0.001). These results suggest that the disturbance of forest conversion and tree species composition are important factors influencing the soil bacterial community among three forest ecosystems in the same climate.}, }
@article {pmid20878521, year = {2010}, author = {Berggren, M and Laudon, H and Jonsson, A and Jansson, M}, title = {Nutrient constraints on metabolism affect the temperature regulation of aquatic bacterial growth efficiency.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {894-902}, pmid = {20878521}, issn = {1432-184X}, mesh = {Bacteria/growth &amp; development/*metabolism ; *Ecosystem ; Fresh Water/analysis/*microbiology ; Nitrogen/metabolism ; Phosphorus/metabolism ; Rivers/chemistry/microbiology ; Temperature ; }, abstract = {Inorganic nutrient availability and temperature are recognized as major regulators of organic carbon processing by aquatic bacteria, but little is known about how these two factors interact to control bacterial metabolic processes. We manipulated the temperature of boreal humic stream water samples within 0-25°C and measured bacterial production (BP) and respiration (BR) with and without inorganic nitrogen + phosphorus addition. Both BP and BR increased exponentially with temperature in all experiments, with Q(10) values varying between 1.2 and 2.4. The bacterial growth efficiency (BGE) showed strong negative relationships with temperature in nutrient-enriched samples and in natural stream water where community-level BP and BR were not limited by nutrients. However, there were no relationships between BGE and temperature in samples where BP and BR were significantly constrained by the inorganic nutrient availability. The results suggest that metabolic responses of aquatic bacterial communities to temperature variations can be strongly dependent on whether the bacterial metabolism is limited by inorganic nutrients or not. Such responses can have consequences for both the carbon flux through aquatic food webs and for the flux of CO(2) from aquatic systems to the atmosphere.}, }
@article {pmid20878276, year = {2010}, author = {Bernstein, CN}, title = {Epidemiologic clues to inflammatory bowel disease.}, journal = {Current gastroenterology reports}, volume = {12}, number = {6}, pages = {495-501}, pmid = {20878276}, issn = {1534-312X}, mesh = {Breast Feeding ; China/epidemiology ; Colitis, Ulcerative/*epidemiology/immunology/microbiology ; Crohn Disease/*epidemiology/immunology/microbiology ; Developing Countries ; Food Contamination ; Humans ; Hygiene ; Intestines/microbiology ; Mycobacterium avium subsp. paratuberculosis/isolation &amp; purification ; Risk Factors ; }, abstract = {In this article, the recent literature exploring the epidemiology of inflammatory bowel disease (IBD) is reviewed. Epidemiologic studies present data on disease burden, but may also provide clues to disease etiology. The emergence of IBD in developing nations warrants a systematic search for environmental changes in those countries to explain the evolution of IBD. The hygiene hypothesis suggests that an alteration in the microbial environment experienced by the host facilitates the evolution of chronic immune-mediated diseases. One complex database study suggested that areas with high species richness of human intestinal helminthes are areas with genetic changes in interleukin gene loci. In other words, over the years, the microbial ecology has affected human genetics, which in turn would have an impact on immune responses. Other factors affect the gut microbiome, and several studies have explored the increase in incidence of IBD in relation to such factors as exogenous infections, use of antibiotics, and diet.}, }
@article {pmid20871988, year = {2010}, author = {Saari, S and Helander, M and Faeth, SH and Saikkonen, K}, title = {The effects of endophytes on seed production and seed predation of tall fescue and meadow fescue.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {928-934}, pmid = {20871988}, issn = {1432-184X}, mesh = {Animals ; Behavior, Animal ; Biomass ; Fungi/*physiology ; Lolium/*growth &amp; development/*microbiology/physiology ; Moths/*physiology ; Seeds/growth &amp; development/microbiology/physiology ; *Symbiosis ; }, abstract = {Fungal endophytes of grasses are often included in agricultural management and in ecological studies of natural grass populations. In European agriculture and ecological studies, however, grass endophytes are largely ignored. In this study, we determined endophyte infection frequencies of 13 European cultivars and 49 wild tall fescue (Schedonorus phoenix) populations in Northern Europe. We then examined seed production and seed predation of endophyte-infected (E+) and endophyte-free (E-) tall fescue (in wild grass populations and in a field experiment) and meadow fescue (Schedonorus pratensis; in a field experiment only). Endophytes were detected in only one of the 13 cultivars. In contrast, >90% of wild tall fescue plants harbored endophytes in 45 wild populations but were absent in three inland populations in Estonia. In three wild tall fescue study sites, 17%, 22%, and 56% of the seeds were preyed upon by the cocksfoot moth. Endophyte infection did not affect seed mass of tall fescue in the field experiment. However, seed predation was lower in E+ than E- grasses in the two tall fescue populations with higher predation rates. For meadow fescue, the mean number of seeds from E+ plants was higher than E- plants, but E- and E+ seeds had equal rates of predation by the moth. Our results suggest that the effects of grass endophytes on seed production and cocksfoot moth seed predation vary considerably among grass species, and the effects may depend on herbivore pressure and other environmental conditions.}, }
@article {pmid20870788, year = {2010}, author = {Pan, Y and Bodrossy, L and Frenzel, P and Hestnes, AG and Krause, S and Lüke, C and Meima-Franke, M and Siljanen, H and Svenning, MM and Bodelier, PL}, title = {Impacts of inter- and intralaboratory variations on the reproducibility of microbial community analyses.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {22}, pages = {7451-7458}, pmid = {20870788}, issn = {1098-5336}, mesh = {*Biodiversity ; Electrophoresis, Polyacrylamide Gel ; Italy ; Metagenomics/*methods/*standards ; Microarray Analysis ; Nucleic Acid Denaturation ; Oryza ; Polymerase Chain Reaction ; Reproducibility of Results ; *Soil Microbiology ; }, abstract = {With the advent of molecular biological techniques, especially next-generation sequencing and metagenomics, the number of microbial biogeography studies is rapidly increasing. However, these studies involve the synthesis of data generated by different laboratories using different protocols, chemicals, etc., all with inherent biases. The aim of this study was to assess inter- as well as intralaboratory variations in microbial community composition when standardized protocols are applied to a single soil sample. Aliquots from a homogenized soil sample from a rice field in Italy were sent to five participating laboratories. DNA was extracted by two investigators per laboratory using an identical protocol. All DNA samples were sent to one laboratory to perform DNA quantification, quantitative PCR (QPCR), and microarray and denaturing gradient gel electrophoresis (DGGE) analyses of methanotrophic communities. Yields, as well as purity of DNA, were significantly different between laboratories but in some cases also between investigators within the same laboratory. The differences in yield and quality of the extracted DNA were reflected in QPCR, microarray, and DGGE analysis results. Diversity indices (Shannon-Wiener, evenness, and richness) differed significantly between laboratories. The observed differences have implications for every project in which microbial communities are compared in different habitats, even if assessed within the same laboratory. To be able to make sensible comparisons leading to valid conclusions, intralaboratory variation should be assessed. Standardization of DNA extraction protocols and possible use of internal standards in interlaboratory comparisons may help in rendering a "quantifiable" bias.}, }
@article {pmid20869859, year = {2011}, author = {Wilson, GS and Raftos, DA and Nair, SV}, title = {Antimicrobial activity of surface attached marine bacteria in biofilms.}, journal = {Microbiological research}, volume = {166}, number = {6}, pages = {437-448}, doi = {10.1016/j.micres.2010.08.003}, pmid = {20869859}, issn = {1618-0623}, mesh = {Anti-Bacterial Agents/*metabolism ; Bacteria/growth &amp; development/isolation &amp; purification/*metabolism ; Bacterial Physiological Phenomena ; *Biofilms ; Microbial Sensitivity Tests ; Seawater/*microbiology ; }, abstract = {Relatively little is known about the microbial ecology of biofilm communities or the diversity of antimicrobial molecules that they produce to regulate these communities. This study tested whether the production of antimicrobial activity in biofilm cultures is enhanced towards competing bacteria found in those biofilms. First, the production of antimicrobial activity of marine bacteria grown in biofilms was tested. Fourteen of the 105 marine isolates tested were found to produce antimicrobial factors when grown in biofilms. The antimicrobial activity produced by these isolates in biofilms was more potent and inhibited a broader range of target bacteria grown in biofilms compared to shaken liquid cultures. In a separate experiment, we found that cultivation in biofilms containing produced metabolites from an 'inducer' bacterium stimulated the production of antimicrobial molecules by 'producer' bacteria that were active against the 'inducer' bacterium. Overall, the study suggests that surface attached marine bacteria can target their antimicrobial activity towards competing bacteria in biofilms.}, }
@article {pmid20865443, year = {2011}, author = {Hennebel, T and Benner, J and Clauwaert, P and Vanhaecke, L and Aelterman, P and Callebaut, R and Boon, N and Verstraete, W}, title = {Dehalogenation of environmental pollutants in microbial electrolysis cells with biogenic palladium nanoparticles.}, journal = {Biotechnology letters}, volume = {33}, number = {1}, pages = {89-95}, doi = {10.1007/s10529-010-0393-7}, pmid = {20865443}, issn = {1573-6776}, mesh = {Biotransformation ; Chlorides/metabolism ; Electrodes/*microbiology ; Electrolysis/methods ; Environmental Pollutants/*metabolism ; Ethane/metabolism ; Hydrogen/*metabolism ; *Nanoparticles ; Palladium/*metabolism ; Trichloroethylene/*metabolism ; Water Purification/*methods ; }, abstract = {Hydrodehalogenation of persistent pollutants, such as the groundwater contaminants trichloroethylene and diatrizoate, are catalyzed by biogenic Pd nanoparticles. As H(2) gas supply for the dehalogenation reactions is still the limiting factor, this study examines in situ H(2) production in the cathode of a microbial electrolysis cell. In a biogenic Pd nanoparticle (bio-Pd) free microbial electrolysis cell (MEC), dechlorination of trichloroethylene (TCE) with concomitant chloride and ethane formation was achieved in the cathode compartment at a removal rate of 120 g TCE m(-3) total cathode compartment (TCC) day(-1), applying -0.8 V with a power source. When the cathode granules were coated with 5 mg bio-Pd g(-1) graphite, chloride and ethane formation increased to 151 g TCE m(-3) TCC day(-1) corresponding with a specific removal rate of 48 mg TCE g(-1) Pd day(-1). In both cases, formation of unwanted byproducts, such as vinyl chloride, was not significant. When the same setup was applied for transformation of the iodinated contrast medium diatrizoate (diaI(3)), reduction in a catalyst-free cathode of a MEC resulted in a removal of 48 ± 9% during the first h corresponding to 3 g diaI(3) m(-3) TCC day(-1). Coating the cathodic graphite granules with bio-Pd enhanced the transformation resulting in a 93 ± 4% removal during the first h corresponding to 6 g diaI(3) m(-3) TCC day(-1). These results suggest that MECs can produce H(2) in a sustainable way to provide an economical interesting reactant for bio-Pd catalyzed dehalogenation reactions.}, }
@article {pmid20865054, year = {2010}, author = {Santos, HF and Cury, JC and Carmo, FL and Rosado, AS and Peixoto, RS}, title = {18S rDNA sequences from microeukaryotes reveal oil indicators in mangrove sediment.}, journal = {PloS one}, volume = {5}, number = {8}, pages = {e12437}, pmid = {20865054}, issn = {1932-6203}, mesh = {Base Sequence ; DNA, Ribosomal/genetics ; Environmental Monitoring/*methods ; Eukaryota/classification/genetics/*isolation &amp; purification ; Geologic Sediments/*chemistry ; Molecular Sequence Data ; Petroleum/*analysis ; RNA, Ribosomal, 18S/genetics ; Water Pollution, Chemical/*analysis ; }, abstract = {BACKGROUND: Microeukaryotes are an effective indicator of the presence of environmental contaminants. However, the characterisation of these organisms by conventional tools is often inefficient, and recent molecular studies have revealed a great diversity of microeukaryotes. The full extent of this diversity is unknown, and therefore, the distribution, ecological role and responses to anthropogenic effects of microeukaryotes are rather obscure. The majority of oil from oceanic oil spills (e.g., the May 2010 accident in the Gulf of Mexico) converges on coastal ecosystems such as mangroves, which are threatened with worldwide disappearance, highlighting the need for efficient tools to indicate the presence of oil in these environments. However, no studies have used molecular methods to assess the effects of oil contamination in mangrove sediment on microeukaryotes as a group.<br><br>We evaluated the population dynamics and the prevailing 18S rDNA phylotypes of microeukaryotes in mangrove sediment microcosms with and without oil contamination, using PCR/DGGE and clone libraries. We found that microeukaryotes are useful for monitoring oil contamination in mangroves. Our clone library analysis revealed a decrease in both diversity and species richness after contamination. The phylogenetic group that showed the greatest sensitivity to oil was the Nematoda. After contamination, a large increase in the abundance of the groups Bacillariophyta (diatoms) and Biosoecida was detected. The oil-contaminated samples were almost entirely dominated by organisms related to Bacillariophyta sp. and Cafeteria minima, which indicates that these groups are possible targets for biomonitoring oil in mangroves. The DGGE fingerprints also indicated shifts in microeukaryote profiles; specific band sequencing indicated the appearance of Bacillariophyta sp. only in contaminated samples and Nematoda only in non-contaminated sediment.<br><br>CONCLUSIONS/SIGNIFICANCE: We believe that the microeukaryotic targets indicated by our work will be of great applicability in biomonitoring hydrocarbons in mangroves under oil contamination risk or during recovery strategies.}, }
@article {pmid20864478, year = {2010}, author = {Roger, LC and Costabile, A and Holland, DT and Hoyles, L and McCartney, AL}, title = {Examination of faecal Bifidobacterium populations in breast- and formula-fed infants during the first 18 months of life.}, journal = {Microbiology (Reading, England)}, volume = {156}, number = {Pt 11}, pages = {3329-3341}, doi = {10.1099/mic.0.043224-0}, pmid = {20864478}, issn = {1465-2080}, mesh = {Bifidobacterium/genetics/growth &amp; development/*isolation &amp; purification ; Biodiversity ; *Breast Feeding ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Denaturing Gradient Gel Electrophoresis ; Feces/*microbiology ; Humans ; Infant ; *Infant Formula ; Longitudinal Studies ; Species Specificity ; Weaning ; }, abstract = {Bifidobacteria in the infant faecal microbiota have been the focus of much interest, especially during the exclusive milk-feeding period and in relation to the fortification of infant formulae to better mimic breast milk. However, longitudinal studies examining the diversity and dynamics of the Bifidobacterium population of infants are lacking, particularly in relation to the effects of weaning. Using a polyphasic strategy, the Bifidobacterium populations of breast- and formula-fed infants were examined during the first 18 months of life. Bifidobacterium-specific denaturing gradient gel electrophoresis demonstrated that breast-fed infants harboured greater diversity than formula-fed infants and the diversity of the infants' Bifidobacterium populations increased with weaning. Twenty-seven distinctive banding profiles were observed from ∼1100 infant isolates using ribosomal intergenic spacer analysis, 14 biotypes of which were confirmed to be members of the genus Bifidobacterium. Two profiles (H, Bifidobacterium longum subsp. infantis; and I, Bifidobacterium bifidum) were common culturable biotypes, seen in 9/10 infants, while profile E (Bifidobacterium breve) was common among breast-fed infants. Overall, inter- and intra-individual differences were observed in the Bifidobacterium populations of infants between 1 and 18 months of age, although weaning was associated with increased diversity of the infant Bifidobacterium populations. Breast-fed infants generally harboured a more complex Bifidobacterium microbiota than formula-fed infants.}, }
@article {pmid20860734, year = {2010}, author = {Vilchez-Vargas, R and Junca, H and Pieper, DH}, title = {Metabolic networks, microbial ecology and 'omics' technologies: towards understanding in situ biodegradation processes.}, journal = {Environmental microbiology}, volume = {12}, number = {12}, pages = {3089-3104}, doi = {10.1111/j.1462-2920.2010.02340.x}, pmid = {20860734}, issn = {1462-2920}, mesh = {Aerobiosis ; Alkanes/metabolism ; *Biodegradation, Environmental ; Ecology ; Genome, Bacterial ; Hydrocarbons, Aromatic/metabolism ; *Metabolomics ; *Metagenomics ; }, abstract = {Microbial degradation is the main mechanism responsible for the recovery of contaminated sites, where a huge body of investigations is available in which most concentrate on single isolates from soils capable of mineralizing pollutants. The rapid development of molecular techniques in recent years allows immense insights into the processes in situ, including identification of organisms active in target sites, community member interactions and catabolic gene structures. Only a detailed understanding of the functioning and interactions within microbial communities will allow their rational manipulation for the purpose of optimizing bioremediation efforts. We will present the status of the current capabilities to assess and predict catabolic potential of environmental sites by applying gene fingerprinting, catabolome arrays, metagenomics and complementary 'omics' technologies. Collectively, this will allow tracking regulation and evolution within microbial communities ultimately aiming to understand the mechanisms taking place in large scale bioremediation treatments for aromatic decontamination.}, }
@article {pmid20857096, year = {2011}, author = {Venieraki, A and Dimou, M and Pergalis, P and Kefalogianni, I and Chatzipavlidis, I and Katinakis, P}, title = {The genetic diversity of culturable nitrogen-fixing bacteria in the rhizosphere of wheat.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {277-285}, pmid = {20857096}, issn = {1432-184X}, mesh = {Azospirillum/classification/enzymology/*genetics/isolation &amp; purification ; Cloning, Molecular ; DNA, Bacterial/genetics ; *Genetic Variation ; Greece ; Indoleacetic Acids/metabolism ; Nitrogen Fixation ; Oxidoreductases/genetics ; Phylogeny ; Pseudomonas stutzeri/classification/enzymology/*genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Sequence Analysis, DNA ; Soil Microbiology ; Triticum/growth &amp; development/*microbiology ; }, abstract = {A total of 17 culturable nitrogen-fixing bacterial strains associated with the roots of wheat growing in different regions of Greece were isolated and characterized for plant-growth-promoting traits such as auxin production and phosphate solubilization. The phylogenetic position of the isolates was first assessed by the analysis of the PCR-amplified 16S rRNA gene. The comparative sequence analysis and phylogenetic analysis based on 16S rRNA gene sequences show that the isolates recovered in this study are grouped with Azospirillum brasilense, Azospirillum zeae, and Pseudomonas stutzeri. The diazotrophic nature of all isolates was confirmed by amplification of partial nifH gene sequences. The phylogenetic tree based on nifH gene sequences is consistent with 16S rRNA gene phylogeny. The isolates belonging to Azospirillum species were further characterized by examining the partial dnaK gene phylogenetic tree. Furthermore, it was demonstrated that the ipdC gene was present in all Azospirillum isolates, suggesting that auxin is mainly synthesized via the indole-3-pyruvate pathway. Although members of P. stutzeri and A. zeae are known diazotrophic bacteria, to the best of our knowledge, this is the first report of isolation and characterization of strains belonging to these bacterial genera associated with wheat.}, }
@article {pmid20854691, year = {2010}, author = {Smith, DM and Snow, DE and Rees, E and Zischkau, AM and Hanson, JD and Wolcott, RD and Sun, Y and White, J and Kumar, S and Dowd, SE}, title = {Evaluation of the bacterial diversity of pressure ulcers using bTEFAP pyrosequencing.}, journal = {BMC medical genomics}, volume = {3}, number = {}, pages = {41}, pmid = {20854691}, issn = {1755-8794}, mesh = {Bacteria/*genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; *Biodiversity ; Biofilms ; Chronic Disease ; DNA, Bacterial/genetics ; Female ; Humans ; Male ; Phenotype ; Pressure Ulcer/*microbiology ; Principal Component Analysis ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Decubitus ulcers, also known as bedsores or pressure ulcers, affect millions of hospitalized patients each year. The microflora of chronic wounds such as ulcers most commonly exist in the biofilm phenotype and have been known to significantly impair normal healing trajectories.<br><br>METHODS: Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP), a universal bacterial identification method, was used to identify bacterial populations in 49 decubitus ulcers. Diversity estimators were utilized and wound community compositions analyzed in relation to metadata such as Age, race, gender, and comorbidities.<br><br>RESULTS: Decubitus ulcers are shown to be polymicrobial in nature with no single bacterium exclusively colonizing the wounds. The microbial community among such ulcers is highly variable. While there are between 3 and 10 primary populations in each wound there can be hundreds of different species present many of which are in trace amounts. There is no clearly significant differences in the microbial ecology of decubitus ulcer in relation to metadata except when considering diabetes. The microbial populations and composition in the decubitus ulcers of diabetics may be significantly different from the communities in non-diabetics.<br><br>CONCLUSIONS: Based upon the continued elucidation of chronic wound bioburdens as polymicrobial infections, it is recommended that, in addition to traditional biofilm-based wound care strategies, an antimicrobial/antibiofilm treatment program can be tailored to each patient's respective wound microflora.}, }
@article {pmid20851963, year = {2010}, author = {Barr, JJ and Cook, AE and Bond, PL}, title = {Granule formation mechanisms within an aerobic wastewater system for phosphorus removal.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {22}, pages = {7588-7597}, pmid = {20851963}, issn = {1098-5336}, mesh = {Aerobiosis ; Bacteria/classification/cytology/*growth &amp; development/*metabolism ; Bacterial Adhesion ; Bioreactors/microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; In Situ Hybridization, Fluorescence ; Microscopy ; Phosphorus/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; }, abstract = {Granular sludge is a novel alternative for the treatment of wastewater and offers numerous operational and economic advantages over conventional floccular-sludge systems. The majority of research on granular sludge has focused on optimization of engineering aspects relating to reactor operation with little emphasis on the fundamental microbiology. In this study, we hypothesize two novel mechanisms for granule formation as observed in three laboratory scale sequencing batch reactors operating for biological phosphorus removal and treating two different types of wastewater. During the initial stages of granulation, two distinct granule types (white and yellow) were distinguished within the mixed microbial population. White granules appeared as compact, smooth, dense aggregates dominated by 97.5% "Candidatus Accumulibacter phosphatis," and yellow granules appeared as loose, rough, irregular aggregates with a mixed microbial population of 12.3% "Candidatus Accumulibacter phosphatis" and 57.9% "Candidatus Competibacter phosphatis," among other bacteria. Microscopy showed white granules as homogeneous microbial aggregates and yellow granules as segregated, microcolony-like aggregates, with phylogenetic analysis suggesting that the granule types are likely not a result of strain-associated differences. The microbial community composition and arrangement suggest different formation mechanisms occur for each granule type. White granules are hypothesized to form by outgrowth from a single microcolony into a granule dominated by one bacterial type, while yellow granules are hypothesized to form via multiple microcolony aggregation into a microcolony-segregated granule with a mixed microbial population. Further understanding and application of these mechanisms and the associated microbial ecology may provide conceptual information benefiting start-up procedures for full-scale granular-sludge reactors.}, }
@article {pmid20848461, year = {2010}, author = {Walk, ST and Blum, AM and Ewing, SA and Weinstock, JV and Young, VB}, title = {Alteration of the murine gut microbiota during infection with the parasitic helminth Heligmosomoides polygyrus.}, journal = {Inflammatory bowel diseases}, volume = {16}, number = {11}, pages = {1841-1849}, pmid = {20848461}, issn = {1536-4844}, support = {T32 HL007749/HL/NHLBI NIH HHS/United States ; R56 DK058755/DK/NIDDK NIH HHS/United States ; DK070875/DK/NIDDK NIH HHS/United States ; R01 DK070875/DK/NIDDK NIH HHS/United States ; R01 DK038327/DK/NIDDK NIH HHS/United States ; T32 HL07749-15/HL/NHLBI NIH HHS/United States ; DK058755/DK/NIDDK NIH HHS/United States ; DK38327/DK/NIDDK NIH HHS/United States ; R01 DK058755/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Disease Models, Animal ; Gastrointestinal Tract/*immunology/*microbiology ; Genes, rRNA ; Ileum/immunology ; Inflammatory Bowel Diseases/*immunology/*microbiology ; Interleukin-10/genetics ; Lactobacillaceae/immunology ; Mice ; Mice, Inbred C57BL ; Mice, Mutant Strains ; Nematospiroides dubius/*immunology ; }, abstract = {BACKGROUND: In a murine model of inflammatory bowel disease (IBD), treatment of colitis in IL-10 gene-deficient mice with the parasitic helminth Heligmosomoides polygyrus ameliorates colonic inflammation. The cellular and molecular mechanisms driving this therapeutic host response are being studied vigorously. One proposed mechanism is that H. polygyrus infection favors the outgrowth or suppression of certain bacteria, which in turn help modulate host immunity.<br><br>METHODS: To quantify the effect of H. polygyrus infection on the composition of the gastrointestinal (GI) tract microbiota, we conducted two independent microbial ecology analyses of C57BL/6 mice. We obtained and analyzed 3,353 bacterial 16S rRNA encoding gene sequences from the ileum and cecum of infected and uninfected mice as well as incective H. polygyrus larvae at the outset of the second experiment and adult worms taken directly from the mouse duodenum at the end of the second experiment.<br><br>RESULTS: We found that a significant shift in the abundance and relative distribution of bacterial species in the ileum of mice is associated with H. polygyrus infection. Members of the bacterial family Lactobacillaceae significantly increased in abundance in the ileum of infected mice reproducibly in two independent experiments despite having different microbiotas present at the outset of each experiment.<br><br>CONCLUSIONS: These data support the concept that helminth infection shifts the composition of intestinal bacteria. The clinical consequences of these shifts in intestinal flora are yet to be explored.}, }
@article {pmid20842497, year = {2011}, author = {Herrera, J and Poudel, R and Khidir, HH}, title = {Molecular characterization of coprophilous fungal communities reveals sequences related to root-associated fungal endophytes.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {239-244}, pmid = {20842497}, issn = {1432-184X}, mesh = {Animals ; Antelopes/microbiology ; Biodiversity ; Bison/microbiology ; Cattle/microbiology ; DNA, Fungal/genetics ; Feces/*microbiology ; Fungi/*classification/genetics ; New Mexico ; Plant Roots/microbiology ; Poaceae/*microbiology ; Sciuridae/microbiology ; South Dakota ; }, abstract = {This paper reports the use of molecular methods to characterize the coprophilous fungal communities (CFC) that inhabit the dung of four species of mammalian herbivores at two sites, Sevilleta National Wildlife Refuge (SNWR) in New Mexico and Wind Cave National Park (WCNP) in South Dakota. Results reveal that CFC from domesticated cattle (Bos taurus) at SNWR, and bison (Bison bison) and black-tailed prairie dogs (Cynomys ludovicianus) at WCNP were diverse but dominated primarily by members within eight taxonomic orders, including the rarely cultured and anaerobic order Neocallimastigales. In addition, 7.7% (138 of 1,788) of the sequences obtained from all dung samples were at least 97% similar to root-associated fungal (RAF) sequences previously described from blue grama (Bouteloua gracilis), a common forage grass found throughout North America and growing at both study sites. In contrast, 95.8% (295 of 308) of the sequences and four of the total seven operational taxonomic units obtained from pronghorn antelope (Antilocapra americana) dung belonged to the Pleosporalean order. We hypothesize that some herbivore vectors disperse non-systemic (non-clavicipitaceous) fungal endophytes. These dispersal events, it is argued, are most likely to occur via herbivores that occasionally forage and masticate root tissue, especially in arid regions where aboveground vegetation is sparse. The results of this study suggest that some (possibly many) members of the RAF community can expand their ecological role to include colonizing dung.}, }
@article {pmid20838787, year = {2011}, author = {Pokharel, A and Mirza, BS and Dawson, JO and Hahn, D}, title = {Frankia populations in soil and root nodules of sympatrically grown Alnus taxa.}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {92-100}, pmid = {20838787}, issn = {1432-184X}, mesh = {Alnus/*microbiology ; Frankia/*classification/*genetics/isolation &amp; purification ; Genes, Bacterial/genetics ; *Genetic Variation ; Molecular Sequence Data ; Oxidoreductases/genetics ; Phylogeny ; Plant Roots/*microbiology ; *Soil Microbiology ; }, abstract = {The genetic diversity of Frankia populations in soil and in root nodules of sympatrically grown Alnus taxa was evaluated by rep-polymerase chain reaction (PCR) and nifH gene sequence analyses. Rep-PCR analyses of uncultured Frankia populations in root nodules of 12 Alnus taxa (n=10 nodules each) growing sympatrically in the Morton Arboretum near Chicago revealed identical patterns for nodules from each Alnus taxon, including replicate trees of the same host taxon, and low diversity overall with only three profiles retrieved. One profile was retrieved from all nodules of nine taxa (Alnus incana subsp. incana, Alnus japonica, Alnus glutinosa, Alnus incana subsp. tenuifolia, Alnus incana subsp. rugosa, Alnus rhombifolia, Alnus mandshurica, Alnus maritima, and Alnus serrulata), the second was found in all nodules of two plant taxa (A. incana subsp. hirsuta and A. glutinosa var. pyramidalis), and the third was unique for all Frankia populations in nodules of A. incana subsp. rugosa var. americana. Comparative sequence analyses of nifH gene fragments in nodules representing these three profiles assigned these frankiae to different subgroups within the Alnus host infection group. None of these sequences, however, represented frankiae detectable in soil as determined by sequence analysis of 73 clones from a Frankia-specific nifH gene clone library. Additional analyses of nodule populations from selected alders growing on different soils demonstrated the presence of different Frankia populations in nodules for each soil, with populations showing identical sequences in nodules from the same soil, but differences between plant taxa. These results suggest that soil environmental conditions and host plant genotype both have a role in the selection of Frankia strains by a host plant for root nodule formation, and that this selection is not merely a function of the abundance of a Frankia strain in soil.}, }
@article {pmid20838786, year = {2011}, author = {Hirsch, MD and Long, ZT and Song, B}, title = {Anammox bacterial diversity in various aquatic ecosystems based on the detection of hydrazine oxidase genes (hzoA/hzoB).}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {264-276}, pmid = {20838786}, issn = {1432-184X}, mesh = {Bacteria/classification/enzymology/*genetics ; *Biodiversity ; Cloning, Molecular ; DNA, Bacterial/genetics ; Genes, Bacterial ; Hydrazines/*metabolism ; Nitrogen/metabolism ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Regression Analysis ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Anammox bacteria belonging to the phylum Planctomycetes are responsible for N removal through NH(4)(+) oxidation coupled with NO(2)(-) reduction. Microbial diversity and ecology of anammox bacteria have not yet been fully revealed due to limitations of 16S rRNA analysis. The hydrazine oxidase gene in cluster 1 (hereafter hzoA/hzoB) was suggested as a proper genetic marker due to its high expression and ubiquitous presence in anammox bacteria. We conducted a comparative analysis of 16S rRNA and hzoA/hzoB genes to reveal anammox bacterial diversity and distribution in various aquatic environments. Phylogenetic analyses of 16S rRNA and hzoA/hzoB genes showed the dominance of Scalindua organisms in marine ecosystems, but there was no congruence of 16S rRNA and hzoA/hzoB gene phylogenies among the freshwater anammox bacteria associated with Brocadia sp., Jettenia sp., and Anammoxoglobus sp. Higher diversity of anammox bacteria was revealed based on hzoA/hzoB genes than 16S rRNA genes in the examined environments. Multiple regression analysis showed that salinity had significant influence on differential distribution and diversity of anammox bacteria in different ecosystems. Thus, molecular detection and resulting phylogeny of the hzoA/hzoB gene generated a better understanding of anammox bacterial diversity and their ecological distribution in various aquatic ecosystems.}, }
@article {pmid20838785, year = {2011}, author = {Rosewarne, CP and Pope, PB and Denman, SE and McSweeney, CS and O'Cuiv, P and Morrison, M}, title = {High-yield and phylogenetically robust methods of DNA recovery for analysis of microbial biofilms adherent to plant biomass in the herbivore gut.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {448-454}, pmid = {20838785}, issn = {1432-184X}, mesh = {Animals ; Biodiversity ; *Biofilms ; Biomass ; Cattle/microbiology ; DNA, Archaeal/*isolation &amp; purification ; DNA, Bacterial/*isolation &amp; purification ; Denaturing Gradient Gel Electrophoresis/methods ; Male ; Plants/*microbiology ; Polymerase Chain Reaction/methods ; Rumen/*microbiology ; }, abstract = {Recent studies have shown the microbial biofilms adherent to plant biomass in the gastrointestinal tracts of humans and other herbivores are quite different to planktonic populations. If these biofilm communities are to be properly characterized by metagenomics methods, then the microbial desorption methods used must ensure the phylogenetic diversity and genetic potential recovered is biologically valid. To that end, we describe here two different methods for desorbing microbes tightly adherent to plant biomass; and used PCR-DGGE analyses of the Bacteria and Archaea rrs genes to show both these desorption methods were effective in recovering the adherent microbial biofilm with no apparent biases in microbe recovery. We also present a derivation of the "repeated bead beating and column (RBB+C) purification" method of DNA extraction that results in the recovery of high molecular weight DNA. These DNA samples can be fragmented and size fractionated by sucrose density gradient centrifugation, bypassing the use of gel-plug lysis and pulsed-field gel electrophoresis separation of DNA for metagenomic library constructions.}, }
@article {pmid20835754, year = {2011}, author = {McSweeney, NJ and Plumb, JJ and Tilbury, AL and Nyeboer, HJ and Sumich, ME and McKinnon, AJ and Franzmann, PD and Sutton, DC and Kaksonen, AH}, title = {Comparison of microbial communities in pilot-scale bioreactors treating Bayer liquor organic wastes.}, journal = {Biodegradation}, volume = {22}, number = {2}, pages = {397-407}, doi = {10.1007/s10532-010-9412-6}, pmid = {20835754}, issn = {1572-9729}, mesh = {Alphaproteobacteria/classification/genetics/metabolism ; Betaproteobacteria/classification/genetics/metabolism ; Bioreactors/*microbiology ; Denaturing Gradient Gel Electrophoresis ; Gammaproteobacteria/classification/genetics/metabolism ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Waste Disposal, Fluid/*methods ; }, abstract = {Western Australian bauxite deposits are naturally associated with high amounts of humic and fulvic materials that co-digest during Bayer processing. Sodium oxalate remains soluble and can co-precipitate with aluminium hydroxide unless it is removed. Removal of sodium oxalate requires a secondary crystallisation step followed by storage. Bioreactors treating oxalate wastes have been developed as economically and environmentally viable treatment alternatives but the microbial ecology and physiology of these treatment processes are poorly understood. Analysis of samples obtained from two pilot-scale moving bed biofilm reactors (MBBRs) and one aerobic suspended growth bioreactor (ASGB) using polymerase chain reaction- denaturing gradient gel electrophoresis of 16S rRNA genes showed that members of the α-, β- and γ-Proteobacteria subgroups were prominent in all three processes. Despite differing operating conditions, the composition of the microbial communities in the three reactors was conserved. MBBR2 was the only configuration that showed complete degradation of oxalate from the influent and the ASGB had the highest degradation rate of all three configurations. Several strains of the genus Halomonas were isolated from the bioreactors and their morphology and physiology was also determined.}, }
@article {pmid20835748, year = {2010}, author = {Bull, AT}, title = {The renaissance of continuous culture in the post-genomics age.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {37}, number = {10}, pages = {993-1021}, pmid = {20835748}, issn = {1476-5535}, mesh = {Bacteria/*growth &amp; development/metabolism ; Biomedical Research/methods/trends ; Fungi/*growth &amp; development/metabolism ; Genomics ; History, 20th Century ; History, 21st Century ; Microbiological Techniques/history/*methods/*trends ; Systems Biology/methods ; }, abstract = {The development of continuous culture techniques 60 years ago and the subsequent formulation of theory and the diversification of experimental systems revolutionised microbiology and heralded a unique period of innovative research. Then, progressively, molecular biology and thence genomics and related high-information-density omics technologies took centre stage and microbial growth physiology in general faded from educational programmes and research funding priorities alike. However, there has been a gathering appreciation over the past decade that if the claims of systems biology are going to be realised, they will have to be based on rigorously controlled and reproducible microbial and cell growth platforms. This revival of continuous culture will be long lasting because its recognition as the growth system of choice is firmly established. The purpose of this review, therefore, is to remind microbiologists, particularly those new to continuous culture approaches, of the legacy of what I call the first age of continuous culture, and to explore a selection of researches that are using these techniques in this post-genomics age. The review looks at the impact of continuous culture across a comprehensive range of microbiological research and development. The ability to establish (quasi-) steady state conditions is a frequently stated advantage of continuous cultures thereby allowing environmental parameters to be manipulated without causing concomitant changes in the specific growth rate. However, the use of continuous cultures also enables the critical study of specified transition states and chemical, physical or biological perturbations. Such dynamic analyses enhance our understanding of microbial ecology and microbial pathology for example, and offer a wider scope for innovative drug discovery; they also can inform the optimization of batch and fed-batch operations that are characterized by sequential transitions states.}, }
@article {pmid20830912, year = {2010}, author = {Ball, PN and MacKenzie, MD and DeLuca, TH and Holben, WE}, title = {Wildfire and charcoal enhance nitrification and ammonium-oxidizing bacterial abundance in dry montane forest soils.}, journal = {Journal of environmental quality}, volume = {39}, number = {4}, pages = {1243-1253}, doi = {10.2134/jeq2009.0082}, pmid = {20830912}, issn = {0047-2425}, mesh = {Bacteria/genetics/*metabolism ; Charcoal/*chemistry ; *Fires ; Nitrogen/*chemistry ; Phylogeny ; Polymerase Chain Reaction ; Quaternary Ammonium Compounds/*metabolism ; Soil Microbiology ; *Trees ; Water ; }, abstract = {All forest fire events generate some quantity of charcoal, which may persist in soils for hundreds to thousands of years. However, few studies have effectively evaluated the potential for charcoal to influence specific microbial communities or processes. To our knowledge, no studies have specifically addressed the effect of charcoal on ammonia-oxidizing bacteria (AOB) in forest soils. Controlled experiments have shown that charcoal amendment of fire-excluded temperate and boreal coniferous forest soil increases net nitrification, suggesting that charcoal plays a major role in maintaining nitrification for extended periods postfire. In this study, we examined the influence of fire history on gross nitrification, nitrification potential, and the nature and abundance of AOB. Soil cores were collected from sites in the Selway-Bitterroot wilderness area in northern Idaho that had been exposed twice (in 1910, 1934) or three times (1910, 1934, and 1992) in the last 94 yr, allowing us to contrast soils recently exposed to fire to those that experienced no recent fire (control). Charcoal content was determined in the O horizon by hand-separation and in the mineral soil by a chemical digestion procedure. Gross and net nitrification, and potential rates of nitrification were measured in mineral soil. Analysis of the AOB community was conducted using primer sets specific for the ammonia mono-oxygenase gene (amoA) or the 16S rRNA gene of AOB. Denaturing gradient gel electrophoresis was used to analyze the AOB community structure, while AOB abundance was determined by quantitative polymerase chain reaction. Recent (12-yr-old) wildfire resulted in greater charcoal contents and nitrification rates compared with sites without fire for 75 yr, and the more recent fire appeared to have directly influenced AOB abundance and community structure. We predicted and observed greater abundance of AOB in soils recently exposed to fire compared with control soils. Interestingly, sequence data revealed that Clusters 3 and 4, and not Cluster 2, of genus Nitrosospira dominated these forest soils, with a shift toward Cluster 3 in recently burned sites.}, }
@article {pmid20829292, year = {2010}, author = {Roger, LC and McCartney, AL}, title = {Longitudinal investigation of the faecal microbiota of healthy full-term infants using fluorescence in situ hybridization and denaturing gradient gel electrophoresis.}, journal = {Microbiology (Reading, England)}, volume = {156}, number = {Pt 11}, pages = {3317-3328}, doi = {10.1099/mic.0.041913-0}, pmid = {20829292}, issn = {1465-2080}, mesh = {Bacteria/genetics/growth &amp; development/*isolation &amp; purification ; Biodiversity ; Breast Feeding ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Feces/*microbiology ; Female ; Humans ; In Situ Hybridization, Fluorescence ; Infant ; Infant Formula ; Longitudinal Studies ; Male ; *Metagenome ; Principal Component Analysis ; Time Factors ; Weaning ; }, abstract = {From birth onwards, the gastrointestinal (GI) tract of infants progressively acquires a complex range of micro-organisms. It is thought that by 2 years of age the GI microbial population has stabilized. Within the developmental period of the infant GI microbiota, weaning is considered to be most critical, as the infant switches from a milk-based diet (breast and/or formula) to a variety of food components. Longitudinal analysis of the biological succession of the infant GI/faecal microbiota is lacking. In this study, faecal samples were obtained regularly from 14 infants from 1 month to 18 months of age. Seven of the infants (including a set of twins) were exclusively breast-fed and seven were exclusively formula-fed prior to weaning, with 175 and 154 faecal samples, respectively, obtained from each group. Diversity and dynamics of the infant faecal microbiota were analysed by using fluorescence in situ hybridization and denaturing gradient gel electrophoresis. Overall, the data demonstrated large inter- and intra-individual differences in the faecal microbiological profiles during the study period. However, the infant faecal microbiota merged with time towards a climax community within and between feeding groups. Data from the twins showed the highest degree of similarity both quantitatively and qualitatively. Inter-individual variation was evident within the infant faecal microbiota and its development, even within exclusively formula-fed infants receiving the same diet. These data can be of help to future clinical trials (e.g. targeted weaning products) to organize protocols and obtain a more accurate outline of the changes and dynamics of the infant GI microbiota.}, }
@article {pmid20821443, year = {2010}, author = {Pavissich, JP and Silva, M and González, B}, title = {Sulfate reduction, molecular diversity, and copper amendment effects in bacterial communities enriched from sediments exposed to copper mining residues.}, journal = {Environmental toxicology and chemistry}, volume = {29}, number = {2}, pages = {256-264}, doi = {10.1002/etc.43}, pmid = {20821443}, issn = {0730-7268}, mesh = {Bacteria/*drug effects/genetics/metabolism ; Biodegradation, Environmental ; Copper/metabolism/*toxicity ; Genetic Variation ; Geologic Sediments/*microbiology ; *Mining ; Oxidation-Reduction ; Phylogeny ; Sulfates/*metabolism ; *Water Microbiology ; }, abstract = {Sulfate-reducing bacterial communities from coastal sediments with a long-term exposure to copper (Cu)-mining residues were studied in lactate enrichments. The toxicity of excess copper may affect sulfate-reducing bacterial communities. Sulfate reduction was monitored by sulfate and organic acid measurements. Molecular diversity was analyzed by 16S rRNA, dissimilatory sulfate reduction dsrAB, and Cu translocating phospho-type adenosine triphosphatases (P-ATPases) cop-like gene sequence profiling. The influence of Cu amendment was tested in these enrichments. Results showed fast sulfate reduction mostly coupled to incomplete organic carbon oxidation and partial sulfate reduction inhibition due to copper amendment. The 16S rRNA clonal libraries analysis indicated that delta- and gamma-Proteobacteria and Cytophaga-Flexibacter-Bacteroides dominated the enrichments. The dsrAB libraries revealed the presence of Desulfobacteraceae and Desulfovibrionaceae families-related sequences. Copper produced significant shifts (i.e., a decrease in the relative abundance of sulfate-reducing microorganisms) in the enriched bacterial community structure as determined by terminal-restriction fragment length polymorphism (T-RFLP) profiling and multivariate analyses. Clonal libraries of cop-like sequences showed low richness in the enriched microbial communities, and a strong effect of copper on its relative abundance. Novel Cu-P(IB)-ATPase sequences encoding Cu resistance were detected. The present study indicates that Cu does not significantly affect sulfate reduction and genetic diversity of taxonomic and dissimilatory sulfate-reduction molecular markers. However, the diversity of Cu resistance genetic determinants was strongly modified by this toxic metal.}, }
@article {pmid20814577, year = {2010}, author = {Rincon, MT and Dassa, B and Flint, HJ and Travis, AJ and Jindou, S and Borovok, I and Lamed, R and Bayer, EA and Henrissat, B and Coutinho, PM and Antonopoulos, DA and Berg Miller, ME and White, BA}, title = {Abundance and diversity of dockerin-containing proteins in the fiber-degrading rumen bacterium, Ruminococcus flavefaciens FD-1.}, journal = {PloS one}, volume = {5}, number = {8}, pages = {e12476}, pmid = {20814577}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*classification/*metabolism ; Carbohydrate Metabolism ; Cell Cycle Proteins/chemistry/metabolism ; Chromosomal Proteins, Non-Histone/chemistry/metabolism ; Conserved Sequence ; Gene Expression Regulation, Bacterial ; Molecular Sequence Data ; Ruminococcus/genetics/*metabolism ; Cohesins ; }, abstract = {BACKGROUND: The cellulosome is a multi-enzyme machine, which plays a key role in the breakdown of plant cell walls in many anaerobic cellulose-degrading microorganisms. Ruminococcus flavefaciens FD-1, a major fiber-degrading bacterium present in the gut of herbivores, has the most intricate cellulosomal organization thus far described. Cellulosome complexes are assembled through high-affinity cohesin-dockerin interactions. More than two-hundred dockerin-containing proteins have been identified in the R. flavefaciens genome, yet the reason for the expansion of these crucial cellulosomal components is yet unknown.<br><br>We have explored the full spectrum of 222 dockerin-containing proteins potentially involved in the assembly of cellulosome-like complexes of R. flavefaciens. Bioinformatic analysis of the various dockerin modules showed distinctive conservation patterns within their two Ca(2+)-binding repeats and their flanking regions. Thus, we established the conceptual framework for six major groups of dockerin types, according to their unique sequence features. Within this framework, the modular architecture of the parent proteins, some of which are multi-functional proteins, was evaluated together with their gene expression levels. Specific dockerin types were found to be associated with selected groups of functional components, such as carbohydrate-binding modules, numerous peptidases, and/or carbohydrate-active enzymes. In addition, members of other dockerin groups were linked to structural proteins, e.g., cohesin-containing proteins, belonging to the scaffoldins.<br><br>CONCLUSIONS/SIGNIFICANCE: This report profiles the abundance and sequence diversity of the R. flavefaciens FD-1 dockerins, and provides the molecular basis for future understanding of the potential for a wide array of cohesin-dockerin specificities. Conserved differences between dockerins may be reflected in their stability, function or expression within the context of the parent protein, in response to their role in the rumen environment.}, }
@article {pmid20813520, year = {2011}, author = {Ma, J and Duong, TH and Smits, M and Verstraete, W and Carballa, M}, title = {Enhanced biomethanation of kitchen waste by different pre-treatments.}, journal = {Bioresource technology}, volume = {102}, number = {2}, pages = {592-599}, doi = {10.1016/j.biortech.2010.07.122}, pmid = {20813520}, issn = {1873-2976}, mesh = {Anaerobiosis ; Biodegradation, Environmental ; Biofuels ; Bioreactors/microbiology ; Cost-Benefit Analysis ; Hydrolysis ; Kinetics ; Methane/*metabolism ; Refuse Disposal/economics/*methods ; Sewage/*analysis ; Solubility ; Time Factors ; }, abstract = {Five different pre-treatments were investigated to enhance the solubilisation and anaerobic biodegradability of kitchen waste (KW) in thermophilic batch and continuous tests. In the batch solubilisation tests, the highest and the lowest solubilisation efficiency were achieved with the thermo-acid and the pressure-depressure pre-treatments, respectively. However, in the batch biodegradability tests, the highest cumulative biogas production was obtained with the pressure-depressure method. In the continuous tests, the best performance in terms of an acceptable biogas production efficiency of 60% and stable in-reactor CODs and VFA concentrations corresponded to the pressure-depressure reactor, followed by freeze-thaw, acid, thermo-acid, thermo and control. The maximum OLR (5 g COD L(-1) d(-1)) applied in the pressure-depressure and freeze-thaw reactors almost doubled the control reactor. From the overall analysis, the freeze-thaw pre-treatment was the most profitable process with a net potential profit of around 11.5 € ton(-1) KW.}, }
@article {pmid20811884, year = {2011}, author = {Principi, P and Villa, F and Sorlini, C and Cappitelli, F}, title = {Molecular studies of microbial community structure on stained pages of Leonardo da Vinci's Atlantic Codex.}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {214-222}, pmid = {20811884}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; *Biodiversity ; DNA, Ribosomal Spacer/genetics ; *Environmental Microbiology ; Fungi/classification/genetics/isolation &amp; purification/*physiology ; Humans ; *Library Materials ; Molecular Sequence Data ; *Paper ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In 2006, after a visual inspection of the Leonardo da Vinci's Atlantic Codex by a scholar, active molds were reported to have been present on Codex pages showing areas of staining. In the present paper, molecular methods were used to assess the current microbiological risk to stained pages of the manuscript. Bacterial and fungal communities were sampled by a non-invasive technique employing nitrocellulose membranes. Denaturing gradient gel electrophoresis of 16 S rRNA gene and internal transcribed space regions were carried out to study the structure of the bacterial and fungal communities and band patterns were analyzed by the multivariate technique of principal component analysis. Any relationship between the presence of an active microbial community and staining was excluded. The presence of potential biodeteriogens was evaluated by constructing bacterial and fungal clone libraries, analyzing them by an operational taxonomic unit (OTU) approach. Among the bacteria, some OTUs were associated with species found on floors in clean room while others were identified with human skin contamination. Some fungal OTU representatives were potential biodeteriogens that, under proper thermo-hygrometric conditions, could grow. The retrieval of these potential biodeteriogens and microorganisms related to human skin suggests the need for a continuous and rigorous monitoring of the environmental conditions, and the need to improve handling procedures.}, }
@article {pmid20811804, year = {2011}, author = {Szczepaniak, S and Polanska, M and Van Assche, A and Moloney, R and Willems, KA}, title = {The synergism of natural compounds in the pursuit of safe and healthier food.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {38}, number = {1}, pages = {215-220}, pmid = {20811804}, issn = {1476-5535}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Biological Products/*pharmacology ; Brochothrix/drug effects/growth &amp; development ; Fatty Acids/pharmacology ; *Food Microbiology ; Food Packaging/methods ; Food Preservation/*methods ; Lactobacillus/drug effects/growth &amp; development ; Meat/microbiology ; Plant Extracts/*pharmacology ; Swine ; Terpenes/pharmacology ; Vacuum ; }, abstract = {Food producers apply modern processing techniques and use a variety of preservative additives to guarantee safe food and a longer shelflife. Regrettably many of these impact the sensory characteristics of the foodstuffs, such as colour, texture, and flavour, which can result in low consumer acceptance. Additionally, strategies used to reduce growth of spoilage and pathogenic bacteria are not selective enough and may inactivate also desired microbiota. Food is usually overdosed with antimicrobials that are supplemented 'just in case.' Consequently, food producers are searching for natural preservation methods that are not harmful to humans. Nature offers a wide spectrum of biologically active (phyto) chemicals that can be used as potential natural preservatives. Compounds with bacterial growth-limiting properties are detected in all parts of plants, including their leaves, flowers, fruits, roots, etc. These are mostly acids, alcohols, medium and long-chain organic acids, terpenic compounds, and their derivatives. This study focused on the effectiveness of plant extracts, i.e., synergism between terpenoids and medium chain fatty acids in cured cooked meat. Bacterial strains that were tested include typical members of the spoilage microflora in vacuum (Lactobacillus curvatus) and MA-packed meats (Brochothrix thermosphacta). These were isolated and identified in a separate study. L. curvatus was observed to be very resistant against either terpenoids or fatty acids when used separately, whereas its growth was strongly inhibited when both chemicals were combined. Growth of B. thermosphacta was significantly inhibited when antimicrobial compounds were solely applied, whereas a blend of terpenoids and fatty acids showed an almost bactericidal effect.}, }
@article {pmid20811742, year = {2011}, author = {Omirou, M and Rousidou, C and Bekris, F and Papadopoulou, KK and Menkissoglou-Spiroudi, U and Ehaliotis, C and Karpouzas, DG}, title = {The impact of biofumigation and chemical fumigation methods on the structure and function of the soil microbial community.}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {201-213}, pmid = {20811742}, issn = {1432-184X}, mesh = {Bacteria/classification/*drug effects/*metabolism ; Brassica/chemistry ; Esters/analysis ; Fatty Acids/analysis ; Fluoresceins/analysis/metabolism ; *Fumigation ; Fungi/*drug effects/genetics/*metabolism ; Molecular Sequence Data ; Pesticides/*pharmacology ; Phospholipids/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/analysis/chemistry ; *Soil Microbiology ; }, abstract = {Biofumigation (BIOF) is carried out mainly by the incorporation of brassica plant parts into the soil, and this fumigation activity has been linked to their high glucosinolate (GSL) content. GSLs are hydrolyzed by the endogenous enzyme myrosinase to release isothiocyanates (ITCs). A microcosm study was conducted to investigate the effects induced on the soil microbial community by the incorporation of broccoli residues into soil either with (BM) or without (B) added myrosinase and of chemical fumigation, either as soil application of 2-phenylethyl ITC (PITC) or metham sodium (MS). Soil microbial activity was evaluated by measuring fluorescein diacetate hydrolysis and soil respiration. Effects on the structure of the total microbial community were assessed by phospholipid fatty acid analysis, while the impact on important fungal (ascomycetes (ASC)) and bacterial (ammonia-oxidizing bacteria (AOB)) guilds was evaluated by denaturating gradient gel electrophoresis (DGGE). Overall, B, and to a lesser extent BM, stimulated microbial activity and biomass. The diminished effect of BM compared to B was particularly evident in fungi and Gram-negative bacteria and was attributed to rapid ITC release following the myrosinase treatment. PITC did not have a significant effect, whereas an inhibitory effect was observed in the MS-treated soil. DGGE analysis showed that the ASC community was temporarily altered by BIOF treatments and more persistently by the MS treatment, while the structure of the AOB community was not affected by the treatments. Cloning of the ASC community showed that MS application had a deleterious effect on potential plant pathogens like Fusarium, Nectria, and Cladosporium compared to BIOF treatments which did not appear to inhibit them. Our findings indicate that BIOF induces changes on the structure and function of the soil microbial community that are mostly related to microbial substrate availability changes derived from the soil amendment with fresh organic materials.}, }
@article {pmid20809326, year = {2010}, author = {Zwirglmaier, K}, title = {Detection of prokaryotic cells with fluorescence in situ hybridization.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {659}, number = {}, pages = {349-362}, doi = {10.1007/978-1-60761-789-1_27}, pmid = {20809326}, issn = {1940-6029}, mesh = {In Situ Hybridization, Fluorescence/*methods ; Oligonucleotide Probes/genetics/metabolism ; Prokaryotic Cells/*cytology/metabolism ; }, abstract = {Fluorescence in situ hybridization with rRNA targeted oligonucleotide probes is nowadays one of the core techniques in microbial ecology, allowing the identification and quantification of microbial cells in environmental samples in situ. Next to the classic FISH protocol, which uses fluorescently monolabelled probes, the more sensitive CARD-FISH (also known as TSA-FISH), which involves an enzyme catalyzed signal amplification step, is becoming increasingly popular. This chapter describes protocols for both methods. While classic FISH has the advantage of being relatively cheap and easy to do on morphologically diverse samples, CARD-FISH offers a significantly higher sensitivity, allowing the detection of slow growing or metabolically inactive cells, which are below the detection limit of classic FISH. The drawback here is the considerably higher price for the probes and advanced cell fixation and permeabilization requirements that have to be optimized for different target cells.}, }
@article {pmid20809289, year = {2011}, author = {Fontes, ML and Suzuki, MT and Cottrell, MT and Abreu, PC}, title = {Primary production in a subtropical stratified coastal lagoon--contribution of anoxygenic phototrophic bacteria.}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {223-237}, pmid = {20809289}, issn = {1432-184X}, mesh = {Bacteria/classification/isolation &amp; purification/*metabolism ; Bacteria, Anaerobic/classification/isolation &amp; purification/*metabolism ; Bacterial Load ; Bacteriochlorophyll A/analysis ; Biomass ; Brazil ; Chlorophyll/analysis ; Cluster Analysis ; *Ecosystem ; Oxygen/*metabolism ; Photosynthesis/*physiology ; Plankton/metabolism ; Principal Component Analysis ; Seasons ; Seawater/chemistry ; *Water Microbiology ; }, abstract = {Anaerobic anoxygenic phototrophic bacteria can be found in the suboxic waters of shallow stratified coastal systems, and may play important roles in the total primary production of subtropical stratified coastal lagoons. We investigated the spatiotemporal variability of light CO(2) fixation and net oxygen production in the stratified Conceição Lagoon (Brazil) in summer and fall of 2007, as well as the contribution of bacteriochlorophyll a (BChl a)-containing bacteria to photosynthetically driven electron transfer. Both chlorophyll a (Chl a) and BChl a varied in space, while only BChl a varied in time (three-fold increase from summer to fall). In summer, net oxygen production and light CO(2) fixation were correlated, with both having higher rates with higher Chl a concentrations in the enclosed region of the lagoon. In fall, CO(2) fixation was decoupled from oxygen production. Denaturing gradient gel electrophoresis revealed that bacterial communities of oxic site 12 and suboxic site 33 formed one cluster, different from other oxic samples within the lagoon. In addition, BChl a/Chl a ratios at these sites were high, 40% and 45%, respectively. Light acted as the main factor controlling the BChl a concentration and CO(2) fixation rates. High turbidity within the enclosed area of the lagoon explained high BChl a and decoupling between CO(2) fixation and oxygen production in oxygenated waters. Contribution of purple sulfur bacteria to total bacterial density in suboxic waters was 1.2%, and their biomass contributed to a much higher percentage (12.2%) due to their large biovolume. Our results indicate a significant contribution of anaerobic anoxygenic bacteria to the primary production of the "dead zone" of Conceição Lagoon.}, }
@article {pmid20809288, year = {2011}, author = {Jackson, CR and Denney, WC}, title = {Annual and seasonal variation in the phyllosphere bacterial community associated with leaves of the southern Magnolia (Magnolia grandiflora).}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {113-122}, pmid = {20809288}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics ; *Bacterial Physiological Phenomena ; Biodiversity ; Gene Library ; Magnolia/*microbiology ; Molecular Sequence Data ; Phylogeny ; Plant Leaves/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Seasons ; }, abstract = {The phyllosphere contains a diverse bacterial community that can be intimately associated with the host plant; however, few studies have examined how the phyllosphere community changes over time. We sampled replicate leaves from a single magnolia (Magnolia grandiflora) tree in the winter of three consecutive years (2007-2009) as well as during four seasons of 1 year (2008) and used molecular techniques to examine seasonal and year-to-year variation in bacterial community structure. Multivariate analysis of denaturing gradient gel electrophoresis profiles of 16S rRNA gene fragments revealed minimal leaf to leaf variation and much greater temporal changes, with the summer (August 2008) leaf community being most distinct from the other seasons. This was confirmed by sequencing and analysis of 16S rRNA gene clone libraries generated for each sample date. All phyllosphere communities were dominated by Alphaproteobacteria, with a reduction in the representation of certain Beijerinckiaceae during the summer and a concurrent increase in the Methylobacteriaceae being the most significant seasonal change. Other important components of the magnolia phyllosphere included members of the Bacteroidetes, Acidobacteria, and Actinobacteria, with the latter two lineages also showing differences in their representation in samples collected at different times. While the leaf-associated bacterial community sampled at the same time of year in three separate years showed some similarities, generally these communities were distinct, suggesting that while there are seasonal patterns, these may not be predictable from year to year. These results suggest that seasonal differences do occur in phyllosphere communities and that broad-leafed evergreen trees such as M. grandiflora may present interesting systems to study these changes in the context of changing environmental conditions.}, }
@article {pmid20806270, year = {2010}, author = {Kurland, CG}, title = {The RNA dreamtime: modern cells feature proteins that might have supported a prebiotic polypeptide world but nothing indicates that RNA world ever was.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {32}, number = {10}, pages = {866-871}, doi = {10.1002/bies.201000058}, pmid = {20806270}, issn = {1521-1878}, mesh = {Amino Acids/metabolism ; Peptides/*metabolism ; *Protein Biosynthesis ; Proteins/*metabolism ; RNA/*metabolism ; Ribonucleoproteins/metabolism ; }, abstract = {Modern cells present no signs of a putative prebiotic RNA world. However, RNA coding is not a sine qua non for the accumulation of catalytic polypeptides. Thus, cellular proteins spontaneously fold into active structures that are resistant to proteolysis. The law of mass action suggests that binding domains are stabilized by specific interactions with their substrates. Random polypeptide synthesis in a prebiotic world has the potential to initially produce only a very small fraction of polypeptides that can fold spontaneously into catalytic domains. However, that fraction can be enriched by proteolytic activities that destroy the unfolded polypeptides and regenerate amino acids that can be recycled into polypeptides. In this open system scenario the stable domains that accumulate and the chemical environment in which they are accumulated are linked through self coding of polypeptide structure. Such open polypeptide systems may have been the precursors to the cellular ribonucleoprotein (RNP) world that evolved subsequently.}, }
@article {pmid20802065, year = {2010}, author = {Llirós, M and Gich, F and Plasencia, A and Auguet, JC and Darchambeau, F and Casamayor, EO and Descy, JP and Borrego, C}, title = {Vertical distribution of ammonia-oxidizing crenarchaeota and methanogens in the epipelagic waters of Lake Kivu (Rwanda-Democratic Republic of the Congo).}, journal = {Applied and environmental microbiology}, volume = {76}, number = {20}, pages = {6853-6863}, pmid = {20802065}, issn = {1098-5336}, mesh = {Ammonia/*metabolism ; Animals ; *Biodiversity ; Cluster Analysis ; Crenarchaeota/*classification/genetics/isolation &amp; purification/*metabolism ; DNA Fingerprinting ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Democratic Republic of the Congo ; Electrophoresis, Polyacrylamide Gel ; Genes, rRNA ; In Situ Hybridization, Fluorescence ; Methane/*metabolism ; Molecular Sequence Data ; Nucleic Acid Denaturation ; Oxidation-Reduction ; Phylogeny ; Polymerase Chain Reaction ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; *Water Microbiology ; }, abstract = {Four stratified basins in Lake Kivu (Rwanda-Democratic Republic of the Congo) were sampled in March 2007 to investigate the abundance, distribution, and potential biogeochemical role of planktonic archaea. We used fluorescence in situ hybridization with catalyzed-reported deposition microscopic counts (CARD-FISH), denaturing gradient gel electrophoresis (DGGE) fingerprinting, and quantitative PCR (qPCR) of signature genes for ammonia-oxidizing archaea (16S rRNA for marine Crenarchaeota group 1.1a [MCG1] and ammonia monooxygenase subunit A [amoA]). Abundance of archaea ranged from 1 to 4.5% of total DAPI (4',6-diamidino-2-phenylindole) counts with maximal concentrations at the oxic-anoxic transition zone (∼50-m depth). Phylogenetic analysis of the archaeal planktonic community revealed a higher level of richness of crenarchaeal 16S rRNA gene sequences (21 of the 28 operational taxonomic units [OTUs] identified [75%]) over euryarchaeotal ones (7 OTUs). Sequences affiliated with the kingdom Euryarchaeota were mainly recovered from the anoxic water compartment and mostly grouped into methanogenic lineages (Methanosarcinales and Methanocellales). In turn, crenarchaeal phylotypes were recovered throughout the sampled epipelagic waters (0- to 100-m depth), with clear phylogenetic segregation along the transition from oxic to anoxic water masses. Thus, whereas in the anoxic hypolimnion crenarchaeotal OTUs were mainly assigned to the miscellaneous crenarchaeotic group, the OTUs from the oxic-anoxic transition and above belonged to Crenarchaeota groups 1.1a and 1.1b, two lineages containing most of the ammonia-oxidizing representatives known so far. The concomitant vertical distribution of both nitrite and nitrate maxima and the copy numbers of both MCG1 16S rRNA and amoA genes suggest the potential implication of Crenarchaeota in nitrification processes occurring in the epilimnetic waters of the lake.}, }
@article {pmid20801480, year = {2010}, author = {Carvalho, G and Marques, R and Lopes, AR and Faria, C and Noronha, JP and Oehmen, A and Nunes, OC and Reis, MA}, title = {Biological treatment of propanil and 3,4-dichloroaniline: kinetic and microbiological characterisation.}, journal = {Water research}, volume = {44}, number = {17}, pages = {4980-4991}, doi = {10.1016/j.watres.2010.08.006}, pmid = {20801480}, issn = {1879-2448}, mesh = {Aniline Compounds/*isolation &amp; purification ; Bacteria/genetics/growth &amp; development/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Biomass ; Bioreactors/microbiology ; Denaturing Gradient Gel Electrophoresis ; Kinetics ; Phylogeny ; Principal Component Analysis ; Propanil/*isolation &amp; purification ; }, abstract = {Propanil (3,4-dichloropropionanilide) is a widely used herbicide, applied worldwide in rice paddies. Propanil is primarily transformed in nature to 3,4-dichloroaniline (DCA), which is more slowly biodegradable. Both compounds have adverse health and ecotoxicity effects. This work investigated the microbial ecology and kinetics of propanil-degrading enrichments obtained from soil in a sequencing batch reactor (SBR) operated with different feeding strategies, aiming at the enhanced biological removal of propanil and DCA from contaminated waters. During SBR operation with a dump feeding strategy, a high propanil concentration led to DCA accumulation, which was only fully degraded after 5 days, likely due to DCA inhibition. For this reason, the operational mode was changed to fed-batch operation with lower initial propanil concentrations, which resulted in faster propanil and DCA biodegradation. Thus a fed-batch operation seems more appropriate for the acclimatisation of an effective propanil- and DCA-degrading population. The changes in performance were accompanied by a shift in the microbial population structure, as determined by DGGE of the 16S rRNA gene, particularly after a feed of DCA as the sole carbon source. Isolates obtained from the acclimatised population included members of the genera Enterococcus and Rhodococcus, as well as Brevundimonas, which displayed >90% propanil biodegradation efficiency.}, }
@article {pmid20740282, year = {2010}, author = {Li, H and Chen, S and Mu, BZ and Gu, JD}, title = {Molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in high-temperature petroleum reservoirs.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {771-783}, pmid = {20740282}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification/*metabolism ; Biodiversity ; DNA, Bacterial/genetics ; Hot Temperature ; Molecular Sequence Data ; Petroleum/*microbiology ; Phylogeny ; Quaternary Ammonium Compounds/*metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Anaerobic ammonium-oxidizing (anammox) process plays an important role in the nitrogen cycle of the worldwide anoxic and mesophilic habitats. Recently, the existence and activity of anammox bacteria have been detected in some thermophilic environments, but their existence in the geothermal subterranean oil reservoirs is still not reported. This study investigated the abundance, distribution and functional diversity of anammox bacteria in nine out of 17 high-temperature oil reservoirs by molecular ecology analysis. High concentration (5.31-39.2 mg l(-1)) of ammonium was detected in the production water from these oilfields with temperatures between 55°C and 75°C. Both 16S rRNA and hzo molecular biomarkers indicated the occurrence of anammox bacteria in nine out of 17 samples. Most of 16S rRNA gene phylotypes are closely related to the known anammox bacterial genera Candidatus Brocadia, Candidatus Kuenenia, Candidatus Scalindua, and Candidatus Jettenia, while hzo gene phylotypes are closely related to the genera Candidatus Anammoxoglobus, Candidatus Kuenenia, Candidatus Scalindua, and Candidatus Jettenia. The total bacterial and anammox bacterial densities were 6.4 ± 0.5 × 10(3) to 2.0 ± 0.18 × 10(6) cells ml(-1) and 6.6 ± 0.51 × 10(2) to 4.9 ± 0.36 × 10(4) cell ml(-1), respectively. The cluster I of 16S rRNA gene sequences showed distant identity (<92%) to the known Candidatus Scalindua species, inferring this cluster of anammox bacteria to be a new species, and a tentative name Candidatus "Scalindua sinooilfield" was proposed. The results extended the existence of anammox bacteria to the high-temperature oil reservoirs.}, }
@article {pmid20740281, year = {2011}, author = {Paziewska, A and Harris, PD and Zwolińska, L and Bajer, A and Siński, E}, title = {Recombination within and between species of the alpha proteobacterium Bartonella infecting rodents.}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {134-145}, pmid = {20740281}, issn = {1432-184X}, mesh = {Animals ; Bartonella/classification/*genetics/isolation &amp; purification ; Bartonella Infections/*microbiology ; Ecosystem ; Genes, Bacterial/genetics ; Genome, Bacterial/genetics ; Haplotypes ; Host-Pathogen Interactions ; Mice ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Recombination, Genetic/*genetics ; Rodent Diseases/*microbiology ; Rodentia/genetics/microbiology ; }, abstract = {Bartonella infections from wild mice and voles (Apodemus flavicollis, Mi. oeconomus, Microtus arvalis and Myodes glareolus) were sampled from a forest and old-field habitats of eastern Poland; a complex network of Bartonella isolates, referrable to B. taylorii, B. grahamii, B. birtlesii and B. doshiae, was identified by the sequencing of a gltA fragment, comparable to previous studies of Bartonella diversity in rodents. Nested clade analysis showed that isolates could be assigned to zero- and one-step clades which correlated with host identity and were probably the result of clonal expansion; however, sequencing of other housekeeping genes (rpoB, ribC, ftsZ, groEl) and the 16S RNA gene revealed a more complex situation with clear evidence of numerous recombinant events in which one or both Bartonella parents could be identified. Recombination within gltA was found to have generated two distinct variant clades, one a hybrid between B. taylorii and B. doshiae, the other between B. taylorii and B. grahamii. These recombinant events characterised the differences between the two-step and higher clades within the total nested cladogram, involved all four species of Bartonella identified in this work and appear to have played a dominant role in the evolution of Bartonella diversity. It is clear, therefore, that housekeeping gene phylogenies are not robust indicators of Bartonella diversity, especially when only a single gene (gltA or 16S RNA) is used. Bartonella clades infecting Microtus were most frequently involved in recombination and were most frequently tip clades within the cladogram. The role of Microtus in influencing the frequency of Bartonella recombination remains unknown.}, }
@article {pmid20738397, year = {2010}, author = {Cattaneo, R and Rouviere, C and Rassoulzadegan, F and Weinbauer, MG}, title = {Association of marine viral and bacterial communities with reference black carbon particles under experimental conditions: an analysis with scanning electron, epifluorescence and confocal laser scanning microscopy.}, journal = {FEMS microbiology ecology}, volume = {74}, number = {2}, pages = {382-396}, doi = {10.1111/j.1574-6941.2010.00953.x}, pmid = {20738397}, issn = {1574-6941}, mesh = {Bacteria/genetics/*growth &amp; development ; Carbon/*chemistry ; Microscopy, Confocal ; Microscopy, Electron, Scanning ; Microscopy, Fluorescence ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Viruses/genetics/*growth &amp; development ; Water Microbiology ; }, abstract = {Black carbon (BC), the product of incomplete combustion of fossil fuels and biomass, constitutes a significant fraction of the marine organic carbon pool. However, little is known about the possible interactions of BC and marine microorganisms. Here, we report the results of experiments using a standard reference BC material in high concentrations to investigate basic principles of the dynamics of natural bacterial and viral communities with BC particles. We assessed the attachment of viral and bacterial communities using scanning electron, epifluorescence and confocal laser scanning microscopy and shifts in bacterial community composition using 16S rRNA gene denaturing gradient gel electrophoresis (DGGE). In 24-h time-course experiments, BC particles showed a strong potential for absorbing viruses and bacteria. Total viral abundance was reduced, whereas total bacterial abundance was stimulated in the BC treatments. Viral and bacterial abundance on BC particles increased with particle size, whereas the abundances of BC-associated viruses and bacteria per square micrometer surface area decreased significantly with BC particle size. DGGE results suggested that BC has the potential to change bacterial community structure and favour phylotypes related to Glaciecola sp. Our study indicates that BC could influence processes mediated by bacteria and viruses in marine ecosystems.}, }
@article {pmid20734040, year = {2011}, author = {Durbán, A and Abellán, JJ and Jiménez-Hernández, N and Ponce, M and Ponce, J and Sala, T and D'Auria, G and Latorre, A and Moya, A}, title = {Assessing gut microbial diversity from feces and rectal mucosa.}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {123-133}, pmid = {20734040}, issn = {1432-184X}, mesh = {Adult ; Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; Feces/*microbiology ; Female ; Humans ; Intestinal Mucosa/*microbiology ; Male ; Middle Aged ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rectum/*microbiology ; }, abstract = {Gut microbiota is the most complex bacterial community in the human body and its study may give important clues to the etiology of different intestinal diseases. Most studies carried out so far have used fecal samples, assuming that these samples have a similar distribution to the communities present throughout the colon. The present study was designed to test this assumption by comparing samples from the rectal mucosa and feces of nine healthy volunteers by sequencing libraries of 16S rRNA genes. At the family taxonomic level, where rarefaction curves indicate that the observed number of taxa is close to the expected one, we observe under different statistical analyses that fecal and mucosal samples cluster separately. The same is found at the level of species considering phylogenetic information. Consequently, it cannot be stated that both samples from a given individual are of similar composition. We believe that the evidence in support of this statement is strong and that it would not change by increasing the number of individuals and/or performing massive sequencing. We do not expect clinicians to stop using feces for research, but we think it is important to caution them on their potential lack of representativeness with respect to the bacterial biofilm on the rectal mucosa.}, }
@article {pmid20731699, year = {2011}, author = {Habicht, KS and Miller, M and Cox, RP and Frigaard, NU and Tonolla, M and Peduzzi, S and Falkenby, LG and Andersen, JS}, title = {Comparative proteomics and activity of a green sulfur bacterium through the water column of Lake Cadagno, Switzerland.}, journal = {Environmental microbiology}, volume = {13}, number = {1}, pages = {203-215}, doi = {10.1111/j.1462-2920.2010.02321.x}, pmid = {20731699}, issn = {1462-2920}, mesh = {Biomass ; Carbon/metabolism ; Carbon Dioxide/metabolism ; Chlorobium/isolation &amp; purification/*metabolism ; Fresh Water/chemistry/microbiology ; Nitrogen/metabolism ; Photosynthesis ; Proteome/*metabolism ; Seasons ; Sulfates/metabolism ; Switzerland ; *Water Microbiology ; }, abstract = {Primary production in the meromictic Lake Cadagno, Switzerland, is dominated by anoxygenic photosynthesis. The green sulfur bacterium Chlorobium clathratiforme is the dominant phototrophic organism in the lake, comprising more than half of the bacterial population, and its biomass increases 3.8-fold over the summer. Cells from four positions in the water column were used for comparative analysis of the Chl. clathratiforme proteome in order to investigate changes in protein composition in response to the chemical and physical gradient in their environment, with special focus on how the bacteria survive in the dark. Although metagenomic data are not available for Lake Cadagno, proteome analysis was possible based on the completely sequenced genome of an isolated strain of Chl. clathratiforme. Using LC-MS/MS we identified 1321 Chl. clathratiforme proteins in Lake Cadagno and quantitatively compared 621 of these in the four samples. Our results showed that compared with cells obtained from the photic zone, cells collected from the dark part of the water column had the same expression level of key enzymes involved in carbon metabolism and photosynthetic light harvesting. However, most proteins participating in nitrogen and sulfur metabolism were twofold less abundant in the dark. From the proteome analysis we were able to show that Chl. clathratiforme in the photic zone contains enzymes for fixation of N(2) and the complete oxidation of sulfide to sulfate while these processes are probably not active in the dark. Instead we propose that Chl. clathratiforme cells in the dark part of the water column obtain energy for maintenance from the fermentation of polyglucose. Based on the observed protein compositions we have constructed possible pathways for C, N and S metabolism in Chl. clathratiforme.}, }
@article {pmid20729323, year = {2010}, author = {Kielak, AM and van Veen, JA and Kowalchuk, GA}, title = {Comparative analysis of acidobacterial genomic fragments from terrestrial and aquatic metagenomic libraries, with emphasis on acidobacteria subdivision 6.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {20}, pages = {6769-6777}, pmid = {20729323}, issn = {1098-5336}, mesh = {Bacteria/*classification/*genetics ; Base Composition ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, Bacterial ; *Metagenome ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Recombination, Genetic ; Sequence Analysis, DNA ; *Soil Microbiology ; Synteny ; *Water Microbiology ; }, abstract = {The bacterial phylum Acidobacteria has a widespread distribution and is one of the most common and diverse phyla in soil habitats. However, members of this phylum have often been recalcitrant to cultivation methods, hampering the study of this presumably important bacterial group. In this study, we used a cultivation-independent metagenomic approach to recover genomic information from soilborne members of this phylum. A soil metagenomic fosmid library was screened by PCR targeting acidobacterial 16S rRNA genes, facilitating the recovery of 17 positive clones. Recovered inserts appeared to originate from a range of Acidobacteria subdivisions, with dominance of subdivision 6 (10 clones). Upon full-length insert sequencing, gene annotation identified a total of 350 open reading frames (ORFs), representing a broad range of functions. Remarkably, six inserts from subdivision 6 contained a region of gene synteny, containing genes involved in purine de novo biosynthesis and encoding tRNA synthetase and conserved hypothetical proteins. Similar genomic regions had previously been observed in several environmental clones recovered from soil and marine sediments, facilitating comparisons with respect to gene organization and evolution. Comparative analyses revealed a general dichotomy between marine and terrestrial genes in both phylogeny and G+C content. Although the significance of this homologous gene cluster across subdivision 6 members is not known, it appears to be a common feature within a large percentage of all acidobacterial genomic fragments recovered from both of these environments.}, }
@article {pmid20729318, year = {2010}, author = {Cardenas, E and Wu, WM and Leigh, MB and Carley, J and Carroll, S and Gentry, T and Luo, J and Watson, D and Gu, B and Ginder-Vogel, M and Kitanidis, PK and Jardine, PM and Zhou, J and Criddle, CS and Marsh, TL and Tiedje, JM}, title = {Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {20}, pages = {6778-6786}, pmid = {20729318}, issn = {1098-5336}, mesh = {Bacteria/*classification/*genetics/metabolism ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil Pollutants, Radioactive/metabolism ; Sulfates/*metabolism ; Tennessee ; Uranium/*metabolism ; }, abstract = {Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared.}, }
@article {pmid20729307, year = {2011}, author = {Peduzzi, S and Welsh, A and Demarta, A and Decristophoris, P and Peduzzi, R and Hahn, D and Tonolla, M}, title = {Thiocystis chemoclinalis sp. nov. and Thiocystis cadagnonensis sp. nov., motile purple sulfur bacteria isolated from the chemocline of a meromictic lake.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {61}, number = {Pt 7}, pages = {1682-1687}, doi = {10.1099/ijs.0.010397-0}, pmid = {20729307}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; Chromatiaceae/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Lakes/*microbiology ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Phylogeny ; Pigments, Biological/chemistry ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Switzerland ; Water Microbiology ; }, abstract = {Two isolates, designated CadH11(T) and Cad448(T), representing uncultured purple sulfur bacterial populations H and 448, respectively, in the chemocline of Lake Cadagno, a crenogenic meromictic lake in Switzerland, were obtained using enrichment and isolation conditions that resembled those used for cultured members of the genus Thiocystis. Phenotypic, genotypic and phylogenetic analyses of these isolates confirmed their assignment to the genus Thiocystis. However, 16S rRNA gene sequence similarities of 98.2 % between CadH11(T) and Cad448(T), and similarities of 97.7 and 98.5 %, respectively, with their closest cultured relative Thiocystis gelatinosa DSM 215(T), as well as differences in DNA G+C content and carbon source utilization suggested that the isolates belonged to two distinct species. DNA-DNA hybridization of CadH11(T) and Cad448(T) with T. gelatinosa DSM 215(T) showed relatedness values of 46.4 and 60.8 %, respectively; the relatedness value between CadH11(T) and Cad448(T) was 59.2 %. Based on this evidence, strains CadH11(T) and Cad448(T) represent two novel species within the genus Thiocystis, for which the names Thiocystis chemoclinalis sp. nov. and Thiocystis cadagnonensis sp. nov. are proposed, respectively. The type strains of T. chemoclinalis sp. nov. and T. cadagnonensis sp. nov. are CadH11(T) (= JCM 15112(T) = KCTC 5954(T)) and Cad448(T) (= JCM 15111(T) = KCTC 15001(T)), respectively.}, }
@article {pmid20729286, year = {2010}, author = {Callaway, TR and Dowd, SE and Edrington, TS and Anderson, RC and Krueger, N and Bauer, N and Kononoff, PJ and Nisbet, DJ}, title = {Evaluation of bacterial diversity in the rumen and feces of cattle fed different levels of dried distillers grains plus solubles using bacterial tag-encoded FLX amplicon pyrosequencing.}, journal = {Journal of animal science}, volume = {88}, number = {12}, pages = {3977-3983}, doi = {10.2527/jas.2010-2900}, pmid = {20729286}, issn = {1525-3163}, mesh = {Animal Feed/*analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Bacteria/*classification/genetics ; Cattle ; DNA, Bacterial/genetics ; Diet/*veterinary ; Edible Grain/chemistry ; Feces/*microbiology ; Rumen/*microbiology ; }, abstract = {Dietary components and changes cause shifts in the gastrointestinal microbial ecology that can play a role in animal health and productivity. However, most information about the microbial populations in the gut of livestock species has not been quantitative. In the present study, we utilized a new molecular method, bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) that can perform diversity analyses of gastrointestinal bacterial populations. In the present study, cattle (n = 6) were fed a basal feedlot diet and were subsequently randomly assigned to 1 of 3 diets (n = 2 cows per diet). In each diet, 0, 25, or 50% of the concentrate portion of the ration was replaced with dried distillers grain (DDGS). Ruminal and fecal bacterial populations were different when animals were fed DDGS compared with controls; ruminal and fecal Firmicute:Bacteroidetes ratios were smaller (P = 0.07) in the 25 and 50% DDG diets compared with controls. Ruminal pH was decreased (P < 0.05) in ruminal fluid from cattle fed diets containing 50% compared with 0% DDGS. Using bTEFAP, the normal microbiota of cattle were examined using modern molecular methods to understand how diets affect gastrointestinal ecology and the gastrointestinal contribution of the microbiome to animal health and production.}, }
@article {pmid20726519, year = {2010}, author = {Gross, G and Jacobs, DM and Peters, S and Possemiers, S and van Duynhoven, J and Vaughan, EE and van de Wiele, T}, title = {In vitro bioconversion of polyphenols from black tea and red wine/grape juice by human intestinal microbiota displays strong interindividual variability.}, journal = {Journal of agricultural and food chemistry}, volume = {58}, number = {18}, pages = {10236-10246}, doi = {10.1021/jf101475m}, pmid = {20726519}, issn = {1520-5118}, mesh = {Adult ; Beverages/*analysis ; Feces/microbiology ; Female ; *Fermentation ; Flavonoids/chemistry/*metabolism ; Fruit/*chemistry ; Humans ; Kinetics ; Male ; Phenols/chemistry/*metabolism ; Polyphenols ; Reproducibility of Results ; Tea/*chemistry ; Vitis/*chemistry ; Wine/*analysis ; }, abstract = {Dietary polyphenols in tea and wine have been associated with beneficial health effects. After ingestion, most polyphenols are metabolized by the colonic microbiota. The current study aimed at exploring the interindividual variation of gut microbial polyphenol bioconversion from 10 healthy human subjects. In vitro fecal batch fermentations simulating conditions in the distal colon were performed using polyphenols from black tea and a mixture of red wine and grape juice. Microbial bioconversion was monitored by NMR- and GC-MS-based profiling of diverse metabolites and phenolics. The complex polyphenol mixtures were degraded to a limited number of key metabolites. Each subject displayed a specific metabolite profile differing in composition and time courses as well as levels of these metabolites. Moreover, clear differences depending on the polyphenol sources were observed. In conclusion, varying metabolite pathways among individuals result in different metabolome profiles and therefore related health effects are hypothesized to differ between subjects.}, }
@article {pmid20725722, year = {2010}, author = {Porat, I and Vishnivetskaya, TA and Mosher, JJ and Brandt, CC and Yang, ZK and Brooks, SC and Liang, L and Drake, MM and Podar, M and Brown, SD and Palumbo, AV}, title = {Characterization of archaeal community in contaminated and uncontaminated surface stream sediments.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {784-795}, pmid = {20725722}, issn = {1432-184X}, mesh = {Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Biodiversity ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Geologic Sediments/*microbiology ; Mercury/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Uranium/metabolism ; Water Pollutants, Chemical/metabolism ; }, abstract = {Archaeal communities from mercury and uranium-contaminated freshwater stream sediments were characterized and compared to archaeal communities present in an uncontaminated stream located in the vicinity of Oak Ridge, TN, USA. The distribution of the Archaea was determined by pyrosequencing analysis of the V4 region of 16S rRNA amplified from 12 streambed surface sediments. Crenarchaeota comprised 76% of the 1,670 archaeal sequences and the remaining 24% were from Euryarchaeota. Phylogenetic analysis further classified the Crenarchaeota as a Freshwater Group, Miscellaneous Crenarchaeota group, Group I3, Rice Cluster VI and IV, Marine Group I and Marine Benthic Group B; and the Euryarchaeota into Methanomicrobiales, Methanosarcinales, Methanobacteriales, Rice Cluster III, Marine Benthic Group D, Deep Sea Hydrothermal Vent Euryarchaeota 1 and Eury 5. All groups were previously described. Both hydrogen- and acetate-dependent methanogens were found in all samples. Most of the groups (with 60% of the sequences) described in this study were not similar to any cultivated isolates, making it difficult to discern their function in the freshwater microbial community. A significant decrease in the number of sequences, as well as in the diversity of archaeal communities was found in the contaminated sites. The Marine Group I, including the ammonia oxidizer Nitrosopumilus maritimus, was the dominant group in both mercury and uranium/nitrate-contaminated sites. The uranium-contaminated site also contained a high concentration of nitrate, thus Marine Group I may play a role in nitrogen cycle.}, }
@article {pmid20724384, year = {2010}, author = {Kemperman, RA and Bolca, S and Roger, LC and Vaughan, EE}, title = {Novel approaches for analysing gut microbes and dietary polyphenols: challenges and opportunities.}, journal = {Microbiology (Reading, England)}, volume = {156}, number = {Pt 11}, pages = {3224-3231}, doi = {10.1099/mic.0.042127-0}, pmid = {20724384}, issn = {1465-2080}, mesh = {Animals ; Bacteria/*metabolism ; Biological Availability ; *Diet ; Flavonoids/*metabolism ; Fruit ; Gastrointestinal Tract/*microbiology ; Gene Expression Profiling ; Humans ; *Metagenome ; Models, Animal ; Phenols/*metabolism ; Polyphenols ; Proteomics ; Vegetables ; }, abstract = {Polyphenols, ubiquitously present in the food we consume, may modify the gut microbial composition and/or activity, and moreover, may be converted by the colonic microbiota to bioactive compounds that influence host health. The polyphenol content of fruit and vegetables and derived products is implicated in some of the health benefits bestowed on eating fruit and vegetables. Elucidating the mechanisms behind polyphenol metabolism is an important step in understanding their health effects. Yet, this is no trivial assignment due to the diversity encountered in both polyphenols and the gut microbial composition, which is further confounded by the interactions with the host. Only a limited number of studies have investigated the impact of dietary polyphenols on the complex human gut microbiota and these were mainly focused on single polyphenol molecules and selected bacterial populations. Our knowledge of gut microbial genes and pathways for polyphenol bioconversion and interactions is poor. Application of specific in vitro or in vivo models mimicking the human gut environment is required to analyse these diverse interactions. A particular benefit can now be gained from next-generation analytical tools such as metagenomics and metatranscriptomics allowing a wider, more holistic approach to the analysis of polyphenol metabolism. Understanding the polyphenol-gut microbiota interactions and gut microbial bioconversion capacity will facilitate studies on bioavailability of polyphenols in the host, provide more insight into the health effects of polyphenols and potentially open avenues for modulation of polyphenol bioactivity for host health.}, }
@article {pmid20723961, year = {2010}, author = {Nielsen, PH and Mielczarek, AT and Kragelund, C and Nielsen, JL and Saunders, AM and Kong, Y and Hansen, AA and Vollertsen, J}, title = {A conceptual ecosystem model of microbial communities in enhanced biological phosphorus removal plants.}, journal = {Water research}, volume = {44}, number = {17}, pages = {5070-5088}, doi = {10.1016/j.watres.2010.07.036}, pmid = {20723961}, issn = {1879-2448}, mesh = {Bacteria/*growth &amp; development/metabolism ; Biodegradation, Environmental ; Biodiversity ; *Ecosystem ; *Models, Biological ; Phosphorus/*isolation &amp; purification ; }, abstract = {The microbial populations in 25 full-scale activated sludge wastewater treatment plants with enhanced biological phosphorus removal (EBPR plants) have been intensively studied over several years. Most of the important bacterial groups involved in nitrification, denitrification, biological P removal, fermentation, and hydrolysis have been identified and quantified using quantitative culture-independent molecular methods. Surprisingly, a limited number of core species was present in all plants, constituting on average approx. 80% of the entire communities in the plants, showing that the microbial populations in EBPR plants are rather similar and not very diverse, as sometimes suggested. By focusing on these organisms it is possible to make a comprehensive ecosystem model, where many important aspects in relation to microbial ecosystems and wastewater treatment can be investigated. We have reviewed the current knowledge about these microorganisms with focus on key ecophysiological factors and combined this into a conceptual ecosystem model for EBPR plants. It includes the major pathways of carbon flow with specific organic substances, the dominant populations involved in the transformations, interspecies interactions, and the key factors controlling their presence and activity. We believe that the EBPR process is a perfect model system for studies of microbial ecology in water engineering systems and that this conceptual model can be used for proposing and testing theories based on microbial ecosystem theories, for the development of new and improved quantitative ecosystem models and is beneficial for future design and management of wastewater treatment systems.}, }
@article {pmid20717661, year = {2011}, author = {Stevens, P and van Overbeek, LS and van Elsas, JD}, title = {Ralstonia solanacearum ΔPGI-1 strain KZR-5 is affected in growth, response to cold stress and invasion of tomato.}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {101-112}, pmid = {20717661}, issn = {1432-184X}, mesh = {Amino Acid Sequence ; Cold Temperature ; Gene Deletion ; Genomic Islands/*genetics ; Solanum lycopersicum/*microbiology ; Microbial Interactions/genetics ; Microbial Viability/genetics ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Ralstonia solanacearum/classification/*genetics/growth &amp; development/*metabolism/pathogenicity ; Sequence Alignment ; }, abstract = {The survival and persistence of Ralstonia solanacearum biovar 2 in temperate climates is still poorly understood. To assess whether genomic variants of the organism show adaptation to local conditions, we compared the behaviour of environmental strain KZR-5, which underwent a deletion of the 17.6 kb genomic island PGI-1, with that of environmental strain KZR-1 and potato-derived strains 1609 and 715. PGI-1 harbours two genes of potential ecological relevance, i.e. one encoding a hypothetical protein with a RelA/SpoT domain and one a putative cellobiohydrolase. We thus assessed bacterial fate under conditions of amino acid starvation, during growth, upon incubation at low temperature and invasion of tomato plants. In contrast to the other strains, environmental strain KZR-5 did not grow on media that induce amino acid starvation. In addition, its maximum growth rate at 28°C in rich medium was significantly reduced. On the other hand, long-term survival at 4°C was significantly enhanced as compared to that of strains 1609, 715 and KZR-1. Although strain KZR-5 showed growth rates (at 28°C) in two different media, which were similar to those of strains 1609 and 715, its ability to compete with these strains under these conditions was reduced. In singly inoculated tomato plants, no significant differences in invasiveness were observed among strains KZR-5, KZR-1, 1609 and 715. However, reduced competitiveness of strain KZR-5 was found in experiments on tomato plant colonisation and wilting when using 1:1 or 5:1 mixtures of strains. The potential role of PGI-1 in plant invasion, response to stress and growth in competition at high and moderate temperatures is discussed.}, }
@article {pmid20717660, year = {2011}, author = {Portillo, MC and Gonzalez, JM}, title = {Moonmilk deposits originate from specific bacterial communities in Altamira Cave (Spain).}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {182-189}, pmid = {20717660}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/growth &amp; development/isolation &amp; purification/metabolism ; *Biodiversity ; Confined Spaces ; Culture Media ; DNA Fingerprinting ; Drug Combinations ; *Environmental Microbiology ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Oils ; Oxygen Consumption ; Phenols ; RNA, Ribosomal, 16S/genetics ; Spain ; }, abstract = {The influence of bacterial communities on the formation of carbonate deposits such as moonmilk was investigated in Altamira Cave (Spain). The study focuses on the relationship between the bacterial communities at moonmilk deposits and those forming white colonizations, which develop sporadically throughout the cave. Using molecular fingerprinting of the metabolically active bacterial communities detected through RNA analyses, the development of white colonizations and moonmilk deposits showed similar bacterial profiles. White colonizations were able to raise the pH as a result of their metabolism (reaching in situ pH values above 8.5), which was proportional to the nutrient supply. Bacterial activity was analyzed by nanorespirometry showing higher metabolic activity from bacterial colonizations than uncolonized areas. Once carbonate deposits were formed, bacterial activity decreased drastically (down to 5.7% of the white colonization activity). This study reports on a specific type of bacterial community leading to moonmilk deposit formation in a cave environment as a result of bacterial metabolism. The consequence of this process is a macroscopic phenomenon of visible carbonate depositions and accumulation in cave environments.}, }
@article {pmid20717659, year = {2010}, author = {Terán-Ventura, E and Roca, M and Martin, MT and Abarca, ML and Martinez, V and Vergara, P}, title = {Characterization of housing-related spontaneous variations of gut microbiota and expression of toll-like receptors 2 and 4 in rats.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {691-702}, pmid = {20717659}, issn = {1432-184X}, mesh = {Animals ; Bacteria/genetics ; Biodiversity ; Cecum/*microbiology ; DNA, Bacterial/genetics ; Gene Expression ; *Housing, Animal ; In Situ Hybridization, Fluorescence ; Male ; Metagenome/*genetics ; Polymorphism, Restriction Fragment Length ; Rats ; Rats, Sprague-Dawley ; Toll-Like Receptor 2/*metabolism ; Toll-Like Receptor 4/*metabolism ; }, abstract = {Gut microbiota has been suggested as a key component of gut homeostasis, affecting immune responses within the gut. We determined changes in intestinal commensal bacteria and expression of toll-like receptors (TLR) 2 and 4 in rats bred under microbiologically controlled conditions (barrier), under standard conditions (conventional), and in barrier animals adapted to standard conditions (barrier/conventional). Cecal microbiota was analyzed by plate culture, and fluorescence in situ hybridization and microbial profiles were assessed by terminal restriction fragment length polymorphism. Cecal expression of TLR-2 and TLR-4 was determined by reverse transcription polymerase chain reaction (PCR). Total number of cecal bacteria was similar in the three groups. However, the barrier group showed a higher number of strict anaerobic bacteria (Bacteroides spp. and Clostridium spp.) while Bifidobacterium spp. were scarce. Re-housing the barrier-bred rats into conventional conditions led to a microbiota with intermediate characteristics between the barrier and conventional groups. Richness of the cecal microbial ecosystem was similar in the three groups, although a relative time-dependent variation, with highest homogeneity in the barrier group, was observed. Expression levels of TLR-2 and TLR-4 had no clear correlation with the microbiota. These results show that the relative composition of the cecal microbiota in rats varies spontaneously with changes in the environmental conditions, with minor impact in the expression of TLR-2 and TLR-4. These observations might be important in the understanding of variability in animal responses, particularly to immune-related stimuli, when assessed in the context of the environmental/microbiological conditions.}, }
@article {pmid20711724, year = {2011}, author = {Václav, R and Ficová, M and Prokop, P and Betáková, T}, title = {Associations between coinfection prevalence of Borrelia lusitaniae, Anaplasma sp., and Rickettsia sp. in hard ticks feeding on reptile hosts.}, journal = {Microbial ecology}, volume = {61}, number = {2}, pages = {245-253}, pmid = {20711724}, issn = {1432-184X}, mesh = {Anaplasma/genetics/isolation &amp; purification/*pathogenicity ; Anaplasmosis/parasitology ; Animals ; Borrelia/genetics/isolation &amp; purification/*pathogenicity ; Borrelia Infections/parasitology/veterinary ; DNA, Bacterial/analysis ; Disease Vectors ; Female ; Ixodes/*microbiology ; Lizards/*microbiology/*parasitology ; Male ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Rickettsia/genetics/isolation &amp; purification/*pathogenicity ; Rickettsia Infections/parasitology/veterinary ; }, abstract = {An increasing number of studies reveal that ticks and their hosts are infected with multiple pathogens, suggesting that coinfection might be frequent for both vectors and wild reservoir hosts. Whereas the examination of associations between coinfecting pathogen agents in natural host-vector-pathogen systems is a prerequisite for a better understanding of disease maintenance and transmission, the associations between pathogens within vectors or hosts are seldom explicitly examined. We examined the prevalence of pathogen agents and the patterns of associations between them under natural conditions, using a previously unexamined host-vector-pathogen system--green lizards Lacerta viridis, hard ticks Ixodes ricinus, and Borrelia, Anaplasma, and Rickettsia pathogens. We found that immature ticks infesting a temperate lizard species in Central Europe were infected with multiple pathogens. Considering I. ricinus nymphs and larvae, the prevalence of Anaplasma, Borrelia, and Rickettsia was 13.1% and 8.7%, 12.8% and 1.3%, and 4.5% and 2.7%, respectively. The patterns of pathogen prevalence and observed coinfection rates suggest that the risk of tick infection with one pathogen is not independent of other pathogens. Our results indicate that Anaplasma can play a role in suppressing the transmission of Borrelia to tick vectors. Overall, however, positive effects of Borrelia on Anaplasma seem to prevail as judged by higher-than-expected Borrelia-Anaplasma coinfection rates.}, }
@article {pmid20705664, year = {2010}, author = {Salonen, A and de Vos, WM and Palva, A}, title = {Gastrointestinal microbiota in irritable bowel syndrome: present state and perspectives.}, journal = {Microbiology (Reading, England)}, volume = {156}, number = {Pt 11}, pages = {3205-3215}, doi = {10.1099/mic.0.043257-0}, pmid = {20705664}, issn = {1465-2080}, mesh = {Bacteria/*genetics/growth &amp; development ; Biomarkers ; DNA, Bacterial/genetics ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Irritable Bowel Syndrome/classification/*microbiology ; *Metagenome ; Phylogeny ; }, abstract = {Irritable bowel syndrome (IBS) is a functional gastrointestinal disorder that has been associated with aberrant microbiota. This review focuses on the recent molecular insights generated by analysing the intestinal microbiota in subjects suffering from IBS. Special emphasis is given to studies that compare and contrast the microbiota of healthy subjects with that of IBS patients classified into different subgroups based on their predominant bowel pattern as defined by the Rome criteria. The current data available from a limited number of patients do not reveal pronounced and reproducible IBS-related deviations of entire phylogenetic or functional microbial groups, but rather support the concept that IBS patients have alterations in the proportions of commensals with interrelated changes in the metabolic output and overall microbial ecology. The lack of apparent similarities in the taxonomy of microbiota in IBS patients may partially arise from the fact that the applied molecular methods, the nature and location of IBS subjects, and the statistical power of the studies have varied considerably. Most recent advances, especially the finding that several uncharacterized phylotypes show non-random segregation between healthy and IBS subjects, indicate the possibility of discovering bacteria specific for IBS. Moreover, tools are being developed for the functional analysis of the relationship between the intestinal microbiota and IBS. These approaches may be instrumental in the evaluation of the ecological dysbiosis hypothesis in the gut ecosystem. Finally, we discuss the future outlook for research avenues and candidate microbial biomarkers that may eventually be used in IBS diagnosis.}, }
@article {pmid20704235, year = {2010}, author = {De Gusseme, B and Du Laing, G and Hennebel, T and Renard, P and Chidambaram, D and Fitts, JP and Bruneel, E and Van Driessche, I and Verbeken, K and Boon, N and Verstraete, W}, title = {Virus removal by biogenic cerium.}, journal = {Environmental science &amp; technology}, volume = {44}, number = {16}, pages = {6350-6356}, doi = {10.1021/es100100p}, pmid = {20704235}, issn = {1520-5851}, mesh = {Bacteriophages/*isolation &amp; purification ; Biodegradation, Environmental ; Biomass ; Cerium/*metabolism ; Leptothrix/*metabolism ; Manganese/metabolism ; Oxidation-Reduction ; Pseudomonas putida/*metabolism/ultrastructure ; Solubility ; Time Factors ; Virus Inactivation ; X-Ray Absorption Spectroscopy ; }, abstract = {The rare earth element cerium has been known to exert antifungal and antibacterial properties in the oxidation states +III and +IV. This study reports on an innovative strategy for virus removal in drinking water by the combination of Ce(III) on a bacterial carrier matrix. The biogenic cerium (bio-Ce) was produced by addition of aqueous Ce(III) to actively growing cultures of either freshwater manganese-oxidizing bacteria (MOB) Leptothrix discophora or Pseudomonas putida MnB29. X-ray absorption spectroscopy results indicated that Ce remained in its trivalent state on the bacterial surface. The spectra were consistent with Ce(III) ions associated with the phosphoryl groups of the bacterial cell wall. In disinfection assays using a bacteriophage as model, it was demonstrated that bio-Ce exhibited antiviral properties. A 4.4 log decrease of the phage was observed after 2 h of contact with 50 mg L(-1) bio-Ce. Given the fact that virus removal with 50 mg L(-1) Ce(III) as CeNO(3) was lower, the presence of the bacterial carrier matrix in bio-Ce significantly enhanced virus removal.}, }
@article {pmid20703315, year = {2011}, author = {Bru, D and Ramette, A and Saby, NP and Dequiedt, S and Ranjard, L and Jolivet, C and Arrouays, D and Philippot, L}, title = {Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale.}, journal = {The ISME journal}, volume = {5}, number = {3}, pages = {532-542}, pmid = {20703315}, issn = {1751-7370}, mesh = {Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; Crenarchaeota/genetics/isolation &amp; purification/*physiology ; *Ecosystem ; France ; Nitrogen/*metabolism ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {Little information is available regarding the landscape-scale distribution of microbial communities and its environmental determinants. However, a landscape perspective is needed to understand the relative importance of local and regional factors and land management for the microbial communities and the ecosystem services they provide. In the most comprehensive analysis of spatial patterns of microbial communities to date, we investigated the distribution of functional microbial communities involved in N-cycling and of the total bacterial and crenarchaeal communities over 107 sites in Burgundy, a 31,500 km(2) region of France, using a 16 × 16 km(2) sampling grid. At each sampling site, the abundance of total bacteria, crenarchaea, nitrate reducers, denitrifiers- and ammonia oxidizers were estimated by quantitative PCR and 42 soil physico-chemical properties were measured. The relative contributions of land use, spatial distance, climatic conditions, time, and soil physico-chemical properties to the spatial distribution of the different communities were analyzed by canonical variation partitioning. Our results indicate that 43-85% of the spatial variation in community abundances could be explained by the measured environmental parameters, with soil chemical properties (mostly pH) being the main driver. We found spatial autocorrelation up to 739 km and used geostatistical modelling to generate predictive maps of the distribution of microbial communities at the landscape scale. The present study highlights the potential of a spatially explicit approach for microbial ecology to identify the overarching factors driving the spatial heterogeneity of microbial communities even at the landscape scale.}, }
@article {pmid20701885, year = {2010}, author = {Shahid, M and Khardori, N and Tripathi, T and Bergman, S}, title = {Pharmaco-EcoMicrobiology: a newer component of medical sciences bridging pharmacovigilance, ecology, and environmental microbiology.}, journal = {Journal of infection and public health}, volume = {3}, number = {1}, pages = {1-4}, doi = {10.1016/j.jiph.2009.11.001}, pmid = {20701885}, issn = {1876-035X}, mesh = {*Drug-Related Side Effects and Adverse Reactions ; *Ecology ; Ecosystem ; *Environmental Microbiology ; Environmental Monitoring ; Humans ; Pharmacoepidemiology ; Risk Assessment ; }, abstract = {Environmental scientists are now raising great concern on the impact of drugs on the environment and microbiologists are concerned about increasing antibiotic resistance due to irrational usage. However, a focus on the impact by the use of antibiotics (irrational/prescribed) to the environment at therapeutic doses has not been instituted. Even the World Health Organization (WHO) defined "Pharmacovigilance" activities as the monitoring, detection, assessment, understanding and prevention of any adverse reactions to drugs at therapeutic concentration on animals and humans. Nevertheless, there is little attention being given to identifying the adverse effects (ADEs) of antimicrobial agents on the environment (given at therapeutic doses). This issue has been highlighted in the present commentary and a new domain, "Pharmaco-EcoMicrobiology", has been proposed which should deal with and monitor such adverse effects. The term "Pharmaco-EcoMicrobiology" has been proposed to define the interplay between antimicrobial pharmacological agents and animate microbial ecology. This new domain, "Pharmaco-EcoMicrobiology", has been derived by the aggregation of three important branches of science (pharmacology+ecology+microbiology) and would be responsible for studying the ADEs due to antimicrobial drugs excreted in environment.}, }
@article {pmid20700590, year = {2010}, author = {Knief, C and Frances, L and Vorholt, JA}, title = {Competitiveness of diverse Methylobacterium strains in the phyllosphere of Arabidopsis thaliana and identification of representative models, including M. extorquens PA1.}, journal = {Microbial ecology}, volume = {60}, number = {2}, pages = {440-452}, pmid = {20700590}, issn = {1432-184X}, mesh = {Arabidopsis/*microbiology ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Methylobacterium/classification/genetics/*isolation &amp; purification ; Phylogeny ; Plant Leaves/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Facultative methylotrophic bacteria of the genus Methylobacterium are consistently found in association with plants, particularly in the phyllosphere. To gain a better understanding of the mechanisms underlying the dispersal and occurrence of Methylobacterium on plants, diverse strains were isolated, identified, and studied with regard to their competitiveness on the model plant Arabidopsis thaliana. As a basis for this study a comprehensive collection of Methylobacterium isolates was established. Isolates were obtained from five different naturally grown A. thaliana populations and diverse other plant genera at these and further sites. They were classified using automated ribosomal internal spacer analysis (ARISA) and a representative subset was identified based on 16S rRNA gene sequence analysis. A comparison of their ARISA patterns with those generated based on a cultivation-independent approach from the same sampling material confirmed that the isolates were abundant colonizers of the studied plants. In competition experiments, colonization efficiency of the strains was found to be linked to phylogeny, rather than to the geographical origin or plant genus from which they were isolated. The most competitive colonizers were related to the species Methylobacterium tardum and Methylobacterium extorquens. Higher cell numbers were observed in the phyllosphere of A. thaliana when a mixture of different strains was applied relative to inoculation with only one strain, suggesting partial niche heterogeneity. Based on the results of the competition experiments, representative strains with different colonization efficiencies were selected, which will serve as models in future studies aiming at a better understanding of plant colonization by this bacterial genus. Among them is the meanwhile genome-sequenced strain M. extorquens PA1, which represents a competitive species of plant colonizers with a broad dispersal. This strain was characterized in more detail including physiological, morphological, and chemotaxonomical properties.}, }
@article {pmid20698885, year = {2010}, author = {He, Z and Gao, F and Zhao, J and Hu, Y and Qiu, G}, title = {Insights into the dynamics of bacterial communities during chalcopyrite bioleaching.}, journal = {FEMS microbiology ecology}, volume = {74}, number = {1}, pages = {155-164}, doi = {10.1111/j.1574-6941.2010.00943.x}, pmid = {20698885}, issn = {1574-6941}, mesh = {Acidithiobacillus/*genetics/metabolism ; Bacteria/*genetics/metabolism ; Biodegradation, Environmental ; Copper/*metabolism ; Culture Media ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Hydrogen-Ion Concentration ; Metals, Heavy/metabolism ; Mining ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The microbial ecology of the bioleaching of chalcopyrite ores is poorly understood and little effort has been made to handle the microbiological components of these processes. In this study, the composition and structure of microbial communities in acid mineral bioleaching systems have been studied using a PCR-based cloning approach. Denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA gene fragments from bacteria was used to evaluate the changes in the bacterial community in the process of chalcopyrite bioleaching in a shaken flask system. The results revealed that the bacterial community was disturbed after the addition of chalcopyrite. Phylogenetic analyses of 16S rRNA gene fragments revealed that the retrieved sequences clustered together with the genera Acidithiobacillus, Leptospirillum, and Acidovorax. Multidimensional scaling analysis of DGGE banding patterns revealed that the process of chalcopyrite bioleaching in 46 days was divided into four stages. In the first stage, Leptospirillum were dominant. In the second stage, Leptospirillum and Acidithiobacillus groups were mainly detected. In the third and fourth stages, the bacterial community was relatively stable and was dominated by Leptospirillum and Acidithiobacillus. These results extend our knowledge on the microbial dynamics in chalcopyrite bioleaching, a key issue required to improve commercial applications.}, }
@article {pmid20697705, year = {2011}, author = {Sridhar, KR and Beaton, M and Bärlocher, F}, title = {Fungal propagules and DNA in feces of two detritus-feeding amphipods.}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {31-40}, pmid = {20697705}, issn = {1432-184X}, mesh = {Amphipoda/*microbiology ; Animals ; Biodiversity ; DNA, Fungal/*genetics ; Feces/chemistry/*microbiology ; Food Chain ; Mitosporic Fungi/classification/*genetics/isolation &amp; purification ; Plant Leaves/microbiology ; Spores, Fungal/genetics ; Water Microbiology ; }, abstract = {Aquatic shredders (leaf-eating invertebrates) preferentially ingest and digest leaves colonized by aquatic hyphomycetes (fungi). This activity destroys leaf-associated fungal biomass and detritial resources in streams. Fungal counter-adaptations may include the ability to survive passage through the invertebrate's digestive tract. When fecal pellets of Gammarus tigrinus and Hyalella azteca were incubated with sterile leaves, spores of nine (G. tigrinus) and seven (H. azteca) aquatic hyphomycete species were subsequently released from the leaves, indicating the presence of viable fungal structures in the feces. Extraction, amplification, and sequencing of DNA from feces revealed numerous fungal phylotypes, two of which could be assigned unequivocally to an aquatic hyphomycete. The estimated contributions of major fungal groups varied depending on whether 18S or ITS sequences were amplified and cloned. We conclude that a variable proportion of fungal DNA in the feces of detritivores may originate from aquatic hyphomycetes. Amplified DNA may be associated with metabolically active, dormant, or dead fungal cells.}, }
@article {pmid20695892, year = {2010}, author = {Hinsa-Leasure, SM and Bhavaraju, L and Rodrigues, JL and Bakermans, C and Gilichinsky, DA and Tiedje, JM}, title = {Characterization of a bacterial community from a Northeast Siberian seacoast permafrost sample.}, journal = {FEMS microbiology ecology}, volume = {74}, number = {1}, pages = {103-113}, doi = {10.1111/j.1574-6941.2010.00945.x}, pmid = {20695892}, issn = {1574-6941}, mesh = {Amino Acid Sequence ; Bacteria/*classification/enzymology/genetics/isolation &amp; purification ; Cold Temperature ; DNA, Bacterial/genetics ; *Ecosystem ; Gene Library ; Genes, Bacterial ; Ice ; Isocitrate Lyase/genetics ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Siberia ; *Soil Microbiology ; }, abstract = {A combination of culture-dependent and -independent techniques was used to characterize a bacterial community, examine cold adaptation of isocitrate lyase (icl) genes, and detect genes with important ecological functions in a permafrost sample from the Bykovsky Peninsula on the Laptev Sea coast of northeast Siberia. According to the 16S rRNA gene sequence, 47 of the cultured isolates were members of the phyla Firmicutes, Proteobacteria, and Actinobacteria, with 85% of the isolates belonging to the genera Arthrobacter and Planococcus. The 16S rRNA gene clone library derived from DNA from the same permafrost sample contained sequences from the same phyla plus a few from Acidobacteria, but favored the Firmicutes at the cost of the Actinobacteria. A partial sequence of the icl gene, a proposed marker for cold adaptation, was determined for 25 isolates that grew at 0 °C. Two Psychrobacter isolates contained two of the four residues shown to be important for low-temperature activity in Colwellia maris or Colwellia psychrerythreaea. The presence in the permafrost DNA of genes with ecosystem functions was determined using geochip 2.0. The highest number of genes identified was from the categories of aromatic and natural polymer degradation genes, perhaps reflecting selection for the use of tundra vegetation-produced carbon.}, }
@article {pmid20685969, year = {2010}, author = {Ikeda, S and Okubo, T and Anda, M and Nakashita, H and Yasuda, M and Sato, S and Kaneko, T and Tabata, S and Eda, S and Momiyama, A and Terasawa, K and Mitsui, H and Minamisawa, K}, title = {Community- and genome-based views of plant-associated bacteria: plant-bacterial interactions in soybean and rice.}, journal = {Plant &amp; cell physiology}, volume = {51}, number = {9}, pages = {1398-1410}, doi = {10.1093/pcp/pcq119}, pmid = {20685969}, issn = {1471-9053}, mesh = {Biota ; Comparative Genomic Hybridization ; *Genome, Bacterial ; *Genome, Plant ; Nitrogen/metabolism ; Oryza/genetics/*microbiology ; Plant Root Nodulation/genetics ; Proteobacteria/*genetics ; Glycine max/genetics/*microbiology ; Symbiosis/*genetics ; }, abstract = {Diverse microorganisms are living as endophytes in plant tissues and as epiphytes on plant surfaces in nature. Questions about driving forces shaping the microbial community associated with plants remain unanswered. Because legumes developed systems to attain endosymbioses with rhizobia as well as mycorrhizae during their evolution, the above questions can be addressed using legume mutants relevant to genes for symbiosis. Analytical methods for the microbial community have recently been advanced by enrichment procedures of plant-associated microbes and culture-independent analyses targeting the small subunit of rRNA in microbial ecology. In this review, we first deal with interdisciplinary works on the global diversity of bacteria associated with field-grown soybeans with different nodulation genotypes and nitrogen application. A subpopulation of Proteobacteria in aerial parts of soybean shoots was likely to be regulated through both the autoregulation system for plant-rhizobium symbiosis and the nitrogen signaling pathway, suggesting that legumes accommodate a taxonomically characteristic microbial community through unknown plant-microbe communications. In addition to the community views, we then show multiphasic analysis of a beneficial rice endophyte for comparative bacterial genomics and plant responses. The significance and perspectives of community- and genome-based approaches are discussed to achieve a better understanding of plant-microbe interactions.}, }
@article {pmid20684970, year = {2010}, author = {Park, H and Rosenthal, A and Jezek, R and Ramalingam, K and Fillos, J and Chandran, K}, title = {Impact of inocula and growth mode on the molecular microbial ecology of anaerobic ammonia oxidation (anammox) bioreactor communities.}, journal = {Water research}, volume = {44}, number = {17}, pages = {5005-5013}, doi = {10.1016/j.watres.2010.07.022}, pmid = {20684970}, issn = {1879-2448}, mesh = {Ammonia/*metabolism ; Anaerobiosis ; Bacteria/*genetics/*growth &amp; development ; Bioreactors/*microbiology ; Denaturing Gradient Gel Electrophoresis ; *Ecological and Environmental Phenomena ; Molecular Sequence Data ; Nitrites/isolation &amp; purification ; Nitrogen/isolation &amp; purification ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The composition of distinctly inoculated granular anammox and biofilm-based completely autotrophic nitrogen removal over nitrite (CANON) bioreactors was investigated from start-up through continuous long-term operation via denaturing gradient gel electrophoresis (DGGE) and sequencing. The granular anammox reactor was seeded with sludge from an operational anammox reactor in Strass, Austria. The CANON reactor was seeded with activated sludge from a local wastewater treatment plant in New York City. The principal anammox bacteria (AMX) shifted from members related to Kuenenia stuttgartiensis present in the initial inoculum to members related to Candidatus Brocadia fulgida during pre-enrichment (before this study) and to members related to Candidatus Brocadia sp. 40 (during this study) in the granular reactor. AMX related to C. Brocadia sp. 40 were also enriched from activated sludge in the CANON reactor. The estimated doubling times of AMX in the granular and CANON reactors were 5.3 and 8.9 days, respectively, which are lower than the value of 11 days, reported previously. Both the granular anammox and CANON reactors also fostered significant amounts of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). The fractions of AMX and two groups of NOB were generally similar in the granular anammox and CANON reactors. However, the diversity and fractions of AOB in the two reactors was markedly different. Therefore, it is suggested that the composition of the feed and extant substrate concentrations in the reactor likely select for the microbial community composition more than the inocula and reactor configuration. Further, such selection is not equivalent for all resident communities.}, }
@article {pmid20683589, year = {2010}, author = {Wang, W and Wang, L and Shao, Z}, title = {Diversity and abundance of oil-degrading bacteria and alkane hydroxylase (alkB) genes in the subtropical seawater of Xiamen Island.}, journal = {Microbial ecology}, volume = {60}, number = {2}, pages = {429-439}, pmid = {20683589}, issn = {1432-184X}, mesh = {Bacteria/classification/enzymology/genetics/*isolation &amp; purification ; Biodegradation, Environmental ; *Biodiversity ; China ; Cytochrome P-450 CYP4A/*genetics ; DNA, Bacterial/genetics ; Petroleum/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Water Microbiology ; }, abstract = {In this report, the diversity of oil-degrading bacteria and alkB gene was surveyed in the seawater around Xiamen Island. Forty-four isolates unique in 16S rRNA sequence were obtained after enrichment with crude oil. Most of the obtained isolates exhibited growth with diesel oil and crude oil. alkB genes were positively detected in 16 isolates by degenerate polymerase chain reaction (PCR). And for the first time, alkB genes were found in bacteria of Gallaecimonas, Castellaniella, Paracoccus, and Leucobacter. Additional 29 alkB sequences were retrieved from genomic DNA of the oil-degrading communities. Phylogenetic analysis showed that the obtained alkB genes formed five groups, most of which exhibited 60-80% similarity at the amino acid level with sequences retrieved from the GenBank database. Furthermore, the abundance of alkB genes in seawater was examined by real-time PCR. The results showed that alkB genes of each group in situ ranged from about 3 × 10(3) to 3 × 10(5) copies L(-1), with the homologs of Alcanivorax and Pseudomonas being the most predominant. Bacteria of Alcanivorax, Acinetobacter, and Pseudomonas are important oil degraders in this area; while those frequently reported in other area, like Oleiphilus spp., Oleispira spp., and Thalassolituus spp. were not found in our report. These results indicate that bacteria and genes involved in oil degradation are quite diverse, and may have restriction in geographic distribution in some species.}, }
@article {pmid20683588, year = {2010}, author = {Bachar, A and Al-Ashhab, A and Soares, MI and Sklarz, MY and Angel, R and Ungar, ED and Gillor, O}, title = {Soil microbial abundance and diversity along a low precipitation gradient.}, journal = {Microbial ecology}, volume = {60}, number = {2}, pages = {453-461}, pmid = {20683588}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; *Climate ; DNA, Bacterial/genetics ; Hydrogen-Ion Concentration ; Mediterranean Region ; Phospholipids/analysis ; Polymorphism, Restriction Fragment Length ; Rain ; Salinity ; Soil/analysis ; *Soil Microbiology ; Water ; }, abstract = {The exploration of spatial patterns of abundance and diversity patterns along precipitation gradients has focused for centuries on plants and animals; microbial profiles along such gradients are largely unknown. We studied the effects of soil pH, nutrient concentration, salinity, and water content on bacterial abundance and diversity in soils collected from Mediterranean, semi-arid, and arid sites receiving approximately 400, 300, and 100 mm annual precipitation, respectively. Bacterial diversity was evaluated by terminal restriction fragment length polymorphism and clone library analyses and the patterns obtained varied with the climatic regions. Over 75% of the sequenced clones were unique to their environment, while ∼2% were shared by all sites, yet, the Mediterranean and semi-arid sites had more common clones (∼9%) than either had with the arid site (4.7% and 6%, respectively). The microbial abundance, estimated by phospholipid fatty acids and real-time quantitative PCR assays, was significantly lower in the arid region. Our results indicate that although soil bacterial abundance decreases with precipitation, bacterial diversity is independent of precipitation gradient. Furthermore, community composition was found to be unique to each ecosystem.}, }
@article {pmid20683587, year = {2011}, author = {Cockell, CS and Pybus, D and Olsson-Francis, K and Kelly, L and Petley, D and Rosser, N and Howard, K and Mosselmans, F}, title = {Molecular characterization and geological microenvironment of a microbial community inhabiting weathered receding shale cliffs.}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {166-181}, pmid = {20683587}, issn = {1432-184X}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; *Ecosystem ; *Environmental Microbiology ; Genes, Archaeal/genetics ; Genome, Bacterial/genetics ; Geologic Sediments/analysis/*microbiology ; Hydrogen-Ion Concentration ; Metagenome/genetics ; Molecular Sequence Data ; Oxidoreductases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Spectrum Analysis ; X-Ray Diffraction ; }, abstract = {Shales play an important role in many earth system processes including coastal erosion, and they form the foundations of many engineering structures. The geobiology of the interior of pyrite-containing receding shale cliffs on the coast of northeast England was examined. The surface of the weathered shales was characterised by a thin layer of disordered authigenic iron oxyhydroxides and localised acicular, platy and aggregated gypsum, which was characterised by Raman spectroscopy, XAS and SEM. These chemical changes are likely to play an important role in causing rock weakening along fractures at the micron scale, which ultimately lead to coastal retreat at the larger scale. The surface of the shale hosts a novel, low-diversity microbial community. The bacterial community was dominated by Proteobacteria, with phylotypes closely associating with Methylocella and other members of the γ-subdivision. The second largest phylogenetic group corresponded to Nitrospira. The archaeal 16S rRNA phylotypes were dominated by a single group of sequences that matched phylotypes reported from South African gold mines and possessed ammonia monooxygenase (amoA) genes. Both the phylogenetic and the mineral data show that acidic microenvironments play an important role in shale weathering, but the shale has a higher microbial diversity than previously described pyritic acid mine drainage sites. The presence of a potentially biogeochemically active microbial population on the rock surface suggests that microorganisms may contribute to early events of shale degradation and coastal erosion.}, }
@article {pmid20680666, year = {2011}, author = {Tyagi, M and da Fonseca, MM and de Carvalho, CC}, title = {Bioaugmentation and biostimulation strategies to improve the effectiveness of bioremediation processes.}, journal = {Biodegradation}, volume = {22}, number = {2}, pages = {231-241}, doi = {10.1007/s10532-010-9394-4}, pmid = {20680666}, issn = {1572-9729}, mesh = {*Biodegradation, Environmental ; Soil Pollutants/metabolism ; }, abstract = {Bioremediation, involving bioaugmentation and/or biostimulation, being an economical and eco-friendly approach, has emerged as the most advantageous soil and water clean-up technique for contaminated sites containing heavy metals and/or organic pollutants. Addition of pre-grown microbial cultures to enhance the degradation of unwanted compounds (bioaugmentation) and/or injection of nutrients and other supplementary components to the native microbial population to induce propagation at a hastened rate (biostimulation), are the most common approaches for in situ bioremediation of accidental spills and chronically contaminated sites worldwide. However, many factors like strain selection, microbial ecology, type of contaminant, environmental constraints, as well as procedures of culture introduction, may lead to their failure. These drawbacks, along with fragmented literature, have opened a gap between laboratory trials and on-field application. The present review discusses the effectiveness as well as the limitations of bioaugmentation and biostimulation processes. A summary of experimental studies both in confined systems under controlled conditions and of real case studies in the field is presented. A comparative account between the two techniques and also the current scenario worldwide for in situ biotreatment using bioaugmentation and biostimulation, are addressed.}, }
@article {pmid20680282, year = {2011}, author = {Lin, WT and Luo, JF and Guo, Y}, title = {Comparison and characterization of microbial communities in sulfide-rich wastewater with and without propidium monoazide treatment.}, journal = {Current microbiology}, volume = {62}, number = {2}, pages = {374-381}, pmid = {20680282}, issn = {1432-0991}, mesh = {Archaea/*classification/genetics ; Azides/metabolism ; Bacteria/*classification/genetics ; *Biodiversity ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Enzyme Inhibitors/metabolism ; Genes, rRNA ; *Microbial Viability ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/methods ; Polymorphism, Restriction Fragment Length ; Propidium/analogs &amp; derivatives/metabolism ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Sewage/chemistry/*microbiology ; Sulfides/*analysis ; }, abstract = {A 16S rRNA gene-based culture-independent approach was used to study the bacterial and archaeal communities in a sulfide-rich wastewater. Propidium Monoazide (PMA) treatment was applied to limit the analysis to the fraction of viable cells in environment. A total of 104 and 68 clones respective from bacterial clone library and archaeal library were picked and analyzed by restriction fragment length polymorphism (RFLP). 35 RFLP patterns from bacterial clone library and 10 RFLP patterns from archaeal clone library were unique and the respective clones were selected for sequencing. BLAST analysis and RFLP analysis showed that the bacterial clone library mainly consisted of Gammaproteobacteria (73%), Anaerolineae (6%), Bacilli (5%), Deltaproteobacteria (7%), Clostridia (4%), Bacteroidetes (1%), and Chlorobia (1%); Methanomicrobia (99%) and Thermococci (1%) were the only two lineages of the archaeal domains. This study gave a first insight into the overall microbial structure in a cloth printing and dyeing wastewater treatment plant with high concentration of sulfide and increased knowledge on the applicability of the PMA treatment in combination with PCR-based molecular techniques to analyze only viable cells in microbial ecology.}, }
@article {pmid20676625, year = {2011}, author = {Warkentin, M and Freese, HM and Schumann, R}, title = {Bacterial activity and bacterioplankton diversity in the eutrophic River Warnow--direct measurement of bacterial growth efficiency and its effect on carbon utilization.}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {190-200}, pmid = {20676625}, issn = {1432-184X}, mesh = {Bacteria/classification/*growth &amp; development/isolation &amp; purification/*metabolism ; *Biodiversity ; Biomass ; Carbon/*metabolism ; Germany ; Plankton/*microbiology ; Rivers/*microbiology ; Seasons ; Temperature ; *Water Microbiology ; }, abstract = {The influence of bacterial activity and diversity on bacterial growth efficiency was investigated in a flatland river. Eutrophic River Warnow drains predominantly agricultural land and is heavily loaded with nutrients, dissolved and particulate organic matter (DOM and POM), especially humic substances. Although the water column bacterial community consists of many inactive or damaged cells, bacterioplankton sustained a high bacterial secondary production of 0.2-14.5 μg C L(-1) h(-1) and a high DNA synthesis (thymidine uptake) of 6.1-15.5 μg C L(-1) h(-1). The direct and short-term measurement of bacterial respiration (by optodes) revealed high respiration rates especially in summer leading to directly estimated bacterial growth efficiencies (BGE) of 2-28%. These values are compared to calculations based only on bacterial production, which considerably overestimated BGEs. From all these data, River Warnow can be characterized as a strongly remineralizing system. River Warnow was dominated among others by Cytophaga/Flavobacteria and Actinobacteria which are typical for organic rich waters because of their ability to degrade high molecular weight compounds. However, community composition did not significantly affect BGE.}, }
@article {pmid20675479, year = {2010}, author = {Heinz, E and Rockey, DD and Montanaro, J and Aistleitner, K and Wagner, M and Horn, M}, title = {Inclusion membrane proteins of Protochlamydia amoebophila UWE25 reveal a conserved mechanism for host cell interaction among the Chlamydiae.}, journal = {Journal of bacteriology}, volume = {192}, number = {19}, pages = {5093-5102}, pmid = {20675479}, issn = {1098-5530}, support = {R01 AI048769/AI/NIAID NIH HHS/United States ; U19 AI031448/AI/NIAID NIH HHS/United States ; AI48769/AI/NIAID NIH HHS/United States ; AI031448/AI/NIAID NIH HHS/United States ; }, mesh = {Acanthamoeba castellanii/microbiology ; Animals ; Bacterial Proteins/genetics/*metabolism ; Blotting, Western ; Chlamydia/genetics/*growth &amp; development/*metabolism/ultrastructure ; Membrane Proteins/genetics/*metabolism ; Microscopy, Immunoelectron ; }, abstract = {Chlamydiae are a group of obligate intracellular bacteria comprising several important human pathogens. Inside the eukaryotic cell, chlamydiae remain within a host-derived vesicular compartment, termed the inclusion. They modify the inclusion membrane through insertion of unique proteins, which are involved in interaction with and manipulation of the host cell. Among chlamydiae, inclusion membrane proteins have been exclusively found in members of the family Chlamydiaceae, which predominantly infect mammalian and avian hosts. Here, the presence of inclusion membrane proteins in Protochlamydia amoebophila UWE25, a chlamydial endosymbiont of free-living amoebae, is reported. A genome-wide screening for secondary structure motifs resulted in the identification of 23 putative inclusion membrane proteins for this organism. Immunofluorescence analysis demonstrated that five of these proteins were expressed, and four of them could be localized to a halo surrounding the intracellular bacteria. Colocalization studies showed an almost complete overlap of the signals obtained for the four putative inclusion membrane proteins, and immuno-transmission electron microscopy unambiguously demonstrated their location in the inclusion membrane. The presence of inclusion membrane proteins (designated IncA, IncQ, IncR, and IncS) in P. amoebophila shows that this strategy for host cell interaction is conserved among the chlamydiae and is used by chlamydial symbionts and pathogens alike.}, }
@article {pmid20662931, year = {2011}, author = {Morales, SE and Holben, WE}, title = {Linking bacterial identities and ecosystem processes: can 'omic' analyses be more than the sum of their parts?.}, journal = {FEMS microbiology ecology}, volume = {75}, number = {1}, pages = {2-16}, doi = {10.1111/j.1574-6941.2010.00938.x}, pmid = {20662931}, issn = {1574-6941}, mesh = {Bacteria/*genetics/isolation &amp; purification/metabolism ; Ecology/*methods/trends ; *Ecosystem ; Environmental Microbiology ; *Metagenomics/trends ; }, abstract = {A major goal in microbial ecology is to link specific microbial populations to environmental processes (e.g. biogeochemical transformations). The cultivation and characterization of isolates using genetic, biochemical and physiological tests provided direct links between organisms and their activities, but did not provide an understanding of the process networks in situ. Cultivation-independent molecular techniques have extended capabilities in this regard, and yet, for two decades, the focus has been on monitoring microbial community diversity and population dynamics by means of rRNA gene abundances or rRNA molecules. However, these approaches are not always well suited for establishing metabolic activity or microbial roles in ecosystem function. The current approaches, microbial community metagenomic and metatranscriptomic techniques, have been developed as other ways to study microbial assemblages, giving rise to exponentially increasing collections of information from numerous environments. This review considers some advantages and limitations of nucleic acid-based 'omic' approaches and discusses the potential for the integration of multiple molecular or computational techniques for a more effective assessment of links between specific microbial populations and ecosystem processes in situ. Establishing such connections will enhance the predictive power regarding ecosystem response to parameters or perturbations, and will bring us closer to integrating microbial data into ecosystem- and global-scale process measurements and models.}, }
@article {pmid20656973, year = {2010}, author = {Price, KL and Totty, HR and Lee, HB and Utt, MD and Fitzner, GE and Yoon, I and Ponder, MA and Escobar, J}, title = {Use of Saccharomyces cerevisiae fermentation product on growth performance and microbiota of weaned pigs during Salmonella infection.}, journal = {Journal of animal science}, volume = {88}, number = {12}, pages = {3896-3908}, doi = {10.2527/jas.2009-2728}, pmid = {20656973}, issn = {1525-3163}, mesh = {Anaerobiosis ; Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Diet/veterinary ; *Dietary Supplements ; Fermentation ; Intestines/pathology ; Saccharomyces cerevisiae/*metabolism ; Salmonella Infections, Animal/*drug therapy/pathology ; Swine ; Swine Diseases/*therapy ; }, abstract = {Anaerobically fermented yeast products are a rich source of nutritional metabolites, mannanoligosaccharides, and β-glucans that may optimize gut health and immunity, which can translate into better growth performance and a reduced risk of foodborne pathogens. The objective of this study was to quantify the effects of Saccharomyces cerevisiae fermentation product (Diamond V Original XPC) inclusion in nursery diets on pig performance and gastrointestinal microbial ecology before, during, and after an oral challenge with Salmonella. Pigs (n = 40) were weaned at 21 d of age, blocked by BW, and assigned in a 2 × 2 factorial arrangement consisting of diet (control or 0.2% XPC) and inoculation (sterile broth or Salmonella). Pigs were fed a 3-phase nursery diet (0 to 7 d, 7 to 21 d, and 21 to 35 d) with ad libitum access to water and feed. On d 14, pigs were orally inoculated with 10(9) cfu of Salmonella enterica serovar Typhimurium DT104 or sterile broth. During d 17 to 20, all pigs were treated with a 5 mg/kg of BW intramuscular injection of ceftiofur-HCl. Growth performance and alterations in the gastrointestinal microbial ecology were measured during preinoculation (PRE; 0 to 14 d), sick (SCK; 14 to 21 d), and postinoculation (POST; 21 to 35 d). Body weight and ADG were measured weekly. Rectal temperature (RT) was measured weekly during PRE and POST, and every 12 h during SCK. Diet had no effect on BW, ADG, or RT during any period (P = 0.12 to 0.95). Inclusion of XPC tended (P < 0.10) to increase Salmonella shedding in feces during SCK. Consumption of XPC altered the composition of the gastrointestinal microbial community, resulting in increased (P < 0.05) populations of Bacteroidetes and Lactobacillus after Salmonella infection. Pigs inoculated with Salmonella had decreased ADG and BW, and increased RT during SCK (P < 0.001). Furthermore, fecal Salmonella cfu (log(10)) was modestly correlated (P = 0.002) with BW (r = -0.22), ADFI (r = -0.27), ADG (r = -0.36), G:F (r = -0.18), and RT (r = 0.52) during SCK. After antibiotic administration, all Salmonella-infected pigs stopped shedding. During POST, an interaction between diet and inoculation (P = 0.009) on ADG indicated that pigs infected with Salmonella grew better when eating XPC than the control diet. The addition of XPC to the diets of weanling pigs resulted in greater compensatory BW gains after infection with Salmonella than in pigs fed conventional nursery diets. This increase in BW gain is likely associated with an increase in beneficial bacteria within the gastrointestinal tract.}, }
@article {pmid20656857, year = {2010}, author = {Garren, M and Azam, F}, title = {New method for counting bacteria associated with coral mucus.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {18}, pages = {6128-6133}, pmid = {20656857}, issn = {1098-5336}, mesh = {Analysis of Variance ; Animals ; Anthozoa/*microbiology ; Bacteria/*isolation &amp; purification/ultrastructure ; Colony Count, Microbial/*methods ; Dinoflagellida/*isolation &amp; purification/ultrastructure ; Hawaii ; Indoles ; Microscopy, Electron, Scanning ; Microscopy, Fluorescence ; Mucus/*microbiology ; }, abstract = {The ability to count bacteria associated with reef-building corals in a rapid, reliable, and cost-effective manner has been hindered by the viscous and highly autofluorescent nature of the coral mucus layer (CML) in which they live. We present a new method that disperses bacterial cells by trypsinization prior to 4',6-diamidino-2-phenylindole (DAPI) staining and quantification by epifluorescence microscopy. We sampled seawater and coral mucus from Porites lobata from 6 reef sites influenced by wastewater intrusion and 2 reef sites unaffected by wastewater in Hawaii. Bacterial and zooxanthella abundances and cell sizes were quantified for each sample. Bacteria were more abundant in coral mucus (ranging from 5.3 x 10(5) +/- 1.0 x 10(5) cells ml(-1) to 1.8 x 10(6) +/- 0.2 x 10(6) cells ml(-1)) than in the surrounding seawater (1.9 x 10(5) +/- 0.1 x 10(5) cells ml(-1) to 4.2 x 10(5) +/- 0.2 x 10(5) cells ml(-1)), and the mucus-associated cells were significantly smaller than their seawater counterparts at all sites (P < 0.0001). The difference in cell size between mucus- and seawater-associated bacteria decreased at wastewater-influenced sites, where simultaneously mucus bacteria were larger and seawater bacteria were smaller than those at uninfluenced sites. The abundance of zooxanthellae in mucus ranged from 1.1 x 10(5) +/- 0.1 x 10(5) cells ml(-1) to 3.4 x 10(5) +/- 0.3 x 10(5) cells ml(-1). The frequency of dividing cells (FDC) was higher in the surrounding seawater than in mucus, despite finding that a 1,000-fold-higher zooxanthella biovolume than bacterial biovolume existed in the CML. Establishment of a standardized protocol for enumeration will provide the field of coral microbial ecology with the urgently needed ability to compare observations across studies and regions.}, }
@article {pmid20655994, year = {2011}, author = {Possemiers, S and Bolca, S and Verstraete, W and Heyerick, A}, title = {The intestinal microbiome: a separate organ inside the body with the metabolic potential to influence the bioactivity of botanicals.}, journal = {Fitoterapia}, volume = {82}, number = {1}, pages = {53-66}, doi = {10.1016/j.fitote.2010.07.012}, pmid = {20655994}, issn = {1873-6971}, mesh = {Bacteria/*metabolism ; Flavonoids/metabolism ; Humans ; Intestines/*microbiology ; *Metagenome ; Phenols/metabolism ; Plant Preparations/*metabolism/pharmacology ; Polyphenols ; Research Design ; }, abstract = {For many years, it was believed that the main function of the large intestine was the resorption of water and salt and the facilitated disposal of waste materials. However, this task definition was far from complete, as it did not consider the activity of the microbial content of the large intestine. Nowadays it is clear that the complex microbial ecosystem in our intestines should be considered as a separate organ within the body, with a metabolic capacity which exceeds the liver with a factor 100. The intestinal microbiome is therefore closely involved in the first-pass metabolism of dietary compounds. This is especially true for botanical supplements, which are now marketed for various health applications. Being of natural origin, their structural building blocks, such as polyphenols, are often highly recognized by the human and especially the intestinal microbial metabolism machinery. Intensive metabolism results in often low circulating levels of the original products, with the consequence that final health effects of botanicals are often related to specific active metabolites which are produced in the body rather than being related to the product's original composition. Understanding how such metabolic processes contribute to the in situ exposure is therefore crucial for the proper interpretation of biological responses. A multidisciplinary approach, characterizing the food and phytochemical intake as well as the metabolic potency of the gut microbiota, while measuring biomarkers of both exposure and response in target tissues, is therefore of critical importance. With polyphenol metabolism as example, this review describes how the incorporation of microbial metabolism as an important variable in the evaluation of the final bioactivity of botanicals strongly increases the relevance and predictive value of the outcome. Moreover, knowledge about intestinal processes may offer innovative strategies for targeted product development.}, }
@article {pmid20652237, year = {2010}, author = {Païssé, S and Goñi-Urriza, M and Coulon, F and Duran, R}, title = {How a bacterial community originating from a contaminated coastal sediment responds to an oil input.}, journal = {Microbial ecology}, volume = {60}, number = {2}, pages = {394-405}, pmid = {20652237}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*metabolism ; Biodegradation, Environmental ; DNA, Bacterial/genetics ; Gas Chromatography-Mass Spectrometry ; Geologic Sediments/chemistry/*microbiology ; Hydrocarbons/metabolism ; *Microbial Consortia ; Petroleum/*metabolism ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Bacterial communities inhabiting coastal sediments are subjected to oil spills. In order to examine the early structural response of a complex bacterial community to oil pollution, a kinetic study of the crude oil impact on bacterial communities inhabiting sediments from the contaminated Etang-de-Berre lagoon was performed. The sediments were maintained in slurries in presence or absence of crude oil and the kinetic study was carried out 14 days. During this period, 54% of crude oil was biodegraded showing the importance of the early degradation step. The metabolically active community (16S rRNA transcript analysis) was immediately impacted by the oil input, observed as an apparent decrease of species richness in the first hour of incubation. Nevertheless, this shift was quickly reversed, highlighting a fast, adaptative and efficient response of the metabolically active bacterial population. The high proportion of sequences related to hydrocarbonoclastic strains or petroleum-associated clones in active oiled community was consistent with significant increasing numbers of cultivable hydrocarbonoclastic bacteria at the end of the experiment. We concluded that "Etang-de-Berre" bacterial communities inhabiting oiled sediments for decades adopted a specific structure depending on oil presence and were able to face hydrocarbon contamination quickly and efficiently.}, }
@article {pmid20652236, year = {2010}, author = {Paver, SF and Kent, AD}, title = {Temporal patterns in glycolate-utilizing bacterial community composition correlate with phytoplankton population dynamics in humic lakes.}, journal = {Microbial ecology}, volume = {60}, number = {2}, pages = {406-418}, pmid = {20652236}, issn = {1432-184X}, mesh = {Alcohol Oxidoreductases/genetics ; Bacteria/classification/genetics/growth &amp; development ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Fresh Water/*microbiology ; Genes, Bacterial ; Glycolates/*metabolism ; *Microbial Consortia ; Phylogeny ; Phytoplankton/*growth &amp; development/microbiology ; Polymorphism, Restriction Fragment Length ; Population Dynamics ; Sequence Analysis, DNA ; Time Factors ; *Water Microbiology ; }, abstract = {Previous observations of correlated community dynamics between phytoplankton and bacteria in lakes indicate that phytoplankton populations may influence bacterial community structure. To investigate the possibility that bacterial use of phytoplankton exudates contributes to observed patterns of community change, we characterized the diversity and dynamics of heterotrophic bacterioplankton with genetic potential to use glycolate, a photorespiration-specific exudate, in five lakes over a 15-week period. Culture-independent approaches were used to track different bacterial phylotypes represented by DNA sequence variation in the functional gene glycolate oxidase subunit D (glcD). glcD gene sequences from freshwater bacteria exhibited broad phylogenetic diversity, including sequences representing the Alpha-, Beta-, and Gammaproteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Verrucomicrobia. The majority of glcD gene sequences were betaproteobacterial, with 48% of the sequences clustering with the glcD gene from the cosmopolitan freshwater species Polynucleobacter necessarius. Terminal restriction fragment length polymorphism fingerprinting of the glcD gene revealed changes in glycolate-utilizing assemblages over time. An average of 39% of within-lake temporal variation in glycolate-utilizing assemblages across five lakes was explained by phytoplankton community composition and dynamics. The interaction between phytoplankton populations and the environment explained an additional 17% of variation on average. These observations offer new insight into the diversity and temporal dynamics of freshwater bacteria with genetic potential to use glycolate and support the hypothesis that algal exudates influence the structure of bacterial communities.}, }
@article {pmid20650504, year = {2010}, author = {Oehmen, A and Carvalho, G and Lopez-Vazquez, CM and van Loosdrecht, MC and Reis, MA}, title = {Incorporating microbial ecology into the metabolic modelling of polyphosphate accumulating organisms and glycogen accumulating organisms.}, journal = {Water research}, volume = {44}, number = {17}, pages = {4992-5004}, doi = {10.1016/j.watres.2010.06.071}, pmid = {20650504}, issn = {1879-2448}, mesh = {Anaerobiosis ; Bacteria/*metabolism ; Citric Acid Cycle ; *Ecological and Environmental Phenomena ; Glycogen/*metabolism ; Glycolysis ; *Models, Biological ; Polyphosphates/*metabolism ; }, abstract = {In the enhanced biological phosphorus removal (EBPR) process, the competition between polyphosphate accumulating organisms (PAO) and glycogen accumulating organisms (GAO) has been studied intensively in recent years by both microbiologists and engineers, due to its important effects on phosphorus removal performance and efficiency. This study addresses the impact of microbial ecology on assessing the PAO-GAO competition through metabolic modelling, focussing on reviewing recent developments, discussion of how the results from molecular studies can impact the way we model the process, and offering perspectives for future research opportunities based on unanswered questions concerning PAO and GAO metabolism. Indeed, numerous findings that are seemingly contradictory could in fact be explained by the metabolic behaviour of different sub-groups of PAOs and/or GAOs exposed to different environmental and operational conditions. Some examples include the glycolysis pathway (i.e. Embden-Meyerhof-Parnas (EMP) vs. Entner-Doudoroff (ED)), denitrification capacity, anaerobic tricarboxylic acid (TCA) cycle activity and PAOs' ability to adjust their metabolism to e.g. a GAO-like metabolism. Metabolic modelling may further yield far-reaching influences on practical applications as well, and serves as a bridge between molecular/biochemical research studies and the optimisation of wastewater treatment plant operation.}, }
@article {pmid20621241, year = {2010}, author = {Wade, WG}, title = {New aspects and new concepts of maintaining "microbiological" health.}, journal = {Journal of dentistry}, volume = {38 Suppl 1}, number = {}, pages = {S21-5}, doi = {10.1016/S0300-5712(10)70007-5}, pmid = {20621241}, issn = {1879-176X}, mesh = {Bacteria/*classification ; *Biofilms ; Dental Plaque/microbiology/*prevention &amp; control ; Humans ; *Microbial Interactions ; Mouth/*microbiology/physiology ; Probiotics ; }, abstract = {The human mouth is host to a diverse collection of microorganisms including bacteria, viruses, fungi and protozoa. Recent advances using molecular methods for the analysis of complex bacterial communities have demonstrated the richness of the oral bacterial biota and the presence of numerous previously undescribed lineages. Dental plaque forms in a structured way with pioneer species able to colonise pellicle-coated enamel followed by secondary plaque formers such as Fusobacterium nucleatum that have the capability of coaggregating with a range of other genera and species. The mature plaque biofilm has many features of multicellular organisms with the constituent organisms cooperating to make nutrients available and resist environmental stresses, and communicating to regulate their overall numbers. Control of the oral microbiota to prevent disease has conventionally been by mechanical means augmented with toothpastes and mouthrinses, but improved knowledge of oral microbial ecology is allowing the development of pre and pro-biotic approaches. Other possibilities include interference with the plaque formation process and the perturbation of bacterial communication networks.}, }
@article {pmid20644925, year = {2010}, author = {Buddrus-Schiemann, K and Schmid, M and Schreiner, K and Welzl, G and Hartmann, A}, title = {Root colonization by Pseudomonas sp. DSMZ 13134 and impact on the indigenous rhizosphere bacterial community of barley.}, journal = {Microbial ecology}, volume = {60}, number = {2}, pages = {381-393}, pmid = {20644925}, issn = {1432-184X}, mesh = {Antibiosis ; DNA, Bacterial/genetics ; Hordeum/*microbiology ; In Situ Hybridization, Fluorescence ; Microscopy, Confocal ; Oligonucleotide Probes ; Phylogeny ; Plant Roots/*microbiology ; Polymorphism, Restriction Fragment Length ; Pseudomonas/genetics/*growth &amp; development ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Over the last few decades, the ability of rhizosphere bacteria to promote plant growth has been considered to be of scientific, ecological, and economic interest. The properties and mechanisms of interaction of these root-colonizing bacteria have been extensively investigated, and plant protection agents that are based on these bacterial strains have been developed for agricultural applications. In the present study, the root colonization of barley by Pseudomonas sp. DSMZ 13134, that is contained in the commercially available plant protection agent Proradix, was examined using the fluorescence in situ hybridization method with oligonucleotide probes and specific gfp-tagging of the inoculant strain in combination with confocal laser scanning microscopy. In the first phase of root colonization, the inoculant strain competed successfully with seed and soil-borne bacteria (including Pseudomonads) for the colonization of the rhizoplane. Pseudomonas sp. DSMZ 13134 could be detected in all parts of the roots, although it did not belong to the dominant members of the root-associated bacterial community. Gfp-tagged cells were localized particularly in the root hair zone, and high cell densities were apparent on the root hair surface. To investigate the impact of the application of Proradix on the structure of the dominant root-associated bacterial community of barley, T-RFLP analyses were performed. Only a transient community effect was found until 3 weeks post-application.}, }
@article {pmid20640571, year = {2010}, author = {Czirják, GA and Møller, AP and Mousseau, TA and Heeb, P}, title = {Microorganisms associated with feathers of barn swallows in radioactively contaminated areas around chernobyl.}, journal = {Microbial ecology}, volume = {60}, number = {2}, pages = {373-380}, pmid = {20640571}, issn = {1432-184X}, mesh = {Animals ; Bacteria/isolation &amp; purification ; *Bacterial Load ; *Chernobyl Nuclear Accident ; Feathers/*microbiology ; Female ; Fungi/isolation &amp; purification ; Male ; Swallows/*microbiology ; }, abstract = {The Chernobyl catastrophe provides a rare opportunity to study the ecological and evolutionary consequences of low-level, environmental radiation on living organisms. Despite some recent studies about negative effects of environmental radiation on macroorganisms, there is little knowledge about the effect of radioactive contamination on diversity and abundance of microorganisms. We examined abundance patterns of total cultivable bacteria and fungi and the abundance of feather-degrading bacterial subset present on feathers of barn swallows (Hirundo rustica), a colonial migratory passerine, around Chernobyl in relation to levels of ground level environmental radiation. After controlling for confounding variables, total cultivable bacterial loads were negatively correlated with environmental radioactivity, whereas abundance of fungi and feather-degrading bacteria was not significantly related to contamination levels. Abundance of both total and feather-degrading bacteria increased with barn swallow colony size, showing a potential cost of sociality. Males had lower abundance of feather-degrading bacteria than females. Our results show the detrimental effects of low-level environmental radiation on total cultivable bacterial assemblage on feathers, while the abundance of other microorganism groups living on barn swallow feathers, such as feather-degrading bacteria, are shaped by other factors like host sociality or host sex. These data lead us to conclude that the ecological effects of Chernobyl may be more general than previously assumed and may have long-term implications for host-microbe interactions and overall ecosystem functioning.}, }
@article {pmid20637597, year = {2010}, author = {Röling, WF and Ferrer, M and Golyshin, PN}, title = {Systems approaches to microbial communities and their functioning.}, journal = {Current opinion in biotechnology}, volume = {21}, number = {4}, pages = {532-538}, doi = {10.1016/j.copbio.2010.06.007}, pmid = {20637597}, issn = {1879-0429}, mesh = {Genome, Bacterial ; *Microbiology ; *Systems Biology ; }, abstract = {Recent advances in molecular microbial ecology and systems biology enhance insight into microbial community structure and functioning. They provide conceptual and technical bases for the translation of species-data and community-data into a model framework accounting for the functioning of and interactions between metabolic networks of species in multispecies environments. Function-directed and single cell-directed approaches supplement and improve metagenomics-derived community information. The topology of the metabolic network, reconstructed from a species' genome sequence, provides insight into its metabolic environments and interactions with other microorganisms. Progress in the theoretical and experimental analysis of flux through metabolic networks paves the way for their application at the community level, contributing to understanding of material flows between and within species and their resilience toward perturbations.}, }
@article {pmid20635180, year = {2010}, author = {Bapiri, A and Bååth, E and Rousk, J}, title = {Drying-rewetting cycles affect fungal and bacterial growth differently in an arable soil.}, journal = {Microbial ecology}, volume = {60}, number = {2}, pages = {419-428}, pmid = {20635180}, issn = {1432-184X}, mesh = {Bacteria/*growth &amp; development ; Biomass ; *Desiccation ; Fungi/*growth &amp; development ; Soil/analysis ; *Soil Microbiology ; Water/metabolism ; }, abstract = {Drying and rewetting is a frequent physiological stress for soil microbial communities; a stress that is predicted to grow more influential with future climate change. We investigated the effect of repeated drying-rewetting cycles on bacterial (leucine incorporation) and fungal (acetate in ergosterol incorporation) growth, on the biomass concentration and composition (PLFA), and on the soil respiration. Using different plant material amendments, we generated soils with different initial fungal:bacterial compositions that we exposed to 6-10 repetitions of a drying-rewetting cycle. Drying-rewetting decreased bacterial growth while fungal growth remained unaffected, resulting in an elevated fungal:bacterial growth ratio. This effect was found irrespective of the initial fungal:bacterial biomass ratio. Many drying-rewetting cycles did not, however, affect the fungal:bacterial growth ratio compared to few cycles. The biomass response of the microbial community differed from the growth response, with fungal and total biomass only being slightly negatively affected by the repeated drying-rewetting. The discrepancy between growth- and biomass-based assessments underscores that microbial responses to perturbations might previously have been misrepresented with biomass-based assessments. In light of this, many aspects of environmental microbial ecology may need to be revisited with attention to what measure of the microbial community is relevant to study.}, }
@article {pmid20632001, year = {2010}, author = {de-Bashan, LE and Hernandez, JP and Nelson, KN and Bashan, Y and Maier, RM}, title = {Growth of quailbush in acidic, metalliferous desert mine tailings: effect of Azospirillum brasilense Sp6 on biomass production and rhizosphere community structure.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {915-927}, pmid = {20632001}, issn = {1432-184X}, support = {P42 ES004940/ES/NIEHS NIH HHS/United States ; 2 P42 ES04940-11/ES/NIEHS NIH HHS/United States ; }, mesh = {Acids/analysis ; Atriplex/*growth &amp; development/*microbiology ; Azospirillum brasilense/genetics/*growth &amp; development/isolation &amp; purification ; Biomass ; Geologic Sediments/analysis ; Metals/analysis ; Mining ; *Rhizosphere ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Mine tailing deposits in semiarid and arid environments frequently remain devoid of vegetation due to the toxicity of the substrate and the absence of a diverse soil microbial community capable of supporting seed germination and plant growth. The contribution of the plant growth promoting bacterium (PGPB) Azospirillum brasilense Sp6 to the growth of quailbush in compost-amended, moderately acidic, high-metal content mine tailings using an irrigation-based reclamation strategy was examined along with its influence on the rhizosphere bacterial community. Sp6 inoculation resulted in a significant (2.2-fold) increase in plant biomass production. The data suggest that the inoculum successfully colonized the root surface and persisted throughout the 60-day experiment in both the rhizosphere, as demonstrated by excision and sequencing of the appropriate denaturing gradient gel electrophoresis (DGGE) band, and the rhizoplane, as indicated by fluorescent in situ hybridization of root surfaces. Changes in rhizosphere community structure in response to Sp6 inoculation were evaluated after 15, 30, and 60 days using DGGE analysis of 16S rRNA polymerase chain reaction amplicons. A comparison of DGGE profiles using canonical correspondence analysis revealed a significant treatment effect (Sp6-inoculated vs. uninoculated plants vs. unplanted) on bacterial community structure at 15, 30, and 60 days (p < 0.05). These data indicate that in an extremely stressed environment such as acid mine tailings, an inoculated plant growth promoting bacterium not only can persist and stimulate plant growth but also can directly or indirectly influence rhizobacterial community development.}, }
@article {pmid20632000, year = {2011}, author = {Fittipaldi, M and Codony, F and Adrados, B and Camper, AK and Morató, J}, title = {Viable real-time PCR in environmental samples: can all data be interpreted directly?.}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {7-12}, pmid = {20632000}, issn = {1432-184X}, mesh = {Bacterial Load/*methods ; *Environmental Microbiology ; Legionella pneumophila/genetics/physiology ; *Microbial Viability ; Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; }, abstract = {Selective nucleic acid intercalating dyes--ethidium monoazide (EMA) and propidium monoazide (PMA)--represent one of the most successful recent approaches to detect viable cells (as defined by an intact cell membrane) by PCR and have been effectively evaluated in different microorganisms. However, some practical limitations were found, especially in environmental samples. The aim of this work was to show that in the application of viable real-time PCR, there may be significant biases and to propose a strategy for overcoming some of these problems. We present an approach based on the combination of three real-time PCR amplifications for each sample that should provide an improved estimation of the number of viable cells. This approach could be useful especially when it is difficult to determine a priori how to optimize methods using PMA or EMA. Although further studies are required to improve viable real-time PCR methods, the concept as outlined here presents an interesting future research direction.}, }
@article {pmid20631808, year = {2011}, author = {Amaral-Zettler, LA and Zettler, ER and Theroux, SM and Palacios, C and Aguilera, A and Amils, R}, title = {Microbial community structure across the tree of life in the extreme Río Tinto.}, journal = {The ISME journal}, volume = {5}, number = {1}, pages = {42-50}, pmid = {20631808}, issn = {1751-7370}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biota ; *Environment ; Eukaryota/classification/genetics ; Genes, rRNA/genetics ; *Rivers ; Spain ; }, abstract = {Understanding biotic versus abiotic forces that shape community structure is a fundamental aim of microbial ecology. The acidic and heavy metal extreme Río Tinto (RT) in southwestern Spain provides a rare opportunity to conduct an ecosystem-wide biodiversity inventory at the level of all three domains of life, because diversity there is low and almost exclusively microbial. Despite improvements in high-throughput DNA sequencing, environmental biodiversity studies that use molecular metrics and consider entire ecosystems are rare. These studies can be prohibitively expensive if domains are considered separately, and differences in copy number of eukaryotic ribosomal RNA genes can bias estimates of relative abundances of phylotypes recovered. In this study we have overcome these barriers (1) by targeting all three domains in a single polymerase chain reaction amplification and (2) by using a replicated sampling design that allows for incidence-based methods to extract measures of richness and carry out downstream analyses that address community structuring effects. Our work showed that combined bacterial and archaeal richness is an order of magnitude higher than eukaryotic richness. We also found that eukaryotic richness was highest at the most extreme sites, whereas combined bacterial and archaeal richness was highest at less extreme sites. Quantitative community phylogenetics showed abiotic forces to be primarily responsible for shaping the RT community structure. Canonical correspondence analysis revealed co-occurrence of obligate symbionts and their putative hosts that may contribute to biotic forces shaping community structure and may further provide a possible mechanism for persistence of certain low-abundance bacteria encountered in the RT.}, }
@article {pmid20629797, year = {2010}, author = {Crab, R and Lambert, A and Defoirdt, T and Bossier, P and Verstraete, W}, title = {The application of bioflocs technology to protect brine shrimp (Artemia franciscana) from pathogenic Vibrio harveyi.}, journal = {Journal of applied microbiology}, volume = {109}, number = {5}, pages = {1643-1649}, doi = {10.1111/j.1365-2672.2010.04791.x}, pmid = {20629797}, issn = {1365-2672}, mesh = {Animals ; Anti-Infective Agents/pharmacology ; Aquaculture ; Artemia/drug effects/*microbiology ; Glycerol/pharmacology ; Larva/microbiology ; Quorum Sensing/drug effects ; Vibrio/physiology ; }, abstract = {AIMS: To study the potential biocontrol activity of bioflocs technology.<br><br>METHODS AND RESULTS: Glycerol-grown bioflocs were investigated for their antimicrobial and antipathogenic properties against the opportunistic pathogen Vibrio harveyi. The bioflocs did not produce growth-inhibitory substances. However, bioflocs and biofloc supernatants decreased quorum sensing-regulated bioluminescence of V. harveyi. This suggested that the bioflocs had biocontrol activity against this pathogen because quorum sensing regulates virulence of vibrios towards different hosts. Interestingly, the addition of live bioflocs significantly increased the survival of gnotobiotic brine shrimp (Artemia franciscana) larvae challenged to V. harveyi.<br><br>CONCLUSIONS: Bioflocs grown on glycerol as carbon source inhibit quorum sensing-regulated bioluminescence in V. harveyi and protect brine shrimp larvae from vibriosis.<br><br>The results presented in this study indicate that in addition to water quality control and in situ feed production, bioflocs technology could help in controlling bacterial infections within the aquaculture pond.}, }
@article {pmid20627208, year = {2010}, author = {Ercolini, D and Casaburi, A and Nasi, A and Ferrocino, I and Di Monaco, R and Ferranti, P and Mauriello, G and Villani, F}, title = {Different molecular types of Pseudomonas fragi have the same overall behaviour as meat spoilers.}, journal = {International journal of food microbiology}, volume = {142}, number = {1-2}, pages = {120-131}, doi = {10.1016/j.ijfoodmicro.2010.06.012}, pmid = {20627208}, issn = {1879-3460}, mesh = {Animals ; Cattle ; Chickens ; Food Contamination/*analysis ; Meat/analysis/*microbiology ; Molecular Sequence Data ; Phylogeny ; Pseudomonas fragi/classification/genetics/*isolation &amp; purification/metabolism ; Swine ; Volatile Organic Compounds/metabolism ; }, abstract = {The functional diversity of a population of sixty-five different strains of P. fragi isolated from fresh and spoiled meat was studied in order to evaluate the population heterogeneity related to meat spoilage potential. The strains were characterized for the proteolytic activity at 4 degrees C on beef sarcoplasmic proteins and only 9 strains were found to be proteolytic. An iron-dependent growth behaviour was shown when each strain was grown in citrate medium containing either myoglobin, haemoglobin or iron chloride as iron sources. Increase of maximum population and mu(max) in presence of different iron sources was registered. The release of volatile organic compounds (VOC) by each strain in beef during aerobic storage at 4 degrees C was evaluated by GC-MS. A considerable variability of occurrence of each molecule in the GC-MS profiles obtained by the different strains was observed ranging from 3% to 79% although the strains showed a high degree of similarity. In particular, ethylhexanoate, ethyloctanoate, ethylnonenoate, ethyldecanoate, 1-octen-3-ol, 3-octanone, 4-methylthiophenol, and 2-pentylfurane were produced by more than 50% of the strains. Representative strains were used to spoil meat in the same conditions used for the VOC analysis and the samples were evaluated by a sensory panel. The results of the sensory analysis indicated that the different strains could significantly affect the odour of meat and strains characterized by production of esters gave fruity odours to the spoiled meat. However, the similarity of strains based on the sensory profiles does not necessarily match the similarity shown in VOC profiles. P. fragi has a significant role in the microbial ecology of meat and the influence of meat-related sources of iron on the growth behaviour of many different strains suggests that meat can be an ecological niche for P. fragi. Regardless of the proteolytic and lipolytic capacities shown in vitro, different molecular types of P. fragi can release odour active volatile molecules and play a similar overall role as spoilage agents of meat.}, }
@article {pmid20625714, year = {2010}, author = {U'ren, JM and Lutzoni, F and Miadlikowska, J and Arnold, AE}, title = {Community analysis reveals close affinities between endophytic and endolichenic fungi in mosses and lichens.}, journal = {Microbial ecology}, volume = {60}, number = {2}, pages = {340-353}, pmid = {20625714}, issn = {1432-184X}, mesh = {Arizona ; *Biodiversity ; Bryophyta/*microbiology ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fungi/*classification/genetics/isolation &amp; purification ; Lichens/*microbiology ; Phylogeny ; Plant Leaves/microbiology ; Sequence Analysis, DNA ; *Symbiosis ; Trees/microbiology ; }, abstract = {Endolichenic fungi live in close association with algal photobionts inside asymptomatic lichen thalli and resemble fungal endophytes of plants in terms of taxonomy, diversity, transmission mode, and evolutionary history. This similarity has led to uncertainty regarding the distinctiveness of endolichenic fungi compared with endophytes. Here, we evaluate whether these fungi represent distinct ecological guilds or a single guild of flexible symbiotrophs capable of colonizing plants or lichens indiscriminately. Culturable fungi were sampled exhaustively from replicate sets of phylogenetically diverse plants and lichens in three microsites in a montane forest in southeastern Arizona (USA). Intensive sampling combined with a small spatial scale permitted us to decouple spatial heterogeneity from host association and to sample communities from living leaves, dead leaves, and lichen thalli to statistical completion. Characterization using data from the nuclear ribosomal internal transcribed spacer and partial large subunit (ITS-LSU rDNA) provided a first estimation of host and substrate use for 960 isolates representing five classes and approximately 16 orders, 32 families, and 65 genera of Pezizomycotina. We found that fungal communities differ at a broad taxonomic level as a function of the phylogenetic placement of their plant or lichen hosts. Endolichenic fungal assemblages differed as a function of lichen taxonomy, rather than substrate, growth form, or photobiont. In plants, fungal communities were structured more by plant lineage than by the living vs. senescent status of the leaf. We found no evidence that endolichenic fungi are saprotrophic fungi that have been "entrapped" by lichen thalli. Instead, our study reveals the distinctiveness of endolichenic communities relative to those in living and dead plant tissues, with one notable exception: we identify, for the first time, an ecologically flexible group of symbionts that occurs both as endolichenic fungi and as endophytes of mosses.}, }
@article {pmid20625713, year = {2010}, author = {He, X and Tian, Y and Guo, L and Lux, R and Zusman, DR and Shi, W}, title = {Oral-derived bacterial flora defends its domain by recognizing and killing intruders--a molecular analysis using Escherichia coli as a model intestinal bacterium.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {655-664}, pmid = {20625713}, issn = {1432-184X}, support = {R01 GM020509/GM/NIGMS NIH HHS/United States ; R01 GM054666/GM/NIGMS NIH HHS/United States ; GM54666/GM/NIGMS NIH HHS/United States ; GM20509/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Antibiosis ; Coculture Techniques ; Escherichia coli/growth &amp; development/*physiology ; Hydrogen Peroxide/metabolism ; Intestines/*microbiology ; Lipopolysaccharides/biosynthesis ; Mice ; Mouth/*microbiology ; Oxidative Stress ; }, abstract = {Within the same human gastrointestinal tract, substantial differences in the bacterial species that inhabit oral cavity and intestinal tract have been noted. Previous research primarily attributed the differences to the influences of host environments and nutritional availabilities ("host habitat" effect). Our recent study indicated that, other than the host habitat effect, an existing microbial community could impose a selective pressure on incoming foreign bacterial species independent of host-mediated selection ("community selection" effect). In this study, we employed in vitro microbial floras representing microorganisms that inhabit the oral cavities and intestinal tract of mice in combination with Escherichia coli as a model intestinal bacterium and demonstrated that E. coli displays a striking community preference. It thrived when introduced into the intestinal microbial community and survived poorly in the microbial flora of foreign origin (oral community). A more detailed examination of this phenomenon showed that the oral community produced oxygen-free radicals in the presence of wild-type E. coli while mutants deficient in lipopolysaccharides (LPS) did not trigger significant production of these cell-damaging agents. Furthermore, mutants of E. coli defective in the oxidative stress response experienced a more drastic reduction in viability when cocultivated with the oral flora, while the exogenous addition of the antioxidant vitamin C was able to rescue it. We concluded that the oral-derived microbial community senses the E. coli LPS and kills the bacterium with oxygen-free radicals. This study reveals a new mechanism of community invasion resistance employed by established microflora to defend their domains.}, }
@article {pmid20625712, year = {2010}, author = {He, X and Tian, Y and Guo, L and Ano, T and Lux, R and Zusman, DR and Shi, W}, title = {In vitro communities derived from oral and gut microbial floras inhibit the growth of bacteria of foreign origins.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {665-676}, pmid = {20625712}, issn = {1432-184X}, support = {R01 GM054666/GM/NIGMS NIH HHS/United States ; GM54666/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Antibiosis ; Bacteria/*growth &amp; development ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Gastrointestinal Tract/*microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Mouth/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The gastrointestinal (GI) tract is home to trillions of microbes. Within the same GI tract, substantial differences in the bacterial species that inhabit the oral cavity and intestinal tract have been noted. While the influence of host environments and nutritional availability in shaping different microbial communities is widely accepted, we hypothesize that the existing microbial flora also plays a role in selecting the bacterial species that are being integrated into the community. In this study, we used cultivable microbial communities isolated from different parts of the GI tract of mice (oral cavity and intestines) as a model system to examine this hypothesis. Microbes from these two areas were harvested and cultured using the same nutritional conditions, which led to two distinct microbial communities, each with about 20 different species as revealed by PCR-based denaturing gradient gel electrophoresis analysis. In vitro community competition assays showed that the two microbial floras exhibited antagonistic interactions toward each other. More interestingly, all the original isolates tested and their closely related species displayed striking community preferences: They persisted when introduced into the bacterial community of the same origin, while their viable count declined more than three orders of magnitude after 4 days of coincubation with the microbial flora of foreign origin. These results suggest that an existing microbial community might impose a selective pressure on incoming foreign bacterial species independent of host selection. The observed inter-flora interactions could contribute to the protective effect of established microbial communities against the integration of foreign bacteria to maintain the stability of the existing communities.}, }
@article {pmid20624973, year = {2010}, author = {Lücker, S and Wagner, M and Maixner, F and Pelletier, E and Koch, H and Vacherie, B and Rattei, T and Damsté, JS and Spieck, E and Le Paslier, D and Daims, H}, title = {A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {30}, pages = {13479-13484}, pmid = {20624973}, issn = {1091-6490}, mesh = {Amino Acid Sequence ; Bacteria/classification/*genetics/*metabolism ; Bacterial Physiological Phenomena ; Bacterial Proteins/classification/genetics/metabolism ; Carbon Dioxide/metabolism ; Chromosomes, Bacterial/genetics ; Citric Acid Cycle/physiology ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Genome, Bacterial/*genetics ; Metagenome/genetics ; Metagenomics ; Molecular Sequence Data ; Nitrite Reductases/genetics/metabolism ; Nitrites/*metabolism ; Oxidation-Reduction ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Sewage/microbiology ; }, abstract = {Nitrospira are barely studied and mostly uncultured nitrite-oxidizing bacteria, which are, according to molecular data, among the most diverse and widespread nitrifiers in natural ecosystems and biological wastewater treatment. Here, environmental genomics was used to reconstruct the complete genome of "Candidatus Nitrospira defluvii" from an activated sludge enrichment culture. On the basis of this first-deciphered Nitrospira genome and of experimental data, we show that Ca. N. defluvii differs dramatically from other known nitrite oxidizers in the key enzyme nitrite oxidoreductase (NXR), in the composition of the respiratory chain, and in the pathway used for autotrophic carbon fixation, suggesting multiple independent evolution of chemolithoautotrophic nitrite oxidation. Adaptations of Ca. N. defluvii to substrate-limited conditions include an unusual periplasmic NXR, which is constitutively expressed, and pathways for the transport, oxidation, and assimilation of simple organic compounds that allow a mixotrophic lifestyle. The reverse tricarboxylic acid cycle as the pathway for CO2 fixation and the lack of most classical defense mechanisms against oxidative stress suggest that Nitrospira evolved from microaerophilic or even anaerobic ancestors. Unexpectedly, comparative genomic analyses indicate functionally significant lateral gene-transfer events between the genus Nitrospira and anaerobic ammonium-oxidizing planctomycetes, which share highly similar forms of NXR and other proteins reflecting that two key processes of the nitrogen cycle are evolutionarily connected.}, }
@article {pmid20624647, year = {2010}, author = {Vassallo, MF and Camargo, CA}, title = {Potential mechanisms for the hypothesized link between sunshine, vitamin D, and food allergy in children.}, journal = {The Journal of allergy and clinical immunology}, volume = {126}, number = {2}, pages = {217-222}, doi = {10.1016/j.jaci.2010.06.011}, pmid = {20624647}, issn = {1097-6825}, support = {T32 AI-060548/AI/NIAID NIH HHS/United States ; }, mesh = {Allergens/immunology/metabolism ; Child ; Child, Preschool ; Epithelium/immunology/metabolism/physiopathology ; Female ; *Food Hypersensitivity/epidemiology/immunology/metabolism/physiopathology ; Gastrointestinal Diseases/epidemiology/immunology/metabolism/physiopathology ; Humans ; Immune Tolerance/immunology/radiation effects ; Immunity, Mucosal/immunology/radiation effects ; Male ; Models, Theoretical ; *Sunlight ; Ultraviolet Rays ; Vitamin D/*immunology/metabolism ; *Vitamin D Deficiency/epidemiology/immunology/metabolism/physiopathology ; }, abstract = {Epidemiologic data suggest that the incidence of food allergy (FA) is increasing among children, yet a satisfactory model of its pathogenesis remains elusive. FA is the consequence of maladaptive immune responses to common and otherwise innocuous food antigens. Concurrent with the increase in FA is an epidemic of vitamin D deficiency (VDD) caused by several factors, especially decreased sunlight/UVB exposure. There is growing appreciation of the importance of the pleiotropic hormone vitamin D in the development of tolerance, immune system defenses, and epithelial barrier integrity. We propose a "multiple-hit" model in which VDD in a developmentally critical period increases susceptibility to colonization with abnormal intestinal microbial flora and gastrointestinal infections, contributing to abnormal intestinal barrier permeability and excess and inappropriate exposure of the immune system to dietary allergens. A compounding effect (and additional "hit") of VDD is the promotion of a pro-sensitization immune imbalance that might compromise immunologic tolerance and contribute to FA. We propose that early correction of VDD might promote mucosal immunity, healthy microbial ecology, and allergen tolerance and thereby blunt the FA epidemic in children.}, }
@article {pmid20624605, year = {2010}, author = {He, Z and Zhao, J and Gao, F and Hu, Y and Qiu, G}, title = {Monitoring bacterial community shifts in bioleaching of Ni-Cu sulfide.}, journal = {Bioresource technology}, volume = {101}, number = {21}, pages = {8287-8293}, doi = {10.1016/j.biortech.2010.05.047}, pmid = {20624605}, issn = {1873-2976}, mesh = {Bacteria/genetics/*metabolism ; Base Sequence ; Biodegradation, Environmental ; Copper/analysis ; Electrophoresis, Agar Gel ; Hydrogen-Ion Concentration ; Industrial Waste/analysis ; Iron/analysis ; Mining ; Nickel/*isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Solutions ; Sulfides/*isolation &amp; purification ; Zinc/analysis ; }, abstract = {The microbial ecology of the bioleaching of Ni-Cu sulfide is poorly understood and little effort has been made to handle the microbiological components of these processes. In this study, denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA genes fragments from bacteria was used to evaluate the changes of the bacterial community in the process of Ni-Cu sulfide bioleaching in a shaken flask system. The results revealed that the bacterial community was disturbed after the addition of Ni-Cu sulfide. Phylogenetic analyses of 16S rRNA fragments revealed that the retrieved sequences clustered together with the genera Acidithiobacillus and Leptospirillum. Multidimensional scaling (MDS) and cluster analysis of DGGE-banding patterns revealed that the process of Ni-Cu sulfide bioleaching in 46days was divided into three stages. During the bioleaching process of Ni-Cu sulfide, Leptospirillum was always dominant. The genera Acidithiobacillus was only detected at early and later stages of the bioleaching process. These results extend our knowledge on microbial dynamics in Ni-Cu sulfide bioleaching, a key issue required to improve commercial applications.}, }
@article {pmid20624475, year = {2010}, author = {Connolly, ML and Lovegrove, JA and Tuohy, KM}, title = {In vitro evaluation of the microbiota modulation abilities of different sized whole oat grain flakes.}, journal = {Anaerobe}, volume = {16}, number = {5}, pages = {483-488}, doi = {10.1016/j.anaerobe.2010.07.001}, pmid = {20624475}, issn = {1095-8274}, mesh = {Avena/*chemistry ; Bacteria/*growth &amp; development/metabolism ; Digestion ; Edible Grain ; Feces/microbiology ; *Fermentation ; Functional Food ; Humans ; *Prebiotics ; }, abstract = {Epidemiological studies and healthy eating guidelines suggest a positive correlation between ingestion of whole grain cereal and food rich in fibre with protection from chronic diseases. The prebiotic potential of whole grains may be related, however, little is known about the microbiota modulatory capability of oat grain or the impact processing has on this ability. In this study the fermentation profile of whole grain oat flakes, processed to produce two different sized flakes (small and large), by human faecal microbiota was investigated in vitro. Simulated digestion and subsequent fermentation by gut bacteria was investigated using pH controlled faecal batch cultures inoculated with human faecal slurry. The different sized oat flakes, Oat 23's (0.53-0.63 mm) and Oat 25's/26's (0.85-1.0 mm) were compared to oligofructose, a confirmed prebiotic, and cellulose, a poorly fermented carbohydrate. Bacterial enumeration was carried out using the culture independent technique, fluorescent in situ hybridisation, and short chain fatty acid (SCFA) production monitored by gas chromatography. Significant changes in total bacterial populations were observed after 24 h incubation for all substrates except Oat 23's and cellulose. Oats 23's fermentation resulted in a significant increase in the Bacteroides-Prevotella group. Oligofructose and Oats 25's/26's produced significant increases in Bifidobacterium in the latter stages of fermentation while numbers declined for Oats 23's between 5 h and 24 h. This is possibly due to the smaller surface area of the larger flakes inhibiting the simulated digestion, which may have resulted in increased levels of resistant starch (Bifidobacterium are known to ferment this dietary fibre). Fermentation of Oat 25's/26's resulted in a propionate rich SCFA profile and a significant increase in butyrate, which have both been linked to benefiting host health. The smaller sized oats did not produce a significant increase in butyrate concentration. This study shows for the first time the impact of oat grain on the microbial ecology of the human gut and its potential to beneficially modulate the gut microbiota through increasing Bifidobacterium population.}, }
@article {pmid20623868, year = {2010}, author = {Zhu, JN and Wang, XD and Zhai, ZH and Ma, WL and Li, RQ and Wang, XL and Li, YH}, title = {[Changes of bacterial community structure on reusing domestic sewage of Daoxianghujing Hotel to landscape water].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {31}, number = {5}, pages = {1299-1306}, pmid = {20623868}, issn = {0250-3301}, mesh = {Actinobacteria/growth &amp; development/isolation &amp; purification ; Bacteria/*classification/growth &amp; development ; China ; Cyanobacteria/growth &amp; development/isolation &amp; purification ; Population Dynamics ; Proteobacteria/*growth &amp; development/isolation &amp; purification ; RNA, Ribosomal, 16S/analysis ; Sewage/*microbiology ; Waste Disposal, Fluid/*methods ; *Water Microbiology ; }, abstract = {A 16S rDNA library was used to evaluate the bacterial diversity and identify dominant groups of bacteria in different treatment pools in the domestic sewage system of the Beijing Daoxianghujing Hotel. The results revealed that there were many types of bacteria in the hotel domestic sewage, and the bacterial Shannon-Weaver diversity index was 3.12. In addition, epsilon Proteobacteria was found to be the dominant group with the ratio of 32%. In addition, both the CFB phylum, Fusobacteria, gamma Proteobacteria and Firmicutes were also reached to 9%-15%. After treated with the reclaimed water station, the bacterial Shannon-Weaver diversity index was reduced to 2. 41 and beta Proteobacteria became the dominant group and occupied 73% of the total clones. However, following artificial wetland training, the bacterial Shannon-Weaver diversity index in the sample increased to 3.38, Actinobacteria arrived to 33% and became the most dominant group; Cyanobacteria reached to 26%, and was the second dominant group. But, the control sample comprised 38% Cyanobacteria, and mainly involved in Cyanobium, Synechoccus and Microcystis, with ratios of 47.1%, 17.6% and 8.8%, respectively. Some bacteria of Microcystis aenruginosa were also detected, which probably resulted in the light bloom finally. Therefore, the bacterial diversity and community structures changed in response to treatment of the hotel domestic sewage; there was no cyanobacteria bloom explosion in the treated water. This study will aid in investigation the changes of microbial ecology in different types of water and providing the useful information for enhancing the cyanobacteria blooms control from ecological angle.}, }
@article {pmid20623278, year = {2010}, author = {Lukjancenko, O and Wassenaar, TM and Ussery, DW}, title = {Comparison of 61 sequenced Escherichia coli genomes.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {708-720}, pmid = {20623278}, issn = {1432-184X}, mesh = {Chromosome Mapping ; Escherichia coli/classification/*genetics ; *Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Escherichia coli is an important component of the biosphere and is an ideal model for studies of processes involved in bacterial genome evolution. Sixty-one publically available E. coli and Shigella spp. sequenced genomes are compared, using basic methods to produce phylogenetic and proteomics trees, and to identify the pan- and core genomes of this set of sequenced strains. A hierarchical clustering of variable genes allowed clear separation of the strains into clusters, including known pathotypes; clinically relevant serotypes can also be resolved in this way. In contrast, when in silico MLST was performed, many of the various strains appear jumbled and less well resolved. The predicted pan-genome comprises 15,741 gene families, and only 993 (6%) of the families are represented in every genome, comprising the core genome. The variable or 'accessory' genes thus make up more than 90% of the pan-genome and about 80% of a typical genome; some of these variable genes tend to be co-localized on genomic islands. The diversity within the species E. coli, and the overlap in gene content between this and related species, suggests a continuum rather than sharp species borders in this group of Enterobacteriaceae.}, }
@article {pmid20623222, year = {2010}, author = {Andrews, G and Lewis, D and Notey, J and Kelly, R and Muddiman, D}, title = {Part I: characterization of the extracellular proteome of the extreme thermophile Caldicellulosiruptor saccharolyticus by GeLC-MS2.}, journal = {Analytical and bioanalytical chemistry}, volume = {398}, number = {1}, pages = {377-389}, pmid = {20623222}, issn = {1618-2650}, support = {T32 GM008776/GM/NIGMS NIH HHS/United States ; 5T32GM00-8776-08/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/analysis/*metabolism ; Chromatography, Liquid ; Electrophoresis, Polyacrylamide Gel ; Extracellular Space/*metabolism ; Gram-Positive Bacteria/*metabolism ; Proteome/*analysis ; Spectrometry, Mass, Electrospray Ionization ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Temperature ; }, abstract = {The proteome of extremely thermophilic microorganisms affords a glimpse into the dynamics of microbial ecology of high temperature environments. The secretome, or extracellular proteome of these microorganisms, no doubt harbors technologically important enzymes and other thermostable biomolecules that, to date, have been characterized only to a limited extent. In the first of a two-part study on selected thermophiles, defining the secretome requires a sample preparation method that has no negative impact on all downstream experiments. Following efficient secretome purification, GeLC-MS(2) analysis and prediction servers suggested probable protein secretion to complement experimental data. In an effort to define the extracellular proteome of the extreme thermophilic bacterium Caldicellulosiruptor saccharolyticus, several techniques were considered regarding sample processing to achieve the most in-depth analysis of secreted proteins. Order of operation experiments, all including the C(18) bead technique, demonstrated that two levels of sample purification were necessary to effectively desalt the sample and provide sufficient protein identifications. Five sample preparation combinations yielded 71 proteins and the majority described, as enzymatic and putative uncharacterized proteins, anticipate consolidated bioprocessing applications. Nineteen proteins were predicted by Phobius, SignalP, SecretomeP, or TatP for extracellular secretion, and 11 contained transmembrane domain stretches suggested by Phobius and transmembrane hidden Markov model. The sample preparation technique demonstrating the most effective outcome for C. saccharolyticus secreted proteins in this study, involved acetone precipitation followed by the C(18) bead method in which 2.4% (63 proteins) of the predicted proteome was identified, including proteins suggested to have secretion and transmembrane moieties.}, }
@article {pmid20620047, year = {2010}, author = {Beristain-Cardoso, R and Gómez, J and Méndez-Pampín, R}, title = {The behavior of nitrifying sludge in presence of sulfur compounds using a floating biofilm reactor.}, journal = {Bioresource technology}, volume = {101}, number = {22}, pages = {8593-8598}, doi = {10.1016/j.biortech.2010.06.084}, pmid = {20620047}, issn = {1873-2976}, mesh = {Bacteria, Anaerobic/*metabolism ; Bioreactors/*microbiology ; Quaternary Ammonium Compounds/*metabolism ; Sewage/*chemistry/*microbiology ; Sulfur Compounds/*chemistry/*metabolism ; }, abstract = {The tolerance, kinetic and oxidizing capability of a nitrifying sludge exposed to different initial concentrations of sulfide (1.7 to 18mg/L) was evaluated in batch experiments. A nitrifying sludge fed with ammonium and thiosulfate and produced in steady state conditions was used as inoculum. Sulfide induced a significant effect either on ammonium consumption rates or nitrite accumulation. In spite of the nitrifying kinetic was affected, the ammonium consumption efficiencies were close to 100%, with nitrate production yields around 1.0. The IC(50) value for ammonium oxidizing-process was 13mg/L of sulfide. Sulfide was oxidized in two steps: first sulfide was oxidized to elemental sulfur and afterward into sulfate. FISH oligonucleotide probes for Thiobacillusdenitrificans, Nitrosomonas spp., and Nitrobacter spp. were used in order to know if these bacteria were part of the microbial ecology. The obtained results showed that under nitrifying conditions are possible to carry out simultaneously two biological processes, nitrification and sulfur oxidation.}, }
@article {pmid20619799, year = {2010}, author = {Fadda, S and López, C and Vignolo, G}, title = {Role of lactic acid bacteria during meat conditioning and fermentation: peptides generated as sensorial and hygienic biomarkers.}, journal = {Meat science}, volume = {86}, number = {1}, pages = {66-79}, doi = {10.1016/j.meatsci.2010.04.023}, pmid = {20619799}, issn = {1873-4138}, mesh = {Biomarkers ; *Fermentation ; Food Handling/*methods ; Food Microbiology ; Food Preservation/methods ; Food, Preserved/analysis/microbiology ; Lactobacillales/*metabolism ; Meat Products/*analysis/*microbiology ; Peptides/*metabolism ; Proteomics/methods ; Quality Control ; *Sensation ; }, abstract = {The microbial ecology of meat fermentation is a complex process in which lactic acid bacteria (LAB) and coagulase-negative cocci play a major role. The present work reviews the most significant developments in which LAB are the main characters acting both as starter cultures improving the sensorial quality and as biopreservative agents. New findings about the identification of low molecular weight peptides arisen from protein hydrolysis in dry fermented sausages and their relation with flavor is presented. Also, a brief description of a proteomic approach is detailed in order to exemplify its application as a tool in the search for improved LAB strains that will contribute to food quality and safety. Finally, the most important features of bacteriocinogenic LAB and its bacteriocins in bioprotection of meat and meat products are analyzed.}, }
@article {pmid20614117, year = {2010}, author = {Ling, Z and Kong, J and Jia, P and Wei, C and Wang, Y and Pan, Z and Huang, W and Li, L and Chen, H and Xiang, C}, title = {Analysis of oral microbiota in children with dental caries by PCR-DGGE and barcoded pyrosequencing.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {677-690}, pmid = {20614117}, issn = {1432-184X}, mesh = {Bacteria/*genetics ; Child ; Child, Preschool ; China ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Dental Caries/*microbiology ; Dental Plaque/microbiology ; Female ; Humans ; Male ; *Metagenome ; Mouth/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; }, abstract = {Oral microbiota plays a vital role in maintaining the homeostasis of oral cavity. Dental caries are among the most common oral diseases in children and pathogenic bacteria contribute to the development of the disease. However, the overall structure of bacterial communities in the oral cavity from children with dental caries has not been explored deeply heretofore. We used high-throughput barcoded pyrosequencing and PCR-denaturing gradient gel electrophoresis (DGGE) to examine bacterial diversity of oral microbiota in saliva and supragingival plaques from 60 children aged 3 to 6 years old with and without dental caries from China. The multiplex barcoded pyrosequencing was performed in a single run, with multiple samples tagged uniquely by multiplex identifiers. As PCR-DGGE analysis is a conventional molecular ecological approach, this analysis was also performed on the same samples and the results of both approaches were compared. A total of 186,787 high-quality sequences were obtained for evaluating bacterial diversity and 41,905 unique sequences represented all phylotypes. We found that the oral microbiota in children was far more diverse than previous studies reported, and more than 200 genera belonging to ten phyla were found in the oral cavity. The phylotypes in saliva and supragingival plaques were significantly different and could be divided into two distinct clusters (p < 0.05). The bacterial diversity in oral microbiome analyzed by PCR-DGGE and barcoded pyrosequencing was employed to cross validate the data sets. The genera of Streptococcus, Veillonella, Actinomyces, Granulicatella, Leptotrichia, and Thiomonas in plaques were significantly associated with dental caries (p < 0.05). The results showed that there was no one specific pathogen but rather pathogenic populations in plaque that significantly correlated with dental caries. The enormous diversity of oral microbiota allowed for a better understanding of oral microecosystem, and these pathogenic populations in plaque provide new insights into the etiology of dental caries and suggest new targets for interventions of the disease.}, }
@article {pmid20614116, year = {2011}, author = {Romeralo, M and Moya-Laraño, J and Lado, C}, title = {Social amoebae: environmental factors influencing their distribution and diversity across south-western Europe.}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {154-165}, pmid = {20614116}, issn = {1432-184X}, mesh = {*Biodiversity ; Dictyosteliida/classification/genetics/isolation &amp; purification/*physiology ; Ecosystem ; Models, Biological ; Portugal ; Soil/*parasitology ; Spain ; }, abstract = {The social amoebae (dictyostelids) are the only truly multicellular lineage within the superkingdom Amoebozoa, the sister group to Ophistokonts (Metazoa+Fungi). Despite the exceptional phylogenetic and evolutionary value of this taxon, the environmental factors that determine their distribution and diversity are largely unknown. We have applied statistical modeling to a set of data obtained from an extensive and detailed survey in the south-western of Europe (The Iberian Peninsula including Spain and Portugal) in order to estimate some of the main environmental factors influencing the distribution and diversity of dictyostelid in temperate climates. It is the first time that this methodology is applied to the study of this unique group of soil microorganisms. Our results show that a combination of climatic (temperature, water availability), physical (pH) and vegetation (species richness) factors favor dictyostelid species richness. In the Iberian Peninsula, dictyostelid diversity is highest in colder and wet environments, indicating that this group has likely diversified in relatively cold places with high levels of water availability.}, }
@article {pmid20614115, year = {2011}, author = {Ben-Dov, E and Siboni, N and Shapiro, OH and Arotsker, L and Kushmaro, A}, title = {Substitution by inosine at the 3'-ultimate and penultimate positions of 16S rRNA gene universal primers.}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {1-6}, pmid = {20614115}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/microbiology ; Bacteria/classification/*genetics ; DNA Primers/*genetics ; Ecology/*methods ; Gene Library ; *Genetic Techniques ; Inosine/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sensitivity and Specificity ; }, abstract = {Universal 16S rRNA gene primers (8F and 518R) bearing inosine substitutions at either the 3'-ultimate or the 3'-ultimate and penultimate base positions were exploited for the first time to study the bacterial community associated with coral polymicrobial Black Band Disease (BBD). Inosine-modified universal primer pairs display some shifting in the composition of 16S rRNA gene libraries, as well as expanding the observed diversity of a BBD bacterial community at the family/class level. Possible explanations for the observed shifts are discussed. These results thus point to the need for adopting multiple approaches in designing 16S rRNA universal primers for PCR amplification and subsequent construction of 16S rRNA gene libraries or pyrosequencing in the exploration of complex microbial communities.}, }
@article {pmid20607532, year = {2010}, author = {Urzì, C and De Leo, F and Bruno, L and Albertano, P}, title = {Microbial diversity in paleolithic caves: a study case on the phototrophic biofilms of the Cave of Bats (Zuheros, Spain).}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {116-129}, pmid = {20607532}, issn = {1432-184X}, mesh = {Archaeology ; Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Biofilms/*growth &amp; development ; Cluster Analysis ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; *Environmental Microbiology ; Photosynthesis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spain ; }, abstract = {The biological colonization of rocks in the Cave of Bats (Cueva de Los Murciélagos, Zuheros, Spain) was studied in order to reveal the diversity of microorganisms involved in the biofilm formation. The culturable, metabolically active fraction of biodeteriogens present on surfaces was investigated focusing on morphological, ultrastructural, and genetic features, and their presence related to the peculiar environmental conditions of the underground site. PCR-ITS analysis and 16S rDNA sequences were used to clusterize and characterize the isolated strains. The presence of bacterial taxa associated to the photosynthetic microflora and fungi within the biofilm contributed to clarify the relationships inside the microbial community and to explain the alteration observed at the different sites. These results will contribute to the application of more successful strategies for the preventive conservation of subterranean archaeological sites.}, }
@article {pmid20607531, year = {2010}, author = {Yamamoto, N and Otawa, K and Nakai, Y}, title = {Diversity and abundance of ammonia-oxidizing bacteria and ammonia-oxidizing archaea during cattle manure composting.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {807-815}, pmid = {20607531}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Animals ; Archaea/classification/genetics/isolation &amp; purification/*metabolism ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; *Biodiversity ; Cattle ; Manure/analysis/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) play important roles in nitrification in various environments. They may also be key communities for ammonia oxidation in composting systems, although few studies have discussed their presence. We investigated the relative diversity and abundance of AOB and AOA using cloning procedures, denaturing gradient gel electrophoresis analysis, and real-time PCR during several stages in the process of cattle manure composting. Our results revealed that the AOB community structure changed during the process. At the high-temperature stage (>60°C), a member of the Nitrosomonas europaea/eutropha cluster dominated while the uncultured Nitrosomonas spp. cluster appeared after the temperature decreased. Additionally, our analysis indicated that AOA sequences, which were classified into a soil/sediment cluster, were present after the temperature decreased during the composting process. At these stages, the number of the archaeal amoA gene copies (3.2 or 3.9 × 10(7) copies per gram freeze-dried compost) was significantly higher than that of bacterial amoA gene copies (2.2-7.2 × 10(6) copies per gram freeze-dried compost). Our results suggest that both AOB and AOA are actively involved in nitrification of composting systems.}, }
@article {pmid20602987, year = {2010}, author = {Marchesi, JR}, title = {Prokaryotic and eukaryotic diversity of the human gut.}, journal = {Advances in applied microbiology}, volume = {72}, number = {}, pages = {43-62}, doi = {10.1016/S0065-2164(10)72002-5}, pmid = {20602987}, issn = {0065-2164}, mesh = {Bacteroidetes/genetics/physiology ; Eukaryota/genetics/*physiology ; Gastrointestinal Tract/*microbiology ; Genetic Variation ; Gram-Positive Bacteria/genetics/physiology ; Humans ; Metagenome/genetics/*physiology ; Phylogeny ; Prokaryotic Cells/*physiology ; }, abstract = {The human intestinal tract is one of the most densely populated ecosystems studied to date. Recently, the gut microbiota have been implicated as an environmental factor in health and disease; however, as with all ecosystems, a significant proportion of these microbiota are as yet uncultured. Hence culture-independent molecular-based methods have been applied and have started to provide insights into the microbes in this system. This review explores the recent significant findings in the last 5 years in the area of gut microbial ecology. Most significant is the observation that the gut microbiota are dominated by species from the phyla Firmicutes and Bacteroidetes. Regardless of whether first- or second-generation sequencing technologies are used to explore the microbial diversity, these two phyla are found throughout the intestinal tract, with other microbes such as the viruses and micro-eukayrotes, which, while being present, are either in low numbers or have not received much attention. Simply put, the Firmicutes and Bacteroidetes have made the gut their own, and the next stage in the study of this fascinating system will be to establish the roles they play in the host's health.}, }
@article {pmid20593174, year = {2010}, author = {Pascault, N and Cécillon, L and Mathieu, O and Hénault, C and Sarr, A and Lévêque, J and Farcy, P and Ranjard, L and Maron, PA}, title = {In situ dynamics of microbial communities during decomposition of wheat, rape, and alfalfa residues.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {816-828}, pmid = {20593174}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Biodiversity ; Brassica rapa/chemistry/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Medicago sativa/chemistry/*microbiology ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Soil/analysis ; *Soil Microbiology ; Triticum/chemistry/*microbiology ; }, abstract = {Microbial communities are of major importance in the decomposition of soil organic matter. However, the identities and dynamics of the populations involved are still poorly documented. We investigated, in an 11-month field experiment, how the initial biochemical quality of crop residues could lead to specific decomposition patterns, linking biochemical changes undergone by the crop residues to the respiration, biomass, and genetic structure of the soil microbial communities. Wheat, alfalfa, and rape residues were incorporated into the 0-15 cm layer of the soil of field plots by tilling. Biochemical changes in the residues occurring during degradation were assessed by near-infrared spectroscopy. Qualitative modifications in the genetic structure of the bacterial communities were determined by bacterial-automated ribosomal intergenic spacer analysis. Bacterial diversity in the three crop residues at early and late stages of decomposition process was further analyzed from a molecular inventory of the 16S rDNA. The decomposition of plant residues in croplands was shown to involve specific biochemical characteristics and microbial community dynamics which were clearly related to the quality of the organic inputs. Decay stage and seasonal shifts occurred by replacement of copiotrophic bacterial groups such as proteobacteria successful on younger residues with those successful on more extensively decayed material such as Actinobacteria. However, relative abundance of proteobacteria depended greatly on the composition of the residues, with a gradient observed from alfalfa to wheat, suggesting that this bacterial group may represent a good indicator of crop residues degradability and modifications during the decomposition process.}, }
@article {pmid20593173, year = {2010}, author = {Lan, W and Li, H and Wang, WD and Katayama, Y and Gu, JD}, title = {Microbial community analysis of fresh and old microbial biofilms on Bayon temple sandstone of Angkor Thom, Cambodia.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {105-115}, pmid = {20593173}, issn = {1432-184X}, mesh = {Archaea/genetics/isolation &amp; purification ; Bacteria/genetics/isolation &amp; purification ; Biodegradation, Environmental ; Biofilms/*growth &amp; development ; Cambodia ; Construction Materials/*microbiology ; *Environmental Microbiology ; Fungi/genetics/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {The temples of Angkor monuments including Angkor Thom and Bayon in Cambodia and surrounding countries were exclusively constructed using sandstone. They are severely threatened by biodeterioration caused by active growth of different microorganisms on the sandstone surfaces, but knowledge on the microbial community and composition of the biofilms on the sandstone is not available from this region. This study investigated the microbial community diversity by examining the fresh and old biofilms of the biodeteriorated bas-relief wall surfaces of the Bayon Temple by analysis of 16S and 18S rRNA gene sequences. The results showed that the retrieved sequences were clustered in 11 bacterial, 11 eukaryotic and two archaeal divisions with disparate communities (Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria; Alveolata, Fungi, Metazoa, Viridiplantae; Crenarchaeote, and Euyarchaeota). A comparison of the microbial communities between the fresh and old biofilms revealed that the bacterial community of old biofilm was very similar to the newly formed fresh biofilm in terms of bacterial composition, but the eukaryotic communities were distinctly different between these two. This information has important implications for understanding the formation process and development of the microbial diversity on the sandstone surfaces, and furthermore to the relationship between the extent of biodeterioration and succession of microbial communities on sandstone in tropic region.}, }
@article {pmid20586937, year = {2010}, author = {Han, F and Ge, B}, title = {Multiplex PCR assays for simultaneous detection and characterization of Vibrio vulnificus strains.}, journal = {Letters in applied microbiology}, volume = {51}, number = {2}, pages = {234-240}, doi = {10.1111/j.1472-765X.2010.02887.x}, pmid = {20586937}, issn = {1472-765X}, mesh = {Animals ; Bacterial Capsules/genetics ; Bacterial Proteins/genetics ; Bacteriological Techniques/*methods ; DNA Primers/genetics ; *Environmental Microbiology ; *Food Microbiology ; Humans ; Ostreidae/*microbiology ; Polymerase Chain Reaction/*methods ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; Time Factors ; United States ; Vibrio vulnificus/*classification/genetics/*isolation &amp; purification ; }, abstract = {AIMS: Vibrio vulnificus is a major cause of seafood-related deaths in the United States. Several biomarkers, e.g. the virulence-correlated gene (vcg), 16S rRNA, and the capsular polysaccharide operon (CPS) have been used to differentiate virulent- from nonvirulent-type V. vulnificus strains. In this study, we combined the use of these biomarkers with a species-specific V. vulnificus cytolysin/haemolysin gene (vvhA) to develop two pairs of multiplex PCR assays that simultaneously detect and characterize V. vulnificus strains.<br><br>METHODS AND RESULTS: The first multiplex PCR pair amplified four genes (vvhA, vcg, 16S rRNA, and CPS), with one for virulent-type and the other one for nonvirulent-type V. vulnificus strains, while the second pair targeted three of those genes excluding CPS. Primer concentration and annealing temperature were optimized for the four multiplex PCR assays. When testing ten V. vulnificus reference strains and 80 field oyster isolates, results from each multiplex PCR matched 100% with known strain characteristics for these target genes.<br><br>CONCLUSIONS: The optimized multiplex PCR assays were capable of simultaneously detecting and characterizing V. vulnificus with high specificity and speed.<br><br>Multiplex PCR assays designed in this study are valuable tools for microbial ecology and epidemiology studies. They may facilitate better control of V. vulnificus risks in oysters, thereby reducing the number of illnesses and deaths because of V. vulnificus in the long run.}, }
@article {pmid20585943, year = {2010}, author = {Purushe, J and Fouts, DE and Morrison, M and White, BA and Mackie, RI and ,  and Coutinho, PM and Henrissat, B and Nelson, KE}, title = {Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {721-729}, pmid = {20585943}, issn = {1432-184X}, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; *Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; Prevotella/classification/enzymology/*genetics/isolation &amp; purification ; Prevotella ruminicola/classification/enzymology/*genetics/isolation &amp; purification ; Rumen/microbiology ; }, abstract = {The Prevotellas comprise a diverse group of bacteria that has received surprisingly limited attention at the whole genome-sequencing level. In this communication, we present the comparative analysis of the genomes of Prevotella ruminicola 23 (GenBank: CP002006) and Prevotella bryantii B(1)4 (GenBank: ADWO00000000), two gastrointestinal isolates. Both P. ruminicola and P. bryantii have acquired an extensive repertoire of glycoside hydrolases that are targeted towards non-cellulosic polysaccharides, especially GH43 bifunctional enzymes. Our analysis demonstrates the diversity of this genus. The results from these analyses highlight their role in the gastrointestinal tract, and provide a template for additional work on genetic characterization of these species.}, }
@article {pmid20579190, year = {2010}, author = {Mair, C and Plitzner, C and Domig, KJ and Schedle, K and Windisch, W}, title = {Impact of inulin and a multispecies probiotic formulation on performance, microbial ecology and concomitant fermentation patterns in newly weaned piglets.}, journal = {Journal of animal physiology and animal nutrition}, volume = {94}, number = {5}, pages = {e164-77}, doi = {10.1111/j.1439-0396.2010.01000.x}, pmid = {20579190}, issn = {1439-0396}, mesh = {Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Diet/veterinary ; Dietary Supplements ; Female ; Fermentation ; Gastrointestinal Contents/chemistry/microbiology ; Gastrointestinal Tract/drug effects/*microbiology/physiology ; Inulin/*pharmacology ; Male ; Probiotics/*pharmacology ; Swine/*physiology ; Synbiotics ; *Weaning ; }, abstract = {The effect of inulin and a multispecies probiotic formulation on performance and microbial parameters in a 28 days feeding trial with newly weaned piglets was assessed. Forty-eight piglets were allocated to a 2 × 2 factorial experiment involving two levels of inulin supplementation (0% or 0.4%) and two levels of probiotics (0 or 1 × 10(9) CFU/kg as fed, comprising enterococci, lactobacilli and bifidobacteria). In digesta samples obtained at slaughter (stomach, jejunum, ileum and colon), selected bacterial groups were enumerated and lactic acid, short chain fatty acids and ammonia concentrations analysed. The overall performance of piglets was unaffected by treatment. Inulin increased total aerobes in stomach and jejunum (p < 0.05), whereas enterococci declined in colon of the inulin group (p < 0.05). Furthermore decreasing colonic acetic acid (p < 0.01) and increasing lactic acid (p < 0.05) was observed for inulin. Probiotics increased total aerobes (p < 0.05) and enterococci (p < 0.01) in ileum and lactobacilli (p < 0.05), enterococci and gram-negative anaerobes (p < 0.01) in colon. Moreover, dry matter content in stomach and colon was lower and acetic acid in colon increased (p < 0.05). A decrease in ileal pH value was noted symbiotically for both additives. However, several parameters showed no synbiotic, but distinct individual effects of inulin and probiotics. Effects occurred along the entire gastrointestinal tract without restriction to the colon.}, }
@article {pmid20577876, year = {2010}, author = {Rineau, F and Garbaye, J}, title = {Effects of liming on potential oxalate secretion and iron chelation of beech ectomycorrhizal root tips.}, journal = {Microbial ecology}, volume = {60}, number = {2}, pages = {331-339}, pmid = {20577876}, issn = {1432-184X}, mesh = {Calcium Compounds/*chemistry ; Chelating Agents/metabolism ; DNA, Fungal/genetics ; Fagus/*microbiology ; Iron/*metabolism ; Meristem/microbiology ; Mycelium/metabolism ; Mycorrhizae/genetics/*metabolism ; Oxalic Acid/*metabolism ; Oxides/*chemistry ; Siderophores/metabolism ; Soil/chemistry ; Soil Microbiology ; Trees/microbiology ; }, abstract = {Liming is used to counteract forest decline induced by soil acidification. It consists of Ca and Mg input to forest soil and not only restores tree mineral nutrition but also modifies the availability of nutrients in soil. Ectomycorrhizal (ECM) fungi are involved in mineral nutrient uptake by trees and can recover them through dissolution of mineral surface. Oxalate and siderophore secretion are considered as the main agents of mineral weathering by ECMs. Here, we studied the effects of liming on the potential oxalate secretion and iron complexation by individual beech ECM root tips. Results show that freshly excised Lactarius subdulcis root tips from limed plots presented a high potential oxalate exudation of 177 μM tip(-1) h(-1). As this ECM species distribution is very dense, it is likely that, in the field, oxalate concentrations in the vicinity of its clusters could be very high. This points out that not only extraradical mycelium but also ECM root tips of certain species can contribute significantly to mineral weathering. Nonmetric multidimensional scaling (NMDS) separated potential oxalate production by ECM root tips in limed and untreated plots, and this activity was mainly driven by L. subdulcis ECMs, but NMDS on potential activity of iron mobilization by ECM root tips did not show a difference between limed and untreated plots. As the mean oxalate secretion did not significantly correlated with the mean iron mobilization by ECM morphotype, we conclude that iron complexation was due to either other organic acids or to siderophores.}, }
@article {pmid20574826, year = {2010}, author = {Grossman, JM and O'Neill, BE and Tsai, SM and Liang, B and Neves, E and Lehmann, J and Thies, JE}, title = {Amazonian anthrosols support similar microbial communities that differ distinctly from those extant in adjacent, unmodified soils of the same mineralogy.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {192-205}, pmid = {20574826}, issn = {1432-184X}, mesh = {Agriculture ; Archaea/genetics/*isolation &amp; purification ; Bacteria/genetics/*isolation &amp; purification ; *Biodiversity ; Brazil ; Cluster Analysis ; DNA Fingerprinting ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Soil/*analysis ; *Soil Microbiology ; }, abstract = {We compared the microbial community composition in soils from the Brazilian Amazon with two contrasting histories; anthrosols and their adjacent non-anthrosol soils of the same mineralogy. The anthrosols, also known as the Amazonian Dark Earths or terra preta, were managed by the indigenous pre-Colombian Indians between 500 and 8,700 years before present and are characterized by unusually high cation exchange capacity, phosphorus (P), and calcium (Ca) contents, and soil carbon pools that contain a high proportion of incompletely combusted biomass as biochar or black carbon (BC). We sampled paired anthrosol and unmodified soils from four locations in the Manaus, Brazil, region that differed in their current land use and soil type. Community DNA was extracted from sampled soils and characterized by use of denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism. DNA bands of interest from Bacteria and Archaea DGGE gels were cloned and sequenced. In cluster analyses of the DNA fingerprints, microbial communities from the anthrosols grouped together regardless of current land use or soil type and were distinct from those in their respective, paired adjacent soils. For the Archaea, the anthrosol communities diverged from the adjacent soils by over 90%. A greater overall richness was observed for Bacteria sequences as compared with those of the Archaea. Most of the sequences obtained were novel and matched those in databases at less than 98% similarity. Several sequences obtained only from the anthrosols grouped at 93% similarity with the Verrucomicrobia, a genus commonly found in rice paddies in the tropics. Sequences closely related to Proteobacteria and Cyanobacteria sp. were recovered only from adjacent soil samples. Sequences related to Pseudomonas, Acidobacteria, and Flexibacter sp. were recovered from both anthrosols and adjacent soils. The strong similarities among the microbial communities present in the anthrosols for both the Bacteria and Archaea suggests that the microbial community composition in these soils is controlled more strongly by their historical soil management than by soil type or current land use. The anthrosols had consistently higher concentrations of incompletely combusted organic black carbon material (BC), higher soil pH, and higher concentrations of P and Ca compared to their respective adjacent soils. Such characteristics may help to explain the longevity and distinctiveness of the anthrosols in the Amazonian landscape and guide us in recreating soils with sustained high fertility in otherwise nutrient-poor soils in modern times.}, }
@article {pmid20574825, year = {2010}, author = {Nakano, Y and Takeshita, T and Yasui, M and Yamashita, Y}, title = {Prediction of plausible bacterial composition based on terminal restriction fragment length polymorphisms using a Monte Carlo method.}, journal = {Microbial ecology}, volume = {60}, number = {2}, pages = {364-372}, pmid = {20574825}, issn = {1432-184X}, mesh = {Algorithms ; Bacteria/classification/*genetics ; Cloning, Molecular ; DNA, Bacterial/genetics ; Humans ; *Metagenome ; *Monte Carlo Method ; *Polymorphism, Restriction Fragment Length ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; Sequence Analysis, DNA/methods ; Time Factors ; }, abstract = {We have developed a new approach for the estimation of bacterial proportional compositions in microbiota based on terminal restriction length polymorphism (T-RFLP) data and a Monte Carlo algorithm. This program estimates proportional compositions by minimizing distances between peak values and the relative abundance of each group, containing several species, estimated from peak areas of capillary electrophoresis for T-RFLP analysis. Oral bacteria in 36 saliva samples obtained from three individuals were analyzed using the program. Upon comparison, the estimated proportional composition obtained from one of the samples matched that from a clone library. Additionally, comparisons among the bacterial proportional compositions of saliva samples obtained from three individuals four times per day for 3 days revealed that the types of microbiota present in each individual did not change within each 24-h time period and were distinguishable from those in other individuals.}, }
@article {pmid20574824, year = {2011}, author = {Gori, K and Bjørklund, MK and Canibe, N and Pedersen, A&#xd8; and Jespersen, L}, title = {Occurrence and identification of yeast species in fermented liquid feed for piglets.}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {146-153}, pmid = {20574824}, issn = {1432-184X}, mesh = {Acids/metabolism ; Animal Feed/*microbiology ; Animals ; *Biodiversity ; Colony Count, Microbial ; DNA, Ribosomal Spacer/genetics ; Fermentation ; Molecular Sequence Data ; Mycological Typing Techniques ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal/genetics ; Swine/*microbiology ; Yeasts/*classification/genetics/isolation &amp; purification/metabolism/*physiology ; }, abstract = {The major objective of the present study was to investigate the occurrence and identity of yeast species in fermented liquid feed (FLF) used for feeding piglets. In total, 40 different Danish farms were included in the analysis. The preparation and composition of FLF was found to be very heterogeneous with high variations in both yeast counts and yeast species composition. The yeast population varied between 6.0 × 10(3) and 4.2 × 10(7) cfug(-1) with an average yeast count of 8.7 × 10(6) ± 1.1 × 10(7) cfug(-1). A total of 766 yeasts were isolated and identified by conventional and/or molecular typing techniques. The predominant yeast species in the FLF samples were found to be Candida milleri (58.4%), Kazachstania exigua (17.5%), Candida pararugosa (6.40%) and Kazachstania bulderi (5.09%). No clear separation between isolates of C. milleri and Candida humilis could be obtained based on sequencing of the D1/D2 region of the 26S rRNA gene. The combined use of ITS-RFLP analysis and phenotypic criteria did meanwhile suggest a closer relationship with C. milleri than C. humilis.}, }
@article {pmid20574458, year = {2011}, author = {van Elsas, JD and Semenov, AV and Costa, R and Trevors, JT}, title = {Survival of Escherichia coli in the environment: fundamental and public health aspects.}, journal = {The ISME journal}, volume = {5}, number = {2}, pages = {173-183}, pmid = {20574458}, issn = {1751-7370}, mesh = {Ecosystem ; *Environmental Microbiology ; Escherichia coli/genetics/*physiology ; Escherichia coli O157/genetics/physiology ; Genomic Islands/genetics ; Genotype ; Humans ; *Microbial Viability ; Public Health ; }, abstract = {In this review, our current understanding of the species Escherichia coli and its persistence in the open environment is examined. E. coli consists of six different subgroups, which are separable by genomic analyses. Strains within each subgroup occupy various ecological niches, and can be broadly characterized by either commensalistic or different pathogenic behaviour. In relevant cases, genomic islands can be pinpointed that underpin the behaviour. Thus, genomic islands of, on the one hand, broad environmental significance, and, on the other hand, virulence, are highlighted in the context of E. coli survival in its niches. A focus is further placed on experimental studies on the survival of the different types of E. coli in soil, manure and water. Overall, the data suggest that E. coli can persist, for varying periods of time, in such terrestrial and aquatic habitats. In particular, the considerable persistence of the pathogenic E. coli O157:H7 is of importance, as its acid tolerance may be expected to confer a fitness asset in the more acidic environments. In this context, the extent to which E. coli interacts with its human/animal host and the organism's survivability in natural environments are compared. In addition, the effect of the diversity and community structure of the indigenous microbiota on the fate of invading E. coli populations in the open environment is discussed. Such a relationship is of importance to our knowledge of both public and environmental health.}, }
@article {pmid20571793, year = {2010}, author = {Li, XS and Sato, T and Ooiwa, Y and Kusumi, A and Gu, JD and Katayama, Y}, title = {Oxidation of elemental sulfur by Fusarium solani strain THIF01 harboring endobacterium Bradyrhizobium sp.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {96-104}, pmid = {20571793}, issn = {1432-184X}, mesh = {Autotrophic Processes ; Bradyrhizobium/*isolation &amp; purification ; Cambodia ; Construction Materials/*microbiology ; DNA, Fungal/genetics ; *Environmental Microbiology ; Fusarium/genetics/*metabolism ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spores, Fungal/growth &amp; development ; Sulfur/*metabolism ; Sulfur Oxides/metabolism ; }, abstract = {Nineteen fungal strains having an ability to oxidize elemental sulfur in mineral salts medium were isolated from deteriorated sandstones of Angkor monuments. These fungi formed clearing zone on agar medium supplemented with powder sulfur due to the dissolution of sulfur. Representative of the isolates, strain THIF01, was identified as Fusarium solani on the basis of morphological characteristics and phylogenetic analyses. PCR amplification targeting 16S rRNA gene and analyses of full 16S rRNA gene sequence indicated strain THIF01 harbors an endobacterium Bradyrhizobium sp.; however, involvement of the bacterium in the sulfur oxidation is still unclear. Strain THIF01 oxidized elemental sulfur to thiosulfate and then sulfate. Germination of the spores of strain THIF01 was observed in a liquid medium containing mineral salts supplemented with elemental sulfur (rate of germinated spores against total spores was 60.2%), and the culture pH decreased from pH 4.8 to 4.0. On the contrary, neither germination (rate of germinated spores against total spores was 1.0%) nor pH decrease was observed without the supplement of elemental sulfur. Strain THIF01 could also degrade 30 ppmv and ambient level (approximate 500 pptv) of carbonyl sulfide.}, }
@article {pmid20571792, year = {2010}, author = {Damiani, C and Ricci, I and Crotti, E and Rossi, P and Rizzi, A and Scuppa, P and Capone, A and Ulissi, U and Epis, S and Genchi, M and Sagnon, N and Faye, I and Kang, A and Chouaia, B and Whitehorn, C and Moussa, GW and Mandrioli, M and Esposito, F and Sacchi, L and Bandi, C and Daffonchio, D and Favia, G}, title = {Mosquito-bacteria symbiosis: the case of Anopheles gambiae and Asaia.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {644-654}, pmid = {20571792}, issn = {1432-184X}, mesh = {Acetobacteraceae/genetics/*physiology ; Animals ; Anopheles/growth &amp; development/*microbiology ; DNA, Bacterial/genetics ; Female ; Organisms, Genetically Modified ; Ovary/microbiology ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; Transformation, Genetic ; }, abstract = {The symbiotic relationship between Asaia, an α-proteobacterium belonging to the family Acetobacteriaceae, and mosquitoes has been studied mainly in the Asian malaria vector Anopheles stephensi. Thus, we have investigated the nature of the association between Asaia and the major Afro-tropical malaria vector Anopheles gambiae. We have isolated Asaia from different wild and laboratory reared colonies of A. gambiae, and it was detected by PCR in all the developmental stages of the mosquito and in all the specimens analyzed. Additionally, we have shown that it localizes in the midgut, salivary glands and reproductive organs. Using recombinant strains of Asaia expressing fluorescent proteins, we have demonstrated the ability of the bacterium to colonize A. gambiae mosquitoes with a pattern similar to that described for A. stephensi. Finally, fluorescent in situ hybridization on the reproductive tract of females of A. gambiae showed a concentration of Asaia at the very periphery of the eggs, suggesting that transmission of Asaia from mother to offspring is likely mediated by a mechanism of egg-smearing. We suggest that Asaia has potential for use in the paratransgenic control of malaria transmitted by A. gambiae.}, }
@article {pmid20570074, year = {2010}, author = {Picot, S and Rakotomalala, RS and Farny, K and Simac, C and Michault, A}, title = {[Evolution of resistance to antibiotics from 1997 to 2005 in the Reunion Island].}, journal = {Medecine et maladies infectieuses}, volume = {40}, number = {11}, pages = {617-624}, doi = {10.1016/j.medmal.2010.04.001}, pmid = {20570074}, issn = {1769-6690}, mesh = {*Drug Resistance, Bacterial ; Humans ; Reunion ; Time Factors ; }, abstract = {OBJECTIVE: The groupe hospitalier Sud Reunion (GHSR) is a 1130-bed hospital center, located on the Reunion Island, (Indian Ocean). We studied the profiles of antibiotic resistance in 2005, and compared those with previous data collected in 1997-1998, and with Metropolitan France and European data.<br><br>MATERIAL AND METHODOLOGY: All bacteriological strains isolated from diagnostic samples in 2005&#xa0;were analyzed according to CA-SFM recommendations.<br><br>RESULTS: Since 1997, the rates of resistance to enterobacteria (betalactam, aminoside, quinolone, trimethoprim-sulfamethoxazole), Pseudomonas aeruginosa (ticarcillin, amikacin, ciprofloxacin, fosfomycin), Acinetobacter baumanii (amikacin) has decreased significantly. The rate of methicillin-resistant Staphylococcus aureus (1997: 3.6&#xa0;%, 2005: 13.4&#xa0;%) has increased but less than in Metropolitan France. The rate of Streptococcuspneumonia with decreased susceptibility to penicillin has increased (1997: 25.5&#xa0;%, 2005: 42.9&#xa0;%), as for Haemophilusinfluenzae which present an important increase of betalactam resistance (1997: 15.5&#xa0;%, 2005: 37.8&#xa0;%).<br><br>CONCLUSION: By comparing our data to 1997&#xa0;and Metropolitan French data, it seems that the GHSR has managed to protect its hospital-based microbial ecology. However, community germs showed increasing resistance, probably because of an increasing antibiotic pressure, but with resistance rates often inferior to Metropolitan French ones.}, }
@article {pmid20568526, year = {2010}, author = {Jasser, I and Karnkowska-Ishikawa, A and Kozłowska, E and Królicka, A and Łukomska-Kowalczyk, M}, title = {Composition of picocyanobacteria community in the Great Mazurian Lakes: isolation of phycoerythrin-rich and phycocyanin-rich ecotypes from the system--comparison of two methods.}, journal = {Polish journal of microbiology}, volume = {59}, number = {1}, pages = {21-31}, pmid = {20568526}, issn = {1733-1331}, mesh = {Bacteriological Techniques ; Colony Count, Microbial ; Culture Media ; Cyanobacteria/chemistry/classification/genetics/*isolation &amp; purification ; Fresh Water/*microbiology ; Phycocyanin/*analysis ; Phycoerythrin/*analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The study showed that the picocyanobacteria community of the Great Mazurian Lakes system (GML) was dominated by phycoerythrin-rich (PE) ecotypes and demonstrated a gradual decrease of the ratio between PE and phycocyanin-rich (PC) ecotypes. The Great Mazurian Lakes offer better conditions for the PE ecotype than for the PC one, despite the considerably high trophic status, probably thanks to low turbidity and attenuation of light in the water column. The successful isolation of PE and PC picocyanobacteria was achieved by two methods: the classic plate method and a modified flow-cytometry method. The modified flow-cytometry method proved to be superior: being more selective for PE picocyanobacteria as well as less time consuming and less laborious. The modifications introduced to the method, such us concentration of cyanobacterial cells by centrifugation to the density required by the flow cytometer, did not hinder the isolation while allowing to skip an intermediate phase of enrichment cultures that had been formerly proposed. The first phylogenetic analyses based on cpcBA operon and 16S rRNA gene demonstrated that picocyanobacteria isolates from GML could, with a high bootstrap support, be grouped into five and four clusters, respectively. Based on a cpcBA-IGS analysis and IGS length the study suggests that at least one of the clusters is new and has not been previously described.}, }
@article {pmid20567814, year = {2010}, author = {Rooney, DC and Hutchens, E and Clipson, N and Baldini, J and McDermott, F}, title = {Microbial community diversity of moonmilk deposits at Ballynamintra Cave, Co. Waterford, Ireland.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {753-761}, pmid = {20567814}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; Ecosystem ; Fungi/classification/genetics/*isolation &amp; purification ; Geologic Sediments/*microbiology ; Ireland ; Molecular Sequence Data ; }, abstract = {Caves are extreme and specialised habitats for terrestrial life that sometimes contain moonmilk, a fine-grained paste-like secondary mineral deposit that is found in subterranean systems worldwide. While previous studies have investigated the possible role of microorganisms in moonmilk precipitation, the microbial community ecology of moonmilk deposits is poorly understood. Bacterial and fungal community structure associated with four spatially isolated microcrystalline, acicular calcite moonmilk deposits at Ballynamintra Cave (S. Ireland) was investigated during this study. Statistical analyses revealed significant differences in microbial activity, number of bacterial species, bacterial richness and diversity, and fungal diversity (Shannon's diversity) among the moonmilk sites over an area of approximately 2.5 m(2). However, the number of fungal species and fungal community richness were unaffected by sampling location. SIMPER analysis revealed significant differences in bacterial and fungal community composition among the sampling sites. These data suggest that a rich assemblage of microorganisms exists associated with moonmilk, with some spatial diversity, which may reflect small-scale spatial differences in cave biogeochemistry.}, }
@article {pmid20567813, year = {2010}, author = {Radwan, S and Mahmoud, H and Khanafer, M and Al-Habib, A and Al-Hasan, R}, title = {Identities of epilithic hydrocarbon-utilizing diazotrophic bacteria from the Arabian Gulf Coasts, and their potential for oil bioremediation without nitrogen supplementation.}, journal = {Microbial ecology}, volume = {60}, number = {2}, pages = {354-363}, pmid = {20567813}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; Biodegradation, Environmental ; DNA Fingerprinting ; Hydrocarbons/*metabolism ; *Microbial Consortia ; Nitrogen/chemistry ; Nitrogen Fixation ; Petroleum/*metabolism ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Gravel particles from four sites along the Arabian Gulf coast in autumn, winter, and spring were naturally colonized with microbial consortia containing between 7 and 400 × 10(2) cm(-2) of cultivable oil-utilizing bacteria. The 16S rRNA gene sequences of 70 representatives of oil-utilizing bacteria revealed that they were predominantly affiliated with the Gammaproteobacteria and the Actinobacteria. The Gammaproteobacteria comprised among others, the genera Pseudomonas, Pseudoalteromonas, Shewanella, Marinobacter, Psychrobacter, Idiomarina, Alcanivorax, Cobetia, and others. Actinobacteria comprised the genera Dietzia, Kocuria, Isoptericola, Rhodococcus, Microbacterium, and others. In autumn, Firmicutes members were isolated from bay and nonbay stations while Alphaproteobacteria were detected only during winter from Anjefa bay station. Fingerprinting by denaturing gradient gel electrophoresis of amplified 16S rRNA genes of whole microbial consortia confirmed the culture-based bacterial diversities in the various epilithons in various sites and seasons. Most of the representative oil-utilizing bacteria isolated from the epilithons were diazotrophic and could attenuate oil also in nitrogen-rich (7.9-62%) and nitrogen-free (4-54%) cultures, which, makes the microbial consortia suitable for oil bioremediation in situ, without need for nitrogen supplementation. This was confirmed in bench-scale experiments in which unfertilized oily seawater was bioremediated by epilithon-coated gravel particles.}, }
@article {pmid20563573, year = {2010}, author = {Chen, Z and Luo, X and Hu, R and Wu, M and Wu, J and Wei, W}, title = {Impact of long-term fertilization on the composition of denitrifier communities based on nitrite reductase analyses in a paddy soil.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {850-861}, pmid = {20563573}, issn = {1432-184X}, mesh = {Bacteria/classification/*enzymology/genetics/*isolation &amp; purification ; Bacterial Proteins/*genetics ; Fertilizers/analysis ; Gene Dosage ; Molecular Sequence Data ; Nitrite Reductases/*genetics ; Phylogeny ; Soil/analysis ; *Soil Microbiology ; }, abstract = {The effect of long-term fertilization on soil-denitrifying communities was determined by measuring the abundance and diversity of the nitrite reductase genes nirK and nirS. Soil samples were collected from plots of a long-term fertilization experiment started in 1990, located in Taoyuan (110°72″ E, 28°52″ N), China. The treatments were no fertilizer (NF), urea (UR), balanced mineral fertilizers (BM), and BM combined with rice straw (BMR). The abundance, diversity, and composition of the soil-denitrifying bacteria were determined by using real-time quantitative PCR, terminal restriction fragment length polymorphism (T-RFLP), and cloning and sequencing of nirK and nirS genes. There was a pronounced difference in the community composition and diversity of nirK-containing denitrifiers responding to the long-term fertilization regimes; however, less variation was observed in communities of nirS-containing denitrifiers, indicating that denitrifiers possessing nirK were more sensitive to the fertilization practices than those with nirS. In contrast, fertilization regimes had similar effects on the copy numbers of nirK and nirS genes. The BMR treatment had the highest copy numbers of nirK and nirS, followed by the two mineral fertilization regimes (UR and BM), and the lowest was in the NF treatment. Of the measured soil parameters, the differences in the community composition of nirK and the abundance of nir denitrifiers were highly correlated with the soil carbon content. Therefore, long-term fertilization resulted in a strong impact on the community structure of nirK populations only, and total organic carbon was the dominant factor in relation to the variations of nir community sizes.}, }
@article {pmid20562281, year = {2010}, author = {Van den Abbeele, P and Grootaert, C and Marzorati, M and Possemiers, S and Verstraete, W and Gérard, P and Rabot, S and Bruneau, A and El Aidy, S and Derrien, M and Zoetendal, E and Kleerebezem, M and Smidt, H and Van de Wiele, T}, title = {Microbial community development in a dynamic gut model is reproducible, colon region specific, and selective for Bacteroidetes and Clostridium cluster IX.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {15}, pages = {5237-5246}, pmid = {20562281}, issn = {1098-5336}, mesh = {Bacteroidetes/*growth &amp; development ; *Biodiversity ; Clostridium/*growth &amp; development ; Colon/*microbiology ; Humans ; *Metagenome ; Models, Biological ; Models, Theoretical ; *Selection, Genetic ; }, abstract = {Dynamic, multicompartment in vitro gastrointestinal simulators are often used to monitor gut microbial dynamics and activity. These reactors need to harbor a microbial community that is stable upon inoculation, colon region specific, and relevant to in vivo conditions. Together with the reproducibility of the colonization process, these criteria are often overlooked when the modulatory properties from different treatments are compared. We therefore investigated the microbial colonization process in two identical simulators of the human intestinal microbial ecosystem (SHIME), simultaneously inoculated with the same human fecal microbiota with a high-resolution phylogenetic microarray: the human intestinal tract chip (HITChip). Following inoculation of the in vitro colon compartments, microbial community composition reached steady state after 2 weeks, whereas 3 weeks were required to reach functional stability. This dynamic colonization process was reproducible in both SHIME units and resulted in highly diverse microbial communities which were colon region specific, with the proximal regions harboring saccharolytic microbes (e.g., Bacteroides spp. and Eubacterium spp.) and the distal regions harboring mucin-degrading microbes (e.g., Akkermansia spp.). Importantly, the shift from an in vivo to an in vitro environment resulted in an increased Bacteroidetes/Firmicutes ratio, whereas Clostridium cluster IX (propionate producers) was enriched compared to clusters IV and XIVa (butyrate producers). This was supported by proportionally higher in vitro propionate concentrations. In conclusion, high-resolution analysis of in vitro-cultured gut microbiota offers new insight on the microbial colonization process and indicates the importance of digestive parameters that may be crucial in the development of new in vitro models.}, }
@article {pmid20561206, year = {2010}, author = {Wallander, H and Johansson, U and Sterkenburg, E and Brandström Durling, M and Lindahl, BD}, title = {Production of ectomycorrhizal mycelium peaks during canopy closure in Norway spruce forests.}, journal = {The New phytologist}, volume = {187}, number = {4}, pages = {1124-1134}, doi = {10.1111/j.1469-8137.2010.03324.x}, pmid = {20561206}, issn = {1469-8137}, mesh = {Base Sequence ; Biodiversity ; Biomass ; Carbon/*physiology ; Ergosterol/analysis ; Fungi/classification/genetics/*physiology ; Light ; Mycelium/*growth &amp; development ; Mycorrhizae/*growth &amp; development ; Photosynthesis ; Picea/*physiology ; *Plant Leaves ; Seasons ; Soil ; Trees/*physiology ; }, abstract = {*Here, species composition and biomass production of actively growing ectomycorrhizal (EM) mycelia were studied over the rotation period of managed Norway spruce (Picea abies) stands in south-western Sweden. *The EM mycelia were collected using ingrowth mesh bags incubated in the forest soil during one growing season. Fungal biomass was estimated by ergosterol analysis and the EM species were identified by 454 sequencing of internal transcribed spacer (ITS) amplicons. Nutrient availability and the fungal biomass in soil samples were also estimated. *Biomass production peaked in young stands (10-30 yr old) before the first thinning phase. Tylospora fibrillosa dominated the EM community, especially in these young stands, where it constituted 80% of the EM amplicons derived from the mesh bags. Species richness increased in older stands. *The establishment of EM mycelial networks in young Norway spruce stands requires large amounts of carbon, while much less is needed to sustain the EM community in older stands. The variation in EM biomass production over the rotation period has implications for carbon sequestration rates in forest soils.}, }
@article {pmid20560344, year = {2010}, author = {Xu, M and Sun, G and Guo, J}, title = {[Advances in microbial eco-systems metabolic network study--a review].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {50}, number = {4}, pages = {438-443}, pmid = {20560344}, issn = {0001-6209}, mesh = {Ecology/*methods ; *Ecosystem ; Gene Expression Regulation, Bacterial/*physiology ; Metabolic Networks and Pathways/*physiology ; }, abstract = {Microbial eco-systems metabolic networks (MEMNs) are ubiquitous in nature and are the major drivers of biosphere processes. Here we try to define MEMNs and describe their significances in microbial ecology studies. We also review recent progresses and approaches of MEMNs including highlights of the major discoveries in these studies based on mixed-cultures, high-throughput sequencing and microarray data, computational approaches, and metabolic reconstruction. In addition, we discuss the potential shortcomings of current approaches and propose that the time is ripe to study the energy-based microbial metabolic networks in bioremediation systems, especially under the anaerobic conditions, which will reclaim the wastes to resources.}, }
@article {pmid20560343, year = {2010}, author = {Jia, Z and Weng, J and Lin, X and Conrad, R}, title = {[Microbial ecology of archaeal ammonia oxidation--a review].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {50}, number = {4}, pages = {431-437}, pmid = {20560343}, issn = {0001-6209}, mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; Bacteria/*metabolism ; Oxidation-Reduction ; }, abstract = {Bacteria have long been considered as the key driver of ammonia oxidation on earth. This concept has been challenged recently by the discovery of chemolithoautotrophic isolate of ammonia-oxidizing archaeon in marine. The relative contribution of bacteria and archaea to ammonia oxidation is essential for our understanding of global nitrogen cycle. Recent study suggested a key role of archaeal ammonia oxidation in the marine nitrogen cycle. Our work however revealed the predominace of bacterial ammonia oxidation in agricultural soil. From the biogeochemical perspective, here we summarized the discovery, progress and prospect of archaeal ammonia oxidation. Of great interest in the future would be to elucidate the metabolisms of ammonia-oxidizing archaeon in natural environment and the underlying mechanism that leads to the physiological divergence of ammonia oxidizers.}, }
@article {pmid20558546, year = {2010}, author = {Widmann, J and Harris, JK and Lozupone, C and Wolfson, A and Knight, R}, title = {Stable tRNA-based phylogenies using only 76 nucleotides.}, journal = {RNA (New York, N.Y.)}, volume = {16}, number = {8}, pages = {1469-1477}, pmid = {20558546}, issn = {1469-9001}, support = {T32 GM008759/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; T32 GM08759/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Pairing ; Cluster Analysis ; Conserved Sequence/genetics ; Gene Transfer, Horizontal ; Genome ; Nucleotides/genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; }, abstract = {tRNAs are among the most ancient, highly conserved sequences on earth, but are often thought to be poor phylogenetic markers because they are short, often subject to horizontal gene transfer, and easily change specificity. Here we use an algorithm now commonly used in microbial ecology, UniFrac, to cluster 175 genomes spanning all three domains of life based on the phylogenetic relationships among their complete tRNA pools. We find that the overall pattern of similarities and differences in the tRNA pools recaptures universal phylogeny to a remarkable extent, and that the resulting tree is similar to the distribution of bootstrapped rRNA trees from the same genomes. In contrast, the trees derived from tRNAs of identical specificity or of individual isoacceptors generally produced trees of lower quality. However, some tRNA isoacceptors were very good predictors of the overall pattern of organismal evolution. These results show that UniFrac can extract meaningful biological patterns from even phylogenies with high level of statistical inaccuracy and horizontal gene transfer, and that, overall, the pattern of tRNA evolution tracks universal phylogeny and provides a background against which we can test hypotheses about the evolution of individual isoacceptors.}, }
@article {pmid20556376, year = {2010}, author = {Tapia-Paniagua, ST and Chabrillón, M and Díaz-Rosales, P and de la Banda, IG and Lobo, C and Balebona, MC and Moriñigo, MA}, title = {Intestinal microbiota diversity of the flat fish Solea senegalensis (Kaup, 1858) following probiotic administration.}, journal = {Microbial ecology}, volume = {60}, number = {2}, pages = {310-319}, pmid = {20556376}, issn = {1432-184X}, mesh = {Animals ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Flatfishes/*microbiology ; Intestines/*microbiology ; *Metagenome ; Phylogeny ; Polymerase Chain Reaction ; *Probiotics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vibrio/*classification/genetics ; }, abstract = {Pleuronectiforms are an important group of fish, and one of their species, Solea senegalensis (Kaup 1858), has been extensively studied at different levels, although information about its intestinal microbiota and the effects of different factors on it is very scarce. Modern aquaculture industry demands strategies which help to maintain a microbiologically healthy environment and an environmentally friendly aquaculture. In this context, probiotics seem to offer an attractive alternative. The intake of probiotics could modify the composition of the intestinal microbiota, which is a key component in excluding potential invaders and maintaining health. The aim of this study was to evaluate by 16S rRNA gene analysis using polymerase chain reaction-denaturing gradient gel electrophoresis the effect of administering fresh or lyophilized cells of Pdp11 on the intestinal microbiota of farmed Senegalese sole, using sodium alginate to facilitate the incorporation of bacterial cells to the feed. The results obtained showed that the composition of fish intestinal microbiota was affected when fish received a diet supplemented with sodium alginate and fresh or lyophilized probiotic cells. In all cases, the dominant bacterial groups belonged to γ-Proteobacteria and mainly the Vibrio species. The use of sodium alginate reduced the incidence of populations with <97% 16S rRNA gene sequence identity to uncultured microorganisms in the intestinal microbiota until non-detected limits. On the other hand, the supplementation of the diet with probiotics produced an increase of the predominant species related to Vibrio genus.}, }
@article {pmid20556375, year = {2010}, author = {Sinsabaugh, RL and Van Horn, DJ and Shah, JJ and Findlay, S}, title = {Ecoenzymatic stoichiometry in relation to productivity for freshwater biofilm and plankton communities.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {885-893}, pmid = {20556375}, issn = {1432-184X}, mesh = {Acetylglucosaminidase/chemistry/metabolism ; Bacteria/chemistry/*enzymology ; Bacterial Physiological Phenomena ; Bacterial Proteins/*chemistry/*metabolism ; *Biofilms ; Ecosystem ; Fresh Water/chemistry/*microbiology ; Glucosidases/chemistry/metabolism ; Kinetics ; Leucyl Aminopeptidase/chemistry/metabolism ; Phosphoric Monoester Hydrolases/chemistry/metabolism ; Plankton/chemistry/*enzymology/physiology ; Protein Transport ; beta-Glucosidase/chemistry/metabolism ; }, abstract = {The degradation of detrital organic matter and assimilation of carbon (C), nitrogen (N), and phosphorus (P) by heterotrophic microbial communities is mediated by enzymes released into the environment (ecoenzymes). For the attached microbial communities of soils and freshwater sediments, the activities of β-glucosidase, β-N-acetylglucosaminidase, leucine aminopeptidase, and phosphatase show consistent stoichiometric patterns. To determine whether similar constraints apply to planktonic communities, we assembled data from nine studies that include measurements of these enzyme activities along with microbial productivity. By normalizing enzyme activity to productivity, we directly compared the ecoenzymatic stoichiometry of aquatic biofilm and bacterioplankton communities. The relationships between β-glucosidase and α-glucosidase and β-glucosidase and β-N-acetylglucosaminidase were statistically indistinguishable for the two community types, while the relationships between β-glucosidase and phosphatase and β-glucosidase and leucine aminopeptidase significantly differed. For β-glucosidase vs. phosphatase, the differences in slope (biofilm 0.65, plankton 1.05) corresponded with differences in the mean elemental C:P ratio of microbial biomass (60 and 106, respectively). For β-glucosidase vs. leucine aminopeptidase, differences in slope (0.80 and 1.02) did not correspond to differences in the mean elemental C:N of biomass (8.6 and 6.6). β-N-Acetylglucosaminidase activity in biofilms was significantly greater than that of plankton, suggesting that aminosaccharides were a relatively more important N source for biofilms, perhaps because fungi are more abundant. The slopes of β-glucosidase vs. (β-N-acetylglucosaminidase + leucine aminopeptidase) regressions (biofilm 1.07, plankton 0.94) corresponded more closely to the estimated difference in mean biomass C:N. Despite major differences in physical structure and trophic organization, biofilm and plankton communities have similar ecoenzymatic stoichiometry in relation to productivity and biomass composition. These relationships can be integrated into the stoichiometric and metabolic theories of ecology and used to analyze community metabolism in relation to resource constraints.}, }
@article {pmid20555400, year = {2010}, author = {de Boer, W and Folman, LB and Gunnewiek, PJ and Svensson, T and Bastviken, D and Oberg, G and del Rio, JC and Boddy, L}, title = {Mechanism of antibacterial activity of the white-rot fungus Hypholoma fasciculare colonizing wood.}, journal = {Canadian journal of microbiology}, volume = {56}, number = {5}, pages = {380-388}, doi = {10.1139/w10-023}, pmid = {20555400}, issn = {1480-3275}, mesh = {Bacteria/growth &amp; development ; Basidiomycota/growth &amp; development/*metabolism ; Fagus/microbiology ; Hydrogen-Ion Concentration ; Pinus/microbiology ; Stem Cells ; Wood/*microbiology ; }, abstract = {In a previous study it was shown that the number of wood-inhabiting bacteria was drastically reduced after colonization of beech (Fagus sylvatica) wood blocks by the white-rot fungus Hypholoma fasciculare, or sulfur tuft (Folman et al. 2008). Here we report on the mechanisms of this fungal-induced antibacterial activity. Hypholoma fasciculare was allowed to invade beech and pine (Pinus sylvestris) wood blocks that had been precolonized by microorganisms from forest soil. The changes in the number of bacteria, fungal biomass, and fungal-related wood properties were followed for 23 weeks. Colonization by the fungus resulted in a rapid and large reduction in the number of bacteria (colony-forming units), which was already apparent after 4 weeks of incubation. The reduction in the number of bacteria coincided with fungal-induced acidification in both beech and pine wood blocks. No evidence was found for the involvement of toxic secondary metabolites or reactive oxygen species in the reduction of the number of bacteria. Additional experiments showed that the dominant bacteria present in the wood blocks were not able to grow under the acidic conditions (pH 3.5) created by the fungus. Hence our research pointed at rapid acidification as the major factor causing reduction of wood-inhabiting bacteria upon colonization of wood by H. fasciculare.}, }
@article {pmid20549199, year = {2010}, author = {Töwe, S and Albert, A and Kleineidam, K and Brankatschk, R and Dümig, A and Welzl, G and Munch, JC and Zeyer, J and Schloter, M}, title = {Abundance of microbes involved in nitrogen transformation in the rhizosphere of Leucanthemopsis alpina (L.) Heywood grown in soils from different sites of the Damma glacier forefield.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {762-770}, pmid = {20549199}, issn = {1432-184X}, mesh = {Asteraceae/metabolism/*microbiology ; Bacteria/enzymology/genetics/isolation &amp; purification/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biotransformation ; Carbon/metabolism ; Ice Cover/microbiology ; Nitrogen/*metabolism ; Nitrogen Cycle ; Nitrogenase/genetics/metabolism ; Plant Roots/metabolism/microbiology ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {Glacier forefields are an ideal playground to investigate the role of development stages of soils on the formation of plant-microbe interactions as within the last decades, many alpine glaciers retreated, whereby releasing and exposing parent material for soil development. Especially the status of macronutrients like nitrogen differs between soils of different development stages in these environments and may influence plant growth significantly. Thus, in this study, we reconstructed major parts of the nitrogen cycle in the rhizosphere soil/root system of Leucanthemopsis alpina (L.) HEYWOOD: as well as the corresponding bulk soil by quantifying functional genes of nitrogen fixation (nifH), nitrogen mineralisation (chiA, aprA), nitrification (amoA AOB, amoA AOA) and denitrification (nirS, nirK and nosZ) in a 10-year and a 120-year ice-free soil of the Damma glacier forefield. We linked the results to the ammonium and nitrate concentrations of the soils as well as to the nitrogen and carbon status of the plants. The experiment was performed in a greenhouse simulating the climatic conditions of the glacier forefield. Samples were taken after 7 and 13 weeks of plant growth. Highest nifH gene abundance in connection with lowest nitrogen content of L. alpina was observed in the 10-year soil after 7 weeks of plant growth, demonstrating the important role of associative nitrogen fixation for plant development in this soil. In contrast, in the 120-year soil copy numbers of genes involved in denitrification, mainly nosZ were increased after 13 weeks of plant growth, indicating an overall increased microbial activity status as well as higher concentrations of nitrate in this soil.}, }
@article {pmid20545842, year = {2010}, author = {Haider, S and Wagner, M and Schmid, MC and Sixt, BS and Christian, JG and Häcker, G and Pichler, P and Mechtler, K and Müller, A and Baranyi, C and Toenshoff, ER and Montanaro, J and Horn, M}, title = {Raman microspectroscopy reveals long-term extracellular activity of Chlamydiae.}, journal = {Molecular microbiology}, volume = {77}, number = {3}, pages = {687-700}, doi = {10.1111/j.1365-2958.2010.07241.x}, pmid = {20545842}, issn = {1365-2958}, mesh = {Bacterial Proteins/chemistry/metabolism ; Cell Line ; Chlamydia/chemistry/*cytology/*growth &amp; development/metabolism ; Chlamydia Infections/diagnosis/*microbiology ; Electrophoresis, Gel, Two-Dimensional ; Humans ; Phenylalanine/metabolism ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Spectrum Analysis, Raman/*methods ; }, abstract = {The phylum Chlamydiae consists exclusively of obligate intracellular bacteria. Some of them are formidable pathogens of humans, while others occur as symbionts of amoebae. These genetically intractable bacteria possess a developmental cycle consisting of replicative reticulate bodies and infectious elementary bodies, which are believed to be physiologically inactive. Confocal Raman microspectroscopy was applied to differentiate between reticulate bodies and elementary bodies of Protochlamydia amoebophila and to demonstrate in situ the labelling of this amoeba symbiont after addition of isotope-labelled phenylalanine. Unexpectedly, uptake of this amino acid was also observed for both developmental stages for up to 3 weeks, if incubated extracellularly with labelled phenylalanine, and P. amoebophila remained infective during this period. Furthermore, P. amoebophila energizes its membrane and performs protein synthesis outside of its host. Importantly, amino acid uptake and protein synthesis after extended extracellular incubation could also be demonstrated for the human pathogen Chlamydia trachomatis, which synthesizes stress-related proteins under these conditions as shown by 2-D gel electrophoresis and MALDI-TOF/TOF mass spectrometry. These findings change our perception of chlamydial biology and reveal that host-free analyses possess a previously not recognized potential for direct experimental access to these elusive microorganisms.}, }
@article {pmid20541022, year = {2010}, author = {Rougé, C and Goldenberg, O and Ferraris, L and Berger, B and Rochat, F and Legrand, A and Göbel, UB and Vodovar, M and Voyer, M and Rozé, JC and Darmaun, D and Piloquet, H and Butel, MJ and de La Cochetière, MF}, title = {Investigation of the intestinal microbiota in preterm infants using different methods.}, journal = {Anaerobe}, volume = {16}, number = {4}, pages = {362-370}, doi = {10.1016/j.anaerobe.2010.06.002}, pmid = {20541022}, issn = {1095-8274}, mesh = {*Biodiversity ; Birth Weight ; DNA Fingerprinting/methods ; Electrophoresis, Polyacrylamide Gel ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Infant, Newborn ; Intensive Care Units, Neonatal ; *Metagenome ; Nucleic Acid Denaturation ; *Premature Birth ; Sequence Analysis, DNA/methods ; }, abstract = {Modifications in microbial colonization of the human gut are believed to affect intestinal homeostasis and increase the risk of gastrointestinal diseases. The present study examined different methods for investigating the dynamic characterization of the intestinal microbiota in preterm infants. Fecal samples were collected weekly from ten preterm infants during their stay in a neonatal intensive care unit. The infants had a mean gestational age of 29 weeks (range: 28-32 weeks) and a mean birth weight of 1233g (range: 935-1450g). Bacterial colonization was assessed using conventional culture techniques and molecular biological methods. More specifically, the recently developed denaturing high performance liquid chromatography (dHPLC) technique was compared to established methods such as temporal temperature gradient gel electrophoresis (TTGE) and rRNA gene library sequencing. Our results indicate that the gastrointestinal tract of preterm infants, born at a gestational age of less than 33 weeks, has a low biodiversity of mainly, culturable bacteria. Finally, dHPLC was evaluated in terms of speed, labor and sensitivity for its use as a tool to analyze microbial colonization in preterm infants. We found that this technique provided major improvements over gel-based fingerprinting methods, such as TTGE, that are commonly used for studying microbial ecology. As such, it may become a common analytical tool for this purpose.}, }
@article {pmid20540779, year = {2010}, author = {Hartman, AL and Riddle, S and McPhillips, T and Ludäscher, B and Eisen, JA}, title = {Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences.}, journal = {BMC bioinformatics}, volume = {11}, number = {}, pages = {317}, pmid = {20540779}, issn = {1471-2105}, mesh = {Base Sequence ; Genes, rRNA ; Genomics/*methods ; Phylogeny ; Ribosomes/*genetics ; Sequence Alignment/*methods ; Sequence Analysis, RNA ; *Software ; }, abstract = {BACKGROUND: For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly.<br><br>RESULTS: We present WATERS, an integrated approach for 16 S rDNA analysis that bundles a suite of publicly available 16 S rDNA analysis software tools into a single software package. The "toolkit" includes sequence alignment, chimera removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological analysis and visualization tools. WATERS employs a flexible, collection-oriented 'workflow' approach using the open-source Kepler system as a platform.<br><br>CONCLUSIONS: By packaging available software tools into a single automated workflow, WATERS simplifies 16 S rDNA analyses, especially for those without specialized bioinformatics, programming expertise. In addition, WATERS, like some of the newer comprehensive rRNA analysis tools, allows researchers to minimize the time dedicated to carrying out tedious informatics steps and to focus their attention instead on the biological interpretation of the results. One advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result interpretation and reproducibility via a data provenance sub-system. Furthermore, new "actors" can be added to the workflow as desired and we see WATERS as an initial seed for a sizeable and growing repository of interoperable, easy-to-combine tools for asking increasingly complex microbial ecology questions.}, }
@article {pmid20535221, year = {2010}, author = {Pester, M and Bittner, N and Deevong, P and Wagner, M and Loy, A}, title = {A 'rare biosphere' microorganism contributes to sulfate reduction in a peatland.}, journal = {The ISME journal}, volume = {4}, number = {12}, pages = {1591-1602}, pmid = {20535221}, issn = {1751-7370}, support = {P 18836/FWF_/Austrian Science Fund FWF/Austria ; P 20185/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacterial Proteins/genetics ; Ecosystem ; Genes, Bacterial ; Methane/metabolism ; Oxidation-Reduction ; Oxidoreductases Acting on Sulfur Group Donors/genetics ; Peptococcaceae/classification/enzymology/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; *Soil Microbiology ; Sulfates/*metabolism ; Sulfur/metabolism ; Sulfur-Reducing Bacteria/classification/enzymology/*genetics ; }, abstract = {Methane emission from peatlands contributes substantially to global warming but is significantly reduced by sulfate reduction, which is fuelled by globally increasing aerial sulfur pollution. However, the biology behind sulfate reduction in terrestrial ecosystems is not well understood and the key players for this process as well as their abundance remained unidentified. Comparative 16S rRNA gene stable isotope probing (SIP) in the presence and absence of sulfate indicated that a Desulfosporosinus species, which constitutes only 0.006% of the total microbial community 16S rRNA genes, is an important sulfate reducer in a long-term experimental peatland field site. Parallel SIP using dsrAB (encoding subunit A and B of the dissimilatory (bi)sulfite reductase) identified no additional sulfate reducers under the conditions tested. For the identified Desulfosporosinus species a high cell-specific sulfate reduction rate of up to 341 fmol SO4[2-] cell[-1] day[-1] was estimated. Thus, the small Desulfosporosinus population has the potential to reduce sulfate in situ at a rate of 4.0-36.8 nmol (g soil w. wt.)[-1] day[-1], sufficient to account for a considerable part of sulfate reduction in the peat soil. Modeling of sulfate diffusion to such highly active cells identified no limitation in sulfate supply even at bulk concentrations as low as 10 μM. Collectively, these data show that the identified Desulfosporosinus species, despite being a member of the 'rare biosphere', contributes to an important biogeochemical process that diverts the carbon flow in peatlands from methane to CO2 and, thus, alters their contribution to global warming.}, }
@article {pmid20534474, year = {2010}, author = {Drigo, B and Pijl, AS and Duyts, H and Kielak, AM and Gamper, HA and Houtekamer, MJ and Boschker, HT and Bodelier, PL and Whiteley, AS and van Veen, JA and Kowalchuk, GA}, title = {Shifting carbon flow from roots into associated microbial communities in response to elevated atmospheric CO2.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {24}, pages = {10938-10942}, pmid = {20534474}, issn = {1091-6490}, mesh = {Atmosphere/chemistry ; Bacteria/genetics/metabolism ; Carbon/*metabolism ; Carbon Dioxide/*metabolism ; Carbon Isotopes/metabolism ; Carex Plant/metabolism/microbiology ; Climate Change ; *Ecosystem ; Festuca/metabolism/microbiology ; Fungi/genetics/metabolism ; Models, Biological ; Molecular Sequence Data ; Mycorrhizae/metabolism ; Plant Roots/*metabolism/*microbiology ; RNA, Bacterial/genetics ; RNA, Fungal/genetics ; Soil/analysis ; Soil Microbiology ; }, abstract = {Rising atmospheric CO(2) levels are predicted to have major consequences on carbon cycling and the functioning of terrestrial ecosystems. Increased photosynthetic activity is expected, especially for C-3 plants, thereby influencing vegetation dynamics; however, little is known about the path of fixed carbon into soil-borne communities and resulting feedbacks on ecosystem function. Here, we examine how arbuscular mycorrhizal fungi (AMF) act as a major conduit in the transfer of carbon between plants and soil and how elevated atmospheric CO(2) modulates the belowground translocation pathway of plant-fixed carbon. Shifts in active AMF species under elevated atmospheric CO(2) conditions are coupled to changes within active rhizosphere bacterial and fungal communities. Thus, as opposed to simply increasing the activity of soil-borne microbes through enhanced rhizodeposition, elevated atmospheric CO(2) clearly evokes the emergence of distinct opportunistic plant-associated microbial communities. Analyses involving RNA-based stable isotope probing, neutral/phosphate lipid fatty acids stable isotope probing, community fingerprinting, and real-time PCR allowed us to trace plant-fixed carbon to the affected soil-borne microorganisms. Based on our data, we present a conceptual model in which plant-assimilated carbon is rapidly transferred to AMF, followed by a slower release from AMF to the bacterial and fungal populations well-adapted to the prevailing (myco-)rhizosphere conditions. This model provides a general framework for reappraising carbon-flow paths in soils, facilitating predictions of future interactions between rising atmospheric CO(2) concentrations and terrestrial ecosystems.}, }
@article {pmid20532498, year = {2010}, author = {Kleineidam, K and Sharma, S and Kotzerke, A and Heuer, H and Thiele-Bruhn, S and Smalla, K and Wilke, BM and Schloter, M}, title = {Effect of sulfadiazine on abundance and diversity of denitrifying bacteria by determining nirK and nirS genes in two arable soils.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {703-707}, pmid = {20532498}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics/metabolism ; *Biodiversity ; Molecular Sequence Data ; Nitrite Reductases/*genetics/metabolism ; Nitrites/*metabolism ; Soil/analysis ; *Soil Microbiology ; Sulfadiazine/*pharmacology ; Veterinary Drugs/pharmacology ; }, abstract = {Sulfadiazine (SDZ) is an antibiotic frequently used in agricultural husbandry. Via manuring of excrements of medicated animals, the drug reaches the soil and might impair important biochemical transformation processes performed by microbes, e.g., the nitrogen turnover. We studied the effect of pig manure and SDZ-spiked pig manure on denitrifying bacteria by quantifying nirK and nirS nitrite reductase genes in two arable soils. Addition of manure entailed mainly an increase of nirK-harboring denitrifiers in both soils, whereas in the SDZ-amended treatments, primarily the nirS denitrifiers increased in abundance after the bioavailable SDZ had declined. However, the community composition of nirS nitrite reducers investigated by denaturing gradient gel electrophoresis did not change despite the observed alterations in abundance.}, }
@article {pmid20532497, year = {2011}, author = {Martínez-García, M and Koblížek, M and López-Legentil, S and Antón, J}, title = {Epibiosis of oxygenic phototrophs containing chlorophylls a, b, c, and d on the colonial ascidian Cystodytes dellechiajei.}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {13-19}, pmid = {20532497}, issn = {1432-184X}, mesh = {Animals ; Chlorophyll/*chemistry ; Cyanobacteria/chemistry/*classification/genetics ; Mediterranean Sea ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; Urochordata/*microbiology ; }, abstract = {The external surfaces of marine animals are colonized by a wide variety of epibionts. Here, we study the phototrophic epibiotic community attached to the colonial ascidian Cystodytes dellechiajei collected in the Mediterranean Sea. Epifluorescence microscopy analysis showed abundant filamentous cyanobacteria on the upper and basal parts of the ascidian that displayed autofluorescence, as well as some unicellular cyanobacteria, diatoms, and structures, which could belong to microscopic rhodophyte algae. In addition, high-performance liquid chromatography of the photosynthetic pigments confirmed that the phototrophic epibionts possess chlorophyll (Chl) d, as well as Chl a, b, and c, which enable them to use far-red light for photosynthesis in that peculiar microenvironment. Furthermore, laser scanning confocal microscopy showed the presence of a few small patches of cells on the basal part of the ascidian displaying fluorescence between 700 and 750 nm after excitement with a 635-nm red laser, typically within the range of Chl d. Denaturing gradient gel electrophoresis of the 16S rRNA gene polymerase chain reaction amplified using specific primers for Cyanobacteria detected sequences related with the genera Planktothricoides, Synechococcus, Phormidium, and Myxosarcina, as well as sequences of chloroplasts of diatoms and rhodophyte algae. Remarkably, only the sequences related to the filamentous cyanobacteria Planktothricoides spp. and some chloroplast sequences were found in almost all specimens collected under different macroecological conditions and geographical areas, suggesting thus certain specificity in the epibiotic association. On the other hand, Prochloron spp. and Acaryochloris marina, typically associated to tropical ascidians, were not detected by denaturing gradient gel electrophoresis. However, given the low abundance of cells displaying Chl d in C. dellechiajei and the fact that molecular fingerprinting techniques not always recover low abundance groups, the presence of these cyanobacteria cannot be ruled out. Nevertheless, our data indicate that tropical ascidians and C. dellechiajei differ in their phototrophic communities, although Chl d-containing cells are present in both microenvironments.}, }
@article {pmid20531404, year = {2010}, author = {Mueller, RS and Denef, VJ and Kalnejais, LH and Suttle, KB and Thomas, BC and Wilmes, P and Smith, RL and Nordstrom, DK and McCleskey, RB and Shah, MB and Verberkmoes, NC and Hettich, RL and Banfield, JF}, title = {Ecological distribution and population physiology defined by proteomics in a natural microbial community.}, journal = {Molecular systems biology}, volume = {6}, number = {}, pages = {374}, pmid = {20531404}, issn = {1744-4292}, mesh = {Bacteria/classification/*growth &amp; development/*metabolism ; *Bacterial Physiological Phenomena ; Bacterial Proteins/metabolism ; Biofilms/growth &amp; development ; Cluster Analysis ; *Ecosystem ; Proteome/metabolism ; Proteomics/*methods ; Species Specificity ; }, abstract = {An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism's metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ.}, }
@article {pmid20526856, year = {2010}, author = {Aouidi, F and Khelifi, E and Asses, N and Ayed, L and Hamdi, M}, title = {Use of cheese whey to enhance Geotrichum candidum biomass production in olive mill wastewater.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {37}, number = {8}, pages = {877-882}, pmid = {20526856}, issn = {1476-5535}, mesh = {Biomass ; Culture Media/chemistry ; *Food Industry ; Geotrichum/*growth &amp; development/*metabolism ; *Industrial Microbiology ; Industrial Waste ; Milk Proteins/isolation &amp; purification/*metabolism ; Olea ; *Water Microbiology ; Whey Proteins ; }, abstract = {Geotrichum candidum is a yeast-like filamentous fungus that has attracted industrial interest. The present work investigated G. candidum biomass production in agro-industrial wastewaters (olive mill wastewater (OMW) and cheese whey (CW)) as the only substrate. Different solid media (Sabouraud dextrose agar (SDA), CW, OMW, and OMW/CW mixtures in different proportions) were tested. OMW/CW mixtures proved to be suitable for optimal mycelia growth of G. candidum with a very high hyphae density. The highest fungal and expansion rate growth of 83 +/- 1 mm and 12.4 day(-1), respectively, were obtained on a 20:80 mixture of OMW/CW, which was incubated for 7 days. This optimal mixture was used to study the biomass production and the OMW decolorization ability of G. candidum in the presence of CW in liquid medium. Liquid cultures were also conducted in OMW and CW separately. After 5 days of incubation, fungal biomass reached 9.26 g l(-1) in the OMW/CW mixture and only 2.83 g l(-1) in CW, while no biomass production was observed in OMW alone. OMW decolorization and dephenolization by G. candidum also improved in the presence of CW with a decolorization efficiency of 54.5% and a total phenolic reduction of 55.3%, compared with the control which yielded values of about 10% and 15%, respectively. These results suggested that OMW/CW--as the only substrate--could be used as a cost-effective medium to produce G. candidum biomass, without the need for water dilution or supplementation with other nutriments.}, }
@article {pmid20523986, year = {2010}, author = {Glad, T and Kristiansen, VF and Nielsen, KM and Brusetti, L and Wright, AD and Sundset, MA}, title = {Ecological characterisation of the colonic microbiota in arctic and sub-arctic seals.}, journal = {Microbial ecology}, volume = {60}, number = {2}, pages = {320-330}, pmid = {20523986}, issn = {1432-184X}, mesh = {Animals ; Archaea/classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Colon/*microbiology ; Gene Library ; *Metagenome ; Microbial Viability ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Seals, Earless/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Dominant colonic bacteria in wild hooded (n = 9), harbour (n = 1) and grey (n = 1) seals were identified using 16S rRNA gene clone libraries (313 clones), revealing 52.7% Bacteroidetes, 41.5% Firmicutes, 4.5% Proteobacteria and 1.0% Fusobacteria. Thirty (77%) of the 39 phylotypes identified were novel, showing <97% sequence similarity to their nearest cultivated relatives. Mean colonic bacterial cell density, determined by real-time PCR, was high (12.8 log(10) cells/g wet wt) for the hooded seals, while the number of methanogenic Archea was low (4.0 log(10) cells/g wet wt). The level of ampicillin (amp(r)) and tetracycline-resistant (tet(r)) isolates was investigated by cultivation. Aerobic amp(r) isolates were only detected in colon contents from four hooded seals, whereas aerobic tet(r) isolates were found in seven of the nine hooded seals. These data provide novel insight to the gut microbiota of Arctic and sub-Arctic seals living in the wild.}, }
@article {pmid20521039, year = {2010}, author = {Costechareyre, D and Rhouma, A and Lavire, C and Portier, P and Chapulliot, D and Bertolla, F and Boubaker, A and Dessaux, Y and Nesme, X}, title = {Rapid and efficient identification of Agrobacterium species by recA allele analysis: Agrobacterium recA diversity.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {862-872}, pmid = {20521039}, issn = {1432-184X}, mesh = {Alleles ; Amplified Fragment Length Polymorphism Analysis ; Bacterial Proteins/*genetics ; Bacterial Typing Techniques/*methods ; *Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Rec A Recombinases/*genetics ; Rhizobium/classification/*enzymology/genetics/*isolation &amp; purification ; Sequence Analysis, DNA ; }, abstract = {The analysis of housekeeping recA gene sequences from 138 strains from 13 species or genomic species of Agrobacterium, nine being biovar 1 genomospecies, and the others Agrobacterium larrymoorei, Agrobacterium rubi, Agrobacterium sp. NCPPB 1650, and Agrobacterium vitis and one "former" Agrobacterium species, Rhizobium rhizogenes, led to the identification of 50 different recA alleles and to a clear delineation of the 14 species or genomospecies entirely consistent with that obtained by amplified fragment length polymorphism (AFLP) analysis. The relevance of a recA sequencing approach for epidemiological analyses was next assessed on agrobacterial Tunisian isolates. All Tunisian isolates were found to belong to the Agrobacterium tumefaciens/biovar 1 species complex by both biochemical tests and rrs sequencing. recA sequence analysis further permitted their unambiguous assignment to A. tumefaciens genomospecies G4, G6, G7, and G8 in total agreement with the results of an AFLP-based analysis. At subspecific level, several Tunisian recA alleles were novel, indicating the power and accuracy of recA-based typing for studies of Agrobacterium spp.}, }
@article {pmid20521038, year = {2010}, author = {Brum, JR and Steward, GF}, title = {Morphological characterization of viruses in the stratified water column of alkaline, hypersaline Mono Lake.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {636-643}, pmid = {20521038}, issn = {1432-184X}, mesh = {Biota ; Capsid/physiology ; Fresh Water/chemistry/virology ; Hydrogen-Ion Concentration ; Microscopy, Electron, Transmission ; Microscopy, Fluorescence ; *Salinity ; Viruses/*isolation &amp; purification/ultrastructure ; *Water Microbiology ; }, abstract = {Concentrations of viruses and prokaryotes in the alkaline, moderately hypersaline, seasonally stratified Mono Lake are among the highest reported for a natural aquatic environment. We used electron microscopy to test whether viral morphological characteristics differed among the epilimnion, metalimnion, and the anoxic hypolimnion of the lake and to determine how the properties of viruses in Mono Lake compare to other aquatic environments. Viral capsid size distributions were more similar in the metalimnion and hypolimnion of Mono Lake, while viral tail lengths were more similar in the epilimnion and metalimnion. The percentage of tailed viruses decreased with depth and the relative percentages of tailed phage families changed with depth. The presence of large (>125 nm capsid), untailed viruses in the metalimnion and hypolimnion suggests that eukaryotic viruses are produced in these suboxic and anoxic, hypersaline environments. Capsid diameters of viruses were larger on average in Mono Lake compared to other aquatic environments, and no lemon-shaped or filamentous viruses were found, in contrast to other high-salinity or high-altitude lakes and seas. Our data suggest that the physically and chemically distinct layers of Mono Lake harbor different viral assemblages, and that these assemblages are distinct from other aquatic environments that have been studied. Furthermore, we found that filtration of a sample through a 0.22-µm pore-size filter significantly altered the distribution of viral capsid diameters and tail lengths, resulting in a relative depletion of viruses having larger capsids and longer tails. This observation highlights the potential for bias in molecular surveys of viral diversity, which typically rely on filtration through 0.2- or 0.22-µm pore-size membrane filters to remove bacteria during sample preparation.}, }
@article {pmid20520654, year = {2010}, author = {Wrighton, KC and Virdis, B and Clauwaert, P and Read, ST and Daly, RA and Boon, N and Piceno, Y and Andersen, GL and Coates, JD and Rabaey, K}, title = {Bacterial community structure corresponds to performance during cathodic nitrate reduction.}, journal = {The ISME journal}, volume = {4}, number = {11}, pages = {1443-1455}, doi = {10.1038/ismej.2010.66}, pmid = {20520654}, issn = {1751-7370}, mesh = {Bacteria/*classification/genetics/*metabolism ; *Biodiversity ; Bioelectric Energy Sources/*microbiology ; Biofilms/growth &amp; development ; DNA, Bacterial/genetics ; DNA, Complementary/genetics ; DNA, Ribosomal/genetics ; Electrodes/*microbiology ; In Situ Hybridization, Fluorescence ; Nitrates/*metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbial fuel cells (MFCs) have applications other than electricity production, including the capacity to power desirable reactions in the cathode chamber. However, current knowledge of the microbial ecology and physiology of biocathodes is minimal, and as a result more research dedicated to understanding the microbial communities active in cathode biofilms is required. Here we characterize the microbiology of denitrifying bacterial communities stimulated by reducing equivalents generated from the anodic oxidation of acetate. We analyzed biofilms isolated from two types of cathodic denitrification systems: (1) a loop format where the effluent from the carbon oxidation step in the anode is subjected to a nitrifying reactor which is fed to the cathode chamber and (2) an alternative non-loop format where anodic and cathodic feed streams are separated. The results of our study indicate the superior performance of the loop reactor in terms of enhanced current production and nitrate removal rates. We hypothesized that phylogenetic or structural features of the microbial communities could explain the increased performance of the loop reactor. We used PhyloChip with 16S rRNA (cDNA) and fluorescent in situ hybridization to characterize the active bacterial communities. Our study results reveal a greater richness, as well as an increased phylogenetic diversity, active in denitrifying biofilms than was previously identified in cathodic systems. Specifically, we identified Proteobacteria, Firmicutes and Chloroflexi members that were dominant in denitrifying cathodes. In addition, our study results indicate that it is the structural component, in terms of bacterial richness and evenness, rather than the phylogenetic affiliation of dominant bacteria, that best corresponds to cathode performance.}, }
@article {pmid20512729, year = {2010}, author = {Selvam, A and Tsai, SH and Liu, CP and Chen, IC and Chang, CH and Yang, SS}, title = {Microbial communities and bacterial diversity of spruce, hemlock and grassland soils of Tatachia Forest, Taiwan.}, journal = {Journal of environmental science and health. Part. B, Pesticides, food contaminants, and agricultural wastes}, volume = {45}, number = {5}, pages = {386-398}, doi = {10.1080/03601231003799960}, pmid = {20512729}, issn = {1532-4109}, mesh = {Bacteria/classification/genetics/*growth &amp; development/metabolism ; *Biodiversity ; Biomass ; Carbon/metabolism ; Gene Library ; Hydrogen-Ion Concentration ; Nitrogen/metabolism ; Picea/*metabolism ; Poaceae/*metabolism ; RNA, Ribosomal, 16S/genetics ; Rain ; Seasons ; *Soil/analysis ; *Soil Microbiology ; Taiwan ; Temperature ; Trees/metabolism ; Tsuga/*metabolism ; }, abstract = {To evaluate the bacterial diversity of Tatachia Forest soils, 16S rDNA clone libraries of the spruce, hemlock and grassland soils were constructed. Further, the influence of physicochemical and biological properties of soil on microbial ecology, pH, moisture content, microbial population and biomass were also analyzed. The soil pH increased with the increasing of soil depth; whereas the microbial population, biomass, moisture content, total organic carbon and total nitrogen were reverse. Microbial populations were the highest in the summer season which also correlated with the highest moisture content. The phylogenetic analyses revealed that the clones from nine 16S rDNA clone libraries represented Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, Planctomycetes, Verrucomicrobia, candidate division TG1 and candidate division TM7. Members of Proteobacteria, Acidobacteria and Actinobacteria constituted 42.2, 35.1 and 7.8 % of the clone libraries, respectively; whereas the remaining bacterial divisions each comprised <3 %. The spruce site had the highest bacterial diversity among the tested sites, followed by the hemlock sites and the grassland sites with the least. The bacterial community is the more diverse in the organic layer than that in deeper horizons. Further, bacterial diversity through the gradient horizons was different, indicating that the bacterial diversity in the deeper horizons is not simply the diluted analogs of the surface soils and some microbes dominate only in the deeper horizons.}, }
@article {pmid20512486, year = {2010}, author = {Slater, FR and Bruce, KD and Ellis, RJ and Lilley, AK and Turner, SL}, title = {Determining the effects of a spatially heterogeneous selection pressure on bacterial population structure at the sub-millimetre scale.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {873-884}, pmid = {20512486}, issn = {1432-184X}, mesh = {Bacteriological Techniques/*methods ; Drug Resistance, Bacterial ; *Ecosystem ; Mercury/metabolism/*pharmacology ; Models, Biological ; Plasmids/genetics ; Pseudomonas fluorescens/drug effects/*genetics/growth &amp; development ; *Selection, Genetic ; }, abstract = {A key interest of microbial ecology is to understand the role of environmental heterogeneity in shaping bacterial diversity and fitness. However, quantifying relevant selection pressures and their effects is challenging due to the number of parameters that must be considered and the multiple scales over which they act. In the current study, a model system was employed to investigate the effects of a spatially heterogeneous mercuric ion (Hg(2+)) selection pressure on a population comprising Hg-sensitive and Hg-resistant pseudomonads. The Hg-sensitive bacteria were Pseudomonas fluorescens SBW25::rfp and Hg-resistant bacteria were P. fluorescens SBW25 carrying a gfp-labelled, Hg resistance plasmid. In the absence of Hg, the plasmid confers a considerable fitness cost on the host, with µ(max) for plasmid-carrying cells relative to plasmid-free cells of only 0.66. Two image analysis techniques were developed to investigate the structure that developed in biofilms about foci of Hg (cellulose fibres imbued with HgCl(2)). Both techniques indicated selection for the resistant phenotype occurred only in small areas of approximately 178-353 μm (manually defined contour region analysis) or 275-350 μm (daime analysis) from foci. Hg also elicited toxic effects that reduced the growth of both Hg-sensitive and Hg-resistant bacteria up to 250 μm from foci. Selection for the Hg resistance phenotype was therefore highly localised when Hg was spatially heterogeneous. As such, for this model system, we define here the spatial scale over which selection operates. The ability to quantify changes in the strength of selection for particular phenotypes over sub-millimetre scales is useful for understanding the scale over which environmental variables affect bacterial populations.}, }
@article {pmid20509607, year = {2010}, author = {Robertson, JA and I'Anson, KJ and Brocklehurst, TF and Faulds, CB and Waldron, KW}, title = {Effect of storage conditions on the microbial ecology and biochemical stability of cell wall components in brewers' spent grain.}, journal = {Journal of agricultural and food chemistry}, volume = {58}, number = {12}, pages = {7266-7272}, doi = {10.1021/jf1001099}, pmid = {20509607}, issn = {1520-5118}, support = {BBS/E/F/00041910/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/00042086/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/00042288/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/isolation &amp; purification ; Bacterial Physiological Phenomena ; Cell Wall/*chemistry/microbiology ; Edible Grain/*chemistry/*microbiology ; Food Handling/*methods ; Fungi/isolation &amp; purification/physiology ; Temperature ; }, abstract = {The composition of brewers' spent grain (BSG) makes it susceptible to microbial attack and chemical deterioration. This can constrain its appeal as an industrial feedstock. The current study has monitored the effects of BSG storage as fresh material (20 degrees C), refrigerated and autoclaved, measured against frozen material in relation to microbial proliferation and modification to plant cell wall polysaccharides and component phenolic acids. At 20 degrees C there was a rapid colonization by microbes and an associated loss of components from BSG. Refrigeration gave a similar but lower level response. When stored frozen, BSG showed no changes in composition but autoclaving resulted in a solubilization of polysaccharides and associated phenolics. Changes were associated with the temperature profile determined during autoclaving and were also partially due to the breakdown of residual starch. Losses of highly branched arabinoxylan (AX) and the related decrease in ferulic acid cross-linking were also found. The results confirm the need for storage stabilization of BSG and demonstrate that the methods selected for stabilization can themselves lead to a substantial modification to BSG.}, }
@article {pmid20505753, year = {2010}, author = {Yilmaz, S and Haroon, MF and Rabkin, BA and Tyson, GW and Hugenholtz, P}, title = {Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations.}, journal = {The ISME journal}, volume = {4}, number = {10}, pages = {1352-1356}, doi = {10.1038/ismej.2010.73}, pmid = {20505753}, issn = {1751-7370}, mesh = {Animals ; Archaea/genetics/*isolation &amp; purification ; Bacteria/genetics/*isolation &amp; purification ; Bioreactors/microbiology ; Flow Cytometry/methods ; Gastrointestinal Tract/microbiology ; In Situ Hybridization, Fluorescence/*methods ; Isoptera/microbiology ; Microbiological Techniques/*methods ; Microscopy, Fluorescence/*methods ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; }, abstract = {We modified the standard ribosomal RNA-targeted fluorescence in situ hybridization (FISH) protocol by removing the fixation steps to allow recovery of unmodified nucleic acids. Using this method, hybridized cells could be visualized in two bioreactor sludges and termite hindgut samples by epifluorescence microscopy. We then targeted one bacterial and one archaeal population in the sludge samples with group-specific oligonucleotide probes using in-solution fixation-free FISH and sorted hybridized populations using fluorescence-activated cell sorting (FACS). We could show that sorted populations were highly enriched for the target organisms based on 16S rRNA gene sequencing, thus confirming probe specificity using the modified FISH protocol. This approach should facilitate subsequent genomic sequencing and analysis of targeted populations as DNA is not compromised by crosslinking during fixation.}, }
@article {pmid20502891, year = {2010}, author = {Finney, JC and Pettay, DT and Sampayo, EM and Warner, ME and Oxenford, HA and LaJeunesse, TC}, title = {The relative significance of host-habitat, depth, and geography on the ecology, endemism, and speciation of coral endosymbionts in the genus Symbiodinium.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {250-263}, pmid = {20502891}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology ; Caribbean Region ; DNA, Ribosomal Spacer/genetics ; Dinoflagellida/classification/*genetics ; *Ecosystem ; Geography ; Microsatellite Repeats ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; }, abstract = {Dinoflagellates in the genus Symbiodinium are among the most abundant and important group of eukaryotic microbes found in coral reef ecosystems. Recent analyses conducted on various host cnidarians indicated that Symbiodinium assemblages in the Caribbean Sea are genetically and ecologically diverse. In order to further characterize this diversity and identify processes important to its origins, samples from six orders of Cnidaria comprising 45 genera were collected from reef habitats around Barbados (eastern Caribbean) and from the Mesoamerican barrier reef off the coast of Belize (western Caribbean). Fingerprinting of the ribosomal internal transcribed spacer 2 identified 62 genetically different Symbiodinium. Additional analyses of clade B Symbiodinium using microsatellite flanker sequences unequivocally characterized divergent lineages, or "species," within what was previously thought to be a single entity (B1 or B184). In contrast to the Indo-Pacific where host-generalist symbionts dominate many coral communities, partner specificity in the Caribbean is relatively high and is influenced little by the host's apparent mode of symbiont acquisition. Habitat depth (ambient light) and geographic isolation appeared to influence the bathymetric zonation and regional distribution for most of the Symbiodinium spp. characterized. Approximately 80% of Symbiodinium types were endemic to either the eastern or western Caribbean and 40-50% were distributed to compatible hosts living in shallow, high-irradiance, or deep, low-irradiance environments. These ecologic, geographic, and phylogenetic patterns indicate that most of the present Symbiodinium diversity probably originated from adaptive radiations driven by ecological specialization in separate Caribbean regions during the Pliocene and Pleistocene periods.}, }
@article {pmid20502890, year = {2010}, author = {Rivas, MO and Vargas, P and Riquelme, CE}, title = {Interactions of Botryococcus braunii cultures with bacterial biofilms.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {628-635}, pmid = {20502890}, issn = {1432-184X}, mesh = {Biofilms/*growth &amp; development ; Chlorophyta/growth &amp; development/*microbiology ; DNA, Bacterial/genetics ; Gram-Negative Bacteria/genetics/*growth &amp; development/isolation &amp; purification ; *Quorum Sensing ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; }, abstract = {Unicellular microalgae generally grow in the presence of bacteria, particularly when they are farmed massively. This study analyzes the bacteria associated with mass culture of Botryococcus braunii: both the planktonic bacteria in the water column and those forming biofilms adhered to the surface of the microalgal cells (∼10[7]-10[8] culturable cells per gram microalgae). Furthermore, we identified the culturable bacteria forming a biofilm in the microalgal cells by 16S rDNA sequencing. At least eight different culturable species of bacteria were detected in the biofilm and were evaluated for the presence of quorum-sensing signals in these bacteria. Few studies have considered the implications of this phenomenon as regards the interaction between bacteria and microalgae. Production of C4-AHL and C6-AHL were detected in two species, Pseudomonas sp. and Rhizobium sp., which are present in the bacterial biofilm associated with B. braunii. This type of signal was not detected in the planktonic bacteria isolated from the water. We also noted that the bacterium, Rhizobium sp., acted as a probiotic bacterium and significantly encouraged the growth of B. braunii. A direct application of these beneficial bacteria associated with B. braunii could be, to use them like inoculants for large-scale microalgal cultures. They could optimize biomass production by enhancing growth, particularly in this microalga that has a low growth rate.}, }
@article {pmid20499112, year = {2011}, author = {Hammer, EC and Nasr, H and Pallon, J and Olsson, PA and Wallander, H}, title = {Elemental composition of arbuscular mycorrhizal fungi at high salinity.}, journal = {Mycorrhiza}, volume = {21}, number = {2}, pages = {117-129}, pmid = {20499112}, issn = {1432-1890}, mesh = {Acacia/chemistry/drug effects/*microbiology ; Desert Climate/adverse effects ; Fatty Acids/analysis ; Glomeromycota/*chemistry/*drug effects/growth &amp; development ; Hyphae/chemistry/drug effects/growth &amp; development ; Mycorrhizae/*chemistry/*drug effects/growth &amp; development ; Plant Roots/chemistry/drug effects/microbiology ; Potassium/analysis ; Salinity ; Sodium/analysis ; Sodium Chloride/pharmacology ; Soil/analysis ; Spectrometry, X-Ray Emission/methods ; Spores, Fungal/chemistry/drug effects/growth &amp; development ; Tunisia ; }, abstract = {We investigated the elemental composition of spores and hyphae of arbuscular mycorrhizal fungi (AMF) collected from two saline sites at the desert border in Tunisia, and of Glomus intraradices grown in vitro with or without addition of NaCl to the medium, by proton-induced X-ray emission. We compared the elemental composition of the field AMF to those of the soil and the associated plants. The spores and hyphae from the saline soils showed strongly elevated levels of Ca, Cl, Mg, Fe, Si, and K compared to their growth environment. In contrast, the spores of both the field-derived AMF and the in vitro grown G. intraradices contained lower or not elevated Na levels compared to their growth environment. This resulted in higher K:Na and Ca:Na ratios in spores than in soil, but lower than in the associated plants for the field AMF. The K:Na and Ca:Na ratios of G. intraradices grown in monoxenic cultures were also in the same range as those of the field AMF and did not change even when those ratios in the growth medium were lowered several orders of magnitude by adding NaCl. These results indicate that AMF can selectively take up elements such as K and Ca, which act as osmotic equivalents while they avoid uptake of toxic Na. This could make them important in the alleviation of salinity stress in their plant hosts.}, }
@article {pmid20495797, year = {2010}, author = {Oliveira, V and Santos, AL and Coelho, F and Gomes, NC and Silva, H and Almeida, A and Cunha, A}, title = {Effects of monospecific banks of salt marsh vegetation on sediment bacterial communities.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {167-179}, pmid = {20495797}, issn = {1432-184X}, mesh = {Amaranthaceae/*growth &amp; development ; Bacteria/enzymology/*growth &amp; development/isolation &amp; purification ; Geologic Sediments/*microbiology ; Poaceae/*growth &amp; development ; Portugal ; *Water Microbiology ; *Wetlands ; }, abstract = {The aim of this study was to understand if two species of salt marsh plants, widely distributed in European estuaries (Spartina maritima and Halimione portulacoides) differently influence the distribution, activity, and metabolic physiology of sediment bacterial communities in monospecific banks, in comparison with uncolonized sediment (control). Microbiological descriptors of abundance and activity were assessed along vertical profiles of sediments. Rates of activity of the extracellular enzymes beta-glucosidase, alpha-glucosidase, aminopeptidase, arylsulfatase, and phosphatase were generally higher in the vegetation banks in relation to control sediments where they were also less variable with depth. This is interpreted as an indirect effect related to supply of plant-derived polymeric substrates for bacterial growth. Parameters related to sediment texture (grain size, percent of fines or water content) showed significant relations with cell abundance or maximum hydrolysis rates, pointing to an indirect effect of plant colonization exerted through the modification of sediment physical properties. The profiles of utilization of sole-carbon-source (Biolog Ecoplates) showed that only the communities from the upper sediment layer of the S. maritima and the H. portulacoides banks exhibit consistent differences in terms of physiological profiles. Bacterial communities in control sediments exhibited the lowest physiological variability between surface and sub-surface communities. The results indicate that microbial colonization and organic matter decomposition are enhanced under the influence of salt marsh plants and confirm that plant coverage is a major determinant of the processes of organic matter recycling in intertidal estuarine sediments.}, }
@article {pmid20495796, year = {2010}, author = {Kampe, H and Dziallas, C and Grossart, HP and Kamjunke, N}, title = {Similar bacterial community composition in acidic mining lakes with different pH and lake chemistry.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {618-627}, pmid = {20495796}, issn = {1432-184X}, mesh = {Acids/analysis ; Bacteria/*genetics/isolation &amp; purification ; Biota ; Carbon/analysis ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Fresh Water/chemistry ; Hydrogen-Ion Concentration ; *Mining ; Oxygen/analysis ; Phylogeny ; Sequence Analysis, DNA ; Temperature ; *Water Microbiology ; }, abstract = {As extreme environmental conditions strongly affect bacterial community composition (BCC), we examined whether differences in pH-even at low pH-and in iron and sulfate concentrations lead to changes in BCC of acidic mining lakes. Thereby, we tested the following hypotheses: (1) diversity of the bacterial community in acidic lakes decreases with reducing pH, (2) BCC differs between epilimnion and hypolimnion, and (3) BCC in extremely acidic environments does not vary much over time. Therefore, we investigated the BCC of three acidic lakes with different pH values (2.3, 2.7, and 3.2) by denaturing gradient gel electrophoresis (DGGE) and subsequent sequencing of DGGE bands as well as catalyzed reporter deposition-FISH (CARD-FISH). BCC did not significantly vary among the studied lakes nor differ much between water layers. In contrast, BCC significantly changed over time, which is contradictory to our hypotheses. Bacterial communities were dominated by Alpha-, Beta-, and Gammaproteobacteria, whereas Actino- and Acidobacteria rarely occurred. Cell numbers of both free and attached bacteria were positively related to DOC concentration. Overall, low pH and extreme chemical conditions of the studied lakes led to similar assemblages of bacteria with pronounced temporal differences. This notion indicates that temporal changes in environmental conditions including food web structure also affect unique communities of bacteria thriving at low pH.}, }
@article {pmid20492238, year = {2010}, author = {Chang, JY and Chang, HC}, title = {Improvements in the quality and shelf life of kimchi by fermentation with the induced bacteriocin-producing strain, Leuconostoc citreum GJ7 as a starter.}, journal = {Journal of food science}, volume = {75}, number = {2}, pages = {M103-10}, doi = {10.1111/j.1750-3841.2009.01486.x}, pmid = {20492238}, issn = {1750-3841}, mesh = {Bacteriocins/*metabolism ; Brassica/*metabolism/microbiology ; Colony Count, Microbial ; Fermentation/*physiology ; Food Microbiology ; Food Preservation/*methods ; Humans ; Hydrogen-Ion Concentration ; Pigmentation ; Sensation ; Taste ; Time Factors ; }, abstract = {UNLABELLED: To improve the quality and self-life of kimchi, the induced bacteriocin-producing lactic acid bacteria (LAB), Leuconostoc citreum GJ7, was introduced into kimchi fermentation as a starter. The kimchi preparations were incubated at 7 degrees C for 12 to 15 d, and then stored at -1 degrees C. Thereafter, changes in their characteristics were monitored for 125 d. When a kimchi starter was introduced into a nonsterile and open kimchi fermentation system, over-ripening of kimchi was prevented during 125 d of storage. In the starter kimchi, Leuc. citreum GJ7 was the dominant organism, comprising 70% to 90% of the total flora, and no yeasts were detected during the entire storage period. However, in the nonstarter kimchi, the predominant LAB could not be determined and yeasts were detected after 50 d of storage. The viable cell number of the starter kimchi was 2 log CFU/mL higher than in the nonstarter kimchi at 125 d of storage. The texture (firmness) of the starter kimchi at 95 to 125 d of storage was similar to that of the nonstarter kimchi at 20 d of storage. Sensory evaluations of texture, off-flavor, and carbonated mouthfeel were significantly improved by the starter-fermentation. The results indicate that the application of the bacteriocin-enhanced Leuc. citreum GJ7 as a starter culture exerts microbial control, prevents over-ripening, and extends the shelf life of kimchi.<br><br>PRACTICAL APPLICATION: Presently, we have shown that under the optimum fermentation condition the induced bacteriocin-producing LAB, Leuc. citreum GJ7, can regulate natural kimchi fermentation and has extended dominance within the microbial ecology of kimchi. The result is improved quality and shelf life of kimchi. Moreover, to control the growth of other microorganisms in open-fermentation and nonsterile conditions, this system may be usefully adapted for other food or environmental control systems.}, }
@article {pmid20486208, year = {2010}, author = {Bolca, S and Li, J and Nikolic, D and Roche, N and Blondeel, P and Possemiers, S and De Keukeleire, D and Bracke, M and Heyerick, A and van Breemen, RB and Depypere, H}, title = {Disposition of hop prenylflavonoids in human breast tissue.}, journal = {Molecular nutrition &amp; food research}, volume = {54 Suppl 2}, number = {0 2}, pages = {S284-94}, pmid = {20486208}, issn = {1613-4133}, support = {P50 AT000155/AT/NCCIH NIH HHS/United States ; P50AT00155/AT/NCCIH NIH HHS/United States ; }, mesh = {Adipose Tissue, White/*metabolism ; Adolescent ; Adult ; Biotransformation ; Breast ; Chromatography, High Pressure Liquid ; *Dietary Supplements ; Female ; Flavanones/administration &amp; dosage/blood/chemistry/*metabolism ; Flavonoids/administration &amp; dosage/blood/chemistry/*metabolism ; Flowers/chemistry ; Humans ; Humulus/*chemistry ; Mammary Glands, Human/*metabolism ; Middle Aged ; Phytoestrogens/administration &amp; dosage/blood/chemistry/metabolism ; Propiophenones/administration &amp; dosage/blood/chemistry/*metabolism ; Spectrometry, Mass, Electrospray Ionization ; Tandem Mass Spectrometry ; Xanthones/administration &amp; dosage/blood/chemistry/*metabolism ; Young Adult ; }, abstract = {Hop-derived products may contain xanthohumol (XN), isoxanthohumol (IX), and the potent phytoestrogen 8-prenylnaringenin (8-PN). To evaluate the potential health effects of these prenylflavonoids on breast tissue, their concentration, nature of metabolites, and biodistribution were assessed and compared with 17beta-estradiol (E(2)) exposure. In this dietary intervention study, women were randomly allocated to hop (n=11; 2.04 mg XN, 1.20 mg IX, and 0.1 mg 8-PN per supplement) or control (n=10). After a run-in of >or=4 days, three supplements were taken daily for 5 days preceding an aesthetic breast reduction. Blood and breast biopsies were analyzed using HPLC-ESI-MS/MS. Upon hop administration, XN and IX concentrations ranged between 0.72 and 17.65 nmol/L and 3.30 and 31.50 nmol/L, and between 0.26 and 5.14 pmol/g and 1.16 and 83.67 pmol/g in hydrolyzed serum and breast tissue, respectively. 8-PN however, was only detected in samples of moderate and strong 8-PN producers (0.43-7.06 nmol/L and 0.78-4.83 pmol/g). Phase I metabolism appeared to be minor (approximately 10%), whereas extensive glucuronidation was observed (> 90%). Total prenylflavonoids showed a breast adipose/glandular tissue distribution of 38/62 and their derived E(2)-equivalents were negligible compared with E(2) in adipose (384.6+/-118.8 fmol/g, p=0.009) and glandular (241.6+/-93.1 fmol/g, p<0.001) tissue, respectively. Consequently, low doses of prenylflavonoids are unlikely to elicit estrogenic responses in breast tissue.}, }
@article {pmid20480364, year = {2011}, author = {Bugla-Płoskońska, G and Korzeniowska-Kowal, A and Guz-Regner, K}, title = {Reptiles as a source of Salmonella O48--clinically important bacteria for children: the relationship between resistance to normal cord serum and outer membrane protein patterns.}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {41-51}, pmid = {20480364}, issn = {1432-184X}, mesh = {Animals ; Bacterial Outer Membrane Proteins/*chemistry/isolation &amp; purification ; *Blood Bactericidal Activity ; Complement Activation/immunology ; Complement C3/analysis ; Complement Pathway, Alternative/immunology ; Fetal Blood/*immunology ; Humans ; Infant, Newborn ; Microbial Viability ; Reptiles/*microbiology ; Salmonella/chemistry/classification/*immunology ; Serum/chemistry/*immunology ; }, abstract = {Bacteria of the Salmonella O48 somatic antigen group are clinically important strains causing intestinal dysfunction and diarrhoea, especially in children. The susceptibility of Salmonella O48 strains containing sialic acid (N-acetylneuraminic acid (NeuAc)) in lipopolysaccharide (LPS) to the bactericidal action of normal cord serum (NCS) was determined. The authors' previous results published in Microbial Ecology in 2010 indicated that neither the presence of NeuAc in LPS nor the length of the O-specific part of LPS containing NeuAc plays a decisive role in determining bacterial resistance to the bactericidal activity of normal human serum (NHS), and that the presence of NeuAc in the LPS structure is not sufficient to block the activation of the alternative pathway of complement in NHS. The current results showed that the tested strains showed various sensitivities also to the bactericidal action of NCS. The authors postulate that the presence of certain outer membrane proteins (OMPs) are characteristic of the resistant and sensitive phenotypes of Salmonella O48 strains. To establish a possible relationship between resistance to NCS and OMPs band patterns, ten Salmonella O48 strains were studied as follows: susceptibility to the bactericidal effect of NCS, the mechanisms of NCS activation and OMP band patterns obtained by sodium dodecyl sulphate-polyacrylamide gel electrophoresis.}, }
@article {pmid20479960, year = {2010}, author = {Caruso, G}, title = {Leucine aminopeptidase, beta-glucosidase and alkaline phosphatase activity rates and their significance in nutrient cycles in some coastal Mediterranean sites.}, journal = {Marine drugs}, volume = {8}, number = {4}, pages = {916-940}, pmid = {20479960}, issn = {1660-3397}, mesh = {Alkaline Phosphatase/*metabolism ; Ecosystem ; Leucyl Aminopeptidase/*metabolism ; Mediterranean Sea ; Nitrates/chemistry ; Phosphorus/chemistry ; Seawater/*chemistry/microbiology ; Water Microbiology ; beta-Glucosidase/*metabolism ; }, abstract = {In aquatic microbial ecology, knowledge of the processes involved in the turnover of organic matter is of utmost importance to understand ecosystem functioning. Microorganisms are major players in the cycling of nutrients (nitrogen, phosphorus) and carbon, thanks to their enzymatic activities (leucine aminopeptidase, LAP, alkaline phosphatase, AP, and beta-glucosidase, beta-GLU) on organic polymers (proteins, organic phosphates and polysaccharides, respectively). Estimates of the decomposition rates of organic polymers are performed using fluorogenic compounds, whose hydrolysis rate allow us to obtain information on the "potential" metabolic activity of the prokaryotic community. This paper refers the enzyme patterns measured during recent oceanographic cruises performed in some coastal Mediterranean sites, not yet fully investigated in terms of microbial biogeochemical processes. Mean enzyme activity rates ranged from 5.24 to 5558.1 nM/h, from 12.68 to 244.73 nM/h and from 0.006 to 9.51 nM/h for LAP, AP and beta-GLU, respectively. The highest LAP and AP activity rates were measured in the Gulf of Milazzo (Tyrrhenian Sea) and in the Straits of Messina, in association with the lowest bacterioplankton abundance; in contrast, the lowest ones were found in the northern Adriatic Sea. beta-GLU was more active in the Straits of Messina. Activity rates were analysed in relation to the main environmental variables. Along the northern Adriatic coastal side affected by the Po river, significant inverse relationships linked LAP and AP with salinity, pointing out that fluvial inputs provided organic substrates for microbial metabolism. Both in the Gulf of Manfredonia and in the Straits of Messina, LAP and AP levels were inversely related with the concentration of nitrate and inorganic phosphorus, respectively. In the Gulf of Milazzo, high cell-specific AP measured in spite of phosphorus availability suggested the role of this enzyme not only in phosphorus, but also in carbon release.}, }
@article {pmid20473491, year = {2010}, author = {Fukuda, A and Hagiwara, H and Ishimura, T and Kouduka, M and Ioka, S and Amano, Y and Tsunogai, U and Suzuki, Y and Mizuno, T}, title = {Geomicrobiological properties of ultra-deep granitic groundwater from the Mizunami Underground Research Laboratory (MIU), central Japan.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {214-225}, pmid = {20473491}, issn = {1432-184X}, mesh = {Caulobacteraceae/*genetics/isolation &amp; purification/metabolism ; DNA, Bacterial/genetics ; Ecosystem ; Fresh Water/*chemistry/*microbiology ; Japan ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Thauera/*genetics/isolation &amp; purification/metabolism ; *Water Microbiology ; }, abstract = {Although deep subterranean crystalline rocks are known to harbor microbial ecosystems, geochemical factors that constrain the biomass, diversity, and metabolic activities of microorganisms remain to be clearly defined. To better understand the geochemical and microbiological relationships, we characterized granitic groundwater collected from a 1,148- to 1,169-m-deep borehole interval at the Mizunami Underground Research Laboratory site, Japan, in 2005 and 2008. Geochemical analyses of the groundwater samples indicated that major electron acceptors, such as NO(3)(-) and SO(4)(2-), were not abundant, while dissolved organic carbon (not including organic acids), CH(4) and H(2), was moderately rich in the groundwater sample collected in 2008. The total number of acridine orange-stained cells in groundwater samples collected in 2005 and 2008 were 1.1 x 10(4) and 5.2 x 10(4) cells/mL, respectively. In 2005 and 2008, the most common phylotypes determined by 16S rRNA gene sequence analysis were both related to Thauera spp., the cultivated members of which can utilize minor electron donors, such as aromatic and aliphatic hydrocarbons. After a 3-5-week incubation period with potential electron donors (organic acids or CH(4) + H(2)) and with/without electron acceptors (O(2) or NO(3)(-)), dominant microbial populations shifted to Brevundimonas spp. These geomicrobiological results suggest that deep granitic groundwater has been stably colonized by Thauera spp. probably owing to the limitation of O(2), NO(3)(-), and organic acids.}, }
@article {pmid20473490, year = {2010}, author = {Kelly, LC and Cockell, CS and Piceno, YM and Andersen, GL and Thorsteinsson, T and Marteinsson, V}, title = {Bacterial diversity of weathered terrestrial Icelandic volcanic glasses.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {740-752}, pmid = {20473490}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/genetics ; Geologic Sediments/analysis/*microbiology ; Glass/analysis ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Volcanic Eruptions/*analysis ; }, abstract = {The diversity of microbial communities inhabiting two terrestrial volcanic glasses of contrasting mineralogy and age was characterised. Basaltic glass from a <0.8 Ma hyaloclastite deposit (Valafell) harboured a more diverse Bacteria community than the younger rhyolitic glass from ∼150-300 AD (Dόmadalshraun lava flow). Actinobacteria dominated 16S rRNA gene clone libraries from both sites, however, Proteobacteria, Acidobacteria and Cyanobacteria were also numerically abundant in each. A significant proportion (15-34%) of the sequenced clones displayed <85% sequence similarities with current database sequences, thus suggesting the presence of novel microbial diversity in each volcanic glass. The majority of clone sequences shared the greatest similarity to uncultured organisms, mainly from soil environments, among these clones from Antarctic environments and Hawaiian and Andean volcanic deposits. Additionally, a large number of clones within the Cyanobacteria and Proteobacteria were more similar to sequences from other lithic environments, included among these Icelandic clones from crystalline basalt and rhyolite, however, no similarities to sequences reported from marine volcanic glasses were observed. PhyloChip analysis detected substantially greater numbers of phylotypes at both sites than the corresponding clone libraries, but nonetheless also identified the basaltic glass community as the richer, containing approximately 29% unique phylotypes compared to rhyolitic glass.}, }
@article {pmid20467813, year = {2010}, author = {Stevens, P and van Elsas, JD}, title = {A putative genomic island, PGI-1, in Ralstonia solanacearum biovar 2 revealed by subtractive hybridization.}, journal = {Antonie van Leeuwenhoek}, volume = {98}, number = {3}, pages = {359-377}, pmid = {20467813}, issn = {1572-9699}, mesh = {Bacterial Typing Techniques ; Bangladesh ; Base Sequence ; DNA Fingerprinting ; DNA Transposable Elements ; DNA, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Fresh Water/microbiology ; *Genomic Islands ; Geologic Sediments/microbiology ; Molecular Sequence Data ; Netherlands ; Nucleic Acid Hybridization ; Plant Diseases/*microbiology ; Plants/microbiology ; Polymerase Chain Reaction ; Ralstonia solanacearum/classification/*genetics/growth &amp; development ; Sequence Analysis, DNA ; Solanum tuberosum/*microbiology ; Virulence ; Water Microbiology ; }, abstract = {Ralstonia solanacearum biovar 2, a key bacterial pathogen of potato, has recently established in temperate climate waters. On the basis of isolates obtained from diseased (potato) plants, its genome has been assumed to be virtually clonal, but information on environmental isolates has been lacking. Based on differences in pulsed-field gel electrophoresis patterns, we compared the genomes of two biovar 2 strains with different life histories. Thus, genomic DNA of the novel environmental strain KZR-5 (The Netherlands) was compared to that of reference potato strain 715 (Bangladesh) by suppressive subtractive hybridization. Various strain-specific sequences were found, all being homologous to those found in the genome of reference potato strain 1609. Approximately 20% of these were related to genes involved in recombinational processes. We found a deletion of a 17.6-Kb region, denoted as a putative genomic island PGI-1, in environmental strain KZR-5. The deleted region was, at both extremes, flanked by a composite of two insertion sequence (IS) elements, identified as ISRso2 and ISRso3. The PGI-1 region contained open reading frames that putatively encoded a (p)ppGpp synthetase, a transporter protein, a transcriptional regulator, a cellobiohydrolase, a site-specific integrase/recombinase, a phage-related protein and seven hypothetical proteins. As yet, no phenotype could be assigned to the loss of PGI-1. The ecological behavior of strain KZR-5 was compared to that of reference strain 715. Strain KZR-5 showed enhanced tolerance to 4°C as compared to the reference strain, but was not affected in its virulence on tomato.}, }
@article {pmid20467736, year = {2010}, author = {De Schamphelaire, L and Boeckx, P and Verstraete, W}, title = {Evaluation of biocathodes in freshwater and brackish sediment microbial fuel cells.}, journal = {Applied microbiology and biotechnology}, volume = {87}, number = {5}, pages = {1675-1687}, doi = {10.1007/s00253-010-2645-9}, pmid = {20467736}, issn = {1432-0614}, mesh = {*Bioelectric Energy Sources ; Biofilms/*growth &amp; development ; Carbon/metabolism ; Electrodes/*microbiology ; Fresh Water/*microbiology ; Molecular Sequence Data ; Proteobacteria/*growth &amp; development/*metabolism ; Stainless Steel ; }, abstract = {Biofilms on biocathodes can catalyze the cathodic oxygen reduction and accordingly guarantee high cathode redox potentials. The present research assessed the use of biocathodes in full-sediment microbial fuel cells. Carbon felt-based biocathodes were evaluated in freshwater systems, and an extension of their application to brackish systems and/or stainless steel webs as base material was considered. Efficient biocathodes could be developed within days through inoculation with active microorganisms. Carbon felt was found most suited for the biocathodes in freshwater with increased performance at salinities around 80-250 mM. Maximum long-term performance reached 12.3 microW cm(-2) cathode. The relative benefit of stainless steel seemed to increase with increasing salinity. A combination of stainless steel cathodes with biofilms could, however, also result in decreased electrical performance. In an efficiently catalyzing cathodic biofilm, an enrichment with an uncultured Proteobacterium--previously correlated with steel waste--was observed.}, }
@article {pmid20461587, year = {2010}, author = {Czerwiński, J and Højberg, O and Smulikowska, S and Engberg, RM and Mieczkowska, A}, title = {Influence of dietary peas and organic acids and probiotic supplementation on performance and caecal microbial ecology of broiler chickens.}, journal = {British poultry science}, volume = {51}, number = {2}, pages = {258-269}, doi = {10.1080/00071661003777003}, pmid = {20461587}, issn = {1466-1799}, mesh = {Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Cecum/*microbiology ; Chickens/*growth &amp; development/microbiology ; Diet/*veterinary ; Dietary Supplements ; Female ; In Situ Hybridization, Fluorescence ; *Pisum sativum ; *Probiotics ; }, abstract = {1. The effect of dietary pea and addition of organic acid blend (OA) or probiotic (Pro) on performance and caecal microbial ecology of broiler chickens was studied. 2. A growth trial was conducted with 160 Ross 308 female broilers from d 1 to 35 of age. There were 8 treatment groups based on either control (S) or white pea (P). Both S and P were supplemented with OA (Galliacid - fumaric acid, calcium formate, calcium propionate and potassium sorbate coated with plant triglycerides, Vetagro) and or with Pro (LABYuc-Probio - lactic acid bacteria, Saccharomyces cerevisiae and Yucca schidigeri extract, Mifarmex GmbH). 3. Inclusion of peas in the diet increased feed intake and decreased gain:feed ratio in comparison to the control diet. Neither probiotic nor OA supplementations affected broiler performance. 4. The caecal microbiota was characterised in 37-d-old birds by fluorescent in situ hybridisation (FISH) and terminal-restriction fragment length polymorphism (T-RFLP). Total bacterial counts in caecal contents were slightly higher for birds fed the pea diets, but were not affected by OA or Pro supplements. 5. Neither pea nor Pro affected the Lactobacillus/Enterococcus and Streptococcus/Lactococcus counts in caecal contents, whereas OA supplementation slightly increased the Lactobacillus/Enterococcus counts. The composition of the Lactobacillus/Enterococcus population was altered by inclusion of peas as revealed by the T-RFLP patterns. 6. The DNA fingerprint further suggested that the caecal microbiota was dominated by the lactic acid bacterium Streptococcus alactolyticus. 7. In ileal contents, the concentration of short-chain fatty acids (SCFA) was decreased only by Pro supplementation. In caecal contents, the SCFA concentration was higher for birds fed on the pea diets, and increased significantly with Pro supplementation 8. In conclusion, the results indicate that the use of pea and probiotics in broiler feed may stimulate the caecal commensal microbiota (growth and/or activity) to some extent and hence prevent establishment of pathogenic and zoonotic enterobacteria in these segments of the gut.}, }
@article {pmid20454959, year = {2010}, author = {Leyton, Y and Riquelme, C}, title = {Marine Bacillus spp. associated with the egg capsule of Concholepas concholepas (common name "loco") have an inhibitory activity toward the pathogen Vibrio parahaemolyticus.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {599-605}, pmid = {20454959}, issn = {1432-184X}, mesh = {Animals ; *Antibiosis ; Bacillus/genetics/isolation &amp; purification/*physiology ; DNA, Bacterial/genetics ; Gastropoda/*microbiology ; Ovum/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vibrio parahaemolyticus/*physiology ; }, abstract = {The pandemic bacterium Vibrio parahaemolyticus, isolated from seawater, sediment, and marine organisms, is responsible for gastroenteric illnesses in humans and also cause diseases in aquaculture industry in Chile and other countries around the world. In this study, bacterial flora with inhibitory activity against pathogenic V. parahaemolyticus were collected from egg capsules of Concholepas concholepas and evaluated. The 16S rRNA fragment was sequenced from each isolated strain to determine its identity using the GenBank database. A phylogenetic analysis was made, and tests for the productions of antibacterial substance were performed using the double-layer method. Forty-five morphotypes of bacterial colonies were isolated, 8 of which presented an inhibitory effect on the growth of V. parahaemolyticus. 16S rRNA sequence and phylogenetic analysis show that these strains constitute taxa that are phylogenetically related to the Bacillus genus and are probably sister species or strains of the species Bacillus pumilus, Bacillus licheniform, or Bacillus sp. It is important to determine the nature of the antibacterial substance to evaluate their potential for use against the pathogen species V. parahaemolyticus.}, }
@article {pmid20452420, year = {2010}, author = {Mocali, S and Benedetti, A}, title = {Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology.}, journal = {Research in microbiology}, volume = {161}, number = {6}, pages = {497-505}, doi = {10.1016/j.resmic.2010.04.010}, pmid = {20452420}, issn = {1769-7123}, mesh = {Biodiversity ; Databases, Genetic ; Gene Library ; Industrial Microbiology ; Internationality ; *Metagenomics/trends ; Phylogeny ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Soil is one of the most complex and challenging environments for microbiologists. In fact, although it contains the largest microbial diversity on the planet, the majority of these microbes are still uncharacterized and represent an enormous unexplored reservoir of genetic and metabolic diversity. Metagenomics, the study of the entire genome of soil biota, currently represents a powerful tool for assessing the diversity of complex microbial communities, providing access to a number of new species, genes or novel molecules that are relevant for biotechnology and agricultural applications. In this paper, the onset of new high-throughput metagenomic approaches and new perspectives in soil microbial ecology and data handling are discussed.}, }
@article {pmid20452073, year = {2010}, author = {Possemiers, S and Marzorati, M and Verstraete, W and Van de Wiele, T}, title = {Bacteria and chocolate: a successful combination for probiotic delivery.}, journal = {International journal of food microbiology}, volume = {141}, number = {1-2}, pages = {97-103}, doi = {10.1016/j.ijfoodmicro.2010.03.008}, pmid = {20452073}, issn = {1879-3460}, mesh = {*Bifidobacterium ; Cacao/*microbiology ; Colony Count, Microbial ; Drug Carriers ; Drug Compounding ; Gastrointestinal Tract/*microbiology ; *Lactobacillus helveticus ; *Probiotics ; Stress, Physiological ; }, abstract = {In this work, chocolate has been evaluated as a potential protective carrier for oral delivery of a microencapsulated mixture of Lactobacillus helveticus CNCM I-1722 and Bifidobacterium longum CNCM I-3470. A sequential in vitro setup was used to evaluate the protection of the probiotics during passage through the stomach and small intestine, when embedded in dark and milk chocolate or liquid milk. Both chocolates offered superior protection (91% and 80% survival in milk chocolate for L. helveticus and B. longum, respectively compared to 20% and 31% found in milk). To simulate long-term administration, the Simulator of the Human Intestinal Microbial Ecosystem (SHIME) was used. Plate counts, Denaturing Gradient Gel Electrophoresis and quantitative PCR showed that the two probiotics successfully reached the simulated colon compartments. This led to an increase in lactobacilli and bifidobacteria counts and the appearance of additional species in the fingerprints. These data indicate that the coating of the probiotics in chocolate is an excellent solution to protect them from environmental stress conditions and for optimal delivery. The simulation with our gastrointestinal model showed that the formulation of a probiotic strain in a specific food matrix could offer superior protection for the delivery of the bacterium into the colon. The chocolate example could act as a trigger for new research to identify new balanced matrices.}, }
@article {pmid20449583, year = {2010}, author = {Michaelsen, A and Piñar, G and Pinzari, F}, title = {Molecular and microscopical investigation of the microflora inhabiting a deteriorated Italian manuscript dated from the thirteenth century.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {69-80}, pmid = {20449583}, issn = {1432-184X}, support = {P 17328/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/genetics/*isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; Electrophoresis, Polyacrylamide Gel ; *Environmental Microbiology ; Fungi/genetics/*isolation &amp; purification ; *Manuscripts as Topic ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Spores, Fungal/isolation &amp; purification ; }, abstract = {This case study shows the application of nontraditional diagnostic methods to investigate the microbial consortia inhabiting an ancient manuscript. The manuscript was suspected to be biologically deteriorated and SEM observations showed the presence of fungal spores attached to fibers, but classic culturing methods did not succeed in isolating microbial contaminants. Therefore, molecular methods, including PCR, denaturing gradient gel electrophoresis (DGGE), and clone libraries, were used as a sensitive alternative to conventional cultivation techniques. DGGE fingerprints revealed a high biodiversity of both bacteria and fungi inhabiting the manuscript. DNA sequence analysis confirmed the existence of fungi and bacteria in manuscript samples. A number of fungal clones identified on the manuscript showed similarity to fungal species inhabiting dry or saline environments, suggesting that the manuscript environment selects for osmophilic or xerophilic fungal species. Most of the bacterial sequences retrieved from the manuscript belong to phylotypes with cellulolytic activities.}, }
@article {pmid20449582, year = {2010}, author = {Yarwood, SA and Bottomley, PJ and Myrold, DD}, title = {Soil microbial communities associated with Douglas-fir and red alder stands at high- and low-productivity forest sites in Oregon, USA.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {606-617}, pmid = {20449582}, issn = {1432-184X}, mesh = {Alnus/*microbiology ; Archaea/classification/genetics/*growth &amp; development ; Bacteria/classification/genetics/*growth &amp; development ; Biota ; DNA, Archaeal/genetics/isolation &amp; purification ; DNA, Bacterial/genetics/isolation &amp; purification ; DNA, Fungal/genetics/isolation &amp; purification ; Ecosystem ; Fungi/classification/genetics/*growth &amp; development ; Gene Dosage ; Oregon ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Pseudotsuga/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Trees/microbiology ; }, abstract = {Communities of archaea, bacteria, and fungi were examined in forest soils located in the Oregon Coast Range and the inland Cascade Mountains. Soils from replicated plots of Douglas-fir (Pseudotsuga menziesii) and red alder (Alnus rubra) were characterized using fungal ITS (internal transcribed spacer region), eubacterial 16S rRNA, and archaeal 16S rRNA primers. Population size was measured with quantitative (Q)-PCR and composition was examined using length heterogeneity (LH)-PCR for fungal composition, terminal restriction fragment length (T-RFLP) profiles for bacterial and archaeal composition, and sequencing to identify dominant community members. Whereas fungal and archaeal composition varied between sites and dominant tree species, bacterial communities only varied between sites. The abundance of archaeal gene copy numbers was found to be greater in coastal compared to montane soils accounting for 11% of the prokaryotic community. Crenarchaea groups 1.1a-associated, 1.1b, 1.1c, and 1.1c-associated were putatively identified. A greater abundance of Crenarchaea 1.1b indicator fragments was found in acidic (pH 4) soils with low C:N ratios under red alder. In coastal soils, 25% of fungal sequences were putatively identified as basidiomycetous yeasts belonging to the genus Cryptococcus. Although the function of these yeasts in soil is not known, they could significantly contribute to decomposition processes in coastal soils distinguished by rapid tree growth, high N content, low pH, and frequent water-saturation events.}, }
@article {pmid20449581, year = {2011}, author = {Pozo, MI and Herrera, CM and Bazaga, P}, title = {Species richness of yeast communities in floral nectar of southern Spanish plants.}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {82-91}, pmid = {20449581}, issn = {1432-184X}, mesh = {Adaptation, Physiological/physiology ; Animals ; *Biodiversity ; Insecta/physiology ; *Plant Nectar ; Plants/*microbiology ; Spain ; Yeasts/*classification/genetics/growth &amp; development/*isolation &amp; purification ; }, abstract = {Floral nectar of insect-pollinated plants often contains dense yeast populations, yet little quantitative information exists on patterns and magnitude of species richness of nectar-dwelling yeasts in natural plant communities. This study evaluates yeast species richness at both the plant community and plant species levels in a montane forest area in southern Spain, and also explores possible correlations between the incidence of different yeast species in nectar and their reported tolerance to high sugar concentrations, and between yeast diversity and pollinator composition. Yeast species occurring in a total of 128 field-collected nectar samples from 24 plant species were identified by sequencing the D1/D2 domain of the large subunit rDNA, and rarefaction-based analyses were used to estimate yeast species richness at the plant community and plant species levels, using nectar drops as elemental sampling units. Individual nectar samples were generally characterized by very low species richness (1.2 yeast species/sample, on average), with the ascomycetous Metschnikowia reukaufii and Metschnikowia gruessii accounting altogether for 84.7% of the 216 isolates identified. Other yeasts recorded included species in the genera Aureobasidium, Rhodotorula, Cryptococcus, Sporobolomyces, and Lecythophora. The shapes and slopes of observed richness accumulation curves were quite similar for the nectar drop and plant species approaches, but the two approaches yielded different expected richness estimates. Expected richness was higher for plant species-based than for nectar drop-based analyses, showing that the coverage of nectar yeast species occurring in the region would be improved by sampling additional host plant species. A significant correlation was found between incidence of yeast species in nectar and their reported ability to grow in a medium containing 50% glucose. Neither diversity nor incidence of yeasts was correlated with pollinator composition across plant species.}, }
@article {pmid20447994, year = {2010}, author = {Schott, J and Griffin, BM and Schink, B}, title = {Anaerobic phototrophic nitrite oxidation by Thiocapsa sp. strain KS1 and Rhodopseudomonas sp. strain LQ17.}, journal = {Microbiology (Reading, England)}, volume = {156}, number = {Pt 8}, pages = {2428-2437}, doi = {10.1099/mic.0.036004-0}, pmid = {20447994}, issn = {1465-2080}, mesh = {Anaerobiosis ; DNA, Bacterial/genetics ; Molecular Sequence Data ; Nitrites/*metabolism ; Oxidation-Reduction ; *Phototrophic Processes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhodopseudomonas/genetics/isolation &amp; purification/*metabolism ; Sewage/microbiology ; Thiocapsa/genetics/isolation &amp; purification/*metabolism ; }, abstract = {In anaerobic enrichment cultures for phototrophic nitrite-oxidizing bacteria from different freshwater sites, two different cell types, i.e. non-motile cocci and motile, rod-shaped bacteria, always outnumbered all other bacteria. Most-probable-number (MPN) dilution series with samples from two freshwater sites yielded only low numbers (<or=3x10(3) cm(-3)) of phototrophic nitrite oxidizers. Slightly higher numbers (about 10(4) cm(-3)) were found in activated sewage sludge. Anaerobic phototrophic oxidation of nitrite was studied with two different isolates, the phototrophic sulfur bacterium strain KS1 and the purple nonsulfur bacterium strain LQ17, both of which were isolated from activated sludge collected from the municipal sewage treatment plant in Konstanz, Germany. Strain KS1 converted 1 mM nitrite stoichiometrically to nitrate with concomitant formation of cell matter within 2-3 days, whereas strain LQ17 oxidized only up to 60 % of the given nitrite to nitrate within several months with the concomitant formation of cell biomass. Nitrite oxidation to nitrate was strictly light-dependent and required the presence of molybdenum in the medium. Nitrite was oxidized in both the presence and absence of oxygen. Nitrite inhibited growth at concentrations higher than 2 mM. Hydroxylamine and hydrazine were found to be toxic to the phototrophs in the range 5-50 muM and did not stimulate phototrophic growth. Based on morphology, substrate-utilization pattern, in vivo absorption spectra, and 16S rRNA gene sequence similarity, strain KS1 was assigned to the genus Thiocapsa and strain LQ17 to the genus Rhodopseudomonas. Also, Thiocapsa roseopersicina strains DSM 217 and DSM 221 were found to oxidize nitrite to nitrate with concomitant growth. We conclude that the ability to use nitrite phototrophically as electron donor is widespread in nature, but low MPN counts indicate that its contribution to nitrite oxidation in the studied habitats is rather limited.}, }
@article {pmid20446084, year = {2010}, author = {Cuzman, OA and Ventura, S and Sili, C and Mascalchi, C and Turchetti, T and D'Acqui, LP and Tiano, P}, title = {Biodiversity of phototrophic biofilms dwelling on monumental fountains.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {81-95}, pmid = {20446084}, issn = {1432-184X}, mesh = {Bacteria/genetics/*isolation &amp; purification ; Biodegradation, Environmental ; *Biodiversity ; Biofilms/*growth &amp; development ; Cyanobacteria/genetics/*isolation &amp; purification ; DNA Fingerprinting ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Italy ; Photosynthesis ; Principal Component Analysis ; *Sculpture ; Spain ; }, abstract = {Among the stone monumental assets, artistic fountains are particularly affected by microbial colonization due to constant contact with water, giving rise to biodegradation processes related with physical-chemical and aesthetical alterations. In this paper, we make an overview of reported biodiversity of the phototrophic patina developed in various fountains of Italy and Spain. The microbial composition of four fountains (two from Florence, Italy and two from Granada, Spain) was investigated using traditional and/or molecular techniques. The results indicated many common similarities with regard the phototrophic biodiversity for all the investigated fountains. Automated ribosomal RNA intergenic spacer analysis (ARISA), a molecular fingerprint tool, was used to examine the eubacterial and cyanobacterial community for two of the investigated fountains. The principal component analysis of ARISA profiles strengthens the results obtained by traditional methods and revealed separate clusters, as a consequence of the differences of micro-environmental conditions for each fountain.}, }
@article {pmid20445636, year = {2010}, author = {Rousk, J and Bååth, E and Brookes, PC and Lauber, CL and Lozupone, C and Caporaso, JG and Knight, R and Fierer, N}, title = {Soil bacterial and fungal communities across a pH gradient in an arable soil.}, journal = {The ISME journal}, volume = {4}, number = {10}, pages = {1340-1351}, doi = {10.1038/ismej.2010.58}, pmid = {20445636}, issn = {1751-7370}, mesh = {Bacteria/*classification/*isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; Fungi/*classification/*isolation &amp; purification ; Hydrogen-Ion Concentration ; Metagenome ; Metagenomics/methods ; North America ; Polymerase Chain Reaction/methods ; Polymorphism, Genetic ; Sequence Analysis, DNA/methods ; Soil/*analysis ; *Soil Microbiology ; South America ; }, abstract = {Soils collected across a long-term liming experiment (pH 4.0-8.3), in which variation in factors other than pH have been minimized, were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial taxa, fungi and bacteria. We hypothesized that bacterial communities would be more strongly influenced by pH than fungal communities. To determine the relative abundance of bacteria and fungi, we used quantitative PCR (qPCR), and to analyze the composition and diversity of the bacterial and fungal communities, we used a bar-coded pyrosequencing technique. Both the relative abundance and diversity of bacteria were positively related to pH, the latter nearly doubling between pH 4 and 8. In contrast, the relative abundance of fungi was unaffected by pH and fungal diversity was only weakly related with pH. The composition of the bacterial communities was closely defined by soil pH; there was as much variability in bacterial community composition across the 180-m distance of this liming experiment as across soils collected from a wide range of biomes in North and South America, emphasizing the dominance of pH in structuring bacterial communities. The apparent direct influence of pH on bacterial community composition is probably due to the narrow pH ranges for optimal growth of bacteria. Fungal community composition was less strongly affected by pH, which is consistent with pure culture studies, demonstrating that fungi generally exhibit wider pH ranges for optimal growth.}, }
@article {pmid20440490, year = {2010}, author = {Miller, AZ and Rogerio-Candelera, MA and Laiz, L and Wierzchos, J and Ascaso, C and Sequeira Braga, MA and Hernández-Mariné, M and Maurício, A and Dionísio, A and Macedo, MF and Saiz-Jimenez, C}, title = {Laboratory-induced endolithic growth in calcarenites: biodeteriorating potential assessment.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {55-68}, pmid = {20440490}, issn = {1432-184X}, mesh = {Biodegradation, Environmental ; Biofilms/*growth &amp; development ; Chlorophyll/analysis ; Construction Materials/analysis/*microbiology ; Cyanobacteria/*growth &amp; development ; Eukaryota/*growth &amp; development ; Microscopy, Electron, Scanning ; Photosynthesis ; Porosity ; }, abstract = {This study is aimed to assess the formation of photosynthetic biofilms on and within different natural stone materials, and to analyse their biogeophysical and biogeochemical deterioration potential. This was performed by means of artificial colonisation under laboratory conditions during 3 months. Monitoring of microbial development was performed by image analysis and biofilm biomass estimation by chlorophyll extraction technique. Microscopy investigations were carried out to study relationships between microorganisms and the mineral substrata. The model applied in this work corroborated a successful survival strategy inside endolithic microhabitat, using natural phototrophic biofilm cultivation, composed by cyanobacteria and algae, which increased intrinsic porosity by active mineral dissolution. We observed the presence of mineral-like iron derivatives (e.g. maghemite) around the cells and intracellularly and the precipitation of hausmannite, suggesting manganese transformations related to the biomineralisation.}, }
@article {pmid20440489, year = {2010}, author = {De Troch, M and Cnudde, C and Willems, A and Moens, T and Vanreusel, A}, title = {Bacterial colonization on fecal pellets of harpacticoid copepods and on their diatom food.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {581-591}, pmid = {20440489}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/*genetics/growth &amp; development ; Copepoda/*microbiology ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Diatoms/*microbiology ; Feces/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Fecal pellets make up a significant fraction of the global flux of organic matter in oceans, and the associated bacterial communities in particular are a potential food source for marine organisms. However, these communities remain largely unknown. In the present study, the bacterial communities on fecal pellets of the benthic copepod Paramphiascella fulvofasciata feeding on the diatoms Navicula phyllepta and Seminavis robusta were analyzed. The aim of this study was to characterize the bacterial communities associated with the diatoms and the fecal pellets by means of DGGE profiling. Furthermore, isolated bacteria were characterized by means of partial 16S rRNA gene sequencing. The composition of the bacterial microflora on fecal pellets was studied in terms of the effect of the original food source, the age of the fecal pellets and the copepod's identity. Alphaproteobacteria, Flavobacteria, and Bacilli were found on the fecal pellets; whereas on diatoms, exclusively Gammaproteobacteria were identified. Especially after eating N. phyllepta, there was an important increase in bacterial diversity, although the diatom N. phyllepta harbored a less diverse bacterial community than S. robusta. Our data suggest that the additional bacteria originate from the copepod's digestive tract and largely depends on the initial food source.}, }
@article {pmid20437259, year = {2011}, author = {Menkis, A and Vasaitis, R}, title = {Fungi in roots of nursery grown Pinus sylvestris: ectomycorrhizal colonisation, genetic diversity and spatial distribution.}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {52-63}, pmid = {20437259}, issn = {1432-184X}, mesh = {DNA, Ribosomal Spacer/genetics ; Fungi/classification/*genetics/*growth &amp; development/isolation &amp; purification ; Genes, Fungal/genetics ; *Genetic Variation ; Genotype ; Molecular Sequence Data ; Mycorrhizae/classification/*genetics/*growth &amp; development/isolation &amp; purification ; Phylogeny ; Pinus sylvestris/*microbiology ; Plant Roots/*microbiology ; Seedlings/microbiology ; Time Factors ; }, abstract = {The aims of this study were to investigate patterns of ectomycorrhizal (ECM) colonisation and community structure on nursery grown seedlings of Pinus sylvestris, spatial distribution of ECMs in the nursery plot and genetic diversity of commonly isolated ECM basidiomycete Hebeloma cavipes. One hundred seedlings were sampled in 225 m(2) area using a systematic grid design. For each seedling, 20 individual root tips were randomly collected, morphotyped, and surface sterilised for fungal isolation in pure culture. Results showed that ECM community was comprised of nine distinct morphotypes among which Thelephora terrestris (39.7%), Hebeloma sp. (17.8%) and Suillus luteus (6.1%) were the most abundant. Spatial distribution of ECMs in the nursery plot was determined by their relative abundance: even in common ECMs and random in rare ones. Fungal isolation yielded 606 pure cultures, representing 71 distinct taxa. The most commonly isolated fungi were the ascomycetes Neonectria macrodidyma (20.3%), Phialocephala fortinii (13.5%), Neonectria radicicola (6.3%) and the ECM basidiomycete H. cavipes (4.5%). Intraspecific genetic diversity within 27 H. cavipes isolates was studied using two methods: restriction digestion of the amplified intergenic spacer of nuclear ribosomal DNA and genealogical concordance of five genetic markers. Five and eight genotypes were revealed by each respective method, but both of those were largely consistent, in particular, in determining the largest genotype (A) composed of 18 isolates. Mapping positions for each H. cavipes isolate and genotype in the field showed that isolates of the A genotype covered a large part of the nursery plot. This suggests that H. cavipes is largely disseminated by vegetative means of local genotypes and that nursery cultivation practices are likely to contribute to the dissemination of this species in the forest nursery soils.}, }
@article {pmid20424834, year = {2011}, author = {Dhanasiri, AK and Brunvold, L and Brinchmann, MF and Korsnes, K and Bergh, &#xd8; and Kiron, V}, title = {Changes in the intestinal microbiota of wild Atlantic cod Gadus morhua L. upon captive rearing.}, journal = {Microbial ecology}, volume = {61}, number = {1}, pages = {20-30}, pmid = {20424834}, issn = {1432-184X}, mesh = {Animals ; Bacteria/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; *Biodiversity ; Fisheries ; Food Deprivation ; Gadus morhua/*microbiology ; Intestines/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The commensal microbiota plays an important role in the well-being of the host organism, and it would be worthwhile to know the tenacious communities among them. Therefore, a study was undertaken to examine the changes in constitution of the intestinal microbiota of wild fish consequential to captivity. At first, the composition of intestinal microorganisms of Atlantic cod caught from the coastal area off Bodø, Norway, was examined. Thereafter, the changes in the bacterial community of the captive fish after offering them artificial feed or subjecting them to starvation were studied. The microbiota from the intestinal contents and wall segments were analyzed quantitatively by spread plate technique and DAPI staining and qualitatively by denaturing gradient gel electrophoresis. The study revealed that the counts of intestinal microbes in wild-caught Atlantic cod were not affected by captive rearing for 6 weeks, either when fed or when starved. However, the diversity of intestinal bacterial community was reduced in response to artificial feeding, whereas the change was restricted upon starvation.}, }
@article {pmid20422409, year = {2010}, author = {Senechkin, IV and Speksnijder, AG and Semenov, AM and van Bruggen, AH and van Overbeek, LS}, title = {Isolation and partial characterization of bacterial strains on low organic carbon medium from soils fertilized with different organic amendments.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {829-839}, pmid = {20422409}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Carbon/*metabolism ; Culture Media/*metabolism ; DNA, Bacterial/genetics ; Fertilizers/analysis ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/analysis ; *Soil Microbiology ; }, abstract = {A total of 720 bacterial strains were isolated from soils with four different organic amendment regimes on a low organic carbon (low-C) agar medium (10 µg C ml(-1)) traditionally used for isolation of oligotrophs. Organic amendments in combination with field history resulted in differences in dissolved organic carbon contents in these soils. There were negative correlations between total and dissolved organic carbon content and the number of isolates on low-C agar medium, whereas these correlations were absent for bacterial strains isolated from the same soil on high-C agar medium (1,000 µg C ml(-1)). Repeated transfers (up to ten times) of the isolates from low-C agar medium to fresh low- and high-C agar media were done to test for exclusive growth under oligotrophic conditions. The number of isolates exclusively growing under oligotrophic conditions dropped after each subsequent transfer from 241 after the first to 98 after the third transfer step. Identification on the basis of partial 16S rRNA gene sequences revealed that most of the 241 isolates (as well as the subset of 98 isolates) belong to widespread genera such as Streptomyces, Rhizobium, Bradyrhizobium, and Mesorhizobium, and the taxonomic composition of dominant genera changed from the first transfer step to the third. A selected subset of 17 isolates were further identified and characterized for exclusive growth on low-C agar medium. Two isolates continued to grow only on low-C agar medium up to the tenth transfer step and matched most closely with Rhizobium sullae and an uncultured bacterium on the basis of the almost full-length 16S rRNA gene. It was concluded that the vast majority of strains which are isolated on low-C agar media belong to the trophic group of microorganisms adapted to a "broad range" of carbon concentrations, including well-known and widespread bacterial genera. Oligotrophy is a physiological, not a taxonomic property, and can only be identified by cultural means so far. We showed that true oligotrophs that are unable to grow on high carbon media are rare and belong to genera that also contain broad-range and copiotrophic strains.}, }
@article {pmid20418443, year = {2010}, author = {Harris, JK and Sahl, JW and Castoe, TA and Wagner, BD and Pollock, DD and Spear, JR}, title = {Comparison of normalization methods for construction of large, multiplex amplicon pools for next-generation sequencing.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {12}, pages = {3863-3868}, pmid = {20418443}, issn = {1098-5336}, support = {U01 HL081335/HL/NHLBI NIH HHS/United States ; U01HL081335-01/HL/NHLBI NIH HHS/United States ; R01 GM083127/GM/NIGMS NIH HHS/United States ; LM009451/LM/NLM NIH HHS/United States ; T15 LM009451/LM/NLM NIH HHS/United States ; }, mesh = {*Gene Library ; Metagenomics/*methods ; Sensitivity and Specificity ; Sequence Analysis, DNA/*methods ; Staining and Labeling/*methods ; }, abstract = {Constructing mixtures of tagged or bar-coded DNAs for sequencing is an important requirement for the efficient use of next-generation sequencers in applications where limited sequence data are required per sample. There are many applications in which next-generation sequencing can be used effectively to sequence large mixed samples; an example is the characterization of microbial communities where <or=1,000 sequences per samples are adequate to address research questions. Thus, it is possible to examine hundreds to thousands of samples per run on massively parallel next-generation sequencers. However, the cost savings for efficient utilization of sequence capacity is realized only if the production and management costs associated with construction of multiplex pools are also scalable. One critical step in multiplex pool construction is the normalization process, whereby equimolar amounts of each amplicon are mixed. Here we compare three approaches (spectroscopy, size-restricted spectroscopy, and quantitative binding) for normalization of large, multiplex amplicon pools for performance and efficiency. We found that the quantitative binding approach was superior and represents an efficient scalable process for construction of very large, multiplex pools with hundreds and perhaps thousands of individual amplicons included. We demonstrate the increased sequence diversity identified with higher throughput. Massively parallel sequencing can dramatically accelerate microbial ecology studies by allowing appropriate replication of sequence acquisition to account for temporal and spatial variations. Further, population studies to examine genetic variation, which require even lower levels of sequencing, should be possible where thousands of individual bar-coded amplicons are examined in parallel.}, }
@article {pmid20417394, year = {2010}, author = {Tu, RJ and Wu, HY and Lock, YS and Chen, MJ}, title = {Evaluation of microbial dynamics during the ripening of a traditional Taiwanese naturally fermented ham.}, journal = {Food microbiology}, volume = {27}, number = {4}, pages = {460-467}, doi = {10.1016/j.fm.2009.12.011}, pmid = {20417394}, issn = {1095-9998}, mesh = {Animals ; Base Sequence ; Colony Count, Microbial ; Culture Media ; DNA, Bacterial/*analysis ; Electrophoresis, Gel, Pulsed-Field ; Fermentation ; Food Microbiology ; Humans ; Lactobacillaceae/*growth &amp; development/isolation &amp; purification ; Meat Products/*microbiology ; Polymerase Chain Reaction ; Population Dynamics ; Staphylococcus/*growth &amp; development/isolation &amp; purification ; Swine ; Taiwan ; }, abstract = {Isolation and identification of the autochthonous starter from a naturally fermented meat allows control of the fermentation process and promises microbiological safety for this specialty. Thus the purpose of this study was to identify the lactic acid bacteria and coagulase-negative cocci present in a traditional Taiwanese naturally fermented ham (TNFH) and to study the microbial dynamics at different ripening stages; the approach was a combination of conventional microbiological cultivation, polymerase chain reaction-denaturing gradient gel electrophoresis and DNA sequencing. In total, twelve different strains of lactic acid bacteria and three Staphylococcus strains were identified in the TNFH samples, whereas only 5 dominant strains were observed in the TNFH samples when the DGGE as a culture-independent method was applied. The bacterial ecology on the surface of the samples was mainly characterized by the stable presence of Lactobacillus sakei and Staphylococcus saprophyticus; nonetheless Leuconostoc mesenteroides and Carnobacterium divergens were the most abundant bacteria found in the final product. These results are also agreed with the findings of the culture-independent method. In addition, Microbacterium spp., Carnobacterium spp., Enterobacter spp., Brochothrix spp., Enterococcus spp., and Bacillus spp. were also present at the beginning of the ripening, but few bacteria were found at the center of the TNFH samples during the early ripening stages. However, after 30 days of ripening, the microbial ecology at the center of the TNFH samples paralleled that of the surface. Finally, as far as we have been able to determine, our report is the first to investigate the microbiological dynamics in fermented meat products using combination of cultivation, the Harrison disc method, DGGE and DNA sequencing as the culture-dependent method. Our report is also the first to show the presence of Staphylococcus arlettae in a fermented sausage and ham product.}, }
@article {pmid20414654, year = {2010}, author = {Saavedra, JM and Acevedo, F and González, M and Seeger, M}, title = {Mineralization of PCBs by the genetically modified strain Cupriavidus necator JMS34 and its application for bioremediation of PCBs in soil.}, journal = {Applied microbiology and biotechnology}, volume = {87}, number = {4}, pages = {1543-1554}, doi = {10.1007/s00253-010-2575-6}, pmid = {20414654}, issn = {1432-0614}, mesh = {Biodegradation, Environmental ; Cupriavidus necator/*genetics/*metabolism ; *Genetic Engineering ; Mutagenesis, Insertional ; Polychlorinated Biphenyls/*metabolism ; Soil Pollutants/metabolism ; }, abstract = {Polychlorobiphenyls (PCBs) are classified as "high-priority pollutants." Diverse microorganisms are able to degrade PCBs. However, bacterial degradation of PCBs is generally incomplete, leading to the accumulation of chlorobenzoates (CBAs) as dead-end metabolites. To obtain a microorganism able to mineralize PCB congeners, the bph locus of Burkholderia xenovorans LB400, which encodes one of the most effective PCB degradation pathways, was incorporated into the genome of the CBA-degrading bacterium Cupriavidus necator JMP134-X3. The bph genes were transferred into strain JMP134-X3, using the mini-Tn5 transposon system and biparental mating. The genetically modified derivative, C. necator strain JMS34, had only one chromosomal insertion of bph locus, which was stable under nonselective conditions. This modified bacterium was able to grow on biphenyl, 3-CBA and 4-CBA, and degraded 3,5-CBA in the presence of m-toluate. The strain JMS34 mineralized 3-CB, 4-CB, 2,4'-CB, and 3,5-CB, without accumulation of CBAs. Bioaugmentation of PCB-polluted soils with C. necator strain JMS34 and with the native B. xenovorans LB400 was monitored. It is noteworthy that strain JMS34 degraded, in 1 week, 99% of 3-CB and 4-CB and approximately 80% of 2,4'-CB in nonsterile soil, as well as in sterile soil. Additionally, the bacterial count of strain JMS34 increased by almost two orders of magnitude in PCB-polluted nonsterile soil. In contrast, the presence of native microflora reduced the degradation of these PCBs by strain LB400 from 73% (sterile soil) to approximately 50% (nonsterile soil). This study contributes to the development of improved biocatalysts for remediation of PCB-contaminated environments.}, }
@article {pmid20414647, year = {2010}, author = {Manter, DK and Delgado, JA and Holm, DG and Stong, RA}, title = {Pyrosequencing reveals a highly diverse and cultivar-specific bacterial endophyte community in potato roots.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {157-166}, pmid = {20414647}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; *Biodiversity ; Biomass ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Plant Roots/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; Solanum tuberosum/*microbiology ; }, abstract = {In this study, we examined the bacterial endophyte community of potato (Solanum tuberosum) cultivar/clones using two different molecular-based techniques (bacterial automated ribosomal intergenic spacer analysis (B-ARISA) and pyrosequencing). B-ARISA profiles revealed a significant difference in the endophytic community between cultivars (perMANOVA, p < 0.001), and canonical correspondence analysis showed a significant correlation between the community structure and plant biomass (p = 0.001). Pyrosequencing detected, on average, 477 +/- 71 bacterial operational taxonomic units (OTUs, 97% genetic similarity) residing within the roots of each cultivar, with a Chao estimated total OTU richness of 1,265 +/- 313. Across all cultivars, a total of 238 known genera from 15 phyla were identified. Interestingly, five of the ten most common genera (Rheinheimera, Dyadobacter, Devosia, Pedobacter, and Pseudoxanthomonas) have not, to our knowledge, been previously reported as endophytes of potato. Like the B-ARISA analysis, the endophytic communities differed between cultivar/clones (integral-libshuff, p < 0.001) and exhibited low similarities on both a presence/absence (0.145 +/- 0.019) and abundance (0.420 +/- 0.081) basis. Seventeen OTUs showed a strong positive (r > 0.600) or negative (r < -0.600) correlation with plant biomass, suggesting a possible link between plant production and endophyte abundance. This study represents one of the most comprehensive assessments of the bacterial endophytic communities to date, and similar analyses in other plant species, cultivars, or tissues could be utilized to further elucidate the potential contribution(s) of endophytic communities to plant physiology and production.}, }
@article {pmid20409700, year = {2010}, author = {Knorr, D and Wacher, C}, title = {Microbial ecology, in foods and at the intestine.}, journal = {Current opinion in biotechnology}, volume = {21}, number = {2}, pages = {123-124}, doi = {10.1016/j.copbio.2010.03.018}, pmid = {20409700}, issn = {1879-0429}, mesh = {*Ecosystem ; *Food Microbiology ; *Food Technology ; Humans ; Intestines/*microbiology ; }, }
@article {pmid20407893, year = {2010}, author = {Holmfeldt, K and Titelman, J and Riemann, L}, title = {Virus production and lysate recycling in different sub-basins of the northern Baltic Sea.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {572-580}, pmid = {20407893}, issn = {1432-184X}, mesh = {Bacteria/metabolism/virology ; Carbon/*metabolism ; DNA, Viral/isolation &amp; purification ; Ecosystem ; Linear Models ; Nitrogen/metabolism ; Oceans and Seas ; Phosphorus/*metabolism ; Seawater/chemistry/*virology ; Sweden ; Temperature ; Viruses/growth &amp; development/*metabolism ; }, abstract = {In the Gulf of Bothnia, northern Baltic Sea, a large freshwater inflow creates north-southerly gradients in physico-chemical and biological factors across the two sub-basins, the Bothnian Bay (BB) and the Bothnian Sea. In particular, the sub-basins differ in nutrient limitation (nitrogen vs. phosphorus; P). Since viruses are rich in P, and virus production is commonly connected with bacterial abundance and growth, we hypothesized that the role of viral lysis differs between the sub-basins. Thus, we examined virus production and the potential importance of lysate recycling in surface waters along a transect in the Gulf of Bothnia. Surprisingly, virus production and total P were negatively correlated. In the BB, virus production rates were double those elsewhere in the system, although bacterial abundance and production were the lowest. In the BB, virus-mediated cell lysates could account for 70-180% and 100-250% of the bacterial carbon and P demand, respectively, while only 4-15% and 8-21% at the other stations. Low concentrations of dissolved DNA (D-DNA) with a high proportion of encapsulated DNA (viruses) in the BB suggested rapid turnover and high uptake of free DNA. The correlation of D-DNA and total P indicates that D-DNA is a particularly important nutrient source in the P-limited BB. Our study demonstrates large and counterintuitive differences in virus-mediated recycling of carbon and nutrients in two basins of the Gulf of Bothnia, which differ in microbial community composition and nutrient limitation.}, }
@article {pmid20405118, year = {2010}, author = {Starič, N and Danevčič, T and Stopar, D}, title = {Vibrio sp. DSM 14379 pigment production--a competitive advantage in the environment?.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {592-598}, pmid = {20405118}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/biosynthesis ; *Antibiosis ; Bacillus/*drug effects ; Coculture Techniques ; Culture Media ; Microbial Sensitivity Tests ; Pigments, Biological/*biosynthesis ; Seawater/*microbiology ; Temperature ; Vibrio/*chemistry/growth &amp; development ; Water Microbiology ; }, abstract = {The ability to produce several antibacterial agents greatly increases the chance of producer's survival. In this study, red-pigmented Vibrio sp. DSM 14379 and Bacillus sp., both isolated from the same sampling volume from estuarine waters of the Northern Adriatic Sea, were grown in a co-culture. The antibacterial activity of the red pigment extract was tested on Bacillus sp. in microtiter plates. The MIC(50) for Bacillus sp. was estimated to be around 10[-5] mg/L. The extract prepared form the nonpigmented mutant of Vibrio sp. had no antibacterial effect. The pigment production of Vibrio sp. was studied under different physicochemical conditions. There was no pigment production at high or low temperatures, high or low salt concentrations in peptone yeast extract (PYE) medium, low glucose concentration in mineral growth medium or high glucose concentration in PYE medium. This indicates that the red pigment production is a luxurious good that Vibrio sp. makes only under favorable conditions. The Malthusian fitness of Bacillus sp. in a co-culture with Vibrio sp. under optimal environmental conditions dropped from 4.0 to -7.6, which corresponds to three orders of magnitude decrease in the number of CFU relative to the monoculture. The nonpigmented mutant of Vibrio sp. in a co-culture with Bacillus sp. had a significant antibacterial activity. This result shows that studying antibacterial properties in isolation (i.e. pigment extract only) may not reveal full antibacterial potential of the bacterial strain. The red pigment is a redundant antibacterial agent of Vibrio sp.}, }
@article {pmid20402776, year = {2010}, author = {Olson, JB and Kellogg, CA}, title = {Microbial ecology of corals, sponges, and algae in mesophotic coral environments.}, journal = {FEMS microbiology ecology}, volume = {73}, number = {1}, pages = {17-30}, doi = {10.1111/j.1574-6941.2010.00862.x}, pmid = {20402776}, issn = {1574-6941}, mesh = {Animals ; Anthozoa/*microbiology ; *Ecosystem ; Eukaryota/*microbiology ; Porifera/*microbiology ; Seawater/microbiology ; *Water Microbiology ; }, abstract = {Mesophotic coral ecosystems that occur at depths from 30 to 200 m have historically been understudied and yet appear to support a diverse biological community. The microbiology of these systems is particularly poorly understood, especially with regard to the communities associated with corals, sponges, and algae. This lack of information is partly due to the problems associated with gaining access to these environments and poor reproducibility across sampling methods. To summarize what is known about the microbiology of these ecosystems and to highlight areas where research is urgently needed, an overview of the current state of knowledge is presented. Emphasis is placed on the characterization of microbial populations, both prokaryotic and eukaryotic, associated with corals, sponges, and algae and the factors that influence microbial community structure. In topic areas where virtually nothing is known from mesophotic environments, the knowledge pertaining to shallow-water ecosystems is summarized to provide a starting point for a discussion on what might be expected in the mesophotic zone.}, }
@article {pmid20401609, year = {2010}, author = {Lazar, CS and Dinasquet, J and Pignet, P and Prieur, D and Toffin, L}, title = {Active archaeal communities at cold seep sediments populated by Siboglinidae tubeworms from the Storegga Slide.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {516-527}, pmid = {20401609}, issn = {1432-184X}, mesh = {Animals ; Crenarchaeota/classification/*genetics ; DNA Fingerprinting ; DNA, Archaeal/genetics ; Denaturing Gradient Gel Electrophoresis ; *Ecosystem ; Gene Library ; Geologic Sediments/*microbiology ; Norway ; Phylogeny ; Polychaeta/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Siboglinid tubeworms in cold seep sediments can locally modify the geochemical gradients of electron acceptors and donors, hence creating potential microhabitats for prokaryotic populations. The archaeal communities associated with sediments populated by Oligobrachia haakonmosbiensis and Sclerolinum contortum Siboglinid tubeworms in the Storegga Slide were examined in this study. Vertical distribution of archaeal communities was investigated using denaturing gradient gel electrophoresis based on 16S rRNA genes. The active fraction of the archaeal community was assessed by using reverse-transcribed rRNA. Archaeal communities associated with sediments colonized by tubeworms were affiliated with uncultivated archaeal lineages of the Crenarchaeota and Euryarchaeota. The composition of the active archaeal populations changed with depth indicating a reorganization of microbial communities. 16S rRNA gene libraries were dominated by sequences affiliated to the Rice Cluster V which are unusual in marine sediment samples. Moreover, this study provides the first evidence of living Crenarchaeota of the Rice Cluster V in cold seep sediments. Furthermore, the Storegga Slide sediments harbored a high diversity of other minor groups of uncultivated lineages including Terrestrial Miscellaneous Euryarchaeotal Group, Marine Benthic Group (MBG)-D, MBG-E, Deep-Sea Hydrothermal Vent Euryarchaeotal Group, Lake Dagow Sediment, Val Kotinen Lake clade III, and Sippenauer Moor 1. Thus, we hypothesize that the vertical geochemical imprint created by the tubeworms could support broad active archaeal populations in the Siboglinidae-populated Storegga Slide sediments.}, }
@article {pmid20400851, year = {2010}, author = {Mandal, SM and Chakraborty, D and Dey, S}, title = {Phenolic acids act as signaling molecules in plant-microbe symbioses.}, journal = {Plant signaling &amp; behavior}, volume = {5}, number = {4}, pages = {359-368}, pmid = {20400851}, issn = {1559-2324}, mesh = {Hydroxybenzoates/*metabolism ; Mycorrhizae/physiology ; Plant Diseases/microbiology ; Plants/*metabolism/*microbiology ; Rhizobium/metabolism/physiology ; *Signal Transduction ; *Symbiosis ; }, abstract = {Phenolic acids are the main polyphenols made by plants. These compounds have diverse functions and are immensely important in plant-microbe interactions/symbiosis. Phenolic compounds act as signaling molecules in the initiation of legumerhizobia symbioses, establishment of arbuscular mycorrhizal symbioses and can act as agents in plant defense. Flavonoids are a diverse class of polyphenolic compounds that have received considerable attention as signaling molecules involved in plant-microbe interactions compared to the more widely distributed, simple phenolic acids; hydroxybenzoic and hydroxycinnamic acids, which are both derived from the general phenylpropanoid pathway. This review describes the well-known roles attributed to phenolic compounds as nod gene inducers of legume-rhizobia symbioses, their roles in induction of the GmGin1 gene in fungus for establishment of arbuscular mycorrhizal symbiosis, their roles in inducing vir gene expression in Agrobacterium, and their roles as defense molecules operating against soil borne pathogens that could have great implications for rhizospheric microbial ecology. Amongst plant phenolics we have a lack of knowledge concerning the roles of phenolic acids as signaling molecules beyond the relatively well-defined roles of flavonoids. This may be addressed through the use of plant mutants defective in phenolic acids biosynthesis or knock down target genes in future investigations.}, }
@article {pmid20397013, year = {2010}, author = {Semenov, AM and Kuprianov, AA and van Bruggen, AH}, title = {Transfer of enteric pathogens to successive habitats as part of microbial cycles.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {239-249}, pmid = {20397013}, issn = {1432-184X}, mesh = {Animals ; Avena/microbiology ; Brassicaceae/microbiology ; Carbon/metabolism ; Cattle ; Colony Count, Microbial ; *Ecosystem ; Escherichia coli O157/*growth &amp; development/metabolism ; Feces/microbiology ; *Food Chain ; Mice ; Salmonella typhimurium/*growth &amp; development/metabolism ; Snails ; *Soil Microbiology ; }, abstract = {Escherichia coli O157:H7 gfp and Salmonella enterica Typhimurium gfp passed through six successive habitats within a microbial cycle. Pathogen cultures were introduced into cow dung or fodder. Microscopically observed cells and CFUs were monitored in fodder, dung, dung-soil mix, rhizosphere and phyllosphere of cress or oat plants grown in infested dung-soil mix, and in excrements of snails or mice fed with contaminated cress or oat shoots. Both methods were sensitive enough to monitor cells and CFUs throughout the chain. There was a positive correlation between cells and CFUs. Both pathogens declined through the successive habitats, but with unexpected increased densities on plants compared to dung-soil mix. Pathogen densities were higher in the phyllosphere than the rhizosphere of cress, but for oat plants this was reverse. Survival in dung was better after passage through the digestive tract of cows than after introduction of cultures into dung. Positive correlations between pathogens and copiotrophic bacteria (CB) and dissolved organic carbon (DOC) were observed in dung and dung-soil mixtures, but at low DOC contents CB densities were higher than pathogen densities. Thus, the pathogens are able to cycle through different habitats, surviving or growing better at high DOC concentrations, but maintaining population densities that are sufficiently high to cause disease in humans.}, }
@article {pmid20393846, year = {2010}, author = {Gertler, C and Näther, DJ and Gerdts, G and Malpass, MC and Golyshin, PN}, title = {A mesocosm study of the changes in marine flagellate and ciliate communities in a crude oil bioremediation trial.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {180-191}, pmid = {20393846}, issn = {1432-184X}, mesh = {Biodegradation, Environmental ; Ciliophora/genetics/growth &amp; development/*isolation &amp; purification ; DNA Fingerprinting ; Dinoflagellida/genetics/growth &amp; development/*isolation &amp; purification ; Petroleum/*microbiology ; Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; Seawater/*microbiology ; }, abstract = {Protozoan grazers play an important role in controlling the density of crude-oil degrading marine communities as has been evidenced in a number of microcosm experiments. However, small bioreactors contain a low initial titre of protozoa and the growth of hydrocarbon-depleting bacteria is accompanied by the fast depletion of mineral nutrients and oxygen, which makes microcosms rather unsuitable for simulating the sequence of events after the oil spill in natural seawater environment. In the present study, the population dynamics of marine protozoan community have been analysed in a 500 l mesocosm experiment involving bioaugmented oil booms that contained oil sorbents and slow-release fertilisers. A significant increase in numbers of marine flagellates and ciliates on biofilms of oil-degrading microbes was microscopically observed as early as 8 days after the start of the experiment, when protozoa exhibited a population density peak making up to 3,000 cells ml(-1). Further, the protozoan density varied throughout the experiment, but never dropped below 80 cells ml(-1). An 18S rRNA gene-based fingerprinting analysis revealed several changes within the eukaryotic community over the whole course of the experiment. Initial growth of flagellates and small ciliates was followed by a predominance of larger protozoa. According to microscopic observations and SSU rRNA molecular analyses, most predominant were the ciliates belonging to Euplotidae and Scuticociliatia. This is the first study to characterise the eukaryotic communities specifically in a large-scale oil bioremediation trial using both microscopy-based and several molecular techniques.}, }
@article {pmid20393845, year = {2010}, author = {Piñar, G and Jimenez-Lopez, C and Sterflinger, K and Ettenauer, J and Jroundi, F and Fernandez-Vivas, A and Gonzalez-Muñoz, MT}, title = {Bacterial community dynamics during the application of a Myxococcus xanthus-inoculated culture medium used for consolidation of ornamental limestone.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {15-28}, pmid = {20393845}, issn = {1432-184X}, support = {T 137/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Calcium Carbonate ; Culture Media ; DNA, Bacterial/genetics ; *Environmental Microbiology ; Metagenome/genetics ; Myxococcus xanthus/genetics/growth &amp; development/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {In this study, we investigated under laboratory conditions the bacterial communities inhabiting quarry and decayed ornamental carbonate stones before and after the application of a Myxococcus xanthus-inoculated culture medium used for consolidation of the stones. The dynamics of the community structure and the prevalence of the inoculated bacterium, M. xanthus, were monitored during the time course of the consolidation treatment (30 days). For this purpose, we selected a molecular strategy combining fingerprinting by denaturing gradient gel electrophoresis (DGGE) with the screening of eubacterial 16S rDNA clone libraries by DGGE and sequencing. Quantification of the inoculated strain was performed by quantitative real-time PCR (qPCR) using M. xanthus-specific primers designed in this work. Results derived from DGGE and sequencing analysis showed that, irrespective of the origin of the stone,the same carbonatogenic microorganisms were activated by the application of a M. xanthus culture. Those microorganisms were Pseudomonas sp., Bacillus sp., and Brevibacillus sp. The monitoring of M. xanthus in the culture media of treated stones during the time course experiment showed disparate results depending on the applied technique. By culture-dependent methods, the detection of this bacterium was only possible in the first day of the treatment, showing the limitation of these conventional techniques. By PCR-DGGE analysis, M. xanthus was detected during the first 3-6 days of the experiment. At this time, the population of this bacterium in the culture media varied between 108-106 cells ml-1, as showed by qPCR analyses. Thereafter, DGGE analyses showed to be not suitable for the detection of M. xanthus in a mixed culture. Nevertheless, qPCR analysis using specific primers for M. xanthus showed to bea more sensitive technique for the detection of thisbacterium, revealing a population of 104 cells ml-1 in the culture media of both treated stones at the end of the consolidation treatment. The molecular strategy used in this study is proposed as an effective monitoring system to evaluate the impact of the application of a bacterially induced carbonate mineralization as restoration/conservation treatment for ornamental stones.}, }
@article {pmid20390264, year = {2010}, author = {López-Legentil, S and Erwin, PM and Pawlik, JR and Song, B}, title = {Effects of sponge bleaching on ammonia-oxidizing Archaea: distribution and relative expression of ammonia monooxygenase genes associated with the barrel sponge Xestospongia muta.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {561-571}, pmid = {20390264}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Animals ; Archaeal Proteins/genetics ; Crenarchaeota/*enzymology/genetics ; Gene Library ; Genes, Archaeal ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Archaeal/genetics ; Xestospongia/*microbiology ; }, abstract = {Sponge-mediated nitrification is an important process in the nitrogen cycle, however, nothing is known about how nitrification and symbiotic Archaea may be affected by sponge disease and bleaching events. The giant barrel sponge Xestospongia muta is a prominent species on Caribbean reefs that contains cyanobacterial symbionts, the loss of which results in two types of bleaching: cyclic, a recoverable condition; and fatal, a condition associated with the disease-like sponge orange band (SOB) syndrome and sponge death. Terminal restriction fragment length polymorphism (TRFLP) analyses, clone libraries, and relative mRNA quantification of ammonia monooxygenase genes (amoA) were performed using a RNA transcript-based approach to characterize the active ammonia-oxidizing Archaea (AOA) community present in bleached, non-bleached, and SOB tissues of cyclically and fatally bleached sponges. We found that non-bleached and cyclically bleached tissues of X. muta harbored a unique Crenarchaeota community closely related to those reported for other sponges. In contrast, bleached tissue from the most degraded sponge contained a Crenarchaeota community that was more similar to those found in sediment and sand. Although there were no significant differences in amoA expression among the different tissues, amoA expression was higher in the most deteriorated tissues. Results suggest that a shift in the Crenarchaeota community precedes an increase in amoA gene expression in fatally bleached sponges, while cyclic bleaching did not alter the AOA community structure and its amoA gene expression.}, }
@article {pmid20386899, year = {2010}, author = {Konkol, NR and Bruckner, JC and Aguilar, C and Lovalvo, D and Maki, JS}, title = {Dominance of epiphytic filamentous Thiothrix spp. on an aquatic macrophyte in a hydrothermal vent flume in Sedge Bay, Yellowstone Lake, Wyoming.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {528-538}, pmid = {20386899}, issn = {1432-184X}, mesh = {DNA, Bacterial/genetics ; *Ecosystem ; Fresh Water ; Genes, Bacterial ; Magnoliopsida/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfur/analysis ; Thiothrix/classification/*genetics ; Water/chemistry ; *Water Microbiology ; Wyoming ; }, abstract = {Sublacustrine hydrothermal vents, geysers, and fumaroles impart regions of Yellowstone Lake with distinctive chemical compositions that generate unique freshwater habitats and support diverse microbial life. Some microbial communities within Sedge Bay manifest themselves as accumulations of white-colored films on the surfaces of aquatic macrophytes located within the hydrothermal flow of vents. It was hypothesized that the white films were the product of microbial growth, particularly sulfur-oxidizing bacteria. An investigation of the relevant biological compounds in the vent waters was conducted. Microscopy, non-culture molecular techniques, and phylogenetic analysis were used to assay the bacterial diversity associated with the films. Microscopic analysis of the white films revealed the presence of long filaments (>200 μm) that contained sulfur granules. Filaments with these characteristics were not detected on the normal macrophyte samples. Nucleic acids were extracted from the surface of macrophyte coated with the white film (SB1, SB2) and from the surface of an uncoated macrophyte (SC). 16S ribosomal (rRNA) genes were amplified with the polymerase chain reaction (PCR) and cloned. Amplified ribosomal DNA restriction analysis (ARDRA) was used to examine 100 clones from each library and identify unique phylotypes. S(Chao1) and the Shannon Index, mathematical measures of richness and heterogeneity, were employed to assess the ARDRA pattern diversity of each sample. The SC community contained 50 unique phylotypes, predominantly cyanobacteria and proteobacteria, and was the most heterogeneous. SB1 and SB2 communities were less heterogeneous and dominated by Thiothrix. Dilution to extinction PCR conducted with specific primers indicated that the relative abundance of Thiothrix 16S rRNA gene copies in all three samples were similar. However, reduced sulfur compounds from the vent resulted in a more narrow habitat that supported the sulfur-oxidizing Thiothrix in the white film to the exclusion of cyanobacteria and other proteobacteria found on the normal macrophyte. The majority of 16S rRNA gene sequences obtained in this study displayed similarities ≤98% to any known sequence in public data bases which suggests an abundance of new bacterial species in Sedge Bay.}, }
@article {pmid20386898, year = {2010}, author = {Rastogi, G and Osman, S and Kukkadapu, R and Engelhard, M and Vaishampayan, PA and Andersen, GL and Sani, RK}, title = {Microbial and mineralogical characterizations of soils collected from the deep biosphere of the former Homestake gold mine, South Dakota.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {539-550}, pmid = {20386898}, issn = {1432-184X}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Gold ; *Mining ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; South Dakota ; }, abstract = {A microbial census on deep biosphere (1.34 km depth) microbial communities was performed in two soil samples collected from the Ross and number 6 Winze sites of the former Homestake gold mine, Lead, South Dakota using high-density 16S microarrays (PhyloChip). Soil mineralogical characterization was carried out using X-ray diffraction, X-ray photoelectron, and Mössbauer spectroscopic techniques which demonstrated silicates and iron minerals (phyllosilicates and clays) in both samples. Microarray data revealed extensive bacterial diversity in soils and detected the largest number of taxa in Proteobacteria phylum followed by Firmicutes and Actinobacteria. The archael communities in the deep gold mine environments were less diverse and belonged to phyla Euryarchaeota and Crenarchaeota. Both the samples showed remarkable similarities in microbial communities (1,360 common OTUs) despite distinct geochemical characteristics. Fifty-seven phylotypes could not be classified even at phylum level representing a hitherto unidentified diversity in deep biosphere. PhyloChip data also suggested considerable metabolic diversity by capturing several physiological groups such as sulfur-oxidizer, ammonia-oxidizers, iron-oxidizers, methane-oxidizers, and sulfate-reducers in both samples. High-density microarrays revealed the greatest prokaryotic diversity ever reported from deep subsurface habitat of gold mines.}, }
@article {pmid20386897, year = {2010}, author = {Tabuchi, K and Kojima, H and Fukui, M}, title = {Seasonal changes in organic matter mineralization in a sublittoral sediment and temperature-driven decoupling of key processes.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {551-560}, pmid = {20386897}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*metabolism ; Biodegradation, Environmental ; Denaturing Gradient Gel Electrophoresis ; Fermentation ; Geologic Sediments/chemistry/*microbiology ; Japan ; Organic Chemicals/metabolism ; Oxidation-Reduction ; Phylogeny ; *Seasons ; Seawater/microbiology ; Sulfates/*metabolism ; *Temperature ; }, abstract = {Seasonal changes in the mineralization of organic compounds in sediments were investigated in temperate, sublittoral zone sediments (Tokyo Bay, Japan). The total mineralization rate and sulfate reduction rate showed large seasonal variations over the year, and although the fluctuations in both rates correlated with temperature, the latter was irregularly high in May. The concentration of organic carbon dissolved in interstitial water was specifically high in April. A culture-based experiment was also conducted under temperatures corresponding to the seasonal changes. In the culture incubated at a temperature corresponding to April (13 °C), hydrolysis and fermentation proceeded, but terminal oxidation was hindered, thereby resulting in acetate accumulation. At a temperature corresponding to May (22 °C), acetate oxidation coupled with sulfate reduction was observed. The temperature-related differences were also reflected in the bacterial community structure in the cultures analyzed by DGGE. In the culture incubated at the lower temperature, sulfate-reducing bacterium of incomplete oxidizer was detected, while sequence found in the culture incubated at the higher temperature was related to complete oxidizers. These results suggest that complete and incomplete-oxidizing sulfate-reducing bacteria act as distinct functional groups, responding to temperature in different ways, particularly in environments characterized by large temperature fluctuations.}, }
@article {pmid20386896, year = {2010}, author = {Blanchette, RA and Held, BW and Arenz, BE and Jurgens, JA and Baltes, NJ and Duncan, SM and Farrell, RL}, title = {An Antarctic hot spot for fungi at Shackleton's historic hut on Cape Royds.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {29-38}, pmid = {20386896}, issn = {1432-184X}, mesh = {Antarctic Regions ; Biodiversity ; DNA, Fungal/genetics ; *Environmental Microbiology ; *Expeditions ; Fungi/classification/genetics/*isolation &amp; purification ; Housing ; Microscopy, Electron, Scanning ; Phylogeny ; Wood/*microbiology/ultrastructure ; }, abstract = {The historic expedition huts located in the Ross Sea Region of the Antarctic and the thousands of artifacts left behind by the early explorers represent important cultural heritage from the "Heroic Era" of Polar exploration. The hut at Cape Royds built by Ernest Shackleton and members of the 1907-1908 British Antarctic Expedition has survived the extreme Antarctic environment for over 100 years, but recent studies have shown many forms of deterioration are causing serious problems, and microbial degradation is evident in the historic wood. Conservation work to reduce moisture at the hut required removal of fodder, wood, and many different types of organic materials from the stables area on the north side of the structure allowing large numbers of samples to be obtained for these investigations. In addition, wood from historic food storage boxes exposed in a ravine adjacent to the hut were also sampled. Fungi were cultured on several different media, and pure cultures were obtained and identified by sequencing of the internal transcribed spacer region of rDNA. From the 69 cultures of filamentous fungi obtained, the most predominant genera were Cadophora (44%) followed by Thielavia (17%) and Geomyces (15%). Other fungi found included Cladosporium, Chaetomium, and isolates identified as being in Pezizomycotina, Onygenales, Nectriaceae, and others. No filamentous basidiomycetes were found. Phylogenetic analyses of the Cadophora species showed great species diversity present revealing Cadophora malorum, Cadophora luteo-olivacea, Cadophora fastigiata, as well as Cadophora sp. 4E71-1, a C. malorum-like species, and Cadophora sp. 7R16-1, a C. fastigiata-like species. Scanning electron microscopy showed extensive decay was present in the wood samples with type 1 and type 2 forms of soft rot evident in pine and birch wood, respectively. Fungi causing decay in the historic wooden structures and artifacts are of great concern, and this investigation provides insight into the identity and species diversity of fungi found at the site. The historic woods and other organic materials at this site represent a large input of carbon into the Antarctic environment. This as well as nutrient additions from the nearby Adélie penguin (Pygoscelis adeliae) colony and favorable conditions for fungal growth at Cape Royds appear responsible for the significant fungal diversity, and where extensive decay is taking place in wood in contact with the ground.}, }
@article {pmid20386895, year = {2010}, author = {Jroundi, F and Fernández-Vivas, A and Rodriguez-Navarro, C and Bedmar, EJ and González-Muñoz, MT}, title = {Bioconservation of deteriorated monumental calcarenite stone and identification of bacteria with carbonatogenic activity.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {39-54}, pmid = {20386895}, issn = {1432-184X}, mesh = {Bacteria/genetics/growth &amp; development/*isolation &amp; purification ; Calcium Carbonate/*analysis ; Construction Materials/*microbiology ; DNA, Bacterial/genetics ; Environmental Microbiology ; Myxococcus xanthus/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Spain ; }, abstract = {The deterioration of the stone built and sculptural heritage has prompted the search and development of novel consolidation/protection treatments that can overcome the limitations of traditional ones. Attention has been drawn to bioconservation, particularly bacterial carbonatogenesis (i.e. bacterially induced calcium carbonate precipitation), as a new environmentally friendly effective conservation strategy, especially suitable for carbonate stones. Here, we study the effects of an in situ bacterial bioconsolidation treatment applied on porous limestone (calcarenite) in the sixteenth century San Jeronimo Monastery in Granada, Spain. The treatment consisted in the application of a nutritional solution (with and without Myxococcus xanthus inoculation) on decayed calcarenite stone blocks. The treatment promoted the development of heterotrophic bacteria able to induce carbonatogenesis. Both the consolidation effect of the treatment and the response of the culturable bacterial community present in the decayed stone were evaluated. A significant surface strengthening (consolidation) of the stone, without altering its surface appearance or inducing any detrimental side effect, was achieved upon application of the nutritional solution. The treatment efficacy was independent of the presence of M. xanthus (which is known as an effective carbonatogenic bacterium). The genetic diversity of 116 bacterial strains isolated from the stone, of which 113 strains showed carbonatogenic activity, was analysed by repetitive extragenic palindromic-polymerase chain reaction (REP-PCR) and 16S rRNA gene sequencing. The strains were distributed into 31 groups on the basis of their REP-PCR patterns, and a representative strain of each group was subjected to 16S rRNA gene sequencing. Analysis of these sequences showed that isolates belong to a wide variety of phylogenetic groups being closely related to species of 15 genera within the Proteobacteria, Firmicutes and the Actinobacteria. This study shows that the abundant carbonatogenic bacteria present in the decayed stone are able to effectively consolidate the degraded stone by producing new calcite (and vaterite) cement if an adequate nutritional solution is used. The implications of these results for the conservation of cultural heritage are discussed.}, }
@article {pmid20381183, year = {2010}, author = {Roh, SW and Abell, GC and Kim, KH and Nam, YD and Bae, JW}, title = {Comparing microarrays and next-generation sequencing technologies for microbial ecology research.}, journal = {Trends in biotechnology}, volume = {28}, number = {6}, pages = {291-299}, doi = {10.1016/j.tibtech.2010.03.001}, pmid = {20381183}, issn = {1879-3096}, mesh = {Ecology/economics/*methods ; *Ecosystem ; *Environmental Microbiology ; Microarray Analysis/economics/*methods ; Sequence Analysis, DNA/economics/*methods ; }, abstract = {Recent advances in molecular biology have resulted in the application of DNA microarrays and next-generation sequencing (NGS) technologies to the field of microbial ecology. This review aims to examine the strengths and weaknesses of each of the methodologies, including depth and ease of analysis, throughput and cost-effectiveness. It also intends to highlight the optimal application of each of the individual technologies toward the study of a particular environment and identify potential synergies between the two main technologies, whereby both sample number and coverage can be maximized. We suggest that the efficient use of microarray and NGS technologies will allow researchers to advance the field of microbial ecology, and importantly, improve our understanding of the role of microorganisms in their various environments.}, }
@article {pmid20370829, year = {2010}, author = {Yao, H and Wu, F}, title = {Soil microbial community structure in cucumber rhizosphere of different resistance cultivars to fusarium wilt.}, journal = {FEMS microbiology ecology}, volume = {72}, number = {3}, pages = {456-463}, doi = {10.1111/j.1574-6941.2010.00859.x}, pmid = {20370829}, issn = {1574-6941}, mesh = {Actinomycetaceae/*isolation &amp; purification ; Bacteria/*isolation &amp; purification ; Cucumis sativus/immunology/*microbiology ; Fatty Acids/analysis ; Fusarium ; Immunity, Innate ; Mycorrhizae/*isolation &amp; purification ; Phospholipids/analysis ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Cucumber fusarium wilt is a common soil-borne disease. We hypothesize that there is a relationship between the severity of disease and soil microbial ecology. In this work, culturable microbial populations, lipid fatty acid and community-level physiological profiles (CLPP) from rhizosphere soils of four different cucumber cultivars were investigated. Comparatively higher actinomycetes, mycorrhizal colonization and higher ratios of bacteria to fungi were found in the two resistant cultivars compared with the two susceptible cultivars. CLPP analysis showed that catabolic diversity indices were higher in the presence of two resistant cultivars. Phospholipid fatty acid (PLFA) profiles suggested that fungal (18:2omega6,9c) PLFA was enriched in the rhizosphere soils of the two susceptible cultivars, but some bacterial (16:0 and 15:0a) PLFAs were found in a lower relative abundance in these soils. The neutral lipid fatty acid 16:1omega5, which is an indicator of arbuscular mycorrhizal fungi, was enriched in the rhizosphere soils of the two resistant cultivars. All the three methods suggested that plant genotype had a significant impact on the soil microbial community composition and activity, and the differences in the rhizosphere microbial community may result in the differences in the resistance to fusarium wilt.}, }
@article {pmid20369877, year = {2010}, author = {Forrez, I and Carballa, M and Verbeken, K and Vanhaecke, L and Ternes, T and Boon, N and Verstraete, W}, title = {Diclofenac oxidation by biogenic manganese oxides.}, journal = {Environmental science &amp; technology}, volume = {44}, number = {9}, pages = {3449-3454}, doi = {10.1021/es9027327}, pmid = {20369877}, issn = {0013-936X}, mesh = {Anti-Inflammatory Agents, Non-Steroidal/pharmacology ; Chromatography, High Pressure Liquid ; Chromatography, Liquid/methods ; Diclofenac/*chemistry ; Hydrogen-Ion Concentration ; Kinetics ; Manganese/chemistry ; Manganese Compounds/*chemistry ; Mass Spectrometry/methods ; Models, Chemical ; Oxides/*chemistry ; Oxygen/*chemistry ; Pseudomonas putida/metabolism ; Water Pollutants, Chemical/analysis ; Water Purification/methods ; }, abstract = {Diclofenac, a nonsteroidal anti-inflammatory drug, is one of the most commonly detected pharmaceuticals in sewage treatment plant (STP) effluents. In this work, biologically produced manganese oxides (BioMnOx) were investigated to remove diclofenac. At neutral pH, the diclofenac oxidation with BioMnOx was 10-fold faster than with chemically produced MnO(2). The main advantage of BioMnOx over chemical MnO(2) is the ability of the bacteria to reoxidize the formed Mn(2+), which inhibits the oxidation of diclofenac. Diclofenac-2,5-iminoquinone was identified as a major transformation product, accounting for 5-10% of the transformed diclofenac. Except for 5-hydroxydiclofenac, which was identified as an intermediate, no other oxidation products were detected. Diclofenac oxidation was proportional to the amount of BioMnOx dosed, and the pseudo first order rate constant k was 6-fold higher when pH was decreased from 6.8 to 6.2. The Mn(2+) levels remained below the drinking water limit (0.05 mg L(-1)), thus indicating the efficient in situ microbiological regeneration of the oxidant. These results combined with previous studies suggest the potential of BioMnOx for STP effluent polishing.}, }
@article {pmid20369357, year = {2010}, author = {Puglisi, E and Cahill, MJ and Lessard, PA and Capri, E and Sinskey, AJ and Archer, JA and Boccazzi, P}, title = {Transcriptional response of Rhodococcus aetherivorans I24 to polychlorinated biphenyl-contaminated sediments.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {505-515}, pmid = {20369357}, issn = {1432-184X}, mesh = {Biodegradation, Environmental ; Culture Media ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Geologic Sediments/*microbiology ; Oligonucleotide Array Sequence Analysis ; Oxidative Stress ; Polychlorinated Biphenyls/*metabolism ; RNA, Bacterial/genetics ; Rhodococcus/*genetics/metabolism ; Sequence Analysis, DNA ; *Soil Microbiology ; Soil Pollutants/*metabolism ; Transcription, Genetic ; }, abstract = {We used a microarray targeting 3,524 genes to assess the transcriptional response of the actinomycete Rhodococcus aetherivorans I24 in minimal medium supplemented with various substrates (e.g., PCBs) and in both PCB-contaminated and non-contaminated sediment slurries. Relative to the reference condition (minimal medium supplemented with glucose), 408 genes were upregulated in the various treatments. In medium and in sediment, PCBs elicited the upregulation of a common set of 100 genes, including gene-encoding chaperones (groEL), a superoxide dismutase (sodA), alkyl hydroperoxide reductase protein C (ahpC), and a catalase/peroxidase (katG). Analysis of the R. aetherivorans I24 genome sequence identified orthologs of many of the genes in the canonical biphenyl pathway, but very few of these genes were upregulated in response to PCBs or biphenyl. This study is one of the first to use microarrays to assess the transcriptional response of a soil bacterium to a pollutant under conditions that more closely resemble the natural environment. Our results indicate that the transcriptional response of R. aetherivorans I24 to PCBs, in both medium and sediment, is primarily directed towards reducing oxidative stress, rather than catabolism.}, }
@article {pmid20368178, year = {2009}, author = {Turnbaugh, PJ and Ridaura, VK and Faith, JJ and Rey, FE and Knight, R and Gordon, JI}, title = {The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice.}, journal = {Science translational medicine}, volume = {1}, number = {6}, pages = {6ra14}, pmid = {20368178}, issn = {1946-6242}, support = {R01 DK070977/DK/NIDDK NIH HHS/United States ; DK70977/DK/NIDDK NIH HHS/United States ; }, mesh = {Adiposity ; Animals ; Bacteria/genetics ; *Diet ; Energy Metabolism ; *Genomics ; Germ-Free Life ; Humans ; Intestines/*microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Diet and nutritional status are among the most important modifiable determinants of human health. The nutritional value of food is influenced in part by a person's gut microbial community (microbiota) and its component genes (microbiome). Unraveling the interrelations among diet, the structure and operations of the gut microbiota, and nutrient and energy harvest is confounded by variations in human environmental exposures, microbial ecology, and genotype. To help overcome these problems, we created a well-defined, representative animal model of the human gut ecosystem by transplanting fresh or frozen adult human fecal microbial communities into germ-free C57BL/6J mice. Culture-independent metagenomic analysis of the temporal, spatial, and intergenerational patterns of bacterial colonization showed that these humanized mice were stably and heritably colonized and reproduced much of the bacterial diversity of the donor's microbiota. Switching from a low-fat, plant polysaccharide-rich diet to a high-fat, high-sugar "Western" diet shifted the structure of the microbiota within a single day, changed the representation of metabolic pathways in the microbiome, and altered microbiome gene expression. Reciprocal transplants involving various combinations of donor and recipient diets revealed that colonization history influences the initial structure of the microbial community but that these effects can be rapidly altered by diet. Humanized mice fed the Western diet have increased adiposity; this trait is transmissible via microbiota transplantation. Humanized gnotobiotic mice will be useful for conducting proof-of-principle "clinical trials" that test the effects of environmental and genetic factors on the gut microbiota and host physiology. Nearly full-length 16S rRNA gene sequences are deposited in GenBank under the accession numbers GQ491120 to GQ493997.}, }
@article {pmid20363788, year = {2010}, author = {Inceoğlu, O and Salles, JF and van Overbeek, L and van Elsas, JD}, title = {Effects of plant genotype and growth stage on the betaproteobacterial communities associated with different potato cultivars in two fields.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {11}, pages = {3675-3684}, pmid = {20363788}, issn = {1098-5336}, mesh = {Betaproteobacteria/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Molecular Sequence Data ; Nucleic Acid Denaturation ; Phylogeny ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Solanum tuberosum/*genetics/*growth &amp; development/microbiology ; }, abstract = {Bacterial communities in the rhizosphere are dynamic and susceptible to changes in plant conditions. Among the bacteria, the betaproteobacteria play key roles in nutrient cycling and plant growth promotion, and hence the dynamics of their community structures in the rhizosphere should be investigated. Here, the effects of plant cultivar, growth stage, and soil type on the communities associated with potato cultivars Aveka, Aventra, Karnico, Modena, Premiere, and Désirée were assessed for two different fields containing sandy soil with either a high or low organic compound content. Thus, bacterial and betaproteobacterial PCR-denaturing gradient gel electrophoresis analyses were performed to analyze the effects of plant cultivar and growth on the rhizosphere community structure. The analyses showed that in both fields all cultivars had a rhizosphere effect on the total bacterial and betaproteobacterial communities. In addition, the plant growth stage strongly affected the betaproteobacterial communities in both fields. Moreover, the community structures were affected by cultivar, and cultivars differed in physiology, as reflected in their growth rates, root development, and estimated tuber starch contents. Analyses of betaproteobacterial clone libraries constructed for two selected cultivars (one cultivar that produced low-starch-content tubers and one cultivar that produced high-starch-content tubers), as well as bulk soil, revealed that the rhizospheres of the two cultivars selected for specific bacteria, including plant-growth-promoting bacteria, such as Variovorax and Achromobacter spp. In addition, quantitative PCR-based quantification of the Variovorax paradoxus-specific functional gene asfA (involved in desulfonation) indicated that there were clear potato rhizosphere effects on the abundance of this gene. Interestingly, both cultivar type and plant growth stage affected the community under some circumstances.}, }
@article {pmid20363786, year = {2010}, author = {Pycke, BF and Vanermen, G and Monsieurs, P and De Wever, H and Mergeay, M and Verstraete, W and Leys, N}, title = {Toxicogenomic response of Rhodospirillum rubrum S1H to the micropollutant triclosan.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {11}, pages = {3503-3513}, pmid = {20363786}, issn = {1098-5336}, mesh = {Bacterial Proteins/biosynthesis/genetics ; Environmental Pollutants/*toxicity ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial/*drug effects ; Microbial Viability/drug effects ; Multigene Family ; Oligonucleotide Array Sequence Analysis ; Rhodospirillum rubrum/*drug effects/growth &amp; development ; Triclosan/*toxicity ; }, abstract = {In the framework of the Micro-Ecological Life Support System Alternative (MELiSSA) project, a pilot study was performed to identify the effects of triclosan on the MELiSSA carbon-mineralizing microorganism Rhodospirillum rubrum S1H. Triclosan is a biocide that is commonly found in human excrement and is considered an emerging pollutant in wastewater and the environment. Chronic exposure to MELiSSA-relevant concentrations (> or =25 microg liter(-1)) of triclosan resulted in a significant extension of the lag phase of this organism but hardly affected the growth rate. Analytical determinations gave no indication of triclosan biodegradation during the growth experiment, and flow cytometric viability analyses revealed that triclosan is bacteriostatic and only slightly toxic to R. rubrum S1H. Using microarray analyses, the genetic mechanisms supporting the reversibility of triclosan-induced inhibition were scrutinized. An extremely triclosan-responsive cluster of four small adjacent genes was identified, for which there was up to 34-fold induction with 25 microg liter(-1) triclosan. These four genes, for which the designation microf (micropollutant-upregulated factor) is proposed, appear to be unique to R. rubrum and are shown here for the first time to be involved in the response to stress. Moreover, numerous other systems that are associated with the proton motive force were shown to be responsive to triclosan, but they were never as highly upregulated as the microf genes. In response to triclosan, R. rubrum S1H induced transcription of the phage shock protein operon (pspABC), numerous efflux systems, cell envelope consolidation mechanisms, the oxidative stress response, beta-oxidation, and carbonic anhydrase, while there was downregulation of bacterial conjugation and carboxysome synthesis genes. The microf genes and three efflux-related genes showed the most potential to be low-dose biomarkers.}, }
@article {pmid20362351, year = {2010}, author = {Marzorati, M and Verhelst, A and Luta, G and Sinnott, R and Verstraete, W and Van de Wiele, T and Possemiers, S}, title = {In vitro modulation of the human gastrointestinal microbial community by plant-derived polysaccharide-rich dietary supplements.}, journal = {International journal of food microbiology}, volume = {139}, number = {3}, pages = {168-176}, doi = {10.1016/j.ijfoodmicro.2010.02.030}, pmid = {20362351}, issn = {1879-3460}, mesh = {Bacteroides/growth &amp; development/isolation &amp; purification ; Bifidobacterium/growth &amp; development/isolation &amp; purification ; *Dietary Supplements ; Fatty Acids, Volatile/analysis/metabolism ; Fermentation ; Galactans/chemistry ; Gastrointestinal Tract/*microbiology ; Humans ; Lactobacillaceae/growth &amp; development/isolation &amp; purification ; Plant Gums/chemistry ; Plants/chemistry ; Polysaccharides/*chemistry ; *Prebiotics ; }, abstract = {The use of prebiotics is a possible strategy to manage and steer the complex gut microbial community towards a health-promoting composition (Gastrointestinal Resource Management). In this study, the Simulator of the Human Intestinal Microbial Ecosystem was used to investigate the effects of two commercially-available plant polysaccharide supplements on the structure, composition and metabolism of an in vitro cultured colon microbial community. Microbial analyses showed both a bifidogenic (up to +1.3 log cfu/mL) and a lactobacillogenic (up to +0.9 log cfu/mL) effect during treatment with the dietary supplements. Quantitative PCR confirmed that the increase of Bifidobacteria spp. was statistically significant (P<0.05) in all of the colon compartments and showed a significant increase of the bacteroides-prevotella group concentration (+0.6 log cells/ml) in the compartment simulating the proximal colon. Denaturant gradient gel electrophoresis analyses and a relative ecological interpretation, in combination with sugar and short-chain fatty acids quantification, provided evidence of a positive effect of both the tested products. Overall, the treatment period was associated with (i) good and selective fermentability of the polysaccharide supplements along the entire colon; (ii) positive and selective bifidogenic effect; (iii) the possibility of enhancing species belonging to Bacteroidetes, a phylum recently associated with body weight management.}, }
@article {pmid20352423, year = {2010}, author = {Wang, Y and Claeys, L and van der Ha, D and Verstraete, W and Boon, N}, title = {Effects of chemically and electrochemically dosed chlorine on Escherichia coli and Legionella beliardensis assessed by flow cytometry.}, journal = {Applied microbiology and biotechnology}, volume = {87}, number = {1}, pages = {331-341}, doi = {10.1007/s00253-010-2526-2}, pmid = {20352423}, issn = {1432-0614}, mesh = {Chlorine/chemistry/*pharmacology ; Disinfection/*methods ; Electrochemistry ; Escherichia coli/cytology/*drug effects/growth &amp; development ; Flow Cytometry ; Legionella/cytology/*drug effects/growth &amp; development ; Microbial Viability/drug effects ; }, abstract = {The present study reports the disinfection effects of chemically and electrochemically dosed chlorine on two models for typical water-borne bacteria (Escherichia coli and Legionella beliardensis) by plating and flow cytometry (FCM) in combination with different fluorescence dyes. The residual effect on various cell functions, including cultivability, esterase activity, membrane polarization, and integrity, was tested at different free chlorine concentrations. In comparison, chemical disinfection yielded on average 60% more E. coli cells entering the viable but nonculturable (VBNC) state than electrochemical disinfection. Here, VBNC is defined as those cells with intact cell membrane but which cannot be cultured on solid nutrient agar plates. L. beliardensis was about five times more resistant to chlorine disinfection than E. coli. The results also suggested the two methods result in different disinfection mechanisms on L. beliardensis, i.e., chemically dosed chlorine targeted cell membrane integrity before enzyme activity, while electrochemically dosed chlorine acted the other way round. In addition, both bacteria lost the integrity of their cell membranes at three times lower chlorine concentration over a longer contact time (i.e., 40 vs. 10 min) by the chemical method. Our results showed that FCM is an appropriate tool to evaluate the effects of water disinfection and the percentage of cells in VBNC in a matter of hours. Electrochemical disinfection is suggested to be a favorable alternative for chemical disinfection.}, }
@article {pmid20352207, year = {2010}, author = {de Castro, AP and Araújo, SD and Reis, AM and Moura, RL and Francini-Filho, RB and Pappas, G and Rodrigues, TB and Thompson, FL and Krüger, RH}, title = {Bacterial community associated with healthy and diseased reef coral Mussismilia hispida from eastern Brazil.}, journal = {Microbial ecology}, volume = {59}, number = {4}, pages = {658-667}, pmid = {20352207}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/genetics/isolation &amp; purification ; Biological Evolution ; Brazil ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Gene Library ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {In order to characterize the bacterial community diversity associated to mucus of the coral Mussismilia hispida, four 16S rDNA libraries were constructed and 400 clones from each library were analyzed from two healthy colonies, one diseased colony and the surrounding water. Nine bacterial phyla were identified in healthy M. hispida, with a dominance of Proteobacteria, Actinobacteria, Acidobacteria, Lentisphaerae, and Nitrospira. The most commonly found species were related to the genera Azospirillum, Hirschia, Fabibacter, Blastochloris, Stella, Vibrio, Flavobacterium, Ochrobactrum, Terasakiella, Alkalibacter, Staphylococcus, Azospirillum, Propionibacterium, Arcobacter, and Paenibacillus. In contrast, diseased M. hispida had a predominance of one single species of Bacteroidetes, corresponding to more than 70% of the sequences. Rarefaction curves using evolutionary distance of 1% showed a greater decrease in bacterial diversity in the diseased M. hispida, with a reduction of almost 85% in OTUs in comparison to healthy colonies. integral-Libshuff analyses show that significant p values obtained were <0.0001, demonstrating that the four libraries are significantly different. Furthermore, the sympatric corals M. hispida and Mussismilia braziliensis appear to have different bacterial community compositions according to Principal Component Analysis and Lineage-specific Analysis. Moreover, lineages that contribute to those differences were identified as alpha-Proteobacteria, Bacteroidetes, and Firmicutes. The results obtained in this study suggest host-microbe co-evolution in Mussismilia, and it was the first study on the diversity of the microbiota of the endemic and endangered of extinction Brazilian coral M. hispida from Abrolhos bank.}, }
@article {pmid20352206, year = {2010}, author = {Pascault, N and Nicolardot, B and Bastian, F and Thiébeau, P and Ranjard, L and Maron, PA}, title = {In situ dynamics and spatial heterogeneity of soil bacterial communities under different crop residue management.}, journal = {Microbial ecology}, volume = {60}, number = {2}, pages = {291-303}, pmid = {20352206}, issn = {1432-184X}, mesh = {Agriculture/*methods ; Bacteria/classification/genetics/*growth &amp; development ; Biodegradation, Environmental ; Biomass ; Crops, Agricultural/microbiology ; DNA Fingerprinting ; DNA, Bacterial/genetics/isolation &amp; purification ; DNA, Ribosomal Spacer/genetics ; Gene Library ; Microbial Consortia ; Nitrogen/analysis ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; Triticum/*microbiology ; }, abstract = {The effect of the location of wheat residues (soil surface vs. incorporated in soil) on their decomposition and on soil bacterial communities was investigated by the means of a field experiment. Bacterial-automated ribosomal intergenic spacer analysis of DNA extracts from residues, detritusphere (soil adjacent to residues), and bulk soil evidenced that residues constitute the zone of maximal changes in bacterial composition. However, the location of the residues influenced greatly their decomposition and the dynamics of the colonizing bacterial communities. Sequencing of 16S rRNA gene in DNA extracts from the residues at the early, middle, and late stages of degradation confirmed the difference of composition of the bacterial community according to the location. Bacteria belonging to the γ-subgroup of proteobacteria were stimulated when residues were incorporated whereas the α-subgroup was stimulated when residues were left at the soil surface. Moreover, Actinobacteria were more represented when residues were left at the soil surface. According to the ecological attributes of the populations identified, our results suggested that climatic fluctuations at the soil surface select populations harboring enhanced catabolic and/or survival capacities whereas residues characteristics likely constitute the main determinant of the composition of the bacterial community colonizing incorporated residues.}, }
@article {pmid20352205, year = {2010}, author = {Zhang, X and Ren, A and Ci, H and Gao, Y}, title = {Genetic diversity and structure of Neotyphodium species and their host Achnatherum sibiricum in a natural grass-endophyte system.}, journal = {Microbial ecology}, volume = {59}, number = {4}, pages = {744-756}, pmid = {20352205}, issn = {1432-184X}, mesh = {China ; DNA, Fungal/genetics ; *Ecosystem ; Gene Flow ; *Genetic Variation ; *Genetics, Population ; Microsatellite Repeats ; Neotyphodium/classification/*genetics/isolation &amp; purification ; Poaceae/*microbiology ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Achnatherum sibiricum (Poaceae) is a perennial bunchgrass native to the Inner Mongolia Steppe of China. This grass is commonly infected by epichloë endophytes with high-infection frequencies. Previously, we identified two predominant Neotyphodium spp., N. sibiricum and N. gansuense. In the present study, genetic diversity and structure were analyzed for the two predominant Neotyphodium spp. as well as the host grass. We obtained 103 fungal isolates from five populations; 33 were identified as N. sibiricum and 61 as N. gansuense. All populations hosted both endophytic species, but genetic variation was much higher for N. gansuense than for N. sibiricum. The majority of fungal isolates were haploid, and 13% of them were heterozygous at one SSR locus, suggesting hybrid origins of those isolates. Significant linkage disequilibrium of fungal SSR loci suggested that both fungal species primarily propagate by clonal growth through plant seeds, whereas variation in genetic diversity and the presence of hybrids in both endophytic species revealed that although clonal propagation was prevalent, occasional recombination might also occur. By comparing genetic differentiation among populations, we found around 4-7-fold greater differentiation of endophyte populations than host populations, implying more restricted gene flow of endophytes than hosts. We proposed that endophyte infection of A. sibiricum might confer the host some selective advantages under certain conditions, which could help to maintain high-endophyte-infection frequencies in host populations, even when their gene flows do not match each other. Furthermore, we suggested that the same genotype of endophyte as well as host should be confirmed if the objective of the study is to know the influence of endophyte or host genotype on their symbiotic relationship, instead of just considering whether the plant is infected by an endophyte or not, since endophytes from the same host species could exhibit high levels of genetic diversity, which is likely to influence the outcome of their symbiotic relationship.}, }
@article {pmid20349058, year = {2010}, author = {Antunes, F and Hinzmann, M and Lopes-Lima, M and Machado, J and Martins da Costa, P}, title = {Association between environmental microbiota and indigenous bacteria found in hemolymph, extrapallial fluid and mucus of Anodonta cygnea (Linnaeus, 1758).}, journal = {Microbial ecology}, volume = {60}, number = {2}, pages = {304-309}, pmid = {20349058}, issn = {1432-184X}, mesh = {Aeromonas/growth &amp; development ; Animals ; Anodonta/*microbiology ; Escherichia coli/growth &amp; development ; Hemolymph/*microbiology ; *Metagenome ; Mucus/*microbiology ; Portugal ; Vibrio/growth &amp; development ; *Water Microbiology ; }, abstract = {Bivalves filter and accumulate large numbers of microorganisms present in the harvesting water. A complete understanding of the balance between Anodonta cygnea and the microbiota present in their surrounding environment remains incomplete. Therefore, the aim of this study was to quantify and identify the indigenous bacteria in the biological fluids of A. cygnea collected from Mira Lagoon in northern Portugal. The results showed Vibrio metschnikovii and Aeromonas sobria as the dominant groups. The median for total bacteria from mucus was 3.1 × 10(3) CFU g(-1), whereas the range in means from fluids was 1.5 × 10(2) to 6.5 × 10(2) CFU ml(-1). During the experimental work, Escherichia coli and enterococci were not detected in healthy A. cygnea. However, the periodic detection of E. coli and enterococci in Mira lagoon revealed its presence in the water. Our observations suggest that A. cygnea has the ability to filter and eliminate E. coli, present in the surrounding environment, through an active phagocytic process conducted by hemolymph circulating cells, the hemocytes.}, }
@article {pmid20348306, year = {2010}, author = {Inceoglu, O and Hoogwout, EF and Hill, P and van Elsas, JD}, title = {Effect of DNA extraction method on the apparent microbial diversity of soil.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {10}, pages = {3378-3382}, pmid = {20348306}, issn = {1098-5336}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; DNA/*chemistry ; DNA Fingerprinting ; Genetic Techniques/*standards ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; *Soil Microbiology ; }, abstract = {Four extraction methods, including a novel one, were compared for their efficiencies in producing DNA from three contrasting agricultural soils. Molecular analyses (PCR-denaturing gradient gel electrophoresis [DGGE] and clone libraries) focusing on different microbial groups were used as assessment criteria. Per soil, the DNA yields differed between extraction methods. Clear effects of method on apparent richness and community structure were found. Actinobacterial diversity based on soil DNA produced by two divergent methods revealed that a hitherto-undescribed group was obtained by the novel method.}, }
@article {pmid20345633, year = {2010}, author = {Verbruggen, E and Röling, WFM and Gamper, HA and Kowalchuk, GA and Verhoef, HA and van der Heijden, MGA}, title = {Positive effects of organic farming on below-ground mutualists: large-scale comparison of mycorrhizal fungal communities in agricultural soils.}, journal = {The New phytologist}, volume = {186}, number = {4}, pages = {968-979}, doi = {10.1111/j.1469-8137.2010.03230.x}, pmid = {20345633}, issn = {1469-8137}, mesh = {Agriculture/*methods ; Crops, Agricultural/growth &amp; development/microbiology ; *Ecosystem ; Mycorrhizae/*physiology ; Poaceae/microbiology ; Principal Component Analysis ; Soil/*analysis ; *Soil Microbiology ; Species Specificity ; Symbiosis/*physiology ; Time Factors ; }, abstract = {*The impact of various agricultural practices on soil biodiversity and, in particular, on arbuscular mycorrhizal fungi (AMF), is still poorly understood, although AMF can provide benefit to plants and ecosystems. Here, we tested whether organic farming enhances AMF diversity and whether AMF communities from organically managed fields are more similar to those of species-rich grasslands or conventionally managed fields. *To address this issue, the AMF community composition was assessed in 26 arable fields (13 pairs of organically and conventionally managed fields) and five semi-natural grasslands, all on sandy soil. Terminal restriction fragment length polymorphism community fingerprinting was used to characterize AMF community composition. *The average number of AMF taxa was highest in grasslands (8.8), intermediate in organically managed fields (6.4) and significantly lower in conventionally managed fields (3.9). Moreover, AMF richness increased significantly with the time since conversion to organic agriculture. AMF communities of organically managed fields were also more similar to those of natural grasslands when compared with those under conventional management, and were less uniform than their conventional counterparts, as expressed by higher beta-diversity (between-site diversity). *We suggest that organic management in agro-ecosystems contributes to the restoration and maintenance of these important below-ground mutualists.}, }
@article {pmid20337927, year = {2010}, author = {De la Iglesia, R and Valenzuela-Heredia, D and Pavissich, JP and Freyhoffer, S and Andrade, S and Correa, JA and González, B}, title = {Novel polymerase chain reaction primers for the specific detection of bacterial copper P-type ATPases gene sequences in environmental isolates and metagenomic DNA.}, journal = {Letters in applied microbiology}, volume = {50}, number = {6}, pages = {552-562}, doi = {10.1111/j.1472-765X.2010.02832.x}, pmid = {20337927}, issn = {1472-765X}, mesh = {Adenosine Triphosphatases/*genetics ; Bacteria/classification/enzymology/genetics/*isolation &amp; purification ; Bacterial Proteins/*genetics ; Copper/metabolism ; DNA Primers/*genetics ; DNA, Bacterial/genetics ; *Environmental Microbiology ; *Metagenomics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/*methods ; Species Specificity ; }, abstract = {AIMS: In the last decades, the worldwide increase in copper wastes release by industrial activities like mining has driven environmental metal contents to toxic levels. For this reason, the study of the biological copper-resistance mechanisms in natural environments is important. Therefore, an appropriate molecular tool for the detection and tracking of copper-resistance genes was developed.<br><br>METHODS AND RESULTS: In this work, we designed a PCR primer pair to specifically detect copper P-type ATPases gene sequences. These PCR primers were tested in bacterial isolates and metagenomic DNA from intertidal marine environments impacted by copper pollution. As well, T-RFLP fingerprinting of these gene sequences was used to compare the genetic composition of such genes in microbial communities, in normal and copper-polluted coastal environments. New copper P-type ATPases gene sequences were found, and a high degree of change in the genetic composition because of copper exposure was also determined.<br><br>CONCLUSIONS: This PCR based method is useful to track bacterial copper-resistance gene sequences in the environment.<br><br>This study is the first to report the design and use of a PCR primer pair as a molecular marker to track bacterial copper-resistance determinants, providing an excellent tool for long-term analysis of environmental communities exposed to metal pollution.}, }
@article {pmid20336290, year = {2010}, author = {Wong, FK and Lacap, DC and Lau, MC and Aitchison, JC and Cowan, DA and Pointing, SB}, title = {Hypolithic microbial community of quartz pavement in the high-altitude tundra of central Tibet.}, journal = {Microbial ecology}, volume = {60}, number = {4}, pages = {730-739}, pmid = {20336290}, issn = {1432-184X}, mesh = {Altitude ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; DNA, Bacterial/genetics ; *Ecosystem ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Phylogeny ; Quartz/metabolism ; RNA, Ribosomal, 16S/genetics ; Tibet ; }, abstract = {The hypolithic microbial community associated with quartz pavement at a high-altitude tundra location in central Tibet is described. A small-scale ecological survey indicated that 36% of quartz rocks were colonized. Community profiling using terminal restriction fragment length polymorphism revealed no significant difference in community structure among a number of colonized rocks. Real-time quantitative PCR and phylogenetic analysis of environmental phylotypes obtained from clone libraries were used to elucidate community structure across all domains. The hypolithon was dominated by cyanobacterial phylotypes (73%) with relatively low frequencies of other bacterial phylotypes, largely represented by the chloroflexi, actinobacteria, and bacteriodetes. Unidentified crenarchaeal phylotypes accounted for 4% of recoverable phylotypes, while algae, fungi, and mosses were indicated by a small fraction of recoverable phylotypes.}, }
@article {pmid20333374, year = {2010}, author = {Hengst, MB and Andrade, S and González, B and Correa, JA}, title = {Changes in epiphytic bacterial communities of intertidal seaweeds modulated by host, temporality, and copper enrichment.}, journal = {Microbial ecology}, volume = {60}, number = {2}, pages = {282-290}, pmid = {20333374}, issn = {1432-184X}, mesh = {Bacteria/*classification/drug effects/genetics ; Chile ; Copper/*chemistry ; Environmental Monitoring ; Gene Library ; *Microbial Consortia ; Mining ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Seaweed/*microbiology ; Time Factors ; Water Pollutants, Chemical/analysis ; }, abstract = {This study reports on the factors involved in regulating the composition and structure of bacterial communities epiphytic on intertidal macroalgae, exploring their temporal variability and the role of copper pollution. Culture-independent, molecular approaches were chosen for this purpose and three host species were used as models: the ephemeral Ulva spp. (Chlorophyceae) and Scytosiphon lomentaria (Phaeophyceae) and the long-living Lessonia nigrescens (Phaeophyceae). The algae were collected from two coastal areas in Northern Chile, where the main contrast was the concentration of copper in the seawater column resulting from copper-mine waste disposals. We found a clear and strong effect in the structure of the bacterial communities associated with the algal species serving as host. The structure of the bacterial communities also varied through time. The effect of copper on the structure of the epiphytic bacterial communities was significant in Ulva spp., but not on L. nigrescens. The use of 16S rRNA gene library analysis to compare bacterial communities in Ulva revealed that they were composed of five phyla and six classes, with approximately 35 bacterial species, dominated by members of Bacteroidetes (Cytophaga-Flavobacteria-Bacteroides) and α-Proteobacteria, in both non-polluted and polluted sites. Less common groups, such as the Verrucomicrobiae, were exclusively found in polluted sites. This work shows that the structure of bacterial communities epiphytic on macroalgae is hierarchically determined by algal species > temporal changes > copper levels.}, }
@article {pmid20333373, year = {2010}, author = {Zhao, J and Zeng, J and de Hoog, GS and Attili-Angelis, D and Prenafeta-Boldú, FX}, title = {Isolation and identification of black yeasts by enrichment on atmospheres of monoaromatic hydrocarbons.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {149-156}, pmid = {20333373}, issn = {1432-184X}, mesh = {Culture Media ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; *Environmental Microbiology ; Hydrocarbons, Aromatic/*metabolism ; Phylogeny ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; Yeasts/classification/genetics/*isolation &amp; purification ; }, abstract = {Black yeast members of the Herpotrichiellaceae present a complex ecological behavior: They are often isolated from rather extreme environments polluted with aromatic hydrocarbons, while they are also regularly involved in human opportunistic infections. A selective technique to promote the in vitro growth of herpotrichiellaceous fungi was applied to investigate their ecophysiology. Samples from natural ecological niches and man-made environments that might contain black yeasts were enriched on an inert solid support at low humidity and under a controlled atmosphere rich in volatile aromatic hydrocarbons. Benzene, toluene, and xylene were provided separately as the sole carbon and energy source via the gas phase. The assayed isolation protocol was highly specific toward mesophilic Exophiala species (70 strains of this genus out of 71 isolates). Those were obtained predominantly from creosote-treated railway ties (53 strains), but isolates were also found on wild berries (11 strains) and in guano-rich soil samples (six strains). Most of the isolates were obtained on toluene (43 strains), but enrichments on xylene and benzene also yielded herpotrichiellaceous fungi (17 and 10 isolates, respectively). Based upon morphological characterizations and DNA sequences of the full internal transcriber spacers (ITS) and the 8.5S rRNA genes, the majority of the obtained isolates were affiliated to the recently described species Exophiala xenobiotica (32 strains) and Exophiala bergeri (nine strains). Members of two other phylogenetic groups (24 and two strains, respectively) somewhat related to E. bergeri were also found, and a last group (three strains) corresponded to an undescribed Exophiala species.}, }
@article {pmid20309538, year = {2010}, author = {Vizcaino, MI and Johnson, WR and Kimes, NE and Williams, K and Torralba, M and Nelson, KE and Smith, GW and Weil, E and Moeller, PD and Morris, PJ}, title = {Antimicrobial resistance of the coral pathogen Vibrio coralliilyticus and Caribbean sister phylotypes isolated from a diseased octocoral.}, journal = {Microbial ecology}, volume = {59}, number = {4}, pages = {646-657}, pmid = {20309538}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology ; Anti-Bacterial Agents/pharmacology ; Caribbean Region ; DNA Fingerprinting ; DNA, Bacterial/genetics ; *Drug Resistance, Bacterial ; Microbial Sensitivity Tests ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Vibrio/drug effects/*genetics/isolation &amp; purification ; }, abstract = {Vibrio coralliilyticus is a global marine pathogen that has been found to cause disease in several marine organisms, including corals. This study is the first report of the isolation of V. coralliilyticus from a diseased Caribbean octocoral, Pseudopterogorgia americana. Five sister phylotypes were positively identified using 16S rRNA gene sequencing, recA probes specific for V. coralliilyticus, and rep-PCR fingerprinting. The antimicrobial resistance was compared between pathogenic strains of V. coralliilyticus and the Caribbean strains. First, the antimicrobial resistance of V. coralliilyticus-type strain ATCC BAA-450 was determined using an agar-overlay antimicrobial bioassay at 24 degrees C and 27 degrees C, temperatures which are relevant to its known temperature-dependent virulence. From 108 distinct bacteria isolated from P. americana, 12 inhibited the V. coralliilyticus-type strain at 24 degrees C and five at 27 degrees C. Next, the phenotypic comparison of two Caribbean phylotypes and three V. coralliilyticus reference strains against a subset of 30 bacteria demonstrated a similar resistance trend. At both temperatures, the reference strains were inhibited by three bacteria isolates, while the Caribbean strains were inhibited by four to nine bacteria. Additionally, V. coralliilyticus-type strain ATCC BAA-450 and one of the Caribbean strains were inhibited by a higher number of bacteria at 24 degrees C compared with 27 degrees C. Together, these results highlight that V. coralliilyticus strains have antimicrobial resistance to the majority of coral-associated bacteria tested, which may be temperature-dependent in some strains. Furthermore, all V. coralliilyticus strains tested showed multi-drug resistance to a range of 11-16 (out of 26) commercial antibiotics. This study establishes V. coralliilyticus in association with a Caribbean octocoral and demonstrates its resistance to the antimicrobial activity of coral-associated bacteria and to commercial antibiotics.}, }
@article {pmid20305019, year = {2010}, author = {Pycke, BF and Crabbé, A and Verstraete, W and Leys, N}, title = {Characterization of triclosan-resistant mutants reveals multiple antimicrobial resistance mechanisms in Rhodospirillum rubrum S1H.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {10}, pages = {3116-3123}, pmid = {20305019}, issn = {1098-5336}, mesh = {Anti-Bacterial Agents/*pharmacology ; Computational Biology ; Drug Resistance, Bacterial/*genetics ; Enoyl-(Acyl-Carrier-Protein) Reductase (NADH)/genetics ; Microbial Sensitivity Tests ; Mutation/genetics ; Rhodospirillum rubrum/*drug effects/*genetics/growth &amp; development/metabolism ; Triclosan/*pharmacology ; }, abstract = {Antimicrobial resistance mechanisms were identified in 11 spontaneous high- and low-level triclosan resistance (Tcs(r)) mutants of Rhodospirillum rubrum S1H by genotyping complemented with transcriptional analyses, antibiotic resistance screening, and membrane permeability analyses. High-end Tcs(r) (MIC = 8 mg/liter) was the result of a FabI1(G98V) mutation. This point mutation led to an even higher level of Tcs(r) (MIC > or = 16 mg/liter) in combination with constitutive upregulation of mexB and mexF efflux pump homologs. Hence, a mechanistic synergy of constitutive efflux pump expression and a FabI1 point mutation could prevent TCS-induced cell permeabilization, which was shown to occur between 4 and 8 mg/liter TCS in the R. rubrum S1H parent strain. Low-level Tcs(r) mutants constitutively upregulated the emrAB, mexAB, and/or mexF homolog. The mutants that overexpressed emrAB also derepressed the micropollutant-upregulated factors mufA1 and mufM. In some cases, low-level Tcs(r) decreased innate resistance to ampicillin and tetracycline, while in others, a triclosan-induced antibiotic cross-resistance was shown for chloramphenicol and carbenicillin. This study showed that the TCS resistance degree is dependent of the initial exposure concentration in Rhodospirillum rubrum S1H and that similar resistance degrees can be the result of different defense mechanisms, which all have distinct antibiotic cross-resistance profiles.}, }
@article {pmid20303564, year = {2010}, author = {Haest, PJ and Springael, D and Smolders, E}, title = {Modelling reactive CAH transport using batch experiment degradation kinetics.}, journal = {Water research}, volume = {44}, number = {9}, pages = {2981-2989}, doi = {10.1016/j.watres.2010.02.031}, pmid = {20303564}, issn = {1879-2448}, mesh = {Bacteria/growth &amp; development ; *Biodegradation, Environmental ; Biomass ; Hydrocarbons, Chlorinated/*metabolism ; Kinetics ; Movement ; Trichloroethylene ; }, abstract = {Models describing transport of degradable organic substances in a porous medium require parameters of the biodegradation kinetics that can be obtained from batch degradation assays. It is rarely assessed if liquid batch biodegradation rates allow extrapolation to reactive transport in a porous medium, i.e. if the cell specific activity in a porous medium with flow-through is identical to that of pelagic cells in liquid cultures. Failure of model predictions can be used to identify the rate-limiting processes in the reactive transport. Column data of anaerobic trichloroethene (TCE) transport and degradation at three flow rates were predicted with a model using biodegradation kinetics derived from a liquid culture. The extent of dechlorination at the column outlet was very well predicted within a factor 1.4 if the specific microbial biomass in the columns was used as an input parameter. This suggests that potential mass transfer limitations in biofilms or differences in microbial ecology between batch and column had minor effects on dechlorination. The model was subsequently extended with Monod kinetics to predict both biomass growth and chlorinated aliphatic hydrocarbon (CAH) degradation in the columns using liquid batch data. These models largely overestimated CAH dechlorination unless microbial transport with cell elution was included and unless a slight batch to column adjustment was made to better predict microbial biomass. With 4 adjustable parameters the model succeeded in predicting the microbial numbers within a factor 4.3 and the extent of dechlorination within a factor 1.2. Our analysis validates the batch to column extrapolation for this dedicated set-up provided that the microbial biomass in columns is well predicted. The sensitivity analysis shows that the extent of dechlorination in the reactive transport is most sensitive to the parameters of TCE degradation kinetics, including microbial growth followed by the residence time.}, }
@article {pmid20298796, year = {2010}, author = {Bolca, S and Verstraete, W}, title = {Microbial equol production attenuates colonic methanogenesis and sulphidogenesis in vitro.}, journal = {Anaerobe}, volume = {16}, number = {3}, pages = {247-252}, doi = {10.1016/j.anaerobe.2010.03.002}, pmid = {20298796}, issn = {1095-8274}, mesh = {Colon/*metabolism/*microbiology ; Culture Media ; Desulfovibrio/metabolism ; Enterococcus faecium/growth &amp; development/metabolism ; Equol ; Euryarchaeota/growth &amp; development/metabolism ; Feces/microbiology ; Female ; Humans ; Hydrogen/metabolism ; Isoflavones/*biosynthesis/metabolism ; Lactobacillus/growth &amp; development/*metabolism ; Methane/*metabolism ; Methanobrevibacter/growth &amp; development/metabolism ; Middle Aged ; Sulfides/*metabolism ; Veillonella/growth &amp; development/metabolism ; }, abstract = {Hydrogen gas produced during colonic fermentation is excreted in breath and flatus, or removed by hydrogen-consuming bacteria such as methanogens and sulphate-reducing bacteria. However, recent research has shown that H2 is also consumed by equol-producing bacteria during the reduction of daidzein into equol. In this study, the interactions between methanogens, sulphate-reducing, and equol-producing bacteria were investigated under in vitro simulated intestinal conditions. In the presence of daidzein, the equol-producing bacterial consortium EPC4 gave rise to equol production in cultures of Methanobrevibacter smithii or Desulfovibrio sp. as well as in faecal samples with methanogenic or sulphate-reducing abilities. Moreover, this supplementation significantly (P<0.001) decreased the methanogenesis and sulphidogenesis. The attenuation did not occur in the absence of a daidzein source. Additionally, there was no influence of soy germ powder, daidzein or equol as such, excluding a possible inhibition by these compounds. Finally, a stronger decrease was observed with increasing amounts of EPC4 and a constant equol production, suggesting that the observed effect was only partly caused by the action of daidzein as a hydrogen sink. These findings are of relevance since abdominal discomfort such as bloating and flatulence, are related to colonic gas production, whereas equol has potential health benefits.}, }
@article {pmid20237775, year = {2010}, author = {Villanueva, L and del Campo, J and Guerrero, R and Geyer, R}, title = {Intact phospholipid and quinone biomarkers to assess microbial diversity and redox state in microbial mats.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {226-238}, pmid = {20237775}, issn = {1432-184X}, mesh = {*Biodiversity ; Chromatography, High Pressure Liquid ; DNA, Bacterial/genetics ; France ; Oxidation-Reduction ; Phospholipids/*analysis ; Proteobacteria/growth &amp; development/isolation &amp; purification/*metabolism ; Quinones/*analysis ; RNA, Ribosomal, 16S/genetics ; Spain ; Tandem Mass Spectrometry ; *Water Microbiology ; }, abstract = {Microbial mats are stratified microbial communities composed by highly inter-related populations and therefore are frequently chosen as model systems to study diversity and ecophysiological strategies. The present study describes an integrated approach to analyze microbial quinones and intact polar lipids (IPLs) in microbial mats within layers as thin as 500 microm by liquid chromatography-tandem mass spectrometry. Quinone profiles revealed important depth-related differences in community composition in two mat systems. The higher abundance of ubiquinones, compared to menaquinones, reflected the clear predominance of microorganisms belonging to aerobic alpha-, beta-, and gamma-Proteobacteria in Ebro delta estuarine mats. Hypersaline photosynthetic Camargue mats (France) showed a predominance of menaquinone-9 at the top of the mat, which is consistent with an important contribution of facultative aerobic or anaerobic bacteria in its photic zone. Quinone indices also indicated a higher diversity of non-phototrophs and a more anaerobic character in the hypersaline mats. Besides, the dissimilarity index suggested that the samples were greatly influenced by a depth-related redox state gradient. In the analysis of IPLs, there was a predominance of phosphatidylglycerols and sulfoquinovosyldiacylglycerols, the latter being an abundant biomarker of Cyanobacteria. This combined approach based on quinone and IPL analysis has proven to be a useful method to establish differences in the microbial diversity and redox state of highly structure microbial mat systems at a fine-scale level.}, }
@article {pmid20221594, year = {2010}, author = {Ortega-Retuerta, E and Duarte, CM and Reche, I}, title = {Significance of bacterial activity for the distribution and dynamics of transparent exopolymer particles in the Mediterranean sea.}, journal = {Microbial ecology}, volume = {59}, number = {4}, pages = {808-818}, pmid = {20221594}, issn = {1432-184X}, mesh = {Bacteria/*chemistry/growth &amp; development ; Mediterranean Sea ; Polysaccharides/*analysis ; Salinity ; Seawater/analysis/*microbiology ; Temperature ; *Water Microbiology ; }, abstract = {The study of transparent exopolymer particles (TEP) in the Mediterranean Sea is particularly relevant as they can be promoters of mucilage events, a frequent phenomenon there. We assessed the influence of bacterioplankton on TEP distribution and dynamics across the west-east axis of the Mediterranean Sea. We performed an extensive study of TEP, dissolved carbohydrates, and their relationships with bacterial abundance and bacterial production (BP). A significant and positive relationship was observed between BP and TEP in the study region (r (2) = 0.51, p < 0.001). The direct release of TEP by bacteria was experimentally corroborated using regrowth cultures where increases in TEP tracked bacterial growth in abundance and production. These TEP increases were positively related to the increases in BP (r (2) = 0.78, p < 0.05). The consistency (similar slopes) of the regression lines between BP and TEP in natural conditions and between the increases of BP and TEP in the experiments underlines the relevant role of bacteria in the formation of TEP in this area.}, }
@article {pmid20217406, year = {2010}, author = {Seyfried, EE and Newton, RJ and Rubert, KF and Pedersen, JA and McMahon, KD}, title = {Occurrence of tetracycline resistance genes in aquaculture facilities with varying use of oxytetracycline.}, journal = {Microbial ecology}, volume = {59}, number = {4}, pages = {799-807}, pmid = {20217406}, issn = {1432-184X}, support = {T32 GM008349/GM/NIGMS NIH HHS/United States ; }, mesh = {Animal Feed/microbiology ; *Aquaculture ; DNA, Bacterial/analysis ; Fresh Water/analysis/microbiology ; Genes, Bacterial ; Geologic Sediments/microbiology ; Microbial Sensitivity Tests ; Oxytetracycline/*pharmacology ; Polymerase Chain Reaction ; Tetracycline Resistance/*genetics ; *Water Microbiology ; }, abstract = {The contribution of human activities to environmental reservoirs of antibiotic resistance is poorly understood. The purpose of this study was to determine if oxytetracycline (OTC) use in aquaculture facilities increased the detection frequency (i.e., prevalence) of tetracycline resistance (tet(R)) genes relative to facilities with no recent OTC treatment. We used polymerase chain reaction to screen water and sediment from four noncommercial fish farms in northwestern Wisconsin for the presence of ten tet(R) determinants: tet(A), tet(B), tet(D), tet(E), tet(G), tet(M), tet(O), tet(Q), tet(S), and tet(W). Water from farms with recent OTC use had significantly higher tet(R) detection frequencies than did water from farms without recent OTC use, with prevalence in raceways and rearing ponds of farms with recent OTC use exceeding by more than twofold that of farms not using OTC. Effluent from all farms, regardless of treatment regime, had higher tet(R) detection frequencies than their corresponding influent for all genes, but the specific combinations of tet(R) genes detected in a sample were not different from their corresponding influent. Although OTC use was associated with the increased occurrence and diversity of tet(R) genes in water samples, it was not found to relate to tet(R) gene occurrence in sediment samples. Sediment samples from facilities with no recent OTC use had significantly higher frequencies of tet(R) gene detection than did samples from facilities with recent OTC use. All of the tet(R) genes were detected in both the medicated and nonmedicated feed samples analyzed in this study. These findings suggest that both OTC treatment in aquaculture facilities and the farms themselves may be sources of tet(R) gene introduction to the environment. To our knowledge, this is the first study to use genotypic and cultivation-independent methods to examine tet(R) gene occurrence associated with OTC use in aquaculture.}, }
@article {pmid20217405, year = {2010}, author = {Wang, Z and Malanoski, AP and Lin, B and Long, NC and Leski, TA and Blaney, KM and Hansen, CJ and Brown, J and Broderick, M and Stenger, DA and Tibbetts, C and Russell, KL and Metzgar, D}, title = {Broad spectrum respiratory pathogen analysis of throat swabs from military recruits reveals interference between rhinoviruses and adenoviruses.}, journal = {Microbial ecology}, volume = {59}, number = {4}, pages = {623-634}, pmid = {20217405}, issn = {1432-184X}, mesh = {Adenoviridae/*isolation &amp; purification ; Adenovirus Infections, Human/*epidemiology ; Adolescent ; Bacteria/isolation &amp; purification ; Base Sequence ; DNA, Viral/analysis ; Female ; Fever/etiology/virology ; Humans ; Male ; *Military Personnel ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Pharynx/virology ; Picornaviridae Infections/*epidemiology ; Respiratory Tract Diseases/etiology/virology ; Rhinovirus/*isolation &amp; purification ; Young Adult ; }, abstract = {Military recruits experience a high incidence of febrile respiratory illness (FRI), leading to significant morbidity and lost training time. Adenoviruses, group A Streptococcus pyogenes, and influenza virus are implicated in over half of the FRI cases reported at recruit training center clinics, while the etiology of the remaining cases is unclear. In this study, we explore the carriage rates and disease associations of adenovirus, enterovirus, rhinovirus, Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis in military recruits using high-density resequencing microarrays. The results showed that rhinoviruses, adenoviruses, S. pneumoniae, H. influenzae, and N. meningitidis were widely distributed in recruits. Of these five agents, only adenovirus showed significant correlation with illness. Among the samples tested, only pathogens associated with FRI, such as adenovirus 4 and enterovirus 68, revealed strong temporal and spatial clustering of specific strains, indicating that they are transmitted primarily within sites. The results showed a strong negative association between adenoviral FRI and the presence of rhinoviruses in recruits, suggesting some form of viral interference.}, }
@article {pmid20217404, year = {2010}, author = {Laque, T and Farjalla, VF and Rosado, AS and Esteves, FA}, title = {Spatiotemporal variation of bacterial community composition and possible controlling factors in tropical shallow lagoons.}, journal = {Microbial ecology}, volume = {59}, number = {4}, pages = {819-829}, pmid = {20217404}, issn = {1432-184X}, mesh = {Bacteria/*growth &amp; development ; Brazil ; Chlorophyll/analysis ; Chlorophyll A ; Geography ; Nitrates/analysis ; Phosphorus/analysis ; Salinity ; Seawater/analysis/*microbiology ; Time Factors ; Tropical Climate ; *Water Microbiology ; }, abstract = {Bacterial community composition (BCC) has been extensively related to specific environmental conditions. Tropical coastal lagoons present great temporal and spatial variation in their limnological conditions, which, in turn, should influence the BCC. Here, we sought for the limnological factors that influence, in space and time, the BCC in tropical coastal lagoons (Rio de Janeiro State, Brazil). The Visgueiro lagoon was sampled monthly for 1 year and eight lagoons were sampled once for temporal and spatial analysis, respectively. BCC was evaluated by bacteria-specific PCR-DGGE methods. Great variations were observed in limnological conditions and BCC on both temporal and spatial scales. Changes in the BCC of Visgueiro lagoon throughout the year were best related to salinity and concentrations of NO (3) (-) , dissolved phosphorus and chlorophyll-a, while changes in BCC between lagoons were best related to salinity and dissolved phosphorus concentration. Salinity has a direct impact on the integrity of the bacterial cell, and it was previously observed that phosphorus is the main limiting nutrient to bacterial growth in these lagoons. Therefore, we conclude that great variations in limnological conditions of coastal lagoons throughout time and space resulted in different BCCs and salinity and nutrient concentration, particularly dissolved phosphorus, are the main limnological factors influencing BCC in these tropical coastal lagoons.}, }
@article {pmid20204349, year = {2010}, author = {Taketani, RG and Tsai, SM}, title = {The influence of different land uses on the structure of archaeal communities in Amazonian anthrosols based on 16S rRNA and amoA genes.}, journal = {Microbial ecology}, volume = {59}, number = {4}, pages = {734-743}, pmid = {20204349}, issn = {1432-184X}, mesh = {Agriculture ; Archaea/classification/enzymology/*genetics/*growth &amp; development ; Brazil ; DNA, Archaeal/genetics ; Gene Library ; Genes, Archaeal ; Genetic Variation ; Oxidoreductases/genetics ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Tropical Climate ; }, abstract = {Soil from the Amazonian region is usually regarded as unsuitable for agriculture because of its low organic matter content and low pH; however, this region also contains extremely rich soil, the Terra Preta Anthrosol. A diverse archaeal community usually inhabits acidic soils, such as those found in the Amazon. Therefore, we hypothesized that this community should be sensitive to changes in the environment. Here, the archaeal community composition of Terra Preta and adjacent soil was examined in four different sites in the Brazilian Amazon under different anthropic activities. The canonical correspondence analysis of terminal restriction fragment length polymorphisms has shown that the archaeal community structure was mostly influenced by soil attributes that differentiate the Terra Preta from the adjacent soil (i.e., pH, sulfur, and organic matter). Archaeal 16S rRNA gene clone libraries indicated that the two most abundant genera in both soils were Candidatus nitrosphaera and Canditatus nitrosocaldus. An ammonia monoxygenase gene (amoA) clone library analysis indicated that, within each site, there was no significant difference between the clone libraries of Terra Preta and adjacent soils. However, these clone libraries indicated there were significant differences between sites. Quantitative PCR has shown that Terra Preta soils subjected to agriculture displayed a higher number of amoA gene copy numbers than in adjacent soils. On the other hand, soils that were not subjected to agriculture did not display significant differences on amoA gene copy numbers between Terra Preta and adjacent soils. Taken together, our findings indicate that the overall archaeal community structure in these Amazonian soils is determined by the soil type and the current land use.}, }
@article {pmid20198369, year = {2010}, author = {Hutalle-Schmelzer, KM and Zwirnmann, E and Krüger, A and Grossart, HP}, title = {Changes in pelagic bacteria communities due to leaf litter addition.}, journal = {Microbial ecology}, volume = {60}, number = {2}, pages = {462-475}, pmid = {20198369}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*growth &amp; development ; *Biota ; Carbon/*chemistry ; Cluster Analysis ; DNA, Bacterial/genetics ; Denaturing Gradient Gel Electrophoresis ; Fresh Water/*microbiology ; Germany ; In Situ Hybridization, Fluorescence ; Phylogeny ; Plant Leaves/*chemistry ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Trees/chemistry ; Water Microbiology ; }, abstract = {In many limnetic systems, the input of allochthonous organic matter, e.g., leaf litter, is a substantial source of dissolved organic carbon (DOC) for pelagic bacteria, especially in fall and winter when autochthonous DOC production is low. However, relatively little is known about community changes of pelagic lake bacteria due to leaf litter input which includes both the release of leaf leachates and microorganisms from the leaf litter into the surrounding water. Therefore, we have experimentally studied the effects of different types of leaf litter (Betula pendula, Fagus silvatica, and Pinus silvestris) on the pelagic bacterial community composition by adding leaves to different treatments of epilimnic water samples (unfiltered, 0.2 µm and 5.0 µm-pre-filtered) from humic Lake Grosse Fuchskuhle (Northeastern Germany). The addition of leaf litter led to a significant increase in DOC concentration in lake water, and each leaf litter type produced significantly different amounts of DOC (p = <0.001) as well as of specific DOC fractions (p = <0.001), except of polysaccharides. DGGE banding patterns varied over time, between types of leaf litter, and among treatments. Bacteria belonging to known bacterial phylotypes in the southwest basin of Lake Grosse Fuchskuhle were frequently found and even persisted after leaf litter additions. Upon leaf litter addition, α-proteobacteria (Azospirillum, Novosphingobium, and Sphingopyxis) as well as β-proteobacteria (Curvibacter and Polynucleobacter) were enriched. Our results indicate that supply of leaf litter DOM shifted the bacterial community in the surrounding water towards specific phylotypes including species capable of assimilating the more recalcitrant DOC pools. Statistical analyses, however, show that DGGE banding patterns are not only affected by DOC pools but also by treatment. This indicates that biological factors such as source community and grazing may be also important for shifts in bacterial community structure following leaf litter input into different lakes.}, }
@article {pmid20195591, year = {2010}, author = {Faeth, SH and Hayes, CJ and Gardner, DR}, title = {Asexual endophytes in a native grass: tradeoffs in mortality, growth, reproduction, and alkaloid production.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {496-504}, pmid = {20195591}, issn = {1432-184X}, mesh = {Biomass ; Ergot Alkaloids/*biosynthesis ; Genotype ; Neotyphodium/*physiology ; Poaceae/genetics/*growth &amp; development/*microbiology ; Reproduction ; Seeds/growth &amp; development ; *Symbiosis ; }, abstract = {Neotyphodium endophytes are asexual, seed-borne fungal symbionts that are thought to interact mutualistically with their grass hosts. Benefits include increased growth, reproduction, and resistance to herbivores via endophytic alkaloids. Although these benefits are well established in infected introduced, agronomic grasses, little is known about the cost and benefits of endophyte infection in native grass populations. These populations exist as mosaics of uninfected and infected plants, with the latter often comprised of plants that vary widely in alkaloid content. We tested the costs and benefits of endophyte infections with varying alkaloids in the native grass Achnatherum robustum (sleepygrass). We conducted a 4-year field experiment, where herbivory and water availability were controlled and survival, growth, and reproduction of three maternal plant genotypes [uninfected plants (E-), infected plants with high levels of ergot alkaloids (E+A+), and infected plants with no alkaloids (E+A-)] were monitored over three growing seasons. Generally, E+A+ plants had reduced growth over the three growing seasons and lower seed production than E- or E+A- plants, suggesting a cost of alkaloid production. The reduction in vegetative biomass in E+A+ plants was most pronounced under supplemented water, contrary to the prediction that additional resources would offset the cost of alkaloid production. Also, E+A+ plants showed no advantage in growth, seed production, or reproductive effort under full herbivory relative to E- or E+A- grasses, contrary to the predictions of the defensive mutualism hypothesis. However, E+A+ plants had higher overwintering survival than E+A- plants in early plant ontogeny, suggesting that alkaloids associated with infection may protect against below ground herbivory or harsh winter conditions. Our results suggest that the mosaic of E-, E+A+, and E+A- plants observed in nature may result from varying biotic and abiotic selective factors that maintain the presence of uninfected plants and infected plants that vary in alkaloid production.}, }
@article {pmid20195499, year = {2010}, author = {Wooley, JC and Godzik, A and Friedberg, I}, title = {A primer on metagenomics.}, journal = {PLoS computational biology}, volume = {6}, number = {2}, pages = {e1000667}, pmid = {20195499}, issn = {1553-7358}, mesh = {Computational Biology ; *Metagenomics ; Sequence Analysis, DNA ; }, abstract = {Metagenomics is a discipline that enables the genomic study of uncultured microorganisms. Faster, cheaper sequencing technologies and the ability to sequence uncultured microbes sampled directly from their habitats are expanding and transforming our view of the microbial world. Distilling meaningful information from the millions of new genomic sequences presents a serious challenge to bioinformaticians. In cultured microbes, the genomic data come from a single clone, making sequence assembly and annotation tractable. In metagenomics, the data come from heterogeneous microbial communities, sometimes containing more than 10,000 species, with the sequence data being noisy and partial. From sampling, to assembly, to gene calling and function prediction, bioinformatics faces new demands in interpreting voluminous, noisy, and often partial sequence data. Although metagenomics is a relative newcomer to science, the past few years have seen an explosion in computational methods applied to metagenomic-based research. It is therefore not within the scope of this article to provide an exhaustive review. Rather, we provide here a concise yet comprehensive introduction to the current computational requirements presented by metagenomics, and review the recent progress made. We also note whether there is software that implements any of the methods presented here, and briefly review its utility. Nevertheless, it would be useful if readers of this article would avail themselves of the comment section provided by this journal, and relate their own experiences. Finally, the last section of this article provides a few representative studies illustrating different facets of recent scientific discoveries made using metagenomics.}, }
@article {pmid20190045, year = {2010}, author = {Zeng, L and Das, S and Burne, RA}, title = {Utilization of lactose and galactose by Streptococcus mutans: transport, toxicity, and carbon catabolite repression.}, journal = {Journal of bacteriology}, volume = {192}, number = {9}, pages = {2434-2444}, pmid = {20190045}, issn = {1098-5530}, support = {R01 DE012236/DE/NIDCR NIH HHS/United States ; DE12236/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Biological Transport/genetics/*physiology ; Carbon/*metabolism ; Galactose/*metabolism ; Galactosephosphates/metabolism ; Lac Operon/genetics ; Lactose/*metabolism ; Models, Biological ; Mutagenesis, Site-Directed ; Mutation ; Phosphoenolpyruvate Sugar Phosphotransferase System/genetics/metabolism ; Promoter Regions, Genetic/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Streptococcus mutans/genetics/growth &amp; development/*metabolism ; }, abstract = {Abundant in milk and other dairy products, lactose is considered to have an important role in oral microbial ecology and can contribute to caries development in both adults and young children. To better understand the metabolism of lactose and galactose by Streptococcus mutans, the major etiological agent of human tooth decay, a genetic analysis of the tagatose-6-phosphate (lac) and Leloir (gal) pathways was performed in strain UA159. Deletion of each gene in the lac operon caused various alterations in expression of a P(lacA)-cat promoter fusion and defects in growth on either lactose (lacA, lacB, lacF, lacE, and lacG), galactose (lacA, lacB, lacD, and lacG) or both sugars (lacA, lacB, and lacG). Failure to grow in the presence of galactose or lactose by certain lac mutants appeared to arise from the accumulation of intermediates of galactose metabolism, particularly galatose-6-phosphate. The glucose- and lactose-PTS permeases, EII(Man) and EII(Lac), respectively, were shown to be the only effective transporters of galactose in S. mutans. Furthermore, disruption of manL, encoding EIIAB(Man), led to increased resistance to glucose-mediated CCR when lactose was used to induce the lac operon, but resulted in reduced lac gene expression in cells growing on galactose. Collectively, the results reveal a remarkably high degree of complexity in the regulation of lactose/galactose catabolism.}, }
@article {pmid20188628, year = {2010}, author = {Gómez, F and Moreira, D and López-García, P}, title = {Molecular phylogeny of noctilucoid dinoflagellates (Noctilucales, Dinophyceae).}, journal = {Protist}, volume = {161}, number = {3}, pages = {466-478}, doi = {10.1016/j.protis.2009.12.005}, pmid = {20188628}, issn = {1618-0941}, mesh = {Atlantic Ocean ; Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Dinoflagellida/*classification/*genetics/isolation &amp; purification ; Genes, rRNA ; Mediterranean Sea ; Molecular Sequence Data ; *Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {The order Noctilucales or class Noctiluciphyceae encompasses three families of aberrant dinoflagellates (Noctilucaceae, Leptodiscaceae and Kofoidiniaceae) that, at least in some life stages, lack typical dinoflagellate characters such as the ribbon-like transversal flagellum or condensed chromosomes. Noctiluca scintillans, the first dinoflagellate to be described, has been intensively investigated. However, its phylogenetic position based on the small subunit ribosomal DNA (SSU rDNA) sequence is unstable and controversial. Noctiluca has been placed either as an early diverging lineage that diverged after Oxyrrhis and before the dinokaryotes -core dinoflagellates- or as a recent lineage branching from unarmoured dino fl agellates in the order Gymnodiniales. So far, the lack of other noctilucoid sequences has hampered the elucidation of their phylogenetic relationships to other dino fl agellates. Furthermore, even the monophyly of the noctilucoids remained uncertain. We have determined SSU rRNA gene sequences for Kofoidiniaceae, those of the type Spatulodinium (=Gymnodinium) pseudonoctiluca and another Spatulodinium species, as well as of two species of Kofoidinium, and the first gene sequence of Leptodiscaceae, that of Abedinium (=Leptophyllus) dasypus. These taxa were collected from their type localities, the English Channel and the NW Mediterranean Sea, respectively. Phylogenetic analyses place the Noctilucales as a monophyletic group at a basal position close to parasites of the Marine Alveolate Group I (MAGI) and the Syndiniales (MAGII), before the core of dinokaryotic dinoflagellates, although with moderate support.}, }
@article {pmid20186408, year = {2010}, author = {de La Cochetière, MF and Montassier, E and Hardouin, JB and Carton, T and Le Vacon, F and Durand, T and Lalande, V and Petit, JC and Potel, G and Beaugerie, L}, title = {Human intestinal microbiota gene risk factors for antibiotic-associated diarrhea: perspectives for prevention. Risk factors for antibiotic-associated diarrhea.}, journal = {Microbial ecology}, volume = {59}, number = {4}, pages = {830-837}, pmid = {20186408}, issn = {1432-184X}, mesh = {Adult ; Analysis of Variance ; Anti-Bacterial Agents/*adverse effects ; Bacteria/*genetics ; Diarrhea/chemically induced/*prevention &amp; control ; Disease Susceptibility/*microbiology ; Genes, Bacterial ; Humans ; Intestines/*microbiology ; Metagenome ; Middle Aged ; Multivariate Analysis ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; Young Adult ; }, abstract = {Antibiotic-associated diarrhea (AAD) is associated with altered intestinal microflora and other symptoms that may lead to possibly death. In critically ill patients, diarrhea increases rates of morbimortality. Assessing diarrhea risks is thus important for clinicians. For this reason, we conducted a hypothesis-generating study focused on AAD to provide insight into methods of prevention. We evaluated the hypothesis of predisposing factors within the resident intestinal microbiota in a cohort of outpatients receiving antibiotherapy. Among the pool of tested variables, only those related to bacterial 16S rRNA genes were found to be relevant. Complex statistical analyses provided further information: amid the bacteria 16S rRNA genes, eight were determined to be essential for diarrhea predisposition and characterized from the most important to the least. Using these markers, AAD risk could be estimated with an error of 2%. This molecular analysis offers new perspectives for clinical applications at the level of prevention.}, }
@article {pmid20182521, year = {2010}, author = {Morales, SE and Cosart, T and Holben, WE}, title = {Bacterial gene abundances as indicators of greenhouse gas emission in soils.}, journal = {The ISME journal}, volume = {4}, number = {6}, pages = {799-808}, doi = {10.1038/ismej.2010.8}, pmid = {20182521}, issn = {1751-7370}, mesh = {Agriculture ; Bacteria/classification/*genetics ; DNA, Bacterial/genetics ; *Genes, Bacterial ; Genes, rRNA ; *Greenhouse Effect ; Nitrous Oxide/*analysis ; Polymerase Chain Reaction ; Principal Component Analysis ; Regression Analysis ; Ribotyping ; Soil/*analysis ; *Soil Microbiology ; }, abstract = {Nitrogen fixing and denitrifying bacteria, respectively, control bulk inputs and outputs of nitrogen in soils, thereby mediating nitrogen-based greenhouse gas emissions in an ecosystem. Molecular techniques were used to evaluate the relative abundances of nitrogen fixing, denitrifying and two numerically dominant ribotypes (based on the > or =97% sequence similarity at the 16S rRNA gene) of bacteria in plots representing 10 agricultural and other land-use practices at the Kellogg biological station long-term ecological research site. Quantification of nitrogen-related functional genes (nitrite reductase, nirS; nitrous oxide reductase, nosZ; and nitrogenase, nifH) as well as two dominant 16S ribotypes (belonging to the phyla Acidobacteria, Thermomicrobia) allowed us to evaluate the hypothesis that microbial community differences are linked to greenhouse gas emissions under different land management practices. Our results suggest that the successional stages of the ecosystem are strongly linked to bacterial functional group abundance, and that the legacy of agricultural practices can be sustained over decades. We also link greenhouse gas emissions with specific compositional responses in the soil bacterial community and assess the use of denitrifying gene abundances as proxies for determining nitrous oxide emissions from soils.}, }
@article {pmid20182510, year = {2010}, author = {Nielsen, LP and Risgaard-Petersen, N and Fossing, H and Christensen, PB and Sayama, M}, title = {Electric currents couple spatially separated biogeochemical processes in marine sediment.}, journal = {Nature}, volume = {463}, number = {7284}, pages = {1071-1074}, pmid = {20182510}, issn = {1476-4687}, mesh = {Bacteria/metabolism ; Cytochromes/metabolism ; Denmark ; Diffusion ; *Electric Conductivity ; Electrochemistry ; Electron Transport ; Electrons ; Geologic Sediments/*chemistry/*microbiology ; Hydrogen Sulfide/analysis/chemistry ; Hydrogen-Ion Concentration ; Iron/chemistry ; Nanowires/microbiology ; Oxygen/analysis/metabolism ; Oxygen Consumption ; Porosity ; Seawater/*microbiology ; Sulfides/chemistry ; }, abstract = {Some bacteria are capable of extracellular electron transfer, thereby enabling them to use electron acceptors and donors without direct cell contact. Beyond the micrometre scale, however, no firm evidence has previously existed that spatially segregated biogeochemical processes can be coupled by electric currents in nature. Here we provide evidence that electric currents running through defaunated sediment couple oxygen consumption at the sediment surface to oxidation of hydrogen sulphide and organic carbon deep within the sediment. Altering the oxygen concentration in the sea water overlying the sediment resulted in a rapid (<1-h) change in the hydrogen sulphide concentration within the sediment more than 12 mm below the oxic zone, a change explicable by transmission of electrons but not by diffusion of molecules. Mass balances indicated that more than 40% of total oxygen consumption in the sediment was driven by electrons conducted from the anoxic zone. A distinct pH peak in the oxic zone could be explained by electrochemical oxygen reduction, but not by any conventional sets of aerobic sediment processes. We suggest that the electric current was conducted by bacterial nanowires combined with pyrite, soluble electron shuttles and outer-membrane cytochromes. Electrical communication between distant chemical and biological processes in nature adds a new dimension to our understanding of biogeochemistry and microbial ecology.}, }
@article {pmid20179919, year = {2010}, author = {Sathe, S and Kaushik, S and Lalremruata, A and Aggarwal, RK and Cavender, JC and Nanjundiah, V}, title = {Genetic heterogeneity in wild isolates of cellular slime mold social groups.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {137-148}, pmid = {20179919}, issn = {1432-184X}, mesh = {Animals ; DNA, Protozoan/genetics ; Dictyostelium/*genetics/*isolation &amp; purification ; Feces/microbiology ; India ; Random Amplified Polymorphic DNA Technique ; *Soil Microbiology ; }, abstract = {This study addresses the issues of spatial distribution, dispersal, and genetic heterogeneity in social groups of the cellular slime molds (CSMs). The CSMs are soil amoebae with an unusual life cycle that consists of alternating solitary and social phases. Because the social phase involves division of labor with what appears to be an extreme form of "altruism", the CSMs raise interesting evolutionary questions regarding the origin and maintenance of sociality. Knowledge of the genetic structure of social groups in the wild is necessary for answering these questions. We confirm that CSMs are widespread in undisturbed forest soil from South India. They are dispersed over long distances via the dung of a variety of large mammals. Consistent with this mode of dispersal, most social groups in the two species examined for detailed study, Dictyostelium giganteum and Dictyostelium purpureum, are multi-clonal.}, }
@article {pmid20179918, year = {2010}, author = {Ghodhbane-Gtari, F and Nouioui, I and Chair, M and Boudabous, A and Gtari, M}, title = {16S-23S rRNA intergenic spacer region variability in the genus Frankia.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {487-495}, pmid = {20179918}, issn = {1432-184X}, mesh = {Base Sequence ; DNA, Bacterial/genetics ; *DNA, Intergenic ; Frankia/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 23S/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {16S-23S rRNA internally transcribed spacer (ITS) sequences from 53 Frankia strains were sequenced and sized from polymerase chain reaction amplification products and compiled with 14 selected 16S-23S ITS sequences from public database. Frankia genomes included two to three ITS copies lacking length polymorphism except for nine strains. No tRNA gene was encountered in this region. Frankia strains exhibited various lengths (369 to 452 nt) and a wide range of sequence similarity (35-100%) in the ITS region. The average pairwise distance varied from 0.368 (clusters 1 and 2) to 0.964 (clusters 3 and 4) and was 0.397, 0.138, 0.129, and 0.016, respectively, for cluster 4 (saprophytic non-infective/non-effective), clusters 1 and 3 (facultative symbiotic), and cluster 2 (obligate symbiotic). This suggests a gradual erosion of Frankia diversity concomitantly with a shift from saprophytic non-infective/non-effective to facultative and symbiotic lifestyle. Comparative sequence analyses of the 16S-23S rRNA intergenic spacer region of Frankia strains are not useful to assign them to their respective cluster or host infection group. Accurate assignment required the inclusion of the adjacent 16S and 23S rRNA gene fragments.}, }
@article {pmid20174790, year = {2010}, author = {Chouari, R and Le Paslier, D and Daegelen, P and Dauga, C and Weissenbach, J and Sghir, A}, title = {Molecular analyses of the microbial community composition of an anoxic basin of a municipal wastewater treatment plant reveal a novel lineage of proteobacteria.}, journal = {Microbial ecology}, volume = {60}, number = {2}, pages = {272-281}, pmid = {20174790}, issn = {1432-184X}, mesh = {Crenarchaeota/classification/genetics ; Euryarchaeota/classification/genetics ; Gene Library ; *Microbial Consortia ; Oligonucleotide Probes/genetics ; *Phylogeny ; Proteobacteria/*classification/genetics ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Waste Disposal, Fluid ; }, abstract = {A culture-independent molecular phylogenetic approach was used to study prokaryotic diversity in an anoxic activated sludge from a municipal wastewater treatment plant. Two 16S rRNA gene libraries were constructed using total genomic DNA and amplified by polymerase chain reaction using primers specific for archaeal or bacterial domains. Phylogenetic analysis of 132 and 249 almost full-length 16S rRNA genes for Archaea and Bacteria, respectively, was done using the ARB software package. Phylogenetic groups affiliated with the Archaea belong to Euryarchaeota (93.8% of the operational taxonomic units [OTUs]) and Crenarchaeota (6.2% of the OTUs). Within the bacterial library, 84.8% of the OTUs represent novel putative phylotypes never described before and affiliated with ten divisions. The Proteobacteria phylum is the most abundant and diversified phylogenetic group representing 60.4% of the OTUs, followed by Bacteroidetes (22.1%) and gram-positives (6.1%). Interestingly, we detected a novel Proteobacteria monophyletic group distinct from the five known subclasses, which we named New Lineage of Proteobacteria (NLP) lineage, and it is composed of eight clones representing 4.6% of the Proteobacteria. A new 16S rRNA-targeted hybridization probe was designed and fluorescent in situ hybridization analyses shows representatives of NLP as cocci-shaped microorganisms. The Chloroflexi, Acidobacterium, and Nitrospira phyla and TM7 candidate division are each represented by ≤3% of clone sequences. A comprehensive set of eight 16S and 23S rRNA-targeted oligonucleotide probes was used to quantify these major groups by dot blot hybridization within 12 samples. The Proteobacteria accounted for 82.5 ± 4.9%, representing the most abundant phyla. The Bacteroidetes and Planctomycetales groups accounted for 4.9 ± 1.3% and 4 ± 1.7%, respectively. Firmicutes and Actinobacteria together accounted for only 1.9 ± 0.5%. The set of probes covers 93.4 ± 14% of the total bacterial population rRNA within the anoxic basin.}, }
@article {pmid20171753, year = {2010}, author = {McMeekin, TA and Hill, C and Wagner, M and Dahl, A and Ross, T}, title = {Ecophysiology of food-borne pathogens: Essential knowledge to improve food safety.}, journal = {International journal of food microbiology}, volume = {139 Suppl 1}, number = {}, pages = {S64-78}, doi = {10.1016/j.ijfoodmicro.2010.01.041}, pmid = {20171753}, issn = {1879-3460}, mesh = {Bacteria/chemistry ; *Bacterial Physiological Phenomena ; *Consumer Product Safety ; Food Analysis/*methods ; Foodborne Diseases/*microbiology ; Humans ; Knowledge ; }, abstract = {The term ecophysiology suggests that a natural connection exists between microbial ecology and microbial physiology, the former being concerned with the responses of microbial populations to environmental influences, and the latter with activities within individual cells. In this contribution we choose to integrate these as far as possible and also indicate how understanding of both is benefiting from advances in molecular biology and informatics. We consider how microbial dispersal relates to microbial survival, recovery and proliferation, including the significance of random factors (stochasticity) in continuation of bacterial lineages, observing that minor environmental changes, can greatly influence the potential for food-borne disease. Homeostasis and membrane transport are identified as potential targets to control food-borne pathogens and the role of compatible solutes in stress protection is presented. Phenotypic variation in genetically homogeneous populations is highlighted as a major component of the overall microbial survival strategy. The marked influence and potential of predictive microbiology as an aid to food safety management is discussed, as is the need for greater knowledge of the ecophysiology of microbes in the growth/no growth region. The application of fundamental scientific principles, including thermodynamics, chemistry and microbial physiology is advocated as the basis for development of theory underpinning microbial ecophysiology. Advancing microbial food safety continues to require development of rapid, quantitative methods as an early warning system and mechanism to curtail microbial food-borne disease outbreaks. However, advances made by technologists and molecular biologists must be combined with knowledge of ecophysiology: e.g. biological rates will continue to constrain resolution of the recalcitrant problem of reducing the time required for enrichment processes. The discussion presented leads to the conclusion that microbial and molecular methods are appropriate for enumeration and prevalence studies but that predictive model development should continue for the purposes of comparative process control and to support the risk assessment paradigm. We conclude also that contributions of human error or complacency to microbial food-borne illness will continue to thwart the best efforts of microbiologists and technologists to reduce its incidence. Decision-support technologies reporting in real-time appear to have potential to make objective food safety decisions thereby reducing the impact of human indifference to the application of simple, but effective, food hygiene rules.}, }
@article {pmid20164865, year = {2010}, author = {Denef, VJ and Mueller, RS and Banfield, JF}, title = {AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature.}, journal = {The ISME journal}, volume = {4}, number = {5}, pages = {599-610}, doi = {10.1038/ismej.2009.158}, pmid = {20164865}, issn = {1751-7370}, mesh = {Archaea/*genetics/physiology/virology ; Bacteria/*genetics/virology ; Bacterial Physiological Phenomena ; *Biofilms ; *Ecosystem ; *Metagenome ; *Mining ; Models, Biological ; }, abstract = {Similar to virtually all components of natural environments, microbial systems are inherently complex and dynamic. Advances in cultivation-independent molecular methods have provided a route to study microbial consortia in their natural surroundings and to begin resolving the community structure, dominant metabolic processes and inter-organism interactions. However, the utility of these methods generally scales inversely with community complexity. By applying genomics-enabled methods to the study of natural microbial communities with reduced levels of species richness, a relatively comprehensive understanding of the metabolic networks and evolutionary processes within these communities can be attained. In such well-defined model systems, it is also possible to link emergent ecological patterns to their molecular and evolutionary underpinnings, facilitating construction of predictive ecosystem models. In this study, we review over a decade of research on one such system-acid mine drainage biofilm communities. We discuss the value and limitations of tractable model microbial communities in developing molecular methods for microbial ecology and in uncovering principles that may explain behavior in more complex systems.}, }
@article {pmid20164861, year = {2010}, author = {Kuramae, EE and Gamper, HA and Yergeau, E and Piceno, YM and Brodie, EL and Desantis, TZ and Andersen, GL and van Veen, JA and Kowalchuk, GA}, title = {Microbial secondary succession in a chronosequence of chalk grasslands.}, journal = {The ISME journal}, volume = {4}, number = {5}, pages = {711-715}, doi = {10.1038/ismej.2010.11}, pmid = {20164861}, issn = {1751-7370}, mesh = {Bacteria/*classification/genetics ; Biodiversity ; *Ecosystem ; Netherlands ; Polymerase Chain Reaction ; *Soil Microbiology ; }, abstract = {Although secondary succession has been studied extensively, we have little knowledge of the succession of soil-borne microbial communities. In this study, we therefore examined the structures of the microbial communities across two separate chronosequences of chalk grasslands in Limburg, the Netherlands, which are at different stages of secondary succession after being abandoned for between 17 and >66 years. Arable fields were also included in the investigation as non-abandoned references. Changes in the soil-borne microbial communities, as determined by phylogenetic microarray and quantitative PCR methodologies, were correlated with the prevailing environmental conditions related to vegetation and soil biochemistry. We observed clear patterns of microbial secondary succession related to soil age, pH and phosphate status, as exemplified by the overrepresentation of Verrucomicrobia, Acidobacteria, Gemmatimonadetes, and alpha-, delta- and epsilon-Proteobacteria at late successional stages. Moreover, effects of secondary succession versus changes in soil pH could be resolved, with pH significantly altering the trajectory of microbial succession.}, }
@article {pmid20164315, year = {2010}, author = {Bolca, S and Urpi-Sarda, M and Blondeel, P and Roche, N and Vanhaecke, L and Possemiers, S and Al-Maharik, N and Botting, N and De Keukeleire, D and Bracke, M and Heyerick, A and Manach, C and Depypere, H}, title = {Disposition of soy isoflavones in normal human breast tissue.}, journal = {The American journal of clinical nutrition}, volume = {91}, number = {4}, pages = {976-984}, doi = {10.3945/ajcn.2009.28854}, pmid = {20164315}, issn = {1938-3207}, mesh = {Adipose Tissue/metabolism ; Adolescent ; Adult ; Breast/*metabolism ; Chromatography, Liquid ; Dietary Supplements ; Estradiol/metabolism ; Estrogen Receptor beta/metabolism ; Female ; Genistein/administration &amp; dosage/metabolism/*pharmacokinetics ; Humans ; Isoflavones/administration &amp; dosage/metabolism/*pharmacokinetics ; Mammary Glands, Human/metabolism ; Middle Aged ; Phytoestrogens/administration &amp; dosage/metabolism/*pharmacokinetics ; Plant Extracts/*pharmacokinetics ; Reference Values ; Soy Foods ; Glycine max/*chemistry ; Tandem Mass Spectrometry ; Tissue Distribution/drug effects ; Young Adult ; }, abstract = {BACKGROUND: Despite decades of research on the relation between soy and breast cancer, questions regarding the absorption, metabolism, and distribution of isoflavones in breast tissue largely remain unanswered.<br><br>OBJECTIVE: We evaluated the potential health effects of isoflavone consumption on normal breast tissue; isoflavone concentrations, metabolites, and biodistribution were investigated and compared with 17beta-estradiol exposure.<br><br>DESIGN: In this dietary intervention study, healthy women were randomly allocated to a soy milk (n = 11; 16.98-mg genistein and 5.40-mg daidzein aglycone equivalents per dose), soy supplement (n = 10; 5.27-mg genistein and 17.56-mg daidzein aglycone equivalents per dose), or control (n = 10) group. After a run-in period > or = 4 d, 3 doses of soy milk or soy supplements were taken daily for 5 d before an esthetic breast reduction. Blood and breast biopsies were collected during surgery and analyzed with liquid chromatography-tandem mass spectrometry.<br><br>RESULTS: After soy administration, genistein and total daidzein concentrations, which were expressed as aglycone equivalents, ranged from 135.1 to 2831 nmol/L and 105.1 to 1397 nmol/L, respectively, in hydrolyzed serum and from 92.33 to 493.8 pmol/g and 22.15 to 770.8 pmol/g, respectively, in hydrolyzed breast tissue. The major metabolites identified in nonhydrolyzed samples were genistein-7-O-glucuronide and daidzein-7-O-glucuronide, with an overall glucuronidation of 98%. Total isoflavones showed a breast adipose/glandular tissue distribution of 40:60, and their mean (+/-SEM) derived 17beta-estradiol equivalents toward estrogen receptor beta were 21 +/- 4-fold and 40 +/- 10-fold higher than the 17beta-estradiol concentrations in adipose (0.283 +/- 0.089 pmol/g, P < 0.001) and glandular (0.246 +/- 0.091 pmol/g, P = 0.001) fractions, respectively.<br><br>CONCLUSION: After intake of soy milk and soy supplements, isoflavones reach exposure levels in breast tissue at which potential health effects may occur.}, }
@article {pmid20154119, year = {2010}, author = {Ayala-del-Río, HL and Chain, PS and Grzymski, JJ and Ponder, MA and Ivanova, N and Bergholz, PW and Di Bartolo, G and Hauser, L and Land, M and Bakermans, C and Rodrigues, D and Klappenbach, J and Zarka, D and Larimer, F and Richardson, P and Murray, A and Thomashow, M and Tiedje, JM}, title = {The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {7}, pages = {2304-2312}, pmid = {20154119}, issn = {1098-5336}, mesh = {Cold Temperature ; DNA, Bacterial/*chemistry/*genetics ; Freezing ; *Genome, Bacterial ; Molecular Sequence Data ; Psychrobacter/*genetics/isolation &amp; purification/physiology ; Sequence Analysis, DNA ; Siberia ; Soil Microbiology ; }, abstract = {Psychrobacter arcticus strain 273-4, which grows at temperatures as low as -10 degrees C, is the first cold-adapted bacterium from a terrestrial environment whose genome was sequenced. Analysis of the 2.65-Mb genome suggested that some of the strategies employed by P. arcticus 273-4 for survival under cold and stress conditions are changes in membrane composition, synthesis of cold shock proteins, and the use of acetate as an energy source. Comparative genome analysis indicated that in a significant portion of the P. arcticus proteome there is reduced use of the acidic amino acids and proline and arginine, which is consistent with increased protein flexibility at low temperatures. Differential amino acid usage occurred in all gene categories, but it was more common in gene categories essential for cell growth and reproduction, suggesting that P. arcticus evolved to grow at low temperatures. Amino acid adaptations and the gene content likely evolved in response to the long-term freezing temperatures (-10 degrees C to -12 degrees C) of the Kolyma (Siberia) permafrost soil from which this strain was isolated. Intracellular water likely does not freeze at these in situ temperatures, which allows P. arcticus to live at subzero temperatures.}, }
@article {pmid20149632, year = {2010}, author = {Critzer, FJ and Doyle, MP}, title = {Microbial ecology of foodborne pathogens associated with produce.}, journal = {Current opinion in biotechnology}, volume = {21}, number = {2}, pages = {125-130}, doi = {10.1016/j.copbio.2010.01.006}, pmid = {20149632}, issn = {1879-0429}, mesh = {*Ecology ; *Food Contamination ; *Food Microbiology ; Foodborne Diseases/*microbiology/*prevention &amp; control ; Fruit/*microbiology ; Humans ; Plants/*microbiology ; }, abstract = {The recent recognition of fresh fruits and vegetables as major vehicles of foodborne illness has led to increased research on mechanisms by which enteric pathogens contaminate and persist on and in this non-host environment. Interactions between foodborne pathogens and plants as well among the naturally occurring microbial communities contribute to endophytic and epiphytic colonization. Scientific findings are just beginning to elucidate the mechanisms that contribute to colonization of produce. This review addresses current knowledge as well as future research needed to increase our understanding of the microbial ecology of enteric pathogens on fruits and vegetables.}, }
@article {pmid20147218, year = {2009}, author = {Daims, H}, title = {Use of fluorescence in situ hybridization and the daime image analysis program for the cultivation-independent quantification of microorganisms in environmental and medical samples.}, journal = {Cold Spring Harbor protocols}, volume = {2009}, number = {7}, pages = {pdb.prot5253}, doi = {10.1101/pdb.prot5253}, pmid = {20147218}, issn = {1559-6095}, mesh = {Bacteria/genetics ; Biofilms ; Biomass ; Computational Biology/methods ; Ecology ; Image Processing, Computer-Assisted ; In Situ Hybridization, Fluorescence/*methods ; *Microbiological Techniques ; Plankton/metabolism ; RNA, Ribosomal/genetics/metabolism ; Software ; }, abstract = {Conventional cultivation-based methods to measure microbial abundance are unsuitable for quantifying uncultured microorganisms that constitute the majority of microbial life in most environmental or medical samples. This problem is solved by the quantification approach described here, which combines fluorescence in situ hybridization (FISH) with rRNA-targeted probes and digital image analysis. By measuring the areas of probe-labeled biomass in randomly recorded image pairs, an unbiased estimate of the relative biovolume of the population of interest can be obtained. This approach expresses abundance as "biovolume fraction" (relative to the total biovolume of the whole microbial community). This value equals the share of biochemical reaction space occupied by the quantified population and thus can be more relevant ecologically than absolute cell numbers (e.g., a few large cells can contain the same biovolume as many small cells). Another advantage lies in the complete independence of this method from the morphology of the quantified organisms. Regardless of whether the target microbes occur as single cells in plankton samples, as filaments, or as dense aggregates in biofilms, this cultivation-independent method allows the composition of complex microbial communities to be determined.}, }
@article {pmid20140610, year = {2010}, author = {Chen, J and Michel, FC and Sreevatsan, S and Morrison, M and Yu, Z}, title = {Occurrence and persistence of erythromycin resistance genes (erm) and tetracycline resistance genes (tet) in waste treatment systems on swine farms.}, journal = {Microbial ecology}, volume = {60}, number = {3}, pages = {479-486}, pmid = {20140610}, issn = {1432-184X}, mesh = {Animal Husbandry ; Animals ; Bacterial Proteins/genetics ; DNA, Bacterial/analysis/*isolation &amp; purification ; *Genes, Bacterial ; Manure/*microbiology ; Metagenome ; Methyltransferases/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Swine ; Tetracycline Resistance/*genetics ; Waste Disposal, Fluid/*methods ; }, abstract = {Animal manure from modern animal agriculture constitutes the single largest source of antibiotic resistance (AR) owing to the use of large quantities of antibiotics. After animal manure enters the environment, the AR disseminates into the environment and can pose a potentially serious threat to the health and well-being of both humans and animals. In this study, we evaluated the efficiency of three different on-farm waste treatment systems in reducing AR. Three classes of erythromycin resistance genes (erm) genes (B, F, and X) conferring resistances to macrolide-lincosamides-streptogramin B (MLS(B)) and one class of tetracycline resistance genes (tet) gene (G) conferring resistance to tetracyclines were used as models. Real-time polymerase chain reaction assays were used to determine the reservoir sizes of these AR genes present in the entire microbiome. These classes of AR genes varied considerably in abundance, with erm(B) being more predominant than erm(F), erm(X), and tet(G). These AR genes also varied in persistence in different waste treatment systems. Aerobic biofiltration reduced erm(X) more effectively than other AR genes, while mesophilic anaerobic digestion and lagoon storage did not appreciably reduce any of these AR genes. Unlike chemical pollutants, some AR genes could increase after reduction in a preceding stage of the treatment processes. Season might also affect the persistence of AR. These results indicate that AR arising from swine-feeding operations can survive typical swine waste treatment processes and thus treatments that are more effective in destructing AR on farms are required.}, }
@article {pmid20135118, year = {2010}, author = {Hatamoto, M and Ohashi, A and Imachi, H}, title = {Peptide nucleic acids (PNAs) antisense effect to bacterial growth and their application potentiality in biotechnology.}, journal = {Applied microbiology and biotechnology}, volume = {86}, number = {2}, pages = {397-402}, doi = {10.1007/s00253-009-2387-8}, pmid = {20135118}, issn = {1432-0614}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects ; Biotechnology/*methods ; Growth Inhibitors/*pharmacology ; Oligonucleotides, Antisense/*pharmacology ; Peptide Nucleic Acids/*pharmacology ; }, abstract = {Peptide nucleic acids (PNAs) are nucleic acid analogs having attractive properties such as quiet stability against nucleases and proteases, and they form strong complexes with complementary strands of DNA or RNA. Because of this attractive nature, PNA is often used in antisense technology to inhibit gene expression and microbial cell growth with high specificity. Many bacterial antisense or antiribosomal studies using PNA oligomers have been reported so far, and parameters to design effective antisense PNAs and to improve PNA cell entry for efficient inhibition of bacterial growth have been presented. However, there are still several obstacles such as low cellular uptake of PNA while applying antisense PNAs to a complex microbial community. On overcoming these problems, the PNA antisense technique might become a very attractive tool not only for controlling the microbial growth but also for further elucidating microbial ecology in complex microbial consortia. Here, we summarize and present recent studies on the development of antimicrobial PNAs targeting mRNAs and rRNAs. In addition, the application potentiality of antisense techniques in nonclinical biotechnology fields is discussed.}, }
@article {pmid20130656, year = {2010}, author = {Godoy-Vitorino, F and Goldfarb, KC and Brodie, EL and Garcia-Amado, MA and Michelangeli, F and Domínguez-Bello, MG}, title = {Developmental microbial ecology of the crop of the folivorous hoatzin.}, journal = {The ISME journal}, volume = {4}, number = {5}, pages = {611-620}, doi = {10.1038/ismej.2009.147}, pmid = {20130656}, issn = {1751-7370}, mesh = {*Aging ; Animals ; Bacteria/*classification/genetics ; Birds/genetics/growth &amp; development/*microbiology ; Cloning, Molecular ; Crop, Avian/*microbiology ; DNA, Bacterial/genetics ; Oligonucleotide Array Sequence Analysis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The hoatzin (Opisthocomus hoazin) is a South American strict folivorous bird, with a crop microbial ecosystem that ferments dietary plants. Chicks progressively become independent from the adult-fed regurgitated crop liquids, and we hypothesized that the crop bacterial ecosystem develops through ecological succession mechanisms, as they grow into adults. The aim of this work was to compare the crop bacterial community in hoatzins from three age groups: newly hatched chicks, juveniles and adults by sequencing 16S rRNA genes and using the G2 PhyloChip. Cloning yielded a total of 2123 nearly full-length sequences binned into 294 operational taxonomic units (OTUs) (with <97% homology) belonging to 7 phyla, with 91% of novel OTUs. The microarray identified a diverse bacterial community dominated by Firmicutes and Bacteroidetes, with approximately 1400 taxa grouped in 40 phyla that included those detected by cloning. In comparison with the adult, the hoatzin chick crop had a greater abundance of Flavobacteriaceae, Clostridiaceae and Lachnospiraceae but lacked phyla DSS1, Deferribacteres and Termite group 1, which were mostly present in adults. The overall community structure of the crop of the hoatzin changes with age in a complex manner, probably responding to new niches made available through dietary changes related to the transition from dependent to independent feeding.}, }
@article {pmid20127086, year = {2010}, author = {Frias, A and Manresa, A and de Oliveira, E and López-Iglesias, C and Mercade, E}, title = {Membrane vesicles: a common feature in the extracellular matter of cold-adapted antarctic bacteria.}, journal = {Microbial ecology}, volume = {59}, number = {3}, pages = {476-486}, pmid = {20127086}, issn = {1432-184X}, mesh = {Bacterial Outer Membrane Proteins/metabolism ; Cell Membrane/*ultrastructure ; Cold Temperature ; Electrophoresis, Polyacrylamide Gel ; Extracellular Space/*metabolism ; Marinobacter/*ultrastructure ; Mass Spectrometry ; Microscopy, Electron, Transmission ; Organelles/metabolism ; Proteome/metabolism ; Pseudoalteromonas/metabolism/*ultrastructure ; Shewanella/*ultrastructure ; }, abstract = {Many Gram-negative, cold-adapted bacteria from the Antarctic environment produce large amounts of extracellular matter, which has potential biotechnology applications. We examined the ultrastructure of extracellular matter from five Antarctic bacteria (Shewanella livingstonensis NF22(T), Shewanella vesiculosa M7(T), Pseudoalteromonas sp. M4.2, Psychrobacter fozii NF23(T), and Marinobacter guineae M3B(T)) by transmission electron microscopy after high-pressure freezing and freeze substitution. All analyzed extracellular matter appeared as a netlike mesh composed of a capsular polymer around cells and large numbers of membrane vesicles (MVs), which have not yet been described for members of the genera Psychrobacter and Marinobacter. MVs showed the typical characteristics described for these structures, and seemed to be surrounded by the same capsular polymer as that found around the cells. The analysis of MV proteins from Antarctic strains by SDS-PAGE showed different banding profiles in MVs compared to the outer membrane, suggesting some kind of protein sorting during membrane vesicle formation. For the psychrotolerant bacterium, S. livingstonensis NF22(T), the growth temperature seemed to influence the amount and morphology of MVs. In an initial attempt to elucidate the functions of MVs for this psychrotolerant bacterium, we conducted a proteomic analysis on membrane vesicles from S. livingstonensis NF22(T) obtained at 4 and 18 degrees C. At both temperatures, MVs were highly enriched in outer membrane proteins and periplasmic proteins related to nutrient processing and transport in Gram-negative bacteria suggesting that MVs could be related with nutrient sensing and bacterial survival. Differences were observed in the expression of some proteins depending on incubation temperature but further studies will be necessary to define their roles and implications in the survival of bacteria in the extreme Antarctic environment.}, }
@article {pmid20112014, year = {2010}, author = {Polo, A and Cappitelli, F and Brusetti, L and Principi, P and Villa, F and Giacomucci, L and Ranalli, G and Sorlini, C}, title = {Feasibility of removing surface deposits on stone using biological and chemical remediation methods.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {1-14}, pmid = {20112014}, issn = {1432-184X}, mesh = {Biodegradation, Environmental ; Biotechnology/*methods ; Biotin/*pharmacology ; Calcium Carbonate/chemistry ; Chlorophyta/isolation &amp; purification ; Cyanobacteria/isolation &amp; purification ; Disinfectants/*pharmacology ; *Environmental Microbiology ; Fungi/isolation &amp; purification ; *Sculpture ; Sulfur-Reducing Bacteria/*metabolism ; }, abstract = {The study was conducted on alterations found on stone artwork and integrates microbial control and a biotechnological method for the removal of undesirable chemical substances. The Demetra and Cronos sculptures are two of 12 stone statues decorating the courtyard of the Buonconsiglio Castle in Trento (Italy). An initial inspection of the statues revealed putative black crusts and highlighted the microbial contamination causing discoloration. In 2006, the Cultural Heritage Superintendence of Trento commissioned us to study and remove these chemical and biological stains. Stereomicroscopy characterised the stone of the sculptures as oolitic limestone, and infrared analyses confirmed the presence of black crusts. To remove the black crusts, we applied a remediation treatment of sulphate-reducing bacteria, which removes the chemical alteration but preserves the original stone and the patina noble. Using traditional and biomolecular methods, we studied the putative microbial contamination and confirmed the presence of biodeteriogens and chose biocide Biotin N for the removal of the agents causing the discolouration. Denaturing gradient gel electrophoresis fluorescent in situ hybridisation established that Cyanobacteria and green algae genera were responsible for the green staining whereas the black microbial contamination was due to dematiaceous fungi. After the biocide Biotin N treatment, we applied molecular methods and demonstrated that the Cyanobacteria, and most of the green algae and dematiaceous fungi, had been efficiently removed. The reported case study reveals that conservators can benefit from an integrated biotechnological approach aimed at the biocleaning of chemical alterations and the abatement of biodeteriogens.}, }
@article {pmid20107781, year = {2010}, author = {Baffico, GD}, title = {Epilithic algae distribution along a chemical gradient in a naturally acidic river, Río Agrio (Patagonia, Argentina).}, journal = {Microbial ecology}, volume = {59}, number = {3}, pages = {533-545}, pmid = {20107781}, issn = {1432-184X}, mesh = {Argentina ; Biodiversity ; Biomass ; Eukaryota/*growth &amp; development ; Hydrogen-Ion Concentration ; Phosphorus/chemistry ; Rivers/*chemistry/*microbiology ; *Water Microbiology ; }, abstract = {The epilithic algae distribution along a pH gradient and the relationship between the chemical gradient and biomass development were studied in Río Agrio, a naturally acidic river located in Patagonia (Argentina). The epilithic community was monitored during the summer of three consecutive years in sites located above and below the entrance of tributaries. The epilithic community showed differences between sites based on the chemical composition of the water and the precipitates that appear on the streambed of the river. The lowest biomass, diversity, and number of species were found at the most extreme part of the river in terms of pH (ca. 2) and element concentrations. Euglena mutabilis was the dominant species in this section of the river. As pH increased (ca. 3), the community changed to be dominated by filamentous green algae (Ulothrix spp., Mougeotia sp., Klebsormidium sp.) showing luxuriant growths in terms of biomass. With the inflow of a neutral tributary, the pH of Río Agrio increased above 3, and the precipitates of orange-red iron hydroxides appeared. The algal community was not affected by these precipitates or the low P concentrations, along the next 30 km of river downstream from this site. The apparent physical stress that the precipitates impose on algae is in fact a dynamic reservoir of P because diel cycle of Fe could be promoting precipitation and redissolution processes that binds and releases P from these precipitates. Where the pH increased above 6, precipitates of aluminum hydroxides appeared. At this site, the epilithic biomass and density decreased, some algae species changed, but the diversity and the number of species in general remained consistent with the upstream values. The physical stress of the Al precipitates on the algae is added to the chemical stress that represents the sequestering of P in these precipitates that are not redissolved, resulting P a limiting nutrient for algae growth.}, }
@article {pmid20107780, year = {2010}, author = {Yutthammo, C and Thongthammachat, N and Pinphanichakarn, P and Luepromchai, E}, title = {Diversity and activity of PAH-degrading bacteria in the phyllosphere of ornamental plants.}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {357-368}, pmid = {20107780}, issn = {1432-184X}, mesh = {Air Pollutants/*metabolism ; Bacteria/classification/genetics/*metabolism ; *Biodiversity ; DNA, Bacterial/genetics ; Electrophoresis, Polyacrylamide Gel ; Plant Leaves/chemistry/microbiology ; Plants/metabolism/*microbiology ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Thailand ; }, abstract = {Phyllosphere bacteria on ornamental plants were characterized based on their diversity and activity towards the removal of polycyclic aromatic hydrocarbons (PAHs), the major air pollutants in urban area. The amounts of PAH-degrading bacteria were about 1-10% of the total heterotrophic phyllosphere populations and consisted of diverse bacterial species such as Acinetobacter, Pseudomonas, Pseudoxanthomonas, Mycobacterium, and uncultured bacteria. Bacterial community structures analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis from each plant species showed distinct band patterns. The uniqueness of these phyllosphere bacterial communities was partly due to the variation in leaf morphology and chemical properties of ornamental plants. The PAH degradation activity of these bacteria was monitored in gas-tight systems containing sterilized or unsterilized leaves. The results indicated that phyllosphere bacteria on unsterilized leaves were able to enhance the activity of leaves for phenanthrene removal. When compared between plant species, phenanthrene removal efficiency corresponded to the size of phenanthrene-degrading bacteria. In addition, phyllosphere bacteria on Wrightia religiosa were able to reduce other PAHs such as acenaphthylene, acenaphthene, and fluorine in 60-ml glass vials and in a 14-l glass chamber. Thus, phyllosphere bacteria on ornamental plants may play an important role in natural attenuation of airborne PAHs in urban areas.}, }
@article {pmid20098985, year = {2010}, author = {Butler, CS and Nerenberg, R}, title = {Performance and microbial ecology of air-cathode microbial fuel cells with layered electrode assemblies.}, journal = {Applied microbiology and biotechnology}, volume = {86}, number = {5}, pages = {1399-1408}, doi = {10.1007/s00253-009-2421-x}, pmid = {20098985}, issn = {1432-0614}, mesh = {Bacteria/*metabolism ; Bioelectric Energy Sources/*microbiology ; Electrodes ; Fluorocarbon Polymers/metabolism ; Geobacter/metabolism ; Graphite/metabolism ; Membranes, Artificial ; Oxygen/metabolism ; Polytetrafluoroethylene/metabolism ; }, abstract = {Microbial fuel cells (MFCs) can be built with layered electrode assemblies, where the anode, proton exchange membrane (PEM), and cathode are pressed into a single unit. We studied the performance and microbial community structure of MFCs with layered assemblies, addressing the effect of materials and oxygen crossover on the community structure. Four MFCs with layered assemblies were constructed using Nafion or Ultrex PEMs and a plain carbon cloth electrode or a cathode with an oxygen-resistant polytetrafluoroethylene diffusion layer. The MFC with Nafion PEM and cathode diffusion layer achieved the highest power density, 381 mW/m(2) (20 W/m(3)). The rates of oxygen diffusion from cathode to anode were three times higher in the MFCs with plain cathodes compared to those with diffusion-layer cathodes. Microsensor studies revealed little accumulation of oxygen within the anode cloth. However, the abundance of bacteria known to use oxygen as an electron acceptor, but not known to have exoelectrogenic activity, was greater in MFCs with plain cathodes. The MFCs with diffusion-layer cathodes had high abundance of exoelectrogenic bacteria within the genus Geobacter. This work suggests that cathode materials can significantly influence oxygen crossover and the relative abundance of exoelectrogenic bacteria on the anode, while PEM materials have little influence on anode community structure. Our results show that oxygen crossover can significantly decrease the performance of air-cathode MFCs with layered assemblies, and therefore limiting crossover may be of particular importance for these types of MFCs.}, }
@article {pmid20097811, year = {2010}, author = {Coci, M and Nicol, GW and Pilloni, GN and Schmid, M and Kamst-van Agterveld, MP and Bodelier, PL and Laanbroek, HJ}, title = {Quantitative assessment of ammonia-oxidizing bacterial communities in the epiphyton of submerged macrophytes in shallow lakes.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {6}, pages = {1813-1821}, pmid = {20097811}, issn = {1098-5336}, mesh = {Ammonia/*metabolism ; Bacteria/classification/*isolation &amp; purification/*metabolism ; Chara/*microbiology ; Cluster Analysis ; Colony Count, Microbial/methods ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Fresh Water ; Molecular Sequence Data ; Netherlands ; Nucleic Acid Denaturation ; Oxidation-Reduction ; Phylogeny ; Polymerase Chain Reaction/*methods ; Potamogetonaceae/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {In addition to the benthic and pelagic habitats, the epiphytic compartment of submerged macrophytes in shallow freshwater lakes offers a niche to bacterial ammonia-oxidizing communities. However, the diversity, numbers, and activity of epiphytic ammonia-oxidizing bacteria have long been overlooked. In the present study, we analyzed quantitatively the epiphytic communities of three shallow lakes by a potential nitrification assay and by quantitative PCR of 16S rRNA genes. On the basis of the m(2) of the lake surface, the gene copy numbers of epiphytic ammonia oxidizers were not significantly different from those in the benthic and pelagic compartments. The potential ammonia-oxidizing activities measured in the epiphytic compartment were also not significantly different from the activities determined in the benthic compartment. No potential ammonia-oxidizing activities were observed in the pelagic compartment. No activity was detected in the epiphyton of Chara aspera, the dominant submerged macrophyte in Lake Nuldernauw in The Netherlands. The presence of ammonia-oxidizing bacterial cells in the epiphyton of Potamogeton pectinatus was also demonstrated by fluorescent in situ hybridization microscopy images. By comparing the community composition as assessed by the 16S rRNA gene PCR-denaturing gradient gel electrophoresis approach, it was concluded that the epiphytic ammonia-oxidizing communities consisted of cells that were also present in the benthic and pelagic compartments. Of the environmental parameters examined, only the water retention time, the Kjeldahl nitrogen content, and the total phosphorus content correlated with potential ammonia-oxidizing activities. None of these parameters correlated with the numbers of gene copies related to ammonia-oxidizing betaproteobacteria.}, }
@article {pmid20097806, year = {2010}, author = {De Schamphelaire, L and Cabezas, A and Marzorati, M and Friedrich, MW and Boon, N and Verstraete, W}, title = {Microbial community analysis of anodes from sediment microbial fuel cells powered by rhizodeposits of living rice plants.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {6}, pages = {2002-2008}, pmid = {20097806}, issn = {1098-5336}, mesh = {Archaea/*classification/isolation &amp; purification ; Bacteria/*classification/isolation &amp; purification ; Bioelectric Energy Sources/*microbiology ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrodes/*microbiology ; Genes, rRNA ; *Metagenomics ; Molecular Sequence Data ; Oryza/*metabolism/*microbiology ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {By placing the anode of a sediment microbial fuel cell (SMFC) in the rhizosphere of a rice plant, root-excreted rhizodeposits can be microbially oxidized with concomitant current generation. Here, various molecular techniques were used to characterize the composition of bacterial and archaeal communities on such anodes, as influenced by electrical circuitry, sediment matrix, and the presence of plants. Closed-circuit anodes in potting soil were enriched with Desulfobulbus-like species, members of the family Geobacteraceae, and as yet uncultured representatives of the domain Archaea.}, }
@article {pmid20094715, year = {2010}, author = {De Schryver, P and Sinha, AK and Kunwar, PS and Baruah, K and Verstraete, W and Boon, N and De Boeck, G and Bossier, P}, title = {Poly-beta-hydroxybutyrate (PHB) increases growth performance and intestinal bacterial range-weighted richness in juvenile European sea bass, Dicentrarchus labrax.}, journal = {Applied microbiology and biotechnology}, volume = {86}, number = {5}, pages = {1535-1541}, doi = {10.1007/s00253-009-2414-9}, pmid = {20094715}, issn = {1432-0614}, mesh = {3-Hydroxybutyric Acid/metabolism ; Animal Feed ; Animals ; Aquaculture/*methods ; Bass/*growth &amp; development/microbiology ; Body Weight ; Hydrogen-Ion Concentration ; Hydroxybutyrates/*pharmacology ; Intestines/microbiology ; Polyesters/*pharmacology ; Survival Analysis ; }, abstract = {The bacterial storage polymer poly-beta-hydroxybutyrate (PHB) has the potential to be used as an alternative anti-infective strategy for aquaculture rearing. In this research, the effects of (partially) replacing the feed of European sea bass juveniles with PHB were investigated. During a 6-week trial period, the PHB showed the ability to act as an energy source for the fish. This indicated that PHB was degraded and used during gastrointestinal passage. The gut pH decreased from 7.7 to 7.2 suggesting that the presence of PHB in the gut led to the increased production of (short-chain fatty) acids. The diets supplemented with 2% and 5% PHB (w/w) induced a gain of the initial fish weight with a factor 2.4 and 2.7, respectively, relative to a factor 2.2 in the normal feed treatment. Simultaneously, these treatments showed the highest bacterial range-weighted richness in the fish intestine. Based on molecular analysis, higher dietary PHB levels induced larger changes in the bacterial community composition. From our results, it seems that PHB can have a beneficial effect on fish growth performance and that the intestinal bacterial community structure may be closely related to this phenomenon.}, }
@article {pmid20093474, year = {2010}, author = {Harris, SR and Feil, EJ and Holden, MT and Quail, MA and Nickerson, EK and Chantratita, N and Gardete, S and Tavares, A and Day, N and Lindsay, JA and Edgeworth, JD and de Lencastre, H and Parkhill, J and Peacock, SJ and Bentley, SD}, title = {Evolution of MRSA during hospital transmission and intercontinental spread.}, journal = {Science (New York, N.Y.)}, volume = {327}, number = {5964}, pages = {469-474}, pmid = {20093474}, issn = {1095-9203}, support = {076964/WT_/Wellcome Trust/United Kingdom ; /DH_/Department of Health/United Kingdom ; }, mesh = {Asia/epidemiology ; Bacterial Typing Techniques ; Cross Infection/epidemiology/*microbiology/transmission ; Europe/epidemiology ; Evolution, Molecular ; *Genome, Bacterial ; Genomics/methods ; Humans ; Likelihood Functions ; Methicillin-Resistant Staphylococcus aureus/*classification/*genetics/isolation &amp; purification ; Molecular Epidemiology ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; South America/epidemiology ; Staphylococcal Infections/epidemiology/*microbiology/transmission ; Time Factors ; United States/epidemiology ; }, abstract = {Current methods for differentiating isolates of predominant lineages of pathogenic bacteria often do not provide sufficient resolution to define precise relationships. Here, we describe a high-throughput genomics approach that provides a high-resolution view of the epidemiology and microevolution of a dominant strain of methicillin-resistant Staphylococcus aureus (MRSA). This approach reveals the global geographic structure within the lineage, its intercontinental transmission through four decades, and the potential to trace person-to-person transmission within a hospital environment. The ability to interrogate and resolve bacterial populations is applicable to a range of infectious diseases, as well as microbial ecology.}, }
@article {pmid20091406, year = {2010}, author = {Ren, Y and Strobel, G and Sears, J and Park, M}, title = {Geobacillus sp., a thermophilic soil bacterium producing volatile antibiotics.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {130-136}, pmid = {20091406}, issn = {1432-184X}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Anti-Infective Agents/*metabolism ; Antibiosis ; DNA, Bacterial/genetics ; Geobacillus/classification/genetics/*isolation &amp; purification/metabolism ; Hot Temperature ; Montana ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Volatile Organic Compounds/*metabolism ; }, abstract = {Geobacillus, a bacterial genus, is represented by over 25 species of Gram-positive isolates from various man-made and natural thermophilic areas around the world. An isolate of this genus (M-7) has been acquired from a thermal area near Yellowstone National Park, MT and partially characterized. The cells of this organism are globose (ca. 0.5 mu diameter), and they are covered in a matrix capsule which gives rise to elongate multicelled bacilliform structures (ranging from 3 to 12 mum) as seen by light and atomic force microscopy, respectively. The organism produces unique petal-shaped colonies (undulating margins) on nutrient agar, and it has an optimum pH of 7.0 and an optimum temperature range of 55-65 degrees C. The partial 16S rRNA sequence of this organism has 97% similarity with Geobacillus stearothermophilus, one of its closest relatives genetically. However, uniquely among all members of this genus, Geobacillus sp. (M-7) produces volatile organic substances (VOCs) that possess potent antibiotic activities. Some of the more notable components of the VOCs are benzaldehyde, acetic acid, butanal, 3-methyl-butanoic acid, 2-methyl-butanoic acid, propanoic acid, 2-methyl-, and benzeneacetaldehyde. An exposure of test organisms such as Aspergillus fumigatus, Botrytis cinerea, Verticillium dahliae, and Geotrichum candidum produced total inhibition of growth on a 48-h exposure to Geobacillus sp.(M-7) cells (ca.10(7)) and killing at a 72-h exposure at higher bacterial cell concentrations. A synthetic mixture of those available volatile compounds, at the ratios occurring in Geobacillus sp. (M-7), mimicked the bioactivity of this organism.}, }
@article {pmid20090946, year = {2010}, author = {Yoder-Himes, DR and Konstantinidis, KT and Tiedje, JM}, title = {Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics.}, journal = {PloS one}, volume = {5}, number = {1}, pages = {e8724}, pmid = {20090946}, issn = {1932-6203}, support = {R21 HL087833/HL/NHLBI NIH HHS/United States ; R21HL087833/HL/NHLBI NIH HHS/United States ; }, mesh = {Burkholderia/genetics/*pathogenicity ; Burkholderia Infections/*drug therapy/microbiology ; *Gene Expression Profiling ; Genes, Bacterial ; Humans ; Oligonucleotide Array Sequence Analysis ; Virulence ; }, abstract = {BACKGROUND: Burkholderia cenocepacia is an endemic soil dweller and emerging opportunistic pathogen in patients with cystic fibrosis (CF). The identification of virulence factors and potential therapeutic targets has been hampered by the genomic diversity within the species as many factors are not shared among the pathogenic members of the species.<br><br>In this study, global identification of putative virulence factors was performed by analyzing the transcriptome of two related strains of B. cenocepacia (one clinical, one environmental) under conditions mimicking cystic fibrosis sputum versus soil. Soil is a natural reservoir for this species; hence, genes induced under CF conditions relative to soil may represent adaptations that have occurred in clinical strains. Under CF conditions, several genes encoding proteins thought to be involved in virulence were induced and many new ones were identified. Our analysis, in combination with previous studies, reveals 458 strain-specific genes, 126 clinical-isolate-specific, and at least four species-specific genes that are induced under CF conditions. The chromosomal distribution of the induced genes was disproportionate to the size of the chromosome as genes expressed under soil conditions by both strains were more frequent on the second chromosome and those differentially regulated between strains were more frequent on the third chromosome. Conservation of these induced genes was established using the 11 available Bcc genome sequences to indicate whether potential therapeutic targets would be species-wide.<br><br>CONCLUSIONS/SIGNIFICANCE: Comparative transcriptomics is a useful way to identify new potential virulence factors and therapeutic targets for pathogenic bacteria. We identified eight genes induced under CF conditions that were also conserved in the Bcc and may constitute particularly attractive therapeutic targets due to their signal sequence, predicted cellular location, and homology to known therapeutic targets.}, }
@article {pmid20087461, year = {2009}, author = {Faith, DP and Lozupone, CA and Nipperess, D and Knight, R}, title = {The cladistic basis for the phylogenetic diversity (PD) measure links evolutionary features to environmental gradients and supports broad applications of microbial ecology's "phylogenetic beta diversity" framework.}, journal = {International journal of molecular sciences}, volume = {10}, number = {11}, pages = {4723-4741}, pmid = {20087461}, issn = {1422-0067}, mesh = {Bacteria/*classification ; Biological Evolution ; Ecological and Environmental Phenomena ; *Models, Biological ; *Phylogeny ; }, abstract = {The PD measure of phylogenetic diversity interprets branch lengths cladistically to make inferences about feature diversity. PD calculations extend conventional species-level ecological indices to the features level. The "phylogenetic beta diversity" framework developed by microbial ecologists calculates PD-dissimilarities between community localities. Interpretation of these PD-dissimilarities at the feature level explains the framework's success in producing ordinations revealing environmental gradients. An example gradients space using PD-dissimilarities illustrates how evolutionary features form unimodal response patterns to gradients. This features model supports new application of existing species-level methods that are robust to unimodal responses, plus novel applications relating to climate change, commercial products discovery, and community assembly.}, }
@article {pmid20082072, year = {2010}, author = {Pleydell, E and Rogers, L and Kwan, E and French, N}, title = {Evidence for the clustering of antibacterial resistance phenotypes of enterococci within integrated poultry companies.}, journal = {Microbial ecology}, volume = {59}, number = {4}, pages = {678-688}, pmid = {20082072}, issn = {1432-184X}, mesh = {Animals ; Bayes Theorem ; Cluster Analysis ; Consumer Product Safety ; *Drug Resistance, Bacterial ; Enterococcus/drug effects/*genetics/isolation &amp; purification ; *Food Contamination ; *Food Microbiology ; Meat-Packing Industry ; Microbial Sensitivity Tests ; Models, Statistical ; New Zealand ; Phenotype ; Poultry/*microbiology ; }, abstract = {From July to December 2006, a panel of 401 enterococci was isolated from carcass rinse samples collected in five poultry processing plants in New Zealand. Agar diffusion assays for nine antibacterial drugs were used to obtain a resistance phenotype for each isolate. Hierarchical clustering techniques and diversity indices showed a high diversity of resistance phenotypes within each plant, with populations of Enterococcus faecalis showing greater heterogeneity than Enterococcus faecium. Bayesian modelling identified three clusters of phenotype patterns within the panel: the E. faecium isolates showed a high probability of containing two distinct clusters, whilst the E. faecalis isolates all grouped together to form the third cluster. The validity of these three clusters was examined using pairwise fixation indices and analysis of variance. Comparing the three clusters to the structure of the participating companies showed that resistance phenotypes for E. faecium isolated from processing plants that were geographically separated but were operated by the same integrated poultry company were more similar than E. faecium isolated from unconnected companies. Company-level management factors, such as the routine use of antibacterial drugs and the genetic line of birds reared, mirrored the structure of these clusters, thus indicating that company-level factors were the dominant selective pressures upon resistance phenotypes across all operating units within these integrated poultry companies.}, }
@article {pmid20082071, year = {2010}, author = {Bondarenko, O and Rahman, PK and Rahman, TJ and Kahru, A and Ivask, A}, title = {Effects of rhamnolipids from Pseudomonas aeruginosa DS10-129 on luminescent bacteria: toxicity and modulation of cadmium bioavailability.}, journal = {Microbial ecology}, volume = {59}, number = {3}, pages = {588-600}, pmid = {20082071}, issn = {1432-184X}, mesh = {Absorption ; Bacteria/*drug effects ; Biodegradation, Environmental ; Biological Availability ; Cadmium/*metabolism ; Cell Membrane Permeability ; DNA, Bacterial/genetics ; Glycolipids/*toxicity ; Luminescence ; Phylogeny ; Pseudomonas aeruginosa/*chemistry/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Toxicity Tests ; }, abstract = {In this study, the mixture of mono- and di-rhamnolipids produced by Pseudomonas aeruginosa DS10-129 was characterized for its toxicity and modulatory effects on Cd availability to different bacteria. Gram-negative naturally bioluminescent Vibrio fischeri and recombinant bioluminescent Pseudomonas fluorescens, P. aeruginosa, Escherichia coli, and Gram-positive Bacillus subtilis were used as model organisms. Rhamnolipids reduced the bioluminescence of these bacteria in less than a second of exposure even in relatively low concentrations (30-min EC(50) 45-167 mg l(-1)). Toxicity of Cd to Gram-negative bacteria (30-min EC(50) values 0.16 mg l(-1) for E. coli, 0.96 mg l(-1) for P. fluorescens, and 4.4 mg l(-1) for V. fischeri) was remarkably (up to 10-fold) reduced in the presence of 50 mg l(-1) rhamnolipids. Interestingly, the toxicity of Cd to Gram-positive B. subtilis (30-min EC(50) value 0.49 mg l(-1)) was not affected by rhamnolipids. Rhamnolipids had an effect on desorption of Cd from soil: 40 mg l(-1) rhamnolipids increased the water-extracted fraction of Cd twice compared with untreated control. However, this additionally desorbed fraction of Cd remained bound with rhamnolipids and was not available to bacteria. Hence, in carefully chosen concentrations (still effectively complexing heavy metals but not yet toxic to soil bacteria), rhamnolipids could be applied in remediation of polluted areas.}, }
@article {pmid20082070, year = {2010}, author = {Yang, C and Hamel, C and Schellenberg, MP and Perez, JC and Berbara, RL}, title = {Diversity and functionality of arbuscular mycorrhizal fungi in three plant communities in semiarid Grasslands National Park, Canada.}, journal = {Microbial ecology}, volume = {59}, number = {4}, pages = {724-733}, pmid = {20082070}, issn = {1432-184X}, mesh = {*Biodiversity ; Biomass ; Canada ; DNA, Fungal/analysis ; Fatty Acids/analysis ; Mycorrhizae/chemistry/*classification/genetics ; Phospholipids/analysis ; Phylogeny ; Plant Roots/microbiology ; Poaceae/*microbiology ; Soil/analysis ; *Soil Microbiology ; Symbiosis ; Time Factors ; }, abstract = {Septate endophytes proliferating in the roots of grasslands' plants shed doubts on the importance of arbuscular mycorrhizal (AM) symbioses in dry soils. The functionality and diversity of the AM symbioses formed in four replicates of three adjacent plant communities (agricultural, native, and restored) in Grasslands National Park, Canada were assessed in periods of moisture sufficiency and deficiency typical of early and late summer in the region. The community structure of AM fungi, as determined by polymerase chain reaction-denaturing gradient gel electrophoresis, varied with sampling time and plant community. Soil properties other than soil moisture did not change significantly with sampling time. The DNA sequences dominating AM extraradical networks in dry soil apparently belonged to rare taxa unreported in GenBank. DNA sequences of Glomus viscosum, Glomus mosseae, and Glomus hoi were dominant under conditions of moisture sufficiency. In total, nine different AM fungal sequences were found suggesting a role for the AM symbioses in semiarid areas. Significant positive linear relationships between plant P and N concentrations and active extraradical AM fungal biomass, estimated by the abundance of the phospholipid fatty acid marker 16:1 omega 5, existed under conditions of moisture sufficiency, but not under dry conditions. Active extraradical AM fungal biomass had significantly positive linear relationship with the abundance of two early season grasses, Agropyron cristatum (L.) Gaertn. and Koeleria gracilis Pers., but no relationship was found under dry conditions. The AM symbioses formed under conditions of moisture sufficiency typical of early summer at this location appear to be important for the nutrition of grassland plant communities, but no evidence of mutualism was found under the dry conditions of late summer.}, }
@article {pmid20077005, year = {2011}, author = {Plasencia, A and Bañeras, L and Llirós, M and Casamayor, EO and Borrego, C}, title = {Maintenance of previously uncultured freshwater archaea from anoxic waters under laboratory conditions.}, journal = {Antonie van Leeuwenhoek}, volume = {99}, number = {2}, pages = {403-408}, doi = {10.1007/s10482-010-9412-x}, pmid = {20077005}, issn = {1572-9699}, mesh = {Anaerobiosis ; Archaea/classification/genetics/*growth &amp; development/*isolation &amp; purification ; Biodiversity ; Cluster Analysis ; Culture Media/chemistry ; DNA Fingerprinting ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Fresh Water/*microbiology ; Hypoxia ; Microbiological Techniques/*methods ; Molecular Sequence Data ; Nucleic Acid Denaturation ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Culture conditions for the maintenance of previously uncultured members of the Archaea thriving in anoxic water layers of stratified freshwater lakes are described. The proposed enrichment conditions, based on the use of defined medium composition and the maintenance of anoxia, have been proven effective for the maintenance of the archaeal community with virtually no changes over time for periods up to 6 months as revealed by a PCR-DGGE analysis. Phylotypes belonging to groups poorly represented in culture collections such as the Deep-Sea Hydrothermal Vent Euryarchaeota (DHVE) and the Miscellaneous Crenarchaeotic Group (MCG) were maintained and selectively enriched when compared to the correspondent indigenous planktonic archaeal community.}, }
@article {pmid20074323, year = {2010}, author = {Glad, T and Bernhardsen, P and Nielsen, KM and Brusetti, L and Andersen, M and Aars, J and Sundset, MA}, title = {Bacterial diversity in faeces from polar bear (Ursus maritimus) in Arctic Svalbard.}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {10}, pmid = {20074323}, issn = {1471-2180}, mesh = {Animals ; Bacteria/classification/*genetics ; *Biodiversity ; Feces/microbiology ; Female ; Gene Library ; Male ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; Svalbard ; Ursidae/*microbiology ; }, abstract = {BACKGROUND: Polar bears (Ursus maritimus) are major predators in the Arctic marine ecosystem, feeding mainly on seals, and living closely associated with sea ice. Little is known of their gut microbial ecology and the main purpose of this study was to investigate the microbial diversity in faeces of polar bears in Svalbard, Norway (74-81 degrees N, 10-33 degrees E). In addition the level of blaTEM alleles, encoding ampicillin resistance (ampr) were determined. In total, ten samples were collected from ten individual bears, rectum swabs from five individuals in 2004 and faeces samples from five individuals in 2006.<br><br>RESULTS: A 16S rRNA gene clone library was constructed, and all sequences obtained from 161 clones showed affiliation with the phylum Firmicutes, with 160 sequences identified as Clostridiales and one sequence identified as unclassified Firmicutes. The majority of the sequences (70%) were affiliated with the genus Clostridium. Aerobic heterotrophic cell counts on chocolate agar ranged between 5.0 x 10(4) to 1.6 x 10(6) colony forming units (cfu)/ml for the rectum swabs and 4.0 x 10(3) to 1.0 x 10(5) cfu/g for the faeces samples. The proportion of ampr bacteria ranged from 0% to 44%. All of 144 randomly selected ampr isolates tested positive for enzymatic beta-lactamase activity. Three % of the ampr isolates from the rectal samples yielded positive results when screened for the presence of blaTEM genes by PCR. BlaTEM alleles were also detected by PCR in two out of three total faecal DNA samples from polar bears.<br><br>CONCLUSION: The bacterial diversity in faeces from polar bears in their natural environment in Svalbard is low compared to other animal species, with all obtained clones affiliating to Firmicutes. Furthermore, only low levels of blaTEM alleles were detected in contrast to their increasing prevalence in some clinical and commensal bacterial populations.}, }
@article {pmid20060292, year = {2010}, author = {Zhang, Y and Henriet, JP and Bursens, J and Boon, N}, title = {Stimulation of in vitro anaerobic oxidation of methane rate in a continuous high-pressure bioreactor.}, journal = {Bioresource technology}, volume = {101}, number = {9}, pages = {3132-3138}, doi = {10.1016/j.biortech.2009.11.103}, pmid = {20060292}, issn = {1873-2976}, mesh = {Anaerobiosis ; Bioreactors/*microbiology ; Methane/*metabolism ; Oxidation-Reduction ; *Pressure ; Sulfides/metabolism ; }, abstract = {Anaerobic oxidation of methane coupled to sulphate reduction (SR-AOM) prevents oceanic methane emissions and is considered as a major environmental process in the deep-sea sediments. To stimulate in vitro SR-AOM activity, we designed a (continuous) high-pressure bioreactor system. Fed-batch mode incubations showed that the elevated methane pressure stimulated SR-AOM activity: when the methane pressure increased from 1 to 4.5 to 8 MPa, the initial SR-AOM activity increased from 3.46 to 8.64 to 9.22 micromol sulphide production/g(dw)/day; the apparent affinity (K(m)) for methane was 37 mM. However, in each fed-batch mode incubation, there was an inhibitory effect observed after 2 days, probably due to the accumulation of sulphide and the increase of pH. When the reactor was operated in a continuous mode, the SR-AOM activity was constantly increasing within 18 days at both 1 and 8 MPa pressures.}, }
@article {pmid20059547, year = {2010}, author = {Janczyk, P and Pieper, R and Smidt, H and Souffrant, WB}, title = {Effect of alginate and inulin on intestinal microbial ecology of weanling pigs reared under different husbandry conditions.}, journal = {FEMS microbiology ecology}, volume = {72}, number = {1}, pages = {132-142}, doi = {10.1111/j.1574-6941.2009.00826.x}, pmid = {20059547}, issn = {1574-6941}, mesh = {Alginates/*administration &amp; dosage ; Animal Feed/analysis ; Animal Husbandry ; Animals ; Bacteria/genetics/*growth &amp; development/isolation &amp; purification ; Cecum/chemistry/microbiology ; Colon/chemistry/microbiology ; Colony Count, Microbial ; Enterococcaceae/genetics/growth &amp; development/isolation &amp; purification ; Genes, rRNA ; Glucuronic Acid/administration &amp; dosage ; Hexuronic Acids/administration &amp; dosage ; Hydrogen-Ion Concentration ; Ileum/chemistry/microbiology ; Intestines/chemistry/*microbiology ; Inulin/*administration &amp; dosage ; Lactobacillus/genetics/growth &amp; development/isolation &amp; purification ; *Prebiotics ; Swine/*microbiology ; Weaning ; Yeasts/genetics/*growth &amp; development/isolation &amp; purification ; }, abstract = {The effects of inulin and alginate on intestinal microbial ecophysiology were investigated in piglets fed a diet (C) with 0.1% alginate (C+A) or 1.5% inulin (C+I) from weaning at day 28. The experiment was performed at an experimental farm (EF) and a commercial farm (CF). Digesta was collected from the ileum, caecum and colon of four piglets from each group on days 29, 30, 33 and 39. The metabolite concentrations changed with age. Colonic and caecal metabolites were affected by prebiotic treatment. Changes in microbiota composition were assessed by cultivation and denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. Enterococci increased in C+A at EF and decreased in C+I at both farms. Lactobacilli decreased in all segments in the experimental groups on days 30 and 33. Yeasts in C+I were five times lower at CF than at EF on day 39. The richness and diversity of DGGE profiles increased in the experimental groups. The evenness of colon digesta-derived DGGE profiles was higher in the experimental groups than in C and this situation was reversed in the distal small intestine. Multivariate redundancy analysis confirmed the recorded effects. In summary, both prebiotics affected the intestinal microbiota, and the changes were more pronounced at the CF.}, }
@article {pmid20055983, year = {2010}, author = {Vitali, B and Ndagijimana, M and Cruciani, F and Carnevali, P and Candela, M and Guerzoni, ME and Brigidi, P}, title = {Impact of a synbiotic food on the gut microbial ecology and metabolic profiles.}, journal = {BMC microbiology}, volume = {10}, number = {}, pages = {4}, pmid = {20055983}, issn = {1471-2180}, mesh = {Adult ; Bifidobacterium/genetics/isolation &amp; purification ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Feces/chemistry/microbiology ; Female ; *Functional Food ; Gas Chromatography-Mass Spectrometry ; Gastrointestinal Tract/metabolism/*microbiology ; Humans ; Lactobacillus helveticus/genetics/isolation &amp; purification ; Male ; *Metabolome ; Middle Aged ; Oligosaccharides/*metabolism ; *Probiotics ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {BACKGROUND: The human gut harbors a diverse community of microorganisms which serve numerous important functions for the host wellbeing. Functional foods are commonly used to modulate the composition of the gut microbiota contributing to the maintenance of the host health or prevention of disease. In the present study, we characterized the impact of one month intake of a synbiotic food, containing fructooligosaccharides and the probiotic strains Lactobacillus helveticus Bar13 and Bifidobacterium longum Bar33, on the gut microbiota composition and metabolic profiles of 20 healthy subjects.<br><br>RESULTS: The synbiotic food did not modify the overall structure of the gut microbiome, as indicated by Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE). The ability of the probiotic L. helveticus and B. longum strains to pass through the gastrointestinal tract was hypothesized on the basis of real-time PCR data. In spite of a stable microbiota, the intake of the synbiotic food resulted in a shift of the fecal metabolic profiles, highlighted by the Gas Chromatography Mass Spectrometry Solid Phase Micro-Extraction (GC-MS/SPME) analysis. The extent of short chain fatty acids (SCFA), ketones, carbon disulfide and methyl acetate was significantly affected by the synbiotic food consumption. Furthermore, the Canonical discriminant Analysis of Principal coordinates (CAP) of GC-MS/SPME profiles allowed a separation of the stool samples recovered before and after the consumption of the functional food.<br><br>CONCLUSION: In this study we investigated the global impact of a dietary intervention on the gut ecology and metabolism in healthy humans. We demonstrated that the intake of a synbiotic food leads to a modulation of the gut metabolic activities with a maintenance of the gut biostructure. In particular, the significant increase of SCFA, ketones, carbon disulfide and methyl acetate following the feeding period suggests potential health promoting effects of the synbiotic food.}, }
@article {pmid21576878, year = {2010}, author = {Okabe, S and Oshiki, M and Kamagata, Y and Yamaguchi, N and Toyofuku, M and Yawata, Y and Tashiro, Y and Nomura, N and Ohta, H and Ohkuma, M and Hiraishi, A and Minamisawa, K}, title = {A great leap forward in microbial ecology.}, journal = {Microbes and environments}, volume = {25}, number = {4}, pages = {230-240}, doi = {10.1264/jsme2.me10178}, pmid = {21576878}, issn = {1347-4405}, mesh = {Bacteria/genetics/growth &amp; development/*isolation &amp; purification ; Biofilms ; Ecology ; *Environmental Microbiology ; Symbiosis ; }, abstract = {Ribosomal RNA (rRNA) sequence-based molecular techniques emerged in the late 1980s, which completely changed our general view of microbial life. Coincidentally, the Japanese Society of Microbial Ecology (JSME) was founded, and its official journal "Microbes and Environments (M&amp;E)" was launched, in 1985. Thus, the past 25 years have been an exciting and fruitful period for M&amp;E readers and microbiologists as demonstrated by the numerous excellent papers published in M&amp;E. In this minireview, recent progress made in microbial ecology and related fields is summarized, with a special emphasis on 8 landmark areas; the cultivation of uncultured microbes, in situ methods for the assessment of microorganisms and their activities, biofilms, plant microbiology, chemolithotrophic bacteria in early volcanic environments, symbionts of animals and their ecology, wastewater treatment microbiology, and the biodegradation of hazardous organic compounds.}, }
@article {pmid20040079, year = {2009}, author = {Heinz, E and Tischler, P and Rattei, T and Myers, G and Wagner, M and Horn, M}, title = {Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {634}, pmid = {20040079}, issn = {1471-2164}, mesh = {Bacterial Outer Membrane Proteins/genetics/*metabolism ; Chlamydia/classification/genetics/*metabolism/physiology ; Chlamydia muridarum/classification/genetics/metabolism/physiology ; Chlamydia trachomatis/classification/genetics/metabolism/physiology ; Computational Biology/*methods ; *Evolution, Molecular ; Lipoproteins/genetics/*metabolism ; Software ; }, abstract = {BACKGROUND: Chlamydiae are obligate intracellular bacteria comprising some of the most important bacterial pathogens of animals and humans. Although chlamydial outer membrane proteins play a key role for attachment to and entry into host cells, only few have been described so far. We developed a comprehensive, multiphasic in silico approach, including the calculation of clusters of orthologues, to predict outer membrane proteins using conservative criteria. We tested this approach using Escherichia coli (positive control) and Bacillus subtilis (negative control), and applied it to five chlamydial species; Chlamydia trachomatis, Chlamydia muridarum, Chlamydia (a.k.a. Chlamydophila) pneumoniae, Chlamydia (a.k.a. Chlamydophila) caviae, and Protochlamydia amoebophila.<br><br>RESULTS: In total, 312 chlamydial outer membrane proteins and lipoproteins in 88 orthologous clusters were identified, including 238 proteins not previously recognized to be located in the outer membrane. Analysis of their taxonomic distribution revealed an evolutionary conservation among Chlamydiae, Verrucomicrobia, Lentisphaerae and Planctomycetes as well as lifestyle-dependent conservation of the chlamydial outer membrane protein composition.<br><br>CONCLUSION: This analysis suggested a correlation between the outer membrane protein composition and the host range of chlamydiae and revealed a common set of outer membrane proteins shared by these intracellular bacteria. The collection of predicted chlamydial outer membrane proteins is available at the online database pCOMP http://www.microbial-ecology.net/pcomp and might provide future guidance in the quest for anti-chlamydial vaccines.}, }
@article {pmid20038697, year = {2010}, author = {De Gusseme, B and Sintubin, L and Baert, L and Thibo, E and Hennebel, T and Vermeulen, G and Uyttendaele, M and Verstraete, W and Boon, N}, title = {Biogenic silver for disinfection of water contaminated with viruses.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {4}, pages = {1082-1087}, pmid = {20038697}, issn = {1098-5336}, mesh = {Animals ; Antiviral Agents/pharmacology ; Bacteriophages/drug effects ; Disinfectants/pharmacology ; Disinfection/instrumentation/*methods ; Enterobacter aerogenes/virology ; Fresh Water/*virology ; Humans ; Limosilactobacillus fermentum/metabolism ; *Metal Nanoparticles ; Mice ; Nanotechnology ; Norovirus/drug effects ; *Silver ; Water Purification/instrumentation/*methods ; Water Supply ; }, abstract = {The presence of enteric viruses in drinking water is a potential health risk. Growing interest has arisen in nanometals for water disinfection, in particular the use of silver-based nanotechnology. In this study, Lactobacillus fermentum served as a reducing agent and bacterial carrier matrix for zerovalent silver nanoparticles, referred to as biogenic Ag(0). The antiviral action of biogenic Ag(0) was examined in water spiked with an Enterobacter aerogenes-infecting bacteriophage (UZ1). Addition of 5.4 mg liter(-1) biogenic Ag(0) caused a 4.0-log decrease of the phage after 1 h, whereas the use of chemically produced silver nanoparticles (nAg(0)) showed no inactivation within the same time frame. A control experiment with 5.4 mg liter(-1) ionic Ag+ resulted in a similar inactivation after 5 h only. The antiviral properties of biogenic Ag(0) were also demonstrated on the murine norovirus 1 (MNV-1), a model organism for human noroviruses. Biogenic Ag(0) was applied to an electropositive cartridge filter (NanoCeram) to evaluate its capacity for continuous disinfection. Addition of 31.25 mg biogenic Ag(0) m(-2) on the filter (135 mg biogenic Ag(0) kg(-1) filter medium) caused a 3.8-log decline of the virus. In contrast, only a 1.5-log decrease could be obtained with the original filter. This is the first report to demonstrate the antiviral efficacy of extracellular biogenic Ag(0) and its promising opportunities for continuous water disinfection.}, }
@article {pmid20037795, year = {2010}, author = {Pitta, DW and Pinchak, E and Dowd, SE and Osterstock, J and Gontcharova, V and Youn, E and Dorton, K and Yoon, I and Min, BR and Fulford, JD and Wickersham, TA and Malinowski, DP}, title = {Rumen bacterial diversity dynamics associated with changing from bermudagrass hay to grazed winter wheat diets.}, journal = {Microbial ecology}, volume = {59}, number = {3}, pages = {511-522}, pmid = {20037795}, issn = {1432-184X}, mesh = {*Animal Feed ; Animals ; *Biodiversity ; Cattle ; Cynodon ; DNA, Bacterial/genetics ; Male ; Nutritive Value ; Population Dynamics ; Prevotella/genetics/*isolation &amp; purification ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Triticum ; }, abstract = {Rumen bacterial communities in forage-fed and grazing cattle continually adapt to a wide range of changing dietary composition, nutrient density, and environmental conditions. We hypothesized that very distinct community assemblages would develop between the fiber and liquid fractions of rumen contents in animals transitioned from bermudagrass hay diet to a grazed wheat diet. To address this hypothesis, we designed an experiment utilizing a 16S-based bTEFAP pyrosequencing technique to characterize and elucidate changes in bacterial diversity among the fiber and liquid rumen fractions and whole rumen contents of 14 (Angus x Hereford) ruminally cannulated steers sequentially fed bermudagrass hay (Cynodon dactylon; 34 days) and grazing wheat forage (28 days). Bermudagrass hay was a conserved C4 perennial grass lower in protein and higher in fiber (11% and 67%, respectively) content than grazed winter wheat (Triticum aestivum), a C3 annual grass with higher protein (20%) and a large (66%) soluble fraction.Significant differences in the OTU estimates (Chao1, Ace,and Rarefaction) were detected between fractions of both diets, with bermudagrass hay supporting greater diversity than wheat forage. Sequences were compared with a 16S database using BLASTn and assigned sequences to respective genera and genera-like units based on the similarity value to known sequences in the database. Predominant genera were Prevotella (up to 33%) and Rikenella-like (upto 28%) genera on the bermudagrass diet and Prevotella (upto 56%) genus on the wheat diet irrespective of the fractions. Principle component analyses accounted for over 95% of variation in 16S estimated bacterial community composition in all three fractions and clearly differentiated communities associated with each diet. Overall, bermudagrass hay diets clustered more clearly than wheat diets.These data are the first to explore bacterial diversity dynamics in a common population of animals in response to contrasting grass forage diets.}, }
@article {pmid20024685, year = {2010}, author = {Bretschger, O and Osterstock, JB and Pinchak, WE and Ishii, S and Nelson, KE}, title = {Microbial fuel cells and microbial ecology: applications in ruminant health and production research.}, journal = {Microbial ecology}, volume = {59}, number = {3}, pages = {415-427}, pmid = {20024685}, issn = {1432-184X}, mesh = {Animal Nutritional Physiological Phenomena ; Animals ; Biodegradation, Environmental ; *Bioelectric Energy Sources ; *Biofilms ; Fermentation ; Hydrogen ; Methane/biosynthesis ; Oxidation-Reduction ; Rumen/*microbiology ; Ruminants/*microbiology ; Waste Disposal, Fluid ; }, abstract = {Microbial fuel cell (MFC) systems employ the catalytic activity of microbes to produce electricity from the oxidation of organic, and in some cases inorganic, substrates. MFC systems have been primarily explored for their use in bioremediation and bioenergy applications; however, these systems also offer a unique strategy for the cultivation of synergistic microbial communities. It has been hypothesized that the mechanism(s) of microbial electron transfer that enable electricity production in MFCs may be a cooperative strategy within mixed microbial consortia that is associated with, or is an alternative to, interspecies hydrogen (H(2)) transfer. Microbial fermentation processes and methanogenesis in ruminant animals are highly dependent on the consumption and production of H(2)in the rumen. Given the crucial role that H(2) plays in ruminant digestion, it is desirable to understand the microbial relationships that control H(2) partial pressures within the rumen; MFCs may serve as unique tools for studying this complex ecological system. Further, MFC systems offer a novel approach to studying biofilms that form under different redox conditions and may be applied to achieve a greater understanding of how microbial biofilms impact animal health. Here, we present a brief summary of the efforts made towards understanding rumen microbial ecology, microbial biofilms related to animal health, and how MFCs may be further applied in ruminant research.}, }
@article {pmid20024684, year = {2010}, author = {Cadillo-Quiroz, H and Yavitt, JB and Zinder, SH and Thies, JE}, title = {Diversity and community structure of Archaea inhabiting the rhizoplane of two contrasting plants from an acidic bog.}, journal = {Microbial ecology}, volume = {59}, number = {4}, pages = {757-767}, pmid = {20024684}, issn = {1432-184X}, mesh = {Archaea/classification/*genetics ; *Biodiversity ; DNA, Archaeal/genetics ; Gene Library ; Magnoliopsida/*microbiology ; New York ; Phylogeny ; Plant Roots/microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil ; *Soil Microbiology ; *Wetlands ; }, abstract = {Plant root exudates increase nutrient availability and influence microbial communities including archaeal members. We examined the archaeal community inhabiting the rhizoplane of two contrasting vascular plants, Dulichium arundinaceum and Sarracenia purpurea, from an acidic bog in upstate NY. Multiple archaeal 16S rRNA gene libraries showed that methanogenic Archaea were dominant in the rhizoplane of both plants. In addition, the community structure (evenness) of the rhizoplane was found markedly different from the bulk peat. The archaeal community in peat from the same site has been found dominated by the E2 group, meanwhile the rhizoplane communities on both plants were co-dominated by Methanosarcinaceae (MS), rice cluster (RC)-I, and E2. Complementary T-RFLP analysis confirmed the difference between bulk peat and rhizoplane, and further characterized the dominance pattern of MS, RC-I, and E2. In the rhizoplane, MS was dominant on both plants although as a less variable fraction in S. purpurea. RC-I was significantly more abundant than E2 on S. purpurea, while the opposite was observed on D. arundinaceum, suggesting a plant-specific enrichment. Also, the statistical analyses of T-RFLP data showed that although both plants overlap in their community structure, factors such as plant type, patch location, and time could explain nearly a third of the variability in the dataset. Other factors such as water table, plant replicate, and root depth had a low contribution to the observed variance. The results of this study illustrate the general effects of roots and the specific effects of plant types on their nearby archaeal communities which in bog-inhabiting plants were mainly composed by methanogenic groups.}, }
@article {pmid20024544, year = {2010}, author = {Luo, JF and Lin, WT and Guo, Y}, title = {Method to detect only viable cells in microbial ecology.}, journal = {Applied microbiology and biotechnology}, volume = {86}, number = {1}, pages = {377-384}, doi = {10.1007/s00253-009-2373-1}, pmid = {20024544}, issn = {1432-0614}, mesh = {*Alcaligenes faecalis/genetics/growth &amp; development/isolation &amp; purification ; Anaerobiosis ; Azides/*pharmacology ; DNA, Bacterial/analysis/isolation &amp; purification ; *Ecosystem ; *Enterobacter aerogenes/genetics/growth &amp; development/isolation &amp; purification ; *Escherichia coli O157/genetics/growth &amp; development/isolation &amp; purification ; Fresh Water/microbiology ; Geologic Sediments/microbiology ; Microbial Viability/*drug effects ; Polymerase Chain Reaction/methods ; Propidium/*analogs &amp; derivatives/pharmacology ; Sewage/microbiology ; *Water Microbiology ; }, abstract = {Propidium monoazide can limit the analysis of microbial communities derived from genetic fingerprints to viable cells with intact cell membranes. However, PMA treatment cannot completely suppress polymerase chain reaction (PCR) amplification when the targeted gene is too short. PMA treatment in combination with two-step nested PCR was designed to overcome this problem. Four experiments were performed to determine the limitation of PMA treatment and to evaluate the suitability of the method by applying the following samples: (1) pure cultures of Escherichia coli O157:H7, Enterobacter aerogenes, and Alcaligenes faecalis; (2) pond water samples spiked with heat-killed E. coli O157:H7 and E. aerogenes; (3) anaerobic sludge samples exposed to increasing heat stress; and (4) selected natural samples of estuarine sediment and lake mud. Results from the first two experiments show that PMA treatment cannot efficiently suppress dead cells from PCR amplification when the targeted gene is as short as 190 bp, however, the two-step nested PCR can overcome this problem. The last two experiments indicate the method that PMA treatment in combination with two-step nested PCR is useful for viable cells detection in microbial ecology.}, }
@article {pmid20023027, year = {2010}, author = {Schmitz-Esser, S and Tischler, P and Arnold, R and Montanaro, J and Wagner, M and Rattei, T and Horn, M}, title = {The genome of the amoeba symbiont "Candidatus Amoebophilus asiaticus" reveals common mechanisms for host cell interaction among amoeba-associated bacteria.}, journal = {Journal of bacteriology}, volume = {192}, number = {4}, pages = {1045-1057}, pmid = {20023027}, issn = {1098-5530}, support = {P 19252/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Amoeba/*microbiology ; Bacterial Proteins/genetics ; Bacteroidetes/*genetics/physiology ; Biosynthetic Pathways/genetics ; DNA Transposable Elements ; DNA, Bacterial/*genetics ; Francisella tularensis/genetics ; *Genome, Bacterial ; Legionella pneumophila/genetics ; Molecular Sequence Data ; Mycobacterium avium/genetics ; Protein Structure, Tertiary ; Rickettsia/genetics ; *Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Protozoa play host for many intracellular bacteria and are important for the adaptation of pathogenic bacteria to eukaryotic cells. We analyzed the genome sequence of "Candidatus Amoebophilus asiaticus," an obligate intracellular amoeba symbiont belonging to the Bacteroidetes. The genome has a size of 1.89 Mbp, encodes 1,557 proteins, and shows massive proliferation of IS elements (24% of all genes), although the genome seems to be evolutionarily relatively stable. The genome does not encode pathways for de novo biosynthesis of cofactors, nucleotides, and almost all amino acids. "Ca. Amoebophilus asiaticus" encodes a variety of proteins with predicted importance for host cell interaction; in particular, an arsenal of proteins with eukaryotic domains, including ankyrin-, TPR/SEL1-, and leucine-rich repeats, which is hitherto unmatched among prokaryotes, is remarkable. Unexpectedly, 26 proteins that can interfere with the host ubiquitin system were identified in the genome. These proteins include F- and U-box domain proteins and two ubiquitin-specific proteases of the CA clan C19 family, representing the first prokaryotic members of this protein family. Consequently, interference with the host ubiquitin system is an important host cell interaction mechanism of "Ca. Amoebophilus asiaticus". More generally, we show that the eukaryotic domains identified in "Ca. Amoebophilus asiaticus" are also significantly enriched in the genomes of other amoeba-associated bacteria (including chlamydiae, Legionella pneumophila, Rickettsia bellii, Francisella tularensis, and Mycobacterium avium). This indicates that phylogenetically and ecologically diverse bacteria which thrive inside amoebae exploit common mechanisms for interaction with their hosts, and it provides further evidence for the role of amoebae as training grounds for bacterial pathogens of humans.}, }
@article {pmid20020121, year = {2010}, author = {Gross, CA and Reddy, CK and Dazzo, FB}, title = {CMEIAS color segmentation: an improved computing technology to process color images for quantitative microbial ecology studies at single-cell resolution.}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {400-414}, pmid = {20020121}, issn = {1432-184X}, mesh = {Algorithms ; Bacteria/genetics/growth &amp; development ; Biofilms ; *Color ; Ecology/methods ; *Environmental Microbiology ; Image Enhancement/*methods ; Microbial Viability ; Pattern Recognition, Automated/methods ; Phylogeny ; Software ; }, abstract = {Quantitative microscopy and digital image analysis are underutilized in microbial ecology largely because of the laborious task to segment foreground object pixels from background, especially in complex color micrographs of environmental samples. In this paper, we describe an improved computing technology developed to alleviate this limitation. The system's uniqueness is its ability to edit digital images accurately when presented with the difficult yet commonplace challenge of removing background pixels whose three-dimensional color space overlaps the range that defines foreground objects. Image segmentation is accomplished by utilizing algorithms that address color and spatial relationships of user-selected foreground object pixels. Performance of the color segmentation algorithm evaluated on 26 complex micrographs at single pixel resolution had an overall pixel classification accuracy of 99+%. Several applications illustrate how this improved computing technology can successfully resolve numerous challenges of complex color segmentation in order to produce images from which quantitative information can be accurately extracted, thereby gain new perspectives on the in situ ecology of microorganisms. Examples include improvements in the quantitative analysis of (1) microbial abundance and phylotype diversity of single cells classified by their discriminating color within heterogeneous communities, (2) cell viability, (3) spatial relationships and intensity of bacterial gene expression involved in cellular communication between individual cells within rhizoplane biofilms, and (4) biofilm ecophysiology based on ribotype-differentiated radioactive substrate utilization. The stand-alone executable file plus user manual and tutorial images for this color segmentation computing application are freely available at http://cme.msu.edu/cmeias/ . This improved computing technology opens new opportunities of imaging applications where discriminating colors really matter most, thereby strengthening quantitative microscopy-based approaches to advance microbial ecology in situ at individual single-cell resolution.}, }
@article {pmid20016981, year = {2010}, author = {Carrasco, L and Gattinger, A and Fliessbach, A and Roldán, A and Schloter, M and Caravaca, F}, title = {Estimation by PLFA of microbial community structure associated with the rhizosphere of Lygeum spartum and Piptatherum miliaceum growing in semiarid mine tailings.}, journal = {Microbial ecology}, volume = {60}, number = {2}, pages = {265-271}, pmid = {20016981}, issn = {1432-184X}, mesh = {Bacteria/metabolism ; Biomass ; Fatty Acids/*analysis ; *Microbial Consortia ; Mining ; Mycorrhizae/metabolism ; Phospholipids/*analysis ; Poaceae/*microbiology ; *Rhizosphere ; *Soil Microbiology ; Soil Pollutants/analysis ; Spain ; }, abstract = {The objective of this study was to compare the microbial community composition and biomass associated with the rhizosphere of a perennial gramineous species (Lygeum spartum L.) with that of an annual (Piptatherum miliaceum L.), both growing in semiarid mine tailings. We also established their relationship with the contents of potentially toxic metals as well as with indicators of soil quality. The total phospholipid fatty acid (PLFA) amount was significantly higher in the rhizosphere soil of the annual species than in the rhizosphere soil of the perennial species. The fungal/bacterial PLFA ratio was significantly greater in the perennial species compared to the annual species. The fatty acid 16:1ω5c, the fungal/bacterial PLFA ratio and monounsaturated/saturated PLFA ratio were correlated negatively with the soluble contents of toxic metals. The cyc/prec (cy17:0 + cy19:0/16:1ω7 + 18:1ω7) ratio was correlated positively with the soluble contents of Pb, Zn, Al, Ni, Cd, and Cu. The results of the PLFA analysis for profiling microbial communities and their stress status of both the plant species indicate that perennial and annual gramineous species appear equally suitable for use in programmes of revegetation of semiarid mine tailings.}, }
@article {pmid20016980, year = {2010}, author = {Lewis, DE and White, JR and Wafula, D and Athar, R and Dickerson, T and Williams, HN and Chauhan, A}, title = {Soil functional diversity analysis of a bauxite-mined restoration chronosequence.}, journal = {Microbial ecology}, volume = {59}, number = {4}, pages = {710-723}, pmid = {20016980}, issn = {1432-184X}, mesh = {Aluminum Oxide/*metabolism ; Bacteria/genetics/*metabolism ; Biodegradation, Environmental ; Biomass ; Carbon/analysis ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Environmental Monitoring ; Jamaica ; Mining ; Multivariate Analysis ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/analysis ; Soil/*analysis ; *Soil Microbiology ; Time Factors ; }, abstract = {Soil microorganisms are sensitive to environmental perturbations such that changes in microbial community structure and function can provide early signs of anthropogenic disturbances and even predict restoration success. We evaluated the bacterial functional diversity of un-mined and three chronosequence sites at various stages of rehabilitation (0, 10, and 20 years old) located in the Mocho Mountains of Jamaica. Samples were collected during the dry and wet seasons and analyzed for metal concentrations, microbial biomass carbon, bacterial numbers, and functional responses of soil microbiota using community-level physiological profile (CLPP) assays. Regardless of the season, un-mined soils consisted of higher microbial biomass and numbers than any of the rehabilitated sites. Additionally, the number and rate of substrates utilized and substrate evenness (the distribution of color development between the substrates) were significantly greater in the un-mined soils with carbohydrates being preferentially utilized than amino acids, polymers, carboxylic acids, and esters. To some extent, functional responses varied with the seasons but the least physiological activity was shown by the site rehabilitated in 1987 indicating long-term perturbation to this ecosystem. Small subunit ribosomal DNA (SSUrDNA)-denaturing gradient-gel electrophoresis analyses on the microbiota collected from the most preferred CLPP substrates followed by taxonomic analyses showed Proteobacteria, specifically the gamma-proteobacteria, as the most functionally active phyla, indicating a propensity of this phyla to out-compete other groups under the prevailing conditions. Additionally, multivariate statistical analyses, Shannon's diversity, and evenness indices, principal component analysis, biplot and un-weighted-pair-group method with arithmetic averages dendrograms further confirmed that un-mined sites were distinctly different from the rehabilitated soils.}, }
@article {pmid20013262, year = {2010}, author = {Lins-de-Barros, MM and Vieira, RP and Cardoso, AM and Monteiro, VA and Turque, AS and Silveira, CB and Albano, RM and Clementino, MM and Martins, OB}, title = {Archaea, Bacteria, and algal plastids associated with the reef-building corals Siderastrea stellata and Mussismilia hispida from Búzios, South Atlantic Ocean, Brazil.}, journal = {Microbial ecology}, volume = {59}, number = {3}, pages = {523-532}, pmid = {20013262}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology ; Archaea/*classification/genetics/isolation &amp; purification ; Atlantic Ocean ; Bacteria/*classification/genetics/isolation &amp; purification ; Brazil ; DNA, Algal/genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; *Ecosystem ; Eukaryota/*classification/genetics/isolation &amp; purification ; Gene Library ; Phylogeny ; Plastids/*genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Symbiosis ; Water Microbiology ; }, abstract = {Reef-building corals may be seen as holobiont organisms, presenting diverse associated microbial communities. Best known is the symbiotic relationship with zooxanthellae, but Archaea, Bacteria, fungi, viruses, and algal plastids are also abundant. Until now, there is little information concerning microbial communities associated with Brazilian corals. The present study aims to describe the diversity of Archaea, Bacteria, and eukaryotic algal plastid communities associated with two sympatric species, Siderastrea stellata and Mussismilia hispida, from Southeastern Brazil, using 16S rRNA gene libraries. Since corals present a high number of other associated invertebrates, coral barcoding (COI) was performed to confirm the exclusive occurrence of coral DNA in our samples. Our analysis yielded 354 distinct microbial OTUs, represented mainly by novel phylotypes. Richness (Chao1 and ACE) and diversity (H') estimations of the microbial communities associated with both species were high and comparable to other studies. Rarefaction analyses showed that microbial diversity of S. stellata is higher than that of M. hispida. Libshuff comparative analyses showed that the highest microbial community similarity between the two coral species occurred in the bacterial libraries, while archaeal and plastidial communities were significantly different. Crenarchaeota dominated archaeal communities, while Proteobacteria was the most abundant bacterial phylum, dominated by alpha-Proteobacteria. Plastids were also represented by novel phylotypes and did not match with any 16S rRNA sequences of Cyanobacteria and zooxanthellae from GenBank. Our data improves the pool of available information on Brazilian coral microbes and shows corals as sources of diverse prokaryotic and picoeukaryotic communities.}, }
@article {pmid20013261, year = {2010}, author = {Azcón, R and Perálvarez, Mdel C and Roldán, A and Barea, JM}, title = {Arbuscular mycorrhizal fungi, Bacillus cereus, and Candida parapsilosis from a multicontaminated soil alleviate metal toxicity in plants.}, journal = {Microbial ecology}, volume = {59}, number = {4}, pages = {668-677}, pmid = {20013261}, issn = {1432-184X}, mesh = {Antioxidants/metabolism ; Bacillus cereus/*metabolism ; Biodegradation, Environmental ; Candida/*metabolism ; Indoleacetic Acids/metabolism ; Metals, Heavy/*metabolism/pharmacology ; Mycorrhizae/*metabolism ; Plant Development ; Plant Root Nodulation ; Plants/drug effects/*microbiology ; Proline/biosynthesis ; *Soil Microbiology ; Soil Pollutants/metabolism/pharmacology ; }, abstract = {We investigated if the limited development of Trifolium repens growing in a heavy metal (HM) multicontaminated soil was increased by selected native microorganisms, bacteria (Bacillus cereus (Bc)), yeast (Candida parapsilosis (Cp)), or arbuscular mycorrhizal fungi (AMF), used either as single or dual inoculants. These microbial inoculants were assayed to ascertain whether the selection of HM-tolerant microorganisms can benefit plant growth and nutrient uptake and depress HM acquisition. The inoculated microorganisms, particularly in dual associations, increased plant biomass by 148% (Bc), 162%, (Cp), and 204% (AMF), concomitantly producing the highest symbiotic (AMF colonisation and nodulation) rates. The lack of AMF colonisation and nodulation in plants growing in this natural, polluted soil was compensated by adapted microbial inoculants. The metal bioaccumulation abilities of the inoculated microorganisms and particularly the microbial effect on decreasing metal concentrations in shoot biomass seem to be involved in such effects. Regarding microbial HM tolerance, the activities of antioxidant enzymes known to play an important role in cell protection by alleviating cellular oxidative damage, such as superoxide dismutase, catalase, glutathione reductase, and ascorbate peroxidase, were here considered as an index of microbial metal tolerance. Enzymatic mechanisms slightly changed in the HM-adapted B. cereus or C. parapsilosis in the presence of metals. Antioxidants seem to be directly involved in the adaptative microbial response and survival in HM-polluted sites. Microbial inoculations showed a bioremediation potential and helped plants to develop in the multicontaminated soil. Thus, they could be used as a biotechnological tool to improve plant development in HM-contaminated environments.}, }
@article {pmid20012275, year = {2010}, author = {Saulnier, D and De Decker, S and Haffner, P and Cobret, L and Robert, M and Garcia, C}, title = {A large-scale epidemiological study to identify bacteria pathogenic to Pacific oyster Crassostrea gigas and correlation between virulence and metalloprotease-like activity.}, journal = {Microbial ecology}, volume = {59}, number = {4}, pages = {787-798}, pmid = {20012275}, issn = {1432-184X}, mesh = {Animals ; Aquaculture ; Bacterial Typing Techniques ; Crassostrea/*microbiology ; France ; Genotype ; Metalloproteases/*genetics/metabolism ; Molecular Epidemiology ; Phylogeny ; Shewanella/classification/enzymology/genetics/pathogenicity ; Vibrio/classification/enzymology/genetics/*pathogenicity ; Vibrio Infections/*epidemiology/microbiology ; Virulence ; Virulence Factors/genetics ; }, abstract = {A 4-year bacteriological survey (2003-2007) of four molluscs cultivated in France and faced with mortality episodes was performed by the French shellfish pathology network. The more abundant bacteria isolated during 92 mortality episodes, occurring mainly in Pacific oyster Crassostrea gigas, were identified by genotyping methods. It allowed us both to confirm the representativeness of Vibrio splendidus and Vibrio aestuarianus bacterial strains and to identify both a large number of Vibrio harveyi-related strains mainly detected during 2007 oyster mortality outbreaks and to a lesser extent bacterial strains identified as Shewanella colwelliana. Because metalloprotease has been reported to constitute a virulence factor in a few Vibrio strains pathogenic for C. gigas, several bacterial strains isolated in this study were screened to evaluate their pathogenicity in C. gigas spat by experimental infection and their ability to produce metalloprotease-like activity in the culture supernatant fluids. A high level (84%) of concordant results between azocaseinase activities and virulence of strains was obtained in this study. Because bacterial metalloprotease activities appeared as a common feature of pathogenic bacteria strains associated with mortality events of C. gigas reared in France, this phenotypic test could be useful for the evaluation of virulence in bacterial strains associated with such mortality episodes.}, }
@article {pmid20011594, year = {2009}, author = {Schloss, PD}, title = {A high-throughput DNA sequence aligner for microbial ecology studies.}, journal = {PloS one}, volume = {4}, number = {12}, pages = {e8230}, pmid = {20011594}, issn = {1932-6203}, mesh = {Algorithms ; Bacteria/*genetics ; Base Sequence ; Databases, Nucleic Acid ; *Ecological and Environmental Phenomena ; High-Throughput Screening Assays/*instrumentation ; Molecular Sequence Data ; Sequence Alignment/*instrumentation ; Sequence Analysis, DNA/*instrumentation ; }, abstract = {As the scope of microbial surveys expands with the parallel growth in sequencing capacity, a significant bottleneck in data analysis is the ability to generate a biologically meaningful multiple sequence alignment. The most commonly used aligners have varying alignment quality and speed, tend to depend on a specific reference alignment, or lack a complete description of the underlying algorithm. The purpose of this study was to create and validate an aligner with the goal of quickly generating a high quality alignment and having the flexibility to use any reference alignment. Using the simple nearest alignment space termination algorithm, the resulting aligner operates in linear time, requires a small memory footprint, and generates a high quality alignment. In addition, the alignments generated for variable regions were of as high a quality as the alignment of full-length sequences. As implemented, the method was able to align 18 full-length 16S rRNA gene sequences and 58 V2 region sequences per second to the 50,000-column SILVA reference alignment. Most importantly, the resulting alignments were of a quality equal to SILVA-generated alignments. The aligner described in this study will enable scientists to rapidly generate robust multiple sequences alignments that are implicitly based upon the predicted secondary structure of the 16S rRNA molecule. Furthermore, because the implementation is not connected to a specific database it is easy to generalize the method to reference alignments for any DNA sequence.}, }
@article {pmid20007908, year = {2010}, author = {De Palma, G and Cinova, J and Stepankova, R and Tuckova, L and Sanz, Y}, title = {Pivotal Advance: Bifidobacteria and Gram-negative bacteria differentially influence immune responses in the proinflammatory milieu of celiac disease.}, journal = {Journal of leukocyte biology}, volume = {87}, number = {5}, pages = {765-778}, doi = {10.1189/jlb.0709471}, pmid = {20007908}, issn = {1938-3673}, mesh = {Bifidobacterium/*immunology ; Caco-2 Cells ; Celiac Disease/*immunology/*microbiology ; Cell Separation ; Coculture Techniques ; Cytokines/biosynthesis ; Flow Cytometry ; Gram-Negative Bacteria/*immunology ; Humans ; Intestinal Mucosa/immunology/microbiology ; Leukocytes, Mononuclear/*immunology ; }, abstract = {CD is a chronic inflammatory disorder of the small intestine that presents in genetically predisposed individuals following gluten consumption. In this study, the effects of Bifidobacterium (Bifidobacterium bifidum IATA-ES2 and Bifidobacterium longum ATCC15707) and Gram-negative bacteria (Bacteroides fragilis DSM2451, Escherichia coli CBL2, and Shigella CBD8 isolated from CD patients), alone and in the presence of CD triggers (gliadins and/or IFN-gamma) on surface marker expression and cytokine production by PBMCs, were determined. These effects were also evaluated in cocultures of PBMCs and Caco-2 cells. The Gram-negative bacteria induced higher secretion of Th1-type proinflammatory cytokines (IL-12 and/or IFN-gamma) than the Bifidobacterium strains. Shigella CBD8 and E. coli CBL2 up-regulated mainly HLA-DR and CD40 expression involved in Th1 activation, and Bifidobacterium strains up-regulated CD83 expression. Specific interactions among the studied bacteria, gliadins, and IFN-gamma, which favored the CD immune features, were also detected. Therefore, intestinal bacteria could be additional factors that regulate the ability of monocytes recruited to the mucosa to respond to gliadins and IFN-gamma in CD patients, influencing the course of the disease.}, }
@article {pmid20002182, year = {2010}, author = {Nazir, R and Warmink, JA and Boersma, H and van Elsas, JD}, title = {Mechanisms that promote bacterial fitness in fungal-affected soil microhabitats.}, journal = {FEMS microbiology ecology}, volume = {71}, number = {2}, pages = {169-185}, doi = {10.1111/j.1574-6941.2009.00807.x}, pmid = {20002182}, issn = {1574-6941}, mesh = {Bacteria/*growth &amp; development/metabolism ; Biodiversity ; Carbon/metabolism ; Microbial Interactions ; Mycorrhizae/*growth &amp; development/metabolism ; Plants/microbiology ; *Soil Microbiology ; }, abstract = {Soil represents a very heterogeneous environment for its microbiota. Among the soil inhabitants, bacteria and fungi are important organisms as they are involved in key biogeochemical cycling processes. A main energy source driving the system is formed by plants through the provision of plant-fixed (reduced) carbon to the soil, whereas soil nitrogen and phosphorus may move from the soil back to the plant. The carbonaceous compounds released form the key energy and nutrient sources for the soil microbiota. In the grossly carbon-limited soil, the emergence of plant roots and the formation of their associated mycorrhizae thus create nutritional hot spots for soil-dwelling bacteria. As there is natural (fitness) selection on bacteria in the soil, those bacteria that are best able to benefit from the hot spots have probably been selected. The purpose of this review is to examine the interactions of bacteria with soil fungi in these hot spots and to highlight the key mechanisms involved in the selection of fungal-responsive bacteria. Salient bacterial mechanisms that are involved in these interactions have emerged from this examination. Thus, the efficient acquisition for specific released nutrients, the presence of type-III secretion systems and the capacity of flagellar movement and to form a biofilm are pinpointed as key aspects of bacterial life in the mycosphere. The possible involvement of functions present on plasmid-borne genes is also interrogated.}, }
@article {pmid19929736, year = {2009}, author = {Bidigare, RR and Christensen, SJ and Wilde, SB and Banack, SA}, title = {Cyanobacteria and BMAA: possible linkage with avian vacuolar myelinopathy (AVM) in the south-eastern United States.}, journal = {Amyotrophic lateral sclerosis : official publication of the World Federation of Neurology Research Group on Motor Neuron Diseases}, volume = {10 Suppl 2}, number = {}, pages = {71-73}, doi = {10.3109/17482960903273056}, pmid = {19929736}, issn = {1471-180X}, support = {P50 ES 012740/ES/NIEHS NIH HHS/United States ; }, mesh = {Amino Acids, Diamino/analysis/*toxicity ; Amino Acids, Dicarboxylic/analysis/*toxicity ; Animals ; *Birds ; Chromatography, Liquid/methods ; Cyanobacteria/chemistry/*physiology ; Demyelinating Diseases/chemically induced/*veterinary ; United States ; }, abstract = {Avian vacuolar myelinopathy (AVM) is a neurological disease that produces uncoordinated behavior in affected birds in wetland ecosystems of the south-eastern United States. Feeding and sentinel trials, field surveys, and genetic studies have implicated the introduced flowering plant species Hydrilla verticillata (Hydrocharitaceae) and an associated epiphytic cyanobacterial species (Order Stigonematales) as a causal link to AVM. All five morphotypes of cyanobacteria have been shown to produce the neurotoxic amino acid BMAA, including cyanobacteria of the Stigonematales that are epiphytic on Hydrilla verticillata. If biomagnification of BMAA occurs in these wetland ecosystems, as has been observed in the Guam ecosystem, then the consumption of fish (e.g. shad and herring) and waterfowl (e.g. Canada geese and mallards) from AVM-confirmed reservoirs in Arkansas, Texas, Georgia, North Carolina and South Carolina could represent a significant human health risk.}, }
@article {pmid19968693, year = {2010}, author = {Ostman, O and Drakare, S and Kritzberg, ES and Langenheder, S and Logue, JB and Lindström, ES}, title = {Regional invariance among microbial communities.}, journal = {Ecology letters}, volume = {13}, number = {1}, pages = {118-127}, doi = {10.1111/j.1461-0248.2009.01413.x}, pmid = {19968693}, issn = {1461-0248}, mesh = {*Bacteria ; *Bacterial Physiological Phenomena ; Biodiversity ; Fresh Water/*microbiology ; Genetic Variation ; Models, Biological ; Phytoplankton/genetics/*physiology ; Population Dynamics ; Sweden ; }, abstract = {Microbial ecology has focused much on causes of between-site variation in community composition. By analysing five data-sets each of aquatic bacteria and phytoplankton, we demonstrated that microbial communities show a large degree of similarity in community composition and that abundant taxa were widespread, a typical pattern for many metazoan metacommunities. The regional abundance of taxa explained on average 85 and 41% of variation in detection frequency and 58 and 31% of variation in local abundances for bacteria and phytoplankton, respectively. However, regional abundance explained less variation in local abundances with increasing environmental variation between sites within data-sets. These findings indicate that the studies of microbial assemblages need to consider similarities between communities to better understand the processes underlying the assembly of microbial communities. Finally, we propose that the degree of regional invariance can be linked to the evolution of microbes and the variation in ecosystem functions performed by microbial communities.}, }
@article {pmid19966029, year = {2010}, author = {Stoecker, K and Dorninger, C and Daims, H and Wagner, M}, title = {Double labeling of oligonucleotide probes for fluorescence in situ hybridization (DOPE-FISH) improves signal intensity and increases rRNA accessibility.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {3}, pages = {922-926}, pmid = {19966029}, issn = {1098-5336}, support = {I 44/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Conserved Sequence/genetics ; Escherichia coli/genetics ; Evolution, Molecular ; Flow Cytometry ; Fluorescence ; Fluorescent Dyes/*chemistry ; In Situ Hybridization, Fluorescence/*methods ; Nucleic Acid Conformation ; Oligonucleotide Probes/*chemistry ; Phylogeny ; RNA, Bacterial/*analysis ; RNA, Ribosomal/*analysis ; RNA, Ribosomal, 16S/analysis ; RNA, Ribosomal, 18S/analysis ; Sequence Alignment ; Species Specificity ; Thermodynamics ; }, abstract = {Fluorescence in situ hybridization (FISH) with singly labeled rRNA-targeted oligonucleotide probes is widely applied for direct identification of microbes in the environment or in clinical specimens. Here we show that a replacement of singly labeled oligonucleotide probes with 5'-, 3'-doubly labeled probes at least doubles FISH signal intensity without causing specificity problems. Furthermore, Cy3-doubly labeled probes strongly increase in situ accessibility of rRNA target sites and thus provide more flexibility for probe design.}, }
@article {pmid19963368, year = {2010}, author = {Rojas-Oropeza, M and Dendooven, L and Garza-Avendaño, L and Souza, V and Philippot, L and Cabirol, N}, title = {Effects of biosolids application on nitrogen dynamics and microbial structure in a saline-sodic soil of the former Lake Texcoco (Mexico).}, journal = {Bioresource technology}, volume = {101}, number = {7}, pages = {2491-2498}, doi = {10.1016/j.biortech.2009.10.088}, pmid = {19963368}, issn = {1873-2976}, mesh = {Ammonia/metabolism ; Bacteria/*growth &amp; development ; Carbon/metabolism ; Carbon Dioxide/metabolism ; DNA, Ribosomal Spacer/genetics ; Fresh Water/*microbiology ; Mexico ; Nitrogen/*metabolism ; *Salinity ; Sewage/*microbiology ; *Soil Microbiology ; Volatilization ; }, abstract = {The saline-sodic soil of the former Lake Texcoco, a large area exposed to desertification, is a unique environment, but little is known about its microbial ecology. The objective of this study was to examine bacterial community structure, activity, and function when biosolids were added to microcosms. The application rates were such that 0, 66, 132, or 265 mg total Nk g(-1) were added with the biosolids (total C and N content 158 and 11.5 g kg(-1) dry biosolids, respectively). Approximately 60% of the biosolids were mineralized within 90 days. Microbial respiration and to a lesser extent ammonification and nitrification, increased after biosolids application. The rRNA intergenic spacer analysis (RISA) patterns for the biosolids and unamended soil bacterial communities were different, indicating that the microorganisms in the biosolids were distinct from the native population. It appears that the survival of the allochthonous microorganisms was short, presumably due to the adverse soil conditions.}, }
@article {pmid19960250, year = {2010}, author = {Stevens, P and van Elsas, JD}, title = {Genetic and phenotypic diversity of Ralstonia solanacearum biovar 2 strains obtained from Dutch waterways.}, journal = {Antonie van Leeuwenhoek}, volume = {97}, number = {2}, pages = {171-188}, pmid = {19960250}, issn = {1572-9699}, mesh = {Bacterial Typing Techniques ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrophoresis, Gel, Pulsed-Field ; Genotype ; Molecular Sequence Data ; Netherlands ; Phylogeny ; Plants/*microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Ralstonia solanacearum/*classification/genetics/*isolation &amp; purification/physiology ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {A novel set of Ralstonia solanacearum biovar 2 isolates was obtained, at several sampling occasions, from Dutch waterways, sediment and bittersweet plants and their genetic and phenotypic diversity was investigated. As reference strains, two previously-described strains obtained from diseased potato plants, denoted 1609 (The Netherlands) and 715 (Bangladesh), were included in the analyses. All novel isolates showed BOX and GTG5 PCR based genomic profiles similar to those of the reference strains. Also, PCR-restriction fragment length polymorphism analysis of the phcA and hrp genomic regions, as well as sequence analysis of six selected genomic loci, revealed great homogeneity across the strains. In contrast, pulsed field gel electrophoresis of restricted genomic DNA revealed the distribution of all strains across four groups, denoted pulsotypes A through D (pulsotypes C and D had one representative each). Moreover, pulsotype B, consisting of five strains, could be separated from the other pulsotypes by a divergent genomic fingerprint when hybridized to a probe specific for insertion element ISRso3. Representatives of pulsotypes A, B and C were selected for growth and metabolic studies. They showed similar growth rates when grown aerobically in liquid media. Assessment of their metabolic capacity using BIOLOG GN-2 revealed a reduced utilization of compounds as compared to the reference strains, with some variation between strains.}, }
@article {pmid19959307, year = {2010}, author = {Hitoto, H and Eveillard, M and Lemarié, C and Cottin, J and Joly-Guillou, ML}, title = {[Assessing the usefulness of a permanently opened clinical microbiology laboratory].}, journal = {Medecine et maladies infectieuses}, volume = {40}, number = {4}, pages = {219-225}, doi = {10.1016/j.medmal.2009.10.011}, pmid = {19959307}, issn = {1769-6690}, mesh = {Bacterial Infections/diagnosis/drug therapy ; Bacteriological Techniques ; Bacteriology/*organization &amp; administration ; Cross Infection/diagnosis/drug therapy ; France ; Hospitals, University/economics/*organization &amp; administration ; Humans ; Laboratories, Hospital/economics/*organization &amp; administration ; Medical Laboratory Personnel ; Microbial Sensitivity Tests ; Night Care/organization &amp; administration ; Process Assessment, Health Care ; Prospective Studies ; Specimen Handling ; Workforce ; }, abstract = {UNLABELLED: Since 2005, the clinical microbiology laboratory of the Angers teaching hospital has implemented after hours service requiring the overnight presence of a technician specialized in bacteriology. During that time, bacterial identifications and antibiotic susceptibility testing to antimicrobial agents can be performed for critical samples.<br><br>OBJECTIVES: The authors wanted to evaluate the impact of the after-hours service on the decrease of delay from sampling to results, and from sampling to the implementation of an appropriate antimicrobial therapy. A therapy could be initiated, changed for more efficient agents, or changed to narrower-spectrum agents (major benefits).<br><br>METHODS: A 4-month prospective study was made. All samples for which identification and/or susceptibility testing were performed during after-hours service (continued analyses) were included in the study. Delays observed were compared with theoretical delays estimated in the absence of the after-hours service.<br><br>RESULTS: A minimum 24 hour-decrease of the delay for results was observed for 97 % of the 430 samples included. Overall, a major benefit was obtained for more than 25 % of the analyses, representing a cumulated 111-day benefit in days of efficient treatments and a cumulated 27-day benefit in days of prescription of narrower-spectrum agents.<br><br>DISCUSSION: This organization, unique in French hospitals, is directly related to the improvement of antimicrobial treatments, like antibiotic practice guidelines or infection disease specialists. It was evaluated as a relevant strategy, potentially cost saving, with a significant impact on both the efficiency of treatments and microbial ecology.}, }
@article {pmid19956939, year = {2010}, author = {Yang, J and Smith, HG and Sherratt, TN and Wilkinson, DM}, title = {Is there a size limit for cosmopolitan distribution in free-living microorganisms? A biogeographical analysis of testate amoebae from polar areas.}, journal = {Microbial ecology}, volume = {59}, number = {4}, pages = {635-645}, pmid = {19956939}, issn = {1432-184X}, mesh = {Amoeba/*classification/genetics/growth &amp; development ; Antarctic Regions ; Arctic Regions ; *Biodiversity ; Geography ; Linear Models ; Logistic Models ; Phylogeny ; Statistics, Nonparametric ; Tibet ; }, abstract = {A long-standing debate in microbial ecology is the extent to which free-living microorganisms exhibit cosmopolitan distributions. We use a comparison of testate amoebae communities in cold "polar" locations (Arctic, Antarctic, and Tibet) to investigate how a microorganism's size affects its probability of having a cosmopolitan distribution. We show that the probability a given taxa being reported in all three locations increases as testate size decreases. Likewise, excluding those testates found only in Tibet, very small testates (<20 microm) are more likely to occur in both the Arctic and Antarctic than in either of these poles alone. Attempting to correct for phylogeny reduces the number of statistically significant relationships--both because of decreased sample size and potentially real phylogenetic patterns, although some size-dependent effects were still apparent. In particular, taxa found in both the Arctic and Antarctic poles were significantly smaller than congeneric taxa found only in Tibet. This pattern may in part be due to habitat effects, with the Tibetan samples being more likely to have come from aquatic sites which may be more suitable for larger taxa. Overall, our analysis suggests that, at least within testate amoebae, a cosmopolitan distribution becomes increasingly common as median taxon size decreases.}, }
@article {pmid19953545, year = {2010}, author = {Schneider, T and Riedel, K}, title = {Environmental proteomics: analysis of structure and function of microbial communities.}, journal = {Proteomics}, volume = {10}, number = {4}, pages = {785-798}, doi = {10.1002/pmic.200900450}, pmid = {19953545}, issn = {1615-9861}, mesh = {Bacterial Proteins ; *Ecological and Environmental Phenomena ; Fungal Proteins ; Proteome/chemistry/isolation &amp; purification/physiology ; Proteomics/*methods ; Viral Proteins ; }, abstract = {Prokaryotic and eukaryotic microorganisms make a vital contribution to biogeochemical cycles by decomposing virtually all natural compounds and thereby exert a lasting effect on biosphere and climate. The rapidly growing number of metagenomic sequences together with revolutionary advances in bioinformatics and protein analyses have opened completely new horizons to investigate the molecular basis of such complex processes. Proteomics has contributed substantially to our understanding of individual organisms at the cellular level as it offers excellent possibilities to probe many protein functions and responses simultaneously. However, it has not yet been widely applied in microbial ecology, although most proteins have an intrinsic metabolic function which can be used to relate microbial activities to the identity of defined organisms in multispecies communities. Albeit still in its infancy, environmental proteomics enables simple protein cataloging, comparative and semi-quantitative proteomics, analyses of protein localization, discovery of post-translational modifications, and even determination of amino-acid sequences and genotypes by strain-resolved proteogenomics. This review traces the historical development of environmental proteomics and summarizes milestone publications in the field. In conclusion, we briefly discuss current limitations of microbial community proteomics but also the potential of emerging technologies to shape the future of metaproteome analyses.}, }
@article {pmid19953241, year = {2010}, author = {Tourlomousis, P and Kemsley, EK and Ridgway, KP and Toscano, MJ and Humphrey, TJ and Narbad, A}, title = {PCR-denaturing gradient gel electrophoresis of complex microbial communities: a two-step approach to address the effect of gel-to-gel variation and allow valid comparisons across a large dataset.}, journal = {Microbial ecology}, volume = {59}, number = {4}, pages = {776-786}, pmid = {19953241}, issn = {1432-184X}, mesh = {Animals ; Bacteria/genetics/isolation &amp; purification ; Birds/microbiology ; DNA, Bacterial/analysis ; Electrophoresis, Polyacrylamide Gel/*methods ; Feces/microbiology ; Image Processing, Computer-Assisted ; Polymerase Chain Reaction/*methods ; Principal Component Analysis ; RNA, Ribosomal, 16S/analysis ; Reference Standards ; Software ; Swine/microbiology ; }, abstract = {Denaturing gradient gel electrophoresis (DGGE) is widely used in microbial ecology to profile complex microbial communities over time and in response to different stimuli. However, inherent gel-to-gel variability has always been a barrier toward meaningful interpretation of DGGE profiles obtained from multiple gels. To address this problem, we developed a two-step methodology to align DGGE profiles across a large dataset. The use of appropriate inter-gel standards was of vital importance since they provided the basis for efficient within- and between-gel alignment and a reliable means to evaluate the final outcome of the process. Pretreatment of DGGE profiles by a commercially available image analysis software package (TL120 v2006, Phoretix 1D Advanced) followed by a simple interpolation step in Matlab minimized the effect of gel-to-gel variation, allowing for comparisons between large numbers of samples with a high degree of confidence. At the same time, data were obtained in the form of whole densitometric curves, rather than as band presence/absence or intensity information, and could be readily analyzed by a collection of well-established multivariate methods. This work clearly demonstrates that there is still room for significant improvements as to the way large DGGE datasets are processed and statistically interrogated.}, }
@article {pmid19953240, year = {2010}, author = {Miletto, M and Loeb, R and Antheunisse, AM and Bodelier, PL and Laanbroek, HJ}, title = {Response of the sulfate-reducing community to the re-establishment of estuarine conditions in two contrasting soils: a mesocosm approach.}, journal = {Microbial ecology}, volume = {59}, number = {1}, pages = {109-120}, pmid = {19953240}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*metabolism ; Ecosystem ; Environment ; Environmental Monitoring ; Fatty Acids/metabolism ; Hydrogensulfite Reductase/genetics/metabolism ; Phylogeny ; Salinity ; Salt Tolerance ; *Soil Microbiology ; Sulfates/*metabolism ; Wetlands ; }, abstract = {We studied the response of the sulfate-reducing prokaryote (SRP) communities to the experimental variation of salinity and tide in an outdoor mesocosm setup. Intact soil monoliths were collected at two areas of the Haringvliet lagoon (The Netherlands): one sampling location consisted of agricultural grassland, drained and fertilized for at least the last century; the other of a freshwater marshland with more recent sea influence. Two factors, i.e., "salinity" (freshwater/oligohaline) and "tide" (nontidal/tidal), were tested in a full-factorial design. Soil samples were collected after 5 months (June-October). Dissimilatory (bi)sulfite reductase beta subunit-based denaturing gradient gel electrophoresis (dsrB-DGGE) analysis revealed that the SRP community composition in the agricultural grassland and in the freshwater marshland was represented mainly by microorganisms related to the Desulfobulbaceae and the Desulfobacteraceae, respectively. Desulfovibrio-related dsrB were detected only in the tidal treatments; Desulfomonile-related dsrB occurrence was related to the presence of oligohaline conditions. Treatments did have an effect on the overall SRP community composition of both soils, but not on the sulfate depletion rates in sulfate-amended anoxic slurry incubations. However, initiation of sulfate reduction upon sulfate addition was clearly different between the two soils.}, }
@article {pmid19953239, year = {2010}, author = {Lamentowicz, M and Lamentowicz, L and van der Knaap, WO and Gabka, M and Mitchell, EA}, title = {Contrasting species-environment relationships in communities of testate amoebae, bryophytes and vascular plants along the fen-bog gradient.}, journal = {Microbial ecology}, volume = {59}, number = {3}, pages = {499-510}, pmid = {19953239}, issn = {1432-184X}, mesh = {*Amoeba ; *Biodiversity ; Bryophyta/*microbiology ; Fresh Water/chemistry ; Hydrogen-Ion Concentration ; Plants/*microbiology ; Switzerland ; Water Microbiology ; *Wetlands ; }, abstract = {We studied the vegetation, testate amoebae and abiotic variables (depth of the water table, pH, electrical conductivity, Ca and Mg concentrations of water extracted from mosses) along the bog to extremely rich fen gradient in sub-alpine peatlands of the Upper Engadine (Swiss Alps). Testate amoeba diversity was correlated to that of mosses but not of vascular plants. Diversity peaked in rich fen for testate amoebae and in extremely rich fen for mosses, while for testate amoebae and mosses it was lowest in bog but for vascular plants in extremely rich fen. Multiple factor and redundancy analyses (RDA) revealed a stronger correlation of testate amoebae than of vegetation to water table and hydrochemical variables and relatively strong correlation between testate amoeba and moss community data. In RDA, hydrochemical variables explained a higher proportion of the testate amoeba and moss data than water table depth. Abiotic variables explained a higher percentage of the species data for testate amoebae (30.3% or 19.5% for binary data) than for mosses (13.4%) and vascular plants (10%). These results show that (1) vascular plant, moss and testate amoeba communities respond differently to ecological gradients in peatlands and (2) testate amoebae are more strongly related than vascular plants to the abiotic factors at the mire surface. These differences are related to vertical trophic gradients and associated niche differentiation.}, }
@article {pmid19948857, year = {2010}, author = {Vlaeminck, SE and Terada, A and Smets, BF and De Clippeleir, H and Schaubroeck, T and Bolca, S and Demeestere, L and Mast, J and Boon, N and Carballa, M and Verstraete, W}, title = {Aggregate size and architecture determine microbial activity balance for one-stage partial nitritation and anammox.}, journal = {Applied and environmental microbiology}, volume = {76}, number = {3}, pages = {900-909}, pmid = {19948857}, issn = {1098-5336}, mesh = {Aerobiosis ; Anaerobiosis ; Autotrophic Processes ; Bacteria, Aerobic/*metabolism ; Biodegradation, Environmental ; Bioreactors/microbiology ; Catalysis ; DNA, Ribosomal/metabolism ; Hydrogen-Ion Concentration ; In Situ Hybridization, Fluorescence ; Nitrates/*metabolism ; Nitrites/*metabolism ; Oxygen/metabolism ; Phylogeny ; Quaternary Ammonium Compounds/*metabolism ; RNA, Ribosomal, 16S/metabolism ; Temperature ; Waste Disposal, Fluid ; Water Microbiology ; Water Pollutants, Chemical/*metabolism ; Water Purification ; }, abstract = {Aerobic ammonium-oxidizing bacteria (AerAOB) and anoxic ammonium-oxidizing bacteria (AnAOB) cooperate in partial nitritation/anammox systems to remove ammonium from wastewater. In this process, large granular microbial aggregates enhance the performance, but little is known about granulation so far. In this study, three suspended-growth oxygen-limited autotrophic nitrification-denitrification (OLAND) reactors with different inoculation and operation (mixing and aeration) conditions, designated reactors A, B, and C, were used. The test objectives were (i) to quantify the AerAOB and AnAOB abundance and the activity balance for the different aggregate sizes and (ii) to relate aggregate morphology, size distribution, and architecture putatively to the inoculation and operation of the three reactors. A nitrite accumulation rate ratio (NARR) was defined as the net aerobic nitrite production rate divided by the anoxic nitrite consumption rate. The smallest reactor A, B, and C aggregates were nitrite sources (NARR, >1.7). Large reactor A and C aggregates were granules capable of autonomous nitrogen removal (NARR, 0.6 to 1.1) with internal AnAOB zones surrounded by an AerAOB rim. Around 50% of the autotrophic space in these granules consisted of AerAOB- and AnAOB-specific extracellular polymeric substances. Large reactor B aggregates were thin film-like nitrite sinks (NARR, <0.5) in which AnAOB were not shielded by an AerAOB layer. Voids and channels occupied 13 to 17% of the anoxic zone of AnAOB-rich aggregates (reactors B and C). The hypothesized granulation pathways include granule replication by division and budding and are driven by growth and/or decay based on species-specific physiology and by hydrodynamic shear and mixing.}, }
@article {pmid19946683, year = {2010}, author = {Iasur-Kruh, L and Hadar, Y and Milstein, D and Gasith, A and Minz, D}, title = {Microbial population and activity in wetland microcosms constructed for improving treated municipal wastewater.}, journal = {Microbial ecology}, volume = {59}, number = {4}, pages = {700-709}, pmid = {19946683}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*growth &amp; development ; Biodiversity ; *Biofilms ; Cluster Analysis ; Electrophoresis, Polyacrylamide Gel ; Phylogeny ; Polymerase Chain Reaction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Waste Disposal, Fluid/*methods ; *Water Microbiology ; *Wetlands ; }, abstract = {The idea of using constructed wetlands for the treatment and improving of wastewater emerged in the second half of the last century. Despite relatively wide use of this environmentally friendly technology, relatively little is known about the microbial populations involved in biotransformation and removal of contaminants in this system. The aim of the current study was to investigate the assembly and function of microbial populations in vertical-flow constructed wetland microcosms designed to improve the quality of wastewater after activated sludge treatment. Also, the performance of 3-year-old wetland ponds was investigated. Even though the quality of the influent water was relatively high, improvement in water parameters such as coliform level, ammonia concentration, BOD, and TSS was observed. The performance of the wetland ponds was comparable to that of the microcosms. The microbial community composition of the biofilm formed on the surface of gravel particles in vegetated and plant-free microcosms was studied by denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rRNA gene fragments. Highly complex bacterial diversity was observed in the biofilm. Cluster analysis of DGGE patterns demonstrated that depth within the wetland microcosm has a stronger effect on microbial community composition of the biofilm formed on wetland matrix than vegetation. Measurements of fluorescein diacetate hydrolysis activity and nitrification potential revealed that hydrolytic activity was affected by both microcosm depth and vegetation presence, whereas nitrification potential was mostly influenced by depth. Resolving the bacterial assemblage of wetland biofilm, which often is considered a black box, will help to understand the interactions involved in the development of diverse and mature biofilm and its function.}, }
@article {pmid19946138, year = {2009}, author = {Zengler, K}, title = {Central role of the cell in microbial ecology.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {73}, number = {4}, pages = {712-729}, pmid = {19946138}, issn = {1098-5557}, mesh = {Bacteria/cytology/genetics/growth &amp; development/isolation &amp; purification ; Ecology ; *Ecosystem ; *Environmental Microbiology ; Genetics, Microbial ; Genome ; Microbiological Techniques ; Species Specificity ; }, abstract = {Over the last few decades, advances in cultivation-independent methods have significantly contributed to our understanding of microbial diversity and community composition in the environment. At the same time, cultivation-dependent methods have thrived, and the growing number of organisms obtained thereby have allowed for detailed studies of their physiology and genetics. Still, most microorganisms are recalcitrant to cultivation. This review not only conveys current knowledge about different isolation and cultivation strategies but also discusses what implications can be drawn from pure culture work for studies in microbial ecology. Specifically, in the light of single-cell individuality and genome heterogeneity, it becomes important to evaluate population-wide measurements carefully. An overview of various approaches in microbial ecology is given, and the cell as a central unit for understanding processes on a community level is discussed.}, }
@article {pmid19943775, year = {2009}, author = {Emami, CN and Petrosyan, M and Giuliani, S and Williams, M and Hunter, C and Prasadarao, NV and Ford, HR}, title = {Role of the host defense system and intestinal microbial flora in the pathogenesis of necrotizing enterocolitis.}, journal = {Surgical infections}, volume = {10}, number = {5}, pages = {407-417}, pmid = {19943775}, issn = {1557-8674}, mesh = {Animals ; *Enterocolitis, Necrotizing/immunology/microbiology/physiopathology ; Humans ; Infant, Newborn ; Infant, Premature ; *Infant, Premature, Diseases/immunology/microbiology/physiopathology ; Intestinal Mucosa/*microbiology ; }, abstract = {BACKGROUND: Necrotizing enterocolitis (NEC) is a devastating disease that affects primarily the intestine of premature infants. Despite recent advances in neonatology, NEC remains a major cause of morbidity and mortality in neonates. Neonatal mucosal defenses and adherence of bacterial pathogens may play an important role in the pathogenesis of NEC.<br><br>METHODS: Review and synthesis of pertinent literature.<br><br>RESULTS: Putative factors that have been implicated in the pathogenesis of NEC include abnormal patterns of gut colonization by bacteria, immaturity of the host immune system and mucosal defense mechanisms, intestinal ischemia, formula feeding, and loss of intestinal epithelial barrier integrity.<br><br>CONCLUSION: Host defenses and intestinal microbial ecology are believed to play important roles in the pathogenesis of NEC. Commensal bacteria and probiotic therapy may be of therapeutic utility in the maintenance of the gut epithelial barrier.}, }
@article {pmid19942690, year = {2010}, author = {Van Immerseel, F and Ducatelle, R and De Vos, M and Boon, N and Van De Wiele, T and Verbeke, K and Rutgeerts, P and Sas, B and Louis, P and Flint, HJ}, title = {Butyric acid-producing anaerobic bacteria as a novel probiotic treatment approach for inflammatory bowel disease.}, journal = {Journal of medical microbiology}, volume = {59}, number = {Pt 2}, pages = {141-143}, doi = {10.1099/jmm.0.017541-0}, pmid = {19942690}, issn = {1473-5644}, mesh = {Bacteria, Anaerobic/*metabolism ; Butyric Acid/*metabolism ; Fermentation ; Humans ; Inflammatory Bowel Diseases/*therapy ; Probiotics/*pharmacology ; }, }
@article {pmid19941629, year = {2010}, author = {Gomez, E and Tuohy, KM and Gibson, GR and Klinder, A and Costabile, A}, title = {In vitro evaluation of the fermentation properties and potential prebiotic activity of Agave fructans.}, journal = {Journal of applied microbiology}, volume = {108}, number = {6}, pages = {2114-2121}, doi = {10.1111/j.1365-2672.2009.04617.x}, pmid = {19941629}, issn = {1365-2672}, mesh = {Adult ; Agave/*chemistry ; Bifidobacterium/*isolation &amp; purification ; Fatty Acids, Volatile/biosynthesis ; Feces/microbiology ; Female ; *Fermentation ; Humans ; In Situ Hybridization, Fluorescence ; Lactobacillaceae/*isolation &amp; purification ; Male ; *Prebiotics ; }, abstract = {AIMS: This study was carried out to evaluate in vitro the fermentation properties and the potential prebiotic activity of Agave-fructans extracted from Agave tequilana (Predilife).<br><br>METHODS AND RESULTS: Five different commercial prebiotics were compared using 24-h pH-controlled anaerobic batch cultures inoculated with human faecal slurries. Measurement of prebiotic efficacy was obtained by comparing bacterial changes, and the production of short-chain fatty acids (SCFA) was also determined. Effects upon major groups of the microbiota were monitored over 24 h incubations by fluorescence in situ hybridization. SCFA were measured by HPLC. Fermentation of the Agave fructans (Predilife) resulted in a large increase in numbers of bifidobacteria and lactobacilli.<br><br>CONCLUSIONS: Under the in vitro conditions used, this study has shown the differential impact of Predilife on the microbial ecology of the human gut.<br><br>This is the first study reporting of a potential prebiotic mode of activity for Agave fructans investigated which significantly increased populations of bifidobacteria and lactobacilli compared to cellulose used as a control.}, }
@article {pmid19939433, year = {2010}, author = {Hennebel, T and De Corte, S and Vanhaecke, L and Vanherck, K and Forrez, I and De Gusseme, B and Verhagen, P and Verbeken, K and Van der Bruggen, B and Vankelecom, I and Boon, N and Verstraete, W}, title = {Removal of diatrizoate with catalytically active membranes incorporating microbially produced palladium nanoparticles.}, journal = {Water research}, volume = {44}, number = {5}, pages = {1498-1506}, doi = {10.1016/j.watres.2009.10.041}, pmid = {19939433}, issn = {1879-2448}, mesh = {Bacteria/*metabolism ; Biodegradation, Environmental ; Catalysis ; Chromatography, High Pressure Liquid ; Diatrizoate/*isolation &amp; purification ; Kinetics ; Mass Spectrometry ; *Membranes, Artificial ; Nanoparticles/*chemistry/ultrastructure ; Palladium/*chemistry ; Polymers/chemistry ; Polyvinyls/chemistry ; Spectrometry, X-Ray Emission ; Sulfones/chemistry ; }, abstract = {There is an increasing concern about the fate of iodinated contrast media (ICM) in the environment. Limited removal efficiencies of currently applied techniques such as advanced oxidation processes require more performant strategies. The aim of this study was to establish an innovative degradation process for diatrizoate, a highly recalcitrant ICM, by using biogenic Pd nanoparticles as free suspension or immobilized in polyvinylidene fluoride (PVDF) and polysulfone (PSf) membranes. As measured by HPLC-UV, the removal of 20mg L(-1) diatrizoate by a 10mg L(-1) Pd suspension was completed after 4h at a pH of 10. LC-MS analysis provided evidence for the sequential hydrodeiodination of diatrizoate. Pd did not lose its activity after incorporation in the PVDF and PSf matrix and the highest activity (k(cat)=30.0+/-0.4h(-1) L g(-1) Pd) was obtained with a casting solution of 10% PSf and 500mg L(-1) Pd. Subsequently, water containing 20mg L(-1) diatrizoate was treated in a membrane contactor, in which the water was supplied at one side of the membrane while hydrogen was provided at the other side. In a fed batch configuration, a removal efficiency of 77% after a time period of 48h was obtained. This work showed that membrane contactors with encapsulated biogenic nanoparticles can be instrumental for treatment of water contaminated with diatrizoate.}, }
@article {pmid19937324, year = {2010}, author = {Wong, FK and Lau, MC and Lacap, DC and Aitchison, JC and Cowan, DA and Pointing, SB}, title = {Endolithic microbial colonization of limestone in a high-altitude arid environment.}, journal = {Microbial ecology}, volume = {59}, number = {4}, pages = {689-699}, pmid = {19937324}, issn = {1432-184X}, mesh = {*Altitude ; Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Calcium Carbonate/*analysis ; Desert Climate ; *Environmental Microbiology ; Geography ; Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal/analysis ; Tibet ; }, abstract = {The morphology of endolithic colonization in a limestone escarpment and surrounding rocky debris (termed float) at a high-altitude arid site in central Tibet was documented using scanning electron microscopy. Putative lichenized structures and extensive coccoid bacterial colonization were observed. Absolute and relative abundance of rRNA gene signatures using real-time quantitative polymerase chain reaction and phylogenetic analysis of environmental phylotypes were used to characterize community structure across all domains. Escarpment endoliths were dominated by eukaryotic phylotypes suggestive of lichenised associations (a Trebouxia lichen phycobiont and Leptodontidium lichen mycobiont), whereas float endoliths were dominated by bacterial phylotypes, including the cyanobacterium Chroococcidiopsis plus several unidentified beta proteobacteria and crenarchaea. Among a range of abiotic variables tested, ultraviolet (UV) transmittance by rock substrates was the factor best able to explain differences in community structure, with eukaryotic lichen phylotypes more abundant under conditions of greater UV-exposure compared to prokaryotes. Variously pigmented float rocks did not support significantly different communities. Estimates of in situ carbon fixation based upon (14)C radio-labelled bicarbonate uptake indicated endolithic productivity of approximately 2.01 g C/m(2)/year(-1), intermediate between estimates for Antarctic and temperate communities.}, }
@article {pmid19936822, year = {2010}, author = {Freese, HM and Eggert, A and Garland, JL and Schumann, R}, title = {Substrate utilization profiles of bacterial strains in plankton from the River Warnow, a humic and eutrophic river in north Germany.}, journal = {Microbial ecology}, volume = {59}, number = {1}, pages = {59-75}, pmid = {19936822}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics/metabolism ; Biodiversity ; Carbon/metabolism ; DNA Fingerprinting ; Environmental Monitoring ; Eutrophication ; Germany ; Humic Substances ; Oxygen/metabolism ; Plankton/*classification/genetics/metabolism ; RNA, Ribosomal, 16S/metabolism ; Rivers/chemistry/*microbiology ; }, abstract = {Bacteria are very important degraders of organic substances in aquatic environments. Despite their influential role in the carbon (and many other element) cycle(s), the specific genetic identity of active bacteria is mostly unknown, although contributing phylogenetic groups had been investigated. Moreover, the degree to which phenotypic potential (i. e., utilization of environmentally relevant carbon substrates) is related to the genomic identity of bacteria or bacterial groups is unclear. The present study compared the genomic fingerprints of 27 bacterial isolates from the humic River Warnow with their ability to utilize 14 environmentally relevant substrates. Acetate was the only substrate utilized by all bacterial strains. Only 60% of the strains respired glucose, but this substrate always stimulated the highest bacterial activity (respiration and growth). Two isolates, both closely related to the same Pseudomonas sp., also had very similar substrate utilization patterns. However, similar substrate utilization profiles commonly belonged to genetically different strains (e.g., the substrate profile of Janthinobacterium lividum OW6/RT-3 and Flavobacterium sp. OW3/15-5 differed by only three substrates). Substrate consumption was sometimes totally different for genetically related isolates. Thus, the genomic profiles of bacterial strains were not congruent with their different substrate utilization profiles. Additionally, changes in pre-incubation conditions strongly influenced substrate utilization. Therefore, it is problematic to infer substrate utilization and especially microbial dissolved organic matter transformation in aquatic systems from bacterial molecular taxonomy.}, }
@article {pmid19924467, year = {2010}, author = {Robinson, CJ and Schloss, P and Ramos, Y and Raffa, K and Handelsman, J}, title = {Robustness of the bacterial community in the cabbage white butterfly larval midgut.}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {199-211}, pmid = {19924467}, issn = {1432-184X}, support = {T32 GM008349/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; 5 T32 GM08349/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/*genetics ; *Biodiversity ; Butterflies/*microbiology ; DNA, Bacterial/genetics ; Digestive System/microbiology ; Larva/microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Microbial communities typically vary in composition and structure over space and time. Little is known about the inherent characteristics of communities that govern various drivers of these changes, such as random variation, changes in response to perturbation, or susceptibility to invasion. In this study, we use 16S ribosomal RNA gene sequences to describe variation among bacterial communities in the midguts of cabbage white butterfly (Pieris rapae) larvae and examine the influence of community structure on susceptibility to invasion. We compared communities in larvae experiencing the same conditions at different times (temporal variation) or fed different diets (perturbation). The most highly represented phylum was Proteobacteria, which was present in all midgut communities. The observed species richness ranged from six to 15, and the most abundant members affiliated with the genera Methylobacteria, Asaia, Acinetobacter, Enterobacter, and Pantoea. Individual larvae subjected to the same conditions at the same time harbored communities that were highly similar in structure and membership, whereas the communities observed within larval populations changed with diet and over time. In addition, structural changes due to perturbation coincided with enhanced susceptibility to invasion by Enterobacter sp. NAB3R and Pantoea stewartii CWB600, suggesting that resistance to invasion is in part governed by community structure. These findings along with the observed conservation of membership at the phylum level, variation in structure and membership at lower taxonomic levels, and its relative simplicity make the cabbage white butterfly larval community an attractive model for studying community dynamics and robustness.}, }
@article {pmid19924466, year = {2010}, author = {Koike, S and Aminov, RI and Yannarell, AC and Gans, HD and Krapac, IG and Chee-Sanford, JC and Mackie, RI}, title = {Molecular ecology of macrolide-lincosamide-streptogramin B methylases in waste lagoons and subsurface waters associated with swine production.}, journal = {Microbial ecology}, volume = {59}, number = {3}, pages = {487-498}, pmid = {19924466}, issn = {1432-184X}, mesh = {Animals ; DNA Primers ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Fresh Water/*microbiology ; Genes, Bacterial ; Lincosamides/pharmacology ; Macrolides/pharmacology ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Streptogramin B/pharmacology ; Streptomyces/drug effects/*enzymology/genetics ; Swine ; Tetracycline Resistance ; *Waste Disposal, Fluid ; Water Microbiology ; tRNA Methyltransferases/genetics/*isolation &amp; purification ; }, abstract = {RNA methylase genes are common antibiotic resistance determinants for multiple drugs of the macrolide, lincosamide, and streptogramin B (MLS(B)) families. We used molecular methods to investigate the diversity, distribution, and abundance of MLS(B) methylases in waste lagoons and groundwater wells at two swine farms with a history of tylosin (a macrolide antibiotic structurally related to erythromycin) and tetracycline usage. Phylogenetic analysis guided primer design for quantification of MLS(B) resistance genes found in tylosin-producing Streptomyces (tlr(B), tlr(D)) and commensal/pathogenic bacteria (erm(A), erm(B), erm(C), erm(F), erm(G), erm(Q)). The near absence of tlr genes at these sites suggested a lack of native antibiotic-producing organisms. The gene combination erm(ABCF) was found in all lagoon samples analyzed. These four genes were also detected with high frequency in wells previously found to be contaminated by lagoon leakage. A weak correlation was found between the distribution of erm genes and previously reported patterns of tetracycline resistance determinants, suggesting that dissemination of these genes into the environment is not necessarily linked. Considerations of gene origins in history (i.e., phylogeny) and gene distributions in the landscape provide a useful "molecular ecology" framework for studying environmental spread of antibiotic resistance.}, }
@article {pmid19921327, year = {2010}, author = {Hamilton, CE and Dowling, TE and Faeth, SH}, title = {Hybridization in endophyte symbionts alters host response to moisture and nutrient treatments.}, journal = {Microbial ecology}, volume = {59}, number = {4}, pages = {768-775}, pmid = {19921327}, issn = {1432-184X}, mesh = {Biomass ; Festuca/*growth &amp; development/*microbiology ; *Hybridization, Genetic ; Neotyphodium/*genetics/growth &amp; development ; Phenotype ; Plant Roots/growth &amp; development/microbiology ; Soil/analysis ; *Soil Microbiology ; Stress, Physiological ; *Symbiosis ; }, abstract = {When a host organism is infected by a symbiont, the resulting symbiotum has a phenotype distinct from uninfected hosts. Genotypic interactions between the partners may increase phenotypic variation of the host at the population level. Neotyphodium is an asexual, vertically transmitted endophytic symbiont of grasses often existing in hybrid form. Hybridization in Neotyphodium rapidly increases the symbiotum's genomic content and is likely to increase the phenotypic variation of the host. This phenotypic variation is predicted to enhance host performance, especially in stressful environments. We tested this hypothesis by comparing the growth, survival, and resource allocation of hybrid and nonhybrid infected host plants exposed to controlled variation in soil moisture and nutrients. Infection by a hybrid endophyte did not fit our predictions of comparatively higher root and total biomass production under low moisture/low nutrient treatments. Regardless of whether the host was infected by a hybrid or nonhybrid endophyte, both produced significantly higher root/total biomass when both nutrient and moisture were high compared to limited nutrient/moisture treatments. However, infection by hybrid Neotyphodium did result in significantly higher total biomass and host survival compared to nonhybrid infected hosts, regardless of treatment. Endophyte hybridization alters host strategies in response to stress by increasing survival in depauperate habitats and thus, potentially increasing the relative long-term host fitness.}, }
@article {pmid19918089, year = {2010}, author = {Filoche, S and Wong, L and Sissons, CH}, title = {Oral biofilms: emerging concepts in microbial ecology.}, journal = {Journal of dental research}, volume = {89}, number = {1}, pages = {8-18}, doi = {10.1177/0022034509351812}, pmid = {19918089}, issn = {1544-0591}, mesh = {Biofilms/*classification ; Dental Plaque/microbiology/*physiopathology ; *Health Status ; Health Status Indicators ; Humans ; Individuality ; Metagenome/*physiology ; Microbial Interactions ; Mouth/*microbiology/physiopathology ; }, abstract = {Oral biofilms develop under a range of different conditions and different environments. This review will discuss emerging concepts in microbial ecology and how they relate to oral biofilm development and the treatment of oral diseases. Clues to how oral biofilms develop may lie in other complex systems, such as interactions between host and gut microbiota, and even in factors that affect biofilm development on leaf surfaces. Most of the conditions under which oral biofilms develop are tightly linked to the overall health and biology of the host. Advances in molecular techniques have led to a greater appreciation of the diversity of human microbiota, the extent of interactions with the human host, and how that relates to inter-individual variation. As a consequence, plaque development may no longer be thought of as a generic process, but rather as a highly individualized process, which has ramifications for the treatment of the diseases it causes.}, }
@article {pmid19914921, year = {2010}, author = {Caporaso, JG and Bittinger, K and Bushman, FD and DeSantis, TZ and Andersen, GL and Knight, R}, title = {PyNAST: a flexible tool for aligning sequences to a template alignment.}, journal = {Bioinformatics (Oxford, England)}, volume = {26}, number = {2}, pages = {266-267}, pmid = {19914921}, issn = {1367-4811}, support = {1U01HG004866-01/HG/NHGRI NIH HHS/United States ; T15LM009451/LM/NLM NIH HHS/United States ; UH2CA140233/CA/NCI NIH HHS/United States ; UH2DK083981/DK/NIDDK NIH HHS/United States ; }, mesh = {Algorithms ; Databases, Genetic ; Sequence Alignment/*methods ; Sequence Analysis, RNA/methods ; *Software ; User-Computer Interface ; }, abstract = {MOTIVATION: The Nearest Alignment Space Termination (NAST) tool is commonly used in sequence-based microbial ecology community analysis, but due to the limited portability of the original implementation, it has not been as widely adopted as possible. Python Nearest Alignment Space Termination (PyNAST) is a complete reimplementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programming interface (API).<br><br>RESULTS: The availability of PyNAST will make the popular NAST algorithm more portable and thereby applicable to datasets orders of magnitude larger by allowing users to install PyNAST on their own hardware. Additionally because users can align to arbitrary template alignments, a feature not available via the original NAST web interface, the NAST algorithm will be readily applicable to novel tasks outside of microbial community analysis.<br><br>AVAILABILITY: PyNAST is available at http://pynast.sourceforge.net.}, }
@article {pmid19906526, year = {2010}, author = {Tsekova, K and Todorova, D and Dencheva, V and Ganeva, S}, title = {Biosorption of copper(II) and cadmium(II) from aqueous solutions by free and immobilized biomass of Aspergillus niger.}, journal = {Bioresource technology}, volume = {101}, number = {6}, pages = {1727-1731}, doi = {10.1016/j.biortech.2009.10.012}, pmid = {19906526}, issn = {1873-2976}, mesh = {Adsorption ; Aspergillus niger/*metabolism ; Biodegradation, Environmental ; *Biomass ; Biotechnology/*methods ; Cadmium/*chemistry ; Copper/*chemistry ; Diffusion ; Fungi/metabolism ; Ions ; Kinetics ; Metals/chemistry ; Solutions ; Spores, Fungal/chemistry ; Time Factors ; }, abstract = {This study investigates the ability of Aspergillus niger resting cells entrapped into poly(vinyl alcohol) (PVA) network to remove Cu(II) and Cd(II) from single ions solutions. The performance of free and immobilized biosorbent was evaluated by equilibrium and kinetic studies. The PVA-immobilized fungal biosorbent removed Cu(II) and Cd(II) rapidly and efficiently with maximum metal removal capacities of 34.13 mg/g and 60.24 mg/g, respectively. These values of heavy metal uptake at equilibrium were higher than the amount of Cu(II) and Cd(II) removal by free biomass (17.60 mg/g and 69.44 mg/g, respectively). Biosorption equilibrium data were best described by Langmuir isotherm model. The biosorption kinetics followed the pseudo-second order model and intraparticle diffusion equation. The results obtained suggest that the immobilized biosorbent holds great potential for wastewater treatment applications.}, }
@article {pmid19906224, year = {2009}, author = {Ahmed, T and Haque, R and Shamsir Ahmed, AM and Petri, WA and Cravioto, A}, title = {Use of metagenomics to understand the genetic basis of malnutrition.}, journal = {Nutrition reviews}, volume = {67 Suppl 2}, number = {}, pages = {S201-6}, doi = {10.1111/j.1753-4887.2009.00241.x}, pmid = {19906224}, issn = {1753-4887}, support = {P30 DK067629/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Biomarkers ; Child Nutrition Disorders/*genetics/microbiology/therapy ; Child, Preschool ; Gastrointestinal Tract/*microbiology ; Genetic Markers ; Genetic Predisposition to Disease ; Humans ; Infant ; Infant, Newborn ; Intestinal Absorption ; *Metagenome ; *Nutrigenomics ; Nutritional Physiological Phenomena/*physiology ; Risk Factors ; }, abstract = {Childhood malnutrition is not just due to lack of nutrients, it can also be caused by enteric infections leading to intestinal inflammation and malabsorption of nutrients. Human genetic polymorphisms can alter host genes that affect nutrient absorption and metabolism. Changes in intestinal microbial ecology and the microbiome (the collective genome of the intestinal microbiota) can also affect the harvest of nutrients from the diet. A substantial proportion of malnourished children fail to recover due to inappropriate treatment. However, there may be other causes for treatment failure, including changes in the microbiome and infection with an enteropathogen, and a genetic predisposition to malnutrition may exist. It is, therefore, logical to undertake the following: 1) investigate genetic predisposition to malnutrition, 2) determine the genetic markers and biomarkers that can help identify children at risk of malnutrition, and 3) look for new treatment modalities that can improve the clinical management of children with malnutrition.}, }
@article {pmid19904569, year = {2010}, author = {Wu, QL and Xing, P and Liu, WT}, title = {East Tibetan lakes harbour novel clusters of picocyanobacteria as inferred from the 16S-23S rRNA internal transcribed spacer sequences.}, journal = {Microbial ecology}, volume = {59}, number = {3}, pages = {614-622}, pmid = {19904569}, issn = {1432-184X}, mesh = {*Biodiversity ; Cluster Analysis ; Colony Count, Microbial ; Cyanobacteria/classification/*genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Fresh Water/*microbiology ; Microscopy, Fluorescence ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Salinity ; Sequence Analysis, DNA ; Tibet ; *Water Microbiology ; }, abstract = {Planktonic picocyanobacteria abundance and diversity were investigated in nine lakes on the East Tibetan Plateau spanning a salinity gradient of 0.4-22.6 g l(-1). The investigation was conducted using epifluorescence microscopy (EFM) and terminal restriction fragment polymorphism analysis of 16S-23S rRNA internal transcribed spacer (ITS) PCR amplicons followed by sequence analyses of large ITS clone libraries of seven selected samples. EFM showed that picocyanobacteria comprised 7-19% of the total prokaryotic cells found in surface water. Most of the clones were classified into six clusters and grouped within the "picocyanobacterial clade", which consists exclusively of freshwater Synechococcus. Four new phylogenetic clusters and one new subcluster of Synechococcus spp. were found, none of which are members of any known picocyanobacterial clusters. The new clusters and subcluster were the most abundant picocyanobacteria (about 96% of the sequences) in the samples collected. Sequence analyses indicated that members of the four new Synechococcus groups were only found in freshwater lakes (<1.0 g l(-1) of total dissolved solid), while members of the new subcluster were found in all the investigated Tibetan lakes, over a large salinity gradient of 0.4-22.6 g l(-1). This suggests that there is ecologically significant microdiversity within the observed Synechococcus group as defined by ITS sequences. Collectively our study demonstrated abundant and potentially novel Synechococcus in East Tibetan lakes that are likely the result of evolutionary adaptations to regional conditions.}, }
@article {pmid19903395, year = {2009}, author = {Ottesen, AR and White, JR and Skaltsas, DN and Newell, MJ and Walsh, CS}, title = {Impact of organic and conventional management on the phyllosphere microbial ecology of an apple crop.}, journal = {Journal of food protection}, volume = {72}, number = {11}, pages = {2321-2325}, doi = {10.4315/0362-028x-72.11.2321}, pmid = {19903395}, issn = {0362-028X}, mesh = {Agriculture/*methods ; Bacteria/classification/*isolation &amp; purification ; *Consumer Product Safety ; DNA, Bacterial/genetics ; Food Contamination/*analysis ; Humans ; Malus/*microbiology ; Plant Leaves/microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bacterial communities associated with the phyllosphere of apple trees (Malus domestica cv. Enterprise) grown under organic and conventional management were assessed to determine if increased biological food safety risks might be linked with the bacterial communities associated with either treatment. Libraries of 16S rRNA genes were generated from phyllosphere DNA extracted from a wash made from the surfaces of leaves and apples from replicated organic and conventional treatments. 16S rRNA gene libraries were analyzed with software designed to identify statistically significant differences between bacterial communities as well as shared and unique phylotypes. The identified diversity spanned eight bacterial phyla and 14 classes in the pooled organic and conventional libraries. Significant differences between organic and conventional communities were observed at four of six time points (P < 0.05). Despite the identification of significantly diverse microfloras associated with organic and conventional treatments, no detectable differences in the presence of potential enteric pathogens could be associated with either organic or conventional management. Neither of the bacterial genera most commonly associated with produce-related illness outbreaks (Salmonella and Escherichia) was observed in any of the libraries. The impressive bacterial diversity that was documented in this study provides a valuable contribution to our developing understanding of the total microbial ecology associated with the preharvest phyllospheres of food crops. The fact that organic and conventional phyllosphere bacterial communities were significantly different at numerous time points suggests that crop management methods may influence the bacterial consortia associated with the surfaces of fruits and vegetables.}, }
@article {pmid19901833, year = {2010}, author = {Ley, RE}, title = {Obesity and the human microbiome.}, journal = {Current opinion in gastroenterology}, volume = {26}, number = {1}, pages = {5-11}, doi = {10.1097/MOG.0b013e328333d751}, pmid = {19901833}, issn = {1531-7056}, mesh = {Animals ; Body Mass Index ; Dietary Fats/metabolism ; Energy Metabolism/genetics ; Gastroenteritis/genetics/physiopathology ; Gastrointestinal Tract/metabolism/*microbiology ; Genetic Predisposition to Disease ; Humans ; Insulin Resistance/*genetics ; Metagenome/*genetics/physiology ; Mice ; Obesity/*genetics/metabolism ; Rats ; Risk Assessment ; Sensitivity and Specificity ; Swine ; }, abstract = {PURPOSE OF REVIEW: Obesity was once rare, but the last few decades have seen a rapid expansion of the proportion of obese individuals worldwide. Recent work has shown obesity to be associated with a shift in the representation of the dominant phyla of bacteria in the gut, both in humans and animal models. This review summarizes the latest research into the association between microbial ecology and host adiposity, and the mechanisms by which microbes in the gut may mediate host metabolism in the context of obesity.<br><br>RECENT FINDINGS: Studies of the effect of excess body fat on the abundances of different bacteria taxa in the gut generally show alterations in the gastrointestinal microbiota, and changes during weight loss. The gastrointestinal microbiota have been shown to impact insulin resistance, inflammation, and adiposity via interactions with epithelial and endocrine cells.<br><br>SUMMARY: Large-scale alterations of the gut microbiota and its microbiome (gene content) are associated with obesity and are responsive to weight loss. Gut microbes can impact host metabolism via signaling pathways in the gut, with effects on inflammation, insulin resistance, and deposition of energy in fat stores. Restoration of the gut microbiota to a healthy state may ameliorate the conditions associated with obesity and help maintain a healthy weight.}, }
@article {pmid19888628, year = {2010}, author = {Vadasz, P and Vadasz, AS}, title = {On the distinction between lag and delay in population growth.}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {233-245}, pmid = {19888628}, issn = {1432-184X}, mesh = {Bacteria/*growth &amp; development ; Colony Count, Microbial ; *Models, Biological ; Population Dynamics ; }, abstract = {The analysis and results presented in this paper provide conclusive evidence to distinguish between the delay effect and the lag as two biologically distinct phenomena. It therefore dispels the incorrect notion that delay effects represented by delay differential equations are the biological reason behind the lag phase in microorganism growth. The resulting consequence so far is that the only other reason for the lag phase is the existence of unstable stationary states. The latter are a result of accounting for the microbial metabolic mass transfer in the population growth process.}, }
@article {pmid19888627, year = {2010}, author = {Rastogi, G and Osman, S and Vaishampayan, PA and Andersen, GL and Stetler, LD and Sani, RK}, title = {Microbial diversity in uranium mining-impacted soils as revealed by high-density 16S microarray and clone library.}, journal = {Microbial ecology}, volume = {59}, number = {1}, pages = {94-108}, pmid = {19888627}, issn = {1432-184X}, mesh = {Bacteria/*classification/drug effects/genetics ; Base Sequence ; *Biodiversity ; Environmental Monitoring ; Gene Library ; Industrial Waste ; *Mining ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/analysis ; Soil Microbiology ; Soil Pollutants/*analysis ; Uranium/*analysis ; }, abstract = {Microbial diversity was characterized in mining-impacted soils collected from two abandoned uranium mine sites, the Edgemont and the North Cave Hills, South Dakota, using a high-density 16S microarray (PhyloChip) and clone libraries. Characterization of the elemental compositions of soils by X-ray fluorescence spectroscopy revealed higher metal contamination including uranium at the Edgemont than at the North Cave Hills mine site. Microarray data demonstrated extensive phylogenetic diversity in soils and confirmed nearly all clone-detected taxonomic levels. Additionally, the microarray exhibited greater diversity than clone libraries at each taxonomic level at both the mine sites. Interestingly, the PhyloChip detected the largest number of taxa in Proteobacteria phylum for both the mine sites. However, clone libraries detected Acidobacteria and Bacteroidetes as the most numerically abundant phyla in the Edgemont and North Cave Hills mine sites, respectively. Several 16S rDNA signatures found in both the microarrays and clone libraries displayed sequence similarities with yet-uncultured bacteria representing a hitherto unidentified diversity. Results from this study demonstrated that highly diverse microbial populations were present in these uranium mine sites. Diversity indices indicated that microbial communities at the North Cave Hills mine site were much more diverse than those at the Edgemont mine site.}, }
@article {pmid19888626, year = {2010}, author = {Nechitaylo, TY and Yakimov, MM and Godinho, M and Timmis, KN and Belogolova, E and Byzov, BA and Kurakov, AV and Jones, DL and Golyshin, PN}, title = {Effect of the earthworms Lumbricus terrestris and Aporrectodea caliginosa on bacterial diversity in soil.}, journal = {Microbial ecology}, volume = {59}, number = {3}, pages = {574-587}, pmid = {19888626}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/*genetics ; DNA Primers ; DNA, Bacterial/genetics ; Gastrointestinal Tract/*microbiology ; Gene Library ; In Situ Hybridization, Fluorescence ; Oligochaeta/*microbiology/physiology ; Phylogeny ; Polymorphism, Single-Stranded Conformational ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Earthworms ingest large amounts of soil and have the potential to radically alter the biomass, activity, and structure of the soil microbial community. In this study, the diversity of eight bacterial groups from fresh soil, gut, and casts of the earthworms Lumbricus terrestris and Aporrectodea caliginosa were studied by single-strand conformation polymorphism (SSCP) analysis using both newly designed 16S rRNA gene-specific primer sets targeting Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Bacteroidetes, Verrucomicrobia, Planctomycetes, and Firmicutes and a conventional universal primer set for SSCP, with RNA and DNA as templates. In parallel, the study of the relative abundance of these taxonomic groups in the same samples was performed using fluorescence in situ hybridization. Bacteroidetes, Alphaproteobacteria, and Betaproteobacteria were predominant in communities from the soil and worm cast samples. Representatives of classes Flavobacteria and Sphingobacteria (Bacteroidetes) and Pseudomonas spp. (low-abundant Gammaproteobacteria) were detected in soil and worm cast samples with conventional and taxon-targeting SSCP and through the sequence analysis of 16S rRNA clone libraries. Physiologically active unclassified Sphingomonadaceae (Alphaproteobacteria) and Alcaligenes spp. (Betaproteobacteria) also maintained their diversities during transit through the earthworm intestine and were found on taxon-targeting SSCP profiles from the soil and worm cast samples. In conclusion, our results suggest that some specific bacterial taxonomic groups maintain their diversity and even increase their relative numbers during transit through the gastrointestinal tract of earthworms.}, }
@article {pmid19888625, year = {2010}, author = {Stabili, L and Gravili, C and Boero, F and Tredici, SM and Alifano, P}, title = {Susceptibility to antibiotics of Vibrio sp. AO1 growing in pure culture or in association with its hydroid host Aglaophenia octodonta (Cnidaria, Hydrozoa).}, journal = {Microbial ecology}, volume = {59}, number = {3}, pages = {555-562}, pmid = {19888625}, issn = {1432-184X}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; *Drug Resistance, Multiple, Bacterial ; Hydrozoa/*microbiology ; Microbial Sensitivity Tests ; Vibrio/*drug effects ; }, abstract = {Vibrio harveyi is the major causal organism of vibriosis, causing potential devastation to diverse ranges of marine invertebrates over a wide geographical area. These microorganisms, however, are phenotypically diverse, and many of the isolates are also resistant to multiple antibiotics. In a previous study, we described a previously unknown association between Vibrio sp. AO1, a luminous bacterium related to the species V. harveyi, and the benthic hydrozoan Aglaophenia octodonta. In this study, we analyzed the susceptibility to antibiotics (ampicillin, streptomycin, tetracycline, or co-trimoxazole = mix of sulfamethoxazole and trimetoprim) of Vibrio sp. AO1 growing in pure culture or in association with its hydroid host by using microcosm experiments. The results of minimum inhibitory concentration (MIC) experiments demonstrated that Vibrio sp. AO1 was highly resistant to ampicillin and streptomycin in pure culture. Nevertheless, these antibiotics, when used at sub-MIC values, significantly reduced the hydroid fluorescence. Co-trimoxazole showed the highest inhibitory effect on fluorescence of A. octodonta. However, in all treatments, the fluorescence was reduced after 48 h, but never disappeared completely around the folds along the hydrocaulus and at the base of the hydrothecae of A. octodonta when the antibiotic was used at concentration completely inhibiting growth in vitro. The apparent discrepancy between the MIC data and the fluorescence patterns may be due to either heterogeneity of the bacterial population in terms of antibiotic susceptibility or specific chemical-physical conditions of the hydroid microenvironment that may decrease the antibiotic susceptibility of the whole population. The latter hypothesis is supported by scanning electron microscope evidence for development of bacterial biofilm on the hydroid surface. On the basis of the results obtained, we infer that A. octodonta might behave as a reservoir of antibiotic multiresistant bacteria, increasing the risk of their transfer into aquaculture farms.}, }
@article {pmid19888561, year = {2010}, author = {Xu, Y and Wang, D and Fan, WL and Mu, XQ and Chen, J}, title = {Traditional Chinese biotechnology.}, journal = {Advances in biochemical engineering/biotechnology}, volume = {122}, number = {}, pages = {189-233}, doi = {10.1007/10_2008_36}, pmid = {19888561}, issn = {0724-6145}, mesh = {Agriculture/*trends ; Biological Products/*chemistry ; Biotechnology/*trends ; Chemical Industry/*trends ; China ; }, abstract = {The earliest industrial biotechnology originated in ancient China and developed into a vibrant industry in traditional Chinese liquor, rice wine, soy sauce, and vinegar. It is now a significant component of the Chinese economy valued annually at about 150 billion RMB. Although the production methods had existed and remained basically unchanged for centuries, modern developments in biotechnology and related fields in the last decades have greatly impacted on these industries and led to numerous technological innovations. In this chapter, the main biochemical processes and related technological innovations in traditional Chinese biotechnology are illustrated with recent advances in functional microbiology, microbial ecology, solid-state fermentation, enzymology, chemistry of impact flavor compounds, and improvements made to relevant traditional industrial facilities. Recent biotechnological advances in making Chinese liquor, rice wine, soy sauce, and vinegar are reviewed.}, }
@article {pmid19888436, year = {2009}, author = {Vermeiren, J and Van de Wiele, T and Verstraete, W and Boeckx, P and Boon, N}, title = {Nitric oxide production by the human intestinal microbiota by dissimilatory nitrate reduction to ammonium.}, journal = {Journal of biomedicine &amp; biotechnology}, volume = {2009}, number = {}, pages = {284718}, pmid = {19888436}, issn = {1110-7251}, mesh = {Anaerobiosis ; Arginine/metabolism ; Buffers ; Colon/microbiology ; Culture Media ; Feces/microbiology ; Female ; Humans ; Intestinal Mucosa/*metabolism ; Intestines/*microbiology ; Middle Aged ; Minerals/metabolism ; Models, Biological ; Nitrates/*metabolism ; Nitric Oxide/*biosynthesis ; Nitrogen Isotopes ; Nitrous Oxide/metabolism ; Oxidation-Reduction ; Quaternary Ammonium Compounds/*metabolism ; }, abstract = {The free radical nitric oxide (NO) is an important signaling molecule in the gastrointestinal tract. Besides eukaryotic cells, gut microorganisms are also capable of producing NO. However, the exact mechanism of NO production by the gut microorganisms is unknown. Microbial NO production was examined under in vitro conditions simulating the gastrointestinal ecosystem using L-arginine or nitrate as substrates. L-arginine did not influence the microbial NO production. However, NO concentrations in the order of 90 ng NO-N per L feed medium were produced by the fecal microbiota from nitrate. (15)N tracer experiments showed that nitrate was mainly reduced to ammonium by the dissimilatory nitrate reduction to ammonium (DNRA) pathway. To our knowledge, this is the first study showing that gastrointestinal microbiota can generate substantial amounts of NO by DNRA and not by the generally accepted denitrification or L-arginine pathway. Further work is needed to elucidate the exact role between NO produced by the gastrointestinal microbiota and host cells.}, }
@article {pmid19885659, year = {2010}, author = {Vanpeteghem, D and Haegeman, B}, title = {An analytical approach to spatio-temporal dynamics of neutral community models.}, journal = {Journal of mathematical biology}, volume = {61}, number = {3}, pages = {323-357}, pmid = {19885659}, issn = {1432-1416}, mesh = {Bacteria/*growth &amp; development ; *Biodiversity ; *Ecosystem ; *Models, Biological ; Population Dynamics ; Stochastic Processes ; }, abstract = {We propose a spatial version of the neutral community model on a network of interconnected patches. The dynamical equations for the abundances and higher order moments of the abundances are established. Due to the neutrality assumption these equations are autonomous, enabling an exact analysis of spatio-temporal dynamics. We compute local (i.e., inside a patch) and global (i.e., between patches) diversities, and illustrate our results with two examples: (1) a non-spatial community, for which we recover previous results, and (2) a model with a finite number of patches which are all connected to each other with equal migration intensity. We discuss the relevance of this model for experiments in microbial ecology.}, }
@article {pmid19882280, year = {2010}, author = {Karpouzas, DG and Singh, BK}, title = {Application of fingerprinting molecular methods in bioremediation studies.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {599}, number = {}, pages = {69-88}, doi = {10.1007/978-1-60761-439-5_5}, pmid = {19882280}, issn = {1940-6029}, mesh = {*Biodegradation, Environmental ; Electrophoresis ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; *Soil Microbiology ; }, abstract = {Bioremediation has been identified as a beneficial and effective strategy for the removal of recalcitrant environmental contaminants. Bioaugmentation of polluted environments with exogenous degrading microorganisms constitutes a major strategy of bioremediation. However, the ecological role of these strains and their impact on the endogenous microbial community of the micro-ecosystems where they are released should be known. Fingerprinting PCR-based methods, like denaturating gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (TRFLP), could be used in studies exploring the ecology of pollutant-degrading microorganisms and their effects on the structure of the soil microbial community. This chapter provides a brief outline of the technical details involved in the application of DGGE and TRFLP fingerprinting in soil microbial ecology, with particular reference to bioremediation studies.}, }
@article {pmid19879146, year = {2009}, author = {Vos, M and Velicer, GJ}, title = {Social conflict in centimeter-and global-scale populations of the bacterium Myxococcus xanthus.}, journal = {Current biology : CB}, volume = {19}, number = {20}, pages = {1763-1767}, pmid = {19879146}, issn = {1879-0445}, support = {R01 GM079690/GM/NIGMS NIH HHS/United States ; GM07690/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Typing Techniques ; Genetic Variation ; *Microbial Interactions ; Myxococcus xanthus/genetics/growth &amp; development/*physiology ; Soil Microbiology ; Spores, Bacterial/genetics/physiology ; }, abstract = {Social interactions among microbes that engage in cooperative behaviors are well studied in laboratory contexts [1, 2], but little is known about the scales at which initially cooperative microbes diversify into socially conflicting genotypes in nature. The predatory soil bacterium Myxococcus xanthus responds to starvation by cooperatively forming multicellular fruiting bodies in which a portion of the population differentiates into stress-resistant spores [3, 4]. Natural M. xanthus populations are spatially structured [5], and genetically divergent isolates from distant origins exhibit striking developmental antagonisms that decrease spore production in chimeric fruiting bodies [6]. Here we show that genetically similar isolates of M. xanthus from a centimeter-scale population [7] also exhibit strong and pervasive antagonisms when mixed in development. Negative responses to chimerism were less intense on average among local strains than among global isolates, although no significant correlation was found between genetic distance at multilocus sequence typing (MLST) loci and the degree of social asymmetry between competitors. A test for self/nonself discrimination during vegetative swarming revealed a great diversity of distinct self-recognition types even among identical MLST genotypes. Such nonself exclusion may serve to direct the benefits of cooperation to close kin within diverse populations in which the probability of social conflict among neighbors is high.}, }
@article {pmid19865185, year = {2010}, author = {Remus-Emsermann, MN and Leveau, JH}, title = {Linking environmental heterogeneity and reproductive success at single-cell resolution.}, journal = {The ISME journal}, volume = {4}, number = {2}, pages = {215-222}, doi = {10.1038/ismej.2009.110}, pmid = {19865185}, issn = {1751-7370}, mesh = {Bacteriological Techniques/*methods ; *Ecosystem ; Erwinia/*cytology/*physiology ; Flow Cytometry ; Green Fluorescent Proteins/*analysis/metabolism ; In Situ Hybridization, Fluorescence ; Microscopy, Fluorescence ; Plant Leaves/microbiology ; }, abstract = {Individual-based microbial ecology (IBME) is a developing field of study in need of experimental tools to quantify the individual experience and performance of microorganisms in their natural habitats. We describe here the conception and application of a single-cell bioreporter approach with broad utility in IBME. It is based on the dilution of stable green fluorescent protein (GFP) in dividing bacteria. In the absence of de novo synthesis, GFP fluorescence of a daughter cell approximates half of that of its mother, from which follows that the fluorescence of a progeny cell is a quantitative measure for the reproductive success of its ancestor. To test this concept, we exposed GFP-filled bacteria to different degrees of environmental heterogeneity and assessed how this affected individual cells by the analysis of GFP content in their progeny. Reporter bacteria growing in rich medium in a shaking flask showed no variation in reproductive success, confirming that life in a broth is experienced much the same from one bacterium to the next. In contrast, when reporter bacteria were released onto plant leaf surfaces, representing a microscopically heterogeneous environment, clear intrapopulation differences in reproductive success were observed. Such variation suggests that individual cells in the founding population experienced different growth-permitting conditions, resulting in unequal contributions of individual bacteria to future offspring and population sizes. Being able to assess population changes bottom-up rather than top-down, the bioreporter offers opportunities to quantify single-cell competitive and facilitative interactions, assess the role of chance events in individual survivorship and reveal causes that underlie individual-based environmental heterogeneity.}, }
@article {pmid19865183, year = {2010}, author = {Zhang, C and Zhang, M and Wang, S and Han, R and Cao, Y and Hua, W and Mao, Y and Zhang, X and Pang, X and Wei, C and Zhao, G and Chen, Y and Zhao, L}, title = {Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice.}, journal = {The ISME journal}, volume = {4}, number = {2}, pages = {232-241}, doi = {10.1038/ismej.2009.112}, pmid = {19865183}, issn = {1751-7370}, mesh = {Animals ; Apolipoprotein A-I/genetics ; *Diet ; Dietary Fats/metabolism ; Gastrointestinal Tract/*microbiology ; Metabolic Syndrome/*genetics/*microbiology ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Molecular Sequence Data ; }, abstract = {Both genetic variations and diet-disrupted gut microbiota can predispose animals to metabolic syndromes (MS). This study assessed the relative contributions of host genetics and diet in shaping the gut microbiota and modulating MS-relevant phenotypes in mice. Together with its wild-type (Wt) counterpart, the Apoa-I knockout mouse, which has impaired glucose tolerance (IGT) and increased body fat, was fed a high-fat diet (HFD) or normal chow (NC) diet for 25 weeks. DNA fingerprinting and bar-coded pyrosequencing of 16S rRNA genes were used to profile gut microbiota structures and to identify the key population changes relevant to MS development by Partial Least Square Discriminate Analysis. Diet changes explained 57% of the total structural variation in gut microbiota, whereas genetic mutation accounted for no more than 12%. All three groups with IGT had significantly different gut microbiota relative to healthy Wt/NC-fed animals. In all, 65 species-level phylotypes were identified as key members with differential responses to changes in diet, genotype and MS phenotype. Most notably, gut barrier-protecting Bifidobacterium spp. were nearly absent in all animals on HFD, regardless of genotype. Sulphate-reducing, endotoxin-producing bacteria of the family, Desulfovibrionaceae, were enhanced in all animals with IGT, most significantly in the Wt/HFD group, which had the highest calorie intake and the most serious MS phenotypes. Thus, diet has a dominating role in shaping gut microbiota and changes of some key populations may transform the gut microbiota of Wt animals into a pathogen-like entity relevant to development of MS, despite a complete host genome.}, }
@article {pmid19860898, year = {2009}, author = {Wolcott, RD and Gontcharova, V and Sun, Y and Dowd, SE}, title = {Evaluation of the bacterial diversity among and within individual venous leg ulcers using bacterial tag-encoded FLX and titanium amplicon pyrosequencing and metagenomic approaches.}, journal = {BMC microbiology}, volume = {9}, number = {}, pages = {226}, pmid = {19860898}, issn = {1471-2180}, mesh = {Bacteria/classification/*genetics ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Genome, Bacterial ; Humans ; Metagenomics/*methods ; Sequence Analysis, DNA ; Varicose Ulcer/*microbiology ; Wound Infection/*microbiology ; }, abstract = {BACKGROUND: Approximately 1 out of every 100 individuals has some form of venous insufficiency, which can lead to chronic venous disease and Venous Leg Ulcer (VLU). There are known underlying pathologies which contribute to the chronic nature of VLU including biofilm phenotype infections.<br><br>RESULTS: Using pyrosequencing based approaches we evaluated VLU to characterize their microbial ecology. Results show that VLU infections are polymicrobial with no single bacterium colonizing the wounds. The most ubiquitous and predominant organisms include a previously uncharacterized bacteroidales, various anaerobes, Staphylococcus, Corynebacterium, and Serratia. Topological analysis of VLU show some notable differences in bacterial populations across the surface of the wounds highlighting the importance of sampling techniques during diagnostics. Metagenomics provide a preliminary indication that there may be protozoa, fungi and possibly an undescribed virus associated with these wounds.<br><br>CONCLUSION: The polymicrobial nature of VLU and previous research on diabetic foot ulcers and surgical site infections suggest that the future of therapy for such wounds lies in the core of the logical and proven multiple concurrent strategy approach, which has been termed "biofilm-based wound care" and the use of individualized therapeutics rather than in a single treatment modality.}, }
@article {pmid19855381, year = {2010}, author = {Salzman, NH and Hung, K and Haribhai, D and Chu, H and Karlsson-Sjöberg, J and Amir, E and Teggatz, P and Barman, M and Hayward, M and Eastwood, D and Stoel, M and Zhou, Y and Sodergren, E and Weinstock, GM and Bevins, CL and Williams, CB and Bos, NA}, title = {Enteric defensins are essential regulators of intestinal microbial ecology.}, journal = {Nature immunology}, volume = {11}, number = {1}, pages = {76-83}, pmid = {19855381}, issn = {1529-2916}, support = {R01 AI032738/AI/NIAID NIH HHS/United States ; R21 AI057757/AI/NIAID NIH HHS/United States ; AI/DK50843/AI/NIAID NIH HHS/United States ; R01 AI085090/AI/NIAID NIH HHS/United States ; AI32738/AI/NIAID NIH HHS/United States ; R37 AI032738/AI/NIAID NIH HHS/United States ; R01 AI057757/AI/NIAID NIH HHS/United States ; R01 AI050843/AI/NIAID NIH HHS/United States ; AI057757/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/growth &amp; development ; Colony Count, Microbial ; *Ecology ; Female ; Flow Cytometry ; Humans ; In Situ Hybridization, Fluorescence ; Interleukin-17/immunology/metabolism ; Intestinal Mucosa/*metabolism ; Intestine, Small/immunology/metabolism/microbiology ; Intestines/immunology/*microbiology ; Male ; Matrix Metalloproteinase 7/genetics/metabolism ; Metagenome ; Mice ; Mice, Inbred Strains ; Mice, Knockout ; Mice, Transgenic ; Microscopy, Fluorescence ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; T-Lymphocytes, Helper-Inducer/cytology/immunology/metabolism ; alpha-Defensins/genetics/immunology/*metabolism ; }, abstract = {Antimicrobial peptides are important effectors of innate immunity throughout the plant and animal kingdoms. In the mammalian small intestine, Paneth cell alpha-defensins are antimicrobial peptides that contribute to host defense against enteric pathogens. To determine if alpha-defensins also govern intestinal microbial ecology, we analyzed the intestinal microbiota of mice expressing a human alpha-defensin gene (DEFA5) and in mice lacking an enzyme required for the processing of mouse alpha-defensins. In these complementary models, we detected significant alpha-defensin-dependent changes in microbiota composition, but not in total bacterial numbers. Furthermore, DEFA5-expressing mice had striking losses of segmented filamentous bacteria and fewer interleukin 17 (IL-17)-producing lamina propria T cells. Our data ascribe a new homeostatic role to alpha-defensins in regulating the makeup of the commensal microbiota.}, }
@article {pmid19851805, year = {2010}, author = {Jiang, N and Wang, Y and Dong, X}, title = {Methanol as the primary methanogenic and acetogenic precursor in the cold Zoige wetland at Tibetan plateau.}, journal = {Microbial ecology}, volume = {60}, number = {1}, pages = {206-213}, pmid = {19851805}, issn = {1432-184X}, mesh = {Acetates/metabolism ; Acetobacterium/genetics/isolation &amp; purification/*metabolism ; China ; Cold Temperature ; DNA, Bacterial/genetics ; Eleocharis/growth &amp; development ; Lactobacillales/genetics/isolation &amp; purification/*metabolism ; Methane/metabolism ; Methanol/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/analysis ; *Soil Microbiology ; *Wetlands ; }, abstract = {Previous studies suggested that methanol and acetate were the likely methanogenic precursors in the cold Zoige wetland. In this study, the contribution of the two substances to methanogenesis and the conversion in Zoige wetland were analyzed. It was determined that methanol supported the highest CH(4) formation rate in the enrichments of the soil grown with Eleocharis valleculosa, and even higher at 15 degrees C than at 30 degrees C; while hydrogenotrophic methanogenesis was higher at 30 degrees C. Both methanol- and acetate-using methanogens were counted at the highest (10(7) g(-1)) in the soil, whereas methanol-using acetogens (10(8) g(-1)) were ten times more abundant than either methanol- or acetate-using methanogens. Both methanol and acetate were detected in the methanogenesis-inhibited soil samples, so that both could be the primary methanogenic precursors in E. valleculosa soil. However, the levels of methanol and acetate accumulated in 2-bromoethane-sulfonate (BES)- and CHCl(3)-treated soils were in reverse, i.e., higher methanol in CHCl(3)- and higher acetate in BES-treated soil, so that methanol-derived methanogenesis could be underestimated due to the consumption by acetogens. Analysis of the soil 16S rRNA genes revealed Acetobacterum bakii and Trichococcus pasteurii to be the dominant methanol-using acetogens in the soil, and a strain of T. pasteurii was isolated, which showed the high conversion of methanol to acetate at 15 degrees C.}, }
@article {pmid19847476, year = {2010}, author = {Fujii, M and Takano, Y and Kojima, H and Hoshino, T and Tanaka, R and Fukui, M}, title = {Microbial community structure, pigment composition, and nitrogen source of red snow in Antarctica.}, journal = {Microbial ecology}, volume = {59}, number = {3}, pages = {466-475}, pmid = {19847476}, issn = {1432-184X}, mesh = {Antarctic Regions ; Bacteria/genetics/*isolation &amp; purification ; Cloning, Molecular ; DNA, Algal/genetics ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; Eukaryota/genetics/*isolation &amp; purification ; Fungi/genetics/isolation &amp; purification ; Genes, rRNA ; Nitrogen/*analysis ; Nitrogen Isotopes/analysis ; Phylogeny ; Pigments, Biological/*analysis ; Sequence Analysis, DNA ; Snow/*microbiology ; }, abstract = {"Red snow" refers to red-colored snow, caused by bloom of cold-adapted phototrophs, so-called snow algae. The red snow found in Langhovde, Antarctica, was investigated from several viewpoints. Various sizes of rounded red cells were observed in the red snow samples under microscopy. Pigment analysis demonstrated accumulation of astaxanthin in the red snow. Community structure of microorganisms was analyzed by culture-independent methods. In the analyses of small subunit rRNA genes, several species of green algae, fungus, and various phylotypes of bacteria were detected. The detected bacteria were closely related to psychrophilic or psychrotolerant heterotrophic strains, or sequences detected from low-temperature environments. As predominant lineage of bacteria, members of the genus Hymenobacter were consistently detected from samples obtained in two different years. Nitrogen isotopic compositions analysis indicated that the red snow was significantly 15N-enriched. Based on an estimation of trophic level, it was suggested that primary nitrogen sources of the red snow were supplied from fecal pellet of seabirds including a marine top predator of Antarctica.}, }
@article {pmid19847475, year = {2010}, author = {Berg, N and Steinberger, Y}, title = {Are biological effects of desert shrubs more important than physical effects on soil microorganisms?.}, journal = {Microbial ecology}, volume = {59}, number = {1}, pages = {121-129}, pmid = {19847475}, issn = {1432-184X}, mesh = {Amaranthaceae/chemistry/*growth &amp; development ; Biomass ; Carbon Dioxide/analysis/chemistry ; *Desert Climate ; *Ecosystem ; Fresh Water/analysis ; Nitrogen/analysis ; Rain ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Vegetation cover plays a major role in providing organic matter and in acting as a physical barrier, with both together contributing to the formation of "fertile islands," which play an active role in prolonging biological activity in desert ecosystems. By undertaking this study, a longterm research, we designed an experiment to separate the two components-the physical and biotic parts of the perennial plants-and to identify the factor that contributes the most to the ecosystem. The study site was located in the northern Negev Desert, Israel, where 50 Hammada scoparia shrubs and 50 artificial plants were randomly marked. Soil samples were collected monthly over 3 years of research at three locations: under the canopy of H. scoparia shrubs, in the vicinity of the artificial plants, and between the shrubs (control). The contribution to microbial activity was measured by evaluation of the microbial community functions in soil. The functional aspects of the microbial community that were measured were CO2 evolution, microbial biomass, microbial functional diversity, and the physiological profile of the community. The results of this study are presented in two ways: (1) according to the three locations/treatments; and (2) according to the phenological situation of the vegetation (annual and perennial plants) in the research field: the growing phase, the drying process, and the absence of annual plants. The only parameters that were found to affect microbial activity were the contribution of the organic matter of perennial shrubs and the growth of vegetation (annual and perennial) during the growing seasons. The physical component was found to have no effect on soil microbial functional diversity, which elucidates the important contribution of the desert shrub in enhancing biological multiplicity and activity.}, }
@article {pmid19844650, year = {2010}, author = {Taylor, EB and Williams, MA}, title = {Microbial protein in soil: influence of extraction method and C amendment on extraction and recovery.}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {390-399}, pmid = {19844650}, issn = {1432-184X}, mesh = {Bacteria/growth &amp; development/isolation &amp; purification ; Bacterial Proteins/*isolation &amp; purification ; Centrifugation, Density Gradient ; Electrophoresis, Polyacrylamide Gel ; Glucose/chemistry ; Multivariate Analysis ; Proteome ; Proteomics/*methods ; Serum Albumin, Bovine/chemistry ; Soil/*analysis ; *Soil Microbiology ; Toluene/chemistry ; }, abstract = {The capacity to study the content and resolve the dynamics of the proteome of diverse microbial communities would help to revolutionize the way microbiologists study the function and activity of microorganisms in soil. To better understand the limitations of a proteomic approach to studying soil microbial communities, we characterized extractable soil microbial proteins using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Two methods were utilized to extract proteins from microorganisms residing in a Quitman and Benfield soil: (1) direct extraction of bulk protein from soil and (2) separation of the microorganisms from soil using density gradient centrifugation and subsequent extraction (DGC-EXT) of microbial protein. In addition, glucose and toluene amendments to soil were used to stimulate the growth of a subset of the microbial community. A bacterial culture and bovine serum albumin (BSA) were added to the soil to qualitatively assess their recovery following extraction. Direct extraction and resolution of microbial proteins using SDS-PAGE generally resulted in smeared and unresolved banding patterns on gels. DGC-EXT of microbial protein from soil followed by separation using SDS-PAGE, however, did resolve six to 10 bands in the Benfield but not the Quitman soil. DGC-EXT of microbial protein, but not direct extraction following the addition of glucose and toluene, markedly increased the number of bands (approximately 40) on the gels in both Benfield and Quitman soils. Low recoveries of added culture and BSA proteins using the direct extraction method suggest that proteins either bind to soil organic matter and mineral particles or that partial degradation takes place during extraction. Interestingly, DGC may have been preferentially selected for actively growing cells, as gauged by the 10-100x lower cy19:0/18:1omega7 ratio of the fatty acid methyl esters in the isolated community compared to that for the whole soil. DGC can be used to isolate soil communities and provide microbial protein that can be characterized using PAGE.}, }
@article {pmid19844649, year = {2010}, author = {Burr, G and Hume, M and Ricke, S and Nisbet, D and Gatlin, D}, title = {In vitro and in vivo evaluation of the prebiotics GroBiotic-A, inulin, mannanoligosaccharide, and galactooligosaccharide on the digestive microbiota and performance of hybrid striped bass (Morone chrysops x Morone saxatilis).}, journal = {Microbial ecology}, volume = {59}, number = {1}, pages = {187-198}, pmid = {19844649}, issn = {1432-184X}, mesh = {Animals ; Bacteria/*classification/drug effects/genetics ; Bass/*microbiology ; Fatty Acids, Volatile/metabolism ; Feeding Behavior/drug effects ; Gastrointestinal Tract/drug effects/metabolism/*microbiology ; Inulin/*pharmacology ; Models, Animal ; Oligosaccharides/*pharmacology ; *Prebiotics ; }, abstract = {Two separate experiments were conducted with hybrid striped bass to evaluate four potential prebiotics: GroBiotic-A (partially autolyzed brewer's yeast, dairy ingredient components, and fermentation products), mannanoligosaccharide (MOS), galactooligosaccharide (GOS), and inulin. In the in vitro experiment, intestinal contents were incubated with the individual prebiotics (0.5% by weight) at 25 degrees C for 24 and 48 h. Analysis of volatile fatty acids in the supernatant showed that GroBiotic-A, MOS, and GOS tended to produce lower acetate levels but higher butyrate levels at 48 h compared to diet alone. However, denaturing gradient gel electrophoresis (DGGE) analysis failed to detect any differences in the composition of the microbial community among treatments. DNA sequencing of a common band for all inoculated samples revealed close similarity to the anaerobic Fusobacteria bacterium. An 8-week feeding trial also was conducted to evaluate the four prebiotics looking at growth performance; weight gain, feed efficiency ratio, protein efficiency ratio, whole-body ash, moisture, and lipid did not vary among fish fed the various diets. However, DGGE analysis revealed that all prebiotics produced a different type of microbial community in the intestinal tract of hybrid striped bass compared to fish fed the basal diet. Thus, GroBiotic-A, FOS, GOS, and MOS exhibited prebiotic effects in hybrid striped bass.}, }
@article {pmid19844648, year = {2010}, author = {Bugla-Płoskońska, G and Rybka, J and Futoma-Kołoch, B and Cisowska, A and Gamian, A and Doroszkiewicz, W}, title = {Sialic acid-containing lipopolysaccharides of Salmonella O48 strains--potential role in camouflage and susceptibility to the bactericidal effect of normal human serum.}, journal = {Microbial ecology}, volume = {59}, number = {3}, pages = {601-613}, pmid = {19844648}, issn = {1432-184X}, mesh = {*Blood Bactericidal Activity ; *Complement Activation ; Complement C3/analysis ; Complement C4/analysis ; Complement Pathway, Alternative ; Gas Chromatography-Mass Spectrometry ; Humans ; Immunoglobulin G/blood ; Immunoglobulin M/blood ; Lipopolysaccharides/*chemistry ; N-Acetylneuraminic Acid/*chemistry ; Salmonella/*chemistry/pathogenicity ; Sugar Acids/chemistry ; }, abstract = {Sialic acid (N-acetylneuraminic acid, NeuAc) plays an essential role in protecting gram-negative bacteria against the bactericidal activity of serum and may contribute to the pathogenicity of bacteria by mimicking epitopes that resemble host tissue components (molecular mimicry). The role of sialic acid (NeuAc)-containing lipopolysaccharides (LPS) of Salmonella O48 strains in the complement activation of normal human serum (NHS) was investigated. NeuAc-containing lipooligosaccharides cause a downregulation of complement activation and may serve to camouflage the bacterial surface from the immunological response of the host. Serotype O48 Salmonella strains have the O-antigen structure containing NeuAc while its serovars differ in outer membrane protein composition. In this study, the mechanisms of complement activation responsible for killing Salmonella O48 serum-sensitive rods by NHS were established. Four of such mechanisms involving pathways, which are important in the bactericidal mechanism of complement activation, were distinguished: only the classical/lectin pathways, independent activation of the classical/lectin or alternative pathway, parallel activation of the classical/lectin and alternative pathways, and only the alternative pathway important in the bactericidal action of human serum. To further study the role of NeuAc, its content in bacterial cells was determined by gas-liquid chromatography-mass spectrometry in relation to 3-deoxy-D-manno-2-octulosonic acid (Kdo), an inherent constituent of LPS. The results indicate that neither the presence of sialic acid in LPS nor the length of the O-specific part of LPS containing NeuAc plays a decisive role in determining bacterial resistance to the bactericidal activity of complement and that the presence of sialic acid in the structure of LPS is not sufficient to block the activation of the alternative pathway of complement. We observed that for three strains with a very high NeuAc/Kdo ratio the alternative pathways were decisive in the bactericidal action of human serum. The results indicated that those strains are not capable of inhibiting the alternative pathway very effectively. As the pathogenicity of most Salmonella serotypes remains undefined, research into the interactions between these bacterial cells and host organisms is indispensable.}, }
@article {pmid19844647, year = {2010}, author = {Vermette, CJ and Russell, AH and Desai, AR and Hill, JE}, title = {Resolution of phenotypically distinct strains of Enterococcus spp. in a complex microbial community using cpn60 universal target sequencing.}, journal = {Microbial ecology}, volume = {59}, number = {1}, pages = {14-24}, pmid = {19844647}, issn = {1432-184X}, mesh = {Animals ; Carbon/metabolism ; Chaperonin 60/*genetics ; Colony Count, Microbial ; Enterococcus/*classification/genetics/metabolism ; Feces/microbiology ; Phenotype ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Swine/microbiology ; }, abstract = {Characterization of complex microbial communities is frequently based on the examination of polymerase chain reaction amplified sequences from a single phylogenetic marker, usually the 16S rRNA gene. However, this commonly used target often does not offer robust resolution of species or sub-species and is thus not a sufficiently informative target for understanding microbial population dynamics occurring at the strain level. We have used the cpn60 universal target sequence to characterize Enterococcus isolates from feces of growing pigs and have shown that sub-species groups, not detected using 16S rRNA sequences, can be resolved. Furthermore, groups resolved by cpn60-based phylogenetic analysis have distinct phenotypes. We report changes in the structure and function of Enterococcus communities in pig feces sampled from individual animals at three times, from suckling through to maturity. Enterococcus faecalis was largely replaced by Enterococcus hirae between suckling and 9 weeks of age, and a shift from one sub-species group of E. hirae to another was observed in all animals between 9 and 15 weeks. Conversely, E. faecalis strains remained consistent throughout the study period. Our results demonstrate that cpn60 sequences can be used to detect strain level changes in Enterococcus populations during succession in the fecal microbiota of growing pigs.}, }
@article {pmid19839490, year = {2009}, author = {Gamboa, F and Chaves, M and Lamby, C and Fajardo, A and Arévalo, A}, title = {Antagonistic action of indigenous Streptococcus mutans strains.}, journal = {Acta odontologica latinoamericana : AOL}, volume = {22}, number = {2}, pages = {129-138}, pmid = {19839490}, issn = {0326-4815}, mesh = {*Antibiosis ; Child ; Dental Caries/prevention &amp; control ; Humans ; Streptococcus mutans/classification/*physiology ; }, abstract = {Dental caries is an infectious process which ultimately destroys the tooth. Streptococcus mutans is considered to be the main agent causing this disease. If microorganisms with antagonistic action on S. mutans were found, they might provide a way of avoiding or controlling the disease. Within the framework of the Oral Microbial Ecology approach, the aim of this project was to identify S. mutans strains with antagonistic effect upon S. mutans. Saliva samples were taken from 66 children and cultured on Blood agar and Mitis Salivarius Bacitracin agar. They were incubated at 37 degrees C in anaerobic atmosphere for 48 hours, after which bacteria were counted and biochemical tests performed on colonies compatible with S. mutans. Antagonistic effect was determined using the double layer in agar technique. In children without and with caries, the frequency of S. mutans was 91.7% and 96.7%, respectively. In the group of patients without caries, only two strains had no antagonistic action, and three strains had full antagonistic action (100%), while the rest showed different kinds of inhibitory action. In the group of patients with caries, only 5 strains had no antagonistic action, 32 strains had full antagonistic action (100%) and the rest had variable inhibitory action. To conclude, 112 S. mutans strains with high antagonistic potential were identified, which, after other requirements are fulfilled, could be used in caries prevention or control strategies.}, }
@article {pmid19834639, year = {2010}, author = {Wornik, S and Grube, M}, title = {Joint dispersal does not imply maintenance of partnerships in lichen symbioses.}, journal = {Microbial ecology}, volume = {59}, number = {1}, pages = {150-157}, pmid = {19834639}, issn = {1432-184X}, mesh = {Eukaryota/growth &amp; development ; Genetics, Population ; Lichens/classification/*growth &amp; development ; Phylogeny ; Population Density ; *Symbiosis ; }, abstract = {Dispersal of symbiotic partners by joint propagules is considered as an efficient strategy to maintain successful associations and to circumvent low symbiont availability. Joint dispersal is widespread in diverse symbioses and a particularly common reproductive mode in lichens. We were interested in the implications of joint symbiont dispersal on population genetic structure and investigated patterns of symbiont association in populations of two closely related lichen species in the genus Physconia, with similar range of compatible algal partners. One of the lichen species is characterized by joint dispersal of both symbionts, whereas the other species propagates by meiotic fungal spores alone. The latter species must reestablish the symbiotic stage with appropriate algae sampled from the environment. Both fungal species have specialized on photobionts representing a monophyletic lineage of the algal genus Trebouxia. The results indicate no correlated association of symbiont genotypes in the species with joint symbiont dispersal. We rather show that algal gene diversity in populations of lichenized fungi with different propagation strategies is not necessarily different. The association with algae that differ from the co-dispersed genotypes during the vegetative development of the thalli is the most likely explanation for the observed pattern. Maintenance of symbiotic associations is an option but not a strict consequence of joint symbiont dispersal in lichens.}, }
@article {pmid19834074, year = {2009}, author = {Baurhoo, B and Ferket, PR and Zhao, X}, title = {Effects of diets containing different concentrations of mannanoligosaccharide or antibiotics on growth performance, intestinal development, cecal and litter microbial populations, and carcass parameters of broilers.}, journal = {Poultry science}, volume = {88}, number = {11}, pages = {2262-2272}, doi = {10.3382/ps.2008-00562}, pmid = {19834074}, issn = {0032-5791}, mesh = {Animal Feed/analysis ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacitracin/*pharmacology ; Bacteria/classification/drug effects/isolation &amp; purification ; Body Composition/drug effects ; Chickens/*growth &amp; development ; Diet/veterinary ; Floors and Floorcoverings ; Gastrointestinal Contents/*microbiology ; Housing, Animal ; Intestines/*growth &amp; development ; Male ; Mannans/*pharmacology ; Virginiamycin/*pharmacology ; }, abstract = {The effects of 2 levels of mannanoligosaccharide (MOS) in feed were compared with antibiotic growth promoters on growth performance, intestinal morphology, cecal and litter microbial populations, and carcass parameters in broilers raised in a sanitary environment. Dietary treatments included: 1) antibiotic growth promoter-free diet (control), 2) VIRG (diet 1 + 16.5 mg/kg of virginiamycin), 3) BACT (diet 1 + 55 mg/kg of bacitracin), 4) LMOS (diet 1 + 0.2% MOS), and 5) HMOS (diet 1 + 0.5% MOS). Birds were randomly assigned to 3 replicate pens/treatment (n = 55/pen). Body weight and feed intake were recorded weekly throughout 38 d. At d 14, 24, and 34, a 1-cm segment of duodenum, jejunum, and ileum was used in morphological analysis (n = 9 birds/d per treatment). At the same bird ages, cecal contents were assayed for lactobacilli, bifidobacteria, Salmonella, Campylobacter, and Escherichia coli, whereas litter was analyzed for Salmonella, Campylobacter, and E. coli. Carcass yields (breast fillet and tenders, thigh, drumstick, and wing) were determined at d 38. Body weight, feed conversion, and carcass yields did not differ among treatments. In contrast to birds fed VIRG or BACT, LMOS and HMOS consistently increased (P < 0.05) villi height and goblet cell number per villus in all intestinal segments at d 24 and 34. Bifidobacteria concentrations were higher (P < 0.05) in LMOS- and HMOS-fed birds at all time points. Birds and litter from all treatments were free of Salmonella. At d 14 and 24, cecal E. coli and Campylobacter counts were not different among treatments. In comparison to birds fed control, at d 34, BACT, LMOS, and HMOS significantly reduced (P < 0.05) cecal E. coli concentrations, whereas Campylobacter counts were reduced (P < 0.05) by VIRG, BACT, and LMOS. Litter bacterial counts were not altered by dietary treatments. In conclusion, under conditions of this study, MOS conferred intestinal health benefits to chickens by improving its morphological development and microbial ecology. But, there were no additional benefits of the higher MOS dosage.}, }
@article {pmid19833519, year = {2009}, author = {Harding, MW and Marques, LL and Howard, RJ and Olson, ME}, title = {Can filamentous fungi form biofilms?.}, journal = {Trends in microbiology}, volume = {17}, number = {11}, pages = {475-480}, doi = {10.1016/j.tim.2009.08.007}, pmid = {19833519}, issn = {1878-4380}, mesh = {Biofilms/*growth &amp; development ; Fungi/growth &amp; development/*physiology ; Models, Biological ; }, abstract = {The discovery of biofilm formation in bacteria and yeasts has led to a better understanding of microbial ecology and to new insights into the mechanisms of virulence and persistence of pathogenic microorganisms. However, it is generally assumed that filamentous fungi, some of which have a significant impact on our health or our economy, do not form biofilms. In contrast to this assumption, here we discuss recent findings supporting the hypothesis that surface-associated filamentous fungi can form biofilms. Based on these findings and on previous models for bacterial and yeast systems, we propose preliminary criteria and a model for biofilm formation by filamentous fungi.}, }
@article {pmid19830478, year = {2010}, author = {Dimitriu, PA and Grayston, SJ}, title = {Relationship between soil properties and patterns of bacterial beta-diversity across reclaimed and natural boreal forest soils.}, journal = {Microbial ecology}, volume = {59}, number = {3}, pages = {563-573}, pmid = {19830478}, issn = {1432-184X}, mesh = {Alberta ; Bacteria/classification/*genetics ; *Biodiversity ; DNA, Bacterial/genetics ; Gene Library ; Hydrogen-Ion Concentration ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/*analysis ; *Soil Microbiology ; Trees/*microbiology ; }, abstract = {Productivity gradients in the boreal forest are largely determined by regional-scale changes in soil conditions, and bacterial communities are likely to respond to these changes. Few studies, however, have examined how variation in specific edaphic properties influences the composition of soil bacterial communities along environmental gradients. We quantified bacterial compositional diversity patterns in ten boreal forest sites of contrasting fertility. Bulk soil (organic and mineral horizons) was sampled from sites representing two extremes of a natural moisture-nutrient gradient and two distinct disturbance types, one barren and the other vegetation-rich. We constructed 16S rRNA gene clone libraries to characterize the bacterial communities under phylogenetic- and species-based frameworks. Using a nucleotide analog to label DNA-synthesizing bacteria, we also assessed the composition of active taxa in disturbed sites. Most sites were dominated by sequences related to the alpha-Proteobacteria, followed by acidobacterial and betaproteobacterial sequences. Non-parametric multivariate regression indicated that pH, which was lowest in the natural sites, explained 34% and 16% of the variability in community structure as determined by phylogenetic-based (UniFrac distances) and species-based (Jaccard similarities) metrics, respectively. Soil pH was also a significant predictor of richness (Chao1) and diversity (Shannon) measures. Within the natural edaphic gradient, soil moisture accounted for 32% of the variance in phylogenetic (but not species) community structure. In the boreal system we studied, bacterial beta-diversity patterns appear to be largely related to "master" variables (e.g., pH, moisture) rather than to observable attributes (e.g., plant cover) leading to regional-scale fertility gradients.}, }
@article {pmid19830477, year = {2010}, author = {Goodenough, AE and Stallwood, B}, title = {Intraspecific variation and interspecific differences in the bacterial and fungal assemblages of blue tit (Cyanistes caeruleus) and great tit (Parus major) nests.}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {221-232}, pmid = {19830477}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/genetics/*growth &amp; development ; DNA, Bacterial/genetics ; Fungi/classification/genetics/*growth &amp; development ; *Models, Biological ; Passeriformes/*microbiology ; Species Specificity ; }, abstract = {Although interest in the relationship between birds and microorganisms is increasing, few studies have compared nest microbial assemblages in wild passerines to determine variation within and between species. Culturing microorganisms from blue tit (Cyanistes caeruleus) and great tit (Parus major) nests from the same study site demonstrated diverse microbial communities with 32 bacterial and 13 fungal species being isolated. Dominant bacteria were Pseudomonas fluorescens, Pseudomonas putida, and Staphylococcus hyicus. Also common in the nests were the keratinolytic bacteria Pseudomonas stutzeri and Bacillus subtilis. Dominant fungi were Cladosporium herbarum and Epicoccum purpurascens. Aspergillus flavous, Microsporum gallinae, and Candida albicans (causative agents of avian aspergillosis, favus, and candidiasis, respectively) were present in 30%, 25%, and 10% of nests, respectively. Although there were no differences in nest mass or materials, bacterial (but not fungal) loads were significantly higher in blue tit nests. Microbial species also differed interspecifically. As regards potential pathogens, the prevalence of Enterobacter cloacae was higher in blue tit nests, while Pseudomonas aeruginosa-present in 30% of blue tit nests-was absent from great tit nests. The allergenic fungus Cladosporium cladosporioides was both more prevalent and abundant in great tit nests. Using discriminant function analysis (DFA), nests were classified to avian species with 100% accuracy using the complete microbial community. Partial DFA models were created using a reduced number of variables and compared using Akaike's information criterion on the basis of model fit and parsimony. The best models classified unknown nests with 72.5-95% accuracy using a small subset of microbes (n = 1-8), which always included Pseudomonas agarici. This suggests that despite substantial intraspecific variation in nest microflora, there are significant interspecific differences-both in terms of individual microbes and the overall microbial community-even when host species are closely related, ecologically similar, sympatric, and construct very similar nests.}, }
@article {pmid19830476, year = {2010}, author = {Vesth, T and Wassenaar, TM and Hallin, PF and Snipen, L and Lagesen, K and Ussery, DW}, title = {On the origins of a Vibrio species.}, journal = {Microbial ecology}, volume = {59}, number = {1}, pages = {1-13}, pmid = {19830476}, issn = {1432-184X}, mesh = {DNA Fingerprinting ; Evolution, Molecular ; Genome, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Vibrio/classification/genetics ; Vibrio cholerae/*classification/genetics ; Vibrionaceae/classification/genetics ; }, abstract = {Thirty-two genome sequences of various Vibrionaceae members are compared, with emphasis on what makes V. cholerae unique. As few as 1,000 gene families are conserved across all the Vibrionaceae genomes analysed; this fraction roughly doubles for gene families conserved within the species V. cholerae. Of these, approximately 200 gene families that cluster on various locations of the genome are not found in other sequenced Vibrionaceae; these are possibly unique to the V. cholerae species. By comparing gene family content of the analysed genomes, the relatedness to a particular species is identified for two unspeciated genomes. Conversely, two genomes presumably belonging to the same species have suspiciously dissimilar gene family content. We are able to identify a number of genes that are conserved in, and unique to, V. cholerae. Some of these genes may be crucial to the niche adaptation of this species.}, }
@article {pmid19830422, year = {2010}, author = {Junier, P and Molina, V and Dorador, C and Hadas, O and Kim, OS and Junier, T and Witzel, JP and Imhoff, JF}, title = {Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment.}, journal = {Applied microbiology and biotechnology}, volume = {85}, number = {3}, pages = {425-440}, pmid = {19830422}, issn = {1432-0614}, mesh = {Ammonia/*metabolism ; Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; *Environmental Microbiology ; *Genes, Archaeal ; *Genes, Bacterial ; Metabolic Networks and Pathways/genetics ; Nitrites/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; }, abstract = {The oxidation of ammonia plays a significant role in the transformation of fixed nitrogen in the global nitrogen cycle. Autotrophic ammonia oxidation is known in three groups of microorganisms. Aerobic ammonia-oxidizing bacteria and archaea convert ammonia into nitrite during nitrification. Anaerobic ammonia-oxidizing bacteria (anammox) oxidize ammonia using nitrite as electron acceptor and producing atmospheric dinitrogen. The isolation and cultivation of all three groups in the laboratory are quite problematic due to their slow growth rates, poor growth yields, unpredictable lag phases, and sensitivity to certain organic compounds. Culture-independent approaches have contributed importantly to our understanding of the diversity and distribution of these microorganisms in the environment. In this review, we present an overview of approaches that have been used for the molecular study of ammonia oxidizers and discuss their application in different environments.}, }
@article {pmid19824401, year = {2009}, author = {Chróst, RJ and Adamczewski, T and Kalinowska, K and Skowrońska, A}, title = {Effect of organic phosphorus and nitrogen enrichment of mesotrophic lake water on dynamics and diversity of planktonic microbial communities--DNA and protein case studies (mesocosm experiments).}, journal = {Polish journal of microbiology}, volume = {58}, number = {2}, pages = {163-180}, pmid = {19824401}, issn = {1733-1331}, mesh = {Bacteria/cytology/growth &amp; development ; Biomass ; DNA/genetics/metabolism ; Food Chain ; Fresh Water/*chemistry ; In Situ Hybridization, Fluorescence ; Nitrogen/*chemistry/pharmacology ; Phosphorus/*chemistry/pharmacology ; Phytoplankton/drug effects/*genetics/*metabolism ; Time Factors ; }, abstract = {Effects of mesotrophic lake water enrichment with organic phosphorus and nitrogen substrates (DNA and model protein, bovine serum albumin--BSA) on dynamics and diversity of natural microbial communities (bacteria, heterotrophic nanoflagellates, ciliates) were studied in mesocosm experiments. Simultaneous enrichment with DNA and BSA strongly increased the abundance and biomass of all studied groups of microorganisms and induced changes in their morphological and taxonomic structure. The increased participation of large heterotrophic nanoflagellates cells (larger than 10 microm) in their total numbers and shifts in taxonomic and trophic structure of the ciliates, from algivorous to small bacterivorous, species were observed. Grazing caused changes in bacterial size distribution in all enriched mesocosms. Large (10-50 microm) filamentous bacteria significantly contributed to the total bacterial numbers and biomass. Pronounced increase in populations of beta- and gamma-Proteobacteria was found in lake water enriched with organic P and N sources, whereas alpha-Proteobacteria did not change markedly in the studied mesocosms. DNA additions stimulated the rates of bacterial secondary production. BSA shortened the rates of bacterial biomass turnover in lake water. Relatively high and constant (approximately 30%) percentage contribution of active bacteria (MEM+) in two mesocosms enriched with DNA and DNA+BSA suggested the important role of nucleic acids as a source of phosphorus for bacterial growth, activity and production. Numerous and statistically significant correlations between bacteria and protists indicated the direct and selective predator-prey relationship.}, }
@article {pmid19822428, year = {2009}, author = {Bourne, DG and Garren, M and Work, TM and Rosenberg, E and Smith, GW and Harvell, CD}, title = {Microbial disease and the coral holobiont.}, journal = {Trends in microbiology}, volume = {17}, number = {12}, pages = {554-562}, doi = {10.1016/j.tim.2009.09.004}, pmid = {19822428}, issn = {1878-4380}, mesh = {Animals ; Anthozoa/growth &amp; development/*microbiology ; Conservation of Natural Resources ; Ecology ; }, abstract = {Tropical coral reefs harbour a reservoir of enormous biodiversity that is increasingly threatened by direct human activities and indirect global climate shifts. Emerging coral diseases are one serious threat implicated in extensive reef deterioration through disruption of the integrity of the coral holobiont - a complex symbiosis between the coral animal, endobiotic alga and an array of microorganisms. In this article, we review our current understanding of the role of microorganisms in coral health and disease, and highlight the pressing interdisciplinary research priorities required to elucidate the mechanisms of disease. We advocate an approach that applies knowledge gained from experiences in human and veterinary medicine, integrated into multidisciplinary studies that investigate the interactions between host, agent and environment of a given coral disease. These approaches include robust and precise disease diagnosis, standardised ecological methods and application of rapidly developing DNA, RNA and protein technologies, alongside established histological, microbial ecology and ecological expertise. Such approaches will allow a better understanding of the causes of coral mortality and coral reef declines and help assess potential management options to mitigate their effects in the longer term.}, }
@article {pmid19820145, year = {2009}, author = {Lee, CW and Bong, CW and Hii, YS}, title = {Temporal variation of bacterial respiration and growth efficiency in tropical coastal waters.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {24}, pages = {7594-7601}, pmid = {19820145}, issn = {1098-5336}, mesh = {Bacteria/*growth &amp; development ; *Bacterial Physiological Phenomena ; Carbon/analysis ; Heterotrophic Processes ; Malaysia ; Nitrogen/analysis ; Salinity ; Seawater/chemistry/*microbiology ; Temperature ; }, abstract = {We investigated the temporal variation of bacterial production, respiration, and growth efficiency in the tropical coastal waters of Peninsular Malaysia. We selected five stations including two estuaries and three coastal water stations. The temperature was relatively stable (averaging around 29.5 degrees C), whereas salinity was more variable in the estuaries. We also measured dissolved organic carbon and nitrogen (DOC and DON, respectively) concentrations. DOC generally ranged from 100 to 900 microM, whereas DON ranged from 0 to 32 microM. Bacterial respiration ranged from 0.5 to 3.2 microM O2 h(-1), whereas bacterial production ranged from 0.05 to 0.51 microM C h(-1). Bacterial growth efficiency was calculated as bacterial production/(bacterial production + respiration), and ranged from 0.02 to 0.40. Multiple correlation analyses revealed that bacterial production was dependent upon primary production (r2 = 0.169, df = 31, and P < 0.02) whereas bacterial respiration was dependent upon both substrate quality (i.e., DOC/DON ratio) (r2 = 0.137, df = 32, and P = 0.03) and temperature (r2 = 0.113, df = 36, and P = 0.04). Substrate quality was the most important factor (r2 = 0.119, df = 33, and P = 0.04) for the regulation of bacterial growth efficiency. Using bacterial growth efficiency values, the average bacterial carbon demand calculated was from 5.30 to 11.28 microM C h(-1). When the bacterial carbon demand was compared with primary productivity, we found that net heterotrophy was established at only two stations. The ratio of bacterial carbon demand to net primary production correlated significantly with bacterial growth efficiency (r2 = 0.341, df = 35, and P < 0.001). From nonlinear regression analysis, we found that net heterotrophy was established when bacterial growth efficiency was <0.08. Our study showed the extent of net heterotrophy in these waters and illustrated the importance of heterotrophic microbial processes in coastal aquatic food webs.}, }
@article {pmid19811538, year = {2010}, author = {Kielak, A and Rodrigues, JL and Kuramae, EE and Chain, PS and van Veen, JA and Kowalchuk, GA}, title = {Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil.}, journal = {FEMS microbiology ecology}, volume = {71}, number = {1}, pages = {23-33}, doi = {10.1111/j.1574-6941.2009.00785.x}, pmid = {19811538}, issn = {1574-6941}, mesh = {*Agriculture ; Bacteria/classification/*genetics ; Base Sequence ; Cloning, Molecular ; DNA, Bacterial/chemistry/isolation &amp; purification ; *Genome, Bacterial ; *Metagenomics ; Molecular Sequence Data ; *Phylogeny ; Poaceae ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {The bacterial phylum Verrucomicrobia has a widespread distribution, and is known to be one of the most common and diverse phyla in soil habitats. However, members of this phylum have typically been recalcitrant to cultivation methods, hampering the study of this presumably important bacterial group. In this study, we examine the phylogenetic diversity of the Verrucomicrobia in a former agricultural field and gain access to genomic information via a metagenomic approach. We examined Verrucomicrobia-like 16S rRNA gene sequences recovered from general bacterial and phylum-specific libraries, revealing a dominance of subdivisions 1 and 2. A PCR-based screening method was developed to identify inserts containing verrucomicrobial 16S rRNA genes within a large-insert metagenomic library, and on screening of 28,800 clones, four fosmids were identified as containing verrucomicrobial genomic DNA. Full-length sequencing of fosmid inserts and gene annotation identified a total of 98 ORFs, representing a range of functions. No conservation of gene order was observed adjacent to the ribosomal operons. Fosmid inserts were further analyzed for tetranucleotide frequencies to identify remnants of past horizontal gene transfer events. The metagenomic approach utilized proved to be suitable for the recovery of verrucomicrobial genomic DNA, thereby providing a window into the genomes of members of this important, yet poorly characterized, bacterial phylum.}, }
@article {pmid19809240, year = {2009}, author = {Ryszard, CJ and Tomasz, A and Kalinowska, K and Skowronska, A}, title = {Abundance and structure of microbial loop components (bacteria and protists) in lakes of different trophic status.}, journal = {Journal of microbiology and biotechnology}, volume = {19}, number = {9}, pages = {858-868}, pmid = {19809240}, issn = {1017-7825}, mesh = {Bacteria/*classification/cytology/isolation &amp; purification ; Biomass ; Cell Membrane/physiology ; Eukaryota/*classification/cytology/isolation &amp; purification ; Fresh Water/*microbiology ; In Situ Hybridization, Fluorescence ; Population Density ; Species Specificity ; Surface Properties ; *Water Microbiology ; }, abstract = {The abundance, biomass, size distribution, and taxonomic composition of bacterial and protistan (heterotrophic and autotrophic nanoflagellates and ciliates) communities were investigated in six lakes of Masurian Lake District (north-eastern Poland) differing in trophic state. Samples were taken from the trophogenic water layer during summer stratification periods in the years of 2004 and 2006. Image analysis techniques with fluorescent in situ hybridization (FISH) as well as [3H]-methyl-thymidine incorporation methods were applied to analyze differences in the composition and activity of bacterial communities. The greatest differences in trophic parameters were found between the humic lake and remaining non-humic ones. The same bacterial and heterotrophic nanoflagellate (HNF) cell size classes dominated in all the studied lakes. However, distinct increases in the contributions of large bacterial (>1.0 microm) and HNF (>10 microm) cells were observed in eutrophic lakes. The bacterial community was dominated by the beta-Proteobacteria group, which accounted for 27% of total DAPI counts. Ciliate communities were largely composed of Oligotrichida. Positive correlations between bacteria and protists, as well as between nanoflagellates (both heterotrophic and autotrophic) and ciliates, suggest that concentrations of food sources may be important in determining the abundance of protists in the studied lakes.}, }
@article {pmid19809137, year = {2009}, author = {Zuo, G and Roberts, DJ and Lehman, SG and Jackson, GW and Fox, GE and Willson, RC}, title = {Molecular assessment of salt-tolerant, perchlorate- and nitrate-reducing microbial cultures.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {60}, number = {7}, pages = {1745-1756}, doi = {10.2166/wst.2009.635}, pmid = {19809137}, issn = {0273-1223}, mesh = {Bacteria/*drug effects/*metabolism ; Nitrates/*metabolism ; Perchlorates/*metabolism ; Sodium Chloride/*pharmacology ; }, abstract = {The microbial ecology of enrichment cultures adapted to the removal of perchlorate and nitrate from high salt solutions and ion-exchange brines was examined over a period of four years using denaturing gradient gel electrophoresis and total DNA extraction with cloning and in each case partial sequencing of the 16S rDNA genes. The cultures studied were a result of enrichment from marine sediment inoculum initiated in 2001. The resulting enrichment cultures were fed perchlorate, or perchlorate and nitrate, in a 3% (w/v) NaCl defined medium or ion-exchange brines (5.6% NaCl) containing perchlorate and nitrate with acetate as the electron donor. All of the sequences' closest matches in the NCBI GenBank database were to marine or salt-tolerant organisms. Strains belonging to the genera Halomonas or Marinobacter were found to dominate in cultures that were fed nitrate in addition to perchlorate, but were effectively absent from cultures fed perchlorate alone. The cultures fed perchlorate as the sole electron acceptor were relatively diverse with the dominant sequences belonging to the genera Dechloromarinus and Denitromonas. A study examining the effects of growing the cultures on different electron acceptors to the cultures revealed that Denitromonas may be more dominant than Dechloromarinus as the salt-tolerant, perchlorate-reducing organism.}, }
@article {pmid19807780, year = {2010}, author = {Louis, P and Young, P and Holtrop, G and Flint, HJ}, title = {Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA:acetate CoA-transferase gene.}, journal = {Environmental microbiology}, volume = {12}, number = {2}, pages = {304-314}, doi = {10.1111/j.1462-2920.2009.02066.x}, pmid = {19807780}, issn = {1462-2920}, mesh = {Acetates/metabolism ; Acyl Coenzyme A/metabolism ; Bacteria/classification/genetics/*metabolism ; Butyrates/*metabolism ; Coenzyme A-Transferases/*genetics/metabolism ; Colon/*microbiology ; Eubacterium/genetics/metabolism ; Fusobacterium/genetics/metabolism ; Genes, Bacterial ; Gram-Positive Bacteria/genetics/metabolism ; Humans ; Inulin/metabolism ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Butyrate-producing bacteria play an important role in the human colon, supplying energy to the gut epithelium and regulating host cell responses. In order to explore the diversity and culturability of this functional group, we designed degenerate primers to amplify butyryl-CoA:acetate CoA-transferase sequences from faecal samples provided by 10 healthy volunteers. Eighty-eight per cent of amplified sequences showed >98% DNA sequence identity to CoA-transferases from cultured butyrate-producing bacteria, and these fell into 12 operational taxonomic units (OTUs). The four most prevalent OTUs corresponded to Eubacterium rectale, Roseburia faecis, Eubacterium hallii and an unnamed cultured species SS2/1. The remaining 12% of sequences, however, belonged to 20 OTUs that are assumed to come from uncultured butyrate-producing strains. Samples taken after ingestion of inulin showed significant (P=0.019) increases in Faecalibacterium prausnitzii. Because several of the dominant butyrate producers differ in their DNA % G+C content, analysis of thermal melt curves obtained for PCR amplicons of the butyryl-CoA:acetate CoA-transferase gene provides a convenient and rapid qualitative assessment of the major butyrate producing groups present in a given sample. This type of analysis therefore provides an excellent source of information on functionally important groups within the colonic microbial community.}, }
@article {pmid19805153, year = {2009}, author = {Hartman, AL and Lough, DM and Barupal, DK and Fiehn, O and Fishbein, T and Zasloff, M and Eisen, JA}, title = {Human gut microbiome adopts an alternative state following small bowel transplantation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {40}, pages = {17187-17192}, pmid = {19805153}, issn = {1091-6490}, support = {R01 ES013932/ES/NIEHS NIH HHS/United States ; R01 ES13932/ES/NIEHS NIH HHS/United States ; }, mesh = {Adult ; Anaerobiosis ; Bacteria/genetics/*growth &amp; development/metabolism ; Bacteroides/growth &amp; development ; Clostridium/growth &amp; development ; DNA, Bacterial/genetics ; Ecosystem ; Enterobacteriaceae/growth &amp; development ; Genotype ; Humans ; Ileostomy ; Ileum/microbiology/surgery/transplantation ; Intestinal Diseases/genetics/microbiology/surgery ; Intestine, Small/*microbiology/surgery/*transplantation ; Lactobacillus/growth &amp; development ; *Metagenome ; Middle Aged ; Mutation ; Nod2 Signaling Adaptor Protein/genetics ; Polymerase Chain Reaction/methods ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Small bowel transplants provide an exceptional opportunity for long-term study of the microbial ecology of the human small bowel. The ileostomy created at time of transplant for ongoing monitoring of the allograft provides access to samples of ileal effluent and mucosal biopsies. In this study, we used qPCR to assay the bacterial population of the small bowel lumen of 17 small bowel transplant patients over time. Surprisingly, the posttransplant microbial community was found to be dominated by Lactobacilli and Enterobacteria, both typically facultative anaerobes. This represents an inversion of the normal community that is dominated instead by the strictly anaerobic Bacteroides and Clostridia. We found this inverted community also in patients with ileostomies who did not receive a transplant, suggesting that the ileostomy itself is the primary ecological determinant shaping the microbiota. After surgical closure of the ileostomy, the community reverted to the normal structure. Therefore, we hypothesized that the ileostomy allows oxygen into the otherwise anaerobic distal ileum, thus driving the transition from one microbial community structure to another. Supporting this hypothesis, metabolomic profiling of both communities demonstrated an enrichment for metabolites associated with aerobic respiration in samples from patients with open ileostomies. Viewed from an ecological perspective, the two communities constitute alternative stable states of the human ileum. That the small bowel appears to function normally despite these dramatic shifts suggests that its ecological resilience is greater than previously realized.}, }
@article {pmid19799631, year = {2009}, author = {He, J and Zhu, Y and Prosser, JI}, title = {Showcasing microbial ecology research in China.}, journal = {FEMS microbiology ecology}, volume = {70}, number = {2}, pages = {7-8}, doi = {10.1111/j.1574-6941.2009.00781.x}, pmid = {19799631}, issn = {1574-6941}, mesh = {China ; *Ecology ; *Environmental Microbiology ; *Research ; }, }
@article {pmid19789910, year = {2010}, author = {Ben Said, O and Goñi-Urriza, M and El Bour, M and Aissa, P and Duran, R}, title = {Bacterial community structure of sediments of the bizerte lagoon (Tunisia), a southern Mediterranean coastal anthropized lagoon.}, journal = {Microbial ecology}, volume = {59}, number = {3}, pages = {445-456}, pmid = {19789910}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; DNA Fingerprinting ; Gene Library ; Geologic Sediments/*microbiology ; Hydrocarbons ; Mediterranean Region ; Metals, Heavy/analysis ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/*analysis ; Polymorphism, Restriction Fragment Length ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Tunisia ; Water Pollutants, Chemical/*analysis ; }, abstract = {In order to estimate how pollution affects the bacterial community structure and composition of sediments, chemical and molecular approaches were combined to investigate eight stations around the Bizerte lagoon. Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified 16S rRNA genes revealed that each station was characterized by a specific bacterial community structure. The combination of this data with those of chemical analysis showed a correlation between the bacterial fingerprint and the pollutant content, principally with hydrocarbon pollution. The composition of the bacterial community of two contrasted stations related to the pollution revealed sequences affiliated to alpha, beta, gamma, delta, epsilon subclass of the Proteobacteria, Actinobacteria, and Acidobacteria in both stations although in different extent. Gamma and delta subclass of the Proteobacteria were dominant and represent 70% of clones in the heavy-metal-contaminated station and 47% in the polyaromatic hydrocarbon (PAH)-contaminated. Nevertheless, most of the sequences found were unaffiliated to cultured bacteria. The adaptation of the bacterial community mainly to PAH compounds demonstrated here and the fact that these bacterial communities are mainly unknown suggest that the Bizerte lagoon is an interesting environment to understand the capacity of bacteria to cope with some pollutants.}, }
@article {pmid19789909, year = {2010}, author = {Obernosterer, I and Lami, R and Larcher, M and Batailler, N and Catala, P and Lebaron, P}, title = {Linkage between bacterial carbon processing and the structure of the active bacterial community at a coastal site in the NW Mediterranean Sea.}, journal = {Microbial ecology}, volume = {59}, number = {3}, pages = {428-435}, pmid = {19789909}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/growth &amp; development/*metabolism ; Biomass ; Carbon/*metabolism ; Chlorophyll/analysis ; Chlorophyll A ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Mediterranean Sea ; Nitrates/analysis ; Oxygen Consumption ; Phosphates/analysis ; Polymorphism, Single-Stranded Conformational ; RNA, Ribosomal, 16S/genetics ; Ribotyping ; Salinity ; Seasons ; Seawater/*microbiology ; }, abstract = {The temporal dynamics in bulk bacterial parameters and in the richness of the total and active bacterial community, determined from CE-SSCP fingerprints of 16S rRNA genes and 16S rRNA transcripts, respectively, were followed weekly to bimonthly at an oligotrophic coastal site in the NW Mediterranean Sea. Bacterial abundance, bacterial heterotrophic production, and bacterial and community respiration determined over two seasonal cycles displayed large short-term variability and no pronounced temporal pattern was detectable for these parameters. Concentrations in inorganic nutrients, salinity, or concentrations of chlorophyll a could not significantly explain the temporal variability of the bacterial parameters determined. By contrast, bacterial respiration and the bacterial carbon demand were both negatively correlated with the richness of the active bacterial community, while the bacterial parameters determined herein were not related to the richness of the total bacterial community present. Our results indicate that a reduced number of ribotypes is active when rates of bacteria-mediated carbon processes are high. Our approach, based on fingerprints of 16S rRNA transcripts, could represent an interesting tool to investigate the relationship between the structure and function of marine bacteria, in particular, on short temporal and spatial scales.}, }
@article {pmid19787390, year = {2010}, author = {Kennedy, PG and Schouboe, JL and Rogers, RH and Weber, MG and Nadkarni, NM}, title = {Frankia and Alnus rubra canopy roots: an assessment of genetic diversity, propagule availability, and effects on soil nitrogen.}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {214-220}, pmid = {19787390}, issn = {1432-184X}, mesh = {Alnus/*microbiology ; DNA, Bacterial/genetics ; Frankia/classification/*genetics ; Genetic Variation ; Genotype ; Nitrogen/*analysis ; Phylogeny ; Plant Roots/microbiology ; Soil/*analysis ; Soil Microbiology ; *Symbiosis ; Trees/genetics ; Washington ; }, abstract = {The ecological importance of microbial symbioses in terrestrial soils is widely recognized, but their role in soils that accumulate in forest canopies is almost entirely unknown. To address this gap, this study investigated the Frankia-Alnus rubra symbiosis in canopy and forest floor roots at Olympic National Park, WA, USA. Sixteen mature A. rubra trees were surveyed and Frankia genetic diversity in canopy and forest floor nodules was assessed with sequence-based nifH analyses. A seedling bioassay experiment was conducted to determine Frankia propagule availability in canopy and forest floor soils. Total soil nitrogen from both environments was also quantified. Nodules were present in the canopies of nine of the 16 trees sampled. Across the study area, Frankia canopy and forest floor assemblages were similar, with both habitats containing the same two genotypes. The composition of forest floor and canopy genotypes on the same tree was not always identical, however, suggesting that dispersal was not a strictly local phenomenon. Frankia seedling colonization was similar in canopy soils regardless of the presence of nodules as well as in forest floor soils, indicating that dispersal was not likely to be a major limiting factor. The total soil nitrogen of canopy soils was higher than that of forest floor soils, but the presence of Frankia nodules in canopy soils did not significantly alter soil nitrogen levels. Overall, this study indicates that the Frankia-A. rubra symbiosis is similar in canopy and forest floor environments. Because canopy roots are exposed to different environmental conditions within very small spatial areas and because those areas can be easily manipulated (e.g., fertilizer or watering treatments), they present microbial ecologists with a unique arena to examine root-microbe interactions.}, }
@article {pmid19783749, year = {2009}, author = {Pieper, R and Bindelle, J and Rossnagel, B and Van Kessel, A and Leterme, P}, title = {Effect of carbohydrate composition in barley and oat cultivars on microbial ecophysiology and proliferation of Salmonella enterica in an in vitro model of the porcine gastrointestinal tract.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {22}, pages = {7006-7016}, pmid = {19783749}, issn = {1098-5336}, mesh = {Animals ; *Avena/chemistry/metabolism ; Bacteria/classification/genetics/growth &amp; development/metabolism ; *Bacterial Physiological Phenomena ; Cell Proliferation ; Colony Count, Microbial ; Dietary Carbohydrates/analysis/*metabolism ; Fermentation ; Gastrointestinal Tract/*microbiology ; *Hordeum/chemistry/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/analysis/metabolism ; Salmonella enterica/growth &amp; development/metabolism/*physiology ; Swine/*microbiology ; }, abstract = {The influence of the carbohydrate (CHO) composition of cereal cultivars on microbial ecophysiology was studied using an in vitro model of the porcine gastrointestinal tract. Ten hull-less barley cultivars, six barley cultivars with hulls, six oat cultivars, and six oat groats that differed in beta-glucan, nonstarch polysaccharide (NSP), and starch contents and starch type were hydrolyzed enzymatically and incubated for 72 h with pig feces. Fermentation kinetics were modeled, and microbial compositions and short-chain fatty acid (SCFA) profiles were analyzed using terminal restriction fragment length polymorphism and gas chromatography. Cluster analysis and canonical ordination revealed different effects on fermentation and microbial ecology depending on the type of CHO and cultivar. First, in cultivars of barley with hulls and oats, the cellulose and insoluble NSP contents (i) increased Ruminococcus flavefaciens-like and Clostridium xylanolyticum-like phylotypes, (ii) increased acetate production, and (iii) decreased fermentation activity. Second, in hull-less barley cultivars the beta-glucan, amylose, amylopectin, crude protein, and soluble NSP contents determined the microbial community composition and activity as follows: (i) the amylose contents of the hull-less barley varieties increased the butyrate production and the abundance of Clostridium butyricum-like phylotypes, (ii) the beta-glucan content determined the total amounts of SCFA, and (iii) the amylopectin and starch contents affected the abundance of Clostridium ramosum-like phylotypes, members of Clostridium cluster XIVa, and Bacteroides-like bacteria. Finally, the effect of CHO on proliferation of Salmonella enterica in the model was determined. Salmonella cell counts were not affected, but the relative proportion of Salmonella decreased with hull-less barley cultivars and increased with oat cultivars as revealed by quantitative PCR. Our results shed light on the complex interactions of cereal CHO with intestinal bacterial ecophysiology and the possible impact on host health.}, }
@article {pmid19783002, year = {2010}, author = {Mshvildadze, M and Neu, J and Shuster, J and Theriaque, D and Li, N and Mai, V}, title = {Intestinal microbial ecology in premature infants assessed with non-culture-based techniques.}, journal = {The Journal of pediatrics}, volume = {156}, number = {1}, pages = {20-25}, pmid = {19783002}, issn = {1097-6833}, support = {M01 RR000082/RR/NCRR NIH HHS/United States ; R01 HD059143/HD/NICHD NIH HHS/United States ; R01 HD 059143/HD/NICHD NIH HHS/United States ; M01RR00082/RR/NCRR NIH HHS/United States ; }, mesh = {DNA, Bacterial/*analysis ; Enterocolitis, Necrotizing/*microbiology ; Feces/*microbiology ; Female ; Humans ; Infant, Newborn ; Infant, Premature ; Infant, Premature, Diseases/*microbiology ; Male ; Meconium/*microbiology ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S ; }, abstract = {OBJECTIVES: To use high throughput techniques to analyze intestinal microbial ecology in premature neonates, who are highly susceptible to perturbations of the luminal environment associated with necrotizing enterocolitis (NEC) and late-onset sepsis.<br><br>STUDY DESIGN: With non-culture-based techniques, we evaluated intestinal microbiota shortly after birth and during hospitalization in 23 neonates born at 23 to 32 weeks gestational age. Microbiota compositions were compared in 6 preterm infants in whom NEC, signs of systemic inflammation, or both developed with matched control subjects by using 16S ribosomal RNA pyrosequencing.<br><br>RESULTS: Microbial DNA was detected in meconium, suggesting an intrauterine origin. Differences in diversity were detected in infants whose mothers intended to breast feed (P = .03), babies born to mothers with chorioamnionitis (P = .06), and in babies born at <30 weeks gestation (P = .03). A 16S ribosomal RNA sequence analysis detected Citrobacter-like sequences only in cases with NEC (3 of 4) and an increased frequency of Enterococcus-like sequences in cases and Klebsiella in control subjects (P = .06). The overall microbiota profiles in cases with NEC were not distinguishable from that in control subjects.<br><br>CONCLUSIONS: Microbial DNA in meconium of premature infants suggests prenatal influences.}, }
@article {pmid19781086, year = {2009}, author = {Rastogi, R and Wu, M and Dasgupta, I and Fox, GE}, title = {Visualization of ribosomal RNA operon copy number distribution.}, journal = {BMC microbiology}, volume = {9}, number = {}, pages = {208}, pmid = {19781086}, issn = {1471-2180}, mesh = {Bacteria/classification/*genetics ; *Gene Dosage ; Genetic Markers ; *Genome, Bacterial ; Phylogeny ; *rRNA Operon ; }, abstract = {BACKGROUND: Results of microbial ecology studies using 16S rRNA sequence information can be deceiving due to differences in rRNA operon copy number and genome size of the detected organisms. It therefore will be useful for investigators to have a better understanding of how these two parameters differ in various organism types. In this study, the number of ribosomal operons and genome size were separately mapped onto a Bacterial phylogenetic tree.<br><br>RESULTS: A representative Bacterial tree was constructed using 31 marker genes found in 578 bacterial genome sequences. Organism names are displayed on the trees using graduations of color such that similar colors indicate similar numbers of operons or genome size. The resulting images provide an intuitive understanding of how copy number and genome size vary in different Bacterial phyla.<br><br>CONCLUSION: Once the phylogenetic position of a novel organism is known the number of rRNA operons, and to a lesser extent the genome size, can be estimated by examination of the colored maps. Further detail can then be obtained for members of relevant taxa from the rrnDB database.}, }
@article {pmid19777880, year = {2009}, author = {Sheffield, CL and Crippen, TL and Andrews, K and Bongaerts, RJ and Nisbet, DJ}, title = {Planktonic and biofilm communities from 7-day-old chicken cecal microflora cultures: characterization and resistance to Salmonella colonization.}, journal = {Journal of food protection}, volume = {72}, number = {9}, pages = {1812-1820}, doi = {10.4315/0362-028x-72.9.1812}, pmid = {19777880}, issn = {0362-028X}, mesh = {Animals ; Animals, Newborn ; Biofilms/*growth &amp; development ; Cecum/*microbiology ; Chickens ; Colony Count, Microbial ; *Consumer Product Safety ; Disease Susceptibility/veterinary ; Food Contamination/*prevention &amp; control ; Humans ; Poultry Diseases/prevention &amp; control ; Ribotyping ; Salmonella Infections, Animal/prevention &amp; control ; Salmonella typhimurium/growth &amp; development/*physiology ; }, abstract = {Information implicating bacterial biofilms as contributory factors in the development of environmental bacterial resistance has been increasing. There is a lack of information regarding the role of biofilms within the microbial ecology of the gastrointestinal tract of food animals. This work used a continuous-flow chemostat model derived from the ceca of 7-day-old chicks to characterize these communities and their ability to neutralize invasion by Salmonella enterica serovar Typhimurium. We characterized and compared the biofilm and planktonic communities within these microcosms using automated ribotyping and the Analytical Profile Index biotyping system. Eleven species from eight different genera were identified from six culture systems. Klebsiella pneumoniae was isolated from all planktonic communities and four of the biofilm communities. Three of the communities resisted colonization by Salmonella enterica serovar Typhimurium, two communities suppressed growth, and one community succumbed to colonization. In cultures that resisted colonization, no Salmonella could be isolated from the biofilm; in cultures that succumbed to colonization, Salmonella was consistently found within the biofilms. This study was one of a series that provided a molecular-based characterization of both the biofilm and planktonic communities from continuous-flow culture systems derived from the cecal microflora of chicks, ranging in age from day-of-hatch to 14 days old. The one common factor relating to successful colonization of the culture was the presence of Salmonella within the biofilm. The capacity to sequester the introduced Salmonella into the biofilm appears to be a contributing factor to the inability of these cultures to withstand colonization by the Salmonella.}, }
@article {pmid19776767, year = {2010}, author = {Iwai, S and Chai, B and Sul, WJ and Cole, JR and Hashsham, SA and Tiedje, JM}, title = {Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment.}, journal = {The ISME journal}, volume = {4}, number = {2}, pages = {279-285}, pmid = {19776767}, issn = {1751-7370}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; 5P42 ES004911-18/19/ES/NIEHS NIH HHS/United States ; }, mesh = {Biodegradation, Environmental ; Czech Republic ; DNA Primers/genetics ; Dioxygenases/*genetics/metabolism ; *Genes, Bacterial ; *Metagenomics ; Phylogeny ; Polymerase Chain Reaction ; *Soil Microbiology ; Soil Pollutants/metabolism ; }, abstract = {Understanding the relationship between gene diversity and function for important environmental processes is a major ecological research goal. We applied gene-targeted metagenomics and pyrosequencing to aromatic dioxygenase genes to obtain greater sequence depth than possible by other methods. A polymerase chain reaction (PCR) primer set designed to target a 524-bp region that confers substrate specificity of biphenyl dioxygenases yielded 2000 and 604 sequences from the 5' and 3' ends of PCR products, respectively, which passed our validity criteria. Sequence alignment showed three known conserved residues, as well as another seven conserved residues not reported earlier. Of the valid sequences, 95% and 41% were assigned to 22 and 3 novel clusters in that they did not include any earlier reported sequences at 0.6 distance by complete linkage clustering for sequenced regions. The greater diversity revealed by this gene-targeted approach provides deeper insights into genes potentially important in environmental processes to better understand their ecology, functional differences and evolutionary origins. We also provide criteria for primer design for this approach, as well as guidance for data processing of diverse functional genes, as gene databases for most genes of environmental relevance are limited.}, }
@article {pmid19769587, year = {2009}, author = {Devi, KK and Kothamasi, D}, title = {Pseudomonas fluorescens CHA0 can kill subterranean termite Odontotermes obesus by inhibiting cytochrome c oxidase of the termite respiratory chain.}, journal = {FEMS microbiology letters}, volume = {300}, number = {2}, pages = {195-200}, doi = {10.1111/j.1574-6968.2009.01782.x}, pmid = {19769587}, issn = {1574-6968}, mesh = {Animals ; Electron Transport Complex IV/*antagonists &amp; inhibitors ; Hydrogen Cyanide/*metabolism/*toxicity ; Isoptera/*microbiology ; Pseudomonas Infections/*microbiology/veterinary ; Pseudomonas fluorescens/*pathogenicity ; Survival Analysis ; }, abstract = {Pseudomonas fluorescens CHA0 has been shown to suppress the growth of a wide range of microbial plant pathogens as well as invertebrate pests such as root nematodes. Hydrogen cyanide, a secondary metabolite produced by the bacterium, has been credited as being one of the determinants of its biocontrol ability. The use of biocontrol agents against social insect pests such as termite Odontotermes obesus has limitations because of behavioural adaptations that include (1) removal of the pathogen when grooming by the termites and (2) isolation of infested members of the colony. In this study, we show that cyanide of bacterial origin may inhibit cytochrome c oxidase (CCO) of the termite respiratory chain and demonstrate that HCN-producing bacteria such as P. fluorescens can actually kill a macroscopic insect pest by cyanide poisoning. This ability of pseudomonad metabolites such as cyanide, which can bring about pest death by blocking respiration through inhibition of CCO rather than infection or predation, can potentially overcome the behavioural adaptations of social insect pests such as termites and represents an attractive option for insect pest management.}, }
@article {pmid19768568, year = {2009}, author = {McIlroy, SJ and Porter, K and Seviour, RJ and Tillett, D}, title = {Extracting nucleic acids from activated sludge which reflect community population diversity.}, journal = {Antonie van Leeuwenhoek}, volume = {96}, number = {4}, pages = {593-605}, doi = {10.1007/s10482-009-9374-z}, pmid = {19768568}, issn = {1572-9699}, mesh = {*Biodiversity ; In Situ Hybridization, Fluorescence ; Molecular Biology/*methods/*standards ; Nucleic Acids/genetics/*isolation &amp; purification/*standards ; Polymerase Chain Reaction/methods ; Sensitivity and Specificity ; Sewage/*microbiology ; }, abstract = {Critical to most studies in molecular microbial ecology is the application of DNA/RNA extraction methods which can reveal the true level of population biodiversity present in samples from the community under investigation. Activated sludge communities have been studied extensively using molecular methods, but rarely have the nucleic acid isolation methods applied been assessed for their ability to achieve this. This study compares eight published RNA and DNA extraction protocols and one commercially available DNA isolation kit for their capacity to provide high quality nucleic acids that reflect the community composition. Each method was assessed on the basis of nucleic acid yield, purity and integrity, and the ability to provide PCR amplifiable RNA and DNA from known marker populations that varied in their resistance to nucleic acid extraction. Only three consistently provided DNA from each of the marker populations known to be present in the samples from fluorescence in situ hybridisation analysis. The failure of the other methods emphasises the need to validate all DNA/RNA extraction protocols. It is recommended that several validated extraction methods be used and the extracts pooled to further minimise any risk of bias.}, }
@article {pmid19768133, year = {2009}, author = {Anderson, CR and Dick, GJ and Chu, ML and Cho, JC and Davis, RE and Bräuer, SL and Tebo, BM}, title = {Aurantimonas manganoxydans, sp. nov. and Aurantimonas litoralis, sp. nov.: Mn(II) oxidizing representatives of a globally distributed clade of alpha-Proteobacteria from the order Rhizobiales.}, journal = {Geomicrobiology journal}, volume = {26}, number = {3}, pages = {189-198}, pmid = {19768133}, issn = {0149-0451}, support = {P42 ES010337/ES/NIEHS NIH HHS/United States ; }, abstract = {Several closely related Mn(II)-oxidizing alpha-Proteobacteria were isolated from very different marine environments: strain SI85-9A1 from the oxic/anoxic interface of a stratified Canadian fjord, strain HTCC 2156 from the surface waters off the Oregon coast, and strain AE01 from the dorsal surface of a hydrothermal vent tubeworm. 16S rRNA analysis reveals that these isolates are part of a tight phylogenetic cluster with previously characterized members of the genus Aurantimonas. Other organisms within this clade have been isolated from disparate environments such as surface waters of the Arctic and Mediterranean seas, a deep-sea hydrothermal plume, and a Caribbean coral. Further analysis of all these strains revealed that many of them are capable of oxidizing dissolved Mn(II) and producing particulate Mn(III/IV) oxides. Strains SI85-9A1 and HTCC 2156 were characterized further. Despite sharing nearly identical 16S rRNA gene sequences with the previously described Aurantimonas coralicida, whole genome DNA-DNA hybridization indicated that their overall genomic similarity is low. Polyphasic phenotype characterization further supported distinguishing characteristics among these bacteria. Thus SI85-9A1 and HTCC 2156 are described as two new species within the family 'Aurantimionadaceae': Aurantimonas manganoxydans sp. nov. and Aurantimonas litoralis sp. nov. This clade of bacteria is widely distributed around the globe and may be important contributors to Mn cycling in many environments. Our results highlight the difficulty in utilizing 16S rRNA-based approaches to investigate the microbial ecology of Mn(II) oxidation.}, }
@article {pmid19763680, year = {2010}, author = {Durham-Colleran, MW and Verhoeven, AB and van Hoek, ML}, title = {Francisella novicida forms in vitro biofilms mediated by an orphan response regulator.}, journal = {Microbial ecology}, volume = {59}, number = {3}, pages = {457-465}, pmid = {19763680}, issn = {1432-184X}, mesh = {Bacterial Proteins/genetics/*metabolism ; Biofilms/*growth &amp; development ; Francisella/genetics/*growth &amp; development ; Gene Expression Regulation, Bacterial ; Genetic Complementation Test ; Mutagenesis ; Orphan Nuclear Receptors/genetics/*metabolism ; Sequence Deletion ; }, abstract = {Francisella tularensis is associated with water and waterways and infects many species of animals, insects, and protists. The mechanism Francisella utilizes to persist in the environment and in tick vectors is currently unknown. We have demonstrated for the first time that Francisella novicida, a model organism of F. tularensis, forms a biofilm in vitro. Selected F. novicida transposon mutants were tested for their ability to form biofilm compared to the wildtype F. novicida strain. Mutation of the putative qseB gene led to an impairment in the ability to form biofilm with no impairment in bacterial growth. A qseC mutant had impaired growth but demonstrated a marked impairment in biofilm production. Mutation in capC affected both bacterial growth and biofilm formation, but no biofilm production impairment was seen with capB or pilE mutants. A deletion mutant in the orphan response regulator FTN_1465, which we propose is the putative QseB, formed significantly less biofilm than the wildtype. When FTN_1465 was complemented back into the deletion mutant, biofilm formation was restored. Thus, the orphan response regulator FTN_1465 is an important factor in biofilm production in vitro in F. novicida. These results demonstrate that Francisella species are able to form biofilms in vitro, suggesting that biofilm formation may be important for the lifecycle of this organism.}, }
@article {pmid19762798, year = {2009}, author = {Ranieri, ML and Boor, KJ}, title = {Short communication: bacterial ecology of high-temperature, short-time pasteurized milk processed in the United States.}, journal = {Journal of dairy science}, volume = {92}, number = {10}, pages = {4833-4840}, doi = {10.3168/jds.2009-2181}, pmid = {19762798}, issn = {1525-3198}, mesh = {Animals ; Bacillus/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Food Handling/methods ; Food Preservation/*methods ; *Hot Temperature ; Milk/*microbiology ; Paenibacillus/classification/genetics/isolation &amp; purification ; Time Factors ; United States ; }, abstract = {To determine the microbial ecology of pasteurized milk within the United States, 2% fat pasteurized fluid milk samples were obtained from 18 dairy plants from 5 geographical areas representing the Northeast, Southeast, South, Midwest, and West. Of the 589 bacterial isolates identified using DNA sequence-based subtyping methods, 346 belonged to genera characterized as gram-positive endospore-forming bacteria (i.e., Bacillus and Paenibacillus). Of the 346 gram-positive endospore-forming bacteria isolated in the present study, 240 were classified into 45 allelic types identical to those previously identified from samples obtained in New York State, indicating the widespread presence of these microbes in fluid milk production and processing systems in the United States. More than 84% of the gram-positive spore-forming isolates characterized at d 1, 7, and 10 were of the genus Bacillus, whereas more than 92% of isolates characterized at d 17 of shelf life were of the genus Paenibacillus, indicating that the predominant gram-positive spoilage genera shifts from Bacillus spp. to Paenibacillus spp. during refrigerated storage.}, }
@article {pmid19762797, year = {2009}, author = {Ranieri, ML and Huck, JR and Sonnen, M and Barbano, DM and Boor, KJ}, title = {High temperature, short time pasteurization temperatures inversely affect bacterial numbers during refrigerated storage of pasteurized fluid milk.}, journal = {Journal of dairy science}, volume = {92}, number = {10}, pages = {4823-4832}, doi = {10.3168/jds.2009-2144}, pmid = {19762797}, issn = {1525-3198}, mesh = {Animals ; Bacillus/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Cold Temperature ; *Colony Count, Microbial ; Food Handling/methods ; Food Preservation/*methods ; *Hot Temperature ; Milk/*microbiology ; Paenibacillus/isolation &amp; purification ; Spores, Bacterial/physiology ; Time Factors ; }, abstract = {The grade A Pasteurized Milk Ordinance specifies minimum processing conditions of 72 degrees C for at least 15 s for high temperature, short time (HTST) pasteurized milk products. Currently, many US milk-processing plants exceed these minimum requirements for fluid milk products. To test the effect of pasteurization temperatures on bacterial numbers in HTST pasteurized milk, 2% fat raw milk was heated to 60 degrees C, homogenized, and treated for 25 s at 1 of 4 different temperatures (72.9, 77.2, 79.9, or 85.2 degrees C) and then held at 6 degrees C for 21 d. Aerobic plate counts were monitored in pasteurized milk samples at d 1, 7, 14, and 21 postprocessing. Bacterial numbers in milk processed at 72.9 degrees C were lower than in milk processed at 85.2 degrees C on each sampling day, indicating that HTST fluid milk-processing temperatures significantly affected bacterial numbers in fluid milk. To assess the microbial ecology of the different milk samples during refrigerated storage, a total of 490 psychrotolerant endospore-forming bacteria were identified using DNA sequence-based subtyping methods. Regardless of processing temperature, >85% of the isolates characterized at d 0, 1, and 7 postprocessing were of the genus Bacillus, whereas more than 92% of isolates characterized at d 14 and 21 postprocessing were of the genus Paenibacillus, indicating that the predominant genera present in HTST-processed milk shifted from Bacillus spp. to Paenibacillus spp. during refrigerated storage. In summary, 1) HTST processing temperatures affected bacterial numbers in refrigerated milk, with higher bacterial numbers in milk processed at higher temperatures; 2) no significant association was observed between genus isolated and pasteurization temperature, suggesting that the genera were not differentially affected by the different processing temperatures; and 3) although typically present at low numbers in raw milk, Paenibacillus spp. are capable of growing to numbers that can exceed Pasteurized Milk Ordinance limits in pasteurized, refrigerated milk.}, }
@article {pmid19760448, year = {2010}, author = {Shade, A and Chiu, CY and McMahon, KD}, title = {Seasonal and episodic lake mixing stimulate differential planktonic bacterial dynamics.}, journal = {Microbial ecology}, volume = {59}, number = {3}, pages = {546-554}, pmid = {19760448}, issn = {1432-184X}, mesh = {*Bacteria/genetics ; DNA Fingerprinting ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Ecosystem ; Fresh Water/*microbiology ; Hydrogen-Ion Concentration ; Population Dynamics ; *Seasons ; Taiwan ; Temperature ; *Water Microbiology ; }, abstract = {Yuan Yang Lake (YYL), Taiwan, experiences both winter and typhoon-initiated mixing, and each type of mixing event is characterized by contrasting environmental conditions. Previous work suggested that after typhoon mixing, bacterial communities in YYL reset to a pioneer composition and then follow a predictable trajectory of change until the next typhoon. Our goal was to continue this investigation by observing bacterial community change after a range of mixing intensities, including seasonal winter mixing. We fingerprinted aquatic bacterial communities in the epilimnion and hypolimnion using automated ribosomal intergenic spacer analysis and then assessed community response using multivariate statistics. We found a significant linear relationship between water column stability and the epilimnion to hypolimnion divergences. In comparison to the summer, we found the winter community had a distinct composition and less variation. We divided the bacterial community into population subsets according to abundance (rare, common, or dominant) and occurrence (transient or persistent) and further explored the contribution of these subsets to the overall community patterns. We found that transient taxa did not drive bacterial community patterns following weak typhoon mixing events, but contributed substantially to patterns observed following strong events. Common taxa generally did not follow the community trajectory after weak or strong events. Our results suggest intensity, frequency, and seasonality jointly contribute to aquatic bacterial response to mixing disturbance.}, }
@article {pmid19759442, year = {2009}, author = {Forrez, I and Verstraete, W}, title = {Bioaugmentation to degrade the organic de-icers acetate and monopropylene glycol at low temperatures.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {60}, number = {6}, pages = {1401-1407}, doi = {10.2166/wst.2009.480}, pmid = {19759442}, issn = {0273-1223}, mesh = {Aircraft ; Bacteria/*metabolism ; Biodegradation, Environmental ; *Ice ; Potassium Acetate/*isolation &amp; purification/*metabolism ; Propylene Glycol/*isolation &amp; purification/*metabolism ; Temperature ; Water Pollutants, Chemical/isolation &amp; purification/metabolism ; }, abstract = {Two de-icers, potassium acetate and monopropylene glycol (MPG), used widespread as a runway and wing de-icer respectively, can exert high BOD in the surrounding waters. A bioaugmentation approach to degrade these de-icer compounds in the drainage water prior to discharge has been tested. A microbial consortium originating from soil was enriched at low temperatures (4 degrees C) in order to adapt to wintertime conditions. With 0.05 g CDW/L of biocatalyst, maximum specific removal rates up to 1.46 and 3.33 g acetate/g CDW d at 4 degrees C were achieved with and without biostimulation respectively. An acetate:MPG mixture of 1:3 at a total COD concentration of 0.80 and 1.20 g/L was degraded in 12 days by 83 and 70% respectively. Bioaugmentation in the field over a period of 25 days showed a removal of 88% MPG compared to 46% in the control. These results demonstrate that bioaugmentation of airport runoff water can be successfully applied to prevent organic de-icer compounds from entering the receiving surface waters.}, }
@article {pmid19756850, year = {2010}, author = {Meyer, C and Gilbert, D and Gaudry, A and Franchi, M and Nguyen, HV and Fabure, J and Bernard, N}, title = {Relationship of atmospheric pollution characterized by gas (NO2) and particles (PM10) to microbial communities living in bryophytes at three differently polluted sites (rural, urban, and industrial).}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {324-334}, pmid = {19756850}, issn = {1432-184X}, mesh = {Air Pollutants/*analysis ; Amoeba/growth &amp; development ; Animals ; Bacteria/growth &amp; development ; Biomass ; Bryophyta/*microbiology ; Environmental Monitoring ; Eukaryota/growth &amp; development ; France ; Metals/analysis ; Nitrogen Dioxide/*analysis ; Particulate Matter/*analysis ; Rotifera/growth &amp; development ; }, abstract = {Atmospheric pollution has become a major problem for modern societies owing to its fatal effects on both human health and ecosystems. We studied the relationships of nitrogen dioxide atmospheric pollution and metal trace elements contained in atmospheric particles which were accumulated in bryophytes to microbial communities of bryophytes at three differently polluted sites in France (rural, urban, and industrial) over an 8-month period. The analysis of bryophytes showed an accumulation of Cr and Fe at the rural site; Cr, Fe, Zn, Cu, Al, and Pb at the urban site; and Fe, Cr, Pb, Al, Sr, Cu, and Zn at the industrial site. During this study, the structure of the microbial communities which is characterized by biomasses of microbial groups evolved differently according to the site. Microalgae, bacteria, rotifers, and testate amoebae biomasses were significantly higher in the rural site. Cyanobacteria biomass was significantly higher at the industrial site. Fungal and ciliate biomasses were significantly higher at the urban and industrial sites for the winter period and higher at the rural site for the spring period. The redundancy analysis showed that the physico-chemical variables ([NO(2)], relative humidity, temperature, and site) and the trace elements which were accumulated in bryophytes ([Cu], [Sr], [Pb]) explained 69.3% of the variance in the microbial community data. Moreover, our results suggest that microbial communities are potential biomonitors of atmospheric pollution. Further research is needed to understand the causal relationship underlined by the observed patterns.}, }
@article {pmid19756849, year = {2010}, author = {Ayarza, JM and Guerrero, LD and Erijman, L}, title = {Nonrandom assembly of bacterial populations in activated sludge flocs.}, journal = {Microbial ecology}, volume = {59}, number = {3}, pages = {436-444}, pmid = {19756849}, issn = {1432-184X}, mesh = {Bacteria/genetics/*growth &amp; development ; *Biomass ; Bioreactors/*microbiology ; DNA Fingerprinting ; Flocculation ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Time Factors ; Waste Disposal, Fluid ; }, abstract = {The aim of this work was to investigate the dynamics of assembly of bacterial populations in activated sludge flocs. We approached this question by following the development of active bacterial populations during floc development in four replicated lab-scale activated sludge reactors, in which solid retention time (SRT) was set at 4 days. The null hypothesis was that the similarities in community composition could be accounted for by the probability that the same organisms occur in more than one replicated reactor. Microscopic imaging showed that the size of flocs in reactors with biomass retention increased during the first few days until a steady-state size was reached. The diversity and community structure of the sludge in all reactors were analyzed during a period of up to ten SRT, using denaturing gradient gel electrophoresis (DGGE) of reverse-transcription polymerase chain reaction-amplified 16S rRNA. High rates of change in DGGE profiles from consecutive sampling points suggested a high level of dynamics in all reactors. This conclusion was confirmed by the application of the Raup and Crick probability-based similarity index (S(RC)) for the comparison of rRNA-based fingerprinting patterns, which indicated that bacterial communities within reactors were not significantly similar after three SRT (0.05 < S(RC) < 0.95) and became significantly dissimilar after five SRT (S(RC) < 0.05). More importantly, significant similarity between replicate reactors was observed at all times analyzed (S(RC) > 0.95). The fact that the patterns between replicates were more reproducible than expected by chance under highly dynamic conditions allowed us to reject the null hypothesis that activated sludge floc communities assemble randomly from the available source pool of bacteria. We suggest that communities progressively recruit from the available pool of bacterial species, each with particular ecological requirements that determine their time of emergence into the community.}, }
@article {pmid19756847, year = {2010}, author = {Beauregard, MS and Hamel, C and Atul-Nayyar,  and St-Arnaud, M}, title = {Long-term phosphorus fertilization impacts soil fungal and bacterial diversity but not AM fungal community in alfalfa.}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {379-389}, pmid = {19756847}, issn = {1432-184X}, mesh = {Agriculture/methods ; Bacteria/genetics/*growth &amp; development ; Biodiversity ; Biomass ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; Fatty Acids/analysis ; *Fertilizers ; Medicago sativa/*microbiology ; Multivariate Analysis ; Mycorrhizae/genetics/*growth &amp; development ; Phospholipids/analysis ; Phosphorus/*chemistry ; Saskatchewan ; Seasons ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Soil function may be affected by cropping practices impacting the soil microbial community. The effect of different phosphorus (P) fertilization rates (0, 20, or 40 kg P(2)O(5) ha(-1)) on soil microbial diversity was studied in 8-year-old alfalfa monocultures. The hypothesis that P fertilization modifies soil microbial community was tested using denaturing gradient gel electrophoresis and phospholipids fatty acid (PLFA) profiling to describe soil bacteria, fungi, and arbuscular mycorrhizal (AM) fungi diversity. Soil parameters related to fertility (soil phosphate flux, soluble P, moisture, phosphatase and dehydrogenase assays, and carbon and nitrogen content of the light fraction of soil organic matter) were also monitored and related to soil microbial ribotype profiles. Change in soil P fertility with the application of fertilizer had no effect on crop yield in 8 years, but on the year of this study was associated with shifts in the composition of fungal and bacterial communities without affecting their richness, as evidenced by the absence of effect on the average number of ribotypes detected. However, variation in soil P level created by a history of differential fertilization did not significantly influence AM fungi ribotype assemblages nor AM fungi biomass measured with the PLFA 16:1omega5. Fertilization increased P flux and soil soluble P level but reduced soil moisture and soil microbial activity, as revealed by dehydrogenase assay. Results suggest that soil P fertility management could influence soil processes involving soil microorganisms. Seasonal variations were also recorded in microbial activity, soil soluble P level as well as in the abundance of specific bacterial and fungal PLFA indicators of soil microbial biomass.}, }
@article {pmid19732933, year = {2009}, author = {Zhang, H and Banaszak, JE and Parameswaran, P and Alder, J and Krajmalnik-Brown, R and Rittmann, BE}, title = {Focused-Pulsed sludge pre-treatment increases the bacterial diversity and relative abundance of acetoclastic methanogens in a full-scale anaerobic digester.}, journal = {Water research}, volume = {43}, number = {18}, pages = {4517-4526}, doi = {10.1016/j.watres.2009.07.034}, pmid = {19732933}, issn = {1879-2448}, mesh = {Acetates/metabolism ; Anaerobiosis ; Archaea/classification/genetics/*metabolism ; Bacteria/classification/genetics/*metabolism ; Bioreactors/*microbiology ; Ecosystem ; Methanomicrobiaceae/metabolism ; Methanosarcinales/genetics/metabolism ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Spirochaetales/genetics/metabolism ; }, abstract = {The low yield of methane in anaerobic digestion systems represents a loss of energy that can be captured as renewable energy when the input sludge is pre-treated to make it more bioavailable. We investigated Focused-Pulsed (FP) pre-treatment, which make complex biological solids more bioavailable by exposing them to rapid pulses of a very strong electric field. We investigated how the microbial ecology in full-scale anaerobic digesters was altered when the digesters' methane production rate was significantly increased by FP pre-treatment. Using clone libraries and quantitative PCR, we demonstrated a shift in methanogenic genera to the acetate-cleaving Methanosaeta and away from the H(2)-oxidizing Methanoculleus. In addition, the acetate concentration in the effluent was very low, probably due to the dominance of Methanosaeta, which are capable of scavenging low acetate concentrations. By analyzing 36,797 pyrosequencing tags from the V6 region of the bacterial 16S rRNA gene, along with archaeal and bacterial clone libraries and quantitative PCR, we compared the microbial community composition before and after FP treatment. The bacterial community became more diverse after FP pre-treatment and was populated more by phylotypes associated with cellulose fermentation (Ruminococcus), scavenging of biomass-derived organic carbon (Chloroflexi), and homo-acetogenesis (Treponema). We interpret that, as the overall activity of the community was stimulated by addition of more bioavailable organic matter, the bacterial community became more phylogenetically diverse to take advantage of the added input of biodegradable material and in response to the more efficient utilization of acetate by Methanosaeta.}, }
@article {pmid19730766, year = {2010}, author = {Koltunov, V and Greenblatt, CL and Goncharenko, AV and Demina, GR and Klein, BY and Young, M and Kaprelyants, AS}, title = {Structural changes and cellular localization of resuscitation-promoting factor in environmental isolates of Micrococcus luteus.}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {296-310}, pmid = {19730766}, issn = {1432-184X}, mesh = {Acetic Acid/metabolism ; Acetylation ; Amino Acid Sequence ; Bacterial Proteins/genetics/*metabolism ; Cell Wall/metabolism ; Cloning, Molecular ; Cytokines/genetics/*metabolism ; Genes, Bacterial ; Genes, Essential ; *Genetic Variation ; Micrococcus luteus/*genetics/growth &amp; development/metabolism ; Molecular Sequence Data ; Muramidase/metabolism ; Recombinant Proteins/genetics/metabolism ; }, abstract = {Dormancy among nonsporulating actinobacteria is now a widely accepted phenomenon. In Micrococcus luteus, the resuscitation of dormant cells is caused by a small secreted protein (resuscitation-promoting factor, or Rpf) that is found in "spent culture medium." Rpf is encoded by a single essential gene in M. luteus. Homologs of Rpf are widespread among the high G + C Gram-positive bacteria, including mycobacteria and streptomycetes, and most organisms make several functionally redundant proteins. M. luteus Rpf comprises a lysozyme-like domain that is necessary and sufficient for activity connected through a short linker region to a LysM motif, which is present in a number of cell-wall-associated enzymes. Muralytic activity is responsible for resuscitation. In this report, we characterized a number of environmental isolates of M. luteus, including several recovered from amber. There was substantial variation in the predicted rpf gene product. While the lysozyme-like and LysM domains showed little variation, the linker region was elongated from ten amino acid residues in the laboratory strains to as many as 120 residues in one isolate. The genes encoding these Rpf proteins have been characterized, and a possible role for the Rpf linker in environmental adaptation is proposed. The environmental isolates show enhanced resistance to lysozyme as compared with the laboratory strains and this correlates with increased peptidoglycan acetylation. In strains that make a protein with an elongated linker, Rpf was bound to the cell wall, rather than being released to the growth medium, as occurs in reference strains. This rpf gene was introduced into a lysozyme-sensitive reference strain. Both rpf genes were expressed in transformants which showed a slight but statistically significant increase in lysozyme resistance.}, }
@article {pmid19730765, year = {2010}, author = {Han, TX and Tian, CF and Wang, ET and Chen, WX}, title = {Associations among rhizobial chromosomal background, nod genes, and host plants based on the analysis of symbiosis of indigenous rhizobia and wild legumes native to Xinjiang.}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {311-323}, pmid = {19730765}, issn = {1432-184X}, mesh = {Bacterial Proteins/*genetics ; Biodiversity ; China ; Chromosomes, Bacterial ; DNA, Bacterial/genetics ; Ecosystem ; Fabaceae/*microbiology ; Genes, Bacterial ; Geography ; N-Acetylglucosaminyltransferases/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizobium/classification/*genetics ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; }, abstract = {The associations among rhizobia chromosomal background, nodulation genes, legume plants, and geographical regions are very attractive but still unclear. To address this question, we analyzed the interactions among rhizobia rDNA genotypes, nodC genotypes, legume genera, as well as geographical regions in the present study. Complex relationships were observed among them, which may be the genuine nature of their associations. The statistical analyses indicate that legume plant is the key factor shaping both rhizobia genetic and symbiotic diversity. In the most cases of our results, the nodC lineages are clearly associated with rhizobial genomic species, demonstrating that nodulation genes have co-evolved with chromosomal background, though the lateral transfer of nodulation genes occurred in some cases in a minority. Our results also support the hypothesis that the endemic rhizobial populations to a certain geographical area prefer to have a wide spectrum of hosts, which might be an important event for the success of both legumes and rhizobia in an isolated region.}, }
@article {pmid19727930, year = {2010}, author = {Lin, YT and Huang, YJ and Tang, SL and Whitman, WB and Coleman, DC and Chiu, CY}, title = {Bacterial community diversity in undisturbed perhumid montane forest soils in Taiwan.}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {369-378}, pmid = {19727930}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics ; *Biodiversity ; DNA, Bacterial/genetics ; Gene Library ; Hydrogen-Ion Concentration ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; Taiwan ; Trees/*microbiology ; }, abstract = {The diversity and composition of soil bacterial communities in three topographic sites (summit, foot slope, and lakeshore) from subtropical montane forest ecosystem in Taiwan were examined by using 16S rRNA gene clone library analysis. This locality is temperate, perhumid, and has low soil acidity (pH < 4), which is an uncommon ecosystem in a monsoonal part of Southeast Asia. A total of 481 clones were sequenced and placed into ten phylogenetic groups according to their similarities to type strains of described organisms. Toposequence of the transect was investigated from summit to foot slope and at the lakeshore. More than 86% of the clones were affiliated with members of the Proteobacteria, Acidobacteria, and Actinobacteria. Within the Proteobacteria, the beta-Proteobacteria was the most abundant, then alpha-Proteobacteria and gamma-Proteobacteria. Based on the Shannon diversity index (H) analysis, the bacterial community in the foot slope was the most diverse (H = 0.86) and that in summit was the least diverse (H = 0.68). The composition and diversity of soil bacterial communities in the three sites suggested no trend with topographic change. Less than 20% of the sequences were Acidobacteria-affiliated clones. The low proportion of Acidobacteria observed may be related to the high soil moisture and anaerobic microhabitats. Moreover, Shannon diversity indices revealed these bacterial communities to have lower diversity than that of other temperate (H = 0.90) and tropical forest (H = 0.82) ecosystems. The extreme acidity of soil pH and high soil moisture of this forest may explain composition and reduced the diversity of these soil bacterial communities.}, }
@article {pmid19727929, year = {2009}, author = {Grimes, DJ and Johnson, CN and Dillon, KS and Flowers, AR and Noriea, NF and Berutti, T}, title = {What genomic sequence information has revealed about Vibrio ecology in the ocean--a review.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {447-460}, pmid = {19727929}, issn = {1432-184X}, mesh = {Bacterial Adhesion ; Chitin/metabolism ; Genes, Bacterial ; *Genome, Bacterial ; Oceans and Seas ; Phylogeny ; Seawater/*microbiology ; Vibrio/classification/*genetics ; *Water Microbiology ; }, abstract = {To date, the genomes of eight Vibrio strains representing six species and three human pathogens have been fully sequenced and reported. This review compares genomic information revealed from these sequencing efforts and what we can infer about Vibrio biology and ecology from this and related genomic information. The focus of the review is on those attributes that allow the Vibrios to survive and even proliferate in their ocean habitats, which include seawater, plankton, invertebrates, fish, marine mammals, plants, man-made structures (surfaces), and particulate matter. Areas covered include general information about the eight genomes, each of which is distributed over two chromosomes; a discussion of expected and unusual genes found; attachment sites and mechanisms; utilization of particulate and dissolved organic matter; and conclusions.}, }
@article {pmid19725865, year = {2010}, author = {Kunin, V and Engelbrektson, A and Ochman, H and Hugenholtz, P}, title = {Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates.}, journal = {Environmental microbiology}, volume = {12}, number = {1}, pages = {118-123}, doi = {10.1111/j.1462-2920.2009.02051.x}, pmid = {19725865}, issn = {1462-2920}, mesh = {*Biodiversity ; Cluster Analysis ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; Genes, Bacterial ; Genetic Variation ; RNA, Ribosomal, 16S/*genetics ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; }, abstract = {Massively parallel pyrosequencing of the small subunit (16S) ribosomal RNA gene has revealed that the extent of rare microbial populations in several environments, the 'rare biosphere', is orders of magnitude higher than previously thought. One important caveat with this method is that sequencing error could artificially inflate diversity estimates. Although the per-base error of 16S rDNA amplicon pyrosequencing has been shown to be as good as or lower than Sanger sequencing, no direct assessments of pyrosequencing errors on diversity estimates have been reported. Using only Escherichia coli MG1655 as a reference template, we find that 16S rDNA diversity is grossly overestimated unless relatively stringent read quality filtering and low clustering thresholds are applied. In particular, the common practice of removing reads with unresolved bases and anomalous read lengths is insufficient to ensure accurate estimates of microbial diversity. Furthermore, common and reproducible homopolymer length errors can result in relatively abundant spurious phylotypes further confounding data interpretation. We suggest that stringent quality-based trimming of 16S pyrotags and clustering thresholds no greater than 97% identity should be used to avoid overestimates of the rare biosphere.}, }
@article {pmid19723545, year = {2009}, author = {Vancov, T and Keen, B}, title = {Rapid isolation and high-throughput determination of cellulase and laminarinase activity in soils.}, journal = {Journal of microbiological methods}, volume = {79}, number = {2}, pages = {174-177}, doi = {10.1016/j.mimet.2009.08.013}, pmid = {19723545}, issn = {1872-8359}, mesh = {Carboxymethylcellulose Sodium/metabolism ; Cellulase/isolation &amp; purification/*metabolism ; Cellulases/isolation &amp; purification/*metabolism ; Glucans ; Glucose/analysis ; Polysaccharides/metabolism ; Reproducibility of Results ; Sensitivity and Specificity ; Soil/*analysis ; }, abstract = {A new method for extracting soil enzymes is described and a microplate method for assaying soil beta-1,4-glucanases (cellulases) and beta-1,3-glucanases (laminarinases). Soil samples were mechanically disrupted to produce crude enzyme extracts, and diluted preps incubated in microplates containing either carboxymethyl cellulose (CMC) to determine cellulase activity or laminarin substrate to determine laminarinase activity. The resulting glucose was measured using the fluorometric Amplex Red glucose assay. The method was reproducible, could be completed in 1 day and measured twice as much enzyme activity than the standard passive soil enzyme extraction procedure. The method described herein facilitates the development of high-throughput soil multiplex enzymatic assays from several soil samples at one time, and is well suited to the study of functional microbial ecology.}, }
@article {pmid19717632, year = {2009}, author = {Zhou, M and Hernandez-Sanabria, E and Guan, LL}, title = {Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {20}, pages = {6524-6533}, pmid = {19717632}, issn = {1098-5336}, mesh = {Animal Feed ; Animal Nutritional Physiological Phenomena ; Animals ; Base Sequence ; Cattle ; DNA Primers/genetics ; Ecosystem ; Euryarchaeota/classification/genetics/*isolation &amp; purification/metabolism ; Fermentation ; Gene Library ; Genes, Archaeal ; Male ; Methane/biosynthesis ; Molecular Sequence Data ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Rumen/microbiology ; }, abstract = {Cattle with high feed efficiencies (designated "efficient") produce less methane gas than those with low feed efficiencies (designated "inefficient"); however, the role of the methane producers in such difference is unknown. This study investigated whether the structures and populations of methanogens in the rumen were associated with differences in cattle feed efficiencies by using culture-independent methods. Two 16S rRNA libraries were constructed using approximately 800-bp amplicons generated from pooled total DNA isolated from efficient (n = 29) and inefficient (n = 29) animals. Sequence analysis of up to 490 randomly selected clones from each library showed that the methanogenic composition was variable: less species variation (22 operational taxonomic units [OTUs]) was detected in the rumens of efficient animals, compared to 27 OTUs in inefficient animals. The methanogenic communities in inefficient animals were more diverse than those in efficient ones, as revealed by the diversity indices of 0.84 and 0.42, respectively. Differences at the strain and genotype levels were also observed and found to be associated with feed efficiency in the host. No difference was detected in the total population of methanogens, but the prevalences of Methanosphaera stadtmanae and Methanobrevibacter sp. strain AbM4 were 1.92 (P < 0.05) and 2.26 (P < 0.05) times higher in inefficient animals, while Methanobrevibacter sp. strain AbM4 was reported for the first time to occur in the bovine rumen. Our data indicate that the methanogenic ecology at the species, strain, and/or genotype level in the rumen may play important roles in contributing to the difference in methane gas production between cattle with different feed efficiencies.}, }
@article {pmid19710082, year = {2009}, author = {He, X and Lux, R and Kuramitsu, HK and Anderson, MH and Shi, W}, title = {Achieving probiotic effects via modulating oral microbial ecology.}, journal = {Advances in dental research}, volume = {21}, number = {1}, pages = {53-56}, pmid = {19710082}, issn = {1544-0737}, support = {MD01831/MD/NIMHD NIH HHS/United States ; R01 GM054666/GM/NIGMS NIH HHS/United States ; R41 MD001831/MD/NIMHD NIH HHS/United States ; DE09821/DE/NIDCR NIH HHS/United States ; R01 DE020102/DE/NIDCR NIH HHS/United States ; R01 DE009821/DE/NIDCR NIH HHS/United States ; R01 DE003258/DE/NIDCR NIH HHS/United States ; GM54666/GM/NIGMS NIH HHS/United States ; DE03258/DE/NIDCR NIH HHS/United States ; R42 MD001831/MD/NIMHD NIH HHS/United States ; }, mesh = {Antimicrobial Cationic Peptides/therapeutic use ; Bacterial Adhesion ; Biofilms ; Dental Caries/*prevention &amp; control ; Dental Plaque/microbiology ; Ecosystem ; Humans ; Immunization, Passive ; *Microbial Interactions ; Probiotics/*therapeutic use ; Quorum Sensing ; Streptococcus mutans/*physiology ; }, abstract = {Unlike many pathogens are foreign invaders, oral “pathogens” such as Streptococcus mutans are part of the “normal” oral microbial flora. While they express certain pathogenic properties, the balance of synergistic and antagonistic interactions determines whether these çommensal pathogens cause damage or not. Recognition of these microbial ecology based pathogeneses argues for new strategies for disease treatment and prevention. Probiotics, potentially beneficial live bacteria or yeasts, have been used to combat dental caries. This includes the application of S. mutans types that cannot produce acids or other bacteria that interfere with the pathogenic effects of S. mutans. While these approaches show therapeutic effects against S. mutans experimentally, the conversion into commercial products remains a challenge, due to safety and shelf life issues. New high-tech approaches, such as quorum sensing interference of pathogenic bacteria or targeted antimicrobial therapies, offer novel ways to achieve probiotic effects against dental caries.}, }
@article {pmid19705193, year = {2010}, author = {Ikenaga, M and Guevara, R and Dean, AL and Pisani, C and Boyer, JN}, title = {Changes in community structure of sediment bacteria along the Florida coastal everglades marsh-mangrove-seagrass salinity gradient.}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {284-295}, pmid = {19705193}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics ; Biodiversity ; Cluster Analysis ; DNA, Bacterial/genetics ; Electrophoresis, Polyacrylamide Gel ; Florida ; Fresh Water/microbiology ; Geologic Sediments/*microbiology ; Phosphorus/analysis ; Phylogeny ; Poaceae/microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Rhizophoraceae/microbiology ; Salinity ; Sequence Alignment ; Sequence Analysis, DNA ; *Water Microbiology ; *Wetlands ; }, abstract = {Community structure of sediment bacteria in the Everglades freshwater marsh, fringing mangrove forest, and Florida Bay seagrass meadows were described based on polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) patterns of 16S rRNA gene fragments and by sequencing analysis of DGGE bands. The DGGE patterns were correlated with the environmental variables by means of canonical correspondence analysis. There was no significant trend in the Shannon-Weiner index among the sediment samples along the salinity gradient. However, cluster analysis based on DGGE patterns revealed that the bacterial community structure differed according to sites. Not only were these salinity/vegetation regions distinct but the sediment bacteria communities were consistently different along the gradient from freshwater marsh, mangrove forest, eastern-central Florida Bay, and western Florida Bay. Actinobacteria- and Bacteroidetes/Chlorobi-like DNA sequences were amplified throughout all sampling sites. More Chloroflexi and members of candidate division WS3 were found in freshwater marsh and mangrove forest sites than in seagrass sites. The appearance of candidate division OP8-like DNA sequences in mangrove sites distinguished these communities from those of freshwater marsh. The seagrass sites were characterized by reduced presence of bands belonging to Chloroflexi with increased presence of those bands related to Cyanobacteria, gamma-Proteobacteria, Spirochetes, and Planctomycetes. This included the sulfate-reducing bacteria, which are prevalent in marine environments. Clearly, bacterial communities in the sediment were different along the gradient, which can be explained mainly by the differences in salinity and total phosphorus.}, }
@article {pmid19705192, year = {2010}, author = {Thomson, BC and Ostle, N and McNamara, N and Bailey, MJ and Whiteley, AS and Griffiths, RI}, title = {Vegetation affects the relative abundances of dominant soil bacterial taxa and soil respiration rates in an upland grassland soil.}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {335-343}, pmid = {19705192}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/growth &amp; development/metabolism ; *Biodiversity ; Carbon/metabolism ; Carbon Dioxide/metabolism ; DNA, Bacterial/genetics ; Poaceae/*microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Scotland ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Plant-derived organic matter inputs are thought to be a key driver of soil bacterial community composition and associated soil processes. We sought to investigate the role of acid grassland vegetation on soil bacterial community structure by assessing bacterial diversity in combination with other soil variables in temporally and spatially distinct samples taken from a field-based plant removal experiment. Removal of aboveground vegetation resulted in reproducible differences in soil properties, soil respiration and bacterial diversity. Vegetated soils had significantly increased carbon and nitrogen concentrations and exhibited higher rates of respiration. Molecular analyses revealed that the soils were broadly dominated by Alphaproteobacterial and Acidobacterial lineages, with increased abundances of Alphaproteobacteria in vegetated soils and more Acidobacteria in bare soils. This field-based study contributes to a growing body of evidence documenting the effect of soil nutrient status on the relative abundances of dominant soil bacterial taxa, with Proteobacterial taxa dominating over Acidobacteria in soils exhibiting higher rates of C turnover. Furthermore, we highlight the role of aboveground vegetation in mediating this effect by demonstrating that plant removal can alter the relative abundances of dominant soil taxa with concomitant changes in soil CO(2)-C efflux.}, }
@article {pmid19705191, year = {2010}, author = {Charpy, L and Palinska, KA and Casareto, B and Langlade, MJ and Suzuki, Y and Abed, RM and Golubic, S}, title = {Dinitrogen-fixing cyanobacteria in microbial mats of two shallow coral reef ecosystems.}, journal = {Microbial ecology}, volume = {59}, number = {1}, pages = {174-186}, pmid = {19705191}, issn = {1432-184X}, mesh = {Animals ; *Anthozoa ; Base Sequence ; Biofilms/*classification ; Cyanobacteria/*classification/genetics/metabolism ; *Ecosystem ; Environmental Monitoring ; Molecular Sequence Data ; Nitrogen/metabolism ; *Nitrogen Fixation ; Nitrogenase/metabolism ; Phylogeny ; Seawater/chemistry/microbiology ; }, abstract = {Dinitrogen-fixing organisms in cyanobacterial mats were studied in two shallow coral reef ecosystems: La Reunion Island, southwestern Indian Ocean, Sesoko (Okinawa) Island, and northwestern Pacific Ocean. Rapidly expanding benthic miniblooms, frequently dominated by a single cyanobacterial taxon, were identified by microscopy and molecular tools. In addition, nitrogenase activity by these blooms was measured in situ. Dinitrogen fixation and its contribution to mat primary production were calculated using (15)N(2) and (13)C methods. Dinitrogen-fixing cyanobacteria from mats in La Reunion and Sesoko showed few differences in taxonomic composition. Anabaena sp. among heterocystous and Hydrocoleum majus and Symploca hydnoides among nonheterocystous cyanobacteria occurred in microbial mats of both sites. Oscillatoria bonnemaisonii and Leptolyngbya spp. occurred only in La Reunion, whereas Hydrocoleum coccineum dominated in Sesoko. Other mats dominated by Hydrocoleum lyngbyaceum, Phormidium laysanense, and Trichocoleus tenerrimus occurred at lower frequencies. The 24-h nitrogenase activity, as measured by acetylene reduction, varied between 11 and 324 nmoles C(2)H(2) reduced microg(-1) Chl a. The highest values were achieved by heterocystous Anabaena sp. performed mostly during the day. Highest values for nonheterocystous cyanobacteria were achieved by H. coccineum mostly during the night. Daily nitrogen fixation varied from nine (Leptolyngbya) to 238 nmoles N(2) microg(-1) Chl day(-1) (H. coccineum). Primary production rates ranged from 1,321 (S. hydnoides) to 9,933 nmoles C microg(-1) Chl day(-1) (H. coccineum). Dinitrogen fixation satisfied between 5% and 21% of the nitrogen required for primary production.}, }
@article {pmid19697077, year = {2009}, author = {Wilson, MK and Lane, AB and Law, BF and Miller, WG and Joens, LA and Konkel, ME and White, BA}, title = {Analysis of the pan genome of Campylobacter jejuni isolates recovered from poultry by pulsed-field gel electrophoresis, multilocus sequence typing (MLST), and repetitive sequence polymerase chain reaction (rep-PCR) reveals different discriminatory capabilities.}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {843-855}, pmid = {19697077}, issn = {1432-184X}, mesh = {Animal Husbandry/methods ; Animals ; Bacterial Typing Techniques/methods ; Campylobacter Infections/microbiology ; Campylobacter jejuni/classification/*genetics ; Chickens/microbiology ; DNA Fingerprinting/methods ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Pulsed-Field/methods ; *Genetic Variation ; *Genome, Bacterial ; Genotype ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; }, abstract = {Campylobacter jejuni is one of the leading bacterial causes of food-borne illness in the USA. Molecular typing methods are often used in food safety for identifying sources of infection and pathways of transmission. Moreover, the identification of genetically related isolates (i.e., clades) may facilitate the development of intervention strategies for control and prevention of food-borne diseases. We analyzed the pan genome (i.e., core and variable genes) of 63 C. jejuni isolates recovered from chickens raised in conventional, organic, and free-range poultry flocks to gain insight into the genetic diversity of C. jejuni isolates recovered from different environments. We assessed the discriminatory power of three genotyping methods [i.e., pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and repetitive extragenic palindromic polymerase chain reaction (rep-PCR)]. The rep-PCR fingerprint was generated by determining the presence of repetitive sequences that are interspersed throughout the genome via repetitive extragenic palindromic PCR, enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR), and BOX element PCR (BOX-PCR) and combining the data to form a composite fingerprint. The genetic fingerprints were subjected to computer-assisted pattern analysis. Comparison of the three genotypic methods revealed that repREB-PCR showed greater discriminatory power than PFGE and MLST. ERIC-PCR and BOX-PCR yielded the highest number of PCR products and greatest reproducibility. Regardless of the genotyping method, C. jejuni isolates recovered from chickens reared in conventional, organic, and free-range environments all exhibit a high level of genotypic diversity.}, }
@article {pmid19694813, year = {2009}, author = {Hoyles, L and McCartney, AL}, title = {What do we mean when we refer to Bacteroidetes populations in the human gastrointestinal microbiota?.}, journal = {FEMS microbiology letters}, volume = {299}, number = {2}, pages = {175-183}, doi = {10.1111/j.1574-6968.2009.01741.x}, pmid = {19694813}, issn = {1574-6968}, mesh = {Adult ; Animals ; Bacteroidetes/*classification/genetics/*isolation &amp; purification ; Colony Count, Microbial ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; In Situ Hybridization, Fluorescence/methods ; Male ; Oligonucleotide Probes/genetics ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Recent large-scale cloning studies have shown that the ratio of Bacteroidetes to Firmicutes may be important in the obesity-associated gut microbiota, but the species these phyla represent in this ecosystem has not been examined. The Bacteroidetes data from the recent Turnbaugh study were examined to determine those members of the phylum detected in human faecal samples. In addition, FISH analysis was performed on faecal samples from 17 healthy, nonobese donors using probe Bac303, routinely used by gut microbiologists to enumerate Bacteroides-Prevotella populations in faecal samples, and another probe (CFB286) whose target range has some overlap with that of Bac303. Sequence analysis of the Turnbaugh data showed that 23/519 clones were chimeras or erroneous sequences; all good sequences were related to species of the order Bacteroidales, but no one species was present in all donors. FISH analysis demonstrated that approximately one-quarter of the healthy, nonobese donors harboured high numbers of Bacteroidales not detected by probe Bac303. It is clear that Bacteroidales populations in human faecal samples have been underestimated in FISH-based studies. New probes and complementary primer sets should be designed to examine numerical and compositional changes in the Bacteroidales during dietary interventions and in studies of the obesity-associated microbiota in humans and animal model systems.}, }
@article {pmid19689880, year = {2009}, author = {Adams, SM and Adams, AS and Holben, WE}, title = {Tri-trophic linkages in disease: pathogen transmission to rainbow trout through stonefly prey.}, journal = {Environmental entomology}, volume = {38}, number = {4}, pages = {1022-1027}, doi = {10.1603/022.038.0409}, pmid = {19689880}, issn = {0046-225X}, mesh = {Aeromonas salmonicida/*physiology ; Animals ; DNA, Bacterial/*isolation &amp; purification ; Environment ; Food Preferences ; Furunculosis/transmission/*veterinary ; Gastrointestinal Tract/microbiology ; *Host-Pathogen Interactions ; Insecta/*microbiology ; Nymph/microbiology ; Oncorhynchus mykiss/*microbiology ; }, abstract = {Relationships between macroinvertebrates and microorganisms in aquatic environments are only poorly understood despite the fact that many aquatic macroinvertebrates feed on microbial biofilms during some life stage. Better understanding of trophic interactions between microbial biofilms, macroinvertebrates, and fish may also help control fish diseases and loss of natural resources. It has also been suggested that pollution, habitat fragmentation, and poor water quality may contribute to increased pathogenesis and mortality in fish. Increased disease incidence is difficult to assess, however, in part because of the complexity of pathogen transmission dynamics. Several environmental pathogens exist whose reservoir(s) and means of transmission remain poorly understood, highlighting the need to study pathogen ecology and interactions with organisms other than susceptible hosts. Aeromonas salmonicida is rarely isolated from freshwater sediments. However, stonefly nymphs were found to frequently harbor A. salmonicida and were shown to preferentially feed on the bacterium. Rainbow trout juveniles were presented with different feeding regimes to determine the transmission capacity of nymphs, and all fish fed stoneflies harboring A. salmonicida expressed symptoms of disease. Although current rates of furunculosis in freshwater ecosystems are unknown, trout primarily feed on stoneflies when water oxygen levels are high and temperatures are low (winter months), which is presumed to correspond to high resistance to the pathogen. Given that furunculosis is associated with physiological stress and higher water temperatures, its natural incidence may change in response to global or regional climatological effects.}, }
@article {pmid19688867, year = {2010}, author = {Madden, P and Chinalia, FA and Enright, AM and Collins, G and O'Flaherty, V}, title = {Perturbation-independent community development in low-temperature anaerobic biological wastewater treatment bioreactors.}, journal = {Biotechnology and bioengineering}, volume = {105}, number = {1}, pages = {79-87}, doi = {10.1002/bit.22507}, pmid = {19688867}, issn = {1097-0290}, mesh = {Anaerobiosis ; Bioreactors/*microbiology ; Cold Temperature ; Electrophoresis, Agar Gel ; *Waste Disposal, Fluid ; }, abstract = {The reproducibility and stability of low- temperature anaerobic wastewater treatment systems undergoing transient perturbations was investigated. Three identical anaerobic expanded granular sludge bed-based bioreactors were used to degrade a volatile fatty acid and glucose-based wastewater under sub-ambient (15 degrees C) conditions. The effect of a variety of environmental perturbations on bioreactor performance was assessed by chemical oxygen demand removal. Temporal microbial community development was monitored by denaturation gradient gel electrophoresis (DGGE) of 16S rRNA genes extracted from sludge granules. Methanogenic activity was monitored using specific methanogenic activity assays. Bioreactor performance and microbial population dynamics were each well replicated between both experimental bioreactors and the control bioreactor prior to, and after the implementation of most of the applied perturbations. Gene fingerprinting data indicated that Methanosaeta sp. were the persistent, keystone members of the archaeal community, and likely were pivotal for the physical stability and maintenance of the granular biofilms. Cluster analyses of DGGE data suggested that temporal shifts in microbial community structure were predominantly independent of the applied perturbations.}, }
@article {pmid19684066, year = {2009}, author = {Pérez-Pantoja, D and Donoso, RA and Sánchez, MA and González, B}, title = {Genuine genetic redundancy in maleylacetate-reductase-encoding genes involved in degradation of haloaromatic compounds by Cupriavidus necator JMP134.}, journal = {Microbiology (Reading, England)}, volume = {155}, number = {Pt 11}, pages = {3641-3651}, doi = {10.1099/mic.0.032086-0}, pmid = {19684066}, issn = {1465-2080}, mesh = {2,4-Dichlorophenoxyacetic Acid/metabolism ; Bacterial Proteins/genetics/*metabolism ; Benzoates/metabolism ; Biodegradation, Environmental ; Chlorobenzoates/metabolism ; Chlorophenols/metabolism ; Cupriavidus necator/*enzymology/*genetics ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Oxidoreductases Acting on CH-CH Group Donors/genetics/*metabolism ; RNA, Bacterial/genetics ; }, abstract = {Maleylacetate reductases (MAR) are required for biodegradation of several substituted aromatic compounds. To date, the functionality of two MAR-encoding genes (tfdF(I) and tfdF(II)) has been reported in Cupriavidus necator JMP134(pJP4), a known degrader of aromatic compounds. These two genes are located in tfd gene clusters involved in the turnover of 2,4-dichlorophenoxyacetate (2,4-D) and 3-chlorobenzoate (3-CB). The C. necator JMP134 genome comprises at least three other genes that putatively encode MAR (tcpD, hqoD and hxqD), but confirmation of their functionality and their role in the catabolism of haloaromatic compounds has not been assessed. RT-PCR expression analyses of C. necator JMP134 cells exposed to 2,4-D, 3-CB, 2,4,6-trichlorophenol (2,4,6-TCP) or 4-fluorobenzoate (4-FB) showed that tfdF(I) and tfdF(II) are induced by haloaromatics channelled to halocatechols as intermediates. In contrast, 2,4,6-TCP only induces tcpD, and any haloaromatic compounds tested did not induce hxqD and hqoD. However, the tcpD, hxqD and hqoD gene products showed MAR activity in cell extracts and provided the MAR function for 2,4-D catabolism when heterologously expressed in MAR-lacking strains. Growth tests for mutants of the five MAR-encoding genes in strain JMP134 showed that none of these genes is essential for degradation of the tested compounds. However, the role of tfdF(I)/tfdF(II) and tcpD genes in the expression of MAR activity during catabolism of 2,4-D and 2,4,6-TCP, respectively, was confirmed by enzyme activity tests in mutants. These results reveal a striking example of genetic redundancy in the degradation of aromatic compounds.}, }
@article {pmid19682245, year = {2009}, author = {Schink, B}, title = {An alternative to the glyoxylate shunt.}, journal = {Molecular microbiology}, volume = {73}, number = {6}, pages = {975-977}, doi = {10.1111/j.1365-2958.2009.06835.x}, pmid = {19682245}, issn = {1365-2958}, mesh = {Acetates/metabolism ; Acetyl Coenzyme A/metabolism ; Acyl Coenzyme A/metabolism ; Bacteria/*metabolism ; Bicarbonates/metabolism ; Carbon Dioxide/metabolism ; Glyoxylates/*metabolism ; Malonyl Coenzyme A/metabolism ; *Metabolic Networks and Pathways ; }, abstract = {A cycle remains a cycle only as long as the spokes of the wheel are not stolen. To keep the citric acid cycle going requires anaplerotic reactions such as the glyoxylate shunt to restore the cycle intermediates that are withdrawn for the biosynthesis of cell constituents, e.g. amino acids and haemin precursors. The article by Erb et al. in this issue of Molecular Microbiology documents an alternative path that replenishes four-carbon intermediates during growth on acetate in the absence of the glyoxylate shunt. The reaction sequence forms malate and succinyl-CoA from three acetyl-CoA, one CO(2) and one HCO(3) in a linear pathway. This new pathway was discovered in phototrophic anoxygenic bacteria and in few aerobic bacteria, but it is probably widespread among many metabolic groups of bacteria.}, }
@article {pmid19674296, year = {2009}, author = {O'Reilly, J and Chinalia, FA and Mahony, T and Collins, G and Wu, J and O'Flaherty, V}, title = {Cultivation of low-temperature (15 degrees C), anaerobic, wastewater treatment granules.}, journal = {Letters in applied microbiology}, volume = {49}, number = {4}, pages = {421-426}, doi = {10.1111/j.1472-765X.2009.02682.x}, pmid = {19674296}, issn = {1472-765X}, mesh = {Anaerobiosis ; Archaea/*chemistry/genetics/isolation &amp; purification/metabolism ; Bacteria/*chemistry/classification/isolation &amp; purification/metabolism ; Biomass ; Bioreactors/microbiology ; Cold Temperature ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Hydrogen/metabolism ; Methane/metabolism ; Particle Size ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sewage/*chemistry/*microbiology ; *Waste Disposal, Fluid ; }, abstract = {AIMS: Anaerobic sludge granules underpin high-rate waste-to-energy bioreactors. Granulation is a microbiological phenomenon involving the self-immobilization of several trophic groups. Low-temperature anaerobic digestion of wastes is of intense interest because of the economic advantages of unheated bioenergy production technologies. However, low-temperature granulation of anaerobic sludge has not yet been demonstrated. The aims of this study were to (i) investigate the feasibility of anaerobic sludge granulation in cold (15 degrees C) bioreactors and (ii) observe the development of methanogenic activity and microbial community structure in developing cold granules.<br><br>METHODS AND RESULTS: One mesophilic (R1; 37 degrees C) and two low-temperature (R2 and R3, 15 degrees C) laboratory-scale, expanded granular sludge bed bioreactors were seeded with crushed (diameter <0.4 mm) granules and were fed a glucose-based wastewater for 194 days. Bioreactor performance was assessed by chemical oxygen demand removal, biogas production, granule growth and temporal methanogenic activity. Granulation was observed in R2 and R3 (up to 33% of the sludge). Elevated hydrogenotrophic methanogenesis was observed in psychrophilically cultivated biomass, but acetoclastic methanogenic activity was also retained. Denaturing gradient gel electrophoresis of archaeal 16S rRNA gene fragments indicated that a distinct community was associated with developing and mature granules in the low-temperature (LT) bioreactors.<br><br>CONCLUSIONS: Granulation was observed at 15 degrees C in anaerobic bioreactors and was associated with H(2)/CO(2)-mediated methanogenesis and distinct community structure development.<br><br>Granulation underpins high-rate anaerobic waste treatment bioreactors. Most LT bioreactor trials have employed mesophilic seed sludge, and granulation <20 degrees C was not previously documented.}, }
@article {pmid19673303, year = {2009}, author = {Vlaeminck, SE and Terada, A and Smets, BF and van der Linden, D and Boon, N and Verstraete, W and Carballa, M}, title = {Nitrogen removal from digested black water by one-stage partial nitritation and anammox.}, journal = {Environmental science &amp; technology}, volume = {43}, number = {13}, pages = {5035-5041}, doi = {10.1021/es803284y}, pmid = {19673303}, issn = {0013-936X}, mesh = {Bacteria/metabolism ; Biofilms ; Bioreactors ; Hypoxia ; In Situ Hybridization, Fluorescence ; Netherlands ; Nitrates/chemistry ; Nitrites/chemistry ; Nitrogen/*analysis/chemistry/isolation &amp; purification ; Pilot Projects ; Quaternary Ammonium Compounds/*analysis/chemistry ; Sewage/*chemistry/microbiology ; Waste Disposal, Fluid/*methods ; Water Purification/*methods ; }, abstract = {This study assessed the technical feasibility to treat digested black water from vacuum toilets (> 1000 mg NH4(+)-N L(-1)) in a lab-scale oxygen-limited autotrophic nitrification/denitrification (OLAND) rotating biological contactor. After an adaptation period of 2.5 months, a stable nitrogen removal rate of ca. 700 mg N L(-1) d(-1) was reached over the subsequent 5 months. Suppression of the nitrite oxidizing bacteria at free ammonia levels above 3 mg N L(-1) resulted in a nitrogen removal efficiency of 76%. The favorable ratios of both organic and inorganic carbon to nitrogen guaranteed endured anammox activity and sufficient buffering capacity, respectively. Quantitative FISH showed that aerobic and anoxic ammonium-oxidizing bacteria (AerAOB and AnAOB) made up 43 and 8% of the biofilm, respectively. Since a part of the AerAOB was probably present in anoxic biofilm zones; their specific ammonium conversion was very low, in contrast to the high specific AnAOB activity. DGGE analysis showed that the dominant AerAOB and AnAOB species were resistant to the transition from synthetic medium to digested black water. This study demonstrates high-rate nitrogen removal from digested black water by one-stage partial nitritation and anammox, which will allow a significant decrease in operational costs compared to conventional nitrification/ denitrification.}, }
@article {pmid19672561, year = {2010}, author = {Parnell, JJ and Denef, VJ and Park, J and Tsoi, T and Tiedje, JM}, title = {Environmentally relevant parameters affecting PCB degradation: carbon source- and growth phase-mitigated effects of the expression of the biphenyl pathway and associated genes in Burkholderia xenovorans LB400.}, journal = {Biodegradation}, volume = {21}, number = {1}, pages = {147-156}, doi = {10.1007/s10532-009-9289-4}, pmid = {19672561}, issn = {1572-9729}, support = {P42 ES 04911-12/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacterial Proteins/*genetics/metabolism ; Biodegradation, Environmental ; Burkholderia/genetics/*growth &amp; development/*metabolism ; Carbon/*metabolism ; *Gene Expression Regulation, Bacterial ; Polychlorinated Biphenyls/*metabolism ; }, abstract = {The principal means for microbial degradation of polychlorinated biphenyls (PCBs) is through the biphenyl pathway. Although molecular aspects of the regulation of the biphenyl pathway have been studied, information on environmental facets such as the effect of alternative carbon sources on (polychlorinated) biphenyl degradation is limited. Here we explore the effect of environmental conditions (e.g., carbon source and growth phase) on the variation in PCB degradation profiles of Burkholderia xenovorans LB400. Genome-wide expression patterns reveal 25 genes commonly up-regulated during PCB degradation and growth on biphenyl to be upregulated in the transition to stationary phase (relative to growth on succinate) including two putative detoxification pathways. Quantitative reverse transcription PCR (Q-RT-PCR) analysis of the upper biphenyl pathway (bphA, bphD, and bphR1), and detoxification genes in response to environmental conditions suggest associated regulation of the biphenyl pathway and chloroacetaldehyde dehydrogenase. The response of genes in the upper biphenyl pathway to carbon source competition and growth phase reveals inhibition of the biphenyl pathway by PCBs. Although PCBs are not degraded during growth on succinate with PCBs, expression data indicate that the biphenyl pathway is induced, suggesting that post-transcriptional regulation or active transport of biphenyl maybe limiting PCB degradation. Identification of the involvement of peripheral pathways in degradation of PCBs is crucial to understanding PCB degradation in an environmental context as bacteria capable of biodegradation experience a range of carbon sources and growth phases.}, }
@article {pmid19669828, year = {2010}, author = {Berrada, ZL and Telford, SR}, title = {Diversity of Francisella species in environmental samples from Martha's Vineyard, Massachusetts.}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {277-283}, pmid = {19669828}, issn = {1432-184X}, support = {R01 AI064218/AI/NIAID NIH HHS/United States ; R21 AI 053411/AI/NIAID NIH HHS/United States ; N01 AI 30050/AI/NIAID NIH HHS/United States ; R01 AI 064218/AI/NIAID NIH HHS/United States ; N01 AI030050/AI/NIAID NIH HHS/United States ; R21 AI053411/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacterial Outer Membrane Proteins/genetics ; *Biodiversity ; DNA Transposable Elements ; DNA, Bacterial/genetics ; Francisella/classification/*genetics ; Massachusetts/epidemiology ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Succinate Dehydrogenase/genetics ; Tularemia/*epidemiology ; *Water Microbiology ; Zoonoses/epidemiology ; }, abstract = {We determined whether Francisella spp. are present in water, sediment, and soil from an active tularemia natural focus on Martha's Vineyard, Massachusetts, during a multiyear outbreak of pneumonic tularemia. Environmental samples were tested by polymerase chain reaction (PCR) targeting Francisella species 16S rRNA gene and succinate dehydrogenase A (sdhA) sequences; evidence of the agent of tularemia was sought by amplification of Francisella tularensis-specific sequences for the insertion element ISFTu2, 17-kDa protein gene tul4, and the 43-kDa outer membrane protein gene fopA. Evidence of F. tularensis subsp. tularensis, the causative agent of the human infections in this outbreak, was not detected from environmental samples despite its active transmission among ticks and animals in the sampling site. Francisella philomiragia was frequently detected from a brackish-water pond using Francisella species PCR targets, and subsequently F. philomiragia was isolated from an individual brackish-water sample. Distinct Francisella sp. sequences that are closely related to F. tularensis and Francisella novicida were detected from samples collected from the brackish-water pond. We conclude that diverse Francisella spp. are present in the environment where human cases of pneumonic tularemia occur.}, }
@article {pmid21180550, year = {2009}, author = {Kovatcheva-Datchary, P and Zoetendal, EG and Venema, K and de Vos, WM and Smidt, H}, title = {Tools for the tract: understanding the functionality of the gastrointestinal tract.}, journal = {Therapeutic advances in gastroenterology}, volume = {2}, number = {4}, pages = {9-22}, pmid = {21180550}, issn = {1756-2848}, abstract = {The human gastrointestinal tract comprises a series of complex and dynamic organs ranging from the stomach to the distal colon, which harbor immense microbial assemblages that are known to be vital for human health. Until recently, most of the details concerning our gut microbiota remained obscure. Over the past several years, however, a number of crucial technological and conceptual innovations have been introduced to shed more light on the composition and functionality of human gut microbiota. Recently developed high throughput approaches, including next-generation sequencing technologies and phylogenetic microarrays targeting ribosomal RNA gene sequences, allow for comprehensive analysis of the diversity and dynamics of the gut microbiota composition. Nevertheless, most of the microbes especially in the human large intestine still remain uncultured, and the in situ functions of distinct groups of the gut microbiota are therefore largely unknown, but pivotal to the understanding of their role in human physiology. Apart from functional and metagenomics approaches, stable isotope probing is a promising tool to link the metabolic activity and diversity of microbial communities, including yet uncultured microbes, in a complex environment. Advancements in current stable isotope probing approaches integrated with the application of high-throughput diagnostic microarray-based phylogenetic profiling and metabolic flux analysis should facilitate the understanding of human microbial ecology and will enable the development of innovative strategies to treat or prevent intestinal diseases of as yet unknown etiology.}, }
@article {pmid21261909, year = {2009}, author = {Zhou, J}, title = {Predictive microbial ecology.}, journal = {Microbial biotechnology}, volume = {2}, number = {2}, pages = {154-156}, pmid = {21261909}, issn = {1751-7915}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Ecology ; *Environmental Microbiology ; Metagenomics ; }, }
@article {pmid21566391, year = {2009}, author = {Tada, Y and Taniguchi, A and Hamasaki, K}, title = {Phylotype-Specific Productivity of Marine Bacterial Populations in Eutrophic Seawater, as Revealed by Bromodeoxyuridine Immunocytochemistry Combined with Fluorescence in situ Hybridization.}, journal = {Microbes and environments}, volume = {24}, number = {4}, pages = {315-321}, doi = {10.1264/jsme2.me09162}, pmid = {21566391}, issn = {1342-6311}, abstract = {Among the fundamental questions in marine microbial ecology are which taxa or phylogenetic groups account for total bacterial productivity and what is the relative contribution of each. We combined bromodeoxyuridine (BrdU) immunocytochemistry and fluorescence in situ hybridization (BIC-FISH) to examine phylotype-specific contributions to total bacterial productivity in eutrophic seawater. We also examined year-round changes in phylotype-specific contributions and explored the factors controlling these changes. Monitoring by BIC-FISH throughout the year revealed the importance of the Roseobacter/Rhodobacter group as a constantly proliferating basic population (27% of all BrdU-positive cells), although their contribution was not significantly correlated with water temperature or with chlorophyll a or organic matter concentration. The Bacteroidetes were another important group, as they greatly increased in abundance after the end of phytoplankton blooms. Two other phylotypes tested, the SAR86 and Vibrio groups, changed their contributions to bacterial productivity with changes in water temperature. To our knowledge, this study was the first to estimate the yearly contribution of major subgroups of marine bacteria to total bacterial productivity in a seawater environment.}, }
@article {pmid21261885, year = {2009}, author = {Sanchez, JI and Marzorati, M and Grootaert, C and Baran, M and Van Craeyveld, V and Courtin, CM and Broekaert, WF and Delcour, JA and Verstraete, W and Van de Wiele, T}, title = {Arabinoxylan-oligosaccharides (AXOS) affect the protein/carbohydrate fermentation balance and microbial population dynamics of the Simulator of Human Intestinal Microbial Ecosystem.}, journal = {Microbial biotechnology}, volume = {2}, number = {1}, pages = {101-113}, pmid = {21261885}, issn = {1751-7915}, mesh = {Bacteria/genetics/isolation &amp; purification/*metabolism ; *Carbohydrate Metabolism ; *Fermentation ; Humans ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Models, Biological ; Oligosaccharides/chemistry/*metabolism ; Polymerization ; Prebiotics/analysis ; Proteins/*metabolism ; Xylans/chemistry/*metabolism ; }, abstract = {Arabinoxylan-oligosaccharides (AXOS) are a recently newly discovered class of candidate prebiotics as - depending on their structure - they are fermented in different regions of gastrointestinal tract. This can have an impact on the protein/carbohydrate fermentation balance in the large intestine and, thus, affect the generation of potentially toxic metabolites in the colon originating from proteolytic activity. In this study, we screened different AXOS preparations for their impact on the in vitro intestinal fermentation activity and microbial community structure. Short-term fermentation experiments with AXOS with an average degree of polymerization (avDP) of 29 allowed part of the oligosaccharides to reach the distal colon, and decreased the concentration of proteolytic markers, whereas AXOS with lower avDP were primarily fermented in the proximal colon. Additionally, prolonged supplementation of AXOS with avDP 29 to the Simulator of Human Intestinal Microbial Ecosystem (SHIME) reactor decreased levels of the toxic proteolytic markers phenol and p-cresol in the two distal colon compartments and increased concentrations of beneficial short-chain fatty acids (SCFA) in all colon vessels (25-48%). Denaturant gradient gel electrophoresis (DGGE) analysis indicated that AXOS supplementation only slightly modified the total microbial community, implying that the observed effects on fermentation markers are mainly caused by changes in fermentation activity. Finally, specific quantitative PCR (qPCR) analysis showed that AXOS supplementation significantly increased the amount of health-promoting lactobacilli as well as of Bacteroides-Prevotella and Clostridium coccoides-Eubacterium rectale groups. These data allow concluding that AXOS are promising candidates to modulate the microbial metabolism in the distal colon.}, }
@article {pmid20209805, year = {2009}, author = {Rydzanicz, K and Lonc, E and Becker, N}, title = {Current procedures of the integrated urban vector-mosquito control as an example in Cotonou (Benin, West Africa) and Wrocław area (Poland).}, journal = {Wiadomosci parazytologiczne}, volume = {55}, number = {4}, pages = {335-340}, pmid = {20209805}, issn = {0043-5163}, mesh = {Africa, Western/epidemiology ; Animals ; Bacillus thuringiensis/physiology ; Disease Outbreaks/prevention &amp; control ; Ecology ; Ecosystem ; Insect Vectors/*microbiology ; Malaria/epidemiology/transmission ; Mosquito Control/*methods/*organization &amp; administration ; Pest Control, Biological/*methods ; Poland/epidemiology ; }, abstract = {Current strategy of Integrated Vector Management (IVM) comprises the general approach of environmentally friendly control measures. With regard to mosquitoes it includes first of all application of microbial insecticides based on Bacillus thuringiensis israelensis (Bti) and B. sphaericus (Bs) delta-endotoxins as well as the reduction of breeding habitats and natural enemy augmentation. It can be achieved thorough implementation of the interdisciplinary program, i. e., understanding of mosquito vector ecology, the appropriate vector-diseases (e. g., malariometric) measurements and training of local personnel responsible for mosquito abatement activities, as well as community involvement. Biocontrol methods as an alternative to chemical insecticides result from the sustainability development concept, growing awareness of environmental pollution and the development of insecticide-resistant strains of vector-mosquito populations in many parts of the world. Although sustainable trends are usually considered in terms of the monetary and training resources within countries, environmental concerns are actually more limiting factors for the duration of an otherwise successful vector control effort. In order to meet these new needs, increasing efforts have been made in search of and application of natural enemies, such as parasites, bacterial pathogens and predators which may control populations of insect vectors. The biological control agent based on the bacterial toxins Bti and Bs has been used in the Wrocław's University and Municipal Mosquito Control Programs since 1998. In West-Africa biocontrol appears to be an effective and safe tool to combat malaria in addition to bed-nets, residual indoor spraying and appropriate diagnosis and treatment of malaria parasites which are the major tools in the WHO Roll Back Malaria Program. IVM studies carried out 2005-2008 in Cotonou (Benin) as well those in Wrocław Irrigated Fields during the last years include the following major steps: 1. Mapping of all breeding sites in the project area and recording data in a geographical information system (GIS/relational database). All districts, streets and houses are numbered for quick reference during the operation; 2. Studying mosquito vector bionomics, migration and vectorial capacity in the project area, before, during and after the routine Bti treatments; 3. Assessment of the optimum for effective larvicide insecticide dosages at major breeding sites against the different target mosquito species; 4. Implementation of the microbial control agents in the integrated routine program. Adaptation of the application equipment to the local situation, training of the field staff, and routine treatments; 5. Conducting surveillance of vector-disease (e. g., malariometric) parameters in the control and experimental area before, during, and after the application of biocontrol agents.}, }
@article {pmid21261871, year = {2008}, author = {Sabirova, JS and Cloetens, LF and Vanhaecke, L and Forrez, I and Verstraete, W and Boon, N}, title = {Manganese-oxidizing bacteria mediate the degradation of 17α-ethinylestradiol.}, journal = {Microbial biotechnology}, volume = {1}, number = {6}, pages = {507-512}, pmid = {21261871}, issn = {1751-7915}, mesh = {Biodegradation, Environmental ; Ethinyl Estradiol/*metabolism ; Leptothrix/*metabolism ; Manganese/*metabolism ; Oxidation-Reduction ; Pseudomonas putida/*metabolism ; Water Pollutants, Chemical/metabolism ; }, abstract = {Manganese (II) and manganese-oxidizing bacteria were used as an efficient biological system for the degradation of the xenoestrogen 17α-ethinylestradiol (EE2) at trace concentrations. Mn(2+)-derived higher oxidation states of Mn (Mn(3+), Mn(4+)) by Mn(2+)-oxidizing bacteria mediate the oxidative cleavage of the polycyclic target compound EE2. The presence of manganese (II) was found to be essential for the degradation of EE2 by Leptothrix discophora, Pseudomonas putida MB1, P. putida MB6 and P. putida MB29. Mn(2+)-dependent degradation of EE2 was found to be a slow process, which requires multi-fold excess of Mn(2+) and occurs in the late stationary phase of growth, implying a chemical process taking place. EE2-derived degradation products were shown to no longer exhibit undesirable estrogenic activity.}, }
@article {pmid21261869, year = {2008}, author = {Pham, HT and Boon, N and Aelterman, P and Clauwaert, P and De Schamphelaire, L and van Oostveldt, P and Verbeken, K and Rabaey, K and Verstraete, W}, title = {High shear enrichment improves the performance of the anodophilic microbial consortium in a microbial fuel cell.}, journal = {Microbial biotechnology}, volume = {1}, number = {6}, pages = {487-496}, pmid = {21261869}, issn = {1751-7915}, mesh = {Bacteria/chemistry/genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; Bioelectric Energy Sources/*microbiology ; Biofilms ; Electrodes/*microbiology ; *Microbial Consortia ; Shear Strength ; }, abstract = {In many microbial bioreactors, high shear rates result in strong attachment of microbes and dense biofilms. In this study, high shear rates were applied to enrich an anodophilic microbial consortium in a microbial fuel cell (MFC). Enrichment at a shear rate of about 120 s(-1) resulted in the production of a current and power output two to three times higher than those in the case of low shear rates (around 0.3 s(-1)). Biomass and biofilm analyses showed that the anodic biofilm from the MFC enriched under high shear rate conditions, in comparison with that under low shear rate conditions, had a doubled average thickness and the biomass density increased with a factor 5. The microbial community of the former, as analysed by DGGE, was significantly different from that of the latter. The results showed that enrichment by applying high shear rates in an MFC can result in a specific electrochemically active biofilm that is thicker and denser and attaches better, and hence has a better performance.}, }
@article {pmid21261866, year = {2008}, author = {De Schamphelaire, L and Rabaey, K and Boeckx, P and Boon, N and Verstraete, W}, title = {Outlook for benefits of sediment microbial fuel cells with two bio-electrodes.}, journal = {Microbial biotechnology}, volume = {1}, number = {6}, pages = {446-462}, pmid = {21261866}, issn = {1751-7915}, mesh = {Bacteria/chemistry/*metabolism ; Bioelectric Energy Sources/*microbiology ; Electrodes/*microbiology ; Geologic Sediments/chemistry/*microbiology ; Oxidation-Reduction ; }, abstract = {The benefits of sediment microbial fuel cells (SMFCs) go beyond energy generation for low-power applications. Aside from producing electrical energy, SMFCs can enhance the oxidation of reduced compounds at the anode, thus bringing about the removal of excessive or unwanted reducing equivalents from submerged soils. Moreover, an SMFC could be applied to control redox-dependent processes in sediment layers. Several cathodic reactions that may drive these sediment oxidation reactions are examined. Special attention is given to two biologically mediated cathodic reactions, respectively employing an oxygen reduction and a manganese cycle. Both reactions imply a low cost and a high electrode potential and are of interest for reactor-type MFCs as well as for SMFCs.}, }
@article {pmid21585769, year = {2008}, author = {Naurin, S and Bensch, S and Hansson, B and Johansson, T and Clayton, DF and Albrekt, AS and VON Schantz, T and Hasselquist, D}, title = {TECHNICAL ADVANCES: A microarray for large-scale genomic and transcriptional analyses of the zebra finch (Taeniopygia guttata) and other passerines.}, journal = {Molecular ecology resources}, volume = {8}, number = {2}, pages = {275-281}, doi = {10.1111/j.1471-8286.2007.01979.x}, pmid = {21585769}, issn = {1755-098X}, abstract = {The microarray technology has revolutionized biological research in the last decade. By monitoring the expression of many genes simultaneously, microarrays can elucidate gene function, as well as scan entire genomes for candidate genes encoding complex traits. However, because of high costs of sequencing and design, microarrays have largely been restricted to a few model species. Cross-species microarray (CSM) analyses, where microarrays are used for other species than the one they were designed for, have had varied success. We have conducted a CSM analysis by hybridizing genomic DNA from the common whitethroat (Sylvia communis) on a newly developed Affymetrix array designed for the zebra finch (Taeniopygia guttata), the Lund-zf array. The results indicate a very high potential for the zebra finch array to act as a CSM utility in other passerine birds. When hybridizing zebra finch genomic DNA, 98% of the gene representatives had higher signal intensities than the background cut-off, and for the common whitethroat, we found the equivalent proportion to be as high as 96%. This was surprising given the fact that finches and warblers diverged 25-50 million years ago, but may be explained by a relatively low sequence divergence between passerines (89-93%). Passerine birds are widely used in studies of ecology and evolution, and a zebra finch array that can be used for many species may have a large impact on future research directions.}, }
@article {pmid21632341, year = {2008}, author = {Shefferson, RP and Kull, T and Tali, K}, title = {Mycorrhizal interactions of orchids colonizing Estonian mine tailings hills.}, journal = {American journal of botany}, volume = {95}, number = {2}, pages = {156-164}, doi = {10.3732/ajb.95.2.156}, pmid = {21632341}, issn = {0002-9122}, abstract = {Northeastern Estonia is home to extensive oil shale mines. Associated with these are desolate and environmentally damaging hills of ash and semicoke tailings. Interestingly, some of the first plants to colonize these hills are rare orchids. Here, we assess the identities of the mycorrhizal fungi associated with these orchids, in particular Epipactis atrorubens, Orchis militaris, and Dactylorhiza baltica, and compare them with mycorrhizal fungi from orchids from pristine habitat. Epipactis atrorubens associated with the widest breadth of fungi, including unnamed members of the basidiomycete family Tulasnellaceae and the potentially ectomycorrhizal ascomycetes Trichophaea woolhopeia and Geopora cooperi. Orchis militaris also associated with unnamed members of the Tulasnellaceae. Dactylorhiza baltica associated with Ceratobasidium albasitensis. In Epipactis and Orchis, the same fungi associated with plants in the pristine habitat as with those on ash hills. The tulasnelloid and ceratobasidioid fungi mycorrhizal with these orchids appear closely related to common orchid mycorrhizal fungi, while one of the ascomycetes mycorrhizal with E. atrorubens is closely related to a mycorrhizal fungus with E. microphylla. Our results suggest that these orchids and their fungi are not limited to pristine habitats and that environmentally polluted sites may present novel habitats that may be exploited for endangered plant conservation.}, }
@article {pmid21585725, year = {2008}, author = {Scallan, U and Liliensiek, A and Clipson, N and Connolly, J}, title = {ribosort: a program for automated data preparation and exploratory analysis of microbial community fingerprints.}, journal = {Molecular ecology resources}, volume = {8}, number = {1}, pages = {95-98}, doi = {10.1111/j.1471-8286.2007.01901.x}, pmid = {21585725}, issn = {1755-098X}, abstract = {ribosort is a computer package for convenient editing of automated ribosomal intergenic spacer analysis (ARISA) and terminal restriction fragment length polymorphism (TRFLP) data. It is designed to eliminate the labourious task of manually classifying community fingerprints in microbial ecology studies. This program automatically assigns detected fragments and their respective relative abundances to appropriate ribotypes. It permits simultaneous sorting of multiple profiles and facilitates direct workflow from TRFLP and ARISA output through to community analyses. ribosort also provides several options to merge repeat profiles of a sample into a single composite profile. By creating a 'ribotypes by samples' matrix ready for statistical analyses, use of the package saves time and simplifies the preparation of DNA fingerprint data sets for statistical analysis. In addition, ribosort performs exploratory analysis on the data by creating multidimensional scaling plots that compare the similarity of sample profiles using the statistical software r.}, }
@article {pmid21558680, year = {2008}, author = {Hiraishi, A}, title = {Biodiversity of dehalorespiring bacteria with special emphasis on polychlorinated biphenyl/dioxin dechlorinators.}, journal = {Microbes and environments}, volume = {23}, number = {1}, pages = {1-12}, doi = {10.1264/jsme2.23.1}, pmid = {21558680}, issn = {1342-6311}, abstract = {A wide variety of haloorganic compounds undergo reductive dehalogenation by certain anaerobic microorganisms. Metabolic reductive dehalogenation is coupled with energy-conserving respiratory electron transport in which a halogenated compound is used as the terminal electron acceptor, the biological process called dehalorespiration or halorespiration. Dehalorespiring bacteria may play important roles in the geochemical cycle with organohalogens in nature and have great promise in their application to the bioremediation of haloorganic contaminants derived from anthropogenic sources. During the past decade, a number of dehalorespiring microorganisms, including a unique group of strictly dehalorespiring bacteria, "Dehalococcoides", have been isolated and characterized at phylogenetic, physiologic, and genetic levels. Also, new perspectives of dehalorespiring bacteria have emerged based on information about genomics and molecular microbial ecology. This review article focuses on up-to-date knowledge of the biodiversity of dehalorespiring bacteria and reductively dehalogenating microbial consortia with special emphasis on those capable of transforming polychlorinated biphenyls and dioxins.}, }
@article {pmid22061795, year = {2007}, author = {Silvestri, G and Santarelli, S and Aquilanti, L and Beccaceci, A and Osimani, A and Tonucci, F and Clementi, F}, title = {Investigation of the microbial ecology of Ciauscolo, a traditional Italian salami, by culture-dependent techniques and PCR-DGGE.}, journal = {Meat science}, volume = {77}, number = {3}, pages = {413-423}, doi = {10.1016/j.meatsci.2007.04.015}, pmid = {22061795}, issn = {0309-1740}, abstract = {The microbial ecology of 22 samples of commercially available Ciauscolo salami were investigated using a polyphasic approach, based on culture-dependent and -independent techniques. The viable counts of pathogen and hygiene indicator microorganisms highlighted the adequate application of good manufacturing practices, while the viable counts of the lactic acid bacteria, coagulase negative cocci, and yeasts showed dominance of the first of these microbial groups. Bacterial and fungal DNA were extracted directly from the salami and amplified by PCR, using two primer sets targeting the 16S and 28S rRNA genes, respectively. Denaturing gradient gel electrophoresis (DGGE) and sequencing of selected bands were used to investigate the microbial ecology of these Ciauscolo salami. The most frequently found bacterial species were Lactobacillus sakei and Lb. curvatus, while Debaryomyces hansenii was the prevalent yeast species detected. Cluster analysis of the DGGE profiles and calculation of biodiversity indices allowed the degree of microbial similarity across these salami to be determined.}, }
@article {pmid21352444, year = {2005}, author = {Ramsey, PW and Rillig, MC and Feris, KP and Gordon, NS and Moore, JN and Holben, WE and Gannon, JE}, title = {Relationship between communities and processes; new insights from a field study of a contaminated ecosystem.}, journal = {Ecology letters}, volume = {8}, number = {11}, pages = {1201-1210}, doi = {10.1111/j.1461-0248.2005.00821.x}, pmid = {21352444}, issn = {1461-023X}, abstract = {We used a 93-year-old mine waste contamination gradient in alluvial soil to explore the relationship between ecosystem level functioning and community structure in a chronically stressed ecosystem. The sensitivity of broad functional parameters (in situ soil respiration, microbial biomass, above and below ground plant biomass) and microbial diversity [phospholipid fatty acid (PLFA) abundance and richness] were compared. Functional responses were linear with respect to contaminants while thresholds were detected in the community structural response to contamination along the gradient. For example, in situ soil respiration was negatively and linearly correlated to contamination concentration (R = -0.783, P < 0.01), but changes in microbial community structure only became evident where contaminant concentrations were greater than 28 times above background levels. Our results suggest that functional redundancy does not prevent depression of ecosystem function in the long-term.}, }
@article {pmid20369918, year = {2005}, author = {Narang, A and Pilyugin, SS}, title = {Toward an integrated physiological theory of microbial growth: from subcellular variables to population dynamics.}, journal = {Mathematical biosciences and engineering : MBE}, volume = {2}, number = {1}, pages = {169-206}, doi = {10.3934/mbe.2005.2.169}, pmid = {20369918}, issn = {1547-1063}, abstract = {The dynamics of microbial growth is a problem of fundamental interest in microbiology, microbial ecology, and biotechnology. The pioneering work of Jacob Monod served as a starting point for developing a wealth of mathematical models that address diferent aspects of microbial growth in batch and continuous cultures. A number of phenomenological models have appeared in the literature over the last half century. These models can capture the steady-state behavior of pure and mixed cultures, but fall short of explaining most of the complex dynamic phenomena. This is because the onset of these complex dynamics is invariably driven by one or more intracellular variables not accounted for by phenomenological models. In this paper, we provide an overview of the experimental data, and introduce a diferent class of mathematical models that can be used to understand microbial growth dynamics. In addition to the standard variables such as the cell and substrate concentrations, these models explicitly include the dynamics of the physiological variables responsible for adaptation of the cells to environmental variations. We present these physiological models in the order of increasing complexity. Thus, we begin with models of single-species growth in environments containing a single growth-limiting substrate, then advance to models of single-species growth in mixed-substrate media, and conclude with models of multiple-species growth in mixed-substrate environments. Throughout the paper, we discuss both the analytical and simulation techniques to illustrate how these models capture and explain various experimental phenomena. Finally, we also present open questions and possible directions for future research that would integrate these models into a global physiological theory of microbial growth.}, }
@article {pmid19712286, year = {2004}, author = {Nicolaisen, MH and Risgaard-Petersen, N and Revsbech, NP and Reichardt, W and Ramsing, NB}, title = {Nitrification-denitrification dynamics and community structure of ammonia oxidizing bacteria in a high yield irrigated Philippine rice field.}, journal = {FEMS microbiology ecology}, volume = {49}, number = {3}, pages = {359-369}, doi = {10.1016/j.femsec.2004.04.015}, pmid = {19712286}, issn = {1574-6941}, mesh = {Agriculture ; Ammonia/*metabolism ; *Ecosystem ; Electrophoresis, Polyacrylamide Gel ; Molecular Sequence Data ; Nitrates/*metabolism ; Nitrogen/metabolism ; Nitrosomonas/classification/enzymology/*growth &amp; development/metabolism ; Oryza/*growth &amp; development ; Oxidation-Reduction ; Oxidoreductases/metabolism ; Philippines ; Phylogeny ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Nitrogen is the single most limiting factor for rice production. Detailed knowledge on nitrogen dynamics in rice fields is therefore of major importance for developing sustainable rice production. A combination of state-of-the-art microsensor, stable isotope tracer, and molecular techniques was used to evaluate coupled nitrification-denitrification potentials and community structure of ammonia-oxidizing bacteria in a high yield irrigated rice cropping system in the Philippines, without the use of microcosm incubations. The multiple approaches showed a high degree of concordance among methods and thereby clarified the investigated processes. Numbers and potential activity of ammonia-oxidizing bacteria in the system reflected the availability of substrate in three defined soil factions with a ranking of: surface soil > rhizosphere > bulk soil. No nitrification activity was measured between spit applications of N fertilizer. However, nitrification was induced upon nitrogen amendment in intact soil cores. Despite induction by nitrogen amendment, the loss of nitrogen through coupled nitrification-denitrification was less than 10% of the plant nitrogen uptake. Denaturant gradient gel electrophoresis of amoA fragments revealed no differences in diversity profiles between the soil fractions, and phylogenetic analysis, based on amoA genes retrieved from the rice paddy soil, identified a set of mutually very similar sequences related to Nitrosomonas nitrosa.}, }
@article {pmid19712417, year = {2004}, author = {Brandt, KK and Jørgensen, NO and Nielsen, TH and Winding, A}, title = {Microbial community-level toxicity testing of linear alkylbenzene sulfonates in aquatic microcosms.}, journal = {FEMS microbiology ecology}, volume = {49}, number = {2}, pages = {229-241}, doi = {10.1016/j.femsec.2004.03.006}, pmid = {19712417}, issn = {0168-6496}, abstract = {Complex microbial communities may serve as ideal and ecologically relevant toxicity indicators. We here report an assessment of frequently used methods in microbial ecology for their feasibility to detect toxic effects of the environmentally important surfactant linear alkylbenzene sulfonate (LAS) on microbial communities in lake water and treated waste water. The two microbial communities were evaluated for changes in community structure and function over a period of 7 weeks in replicated aquatic microcosms amended with various levels of LAS (0, 0.1, 1, 10 or 100 mg l(-1)) and inorganic nutrients. In general, the two communities behaved similarly when challenged with LAS. Following lag periods of 1-3 weeks, LAS was degraded to non-toxic substances. Denaturing gradient gel electrophoresis of 16S rRNA gene fragments and [3H]leucine incorporation were the most sensitive assays with effect levels of 0-1 and 1-10 mg LAS l(-1), respectively. Community-level physiological profiles and pollution-induced community tolerance determinations using Biolog microplates demonstrated less sensitivity with effect levels of 10-100 mg LAS l(-1). Total cell counts and net uptake of inorganic N and P were unaffected even at 100 mg LAS l(-1). Interestingly, different microbial communities developed in some replicate microcosms, indicating the importance of stochastic events for community succession. We conclude that microbial community-level toxicity testing holds great promise and suggest a polyphasic approach involving a range of independent methods targeting both the structure and function of the tested microbial communities.}, }
@article {pmid19712382, year = {2004}, author = {Gruden, C and Skerlos, S and Adriaens, P}, title = {Flow cytometry for microbial sensing in environmental sustainability applications: current status and future prospects.}, journal = {FEMS microbiology ecology}, volume = {49}, number = {1}, pages = {37-49}, doi = {10.1016/j.femsec.2004.01.014}, pmid = {19712382}, issn = {1574-6941}, mesh = {Bacteria/isolation &amp; purification ; *Environmental Microbiology ; Environmental Monitoring/*methods ; Flow Cytometry/*methods ; Micro-Electrical-Mechanical Systems ; }, abstract = {Practical and accurate microbial assessment of environmental systems is predicated on the detection and quantification of various microbial parameters in complex matrices. Traditional growth-based assays, considered to be both slow and biased, are increasingly being replaced by optical detection methods such as flow cytometry. Flow cytometry (FCM) offers high-speed multi-parametric data acquisition, compatibility with current molecular-based microbial detection technologies, and is a proven technology platform. The unique technical properties of flow cytometry have allowed the discrimination of bacteria based on nucleic acid staining, microbial identification based on genomic and immunologic characteristics, and determination of cell viability. For this technology to achieve the ultimate goal of monitoring the microbial ecology of distributed systems, it will be necessary to develop a fully functional, low cost, and networkable microsystem platform capable of rapid detection of multiple species of microorganisms simultaneously under realistic environmental conditions. One such microsystem, miniaturized and integrated in accordance with recent advances in micro-electro-mechanical systems technology, is named the Micro Integrated Flow Cytometer. This manuscript is a minireview of the current status and future prospects for environmental application of flow cytometry in general, and micro-flow cytometry in particular.}, }
@article {pmid19712315, year = {2004}, author = {Bodelier, PL and Laanbroek, HJ}, title = {Nitrogen as a regulatory factor of methane oxidation in soils and sediments.}, journal = {FEMS microbiology ecology}, volume = {47}, number = {3}, pages = {265-277}, doi = {10.1016/S0168-6496(03)00304-0}, pmid = {19712315}, issn = {1574-6941}, mesh = {Bacteria/drug effects/*metabolism ; Fertilizers ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Nitrogen/*metabolism ; Nitrogen Compounds/*metabolism ; Oxidation-Reduction ; *Soil Microbiology ; }, abstract = {The oxidation of methane by methane-oxidising microorganisms is an important link in the global methane budget. Oxic soils are a net sink while wetland soils are a net source of atmospheric methane. It has generally been accepted that the consumption of methane in upland as well as lowland systems is inhibited by nitrogenous fertiliser additions. Hence, mineral nitrogen (i.e. ammonium/nitrate) has conceptually been treated as a component with the potential to enhance emission of methane from soils and sediments to the atmosphere, and results from numerous studies have been interpreted as such. Recently, ammonium-based fertilisation was demonstrated to stimulate methane consumption in rice paddies. Growth and activity of methane-consuming bacteria in microcosms as well as in natural rice paddies was N limited. Analysing the available literature revealed that indications for N limitation of methane consumption have been reported in a variety of lowland soils, upland soils, and sediments. Obviously, depriving methane-oxidising bacteria of a suitable source of N hampers their growth and activity. However, an almost instantaneous link between the presence of mineral nitrogen (i.e. ammonium, nitrate) and methane-oxidising activity, as found in rice soils and culture experiments, requires an alternative explanation. We propose that switching from mineral N assimilation to the fixation of molecular nitrogen may explain this phenomenon. However, there is as yet no experimental evidence for any mechanism of instantaneous stimulation, since most studies have assumed that nitrogenous fertiliser is inhibitory of methane oxidation in soils and have focused only on this aspect. Nitrogen as essential factor on the sink side of the global methane budget has been neglected, leading to erroneous interpretation of methane emission dynamics, especially from wetland environments. The purpose of this minireview is to summarise and balance the data on the regulatory role of nitrogen in the consumption of methane by soils and sediments, and thereby stimulate the scientific community to embark on experiments to close the existing gap in knowledge.}, }
@article {pmid19712331, year = {2004}, author = {Müller, T and Müller, M and Behrendt, U}, title = {Leucine arylamidase activity in the phyllosphere and the litter layer of a Scots pine forest.}, journal = {FEMS microbiology ecology}, volume = {47}, number = {2}, pages = {153-159}, doi = {10.1016/S0168-6496(03)00258-7}, pmid = {19712331}, issn = {1574-6941}, mesh = {Bacteria/*enzymology/isolation &amp; purification ; Culture Media ; Ecosystem ; Leucyl Aminopeptidase/*metabolism ; Nitrogen/metabolism ; *Pinus sylvestris/metabolism/microbiology ; Plant Leaves/*microbiology ; Soil/*analysis ; Trees/*metabolism/microbiology ; Yeasts/*enzymology/isolation &amp; purification ; }, abstract = {The activity of the leucine arylamidase (EC 3.4.11.2) was measured in washings of green needles from the canopy and dead needles from the litter of Scots pine throughout one year. It was highest in the litter and markedly higher in 2-year-old needles than in young ones, which were colonized by only a few bacteria. The leucine arylamidase activity largely arose from microbial epiphytes. Screenings for the potential of the enzyme activity among strains of a collection of phyllosphere microorganisms isolated from forest trees revealed that the leucine arylamidase activity was more abundant among bacteria (79%) and yeasts (57%) than among filamentous fungi, whereas the opposite was true in degrading complex proteins by proteinases.}, }
@article {pmid19712353, year = {2004}, author = {Boucard, TK and Parry, J and Jones, K and Semple, KT}, title = {Effects of organophosphate and synthetic pyrethroid sheep dip formulations on protozoan survival and bacterial survival and growth.}, journal = {FEMS microbiology ecology}, volume = {47}, number = {1}, pages = {121-127}, doi = {10.1016/S0168-6496(03)00253-8}, pmid = {19712353}, issn = {1574-6941}, mesh = {Agar ; Amoeba/classification/drug effects/growth &amp; development/isolation &amp; purification ; Animals ; Bacteria/classification/*drug effects/growth &amp; development/isolation &amp; purification ; Culture Media ; Ectoparasitic Infestations/*prevention &amp; control ; Environmental Pollutants/pharmacology ; Environmental Pollution ; Eukaryota/classification/*drug effects/growth &amp; development/isolation &amp; purification ; Microbial Sensitivity Tests ; Organophosphates/administration &amp; dosage/*pharmacology ; Parasitic Sensitivity Tests ; Pyrethrins/administration &amp; dosage/*pharmacology ; Risk Assessment ; Sheep Diseases/parasitology/*prevention &amp; control ; }, abstract = {Sheep dipping with organophosphate or synthetic pyrethroid-based formulations is still widely used by farmers in the UK to control ectoparasites and results in 175-220 million litres of spent sheep dip produced each year. Spent sheep dip may be diluted in animal slurry or water prior to disposal onto land. However, the effects of this practice on the microbial ecology of animal slurries, soil and aquatic systems are still relatively unknown. This paper investigated the effect of Bayticol (synthetic pyrethroid sheep dip) and Ectomort (organophosphate sheep dip) concentrations on (i) the survival of 15 protozoan species, (ii) the recovery of the four species of amoebae, and (iii) bacterial survival and growth. This investigation found that overall Bayticol was less toxic to protozoa than Ectomort, with minimum inhibitory concentrations ranging from 0.01 to 0.03% (v/v) and 0.005 to 0.06% (v/v), respectively. Amoebic cysts remained viable and emerged from dormancy, thereby pointing to the potential for recovery of protozoan communities in contaminated environments. The presence of sheep dips did not affect bacterial survival and growth on agar; however, the five test bacteria were not able to utilise the sheep dips as sole carbon sources. These findings have implications for the contamination of animal slurries, soil and aquatic systems, in that there is the potential for significant increases in microbial numbers, containing putative pathogens due to the diminution of bacteriophagous protozoan populations.}, }
@article {pmid19719569, year = {2003}, author = {Collins, G and Woods, A and McHugh, S and Carton, MW and O'Flaherty, V}, title = {Microbial community structure and methanogenic activity during start-up of psychrophilic anaerobic digesters treating synthetic industrial wastewaters.}, journal = {FEMS microbiology ecology}, volume = {46}, number = {2}, pages = {159-170}, doi = {10.1016/S0168-6496(03)00217-4}, pmid = {19719569}, issn = {1574-6941}, abstract = {Culture-independent, molecular techniques were applied to the characterization of microbial communities of an anaerobic granular sludge obtained from a full-scale digester. Procedures were optimised for total DNA recovery and polymerase chain reaction (PCR) amplification of 16S rDNA using archaea- and eubacteria-specific oligonucleotide primers. Cloned PCR products were subsequently screened by amplified rDNA restriction analysis to identify operational taxonomic units (OTUs). Inserts from clones representing each OTU were sequenced and phylogenetic trees were prepared. In addition, the microbial communities were characterised using terminal restriction fragment length polymorphism (T-RFLP). The specific methanogenic activity of the biomass, against various substrates, was also ascertained. Two anaerobic bioreactors were seeded with granular and non-granular (i.e. crushed) aliquots of the characterised sludge, respectively, and used to investigate the treatment of a volatile fatty acid (VFA)-based synthetic wastewater, at a loading rate of 5 kg COD m(-3) day(-1) at low ambient temperatures (18 degrees C). DNA was isolated from sludge samples during the test period and shifts in archaeal and eubacterial population structures were elucidated. The start-up period was successful with methane yields and COD removal efficiencies of 60-75% and 65-85%, respectively. Specific methanogenic activities of reactor biomass, obtained at the conclusion of the trial, indicated the development of psychrotolerant biomass during the 90-day experiment. Furthermore, the efficacy of T-RFLP as a molecular tool for use in the surveyance of engineered ecosystems was confirmed.}, }
@article {pmid19719567, year = {2003}, author = {Seghers, D and Verthé, K and Reheul, D and Bulcke, R and Siciliano, SD and Verstraete, W and Top, EM}, title = {Effect of long-term herbicide applications on the bacterial community structure and function in an agricultural soil.}, journal = {FEMS microbiology ecology}, volume = {46}, number = {2}, pages = {139-146}, doi = {10.1016/S0168-6496(03)00205-8}, pmid = {19719567}, issn = {1574-6941}, abstract = {Little is known about the chronic effect of herbicides on the soil microbial community, with most studies focusing on acute impacts. In this study, we investigated the effect of 20 years of atrazine and metolachlor application on the community structure, abundance and function of bacterial groups in the bulk soil of a maize monoculture. Group-specific PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) of 16S rRNA genes was used to characterize the composition of the microbial community. Primers specific for the entire bacterial group, as well as for the Acidobacterium group, the actinomycetes, the ammonium oxidizers, and the Type I and II methanotrophs were used in the PCR-DGGE analysis. Cluster analysis of the DGGE patterns obtained with the different primer sets differentiated between the herbicide-treated and the non-treated control soil. In particular the methanotrophic community differed, with three bands (phylotypes) being absent (or showing a lower intensity) in the DGGE patterns of the herbicide-treated soils compared to the patterns of the control soil. The differences in the methanotrophic community structure were not reflected in the methane oxidation capacity, which was similar for the two treatments. The prevalence of methanotrophs as evaluated with real-time PCR analysis also did not differ between the herbicide-treated and non-treated soil. Our results indicate that the long-term use of the herbicides atrazine and metolachlor resulted in an altered soil community structure, in particular for the methanotrophic bacteria. These observed changes did not cause a decreased community function (methane oxidation), probably because the total abundance of the methanotrophs in the soil system was preserved.}, }
@article {pmid19719566, year = {2003}, author = {Ingvorsen, K and Yde Nielsen, M and Joulian, C}, title = {Kinetics of bacterial sulfate reduction in an activated sludge plant.}, journal = {FEMS microbiology ecology}, volume = {46}, number = {2}, pages = {129-137}, doi = {10.1016/S0168-6496(03)00209-5}, pmid = {19719566}, issn = {1574-6941}, abstract = {The kinetics of sulfate reduction and cell densities of sulfate-reducing bacteria (SRB) were determined in activated sludge at Aalborg East wastewater treatment plant, a modern 100 000 person equivalent plant, where SRB are subjected to alternating cycles of oxic and anoxic conditions. The number of SRB was relatively constant over the year, ranging from 2.1x10(5) to 1.1x10(6) cells ml(-1) as determined by (35)S-radiotracer most probable number (MPN) in a growth medium prepared from anaerobic, sterilized sludge. Under anoxic conditions, the sulfide production in the activated sludge followed a biphasic pattern, being linear for approximately 5 h, followed by an exponential phase with doubling times of sulfide production of 4.2-12.6 h. Sulfate reduction started immediately after the onset of the anoxic cycle. Addition of antibiotics (chloramphenicol and streptomycin) to the activated sludge prevented the exponential phase of sulfate reduction for up to 100 h and this treatment was found to yield precise estimates of potential sulfate reduction rates. The addition of sulfate, sodium dithionite or single carbon compounds (lactate, acetate and glucose) did not decrease the length of the linear phase of sulfate reduction, nor did it affect the sulfate reduction rate. Our results indicate a tight and efficient metabolic coupling between populations of SRB and fermenting bacteria in activated sludge and a high capacity for sulfate reduction in sludge stored in settling tanks. Bacterial sulfate reduction may therefore be an important process in the destabilization of the floc structure when activated sludge is stored anaerobically for several days prior to dewatering.}, }
@article {pmid19719594, year = {2003}, author = {Meyer, RL and Saunders, AM and Zeng, RJ and Keller, J and Blackall, LL}, title = {Microscale structure and function of anaerobic-aerobic granules containing glycogen accumulating organisms.}, journal = {FEMS microbiology ecology}, volume = {45}, number = {3}, pages = {253-261}, doi = {10.1016/S0168-6496(03)00159-4}, pmid = {19719594}, issn = {1574-6941}, abstract = {The spatial arrangement and metabolic activity of 'Candidatus Competibacter phosphatis' was investigated in granular sludge from an anaerobic-aerobic sequencing batch reactor enriched for glycogen-accumulating organisms. In this process, the electron donor (acetate) and the electron acceptor (oxygen) were supplied sequentially in each phase. The organism, identified by fluorescence in situ hybridisation, was present throughout the granules; however, metabolic activity was limited to a 100-mum-thick layer immediately below the surface of the granules. To investigate the cause of this, oxygen microsensors and a novel microscale biosensor for volatile fatty acids were used in conjunction with chemical staining for intracellular storage polymers. It was found that the limited distribution of activity was caused by mass transport limitation of oxygen into the granules during the aerobic phase.}, }
@article {pmid19719629, year = {2003}, author = {Gavito, ME and Olsson, PA}, title = {Allocation of plant carbon to foraging and storage in arbuscular mycorrhizal fungi.}, journal = {FEMS microbiology ecology}, volume = {45}, number = {2}, pages = {181-187}, doi = {10.1016/S0168-6496(03)00150-8}, pmid = {19719629}, issn = {1574-6941}, abstract = {Abstract Foraging strategies, the cost-benefit associated with the search for new resources, have only begun to be explored in arbuscular mycorrhizal fungi (AMF). We show the use of (13)C-labelling, via shoot photosynthesis, of the 16:1omega5 fatty acid biomarker (the dominant and rather specific fatty acid in AMF storage lipids) to study the immediate patterns of carbon allocation to fungal lipids in response to inorganic and organic nutrient amendments. Signature fatty acid measurements, the incorporation of the label and complementary hyphal length density measurements showed that the extraradical mycelium of AMF proliferated in response to all the amendments provided whereas its development into unamended sand was minor in all treatments. We demonstrate the foraging capacity of AMF, linked to plant carbon, through their hyphal proliferation and accumulation of energy reserves.}, }
@article {pmid19719602, year = {2003}, author = {Pettersson, M and Bååth, E}, title = {Temperature-dependent changes in the soil bacterial community in limed and unlimed soil.}, journal = {FEMS microbiology ecology}, volume = {45}, number = {1}, pages = {13-21}, doi = {10.1016/S0168-6496(03)00106-5}, pmid = {19719602}, issn = {1574-6941}, abstract = {Abstract A humus soil with a pH(H(2)O) of 4.9 was limed to a pH of 7.5 and was incubated together with samples from unlimed and field limed (pH 6.1) soils at 5, 20 and 30 degrees C for up to 80 days. The changes in the phospholipid fatty acid (PLFA) pattern were most rapid for the bacterial community of the soil incubated at 30 degrees C, while no changes were found in the soil incubated at 5 degrees C. The response of the community activity to temperature was measured using the thymidine incorporation method on bacteria extracted from the soil. The bacterial community in soil incubated at 30 degrees C became more adapted to high temperature than that in soil samples incubated at 5 degrees C. When soil samples incubated at 30 degrees C and 20 degrees C were returned to 5 degrees C for 35 days, only small changes in the PLFA pattern were found. No significant shift in community temperature adaptation was found. Thus, higher temperatures (with higher turnover) led to higher rates of change in both the PLFA pattern and the activity response to temperature, compared with lower temperatures. No effect of liming as a way of increasing substrate availability and turnover on the rate of change was observed. Changes in the PLFA pattern appeared sooner than changes in the activity response to temperature, indicating that changes in the PLFA pattern were mainly due to phenotypic acclimation and not to species replacement.}, }
@article {pmid19719657, year = {2003}, author = {Mouné, S and Caumette, P and Matheron, R and Willison, JC}, title = {Molecular sequence analysis of prokaryotic diversity in the anoxic sediments underlying cyanobacterial mats of two hypersaline ponds in Mediterranean salterns.}, journal = {FEMS microbiology ecology}, volume = {44}, number = {1}, pages = {117-130}, doi = {10.1016/S0168-6496(03)00017-5}, pmid = {19719657}, issn = {1574-6941}, abstract = {Abstract Small-subunit (16S) ribosomal DNA clone libraries were constructed using DNA isolated from the anoxic sediments underlying the cyanobacterial mats from two sampling stations of different salinity (Station A, 150-200 per thousand salinity; Station B, 250-320 per thousand salinity) located in the Mediterranean salterns of Salin-de-Giraud (France). Previous studies have shown that the mats at these two sites differ greatly in physicochemical and microbial composition. Sequence analysis of the clone libraries indicated that prokaryotic diversity was high in the sediments from both stations, in both the Bacteria and Archaea domains. Clones related to the alpha- and delta-Proteobacteria (phylum Proteobacteria), the strictly anaerobic fermentative bacteria (phylum Firmicutes), and the Cytophaga-Flavobacterium-Bacteroides (CFB) group (phylum Bacteroidetes) were found in the libraries from both sediments and accounted for the majority of Bacteria domain clones. The results indicated that the populations of delta-Proteobacteria (principally sulfate-reducing bacteria) were significantly different in the two sediments. In addition, several clones from Station A were related either to the gamma-Proteobacteria (phylum Proteobacteria) or to the Spirochaeta, whereas the library from Station B contained several clones related to the uncultured, deep-branching 'KTK group' of Bacteria. Among the Archaea domain clones, all from Station B and the majority from Station A were related to the order Halobacteriales (phylum Euryarchaeota, class Halobacteria). In addition, 12% of the Archaea domain clones from Station A were related to the Methanococci group (phylum Euryarchaeota, class Methanobacteria) and 32% to the phylum Crenarchaeota. This study represents the first molecular analysis of the diversity of halophilic prokaryotes present in these sediments and the results are discussed in the light of our current knowledge of the microbial ecology of these hypersaline ecosystems.}, }
@article {pmid19719651, year = {2003}, author = {Wallander, H and Mahmood, S and Hagerberg, D and Johansson, L and Pallon, J}, title = {Elemental composition of ectomycorrhizal mycelia identified by PCR-RFLP analysis and grown in contact with apatite or wood ash in forest soil.}, journal = {FEMS microbiology ecology}, volume = {44}, number = {1}, pages = {57-65}, doi = {10.1111/j.1574-6941.2003.tb01090.x}, pmid = {19719651}, issn = {1574-6941}, abstract = {Abstract The aim of this study was to identify ectomycorrhizal species with a potential to release elements from apatite and wood ash and accumulate them in the mycelia. Fungal rhizomorphs and mycelia were sampled from sand-filled mesh bags with or without amendment of apatite or wood ash. The mesh bags were buried in forest soil in the field for 13 or 24 months. Elemental composition of the samples was analyzed with particle-induced X-ray emission and the fungus was identified by polymerase chain reaction-restriction fragment length polymorphism analysis of the ITS-region of ribosomal DNA. The majority of rhizomorphs and mycelia collected from the mesh bags were of mycorrhizal origin with Paxillus involutus being the most common species (31%). Other identified species were Thelephora terrestris, Suillus granulatus and Tylospora fibillosa. S. granulatus contained 3-15 times more K (3 mg g(-1)) than the other species and had large calcium-rich crystals deposited on the surface of rhizomorphs when grown in contact with apatite. P. involutus contained the largest amount of Ca (2-7 mg g(-1)). Wood ash addition increased the amount of Ti, Mn and Pb in the rhizomorphs while apatite addition increased the amount of Ca in the rhizomorphs. The high concentration of K in S. granulatus rhizomorphs suggests that this fungus is a good accumulator of K while P. involutus appeared to accumulate heavy metals originating from wood ash.}, }
@article {pmid19719632, year = {2003}, author = {Baker, BJ and Banfield, JF}, title = {Microbial communities in acid mine drainage.}, journal = {FEMS microbiology ecology}, volume = {44}, number = {2}, pages = {139-152}, doi = {10.1016/S0168-6496(03)00028-X}, pmid = {19719632}, issn = {1574-6941}, abstract = {The dissolution of sulfide minerals such as pyrite (FeS2), arsenopyrite (FeAsS), chalcopyrite (CuFeS2), sphalerite (ZnS), and marcasite (FeS2) yields hot, sulfuric acid-rich solutions that contain high concentrations of toxic metals. In locations where access of oxidants to sulfide mineral surfaces is increased by mining, the resulting acid mine drainage (AMD) may contaminate surrounding ecosystems. Communities of autotrophic and heterotrophic archaea and bacteria catalyze iron and sulfur oxidation, thus may ultimately determine the rate of release of metals and sulfur to the environment. AMD communities contain fewer prokaryotic lineages than many other environments. However, it is notable that at least two archaeal and eight bacterial divisions have representatives able to thrive under the extreme conditions typical of AMD. AMD communities are characterized by a very limited number of distinct species, probably due to the small number of metabolically beneficial reactions available. The metabolisms that underpin these communities include organoheterotrophy and autotrophic iron and sulfur oxidation. Other metabolic activity is based on anaerobic sulfur oxidation and ferric iron reduction. Evidence for physiological synergy in iron, sulfur, and carbon flow in these communities is reviewed. The microbial and geochemical simplicity of these systems makes them ideal targets for quantitative, genomic-based analyses of microbial ecology and evolution and community function.}, }
@article {pmid19719702, year = {2003}, author = {Mahmood, S and Finlay, RD and Fransson, AM and Wallander, H}, title = {Effects of hardened wood ash on microbial activity, plant growth and nutrient uptake by ectomycorrhizal spruce seedlings.}, journal = {FEMS microbiology ecology}, volume = {43}, number = {1}, pages = {121-131}, doi = {10.1111/j.1574-6941.2003.tb01051.x}, pmid = {19719702}, issn = {1574-6941}, abstract = {Abstract Plant growth, nutrient uptake, microbial biomass and activity were studied in pot systems containing spruce seedlings colonised with different ectomycorrhizal fungi from an ash-fertilised forest. The seedling root systems were enclosed in mesh bags inside an outer compartment containing crushed, hardened wood ash. Three different species of mycorrhizal fungi and a non-mycorrhizal control were exposed to factorial combinations of ash and N addition. Ash treatment had a highly significant, positive effect on plant growth and on shoot and root concentrations of K, Ca and P, irrespective of mycorrhizal status. Mycorrhizal inoculation had a significant effect on plant growth, which was proportionally greater in the absence of ash. N addition had a significant positive effect on plant biomass in mycorrhizal treatments with ash, but no effect in non-mycorrhizal treatments or most of the mycorrhizal treatments without ash. Piloderma sp. 1, which was earlier found to colonise wood ash granules in field studies, appeared to accumulate Ca from ash in the mycorrhizal roots. 5-6.7% of the total P in the ash was solubilised, with 0.9-1.5% in solution, 3.6-4.6% in the plants and 0.5-1.5% in microbial biomass. Bacterial activity as determined by [(3)H]-thymidine and [(14)C]-leucine incorporation was significantly greater in ash treatments than in controls with no ash addition. Principal component analysis (PCA) of phospholipid fatty acids (PLFAs) showed a clear difference in bacterial community structure between samples collected from ash-treated pots and controls without ash.}, }
@article {pmid19719699, year = {2003}, author = {Tonolla, M and Peduzzi, S and Hahn, D and Peduzzi, R}, title = {Spatio-temporal distribution of phototrophic sulfur bacteria in the chemocline of meromictic Lake Cadagno (Switzerland).}, journal = {FEMS microbiology ecology}, volume = {43}, number = {1}, pages = {89-98}, doi = {10.1111/j.1574-6941.2003.tb01048.x}, pmid = {19719699}, issn = {1574-6941}, abstract = {Abstract In situ hybridization was used to study the spatio-temporal distribution of phototrophic sulfur bacteria in the permanent chemocline of meromictic Lake Cadagno, Switzerland. At all four sampling times during the year the numerically most important phototrophic sulfur bacteria in the chemocline were small-celled purple sulfur bacteria of two yet uncultured populations designated D and F. Other small-celled purple sulfur bacteria (Amoebobacter purpureus and Lamprocystis roseopersicina) were found in numbers about one order of magnitude lower. These numbers were similar to those of large-celled purple sulfur bacteria (Chromatium okenii) and green sulfur bacteria that almost entirely consisted of Chlorobium phaeobacteroides. In March and June when low light intensities reached the chemocline, cell densities of all populations, with the exception of L. roseopersicina, were about one order of magnitude lower than in August and October when light intensities were much higher. Most populations were evenly distributed throughout the whole chemocline during March and June, while in August and October a microstratification of populations was detected suggesting specific eco-physiological adaptations of different populations of phototrophic sulfur bacteria to the steep physico-chemical gradients in the chemocline of Lake Cadagno.}, }
@article {pmid19719694, year = {2003}, author = {Griffiths, RI and Whiteley, AS and O'Donnell, AG and Bailey, MJ}, title = {Influence of depth and sampling time on bacterial community structure in an upland grassland soil.}, journal = {FEMS microbiology ecology}, volume = {43}, number = {1}, pages = {35-43}, doi = {10.1111/j.1574-6941.2003.tb01043.x}, pmid = {19719694}, issn = {1574-6941}, abstract = {Abstract Temporal and spatial variation of soil bacterial communities was evaluated with both molecular and metabolic profiling techniques. Soil cores (20 cm deep) were taken from an upland grassland in the Scottish Borders (UK) over 3 days in July 1999, and on single days in October 1999, April 2000, and August 2000. Cores were separated into four 5-cm depths to examine vertical spatial distribution. The 0-5-, 5-10- and 10-15-cm samples represented organic horizons whilst the 15-20-cm depths were from a mineral horizon. The potential metabolic activities were analysed using BIOLOG-GN plates, whereas genotypic diversity was evaluated using molecular profiling of amplified 16S rRNA and 16S rDNA gene fragments (denaturing gradient gel electrophoresis (DGGE)). BIOLOG-GN analysis revealed decreased substrate utilisation in the lowest depths, which was coupled with changes in the DNA and RNA DGGE profiles. Seasonal variation was pronounced in the 5-10-cm and 10-15-cm organic horizons for the July samplings whilst the 15-20-cm depths appeared more stable. Potential factors influencing the observed changes in bacterial communities resulting from soil depth and sampling time are discussed.}, }
@article {pmid19709291, year = {2002}, author = {Dejonghe, W and Goris, J and Dierickx, A and De Dobbeleer, V and Crul, K and De Vos, P and Verstraete, W and Top, EM}, title = {Diversity of 3-chloroaniline and 3,4-dichloroaniline degrading bacteria isolated from three different soils and involvement of their plasmids in chloroaniline degradation.}, journal = {FEMS microbiology ecology}, volume = {42}, number = {2}, pages = {315-325}, doi = {10.1111/j.1574-6941.2002.tb01021.x}, pmid = {19709291}, issn = {1574-6941}, abstract = {Attempts were made to isolate 3-chloroaniline (3-CA) and 3,4-dichloroaniline (3,4-DCA) degrading bacteria from the A- and B-horizon of three different soils. A variety of 3-CA degrading bacteria was obtained from all soils, whereas 3,4-DCA degrading strains were only isolated from one soil. Amongst the 3-CA and 3,4-DCA degraders, two belong to the gamma-Proteobacteria and seven to the beta-Proteobacteria. Of the latter group, five are members of the family of the Comamonadaceae. Interestingly, all isolates contained an IncP-1beta plasmid. These plasmids could be divided into four major groups based on restriction digest patterns. While all plasmids that were detected in the isolates, except one, encode total degradation of 3-CA, no indigenous plasmid that codes for total degradation of 3,4-DCA was found. This is the first study that reports the presence of diverse transferable plasmids that encode mineralisation of 3-CA in different 3-CA degrading species.}, }
@article {pmid19709286, year = {2002}, author = {Haagensen, JA and Hansen, SK and Johansen, T and Molin, S}, title = {In situ detection of horizontal transfer of mobile genetic elements.}, journal = {FEMS microbiology ecology}, volume = {42}, number = {2}, pages = {261-268}, doi = {10.1111/j.1574-6941.2002.tb01016.x}, pmid = {19709286}, issn = {1574-6941}, abstract = {Plasmid transfer was investigated in microbial populations associated with different types of surfaces. The general strategy behind these investigations was to label the transferable plasmid with a gene encoding a fluorescent protein in order to make it a transfer reporter. This was achieved by fusing the reporter gene with a lac promoter expression cassette and combining this with a donor cell-associated lacI repressor cassette. After construction of a range of strains and plasmids with combinations of genes expressing fluorescent proteins from constitutive (cell tagging) or regulated promoters (transfer reporters) it was thus possible to detect transfer events in situ and correlate these with either the location of donor and recipient cells or with the growth activity of the cells. In some cases, expression of unstable Gfp from a growth-controlled promoter, rrnB from Escherichia coli, was used to monitor bacterial growth activity in situ. Differential tagging of mobilizing and mobilizable plasmids with different genes encoding fluorescent proteins with varying emission wavelengths allowed in situ detection of plasmid mobilization and detection of retro-transfer on agar surfaces. The obtained data show that the several different types of fluorescent reporters, which are now available, allow more informative in situ investigations of horizontal gene transfer to be carried out, and by combining these genes with various expression systems it is possible to simultaneously monitor donor/recipient positioning, cellular activity and appearance of transconjugants.}, }
@article {pmid19709284, year = {2002}, author = {Lilley, AK and Bailey, MJ}, title = {The transfer dynamics of Pseudomonas sp. plasmid pQBR11 in biofilms.}, journal = {FEMS microbiology ecology}, volume = {42}, number = {2}, pages = {243-250}, doi = {10.1111/j.1574-6941.2002.tb01014.x}, pmid = {19709284}, issn = {1574-6941}, abstract = {Plasmid pQBR11 (294 kb) is one of a group of genetically similar conjugative plasmids that are common to and persist in pseudomonad populations colonising leaves and roots of crops and wild plants. This plasmid was marked by insertion of a green fluorescent protein reporter cassette to facilitate epifluorescence microscopy tracking and enumeration of transconjugant formation in biofilms. The intrinsic transfer activity of the plasmid, the conditions which affect this activity and the patterns of infectious spread of the plasmid in simple biofilms were evaluated. Transfer was observed over a range of nutritional and other conditions but no transitory de-repression of plasmid transfer was observed from new transconjugants and re-transfer of the plasmid by transconjugant cells played only a secondary role in the establishment of the plasmid in biofilm populations. As the plasmid was poorly invasive the parasitic persistence of pQBR11 by transfer alone is highly unlikely. The key factors for establishment of this plasmid in these biofilm populations were the size and activity of the donor population and the effect of plasmid carriage on host fitness.}, }
@article {pmid19709280, year = {2002}, author = {Turner, SL and Lilley, AK and Bailey, MJ}, title = {Two dnaB genes are associated with the origin of replication of pQBR55, an exogenously isolated plasmid from the rhizosphere of sugar beet.}, journal = {FEMS microbiology ecology}, volume = {42}, number = {2}, pages = {209-215}, doi = {10.1111/j.1574-6941.2002.tb01010.x}, pmid = {19709280}, issn = {1574-6941}, abstract = {Plasmid pQBR55 (approximately 149 kb) represents one of five (Groups I-V) genetically distinct transfer proficient, mercury resistance plasmid groups that have been observed in the phytosphere pseudomonad community at a single geographic location in Oxford, UK. A 4.9-kb HindIII fragment was cloned from pQBR55 (a Group III plasmid) that facilitates autonomous replication of a narrow host range cloning vector, pKIL29, in the non-permissive host Pseudomonas putida UWC1. Sequencing revealed that the fragment contains a unique tandem array of dnaB genes (one partial and one complete), a homologue of the traA gene of plasmid RP4 and several potential open reading frames with little homology to any known sequences. The fragment also contains: a short region of direct and indirect repeats, two sequences that resemble the consensus Escherichia coli DnaA box motif, an A+T rich region and evidence of a GC-skew inversion. All features associated with origins of replication. Two specific oligonucleotide primer pairs, one targeted at the tandem dnaB genes and the other at the dnaB-traA arrangement were used for PCR analysis of other plasmids isolated from the same field site. PCR generated amplification products were only amplified from Group III plasmids (defined by RFLP typing) but not from plasmids belonging to Group I, II, IV or V. The nucleotide sequences of the amplified fragments were identical to those of pQBR55, even though the other Group III plasmids had distinct RFLP patterns. The results of a more general PCR screen, using primers to amplify a 389-bp fragment of all described pseudomonad dnaB genes, suggests that closely related dnaB sequences are only associated with Group III plasmids.}, }
@article {pmid19709277, year = {2002}, author = {Turner, SL and Bailey, MJ and Lilley, AK and Thomas, CM}, title = {Ecological and molecular maintenance strategies of mobile genetic elements.}, journal = {FEMS microbiology ecology}, volume = {42}, number = {2}, pages = {177-185}, doi = {10.1111/j.1574-6941.2002.tb01007.x}, pmid = {19709277}, issn = {1574-6941}, abstract = {This review considers the influence of selection pressure, fitness and population structures on the evolution of mobile genetic elements (including plasmids, phage, pathogenicity islands, transposons and insertion sequences) that constitute the horizontal gene pool of bacteria. These are considered at different scales using examples from in vitro evolutionary studies of Escherichia coli and associated bacteriophage, detailed molecular analyses of the broad host-range IncP-1 plasmids, population surveys of pseudomonad plasmids and genomic comparisons of members of the Rhizobiaceae. All biological systems show genetic redundancy (the existence of allelic variation) at some population level, i.e. within a cell, a clone, population or community. We consider the level(s) at which redundancy is expressed and how this will affect and has influenced the evolution of mobile genetic elements.}, }
@article {pmid19709258, year = {2002}, author = {Connally, R and Veal, D and Piper, J}, title = {High resolution detection of fluorescently labeled microorganisms in environmental samples using time-resolved fluorescence microscopy.}, journal = {FEMS microbiology ecology}, volume = {41}, number = {3}, pages = {239-245}, doi = {10.1111/j.1574-6941.2002.tb00985.x}, pmid = {19709258}, issn = {1574-6941}, abstract = {The high level of discrimination offered by fluorescence microscopy has led to its widespread use for the analysis of individual microbial cells. The major limitation of fluorescence microscopy in microbial ecology is that many types of environmental samples contain autofluorescent material that can obscure emission from a fluorescent label. Time-resolved fluorescence microscopy (TRFM) is a technique that greatly reduces background autofluorescence whilst maintaining signal strength of the fluorescent target. TRFM differs from fluorescent microscopy in the use of fluorophores that are characterized by long-lived luminescence. Samples are briefly illuminated to excite fluorescence then capture of luminescence is delayed for a time interval sufficient to ensure autofluorescence has largely faded. TRFM has not been extensively used in microbiology because of the limitations and cost of available time-resolved microscopes and the lack of suitable long-lived fluorescent labels. Here we describe modification of a commercial fluorescence microscope for time-resolved operation through the addition of an image-intensified camera and low cost flashlamp. The TRFM was used in combination with a novel immunofluorophore for the specific detection of Giardia cysts in a water sample containing large amounts of autofluorescent material. A 60-mus gate delay between excitation and detection resulted in a 30-fold increase in contrast of labeled parasites compared to conventional immunostaining. To our knowledge, this is the first report of the use of TRFM for the detection of microorganisms in environmental samples.}, }
@article {pmid19709230, year = {2002}, author = {Söderberg, KH and Olsson, PA and Bååth, E}, title = {Structure and activity of the bacterial community in the rhizosphere of different plant species and the effect of arbuscular mycorrhizal colonisation.}, journal = {FEMS microbiology ecology}, volume = {40}, number = {3}, pages = {223-231}, doi = {10.1111/j.1574-6941.2002.tb00955.x}, pmid = {19709230}, issn = {1574-6941}, abstract = {The aim of this study was to determine if arbuscular mycorrhizal (AM) colonisation influences rhizosphere bacteria differently depending on plant species. Thus, the effect of AM colonisation (Glomus intraradices) on rhizosphere bacteria of subterranean clover, cucumber, leek and maize was studied. The bacterial activity was measured as thymidine or leucine incorporation and bacterial numbers as colony forming units and acridine orange direct counts. The phospholipid fatty acid (PLFA) pattern was used to characterise the bacterial community structure and was compared with the community substrate utilisation pattern using Biolog. The bacterial activity and bacterial densities differed between the rhizospheres of the plant species. AM colonisation had a low impact on bacterial activity, but affected bacterial numbers differently depending on the plant species. Only small effects of AM colonisation were detected with the PLFA technique, and no effects were seen with Biolog, while similar effects of the plant species were found for these techniques. Thus, the plant species had greater effects on the bacterial community in the rhizosphere than AM colonisation and the effect of AM differed between plant species.}, }
@article {pmid19709215, year = {2002}, author = {Boschker, HT and Middelburg, JJ}, title = {Stable isotopes and biomarkers in microbial ecology.}, journal = {FEMS microbiology ecology}, volume = {40}, number = {2}, pages = {85-95}, doi = {10.1111/j.1574-6941.2002.tb00940.x}, pmid = {19709215}, issn = {1574-6941}, abstract = {The use of biomarkers in combination with stable isotope analysis is a new approach in microbial ecology and a number of papers on a variety of subjects have appeared. We will first discuss the techniques for analysing stable isotopes in biomarkers, primarily gas chromatography-combustion-isotope ratio mass spectrometry, and then describe a number of applications in microbial ecology based on 13C. Natural abundance isotope ratios of biomarkers can be used to study organic matter sources utilised by microorganisms in complex ecosystems and for identifying specific groups of bacteria like methanotrophs. Addition of labelled substrates in combination with biomarker analysis enables direct identification of microbes involved in specific processes and also allows for the incorporation of bacteria into food web studies. We believe that the full potential of the technique in microbial ecology has just started to be exploited.}, }
@article {pmid19709206, year = {2002}, author = {Tornberg, K and Olsson, S}, title = {Detection of hydroxyl radicals produced by wood-decomposing fungi.}, journal = {FEMS microbiology ecology}, volume = {40}, number = {1}, pages = {13-20}, doi = {10.1111/j.1574-6941.2002.tb00931.x}, pmid = {19709206}, issn = {1574-6941}, abstract = {The hydroxyl radical ((*)OH) is believed to act as the small non-enzymatic agent involved in the brown-rot decay of wood. However, knowledge about the relation between hydroxyl radical production and the activity of wood-decomposing fungi in wood or about the significance of these radicals during interactions with other organisms is limited due to a lack of reliable methods for detecting the radicals. A sensitive and specific fluorescence method was developed in this study to detect the production of (*)OH by wood-decomposing fungal species. The method was based on the hydroxylation of coumarin-3-carboxylic acid, which produces 7-hydroxy-coumarin-3-carboxylic acid (7-OHCCA), a fluorescent, stable and specific product. Wood discs colonized by fungi were placed on water agar containing coumarin-3-carboxylic acid, where the formation of 7-OHCCA occurred and the fluorescence could be measured. The production of (*)OH was above the detection limit for eight of the 10 fungal species. The highest level, 8-25 times that of the detection limit, was produced by the brown-rot fungus Antrodia vaillantii. In interaction experiments where A. vaillantii had established contact with the antagonistic bacterium Pseudomonas fluorescens, the production of (*)OH increased, whereas contact with Bacillus subtilis did not change the amount of (*)OH generated compared with controls containing only the fungus. In contrast, the production of (*)OH increased above the control level when the fungus Coniophora puteana was in contact with any of these bacteria. The method was also tested in soil, with the result that 40% of 7-OHCCA added to the soil could be recovered with K2HPO4 buffer.}, }
@article {pmid19709194, year = {2002}, author = {Wallander, H and Johansson, L and Pallon, J}, title = {PIXE analysis to estimate the elemental composition of ectomycorrhizal rhizomorphs grown in contact with different minerals in forest soil.}, journal = {FEMS microbiology ecology}, volume = {39}, number = {2}, pages = {147-156}, doi = {10.1111/j.1574-6941.2002.tb00916.x}, pmid = {19709194}, issn = {1574-6941}, abstract = {The aim of this study was to investigate possible interactions between minerals and ectomycorrhizal (EM) mycelia. Fungal rhizomorphs growing in association with apatite and/or biotite were sampled both from a laboratory experimental system (Rhizopogon sp. and Pinus muricata) and from mesh bags buried in forest soil in the field. The elemental composition of the samples was analyzed with particle-induced X-ray emission (PIXE). Many EM rhizomorphs associated with apatite in laboratory systems and in mesh bags contained larger amounts of Ca (mean ranges between 12 and 31 mg Ca g(-1)) than similar rhizomorphs connected to acid-washed sand (range 0.3-3.5 mg Ca g(-1)). Ca originating from apatite was deposited as calcium oxalate crystals on the surface of the rhizomorphs. EM mycelium produced in mesh bags had a capacity to mobilize 0.6 mg P kg(-1) year(-1) from apatite-amended sand (which is 0.04% of the added apatite). A high concentration of K in some rhizomorphs (up to 11 mg K g(-1)) suggests that these fungi are good accumulators of K and may have a significant role in transporting K to trees.}, }
@article {pmid19709193, year = {2002}, author = {Hagerberg, D and Wallander, H}, title = {The impact of forest residue removal and wood ash amendment on the growth of the ectomycorrhizal external mycelium.}, journal = {FEMS microbiology ecology}, volume = {39}, number = {2}, pages = {139-146}, doi = {10.1111/j.1574-6941.2002.tb00915.x}, pmid = {19709193}, issn = {1574-6941}, abstract = {Intensive harvesting of forest residues for energy production may lead to the depletion of organic matter and mineral nutrients in the forest floor. In order to restore nutrient content wood ash has been suggested as a fertiliser. Ectomycorrhizal (EM) fungi are involved in the nutrient uptake of forest trees and this study investigates the influence of intensive harvesting and wood ash fertilisation on the external EM mycelium in forest soil. Nylon mesh bags filled with sand were buried in September 1997 in field plots which had or had not been intensively harvested. The effect of wood ash on the production of external EM mycelium was studied in mesh bags amended with wood ash. Mesh bags were retrieved in May and October 1998. The relative amount of fungal mycelia in the mesh bags was estimated with phospholipid fatty acid analysis. The fungi colonising the mesh bags were mainly (>90%) ectomycorrhizal. Fungal biomass in the mesh bags was low in the spring but high in the autumn. No significant effect on EM fungal biomass was observed in the mesh bags collected from intensively harvested plots compared with those from control plots, but wood ash amendment resulted in 2.4 times more EM fungal biomass (P<0.05). The effect of external EM mycelium on the dissolution of wood ash was studied in mesh bags filled with wood ash, using mesh bags buried in soil isolated from roots as EM-free controls. The external EM mycelium had no effect on the dissolution rate of the wood ash. 80% of the potassium was lost from the wood ash within a month, whereas no phosphorus was lost during the experimental period (up to 13 months).}, }
@article {pmid19709189, year = {2002}, author = {Boon, N and Windt, W and Verstraete, W and Top, EM}, title = {Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants.}, journal = {FEMS microbiology ecology}, volume = {39}, number = {2}, pages = {101-112}, doi = {10.1111/j.1574-6941.2002.tb00911.x}, pmid = {19709189}, issn = {1574-6941}, abstract = {The diversity of bacterial groups of activated sludge samples that received wastewater from four different types of industry was investigated by a nested PCR-DGGE (denaturing gradient gel electrophoresis) approach. Specific 16S rRNA primers were chosen for large bacterial groups (Bacteria and alpha-Proteobacteria in particular), which dominate activated sludge communities, as well as for actinomycetes, ammonium oxidisers and methanotrophs (types I and II). In addition primers for the new Acidobacterium kingdom were used to observe their community structure in activated sludge. After this first PCR amplification, a second PCR with bacterial primers yielded 16S rRNA gene fragments that were subsequently separated by DGGE, thus generating 'group-specific DGGE patterns'. The community structure and diversity of the bacterial groups from the different samples was further analysed using different techniques, such as statistical analysis and Shannon diversity index evaluation of the band patterns. By combining the seven DGGE gels, cluster analysis, multidimensional scaling and principal component analysis clearly clustered two of the four activated sludge types separately. It was shown that the combination of molecular and statistical methods can be very useful to differentiate microbial communities.}, }
@article {pmid19709183, year = {2002}, author = {Kielemoes, J and Bultinck, I and Storms, H and Boon, N and Verstraete, W}, title = {Occurrence of manganese-oxidizing microorganisms and manganese deposition during biofilm formation on stainless steel in a brackish surface water.}, journal = {FEMS microbiology ecology}, volume = {39}, number = {1}, pages = {41-55}, doi = {10.1111/j.1574-6941.2002.tb00905.x}, pmid = {19709183}, issn = {1574-6941}, abstract = {Abstract Biofilm formation on 316L stainless steel was investigated in a pilotscale flow-through system fed with brackish surface water using an alternating flow/stagnation/flow regime. Microbial community analysis by denaturing gradient gel electrophoresis and sequencing revealed the presence of complex microbial ecosystems consisting of, amongst others, Leptothrix-related manganese-oxidizing bacteria in the adjacent water, and sulfur-oxidizing, sulfate-reducing and slime-producing bacteria in the biofilm. Selective plating of the biofilm indicated the presence of high levels of manganese-oxidizing microorganisms, while microscopic and chemical analyses of the biofilm confirmed the presence of filamentous manganese-precipitating microorganisms, most probably Leptothrix species. Strong accumulation of iron and manganese occurred in the biofilm relative to the adjacent water. No evidence of selective colonization of the steel surface or biocorrosion was found over the experimental period. The overall results of this study highlight the potential formation of complex microbial biofilm communities in flow-through systems thriving on minor concentrations of manganese.}, }
@article {pmid21669705, year = {2001}, author = {Saxena, D and Stotzky, G}, title = {Bt corn has a higher lignin content than non-Bt corn.}, journal = {American journal of botany}, volume = {88}, number = {9}, pages = {1704-1706}, pmid = {21669705}, issn = {0002-9122}, abstract = {Bt corn has been genetically modified to express the Cry1Ab protein of Bacillus thuringiensis to kill lepidopteran pests. Fluorescence microscopy and staining with toluidine blue indicated a higher content of lignin in the vascular bundle sheaths and in the sclerenchyma cells surrounding the vascular bundle in all ten Bt corn hybrids, representing three different transformation events, studied than of their respective non-Bt isolines. Chemical analysis confirmed that the lignin content of all hybrids of Bt corn, whether grown in a plant growth room or in the field, was significantly higher (33-97% higher) than that of their respective non-Bt isolines. As lignin is a major structural component of plant cells, modifications in lignin content may have ecological implications.}, }
@article {pmid21182702, year = {1998}, author = {Colwell, RR and Huq, A}, title = {Global microbial ecology: biogeography and diversity of Vibrios as a model.}, journal = {Journal of applied microbiology}, volume = {85 Suppl 1}, number = {}, pages = {134S-137S}, doi = {10.1111/j.1365-2672.1998.tb05292.x}, pmid = {21182702}, issn = {1365-2672}, mesh = {Animals ; Bangladesh/epidemiology ; *Biodiversity ; Cholera/epidemiology/microbiology/prevention &amp; control ; *Ecology ; El Nino-Southern Oscillation ; Epidemics/prevention &amp; control ; Filtration ; Humans ; India/epidemiology ; Models, Biological ; Oceans and Seas ; Phylogeography ; Vibrio cholerae/*physiology ; *Water Microbiology ; Zooplankton/microbiology ; }, abstract = {An environmental source of cholera was hypothesized as early as the late nineteenth century by Robert Koch, but not proven because of the ability of Vibrio cholera, the causative agent of cholera, to enter a dormant phase between epidemics. Standard bacteriological procedures for isolation of the vibrios from the environmental samples, including water, between epidemics generally were unsuccessful. Vibrio cholera, a marine vibrio requiring salt for growth, enters into a dormant 'viable but non-culturable' stage when conditions are unfavourable for growth and reproduction. The association of V. cholera with plankton, notably copepods, provides evidence for the environmental origin of cholera, as well as an explanation for the sporadic and erratic nature of cholera epidemics. Thus, the association of V. cholera with plankton was established only recently, allowing analysis of epidemic patterns of cholera, especially in those countries where cholera is endemic. The sporadic and erratic nature of cholera epidemics can now be related to climate and climate events, such as El Niño. Since zooplankton have been shown to harbour the bacterium and zooplankton blooms follow phytoplankton blooms, remote sensing can be employed to determine the relationship of cases of cholera with chlorophyll, as well as sea surface temperature (SST), ocean height, and turbidity. Cholera occurs seasonally in Bangladesh with two annual peaks in the number of cases occurring each year. From the data obtained and analysed to date, when the height of the ocean is high and sea surface temperature is also elevated, cholera cases are numerous. When the height is low and sea surface temperature is also low, little or no cholera is recorded. From the examination of data for the 1992-1993 cholera epidemic in India, preliminary comparisons of cholera data for Calcutta show a similar relationship between cholera cases, ocean height and SST. In conclusion, from results of studies of SST, phytoplankton and zooplankton, and their relationships to incidence of cholera, correlation of selected climatological factors and incidence of V. cholera appears to be significant, bringing the potential of predicting conditions conducive to cholera outbreaks closer to reality.}, }
@article {pmid21238259, year = {1998}, author = {Aravalli, RN and She, Q and Garrett, RA}, title = {Archaea and the new age of microorganisms.}, journal = {Trends in ecology &amp; evolution}, volume = {13}, number = {5}, pages = {190-194}, doi = {10.1016/S0169-5347(98)01343-3}, pmid = {21238259}, issn = {0169-5347}, abstract = {Archaea were, until recently, considered to be confined to specialized environments including those at high temperature, high salinity, extremes of pH and ambients that permit methanogenesis. Recently developed molecular methods for studying microbial ecology, which do not necessitate cell culturing, have demonstrated their presence in a wide variety of temperate and cold environments including agricultural and forest soils, fresh water lake sediments, marine picoplankton and deep-sea locations. These discoveries mark the beginning of a new era for investigating the Archaea and in particular their physiological and metabolic properties and their biological roles in complex microbial populations.}, }
@article {pmid21238138, year = {1997}, author = {Loewe, L and Scherer, S}, title = {Mitochondrial Eve: the plot thickens.}, journal = {Trends in ecology &amp; evolution}, volume = {12}, number = {11}, pages = {422-423}, doi = {10.1016/s0169-5347(97)01204-4}, pmid = {21238138}, issn = {0169-5347}, }
@article {pmid21639276, year = {1997}, author = {Larsen, LH and Kjær, T and Revsbech, NP}, title = {A Microscale NO(3)(-) Biosensor for Environmental Applications.}, journal = {Analytical chemistry}, volume = {69}, number = {17}, pages = {3527-3531}, doi = {10.1021/ac9700890}, pmid = {21639276}, issn = {0003-2700}, abstract = {A biosensor for NO(3)(-) containing immobilized dentrifying bacteria and a reservoir of liquid growth medium for the bacteria was constructed. The bacteria did not have a N(2)O reductase and therefore reduced NO(3)(-) to N(2)O, which was then subsequently quantified by a built-in electrochemical transducer for N(2)O. The only agents interfering with the determination of NO(3)(-) were NO(2)(-) and N(2)O. The sensitivity for NO(2)(-) was identical to the one for NO(3)(-) whereas the sensitivity for N(2)O was 2.4 times higher than for NO(3)(-). Diffusive supply of electron donors to the bacteria from the built-in reservoir of growth medium ensured that the biosensor could work for 2-4 days. The tip diameter was down to 20 μm, and the sensors exhibited perfectly linear responses to nitrate in both freshwater and seawater. The detection limit was ∼1 μM. The 90% response time to changes in NO(3)(-) concentration was from 15 to 60 s at room temperature and about twice that at 6 °C, which was the lowest temperature for successful operation. The new NO(3)(-) biosensor is a very useful tool for the study of nitrogen metabolism in nature.}, }
@article {pmid21639359, year = {1997}, author = {Damgaard, LR and Revsbech, NP}, title = {A microscale biosensor for methane containing methanotrophic bacteria and an internal oxygen reservoir.}, journal = {Analytical chemistry}, volume = {69}, number = {13}, pages = {2262-2267}, doi = {10.1021/ac9611576}, pmid = {21639359}, issn = {0003-2700}, abstract = {A microscale biosensor for continuous measurement of methane partial pressure based on a novel counterdiffusion principle is presented. Methane-oxidizing bacteria placed in the microsensor utilize oxygen from an internal oxygen reservoir when methane from the exterior diffuses through the tip membrane. The transducer is an internal oxygen microsensor with its tip positioned between the oxygen reservoir and the sensor tip membrane. The external partial pressure of methane determines the rate of bacterial oxygen consumption within the sensor, which in turn is reflected by the signal from the transducer. Tip diameters were down to 20 μm, enabling us to study methane distribution on a microscale. The microscale construction also results in a low stirring sensitivity and a 95% response time down to 20 s. By tailoring the geometry, sensors can be made to exhibit a linear response in the full range of 0-1 atm partial pressure of methane or, alternatively, to exhibit a linear response only at lower concentrations, improving the sensitivity to below 0.1 kPa, corresponding to ∼1 μM in aqueous solution. Temperature, oxygen, and H(2)S interfere with the signal; no interferences were detected from H(2), NH(3), CO(2), or acetate.}, }
@article {pmid21236874, year = {1994}, author = {Brul, S and Stumm, CK}, title = {Symbionts and organelles in ancrobic protozoa and fungi.}, journal = {Trends in ecology &amp; evolution}, volume = {9}, number = {9}, pages = {319-324}, doi = {10.1016/0169-5347(94)90151-1}, pmid = {21236874}, issn = {0169-5347}, abstract = {The discovery of methanogenic bacteria as endosymbionts of free-living anaerobic protozoa opened new fields of research in microbial ecology, cell physiology and molecular biology. Recent information from 16S rRNA sequence studies has shown in three cases that endosymbiotic methanogenic bacteria differ from free-living species. Frequently, endosymbiotic methanogens are localized in anaerobic protozoa near hydrogenosomes - organelles that produce H2, C02 and acetate, all of which are substrates for methanogenesis. Hydrogenosomes are also present in anaerobic fungi. The current view is that the organelles are endosymbllont-derived and were probably acquired on several distinct occasions during evolution.}, }
@article {pmid19669227, year = {2010}, author = {Li, CH and Zhao, MW and Tang, CM and Li, SP}, title = {Population dynamics and identification of endophytic bacteria antagonistic toward plant-pathogenic fungi in cotton root.}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {344-356}, pmid = {19669227}, issn = {1432-184X}, mesh = {*Antibiosis ; Bacteria/classification/genetics/*isolation &amp; purification ; Cluster Analysis ; DNA, Bacterial/genetics ; Fusarium/*growth &amp; development ; Genetic Variation ; Gossypium/growth &amp; development/*microbiology ; Multivariate Analysis ; Plant Diseases/microbiology ; Plant Roots/microbiology ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Verticillium/*growth &amp; development ; }, abstract = {The antagonistic potentials of endophytic bacteria isolated from the roots of six cotton cultivars at different developmental stages were determined in vitro toward three pathogens: Verticillium dahliae Kleb V107 and V396 and Fusarium oxysporum f.sp. vasinfectum (F108). The populations of antagonistic endophytic bacteria (AEB) toward V107, V396, and F108 at the flowering and maturation stages were significantly higher than those at the seedling stage were. More AEB were found to be antagonistic toward pathogens V396 and F108 than V107. Results from the multivariate analysis of variance showed that the populations of AEB were significantly different for the main factors of cultivars, stages, and their interactions. Based on 16S rDNA sequence analysis, the 39 AEB isolates that antagonized V107, V396, and F108 (BAEB) consisted of seven genera, in which the genus of Enterobacter (17 out of 39) and Pantoea (14 out of 39) were predominant among the BAEB isolates. Characterized by BOX-PCR fingerprints, these 39 BAEB isolates represented 35 different cluster types. To explore the antagonistic mechanisms, the agar diffusion method was used to detect cell-wall-degrading enzyme activity and siderophore secretion. Nearly half of these BAEB isolates showed protease and chitinase activity, while all 39 BAEB isolates excreted siderophores. However, pectinase, cellulase, and xylanase activity were hardly detected. A germination experiment revealed that nine of the 39 BAEB isolates significantly improved the vigor index of the cotton seedlings.}, }
@article {pmid19663913, year = {2009}, author = {Tang, H and Xiao, C and Ma, J and Yu, M and Li, Y and Wang, G and Zhang, L}, title = {Prokaryotic diversity in continuous cropping and rotational cropping soybean soil.}, journal = {FEMS microbiology letters}, volume = {298}, number = {2}, pages = {267-273}, doi = {10.1111/j.1574-6968.2009.01730.x}, pmid = {19663913}, issn = {1574-6968}, mesh = {Agriculture/*methods ; Bacteria/*classification/*genetics/isolation &amp; purification ; *Biodiversity ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Genetic ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Glycine max/*growth &amp; development ; }, abstract = {In spite of the techniques based on the amplification of 16S rRNA genes (16S rDNA) to compare bacterial communities that are now widely in use in microbial ecology, little is known about the composition of the soybean continuous cropping (CC) and rotational cropping (RC) soil microbial community. To address this, we compared the levels of bacterial community diversity in RC and 5-year CC rhizosphere soil samples. We selected 407 clones in RC and 490 clones in CC for restriction fragment length polymorphism analysis. A total of 123 phylotypes were identified among the 16S rDNA clones, while 78 unique and 21 common phylotypes were identified among the CC soil isolates. Analysis of sequences from a subset of the phylotypes showed that at least 11 bacterial divisions were represented in the clone libraries. The phylotype richness, frequency distribution (evenness), and composition of the two clone libraries were investigated using a variety of diversity indices. Although the analysis of diversity indices and LIBSHUFF comparisons revealed that the compared libraries were not significantly different (P=0.05) between the RC vs. CC soils, some differences could be observed in terms of specific phyla and groups. We concluded that the group variance was not determined immediately by the cropping system's induction, but was a long-term and slow process.}, }
@article {pmid19662454, year = {2009}, author = {Ikeda, S and Kaneko, T and Okubo, T and Rallos, LE and Eda, S and Mitsui, H and Sato, S and Nakamura, Y and Tabata, S and Minamisawa, K}, title = {Development of a bacterial cell enrichment method and its application to the community analysis in soybean stems.}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {703-714}, pmid = {19662454}, issn = {1432-184X}, mesh = {Bacteria/genetics/*growth &amp; development ; Bacteriological Techniques/*methods ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Gene Library ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Glycine max/*microbiology ; }, abstract = {A method was developed for enriching bacterial cells from soybean stems which was recalcitrant for a culture-independent analysis of bacterial community due to the interference with plant DNA. Stem homogenates were fractionated by a series of differential centrifugations followed by a Nycodenz density gradient centrifugation. The efficiency of bacterial cell enrichment was assessed by ribosomal intergenic spacer analysis (RISA). The intensity and the number of bacterial amplicons of RISA were markedly increased in the DNA extracted from the enriched bacterial cells compared to that in the DNA directly extracted from soybean stems. The phylogenetic diversity of the enriched bacterial cells was evaluated by analyzing a clone library of 16S rRNA gene in comparison with those of the culturable fractions of the enriched and non-enriched stem-associated bacteria, endophytic bacteria, and epiphytic bacteria. The results indicated that the method was able to enrich both endophytic and epiphytic bacteria from soybean stems, and was useful to assess the bacterial diversity based on a 16S rRNA gene clone library. When the sequence data from all clones (1,332 sequences) were combined, 72 operational taxonomic units were affiliated with Proteobacteria (Alpha-, Beta-, and Gammaproteobacteria), Actinobacteria, Firmicutes, and Bacteroidetes, which also provided the most comprehensive set of data on the bacterial diversity in the aerial parts of soybeans.}, }
@article {pmid19655080, year = {2009}, author = {Chan, YF and Tsai, AY and Chiang, KP and Hsieh, CH}, title = {Pigmented nanoflagellates grazing on Synechococcus: seasonal variations and effect of flagellate size in the coastal ecosystem of subtropical Western Pacific.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {548-557}, pmid = {19655080}, issn = {1432-184X}, mesh = {Animals ; Ecosystem ; Eukaryota/*physiology ; Feeding Behavior ; Population Dynamics ; *Seasons ; Seawater/microbiology ; Synechococcus/*growth &amp; development ; Temperature ; *Water Microbiology ; }, abstract = {We investigated seasonal variation of grazing impact of the pigmented nanoflagellates (PNF) with different sizes upon Synechococcus in the subtropical western Pacific coastal waters using grazing experiments with fluorescently labeled Synechococcus (FLS). For total PNF, conspicuous seasonal variations of ingestion rates on Synechococcus were found, and a functional response was observed. To further investigate the impact of different size groups, we separated the PNF into four categories (<3, 3-5, 5-10, and >10 microm). Our results indicated that the smallest PNF (<3 microm PNF) did not ingest FLS and was considered autotrophic. PNF of 3-5 microm in size made up most of the PNF community; however, their ingestion on Synechococcus was too low (0.1-1.9 Syn PNF(-1) h(-1)) to support their growth, and they had to depend on other prey or photosynthesis to survive. The ingestion rate of the 3-5 microm group exhibited no significant seasonal variation; by contrast, the ingestion rates of 5-10 and >10 microm PNFs showed significant seasonal variation. During the warm season, 3-5 microm PNF were responsible for the grazing of 12% of Synechococcus production, 5-10 microm PNF for 48%, and >10 microm PNF for 2%. Taken together, our results demonstrate that the PNF of 3-10 microm consumed most Synechococcus during the warm season and exhibited a significant functional response to the increase in prey concentration.}, }
@article {pmid19653495, year = {2009}, author = {Rydzanicz, K and Lonc, E and Kiewra, D and Dechant, P and Krause, S and Becker, N}, title = {Evaluation of three microbial formulations against Culex pipiens pipiens larvae in irrigation fields in Wroclaw, Poland.}, journal = {Journal of the American Mosquito Control Association}, volume = {25}, number = {2}, pages = {140-148}, doi = {10.2987/08-5822.1}, pmid = {19653495}, issn = {8756-971X}, mesh = {Animals ; *Bacillus thuringiensis ; Culex/*microbiology ; Fresh Water/*parasitology ; *Insecticides ; Larva/microbiology ; Mosquito Control/*methods ; Poland ; }, abstract = {Two evaluations of microbial mosquito larvicides were conducted in irrigation fields located along the Odra River near the city of Wroclaw, Poland. In the first evaluation, 3 dosages each of Bacillus thuringiensis israelensis (Bti)--VectoBac water dispersible granule (WDG) and VectoBac aqueous suspension formulation (12AS)--and Bacillus sphaericus (Bs)--VectoLex WDG--were tested against larvae of Culex pipiens pipiens. There was little difference between formulations and rates of application between day 2 and 7 following the treatment. VectoBac WDG at 300 g/ha resulted in 100% mortality of Cx. p. pipiens. Between 0.5 and 1 liter of VectoBac 12AS caused sufficient mortality for up to 7 days. The effective shortterm application rate of VectoLex WDG was found to be 400 g/ha. The above doses can be recommended for up to 7-day control in this habitat. In the second evaluation, using VectoBac WDG at 800 g/ha, the residual efficacies of 2 ground application methods, a knapsack sprayer configured for large droplet application and a motorized backpack blower configured for small droplet application, were compared. The results indicated no significant difference between the 2 application methods, but a significant long-term effect of VectoBac WDG was observed at the rate of 800 g/ha.}, }
@article {pmid19648381, year = {2009}, author = {Sul, WJ and Park, J and Quensen, JF and Rodrigues, JL and Seliger, L and Tsoi, TV and Zylstra, GJ and Tiedje, JM}, title = {DNA-stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {17}, pages = {5501-5506}, pmid = {19648381}, issn = {1098-5336}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; P42-ES004911/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Biphenyl Compounds/metabolism ; Carbon Isotopes/*metabolism ; Cluster Analysis ; DNA/*genetics/isolation &amp; purification ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Dioxygenases/*genetics/isolation &amp; purification ; Gene Library ; Gene Order ; *Geologic Sediments ; Molecular Sequence Data ; Phylogeny ; Polychlorinated Biphenyls/*analysis ; RNA, Ribosomal, 16S/genetics ; Rivers ; Sequence Analysis, DNA ; Water/chemistry ; Water Pollutants, Chemical/*analysis ; }, abstract = {Stable isotope probing with [(13)C]biphenyl was used to explore the genetic properties of indigenous bacteria able to grow on biphenyl in PCB-contaminated River Raisin sediment. A bacterial 16S rRNA gene clone library generated from [(13)C]DNA after a 14-day incubation with [(13)C]biphenyl revealed the dominant organisms to be members of the genera Achromobacter and Pseudomonas. A library built from PCR amplification of genes for aromatic-ring-hydroxylating dioxygenases from the [(13)C]DNA fraction revealed two sequence groups similar to bphA (encoding biphenyl dioxygenase) of Comamonas testosteroni strain B-356 and of Rhodococcus sp. RHA1. A library of 1,568 cosmid clones was produced from the [(13)C]DNA fraction. A 31.8-kb cosmid clone, detected by aromatic dioxygenase primers, contained genes of biphenyl dioxygenase subunits bphAE, while the rest of the clone's sequence was similar to that of an unknown member of the Gammaproteobacteria. A discrepancy in G+C content near the bphAE genes implies their recent acquisition, possibly by horizontal transfer. The biphenyl dioxygenase from the cosmid clone oxidized biphenyl and unsubstituted and para-only-substituted rings of polychlorinated biphenyl (PCB) congeners. A DNA-stable isotope probing-based cosmid library enabled the retrieval of functional genes from an uncultivated organism capable of PCB metabolism and suggest dispersed dioxygenase gene organization in nature.}, }
@article {pmid19641948, year = {2010}, author = {Ponnusamy, L and Wesson, DM and Arellano, C and Schal, C and Apperson, CS}, title = {Species composition of bacterial communities influences attraction of mosquitoes to experimental plant infusions.}, journal = {Microbial ecology}, volume = {59}, number = {1}, pages = {158-173}, pmid = {19641948}, issn = {1432-184X}, support = {U01 AI058303/AI/NIAID NIH HHS/United States ; U01-AI-58303-01/AI/NIAID NIH HHS/United States ; }, mesh = {Aedes/*physiology ; Animals ; Bacteria/*classification/genetics/growth &amp; development ; Behavior, Animal/drug effects ; *Biodiversity ; Colony Count, Microbial ; Culture Media/classification ; Ecosystem ; Female ; Fermentation ; Phylogeny ; }, abstract = {In the container habitats of immature mosquitoes, catabolism of plant matter and other organic detritus by microbial organisms produces metabolites that mediate the oviposition behavior of Aedes aegypti and Aedes albopictus. Public health agencies commonly use oviposition traps containing plant infusions for monitoring populations of these mosquito species, which are global vectors of dengue viruses. In laboratory experiments, gravid females exhibited significantly diminished responses to experimental infusions made with sterilized white oak leaves, showing that attractive odorants were produced through microbial metabolic activity. We evaluated effects of infusion concentration and fermentation time on attraction of gravid females to infusions made from senescent bamboo or white oak leaves. We used plate counts of heterotrophic bacteria, total counts of 4',6-diamidino-2-phenylindole-stained bacterial cells, and 16S ribosomal DNA (rDNA) polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) to show that changes in the relative abundance of bacteria and the species composition of bacterial communities influenced attraction of gravid A. aegypti and A. albopictus mosquitoes to infusions. DGGE profiles showed that bacterial species composition in infusions changed over time. Principal components analysis indicated that oviposition responses to plant infusions were in general most affected by bacterial diversity and abundance. Analysis of bacterial 16S rDNA sequences derived from DGGE bands revealed that Proteobacteria (Alpha-, Beta-, Delta-, and Gamma-) were the predominant bacteria detected in both types of plant infusions. Gravid A. aegypti were significantly attracted to a mix of 14 bacterial species cultured from bamboo leaf infusion. The oviposition response of gravid mosquitoes to plant infusions is strongly influenced by abundance and diversity of bacterial species, which in turn is affected by plant species, leaf biomass, and fermentation time.}, }
@article {pmid19638171, year = {2009}, author = {Philippot, L and Bru, D and Saby, NP and Cuhel, J and Arrouays, D and Simek, M and Hallin, S}, title = {Spatial patterns of bacterial taxa in nature reflect ecological traits of deep branches of the 16S rRNA bacterial tree.}, journal = {Environmental microbiology}, volume = {11}, number = {12}, pages = {3096-3104}, doi = {10.1111/j.1462-2920.2009.02014.x}, pmid = {19638171}, issn = {1462-2920}, mesh = {Bacteria/*classification/genetics ; Biostatistics ; Ecology ; Environmental Monitoring/*methods ; Geography ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Soil Microbiology ; }, abstract = {Whether bacteria display spatial patterns of distribution and at which level of taxonomic organization such patterns can be observed are central questions in microbial ecology. Here we investigated how the total and relative abundances of eight bacterial taxa at the phylum or class level were spatially distributed in a pasture by using quantitative PCR and geostatistical modelling. The distributions of the relative abundance of most taxa varied by a factor of 2.5-6.5 and displayed strong spatial patterns at the field scale. These spatial patterns were taxon-specific and correlated to soil properties, which indicates that members of a bacterial clade defined at high taxonomical levels shared specific ecological traits in the pasture. Ecologically meaningful assemblages of bacteria at the phylum or class level in the environment provides evidence that deep branching patterns of the 16S rRNA bacterial tree are actually mirrored in nature.}, }
@article {pmid19633807, year = {2009}, author = {Thomas, P and Soly, TA}, title = {Endophytic bacteria associated with growing shoot tips of banana (Musa sp.) cv. Grand Naine and the affinity of endophytes to the host.}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {952-964}, pmid = {19633807}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Musa/*microbiology ; Phylogeny ; Plant Shoots/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {A cultivation-based assessment of endophytic bacteria present in deep-seated shoot tips of banana suckers was made with a view to generate information on the associated organisms, potential endophytic contaminants in tissue-cultured bananas and to assess if the endophytes shared a beneficial relationship with the host. Plating the tissue homogenate from the central core of suckers showed colony growth on nutrient agar from just 75% and 42% of the 12 stocks during May and November, respectively (average 58%; 6 x 10(3) colony-forming units per gram), yielding diverse organisms belonging to firmicutes (Bacillus, Brevibacillus, Paenibacillus, Virgibacillus, Staphylococcus spp.), actinobacteria (Cellulomonas, Micrococcus, Corynebacterium, Kocuria spp.), alpha-proteobacteria (Paracoccus sp.), and gamma-proteobacteria (Pseudomonas, Acinetobacter spp.). Each shoot tip showed one to three different organisms and no specific organism appeared common to different sucker tips. Tissue homogenate from shoot tips including the ones that did not yield culturable bacteria displayed abundant bacterial cells during microscopic examination suggesting that a high proportion of cells were in viable-but-nonculturable state, or their cultivation requirements were not met. Direct application of cultivation-independent approach to study endophytic bacterial community using bacterial 16S ribosomal RNA universal primers resulted in high interference from chloroplast and mitochondrial genome sequences. Dislodging the bacterial cells from shoot tips that did not show cultivable bacteria and incubating the tissue crush in dilute-nutrient broth led to the activation of four organisms (Klebsiella, Agrobacterium, Pseudacidovorax spp., and an unidentified isolate). The endophytic organisms in general showed better growth at 30-37 degrees C compared with 25 degrees C, and the growth of endophytes as well as pathogenic Erwinia carotovora were promoted with the supply of host tissue extract (HTE) while that of the isolates from nonplant sources were inhibited or unaffected by HTE, suggesting an affinity or dependence of the endophytes on the host and the prospect of an HTE-based assay for discriminating the nonendophytes from endophytes.}, }
@article {pmid19633806, year = {2009}, author = {Santos, A and Cerrada, A and García, S and San Andrés, M and Abrusci, C and Marquina, D}, title = {Application of molecular techniques to the elucidation of the microbial community structure of antique paintings.}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {692-702}, pmid = {19633806}, issn = {1432-184X}, mesh = {Bacteria/*isolation &amp; purification ; Biofilms ; Coloring Agents/chemistry ; DNA, Bacterial/analysis ; DNA, Fungal/analysis ; Electrophoresis, Polyacrylamide Gel/methods ; *Environmental Microbiology ; Fungi/*isolation &amp; purification ; In Situ Hybridization, Fluorescence ; Microscopy, Electron, Scanning ; Paint/microbiology ; *Paintings ; Spectrometry, X-Ray Emission ; }, abstract = {This paper uses molecular techniques to describe the microstructure and microbiological communities of sixteenth century artwork and their relationships. The microbiological populations, analysed by denaturing gradient gel electrophoresis (DGGE), were highly influenced by the chemical composition of the pictorial layers detected by energy-dispersive X-ray analysis. DGGE revealed that the diversity of microbial communities was lower in pictorial layers composed of pigments with metals, such as Pb, Cu and Hg, than in those found in pictorial layers without such compounds. The number of cultivable microorganisms, mainly fungi and bacteria, was very low in comparison to those found by DGGE, revealing the presence of both cultivable and as-yet-uncultivated (or not viable) species in the samples analysed. Both fungi and bacteria were present in a non-random spatial distribution. Environmental scanning electron microscopy and fluorescent in situ hybridisation analyses revealed that bacterial populations were usually found in close contact with the surface of the pictorial layers, and fungal populations were located on the bacterial biofilm. This work shows, for the first time, the correlation between the diversity of the microbial populations and the chemical composition of the pictorial layers of an artwork.}, }
@article {pmid19629578, year = {2009}, author = {Edmonds, JW and Weston, NB and Joye, SB and Mou, X and Moran, MA}, title = {Microbial community response to seawater amendment in low-salinity tidal sediments.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {558-568}, pmid = {19629578}, issn = {1432-184X}, mesh = {Archaea/genetics/*growth &amp; development ; Bacteria/genetics/*growth &amp; development ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Ecosystem ; Gene Library ; Geologic Sediments/*microbiology ; Georgia ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Rivers/microbiology ; Salinity ; Seawater/microbiology ; Sequence Analysis, DNA ; Time Factors ; *Water Microbiology ; }, abstract = {Rising sea levels and excessive water withdrawals upstream are making previously freshwater coastal ecosystems saline. Plant and animal responses to variation in the freshwater-saline interface have been well studied in the coastal zone; however, microbial community structure and functional response to seawater intrusion remains relatively unexplored. Here, we used molecular approaches to evaluate the response of the prokaryotic community to controlled changes in porewater salinity levels in freshwater sediments from the Altamaha River, Georgia, USA. This work is a companion to a previously published study describing results from an experiment using laboratory flow-through sediment core bioreactors to document biogeochemical changes as porewater salinity was increased from 0 to 10 over 35 days. As reported in Weston et al. (Biogeochemistry, 77:375-408, 62), porewater chemistry was monitored, and cores were sacrificed at 0, 9, 15, and 35 days, at which time we completed terminal restriction fragment length polymorphism and 16S rRNA clone library analyses of sediment microbial communities. The biogeochemical study documented changes in mineralization pathways in response to artificial seawater additions, with a decline in methanogenesis, a transient increase in iron reduction, and finally a dominance of sulfate reduction. Here, we report that, despite these dramatic and significant changes in microbial activity at the biogeochemical level, no significant differences were found between microbial community composition of control vs. seawater-amended treatments for either Bacterial or Archaeal members. Further, taxa in the seawater-amended treatment community did not become more "marine-like" through time. Our experiment suggests that, as seawater intrudes into freshwater sediments, observed changes in metabolic activity and carbon mineralization on the time scale of weeks are driven more by shifts in gene expression and regulation than by changes in the composition of the microbial community.}, }
@article {pmid19629577, year = {2010}, author = {Pascoal, C and Cássio, F and Nikolcheva, L and Bärlocher, F}, title = {Realized fungal diversity increases functional stability of leaf litter decomposition under zinc stress.}, journal = {Microbial ecology}, volume = {59}, number = {1}, pages = {84-93}, pmid = {19629577}, issn = {1432-184X}, mesh = {Biodegradation, Environmental/drug effects ; Biodiversity ; Ecosystem ; Fungi/*drug effects/growth &amp; development/metabolism ; Plant Leaves/*microbiology ; *Stress, Physiological ; Water Pollutants, Chemical/*toxicity ; Zinc/*toxicity ; }, abstract = {Freshwaters include some of the most impaired systems on Earth with high rates of species loss, underscoring the significance of investigating whether ecosystems with fewer species will be able to maintain ecological processes. The environmental context is expected to modulate the effects of declining diversity. We conducted microcosm experiments manipulating fungal inoculum diversity and zinc concentration to test the hypothesis that fungal diversity determines the susceptibility of leaf litter decomposition to Zn stress. Realized fungal diversity was estimated by counting released spores and by measuring species-specific biomasses via denaturing gradient gel electrophoresis. In the absence of Zn, positive diversity effects were found for leaf mass loss and fungal biomass through complementary interactions and due to the presence of key species. The variability of leaf decomposition decreased with increasing species number (portfolio effect), particularly under Zn stress. Results suggest that the effect of species loss on ecosystem stability may be exacerbated at higher stress levels.}, }
@article {pmid19627483, year = {2009}, author = {Plominsky, AM and Soto-Liebe, K and Vásquez, M}, title = {Optimization of 2D-PAGE protocols for proteomic analysis of two nonaxenic toxin-producing freshwater cyanobacteria: Cylindrospermopsis raciborskii and Raphidiopsis sp.}, journal = {Letters in applied microbiology}, volume = {49}, number = {3}, pages = {332-337}, doi = {10.1111/j.1472-765X.2009.02665.x}, pmid = {19627483}, issn = {1472-765X}, mesh = {Bacterial Proteins/*analysis ; Chromatography, High Pressure Liquid ; Cyanobacteria/*chemistry ; Cylindrospermopsis/chemistry ; Electrophoresis, Gel, Two-Dimensional/*methods ; Fresh Water/*microbiology ; Mass Spectrometry ; Proteome/*analysis ; }, abstract = {AIMS: To optimize a protocol for the extraction and an in-depth analysis of the soluble protein fraction of two nonaxenic toxin-producing cyanobacteria Cylindrospermopsis raciborskii (hepatotoxin-producing), and Raphidiopsis sp. (neurotoxin-producing), using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE).<br><br>METHODS AND RESULTS: The soluble protein fractions from strains of C. raciborskii and Raphidiosis sp. with different toxicity phenotypes were analysed by 2D-PAGE. Specific protocols were optimized specifically for each strain. Between 500 and 700 sharp protein spots were distinguished in a single 4-7 pH range 2D-PAGE for each cyanobacterium. Comparison of the protein maps of C. raciborskii CS-505 (a cylindrospermopsin-producing strain) and Raphidiopsis sp. D9 (saxitoxin-producing strain) against the nontoxic C. raciborskii strain CS-509 revealed many unique proteins in each protein map. We confirmed that the resolved proteins were cyanobacterial by identifying three randomly chosen protein spots from a Raphidiopsis sp. strain D9 2D-PAGE, using high-performance liquid chromatography (HPLC) tandem mass spectrometry (MS).<br><br>CONCLUSIONS: The 2D-PAGE conditions presented here provide a robust protocol for proteomic studies in two CYN- and STX-producing model organisms, C. raciborskii and Raphidiopsis sp.<br><br>We present the first protocols for proteomic analyses of Cylindrospermopsis raciborskii and Raphidiopsis sp.}, }
@article {pmid19626265, year = {2010}, author = {Gamble, MD and Bagwell, CE and LaRocque, J and Bergholz, PW and Lovell, CR}, title = {Seasonal variability of diazotroph assemblages associated with the rhizosphere of the salt marsh cordgrass, Spartina alterniflora.}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {253-265}, pmid = {19626265}, issn = {1432-184X}, mesh = {*Biodiversity ; DNA, Bacterial/genetics ; Ecosystem ; Gammaproteobacteria/genetics/*growth &amp; development ; Genes, Bacterial ; Geologic Sediments ; Phylogeny ; Poaceae/*microbiology ; Principal Component Analysis ; *Seasons ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Nitrogen fixation is the primary N source in the highly productive but N-limited North Inlet, SC, USA salt marsh system. The diverse assemblages of nitrogen-fixing (diazotrophic) bacteria associated with the rhizospheres of the short and tall growth forms of Spartina alterniflora were analyzed at two sites, Crab Haul Creek and Goat Island, which are in different tidal creek drainage systems in this marsh. The sites differed in proximity to the main channel for tidal intrusion and in several edaphic parameters. We hypothesized that either the differing abiotic environmental regimes of the two sites or the variation due to seasonal effects result in differences in the diazotroph assemblage. Rhizosphere samples were collected seasonally during 1999 and 2000. DNA was purified and nifH amplified for denaturing gradient gel electrophoresis (DGGE) analysis of diazotroph assemblage composition. Principal components analysis was used to analyze the binary DGGE band position data. Season strongly influenced assemblage composition and biplots were used to identify bands that significantly affected the seasonal and site-specific clustering. The types of organisms that were most responsive to seasonal or site variability were identified on the basis of DGGE band sequences. Seasonally responsive members of the anaerobic diazotrophs were detected during the winter and postsenescence conditions and may have been responsible for elevated pore water sulfide concentrations. Sequences from a diverse assemblage of Gammaproteobacteria were predominant during growth periods of S. alterniflora. Abiotic environmental parameters strongly influenced both the S. alterniflora and the diazotrophic bacterial assemblages associated with this keystone salt marsh plant species.}, }
@article {pmid19624130, year = {2009}, author = {White, PM and Potter, TL and Strickland, TC}, title = {Pressurized liquid extraction of soil microbial phospholipid and neutral lipid fatty acids.}, journal = {Journal of agricultural and food chemistry}, volume = {57}, number = {16}, pages = {7171-7177}, doi = {10.1021/jf901257n}, pmid = {19624130}, issn = {1520-5118}, mesh = {Bacteria/chemistry ; Chemical Fractionation/*methods ; Eukaryota/chemistry ; Fatty Acids/analysis/*isolation &amp; purification ; Fungi/chemistry ; Phospholipids/analysis/*isolation &amp; purification ; *Soil Microbiology ; }, abstract = {Soil microbial lipid biomarkers are indicators of viable microbial biomass and community structure. Pressurized liquid extraction (PLE) of soil phospholipid fatty acids (PLFA) and neutral lipid fatty acids (NLFA) was compared to a conventional extraction method in four soils with differing physical and chemical properties. PLE efficiency was greater than that of the conventional method for about half of the saturated PLFA and for selected other Gram-positive (i16:0) and Gram-negative bacteria (18:1omega7c) PLFA, fungal PLFA (18:2omega6,9c), and eukaryotic NLFA from a coarse-textured soil. Lipids extracted by the two methods did not indicate a significant difference in microbial community structure data. Principle component analysis revealed that PLFA clustered by location, with data indicating that the group of microbes contributing the greatest weight differed among soils. Overall, the PLE method proved to be more efficient at extracting soilborne microbial lipids while not altering microbial community information. These advantages indicate the PLE method is robust and well-suited to soil microbial ecology research.}, }
@article {pmid19618099, year = {2009}, author = {Muthukumarasamy, R and Revathi, G}, title = {Letter with regard to the publication of the manuscript entitled "Effects of the inoculation of Burkholderia vietnamiensis and related endophytic diazotrophic bacteria on grain yield of rice".}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {970-971}, pmid = {19618099}, issn = {1432-184X}, mesh = {Burkholderia cepacia complex/*physiology ; Oryza/*growth &amp; development/*microbiology ; }, }
@article {pmid19617514, year = {2009}, author = {Dimitroglou, A and Merrifield, DL and Moate, R and Davies, SJ and Spring, P and Sweetman, J and Bradley, G}, title = {Dietary mannan oligosaccharide supplementation modulates intestinal microbial ecology and improves gut morphology of rainbow trout, Oncorhynchus mykiss (Walbaum).}, journal = {Journal of animal science}, volume = {87}, number = {10}, pages = {3226-3234}, doi = {10.2527/jas.2008-1428}, pmid = {19617514}, issn = {1525-3163}, mesh = {Animals ; Aquaculture ; Colony Count, Microbial/veterinary ; DNA, Bacterial/chemistry/genetics ; Dietary Carbohydrates/*pharmacology ; Electrophoresis, Polyacrylamide Gel/veterinary ; Histocytochemistry/veterinary ; Intestinal Mucosa/metabolism ; Intestines/*microbiology/ultrastructure ; Mannans/*pharmacology ; Microscopy, Electron, Scanning/veterinary ; Microscopy, Electron, Transmission/*veterinary ; Oligosaccharides/*pharmacology ; Oncorhynchus mykiss/*metabolism/microbiology ; Polymerase Chain Reaction/veterinary ; RNA, Ribosomal, 16S/chemistry/genetics ; }, abstract = {A study was conducted to investigate the effect of mannan oligosaccharide (MOS) on the gut microbiota and intestinal morphology of rainbow trout under commercial farming conditions. Juvenile (mean initial BW 38.2 +/- 1.7 g) and subadult (111.7 +/- 11.6 g) trout were fed 2 dietary treatments for 111 and 58 d, respectively. The control treatment consisted of a standard commercial diet, and the MOS treatment consisted of the control diet supplemented with 0.2% MOS. Morphology of the anterior and the posterior intestine was examined with light and electron microscopy. Light microscopy demonstrated increased gut absorptive surface area in the subadult MOS group. Additionally, electron microscopy revealed an increase in microvilli length and density in the subadult MOS group compared with the control (P < 0.05). However, no significant improvements were detected in the juvenile group. Culture-based evaluation of the intestinal microbiota showed that MOS significantly reduced (P < 0.05) the viable intestinal bacterial populations (by approximately 2 log scales in all cases). Levels of Aeromonas/Vibrio spp. were significantly decreased (P < 0.05) in the juvenile MOS group (9% of the total microbiota) compared with the juvenile control group (37%). Additionally, analysis of microbial communities was conducted using denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA. The denaturing gradient gel electrophoresis fingerprinting revealed an alteration of bacterial populations; analysis of similarity, similarity percentages, and nonmetric multidimensional scaling analysis showed that MOS reduced species richness and increased similarity of bacterial populations found within the subadult and juvenile groups. The current study shows that MOS modulates intestinal microbial communities, which subsequently improve gut morphology and epithelial brush border.}, }
@article {pmid19609599, year = {2010}, author = {Morrison, M and Daugherty, SC and Nelson, WC and Davidsen, T and Nelson, KE and , }, title = {The FibRumBa database: a resource for biologists with interests in gastrointestinal microbial ecology, plant biomass degradation, and anaerobic microbiology.}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {212-213}, doi = {10.1007/s00248-009-9562-4}, pmid = {19609599}, issn = {1432-184X}, mesh = {Animals ; *Databases, Genetic ; Fibrobacter/*genetics ; Genome, Bacterial ; Genomic Library ; Rumen/*microbiology/physiology ; }, }
@article {pmid19609598, year = {2010}, author = {Coppotelli, BM and Ibarrolaza, A and Dias, RL and Del Panno, MT and Berthe-Corti, L and Morelli, IS}, title = {Study of the degradation activity and the strategies to promote the bioavailability of phenanthrene by Sphingomonas paucimobilis strain 20006FA.}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {266-276}, pmid = {19609598}, issn = {1432-184X}, mesh = {Biodegradation, Environmental ; Biological Availability ; Carbon/metabolism ; Culture Media ; Hydrophobic and Hydrophilic Interactions ; Microscopy, Electron, Scanning ; Naphthols/metabolism ; Phenanthrenes/*metabolism ; Salicylic Acid/metabolism ; *Soil Microbiology ; Sphingomonas/*metabolism/ultrastructure ; Surface-Active Agents/metabolism ; }, abstract = {The present study describes the phenanthrene-degrading activity of Sphingomonas paucimobilis 20006FA and its ability to promote the bioavailability of phenanthrene. S. paucimobilis 20006FA was isolated from a phenanthrene-contaminated soil microcosm. The strain was able to grow in liquid mineral medium saturated with phenanthrene as the sole carbon source, showing high phenanthrene elimination (52.9% of the supplied phenanthrene within 20 days). The accumulation of 1-hydroxy-2-naphthoic acid and salicylic acid as major phenanthrene metabolites and the capacity of the strain to grow with sodium salicylate as the sole source of carbon and energy indicated that the S. paucimobilis 20006FA possesses a complete phenanthrene degradation pathway. However, under the studied conditions, the strain was able to mineralize only the 10% of the consumed phenanthrene. Investigations on the cell ability to promote bioavailability of phenanthrene showed that the S. paucimobilis strain 20006FA exhibited low cell hydrophobicity (0.13), a pronounced chemotaxis toward phenanthrene, and it was able to reduce the surface tension of mineral liquid medium supplemented with phenanthrene as sole carbon source. Scanning electron micrographs revealed that: (1) in suspension cultures, cells formed flocks and showed small vesicles on the cell surface and (2) cells were also able to adhere to phenanthrene crystals and to produce biofilms. Clearly, the strain seems to exhibit two different mechanisms to enhance phenanthrene bioavailability: biosurfactant production and adhesion to the phenanthrene crystals.}, }
@article {pmid19597862, year = {2010}, author = {Kaszab, E and Kriszt, B and Atzél, B and Szabó, G and Szabó, I and Harkai, P and Szoboszlay, S}, title = {The occurrence of multidrug-resistant Pseudomonas aeruginosa on hydrocarbon-contaminated sites.}, journal = {Microbial ecology}, volume = {59}, number = {1}, pages = {37-45}, pmid = {19597862}, issn = {1432-184X}, mesh = {*Drug Resistance, Multiple, Bacterial ; Environmental Monitoring ; Hungary ; Hydrocarbons/*analysis ; Pseudomonas aeruginosa/drug effects/genetics/*isolation &amp; purification ; Soil Pollutants/*analysis ; }, abstract = {The main aim of this paper was the comprehensive estimation of the occurrence rate and the antibiotic-resistance conditions of opportunistic pathogen Pseudomonas aeruginosa in hydrocarbon-contaminated environments. From 2002 to 2007, 26 hydrocarbon-contaminated sites of Hungary were screened for the detection of environmental isolates. Altogether, 156 samples were collected and examined for the determination of appearance, representative cell counts, and antibiotic-resistance features of P. aeruginosa. The detected levels of minimal inhibitory concentrations of ten different drugs against 36 environmental strains were compared to the results of a widely used reference strain ATCC 27853 and four other clinical isolates of P. aeruginosa. Based on our long-term experiment, it can be established that species P. aeruginosa was detectable in case of 61.5% of the investigated hydrocarbon-contaminated sites and 35.2% of the examined samples that shows its widespread occurrence in polluted soil-groundwater systems. In the course of the antibiotic-resistance assay, our results determined that 11 of the examined 36 environmental strains had multiple drug-resistance against several clinically effective antimicrobial classes: cephalosporins, wide spectrum penicillins, carbapenems, fluoroquinolones, and aminoglycosides. The fact that these multiresistant strains were isolated from 8 different hydrocarbon-contaminated sites, mainly from outskirts, confirms that multiple drug-resistance of P. aeruginosa is widespread not only in clinical, but also in natural surroundings as well.}, }
@article {pmid19596129, year = {2009}, author = {Wittebolle, L and Verstraete, W and Boon, N}, title = {The inoculum effect on the ammonia-oxidizing bacterial communities in parallel sequential batch reactors.}, journal = {Water research}, volume = {43}, number = {17}, pages = {4149-4158}, doi = {10.1016/j.watres.2009.06.034}, pmid = {19596129}, issn = {1879-2448}, mesh = {Ammonia/*metabolism ; Bacteria/*metabolism ; *Bioreactors ; Electrophoresis, Polyacrylamide Gel ; In Situ Hybridization, Fluorescence ; Oxidation-Reduction ; Polymerase Chain Reaction ; Reproducibility of Results ; }, abstract = {Three identical sequential batch reactors (SBRs) were each inoculated with sludge from a full-scale wastewater treatment plant (WWTP) treating a waste stream of different origin, i.e. a hospital, a meat processing company, and a municipal WWTP. The SBRs were run in parallel for 84 consecutive days to investigate whether the reactors would become more phylogenetically similar or stay separated concerning their functionality and microbial communities. Overall, the nitrification functionality was high throughout the experiment, and the size and structure of the sludge flocs were very similar. The total bacterial and ammonia-oxidizing bacterial (AOB) communities were analyzed by PCR-DGGE. Cluster analysis demonstrated very distinct bacterial communities in the three SBRs, not showing any trend becoming more similar. The carrying capacity, dynamics and functional organization of the communities were assessed by DGGE analysis and based on these patterns the range-weighted richness, moving window analysis, and constructing Pareto-Lorenz evenness distribution curves were calculated. Between the SBRs, highly comparable internal structure and dynamics of the AOB communities were observed, although they had only one AOB DGGE band in common. These observations indicate that community characteristics such as the extent of biodiversity and dynamics are more important indicators of good microbial functionality than the presence of certain specific species.}, }
@article {pmid19593555, year = {2010}, author = {Angel, R and Asaf, L and Ronen, Z and Nejidat, A}, title = {Nitrogen transformations and diversity of ammonia-oxidizing bacteria in a desert ephemeral stream receiving untreated wastewater.}, journal = {Microbial ecology}, volume = {59}, number = {1}, pages = {46-58}, pmid = {19593555}, issn = {1432-184X}, mesh = {Ammonia/analysis/*metabolism ; Bacteria/classification/isolation &amp; purification/*metabolism ; Biodiversity ; Biotransformation ; Desert Climate ; Environmental Monitoring ; Eutrophication ; Geologic Sediments/chemistry/microbiology ; Nitrogen/analysis/*metabolism ; Oxidation-Reduction ; Phylogeny ; Rivers/chemistry/*microbiology ; Water Pollutants, Chemical/analysis/*metabolism ; }, abstract = {Levels of inorganic nitrogen species (ammonia, nitrite, and nitrate), ammonia oxidation potential (AOP), and diversity of ammonia-oxidizing bacteria (AOB) were studied in the sediments of a 50-km-long segment of an ephemeral stream in the Negev desert, receiving untreated wastewater. Water analysis in downstream sampling points showed reductions of 91.7% in biological oxygen demand, 87.7% in chemical oxygen demand, 73.9% in total nitrogen, and 72.8% in total ammonia nitrogen. Significant AOP levels in the sediment were detected mainly in the fall and spring seasons. Denaturing gradient gel electrophoresis of AOB 16S rRNA gene fragments showed that in most sampling points, the streambed was dominated by Nitrosospira cluster 3 strains similar to those dominating the stream bank's soils and sediments in nearby springs. Nitrosomonas strains introduced by discharged wastewater and others dominated some sections of the stream characterized by high organic carbon levels. The results suggest that climatic conditions in the Negev desert select for AOB belonging to Nitrosospira cluster 3, and these conditions dominate the aquatic environment effect along most of the stream sections. In addition, the nitrification-denitrification processes were not sufficient to reduce nitrogen levels in the sediment and prevent the eutrophication of some sections of the stream ecosystem. Thus, the discharge of high nitrogen wastewater into desert streams should be done carefully as it may endanger the already fragile ecosystem.}, }
@article {pmid19590809, year = {2009}, author = {Abdulla, H}, title = {Bioweathering and biotransformation of granitic rock minerals by actinomycetes.}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {753-761}, pmid = {19590809}, issn = {1432-184X}, mesh = {Actinobacteria/growth &amp; development/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Biotransformation ; Metals/metabolism ; Mycolic Acids/metabolism ; Silicon Dioxide/*metabolism ; *Soil Microbiology ; }, abstract = {Actinomycetes inhabiting granitic rocks at St. Katherine, Egypt were investigated for their bioweathering potential. Actinomycete counts ranged between 174 and 360 colony forming units per gram. Counts were positively correlated to rock porosity (r = 0.65) and negatively correlated to rock salinity (r = -0.56). Sixty-six actinomycete isolates originating from rocks could be assigned into eight genera, with a high frequency of Nocardioides and Streptomyces. Organic acids were produced by 97% of the isolates. Strains belonging to Actinopolyspora, Actinomadura, Kitasatospora, Nocardioides, and Kibdelosporangium showed the highest acid production indices. Representatives from all eight genera could precipitate metals Cu, Fe, Zn, Cd, and Ag up to concentrations of 2.5 mM each. An actinomycete consortium of two Nocardioides strains and one Kibdelosporangium strain was studied for its potential to cause rock weathering in batch experiments. Results indicated a high ability of the consortium to leach the metals Cu, Zn, and Fe up to 2.6-, 2.1-, and 1.3-fold, respectively, compared to the control after 4 weeks. The pH significantly decreased after 1 week, which was parallel to an increased release of phosphate and sulfate reaching a 2.2- and 2.5-fold increase, respectively, compared to control. Highly significant weight loss (p = 0.005) was achieved by the consortium, indicating a potential multiple role of actinomycetes in weathering by acid production, metal leaching, and solubilization of phosphate and sulfate. This study emphasizes the diverse and unique abilities of actinomycetes inhabiting rock surfaces which could be of potential biotechnological applications, such as in the bioremediation of metal-contaminated environments and metal biorecovery.}, }
@article {pmid19588186, year = {2009}, author = {Gerçe, B and Schwartz, T and Voigt, M and Rühle, S and Kirchen, S and Putz, A and Proksch, P and Obst, U and Syldatk, C and Hausmann, R}, title = {Morphological, bacterial, and secondary metabolite changes of Aplysina aerophoba upon long-term maintenance under artificial conditions.}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {865-878}, pmid = {19588186}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/*genetics ; Chromatography, High Pressure Liquid ; Cluster Analysis ; DNA, Bacterial/genetics ; Electrophoresis, Polyacrylamide Gel ; Light ; *Phylogeny ; Porifera/anatomy &amp; histology/*metabolism/*microbiology ; Seawater/microbiology ; Sequence Analysis, DNA ; Temperature ; }, abstract = {The aim of this study was to analyze successional changes in the bacterial community over a period of 6 months of cultivation of Aplysina aerophoba sponges under different artificial cultivation conditions by use of denaturing gradient gel electrophoresis (DGGE). The cultivation conditions varied concerning the water temperature (20 +/- 2 degrees C and 25 +/- 2 degrees C) of the aquaria, additional illumination of one aquarium, and feeding of the sponges. Amplicons from DGGE separation of dominant colonizing or variably appearing bacteria were sequenced and aligned for taxonomical identification. In addition, secondary metabolites typically found in A. aerophoba were analyzed to investigate changes in the natural product profile during cultivation. The cultivation of sponges under any given condition did not lead to a depletion of their bacterial community in the course of the experiment. On the contrary, the distinctive set of associated bacteria was maintained in spite of a dramatic loss of biomass and morphological degradation during the cultivation period. Generally, all sequences obtained from the DGGE gels were related to bacteria of five phyla: Actinobacteria, Cyanobacteria, alpha-Proteobacteria, gamma-Proteobacteria, and Chloroflexi. Despite the overall stability of the bacterial community in A. aerophoba, an unambiguous variability was detected for the Cyanobacteria "A. aerophoba clone TK09". This variability was ascribed to the predominant light conditions. The analysis of the metabolic pattern revealed that the concentration of a class of characteristic-brominated compounds typically found in A. aerophoba, like aeroplysinin-1, aerophobin-1, aerophobin-2, and isofistularin-3, increased over the 6 months of cultivation.}, }
@article {pmid19582501, year = {2010}, author = {Odić, D and Budic, B and Mandić-Mulec, I and Stopar, D}, title = {Influence of bacterial lysate quality on growth of two bacterioplankton species.}, journal = {Microbial ecology}, volume = {59}, number = {2}, pages = {246-252}, pmid = {19582501}, issn = {1432-184X}, mesh = {Bacteria/*chemistry ; Cell Extracts/*chemistry ; Culture Media ; Hydrogen-Ion Concentration ; Pseudoalteromonas/chemistry/*growth &amp; development ; Salinity ; Temperature ; Vibrio/chemistry/*growth &amp; development ; *Water Microbiology ; Zinc/chemistry ; }, abstract = {All physico-chemical parameters that affect bacterial growth rate will also affect bacterial molecular composition, which in turn influences the chemical composition of bacterial lysate and its turnover rate in the ecosystem. To produce qualitatively different lysates, Vibrio sp. cells were grown under different pH, salt, or temperature conditions in rich growth media and then washed and lysed by autoclaving. Both the absolute concentrations and the ratios between elements in the lysates varied with different growth conditions, implying differences in lysate quality. Either Pseudoalteromonas sp. or Vibrio sp. was grown on the lysates at non-limiting lysate concentrations. Different lysates supported growth rates of Pseudoalteromonas sp. in the range from 0.25 to 1.53 h(-1). On the other hand, growth rates of Vibrio sp. grown on its own lysates were around 0.4 h(-1) and were not dependent on lysate quality. Two orders of magnitude decrease in Zn concentration in Vibrio sp. cells grown on different lysates as compared to cells grown on rich growth medium suggested that Zn might be a factor limiting growth. In the simple microbial loop studied, the initial difference in lysate quality was preserved in Pseudoalteromonas sp., whereas Vibrio sp. decreased the initial differences in lysate quality, thereby neutralizing the primary effect of environmental conditions on carbon turnover.}, }
@article {pmid19577958, year = {2009}, author = {Pizay, MD and Lemée, R and Simon, N and Cras, AL and Laugier, JP and Dolan, JR}, title = {Night and day morphologies in a planktonic dinoflagellate.}, journal = {Protist}, volume = {160}, number = {4}, pages = {565-575}, doi = {10.1016/j.protis.2009.04.003}, pmid = {19577958}, issn = {1618-0941}, mesh = {*Circadian Rhythm ; Dinoflagellida/*cytology/*physiology ; Microscopy ; Microscopy, Electron, Scanning ; Microscopy, Fluorescence ; Microscopy, Video ; Organelles/*physiology ; }, abstract = {We describe remarkable diurnal changes in the morphology of the planktonic dinoflagellate Ceratium ranipes. The species is distinguished by the unusual appendages, known as toes or fingers, protruding from its horns. Varieties have been described based on the characteristics of the fingers. We discovered that cultures, maintained on a 12:12 photoperiod, when examined during the dark period were composed of 'finger-less' cells. Monitoring of isolated cells revealed a diurnal cycle of distinct changes in morphology with daytime cells showing appendages, well-stocked with chlorophyll, and the absence of the fingers at the end of the photoperiod. Fingers are absorbed at the end of the light period and re-grown at the end of the dark period. Sampling the Bay of Villefranche, we found the distinct morphologies in a natural population at night and during the day.}, }
@article {pmid19577923, year = {2009}, author = {Verstraete, W and Van de Caveye, P and Diamantis, V}, title = {Maximum use of resources present in domestic "used water".}, journal = {Bioresource technology}, volume = {100}, number = {23}, pages = {5537-5545}, doi = {10.1016/j.biortech.2009.05.047}, pmid = {19577923}, issn = {1873-2976}, mesh = {Bioreactors ; Cities ; Conservation of Natural Resources/economics ; *Energy-Generating Resources ; Environmental Monitoring ; Equipment Design ; Metals/chemistry ; Refuse Disposal/methods ; *Sewage ; Waste Disposal, Fluid/economics/methods ; Water Purification/*methods ; }, abstract = {Environmental protection and the sustainable management of natural resources stand at the foreground of economic and technological activities worldwide. Current sewage technologies, however, deal with diluted wastes and do not focus on recovery and are therefore not sustainable. Here, the most promising methods available for the recovery of nutrients (nitrogen, phosphorus), organic material and energy from "used waters" are examined both at the decentralised and centralised level. Novel approaches for water processing, not implementing aerobic biological treatment as a core technology, are conceived and critically evaluated regarding efficiency, diffuse emissions and requisite costs. By implementing up-concentration of dilute wastewaters, the concentrated stream becomes suitable for the waste-to-energy strategy. The approach of up-concentration of municipal effluent at arrival at the water treatment plant followed by anaerobic digestion of organics and maximal reuse of the mineral nutrients and water is estimated to have a total cost of the order 0.9 euros/m(3); the latter is comparable to that of conventional aerobic treatment technologies which has little or no reuse. It is argued that in view of the fact that recovered nutrients will become of increasing economic and ecological value, this new conceptual design for the treatment of "used water" will become feasible in the next decade.}, }
@article {pmid19572164, year = {2009}, author = {Li, M and Yang, H and Gu, JD}, title = {Phylogenetic diversity and axial distribution of microbes in the intestinal tract of the polychaete Neanthes glandicincta.}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {892-902}, pmid = {19572164}, issn = {1432-184X}, mesh = {Animals ; Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/classification/*genetics/isolation &amp; purification ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Intestines/microbiology ; *Phylogeny ; Polychaeta/*microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The phylogenetic diversity and axial distribution of microorganisms in three sections of the gastrointestinal tracts of the polychaete Neanthes glandicincta was evaluated using both most probable number method and cloning analyses of 16S rRNA genes in this study. Quantification of the density of microorganisms in the gut showed that aerobic microorganisms decreased from anterior to posterior, while anaerobic ones showed a reverse trend. The total numbers of microorganisms decreased significantly (p < 0.05, analysis of variance) but more rapidly from the anterior to the middle segment. Phylogenetic analysis showed that the dominating phylogenetic groups included Methanomicrobiales I: Methanosaetaceae (up to 66% of archaeal clones), delta-Proteobacteria (up to 42% of bacterial clones), and gamma-Proteobacteria (up to 30% of bacterial clones) widely distributed throughout the entire gut. Other microbiota distributed in different gut sections were Methanomicrobiales II: Methanospirillaceae, Methanomicrobiales III, Thermoplasmatales, Crenarchaea, Methanobacteriaceae, and Methanosarcinales for archaea; and alpha-Proteobacteria, beta-Proteobacteria, Fusobacteria, Clostridia, Chloroflexi, and Planctomycetes for bacteria. The results reveal a difference in microbial community structure along the gut of N. glandicincta. The various phylogenetic diversity and axial distribution of microbes along the gut might indicate an environmental gradient from anterior to posterior sections affecting the structure of the microbial community.}, }
@article {pmid19568805, year = {2009}, author = {Onstott, TC and McGown, DJ and Bakermans, C and Ruskeeniemi, T and Ahonen, L and Telling, J and Soffientino, B and Pfiffner, SM and Sherwood-Lollar, B and Frape, S and Stotler, R and Johnson, EJ and Vishnivetskaya, TA and Rothmel, R and Pratt, LM}, title = {Microbial communities in subpermafrost saline fracture water at the Lupin Au mine, Nunavut, Canada.}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {786-807}, pmid = {19568805}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; *Ecosystem ; Lipids/analysis ; Mining ; Nunavut ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Sulfur/analysis ; Water/*analysis/chemistry ; *Water Microbiology ; }, abstract = {We report the first investigation of a deep subpermafrost microbial ecosystem, a terrestrial analog for the Martian subsurface. Our multidisciplinary team analyzed fracture water collected at 890 and 1,130 m depths beneath a 540-m-thick permafrost layer at the Lupin Au mine (Nunavut, Canada). 14C, 3H, and noble gas isotope analyses suggest that the Na-Ca-Cl, suboxic, fracture water represents a mixture of geologically ancient brine, approximately25-kyr-old, meteoric water and a minor modern talik-water component. Microbial planktonic concentrations were approximately10(3) cells mL(-1). Analysis of the 16S rRNA gene from extracted DNA and enrichment cultures revealed 42 unique operational taxonomic units in 11 genera with Desulfosporosinus, Halothiobacillus, and Pseudomonas representing the most prominent phylotypes and failed to detect Archaea. The abundance of terminally branched and midchain-branched saturated fatty acids (5 to 15 mol%) was consistent with the abundance of Gram-positive bacteria in the clone libraries. Geochemical data, the ubiquinone (UQ) abundance (3 to 11 mol%), and the presence of both aerobic and anaerobic bacteria indicated that the environment was suboxic, not anoxic. Stable sulfur isotope analyses of the fracture water detected the presence of microbial sulfate reduction, and analyses of the vein-filling pyrite indicated that it was in isotopic equilibrium with the dissolved sulfide. Free energy calculations revealed that sulfate reduction and sulfide oxidation via denitrification and not methanogenesis were the most thermodynamically viable consistent with the principal metabolisms inferred from the 16S rRNA community composition and with CH4 isotopic compositions. The sulfate-reducing bacteria most likely colonized the subsurface during the Pleistocene or earlier, whereas aerobic bacteria may have entered the fracture water networks either during deglaciation prior to permafrost formation 9,000 years ago or from the nearby talik through the hydrologic gradient created during mine dewatering. Although the absence of methanogens from this subsurface ecosystem is somewhat surprising, it may be attributable to an energy bottleneck that restricts their migration from surface permafrost deposits where they are frequently reported. These results have implications for the biological origin of CH4 on Mars.}, }
@article {pmid19562247, year = {2009}, author = {Chénier, MR and Juteau, P}, title = {Impact of an aerobic thermophilic sequencing batch reactor on antibiotic-resistant anaerobic bacteria in swine waste.}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {773-785}, pmid = {19562247}, issn = {1432-184X}, mesh = {Animal Feed ; Animals ; Bacteria, Anaerobic/drug effects/*genetics/isolation &amp; purification ; Bioreactors/*microbiology ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/*genetics ; Genes, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Swine ; Waste Disposal, Fluid/*methods ; }, abstract = {The introduction of antibiotics to animal feed has contributed to the selection of antibiotic-resistant bacteria in concentrated animal feeding operations. The aim of this work was to characterize the impact of an aerobic thermophilic biotreatment on anaerobic antibiotic-resistant bacteria in swine waste. Despite 162- to 6,166-fold reduction in antibiotic-resistant populations enumerated in the swine waste at 25 degrees C and 37 degrees C, resistant populations remained significant (10(4) to 10(5) most probable number per milliliter) in the treated swine waste. Five resistance genes were detected before [tet(LMOS) erm(B)], and six resistance genes were detected after [tet(LMOSY) erm(B)] biotreatment. However, the biotreatment decreased the frequency of detection of resistance genes by 57%. Analysis by denaturing gradient gel electrophoresis of polymerase chain reaction-amplified 16 S ribosomal DNA (rDNA) fragments showed that the biotreatment reduced the bacterial diversity of resistant populations enumerated at 37 degrees C. Cloning and sequencing of the 16 S rDNA of these populations revealed that most clones in the treated swine waste were closely similar to some of the clones retrieved from the untreated swine waste. This study revealed that the aerobic thermophilic biotreatment developed in our laboratory does not prevent the introduction of facultatively anaerobic antibiotic-resistant bacteria and their resistance genes into agricultural ecosystems. Horizontal transfer of ecologically advantageous genes within microbial communities are likely to prevent thermophilic biotreatments from completely eliminating antibiotic-resistant bacteria and their resistance genes in animal wastes.}, }
@article {pmid19562246, year = {2010}, author = {Payne, R and Gauci, V and Charman, DJ}, title = {The impact of simulated sulfate deposition on peatland testate amoebae.}, journal = {Microbial ecology}, volume = {59}, number = {1}, pages = {76-83}, pmid = {19562246}, issn = {1432-184X}, mesh = {Biodiversity ; Environmental Monitoring ; Eukaryota/classification/*drug effects/growth &amp; development ; Soil ; Soil Pollutants/*toxicity ; *Sphagnopsida ; Statistics, Nonparametric ; Sulfates/*toxicity ; }, abstract = {Peatlands subjected to sulfate deposition have been shown to produce less methane, believed to be due to competitive exclusion of methanogenic archaea by sulfate-reducing bacteria. Here, we address whether sulfate deposition produces impacts on a higher microbial group, the testate amoebae. Sodium sulfate was applied to experimental plots on a Scottish peatland and samples extracted after a period of more than 10 years. Impacts on testate amoebae were tested using redundancy analysis and Mann-Whitney tests. Results showed statistically significant impacts on amoebae communities particularly noted by decreased abundance of Trinema lineare, Corythion dubium, and Euglypha rotunda. As the species most reduced in abundance are all small bacterivores we suggest that our results support the hypothesis of a shift in dominant prokaryotes, although other explanations are possible. Our results demonstrate the sensitivity of peatland microbial communities to sulfate deposition and suggest sulfate may be a potentially important secondary control on testate amoebae communities.}, }
@article {pmid19562245, year = {2009}, author = {Wu, L and Ma, K and Li, Q and Ke, X and Lu, Y}, title = {Composition of archaeal community in a paddy field as affected by rice cultivar and N fertilizer.}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {819-826}, pmid = {19562245}, issn = {1432-184X}, mesh = {Archaea/classification/*genetics/metabolism ; DNA Fingerprinting ; DNA, Archaeal/genetics ; *Ecosystem ; Fertilizers/*microbiology ; Multivariate Analysis ; Nitrogen/*metabolism ; Oryza/*microbiology ; Phylogeny ; Plant Roots/microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Methanogenesis in paddy fields is significantly influenced by environmental and field management factors such as rice cultivar and nitrogenous fertilizer. However, it has been unclear whether such effects are reflected in the structure of methanogenic archaeal populations. In the present study, molecular analyses including cloning and sequencing and terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of archaeal 16S rRNA genes were used to characterize the methanogenic archaeal assemblages and to identify the effect of environmental variables including rice cultivar and N fertilizer on archaeal community compositions in a Chinese paddy field soil. The correlation between methanogenic archaeal composition and environmental variables was explored by correspondence analysis. The results showed that the spatial or niche factor (rice roots versus rhizosphere, surface, and the deeper layer soils) had the greatest influence on the archaeal community composition. There was an obvious enrichment or selection of hydrogenotrophic as opposed to acetoclastic methanogens by rice roots. The archaeal community also changed, though slightly, between the rhizosphere and bulk soils and between the surface soil and the deeper layer soil. However, rice cultivar and N fertilizer appear to have an effect only on methanogens tightly associated with rice roots.}, }
@article {pmid19560796, year = {2009}, author = {Hennebel, T and Verhagen, P and Simoen, H and De Gusseme, B and Vlaeminck, SE and Boon, N and Verstraete, W}, title = {Remediation of trichloroethylene by bio-precipitated and encapsulated palladium nanoparticles in a fixed bed reactor.}, journal = {Chemosphere}, volume = {76}, number = {9}, pages = {1221-1225}, doi = {10.1016/j.chemosphere.2009.05.046}, pmid = {19560796}, issn = {1879-1298}, mesh = {Biodegradation, Environmental ; *Bioreactors ; Catalysis ; Kinetics ; Metal Nanoparticles/*chemistry/microbiology ; Palladium/*chemistry ; Polymers/chemistry ; Shewanella/metabolism ; Trichloroethylene/*metabolism ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Trichloroethylene is a toxic and recalcitrant groundwater pollutant. Palladium nanoparticles bio-precipitated on Shewanella oneidensis were encapsulated in polyurethane, polyacrylamide, alginate, silica or coated on zeolites. The reactivity of these bio-Pd beads and zeolites was tested in batch experiments and trichloroethylene dechlorination followed first order reaction kinetics. The calculated k-values of the encapsulated catalysts were a factor of six lower compared to non-encapsulated bio-Pd. Bio-Pd, used as a catalyst, was able to dechlorinate 100 mgL(-1) trichloroethylene within a time period of 1h. The main reaction product was ethane; yet small levels of chlorinated intermediates were detected. Subsequently polyurethane cubes empowered with bio-Pd were implemented in a fixed bed reactor for the treatment of water containing trichloroethylene. The influent recycle configuration resulted in a cumulative removal of 98% after 22 h. The same reactor in a flow through configuration achieved removal rates up to 1059 mg trichloroethylene g Pd(-1)d(-1). This work showed that fixed bed reactors with bio-Pd polyurethane cubes can be instrumental for remediation of water contaminated with trichloroethylene.}, }
@article {pmid19558511, year = {2009}, author = {Sandaa, RA and Gómez-Consarnau, L and Pinhassi, J and Riemann, L and Malits, A and Weinbauer, MG and Gasol, JM and Thingstad, TF}, title = {Viral control of bacterial biodiversity--evidence from a nutrient-enriched marine mesocosm experiment.}, journal = {Environmental microbiology}, volume = {11}, number = {10}, pages = {2585-2597}, doi = {10.1111/j.1462-2920.2009.01983.x}, pmid = {19558511}, issn = {1462-2920}, mesh = {Bacteria/genetics/*growth &amp; development/metabolism/*virology ; Bacteriophages/genetics/*growth &amp; development ; *Biodiversity ; Chlorophyll/biosynthesis ; Chlorophyll A ; DNA, Bacterial/analysis/genetics ; DNA, Viral/analysis/genetics ; Electrophoresis, Gel, Pulsed-Field ; Flow Cytometry ; Food ; Glucose/chemistry/metabolism ; Host-Pathogen Interactions ; Phosphates/chemistry/metabolism ; Seawater/chemistry/*microbiology ; Water Microbiology ; }, abstract = {We demonstrate here results showing that bottom-up and top-down control mechanisms can operate simultaneously and in concert in marine microbial food webs, controlling prokaryote diversity by a combination of viral lysis and substrate limitation. Models in microbial ecology predict that a shift in the type of bacterial growth rate limitation is expected to have a major effect on species composition within the community of bacterial hosts, with a subsequent shift in the composition of the viral community. Only moderate effects would, however, be expected in the absolute number of coexisting virus-host pairs. We investigated these relationships in nutrient-manipulated systems, under simulated in situ conditions. There was a strong correlation in the clustering of the viral and bacterial community data supporting the existence of an important link between the bacterial and viral communities. As predicted, the total number of viral populations was the same in all treatments, while the composition of the viral community varied. Our results support the theoretical prediction that there is one control mechanism for the number of niches for coexisting virus-host pairs (top-down control), and another mechanism that controls which virus-host pairs occupy these niches (bottom-up control).}, }
@article {pmid19557310, year = {2009}, author = {Clauwaert, P and Desloover, J and Shea, C and Nerenberg, R and Boon, N and Verstraete, W}, title = {Enhanced nitrogen removal in bio-electrochemical systems by pH control.}, journal = {Biotechnology letters}, volume = {31}, number = {10}, pages = {1537-1543}, doi = {10.1007/s10529-009-0048-8}, pmid = {19557310}, issn = {1573-6776}, mesh = {*Bioelectric Energy Sources ; Electricity ; Hydrogen-Ion Concentration ; Nitrogen/*metabolism ; *Water Microbiology ; }, abstract = {Microbial fuel cells can be designed to remove nitrogenous compounds out of wastewater, but their performance is at present limited to 0.33 kg NO(3) (-)-Nm(-3) net cathode compartment (NCC) d(-1). By maintaining the pH in the cathode at 7.2, nitrogen removal was increased from 0.22 to 0.50 kg NO(3) (-)-Nm(-3) NCC d(-1). Bio-electrochemical active microorganisms seem to struggle with the deterioration of their own environment due to slow proton fluxes. Therefore, the results suggest that an appropriate pH adjustment strategy is necessary to allow a sustained and enhanced biological activity in bio-electrochemical systems.}, }
@article {pmid19554362, year = {2009}, author = {Gantar, M and Sekar, R and Richardson, LL}, title = {Cyanotoxins from black band disease of corals and from other coral reef environments.}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {856-864}, pmid = {19554362}, issn = {1432-184X}, support = {S06 GM008205/GM/NIGMS NIH HHS/United States ; S11 ES011181/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Anthozoa/*microbiology ; Bacterial Toxins/*biosynthesis ; Cyanobacteria/classification/growth &amp; development/isolation &amp; purification/*metabolism ; Cyanobacteria Toxins ; DNA, Bacterial/genetics ; Environment ; Glucose/metabolism ; Light ; Marine Toxins/*biosynthesis ; Microcystins/*biosynthesis ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; }, abstract = {Many cyanobacteria produce cyanotoxins, which has been well documented from freshwater environments but not investigated to the same extent in marine environments. Cyanobacteria are an obligate component of the polymicrobial disease of corals known as black band disease (BBD). Cyanotoxins were previously shown to be present in field samples of BBD and in a limited number of BBD cyanobacterial cultures. These toxins were suggested as one of the mechanisms contributing to BBD-associated coral tissue lysis and death. In this work, we tested nine cyanobacterial isolates from BBD and additionally nine isolated from non-BBD marine sources for their ability to produce toxins. The presence of toxins was determined using cell extracts of laboratory grown cyanobacterial cultures using ELISA and the PP2A assay. Based on these tests, it was shown that cyanobacterial toxins belonging to the microcystin/nodularin group were produced by cyanobacteria originating from both BBD and non-BBD sources. Several environmental factors that can be encountered in the highly dynamic microenvironment of BBD were tested for their effect on both cyanobacterial growth yield and rate of toxin production using two of the BBD isolates of the genera Leptolyngbya and Geitlerinema. While toxin production was the highest under mixotrophic conditions (light and glucose) for the Leptolyngbya isolate, it was highest under photoautotrophic conditions for the Geitlerinema isolate. Our results show that toxin production among marine cyanobacteria is more widespread than previously documented, and we present data showing three marine cyanobacterial genera (Phormidium, Pseudanabaena, and Spirulina) are newly identified as cyanotoxin producers. We also show that cyanotoxin production by BBD cyanobacteria can be affected by environmental factors that are present in the microenvironment associated with this coral disease.}, }
@article {pmid19554037, year = {2009}, author = {McKeown, RM and Scully, C and Enright, AM and Chinalia, FA and Lee, C and Mahony, T and Collins, G and O'Flaherty, V}, title = {Psychrophilic methanogenic community development during long-term cultivation of anaerobic granular biofilms.}, journal = {The ISME journal}, volume = {3}, number = {11}, pages = {1231-1242}, doi = {10.1038/ismej.2009.67}, pmid = {19554037}, issn = {1751-7370}, mesh = {Anaerobiosis ; Bacteria/classification/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; *Biofilms ; Bioreactors/microbiology ; *Culture Techniques ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Hydrogen/metabolism ; Methane/*metabolism ; Methanosarcinaceae/classification/genetics/isolation &amp; purification/*physiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Temperature ; }, abstract = {Granular biomass was temporally sampled from a cold (4-15 degrees C) anaerobic bioreactor, which was inoculated with mesophilic biomass and used to treat industrial wastewater in a long-term (3.4 year) study. Data from 16S rRNA gene clone libraries, quantitative PCR and terminal restriction fragment length polymorphism analyses indicated that microbial community structure was dynamic, with shifts in the archaeal and bacterial communities' structures observed following start-up and during temperature decreases from 15 to 9.5 degrees C (phase 1). Specifically, the relative abundance of architecturally important Methanosaeta-like (acetoclastic) methanogens decreased, which was concomitant with granule disintegration and the development of a putatively psychrophilic hydrogenotrophic methanogenic community. Genetic fingerprinting suggested the development of a psychroactive methanogenic community between 4 and 10 degrees C (phase 2), which was dominated by acetogenic bacteria and Methanocorpusculum-like (hydrogenotrophic) methanogens. High levels of Methanosaeta-like acetoclastic methanogens and granular biofilm integrity were maintained during phase 2. Overall, decreasing temperature resulted in distinctly altered microbial community structure during phase 1, and the development of a less dynamic psychroactive methanogenic consortium during phase 2. Moreover, psychrophilic H(2)-oxidizing methanogens emerged as important members of the psychroactive consortia after >1200 days of low-temperature cultivation. The data suggest that prolonged psychrophilic cultivation of mesophilic biomass can establish a well-functioning psychroactive methanogenic consortium, thus highlighting the potential of low-temperature anaerobic digestion technology.}, }
@article {pmid19549860, year = {2009}, author = {Crawford, PA and Crowley, JR and Sambandam, N and Muegge, BD and Costello, EK and Hamady, M and Knight, R and Gordon, JI}, title = {Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {27}, pages = {11276-11281}, pmid = {19549860}, issn = {1091-6490}, support = {R01 DK070977/DK/NIDDK NIH HHS/United States ; P30 DK056341/DK/NIDDK NIH HHS/United States ; DK052574/DK/NIDDK NIH HHS/United States ; DK70977/DK/NIDDK NIH HHS/United States ; P30 DK020579/DK/NIDDK NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; DK020579/DK/NIDDK NIH HHS/United States ; P60 DK020579/DK/NIDDK NIH HHS/United States ; DK073282/DK/NIDDK NIH HHS/United States ; T32 GM065103/GM/NIGMS NIH HHS/United States ; DK56341/DK/NIDDK NIH HHS/United States ; K08 DK073282/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Fasting/*physiology ; Food ; Gastrointestinal Tract/*microbiology ; Genomics ; Germ-Free Life ; Glucose/metabolism ; Hypertrophy ; In Vitro Techniques ; Ketone Bodies/*metabolism ; Liver/metabolism ; *Metagenome ; Mice ; Myocardium/*metabolism/pathology ; Organ Size ; Oxidation-Reduction ; Perfusion ; Physical Endurance ; }, abstract = {Studies in mice indicate that the gut microbiota promotes energy harvest and storage from components of the diet when these components are plentiful. Here we examine how the microbiota shapes host metabolic and physiologic adaptations to periods of nutrient deprivation. Germ-free (GF) mice and mice who had received a gut microbiota transplant from conventionally raised donors were compared in the fed and fasted states by using functional genomic, biochemical, and physiologic assays. A 24-h fast produces a marked change in gut microbial ecology. Short-chain fatty acids generated from microbial fermentation of available glycans are maintained at higher levels compared with GF controls. During fasting, a microbiota-dependent, Ppar alpha-regulated increase in hepatic ketogenesis occurs, and myocardial metabolism is directed to ketone body utilization. Analyses of heart rate, hydraulic work, and output, mitochondrial morphology, number, and respiration, plus ketone body, fatty acid, and glucose oxidation in isolated perfused working hearts from GF and colonized animals (combined with in vivo assessments of myocardial physiology) revealed that the fasted GF heart is able to sustain its performance by increasing glucose utilization, but heart weight, measured echocardiographically or as wet mass and normalized to tibial length or lean body weight, is significantly reduced in both fasted and fed mice. This myocardial-mass phenotype is completely reversed in GF mice by consumption of a ketogenic diet. Together, these results illustrate benefits provided by the gut microbiota during periods of nutrient deprivation, and emphasize the importance of further exploring the relationship between gut microbes and cardiovascular health.}, }
@article {pmid19547939, year = {2009}, author = {Palacios, C and Zbinden, M and Pailleret, M and Gaill, F and Lebaron, P}, title = {Highly similar prokaryotic communities of sunken wood at shallow and deep-sea sites across the oceans.}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {737-752}, pmid = {19547939}, issn = {1432-184X}, mesh = {Archaea/*growth &amp; development/isolation &amp; purification ; Bacteria/*growth &amp; development/isolation &amp; purification ; Biodegradation, Environmental ; DNA, Archaeal/analysis ; DNA, Bacterial/analysis ; Microscopy, Electron ; Oceans and Seas ; Polymorphism, Single-Stranded Conformational ; Seawater/*microbiology ; *Water Microbiology ; Wood/*microbiology ; }, abstract = {With an increased appreciation of the frequency of their occurrence, large organic falls such as sunken wood and whale carcasses have become important to consider in the ecology of the oceans. Organic-rich deep-sea falls may play a major role in the dispersal and evolution of chemoautotrophic communities at the ocean floor, and chemosynthetic symbiotic, free-living, and attached microorganisms may drive the primary production at these communities. However, little is known about the microbiota thriving in and around organic falls. Our aim was to investigate and compare free-living and attached communities of bacteria and archaea from artificially immersed and naturally sunken wood logs with varying characteristics at several sites in the deep sea and in shallow water to address basic questions on the microbial ecology of sunken wood. Multivariate indirect ordination analyses of capillary electrophoresis single-stranded conformation polymorphisms (CE-SSCP) fingerprinting profiles demonstrated high similarity of bacterial and archaeal assemblages present in timbers and logs situated at geographically distant sites and at different depths of immersion. This similarity implies that wood falls harbor a specialized microbiota as observed in other ecosystems when the same environmental conditions reoccur. Scanning and transmission electron microscopy observations combined with multivariate direct gradient analysis of Bacteria CE-SSCP profiles demonstrate that type of wood (hard vs. softwood), and time of immersion are important in structuring sunken wood bacterial communities. Archaeal populations were present only in samples with substantial signs of decay, which were also more similar in their bacterial assemblages, providing indirect evidence of temporal succession in the microbial communities that develop in and around wood falls.}, }
@article {pmid19547938, year = {2010}, author = {Maeda, K and Morioka, R and Hanajima, D and Osada, T}, title = {The impact of using mature compost on nitrous oxide emission and the denitrifier community in the cattle manure composting process.}, journal = {Microbial ecology}, volume = {59}, number = {1}, pages = {25-36}, pmid = {19547938}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/*genetics/metabolism ; Base Sequence ; Cattle ; Genes, Bacterial/genetics ; Manure/*microbiology ; Molecular Sequence Data ; Nitrous Oxide/*metabolism ; Phylogeny ; Pseudomonas/genetics/metabolism ; *Soil ; Waste Management/*methods ; }, abstract = {The diversity and dynamics of the denitrifying genes (nirS, nirK, and nosZ) encoding nitrite reductase and nitrous oxide (N(2)O) reductase in the dairy cattle manure composting process were investigated. A mixture of dried grass with a cattle manure compost pile and a mature compost-added pile were used, and denaturing gradient gel electrophoresis was used for denitrifier community analysis. The diversity of nirK and nosZ genes significantly changed in the initial stage of composting. These variations might have been induced by the high temperature. The diversity of nirK was constant after the initial variation. On the other hand, the diversity of nosZ changed in the latter half of the process, a change which might have been induced by the accumulation of nitrate and nitrite. The nirS gene fragments could not be detected. The use of mature compost that contains nitrate and nitrite promoted the N(2)O emission and significantly affected the variation of nosZ diversity in the initial stage of composting, but did not affect the variation of nirK diversity. Many Pseudomonas-like nirK and nosZ gene fragments were detected in the stage in which N(2)O was actively emitted.}, }
@article {pmid19543938, year = {2009}, author = {Vezzulli, L and Pezzati, E and Moreno, M and Fabiano, M and Pane, L and Pruzzo, C and , }, title = {Benthic ecology of Vibrio spp. and pathogenic Vibrio species in a coastal Mediterranean environment (La Spezia Gulf, Italy).}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {808-818}, pmid = {19543938}, issn = {1432-184X}, mesh = {Biodiversity ; DNA, Bacterial/analysis ; *Ecosystem ; Geologic Sediments/*microbiology ; Mediterranean Sea ; Regression Analysis ; Seasons ; Seawater/*microbiology ; Temperature ; Vibrio/growth &amp; development/*isolation &amp; purification ; *Water Microbiology ; }, abstract = {We carried out a 16-month in situ study to investigate the ecology of Vibrio spp. and pathogenic Vibrio species in coastal sediments of the Mediterranean Sea, employing multiple-regression analysis to reveal the major environmental factors controlling their occurrence in the benthic environment. In addition, association between vibrios and sediment-inhabiting meiofauna, which is a major component of benthic ecosystems, was investigated. Culturable and total Vibrio spp. estimates by most-probable-number technique coupled with standard polymerase chain reaction (PCR) and real-time PCR methods, respectively, were at least one order of magnitude higher in sediment than in seawater. In addition, potential human pathogenic species Vibrio cholerae, Vibrio vulnificus and Vibrio parahaemolyticus occurred in the sediment with V. parahaemolyticus being the most frequently found. In the pelagic environment, 60% of total variance in culturable Vibrio data was explained by sea surface temperature (40%), salinity (13%) and organic matter concentration (7%). In the benthic environment, sea surface temperature was the only factor that significantly affected culturable Vibrio occurrence although it explained only 25% of total variance, suggesting that additional unexplored factors may play a role as well. No correlation was found between culturable Vibrio spp. concentrations and the abundance of harpacticoid copepods in the sediment whilst a negative correlation was found between Vibrio spp. and nematode abundance which accounted for almost 90% of the total meiofaunal density. Taxonomic analysis revealed that selective bacterial feeders accounted for nearly 50% of the total nematode community and included genera such as Terschellingia, Molgolaimus and Halalaimus, suggesting that top-down control by nematode grazing may be an important factor affecting Vibrio occurrence in these sediments. It is concluded that the benthic marine environment may function as a reservoir of Vibrio spp. and potential pathogenic vibrios whose ecological features appeared substantially different from the ones recognised in the pelagic environment.}, }
@article {pmid19543937, year = {2009}, author = {Morales-Jiménez, J and Zúñiga, G and Villa-Tanaca, L and Hernández-Rodríguez, C}, title = {Bacterial community and nitrogen fixation in the red turpentine beetle, Dendroctonus valens LeConte (Coleoptera: Curculionidae: Scolytinae).}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {879-891}, pmid = {19543937}, issn = {1432-184X}, mesh = {Acetylene/metabolism ; Animals ; Bacteria/classification/*genetics/isolation &amp; purification ; Biodiversity ; Coleoptera/*metabolism/*microbiology ; DNA, Bacterial/genetics ; Gastrointestinal Tract/microbiology ; Gene Library ; *Nitrogen Fixation ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The red turpentine beetle, Dendroctonus valens LeConte (Coleoptera: Curculionidae: Scolytinae), colonizes all pines species within its native range throughout North and Central America. Recently, this species was accidentally introduced to China, where it has caused severe damage in pine forests. It belongs to a group of beetles that spend most of their lives between the tree bark and sapwood, where it feeds on phloem: a poor substrate with very low nutritional value of nitrogen and toxic properties due to its high content of secondary defensive compounds. The aim of this study was to characterize the bacterial community of the D. valens gut by culture-dependent and -independent methods. Polymerase chain reaction denaturing gradient gel electrophoresis and ribosomal gene library analyses revealed that species diversity in the D. valens gut was relatively low, containing between six and 17 bacterial species. The bacterial community associated with larvae and adults was dominated by members of the following genera: Lactococcus, Acinetobacter, Pantoea, Rahnella, Stenothrophomonas, Erwinia, Enterobacter, Serratia, Janibacter, Leifsonia, Cellulomonas, and Cellulosimicrobium. The members of the last four genera showed cellulolytic activity in vitro and could be involved in cellulose breakdown in the insect gut. Finally, nitrogen fixation was demonstrated in live larvae and adults; however, capacity of nitrogen fixing in vitro was not found among enterobacterial species isolated in nitrogen-free media; neither were nifD nor nifH genes detected. In contrast, nifD gen was detected in metagenomic DNA from insect guts. The identification of bacterial species and their potential physiological capacities will allow exploring the role of gut symbiotic bacteria in the adaptation and survival of D. valens in a harsh chemical habitat poor in nitrogen sources.}, }
@article {pmid19542109, year = {2009}, author = {Gordon, NS and Valenzuela, A and Adams, SM and Ramsey, PW and Pollock, JL and Holben, WE and Gannon, JE}, title = {Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {59}, number = {Pt 7}, pages = {1720-1726}, doi = {10.1099/ijs.0.000158-0}, pmid = {19542109}, issn = {1466-5026}, mesh = {Bacterial Typing Techniques ; Bacteroidetes/*classification/genetics/isolation &amp; purification/physiology ; DNA, Bacterial/analysis ; *Floods ; Genes, rRNA ; Genotype ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Montana ; Phenotype ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Species Specificity ; Tracheophyta ; *Trees ; }, abstract = {Three Gram-negative, rod-shaped, non-spore-forming eubacterial strains were isolated in western Montana, USA, and subjected to taxonomic studies. Strains NWG-II14(T) and NWER-II11(T) were isolated from hyporheic sediments of a large alluvial flood plain, whereas strain G-1(T) was isolated from a conifer forest soil. On the basis of 16S rRNA gene sequence similarity, strains NWG-II14(T), NWER-II11(T) and G-1(T) were shown to belong to the family Sphingobacteriaceae and are most closely related to various species of the genus Pedobacter. The results of molecular, physiological and biochemical tests allowed genotypic and phenotypic differentiation of these three strains from 23 Pedobacter species with validly published names. The three isolates therefore represent novel species, for which the names Pedobacter nyackensis sp. nov. (type strain NWG-II14(T) =DSM 19625(T) =LMG 24260(T)), Pedobacter alluvionis sp. nov. (type strain NWER-II11(T) =DSM 19624(T) =LMG 24258(T)) and Pedobacter borealis sp. nov. (type strain G-1(T) =DSM 19626(T) =LMG 24259(T)) are proposed.}, }
@article {pmid19539975, year = {2009}, author = {O'Reilly, J and Lee, C and Collins, G and Chinalia, F and Mahony, T and O'Flaherty, V}, title = {Quantitative and qualitative analysis of methanogenic communities in mesophilically and psychrophilically cultivated anaerobic granular biofilims.}, journal = {Water research}, volume = {43}, number = {14}, pages = {3365-3374}, doi = {10.1016/j.watres.2009.03.039}, pmid = {19539975}, issn = {1879-2448}, mesh = {Anaerobiosis ; Archaea/genetics/*growth &amp; development ; Biofilms/*growth &amp; development ; Bioreactors/microbiology ; *Cold Temperature ; Electrophoresis ; Methane/*metabolism ; Oxygen/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Anaerobic granulation describes the self-immobilisation of methanogenic consortia into dense, particulate biofilms. This procedure underpins the operation of several categories of high-rate anaerobic wastewater treatment system. Full-scale anaerobic granular sludge plants have been generally operated in the mesophilic (20-45 degrees C) or thermophilic (45-65 degrees C) temperature range. On the other hand, recent studies highlighted the economic advantages of treating wastewaters at their discharge temperatures (mostly under 18 degrees C), removing a costly heating process and increasing net biogas yield. However, as yet, relatively little information is available about the microbial behaviour and interactions in anaerobic granular sludge formed under psychrophilic conditions. To this end, and in order to provide a microbial insight into low-temperature anaerobic granulation, we monitored the changes in methanogenic community structure, associated with the changes in process performance. Three, laboratory-scale, expanded granular sludge bed (EGSB) bioreactors treating a synthetic glucose wastewater were tested at two temperatures of 37+/-1 degrees C (R1) and 15+/-1 degrees C (R2 and 3). Quantitative real-time PCR and specific methanogenic activity assays highlighted a community shift towards hydrogenotrophic methanogens, particularly the order Methanomicrobiales in the low-temperature bioreactors. Corresponding to this, denaturing gradient gel electrophoresis (DGGE) analysis identified the emergence and maintenance of a Methanocorpusculum-like organism. Our results indicate that hydrogenotrophic methanogens, particularly the Methanomicrobiales-related populations, are likely to play important roles in low-temperature anaerobic granular sludge systems. This suggests that the process efficiency could be improved by facilitating the growth and retention of this group.}, }
@article {pmid19536588, year = {2010}, author = {Segarra, G and Casanova, E and Avilés, M and Trillas, I}, title = {Trichoderma asperellum strain T34 controls Fusarium wilt disease in tomato plants in soilless culture through competition for iron.}, journal = {Microbial ecology}, volume = {59}, number = {1}, pages = {141-149}, pmid = {19536588}, issn = {1432-184X}, mesh = {Culture Media/chemistry ; Food Chain ; Fusarium/growth &amp; development/*metabolism ; Iron/analysis/*metabolism ; Solanum lycopersicum/metabolism/*microbiology ; Microbial Interactions ; Pest Control, Biological ; Plant Diseases/*microbiology ; Trichoderma/growth &amp; development/*metabolism ; }, abstract = {Trichoderma asperellum strain T34 has been reported to control the disease caused by Fusarium oxysporum f.sp. lycopersici (Fol) on tomato plants. To study the importance of iron concentration in the growth media for the activity and competitiveness of T34 and the pathogen, we tested four iron concentrations in the nutrient solution [1, 10, 100, and 1000 microM provided as EDTA/Fe(III)] in a biological control experiment with T34 and Fol in tomato plants. The reduction of the Fusarium-infected shoot by T34 was only significant at 10 microM Fe. We hypothesized that Fe competition is one of the key factors in the biocontrol activity exerted by T34 against Fol, as an increase in Fe concentration over 10 microM would lead to the suppression of T34 siderophore synthesis and thus inhibition of Fe competition with Fol. T34 significantly reduced the populations of Fol at all the doses of Fe assayed. In contrast, Fol enhanced the populations of T34 at 1 and 10 microM Fe. Nevertheless, several plant physiological parameters like net CO(2) assimilation (A), stomatal conductance (g(s)), relative quantum efficiency of PSII (Phi(PSII)), and efficiency of excitation energy capture by open PSII reactive centers (Fv'/Fm') demonstrated the protection against Fol damage by treatment with T34 at 100 microM Fe. The first physiological parameter affected by the disease progression was g(s). Plant dry weight was decreased by Fe toxicity at 100 and 1,000 microM. T34-treated plants had significantly greater heights and dry weights than control plants at 1,000 microM Fe, even though T34 did not reduce the Fe content in leaves or stems. Furthermore, T34 enhanced plant height even at the optimal Fe concentration (10 microM) compared to control plants. In conclusion, T. asperellum strain T34 protected tomato plants from both biotic (Fusarium wilt disease) and abiotic stress [Fe(III) toxic effects].}, }
@article {pmid19536195, year = {2009}, author = {Drigo, B and van Veen, JA and Kowalchuk, GA}, title = {Specific rhizosphere bacterial and fungal groups respond differently to elevated atmospheric CO(2).}, journal = {The ISME journal}, volume = {3}, number = {10}, pages = {1204-1217}, doi = {10.1038/ismej.2009.65}, pmid = {19536195}, issn = {1751-7370}, mesh = {Bacteria/*classification/*isolation &amp; purification/metabolism ; Carbohydrate Metabolism ; Carbon Dioxide/*metabolism ; Chromatography, High Pressure Liquid ; Cyperaceae/metabolism/microbiology ; DNA Fingerprinting ; Electrophoresis, Polyacrylamide Gel ; Festuca/metabolism/microbiology ; Fungi/*classification/*isolation &amp; purification/metabolism ; Nucleic Acid Denaturation ; Peptide Elongation Factor 1/genetics ; Plant Roots/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Soil community responses to increased atmospheric CO(2) concentrations are expected to occur mostly through interactions with changing vegetation patterns and plant physiology. To gain insight into the effects of elevated atmospheric CO(2) on the composition and functioning of microbial communities in the rhizosphere, Carex arenaria (a non-mycorrhizal plant species) and Festuca rubra (a mycorrhizal plant species) were grown under defined atmospheric conditions with either ambient (350 p.p.m.) or elevated (700 p.p.m.) CO(2) concentrations. PCR-DGGE (PCR-denaturing gradient gel electrophoresis) and quantitative-PCR were carried out to analyze, respectively, the structure and abundance of the communities of actinomycetes, Fusarium spp., Trichoderma spp., Pseudomonas spp., Burkholderia spp. and Bacillus spp. Responses of specific functional groups, such as phloroglucinol, phenazine and pyrrolnitrin producers, were also examined by quantitative-PCR, and HPLC (high performance liquid chromatography) was employed to assess changes in exuded sugars in the rhizosphere. Multivariate analysis of group-specific community profiles showed disparate responses to elevated CO(2) for the different bacterial and fungal groups examined, and these responses were dependent on plant type and soil nutrient availability. Within the bacterial community, the genera Burkholderia and Pseudomonas, typically known as successful rhizosphere colonizers, were significantly influenced by elevated CO(2), whereas the genus Bacillus and actinomycetes, typically more dominant in bulk soil, were not. Total sugar concentrations in the rhizosphere also increased in both plants in response to elevated CO(2). The abundances of phloroglucinol-, phenazine- and pyrrolnitrin-producing bacterial communities were also influenced by elevated CO(2), as was the abundance of the fungal genera Fusarium and Trichoderma.}, }
@article {pmid19535244, year = {2009}, author = {De Clippeleir, H and Vlaeminck, SE and Carballa, M and Verstraete, W}, title = {A low volumetric exchange ratio allows high autotrophic nitrogen removal in a sequencing batch reactor.}, journal = {Bioresource technology}, volume = {100}, number = {21}, pages = {5010-5015}, doi = {10.1016/j.biortech.2009.05.031}, pmid = {19535244}, issn = {1873-2976}, mesh = {Aerobiosis ; Anaerobiosis ; *Autotrophic Processes ; Biodegradation, Environmental ; Biomass ; Bioreactors/*microbiology ; Nitrates/analysis ; Nitrites/analysis ; Nitrogen/*isolation &amp; purification ; Quaternary Ammonium Compounds/analysis ; Rotation ; }, abstract = {Sequencing batch reactors (SBRs) have several advantages, such as a lower footprint and a higher flexibility, compared to biofilm based reactors, such as rotating biological contactors. However, the critical parameters for a fast start-up of the nitrogen removal by oxygen-limited autotrophic nitrification/denitrification (OLAND) in a SBR are not available. In this study, a low critical minimum settling velocity (0.7 m h(-1)) and a low volumetric exchange ratio (25%) were found to be essential to ensure a fast start-up, in contrast to a high critical minimum settling velocity (2 m h(-1)) and a high volumetric exchange ratio (40%) which yielded no successful start-up. To prevent nitrite accumulation, two effective actions were found to restore the microbial activity balance between aerobic and anoxic ammonium-oxidizing bacteria (AerAOB and AnAOB). A daily biomass washout at a critical minimum settling velocity of 5 m h(-1) removed small aggregates rich in AerAOB activity, and the inclusion of an anoxic phase enhanced the AnAOB to convert the excess nitrite. This study showed that stable physicochemical conditions were needed to obtain a competitive nitrogen removal rate of 1.1 g N L(-1) d(-1).}, }
@article {pmid19534605, year = {2009}, author = {Denou, E and Rezzonico, E and Panoff, JM and Arigoni, F and Brüssow, H}, title = {A Mesocosm of Lactobacillus johnsonii, Bifidobacterium longum, and Escherichia coli in the mouse gut.}, journal = {DNA and cell biology}, volume = {28}, number = {8}, pages = {413-422}, doi = {10.1089/dna.2009.0873}, pmid = {19534605}, issn = {1557-7430}, mesh = {Animals ; Antibiosis ; Bifidobacterium/genetics/*growth &amp; development ; Cecum/microbiology ; Colon/microbiology ; Colony Count, Microbial ; Ecosystem ; Escherichia coli/growth &amp; development ; Escherichia coli K12/*growth &amp; development ; Feces/microbiology ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Germ-Free Life ; Ileum/microbiology ; Intestinal Mucosa/microbiology ; Intestines/*microbiology ; Jejunum/microbiology ; Lactobacillus/genetics/*growth &amp; development ; Mice ; Mice, Inbred C3H ; Oligonucleotide Array Sequence Analysis ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {The relative contribution of competition and cooperation at the microbe-microbe level is not well understood for the bacteria constituting the gut microbiota. The high number and variability of human gut commensals have hampered the analysis. To get some insight into the question how so many different bacterial species can coexist in the mammalian gut, we studied the interaction between three human gut commensals (Escherichia coli K-12, Lactobacillus johnsonii NCC533, and Bifidobacterium longum NCC2705) in the intestine of gnotobiotic mice. The bacterial titers and their anatomical distribution were studied in the colonized mice. L. johnsonii achieved the highest cell counts in the stomach, while B. longum dominated the colon. The colon was also the intestinal location in which B. longum displayed the highest number of expressed genes, followed by the cecum and the small intestine. Addition of further bacterial strains led to strikingly different results. A Lactobacillus paracasei strain coexisted, while a second B. longum strain was excluded from the system. Notably, this strain lacked an operon involved in the degradation, import, and metabolism of mannosylated glycans. Subsequent introduction of the E. coli Nissle strain resulted in the elimination of L. johnsonii NCC533 and E. coli K-12, while B. longum NCC2705 showed a transient decrease in population size, demonstrating the dynamic nature of microbe-microbe interactions. The study of such simple interacting bacterial systems might help to derive some basic rules governing microbial ecology within the mammalian gut.}, }
@article {pmid19530077, year = {2009}, author = {Lee, HS and Krajmalinik-Brown, R and Zhang, H and Rittmann, BE}, title = {An electron-flow model can predict complex redox reactions in mixed-culture fermentative bioH2: microbial ecology evidence.}, journal = {Biotechnology and bioengineering}, volume = {104}, number = {4}, pages = {687-697}, doi = {10.1002/bit.22442}, pmid = {19530077}, issn = {1097-0290}, mesh = {Acetates/metabolism ; Bacteria/*metabolism ; *Biodiversity ; Bioreactors/*microbiology ; Clostridium/growth &amp; development/metabolism ; *Ecosystem ; Hydrogen/*metabolism ; Hydrogen-Ion Concentration ; Klebsiella pneumoniae/growth &amp; development/metabolism ; Lactic Acid/metabolism ; Models, Theoretical ; Oxidation-Reduction ; }, abstract = {We developed the first model for predicting community structure in mixed-culture fermentative biohydrogen production using electron flows and NADH2 balances. A key assumption of the model is that H2 is produced only via the pyruvate decarboxylation-ferredoxin-hydrogenase pathway, which is commonly the case for fermentation by Clostridium and Ethanoligenens species. We experimentally tested the model using clone libraries to gauge community structures with mixed cultures in which we did not pre-select for specific bacterial groups, such as spore-formers. For experiments having final pHs 3.5 and 4.0, where H2 yield and soluble end-product distribution were distinctly different, we established stoichiometric reactions for each condition by using experimentally determined electron equivalent balances. The error in electron balancing was only 3% at final pH 3.5, in which butyrate and acetate were dominant organic products and the H2 yield was 2.1 mol H2/mol glucose. Clone-library analysis showed that clones affiliated with Clostridium sp. BL-22 and Clostridium sp. HPB-16 were dominant at final pH 3.5. For final pH 4.0, the H2 yield was 0.9 mol H2/mol glucose, ethanol, and acetate were the dominant organic products, and the electron balance error was 13%. The significant error indicates that a second pathway for H2 generation was active. The most abundant clones were affiliated with Klebsiella pneumoniae, which uses the formate-cleavage pathway for H2 production. Thus, the clone-library analyses confirmed that the model predictions for when the pyruvate decarboxylation-ferredoxin-hydrogenase pathway was (final pH 3.5) or was not (final pH 4.0) dominant. With the electron-flow model, we can easily assess the main mechanisms for H2 formation and the dominant H2-producing bacteria in mixed-culture fermentative bioH2.}, }
@article {pmid19525871, year = {2009}, author = {Abrahamsson, TR and Sinkiewicz, G and Jakobsson, T and Fredrikson, M and Björkstén, B}, title = {Probiotic lactobacilli in breast milk and infant stool in relation to oral intake during the first year of life.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {49}, number = {3}, pages = {349-354}, doi = {10.1097/MPG.0b013e31818f091b}, pmid = {19525871}, issn = {1536-4801}, mesh = {Adult ; Bifidobacterium/isolation &amp; purification ; Clostridioides difficile/isolation &amp; purification ; Colony Count, Microbial ; Colostrum/*microbiology ; *Dietary Supplements ; Double-Blind Method ; Feces/*microbiology ; Female ; Humans ; Hypersensitivity ; Infant ; Limosilactobacillus reuteri/*isolation &amp; purification ; Milk, Human/*microbiology ; Pregnancy ; Probiotics/*administration &amp; dosage/isolation &amp; purification ; }, abstract = {OBJECTIVES: This is to identify factors affecting the prevalence of Lactobacillus reuteri in maternal faeces and breast milk and infant faeces after oral supplementation with L reuteri and to assess the influence on microbial ecology, particularly Clostridium difficile and Bifidobacterium colonization.<br><br>MATERIALS AND METHODS: In this double-blind trial, 232 mothers with a family history of atopic disease were randomized to a daily intake of either L reuteri American-type culture collection (ATCC) 55730 (1 x 10 colony-forming units [CFU]) or placebo for the last 4 weeks of pregnancy. Their babies then continued with the same study product daily from birth until 12 months of age. Bacterial counts and prevalence were assessed in maternal breast milk and faeces and infant faeces, using conventional cultivation methods.<br><br>RESULTS: The prevalence of L reuteri was higher during the first year of life in the stool samples from infants in the active as compared with the placebo-treated group. The highest prevalence was recorded at 5 to 6 days of age (82% in the treated vs 20% in the placebo group, P < 0.001). Lactobacillus reuteri was isolated from 12% and 2%, respectively, in the colostrum samples (P < 0.05). Breast-feeding seemed to reduce faecal L reuteri counts, although antibiotics did not influence the levels of L reuteri. The administration of L reuteri did not affect bifidobacteria or C difficile colonization.<br><br>CONCLUSION: Lactobacillus reuteri may be detected in breast milk after oral supplementation to the mother and in almost all infants after oral supplementation during the first year of life, as well as occasionally in many untreated infants.}, }
@article {pmid19521866, year = {2009}, author = {Hiett, KL and Seal, BS}, title = {Use of repetitive element palindromic PCR (rep-PCR) for the epidemiologic discrimination of foodborne pathogens.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {551}, number = {}, pages = {49-58}, doi = {10.1007/978-1-60327-999-4_5}, pmid = {19521866}, issn = {1064-3745}, mesh = {Campylobacter/genetics/isolation &amp; purification/pathogenicity ; Clostridium/genetics/isolation &amp; purification/pathogenicity ; DNA, Bacterial/*genetics/isolation &amp; purification ; Escherichia coli/genetics/isolation &amp; purification/pathogenicity ; *Food Microbiology ; Genome, Bacterial ; Humans ; *Inverted Repeat Sequences ; Molecular Epidemiology/*methods ; Polymerase Chain Reaction/*methods ; Salmonella/genetics/isolation &amp; purification/pathogenicity ; }, abstract = {The use of defined primers for polymerase chain reaction (PCR) amplification of interspersed repetitive DNA elements present at distinct locations in prokaryotic genomes is referred to as repetitive element sequence based-polymerase chain reaction (rep-PCR). The initial discovery of repetitive extragenic palindromic (REP) elements occurred in the genomes of Escherichia coli and Salmonella. The family of REP elements is generally between 33 and 40 bp in length, has 500 to 1,000 copies per genome, and comprises about 1% of the bacterial genomes of E. coli or Salmonella. The amplified DNA fragments, when separated by electrophoresis, constitute a genomic fingerprint that can be employed for subspecies discrimination and strain delineation of bacteria and fungi. The application of rep-PCR to microbes has proven a discriminatory and reproducible tool for microbial subtype analyses and for microbial ecology investigations.}, }
@article {pmid19519443, year = {2009}, author = {Possemiers, S and Grootaert, C and Vermeiren, J and Gross, G and Marzorati, M and Verstraete, W and Van de Wiele, T}, title = {The intestinal environment in health and disease - recent insights on the potential of intestinal bacteria to influence human health.}, journal = {Current pharmaceutical design}, volume = {15}, number = {18}, pages = {2051-2065}, doi = {10.2174/138161209788489159}, pmid = {19519443}, issn = {1873-4286}, mesh = {Animals ; Bacteria/enzymology/genetics/metabolism ; *Disease ; *Health ; Humans ; Intestines/*microbiology/pathology/physiology ; Metagenome/*physiology ; Obesity/etiology/microbiology ; Symbiosis/physiology ; Xenobiotics/metabolism ; }, abstract = {The human intestine is colonized by a complex microbial ecosystem, which could be considered as a separate organ within the human host, having a coding capacity which exceeds the liver by a factor 100. On the one hand, this extensive microbiome is closely involved in the first-pass metabolism and bioavailability of food and drug compounds. Understanding to which extent each individual's gut microbiota affects the bioavailability and response to orally administered drugs is therefore a first important challenge towards novel drug development strategies. On the other hand, as our microbiota is directly or indirectly involved in the onset of a number of disease states, a new generation of therapeutics may be developed that affect the structure and functioning of the intestinal microbiota and interfere with their specific cross-talk with the human host. Ultimately, the intestinal microbiota may even be used as a biomarker for impending diseases inside or outside the gastrointestinal tract and for the evaluation of responses to specific therapeutic interventions. This review will therefore highlight the importance of the indigenous microbial community and its enormous metabolic potential, microbe-microbe interactions, mechanisms of host-bacterium cross-talk and will discuss the onset of obesity, a specific disease state in which the role of intestinal bacteria becomes more and more apparent. Understanding the importance of the intestinal ecosystem in these phenomena may open the door for new strategies which target the management of the intestinal microbiome into the desired direction and therefore to a completely new type of nutrition research and pharmaceutical design.}, }
@article {pmid19517721, year = {2009}, author = {Sheffield, CL and Crippen, TL and Andrews, K and Bongaerts, RJ and Nisbet, DJ}, title = {Characterization of planktonic and biofilm communities of day-of-hatch chicks cecal microflora and their resistance to Salmonella colonization.}, journal = {Journal of food protection}, volume = {72}, number = {5}, pages = {959-965}, doi = {10.4315/0362-028x-72.5.959}, pmid = {19517721}, issn = {0362-028X}, mesh = {Animals ; Animals, Newborn ; Biofilms/*growth &amp; development ; Cecum/*microbiology ; Chickens ; Colony Count, Microbial ; *Consumer Product Safety ; Disease Susceptibility/veterinary ; Food Contamination/*prevention &amp; control ; Humans ; Poultry Diseases/prevention &amp; control ; Ribotyping ; Salmonella Infections, Animal/prevention &amp; control ; Salmonella typhimurium/growth &amp; development/*physiology ; }, abstract = {Recent concerns about the use of antimicrobials in food animals have increased interest in the microbial ecology and biofilms within their gastrointestinal tract. This work used a continuous-flow chemostat system to model the microbial community within the ceca from day-of-hatch chicks and its ability to resist colonization by Salmonella enterica serovar Typhimurium. We characterized the biofilm and planktonic communities from five cultures by using automated ribotyping. Eight species from six different genera were identified. Overall, the planktonic communities were more diverse, with 40% of the cultures containing four or more bacterial species. Eighty percent of the biofilm communities contained only one or two species of bacteria. Enterococcus faecalis was the only species isolated from all communities. None of the resulting microbial communities was able to resist colonization by S. enterica serovar Typhimurium. This is the first study to provide a molecular-based characterization of the biofilm and planktonic communities found in day-of-hatch chicken cecal microflora cultures.}, }
@article {pmid19517158, year = {2009}, author = {Pan, JJ and May, G}, title = {Fungal-fungal associations affect the assembly of endophyte communities in maize (Zea mays).}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {668-678}, pmid = {19517158}, issn = {1432-184X}, mesh = {DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; *Ecosystem ; Fungi/genetics/*isolation &amp; purification ; Genotype ; Population Dynamics ; Sequence Analysis, DNA ; Species Specificity ; Zea mays/genetics/*microbiology ; }, abstract = {Many factors can affect the assembly of communities, ranging from species pools to habitat effects to interspecific interactions. In microbial communities, the predominant focus has been on the well-touted ability of microbes to disperse and the environment acting as a selective filter to determine which species are present. In this study, we investigated the role of biotic interactions (e.g., competition, facilitation) in fungal endophyte community assembly by examining endophyte species co-occurrences within communities using null models. We used recombinant inbred lines (genotypes) of maize (Zea mays) to examine community assembly at multiple habitat levels, at the individual plant and host genotype levels. Both culture-dependent and culture-independent approaches were used to assess endophyte communities. Communities were analyzed using the complete fungal operational taxonomic unit (OTU) dataset or only the dominant (most abundant) OTUs in order to ascertain whether species co-occurrences were different for dominant members compared to when all members were included. In the culture-dependent approach, we found that for both datasets, OTUs co-occurred on maize genotypes more frequently than expected under the null model of random species co-occurrences. In the culture-independent approach, we found that OTUs negatively co-occurred at the individual plant level but were not significantly different from random at the genotype level for either the dominant or complete datasets. Our results showed that interspecific interactions can affect endophyte community assembly, but the effects can be complex and depend on host habitat level. To our knowledge, this is the first study to examine endophyte community assembly in the same host species at multiple habitat levels. Understanding the processes and mechanisms that shape microbial communities will provide important insights into microbial community structure and the maintenance of microbial biodiversity.}, }
@article {pmid19516279, year = {2009}, author = {Pearce, DA}, title = {Antarctic subglacial lake exploration: a new frontier in microbial ecology.}, journal = {The ISME journal}, volume = {3}, number = {8}, pages = {877-880}, doi = {10.1038/ismej.2009.53}, pmid = {19516279}, issn = {1751-7370}, mesh = {Antarctic Regions ; Bacteria/*classification/*isolation &amp; purification ; *Biodiversity ; *Ecology ; Fresh Water/*microbiology ; }, }
@article {pmid19515396, year = {2009}, author = {Ma, J and Carballa, M and Van De Caveye, P and Verstraete, W}, title = {Enhanced propionic acid degradation (EPAD) system: proof of principle and feasibility.}, journal = {Water research}, volume = {43}, number = {13}, pages = {3239-3248}, doi = {10.1016/j.watres.2009.04.046}, pmid = {19515396}, issn = {1879-2448}, mesh = {Anaerobiosis ; Bacteria, Anaerobic/metabolism ; Biodegradation, Environmental ; Bioreactors/microbiology ; Chemical Fractionation/instrumentation ; Feasibility Studies ; Propionates/*metabolism ; Ultrafiltration/instrumentation ; *Waste Disposal, Fluid ; Water Purification ; }, abstract = {Full-scale anaerobic single-phase digesters can be confronted with process instabilities, which often result in the accumulation of propionic acid (HPr). As a solution, an enhanced propionic acid degradation (EPAD) system has been conceptually designed and experimentally tested at lab-scale. The system consisted of two components: a liquid/solid separator containing a microfiltration membrane and an up-flow anaerobic sludge bed (UASB) reactor specialized in HPr degradation. Two lab-scale continuous stirred tank reactors (CSTR) were used, i.e. the CSTR(control) and the CSTR(treatment). Firstly, the CSTRs were stressed by organic overloading to obtain high HPr levels. During the recovery period, besides stop feeding, no actions were taken to decrease the residual HPr concentration in the CSTR(control), while the CSTR(treatment) was connected to EPAD system in order to accelerate its recovery. By the end of the experiment, the CSTR(treatment) completely recovered from HPr accumulation, while no significant decrease of the HPr level in the CSTR(control) was observed. Based on the experimental results, the up-scaling of EPAD system was evaluated and it would only account for about 2% of the volume of the full-scale digester, thus suggesting that the implementation of a mobile EPAD system in full-scale practice should be feasible.}, }
@article {pmid19514853, year = {2009}, author = {Wagner, M}, title = {Single-cell ecophysiology of microbes as revealed by Raman microspectroscopy or secondary ion mass spectrometry imaging.}, journal = {Annual review of microbiology}, volume = {63}, number = {}, pages = {411-429}, doi = {10.1146/annurev.micro.091208.073233}, pmid = {19514853}, issn = {1545-3251}, mesh = {Eukaryotic Cells/*chemistry/metabolism ; Image Processing, Computer-Assisted/methods ; Isotopes/*metabolism ; Prokaryotic Cells/*chemistry/metabolism ; Spectrometry, Mass, Secondary Ion/*methods ; Spectrum Analysis, Raman/*methods ; }, abstract = {An astonishing diversity of microorganisms thrives on our planet and their activities are fundamental for the functioning of all ecosystems including the human body. Consequently, detailed insights into the functions performed by microorganisms in their natural environment are required to understand human biology and the biology of the world around us and to lay the foundations for targeted manipulation of microbial communities. Isotope-labeling techniques combined with molecular detection tools are frequently used by microbial ecologists to directly link structure and function of microbial communities and to monitor metabolic properties of uncultured microbes at the single-cell level. However, only the recent combination of such techniques with Raman microspectroscopy or secondary ion mass spectrometry enables functional studies of microbes on a single-cell level by using stable isotopes as labels. This review provides an overview of these new techniques and their applications in microbial ecology, which allow us to investigate the ecophysiology of uncultured microbes to an extent that was unimaginable just a few years ago.}, }
@article {pmid19513849, year = {2009}, author = {Gein, SV and Gorshkova, KG and Tendryakova, SP}, title = {Regulation of interleukin-1beta and interleukin-8 production by agonists of mu and delta opiate receptors in vitro.}, journal = {Neuroscience and behavioral physiology}, volume = {39}, number = {6}, pages = {591-595}, pmid = {19513849}, issn = {1573-899X}, mesh = {Adult ; Cells, Cultured ; Enkephalin, Ala(2)-MePhe(4)-Gly(5)-/pharmacology ; Enkephalin, Leucine-2-Alanine/pharmacology ; Humans ; Interleukin-1beta/*biosynthesis ; Interleukin-8/*biosynthesis ; Leukocytes/drug effects/*metabolism ; Leukocytes, Mononuclear/drug effects/metabolism ; Lipopolysaccharides/pharmacology ; Male ; Neutrophils/drug effects/metabolism ; Oligopeptides/pharmacology ; Receptors, Opioid, delta/*agonists/antagonists &amp; inhibitors ; Receptors, Opioid, mu/*agonists/antagonists &amp; inhibitors ; beta-Endorphin/pharmacology ; }, abstract = {The studies reported here showed that beta-endorphin at concentrations of 10(-7)-10(-11) M increased interleukin-1beta (IL-1beta) production in unfractionated leukocyte suspensions both in the presence of 0.1 microg/ml lipopolysaccharide (LPS) and in cultures not stimulated with LPS. Interleukin-8 (IL-8) production by leukocytes was inhibited by beta-endorphin at concentrations of 10(-7) and 10(-11) M in the presence of LPS. The stimulatory effect of beta-endorphin on IL-1beta production was not blocked by naloxone or naltrindole. Suppression of IL-8 production was blocked by naloxone and naltrindole. In the mononuclear cell and neutrophil fractions, beta-endorphin and the delta agonist DADLE increased IL-1beta synthesis in both the spontaneous and stimulated versions of the test, while beta-endorphin and the delta agonist DADLE inhibited IL-8 production in the mononuclear cell and neutrophil fractions only in LPS-stimulated cultures. The mu agonist DAGO had no effect on IL-1beta production by mononuclear cells or neutrophils, though it suppressed LPS-induced secretion of IL-8 by neutrophils.}, }
@article {pmid19508502, year = {2009}, author = {Grootaert, C and Van den Abbeele, P and Marzorati, M and Broekaert, WF and Courtin, CM and Delcour, JA and Verstraete, W and Van de Wiele, T}, title = {Comparison of prebiotic effects of arabinoxylan oligosaccharides and inulin in a simulator of the human intestinal microbial ecosystem.}, journal = {FEMS microbiology ecology}, volume = {69}, number = {2}, pages = {231-242}, doi = {10.1111/j.1574-6941.2009.00712.x}, pmid = {19508502}, issn = {1574-6941}, mesh = {Bacteroidaceae/*metabolism ; Butyrates/metabolism ; Colon/*microbiology ; Colony Count, Microbial ; DNA, Bacterial/analysis ; Fermentation ; Humans ; Inulin/*pharmacology ; Lactic Acid/metabolism ; Oligosaccharides/*pharmacology ; Propionates/metabolism ; Quaternary Ammonium Compounds/metabolism ; Xylans/*pharmacology ; }, abstract = {In this study, the prebiotic potential of arabinoxylan oligosaccharides (AXOS) was compared with inulin in two simulators of the human intestinal microbial ecosystem. Microbial breakdown of both oligosaccharides and short-chain fatty acid production was colon compartment specific, with ascending and transverse colon being the predominant site of inulin and AXOS degradation, respectively. Lactate levels (+5.5 mM) increased in the ascending colon during AXOS supplementation, while propionate levels (+5.1 mM) increased in the transverse colon. The concomitant decrease in lactate in the transverse colon suggests that propionate was partially formed over the acrylate pathway. Furthermore, AXOS supplementation strongly decreased butyrate in the ascending colon, this in parallel with a decrease in Roseburia spp. and Bacteroides/Prevotella/Porphyromonas (-1.4 and -2.0 log CFU) levels. Inulin treatment had moderate effects on lactate, propionate and butyrate levels. Denaturing gradient gel electrophoresis analysis revealed that inulin changed microbial metabolism by modulating the microbial community composition. In contrast, AXOS primarily affected microbial metabolism by 'switching on' AXOS-degrading enzymes (xylanase, arabinofuranosidase and xylosidase), without significantly affecting microbial community composition. Our results demonstrate that AXOS has a higher potency than inulin to shift part of the sugar fermentation toward the distal colon parts. Furthermore, due to its stronger propionate-stimulating effect, AXOS is a candidate prebiotic capable of lowering cholesterol and beneficially affecting fat metabolism of the host.}, }
@article {pmid19508345, year = {2009}, author = {Haruta, S and Kato, S and Yamamoto, K and Igarashi, Y}, title = {Intertwined interspecies relationships: approaches to untangle the microbial network.}, journal = {Environmental microbiology}, volume = {11}, number = {12}, pages = {2963-2969}, doi = {10.1111/j.1462-2920.2009.01956.x}, pmid = {19508345}, issn = {1462-2920}, mesh = {Coculture Techniques/methods ; Ecology/*methods ; *Ecosystem ; *Microbial Interactions ; }, abstract = {In nature, microorganisms live by interacting with each other. Microbiological studies that only consider pure cultures are not sufficient to adequately describe the natural behaviour of microbes. Several microbial interactions have been recognized to affect the growth or metabolism of others; e.g. syntrophic cometabolism, competition, production of inhibitors or activators, and predation. It is believed that third-party organisms easily affect the two-species relationships and these relationships form the basis of interspecies networks within microbial communities. A microbial network contributes to 'functional redundancy' or 'structural diversity' and the microbial communities effectively act as a multicellular organism. It is necessary to understand not only the physiological activity of members within microbial communities but also their roles to regulate the activity or population of others. To access the microbial network, we require (i) comprehensive determination of all possible interspecies relationships among microbes, (ii) knock-out experiments by which certain members can be removed or suppressed, and (iii) supplemental addition of microbes or activation of certain members. Microbial network studies have started using defined microbial communities, i.e. a mixed culture that is composed of three or four species. In order to expand these studies to microflora in nature, microbial ecology requires the help of mathematical biology.}, }
@article {pmid19508296, year = {2009}, author = {Li, M and Penner, GB and Hernandez-Sanabria, E and Oba, M and Guan, LL}, title = {Effects of sampling location and time, and host animal on assessment of bacterial diversity and fermentation parameters in the bovine rumen.}, journal = {Journal of applied microbiology}, volume = {107}, number = {6}, pages = {1924-1934}, doi = {10.1111/j.1365-2672.2009.04376.x}, pmid = {19508296}, issn = {1365-2672}, mesh = {Animal Feed ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Cattle/*microbiology ; Fermentation ; Rumen/anatomy &amp; histology/*microbiology ; }, abstract = {AIMS: To investigate, using culture-independent methods, whether the ruminal bacterial structure, population and fermentation parameters differed between sampling locations and time.<br><br>METHODS AND RESULTS: The detectable bacteria and fermentation parameters in the digesta from five locations in the rumen of three cows at three time points were analysed. The PCR-denaturing gradient gel electrophoresis (PCR-DGGE) profiles were similar among digesta samples from five locations (95.4%) and three time points (93.4%) within cows; however, a lower similarity was observed for samples collected from different host animals (85.5%). Rumen pH and concentration of volatile fatty acids (VFA) were affected by time points of sampling relative to feeding.<br><br>CONCLUSIONS: The detectable bacterial structure in the rumen is highly conserved among different locations and over time, while the quantity of individual bacterial species may change diurnally in response to the feeding.<br><br>This study supplies the fundamental understanding of the microbial ecology in the rumen, which is essential for manipulation of ruminal microflora and subsequent improvement in animal production.}, }
@article {pmid19504148, year = {2009}, author = {Pontes, DS and Pinheiro, FA and Lima-Bittencourt, CI and Guedes, RL and Cursino, L and Barbosa, F and Santos, FR and Chartone-Souza, E and Nascimento, AM}, title = {Multiple antimicrobial resistance of gram-negative bacteria from natural oligotrophic lakes under distinct anthropogenic influence in a tropical region.}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {762-772}, pmid = {19504148}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/*pharmacology ; DNA, Bacterial/genetics ; *Drug Resistance, Multiple, Bacterial ; Fresh Water/analysis/microbiology ; Genes, Bacterial ; Gram-Negative Bacteria/*drug effects/genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; beta-Lactamases/genetics ; }, abstract = {The aim of this study was to evaluate the resistance to ten antimicrobial agents and the presence of bla (TEM1) gene of Gram-negative bacteria isolated from three natural oligotrophic lakes with varying degrees of anthropogenic influence. A total of 272 indigenous bacteria were recovered on eosin methylene blue medium; they were characterized for antimicrobial resistance and identified taxonomically by homology search and phylogenetic comparisons. Based on 16S ribosomal RNA sequences analysis, 97% of the isolates were found to be Gram-negative bacteria; they belonged to 11 different genera. Members of the genera Acinetobacter, Enterobacter, and Pseudomonas predominated. Most of the bacteria were resistant to at least one antimicrobial. The incidence of resistance to beta-lactams, chloramphenicol, and mercury was high, whereas resistance to tetracycline, aminoglycosides, and nalidixic acid was low. There was a great frequency of multiple resistances among the isolates from the three lakes, although no significant differences were found among the disturbed and reference lakes. The ampicillin resistance mechanism of 71% of the isolates was due to the gene bla (TEM1). Our study suggests that multiresistant Gram-negative bacteria and the bla (TEM1) gene are common in freshwater oligotrophic lakes, which are subject to different levels of anthropogenic inputs.}, }
@article {pmid19502434, year = {2009}, author = {Rodríguez-Minguela, CM and Apajalahti, JH and Chai, B and Cole, JR and Tiedje, JM}, title = {Worldwide prevalence of class 2 integrases outside the clinical setting is associated with human impact.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {15}, pages = {5100-5110}, pmid = {19502434}, issn = {1098-5336}, mesh = {Amino Acid Sequence ; Animals ; Cluster Analysis ; DNA, Bacterial/chemistry/*genetics ; *Environmental Microbiology ; Gram-Positive Bacteria/classification/*genetics/isolation &amp; purification ; Human Activities ; Humans ; Integrases/classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/*methods ; Prevalence ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {An intI-targeted PCR assay was optimized to evaluate the frequency of partial class 2-like integrases relative to putative, environmental IntI elements in clone libraries generated from 17 samples that included various terrestrial, marine, and deep-sea habitats with different exposures to human influence. We identified 169 unique IntI phylotypes (< or =98% amino acid identity) relative to themselves and with respect to those previously described. Among these, six variants showed an undescribed, extended, IntI-specific additional domain. A connection between human influence and the dominance of IntI-2-like variants was also observed. IntI phylotypes 80 to 99% identical to class 2 integrases comprised approximately 70 to 100% (n = 65 to 87) of the IntI elements detected in samples with a high input of fecal waste, whereas IntI2-like sequences were undetected in undisturbed settings and poorly represented (1 to 10%; n = 40 to 79) in environments with moderate or no recent fecal or anthropogenic impact. Eleven partial IntI2-like sequences lacking the signature ochre 179 codon were found among samples of biosolids and agricultural soil supplemented with swine manure, indicating a wider distribution of potentially functional IntI2 variants than previously reported. To evaluate IntI2 distribution patterns beyond the usual hosts, namely, the Enterobacteriaceae, we coupled PCR assays targeted at intI and 16S rRNA loci to G+C fractionation of total DNA extracted from manured cropland. IntI2-like sequences and 16S rRNA phylotypes related to Firmicutes (Clostridium and Bacillus) and Bacteroidetes (Chitinophaga and Sphingobacterium) dominated a low-G+C fraction (approximately 40 to 45%), suggesting that these groups could be important IntI2 hosts in manured soil. Moreover, G+G fractionation uncovered an additional set of 36 novel IntI phylotypes (< or =98% amino acid identity) undetected in bulk DNA and revealed the prevalence of potentially functional IntI2 variants in the low-G+C fraction.}, }
@article {pmid19501962, year = {2009}, author = {Gannoun, H and Bouallagui, H and Okbi, A and Sayadi, S and Hamdi, M}, title = {Mesophilic and thermophilic anaerobic digestion of biologically pretreated abattoir wastewaters in an upflow anaerobic filter.}, journal = {Journal of hazardous materials}, volume = {170}, number = {1}, pages = {263-271}, doi = {10.1016/j.jhazmat.2009.04.111}, pmid = {19501962}, issn = {1873-3336}, mesh = {*Abattoirs ; Anaerobiosis ; Animals ; Bacillus/metabolism ; *Biodegradation, Environmental ; Fats/metabolism ; Filtration ; Hydrolysis ; Industrial Waste/*prevention &amp; control ; Proteins/metabolism ; Solubility ; Waste Disposal, Fluid/*methods ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The hydrolysis pretreatment of abattoir wastewaters (AW), rich in organic suspended solids (fats and protein) was studied in static and stirred batch reactors without aeration in the presence of natural microbial population acclimated in a storage tank of AW. Microbial analysis showed that the major populations which contribute to the pretreatment of AW belong to the genera Bacillus. Contrary to the static pretreatment, the stirred conditions favoured the hydrolysis and solubilization of 80% of suspended matter into soluble pollution. The pretreated AW, in continuous stirred tank reactor (CSTR) at a hydraulic retention time (HRT) of 2 days, was fed to an upflow anaerobic filter (UAF) at an HRT of 2 days. The performance of anaerobic digestion of biologically pretreated AW was examined under mesophilic (37 degrees C) and thermophilic (55 degrees C) conditions. The shifting from a mesophilic to a thermophilic environment in the UAF was carried out with a short start-up of thermophilic condition. The UAF ran at organic loading rates (OLRs) ranging from 0.9 to 6g COD/Ld in mesophilic conditions and at OLRs from 0.9 to 9 g COD/Ld in thermophilic conditions. COD removal efficiencies of 80-90% were achieved for OLRs up to 4.5 g COD/Ld in mesophilic conditions, while the highest OLRs i.e. 9 g COD/Ld led to efficiencies of 70-72% in thermophilic conditions. The biogas yield in thermophilic conditions was about 0.32-0.45 L biogas/g of COD removed for OLRs up to 4.5 g COD/Ld. For similar OLR, the UAF in mesophilic conditions showed lower percentage of methanization. Mesophilic anaerobic digestion has been shown to destroy pathogens partially, whereas the thermophilic process was more efficient in the removal of indicator microorganisms and pathogenic bacteria at different organic loading rates.}, }
@article {pmid19495855, year = {2009}, author = {Ordoñez, OF and Flores, MR and Dib, JR and Paz, A and Farías, ME}, title = {Extremophile culture collection from Andean lakes: extreme pristine environments that host a wide diversity of microorganisms with tolerance to UV radiation.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {461-473}, pmid = {19495855}, issn = {1432-184X}, mesh = {Altitude ; Argentina ; Bacteria/classification/genetics/*isolation &amp; purification/radiation effects ; Biodiversity ; DNA, Bacterial/genetics ; Ecosystem ; Fresh Water/*microbiology ; Salinity ; Sequence Analysis, DNA ; *Ultraviolet Rays ; *Water Microbiology ; }, abstract = {A total of 88 bacterial strains were isolated from six Andean lakes situated at altitudes ranging from 3,400 to 4,600 m above sea level: L. Aparejos (4,200 m), L. Negra (4,400 m), L. Verde (4,460 m), L. Azul (4,400 m), L. Vilama (4,600 m), and Salina Grande (3,400 m). Salinity ranged from 0.4 to 117 ppm. General diversity was determined by denaturing gradient gel electrophoresis (DGGE) analysis. From the excised DGGE bands, 182 bacterial sequences of good quality were obtained. Gammaproteobacteria and Cytophaga/Flavobacterium/Bacteroides (CFB) were the most abundant phylogenetic groups with 42% and 18% of identified bands, respectively. The isolated strains were identified by sequence analysis. Isolated bacteria were subjected to five different UV-B exposure times: 0.5, 3, 6, 12, and 24 h. Afterwards, growth of each isolate was monitored and resistance was classified according to the growth pattern. A wide interspecific variation among the 88 isolates was observed. Medium and highly resistant strains accounted for 43.2% and 28.4% of the isolates, respectively, and only 28.4% was sensitive. Resistance to solar radiation was equally distributed among the isolates from the different lakes regardless of the salinity of the lakes and pigmentation of isolates. Of the highly resistant isolates, 44.5% belonged to gammaproteobacteria, 33.3% to betaproteobacteria, 40% to alphaproteobacteria, 50% to CFB, and among gram-positive organisms, 33.3% were HGC and 44.5% were Firmicutes. Most resistant strains belonged to genera like Exiguobaceterium sp., Acinetobacter sp., Bacillus sp., Micrococcus sp., Pseudomonas sp., Sphyngomonas sp., Staphylococcus sp., and Stenotrophomonas sp. The current study provides further evidence that gammaproteobacteria are the most abundant and the most UV-B-resistant phylogenetic group in Andean lakes and that UV resistance in bacteria isolated from these environments do not depend on pigmentation and tolerance to salinity.}, }
@article {pmid19495854, year = {2010}, author = {Poll, C and Brune, T and Begerow, D and Kandeler, E}, title = {Small-scale diversity and succession of fungi in the detritusphere of rye residues.}, journal = {Microbial ecology}, volume = {59}, number = {1}, pages = {130-140}, pmid = {19495854}, issn = {1432-184X}, mesh = {*Biodiversity ; Ecosystem ; Fungi/*classification/genetics/isolation &amp; purification ; Phylogeny ; Secale/microbiology ; *Soil Microbiology ; }, abstract = {Transport of litter carbon in the detritusphere might determine fungal abundance and diversity at the small scale. Rye residues were applied to the surface of soil cores with two different water contents and incubated at 10 degrees C for 2 and 12 weeks. Fungal community structure was analysed by constructing clone libraries of 18S rDNA and subsequent sequencing. Litter addition induced fungal succession in the adjacent soil and decreased detectable fungal diversity mainly due to the huge supply of substrates. Ergosterol content and N-acetyl-glucosaminidase activity indicated fungal growth after 2 weeks. Simultaneously, the structure of the fungal community changed, with Mortierellaceae proliferating during the initial phase of litter decomposition. Ergosterol measurements were unable to detect this early fungal growth because Mortierellaceae do not produce ergosterol. In the late phase during decomposition of polymeric substrates, like cellulose and chitin, the fungal community was dominated by Trichocladium asperum. Water content influenced community composition only during the first 2 weeks due to its influence on transport processes in the detritusphere and on competition between fungal species. Our results underline the importance of species identification in understanding decomposition processes in soil.}, }
@article {pmid19495853, year = {2009}, author = {Alguacil, Mdel M and Kohler, J and Caravaca, F and Roldán, A}, title = {Differential effects of Pseudomonas mendocina and Glomus intraradices on lettuce plants physiological response and aquaporin PIP2 gene expression under elevated atmospheric CO2 and drought.}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {942-951}, pmid = {19495853}, issn = {1432-184X}, mesh = {Aquaporins/genetics/*metabolism ; Biomass ; Carbon Dioxide/*metabolism ; *Droughts ; Gene Expression Regulation, Plant ; Genes, Plant ; Lactuca/genetics/*microbiology/physiology ; Mycorrhizae/*growth &amp; development ; Phosphorus/metabolism ; Plant Leaves/metabolism ; Plant Proteins/genetics/*metabolism ; Plant Roots/genetics/metabolism ; Plant Transpiration ; Pseudomonas mendocina/*growth &amp; development ; Symbiosis ; Water/metabolism ; }, abstract = {Arbuscular mycorrhizal (AM) symbiosis and plant-growth-promoting rhizobacterium (PGPR) can alleviate the effects of water stress in plants, but it is unknown whether these benefits can be maintained at elevated CO2. Therefore, we carried out a study where seedlings of Lactuca sativa were inoculated with the AM fungus (AMF) Glomus intraradices N.C. Schenk &amp; G.S. Sm. or the PGPR Pseudomonas mendocina Palleroni and subjected to two levels of watering and two levels of atmospheric CO2 to ascertain their effects on plant physiological parameters and gene expression of one PIP aquaporin in roots. The inoculation with PGPR produced the greatest growth in lettuce plants under all assayed treatments as well as the highest foliar potassium concentration and leaf relative water content under elevated [CO2] and drought. However, under such conditions, the PIP2 gene expression remained almost unchanged. G. intraradices increased significantly the AMF colonization, foliar phosphorus concentration and leaf relative water content in plants grown under drought and elevated [CO2]. Under drought and elevated [CO2], the plants inoculated with G. intraradices showed enhanced expression of the PIP2 gene as compared to P. mendocina or control plants. Our results suggest that both microbial inoculation treatments could help to alleviate drought at elevated [CO2]. However, the PIP2 gene expression was increased only by the AMF but not by the PGPR under these conditions.}, }
@article {pmid19490339, year = {2009}, author = {Reale, A and Sorrentino, E and Iacumin, L and Tremonte, P and Manzano, M and Maiuro, L and Comi, G and Coppola, R and Succi, M}, title = {Irradiation treatments to improve the shelf life of fresh black truffles (truffles preservation by gamma-rays).}, journal = {Journal of food science}, volume = {74}, number = {4}, pages = {M196-200}, doi = {10.1111/j.1750-3841.2009.01142.x}, pmid = {19490339}, issn = {1750-3841}, mesh = {*Ascomycota/ultrastructure ; *Food Irradiation ; Food Microbiology ; Gamma Rays ; Humans ; Hydrogen-Ion Concentration ; Microscopy, Electron, Scanning ; Sensation ; Time Factors ; }, abstract = {The aim of this study was to individuate a method to improve the shelf life of fresh truffles, hypogeous fungi highly prized but very perishable as well. Microbial ecology of fresh products was investigated and the effect of irradiation at different doses on microbial and sensorial parameters was assayed. Data showed that fresh truffles are strongly contaminated from different groups of microorganisms. Irradiation was able to influence their growth, determining an impressive reduction. Treatments at 5 and 10 kGy doses produced the highest microbial decontamination but negatively influenced sensorial parameters. Irradiation at a 1.5 kGy dose was the best solution to improve the shelf life of truffles.}, }
@article {pmid19488750, year = {2009}, author = {Sintubin, L and De Windt, W and Dick, J and Mast, J and van der Ha, D and Verstraete, W and Boon, N}, title = {Lactic acid bacteria as reducing and capping agent for the fast and efficient production of silver nanoparticles.}, journal = {Applied microbiology and biotechnology}, volume = {84}, number = {4}, pages = {741-749}, doi = {10.1007/s00253-009-2032-6}, pmid = {19488750}, issn = {1432-0614}, mesh = {Gram-Negative Bacteria/growth &amp; development/metabolism ; Gram-Positive Bacteria/*growth &amp; development/*metabolism ; Lactic Acid/*metabolism ; Microscopy, Electron, Transmission ; *Nanoparticles ; Oxidation-Reduction ; Silver/*metabolism ; }, abstract = {There is a growing demand for silver-based biocides, including both ionic silver forms and metallic nanosilver. The use of metallic nanosilver, typically chemically produced, faces challenges including particle agglomeration, high costs, and upscaling difficulties . Additionally, there exists a need for the development of a more eco-friendly production of nanosilver. In this study, Gram-positive and Gram-negative bacteria were utilized in the non-enzymatic production of silver nanoparticles via the interaction of silver ions and organic compounds present on the bacterial cell. Only lactic acid bacteria, Lactobacillus spp., Pediococcus pentosaceus, Enterococcus faecium, and Lactococcus garvieae, were able to reduce silver. The nanoparticles of the five best producing Lactobacillus spp. were examined more into detail with transmission electron microscopy. Particle localization inside the cell, the mean particle size, and size distribution were species dependent, with Lactobacillus fermentum having the smallest mean particle size of 11.2 nm, the most narrow size distribution, and most nanoparticles associated with the outside of the cells. Furthermore, influence of pH on the reduction process was investigated. With increasing pH, silver recovery increased as well as the reduction rate as indicated by UV-VIS analyses. This study demonstrated that Lactobacillus spp. can be used for a rapid and efficient production of silver nanoparticles.}, }
@article {pmid19486432, year = {2009}, author = {Wittebolle, L and Van Vooren, N and Verstraete, W and Boon, N}, title = {High reproducibility of ammonia-oxidizing bacterial communities in parallel sequential batch reactors.}, journal = {Journal of applied microbiology}, volume = {107}, number = {2}, pages = {385-394}, doi = {10.1111/j.1365-2672.2009.04222.x}, pmid = {19486432}, issn = {1365-2672}, mesh = {Ammonia/metabolism ; Bacteria/genetics/*growth &amp; development/*isolation &amp; purification ; *Bioreactors ; Electrophoresis, Polyacrylamide Gel ; Kinetics ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; *Sewage ; Time Factors ; }, abstract = {AIMS: To investigate whether the ammonia-oxidizing bacterial (AOB) communities of replicate nitrifying bioreactors (i) co-evolve or diverge over time and (ii) are stable or dynamic during periods of complete nitrification.<br><br>METHODS AND RESULTS: Three sequential batch reactors (SBR) were inoculated with sludge from a municipal wastewater treatment plant, fed with ammonium-enriched tap water and operated in parallel for 134 days. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) demonstrated co-evolvement of the AOB communities over time. During start-up, temporary decreases in nitrification were noticed, and the AOB community rate of change values (Delta(t(week))) were medium to high (12-22%). During the adjacent period of complete nitrification, low AOB community dynamics were observed (Delta(t(week)) < 5%). Further pragmatic processing of the DGGE profiles revealed a high range-weighted richness and a medium functional organization of the AOB communities.<br><br>CONCLUSIONS: After a start-up period, high functional stability and low dynamics of the AOB communities were observed. Deterministic rather than stochastic driving forces led to AOB community co-evolvement in the replicate SBR.<br><br>Replicates in identical set-ups are reproducible, and pragmatic processing of DGGE patterns is a straightforward tool to score and compare the functionality of the bacterial communities.}, }
@article {pmid19486425, year = {2009}, author = {Rasmussen, HE and Martínez, I and Lee, JY and Walter, J}, title = {Alteration of the gastrointestinal microbiota of mice by edible blue-green algae.}, journal = {Journal of applied microbiology}, volume = {107}, number = {4}, pages = {1108-1118}, doi = {10.1111/j.1365-2672.2009.04288.x}, pmid = {19486425}, issn = {1365-2672}, mesh = {Animals ; Bacteria/genetics/*isolation &amp; purification ; Colon/microbiology ; Colony Count, Microbial ; Cyanobacteria/*physiology ; DNA, Bacterial/genetics ; Diet/veterinary ; Electrophoresis, Polyacrylamide Gel ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Ileum/microbiology ; Mice ; Mice, Inbred C57BL/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {AIMS: To characterize the effect of edible blue-green algae (cyanobacteria) on the gastrointestinal microbiota of mice.<br><br>METHODS AND RESULTS: C57BL/6J mice were fed a diet supplemented with 0% or 5% dried Nostoc commune, Spirulina platensis or Afanizominon flos-aquae (w/w) for 4 weeks. Molecular fingerprinting of the colonic microbiota using denaturing gradient gel electrophoresis revealed that administration of N. commune induced major alterations in colonic microbiota composition, while administration of S. platensis or A. flos-aquae had a more subtle impact. Community profile analysis revealed that administration of N. commune did not reduce microbial diversity indices of the colonic microbiota. Despite its pronounced effects on the bacterial composition in the colon, total bacterial numbers in the gut of mice fed N. commune were not reduced as assessed by quantitative real-time PCR and bacteriological culture.<br><br>CONCLUSIONS: The results presented here show that administration of blue-green algae, and especially N. commune, alters colonic microbiota composition in mice with limited effects on total bacterial numbers or microbial diversity.<br><br>Blue-green algae are consumed in many countries as a source of nutrients and to promote health, and they are intensively studied for their pharmaceutical value. Given the importance of the gut microbiota for many host functions, the effects of blue-green algae on gut microbial ecology revealed during this study should be considered when using them as food supplements or when studying their pharmaceutical properties.}, }
@article {pmid19484283, year = {2010}, author = {Sánchez-Peinado, Mdel M and González-López, J and Martínez-Toledo, MV and Pozo, C and Rodelas, B}, title = {Influence of linear alkylbenzene sulfonate (LAS) on the structure of Alphaproteobacteria, Actinobacteria, and Acidobacteria communities in a soil microcosm.}, journal = {Environmental science and pollution research international}, volume = {17}, number = {3}, pages = {779-790}, pmid = {19484283}, issn = {1614-7499}, mesh = {Actinobacteria/classification/*drug effects/isolation &amp; purification ; Alkanesulfonic Acids/*toxicity ; Alphaproteobacteria/classification/*drug effects/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/metabolism ; Soil Pollutants/*toxicity ; Surface-Active Agents/*toxicity ; Toxicity Tests ; }, abstract = {BACKGROUND, AIM, AND SCOPE: Linear alkylbenzene sulfonate (LAS) is the most used anionic surfactant in a worldwide scale and is considered a high-priority pollutant. LAS is regarded as a readily biodegradable product under aerobic conditions in aqueous media and is mostly removed in wastewater treatment plants, but an important fraction (20-25%) is immobilized in sewage sludge and persists under anoxic conditions. Due to the application of the sludge as a fertilizer, LAS reaches agricultural soil, and therefore, microbial toxicity tests have been widely used to evaluate the influence of LAS on soil microbial ecology. However, molecular-based community-level analyses have been seldom applied in studies regarding the effects of LAS on natural or engineered systems, and, to our knowledge, there are no reports of their use for such appraisals in agricultural soil. In this study, a microcosm system is used to evaluate the effects of a commercial mixture of LAS on the community structure of Alphaproteobacteria, Actinobacteria, and Acidobacteria in an agricultural soil.<br><br>MATERIAL AND METHODS: The microcosms consisted of agricultural soil columns (800 g) fed with sterile water (8 ml h(-1)) added of different concentration of LAS (10 or 50 mg l(-1)) for periods of time up to 21 days. Sterile water was added to control columns for comparison. The structures of Alphaproteobacteria, Actinobacteria, and Acidobacteria communities were analyzed by a cultivation independent method (temperature gradient gel electrophoresis (TGGE) separation of polymerase chain reaction (PCR)-amplified partial 16S rRNA genes). Relevant populations were identified by subsequent reamplification, DNA sequencing, and database comparisons.<br><br>RESULTS: Cluster analysis of the TGGE fingerprints taking into consideration both the number of bands and their relative intensities revealed that the structure of the Alphaproteobacteria community was significantly changed in the presence of LAS, at both concentrations tested. The average number of bands was significantly lower in the microcosms receiving 50 mg l(-1) LAS and in the lower portion of soil cores. The clear differentiation of the samples of the upper portion of the soil columns amended with LAS was specifically related to the presence and intensity of a distinctive major band (named band class 7). There was a statistically significant positive correlation between the concentrations of LAS detected in soil portions taken from LAS 10 mg l(-1) and LAS 50 mg l(-1) microcosms and the relative intensity of band class 7 in the corresponding TGGE profiles. Prevalent Alphaproteobacteria populations in the soil microcosms had close similarity (>99%) to cultivated species affiliated to genera of the Rhizobiaceae, Methylocystaceae, Hyphomicrobiaceae, Rhodospirillaceae, Brucellaceae, Bradyrhizobiaceae, and Caulobacteraceae families. The population represented by band class 7 was found closely related to the genus Phenylobacterium (Caulobacteraceae). According to cluster analysis of TGGE profiles, the structure of both Actinobacteria and Acidobacteria communities in the soil microcosms was remarkably stable in the presence of LAS at the two concentrations tested, as most bands were universally present in all samples and displayed fairly similar relative intensities.<br><br>DISCUSSION: Previous studies by others authors, based on biological and chemical tests, concluded that LAS toxicity was not an important microbial selection factor in sludge amended soil, while work based on the use of molecular fingerprinting to evaluate the impact of LAS in aqueous media and marine sediments showed that concentrations as low as 1 mg l(-1) significantly influence the development of the bacterial community structure. Although TGGE is not a strictly quantitative method due to the bias introduced by the PCR reaction, changes of band intensity through experiments are a consequence of a change in the relative abundance of the corresponding populations in the community and can be used as a semiquantitative measure of bacterial diversity. Our results evidence that the Phenylobacterium population represented by band class 7 was favored by the presence of increasing concentrations of LAS in the soil and turned into a dominant population, suggesting its possible ability to use LAS in soil as a source of nutrients. As studies with pure cultures are required to confirm the ability of this population to degrade LAS, isolation strategies are currently under development in our laboratory. The weak effect of LAS on the structure of Actinobacteria and Acidobacteria communities is particularly interesting, as to our knowledge, there are no previous reports regarding the effects of LAS on these bacterial groups in soil. CONCLUSIONS, RECOMMENDATIONS, AND PERSPECTIVES: The Phenylobacterium-related alphaproteobacterial population identified in this work was selectively enriched in LAS polluted soil and is a plausible candidate to play a relevant role in the biotransformation of the surfactant under the conditions tested. The surfactant had no remarkable effects on the Actinobacteria and Acidobacteria fingerprints in soil, even when present at concentrations widely exceeding those reached in soil immediately after sludge application. TGGE fingerprinting provides a reliable and low time-consuming method for the monitoring of the bacterial community structure and dynamics, and we recommend its integration with the biological and chemical analyses usually applied in risk assessment of LAS in the environment.}, }
@article {pmid19480952, year = {2009}, author = {Warnecke, F and Hess, M}, title = {A perspective: metatranscriptomics as a tool for the discovery of novel biocatalysts.}, journal = {Journal of biotechnology}, volume = {142}, number = {1}, pages = {91-95}, doi = {10.1016/j.jbiotec.2009.03.022}, pmid = {19480952}, issn = {1873-4863}, mesh = {Archaea/*enzymology/genetics ; Bacteria/*enzymology/genetics ; *Biocatalysis ; Enzymes/*metabolism ; *Gene Expression Profiling ; Genome, Archaeal ; Genome, Bacterial ; Genomics/*methods ; Sequence Analysis, DNA ; }, abstract = {In this mini-review, advantages and current bottlenecks of metatranscriptomic-sequencing for the discovery of novel enzymes for biotechnological applications will be discussed. Comparison of this innovative approach to traditional metagenomic-sequencing will illustrate that expression profiling has a promising future as a direct and very efficient method for the discovery of novel biocatalysts, even from complex microbial communities.}, }
@article {pmid19479305, year = {2009}, author = {Langhans, TM and Storm, C and Schwabe, A}, title = {Community assembly of biological soil crusts of different successional stages in a temperate sand ecosystem, as assessed by direct determination and enrichment techniques.}, journal = {Microbial ecology}, volume = {58}, number = {2}, pages = {394-407}, pmid = {19479305}, issn = {1432-184X}, mesh = {Biomass ; Chlorophyll/analysis ; Chlorophyll A ; Cyanobacteria/classification/genetics/isolation &amp; purification ; *Ecosystem ; Eukaryota/classification/genetics/isolation &amp; purification ; Germany ; Lichens/classification/genetics/isolation &amp; purification ; Silicon Dioxide/*analysis ; *Soil Microbiology ; Time Factors ; }, abstract = {In temperate regions, biological soil crusts (BSCs: complex communities of cyanobacteria, eukaryotic algae, bryophytes, and lichens) are not well investigated regarding community structure and diversity. Furthermore, studies on succession are rare. For that reason, the community assembly of crusts representing two successional stages (initial, 5 years old; and stable, >20 years old) were analyzed in an inland sand ecosystem in Germany in a plot-based approach (2 x 18 plots, each 20 x 20 cm). Two different methods were used to record the cyanobacteria and eukaryotic algae in these communities comprehensively: determination directly out of the soil and enrichment culture techniques. Additionally, lichens, bryophytes, and phanerogams were determined. We examine four hypotheses: (1) A combination of direct determination and enrichment culture technique is necessary to detect cyanobacteria and eukaryotic algae comprehensively. In total, 45 species of cyanobacteria and eukaryotic algae were detected in the study area with both techniques, including 26 eukaryotic algae and 19 cyanobacteria species. With both determination techniques, 22 identical taxa were detected (11 eukaryotic algae and 11 cyanobacteria). Thirteen taxa were only found by direct determination, and ten taxa were only found in enrichment cultures. Hence, the hypothesis is supported. Additionally, five lichen species (three genera), five bryophyte species (five genera), and 24 vascular plant species occurred. (2) There is a clear difference between the floristic structure of initial and stable crusts. The different successional stages are clearly separated by detrended correspondence analysis, showing a distinct structure of the community assembly in each stage. In the initial crusts, Klebsormidium flaccidum, Klebsormidium cf. klebsii, and Stichococcus bacillaris were important indicator species, whereas the stable crusts are especially characterized by Tortella inclinata. (3) The biodiversity of BSC taxa and vascular plant species increases from initial to stable BSCs. There are significantly higher genera and species numbers of cyanobacteria and eukaryotic algae in initial BSCs. Stable BSCs are characterized by significantly higher species numbers of bryophytes and vascular plant species. The results show that, in the investigated temperate region, the often-assumed increase of biodiversity in the course of succession is clearly taxa-dependent. Both successional stages of BSCs are diversity "hot spots" with about 29 species of all taxa per 20 x 20 cm plot. (4) Nitrogen and chlorophyll a concentrations increase in the course of succession. The chlorophyll a content of the crusts (cyanobacteria, eukaryotic algae, bryophyte protonemata) is highly variable across the studied samples, with no significant differences between initial and stable BSCs; nor were ecologically significant differences in soil nutrient contents observed. According to our results, we cannot confirm this hypothesis; the age difference between our two stages is probably not big enough to show such an increase.}, }
@article {pmid19479304, year = {2009}, author = {Mengoni, A and Pini, F and Huang, LN and Shu, WS and Bazzicalupo, M}, title = {Plant-by-plant variations of bacterial communities associated with leaves of the nickel hyperaccumulator Alyssum bertolonii Desv.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {660-667}, pmid = {19479304}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Brassicaceae/metabolism/*microbiology ; DNA, Bacterial/genetics ; Italy ; Nickel/*metabolism ; Plant Leaves/metabolism/microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/analysis ; Soil Pollutants/metabolism ; }, abstract = {Bacteria associated with tissues of metal-hyperaccumulating plants are of great interest due to the multiple roles they may play with respect to plant growth and resistance to heavy metals. The variability of bacterial communities associated with plant tissues of three populations of Alyssum bertolonii, a Ni hyperaccumulator endemic of serpentine outcrops of Central Italy, was investigated. Terminal-restriction fragment length polymorphism (T-RFLP) analysis of bacterial 16S rRNA genes was applied to DNA extracted from leaf tissues of 30 individual plants from three geographically separated serpentine outcrops. Moreover, T-RFLP fingerprinting was also performed on DNA extracted from the same soils from which the plants were collected. Fifty-nine unique terminal-restriction fragments (TRFs) were identified, with more than half of the taxonomically interpreted TRFs assigned to Alpha- and Gamma-Proteobacteria and Clostridia. Data were then used to define the extent of variation of bacterial communities due to single plants or to plant populations. Results indicated a very high plant-by-plant variation of leaf-associated community (more than 93% of total variance observed). However, a core (numerically small) of plant-specific TRFs was found. This work demonstrates that plant-associated bacterial communities represent a large reservoir of biodiversity and that the high variability existing between plants, even from the same population, should be taken into account in future studies on association between bacteria and metal-hyperaccumulating plants.}, }
@article {pmid19477544, year = {2009}, author = {Cocolin, L and Nucera, D and Alessandria, V and Rantsiou, K and Dolci, P and Grassi, MA and Lomonaco, S and Civera, T}, title = {Microbial ecology of Gorgonzola rinds and occurrence of different biotypes of Listeria monocytogenes.}, journal = {International journal of food microbiology}, volume = {133}, number = {1-2}, pages = {200-205}, doi = {10.1016/j.ijfoodmicro.2009.05.003}, pmid = {19477544}, issn = {1879-3460}, mesh = {Bacteria/*isolation &amp; purification ; Cheese/*microbiology ; Electrophoresis ; *Food Microbiology ; Genetic Variation ; Humans ; Listeria monocytogenes/*isolation &amp; purification ; Polymerase Chain Reaction ; Yeasts/*isolation &amp; purification ; }, abstract = {In this study we investigated the microbiota of Gorgonzola rinds and maturing shelf swabs collected in 5 different maturing cellars in the Northwest part of Italy, in association with the detection and characterization of Listeria monocytogenes. Culture-dependent and -independent methods were performed in order to profile the main microbial populations present on the rinds and in the maturing shelves and species-specific PCR and Pulsed Field Gel Electrophoresis (PFGE) were used to identify and type L. monocytogenes isolates. The microflora was predominated by lactic acid bacteria and coagulase negative cocci, while enterococci and yeasts were very variable between the samples. Arthrobacter sp., Carnobacterium sp., Staphylococcus sp. and Brevibacterium linens, as bacteria, and Debaryomyces hansenii, as yeast, were detected by Denaturing Gradient Gel Electrophoresis (DGGE). Cluster analysis of the DGGE profiles clearly highlighted a cellar-specific microflora. L. monocytogenes was isolated in 11.1% of the rinds and 29.4% of the swabs and the molecular characterization of the isolates suggests a route of contamination from the maturing shelves to the rinds. No correlation was found between DGGE profiles and presence or absence of L. monocytogenes.}, }
@article {pmid19475445, year = {2009}, author = {Akhtar, M and Hirt, H and Zurek, L}, title = {Horizontal transfer of the tetracycline resistance gene tetM mediated by pCF10 among Enterococcus faecalis in the house fly (Musca domestica L.) alimentary canal.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {509-518}, pmid = {19475445}, issn = {1432-184X}, mesh = {Animals ; Conjugation, Genetic ; Enterococcus faecalis/drug effects/*genetics ; Gastrointestinal Tract/*microbiology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Houseflies/*microbiology ; Microbial Sensitivity Tests ; Plasmids ; Tetracycline Resistance/drug effects/*genetics ; }, abstract = {The house fly (Musca domestica L.) alimentary canal was evaluated for the potential of horizontal transfer of tetM on plasmid pCF10 among Enterococcus faecalis. Two sets of experiments were conducted: (1) house flies without surface sterilization and (2) surface-sterilized flies. Both sets of flies were exposed to E. faecalis OG1RF:pCF10 as donor for 12 h and then E. faecalis OG1SSp as recipient for 1 h. Another group of flies received the recipient first for 12 h followed by exposure to the donor strain for 1 h. House flies were screened daily to determine the donor, recipient, and transconjugant bacterial load for up to 5 days. In addition, the sponge-like mouth parts used for food uptake (labellum) of surface-sterilized house flies were removed and analyzed for donors, recipients, and transconjugants, separately. In both groups of flies (n = 90 flies/group), transfer occurred within 24 h after exposure with a transconjugant/donor rate from 8.6 x 10(-5) to 4.5 x 10(1). Transconjugants were also isolated from the house fly labellum. Our data suggest that the house fly digestive tract provides a suitable environment for horizontal transfer of conjugative plasmids and antibiotic resistance genes among enterococci. Our results emphasize the importance of this insect as a potential vector of antibiotic-resistant bacterial strains.}, }
@article {pmid19475444, year = {2009}, author = {Colombet, J and Charpin, M and Robin, A and Portelli, C and Amblard, C and Cauchie, HM and Sime-Ngando, T}, title = {Seasonal depth-related gradients in virioplankton: standing stock and relationships with microbial communities in Lake Pavin (France).}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {728-736}, pmid = {19475444}, issn = {1432-184X}, mesh = {Chlorophyll/analysis ; Ecosystem ; France ; Fresh Water/analysis/*virology ; Light ; Oxygen/analysis ; *Seasons ; Viruses/*growth &amp; development/isolation &amp; purification ; Water Microbiology ; }, abstract = {This study presents a depth-related survey of virioplankton abundance in Lake Pavin (Massif Central, France), in relation to the abundances of heterotrophic prokaryotes, picocyanobacteria (Pcy), autotrophic picoeukaryotes (Peu), and of autotrophic (ANF) and heterotrophic (HNF) nanoflagellates. The sampling strategy was designed to be representative of the physico-chemical gradients of the whole water column of the lake, and the seasonal variability as well. In mixolimnic surface waters, all communities were present and viral abundance peaked in summer and autumn. Viral abundance was significantly correlated (p < 0.001) with Pcy, Peu, and ANF, indicating that cyanophages and perhaps other phytoplankton viruses represent a significant pool of viral standing stocks in the mixolimnion of Lake Pavin. Microautotrophs were absent in the deep monimolimnic water masses, where viruses and heterotrophic prokaryotes exhibited highest seasonal abundances in summer and/or autumn and were significantly correlated (p < 0.001) to each other. This indicates that the anoxic monimolimnion of Lake Pavin is an exclusive habitat for viruses and heterotrophic prokaryotes. We conclude that in this habitat, host availability is prevalent over other factors (temperature, oxygen, nutrients, grazers) in favoring viral proliferation.}, }
@article {pmid19474491, year = {2009}, author = {Martin, KJ and Downing, LS and Nerenberg, R}, title = {Evidence of specialized bromate-reducing bacteria in a hollow fiber membrane biofilm reactor.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {59}, number = {10}, pages = {1969-1974}, doi = {10.2166/wst.2009.216}, pmid = {19474491}, issn = {0273-1223}, mesh = {Betaproteobacteria/*metabolism ; Biofilms ; Bioreactors ; Bromates/*metabolism ; Carcinogens/metabolism ; Equipment Design ; Kinetics ; Nitrates/metabolism ; Oxidation-Reduction ; Perchlorates/*metabolism ; Water Purification/methods ; }, abstract = {Bromate is a carcinogenic disinfection by-product formed from bromide during ozonation or advanced oxidation. We previously observed bromate reduction in a hydrogen-based, denitrifying hollow fiber membrane biofilm reactor (MBfR). In this research, we investigated the potential existence of specialized bromate-reducing bacteria. Using denaturing gradient gel electrophoresis (DGGE), we compared the microbial ecology of two denitrifying MBfRs, one amended with nitrate as the electron acceptor and the other with nitrate plus bromate. The DGGE results showed that bromate exerted a selective pressure for a putative, specialized bromate-reducing bacterium, which developed a strong presence only in the reactor with bromate. To gain further insight into the capabilities of specialized, bromate-reducing bacteria, we explored bromate reduction in a control MBfR without any primary electron acceptors. A grown biofilm in the control MBfR reduced bromate without previous exposure, but the rate of reduction decreased over time, especially after perturbations resulting in biomass loss. The decrease in bromate reduction may have been the result of the toxic effects of bromate. We also used batch tests of the perchlorate-reducing pure culture, Dechloromonas sp. PC1 to test bromate reduction and growth. Bromate was reduced without measurable growth. Based on these results, we speculate bromate's selective pressure for the putative, specialized BRB observed in the DGGE was not growth related, but possibly based on resistance to bromate toxicity.}, }
@article {pmid19471996, year = {2009}, author = {Sipkema, D and Holmes, B and Nichols, SA and Blanch, HW}, title = {Biological characterisation of Haliclona (?gellius) sp.: sponge and associated microorganisms.}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {903-920}, pmid = {19471996}, issn = {1432-184X}, mesh = {Animals ; Archaea/classification/*genetics/isolation &amp; purification ; Bacteria/classification/*genetics/isolation &amp; purification ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Genomic Library ; Haliclona/*microbiology ; Microscopy, Electron, Transmission ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Species Specificity ; }, abstract = {We have characterised the northern Pacific undescribed sponge Haliclona (?gellius) sp. based on rDNA of the sponge and its associated microorganisms. The sponge is closely related to Amphimedon queenslandica from the Great Barrier Reef as the near-complete 18S rDNA sequences of both sponges were identical. The microbial fingerprint of three specimens harvested at different times and of a transplanted specimen was compared to identify stably associated microorganisms. Most bacterial phyla were detected in each sample, but only a few bacterial species were determined to be stably associated with the sponge. A sponge-specific beta- and gamma-Proteobacterium were abundant clones and both of them were present in three of the four specimens analysed. In addition, a Planctomycete and a Crenarchaea were detected in all sponge individuals. Both were closely related to operational taxonomic units that have been found in other sponges, but not exclusively in sponges. Interestingly, also a number of clones that are closely related to intracellular symbionts from insects and amoeba were detected.}, }
@article {pmid19469290, year = {2009}, author = {Chróst, RJ and Adamczewski, T and Kalinowska, K and Skowrońska, A}, title = {Inorganic phosphorus and nitrogen modify composition and diversity of microbial communities in water of mesotrophic lake.}, journal = {Polish journal of microbiology}, volume = {58}, number = {1}, pages = {77-90}, pmid = {19469290}, issn = {1733-1331}, mesh = {Animals ; Bacteria/*growth &amp; development/metabolism/ultrastructure ; *Biodiversity ; Biomass ; Cell Membrane/ultrastructure ; Chlorophyll/analysis ; Chlorophyll A ; Ecosystem ; Eukaryota/growth &amp; development/ultrastructure ; Fresh Water/analysis/*chemistry/*microbiology ; In Situ Hybridization, Fluorescence ; Nitrogen/*metabolism ; Phosphorus/*metabolism ; Photosynthesis ; Phytoplankton/metabolism ; *Water Microbiology ; }, abstract = {The effects of inorganic nutrients (N, P) enrichment of mesotrophic lake water on changes in bacterial and protistan (heterotrophic nanoflagellates and ciliates) communities compositions were studied in the mesocosm experiment. Phosphorus (PO4(3-)) and nitrogen (NH4+) alone and in combination were added to three types of experimental mesocosms. Mesocosms results suggested that simultaneous addition of P and N stimulated phytoplankton growth and production rates of bacterial biomass its turnover rate. Strong positive correlations between chlorophyll a and bacterial secondary production rates suggested that bacteria were mainly controlled by organic substrates released in course ofphytoplankton photosynthesis. Both nutrients increased distinctly protistan biomass and resulted in the shift in ciliate community composition from algivorous to large omnivorous species. The response of bacterial numbers and biomass to nutrients addition was less evident. However, intensive grazing caused their dynamic changes. Fluorescence in situ hybridization (FISH) revealed only small changes in bacterial taxonomic composition. There was an apparent shift in dominance from Cytophaga-Flavobacterium to the Alphaproteobacteria group in the mesocosm with simultaneous addition of P and N, which positively related to increased abundance of bacterivorous protists. Experiment demonstrated that inorganic N and P nutrients directly influenced the bottom-down control of microbial communities, which had a crucial effect on morphological diversity of bacteria.}, }
@article {pmid19468701, year = {2009}, author = {Kim, J and Shepherd, MW and Jiang, X}, title = {Evaluating the effect of environmental factors on pathogen regrowth in compost extract.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {498-508}, pmid = {19468701}, issn = {1432-184X}, mesh = {Animals ; Antibiosis ; Cattle ; Colony Count, Microbial ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli O157/*growth &amp; development ; Listeria monocytogenes/*growth &amp; development ; Manure/microbiology ; Salmonella/*growth &amp; development ; *Soil ; }, abstract = {Pathogenic microorganisms may survive the composting process in low numbers and subsequently regrow to high levels under favorable conditions. The objective of this study was to investigate the regrowth potential of Salmonella spp., Escherichia coli O157:H7, and Listeria monocytogenes in dairy-based composts under different environmental conditions. Water extract of commercially available dairy compost was used as a model system. Cocktails of five rifampin-resistant strains of each pathogen previously grown in reduced nutrient media (1/2 or 1/10 strength of tryptic soy broth, TSB) were inoculated into water extract of compost of different ratios (1:2,1:5, and 1:10, w/v), and then stored at 35 degrees C or 22 degrees C for 7 days. The strains exhibiting greatest survival or regrowth were identified by pulsed-field gel electrophoresis (PFGE). At 22 degrees C, both E. coli O157:H7 and L. monocytogenes multiplied in all compost extracts, whereas Salmonella spp. regrew in both 1:2 and 1:5 compost extracts but not in 1:10. For all three pathogens, incubation at 22 degrees C provides better conditions for regrowth than at 35 degrees C. Both Salmonella and E. coli O157:H7 previously adapted to nutrient-limited broth (1/10 strength of TSB) regrew in compost extracts to higher populations than the control cultures grown previously in full strength of TSB. In the absence of indigenous microorganisms, all three pathogens regrew even in the most diluted sterile compost extract (1:10) with growth potentials ranging from 2.30 to 3.59 log CFU/ml. In nonsterile compost extract with ca. 5 log CFU/ml of background microorganisms, all three pathogens regrew only in the most concentrated compost extract (1:2) with much less population increases ranging from 0.70 to 1.43 log CFU/ml. Compost extract samples of all ages supported the regrowth of both Salmonella and E. coli O157:H7 with population increases ranging from 0.95 to 2.32 log CFU/ml. The PFGE patterns for E. coli O157:H7 isolates from sterile compost extracts matched with either the spinach outbreak strain or an avirulent B6914 strain. These results demonstrated that compost extract of dairy-based compost contained sufficient nutrients for pathogen regrowth. Cultures previously adapted to low nutrient media regrew to higher populations than control cultures; however, indigenous microflora suppressed the pathogen regrowth in compost extract, especially at 35 degrees C.}, }
@article {pmid19468700, year = {2009}, author = {Alexandre, A and Brígido, C and Laranjo, M and Rodrigues, S and Oliveira, S}, title = {Survey of Chickpea Rhizobia diversity in Portugal reveals the predominance of species distinct from Mesorhizobium ciceri and Mesorhizobium mediterraneum.}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {930-941}, pmid = {19468700}, issn = {1432-184X}, mesh = {Biodiversity ; Cicer/*microbiology ; Cluster Analysis ; DNA, Bacterial/genetics ; Geography ; *Phylogeny ; Plasmids ; Portugal ; RNA, Ribosomal, 16S/genetics ; Rhizobiaceae/classification/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; *Soil Microbiology ; *Symbiosis ; }, abstract = {Several Mesorhizobium species are able to induce effective nodules in chickpea, one of the most important legumes worldwide. Our aims were to examine the biogeography of chickpea rhizobia, to search for a predominant species, and to identify the most efficient microsymbiont, considering Portugal as a case study. One hundred and ten isolates were obtained from continental Portugal and Madeira Island. The 16S ribosomal RNA gene phylogeny revealed that isolates are highly diverse, grouping with most Mesorhizobium type strains, in four main clusters (A-D). Interestingly, only 33% of the isolates grouped with Mesorhizobium ciceri (cluster B) or Mesorhizobium mediterraneum (cluster D), the formerly described specific chickpea microsymbionts. Most isolates belong to cluster A, showing higher sequence similarity with Mesorhizobium huakuii and Mesorhizobium amorphae. The association found between the province of origin and species cluster of the isolates suggests biogeography patterns: most isolates from the north, center, and south belong to clusters B, A, and D, respectively. Most of the highly efficient isolates (symbiotic effectiveness >75%) belong to cluster B. A correlation was found between species cluster and origin soil pH of the isolates, suggesting that pH is a key environmental factor, which influences the species geographic distribution. To our knowledge, this is one of the few surveys on chickpea rhizobia and the first systematic assessment of indigenous rhizobia in Portugal.}, }
@article {pmid19466479, year = {2009}, author = {Bell, CW and Acosta-Martinez, V and McIntyre, NE and Cox, S and Tissue, DT and Zak, JC}, title = {Linking microbial community structure and function to seasonal differences in soil moisture and temperature in a Chihuahuan desert grassland.}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {827-842}, pmid = {19466479}, issn = {1432-184X}, mesh = {Bacteria/enzymology/*growth &amp; development ; Biomass ; Carbon/metabolism ; *Desert Climate ; Ecosystem ; Fungi/enzymology/*growth &amp; development ; *Seasons ; Soil/analysis ; *Soil Microbiology ; *Temperature ; Texas ; }, abstract = {Global and regional climate models predict higher air temperature and less frequent, but larger precipitation events in arid regions within the next century. While many studies have addressed the impact of variable climate in arid ecosystems on plant growth and physiological responses, fewer studies have addressed soil microbial community responses to seasonal shifts in precipitation and temperature in arid ecosystems. This study examined the impact of a wet (2004), average (2005), and dry (2006) year on subsequent responses of soil microbial community structure, function, and linkages, as well as soil edaphic and nutrient characteristics in a mid-elevation desert grassland in the Chihuahuan Desert. Microbial community structure was classified as bacterial (Gram-negative, Gram-positive, and actinomycetes) and fungal (saprophytic fungi and arbuscular mycorrhiza) categories using (fatty acid methyl ester) techniques. Carbon substrate use and enzymic activity was used to characterize microbial community function annually and seasonally (summer and winter). The relationship between saprophytic fungal community structure and function remained consistent across season independent of the magnitude or frequency of precipitation within any given year. Carbon utilization by fungi in the cooler winter exceeded use in the warmer summer each year suggesting that soil temperature, rather than soil moisture, strongly influenced fungal carbon use and structure and function dynamics. The structure/function relationship for AM fungi and soil bacteria notably changed across season. Moreover, the abundance of Gram-positive bacteria was lower in the winter compared to Gram-negative bacteria. Bacterial carbon use, however, was highest in the summer and lower during the winter. Enzyme activities did not respond to either annual or seasonal differences in the magnitude or timing of precipitation. Specific structural components of the soil microbiota community became uncoupled from total microbial function during different seasons. This change in the microbial structure/function relationship suggests that different components of the soil microbial community may provide similar ecosystem function, but differ in response to seasonal temperature and precipitation. As soil microbes encounter increased soil temperatures and altered precipitation amounts and timing that are predicted for this region, the ability of the soil microbial community to maintain functional resilience across the year may be reduced in this Chihuahuan Desert ecosystem.}, }
@article {pmid19466478, year = {2009}, author = {Adesemoye, AO and Torbert, HA and Kloepper, JW}, title = {Plant growth-promoting rhizobacteria allow reduced application rates of chemical fertilizers.}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {921-929}, pmid = {19466478}, issn = {1432-184X}, mesh = {Bacillus/*physiology ; Crops, Agricultural/growth &amp; development/microbiology ; *Fertilizers ; Solanum lycopersicum/*growth &amp; development/*microbiology ; Mycorrhizae/*physiology ; Nitrogen/metabolism ; Phosphorus/metabolism ; Soil/analysis ; *Soil Microbiology ; }, abstract = {The search for microorganisms that improve soil fertility and enhance plant nutrition has continued to attract attention due to the increasing cost of fertilizers and some of their negative environmental impacts. The objectives of this greenhouse study with tomato were to determine (1) if reduced rates of inorganic fertilizer coupled with microbial inoculants will produce plant growth, yield, and nutrient uptake levels equivalent to those with full rates of the fertilizer and (2) the minimum level to which fertilizer could be reduced when inoculants were used. The microbial inoculants used in the study were a mixture of plant growth-promoting rhizobacteria (PGPR) strains Bacillus amyloliquefaciens IN937a and Bacillus pumilus T4, a formulated PGPR product, and the arbuscular mycorrhiza fungus (AMF), Glomus intraradices. Results showed that supplementing 75% of the recommended fertilizer rate with inoculants produced plant growth, yield, and nutrient (nitrogen and phosphorus) uptake that were statistically equivalent to the full fertilizer rate without inoculants. When inoculants were used with rates of fertilizer below 75% of the recommended rate, the beneficial effects were usually not consistent; however, inoculation with the mixture of PGPR and AMF at 70% fertility consistently produced the same yield as the full fertility rate without inoculants. Without inoculants, use of fertilizer rates lower than the recommended resulted in significantly less plant growth, yield, and nutrient uptake or inconsistent impacts. The results suggest that PGPR-based inoculants can be used and should be further evaluated as components of integrated nutrient management strategies.}, }
@article {pmid19462196, year = {2009}, author = {Lowell, JL and Gordon, N and Engstrom, D and Stanford, JA and Holben, WE and Gannon, JE}, title = {Habitat heterogeneity and associated microbial community structure in a small-scale floodplain hyporheic flow path.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {611-620}, pmid = {19462196}, issn = {1432-184X}, mesh = {Bacteria/genetics/*growth &amp; development ; Biodiversity ; Biofilms ; Carbon/analysis ; Colony Count, Microbial ; DNA, Bacterial/genetics ; *Ecosystem ; Geologic Sediments/chemistry/microbiology ; Montana ; Nitrates/analysis ; Nitrogen/analysis ; Oxygen/analysis ; Phosphorus/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rivers/chemistry/microbiology ; Seasons ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {The Nyack floodplain is located on the Middle Fork of the Flathead River, an unregulated, pristine, fifth-order stream in Montana, USA, bordering Glacier National Park. The hyporheic zone is a nutritionally heterogeneous floodplain component harboring a diverse array of microbial assemblages essential in fluvial biogeochemical cycling, riverine ecosystem productivity, and trophic interactions. Despite these functions, microbial community structure in pristine hyporheic systems is not well characterized. The current study was designed to assess whether physical habitat heterogeneity within the hyporheic zone of the Nyack floodplain was sufficient to drive bacterial beta diversity between three different hyporheic flow path locations. Habitat heterogeneity was assessed by measuring soluble reactive phosphorous, nitrate, dissolved organic carbon, dissolved oxygen, and soluble total nitrogen levels seasonally at surface water infiltration, advection, and exfiltration zones. Significant spatial differences were detected in dissolved oxygen and nitrate levels, and seasonal differences were detected in dissolved oxygen, nitrate, and dissolved organic carbon levels. Denaturing gradient gel electrophoresis (DGGE) and cell counts indicated that bacterial diversity increased with abundance, and DGGE fingerprints covaried with nitrate levels where water infiltrated the hyporheic zone. The ribosomal gene phylogeny revealed that hyporheic habitat heterogeneity was sufficient to drive beta diversity between bacterial assemblages. Phylogenetic (P) tests detected sequence disparity between the flow path locations. Small distinct lineages of Firmicutes, Actinomycetes, Planctomycetes, and Acidobacteria defined the infiltration zone and alpha- and beta-proteobacterial lineages delineated the exfiltration and advection zone communities. These data suggest that spatial habitat heterogeneity drives hyporheic microbial community development and that attempts to understand functional differences between bacteria inhabiting nutritionally heterogeneous hyporheic environments might begin by focusing on the biology of these taxa.}, }
@article {pmid19462194, year = {2009}, author = {Farjalla, VF and Amado, AM and Suhett, AL and Meirelles-Pereira, F}, title = {DOC removal paradigms in highly humic aquatic ecosystems.}, journal = {Environmental science and pollution research international}, volume = {16}, number = {5}, pages = {531-538}, pmid = {19462194}, issn = {0944-1344}, mesh = {Brazil ; Carbon/*chemistry ; *Ecosystem ; Humic Substances/*analysis ; Seawater/*chemistry ; }, abstract = {BACKGROUND, AIM, AND SCOPE: Dissolved humic substances (HS) usually comprise 50-80% of the dissolved organic carbon (DOC) in aquatic ecosystems. From a trophic and biogeochemical perspective, HS has been considered to be highly refractory and is supposed to accumulate in the water. The upsurge of the microbial loop paradigm and the studies on HS photo-degradation into labile DOC gave rise to the belief that microbial processing of DOC should sustain aquatic food webs in humic waters. However, this has not been extensively supported by the literature, since most HS and their photo-products are often oxidized by microbes through respiration in most nutrient-poor humic waters. Here, we review basic concepts, classical studies, and recent data on bacterial and photo-degradation of DOC, comparing the rates of these processes in highly humic ecosystems and other aquatic ecosystems.<br><br>MATERIALS AND METHODS: We based our review on classical and recent findings from the fields of biogeochemistry and microbial ecology, highlighting some odd results from highly humic Brazilian tropical lagoons, which can reach up to 160 mg C L(-1).<br><br>RESULTS AND DISCUSSION: Highly humic tropical lagoons showed proportionally lower bacterial production rates and higher bacterial respiration rates (i.e., lower bacterial growth efficiency) than other lakes. Zooplankton showed similar delta(13)C to microalgae but not to humic DOC in these highly humic lagoons. Thus, the data reviewed here do not support the microbial loop as an efficient matter transfer pathway in highly humic ecosystems, where it is supposed to play its major role. In addition, we found that some tropical humic ecosystems presented the highest potential DOC photo-chemical mineralization (PM) rates reported in the literature, exceeding up to threefold the rates reported for temperate humic ecosystems. We propose that these atypically high PM rates are the result of a joint effect of the seasonal dynamics of allochthonous humic DOC input to these ecosystems and the high sunlight incidence throughout the year. The sunlight action on DOC is positive to microbial consumption in these highly humic lagoons, but little support is given to the enhancement of bacterial growth efficiency, since the labile photo-chemical products are mostly respired by microbes in the nutrient-poor humic waters.<br><br>CONCLUSIONS: HS may be an important source of energy for aquatic bacteria in humic waters, but it is probably not as important as a substrate to bacterial growth and to aquatic food webs, since HS consumption is mostly channeled through microbial respiration. This especially seems to be the case of humic-rich, nutrient-poor ecosystems, where the microbial loop was supposed to play its major role. Highly humic ecosystems also present the highest PM rates reported in the literature. Finally, light and bacteria can cooperate in order to enhance total carbon degradation in highly humic aquatic ecosystems but with limited effects on aquatic food webs.<br><br>More detailed studies using C- and N-stable isotope techniques and modeling approaches are needed to better understand the actual importance of HS to carbon cycling in highly humic waters.}, }
@article {pmid19458658, year = {2009}, author = {Bertics, VJ and Ziebis, W}, title = {Biodiversity of benthic microbial communities in bioturbated coastal sediments is controlled by geochemical microniches.}, journal = {The ISME journal}, volume = {3}, number = {11}, pages = {1269-1285}, doi = {10.1038/ismej.2009.62}, pmid = {19458658}, issn = {1751-7370}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; *Biodiversity ; Decapoda/chemistry/*metabolism ; Geologic Sediments/*chemistry/*microbiology ; Molecular Sequence Data ; Phylogeny ; Seawater/chemistry/microbiology ; }, abstract = {We used a combination of field and laboratory approaches to address how the bioturbation activity of two crustaceans, the ghost shrimp Neotrypaea californiensis and the fiddler crab Uca crenulata, affects the microbial diversity in the seabed of a coastal lagoon (Catalina Harbor, Santa Catalina Island, CA, USA). Detailed geochemical analyses, including oxygen microsensor measurements, were performed to characterize environmental parameters. We used a whole-assemblage fingerprinting approach (ARISA: amplified ribosomal intergenic spacer analysis) to compare bacterial diversity along geochemical gradients and in relation to subsurface microniches. The two crustaceans have different burrowing behaviors. The ghost shrimp maintains complex, deep-reaching burrows and permanently lives subterranean, supplying its burrow with oxygen-rich water. In contrast, the fiddler crab constructs simpler, J-shaped burrows, which it does not inhabit permanently and does not actively ventilate. Our goal was to address how varying environmental parameters affect benthic microbial communities. An important question in benthic microbial ecology has been whether burrows support similar or unique communities compared with the sediment surface. Our results showed that sediment surface microbial communities are distinct from subsurface assemblages and that different burrow types support diverse bacterial taxa. Statistical comparisons by canonical correspondence analysis indicated that the availability of oxidants (oxygen, nitrate, ferric iron) play a key role in determining the presence and abundance of different taxa. When geochemical parameters were alike, microbial communities associated with burrows showed significant similarity to sediment surface communities. Our study provides implications on the community structure of microbial communities in marine sediments and the factors controlling their distribution.}, }
@article {pmid19458653, year = {2009}, author = {Shade, A and Carey, CC and Kara, E and Bertilsson, S and McMahon, KD and Smith, MC}, title = {Can the black box be cracked? The augmentation of microbial ecology by high-resolution, automated sensing technologies.}, journal = {The ISME journal}, volume = {3}, number = {8}, pages = {881-888}, doi = {10.1038/ismej.2009.56}, pmid = {19458653}, issn = {1751-7370}, mesh = {Automation/methods ; *Biodiversity ; Ecology/*methods ; Time Factors ; *Water Microbiology ; }, abstract = {Automated sensing technologies, 'ASTs,' are tools that can monitor environmental or microbial-related variables at increasingly high temporal resolution. Microbial ecologists are poised to use AST data to couple microbial structure, function and associated environmental observations on temporal scales pertinent to microbial processes. In the context of aquatic microbiology, we discuss three applications of ASTs: windows on the microbial world, adaptive sampling and adaptive management. We challenge microbial ecologists to push AST potential in helping to reveal relationships between microbial structure and function.}, }
@article {pmid19457423, year = {2009}, author = {Camp, JG and Kanther, M and Semova, I and Rawls, JF}, title = {Patterns and scales in gastrointestinal microbial ecology.}, journal = {Gastroenterology}, volume = {136}, number = {6}, pages = {1989-2002}, pmid = {19457423}, issn = {1528-0012}, support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; DK081426/DK/NIDDK NIH HHS/United States ; T32 GM007092/GM/NIGMS NIH HHS/United States ; K01 DK073695/DK/NIDDK NIH HHS/United States ; DK073695/DK/NIDDK NIH HHS/United States ; T32 HD046369/HD/NICHD NIH HHS/United States ; R01 DK081426/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Bacteria/genetics/isolation &amp; purification/pathogenicity ; Gastrointestinal Tract/*microbiology ; Humans ; Intestinal Mucosa/microbiology ; RNA, Bacterial/genetics ; }, abstract = {The body surfaces of humans and other animals are colonized at birth by microorganisms. The majority of microbial residents on the human body exist within gastrointestinal (GI) tract communities, where they contribute to many aspects of host biology and pathobiology. Recent technological advances have expanded our ability to perceive the membership and physiologic traits of microbial communities along the GI tract. To translate this information into a mechanistic and practical understanding of host-microbe and microbe-microbe relationships, it is necessary to recast our conceptualization of the GI tract and its resident microbial communities in ecological terms. This review depicts GI microbial ecology in the context of 2 fundamental ecological concepts: (1) the patterns of biodiversity within the GI tract and (2) the scales of time, space, and environment within which we perceive those patterns. We show how this conceptual framework can be used to integrate our existing knowledge and identify important open questions in GI microbial ecology.}, }
@article {pmid19453743, year = {2009}, author = {Zhang, M and Zhang, M and Zhang, C and Du, H and Wei, G and Pang, X and Zhou, H and Liu, B and Zhao, L}, title = {Pattern extraction of structural responses of gut microbiota to rotavirus infection via multivariate statistical analysis of clone library data.}, journal = {FEMS microbiology ecology}, volume = {70}, number = {2}, pages = {21-29}, doi = {10.1111/j.1574-6941.2009.00694.x}, pmid = {19453743}, issn = {1574-6941}, mesh = {Bacteroides/classification/genetics/*growth &amp; development ; Biodiversity ; Child, Preschool ; DNA, Bacterial/genetics ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Gene Library ; Humans ; Infant ; Least-Squares Analysis ; Male ; Multivariate Analysis ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Rotavirus ; Rotavirus Infections/*microbiology ; Sequence Analysis, DNA ; }, abstract = {This study developed a new statistical strategy for analyzing clone library data to observe whether there is a defined pattern in structural responses of gut microbiota to environmental perturbations. A large clone library of genus Bacteroides was constructed with fecal samples for each subject in rotavirus-infected (Group R) and healthy children (Group H). In all, 665 clones of the 12 Group H subjects and 284 clones of the nine Group R subjects were sequenced and classified into 34 operational taxonomic units (OTUs) with a similarity cutoff at 98%. Partial least squares-discriminant analysis was used to observe the change of the Bacteroides spp. composition caused by rotavirus infection and to identify the most relevant species contributing to this shift. It was revealed that H subjects and R subjects were well separated. Bacteroides vulgatus, Bacteroides stercoris and Bacteroides fragilis were identified as the most important discriminating OTUs between two groups. The increased abundance of B. fragilis and the decreased populations of B. vulgatus and B. stercoris in infected guts observed in this study were in agreement with previous culture-based studies. The strategy developed in this work can be used to reveal patterns in structural responses of gut microbiota to environmental perturbations from large-scale 16S rRNA gene-based sequencing data.}, }
@article {pmid19453612, year = {2009}, author = {Bengtson, P and Bastviken, D and de Boer, W and Oberg, G}, title = {Possible role of reactive chlorine in microbial antagonism and organic matter chlorination in terrestrial environments.}, journal = {Environmental microbiology}, volume = {11}, number = {6}, pages = {1330-1339}, doi = {10.1111/j.1462-2920.2009.01915.x}, pmid = {19453612}, issn = {1462-2920}, mesh = {Anti-Infective Agents/chemical synthesis/metabolism ; *Antibiosis ; Bacteria/growth &amp; development ; Chloride Peroxidase/metabolism ; Chlorine/analysis/*metabolism ; *Environmental Microbiology ; Fungi/growth &amp; development ; Hypochlorous Acid/chemical synthesis/metabolism ; Organic Chemicals/chemistry ; Plants/chemistry ; Soil/analysis ; }, abstract = {Several studies have demonstrated that extensive formation of organically bound chlorine occurs both in soil and in decaying plant material. Previous studies suggest that enzymatic formation of reactive chlorine outside cells is a major source. However, the ecological role of microbial-induced extracellular chlorination processes remains unclear. In the present paper, we assess whether or not the literature supports the hypothesis that extracellular chlorination is involved in direct antagonism against competitors for the same resources. Our review shows that it is by no means rare that biotic processes create conditions that render biocidal concentrations of reactive chlorine compounds, which suggest that extracellular production of reactive chlorine may have an important role in antagonistic microbial interactions. To test the validity, we searched the UniprotPK database for microorganisms that are known to produce haloperoxidases. It appeared that many of the identified haloperoxidases from terrestrial environments are originating from organisms that are associated with living plants or decomposing plant material. The results of the in silico screening were supported by various field and laboratory studies on natural chlorination. Hence, the ability to produce reactive chlorine seems to be especially common in environments that are known for antibiotic-mediated competition for resources (interference competition). Yet, the ability to produce haloperoxidases is also recorded, for example, for plant endosymbionts and parasites, and there is little or no empirical evidence that suggests that these organisms are antagonistic.}, }
@article {pmid19453611, year = {2009}, author = {Dumont, M and Harmand, J and Rapaport, A and Godon, JJ}, title = {Towards functional molecular fingerprints.}, journal = {Environmental microbiology}, volume = {11}, number = {7}, pages = {1717-1727}, doi = {10.1111/j.1462-2920.2009.01898.x}, pmid = {19453611}, issn = {1462-2920}, mesh = {*Biodiversity ; DNA Fingerprinting/*methods ; Ecology/*methods ; Mathematics/methods ; Metagenomics/*methods ; Nitrates/metabolism ; Nitrites/metabolism ; Nitrogen/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {One of the most important challenges in microbial ecology is to determine the ecological function of dominant microbial populations in their environment. In this paper we propose a generic method coupling fingerprinting and mathematical tools to achieve the functional assigning of bacteria detected in microbial consortia. This approach was tested on a nitrification bioprocess where two functions carried out by two different communities could be clearly distinguished. The mathematical theory of observers of dynamical systems has been used to design a dynamic estimator of the active biomass concentration of each functional community from the available measurements on nitrifying performance. Then, the combination of phylotypes obtained by fingerprinting that best approximated the estimated trajectories of each functional biomass was selected through a random optimization method. By this way, a nitritation or nitratation function was assigned to each phylotype detected in the ecosystem by means of functional molecular fingerprints. The results obtained by this approach were successfully compared with the information obtained from 16S rDNA identification. This original approach can be used on any biosystem involving n successive cascading bioreactions performed by n communities.}, }
@article {pmid19453522, year = {2009}, author = {Erguder, TH and Boon, N and Wittebolle, L and Marzorati, M and Verstraete, W}, title = {Environmental factors shaping the ecological niches of ammonia-oxidizing archaea.}, journal = {FEMS microbiology reviews}, volume = {33}, number = {5}, pages = {855-869}, doi = {10.1111/j.1574-6976.2009.00179.x}, pmid = {19453522}, issn = {1574-6976}, mesh = {Ammonia/metabolism ; Archaea/*enzymology/growth &amp; development ; Crenarchaeota/enzymology/growth &amp; development ; *Ecosystem ; *Hot Springs/chemistry/microbiology ; Hydrogen-Ion Concentration ; Oxidation-Reduction ; Oxidoreductases/*metabolism ; Phosphates/analysis ; Seawater/chemistry/microbiology ; Sulfides/analysis ; }, abstract = {For more than 100 years it was believed that bacteria were the only group responsible for the oxidation of ammonia. However, recently, a new strain of archaea bearing a putative ammonia monooxygenase subunit A (amoA) gene and able to oxidize ammonia was isolated from a marine aquarium tank. Ammonia-oxidizing archaea (AOA) were subsequently discovered in many ecosystems of varied characteristics and even found as the predominant causal organisms in some environments. Here, we summarize the current knowledge on the environmental conditions related to the presence of AOA and discuss the possible site-related properties. Considering these data, we deduct the possible niches of AOA based on pH, sulfide and phosphate levels. It is proposed that the AOA might be important actors within the nitrogen cycle in low-nutrient, low-pH, and sulfide-containing environments.}, }
@article {pmid19453435, year = {2009}, author = {Rajashekar, B and Kohler, A and Johansson, T and Martin, F and Tunlid, A and Ahrén, D}, title = {Expansion of signal pathways in the ectomycorrhizal fungus Laccaria bicolor- evolution of nucleotide sequences and expression patterns in families of protein kinases and RAS small GTPases.}, journal = {The New phytologist}, volume = {183}, number = {2}, pages = {365-379}, doi = {10.1111/j.1469-8137.2009.02860.x}, pmid = {19453435}, issn = {1469-8137}, mesh = {Base Sequence ; *Evolution, Molecular ; *Gene Expression Regulation, Fungal ; Genetic Variation ; Laccaria/enzymology/*genetics ; Multigene Family/genetics ; Mycorrhizae/enzymology/*genetics ; Phylogeny ; Protein Kinases/*genetics/metabolism ; Sequence Homology, Amino Acid ; *Signal Transduction ; ras Proteins/classification/*genetics/metabolism ; }, abstract = {The ectomycorrhizal fungus Laccaria bicolor has the largest genome of all fungi yet sequenced. The large genome size is partly a result of an expansion of gene family sizes. Among the largest gene families are protein kinases and RAS small guanosine triphosphatases (GTPases), which are key components of signal transduction pathways. Comparative genomics and phylogenetic analyses were used to examine the evolution of the two largest families of protein kinases and RAS small GTPases in L. bicolor. Expression levels in various tissues and growth conditions were inferred from microarray data. The two families possessed a large number of young duplicates (paralogs) that had arisen in the Laccaria lineage following the separation from the saprophyte Coprinopsis cinerea. The protein kinase paralogs were dispersed in many small clades and the majority were pseudogenes. By contrast, the RAS paralogs were found in three large groups of RAS1-, RAS2- and RHO1-like GTPases with few pseudogenes. Duplicates of protein kinases and RAS small GTPase have either retained, gained or lost motifs found in the coding regions of their ancestors. Frequent outcomes during evolution were the formation of pseudogenes (nonfunctionalization) or proteins with novel structures and expression patterns (neofunctionalization).}, }
@article {pmid19452680, year = {2009}, author = {Zhang, L and De Gusseme, B and De Schryver, P and Mendoza, L and Marzorati, M and Verstraete, W}, title = {Decreasing sulfide generation in sewage by dosing formaldehyde and its derivatives under anaerobic conditions.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {59}, number = {6}, pages = {1248-1254}, pmid = {19452680}, issn = {0273-1223}, mesh = {Anaerobiosis/drug effects ; City Planning/economics ; Environment Design/economics ; Formaldehyde/analogs &amp; derivatives/*chemistry/*metabolism/pharmacology ; Occupational Exposure ; Sewage/*chemistry/*microbiology ; Sulfides/*analysis/*metabolism ; }, abstract = {Hydrogen sulfide emission in sewers is associated with toxicity, corrosion, odour nuisance and high costs. In this study, a new method to inhibit sulfide generation by means of formaldehyde and its derivatives has been evaluated under anaerobic conditions. The possible impact of formaldehyde on an activated sludge system and an appraisal of the economic aspects are presented as well. A dosage of 19 mg L(-1) formaldehyde resulted in a decrease of the sulfide production of 90%. Dosing of 32 mg L(-1) paraformaldehyde and addition of 111 mg L(-1) ureaformaldehyde were not sufficient to inhibit the sulfide generation in sewage to the same extent. The impacts of 19 mg L(-1) formaldehyde on activated sludge, in terms of COD removal, nitrification rate and oxygen uptake rates, were negligible. This suggests that formaldehyde dosage is a feasible technique to abate the sulfide problem in sewers.}, }
@article {pmid19452199, year = {2009}, author = {Baschien, C and Rode, G and Böckelmann, U and Götz, P and Szewzyk, U}, title = {Interactions between hyphosphere-associated bacteria and the fungus Cladosporium herbarum on aquatic leaf litter.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {642-650}, pmid = {19452199}, issn = {1432-184X}, mesh = {Antibiosis ; Biodegradation, Environmental ; Carbon/analysis ; Cellulases/metabolism ; Chryseobacterium/growth &amp; development/isolation &amp; purification/metabolism ; Cladosporium/enzymology/*growth &amp; development/isolation &amp; purification ; Coculture Techniques ; Hyphae ; Nitrogen/analysis ; Plant Leaves/*microbiology ; Ralstonia pickettii/*growth &amp; development/isolation &amp; purification ; Rivers/microbiology ; *Water Microbiology ; beta-Glucosidase/metabolism ; }, abstract = {We investigated microbial interactions of aquatic bacteria associated with hyphae (the hyphosphere) of freshwater fungi on leaf litter. Bacteria were isolated directly from the hyphae of fungi from sedimented leaves of a small stream in the National Park "Lower Oder," Germany. To investigate interactions, bacteria and fungi were pairwise co-cultivated on leaf-extract medium and in microcosms loaded with leaves. The performance of fungi and bacteria was monitored by measuring growth, enzyme production, and respiration of mono- and co-cultures. Growth inhibition of the fungus Cladosporium herbarum by Ralstonia pickettii was detected on leaf extract agar plates. In microcosms, the presence of Chryseobacterium sp. lowered the exocellulase, endocellulase, and cellobiase activity of the fungus. Additionally, the conversion of leaf material into microbial biomass was retarded in co-cultures. The respiration of the fungus was uninfluenced by the presence of the bacterium.}, }
@article {pmid19452174, year = {2009}, author = {Hedh, J and Johansson, T and Tunlid, A}, title = {Variation in host specificity and gene content in strains from genetically isolated lineages of the ectomycorrhizal fungus Paxillus involutus s. lat.}, journal = {Mycorrhiza}, volume = {19}, number = {8}, pages = {549-558}, pmid = {19452174}, issn = {1432-1890}, mesh = {Basidiomycota/*genetics/*growth &amp; development ; Betula/*microbiology ; Comparative Genomic Hybridization ; DNA, Fungal/genetics ; *Genes, Fungal ; Microarray Analysis ; Mycorrhizae/*genetics/*growth &amp; development ; Picea/*microbiology ; }, abstract = {Ectomycorrhizal fungi are known to vary in host range. Some fungi can enter into symbiosis with multiple plant species, while others have restricted host ranges. The aim of this study was to examine variation in host specificity among strains from the basidiomycete Paxillus involutus s. lat. Recent studies have shown that this fungus consists of at least four genetically isolated lineages, phylogenetic species (PS) I (which corresponds to the morphological species Paxillus obscurosporus), PS II (P. involutus s. str.), PS III (Paxillus validus), and PS IV (not yet supported by any reference material). Thirty-five Paxillus strains of PS I to IV were examined in microcosms for their capacity to infect birch (Betula pendula) and spruce (Picea abies). Seventeen strains were compatible and formed mycorrhizae with both tree species. Seven strains were incompatible with both birch and spruce. The gene content in three pairs of incompatible and compatible strains PS I, II, and III were compared using microarray-based comparative genomic hybridizations. Of 4,113 P. involutus gene representatives analyzed, 390 varied in copy numbers in at least one of the three pairwise comparisons. Only three reporters showed significant changes in all three pairwise comparisons, and none of these were changed in a similar way in three comparisons. Our data indicate that changes in host range have occurred frequently and independently among strains in P. obscurosporus, P. involutus s. str., and P. validus. No evidence was obtained demonstrating that these changes have been associated with the gain or loss of similar genes in these three species.}, }
@article {pmid19444498, year = {2009}, author = {Persson, Y and Vasaitis, R and Långström, B and Ohrn, P and Ihrmark, K and Stenlid, J}, title = {Fungi vectored by the bark beetle Ips typographus following hibernation under the bark of standing trees and in the forest litter.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {651-659}, pmid = {19444498}, issn = {1432-184X}, mesh = {Animals ; Coleoptera/*microbiology ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fungi/classification/genetics/*isolation &amp; purification ; Hibernation ; Plant Bark/*microbiology ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Soil Microbiology ; Sweden ; Trees/microbiology ; }, abstract = {The bark beetle Ips typographus has different hibernation environments, under the bark of standing trees or in the forest litter, which is likely to affect the beetle-associated fungal flora. We isolated fungi from beetles, standing I. typographus-attacked trees, and forest litter below the attacked trees. Fungal identification was done using cultural and molecular methods. The results of the two methods in detecting fungal species were compared. Fungal communities associated with I. typographus differed considerably depending on the hibernation environment. In addition to seven taxa of known ophiostomoid I. typographus-associated fungi, we detected 18 ascomycetes and anamorphic fungi, five wood-decaying basidomycetes, 11 yeasts, and four zygomycetes. Of those, 14 fungal taxa were detected exclusively from beetles that hibernated under bark, and six taxa were detected exclusively from beetles hibernating in forest litter. The spruce pathogen, Ceratocystis polonica, was detected occasionally in bark, while another spruce pathogen, Grosmannia europhioides, was detected more often from beetles hibernating under the bark as compared to litter. The identification method had a significant impact on which taxa were detected. Rapidly growing fungal taxa, e.g. Penicillium, Trichoderma, and Ophiostoma, dominated pure culture isolations; while yeasts dominated the communities detected using molecular methods. The study also demonstrated low frequencies of tree pathogenic fungi carried by I. typographus during its outbreaks and that the beetle does not require them to successfully attack and kill trees.}, }
@article {pmid19444497, year = {2009}, author = {Cooney, TJ and Simon, KS}, title = {Influence of dissolved organic matter and invertebrates on the function of microbial films in groundwater.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {599-610}, pmid = {19444497}, issn = {1432-184X}, mesh = {Amphipoda/*physiology ; Animals ; Bacteria/enzymology/*growth &amp; development ; Biofilms/*growth &amp; development ; Carbon/metabolism ; Ecosystem ; Fresh Water/chemistry/microbiology ; Geologic Sediments/microbiology ; Glucose/metabolism ; Organic Chemicals/*metabolism ; *Water Microbiology ; }, abstract = {Microbial films play a central role in mediating energy flux in groundwater ecosystems. The activity of these microbes is likely to be influenced by the availability of resources, especially dissolved organic matter (DOM), and also by consumers, such as invertebrates that feed on microbial films. We used microcosm experiments to examine how bacterial production and extracellular enzyme activity on rocks and fine sediments from cave streams responded to amendments of DOM of varying form and to cave amphipods (Gammarus minus) that feed on microbial films. Glucose and mixtures of DOM extracted from soils and leaves stimulated bacterial production on rocks by 89-166% relative to unamended controls. In contrast, tannic acid amendment did not influence production. Microbial films on fine sediment were not consistently responsive to DOM amendment. Glucose amendment led to increased activity of enzymes associated with C acquisition, but other forms of DOM generally did not alter enzyme activity. DOM amendment led to removal of nitrate and this was correlated with bacterial production, suggesting microbes can link carbon and nitrogen cycling in groundwater as is the case in surface systems. Amphipods reduced bacterial production on rocks, but not fine sediments. The reduction caused by amphipods offset the stimulatory effect of glucose amendment, but there was no interactive effect of DOM and grazing on bacterial production or enzyme activity. Both resources and consumers play important roles in regulating microbial activity in groundwater with important implications for higher trophic levels that use microbes for food.}, }
@article {pmid19444496, year = {2009}, author = {Wu, QL and Chatzinotas, A and Wang, J and Boenigk, J}, title = {Genetic diversity of eukaryotic plankton assemblages in Eastern Tibetan Lakes differing by their salinity and altitude.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {569-581}, pmid = {19444496}, issn = {1432-184X}, support = {P 19706/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Altitude ; Cluster Analysis ; Colony Count, Microbial ; Cyanobacteria/classification/genetics/isolation &amp; purification ; Ecosystem ; Electrophoresis, Polyacrylamide Gel ; Eukaryota/classification/genetics/isolation &amp; purification ; Fresh Water/analysis/microbiology ; *Genetic Variation ; Phylogeny ; Plankton/classification/*genetics/isolation &amp; purification ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 18S/genetics ; *Salinity ; Sequence Analysis, DNA ; Tibet ; *Water Microbiology ; }, abstract = {Eukaryotic plankton assemblages in 11 high-mountain lakes located at altitudes of 2,817 to 5,134 m and over a total area of ca. one million square kilometers on the Eastern Tibet Plateau, spanning a salinity gradient from 0.2 (freshwater) to 187.1 g l(-1) (hypersaline), were investigated by cultivation independent methods. Two 18S rRNA gene-based fingerprint approaches, i.e., the terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis (DGGE) with subsequent band sequencing were applied. Samples of the same lake type (e.g., freshwater) generally shared more of the same bands or T-RFs than samples of different types (e.g., freshwater versus saline). However, a certain number of bands or T-RFs among the samples within each lake were distinct, indicating the potential presence of significant genetic diversity within each lake. PCA indicated that the most significant environmental gradient among the investigated lakes was salinity. The observed molecular profiles could be further explained (17-24%) by ion percentage of chloride, carbonate and bicarbonate, and sulfate, which were also covaried with change of altitude and latitude. Sequence analysis of selected major DGGE bands revealed many sequences (largely protist) that are not related to any known cultures but to uncultured eukaryotic picoplankton and unidentified eukaryotes. One fourth of the retrieved sequences showed < or =97% similarity to the closest sequences in the GenBank. Sequences related to well-known heterotrophic nanoflagellates were not retrieved from the DGGE gels. Several groups of eukaryotic plankton, which were found worldwide and detected in low land lakes, were also detected in habitats located above 4,400 m, suggesting a cosmopolitan distribution of these phylotypes. Collectively, our study suggests that there was a high beta-diversity of eukaryotic plankton assemblages in the investigated Tibetan lakes shaped by multiple geographic and environmental factors.}, }
@article {pmid19444360, year = {2009}, author = {Icoz, I and Andow, D and Zwahlen, C and Stotzky, G}, title = {Is the Cry1Ab protein from Bacillus thuringiensis (Bt) taken up by plants from soils previously planted with Bt corn and by carrot from hydroponic culture?.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {83}, number = {1}, pages = {48-58}, doi = {10.1007/s00128-009-9760-2}, pmid = {19444360}, issn = {1432-0800}, mesh = {Bacillus thuringiensis/*metabolism ; Bacillus thuringiensis Toxins ; Bacterial Proteins/analysis/*metabolism ; Blotting, Western ; Daucus carota/*metabolism ; Endotoxins/analysis/*metabolism ; Enzyme-Linked Immunosorbent Assay ; Hemolysin Proteins/analysis/*metabolism ; Hydroponics ; Insecticides/*metabolism ; Plants/metabolism ; Soil/analysis ; Zea mays/*metabolism ; }, abstract = {The uptake of the insecticidal Cry1Ab protein from Bacillus thuringiensis (Bt) by various crops from soils on which Bt corn had previously grown was determined. In 2005, the Cry1Ab protein was detected by Western blot in tissues (leaves plus stems) of basil, carrot, kale, lettuce, okra, parsnip, radish, snap bean, and soybean but not in tissues of beet and spinach and was estimated by enzyme-linked immunosorbent assay (ELISA) to be 0.05 +/- 0.003 ng g(-1) of fresh plant tissue in basil, 0.02 +/- 0.014 ng g(-1) in okra, and 0.34 +/- 0.176 ng g(-1) in snap bean. However, the protein was not detected by ELISA in carrot, kale, lettuce, parsnip, radish, and soybean or in the soils by Western blot. In 2006, the Cry1Ab protein was detected by Western blot in tissues of basil, carrot, kale, radish, snap bean, and soybean from soils on which Bt corn had been grown the previous year and was estimated by ELISA to be 0.02 +/- 0.014 ng g(-1) of fresh plant tissue in basil, 0.19 +/- 0.060 ng g(-1) in carrot, 0.05 +/- 0.018 ng g(-1) in kale, 0.04 +/- 0.022 ng g(-1) in radish, 0.53 +/- 0.170 ng g(-1) in snap bean, and 0.15 +/- 0.071 ng g(-1) in soybean. The Cry1Ab protein was also detected by Western blot in tissues of basil, carrot, kale, radish, and snap bean but not of soybean grown in soil on which Bt corn had not been grown since 2002; the concentration was estimated by ELISA to be 0.03 +/- 0.021 ng g(-1) in basil, 0.02 +/- 0.008 ng g(-1) in carrot, 0.04 +/- 0.017 ng g(-1) in kale, 0.02 +/- 0.012 ng g(-1) in radish, 0.05 +/- 0.004 ng g(-1) in snap bean, and 0.09 +/- 0.015 ng g(-1) in soybean. The protein was detected by Western blot in 2006 in most soils on which Bt corn had or had not been grown since 2002. The Cry1Ab protein was detected by Western blot in leaves plus stems and in roots of carrot after 56 days of growth in sterile hydroponic culture to which purified Cry1Ab protein had been added and was estimated by ELISA to be 0.08 +/- 0.021 and 0.60 +/- 0.148 ng g(-1) of fresh leaves plus stems and roots, respectively. No Cry1Ab protein was detected in the tissues of carrot grown in hydroponic culture to which no Cry1Ab protein had been added. Because of the different results obtained with different commercial Western blot (i.e., from Envirologix and Agdia) and ELISA kits (i.e., from Envirologix, Agdia, and Abraxis), it is not clear whether the presence of the Cry1Ab protein in the tissues of some plants under field condition and in carrot in sterile hydroponic culture was the result of the uptake of the protein by the plants or of the accuracy and sensitivity of the different commercial kits used. More detailed studies with additional techniques are obviously needed to confirm the uptake of Cry proteins from soil by plants subsequently planted after a Bt crop.}, }
@article {pmid19443006, year = {2009}, author = {Pham, H and Boon, N and Marzorati, M and Verstraete, W}, title = {Enhanced removal of 1,2-dichloroethane by anodophilic microbial consortia.}, journal = {Water research}, volume = {43}, number = {11}, pages = {2936-2946}, doi = {10.1016/j.watres.2009.04.004}, pmid = {19443006}, issn = {0043-1354}, mesh = {Bacteria/*metabolism ; Biodegradation, Environmental ; Carbon Dioxide ; Chlorides ; Electrodes ; Ethylene Dichlorides/*metabolism ; Hydrogen-Ion Concentration ; Water Pollutants, Chemical/*metabolism ; }, abstract = {1,2-Dichloroethane (1,2-DCA) is a well-known recalcitrant groundwater contaminant. New environment-friendly approaches for the removal of 1,2-DCA that does not bring about volatilization of the compound are required. In this study, different anodophilic consortia enriched in microbial fuel cells (MFCs) operated under airtight conditions were shown to effectively degrade 1,2-DCA (up to 102mg per liter reactor volume per day), while concomitantly generating a current. An anodophilic consortium previously enriched with acetate as the electron donor changed its composition at the rate of 48% per week and increased its richness (Rr) 3-fold, upon adapting to 1,2-DCA as the new electron donor. After being stable, during 1month of operation, it removed up to 95% of the 1,2-DCA amount in the medium in the first 2weeks, while converting 43+/-4% of electrons available from the removal to electricity. A natural consortium from a 1,2-DCA contaminated site changed its composition at the rate of 9% per week and increased its Rr 2-fold, upon adapting to the MFC anode conditions with 1,2-DCA as the electron donor. After being stable, during 1month of operation, it removed up to 85% of the 1,2-DCA amount in the medium in the first 2weeks and the coulombic efficiency was 25+/-4%. The operation of the MFCs under closed circuit conditions resulted in higher 1,2-DCA removal rates than the operation under open circuit conditions, indicating that bioelectrochemical activities enhanced the removal of 1,2-DCA in the MFC anode. The production of ethylene glycol, acetate and carbon dioxide indicated that the anodophilic bacteria oxidatively metabolized 1,2-DCA, probably by means of a hydrolysis-based pathway. The results show that MFCs can be potentially used as a practically convenient technology for the biological removal of 1,2-DCA.}, }
@article {pmid19440648, year = {2009}, author = {Spyrou, IM and Karpouzas, DG and Menkissoglu-Spiroudi, U}, title = {Do botanical pesticides alter the structure of the soil microbial community?.}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {715-727}, pmid = {19440648}, issn = {1432-184X}, mesh = {Fatty Acids/analysis ; Fungi/*drug effects/growth &amp; development ; Gram-Negative Bacteria/*drug effects/growth &amp; development ; Limonins/pharmacology ; Oleanolic Acid/analogs &amp; derivatives/pharmacology ; Organophosphorus Compounds/pharmacology ; Pesticides/*pharmacology ; Phospholipids/analysis ; Principal Component Analysis ; Soil/analysis ; *Soil Microbiology ; Sulfur Compounds/*pharmacology ; Thiazolidines/pharmacology ; }, abstract = {The effects of synthetic pesticides on the soil microbial community have been thoroughly investigated in the past mostly by culture-dependent methods and only few recent studies have used culture-independent approaches for this purpose. However, it should be noted that most of these studies have been conducted in microcosms where the soil microbial community is exposed to unrealistic concentrations of the pesticides, providing an unrealistic exposure scheme for soil microorganism. On the other hand, little is known regarding the potential impact of botanical pesticides on the soil microbial community. Therefore, a laboratory study and a field study were conducted to investigate the effects of synthetic (metham sodium [MS], sodium tetrathiocarbonate [SoTe], and fosthiazate) and botanical pesticides (azadirachtin, quillaja, and pulverized Melia azedarach fruits [PMF]) on the soil microbial community using phospholipid fatty acids (PLFA) analysis. Principal component analysis (PCA) on the results of the laboratory study indicated that the application of PMF resulted in significant changes in the soil microbial community. This was obvious by the proportional increase in the abundance of fatty acids 18:1omega9cis, 18:1omega9trans, which are common in gram-negative bacteria and saprotrophic fungi, and 18:2omega6,9, which is a fungal indicator. This response was attributed to the release of copious amounts of organic carbon and nutrients in the soil by the PMF. On the other hand, MS inhibited fungi and gram-negative bacteria, while fosthiazate and the botanical pesticides quillaja and azadirachtin did not impose significant changes in the soil microbial community. Similar results were obtained by the field study where application of the fumigants MS and SoTe significantly altered the structure of the soil microbial community with the former having a more prominent effect. Fosthiazate imposed mild changes in the soil microbial community, whereas quillaja and azadirachtin again did not show a significant effect. Overall, botanical pesticides, at their recommended dose, did not alter the structure of the soil microbial community compared to synthetic nonfumigant and fumigant pesticides which induced significant changes.}, }
@article {pmid19440274, year = {2009}, author = {Bolca, S and Huybrechts, I and Verschraegen, M and De Henauw, S and Van de Wiele, T}, title = {Validity and reproducibility of a self-administered semi-quantitative food-frequency questionnaire for estimating usual daily fat, fibre, alcohol, caffeine and theobromine intakes among Belgian post-menopausal women.}, journal = {International journal of environmental research and public health}, volume = {6}, number = {1}, pages = {121-150}, pmid = {19440274}, issn = {1660-4601}, mesh = {Aged ; Alcohol Drinking ; Belgium ; Caffeine ; *Diet ; *Diet Records ; Dietary Fats ; Dietary Fiber ; Female ; Humans ; Middle Aged ; Postmenopause ; Reproducibility of Results ; Surveys and Questionnaires ; Theobromine ; }, abstract = {A novel food-frequency questionnaire (FFQ) was developed and validated to assess the usual daily fat, saturated, mono-unsaturated and poly-unsaturated fatty acid, fibre, alcohol, caffeine, and theobromine intakes among Belgian post-menopausal women participating in dietary intervention trials with phyto-oestrogens. The relative validity of the FFQ was estimated by comparison with 7 day (d) estimated diet records (EDR, n 64) and its reproducibility was evaluated by repeated administrations 6 weeks apart (n 79). Although the questionnaire underestimated significantly all intakes compared to the 7 d EDR, it had a good ranking ability (r 0.47-0.94; weighted kappa 0.25-0.66) and it could reliably distinguish extreme intakes for all the estimated nutrients, except for saturated fatty acids. Furthermore, the correlation between repeated administrations was high (r 0.71-0.87) with a maximal misclassification of 7% (weighted kappa 0.33-0.80). In conclusion, these results compare favourably with those reported by others and indicate that the FFQ is a satisfactorily reliable and valid instrument for ranking individuals within this study population.}, }
@article {pmid19440233, year = {2009}, author = {da C Jesus, E and Marsh, TL and Tiedje, JM and de S Moreira, FM}, title = {Changes in land use alter the structure of bacterial communities in Western Amazon soils.}, journal = {The ISME journal}, volume = {3}, number = {9}, pages = {1004-1011}, doi = {10.1038/ismej.2009.47}, pmid = {19440233}, issn = {1751-7370}, mesh = {Agriculture ; Aluminum/analysis ; Bacteria/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; Brazil ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geography ; *Human Activities ; Humans ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Here we show how agricultural practices by indigenous peoples as well as forest recovery relate to the structure and composition of Amazon soil bacterial communities. Soil samples were collected in different land use systems and bacterial community composition and diversity were explored by T-RFLP, cloning and sequencing, and data were analyzed with multivariate techniques. The main differences in bacterial community structure were related to changes in the soil attributes that, in turn, were correlated to land use. Community structure changed significantly along gradients of base saturation, [Al3+] and pH. The relationship with soil attributes accounted for about 31% of the variation of the studied communities. Clear differences were observed in community composition as shown by the differential distribution of Proteobacteria, Bacteroidetes, Firmicutes, Acidobacteria and Actinobacteria. Similarity between primary and secondary forest communities indicates the recovery of bacterial community structure during succession. Pasture and crop soil communities were among the most diverse, showing that these land use types did not deplete bacterial diversity under the conditions found in our sites.}, }
@article {pmid19433544, year = {2009}, author = {Garner, CD and Antonopoulos, DA and Wagner, B and Duhamel, GE and Keresztes, I and Ross, DA and Young, VB and Altier, C}, title = {Perturbation of the small intestine microbial ecology by streptomycin alters pathology in a Salmonella enterica serovar typhimurium murine model of infection.}, journal = {Infection and immunity}, volume = {77}, number = {7}, pages = {2691-2702}, pmid = {19433544}, issn = {1098-5522}, support = {N01 AI030054/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*therapeutic use ; Bacteria/*drug effects ; Bacterial Translocation/drug effects ; *Biodiversity ; Cecum/chemistry/microbiology ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fatty Acids, Volatile/*analysis ; Female ; Humans ; Intestine, Small/*chemistry/*microbiology ; Mice ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salmonella Infections, Animal/microbiology/pathology ; Salmonella typhimurium/drug effects ; Sequence Analysis, DNA ; Streptomycin/*therapeutic use ; }, abstract = {The small intestine is an important site of infection for many enteric bacterial pathogens, and murine models, including the streptomycin-treated mouse model of infection, are frequently used to study these infections. The environment of the mouse small intestine and the microbiota with which enteric pathogens are likely to interact, however, have not been well described. Therefore, we compared the microbiota and the concentrations of short-chain fatty acids (SCFAs) present in the ileum and cecum of streptomycin-treated mice and untreated controls. We found that the microbiota in the ileum of untreated mice differed greatly from that of the cecum of the same mice, primarily among families of the phylum Firmicutes. Upon treatment with streptomycin, substantial changes in the microbial composition occurred, with a marked loss of population complexity. Characterization of the metabolic products of the microbiota, the SCFAs, showed that formate was present in the ileum but low or not detectable in the cecum while butyrate was present in the cecum but not the ileum. Treatment with streptomycin altered the SCFAs in the cecum, significantly decreasing the concentration of acetate, propionate, and butyrate. In this work, we also characterized the pathology of Salmonella infection in the ileum. Infection of streptomycin-treated mice with Salmonella was characterized by a significant increase in the relative and absolute levels of the pathogen and was associated with more severe ileal inflammation and pathology. Together these results provide a better understanding of the ileal environment in the mouse and the changes that occur upon streptomycin treatment.}, }
@article {pmid19426267, year = {2009}, author = {Deetae, P and Mounier, J and Bonnarme, P and Spinnler, HE and Irlinger, F and Helinck, S}, title = {Effects of Proteus vulgaris growth on the establishment of a cheese microbial community and on the production of volatile aroma compounds in a model cheese.}, journal = {Journal of applied microbiology}, volume = {107}, number = {4}, pages = {1404-1413}, doi = {10.1111/j.1365-2672.2009.04315.x}, pmid = {19426267}, issn = {1365-2672}, mesh = {Animals ; Bacteria/*growth &amp; development/isolation &amp; purification ; Cheese/*analysis/*microbiology ; Colony Count, Microbial ; Color ; Ecosystem ; Food Microbiology ; Gas Chromatography-Mass Spectrometry ; Hydrogen-Ion Concentration ; Organic Chemicals/*analysis ; Proteus vulgaris/*growth &amp; development ; Smell ; Sulfur Compounds/*analysis ; Volatilization ; Yeasts/*growth &amp; development/isolation &amp; purification ; }, abstract = {AIMS: To investigate the impact of Proteus vulgaris growth on a multispecies ecosystem and on volatile aroma compound production during cheese ripening.<br><br>METHODS AND RESULTS: The microbial community dynamics and the production of volatile aroma compounds of a nine-species cheese ecosystem were compared with or without the presence of P. vulgaris in the initial inoculum. Proteus vulgaris was able to colonize the cheese surface and it was one of the dominant species, representing 37% of total isolates at the end of ripening with counts of 9.2 log(10) CFU g(-1). In the presence of P. vulgaris, counts of Arthrobacter arilaitensis, Brevibacterium aurantiacum and Hafnia alvei significantly decreased. Proteus vulgaris influenced the production of total volatile aroma compounds with branched-chain aldehydes and their corresponding alcohols being most abundant.<br><br>CONCLUSIONS: Proteus vulgaris was able to successfully implant itself in a complex cheese ecosystem and significantly contributed to the organoleptic properties of cheese during ripening. This bacterium also interacted negatively with other bacteria in the ecosystem studied.<br><br>This is the first time that the impact of a Gram-negative bacterium on cheese microbial ecology and functionality has been described.}, }
@article {pmid19423632, year = {2009}, author = {Ledger, T and Aceituno, F and González, B}, title = {3-Chlorobenzoate is taken up by a chromosomally encoded transport system in Cupriavidus necator JMP134.}, journal = {Microbiology (Reading, England)}, volume = {155}, number = {Pt 8}, pages = {2757-2765}, doi = {10.1099/mic.0.029207-0}, pmid = {19423632}, issn = {1350-0872}, mesh = {Anti-Infective Agents/pharmacology ; Benzoates/pharmacology ; Biological Transport/drug effects ; Chlorobenzoates/*metabolism ; Chromosomes/*metabolism ; Cupriavidus necator/drug effects/*genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Multigene Family ; Plasmids ; RNA, Bacterial/analysis/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Transcriptional Activation ; }, abstract = {Cupriavidus necator JMP134(pJP4) is able to grow on 3-chlorobenzoate (3-CB), a model chloroaromatic pollutant. Catabolism of 3-CB is achieved via the expression of the chromosomally encoded benABCD genes and the tfd genes from plasmid pJP4. Since passive diffusion of benzoic acid derivatives at physiological pH is negligible, the uptake of this compound should be facilitated by a transport system. However, no transporter has so far been described to perform this function, and identification of chloroaromatic compound transporters has been limited. In this work, uptake experiments using 3-[ring-UL-(14)C]CB showed an inducible transport system in strain JMP134, whose expression is activated by 3-CB and benzoate. A similar level of 3-CB uptake was found for a mutant strain of JMP134, defective in chlorobenzoate degradation, indicating that metabolic drag is not an important component of the measured uptake rate. Competitive inhibitor assays showed that uptake of 3-CB was inhibited by benzoate and, to a lesser degree, by 3-CB and 3,5-dichlorobenzoate, but not by any of 12 other substituted benzoates tested. The expression of several gene candidates for this transport function was analysed by RT-PCR, including both permease-type and ABC-type ATP-dependent transporters. Induction of a chromosomally encoded putative permease transporter (benP gene) was found specifically in the presence of 3-CB or benzoate. A benP knockout mutant of strain JMP134 displayed an almost complete loss of 3-CB transport activity. This is to our knowledge the first report of a 3-CB transporter.}, }
@article {pmid19422908, year = {2009}, author = {Defoirdt, T and Boon, N and Sorgeloos, P and Verstraete, W and Bossier, P}, title = {Short-chain fatty acids and poly-beta-hydroxyalkanoates: (New) Biocontrol agents for a sustainable animal production.}, journal = {Biotechnology advances}, volume = {27}, number = {6}, pages = {680-685}, doi = {10.1016/j.biotechadv.2009.04.026}, pmid = {19422908}, issn = {1873-1899}, mesh = {*Animal Husbandry ; Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Fatty Acids/*pharmacology ; Polyhydroxyalkanoates/*pharmacology ; }, abstract = {Because of the risk of antibiotic resistance development, there is a growing awareness that antibiotics should be used more carefully in animal production. However, a decreased use of antibiotics could result in a higher frequency of pathogenic bacteria, which in its turn could lead to a higher incidence of infections. Short-chain fatty acids (SCFAs) have long been known to exhibit bacteriostatic activity. These compounds also specifically downregulate virulence factor expression and positively influence the gastrointestinal health of the host. As a consequence, there is currently considerable interest in SCFAs as biocontrol agents in animal production. Polyhydroxyalkanoates (PHAs) are polymers of beta-hydroxy short-chain fatty acids. Currently, PHAs are applied as replacements for synthetic polymers. These biopolymers can be depolymerised by many different microorganisms that produce extracellular PHA depolymerases. Interestingly, different studies provided some evidence that PHAs can also be degraded upon passage through the gastrointestinal tract of animals and consequently, adding these compounds to the feed might result in biocontrol effects similar to those described for SCFAs.}, }
@article {pmid19418092, year = {2009}, author = {Ki, JS and Zhang, R and Zhang, W and Huang, YL and Qian, PY}, title = {Analysis of RNA polymerase beta subunit (rpoB) gene sequences for the discriminative power of marine Vibrio species.}, journal = {Microbial ecology}, volume = {58}, number = {4}, pages = {679-691}, pmid = {19418092}, issn = {1432-184X}, mesh = {DNA Primers ; DNA, Bacterial/genetics ; DNA-Directed RNA Polymerases/*genetics ; Genes, Bacterial ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Vibrio/classification/*genetics/isolation &amp; purification ; }, abstract = {In the present study, we sequenced the RNA polymerase beta subunit (rpoB) gene of marine Vibrio species and assessed its discriminative power in identifying vibrios. Both the rpoB and 16S rRNA sequences of 29 phenotypically different Vibrio strains isolated from coastal waters were determined. Molecular and phylogenetic comparisons of the sequences of these two genes classified the 29 strains into 11 different species. The resolution of the Vibrio spp. on the rpoB phylogenetic tree was approximately three times greater than that on the 16S rRNA phylogenetic tree. Moreover, by comparing the rpoB sequences of 98 marine gamma-Proteobacteria, including 38 marine Vibrio species, Vibrio-specific primers were developed to amplify a 730-bp fragment of the rpoB gene. Using these primers, we successfully detected Vibrio signals in environmental samples and determined their relative abundances via comparisons with known standards. This rpoB-targeting polymerase chain reaction assay can be used efficiently to monitor relative Vibrio abundance in marine waters.}, }
@article {pmid19416353, year = {2009}, author = {Luef, B and Neu, TR and Peduzzi, P}, title = {Imaging and quantifying virus fluorescence signals on aquatic aggregates: a new method and its implication for aquatic microbial ecology.}, journal = {FEMS microbiology ecology}, volume = {68}, number = {3}, pages = {372-380}, pmid = {19416353}, issn = {1574-6941}, support = {P 17798/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/isolation &amp; purification ; Fluorescence ; Microscopy, Confocal/*methods ; Microscopy, Fluorescence/*methods ; Software ; Viruses/*isolation &amp; purification ; *Water Microbiology ; }, abstract = {The development of accurate methods to detect and enumerate viruses is an important issue in aquatic microbial ecology. In particular, viruses attached to floating aggregates are a largely ignored field both in marine and inland water ecology. Data on the total abundance and the colonization of aggregates by viruses are rare, mainly due to methodological difficulties. In the present study, we used confocal laser scanning microscopy (CLSM) to resolve fluorescence signals of single viruses and bacterial cells in a complex three-dimensional matrix of riverine aggregates. CLSM in combination with different fluorochromes is a very promising approach for obtaining information both on the aggregate architecture and on the spatial distribution of viruses attached to fully hydrated aggregates. Aggregates from the Danube River harbored up to 5.39 x 10(9) viruses cm(-3). We discuss the problems associated with different methods such as sonication or directly counting viruses on aggregates, both combined with epifluorescence microscopy and CLSM, to quantify viruses on suspended particles.}, }
@article {pmid19411417, year = {2009}, author = {Martínez, I and Wallace, G and Zhang, C and Legge, R and Benson, AK and Carr, TP and Moriyama, EN and Walter, J}, title = {Diet-induced metabolic improvements in a hamster model of hypercholesterolemia are strongly linked to alterations of the gut microbiota.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {12}, pages = {4175-4184}, pmid = {19411417}, issn = {1098-5336}, mesh = {Animals ; Bacteria/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; Cluster Analysis ; Cricetinae ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Diet Therapy/*methods ; Electrophoresis, Polyacrylamide Gel ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Hypercholesterolemia/*therapy ; Nucleic Acid Denaturation ; Phylogeny ; Plant Extracts/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sorghum/chemistry ; }, abstract = {The mammalian gastrointestinal microbiota exerts a strong influence on host lipid and cholesterol metabolism. In this study, we have characterized the interplay among diet, gut microbial ecology, and cholesterol metabolism in a hamster model of hypercholesterolemia. Previous work in this model had shown that grain sorghum lipid extract (GSL) included in the diet significantly improved the high-density lipoprotein (HDL)/non-HDL cholesterol equilibrium (T. P. Carr, C. L. Weller, V. L. Schlegel, S. L. Cuppett, D. M. Guderian, Jr., and K. R. Johnson, J. Nutr. 135:2236-2240, 2005). Molecular analysis of the hamsters' fecal bacterial populations by pyrosequencing of 16S rRNA tags, PCR-denaturing gradient gel electrophoresis, and Bifidobacterium-specific quantitative real-time PCR revealed that the improvements in cholesterol homeostasis induced through feeding the hamsters GSL were strongly associated with alterations of the gut microbiota. Bifidobacteria, which significantly increased in abundance in hamsters fed GSL, showed a strong positive association with HDL plasma cholesterol levels (r = 0.75; P = 0.001). The proportion of members of the family Coriobacteriaceae decreased when the hamsters were fed GSL and showed a high positive association with non-HDL plasma cholesterol levels (r = 0.84; P = 0.0002). These correlations were more significant than those between daily GSL intake and animal metabolic markers, implying that the dietary effects on host cholesterol metabolism are conferred, at least in part, through an effect on the gut microbiota. This study provides evidence that modulation of the gut microbiota-host metabolic interrelationship by dietary intervention has the potential to improve mammalian cholesterol homeostasis, which has relevance for cardiovascular health.}, }
@article {pmid19411407, year = {2009}, author = {Humblot, C and Guyot, JP}, title = {Pyrosequencing of tagged 16S rRNA gene amplicons for rapid deciphering of the microbiomes of fermented foods such as pearl millet slurries.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {13}, pages = {4354-4361}, pmid = {19411407}, issn = {1098-5336}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Biodiversity ; Burkina Faso ; Cluster Analysis ; DNA, Bacterial/chemistry/*genetics ; DNA, Ribosomal/chemistry/*genetics ; *Food Microbiology ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; Sequence Homology ; }, abstract = {Pearl millet slurries, mixed with groundnuts or not, were chosen as a model to investigate the feasibility of obtaining a rapid overview of community structure and population dynamics of fermented foods using pyrosequencing of tagged 16S rRNA gene amplicons. From 14 fermented samples collected either in a traditional small-scale processing unit in Burkina Faso or at laboratory scale, 137,469 sequences of bacterial 16S rRNA gene amplicons were characterized. Except for a few Proteobacteria, almost all the bacterial sequences were attributed to cultivable bacteria. This approach enabled 80.7% of the sequences to be attributed to a family and 70% to a genus but did not enable identification to the species level. The bacterial sequences were assigned to four phyla, with Firmicutes representing the highest diversity, followed by Proteobacteria, Actinobacteria, and Bacteroidetes, which were found only in the slurries prepared in traditional production units. Most of the Firmicutes were lactic acid bacteria, mainly represented by members of the Lactobacillus, Pediococcus, Leuconostoc, and Weissella genera, whose ratio varied from the onset to the end of the fermentation. The other bacteria present at the beginning of fermentation were generally no longer detected at the end, which is consistent with already-known patterns in the microbial ecology of fermented foods. In conclusion, this method seems very promising for rapid and preliminary microbial characterization in many samples of an unknown food sample, by determining numerous nucleic sequences simultaneously without the need for cloning and cultivation-dependent methods.}, }
@article {pmid19397676, year = {2009}, author = {Duncan, SH and Louis, P and Thomson, JM and Flint, HJ}, title = {The role of pH in determining the species composition of the human colonic microbiota.}, journal = {Environmental microbiology}, volume = {11}, number = {8}, pages = {2112-2122}, doi = {10.1111/j.1462-2920.2009.01931.x}, pmid = {19397676}, issn = {1462-2920}, mesh = {Base Sequence ; Colon/metabolism/*microbiology ; Dietary Carbohydrates/metabolism ; Fatty Acids, Volatile/metabolism ; Gram-Negative Bacteria/classification/*growth &amp; development/isolation &amp; purification/metabolism ; Gram-Positive Bacteria/classification/*growth &amp; development/isolation &amp; purification/metabolism ; Humans ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Starch/metabolism ; }, abstract = {The pH of the colonic lumen varies with anatomical site and microbial fermentation of dietary residue. We have investigated the impact of mildly acidic pH, which occurs in the proximal colon, on the growth of different species of human colonic bacteria in pure culture and in the complete microbial community. Growth was determined for 33 representative human colonic bacteria at three initial pH values (approximately 5.5, 6.2 and 6.7) in anaerobic YCFA medium, which includes a mixture of short-chain fatty acids (SCFA) with 0.2% glucose as energy source. Representatives of all eight Bacteroides species tested grew poorly at pH 5.5, as did Escherichia coli, whereas 19 of the 23 gram-positive anaerobes tested gave growth rates at pH 5.5 that were at least 50% of those at pH 6.7. Growth inhibition of B. thetaiotaomicron at pH 5.5 was increased by the presence of the SCFA mix (33 mM acetate, 9 mM propionate and 1 mM each of iso-valerate, valerate and iso-butyrate). Analysis of amplified 16S rRNA sequences demonstrated a major pH-driven shift within a human faecal bacterial community in a continuous flow fermentor. Bacteroides spp. accounted for 27% of 16S rRNA sequences detected at pH 5.5, but 86% of sequences at pH 6.7. Conversely, butyrate-producing gram-positive bacteria related to Eubacterium rectale represented 50% of all 16S rRNA sequences at pH 5.5, but were not detected at pH 6.7. Inhibition of the growth of a major group of gram-negative bacteria at mildly acidic pH apparently creates niches that can be exploited by more low pH-tolerant microorganisms.}, }
@article {pmid19395520, year = {2009}, author = {Opapeju, FO and Krause, DO and Payne, RL and Rademacher, M and Nyachoti, CM}, title = {Effect of dietary protein level on growth performance, indicators of enteric health, and gastrointestinal microbial ecology of weaned pigs induced with postweaning colibacillosis.}, journal = {Journal of animal science}, volume = {87}, number = {8}, pages = {2635-2643}, doi = {10.2527/jas.2008-1310}, pmid = {19395520}, issn = {1525-3163}, mesh = {Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Anti-Bacterial Agents/pharmacology ; Ciprofloxacin/pharmacology ; Diarrhea/microbiology/veterinary ; Diet/veterinary ; Dietary Proteins/*pharmacology ; Drug Resistance, Bacterial ; Escherichia coli Infections/pathology/prevention &amp; control/*veterinary ; Female ; Gastrointestinal Contents/chemistry/microbiology ; Gastrointestinal Tract/*microbiology/pathology ; Male ; Swine ; Swine Diseases/*microbiology/pathology/prevention &amp; control ; Weaning ; }, abstract = {The effect of dietary CP level on performance, enteric health, and gastrointestinal microbial ecology of weaned pigs challenged with enterotoxigenic Escherichia coli (ETEC) K88 was investigated in a 14-d study. Forty weaned pigs (BW = 5.32 +/- 0.24 kg, mean +/- SD), housed 4 per pen, were randomly assigned to 2 diets (5 pens/diet): 1) 22.5% CP or 2) 17.6% CP supplemented with AA. Diets contained the same amount of ME and standardized ileal digestible Lys, Met + Cys, Thr, and Trp based on the ideal protein ratio. Isoleucine and Val were added to the 17.6% CP diet up to the level in the 22.5% CP diet. On d 8 postweaning, pigs were challenged with 6 mL of ETEC suspension (10(10) cfu/mL) by gavage. Feed disappearance and BW were measured on d 7, 9, 10, 12, and 14 for determination of ADG, ADFI, and G:F. One pig from each pen was serially slaughtered on -1, 3, and 7 d postchallenge (10 pigs/d of slaughter) to evaluate gut morphology, and gut microbial ecology and metabolites. Pigs fed the 22.5% CP diet had greater (P < 0.05) ADG and G:F than those fed the 17.6% CP diet before infection, but performance was similar between the 2 diets after ETEC challenge and overall. On d 3 after challenge, ETEC was not detected in the ileal digesta of pigs fed the 17.6% CP diet but was detected in the ileal digesta of 80% of pigs fed the 22.5% CP diet (5.22 +/- 1.07 cfu/g, mean +/- SD). Pigs fed the 17.6% CP diet had a greater (P < 0.01) prevalence of order Clostridiales (73 vs. 50%), family Lachnospiraceae (43 vs. 18%), and genus Roseburia (13 vs. 3%) in the colon digesta 7 d after challenge compared with those fed the 22.5% CP diet. The richness and diversity of bacteria in the colon digesta were less (P < 0.05) in pigs fed the 17.6% CP diet than in those fed the 22.5% CP diet at -1, 3, and 7 d postchallenge. Pigs fed the 22.5% CP diet had greater (P < 0.05) ammonia N concentration in the colon digesta on -1 and 7 d after challenge compared with those fed the 17.6% CP diet. Pigs fed the 22.5% CP diet had deeper (P < 0.05) crypts 1 d before challenge, shorter villi 3 d after challenge, and reduced villus height:crypt depth 1 d before and 3 d after challenge compared with those fed the 17.6% CP diet. In conclusion, a reduction in the dietary CP level of weaned pigs from 22.5 to 17.6% with AA supplementation impaired growth performance before, but not after, the ETEC challenge and increased the relative composition of butyrate producing bacteria in the colon digesta after ETEC challenge.}, }
@article {pmid19393086, year = {2009}, author = {Hooper, SD and Mavromatis, K and Kyrpides, NC}, title = {Microbial co-habitation and lateral gene transfer: what transposases can tell us.}, journal = {Genome biology}, volume = {10}, number = {4}, pages = {R45}, pmid = {19393086}, issn = {1474-760X}, mesh = {Bacillus cereus/genetics/growth &amp; development ; Bacteria/classification/*genetics/growth &amp; development ; Bacterial Proteins/genetics ; Databases, Genetic ; *Ecosystem ; Escherichia coli/genetics/growth &amp; development ; Fresh Water/microbiology ; Gene Transfer, Horizontal/*genetics ; Phylogeny ; Proteobacteria/genetics/growth &amp; development ; Salmonella enterica/genetics/growth &amp; development ; Seawater/microbiology ; Soil Microbiology ; Transposases/genetics ; Water Microbiology ; }, abstract = {BACKGROUND: Determining the habitat range for various microbes is not a simple, straightforward matter, as habitats interlace, microbes move between habitats, and microbial communities change over time. In this study, we explore an approach using the history of lateral gene transfer recorded in microbial genomes to begin to answer two key questions: where have you been and who have you been with?<br><br>RESULTS: All currently sequenced microbial genomes were surveyed to identify pairs of taxa that share a transposase that is likely to have been acquired through lateral gene transfer. A microbial interaction network including almost 800 organisms was then derived from these connections. Although the majority of the connections are between closely related organisms with the same or overlapping habitat assignments, numerous examples were found of cross-habitat and cross-phylum connections.<br><br>CONCLUSIONS: We present a large-scale study of the distributions of transposases across phylogeny and habitat, and find a significant correlation between habitat and transposase connections. We observed cases where phylogenetic boundaries are traversed, especially when organisms share habitats; this suggests that the potential exists for genetic material to move laterally between diverse groups via bridging connections. The results presented here also suggest that the complex dynamics of microbial ecology may be traceable in the microbial genomes.}, }
@article {pmid19387721, year = {2009}, author = {Trifonova, R and Postma, J and Schilder, MT and van Elsas, JD}, title = {Microbial enrichment of a novel growing substrate and its effect on plant growth.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {632-641}, pmid = {19387721}, issn = {1432-184X}, mesh = {Ascomycota/*growth &amp; development ; Bacteria/*growth &amp; development ; Bacteriological Techniques ; Colony Count, Microbial ; DNA, Bacterial/isolation &amp; purification ; DNA, Fungal/isolation &amp; purification ; Germination ; Solanum lycopersicum/*growth &amp; development ; Plant Leaves/growth &amp; development ; Poaceae ; Seeds/growth &amp; development ; Soil/analysis ; *Soil Microbiology ; }, abstract = {The quality of torrefied grass fibers (TGF) as a new potting soil ingredient was tested in a greenhouse experiment. TGF was colonized with previously selected microorganisms. Four colonization treatments were compared: (1) no inoculants, (2) the fungus Coniochaeta ligniaria F/TGF15 alone, (3) the fungus followed by inoculation with two selected bacteria, and (4) the fungus with seven selected bacteria. Cultivation-based and DNA-based methods, i.e., PCR-DGGE and BOX-PCR, were applied to assess the bacterial and fungal communities established in the TGF. Although colonization was not performed under sterile conditions, all inoculated strains were recovered from TGF up to 26 days incubation. Stable fungal and bacterial populations of 10(8) and 10(9) CFU/g TGF, respectively, were reached. As a side effect of the torrefaction process that aimed at the chemical stabilization of grass fibers, potentially phytotoxic compounds were generated. These phytotoxic compounds were cold-extracted from the fibers and analyzed by gas chromatography mass spectrometry. Four of 15 target compounds that had previously been found in the extract of TGF were encountered, namely phenol, 2-methoxyphenol, benzopyran-2-one, and tetrahydro-5,6,7,7a-benzofuranone. The concentration of these compounds decreased significantly during incubation. The colonized TGF was mixed with peat (P) in a range of 100%:0%, 50%:50%, 20%:80%, and 0%:100% TGF/P (w/w), respectively, to assess suitability for plant growth. Germination of tomato seeds was assessed three times, i.e., with inoculated TGF that had been incubated for 12, 21, and 26 days. In these tests, 90-100% of the seeds germinated in 50%:50% and 20%:80% TGF/P, whereas on average only 50% of the seeds germinated in pure TGF. Germination was not improved by the microbial inoculants. However, plant fresh weight as well as leaf area of 28-day-old tomato plants were significantly increased in all treatments where C. ligniaria F/TGF15 was inoculated compared to the control treatment without microbial inoculants. Colonization with C. ligniaria also protected the substrate from uncontrolled colonization by other fungi. The excellent colonization of TGF by the selected plant-health promoting bacteria in combination with the fungus C. ligniaria offers the possibility to create disease suppressive substrate, meanwhile replacing 20% to 50% of peat in potting soil by TGF.}, }
@article {pmid19381712, year = {2009}, author = {O'Neill, B and Grossman, J and Tsai, MT and Gomes, JE and Lehmann, J and Peterson, J and Neves, E and Thies, JE}, title = {Bacterial community composition in Brazilian Anthrosols and adjacent soils characterized using culturing and molecular identification.}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {23-35}, pmid = {19381712}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/*isolation &amp; purification ; Brazil ; Culture Media ; DNA, Bacterial/genetics ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; Tropical Climate ; }, abstract = {Microbial community composition was examined in two soil types, Anthrosols and adjacent soils, sampled from three locations in the Brazilian Amazon. The Anthrosols, also known as Amazonian dark earths, are highly fertile soils that are a legacy of pre-Columbian settlement. Both Anthrosols and adjacent soils are derived from the same parent material and subject to the same environmental conditions, including rainfall and temperature; however, the Anthrosols contain high levels of charcoal-like black carbon from which they derive their dark color. The Anthrosols typically have higher cation exchange capacity, higher pH, and higher phosphorus and calcium contents. We used culture media prepared from soil extracts to isolate bacteria unique to the two soil types and then sequenced their 16S rRNA genes to determine their phylogenetic placement. Higher numbers of culturable bacteria, by over two orders of magnitude at the deepest sampling depths, were counted in the Anthrosols. Sequences of bacteria isolated on soil extract media yielded five possible new bacterial families. Also, a higher number of families in the bacteria were represented by isolates from the deeper soil depths in the Anthrosols. Higher bacterial populations and a greater diversity of isolates were found in all of the Anthrosols, to a depth of up to 1 m, compared to adjacent soils located within 50-500 m of their associated Anthrosols. Compared to standard culture media, soil extract media revealed diverse soil microbial populations adapted to the unique biochemistry and physiological ecology of these Anthrosols.}, }
@article {pmid19380465, year = {2009}, author = {Croswell, A and Amir, E and Teggatz, P and Barman, M and Salzman, NH}, title = {Prolonged impact of antibiotics on intestinal microbial ecology and susceptibility to enteric Salmonella infection.}, journal = {Infection and immunity}, volume = {77}, number = {7}, pages = {2741-2753}, pmid = {19380465}, issn = {1098-5522}, support = {R01 AI057757/AI/NIAID NIH HHS/United States ; R21 AI057757/AI/NIAID NIH HHS/United States ; AI057757/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*therapeutic use ; Bacteria/classification/*drug effects ; Bacterial Translocation/*drug effects ; *Biodiversity ; Cecum/microbiology/pathology ; Colony Count, Microbial ; Disease Susceptibility ; *Ecosystem ; Female ; Gastrointestinal Tract/*microbiology ; Ileum/microbiology/pathology ; In Situ Hybridization, Fluorescence ; Mice ; *Salmonella Infections, Animal ; }, abstract = {The impact of antibiotics on the host's protective microbiota and the resulting increased susceptibility to mucosal infection are poorly understood. In this study, antibiotic regimens commonly applied to murine enteritis models are used to examine the impact of antibiotics on the intestinal microbiota, the time course of recovery of the biota, and the resulting susceptibility to enteric Salmonella infection. Molecular analysis of the microbiota showed that antibiotic treatment has an impact on the colonization of the murine gut that is site and antibiotic dependent. While combinations of antibiotics were able to eliminate culturable bacteria, none of the antibiotic treatments were effective at sterilizing the intestinal tract. Recovery of total bacterial numbers occurs within 1 week after antibiotic withdrawal, but alterations in specific bacterial groups persist for several weeks. Increased Salmonella translocation associated with antibiotic pretreatment corrects rapidly in association with the recovery of the most dominant bacterial group, which parallels the recovery of total bacterial numbers. However, susceptibility to intestinal colonization and mucosal inflammation persists when mice are infected several weeks after withdrawal of antibiotics, correlating with subtle alterations in the intestinal microbiome involving alterations of specific bacterial groups. These results show that the colonizing microbiotas are integral to mucosal host protection, that specific features of the microbiome impact different aspects of enteric Salmonella pathogenesis, and that antibiotics can have prolonged deleterious effects on intestinal colonization resistance.}, }
@article {pmid19376925, year = {2009}, author = {Zhang, Y and Min, B and Huang, L and Angelidaki, I}, title = {Generation of electricity and analysis of microbial communities in wheat straw biomass-powered microbial fuel cells.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {11}, pages = {3389-3395}, pmid = {19376925}, issn = {1098-5336}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; Bioelectric Energy Sources/*microbiology ; Biofilms/growth &amp; development ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electricity ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Triticum/metabolism ; }, abstract = {Electricity generation from wheat straw hydrolysate and the microbial ecology of electricity-producing microbial communities developed in two-chamber microbial fuel cells (MFCs) were investigated. The power density reached 123 mW/m(2) with an initial hydrolysate concentration of 1,000 mg chemical oxygen demand (COD)/liter, while coulombic efficiencies ranged from 37.1 to 15.5%, corresponding to the initial hydrolysate concentrations of 250 to 2,000 mg COD/liter. The suspended bacteria found were different from the bacteria immobilized in the biofilm, and they played different roles in electricity generation from the hydrolysate. The bacteria in the biofilm were consortia with sequences similar to those of Bacteroidetes (40% of sequences), Alphaproteobacteria (20%), Bacillus (20%), Deltaproteobacteria (10%), and Gammaproteobacteria (10%), while the suspended consortia were predominately Bacillus (22.2%). The results of this study can contribute to improving understanding of and optimizing electricity generation in microbial fuel cells.}, }
@article {pmid19370165, year = {2009}, author = {de Groot, A and Dulermo, R and Ortet, P and Blanchard, L and Guérin, P and Fernandez, B and Vacherie, B and Dossat, C and Jolivet, E and Siguier, P and Chandler, M and Barakat, M and Dedieu, A and Barbe, V and Heulin, T and Sommer, S and Achouak, W and Armengaud, J}, title = {Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti.}, journal = {PLoS genetics}, volume = {5}, number = {3}, pages = {e1000434}, pmid = {19370165}, issn = {1553-7404}, mesh = {Africa, Northern ; Bacterial Proteins/chemistry/genetics/metabolism ; Deinococcus/*chemistry/genetics/radiation effects ; Desert Climate ; Gamma Rays ; Genome, Bacterial ; *Genomics ; Molecular Sequence Data ; *Proteomics ; Ultraviolet Rays ; }, abstract = {To better understand adaptation to harsh conditions encountered in hot arid deserts, we report the first complete genome sequence and proteome analysis of a bacterium, Deinococcus deserti VCD115, isolated from Sahara surface sand. Its genome consists of a 2.8-Mb chromosome and three large plasmids of 324 kb, 314 kb, and 396 kb. Accurate primary genome annotation of its 3,455 genes was guided by extensive proteome shotgun analysis. From the large corpus of MS/MS spectra recorded, 1,348 proteins were uncovered and semiquantified by spectral counting. Among the highly detected proteins are several orphans and Deinococcus-specific proteins of unknown function. The alliance of proteomics and genomics high-throughput techniques allowed identification of 15 unpredicted genes and, surprisingly, reversal of incorrectly predicted orientation of 11 genes. Reversal of orientation of two Deinococcus-specific radiation-induced genes, ddrC and ddrH, and identification in D. deserti of supplementary genes involved in manganese import extend our knowledge of the radiotolerance toolbox of Deinococcaceae. Additional genes involved in nutrient import and in DNA repair (i.e., two extra recA, three translesion DNA polymerases, a photolyase) were also identified and found to be expressed under standard growth conditions, and, for these DNA repair genes, after exposure of the cells to UV. The supplementary nutrient import and DNA repair genes are likely important for survival and adaptation of D. deserti to its nutrient-poor, dry, and UV-exposed extreme environment.}, }
@article {pmid19367430, year = {2009}, author = {Männistö, MK and Tiirola, M and Häggblom, MM}, title = {Effect of freeze-thaw cycles on bacterial communities of arctic tundra soil.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {621-631}, pmid = {19367430}, issn = {1432-184X}, mesh = {Arctic Regions ; Bacteria/classification/*genetics ; Cold Temperature ; DNA, Bacterial/genetics ; Ecosystem ; Finland ; *Freezing ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The effect of freeze-thaw (FT) cycles on Arctic tundra soil bacterial community was studied in laboratory microcosms. FT-induced changes to the bacterial community were followed over a 60-day period by terminal restriction fragment length polymorphism (T-RFLP) profiles of amplified 16S rRNA genes and reverse transcribed 16S rRNA. The main phylotypes of the active, RNA-derived bacterial community were identified using clone analysis. Non-metric multidimensional scaling ordination of the T-RFLP profiles indicated some shifts in the bacterial communities after three to five FT cycles at -2, -5, and -10 degrees C as analyzed both from the DNA and rRNA. The dominating T-RFLP peaks remained the same, however, and only slight variation was generally detected in the relative abundance of the main T-RF sizes of either DNA or rRNA. T-RFLP analysis coupled to clone analysis of reverse transcribed 16S rRNA indicated that the initial soil was dominated by members of Bacteroidetes, Acidobacteria, Alpha-, Beta-, and Gammaproteobacteria. The most notable change in the rRNA-derived bacterial community was a decrease in the relative abundance of a Betaproteobacteria-related phylotype after the FT cycles. This phylotype decreased, however, also in the control soil incubated at constant +5 degrees C suggesting that the decrease was not directly related to FT sensitivity. The results indicate that FT caused only minor changes in the bacterial community structure.}, }
@article {pmid19365668, year = {2009}, author = {Taylor, M and Ross, K and Bentham, R}, title = {Legionella, protozoa, and biofilms: interactions within complex microbial systems.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {538-547}, pmid = {19365668}, issn = {1432-184X}, mesh = {Animals ; *Biofilms ; Coculture Techniques ; Eukaryota/*microbiology ; Host-Pathogen Interactions ; Legionella/growth &amp; development/*physiology ; }, abstract = {Currently, the investigation of Legionella ecology falls into two distinct areas of research activity: (1) that Legionella multiply within water sources by parasitizing amoebic or ciliate hosts or (2) that Legionella grows extracellularly within biofilms. Less focus has been given to the overlaps that may occur between these two areas or the likelihood that Legionella employs multiple survival strategies to persist in water sources. It is likely that Legionella interacts with protozoa, bacteria, algae, fungi, etc., and biofilm components in a more complex fashion than multiplication or death due to the presence or absence of single components of these complex microbial systems. This paper addresses gaps that exist in the understanding of Legionella ecology and serves to pinpoint areas of future research. To assume that only one other class of organism is important to Legionella ecology may limit our understanding of how this bacterium proliferates in heated water sources and also limit our strategies for its control in the built environment.}, }
@article {pmid19363072, year = {2009}, author = {Rinnan, R and Bååth, E}, title = {Differential utilization of carbon substrates by bacteria and fungi in tundra soil.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {11}, pages = {3611-3620}, pmid = {19363072}, issn = {1098-5336}, mesh = {Acetic Acid/metabolism ; Arctic Regions ; Bacteria/*metabolism ; Carbon/*metabolism ; Carbon Isotopes/metabolism ; Fatty Acids/metabolism ; Fungi/*metabolism ; Glucose/metabolism ; Glycine/metabolism ; Phospholipids/metabolism ; *Soil Microbiology ; Starch/metabolism ; }, abstract = {Little is known about the contribution of bacteria and fungi to decomposition of different carbon compounds in arctic soils, which are an important carbon store and possibly vulnerable to climate warming. Soil samples from a subarctic tundra heath were incubated with (13)C-labeled glucose, acetic acid, glycine, starch, and vanillin, and the incorporation of (13)C into different phospholipid fatty acids (PLFA; indicative of growth) and neutral lipid fatty acids (NLFA; indicative of fungal storage) was measured after 1 and 7 days. The use of (13)C-labeled substrates allowed the addition of substrates at concentrations low enough not to affect the total amount of PLFA. The label of glucose and acetic acid was rapidly incorporated into the PLFA in a pattern largely corresponding to the fatty acid concentration profile, while glycine and especially starch were mainly taken up by bacteria and not fungi, showing that different groups of the microbial community were responsible for substrate utilization. The (13)C-incorporation from the complex substrates (starch and vanillin) increased over time. There was significant allocation of (13)C into the fungal NLFA, except for starch. For glucose, acetic acid, and glycine, the allocation decreased over time, indicating use of the storage products, whereas for vanillin incorporation into fungal NLFA increased during the incubation. In addition to providing information on functioning of the microbial communities in an arctic soil, our study showed that the combination of PLFA and NLFA analyses yields additional information on the dynamics of substrate degradation.}, }
@article {pmid19352771, year = {2009}, author = {Long, T and Or, D}, title = {Dynamics of microbial growth and coexistence on variably saturated rough surfaces.}, journal = {Microbial ecology}, volume = {58}, number = {2}, pages = {262-275}, pmid = {19352771}, issn = {1432-184X}, mesh = {Bacteria/*growth &amp; development ; Computer Simulation ; *Models, Biological ; Porosity ; *Soil Microbiology ; Surface Properties ; Time Factors ; Water ; }, abstract = {The high degree of microbial diversity found in soils is attributed to the highly heterogeneous pore space and the dynamic aqueous microenvironments. Previous studies have shown that spatial and temporal variations in aqueous diffusion pathways play an important role in shaping microbial habitats and biological activity in unsaturated porous media. A new modeling framework was developed for the quantitative description of diffusion-dominated microbial interactions focusing on competitive growth of two microbial species inhabiting partially saturated rough surfaces. Surface heterogeneity was represented by patches with different porosities and water retention properties, yielding heterogeneous distribution of water contents that varies with changes in relative humidity or soil matric potential. Nutrient diffusion and microbial growth on the variably hydrated and heterogeneous surface was modeled using a hybrid method that combines a reaction diffusion method for nutrient field with individual based model for microbial growth and expansion. The model elucidated the effects of hydration dynamics and heterogeneity on nutrient fluxes and mobility affecting microbial population growth, expansion, and coexistence at the microscale. In contrast with single species dominance under wet conditions, results demonstrated prolonged coexistence of two competing species under drier conditions where nutrient diffusion and microbial movement were both limited. The uneven distribution of resources and diffusion pathways in heterogeneous surfaces highlighted the importance of position in the landscape for survival that may compensate for competitive disadvantages conferred by physiological traits. Increased motility was beneficial for expansion and survival. Temporal variations in hydration conditions resulted in fluctuations in microbial growth rate and population size. Population growth dynamics of the dominant species under wet-dry cycles were similar to growth under average value of diffusion coefficients for dry and wet conditions, respectively, suggesting that the time-averaged diffusion coefficient could serve as a useful indicator for estimation of microbial activities in a highly dynamic system such as that found in soils.}, }
@article {pmid19352770, year = {2009}, author = {Fierer, N and Carney, KM and Horner-Devine, MC and Megonigal, JP}, title = {The biogeography of ammonia-oxidizing bacterial communities in soil.}, journal = {Microbial ecology}, volume = {58}, number = {2}, pages = {435-445}, pmid = {19352770}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; *Ecosystem ; Nitrogen/metabolism ; Nitrosomonadaceae/classification/*genetics/metabolism ; North America ; Oxidation-Reduction ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Although ammonia-oxidizing bacteria (AOB) are likely to play a key role in the soil nitrogen cycle, we have only a limited understanding of how the diversity and composition of soil AOB communities change across ecosystem types. We examined 23 soils collected from across North America and used sequence-based analyses to compare the AOB communities in each of the distinct soils. Using 97% 16S rRNA sequence similarity groups, we identified only 24 unique AOB phylotypes across all of the soils sampled. The majority of the sequences collected were in the Nitrosospira lineages (representing 80% of all the sequences collected), and AOB belonging to Nitrosospira cluster 3 were particularly common in our clone libraries and ubiquitous across the soil types. Community composition was highly variable across the collected soils, and similar ecosystem types did not always harbor similar AOB communities. We did not find any significant correlations between AOB community composition and measures of N availability. From the suite of environmental variables measured, we found the strongest correlation between temperature and AOB community composition; soils exposed to similar mean annual temperatures tended to have similar AOB communities. This finding is consistent with previous studies and suggests that temperature selects for specific AOB lineages. Given that distinct AOB taxa are likely to have unique functional attributes, the biogeographical patterns exhibited by soil AOB may be directly relevant to understanding soil nitrogen dynamics under changing environmental conditions.}, }
@article {pmid19342228, year = {2009}, author = {Ma, J and Mungoni, LJ and Verstraete, W and Carballa, M}, title = {Maximum removal rate of propionic acid as a sole carbon source in UASB reactors and the importance of the macro- and micro-nutrients stimulation.}, journal = {Bioresource technology}, volume = {100}, number = {14}, pages = {3477-3482}, doi = {10.1016/j.biortech.2009.02.060}, pmid = {19342228}, issn = {1873-2976}, mesh = {Bacteria, Anaerobic/*physiology ; *Bioreactors ; Biotechnology/*methods ; Chemistry, Organic/methods ; Equipment Design ; Facility Design and Construction ; Fatty Acids/chemistry ; Filtration ; Micronutrients/*chemistry ; Models, Theoretical ; Propionates/*analysis/chemistry ; Sewage/chemistry/*microbiology ; Trace Elements/analysis ; Waste Disposal, Fluid/*methods ; }, abstract = {The maximum propionic acid (HPr) removal rate (R(HPr)) was investigated in two lab-scale Upflow Anaerobic Sludge Bed (UASB) reactors. Two feeding strategies were applied by modifying the hydraulic retention time (HRT) in the UASB(HRT) and the influent HPr concentration in the UASB(HPr), respectively. The experiment was divided into three main phases: phase 1, influent with only HPr; phase 2, HPr with macro-nutrients supplementation and phase 3, HPr with macro- and micro-nutrients supplementation. During phase 1, the maximum R(HPr) achieved was less than 3 g HPr-CODL(-1)d(-1) in both reactors. However, the subsequent supplementation of macro- and micro-nutrients during phases 2 and 3 allowed to increase the R(HPr) up to 18.1 and 32.8 g HPr-CODL(-1)d(-1), respectively, corresponding with an HRT of 0.5h in the UASB(HRT) and an influent HPr concentration of 10.5 g HPr-CODL(-1) in the UASB(HPr). Therefore, the high operational capacity of these reactor systems, specifically converting HPr with high throughput and high influent HPr level, was demonstrated. Moreover, the presence of macro- and micro-nutrients is clearly essential for stable and high HPr removal in anaerobic digestion.}, }
@article {pmid19338635, year = {2009}, author = {Gamper, HA and Walker, C and Schüßler, A}, title = {Diversispora celata sp. nov: molecular ecology and phylotaxonomy of an inconspicuous arbuscular mycorrhizal fungus.}, journal = {The New phytologist}, volume = {182}, number = {2}, pages = {495-506}, doi = {10.1111/j.1469-8137.2008.02750.x}, pmid = {19338635}, issn = {1469-8137}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Geography ; Glomeromycota/*classification/genetics/isolation &amp; purification ; Mycorrhizae/*classification/genetics/isolation &amp; purification ; *Phylogeny ; RNA, Ribosomal ; Sequence Analysis, RNA ; Spores, Fungal ; Switzerland ; }, abstract = {The increasing numbers of taxonomically unassigned phylotypes reported in molecular ecological studies contrast with the few formally described arbuscular mycorrhizal fungi (AMF; Glomeromycota). Here, a species new to science with Glomus-like spores is phylogenetically, morphologically and ecologically characterized. From single spore isolates of a previously recognized member of the Diversisporaceae from Swiss agricultural grassland, 17 new nuclear internal transcribed spacer (ITS), large subunit (LSU) and small subunit (SSU) ribosomal RNA (rRNA) gene sequences were determined and compared with 14 newly generated sequences of two close relatives and public database sequences, including environmental sequences, of known geographic origin. SSU ribosomal DNA (rDNA) sequence signatures and phylogenies based on ITS, LSU and SSU rDNA sequences show that the fungus belongs to the genus Diversispora. It is described as Diversispora celata sp. nov. Comparison with environmental sequences in the public domain confirmed its molecular genetic distinctiveness and revealed a cross-continental distribution of close relatives. The value of combining morphology and phylogeny to characterize AMF was reinforced by the morphological similarity to other species and the inconspicuous nature of D. celata spores and mycorrhizas. Inclusion of all three nuclear rDNA regions in species descriptions will facilitate species determination from environmental phylotypes.}, }
@article {pmid19330551, year = {2009}, author = {Chaer, G and Fernandes, M and Myrold, D and Bottomley, P}, title = {Comparative resistance and resilience of soil microbial communities and enzyme activities in adjacent native forest and agricultural soils.}, journal = {Microbial ecology}, volume = {58}, number = {2}, pages = {414-424}, pmid = {19330551}, issn = {1432-184X}, mesh = {Agriculture ; *Biomass ; Brazil ; Cellulase/metabolism ; Ecosystem ; Enzyme Stability ; Fluoresceins/metabolism ; Hot Temperature ; Laccase/metabolism ; Soil/*analysis ; *Soil Microbiology ; Trees/*microbiology ; }, abstract = {Degradation of soil properties following deforestation and long-term soil cultivation may lead to decreases in soil microbial diversity and functional stability. In this study, we investigated the differences in the stability (resistance and resilience) of microbial community composition and enzyme activities in adjacent soils under either native tropical forest (FST) or in agricultural cropping use for 14 years (AGR). Mineral soil samples (0 to 5 cm) from both areas were incubated at 40 degrees C, 50 degrees C, 60 degrees C, or 70 degrees C for 15 min in order to successively reduce the microbial biomass. Three and 30 days after the heat shocks, fluorescein diacetate (FDA) hydrolysis, cellulase and laccase activities, and phospholipid-derived fatty acids-based microbial community composition were measured. Microbial biomass was reduced up to 25% in both soils 3 days after the heat shocks. The higher initial values of microbial biomass, enzyme activity, total and particulate soil organic carbon, and aggregate stability in the FST soil coincided with higher enzymatic stability after heat shocks. FDA hydrolysis activity was less affected (more resistance) and cellulase and laccase activities recovered more rapidly (more resilience) in the FST soil relative to the AGR counterpart. In the AGR soil, laccase activity did not show resilience to any heat shock level up to 30 days after the disturbance. Within each soil type, the microbial community composition did not differ between heat shock and control samples at day 3. However, at day 30, FST soil samples treated at 60 degrees C and 70 degrees C contained a microbial community significantly different from the control and with lower biomass regardless of high enzyme resilience. Results of this study show that deforestation followed by long-term cultivation changed microbial community composition and had differential effects on microbial functional stability. Both soils displayed similar resilience to FDA hydrolysis, a composite measure of a broad range of hydrolases, supporting the concept of high functional redundancy in soil microbial communities. In contrast, the resilience of the substrate-specific activities of laccase and cellulase were lower in AGR soils, indicating a less diverse community of microorganisms capable of producing these enzymes and confirming that specific microbial functions are more sensitive measurements for evaluating change in the ecological stability of soils.}, }
@article {pmid19330550, year = {2009}, author = {Mirza, BS and Welsh, A and Rasul, G and Rieder, JP and Paschke, MW and Hahn, D}, title = {Variation in Frankia populations of the Elaeagnus host infection group in nodules of six host plant species after inoculation with soil.}, journal = {Microbial ecology}, volume = {58}, number = {2}, pages = {384-393}, pmid = {19330550}, issn = {1432-184X}, mesh = {DNA, Bacterial/genetics ; Elaeagnaceae/*microbiology ; Frankia/classification/*genetics/isolation &amp; purification ; Genes, Bacterial ; Nitrogen Fixation ; Oxidoreductases/genetics ; Phylogeny ; Root Nodules, Plant/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; Symbiosis ; }, abstract = {The potential role of host plant species in the selection of symbiotic, nitrogen-fixing Frankia strains belonging to the Elaeagnus host infection group was assessed in bioassays with two Morella, three Elaeagnus, and one Shepherdia species as capture plants, inoculated with soil slurries made with soil collected from a mixed pine/grassland area in central Wisconsin, USA. Comparative sequence analysis of nifH gene fragments amplified from homogenates of at least 20 individual lobes of root nodules harvested from capture plants of each species confirmed the more promiscuous character of Morella cerifera and Morella pensylvanica that formed nodules with frankiae of the Alnus and the Elaeagnus host infection groups, while frankiae in nodules formed on Elaeagnus umbellata, Elaeagnus angustifolia, Elaeagnus commutata, and Shepherdia argentea generally belonged to the Elaeagnus host infection group. Diversity of frankiae of the Elaeagnus host infection groups was larger in nodules on both Morella species than in nodules formed on the other plant species. None of the plants, however, captured the entire diversity of nodule-forming frankiae. The distribution of clusters of Frankia populations and their abundance in nodules was unique for each of the plant species, with only one cluster being ubiquitous and most abundant while the remaining clusters were only present in nodules of one (six clusters) or two (two clusters) host plant species. These results demonstrate large effects of the host plant species in the selection of Frankia strains from soil for potential nodule formation and thus the significant effect of the choice of capture plant species in bioassays on diversity estimates in soil.}, }
@article {pmid19326159, year = {2009}, author = {Lee, C and Kim, J and Chinalia, FA and Shin, SG and Hwang, S}, title = {Unusual bacterial populations observed in a full-scale municipal sludge digester affected by intermittent seawater inputs.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {36}, number = {5}, pages = {769-773}, pmid = {19326159}, issn = {1476-5535}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; Seasons ; Seawater/*analysis ; Sewage/*microbiology ; }, abstract = {This study investigated the bacterial community of a full-scale anaerobic digester, which suffers from intermittent seawater contaminations, using 16S rRNA gene clone analysis over different seasons. Bacteroidetes, Proteobacteria, and unclassifiable bacteria were the three major bacterial groups within the clone library (a total of 290 clones). A significant portion of the total clones (29.3%) was not affiliated to any previously reported phylum, and 55.3% of the unclassifiable clones (16.9% of the total clones) showed potential relations to the species of Thermotogae, rarely present under normal mesophilic anaerobic conditions. These results suggested that the novel populations may have the potential to play an important role in anaerobic processes, particularly under abnormal environmental conditions. Additionally, statistical analysis supported that seasonal variations in influent characteristics, and potential competitions among different populations, may be related to the unusual bacterial diversity and community dynamics observed over the study period.}, }
@article {pmid19324389, year = {2009}, author = {De Gusseme, B and Pycke, B and Hennebel, T and Marcoen, A and Vlaeminck, SE and Noppe, H and Boon, N and Verstraete, W}, title = {Biological removal of 17alpha-ethinylestradiol by a nitrifier enrichment culture in a membrane bioreactor.}, journal = {Water research}, volume = {43}, number = {9}, pages = {2493-2503}, doi = {10.1016/j.watres.2009.02.028}, pmid = {19324389}, issn = {0043-1354}, mesh = {*Biodegradation, Environmental ; *Bioreactors ; Ethinyl Estradiol/*isolation &amp; purification ; Membranes, Artificial ; Nitrates/*metabolism ; Waste Disposal, Fluid/*methods ; Water Purification/methods ; }, abstract = {Increasing concern about the fate of 17alpha-ethinylestradiol (EE2) in the environment stimulates the search for alternative methods for wastewater treatment plant (WWTP) effluent polishing. The aim of this study was to establish an innovative and effective biological removal technique for EE2 by means of a nitrifier enrichment culture (NEC) applied in a membrane bioreactor (MBR). In batch incubation tests, the microbial consortium was able to remove EE2 from both a synthetic minimal medium and WWTP effluent. A maximum EE2 removal rate of 9.0 microg EE2 g(-1)biomass-VSS h(-1) was achieved (>94% removal efficiency). Incubation of the heterotrophic bacteria isolated from the NEC did not result in a significant EE2 removal, indicating the importance of nitrification as driving force in the mechanism. Application of the NEC in a MBR to treat a synthetic influent with an EE2 concentration of 83 ng EE2 L(-1) resulted in a removal efficiency of 99% (loading rates up to 208 ng EE2 L(-1)d(-1); membrane flux rate: 6.9 L m(-2) h(-1)). Simultaneously, complete nitrification was achieved at an optimal ammonium influent concentration of 1.0 mg NH(4)(+)-N L(-1). This minimal NH(4)(+)-N input is very advantageous for effluent polishing since the concomitant effluent nitrate concentrations will be low as well and it offers opportunities for the nitrifying MBR as a promising add-on technology for WWTP effluent polishing.}, }
@article {pmid19322604, year = {2009}, author = {Dar, SA and Bijmans, MF and Dinkla, IJ and Geurkink, B and Lens, PN and Dopson, M}, title = {Population dynamics of a single-stage sulfidogenic bioreactor treating synthetic zinc-containing waste streams.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {529-537}, pmid = {19322604}, issn = {1432-184X}, mesh = {Bioreactors/*microbiology ; DNA, Bacterial/genetics ; Desulfovibrio/classification/genetics/*growth &amp; development/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfides/metabolism ; *Waste Disposal, Fluid ; Zinc/*metabolism ; }, abstract = {Waste streams from industrial processes such as metal smelting or mining contain high concentrations of sulfate and metals with low pH. Dissimilatory sulfate reduction carried out by sulfate-reducing bacteria (SRB) at low pH can combine sulfate reduction with metal-sulfide precipitation and thus open possibilities for selective metal recovery. This study investigates the microbial diversity and population changes of a single-stage sulfidogenic gas-lift bioreactor treating synthetic zinc-rich waste water at pH 5.5 by denaturing gradient gel electrophoresis of 16S rRNA gene fragments and quantitative polymerase chain reaction. The results indicate the presence of a diverse range of phylogenetic groups with the predominant microbial populations belonging to the Desulfovibrionaceae from delta-Proteobacteria. Desulfovibrio desulfuricans-like populations were the most abundant among the SRB during the three stable phases of varying sulfide and zinc concentrations and increased from 13% to 54% of the total bacterial populations over time. The second largest group was Desulfovibrio marrakechensis-like SRB that increased from 1% to about 10% with decreasing sulfide concentrations. Desulfovibrio aminophilus-like populations were the only SRB to decrease in numbers with decreasing sulfide concentrations. However, their population was <1% of the total bacterial population in the reactor at all analyzed time points. The number of dissimilatory sulfate reductase (DsrA) gene copies per number of SRB cells decreased from 3.5 to 2 DsrA copies when the sulfide concentration was reduced, suggesting that the cells' sulfate-reducing capacity was also lowered. This study has identified the species present in a single-stage sulfidogenic bioreactor treating zinc-rich wastewater at low pH and provides insights into the microbial ecology of this biotechnological process.}, }
@article {pmid19322243, year = {2009}, author = {Rodrigues, DF and da C Jesus, E and Ayala-Del-Río, HL and Pellizari, VH and Gilichinsky, D and Sepulveda-Torres, L and Tiedje, JM}, title = {Biogeography of two cold-adapted genera: Psychrobacter and Exiguobacterium.}, journal = {The ISME journal}, volume = {3}, number = {6}, pages = {658-665}, doi = {10.1038/ismej.2009.25}, pmid = {19322243}, issn = {1751-7370}, mesh = {Antarctic Regions ; Climate ; Cluster Analysis ; Colony Count, Microbial/methods ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gram-Positive Bacteria/*isolation &amp; purification ; Michigan ; Molecular Sequence Data ; Phylogeny ; Psychrobacter/*isolation &amp; purification ; Puerto Rico ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; *Soil Microbiology ; }, abstract = {The genera Exiguobacterium and Psychrobacter have been frequently detected in and isolated from polar permafrost and ice. These two genera have members that can grow at temperatures as low as -5 and -10 degrees C, respectively. We used quantitative PCR (Q-PCR) to quantify members of these genera in 54 soil or sediment samples from polar, temperate and tropical environments to determine to what extent they are selected by cold environments. These results were further analyzed by multiple linear regression to identify the most relevant environmental factors corresponding to their distribution. Exiguobacterium was detected in all three climatic zones at similar densities, but was patchier in the temperate and tropical samples. Psychrobacter was present in almost all polar samples, was at highest densities in Antarctica sediment samples, but was in very low densities and infrequently detected in temperate and tropical soils. Clone libraries, specific for the 16S rRNA gene for each genus, were constructed from a sample from each climatic region. The clone libraries were analyzed for alpha and beta diversities, as well as for variation in population structure by using analysis of molecular variance. Results confirm that both genera were found in all three climatic zones; however, Psychrobacter populations seemed to be much more diverse than Exiguobacterium in all three climatic zones. Furthermore, Psychrobacter populations from Antarctica are different from those in Michigan and Puerto Rico, which are similar to each other.}, }
@article {pmid19319589, year = {2009}, author = {Vyas, P and Rahi, P and Gulati, A}, title = {Stress tolerance and genetic variability of phosphate-solubilizing fluorescent Pseudomonas from the cold deserts of the trans-Himalayas.}, journal = {Microbial ecology}, volume = {58}, number = {2}, pages = {425-434}, pmid = {19319589}, issn = {1432-184X}, mesh = {Asia ; Cluster Analysis ; Cold Temperature ; *Desert Climate ; Genetic Variation ; Geography ; Hydrogen-Ion Concentration ; Phosphates/*metabolism ; Phylogeny ; Pseudomonas/classification/*genetics/*growth &amp; development/isolation &amp; purification ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Salinity ; *Soil Microbiology ; Stress, Physiological ; }, abstract = {Nineteen efficient phosphate-solubilizing fluorescent Pseudomonas from the cold deserts of the trans-Himalayas were screened for stress tolerance against temperature, alkalinity, salinity, calcium salts, and desiccation. Phylogenetic analysis based on 16S rRNA gene sequencing placed these bacteria under three groups with fourteen strains in Group I including Pseudomonas trivialis and P. poae, two strains in Group II together with Pseudomonas kilonensis and P. corrugata, and three strains in Group III along with Pseudomonas jessenii and P. moraviensis. Genetic diversity assessed by ERIC and BOX-PCR revealed variability among strains belonging to the same phylogenetic groups. Cluster analysis based on the growth characteristics under regimes of different stress levels placed the strains into three distinct clusters displaying no correlation to their phylogenetic groups. Stress-tolerant strains differed in the level of decline in phosphate solubilization under increasing intensity of various stress parameters. The highest decrease occurred with 5% CaCO(3,) followed by 2.5% CaCO(3), pH 11, 5% NaCl, temperature of 37 degrees C, 40% PEG, 5% CaSO(4), 2.5% NaCl, 2.5% CaSO(4), pH 9 and temperature of 15 degrees C. Two strains belonging to Phylogenetic Group I exhibited higher phosphate solubilization at lower temperature. The results revealed that stress-tolerance ability was not limited to any particular phylogenetic group. Knowledge about the genetic variants of phosphate-solubilizing fluorescent Pseudomonas with potential for tolerance to desiccation, alkalinity, temperature, and salinity could be useful in understanding their ecological role under stressful environments of low phosphate availability.}, }
@article {pmid19319588, year = {2009}, author = {Smart, KA and Jackson, CR}, title = {Fine scale patterns in microbial extracellular enzyme activity during leaf litter decomposition in a stream and its floodplain.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {591-598}, pmid = {19319588}, issn = {1432-184X}, mesh = {Bacteria/*enzymology ; Biodegradation, Environmental ; Cellulose/metabolism ; Ecosystem ; Lignin/metabolism ; Plant Leaves/*microbiology ; Rivers/*microbiology ; *Water Microbiology ; }, abstract = {Microorganisms mediate the decomposition of leaf-litter through the release of extracellular enzymes. The surfaces of decomposing leaves are both chemically and physically heterogeneous, and spatial patterns in microbial enzyme activity on the litter surface should provide insights into fine-scale patterns of leaf-litter decomposition. Platanus occidentalis leaves were collected from the floodplain of a third-order stream in northern Mississippi, enclosed in individual litter bags, and placed in the stream channel and in the floodplain. Replicate leaves were collected approximately monthly over a 9-month period and assayed for spatial variation in microbial extracellular enzyme activity and rates of organic matter (OM) decomposition. Spatial variation in enzyme activity was measured by sampling 96 small discs (5-mm diameter) cut from each leaf. Discs were assayed for the activity of enzymes involved in lignin (oxidative enzymes) and cellulose (beta-glucosidase, cellobiohydrolase) degradation. Rates of OM loss were greater in the stream than the floodplain. Activities of all enzymes displayed high variability in both environments, with severalfold differences across individual leaves, and replicate leaves varied greatly in their distribution of activities. Geostatistical analysis revealed no clear patterns in spatial distribution of activity over time or among replicates, and replicate leaves were highly variable. These results show that fine-scale spatial heterogeneity occurs on decomposing leaves, but the level of spatial variability varies among individual leaves at the measured spatial scales. This study is the first to use geostatistical analyses to analyze landscape patterns of microbial activity on decomposing leaf litter and in conjunction with studies of the microbial community composition and/or substrate characteristics, should provide key insights into the function of these processes.}, }
@article {pmid19308405, year = {2009}, author = {Van den Abbeele, P and Grootaert, C and Possemiers, S and Verstraete, W and Verbeken, K and Van de Wiele, T}, title = {In vitro model to study the modulation of the mucin-adhered bacterial community.}, journal = {Applied microbiology and biotechnology}, volume = {83}, number = {2}, pages = {349-359}, doi = {10.1007/s00253-009-1947-2}, pmid = {19308405}, issn = {1432-0614}, mesh = {Bacteria/chemistry ; *Bacterial Adhesion ; *Bacterial Physiological Phenomena ; Bacteriological Techniques/*methods ; Humans ; Intestinal Mucosa/metabolism/*microbiology ; Models, Biological ; Mucins/*metabolism ; }, abstract = {There is an upsurge of interest in gastro-intestinal microbiology to improve the balance between positive and negative commensals. Mucosal bacteria make closer contact with the host than luminal ones and can therefore have a stronger health impact. An in vitro adhesion assay was developed to study the mucin colonization of bacteria from the mixed microbial communities of the Simulator of the Human Intestinal Microbial Ecosystem. Adhesion capacity differed substantially between bacteria and decreased from lactobacilli over fecal coliforms, bifidobacteria, and clostridia to total anaerobes. Lactobacillus rhamnosus GG adhered most selectively. Further, intestinal water lowered adhesion compared to phosphate-buffered saline. By processing the data to an Adhesion-Related Prebiotic Index, it was found that intestinal water stimulated adherence of positive commensals. Arabinoxylans decreased the adhesion capacity matrix independently, whereas inulin had less or no influence. Measurements of bacterial surface tension, surface hydrophobicity, liquid surface tension, and viscosity showed that bacterial adhesion to mucin agar is a matter of both non-specific and specific interactions. The developed methodology can be useful for the characterization of the relevant but barely investigated mucin-associated bacterial community in health and disease (e.g., IBD) as well as for its modulation with functional foods like prebiotics.}, }
@article {pmid19306116, year = {2009}, author = {Caton, TM and Caton, IR and Witte, LR and Schneegurt, MA}, title = {Archaeal diversity at the great salt plains of Oklahoma described by cultivation and molecular analyses.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {519-528}, pmid = {19306116}, issn = {1432-184X}, support = {P20 GM103418/GM/NIGMS NIH HHS/United States ; P20 RR016475/RR/NCRR NIH HHS/United States ; P20 RR16475/RR/NCRR NIH HHS/United States ; }, mesh = {Biodiversity ; DNA, Archaeal/genetics ; Gene Library ; Halobacteriaceae/classification/genetics/*isolation &amp; purification ; Oklahoma ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sequence Analysis, DNA ; *Sodium Chloride ; *Soil Microbiology ; }, abstract = {The Great Salt Plains of Oklahoma is a natural inland terrestrial hypersaline environment that forms evaporite crusts of mainly NaCl. Previous work described the bacterial community through the characterization of 105 isolates from 46 phylotypes. The current report describes the archaeal community through both microbial isolation and culture-independent techniques. Nineteen distinct archaea were isolated, and ten were characterized phenetically. Included were isolates phylogenetically related to Haloarcula, Haloferax, Halorubrum, Haloterrigena, and Natrinema. The isolates were aerobic, non-motile, Gram-negative organisms and exhibited little capacity for fermentation. All of the isolates were halophilic, with most requiring at least 15% salinity for growth, and all grew at 30% salinity. The isolates were mainly mesothermic and could grow at alkaline pH (8.5). A 16S rRNA gene library was generated by polymerase chain reaction amplification of direct soil DNA extracts, and 200 clones were sequenced and analyzed. At 99% and 94% sequence identity, 36 and 19 operational taxonomic units (OTUs) were detected, respectively, while 53 and 22 OTUs were estimated by Chao1, respectively. Coverage was relatively high (100% and 59% at 89% and 99% sequence identity, respectively), and the Shannon Index was 3.01 at 99% sequence identity, comparable to or somewhat lower than hypersaline habitats previously studied. Only sequences from Euryarchaeota in the Halobacteriales were detected, and the strength of matches to known sequences was generally low, most near 90% sequence identity. Large clusters were observed that are related to Haloarcula and Halorubrum. More than two-thirds of the sequences were in clusters that did not have close relatives reported in public databases.}, }
@article {pmid19304829, year = {2009}, author = {Hardoim, CC and Costa, R and Araújo, FV and Hajdu, E and Peixoto, R and Lins, U and Rosado, AS and van Elsas, JD}, title = {Diversity of bacteria in the marine sponge Aplysina fulva in Brazilian coastal waters.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {10}, pages = {3331-3343}, pmid = {19304829}, issn = {1098-5336}, mesh = {Animals ; Bacteria/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; Brazil ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Molecular Sequence Data ; Phylogeny ; Porifera/*microbiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Microorganisms can account for up to 60% of the fresh weight of marine sponges. Marine sponges have been hypothesized to serve as accumulation spots of particular microbial communities, but it is unknown to what extent these communities are directed by the organism or the site or occur randomly. To address this question, we assessed the composition of specific bacterial communities associated with Aplysina fulva, one of the prevalent sponge species inhabiting Brazilian waters. Specimens of A. fulva and surrounding seawater were collected in triplicate in shallow water at two sites, Caboclo Island and Tartaruga beach, Búzios, Brazil. Total community DNA was extracted from the samples using "direct" and "indirect" approaches. 16S rRNA-based PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analyses of the total bacterial community and of specific bacterial groups--Pseudomonas and Actinobacteria--revealed that the structure of these assemblages in A. fulva differed drastically from that observed in seawater. The DNA extraction methodology and sampling site were determinative for the composition of actinobacterial communities in A. fulva. However, no such effects could be gleaned from total bacterial and Pseudomonas PCR-DGGE profiles. Bacterial 16S rRNA gene clone libraries constructed from directly and indirectly extracted DNA did not differ significantly with respect to diversity and composition. Altogether, the libraries encompassed 15 bacterial phyla and the candidate division TM7. Clone sequences affiliated with the Cyanobacteria, Chloroflexi, Gamma- and Alphaproteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria were, in this order, most abundant. The bacterial communities associated with the A. fulva specimens were distinct and differed from those described in studies of sponge-associated microbiota performed with other sponge species.}, }
@article {pmid19303731, year = {2009}, author = {Li, M and Zhou, H and Hua, W and Wang, B and Wang, S and Zhao, G and Li, L and Zhao, L and Pang, X}, title = {Molecular diversity of Bacteroides spp. in human fecal microbiota as determined by group-specific 16S rRNA gene clone library analysis.}, journal = {Systematic and applied microbiology}, volume = {32}, number = {3}, pages = {193-200}, doi = {10.1016/j.syapm.2009.02.001}, pmid = {19303731}, issn = {0723-2020}, mesh = {Adolescent ; Adult ; Aged, 80 and over ; Bacteroides/*classification/genetics/isolation &amp; purification ; China ; *Cloning, Molecular ; DNA Primers ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Feces/*microbiology ; Female ; *Gene Library ; Genes, rRNA ; *Genetic Variation ; Humans ; Infant ; Male ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Bacteroides spp. represent a prominent bacterial group in human intestinal microbiota with roles in symbiosis and pathogenicity; however, the detailed composition of this group in human feces has yet to be comprehensively characterized. In this study, the molecular diversity of Bacteroides spp. in human fecal microbiota was analyzed from a seven-member, four-generation Chinese family using Bacteroides spp. group-specific 16S rRNA gene clone library analysis. A total of 549 partial 16S rRNA sequences amplified by Bacteroides spp.-specific primers were classified into 52 operational taxonomic units (OTUs) with a 99% sequence identity cut-off. Twenty-three OTUs, representing 83% of all clones, were related to 11 validly described Bacteroides species, dominated by Bacteroides coprocola, B. uniformis, and B. vulgatus. Most of the OTUs did not correspond to known species and represented hitherto uncharacterized bacteria. Relative to 16S rRNA gene universal libraries, the diversity of Bacteroides spp. detected by the group-specific libraries was much higher than previously described. Remarkable inter-individual differences were also observed in the composition of Bacteroides spp. in this family cohort. The comprehensive observation of molecular diversity of Bacteroides spp. provides new insights into potential contributions of various species in this group to human health and disease.}, }
@article {pmid19303285, year = {2009}, author = {Aldrovandi, A and Marsili, E and Stante, L and Paganin, P and Tabacchioni, S and Giordano, A}, title = {Sustainable power production in a membrane-less and mediator-less synthetic wastewater microbial fuel cell.}, journal = {Bioresource technology}, volume = {100}, number = {13}, pages = {3252-3260}, doi = {10.1016/j.biortech.2009.01.041}, pmid = {19303285}, issn = {1873-2976}, mesh = {Ammonia/chemistry ; Biodegradation, Environmental ; Bioelectric Energy Sources/microbiology ; Biomass ; Bioreactors ; Conservation of Energy Resources ; Electricity ; Electrodes ; Electrophoresis, Polyacrylamide Gel/methods ; Energy Transfer/physiology ; Equipment Design ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/metabolism ; Water Purification/*instrumentation/methods ; }, abstract = {Microbial fuel cells (MFCs) fed with wastewater are currently considered a feasible strategy for production of renewable electricity. A membrane-less MFC with biological cathode was built from a compact wastewater treatment reactor and fed with synthetic wastewater. When operated with an external resistance of 250 Omega, the MFC produced a long-term power of about 70 mW/m(2) for 10 months. Denaturing Gradient Gel Electrophoresis (DGGE) analysis of the cathode biomass when the MFC was closed on a 2100 Omega external resistance showed that the sequenced bands were affiliated with Firmicutes, alpha-Proteobacteria,beta-Proteobacteria, gamma-Proteobacteria, and Bacteroidetes groups. When the external resistance was varied between 250 and 2100 Omega, minimum sustainable resistance decreased from 900 to 750 Omega, while maximum sustainable power output decreased from 32 to 28 mW/m(2). It is likely that these effects were caused by changes in the microbial ecology of anodic and cathodic biomass attached to the electrodes. Results suggest that cathodic biomass enrichment in "electroactive" bacteria may improve MFCs power output in a similar fashion to what has been already observed for anodic biomass.}, }
@article {pmid19301066, year = {2009}, author = {Zhou, MY and Chen, XL and Zhao, HL and Dang, HY and Luan, XW and Zhang, XY and He, HL and Zhou, BC and Zhang, YZ}, title = {Diversity of both the cultivable protease-producing bacteria and their extracellular proteases in the sediments of the South China sea.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {582-590}, pmid = {19301066}, issn = {1432-184X}, mesh = {Biodiversity ; China ; DNA, Bacterial/genetics ; Gammaproteobacteria/classification/enzymology/*genetics ; Geologic Sediments/*microbiology ; Oceans and Seas ; Peptide Hydrolases/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Protease-producing bacteria are known to play an important role in degrading sedimentary particular organic nitrogen, and yet, their diversity and extracellular proteases remain largely unknown. In this paper, the diversity of the cultivable protease-producing bacteria and their extracellular proteases in the sediments of the South China Sea was investigated. The richness of the cultivable protease-producing bacteria reached 10(6) cells/g in all sediment samples. Analysis of the 16S rRNA gene sequences revealed that the predominant cultivated protease-producing bacteria are Gammaproteobacteria affiliated with the genera Pseudoalteromonas, Alteromonas, Marinobacter, Idiomarina, Halomonas, Vibrio, Shewanella, Pseudomonas, and Rheinheimera, with Alteromonas (34.6%) and Pseudoalteromonas (28.2%) as the predominant groups. Inhibitor analysis showed that nearly all the extracellular proteases from the bacteria are serine proteases or metalloproteases. Moreover, these proteases have different hydrolytic ability to different proteins, reflecting they may belong to different kinds of serine proteases or metalloproteases. To our knowledge, this study represents the first report of the diversity of bacterial proteases in deep-sea sediments.}, }
@article {pmid19295641, year = {2009}, author = {Sime-Ngando, T and Colombet, J}, title = {[Virus and prophages in aquatic ecosystems].}, journal = {Canadian journal of microbiology}, volume = {55}, number = {2}, pages = {95-109}, doi = {10.1139/w08-099}, pmid = {19295641}, issn = {0008-4166}, mesh = {Bacteriophages/genetics/isolation &amp; purification/*physiology/ultrastructure ; *Ecosystem ; Prophages/genetics/isolation &amp; purification/*physiology/ultrastructure ; *Water Microbiology ; }, abstract = {In this review, available data on the structure (diversity, abundance, biomass) and functional imprints (bacteriolysis, lysogeny, gene transfers, regulation of prokaryotic diversity) of natural viruses in the context of food webs in aquatic microbial ecology, and the related biogeochemical cycles, are summarized. Viruses are the most abundant, and probably the most diverse, biological entities in aquatic ecosystems and in the biosphere (i.e., viriosphere). Aquatic viruses typically exceed 107 particles/mL in mesotrophic conditions, the majority being represented by phages without tails and by tailed-phages such as members of the family Siphoviridae. Both types of phages have a small capsid and a small genome size, which is considered an evolutionary adaptation to planktonic life. Their contribution to microbial mortality is significant. There is strong evidence that phages exert a significant pressure on the community structure and diversity and on the diversification of potential hosts, mainly through two major pathways: biogeochemical catalysis from lysis products and horizontal gene transfers. In turn, phages are sensitive to environmental factors, both in terms of integrity and of infectivity. Some phages contain typical viral genes that code for biological functions of interest, such as photosynthesis. In general, development in viral ecology is a source of new knowledge for the scientific community in the domain of environmental sciences, but also in the context of evolutionary biology of living cellular organisms, the obligatory hosts for viruses. For example, the recent discovery of a giant virus that becomes ill through infection by another virus (i.e., a viriophage) is fuelling debate about whether viruses are alive. Finally, future research directions are identified in the context of general aquatic ecology, including ecological researches on cyanophages and other phytoplanktonic phages as a priority, primarily in freshwater lakes.}, }
@article {pmid19294463, year = {2009}, author = {Bugla-Płoskońska, G and Kiersnowski, A and Futoma-Kołoch, B and Doroszkiewicz, W}, title = {Killing of Gram-negative bacteria with normal human serum and normal bovine serum: use of lysozyme and complement proteins in the death of Salmonella strains O48.}, journal = {Microbial ecology}, volume = {58}, number = {2}, pages = {276-289}, pmid = {19294463}, issn = {1432-184X}, mesh = {Adsorption ; Animals ; Bentonite/chemistry ; Blood Bactericidal Activity ; Calcium/metabolism ; Cattle ; Complement Activation ; Complement System Proteins/*immunology/metabolism ; Humans ; Muramidase/*immunology/metabolism ; Salmonella/*growth &amp; development ; Serum/*immunology/metabolism ; X-Ray Diffraction ; }, abstract = {Serum is an environment in which bacterial cells should not exist. The serum complement system provides innate defense against microbial infections. It consists of at least 35 proteins, mostly in pre-activated enzymatic forms. The activation of complement is achieved through three major pathways: the classical, alternative, and lectin. Lysozyme, widely present in body fluids, catalyzes the hydrolysis of beta 1,4 linkage between N-acetyloglucosamine and N-acetylmuramic acid in the bacterial cell wall and cooperates with the complement system in the bactericidal action of serum. In this study, ten strains of serotype O48 Salmonella, mainly associated with warm-blooded vertebrates and clinically important causing diarrhea in infants and children, were tested. The results demonstrated that the most efficient killing of Salmonella O48 occurred when all the components of normal bovine serum (NBS) and normal human serum (NHS) cooperated. To prove the role of lysozyme in the bactericidal activity of bovine and human serum, the method of serum adsorption onto bentonite (montmorillonite, MMT) was used. In order to investigate structural transitions accompanying the adsorption of serum components, we applied X-ray diffraction methods. The results of this investigation suggested that apart from lysozyme, other proteins (as, e.g., C3 protein or IgG immunoglobulin) were adsorbed on MMT particles. It was also shown that Ca(2+) cations can be adsorbed on bentonite. This may explain the different sensitivities of the serovars belonging to the same O48 Salmonella serotype to NBS and NHS devoid of lysozyme.}, }
@article {pmid19290881, year = {2009}, author = {Nikolausz, M and Chatzinotas, A and Táncsics, A and Imfeld, G and Kästner, M}, title = {The single-nucleotide primer extension (SNuPE) method for the multiplex detection of various DNA sequences: from detection of point mutations to microbial ecology.}, journal = {Biochemical Society transactions}, volume = {37}, number = {Pt 2}, pages = {454-459}, doi = {10.1042/BST0370454}, pmid = {19290881}, issn = {1470-8752}, mesh = {DNA/*genetics ; DNA Primers ; Humans ; Microbiology ; *Point Mutation ; *Polymorphism, Single Nucleotide ; Sensitivity and Specificity ; *Sequence Analysis, DNA ; }, abstract = {Methods based on SNuPE (single-nucleotide primer extension) have become invaluable tools for the rapid and highly specific detection of point mutations and single-nucleotide polymorphisms in the field of human genetics. In the primer extension reaction, a DNA polymerase is used to label a specific primer hybridized to the target sequence by incorporating a single labelled ddNTP (dideoxynucleotide). This labelling provides not only information about the complementary nucleotide of interest in the opposite strand but also a semiquantitative analysis of the sequence targeted by the primer. Since several subdisciplines of microbiology increasingly require cultivation-independent molecular screening tools for elucidating differences between either strains or community structures based on sequence variations of marker genes, SNuPE offers a promising alternative to the existing tool box. The present review describes the method in detail and reports the state-of-the-art applications of this technique both in the field of nucleic acid detections in human genetics and in microbiology.}, }
@article {pmid19290566, year = {2009}, author = {Hamilton, CE and Faeth, SH and Dowling, TE}, title = {Distribution of hybrid fungal symbionts and environmental stress.}, journal = {Microbial ecology}, volume = {58}, number = {2}, pages = {408-413}, pmid = {19290566}, issn = {1432-184X}, mesh = {*Adaptation, Physiological ; Arizona ; Chimera ; Ecosystem ; Epichloe/*growth &amp; development ; Festuca/*microbiology ; Hybridization, Genetic ; Neotyphodium/*growth &amp; development ; Population Dynamics ; Soil Microbiology ; *Symbiosis ; }, abstract = {Most asexual fungal symbionts of grasses in the genus Neotyphodium occurring in nature are of hybrid origin. Most hybrid Neotyphodium species result from interspecific hybridization events between pathogenic Epichloë species or co-occurring non-hybrid Neotyphodium species. Current hypotheses for the prevalence of hybrid Neotyphodium species include reduction of mutation accumulation and increased adaptive response to environmental extremes. We tested the adaptive response hypothesis by characterizing the distribution of uninfected, hybrid, and non-hybrid Neotyphodium endophytes in 24 native Arizona fescue host populations and abiotic parameters at each locality. Infection was high in all host populations (>70%), but the majority of host populations were infected by non-hybrid Neotyphodium (>50% on average). Principal component analysis indicates the frequency of plants infected with hybrid fungi is negatively related to soil nutrients and positively correlated with early spring moisture. Non-hybrid infected hosts are positively associated with soil nutrients and show a complex relationship with soil moisture (negative in early spring moisture, positive with late summer soil moisture). These results suggest the frequency of uninfected, hybrid, and non-hybrid infected plants is related to resource availability and abiotic stress factors. This supports the hypothesis that hybridization in asexual fungal symbionts increases host adaptability to extreme environments.}, }
@article {pmid19286795, year = {2009}, author = {Warmink, JA and van Elsas, JD}, title = {Migratory response of soil bacteria to Lyophyllum sp. strain Karsten in soil microcosms.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {9}, pages = {2820-2830}, pmid = {19286795}, issn = {1098-5336}, mesh = {*Agaricales ; Bacteria/classification/genetics/*growth &amp; development/isolation &amp; purification ; *Bacterial Physiological Phenomena ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; *Locomotion ; Molecular Sequence Data ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; *Soil Microbiology ; }, abstract = {In this study, the selection of bacteria on the basis of their migration via fungal hyphae in soil was investigated in microcosm experiments containing Lyophyllum sp. strain Karsten (DSM2979). One week following inoculation with a bacterial community obtained from soil, selection of a few specific bacterial types was noticed at 30 mm in the growth direction of Lyophyllum sp. strain Karsten in sterile soil. Cultivation-based analyses showed that the migration-proficient types encompassed 10 bacterial groups, as evidenced by (GTG)(5) genomic fingerprinting as well as 16S rRNA gene sequencing. These were (>97% similarity) Burkholderia terrae BS001, Burkholderia sordidicola BS026, Burkholderia sediminicola BS010, and Burkholderia phenazinium BS028; Dyella japonica BS013, BS018, and BS021; "Sphingoterrabacterium pocheensis" BS024; Sphingobacterium daejeonense BS025; and Ralstonia basilensis BS017. Migration as single species was subsequently found for B. terrae BS001, D. japonica BS018 and BS021, and R. basilensis BS017. Typically, migration occurred only when these organisms were introduced at the fungal growth front and only in the direction of hyphal growth. Migration proficiency showed a one-sided correlation with the presence of the hrcR gene, used as a marker for the type III secretion system (TTSS), as all single-strain migrators were equipped with this system and most non-single-strain migrators were not. The presence of the TTSS stood in contrast to the low prevalence of TTSSs within the bacterial community used as an inoculum (<3%). Microscopic examination of B. terrae BS001 in contact with Lyophyllum sp. strain Karsten hyphae revealed the development of a biofilm surrounding the hyphae. Migration-proficient bacteria interacting with Lyophyllum sp. strain Karsten may show complex behavior (biofilm formation) at the fungal tip, leading to their translocation and growth in novel microhabitats in soil.}, }
@article {pmid19279070, year = {2009}, author = {Lacerda, CM and Reardon, KF}, title = {Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology.}, journal = {Briefings in functional genomics &amp; proteomics}, volume = {8}, number = {1}, pages = {75-87}, doi = {10.1093/bfgp/elp005}, pmid = {19279070}, issn = {1477-4062}, mesh = {Bacteria/*genetics ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/*metabolism ; Biotechnology/*methods ; Computational Biology/*methods ; Ecology ; *Environmental Microbiology ; Genome, Bacterial ; Protein Engineering ; Proteome/genetics/*metabolism ; Proteomics/*methods/trends ; Water Microbiology ; Water Purification ; }, abstract = {In this review, we present the use of proteomics to advance knowledge in the field of environmental biotechnology, including studies of bacterial physiology, metabolism and ecology. Bacteria are widely applied in environmental biotechnology for their ability to catalyze dehalogenation, methanogenesis, denitrification and sulfate reduction, among others. Their tolerance to radiation and toxic compounds is also of importance. Proteomics has an important role in helping uncover the pathways behind these cellular processes. Environmental samples are often highly complex, which makes proteome studies in this field especially challenging. Some of these challenges are the lack of genome sequences for the vast majority of environmental bacteria, difficulties in isolating bacteria and proteins from certain environments, and the presence of complex microbial communities. Despite these challenges, proteomics offers a unique dynamic view into cellular function. We present examples of environmental proteomics of model organisms, and then discuss metaproteomics (microbial community proteomics), which has the potential to provide insights into the function of a community without isolating organisms. Finally, the environmental proteomics literature is summarized as it pertains to the specific application areas of wastewater treatment, metabolic engineering, microbial ecology and environmental stress responses.}, }
@article {pmid19277770, year = {2009}, author = {Geib, SM and Jimenez-Gasco, Mdel M and Carlson, JE and Tien, M and Jabbour, R and Hoover, K}, title = {Microbial community profiling to investigate transmission of bacteria between life stages of the wood-boring beetle, Anoplophora glabripennis.}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {199-211}, pmid = {19277770}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/*genetics/isolation &amp; purification ; Cluster Analysis ; Coleoptera/*microbiology/physiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Gastrointestinal Tract/microbiology ; Larva/microbiology ; Multivariate Analysis ; Ovum/microbiology ; Sequence Analysis, DNA ; Symbiosis ; Wood/microbiology ; }, abstract = {Many insects harbor specific bacteria in their digestive tract, and these gut microbiota often play important roles in digestion and nutrient provisioning. While it is common for a given insect species to harbor a representative gut microbial community as a population, how this community is acquired and maintained from generation to generation is not known for most xylophagous insects, except termites. In this study, we examined acquisition of gut microbiota by the wood-feeding beetle, Anoplophora glabripennis, by identifying and comparing microbial community members among different life stages of the insect and with microbes it encounters in the environment. Automated ribosomal intergenic spacer analysis was employed to compare bacterial communities present in the egg and larval stages of A. glabripennis as well as with microbes found in the oviposition site and the surrounding woody tissue. Multivariate analyses were used to identify relationships between sample type and specific bacterial types (operational taxonomic units). From this analysis, bacteria that were derived from the environment, the oviposition site, and/or the egg were identified and compared with taxa found in larvae. Results showed that while some larval microbes were derived from environmental sources, other members of the larval microbial community appear to be vertically transmitted. These findings could lead to a better understanding of which microbial species are critical for the survival of this insect and to development of techniques that could be used to alter this community to disrupt the digestive physiology of the host insect as a biological control measure.}, }
@article {pmid19277769, year = {2009}, author = {Porsch, K and Meier, J and Kleinsteuber, S and Wendt-Potthoff, K}, title = {Importance of different physiological groups of iron reducing microorganisms in an acidic mining lake remediation experiment.}, journal = {Microbial ecology}, volume = {57}, number = {4}, pages = {701-717}, pmid = {19277769}, issn = {1432-184X}, mesh = {Acids/metabolism ; Biodegradation, Environmental ; DNA, Bacterial/genetics ; Environmental Monitoring ; Environmental Pollutants/*metabolism ; Ferric Compounds/metabolism ; Fresh Water/chemistry/microbiology ; Geologic Sediments/chemistry/microbiology ; Hydrogen-Ion Concentration ; Iron/*metabolism ; *Mining ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfur-Reducing Bacteria/classification/genetics/*metabolism ; }, abstract = {Iron- and sulfate-reducing microorganisms play an important role for alkalinity-generating processes in mining lakes with low pH. In the acidic mining lake 111 in Lusatia, Germany, a passive in situ remediation method was tested in a large scale experiment, in which microbial iron and sulfate reduction are stimulated by addition of Carbokalk (a mixture of the nonsugar compounds of sugar beets and lime) and straw. The treated surface sediment consisted of three layers of different pH and geochemical composition. The top layer was acidic and rich in Fe(III), the second and third layer both showed moderately acidic to circum-neutral pH values, but only the second was rich in organics, strongly reduced and sulfidic. Aim of the study was to elucidate the relative importance of neutrophilic heterotrophic, acidophilic heterotrophic, and acidophilic autotrophic iron-reducing microorganisms in each of the three layers. In order to distinguish between them, the effect of their respective characteristic electron donors acetate, glucose, and elemental sulfur on potential iron reduction rates was investigated. Limitation of iron reduction by the availability of Fe(III) was revealed by the addition of Fe(OH)(3). The three groups of iron-reducing microorganisms were quantified by most probable number (MPN) technique and their community composition was analyzed by cloning and sequencing of 16S rRNA genes. In the acidic surface layer, none of the three electron donors stimulated iron reduction; acetate even had an inhibiting effect. In agreement with this, no decrease of the added electron donors was observed. Iron reduction rates were low in comparison to the other layers. Iron reduction in layers 2 and 3 was enhanced by glucose and acetate, accompanied by a decrease of these electron donors. Addition of elemental sulfur did not enhance iron reduction in either layer. Layer 2 exhibited the highest iron reduction rate (4.08 mmol dm(-3) d(-1)) and the highest cell numbers in MPN media. In MPN enrichments from all layers, Acidithiobacillus-like sequences were frequent. In addition to these, sequences related to Fulvimonas and Clostridium dominated in layer 1. MPN enrichments of layer 2 were diverse, containing Rhodocyclaceae-related sequences and surprisingly low numbers of Geobacteraceae. In layer 3, Sulfobacillus and Trichococcus spp. were also important. It was concluded that in the surface layer mainly acidophilic, probably autotrophic and heterotrophic, iron reducers were active, whereas in layers 2 and 3 mainly neutrophilic heterotrophs were important for iron reduction. These differ from well-studied Fe(III) reducers in other environments, so they deserve further study. The potential for acid-producing sulfur-driven Fe(III) reduction seemed not to be critical for in situ remediation.}, }
@article {pmid19271192, year = {2009}, author = {Smets, BF and Lardon, L}, title = {Mass action models describing extant horizontal transfer of plasmids: inferences and parameter sensitivities.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {289-305}, doi = {10.1007/978-1-60327-853-9_17}, pmid = {19271192}, issn = {1064-3745}, mesh = {Computer Simulation ; *Gene Transfer, Horizontal ; Genetics, Microbial ; *Models, Genetic ; Plasmids/*genetics ; Software ; }, abstract = {Predicting the fate of horizontally transmissible elements in extant microbial communities might be facilitated by the availability of suitable mathematical models. Since the mid-1970s, mass action models have been introduced to describe the transfer of conjugal and mobilizable genetic elements. This chapter will summarize and explain the assumptions behind spatially homogenous models, and show the predictions by these models under typical scenarios, such as evaluating existence conditions of conjugal plasmids under chemostat or seasonal growth conditions. Special attention is given to the sensitivity of the outcomes to the various plasmid dynamic parameters. For our analysis, we developed a set of user-friendly MatLab routines, which are deposited in the public domain. We hope that the availability of these routines will encourage the computationally untrained microbiologist to make use of these mathematical models. Finally, further permutations, as well as limitations of these mass action models in view of the structured complexity of most microbial systems are addressed.}, }
@article {pmid19270679, year = {2009}, author = {Wittebolle, L and Marzorati, M and Clement, L and Balloi, A and Daffonchio, D and Heylen, K and De Vos, P and Verstraete, W and Boon, N}, title = {Initial community evenness favours functionality under selective stress.}, journal = {Nature}, volume = {458}, number = {7238}, pages = {623-626}, pmid = {19270679}, issn = {1476-4687}, mesh = {Bacteria/genetics/*metabolism ; *Biodiversity ; *Models, Biological ; Nitrates/metabolism ; Nitrites/metabolism ; RNA, Ribosomal, 16S/genetics ; *Selection, Genetic ; Stress, Physiological ; }, abstract = {Owing to the present global biodiversity crisis, the biodiversity-stability relationship and the effect of biodiversity on ecosystem functioning have become major topics in ecology. Biodiversity is a complex term that includes taxonomic, functional, spatial and temporal aspects of organismic diversity, with species richness (the number of species) and evenness (the relative abundance of species) considered among the most important measures. With few exceptions (see, for example, ref. 6), the majority of studies of biodiversity-functioning and biodiversity-stability theory have predominantly examined richness. Here we show, using microbial microcosms, that initial community evenness is a key factor in preserving the functional stability of an ecosystem. Using experimental manipulations of both richness and initial evenness in microcosms with denitrifying bacterial communities, we found that the stability of the net ecosystem denitrification in the face of salinity stress was strongly influenced by the initial evenness of the community. Therefore, when communities are highly uneven, or there is extreme dominance by one or a few species, their functioning is less resistant to environmental stress. Further unravelling how evenness influences ecosystem processes in natural and humanized environments constitutes a major future conceptual challenge.}, }
@article {pmid19267151, year = {2009}, author = {Williams, HN and Turng, BF and Kelley, JI}, title = {Survival response of Bacteriovorax in surface biofilm versus suspension when stressed by extremes in environmental conditions.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {474-484}, pmid = {19267151}, issn = {1432-184X}, mesh = {*Biofilms ; Cold Temperature ; Deltaproteobacteria/growth &amp; development/*physiology ; Hot Temperature ; Microbial Viability ; Rivers/microbiology ; Salinity ; Stress, Physiological ; *Water Microbiology ; }, abstract = {The Bacteriovorax, previously in the genus Bdellovibrio, are prokaryotes that prey upon many Gram-negative bacteria. They are ubiquitous in salt-water environments and have been reported to have a strong association with biofilms. The purpose of this study was to test the hypothesis that this association affords protection for the Bacteriovorax and enhances their survival in nature when exposed to extreme environmental conditions. Experiments were designed to compare their survival in biofilms versus in suspension when exposed to extremes in salinity and temperature. Natural mixed-population biofilms generated in moderate-salinity (16 per thousand) Patuxent River water and containing Bacteriovorax were exposed to drastic changes in salinity by placing in low-salinity (1 per thousand) river water and salt-free (no measurable salinity) distilled water for up to 14 days. In a separate trial, the biofilm was exposed to extremes in temperature, 5 degrees C and 35 degrees C, for up to 12 weeks in aquarium mesocosms. Simultaneously, suspensions of the Bacteriovorax were exposed to the same extremes in salinity and temperature as biofilms. The results revealed that the Bacteriovorax typically were able to survive for a week or longer while in association with biofilms than when in suspension. These results are consistent with observations from nature and establish that biofilms are important in the survival and ecology of the Bacteriovorax.}, }
@article {pmid19267150, year = {2009}, author = {Garbeva, P and de Boer, W}, title = {Inter-specific interactions between carbon-limited soil bacteria affect behavior and gene expression.}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {36-46}, pmid = {19267150}, issn = {1432-184X}, mesh = {Antibiosis/genetics ; Bacteroidetes/*genetics/growth &amp; development/metabolism ; Carbon/*metabolism ; Colony Count, Microbial ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Pseudomonas/*genetics/growth &amp; development/metabolism ; RNA, Bacterial/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Recent publications indicate that inter-specific interactions between soil bacteria may strongly affect the behavior of the strains involved, e.g., by increased production of antibiotics or extracellular enzymes. This may point at an enhanced competitive ability due to inter-specific triggering of gene expression. However, it is not known if such inter-specific interactions also occur during competition for carbon which is the normal situation in soil. Here, we report on competitive interactions between two taxonomically non-related bacterial strains, Pseudomonas sp. A21 and Pedobacter sp. V48, that were isolated from a dune soil. The strains showed strong effects on each other's behavior and gene expression patterns when growing together under carbon-limited conditions on agar. The most pronounced observed visual changes in mixed cultures as compared to monocultures were (1) strong inhibition of a bioindicator fungus, suggesting the production of a broad-spectrum antibiotic, and (2) the occurrence of gliding-like movement of Pedobacter cells. Two independent techniques, namely random arbitrary primed-PCR (RAP-PCR) and suppressive subtractive hybridization (SSH), identified in total 24 genes that had higher expression in mixed cultures compared to monocultures. Microbial interactions were clearly bidirectional, as differentially expressed genes were detected for both bacteria in mixed cultures. Sequence analysis of the differentially expressed genes indicated that several of them were most related to genes involved in motility and chemotaxis, secondary metabolite production and two-component signal transduction systems. The gene expression patterns suggest an interference competition strategy by the Pseudomonas strain and an escape/explorative strategy by the Pedobacter strain during confrontation with each other. Our results show that the bacterial strains can distinguish between intra- and inter-specific carbon competition.}, }
@article {pmid19259627, year = {2009}, author = {Watcharasukarn, M and Kaparaju, P and Steyer, JP and Krogfelt, KA and Angelidaki, I}, title = {Screening Escherichia coli, Enterococcus faecalis, and Clostridium perfringens as indicator organisms in evaluating pathogen-reducing capacity in biogas plants.}, journal = {Microbial ecology}, volume = {58}, number = {2}, pages = {221-230}, pmid = {19259627}, issn = {1432-184X}, mesh = {Animals ; Cattle ; Clostridium perfringens/*growth &amp; development/isolation &amp; purification ; Enterococcus faecalis/*growth &amp; development/isolation &amp; purification ; Escherichia coli/*growth &amp; development/isolation &amp; purification ; Hot Temperature ; Manure/analysis/*microbiology ; Microbial Viability ; Time Factors ; }, abstract = {This study was conducted to identify an indicator organism(s) in evaluating the pathogen-reducing capacity of biogas plants. Fresh cow manure containing 10(4) to 10(5) colony forming unit (CFU) per milliliter of Escherichia coli and Enterococcus faecalis along with an inoculated Clostridium perfringens strain were exposed to 37 degrees C for 15 days, 55 degrees C for 48 h, and 70 degrees C for 24 h. C. perfringens was the most heat-resistant organism followed by E. faecalis, while E. coli was the most heat-sensitive organism. E. coli was reduced below detection limit at all temperatures with log(10) reductions of 4.94 (10 s), 4.37 (40 min), and 2.6 (5 days) at 70 degrees C, 55 degrees C, and 37 degrees C, respectively. Maximum log(10) reductions for E. faecalis were 1.77 at 70 degrees C (1 day), 1.7 at 55 degrees C (2 days) and 3.13 at 37 degrees C (15 days). For C. perfringens, maximum log(10) reduction at 37 degrees C was 1.35 log(10) units (15 days) compared to less than 1 unit at 55 and 70 degrees C. Modeling results showed that E. faecalis and C. perfringens had higher amount of heat-resistant fraction than E. coli. Thus, E. faecalis and C. perfringens can be used as indicator organisms to evaluate pathogen-reducing capacity in biogas plants at high temperatures of 55 degrees C and 70 degrees C while at 37 degrees C E. coli could also be included as indicator organism.}, }
@article {pmid19259626, year = {2009}, author = {Azúa-Bustos, A and González-Silva, C and Mancilla, RA and Salas, L and Palma, RE and Wynne, JJ and McKay, CP and Vicuña, R}, title = {Ancient photosynthetic eukaryote biofilms in an Atacama Desert coastal cave.}, journal = {Microbial ecology}, volume = {58}, number = {3}, pages = {485-496}, pmid = {19259626}, issn = {1432-184X}, mesh = {*Biofilms ; Chile ; DNA, Algal/genetics ; *Desert Climate ; Ecosystem ; Humidity ; Hydrogen-Ion Concentration ; Microscopy, Confocal ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Photosynthesis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhodophyta/classification/genetics/*growth &amp; development/ultrastructure ; Temperature ; }, abstract = {Caves offer a stable and protected environment from harsh and changing outside prevailing conditions. Hence, they represent an interesting habitat for studying life in extreme environments. Here, we report the presence of a member of the ancient eukaryote red algae Cyanidium group in a coastal cave of the hyperarid Atacama Desert. This microorganism was found to form a seemingly monospecific biofilm growing under extremely low photon flux levels. Our work suggests that this species, Cyanidium sp. Atacama, is a new member of a recently proposed novel monophyletic lineage of mesophilic "cave" Cyanidium sp., distinct from the remaining three other lineages which are all thermo-acidophilic. The cave described in this work may represent an evolutionary island for life in the midst of the Atacama Desert.}, }
@article {pmid19258530, year = {2009}, author = {Woese, CR and Goldenfeld, N}, title = {How the microbial world saved evolution from the scylla of molecular biology and the charybdis of the modern synthesis.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {73}, number = {1}, pages = {14-21}, pmid = {19258530}, issn = {1098-5557}, mesh = {*Biological Evolution ; Ecology/*history ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Microbiology/*history/trends ; Molecular Biology/*history/trends ; }, abstract = {In this commentary, we provide a personal overview of the conceptual history of microbiology and molecular biology over the course of the last hundred years, emphasizing the relationship of these fields to the problem of evolution. We argue that despite their apparent success, all three reached an impasse that arose from the influence of dogmatic or overly narrow perspectives. Finally, we describe how recent developments in microbiology are realizing Beijerinck's vision of a field that is fully integrated with molecular biology, microbial ecology, thereby challenging and extending current thinking in evolution.}, }
@article {pmid19252940, year = {2009}, author = {Bascom-Slack, CA and Ma, C and Moore, E and Babbs, B and Fenn, K and Greene, JS and Hann, BD and Keehner, J and Kelley-Swift, EG and Kembaiyan, V and Lee, SJ and Li, P and Light, DY and Lin, EH and Schorn, MA and Vekhter, D and Boulanger, LA and Hess, WM and Vargas, PN and Strobel, GA and Strobel, SA}, title = {Multiple, novel biologically active endophytic actinomycetes isolated from upper Amazonian rainforests.}, journal = {Microbial ecology}, volume = {58}, number = {2}, pages = {374-383}, pmid = {19252940}, issn = {1432-184X}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Actinobacteria/classification/*genetics/*isolation &amp; purification/ultrastructure ; Antibiosis ; *Biodiversity ; DNA, Ribosomal/genetics ; Molecular Sequence Data ; Peru ; *Phylogeny ; RNA, Bacterial/genetics ; Sequence Analysis, DNA ; Trees/*microbiology ; Tropical Climate ; }, abstract = {Microbial biodiversity provides an increasingly important source of medically and industrially useful compounds. We have isolated 14 actinomycete species from a collection of approximately 300 plant stem samples from the upper Amazonian rainforest in Peru. All of the cultured isolates produce substances with inhibitory activity directed at a range of potential fungal and bacterial pathogens. For some organisms, this activity is very broad in spectrum while other organisms show specific activity against a limited number of organisms. Two of these organisms preferentially inhibit bacterial test organisms over eukaryotic organisms. rDNA sequence analysis indicates that these organisms are not equivalent to any other cultured deposits in GenBank. Our results provide evidence of the untapped biodiversity in the form of biologically active microbes present within the tissues of higher plants.}, }
@article {pmid19251890, year = {2009}, author = {Morales, SE and Holben, WE}, title = {Empirical testing of 16S rRNA gene PCR primer pairs reveals variance in target specificity and efficacy not suggested by in silico analysis.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {9}, pages = {2677-2683}, pmid = {19251890}, issn = {1098-5336}, mesh = {DNA Primers/*genetics ; DNA, Bacterial/*genetics ; DNA, Ribosomal/*genetics ; *Genes, rRNA ; Polymerase Chain Reaction/*methods/*standards ; Reproducibility of Results ; Sensitivity and Specificity ; }, abstract = {Phylogenetic and "fingerprinting" analyses of the 16S rRNA genes of prokaryotes have been a mainstay of microbial ecology during the last two decades. However, many methods and results from studies that rely on the 16S rRNA gene for detection and quantification of specific microbial taxa have seemingly received only cursory or even no validation. To directly examine the efficacy and specificity of 16S rRNA gene-based primers for phylum-, class-, and operational taxonomic unit-specific target amplification in quantitative PCR, we created a collection of primers based solely on an extensive soil bacterial 16S rRNA gene clone library containing approximately 5,000 sequences from a single soil sample (i.e., a closed site-specific library was used to create PCR primers for use at this site). These primers were initially tested in silico prior to empirical testing by PCR amplification of known target sequences and of controls based on disparate phylogenetic groups. Although all primers were highly specific according to the in silico analysis, the empirical analyses clearly exhibited a high degree of nonspecificity for many of the phyla or classes, while other primers proved to be highly specific. These findings suggest that significant care must be taken when interpreting studies whose results were obtained with target specific primers that were not adequately validated, especially where population densities or dynamics have been inferred from the data. Further, we suggest that the reliability of quantification of specific target abundance using 16S rRNA-based quantitative PCR is case specific and must be determined through rigorous empirical testing rather than solely in silico.}, }
@article {pmid19246763, year = {2009}, author = {Lücking, G and Dommel, MK and Scherer, S and Fouet, A and Ehling-Schulz, M}, title = {Cereulide synthesis in emetic Bacillus cereus is controlled by the transition state regulator AbrB, but not by the virulence regulator PlcR.}, journal = {Microbiology (Reading, England)}, volume = {155}, number = {Pt 3}, pages = {922-931}, doi = {10.1099/mic.0.024125-0}, pmid = {19246763}, issn = {1350-0872}, mesh = {Amino Acid Sequence ; Bacillus cereus/*genetics/growth &amp; development/metabolism ; Bacterial Proteins/genetics/*metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Depsipeptides/*biosynthesis ; Gene Expression Regulation, Bacterial ; Molecular Sequence Data ; Operon ; Promoter Regions, Genetic ; RNA, Bacterial/genetics ; Sequence Deletion ; Spores, Bacterial/genetics/metabolism ; Trans-Activators/genetics/*metabolism ; Transcription Factors/genetics/*metabolism ; }, abstract = {Cereulide, a depsipeptide structurally related to the antibiotic valinomycin, is responsible for the emetic type of gastrointestinal disease caused by Bacillus cereus. Recently, it has been shown that cereulide is produced non-ribosomally by the plasmid-encoded peptide synthetase Ces. Using deletion mutants of the emetic reference strain B. cereus F4810/72, the influence of the well-known transcription factors PlcR, Spo0A and AbrB on cereulide production and on the transcription of the cereulide synthetase gene cluster was investigated. Our data demonstrate that cereulide synthesis is independent of the B. cereus specific virulence regulator PlcR but belongs to the Spo0A-AbrB regulon. Although cereulide production turned out to be independent of sporulation, it required the activity of the sporulation factor Spo0A. The sigma(A)-promoted transcription of spo0A was found to be crucial for cereulide production, while the sigma(H)-driven transcription of spo0A did not affect cereulide synthesis. Overexpression of the transition state factor AbrB in B. cereus F4810/72 resulted in a non-toxic phenotype. Moreover, AbrB was shown to bind efficiently to the main promoter region of the ces operon, indicating that AbrB acts as a repressor of cereulide production by negatively affecting ces transcription.}, }
@article {pmid19246073, year = {2009}, author = {Whang, LM and Chien, IC and Yuan, SL and Wu, YJ}, title = {Nitrifying community structures and nitrification performance of full-scale municipal and swine wastewater treatment plants.}, journal = {Chemosphere}, volume = {75}, number = {2}, pages = {234-242}, doi = {10.1016/j.chemosphere.2008.11.059}, pmid = {19246073}, issn = {1879-1298}, mesh = {Animals ; Molecular Sequence Data ; Nitrites/*metabolism ; Nitrobacter/classification/genetics/isolation &amp; purification/metabolism ; Nitrosomonas/classification/genetics/isolation &amp; purification/metabolism ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Swine ; Waste Disposal, Fluid/*methods ; }, abstract = {This study evaluated nitrification performance and microbial ecology of nitrifying sludge in two full-scale wastewater treatment plants (WWTPs) including a municipal WWTP treating 20mgNL(-1) of ammonium and a swine WWTP treating 220mgNL(-1) of ammonium. These two plants differed in both wastewater characteristics and operating parameters, such as influent COD, TKN, ammonium, hydraulic retention time, and solids retention time, even though both plants achieve >85% nitrification efficiency. By employing molecular techniques, including terminal restriction fragment length polymorphism, cloning-sequencing and phylogenetic analyses targeting the 16S ribosomal RNA and group specific ammonia-monooxygenase functional gene (amoA), microbial community structures of nitrifying sludge and their significance to nitrification performance were evaluated. The results reveal that for the municipal WWTP Nitrosomonas marina-like AOB (ammonia-oxidizing bacteria) and Nitrospira-like NOB (nitrite-oxidizing bacteria) were the ubiquitously dominant nitrifiers, while Nitrosomonas europaea-, Nitrosomonas oligotropha-, and Nitrosospira-like AOB and Nitrobacter- and Nitrospira-like NOB were the major nitrifying populations found in the swine WWTP. The observed dissimilar nitrifying populations prevailing in these two plants may be related to niche differentiation concerning ammonium concentrations, system operation, and salinity. Moreover, our results suggest that the swine nitrifying sludge, involving relatively diverse AOB and NOB populations that perform the same task but with distinct growth and survival characters, may allow communities to maintain nitrifying capabilities when conditions change such as sudden increases in ammonium concentrations as examined with nitrification kinetic batch tests.}, }
@article {pmid19243502, year = {2009}, author = {Goh, SH and Mabbett, AN and Welch, JP and Hall, SJ and McEwan, AG}, title = {Molecular ecology of a facultative swine waste lagoon.}, journal = {Letters in applied microbiology}, volume = {48}, number = {4}, pages = {486-492}, doi = {10.1111/j.1472-765X.2009.02560.x}, pmid = {19243502}, issn = {1472-765X}, mesh = {Animal Husbandry/methods ; Animals ; *Bacteria/classification/genetics/isolation &amp; purification ; Carbon/metabolism ; Chromatiaceae/classification/genetics/isolation &amp; purification ; *Ecosystem ; Gene Library ; Genes, rRNA ; Hydrogen/metabolism ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfates/metabolism ; Sulfur/*metabolism ; *Swine ; Waste Disposal, Fluid/*methods ; *Water Microbiology ; }, abstract = {AIMS: To investigate the microbial ecology of three facultative swine waste lagoons.<br><br>METHODS AND RESULTS: Phylogenetic analysis of sequences in a 16S rRNA gene clone library and fluorescence in situ hybridization (FISH) analyses were used to assess bacterial diversity in a swine waste lagoon. FISH analysis and Gram-staining were used to compare the microbial communities of all three swine waste lagoons. Six operational taxonomic units were in high relative abundance and corresponded to the following phylotypes; Thiolamprovum, Verrucomicrobia, Acholeplasma, Turicibacter, Clostridium and Bacteroides. PCR was employed to detect the genes apsA and dsrAB which encode for enzymes specifically associated with dissimilatory sulfate-reduction within sulfate-reducing bacteria (SRB). Amplification of these genes confirmed their presence within the lagoons.<br><br>CONCLUSIONS: All lagoons were dominated by purple sulfur bacteria, affiliated to Thiolamprovum pedioforme. The molecular identification of fermentative bacteria and SRB indicate the following metabolic processes within such facultative ponds: sulfur-cycling, fermentation, inter-species hydrogen transfer and carbon cycling.<br><br>This study provides the first molecular evidence for the existence of a sulfur cycle which is linked to phototrophic sulfide oxidation by purple bacteria and organotrophic sulfate-reduction by SRB.}, }
@article {pmid19242746, year = {2009}, author = {Gerbersdorf, SU and Westrich, B and Paterson, DM}, title = {Microbial extracellular polymeric substances (EPS) in fresh water sediments.}, journal = {Microbial ecology}, volume = {58}, number = {2}, pages = {334-349}, pmid = {19242746}, issn = {1432-184X}, mesh = {Algal Proteins/analysis ; Bacteria/growth &amp; development/metabolism ; Bacterial Proteins/analysis ; Biomass ; Biopolymers/*analysis ; Carbohydrates/analysis ; Diatoms/growth &amp; development/metabolism ; Ecosystem ; Fresh Water/microbiology ; Geologic Sediments/*analysis/*microbiology ; Principal Component Analysis ; Rivers/microbiology ; *Water Microbiology ; }, abstract = {Microbially produced extracellular polymeric substances (EPS) have been linked with many important ecological functions in natural sediments; yet, most information has been derived from marine systems. The present paper is the first comprehensive study on EPS (i.e., carbohydrates and proteins) dynamics in riverine sediments addressing spatial (six reservoirs and four groyne fields across three European rivers), temporal (all seasons in 2003-2005), and vertical (over a 50-cm sediment depth transect) pattern. The variation in hydrodynamic regime found in the reservoirs and groyne fields was reflected in the biomass and composition of the benthic microorganisms that produce EPS. The microphytobenthic communities consisted mainly of diatoms and a higher algal biomass (up to 248 microg g(-1) dry weight, DW) seemed to be indicative for higher amounts of secreted colloidal carbohydrates. Consequently, the model proposed by Underwood and Smith (1998) for the relation chlorophyll-colloidal carbohydrates was also applicable for upper riverine sediment layers. The close relation between algal biomass and bacterial cell counts (10(8)-10(9) cells g(-1) DW) supports the idea of bacterial use of the secreted EPS. However, the data also suggest a contribution to the EPS pool through bacterial secretion of proteins/extracellular enzymes and possibly carbohydrates. Over depth, the relationships between microorganisms and EPS became increasingly decoupled along with increasing ratios of bound (refractory) to colloidal (labile) EPS. These data suggest fresh production of polymeric substances in upper sediment layers and mainly accumulation of refractory, biodegraded material in deeper layers. The high contents of EPS colloidal and bound carbohydrates (0.1-1.8 and 1.3-6.7 mg g(-1) DW, respectively) and EPS proteins (0.4-12.9 mg g(-1) DW) at the freshwater study sites might indicate an important role in sediment ecology.}, }
@article {pmid19239486, year = {2009}, author = {Burgaud, G and Le Calvez, T and Arzur, D and Vandenkoornhuyse, P and Barbier, G}, title = {Diversity of culturable marine filamentous fungi from deep-sea hydrothermal vents.}, journal = {Environmental microbiology}, volume = {11}, number = {6}, pages = {1588-1600}, doi = {10.1111/j.1462-2920.2009.01886.x}, pmid = {19239486}, issn = {1462-2920}, mesh = {*Biodiversity ; Ecosystem ; Fungi/*classification/isolation &amp; purification/physiology ; Hot Springs/*microbiology ; Phylogeny ; Seawater/*microbiology ; Water Microbiology ; }, abstract = {As now very few studies have been carried out on deep-sea marine fungi, this field remains relatively unknown. However, their presence inside benthic microbial eukaryotes at deep-sea vents was recently pointed out from molecular microbial ecology studies. We report here an attempt to describe the culturable part of mycological communities in deep-sea vent ecosystems that is an important step in understanding their diversity, abundance and function. Physiological characterization revealed strains that are more or less adapted to deep-sea conditions. Those results suggest the presence of true marine organisms and other more ubiquitous. Phylogenetical characterization highly correlated to physiological data revealed the presence of fungi that have been previously described and unknown ones until now, belonging to new taxonomic groups. This survey encourages for further work in order to complete descriptions and also to describe the ecological role of these organisms in such extreme environments.}, }
@article {pmid19238477, year = {2009}, author = {Jayakumar, A and O'Mullan, GD and Naqvi, SW and Ward, BB}, title = {Denitrifying bacterial community composition changes associated with stages of denitrification in oxygen minimum zones.}, journal = {Microbial ecology}, volume = {58}, number = {2}, pages = {350-362}, pmid = {19238477}, issn = {1432-184X}, mesh = {Bacteria/enzymology/*genetics ; Biodiversity ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Genes, Bacterial ; Nitrogen/*metabolism ; Oceans and Seas ; Oxygen/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {Denitrification in the ocean is a major sink for fixed nitrogen in the global N budget, but the process is geographically restricted to a few oceanic regions, including three oceanic oxygen minimum zones (OMZ) and hemipelagic sediments worldwide. Here, we describe the diversity and community composition of microbes responsible for denitrification in the OMZ using polymerase chain reaction, sequence and fragment analysis of clone libraries of the signature genes (nirK and nirS) that encode the enzyme nitrite reductase, responsible for key denitrification transformation steps. We show that denitrifying assemblages vary in space and time and exhibit striking changes in diversity associated with the progression of denitrification from initial anoxia through nitrate depletion. The initial denitrifying assemblage is highly diverse, but succession on the scale of 3-12 days leads to a much less diverse assemblage and dominance by one or a few phylotypes. This progression occurs in the natural environment as well as in enclosed incubations. The emergence of dominants from a vast reservoir of rare types has implications for the maintenance of diversity of the microbial population and suggests that a small number of microbial dominants may be responsible for the greatest rates of transformations involving nitrous oxide and global fixed nitrogen loss. Denitrifying blooms, driven by a few types responding to episodic environmental changes and distributed unevenly in time and space, are consistent with the sampling effect model of diversity-function relationships. Canonical denitrification thus appears to have important parallels with both primary production and nitrogen fixation, which are typically dominated by regionally and temporally restricted blooms that account for a disproportionate share of these processes worldwide.}, }
@article {pmid19234113, year = {2009}, author = {Yoder-Himes, DR and Chain, PS and Zhu, Y and Wurtzel, O and Rubin, EM and Tiedje, JM and Sorek, R}, title = {Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {10}, pages = {3976-3981}, pmid = {19234113}, issn = {1091-6490}, support = {R21 HL087833/HL/NHLBI NIH HHS/United States ; R21HL087833/HL/NHLBI NIH HHS/United States ; }, mesh = {Burkholderia cepacia complex/*genetics/growth &amp; development ; DNA, Complementary/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Sequence Analysis, RNA/*methods ; }, abstract = {Determining how an organism responds to its environment by altering gene expression is key to understanding its ecology. Here, we used RNA-seq to comprehensively and quantitatively assess the transcriptional response of the bacterial opportunistic cystic fibrosis (CF) pathogen and endemic soil dweller, Burkholderia cenocepacia, in conditions mimicking these 2 environments. By sequencing 762 million bases of cDNA from 2 closely related B. cenocepacia strains (one isolated from a CF patient and one from soil), we identified a number of potential virulence factors expressed under CF-like conditions, whereas genes whose protein products are involved in nitrogen scavenging and 2-component sensing were among those induced under soil-like conditions. Interestingly, 13 new putative noncoding RNAs were discovered using this technique, 12 of which are preferentially induced in the soil environment, suggesting that ncRNAs play an important role in survival in the soil. In addition, we detected a surprisingly large number of regulatory differences between the 2 strains, which may represent specific adaptations to the niches from which each strain was isolated, despite their high degree of DNA sequence similarity. Compared with the CF strain, the soil strain shows a stronger global gene expression response to its environment, which is consistent with the need for a more dynamic reaction to the heterogeneous conditions of soil.}, }
@article {pmid19224271, year = {2009}, author = {Jha, P and Kumar, A}, title = {Characterization of novel plant growth promoting endophytic bacterium Achromobacter xylosoxidans from wheat plant.}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {179-188}, pmid = {19224271}, issn = {1432-184X}, mesh = {Achromobacter denitrificans/genetics/growth &amp; development/*isolation &amp; purification/metabolism ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Indoleacetic Acids/metabolism ; Nitrogenase/genetics/*metabolism ; Phosphorus/metabolism ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Triticum/growth &amp; development/*microbiology ; }, abstract = {Nine diazotrophic bacteria were isolated from surface-sterilized roots and culms of wheat variety Malviya-234, which is grown with very low or no inputs of nitrogen fertilizer. Out of the nine bacteria, four showed indole acetic acid (IAA) production, and five were positive for P solubilization. One isolate, WM234C-3, showed appreciable level of nitrogenase activity, IAA production, and P solubilization ability, and was further characterized with a view to exploiting its plant growth promoting activity. Based on 16S rDNA sequence analysis, this isolate was identified as Achromobacter xylosoxidans. Diazotrophic nature of this particular isolate was confirmed by Western blot analysis of dinitrogenase reductase and amplification of nifH. Analysis of the nifH sequence showed close homology with typical diazotrophic bacteria. Endophytic nature and cross-infection ability of WM234C-3 were tested by molecular tagging with gusA fused to a constitutive promoter followed by inoculation onto rice seedlings in axenic conditions. At 21 days after inoculation, the roots showed blue staining, the most intense color being at the emergence of lateral roots and root tips. Microscopic observation confirmed colonization of gus-tagged WM234C-3 in the intercellular spaces of cortical as well as vascular zones of roots. Inoculation of gus-tagged WM234C-3 to rice plants resulted in significant increase in root/shoot length, fresh weight, and chlorophyll a content. Plant growth promoting features coupled with cross-infection ability suggest that this endophytic bacterium may be exploited as agricultural agent for various crops after a thorough and critical pathogenicity test.}, }
@article {pmid19224270, year = {2009}, author = {Fliessbach, A and Winkler, M and Lutz, MP and Oberholzer, HR and Mäder, P}, title = {Soil amendment with Pseudomonas fluorescens CHA0: lasting effects on soil biological properties in soils low in microbial biomass and activity.}, journal = {Microbial ecology}, volume = {57}, number = {4}, pages = {611-623}, pmid = {19224270}, issn = {1432-184X}, mesh = {Agriculture/*methods ; *Biomass ; Colony Count, Microbial ; Crops, Agricultural/microbiology ; Ecosystem ; Plant Roots/microbiology ; Pseudomonas fluorescens/*growth &amp; development/metabolism ; Soil/*analysis ; *Soil Microbiology ; Triticum/microbiology ; }, abstract = {Pseudomonas fluorescens strains are used in agriculture as plant growth-promoting rhizobacteria (PGPR). Nontarget effects of released organisms should be analyzed prior to their large-scale use, and methods should be available to sensitively detect possible changes in the environments the organism is released to. According to ecological theory, microbial communities with a greater diversity should be less susceptible to disturbance by invading organisms. Based on this principle, we laid out a pot experiment with field-derived soils different in their microbial biomass and activity due to long-term management on similar parent geological material (loess). We investigated the survival of P. fluorescens CHA0 that carried a resistance toward rifampicin and the duration of potential changes of the soil microflora caused by the inoculation with the bacterium at the sowing date of spring wheat. Soil microbial biomass (C(mic), N(mic)) basal soil respiration (BR), qCO(2), dehydrogenase activity (DHA), bacterial plate counts, mycorrhiza root colonization, and community level substrate utilization were analyzed after 18 and 60 days. At the initial stage, soils were clearly different with respect to most of the parameters measured, and a time-dependent effect between the first and the second set point were attributable to wheat growth and the influence of roots. The effect of the inoculum was small and merely transient, though significant long-term changes were found in soils with a relatively low level of microbial biomass. Community level substrate utilization as an indicator of changes in microbial community structure was mainly changed by the growth of wheat, while other experimental factors were negligible. The sensitivity of the applied methods to distinguish the experimental soils was in decreasing order N(mic), DHA, C(mic), and qCO(2). Besides the selective enumeration of P. fluorescens CHA0 rif(+), which was only found in amended soils, methods to distinguish the inoculum effect were DHA, C(mic), and the ratio of C(mic) to N(mic). The sampling time was most sensitively indicated by N(mic), DHA, C(mic), and qCO(2). Our data support the hypothesis-based on ecosystem theory-that a rich microflora is buffering changes due to invading species. In other words, a soil-derived bacterium was more effective in a relatively poor soil than in soils that are rich in microorganisms.}, }
@article {pmid19224269, year = {2009}, author = {Han, J and Xia, D and Li, L and Sun, L and Yang, K and Zhang, L}, title = {Diversity of culturable bacteria isolated from root domains of moso bamboo (Phyllostachys edulis).}, journal = {Microbial ecology}, volume = {58}, number = {2}, pages = {363-373}, pmid = {19224269}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; *Biodiversity ; China ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Phylogeny ; Plant Roots/*microbiology ; Poaceae/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The distribution of culturable bacteria in the rhizosphere, rhizoplane, and interior root tissues of moso bamboo plants was investigated in this study. Of the 182 isolates showing different colony characteristics on Luria-Bertani and King B plates, 56 operational taxonomic units of 22 genera were identified by 16S ribosomal RNA gene sequence analysis. The majority of root endophytic bacteria were Proteobacteria (67.5%), while the majority of rhizospheric and rhizoplane bacteria were Firmicutes (66.3% and 70.4%, respectively). The most common genus in both the rhizosphere and on the rhizoplane was Bacillus (42.4% and 44.4%, respectively), while Burkholderia was the most common genus inside the roots, comprising 35.0% of the isolates from this root domain. The endophytic bacterial community was less diverse than the rhizoplane and rhizospheric bacterial communities. Members of Lysinibacillus, Bacillus, and Burkholderia were found in all three root domains, whereas many isolates were found in only a single domain. Our results show that the population diversity of culturable bacteria is abundant in the root domains of moso bamboo plants and that obvious differences exist among the rhizospheric, rhizoplane, and endophytic bacterial communities.}, }
@article {pmid19222573, year = {2009}, author = {Louis, P and Flint, HJ}, title = {Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine.}, journal = {FEMS microbiology letters}, volume = {294}, number = {1}, pages = {1-8}, doi = {10.1111/j.1574-6968.2009.01514.x}, pmid = {19222573}, issn = {1574-6968}, mesh = {*Biodiversity ; Butyrates/*metabolism ; Coenzyme A-Transferases/metabolism ; Gram-Positive Bacteria/*classification/genetics/isolation &amp; purification/*metabolism ; Humans ; Intestine, Large/*microbiology ; Phosphotransferases (Carboxyl Group Acceptor)/metabolism ; }, abstract = {Butyrate-producing bacteria play a key role in colonic health in humans. This review provides an overview of the current knowledge of the diversity, metabolism and microbial ecology of this functionally important group of bacteria. Human colonic butyrate producers are Gram-positive firmicutes, but are phylogenetically diverse, with the two most abundant groups related to Eubacterium rectale/Roseburia spp. and to Faecalibacterium prausnitzii. Five different arrangements have been identified for the genes of the central pathway involved in butyrate synthesis, while in most cases butyryl-CoA : acetate CoA-transferase, rather than butyrate kinase, appears to perform the final step in butyrate synthesis. Mechanisms have been proposed recently in non-gut Clostridium spp. whereby butyrate synthesis can result in energy generation via both substrate-level phosphorylation and proton gradients. Here we suggest that these mechanisms also apply to the majority of butyrate producers from the human colon. The roles of these bacteria in the gut community and their influence on health are now being uncovered, taking advantage of the availability of cultured isolates and molecular methodologies. Populations of F. prausnitzii are reported to be decreased in Crohn's disease, for example, while populations of Roseburia relatives appear to be particularly sensitive to the diet composition in human volunteer studies.}, }
@article {pmid19221834, year = {2009}, author = {Redford, AJ and Fierer, N}, title = {Bacterial succession on the leaf surface: a novel system for studying successional dynamics.}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {189-198}, pmid = {19221834}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*growth &amp; development ; *Biodiversity ; DNA, Bacterial/genetics ; Phylogeny ; Plant Leaves/*microbiology ; Populus/*microbiology ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Succession is a widely studied process in plant and animal systems, but succession in microbial communities has received relatively little attention despite the ubiquity of microorganisms in natural habitats. One important microbial habitat is the phyllosphere, or leaf surface, which harbors large, diverse populations of bacteria and offers unique opportunities for the study of succession and temporal community assembly patterns. To explore bacterial community successional patterns, we sampled phyllosphere communities on cottonwood (Populus deltoides) trees multiple times across the growing season, from leaf emergence to leaf fall. Bacterial community composition was highly variable throughout the growing season; leaves sampled as little as a week apart were found to harbor significantly different communities, and the temporal variability on a given tree exceeded the variability in community composition between individual trees sampled on a given day. The bacterial communities clearly clustered into early-, mid-, and late-season clusters, with early- and late-season communities being more similar to each other than to the mid-season communities, and these patterns appeared consistent from year to year. Although we observed clear and predictable changes in bacterial community composition during the course of the growing season, changes in phyllosphere bacterial diversity were less predictable. We examined the species-time relationship, a measure of species turnover rate, and found that the relationship was fundamentally similar to that observed in plant and invertebrate communities, just on a shorter time scale. The temporal dynamics we observed suggest that although phyllosphere bacterial communities have high levels of phylogenetic diversity and rapid turnover rates, these communities follow predictable successional patterns from season to season.}, }
@article {pmid19219487, year = {2009}, author = {Inoue, K and Kabeya, H and Kosoy, MY and Bai, Y and Smirnov, G and McColl, D and Artsob, H and Maruyama, S}, title = {Evolutional and geographical relationships of Bartonella grahamii isolates from wild rodents by multi-locus sequencing analysis.}, journal = {Microbial ecology}, volume = {57}, number = {3}, pages = {534-541}, pmid = {19219487}, issn = {1432-184X}, mesh = {Animals ; Bacterial Typing Techniques ; Bartonella/classification/*genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; *Evolution, Molecular ; Geography ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rodentia/*microbiology ; Sequence Analysis, DNA ; }, abstract = {To clarify the relationship between Bartonella grahamii strains and both the rodent host species and the geographic location of the rodent habitat, we have investigated 31 B. grahamii strains from ten rodent host species from Asia (Japan and China), North America (Canada and the USA), and Europe (Russia and the UK). On the basis of multi-locus sequencing analysis of 16S rRNA, ftsZ, gltA, groEL, ribC, and rpoB, the strains were classified into two large groups, an Asian group and an American/European group. In addition, the strains examined were clearly clustered according to the geographic locations where the rodents had been captured. In the phylogenetic analysis based on gltA, the Japanese strains were divided into two subgroups: one close to strains from China, and the other related to strains from Far Eastern Russia. Thus, these observations suggest that the B. grahamii strains distributed in Japanese rodents originated from two different geographic regions. In the American/European group, B. grahamii from the North American continent showed an ancestral lineage and strict host specificity; by contrast, European strains showed low host specificity. The phylogenetic analysis and host specificity of B. grahamii raise the possibility that B. grahamii strains originating in the North American continent were distributed to European countries by adapting to various rodent hosts.}, }
@article {pmid19219053, year = {2009}, author = {VerBerkmoes, NC and Denef, VJ and Hettich, RL and Banfield, JF}, title = {Systems biology: Functional analysis of natural microbial consortia using community proteomics.}, journal = {Nature reviews. Microbiology}, volume = {7}, number = {3}, pages = {196-205}, pmid = {19219053}, issn = {1740-1534}, mesh = {Bacteria/*genetics/*metabolism ; Chromatography, Liquid ; *Ecosystem ; Electrophoresis, Gel, Two-Dimensional ; *Environmental Microbiology ; *Genomics/trends ; Mass Spectrometry ; *Proteomics/trends ; }, abstract = {We know very little about the metabolic functioning and evolutionary dynamics of microbial communities. Recent advances in comprehensive, sequencing-based methods, however, are laying a molecular foundation for new insights into how microbial communities shape the Earth's biosphere. Here we explore the convergence of microbial ecology, genomics, biological mass spectrometry and informatics that form the new field of microbial community proteogenomics. We discuss the first applications of proteogenomics and its potential for studying the physiology, ecology and evolution of microbial populations and communities.}, }
@article {pmid19217137, year = {2009}, author = {McKeown, RM and Scully, C and Mahony, T and Collins, G and O'Flaherty, V}, title = {Long-term (1,243 days), low-temperature (4-15 degrees C), anaerobic biotreatment of acidified wastewaters: bioprocess performance and physiological characteristics.}, journal = {Water research}, volume = {43}, number = {6}, pages = {1611-1620}, doi = {10.1016/j.watres.2009.01.015}, pmid = {19217137}, issn = {0043-1354}, mesh = {Anaerobiosis ; Biodegradation, Environmental ; Biomass ; *Bioreactors ; Cold Temperature ; Gases/analysis ; Methane/analysis ; Oxygen/analysis ; Sewage/*analysis ; Time Factors ; Waste Disposal, Fluid/*methods ; }, abstract = {The feasibility of long-term (>3 years), low-temperature (4-15 degrees C) and anaerobic bioreactor operation, for the treatment of acidified wastewater, was investigated. A hybrid, expanded granular sludge bed-anaerobic filter bioreactor was seeded with a mesophilic inoculum and employed for the mineralization of moderate-strength (3.75-10 kg chemical oxygen demand (COD)m(-3)) volatile fatty acid-based wastewaters at 4-15 degrees C. Bioprocess performance was assessed in terms of COD removal efficiency (CODRE), methane biogas concentration, and yield, and biomass retention. Batch specific methanogenic activity assays were performed to physiologically characterise reactor biomass. Despite transient disimprovements, CODRE and methane biogas concentrations exceeded 80% and 65%, respectively, at an applied organic loading rate (OLR) of 10 kgCODm(-3)d(-1) between 9.5 and 15 degrees C (sludge loading rate (SLR), 0.6 kgCOD kg[VSS](-1)d(-1)). Over 50% of the granular sludge bed was lost to disintegration during operation at 9.5 degrees C, warranting a reduction in the applied OLR to 3.75-5 kgCODm(-3)d(-1) (SLR, c. 0.4-0.5kgCOD kg[VSS](-1)d(-1)). From that point forward, remarkably stable and efficient performance was observed during operation at 4-10 degrees C, with respect to CODRE (>or=82%), methane biogas concentration (>70%) and methane yields (>4l(Methane)d(-1)), suggesting the adaptation of our mesophilic inoculum to psychrophilic operating conditions. Physiological activity assays indicated the development of psychroactive syntrophic and methanogenic populations, including the emergence of putatively psychrophilic propionate-oxidising and hydrogenotrophic methanogenic activity. The data suggest that mesophilic inocula can physiologically adapt to sub-optimal operational temperatures: treatment efficiencies and sludge loading rates at 4 degrees C (day, 1243) were comparable to those achieved at 15 degrees C (day 0). Furthermore, long-term, low-temperature bioreactor operation may act as a selective enrichment for psychrophilic methanogenic activity from mesophilic inocula. The observed efficient and stable bioprocess performance highlights the potential for long-term, low-temperature bioreactor operation.}, }
@article {pmid19214623, year = {2009}, author = {Ostermaier, V and Kurmayer, R}, title = {Distribution and abundance of nontoxic mutants of cyanobacteria in lakes of the Alps.}, journal = {Microbial ecology}, volume = {58}, number = {2}, pages = {323-333}, pmid = {19214623}, issn = {1432-184X}, support = {P 20231/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Austria ; Bacterial Toxins/genetics ; Colony Count, Microbial ; Cyanobacteria/*genetics ; DNA, Bacterial/genetics ; Ecosystem ; Eutrophication ; Fresh Water/microbiology ; Genes, Bacterial ; Genetics, Population ; Genotype ; Germany ; Microcystins/*genetics ; *Multigene Family ; Mutagenesis, Insertional ; Population Density ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Sequence Deletion ; Switzerland ; *Water Microbiology ; }, abstract = {The filamentous cyanobacterium Planktothrix rubescens frequently occurs in deep and stratified lakes in the temperate region of the northern hemisphere and is a known producer of the hepatotoxic secondary metabolite microcystin. These cyclic heptapeptides are synthesized nonribosomally via large enzyme complexes encoded by the microcystin (mcy) synthetase gene cluster. The occurrence of cyanobacterial strains lacking microcystin, but containing the mcy gene cluster has been reported repeatedly; it was shown that this inactivation is due to mutations such as gene deletion events and the insertion of transposable elements. In the present study, 12 lakes in Austria, Germany, and Switzerland were sampled from July 2005 to October 2007, and the proportion of inactive mcy genotypes was quantified in relation to the total population of the red-pigmented filamentous cyanobacterium Planktothrix by means of quantitative polymerase chain reaction. In total, four different mutations were quantified, namely two insertions affecting mcyD, one insertion affecting mcyA, and a deletion within mcyH and mcyA. The mutations occurred over a wide range of population densities (40-570,000 filaments L(-1)), and their abundance was found to be positively correlated with population density. However, on average, all nontoxic mutants were found in a low proportion only (min 0%, mean 6.5% +/- 1.1 (SE), max 52% of the total population). The genotype containing the mcyHA deletion had a significantly higher proportion (min 0%, mean 3.7% +/- 1, max 52%) when compared with all the genotypes containing insertions within the mcy gene cluster (min 0%, mean 2.8% +/- 0.7, max 24%). The results demonstrate that the occurrence of inactive mcy genotypes is linearly related to the population density, and selective sweeps of nontoxic mutants did not occur during the transition from prebloom to bloom conditions.}, }
@article {pmid19212699, year = {2009}, author = {Lasher, C and Dyszynski, G and Everett, K and Edmonds, J and Ye, W and Sheldon, W and Wang, S and Joye, SB and Moran, MA and Whitman, WB}, title = {The diverse bacterial community in intertidal, anaerobic sediments at Sapelo Island, Georgia.}, journal = {Microbial ecology}, volume = {58}, number = {2}, pages = {244-261}, pmid = {19212699}, issn = {1432-184X}, mesh = {Bacteria/*classification/genetics ; Biodiversity ; Gene Library ; Geography ; Geologic Sediments/chemistry/*microbiology ; Georgia ; *Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {The phylogenetic diversity and composition of the bacterial community in anaerobic sediments from Sapelo Island, GA, USA were examined using 16S rRNA gene libraries. The diversity of this community was comparable to that of soil, and 1,186 clones formed 817 OTUs at 99% sequence similarity. Chao1 estimators for the total richness were also high, at 3,290 OTUs at 99% sequence similarity. The program RDPquery was developed to assign clones to taxonomic groups based upon comparisons to the RDP database. While most clones could be assigned to describe phyla, fewer than 30% of the clones could be assigned to a described order. Similarly, nearly 25% of the clones were only distantly related (<90% sequence similarity) to other environmental clones, illustrating the unique composition of this community. One quarter of the clones were related to one or more undescribed orders within the gamma-Proteobacteria. Other abundant groups included the delta-Proteobacteria, Bacteroidetes, and Cyanobacteria. While these phyla were abundant in other estuarine sediments, the specific members at Sapelo Island appeared to be different from those previously described in other locations, suggesting that great diversity exists between as well as within estuarine intertidal sediments. In spite of the large differences in pore water chemistry with season and depth, differences in the bacterial community were modest over the temporal and spatial scales examined and generally restricted to only certain taxa.}, }
@article {pmid19212698, year = {2009}, author = {Bisson, IA and Marra, PP and Burtt, EH and Sikaroodi, M and Gillevet, PM}, title = {Variation in plumage microbiota depends on season and migration.}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {212-220}, pmid = {19212698}, issn = {1432-184X}, mesh = {*Animal Migration ; Animals ; Bacteria/classification/*genetics ; Birds/*microbiology ; DNA, Bacterial/genetics ; Feathers/*microbiology ; RNA, Ribosomal, 16S/genetics ; *Seasons ; Sequence Analysis, DNA ; Soil/analysis ; Soil Microbiology ; }, abstract = {Migratory birds can be efficient dispersers of pathogens, yet we know little about the effect of migration and season on the microbial community in avian plumage. This is the first study to describe and compare the microbial plumage community of adult and juvenile migratory birds during the annual cycle and compare the plumage community of migrants to that of resident birds at both neotropical and nearctic locations. We used length heterogeneity PCR (16S rRNA) to describe the microbial assemblage sampled from the plumage of 66 birds in two age classes and from 16 soil samples. Resident birds differed significantly in plumage microbial community composition from migrants (R > or = 0.238, P < 0.01). Nearctic resident birds had higher plumage microbial diversity than nearctic migrants (R = 0.402, P < 0.01). Plumage microbial composition differed significantly between fall premigratory and either breeding (R > or = 0.161, P < 0.05) or nonbreeding stages (R = 0.267, P < 0.01). Six bacterial operational taxonomic units contributed most to the dissimilarities found in this assay. Soil microbial community composition was significantly different from all samples of plumage microbial communities (R > or = 0.700, P < 0.01). The plumage microbial community varies in relation to migration strategy and stage of the annual cycle. We suggest that plumage microbial acquisition begins in the first year at natal breeding locations and reaches equilibrium at the neotropical wintering sites. These data lead us to conclude that migration and season play an important role in the dynamics of the microbial community in avian plumage and may reflect patterns of pathogen dispersal by birds.}, }
@article {pmid19212428, year = {2009}, author = {Morono, Y and Terada, T and Masui, N and Inagaki, F}, title = {Discriminative detection and enumeration of microbial life in marine subsurface sediments.}, journal = {The ISME journal}, volume = {3}, number = {5}, pages = {503-511}, doi = {10.1038/ismej.2009.1}, pmid = {19212428}, issn = {1751-7370}, mesh = {Automation ; Bacteria/*isolation &amp; purification ; Benzothiazoles ; Colony Count, Microbial/*methods ; Diamines ; Geologic Sediments/*microbiology ; Hydrofluoric Acid/metabolism ; Image Processing, Computer-Assisted ; Japan ; Microscopy, Fluorescence/methods ; Organic Chemicals/metabolism ; Peru ; Quinolines ; Sensitivity and Specificity ; Specimen Handling/*methods ; Staining and Labeling/methods ; }, abstract = {Detection and enumeration of microbial life in natural environments provide fundamental information about the extent of the biosphere on Earth. However, it has long been difficult to evaluate the abundance of microbial cells in sedimentary habitats because non-specific binding of fluorescent dye and/or auto-fluorescence from sediment particles strongly hampers the recognition of cell-derived signals. Here, we show a highly efficient and discriminative detection and enumeration technique for microbial cells in sediments using hydrofluoric acid (HF) treatment and automated fluorescent image analysis. Washing of sediment slurries with HF significantly reduced non-biological fluorescent signals such as amorphous silica and enhanced the efficiency of cell detachment from the particles. We found that cell-derived SYBR Green I signals can be distinguished from non-biological backgrounds by dividing green fluorescence (band-pass filter: 528/38 nm (center-wavelength/bandwidth)) by red (617/73 nm) per image. A newly developed automated microscope system could take a wide range of high-resolution image in a short time, and subsequently enumerate the accurate number of cell-derived signals by the calculation of green to red fluorescence signals per image. Using our technique, we evaluated the microbial population in deep marine sediments offshore Peru and Japan down to 365 m below the seafloor, which provided objective digital images as evidence for the quantification of the prevailing microbial life. Our method is hence useful to explore the extent of sub-seafloor life in the future scientific drilling, and moreover widely applicable in the study of microbial ecology.}, }
@article {pmid19207574, year = {2009}, author = {Ishii, S and Sadowsky, MJ}, title = {Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution.}, journal = {Environmental microbiology}, volume = {11}, number = {4}, pages = {733-740}, doi = {10.1111/j.1462-2920.2008.01856.x}, pmid = {19207574}, issn = {1462-2920}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Biodiversity ; *Biological Evolution ; DNA Fingerprinting/*methods ; Ecology/*methods ; *Ecosystem ; Repetitive Sequences, Nucleic Acid ; }, abstract = {A large number of repetitive DNA sequences are found in multiple sites in the genomes of numerous bacteria, archaea and eukarya. While the functions of many of these repetitive sequence elements are unknown, they have proven to be useful as the basis of several powerful tools for use in molecular diagnostics, medical microbiology, epidemiological analyses and environmental microbiology. The repetitive sequence-based PCR or rep-PCR DNA fingerprint technique uses primers targeting several of these repetitive elements and PCR to generate unique DNA profiles or 'fingerprints' of individual microbial strains. Although this technique has been extensively used to examine diversity among variety of prokaryotic microorganisms, rep-PCR DNA fingerprinting can also be applied to microbial ecology and microbial evolution studies since it has the power to distinguish microbes at the strain or isolate level. Recent advancement in rep-PCR methodology has resulted in increased accuracy, reproducibility and throughput. In this minireview, we summarize recent improvements in rep-PCR DNA fingerprinting methodology, and discuss its applications to address fundamentally important questions in microbial ecology and evolution.}, }
@article {pmid19201983, year = {2009}, author = {Prat, C and Ruiz-Rueda, O and Trias, R and Anticó, E and Capone, D and Sefton, M and Bañeras, L}, title = {Molecular fingerprinting by PCR-denaturing gradient gel electrophoresis reveals differences in the levels of microbial diversity for musty-earthy tainted corks.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {7}, pages = {1922-1931}, pmid = {19201983}, issn = {1098-5336}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; *Biodiversity ; DNA Fingerprinting/methods ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel/methods ; *Environmental Microbiology ; *Food Industry ; Fungi/*classification/genetics/isolation &amp; purification ; Molecular Sequence Data ; Plants/*microbiology ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; }, abstract = {The microbial community structure of cork with marked musty-earthy aromas was analyzed using denaturing gradient gel electrophoresis of amplified ribosomal DNA. Cork stoppers and discs were used for DNA extraction and were analyzed by using selective primers for bacteria and fungi. Stoppers clearly differed from discs harboring a different fungal community. Moreover, musty-earthy samples of both types were shown to have a specific microbiota. The fungi Penicillium glabrum and Neurospora spp. were present in all samples and were assumed to make only a small contribution to off-odor development. In contrast, Penicillium islandicum and Penicillium variabile were found almost exclusively in 2,4,6-trichloroanisole (TCA) tainted discs. Conversely, Rhodotorula minuta and Rhodotorula sloofiae were most common in cork stoppers, where only small amounts of TCA were detected. Alpha- and gammaproteobacteria were the most commonly found bacteria in either control or tainted cork stoppers. Specific Pseudomonas and Actinobacteria were detected in stoppers with low amounts of TCA and 2-methoxy-3,5-dimethylpyrazine. These results are discussed in terms of biological degradation of taint compounds by specific microorganisms. Reliable and straightforward microbial identification methods based on a molecular approach provided useful data to determine and evaluate the risk of taint formation in cork.}, }
@article {pmid19200315, year = {2009}, author = {Vanhaecke, L and Grootaert, C and Verstraete, W and Van de Wiele, T}, title = {Chemopreventive effects from prebiotic inulin towards microbial 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine bioactivation.}, journal = {Journal of applied microbiology}, volume = {106}, number = {2}, pages = {474-485}, doi = {10.1111/j.1365-2672.2008.04015.x}, pmid = {19200315}, issn = {1365-2672}, mesh = {Bacteria/genetics/growth &amp; development/metabolism ; Cichorium intybus/chemistry ; Colon/metabolism/microbiology ; Colony Count, Microbial ; DNA Fingerprinting ; Fatty Acids, Volatile/metabolism ; Fermentation ; Humans ; Imidazoles/*metabolism ; Inulin/*pharmacology ; Mutagens/*metabolism ; *Prebiotics ; Pyrimidines/metabolism ; }, abstract = {AIMS: Using a Simulator of the Human Intestinal Microbial Ecosystem (SHIME), we investigated the chemopreventive potential of prebiotic chicory inulin towards the in vitro bioactivation of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) by human intestinal microbiota.<br><br>METHODS AND RESULTS: HPLC data revealed that inulin significantly decreased the formation of the genotoxic PhIP-M1 metabolite, with the highest inhibitory activity in the colon ascendens (87% decrease). Interestingly, this chemopreventive effect correlated with alterations of bacterial community composition and metabolism in the different colon compartments. Conventional culture-based techniques and PCR-DGGE analysis on the SHIME colon suspension revealed significant bifidogenic effects during inulin treatment, whereas the overall microbial community kept relatively unchanged. Additionally, the production of short-chain fatty acids increased with 12%, 3% and 7%, while ammonia concentrations decreased with 3%, 4% and 3% in the ascending, transverse and descending colon compartments, respectively.<br><br>CONCLUSIONS: These results indicate that the prebiotic effects from inulin may also purport protective effects towards microbial PhIP bioactivation.<br><br>As the colonic microbiota may contribute significantly to the carcinogenic potential of PhIP, the search for dietary constituents that decrease the formation of this harmful metabolite, may help in preventing its risk towards human health.}, }
@article {pmid19196267, year = {2009}, author = {Warmink, JA and Nazir, R and van Elsas, JD}, title = {Universal and species-specific bacterial 'fungiphiles' in the mycospheres of different basidiomycetous fungi.}, journal = {Environmental microbiology}, volume = {11}, number = {2}, pages = {300-312}, doi = {10.1111/j.1462-2920.2008.01767.x}, pmid = {19196267}, issn = {1462-2920}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Bacterial Typing Techniques ; *Basidiomycota ; *Biodiversity ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; *Fruiting Bodies, Fungal ; Genes, rRNA ; Molecular Sequence Data ; Nucleic Acid Denaturation ; Phylogeny ; Polymerase Chain Reaction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {In previous work, several bacterial groups that show a response to fruiting bodies (the mycosphere) of the ectomycorrhizal fungus Laccaria proxima were identified. We here extend this work to a broader range of fungal fruiting bodies sampled at two occasions. PCR-DGGE analyses showed clear effects of the mycosphere of diverse fungi on the total bacterial and Pseudomonas communities in comparison with those in the corresponding bulk soil. The diversities of the Pseudomonas communities increased dramatically in most of the mycospheres tested, which contrasted with a decrease of the diversity of the total bacterial communities in these habitats. The data also indicated the existence of universal (i.e. Pseudomonas poae, P. lini, P. umsongensis, P. corrugata, P. antarctica and Rahnella aquatilis) as well as specific (i.e. P. viridiflava and candidatus Xiphinematobacter americani) fungiphiles, defined as bacteria adapted to the mycospheres of, respectively, three or more or just one fungal species. The selection of such fungiphiles was shown to be strongly related to their capacities to use particular carbonaceous compounds, as evidenced using principal components analyses of BIOLOG-based substrate utilization tests. The differentiating compounds, i.e. L-arabinose, L-leucine, m-inositol, m-arabitol, D-mannitol and D-trehalose, were tentatively linked to compounds known to occur in mycosphere exudates.}, }
@article {pmid19194750, year = {2009}, author = {Nisbet, DJ and Callaway, TR and Edrington, TS and Anderson, RC and Krueger, N}, title = {Effects of the dicarboxylic acids malate and fumarate on E. coli O157:H7 and Salmonella enterica typhimurium populations in pure culture and in mixed ruminal microorganism fermentations.}, journal = {Current microbiology}, volume = {58}, number = {5}, pages = {488-492}, pmid = {19194750}, issn = {1432-0991}, mesh = {Animals ; Body Fluids/chemistry/microbiology ; Cattle ; Colony Count, Microbial ; Escherichia coli O157/drug effects/*growth &amp; development ; Fermentation ; Fumarates/*pharmacology ; Growth Inhibitors/*pharmacology ; Hydrogen-Ion Concentration ; Malates/*pharmacology ; Rumen/*microbiology ; Salmonella typhimurium/drug effects/*growth &amp; development ; }, abstract = {The dicarboxylic acids malate and fumarate increase ruminal pH, reduce methane production, increase propionate and total volatile fatty acid (VFA) production, and reduce lactic acid accumulation in a manner similar to ionophores. These acids stimulate the ruminal bacterium Selenomonas ruminantium to ferment lactate to produce propionate. Thus, dicarboxylic acids have been suggested as nonantibiotic modifiers of the ruminal fermentation, but their impact on ruminal microbial ecology remains unknown. This study was designed to examine what effects these modifiers may have on intestinal pathogen populations such as Escherichia coli O157:H7 and S. enterica Typhimurium prior to their widespread incorporation into cattle rations. Pure cultures of E. coli O157:H7 strain 933 and S. enterica Typhimurium were grown with malate and fumarate added at 0, 1, 5, 10, and 20 mM (v/v; n = 3). Neither dicarboxylic acid inhibited (p > 0.1) the growth rate or final populations of E. coli O157:H7 or S. enterica Typhimurium. Ruminal fluid was collected from cattle (n = 2) and E. coli O157:H7 and S. enterica Typhimurium were added to separate ruminal fermentations incubated for 24 h at 39 degrees C. Fumarate and malate were added at concentrations of 0, 5, 10, and 20 mM (v/v; n = 2) and incubated for 24 h at 39 degrees C. Malate or fumarate addition did not affect (p > 0.1) populations of E. coli O157:H7 or S. enterica Typhimurium. However, the final pH was increased (p < 0.05), the acetate:propionate ratio was decreased (p < 0.05), and the total VFA production was increased (p < 0.05) by > or =10 mM dicarboxylic acid addition. These results confirm that dicarboxylic acids can modify ruminal fermentation, but they do not affect populations of critical foodborne pathogens.}, }
@article {pmid19194481, year = {2009}, author = {Bodelier, PL and Gillisen, MJ and Hordijk, K and Damsté, JS and Rijpstra, WI and Geenevasen, JA and Dunfield, PF}, title = {A reanalysis of phospholipid fatty acids as ecological biomarkers for methanotrophic bacteria.}, journal = {The ISME journal}, volume = {3}, number = {5}, pages = {606-617}, doi = {10.1038/ismej.2009.6}, pmid = {19194481}, issn = {1751-7370}, mesh = {Alphaproteobacteria/*chemistry/*classification/metabolism ; Biomarkers/analysis ; Cell Membrane/chemistry ; Cluster Analysis ; Fatty Acids/*analysis ; Methane/metabolism ; Methanol/metabolism ; Oxidation-Reduction ; Phospholipids/*analysis ; *Soil Microbiology ; }, abstract = {Aerobic methane-oxidizing bacteria (MB) are the primary terrestrial sinks for the greenhouse gas methane. A distinct characteristic of MB is the presence of specific phospholipid ester-linked fatty acids (PLFA) in their membranes that differentiate them from each other and also from all other organisms. These distinct PLFA patterns facilitate microbial ecology studies. For example, the assimilation of C from methane into PLFA can be traced in environmental samples using stable isotope ((13)C) probing (SIP), which links the activity of MB to their community composition in situ. However, the phylogenetic resolution of this method is low because of a lack of PLFA profiles from cultured MB species. In this study, PLFA profiles of 22 alphaproteobacterial (type II) MB were analysed after growth on methane, methanol or both substrates together. Growth on different substrates did not affect the PLFA profiles of the investigated strains. A number of Methylocystis strains contained novel C18:2 fatty acids (omega 7c,12c and omega 6c,12c) that can be used as diagnostic biomarkers. The detection of these novel PLFA, combined with the analyses of multiple type II strains, increased the phylogenetic resolution of PLFA analysis substantially. Multivariate analysis of the expanded MB PLFA database identified species groups that closely reflected phylogenies based on 16S rRNA and pmoA gene sequences. The PLFA database therefore provides a robust framework for linking identity to activity in MB communities with a higher resolution than was previously possible.}, }
@article {pmid19193706, year = {2009}, author = {Cildir, SK and Germec, D and Sandalli, N and Ozdemir, FI and Arun, T and Twetman, S and Caglar, E}, title = {Reduction of salivary mutans streptococci in orthodontic patients during daily consumption of yoghurt containing probiotic bacteria.}, journal = {European journal of orthodontics}, volume = {31}, number = {4}, pages = {407-411}, doi = {10.1093/ejo/cjn108}, pmid = {19193706}, issn = {1460-2210}, mesh = {Adolescent ; Bifidobacterium/physiology ; Child ; Colony Count, Microbial ; Cross-Over Studies ; Double-Blind Method ; Female ; Follow-Up Studies ; Humans ; Lactobacillus/*isolation &amp; purification ; Male ; *Orthodontic Appliances ; Probiotics/*therapeutic use ; Saliva/*microbiology ; Streptococcus mutans/*isolation &amp; purification ; *Yogurt/microbiology ; }, abstract = {Previous studies have suggested that probiotic supplements in dairy products may affect the oral microbial ecology, but the effect in orthodontic patients has not previously been reported. The aim of the present study was to examine whether short-term consumption of fruit yogurt containing probiotic bifidobacteria would affect the levels of salivary mutans streptococci and lactobacilli in patients with fixed orthodontic appliances. A double-blind, randomized crossover study was performed and 24 healthy adolescents (12-16 years) undergoing orthodontic treatment were followed over four periods. During periods 2 and 4 (2 weeks each), the subjects ingested 200 g fruit yogurt containing Bifidobacterium animalis subsp. lactis DN-173010 (2 x 10(8) colony forming units/g) once daily or a control yogurt without viable bacteria. Periods 1 and 3 were run-in and wash-out periods of 1 and 6 weeks, respectively. Salivary mutans streptococci and lactobacilli were enumerated with chair-side kits before and after the yogurt consumption periods. Pre- and post-treatment values within each regimen were compared with a two-tailed marginal homogeneity test for categorical data. A statistically significant reduction of salivary mutans streptococci was recorded after probiotic yogurt consumption (P < 0.05), which was in contrast to the control yogurt. No significant alterations of the salivary lactobacilli counts were observed. Short-term daily consumption of fruit yogurt containing Bifidobacterium animalis subsp. lactis DN-173010 may reduce the levels of mutans streptococci in saliva during orthodontic treatment with fixed appliances.}, }
@article {pmid19192787, year = {2008}, author = {Erguder, TH and Boon, N and Vlaeminck, SE and Verstraete, W}, title = {Partial nitrification achieved by pulse sulfide doses in a sequential batch reactor.}, journal = {Environmental science &amp; technology}, volume = {42}, number = {23}, pages = {8715-8720}, doi = {10.1021/es801391u}, pmid = {19192787}, issn = {0013-936X}, mesh = {Aerobiosis ; Ammonia/metabolism ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; *Bioreactors ; Electrophoresis ; Nitrates/metabolism ; Nitrites/metabolism ; Nitrogen/*metabolism ; Oxidation-Reduction ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/analysis/genetics ; Sulfides/*metabolism ; }, abstract = {A nitrifying sequential batch reactor operated under 2-day cyclic aerobic and anoxic conditions was pulse dosed with incremental sulfide concentrations during anoxic conditions. The nitrite-oxidizing bacteria were found to be more sensitive to sulfide than the ammonia oxidizers. A maximum of nitrite-N to (nitrite-N + nitrate-N) accumulation ratio of 0.75 was obtained at an initial pulse sulfide-S concentration of 45 mg/L under pH control at 7.5 +/- 0.2 and fully mixing conditions. Total ammonium nitrogen was removed almost 100% at a removal rate of 0.73 +/- 0.05 g/L x day, achieved during the aerobic days of the cycles. Denaturing gradientgel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH) analyses indicated the shift in the ammonia- and nitrite-oxidizing populations triggered by sulfide addition, partial nitrification, and subsequent recovery to complete nitrification. Interestingly, archaeal amoA genes were retrieved under the conditions of sulfide addition. These results indicate that the pulse sulfide application can be used as a tool to accumulate nitrite, which is of importance for the subsequent anaerobic ammonium oxidation (anammox) process in the achievement of complete nitrogen removal.}, }
@article {pmid19190702, year = {2009}, author = {Marx, JG and Carpenter, SD and Deming, JW}, title = {Production of cryoprotectant extracellular polysaccharide substances (EPS) by the marine psychrophilic bacterium Colwellia psychrerythraea strain 34H under extreme conditions.}, journal = {Canadian journal of microbiology}, volume = {55}, number = {1}, pages = {63-72}, doi = {10.1139/W08-130}, pmid = {19190702}, issn = {0008-4166}, mesh = {Cold Temperature ; Cryoprotective Agents/*metabolism ; Culture Media ; Freezing ; Gammaproteobacteria/*metabolism ; Hydrostatic Pressure ; Polysaccharides, Bacterial/*biosynthesis ; Salinity ; *Water Microbiology ; }, abstract = {Extracellular polysaccharide substances (EPS) play critical roles in microbial ecology, including the colonization of extreme environments in the ocean, from sea ice to the deep sea. After first developing a sugar-free growth medium, we examined the relative effects of temperature, pressure, and salinity on EPS production (on a per cell basis) by the obligately marine and psychrophilic gamma-proteobacterium, Colwellia psychrerythraea strain 34H. Over growth-permissive temperatures of approximately 10 to -4 degrees C, EPS production did not change, but from -8 to -14 degrees C when samples froze, EPS production rose dramatically. Similarly, at growth-permissive hydrostatic pressures of 1-200 atm (1 atm = 101.325 kPa) (at -1 and 8 degrees C), EPS production was unchanged, but at higher pressures of 400 and 600 atm EPS production rose markedly. In salinity tests at 10-100 parts per million (and -1 and 5 degrees C), EPS production increased at the freshest salinity tested. Extreme environmental conditions thus appear to stimulate EPS production by this strain. Furthermore, strain 34H recovered best from deep-freezing to -80 degrees C (not found for Earthly environments) if first supplemented with a preparation of its own EPS, rather than other cryoprotectants like glycerol, suggesting EPS production as both a survival strategy and source of compounds with potentially novel properties for biotechnological and other applications.}, }
@article {pmid19187991, year = {2009}, author = {Pham, TH and Aelterman, P and Verstraete, W}, title = {Bioanode performance in bioelectrochemical systems: recent improvements and prospects.}, journal = {Trends in biotechnology}, volume = {27}, number = {3}, pages = {168-178}, doi = {10.1016/j.tibtech.2008.11.005}, pmid = {19187991}, issn = {0167-7799}, mesh = {*Bacterial Physiological Phenomena ; Bioelectric Energy Sources/*microbiology ; Bioreactors/*microbiology ; Cell Culture Techniques/*instrumentation ; Electrochemistry/*instrumentation ; *Electrodes ; Equipment Design ; }, abstract = {In a bioelectrochemical system (BES) operated with a bioanode, the anode performance plays an important part in the overall performance. Fundamental aspects of bioanodes have been intensively investigated, enabling us to better understand the growth, kinetics functioning and interactions of anodophilic microorganisms. Recently, various technological advances have improved the properties and operation of anodes and have increased bioanode performance by up to tenfold. To further boost the performance of bioanodes by several orders of magnitude, practical microbiological approaches deserve more investigation. This article reviews the factors affecting bioanode performance, the recent advances and the prospective strategies for improving it. Future application perspectives of bioanodes are also proposed.}, }
@article {pmid19184185, year = {2009}, author = {Grover, JP and Chrzanowski, TH}, title = {Dynamics and nutritional ecology of a nanoflagellate preying upon bacteria.}, journal = {Microbial ecology}, volume = {58}, number = {2}, pages = {231-243}, pmid = {19184185}, issn = {1432-184X}, mesh = {Animals ; Carbon/metabolism ; Models, Biological ; Nitrogen/metabolism ; Ochromonas/growth &amp; development/*physiology ; *Predatory Behavior ; Pseudomonas fluorescens/*chemistry/growth &amp; development ; }, abstract = {Ingestion and growth rates of the nanoflagellate predator Ochromonas danica feeding on the bacterium Pseudomonas fluorescens were quantified in laboratory cultures. Bacterial prey were grown under four nutritional conditions with respect to macronutrient elements: C-limited, N-limited, P-limited, and balanced. Ingestion and growth rates were saturating functions of prey abundance when preying upon nutritionally balanced, C-limited, and P-limited bacteria but were unimodal functions of abundance when preying on N-limited bacteria. At saturating prey concentrations, the ingestion rate of C-limited prey was about twice that of prey in other nutritional states, while at subsaturating prey concentrations, the ingestion rates of both C- and N-limited prey were higher than those of prey in other nutritional states. Over all prey concentrations, growth was most rapid on balanced and C-limited prey and generally lowest for P-limited prey. Due to the unimodal response of growth rate to abundance of N-limited prey, growth rate on N-limited prey approached that obtained on balanced and C-limited prey when prey were available at intermediate abundances. The accumulation of recycled N increased with the growth rate of O. danica. Recycling of N was highest when O. danica was feeding upon P-limited prey. The accumulation of recycled P increased with growth rate for balanced and N-limited prey, but not for P-limited prey, which consistently had low accumulation of recycled P. The low growth rate and negligible recycling of P for O. danica preying on P-limited prey is consistent with the theory of ecological stoichiometry and resembles results found for crustacean zooplankton, especially in the genus Daphnia. Potentially, the major predators of bacterioplankton and a major predator of phytoplankton play analogous roles in the trophic dynamics and biogeochemistry of aquatic ecosystems.}, }
@article {pmid19183981, year = {2009}, author = {Clauwaert, P and Mulenga, S and Aelterman, P and Verstraete, W}, title = {Litre-scale microbial fuel cells operated in a complete loop.}, journal = {Applied microbiology and biotechnology}, volume = {83}, number = {2}, pages = {241-247}, doi = {10.1007/s00253-009-1876-0}, pmid = {19183981}, issn = {1432-0614}, mesh = {*Bioelectric Energy Sources ; Conservation of Energy Resources/methods ; Electricity ; *Electrodes ; Equipment Design ; Hydrogen-Ion Concentration ; }, abstract = {Using the anode effluent to compensate the alkalinization in a bio-cathode has recently been proposed as a way to operate a microbial fuel cell (MFC) in a continuous and pH neutral way. In this research, we successfully demonstrated that the operation of a MFC without any pH adjustments is possible by completing the liquid loop over cathode and anode. During the complete loop operation, a stable current production of 23.2 +/- 2.5 A m(-3) MFC was obtained, even in the presence of 3.2-5.2 mg O(2) L(-1) in the anode. The use of current collectors and subdivided electrical circuitries for relative large 2.5-L-scale MFCs resulted in ohmic cell resistances in the order of 1.4-1.7 mOmega m(3) MFC, which were comparable to values of ten times smaller MFCs. Nevertheless, the bio-cathode activity still needs to be improved significantly with a factor 10-50 in order achieve desirable current densities of 1,000 A m(-3) MFC.}, }
@article {pmid19182331, year = {2009}, author = {Whang, LM and Yang, KH and Yang, YF and Han, YL and Chen, YJ and Cheng, SS}, title = {Microbial ecology and performance of ammonia oxidizing bacteria (AOB) in biological processes treating petrochemical wastewater with high strength of ammonia: effect of Na(2)CO(3) addition.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {59}, number = {2}, pages = {223-231}, doi = {10.2166/wst.2009.848}, pmid = {19182331}, issn = {0273-1223}, mesh = {Ammonia/*metabolism ; Bacteria/*drug effects/*metabolism ; Bioreactors/*microbiology ; Carbonates/*pharmacology ; Hydrogen-Ion Concentration ; Models, Theoretical ; Oxidation-Reduction ; Waste Disposal, Fluid/*methods ; }, abstract = {This study evaluated nitrification performance and microbial ecology of AOB in a full-scale biological process, powder activated carbon treatment (PACT), and a pilot-scale biological process, moving bed biofilm reactor (MBBR), treating wastewater collected from a petrochemical industry park. The petrochemical influent wastewater characteristics showed a relative low carbon to nitrogen ratio around 1 with average COD and ammonia concentrations of 310 mg/L and 325 mg-N/L, respectively. The average nitrification efficiency of the full-scale PACT process was around 11% during this study. For the pilot-scale MBBR, the average nitrification efficiency was 24% during the Run I operation mode, which provided a slightly better performance in nitrification than that of the PACT process. During the Run II operation, the pH control mode was switched from addition of NaOH to Na(2)CO(3), leading to a significant improvement in nitrification efficiency of 51%. In addition to a dramatic change in nitrification performance, the microbial ecology of AOB, monitored with the terminal restriction fragment length polymorphism (T-RFLP) molecular methodology, was found to be different between Runs I and II. The amoA-based TRFLP results indicated that Nitrosomonas europaea lineage was the dominant AOB population during Run I operation, while Nitrosospira-like AOB was dominant during Run II operation. To confirm the effects of Na(2)CO(3) addition on the nitrification performance and AOB microbial ecology observed in the MBBR process, batch experiments were conducted. The results suggest that addition of Na(2)CO(3) as a pH control strategy can improve nitrification performance and also influence AOB microbial ecology as well. Although the exact mechanisms are not clear at this time, the results showing the effects of adding different buffering chemicals such as NaOH or Na(2)CO(3) on AOB populations have never been demonstrated until this study.}, }
@article {pmid19181827, year = {2009}, author = {Boersma, FG and Warmink, JA and Andreote, FA and van Elsas, JD}, title = {Selection of Sphingomonadaceae at the base of Laccaria proxima and Russula exalbicans fruiting bodies.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {7}, pages = {1979-1989}, pmid = {19181827}, issn = {1098-5336}, mesh = {*Basidiomycota ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel/methods ; *Fruiting Bodies, Fungal ; Laccaria ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Sequence Homology ; *Soil Microbiology ; Sphingomonadaceae/classification/*genetics/*isolation &amp; purification ; }, abstract = {The dense hyphal network directly underneath the fruiting bodies of ectomycorrhizal fungi might exert strong influences on the bacterial community of soil. Such fruiting bodies might serve as hot spots for bacterial activity, for instance by providing nutrients and colonization sites in soil. Here, we assessed the putative selection of specific members of the Sphingomonadaceae family at the bases of the fruiting bodies of the ectomycorrhizal fungi Laccaria proxima and Russula exalbicans in comparison to the adjacent bulk soil. To do so, we used a previously designed Sphingomonadaceae-specific PCR-denaturing gradient gel electrophoresis (DGGE) system and complemented this with analyses of sequences from a Sphingomonadaceae-specific clone library. The analyses showed clear selective effects of the fruiting bodies of both fungi on the Sphingomonadaceae community structures. The effect was especially prevalent with R. exalbicans. Strikingly, similar fungi sampled approximately 100 m apart showed similar DGGE patterns, while corresponding bulk soil-derived patterns differed from each other. However, the mycospheres of L. proxima and R. exalbicans still revealed divergent community structures, indicating that different fungi select for different members of the Sphingomonadaceae family. Excision of specific bands from the DGGE patterns, as well as analyses of the clone libraries generated from both habitats, revealed fruiting body-specific Sphingomonadaceae types. It further showed that major groups from the mycospheres of R. exalbicans and L. proxima did not cluster with known bacteria from the database, indicating new groups within the family of Sphingomonadaceae present in these environments.}, }
@article {pmid19180645, year = {2009}, author = {De Schamphelaire, L and Verstraete, W}, title = {Revival of the biological sunlight-to-biogas energy conversion system.}, journal = {Biotechnology and bioengineering}, volume = {103}, number = {2}, pages = {296-304}, doi = {10.1002/bit.22257}, pmid = {19180645}, issn = {1097-0290}, mesh = {Carbon Dioxide/*metabolism ; Electricity ; Eukaryota/*metabolism ; Gases ; Methane/*metabolism ; *Sunlight ; }, abstract = {In the quest for renewable resources, algae are increasingly receiving attention. Their high growth rate, high CO(2) fixation and their lack of requirement for fertile soil surface represent several advantages as compared to conventional (energy) crops. Through their ability to store large amounts of oils, they qualify as a source for biodiesel. Algal biomass, however, can also be used as such, namely as a substrate for anaerobic digestion. In the present research, we investigated the use of algae for energy generation in a stand-alone, closed-loop system. The system encompasses an algal growth unit for biomass production, an anaerobic digestion unit to convert the biomass to biogas and a microbial fuel cell to polish the effluent of the digester. Nutrients set free during digestion can accordingly be returned to the algal growth unit for a sustained algal growth. Hence, a system is presented that continuously transforms solar energy into energy-rich biogas and electricity. Algal productivities of 24-30 ton VS ha(-1) year(-1) were reached, while 0.5 N m(3) biogas could be produced kg(-1) algal VS. The system described resulted in a power plant with a potential capacity of about 9 kW ha(-1) of solar algal panel, with prospects of 23 kW ha(-1).}, }
@article {pmid19177226, year = {2009}, author = {Liu, Y and Zhang, W and Sileika, T and Warta, R and Cianciotto, NP and Packman, A}, title = {Role of bacterial adhesion in the microbial ecology of biofilms in cooling tower systems.}, journal = {Biofouling}, volume = {25}, number = {3}, pages = {241-253}, pmid = {19177226}, issn = {1029-2454}, support = {R01 AI081983/AI/NIAID NIH HHS/United States ; K25 AI062977/AI/NIAID NIH HHS/United States ; 5K25AI062977/AI/NIAID NIH HHS/United States ; R01 AI034937/AI/NIAID NIH HHS/United States ; R01 AI043987/AI/NIAID NIH HHS/United States ; }, mesh = {*Bacterial Adhesion ; *Biofilms ; *Cold Temperature ; Electrons ; Industry/*instrumentation ; Kinetics ; Surface Properties ; Time Factors ; Water ; }, abstract = {The fate of the three heterotrophic biofilm forming bacteria, Pseudomonas aeruginosa, Klebsiella pneumoniae and Flavobacterium sp. in pilot scale cooling towers was evaluated both by observing the persistence of each species in the recirculating water and the formation of biofilms on steel coupons placed in each cooling tower water reservoir. Two different cooling tower experiments were performed: a short-term study (6 days) to observe the initial bacterial colonization of the cooling tower, and a long-term study (3 months) to observe the ecological dynamics with repeated introduction of the test strains. An additional set of batch experiments (6 days) was carried out to evaluate the adhesion of each strain to steel surfaces under similar conditions to those found in the cooling tower experiments. Substantial differences were observed in the microbial communities that developed in the batch systems and cooling towers. P. aeruginosa showed a low degree of adherence to steel surfaces both in batch and in the cooling towers, but grew much faster than K. pneumoniae and Flavobacterium in mixed-species biofilms and ultimately became the dominant organism in the closed batch systems. However, the low degree of adherence caused P. aeruginosa to be rapidly washed out of the open cooling tower systems, and Flavobacterium became the dominant microorganism in the cooling towers in both the short-term and long-term experiments. These results indicate that adhesion, retention and growth on solid surfaces play important roles in the bacterial community that develops in cooling tower systems.}, }
@article {pmid19172216, year = {2009}, author = {Horath, T and Bachofen, R}, title = {Molecular characterization of an endolithic microbial community in dolomite rock in the central Alps (Switzerland).}, journal = {Microbial ecology}, volume = {58}, number = {2}, pages = {290-306}, pmid = {19172216}, issn = {1432-184X}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; *Biodiversity ; Calcium Carbonate/analysis ; Gene Library ; Magnesium/analysis ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Switzerland ; }, abstract = {Endolithic microorganisms colonize the pores in exposed dolomite rocks in the Piora Valley in the Swiss Alps. They appear as distinct grayish-green bands about 1-8 mm below the rock surface. Based on environmental small subunit ribosomal RNA gene sequences, a diverse community driven by photosynthesis has been found. Cyanobacteria (57 clones), especially the genus Leptolyngbya, form the functional basis for an endolithic community which contains a wide spectrum of so far not characterized species of chemotrophic Bacteria (64 clones) with mainly Actinobacteria, Alpha-Proteobacteria, Bacteroidetes, and Acidobacteria, as well as a cluster within the Chloroflexaceae. Furthermore, a cluster within the Crenarchaeotes (40 clones) has been detected. Although the eukaryotic diversity was outside the scope of the study, an amoeba (39 clones), and several green algae (51 clones) have been observed. We conclude that the bacterial diversity in this endolithic habitat, especially of chemotrophic, nonpigmented organisms, is considerable and that Archaea are present as well.}, }
@article {pmid19171253, year = {2009}, author = {Iacumin, L and Cecchini, F and Manzano, M and Osualdini, M and Boscolo, D and Orlic, S and Comi, G}, title = {Description of the microflora of sourdoughs by culture-dependent and culture-independent methods.}, journal = {Food microbiology}, volume = {26}, number = {2}, pages = {128-135}, doi = {10.1016/j.fm.2008.10.010}, pmid = {19171253}, issn = {1095-9998}, mesh = {Base Sequence ; Biodiversity ; Bread/*microbiology ; Candida/genetics/*growth &amp; development/isolation &amp; purification ; Colony Count, Microbial/*methods ; DNA, Bacterial/analysis ; Fermentation ; *Food Microbiology ; Hydrogen-Ion Concentration ; Italy ; Lactobacillus/genetics/*growth &amp; development/isolation &amp; purification ; Levilactobacillus brevis/genetics/growth &amp; development/isolation &amp; purification ; Lactobacillus plantarum/genetics/growth &amp; development/isolation &amp; purification ; Polymerase Chain Reaction/methods ; Saccharomyces cerevisiae/genetics/*growth &amp; development/isolation &amp; purification ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Four types of sourdoughs (L, C, B, Q) from artisanal bakeries in Northern Italy were studied using culture-dependent and culture-independent methods. In all samples, the yeast numbers ranged from 160 to 10(7)cfu/g, and the numbers of lactic acid bacteria (LAB) ranged from 10(3) to 10(9)cfu/g. The isolated LAB were sequenced, and a similarity was noted between two samples (C, Q), both in terms of the species that were present and in terms of the percentage of isolates. In these two samples, Lactobacillus plantarum accounted for 73% and 89% of the bacteria, and Lactobacillus brevis represented 27% and 11%. In the third sample (B), however, the dominant LAB isolate was Lb. brevis (73%), while Lb. plantarum accounted for only 27%. The fourth sourdough (L) was completely different from the others. In this sample, the most prominent isolate was Weisella cibaria (56%), followed by Lb. plantarum (36%) and Pediococcus pentosaceus (8%). In three out of four samples (L, C and Q), all of the yeasts isolated were identified as Saccharomyces cerevisiae, yet only Candida humilis (90%) and Candida milleri (10%) were isolated in the fourth sample (B). The microbial ecology of the sourdoughs was also examined with direct methods. The results obtained by culture-independent methods and DGGE analysis underline a partial correspondence between the DNA and RNA analysis. These results demonstrate the importance of using a combined analytical approach to explore the microbial communities of sourdoughs.}, }
@article {pmid19171024, year = {2009}, author = {Sullivan, A and Nord, CE and Evengård, B}, title = {Effect of supplement with lactic-acid producing bacteria on fatigue and physical activity in patients with chronic fatigue syndrome.}, journal = {Nutrition journal}, volume = {8}, number = {}, pages = {4}, pmid = {19171024}, issn = {1475-2891}, mesh = {Adult ; Bifidobacterium ; *Dietary Supplements ; *Fatigue ; Fatigue Syndrome, Chronic/psychology/*therapy ; Feces/chemistry/microbiology ; Female ; Humans ; Lactobacillus ; Lactobacillus acidophilus ; Leukocyte L1 Antigen Complex/analysis ; Male ; Middle Aged ; *Motor Activity ; Pilot Projects ; Probiotics/*therapeutic use ; }, abstract = {Disturbances in intestinal microbial ecology and in the immune system of the host have been implicated as a part of the pathogenesis in chronic fatigue syndrome. Probiotic lactic acid producing bacteria have been shown to prevent and alleviate gastrointestinal disturbances and to normalize the cytokine profile which might be of an advantage for patients suffering from chronic fatigue syndrome. The aim of the study was to evaluate the effect of Lactobacillus paracasei ssp. paracasei F19, Lactobacillus acidophilus NCFB 1748 and Bifidobacterium lactis Bb12 on fatigue and physical activity in CFS patients. Fifteen patients fulfilling the criteria set by international researchers in the field at the US Centre for Disease Control and Prevention in 1994 for chronic fatigue syndrome, were included in the study. The patients had high fatigue severity scores and high disability scores. During the first two weeks baseline observations without treatment were assessed, succeeded by four weeks of intake of a probiotic product and a four-week follow-up period. The fatigue, health and physical activity was assessed by the use of the Visual Analogue Scales and the SF-12 Health Survey. Faecal samples were collected and the normal microflora was analysed. Neurocognitive functions improved during the study period while there were no significant changes in fatigue and physical activity scores. No major changes occurred in the gastrointestinal microflora. At the end of the study 6 of 15 patients reported that they had improved according to the assessment described. The findings in this study that improvement of health is possible to achieve should encourage further studies with interventions with probiotics in patients with CFS.}, }
@article {pmid19169740, year = {2009}, author = {Tang, X and Gao, G and Qin, B and Zhu, L and Chao, J and Wang, J and Yang, G}, title = {Characterization of bacterial communities associated with organic aggregates in a large, shallow, eutrophic freshwater lake (Lake Taihu, China).}, journal = {Microbial ecology}, volume = {58}, number = {2}, pages = {307-322}, pmid = {19169740}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; China ; Colony Count, Microbial ; Ecosystem ; Food Chain ; Fresh Water/analysis/microbiology ; *Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Although organic-aggregate-associated bacteria play a pivotal role in microbial food webs and in the cycling of major elements, their community composition and diversity have not been extensively studied, especially in shallow freshwater systems. This study is among the first to explore intra-lake horizontal heterogeneity of organic-aggregate-associated bacterial community composition (OABC) in the large, shallow, and eutrophic Lake Taihu. During November 2006, samples were collected at four locations representing different trophic states and food web structures. Regional variability of OABC and diversity were studied by amplified ribosomal DNA restriction analysis and comparative analysis of four large 16S ribosomal RNA clone libraries. Our results demonstrate that OABC were numerically dominated by members of the beta-proteobacteria (19.2-38.6%), Bacteroidetes (3.6-20.0%), and alpha-proteobacteria (11.5-19.2%) groups. The dominance of the Bacteroidetes group was related to algae-based aggregates. Horizontal heterogeneity of OABC exists within habitats, suggesting that the trophic state of the water and the physicochemical properties of organic aggregates (OA) play a key role. Diverse bacterial communities found on OA were substantially different from free-living ones. Comparative statistical analyses of the habitats of OA-associated bacteria highlight the potential ecological importance of the exchange between OABC and the surrounding planktonic community. Lastly, we found at least 45% of sequences closely related to ones previously found in soils, sludge, sediments, and other habitats. This demonstrates that microorganisms from terrestrial and sediment habitats are an important component of OA.}, }
@article {pmid19169713, year = {2009}, author = {Wallander, H and Mörth, CM and Giesler, R}, title = {Increasing abundance of soil fungi is a driver for (15)N enrichment in soil profiles along a chronosequence undergoing isostatic rebound in northern Sweden.}, journal = {Oecologia}, volume = {160}, number = {1}, pages = {87-96}, pmid = {19169713}, issn = {1432-1939}, mesh = {Carbon Isotopes/analysis ; Fatty Acids/analysis ; Mycorrhizae/metabolism/*physiology ; Nitrogen Isotopes/*analysis ; Phospholipids/analysis ; Principal Component Analysis ; Soil/*analysis ; *Soil Microbiology ; Sweden ; }, abstract = {Soil organic material (SOM) is usually enriched in (15)N in deeper soil layers. This has been explained by discrimination against the heavier isotope during decomposition or by the accumulation of (15)N-enriched microbial biomass versus plant biomass in older SOM. In particular, ectomycorrhizal (EM) fungi have been suggested to accumulate in old SOM since this group is among the most (15)N-enriched components of the microbial community. In the present study we investigated the microbial community in soil samples along a chronosequence (7,800 years) of sites undergoing isostatic rebound in northern Sweden. The composition of the microbial community was analyzed and related to the delta(15)N and delta(13)C isotope values of the SOM in soil profiles. A significant change in the composition of the microbial community was found during the first 2,000 years, and this was positively related to an increase in the delta(15)N values of the E and B horizons in the mineral soil. The proportion of fungal phospholipid fatty acids increased with time in the chronosequence and was positively related to the (15)N enrichment of the SOM. The increase in delta(13)C in the SOM was much less than the increase in delta(15)N, and delta(13)C values in the mineral soil were only weakly related to soil age. The C:N ratio and the pH of the soil were important factors determining the composition of the microbial community. We suggest that the N being transported from the soil to aboveground tissue by EM fungi is a driver for (15)N enrichment of soil profiles.}, }
@article {pmid19168616, year = {2009}, author = {Bergholz, PW and Bakermans, C and Tiedje, JM}, title = {Psychrobacter arcticus 273-4 uses resource efficiency and molecular motion adaptations for subzero temperature growth.}, journal = {Journal of bacteriology}, volume = {191}, number = {7}, pages = {2340-2352}, pmid = {19168616}, issn = {1098-5530}, mesh = {Adaptation, Physiological ; Bacterial Proteins/genetics/metabolism ; Cold Temperature ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Psychrobacter/enzymology/genetics/growth &amp; development/*physiology ; }, abstract = {Permafrost soils are extreme environments that exert low-temperature, desiccation, and starvation stress on bacteria over thousands to millions of years. To understand how Psychrobacter arcticus 273-4 survived for >20,000 years in permafrost, transcriptome analysis was performed during growth at 22 degrees C, 17 degrees C, 0 degrees C, and -6 degrees C using a mixed-effects analysis of variance model. Genes for transcription, translation, energy production, and most biosynthetic pathways were downregulated at low temperatures. Evidence of isozyme exchange was detected over temperature for D-alanyl-D-alanine carboxypeptidases (dac1 and dac2), DEAD-box RNA helicases (csdA and Psyc_0943), and energy-efficient substrate incorporation pathways for ammonium and acetate. Specific functions were compensated by upregulation of genes at low temperature, including genes for the biosynthesis of proline, tryptophan, and methionine. RNases and peptidases were generally upregulated at low temperatures. Changes in energy metabolism, amino acid metabolism, and RNase gene expression were consistent with induction of a resource efficiency response. In contrast to results observed for other psychrophiles and mesophiles, only clpB and hsp33 were upregulated at low temperature, and there was no upregulation of other chaperones and peptidyl-prolyl isomerases. relA, csdA, and dac2 knockout mutants grew more slowly at low temperature, but a dac1 mutant grew more slowly at 17 degrees C. The combined data suggest that the basal biological machinery, including translation, transcription, and energy metabolism, is well adapted to function across the growth range of P. arcticus from -6 degrees C to 22 degrees C, and temperature compensation by gene expression was employed to address specific challenges to low-temperature growth.}, }
@article {pmid19151179, year = {2009}, author = {Rousk, J and Brookes, PC and Bååth, E}, title = {Contrasting soil pH effects on fungal and bacterial growth suggest functional redundancy in carbon mineralization.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {6}, pages = {1589-1596}, pmid = {19151179}, issn = {1098-5336}, mesh = {Bacteria/*drug effects/growth &amp; development/*metabolism ; Carbon/*metabolism ; Fungi/*drug effects/growth &amp; development/*metabolism ; Hordeum/growth &amp; development ; Hydrogen-Ion Concentration ; *Soil Microbiology ; United Kingdom ; }, abstract = {The influence of pH on the relative importance of the two principal decomposer groups in soil, fungi and bacteria, was investigated along a continuous soil pH gradient at Hoosfield acid strip at Rothamsted Research in the United Kingdom. This experimental location provides a uniform pH gradient, ranging from pH 8.3 to 4.0, within 180 m in a silty loam soil on which barley has been continuously grown for more than 100 years. We estimated the importance of fungi and bacteria directly by measuring acetate incorporation into ergosterol to measure fungal growth and leucine and thymidine incorporation to measure bacterial growth. The growth-based measurements revealed a fivefold decrease in bacterial growth and a fivefold increase in fungal growth with lower pH. This resulted in an approximately 30-fold increase in fungal importance, as indicated by the fungal growth/bacterial growth ratio, from pH 8.3 to pH 4.5. In contrast, corresponding effects on biomass markers for fungi (ergosterol and phospholipid fatty acid [PLFA] 18:2omega6,9) and bacteria (bacterial PLFAs) showed only a two- to threefold difference in fungal importance in the same pH interval. The shift in fungal and bacterial importance along the pH gradient decreased the total carbon mineralization, measured as basal respiration, by only about one-third, possibly suggesting functional redundancy. Below pH 4.5 there was universal inhibition of all microbial variables, probably derived from increased inhibitory effects due to release of free aluminum or decreasing plant productivity. To investigate decomposer group importance, growth measurements provided significantly increased sensitivity compared with biomass-based measurements.}, }
@article {pmid19139953, year = {2009}, author = {Pruvost, O and Savelon, C and Boyer, C and Chiroleu, F and Gagnevin, L and Jacques, MA}, title = {Populations of Xanthomonas citri pv. mangiferaeindicae from asymptomatic mango leaves are primarily endophytic.}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {170-178}, pmid = {19139953}, issn = {1432-184X}, mesh = {*Biofilms ; Chloroform/pharmacology ; Mangifera/*microbiology ; Plant Diseases/*microbiology ; Plant Leaves/microbiology ; Xanthomonas/drug effects/*growth &amp; development/isolation &amp; purification ; }, abstract = {Epiphytic survival of several Xanthomonas pathovars has been reported, but most studies failed to determine whether such populations were resident epiphytes, resulting from latent infections, or casual epiphytes. This study aimed at understanding the nature of Xanthomonas citri pv. mangiferaeindicae populations associated with asymptomatic leaves. When spray-inoculated on mango leaves cv. Maison Rouge, the pathogen multiplied markedly in association with juvenile leaves, but was most often detected as low population sizes (<1 x 10(3) cfu g(-1)) in association with mature leaves. Our results suggest a very low biological significance of biofilm-associated populations of X. citri pv. mangiferaeindicae, while saprophytic microbiota associated with mango leaves survived frequently as biofilms. A chloroform vapor-based disinfestation assay which kills cells specifically located on the leaf surface and not those located within the leaf mesophyll was developed. When applied to spray-inoculated leaves maintained under controlled environmental conditions, 155 out of the 168 analyzed datasets collected over three assessment dates for seven bacterial strains representative of the genetic diversity of the pathogen failed to demonstrate a significant X. citri pv. mangiferaeindicae population decrease on chloroform treated leaves up to 13 days after inoculation. We conclude that an efficient survival of X. citri pv. mangiferaeindicae present on mango leaf surfaces following a limited dissemination event is largely dependent on the availability of juvenile plant tissues. The bacterium gains access to protected sites (e.g., mesophyll) through stomata where it becomes endophytic and eventually causes disease. Chloroform vapor-based disinfestation assays should be useful for further studies aiming at evaluating survival sites of bacteria associated with the phyllosphere.}, }
@article {pmid19138432, year = {2009}, author = {Ye, P and Nadkarni, MA and Simonian, M and Hunter, N}, title = {CD24 regulated gene expression and distribution of tight junction proteins is associated with altered barrier function in oral epithelial monolayers.}, journal = {BMC cell biology}, volume = {10}, number = {}, pages = {2}, pmid = {19138432}, issn = {1471-2121}, mesh = {Actins/metabolism ; CD24 Antigen/genetics/*metabolism ; Cadherins/*genetics/metabolism ; Cell Line, Tumor ; Connexins/metabolism ; Dextrans/metabolism ; Epithelial Cells/*metabolism/ultrastructure ; *Gene Expression Regulation ; Humans ; Microscopy, Electron, Transmission ; Models, Biological ; Mouth/*cytology ; RNA, Messenger/metabolism ; RNA, Small Interfering ; Tight Junctions/metabolism ; }, abstract = {BACKGROUND: Control of intercellular penetration of microbial products is critical for the barrier function of oral epithelia. We demonstrated that CD24 is selectively and strongly expressed in the cells of the epithelial attachment to the tooth and the epithelial lining of the diseased periodontal pocket and studies in vitro showed that CD24 regulated expression of the epithelial intercellular adhesion protein E-cadherin.<br><br>RESULTS: In the present study, the barrier function of oral epithelial cell monolayers to low molecular weight dextran was assayed as a model for the normal physiological function of the epithelial attachment to limit ingress of microbial products from oral microbial biofilms. Paracellular transfer of low molecular weight dextran across monolayers of oral epithelial cells was specifically decreased following incubation with anti-CD24 peptide antibody whereas passage of dextran across the monolayer was increased following silencing of mRNA for CD24. Changes in barrier function were related to the selective regulation of the genes encoding zonula occludens-1, zonula occludens-2 and occludin, proteins implicated in tight junctions. More particularly, enhanced barrier function was related to relocation of these proteins to the cell periphery, compatible with tight junctions.<br><br>CONCLUSION: CD24 has the constitutive function of maintaining expression of selected genes encoding tight junction components associated with a marginal barrier function of epithelial monolayers. Activation by binding of an external ligand to CD24 enhances this expression but is also effective in re-deployment of tight junction proteins that is aligned with enhanced intercellular barrier function. These results establish the potential of CD24 to act as a potent regulator of the intercellular barrier function of epithelia in response to local microbial ecology.}, }
@article {pmid19125306, year = {2009}, author = {Perez, JL and French, JV and Summy, KR and Baines, AD and Little, CR}, title = {Fungal phyllosphere communities are altered by indirect interactions among trophic levels.}, journal = {Microbial ecology}, volume = {57}, number = {4}, pages = {766-774}, pmid = {19125306}, issn = {1432-184X}, mesh = {Animals ; Citrus paradisi/microbiology ; Diptera/*parasitology ; *Ecosystem ; *Food Chain ; Fungi/classification/*growth &amp; development/isolation &amp; purification ; Plant Leaves/microbiology ; Population Dynamics ; Texas ; Wasps/*physiology ; }, abstract = {Trophic interactions involving predators, herbivores, and plants have been described in terrestrial systems. However, there is almost no information on the effect of trophic interactions on microbial phyllosphere community abundance, diversity, or structure. In this study, the interaction between a parasitoid, an insect herbivore, and the fungal phyllosphere community is examined. Parasitoid wasps have an indirect negative impact on fungal community diversity. On the citrus phyllosphere, the exotic wasp species, Amitus hesperidum and Encarsia opulenta, may parasitize the citrus blackfly (Aleurocanthus woglumi). If parasitism levels are low, the blackfly may produce significant amounts of honeydew secretions on the surface of the leaf. Honeydew deposition provides a carbon-rich substrate for the development of fungal growth persisting as sooty mold on the leaves. Leaves from sooty mold-infested grapefruit (Citrus paradisi) trees were collected from multiple orchards in south Texas. The effect of different levels of exotic parasite activity, citrus blackfly, and sooty mold infestation on phyllosphere mycobiota community structure and diversity was examined. Our results suggest the presence of the parasitoid may lead to a top-down trophic cascade affecting phyllosphere fungal community diversity and structure. Additionally, persistent sooty mold deposits that have classically been referred to as Capnodium citri (and related asexual morphological forms) actually comprise a myriad of fungal species including many saprophytes and potential fruit and foliar pathogens of citrus.}, }
@article {pmid19125305, year = {2009}, author = {Chénier, MR and Juteau, P}, title = {Fate of chlortetracycline- and tylosin-resistant bacteria in an aerobic thermophilic sequencing batch reactor treating swine waste.}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {86-97}, pmid = {19125305}, issn = {1432-184X}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics/*growth &amp; development ; Bioreactors/microbiology ; Chlortetracycline/pharmacology ; Colony Count, Microbial ; DNA, Bacterial/analysis ; Drug Resistance, Bacterial/*genetics ; Genes, Bacterial ; Hot Temperature ; Phylogeny ; RNA, Ribosomal, 16S/analysis ; Swine/microbiology ; Tylosin/pharmacology ; Waste Disposal, Fluid/*methods ; }, abstract = {Antibiotics have been added to animal feed for decades. Consequently, food animals and their wastes constitute a reservoir of antibiotic-resistant bacteria. The objective of this work was to characterize the impact of an aerobic thermophilic biotreatment on aerobic, antibiotic-resistant bacteria in swine waste. The proportion of tylosin- and chlortetracycline-resistant bacteria grown at 25 degrees C, 37 degrees C, and 60 degrees C decreased after treatment, but they were still abundant (10(2) to 10(8) most probable number ml(-1)) in the treated swine waste. The presence of 14 genes conferring resistance to tylosin and chlortetracycline was assessed by polymerase chain reaction in bacterial populations grown at 25 degrees C, 37 degrees C, and 60 degrees C, with or without antibiotics. In 22 cases, genes were detected before but not after treatment. The overall gene diversity was wider before [tet(BLMOSY), erm(AB)] than after [tet(LMOS), erm(B)] treatment. Analysis by denaturing gradient gel electrophoresis of amplified 16S ribosomal DNA (rDNA) fragments generally showed a reduction of the bacterial diversity, except for total populations grown at 60 degrees C and for tylosin-resistant populations grown at 37 degrees C. The latter were further investigated by cloning and sequencing their 16S rDNA. Phylotypes found before treatment were all closely related to Enterococcus hirae, whereas six different phylotypes, related to Pseudomonas, Alcaligenes, and Pusillimonas, were found after treatment. This work demonstrated that the aerobic thermophilic biotreatment cannot be considered as a means for preventing the dissemination of aerobic antibiotic-resistant bacteria and their resistance genes to the environment. However, since pathogens do not survive the biotreatment, the effluent does not represent an immediate threat to animal or human health.}, }
@article {pmid19120664, year = {2008}, author = {Albano, H and Henriques, I and Correia, A and Hogg, T and Teixeira, P}, title = {Characterization of microbial population of 'Alheira' (a traditional Portuguese fermented sausage) by PCR-DGGE and traditional cultural microbiological methods.}, journal = {Journal of applied microbiology}, volume = {105}, number = {6}, pages = {2187-2194}, doi = {10.1111/j.1365-2672.2008.03947.x}, pmid = {19120664}, issn = {1365-2672}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Bacteriological Techniques ; DNA Primers/genetics ; DNA, Bacterial/*analysis ; Fermentation ; *Food Microbiology ; Lactobacillus/genetics ; Meat Products/*microbiology ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; Portugal ; RNA, Ribosomal, 16S/analysis ; }, abstract = {AIMS: This study evaluates the microbial ecology of 'Alheira' by traditional microbiological analysis and a PCR-denaturing gradient gel electrophoresis (DGGE) protocol.<br><br>METHODS AND RESULTS: Total microbial DNA from 'Alheiras' was extracted directly from the products and subjected to PCR using Eubacterial primers for 16S rDNA. The amplicons were separated by DGGE. The results demonstrated that different products of the same batch display identical profiles, whereas products from different batches of the same producer could display different DGGE profiles. 'Alheiras' from different producers were distinguishable based on the respective DGGE profiles. The obtained sequences from prevalent phylotypes affiliated with order Lactobacillales and order Bacillales and class Gammaproteobacteria. The same samples were subjected to traditional microbiological analysis. In both methods, lactic acid bacteria were dominant and were present together with other organisms, mainly members of the family Micrococcaceae.<br><br>CONCLUSIONS: The approach explored in this study allowed the description of the microbial community present in 'Alheira' in particular the diversity of lactic acid bacteria.<br><br>This can be useful for the microbiological characterization of traditional products in order to develop new methods of quality control capable of supporting a standardization of the processes, while preserving their typical traits.}, }
@article {pmid19120464, year = {2009}, author = {De Gusseme, B and De Schryver, P and De Cooman, M and Verbeken, K and Boeckx, P and Verstraete, W and Boon, N}, title = {Nitrate-reducing, sulfide-oxidizing bacteria as microbial oxidants for rapid biological sulfide removal.}, journal = {FEMS microbiology ecology}, volume = {67}, number = {1}, pages = {151-161}, doi = {10.1111/j.1574-6941.2008.00598.x}, pmid = {19120464}, issn = {0168-6496}, mesh = {*Arcobacter/classification/genetics/growth &amp; development/metabolism ; *Bacteria, Anaerobic/classification/genetics/growth &amp; development/metabolism ; Bioreactors ; Biotechnology/methods ; Culture Media ; Ecosystem ; Hydrogen Sulfide/metabolism ; Molecular Sequence Data ; Nitrates/*metabolism ; Oxidants/*metabolism ; Oxidation-Reduction ; Sequence Analysis, DNA ; Sewage/microbiology ; Sulfides/*metabolism ; Time Factors ; }, abstract = {The emission of hydrogen sulfide into the atmosphere of sewer systems induces the biological production of sulfuric acid, causing severe concrete corrosion. As a possible preventive solution, a microbial consortium of nitrate-reducing, sulfide-oxidizing bacteria (NR-SOB) was enriched in a continuously stirred tank reactor in order to develop a biological technique for the removal of dissolved sulfide. The consortium, dominated by Arcobacter sp., was capable of removing 99% of sulfide. Stable isotope fractioning of the sulfide indicated that the oxidation was a biological process. The capacity of the NR-SOB consortium for rapid removal of sulfide was demonstrated by using it as an inoculum in synthetic and real sewage. Removal rates up to 52 mg sulfide-S g VSS(-1) h(-1) were achieved, to our knowledge the highest removal rate reported so far for freshwater species in the absence of molecular oxygen. Further long-term incubation experiments revealed the capacity of the bacteria to oxidize sulfide without the presence of nitrate, suggesting that an oxidized redox reserve is present in the culture.}, }
@article {pmid19120456, year = {2009}, author = {Smith, CJ and Osborn, AM}, title = {Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology.}, journal = {FEMS microbiology ecology}, volume = {67}, number = {1}, pages = {6-20}, doi = {10.1111/j.1574-6941.2008.00629.x}, pmid = {19120456}, issn = {0168-6496}, mesh = {Ecology/*methods ; *Environmental Microbiology ; Polymerase Chain Reaction/*methods ; RNA, Messenger/analysis ; RNA, Ribosomal, 16S/genetics ; Reverse Transcriptase Polymerase Chain Reaction/*methods ; }, abstract = {Quantitative PCR (Q-PCR or real-time PCR) approaches are now widely applied in microbial ecology to quantify the abundance and expression of taxonomic and functional gene markers within the environment. Q-PCR-based analyses combine 'traditional' end-point detection PCR with fluorescent detection technologies to record the accumulation of amplicons in 'real time' during each cycle of the PCR amplification. By detection of amplicons during the early exponential phase of the PCR, this enables the quantification of gene (or transcript) numbers when these are proportional to the starting template concentration. When Q-PCR is coupled with a preceding reverse transcription reaction, it can be used to quantify gene expression (RT-Q-PCR). This review firstly addresses the theoretical and practical implementation of Q-PCR and RT-Q-PCR protocols in microbial ecology, highlighting key experimental considerations. Secondly, we review the applications of (RT)-Q-PCR analyses in environmental microbiology and evaluate the contribution and advances gained from such approaches. Finally, we conclude by offering future perspectives on the application of (RT)-Q-PCR in furthering understanding in microbial ecology, in particular, when coupled with other molecular approaches and more traditional investigations of environmental systems.}, }
@article {pmid19117663, year = {2009}, author = {Bouallagui, H and Lahdheb, H and Ben Romdan, E and Rachdi, B and Hamdi, M}, title = {Improvement of fruit and vegetable waste anaerobic digestion performance and stability with co-substrates addition.}, journal = {Journal of environmental management}, volume = {90}, number = {5}, pages = {1844-1849}, doi = {10.1016/j.jenvman.2008.12.002}, pmid = {19117663}, issn = {1095-8630}, mesh = {Abattoirs ; Analysis of Variance ; Animals ; Bacteria, Anaerobic/*metabolism ; *Biodegradation, Environmental ; Carbon/metabolism ; Fishes/metabolism ; Fruit/metabolism ; Nitrogen/metabolism ; Refuse Disposal/*methods ; Sewage/chemistry/*microbiology ; Vegetables/metabolism ; }, abstract = {The effect of fish waste (FW), abattoir wastewater (AW) and waste activated sludge (WAS) addition as co-substrates on the fruit and vegetable waste (FVW) anaerobic digestion performance was investigated under mesophilic conditions using four anaerobic sequencing batch reactors (ASBR) with the aim of finding the better co-substrate for the enhanced performance of co-digestion. The reactors were operated at an organic loading rate of 2.46-2.51 g volatile solids (VS)l(-1)d(-1), of which approximately 90% were from FVW, and a hydraulic retention time of 10 days. It was observed that AW and WAS additions with a ratio of 10% VS enhanced biogas yield by 51.5% and 43.8% and total volatile solids removal by 10% and 11.7%, respectively. However FW addition led to improvement of the process stability, as indicated by the low VFAs/Alkalinity ratio of 0.28, and permitted anaerobic digestion of FVW without chemical alkali addition. Despite a considerable decrease in the C/N ratio from 34.2 to 27.6, the addition of FW slightly improved the gas production yield (8.1%) compared to anaerobic digestion of FVW alone. A C/N ratio between 22 and 25 seemed to be better for anaerobic co-digestion of FVW with its co-substrates. The most significant factor for enhanced FVW digestion performance was the improved organic nitrogen content provided by the additional wastes. Consequently, the occurrence of an imbalance between the different groups of anaerobic bacteria which may take place in unstable anaerobic digestion of FVW could be prevented.}, }
@article {pmid19108975, year = {2009}, author = {Enright, AM and McGrath, V and Gill, D and Collins, G and O'Flaherty, V}, title = {Effect of seed sludge and operation conditions on performance and archaeal community structure of low-temperature anaerobic solvent-degrading bioreactors.}, journal = {Systematic and applied microbiology}, volume = {32}, number = {1}, pages = {65-79}, doi = {10.1016/j.syapm.2008.10.003}, pmid = {19108975}, issn = {0723-2020}, mesh = {Anaerobiosis ; Archaea/classification/genetics/*growth &amp; development/metabolism ; *Bioreactors ; Biotechnology ; DNA, Archaeal/analysis ; Drug Industry ; *Ecosystem ; In Situ Hybridization, Fluorescence ; Methane/biosynthesis ; Methanosarcinales/classification/genetics/growth &amp; development/metabolism ; Molecular Sequence Data ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; Solvents/chemistry/*metabolism ; *Temperature ; Waste Disposal, Fluid/methods ; }, abstract = {Two laboratory-scale expanded granular sludge bed (EGSB) anaerobic bioreactors (R1 and R2) were inoculated with biomass from different mesophilic (37 degrees C) treatment plants, and used for the treatment of an organic solvent-based wastewater at 9-14 degrees C at applied organic loading rates (OLRs) of 1.2-3.6kg chemical oxygen demand (COD)m(-3)d(-1). Replicated treatment performance was observed at 10-14 degrees C, which suggested the feasibility of the process at pilot-scale. Stable and efficient COD removal, along with high methane productivity, was demonstrated at 9 degrees C at an applied OLR of 2.4kgCODm(-3)d(-1). Clonal libraries and fluorescence in situ hybridization (FISH) indicated that the seed sludges were dominated (>60%) by acetoclastic Methanosaeta-like organisms. Specific methanogenic activity (SMA) profiles indicated shifts in the physiological profiles of R1 and R2 biomass, including the development of psychrotolerant methanogenic activity. Acetoclastic methanogenesis represented the primary route of methane production in R1 and R2, which is in contrast with several previous reports from low-temperature bioreactor trials. A reduction in the abundance of Methanosaeta-like clones (R2), along with the detection of hydrogenotrophic methanogenic species, coincided with altered granule (sludge) morphology and the development of hydrogenotrophic SMA after prolonged operation at 9 degrees C.}, }
@article {pmid19107315, year = {2009}, author = {Campbell, JH and Clark, JS and Zak, JC}, title = {PCR-DGGE comparison of bacterial community structure in fresh and archived soils sampled along a Chihuahuan Desert elevational gradient.}, journal = {Microbial ecology}, volume = {57}, number = {2}, pages = {261-266}, pmid = {19107315}, issn = {0095-3628}, mesh = {Bacteria/classification/*genetics ; *Biodiversity ; Biomass ; DNA, Bacterial/genetics ; *Desert Climate ; Electrophoresis, Polyacrylamide Gel ; RNA, Ribosomal, 16S/genetics ; Soil ; *Soil Microbiology ; Specimen Handling ; Texas ; }, abstract = {The polymerase chain reaction coupled with denaturing gradient gel electrophoresis (PCR-DGGE) has been used widely to determine species richness and structure of microbial communities in a variety of environments. Researchers commonly archive soil samples after routine chemical or microbial analyses, and applying PCR-DGGE technology to these historical samples offers evaluation of long-term patterns in bacterial species richness and community structure that was not available with previous technology. However, use of PCR-DGGE to analyze microbial communities of archived soils has been largely unexplored. To evaluate the stability of DGGE patterns in archived soils in comparison with fresh soils, fresh and archived soils from five sites along an elevational gradient in the Chihuahuan Desert were compared using PCR-DGGE of 16S rDNA. DNA from all archived samples was extracted reliably, but DNA in archived soils collected from a closed-canopy oak forest site could not be amplified. DNA extraction yields were lower for most archived soils, but minimal changes in bacterial species richness and structure due to archiving were noted in bacterial community profiles from four sites. Use of archived soils to determine long-term changes in bacterial community structure via PCR-DGGE appears to be a viable option for addressing microbial community dynamics for particular ecosystems or landscapes.}, }
@article {pmid19101008, year = {2009}, author = {Flores, C and Morgante, V and González, M and Navia, R and Seeger, M}, title = {Adsorption studies of the herbicide simazine in agricultural soils of the Aconcagua valley, central Chile.}, journal = {Chemosphere}, volume = {74}, number = {11}, pages = {1544-1549}, doi = {10.1016/j.chemosphere.2008.10.060}, pmid = {19101008}, issn = {1879-1298}, mesh = {Adsorption ; Agriculture ; Chile ; Herbicides/*chemistry ; Hydrogen Bonding ; Simazine/*chemistry ; *Soil ; Soil Pollutants/*chemistry ; Thermodynamics ; }, abstract = {Simazine is a s-triazine herbicide that has been applied worldwide for agriculture. This herbicide is the second most commonly detected pesticide in surface and groundwater in the United States, Europe and Australia. In this study, simazine adsorption behaviour was studied in two agricultural soils of the Aconcagua valley, central Chile. The two studied soils were soil A (loam, 8.5% organic matter content) and soil B (clay-loam, 3.5% organic matter content). Three times higher simazine adsorption capacity was observed in soil A (68.03 mg kg(-1)) compared to soil B (22.03 mg kg(-1)). The simazine adsorption distribution coefficients (K(d)) were 9.32 L kg(-1) for soil A and 7.74 L kg(-1) for soil B. The simazine adsorption enthalpy in soil A was -21.0 kJ mol(-1) while in soil B the adsorption enthalpy value was -11.5 kJ mol(-1). These results indicate that simazine adsorption process in these soils is exothermic, governing H bonds the adsorption process of simazine in both the loam and clay-loam soils. These results and the potentiometric profiles of both soils, suggest that simazine adsorption in soil A is mainly governed by simazine-organic matter interactions and in soil B by simazine-clay interactions. The understanding of simazine sorption-desorption processes is essential to determine the pesticide fate and availability in soil for pest control, biodegradation, runoff and leaching.}, }
@article {pmid19097144, year = {2009}, author = {Baytshtok, V and Lu, H and Park, H and Kim, S and Yu, R and Chandran, K}, title = {Impact of varying electron donors on the molecular microbial ecology and biokinetics of methylotrophic denitrifying bacteria.}, journal = {Biotechnology and bioengineering}, volume = {102}, number = {6}, pages = {1527-1536}, doi = {10.1002/bit.22213}, pmid = {19097144}, issn = {1097-0290}, mesh = {Biomass ; *Bioreactors ; Carbon Isotopes/metabolism ; Ethanol/metabolism ; Hyphomicrobium/genetics/*metabolism ; Kinetics ; Linear Models ; Methanol/*metabolism ; Nitrates/*metabolism ; Nitrites/*metabolism ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics/metabolism ; Rhodocyclaceae/genetics/*metabolism ; Sewage/microbiology ; }, abstract = {The goal of this study was to identify bacterial populations that assimilated methanol in a denitrifying sequencing batch reactor (SBR), using stable isotope probing (SIP) of (13)C labeled DNA and quantitatively track changes in these populations upon changing the electron donor from methanol to ethanol in the SBR feed. Based on SIP derived (13)C 16S rRNA gene clone libraries, dominant SBR methylotrophic bacteria were related to Methyloversatilis spp. and Hyphomicrobium spp. These methylotrophic populations were quantified via newly developed real-time PCR assays. Upon switching the electron donor from methanol to ethanol, Hyphomicrobium spp. concentrations decreased significantly in accordance with their obligately methylotrophic nutritional mode. In contrast, Methyloversatilis spp. concentrations were relatively unchanged, in accordance with their ability to assimilate both methanol and ethanol. Direct assimilation of ethanol by Methyloversatilis spp. but not Hyphomicrobium spp. was also confirmed via SIP. The reduction in methylotrophic bacterial concentration upon switching to ethanol was paralleled by a significant decrease in the methanol supported denitrification biokinetics of the SBR on nitrate. In sum, the results of this study demonstrate that the metabolic capabilities (methanol assimilation and metabolism) and substrate specificity (obligately or facultatively methylotrophic) of two distinct methylotrophic bacterial populations contributed to their survival or washout in denitrifying bioreactors.}, }
@article {pmid19092215, year = {2008}, author = {Whang, LM and Yang, YF and Huang, SJ and Cheng, SS}, title = {Microbial ecology and performance of nitrifying bacteria in an aerobic membrane bioreactor treating thin-film transistor liquid crystal display wastewater.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {58}, number = {12}, pages = {2365-2371}, doi = {10.2166/wst.2008.580}, pmid = {19092215}, issn = {0273-1223}, mesh = {Aerobiosis ; Bacteria/*metabolism ; Biodegradation, Environmental ; Bioreactors/*microbiology ; Dimethyl Sulfoxide/chemistry/metabolism ; *Ecology ; Ethanolamine/chemistry/metabolism ; Liquid Crystals/*microbiology ; Membranes, Artificial ; Nitrogen/*metabolism ; Polymorphism, Restriction Fragment Length ; Quaternary Ammonium Compounds/chemistry/metabolism ; Transistors, Electronic/*microbiology ; Waste Disposal, Fluid ; Water Purification/*methods ; }, abstract = {This study was conducted to evaluate the long-term performance of an aerobic membrane bioreactor (MBR), treating TFT-LCD wastewater containing dimethyl sulphoxide (DMSO), monoethanolamine (MEA) and tetra-methyl ammonium hydroxide (TMAH), which are recognized as slow-biodegradable organic compounds containing nitrogen and can release significant amount of ammonia during biodegradation. Moreover, many studies have reported that certain organic compounds can potentially inhibit nitrification of AOB, but limited information is available regarding the effects of TFT-LCD wastewater compounds on nitrification performance and microbial ecology of nitrifying bacteria. In general, the aerobic MBR achieved satisfactory conversion efficiency for DMSO, MEA, TMAH, and ammonia, except that a sudden inhibition on MEA degradation was observed for a transition period when the influent feed switched from synthetic to real TFT-LCD wastewater. Furthermore, the terminal restriction fragment length polymorphism (T-RFLP) methodology was applied to monitor the microbial ecology of nitrifying bacteria in the aerobic MBR. The results suggested that Nm. marina or Nm. cummunis were the dominant AOB population in the aerobic MBR fed with synthetic TFT-LCD wastewater, while Nitrosospira became dominant in the aerobic MBR fed with real TFT-LCD wastewater. For the NOB population, both Nitrobacter and Nitrospira were present during this study. Finally, the results of batch experiments, which were conducted to evaluate the effects of DMSO, MEA, and TMAH on nitrification activity, indicated that MEA and TMAH became inhibitory to nitrifying bacteria at concentrations of 250 and 50 mg/L, respectively, while DMSO did not at concentrations up to 100 mg/L.}, }
@article {pmid19088311, year = {2009}, author = {Wagner, AO and Malin, C and Illmer, P}, title = {Application of denaturing high-performance liquid chromatography in microbial ecology: fermentor sludge, compost, and soil community profiling.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {4}, pages = {956-964}, pmid = {19088311}, issn = {1098-5336}, mesh = {Bacteria/*classification/*genetics ; Chromatography, High Pressure Liquid/*methods ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Genetic fingerprinting methods, such as denaturing gradient gel electrophoresis (DGGE), are used in microbial ecology for the analysis of mixed microbial communities but are associated with various problems. In the present study we used a new alternative method: denaturing high-performance liquid chromatography (dHPLC). This method was previously shown to work with samples from water and gut flora but had not yet been applied to complex environmental samples. In contrast to other publications dealing with dHPLC, we used a commonly available HPLC system. Samples from different origins (fermentor sludge, compost, and soil), all ecologically significant, were tested, and the 16S rRNA gene was amplified via PCR. After optimization of the HPLC elution conditions, amplicons of pure cultures and mixed microbial populations could be separated successfully. Systematic differentiation was carried out by a cloning approach, since fraction collection of the peaks did not result in satisfactory fragment separation. dHPLC was evaluated as a tool for microbial community analysis on a genetic level and demonstrated major improvements compared to gel-based fingerprinting methods, such as DGGE, that are commonly used in microbial ecology.}, }
@article {pmid19085182, year = {2009}, author = {Kramp, B and Donat, M and Dommerich, S and Pau, HW and Podbielski, A}, title = {Prospective controlled study of microbial colonization of the trachea in tracheotomized and laryngectomized patients with HME (heat and moisture exchanger).}, journal = {Acta oto-laryngologica}, volume = {129}, number = {10}, pages = {1136-1144}, doi = {10.1080/00016480802572517}, pmid = {19085182}, issn = {1651-2251}, mesh = {Female ; Humans ; *Laryngectomy ; Male ; Middle Aged ; Prospective Studies ; Prostheses and Implants/*microbiology ; Trachea/*microbiology ; *Tracheostomy ; }, abstract = {CONCLUSION: The use of heat and moisture exchangers (HMEs) does not endanger tracheostomy patients in terms of additional exposure to pathogenic microorganisms.<br><br>OBJECTIVE: Stoma filters in the form of HMEs cause a beneficial convection of respiratory air in tracheotomized and laryngectomized patients. We investigated whether or not this may lead to an altered microbial ecology in the non-physiologically colonized lower respiratory tract.<br><br>MATERIALS AND METHODS: To test this hypothesis, material from the trachea of stoma patients was prospectively collected utilizing a standardized swab technique and subsequent aerobic quantitative culture assays of the suspended and serially diluted material. With this approach, we examined the microbial flora in 6 and 5 patients after laryngectomy/tracheostomy, respectively, without any protection, in 11 patients after laryngectomy with a bib, and in 8 laryngectomized patients with an HME.<br><br>RESULTS: In all three groups, Staphylococcus aureus and Candida albicans were most frequently demonstrated. The microbial count of facultative pathogenic agents ranged between 3&#xd7;10(2) colony forming units (cfu)/ml and 10(6) cfu/ml and was similar in the three groups. With respect to the absence of inflammatory symptoms in every patient, all isolates could be regarded as colonizers. Among the antibiotics tested with each isolate, cefuroxime proved to be the most effective against the facultative pathogenic bacteria.}, }
@article {pmid19079040, year = {2008}, author = {Schleper, C}, title = {Microbial ecology: Metabolism of the deep.}, journal = {Nature}, volume = {456}, number = {7223}, pages = {712-714}, doi = {10.1038/456712a}, pmid = {19079040}, issn = {1476-4687}, mesh = {Ammonia/metabolism ; Atlantic Ocean ; Autotrophic Processes/genetics/physiology ; Crenarchaeota/genetics/metabolism/*physiology ; Ecosystem ; Heterotrophic Processes/physiology ; Nitrogen/*metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics ; }, }
@article {pmid19074609, year = {2009}, author = {Polerecky, L and Bissett, A and Al-Najjar, M and Faerber, P and Osmers, H and Suci, PA and Stoodley, P and de Beer, D}, title = {Modular spectral imaging system for discrimination of pigments in cells and microbial communities.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {3}, pages = {758-771}, pmid = {19074609}, issn = {1098-5336}, mesh = {Ecosystem ; Environmental Microbiology ; Image Processing, Computer-Assisted/methods ; Pigments, Biological/*analysis ; Spectrum Analysis/*methods ; }, abstract = {Here we describe a spectral imaging system for minimally invasive identification, localization, and relative quantification of pigments in cells and microbial communities. The modularity of the system allows pigment detection on spatial scales ranging from the single-cell level to regions whose areas are several tens of square centimeters. For pigment identification in vivo absorption and/or autofluorescence spectra are used as the analytical signals. Along with the hardware, which is easy to transport and simple to assemble and allows rapid measurement, we describe newly developed software that allows highly sensitive and pigment-specific analyses of the hyperspectral data. We also propose and describe a number of applications of the system for microbial ecology, including identification of pigments in living cells and high-spatial-resolution imaging of pigments and the associated phototrophic groups in complex microbial communities, such as photosynthetic endolithic biofilms, microbial mats, and intertidal sediments. This system provides new possibilities for studying the role of spatial organization of microorganisms in the ecological functioning of complex benthic microbial communities or for noninvasively monitoring changes in the spatial organization and/or composition of a microbial community in response to changing environmental factors.}, }
@article {pmid19067331, year = {2008}, author = {Bunge, J and Barger, K}, title = {Parametric models for estimating the number of classes.}, journal = {Biometrical journal. Biometrische Zeitschrift}, volume = {50}, number = {6}, pages = {971-982}, doi = {10.1002/bimj.200810452}, pmid = {19067331}, issn = {1521-4036}, mesh = {*Biodiversity ; *Ecosystem ; *Epidemiologic Methods ; *Models, Biological ; *Models, Statistical ; Numerical Analysis, Computer-Assisted ; }, abstract = {We consider parametric distributions intended to model heterogeneity in population size estimation, especially parametric stochastic abundance models for species richness estimation. We briefly review (conditional) maximum likelihood estimation of the number of species, and summarize the results of fitting 7 candidate models to frequency-count data, from a database of >40000 such instances, mostly arising from microbial ecology. We consider error estimation, goodness-of-fit assessment, data subsetting, and other practical matters. We find that, although the array of candidate models can be improved, finite mixtures of a small number of components (point masses or simple diffuse distributions) represent a promising direction. Finally we consider the connections between parametric models for abundance and incidence data, again noting the usefulness of finite mixture models.}, }
@article {pmid19067032, year = {2009}, author = {Norf, H and Arndt, H and Weitere, M}, title = {Responses of biofilm-dwelling ciliate communities to planktonic and benthic resource enrichment.}, journal = {Microbial ecology}, volume = {57}, number = {4}, pages = {687-700}, pmid = {19067032}, issn = {1432-184X}, mesh = {Animals ; Bacteria/*growth &amp; development ; Biofilms/*growth &amp; development ; Carbon/metabolism ; Ciliophora/growth &amp; development/*physiology ; Ecosystem ; Eukaryota/growth &amp; development/*physiology ; Rivers/microbiology ; *Water Microbiology ; }, abstract = {Four experiments covering different seasons were performed to test the impact of increased benthic and planktonic resource availability on the structure of biofilm-dwelling ciliate communities which were cultivated in river bypass systems. The growth of benthic bacteria was stimulated by the addition of dissolved organic carbon. The enrichment of the planktonic resource was achieved by supplementation with suspended bacteria. It was shown that both resource enrichments can differentially influence abundance and taxonomic structure of ciliate communities. Furthermore, both resources can influence different stages during biofilm colonization. Increased benthic bacterial growth mainly resulted in both an accumulation of primarily grazing-resistant bacterial filaments and in an increase in the number of vagile heterotrophic flagellates. This can stimulate nanophagous ciliates (feeding on flagellates) in addition to the direct stimulation of bacteriovorous ciliates. The effects of the planktonic bacteria enrichments were twofold: They could have been utilized either directly by suspension-feeding ciliates or indirectly through an enhanced growth of suspension-feeding attached heterotrophic flagellates, which were then in turn grazed upon by ciliates. The magnitude of responses of the total ciliate abundance to the two resource enrichments further depended on the background conditions, thereby showing temporarily variable limitations of these resources. Furthermore, the particular taxonomic groups stimulated by one resource type sometimes differed between the experiments, an observation which demonstrates that the response depends on different environmental factors and is not easily predictable based simply on resource type. Taken together, our results emphasize the need of a differentiated view on the effects of resources on complex biofilm-dwelling consumer communities with respect to both the origin of carbon source as well as the particular environmental conditions.}, }
@article {pmid19067031, year = {2009}, author = {Clark, JS and Campbell, JH and Grizzle, H and Acosta-Martìnez, V and Zak, JC}, title = {Soil microbial community response to drought and precipitation variability in the Chihuahuan Desert.}, journal = {Microbial ecology}, volume = {57}, number = {2}, pages = {248-260}, pmid = {19067031}, issn = {0095-3628}, mesh = {Altitude ; Bacteria/metabolism ; DNA, Bacterial/analysis ; DNA, Fungal/analysis ; *Desert Climate ; *Droughts ; Ecosystem ; Fungi/metabolism ; *Rain ; Seasons ; Soil/analysis ; *Soil Microbiology ; Texas ; }, abstract = {Increases in the magnitude and variability of precipitation events have been predicted for the Chihuahuan Desert region of West Texas. As patterns of moisture inputs and amounts change, soil microbial communities will respond to these alterations in soil moisture windows. In this study, we examined the soil microbial community structure within three vegetation zones along the Pine Canyon Watershed, an elevation and vegetation gradient in Big Bend National Park, Chihuahuan Desert. Soil samples at each site were obtained in mid-winter (January) and in mid-summer (August) for 2 years to capture a component of the variability in soil temperature and moisture that can occur seasonally and between years along this watershed. Precipitation patterns and amounts differed substantially between years with a drought characterizing most of the second year. Soils were collected during the drought period and following a large rainfall event and compared to soil samples collected during a relatively average season. Structural changes within microbial community in response to site, season, and precipitation patterns were evaluated using fatty acid methyl ester (FAME) and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analyses. Fungal FAME amounts differed significantly across seasons and sites and greatly outweighed the quantity of bacterial and actinomycete FAME levels for all sites and seasons. The highest fungal FAME levels were obtained in the low desert scrub site and not from the high elevation oak-pine forests. Total bacterial and actinomycete FAME levels did not differ significantly across season and year within any of the three locations along the watershed. Total bacterial and actinomycete FAME levels in the low elevation desert-shrub and grassland sites were slightly higher in the winter than in the summer. Microbial community structure at the high elevation oak-pine forest site was strongly correlated with levels of NH4+-N, % soil moisture, and amounts of soil organic matter irrespective of season. Microbial community structure at the low elevation desert scrub and sotol grasslands sites was most strongly related to soil pH with bacterial and actinobacterial FAME levels accounting for site differences along the gradient. DGGE band counts of amplified soil bacterial DNA were found to differ significantly across sites and season with the highest band counts found in the mid-elevation grassland site. The least number of bands was observed in the high elevation oak-pine forest following the large summer-rain event that occurred after a prolonged drought. Microbial responses to changes in precipitation frequency and amount due to climate change will differ among vegetation zones along this Chihuahuan Desert watershed gradient. Soil bacterial communities at the mid-elevation grasslands site are the most vulnerable to changes in precipitation frequency and timing, while fungal community structure is most vulnerable in the low desert scrub site. The differential susceptibility of the microbial communities to changes in precipitation amounts along the elevation gradient reflects the interactive effects of the soil moisture window duration following a precipitation event and differences in soil heat loads. Amounts and types of carbon inputs may not be as important in regulating microbial structure among vegetation zones within in an arid environment as is the seasonal pattern of soil moisture and the soil heat load profile that characterizes the location.}, }
@article {pmid19067030, year = {2009}, author = {Tsibakhashvili, NY and Kalabegishvili, TL and Rcheulishvili, AN and Murusidze, IG and Rcheulishvili, OA and Kerkenjia, SM and Holman, HY}, title = {Decomposition of Cr(V)-diols to Cr(III) complexes by Arthrobacter oxydans.}, journal = {Microbial ecology}, volume = {57}, number = {2}, pages = {360-366}, pmid = {19067030}, issn = {0095-3628}, mesh = {Arthrobacter/*metabolism ; Biodegradation, Environmental ; Chromium Compounds/*metabolism ; Electron Spin Resonance Spectroscopy ; Kinetics ; Models, Biological ; Spectrophotometry, Atomic ; Time Factors ; }, abstract = {We demonstrated previously that Cr(VI) is readily reduced to oxoCr(V)-diols at the surface of Arthrobacter oxydans-a Gram-positive aerobic bacteria isolated from Columbia basalt rocks originated from a highly contaminated site in the USA. Here, we report an electron spin resonance (ESR) study of Cr(III) hydroxide formation from Cr(V)-diols by this bacterial strain as cells were exposed to 35, 200, and 400 mg/L of Cr(VI) under aerobic conditions as a batch culture and as lyophilized cells. The time-dependent ESR measurements show that the half-time of Cr(III) formation is almost equal to that of Cr(V) decomposition, which is in the range of 3-6 days for all cases. This rate is at least 300 times slower than that of Cr(V) formation. Additionally, atomic absorption spectrometry was also employed to examine the time course of total chromium in bacterial cells. This is the first time the kinetics of Cr(III) complexes formation in bacteria is evaluated.}, }
@article {pmid19062077, year = {2009}, author = {Albuquerque, P and Mendes, MV and Santos, CL and Moradas-Ferreira, P and Tavares, F}, title = {DNA signature-based approaches for bacterial detection and identification.}, journal = {The Science of the total environment}, volume = {407}, number = {12}, pages = {3641-3651}, doi = {10.1016/j.scitotenv.2008.10.054}, pmid = {19062077}, issn = {0048-9697}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Bacterial Typing Techniques/*methods ; DNA Probes ; DNA, Bacterial/chemistry ; Environmental Microbiology ; Polymerase Chain Reaction ; }, abstract = {During the late eighties, environmental microbiologists realized the potential of the polymerase chain reaction (PCR) for the design of innovative approaches to study microbial communities or to detect and identify microorganisms in diverse and complex environments. In contrast to long-established methods of cultivation-based microbial identification, PCR-based techniques allow for the identification of microorganisms regardless of their culturability. A large number of reports have been published that describe PCR-inspired methods, frequently complemented by sequencing or hybridization profiling, to infer taxonomic and clonal microbial diversity or to detect and identify microorganisms using taxa-specific genomic markers. Typing methods have been particularly useful for microbial ecology-driven studies; however, they are not suitable for diagnostic purposes, such as the detection of specific species, strains or clones. Recently, comprehensive reviews have been written describing the panoply of typing methods available and describing their advantages and limitations; however, molecular approaches for bacterial detection and identification were either not considered or only vaguely discussed. This review focuses on DNA-based methods for bacterial detection and identification, highlighting strategies for selecting taxa-specific loci and emphasizing the molecular techniques and emerging technological solutions for increasing the detection specificity and sensitivity. The massive and increasing number of available bacterial sequences in databases, together with already employed bioinformatics tools, hold promise of more reliable, fast and cost-effective methods for bacterial identification in a wide range of samples in coming years. This tendency will foster the validation and certification of these methods and their routine implementation by certified diagnostic laboratories.}, }
@article {pmid19056488, year = {2009}, author = {Basso, O and Lascourreges, JF and Le Borgne, F and Le Goff, C and Magot, M}, title = {Characterization by culture and molecular analysis of the microbial diversity of a deep subsurface gas storage aquifer.}, journal = {Research in microbiology}, volume = {160}, number = {2}, pages = {107-116}, doi = {10.1016/j.resmic.2008.10.010}, pmid = {19056488}, issn = {0923-2508}, mesh = {Autotrophic Processes ; *Biodiversity ; DNA, Bacterial/isolation &amp; purification ; Deltaproteobacteria/*genetics/*isolation &amp; purification/metabolism ; Desulfovibrio/genetics/isolation &amp; purification/metabolism ; Ecosystem ; Fossil Fuels/*microbiology ; Genes, rRNA/genetics ; Geologic Sediments/microbiology ; Gram-Positive Bacteria/*genetics/*isolation &amp; purification/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Water Microbiology ; }, abstract = {The bacterial diversity of a subsurface water sample collected from a gas storage aquifer in an Upper Jurassic calcareous formation was investigated by culture of microorganisms and construction of a 16S rRNA gene library. Both culture and molecular techniques showed that members of the phyla Firmicutes and class delta-proteobacteria dominated the bacterial community. The presence of hydrogen-utilizing autotrophic bacteria including sulfate reducers (e.g. Desulfovibrio aespoeensis) and homoacetogens (e.g. Acetobacterium carbinolicum) suggested that CO(2) and H(2) are the main carbon and energy sources sustaining a nutrient-limited subsurface lithoautotrophic microbial ecosystem (SLiME). Gram-positive SRB belonging to the genus Desulfotomaculum, frequently observed in subsurface environments, represented 25% of the clone library and 4 distinct phylotypes. No Archaea were detected by both experimental approaches. Water samples were collected in an area of the rauracian geological formation located outside the maximum seasonal extension of underground gas storage. Considering the observed microbial diversity, there is no evidence of any influence on the microbial ecology of the aquifer in the surroundings of maximum extension reached by the gas bubble of the underground storage, which should have resulted from the introduction of exogenous carbon and energy sources in a nutrient-limited ecosystem.}, }
@article {pmid19052647, year = {2008}, author = {Palacios, C and Zettler, E and Amils, R and Amaral-Zettler, L}, title = {Contrasting microbial community assembly hypotheses: a reconciling tale from the Río Tinto.}, journal = {PloS one}, volume = {3}, number = {12}, pages = {e3853}, pmid = {19052647}, issn = {1932-6203}, mesh = {Bacteria/classification/growth &amp; development ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/analysis ; Ecosystem ; Rivers/*microbiology ; *Water Microbiology ; }, abstract = {BACKGROUND: The Río Tinto (RT) is distinguished from other acid mine drainage systems by its natural and ancient origins. Microbial life from all three domains flourishes in this ecosystem, but bacteria dominate metabolic processes that perpetuate environmental extremes. While the patchy geochemistry of the RT likely influences the dynamics of bacterial populations, demonstrating which environmental variables shape microbial diversity and unveiling the mechanisms underlying observed patterns, remain major challenges in microbial ecology whose answers rely upon detailed assessments of community structures coupled with fine-scale measurements of physico-chemical parameters.<br><br>By using high-throughput environmental tag sequencing we achieved saturation of richness estimators for the first time in the RT. We found that environmental factors dictate the distribution of the most abundant taxa in this system, but stochastic niche differentiation processes, such as mutation and dispersal, also contribute to observed diversity patterns.<br><br>CONCLUSIONS/SIGNIFICANCE: We predict that studies providing clues to the evolutionary and ecological processes underlying microbial distributions will reconcile the ongoing debate between the Baas Becking vs. Hubbell community assembly hypotheses.}, }
@article {pmid19052320, year = {2008}, author = {Kunin, V and Copeland, A and Lapidus, A and Mavromatis, K and Hugenholtz, P}, title = {A bioinformatician's guide to metagenomics.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {72}, number = {4}, pages = {557-78, Table of Contents}, pmid = {19052320}, issn = {1098-5557}, mesh = {*Database Management Systems ; Databases, Genetic ; Environmental Microbiology ; Genome/*genetics ; Genomics/*methods/standards ; Information Storage and Retrieval/*methods ; Sequence Analysis, DNA ; }, abstract = {As random shotgun metagenomic projects proliferate and become the dominant source of publicly available sequence data, procedures for the best practices in their execution and analysis become increasingly important. Based on our experience at the Joint Genome Institute, we describe the chain of decisions accompanying a metagenomic project from the viewpoint of the bioinformatic analysis step by step. We guide the reader through a standard workflow for a metagenomic project beginning with presequencing considerations such as community composition and sequence data type that will greatly influence downstream analyses. We proceed with recommendations for sampling and data generation including sample and metadata collection, community profiling, construction of shotgun libraries, and sequencing strategies. We then discuss the application of generic sequence processing steps (read preprocessing, assembly, and gene prediction and annotation) to metagenomic data sets in contrast to genome projects. Different types of data analyses particular to metagenomes are then presented, including binning, dominant population analysis, and gene-centric analysis. Finally, data management issues are presented and discussed. We hope that this review will assist bioinformaticians and biologists in making better-informed decisions on their journey during a metagenomic project.}, }
@article {pmid19050859, year = {2009}, author = {Clauwaert, P and Verstraete, W}, title = {Methanogenesis in membraneless microbial electrolysis cells.}, journal = {Applied microbiology and biotechnology}, volume = {82}, number = {5}, pages = {829-836}, doi = {10.1007/s00253-008-1796-4}, pmid = {19050859}, issn = {1432-0614}, mesh = {Bioreactors/*microbiology ; *Cation Exchange Resins ; Chemical Industry/instrumentation/methods ; Electrochemistry ; Electrodes ; *Electrolysis/instrumentation/methods ; Hydrogen/chemistry/metabolism ; Hydrogen-Ion Concentration ; Methane/chemistry/*metabolism ; }, abstract = {Operation of microbial electrolysis cells (MECs) without an ion exchange membrane could help to lower the construction costs while lowering the ohmic cell resistance and improving MEC conversion rates by minimizing the pH gradient between anode and cathode. In this research, we demonstrate that membraneless MECs with plain graphite can be operated for methane production without pH adjustment and that the ohmic cell resistance could be lowered with approximately 50% by removing the cation exchange membrane. As a result, the current production increased from 66 +/- 2 to 156 +/- 1 A m(-3) MEC by removing the membrane with an applied voltage of -0.8 V. Methane was the main energetic product despite continuous operation under carbonate-limited and slightly acidified conditions (pH 6.1-6.2). Our results suggest that continuous production of hydrogen in membraneless MECs will be challenging since methane production might not be avoided easily. The electrical energy invested was not always completely recovered under the form of an energy-rich biogas; however, our results indicate that membraneless MECs might be a viable polishing step for the treatment of the effluent of anaerobic digesters as methane was produced under low organic loading conditions and at room temperature.}, }
@article {pmid19049502, year = {2009}, author = {Ruiz-Rueda, O and Hallin, S and Bañeras, L}, title = {Structure and function of denitrifying and nitrifying bacterial communities in relation to the plant species in a constructed wetland.}, journal = {FEMS microbiology ecology}, volume = {67}, number = {2}, pages = {308-319}, doi = {10.1111/j.1574-6941.2008.00615.x}, pmid = {19049502}, issn = {1574-6941}, mesh = {Ammonia/metabolism ; *Bacteria/enzymology/growth &amp; development/metabolism ; *Ecosystem ; Electrophoresis ; Geologic Sediments/microbiology ; Molecular Sequence Data ; Nitrates/*metabolism ; Nitrosomonas/enzymology/growth &amp; development/metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics ; Plant Roots/microbiology ; Poaceae/growth &amp; development/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Typhaceae/growth &amp; development/*microbiology ; *Wetlands ; }, abstract = {The community structure and potential activities of nitrifying and denitrifying bacteria were studied in the rhizosphere of Typha latifolia and Phragmites australis present in a free water system constructed wetland (CW). Potential nitrate reduction and nitrification activities were shown to be significantly higher in the rhizosphere when compared with the nonvegetated sediment. Higher rates were generally obtained for P. australis. The community structure of denitrifying bacteria in the rhizosphere differed from that found at the bulk sediment, as revealed by PCR-denaturing gradient gel electrophoresis (DGGE) of the nitrous oxide reductase encoding gene nosZ. Results also show a greater nosZ genotype diversification and suggest a plant species effect in rhizosphere samples obtained during events of low hydraulic retention times. Ammonia-oxidizing communities were less complex on the basis of PCR-DGGE analysis of the 16S rRNA gene. Retrieved sequences were all related to Nitrosomonas marina and Nitrosomonas ureae, being both present in rhizosphere and bulk sediment regardless of environmental changes. The results demonstrate the effect of vegetation on the functioning and structure of bacterial communities involved in the removal of nitrogen in the treatment cells of a CW and point to the use of vegetation coverage to promote nitrification or denitrification in particular areas.}, }
@article {pmid19048329, year = {2009}, author = {Locsei, JT and Pedley, TJ}, title = {Bacterial tracking of motile algae assisted by algal cell's vorticity field.}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {63-74}, pmid = {19048329}, issn = {1432-184X}, mesh = {*Bacteria ; *Bacterial Physiological Phenomena ; Eukaryota/*physiology ; *Models, Biological ; }, abstract = {Previously published experimental work by other authors has shown that certain motile marine bacteria are able to track free-swimming algae by executing a zigzag path and steering toward the algae at each turn. Here, we propose that the apparent steering behaviour could be a hydrodynamic effect, whereby an algal cell's vorticity and strain-rate fields rotate a pursuing bacterial cell in the appropriate direction. Using simplified models for the bacterial and algal cells, we numerically compute the trajectory of a bacterial cell and demonstrate the plausibility of this hypothesis.}, }
@article {pmid19043657, year = {2009}, author = {Gião, MS and Wilks, SA and Azevedo, NF and Vieira, MJ and Keevil, CW}, title = {Validation of SYTO 9/propidium iodide uptake for rapid detection of viable but noncultivable Legionella pneumophila.}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {56-62}, pmid = {19043657}, issn = {1432-184X}, mesh = {Chlorine/pharmacology ; Coloring Agents/metabolism ; Disinfection/methods ; Legionella pneumophila/drug effects/*isolation &amp; purification/metabolism ; *Microbial Viability ; Organic Chemicals/*metabolism ; Propidium/*metabolism ; Water Microbiology ; }, abstract = {Legionella pneumophila is an ubiquitous environmental microorganism that can cause Legionnaires' disease or Pontiac fever. As a waterborne pathogen, it has been found to be resistant to chlorine disinfection and survive in drinking water systems, leading to potential outbreaks of waterborne disease. In this work, the effect of different concentrations of free chlorine was studied (0.2, 0.7, and 1.2 mg l(-1)), the cultivability of cells assessed by standard culture techniques (buffered charcoal yeast extract agar plates) and viability using the SYTO 9/propidium iodide fluorochrome uptake assay (LIVE/DEAD BacLight). Results demonstrate that L. pneumophila loses cultivability after exposure for 30 min to 0.7 mg l(-1) of free chlorine and in 10 min when the concentration is increased to 1.2 mg l(-1). However, the viability of the cells was only slightly affected even after 30 min exposure to the highest concentration of chlorine; good correlation was obtained between the rapid SYTO 9/propidium iodide fluorochrome uptake assay and a longer cocultivation with Acanthamoeba polyphaga assay, confirming that these cells could still recover their cultivability. These results raise new concerns about the assessment of drinking water disinfection efficiency and indicate the necessity of further developing new validated rapid methods, such as the SYTO 9/propidium iodide uptake assay, to assess viable but noncultivable L. pneumophila cells in the environment.}, }
@article {pmid19040453, year = {2009}, author = {de Goffau, MC and Yang, X and van Dijl, JM and Harmsen, HJ}, title = {Bacterial pleomorphism and competition in a relative humidity gradient.}, journal = {Environmental microbiology}, volume = {11}, number = {4}, pages = {809-822}, doi = {10.1111/j.1462-2920.2008.01802.x}, pmid = {19040453}, issn = {1462-2920}, mesh = {*Bacterial Physiological Phenomena ; Cell Wall/ultrastructure ; Gram-Negative Bacteria/*cytology/growth &amp; development ; Gram-Positive Bacteria/*cytology/growth &amp; development ; *Humidity ; Microscopy, Electron, Transmission ; }, abstract = {The response of different bacterial species to reduced water availability was studied using a simple relative humidity gradient technique. Interestingly, distinct differences in morphology and growth patterns were observed between populations of the same species growing at different relative humidity. Gram-positive cocci increased in cell size as they approached humidity growth limits and staphylococcal species started growing in tetrad/cubical formations instead of their normal grape-like structures. Gram-negative rods displayed wave-like patterns, forming larger waves as they became increasingly filamentous at low humidity. In contrast, cells of the Gram-positive bacterium Bacillus subtilis became shorter, curved, and eventually almost coccoid. Moreover, B. subtilis started to sporulate at low humidity. The altered morphology and/or growth patterns of bacteria growing at low humidity might be more ecologically relevant than their textbook appearance at high humidity since their natural habitats are often dry. Transmission electron microscopic analyses revealed that staphylococci grown at low humidity have significantly thickened cell walls, which may explain why these cells displayed increased resistance to vancomycin. We conclude that our relative humidity gradient technique is widely applicable for investigating effects of relative humidity on microbial survival, growth and competitive success at solid-air interfaces, making it a versatile tool in microbial ecology.}, }
@article {pmid19034559, year = {2009}, author = {Sandhu, A and Halverson, LJ and Beattie, GA}, title = {Identification and genetic characterization of phenol-degrading bacteria from leaf microbial communities.}, journal = {Microbial ecology}, volume = {57}, number = {2}, pages = {276-285}, pmid = {19034559}, issn = {0095-3628}, mesh = {Acinetobacter/enzymology/*genetics/isolation &amp; purification ; Alcaligenes/enzymology/*genetics/isolation &amp; purification ; Biodegradation, Environmental ; Biodiversity ; Catechol 1,2-Dioxygenase/genetics/metabolism ; Catechol 2,3-Dioxygenase/genetics/metabolism ; DNA, Bacterial/genetics ; Fraxinus/*microbiology ; Genes, Bacterial ; Phenol/*metabolism ; Plant Leaves/microbiology ; RNA, Ribosomal, 16S/genetics ; Rhodococcus/enzymology/*genetics/isolation &amp; purification ; }, abstract = {Microbial communities on aerial plant leaves may contribute to the degradation of organic air pollutants such as phenol. Epiphytic bacteria capable of phenol degradation were isolated from the leaves of green ash trees grown at a site rich in airborne pollutants. Bacteria from these communities were subjected, in parallel, to serial enrichments with increasing concentrations of phenol and to direct plating followed by a colony autoradiography screen in the presence of radiolabeled phenol. Ten isolates capable of phenol mineralization were identified. Based on 16S rDNA sequence analysis, these isolates included members of the genera Acinetobacter, Alcaligenes, and Rhodococcus. The sequences of the genes encoding the large subunit of a multicomponent phenol hydroxylase (mPH) in these isolates indicated that the mPHs of the gram-negative isolates belonged to a single kinetic class, and that is one with a moderate affinity for phenol; this affinity was consistent with the predicted phenol levels in the phyllosphere. PCR amplification of genes for catechol 1,2-dioxygenase (C12O) and catechol 2,3-dioxygenase (C23O) in combination with a functional assay for C23O activity provided evidence that the gram-negative strains had the C12O-, but not the C23O-, phenol catabolic pathway. Similarly, the Rhodococcus isolates lacked C23O activity, although consensus primers to the C12O and C23O genes of Rhodococcus could not be identified. Collectively, these results demonstrate that these leaf surface communities contained several taxonomically distinct phenol-degrading bacteria that exhibited diversity in their mPH genes but little diversity in the catabolic pathways they employ for phenol degradation.}, }
@article {pmid19030917, year = {2009}, author = {Anderson, JA and Hooper, MJ and Zak, JC and Cox, SB}, title = {Molecular and functional assessment of bacterial community convergence in metal-amended soils.}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {10-22}, pmid = {19030917}, issn = {1432-184X}, support = {ES04696/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/*drug effects/genetics/metabolism ; Biodiversity ; Biomass ; DNA, Bacterial/analysis ; Ecosystem ; Hydrogen-Ion Concentration ; Metals, Heavy/*pharmacology ; Soil/analysis ; *Soil Microbiology ; Soil Pollutants/pharmacology ; }, abstract = {Species diversity and the structure of microbial communities in soils are thought to be a function of the cumulative selective pressures within the local environment. Shifts in microbial community structure, as a result of metal stress, may have lasting negative effects on soil ecosystem dynamics if critical microbial community functions are compromised. Three soils in the vicinity of a copper smelter, previously contaminated with background, low and high levels of aerially deposited metals, were amended with metal-salts to determine the potential for metal contamination to shape the structural and functional diversity of microbial communities in soils. We hypothesized that the microbial communities native to the three soils would initially be unique to each site, but would converge on a microbial community with similar structure and function, as a result of metal stress. Initially, the three different sites supported microbial communities with unique structural and functional diversity, and the nonimpacted site supported inherently higher levels of microbial activity and biomass, relative to the metal-contaminated sites. Amendment of the soils with metal-salts resulted in a decrease in microbial activity and biomass, as well as shifts in microbial community structure and function at each site. Soil microbial communities from each site were also observed to be sensitive to changes in soil pH as a result of metal-salt amendment; however, the magnitude of these pH-associated effects varied between soils. Microbial communities from each site did not converge on a structurally or functionally similar community following metal-salt amendment, indicating that other factors may be equally important in shaping microbial communities in soils. Among these factors, soil physiochemical parameters like organic matter and soil pH, which can both influence the bioavailability and toxicity of metals in soils, may be critical.}, }
@article {pmid19030916, year = {2009}, author = {Jamali, F and Sharifi-Tehrani, A and Lutz, MP and Maurhofer, M}, title = {Influence of host plant genotype, presence of a pathogen, and coinoculation with Pseudomonas fluorescens strains on the rhizosphere expression of hydrogen cyanide- and 2,4-diacetylphloroglucinol biosynthetic genes in P. fluorescens biocontrol strain CHA0.}, journal = {Microbial ecology}, volume = {57}, number = {2}, pages = {267-275}, pmid = {19030916}, issn = {0095-3628}, mesh = {Antibiosis ; DNA, Bacterial/genetics ; Fabaceae/*genetics/microbiology ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Genotype ; *Host-Pathogen Interactions ; Hydrogen Cyanide/*metabolism ; Phloroglucinol/analogs &amp; derivatives/metabolism ; Plant Diseases/microbiology ; Plant Roots/genetics/microbiology ; Pseudomonas fluorescens/genetics/isolation &amp; purification/*metabolism ; Rhizoctonia/pathogenicity ; Soil Microbiology ; }, abstract = {The production of hydrogen cyanide (HCN) and 2,4-diacetylphloroglucinol (DAPG) is a major factor in the control of soil-borne diseases by Pseudomonas fluorescens CHA0. We investigated the impact of different biotic factors on the expression of HCN-in comparison to DAPG biosynthetic genes in the rhizosphere. To this end, the influence of plant cultivar, pathogen infection, and coinoculation with other biocontrol strains on the expression of hcnA-lacZ and phlA-lacZ fusion in strain CHA0 was monitored on the roots of bean. Interestingly, all the tested factors influenced the expression of the two biocontrol traits in a similar way. For both genes, we observed a several-fold higher expression in the rhizosphere of cv. Derakhshan compared with cvs. Goli and Naz, although bacterial rhizosphere colonization levels were similar on all cultivars tested. Root infection by Rhizoctonia solani stimulated total phlA and hcnA gene expression in the bean rhizosphere. Coinoculation of strain CHA0 with DAPG-producing P. fluorescens biocontrol strains Pf-68 and Pf-100 did neither result in a substantial alteration of hcnA nor of phlA expression in CHA0 on bean roots. To our best knowledge, this is the first study investigating the impact of biotic factors on HCN production by a bacterial biocontrol strain in the rhizosphere.}, }
@article {pmid19020558, year = {2009}, author = {Kielak, A and Pijl, AS and van Veen, JA and Kowalchuk, GA}, title = {Phylogenetic diversity of Acidobacteria in a former agricultural soil.}, journal = {The ISME journal}, volume = {3}, number = {3}, pages = {378-382}, doi = {10.1038/ismej.2008.113}, pmid = {19020558}, issn = {1751-7370}, mesh = {Bacteria/*classification/*isolation &amp; purification ; *Biodiversity ; Cloning, Molecular ; DNA Primers/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gene Library ; Genes, rRNA ; Molecular Sequence Data ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; *Soil Microbiology ; }, abstract = {Although Acidobacteria represent the most abundant bacterial phylum in many soils, knowledge of acidobacterial diversity is still rather incomplete. We, therefore, examined the diversity of 16S rRNA genes affiliated with this phylum in a former arable soil via three independent approaches: (1) screening of a fosmid metagenome library for inserts containing Acidobacteria-like 16S rRNA genes; (2) PCR-cloning using general bacterial primers; and (3) PCR-cloning with acidobacterial-specific primers. Bacterial-specific libraries compared rhizosphere versus bulk soil samples, revealing a higher proportion of acidobacterial sequences in bulk soil libraries (P<0.001). Bacterial libraries recovered the greatest diversity, and sequence examination suggested that sequence mismatches with the Acidobacteria-specific primers limited the coverage of the metagenome library screening and specific library approaches. Together, these results expand knowledge of the distribution and diversity of Acidobacteria in soil environments and highlight important technical considerations in the molecular analysis of Acidobacteria diversity.}, }
@article {pmid19019206, year = {2008}, author = {Rodrigues, DF and Ivanova, N and He, Z and Huebner, M and Zhou, J and Tiedje, JM}, title = {Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach.}, journal = {BMC genomics}, volume = {9}, number = {}, pages = {547}, pmid = {19019206}, issn = {1471-2164}, mesh = {Acclimatization/*genetics/physiology ; Amino Acids/metabolism ; Carbohydrate Metabolism ; *Cold Temperature ; DNA Replication ; Energy Metabolism ; Gene Expression Profiling ; Genome, Bacterial/*genetics ; Gram-Positive Asporogenous Rods/*genetics/metabolism/ultrastructure ; Microscopy, Electron, Transmission ; Nucleotides/metabolism ; Siberia ; Transcription, Genetic ; }, abstract = {BACKGROUND: Many microorganisms have a wide temperature growth range and versatility to tolerate large thermal fluctuations in diverse environments, however not many have been fully explored over their entire growth temperature range through a holistic view of its physiology, genome, and transcriptome. We used Exiguobacterium sibiricum strain 255-15, a psychrotrophic bacterium from 3 million year old Siberian permafrost that grows from -5 degrees C to 39 degrees C to study its thermal adaptation.<br><br>RESULTS: The E. sibiricum genome has one chromosome and two small plasmids with a total of 3,015 protein-encoding genes (CDS), and a GC content of 47.7%. The genome and transcriptome analysis along with the organism's known physiology was used to better understand its thermal adaptation. A total of 27%, 3.2%, and 5.2% of E. sibiricum CDS spotted on the DNA microarray detected differentially expressed genes in cells grown at -2.5 degrees C, 10 degrees C, and 39 degrees C, respectively, when compared to cells grown at 28 degrees C. The hypothetical and unknown genes represented 10.6%, 0.89%, and 2.3% of the CDS differentially expressed when grown at -2.5 degrees C, 10 degrees C, and 39 degrees C versus 28 degrees C, respectively.<br><br>CONCLUSION: The results show that E. sibiricum is constitutively adapted to cold temperatures stressful to mesophiles since little differential gene expression was observed between 4 degrees C and 28 degrees C, but at the extremities of its Arrhenius growth profile, namely -2.5 degrees C and 39 degrees C, several physiological and metabolic adaptations associated with stress responses were observed.}, }
@article {pmid19018587, year = {2009}, author = {Dang, H and Wang, C and Li, J and Li, T and Tian, F and Jin, W and Ding, Y and Zhang, Z}, title = {Diversity and distribution of sediment nirS-encoding bacterial assemblages in response to environmental gradients in the eutrophied Jiaozhou Bay, China.}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {161-169}, pmid = {19018587}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; China ; Cluster Analysis ; DNA, Bacterial/genetics ; *Eutrophication ; Genes, Bacterial ; Geologic Sediments/*microbiology ; Multivariate Analysis ; Seawater/*microbiology ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {A gene-clone-library-based molecular approach was used to study the nirS-encoding bacteria-environment relationship in the sediments of the eutrophic Jiaozhou Bay. Diverse nirS sequences were recovered and most of them were related to the marine cluster I group, ubiquitous in estuarine, coastal, and marine environments. Some NirS sequences were unique to the Jiaozhou Bay, such as the marine subcluster VIIg sequences. Most of the Jiaozhou Bay NirS sequences had their closest matches originally detected in estuarine and marine sediments, especially from the Chesapeake Bay, indicating similarity of the denitrifying bacterial communities in similar coastal environments in spite of geographical distance. Multivariate statistical analyses indicated that the spatial distribution of the nirS-encoding bacterial assemblages is highly correlated with environmental factors, such as sediment silt content, NH4+ concentration, and OrgC/OrgN. The nirS-encoding bacterial assemblages in the most hypernutrified stations could be easily distinguished from that of the least eutrophic station. For the first time, the sedimentological condition was found to influence the structure and distribution of the sediment denitrifying bacterial community.}, }
@article {pmid19015912, year = {2009}, author = {Snyder, LA and Loman, N and Pallen, MJ and Penn, CW}, title = {Next-generation sequencing--the promise and perils of charting the great microbial unknown.}, journal = {Microbial ecology}, volume = {57}, number = {1}, pages = {1-3}, pmid = {19015912}, issn = {0095-3628}, mesh = {Archaea/genetics ; Bacteria/genetics ; Computational Biology/methods/*trends ; *Environmental Microbiology ; *Genomics ; Sequence Analysis, DNA/methods/*trends ; }, }
@article {pmid19011974, year = {2009}, author = {Bouallagui, H and Rachdi, B and Gannoun, H and Hamdi, M}, title = {Mesophilic and thermophilic anaerobic co-digestion of abattoir wastewater and fruit and vegetable waste in anaerobic sequencing batch reactors.}, journal = {Biodegradation}, volume = {20}, number = {3}, pages = {401-409}, doi = {10.1007/s10532-008-9231-1}, pmid = {19011974}, issn = {1572-9729}, mesh = {*Abattoirs ; Anaerobiosis ; Bioreactors/*microbiology ; *Fruit ; Industrial Waste/*analysis ; Temperature ; *Vegetables ; Waste Disposal, Fluid/*instrumentation ; Waste Management/*instrumentation ; }, abstract = {Anaerobic co-digestion of fruit and vegetable waste (FVW) and abattoir wastewater (AW) was investigated using anaerobic sequencing batch reactors (ASBRs). The effects of hydraulic retention time (HRT) and temperature variations on digesters performances were examined. At both 20 and 10 days biogas production for co-digestion was greater thanks to the improved balance of nutrients. The high specific gas productions for the different digestion processes were 0.56, 0.61 and 0.85 l g(-1) total volatile solids (TVS) removal for digesters treating AW, FVW and AW + FVW, respectively. At an HRT of 20 days, biogas production rates from thermophilic digesters were higher on average than from mesophilic AW, FVW and AW + FVW digestion by 28.5, 44.5 and 25%, respectively. However, at 10 days of HRT results showed a decrease of biogas production rate for AW and AW + FVW digestion processes due to the high amount of free ammonia at high organic loading rate (OLR).}, }
@article {pmid19011079, year = {2009}, author = {Morales, SE and Cosart, TF and Johnson, JV and Holben, WE}, title = {Extensive phylogenetic analysis of a soil bacterial community illustrates extreme taxon evenness and the effects of amplicon length, degree of coverage, and DNA fractionation on classification and ecological parameters.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {3}, pages = {668-675}, pmid = {19011079}, issn = {1098-5336}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; Cluster Analysis ; DNA Primers/genetics ; DNA, Bacterial/chemistry/genetics/isolation &amp; purification ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Molecular Biology/*methods ; Molecular Sequence Data ; *Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; *Soil Microbiology ; }, abstract = {To thoroughly investigate the bacterial community diversity present in a single composite sample from an agricultural soil and to examine potential biases resulting from data acquisition and analytical approaches, we examined the effects of percent G+C DNA fractionation, sequence length, and degree of coverage of bacterial diversity on several commonly used ecological parameters (species estimation, diversity indices, and evenness). We also examined variation in phylogenetic placement based on multiple commonly used approaches (ARB alignments and multiple RDP tools). The results demonstrate that this soil bacterial community is highly diverse, with 1,714 operational taxonomic units demonstrated and 3,555 estimated (based on the Chao1 richness estimation) at 97% sequence similarity using the 16S rRNA gene. The results also demonstrate a fundamental lack of dominance (i.e., a high degree of evenness), with 82% of phylotypes being encountered three times or less. The data also indicate that generally accepted cutoff values for phylum-level taxonomic classification might not be as applicable or as general as previously assumed and that such values likely vary between prokaryotic phyla or groups.}, }
@article {pmid19004872, year = {2009}, author = {Cole, JR and Wang, Q and Cardenas, E and Fish, J and Chai, B and Farris, RJ and Kulam-Syed-Mohideen, AS and McGarrell, DM and Marsh, T and Garrity, GM and Tiedje, JM}, title = {The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.}, journal = {Nucleic acids research}, volume = {37}, number = {Database issue}, pages = {D141-5}, pmid = {19004872}, issn = {1362-4962}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; P42ES04911/ES/NIEHS NIH HHS/United States ; }, mesh = {Computer Graphics ; *Databases, Nucleic Acid ; Internet ; RNA, Archaeal/*chemistry/classification ; RNA, Bacterial/*chemistry/classification ; RNA, Ribosomal/*chemistry/classification ; Sequence Alignment ; *Sequence Analysis, RNA ; Software ; }, abstract = {The Ribosomal Database Project (RDP) provides researchers with quality-controlled bacterial and archaeal small subunit rRNA alignments and analysis tools. An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences. Substantial new analysis features include a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data. This pipeline offers a collection of tools that automate the data processing and simplify the computationally intensive analysis of large sequencing libraries. In addition, a new Taxomatic visualization tool allows rapid visualization of taxonomic inconsistencies and suggests corrections, and a new class Assignment Generator provides instructors with a lesson plan and individualized teaching materials. Details about RDP data and analytical functions can be found at http://rdp.cme.msu.edu/.}, }
@article {pmid19004758, year = {2008}, author = {Fierer, N and Hamady, M and Lauber, CL and Knight, R}, title = {The influence of sex, handedness, and washing on the diversity of hand surface bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {46}, pages = {17994-17999}, pmid = {19004758}, issn = {1091-6490}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; T32 GM065103/GM/NIGMS NIH HHS/United States ; P01DK078669/DK/NIDDK NIH HHS/United States ; T32GM065103/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Functional Laterality/*physiology ; *Genetic Variation ; Hand/*microbiology ; Humans ; *Sex Characteristics ; *Skin Care ; }, abstract = {Bacteria thrive on and within the human body. One of the largest human-associated microbial habitats is the skin surface, which harbors large numbers of bacteria that can have important effects on health. We examined the palmar surfaces of the dominant and nondominant hands of 51 healthy young adult volunteers to characterize bacterial diversity on hands and to assess its variability within and between individuals. We used a novel pyrosequencing-based method that allowed us to survey hand surface bacterial communities at an unprecedented level of detail. The diversity of skin-associated bacterial communities was surprisingly high; a typical hand surface harbored >150 unique species-level bacterial phylotypes, and we identified a total of 4,742 unique phylotypes across all of the hands examined. Although there was a core set of bacterial taxa commonly found on the palm surface, we observed pronounced intra- and interpersonal variation in bacterial community composition: hands from the same individual shared only 17% of their phylotypes, with different individuals sharing only 13%. Women had significantly higher diversity than men, and community composition was significantly affected by handedness, time since last hand washing, and an individual's sex. The variation within and between individuals in microbial ecology illustrated by this study emphasizes the challenges inherent in defining what constitutes a "healthy" bacterial community; addressing these challenges will be critical for the International Human Microbiome Project.}, }
@article {pmid19002248, year = {2008}, author = {Tito, RY and Macmil, S and Wiley, G and Najar, F and Cleeland, L and Qu, C and Wang, P and Romagne, F and Leonard, S and Ruiz, AJ and Reinhard, K and Roe, BA and Lewis, CM}, title = {Phylotyping and functional analysis of two ancient human microbiomes.}, journal = {PloS one}, volume = {3}, number = {11}, pages = {e3703}, pmid = {19002248}, issn = {1932-6203}, mesh = {Bacteria/classification/isolation &amp; purification ; DNA, Bacterial/analysis ; Evolution, Molecular ; Gastrointestinal Tract/*microbiology ; Genome, Bacterial ; Geography ; Humans ; Metagenome/*genetics ; Mexico ; *Phylogeny ; }, abstract = {BACKGROUND: The Human Microbiome Project (HMP) is one of the U.S. National Institutes of Health Roadmap for Medical Research. Primary interests of the HMP include the distinctiveness of different gut microbiomes, the factors influencing microbiome diversity, and the functional redundancies of the members of human microbiotas. In this present work, we contribute to these interests by characterizing two extinct human microbiotas.<br><br>We examine two paleofecal samples originating from cave deposits in Durango Mexico and dating to approximately 1300 years ago. Contamination control is a serious issue in ancient DNA research; we use a novel approach to control contamination. After we determined that each sample originated from a different human, we generated 45 thousand shotgun DNA sequencing reads. The phylotyping and functional analysis of these reads reveals a signature consistent with the modern gut ecology. Interestingly, inter-individual variability for phenotypes but not functional pathways was observed. The two ancient samples have more similar functional profiles to each other than to a recently published profile for modern humans. This similarity could not be explained by a chance sampling of the databases.<br><br>CONCLUSIONS/SIGNIFICANCE: We conduct a phylotyping and functional analysis of ancient human microbiomes, while providing novel methods to control for DNA contamination and novel hypotheses about past microbiome biogeography. We postulate that natural selection has more of an influence on microbiome functional profiles than it does on the species represented in the microbial ecology. We propose that human microbiomes were more geographically structured during pre-Columbian times than today.}, }
@article {pmid18998189, year = {2009}, author = {Díaz-Pérez, M and Camacho-Ferre, F and Diánez-Martínez, F and De Cara-García, M and Tello-Marquina, JC}, title = {Evaluation of alternatives to methyl bromide in melon crops in Guatemala.}, journal = {Microbial ecology}, volume = {57}, number = {2}, pages = {379-383}, doi = {10.1007/s00248-008-9460-1}, pmid = {18998189}, issn = {0095-3628}, mesh = {Agriculture/*methods ; Allyl Compounds/pharmacology ; *Cucumis melo ; Disinfectants/pharmacology ; Guatemala ; Hydrocarbons, Brominated/*pharmacology ; Hydrocarbons, Chlorinated ; Models, Statistical ; *Plant Diseases ; Soil ; Soil Microbiology ; Sterilization ; Thiocarbamates/pharmacology ; }, abstract = {The monoculture of melon in Guatemala has caused the massive appearance of plants with an analogous syndrome for the well-known disease commonly called melon collapse, or vine decline, causing significant losses in crops. Methyl bromide is commonly used to sterilize soil prior to planting in Guatemala, but it must be phased out by 2015. The objective of this study was to evaluate the technique of grafting melon onto hybrids of Cucurbita (Cucurbita maxima x Cucurbita moschata), as an alternative to using soil disinfectants (such as Metam sodium, 1,3-dichloropropene, and methyl bromide) for the control of collapse. The results suggested that both soil disinfection and grafting were not necessary in these locations, since there were no statistical differences in terms of yields between the treatments and the untreated control. Furthermore, these results demonstrate that decisions to disinfect the soil must be based on the firm identification of the causal agents, in addition to preliminary assessments of yield losses.}, }
@article {pmid18990419, year = {2009}, author = {Forrez, I and Carballa, M and Noppe, H and De Brabander, H and Boon, N and Verstraete, W}, title = {Influence of manganese and ammonium oxidation on the removal of 17 alpha-ethinylestradiol (EE2).}, journal = {Water research}, volume = {43}, number = {1}, pages = {77-86}, doi = {10.1016/j.watres.2008.10.006}, pmid = {18990419}, issn = {0043-1354}, mesh = {Biodegradation, Environmental/drug effects ; Bioreactors ; Ethinyl Estradiol/*isolation &amp; purification ; Manganese/*pharmacology ; Nitrogen/metabolism ; Oxidation-Reduction/drug effects ; Pseudomonas putida/drug effects/metabolism ; Quaternary Ammonium Compounds/*pharmacology ; Waste Disposal, Fluid ; }, abstract = {Flow-through reactors with manganese oxides were examined for their capacity to remove 17 alpha-ethinylestradiol (EE2) at microg L(-1) and ng L(-1) range from synthetic wastewater treatment plant (WWTP) effluent. The mineral MnO(2) reactors removed 93% at a volumetric loading rate (B(V)) of 5 microg EE2 L(-1) d(-1) and from a B(V) of 40 microg EE2 L(-1) d(-1) on, these reactors showed 75% EE2 removal. With the biologically produced manganese oxides, only 57% EE2 was removed at 40 microg EE2 L(-1) d(-1). EE2 removal in the ng L(-1) range was 84%. The ammonium present in the influent (10 mg N L(-1)) was nitrified and ammonia-oxidizing bacteria (AOB) were found to be of prime importance for the degradation of EE2. Remarkably, EE2 removal by AOB continued for a period of 4 months after depleting NH(4)(+) in the influent. EE2 removal by manganese-oxidizing bacteria was inhibited by NH(4)(+). These results indicate that the metabolic properties of nitrifiers can be employed to polish water containing EE2 based estrogenic activity.}, }
@article {pmid18989608, year = {2009}, author = {Corso, CR and Maganha de Almeida, AC}, title = {Bioremediation of dyes in textile effluents by Aspergillus oryzae.}, journal = {Microbial ecology}, volume = {57}, number = {2}, pages = {384-390}, pmid = {18989608}, issn = {0095-3628}, mesh = {Adsorption ; Animals ; Aspergillus oryzae/*metabolism ; Azo Compounds/*metabolism/pharmacokinetics/toxicity ; Biodegradation, Environmental ; Coloring Agents/*metabolism/pharmacokinetics/toxicity ; Culture Media ; Daphnia/drug effects ; Hydrogen-Ion Concentration ; Industrial Waste ; *Textile Industry ; Toxicity Tests ; Waste Disposal, Fluid/*methods ; }, abstract = {In this study Aspergillus oryzae was utilized to remove azo dyes from aqueous solution. Physically induced in its paramorphogenic form to produce standardized mycelial pellets, the non-autoclaved and autoclaved hyphae biomass was applied to biosorb the reactive dyes Procion Red HE7B (PR-HE7B) and Procion Violet H3R (PV-H3R) at different pH values (2.50, 4.50, and 6.50). The best pH for biosorption was 2.50, though the autoclaved demonstrated a higher biosorption capacity than the non-autoclaved pellets. The toxicity level was determined using the Trimmed Spearman-Karber method with Daphnia similis in all bioassays. The calculated toxicity of PV-H3R (LC100 62.50 microg mL(-1)) was higher than to PR-HE7B (LC100 300.00 microg mL(-1)), and its results brought out that the decrease of toxicity levels to zero might be accomplished by adding small quantities of pelletized A. oryzae to the solutions.}, }
@article {pmid18985269, year = {2009}, author = {Farjalla, VF and Marinho, CC and Faria, BM and Amado, AM and Esteves, Fde A and Bozelli, RL and Giroldo, D}, title = {Synergy of fresh and accumulated organic matter to bacterial growth.}, journal = {Microbial ecology}, volume = {57}, number = {4}, pages = {657-666}, pmid = {18985269}, issn = {1432-184X}, mesh = {Bacteria/*growth &amp; development/metabolism ; Carbon/metabolism ; Ecosystem ; Fresh Water/microbiology ; Nitrogen/metabolism ; Nymphaea/chemistry ; Organic Chemicals/*metabolism ; Phosphorus/metabolism ; Potamogetonaceae/chemistry ; Typhaceae/chemistry ; *Water Microbiology ; }, abstract = {The main goal of this research was to evaluate whether the mixture of fresh labile dissolved organic matter (DOM) and accumulated refractory DOM influences bacterial production, respiration, and growth efficiency (BGE) in aquatic ecosystems. Bacterial batch cultures were set up using DOM leached from aquatic macrophytes as the fresh DOM pool and DOM accumulated from a tropical humic lagoon. Two sets of experiments were performed and bacterial growth was followed in cultures composed of each carbon substrate (first experiment) and by carbon substrates combined (second experiment), with and without the addition of nitrogen and phosphorus. In both experiments, bacterial production, respiration, and BGE were always higher in cultures with N and P additions, indicating a consistent inorganic nutrient limitation. Bacterial production, respiration, and BGE were higher in cultures set up with leachate DOM than in cultures set up with humic DOM, indicating that the quality of the organic matter pool influenced the bacterial growth. Bacterial production and respiration were higher in the mixture of substrates (second experiment) than expected by bacterial production and respiration in single substrate cultures (first experiment). We suggest that the differences in the concentration of some compounds between DOM sources, the co-metabolism on carbon compound decomposition, and the higher diversity of molecules possibly support a greater bacterial diversity which might explain the higher bacterial growth observed. Finally, our results indicate that the mixture of fresh labile and accumulated refractory DOM that naturally occurs in aquatic ecosystems could accelerate the bacterial growth and bacterial DOM removal.}, }
@article {pmid18984052, year = {2008}, author = {Cardenas, E and Tiedje, JM}, title = {New tools for discovering and characterizing microbial diversity.}, journal = {Current opinion in biotechnology}, volume = {19}, number = {6}, pages = {544-549}, doi = {10.1016/j.copbio.2008.10.010}, pmid = {18984052}, issn = {1879-0429}, support = {5P42 ES004911-18/ES/NIEHS NIH HHS/United States ; 5P42 ES004911-19/ES/NIEHS NIH HHS/United States ; }, mesh = {Archaea/classification/genetics/*isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Microfluidics ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Proteomics ; RNA, Messenger/genetics ; Species Specificity ; }, abstract = {To discover and characterize microbial diversity, approaches based on new sequencing technologies, novel isolation techniques, microfluidics, and metagenomics among others are being used. These approaches have contributed to discovery of novel genes from environmental samples, to massive characterization of functional and phylogenetic genes and to isolation of members of formerly uncultured yet ubiquitous groups like Verrucomicrobia, Acidobacteria, OP10, and methanogenic Archaea. Cheaper sequencing is key in this process by making available applications that were previously restricted to big research centers, complementing previously available methodologies and potentially replacing some of them. The new tools are reshaping the way we study the environment, increasing the resolution at which microbial communities, their complexities and dynamics, can be studied to reveal their genetic potential and their functional diversity.}, }
@article {pmid18982382, year = {2009}, author = {Kubartová, A and Ranger, J and Berthelin, J and Beguiristain, T}, title = {Diversity and decomposing ability of saprophytic fungi from temperate forest litter.}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {98-107}, pmid = {18982382}, issn = {1432-184X}, mesh = {*Biodiversity ; DNA, Fungal/analysis ; Fungi/*genetics/isolation &amp; purification/metabolism ; *Soil Microbiology ; Species Specificity ; Trees/*microbiology ; }, abstract = {This study was designed to examine saprophytic fungi diversity under different tree species situated in the same ecological context. Further, the link between the diversity and decomposition rate of two broadleaved, two coniferous and two mixed broadleaved-coniferous litter types was targeted. Litter material was decomposed in litter bags for 4 and 24 months to target both early and late stages of the decomposition. Fungal diversity of L and F layers were also investigated as a parallel to the litter bag method. Temperature gradient gel electrophoresis fingerprinting was used to assess fungal diversity in the samples. Mass loss values and organic and nutrient composition of the litter were also measured. The results showed that the species richness was not strongly affected by the change of the tree species. Nevertheless, the community compositions differed within tree species and decomposition stages. The most important shift was found in the mixed litters from the litter bag treatment for both variables. Both mixed litters displayed the highest species richness (13.3 species both) and the most different community composition as compared to pure litters (6.3-10.7 species) after 24 months. The mass loss after 24 months was similar or greater in the mixed litter (70.5% beech-spruce, 76.2% oak-Douglas-fir litter) than in both original pure litter types. This was probably due to higher niche variability and to the synergistic effect of nutrient transfer between litter types. Concerning pure litter, mass loss values were the highest in oak and beech litter (72.8% and 69.8%) compared to spruce and D. fir (59.4% and 66.5%, respectively). That was probably caused by a more favourable microclimate and litter composition in broadleaved than in coniferous plantations. These variables also seemed to be more important to pure litter decomposition rates than were fungal species richness or community structure.}, }
@article {pmid18982381, year = {2009}, author = {Solé, A and Diestra, E and Esteve, I}, title = {Confocal laser scanning microscopy image analysis for cyanobacterial biomass determined at microscale level in different microbial mats.}, journal = {Microbial ecology}, volume = {57}, number = {4}, pages = {649-656}, pmid = {18982381}, issn = {1432-184X}, mesh = {*Biomass ; Cyanobacteria/*isolation &amp; purification ; Ecosystem ; Geologic Sediments/microbiology ; Image Processing, Computer-Assisted/*methods ; *Microscopy, Confocal ; *Water Microbiology ; }, abstract = {We recently published a new method based on determining cyanobacterial biomass by confocal laser scanning microscopy image analysis (CLSM-IA) (Solé et al., Ultramicrosc 107:669-673, 2007). CLSM-IA allows biomass calculation for microorganisms of a small size, since the limit of the technique's resolution is that generated by a voxel, the smallest unit of a three-dimensional digital image, equivalent to 1.183 x 10(-3) mgC/cm(3) of sediment. This method is especially suitable for the quantitative analysis of a large number of CLSM images generated from benthic sediments in which complex populations of cyanobacteria are abundant, such as microbial mats. In order to validate the new CLSM approach, mats with varying structural characteristics were studied. We have grouped them into three types: Microcoleus mats (laminated), sandy mats (nonlaminated and composed of well-sorted quartz sands), and oil-polluted mats. In this work, we applied CLSM-IA in natural [the Ebro delta and Sant Jordi colony (Spain), Salins-de-Giraud and Etang de Berre (France), and Orkney Islands (Scotland)] and artificial [mesocosms (Israel)] microbial mats. A total of 4,103 confocal images were obtained in order to determine total and individual cyanobacteria biomass profiles, at microscale level. The data presented in this paper show the efficacy of the method, as it can be applied to highly diverse mat samples.}, }
@article {pmid18979007, year = {2007}, author = {Seymour, JR and Marcos,  and Stocker, R}, title = {Chemotactic response of marine micro-organisms to micro-scale nutrient layers.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {4}, pages = {203}, pmid = {18979007}, issn = {1940-087X}, mesh = {Animals ; Bacterial Physiological Phenomena ; *Chemotaxis ; *Microbiological Phenomena ; Microfluidics/instrumentation ; *Micronutrients ; Oceans and Seas ; Phytoplankton/physiology ; *Water Microbiology ; }, abstract = {The degree to which planktonic microbes can exploit microscale resource patches will have considerable implications for oceanic trophodynamics and biogeochemical flux. However, to take advantage of nutrient patches in the ocean, swimming microbes must overcome the influences of physical forces including molecular diffusion and turbulent shear, which will limit the availability of patches and the ability of bacteria to locate them. Until recently, methodological limitations have precluded direct examinations of microbial behaviour within patchy habitats and realistic small-scale flow conditions. Hence, much of our current knowledge regarding microbial behaviour in the ocean has been procured from theoretical predictions. To obtain new information on microbial foraging behaviour in the ocean we have applied soft lithographic fabrication techniques to develop 2 microfluidic devices, which we have used to create (i) microscale nutrient patches with dimensions and diffusive characteristics relevant to oceanic processes and (ii) microscale vortices, with shear rates corresponding to those expected in the ocean. These microfluidic devices have permitted a first direct examination of microbial swimming and chemotactic behaviour within a heterogeneous and dynamic seascape. The combined use of epifluorescence and phase contrast microscopy allow direct examinations of the physical dimensions and diffusive characteristics of nutrient patches, while observing the population-level aggregative response, in addition to the swimming behaviour of individual microbes. These experiments have revealed that some species of phytoplankton, heterotrophic bacteria and phagotrophic protists are adept at locating and exploiting diffusing microscale resource patches within very short time frames. We have also shown that up to moderate shear rates, marine bacteria are able to fight the flow and swim through their environment at their own accord. However, beyond a threshold high shear level, bacteria are aligned in the shear flow and are less capable of swimming without disturbance from the flow. Microfluidics represents a novel and inexpensive approach for studying aquatic microbial ecology, and due to its suitability for accurately creating realistic flow fields and substrate gradients at the microscale, is ideally applicable to examinations of microbial behaviour at the smallest scales of interaction. We therefore suggest that microfluidics represents a valuable tool for obtaining a better understanding of the ecology of microorganisms in the ocean.}, }
@article {pmid18977658, year = {2009}, author = {Habiba, L and Hassib, B and Moktar, H}, title = {Improvement of activated sludge stabilisation and filterability during anaerobic digestion by fruit and vegetable waste addition.}, journal = {Bioresource technology}, volume = {100}, number = {4}, pages = {1555-1560}, doi = {10.1016/j.biortech.2008.09.019}, pmid = {18977658}, issn = {1873-2976}, mesh = {Anaerobiosis ; Bioreactors ; Fatty Acids, Volatile/analysis ; Filtration ; Fruit/*metabolism ; Gases ; Hydrogen-Ion Concentration ; *Refuse Disposal ; Sewage/*chemistry ; Vegetables/*metabolism ; Volatilization ; }, abstract = {Anaerobic co-digestion of fruit and vegetable waste (FVW) and activated sludge (AS) was investigated using anaerobic sequencing batch reactors (ASBRs). The effects of AS:FVW ratio and the organic loading rate (OLR) on digesters performances were examined. The mixtures having AS:FVW ratios of 100:00, 65:35, 35:65, by a total solid (TS) basis were operated at an hydraulic retention time (HRT) of 20d. However, 30:70, 20:80, 15:85, 10:90 and 0:100 ratios were tested at an HRT of 10d. To investigate effects of aerobic and anaerobic digestion on the sludge filterability, specific resistance to filtration (R) was also determined. Increasing FVW proportions in the feedstock significantly improved the biogas production yield. The reactor that was fed with a 30:70 ratio showed the highest VS removal and biogas production yield of 88% and 0.57 L g(-1) VS added, respectively. The filterability results showed that the anaerobic effluent was characterised by a slightly better filterability efficiency of 1.6 x 10(16) m kg(-1) than 1.74 x 10(16) m kg(-1) of aerobic effluent. However, FVW addition improved the anaerobic co-digestion effluent filterability (5.52 x 10(14) m kg(-1)).}, }
@article {pmid18975025, year = {2009}, author = {Pedersen, AL and Nybroe, O and Winding, A and Ekelund, F and Bjørnlund, L}, title = {Bacterial feeders, the nematode Caenorhabditis elegans and the flagellate Cercomonas longicauda, have different effects on outcome of competition among the Pseudomonas biocontrol strains CHA0 and DSS73.}, journal = {Microbial ecology}, volume = {57}, number = {3}, pages = {501-509}, pmid = {18975025}, issn = {1432-184X}, mesh = {Animals ; Caenorhabditis elegans/*physiology ; Ecosystem ; Eukaryota/*physiology ; *Feeding Behavior ; Flow Cytometry ; Predatory Behavior ; Pseudomonas fluorescens/*growth &amp; development ; Soil Microbiology ; }, abstract = {How bacterial feeding fauna affects colonization and survival of bacteria in soil is not well understood, which constrains the applicability of bacterial inoculants in agriculture. This study aimed to unravel how food quality of bacteria and bacterial feeders with different feeding habits (the selective feeding flagellate Cercomonas longicauda versus the non-selective feeding nematode Caenorhabditis elegans) influence the abundance of two bacteria that compete for resources in simple model communities. Microcosms consisted of either one gfp-tagged bacterial strain (Pseudomonas fluorescens DSM50090 or one of two biocontrol strains P. fluorescens CHA0 or Pseudomonas sp. DSS73) or combinations of two bacterial strains. DSM50090 is a suitable food bacterium, DSS73 is of intermediate food quality, and CHA0 is inedible to the bacterial feeders. Bacterial and protozoan cell numbers were measured by flow cytometry. In the presence of flagellates, CHA0 increased its abundance as compared to the other biocontrol strain DSS73 or to DSM50090, which were both eaten by the flagellates. In contrast, the number of CHA0 declined as compared to DSS73 when the model community was subjected to nematode predation pressure. Hence, the results suggested that the outcome of competition among bacteria depended on their ability to cope with the prevailing bacterial predator.}, }
@article {pmid18972149, year = {2009}, author = {Van Houdt, R and De Boever, P and Coninx, I and Le Calvez, C and Dicasillati, R and Mahillon, J and Mergeay, M and Leys, N}, title = {Evaluation of the airborne bacterial population in the periodically confined Antarctic base Concordia.}, journal = {Microbial ecology}, volume = {57}, number = {4}, pages = {640-648}, pmid = {18972149}, issn = {1432-184X}, mesh = {*Air Microbiology ; Air Pollution, Indoor ; Antarctic Regions ; Bacillus/isolation &amp; purification ; Biodiversity ; Colony Count, Microbial ; *Environment, Controlled ; *Environmental Monitoring ; Humans ; Inhalation Exposure ; Occupational Exposure/analysis ; Sphingomonas/isolation &amp; purification ; Staphylococcus/isolation &amp; purification ; }, abstract = {The environmental airborne bacterial population in relation to human confinement was investigated over a period of 1 year in the Concordia Research Station, which is located on the Eastern Antarctic plateau. The unique location of the station makes it suitable for different research domains such as glaciology, atmospheric sciences, astronomy, etc. Furthermore, it is used as a test bed for long-duration spaceflights to study the physiologic and psychological adaptation to isolated environments. A total of 96 samples were collected at eight different locations in the station at regular intervals. The airborne bacterial contamination was for 90% of the samples lower than 10.0 x 10(2) colony-forming units per cubic meter of air (CFU/m(3)) and the total bacterial contamination increased over time during confinement but diminished after re-opening of the base. Viable airborne bacteria with different morphology were identified by biochemical analyses. The predominant microflora was identified as Staphylococcus sp. (24.9% of total) and Bacillus sp. (11.6% of total) and was associated with human activity, but also environmental species such as Sphingomonas paucimobilis (belonging to the alpha-Proteobacteria) could establish themselves in the airborne population. A few opportunistic pathogens (6%) were also identified.}, }
@article {pmid18958515, year = {2009}, author = {Zhou, HW and Wong, AH and Yu, RM and Park, YD and Wong, YS and Tam, NF}, title = {Polycyclic aromatic hydrocarbon-induced structural shift of bacterial communities in mangrove sediment.}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {153-160}, pmid = {18958515}, issn = {1432-184X}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; Electrophoresis, Gel, Two-Dimensional ; Geologic Sediments/chemistry/*microbiology ; Polycyclic Aromatic Hydrocarbons/*chemistry ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Rhizophoraceae/*microbiology ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Mangrove sediment is well known for its susceptibility to anthropogenic pollution, including polycyclic aromatic hydrocarbons (PAHs), but knowledge of the sediment microbial community structure with regards to exposure to PAHs is limited. The study aims to assess the effects of PAHs on the bacterial community of mangrove sediment using both 16s rDNA polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and traditional enrichment methods. Both the exposure time and the PAH concentration reduced the microbial diversity, as determined by the DGGE bands. Although PAHs could act as carbon sources for microorganisms, PAHs, at a concentration as low as 20 mg l(-1), posed a toxic effect to the microbial community. Sequencing of DGGE bands showed that marine bacteria from the genera of Vibrio, Roseobacter, and Ferrimonas were most abundant after PAH exposure, which suggests that both marine and terrestrial bacteria coexisted in the mangrove sediment, but that the marine microbes were more difficult to isolate using the traditional culture method. DGGE determination further demonstrated that the consistency among triplicates of the enriched consortia was significantly less than that of the sediment slurries. The present study reveals that the mangrove sediment microbial structure is susceptible to PAH contamination, and complex microbial community interactions occur in mangrove sediment.}, }
@article {pmid18958514, year = {2009}, author = {Cloete, KJ and Valentine, AJ and Stander, MA and Blomerus, LM and Botha, A}, title = {Evidence of symbiosis between the soil yeast Cryptococcus laurentii and a sclerophyllous medicinal shrub, Agathosma betulina (Berg.) Pillans.}, journal = {Microbial ecology}, volume = {57}, number = {4}, pages = {624-632}, pmid = {18958514}, issn = {1432-184X}, mesh = {Cryptococcus/genetics/*growth &amp; development/isolation &amp; purification/metabolism ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer ; Plant Roots/microbiology ; Polyamines/metabolism ; Rutaceae/*microbiology ; *Soil Microbiology ; *Symbiosis ; }, abstract = {The interaction between a common soil yeast, Cryptococcus laurentii, and a slow-growing medicinal plant adapted to low-nutrient soils, Agathosma betulina (Berg.) Pillans, was studied. C. laurentii CAB 578 was isolated from the rhizosphere of wild A. betulina, and liquid chromatography-tandem mass spectrometry (LC-MS-MS) analysis revealed that the yeast was capable of producing polyamines, such as cadaverine and spermine, while growing in vitro in a chemically defined medium. Since the exogenous application of polyamines are known to impact on root growth, these findings supported the results obtained when axenic cultures of A. betulina seedlings were inoculated with C. laurentii CAB 578 and cultivated for 5 months under glasshouse conditions. The presence of the yeast increased root growth by 51%. Using soil dilution plates, it was demonstrated that yeast numbers were greater in the vicinity of the roots than in the bulk soil. In addition, fluoromicroscopy, in combination with the fluorescent probes Fungolight and Calcofluor white, revealed the presence of metabolic active yeast colonies on the rhizoplane 5 months after initiation of the experimentation. The study provided evidence for a symbiosis between C. laurentii and A. betulina.}, }
@article {pmid18958513, year = {2009}, author = {Brown, AL and Garland, JL and Day, FP}, title = {Physiological profiling of soil microbial communities in a Florida scrub-oak ecosystem: spatial distribution and nutrient limitations.}, journal = {Microbial ecology}, volume = {57}, number = {1}, pages = {14-24}, pmid = {18958513}, issn = {0095-3628}, mesh = {Arecaceae/*growth &amp; development/microbiology ; *Biosensing Techniques/instrumentation/methods ; Carbon Dioxide/metabolism/pharmacology ; *Ecosystem ; Florida ; Glucose/metabolism ; Nitrogen/metabolism ; Oxygen Consumption/*physiology ; Phosphates/metabolism ; Plant Roots/microbiology ; Quercus/*growth &amp; development/microbiology ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Rapid physiological profiling of heterotrophic microbial communities enables intensive analysis of the factors affecting activity in aerobic habitats, such as soil. Previous methods for performing such profiling were severely limited due to enrichment bias and inflexibility in incubation conditions. We tested a new physiological profiling approach based on a microtiter plate oxygen sensor system (Becton Dickinson Oxygen Biosensor System (BDOBS)), which allows for testing of lower substrate addition (i.e., lower enrichment potential) and manipulation of physiochemical assay conditions, such as pH and nutrients. Soil microbial communities associated with a scrub-oak forest ecosystem on Merritt Island Wildlife Refuge in central Florida, USA, were studied in order to evaluate microbial activity in a nutrient poor soil and to provide baseline data on the site for subsequent evaluation of the effects of elevated CO(2) on ecosystem function. The spatial variation in physiological activity amongst different habitats (litter, bulk soil, and rhizosphere) was examined as a function of adaptation to local resources (i.e., water soluble extracts of roots and leaf litter) and the degree of N and P limitation. All the communities were primarily N-limited, with a secondary P limitation, which was greater in the rhizosphere and bulk soil. The litter community showed greater overall oxygen consumption when exposed to litter extracts relative to the rhizosphere or soil, suggesting acclimation toward greater use of the mixed substrates in the extract. Root extracts were readily used by communities from all the habitats with no habitat specific acclimation observed. A priming effect was detected in all habitats; addition of glucose caused a significant increase in the use of soil organic carbon. Response to added glucose was only observed with N and P addition, suggesting that C may be lost to the groundwater from these porous soils because nutrient limitation prevents C immobilization.}, }
@article {pmid18958512, year = {2009}, author = {Pueyo, MT and Bloch, C and Carmona-Ribeiro, AM and di Mascio, P}, title = {Lipopeptides produced by a soil Bacillus megaterium strain.}, journal = {Microbial ecology}, volume = {57}, number = {2}, pages = {367-378}, pmid = {18958512}, issn = {0095-3628}, mesh = {Anti-Bacterial Agents/*biosynthesis/chemistry ; Bacillus megaterium/isolation &amp; purification/*metabolism ; Bacterial Proteins/*biosynthesis/chemistry ; Culture Media ; Lipopeptides/*biosynthesis/chemistry ; Microbial Sensitivity Tests ; Molecular Structure ; Peptides, Cyclic ; Soil Microbiology ; Spectrometry, Mass, Electrospray Ionization ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Surface Tension ; Surface-Active Agents/pharmacology ; }, abstract = {A soil microorganism identified as Bacillum megaterium was found to produce several antibiotics substances after growth for 20 h at 37 degrees C in a mineral culture medium. Analysis both by electron spray ionization (ESI) and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) identified these substances as lipopeptides. Predominant peaks at m/z 1,041 and m/z 1,065 revealed ions which are compatible with surfactins and lichenysins, respectively. Two other ions m/z 1,057 and m/z 1,464 were further studied by collision-induced dissociation (CID) unveiling an iturin A at the first and fengycins A and B at the second m/z peaks. The CID spectrum of the m/z 1,464 ion also suggests the existence of fengycins A and B variants in which Ile was changed to Val in the position 10 of the peptide moiety. Raw mixtures of all these compounds were also assayed for antibiotic features. The data enlighten the unusual diversity of the lipopeptide mixture produced by a sole Bacillus species.}, }
@article {pmid18953593, year = {2009}, author = {Fontes, ML and Abreu, PC}, title = {Spatiotemporal variation of bacterial assemblages in a shallow subtropical coastal lagoon in Southern Brazil.}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {140-152}, pmid = {18953593}, issn = {1432-184X}, mesh = {Bacteria/*isolation &amp; purification ; Biomass ; Brazil ; Chlorophyll/analysis ; Chlorophyll A ; Ecosystem ; Fresh Water/analysis/*microbiology ; Heterotrophic Processes ; Light ; Oxygen/analysis ; Principal Component Analysis ; Salinity ; Seasons ; Temperature ; *Water Microbiology ; }, abstract = {A study on the bacterioplankton of Conceição Lagoon (27 degrees 34' S-48 degrees 27' W), Southern Brazil, was carried out in July 2005 (austral winter) and January 2006 (austral summer) to characterize the bacterial spatiotemporal distribution and to determine the heterotrophic and photoautotrophic bacterial dominance in hypoxic/oxic stratified waters. Bacterial abundance increased significantly (p < 0.05) in summer with averages of coccus cyanobacteria (CCY) ranging from 1.02 x 10(5) (winter) to 3.21 x 10(6) cells mL(-1) (summer), heterotrophic coccus/rod-shaped (HCR) cells from 7.00 x 10(4) to 3.60 x 10(6) cells mL(-1), and heterotrophic filamentous (HF) bacteria from 2.90 x 10(3) to 2.74 x 10(5) cells mL(-1). Bacterial biovolumes also increased in summer with mean biovolumes of CCY ranging from 0.38 to 1.37 microm3, HCR cells from 0.31 to 1.12 microm3, and HF from 3.32 to 11.34 microm3. Principal component analysis showed that salinity, temperature, and light were the abiotic factors that better explained the temporal variability of bacterial assemblages. Bacterial heterotrophy dominated in the lagoon, excepted by the southern and part of central sector in January 2006, when autotrophic-dominated microbial community occurred. Spatially, bacterial assemblages were influenced by nutrient gradient, oxygen, and salinity with a positive relationship between biovolumes and nutrients and a negative relationship between abundance of coccus cyanobacteria and nutrients. The stratified [corrected] area revealed a singular temporal pattern with hypoxic bottom waters in winter and oxygen-rich waters appearing in summer related with the availability of light and predominant microbes. Thus, oxygen consumption/production is likely to be regulated by the amount of light reaching the bottom, stimulating the production of oxygen by oxygenic phototrophs.}, }
@article {pmid18952739, year = {2009}, author = {Bhandari, SK and Nyachoti, CM and Krause, DO}, title = {Raw potato starch in weaned pig diets and its influence on postweaning scours and the molecular microbial ecology of the digestive tract.}, journal = {Journal of animal science}, volume = {87}, number = {3}, pages = {984-993}, doi = {10.2527/jas.2007-0747}, pmid = {18952739}, issn = {1525-3163}, mesh = {Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Bacteria/genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; Biodiversity ; Body Weight/physiology ; Colon/microbiology ; Diet/*veterinary ; Gastrointestinal Contents/chemistry ; Gastrointestinal Tract/*microbiology ; Intestinal Mucosa/microbiology ; Organ Size/physiology ; Polymorphism, Restriction Fragment Length ; Random Allocation ; Solanum tuberosum/*metabolism ; Starch/*administration &amp; dosage ; Swine/*metabolism/*microbiology ; *Weaning ; }, abstract = {We evaluated the effect of raw potato starch (RPS) on growth performance, postweaning diarrhea, and gastrointestinal microbial populations in weaned piglets. Eighty-four piglets were weaned at 17 +/- 2 d of age with an average BW of 6.0 +/- 0.9 kg. Pigs were blocked by BW and assigned to 1 of 4 diets in a randomized complete block design with 7 replicate pens per diet and 3 pigs per pen. Treatments were 1) a positive control (PC) containing an antibiotic, 2) a negative control (NC) with no RPS and no antibiotic, 3) NC + 7% RPS (7% RPS), and 4) NC + 14% RPS (14% RPS). Diets were corn-wheat-soybean meal-based and formulated to meet NRC (1998) recommendations. The ADG, ADFI, and G:F ratio were determined weekly. Fecal consistency (FC) scoring was determined daily. After wk 3, 1 pig with a BW closest to the pen mean was killed to evaluate ileal and colonic mucosal-attached Escherichia coli and lactic acid bacteria, as well as digesta pH, VFA, and ammonia N concentrations. The DNA was extracted from ileum and colon digesta and used for molecular microbial evaluations using terminal-RFLP analysis of 16S rDNA genes. The ADG for wk 1 was greater (P < 0.01) for the PC diet, but diet had no effect on ADG during wk 3. The ADFI did not differ among treatments during the first 2 wk, and ADFI was least for 7% RPS diet during wk 3. The NC diet had a greater (P < 0.05) FC score during wk 1 than other treatments, but diet had no effect on FC score during wk 2 and 3. Diets had no effect on the colon lactic acid bacterial counts; however, the PC diet had decreased (P < 0.05) colon E. coli counts than other treatments. Ileum and colon digesta pH and total VFA concentrations did not differ among treatments. Pigs fed with 7 and 14% RPS diets had greater (P < 0.05) ileum ammonia N concentration compared with pigs fed with other diets. There was more diarrhea (P < 0.05) in the 14% than the 7% RPS and control treatments at d 21. This difference correlated with a decline (P < 0.05) in microbial diversity in the colon. We concluded that 7% RPS can be used to prevent postweaning diarrhea in weaned piglets, but there are no effects on growth performance.}, }
@article {pmid18949748, year = {2009}, author = {Hennebel, T and Simoen, H and De Windt, W and Verloo, M and Boon, N and Verstraete, W}, title = {Biocatalytic dechlorination of trichloroethylene with bio-palladium in a pilot-scale membrane reactor.}, journal = {Biotechnology and bioengineering}, volume = {102}, number = {4}, pages = {995-1002}, doi = {10.1002/bit.22138}, pmid = {18949748}, issn = {1097-0290}, mesh = {*Bioreactors ; Chlorine/*metabolism ; Environmental Restoration and Remediation/methods ; Ethane/metabolism ; Formates/metabolism ; Hydrogen/metabolism ; Palladium/*metabolism ; Shewanella/*metabolism ; Trichloroethylene/*metabolism ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Trichloroethylene (TCE) is a toxic and recalcitrant groundwater pollutant. An innovative technology using microbial produced Pd(0) nanoparticles for the remediation of TCE contaminated groundwater was developed. The nanoscale bio-Pd particles were precipitated on the biomass of Shewanella oneidensis and hydrogen gas, formate, or formic acid were used as hydrogen donors. Ethane turned out to be the only organic degradation product and no intermediate chlorinated reaction products were detected. Subsequently bio-Pd was implemented in a plate membrane reactor (MR) for the treatment of water containing TCE. In a continuous MR system, containing 50 mg L(-1) bio-Pd, removal rates up to 2,515 mg TCE day(-1) g(-1) Pd were achieved with H(2) gas as hydrogen donor. The measured chloride mass balance confirmed the removal rates. This work shows that a complete, efficient and rapid removal of TCE was achieved with bio-Pd and that a MR system containing bio-Pd and supplied with hydrogen gas offers an alternative for the current remediation technologies of water contaminated with TCE.}, }
@article {pmid18945471, year = {2009}, author = {Lee, C and Kim, J and Hwang, K and O'Flaherty, V and Hwang, S}, title = {Quantitative analysis of methanogenic community dynamics in three anaerobic batch digesters treating different wastewaters.}, journal = {Water research}, volume = {43}, number = {1}, pages = {157-165}, doi = {10.1016/j.watres.2008.09.032}, pmid = {18945471}, issn = {0043-1354}, mesh = {Anaerobiosis ; Bacteria/*metabolism ; Biodegradation, Environmental ; *Bioreactors ; Methane/*metabolism ; RNA, Ribosomal, 16S/genetics ; Time Factors ; *Waste Disposal, Fluid ; *Water Purification ; }, abstract = {Quantitative changes in methanogenic community structures, associated with performance data, were investigated in three anaerobic batch digesters treating synthetic glucose medium, whey permeate, and liquefied sewage sludge. All digesters were initially seeded with anaerobic sludge obtained from a local municipal wastewater treatment plant. Dynamics of methanogenic populations were monitored, at order and family levels, using real-time PCR based on the 16S rRNA gene. The molecular monitoring revealed that, in each digester, the quantitative structure of methanogenic community varied continuously over treatment time and the variation corresponded well to the changes in chemical profiles. Biphasic production of methane, associated with successive increases in aceticlastic (mainly Methanosarcinaceae) and hydrogenotrophic (mainly Methanomicrobiales) methanogenic groups, was observed in each digester. This corresponded to the diauxic utilization of acetate and longer-chain volatile fatty acids (C(3)-C(6)), mainly propionate. Additionally, the non-metric multidimensional scaling (NMDS) analysis of the quantification results demonstrated that the community shift patterns in three digesters were totally different from each other. Considering that the operating conditions in all trials were identical except substrates, the differences in quantitative shift profiles were suggested to be due to the different substrate compositions. This implied that the composition of wastewater could affect the evolution of quantitative methanogenic community structure in an anaerobic process. Overall, our results suggested that more attention to quantitative as well as qualitative approaches on microbial communities is needed for fundamental understanding of anaerobic processes, particularly under dynamic or transitional conditions.}, }
@article {pmid18944463, year = {2004}, author = {McSpadden Gardener, BB}, title = {Ecology of Bacillus and Paenibacillus spp. in Agricultural Systems.}, journal = {Phytopathology}, volume = {94}, number = {11}, pages = {1252-1258}, doi = {10.1094/PHYTO.2004.94.11.1252}, pmid = {18944463}, issn = {0031-949X}, abstract = {Diverse populations of aerobic endospore-forming bacteria occur in agricultural fields and may directly and indirectly contribute to crop productivity. This paper describes recent advances in our understanding of the ecology of Bacillus and Paenibacillus spp. and how different subpopulations of these two genera can promote crop health. The abundance, diversity, and distribution of native populations and inoculant strains in agricultural fields have been characterized using a variety of methods. While native populations of these two genera occur abundantly in most agricultural soils, plant tissues are differentially colonized by distinct subpopulations. Multiple Bacillus and Paenibacillus spp. can promote crop health in a variety of ways. Some populations suppress plant pathogens and pests by producing antibiotic metabolites, while others may directly stimulate plant host defenses prior to infection. Some strains can also stimulate nutrient uptake by plants, either by promoting rhizobial and mycorrhizal symbioses or by fixing atmospheric nitrogen directly. Despite a wealth of new information on the genetics and physiology of Bacillus and related species, a better understanding of the microbial ecology of these two genera must be developed. To this end, several important, but unanswered, questions related to the ecological significance and potential for managing the beneficial activities of these bacteria are discussed.}, }
@article {pmid18944378, year = {2007}, author = {McSpadden Gardener, BB}, title = {Diversity and Ecology of Biocontrol Pseudomonas spp. in Agricultural Systems.}, journal = {Phytopathology}, volume = {97}, number = {2}, pages = {221-226}, doi = {10.1094/PHYTO-97-2-0221}, pmid = {18944378}, issn = {0031-949X}, abstract = {Diverse Pseudomonas spp. may act as biological controls of plant pathogens, but the ecology of those natural populations is not well understood. And, while biocontrol potential has been identified in multiple pseudomonad strains, the linkages between genotype and phenotype have yet to be fully delineated. However, intensive studies of one class of biocontrol strains, i.e., those that can produce 2,4-diacetylphloroglucionl (DAPG), have provided new insights into the diversity, distribution, and interactions of biocontrol pseudomonads. Those studies also laid the foundation for future research and development of pseudomonad-based biocontrol strategies. Over the past several years, numerous studies have also revealed that biocontrol pseudomonads are widely distributed in agricultural soils, and that multiple crop and soil factors can affect their abundance and activities. Recent work has shown that a variety of farm management practices that reduce soilborne disease pressure can also alter the rhizosphere abundance of DAPG producers in complex ways. Such studies provide support for the hypothesis of an ecological feedback mechanism whereby a native biocontrol population increase and subsequently reduce root disease severity following infection. It is well established that complex biological interactions can take place among bio-control pseudomonads, plant pathogens, their hosts, and other members of the microbial community. The net result of such interactions likely dilutes biocontrol efficacy at the field scale. Nonetheless, inoculation can be effective, and several successful applications of biocontrol pseudomonads have been developed. Future applications of microbial ecology research will hopefully improve the consistency and efficacy of bio-control mediated by Pseudomonas spp. Current applications and future opportunities for improving pseudomonad-based biological control are discussed.}, }
@article {pmid18931821, year = {2009}, author = {Smith, ME and Jaffee, BA}, title = {PCR primers with enhanced specificity for nematode-trapping fungi (Orbiliales).}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {117-128}, pmid = {18931821}, issn = {1432-184X}, mesh = {Animals ; Ascomycota/classification/genetics/*isolation &amp; purification ; *DNA Primers ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; Nematoda/*microbiology ; Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 28S/genetics ; Sensitivity and Specificity ; *Soil Microbiology ; }, abstract = {Nematode-trapping fungi, a monophyletic lineage within the Orbiliales (Ascomycota), use specialized structures to capture and consume nematodes in soil, leaf litter, and other substrates. These fungi have been studied both because of their unique predatory life history and because they are potential control agents of important plant- and animal-parasitic nematodes. Ecological studies of nematode-trapping fungi have primarily used culture-based methods, but molecular detection techniques are now available and should be useful for studying this group. We developed Orbiliales-specific PCR primers for the ITS and 28s rDNA to directly detect nematode-trapping fungi without culturing and also to screen fungal isolates for phylogenetic placement in the Orbiliales. We used these primers to selectively amplify, clone, and sequence Orbiliales DNA extracted from soil, litter, and wood, and we compared the results of molecular detection with those obtained using a culture-based method. Of the eight species of nematode-trapping Orbiliales detected with the culture-based assay, only three were detected with PCR. The molecular assay, however, detected 18 species of uncultured Orbiliales, many of which are closely related to nematode-trapping fungi and fungal parasites of nematode eggs. Our results suggest that the combined use of Orbiliales-specific primers and culture-based techniques may benefit future studies of nematophagous fungi.}, }
@article {pmid18931299, year = {2008}, author = {Galkiewicz, JP and Kellogg, CA}, title = {Cross-kingdom amplification using bacteria-specific primers: complications for studies of coral microbial ecology.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {24}, pages = {7828-7831}, pmid = {18931299}, issn = {1098-5336}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/*genetics/isolation &amp; purification ; Base Sequence ; DNA Primers/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Eukaryotic Cells ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 18S/genetics ; Sensitivity and Specificity ; }, abstract = {PCR amplification of pure bacterial DNA is vital to the study of bacterial interactions with corals. Commonly used Bacteria-specific primers 8F and 27F paired with the universal primer 1492R amplify both eukaryotic and prokaryotic rRNA genes. An alternative primer set, 63F/1542R, is suggested to resolve this problem.}, }
@article {pmid18855043, year = {2009}, author = {Val, G and Marín, S and Mellado, RP}, title = {A sensitive method to monitor Bacillus subtilis and Streptomyces coelicolor-related [corrected] bacteria in maize rhizobacterial communities: the use of genome-wide microarrays.}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {108-115}, pmid = {18855043}, issn = {1432-184X}, mesh = {Bacillus subtilis/*genetics ; Bacillus thuringiensis Toxins ; Bacterial Proteins/genetics ; DNA, Bacterial/genetics ; Endotoxins/genetics ; Genome, Bacterial ; Hemolysin Proteins/genetics ; Oligonucleotide Array Sequence Analysis ; Plants, Genetically Modified/genetics/microbiology ; Sensitivity and Specificity ; *Soil Microbiology ; Streptomyces coelicolor/*genetics ; Zea mays/genetics/*microbiology ; }, abstract = {Commercially available DNA microarrays containing genome-wide spotted oligonucleotides encompass the soil bacteria Bacillus subtilis or Streptomyces coelicolor genomes. These have been used to analyse potential differences in rhizobacterial communities of transgenic maize engineered to express the Bacillus thuringensis Cry toxin (Bt maize) in three different agricultural soils. No differences in hybridisation were observed between genetically and non-genetically modified maize rhizobacteria from two Bt lines with a detection sensitivity of five copies of a particular gene above the background. Soil-specific hybridisation results were obtained when rhizobacterial DNA was compared to the corresponding genomic DNA spotted in the microarrays suggesting that the use of genome-wide DNA arrays could serve as a useful tool for the molecular monitoring of rhizobacterial communities.}, }
@article {pmid18853809, year = {2008}, author = {Demoling, LA and Bååth, E}, title = {No long-term persistence of bacterial pollution-induced community tolerance in tylosin-polluted soil.}, journal = {Environmental science &amp; technology}, volume = {42}, number = {18}, pages = {6917-6921}, doi = {10.1021/es8004706}, pmid = {18853809}, issn = {0013-936X}, mesh = {Bacteria/*drug effects/growth &amp; development ; Dose-Response Relationship, Drug ; Drug Resistance, Bacterial/*drug effects ; *Environmental Pollution ; Medicago sativa ; Soil Microbiology ; Soil Pollutants/*toxicity ; Time Factors ; Toxicity Tests ; Tylosin/*toxicity ; }, abstract = {Pollution-induced community tolerance (PICT) of soil bacteria to the antibiotic tylosin was studied over 95 days. Tylosin was added at increasing concentrations, together with different amounts of alfalfa to study the effects of substrate addition on PICT and bacterial growth in soil. The leucine incorporation technique was used to estimate bacterial growth and as a detection method in the PICT concept. Direct inhibition of the bacterial growth rates, resulting in a dose-response curve, was found above 50 mg of tylosin kg(-1) of soil two days after tylosin addition (IC50 value of 960 mg tylosin kg(-1)). After 10 days of exposure to at least 50 mg of tylosin kg(-1), the PICT was observed and correlated to inhibition of bacterial growth by tylosin. A return of the PICT to control levels was found over time, and after 95 days at 1500 mg of tylosin kg(-1), essentially no PICT was found, as compared to the unpolluted control soil. The return of PICT to pre-exposure levels was not totally reflected in the recovery of bacterial growth. Alfalfa addition did not affect the inhibitory effect of tylosin on bacterial growth rates; neither did it alter the PICT. Since tylosin is relatively rapidly degraded in soil, our results indicate that the PICT will return to prepollution levels when the selective pressure of the toxicant is removed and will thus be a useful technique for monitoring remediation measures.}, }
@article {pmid18853084, year = {2009}, author = {Verma, VC and Gond, SK and Kumar, A and Mishra, A and Kharwar, RN and Gange, AC}, title = {Endophytic actinomycetes from Azadirachta indica A. Juss.: isolation, diversity, and anti-microbial activity.}, journal = {Microbial ecology}, volume = {57}, number = {4}, pages = {749-756}, pmid = {18853084}, issn = {1432-184X}, mesh = {Actinobacteria/*chemistry/classification/*isolation &amp; purification ; *Antibiosis ; Azadirachta/*microbiology ; Bacteria/growth &amp; development ; *Biodiversity ; India ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Plant Stems/microbiology ; }, abstract = {Endophytic actinomycetes from Azadirachta indica A. Juss. were screened and evaluated for their anti-microbial activity against an array of pathogenic fungi and bacteria. A total of 55 separate isolates were obtained from 20 plants, and 60% of these showed inhibitory activity against one or more pathogenic fungi and bacteria. Actinomycetes were most commonly recovered from roots (54.5% of all isolates), followed by stems (23.6%), and leaves (21.8%). The dominant genus was Streptomyces (49.09% of all isolates), while Streptosporangium (14.5%), Microbispora (10.9%), Streptoverticillium (5.5%), Sacchromonospora sp. (5.5%), and Nocardia (3.6%) were also recovered. Streptomyces isolates AzR 006, 011, and 031 (all from roots) had acute activity against Pseudomonas fluorescens, while AzR027, 032, and 051 (also all from roots) showed activity against Escherichia coli. Meanwhile, an isolate of Nocardia sp. from leaves (AzL025) showed antagonism against Bacillus subtilis. Overall, 32 of the 55 were found to have broad spectrum significant antimicrobial activity, while about 4% of them showed strong and acute inhibition to pathogenic fungi and bacteria. Isolates of Streptomyces AzR031, 008, and 047, Nocardia sp. AzL025, and Streptosporangium sp. AzR 021 and 048 are of particular interest because they showed significant antagonistic activity against root pathogens, including Pythium and Phytophthora sp. Thus, many of the isolates recovered from A. indica in this study may be used in developing potential bio-control agents against a range of pathogenic fungi and bacteria and in the production of novel natural antimicrobial compounds. These results not only further our understanding of plant-microbe interactions but also indicate that there is an untapped resource of endophytic microorganisms that could be exploited in the biotechnological, medicinal, and agricultural industries.}, }
@article {pmid18850242, year = {2009}, author = {Büdel, B and Darienko, T and Deutschewitz, K and Dojani, S and Friedl, T and Mohr, KI and Salisch, M and Reisser, W and Weber, B}, title = {Southern African biological soil crusts are ubiquitous and highly diverse in drylands, being restricted by rainfall frequency.}, journal = {Microbial ecology}, volume = {57}, number = {2}, pages = {229-247}, pmid = {18850242}, issn = {0095-3628}, mesh = {*Biodiversity ; Biomass ; Carbon/analysis ; Chlorophyll/analysis ; Climate ; Cyanobacteria/genetics/isolation &amp; purification ; Lichens/genetics/isolation &amp; purification ; Namibia ; Nitrogen/analysis ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Rain ; Seasons ; *Soil Microbiology ; }, abstract = {Biological soil crusts (BSCs) are found in all dryland regions of the world, including the polar regions. They are also known to occur in the southern African region. Although there were a number of case studies on BSCs from that region, we did not know if they are a normal part of the vegetation cover or just a phenomenon that occasionally occurs here and there. In order to investigate diversity, distribution patterns, and the driving factors of both, we followed a random sampling system of observatories along a transect, stretching from the Namibian-Angolan border down south to the Cape Peninsula, covering seven different major biomes. Biological soil crusts were found to occur in six out of seven biomes. Despite the fact that soil-dwelling algae occurred in the Fynbos biome, crust formation was not observed for hitherto unknown reasons. Seven BSC types were distinguished on the basis of morphology and taxonomic composition: three of them were cyanobacteria-dominated, one with additional chlorolichens, two with bryophytes, one hypolithic type restricted to quartz gravel pavements, and the unique lichen fields of the Namib Desert. Besides 29 green algal species in 21 genera, one heterokont alga, 12 cyanolichens, 14 chlorolichens, two genera of liverworts, and three genera of mosses, these crusts are positioned among the most diverse BSCs worldwide mainly because of the unusual high cyanobacterial species richness comprising 58 species in 21 genera. They contribute considerably to the biodiversity of arid and semi-arid bioregions. Taxonomic diversity of cyanobacteria was significantly higher in the winter rain zone than in the summer rain zone (54 versus 32 species). The soil photosynthetic biomass (chlorophylla/m2), the carbon content of the soil and the number of BSC types were significantly higher in the winter rain zone (U27, 29=215.0, p=0.004 [chla]; U21, 21=135.0, p=0.031 [C]; U27, 29=261.5, p=0.028 [BSC types]; excluding the fog-dominated Namib biome). The winter rain zone is characterized by a lower precipitation amount, but a higher rain frequency with the number of rainy days more evenly distributed over the year. The dry period is significantly shorter per year in the winter rain zone (U8, 9=5.0, p=0.003). We conclude that rain frequency and duration of dry periods rather than the precipitation amount is the main factor for BSC growth and succession. Nitrogen content of the soils along the transect was generally very low and correlated with soil carbon content. There was a weak trend that an increasing proportion of silt and clay (<0.63 mm) in the soil is associated with higher values of BSC chlorophyll content (Pearson correlation coefficient=0.314, p=0.237). Furthermore, we found a significant positive correlation between silt and clay and the number of BSC types (Pearson correlation coefficient=0.519, p=0.039), suggesting that fine grain-size promotes BSC succession and their biomass content. Lichens and bryophytes occurred in BSCs with lower disturbance frequencies (e.g. trampling) only. Crust thickness and chlorophyll content increased significantly from crusts of the early successional type to the late successional crust types. From our results, we conclude that BSCs are a normal and frequent element of the vegetation in arid and semi-arid southwestern Africa, and that rain frequency and duration of dry periods rather than the precipitation amount are the key factors for the development, differentiation and composition of BSCs.}, }
@article {pmid18850241, year = {2009}, author = {Botes, A and Boekhout, T and Hagen, F and Vismer, H and Swart, J and Botha, A}, title = {Growth and mating of Cryptococcus neoformans var. grubii on woody debris.}, journal = {Microbial ecology}, volume = {57}, number = {4}, pages = {757-765}, pmid = {18850241}, issn = {1432-184X}, mesh = {Acacia/microbiology ; Cellulases/metabolism ; Cryptococcus neoformans/enzymology/genetics/*growth &amp; development ; Culture Media ; Endo-1,4-beta Xylanases/metabolism ; Eucalyptus/microbiology ; Genes, Mating Type, Fungal ; Genotype ; South Africa ; Wood/chemistry/*microbiology ; Xylans/metabolism ; }, abstract = {A total of 36 Cryptococcus neoformans strains originating from South Africa were screened for wood degrading enzymes. All strains tested positive for cellulase activity while none where capable of xylan degradation. Three C. neoformans var. grubii strains, originating from clinical and environmental samples, representing the same genotype (VNI/AFLP1-C. neoformans var. grubii) and MATalpha, were evaluated for growth on debris of two common tree species in South Africa: Acacia mearnsii and Eucalyptus camaldulensis. The mating capability of all the C. neoformans strains was evaluated on similar debris. Strains grown on A. mearnsii yielded substantially greater yeast populations. A total of 26%, 6%, 46%, and 80% of the 36 C. neoformans strains tested were either able to mate or develop filaments when crossed on A. mearnsii and E. camaldulensis debris, V8 juice, and yeast carbon base (YCB) agar, respectively. Filamentation and monokaryotic fruiting was observed in 3% of strains when C. neoformans was cultured on either A. mearnsii, E. camaldulensis debris, or YCB. The results indicate that this fungus is capable of completing its life cycle and can produce basidiospores on woody debris. In the future, these findings should be considered when studying the epidemiology, microbial ecology, and proposed infection process of this global pathogen.}, }
@article {pmid18846553, year = {2009}, author = {Harper, WF and Terada, A and Poly, F and Le Roux, X and Kristensen, K and Mazher, M and Smets, BF}, title = {The effect of hydroxylamine on the activity and aggregate structure of autotrophic nitrifying bioreactor cultures.}, journal = {Biotechnology and bioengineering}, volume = {102}, number = {3}, pages = {714-724}, doi = {10.1002/bit.22121}, pmid = {18846553}, issn = {1097-0290}, mesh = {Ammonia/metabolism ; Autotrophic Processes/*drug effects ; Bacteria/enzymology/genetics/*metabolism ; Biomass ; *Bioreactors ; Cell Culture Techniques ; Gene Expression Regulation, Bacterial/drug effects ; Hydroxylamine/metabolism/*pharmacology ; In Situ Hybridization, Fluorescence ; Nitrite Reductases/genetics/metabolism ; Nitrosomonas/enzymology/genetics/metabolism ; Oxidoreductases/genetics/metabolism ; Polymerase Chain Reaction ; }, abstract = {Addition of hydroxylamine (NH2OH) to autotrophic biomass in nitrifying bioreactors affected the activity, physical structure, and microbial ecology of nitrifying aggregates. When NH2OH is added to nitrifying cultures in 6-h batch experiments, the initial NH3-N uptake rates were physiologically accelerated by a factor of 1.4-13. NH2OH addition caused a 20-40% decrease in the median aggregate size, broadened the shape of the aggregate size distribution by up to 230%, and caused some of the microcolonies to appear slightly more dispersed. Longer term NH2OH addition in fed batch bioreactors decreased the median aggregate size, broadened the aggregate size distribution, and decreased NH3-N removal from >90% to values ranging between 75% and 17%. This altered performance is explained by quantitative fluorescence in situ hybridization (FISH) results that show inhibition of nitrifying populations, and by qPCR results showing that the copy numbers of amoA and nxrA genes gradually decreased by up to an order-of-magnitude. Longer term NH2OH addition damaged the active biomass. This research clarifies the effect of NH2OH on nitrification and demonstrates the need to incorporate NH2OH-related dynamics of the nitrifying biomass into mathematical models, accounting for both ecophysiological and structural responses.}, }
@article {pmid18842400, year = {2009}, author = {De Schryver, P and Verstraete, W}, title = {Nitrogen removal from aquaculture pond water by heterotrophic nitrogen assimilation in lab-scale sequencing batch reactors.}, journal = {Bioresource technology}, volume = {100}, number = {3}, pages = {1162-1167}, doi = {10.1016/j.biortech.2008.08.043}, pmid = {18842400}, issn = {1873-2976}, mesh = {Aquaculture/*instrumentation ; Bacteria, Anaerobic/*metabolism ; Bioreactors/*microbiology ; Equipment Design ; Equipment Failure Analysis ; Fresh Water/*microbiology ; Nitrogen/isolation &amp; purification/*metabolism ; Pilot Projects ; Water Pollutants, Chemical/isolation &amp; purification/*metabolism ; Water Purification/*instrumentation ; }, abstract = {The potential use of sequencing batch reactors (SBRs) as an alternative bio-flocs technology (BFT) approach in aquaculture was explored. One SBR was dosed with glycerol and one with acetate for the decrease of the nitrogen concentration in simulated aquaculture water by microbial assimilation. At an optimal C/N ratio between 10 and 15, the nitrogen removal efficiency reached up to 98% (=110 mg N L(-1) reactor day(-1)) for both SBRs. The estimated biomass productivity reached 0.62-0.94 g C L(-1)r eactor day(-1) for the glycerol SBR and 0.54-0.82 g C L(-1) reactor day(-1) for the acetate SBR. The floc protein content, indicating biomass quality, reached up to 57% if grown on glycerol. With acetate, it attained a value of 61%. The highest average poly-beta-hydroxybutyrate (PHB) content was 16% on a dry weight basis for the acetate biomass.}, }
@article {pmid18841701, year = {2008}, author = {Young, VB and Schmidt, TM}, title = {Overview of the gastrointestinal microbiota.}, journal = {Advances in experimental medicine and biology}, volume = {635}, number = {}, pages = {29-40}, pmid = {18841701}, issn = {0065-2598}, support = {R01 DK070875/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome ; Microbiological Techniques ; }, abstract = {The community of microbes that inhabits the mammalian intestinal tract exists in a symbiosis with their host. The structure of this community represents the combined effects of selection pressure on the part of the host and on the part of the microbes themselves. Through recent advances in the field of microbial ecology we are beginning to understand the forces that shape this complex community. We will review what is known about the interaction between the host and the indigenous microbial community. Following this discussion we will introduce methods that have been used to study the structure, function and dynamics of this community.}, }
@article {pmid18840282, year = {2008}, author = {Frank, DN}, title = {XplorSeq: a software environment for integrated management and phylogenetic analysis of metagenomic sequence data.}, journal = {BMC bioinformatics}, volume = {9}, number = {}, pages = {420}, pmid = {18840282}, issn = {1471-2105}, mesh = {Artificial Intelligence ; Base Sequence ; *Database Management Systems ; Genes, rRNA ; *Genome ; Information Storage and Retrieval ; Meta-Analysis as Topic ; *Phylogeny ; Sequence Analysis, DNA/*methods ; Systems Integration ; *User-Computer Interface ; }, abstract = {BACKGROUND: Advances in automated DNA sequencing technology have accelerated the generation of metagenomic DNA sequences, especially environmental ribosomal RNA gene (rDNA) sequences. As the scale of rDNA-based studies of microbial ecology has expanded, need has arisen for software that is capable of managing, annotating, and analyzing the plethora of diverse data accumulated in these projects.<br><br>RESULTS: XplorSeq is a software package that facilitates the compilation, management and phylogenetic analysis of DNA sequences. XplorSeq was developed for, but is not limited to, high-throughput analysis of environmental rRNA gene sequences. XplorSeq integrates and extends several commonly used UNIX-based analysis tools by use of a Macintosh OS-X-based graphical user interface (GUI). Through this GUI, users may perform basic sequence import and assembly steps (base-calling, vector/primer trimming, contig assembly), perform BLAST (Basic Local Alignment and Search Tool; 123) searches of NCBI and local databases, create multiple sequence alignments, build phylogenetic trees, assemble Operational Taxonomic Units, estimate biodiversity indices, and summarize data in a variety of formats. Furthermore, sequences may be annotated with user-specified meta-data, which then can be used to sort data and organize analyses and reports. A document-based architecture permits parallel analysis of sequence data from multiple clones or amplicons, with sequences and other data stored in a single file.<br><br>CONCLUSION: XplorSeq should benefit researchers who are engaged in analyses of environmental sequence data, especially those with little experience using bioinformatics software. Although XplorSeq was developed for management of rDNA sequence data, it can be applied to most any sequencing project. The application is available free of charge for non-commercial use at http://vent.colorado.edu/phyloware.}, }
@article {pmid18831268, year = {2008}, author = {Ma, J and Mungoni, LJ and Carballa, M and Verstraete, W}, title = {Maximum removal rate of propionic acid as sole carbon source in UASB reactors by macro and micro nutrients stimulation.}, journal = {Communications in agricultural and applied biological sciences}, volume = {73}, number = {1}, pages = {173-176}, pmid = {18831268}, issn = {1379-1176}, mesh = {*Anaerobiosis ; Bacteria, Anaerobic/*metabolism ; Biodegradation, Environmental ; Biomass ; *Bioreactors ; Carbon ; Kinetics ; Methane/*metabolism ; Propionates/chemistry/*metabolism ; }, }
@article {pmid18831258, year = {2008}, author = {De Schryver, P and Verstraete, W}, title = {Sequential batch reactors as an alternative approach for bio-flocs technology in aquaculture: from waste to fish.}, journal = {Communications in agricultural and applied biological sciences}, volume = {73}, number = {1}, pages = {127-131}, pmid = {18831258}, issn = {1379-1176}, mesh = {Animals ; Aquaculture/*instrumentation/*methods ; Bacteria/*metabolism ; Bioreactors ; Carbon/*metabolism ; Nitrogen/adverse effects/*metabolism ; Oxygen/metabolism ; *Water Microbiology ; }, }
@article {pmid18831254, year = {2008}, author = {Crab, R and Kochva, M and Verstraete, W and Avnimelech, Y}, title = {Bio-flocs technology for overwintering of tilapia.}, journal = {Communications in agricultural and applied biological sciences}, volume = {73}, number = {1}, pages = {109-113}, pmid = {18831254}, issn = {1379-1176}, mesh = {Ammonia/analysis ; Animals ; Aquaculture/*methods ; Carbon/analysis ; Environmental Monitoring/methods ; Nitrogen/analysis ; Oxygen/analysis ; Population Density ; Seasons ; Starch/analysis/metabolism ; *Temperature ; Tilapia/growth &amp; development/metabolism/*physiology ; Water/*standards ; *Water Microbiology ; Water Pollution, Chemical/analysis/*prevention &amp; control ; }, }
@article {pmid18831250, year = {2008}, author = {Aelterman, P and Freguia, S and Keller, J and Rabaey, K and Verstraete, W}, title = {The anode potential regulates the bacterial activity in microbial fuel cells.}, journal = {Communications in agricultural and applied biological sciences}, volume = {73}, number = {1}, pages = {85-89}, pmid = {18831250}, issn = {1379-1176}, mesh = {Acetates/metabolism ; *Bacterial Physiological Phenomena ; *Bioelectric Energy Sources ; Biomass ; Bioreactors ; Carbon Dioxide/metabolism ; Electricity ; Electrodes/*microbiology ; }, }
@article {pmid18831243, year = {2008}, author = {Vlaeminck, SE and Terada, A and Carballa, M and De Clippeleir, H and Boon, N and Smets, BF and Verstraete, W}, title = {Fluorescence in situ hybridization (FISH) to elucidate structure and diversity in granular biomass for the treatment of nitrogenous wastewater.}, journal = {Communications in agricultural and applied biological sciences}, volume = {73}, number = {1}, pages = {43-47}, pmid = {18831243}, issn = {1379-1176}, mesh = {Anaerobiosis ; Bacteria/classification/*metabolism/ultrastructure ; Bacteria, Anaerobic/classification/*metabolism/ultrastructure ; *Biomass ; Bioreactors ; In Situ Hybridization, Fluorescence/*methods ; Industrial Microbiology ; Industrial Waste ; Particle Size ; Phylogeny ; Sewage/*microbiology ; Waste Disposal, Fluid ; }, }
@article {pmid18831237, year = {2008}, author = {De Schamphelaire, L and Verstraete, W}, title = {Microalgae and the biological sunlight-to-biogas energy conversion system.}, journal = {Communications in agricultural and applied biological sciences}, volume = {73}, number = {1}, pages = {15-18}, pmid = {18831237}, issn = {1379-1176}, mesh = {Anaerobiosis ; Animals ; *Biomass ; Bioreactors ; Biotransformation ; Carbon Dioxide/*pharmacology ; *Energy-Generating Resources ; Eukaryota/*metabolism ; Oxygen/metabolism ; Photosynthesis ; *Sunlight ; }, }
@article {pmid18830662, year = {2009}, author = {Rastogi, G and Sani, RK and Peyton, BM and Moberly, JG and Ginn, TR}, title = {Molecular studies on the microbial diversity associated with mining-impacted Coeur d'Alene River sediments.}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {129-139}, pmid = {18830662}, issn = {1432-184X}, mesh = {Archaea/classification/*genetics/isolation &amp; purification ; Bacteria/classification/*genetics/isolation &amp; purification ; Biodiversity ; Gene Library ; Geologic Sediments/analysis/*microbiology ; Idaho ; Metals/analysis ; Mining ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; Rivers/*microbiology ; *Water Microbiology ; Water Pollutants/analysis ; }, abstract = {The prokaryotic diversity associated with highly metal-contaminated sediment samples collected from the Coeur d'Alene River (CdAR) was investigated using a cultivation-independent approach. Bacterial community structure was studied by constructing an RNA polymerase beta subunit (rpoB) gene library. Phylogenetic analysis revealed that 75.8% of the rpoB clones were associated with beta-Proteobacteria while the remaining 24.2% were with gamma-Proteobacteria. All phylotypes showed close similarity to previously reported cultivable lineages from metal or organic contaminant-rich environments. In an archaeal 16S rRNA gene library, 70% of the clones were affiliated to Crenarchaeota, while 30% belonged to Euryarchaeota. Most of the Euryarchaeota sequences were related to acetoclastic lineages belonging to Methanosarcinales. A single phylotype within the Euryarchaeota showed no association with cultivable euryarchaeotal lineages and might represent novel taxon. Diversity indices demonstrated greater diversity of Bacteria compared to Archaea in CdAR sediments. Sediment characterization by the X-ray fluorescence spectroscopy revealed high amount of toxic metals. To our knowledge, this is the first culture-independent survey on the prokaryotic diversity present in mining-impacted sediments of CdAR.}, }
@article {pmid18826437, year = {2009}, author = {Loy, A and Duller, S and Baranyi, C and Mussmann, M and Ott, J and Sharon, I and Béjà, O and Le Paslier, D and Dahl, C and Wagner, M}, title = {Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur-oxidizing prokaryotes.}, journal = {Environmental microbiology}, volume = {11}, number = {2}, pages = {289-299}, pmid = {18826437}, issn = {1462-2920}, support = {P 18836/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Archaea/*classification/*enzymology/genetics ; Bacteria/*classification/*enzymology/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Hydrogensulfite Reductase/*genetics ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfur Compounds/*metabolism ; }, abstract = {Sulfur-oxidizing prokaryotes (SOP) catalyse a central step in the global S-cycle and are of major functional importance for a variety of natural and engineered systems, but our knowledge on their actual diversity and environmental distribution patterns is still rather limited. In this study we developed a specific PCR assay for the detection of dsrAB that encode the reversely operating sirohaem dissimilatory sulfite reductase (rDSR) and are present in many but not all published genomes of SOP. The PCR assay was used to screen 42 strains of SOP (most without published genome sequence) representing the recognized diversity of this guild. For 13 of these strains dsrAB was detected and the respective PCR product was sequenced. Interestingly, most dsrAB-encoding SOP are capable of forming sulfur storage compounds. Phylogenetic analysis demonstrated largely congruent rDSR and 16S rRNA consensus tree topologies, indicating that lateral transfer events did not play an important role in the evolutionary history of known rDSR. Thus, this enzyme represents a suitable phylogenetic marker for diversity analyses of sulfur storage compound-exploiting SOP in the environment. The potential of this new functional gene approach was demonstrated by comparative sequence analyses of all dsrAB present in published metagenomes and by applying it for a SOP census in selected marine worms and an alkaline lake sediment.}, }
@article {pmid18825450, year = {2009}, author = {Rudi, K}, title = {Environmental shaping of ribosomal RNA nucleotide composition.}, journal = {Microbial ecology}, volume = {57}, number = {3}, pages = {469-477}, pmid = {18825450}, issn = {1432-184X}, mesh = {Analysis of Variance ; Bacteria/classification/*genetics ; Base Composition ; Ecosystem ; *Environment ; Multivariate Analysis ; Principal Component Analysis ; RNA, Bacterial/*genetics ; RNA, Ribosomal/*genetics ; Regression Analysis ; Sequence Analysis, RNA ; }, abstract = {Ribosomal RNA (rRNA) is one of the most important macromolecules in the cell. It is well established that high-temperature environmental conditions destabilize rRNA, leading to a selection for G+C-rich stabilizing structures. Our knowledge about the nucleotide composition effect of other environmental conditions, however, is limited. In the present work, I addressed this by correlating the rRNA nucleotide composition to known environmental habitats for bacteria. The bacterial phyla Firmicutes, Actinobacteria, and Proteobacteria were chosen for in-depth analyses due to the abundance of information available in the databases. Major differences in nucleotide composition were identified between these phyla. In addition to the G+C-->A+T gradients, a main gradient of G+A-->C+T was identified for Firmicutes, while a G+T-->A+C gradient was identified for Actinobacteria. With respect to correlation to environmental conditions, the Firmicutes showed a main structure of high G+C being correlated to thermophilic conditions, high A+T to anaerobic conditions, and high C+T to halophilic conditions. The main patterns detected for Firmicutes can be explained by structural stability for high G+C, chemical instability of G under aerobic conditions, and structural stability by purine/pyrimidine skew for halophilic conditions. On the contrary, the correlations for Actinobacteria cannot easily be explained by chemical and/or structural stability. This may indicate interference with factors not included in my work. Finally, I found a main correlation between high A+T and endosymbiosis for Proteobacteria. High A+T probably reflects adaptation to cell internal growth. Further support for environmentally driven nucleotide composition shaping was found and that polyphyletic bacteria were associated with the same environment/nucleotide correlations. My conclusion is that environmental conditions and habitats have a major effect on rRNA nucleotide composition but that the effects may differ between the bacterial phyla.}, }
@article {pmid18824812, year = {2008}, author = {Vlaeminck, SE and Cloetens, LF and Carballa, M and Boon, N and Verstraete, W}, title = {Granular biomass capable of partial nitritation and anammox.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {58}, number = {5}, pages = {1113-1120}, doi = {10.2166/wst.2008.731}, pmid = {18824812}, issn = {0273-1223}, mesh = {Ammonia/*metabolism ; Biodegradation, Environmental ; *Biomass ; Bioreactors/microbiology ; Nitrogen/*metabolism ; Water Microbiology ; Water Purification/*instrumentation/methods ; }, abstract = {A novel and efficient way of removing nitrogen from wastewater poor in biodegradable organic carbon, is the combination of partial nitritation and anoxic ammonium oxidation (anammox), as in the one-stage oxygen-limited autotrophic nitrification/denitrification (OLAND) process. Since anoxic ammonium-oxidizing bacteria grow very slowly, maximum biomass retention in the reactor is required. In this study, a lab-scale sequencing batch reactor (SBR) was used to develop granular, rapidly settling biomass. With SBR cycles of one hour and a minimum biomass settling velocity of 0.7 m/h, OLAND granules were formed in 1.5 months and the nitrogen removal rate increased from 50 to 450 mg N L(-1) d(-1) in 2 months. The granules had a mean diameter of 1.8 mm and their aerobic and anoxic ammonium-oxidizing activities were well equilibrated to perform the OLAND reaction. Fluorescent in-situ hybridization (FISH) demonstrated the presence of both beta-proteobacterial aerobic ammonium oxidizers and planctomycetes (among which anoxic ammonium oxidizers) in the granules. The presented results show the applicability of rapidly settling granular biomass for one-stage partial nitritation and anammox.}, }
@article {pmid18824808, year = {2008}, author = {Wu, YJ and Whang, LM and Huang, SJ and Yang, YF and Lei, CN and Cheng, SS}, title = {Evaluation of performance and microbial ecology of sequencing batch reactor and membrane bioreactor treating thin-film transistor liquid crystal display wastewater.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {58}, number = {5}, pages = {1085-1093}, doi = {10.2166/wst.2008.464}, pmid = {18824808}, issn = {0273-1223}, mesh = {Aerobiosis ; Bacteria, Aerobic/genetics/metabolism ; Biodegradation, Environmental ; Bioreactors/*microbiology ; Dimethyl Sulfoxide/metabolism ; *Ecology ; Ethanolamine/metabolism ; Filtration/instrumentation/methods ; Membranes, Artificial ; Quaternary Ammonium Compounds/metabolism ; Reproducibility of Results ; Waste Disposal, Fluid/*methods ; }, abstract = {In Taiwan, a substantial amount of thin-film transistor liquid crystal display (TFT-LCD) wastewater is produced daily due to an increasing production of the opto-electronic industry in recent years. The main components of TFT-LCD wastewater include dimethyl sulphoxide (DMSO), monoethanolamine (MEA), and tetra-methyl ammonium hydroxide (TMAH), which are recognized as non-or slow-biodegradable organic compounds and limited information is available regarding their biological treatablility. This study was conducted to evaluate the long-term performance of two bioreactors, anaerobic-aerobic (A/O) sequencing batch reactor (SBR) and aerobic membrane bioreactor (MBR), treating synthetic TFT-LCD wastewater containing DMSO, MEA, and TMAH with different loadings. For the A/O SBR, the influent wastewater was composed of 800 mg MEA/L, 430 mg DMSO/L, and 90 mg TMAH/L, respectively. After reaching steady-state, SBR was able to achieve more than 99% degradation efficiencies for the three compounds examined. For the case of aerobic MBR, the influent wastewater was composed of 550 mg MEA/L, 270 mg DMSO/L, and 330 mg TMAH/L, respectively, and degradation efficiencies for the three compounds achieved more than 99%. Although both different reactors shared similar and satisfactory degradation efficiencies for DMSO, MEA, and TMAH, the microbial ecology of these two reactors, as elucidated with molecular methods, was apparently different. The 16S rDNA-based cloning/sequencing results indicated that the dominant sequences retrieved from the aerobic MBR, including Hyphomicrobium denitrificans, Hyphomicrobium zavarzinii, Rhodobacter sp., and Methyloversatilis universalis, showed a clear linkage to their physiological properties of DMSO and TMAH degradation. On the other hand, Zoogloea sp., Chlorobium chlorochromatii, Agricultural soil bacterium, and Flavosolibacter ginsengiterrae were proliferated in the A/O SBR Run1, while Thiobacillus sp., Nitrosomonas sp., Thauera aromatica and Azoarcus sp. became dominant in Run2. Furthermore, the sequences retrieved from different reactors were used to establish the terminal restriction fragment length polymorphism (TRFLP) fingerprint methodology for monitoring the dynamics of dominant degrading bacteria in the aerobic MBR treating TFT-LCD wastewater.}, }
@article {pmid18824273, year = {2008}, author = {Wilkinson, DM}, title = {Testate amoebae and nutrient cycling: peering into the black box of soil ecology.}, journal = {Trends in ecology &amp; evolution}, volume = {23}, number = {11}, pages = {596-599}, doi = {10.1016/j.tree.2008.07.006}, pmid = {18824273}, issn = {0169-5347}, mesh = {Amoeba/*metabolism/microbiology/ultrastructure ; Animals ; Mycorrhizae/metabolism/physiology ; Nitrogen/*metabolism ; Rhododendron/microbiology ; Silicon Dioxide/metabolism ; *Soil ; Soil Microbiology ; }, abstract = {In some areas of ecology and evolution, such as the behavioural ecology of many well-studied bird species, it is increasingly difficult to make surprising new discoveries. However, this is not the case in many areas of soil and/or microbial ecology. Two recent studies suggest that the testate amoebae, a microbial group unfamiliar to most biologists, might play a much larger role in soil nutrient cycling than has hitherto been suspected.}, }
@article {pmid18818866, year = {2009}, author = {Bakermans, C and Sloup, RE and Zarka, DG and Tiedje, JM and Thomashow, MF}, title = {Development and use of genetic system to identify genes required for efficient low-temperature growth of Psychrobacter arcticus 273-4.}, journal = {Extremophiles : life under extreme conditions}, volume = {13}, number = {1}, pages = {21-30}, pmid = {18818866}, issn = {1433-4909}, mesh = {Adaptation, Physiological ; *Cold Temperature ; Electroporation ; *Genes, Bacterial ; Genetic Vectors ; Membrane Fluidity ; Plasmids ; Psychrobacter/genetics/*growth &amp; development/physiology ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {We describe the development of genetic tools (electroporation, conjugation, vector for targeted gene replacement) for use in the psychrophile Psychrobacter arcticus 273-4 to test hypotheses about cold adaptation. Successful electroporation only occurred with nonstandard parameters, such as: electrocompetent cells freshly prepared from stationary-phase cultures, high field strengths (25 kV cm(-1)), long recovery times (16-24 h), and selection with low concentrations of antibiotics. Transformation frequencies were greatly affected by a methylation-dependent restriction barrier homologous to DpnI. The vector pJK100 (which was self-transmissible and contained a Pir-dependent R6K origin of replication) proved effective as a suicide plasmid that could be used to recombine mutations into the P. arcticus 273-4 genome. We used this vector for targeted replacement of dctT, the substrate-binding periplasmic subunit of a TRAP (tripartite ATP-independent periplasmic) transporter (which we have named dctTUF), as it was more highly expressed at cold temperatures. The replacement of dctT (with kan) decreased the rate of growth at low temperatures in mineral medium with glutamate, acetate, butyrate, and fumarate, but not with pyruvate suggesting that DctTUF participates in the transport of glutamate, acetate, butyrate, and fumarate at cold temperatures. This is the first report to demonstrate the creation of site-specific mutants in the genus Psychrobacter, their affect on low-temperature growth, and a substrate range for TAXI proteins of TRAP transporters.}, }
@article {pmid18818861, year = {2009}, author = {Franke-Whittle, IH and Knapp, BA and Fuchs, J and Kaufmann, R and Insam, H}, title = {Application of COMPOCHIP microarray to investigate the bacterial communities of different composts.}, journal = {Microbial ecology}, volume = {57}, number = {3}, pages = {510-521}, pmid = {18818861}, issn = {1432-184X}, mesh = {Bacteria/classification/*genetics ; DNA, Bacterial/genetics ; Multivariate Analysis ; Oligonucleotide Array Sequence Analysis/*methods ; RNA Probes ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; *Soil ; *Soil Microbiology ; }, abstract = {A microarray spotted with 369 different 16S rRNA gene probes specific to microorganisms involved in the degradation process of organic waste during composting was developed. The microarray was tested with pure cultures, and of the 30,258 individual probe-target hybridization reactions performed, there were only 188 false positive (0.62%) and 22 false negative signals (0.07%). Labeled target DNA was prepared by polymerase chain reaction amplification of 16S rRNA genes using a Cy5-labeled universal bacterial forward primer and a universal reverse primer. The COMPOCHIP microarray was applied to three different compost types (green compost, manure mix compost, and anaerobic digestate compost) of different maturity (2, 8, and 16 weeks), and differences in the microorganisms in the three compost types and maturity stages were observed. Multivariate analysis showed that the bacterial composition of the three composts was different at the beginning of the composting process and became more similar upon maturation. Certain probes (targeting Sphingobacterium, Actinomyces, Xylella/Xanthomonas/Stenotrophomonas, Microbacterium, Verrucomicrobia, Planctomycetes, Low G + C and Alphaproteobacteria) were more influential in discriminating between different composts. Results from denaturing gradient gel electrophoresis supported those of microarray analysis. This study showed that the COMPOCHIP array is a suitable tool to study bacterial communities in composts.}, }
@article {pmid18817891, year = {2008}, author = {Tringe, SG and Hugenholtz, P}, title = {A renaissance for the pioneering 16S rRNA gene.}, journal = {Current opinion in microbiology}, volume = {11}, number = {5}, pages = {442-446}, doi = {10.1016/j.mib.2008.09.011}, pmid = {18817891}, issn = {1369-5274}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Culture-independent molecular surveys using the 16S rRNA gene have become a mainstay for characterizing microbial community structure over the past quarter century. More recently this approach has been overshadowed by metagenomics, which provides a global overview of a community's functional potential rather than just an inventory of its inhabitants. However, the pioneering 16S rRNA gene is making a comeback in its own right thanks to a number of methodological advancements including higher resolution (more sequences), analysis of multiple related samples (e.g. spatial and temporal series) and improved metadata, and use of metadata. The standard conclusion that microbial ecosystems are remarkably complex and diverse is now being replaced by detailed insights into microbial ecology and evolution based only on this one historically important marker gene.}, }
@article {pmid18797957, year = {2009}, author = {Rousk, J and Demoling, LA and Bååth, E}, title = {Contrasting short-term antibiotic effects on respiration and bacterial growth compromises the validity of the selective respiratory inhibition technique to distinguish fungi and bacteria.}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {75-85}, pmid = {18797957}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/growth &amp; development/metabolism ; Benomyl/pharmacology ; Biomass ; Captan/pharmacology ; Fungi/*drug effects/growth &amp; development/metabolism ; Fungicides, Industrial/*pharmacology ; Glucose/metabolism ; Leucine/metabolism ; *Soil Microbiology ; Streptomycin/pharmacology ; }, abstract = {The selective inhibition (SI) technique has been widely used to resolve fungal and bacterial biomass. By studying bacterial growth (leucine/thymidine incorporation) and respiration simultaneously, this study demonstrates that the inhibitors the SI technique is based on do not efficiently or specifically resolve fungal and bacterial contributions to respiration. At concentrations that completely inhibited bacterial growth, the bactericide streptomycin had no influence on the SI technique's respiration measurement, and complete inhibition of bacterial growth using oxytetracycline resulted in marginal respiration reductions. The fungicides captan and benomyl severely inhibited non-target bacterial growth. Cycloheximide did not reduce bacterial growth at moderate concentrations, but the cycloheximide respiration reduction was no higher in a soil with more fungal biomass, casting doubt on its ability to discriminate fungal respiration contribution. Conclusions regarding bacteria and fungi based on the SI technique using these inhibitors are thus compromised. The inhibition of glucose-activated respiration by the bactericide bronopol appeared to correlate with bacterial growth inhibition, however. Bronopol, combined with growth-based techniques, could aid development of a new framework to resolve decomposer ecology in soil.}, }
@article {pmid18797956, year = {2009}, author = {Gundel, PE and Garibaldi, LA and Tognetti, PM and Aragón, R and Ghersa, CM and Omacini, M}, title = {Imperfect vertical transmission of the endophyte Neotyphodium in exotic grasses in grasslands of the flooding pampa.}, journal = {Microbial ecology}, volume = {57}, number = {4}, pages = {740-748}, pmid = {18797956}, issn = {1432-184X}, mesh = {Animals ; Argentina ; Cattle ; *Ecosystem ; Floods ; Neotyphodium/*physiology ; Poaceae/*microbiology ; Seeds/microbiology ; *Soil Microbiology ; *Symbiosis ; }, abstract = {Cool-season grasses establish symbioses with vertically transmitted Neotyphodium endophytes widespread in nature. The frequency of endophyte-infected plants in closed populations (i.e., without migrations) depends on both the differential fitness between infected and non-infected plants, and the endophyte-transmission efficiency. Most studies have been focused on the first mechanism ignoring the second. Infection frequency and endophyte transmission from vegetative tissues to seeds were surveyed in two grasses growing in vegetation units that differ in flood and grazing regimes, and soil salinity. Transmission efficiency and infection frequency for tall fescue did not vary significantly and were 0.98 and 1.00, respectively. For Italian ryegrass, transmission efficiency and infection frequency were 0.88 and 0.57 in humid prairies, and 0.96 and 0.96 in the other vegetation units. Only in humid mesophytic meadows, the observed pattern was irrespective of the presence or absence of grazers. Our results suggest that selection forces for endophyte infection are different for both species. Imperfect transmission was only compensated in tall fescue through an increased fitness of infected plants. Interpreting variations of infection frequency only in terms of differential fitness can be misleading, considering that endophyte transmission can be imperfect and variable in nature. Therefore, this study highlights the importance of measuring transmission efficiency.}, }
@article {pmid18797955, year = {2009}, author = {Navarrete, P and Espejo, RT and Romero, J}, title = {Molecular analysis of microbiota along the digestive tract of juvenile Atlantic salmon (Salmo salar L.).}, journal = {Microbial ecology}, volume = {57}, number = {3}, pages = {550-561}, pmid = {18797955}, issn = {1432-184X}, mesh = {Animals ; Colony Count, Microbial ; DNA, Bacterial/genetics ; DNA, Intergenic/genetics ; Ecosystem ; Gastrointestinal Tract/*microbiology ; Polymorphism, Restriction Fragment Length ; Pseudomonas/classification/*genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Salmo salar/*microbiology ; Sequence Analysis, DNA ; Shewanella/classification/*genetics/isolation &amp; purification ; }, abstract = {Dominant bacterial microbiota of the gut of juvenile farmed Atlantic salmon was investigated using a combination of molecular approaches. Bacterial community composition from the stomach, the pyloric caeca, and the intestine was assessed by extracting DNA directly from each gut compartment. Temporal temperature gradient gel electrophoresis (TTGE) analysis of 16S ribosomal DNA (rDNA) amplicons showed very similar bacterial compositions throughout the digestive tract. Band sequencing revealed a narrow diversity of species with a dominance of Pseudomonas in the three compartments. However, cloning revealed more diversity among the Pseudomonas sequences. To confirm these results, we analyzed the bacterial community by amplifying the variable 16S-23S rDNA intergenic spacer region (ITS). Similar ITS profiles were observed among gastrointestinal compartments of salmon, confirming the TTGE results. Moreover, the dominant ITS band at 650 bp, identified as Pseudomonas, was observed in the ITS profile from fish collected in two seasons (July 2003 and 2004). In contrast, aerobic culture analysis revealed Shewanella spp. as the most prevalent isolate. This discrepancy was resolved by evaluating 16S rDNA and ITS polymerase chain reaction amplification efficiency from both Shewanella and Pseudomonas isolates. Very similar efficiencies were observed in the two bacteria. Hence, this discrepancy may be explained by preferential cultivation of Shewanella spp. under the experimental conditions. Also, we included analyses of pelleted feed and the water influent to explore environmental influences on the bacterial composition of the gut microbiota. Overall, these results indicate a homogeneous composition of the bacterial community composition along the gastrointestinal tract of reared juvenile salmon. This community is mainly composed of Pseudomonas spp., which could be derived from water influent and may be selectively associated with salmon in this hatchery.}, }
@article {pmid18793360, year = {2008}, author = {Coco, BJ and Bagg, J and Cross, LJ and Jose, A and Cross, J and Ramage, G}, title = {Mixed Candida albicans and Candida glabrata populations associated with the pathogenesis of denture stomatitis.}, journal = {Oral microbiology and immunology}, volume = {23}, number = {5}, pages = {377-383}, doi = {10.1111/j.1399-302X.2008.00439.x}, pmid = {18793360}, issn = {1399-302X}, mesh = {Aged ; Aged, 80 and over ; Biofilms ; Candida albicans/*isolation &amp; purification ; Candida glabrata/*isolation &amp; purification ; Candidiasis, Oral/classification/*diagnosis ; Cohort Studies ; Colony Count, Microbial ; Denture Cleansers/therapeutic use ; Denture, Complete/microbiology ; Erythema/microbiology ; Humans ; Hyperplasia ; Middle Aged ; Oral Hygiene ; Saccharomyces cerevisiae/isolation &amp; purification ; Smoking ; Stomatitis, Denture/classification/*microbiology ; Toothbrushing ; }, abstract = {INTRODUCTION: Oral yeasts are an important component of the resident microbial ecology of the oral cavity, but they are also associated with various forms of oral candidosis, such as denture stomatitis. Although Candida albicans is the predominant oral fungal pathogen, other species may also play an integral role in pathogenesis. The aim of this study was to examine the mycological ecology in patients with denture stomatitis, using an improved sampling technique, to determine whether species diversity and species quantity were related to oral pathology.<br><br>METHODS: Thirty-seven patients attending the Glasgow Dental Hospital were enrolled in this study following informed consent. A full clinical history was obtained, including details of their oral hygiene practices and the levels of erythema based on Newton's classification scale. Oral rinse, denture sonicate, and swab samples were taken, which were processed for quantitative and qualitative analysis of oral yeasts.<br><br>RESULTS: The proportion of patients with no inflammation or Newton's Types I, II, and III were 31, 33, 25, and 14%, respectively. Denture sonication was a superior sampling procedure, with statistically greater quantities of yeasts isolated using this methodology (P < 0.01). The predominant oral yeasts isolated were C. albicans (75%) and Candida glabrata (30%), which were isolated in higher proportions in patients with the highest grades of inflammation (100 and 80%), and in combination from 80% of these patients.<br><br>CONCLUSIONS: This study has demonstrated that mixed C. albicans and C. glabrata biofilms may play an important role in the pathogenesis associated with severe inflammation in denture wearers.}, }
@article {pmid18793314, year = {2009}, author = {Costa, R and van Aarle, IM and Mendes, R and van Elsas, JD}, title = {Genomics of pyrrolnitrin biosynthetic loci: evidence for conservation and whole-operon mobility within gram-negative bacteria.}, journal = {Environmental microbiology}, volume = {11}, number = {1}, pages = {159-175}, doi = {10.1111/j.1462-2920.2008.01750.x}, pmid = {18793314}, issn = {1462-2920}, mesh = {Biosynthetic Pathways/*genetics ; Burkholderia/*genetics ; Cluster Analysis ; Conserved Sequence ; DNA, Bacterial/genetics ; Evolution, Molecular ; Gene Order ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Molecular Sequence Data ; *Operon ; Phylogeny ; Polymorphism, Genetic ; Pseudomonas/*genetics ; Pyrrolnitrin/*biosynthesis ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Serratia/*genetics ; Synteny ; }, abstract = {Pyrrolnitrin (PRN) is a tryptophan-derived secondary metabolite produced by a narrow range of gram-negative bacteria. The PRN biosynthesis by rhizobacteria presumably has a key role in their life strategies and in the biocontrol of plant diseases. The biosynthetic operon that encodes the pathway that converts tryptophan to PRN is composed of four genes, prnA through D, whose diversity, genomic context and spread over bacterial genomes are poorly understood. Therefore, we launched an endeavour aimed at retrieving, by in vitro and in silico means, diverse bacteria carrying the prnABCD biosynthetic loci in their genomes. Analysis of polymorphisms of the prnD gene sequences revealed a high level of conservation between Burkholderia, Pseudomonas and Serratia spp. derived sequences. Whole-operon- and prnD-based phylogeny resulted in tree topologies that are incongruent with the taxonomic status of the evaluated strains as predicted by 16S rRNA gene phylogeny. The genomic composition of c. 20 kb DNA fragments containing the PRN operon varied in different strains. Highly conserved and distinct transposase-encoding genes surrounding the PRN biosynthetic operons of Burkholderia pseudomallei strains were found. A prnABCD-deprived genomic region in B. pseudomallei strain K96243 contained the same gene composition as, and shared high homology with, the flanking regions of the PRN operon in B. pseudomallei strains 668, 1106a and 1710b. Our results strongly suggest that the PRN biosynthetic operon is mobile. The extent, frequency and promiscuity of this mobility remain to be understood.}, }
@article {pmid18791762, year = {2009}, author = {Hassett, JE and Zak, DR and Blackwood, CB and Pregitzer, KS}, title = {Are basidiomycete laccase gene abundance and composition related to reduced lignolytic activity under elevated atmospheric NO3(-) deposition in a northern hardwood forest?.}, journal = {Microbial ecology}, volume = {57}, number = {4}, pages = {728-739}, pmid = {18791762}, issn = {1432-184X}, mesh = {Basidiomycota/*enzymology/genetics ; DNA, Fungal/analysis ; Ecosystem ; Laccase/*analysis/genetics ; Nitrates/*metabolism ; Soil/analysis ; *Soil Microbiology ; Trees/metabolism/*microbiology ; }, abstract = {Anthropogenic release of biologically available N has increased atmospheric N deposition in forest ecosystems, which may slow decomposition by reducing the lignolytic activity of white-rot fungi. We investigated the potential for atmospheric N deposition to reduce the abundance and alter the composition of lignolytic basidiomycetes in a regional network of four northern hardwood forest stands receiving experimental NO(3)(-) deposition (30 kg NO(3)(-)-N ha(-1) year(-1)) for a decade. To estimate the abundance of basidiomycetes with lignolytic potential, we used PCR primers targeting laccase (polyphenol oxidase) and quantitative fluorescence PCR to estimate gene copy number. Natural variation in laccase gene size permitted use of length heterogeneity PCR to profile basidiomycete community composition across two sampling dates in forest floor and mineral soil. Although past work has identified significant and consistent negative effects of NO(3)(-) deposition on lignolytic enzyme activity, microbial biomass, soil respiration, and decomposition rate, we found no consistent effect of NO(3)(-) deposition on basidiomycete laccase gene abundance or community profile. Rather, laccase abundance under NO(3)(-) deposition was lower (-52%), higher (+223%), or unchanged, depending on stand. Only a single stand exhibited a significant change in basidiomycete laccase gene profile. Basidiomycete laccase genes occurring in mineral soil were a subset of the genes observed in the forest floor. Moreover, significant effects on laccase abundance were confined to the forest floor, suggesting that species composition plays some role in determining how lignolytic basidiomycetes are affected by N deposition. Community profiles differed between July and October sampling dates, and basidiomycete communities sampled in October had lower laccase gene abundance in the forest floor, but higher laccase abundance in mineral soil. Although experimental N deposition significantly suppresses lignolytic activity in these forests, this change is not related to the abundance or community composition of basidiomycete fungi with laccase genes. Understanding the expression of laccases and other lignolytic enzymes by basidiomycete fungi and other lignin-decaying organisms appears to hold promise for explaining the consistent decline in lignolytic activity elicited by experimental N deposition.}, }
@article {pmid18789693, year = {2008}, author = {Hardoim, PR and van Overbeek, LS and Elsas, JD}, title = {Properties of bacterial endophytes and their proposed role in plant growth.}, journal = {Trends in microbiology}, volume = {16}, number = {10}, pages = {463-471}, doi = {10.1016/j.tim.2008.07.008}, pmid = {18789693}, issn = {0966-842X}, mesh = {*Bacterial Physiological Phenomena ; Bacterial Proteins/metabolism ; Ethylenes/metabolism ; *Plant Development ; Plant Growth Regulators/metabolism ; Plant Roots/growth &amp; development/metabolism/microbiology ; Plants/metabolism/*microbiology ; }, abstract = {Bacterial endophytes live inside plants for at least part of their life cycle. Studies of the interaction of endophytes with their host plants and their function within their hosts are important to address the ecological relevance of endophytes. The modulation of ethylene levels in plants by bacterially produced 1-aminocyclopropane-1-carboxylate deaminase is a key trait that enables interference with the physiology of the host plant. Endophytes with this capacity might profit from association with the plant, because colonization is enhanced. In turn, host plants benefit by stress reduction and increased root growth. This mechanism leads to the concept of 'competent' endophytes, defined as endophytes that are equipped with genes important for maintenance of plant-endophyte associations. The ecological role of these endophytes and their relevance for plant growth are discussed here.}, }
@article {pmid18785930, year = {2008}, author = {Guan, LL and Nkrumah, JD and Basarab, JA and Moore, SS}, title = {Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle's feed efficiency.}, journal = {FEMS microbiology letters}, volume = {288}, number = {1}, pages = {85-91}, doi = {10.1111/j.1574-6968.2008.01343.x}, pmid = {18785930}, issn = {0378-1097}, mesh = {*Animal Feed/analysis ; Animals ; Bacteria/classification/*genetics/isolation &amp; purification/metabolism ; Cattle/microbiology/*physiology ; Cluster Analysis ; DNA Fingerprinting ; Digestion ; Eating ; Phenotype ; Phylogeny ; Rumen/*microbiology/physiology ; }, abstract = {Linkage of rumen microbial structure to host phenotypical traits may enhance the understanding of host-microbial interactions in livestock species. This study used culture-independent PCR-denaturing gradient gel electrophoresis (PCR-DGGE) to investigate the microbial profiles in the rumen of cattle differing in feed efficiency. The analysis of detectable bacterial PCR-DGGE profiles showed that the profiles generated from efficient steers clustered together and were clearly separated from those obtained from inefficient steers, indicating that specific bacterial groups may only inhabit in efficient steers. In addition, the bacterial profiles were more likely clustered within a certain breed, suggesting that host genetics may play an important role in rumen microbial structure. The correlations between the concentrations of volatile fatty acids and feed efficiency traits were also observed. Significantly higher concentrations of butyrate (P < 0.001) and valerate (P = 0.006) were detected in the efficient steers. Our results revealed potential associations between the detectable rumen microbiota and its fermentation parameters with the feed efficiency of cattle.}, }
@article {pmid18779355, year = {2008}, author = {Kazimierczak, KA and Rincon, MT and Patterson, AJ and Martin, JC and Young, P and Flint, HJ and Scott, KP}, title = {A new tetracycline efflux gene, tet(40), is located in tandem with tet(O/32/O) in a human gut firmicute bacterium and in metagenomic library clones.}, journal = {Antimicrobial agents and chemotherapy}, volume = {52}, number = {11}, pages = {4001-4009}, pmid = {18779355}, issn = {1098-6596}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics/metabolism ; Carrier Proteins/genetics/metabolism ; Cloning, Molecular ; Clostridium/drug effects/genetics/isolation &amp; purification ; Conjugation, Genetic ; DNA Transposable Elements/genetics ; DNA, Bacterial/genetics ; Digestive System/*microbiology ; Enterococcus faecalis/drug effects/genetics ; Escherichia coli/drug effects/genetics ; *Genes, Bacterial ; Genomic Library ; Humans ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; Tetracycline/*metabolism/pharmacology ; Tetracycline Resistance/*genetics ; }, abstract = {The bacterium Clostridium saccharolyticum K10, isolated from a fecal sample obtained from a healthy donor who had received long-term tetracycline therapy, was found to carry three tetracycline resistance genes: tet(W) and the mosaic tet(O/32/O), both conferring ribosome protection-type resistance, and a novel, closely linked efflux-type resistance gene designated tet(40). tet(40) encodes a predicted membrane-associated protein with 42% amino acid identity to tetA(P). Tetracycline did not accumulate in Escherichia coli cells expressing the Tet(40) efflux protein, and resistance to tetracycline was reduced when cells were incubated with an efflux pump inhibitor. E. coli cells carrying tet(40) had a 50% inhibitory concentration of tetracycline of 60 microg/ml. Analysis of a transconjugant from a mating between donor strain C. saccharolyticum K10 and the recipient human gut commensal bacterium Roseburia inulinivorans suggested that tet(O/32/O) and tet(40) were cotransferred on a mobile element. Sequence analysis of a 37-kb insert identified on the basis of tetracycline resistance from a metagenomic fosmid library again revealed a tandem arrangement of tet(O/32/O) and tet(40), flanked by regions with homology to parts of the VanG operon previously identified in Enterococcus faecalis. At least 10 of the metagenomic inserts that carried tet(O/32/O) also carried tet(40), suggesting that tet(40), although previously undetected, may be an abundant efflux gene.}, }
@article {pmid18778739, year = {2008}, author = {van Elsas, JD and Speksnijder, AJ and van Overbeek, LS}, title = {A procedure for the metagenomics exploration of disease-suppressive soils.}, journal = {Journal of microbiological methods}, volume = {75}, number = {3}, pages = {515-522}, doi = {10.1016/j.mimet.2008.08.004}, pmid = {18778739}, issn = {0167-7012}, mesh = {Antibiosis ; Antifungal Agents/metabolism ; Bacteria/*genetics/isolation &amp; purification/metabolism ; Bacterial Physiological Phenomena ; DNA, Bacterial/genetics/isolation &amp; purification ; *Genetic Techniques ; Genomic Library ; *Genomics ; Plant Diseases/*microbiology ; Rhizoctonia/physiology ; *Soil Microbiology ; }, abstract = {The microbiota of, in particular, disease-suppressive soils contains a wealth of antibiotic biosynthetic loci that are inaccessible by traditional cultivation-based techniques. Hence, we developed a methodology based on soil microbial DNA, which allowed the metagenomics-based unlocking of the relevant genes. Here, a streamlined soil metagenomics protocol is presented. The protocol consists of an optimized method to extract bacterial cells from a Rhizoctonia solani AG3 suppressive loamy sand soil followed by DNA extraction and purification, and the preparation of a clone library in an efficient host/vector system. Methods for the functional and genetic screening of the library for antibiotic production loci are also described. Using the suppressive soil, we thus produced, screened and tested an approximate 15,000-membered metagenomic library of fosmids in an Escherichia coli host. Functional screens, based on dual culturing of clone arrays with R. solani AG3 and Bacillus subtilis 168, were largely negative. Genetic screens, based on hybridizations with soil-generated probes for polyketide biosynthesis, non-ribosomal protein synthesis and gacA, revealed several inserts, of around 40-kb in size, with potential antibiotic production capacity. We present the full sequences of three selected clones. We further examine the challenges that still impinge on the metagenomic exploration of disease-suppressive soil.}, }
@article {pmid18777188, year = {2009}, author = {Videmsek, U and Hagn, A and Suhadolc, M and Radl, V and Knicker, H and Schloter, M and Vodnik, D}, title = {Abundance and diversity of CO2-fixing bacteria in grassland soils close to natural carbon dioxide springs.}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {1-9}, pmid = {18777188}, issn = {1432-184X}, mesh = {Bacteria/genetics/*metabolism ; Carbon Dioxide/*metabolism ; DNA, Bacterial/analysis ; Ecosystem ; Genetic Variation ; Phylogeny ; Ribulose-Bisphosphate Carboxylase/genetics ; Soil/*analysis ; *Soil Microbiology ; }, abstract = {Gaseous conditions at natural CO2 springs (mofettes) affect many processes in these unique ecosystems. While the response of plants to extreme and fluctuating CO2 concentrations ([CO2]) is relatively well documented, little is known on microbial life in mofette soil. Therefore, it was the aim of this study to investigate the abundance and diversity of CO2-fixing bacteria in grassland soils in different distances to a natural carbon dioxide spring. Samples of the same soil type were collected from the Stavesinci mofette, a natural CO2 spring which is known for very pure CO2 emissions, at different distances from the CO2 releasing vents, at locations that clearly differed in soil CO2 efflux (from 12.5 to over 200 micromol CO2 m(-2) s(-1) yearly average). Bulk and rhizospheric soil samples were included into analyses. The microbial response was followed by a molecular analysis of cbbL genes, encoding for the large subunit of RubisCO, a carboxylase which is of crucial importance for C assimilation in chemolitoautotrophic microbes. In all samples analyzed, the "red-like" type of cbbL genes could be detected. In contrast, the "green-like" type of cbbL could not be measured by the applied technique. Surprisingly, a reduction of "red-like" cbbL genes copies was observed in bulk soil and rhizosphere samples from the sites with the highest CO2 concentrations. Furthermore, the diversity pattern of "red-like" cbbL genes changed depending on the CO(2) regime. This indicates that only a part of the autotrophic CO2-fixing microbes could adapt to the very high CO2 concentrations and adverse life conditions that are governed by mofette gaseous regime.}, }
@article {pmid18777187, year = {2009}, author = {Freese, E and Rütters, H and Köster, J and Rullkötter, J and Sass, H}, title = {Gammaproteobacteria as a possible source of eicosapentaenoic acid in anoxic intertidal sediments.}, journal = {Microbial ecology}, volume = {57}, number = {3}, pages = {444-454}, pmid = {18777187}, issn = {1432-184X}, mesh = {Cardiolipins/biosynthesis ; Eicosapentaenoic Acid/*biosynthesis ; Gammaproteobacteria/genetics/isolation &amp; purification/*metabolism ; Geologic Sediments/*microbiology ; Phosphatidylethanolamines/biosynthesis ; Phosphatidylglycerols/biosynthesis ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Temperature ; }, abstract = {Eicosapentaenoic acid (EPA; n-20:5omega3) was found to be a constituent of phospholipids in three mesophilic strains of Gammaproteobacteria, which were isolated from anoxic most probable number series prepared with sediments from an intertidal flat of the German North Sea coast. Their partial 16S rRNA gene sequences identified the isolates as close relatives of Shewanella colwelliana, Vibrio splendidus, and Photobacterium lipolyticum. So far, eicosapentaenoic acid has mainly been reported to occur in eukaryotes and some piezophilic or psychrophilic bacteria. With decreasing temperature, relative contents of EPA (up to 14% of total fatty acids) increased in all strains. Additionally, Shewanella and Vibrio spp. showed a significant increase in monounsaturated fatty acids with lower growth temperature. Analysis of the phospholipid compositions revealed that EPA was present in all three major phospholipid types, namely, phosphatidyl glycerol (PG), cardiolipin and phosphatidyl ethanolamine (PE). However, EPA was enriched in PG and cardiolipin relative to PE. In the tidal flat sediments from which the isolates were obtained, substantial amounts of EPA-containing PG were detected, whereas other typical microeukaryotic phospholipids-being also a possible source of EPA-were abundant at the sediment surface but were present in clearly lower amounts in the anoxic layers beneath 5 cm depth. Therefore, the EPA-containing PG species in the deeper layers in these sediments may indicate the presence of Gammaproteobacteria closely related to the isolates. These bacteria appear to be an important source of EPA in buried, anoxic sediments beneath the layers harboring significant populations of benthic eukaryotes.}, }
@article {pmid18777048, year = {2009}, author = {Yan, Q and Yu, Y and Feng, W and Pan, G and Chen, H and Chen, J and Yang, B and Li, X and Zhang, X}, title = {Plankton community succession in artificial systems subjected to cyanobacterial blooms removal using chitosan-modified soils.}, journal = {Microbial ecology}, volume = {58}, number = {1}, pages = {47-55}, pmid = {18777048}, issn = {1432-184X}, mesh = {*Chitosan ; Cyanobacteria/genetics/*growth &amp; development ; DNA Fingerprinting ; Ecosystem ; Electrophoresis, Polyacrylamide Gel ; *Eutrophication ; Phosphorus/analysis ; Plankton/genetics/*growth &amp; development ; RNA, Bacterial/genetics ; Soil ; *Water Microbiology ; }, abstract = {Using artificial systems to simulate natural lake environments with cyanobacterial blooms, we investigated plankton community succession by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprinting and morphological method. With this approach, we explored potential ecological effects of a newly developed cyanobacterial blooms removal method using chitosan-modified soils. Results of PCR-DGGE and morphological identification showed that plankton communities in the four test systems were nearly identical at the beginning of the experiment. After applying the newly developed and standard removal methods, there was a shift in community composition, but neither chemical conditions nor plankton succession were significantly affected by the cyanobacteria removal process. The planted Vallisneria natans successfully recovered after cyanobacteria removal, whereas that in the box without removal process did not. Additionally, canonical correspondence analysis indicated that other than for zooplankton abundance, total phosphorus was the most important environmental predictor of planktonic composition. The present study and others suggest that dealing with cyanobacteria removal using chitosan-modified soils can play an important role in controlling cyanobacterial blooms in eutrophicated freshwater systems.}, }
@article {pmid18774191, year = {2008}, author = {van Elsas, JD and Costa, R and Jansson, J and Sjöling, S and Bailey, M and Nalin, R and Vogel, TM and van Overbeek, L}, title = {The metagenomics of disease-suppressive soils - experiences from the METACONTROL project.}, journal = {Trends in biotechnology}, volume = {26}, number = {11}, pages = {591-601}, doi = {10.1016/j.tibtech.2008.07.004}, pmid = {18774191}, issn = {0167-7799}, mesh = {*Biotechnology ; DNA/analysis/chemistry ; *Gene Library ; Genetic Vectors ; *Genomics ; Microbiological Techniques ; Phylogeny ; *Soil Microbiology ; }, abstract = {Soil teems with microbial genetic information that can be exploited for biotechnological innovation. Because only a fraction of the soil microbiota is cultivable, our ability to unlock this genetic complement has been hampered. Recently developed molecular tools, which make it possible to utilize genomic DNA from soil, can bypass cultivation and provide information on the collective soil metagenome with the aim to explore genes that encode functions of key interest to biotechnology. The metagenome of disease-suppressive soils is of particular interest given the expected prevalence of antibiotic biosynthetic clusters. However, owing to the complexity of soil microbial communities, deciphering this key genetic information is challenging. Here, we examine crucial issues and challenges that so far have hindered the metagenomic exploration of soil by drawing on experience from a trans-European project on disease-suppressive soils denoted METACONTROL.}, }
@article {pmid18773234, year = {2009}, author = {Bonjoch, X and Blanch, AR}, title = {Resistance of faecal coliforms and enterococci populations in sludge and biosolids to different hygienisation treatments.}, journal = {Microbial ecology}, volume = {57}, number = {3}, pages = {478-483}, pmid = {18773234}, issn = {1432-184X}, mesh = {Anaerobiosis ; Bioreactors ; Cluster Analysis ; Colony Count, Microbial ; Enterobacteriaceae/growth &amp; development/*physiology ; Enterococcus/growth &amp; development/*physiology ; Feces/microbiology ; Hot Temperature ; Sewage/*microbiology ; Waste Disposal, Fluid/*methods ; }, abstract = {The composition of the most abundant facultative anaerobic bacteria populations [faecal coliforms (FC) and enterococci (ENT)] in sludge can be modified after different treatments. These involve the disposal or reuse of sludge and include: anaerobic digesters, incineration, composting, pasteurization and lime treatments. In this study, three treatment types (mesophilic anaerobic digestion, composting and pasteurization) were compared in terms of their ability to reduce both bacterial populations. The diversity and any changes in composition of main phenotypic groups for both populations were also analyzed. Mesophilic anaerobic digestion (MAD) was carried out at 35 degrees C for 20 days. Digested sludge was then dehydrated by centrifugation at 2,500 rpm. Composting (COM) was performed at 55 degrees C with windrow phases. Pasteurization was assayed at 60 degrees C for 90 min (P60), at 80 degrees C for 60 min (P80). A 1-1.5 log unit reduction was observed for FC, and 1 log unit reduction was noted for ENT by MAD treatment. In composting, this reduction proved higher for FC than for ENT (6 log and 3-4 log units, respectively). Optimal pasteurization was obtained at 80 degrees C for 60 min, resulting in a 5 log unit reduction for FC and a 2 log unit reduction for ENT. High diversity indices (Di) for both bacterial populations were detected both before and after implementation of the different treatments. Analyses of the population's similarity provided that FC were diverse both before and after COM, P60 and P80 treatments. However, no differences were observed on the composition of ENT populations after the different treatments assayed.}, }
@article {pmid18772943, year = {2008}, author = {Rooney, DC and Clipson, N}, title = {Impact of sheep urine deposition and plant species on ammonia-oxidizing bacteria in upland grassland soil.}, journal = {Canadian journal of microbiology}, volume = {54}, number = {9}, pages = {791-796}, doi = {10.1139/w08-065}, pmid = {18772943}, issn = {0008-4166}, mesh = {Ammonia/*metabolism ; Animals ; Bacteria/genetics/*isolation &amp; purification/metabolism ; *Ecosystem ; Poaceae/*microbiology ; Sheep ; *Soil Microbiology ; Urine/*chemistry ; }, abstract = {The effects of different concentrations of synthetic sheep urine and plant species on ammonia-oxidizing bacterial (AOB) communities in an upland grassland soil were investigated using a microcosm approach. Plant species characteristic of unimproved and improved agricultural pastures (Agrostis capillaris and Lolium perenne, respectively) were planted in soil microcosms, and different levels of synthetic sheep urine were applied, with harvests 10 and 50 days following urine application. Shifts in the community structure of the AOB were investigated using terminal restriction fragment length polymorphism of amoA amplicons. Species richness and diversity were significantly altered by synthetic sheep urine addition and time depending on plant species type. Principal coordinate analysis revealed that AOB community structure was largely dependent on interactions between sheep urine deposition, plant species, and time after urine application, while significant changes in AOB structure were also revealed by similarity percentage analysis. The results of this study suggested that high levels of sheep urine, combined with floristic changes that are characteristic of agricultural intensification, can contribute to temporal and spatial changes in the structure of key bacterial communities in upland grassland soil. Changes in AOB community structure could potentially affect important soil processes, such as nitrification, with subsequent implications for nutrient cycling in agricultural systems.}, }
@article {pmid18769457, year = {2009}, author = {Hwang, C and Wu, W and Gentry, TJ and Carley, J and Corbin, GA and Carroll, SL and Watson, DB and Jardine, PM and Zhou, J and Criddle, CS and Fields, MW}, title = {Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths.}, journal = {The ISME journal}, volume = {3}, number = {1}, pages = {47-64}, doi = {10.1038/ismej.2008.77}, pmid = {18769457}, issn = {1751-7370}, mesh = {Bacteria/*classification/*isolation &amp; purification/metabolism ; *Biodegradation, Environmental ; *Biodiversity ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Ethanol/metabolism ; Genes, rRNA ; Metals/metabolism ; Oxidation-Reduction ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Sulfates/metabolism ; Uranium/*metabolism ; }, abstract = {Bacterial community succession was investigated in a field-scale subsurface reactor formed by a series of wells that received weekly ethanol additions to re-circulating groundwater. Ethanol additions stimulated denitrification, metal reduction, sulfate reduction and U(VI) reduction to sparingly soluble U(IV). Clone libraries of SSU rRNA gene sequences from groundwater samples enabled tracking of spatial and temporal changes over a 1.5-year period. Analyses showed that the communities changed in a manner consistent with geochemical variations that occurred along temporal and spatial scales. Canonical correspondence analysis revealed that the levels of nitrate, uranium, sulfide, sulfate and ethanol were strongly correlated with particular bacterial populations. As sulfate and U(VI) levels declined, sequences representative of sulfate reducers and metal reducers were detected at high levels. Ultimately, sequences associated with sulfate-reducing populations predominated, and sulfate levels declined as U(VI) remained at low levels. When engineering controls were compared with the population variation through canonical ordination, changes could be related to dissolved oxygen control and ethanol addition. The data also indicated that the indigenous populations responded differently to stimulation for bioreduction; however, the two biostimulated communities became more similar after different transitions in an idiosyncratic manner. The strong associations between particular environmental variables and certain populations provide insight into the establishment of practical and successful remediation strategies in radionuclide-contaminated environments with respect to engineering controls and microbial ecology.}, }
@article {pmid18766400, year = {2009}, author = {Alguacil, MM and Roldán, A and Torres, MP}, title = {Complexity of semiarid gypsophilous shrub communities mediates the AMF biodiversity at the plant species level.}, journal = {Microbial ecology}, volume = {57}, number = {4}, pages = {718-727}, pmid = {18766400}, issn = {1432-184X}, mesh = {*Biodiversity ; Caryophyllaceae/*microbiology ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; Glomeromycota/classification/*genetics ; Mycorrhizae/classification/*genetics ; Phylogeny ; Plant Roots/microbiology ; Polymorphism, Restriction Fragment Length ; Soil/analysis ; *Soil Microbiology ; Species Specificity ; Spores, Fungal/classification/genetics ; }, abstract = {The community composition of arbuscular mycorrhizal fungi (AMF) was analyzed in roots of Gypsophila struthium growing in gypsum soils under semiarid conditions. In order to investigate the effect of plant community degradation on the AMF biodiversity at the single species level, on the basis of the plant community complexity level, we selected four areas affected by degradation and shrub species spatial heterogeneity. The AM fungal community colonizing G. struthium was investigated from the morphological and molecular points of view. All plants were well colonized and showed a high level of infective AM propagules. Roots were analyzed by polymerase chain reaction, restriction fragment length polymorphism screening, and sequence analyses of the ribosomal DNA small subunit region. Four AM fungal types were identified and clustered into the AM fungal family: Glomeraceae, Glomus being the only taxon present. One fungal type was present in all the selected areas. Two fungal types are distinct from any previously published sequences and could be specific to gypsum soils. The chemical-physical properties of the soil were not correlated with the AMF diversity in roots. Our data show vegetation cover complexity-dependent differences in the AM fungal community composition.}, }
@article {pmid18762854, year = {2009}, author = {Sommaruga, R and Chen, Y and Liu, Z}, title = {Multiple strategies of bloom-forming Microcystis to minimize damage by solar ultraviolet radiation in surface waters.}, journal = {Microbial ecology}, volume = {57}, number = {4}, pages = {667-674}, pmid = {18762854}, issn = {1432-184X}, mesh = {Adaptation, Physiological ; Amino Acids/metabolism ; Biomass ; Chlorophyll/analysis ; Chlorophyll A ; *Eutrophication ; Fresh Water/microbiology ; Hexuronic Acids/analysis ; Microcystis/*metabolism/*radiation effects ; Phytoplankton/metabolism/radiation effects ; Ultraviolet Rays/*adverse effects ; *Water Microbiology ; }, abstract = {The occurrence of bloom-forming cyanobacteria is one of the most obvious sign of eutrophication in freshwaters. Although in eutrophic lakes water transparency in the ultraviolet (UV) region is strongly reduced, bloom-forming cyanobacteria are exposed to high solar UV radiation at the surface. Here, we show that, in a natural phytoplankton community from a very eutrophic lake, Microcystis synthesizes UV sunscreen compounds identified as mycosporine-like amino acids (MAAs). The biomass-specific MAA concentration was significantly correlated with the occurrence of Microcystis but not with other algal groups, even though they were dominant in terms of biomass. Based on a photo-optical model, we estimated that the maximum MAA concentration per cell observed (2.5% dry weight) will confer only approximately 40% of internal screening to a single layer of Microcystis cells. Thus, the formation of a colony with several layers of cells is important to afford an efficient UV screening by internal self-shading. Overall, we propose that Microcystis uses a combination of photoprotective strategies (MAAs, carotenoids) to cope with high solar UV radiation at the water surface. These strategies include also the screening of UV radiation by D-galacturonic acid, one of the main chemical components of the slime layer in Microcystis.}, }
@article {pmid18762853, year = {2009}, author = {Islam, SM and Hong, SJ and Cho, KM and Math, RK and Heo, JY and Lee, YH and Lee, KS and Yun, HD}, title = {Bacterial diversity and structural changes of oyster shell during 1-year storage.}, journal = {Microbial ecology}, volume = {57}, number = {2}, pages = {221-228}, pmid = {18762853}, issn = {0095-3628}, mesh = {Animals ; Bacteria/classification/*genetics/isolation &amp; purification ; Biodegradation, Environmental ; *Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; *Environmental Microbiology ; *Hot Temperature ; Ostreidae/ultrastructure ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {We examined the biodiversity of bacteria associated with oyster-shell waste during a 1-year storage period using 16S ribosomal DNA analysis. Temperature variation and structural changes of oyster shell were observed during storage. Initial and final temperatures were at 16-17 degrees C, but a high temperature of about 60 degrees C was recorded after approximately 6 months of storage. The crystal structure and nanograin of the oyster shell surface were sharp and large in size initially and became gradually blunter and smaller over time. Phylogenetic analysis revealed that Firmicutes were dominant in the oyster-shell waste initially, during the high-temperature stage, and after 1 year of storage (making up >65% of the biodiversity at all three sampling times). Bacillus licheniformis was presumed as the predominate Firmicutes present. These bacteria are likely to have important roles in the biodegradation of oyster shell.}, }
@article {pmid18762628, year = {2008}, author = {Stoodley, P and Wefel, J and Gieseke, A and Debeer, D and von Ohle, C}, title = {Biofilm plaque and hydrodynamic effects on mass transfer, fluoride delivery and caries.}, journal = {Journal of the American Dental Association (1939)}, volume = {139}, number = {9}, pages = {1182-1190}, doi = {10.14219/jada.archive.2008.0333}, pmid = {18762628}, issn = {0002-8177}, mesh = {*Biofilms/drug effects ; Cariostatic Agents/*administration &amp; dosage ; Dental Caries/*microbiology ; Dental Plaque/*microbiology ; Ecology ; Fluorides/*administration &amp; dosage ; Humans ; Rheology ; Streptococcus mutans/drug effects/physiology ; }, abstract = {BACKGROUND: The biofilm concept of dental plaque now is widely accepted in the dental clinic, particularly with respect to its importance to oral hygiene. A number of reviews have focused on the microbial ecology of biofilm with regard to oral health; however, there has been less focus on how the interaction of biofilms and hydrodynamics with mass transfer (the movement of molecules and particulates) and physiological processes may relate to caries.<br><br>TYPES OF STUDIES REVIEWED: The authors reviewed reports in the microbiology and dental literature addressing microbiological, engineering and clinical aspects of biofilms with respect to mass transport and microbial physiology, with an emphasis on fluoride ions (F(-)).<br><br>CONCLUSIONS: and Practical Implications. These data illustrate how dental plaque biofilms may affect the delivery of cariogenic agents, such as sucrose, or anticariogenic agents, such as F(-), into and out of the biofilm, with subsequent consequences for the development of physio-chemical microenvironments at the tooth surface. Increasing the flow rate in an overlying fluid (such as saliva or mouthrinse) increases transport from the fluid into and through biofilms. Increasing the delivery of anticariogenic agents such as F(-) into the plaque biofilm, by generating strong fluid flows, may be a useful strategy for enhancing the anticaries effects of F(-) in areas of the mouth where complete biofilm removal is not possible with routine daily cleaning techniques.}, }
@article {pmid18758846, year = {2009}, author = {Navarro, JB and Moser, DP and Flores, A and Ross, C and Rosen, MR and Dong, H and Zhang, G and Hedlund, BP}, title = {Bacterial succession within an ephemeral hypereutrophic Mojave Desert playa Lake.}, journal = {Microbial ecology}, volume = {57}, number = {2}, pages = {307-320}, pmid = {18758846}, issn = {0095-3628}, support = {P20 RR016464/RR/NCRR NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; California ; Colony Count, Microbial ; DNA, Bacterial/genetics ; *Desert Climate ; Ecosystem ; Gene Library ; Geologic Sediments/chemistry/microbiology ; Phylogeny ; Plankton/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Seasons ; *Water Microbiology ; }, abstract = {Ephemerally wet playas are conspicuous features of arid landscapes worldwide; however, they have not been well studied as habitats for microorganisms. We tracked the geochemistry and microbial community in Silver Lake playa, California, over one flooding/desiccation cycle following the unusually wet winter of 2004-2005. Over the course of the study, total dissolved solids increased by approximately 10-fold and pH increased by nearly one unit. As the lake contracted and temperatures increased over the summer, a moderately dense planktonic population of approximately 1x10(6) cells ml(-1) of culturable heterotrophs was replaced by a dense population of more than 1x10(9) cells ml(-1), which appears to be the highest concentration of culturable planktonic heterotrophs reported in any natural aquatic ecosystem. This correlated with a dramatic depletion of nitrate as well as changes in the microbial community, as assessed by small subunit ribosomal RNA gene sequencing of bacterial isolates and uncultivated clones. Isolates from the early-phase flooded playa were primarily Actinobacteria, Firmicutes, and Bacteroidetes, yet clone libraries were dominated by Betaproteobacteria and yet uncultivated Actinobacteria. Isolates from the late-flooded phase ecosystem were predominantly Proteobacteria, particularly alkalitolerant isolates of Rhodobaca, Porphyrobacter, Hydrogenophaga, Alishwenella, and relatives of Thauera; however, clone libraries were composed almost entirely of Synechococcus (Cyanobacteria). A sample taken after the playa surface was completely desiccated contained diverse culturable Actinobacteria typically isolated from soils. In total, 205 isolates and 166 clones represented 82 and 44 species-level groups, respectively, including a wide diversity of Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Gemmatimonadetes, Acidobacteria, and Cyanobacteria.}, }
@article {pmid18758845, year = {2009}, author = {Gibson, CM and Hunter, MS}, title = {Inherited fungal and bacterial endosymbionts of a parasitic wasp and its cockroach host.}, journal = {Microbial ecology}, volume = {57}, number = {3}, pages = {542-549}, pmid = {18758845}, issn = {1432-184X}, mesh = {Animals ; Bacteria/classification/*genetics/isolation &amp; purification ; Bayes Theorem ; *Biological Evolution ; Cockroaches/*microbiology/parasitology ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; Fungi/classification/*genetics/isolation &amp; purification ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; *Symbiosis ; Wasps/*microbiology ; }, abstract = {Bacterial endosymbionts of insects are increasingly being recognized as common, diverse, and integral to the biology of their hosts. Inherited fungal symbionts have been largely overlooked, however, even though insect guts appear to be a key habitat for an incredible array of fungal diversity. Like bacteria, fungal symbionts also likely play important roles in the ecology and evolution of their insect associates. The objective of this study was to lay the foundations for understanding the roles of the vertically transmitted fungal and bacterial associates of both the brownbanded cockroach, Supella longipalpa, and its parasitic wasp, Comperia merceti. We used culture-dependent and culture-independent molecular methods and phylogenetic analyses in order to identify the symbionts. Two fungal associates of brownbanded cockroaches were found. To our knowledge, this is the first record of vertically transmitted fungal symbionts in the order Blattaria. The wasp was found to house a close relative of one of the cockroach fungi but no bacterial symbionts. Finally, the brownbanded cockroaches also harbored three lineages of bacterial symbionts: Blattabacterium and two lineages of Wolbachia, indicating the number of vertically transmitted symbionts in this insect may be as many as five.}, }
@article {pmid18758844, year = {2009}, author = {Lauber, CL and Sinsabaugh, RL and Zak, DR}, title = {Laccase gene composition and relative abundance in oak forest soil is not affected by short-term nitrogen fertilization.}, journal = {Microbial ecology}, volume = {57}, number = {1}, pages = {50-57}, pmid = {18758844}, issn = {0095-3628}, mesh = {Basidiomycota/*enzymology/genetics/growth &amp; development ; DNA, Ribosomal Spacer/analysis ; Fertilizers ; Laccase/*genetics/metabolism ; Nitrogen/*metabolism ; Polymerase Chain Reaction/methods ; Quercus/*growth &amp; development ; Sequence Analysis, DNA ; Soil/*analysis ; Soil Microbiology ; *Trees ; }, abstract = {Anthropogenic nitrogen (N) deposition affects a wide range of soil processes including phenol oxidase (PO) activity and soil organic matter dynamics. Depression of phenol oxidase activity in response to N saturation is believed to be mediated by the activity of white-rot basidiomycetes, whose production of extracellular oxidative enzymes can be limited by high N availability. We examined the effect of short-term N deposition on basidiomycete laccase gene diversity and relative abundance in temperate oak forest soil in which significant decreases in phenol oxidase and increased SOM have been recorded in response to experimental N deposition. UniFrac was used to compare the composition of laccase genes between three control- and three nitrogen-fertilized (80 kg(-1) ha(-1) per year) oak forest soils. The relative abundance of laccase genes was determined from qPCR analysis of laccase and basidiomycete ITS gene abundances. Our results indicate that there was no significant shift in the composition of laccase genes between control- and N-fertilized soils, nor was there a significant change in the relative abundance of laccase genes. These data suggest that N deposition effects on mineral soil PO activity do not result from changes in laccase gene diversity of white-rot basidiomycetes but are likely the result of altered microbial abundance or expression in this ecosystem type. Furthermore, laccase gene composition may be tied to factors that structure microbial communities in general, as soil laccase gene communities are more similar to other forest soils than with the corresponding litter.}, }
@article {pmid18757794, year = {2008}, author = {Justé, A and Lievens, B and Frans, I and Marsh, TL and Klingeberg, M and Michiels, CW and Willems, KA}, title = {Genetic and physiological diversity of Tetragenococcus halophilus strains isolated from sugar- and salt-rich environments.}, journal = {Microbiology (Reading, England)}, volume = {154}, number = {Pt 9}, pages = {2600-2610}, doi = {10.1099/mic.0.2008/018168-0}, pmid = {18757794}, issn = {1350-0872}, mesh = {Beta vulgaris/microbiology ; DNA Fingerprinting ; DNA, Bacterial/genetics ; *Food Microbiology ; Genes, Bacterial ; Genes, rRNA ; Gram-Positive Cocci/*genetics/*metabolism ; Nucleic Acid Hybridization ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Random Amplified Polymorphic DNA Technique ; Sodium Chloride/*metabolism ; Sucrose/*metabolism ; }, abstract = {Tetragenococcus halophilus is known to flourish in extreme salt environments. Recently, this halophilic bacterium also appeared as the dominant microflora during storage of sugar thick juice, an intermediate product of beet sugar production. Although T. halophilus can cause degradation of thick juice, dominance of this bacterium does not always result in degradation. In this study T. halophilus strains from high-salt and high-sugar environments, and in particular from degraded and non-degraded thick juice, were compared in detail. Both physiological and genetic characterization using Biolog, repetitive PCR fingerprinting (rep-PCR) and random amplified polymorphic DNA (RAPD) technology, revealed clear differences between T. halophilus strains isolated from salt- and sugar-rich environments. However, no strain pattern could be specifically and systematically associated with degraded or non-degraded thick juice. Remarkably, halophilic T. halophilus strains were not able to grow in sugar thick juice. Irrespective of the differences between the strains from high-salt or high-sugar environments, DNA-DNA hybridization grouped all strains within the species T. halophilus, except one isolate from sugar thick juice that showed different physiological and genetic characteristics, and that may represent a new species of Tetragenococcus.}, }
@article {pmid18757134, year = {2009}, author = {Khelifi, E and Ayed, L and Bouallagui, H and Touhami, Y and Hamdi, M}, title = {Effect of nitrogen and carbon sources on Indigo and Congo red decolourization by Aspergillus alliaceus strain 121C.}, journal = {Journal of hazardous materials}, volume = {163}, number = {2-3}, pages = {1056-1062}, doi = {10.1016/j.jhazmat.2008.07.060}, pmid = {18757134}, issn = {1873-3336}, mesh = {Aspergillus/enzymology/*metabolism ; *Biodegradation, Environmental ; Carbon/metabolism/pharmacology ; Coloring Agents/metabolism ; Congo Red/*metabolism ; Indigo Carmine ; Indoles/*metabolism ; Laccase ; Nitrogen/metabolism/pharmacology ; Peroxidases ; }, abstract = {The decolourizing ability of Aspergillus alliaceus 121C was investigated on solid medium. The effects of nitrogen (N), carbon (C) sources and supplements on the decolourization of Indigo and Congo red dyes were studied. It has been shown that both the nature and the quantity of available N- and C-sources exert an influence on growth and decolourization. For the six N-sources (NH(4)Cl, Diammonium Tartrate, urea, malt extract, peptone and yeast extract) tested for Congo red decolourization, 8mM yeast extract provided the higher decolourized zone diameter (80 mm) and colony diameter (80 mm). 12 mM urea provided the higher decolourized zone diameter (76+/-2mm) and colony diameter (80 mm) for Indigo decolourization. For the C-sources tested (glucose, starch, glycerol and lactose), above 12.5mM of glucose and 62.5mM of starch provided the higher decolourized zones diameters of 80 mm and 77+/-3mm for Indigo and Congo red, respectively. When the fungi was grown in liquid medium containing optimum carbon and nitrogen sources supplemented with oak sawdust and wheat bran, more than 98.6% and 98% of colour removal are obtained for Indigo and Congo red dyes, respectively. The detection of ligninolytic enzymes proved that laccase and lignine-peroxidase (LiP) are the two enzymes responsible of the decolourization of the two dyes.}, }
@article {pmid18754782, year = {2008}, author = {Llirós, M and Casamayor, EO and Borrego, C}, title = {High archaeal richness in the water column of a freshwater sulfurous karstic lake along an interannual study.}, journal = {FEMS microbiology ecology}, volume = {66}, number = {2}, pages = {331-342}, doi = {10.1111/j.1574-6941.2008.00583.x}, pmid = {18754782}, issn = {0168-6496}, mesh = {*Crenarchaeota/classification/genetics/isolation &amp; purification ; DNA Fingerprinting/methods ; DNA, Archaeal/analysis/isolation &amp; purification ; *Ecosystem ; *Euryarchaeota/classification/genetics/isolation &amp; purification ; Fresh Water/chemistry/*microbiology ; Molecular Sequence Data ; Oxygen/analysis ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; Sulfur/analysis ; }, abstract = {We surveyed the archaeal assemblage in a stratified sulfurous lake (Lake Vilar, Banyoles, Spain) over 5 consecutive years to detect potential seasonal and interannual trends in the free-living planktonic Archaea composition. The combination of different primer pairs and nested PCR steps revealed an unexpectedly rich archaeal community. Overall, 140 samples were analyzed, yielding 169 different 16S rRNA gene sequences spread over 14 Crenarchaeota (109 sequences) and six Euryarchaeota phylogenetic clusters. Most of the Crenarchaeota (98% of the total crenarchaeotal sequences) affiliated within the Miscellaneous Crenarchaeota Group (MCG) and were related to both marine and freshwater phylotypes. Euryarchaeota mainly grouped within the Deep Hydrothermal Vent Euryarchaeota (DHVE) cluster (80% of the euryarchaeotal sequences) and the remaining 20% distributed into three less abundant taxa, most of them composed of soil and sediment clones. The largest fraction of phylotypes from the two archaeal kingdoms (79% of the Crenarchaeota and 54% of the Euryarchaeota) was retrieved from the anoxic hypolimnion, indicating that these cold and sulfide-rich waters constitute an unexplored source of archaeal richness. The taxon rank-frequency distribution showed two abundant taxa (MCG and DHVE) that persisted in the water column through seasons, plus several rare ones that were only detected occasionally. Differences in richness distribution and seasonality were observed, but no clear correlations were obtained when multivariate statistical analyses were carried out.}, }
@article {pmid18752018, year = {2009}, author = {Cappitelli, F and Abbruscato, P and Foladori, P and Zanardini, E and Ranalli, G and Principi, P and Villa, F and Polo, A and Sorlini, C}, title = {Detection and elimination of cyanobacteria from frescoes: the case of the St. Brizio Chapel (Orvieto Cathedral, Italy).}, journal = {Microbial ecology}, volume = {57}, number = {4}, pages = {633-639}, pmid = {18752018}, issn = {1432-184X}, mesh = {Benzalkonium Compounds/*pharmacology ; Chlorophyll/analysis ; Culture Media ; Cyanobacteria/chemistry/drug effects/genetics/*isolation &amp; purification ; DNA, Bacterial/analysis ; Disinfectants/*pharmacology ; Flow Cytometry ; Italy ; Microscopy, Electron ; Microscopy, Fluorescence ; Molecular Sequence Data ; *Paintings ; Phycoerythrin/analysis ; }, abstract = {A rosy discoloration partly masking the Luca Signorelli frescoes in St. Brizio Chapel (Orvieto Cathedral, Italy) for many years proved to be a biological alteration, so the present research focused on investigating biodeteriogens and selecting an appropriate biocide to treat them. Optical epifluorescence and electronic microscopic observations of the rosy powder revealed a prevalent autofluorescent coccoid form with a diameter bigger than 5 microm. Chlorophylls a and b were extracted, suggesting the presence of cyanobacteria, a thesis subsequently confirmed by flow cytometry. Cultural media were inoculated with the rosy powder, and microorganisms grew as a green patina in phototrophic conditions and as a rosy patina when organic compounds were added to the mineral medium. The rosy discoloration was most likely caused by the presence of phycoerythrin. The sequencing of the cyanobacteria-specific polymerase chain reaction (PCR)-DGGE bands matched, with a similarity percentage >94, uncultured cyanobacteria, and the sequences were deposited in the GenBank under EU874241, EU874242, EU874243, EU874244, EU874245, EU874246, and EU874247. Finally, the efficiency of the two biocides Neo Desogen and Metatin 5810-101, both based on benzalkonium chloride, was evaluated using adenosine triphosphate measurements and PCR-based detection of cyanobacteria. Metatin, used in situ at 2% of the trade product, proved to be the better biocide, no cyanobacteria being detected after the Metatin treatment.}, }
@article {pmid18725730, year = {2008}, author = {Ren, Z and Steinberg, LM and Regan, JM}, title = {Electricity production and microbial biofilm characterization in cellulose-fed microbial fuel cells.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {58}, number = {3}, pages = {617-622}, doi = {10.2166/wst.2008.431}, pmid = {18725730}, issn = {0273-1223}, mesh = {*Bioelectric Energy Sources ; *Biofilms ; Cellulose/*metabolism ; Clostridium cellulolyticum/genetics/metabolism/physiology ; *Electricity ; Electrochemistry ; Geobacter/genetics/metabolism/physiology ; In Situ Hybridization, Fluorescence ; Polymerase Chain Reaction ; }, abstract = {Converting biodegradable materials into electricity, microbial fuel cells (MFCs) present a promising technology for renewable energy production in specific applications. Unlike typical soluble substrates that have been used as electron donors in MFC studies, cellulose is unique because it requires a microbial consortium that can metabolize both an insoluble electron donor (cellulose) and electron acceptor (electrode). In this study, electricity generation and the microbial ecology of cellulose-fed MFCs were analyzed using a defined co-culture of Clostridium cellulolyticum and Geobacter sulfurreducens. Fluorescent in situ hybridization and quantitative PCR showed that when particulate MN301 cellulose was used as sole substrate, most Clostridium cells were found adhered to cellulose particles in suspension, while most Geobacter cells were attached to the electrode. By comparison, both bacteria resided in suspension and biofilm samples when soluble carboxymethyl cellulose was used. This distinct function-related distribution of the bacteria suggests an opportunity to optimize reactor operation by settling cellulose and decanting supernatant to extend cellulose hydrolysis and improve cellulose-electricity conversion.}, }
@article {pmid18725251, year = {2008}, author = {Coucheney, E and Daniell, TJ and Chenu, C and Nunan, N}, title = {Gas chromatographic metabolic profiling: a sensitive tool for functional microbial ecology.}, journal = {Journal of microbiological methods}, volume = {75}, number = {3}, pages = {491-500}, doi = {10.1016/j.mimet.2008.07.029}, pmid = {18725251}, issn = {0167-7012}, mesh = {Bacteria/chemistry/isolation &amp; purification/*metabolism ; Chromatography, Gas/*methods ; *Ecology ; *Metabolome ; *Soil Microbiology ; }, abstract = {Microbial metabolomics, which consists of a non-targeted analysis of the metabolites released from ('exometabolome') or existing in ('endometabolome') a cell has mostly been used to study the metabolism of particular microbes. Metabolomes also represent a picture of microbial activity and we suggest that the exometabolome may also contain pertinent information for studying microbial interaction networks. Gas chromatography coupled to mass spectrometry is the most commonly used technique in metabolomics studies. It allows a wide range of metabolites to be detected but requires the derivatisation of compounds prior to detection. This type of non-targeted analysis can introduce biases to the detection and quantification of the different metabolites, particularly at the extraction and derivatisation steps. The aims of this study, therefore, were to quantify the sources of variability and to test the sensitivity of the GC metabolic profiling approach to small environmental changes such as shifts in temperature. The temperature sensitivity of metabolic profiles was compared with that of catabolic profiles obtained using Biolog microplates. Analytical variability was compared with biological variability by incubating bacterial strains isolated from soil with fructose at 20 degrees C and by replicating each step of the protocol (incubation, extraction and derivatisation). For both the endo- and the exometabolome, more than 70% of the total variability was of biological origin and principal components analysis clearly separated the strains along the first ordination axis. The endometabolome distinguished bacterial strains at the species level only, whereas separation was evident at the species and group level with the exometabolome. Temperature had a significant but differential effect on the metabolite production of the bacterial strains whilst their catabolic profiles remained relatively unaffected. The exometabolome was more sensitive to temperature shifts than the endometabolome, suggesting that this pool may be of interest for studies in environmental functional ecology.}, }
@article {pmid18722066, year = {2008}, author = {Thorin, C and Rigaud, E and Capek, I and André-Fontaine, G and Oster, B and Gastinger, G and Abadia, G}, title = {[Seroprevalence of Lyme Borreliosis and tick-borne encephalitis in workers at risk, in eastern France].}, journal = {Medecine et maladies infectieuses}, volume = {38}, number = {10}, pages = {533-542}, doi = {10.1016/j.medmal.2008.06.008}, pmid = {18722066}, issn = {0399-077X}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Animals ; Antibodies, Bacterial/blood ; Antibodies, Viral/blood ; Arachnid Vectors/microbiology/virology ; Bites and Stings/epidemiology/microbiology/virology ; Borrelia burgdorferi/immunology ; Encephalitis Viruses, Tick-Borne/immunology ; Encephalitis, Tick-Borne/*epidemiology/prevention &amp; control/transmission ; Female ; *Forestry ; France/epidemiology ; Humans ; Lyme Disease/*epidemiology/prevention &amp; control/transmission ; Male ; Middle Aged ; Occupational Diseases/*epidemiology/prevention &amp; control ; Seroepidemiologic Studies ; Ticks/microbiology/virology ; Young Adult ; }, abstract = {OBJECTIVE: The aim of this article was to assess the seroprevalence of Lyme Borreliosis and tick-borne encephalitis (TBE) among occupationally exposed forest workers.<br><br>METHODS: Workers exposed to tick bites in Eastern France were interviewed by occupational health physicians of the mutualit&#xe9; sociale agricole (MSA) on their sociodemographic features, their occupational activity, their last tick bite, their clinical history, and their means of prevention. Blood sampling was carried out for antibody detection.<br><br>RESULTS: Among the 2975 subjects included in the study, the observed seroprevalence was 14.1% for Lyme borreliosis and 3.4% for TBE. Age, occupational activity, and place of residence significantly influenced the serological status of Lyme borreliosis. The seroprevalence was significantly higher among woodcutters (17.5%) than among other occupational categories (p<.001). Seroprevalence in Alsace (26.9%) and Lorraine (16.5%) were significantly higher than in other regions (p<0.001 and p<0.01, respectively). The seroprevalence of TBE was significantly higher in Alsace (5.5%; p<0.001). The rates of seroprevalence for both infections varied according to forest areas. The multifactorial analysis of prevention practices revealed three types of behaviors as far as protection was concerned: "rigorous", "partial", or "insufficient".<br><br>CONCLUSION: These results do not change the present French indications for use of TBE vaccine. They highlight the importance of information on these diseases and the need for further studies on microbial ecology and risk-factors identification.}, }
@article {pmid18716312, year = {2009}, author = {Simeonova, DD and Susnea, I and Moise, A and Schink, B and Przybylski, M}, title = {"Unknown genome" proteomics: a new NADP-dependent epimerase/dehydratase revealed by N-terminal sequencing, inverted PCR, and high resolution mass spectrometry.}, journal = {Molecular &amp; cellular proteomics : MCP}, volume = {8}, number = {1}, pages = {122-131}, doi = {10.1074/mcp.M800242-MCP200}, pmid = {18716312}, issn = {1535-9484}, mesh = {Amino Acid Sequence ; Bacteria/*enzymology/genetics ; Bacterial Proteins/chemistry/genetics ; DNA Primers/metabolism ; Electrophoresis, Gel, Two-Dimensional ; Genes, Bacterial ; Genome, Bacterial/*genetics ; *Mass Spectrometry ; Molecular Sequence Data ; Molecular Weight ; NADP/*metabolism ; Open Reading Frames/genetics ; Peptides/chemistry/isolation &amp; purification ; Phosphorylation ; Polymerase Chain Reaction ; Proteomics/*methods ; Racemases and Epimerases/genetics/*metabolism ; Reproducibility of Results ; Sequence Analysis, Protein/*methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {We present here a new approach that enabled the identification of a new protein from a bacterial strain with unknown genomic background using a combination of inverted PCR with degenerate primers derived from N-terminal protein sequences and high resolution peptide mass determination of proteolytic digests from two-dimensional electrophoretic separation. Proteins of the sulfate-reducing bacterium Desulfotignum phosphitoxidans specifically induced in the presence of phosphite were separated by two-dimensional gel electrophoresis as a series of apparent soluble and membrane-bound isoforms with molecular masses of approximately 35 kDa. Inverted PCR based on N-terminal sequences and high resolution peptide mass fingerprinting by Fourier transform-ion cyclotron resonance mass spectrometry provided the identification of a new NAD(P) epimerase/dehydratase by specific assignment of peptide masses to a single ORF, excluding other possible ORF candidates. The protein identification was ascertained by chromatographic separation and sequencing of internal proteolytic peptides. Metal ion affinity isolation of tryptic peptides and high resolution mass spectrometry provided the identification of five phosphorylations identified in the domains 23-47 and 91-118 of the protein. In agreement with the phosphorylations identified, direct molecular weight determination of the soluble protein eluted from the two-dimensional gels by mass spectrometry provided a molecular mass of 35,400 Da, which is consistent with an average degree of three phosphorylations.}, }
@article {pmid18713272, year = {2008}, author = {Walker, AW and Duncan, SH and Harmsen, HJ and Holtrop, G and Welling, GW and Flint, HJ}, title = {The species composition of the human intestinal microbiota differs between particle-associated and liquid phase communities.}, journal = {Environmental microbiology}, volume = {10}, number = {12}, pages = {3275-3283}, doi = {10.1111/j.1462-2920.2008.01717.x}, pmid = {18713272}, issn = {1462-2920}, mesh = {Adult ; Bacteria/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; Colon/*microbiology ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Feces/microbiology ; Genes, rRNA ; Humans ; In Situ Hybridization, Fluorescence ; Microscopy, Fluorescence ; Molecular Sequence Data ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Many of the substrates available as energy sources for microorganisms in the human colon, including dietary plant fibre and secreted mucin, are insoluble. It seems likely that such insoluble substrates support a specialized microbiota, and in order to test this hypothesis, faecal samples from four healthy subjects were fractionated into insoluble (washed particulate) and liquid fractions. Analysis of 1252 PCR-amplified 16S rRNA sequences revealed a significantly lower percentage of Bacteroidetes (P = 0.021) and a significantly higher percentage of Firmicutes (P = 0.029) among bacterial sequences amplified from particle-associated (mean 76.8% Firmicutes, 18.5% Bacteroidetes) compared with liquid phase (mean 65.8% Firmicutes, 28.5% Bacteroidetes). Within the Firmicutes, the most significant association with solid particles was found for relatives of Ruminococcus-related clostridial cluster IV species that include Ruminococcus flavefaciens and R. bromii, which together accounted for 12.2% of particle-associated, but only 3.3% of liquid phase, sequences. These findings were strongly supported by microscopy, using group-specific FISH probes able to detect these species. This work suggests that the primary colonizers of insoluble substrates found in the gut are restricted to certain specialized groups of bacteria. The abundance of such primary degraders may often be underestimated because of the difficulty in recovering these bacteria and their nucleic acids from the insoluble substrate.}, }
@article {pmid18709402, year = {2009}, author = {Mohlin, M and Wulff, A}, title = {Interaction effects of ambient UV radiation and nutrient limitation on the toxic cyanobacterium Nodularia spumigena.}, journal = {Microbial ecology}, volume = {57}, number = {4}, pages = {675-686}, pmid = {18709402}, issn = {1432-184X}, mesh = {Amino Acids/metabolism ; Canthaxanthin/metabolism ; *Eutrophication ; Nitrogen/metabolism ; Nodularia/growth &amp; development/*metabolism/*radiation effects ; Phosphorus/metabolism ; Photosynthesis ; Seawater/microbiology ; *Ultraviolet Rays ; *Water Microbiology ; }, abstract = {Nodularia spumigena is one of the dominating species during the extensive cyanobacterial blooms in the Baltic Sea. The blooms coincide with strong light, stable stratification, low ratios of dissolved inorganic nitrogen, and dissolved inorganic phosphorus. The ability of nitrogen fixation, a high tolerance to phosphorus starvation, and different photo-protective strategies (production of mycosporine-like amino acids, MAAs) may give N. spumigena a competitive advantage over other phytoplankton during the blooms. To elucidate the interactive effects of ambient UV radiation and nutrient limitation on the performance of N. spumigena, an outdoor experiment was designed. Two radiation treatments photosynthetic active radiation (PAR) and PAR +UV-A + UV-B (PAB) and three nutrient treatments were established: nutrient replete (NP), nitrogen limited (-N), and phosphorus limited (-P). Variables measured were specific growth rate, heterocyst frequency, cell volume, cell concentrations of MAAs, photosynthetic pigments, particulate carbon (POC), particulate nitrogen (PON), and particulate phosphorus (POP). Ratios of particulate organic matter were calculated: POC/PON, POC/POP, and PON/POP. There was no interactive effect between radiation and nutrient limitation on the specific growth rate of N. spumigena, but there was an overall effect of phosphorus limitation on the variables measured. Interaction effects were observed for some variables; cell size (larger cells in -P PAB compared to other treatments) and the carotenoid canthaxanthin (highest concentration in -N PAR). In addition, significantly less POC and PON (mol cell(-1)) were found in -P PAR compared to -P PAB, and the opposite radiation effect was observed in -N. Our study shows that despite interactive effects on some of the variables studied, N. spumigena tolerate high ambient UVR also under nutrient limiting conditions and maintain positive growth rate even under severe phosphorus limitation.}, }
@article {pmid18704556, year = {2009}, author = {Schlatter, D and Fubuh, A and Xiao, K and Hernandez, D and Hobbie, S and Kinkel, L}, title = {Resource amendments influence density and competitive phenotypes of Streptomyces in soil.}, journal = {Microbial ecology}, volume = {57}, number = {3}, pages = {413-420}, pmid = {18704556}, issn = {1432-184X}, mesh = {Cellulose/metabolism ; Glucose/metabolism ; Lignin/metabolism ; *Phenotype ; *Soil ; *Soil Microbiology ; Streptomyces/genetics/*metabolism ; }, abstract = {Carbon from plant rhizospheres is a source of energy for soil microbial communities in native habitats. Soil amendments have been used as a means for deliberately altering soil community composition in agricultural soils to enhance plant health. However, little information is available in agricultural or natural soils on how specific carbon compounds or quantities influence soil microbial communities. Streptomyces are important soil saprophytes noted for their ability to produce antibiotics and influence plant health. To explore how specific types and amounts of carbon compounds influence Streptomyces in soil, glucose, cellulose, and lignin were added alone and in combination with six other carbon substrates of varying complexity to mesocosms of native prairie soil for 9 months at amounts equivalent to natural inputs from plants. Estimated culturable population densities, antibiotic inhibitory phenotypes, and resource utilization profiles were examined for Streptomyces communities from each treatment. The type and quantity of carbon compounds influenced densities, proportions, antibiotic phenotypes, and substrate utilization profiles of Streptomyces. Cellulose and lignin inputs produced the largest Streptomyces densities. Also, Streptomyces communities receiving high-resource inputs were more inhibitory whereas those receiving low-resource inputs used substrates more efficiently. Knowledge of how the availability and quantity of particular carbon compounds influences Streptomyces communities and their function, specifically resource use and inhibitory phenotypes, may be helpful in understanding the roles of resource availability in Streptomyces community dynamics and the potential of Streptomyces to suppress pathogens and enhance plant fitness in native and agricultural soils.}, }
@article {pmid18703094, year = {2008}, author = {Morales, SE and Cosart, T and Johnson, JV and Holben, WE}, title = {Supplemental programs for enhanced recovery of data from the DOTUR application.}, journal = {Journal of microbiological methods}, volume = {75}, number = {3}, pages = {572-575}, doi = {10.1016/j.mimet.2008.07.017}, pmid = {18703094}, issn = {0167-7012}, mesh = {*Databases, Nucleic Acid ; *Software ; }, abstract = {In order to retrieve phylogenetic information from distance matrices generated from large-scale clone libraries, and to explore OTU distribution among them, we have developed downstream applications for use with the already available DOTUR program. These programs enhance and ease data extraction, providing phylogeny to the already generated distance data.}, }
@article {pmid18691224, year = {2008}, author = {Pérez-Pantoja, D and De la Iglesia, R and Pieper, DH and González, B}, title = {Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacterium Cupriavidus necator JMP134.}, journal = {FEMS microbiology reviews}, volume = {32}, number = {5}, pages = {736-794}, doi = {10.1111/j.1574-6976.2008.00122.x}, pmid = {18691224}, issn = {0168-6445}, mesh = {Bacterial Proteins/genetics/metabolism ; *Biodegradation, Environmental ; Cupriavidus necator/genetics/growth &amp; development/*metabolism ; Feedback, Physiological ; Gene Expression Regulation, Bacterial/*genetics ; Gene Regulatory Networks/*physiology ; Genes, Bacterial/physiology ; Hydrocarbons, Aromatic/*metabolism ; Protein Biosynthesis/physiology ; Systems Biology/*methods ; Transcription, Genetic/physiology ; }, abstract = {Cupriavidus necator JMP134 is a model for chloroaromatics biodegradation, capable of mineralizing 2,4-D, halobenzoates, chlorophenols and nitrophenols, among other aromatic compounds. We performed the metabolic reconstruction of aromatics degradation, linking the catabolic abilities predicted in silico from the complete genome sequence with the range of compounds that support growth of this bacterium. Of the 140 aromatic compounds tested, 60 serve as a sole carbon and energy source for this strain, strongly correlating with those catabolic abilities predicted from genomic data. Almost all the main ring-cleavage pathways for aromatic compounds are found in C. necator: the beta-ketoadipate pathway, with its catechol, chlorocatechol, methylcatechol and protocatechuate ortho ring-cleavage branches; the (methyl)catechol meta ring-cleavage pathway; the gentisate pathway; the homogentisate pathway; the 2,3-dihydroxyphenylpropionate pathway; the (chloro)hydroxyquinol pathway; the (amino)hydroquinone pathway; the phenylacetyl-CoA pathway; the 2-aminobenzoyl-CoA pathway; the benzoyl-CoA pathway and the 3-hydroxyanthranilate pathway. A broad spectrum of peripheral reactions channel substituted aromatics into these ring cleavage pathways. Gene redundancy seems to play a significant role in the catabolic potential of this bacterium. The literature on the biochemistry and genetics of aromatic compounds degradation is reviewed based on the genomic data. The findings on aromatic compounds biodegradation in C. necator reviewed here can easily be extrapolated to other environmentally relevant bacteria, whose genomes also possess a significant proportion of catabolic genes.}, }
@article {pmid18690405, year = {2009}, author = {Auguet, JC and Montanié, H and Hartmann, HJ and Lebaron, P and Casamayor, EO and Catala, P and Delmas, D}, title = {Potential effect of freshwater virus on the structure and activity of bacterial communities in the Marennes-Oléron Bay (France).}, journal = {Microbial ecology}, volume = {57}, number = {2}, pages = {295-306}, pmid = {18690405}, issn = {0095-3628}, mesh = {Bacteria/genetics/*growth &amp; development/*virology ; Biodiversity ; Colony Count, Microbial ; DNA Fingerprinting ; DNA, Bacterial/genetics ; France ; Fresh Water/virology ; Polymorphism, Single-Stranded Conformational ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; Seasons ; Seawater/microbiology/virology ; Viruses/*growth &amp; development ; *Water Microbiology ; }, abstract = {Batch culture experiments using viral enrichment were conducted to test the response of a coastal bacterial community to autochthonous (i.e., co-existing) or allochthonous riverine viruses. The effects of viral infections on bacterial dynamics and activity were assessed by epifluorescence microscopy and thymidine incorporation, respectively, whereas the effect of viral infection on bacterial community composition was examined by polymerase chain reaction-single strand conformation polymorphism 16S ribosomal RNA fingerprinting. The percentages of high nucleic acid-containing cells, evaluated by flow cytometry, were significantly correlated (r2=0.91, n=12, p<0.0001) to bacterial production, making this value a good predictor of active cell dynamics along the study. While confinement and temperature were the two principal experimental factors affecting bacterial community composition and dynamics, respectively, additions of freshwater viruses had significant effects on coastal bacterial communities. Thus, foreign viruses significantly reduced net bacterial population increase as compared to the enrichment treated with inactivated virus. Moreover, freshwater viruses recurrently and specifically affected bacterial community composition, as compared to addition of autochthonous viruses. In most cases, the combined treatment viruses and freshwater dissolved organic matter helped to maintain or even enhance species richness in coastal bacterial communities in agreement to the 'killing the winner' hypothesis. Thus, riverine virus input could potentially influence bacterial community composition of the coastal bay albeit with modest modification of bulk bacterial growth.}, }
@article {pmid18688612, year = {2008}, author = {Pham, TH and Boon, N and De Maeyer, K and Höfte, M and Rabaey, K and Verstraete, W}, title = {Use of Pseudomonas species producing phenazine-based metabolites in the anodes of microbial fuel cells to improve electricity generation.}, journal = {Applied microbiology and biotechnology}, volume = {80}, number = {6}, pages = {985-993}, doi = {10.1007/s00253-008-1619-7}, pmid = {18688612}, issn = {1432-0614}, mesh = {*Electricity ; Electrodes/*microbiology ; Phenazines/*metabolism ; Pseudomonas/*metabolism ; }, abstract = {The rate of anodic electron transfer is one of the factors limiting the performance of microbial fuel cells (MFCs). It is known that phenazine-based metabolites produced by Pseudomonas species can function as electron shuttles for Pseudomonas themselves and also, in a syntrophic association, for Gram-positive bacteria. In this study, we have investigated whether phenazine-based metabolites and their producers could be used to improve the electricity generation of a MFC operated with a mixed culture. Both anodic supernatants obtained from MFCs operated with a Pseudomonas strain (P-PCA) producing phenazine-1-carboxylic acid (PCA) and those from MFCs operated with a strain (P-PCN) producing phenazine-1-carboxamide (PCN) exerted similarly positive effects on the electricity generation of a mixed culture. Replacing supernatants of MFCs operated with a mixed culture with supernatants of MFCs operated with P-PCN could double the currents generated. Purified PCA and purified PCN had similar effects. If the supernatant of an engineered strain overproducing PCN was used, the effect could be maintained over longer time courses, resulting in a 1.5-fold increase in the production of charge. Bioaugmentation of the mixed culture MFCs using slow release tubes containing P-PCN not only doubled the currents but also maintained the effect over longer periods. The results demonstrated the electron-shuttling effect of phenazine-based compounds produced by Pseudomonas species and their capacity to improve the performance of MFCs operated with mixed cultures.}, }
@article {pmid18685886, year = {2009}, author = {Vázquez, S and Nogales, B and Ruberto, L and Hernández, E and Christie-Oleza, J and Lo Balbo, A and Bosch, R and Lalucat, J and Mac Cormack, W}, title = {Bacterial community dynamics during bioremediation of diesel oil-contaminated Antarctic soil.}, journal = {Microbial ecology}, volume = {57}, number = {4}, pages = {598-610}, pmid = {18685886}, issn = {1432-184X}, mesh = {Antarctic Regions ; Bacteria/classification/genetics/*metabolism ; Biodegradation, Environmental ; Biodiversity ; DNA, Bacterial/genetics ; Gasoline/*microbiology ; Hydrocarbons/*metabolism ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Soil/analysis ; *Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {The effect of nutrient and inocula amendment in a bioremediation field trial using a nutrient-poor Antarctic soil chronically contaminated with hydrocarbons was tested. The analysis of the effects that the treatments caused in bacterial numbers and hydrocarbon removal was combined with the elucidation of the changes occurring on the bacterial community, by 16S rDNA-based terminal restriction fragment length polymorphism (T-RFLP) typing, and the detection of some of the genes involved in the catabolism of hydrocarbons. All treatments caused a significant increase in the number of bacteria able to grow on hydrocarbons and a significant decrease in the soil hydrocarbon content, as compared to the control. However, there were no significant differences between treatments. Comparison of the soil T-RFLP profiles indicated that there were changes in the structure and composition of bacterial communities during the bioremediation trial, although the communities in treated plots were highly similar irrespective of the treatment applied, and they had a similar temporal dynamics. These results showed that nutrient addition was the main factor contributing to the outcome of the bioremediation experiment. This was supported by the lack of evidence of the establishment of inoculated consortia in soils, since their characteristic electrophoretic peaks were only detectable in soil profiles at the beginning of the experiment. Genetic potential for naphthalene degradation, evidenced by detection of nahAc gene, was observed in all soil plots including the control. In treated plots, an increase in the detection of catechol degradation genes (nahH and catA) and in a key gene of denitrification (nosZ) was observed as well. These results indicate that treatments favored the degradation of aromatic hydrocarbons and probably stimulated denitrification, at least transiently. This mesocosm study shows that recovery of chronically contaminated Antarctic soils can be successfully accelerated using biostimulation with nutrients, and that this causes a change in the indigenous bacterial communities and in the genetic potential for hydrocarbon degradation.}, }
@article {pmid18685245, year = {2008}, author = {Wei, H and Shen, J and Pang, X and Ding, D and Zhang, Y and Zhang, B and Lu, H and Wang, T and Zhang, C and Hua, X and Cui, L and Zhao, L}, title = {Fatal infection in human flora-associated piglets caused by the opportunistic pathogen Klebsiella pneumoniae from an apparently healthy human donor.}, journal = {The Journal of veterinary medical science}, volume = {70}, number = {7}, pages = {715-717}, doi = {10.1292/jvms.70.715}, pmid = {18685245}, issn = {0916-7250}, mesh = {Animals ; Animals, Newborn ; Gastrointestinal Tract/*microbiology ; Humans ; Klebsiella Infections/microbiology/*veterinary ; Klebsiella pneumoniae/*growth &amp; development ; Models, Animal ; Opportunistic Infections/microbiology/*veterinary ; Swine ; Swine Diseases/*microbiology ; }, abstract = {Seventeen out of 24 human flora-associated (HFA) piglets died after oral administration of whole fecal flora from an apparently healthy human donor. The bacteria isolated from the organs of the infected piglets were identified as Klebsiella pneumoniae by bacteriological and biochemical tests and 16S rRNA gene sequence analysis. The identical K. pneumoniae strain was also isolated from the donor's fecal flora. All three neonatal piglets inoculated with K. pneumoniae from the donor's fecal flora developed severe diarrhea, with 2 eventually dying. This strongly suggests that the opportunistic pathogen K. pneumoniae from the human donor caused the fatal infection in the HFA piglets. The results underscore the importance of safety evaluation of the human donor's fecal flora for HFA piglet development.}, }
@article {pmid18680487, year = {2008}, author = {Lehmann, K and Crombie, A and Singer, AC}, title = {Reproducibility of a microbial river water community to self-organize upon perturbation with the natural chemical enantiomers, R- and S-carvone.}, journal = {FEMS microbiology ecology}, volume = {66}, number = {2}, pages = {208-220}, doi = {10.1111/j.1574-6941.2008.00554.x}, pmid = {18680487}, issn = {0168-6496}, mesh = {Animals ; *Bacteria/genetics/growth &amp; development/metabolism ; Biodegradation, Environmental ; Cyclohexane Monoterpenes ; *Ecosystem ; *Eukaryota/growth &amp; development/physiology ; *Monoterpenes/metabolism/pharmacology ; Polymerase Chain Reaction ; Reproducibility of Results ; Rivers/chemistry/*microbiology/*parasitology ; }, abstract = {A river water microbial community was studied in response to perturbation with the monoterpene enantiomers R- and S-carvone. The microbial community structure and function was also evaluated after enantiomers exposure was switched. Microbial communities were evaluated by length heterogeneity PCR. The addition of R- and S-carvone enriched for a range of functionally different communities: enantiomer-selective, racemic and ones that contain both. After 5 days incubation, the R- and S-carvone treatments developed a range of dominant microbial communities, which were increasingly dissimilar from the ones in which no carvone degradation had taken place (R-values: R-carvone 0.743, S-carvone 0.5007). There was an increase in the evenness of the microbial community structure upon carvone depletion. After the cross-over, the rate of carvone utilization was significantly faster than after the first carvone addition (P=0.008) as demonstrated by concomitant carvone and oxygen depletion. The main R-degrading community (450-456 bp) appeared enantioselective and largely unable to degrade S-carvone, whereas the S-carvone-degrading community (502-508 bp) appeared to have racemic catabolic capacity. In conclusion, chemical perturbations, such as enantiomers, might generate a significant shift in the river microbial ecology that can have implications for the function of a river in both a spatial and temporal context.}, }
@article {pmid18677528, year = {2009}, author = {Brown, MG and Balkwill, DL}, title = {Antibiotic resistance in bacteria isolated from the deep terrestrial subsurface.}, journal = {Microbial ecology}, volume = {57}, number = {3}, pages = {484-493}, pmid = {18677528}, issn = {1432-184X}, mesh = {Bacteria/*drug effects/*genetics/isolation &amp; purification ; *Drug Resistance, Bacterial ; Geologic Sediments/*microbiology ; Microbial Sensitivity Tests ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; South Carolina ; Washington ; }, abstract = {Various natural environments have been examined for the presence of antibiotic-resistant bacteria and/or novel resistance mechanisms, but little is known about resistance in the terrestrial deep subsurface. This study examined two deep environments that differ in their known period of isolation from surface environments and the bacteria therein. One hundred fifty-four strains of bacteria were isolated from sediments located 170-259 m below land surface at the US Department of Energy Savannah River Site (SRS) in South Carolina and Hanford Site (HS) in Washington. Analyses of 16S rRNA gene sequences showed that both sets of strains were phylogenetically diverse and could be assigned to several genera in three to four phyla. All of the strains were screened for resistance to 13 antibiotics by plating on selective media and 90% were resistant to at least one antibiotic. Eighty-six percent of the SRS and 62% of the HS strains were resistant to more than one antibiotic. Resistance to nalidixic acid, mupirocin, or ampicillin was noted most frequently. The results indicate that antibiotic resistance is common among subsurface bacteria. The somewhat higher frequencies of resistance and multiple resistance at the SRS may, in part, be due to recent surface influence, such as exposure to antibiotics used in agriculture. However, the HS strains have never been exposed to anthropogenic antibiotics but still had a reasonably high frequency of resistance. Given their long period of isolation from surface influences, it is possible that they possess some novel antibiotic resistance genes and/or resistance mechanisms.}, }
@article {pmid18677527, year = {2009}, author = {Principi, P and Villa, F and Giussani, B and Zanardini, E and Cappitelli, F and Sorlini, C}, title = {The effect of copper on the structure of the ammonia-oxidizing microbial community in an activated sludge wastewater treatment plant.}, journal = {Microbial ecology}, volume = {57}, number = {2}, pages = {215-220}, pmid = {18677527}, issn = {0095-3628}, mesh = {Ammonia/*metabolism ; Bacteria/drug effects/genetics/*metabolism ; Biomass ; Bioreactors/microbiology ; Copper/*pharmacology ; DNA, Bacterial/genetics ; Multivariate Analysis ; Oxidoreductases/genetics/metabolism ; Sewage/*microbiology ; Time Factors ; Waste Disposal, Fluid ; }, abstract = {Molecular approaches based on both whole-cell and extracted DNA were applied to assess chronic and acute effects of copper on the ammonia oxidizing bacteria (AOB) community in an activated sludge system. The ammonia monooxygenase amoA gene was chosen as the functional marker to evaluate changes in the AOB community. Using in situ polymerase chain reaction, we were able to visualize the peripheric distribution of the amoA gene-possessing bacteria in activated sludge flocs. The AOB biomass content was constant in both chronic and acute toxicity experiments, but the ammonia oxidizing activity, measured as ammonia uptake rate, was different. The AOB community structural changes due to the copper presence were evaluated by multivariate analysis of the DGGE bands profiles. The chronic contamination caused a change in the AOB community compared to the control. In contrast, acute inputs led to a temporary change in the AOB community, after which the community was similar to the control. Recovery after acute intoxication was achieved after 72 h. The present study reports on the effects of chronic and acute copper contamination on the ammonia uptake ability of the AO microorganisms and the structure of the AOB community in a wastewater system and, as a consequence, gives indications on the response of wastewater plants under similar conditions.}, }
@article {pmid18670729, year = {2009}, author = {Riemann, L and Holmfeldt, K and Titelman, J}, title = {Importance of viral lysis and dissolved DNA for bacterioplankton activity in a P-limited estuary, Northern Baltic Sea.}, journal = {Microbial ecology}, volume = {57}, number = {2}, pages = {286-294}, pmid = {18670729}, issn = {0095-3628}, mesh = {Bacteria/growth &amp; development/*metabolism/*virology ; Carbon/metabolism ; DNA/*metabolism ; Ecosystem ; North Sea ; Phosphorus/metabolism ; Plankton/growth &amp; development/*metabolism/*virology ; *Water Microbiology ; }, abstract = {Through lysis of bacterioplankton cells, viruses mediate an important, but poorly understood, pathway of carbon and nutrients from the particulate to the dissolved form. Via this activity, nutrient-rich cell lysates may become available to noninfected cells and support significant growth. However, the nutritional value of lysates for noninfected bacteria presumably depends on the prevailing nutrient limitation. In the present study, we examined dynamics of dissolved DNA (D-DNA) and viruses along a transect in the phosphorus (P)-limited Ore Estuary, northern Baltic Sea. We found that viruses were an important mortality factor for bacterioplankton and that their activity mediated a significant recycling of carbon and especially of P. Uptake of dissolved DNA accounted for up to 70% of the bacterioplankton P demand, and about a quarter of the D-DNA pool was supplied through viral lysis of bacterial cells. Generally, the importance of viral lysates and uptake of D-DNA was highest at the estuarine and offshore stations and was positively correlated with P limitation measured as alkaline phosphatase activity. Our results highlight the importance of viral activity for the internal recycling of principal nutrients and pinpoints D-DNA as a particularly relevant compound in microbial P dynamics.}, }
@article {pmid18665274, year = {2008}, author = {Andersson, AF and Lindberg, M and Jakobsson, H and Bäckhed, F and Nyrén, P and Engstrand, L}, title = {Comparative analysis of human gut microbiota by barcoded pyrosequencing.}, journal = {PloS one}, volume = {3}, number = {7}, pages = {e2836}, pmid = {18665274}, issn = {1932-6203}, mesh = {Adult ; Aged ; Biopsy ; DNA Primers ; Ecology ; Endoscopy ; *Genetic Techniques ; Humans ; Intestines/*microbiology ; *Microbiological Techniques ; Middle Aged ; Models, Biological ; Phylogeny ; Sequence Analysis, DNA ; Stomach/*microbiology ; }, abstract = {Humans host complex microbial communities believed to contribute to health maintenance and, when in imbalance, to the development of diseases. Determining the microbial composition in patients and healthy controls may thus provide novel therapeutic targets. For this purpose, high-throughput, cost-effective methods for microbiota characterization are needed. We have employed 454-pyrosequencing of a hyper-variable region of the 16S rRNA gene in combination with sample-specific barcode sequences which enables parallel in-depth analysis of hundreds of samples with limited sample processing. In silico modeling demonstrated that the method correctly describes microbial communities down to phylotypes below the genus level. Here we applied the technique to analyze microbial communities in throat, stomach and fecal samples. Our results demonstrate the applicability of barcoded pyrosequencing as a high-throughput method for comparative microbial ecology.}, }
@article {pmid18661115, year = {2009}, author = {Pringault, O and Tesson, S and Rochelle-Newall, E}, title = {Respiration in the light and bacterio-phytoplankton coupling in a coastal environment.}, journal = {Microbial ecology}, volume = {57}, number = {2}, pages = {321-334}, pmid = {18661115}, issn = {0095-3628}, mesh = {Bacteria/growth &amp; development/*metabolism ; Chlorophyll/analysis ; Chlorophyll A ; Ecosystem ; *Light ; Oxygen/metabolism ; *Photosynthesis ; Phytoplankton/*metabolism ; Seawater/microbiology ; *Water Microbiology ; }, abstract = {In pelagic ecosystems, the principal source of organic matter is via autotrophic production and the primary sink is through heterotrophic respiration. One would therefore anticipate that there is some degree of linkage between these two compartments. Recent work has shown that respiration in the light is higher than dark respiration. Consequently, many of the methods used to determine respiration and production are biased as they require the assumption that light and dark respiration rates are equivalent. We show here that, in a coastal ecosystem, under visible light exposure, respiration in the light is related to gross production. More than 60% of the variation of respiration in the light, measured at 1 to 40 microg L(-1) of chlorophyll a (Chla), could be explained by the variations of gross production. Secondly, the relative contribution of bacterial respiration to community respiration in the light represented up to 79% at low Chla (1 microg L(-1)) and was negatively correlated with Chla concentration. Although bacterial production and bacterial respiration were both enhanced in the light, bacterial respiration in the light was more stimulated than bacterial production, which resulted in a decrease in bacterial growth efficiency during light exposure. These results show that the impact of light on the functioning of the microbial loop needs to be taken into account for a better understanding of the oceanic carbon cycle.}, }
@article {pmid18661114, year = {2009}, author = {Berggren, M and Laudon, H and Jansson, M}, title = {Hydrological control of organic carbon support for bacterial growth in boreal headwater streams.}, journal = {Microbial ecology}, volume = {57}, number = {1}, pages = {170-178}, pmid = {18661114}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development/metabolism ; Carbon/*metabolism ; Organic Chemicals/*metabolism ; Oxygen Consumption ; Picea/growth &amp; development ; Pinus/growth &amp; development ; Rivers/*chemistry/*microbiology ; Sphagnopsida/growth &amp; development ; Sweden ; Trees/growth &amp; development ; }, abstract = {Terrestrial organic carbon is exported to freshwater systems where it serves as substrate for bacterial growth. Temporal variations in the terrigenous organic carbon support for aquatic bacteria are not well understood. In this paper, we demonstrate how the combined influence of landscape characteristics and hydrology can shape such variations. Using a 13-day bioassay approach, the production and respiration of bacteria were measured in water samples from six small Swedish streams (64 degrees N, 19 degrees E), draining coniferous forests, peat mires, and mixed catchments with typical boreal proportions between forest and mire coverage. Forest drainage supported higher bacterial production and higher bacterial growth efficiency than drainage from mires. The areal export of organic carbon was several times higher from mire than from forest at low runoff, while there was no difference at high flow. As a consequence, mixed streams (catchments including both mire and forest) were dominated by mire organic carbon with low support of bacterial production at low discharge situations but dominated by forest carbon supporting higher bacterial production at high flow. The stimulation of bacterial growth during high-flow episodes was a result of higher relative export of organic carbon via forest drainage rather than increased drainage of specific "high-quality" carbon pools in mire or forest soils.}, }
@article {pmid18654815, year = {2009}, author = {Székely, AJ and Sipos, R and Berta, B and Vajna, B and Hajdú, C and Márialigeti, K}, title = {DGGE and T-RFLP analysis of bacterial succession during mushroom compost production and sequence-aided T-RFLP profile of mature compost.}, journal = {Microbial ecology}, volume = {57}, number = {3}, pages = {522-533}, pmid = {18654815}, issn = {1432-184X}, mesh = {Agaricales/metabolism ; Bacteria/classification/*genetics/isolation &amp; purification ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Ecosystem ; Electrophoresis, Gel, Pulsed-Field ; Phylogeny ; *Polymorphism, Restriction Fragment Length ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; Soil/*analysis ; *Soil Microbiology ; Temperature ; }, abstract = {The amount of button mushroom (Agaricus bisporus) harvested from compost is largely affected by the microbial processes taking place during composting and the microbes inhabiting the mature compost. In this study, the microbial changes during the stages of this specific composting process were monitored, and the dominant bacteria of the mature compost were identified to reveal the microbiological background of the favorable properties of the heat-treated phase II mushroom compost. 16S ribosomal deoxyribonucleic acid (rDNA)-based denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) molecular fingerprinting methods were used to track the succession of microbial communities in summer and winter composting cycles. DNA from individual DGGE bands were reamplified and subjected to sequence analysis. Principal component analysis of fingerprints of the composting processes showed intensive changes in bacterial community during the 22-day procedure. Peak temperature samples grouped together and were dominated by Thermus thermophilus. Mature compost patterns were almost identical by both methods (DGGE, T-RFLP). To get an in-depth analysis of the mature compost bacterial community, the sequence data from cultivation of the bacteria and cloning of environmental 16S rDNA were uniquely coupled with the output of the environmental T-RFLP fingerprints (sequence-aided T-RFLP). This method revealed the dominance of a supposedly cellulose-degrading consortium composed of phylotypes related to Pseudoxanthomonas, Thermobifida, and Thermomonospora.}, }
@article {pmid18648871, year = {2009}, author = {Fuka, MM and Engel, M and Hagn, A and Munch, JC and Sommer, M and Schloter, M}, title = {Changes of diversity pattern of proteolytic bacteria over time and space in an agricultural soil.}, journal = {Microbial ecology}, volume = {57}, number = {3}, pages = {391-401}, pmid = {18648871}, issn = {1432-184X}, mesh = {*Agriculture ; Bacteria/enzymology/*genetics/isolation &amp; purification ; Bacterial Proteins/genetics ; *Biodiversity ; DNA, Bacterial/genetics ; Environment ; Metalloproteases/genetics ; Polymorphism, Restriction Fragment Length ; Seasons ; Sequence Analysis, DNA ; *Soil Microbiology ; Time Factors ; }, abstract = {The genetic heterogeneity of neutral metalloprotease (npr) gene fragments from soil proteolytic bacteria was investigated at a cultivated field site with four different soil types and at three different depths in April, July, and October. Terminal restriction fragment length polymorphism (T-RFLP) analyses of polymerase chain reaction-amplified npr gene fragments were applied to study the dynamic of the npr gene pool with regard to environmental conditions. The aim of this study was to relate differences in npr community structure and richness to the vertical, site, and seasonal variations naturally occurring at the field site under investigation. T-RFLP analysis revealed a noticeable seasonal variability in the community structure of npr-containing bacteria. The data suggest that the composition of the npr proteolytic bacterial population in July differed from those at the other dates. Additionally, the diversity of npr genes decreased with increasing soil depth revealing the highest values in upper layers. The reasons behind the observed patterns in the community structure might be mainly seasonal and vertical variation of the quantity and heterogeneity of available substrates as well as spatial isolation caused by a varying water amount and the connectivity of soil particles among the soil profile. Sequencing and phylogenetical analysis of 120 npr clones from the top soils collected in July revealed that most of the clones exhibit only poor homology to npr genes of isolates previously obtained from various environments, indicating the presence of until now uncharacterized npr coding proteolytic bacteria at the study site.}, }
@article {pmid18648058, year = {2008}, author = {Thompson, K and Burkholder, K and Patterson, J and Applegate, TJ}, title = {Microbial ecology shifts in the ileum of broilers during feed withdrawal and dietary manipulations.}, journal = {Poultry science}, volume = {87}, number = {8}, pages = {1624-1632}, doi = {10.3382/ps.2007-00324}, pmid = {18648058}, issn = {0032-5791}, mesh = {Animals ; Bacitracin/*pharmacology ; Chickens/metabolism/*microbiology ; Copper Sulfate/*pharmacology ; DNA, Bacterial/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel/veterinary ; *Food Deprivation ; Ileum/metabolism/*microbiology ; Intestinal Mucosa/metabolism/*microbiology ; Male ; Polymerase Chain Reaction/veterinary ; Salicylates/*pharmacology ; }, abstract = {Broilers are withheld from feed for 8 to 24 h before processing to empty the gastrointestinal tract and reduce potential carcass contamination from gastrointestinal tract contents. Intestinal microbial changes during feed withdrawal (FW) have not been thoroughly defined. Two experiments were conducted to examine the effects of diet and FW on the microbial ecology in the small intestine. In experiment 1, 42-d-old broilers were fed diets containing no additive (control), 250 ppm of CuSO(4), or bacitracin (BMD; 30 ppm) and were also subjected to FW for 0, 10, and 24 h. Six birds from each dietary treatment were killed at each FW time point and ileal mucosa and digesta were collected. Microbial communities were determined by isolating bacterial DNA, amplifying the V3 region of 16S ribosomal DNA, and performing denaturing gradient gel electrophoresis. The mucosal microbial profiles from birds at 0 h of FW had higher similarity values than those at 24 h of FW, indicating that as FW time increased, uniformity of intestinal microbial populations decreased. Numbers of bands (an indicator of numbers of bacterial species present) at 0 h (9.38) were greater than those at 10 and 24 h (5.39 and 5.78, respectively), suggesting a reduction in microbial species and diversity as FW time increased. Copper-fed birds had greater similarity coefficients than either the control or BMD-fed birds, but BMD-fed birds had greater band numbers. No interaction between diet and FW was observed and no digesta differences were observed. In experiment 2, 62-d-old birds fed corn-soy diets in floor pens were subjected to 0, 8, 12, and 24 h of FW. Ileal mucosal tissue was collected and analyzed as in experiment 1. Mucosal microbiota similarities were greater at 0 h of FW than at 8, 12, or 24 h of FW and band numbers were reduced between 0 and 24 h of FW. Data from these studies suggest that FW and dietary treatments alter the microbial community of the intestine by decreasing bacterial diversity in the ileum.}, }
@article {pmid18647357, year = {2008}, author = {Hernández, M and Villalobos, P and Morgante, V and González, M and Reiff, C and Moore, E and Seeger, M}, title = {Isolation and characterization of a novel simazine-degrading bacterium from agricultural soil of central Chile, Pseudomonas sp. MHP41.}, journal = {FEMS microbiology letters}, volume = {286}, number = {2}, pages = {184-190}, doi = {10.1111/j.1574-6968.2008.01274.x}, pmid = {18647357}, issn = {0378-1097}, mesh = {Atrazine/metabolism ; Bacterial Typing Techniques ; Biomass ; Biotransformation ; Chile ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, Bacterial ; Metabolic Networks and Pathways ; Nitrogen/metabolism ; Phylogeny ; Pseudomonas/*classification/isolation &amp; purification/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Simazine/*metabolism ; *Soil Microbiology ; }, abstract = {s-Triazine herbicides are used extensively in South America in agriculture and forestry. In this study, a bacterium designated as strain MHP41, capable of degrading simazine and atrazine, was isolated from agricultural soil in the Quillota valley, central Chile. Strain MHP41 is able to grow in minimal medium, using simazine as the sole nitrogen source. In this medium, the bacterium exhibited a growth rate of mu=0.10 h(-1), yielding a high biomass of 4.2 x 10(8) CFU mL(-1). Resting cells of strain MHP41 degrade more than 80% of simazine within 60 min. The atzA, atzB, atzC, atzD, atzE and atzF genes encoding the enzymes of the simazine upper and lower pathways were detected in strain MHP41. The motile Gram-negative bacterium was identified as a Pseudomonas sp., based on the Biolog microplate system and comparative sequence analyses of the 16S rRNA gene. Amplified ribosomal DNA restriction analysis allowed the differentiation of strain MHP41 from Pseudomonas sp. ADP. The comparative 16S rRNA gene sequence analyses suggested that strain MHP41 is closely related to Pseudomonas nitroreducens and Pseudomonas multiresinovorans. This is the first s-triazine-degrading bacterium isolated in South America. Strain MHP41 is a potential biocatalyst for the remediation of s-triazine-contaminated environments.}, }
@article {pmid18647356, year = {2008}, author = {Lee, C and Kim, J and Shin, SG and Hwang, S}, title = {Monitoring bacterial and archaeal community shifts in a mesophilic anaerobic batch reactor treating a high-strength organic wastewater.}, journal = {FEMS microbiology ecology}, volume = {65}, number = {3}, pages = {544-554}, doi = {10.1111/j.1574-6941.2008.00530.x}, pmid = {18647356}, issn = {0168-6496}, mesh = {Anaerobiosis ; Archaea/genetics/*growth &amp; development/metabolism ; Bacteria/genetics/*growth &amp; development/metabolism ; Biodegradation, Environmental ; *Bioreactors ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Dairying ; Electrophoresis, Gel, Pulsed-Field ; Fermentation ; Genes, Archaeal ; Genes, Bacterial ; Genes, rRNA ; Methane/metabolism ; Molecular Sequence Data ; Oxygen Consumption ; Phylogeny ; Polymerase Chain Reaction ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; *Waste Disposal, Fluid ; *Water Microbiology ; }, abstract = {Shifts in bacterial and archaeal communities, associated with changes in chemical profiles, were investigated in an anaerobic batch reactor treating dairy-processing wastewater prepared with whey permeate powder. The dynamics of bacterial and archaeal populations were monitored by quantitative real-time PCR and showed good agreement with the process data. A rapid increase in bacterial populations and a high rate of substrate fermentation were observed during the initial period. Growth and regrowth of archaeal populations occurred with biphasic production of methane, corresponding to the diauxic consumption of acetate and propionate. Bacterial community structure was examined by denaturing gel gradient electrophoresis (DGGE) targeting 16S rRNA genes. An Aeromonas-like organism was suggested to be mainly responsible for the rapid fermentation of carbohydrate during the initial period. Several band sequences closely related to the Clostridium species, capable of carbohydrate fermentation, lactate or ethanol fermentation, and/or homoacetogenesis, were also detected. Statistical analyses of the DGGE profiles showed that the bacterial community structure, as well as the process performance, varied with the incubation time. Our results demonstrated that the bacterial community shifted, reflecting the performance changes and, particularly, that a significant community shift corresponded to a considerable process event. This suggested that the diagnosis of an anaerobic digestion process could be possible by monitoring bacterial community shifts.}, }
@article {pmid18647333, year = {2008}, author = {Loy, A and Arnold, R and Tischler, P and Rattei, T and Wagner, M and Horn, M}, title = {probeCheck--a central resource for evaluating oligonucleotide probe coverage and specificity.}, journal = {Environmental microbiology}, volume = {10}, number = {10}, pages = {2894-2898}, pmid = {18647333}, issn = {1462-2920}, support = {P 18836/FWF_/Austrian Science Fund FWF/Austria ; P 20185/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Databases, Genetic ; Molecular Biology/*methods ; Nucleic Acid Hybridization/*methods ; Oligonucleotide Probes/*genetics ; Sensitivity and Specificity ; }, abstract = {The web server probeCheck, freely accessible at http://www.microbial-ecology.net/probecheck, provides a pivotal forum for rapid specificity and coverage evaluations of probes and primers against selected databases of phylogenetic and functional marker genes. Currently, 24 widely used sequence collections including the Ribosomal Database Project (RDP) II, Greengenes, SILVA and the Functional Gene Pipeline/Repository can be queried. For this purpose, probeCheck integrates a new online version of the popular ARB probe match tool with free energy (DeltaG) calculations for each perfectly matched and mismatched probe-target hybrid, allowing assessment of the theoretical binding stabilities of oligo-target and non-target hybrids. For each output sequence, the accession number, the GenBank taxonomy and a link to the respective entry at GenBank, EMBL and, if applicable, the query database are displayed. Filtering options allow customizing results on the output page. In addition, probeCheck is linked with probe match tools of RDP II and Greengenes, NCBI blast, the Oligonucleotide Properties Calculator, the two-state folding tool of the DINAMelt server and the rRNA-targeted probe database probeBase. Taken together, these features provide a multifunctional platform with maximal flexibility for the user in the choice of databases and options for the evaluation of published and newly developed probes and primers.}, }
@article {pmid18642607, year = {2008}, author = {Tzeneva, VA and Heilig, HG and van Vliet, WA and Akkermans, AD and de Vos, WM and Smidt, H}, title = {16S rRNA targeted DGGE fingerprinting of microbial communities.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {410}, number = {}, pages = {335-349}, doi = {10.1007/978-1-59745-548-0_17}, pmid = {18642607}, issn = {1064-3745}, mesh = {Biodiversity ; DNA Fingerprinting/methods ; Electrophoresis, Polyacrylamide Gel/*methods ; Environmental Microbiology/*standards ; Genetic Variation ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The past decades have seen the staggering development of molecular microbial ecology as a discipline that uses the detection of so-called biomarkers to monitor microbial communities in environment samples. A variety of molecules can be used as biomarkers, including cell-wall components, proteins, lipids, DNA or RNA. Especially, the application of small subunit ribosomal RNA (rRNA) and the corresponding genes have proven invaluable for advances in microbial ecology. Several types of fingerprinting methods have been developed for the description of microbial communities in environmental samples. Among the most commonly used approaches is denaturing gradient gel electrophoresis (DGGE) of PCR-amplified fragments. DGGE allows separation of DNA fragment mixtures of equal length depending on their sequence. The separation is based on their sequence-specific melting point in a polyacrylamide gel with a gradient of a denaturant chemical (generally a combination of urea and formamide). DGGE allows for a rapid analysis and comparison of microbial communities. Compositional diversity can be visualized using DGGE where each band in principle represents a bacterial phylotype. After staining bands are visualized at each position in the gel where DNA molecules stopped migration. In principle, DGGE fingerprinting can resolve single base pair differences.}, }
@article {pmid18642270, year = {1997}, author = {Chang, WK and Criddle, CS}, title = {Experimental evaluation of a model for cometabolism: Prediction of simultaneous degradation of trichloroethylene and methane by a methanotrophic mixed culture.}, journal = {Biotechnology and bioengineering}, volume = {56}, number = {5}, pages = {492-501}, doi = {10.1002/(SICI)1097-0290(19971205)56:5&lt;492::AID-BIT3&gt;3.0.CO;2-D}, pmid = {18642270}, issn = {0006-3592}, abstract = {A model for cometabolism is verified experimentally for a defined methanotrophic mixed culture. The model includes the effects of cell growth, endogenous cell decay, product toxicity, and competitive inhibition with the assumption that cometabolic transformation rates are enhanced by reducing power obtained from oxidation of growth substrates. A theoretical transformation yield is used to quantify the enhancement resulting from growth substrate oxidation. A systematic method for evaluating model parameters independently is described. The applicability of the model is evaluated by comparing experimental data for methanotrophic cometabolism of TCE with model predictions from independently measured model parameters. Propagation of errors is used to quantify errors in parameter estimates and in the final prediction. The model successfully predicts TCE transformation and methane utilization for a wide range of concentrations of TCE (0.5 to 9 mg/L) and methane (0.05 to 6 mg/L). (c) 1997 John Wiley &amp; Sons, Inc. Biotechnol Bioeng 56: 492-501, 1997.}, }
@article {pmid18642041, year = {2009}, author = {Baker-Austin, C and McArthur, JV and Lindell, AH and Wright, MS and Tuckfield, RC and Gooch, J and Warner, L and Oliver, J and Stepanauskas, R}, title = {Multi-site analysis reveals widespread antibiotic resistance in the marine pathogen Vibrio vulnificus.}, journal = {Microbial ecology}, volume = {57}, number = {1}, pages = {151-159}, pmid = {18642041}, issn = {0095-3628}, mesh = {Anti-Infective Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Genotype ; Geologic Sediments/*microbiology ; Humans ; Microbial Sensitivity Tests ; Seawater/*microbiology ; Vibrio Infections/*microbiology ; Vibrio vulnificus/classification/*drug effects/genetics/isolation &amp; purification ; }, abstract = {Vibrio vulnificus is a serious opportunistic human pathogen commonly found in subtropical coastal waters, and is the leading cause of seafood-borne mortality in the USA. This taxon does not sustain prolonged presence in clinical or agricultural settings, where it would undergo human-induced selection for antibiotic resistance. Therefore, few studies have verified the effectiveness of commonly prescribed antibiotics in V. vulnificus treatment. Here we screened 151 coastal isolates and 10 primary septicaemia isolates against 26 antimicrobial agents representing diverse modes of action. The frequency of multiple resistances to antibiotics from all sources was unexpectedly high, particularly during summer months, and a substantial proportion of isolates (17.3%) were resistant to eight or more antimicrobial agents. Numerous isolates demonstrated resistance to antibiotics routinely prescribed for V. vulnificus infections, such as doxycycline, tetracycline, aminoglycosides and cephalosporins. These resistances were detected at similar frequencies in virulent and non-virulent strains (PCR-based virulence typing) and were present in septicaemia isolates, underlying the public health implications of our findings. Among environmental isolates, there were no consistent differences in the frequency of resistance between pristine and anthropogenically impacted estuaries, suggesting natural rather than human-derived sources of resistance traits. This report is the first to demonstrate prevalent antibiotic resistance in a human pathogen with no clinical reservoirs, implying the importance of environmental studies in understanding the spread, evolution and public health relevance of antibiotic resistance factors.}, }
@article {pmid18642040, year = {2009}, author = {Martel, CM}, title = {Conceptual bases for prey biorecognition and feeding selectivity in the microplanktonic marine phagotroph Oxyrrhis marina.}, journal = {Microbial ecology}, volume = {57}, number = {4}, pages = {589-597}, pmid = {18642040}, issn = {1432-184X}, mesh = {Animals ; Cell Wall/metabolism ; Dinoflagellida/*metabolism ; Mannose-Binding Lectins/metabolism ; Phagocytosis ; Phytoplankton/*chemistry ; *Predatory Behavior ; Receptors, Mitogen/metabolism ; Superoxides/metabolism ; }, abstract = {It is suspected that phagotrophic marine protozoa might possess feeding receptors that enable them to discern the nutritional quality of individual prey items (during prey-handling) on the basis of their cell-surface biochemistry. This article reviews advances in our understanding of the molecular mechanisms that mediate the biorecognition and selection of nonself (microalgal) prey items by the microplanktonic marine phagotroph Oxyrrhis marina. The potential importance of lectin-glycan interactions is first considered in view of findings which demonstrate that O. marina possesses lectin-like feeding receptors specific for prey-surface (mannose) glycoconjugates. Secondly, some conceptual bases for indirect or 'opsonic' modes of prey biorecognition mediated by soluble prey-labelling proteins are presented. Finally, the possibility that some accounts of selective feeding in O. marina might result from the noxious effects of prey-associated chemicals rather than active 'distaste' by phagotrophic cells is discussed. Recent evidence for toxic superoxide (O(2)(-)) production by marine microalgae is afforded particular attention given that release of O(2)(-) anions can be exacerbated by the binding of mannose-specific lectins to the microalgal cell wall; a novel model for grazing-activated chemical defence is proposed.}, }
@article {pmid18641160, year = {2008}, author = {Schmitz-Esser, S and Toenshoff, ER and Haider, S and Heinz, E and Hoenninger, VM and Wagner, M and Horn, M}, title = {Diversity of bacterial endosymbionts of environmental acanthamoeba isolates.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {18}, pages = {5822-5831}, pmid = {18641160}, issn = {1098-5336}, support = {P 19252/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Acanthamoeba/genetics/*microbiology ; Animals ; Bacteria/*classification/genetics ; *Biodiversity ; DNA, Bacterial/genetics ; DNA, Protozoan/genetics ; Genes, Bacterial ; Genes, Protozoan ; Genes, rRNA ; Geologic Sediments/microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Soil Microbiology ; *Symbiosis ; Water Microbiology ; }, abstract = {Free-living amoebae are frequent hosts for bacterial endosymbionts. In this study, the symbionts of eight novel environmental Acanthamoeba strains isolated from different locations worldwide were characterized. Phylogenetic analysis revealed that they were related to one of four evolutionary lineages of amoeba symbionts recognized previously. This study provides evidence for the existence of only a small number of phylogenetically well-separated groups of obligate intracellular endosymbionts of acanthamoebae with global distribution.}, }
@article {pmid18615233, year = {2009}, author = {Lafortune, I and Juteau, P and Déziel, E and Lépine, F and Beaudet, R and Villemur, R}, title = {Bacterial diversity of a consortium degrading high-molecular-weight polycyclic aromatic hydrocarbons in a two-liquid phase biosystem.}, journal = {Microbial ecology}, volume = {57}, number = {3}, pages = {455-468}, pmid = {18615233}, issn = {1432-184X}, mesh = {Bacteria/*genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Biodiversity ; Genes, Bacterial ; Geologic Sediments/microbiology ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/*metabolism ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {High-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs) are pollutants that persist in the environment due to their low solubility in water and their sequestration by soil and sediments. Although several PAH-degrading bacterial species have been isolated, it is not expected that a single isolate would exhibit the ability to degrade completely all PAHs. A consortium composed of different microorganisms can better achieve this. Two-liquid phase (TLP) culture systems have been developed to increase the bioavailability of poorly soluble substrates for uptake and biodegradation by microorganisms. By combining a silicone oil-water TLP system with a microbial consortium capable of degrading HMW PAHs, we previously developed a highly efficient PAH-degrading system. In this report, we characterized the bacterial diversity of the consortium with a combination of culture-dependent and culture-independent methods. Polymerase chain reaction (PCR) of part of the 16S ribosomal RNA gene (rDNA) sequences combined with denaturing gradient gel electrophoresis was used to monitor the bacterial population changes during PAH degradation of the consortium when pyrene, chrysene, and benzo[a]pyrene were provided together or separately in the TLP cultures. No substantial changes in bacterial profiles occurred during biodegradation of pyrene and chrysene in these cultures. However, the addition of the low-molecular-weight PAHs phenanthrene or naphthalene in the system favored one bacterial species related to Sphingobium yanoikuyae. Eleven bacterial strains were isolated from the consortium but, interestingly, only one-IAFILS9 affiliated to Novosphingobium pentaromativorans-was capable of growing on pyrene and chrysene as sole source of carbon. A 16S rDNA library was derived from the consortium to identify noncultured bacteria. Among 86 clones screened, 20 were affiliated to different bacterial species-genera. Only three strains were represented in the screened clones. Eighty-five percent of clones and strains were affiliated to Alphaproteobacteria and Betaproteobacteria; among them, several were affiliated to bacterial species known for their PAH degradation activities such as those belonging to the Sphingomonadaceae. Finally, three genes involved in the degradation of aromatic molecules were detected in the consortium and two in IAFILS9. This study provides information on the bacterial composition of a HWM PAH-degrading consortium and its dynamics in a TLP biosystem during PAH degradation.}, }
@article {pmid18615117, year = {2008}, author = {Bardgett, RD and Freeman, C and Ostle, NJ}, title = {Microbial contributions to climate change through carbon cycle feedbacks.}, journal = {The ISME journal}, volume = {2}, number = {8}, pages = {805-814}, doi = {10.1038/ismej.2008.58}, pmid = {18615117}, issn = {1751-7370}, mesh = {Carbon/*metabolism ; *Climate ; *Environmental Microbiology ; Plants/metabolism ; }, abstract = {There is considerable interest in understanding the biological mechanisms that regulate carbon exchanges between the land and atmosphere, and how these exchanges respond to climate change. An understanding of soil microbial ecology is central to our ability to assess terrestrial carbon cycle-climate feedbacks, but the complexity of the soil microbial community and the many ways that it can be affected by climate and other global changes hampers our ability to draw firm conclusions on this topic. In this paper, we argue that to understand the potential negative and positive contributions of soil microbes to land-atmosphere carbon exchange and global warming requires explicit consideration of both direct and indirect impacts of climate change on microorganisms. Moreover, we argue that this requires consideration of complex interactions and feedbacks that occur between microbes, plants and their physical environment in the context of climate change, and the influence of other global changes which have the capacity to amplify climate-driven effects on soil microbes. Overall, we emphasize the urgent need for greater understanding of how soil microbial ecology contributes to land-atmosphere carbon exchange in the context of climate change, and identify some challenges for the future. In particular, we highlight the need for a multifactor experimental approach to understand how soil microbes and their activities respond to climate change and consequences for carbon cycle feedbacks.}, }
@article {pmid18607657, year = {2009}, author = {Johnson, CN and Flowers, AR and Young, VC and Gonzalez-Escalona, N and DePaola, A and Noriea, NF and Grimes, DJ}, title = {Genetic relatedness among tdh+ and trh+ Vibrio parahaemolyticus cultured from Gulf of Mexico oysters (Crassostrea virginica) and surrounding water and sediment.}, journal = {Microbial ecology}, volume = {57}, number = {3}, pages = {437-443}, pmid = {18607657}, issn = {1432-184X}, mesh = {Animals ; Bacterial Toxins/*genetics ; Bacterial Typing Techniques ; Crassostrea/*microbiology ; DNA, Bacterial/genetics ; Geologic Sediments/microbiology ; Hemolysin Proteins/*genetics ; Mississippi ; Phylogeny ; Sequence Analysis, DNA ; Vibrio parahaemolyticus/classification/*genetics ; }, abstract = {Pathogenic Vibrio parahaemolyticus (Vp) (tdh(+)/trh(+)) represent a small percentage of environmental Vp populations, and very little is known about this subpopulation. Repetitive extragenic palindromic PCR and multilocus sequence analysis revealed heterogeneity among 41 Vp containing thermostable direct hemolysin (tdh) and tdh-related hemolysin (trh) that were isolated from Mississippi coastal environments from October 2006 to April 2007. There was no source-specific sequestering in oysters, water, or sediment.}, }
@article {pmid18604649, year = {2009}, author = {Vohník, M and Burdíková, Z and Albrechtová, J and Vosátka, M}, title = {Testate amoebae (Arcellinida and Euglyphida) vs. Ericoid mycorrhizal and DSE fungi: a possible novel interaction in the mycorrhizosphere of ericaceous plants?.}, journal = {Microbial ecology}, volume = {57}, number = {1}, pages = {203-214}, pmid = {18604649}, issn = {0095-3628}, mesh = {*Amoeba/classification/isolation &amp; purification/microbiology ; Animals ; *Ascomycota/classification/growth &amp; development/isolation &amp; purification/metabolism ; Ecosystem ; *Ericaceae/classification/growth &amp; development/microbiology/parasitology ; *Mycorrhizae ; *Plant Roots/microbiology/parasitology ; Rhododendron/classification/microbiology/parasitology ; Soil/*parasitology ; *Soil Microbiology ; }, abstract = {Common occurrence of testate amoebae (TA) in the rhizosphere of mycorrhizal plants indicates existence of yet undocumented ecological interactions, involving three distinct groups of organisms: soil protists, mycorrhizal fungi, and their host plants. This tripartite relationship was to date investigated only to a limited extent, despite its probable importance for processes taking place in the mycorrhizosphere. In this study, we (1) explored spectra of different TA genera naturally associated with the rhizoplane of three autochthonous European Rhododendron species, (2) screened natural fungal colonization of the TA shells occupying the rhizoplane of selected rhododendrons, and (3) carried out two in vitro experiments addressing the question whether TA shells may serve as a nutrient source for ericoid mycorrhizal fungi (ErMF) and dark septate endophytes (DSE). Our field observations indicated that TA regularly associated with the rhizoplane of all screened rhododendrons and that ErMF and/or DSE associated with their roots possibly exploited the TA shells as a nutrient source. We were unable to detect any major differences among the TA spectra from the rhizoplanes with respect to the three Rhododendron species. The spectra were dominated by Diplochlamys, Centropyxis, Cyclopyxis, Euglypha, Trinema, and Assulina. Positive, neutral, and negative associations were found for various TA genera x Rhododendron species combinations. The highest fungal colonization was observed in Centropyxidae and Trigonopyxidae, reaching up to 45% of the shells in the case of Trigonopyxis. In the in vitro experiments, both ErMF Rhizoscyphus ericae and DSE Phialocephala fortinii regularly colonized TA shells, utilizing them as a source of nutrients. We hypothesize a complex relationship between ErMF-DSE and TA. If corroborated, it would represent an interesting nutrient loop in the mycorrhizosphere of ericaceous plants.}, }
@article {pmid18604648, year = {2009}, author = {Sundset, MA and Edwards, JE and Cheng, YF and Senosiain, RS and Fraile, MN and Northwood, KS and Praesteng, KE and Glad, T and Mathiesen, SD and Wright, AD}, title = {Molecular diversity of the rumen microbiome of Norwegian reindeer on natural summer pasture.}, journal = {Microbial ecology}, volume = {57}, number = {2}, pages = {335-348}, pmid = {18604648}, issn = {0095-3628}, support = {BBS/E/W/00003135A/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/W/00003135B/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biodiversity ; DNA, Archaeal/genetics ; DNA, Fungal/genetics ; DNA, Protozoan/genetics ; Eukaryota/classification/genetics ; Female ; Gene Library ; *Metagenome ; Neocallimastigales/classification/genetics ; Norway ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Reindeer/*microbiology ; Rumen/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The molecular diversity of the rumen microbiome was investigated in five semi-domesticated adult female Norwegian reindeer (Rangifer tarandus tarandus) grazing on natural summer pastures on the coast of northern Norway (71.00 degrees N, 25.30 degrees E). Mean population densities (numbers per gram wet weight) of methanogenic archaea, rumen bacteria and ciliate protozoa, estimated using quantitative real-time polymerase chain reaction (PCR), were 3.17x10(9), 5.17x10(11) and 4.02x10(7), respectively. Molecular diversity of rumen methanogens was revealed using a 16S rRNA gene library (54 clones) constructed using pooled PCR products from the whole rumen contents of the five individual reindeer. Based upon a similarity criterion of <97%, a total of 19 distinct operational taxonomic units (OTUs) were identified, nine of which are potential new species. The 16S rRNA sequences generated from the reindeer rumen exhibited a high degree of sequence similarity to methanogens affiliated with the families Methanobacteriaceae (14 OTUs) and Methanosarcinaceae (one OTU). Four of the OTUs detected belonged to a group of uncultivated archaea previously found in domestic ruminants and thought to be dominant in the rumen together with Methanobrevibacter spp. Denaturing gradient gel electrophoresis profiling of the rumen bacterial 16S rRNA gene and the protozoal 18S rRNA gene indicated a high degree of animal variation, although some bands were common to all individuals. Automated ribosomal intergenic spacer analysis (ARISA) profiling of the ruminal Neocallimastigales population indicated that the reindeer are likely to contain more than one type of anaerobic fungus. The ARISA profile from one animal was distinct from the other four. This is the first molecular investigation of the ruminal methanogenic archaea in reindeer, revealing higher numbers than expected based on methane emission data available. Also, many of the reindeer archaeal 16S rRNA gene sequences were similar to those reported in domesticated ruminants in Australia, Canada, China, New Zealand and Venezuela, supporting previous findings that there seems to be no host type or geographical effect on the methanogenic archaea community structure in ruminants.}, }
@article {pmid18599726, year = {2008}, author = {Duncan, SH and Flint, HJ}, title = {Proposal of a neotype strain (A1-86) for Eubacterium rectale. Request for an opinion.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {58}, number = {Pt 7}, pages = {1735-1736}, doi = {10.1099/ijs.0.2008/004580-0}, pmid = {18599726}, issn = {1466-5026}, mesh = {Eubacterium/*classification/growth &amp; development/metabolism ; Feces/microbiology ; Fermentation ; Humans ; Species Specificity ; }, abstract = {Eubacterium rectale is one of the most abundant bacterial species recovered from human faeces. E. rectale (Hauduroy et al. 1937) appears in the 'List of Bacterial Names with Standing in Nomenclature', but it is noted that the originally proposed type strain, VPI 0989(T), has been lost and its possible replacement by another strain (VPI 0990) from the same faecal sample has never been formally proposed. It is therefore proposed that strain A1-86 (=DSM 17629=NCIMB 14373), isolated from human adult faeces, be formally recognized as the neotype strain of Eubacterium rectale.}, }
@article {pmid18592300, year = {2009}, author = {Liebner, S and Rublack, K and Stuehrmann, T and Wagner, D}, title = {Diversity of aerobic methanotrophic bacteria in a permafrost active layer soil of the Lena Delta, Siberia.}, journal = {Microbial ecology}, volume = {57}, number = {1}, pages = {25-35}, pmid = {18592300}, issn = {0095-3628}, mesh = {Aerobiosis ; Arctic Regions ; DNA, Bacterial/*analysis ; DNA, Ribosomal/analysis ; *Genetic Variation ; *Ice ; Methane/*metabolism ; Methylococcaceae/*classification/genetics/isolation &amp; purification ; Molecular Sequence Data ; Oxygenases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Siberia ; Soil ; *Soil Microbiology ; }, abstract = {With this study, we present first data on the diversity of aerobic methanotrophic bacteria (MOB) in an Arctic permafrost active layer soil of the Lena Delta, Siberia. Applying denaturing gradient gel electrophoresis and cloning of 16S ribosomal ribonucleic acid (rRNA) and pmoA gene fragments of active layer samples, we found a general restriction of the methanotrophic diversity to sequences closely related to the genera Methylobacter and Methylosarcina, both type I MOB. In contrast, we revealed a distinct species-level diversity. Based on phylogenetic analysis of the 16S rRNA gene, two new clusters of MOB specific for the permafrost active layer soil of this study were found. In total, 8 out of 13 operational taxonomic units detected belong to these clusters. Members of these clusters were closely related to Methylobacter psychrophilus and Methylobacter tundripaludum, both isolated from Arctic environments. A dominance of MOB closely related to M. psychrophilus and M. tundripaludum was confirmed by an additional pmoA gene analysis. We used diversity indices such as the Shannon diversity index or the Chao1 richness estimator in order to compare the MOB community near the surface and near the permafrost table. We determined a similar diversity of the MOB community in both depths and suggest that it is not influenced by the extreme physical and geochemical gradients in the active layer.}, }
@article {pmid18590586, year = {2009}, author = {Ramirez-Farias, C and Slezak, K and Fuller, Z and Duncan, A and Holtrop, G and Louis, P}, title = {Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii.}, journal = {The British journal of nutrition}, volume = {101}, number = {4}, pages = {541-550}, doi = {10.1017/S0007114508019880}, pmid = {18590586}, issn = {1475-2662}, mesh = {Adult ; Analysis of Variance ; Base Sequence ; Bifidobacterium/classification/genetics/*physiology ; Colony Count, Microbial ; DNA Fingerprinting ; DNA Primers/genetics ; DNA, Bacterial/analysis ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; *Food Microbiology ; Gene Library ; Humans ; Hydrogen-Ion Concentration ; Intestinal Mucosa/*microbiology ; Inulin/*pharmacology ; Linear Models ; Molecular Sequence Data ; *Probiotics ; Reverse Transcriptase Polymerase Chain Reaction/methods ; Species Specificity ; Stimulation, Chemical ; }, abstract = {Prebiotics are food ingredients that improve health by modulating the colonic microbiota. The bifidogenic effect of the prebiotic inulin is well established; however, it remains unclear which species of Bifidobacterium are stimulated in vivo and whether bacterial groups other than lactic acid bacteria are affected by inulin consumption. Changes in the faecal microbiota composition were examined by real-time PCR in twelve human volunteers after ingestion of inulin (10 g/d) for a 16-d period in comparison with a control period without any supplement intake. The prevalence of most bacterial groups examined did not change after inulin intake, although the low G+C % Gram-positive species Faecalibacterium prausnitzii exhibited a significant increase (10.3% for control period v. 14.5% during inulin intake, P=0.019). The composition of the genus Bifidobacterium was studied in four of the volunteers by clone library analysis. Between three and five Bifidobacterium spp. were found in each volunteer. Bifidobacterium adolescentis and Bifidobacterium longum were present in all volunteers, and Bifidobacterium pseudocatenulatum, Bifidobacterium animalis, Bifidobacterium bifidum and Bifidobacterium dentium were also detected. Real-time PCR was employed to quantify the four most prevalent Bifidobacterium spp., B. adolescentis, B. longum, B. pseudocatenulatum and B. bifidum, in ten volunteers carrying detectable levels of bifidobacteria. B. adolescentis showed the strongest response to inulin consumption, increasing from 0.89 to 3.9% of the total microbiota (P=0.001). B. bifidum was increased from 0.22 to 0.63% (P<0.001) for the five volunteers for whom this species was present.}, }
@article {pmid18587611, year = {2009}, author = {Lemke, MJ and Lienau, EK and Rothe, J and Pagioro, TA and Rosenfeld, J and Desalle, R}, title = {Description of freshwater bacterial assemblages from the upper paraná river floodpulse system, Brazil.}, journal = {Microbial ecology}, volume = {57}, number = {1}, pages = {94-103}, pmid = {18587611}, issn = {0095-3628}, mesh = {Actinobacteria/classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/*isolation &amp; purification ; Bacteroidetes/classification/genetics/isolation &amp; purification ; Brazil ; Cloning, Molecular ; DNA, Bacterial/analysis ; *Disasters ; Ecosystem ; *Floods ; Genetic Variation ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Phylogeny ; Proteobacteria/classification/genetics/isolation &amp; purification ; Rivers/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Bacteria were identified from a large, seasonally flooded river (Paraná River, Brazil) and two floodplain habitats that were part of the same river system yet very different in nature: clearwater Garças Lagoon and the highly humic waters of Patos Lagoon. Bacterioplankton were collected during mid-summer (Jan. 2002) from water samples (2 l) filtered first through a 1.2-microm filter then a 0.2-microm membrane filter representing the particle-attached and free-living sub-communities, respectively. DNA was extracted from filters and purified and a 16S rRNA clone library established for each habitat. Over 300 clones were sequenced and checked for similarity to existing 16S sequences in GenBank using the BLAST algorithm with default parameters. Further classification of clones was done using a species "backbone" attachment followed by parsimony analysis. The majority (85%) of sequences, referred to here as operational taxonomic units (OTUs), were most similar to uncultured bacterium 16S sequences. OTUs from each Proteobacteria sub-phylum (alpha, beta, gamma, delta, epsilon) were present in the Upper Paraná River system, as well as members of the Bacteroidetes. The microbial assemblage from Patos Lagoon was least like other samples in that it had no Firmicutes present and was dominated by Actinobacteria. Verrucomicrobia OTUs were only found in the free-living assemblage. This study documents the presence of globally distributed phyla in Upper Paraná River and taxa unique to habitat and particle attachment.}, }
@article {pmid18587610, year = {2009}, author = {Liang, C and Read, HW and Balser, TC}, title = {Reliability of muramic acid as a bacterial biomarker is influenced by methodological artifacts from streptomycin.}, journal = {Microbial ecology}, volume = {57}, number = {3}, pages = {494-500}, pmid = {18587610}, issn = {1432-184X}, mesh = {*Artifacts ; Bacteria/*chemistry ; Biomarkers/*analysis/chemistry ; Chromatography, Gas/methods ; Mass Spectrometry/methods ; Muramic Acids/*analysis/chemistry ; Streptomycin/*analysis/chemistry ; }, abstract = {The muramic acid (MurA) assay is a powerful tool for the detection and quantification of bacteria with no need to enrich samples by culturing. However, the analysis of MurA in mixed biological and environmental matrices is potentially more complex than analysis in isolated bacterial cells. In this study, we employed one commonly used procedure for extraction of MurA from environmental samples and found that the presence of streptomycin interfered with the determination of MurA by creating chemical species that coeluted with the aldononitrile derivative of MurA prepared in this method. On a molar basis, streptomycin yields a signal that is approximately 0.67 times that of MurA. Mass spectrometry analysis confirmed that the interference from hydrolyzed streptomycin is not actually by MurA, but rather is likely to be N-methyl glucosamine. Because streptomycin is widely applied for selective growth of eukaryotes both in situ and in vitro, our findings may have implications for the significance of results from MurA assays. We conclude that MurA remains an effectual bacterial biomarker due to its unique bacterial origin, but care must be applied in interpreting results from the assay when performed in the presence of streptomycin.}, }
@article {pmid18587609, year = {2009}, author = {Soto, W and Gutierrez, J and Remmenga, MD and Nishiguchi, MK}, title = {Salinity and temperature effects on physiological responses of Vibrio fischeri from diverse ecological niches.}, journal = {Microbial ecology}, volume = {57}, number = {1}, pages = {140-150}, pmid = {18587609}, issn = {0095-3628}, support = {R25 GM061222/GM/NIGMS NIH HHS/United States ; S06 GM008136/GM/NIGMS NIH HHS/United States ; GM-61222-01/GM/NIGMS NIH HHS/United States ; 52005881/HHMI/Howard Hughes Medical Institute/United States ; S06 GM008136-32S2-1/GM/NIGMS NIH HHS/United States ; SC1 AI081659/AI/NIAID NIH HHS/United States ; }, mesh = {Aliivibrio fischeri/growth &amp; development/*isolation &amp; purification/*physiology ; Animals ; Decapodiformes/classification/microbiology ; *Ecosystem ; Fishes/classification/microbiology ; Light ; *Salinity ; Seawater/microbiology ; Species Specificity ; Symbiosis ; *Temperature ; }, abstract = {Vibrio fischeri is a bioluminescent bacterial symbiont of sepiolid squids (Cephalopoda: Sepiolidae) and monocentrid fishes (Actinopterygii: Monocentridae). V. fischeri exhibit competitive dominance within the allopatrically distributed squid genus Euprymna, which have led to the evolution of V. fischeri host specialists. In contrast, the host genus Sepiola contains sympatric species that is thought to have given rise to V. fischeri that have evolved as host generalists. Given that these ecological lifestyles may have a direct effect upon the growth spectrum and survival limits in contrasting environments, optimal growth ranges were obtained for numerous V. fischeri isolates from both free-living and host environments. Upper and lower limits of growth were observed in sodium chloride concentrations ranging from 0.0% to 9.0%. Sepiola symbiotic isolates possessed the least variation in growth throughout the entire salinity gradient, whereas isolates from Euprymna were the least uniform at <2.0% NaCl. V. fischeri fish symbionts (CG101 and MJ101) and all free-living strains were the most dissimilar at >5.0% NaCl. Growth kinetics of symbiotic V. fischeri strains were also measured under a range of salinity and temperature combinations. Symbiotic V. fischeri ES114 and ET101 exhibited a synergistic effect for salinity and temperature, where significant differences in growth rates due to salinity existed only at low temperatures. Thus, abiotic factors such as temperature and salinity have differential effects between free-living and symbiotic strains of V. fischeri, which may alter colonization efficiency prior to infection.}, }
@article {pmid18587608, year = {2009}, author = {Lehman, RM and Lundgren, JG and Petzke, LM}, title = {Bacterial communities associated with the digestive tract of the predatory ground beetle, Poecilus chalcites, and their modification by laboratory rearing and antibiotic treatment.}, journal = {Microbial ecology}, volume = {57}, number = {2}, pages = {349-358}, pmid = {18587608}, issn = {0095-3628}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/drug effects/*genetics/isolation &amp; purification ; Biodiversity ; Coleoptera/*microbiology ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Gastrointestinal Tract/*microbiology ; Gene Library ; Genes, rRNA ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Ground beetles such as Poecilus chalcites (Coleoptera: Carabidae) are beneficial insects in agricultural systems where they contribute to the control of insect and weed pests. We assessed the complexity of bacterial communities occurring in the digestive tracts of field-collected P. chalcites using terminal restriction fragment length polymorphism analyses of polymerase chain reaction-amplified 16S rRNA genes. Bacterial identification was performed by the construction of 16S rRNA gene clone libraries and sequence analysis. Intestinal bacteria in field-collected beetles were then compared to those from groups of beetles that were reared in the lab on an artificial diet with and without antibiotics. Direct cell counts estimated 1.5x10(8) bacteria per milliliter of gut. The digestive tract of field-collected P. chalcites produced an average of 4.8 terminal restriction fragments (tRF) for each beetle. The most abundant clones were affiliated with the genus Lactobacillus, followed by the taxa Enterobacteriaceae, Clostridia, and Bacteriodetes. The majority of the sequences recovered were closely related to those reported from other insect gastrointestinal tracts. Lab-reared beetles produced fewer tRF, an average of 3.1 per beetle, and a reduced number of taxa with a higher number of clones from the family Enterobacteriaceae compared to the field-collected beetles. Antibiotic treatment significantly (p<0.05) reduced the number of tRF per beetle and selected for a less diverse set of bacterial taxa. We conclude that the digestive tract of P. chalcites is colonized by a simple community of bacteria that possess autochthonous characteristics. Laboratory-reared beetles harbored the most common bacteria found in field-collected beetles, and these bacterial communities may be manipulated in the laboratory with the addition of antibiotics to the diet to allow study of functional roles.}, }
@article {pmid18587180, year = {2008}, author = {Smith, RC and Saikaly, PE and Zhang, K and Thomatos, S and Oerther, DB}, title = {Ecological engineering of bioaugmentation from side-stream nitrification.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {57}, number = {12}, pages = {1927-1933}, doi = {10.2166/wst.2008.628}, pmid = {18587180}, issn = {0273-1223}, mesh = {Bacteria/classification/genetics/metabolism ; Biodegradation, Environmental ; Bioreactors/*microbiology ; Nitrites/*metabolism ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Waste Disposal, Fluid/*methods ; }, abstract = {Wastewater treatment relies on careful integration of environmental engineering with microbial ecology. This would seem to be particularly the case when attempting to enhance survivability of organisms introduced from outside the main-stream reactor, i.e. bioaugmentation. Molecular biology tools were utilised in this study to assist in understanding the mechanisms of successful bioaugmentation. Molecular fingerprinting showed that side-stream reactor configuration strongly influenced ammonia-oxidising bacteria (AOB) community structure. In both lab-scale and full-scale systems, AOB communities in the side-stream and main-stream were very similar. The experimental systems revealed that a PFR side-stream produced greater diversity of AOB than a CSTR side-stream in a PFR main-stream system, whereas the full-scale side-stream resulted in essentially an AOB monoculture. Phylogenetic analysis revealed less diversity than molecular fingerprinting perhaps due to biases in the cloning/transformation procedure.}, }
@article {pmid18582331, year = {2008}, author = {Liy, Y and Dan, J and Tao, H and Xuedong, Z}, title = {Regulation of urease expression of Actinomyces naeslundii in biofilms in response to pH and carbohydrate.}, journal = {Oral microbiology and immunology}, volume = {23}, number = {4}, pages = {315-319}, doi = {10.1111/j.1399-302X.2008.00430.x}, pmid = {18582331}, issn = {1399-302X}, mesh = {Actinomyces/*enzymology/physiology ; Bacterial Proteins/analysis/genetics ; Bacteriological Techniques ; *Biofilms ; Biomass ; Bioreactors ; Colony Count, Microbial ; Culture Media ; Gene Expression Regulation, Enzymologic/genetics ; Glucose/analysis/pharmacology ; Humans ; Hydrogen-Ion Concentration ; Microscopy, Confocal ; RNA, Messenger/analysis ; Reverse Transcriptase Polymerase Chain Reaction ; Sucrose/metabolism/*pharmacology ; Temperature ; Time Factors ; Transcription, Genetic/genetics ; Up-Regulation ; Urease/*analysis/genetics ; }, abstract = {INTRODUCTION: The hydrolysis of urea by the urease enzymes of oral bacteria is believed to have a major impact on oral microbial ecology and to be intimately involved in oral health and diseases. Actinomyces naeslundii is a ureolytic bacterium that is adapted to tolerate the rapid and dramatic fluctuations in nutrient availability, carbohydrate source, and pH in dental biofilms. Our research objectives were to better understand the regulation of the expression of urease under environmental conditions that closely mimic those in dental biofilms.<br><br>METHODS: A. naeslundii ATCC12104 were grown in a chemostat biofilm reactor with carbohydrate-limited medium for 3 days followed by a carbohydrate pulse, at pH 7.0 and at pH 5.5. Urease activities and ureC gene messenger RNA levels of cells in the biofilm were measured before and after the carbohydrate pulse.<br><br>RESULTS: We found that the neutral pH environments and excess carbohydrate availability could both result in enhancement of urease activity in biofilm cells. The ureC messenger RNA level of A. naeslundii biofilm cells cultivated at pH 7.0 was approximately 10-fold higher than that of cells grown at pH 5.5, but no changes in ureC gene expression were detected after the carbohydrate pulse.<br><br>CONCLUSIONS: Neutral pH environments and excess carbohydrate availability could promote urease expression of A. naeslundii in biofilms, but only neutral pH environments could up-regulate the ureC gene expression and the pH regulates ureC gene expression at a transcriptional level.}, }
@article {pmid18581037, year = {2009}, author = {Rooney, DC and Clipson, NJ}, title = {Phosphate addition and plant species alters microbial community structure in acidic upland grassland soil.}, journal = {Microbial ecology}, volume = {57}, number = {1}, pages = {4-13}, pmid = {18581037}, issn = {0095-3628}, mesh = {Agrostis/growth &amp; development ; Bacteria/classification/drug effects/genetics/*growth &amp; development ; DNA, Bacterial/analysis ; DNA, Fungal/analysis ; DNA, Ribosomal Spacer/analysis ; *Ecosystem ; Festuca/growth &amp; development ; Fungi/classification/drug effects/genetics/*growth &amp; development ; Hydrogen-Ion Concentration ; Lolium/growth &amp; development ; Phosphates/metabolism/*pharmacology ; Poaceae/*classification/*growth &amp; development ; Ribotyping ; Soil/analysis ; *Soil Microbiology ; Species Specificity ; }, abstract = {Agricultural improvement (addition of fertilizers, liming) of seminatural acidic grasslands across Ireland and the UK has resulted in significant shifts in floristic composition, soil chemistry, and microbial community structure. Although several factors have been proposed as responsible for driving shifts in microbial communities, the exact causes of such changes are not well defined. Phosphate was added to grassland microcosms to investigate the effect on fungal and bacterial communities. Plant species typical of unimproved grasslands (Agrostis capillaris, Festuca ovina) and agriculturally improved grasslands (Lolium perenne) were grown, and phosphate was added 25 days after seed germination, with harvesting after a further 50 days. Phosphate addition significantly increased root biomass (p < 0.001) and shoot biomass (p < 0.05), soil pH (by 0.1 U), and microbial activity (by 5.33 mg triphenylformazan [TPF] g(-1) soil; p < 0.001). A slight decrease (by 0.257 mg biomass-C g(-1) soil; p < 0.05) in microbial biomass after phosphate addition was found. The presence of plant species significantly decreased soil pH (p < 0.05; by up to 0.2 U) and increased microbial activity (by up to 6.02 mg TPF g(-1) soil) but had no significant effect on microbial biomass. Microbial communities were profiled using automated ribosomal intergenic spacer analysis. Multidimensional scaling plots and canonical correspondence analysis revealed that phosphate addition and its interactions with upland grassland plant species resulted in considerable changes in the fungal and bacterial communities of upland soil. The fungal community structure was significantly affected by both phosphate (R = 0.948) and plant species (R = 0.857), and the bacterial community structure was also significantly affected by phosphate (R = 0.758) and plant species (R = 0.753). Differences in microbial community structure following P addition were also revealed by similarity percentage analysis. These data suggest that phosphate application may be an important contributor to microbial community structural change during agricultural management of upland grasslands.}, }
@article {pmid18580970, year = {2008}, author = {Milinovich, GJ and Burrell, PC and Pollitt, CC and Klieve, AV and Blackall, LL and Ouwerkerk, D and Woodland, E and Trott, DJ}, title = {Microbial ecology of the equine hindgut during oligofructose-induced laminitis.}, journal = {The ISME journal}, volume = {2}, number = {11}, pages = {1089-1100}, doi = {10.1038/ismej.2008.67}, pmid = {18580970}, issn = {1751-7370}, mesh = {Animals ; Bacteria/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; Cecum/chemistry/microbiology ; Escherichia coli/classification/isolation &amp; purification ; Fatty Acids, Volatile/analysis ; Gastrointestinal Tract/*microbiology ; Horse Diseases/*microbiology ; Horses ; Lactic Acid/analysis ; Oligosaccharides/*administration &amp; dosage/analysis ; Streptococcus/classification/isolation &amp; purification ; Veillonellaceae/classification/isolation &amp; purification ; }, abstract = {Alimentary carbohydrate overload is a significant cause of laminitis in horses and is correlated with drastic shifts in the composition of hindgut microbiota. Equine hindgut streptococcal species (EHSS), predominantly Streptococcus lutetiensis, have been shown to be the most common microorganisms culturable from the equine caecum prior to the onset of laminitis. However, the inherent biases of culture-based methods are estimated to preclude up to 70% of the normal caecal microbiota. The objective of this study was to evaluate bacterial population shifts occurring in the equine caecum throughout the course of oligofructose-induced laminitis using several culture-independent techniques and to correlate these with caecal lactate, volatile fatty acid and degrees of polymerization 3-7 fructo-oligosaccharide concentrations. Our data conclusively show that of the total microbiota present in the equine hindgut, the EHSS S. lutetiensis is the predominant microorganism that proliferates prior to the onset of laminitis, utilizing oligofructose to produce large quantities of lactate. Population shifts in lactobacilli and Escherichia coli subpopulations occur secondarily to the EHSS population shifts, thus confirming that lactobacilli and coliforms have no role in laminitis. A large, curved, Gram-negative rod previously observed during the early phases of laminitis induction was most closely related to the Anaerovibrio genus and most likely represents a new, yet to be cultured, genus and species. Correlation of fluorescence in situ hybridization and quantitative real-time PCR results provide evidence supporting the hypothesis that laminitis is associated with the death en masse and rapid cell lysis of EHSS. If EHSS are lysed, liberated cellular components may initiate laminitis.}, }
@article {pmid18577459, year = {2009}, author = {Dunkley, KD and Callaway, TR and Chalova, VI and McReynolds, JL and Hume, ME and Dunkley, CS and Kubena, LF and Nisbet, DJ and Ricke, SC}, title = {Foodborne Salmonella ecology in the avian gastrointestinal tract.}, journal = {Anaerobe}, volume = {15}, number = {1-2}, pages = {26-35}, doi = {10.1016/j.anaerobe.2008.05.007}, pmid = {18577459}, issn = {1095-8274}, mesh = {Animals ; *Ecology ; Eggs/*microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Meat Products/*microbiology ; Poultry ; Poultry Diseases/*microbiology ; Salmonella Infections, Animal/*microbiology/*transmission ; Salmonella enteritidis/isolation &amp; purification/pathogenicity ; Salmonella typhimurium/isolation &amp; purification/pathogenicity ; }, abstract = {Foodborne Salmonella continues to be a major cause of salmonellosis with Salmonella Enteritidis and S. Typhimurium considered to be responsible for most of the infections. Investigation of outbreaks and sporadic cases has indicated that food vehicles such as poultry and poultry by-products including raw and uncooked eggs are among the most common sources of Salmonella infections. The dissemination and infection of the avian intestinal tract remain somewhat unclear. In vitro incubation of Salmonella with mammalian tissue culture cells has shown that invasion into epithelial cells is complex and involves several genetic loci and host factors. Several genes are required for the intestinal phase of Salmonella invasion and are located on Salmonella pathogenicity island 1 (SPI 1). Salmonella pathogenesis in the gastrointestinal (GI) tract and the effects of environmental stimuli on gene expression influence bacterial colonization and invasion. Furthermore, significant parameters of Salmonella including growth physiology, nutrient availability, pH, and energy status are considered contributing factors in the GI tract ecology. Approaches for limiting Salmonella colonization have been primarily based on the microbial ecology of the intestinal tract. In vitro studies have shown that the toxic effects of short chain fatty acids (SCFA) to some Enterobacteriaceae, including Salmonella, have resulted in a reduction in population. In addition, it has been established that native intestinal microorganisms such as Lactobacilli provide protective mechanisms against Salmonella in the ceca. A clear understanding of the key factors involved in Salmonella colonization in the avian GI tract has the potential to lead to better approach for more effective control of this foodborne pathogen.}, }
@article {pmid18575805, year = {2008}, author = {Clauwaert, P and van der Ha, D and Verstraete, W}, title = {Energy recovery from energy rich vegetable products with microbial fuel cells.}, journal = {Biotechnology letters}, volume = {30}, number = {11}, pages = {1947-1951}, doi = {10.1007/s10529-008-9778-2}, pmid = {18575805}, issn = {1573-6776}, mesh = {*Bioelectric Energy Sources ; Bioreactors/*microbiology ; Glycerol/metabolism ; Medicago/*metabolism ; Oxidation-Reduction ; }, abstract = {Two types of rapidly biodegradable vegetable products (the liquid fraction of clover and the glycerol-containing sidestream from biodiesel production) were selected for anodic oxidation in microbial fuel cells (MFC) equipped with a biocathode. As benchmark references, five abundant amino-acids in plant sap (L: -glutamine, L: -glutamic acid, L: -asparagine, L: -aspartic acid and L: -alanine) were tested separately. Their performance was in the same order of magnitude of clover sap oxidation (145-225 A m(-3) MFC; 39-95 W m(-3) MFC). Glycerol oxidation resulted in competitive current and power outputs (111 A m(-3) MFC; 23 W m(-3) MFC).}, }
@article {pmid18575584, year = {2008}, author = {Urich, T and Lanzén, A and Qi, J and Huson, DH and Schleper, C and Schuster, SC}, title = {Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome.}, journal = {PloS one}, volume = {3}, number = {6}, pages = {e2527}, pmid = {18575584}, issn = {1932-6203}, mesh = {Ecosystem ; RNA, Bacterial/*genetics ; RNA, Messenger/*genetics ; RNA, Ribosomal/*genetics ; *Soil Microbiology ; Species Specificity ; }, abstract = {BACKGROUND: Soil ecosystems harbor the most complex prokaryotic and eukaryotic microbial communities on Earth. Experimental approaches studying these systems usually focus on either the soil community's taxonomic structure or its functional characteristics. Many methods target DNA as marker molecule and use PCR for amplification.<br><br>Here we apply an RNA-centered meta-transcriptomic approach to simultaneously obtain information on both structure and function of a soil community. Total community RNA is random reversely transcribed into cDNA without any PCR or cloning step. Direct pyrosequencing produces large numbers of cDNA rRNA-tags; these are taxonomically profiled in a binning approach using the MEGAN software and two specifically compiled rRNA reference databases containing small and large subunit rRNA sequences. The pyrosequencing also produces mRNA-tags; these provide a sequence-based transcriptome of the community. One soil dataset of 258,411 RNA-tags of approximately 98 bp length contained 193,219 rRNA-tags with valid taxonomic information, together with 21,133 mRNA-tags. Quantitative information about the relative abundance of organisms from all three domains of life and from different trophic levels was obtained in a single experiment. Less frequent taxa, such as soil Crenarchaeota, were well represented in the data set. These were identified by more than 2,000 rRNA-tags; furthermore, their activity in situ was revealed through the presence of mRNA-tags specific for enzymes involved in ammonia oxidation and CO(2) fixation.<br><br>CONCLUSIONS/SIGNIFICANCE: This approach could be widely applied in microbial ecology by efficiently linking community structure and function in a single experiment while avoiding biases inherent in other methods.}, }
@article {pmid18573518, year = {2009}, author = {Uhlík, O and Jecná, K and Leigh, MB and Macková, M and Macek, T}, title = {DNA-based stable isotope probing: a link between community structure and function.}, journal = {The Science of the total environment}, volume = {407}, number = {12}, pages = {3611-3619}, doi = {10.1016/j.scitotenv.2008.05.012}, pmid = {18573518}, issn = {0048-9697}, mesh = {Bacteria/*classification/*genetics ; Biodegradation, Environmental ; Carbon Isotopes ; DNA, Bacterial/chemistry ; Ecosystem ; Isotope Labeling/*methods ; }, abstract = {DNA-based molecular techniques permit the comprehensive determination of microbial diversity but generally do not reveal the relationship between the identity and the function of microorganisms. The first direct molecular technique to enable the linkage of phylogeny with function is DNA-based stable isotope probing (DNA-SIP). Applying this method first helped describe the utilization of simple compounds, such as methane, methanol or glucose and has since been used to detect microbial communities active in the utilization of a wide variety of compounds, including various xenobiotics. The principle of the method lies in providing (13)C-labeled substrate to a microbial community and subsequent analyses of the (13)C-DNA isolated from the community. Isopycnic centrifugation permits separating (13)C-labeled DNA of organisms that utilized the substrate from (12)C-DNA of the inactive majority. As the whole metagenome of active populations is isolated, its follow-up analysis provides successful taxonomic identification as well as the potential for functional gene analyses. Because of its power, DNA-SIP has become one of the leading techniques of microbial ecology research. But from other point of view, it is a labor-intensive method that requires careful attention to detail during each experimental step in order to avoid misinterpretation of results.}, }
@article {pmid18568286, year = {2009}, author = {Hou, BC and Wang, ET and Li, Y and Jia, RZ and Chen, WF and Man, CX and Sui, XH and Chen, WX}, title = {Rhizobial resource associated with epidemic legumes in Tibet.}, journal = {Microbial ecology}, volume = {57}, number = {1}, pages = {69-81}, pmid = {18568286}, issn = {0095-3628}, mesh = {Acyltransferases/genetics ; Alphaproteobacteria/*classification/genetics/*isolation &amp; purification/metabolism ; Bacterial Proteins/genetics ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; DNA, Ribosomal Spacer/analysis ; Fabaceae/classification/*microbiology ; N-Acetylglucosaminyltransferases/genetics ; Nitrogen Fixation ; Phylogeny ; Plant Roots/*microbiology ; Polymerase Chain Reaction/methods ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Restriction Mapping ; Rhizobiaceae/classification/genetics/isolation &amp; purification/metabolism ; Symbiosis/genetics ; Tibet ; }, abstract = {A total of 128 bacterial test strains originated from Astragalus, Caragana, Gueldenstaedtia, Medicago, Melilotus, Oxytropis, Trifolium, and Vicia grown in Tibet were characterized phenotypically and genomically. Based upon the consensus of grouping results, they were identified as 16 putative species. Twenty-five test strains belonging to seven putative species of Agrobacterium, Bradyrhizobium, and Rhizobium might be nonsymbiotic bacteria and the remaining 103 test strains were symbiotic bacteria belonging to Mesorhizobium, Rhizobium, and Sinorhizobium meliloti. Although no novel taxon was detected in the symbiotic bacteria, several characters including the alkaliphilic psychrotolerance revealed that the Tibetan rhizobia could be ecotypes adapted to the local conditions. The results also demonstrated that frequent lateral transfer of symbiotic genes might have happened in the Tibetan rhizobia since nodC genes similar to that of S. meliloti were found in several Rhizobium test strains and all the Mesorhizobium species had very similar nodC genes despite their genomic background. All of these findings demonstrated that the Tibetan rhizobia were an important resource for further studies on rhizobial ecology and application.}, }
@article {pmid18567753, year = {2008}, author = {Possemiers, S and Rabot, S and Espín, JC and Bruneau, A and Philippe, C and González-Sarrías, A and Heyerick, A and Tomás-Barberán, FA and De Keukeleire, D and Verstraete, W}, title = {Eubacterium limosum activates isoxanthohumol from hops (Humulus lupulus L.) into the potent phytoestrogen 8-prenylnaringenin in vitro and in rat intestine.}, journal = {The Journal of nutrition}, volume = {138}, number = {7}, pages = {1310-1316}, doi = {10.1093/jn/138.7.1310}, pmid = {18567753}, issn = {1541-6100}, mesh = {Animals ; Base Sequence ; Biotransformation ; DNA Primers/genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; Diet ; Eubacterium/genetics/*metabolism ; Female ; Flavanones/*metabolism ; Germ-Free Life ; Humans ; Humulus/*metabolism ; In Vitro Techniques ; Intestinal Mucosa/metabolism ; Intestines/microbiology ; Male ; Phytoestrogens/*metabolism ; Polymerase Chain Reaction ; Probiotics ; Rats ; Rats, Inbred F344 ; Xanthones/*metabolism ; }, abstract = {Recently, it was shown that the exposure to the potent hop phytoestrogen 8-prenylnaringenin (8-PN) depends on intestinal bacterial activation of isoxanthohumol (IX), but this occurs in only one-third of tested individuals. As the butyrate-producing Eubacterium limosum can produce 8-PN from IX, a probiotic strategy was applied to investigate whether 8-PN production could be increased in low 8-PN producers, thus balancing phytoestrogen exposure. Using fecal samples from high (Hop +) and low (Hop -) 8-PN-producing individuals, a Hop + and Hop - dynamic intestinal model was developed. In parallel, Hop + and Hop - human microbiota-associated rats were developed, germ-free (GF) rats acting as negative controls. IX and then IX + E. limosum were administered in the intestinal model and to the rats, and changes in 8-PN production and exposure were assessed. After dosing IX, 80% was converted into 8-PN in the Hop + model and highest 8-PN production, plasma concentrations, and urinary and fecal excretion occurred in the Hop + rats. Administration of the bacterium triggered 8-PN production in the GF rats and increased 8-PN production in the Hop - model and Hop - rats. 8-PN excretion was similar in the feces (294.1 +/- 132.2 nmol/d) and urine (8.5 +/- 1.1 nmol/d) of all rats (n = 18). In addition, butyrate production increased in all rats. In conclusion, intestinal microbiota determined 8-PN production and exposure after IX intake. Moreover, E. limosum administration increased 8-PN production in low producers, resulting in similar 8-PN production in all rats.}, }
@article {pmid18566261, year = {2008}, author = {Pala, C}, title = {Microbial ecology. Out of thin air.}, journal = {Science (New York, N.Y.)}, volume = {320}, number = {5883}, pages = {1582-1583}, doi = {10.1126/science.320.5883.1582}, pmid = {18566261}, issn = {1095-9203}, mesh = {Atmosphere/chemistry ; Bacteria/isolation &amp; purification/*metabolism ; Carbon/metabolism ; Carbon Dioxide/metabolism ; Carbon Monoxide/analysis/*metabolism ; *Ecosystem ; Hydrogen/analysis ; Nitrogen/metabolism ; Oxidation-Reduction ; Plant Development ; *Soil Microbiology ; Symbiosis ; Trees/growth &amp; development ; *Volcanic Eruptions ; }, }
@article {pmid18563478, year = {2009}, author = {Duc, L and Noll, M and Meier, BE and Bürgmann, H and Zeyer, J}, title = {High diversity of diazotrophs in the forefield of a receding alpine glacier.}, journal = {Microbial ecology}, volume = {57}, number = {1}, pages = {179-190}, pmid = {18563478}, issn = {0095-3628}, mesh = {*Altitude ; Asteraceae/genetics/growth &amp; development/microbiology ; DNA, Bacterial/analysis ; Genetic Variation ; Geobacter ; Gram-Negative Bacteria/*classification/*genetics/metabolism ; Ice Cover/*microbiology ; Molecular Sequence Data ; *Nitrogen Fixation ; Oxidoreductases/genetics/metabolism ; Phylogeny ; Plant Roots/microbiology ; Poaceae/genetics/growth &amp; development/microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; Switzerland ; Time Factors ; }, abstract = {Forefields of receding glaciers are unique and sensitive environments representing natural chronosequences. In such habitats, microbial nitrogen fixation is of particular interest since the low concentration of bioavailable nitrogen is one of the key limitations for growth of plants and soil microorganisms. Asymbiotic nitrogen fixation in the Damma glacier (Swiss Central Alps) forefield soils was assessed using the acetylene reduction assay. Free-living diazotrophic diversity and population structure were resolved by assembling four NifH sequence libraries for bulk and rhizosphere soils at two soil age classes (8- and 70-year ice-free forefield). A total of 318 NifH sequences were analyzed and grouped into 45 unique phylotypes. Phylogenetic analyses revealed a higher diversity as well as a broader distribution of NifH sequences among phylogenetic clusters than formerly observed in other environments. This illustrates the importance of free-living diazotrophs and their potential contribution to the global nitrogen input in this nutrient-poor environment. NifH diversity in bulk soils was higher than in rhizosphere soils. Moreover, the four libraries displayed low similarity values. This indicated that both soil age and the presence of pioneer plants influence diversification and population structure of free-living diazotrophs.}, }
@article {pmid18563187, year = {2008}, author = {Morris, BE and Crable, BR and Suflita, JM}, title = {On the contributions of David Cleaveland White, MD, PhD to microbial ecology: celebrating the life of a pioneer.}, journal = {The ISME journal}, volume = {2}, number = {8}, pages = {797-804}, doi = {10.1038/ismej.2008.65}, pmid = {18563187}, issn = {1751-7370}, mesh = {Ecology/*history ; *Environmental Microbiology ; History, 20th Century ; History, 21st Century ; }, }
@article {pmid18558332, year = {2008}, author = {Furukawa, K and Fujihara, H}, title = {Microbial degradation of polychlorinated biphenyls: biochemical and molecular features.}, journal = {Journal of bioscience and bioengineering}, volume = {105}, number = {5}, pages = {433-449}, doi = {10.1263/jbb.105.433}, pmid = {18558332}, issn = {1347-4421}, mesh = {*Bacterial Physiological Phenomena ; Biodegradation, Environmental ; Environmental Pollutants/*metabolism ; Polychlorinated Biphenyls/*chemistry/isolation &amp; purification/*metabolism ; }, abstract = {It is more than 40 years since the environmental contamination of polychlorinated biphenyls (PCBs) was first reported in wildlife samples. Since then, a huge number of papers on PCBs have been published, which include the biodegradation of PCBs and toxicology of PCBs. The studies on the microbial degradation of PCBs during the few decades provided significant insight into the areas of microbial ecology, biochemistry, and molecular genetics.}, }
@article {pmid18555549, year = {2008}, author = {Rantsiou, K and Urso, R and Dolci, P and Comi, G and Cocolin, L}, title = {Microflora of Feta cheese from four Greek manufacturers.}, journal = {International journal of food microbiology}, volume = {126}, number = {1-2}, pages = {36-42}, doi = {10.1016/j.ijfoodmicro.2008.04.031}, pmid = {18555549}, issn = {0168-1605}, mesh = {Cheese/*microbiology ; Cluster Analysis ; Colony Count, Microbial/*methods ; DNA, Bacterial/analysis ; Ecosystem ; Electrophoresis, Polyacrylamide Gel/methods ; Fermentation ; *Food Microbiology ; Greece ; Humans ; Lactobacillus/genetics/*isolation &amp; purification ; Polymerase Chain Reaction/methods ; Population Dynamics ; RNA, Bacterial/analysis ; Sensitivity and Specificity ; Species Specificity ; Temperature ; Yeasts/genetics/*isolation &amp; purification ; }, abstract = {The components of the microflora of four Feta cheeses, produced by different Greek manufacturers, were determined by culture dependent and independent techniques. Isolates from microbiological media were first grouped by Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) and then representatives of each DGGE group were sequenced for identification purposes. DNA and RNA, extracted directly from the cheese, were subjected to PCR-DGGE. Moreover, Feta cheeses were subjected to FISH analysis in order to identify viable bacterial populations. The microbial ecology, as represented by the Lactic Acid Bacteria (LAB) and yeast populations, was different for the four cheeses. The main LAB species isolated were Lactobacillus plantarum, Lactobacillus brevis, Lactobacillus coryniformis and Lactobacillus fermentum. However, some inconsistencies were observed between the results obtained with the culture dependent and the culture independent approach. In the case of the yeasts, the results obtained by PCR-DGGE compared very well with those obtained by the conventional microbiological analysis and the main species found were Kluyveromyces lactis, Pichia fermentans and C. zeylanoides. FISH analysis highlighted viable but not culturable populations of Streptococcus thermophilus and Lactococcus spp. RAPD-PCR performed on the L. plantarum isolates revealed a cheese specific distribution and a temperature dependent clustering.}, }
@article {pmid18554975, year = {2008}, author = {Allen, MJ and Wilson, WH}, title = {Aquatic virus diversity accessed through omic techniques: a route map to function.}, journal = {Current opinion in microbiology}, volume = {11}, number = {3}, pages = {226-232}, doi = {10.1016/j.mib.2008.05.004}, pmid = {18554975}, issn = {1369-5274}, mesh = {Archaea/virology ; *Biodiversity ; Ecosystem ; Eukaryotic Cells/virology ; *Genomics ; Oligonucleotide Array Sequence Analysis ; Prokaryotic Cells/virology ; *Proteomics ; Sequence Analysis, DNA ; Viruses/*classification/genetics ; *Water Microbiology ; }, abstract = {Viruses are arguably the simplest form of life yet they play a crucial role in regulating planetary processes. From shuttling genes to 'lubricating' microbial loop dynamics, viruses are integral in shaping microbial ecology. In every environment on Earth the role of viruses goes far beyond the simple infect-replicate-kill cycle. Their enormous abundance and seemingly infinite diversity provide the vital clues to the true function of viruses. New 'omic' approaches are now allowing researchers to gain extraordinary insights into virus diversity and inferred function, particularly within aquatic environments. The development of molecular markers and application of techniques including microarrays, metagenomic sequencing and proteomic analysis are now being applied to virus communities. Despite this shift towards culture-independent approaches it has proved difficult to derive useful information about infection strategies since so much of the sequence information has no database matches. Future advances will involve tools such as microarrays to help determine the functionality of unknown genes. Sequence information should be considered as a starting point for asking questions and developing hypotheses about the role of viruses. It is an exciting new era for virus ecology and when used in combination with more traditional approaches, virus genomics will give us access to their ecological function on an unprecedented scale.}, }
@article {pmid18554888, year = {2008}, author = {Hedh, J and Samson, P and Erland, S and Tunlid, A}, title = {Multiple gene genealogies and species recognition in the ectomycorrhizal fungus Paxillus involutus.}, journal = {Mycological research}, volume = {112}, number = {Pt 8}, pages = {965-975}, doi = {10.1016/j.mycres.2008.01.026}, pmid = {18554888}, issn = {0953-7562}, mesh = {Basidiomycota/*classification/*genetics/isolation &amp; purification ; DNA, Fungal/genetics ; Ecosystem ; *Environmental Microbiology ; Fungal Proteins/genetics ; Host-Pathogen Interactions ; Molecular Sequence Data ; Mycorrhizae/*classification/*genetics/isolation &amp; purification ; Phylogeny ; Polymorphism, Genetic ; }, abstract = {Paxillus involutus (basidiomycetes, Boletales) is a common ectomycorrhizal fungus in the Northern Hemisphere. The fungus displays significant variation in phenotypic characters related to morphology, physiology, and ecology. Previous studies have shown that P. involutus contains several intersterility groups and morphological species. In this study, we have used concordance of multiple gene genealogies to identify genetically isolated species of P. involutus. Fragments from five protein coding genes in 50 isolates of P. involutus collected from different hosts and environments in Europe and one location in Canada were analysed using phylogenetic methods. Concordance of the five gene genealogies showed that P. involutus comprises at least four distinct phylogenetic lineages: phylogenetic species I (with nine isolates), II (33 isolates), III (three isolates), and IV (five isolates). The branches separating the four species were long and well supported compared with the species internodes. A low level of shared polymorphisms was observed among the four lineages indicating a long time since the genetic isolation began. Three of the phylospecies corresponded to earlier identified morphological species: I to P. obscurosporus, II to P. involutus s. str., and III to P. validus. The phylogenetic species had an overlapping geographical distribution. Species I and II differed partly in habitat and host preferences.}, }
@article {pmid18553170, year = {2009}, author = {Baniulyte, D and Favila, E and Kelly, JJ}, title = {Shifts in microbial community composition following surface application of dredged river sediments.}, journal = {Microbial ecology}, volume = {57}, number = {1}, pages = {160-169}, pmid = {18553170}, issn = {0095-3628}, mesh = {*Bacteria/classification/genetics/growth &amp; development/isolation &amp; purification ; Biomass ; Chicago ; Cloning, Molecular ; Conservation of Natural Resources ; *Ecosystem ; Fatty Acids/analysis ; *Fungi/classification/genetics/growth &amp; development/isolation &amp; purification ; Gene Library ; Geologic Sediments/chemistry/*microbiology ; Illinois ; Molecular Sequence Data ; Polymorphism, Restriction Fragment Length ; Rivers/*microbiology ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Sediment input to the Illinois River has drastically decreased river depth and reduced habitats for aquatic organisms. Dredging is being used to remove sediment from the Illinois River, and the dredged sediment is being applied to the surface of a brownfield site in Chicago with the goal of revegetating the site. In order to determine the effects of this drastic habitat change on sediment microbial communities, we examined sediment physical, chemical, and microbial characteristics at the time of sediment application to the soil surface as well as 1 and 2 years after application. Microbial community biomass was determined by measurement of lipid phosphate. Microbial community composition was assessed using phospholipid fatty acid (PLFA) analysis, terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes, and clone library sequencing of 16S rRNA genes. Results indicated that the moisture content, organic carbon, and total nitrogen content of the sediment all decreased over time. Total microbial biomass did not change over the course of the study, but there were significant changes in the composition of the microbial communities. PLFA analysis revealed relative increases in fungi, actinomycetes, and Gram positive bacteria. T-RFLP analysis indicated a significant shift in bacterial community composition within 1 year of application, and clone library analysis revealed relative increases in Proteobacteria, Gemmatimonadetes, and Bacteriodetes and relative decreases in Acidobacteria, Spirochaetes, and Planctomycetes. These results provide insight into microbial community shifts following land application of dredged sediment.}, }
@article {pmid18548185, year = {2009}, author = {Rojas, R and Miranda, CD and Amaro, AM}, title = {Pathogenicity of a highly exopolysaccharide-producing Halomonas strain causing epizootics in larval cultures of the Chilean scallop Argopecten purpuratus (Lamarck, 1819).}, journal = {Microbial ecology}, volume = {57}, number = {1}, pages = {129-139}, pmid = {18548185}, issn = {0095-3628}, mesh = {Animals ; Aquaculture ; Chile ; DNA, Bacterial/analysis ; Halomonas/*classification/genetics/metabolism/*pathogenicity ; Larva/growth &amp; development/microbiology/ultrastructure ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; Pectinidae/growth &amp; development/*microbiology/ultrastructure ; Polymerase Chain Reaction ; Polysaccharides, Bacterial/*biosynthesis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Shellfish/*microbiology ; }, abstract = {Mass mortalities of larval cultures of Chilean scallop Argopecten purpuratus have repeatedly occurred in northern Chile, characterized by larval agglutination and accumulation in the bottom of rearing tanks. The exopolysaccharide slime (EPS) producing CAM2 strain was isolated as the primary organism from moribund larvae in a pathogenic outbreak occurring in a commercial hatchery producing larvae of the Chilean scallop Argopecten purpuratus located in Bahía Inglesa, Chile. The CAM2 strain was characterized biochemically and was identified by polymerase chain reaction amplification of 16S rRNA as Halomonas sp. (Accession number DQ885389.1). Healthy 7-day-old scallop larvae cultures were experimentally infected for a 48-h period with an overnight culture of the CAM2 strain at a final concentration of ca. 10(5) cells per milliliter, and the mortality and vital condition of larvae were determined by optical and scanning electron microscopy (SEM) to describe the chronology of the disease. Pathogenic action of the CAM2 strain was clearly evidenced by SEM analysis, showing a high ability to adhere and detach larvae velum cells by using its "slimy" EPS, producing agglutination, loss of motility, and a posterior sinking of scallop larvae. After 48 h, a dense bacterial slime on the shell surface was observed, producing high percentages of larval agglutination (63.28 +/- 7.87%) and mortality (45.03 +/- 4.32%) that were significantly (P < 0.05) higher than those of the unchallenged control cultures, which exhibited only 3.20 +/- 1.40% dead larvae and no larval agglutination. Furthermore, the CAM2 strain exhibited a high ability to adhere to fiberglass pieces of tanks used for scallop larvae rearing (1.64 x 10(5) cells adhered per square millimeters at 24 h postinoculation), making it very difficult to eradicate it from the culture systems. This is the first report of a pathogenic activity on scallop larvae of Halomonas species, and it prompts the necessity of an appraisal on biofilm-producing bacteria in Chilean scallop hatcheries.}, }
@article {pmid18548184, year = {2009}, author = {Wu, L and Ma, K and Lu, Y}, title = {Prevalence of betaproteobacterial sequences in nifH gene pools associated with roots of modern rice cultivars.}, journal = {Microbial ecology}, volume = {57}, number = {1}, pages = {58-68}, pmid = {18548184}, issn = {0095-3628}, mesh = {Alphaproteobacteria/enzymology/genetics/growth &amp; development ; Azoarcus/classification/enzymology/growth &amp; development ; Betaproteobacteria/*enzymology/*genetics/growth &amp; development ; Cloning, Molecular ; Molecular Sequence Data ; Oryza/classification/growth &amp; development/*microbiology ; Oxidoreductases/*genetics ; Phylogeny ; Plant Roots/*microbiology ; Polymorphism, Restriction Fragment Length ; Prevalence ; Sequence Analysis, DNA ; }, abstract = {The diversity and function of nitrogen-fixing bacteria colonizing rice roots are not well understood. A field experiment was conducted to determine the diversity of diazotrophic communities associated with roots of modern rice cultivars using culture-independent molecular analyses of nitrogenase gene (nifH) fragments. Experimental treatments included four modern rice cultivars (Oryza sativa, one Indica, one Japonica and two hybrid rice varieties) and three levels (0, 50, and 100 kg N ha(-1)) of N (urea) fertilizer application. Cloning and sequencing of 103 partial nifH genes showed that a diverse community of diazotrophs was associated with rice roots. However, the nifH gene fragments belonging to betaproteobacteria were dominant, accounting for nearly half of nifH sequences analyzed across the clone libraries. Most of them were similar to nifH fragments retrieved from wild rice and Kallar grass, with Azoarcus spp. being the closest cultured relatives. Alphaproteobacteria were also detected, but their relative abundance in the nifH gene pools was dramatically decreased with N fertilizer application. In addition, a high fraction of nifH gene pools was affiliated with methylotrophs and methane oxidizers. The sequence analysis was consistent with the terminal restriction fragment-length polymorphism (T-RFLP) fingerprinting of the nifH gene fragments, which showed three of four dominant terminal restriction fragments were mainly related to betaproteobacteria based on in silico digestion of nifH sequences. T-RFLP analyses also revealed that the effects of N fertilizer on the nifH gene diversity retrieved from roots varied according to rice cultivars. In summary, the present study revealed the prevalence of betaproteobacterial sequences among the proteobacteria associated with roots of modern rice cultivars. This group of diazotrophs appeared less sensitive to N fertilizer application than diazotrophic alphaproteobacteria. Furthermore, methylotrophs may also play a role in nitrogen fixation on rice roots. However, it must be noted that due to the potential bias of polymerase chain reaction protocol, the significance of non-proteobacterial diazotrophs such as Firmicutes and anaerobic bacteria is possibly underestimated.}, }
@article {pmid18548183, year = {2009}, author = {Duan, J and Müller, KM and Charles, TC and Vesely, S and Glick, BR}, title = {1-aminocyclopropane-1-carboxylate (ACC) deaminase genes in rhizobia from southern Saskatchewan.}, journal = {Microbial ecology}, volume = {57}, number = {3}, pages = {423-436}, pmid = {18548183}, issn = {1432-184X}, mesh = {Bacterial Proteins/genetics/*metabolism ; Base Sequence ; Carbon-Carbon Lyases/genetics/*metabolism ; Gene Dosage ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Molecular Sequence Data ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rhizobium/enzymology/*genetics/isolation &amp; purification ; Saskatchewan ; Sequence Analysis, DNA ; }, abstract = {A collection of 233 rhizobia strains from 30 different sites across Saskatchewan, Canada was assayed for 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, with 27 of the strains displaying activity. When all 27 strains were characterized based on 16S rRNA gene sequences, it was noted that 26 strains are close to Rhizobium leguminosarum and one strain is close to Rhizobium gallicum. Polymerase chain reaction (PCR) was used to rapidly isolate ACC deaminase structural genes from the above-mentioned 27 strains; 17 of them have 99% identities with the previously characterized ACC deaminase structural gene (acdS) from R. leguminosarum bv. viciae 128C53K, whereas the other ten strains are 84% identical (864-866/1,020 bp) compared to the acdS from strain 128C53K. Southern hybridization showed that each strain has only one ACC deaminase gene. Using inverse PCR, the region upstream of the ACC deaminase structural genes was characterized for all 27 strains, and 17 of these strains were shown to encode a leucine-responsive regulatory protein. The results are discussed in the context of a previously proposed model for the regulation of bacterial ACC deaminase in R. leguminosarum 128C53K.}, }
@article {pmid18548182, year = {2009}, author = {Jackson, CR and Liew, KC and Yule, CM}, title = {Structural and functional changes with depth in microbial communities in a tropical Malaysian peat swamp forest.}, journal = {Microbial ecology}, volume = {57}, number = {3}, pages = {402-412}, pmid = {18548182}, issn = {1432-184X}, mesh = {Archaea/classification/enzymology/*genetics ; Bacteria/classification/enzymology/*genetics ; *Ecosystem ; Gene Library ; Geologic Sediments/microbiology ; RNA, Archaeal/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Trees/*microbiology ; Wetlands ; }, abstract = {Tropical peat swamp forests are important and endangered ecosystems, although little is known of their microbial diversity and ecology. We used molecular and enzymatic techniques to examine patterns in prokaryotic community structure and overall microbial activity at 0-, 10-, 20-, and 50-cm depths in sediments in a peat swamp forest in Malaysia. Denaturing gradient gel electrophoresis profiles of amplified 16S ribosomal ribonucleic acid (rRNA) gene fragments showed that different depths harbored different bacterial assemblages and that Archaea appeared to be limited to the deeper samples. Cloning and sequencing of longer 16S rRNA gene fragments suggested reduced microbial diversity in the deeper samples compared to the surface. Bacterial clone libraries were largely dominated by ribotypes affiliated with the Acidobacteria, which accounted for at least 27-54% of the sequences obtained. All of the sequenced representatives from the archaeal clone libraries were Crenarchaeota. Activities of microbial extracellular enzymes involved in carbon, nitrogen, and phosphorus cycling declined appreciably with depth, the only exception being peroxidase. These results show that tropical peat swamp forests are unusual systems with microbial assemblages dominated by members of the Acidobacteria and Crenarchaeota. Microbial communities show clear changes with depth, and most microbial activity is likely confined to populations in the upper few centimeters, the site of new leaf litter fall, rather than the deeper, older, peat layers.}, }
@article {pmid18547324, year = {2008}, author = {Iovieno, P and Bååth, E}, title = {Effect of drying and rewetting on bacterial growth rates in soil.}, journal = {FEMS microbiology ecology}, volume = {65}, number = {3}, pages = {400-407}, doi = {10.1111/j.1574-6941.2008.00524.x}, pmid = {18547324}, issn = {0168-6496}, mesh = {Bacteria/*growth &amp; development/metabolism ; *Desiccation ; Glucose/metabolism ; Leucine/metabolism ; Oxygen Consumption ; *Soil Microbiology ; Thymidine/metabolism ; *Water ; }, abstract = {The effect of soil moisture on bacterial growth was investigated, and the effects of rewetting were compared with glucose addition because both treatments increase substrate availability. Bacterial growth was estimated as thymidine and leucine incorporation, and was compared with respiration. Low growth rates were found in air-dried soil, increasing rapidly to high stable values in moist soils. Respiration and bacterial growth at different soil moisture contents were correlated. Rewetting air-dried soil resulted in a linear increase in bacterial growth with time, reaching the levels in moist soil (10 times higher) after about 7 h. Respiration rates increased within 1 h to a level >10 times higher than that in moist soil. After the initial flush, there was a gradual decrease in respiration rate, while bacterial growth increased to levels twice that of moist soil 24 h after rewetting, and decreased to levels similar to those in moist soil after 2 days. Adding glucose resulted in no positive effect on bacterial growth during the first 9 h, despite resulting in more than five times higher respiration. This indicated that the initial increase in bacterial growth after rewetting was not due to increased substrate availability.}, }
@article {pmid18545867, year = {2009}, author = {Bleiker, KP and Six, DL}, title = {Competition and coexistence in a multi-partner mutualism: interactions between two fungal symbionts of the mountain pine beetle in beetle-attacked trees.}, journal = {Microbial ecology}, volume = {57}, number = {1}, pages = {191-202}, pmid = {18545867}, issn = {0095-3628}, mesh = {Animals ; Coleoptera/*growth &amp; development/physiology ; Ecosystem ; Host-Parasite Interactions ; Ophiostoma/*growth &amp; development ; Ophiostomatales/classification/*growth &amp; development ; Phloem/*microbiology ; Pinus/*microbiology/*parasitology ; *Symbiosis ; }, abstract = {Despite overlap in niches, two fungal symbionts of the mountain pine beetle (Dendroctonus ponderosae), Grosmannia clavigera and Ophiostoma montium, appear to coexist with one another and their bark beetle host in the phloem of trees. We sampled the percent of phloem colonized by fungi four times over 1 year to investigate the nature of the interaction between these two fungi and to determine how changing conditions in the tree (e.g., moisture) affect the interaction. Both fungi colonized phloem at similar rates; however, G. clavigera colonized a disproportionately larger amount of phloem than O. montium considering their relative prevalence in the beetle population. High phloem moisture appeared to inhibit fungal growth shortly after beetle attack; however, by 1 year, low phloem moisture likely inhibited fungal growth and survival. There was no inverse relationship between the percent of phloem colonized by G. clavigera only and O. montium only, which would indicate competition between the species. However, the percent of phloem colonized by G. clavigera and O. montium together decreased after 1 year, while the percent of phloem from which no fungi were isolated increased. A reduction in living fungi in the phloem at this time may have significant impacts on both beetles and fungi. These results indicate that exploitation competition occurred after a year when the two fungi colonized the phloem together, but we found no evidence of strong interference competition. Each species also maintained an exclusive area, which may promote coexistence of species with similar resource use.}, }
@article {pmid18545866, year = {2009}, author = {Frette, L and Jørgensen, NO and Nybroe, O and Del Giorgio, PA and Kroer, N}, title = {Effect of availability of nitrogen compounds on community structure of aquatic bacteria in model systems.}, journal = {Microbial ecology}, volume = {57}, number = {1}, pages = {104-116}, pmid = {18545866}, issn = {0095-3628}, mesh = {Bacillus/classification/growth &amp; development/isolation &amp; purification/metabolism ; Bacteria/*classification/*growth &amp; development/isolation &amp; purification/metabolism ; Culture Media ; *Ecosystem ; Models, Biological ; Nitrogen/metabolism ; Nitrogen Compounds/classification/*metabolism ; Pseudomonas/classification/growth &amp; development/isolation &amp; purification/metabolism ; Seawater/chemistry/*microbiology ; Sphingomonadaceae/classification/growth &amp; development/isolation &amp; purification/metabolism ; }, abstract = {To test if the quality and concentration of dissolved nitrogen (N) species could be a selective force in shaping bacterioplankton community structure, competition for various N compounds among five heterotrophic marine bacteria (Pseudomonas strains B, B25, and AX; Bacillus strain A6; Erythrobacter strain F19) was examined. Two of the five strains (AX and B25) were capable of utilizing urea for growth. The five strains were inoculated into dilute (1/1,000 strength) ZoBell medium enriched with various N sources (free amino acids, casein, ammonium, nitrate, or urea). Regardless of the added N source, the communities were either dominated by strain B (at 50 microM N) or strain AX (at 250 microM N). Without any addition of N, strain F19 dominated. If F19 was not included in the community, strain B25 dominated. Despite these differences in community structure, consumption of the added N compounds was surprisingly similar and no advantages of urea for the urea-utilizing bacterium B25 were obvious. To examine if urea could be of selective advantage to the urea-degrading strains B25 and AX, communities with and without B25 were amended with urea N. As expected, strain B25 became dominant when present, but without this strain the non-urea-utilizing strain B outcompeted the urea-utilizing strain AX. Possibly, strain B benefited from N released during catabolism of urea by strain AX. Changes in community composition did not result in major changes in the nitrogen dynamics. The results indicate that dissolved N species can be a selective force in shaping microbial communities. Relative to nutrient generalists, nutrient specialists may either have competitive advantages or stimulate growth of other species by synergetic interactions. Results from the model communities suggest that there may be a large degree of unpredictability in the making of microbial communities, whereas major ecosystem functions such as N cycling appear relatively stable.}, }
@article {pmid18545660, year = {2008}, author = {Lefèvre, E and Roussel, B and Amblard, C and Sime-Ngando, T}, title = {The molecular diversity of freshwater picoeukaryotes reveals high occurrence of putative parasitoids in the plankton.}, journal = {PloS one}, volume = {3}, number = {6}, pages = {e2324}, pmid = {18545660}, issn = {1932-6203}, mesh = {Bayes Theorem ; Ecology ; Eukaryotic Cells ; Fresh Water/microbiology ; Phylogeny ; Plankton/*microbiology ; RNA, Ribosomal, 18S/genetics ; Species Specificity ; *Water Microbiology ; }, abstract = {Eukaryotic microorganisms have been undersampled in biodiversity studies in freshwater environments. We present an original 18S rDNA survey of freshwater picoeukaryotes sampled during spring/summer 2005, complementing an earlier study conducted in autumn 2004 in Lake Pavin (France). These studies were designed to detect the small unidentified heterotrophic flagellates (HF, 0.6-5 microm) which are considered the main bacterivores in aquatic systems. Alveolates, Fungi and Stramenopiles represented 65% of the total diversity and differed from the dominant groups known from microscopic studies. Fungi and Telonemia taxa were restricted to the oxic zone which displayed two fold more operational taxonomic units (OTUs) than the oxycline. Temporal forcing also appeared as a driving force in the diversification within targeted organisms. Several sequences were not similar to those in databases and were considered as new or unsampled taxa, some of which may be typical of freshwater environments. Two taxa known from marine systems, the genera Telonema and Amoebophrya, were retrieved for the first time in our freshwater study. The analysis of potential trophic strategies displayed among the targeted HF highlighted the dominance of parasites and saprotrophs, and provided indications that these organisms have probably been wrongfully regarded as bacterivores in previous studies. A theoretical exercise based on a new 'parasite/saprotroph-dominated HF hypothesis' demonstrates that the inclusion of parasites and saprotrophs may increase the functional role of the microbial loop as a link for carbon flows in pelagic ecosystems. New interesting perspectives in aquatic microbial ecology are thus opened.}, }
@article {pmid18544040, year = {2008}, author = {Little, AE and Robinson, CJ and Peterson, SB and Raffa, KF and Handelsman, J}, title = {Rules of engagement: interspecies interactions that regulate microbial communities.}, journal = {Annual review of microbiology}, volume = {62}, number = {}, pages = {375-401}, doi = {10.1146/annurev.micro.030608.101423}, pmid = {18544040}, issn = {0066-4227}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Biological Evolution ; *Ecosystem ; Gene Transfer, Horizontal ; Genetics, Microbial ; Genomics ; *Microbiological Phenomena ; Species Specificity ; }, abstract = {Microbial communities comprise an interwoven matrix of biological diversity modified by physical and chemical variation over space and time. Although these communities are the major drivers of biosphere processes, relatively little is known about their structure and function, and predictive modeling is limited by a dearth of comprehensive ecological principles that describe microbial community processes. Here we discuss working definitions of central ecological terms that have been used in various fashions in microbial ecology, provide a framework by focusing on different types of interactions within communities, review the status of the interface between evolutionary and ecological study, and highlight important similarities and differences between macro- and microbial ecology. We describe current approaches to study microbial ecology and progress toward predictive modeling.}, }
@article {pmid18541218, year = {2008}, author = {Peterson, DA and Frank, DN and Pace, NR and Gordon, JI}, title = {Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases.}, journal = {Cell host &amp; microbe}, volume = {3}, number = {6}, pages = {417-427}, pmid = {18541218}, issn = {1934-6069}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/immunology/*isolation &amp; purification ; Biodiversity ; *Host-Pathogen Interactions ; Humans ; Immunoglobulin A/immunology ; Inflammatory Bowel Diseases/*immunology/*microbiology/therapy ; Intestinal Mucosa/immunology/microbiology/physiopathology ; Mice ; Probiotics/administration &amp; dosage ; }, abstract = {The human gastrointestinal tract is home to immense and complex populations of microorganisms. Using recent technical innovations, the diversity present in this human body habitat is now being analyzed in detail. This review focuses on the microbial ecology of the gut in inflammatory bowel diseases and on how recent studies provide an impetus for using carefully designed, comparative metagenomic approaches to delve into the structure and activities of the gut microbial community and its interrelationship with the immune system.}, }
@article {pmid18537837, year = {2008}, author = {Dabek, M and McCrae, SI and Stevens, VJ and Duncan, SH and Louis, P}, title = {Distribution of beta-glucosidase and beta-glucuronidase activity and of beta-glucuronidase gene gus in human colonic bacteria.}, journal = {FEMS microbiology ecology}, volume = {66}, number = {3}, pages = {487-495}, doi = {10.1111/j.1574-6941.2008.00520.x}, pmid = {18537837}, issn = {0168-6496}, mesh = {Bacteria/*enzymology/*genetics/growth &amp; development/isolation &amp; purification ; Carbon/metabolism ; Colon/*microbiology ; Feces/microbiology ; Genes, Bacterial/*genetics ; Glucuronidase/*metabolism ; Glycoside Hydrolases/metabolism ; Humans ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; beta-Glucosidase/*metabolism ; }, abstract = {beta-Glycosidase activities present in the human colonic microbiota act on glycosidic plant secondary compounds and xenobiotics entering the colon, with potential health implications for the human host. Information on beta-glycosidases is currently limited to relatively few species of bacteria from the human colonic ecosystem. We therefore screened 40 different bacterial strains that are representative of dominant bacterial groups from human faeces for beta-glucosidase and beta-glucuronidase activity. More than half of the low G+C% Gram-positive firmicutes harboured beta-glucosidase activity, while beta-glucuronidase activity was only found in some firmicutes within clostridial clusters XIVa and IV. Most of the Bifidobacterium spp. and Bacteroides thetaiotaomicron carried beta-glucosidase activity. A beta-glucuronidase gene belonging to family 2 glycosyl hydrolases was detected in 10 of the 40 isolates based on degenerate PCR. These included all nine isolates that gave positive assays for beta-glucuronidase activity, suggesting that the degenerate PCR could provide a useful assay for the capacity to produce beta-glucuronidase in the gut community. beta-Glucuronidase activity was induced by growth on d-glucuronic acid, or by addition of 4-nitrophenol-glucuronide, in Roseburia hominis A2-183, while beta-glucosidase activity was induced by 4-nitrophenol-glucopyranoside. Inducibility varied between strains.}, }
@article {pmid18536862, year = {2009}, author = {Andreote, FD and Carneiro, RT and Salles, JF and Marcon, J and Labate, CA and Azevedo, JL and Araújo, WL}, title = {Culture-independent assessment of Rhizobiales-related alphaproteobacteria and the diversity of Methylobacterium in the rhizosphere and rhizoplane of transgenic eucalyptus.}, journal = {Microbial ecology}, volume = {57}, number = {1}, pages = {82-93}, pmid = {18536862}, issn = {0095-3628}, mesh = {Alphaproteobacteria/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/analysis ; Ecosystem ; Electrophoresis/methods ; Eucalyptus/*microbiology ; Gene Library ; Genes, rRNA ; Genetic Variation ; Methylobacterium/classification/genetics/*isolation &amp; purification ; Plant Roots/*microbiology ; Plants, Genetically Modified/*microbiology ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {The rhizosphere is an ecosystem exploited by a variety of organisms involved in plant health and environmental sustainability. Abiotic factors influence microorganism-plant interactions, but the microbial community is also affected by expression of heterologous genes from host plants. In the present work, we assessed the community shifts of Alphaproteobacteria phylogenetically related to the Rhizobiales order (Rhizobiales-like community) in rhizoplane and rhizosphere soils of wild-type and transgenic eucalyptus. A greenhouse experiment was performed and the bacterial communities associated with two wild-type (WT17 and WT18) and four transgenic (TR-9, TR-15, TR-22, and TR-23) eucalyptus plant lines were evaluated. The culture-independent approach consisted of the quantification, by real-time polymerase chain reaction (PCR), of a targeted subset of Alphaproteobacteria and the assessment of its diversity using PCR-denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone libraries. Real-time quantification revealed a lesser density of the targeted community in TR-9 and TR-15 plants and diversity analysis by principal components analysis, based on PCR-DGGE, revealed differences between bacterial communities, not only between transgenic and nontransgenic plants, but also among wild-type plants. The comparison between clone libraries obtained from the transgenic plant TR-15 and wild-type WT17 revealed distinct bacterial communities associated with these plants. In addition, a culturable approach was used to quantify the Methylobacterium spp. in the samples where the identification of isolates, based on 16S rRNA gene sequences, showed similarities to the species Methylobacterium nodulans, Methylobacterium isbiliense, Methylobacterium variable, Methylobacterium fujisawaense, and Methylobacterium radiotolerans. Colonies classified into this genus were not isolated from the rhizosphere but brought in culture from rhizoplane samples, except for one line of the transgenic plants (TR-15). In general, the data suggested that, in most cases, shifts in bacterial communities due to cultivation of transgenic plants are similar to those observed when different wild-type cultivars are compared, although shifts directly correlated to transgenic plant cultivation may be found.}, }
@article {pmid18535850, year = {2009}, author = {Arboleda, M and Reichardt, W}, title = {Epizoic communities of prokaryotes on healthy and diseased scleractinian corals in Lingayen Gulf, Philippines.}, journal = {Microbial ecology}, volume = {57}, number = {1}, pages = {117-128}, pmid = {18535850}, issn = {0095-3628}, mesh = {Animals ; Anthozoa/growth &amp; development/*microbiology ; *Archaea/classification/genetics/growth &amp; development/pathogenicity ; *Bacteria/classification/genetics/growth &amp; development/pathogenicity ; Biofilms/growth &amp; development ; *Ecosystem ; In Situ Hybridization, Fluorescence ; *Marine Biology ; Philippines ; Seawater/*microbiology ; }, abstract = {In search for microbiological indicators of coral health and coral diseases, community profiles of coral-associated epizoic prokaryotes were investigated because of their dual potential as a source of coral pathogens and their antagonists. In pairwise samples of visually healthy and diseased coral specimens from Bolinao Bay (Pangasinan, Philippines), mixed biofilm communities of ectoderm- and mucus-colonizing epizoic prokaryotes were compared using fluorescent in situ hybridization (FISH). Oligonucleotide probes targeted 13 phylotypes representing the main taxonomic groups of marine prokaryotes. Coral taxa tended to show specific community profiles. An attempt to separate the profiles of healthy and diseased specimens by applying principal component analysis (PCA) to a (nonselective) collection of corals (affected by various diseases) proved unsuccessful. On the other hand, separate PCA clusters were obtained from healthy and diseased corals belonging to a single species (Pocillopora damicornis) only. This cluster formation was dominated by principal component 1 with the genus Vibrio accounting for 18%. At the same time, reef-site-specific clusters were formed as well. At a reef site exposed to pollution from intensive fish cage (Chanos chanos) farming, healthy P. damicornis were mainly (93%) colonized by unicellular cyanobacteria. The formal calculation of diversity parameters suggested that evenness in particular was driven by both health status and reef site location. Despite the low resolution of taxonomic levels achieved with FISH probes targeting only large phylotype groups, significant differences between healthy and diseased corals and also between polluted and nonpolluted reef sites were observed.}, }
@article {pmid18524640, year = {2008}, author = {Guo, X and Xia, X and Tang, R and Wang, K}, title = {Real-time PCR quantification of the predominant bacterial divisions in the distal gut of Meishan and Landrace pigs.}, journal = {Anaerobe}, volume = {14}, number = {4}, pages = {224-228}, doi = {10.1016/j.anaerobe.2008.04.001}, pmid = {18524640}, issn = {1095-8274}, mesh = {Adipose Tissue ; Animals ; Bacteroides/*classification/genetics/*isolation &amp; purification ; Colony Count, Microbial/*methods ; Gastrointestinal Tract/*microbiology ; Gram-Positive Bacteria/*classification/genetics/*isolation &amp; purification ; Polymerase Chain Reaction/*methods ; Statistics as Topic ; Swine/*microbiology ; }, abstract = {Firmicutes and Bacteroidetes are closely related to body fat in humans and mice, which are the two dominant bacterial divisions of gut microbiota in mammals. Here real-time PCR analysis indicated that Meishan pigs had a 34% reduction in percentage Bacteroidetes (P = 0.008) and a significantly lower proportion of Bacteroides (P = 0.013) than Landrace pigs. The percentage of Bacteroidetes or Bacteroides had a negative correlation with body fat (R2 was 0.63 for Bacteroidetes and 0.57 for Bacteroides, P < 0.05). There was a trend that the percentage of Firmicutes in Meishan pigs was higher in numerical value than in Landrace pigs, although this difference was not statistically significant (P = 0.290) between the two breeds. These suggested that body fat correlated with the percentage of Bacteroidetes division of the gut microbiota in the common pig breeds, and the differences of gut microbial ecology in obese versus lean animals may be analogous.}, }
@article {pmid18523433, year = {2008}, author = {Kunin, V and Raes, J and Harris, JK and Spear, JR and Walker, JJ and Ivanova, N and von Mering, C and Bebout, BM and Pace, NR and Bork, P and Hugenholtz, P}, title = {Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat.}, journal = {Molecular systems biology}, volume = {4}, number = {}, pages = {198}, pmid = {18523433}, issn = {1744-4292}, mesh = {Amino Acids/metabolism ; *Genetics, Microbial ; Mexico ; *Salinity ; *Selection, Genetic ; }, abstract = {To investigate the extent of genetic stratification in structured microbial communities, we compared the metagenomes of 10 successive layers of a phylogenetically complex hypersaline mat from Guerrero Negro, Mexico. We found pronounced millimeter-scale genetic gradients that were consistent with the physicochemical profile of the mat. Despite these gradients, all layers displayed near-identical and acid-shifted isoelectric point profiles due to a molecular convergence of amino-acid usage, indicating that hypersalinity enforces an overriding selective pressure on the mat community.}, }
@article {pmid18522451, year = {2008}, author = {Morán, AC and Hengst, MB and De La Iglesia, R and Andrade, S and Correa, JA and González, B}, title = {Changes in bacterial community structure associated with coastal copper enrichment.}, journal = {Environmental toxicology and chemistry}, volume = {27}, number = {11}, pages = {2239-2245}, doi = {10.1897/08-112.1}, pmid = {18522451}, issn = {0730-7268}, mesh = {Bacteria/classification/*drug effects ; Copper/*pharmacology ; *Ecosystem ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Marine bacterial communities isolated from the water column, sediment, the rock surface, and the green seaweed Ulva compressa were studied in an intertidal ecosystem. The study area included a coastal zone chronically affected by copper mine waste disposals. Bacterial community composition was analyzed by terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes, and multivariate analyses of T-RFLP data sets were used for comparisons. Results showed that diversity and richness indexes were not able to detect differences among compartments. However, comparisons within the same compartment clearly showed that copper enrichment was associated with changes in the composition of the bacterial communities and revealed that the magnitude of the effect depends on the compartment being considered. In this context, communities from sediments appeared as the most affected by copper enrichment. The present study also demonstrated that intertidal bacterial communities were dominated by Gammaproteobacteria, Firmicutes, and Actinobacteria and the changes in these communities were mainly due to changes in their relative abundances.}, }
@article {pmid18521656, year = {2009}, author = {Barness, G and Rodriguez Zaragoza, S and Shmueli, I and Steinberger, Y}, title = {Vertical distribution of a soil microbial community as affected by plant ecophysiological adaptation in a desert system.}, journal = {Microbial ecology}, volume = {57}, number = {1}, pages = {36-49}, pmid = {18521656}, issn = {0095-3628}, mesh = {*Adaptation, Physiological ; Amaranthaceae/classification/growth &amp; development/*physiology ; Bacteria/growth &amp; development/metabolism ; Biomass ; Carbon Dioxide/metabolism ; Colony Count, Microbial ; *Desert Climate ; *Ecosystem ; Fungi/growth &amp; development/metabolism ; *Soil Microbiology ; Species Specificity ; }, abstract = {The spatial and temporal patterns of resource distribution in a desert system have been shown to influence a number of soil biota components and processes. The pattern of possible different resources supplied by two typical halophyte shrubs with different ecophysiological adaptations, Atriplex halimus and Hammada scoparia, was found to be the trigger in the present study on the microbial community temporal and spatial (vertical) scale. The uniqueness of A. halimus, a saltbush plant, is in the creation of 'islands of salinity' in its rhizosphere system and the relatively high percentage of organic matter beneath its canopy, whereas the H. scoparia shrub has a leafless stem with a relatively lower amount of organic matter accumulation beneath its canopy. Soil samples from 0 to 50 cm depths were collected at 10-cm intervals during each of the four seasons. The vertical distribution of the microbial community was measured in the vicinity of the above plant shrubs and in the open spaces between them. The results obtained from the field study demonstrated that plant ecophysiological adaptation played an important role in the temporal and spatial distribution of abiotic conditions and microbial community levels such as microbial biomass, CO(2) evolution, and colony-forming units (CFUs) of both bacteria and fungi. However, we did not find consistency in the positive effect of plant cover on the microbial community. The shrub effect was observed to have a major outcome on microbial variables not only on a temporal but also on a spatial (vertical) basis. This contributed to the understanding of the controversy regarding the difference between the shrubs.}, }
@article {pmid18506502, year = {2008}, author = {Gramss, G and Bergmann, H}, title = {Role of plants in the vegetative and reproductive growth of saprobic basidiomycetous ground fungi.}, journal = {Microbial ecology}, volume = {56}, number = {4}, pages = {660-670}, pmid = {18506502}, issn = {0095-3628}, mesh = {Basidiomycota/classification/*growth &amp; development/metabolism ; Plant Roots/microbiology ; Plants/*microbiology ; Soil Microbiology ; Species Specificity ; }, abstract = {Non-symbiotic microorganisms engineered or expensively selected to degrade xenobiotic hydrocarbons or modify heavy-metal uptake of plants in soil remediations die back after their introduction into the target soils. Mycelia of saprobic basidiomycetes were therefore inoculated into soil samples of 1 l in glass vessels to record mycelial growth and reproduction in the immediate rhizosphere of up to 11 herbaceous plant species, or to study their responses to the separate volatiles from whole plant swards or their root balls whose emanations had been collected in 1.5-l plastic bags fixed to the glass vessels. Excess CO2 was controlled with NaOH solution. Volatiles from root balls of parsley and pea but not wheat, from unplanted soils, from the fungus-permeated, unplanted substrate soil itself, and from the rooting soil of whole wheat sward increased mycelial densities in Clitocybe sp. more than in Agaricus macrocarpus and indicated thus a higher nutrient state of the mycelia. Organic volatiles proved therefore to be a significant carbon source for certain basidiomycetes in poor natural soils. The contemporary decline in the number of basidiocarp initials to 0 to 36% in both fungi relative to the unplanted and aerated controls was caused by volatiles from rooted and unplanted soil and pointed thus to their ecological role as antibiotics, fumigants, toxins, and hormonal compounds. Aqueous extracts from root balls of wheat stimulated mycelial density and fruiting in A. macrocarpus contemporarily because of their contents in soil-derived macronutrients. They suppressed once more fruiting in the more sensitive Clitocybe sp. by active agents in the aqueous phase. Within plant rhizospheres, densities of Clitocybe sp. mycelia were stimulated in the presence of alfalfa, carrot, red clover, ryegrass, and spinach, whereas those of A. macrocarpus were halved by 7 of 10 plant species including alfalfa, red clover, ryegrass, and spinach. Mycelia of A. macrocarpus may thereby have responded to differences in concentration and composition of volatile compounds. The contemporary repression of fruiting in both fungi and in nearly all treatments was not due to plant competition for macronutrients. Mycelia of basidiomycetes over-compensated for losses in macronutrients to the plant by decomposing soil matrix constituents. It is concluded that organic volatiles emitted by several plant organs and natural soils improved the nutritional state of A. macrocarpus and Clitocybe sp. but not of Agaricus bisporus mycelia and could therefore help establish certain ground fungi in the field. The contemporary and general suppression of fruiting by constituents of the gaseous (and liquid) phase in all fungi examined suggests interference with basic physiological processes and recommends an urgent re-examination of the degradative ability of basidiomycetes in the presence of volatiles.}, }
@article {pmid18506439, year = {2008}, author = {Clauwaert, P and Aelterman, P and Pham, TH and De Schamphelaire, L and Carballa, M and Rabaey, K and Verstraete, W}, title = {Minimizing losses in bio-electrochemical systems: the road to applications.}, journal = {Applied microbiology and biotechnology}, volume = {79}, number = {6}, pages = {901-913}, doi = {10.1007/s00253-008-1522-2}, pmid = {18506439}, issn = {0175-7598}, mesh = {Bacteria/chemistry/*metabolism ; Bioelectric Energy Sources/*economics ; *Biosensing Techniques ; Conservation of Energy Resources/*economics ; Electrodes/microbiology ; *Energy Metabolism ; Energy-Generating Resources ; Oxidation-Reduction ; Water Purification ; }, abstract = {Bio-electrochemical systems (BESs) enable microbial catalysis of electrochemical reactions. Plain electrical power production combined with wastewater treatment by microbial fuel cells (MFCs) has been the primary application purpose for BESs. However, large-scale power production and a high chemical oxygen demand conversion rates must be achieved at a benchmark cost to make MFCs economical competitive in this context. Recently, a number of valuable oxidation or reduction reactions demonstrating the versatility of BESs have been described. Indeed, BESs can produce hydrogen, bring about denitrification, or reductive dehalogenation. Moreover, BESs also appear to be promising in the field of online biosensors. To effectively apply BESs in practice, both biological and electrochemical losses need to be further minimized. At present, the costs of reactor materials have to be decreased, and the volumetric biocatalyst activity in the systems has to be increased substantially. Furthermore, both the ohmic cell resistance and the pH gradients need to be minimized. In this review, these losses and constraints are discussed from an electrochemical viewpoint. Finally, an overview of potential applications and innovative research lines is given for BESs.}, }
@article {pmid18504955, year = {2008}, author = {Feris, K and Mackay, D and de Sieyes, N and Chakraborty, I and Einarson, M and Hristova, K and Scow, K}, title = {Effect of ethanol on microbial community structure and function during natural attenuation of benzene, toluene, and o-xylene in a sulfate-reducing aquifer.}, journal = {Environmental science &amp; technology}, volume = {42}, number = {7}, pages = {2289-2294}, doi = {10.1021/es702603q}, pmid = {18504955}, issn = {0013-936X}, support = {5P42 ES04699-16/ES/NIEHS NIH HHS/United States ; }, mesh = {Benzene/*metabolism ; Ethanol/*pharmacology ; Fermentation ; Oxidation-Reduction ; Polymerase Chain Reaction ; Sulfates/*metabolism ; Toluene/*metabolism ; *Water Microbiology ; Water Pollutants, Chemical/*metabolism ; Xylenes/*metabolism ; }, abstract = {Ethanol (EtOH) is a commonly used fuel oxygenate in reformulated gasoline and is an alternative fuel and fuel supplement. Effects of EtOH release on aquifer microbial ecology and geochemistry have not been well characterized in situ. We performed a controlled field release of petroleum constituents (benzene (B), toluene (T), o-xylene (o-X) at approximately 1-3 mg/L each) with and without EtOH (approximately 500 mg/L). Mixed linear modeling (MLM) assessed effects on the microbial ecology of a naturally sulfidic aquifer and how the microbial community affected B, T, and o-X plume lengths and aquifer geochemistry. Changes in microbial community structure were determined by quantitative polymerase chain reaction (qPCR) targeting Bacteria, Archaea, and sulfate reducing bacteria (SRB); SRB were enumerated using a novel qPCR method targeting the adenosine-5'-phosphosulfate reductase gene. Bacterial and SRB densities increased with and without EtOH-amendment (1-8 orders of magnitude). Significant increases in Archaeal species richness; Archaeal cell densities (3-6 orders of magnitude); B, T, and o-X plume lengths; depletion of sulfate; and induction of methanogenic conditions were only observed with EtOH-amendment MLM supported the conclusion that EtOH-amendment altered microbial community structure and function, which in turn lowered the aquifer redox state and led to a reduction in bioattenuation rates of B, T, and o-X.}, }
@article {pmid18503550, year = {2008}, author = {Zhang, R and Thiyagarajan, V and Qian, PY}, title = {Evaluation of terminal-restriction fragment length polymorphism analysis in contrasting marine environments.}, journal = {FEMS microbiology ecology}, volume = {65}, number = {1}, pages = {169-178}, doi = {10.1111/j.1574-6941.2008.00493.x}, pmid = {18503550}, issn = {0168-6496}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; DNA, Bacterial/*analysis/genetics/isolation &amp; purification ; *Ecosystem ; Genes, rRNA ; Genetic Variation ; Phylogeny ; Polymerase Chain Reaction/methods ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Species Specificity ; }, abstract = {Terminal-restriction fragment length polymorphism (T-RFLP) analysis is widely used in microbial ecology studies. In the present study, T-RFLP analysis of PCR products digested by five restriction enzymes (AluI, HaeIII, MspI, Sau3AI and TaqI) was applied for 20 samples from three contrasting coastal environments to assess the biases associated with the choice of enzyme digestion and T-RF analysis. The five enzyme digestions produced highly variable species richness (in terms of number of T-RFs). Analysis of peak areas with a threshold of 0.5% of the total peak area, which recovered 92-96% of the total peak area, revealed different diversity indexes from the five enzyme digestions. Multidimensional scaling, based on matrices that were generated by scoring peak presence/absence and area, revealed similar bacterial community structure patterns among the 20 samples, regardless of the choice of restriction enzymes. Our results strongly argue that the choice of different digestion enzymes in the T-RFLP technique generated valid and consistent bacterial community structures but highly variable species richness and diversity indices. The biases associated with the choice of digestion enzymes needs to be evaluated carefully or at least to be addressed when using T-RFLP analysis.}, }
@article {pmid18497289, year = {2008}, author = {Strom, SL}, title = {Microbial ecology of ocean biogeochemistry: a community perspective.}, journal = {Science (New York, N.Y.)}, volume = {320}, number = {5879}, pages = {1043-1045}, doi = {10.1126/science.1153527}, pmid = {18497289}, issn = {1095-9203}, mesh = {Animals ; Antibiosis ; Archaea/genetics/growth &amp; development/*physiology ; Bacteria/genetics/growth &amp; development ; *Bacterial Physiological Phenomena ; *Ecosystem ; Genomics ; Geological Phenomena ; Geology ; Nitrogen/metabolism ; Oceans and Seas ; Plankton/physiology ; Seawater/*microbiology ; Sulfur/metabolism ; Surface Properties ; Symbiosis ; }, abstract = {The oceans harbor a tremendous diversity of marine microbes. Different functional groups of bacteria, archaea, and protists arise from this diversity to dominate various habitats and drive globally important biogeochemical cycles. Explanations for the distribution of microbial taxa and their associated activity often focus on resource availability and abiotic conditions. However, the continual reshaping of communities by mortality, allelopathy, symbiosis, and other processes shows that community interactions exert strong selective pressure on marine microbes. Deeper exploration of microbial interactions is now possible via molecular prospecting and taxon-specific experimental approaches. A holistic outlook that encompasses the full array of selective pressures on individuals will help elucidate the maintenance of microbial diversity and the regulation of biogeochemical reactions by planktonic communities.}, }
@article {pmid18497288, year = {2008}, author = {Green, JL and Bohannan, BJ and Whitaker, RJ}, title = {Microbial biogeography: from taxonomy to traits.}, journal = {Science (New York, N.Y.)}, volume = {320}, number = {5879}, pages = {1039-1043}, doi = {10.1126/science.1153475}, pmid = {18497288}, issn = {1095-9203}, mesh = {Animals ; Archaea/classification/genetics/metabolism/physiology ; Bacteria/*classification/genetics/metabolism ; *Bacterial Physiological Phenomena ; Biodiversity ; DNA, Ribosomal/genetics ; Ecology ; *Ecosystem ; Environment ; Gene Dosage ; Genes, Bacterial ; Genomics ; Plant Physiological Phenomena ; }, abstract = {The biogeographic variation of life has predominantly been studied using taxonomy, but this focus is changing. There is a resurging interest in understanding patterns in the distribution not only of taxa but also of the traits those taxa possess. Patterns of trait variation shed light on fundamental questions in biology, including why organisms live where they do and how they will respond to environmental change. Technological advances such as environmental genomics place microbial ecology in a unique position to move trait-based biogeography forward. We anticipate that as trait-based biogeography continues to evolve, micro- and macroorganisms will be studied in concert, establishing a science that is informed by and relevant to all domains of life.}, }
@article {pmid18497286, year = {2008}, author = {Bohannon, J}, title = {Microbial ecology. Confusing kinships.}, journal = {Science (New York, N.Y.)}, volume = {320}, number = {5879}, pages = {1031-1033}, doi = {10.1126/science.320.5879.1031}, pmid = {18497286}, issn = {1095-9203}, mesh = {Adaptation, Physiological ; Archaea/*classification/genetics/physiology ; Bacteria/*classification/genetics ; Bacterial Physiological Phenomena ; Biodiversity ; Biological Evolution ; Ecology ; *Ecosystem ; Environment ; Gene Transfer, Horizontal ; Genome, Archaeal ; Genome, Bacterial ; Phylogeny ; Recombination, Genetic ; Terminology as Topic ; }, }
@article {pmid18497284, year = {2008}, author = {Ash, C and Foley, J and Pennisi, E}, title = {Microbial ecology. Lost in microbial space. Special section introduction.}, journal = {Science (New York, N.Y.)}, volume = {320}, number = {5879}, pages = {1027}, doi = {10.1126/science.320.5879.1027}, pmid = {18497284}, issn = {1095-9203}, mesh = {Animals ; Archaea/*physiology ; Archaeal Viruses/physiology ; *Bacterial Physiological Phenomena ; Bacteriophages/physiology ; Biodiversity ; *Ecosystem ; Fungi/*physiology/virology ; Humans ; *Virus Physiological Phenomena ; }, }
@article {pmid18497165, year = {2008}, author = {De Schamphelaire, L and Van den Bossche, L and Dang, HS and Höfte, M and Boon, N and Rabaey, K and Verstraete, W}, title = {Microbial fuel cells generating electricity from rhizodeposits of rice plants.}, journal = {Environmental science &amp; technology}, volume = {42}, number = {8}, pages = {3053-3058}, doi = {10.1021/es071938w}, pmid = {18497165}, issn = {0013-936X}, mesh = {*Bioelectric Energy Sources ; Electricity ; Electrochemistry ; *Oryza ; Oxidation-Reduction ; Plant Roots ; }, abstract = {Living plants transport substantial amounts of organic material into the soil. This process, called rhizodeposition, provides the substrate for the rhizospheric microbial community. In this study, a laboratory-scale sediment microbial fuel cell, of which the anode is positioned in the rhizosphere of the rice plants, is used to microbially oxidize the plant-derived organics. An electrical current was generated through the in situ oxidation of rhizodeposits from living rice plants. The electrical power output of a sediment microbial fuel cell was found to be a factor 7 higher in the presence of actively growing plants. This process offers the potential of light-driven power generation from living plants in a nondestructive way. Sustainable power productions up to 330 W ha(-1) could be attributed to the oxidation of the plant-derived compounds.}, }
@article {pmid18495461, year = {2009}, author = {Amit-Romach, E and Uni, Z and Cheled, S and Berkovich, Z and Reifen, R}, title = {Bacterial population and innate immunity-related genes in rat gastrointestinal tract are altered by vitamin A-deficient diet.}, journal = {The Journal of nutritional biochemistry}, volume = {20}, number = {1}, pages = {70-77}, doi = {10.1016/j.jnutbio.2008.01.002}, pmid = {18495461}, issn = {0955-2863}, mesh = {Animal Feed ; Animals ; Bacterial Infections/*diet therapy ; Diet ; Disease Models, Animal ; Escherichia coli/*metabolism ; Gastrointestinal Tract/*microbiology/*pathology ; Immunity, Innate ; Intestinal Mucosa/*microbiology/*pathology ; Male ; RNA, Messenger/metabolism ; RNA, Ribosomal, 16S/metabolism ; Rats ; Rats, Wistar ; Vitamin A Deficiency/*complications/pathology ; }, abstract = {Vitamin A and its derivatives have been shown to regulate the growth and differentiation of gastrointestinal epithelial cells; in addition, vitamin A deficiency has been convincingly shown to be associated with increased susceptibility to infection. The gastrointestinal mucosal barrier, which is a component of the innate immune system, is considered the first line of defense, as it provides a barrier between the external environment and the internal milieu. A disturbance in the integrity of the intestinal epithelium is one of the main factors involved in increased incidence of infections during vitamin A deficiency. In this study, the effects of vitamin A deficiency on microbial ecology and the expression of genes related to the intestinal mucosa's innate immunity were examined in a rat model. Using the 16s rDNA method, we demonstrate that a vitamin A-deficient (VAD) diet increases the total amount of bacteria in the gastrointestinal tract and alters the intestinal microflora. Results show a decrease in the relative proportion of Lactobacillus spp. and the simultaneous appearance of Escherichia coli strains. Lack of vitamin A significantly changed mucin (MUC) dynamics, as reflected by the enlarged goblet-cell "cup" area relative to controls; decreased MUC2 mRNA expression in the jejunum, ileum and colon of VAD rats and increased MUC3 mRNA expression in the ileum and colon of these rats. In addition, vitamin A deficiency down-regulated defensin 6 mRNA expression while up-regulating toll-like receptors 2 and 5 mRNA expressions. The current study indicates that vitamin A deficiency interferes with the integrity of the gastrointestinal mucosal barrier.}, }
@article {pmid18495448, year = {2008}, author = {Hedh, J and Wallander, H and Erland, S}, title = {Ectomycorrhizal mycelial species composition in apatite amended and non-amended mesh bags buried in a phosphorus-poor spruce forest.}, journal = {Mycological research}, volume = {112}, number = {Pt 6}, pages = {681-688}, doi = {10.1016/j.mycres.2007.11.008}, pmid = {18495448}, issn = {0953-7562}, mesh = {Apatites/*analysis/metabolism ; Basidiomycota/genetics/growth &amp; development/*isolation &amp; purification/metabolism ; Biodiversity ; Biomass ; DNA, Fungal/genetics ; Molecular Sequence Data ; Mycelium/genetics/isolation &amp; purification/metabolism ; Mycorrhizae/genetics/growth &amp; development/*isolation &amp; purification/metabolism ; Phosphorus/*analysis/metabolism ; Soil/analysis ; *Soil Microbiology ; Trees/*microbiology ; }, abstract = {We studied the effect of apatite amendment on ectomycorrhizal (EM) mycelial biomass production and species composition in a phosphorus-poor spruce forest using sand-filled mesh bags. Control and apatite-amended bags were buried in pairs in the lower part of the organic horizon for one growth season. DNA extraction, PCR of the ITS region, cloning and random sequencing were used to examine the fungal species composition in each bag. Sequences were identified by comparison with the UNITE database and GenBank. Our study confirmed previous results that the major fungal ingrowth in mesh bags was of EM origin. On average 13 species were detected in each bag. Tylospora fibrillosa, Amphinema sp., Tomentellopsis submollis, and Xerocomus badius made up almost 80% of the EM sequences. High biomass was related to increased dominance of specific species. There were no statistically significant differences in biomass production estimated from PLFA 18:2omega6, 9, or between fungal communities of apatite-amended and control bags estimated from DNA after one growth season. The potential of the mesh bag method in studies of functional diversity of EM mycelia in the field is discussed.}, }
@article {pmid18494895, year = {2003}, author = {Taylor, D and Daulby, A and Grimshaw, S and James, G and Mercer, J and Vaziri, S}, title = {Characterization of the microflora of the human axilla.}, journal = {International journal of cosmetic science}, volume = {25}, number = {3}, pages = {137-145}, doi = {10.1046/j.1467-2494.2003.00181.x}, pmid = {18494895}, issn = {1468-2494}, abstract = {It is widely accepted that axillary malodour is attributable to the microbial biotransformation of odourless, natural secretions into volatile odorous products. Consequently, there is a need to understand the microbial ecology of the axilla in order that deodorant products, which control microbial action in this region, can be developed in the appropriate manner. A detailed characterization of the axillary microflora of a group of human volunteers has been performed. The axillary microflora is composed of four principal groups of bacteria (staphylococci, aerobic coryneforms, micrococci and propionibacteria), and the yeast genus Malassezia. Results indicated that the axillary microflora was dominated by either staphylococcal or aerobic coryneform species. Comparisons between axillary bacterial numbers and levels of axillary odour demonstrated the greatest association between odour levels and the presence of aerobic coryneforms in the under-arm. As the taxonomy of cutaneous aerobic coryneforms is poorly understood, a further study was conducted to characterize selected axillary aerobic coryneform isolates. Using the molecular technique of 16S rDNA sequencing, selected genomic sequences of a number of axillary aerobic coryneform isolates were obtained. Comparisons with sequence databases indicated the likely presence of a range of Corynebacterium species on axillary skin, although the majority of isolates were most similar to either Corynebacterium G-2 CDC G5840 or C. mucifaciens DMMZ 2278. Although for a panel of individuals differences in the carriage of Corynebacterium species were noted, similar species were carried by a number of panellists. All isolates examined in this limited evaluation failed to demonstrate the capability to metabolize long-chain fatty acids (LCFAs) to shorter chain, more volatile products. The application of this modern molecular phylogenetic technique has increased understanding of the diversity of aerobic coryneform carriage in the axilla, and on human skin. The application of this technique in other studies to assess the ethnic differences in cutaneous bacterial ecology, or the effects on the microflora of specific product use, will assist in the future development of novel deodorant systems.}, }
@article {pmid18494490, year = {2008}, author = {Eeckhaut, E and Struijs, K and Possemiers, S and Vincken, JP and Keukeleire, DD and Verstraete, W}, title = {Metabolism of the lignan macromolecule into enterolignans in the gastrointestinal lumen as determined in the simulator of the human intestinal microbial ecosystem.}, journal = {Journal of agricultural and food chemistry}, volume = {56}, number = {12}, pages = {4806-4812}, doi = {10.1021/jf800101s}, pmid = {18494490}, issn = {1520-5118}, mesh = {Bacteria/metabolism ; Butylene Glycols/metabolism ; Diet ; Ecosystem ; Estrogens/metabolism ; Gastrointestinal Tract/*metabolism/*microbiology ; Glucosides/metabolism ; Humans ; Lignans/*metabolism ; Macromolecular Substances/metabolism ; Models, Biological ; }, abstract = {Estrogenic plant compounds from the human diet such as the lignan secoisolariciresinol diglucoside (SDG, 1) can exert biological activity in the human body upon ingestion and bioactivation to enterodiol (END, 5) and enterolactone (ENL, 6). Bioavailability of lignans is influenced by the food matrix and gut microbial action, of which the latter is subject to a large interindividual variation. In this study, the fate of the lignan precursor SDG, present in the lignan macromolecule of flax seed (Linum usitatissimum), was determined during an artificial stomach and small intestinal digestion and during metabolism by two different enterolignan phenotypes in a TWINSHIME environment (TWIN Simulator of the Human Intestinal Microbial Ecosystem). The lignan macromolecule acted as a delivery system of SDG in the large intestine. SDG was only hydrolyzed into secoisolariciresinol (SECO, 2) through microbial action in the ascending colon, after which it was bioactivated into enterolignans from the transverse colon onward. Single demethylation was a first step in the bioactivation, followed by dehydroxylation. Enterolignan phenotypes remained stable throughout the experimental period. The establishment of END and ENL production equilibria reflected the subdominance of ENL-producing bacteria in the gastrointestinal tract.}, }
@article {pmid18493202, year = {2008}, author = {Barclay, AR and Morrison, DJ and Weaver, LT}, title = {What is the role of the metabolic activity of the gut microbiota in inflammatory bowel disease? Probing for answers with stable isotopes.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {46}, number = {5}, pages = {486-495}, doi = {10.1097/MPG.0b013e3181615b3a}, pmid = {18493202}, issn = {1536-4801}, mesh = {Bacteria/genetics/*immunology/isolation &amp; purification ; DNA, Bacterial/chemistry/genetics ; Genetic Predisposition to Disease ; Humans ; Inflammatory Bowel Diseases/genetics/*immunology/*microbiology ; Intestinal Mucosa/immunology/microbiology ; Isotope Labeling ; RNA, Bacterial/chemistry/genetics ; Species Specificity ; }, abstract = {The pathogenesis of inflammatory bowel disease remains obscure. However, there has been increasing interest in the role of the gut microbiota, focusing in particular on the "unculturable majority" of luminal and mucosal bacteria, which until recently have been difficult to study owing to the technical challenges of identification and elucidating function. Bacterial components and metabolites have been implicated in signalling to host immune systems and regulating inflammatory responses. Although the rapid expansion in techniques of molecular microbiology has increased our understanding of bacterial diversity, the tools to assess bacterial metabolic activity, and to link the 2, lag behind. Stable isotope probing is a powerful technique to link the metabolic activity and diversity of "unculturable" bacteria through isotopic labelling of biomarkers such as DNA and RNA. Progression of current stable isotope probing methodology with high-resolution oligonucleotide 16s rRNA probe technology and high precision liquid chromatographic isotope ratio mass spectrometry may facilitate application in human microbial ecology. Progress towards stable isotope probing use in vivo, in concert with other advances in bacterial metabolome analysis, will lead to the development of a dynamic picture of the metabolic activity and diversity of intestinal bacteria in inflammatory bowel disease. Such insights will, over time, lead to fuller understanding of inflammatory bowel disease pathogenesis and the development of targeted therapies to reverse the "dysbiosis" that precedes disease relapse.}, }
@article {pmid18491176, year = {2008}, author = {Feldman, TS and O'Brien, HE and Arnold, AE}, title = {Moths that vector a plant pathogen also transport endophytic fungi and mycoparasitic antagonists.}, journal = {Microbial ecology}, volume = {56}, number = {4}, pages = {742-750}, pmid = {18491176}, issn = {0095-3628}, mesh = {Animals ; Claviceps/genetics/*growth &amp; development/metabolism ; DNA, Ribosomal Spacer/genetics ; Ecosystem ; Fungi/genetics/growth &amp; development ; Fusarium/genetics/*growth &amp; development ; Moths/*microbiology ; Plant Diseases/*microbiology ; Poaceae/microbiology ; Polymerase Chain Reaction ; }, abstract = {Claviceps paspali, a common fungal pathogen of Paspalum grasses, attracts moth vectors by producing sugary exudates in the grass florets it infects. These exudates also support mycoparasitic Fusarium species that may negatively influence C. paspali fitness. We examined the potential for moths on which C. paspali depends to also transmit mycoparasitic Fusarium and fungal endophytes, which inhabit asymptomatic plant tissue and may influence host susceptibility to pathogens. We quantified infections by C. paspali, Fusarium spp., and endophytic fungi associated with Paspalum spp. at focal sites in the southeastern USA and used data from the nuclear internal transcribed spacer (ITS rDNA) to compare communities of plant-associated and moth-borne fungi. ITS sequences of moth-borne fungi were identical to reference sequences of mycoparasitic Fusarium heterosporum and to three distinct endophytic fungi isolated from Paspalum species. Our results demonstrate an unexpected overlap of fungal communities between disparate locations and among plant species and plant tissues, and suggest an unexpected role of moths, which vector a plant pathogen, to transmit other guilds of fungi. In turn, the potential for insects to transmit plant pathogens as well as mycoparasites and endophytic fungi suggests complex interactions underlying a commonly observed grass-pathogen system.}, }
@article {pmid18487399, year = {2008}, author = {Oakley, BB and Fiedler, TL and Marrazzo, JM and Fredricks, DN}, title = {Diversity of human vaginal bacterial communities and associations with clinically defined bacterial vaginosis.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {15}, pages = {4898-4909}, pmid = {18487399}, issn = {1098-5336}, support = {R01 AI61628/AI/NIAID NIH HHS/United States ; R56 AI052228/AI/NIAID NIH HHS/United States ; AI052228/AI/NIAID NIH HHS/United States ; R01 AI061628/AI/NIAID NIH HHS/United States ; R01 AI052228/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*genetics/isolation &amp; purification/pathogenicity ; DNA Primers ; Female ; Genetic Variation ; Gram-Negative Bacteria/classification/genetics/isolation &amp; purification/pathogenicity ; Gram-Positive Bacteria/classification/genetics/isolation &amp; purification/pathogenicity ; Humans ; Molecular Sequence Data ; Polymerase Chain Reaction ; Vagina/*microbiology ; Vaginal Smears ; Vaginosis, Bacterial/*microbiology ; }, abstract = {Bacterial vaginosis (BV) is a common syndrome associated with numerous adverse health outcomes in women. Despite its medical importance, the etiology and microbial ecology of BV remain poorly understood. We used broad-range PCR to census the community structure of the healthy and BV-affected vaginal microbial ecosystems and synthesized current publicly available bacterial 16S rRNA gene sequence data from this environment. The community of vaginal bacteria detected in subjects with BV was much more taxon rich and diverse than in subjects without BV. At a 97% sequence similarity cutoff, the number of operational taxonomic units (OTUs) per patient in 28 subjects with BV was nearly three times greater than in 13 subjects without BV: 14.8 +/- 0.7 versus 5.2 +/- 0.75 (mean +/- standard error). OTU-based analyses revealed previously hidden diversity for many vaginal bacteria that are currently poorly represented in GenBank. Our sequencing efforts yielded many novel phylotypes (123 of our sequences represented 38 OTUs not previously found in the vaginal ecosystem), including several novel BV-associated OTUs, such as those belonging to the Prevotella species complex, which remain severely underrepresented in the current NCBI database. Community composition was highly variable among subjects at a fine taxonomic scale, but at the phylum level, Actinobacteria and Bacteroidetes were strongly associated with BV. Our data describe a previously unrecognized extent of bacterial diversity in the vaginal ecosystem. The human vagina hosts many bacteria that are only distantly related to known species, and subjects with BV harbor particularly taxon-rich and diverse bacterial communities.}, }
@article {pmid18487133, year = {2008}, author = {Nisbet, EG and Nisbet, RE}, title = {Methane, oxygen, photosynthesis, rubisco and the regulation of the air through time.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {363}, number = {1504}, pages = {2745-2754}, pmid = {18487133}, issn = {0962-8436}, mesh = {Archaea/genetics/metabolism ; Atmosphere ; Biological Evolution ; Carbon Dioxide/metabolism ; Evolution, Molecular ; Methane/*metabolism ; Models, Biological ; Oceans and Seas ; Oxygen/*metabolism ; *Photosynthesis ; Phylogeny ; Ribulose-Bisphosphate Carboxylase/genetics/*metabolism ; Temperature ; Time Factors ; }, abstract = {Rubisco I's specificity, which today may be almost perfectly tuned to the task of cultivating the global garden, controlled the balance of carbon gases and O(2) in the Precambrian ocean and hence, by equilibration, in the air. Control of CO(2) and O(2) by rubisco I, coupled with CH(4) from methanogens, has for the past 2.9 Ga directed the global greenhouse warming, which maintains liquid oceans and sustains microbial ecology.Both rubisco compensation controls and the danger of greenhouse runaway (e.g. glaciation) put limits on biological productivity. Rubisco may sustain the air in either of two permissible stable states: either an anoxic system with greenhouse warming supported by both high methane mixing ratios as well as carbon dioxide, or an oxygen-rich system in which CO(2) largely fulfils the role of managing greenhouse gas, and in which methane is necessarily only a trace greenhouse gas, as is N(2)O. Transition from the anoxic to the oxic state risks glaciation. CO(2) build-up during a global snowball may be an essential precursor to a CO(2)-dominated greenhouse with high levels of atmospheric O(2). Photosynthetic and greenhouse-controlling competitions between marine algae, cyanobacteria, and terrestrial C3 and C4 plants may collectively set the CO(2) : O(2) ratio of the modern atmosphere (last few million years ago in a mainly glacial epoch), maximizing the productivity close to rubisco compensation and glacial limits.}, }
@article {pmid18485285, year = {2008}, author = {van der Gast, CJ}, title = {Islands shaping thought in microbial ecology.}, journal = {Advances in applied microbiology}, volume = {64}, number = {}, pages = {167-182}, doi = {10.1016/S0065-2164(08)00406-1}, pmid = {18485285}, issn = {0065-2164}, mesh = {Bacteria/*classification/*isolation &amp; purification ; *Biodiversity ; *Ecosystem ; *Geography ; Time Factors ; }, }
@article {pmid18481138, year = {2008}, author = {Cai, H and Jiao, N}, title = {Diversity and abundance of nitrate assimilation genes in the northern South china sea.}, journal = {Microbial ecology}, volume = {56}, number = {4}, pages = {751-764}, pmid = {18481138}, issn = {0095-3628}, mesh = {Bacterial Proteins/*genetics/metabolism ; Biodiversity ; China ; Cyanobacteria/classification/genetics/metabolism ; Flow Cytometry ; Genetic Variation ; Geography ; Nitrates/*metabolism ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Proteobacteria/classification/genetics/metabolism ; Seawater/*microbiology ; }, abstract = {Marine heterotrophic microorganisms that assimilate nitrate play an important role in nitrogen and carbon cycling in the water column. The nasA gene, encoding the nitrate assimilation enzyme, was selected as a functional marker to examine the nitrate assimilation community in the South China Sea (SCS). PCR amplification, restriction fragment length polymorphism (RFLP) screening, and phylogenetic analysis of nasA gene sequences were performed to characterize in situ nitrate assimilatory bacteria. Furthermore, the effects of nutrients and other environmental factors on the genetic heterogeneity of nasA fragments from the SCS were evaluated at the surface in three stations, and at two other depths in one of these stations. The diversity indices and rarefaction curves indicated that the nasA gene was more diverse in offshore waters than in the Pearl River estuary. The phylotype rank abundance curve showed an abundant and unique RFLP pattern in all five libraries, indicating that a high diversity but low abundance of nasA existed in the study areas. Phylogenetic analysis of environmental nasA gene sequences further revealed that the nasA gene fragments came from several common aquatic microbial groups, including the Proteobacteria, Cytophaga-Flavobacteria (CF), and Cyanobacteria. In addition to the direct PCR/sequence analysis of environmental samples, we also cultured a number of nitrate assimilatory bacteria isolated from the field. Comparison of nasA genes from these isolates and from the field samples indicated the existence of horizontal nasA gene transfer. Application of real-time quantitative PCR to these nasA genes revealed a great variation in their abundance at different investigation sites and water depths.}, }
@article {pmid18478424, year = {2007}, author = {Brown, SD and Raman, B and McKeown, CK and Kale, SP and He, Z and Mielenz, JR}, title = {Construction and evaluation of a Clostridium thermocellum ATCC 27405 whole-genome oligonucleotide microarray.}, journal = {Applied biochemistry and biotechnology}, volume = {137-140}, number = {1-12}, pages = {663-674}, doi = {10.1007/s12010-007-9087-6}, pmid = {18478424}, issn = {1559-0291}, mesh = {Chromosome Mapping/*instrumentation ; Clostridium thermocellum/*genetics ; DNA Probes/*genetics ; DNA, Bacterial/*genetics ; Equipment Design ; Equipment Failure Analysis ; Gene Expression Profiling/*instrumentation/methods ; Genome, Bacterial/*genetics ; Oligonucleotide Array Sequence Analysis/*instrumentation/methods ; Sensitivity and Specificity ; }, abstract = {Clostridium thermocellum is an anaerobic, thermophilic bacterium that can directly convert cellulosic substrates into ethanol. Microarray technology is a powerful tool to gain insights into cellular processes by examining gene expression under various physiological states. Oligonucleotide microarray probes were designed for 96.7% of the 3163 C. thermocellum ATCC 27405 candidate protein-encoding genes and then a partial-genome microarray containing 70 C. thermocellum specific probes was constructed and evaluated. We detected a signal-to-noise ratio of three with as little as 1.0 ng of genomic DNA and only low signals from negative control probes (nonclostridial DNA), indicating the probes were sensitive and specific. In order to further test the specificity of the array we amplified and hybridized 10 C. thermocellum polymerase chain reaction products that represented different genes and found gene specific hybridization in each case. We also constructed a whole-genome microarray and prepared total cellular RNA from the same point in early-logarithmic growth phase from two technical replicates during cellobiose fermentation. The reliability of the microarray data was assessed by cohybridization of labeled complementary DNA from the cellobiose fermentation samples and the pattern of hybridization revealed a linear correlation. These results taken together suggest that our oligonucleotide probe set can be used for sensitive and specific C. thermocellum transcriptomic studies in the future.}, }
@article {pmid18478288, year = {2008}, author = {Huang, CY and Lee, CY and Wu, HC and Kuo, MH and Lai, CY}, title = {Interactions of chaperonin with a weakly active anthranilate synthase from the aphid endosymbiont Buchnera aphidicola.}, journal = {Microbial ecology}, volume = {56}, number = {4}, pages = {696-703}, pmid = {18478288}, issn = {0095-3628}, mesh = {Animals ; Anthranilate Synthase/genetics/*metabolism ; Aphids/*microbiology ; Bacterial Proteins/genetics/*metabolism ; Buchnera/*enzymology ; Chaperonins/*metabolism ; Escherichia coli/genetics ; Genetic Complementation Test ; Mutation ; Polymerase Chain Reaction ; Protein Binding ; Recombinant Proteins/metabolism ; Symbiosis ; }, abstract = {The endosymbiotic bacterium Buchnera provides its aphid host with essential amino acids. Buchnera is typical of intracellular symbiotic and parasitic microorganisms in having a small effective population size, which is believed to accelerate genetic drift and reduce the stability of gene products. It is hypothesized that Buchnera mitigates protein instability with an increased production of the chaperonins GroESL. In this paper, we report the expression and functional analysis of trpE, a plasmid-borne fast-evolving gene encoding the tryptophan biosynthesis enzyme anthranilate synthase. We overcame the problem of low enzyme stability by using an anthranilate synthase-deficient mutant of E. coli as the expression host and the method of genetic complementation for detection of the enzyme activity. We showed that the Buchnera anthranilate synthase was only weakly active at the temperature of 26 degrees C but became inactive at the higher temperatures of 32 degrees C and 37 degrees C and that the coexpression with chaperonin genes groESL of E. coli enhanced the function of the Buchnera enzyme. These findings are consistent with the proposed role of groESL in the Buchnera-aphid symbiosis.}, }
@article {pmid18473699, year = {2008}, author = {Horn, M}, title = {Chlamydiae as symbionts in eukaryotes.}, journal = {Annual review of microbiology}, volume = {62}, number = {}, pages = {113-131}, doi = {10.1146/annurev.micro.62.081307.162818}, pmid = {18473699}, issn = {0066-4227}, mesh = {Amoeba/microbiology ; Animals ; Biological Evolution ; Chlamydiales/genetics/growth &amp; development/pathogenicity/*physiology ; Ecosystem ; Eukaryotic Cells/*microbiology ; Humans ; Plants/genetics/microbiology ; Public Health ; Symbiosis ; }, abstract = {Members of the phylum Chlamydiae are obligate intracellular bacteria that were discovered about a century ago. Although Chlamydiae are major pathogens of humans and animals, they were long recognized only as a phylogenetically well-separated, small group of closely related microorganisms. The diversity of chlamydiae, their host range, and their occurrence in the environment had been largely underestimated. Today, several chlamydia-like bacteria have been described as symbionts of free-living amoebae and other eukaryotic hosts. Some of these environmental chlamydiae might also be of medical relevance for humans. Their analysis has contributed to a broader understanding of chlamydial biology and to novel insights into the evolution of these unique microorganisms.}, }
@article {pmid18473135, year = {2008}, author = {Granado, J and Thürig, B and Kieffer, E and Petrini, L and Fliessbach, A and Tamm, L and Weibel, FP and Wyss, GS}, title = {Culturable fungi of stored 'golden delicious' apple fruits: a one-season comparison study of organic and integrated production systems in Switzerland.}, journal = {Microbial ecology}, volume = {56}, number = {4}, pages = {720-732}, pmid = {18473135}, issn = {0095-3628}, mesh = {Biodiversity ; Fruit/*microbiology ; Fungi/classification/*growth &amp; development/isolation &amp; purification ; Malus/*microbiology ; Switzerland ; }, abstract = {The effects of organic and integrated production systems on the culturable fungal microflora of stored apple fruits from five matched pairs of certified organic and integrated 'Golden Delicious' farms were studied at five representative production sites in Switzerland. Isolated fungi were identified morphologically. Colonization frequency (percentage of apples colonized), abundance (colony numbers), and diversity (taxon richness) were assessed for each orchard. The standard quality of the stored fruits was comparable for both organic and integrated apples and complied with national food hygiene standards. Yeasts (six taxa) and the yeast-like fungus Aureobasidium pullulans were the dominant epiphytes, filamentous fungi (21 taxa) the dominant endophytes. The most common fungi occurred at all sites and belonged to the "white" and "pink" yeasts, yeast-like A. pullulans, filamentous fungi Cladosporium spp., Alternaria spp., and sterile filamentous fungi. Canonical correspondence analysis of the total fungal community revealed a clear differentiation among production systems and sites. Compared to integrated apples, organic apples had significantly higher frequencies of filamentous fungi, abundance of total fungi, and taxon diversity. The effects of the production system on the fungal microflora are most likely due to the different plant protection strategies. The incidence of potential mycotoxin producers such as Penicillium and Alternaria species was not different between production systems. We suggest that higher fungal diversity may generally be associated with organic production and may increase the level of beneficial and antagonistically acting species known for their potential to suppress apple pathogens, which may be an advantage to organic apples, e.g., in respect to natural disease control.}, }
@article {pmid18465167, year = {2008}, author = {Laurin, V and Labbé, N and Parent, S and Juteau, P and Villemur, R}, title = {Microeukaryote diversity in a marine methanol-fed fluidized denitrification system.}, journal = {Microbial ecology}, volume = {56}, number = {4}, pages = {637-648}, pmid = {18465167}, issn = {0095-3628}, mesh = {Amoebida/classification/genetics/*growth &amp; development ; Animals ; Biodiversity ; Biofilms/growth &amp; development ; Eukaryota/classification/genetics/*growth &amp; development ; Fungi/classification/genetics/*growth &amp; development ; In Situ Hybridization, Fluorescence ; Methanol/*metabolism ; Nematoda/classification/genetics/*growth &amp; development ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Seawater/microbiology/parasitology ; }, abstract = {The marine methanol-fed fluidized denitrification system operated by the Montreal Biodome includes carriers on which a denitrifying biofilm has developed. Previous observations showed a high abundance of microeukaryotes living in and around the biofilm. These eukaryotes may influence the system's denitrification efficiency. The composition of the microeukaryote population was determined. Microscopic observations showed at least 20 different morphologies that included large numbers of ciliates. Molecular analyses of an 18S ribosomal RNA (rDNA) gene library revealed 31 different phylotypes. Alveolobiontes were the most abundant phylotypes and made up 75% of the 159 screened clones. Other eukaryotic groups, including Stramenopiles, Fungi, Amoebozoa, and nematodes, were also present. From 18S rDNA specific sequences, one of the Amoebozoa-affiliated phylotypes was visualized by fluorescence in situ hybridization. It had a rod-like irregular shape and measured less than 5 mum in length. We determined the impact of protozoans on the denitrifying activity. In a laboratory-scale batch culture assays, the denitrifying biofilm was treated with cycloheximide and nystatin that eliminated the protozoans. No difference in the denitrification rate was found. However, planktonic bacteria were more abundant in the treated culture medium.}, }
@article {pmid18463726, year = {2007}, author = {Bowman, JP}, title = {Bioactive compound synthetic capacity and ecological significance of marine bacterial genus pseudoalteromonas.}, journal = {Marine drugs}, volume = {5}, number = {4}, pages = {220-241}, pmid = {18463726}, issn = {1660-3397}, abstract = {The genus Pseudoalteromonas is a marine group of bacteria belonging to the class Gammaproteobacteria that has come to attention in the natural product and microbial ecology science fields in the last decade. Pigmented species of the genus have been shown to produce an array of low and high molecular weight compounds with antimicrobial, anti-fouling, algicidal and various pharmaceutically-relevant activities. Compounds formed include toxic proteins, polyanionic exopolymers, substituted phenolic and pyrolle-containing alkaloids, cyclic peptides and a range of bromine-substituted compounds. Ecologically, Pseudoalteromonas appears significant and to date has been shown to influence biofilm formation in various marine econiches; involved in predator-like interactions within the microbial loop; influence settlement, germination and metamorphosis of various invertebrate and algal species; and may also be adopted by marine flora and fauna as defensive agents. Studies have been so far limited to a relatively small subset of strains compared to the known diversity of the genus suggesting that many more discoveries of novel natural products as well as ecological connections these may have in the marine ecosystem remain to be made.}, }
@article {pmid18461781, year = {2008}, author = {Wilhelm, SW}, title = {Field methods in the study of toxic cyanobacterial blooms: results and insights from Lake Erie research.}, journal = {Advances in experimental medicine and biology}, volume = {619}, number = {}, pages = {501-512}, doi = {10.1007/978-0-387-75865-7_22}, pmid = {18461781}, issn = {0065-2598}, mesh = {Animals ; Bacterial Toxins/analysis/toxicity ; Cyanobacteria/classification/genetics/isolation &amp; purification/*pathogenicity ; Cyanobacteria Toxins ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Environmental Monitoring/*methods ; *Eutrophication ; Fresh Water/analysis/*microbiology ; Great Lakes Region ; Humans ; Marine Toxins/analysis/toxicity ; Microcystins/analysis/toxicity ; Phylogeny ; Spacecraft ; }, abstract = {Sound field methodologies are an essential prerequisite in the development of a basic understanding of toxic cyanobacteria blooms. Sample collection, on-site processing, storage and transportation, and subsequent analysis and documentation are all critically dependent on a sound field program that allows the researcher to construct, with minimal uncertainty, linkages between bloom events and cyanotoxin production with the ecology of the studied system. Since 1999, we have collected samples in Lake Erie as part of the MELEE (Microbial Ecology of the Lake Erie Ecosystem) and MERHAB-LGL (Monitoring Event Responses for Harmful Algal Blooms in the Lower Great Lakes) research programs to develop appropriate tools and refine methods necessary to characterize the ecology of the reoccurring cyanobacterial blooms in the systems. Satellite imagery, large ship expeditions, classical and novel molecular tools have been combined to provide insight into both the cyanobacteria responsible for these events as well as into some of the environmental cues that may facilitate the formation of toxic blooms. This information, as well new directions in cyano-specific monitoring will be presented to highlight needs for field program monitoring and/or researching toxic freshwater cyanobacteria.}, }
@article {pmid18458997, year = {2008}, author = {Kageyama, D and Narita, S and Noda, H}, title = {Transfection of feminizing Wolbachia endosymbionts of the butterfly, Eurema hecabe, into the cell culture and various immature stages of the silkmoth, Bombyx mori.}, journal = {Microbial ecology}, volume = {56}, number = {4}, pages = {733-741}, pmid = {18458997}, issn = {0095-3628}, mesh = {Animals ; Bombyx/cytology/genetics/*microbiology ; Butterflies/*microbiology ; Cell Line ; Female ; Male ; Oocytes/metabolism ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Wolbachia/genetics/*growth &amp; development ; }, abstract = {Wolbachia are maternally inherited endosymbiotic bacteria of invertebrates that can manipulate the reproductive systems of their arthropod hosts in a variety of ways. To establish a useful model system for investigating the mechanism of Wolbachia-induced host feminization, we conducted the following series of experiments: (1) feminizing Wolbachia of the butterfly, Eurema hecabe, were transferred into cell cultures of the silkmoth, Bombyx mori, and (2) the transfected Wolbachia in cell cultures were inoculated into B. mori at four immature stages. Wolbachia were successfully transfected into the cell cultures and stably maintained for more than 1 year (>30 passages). However, none of the inoculated insects produced mature oocytes that were Wolbachia-positive. This finding was consistent with the fact that Wolbachia was not detected in individuals in subsequent generations. In contrast, Wolbachia were detected at relatively high frequencies (60-80% of individuals) in the somatic tissues of inoculated insects. Real-time quantitative polymerase chain reaction revealed that the Wolbachia densities in the cultured cells were approximately tenfold higher than those in the native host E. hecabe. Among B. mori individuals inoculated at various developmental stages, those inoculated at early stages exhibited higher Wolbachia densities at the adult stage. The Wolbachia densities in individuals inoculated at the second-instar stage were comparable to those in intact E. hecabe. These results suggest that infection and/or proliferation of Wolbachia in germline cells are actively hindered by regulation in B. mori but feasible in somatic cells and that the Wolbachia densities in somatic tissues are regulated by the living host insects.}, }
@article {pmid18458132, year = {2008}, author = {Haanperä, M and Forssten, SD and Huovinen, P and Jalava, J}, title = {Typing of SHV extended-spectrum beta-lactamases by pyrosequencing in Klebsiella pneumoniae strains with chromosomal SHV beta-lactamase.}, journal = {Antimicrobial agents and chemotherapy}, volume = {52}, number = {7}, pages = {2632-2635}, pmid = {18458132}, issn = {1098-6596}, mesh = {Amino Acid Substitution ; Base Sequence ; Chromosomes, Bacterial/genetics ; DNA Primers/genetics ; DNA, Bacterial/genetics ; Genes, Bacterial ; Humans ; Klebsiella pneumoniae/classification/*enzymology/*genetics/isolation &amp; purification ; Point Mutation ; Sequence Analysis, DNA ; beta-Lactamases/classification/*genetics ; }, abstract = {In Klebsiella pneumoniae, the cooccurrence of chromosomal and plasmid-mediated beta-lactamases can hinder their accurate molecular detection. We developed a fast and reliable method that allows the typing of isolates carrying more than one SHV gene. The method is based on pyrosequencing the DNA sequence corresponding to amino acid positions 35, 238, and 240.}, }
@article {pmid18456853, year = {2008}, author = {Cardenas, E and Wu, WM and Leigh, MB and Carley, J and Carroll, S and Gentry, T and Luo, J and Watson, D and Gu, B and Ginder-Vogel, M and Kitanidis, PK and Jardine, PM and Zhou, J and Criddle, CS and Marsh, TL and Tiedje, JM}, title = {Microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levels.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {12}, pages = {3718-3729}, pmid = {18456853}, issn = {1098-5336}, mesh = {Bacteria/*classification/*genetics/isolation &amp; purification ; *Biodegradation, Environmental ; *Biodiversity ; Cluster Analysis ; Colony Count, Microbial ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Ethanol/metabolism ; Genes, rRNA ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; United States ; Uranium/*metabolism ; }, abstract = {Microbial enumeration, 16S rRNA gene clone libraries, and chemical analysis were used to evaluate the in situ biological reduction and immobilization of uranium(VI) in a long-term experiment (more than 2 years) conducted at a highly uranium-contaminated site (up to 60 mg/liter and 800 mg/kg solids) of the U.S. Department of Energy in Oak Ridge, TN. Bioreduction was achieved by conditioning groundwater above ground and then stimulating growth of denitrifying, Fe(III)-reducing, and sulfate-reducing bacteria in situ through weekly injection of ethanol into the subsurface. After nearly 2 years of intermittent injection of ethanol, aqueous U levels fell below the U.S. Environmental Protection Agency maximum contaminant level for drinking water and groundwater (<30 microg/liter or 0.126 microM). Sediment microbial communities from the treatment zone were compared with those from a control well without biostimulation. Most-probable-number estimations indicated that microorganisms implicated in bioremediation accumulated in the sediments of the treatment zone but were either absent or in very low numbers in an untreated control area. Organisms belonging to genera known to include U(VI) reducers were detected, including Desulfovibrio, Geobacter, Anaeromyxobacter, Desulfosporosinus, and Acidovorax spp. The predominant sulfate-reducing bacterial species were Desulfovibrio spp., while the iron reducers were represented by Ferribacterium spp. and Geothrix spp. Diversity-based clustering revealed differences between treated and untreated zones and also within samples of the treated area. Spatial differences in community structure within the treatment zone were likely related to the hydraulic pathway and to electron donor metabolism during biostimulation.}, }
@article {pmid18449467, year = {2008}, author = {Appoloni, S and Lekberg, Y and Tercek, MT and Zabinski, CA and Redecker, D}, title = {Molecular community analysis of arbuscular mycorrhizal fungi in roots of geothermal soils in Yellowstone National Park (USA).}, journal = {Microbial ecology}, volume = {56}, number = {4}, pages = {649-659}, pmid = {18449467}, issn = {0095-3628}, mesh = {DNA, Ribosomal Spacer/genetics ; *Ecosystem ; Molecular Sequence Data ; Mycorrhizae/classification/*genetics/growth &amp; development ; Phylogeny ; Plant Roots/*microbiology ; Poaceae/microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 5.8S/genetics ; Sequence Analysis, DNA ; Soil/analysis ; Wyoming ; }, abstract = {To better understand adaptation of plants and their mycorrhizae to extreme environmental conditions, we analyzed the composition of communities of arbuscular mycorrhizal fungi (AMF) in roots from geothermal sites in Yellowstone National Park (YNP), USA. Arbuscular mycorrhizal fungi were identified using molecular methods including seven specific primer pairs for regions of the ribosomal DNA that amplify different subgroups of AMF. Roots of Dichanthelium lanuginosum, a grass only occurring in geothermal areas, were sampled along with thermal and nonthermal Agrostis scabra and control plants growing outside the thermally influenced sites. In addition, root samples of Agrostis stolonifera from geothermal areas of Iceland were analyzed to identify possible common mycosymbionts between these geographically isolated locations. In YNP, 16 ribosomal DNA phylotypes belonging to the genera Archaeospora, Glomus, Paraglomus, Scutellospora, and Acaulospora were detected. Eight of these phylotypes could be assigned to known morphospecies, two others have been reported previously in molecular studies from different environments, and six were new to science. The most diverse and abundant lineage was Glomus group A, with the most frequent phylotype corresponding to Glomus intraradices. Five of the seven phylotypes detected in a preliminary sampling in a geothermal area in Iceland were also found in YNP. Nonthermal vegetation was dominated by a high diversity of Glomus group A phylotypes while nonthermal plants were not. Using multivariate analyses, a subset of three phylotypes were determined to be associated with geothermal conditions in the field sites analyzed. In conclusion, AMF communities in geothermal soils are distinct in their composition, including both unique phylotypes and generalist fungi that occur across a broad range of environmental conditions.}, }
@article {pmid18443848, year = {2008}, author = {Liu, X and Kong, S and Shi, M and Fu, L and Gao, Y and An, C}, title = {Genomic analysis of freshwater cyanophage Pf-WMP3 Infecting cyanobacterium Phormidium foveolarum: the conserved elements for a phage.}, journal = {Microbial ecology}, volume = {56}, number = {4}, pages = {671-680}, pmid = {18443848}, issn = {0095-3628}, mesh = {Bacteriophages/classification/*genetics/growth &amp; development ; Cyanobacteria/*virology ; Fresh Water/microbiology/*virology ; Genome, Viral/*genetics ; Genomics/methods ; Molecular Sequence Data ; Sequence Analysis, DNA ; }, abstract = {Cyanophages are ecologically abundant, genetically diverse in aquatic environments, and affect the population and evolutionary trajectories of their hosts. After reporting the cyanophage Pf-WMP4 genome (Liu et al. in Virology 366:28-39, 2007), we hereby present a related cyanophage, Pf-WMP3, which also infects the freshwater cyanobacterium Phormidium foveolarum. The Pf-WMP3 genome contains 43,249 bp with 234 bp direct terminal repeats. The overall genome organization and core genes of the two phages are comparable to those of the T7 supergroup phages. Compared with Pf-WMP4, cyanophage Pf-WMP3 has diverged extensively at the DNA level; however, they are closely related at the protein level and genome architecture. The left arm genes for the two phages, which mainly encode the DNA replication machinery, are not conserved in the gene order. Whereas the right arm genes of the two phages coding for structural proteins show high similarity in amino acid sequences and modular architecture, indicating that they have retained similar development strategies. The differences in similarity levels between the left and right arm genes suggest that the structural genes are the most conserved elements for a phage.}, }
@article {pmid18443847, year = {2008}, author = {Schmidt, SK and Wilson, KL and Meyer, AF and Gebauer, MM and King, AJ}, title = {Phylogeny and ecophysiology of opportunistic "snow molds" from a subalpine forest ecosystem.}, journal = {Microbial ecology}, volume = {56}, number = {4}, pages = {681-687}, pmid = {18443847}, issn = {0095-3628}, mesh = {Colorado ; *Ecosystem ; Fungi/classification/genetics/*growth &amp; development ; *Phylogeny ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; *Snow ; Temperature ; Trees/*microbiology ; }, abstract = {Mats of coenocytic "snow molds" are commonly observed covering the soil and litter of alpine and subalpine areas immediately following snow melt. Here, we describe the phylogenetic placement, growth rates, and metabolic potential of cold-adapted fungi from under-snow mats in the subalpine forests of Colorado. SSU rDNA sequencing revealed that these fungi belong to the zygomycete orders Mucorales and Mortierellales. All of the isolates could grow at temperatures observed under the snow at our sites (0 degrees C and -2 degrees C) but were unable to grow at temperatures above 25 degrees C and were unable to grow anaerobically. Growth rates for these fungi were very high at -2 degrees C, approximately an order of magnitude faster than previously studied cold-tolerant fungi from Antarctic soils. Given the rapid aerobic growth of these fungi at low temperatures, we propose that they are uniquely adapted to take advantage of the flush of nutrient that occurs at the soil-snow interface beneath late winter snow packs. In addition, extracellular enzyme production was relatively high for the Mucorales, but quite low for the Mortierellales, perhaps indicating some niche separation between these fungi beneath the late winter snow pack.}, }
@article {pmid18443846, year = {2008}, author = {Duarte, S and Pascoal, C and Cássio, F}, title = {High diversity of fungi may mitigate the impact of pollution on plant litter decomposition in streams.}, journal = {Microbial ecology}, volume = {56}, number = {4}, pages = {688-695}, pmid = {18443846}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development/metabolism ; Biodegradation, Environmental ; Biomass ; Environmental Pollution/*prevention &amp; control ; Fungi/*growth &amp; development/metabolism ; Plant Leaves/metabolism/microbiology ; Rivers/*microbiology ; Water Microbiology ; }, abstract = {We investigated how a community of microbial decomposers adapted to a reference site responds to a sudden decrease in the water quality. For that, we assessed the activity and diversity of fungi and bacteria on decomposing leaves that were transplanted from a reference (E1) to a polluted site (E2), and results were compared to those from decomposing leaves either at E1 or E2. The two sites had contrasting concentrations of organic and inorganic nutrients and heavy metals in the stream water. At E2, leaf decomposition rates, fungal biomass, and sporulation were reduced, while bacterial biomass was stimulated. Fungal diversity was four times lower at the polluted site. The structure of fungal community on leaves decomposing at E2 significantly differed from that decomposing at E1, as indicated by the principal response curves analysis. Articulospora tetracladia, Anguillospora filiformis, and Lunulospora curvula were dominant species on leaves decomposing at E1 and were the most negatively affected by the transfer to the polluted site. The transfer of leaves colonized at the reference site to the polluted site reduced fungal diversity and sporulation but not fungal biomass and leaf decomposition. Overall, results suggest that the high diversity on leaves from the upstream site might have mitigated the impact of anthropogenic stress on microbial decomposition of leaves transplanted to the polluted site.}, }
@article {pmid18443845, year = {2008}, author = {Aroca, R and Del Mar Alguacil, M and Vernieri, P and Ruiz-Lozano, JM}, title = {Plant responses to drought stress and exogenous ABA application are modulated differently by mycorrhization in tomato and an ABA-deficient mutant (sitiens).}, journal = {Microbial ecology}, volume = {56}, number = {4}, pages = {704-719}, pmid = {18443845}, issn = {0095-3628}, mesh = {Abscisic Acid/metabolism/*pharmacology ; Adaptation, Physiological/*drug effects/genetics/physiology ; *Droughts ; Solanum lycopersicum/genetics/metabolism/*microbiology ; Mutation ; Mycorrhizae/*physiology ; Plant Roots/genetics/metabolism/microbiology ; Symbiosis ; }, abstract = {The aims of the present study are to find out whether the effects of arbuscular mycorrhizal (AM) symbiosis on plant resistance to water deficit are mediated by the endogenous abscisic acid (ABA) content of the host plant and whether the exogenous ABA application modifies such effects. The ABA-deficient tomato mutant sitiens and its near-isogenic wild-type parental line were used. Plant development, physiology, and expression of plant genes expected to be modulated by AM symbiosis, drought, and ABA were studied. Results showed that only wild-type tomato plants responded positively to mycorrhizal inoculation, while AM symbiosis was not observed to have any effect on plant development in sitiens plants grown under well-watered conditions. The application of ABA to sitiens plants enhanced plant growth both under well-watered and drought stress conditions. In respect to sitiens plants subjected to drought stress, the addition of ABA had a cumulative effect in relation to that of inoculation with G. intraradices. Most of the genes analyzed in this study showed different regulation patterns in wild-type and sitiens plants, suggesting that their gene expression is modulated by the plant ABA phenotype. In the same way, the colonization of roots with the AM fungus G. intraradices differently regulated the expression of these genes in wild-type and in sitiens plants, which could explain the distinctive effect of the symbiosis on each plant ABA phenotype. This also suggests that the effects of the AM symbiosis on plant responses and resistance to water deficit are mediated by the plant ABA phenotype.}, }
@article {pmid18441792, year = {2008}, author = {Hand, VL and Lloyd, JR and Vaughan, DJ and Wilkins, MJ and Boult, S}, title = {Experimental studies of the influence of grain size, oxygen availability and organic carbon availability on bioclogging in porous media.}, journal = {Environmental science &amp; technology}, volume = {42}, number = {5}, pages = {1485-1491}, doi = {10.1021/es072022s}, pmid = {18441792}, issn = {0013-936X}, mesh = {Bacteria, Aerobic/genetics/metabolism ; Bacteria, Anaerobic/genetics/metabolism ; Carbon/*chemistry/metabolism ; Microscopy, Electron, Scanning ; Oxygen/*chemistry/metabolism ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {Changes in the hydraulic properties of porous material due to bioclogging have been observed in many laboratory simulations and field studies. Because such changes in hydraulic properties influence the movement of fluids and contaminants, microbial ecology data are required for improved transport modeling. Here we investigate the effects of environmental variables previously shown to influence bioclogging, specifically oxygen availability, sediment grain size, and organic carbon (nutrient) concentration on the hydraulic properties of simulated subsurface environments. Our study provides evidence of a different clogging mechanism for aerobic and anaerobic microbial communities under high organic carbon concentrations (400 mg L(-1)). This work also suggests that the clogging mechanism operating in anaerobic microbial communities is more sensitive to carbon availability than that in the aerobic microbial communities. We found that grain size does have an effect on clogging, but it appears that there is a threshold carbon concentration, and therefore biomass, below which these effects are insignificant. Differences between the microbial communities that developed under different oxygenation conditions were detected using 16s rRNA analysis.}, }
@article {pmid18437449, year = {2008}, author = {Kamnev, AA and Sadovnikova, JN and Tarantilis, PA and Polissiou, MG and Antonyuk, LP}, title = {Responses of Azospirillum brasilense to nitrogen deficiency and to wheat lectin: a diffuse reflectance infrared fourier transform (DRIFT) spectroscopic study.}, journal = {Microbial ecology}, volume = {56}, number = {4}, pages = {615-624}, pmid = {18437449}, issn = {0095-3628}, mesh = {Aerobiosis ; Azospirillum brasilense/*drug effects/growth &amp; development/metabolism ; Hydroxybutyrates/metabolism ; Nitrogen/*metabolism/pharmacology ; Polyesters/metabolism ; Spectroscopy, Fourier Transform Infrared/*methods ; Wheat Germ Agglutinins/*pharmacology ; }, abstract = {For the rhizobacterium Azospirillum brasilense, the optimal nutritional range of C:N ratios corresponds to the presence of malate (ca. 3 to 5 g l(-1) of its sodium salt) and ammonium (ca. 0.5 to 3 g l(-1) of NH4Cl) as preferred carbon and nitrogen sources, respectively. This microaerophilic aerotactic bacterium is known to have a narrow optimal oxygen concentration range of ca. 3 to 5 microM, which is 1.2% to 2% of oxygen solubility in air-saturated water under normal conditions. In this work, the effects of stress conditions (bound-nitrogen deficiency related to a high C:N ratio in the medium; excess of oxygen) on aerobically grown A. brasilense Sp245, a native wheat-associated endophyte, were investigated in the absence and presence of wheat germ agglutinin (WGA, plant stress protein and a molecular host-plant signal for the bacterium) using FTIR spectroscopy of whole cells in the diffuse reflectance mode (DRIFT). The nutritional stress resulted in the appearance of prominent spectroscopic signs of poly-3-hydroxybutyrate (PHB) accumulation in the bacterial cells; in addition, splitting of the amide I band related to bacterial cellular proteins indicated some stress-induced alterations in their secondary structure components. Similar structural changes were observed in the presence of nanomolar WGA both in stressed A. brasilense cells and under normal nutritional conditions. Comparative analysis of the data obtained and the relevant literature data indicated that the stress conditions applied (which resulted in the accumulation of PHB involved in stress tolerance) and/or the presence of nanomolar concentrations of WGA induced synthesis of bacterial cell-surface (glyco)proteins rich in beta-structures, that could be represented by hemagglutinin and/or porin.}, }
@article {pmid18437448, year = {2008}, author = {Stabili, L and Gravili, C and Tredici, SM and Piraino, S and Talà, A and Boero, F and Alifano, P}, title = {Epibiotic Vibrio luminous bacteria isolated from some hydrozoa and bryozoa species.}, journal = {Microbial ecology}, volume = {56}, number = {4}, pages = {625-636}, pmid = {18437448}, issn = {0095-3628}, mesh = {Animals ; Bryozoa/*microbiology ; Geography ; Hydrozoa/*microbiology ; Italy ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vibrio/classification/*genetics/ultrastructure ; }, abstract = {Luminous bacteria are isolated from both Hydrozoa and Bryozoa with chitinous structures on their surfaces. All the specimens of the examined hydroid species (Aglaophenia kirchenpaueri, Aglaophenia octodonta, Aglaophenia tubiformis, Halopteris diaphana, Plumularia setacea, Ventromma halecioides), observed under blue light excitation, showed a clear fluorescence on the external side of the perisarc (chitinous exoskeleton) around hydrocladia. In the bryozoan Myriapora truncata, luminous bacteria are present on the chitinous opercula. All the isolated luminous bacteria were identified on the basis of both phenotypic and genotypic analysis. The isolates from A. tubiformis and H. diaphana were unambiguously assigned to the species Vibrio fischeri. In contrast, the isolates from the other hydroids, phenotypically assigned to the species Vibrio harveyi, were then split into two distinct species by phylogenetic analysis of 16S rRNA gene sequences and DNA-DNA hybridization experiments. Scanning electron microscopy analysis and results of culture-based and culture-independent approaches enabled us to establish that luminous vibrios represent major constituents of the bacterial community inhabiting the A. octodonta surface suggesting that the interactions between luminous bacteria and the examined hydrozoan and bryozoan species are highly specific. These interactions might have epidemiological as well as ecological implications because of the opportunistic pathogenicity of luminous Vibrio species for marine organisms and the wide-distribution of the hydrozoan and bryozoan functioning as carriers.}, }
@article {pmid18435506, year = {2008}, author = {Baggs, EM}, title = {A review of stable isotope techniques for N2O source partitioning in soils: recent progress, remaining challenges and future considerations.}, journal = {Rapid communications in mass spectrometry : RCM}, volume = {22}, number = {11}, pages = {1664-1672}, doi = {10.1002/rcm.3456}, pmid = {18435506}, issn = {0951-4198}, support = {BB/D525099/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; D19035/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Environmental Monitoring ; Mass Spectrometry ; Nitrogen/analysis/*metabolism ; Nitrogen Isotopes/analysis ; Nitrous Oxide/chemistry/*metabolism ; Oxygen Isotopes/analysis ; Soil/*analysis ; *Soil Microbiology ; Waste Disposal, Fluid/methods ; }, abstract = {Nitrous oxide is produced in soil during several processes, which may occur simultaneously within different micro-sites of the same soil. Stable isotope techniques have a crucial role to play in the attribution of N(2)O emissions to different microbial processes, through estimation (natural abundance, site preference) or quantification (enrichment) of processes based on the (15)N and (18)O signatures of N(2)O determined by isotope ratio mass spectrometry. These approaches have the potential to become even more powerful when linked with recent developments in secondary isotope mass spectrometry, with microbial ecology, and with modelling approaches, enabling sources of N(2)O to be considered at a wide range of scales and related to the underlying microbiology. Such source partitioning of N(2)O is inherently challenging, but is vital to close the N(2)O budget and to better understand controls on the different processes, with a view to developing appropriate management practices for mitigation of N(2)O. In this respect, it is essential that as many of the contributing processes as possible are considered in any study aimed at source attribution, as mitigation strategies for one process may not be appropriate for another. To aid such an approach, here the current state of the art is critically examined, remaining challenges are highlighted, and recommendations are made for future direction.}, }
@article {pmid18434131, year = {2008}, author = {Signoretto, C and Canepari, P}, title = {Towards more accurate detection of pathogenic Gram-positive bacteria in waters.}, journal = {Current opinion in biotechnology}, volume = {19}, number = {3}, pages = {248-253}, doi = {10.1016/j.copbio.2008.03.001}, pmid = {18434131}, issn = {0958-1669}, mesh = {Animals ; Bacteriological Techniques/*methods ; Biotechnology ; Enterococcus/genetics/isolation &amp; purification/pathogenicity/physiology ; Gram-Positive Bacteria/genetics/*isolation &amp; purification/*pathogenicity/physiology ; Gram-Positive Bacterial Infections/transmission ; Humans ; *Water Microbiology ; }, abstract = {Medically important bacteria can persist in surface waters longer than was previously thought, by activating specific survival strategies and, thus, may represent a further threat to human health, in that they are non-detectable by the traditional culture methods currently used for the evaluation of microbiological quality. Combining microbial physiology, microbial biochemistry, microbial genetics, microbial ecology and molecular biology techniques allow us to achieve more accurate detection of human pathogens located in natural environments external to the human body.}, }
@article {pmid18429330, year = {2008}, author = {Gury, J and Zinger, L and Gielly, L and Taberlet, P and Geremia, RA}, title = {Exonuclease activity of proofreading DNA polymerases is at the origin of artifacts in molecular profiling studies.}, journal = {Electrophoresis}, volume = {29}, number = {11}, pages = {2437-2444}, doi = {10.1002/elps.200700667}, pmid = {18429330}, issn = {0173-0835}, mesh = {*Artifacts ; DNA Fingerprinting/*methods ; DNA-Directed DNA Polymerase/*metabolism ; Electrophoresis, Capillary/methods ; Exonucleases/*metabolism ; Polymerase Chain Reaction/methods ; Polymorphism, Single-Stranded Conformational ; }, abstract = {CE fingerprint methods are commonly used in microbial ecology. We have previously noticed that the position and number of peaks in CE-SSCP (single-strand conformation polymorphism) profiles depend on the DNA polymerase used in PCR [1]. Here, we studied the fragments produced by Taq polymerase as well as four commercially available proofreading polymerases, using the V3 region of the Escherichia coli rss gene as a marker. PCR products rendered multiple peaks in denaturing CE; Taq polymerase was observed to produce the longest fragments. Incubation of the fragments with T4 DNA polymerase indicated that the 3'-ends of the proofreading polymerase amplicons were recessed, while the Taq amplicon was partially +A tailed. Treatment of the PCR product with proofreading DNA polymerase rendered trimmed fragments. This was due to the 3'-5' exonuclease activity of these enzymes, which is essential for proofreading. The nuclease activity was reduced by increasing the concentration of dNTP. The Platinum Pfx DNA polymerase generated very few artifacts and could produce 85% of blunted PCR products. Nevertheless, despite the higher error rate, we recommend the use of Taq polymerase rather than proofreading in the framework for molecular fingerprint studies. They are more cost-effective and therefore ideally suited for high-throughput analysis; the +A tail artifact rate can be controlled by modifying the PCR primers and the reaction conditions.}, }
@article {pmid18422633, year = {2008}, author = {Heijs, SK and Laverman, AM and Forney, LJ and Hardoim, PR and van Elsas, JD}, title = {Comparison of deep-sea sediment microbial communities in the Eastern Mediterranean.}, journal = {FEMS microbiology ecology}, volume = {64}, number = {3}, pages = {362-377}, doi = {10.1111/j.1574-6941.2008.00463.x}, pmid = {18422633}, issn = {0168-6496}, mesh = {Archaea/*classification/genetics/*isolation &amp; purification ; Bacteria/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal ; Geologic Sediments/*microbiology ; Mediterranean Sea ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Bacterial and archaeal communities in sediments obtained from three geographically-distant mud volcanoes, a control site and a microbial mat in the Eastern Mediterranean deep-sea were characterized using direct 16S rRNA gene analyses. The data were thus in relation to the chemical characteristics of the (stratified) habitats to infer community structure-habitat relationships. The bacterial sequences in the different habitats were related to those of Actinobacteria, Bacilli, Chloroflexi, Alpha-, Beta-, Gamma-, Delta- and Epsilonproteobacteria and unclassified bacteria, including the JS1 group. The archaeal sequences found were affiliated with those of the Methanosarcinales, Thermoplasmales, Halobacteriales and Crenarchaea belonging to marine benthic group I and B, as well as MCG group archaea. In each sample, the communities were diverse and unique at the phylotype level. However, at higher taxonomic levels, similar groups were found in different sediments, and similar depth layers tended to contain similar communities. The sequences that dominated in all top layers (as well as in the mat) probably represented organisms involved in aerobic heterotrophy, sulfide-based chemoautotrophy and methanotrophy and/or methylotrophy. Sequences of organisms most likely involved in anaerobic methane oxidation, sulfate reduction and anaerobic heterotrophy were predominantly found in deeper layers. The data supported the notion of (1) uniqueness of each habitat at fine taxonomic levels, (2) stratification in depth and (3) conservation of function in the sediments.}, }
@article {pmid18421258, year = {2008}, author = {Warmink, JA and van Elsas, JD}, title = {Selection of bacterial populations in the mycosphere of Laccaria proxima: is type III secretion involved?.}, journal = {The ISME journal}, volume = {2}, number = {8}, pages = {887-900}, doi = {10.1038/ismej.2008.41}, pmid = {18421258}, issn = {1751-7370}, mesh = {Agaricales/*physiology ; *Antibiosis ; Bacteria/*classification/*genetics/isolation &amp; purification ; Bacterial Proteins/genetics ; Base Sequence ; *Biodiversity ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Electrophoresis, Polyacrylamide Gel ; Membrane Transport Proteins/genetics ; Molecular Sequence Data ; Nucleic Acid Denaturation ; Phylogeny ; Polymerase Chain Reaction ; *Selection, Genetic ; Sequence Homology, Nucleic Acid ; *Soil Microbiology ; }, abstract = {The bacterial communities in the Laccaria proxima mycosphere (soil from beneath fruiting bodies) and the corresponding bulk soil were compared by cultivation-dependent and cultivation-independent methods. To assess the distribution of type III secretion systems (TTSS), a PCR-based system for the broad detection of a highly conserved gene involved in TTSS, that is hrcR, was developed and used to assay the cultured bacteria from the L. proxima mycosphere and surrounding bulk soil. PCR-DGGE based on the 16S ribosomal RNA gene showed the selection of presumably mycosphere-specific bacterial groups in the mycosphere of L. proxima compared to the bulk soil in 3 sampling years. Moreover, plate counts revealed that the numbers of culturable heterotrophic bacteria were increased in the mycosphere as compared to the bulk soil. Strikingly, the percentage of randomly picked isolates that carried the hrcR gene showed a significant increase, from 2.8 in the bulk to 13.4 in the mycosphere soil. The increase could be mainly attributed to the emergence of a hrcR positive Pseudomonas fluorescens, denoted BS053, which constituted the most dominant species in the culturable mycosphere communities. This organism was, together with a hrcR-positive Burkholderia terrae BS110, exclusively found in mycosphere soil. Direct detection of hrcR genes using a cultivation-independent approach showed the selection of several hrcR gene types uniquely in the mycosphere, indicating the selection of several TTSS-harboring bacterial species. Thus, different bacteria were found to be enriched in the L. proxima mycosphere and TTSS can be involved in some of the interactions with the fungal host.}, }
@article {pmid18419193, year = {2008}, author = {Törneman, N and Yang, X and Bååth, E and Bengtsson, G}, title = {Spatial covariation of microbial community composition and polycyclic aromatic hydrocarbon concentration in a creosote-polluted soil.}, journal = {Environmental toxicology and chemistry}, volume = {27}, number = {5}, pages = {1039-1046}, doi = {10.1897/07-440.1}, pmid = {18419193}, issn = {0730-7268}, mesh = {Creosote/*analysis ; Polycyclic Compounds/*analysis ; *Soil Microbiology ; Soil Pollutants/*analysis ; }, abstract = {Little is known about the spatial connection between soil microbial community composition and polycyclic aromatic hydrocarbon (PAH) concentration. A spatially explicit survey at a creosote-contaminated site demonstrated that microbial biomass (total concentration of phospholipid fatty acids [PLFAs]) and microbial community composition (PLFA fingerprints) were spatially autocorrelated, mostly within a distance of 25 m, and covaried with PAH concentrations. The concentration of PLFAs indicative of gram-negative bacteria (16:1omega7c, 16:1omega7t, 18:1omega7, cy17:0, and cy19:0) increased in the PAH hot spots, whereas PLFAs representing fungi and gram-positive bacteria (including actinomycetes) were negatively correlated to PAH concentrations. Most PLFAs were spatially autocorrelated, with distances varying between 4 and 25 m. Those PLFAs that increased in PAH-contaminated soil had autocorrelation ranges between 4 and 16 m, whereas the fungal indicator PLFA 18:2omega6,9 had the largest autocorrelation range (25 m). Bacterial strains isolated using a spray-plate technique and with the same PLFA composition as that in contaminated soil samples were capable of degrading phenanthrene, fluoranthene, and pyrene, indicating that the main PAH degraders could be isolated.}, }
@article {pmid18413953, year = {2008}, author = {Zhang, L and Mendoza, L and Marzorati, M and Verstraete, W}, title = {Inhibition of sulfide generation by dosing formaldehyde and its derivatives in sewage under anaerobic conditions.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {57}, number = {6}, pages = {915-919}, doi = {10.2166/wst.2008.087}, pmid = {18413953}, issn = {0273-1223}, mesh = {Anaerobiosis ; Formaldehyde/*chemistry/toxicity ; Hydrogen Sulfide/*chemistry/metabolism ; Polymers/toxicity ; Sewage/*chemistry/microbiology ; Sulfur-Reducing Bacteria/drug effects/growth &amp; development/metabolism ; Urea/toxicity ; Waste Disposal, Fluid/economics/*methods ; }, abstract = {Hydrogen sulfide emission in sewers is associated with toxicity, corrosion, odor nuisance and a lot of costs. The possibility to inhibit sulfide generation by formaldehyde and its derivatives (paraformaldehyde and urea formaldehyde) has been evaluated under anaerobic conditions. The impact of formaldehyde on an activated sludge system and an appraisal of the economic aspects are also presented. The optimum dosage to inhibit sulfide generation in sewage was 12-19 mg L(-1) formaldehyde. The dosages of 32 mg L(-1) paraformaldehyde or 100 mg L(-1) urea formaldehyde were not capable of inhibiting sulfide generation in sewage. The impact of 19 mg L(-1) formaldehyde on activated sludge system was negligible in terms of COD removal, nitrification rate and oxygen uptake rate.}, }
@article {pmid18407065, year = {2008}, author = {Turnbaugh, PJ and Bäckhed, F and Fulton, L and Gordon, JI}, title = {Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome.}, journal = {Cell host &amp; microbe}, volume = {3}, number = {4}, pages = {213-223}, pmid = {18407065}, issn = {1934-6069}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; R01 DK030292/DK/NIDDK NIH HHS/United States ; R01 DK070977/DK/NIDDK NIH HHS/United States ; P30 DK056341/DK/NIDDK NIH HHS/United States ; DK30292/DK/NIDDK NIH HHS/United States ; DK70977/DK/NIDDK NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Carbohydrate Metabolism ; Carbohydrates/administration &amp; dosage/adverse effects ; Cecum/*microbiology ; Diet/*adverse effects ; Disease Models, Animal ; Energy Metabolism ; Eubacterium/genetics/isolation &amp; purification ; Fats/administration &amp; dosage/adverse effects ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Obese ; Molecular Sequence Data ; Obesity/chemically induced/metabolism/*microbiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Specific Pathogen-Free Organisms ; Tenericutes/classification/genetics/isolation &amp; purification ; }, abstract = {We have investigated the interrelationship between diet, gut microbial ecology, and energy balance using a mouse model of obesity produced by consumption of a prototypic Western diet. Diet-induced obesity (DIO) produced a bloom in a single uncultured clade within the Mollicutes class of the Firmicutes, which was diminished by subsequent dietary manipulations that limit weight gain. Microbiota transplantation from mice with DIO to lean germ-free recipients promoted greater fat deposition than transplants from lean donors. Metagenomic and biochemical analysis of the gut microbiome together with sequencing and metabolic reconstructions of a related human gut-associated Mollicute (Eubacterium dolichum) revealed features that may provide a competitive advantage to members of the bloom in the Western diet nutrient milieu, including import and processing of simple sugars. Our study illustrates how combining comparative metagenomics with gnotobiotic mouse models and specific dietary manipulations can disclose the niches of previously uncharacterized members of the gut microbiota.}, }
@article {pmid18397300, year = {2008}, author = {Anderson-Glenna, MJ and Bakkestuen, V and Clipson, NJ}, title = {Spatial and temporal variability in epilithic biofilm bacterial communities along an upland river gradient.}, journal = {FEMS microbiology ecology}, volume = {64}, number = {3}, pages = {407-418}, doi = {10.1111/j.1574-6941.2008.00480.x}, pmid = {18397300}, issn = {0168-6496}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; *Biofilms ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geography ; Longitudinal Studies ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ribotyping ; Rivers ; Sequence Analysis, DNA ; *Soil Microbiology ; Time Factors ; *Water Microbiology ; }, abstract = {Riverine biofilms remain one of the least-studied habitats despite the significant increase in the examination of aquatic microbial communities in recent years. In this study, the dynamics of epilithic biofilm communities native on rocks from a low-order upland stream were examined over a period of 3 years. Spatial and temporal variations in bacterial communities were assessed using terminal restriction fragment length polymorphism, based on analysis of the 16S rRNA gene. In total, 108 epilithic biofilm samples were analysed and 170 different ribotypes were detected. A strong temporal gradient in ribotype composition was noticed, especially between samples collected in 2001 and those collected in 2002 and 2003, most likely reflecting interannual differences in weather conditions, such as temperature. A spatial gradient in ribotype composition, from upstream sites to the low-lying sites, was also evident and interpreted as an environmental variation gradient along the river course. Distinct biofilm communities consistently occurred at the first site along the river, which was significantly correlated to low pH. Temporal factors explained the highest degree of variation within the epilithic biofilms. Recurrent blooms of certain bacteria were noted within the system. Phylogenetic relationships of bacteria at one point in the river were determined using a cloning and sequencing approach, with Alphaproteobacteria dominating the community, followed by Cyanobacteria, Bacteroidetes and Betaproteobacteria.}, }
@article {pmid18396552, year = {2008}, author = {Icoz, I and Saxena, D and Andow, DA and Zwahlen, C and Stotzky, G}, title = {Microbial populations and enzyme activities in soil in situ under transgenic corn expressing cry proteins from Bacillus thuringiensis.}, journal = {Journal of environmental quality}, volume = {37}, number = {2}, pages = {647-662}, doi = {10.2134/jeq2007.0352}, pmid = {18396552}, issn = {0047-2425}, mesh = {Acid Phosphatase/metabolism ; Alkaline Phosphatase/metabolism ; Animals ; Arylsulfatases/metabolism ; Bacillus thuringiensis Toxins ; Bacteria/genetics/isolation &amp; purification ; Bacterial Proteins/analysis/*genetics ; Colony Count, Microbial ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Endotoxins/analysis/*genetics ; Eukaryota/isolation &amp; purification ; Fungi/isolation &amp; purification ; Hemolysin Proteins/analysis/*genetics ; Oxidoreductases/metabolism ; Peptide Hydrolases/metabolism ; Plants, Genetically Modified/*genetics ; *Soil Microbiology ; Zea mays/*genetics ; }, abstract = {Transgenic Bt crops produce insecticidal Cry proteins that are released to soil in plant residues, root exudates, and pollen and that may affect soil microorganisms. As a continuation of studies in the laboratory and a plant-growth room, a field study was conducted at the Rosemount Experiment Station of the University of Minnesota. Three Bt corn varieties that express the Cry1Ab protein, which is toxic to the European corn borer (Ostrinia nubilalis Hübner), and one Bt corn variety that expresses the Cry3Bb1 protein, which is toxic to the corn rootworm complex (Diabrotica spp.), and their near-isogenic non-Bt varieties were evaluated for their effects on microbial diversity by classical dilution plating and molecular (polymerase chain reaction-denaturing gradient gel electrophoresis) techniques and for the activities of some enzymes (arylsulfatases, acid and alkaline phosphatases, dehydrogenases, and proteases) involved in the degradation of plant biomass. After 4 consecutive years of corn cultivation (2003-2006), there were, in general, no consistent statistically significant differences in the numbers of different groups of microorganisms, the activities of the enzymes, and the pH between soils planted with Bt and non-Bt corn. Numbers and types of microorganisms and enzyme activities differed with season and with the varieties of corn, but these differences were not related to the presence of the Cry proteins in soil. The Cry1Ab protein of Bt corn (events Bt11 and MON810) was detected in most soils during the 4 yr, whereas the Cry3Bb1 protein was not detected in soils of Bt corn (event MON863) expressing the cry3Bb1 gene.}, }
@article {pmid18393990, year = {2008}, author = {Jones, SE and Newton, RJ and McMahon, KD}, title = {Potential for atmospheric deposition of bacteria to influence bacterioplankton communities.}, journal = {FEMS microbiology ecology}, volume = {64}, number = {3}, pages = {388-394}, doi = {10.1111/j.1574-6941.2008.00476.x}, pmid = {18393990}, issn = {0168-6496}, mesh = {Bacteria/*classification/growth &amp; development/*isolation &amp; purification ; Colony Count, Microbial ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fresh Water/*microbiology ; Genes, rRNA ; Molecular Sequence Data ; Phylogeny ; Plankton/*microbiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rain/*microbiology ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Biogeographic patterns in microbial communities are an exciting but controversial topic in microbial ecology. Advances in theory pertaining to assembly of microbial communities have made strong assumptions about dispersal of bacteria without exploration. For this reason, we investigated rates of atmospheric bacterial deposition and compared the taxonomic composition of bacteria in rain with that of common freshwater bacterial communities. Our findings suggest that it is not appropriate to take for granted that atmospheric deposition of bacteria is a significant vector of immigration to freshwater ecosystems.}, }
@article {pmid18393313, year = {2008}, author = {Ahn, JH and Yu, R and Chandran, K}, title = {Distinctive microbial ecology and biokinetics of autotrophic ammonia and nitrite oxidation in a partial nitrification bioreactor.}, journal = {Biotechnology and bioengineering}, volume = {100}, number = {6}, pages = {1078-1087}, doi = {10.1002/bit.21863}, pmid = {18393313}, issn = {1097-0290}, mesh = {Ammonia/metabolism ; Biodegradation, Environmental ; Biomass ; Bioreactors/*microbiology ; Ecology ; Kinetics ; Nitrates/metabolism ; Nitrites/metabolism ; Nitrobacter/*cytology/*enzymology ; *Nitrogen Fixation ; Nitrosomonas europaea/*cytology/*enzymology ; Oxidation-Reduction ; *Water Microbiology ; }, abstract = {Biological nitrogen removal (BNR) based on partial nitrification and denitrification via nitrite is a cost-effective alternate to conventional nitrification and denitrification (via nitrate). The goal of this study was to investigate the microbial ecology, biokinetics, and stability of partial nitrification. Stable long-term partial nitrification resulting in 82.1 +/- 17.2% ammonia oxidation, primarily to nitrite (77.3 +/- 19.5% of the ammonia oxidized) was achieved in a lab-scale bioreactor by operation at a pH, dissolved oxygen and solids retention time of 7.5 +/- 0.1, 1.54 +/- 0.87 mg O(2)/L, and 3.0 days, respectively. Bioreactor ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) populations were most closely related to Nitrosomonas europaea and Nitrobacter spp., respectively. The AOB population fraction varied in the range 61 +/- 45% and was much higher than the NOB fraction, 0.71 +/- 1.1%. Using direct measures of bacterial concentrations in conjunction with independent activity measures and mass balances, the maximum specific growth rate (micro(max)), specific decay (b) and observed biomass yield coefficients (Y(obs)) for AOB were 1.08 +/- 1.03 day(-1), 0.32 +/- 0.34 day(-1), and 0.15 +/- 0.06 mg biomass COD/mg N oxidized, respectively. Corresponding micro(max), b, and Y(obs) values for NOB were 2.6 +/- 2.05 day(-1), 1.7 +/- 1.9 day(-1), and 0.04 +/- 0.02 mg biomass COD/mg N oxidized, respectively. The results of this study demonstrate that the highly selective partial nitrification operating conditions enriched for a narrow diversity of rapidly growing AOB and NOB populations unlike conventional BNR reactors, which host a broader diversity of nitrifying bacteria. Further, direct measures of microbial abundance enabled not only elucidation of mixed community microbial ecology but also estimation of key engineering parameters describing bioreactor systems supporting these communities.}, }
@article {pmid18385770, year = {2008}, author = {Trosvik, P and Rudi, K and Naes, T and Kohler, A and Chan, KS and Jakobsen, KS and Stenseth, NC}, title = {Characterizing mixed microbial population dynamics using time-series analysis.}, journal = {The ISME journal}, volume = {2}, number = {7}, pages = {707-715}, doi = {10.1038/ismej.2008.36}, pmid = {18385770}, issn = {1751-7370}, mesh = {Bacteria/*chemistry/genetics/growth &amp; development/metabolism ; *Biodiversity ; Bioreactors ; *Ecology ; Electronic Data Processing ; Fermentation ; *Models, Biological ; Multivariate Analysis ; Sequence Analysis, DNA ; }, abstract = {Due to a general shortage of temporal population data, dynamic structures in microbial communities remain largely unexplored. Knowledge of community dynamics is, however, essential for understanding the mechanisms by which microbes interact. Here, we have used a computational approach for quantification of bacteria in multispecies populations, generating data for time-series modeling. Moreover, we have used online FR-IR spectroscopy to monitor the main metabolic processes. The approach enabled us to provide a functional description of the parameters governing the population dynamics in a three-species model bacterial community, demonstrating density-dependent regulation, interspecies competition and even a case of cooperation between two species. Since the field of microbial ecology has yet to embrace many of the concepts and methods developed for the study of ecology of higher plants and animals, the realization that microbial systems can be analyzed within the same conceptual framework as other ecosystems is of fundamental importance.}, }
@article {pmid18382642, year = {2006}, author = {Reid, G}, title = {Probiotics to prevent the need for, and augment the use of, antibiotics.}, journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {17}, number = {5}, pages = {291-295}, pmid = {18382642}, issn = {1712-9532}, abstract = {Although humans and microbes are inseparable, our knowledge and understanding of the majority of microbes that help keep us alive and well is in desperate need of further investigation. Of the organisms that influence humans before birth and inhabit various niches from birth to old age, we know little about their identity, origin, metabolic properties, attributes and mechanisms of interactions with the host and surrounding microbes. The use of probiotics ("live microorganisms which when administered in adequate amounts confer a health benefit on the host") has re-emerged as a means to restore and boost the beneficial microbes in our bodies. The timing of resurgent interest in this ancient field coincides with the need to augment or replace antibiotics whose side effects are unwelcome and whose efficacy is diminishing due to drug resistance. Evidence that probiotic strains can act as adjuncts to antibiotic therapy by reducing adverse effects, improving antibiotic function and enhancing mucosal immunity is mounting. It is to our discredit that basic research on microbial ecology has been stalled in Canada for the past 20 years. If supported, research into indigenous and probiotic microbes will form an important part of future research that sheds light on health, disease and a basic understanding of life itself. In some cases, probiotics will be the difference between a good quality of life and a bad one, or perhaps even life over death. Improvements in clinical studies, manufacturing and regulatory standards must coincide with this progress to ensure that physicians and consumers have reliable, proven products for safe and efficacious use.}, }
@article {pmid18380992, year = {2008}, author = {DiBaise, JK and Zhang, H and Crowell, MD and Krajmalnik-Brown, R and Decker, GA and Rittmann, BE}, title = {Gut microbiota and its possible relationship with obesity.}, journal = {Mayo Clinic proceedings}, volume = {83}, number = {4}, pages = {460-469}, doi = {10.4065/83.4.460}, pmid = {18380992}, issn = {0025-6196}, mesh = {Animals ; *Bacterial Physiological Phenomena ; Energy Metabolism ; Humans ; Intestines/*microbiology ; Obesity/metabolism/*prevention &amp; control ; Probiotics/*therapeutic use ; Prognosis ; }, abstract = {Obesity results from alterations in the body's regulation of energy intake, expenditure, and storage. Recent evidence, primarily from investigations in animal models, suggests that the gut microbiota affects nutrient acquisition and energy regulation. Its composition has also been shown to differ in lean vs obese animals and humans. In this article, we review the published evidence supporting the potential role of the gut microbiota in the development of obesity and explore the role that modifying the gut microbiota may play in its future treatment. Evidence suggests that the metabolic activities of the gut microbiota facilitate the extraction of calories from ingested dietary substances and help to store these calories in host adipose tissue for later use. Furthermore, the gut bacterial flora of obese mice and humans include fewer Bacteroidetes and correspondingly more Firmicutes than that of their lean counterparts, suggesting that differences in caloric extraction of ingested food substances may be due to the composition of the gut microbiota. Bacterial lipopolysaccharide derived from the intestinal microbiota may act as a triggering factor linking inflammation to high-fat diet-induced metabolic syndrome. Interactions among microorganisms in the gut appear to have an important role in host energy homeostasis, with hydrogen-oxidizing methanogens enhancing the metabolism of fermentative bacteria. Existing evidence warrants further investigation of the microbial ecology of the human gut and points to modification of the gut microbiota as one means to treat people who are over-weight or obese.}, }
@article {pmid18378598, year = {2008}, author = {Flint, HJ and Bayer, EA}, title = {Plant cell wall breakdown by anaerobic microorganisms from the Mammalian digestive tract.}, journal = {Annals of the New York Academy of Sciences}, volume = {1125}, number = {}, pages = {280-288}, doi = {10.1196/annals.1419.022}, pmid = {18378598}, issn = {0077-8923}, mesh = {Animals ; Bacteria, Anaerobic/*metabolism ; Cell Wall/*metabolism ; Cellulose/*metabolism ; Digestive System/*microbiology ; Energy Metabolism ; Humans ; Intestines/microbiology ; Mammals/*microbiology ; Plants/*metabolism ; Ruminococcus/*metabolism ; }, abstract = {Degradation of lignocellulosic plant material in the mammalian digestive tract is accomplished by communities of anaerobic microorganisms that exist in symbiotic association with the host. Catalytic domains and substrate-binding modules concerned with plant polysaccharide degradation are found in a variety of anaerobic bacteria, fungi, and protozoa from the mammalian gut. The organization of plant cell wall-degrading enzymes, however, varies widely. The cellulolytic gram-positive bacterium Ruminococcus flavefaciens produces an elaborate cellulosomal enzyme complex that is anchored to the bacterial cell wall; assembly of the complex involves at least five different dockerin:cohesin specificities, and the R. flavefaciens genome encodes at least 180 dockerin-containing proteins that encompass a wide array of catalytic and binding activities. On the other hand, in the cellulolytic protozoan, Polyplastron multivesiculatum, individual plant cell wall-degrading enzymes appear to be secreted into food vacuoles, while the gram-negative bacterium Prevotella bryantii appears to possess a sequestration-type system for the utilization of soluble xylans. The system that is employed for polysaccharide utilization must play a major role in defining the ecological niche that each organism occupies within a complex gut community. 16S rRNA analyses are also revealing uncultured bacterial species closely adherent to fibrous substrates in the rumen and in the large intestine of animals and humans. The true complexity, both at a single organism and community level, of the microbial enzyme systems that allow animals to digest plant material is beginning to become apparent.}, }
@article {pmid18375078, year = {2008}, author = {Vanhaecke, L and Derycke, L and Le Curieux, F and Lust, S and Marzin, D and Verstraete, W and Bracke, M}, title = {The microbial PhIP metabolite 7-hydroxy-5-methyl-3-phenyl-6,7,8,9-tetrahydropyrido[3',2':4,5]imidazo[1,2-a]pyrimidin-5-ium chloride (PhIP-M1) induces DNA damage, apoptosis and cell cycle arrest towards Caco-2 cells.}, journal = {Toxicology letters}, volume = {178}, number = {1}, pages = {61-69}, doi = {10.1016/j.toxlet.2008.02.004}, pmid = {18375078}, issn = {0378-4274}, mesh = {*Apoptosis ; Caco-2 Cells ; Carcinogens/*metabolism ; Cell Cycle/*drug effects ; Cell Proliferation/drug effects ; Cell Survival/drug effects ; Comet Assay ; *DNA Damage ; Humans ; Imidazoles/*metabolism/*toxicity ; Mutagens/*toxicity ; Pyrimidines/*toxicity ; }, abstract = {7-Hydroxy-5-methyl-3-phenyl-6,7,8,9-tetrahydropyrido[3',2':4,5]imidazo[1,2-a]pyrimidin-5-ium chloride (PhIP-M1) is a newly identified intestinal microbial metabolite from the food carcinogen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP). Although the mutagenic potential of the endogenous N-hydroxy PhIP derivate has been reported, the risks associated with PhIP-M1 have not yet been explored. In this work, the cytotoxic and genotoxic effects originating from PhIP-M1 were assessed in the epithelial intestinal Caco-2 cell line. PhIP-M1 significantly decreased in a time- and dose-dependent manner mitochondrial dehydrogenase activity and protein synthesis, with IC50 values of, respectively, 180+/-39.4 and 173+/-20.3 microM after 24h, and 33.8+/-3.5 and 37.3+/-10.9 microM after 72 h. Apoptosis within the concentration ranges of cytotoxicity was confirmed by morphological examination, DAPI nuclear staining and annexin V staining. PhIP-M1 provoked cell cycle arrest, characterized by a significant increase in the number of nucleoids in the G2/M phase. A dose-dependent increase in DNA damage, as quantified by the alkaline comet assay, was observed after 3h in the 50-200 microM range. Because these PhIP-M1-induced genomic and cellular events may contribute to the carcinogenicity of PhIP, the potency of the colon microbiota to bioactivate PhIP must be included in future risk assessments.}, }
@article {pmid18373113, year = {2008}, author = {Ponnusamy, L and Xu, N and Stav, G and Wesson, DM and Schal, C and Apperson, CS}, title = {Diversity of bacterial communities in container habitats of mosquitoes.}, journal = {Microbial ecology}, volume = {56}, number = {4}, pages = {593-603}, pmid = {18373113}, issn = {0095-3628}, support = {U01 AI058303/AI/NIAID NIH HHS/United States ; U01-AI-58303-01/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/*growth &amp; development ; Biodiversity ; Culicidae/*growth &amp; development ; *Ecosystem ; Fresh Water/microbiology/parasitology ; Genetic Variation ; Molecular Sequence Data ; New Orleans ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; }, abstract = {We investigated the bacterial diversity of microbial communities in water-filled, human-made and natural container habitats of the mosquitoes Aedes aegypti and Aedes albopictus in suburban landscapes of New Orleans, Louisiana in 2003. We collected water samples from three classes of containers, including tires (n = 12), cemetery urns (n = 23), and miscellaneous containers that included two tree holes (n = 19). Total genomic DNA was extracted from water samples, and 16S ribosomal DNA fragments (operational taxonomic units, OTUs) were amplified by PCR and separated by denaturing gradient gel electrophoresis (DGGE). The bacterial communities in containers represented diverse DGGE-DNA banding patterns that were not related to the class of container or to the local spatial distribution of containers. Mean richness and evenness of OTUs were highest in water samples from tires. Bacterial phylotypes were identified by comparative sequence analysis of 90 16S rDNA DGGE band amplicons. The majority of sequences were placed in five major taxa: Alpha-, Beta- and Gammaproteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and an unclassified group; Proteobacteria and Bacteroidetes were the predominant heterotrophic bacteria in containers. The bacterial communities in human-made containers consisted mainly of undescribed species, and a phylogenetic analysis based on 16S rRNA sequences suggested that species composition was independent of both container type and the spatial distribution of containers. Comparative PCR-based, cultivation-independent rRNA surveys of microbial communities associated with mosquito habitats can provide significant insight into community organization and dynamics of bacterial species.}, }
@article {pmid18369523, year = {2008}, author = {Rodrigues, A and Bacci, M and Mueller, UG and Ortiz, A and Pagnocca, FC}, title = {Microfungal "weeds" in the leafcutter ant symbiosis.}, journal = {Microbial ecology}, volume = {56}, number = {4}, pages = {604-614}, pmid = {18369523}, issn = {0095-3628}, mesh = {Agaricales/classification/genetics/*growth &amp; development ; Animals ; Ants/*microbiology ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; *Symbiosis ; }, abstract = {Leafcutter ants (Formicidae: tribe Attini) are well-known insects that cultivate basidiomycete fungi (Agaricales: Lepiotaceae) as their principal food. Fungus gardens are monocultures of a single cultivar strain, but they also harbor a diverse assemblage of additional microbes with largely unknown roles in the symbiosis. Cultivar-attacking microfungi in the genus Escovopsis are specialized parasites found only in association with attine gardens. Evolutionary theory predicts that the low genetic diversity in monocultures should render ant gardens susceptible to a wide range of diseases, and additional parasites with roles similar to that of Escovopsis are expected to exist. We profiled the diversity of cultivable microfungi found in 37 nests from ten Acromyrmex species from Southern Brazil and compared this diversity to published surveys. Our study revealed a total of 85 microfungal strains. Fusarium oxysporum and Escovopsis were the predominant species in the surveyed gardens, infecting 40.5% and 27% of the nests, respectively. No specific relationship existed regarding microfungal species and ant-host species, ant substrate preference (dicot versus grass) or nesting habit. Molecular data indicated high genetic diversity among Escovopsis isolates. In contrast to the garden parasite, F. oxysporum strains are not specific parasites of the cultivated fungus because strains isolated from attine gardens have similar counterparts found in the environment. Overall, the survey indicates that saprophytic microfungi are prevalent in South American leafcutter ants. We discuss the antagonistic potential of these microorganisms as "weeds" in the ant-fungus symbiosis.}, }
@article {pmid18368438, year = {2008}, author = {Trifonova, R and Postma, J and Ketelaars, JJ and van Elsas, JD}, title = {Thermally treated grass fibers as colonizable substrate for beneficial bacterial inoculum.}, journal = {Microbial ecology}, volume = {56}, number = {3}, pages = {561-571}, pmid = {18368438}, issn = {0095-3628}, mesh = {Bacteria/genetics/*growth &amp; development ; Bacteriological Techniques/methods ; Base Sequence ; Cluster Analysis ; Colony Count, Microbial ; DNA, Bacterial/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Hot Temperature ; Lactuca/growth &amp; development ; Molecular Sequence Data ; Poaceae/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {This study investigates how thermally treated (i.e., torrefied) grass, a new prospective ingredient of potting soils, is colonized by microorganisms. Torrefied grass fibers (TGF) represent a specific colonizable niche, which is potentially useful to establish a beneficial microbial community that improves plant growth. TGF and torrefied grass extracts (TGE) were inoculated with a suspension of microorganisms obtained from soil. Sequential microbial enrichment steps were then performed in both substrates. The microbial communities developing in the substrates were assessed using cultivation-based and cultivation-independent approaches. Thus, bacterial isolates were obtained, and polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) analyses for bacterial communities were performed. Partial sequencing of the 16S ribosomal RNA gene from isolates and bands from DGGE gels showed diverse communities after enrichment in TGE and TGF. Bacterial isolates affiliated with representatives of the alpha-proteobacteria (Methylobacterium radiotolerans, Rhizobium radiobacter), gamma-proteobacteria (Serratia plymuthica, Pseudomonas putida), Cytophaga-Flavobacterium-Bacteroides (CFB) group (Flavobacterium denitrificans), beta-proteobacteria (Ralstonia campinensis), actinobacteria (Cellulomonas parahominis, Leifsonia poae, L. xyli subsp. xyli, and Mycobacterium anthracenicum), and the firmicutes (Bacillus megaterium) were found. In TGE, gamma-proteobacteria were dominant (61.5% of the culturable community), and 20% belonged to the CFB group, whereas actinobacteria (67.4%) and alpha-proteobacteria (21.7%) were prevalent in TGF. A germination assay with lettuce seeds showed that the phytotoxicity of TGF and TGE decreased due to the microbial enrichment.}, }
@article {pmid18368437, year = {2008}, author = {Chen, M and Chen, F and Yu, Y and Ji, J and Kong, F}, title = {Genetic diversity of eukaryotic microorganisms in Lake Taihu, a large shallow subtropical lake in china.}, journal = {Microbial ecology}, volume = {56}, number = {3}, pages = {572-583}, pmid = {18368437}, issn = {0095-3628}, mesh = {Animals ; Base Sequence ; DNA/chemistry/genetics ; Euglenida/genetics ; Eukaryota/genetics ; Eukaryotic Cells/*physiology ; Fresh Water/*microbiology ; Fungi/genetics ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 18S/chemistry/genetics ; Sequence Alignment ; *Water Microbiology ; }, abstract = {We investigated the genetic diversity of eukaryotic microorganisms (0.8-20 microm) by sequencing cloned 18S rRNA genes in six genetic libraries constructed from six locations in Lake Taihu, a large shallow subtropical lake in China. Genetic libraries of eukaryotic ribosomal RNA were screened by restriction fragment length polymorphism (RFLP) analysis, and one clone representative of each RFLP pattern was partially sequenced. A total of 528 clones were clustered into 165 RFLP patterns and finally into 131 operational taxonomic unit (OTUs). Phylogenetic analysis revealed that each library included many unique OTUs, as well as members of distantly related phylogenetic groups. A majority of the clones were from alveolates, stramenopiles, cercozoa, cryptophytes, chlorophytes, and fungi, with members of choanoflagellida, euglenida, centroheliozoa, ancyromonadidae, ichthyosporea, and kathablepharid representing a minor fraction of the library. Six OTUs (15 clones) were not related to any known eukaryotic group. Canonical correspondence analysis suggested that the differences in eukaryotic microorganism community composition of in the six regions were partially related to trophic status, sediment resuspension, and top-down regulation by metazooplankton.}, }
@article {pmid18367280, year = {2008}, author = {Diez, AM and Urso, R and Rantsiou, K and Jaime, I and Rovira, J and Cocolin, L}, title = {Spoilage of blood sausages morcilla de Burgos treated with high hydrostatic pressure.}, journal = {International journal of food microbiology}, volume = {123}, number = {3}, pages = {246-253}, doi = {10.1016/j.ijfoodmicro.2008.02.017}, pmid = {18367280}, issn = {0168-1605}, mesh = {Colony Count, Microbial ; Food Contamination/*analysis ; Food Handling/*methods ; Food Microbiology ; Food Preservation/*methods ; *Hydrostatic Pressure ; Lactobacillus/growth &amp; development ; Meat Products/*microbiology ; Species Specificity ; Temperature ; Time Factors ; }, abstract = {In this study, the microbial ecology of the blood sausage morcilla de Burgos, subjected to high hydrostatic pressure treatment (HPP), was studied by culture-dependent and -independent methods. Morcilla de Burgos is the most traditional and famous blood sausage in Spain. The producers are interested in extending its shelf-life in order to expand their market and to reduce losses attributed to spoilage. Sausage batter prior to stuffing and blood sausages HPP treated or not (control) were analyzed at 0, 9, 14, 21, 28 and 35 days of storage at 4 degrees C. Lactic acid bacteria, Pseudomonas spp. and aerobic mesophilic bacteria were investigated by traditional plating. PCR-denaturing gradient gel electrophoresis (DGGE) was used to analyze the DNA and the RNA extracted directly from the blood sausages, as well as bulk cells of LAB and Pseudomonas spp. The results showed that HPP improved the shelf life of morcilla de Burgos to 28 days in comparison with control samples. The populations responsible for spoilage, namely LAB, remained lower in HPP treated samples when compared with the control samples. Only at 35 days of storage they reached values of 10(8) cfu/g, leading to the spoilage of the product. Although, HPP affected the LAB population, they were able to recover the injury provoked by the treatment. Lastly, HPP seemed to affect differently LAB species detected. While Leuconostoc mesenteroides was completely inactivated by HPP, Weissella viridescens was able to recover and carry out the typical spoilage of the product. Pseudomonas spp. remained under detection level (<10(2) CFU/g) after the HPP treatment.}, }
@article {pmid18363715, year = {2008}, author = {Huang, WE and Singer, AC and Spiers, AJ and Preston, GM and Whiteley, AS}, title = {Characterizing the regulation of the Pu promoter in Acinetobacter baylyi ADP1.}, journal = {Environmental microbiology}, volume = {10}, number = {7}, pages = {1668-1680}, doi = {10.1111/j.1462-2920.2008.01583.x}, pmid = {18363715}, issn = {1462-2920}, mesh = {Acinetobacter/*genetics ; DNA-Binding Proteins/physiology ; DNA-Directed RNA Polymerases/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Promoter Regions, Genetic/*genetics/physiology ; Pseudomonas putida/genetics/metabolism ; RNA Polymerase Sigma 54/physiology ; Regulatory Sequences, Nucleic Acid ; Sigma Factor/metabolism ; }, abstract = {Effective gene trapping and screening requires sensory and regulatory compatibility of both host and exogenous systems. The naturally competent bacterium Acinetobacter baylyi ADP1 is able to efficiently take up and integrate exogenous DNA into the chromosome, making it an attractive host system for a wide range of metagenomic applications. To test the ability of A. baylyi ADP1 to express the XylR-regulated Pu promoter from Pseudomonas putida mt-2, we have constructed and examined an A. baylyi ADP1 strain, ADPWH-Pu-lux-xylR. The Pu promoter in ADPWH-Pu-lux-xylR was specifically induced by toluene, m-, p- and o-xylene. The substrate-induced Pu promoter was highly dependent on the growth medium: it was repressed in rich media until stationary phase, but was immediately induced in minimal medium with glucose as the sole carbon source (MMG). However, the Pu promoter was repressed in MMG when it was supplemented with 5 g l(-1) yeast extract. Further investigation showed that the Pu promoter in MMG was repressed by 0.5 g l(-1) aspartic acid or asparagine, but not repressed by glutamine. Changing the carbon/nitrogen ratios by addition of ammonia did not significantly affect the Pu promoter activity but addition of nitrate did. These results show that A. baylyi ADP1 reproduced characteristics of the XylR-regulated Pu promoter observed in its original host. It demonstrates that A. baylyi could provide an excellent genetic host for a wide range of functional metagenomic applications.}, }
@article {pmid18359998, year = {2008}, author = {Clauwaert, P and Tolêdo, R and van der Ha, D and Crab, R and Verstraete, W and Hu, H and Udert, KM and Rabaey, K}, title = {Combining biocatalyzed electrolysis with anaerobic digestion.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {57}, number = {4}, pages = {575-579}, doi = {10.2166/wst.2008.084}, pmid = {18359998}, issn = {0273-1223}, mesh = {Acetates/metabolism ; Anaerobiosis ; *Bioelectric Energy Sources ; Catalysis ; Electrodes ; Electrolysis ; Hydrogen/*chemistry ; Methane/*metabolism ; Quaternary Ammonium Compounds/*metabolism ; Temperature ; }, abstract = {Biocatalyzed electrolysis is a microbial fuel cell based technology for the generation of hydrogen gas and other reduced products out of electron donors. Examples of electron donors are acetate and wastewater. An external power supply can support the process and therefore circumvent thermodynamical constraints that normally render the generation of compounds such as hydrogen unlikely. We have investigated the possibility of biocatalyzed electrolysis for the generation of methane. The cathodically produced hydrogen could be converted into methane at a ratio of 0.41 mole methane mole(-1) acetate, at temperatures of 22+/-2 degrees C. The anodic oxidation of acetate was not hampered by ammonium concentrations up to 5 g N L(-1). An overview is given of potential applications for biocatalyzed electrolysis.}, }
@article {pmid18359987, year = {2008}, author = {McKeown, RM and Collins, G and Chinalia, FA and Mahony, T and O'Flaherty, V}, title = {Low temperature anaerobic biotreatment of priority pollutants.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {57}, number = {4}, pages = {499-503}, doi = {10.2166/wst.2008.056}, pmid = {18359987}, issn = {0273-1223}, mesh = {Anaerobiosis ; *Bioreactors ; Fatty Acids, Volatile/metabolism ; Pentachlorophenol/*metabolism ; Temperature ; Toluene/*metabolism ; Waste Disposal, Fluid/*methods ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The effect of low operating temperature and pollutant concentration on the performance of five anaerobic hybrid reactors was investigated. Stable and efficient long-term (>400 days) treatment of a cold (6-13 degrees C), volatile fatty acid (VFA)-based, wastewater was achieved at applied organic loading rates (OLRs) of 5 kg chemical oxygen demand (COD) m(-3) d(-1) with COD removal efficiencies c. 84% at 6 degrees C (sludge loading rate (SLR) 1.04-1.46 kg COD kg [VSS](-1) d(-1)). VFA-based wastewaters, containing up to 14 g pentachlorophenol (PCP) m(-3) d(-1) or 155 g toluene m(-3) d(-1) were successfully treated at applied OLRs of 5-7 kg COD m(-3) d(-1). Despite transient declines in reactor performance in response to increasing toxicant loading rates, stable operation (COD removal efficiencies > 90%) and satisfactory toxicant removal efficiencies (>88%) were demonstrated by the systems.}, }
@article {pmid18359835, year = {2008}, author = {Stanton, TB and Humphrey, SB and Sharma, VK and Zuerner, RL}, title = {Collateral effects of antibiotics: carbadox and metronidazole induce VSH-1 and facilitate gene transfer among Brachyspira hyodysenteriae strains.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {10}, pages = {2950-2956}, pmid = {18359835}, issn = {1098-5336}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteriophages/drug effects/growth &amp; development/ultrastructure ; Brachyspira hyodysenteriae/*drug effects/*genetics/growth &amp; development/virology ; Carbadox/*pharmacology ; Culture Media/chemistry ; DNA, Viral/analysis ; Drug Resistance, Bacterial/genetics ; Genes, Viral ; Hydrogen Peroxide/pharmacology ; Metronidazole/*pharmacology ; Microscopy, Electron, Transmission ; Mitomycin/pharmacology ; Polymerase Chain Reaction ; Prophages/*drug effects ; RNA, Viral/biosynthesis/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Transcription, Genetic/drug effects ; *Transduction, Genetic ; Viral Proteins/genetics ; }, abstract = {Brachyspira hyodysenteriae is an anaerobic spirochete and the etiologic agent of swine dysentery. The genome of this spirochete contains a mitomycin C-inducible, prophage-like gene transfer agent designated VSH-1. VSH-1 particles package random 7.5-kb fragments of the B. hyodysenteriae genome and transfer genes between B. hyodysenteriae cells. The chemicals and conditions inducing VSH-1 production are largely unknown. Antibiotics used in swine management and stressors inducing traditional prophages might induce VSH-1 and thereby stimulate lateral gene transfer between B. hyodysenteriae cells. In these studies, VSH-1 induction was initially detected by a quantitative real-time reverse transcriptase PCR assay evaluating increased transcription of hvp38 (VSH-1 head protein gene). VSH-1 induction was confirmed by detecting VSH-1-associated 7.5-kb DNA and VSH-1 particles in B. hyodysenteriae cultures. Nine antibiotics (chlortetracycline, lincomycin, tylosin, tiamulin, virginiamycin, ampicillin, ceftriaxone, vancomycin, and florfenicol) at concentrations affecting B. hyodysenteriae growth did not induce VSH-1 production. By contrast, VSH-1 was detected in B. hyodysenteriae cultures treated with mitomycin C (10 microg/ml), carbadox (0.5 microg/ml), metronidazole (0.5 microg/ml), and H(2)O(2) (300 microM). Carbadox- and metronidazole-induced VSH-1 particles transmitted tylosin and chloramphenicol resistance determinants between B. hyodysenteriae strains. The results of these studies suggest that certain antibiotics may induce the production of prophage or prophage-like elements by intestinal bacteria and thereby impact intestinal microbial ecology.}, }
@article {pmid18351077, year = {2008}, author = {Wang, S and Holzem, RM and Gunsch, CK}, title = {Effects of pharmaceutically active compounds on a mixed microbial community originating from a municipal wastewater treatment plant.}, journal = {Environmental science &amp; technology}, volume = {42}, number = {4}, pages = {1091-1095}, doi = {10.1021/es072026x}, pmid = {18351077}, issn = {0013-936X}, mesh = {Chromatography, High Pressure Liquid ; Electrophoresis, Polyacrylamide Gel ; *Environmental Restoration and Remediation ; *Pharmaceutical Preparations ; Spectrophotometry, Ultraviolet ; *Water Microbiology ; Water Pollutants, Chemical/*pharmacology ; }, abstract = {The growth and composition of microorganisms found in a municipal wastewater treatment plant were investigated in the presence of four pharmaceutically active compounds (PhACs) [ketoprofen, naproxen, carbamazepine, and clofibric acid] in batch reactors at varying organic loadings. Overall, the data suggest that microbial growth inhibition was correlated to organic loading rather than PhAC concentration. Significant inhibition ranging from 34 to 43% was observed under the lowest organic loading for all PhACs other than clofibric acid. No inhibition was observed at the highest organic loading. Higher microbial inhibition was not observed with increased PhAC concentration for a given organic loading. These results indicatethatthe presence of PhAC may affect microbial growth especially under lower organic loading conditions. Further validation is required with additional PhACs, organic substrates, and a wider loading range. In addition, significant microbial shifts were observed in the presence of ketoprofen and naproxen. These data suggest that, in addition to their effect on overall microbial growth, PhACs may affect the microbial ecology and additional research should be carried out to identify PhACs that have the potential of affecting ecologically important microorganisms in wastewater treatment processes and aquatic environments in general.}, }
@article {pmid18348637, year = {2008}, author = {Demoling, LA and Bååth, E}, title = {Use of pollution-induced community tolerance of the bacterial community to detect phenol toxicity in soil.}, journal = {Environmental toxicology and chemistry}, volume = {27}, number = {2}, pages = {334-340}, doi = {10.1897/07-289R.1}, pmid = {18348637}, issn = {0730-7268}, mesh = {Bacteria/*drug effects ; Biological Assay ; Dose-Response Relationship, Drug ; Ecosystem ; Phenol/administration &amp; dosage/*toxicity ; *Soil Microbiology ; Soil Pollutants/administration &amp; dosage/*analysis/*toxicity ; Time Factors ; }, abstract = {Pollution-induced community tolerance (PICT) was used to study effects of phenol on soil bacteria. Phenol was added to an agricultural soil in a microcosm experiment. The effects were studied for up to four months. Bacterial growth rates were estimated with the leucine incorporation technique. This technique was also used as detection method for PICT. Changes in community structure were studied using the phospholipid fatty acid (PLFA) pattern. Increased phenol PICT of the bacterial community was found at phenol concentrations above 1 micromol/g wet weight soil. Direct inhibiting effect on bacterial growth rates 1 d after adding phenol was correlated to PICT. Phenol toxicity was reflected by changes in the structure of the bacterial community, although PICT appeared more sensitive than the PLFA method. In soil amended with 1 to 10 micromol phenol/g soil, bacterial growth recovered within one week. In the soil amended with the highest phenol concentration (30 micromol/g soil), bacterial growth rate recovered from total inhibition after 27 d, eventually reaching values six times higher than in the control. However, PICT did not change during the four months the experiment was performed. The specificity of PICT was also studied by examining cotolerance to 2-chlorophenol, 2,4-dichlorophenol, 2,3,6-trichlorophenol, Cu, and Zn. Adding phenol induced cotolerance of the bacterial community to the other phenols, although always at a lover level than to phenol. No cotolerance was found to metals in phenol-polluted soil. We conclude that the PICT concept is a valuable tool in determining phenol toxicity to bacterial communities, especially in situations where bacterial growth has recovered. Cotolerance between different phenols can, however, make interpretations of PICT more complicated.}, }
@article {pmid18347847, year = {2008}, author = {Naik, PR and Sahoo, N and Goswami, D and Ayyadurai, N and Sakthivel, N}, title = {Genetic and functional diversity among fluorescent pseudomonads isolated from the rhizosphere of banana.}, journal = {Microbial ecology}, volume = {56}, number = {3}, pages = {492-504}, pmid = {18347847}, issn = {0095-3628}, mesh = {Antifungal Agents/metabolism ; Base Sequence ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Genetic Variation ; Molecular Sequence Data ; Musa/*microbiology ; Phenazines/metabolism ; Phenols/metabolism ; Phylogeny ; Polymerase Chain Reaction ; Pseudomonas/genetics/growth &amp; development/metabolism/*physiology ; Pyrroles/metabolism ; Pyrrolnitrin/metabolism ; RNA, Ribosomal, 16S/chemistry/genetics ; Rhizome/microbiology ; Sequence Alignment ; *Soil Microbiology ; }, abstract = {Fluorescent pseudomonads from banana rhizospheric soil were isolated and screened for the production of enzymes and hormones such as phosphatase, indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate (ACC) deaminase, protease, and antifungal metabolites. Of 95 isolates, 50 (52%) isolates solubilized tri-calcium phosphate (TCP), 63 (66%) isolates produced plant growth hormone IAA, 10 (11%) isolates exhibited ACC deaminase, and 23 (24%) isolates produced protease. Isolates were screened for antifungal activity toward phytopathogenic fungi. Gene-specific primers have identified the putative antibiotic producing isolates. These putative isolates were grown in the production media and production of antibiotics was confirmed by thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC). Genotypic analysis by BOX (bacterial repetitive BOX element)-polymerase chain reaction (PCR) resulted into three distinct genomic clusters at a 50% similarity level and 62 distinct BOX profiles. Based on the sequence similarity of 16S rRNA and construction of subsequent phylogenetic tree analysis, isolates were designated as Pseudomonas monteilii, P. plecoglossicida, P. fluorescens, P. fulva, P. mosselii, P. aeruginosa, P. alcaligenes, and P. pseudoalcaligenes. Present study revealed the genetic and functional diversity among isolates of fluorescent pseudomonads associated with rhizospheric soil of banana and also identified P. monteilii as dominant species. The knowledge on genetic and functional diversity of fluorescent pseudomonads associated with banana rhizosphere is useful to understand their ecological role and for their utilization in sustainable agriculture.}, }
@article {pmid18347846, year = {2008}, author = {Riemann, L and Grossart, HP}, title = {Elevated lytic phage production as a consequence of particle colonization by a marine Flavobacterium (Cellulophaga sp.).}, journal = {Microbial ecology}, volume = {56}, number = {3}, pages = {505-512}, pmid = {18347846}, issn = {0095-3628}, mesh = {Bacteriophages/*growth &amp; development ; Colony Count, Microbial ; *Ecosystem ; Flavobacterium/*virology ; Geologic Sediments/*microbiology ; *Water Microbiology ; }, abstract = {Bacteria growing on marine particles generally have higher densities and cell-specific activities than free-living bacteria. Since rapidity of phage adsorption is dependent on host density, while infection productivity is a function of host physiological status, we hypothesized that marine particles are sites of elevated phage production. In the present study, organic-matter-rich agarose beads and a marine phage-host pair (Cellulophaga sp., PhiS(M)) were used as a model system to examine whether bacterial colonization of particles increases phage production. While no production of phages was observed in plain seawater, the presence of beads enhanced attachment and growth of bacteria, as well as phage production. This was observed because of extensive lysis of bacteria in the presence of beads and a subsequent increase in phage abundance both on beads and in the surrounding water. After 12 h, extensive phage lysis reduced the density of attached bacteria; however, after 32 h, bacterial abundance increased again. Reexposure to phages and analyses of bacterial isolates suggested that this regrowth on particles was by phage-resistant clones. The present demonstration of elevated lytic phage production associated with model particles illustrates not only that a marine phage has the ability to successfully infect and lyse surface-attached bacteria but also that acquisition of resistance may affect temporal phage-host dynamics on particles. These findings from a model system may have relevance to the distribution of phage production in environments rich in particulate matter (e.g., in coastal areas or during phytoplankton blooms) where a significant part of phage production may be directly linked to these nutrient-rich "hot spots."}, }
@article {pmid18347845, year = {2008}, author = {Ogilvie, LA and Hirsch, PR and Johnston, AW}, title = {Bacterial diversity of the broadbalk 'classical' winter wheat experiment in relation to long-term fertilizer inputs.}, journal = {Microbial ecology}, volume = {56}, number = {3}, pages = {525-537}, pmid = {18347845}, issn = {0095-3628}, support = {BBS/E/C/00004175/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/C/00004961/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Bacteria/*genetics/*growth &amp; development ; Base Sequence ; Cation Transport Proteins/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Fertilizers/*microbiology ; Genetic Variation/drug effects ; Molecular Sequence Data ; Oxidoreductases/chemistry/genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry/genetics ; *Soil Microbiology ; }, abstract = {With more than 160 years of contrasting fertilizer regimes, the Broadbalk winter wheat experiment represents a unique experimental resource for studying the effects of long-term fertilizer application on microbial population diversity. Using DGGE and clone library analysis, we report here on eubacterial species diversity (16S rRNA gene) and diversity within two sets of gene products associated with microbial N acquisition: NifH (nitrogen fixation) and AmtB (ammonium transport). Comparisons were made within and between soils treated with mineral N fertilizer, farmyard manure or receiving no fertilizer. Analysis of 16S rRNA gene DGGE profiles showed no clear patterns to qualitatively distinguish bacterial community structure between the three different treatments (P > 0.05), with all samples containing a range of eubacterial taxa similar to those that are characteristic of soil bacteria reported elsewhere. Intra-plot heterogeneity was high and of a similar magnitude to that between treatments. This lack of qualitative between plot differences was echoed in the representative sequences of 16S rRNA, nifH, and amtB genes in the various samples. Taken together, both phylogenetic and functional gene analyses showed bacterial communities in the Broadbalk-trial soil were very stable and relatively non-responsive to long-term management of balanced fertilizer inputs.}, }
@article {pmid18347844, year = {2008}, author = {Pagliaccia, D and Merhaut, D and Colao, MC and Ruzzi, M and Saccardo, F and Stanghellini, ME}, title = {Selective enhancement of the fluorescent pseudomonad population after amending the recirculating nutrient solution of hydroponically grown plants with a nitrogen stabilizer.}, journal = {Microbial ecology}, volume = {56}, number = {3}, pages = {538-554}, pmid = {18347844}, issn = {0095-3628}, mesh = {Asteraceae/growth &amp; development/*microbiology ; Base Sequence ; Capsicum/growth &amp; development/*microbiology ; Chelating Agents/*pharmacology ; DNA, Bacterial/chemistry/genetics ; Hydroponics/*methods ; Molecular Sequence Data ; Picolines/*pharmacology ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Pseudomonas putida/drug effects/genetics/*growth &amp; development ; Random Allocation ; Siderophores/analysis/metabolism ; }, abstract = {Fluorescent pseudomonads have been associated, via diverse mechanisms, with suppression of root disease caused by numerous fungal and fungal-like pathogens. However, inconsistent performance in disease abatement, after their employment, has been a problem. This has been attributed, in part, to the inability of the biocontrol bacterium to maintain a critical threshold population necessary for sustained biocontrol activity. Our results indicate that a nitrogen stabilizer (N-Serve, Dow Agrosciences) selectively and significantly enhanced, by two to three orders of magnitude, the resident population of fluorescent pseudomonads in the amended (i.e., 25 microg ml(-1) nitrapyrin, the active ingredient) and recycled nutrient solution used in the cultivation of hydroponically grown gerbera and pepper plants. Pseudomonas putida was confirmed as the predominant bacterium selectively enhanced. Terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rDNA suggested that N-Serve selectively increased P. putida and reduced bacterial diversity 72 h after application. In vitro tests revealed that the observed population increases of fluorescent pseudomonads were preceded by an early growth suppression of indigenous aerobic heterotrophic bacteria (AHB) population. Interestingly, the fluorescent pseudomonad population did not undergo this decrease, as shown in competition assays. Xylene and 1,2,4-trimethylbenzene (i.e., the inert ingredients in N-Serve) were responsible for a significant percentage of the fluorescent pseudomonad population increase. Furthermore, those increases were significantly higher when the active ingredient (i.e., nitrapyrin) and the inert ingredients were combined, which suggests a synergistic response. P. putida strains were screened for the ability to produce antifungal compounds and for the antifungal activity against Pythium aphanidermatum and Phytophthora capsici. The results of this study suggest the presence of diverse mechanisms with disease-suppressing potential. This study demonstrates the possibility of using a specific substrate to selectively enhance and maintain desired populations of a natural-occurring bacterium such as P. putida, a trait considered to have great potential in biocontrol applications for plant protection.}, }
@article {pmid18345476, year = {2008}, author = {Reinoso, R and Bécares, E}, title = {Environmental inactivation of Cryptosporidium parvum oocysts in waste stabilization ponds.}, journal = {Microbial ecology}, volume = {56}, number = {4}, pages = {585-592}, pmid = {18345476}, issn = {0095-3628}, mesh = {Animals ; Cryptosporidium parvum/*growth &amp; development/radiation effects ; Fresh Water/*parasitology ; Oocysts/*growth &amp; development/radiation effects ; Spain ; Sunlight ; Water Supply ; }, abstract = {The survival of Cryptosporidium parvum oocysts in a waste stabilization pond system in northwestern Spain and the effects of sunlight and the depth and type of pond on oocyst viability were evaluated using an assay based on the exclusion or inclusion of two fluorogenic vital dyes, 4',6-diamidino-2-phenylindole (DAPI) and propidium iodide (PI). All tested factors had significant effects (P < 0.01) over time on C. parvum oocyst viability. Sunlight exposure was the most influential factor for oocyst inactivation. A 40% reduction was observed after 4 days exposure to sunlight conditions compared with dark conditions. The type of pond also caused a significant reduction in C. parvum oocyst viability (P < 0.01). Inactivation rates reflected that the facultative pond was the most aggressive environment for oocysts placed both at the surface (presence of sunlight) and at the bottom (absence of sunlight) of the pond, followed by the maturation pond and the anaerobic pond. The mean inactivation rates of oocysts in the ponds ranged from 0.0159 to 0.3025 day(-1).}, }
@article {pmid18340001, year = {2008}, author = {Rehman, H and Hellweg, P and Taras, D and Zentek, J}, title = {Effects of dietary inulin on the intestinal short chain fatty acids and microbial ecology in broiler chickens as revealed by denaturing gradient gel electrophoresis.}, journal = {Poultry science}, volume = {87}, number = {4}, pages = {783-789}, doi = {10.3382/ps.2007-00271}, pmid = {18340001}, issn = {0032-5791}, mesh = {Animal Feed ; *Animal Nutritional Physiological Phenomena ; Animals ; Body Weight/physiology ; Chickens/*metabolism/microbiology ; DNA, Bacterial/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel/veterinary ; Fatty Acids, Volatile/*metabolism ; Feces/chemistry/microbiology ; Intestinal Mucosa/*metabolism ; Intestines/drug effects/microbiology ; Inulin/*administration &amp; dosage ; Polymerase Chain Reaction/veterinary ; RNA, Ribosomal, 16S/chemistry/genetics ; Random Allocation ; Statistics, Nonparametric ; }, abstract = {Inulin can stimulate the growth of the intestinal bacteria as well as alter the ratio among various short chain fatty acids (SCFA) produced. In the present study, we analyzed the effect of dietary inulin on the intestinal bacterial community as determined by denaturing gradient gel electrophoresis analysis of universal 16S rDNA after amplication with PCR and SCFA profile. Broilers were fed a diet primarily composed of corn-soybean meal or same diet with 1% inulin for 42 d. The relative weight of digesta-filled ceca of the inulin-fed group was higher (P<0.01) than in the control group. Amongst SCFA, only acetate could be detected in the jejunal digesta, which tended to be higher (P=0.09) in inulin-fed group compared with the control group. Inulin did not affect the total concentration of SCFA in the cecal digesta. The relative proportion of n-butyrate was elevated (P=0.05) with a concomitant decrease in the concentration of n-valerate (P<0.05) in the inulin-fed group compared with the control group. Dietary inulin did not affect the number of PCR-denaturing gradient gel electrophoresis bands nor their diversity in the jejunal and cecal digesta. Intragroup similarities were not different between the groups, nor were any differences between intra-and intergroup similarities in the jejunal and cecal samples. In conclusion, inulin altered the cecal microbial metabolic activity without any major impact on the composition of intestinal bacterial communities as measured by the present techniques.}, }
@article {pmid18335238, year = {2008}, author = {Gagneur, A and Vallet, S and Talbot, PJ and Legrand-Quillien, MC and Picard, B and Payan, C and Sizun, J}, title = {Outbreaks of human coronavirus in a pediatric and neonatal intensive care unit.}, journal = {European journal of pediatrics}, volume = {167}, number = {12}, pages = {1427-1434}, pmid = {18335238}, issn = {1432-1076}, mesh = {*Coronavirus 229E, Human/genetics/isolation &amp; purification ; Coronavirus Infections/diagnosis/*epidemiology/virology ; Cross Infection/diagnosis/*epidemiology/virology ; *Disease Outbreaks ; Female ; France/epidemiology ; Health Surveys ; Hospitals, University ; Humans ; Incidence ; Infant ; Infant, Newborn ; Intensive Care Units, Neonatal/statistics &amp; numerical data ; Intensive Care Units, Pediatric/*statistics &amp; numerical data ; Male ; Nasal Mucosa/virology ; Prevalence ; Prospective Studies ; Respiratory Tract Infections/diagnosis/*epidemiology/virology ; Reverse Transcriptase Polymerase Chain Reaction ; Risk Factors ; Seasons ; }, abstract = {Human coronavirus 229E (HCoV) has been recently recognized as a potential agent of nosocomial viral respiratory infections (NRVI) in high-risk infants. We have confirmed this as fact through the study of a 1-year period of HCoV outbreaks occurring during a prospective survey of NRVI in a paediatric and neonatal intensive care unit (PNICU) using new molecular techniques for HCoV detection. Nasal samples obtained at admission and weekly thereafter for all hospitalised children, as well as monthly nasal samples from staff, were analysed using immunofluorescence for respiratory syncytial virus (RSV), influenza viruses A and B, paramyxoviruses 1, 2, 3 and adenoviruses. RT-PCR was used for HCoV detection. During the year 1998, 43 HCoV-related NRVI were detected in 152 neonates (incidence 28.3%), and 7 HCoV-related NRVI were found in 92 children (incidence 7.6%). Three HCoV-related outbreaks were observed (February, August and December), associated with a high prevalence of HCoV infection in the staff. During the August outbreak, 50% to 78% of hospitalised neonates and children were infected. Seventy-five percent of hospitalised preterm neonates with a gestational age less than 32 weeks and 52.4% of staff members were infected. Risk factors for NRVI in neonates were birth weight, gestational age, ventilation, oxygenation and hospitalisation length. Ninety-two percent of infected preterm neonates were symptomatic, mainly with bradycardia and respiratory worsening. These data provide additional evidence for a possibly significant role of HCoV in NRVI in a PNICU. The role of staff or hospitalised children in spreading HCoV is hypothesised.}, }
@article {pmid18335158, year = {2008}, author = {Kamp, A and Røy, H and Schulz-Vogt, HN}, title = {Video-supported analysis of Beggiatoa filament growth, breakage, and movement.}, journal = {Microbial ecology}, volume = {56}, number = {3}, pages = {484-491}, pmid = {18335158}, issn = {0095-3628}, mesh = {Bacterial Proteins/physiology ; Beggiatoa/genetics/*growth &amp; development/physiology ; Cytoskeleton/*physiology ; DNA, Bacterial/chemistry/genetics ; In Situ Hybridization, Fluorescence ; Video Recording ; }, abstract = {A marine Beggiatoa sp. was cultured in semi-solid agar with opposing oxygen-sulfide gradients. Growth pattern, breakage of filaments for multiplication, and movement directions of Beggiatoa filaments in the transparent agar were investigated by time-lapse video recording. The initial doubling time of cells was 15.7 +/- 1.3 h (mean +/- SD) at room temperature. Filaments grew up to an average length of 1.7 +/- 0.2 mm, but filaments of up to approximately 6 mm were also present. First breakages of filaments occurred approximately 19 h after inoculation, and time-lapse movies illustrated that a parent filament could break into several daughter filaments within a few hours. In >20% of the cases, filament breakage occurred at the tip of a former loop. As filament breakage is accomplished by the presence of sacrificial cells, loop formation and the presence of sacrificial cells must coincide. We hypothesize that sacrificial cells enhance the chance of loop formation by interrupting the communication between two parts of one filament. With communication interrupted, these two parts of one filament can randomly move toward each other forming the tip of a loop at the sacrificial cell.}, }
@article {pmid18335091, year = {2008}, author = {Mendez, MO and Maier, RM}, title = {Phytostabilization of mine tailings in arid and semiarid environments--an emerging remediation technology.}, journal = {Environmental health perspectives}, volume = {116}, number = {3}, pages = {278-283}, pmid = {18335091}, issn = {0091-6765}, support = {P42 ES004940/ES/NIEHS NIH HHS/United States ; 2 P42 ES04940-11/ES/NIEHS NIH HHS/United States ; }, mesh = {*Biodegradation, Environmental ; Conservation of Natural Resources/methods ; Desert Climate ; *Ecosystem ; *Environmental Pollution ; Humans ; *Industrial Waste ; Metals, Heavy/metabolism ; *Mining ; Plant Development ; *Plants/metabolism/microbiology ; United States ; }, abstract = {OBJECTIVE: Unreclaimed mine tailings sites are a worldwide problem, with thousands of unvegetated, exposed tailings piles presenting a source of contamination for nearby communities. Tailings disposal sites in arid and semiarid environments are especially subject to eolian dispersion and water erosion. Phytostabilization, the use of plants for in situ stabilization of tailings and metal contaminants, is a feasible alternative to costly remediation practices. In this review we emphasize considerations for phytostabilization of mine tailings in arid and semiarid environments, as well as issues impeding its long-term success.<br><br>DATA SOURCES: We reviewed literature addressing mine closures and revegetation of mine tailings, along with publications evaluating plant ecology, microbial ecology, and soil properties of mine tailings.<br><br>DATA EXTRACTION: Data were extracted from peer-reviewed articles and books identified in Web of Science and Agricola databases, and publications available through the U.S. Department of Agriculture, U.S. Environmental Protection Agency, and the United Nations Environment Programme.<br><br>DATA SYNTHESIS: Harsh climatic conditions in arid and semiarid environments along with the innate properties of mine tailings require specific considerations. Plants suitable for phytostabilization must be native, be drought-, salt-, and metal-tolerant, and should limit shoot metal accumulation. Factors for evaluating metal accumulation and toxicity issues are presented. Also reviewed are aspects of implementing phytostabilization, including plant growth stage, amendments, irrigation, and evaluation.<br><br>CONCLUSIONS: Phytostabilization of mine tailings is a promising remedial technology but requires further research to identify factors affecting its long-term success by expanding knowledge of suitable plant species and mine tailings chemistry in ongoing field trials.}, }
@article {pmid18331337, year = {2008}, author = {Marzorati, M and Wittebolle, L and Boon, N and Daffonchio, D and Verstraete, W}, title = {How to get more out of molecular fingerprints: practical tools for microbial ecology.}, journal = {Environmental microbiology}, volume = {10}, number = {6}, pages = {1571-1581}, doi = {10.1111/j.1462-2920.2008.01572.x}, pmid = {18331337}, issn = {1462-2920}, mesh = {Bacteria/classification/*genetics ; DNA Fingerprinting/methods/*standards ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Electrophoresis, Polyacrylamide Gel/methods ; Genetics, Microbial/*methods/standards ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Community-level molecular techniques are widely used in comparative microbial ecology to assess the diversity of microbial communities and their response to changing environments. These include among others denaturing and temperature gradient gel electrophoresis (DGGE/TGGE), single-strand conformation polymorphism (SSCP), length heterogeneity-PCR (LH-PCR), terminal-restriction fragment length polymorphism (tRFLP) and 16S rRNA gene clone libraries. The amount of data derived from these techniques available in literature is continuously increasing and the lack of a universal way to interpret the raw fingerprint itself makes it difficult to compare between different results. Taking the DGGE technique as an example, we propose a setting-independent theoretical interpretation of the DGGE pattern, based on a straightforward processing on three levels of analysis: (i) the range-weighted richness (Rr) reflecting the carrying capacity of the system, (ii) the dynamics (Dy) reflecting the specific rate of species coming to significance, and (iii) functional organization (Fo), defined through a relation between the structure of a microbial community and its functionality. These Rr, Dy and Fo values, each representing a score to describe a microbial community, can be plotted in a 3D graph. The latter represents a visual ecological interpretation of the initial raw fingerprinting pattern.}, }
@article {pmid18331336, year = {2008}, author = {Ellis, DG and Bizzoco, RW and Kelley, ST}, title = {Halophilic Archaea determined from geothermal steam vent aerosols.}, journal = {Environmental microbiology}, volume = {10}, number = {6}, pages = {1582-1590}, doi = {10.1111/j.1462-2920.2008.01574.x}, pmid = {18331336}, issn = {1462-2920}, mesh = {*Aerosols ; Archaea/*classification/cytology/*isolation &amp; purification ; California ; Cell Count ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Hawaii ; Hot Springs/*microbiology ; Molecular Sequence Data ; New Mexico ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Russia ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Sodium Chloride/metabolism ; *Steam ; Wyoming ; }, abstract = {Hydrothermal vents, known as 'fumaroles', are ubiquitous features of geothermal areas. Although their geology has been extensively characterized, little is known about the subsurface microbial ecology of fumaroles largely because of the difficulty in collecting sufficient numbers of cells from boiling steam water for DNA extraction and culture isolation. Here we describe the first collection, molecular analysis and isolation of microbes from fumarole steam waters in Russia (Kamchatka) and the USA (Hawaii, New Mexico, California and Wyoming). Surprisingly, the steam vent waters from all the fumaroles contained halophilic Archaea closely related to the Haloarcula spp. found in non-geothermal salt mats, saline soils, brine pools and salt lakes around the world. Microscopic cell counting estimated the cell dispersal rate at approximately 1.6 x 10(9) cells year(-1) from a single fumarole. We also managed to enrich microbes in high-salt media from every vent sample, and to isolate Haloarcula from a Yellowstone vent in a 20% salt medium after a month-long incubation, demonstrating both salt tolerance and viability of cells collected from high-temperature steam. Laboratory tests determined that microbes enriched in salt media survived temperatures greater than 75 degrees C for between 5 and 30 min during the collection process. Hawaiian fumaroles proved to contain the greatest diversity of halophilic Archaea with four new lineages that may belong to uncultured haloarchaeal genera. This high diversity may have resulted from the leaching of salts and minerals through the highly porous volcanic rock, creating a chemically complex saline subsurface.}, }
@article {pmid18328562, year = {2009}, author = {Wang, F and Yao, J and Chen, H and Zhou, Y and Chen, Y and Chen, H and Gai, N and Zhuang, R and Tian, L and Maskow, T and Ceccanti, B and Trebse, P and Zaray, G}, title = {Microcalorimetric measurements of the microbial activities of single- and mixed-species with trivalent iron in soil.}, journal = {Ecotoxicology and environmental safety}, volume = {72}, number = {1}, pages = {128-135}, doi = {10.1016/j.ecoenv.2008.01.012}, pmid = {18328562}, issn = {1090-2414}, mesh = {Bacillus subtilis/drug effects/growth &amp; development ; Calcium/analysis ; Calorimetry/methods ; Candida/drug effects/growth &amp; development ; Chlorides ; Ferric Compounds/*pharmacology ; Magnesium/analysis ; Microchemistry/methods ; Oxygen/analysis ; Phosphorus/analysis ; Potassium/analysis ; Sodium/analysis ; Soil/*analysis ; *Soil Microbiology ; Spectrophotometry ; }, abstract = {A microcalorimetric technique was applied to a series of experiments to follow the toxic effect caused by the trivalent iron on the single and mixed microbes in sterilized soil that was inoculated with the single Bacillus subtilis (B. subtilis) (prokaryotic bacterium), single Candida humicola (C. humicola) (eukaryotic fungus) and the mixed-species. The microbial activity was stimulated by the addition of 5.0mg glucose and 5.0mg ammonium sulfate under a 35% controlled humidity in the studied soil samples of 1.2g. The power-time curves from every experiment were analyzed, and from these analyses characteristic parameters, such as growth rate constant (k) and total thermal effect (Q) which can reflect the biochemical reactions were determined. The mixed-species have moderate tolerance to the iron overload, comparing with single species, and exhibit synergistic interaction in exponential growth phase (0-400.0 microg mL(-1)). Meanwhile, there is no much difference in the thermal effect (Q) per gram soil sample for the single and mixed culture. This also validates that the nutrient substances in natural environment determine the organisms' metabolic activities. Ultraviolet-visible spectrophotometry and dissolved oxygen sensor also were successfully applied to reflect the activities of B. subtilis and C. humicola in the pure culture. The investigation could provide insight into the microbial ecology of bacteria and fungi in ecological niches.}, }
@article {pmid18322729, year = {2008}, author = {Williamson, KE and Schnitker, JB and Radosevich, M and Smith, DW and Wommack, KE}, title = {Cultivation-based assessment of lysogeny among soil bacteria.}, journal = {Microbial ecology}, volume = {56}, number = {3}, pages = {437-447}, pmid = {18322729}, issn = {0095-3628}, mesh = {Bacteria/genetics/radiation effects/*virology ; Bacteriophages/drug effects/genetics/*physiology/radiation effects ; Base Sequence ; Colony Count, Microbial ; DNA/chemistry/genetics ; Electrophoresis, Gel, Pulsed-Field ; Lysogeny/drug effects/*physiology/radiation effects ; Microscopy, Electron, Transmission ; Mitomycin/pharmacology ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal/chemistry/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Ultraviolet Rays ; Virus Activation/drug effects/physiology/radiation effects ; }, abstract = {Lysogeny has long been proposed as an important long-term maintenance strategy for autochthonous soil bacteriophages (phages). Whole genome sequence data indicate that prophage-derived sequences pervade prokaryotic genomes, but the connection between inferred prophage sequence and an active temperate phage is tenuous. Thus, definitive evidence of phage production from lysogenic prokaryotes will be critical in determining the presence and extent of temperate phage diversity existing as prophage within bacterial genomes and within environmental contexts such as soils. This study optimized methods for systematic and definitive determination of lysogeny within a collection of autochthonous soil bacteria. Twenty bacterial isolates from a range of Delaware soil environments (five from each soil) were treated with the inducing agents mitomycin C (MC) or UV light. Six isolates (30%) carried inducible temperate phages as evidenced by an increase in virus direct counts. The magnitude of induction response was highly dependent upon specific induction conditions, and corresponding burst sizes ranged from 1 to 176. Treatment with MC for 30 min yielded the largest induction responses for three of the six lysogens. Morphological analysis revealed that four of the lysogens produced lambda-like Siphoviridae particles, whereas two produced Myoviridae particles. Additionally, pulsed-field gel electrophoresis data indicated that two of the six lysogens were polylysogens, producing more than one distinct type of phage particle. These results suggest that lysogeny is relatively common among soil bacteria.}, }
@article {pmid18322728, year = {2008}, author = {Adams, AS and Six, DL and Adams, SM and Holben, WE}, title = {In vitro interactions between yeasts and bacteria and the fungal symbionts of the mountain pine beetle (Dendroctonus ponderosae).}, journal = {Microbial ecology}, volume = {56}, number = {3}, pages = {460-466}, pmid = {18322728}, issn = {0095-3628}, mesh = {Animals ; Base Sequence ; Basidiomycota/genetics/*growth &amp; development ; Coleoptera/*microbiology ; Fungi/genetics/*growth &amp; development ; Molecular Sequence Data ; Phloem ; Pinus ; Polymerase Chain Reaction ; RNA, Fungal/chemistry/genetics ; RNA, Ribosomal, 16S/chemistry/genetics ; RNA, Ribosomal, 18S/chemistry/genetics ; Sequence Analysis, DNA ; Symbiosis/physiology ; }, abstract = {Multi-trophic interactions between prokaryotes, unicellular eukaryotes, and ecologically intertwined metazoans are presumably common in nature, yet rarely described. The mountain pine beetle, Dendroctonus ponderosae, is associated with two filamentous fungi, Grosmannia clavigera and Ophiostoma montium. Other microbes, including yeasts and bacteria, are also present in the phloem, but it is not known whether they interact with the symbiotic fungi or the host beetle. To test whether such interactions occur, we performed a suite of in vitro assays. Overall, relative yield of O. montium grown with microbes isolated from larval galleries was significantly greater than when the fungus was grown alone. Conversely, the yield of G. clavigera grown with these same microbes was less than or equal to when it was grown alone, suggesting that O. montium, and at least some microbes in larval galleries, have a mutualistic or commensal relationship, while G. clavigera and those same microbes have an antagonistic relationship. A bacterium isolated from phloem not colonized by beetles was found to inhibit growth of both G. clavigera and O. montium and appears to be an antagonist to both fungi. Our results suggest that bacteria and yeasts likely influence the distribution of mycangial fungi in the host tree, which, in turn, may affect the fitness of D. ponderosae.}, }
@article {pmid18322727, year = {2008}, author = {Singh, P and Srivastava, B and Kumar, A and Dubey, NK}, title = {Fungal contamination of raw materials of some herbal drugs and recommendation of Cinnamomum camphora oil as herbal fungitoxicant.}, journal = {Microbial ecology}, volume = {56}, number = {3}, pages = {555-560}, pmid = {18322727}, issn = {0095-3628}, mesh = {Aflatoxin B1/metabolism ; Antifungal Agents/*pharmacology ; Cinnamomum camphora/*chemistry ; Fungi/drug effects/*isolation &amp; purification/metabolism ; Plant Oils/*pharmacology ; Plants, Medicinal/*microbiology ; }, abstract = {The paper explores fungal infection and aflatoxin B1 contamination of six medicinal plant samples viz. Adhatoda vasica Nees, Asparagus racemosus Linn., Evolvulus alsinoides Linn., Glycyrrhiza glabra Linn., Plumbago zeylanica Linn. and Terminalia chebula Retz. A total of 858 fungal isolates were detected from the raw materials. Maximum number of fungal isolates was detected from A. racemosus (228). The genus Aspergillus was found to be the most dominant genus causing infection to most of the raw materials. Among the 32 isolates of A. flavus tested, 13 isolates were found to be toxigenic elaborating aflatoxin B1. The highest elaboration of aflatoxin B1 was 394.95 ppb by the isolates of A. flavus from G. glabra. The essential oil of Cinnamomum camphora (L.) Presl showed efficacy in arresting aflatoxin B1 by the toxigenic strain. The growth of a toxigenic strain of A. flavus decreased progressively with increasing concentration of essential oil from leaves of C. camphora. The oil completely inhibited aflatoxin B1 production even at 750 ppm. Hence, the oil of C. camphora is recommended as herbal fungitoxicant against the fungal contamination of the raw materials.}, }
@article {pmid18312573, year = {2008}, author = {Haider, S and Collingro, A and Walochnik, J and Wagner, M and Horn, M}, title = {Chlamydia-like bacteria in respiratory samples of community-acquired pneumonia patients.}, journal = {FEMS microbiology letters}, volume = {281}, number = {2}, pages = {198-202}, doi = {10.1111/j.1574-6968.2008.01099.x}, pmid = {18312573}, issn = {0378-1097}, mesh = {Adult ; Aged ; Chlamydia/genetics/*isolation &amp; purification ; Chlamydia Infections/*microbiology ; Community-Acquired Infections/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Female ; Humans ; Male ; Middle Aged ; Molecular Sequence Data ; Pneumonia/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {Chlamydia-like bacteria, obligate intracellular relatives of Chlamydia trachomatis and Chlamydophila pneumoniae, are widely distributed in nature. Using a two-step nested and semi-nested PCR approach targeting the 16S rRNA gene, we found DNA of Chlamydia-like bacteria in respiratory samples from patients with community-acquired pneumonia. Of 387 cases tested, four (1.03%) tested positive if only sequences showing less than 99.9% 16S rRNA gene sequence similarity to known Chlamydiae were considered. These included for the first time Protochlamydia amoebophila, Waddlia chondrophila, and 'Candidatus Rhabdochlamydia porcellionis'-related sequences. This study extends previous findings suggesting an association of Chlamydia-like bacteria with respiratory disease, but a causal link between these microorganisms and respiratory tract infections has yet to be established.}, }
@article {pmid18312392, year = {2008}, author = {Pruzzo, C and Vezzulli, L and Colwell, RR}, title = {Global impact of Vibrio cholerae interactions with chitin.}, journal = {Environmental microbiology}, volume = {10}, number = {6}, pages = {1400-1410}, doi = {10.1111/j.1462-2920.2007.01559.x}, pmid = {18312392}, issn = {1462-2920}, mesh = {Animals ; Chitin/*metabolism ; Cholera/*microbiology ; Evolution, Molecular ; Humans ; Vibrio cholerae/pathogenicity/*physiology ; Virulence ; *Water Microbiology ; }, abstract = {The interaction of Vibrio cholerae with chitin exemplifies for microbial ecology a successful bacteria-substrate interaction with complex and significant influence on the lifestyle of the bacterium. Chitin is one of the most abundant polymers on earth and possibly the most abundant in the aquatic environment, where its association with V. cholerae has provided the microorganism with a number of advantages, including food availability, adaptation to environmental nutrient gradients, tolerance to stress and protection from predators. Emergent properties of V. cholerae-chitin interactions occur at multiple hierarchical levels in the environment and include cell metabolic and physiological responses e.g. chemotaxis, cell multiplication, induction of competence, biofilm formation, commensal and symbiotic relationship with higher organisms, cycling of nutrients, and pathogenicity for humans and aquatic animals. As factors mediating virulence of V. cholerae for humans and aquatic animals derive from mechanisms of adaptation to its environment, at different levels of hierarchical scale, V. cholerae interactions with chitin represent a useful model for examination of the role of primary habitat selection in the development of traits that have been identified as virulence factors in human disease.}, }
@article {pmid18311472, year = {2008}, author = {Pieper, R and Janczyk, P and Zeyner, A and Smidt, H and Guiard, V and Souffrant, WB}, title = {Ecophysiology of the developing total bacterial and lactobacillus communities in the terminal small intestine of weaning piglets.}, journal = {Microbial ecology}, volume = {56}, number = {3}, pages = {474-483}, pmid = {18311472}, issn = {0095-3628}, mesh = {Animals ; Base Sequence ; Colony Count, Microbial/veterinary ; DNA, Bacterial/chemistry/genetics ; Female ; Gastrointestinal Contents/microbiology ; Intestine, Small/*microbiology ; Lactobacillus/genetics/isolation &amp; purification/*physiology ; Male ; Molecular Sequence Data ; Polymerase Chain Reaction/veterinary ; RNA, Ribosomal, 16S/chemistry/genetics ; Random Allocation ; Sequence Analysis, DNA ; Swine/*microbiology ; Weaning ; }, abstract = {Weaning of the pig is generally regarded as a stressful event which could lead to clinical implications because of the changes in the intestinal ecosystem. The functional properties of microbiota inhabiting the pig's small intestine (SI), including lactobacilli which are assumed to exert health-promoting properties, are yet poorly described. Thus, we determined the ecophysiology of bacterial groups and within genus Lactobacillus in the SI of weaning piglets and the impact of dietary changes. The SI contents of 20 piglets, 4 killed at weaning (only sow milk and no creep feed) and 4 killed at 1, 2, 5, and 11 days post weaning (pw; cereal-based diet) were examined for bacterial cell count and bacterial metabolites by fluorescence in situ hybridization (FISH). Lactobacilli were the predominant group in the SI except at 1 day pw because of a marked reduction in their number. On day 11 pw, bifidobacteria and E. coli were not detected, and Enterobacteriaceae and members of the Clostridium coccoides/Eubacterium rectale cluster were only found occasionally. L. sobrius/L. amylovorus became dominant species whereas the abundance of L. salivarius and L. gasseri/johnsonii declined. Concentration of lactic acid increased pw whereas pH, volatile fatty acids, and ammonia decreased. Carbohydrate utilization of 76 Lactobacillus spp. isolates was studied revealing a shift from lactose and galactose to starch, cellobiose, and xylose, suggesting that the bacteria colonizing the SI of piglets adapt to the newly introduced nutrients during the early weaning period. Identification of isolates based on partial 16S rRNA gene sequence data and comparison with fermentation data furthermore suggested adaptation processes below the species level. The results of our study will help to understand intestinal bacterial ecophysiology and to develop nutritional regimes to prevent or counteract complications during the weaning transition.}, }
@article {pmid18310425, year = {2008}, author = {Brons, JK and van Elsas, JD}, title = {Analysis of bacterial communities in soil by use of denaturing gradient gel electrophoresis and clone libraries, as influenced by different reverse primers.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {9}, pages = {2717-2727}, pmid = {18310425}, issn = {1098-5336}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; *Biodiversity ; Cluster Analysis ; DNA Fingerprinting/methods ; DNA Primers/genetics ; DNA, Bacterial/chemistry/*genetics ; DNA, Ribosomal/chemistry/genetics ; *Electrophoresis, Polyacrylamide Gel ; Molecular Sequence Data ; Nucleic Acid Denaturation ; Phylogeny ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {To assess soil bacterial diversity, PCR systems consisting of several slightly different reverse primers together with forward primer F968-GC were used along with subsequent denaturing gradient gel electrophoresis (DGGE) or clone library analyses. In this study, a set of 13 previously used and novel reverse primers was tested with the canonical forward primer as to the DGGE fingerprints obtained from grassland soil. Analysis of these DGGE profiles by GelCompar showed that they all fell into two main clusters separated by a G/A alteration at position 14 in the reverse primer used. To assess differences between the dominant bacteria amplified, we then produced four (100-membered) 16S rRNA gene clone libraries by using reverse primers with either an A or a G at position 14, designated R1401-1a, R1401-1b, R1401-2a, and R1401-2b. Subsequent sequence analysis revealed that, on the basis of the about 410-bp sequence information, all four primers amplified similar, as well as different (including novel), bacterial groups from soil. Most of the clones fell into two main phyla, Firmicutes and Proteobacteria. Within Firmicutes, the majority of the clones belonged to the genus Bacillus. Within Proteobacteria, the majority of the clones fell into the alpha or gamma subgroup whereas a few were delta and beta proteobacteria. The other phyla found were Actinobacteria, Acidobacteria, Verrucomicrobia, Chloroflexi, Gemmatimonadetes, Chlorobi, Bacteroidetes, Chlamydiae, candidate division TM7, Ferribacter, Cyanobacteria, and Deinococcus. Statistical analysis of the data revealed that reverse primers R1401-1b and R1401-1a both produced libraries with the highest diversities yet amplified different types. Their concomitant use is recommended.}, }
@article {pmid18305983, year = {2008}, author = {Carriconde, F and Gardes, M and Jargeat, P and Heilmann-Clausen, J and Mouhamadou, B and Gryta, H}, title = {Population evidence of cryptic species and geographical structure in the cosmopolitan ectomycorrhizal fungus, Tricholoma scalpturatum.}, journal = {Microbial ecology}, volume = {56}, number = {3}, pages = {513-524}, pmid = {18305983}, issn = {0095-3628}, mesh = {Agaricales/*genetics/growth &amp; development ; Base Sequence ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Europe ; Genetic Variation ; Microsatellite Repeats/genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Polymorphism, Restriction Fragment Length ; }, abstract = {Tricholoma scalpturatum is an ectomycorrhizal fungus that forms symbioses with roots of diverse trees and shrubs. It is commonly encountered in a wide range of habitats, across temperate ecosystems. A previous study has revealed a high genetic diversity at a local scale, and ruderal abilities. To examine genetic structure at a large geographical scale, a total of 164 basidiocarps were collected from 30 populations located in Western Europe, from Spain to Scandinavia. These samples were analyzed by three molecular methods with different levels of resolution: inter-simple sequence repeats (ISSRs), restriction fragment length polymorphisms (RFLPs) in the rDNA internal transcribed spacer (ITS), and ITS sequence analysis. Considerable genetic variation was found, and the morphospecies was separated into two genetic groups that were distinct from each other. The ISSR data and the relatively low percentage value (96%) of shared sequence polymorphisms in the ITS between isolates from the two groups, strongly suggest cryptic species and long-lasting separation. No geographical exclusion was detected for these two widely distributed taxa. However, high estimates of population differentiation were observed in each group, including between populations less than a few kilometers apart. This result provides evidence for limited gene flow and/or founding effects. It also indicates that T. scalpturatum does not constitute a random mating population, and the hypothesis of endemism cannot be excluded for this cosmopolitan wind-dispersed fungus.}, }
@article {pmid18301735, year = {2008}, author = {Dinsdale, EA and Pantos, O and Smriga, S and Edwards, RA and Angly, F and Wegley, L and Hatay, M and Hall, D and Brown, E and Haynes, M and Krause, L and Sala, E and Sandin, SA and Thurber, RV and Willis, BL and Azam, F and Knowlton, N and Rohwer, F}, title = {Microbial ecology of four coral atolls in the Northern Line Islands.}, journal = {PloS one}, volume = {3}, number = {2}, pages = {e1584}, pmid = {18301735}, issn = {1932-6203}, mesh = {Animal Diseases/microbiology ; Animals ; Anthozoa/*microbiology ; *Ecosystem ; *Geography ; Humans ; Marine Biology ; Water/chemistry ; *Water Microbiology ; }, abstract = {Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Kingman, a small uninhabited atoll which lies most northerly in the chain, had microbial and water chemistry characteristic of an open ocean ecosystem. On this atoll the microbial community was equally divided between autotrophs (mostly Prochlorococcus spp.) and heterotrophs. In contrast, Kiritimati, a large and populated (approximately 5500 people) atoll, which is most southerly in the chain, had microbial and water chemistry characteristic of a near-shore environment. On Kiritimati, there were 10 times more microbial cells and virus-like particles in the water column and these microbes were dominated by heterotrophs, including a large percentage of potential pathogens. Culturable Vibrios were common only on Kiritimati. The benthic community on Kiritimati had the highest prevalence of coral disease and lowest coral cover. The middle atolls, Palmyra and Tabuaeran, had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati. The differences in microbial communities across atolls could reflect variation in 1) oceaonographic and/or hydrographic conditions or 2) human impacts associated with land-use and fishing. The fact that historically Kingman and Kiritimati did not differ strongly in their fish or benthic communities (both had large numbers of sharks and high coral cover) suggest an anthropogenic component in the differences in the microbial communities. Kingman is one of the world's most pristine coral reefs, and this dataset should serve as a baseline for future studies of coral reef microbes. Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation of coral reef ecosystems worldwide.}, }
@article {pmid18291426, year = {2008}, author = {Vanpeteghem, D and Zemb, O and Haegeman, B}, title = {Dynamics of neutral biodiversity.}, journal = {Mathematical biosciences}, volume = {212}, number = {1}, pages = {88-98}, doi = {10.1016/j.mbs.2008.01.002}, pmid = {18291426}, issn = {0025-5564}, mesh = {*Biodiversity ; Computer Simulation ; *Ecosystem ; *Models, Biological ; Stochastic Processes ; }, abstract = {Hubbell's neutral model has become a major paradigm in ecology. Whereas the steady-state structure is well understood, results about the dynamical aspects of the model are scarce. Here we derive dynamical equations for the Simpson diversity index. Both mean and variance of the diversity are proven to satisfy stable linear system dynamics. We show that in the stationary limit we indeed recover previous results, and we supplement this with numerical simulations to validate the dynamical part of our analytical computations. These findings are especially relevant for experiments in microbial ecology, where the Simpson diversity index can be accurately measured as a function of time.}, }
@article {pmid18290451, year = {2007}, author = {Jiang, YX and Ai, CX}, title = {[Main bottleneck and developments of metagenomic technology].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {28}, number = {12}, pages = {2861-2866}, pmid = {18290451}, issn = {0250-3301}, mesh = {*Ecology ; *Genome, Bacterial ; Genomic Library ; Genomics/*methods ; Soil/analysis ; *Soil Microbiology ; }, abstract = {This review analyzed the main bottleneck of metagenomic technology on construction and screening of environmental library, discussed the recent developments towards overcoming the main bottleneck. Finally, the enormous scope and potential for both fundamental microbial ecology and biotechnological development of metagenomics was highlighted.}, }
@article {pmid18283507, year = {2008}, author = {Fermoso, FG and Collins, G and Bartacek, J and Lens, PN}, title = {Zinc deprivation of methanol fed anaerobic granular sludge bioreactors.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {35}, number = {6}, pages = {543-557}, pmid = {18283507}, issn = {1367-5435}, mesh = {Bacteria, Anaerobic/growth &amp; development/metabolism ; Bioreactors/*microbiology ; Culture Media/chemistry ; Euryarchaeota/growth &amp; development/metabolism ; Fatty Acids, Volatile/metabolism ; Hydrogen-Ion Concentration ; Methane/metabolism ; Methanol/*metabolism ; Sewage/*microbiology ; Time Factors ; Zinc/*metabolism ; }, abstract = {The effect of omitting zinc from the influent of mesophilic (30 degrees C) methanol fed upflow anaerobic sludge bed (UASB) reactors, and latter zinc supplementation to the influent to counteract the deprivation, was investigated by coupling the UASB reactor performance to the microbial ecology of the bioreactor sludge. Limitation of the specific methanogenic activity (SMA) on methanol due to the absence of zinc from the influent developed after 137 days of operation. At that day, the SMA in medium with a complete trace metal solution except Zn was 3.4 g CH4-COD g VSS(-1) day(-1), compared to 4.2 g CH4-COD g VSS(-1) day(-1) in a medium with a complete (including zinc) trace metal solution. The methanol removal capacity during these 137 days was 99% and no volatile fatty acids accumulated. Two UASB reactors, inoculated with the zinc-deprived sludge, were operated to study restoration of the zinc limitation by zinc supplementation to the bioreactor influent. In a first reactor, no changes to the operational conditions were made. This resulted in methanol accumulation in the reactor effluent after 12 days of operation, which subsequently induced acetogenic activity 5 days after the methanol accumulation started. Methanogenesis could not be recovered by the continuous addition of 0.5 microM ZnCl2 to the reactor for 13 days. In the second reactor, 0.5 microM ZnCl2 was added from its start-up. Although the reactor stayed 10 days longer methanogenically than the reactor operated without zinc, methanol accumulation was observed in this reactor (up to 1.1 g COD-MeOH L(-1)) as well. This study shows that zinc limitation can induce failure of methanol fed UASB reactors due to acidification, which cannot be restored by resuming the continuous supply of the deprived metal.}, }
@article {pmid18272490, year = {2008}, author = {Koeppel, A and Perry, EB and Sikorski, J and Krizanc, D and Warner, A and Ward, DM and Rooney, AP and Brambilla, E and Connor, N and Ratcliff, RM and Nevo, E and Cohan, FM}, title = {Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {7}, pages = {2504-2509}, pmid = {18272490}, issn = {1091-6490}, mesh = {Algorithms ; Bacillus/*classification ; Computer Simulation ; *Ecology ; Environmental Pollution ; Molecular Sequence Data ; Phylogeny ; }, abstract = {The central questions of bacterial ecology and evolution require a method to consistently demarcate, from the vast and diverse set of bacterial cells within a natural community, the groups playing ecologically distinct roles (ecotypes). Because of a lack of theory-based guidelines, current methods in bacterial systematics fail to divide the bacterial domain of life into meaningful units of ecology and evolution. We introduce a sequence-based approach ("ecotype simulation") to model the evolutionary dynamics of bacterial populations and to identify ecotypes within a natural community, focusing here on two Bacillus clades surveyed from the "Evolution Canyons" of Israel. This approach has identified multiple ecotypes within traditional species, with each predicted to be an ecologically distinct lineage; many such ecotypes were confirmed to be ecologically distinct, with specialization to different canyon slopes with different solar exposures. Ecotype simulation provides a long-needed natural foundation for microbial ecology and systematics.}, }
@article {pmid18269340, year = {2008}, author = {Mitsuyama, K and Sata, M}, title = {Gut microflora: a new target for therapeutic approaches in inflammatory bowel disease.}, journal = {Expert opinion on therapeutic targets}, volume = {12}, number = {3}, pages = {301-312}, doi = {10.1517/14728222.12.3.301}, pmid = {18269340}, issn = {1744-7631}, mesh = {Animals ; Drug Delivery Systems/*methods ; Gastrointestinal Agents/administration &amp; dosage ; Gastrointestinal Tract/drug effects/*microbiology ; Humans ; Inflammatory Bowel Diseases/*microbiology/*therapy ; Probiotics/*administration &amp; dosage ; }, abstract = {BACKGROUND: Intestinal microflora contribute to the pathogenesis of inflammatory bowel disease, including ulcerative colitis and Crohn's disease.<br><br>OBJECTIVE: This review summarizes current clinical knowledge about the role of intestinal microflora in inflammatory bowel disease and their importance as targets for new forms of therapy.<br><br>METHODS: Recent knowledge on gut microbial ecology, role of microflora, and pattern recognition receptors is summarized in relation to inflammatory bowel disease. The results of in vitro experiments, in vivo animal studies and human clinical trials with the use of agents targeting microflora, including prebiotics, probiotics and synbiotics, are described briefly.<br><br>CONCLUSION: Altering the composition of intestinal microflora through prebiotics, probiotics and synbiotics may improve the clinical outcome of patients with inflammatory bowel disease.}, }
@article {pmid18264658, year = {2008}, author = {Manerkar, MA and Seena, S and Bärlocher, F}, title = {Q-RT-PCR for assessing archaea, bacteria, and fungi during leaf decomposition in a stream.}, journal = {Microbial ecology}, volume = {56}, number = {3}, pages = {467-473}, pmid = {18264658}, issn = {0095-3628}, mesh = {Archaea/genetics/*growth &amp; development ; Bacteria/genetics/*growth &amp; development ; Biomass ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Ecosystem ; Ergosterol/metabolism ; Fungi/genetics/*growth &amp; development ; Plant Leaves/metabolism/*microbiology ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/chemistry/genetics ; RNA, Ribosomal, 5.8S/chemistry/genetics ; Rivers ; }, abstract = {Leaf disks of Tilia cordata were exposed for up to 5 weeks in a first-order stream in Nova Scotia, Canada. The exponential decay rate k was 0.008 day(-1). Ergosterol levels increased linearly to a maximum of 134 microg g(-1) dry leaf mass. Release of conidia peaked at 700 day(-1) mg(-1) on leaves that had been exposed for 3 weeks; after 5 weeks, it declined to 15 mg(-1). In total, 23 taxa of aquatic hyphomycetes were distinguished. Anguillospora filiformis contributed over 76% of the conidia during weeks 1, 2, and 3, and 16.5% in week 5. Three sets of primers specific for Bacteria, Archaea, and Fungi were applied in quantitative real-time polymerase chain reaction (Q-RT-PCR) to estimate relative DNA amounts. Archaeal DNA was consistently present at low levels. Bacterial and fungal DNA peaked between weeks 2 and 3, and declined in week 5. With the exception of week 1, fungal DNA exceeded bacterial DNA by between 12 and 110%.}, }
@article {pmid18256705, year = {2008}, author = {Binga, EK and Lasken, RS and Neufeld, JD}, title = {Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology.}, journal = {The ISME journal}, volume = {2}, number = {3}, pages = {233-241}, doi = {10.1038/ismej.2008.10}, pmid = {18256705}, issn = {1751-7362}, mesh = {DNA/analysis ; Ecology/*methods ; Ecosystem ; Genetics, Microbial/*methods ; Genomics/methods ; Nucleic Acid Amplification Techniques/*methods ; }, abstract = {Microbial ecology is a field that applies molecular techniques to analyze genes and communities associated with a plethora of unique environments on this planet. In the past, low biomass and the predominance of a few abundant community members have impeded the application of techniques such as PCR, microarray analysis and metagenomics to complex microbial populations. In the absence of suitable cultivation methods, it was not possible to obtain DNA samples from individual microorganisms. Recently, a method called multiple displacement amplification (MDA) has been used to circumvent these limitations by amplifying DNA from microbial communities in low-biomass environments, individual cells from uncultivated microbial species and active organisms obtained through stable isotope probing incubations. This review describes the development and applications of MDA, discusses its strengths and limitations and highlights the impact of MDA on the field of microbial ecology. Whole genome amplification via MDA has increased access to the genomic DNA of uncultivated microorganisms and low-biomass environments and represents a 'power tool' in the molecular toolbox of microbial ecologists.}, }
@article {pmid18253776, year = {2008}, author = {Connell, L and Redman, R and Craig, S and Scorzetti, G and Iszard, M and Rodriguez, R}, title = {Diversity of soil yeasts isolated from South Victoria Land, Antarctica.}, journal = {Microbial ecology}, volume = {56}, number = {3}, pages = {448-459}, pmid = {18253776}, issn = {0095-3628}, mesh = {Antarctic Regions ; Base Sequence ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Principal Component Analysis ; RNA, Ribosomal/chemistry/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; *Soil Microbiology ; Yeasts/genetics/*isolation &amp; purification ; }, abstract = {Unicellular fungi, commonly referred to as yeasts, were found to be components of the culturable soil fungal population in Taylor Valley, Mt. Discovery, Wright Valley, and two mountain peaks of South Victoria Land, Antarctica. Samples were taken from sites spanning a diversity of soil habitats that were not directly associated with vertebrate activity. A large proportion of yeasts isolated in this study were basidiomycetous species (89%), of which 43% may represent undescribed species, demonstrating that culturable yeasts remain incompletely described in these polar desert soils. Cryptococcus species represented the most often isolated genus (33%) followed by Leucosporidium (22%). Principle component analysis and multiple linear regression using stepwise selection was used to model the relation between abiotic variables (principle component 1 and principle component 2 scores) and yeast biodiversity (the number of species present at a given site). These analyses identified soil pH and electrical conductivity as significant predictors of yeast biodiversity. Species-specific PCR primers were designed to rapidly discriminate among the Dioszegia and Leucosporidium species collected in this study.}, }
@article {pmid18250313, year = {2008}, author = {Hatzenpichler, R and Lebedeva, EV and Spieck, E and Stoecker, K and Richter, A and Daims, H and Wagner, M}, title = {A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {6}, pages = {2134-2139}, pmid = {18250313}, issn = {1091-6490}, mesh = {Ammonia/*metabolism ; Archaea/genetics/*metabolism ; Catalysis ; Hot Temperature ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; RNA, Messenger/genetics ; RNA, Ribosomal, 16S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; *Water Microbiology ; }, abstract = {The recent discovery of ammonia-oxidizing archaea (AOA) dramatically changed our perception of the diversity and evolutionary history of microbes involved in nitrification. In this study, a moderately thermophilic (46 degrees C) ammonia-oxidizing enrichment culture, which had been seeded with biomass from a hot spring, was screened for ammonia oxidizers. Although gene sequences for crenarchaeotal 16S rRNA and two subunits of the ammonia monooxygenase (amoA and amoB) were detected via PCR, no hints for known ammonia-oxidizing bacteria were obtained. Comparative sequence analyses of these gene fragments demonstrated the presence of a single operational taxonomic unit and thus enabled the assignment of the amoA and amoB sequences to the respective 16S rRNA phylotype, which belongs to the widely distributed group I.1b (soil group) of the Crenarchaeota. Catalyzed reporter deposition (CARD)-FISH combined with microautoradiography (MAR) demonstrated metabolic activity of this archaeon in the presence of ammonium. This finding was corroborated by the detection of amoA gene transcripts in the enrichment. CARD-FISH/MAR showed that the moderately thermophilic AOA is highly active at 0.14 and 0.79 mM ammonium and is partially inhibited by a concentration of 3.08 mM. The enriched AOA, which is provisionally classified as "Candidatus Nitrososphaera gargensis," is the first described thermophilic ammonia oxidizer and the first member of the crenarchaeotal group I.1b for which ammonium oxidation has been verified on a cellular level. Its preference for thermophilic conditions reinvigorates the debate on the thermophilic ancestry of AOA.}, }
@article {pmid18246293, year = {2008}, author = {Bell, C and McIntyre, N and Cox, S and Tissue, D and Zak, J}, title = {Soil microbial responses to temporal variations of moisture and temperature in a chihuahuan desert grassland.}, journal = {Microbial ecology}, volume = {56}, number = {1}, pages = {153-167}, pmid = {18246293}, issn = {0095-3628}, mesh = {Bacteria/classification/*growth &amp; development/isolation &amp; purification ; Carbon/metabolism ; *Desert Climate ; Ecosystem ; Fungi/classification/*growth &amp; development/isolation &amp; purification ; Hydrogen-Ion Concentration ; Nitrogen/metabolism ; Poaceae/*growth &amp; development ; *Rain ; Seasons ; Soil/analysis ; *Soil Microbiology ; *Temperature ; Texas ; Water/analysis ; }, abstract = {Global climate change models indicate that storm magnitudes will increase in many areas throughout southwest North America, which could result in up to a 25% increase in seasonal precipitation in the Big Bend region of the Chihuahuan Desert over the next 50 years. Seasonal precipitation is a key limiting factor regulating primary productivity, soil microbial activity, and ecosystem dynamics in arid and semiarid regions. As decomposers, soil microbial communities mediate critical ecosystem processes that ultimately affect the success of all trophic levels, and the activity of these microbial communities is primarily regulated by moisture availability. This research is focused on elucidating soil microbial responses to seasonal and yearly changes in soil moisture, temperature, and selected soil nutrient and edaphic properties in a Sotol Grassland in the Chihuahuan Desert at Big Bend National Park. Soil samples were collected over a 3-year period in March and September (2004-2006) at 0-15 cm soil depth from 12 3 x 3 m community plots. Bacterial and fungal carbon usage (quantified using Biolog 96-well micro-plates) was related to soil moisture patterns (ranging between 3.0 and 14%). In addition to soil moisture, the seasonal and yearly variability of soil bacterial activity was most closely associated with levels of soil organic matter, extractable NH(4)-N, and soil pH. Variability in fungal activity was related to soil temperatures ranging between 13 and 26 degrees C. These findings indicate that changes in soil moisture, coupled with soil temperatures and resource availability, drive the functioning of soil-microbial dynamics in these desert grasslands. Temporal patterns in microbial activity may reflect the differences in the ability of bacteria and fungi to respond to seasonal patterns of moisture and temperature. Bacteria were more able to respond to moisture pulses regardless of temperature, while fungi only responded to moisture pulses during cooler seasons with the exception of substantial increased magnitudes in precipitation occurring during warmer months. Changes in the timing and magnitude of precipitation will alter the proportional contribution of bacteria and fungi to decomposition and nitrogen mineralization in this desert grassland.}, }
@article {pmid18242084, year = {2008}, author = {Gannoun, H and Khelifi, E and Bouallagui, H and Touhami, Y and Hamdi, M}, title = {Ecological clarification of cheese whey prior to anaerobic digestion in upflow anaerobic filter.}, journal = {Bioresource technology}, volume = {99}, number = {14}, pages = {6105-6111}, doi = {10.1016/j.biortech.2007.12.037}, pmid = {18242084}, issn = {0960-8524}, mesh = {*Anaerobiosis ; *Cheese ; *Ecology ; Industrial Waste ; Lactobacillus/metabolism ; }, abstract = {Anaerobic digestion of cheese whey wastewaters (CW) was investigated in a system consisting of an ecological pretreatment followed by upflow anaerobic filter (UAF). The pretreatment was conducted to solve the inhibition problems during anaerobic treatment of CW caused by the amounts of fats, proteins and carbohydrates and to avoid the major problems of clogging in the reactor. The optimized ecological pretreatment of diluted CW induce removal yields of 50% of chemical oxygen demand (COD) and 60% of total suspended solids (TSS) after acidification by Lactobacillus paracasei at 32 degrees C during 20 h and neutralization with lime. The pretreated CW was used to feed UAF (35 degrees C). The effects of organic loading rate (OLR) and hydraulic retention time (HRT) on the pretreated CW anaerobic degradation were examined. The average total COD removals achieved was 80-90%. The performance of the reactor was depressed by increasing the COD concentration to 20 g/l (OLR = 4 gCOD/ld) and the COD removal efficiency was reduced to 72%. Significant methane yield (280 l/kg COD removal) was obtained at an HRT of 2 days.}, }
@article {pmid18239608, year = {2008}, author = {Schloss, PD}, title = {Evaluating different approaches that test whether microbial communities have the same structure.}, journal = {The ISME journal}, volume = {2}, number = {3}, pages = {265-275}, doi = {10.1038/ismej.2008.5}, pmid = {18239608}, issn = {1751-7362}, mesh = {Cluster Analysis ; Computational Biology/*methods ; *Ecosystem ; *Environmental Microbiology ; *Monte Carlo Method ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {As microbial ecology investigations have progressed from descriptive characterizations of a community to hypothesis-driven ecological research, a number of different statistical techniques have been developed to describe and compare the structure of microbial communities. Thus far, these methods have only been evaluated using 16S rRNA gene sequence data obtained from incomplete characterizations of microbial communities. In this investigation, simulations were designed to test the statistical power of different methods to differentiate between communities with known memberships and structures. These simulations revealed three important results that affect how the results of the tests are interpreted. First, integral-LIBSHUFF, TreeClimber, UniFrac, analysis of molecular variance (AMOVA) and homogeneity of molecular variance (HOMOVA) compare the structure of communities and not just their memberships. Second, integral-LIBSHUFF is unable to detect cases when one community structure is a subset of another. Third, AMOVA determines whether the genetic diversity within two or more communities is greater than their pooled genetic diversity, and HOMOVA determines whether the amount of genetic diversity in each community is significantly different. integral-LIBSHUFF, TreeClimber and UniFrac lump these and other factors together when performing their analysis making it difficult to discern the nature of the differences that are detected between communities. These findings demonstrate that when correctly employed, the current statistical toolbox has the ability to address specific ecological questions concerning the differences between microbial communities.}, }
@article {pmid18232226, year = {2007}, author = {Cai, P and Huang, QY and Lu, YD and Chen, WL and Jiang, DH and Liang, W}, title = {Amplification of plasmid DNA bound on soil colloidal particles and clay minerals by the polymerase chain reaction.}, journal = {Journal of environmental sciences (China)}, volume = {19}, number = {11}, pages = {1326-1329}, doi = {10.1016/s1001-0742(07)60216-2}, pmid = {18232226}, issn = {1001-0742}, mesh = {Aluminum Silicates/*chemistry ; Animals ; Bentonite/chemistry ; Cattle ; Clay ; Colloids/*chemistry ; DNA, Bacterial/chemistry/genetics ; Iron Compounds/chemistry ; Kaolin/chemistry ; Minerals ; Plasmids/*chemistry/*genetics ; Polymerase Chain Reaction/*methods ; *Soil ; }, abstract = {Polymerase chain reaction (PCR) was used to amplify a 600-base pair (bp) sequence of plasmid pGEX-2T DNA bound on soil colloidal particles from Brown soil (Alfisol) and Red soil (Ultisol), and three different minerals (goethite, kaolinite, montmorillonite). DNA bound on soil colloids, kaolinite, and montmorillonite was not amplified when the complexes were used directly but amplification occurred when the soil colloid or kaolinite-DNA complex was diluted, 10- and 20-fold. The montmorillonite-DNA complex required at least 100-fold dilution before amplification could be detected. DNA bound on goethite was amplified irrespective of whether the complex was used directly, or diluted 10- and 20-fold. The amplification of mineral-bound plasmid DNA by PCR is, therefore, markedly influenced by the type and concentration of minerals used. This information is of fundamental importance to soil molecular microbial ecology with particular reference to monitoring the fate of genetically engineered microorganisms and their recombinant DNA in soil environments.}, }
@article {pmid18227962, year = {2008}, author = {Romaní, AM and Fund, K and Artigas, J and Schwartz, T and Sabater, S and Obst, U}, title = {Relevance of polymeric matrix enzymes during biofilm formation.}, journal = {Microbial ecology}, volume = {56}, number = {3}, pages = {427-436}, pmid = {18227962}, issn = {0095-3628}, mesh = {Acetylglucosaminidase/*metabolism ; Biofilms/*growth &amp; development ; Carbon/metabolism ; Cell Adhesion/physiology ; Extracellular Matrix/*enzymology ; Fresh Water ; Leucyl Aminopeptidase/*metabolism ; Nitrogen/metabolism ; Polysaccharides, Bacterial/metabolism ; Rivers ; beta-Glucosidase/*metabolism ; }, abstract = {Extracellular polymeric substances (EPS) contribute to biofilm stability and adhesion properties. The EPS matrix might also be a site for free extracellular enzyme activity; however, little is known about participation of enzyme activity in EPS during biofilm formation. In this study, we analyzed the activities of beta-glucosidase, leu-aminopeptidase, and beta-glucosaminidase during the colonization of artificial substrata (glass tiles) in a stream distinguishing enzyme activity in EPS matrix (matrix-enzymes) and total biofilm extracellular enzyme activity. The 1-h incubation of a biofilm suspension and cation-exchange resin followed by centrifugation seems appropriate to extract the matrix fraction (supernatant) and measure matrix enzymes (including free and linked to EPS) in freshwater biofilms, although there is a methodological limitation for using a biofilm suspension instead of an undisrupted biofilm. Total biofilm activities and matrix-enzyme activities showed similar capabilities to decompose organic matter compounds, with a greater capacity for peptide decomposition (leu-aminopeptidase) than for polysaccharides (beta-glucosidase), and a low decomposition of chitin and peptidoglycan (beta-glucosaminidase). Matrix-enzyme activity increased with colonization time, but more slowly than that of total enzyme activity. At the beginning of the colonization experiment (days 1-4) matrix enzymes accounted for 65-81% of total biofilm enzyme activity. Higher proportion of polysaccharides in EPS versus total biofilm, and higher matrix-enzyme activities per microgram of polysaccharides in the EPS were measured during the first 1-3 days of biofilm formation, indicating a high rate of enzyme release into the matrix during this period. Relative contribution of matrix-enzyme activities decreased as biofilm matures, but was maintained at 13-37% of total enzyme activity at the 42- to 49-day-old biofilm. These enzymes, retained and conserved in the EPS, may contribute to community metabolism. When analyzing extracellular enzymes in biofilms, the contribution of matrix enzymes must be considered, especially for young biofilms.}, }
@article {pmid18209965, year = {2008}, author = {De La Cochetière, MF and Durand, T and Lalande, V and Petit, JC and Potel, G and Beaugerie, L}, title = {Effect of antibiotic therapy on human fecal microbiota and the relation to the development of Clostridium difficile.}, journal = {Microbial ecology}, volume = {56}, number = {3}, pages = {395-402}, pmid = {18209965}, issn = {0095-3628}, mesh = {Adult ; Aged ; Amoxicillin-Potassium Clavulanate Combination/adverse effects/pharmacology ; Anti-Bacterial Agents/adverse effects/*pharmacology ; Base Sequence ; Clostridioides difficile/genetics/*growth &amp; development ; DNA, Bacterial/chemistry/genetics ; Discriminant Analysis ; Electrophoresis, Polyacrylamide Gel ; Enterocolitis, Pseudomembranous/microbiology ; Feces/*microbiology ; Female ; Gastrointestinal Tract/*drug effects/*microbiology ; Humans ; Male ; Middle Aged ; Molecular Sequence Data ; Polymerase Chain Reaction ; Pristinamycin/adverse effects/pharmacology ; RNA, Ribosomal, 16S/chemistry/genetics ; beta-Lactams/adverse effects/pharmacology ; }, abstract = {The gastrointestinal tract is a complex ecosystem. Recent studies have shown that the human fecal microbiota is composed of a consortium of microorganism. It is known that antibiotic treatment alters the microbiota, facilitating the proliferation of opportunists that may occupy ecological niches previously unavailable to them. It is therefore important to characterize resident microbiota to evaluate its latent ability to permit the development of pathogens such as Clostridium difficile. Using samples from 260 subjects enrolled in a previously published clinical study on antibiotic-associated diarrhea, we investigated the possible relationship between the fecal dominant resident microbiota and the subsequent development of C. difficile. We used molecular profiling of bacterial 16S rDNA coupled with partial least square (PLS) regression analysis. Fecal samples were collected on day 0 (D0) before antibiotic treatment and on day 14 (D14) after the beginning of the treatment. Fecal DNA was isolated, and V6-to-V8 regions of the 16S rDNA were amplified by polymerase chain reaction with general primers and analyzed by temporal temperature gradient gel electrophoresis (TTGE). Main bacteria profiles were compared on the basis of similarity (Pearson correlation coefficient). The characteristics of the microbiota were determined using PLS discriminant analysis model. Eighty-seven TTGE profiles on D0 have been analyzed. The banding pattern was complex in all cases. The subsequent onset of C. difficile was not revealed by any clustering of TTGE profiles, but was explained up to 46% by the corresponding PLS model. Furthermore, 6 zones out of the 438 dispatched from the TTGE profiles by the software happened to be specific for the group of patients who acquired C. difficile. The first approach in the molecular phylogenetic analysis showed related sequences to uncultured clones. As for the 87 TTGE profiles on D14, no clustering could be found either, but the subsequent onset of C. difficile was explained up to 74.5% by the corresponding PLS model, thus corroborating the results found on D0. The non exhaustive data of the microbiota we found should be taken as the first step to assess the hypothesis of permissive microbiota. The PLS model was used successfully to predict C. difficile development. We found that important criteria in terms of main bacteria could be markedly considered as predisposing factors for C. difficile development. Yet, the resident microbiota in case of antibiotic-associated diarrhea has still to be analyzed. Furthermore, these findings suggest that strategies reinforcing the ability of the fecal microbiota to resist to modifications would be of clinical relevance.}, }
@article {pmid18206774, year = {2008}, author = {Gounadaki, AS and Skandamis, PN and Drosinos, EH and Nychas, GJ}, title = {Microbial ecology of food contact surfaces and products of small-scale facilities producing traditional sausages.}, journal = {Food microbiology}, volume = {25}, number = {2}, pages = {313-323}, doi = {10.1016/j.fm.2007.10.001}, pmid = {18206774}, issn = {1095-9998}, mesh = {Animals ; Colony Count, Microbial ; Consumer Product Safety ; *Equipment Contamination ; Fermentation ; Food Contamination/*analysis ; Food Microbiology ; Food-Processing Industry/*standards ; Humans ; *Hygiene ; Listeria monocytogenes/growth &amp; development/isolation &amp; purification ; Meat Products/*microbiology/standards ; Risk Assessment ; Safety Management ; Salmonella/growth &amp; development/isolation &amp; purification ; Swine ; }, abstract = {The microbial status in 7 small-scale facilities (SSFs) producing traditional fermented and/or dry sausages was investigated. It was shown that the hygienic status of the processing environment and equipment plays an essential role in the microbial stability and safety of the final products. The current study revealed that the majority of the sampling sites (control points) tested were highly (>4 log CFU/cm(2)) contaminated by spoilage flora (i.e. Pseudomonas, Enterobacteriaceae), with knives, tables and mincing machines being the most heavily contaminated surfaces. Moreover, Listeria monocytogenes, Salmonella spp. and Staphylococcus aureus were detected in 11.7%, 26.4%, and 11.7% of the food contact surfaces, respectively. The presence of these pathogens seemed to be associated with high numbers of one or more specific groups of the 'house-flora' on the sampling sites of the facilities; however, high numbers of 'house-flora' do not always suggest the presence of pathogens. With regard to product samples, batter samples were heavily contaminated with the 'house-flora' present on surfaces and equipment of the processing facilities while by the end of processing (final products) LAB constituted the predominant microbial flora of all products. The low initial levels of S. aureus and Salmonella found in batter samples as well as the combination of hurdles (mainly a(w)<0.92, average pH ca. <5.0 and competitive effect of natural flora) in the final products were able to inhibit and/or eliminate these pathogens; however, the detection of L. monocytogenes in 3 out of the 7 final products examined is indicative of cross-contamination. Our findings further indicate that inadequate hygiene practices within small-scale-processing facilities may result in loss of microbial control. Therefore, this study addresses the need for strict control measures within SSFs producing traditional fermented sausages.}, }
@article {pmid18205822, year = {2008}, author = {van der Gast, CJ and Ager, D and Lilley, AK}, title = {Temporal scaling of bacterial taxa is influenced by both stochastic and deterministic ecological factors.}, journal = {Environmental microbiology}, volume = {10}, number = {6}, pages = {1411-1418}, doi = {10.1111/j.1462-2920.2007.01550.x}, pmid = {18205822}, issn = {1462-2920}, mesh = {Bacteria/*classification/*isolation &amp; purification ; *Biodiversity ; Bioreactors ; Colony Count, Microbial ; DNA Fingerprinting ; DNA, Bacterial/genetics ; *Ecology ; Industrial Waste ; Time Factors ; *Water Microbiology ; }, abstract = {Microorganisms operate at a range of spatial and temporal scales acting as key drivers of ecosystem properties. Therefore, many key questions in microbial ecology require the consideration of both spatial and temporal scales. Spatial scaling, in particular the species-area relationship (SAR), has a long history in ecology and has recently been addressed in microbial ecology. However, the temporal analogue of the SAR, the species-time relationship, has received far less attention even in the science of general ecology. Here we focus upon the role of temporal scaling in microbial ecological patterns by coupling molecular characterization of bacterial communities in discrete island (bioreactor) systems with a macroecological approach. Our findings showed that the temporal scaling exponent (slope), and therefore taxa turnover of the bacterial taxa-time relationship decreased as selective pressure (industrial wastewater concentration) increased. Also, as the concentration of industrial wastewater increased across the bioreactors, we observed a gradual switch from stochastic community assembly to more deterministic (niche)-based considerations. The identification of broad-scale statistical patterns is particularly relevant to microbial ecology, as it is frequently difficult to identify individual species or their functions. In this study, we identify wide-reaching statistical patterns of diversity and show that they are shaped by the prevalent underlying ecological factors.}, }
@article {pmid18205817, year = {2008}, author = {Kielak, A and Pijl, AS and van Veen, JA and Kowalchuk, GA}, title = {Differences in vegetation composition and plant species identity lead to only minor changes in soil-borne microbial communities in a former arable field.}, journal = {FEMS microbiology ecology}, volume = {63}, number = {3}, pages = {372-382}, doi = {10.1111/j.1574-6941.2007.00428.x}, pmid = {18205817}, issn = {0168-6496}, mesh = {Agriculture ; Asteraceae/growth &amp; development ; Bacteria/*classification/genetics ; Biodiversity ; DNA, Bacterial/analysis ; Ecosystem ; Electrophoresis/methods ; Lotus/growth &amp; development ; Magnoliopsida/*classification/*growth &amp; development ; Molecular Sequence Data ; Plant Roots/microbiology ; Poaceae/growth &amp; development ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {To examine the relationship between plant species composition and microbial community diversity and structure, we carried out a molecular analysis of microbial community structure and diversity in two field experiments. In the first experiment, we examined bacterial community structure in bulk and rhizosphere soils in fields exposed to different plant diversity treatments, via a 16S rRNA gene clone library approach. Clear differences were observed between bacterial communities of the bulk soil and the rhizosphere, with the latter containing lower bacterial diversity. The second experiment focused on the influence of 12 different native grassland plant species on bacterial community size and structure in the rhizosphere, as well as the structure of Acidobacteria and Verrucomicrobia community structures. In general, bacterial and phylum-specific quantitative PCR and PCR-denaturing gradient gel electrophoresis revealed only weak influences of plant species on rhizosphere communities. Thus, although plants did exert an influence on microbial species composition and diversity, these interactions were not specific and selective enough to lead to major impacts of vegetation composition and plant species on below-ground microbial communities.}, }
@article {pmid18205814, year = {2008}, author = {Rousk, J and Demoling, LA and Bahr, A and Bååth, E}, title = {Examining the fungal and bacterial niche overlap using selective inhibitors in soil.}, journal = {FEMS microbiology ecology}, volume = {63}, number = {3}, pages = {350-358}, doi = {10.1111/j.1574-6941.2008.00440.x}, pmid = {18205814}, issn = {0168-6496}, mesh = {Acetates/metabolism ; Anti-Bacterial Agents/pharmacology ; *Antibiosis ; Bacteria/drug effects/*growth &amp; development ; *Ecosystem ; Fungi/drug effects/*growth &amp; development ; Leucine/metabolism ; Medicago sativa/metabolism ; Oxygen Consumption ; Soil/analysis ; *Soil Microbiology ; }, abstract = {It is important to know the contributions of bacteria and fungi to decomposition in connection with both the structure of the food web and the functioning of the ecosystem. However, the extent of the competition between these groups of organisms is largely unknown. The bacterial influence on fungal growth in a soil system was studied by applying three different bacterial inhibitors - bronopol, tylosin and oxytetracycline - in a series of increasing concentrations, and comparing the resulting bacterial and fungal growth rates measured using leucine and acetate-in-ergosterol incorporation, respectively. Direct measurements of growth showed that fungi increased after adding inhibitors; the level of increase in fungal growth corresponded to that of the decrease in bacterial growth, irrespective of the bacterial inhibitor used. Similar antagonistic effects of the bacteria on fungal growth were also found after adding the bacterial inhibitors together with additional substrate (alfalfa or straw plant material). The resulting responses in bacterial and fungal growth indirectly indicated that the negative interaction between fungi and bacteria was mostly attributable to exploitation competition. The results of this study also emphasize the increased sensitivity of using growth-related, instead of biomass-based, measurements when studying bacterial and fungal interactions in soil.}, }
@article {pmid18204798, year = {2008}, author = {Adair, KL and Schwartz, E}, title = {Evidence that ammonia-oxidizing archaea are more abundant than ammonia-oxidizing bacteria in semiarid soils of northern Arizona, USA.}, journal = {Microbial ecology}, volume = {56}, number = {3}, pages = {420-426}, pmid = {18204798}, issn = {0095-3628}, mesh = {Ammonia/*metabolism ; Archaea/enzymology/genetics/*metabolism ; Arizona ; Bacteria/enzymology/genetics/*metabolism ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; Desert Climate ; Ecosystem ; Gene Dosage ; Linear Models ; Multivariate Analysis ; Oxidation-Reduction ; Oxidoreductases/genetics/*isolation &amp; purification/metabolism ; Polymerase Chain Reaction ; *Soil Microbiology ; }, abstract = {Autotrophic ammonia-oxidizing communities, which are responsible for the rate-limiting step of nitrification in most soils, have not been studied extensively in semiarid ecosystems. Abundances of soil archaeal and bacterial amoA were measured with real-time polymerase chain reaction along an elevation gradient in northern Arizona. Archaeal amoA was the predominant form of amoA at all sites; however, ratios of archaeal to bacterial amoA ranged from 17 to more than 1,600. Although size of ammonia-oxidizing bacteria populations was correlated with precipitation, temperature, percent sand, and soil C/N, there were no significant relationships between ammonia-oxidizing archaea populations and any of the environmental parameters evaluated in this study. Our results suggest that in these soils, archaea may be the primary ammonia oxidizers, and that ammonia-oxidizing archaea and ammonia-oxidizing bacteria occupy different niches.}, }
@article {pmid18203855, year = {2008}, author = {Rodrigues, DF and Tiedje, JM}, title = {Coping with our cold planet.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {6}, pages = {1677-1686}, pmid = {18203855}, issn = {1098-5336}, mesh = {Adaptation, Physiological/genetics/*physiology ; Bacteria/genetics/*growth &amp; development/metabolism ; Bacterial Proteins/genetics/metabolism ; *Cold Temperature ; *Earth, Planet ; Water/analysis ; }, }
@article {pmid18202885, year = {2008}, author = {Baudoin, JM and Guérold, F and Felten, V and Chauvet, E and Wagner, P and Rousselle, P}, title = {Elevated aluminium concentration in acidified headwater streams lowers aquatic hyphomycete diversity and impairs leaf-litter breakdown.}, journal = {Microbial ecology}, volume = {56}, number = {2}, pages = {260-269}, pmid = {18202885}, issn = {0095-3628}, mesh = {Aluminum/*analysis ; Biodegradation, Environmental ; Biomass ; *Ecosystem ; *Fagus ; Hydrogen-Ion Concentration ; Mitosporic Fungi/*classification/growth &amp; development ; Plant Leaves/*metabolism ; Principal Component Analysis ; *Rivers/chemistry/microbiology ; }, abstract = {Aquatic hyphomycetes play an essential role in the decomposition of allochthonous organic matter which is a fundamental process driving the functioning of forested headwater streams. We studied the effect of anthropogenic acidification on aquatic hyphomycetes associated with decaying leaves of Fagus sylvatica in six forested headwater streams (pH range, 4.3-7.1). Non-metric multidimensional scaling revealed marked differences in aquatic hyphomycete assemblages between acidified and reference streams. We found strong relationships between aquatic hyphomycete richness and mean Al concentration (r = -0.998, p < 0.0001) and mean pH (r = 0.962, p < 0.002), meaning that fungal diversity was severely depleted in acidified streams. By contrast, mean fungal biomass was not related to acidity. Leaf breakdown rate was drastically reduced under acidic conditions raising the issue of whether the functioning of headwater ecosystems could be impaired by a loss of aquatic hyphomycete species.}, }
@article {pmid18196313, year = {2008}, author = {Kato, S and Haruta, S and Cui, ZJ and Ishii, M and Igarashi, Y}, title = {Network relationships of bacteria in a stable mixed culture.}, journal = {Microbial ecology}, volume = {56}, number = {3}, pages = {403-411}, pmid = {18196313}, issn = {0095-3628}, mesh = {Bacillus/genetics/*growth &amp; development/metabolism ; Cellulose/metabolism ; Clostridium/genetics/*growth &amp; development/metabolism ; DNA, Bacterial/chemistry/genetics ; Polymerase Chain Reaction ; Symbiosis/physiology ; Xanthomonadaceae/genetics/*growth &amp; development/metabolism ; }, abstract = {We investigated the network relationships of bacteria in a structurally stable mixed culture degrading cellulose. The mixed culture consists of four bacterial strains (a cellulose-degrading anaerobe [strain S], a saccharide-utilizing anaerobe [strain F], a peptide- and acetate-utilizing aerobe [strain 3] and a peptide-, glucose-, and ethanol-utilizing aerobe [strain 5]). Interspecies interactions were examined by analyzing the effects of culture filtrates on the growth of the other strains and by comprehensively analyzing population dynamics in the mixed-culture systems with all possible combinations of the four bacterial strains. The persistence of strain S depends on the effects of strain 5. However, strain 5 is a disadvantaged strain because strain 3 has bacteriocidal activity on strain 5. The extinction of strain 5 is indirectly prevented by strain F that suppresses the growth of strain 3. Although strain F directly has suppressive effects on the growth of strain S, strain F is essential for the persistence of strain S, considering the indirect effects (maintaining strain 5, which is essential for the survival of strain S, by inhibiting strain 3). These indirect relationships form a bacterial network in which all the relationships including suppressive effects were well balanced to maintain the structural stability. In addition to direct metabolite interactions, such kind of indirect relationships could have a great impact on microbial community structure in the natural environment.}, }
@article {pmid18193419, year = {2008}, author = {Aelterman, P and Freguia, S and Keller, J and Verstraete, W and Rabaey, K}, title = {The anode potential regulates bacterial activity in microbial fuel cells.}, journal = {Applied microbiology and biotechnology}, volume = {78}, number = {3}, pages = {409-418}, doi = {10.1007/s00253-007-1327-8}, pmid = {18193419}, issn = {0175-7598}, mesh = {Acetates/metabolism ; *Bacterial Physiological Phenomena ; *Bioelectric Energy Sources ; Biomass ; Bioreactors ; Carbon Dioxide/metabolism ; Electricity ; Electrodes/*microbiology ; }, abstract = {The anode potential in microbial fuel cells controls both the theoretical energy gain for the microorganisms as the output of electrical energy. We operated three reactors fed with acetate continuously at a poised anode potential of 0 (R0), -200 (R(-200)) and -400 (R(-400)) mV versus Ag/AgCl and investigated the resulting bacterial activity. The anode potential had no influence on the start-up time of the three reactors. During a 31-day period, R(-200) produced 15% more charge compared to R0 and R(-400). In addition, R(-200) had the highest maximal power density (up to 199 W m(-3) total anode compartment during polarization) but the three reactors evolved to the same power density at the end of the experimental period. During polarization, only the current of R(-400) levelled off at an anode potential of -300 mV versus Ag/AgCl. The maximum respiration rate of the bacteria during batch tests was also considerably lower for R(-400). The specific biomass activity however, was the highest for R(-400) (6.93 g chemical oxygen demand g(-1) biomass-volatile suspended solids (VSS) d(-1) on day 14). This lowered during the course of the experiment due to an increase of the biomass concentration to an average level of 578+/-106 mg biomass-VSS L(-1) graphite granules for the three reactors. This research indicated that an optimal anode potential of -200 mV versus Ag/AgCl exists, regulating the activity and growth of bacteria to sustain an enhanced current and power generation.}, }
@article {pmid18193317, year = {2008}, author = {Meyer, B and Kuever, J}, title = {Phylogenetic diversity and spatial distribution of the microbial community associated with the Caribbean deep-water sponge Polymastia cf. corticata by 16S rRNA, aprA, and amoA gene analysis.}, journal = {Microbial ecology}, volume = {56}, number = {2}, pages = {306-321}, pmid = {18193317}, issn = {0095-3628}, mesh = {Alphaproteobacteria/classification/genetics/isolation &amp; purification ; Animals ; Archaea/classification/genetics/isolation &amp; purification ; Caribbean Region ; *Ecosystem ; Gammaproteobacteria/classification/genetics/isolation &amp; purification ; *Genetic Variation ; Geologic Sediments/microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/*genetics ; Oxidoreductases Acting on Sulfur Group Donors/*genetics ; *Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S/*genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Sulfur/metabolism ; }, abstract = {Denaturing gradient gel electrophoresis (DGGE)-based analyses of 16S rRNA, aprA, and amoA genes demonstrated that a phylogenetically diverse and complex microbial community was associated with the Caribbean deep-water sponge Polymastia cf. corticata Ridley and Dendy, 1887. From the 38 archaeal and bacterial 16S rRNA phylotypes identified, 53% branched into the sponge-specific, monophyletic sequence clusters determined by previous studies (considering predominantly shallow-water sponge species), whereas 26% appeared to be P. cf. corticata specifically associated microorganisms ("specialists"); 21% of the phylotypes were confirmed to represent seawater- and sediment-derived proteobacterial species ("contaminants") acquired by filtration processes from the host environment. Consistently, the aprA and amoA gene-based analyses indicated the presence of environmentally derived sulfur- and ammonia-oxidizers besides putative sponge-specific sulfur-oxidizing Gammaproteobacteria and Alphaproteobacteria and a sulfate-reducing archaeon. A sponge-specific, endosymbiotic sulfur cycle as described for marine oligochaetes is proposed to be also present in P. cf. corticata. Overall, the results of this work support the recent studies that demonstrated the sponge species specificity of the associated microbial community while the biogeography of the host collection site has only a minor influence on the composition. In P. cf. corticata, the specificity of the sponge-microbe associations is even extended to the spatial distribution of the microorganisms within the sponge body; distinct bacterial populations were associated with the different tissue sections, papillae, outer and inner cortex, and choanosome. The local distribution of a phylotype within P. cf. corticata correlated with its (1) phylogenetic affiliation, (2) classification as sponge-specific or nonspecifically associated microorganism, and (3) potential ecological role in the host sponge.}, }
@article {pmid18192551, year = {2008}, author = {Bhandari, SK and Xu, B and Nyachoti, CM and Giesting, DW and Krause, DO}, title = {Evaluation of alternatives to antibiotics using an Escherichia coli K88+ model of piglet diarrhea: effects on gut microbial ecology.}, journal = {Journal of animal science}, volume = {86}, number = {4}, pages = {836-847}, doi = {10.2527/jas.2006-822}, pmid = {18192551}, issn = {1525-3163}, mesh = {*Animal Feed ; Animal Nutritional Physiological Phenomena ; Animals ; Animals, Newborn/growth &amp; development ; Anti-Bacterial Agents/administration &amp; dosage/adverse effects ; Bacillus subtilis/physiology ; Colon/*microbiology ; DNA, Ribosomal/genetics ; Diarrhea/microbiology/prevention &amp; control/veterinary ; Enterotoxigenic Escherichia coli/*immunology/isolation &amp; purification/pathogenicity ; Escherichia coli Infections/prevention &amp; control/veterinary ; *Plasma ; Polymorphism, Restriction Fragment Length ; Probiotics ; Random Allocation ; Swine/*growth &amp; development ; Swine Diseases/microbiology/prevention &amp; control ; Weight Gain ; }, abstract = {Enterotoxigenic Escherichia coli is a major problem in the swine industry and results in scouring, increased mortality, and poor performance in the period immediately postweaning. The traditional way to control this problem is to include subtherapeutic antibiotics in the feed, but this is no longer acceptable to consumers; thus, alternatives to antibiotics are needed. One of the supplements that has been effective in reducing scouring in the absence of antibiotics is animal blood products produced from the rendering process. This is also becoming a problem because of concerns regarding the transfer of transmissible spongiform encephalopathies to humans from animals. In this research, we investigated the effects of spray-dried porcine plasma (SDPP), a Bacillus subtilis direct-fed microbial (DFM), a blend of organic acids, and sweeteners on E. coli-induced scouring. A total of 108 pigs of approximately 17 d of age were assigned to 6 treatments, with 3 pigs per pen, in 2 blocks, with each block having 3 replicates. The 2 blocks were initiated approximately 2 mo apart, because a sufficient number of pigs were not available that met our inclusion criteria in the first block. Diet 1 was a negative control containing no antibiotics (NC). Diet 2 was the positive control and included the same ingredient composition as NC except that antibiotics (110 mg/kg of chlortetracycline, 110 mg/kg of sulfamethazine, and 55 mg/kg of penicillin) were added (PC). Diet 3 was equal to the NC, but with a B. subtilis probiotic (DFM). Diet 4 was the NC to which SDPP was added. Diet 5 was the NC plus a combination of SDPP and DFM (SDPP + DFM). Diet 6 was the NC plus a combination of supplements, including SDPP and a blend of organic acids, DFM, and a sweetener (Blend). At 24 d of age, the pigs were experimentally infected with 6.3 x 10(9) cfu/mL of E. coli K88. All pigs were euthanized 7 d after infection and tissues were obtained for analysis. There were no significant differences among treatments for ADG, ADFI, G:F, plasma urea nitrogen, alpha-acid glycoprotein, tumor necrosis factor-alpha, intestinal ammonia, pH, or VFA. However, the PC and DFM treatments showed decreased (P < 0.05) scours at 24 h postinfection compared with the NC, SDPP, and SDPP + DFM diets. Mortality in the NC treatment, which did not contain antibiotics, was greater (P < 0.05) than in the other treatments. Terminal restriction fragment length polymorphism analysis of the 16S rDNA genes of digesta showed a greater incidence (P < 0.05) of Bacteroidetes in the PC and DFM diets than in the NC diet. When SDPP and DFM were included in the diet, the incidence of Bacteroidetes was also greater than in the NC diet (P < 0.05).}, }
@article {pmid18192423, year = {2008}, author = {Vanhaecke, L and Vercruysse, F and Boon, N and Verstraete, W and Cleenwerck, I and De Wachter, M and De Vos, P and van de Wiele, T}, title = {Isolation and characterization of human intestinal bacteria capable of transforming the dietary carcinogen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {5}, pages = {1469-1477}, pmid = {18192423}, issn = {1098-5336}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Base Sequence ; Carcinogens/*metabolism ; Chromatography, High Pressure Liquid ; Enterococcus faecium/genetics/*metabolism ; Feces/microbiology ; Fermentation ; Glycerol ; Humans ; Hydrogen-Ion Concentration ; Imidazoles/*metabolism ; Intestines/*microbiology ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is a carcinogenic heterocyclic aromatic amine formed in meat products during cooking. Although the formation of hazardous PhIP metabolites by mammalian enzymes has been extensively reported, research on the putative involvement of the human intestinal microbiota in PhIP metabolism remains scarce. In this study, the in vitro conversion of PhIP into its microbial derivate, 7-hydroxy-5-methyl-3-phenyl-6,7,8,9-tetrahydropyrido[3',2':4,5]imidazo[1,2-a]pyrimidin-5-ium chloride (PhIP-M1), by fecal samples from 18 human volunteers was investigated. High-performance liquid chromatography analysis showed that all human fecal samples transformed PhIP but with efficiencies ranging from 1.8 to 96% after 72 h of incubation. Two PhIP-transforming strains, PhIP-M1-a and PhIP-M1-b, were isolated from human feces and identified by fluorescent amplified fragment length polymorphism and pheS sequence analyses as Enterococcus faecium strains. Some strains from culture collections belonging to the species E. durans, E. avium, E. faecium, and Lactobacillus reuteri were also able to perform this transformation. Yeast extract, special peptone, and meat extract supported PhIP transformation by the enriched E. faecium strains, while tryptone, monomeric sugars, starch, and cellulose did not. Glycerol was identified as a fecal matrix constituent required for PhIP transformation. Abiotic synthesis of PhIP-M1 and quantification of the glycerol metabolite 3-hydroxypropionaldehyde (3-HPA) confirmed that the anaerobic fermentation of glycerol via 3-HPA is the critical bacterial transformation process responsible for the formation of PhIP-M1. Whether it is a detoxification is still a matter of debate, since PhIP-M1 has been shown to be cytotoxic toward Caco-2 cells but is not mutagenic in the Ames assay.}, }
@article {pmid18188535, year = {2008}, author = {Pumbwe, L and Skilbeck, CA and Wexler, HM}, title = {Presence of quorum-sensing systems associated with multidrug resistance and biofilm formation in Bacteroides fragilis.}, journal = {Microbial ecology}, volume = {56}, number = {3}, pages = {412-419}, pmid = {18188535}, issn = {0095-3628}, mesh = {Acyl-Butyrolactones/metabolism ; Bacteroides fragilis/genetics/growth &amp; development/*physiology ; Biofilms/*growth &amp; development ; Carbonyl Cyanide m-Chlorophenyl Hydrazone/pharmacology ; DNA, Bacterial/chemistry/genetics ; Drug Resistance, Multiple, Bacterial/*physiology ; Gene Expression Regulation, Bacterial ; Kinetics ; Microbial Sensitivity Tests ; Quorum Sensing/drug effects/*physiology ; RNA, Bacterial/chemistry/genetics ; RNA, Ribosomal, 16S/chemistry/genetics ; Repressor Proteins/genetics/*physiology ; Reverse Transcriptase Polymerase Chain Reaction ; Trans-Activators/genetics/*physiology ; Uncoupling Agents/pharmacology ; }, abstract = {Bacteroides fragilis constitutes 1-2% of the natural microbiota of the human digestive tract and is the predominant anaerobic opportunistic pathogen in gastrointestinal infections. Most bacteria use quorum sensing (QS) to monitor cell density in relation to other cells and their environment. In Gram-negative bacteria, the LuxRI system is common. The luxR gene encodes a transcriptional activator inducible by type I acyl-homoserine lactone autoinducers (e.g., N-[3-oxohexanoyl] homoserine lactone and hexanoyl homoserine lactone [C6-HSL]). This study investigated the presence of QS system(s) in B. fragilis. The genome of American-type culture collection strain no. ATCC25285 was searched for QS genes. The strain was grown to late exponential phase in the presence or absence of synthetic C6-HSL and C8-HSL or natural homoserine lactones from cell-free supernatants from spent growth cultures of other bacteria. Growth, susceptibility to antimicrobial agents, efflux pump gene (bmeB) expression, and biofilm formation were measured. Nine luxR and no luxI orthologues were found. C6-HSL and supernatants from Yersinia enterocolitica, Vibrio cholerae, and Pseudomonas aeruginosa caused a significant (1) reduction in cellular density and (2) increases in expression of four putative luxR genes, bmeB3, bmeB6, bmeB7, and bmeB10, resistance to various antibiotics, which was reduced by carbonyl cyanide-m-chlorophenyl hydrazone (CCCP, an uncoupler that dissipates the transmembrane proton gradient, which is also the driving force of resistance nodulation division efflux pumps) and (3) increase in biofilm formation. Susceptibility of ATCC25285 to C6-HSL was also reduced by CCCP. These data suggest that (1) B. fragilis contains putative luxR orthologues, which could respond to exogenous homoserine lactones and modulate biofilm formation, bmeB efflux pump expression, and susceptibility to antibiotics, and (2) BmeB efflux pumps could transport homoserine lactones.}, }
@article {pmid18183454, year = {2008}, author = {Scupham, AJ and Patton, TG and Bent, E and Bayles, DO}, title = {Comparison of the cecal microbiota of domestic and wild turkeys.}, journal = {Microbial ecology}, volume = {56}, number = {2}, pages = {322-331}, pmid = {18183454}, issn = {0095-3628}, mesh = {Animals ; Animals, Wild/*microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Cecum/*microbiology ; Cloning, Molecular ; DNA Fingerprinting/methods ; DNA, Bacterial/analysis/isolation &amp; purification ; Ecosystem ; Gene Library ; Genes, rRNA ; Immunoblotting ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Turkeys/*microbiology ; }, abstract = {The extent to which production methods alter intestinal microbial communities of livestock is currently unknown. As the intestinal microbiota may affect animal health, nutrition, and food safety, a baseline comparison of the cecal communities of domestic and wild turkeys was performed. Oligonucleotide fingerprinting of ribosomal RNA (rRNA) genes (OFRG) of 2,990 16S rRNA clones and dot blot quantification of dominant populations were used to identify the dominant bacterial taxa. Seventy-three percent of all the clones belonged to as yet uncultured genera. However, at a higher phylogenetic level, the OFRG library was composed of 54% Bacteroidetes clones (52% of the domestic library clones, 56% of the wild library clones), 30% Firmicutes clones (33% of the domestic library clones, 32% of the wild library clones), 3% Proteobacteria clones (5% domestic, 2% wild), and 3% Deferribacteres clones (4% domestic, 1% wild). Seven percent of the clones were unidentifiable (6% domestic, 9% wild). Bacteroidetes clones included the genera Alistipes, Prevotella, Megamonas, and Bacteroides. Of the Clostridiales clones, groups IV, IX, and XIV including genera Faecalibacterium, Megasphaera, Phascolarctobacterium, and Papillibacter were predominant. Lactobacillus, Enterococcus, and Streptococcus bacilli were also identified. beta- delta- and gamma-proteobacterial genera included Acinetobacter, Sutterella, and Escherichia. Deferribacteres clones showed high similarity to Mucispirillum schaedleri. Statistical comparison of the domestic and wild turkey clone libraries indicated similar levels of community richness and evenness despite the fact that the two libraries shared only 30% of the total clone operational taxonomic units. Together these results indicate that although high level taxonomic community structure is similar, high-density turkey production causes considerable divergence of the genera found in the ceca of commercial birds from those of their wild counterparts.}, }
@article {pmid18183453, year = {2008}, author = {Ruppel, S and Krumbein, A and Schreiner, M}, title = {Composition of the phyllospheric microbial populations on vegetable plants with different glucosinolate and carotenoid compositions.}, journal = {Microbial ecology}, volume = {56}, number = {2}, pages = {364-372}, pmid = {18183453}, issn = {0095-3628}, mesh = {Amaranthaceae/chemistry/microbiology ; Asteraceae/chemistry/microbiology ; Bacteria/genetics/growth &amp; development/isolation &amp; purification ; Brassica/chemistry/microbiology ; Carotenoids/*analysis ; Chromatography, High Pressure Liquid ; Colony Count, Microbial ; Glucosinolates/*analysis ; Plant Leaves/chemistry/microbiology ; RNA, Ribosomal, 16S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Species Specificity ; Vegetables/*chemistry/*microbiology ; }, abstract = {The plant phyllosphere is intensely colonized by a complex and highly diverse microbial population and shows pronounced plant-species-specific differences. The mechanisms and influencing factors determining whether and in which density microorganisms colonize plant phyllosphere tissues are not yet fully understood. One of the key influencing factors is thought to be phytochemical concentration and composition. Therefore, correlations between various concentrations of individual glucosinolates and carotenoids in four different plant species-Brassica juncea, Brassica campestris, Cichorium endivia, and Spinacea oleracea-and the phyllospheric bacterial population size associated with the aerial parts of the same plants were analyzed. The concentration of various individual glucosinolates and carotenoids were measured using high-performance liquid chromatography. The phyllospheric bacterial population size including both nonculturable and culturable organisms was assessed using quantitative real-time polymerase chain reaction, and the physiological profile of the culturable microbial community was analyzed using the Biolog system. Results show significant differences between plant species in both concentration and composition of secondary metabolites, bacterial population size, and microbial community composition in three consecutively performed experiments. An interesting and underlying trend was that bacterial density was positively correlated to concentrations of beta-carotene in the plant phyllosphere of the four plant species examined. Likewise, the alkenyl glucosinolates, 2-propenyl, 3-butenyl, and 4-pentenyl, concentrations were positively correlated to the bacterial population density, whereas the aromatic glucosinolate 2-phenylethyl showed a negative correlation to the phyllospheric bacterial population size. Thus, we report for the first time the relationship between individual glucosinolate and carotenoid concentrations and the phyllospheric bacterial population size of nonculturable and culturable organisms and the phyllospheric microbial physiological profiles.}, }
@article {pmid18181025, year = {2008}, author = {Pauwels, B and Wille, K and Noppe, H and De Brabander, H and Van de Wiele, T and Verstraete, W and Boon, N}, title = {17alpha-ethinylestradiol cometabolism by bacteria degrading estrone, 17beta-estradiol and estriol.}, journal = {Biodegradation}, volume = {19}, number = {5}, pages = {683-693}, doi = {10.1007/s10532-007-9173-z}, pmid = {18181025}, issn = {0923-9820}, mesh = {Chromatography, High Pressure Liquid ; Estradiol/*metabolism ; Estriol/*metabolism ; Estrone/*metabolism ; Ethinyl Estradiol/*metabolism ; Phylogeny ; Polymerase Chain Reaction ; Proteobacteria/classification/*metabolism ; }, abstract = {17alpha-ethinylestradiol (EE2), the active compound of the contraceptive pill, is a recalcitrant estrogen, which is encountered at ng/l levels in wastewater treatment plant (WWTP) effluents and rivers and can cause feminization of aquatic organisms. The aim of this study was to isolate micro-organisms that could remove such low EE2 concentrations. In this study, six bacterial strains were isolated from compost that co-metabolize EE2 when metabolizing estrone (E1), 17beta-estradiol (E2) and estriol (E3). The strains belong to the alpha, beta and gamma-Proteobacteria. All six strains metabolize E2 over E1, at microg/l to ng/l concentrations. In 4 days, initial concentrations of 0.5 microg E2/l and 0.6 microg EE2/l were degraded to 1.8 +/- 0.4 ng E2/l and 85 +/- 16 ng EE2/l, respectively. No other metabolites besides E1, E2, E3 or EE2 were detected, suggesting that total degradation and cleavage of the aromatic ring occurred. This is the first study describing that bacteria able to metabolize E2, can subsequently co-metabolize EE2 at low microg/l levels.}, }
@article {pmid18180751, year = {2008}, author = {Flint, HJ and Bayer, EA and Rincon, MT and Lamed, R and White, BA}, title = {Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis.}, journal = {Nature reviews. Microbiology}, volume = {6}, number = {2}, pages = {121-131}, doi = {10.1038/nrmicro1817}, pmid = {18180751}, issn = {1740-1534}, mesh = {Animals ; Bacteria, Anaerobic/classification/enzymology/*metabolism ; Bacterial Proteins/genetics/metabolism ; Cattle ; *Genomics ; Humans ; Intestine, Large/*microbiology ; Polysaccharides/*metabolism ; Rumen/*microbiology ; }, abstract = {The microbiota of the mammalian intestine depend largely on dietary polysaccharides as energy sources. Most of these polymers are not degradable by the host, but herbivores can derive 70% of their energy intake from microbial breakdown--a classic example of mutualism. Moreover, dietary polysaccharides that reach the human large intestine have a major impact on gut microbial ecology and health. Insight into the molecular mechanisms by which different gut bacteria use polysaccharides is, therefore, of fundamental importance. Genomic analyses of the gut microbiota could revolutionize our understanding of these mechanisms and provide new biotechnological tools for the conversion of polysaccharides, including lignocellulosic biomass, into monosaccharides.}, }
@article {pmid18180744, year = {2008}, author = {Defoirdt, T and Boon, N and Sorgeloos, P and Verstraete, W and Bossier, P}, title = {Quorum sensing and quorum quenching in Vibrio harveyi: lessons learned from in vivo work.}, journal = {The ISME journal}, volume = {2}, number = {1}, pages = {19-26}, doi = {10.1038/ismej.2007.92}, pmid = {18180744}, issn = {1751-7362}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Aquaculture ; Drug Resistance ; Furans/pharmacology ; Halogenation ; Lactones/pharmacology ; Penaeidae/*microbiology ; Quorum Sensing/*drug effects ; Vibrio/*drug effects/*metabolism/pathogenicity ; Virulence ; }, abstract = {Luminescent vibrios, bacteria belonging to the species Vibrio harveyi and closely related species, are important pathogens in aquaculture that can affect almost all types of cultured animals. Due to large-scale use of antibiotics, many luminescent vibrios have acquired (multiple) resistance, which render antibiotic treatments ineffective. One of the alternative strategies that has recently been developed to control infections caused by antibiotic-resistant bacteria is the disruption of quorum sensing, bacterial cell-to-cell communication. The quorum sensing system of V. harveyi has been studied quite intensively in vitro. Recent studies have been directed towards understanding the impact of quorum sensing and quorum sensing disruption on the virulence of luminescent vibrios towards different host organisms in vivo. This mini-review aims at discussing the current knowledge of quorum sensing in luminescent vibrios in vivo. Subsequently, quorum quenching by halogenated furanones is discussed and finally, some directions for further research are presented.}, }
@article {pmid18180743, year = {2008}, author = {Teske, A and Sørensen, KB}, title = {Uncultured archaea in deep marine subsurface sediments: have we caught them all?.}, journal = {The ISME journal}, volume = {2}, number = {1}, pages = {3-18}, doi = {10.1038/ismej.2007.90}, pmid = {18180743}, issn = {1751-7362}, mesh = {Archaea/*classification/*genetics/isolation &amp; purification ; DNA Primers ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Geologic Sediments/*microbiology ; Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Deep marine subsurface sediments represent a novel archaeal biosphere with unknown physiology; the sedimentary subsurface harbors numerous novel phylogenetic lineages of archaea that are at present uncultured. Archaeal 16S rRNA analyses of deep subsurface sediments demonstrate their global occurrence and wide habitat range, including deep subsurface sediments, methane seeps and organic-rich coastal sediments. These subsurface archaeal lineages were discovered by PCR of extracted environmental DNA; their detection ultimately depends on the specificity of the archaeal PCR 16S rRNA primers. Surprisingly high mismatch frequencies for some archaeal PCR primers result in amplification bias against the corresponding archaeal lineages; this review presents some examples. Obviously, most archaeal 16S rRNA PCR primers were developed either before the discovery of these deep subsurface archaeal lineages, or without taking their sequence variants into account. PCR surveys with multiple primer combinations, revision and updates of primers whenever possible, and increasing use of PCR-independent methods in molecular microbial ecology will contribute to a more comprehensive view of subsurface archaeal communities.}, }
@article {pmid18177506, year = {2007}, author = {Warnecke, F and Hugenholtz, P}, title = {Building on basic metagenomics with complementary technologies.}, journal = {Genome biology}, volume = {8}, number = {12}, pages = {231}, pmid = {18177506}, issn = {1474-760X}, mesh = {Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; *Genetics, Microbial ; Genomics/*methods ; }, abstract = {Metagenomics, the application of random shotgun sequencing to environmental samples, is a powerful approach for characterizing microbial communities. However, this method only represents the cornerstone of what can be achieved using a range of complementary technologies such as transcriptomics, proteomics, cell sorting and microfluidics. Together, these approaches hold great promise for the study of microbial ecology and evolution.}, }
@article {pmid18177367, year = {2008}, author = {Steger, D and Ettinger-Epstein, P and Whalan, S and Hentschel, U and de Nys, R and Wagner, M and Taylor, MW}, title = {Diversity and mode of transmission of ammonia-oxidizing archaea in marine sponges.}, journal = {Environmental microbiology}, volume = {10}, number = {4}, pages = {1087-1094}, doi = {10.1111/j.1462-2920.2007.01515.x}, pmid = {18177367}, issn = {1462-2920}, mesh = {Ammonia/metabolism ; Animals ; Archaeal Proteins/genetics ; Biodiversity ; Caribbean Region ; Crenarchaeota/*classification/genetics/metabolism ; Genes, Archaeal ; Larva/microbiology ; *Marine Biology ; Mediterranean Sea ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Pacific Ocean ; Phylogeny ; Porifera/growth &amp; development/metabolism/*microbiology ; Protein Subunits/genetics ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The model marine crenarchaeote 'Cenarchaeum symbiosum' is until now the only ammonia-oxidizing archaeon known from a marine sponge. Here, phylogenetic analyses based on the 16S rRNA and ammonia monooxygenase subunit A (amoA) genes revealed the presence of putative ammonia-oxidizing archaea (AOA) in a diverse range of sponges from the western Pacific, Caribbean and Mediterranean. amoA diversity was limited even between different oceans, with many of the obtained sequences (75.9%; n(total) = 83) forming a monophyletic, apparently sponge- (and coral-) specific lineage, analogous to those previously inferred from comparative 16S rRNA gene studies of sponge-associated microbes. The presence of AOA in sponge larvae, as detected by 16S rRNA and amoA PCR assays as well as by fluorescence in situ hybridization, suggests they are vertically transmitted and thus might be of importance for ammonia detoxification within the sponge.}, }
@article {pmid18176820, year = {2008}, author = {Bai, Y and Kosoy, MY and Ray, C and Brinkerhoff, RJ and Collinge, SK}, title = {Temporal and spatial patterns of Bartonella infection in black-tailed prairie dogs (Cynomys ludovicianus).}, journal = {Microbial ecology}, volume = {56}, number = {2}, pages = {373-382}, pmid = {18176820}, issn = {0095-3628}, mesh = {Animals ; *Animals, Wild/microbiology/physiology ; Bacteremia/epidemiology/microbiology/*veterinary ; Bartonella/classification/genetics/*isolation &amp; purification ; Bartonella Infections/epidemiology/microbiology/*veterinary ; Body Mass Index ; Colorado/epidemiology ; Female ; Host-Pathogen Interactions ; Male ; Population Density ; Prevalence ; Rodent Diseases/*epidemiology/microbiology ; *Sciuridae/microbiology/physiology ; Seasons ; }, abstract = {We describe the temporal dynamics and spatial distribution of Bartonella in black-tailed prairie dogs (Cynomys ludovicianus) based on a longitudinal study conducted in 20 black-tailed prairie dog (BTPD) colonies in Boulder County, CO from 2003 to 2005. Bartonella infection was widely distributed in all colonies with an overall prevalence of 23.1%, but varied by colony from 4.8% to 42.5% and by year from 9.1 to 39.0%, with a marked increase in Bartonella activity in 2005. Levels of bacteremia varied from 40 to 12,000 colony forming units (CFU) per milliliter of BTPD blood, but were highly skewed with a median of 240 CFU. Bartonella infection rates were unimodal with respect to BTPD body mass, first increasing among growing juveniles, then declining among adults. Infection rates exhibited a sigmoidal response to body mass, such that 700g may prove to be a useful threshold value to evaluate the likelihood of Bartonella infection in BTPDs. Bartonella prevalence increased throughout the testing season for each year, as newly emerged juveniles developed bacteremia. Data from recaptured animals suggest that Bartonella infections did not persist in individual BTPDs, which may explain the relatively low prevalence of Bartonella in BTPDs compared to other rodent species. No association was found between Bartonella prevalence and host population density. Prevalence did not differ between males and females. The spatio-temporal pattern of Bartonella infection among colonies suggests epizootic spread from northern to central and southern portions of the study area. The potential significance of the BTPD-associated Bartonella for public health needs to be further investigated.}, }
@article {pmid19277109, year = {2008}, author = {Walk, ST and Young, VB}, title = {Emerging Insights into Antibiotic-Associated Diarrhea and Clostridium difficile Infection through the Lens of Microbial Ecology.}, journal = {Interdisciplinary perspectives on infectious diseases}, volume = {2008}, number = {}, pages = {125081}, pmid = {19277109}, issn = {1687-708X}, support = {R01 DK070875/DK/NIDDK NIH HHS/United States ; }, abstract = {Antibiotics are the main, and often only, clinical intervention for prophylactic and active treatment of bacterial infections in humans. Perhaps it is not surprising that these drugs also shift the composition of commensal bacteria inside our bodies, especially those within the gut microbial community (microbiota). How these dynamics ultimately affect the function of the gut microbiota, however, is not fully appreciated. Likewise, how antibiotic induced changes facilitate the outgrowth and pathogenicity of certain bacterial strains remains largely enigmatic. Here, we discuss the merits of a microbial ecology approach toward understanding a common side effect of antibiotic use, antibiotic-associated diarrhea (AAD), and the opportunistic bacterial infections that sometimes underlie it. As an example, we discuss how this approach is being used to address complex disease dynamics during Clostridium difficile infection.}, }
@article {pmid19277102, year = {2008}, author = {Huys, G and Vanhoutte, T and Vandamme, P}, title = {Application of sequence-dependent electrophoresis fingerprinting in exploring biodiversity and population dynamics of human intestinal microbiota: what can be revealed?.}, journal = {Interdisciplinary perspectives on infectious diseases}, volume = {2008}, number = {}, pages = {597603}, pmid = {19277102}, issn = {1687-708X}, abstract = {Sequence-dependent electrophoresis (SDE) fingerprinting techniques such as denaturing gradient gel electrophoresis (DGGE) have become commonplace in the field of molecular microbial ecology. The success of the SDE technology lays in the fact that it allows visualization of the predominant members of complex microbial ecosystems independent of their culturability and without prior knowledge on the complexity and diversity of the ecosystem. Mainly using the prokaryotic 16S rRNA gene as PCR amplification target, SDE-based community fingerprinting turned into one of the leading molecular tools to unravel the diversity and population dynamics of human intestinal microbiota. The first part of this review covers the methodological concept of SDE fingerprinting and the technical hurdles for analyzing intestinal samples. Subsequently, the current state-of-the-art of DGGE and related techniques to analyze human intestinal microbiota from healthy individuals and from patients with intestinal disorders is surveyed. In addition, the applicability of SDE analysis to monitor intestinal population changes upon nutritional or therapeutic interventions is critically evaluated.}, }
@article {pmid19277099, year = {2008}, author = {O'Toole, PW and Cooney, JC}, title = {Probiotic bacteria influence the composition and function of the intestinal microbiota.}, journal = {Interdisciplinary perspectives on infectious diseases}, volume = {2008}, number = {}, pages = {175285}, pmid = {19277099}, issn = {1687-708X}, abstract = {Probiotics have a range of proposed health benefits for the consumer, which may include modulating the levels of beneficial elements in the microbiota. Recent investigations using molecular approaches have revealed a human intestinal microbiota comprising over 1000 phylotypes. Mechanisms whereby probiotics impact on the intestinal microbiota include competition for substrates, direct antagonism by inhibitory substances, competitive exclusion, and potentially host-mediated effects such as improved barrier function and altered immune response. We now have the microbial inventories and genetic blueprints to begin tackling intestinal microbial ecology at an unprecedented level of detail, aided by the understanding that dietary components may be utilized differentially by individual phylotypes. Controlled intervention studies in humans, utilizing latest molecular technologies, are required to consolidate evidence for bacterial species that impact on the microbiota. Mechanistic insights should be provided by metabolomics and other analytical techniques for small molecules. Rigorous characterization of interactions between the diet, microbiota, and probiotic bacteria will provide new opportunities for modulating the microbiota towards improving human health.}, }
@article {pmid18165875, year = {2008}, author = {Wright, AD and Ma, X and Obispo, NE}, title = {Methanobrevibacter phylotypes are the dominant methanogens in sheep from Venezuela.}, journal = {Microbial ecology}, volume = {56}, number = {2}, pages = {390-394}, pmid = {18165875}, issn = {0095-3628}, mesh = {Animals ; DNA, Archaeal/analysis ; DNA, Ribosomal/analysis ; Electrophoresis, Polyacrylamide Gel ; Female ; Genes, rRNA ; Male ; Methanobacterium/classification/genetics/isolation &amp; purification ; Methanobrevibacter/*classification/genetics/*isolation &amp; purification ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; Sheep/*microbiology ; Venezuela ; }, abstract = {Rumen methanogens in sheep from Venezuela were examined using 16S rRNA gene libraries and denaturing gradient gel electrophoresis (DGGE) profiles prepared from pooled and individual PCR products from the rumen contents from 10 animals. A total of 104 clones were examined, revealing 14 different 16S rRNA gene sequences or phylotypes. Of the 14 phylotypes, 13 (99 of 104 clones) belonged to the genus Methanobrevibacter, indicating that the genus Methanobrevibacter is the most dominant component of methanogen populations in sheep in Venezuela. The largest group of clones (41 clones) was 97.9-98.5% similar to Methanobrevibacter gottschalkii. Two sequences were identified as possible new species, one belonging to the genus Methanobrevibacter and the other belonging to the genus Methanobacterium. DGGE analysis of the rumen contents from individual animals also revealed 14 different bands with a range of 4-9 bands per animal.}, }
@article {pmid18165874, year = {2008}, author = {Jones, MD and Singleton, DR and Carstensen, DP and Powell, SN and Swanson, JS and Pfaender, FK and Aitken, MD}, title = {Effect of incubation conditions on the enrichment of pyrene-degrading bacteria identified by stable-isotope probing in an aged, PAH-contaminated soil.}, journal = {Microbial ecology}, volume = {56}, number = {2}, pages = {341-349}, pmid = {18165874}, issn = {0095-3628}, support = {5 P42 ES05948/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics/*growth &amp; development/metabolism ; Carbon Isotopes/metabolism ; DNA, Bacterial/analysis/isolation &amp; purification ; Genes, rRNA ; Molecular Sequence Data ; Nitrogen/metabolism ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Pyrenes/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {To determine whether the diversity of pyrene-degrading bacteria in an aged polycyclic aromatic hydrocarbon-contaminated soil is affected by the addition of inorganic nutrients or by slurrying the soil, various incubation conditions (all including phosphate buffer) were examined by mineralization studies and stable-isotope probing (SIP). The addition of nitrogen to either continuously mixed slurry or static field-wet soil incubations increased the rate and extent of mineralization of [(14)C]pyrene, with the most rapid mineralization observed in slurried, nitrogen-amended soil. Microcosms of slurry and static field-wet soil amended with nitrogen were also examined by SIP with [U-(13)C]pyrene. Recovered (13)C-enriched deoxyribonucleic acid (DNA) was analyzed by denaturing-gradient gel electrophoresis (DGGE) and 16S ribosomal ribonucleic acid (rRNA) gene clone libraries. DGGE profiles of (13)C-enriched DNA fractions from both incubation conditions were similar, suggesting that pyrene-degrading bacterial community diversity may be independent of treatment method. The vast majority (67 of 71) of the partial sequences recovered from clone libraries were greater than or equal to 97% similar to one another, 98% similar to sequences of pyrene-degrading bacteria previously detected by SIP with pyrene in different soil, and only 89% similar to the closest cultivated genus. All of the sequences recovered from the field-wet incubation and most of the sequences recovered from the slurry incubation were in this clade. Of the four sequences from slurry incubations not within this clade, three possessed greater than 99% similarity to the 16S rRNA gene sequences of phylogenetically dissimilar Caulobacter spp.}, }
@article {pmid18165873, year = {2008}, author = {Carrillo, P and Villar-Argaiz, M and Medina-Sánchez, JM}, title = {Does microorganism stoichiometry predict microbial food web interactions after a phosphorus pulse?.}, journal = {Microbial ecology}, volume = {56}, number = {2}, pages = {350-363}, pmid = {18165873}, issn = {0095-3628}, mesh = {Animals ; *Bacteria/growth &amp; development/metabolism ; *Ciliophora/growth &amp; development/metabolism ; Ecosystem ; *Eukaryota/growth &amp; development/metabolism ; *Food Chain ; Fresh Water/microbiology/parasitology ; Heterotrophic Processes ; Nitrogen/metabolism ; Phosphorus/*metabolism ; Seasons ; Spain ; }, abstract = {Knowledge of variations in microbial food web interactions resulting from atmospheric nutrient loads is crucial to improve our understanding of aquatic food web structure in pristine ecosystems. Three experiments mimicking atmospheric inputs at different nitrogen/phosphorus (N/P) ratios were performed in situ covering the seasonal biological succession of the pelagic zone in a high-mountain Spanish lake. In all experiments, abundance, biomass, algal cell biovolume, P-incorporation rates, P-cell quota, and N/P ratio of algae strongly responded to P-enrichment, whereas heterotrophic bacteria remained relatively unchanged. Ciliates were severely restricted when a strong algal exploitation of the available P (bloom growth or storage strategies) led to transient (mid-ice-free experiment) or chronic (late ice-free experiment) P-deficiencies in bacteria. In contrast, maximum development of ciliates was reached when bacteria remained P-rich (N/P < 20) and algae approached Redfield proportions (N/P approximately 16). Evidence of a higher P-incorporation rate supports the proposition that algae and bacteria shifted from a mainly commensalistic-mutualistic to a competitive relationship for the available P when bacterial P-deficiency increased, as reflected by their unbalanced N/P ratio (N/P > 20-24). Hence, the bacterial N/P ratio proved be a key factor to understand the algae-bacteria relationship and microbial food web development. This study not only demonstrates the interdependence of life history strategies, stoichiometric nutrient content, and growth but also supports the use of bacterial N/P thresholds for diagnosing ciliate development, a little-studied aspect worthy of further attention.}, }
@article {pmid18160481, year = {2008}, author = {Barman, M and Unold, D and Shifley, K and Amir, E and Hung, K and Bos, N and Salzman, N}, title = {Enteric salmonellosis disrupts the microbial ecology of the murine gastrointestinal tract.}, journal = {Infection and immunity}, volume = {76}, number = {3}, pages = {907-915}, pmid = {18160481}, issn = {1098-5522}, support = {R01 AI057757/AI/NIAID NIH HHS/United States ; R21 AI057757/AI/NIAID NIH HHS/United States ; AI057757/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification/genetics ; *Biodiversity ; Colony Count, Microbial ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; *Ecosystem ; Female ; Gastrointestinal Tract/*microbiology/pathology ; Genomic Islands ; In Situ Hybridization, Fluorescence ; Lethal Dose 50 ; Male ; Mice ; Mutation ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Salmonella Infections, Animal/*microbiology ; Salmonella typhimurium/*physiology ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {The commensal microbiota protects the murine host from enteric pathogens. Nevertheless, specific pathogens are able to colonize the intestinal tract and invade, despite the presence of an intact biota. Possibly, effective pathogens disrupt the indigenous microbiota, either directly through pathogen-commensal interaction, indirectly via the host mucosal immune response to the pathogen, or by a combination of these factors. This study investigates the effect of peroral Salmonella enterica serovar Typhimurium infection on the intestinal microbiota. Since the majority of the intestinal microbiota cannot be cultured by conventional techniques, molecular approaches using 16S rRNA sequences were applied. Several major bacterial groups were assayed using quantitative PCR. Administration of either the 50% lethal dose (LD(50)) or 10x LD(50) of Salmonella enterica serovar Typhimurium caused changes in the microbiota throughout the intestinal tract over the time course of infection. A 95% decrease in total bacterial number was noted in the cecum and large intestine with 10x LD(50) S. enterica serovar Typhimurium challenge at 7 days postinfection, concurrent with gross evidence of diarrhea. In addition, alterations in microbiota composition preceded the onset of diarrhea, suggesting the involvement of pathogen-commensal interactions and/or host responses unrelated to diarrhea. Microbiota alterations were not permanent and reverted to the microbiota of uninfected mice by 1 month postinfection. Infection with a Salmonella pathogenicity island 1 (SPI1) mutant did not result in microbiota alterations, while SPI2 mutant infections triggered partial changes. Neither mutant was capable of prolonged colonization or induction of mucosal inflammation. These data suggest that several Salmonella virulence factors, particularly those involved in the local mucosal host response, are required for disruption of the intestinal ecosystem.}, }
@article {pmid18159390, year = {2002}, author = {Allard, DG}, title = {The 'farm to plate' approach to food safety - Everyone's business.}, journal = {The Canadian journal of infectious diseases = Journal canadien des maladies infectieuses}, volume = {13}, number = {3}, pages = {185-190}, pmid = {18159390}, issn = {1180-2332}, abstract = {Food safety is growing in importance as a public health concern for health practitioners and the general public. The Canadian public is exposed more extensively than ever before to exotic foods and pathogens via international travel, changing lifestyles and domestic contact with fresh foodstuff that is imported from faraway lands. Global warming, changing microbial ecology and resistance, and reduced host immunity are also having their effect in increasing the risk. To manage the risk adequately, interventions must be implemented at every point of the food supply chain, from production and processing to distribution, preparation and consumption, at home and in retail food service establishments. The role of government is explained, and the roles of other stakeholders, including physicians, are reviewed briefly.}, }
@article {pmid18159282, year = {2000}, author = {Griffiths, MW}, title = {How novel methods can help discover more information about foodborne pathogens.}, journal = {The Canadian journal of infectious diseases = Journal canadien des maladies infectieuses}, volume = {11}, number = {3}, pages = {142-153}, pmid = {18159282}, issn = {1180-2332}, abstract = {Considerable emphasis is being placed on quantitative risk assessment modelling as a basis for regulation of trade in food products. However, for models to be accurate, information about the behaviour of potential pathogens in foods needs to be available. The question is how to obtain this knowledge in a simple and cost effective way. One technique that has great potential is the use of reporter bacteria which have been genetically modified to express a phenotype that can be easily monitored, such as light production in luminescent organisms. Bacteria carrying these (lux) genes can easily be detected using simple luminometers or more sophisticated low light imaging equipment.By monitoring light output from these bacteria over time, it can easily be determined if the organism is growing (resulting in an increase in light emission), is dead (causing a decrease in light production) or is injured (light output remains constant). The use of imaging systems allows the response of bioluminescent bacteria to be studied directly on the food, making the technique even more useful. Applications of bioluminescence are discussed below and include use as reporters of gene expression; biocide efficacy and antibiotic susceptibility; sub-lethal injury; adhesion and biofilm formation; the microbial ecology of foods; pathogenesis; and as biosensors.}, }
@article {pmid18156331, year = {2008}, author = {Xing, D and Ren, N and Rittmann, BE}, title = {Genetic diversity of hydrogen-producing bacteria in an acidophilic ethanol-H2-coproducing system, analyzed using the [Fe]-hydrogenase gene.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {4}, pages = {1232-1239}, pmid = {18156331}, issn = {1098-5336}, mesh = {Alcohol Dehydrogenase/genetics ; Base Composition ; Base Sequence ; Cluster Analysis ; DNA Primers/genetics ; Electrophoresis ; Ethanol/*metabolism ; Fermentation ; *Genetic Variation ; Gram-Positive Endospore-Forming Rods/*genetics/*metabolism ; Hydrogen/*metabolism ; Molasses ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Hydrogen gas (H2) produced by bacterial fermentation of biomass can be a sustainable energy source. The ability to produce H2 gas during anaerobic fermentation was previously thought to be restricted to a few species within the genera Clostridium and Enterobacter. This work reports genomic evidence for the presence of novel H2-producing bacteria (HPB) in acidophilic ethanol-H2-coproducing communities that were enriched using molasses wastewater. The majority of the enriched dominant populations in the acidophilic ethanol-H2-coproducing system were affiliated with low-G+C-content gram-positive bacteria, Bacteroidetes, and Actinobacteria, based on the 16S rRNA gene. However, PCR primers designed to specifically target bacterial hydA yielded 17 unique hydA sequences whose amino acid sequences differed from those of known HPB. The putative ethanol-H2-coproducing bacteria comprised 11 novel phylotypes closely related to Ethanoligenens harbinense, Clostridium thermocellum, and Clostridium saccharoperbutylacetonicum. Furthermore, analysis of the alcohol dehydrogenase isoenzyme also pointed to an E. harbinense-like organism, which is known to have a high conversion rate of carbohydrate to H2 and ethanol. We also found six novel HPB that were associated with lactate-, propionate-, and butyrate-oxidizing bacteria in the acidophilic H2-producing sludge. Thus, the microbial ecology of mesophilic and acidophilic H2 fermentation involves many other bacteria in addition to Clostridium and Enterobacter.}, }
@article {pmid18097714, year = {2008}, author = {Munshi, TK and Chattoo, BB}, title = {Bacterial population structure of the jute-retting environment.}, journal = {Microbial ecology}, volume = {56}, number = {2}, pages = {270-282}, pmid = {18097714}, issn = {0095-3628}, mesh = {Bacteria/*classification/genetics/*growth &amp; development/metabolism ; Biodegradation, Environmental ; Cloning, Molecular ; Culture Media ; DNA, Bacterial/analysis/isolation &amp; purification ; DNA, Ribosomal ; *Ecosystem ; Gene Library ; Genes, rRNA ; In Situ Hybridization, Fluorescence ; India ; Malvaceae/*metabolism/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {Jute is one of the most versatile bast fibers obtained through the process of retting, which is a result of decomposition of stalks by the indigenous microflora. However, bacterial communities associated with the retting of jute are not well characterized. To investigate the presence of microorganisms during the process of jute retting, full-cycle rRNA approach was followed, and two 16S rRNA gene libraries, from jute-retting locations of Krishnanagar and Barrackpore, were constructed. Phylotypes affiliating to seven bacterial divisions were identified in both libraries. The bulk of clones came from Proteobacteria (approximately 37, 41%) and a comparatively smaller proportion of clones from the divisions-Firmicutes (approximately 11, 12%), Cytophaga-Flexibacter-Bacteroidetes group (CFB; approximately 9, 7%), Verrucomicrobia (approximately 6, 5%), Acidobacteria (approximately 4, 5%), Chlorobiales (approximately 5, 5%), and Actinobacteria (approximately 4, 2%) were identified. Percent coverage value and diversity estimations of phylotype richness, Shannon-Weiner index, and evenness confirmed the diverse nature of both the libraries. Evaluation of the retting waters by whole cell rRNA-targeted flourescent in situ hybridization, as detected by domain- and group-specific probes, we observed a considerable dominance of the beta-Proteobacteria (25.9%) along with the CFB group (24.4%). In addition, 32 bacterial species were isolated on culture media from the two retting environments and identified by 16S rDNA analysis, confirming the presence of phyla, Proteobacteria (approximately 47%), Firmicutes (approximately 22%), CFB group (approximately 19%), and Actinobacteria (approximately 13%) in the retting niche. Thus, our study presents the first quantification of the dominant and diverse bacterial phylotypes in the retting ponds, which will further help in improving the retting efficiency, and hence the fiber quality.}, }
@article {pmid18095440, year = {2007}, author = {Martínez, AJ and Bossio, CP and Durango, AC and Vanegas, MC}, title = {Characterization of Shiga toxigenic Escherichia coli isolated from foods.}, journal = {Journal of food protection}, volume = {70}, number = {12}, pages = {2843-2846}, doi = {10.4315/0362-028x-70.12.2843}, pmid = {18095440}, issn = {0362-028X}, mesh = {Colombia ; Escherichia coli O157/genetics/isolation &amp; purification/metabolism ; Food Contamination/*analysis ; Food Microbiology ; Meat Products/*microbiology ; Mutation ; Polymerase Chain Reaction/*methods ; Prevalence ; Shiga Toxin 1/biosynthesis/genetics ; Shiga Toxin 2/biosynthesis/genetics ; Shiga Toxins/biosynthesis/*genetics ; Shiga-Toxigenic Escherichia coli/genetics/*isolation &amp; purification/metabolism ; }, abstract = {The aim of this study was to characterize Shiga toxigenic Escherichia coli (STEC) by PCR using strains isolated from ham, beef, and cattle in Colombia. A total of 189 E. coli strains were tested for the presence of the uidA, stx1, and stx2 genes, and identification was confirmed by the automated PCR BAX system for E. coli O157:H7. Genes encoding Shiga-like toxins (stx) were found in eight (6.06%) of 132 strains previously isolated from minced beef; four (50%) of these strains yielded amplification products for both toxin genes (stx1 and stx2), and four (50%) yielded products only for the stx2 toxin. None of the strains analyzed were positive by PCR for the presence of the single base-pair mutation in the uidA gene from E. coli O157:H7; these results were confirmed by the BAX system analysis. A multiplex PCR assay was standardized for the three genes. Results from this study confirmed previous data about the low prevalence of E. coli O157:H7 and Shiga-like toxins in Colombia and is the first known report of the prevalence of non-O157 enterohemorrhagic E. coli in this country.}, }
@article {pmid18095016, year = {2008}, author = {Przybył, K and Karolewski, P and Oleksyn, J and Labedzki, A and Reich, PB}, title = {Fungal diversity of Norway spruce litter: effects of site conditions and premature leaf fall caused by bark beetle outbreak.}, journal = {Microbial ecology}, volume = {56}, number = {2}, pages = {332-340}, pmid = {18095016}, issn = {0095-3628}, mesh = {Animals ; Fungi/*classification/isolation &amp; purification ; Phenols/analysis ; Picea/*microbiology ; Plant Bark/*parasitology ; Plant Diseases/parasitology ; Plant Leaves/chemistry/metabolism/*microbiology ; Poland ; Seasons ; Trees ; Weevils/classification/*physiology ; }, abstract = {Fungi play an important role in leaf litter decomposition due to their ability to break down the lignocellulose matrix, which other organisms are unable to digest. However, little is known regarding the factors affecting components of fungal diversity. Here, we quantified richness of internal fungi in relation to litter nutrient and phenolic concentrations, sampling season (spring or fall), and premature leaf shedding due to low precipitation and infestation of bark beetles (mainly Ips typographus and Ips duplicatus). The study was conducted in 37-year-old Norway spruce [Picea abies (L.) Karst.] stands, with three plots each in mixed forest (MF) and coniferous forest (CF) site conditions in south-central Poland. Fifty-four species of sporulating fungi were identified in 2,330 freshly fallen needles sampled during 2003-2005, including 45 species in MF and 31 in CF. The significantly higher number of species in MF was likely related to moister conditions at that site. Among isolated fungi, 22% (12 species) were identified as endophytes of Norway spruce in prior studies. During spring of 2005, we found less than half the number of isolates and fungal species at each forest site as compared to fall for the two prior years. This pattern was observed in typical soil fungi (e.g., Penicillium daleae, Penicillium purpurogenum) and endophytes/epiphytes (e.g., Aureobasidium pullulans, Alternaria alternata, Cladosporium spp., and Lophodermium piceae). Premature shedding of needles was the most likely cause of this decline because it shortened the time period for fungi to infect green needles while on the tree. For all sites and sampling periods, richness of internal fungi was strongly and positively related to the age of freshly fallen litter (assessed using needle Ca concentration as a needle age tracer) and was also negatively related to litter phenolic concentration. Richness of internal fungi in freshly fallen litter may be adversely affected by low soil moisture status, natural inhibitors slowing fungal colonization (e.g., phenolics) and biotic (e.g., insect infestation) and abiotic (e.g., drought) factors that shorten leaf life span.}, }
@article {pmid18085514, year = {2008}, author = {Jacobs, DM and Deltimple, N and van Velzen, E and van Dorsten, FA and Bingham, M and Vaughan, EE and van Duynhoven, J}, title = {(1)H NMR metabolite profiling of feces as a tool to assess the impact of nutrition on the human microbiome.}, journal = {NMR in biomedicine}, volume = {21}, number = {6}, pages = {615-626}, doi = {10.1002/nbm.1233}, pmid = {18085514}, issn = {0952-3480}, mesh = {Cross-Over Studies ; Double-Blind Method ; Feces/*chemistry/*microbiology ; Female ; Flavonoids/*administration &amp; dosage ; Humans ; Intestinal Mucosa/*metabolism ; Intestines/drug effects/*microbiology ; Magnetic Resonance Spectroscopy/*methods ; Male ; Middle Aged ; Nutritional Physiological Phenomena/drug effects/*physiology ; Phenols/*administration &amp; dosage ; Polyphenols ; Protons ; }, abstract = {Current research increasingly recognizes the human gut microbiome as a metabolically versatile biological 'digester' that plays an essential role in regulating the host metabolome. Gut microbiota recover energy and biologically active molecules from food that would otherwise be washed out of the intestinal tract without benefit. In this study, a protocol for NMR-based metabolite profiling has been developed to access the activity of the microbiome. The physicochemical properties of fecal metabolites have been found to strongly affect the reproducibility and coverage of the profiles obtained. Metabolite profiles generated by water and methanol extraction of lyophilized feces are reproducible and comprise a variety of different compounds including, among others, short-chain fatty acids (e.g. acetate, propionate, butyrate, isobutyrate, isovalerate, malate), organic acids (e.g. succinate, pyruvate, fumarate, lactate), amino acids, uracil, trimethylamine, ethanol, glycerol, glucose, phenolic acids, cholate, and lipid components. The NMR profiling approach was validated on fecal samples from a double-blinded, placebo-controlled, randomized cross-over study, in which healthy human subjects consumed a placebo and either a grape juice extract or a mix of grape juice and wine extract over a period of 4 weeks, each. The considerable inter- and intra-individual variability observed originates in the first instance from variable metabolite concentrations rather than from variable metabolite compositions, suggesting that different colonic flora share general biochemical characteristics metabolizing different substrates to specific metabolic patterns. Whereas the grape juice extract did not induce changes in the metabolite profiles as compared with the placebo, the mixture of grape juice and wine extract induced a reduction in isobutyrate, which may indicate that polyphenols are able to modulate the microbial ecology of the gut.}, }
@article {pmid18083877, year = {2008}, author = {Isenbarger, TA and Finney, M and Ríos-Velázquez, C and Handelsman, J and Ruvkun, G}, title = {Miniprimer PCR, a new lens for viewing the microbial world.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {3}, pages = {840-849}, pmid = {18083877}, issn = {1098-5336}, support = {F32 AI065067/AI/NIAID NIH HHS/United States ; F32AI065067/AI/NIAID NIH HHS/United States ; }, mesh = {Computational Biology ; DNA Primers/*genetics ; DNA, Archaeal/analysis/genetics ; DNA, Bacterial/analysis/genetics ; DNA-Directed DNA Polymerase/*genetics ; Escherichia coli/genetics ; Gene Library ; Geologic Sediments/*microbiology ; Halobacterium/genetics ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Taq Polymerase/genetics ; }, abstract = {Molecular methods based on the 16S rRNA gene sequence are used widely in microbial ecology to reveal the diversity of microbial populations in environmental samples. Here we show that a new PCR method using an engineered polymerase and 10-nucleotide "miniprimers" expands the scope of detectable sequences beyond those detected by standard methods using longer primers and Taq polymerase. After testing the method in silico to identify divergent ribosomal genes in previously cloned environmental sequences, we applied the method to soil and microbial mat samples, which revealed novel 16S rRNA gene sequences that would not have been detected with standard primers. Deeply divergent sequences were discovered with high frequency and included representatives that define two new division-level taxa, designated CR1 and CR2, suggesting that miniprimer PCR may reveal new dimensions of microbial diversity.}, }
@article {pmid18080704, year = {2008}, author = {Maira, MA and Sebastian, MA and Sergi, RM and Elena, GT and Amils, R and Gaju, N}, title = {Spatial heterogeneity of bacterial populations in monomictic Lake Estanya (Huesca, Spain).}, journal = {Microbial ecology}, volume = {55}, number = {4}, pages = {737-750}, pmid = {18080704}, issn = {0095-3628}, mesh = {Bacteria/cytology/*genetics/growth &amp; development ; DNA, Bacterial/genetics ; Ecosystem ; Electrophoresis, Gel, Pulsed-Field ; Fresh Water/*chemistry/*microbiology ; Genes, Bacterial ; Genes, rRNA ; Microscopy, Phase-Contrast ; Molecular Sequence Data ; Polymorphism, Restriction Fragment Length ; Population Dynamics ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; Spain ; Time Factors ; *Water Microbiology ; }, abstract = {Bacterial population changes were investigated in the monomictic Lake Estanya by combining microscopic analysis and two molecular methods involving the amplification of 16S rDNA genes using primers for the domain Bacteria and subsequent restriction fragment length polymorphism (PCR-RFLP) and denaturing gradient gel electrophoresis (PCR-DGGE). Both approaches revealed the vertical distribution of predominant microbial morphotypes and phylotypes in both holomictic and stratified periods, respectively, and showed that variations in structure and composition of bacterial populations are occurring in this lake as a function of depth and time. Through principal component analysis (PCA), these shifts could be related to different physicochemical parameters with temperature, oxygen concentration, and the incident light being of paramount importance as structuring variables. Comparison of RFLP and DGGE profiles by scoring similarities using the Jaccard coefficient and then building a multidimensional scaling map (MDS) showed equivalent results. Both techniques revealed that bacterial populations, present in the whole water column in the holomictic period, showed a high similarity with those located in the deeper part of the lake in the stratified period, evidencing that other factors, both biotic and abiotic, should also be considered as a force driving change in the composition of the bacterial community. Furthermore, DGGE analysis showed that sequences from prominent bands were affiliated to members of four major phyla of the domain Bacteria: Cyanobacteria, Bacteroidetes, Proteobacteria, and Actinobacteria, most of which corresponded to heterotrophic bacterial populations involved in carbon, sulfide, and nitrogen biogeochemical cycles, which were indistinguishable under the light microscope.}, }
@article {pmid18080156, year = {2008}, author = {Wilson, MS and Siering, PL and White, CL and Hauser, ME and Bartles, AN}, title = {Novel archaea and bacteria dominate stable microbial communities in North America's Largest Hot Spring.}, journal = {Microbial ecology}, volume = {56}, number = {2}, pages = {292-305}, pmid = {18080156}, issn = {0095-3628}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {*Archaea/classification/genetics/growth &amp; development/isolation &amp; purification ; *Bacteria/classification/genetics/growth &amp; development/isolation &amp; purification ; California ; Cloning, Molecular ; DNA, Ribosomal/analysis ; *Ecosystem ; Fungi/classification/genetics/growth &amp; development/isolation &amp; purification ; Gene Library ; Genes, rRNA ; Hot Springs/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {Boiling Springs Lake is an approximately 12,000 m(2), 55 degrees C, pH 2 thermal feature located in Lassen Volcanic National Park in northern California, USA. We assessed the microbial diversity in the lake by analyzing approximately 500 sequences from clone libraries constructed using three different primer sets targeted at 16S rRNA genes and one targeted at 18S rRNA genes. We assessed the stability of the microbial community by constructing terminal restriction fragment length polymorphism (T-RFLP) profiles using DNA extracts collected in four separate years over a 7-year period. The four most prevalent phylotypes in the clone libraries shared an average approximately 85% sequence identity with their closest cultured relatives, and three fourths of the prokaryotic sequences shared less than 91% identity. Phylogenetic analyses revealed novel lineages devoid of cultivated representatives in the Bacterial and Archaeal domains. Many detected phylotypes were related to taxonomically diverse genera previously associated with high-temperature environments, while others were related to diverse Proteobacteria and Firmicutes that would not be expected to grow within BSL conditions. All of the 18S rRNA sequences most closely matched fungi in the phyla Ascomycota and Basidiomycota (91-99% identity). T-RFLP detected fragments corresponding to the most prevalent phylotypes detected in 16S rRNA gene libraries. The T-RFLPs from separate years were similar, and the water-derived T-RFLPs were similar to the sediment-derived (average pairwise Sorenson's similarity index of 0.74, and 0.78, respectively). Collectively, these results indicate that a stable community of diverse novel microorganisms exists in Boiling Springs Lake.}, }
@article {pmid18077539, year = {2008}, author = {Kunin, V and He, S and Warnecke, F and Peterson, SB and Garcia Martin, H and Haynes, M and Ivanova, N and Blackall, LL and Breitbart, M and Rohwer, F and McMahon, KD and Hugenholtz, P}, title = {A bacterial metapopulation adapts locally to phage predation despite global dispersal.}, journal = {Genome research}, volume = {18}, number = {2}, pages = {293-297}, pmid = {18077539}, issn = {1088-9051}, mesh = {Adaptation, Biological/*genetics ; Bacteria/*genetics/*virology ; Bacteriophages/*genetics ; Base Sequence ; Computational Biology/methods ; Demography ; Gene Components ; Gene Expression Profiling ; *Genetics, Population ; Microarray Analysis ; Molecular Sequence Data ; *Phylogeny ; Population Dynamics ; Queensland ; Sequence Analysis, DNA ; Sewage/*microbiology ; Wisconsin ; }, abstract = {Using a combination of bacterial and phage-targeted metagenomics, we analyzed two geographically remote sludge bioreactors enriched in a single bacterial species Candidatus Accumulibacter phosphatis (CAP). We inferred unrestricted global movement of this species and identified aquatic ecosystems as the primary environmental reservoirs facilitating dispersal. Highly related and geographically remote CAP strains differed principally in genomic regions encoding phage defense mechanisms. We found that CAP populations were high density, clonal, and nonrecombining, providing natural targets for "kill-the-winner" phage predation. Community expression analysis demonstrated that phages were consistently active in the bioreactor community. Genomic signatures linking CAP to past phage exposures were observed mostly between local phage and host. We conclude that CAP strains disperse globally but must adapt to phage predation pressure locally.}, }
@article {pmid18076003, year = {2007}, author = {Dinamarca, MA and Cereceda-Balic, F and Fadic, X and Seeger, M}, title = {Analysis of s-triazine-degrading microbial communities in soils using most-probable-number enumeration and tetrazolium-salt detection.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {10}, number = {3}, pages = {209-215}, pmid = {18076003}, issn = {1139-6709}, mesh = {Biodegradation, Environmental ; Biotechnology/methods ; Colony Count, Microbial ; *Ecosystem ; Herbicides/*metabolism ; Oxidation-Reduction ; Pseudomonas/classification/growth &amp; development/*metabolism ; *Soil Microbiology ; Tetrazolium Salts/*metabolism ; Triazines/*metabolism ; }, abstract = {A simple and sensitive method for the detection and enumeration of microbial s-triazine-degrading microorganisms in soil was designed. The procedure is based on the ability of some microbes to use s-triazines, such as simazine, atrazine, and cyanuric acid, as sole nitrogen source. It employs the respiration indicator 2,3,5-triphenyl-2H-tetrazolium chloride (TTC) to detect metabolic activity and the most-probable-number (MPN) enumeration in microtiter plates. The method was used to identify simazine- and cyanuric acid-degrading activities in agricultural soils treated with the herbicide simazine. The MPN-TTC method showed that the number of simazine- and cyanuric acid-degrading microorganisms increased four weeks after the herbicide simazine had been applied.}, }
@article {pmid18075710, year = {2008}, author = {Ohene-Adjei, S and Chaves, AV and McAllister, TA and Benchaar, C and Teather, RM and Forster, RJ}, title = {Evidence of increased diversity of methanogenic archaea with plant extract supplementation.}, journal = {Microbial ecology}, volume = {56}, number = {2}, pages = {234-242}, pmid = {18075710}, issn = {0095-3628}, mesh = {Animals ; Cinnamomum zeylanicum/chemistry ; DNA, Archaeal/analysis ; DNA, Ribosomal/analysis ; Ecosystem ; Female ; Garlic/chemistry ; Genes, rRNA ; *Genetic Variation ; Methane/*metabolism ; *Methanobacteriaceae/classification/drug effects/genetics/growth &amp; development ; Molecular Sequence Data ; Phylogeny ; Plant Oils/administration &amp; dosage/*pharmacology ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sequence Analysis, DNA ; Sheep ; }, abstract = {This study evaluated the effects of selected essential oils on archaeal communities using the ovine rumen model. Forty weaned Canadian Arcott ewes, fed with barley-based diet, were allotted to one of three essential oil supplementation treatments or a control (10 ewes per treatment) for 13 weeks. The treatments were cinnamaldehyde, garlic oil, juniper berry oil, and a control with no additive. Rumen content was sampled after slaughter and grouped by treatment by combining subsamples from each animal. DNA was extracted from the pooled samples and analyzed for methanogenic archaea using quantitative polymerase chain reaction, denaturing gradient gel electrophoresis, cloning, and sequencing. Our results suggest that the total copy number of archaeal 16S rRNA was not significantly affected by the treatments. The phylogenetic analysis indicated a trend toward an increased diversity of methanogenic archaea related to Methanosphaera stadtmanae, Methanobrevibacter smithii, and some uncultured groups with cinnamaldehyde, garlic, and juniper berry oil supplementation. The trends in the diversity of methanogenic archaea observed with the essential oil supplementation may have resulted from changes in associated protozoal species. Supplementation of ruminant diets with essential oils may alter the diversity of rumen methanogens without affecting the methanogenic capacity of the rumen.}, }
@article {pmid18074169, year = {2008}, author = {Delille, D and Coulon, F}, title = {Comparative mesocosm study of biostimulation efficiency in two different oil-amended sub-antarctic soils.}, journal = {Microbial ecology}, volume = {56}, number = {2}, pages = {243-252}, pmid = {18074169}, issn = {0095-3628}, mesh = {Antarctic Regions ; Bacteria/*growth &amp; development/metabolism ; Biodegradation, Environmental ; *Ecosystem ; Fertilizers ; *Gasoline ; Hydrocarbons/*metabolism ; *Petroleum/metabolism ; Rosaceae/growth &amp; development ; Soil/analysis ; *Soil Microbiology ; Soil Pollutants/metabolism ; Temperature ; }, abstract = {Biological treatment has become increasingly popular as a remediation method for soils and groundwater contaminated with petroleum hydrocarbon, chlorinated solvents, and pesticides. Bioremediation has been considered for application in cold regions such as Arctic and sub-Arctic climates and Antarctica. Studies to date suggest that indigenous microbes suitable for bioremediation exist in soils in these regions. This paper reports on two case studies at the sub-Antarctic Kerguelen Island in which indigenous bacteria were found that were capable of mineralizing petroleum hydrocarbons in soil contaminated with crude oil and diesel fuel. All results demonstrate a serious influence of the soil properties on the biostimulation efficiency. Both temperature elevation and fertilizer addition have a more significant impact on the microbial assemblages in the mineral soil than in the organic one. Analysis of the hydrocarbons remaining at the end of the experiments confirmed the bacterial observations. Optimum temperature seems to be around 10 degrees C in organic soil, whereas it was higher in mineral soil. The benefit of adding nutrients was much stronger in mineral than in the organic soil. Overall, this study suggests that biostimulation treatments were driven by soil properties and that ex situ bioremediation for treatment of cold contaminated soils will allow greater control over soil temperature, a limiting factor in cold climates.}, }
@article {pmid18074129, year = {2008}, author = {Lee, C and Lee, S and Shin, SG and Hwang, S}, title = {Real-time PCR determination of rRNA gene copy number: absolute and relative quantification assays with Escherichia coli.}, journal = {Applied microbiology and biotechnology}, volume = {78}, number = {2}, pages = {371-376}, doi = {10.1007/s00253-007-1300-6}, pmid = {18074129}, issn = {0175-7598}, mesh = {Escherichia coli/genetics ; *Gene Dosage ; *Genes, rRNA ; Polymerase Chain Reaction/*methods ; Reproducibility of Results ; Transferases/genetics ; }, abstract = {Real-time polymerase chain reaction (PCR)-based methodology for the determination of rRNA gene (rrn) copy number was introduced and demonstrated. Both absolute and relative quantifications were tested with Escherichia coli. The separate detection of rRNA gene and chromosomal DNA was achieved using two primer sets, specific for 16S rRNA gene and for D-1-deoxyxylulose 5-phosphate synthase gene (dxs), respectively. As dxs is a single-copy gene of E. coli chromosomal DNA, the rrn copy number can be determined as the copy ratio of rrn to dxs. This methodology was successfully applied to determine the rrn copy number in E. coli cells. The results from absolute and relative quantifications were identical and highly reproducible with coefficient of variation (CV) values of 1.8-4.6%. The estimated rrn copy numbers also corresponded to the previously reported value in E. coli (i.e., 7), indicating that the results were reliable. The methodology introduced in this study is faster and cost-effective without safety problems compared to the traditionally used Southern blot analysis. The fundamentals in our methodology would be applicable to any microorganism, as long as having the sequence information of the rRNA gene and another chromosomal gene with a known copy number.}, }
@article {pmid18070032, year = {2008}, author = {Defoirdt, T and Verstraete, W and Bossier, P}, title = {Luminescence, virulence and quorum sensing signal production by pathogenic Vibrio campbellii and Vibrio harveyi isolates.}, journal = {Journal of applied microbiology}, volume = {104}, number = {5}, pages = {1480-1487}, doi = {10.1111/j.1365-2672.2007.03672.x}, pmid = {18070032}, issn = {1365-2672}, mesh = {Animals ; Artemia/microbiology ; Homoserine/analogs &amp; derivatives/analysis ; Lactones/analysis ; Luminescence ; Microbial Viability ; Quorum Sensing ; Species Specificity ; Vibrio/pathogenicity/*physiology ; Virulence ; }, abstract = {AIMS: To study the relationship between luminescence, autoinducer production and virulence of pathogenic vibrios.<br><br>METHODS AND RESULTS: Luminescence, quorum sensing signal production and virulence towards brine shrimp nauplii of 13 Vibrio campbellii and Vibrio harveyi strains were studied. Although only two of the tested strains were brightly luminescent, all of them were shown to produce the three different types of quorum sensing signals known to be produced by Vibrio harveyi. Cell-free culture fluids of all strains significantly induced bioluminescence in the cholerae autoinducer 1, autoinducer 2 and harveyi autoinducer 1 reporter strains JAF375, JMH597 and JMH612, respectively. There was no relation between luminescence and signal production and virulence towards brine shrimp.<br><br>CONCLUSIONS: There is a large difference between different strains of Vibrio campbellii and Vibrio harveyi with respect to bioluminescence. However, this is not reflected in signal production and virulence towards gnotobiotic brine shrimp. Moreover, there seems to be no relation between quorum sensing signal production and virulence towards brine shrimp.<br><br>The results presented here indicate that strains that are most brightly luminescent are not necessarily the most virulent ones and that the lower virulence of some of the strains is not due to a lack of autoinducer production.}, }
@article {pmid18066486, year = {2008}, author = {Vladár, P and Rusznyák, A and Márialigeti, K and Borsodi, AK}, title = {Diversity of sulfate-reducing bacteria inhabiting the rhizosphere of Phragmites australis in Lake Velencei (Hungary) revealed by a combined cultivation-based and molecular approach.}, journal = {Microbial ecology}, volume = {56}, number = {1}, pages = {64-75}, pmid = {18066486}, issn = {0095-3628}, mesh = {Colony Count, Microbial ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Desulfotomaculum/classification/genetics/growth &amp; development ; Desulfovibrio/classification/genetics/growth &amp; development ; Fresh Water/*microbiology ; *Genetic Variation ; Hungary ; Hydrogensulfite Reductase/genetics ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Plant Roots/*microbiology ; Poaceae/*microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Sulfates/*metabolism ; Sulfur-Reducing Bacteria/*classification/genetics/growth &amp; development ; }, abstract = {The community structure of sulfate-reducing bacteria (SRB) associated with reed (Phragmites australis) rhizosphere in Lake Velencei (Hungary) was investigated by using cultivation-based and molecular methods. The cultivation methods were restricted to recover lactate-utilizing species with the exclusion of Desulfobacter and some Desulfobacterium species presumably not being dominant members of the examined community. The most-probable-number (MPN) estimations of lactate-utilizing SRB showed that the cell counts in reed rhizosphere were at least one order of magnitude higher than that in the bulk sediment. The number of endospores was low compared to the total SRB counts. From the highest positive dilution of MPN series, 47 strains were isolated and grouped by restriction fragment length polymorphism (RFLP) analysis of the amplified 16S ribosomal RNA (rRNA) and dsrAB (dissimilatory sulfite reductase) genes. Contrary to the physiological diversity of the isolates, the combined results of RFLP analysis revealed higher diversity at species as well as at subspecies level. Based on the partial 16S rRNA sequences, the representative strains were closely affiliated with the genera Desulfovibrio and Desulfotomaculum. The partial dsrAB sequences of the clones, recovered after isolation and PCR amplification of the community DNA, were related to hitherto uncultured species of the genera Desulfovibrio and Desulfobulbus. Nevertheless, the representative of the second largest clone group was shown to be closely affiliated with the sequenced dsrAB gene of a strain isolated from the same environment and identified as Desulfovibrio alcoholivorans. Another clone sequence was closely related to a possible novel species also isolated within the scope of this work.}, }
@article {pmid18066485, year = {2008}, author = {Winter, C and Moeseneder, MM and Herndl, GJ and Weinbauer, MG}, title = {Relationship of geographic distance, depth, temperature, and viruses with prokaryotic communities in the eastern tropical Atlantic Ocean.}, journal = {Microbial ecology}, volume = {56}, number = {2}, pages = {383-389}, pmid = {18066485}, issn = {0095-3628}, mesh = {*Archaea/genetics/isolation &amp; purification/virology ; Atlantic Ocean ; *Bacteria/genetics/isolation &amp; purification/virology ; Chlorophyll/analysis ; DNA, Archaeal/analysis ; DNA, Bacterial/analysis ; Deoxyribonucleases, Type II Site-Specific ; *Ecosystem ; Geography ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Seasons ; *Seawater/chemistry/microbiology/virology ; Sodium Chloride/analysis ; Temperature ; }, abstract = {The richness and biogeographical distribution pattern of bacterial and archaeal communities was assessed by terminal restriction fragment length polymorphism analysis of polymerase chain reaction-amplified fragments of the 16S rRNA gene at the surface (15-25 m depth), in the deep chlorophyll maximum layer (DCM; 50 m depth), and deep waters (75-1000 m depth) of the eastern tropical Atlantic Ocean. Additionally, prokaryotic and viral abundance and the frequency of infected prokaryotic cells (FIC) were determined along with physico-chemical parameters to identify factors influencing prokaryotic richness and biogeography. Viral abundance was highest in the DCM layer averaging 45.5 x 10(6) ml(-1), whereas in the mixed surface layer and in the waters below the DCM, average viral abundance was 11.3 x 10(6) and 4.3 x 10(6) ml(-1), respectively. The average estimate of FIC was 8.3% in the mixed surface layer and the DCM and 2.4% in deeper waters. FIC was positively related to prokaryotic and viral abundance and negatively to archaeal richness. There was no detectable effect of geographic distance (maximum distance between stations approximately 4600 km) or differences between water masses on bacterial and archaeal community composition. Bacterial communities showed a clear depth zonation, whereas changes in archaeal community composition were related to temperature and FIC. The results indicate that planktonic archaeal virus host systems are a dynamic component of marine ecosystems under natural conditions.}, }
@article {pmid18062325, year = {2007}, author = {Chen, YX and Ding, Y and Han, ZY and Wu, WX}, title = {[Research advances in microbial ecology of biofilter and biotrickling filter for waste gases treatment].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {18}, number = {9}, pages = {2133-2138}, pmid = {18062325}, issn = {1001-9332}, mesh = {*Air Microbiology ; Air Pollutants/*metabolism ; Air Pollution/*prevention &amp; control ; Biodegradation, Environmental ; Biofilms ; *Ecology ; Filtration/instrumentation ; }, abstract = {Waste gases biofiltration is an emerging technology, and has played important roles in air pollution control. In this paper, the structure of biofilter and biotrickling filter and their mechanisms in air pollution removal were introduced, with focus on the research advances in the isolation and identification of microbes in the filters, correlations between microbial abundance, activity and community diversity, influences of operation conditions on microbial community, spatiotemporal change patterns of microbial community structure during operation, development of biofilm, and biodegrading dynamic models. The research perspectives in microbial ecology during biofiltration of waste gases were discussed.}, }
@article {pmid18060602, year = {2008}, author = {Ma, J and Van Wambeke, M and Carballa, M and Verstraete, W}, title = {Improvement of the anaerobic treatment of potato processing wastewater in a UASB reactor by co-digestion with glycerol.}, journal = {Biotechnology letters}, volume = {30}, number = {5}, pages = {861-867}, doi = {10.1007/s10529-007-9617-x}, pmid = {18060602}, issn = {1573-6776}, mesh = {Anaerobiosis ; *Bioreactors ; Fatty Acids, Volatile/metabolism ; Fermentation ; *Food Handling ; Glycerol/*metabolism ; Methane/metabolism ; Oxygen/metabolism ; Solanum tuberosum/metabolism ; Time Factors ; Waste Disposal, Fluid/*methods ; }, abstract = {The effect of three different types of glycerol on the performance of up-flow anaerobic sludge blanket (UASB) reactors treating potato processing wastewater was investigated. High COD removal efficiencies were obtained in both control and supplemented UASB reactors (around 85%). By adding 2 ml glycerol product per liter of raw wastewater, the biogas production could be increased by 0.74 l biogas ml(-1) glycerol product, which leads to energy values in the range of 810-1270 kWh(electric) per m(3) product. Moreover, a better in-reactor biomass yield was observed for the supplemented UASB reactor (0.012 g VSS g(-1) COD(removed)) compared to the UASB control (0.002 g VSS g(-1) COD(removed)), which suggests a positive effect of glycerol on the sludge blanket growth.}, }
@article {pmid18060449, year = {2008}, author = {Zachow, C and Tilcher, R and Berg, G}, title = {Sugar beet-associated bacterial and fungal communities show a high indigenous antagonistic potential against plant pathogens.}, journal = {Microbial ecology}, volume = {55}, number = {1}, pages = {119-129}, pmid = {18060449}, issn = {0095-3628}, support = {L 312/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Antibiosis ; Aphanomyces/growth &amp; development/pathogenicity ; Ascomycota/growth &amp; development/pathogenicity ; *Bacteria/classification/genetics/growth &amp; development/isolation &amp; purification ; Beta vulgaris/*microbiology ; *Ecosystem ; *Fungi/classification/genetics/growth &amp; development/isolation &amp; purification ; Molecular Sequence Data ; Plant Diseases/*microbiology ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Polymorphism, Single-Stranded Conformational ; Pythium/growth &amp; development/pathogenicity ; RNA, Ribosomal, 16S/genetics ; Rhizoctonia/growth &amp; development/pathogenicity ; Sequence Analysis, DNA ; }, abstract = {The aim of this study was to analyze microbial communities in/on sugar beet with special focus on antagonists toward plant pathogens. For this purpose, the composition of microorganisms isolated from the rhizosphere, phyllosphere, endorhiza, and endosphere of field-grown sugar beet plants was analyzed by a multiphasic approach at three different plant development stages at six locations in Europe. The analysis of microbial communities by Single Strand Conformation Polymorphism (SSCP) of 16S/18S rRNA clearly revealed the existence of discrete microenvironment- and site-specific patterns. A total of 1952 bacterial and 1344 fungal isolates screened by dual testing for antagonism toward the pathogens Aphanomyces cochlioides, Phoma betae, Pythium ultimum, and Rhizoctonia solani resulted in 885 bacterial (=45%) and 437 fungal (=33%) antagonists. In general, the indigenous antagonistic potential was very high and influenced by (a) the location, (b) the plant developmental stage, and (3) the microenvironment. Furthermore, we showed for the first time that the antagonistic potential was highly specific for each target pathogen. The majority of antagonistic microorganisms suppressed only one pathogen (bacteria: 664 = 75%; fungi: 256 = 59%), whereas the minority showed a broad host range (bacteria: 4 = 0.5%; fungi: 7 = 1.6%). The bacterial communities harbored the highest antagonistic potential against P. ultimum, whereas the fungal communities contained more antagonists against A. cochlioides and R. solani. In contrast to their high proportion, only a low diversity of antagonists at genotypic and species level was found. Novel antagonistic species, e.g., Subtercola pratensis or Microbacterium testaceum were found in the internal part of the sugar beet body.}, }
@article {pmid18060448, year = {2008}, author = {Rincón, A and Arenal, F and González, I and Manrique, E and Lucas, MM and Pueyo, JJ}, title = {Diversity of rhizobial bacteria isolated from nodules of the Gypsophyte Ononis tridentata L. growing in Spanish soils.}, journal = {Microbial ecology}, volume = {56}, number = {2}, pages = {223-233}, pmid = {18060448}, issn = {0095-3628}, mesh = {*Alphaproteobacteria/classification/genetics/growth &amp; development/isolation &amp; purification ; Bacterial Proteins/genetics ; Calcium Sulfate ; DNA Fingerprinting/methods ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Fabaceae/*microbiology ; Genes, rRNA ; *Genetic Variation ; N-Acetylglucosaminyltransferases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Restriction Mapping/methods ; *Rhizobium/classification/genetics/growth &amp; development/isolation &amp; purification ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; Spain ; }, abstract = {The aim of this work is to describe the diversity and phylogeny of rhizobial bacteria associated to nodules of Ononis tridentata L. in different geographical regions of Spain. Twenty-two bacterial isolates were characterized using several molecular techniques (16S amplified ribosomal deoxyribonucleic acid restriction analysis, fingerprinting, and sequencing) and phylogenies were inferred from their 16S and nodC gene sequences. Phylogenetically, the isolates grouped with the genera Rhizobium, Mesorhizobium, Phylobacterium, and Bosea. The nodC gene, essential for nodulation, was detected for the first time in isolates close to the genera Bosea and Phyllobacterium. The bacteria isolated showed a high diversity at the genus, species, and strain level regardless of the geographical origin of the host plant. This is the first report describing bacteria associated to nodules of O. tridentata. This shrub legume is highly prized for the revegetation of gypsum soils in semiarid Mediterranean areas. Our molecular description of bacteria associated to this legume improves the current understanding of the ecology of this plant species. Our findings have implications for formulating suitable bacterial inocula to recover gypsum ecosystems.}, }
@article {pmid18059488, year = {2008}, author = {Ainsworth, TD and Fine, M and Roff, G and Hoegh-Guldberg, O}, title = {Bacteria are not the primary cause of bleaching in the Mediterranean coral Oculina patagonica.}, journal = {The ISME journal}, volume = {2}, number = {1}, pages = {67-73}, doi = {10.1038/ismej.2007.88}, pmid = {18059488}, issn = {1751-7362}, mesh = {Animals ; Anthozoa/*microbiology/physiology/ultrastructure ; Bacterial Physiological Phenomena ; Ecosystem ; In Situ Hybridization, Fluorescence ; Israel ; Microscopy, Electron, Scanning Transmission ; Symbiosis ; Vibrio/*physiology ; }, abstract = {Coral bleaching occurs when the endosymbiosis between corals and their symbionts disintegrates during stress. Mass coral bleaching events have increased over the past 20 years and are directly correlated with periods of warm sea temperatures. However, some hypotheses have suggested that reef-building corals bleach due to infection by bacterial pathogens. The 'Bacterial Bleaching' hypothesis is based on laboratory studies of the Mediterranean invading coral, Oculina patagonica, and has further generated conclusions such as the coral probiotic hypothesis and coral hologenome theory of evolution. We aimed to investigate the natural microbial ecology of O. patagonica during the annual bleaching using fluorescence in situ hybridization to map bacterial populations within the coral tissue layers, and found that the coral bleaches on the temperate rocky reefs of the Israeli coastline without the presence of Vibrio shiloi or bacterial penetration of its tissue layers. Bacterial communities were found associated with the endolithic layer of bleached coral regions, and a community dominance shift from an apparent cyanobacterial-dominated endolithic layer to an algal-dominated layer was found in bleached coral samples. While bacterial communities certainly play important roles in coral stasis and health, we suggest environmental stressors, such as those documented with reef-building corals, are the primary triggers leading to bleaching of O. patagonica and suggest that bacterial involvement in patterns of bleaching is that of opportunistic colonization.}, }
@article {pmid18058162, year = {2008}, author = {Paparu, P and Dubois, T and Gold, CS and Niere, B and Adipala, E and Coyne, D}, title = {Screenhouse and field persistence of nonpathogenic endophytic Fusarium oxysporum in Musa tissue culture plants.}, journal = {Microbial ecology}, volume = {55}, number = {3}, pages = {561-568}, pmid = {18058162}, issn = {0095-3628}, mesh = {Animals ; Fusarium/genetics/*growth &amp; development/isolation &amp; purification/physiology ; Genetic Complementation Test ; Meristem/*microbiology ; Musa/*microbiology/physiology ; Pest Control, Biological ; Rhizome/microbiology ; *Symbiosis ; Tissue Culture Techniques/*methods ; Tylenchoidea ; Uganda ; Weevils ; }, abstract = {Two major biotic constraints to highland cooking banana (Musa spp., genome group AAA-EA) production in Uganda are the banana weevil Cosmopolites sordidus and the burrowing nematode Radopholus similis. Endophytic Fusarium oxysporum strains inoculated into tissue culture banana plantlets have shown control of the banana weevil and the nematode. We conducted screenhouse and field experiments to investigate persistence in the roots and rhizome of two endophytic Fusarium oxysporum strains, V2w2 and III4w1, inoculated into tissue-culture banana plantlets of highland cooking banana cultivars Kibuzi and Nabusa. Re-isolation of F. oxysporum showed that endophyte colonization decreased faster from the rhizomes than from the roots of inoculated plants, both in the screenhouse and in the field. Whereas rhizome colonization by F. oxysporum decreased in the screenhouse (4-16 weeks after inoculation), root colonization did not. However, in the field (17-33 weeks after inoculation), a decrease was observed in both rhizome and root colonization. The results show a better persistence in the roots than rhizomes of endophytic F. oxysporum strains V2w2 and III4w1.}, }
@article {pmid18058161, year = {2008}, author = {Cazorla, FM and Codina, JC and Abad, C and Arrebola, E and Torés, JA and Murillo, J and Pérez-García, A and de Vicente, A}, title = {62-kb plasmids harboring rulAB homologues confer UV-tolerance and epiphytic fitness to Pseudomonas syringae pv. syringae mango isolates.}, journal = {Microbial ecology}, volume = {56}, number = {2}, pages = {283-291}, pmid = {18058161}, issn = {0095-3628}, mesh = {Bacterial Proteins/*genetics ; Colony Count, Microbial ; Conjugation, Genetic ; Electroporation ; Mangifera/*microbiology ; Plant Leaves/microbiology ; Plasmids/*genetics ; Pseudomonas syringae/genetics/growth &amp; development/isolation &amp; purification/*radiation effects ; Radiation Tolerance/*genetics ; Sunlight ; *Ultraviolet Rays ; }, abstract = {The presence of genetic determinants homologous to rulAB genes for ultraviolet (UV) radiation resistance was determined in a collection of Pseudomonas syringae pv. syringae strains isolated from mango. The potential role of these plasmids in UV tolerance and ecological fitness in the mango phyllosphere was also evaluated. Nearly all of the 62-kb plasmids present in the P. syringae pv. syringae strains hybridized with a rulAB probe, but these 62-kb plasmids showed differences in restriction patterns. In vitro assays of tolerance to UV radiation of P. syringae pv. syringae strains showed a higher survival of the strains harboring the 62-kb plasmids compared to strains lacking plasmids when exposed to UVC or UVA+B fractions. Similar results were observed when transconjugants harboring the 62-kb plasmid were tested. Survival assays were carried out under field conditions, and a higher survival of P. syringae pv. syringae strains harboring 62-kb plasmids under direct solar radiation on the adaxial surface of leaves was also observed. When the assays were carried out in shady areas or on the abaxial surface of leaves, survival time was comparable for all the assayed strains, whether or not they contained a 62-kb plasmid hybridizing to rulAB. Our results indicate that P. syringae pv. syringae strains harboring 62-kb plasmids show an increase in ecological fitness when colonizing the mango phyllosphere.}, }
@article {pmid18055136, year = {2008}, author = {Norris, BJ and Colditz, IG and Dixon, TJ}, title = {Fleece rot and dermatophilosis in sheep.}, journal = {Veterinary microbiology}, volume = {128}, number = {3-4}, pages = {217-230}, doi = {10.1016/j.vetmic.2007.10.024}, pmid = {18055136}, issn = {0378-1135}, mesh = {Actinomycetales/immunology ; Actinomycetales Infections/microbiology/pathology/prevention &amp; control/*veterinary ; Animals ; *Bacterial Vaccines ; Dermatitis/microbiology/pathology/prevention &amp; control/*veterinary ; Disease Susceptibility/immunology/veterinary ; Genetic Predisposition to Disease ; Immunity, Innate/genetics/immunology ; Pseudomonas Infections/microbiology/pathology/prevention &amp; control/*veterinary ; Pseudomonas aeruginosa/immunology ; Sheep ; Sheep Diseases/*microbiology/pathology/prevention &amp; control ; Wool/*microbiology ; }, abstract = {Fleece rot and dermatophilosis reduce health and production of sheep and predispose them to blow fly strike. This paper reviews aetiology, prevalence, pathogenesis, resistance, attempts to develop vaccines and prospects for new control strategies to these important skin diseases. Although the severity of fleece rot is associated with the abundance of Pseudomonas aeruginosa on skin, microbial ecology studies are providing new insights into the contribution of other bacteria to the disease. Wool traits and body conformation traits that predispose sheep to fleece rot and dermatophilosis are heritable and have been used as indirect selection criteria for resistance for many years. Selection against BoLA-DRB3-DQB class II haplotype in cattle can substantially reduce the prevalence of dermatophilosis and holds promise for identification of gene markers for resistance to these bacterial diseases in sheep. Immune responses in skin and systemic antibody responses to bacterial antigens are acquired through natural infection and contribute to resistance; however, prototype antibacterial vaccines have to date failed to provide protection against the diversity of isolates of Dermatophilus congolensis and Pseudomonas species present in the field. Opportunities for future control through breeding for resistance, vaccines and non-vaccine strategies for controlling the microbial ecology of fleece are discussed. In combination, control strategies need to reduce the risk of transmission, minimise exposure of animals to stressors that enhance the risk of infection, and enhance resistance though genetics or vaccines.}, }
@article {pmid18051265, year = {2007}, author = {Olaniran, AO and Stafford, WH and Cowan, DA and Pillay, D and Pillay, B}, title = {Microbial community profiling in cis- and trans-dichloroethene enrichment systems using denaturing gradient gel electrophoresis.}, journal = {Journal of microbiology and biotechnology}, volume = {17}, number = {4}, pages = {560-570}, pmid = {18051265}, issn = {1017-7825}, mesh = {Bacteria/*classification/genetics/metabolism ; Biodegradation, Environmental ; *Biodiversity ; Cluster Analysis ; Dichloroethylenes/*metabolism ; Electrophoresis ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; Soil Microbiology ; Water Microbiology ; }, abstract = {The effective and accurate assessment of the total microbial community diversity is one of the primary challenges in modem microbial ecology, especially for the detection and characterization of unculturable populations and populations with a low abundance. Accordingly, this study was undertaken to investigate the diversity of the microbial community during the biodegradation of cis- and trans-dichloroethenes in soil and wastewater enrichment cultures. Community profiling using PCR targeting the 16S rRNA gene and denaturing gradient gel electrophoresis (PCR-DGGE) revealed an alteration in the bacterial community profiles with time. Exposure to cis- and trans-dichloroethenes led to the disappearance of certain genospecies that were initially observed in the untreated samples. A cluster analysis of the bacterial DGGE community profiles at various sampling times during the degradation process indicated that the community profile became stable after day 10 of the enrichment. DNA sequencing and phylogenetic analysis of selected DGGE bands revealed that the genera Acinetobacter, Pseudomonas, Bacillus, Comamonas, and Arthrobacter, plus several other important uncultured bacterial phylotypes, dominated the enrichment cultures. Thus, the identified dominant phylotypes may play an important role in the degradation of cis- and trans-dichloroethenes.}, }
@article {pmid18050906, year = {2007}, author = {Siuda, W and Kiersztyn, B and Chróst, RJ}, title = {The dynamics of protein decomposition in lakes of different trophic status--reflections on the assessment of the real proteolytic activity in situ.}, journal = {Journal of microbiology and biotechnology}, volume = {17}, number = {6}, pages = {897-904}, pmid = {18050906}, issn = {1017-7825}, mesh = {Amino Acids/metabolism ; Biodegradation, Environmental ; *Eutrophication ; Fresh Water/*chemistry/microbiology ; Half-Life ; Hydrolysis ; Oligopeptides/metabolism ; Proteins/*metabolism ; }, abstract = {Abstract The aim of this paper is to discuss the methodology of our investigation of the dynamics of protein degradation and the total in situ proteolytic activity in meso/eutrophic, eutrophic, and hypereutrophic freshwater environments. Analysis of the kinetics and rates of enzymatic release of amino acids in water samples preserved with sodium azide allows determination of the concentrations of labile proteins (C(LAB)), and their half-life time (T(1/2)). Moreover, it gives more realistic information on resultant activity in situ (V(T(1/2))) of ecto- and extracellular proteases that are responsible for the biological degradation of these compounds. Although the results provided by the proposed method are generally well correlated with those obtained by classical procedures, they better characterize the dynamics of protein degradation processes, especially in eutrophic or hypereutrophic lakes. In these environments, processes of protein decomposition occur mainly on the particles and depend primarily on a metabolic activity of seston-attached bacteria. The method was tested in three lakes. The different degree of eutrophication of these lakes was clearly demonstrated by the measured real proteolytic pattern and confirmed by conventional trophic state determinants.}, }
@article {pmid18049456, year = {2008}, author = {Boon, C and Deng, Y and Wang, LH and He, Y and Xu, JL and Fan, Y and Pan, SQ and Zhang, LH}, title = {A novel DSF-like signal from Burkholderia cenocepacia interferes with Candida albicans morphological transition.}, journal = {The ISME journal}, volume = {2}, number = {1}, pages = {27-36}, doi = {10.1038/ismej.2007.76}, pmid = {18049456}, issn = {1751-7362}, mesh = {*Antibiosis ; Bacterial Proteins/chemistry/metabolism ; Biofilms/growth &amp; development ; Burkholderia Infections/microbiology ; Burkholderia cepacia/enzymology/genetics/isolation &amp; purification/*metabolism ; Candida albicans/cytology/*drug effects/growth &amp; development ; Enoyl-CoA Hydratase/chemistry/genetics/metabolism ; Fatty Acids, Monounsaturated/chemistry/*metabolism/pharmacology ; Gene Expression Regulation, Bacterial ; Genetic Complementation Test ; Mutant Proteins/genetics ; Open Reading Frames ; Polysaccharides, Bacterial/biosynthesis ; Sequence Alignment ; Sequence Deletion ; *Signal Transduction ; Xanthomonas campestris/chemistry/genetics/metabolism ; }, abstract = {In addition to producing lethal antibiotics, microorganisms may also use a new form of antagonistic mechanism in which signal molecules are exported to influence the gene expression and hence the ecological competence of their competitors. We report here the isolation and characterization of a novel signaling molecule, cis-2-dodecenoic acid (BDSF), from Burkholderia cenocepacia. BDSF is structurally similar to the diffusible signal factor (DSF) that is produced by the RpfF enzyme of Xanthomonas campestris. Deletion analysis demonstrated that Bcam0581, which encodes an RpfF homologue, was essential for BDSF production. The gene is highly conserved and widespread in the Burkholderia cepacia complex. Exogenous addition of BDSF restored the biofilm and extracellular polysaccharide production phenotypes of Xanthomonas campestris pv. campestris DSF-deficient mutants, highlighting its potential role in inter-species signaling. Further analyses showed that Candida albicans germ tube formation was strongly inhibited by either coculture with B. cenocepacia or by exogenous addition of physiological relevant levels of BDSF, whereas deletion of Bcam0581 abrogated the inhibitory ability of the bacterial pathogen. As B. cenocepacia and C. albicans are frequently encountered human pathogens, identification of the BDSF signal and its activity thus provides a new insight into the molecular grounds of their antagonistic interactions whose importance to microbial ecology and pathogenesis is now becoming evident.}, }
@article {pmid18048744, year = {2007}, author = {Borchert, MS and Nielsen, P and Graeber, I and Kaesler, I and Szewzyk, U and Pape, T and Antranikian, G and Schäfer, T}, title = {Bacillus plakortidis sp. nov. and Bacillus murimartini sp. nov., novel alkalitolerant members of rRNA group 6.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {57}, number = {Pt 12}, pages = {2888-2893}, doi = {10.1099/ijs.0.65177-0}, pmid = {18048744}, issn = {1466-5026}, mesh = {Animals ; Bacillus/chemistry/*classification/genetics/*isolation &amp; purification ; Base Composition ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fatty Acids/analysis ; Genes, rRNA ; Germany ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phylogeny ; Plakortis/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Sodium Chloride/metabolism ; Temperature ; }, abstract = {The Gram-positive, alkali- and salt-tolerant marine bacterium strain P203(T) is described together with its closest phylogenetic neighbour, terrestrial isolate LMG 21005(T). Strain P203(T) was isolated from material from the sponge Plakortis simplex that was obtained from the Sula-Ridge, Norwegian Sea. Strain LMG 21005(T) was an undescribed strain that was isolated from a church wall mural in Germany. Strains P203(T) and LMG 21005(T) were identified as novel alkalitolerant members of the Bacillus rRNA group 6 with a 16S rRNA gene sequence similarity of 99.5 %. The closest described neighbour, Bacillus gibsonii DSM 8722(T), showed 99.0 % gene sequence similarity with P203(T) and 98.8 % similarity with strain LMG 21005(T). Despite the high 16S rRNA gene sequence similarity, DNA-DNA cross-hybridization revealed only 25.8-34.1 % similarity amongst the three strains. The DNA G+C contents were 41.1 mol% for strain P203(T) and 39.6 mol% for strain LMG 21005(T). Both strains grew well between pH 7 and pH 11. Strain P203(T) showed growth at moderate temperatures (from 4 to 30 degrees C) and in the presence of up to 12 % (w/v) NaCl at pH 9.7, whereas strain LMG 21005(T) was not salt tolerant (up to 4 % NaCl) and no growth was observed at 4 degrees C. The major fatty acids of strains P203(T), LMG 21005(T) and the type strain of B. gibsonii were the saturated terminally methyl-branched compounds iso-C(15 : 0) (19.8, 15.6 and 28.0 %, respectively) and anteiso-C(15 : 0) (57.1, 48.6 and 45.2 %, respectively). Physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains P203(T) and LMG 21005(T) from the six related Bacillus species with validly published names and supported the proposal of two novel species, Bacillus plakortidis [type strain P203(T) (=DSM 19153(T)=NCIMB 14288(T))] and Bacillus murimartini [type strain LMG 21005(T) (=NCIMB 14102(T))].}, }
@article {pmid18046600, year = {2008}, author = {Lindström, A}, title = {Distribution of Paenibacillus larvae spores among adult honey bees (Apis mellifera) and the relationship with clinical symptoms of American foulbrood.}, journal = {Microbial ecology}, volume = {56}, number = {2}, pages = {253-259}, pmid = {18046600}, issn = {0095-3628}, mesh = {Animals ; Bees/growth &amp; development/*microbiology ; Colony Count, Microbial ; Gram-Positive Endospore-Forming Rods/*isolation &amp; purification/*pathogenicity/physiology ; Larva/*microbiology ; Spores, Bacterial/*isolation &amp; purification ; United States ; }, abstract = {Knowledge of the distribution of Paenibacillus larvae spores, the causative agent of American foulbrood (AFB), among individual adult honey bees is crucial for determining the appropriate number of adult bees to include in apiary composite samples when screening for diseased colonies. To study spore distribution at the individual bee level, 500 honey bees were collected from different parts of eight clinically diseased colonies and individually analyzed for P. larvae. From the brood chamber and from the super, bees were randomly collected and individually put in Eppendorf vials. The samples were frozen as soon as possible after collection. Concurrently with sampling, each colony was visually inspected for clinical symptoms of AFB. The number of clinically diseased cells in the colony was visually estimated. All samples were cultured in the laboratory for P. larvae. The results demonstrate that the spores are not randomly distributed among the bees; some bees have much higher spore loads than others. It is also clear that as the proportion of contaminated bees increase, the number of spores from each positive bee also increases. The data also demonstrated a relationship between the number of clinically diseased cells and the proportion of positive bees in individual colonies. This relationship was used to develop a mathematical formula for estimating the minimum number of bees in a sample to detect clinical disease. The formula takes into account the size of the apiary and the degree of certainty with which one aims to discover clinical symptoms. Calculations using the formula suggest that adult bee samples at the colony level will detect light AFB infections with a high probability. However, the skewed spore distribution of the adult bees makes composite sampling at the apiary level more problematic, if the aim of the sampling is to locate lightly infected individual colonies within apiaries. The results suggest that false-negative culturing results from composite samples of adult bees from individual colonies with clinical symptoms of AFB are highly improbable. However, if single colonies have light infections in large apiaries, the dilution effect from uncontaminated bees from healthy colonies on the positive bees from diseased colonies may yield false-negative results at the apiary level.}, }
@article {pmid18044542, year = {2007}, author = {Clauwaert, P and Van der Ha, D and Boon, N and Verbeken, K and Verhaege, M and Rabaey, K and Verstraete, W}, title = {Open air biocathode enables effective electricity generation with microbial fuel cells.}, journal = {Environmental science &amp; technology}, volume = {41}, number = {21}, pages = {7564-7569}, doi = {10.1021/es0709831}, pmid = {18044542}, issn = {0013-936X}, mesh = {Acetates/metabolism ; Bacteria/genetics/metabolism ; *Bioelectric Energy Sources ; Bioreactors ; DNA, Bacterial/genetics ; Electricity ; Electrodes ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The reduction of oxygen at the cathode is one of the major bottlenecks of microbial fuel cells (MFCs). While research so far has mainly focused on chemical catalysis of this oxygen reduction, here we present a continuously wetted cathode with microorganisms that act as biocatalysts for oxygen reduction. We combined the anode of an acetate oxidizing tubular microbial fuel cell with an open air biocathode for electricity production. The maximum power production was 83 +/- 11 W m(-3) MFC (0.183 L MFC) for batch-fed systems (20-40% Coulombic yield) and 65 +/- 5 W m(-3) MFC for a continuous system with an acetate loading rate of 1.5 kg COD m(-3) day(-1) (90 +/- 3% Coulombic yield). Electrochemical precipitation of manganese oxides on the cathodic graphite felt decreased the start-up period with approximately 30% versus a non-treated graphite felt. After the start-up period, the cell performance was similar for the pretreated and non-treated cathodic electrodes. Several reactor designs were tested, and it was found that enlargement of the 0.183 L MFC reactor by a factor 2.9-3.8 reduced the volumetric power output by 60-67%. Biocathodes alleviate the need to use noble or non-noble catalysts for the reduction of oxygen, which increases substantially the viability and sustainability of MFCs.}, }
@article {pmid18043672, year = {2007}, author = {Santiago-Vázquez, LZ and Brück, TB and Brück, WM and Duque-Alarcón, AP and McCarthy, PJ and Kerr, RG}, title = {The diversity of the bacterial communities associated with the azooxanthellate hexacoral Cirrhipathes lutkeni.}, journal = {The ISME journal}, volume = {1}, number = {7}, pages = {654-659}, doi = {10.1038/ismej.2007.77}, pmid = {18043672}, issn = {1751-7362}, mesh = {Actinobacteria/classification/genetics ; Alphaproteobacteria/classification/genetics ; Animals ; Anthozoa/*microbiology ; Bacteria/classification/*genetics/growth &amp; development ; *Biodiversity ; Chloroflexi/classification/genetics ; Cytophagaceae/classification/genetics ; Flavobacterium/classification/genetics ; Gammaproteobacteria/classification/genetics ; Genetic Variation ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {This study examined the symbiotic microbiota of the hexacoral Cirrhipathes lutkeni using traditional plate culture, fluorescence in situ hybridization (FISH) and 16S rDNA characterization. FISH counts for the whole coral (holobiont) showed a major presence of gamma-Proteobacteria (22%) and Actinobacteria (19%), followed by alpha-Proteobacteria (14%), Firmicutes (9%), Cytophaga-Flavobacterium (7%), beta-Proteobacteria (6%) and Chloroflexi (2%). In contrast to the diversity observed by FISH, plate cultures were found to be selective for gamma-Proteobacteria (22 cultures) with the exception of an Actinobacterium. The methods employed in this study detected 76% of all microbes estimated by DAPI staining of C. lutkeni homogenates. The absence of zooxanthellae in this particular hexacoral was confirmed by PCR and spectrophotometry using fresh tissue isolated from the holobiont. This is the first study describing the microbial associations of shallow-water hexacorallia, which opens further insight into coral microbial ecology and may enhance the search for novel natural products in the near future.}, }
@article {pmid18043636, year = {2007}, author = {Kassem, II and Sigler, V and Esseili, MA}, title = {Public computer surfaces are reservoirs for methicillin-resistant staphylococci.}, journal = {The ISME journal}, volume = {1}, number = {3}, pages = {265-268}, doi = {10.1038/ismej.2007.36}, pmid = {18043636}, issn = {1751-7362}, mesh = {Anti-Bacterial Agents/pharmacology ; *Computers ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Genes, rRNA ; *Methicillin Resistance ; Molecular Sequence Data ; Oxacillin/pharmacology ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Staphylococcus/*drug effects/*isolation &amp; purification ; Universities ; }, abstract = {The role of computer keyboards used by students of a metropolitan university as reservoirs of antibiotic-resistant staphylococci was determined. Putative methicillin (oxacillin)-resistant staphylococci isolates were identified from keyboard swabs following a combination of biochemical and genetic analyses. Of 24 keyboards surveyed, 17 were contaminated with staphylococci that grew in the presence of oxacillin (2 mg l(-1)). Methicillin (oxacillin)-resistant Staphylococcus aureus (MRSA), -S. epidermidis (MRSE) and -S. hominis (MRSH) were present on two, five and two keyboards, respectively, while all three staphylococci co-contaminated one keyboard. Furthermore, these were found to be part of a greater community of oxacillin-resistant bacteria. Combined with the broad user base common to public computers, the presence of antibiotic-resistant staphylococci on keyboard surfaces might impact the transmission and prevalence of pathogens throughout the community.}, }
@article {pmid18043631, year = {2007}, author = {van Elsas, JD and Hill, P and Chronáková, A and Grekova, M and Topalova, Y and Elhottová, D and Kristůfek, V}, title = {Survival of genetically marked Escherichia coli O157:H7 in soil as affected by soil microbial community shifts.}, journal = {The ISME journal}, volume = {1}, number = {3}, pages = {204-214}, doi = {10.1038/ismej.2007.21}, pmid = {18043631}, issn = {1751-7362}, mesh = {*Biodiversity ; Cluster Analysis ; Colony Count, Microbial ; DNA Fingerprinting ; DNA, Bacterial/genetics/isolation &amp; purification ; Escherichia coli O157/genetics/*growth &amp; development ; *Fumigation ; *Microbial Viability ; Netherlands ; Nucleic Acid Denaturation ; Polymerase Chain Reaction ; *Soil Microbiology ; }, abstract = {A loamy sand soil sampled from a species-rich permanent grassland at a long-term experimental site (Wildekamp, Bennekom, The Netherlands) was used to construct soil microcosms in which the microbial community compositions had been modified by fumigation at different intensities (depths). As expected, increasing depth of fumigation was shown to result in progressively increasing effects on the microbiological soil parameters, as determined by cultivation-based as well as cultivation-independent (PCR-DGGE, PLFA) methods. Both at 7 and at 60 days after fumigation, shifts in the bacterial, fungal and protozoan communities were noted, indicating that altered community compositions had emerged following a transition phase. At the level of bacteria culturable on plates, an increase of the prevalence of bacterial r-strategists was noted at 7 days followed by a decline at 60 days, which also hinted at the effectiveness of the fumigation treatments. The survival of a non-toxigenic Escherichia coli O157:H7 derivative, strain T, was then assessed over 60 days in these microcosms, using detection via colony forming units counts as well as via PCR-DGGE. Both data sets were consistent with each other. Thus, a clear effect of fumigation depth on the survival of the invading strain T was noted, as a progressive increase of depth coincided with a progressively enhanced inoculant survival rate. As fumigation depth was presumably inversely related to community complexity, this was consistent with the hypothesis that soil systems with reduced biological complexity offer enhanced opportunities for invading microbial species to establish and persist. The significance of this finding is discussed in the light of the ongoing discussion about the complexity-invasiveness relationship within microbial communities, in particular regarding the opportunities of pathogens to persist.}, }
@article {pmid18043629, year = {2007}, author = {Taylor, MW and Hill, RT and Piel, J and Thacker, RW and Hentschel, U}, title = {Soaking it up: the complex lives of marine sponges and their microbial associates.}, journal = {The ISME journal}, volume = {1}, number = {3}, pages = {187-190}, doi = {10.1038/ismej.2007.32}, pmid = {18043629}, issn = {1751-7362}, mesh = {Animals ; Archaea/*classification/*isolation &amp; purification ; Bacteria/*classification/*isolation &amp; purification ; *Biodiversity ; Porifera/*microbiology ; }, }
@article {pmid18043623, year = {2007}, author = {Leigh, MB and Pellizari, VH and Uhlík, O and Sutka, R and Rodrigues, J and Ostrom, NE and Zhou, J and Tiedje, JM}, title = {Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs).}, journal = {The ISME journal}, volume = {1}, number = {2}, pages = {134-148}, doi = {10.1038/ismej.2007.26}, pmid = {18043623}, issn = {1751-7362}, support = {2P42ES04911/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Biphenyl Compounds/*metabolism ; Carbon Isotopes/metabolism ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Pinus/*microbiology ; Plant Roots/*microbiology ; Polychlorinated Biphenyls/*metabolism ; Sequence Analysis, DNA ; *Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {Bacteria and functional genes associated with biphenyl (BP) degradation in the root zone of an Austrian pine (Pinus nigra L.) growing naturally in polychlorinated-BP (PCB)-contaminated soil were identified using stable isotope probing (SIP) integrated with comprehensive functional gene analyses. SIP revealed 75 different genera that derived carbon from 13C-BP, with Pseudonocardia, Kribella, Nocardiodes and Sphingomonas predominating carbon acquisition. Rhodococcus spp. were not detected with SIP, despite being the most abundant BP utilizers isolated from agar plates. Only one organism, an Arthrobacter spp., was detected as a BP utilizer by both cultivation and SIP methods. Time-course SIP analyses indicated that secondary carbon flow from BP-utilizing bacteria into other soil organisms may have occurred largely between 4 and 14 days incubation. Functional gene contents of the BP-utilizing metagenome (13C-DNA) were explored using the GeoChip, a functional gene array containing 6465 probes targeting aromatic degradative genes. The GeoChip detected 27 genes, including several associated with catabolism of BP, benzoate and a variety of aromatic ring hydroxylating dioygenase (ARHD) subunits. Genes associated with the beta-ketoadipate pathway were also detected, suggesting a potential role for this plant aromatic catabolic pathway in PCB degradation. Further ARHD analyses using targeted polymerase chain reaction primers and sequence analyses revealed novel dioxygenase sequences in 13C-DNA, including several sequences that clustered distantly from all known ARHDs and others that resembled known Rhodococcus ARHDs. The findings improve our understanding of BP degradation and carbon flow in soil, reveal the extent of culture bias, and may benefit bioremediation research by facilitating the development of molecular tools to detect, quantify and monitor populations involved in degradative processes.}, }
@article {pmid18043611, year = {2007}, author = {van der Putten, WH and Klironomos, JN and Wardle, DA}, title = {Microbial ecology of biological invasions.}, journal = {The ISME journal}, volume = {1}, number = {1}, pages = {28-37}, doi = {10.1038/ismej.2007.9}, pmid = {18043611}, issn = {1751-7362}, mesh = {Animals ; *Bacterial Physiological Phenomena ; *Ecosystem ; Fungi/*physiology ; *Plant Physiological Phenomena ; Plants/*microbiology ; Soil Microbiology ; Symbiosis ; }, abstract = {Invasive microbes, plants and animals are a major threat to the composition and functioning of ecosystems; however, the mechanistic basis of why exotic species can be so abundant and disruptive is not well understood. Most studies have focused on invasive plants and animals, although few have considered the effects of invasive microbes, or interactions of invasive plant and animal species with microbial communities. Here, we review effects of invasive plants on soil microbial communities and discuss consequences for plant performance, plant community structure and ecosystem processes. In addition, we briefly discuss effects of invasive soil microbes on plant communities, which has been less well studied, and effects of invasive animals on soil decomposers and ecosystem functioning. We do this by considering each of three important functional groups of microbes, namely soil microbial parasites and pathogens, mutualistic symbionts and decomposers. We conclude that invasive plants, pathogenic and symbiotic soil microbes will have strongest effects on the abundance of individual species, community diversity and ecosystem functioning. Invasive decomposer microbes probably have little impact, because of limited specificity and great functional redundancy. However, invasive plants and animals can have major effects on microbial decomposition in soil. We propose that understanding, predicting and counteracting consequences of enhanced global homogenization of natural communities through introducing exotic plants, animals and microbes will require future studies on how pathogenic, symbiotic and decomposer soil microbes interact, how they are influenced by higher trophic level organisms and how their combined effects are influencing the composition and functioning of ecosystems.}, }
@article {pmid18043610, year = {2007}, author = {Francis, CA and Beman, JM and Kuypers, MM}, title = {New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation.}, journal = {The ISME journal}, volume = {1}, number = {1}, pages = {19-27}, doi = {10.1038/ismej.2007.8}, pmid = {18043610}, issn = {1751-7362}, mesh = {Ammonia/*metabolism ; Archaea/*metabolism ; Bacteria, Anaerobic/*metabolism ; Ecology ; Nitrogen/*metabolism ; Oceans and Seas ; Oxidation-Reduction ; Water Microbiology ; }, abstract = {Microbial activities drive the global nitrogen cycle, and in the past few years, our understanding of nitrogen cycling processes and the micro-organisms that mediate them has changed dramatically. During this time, the processes of anaerobic ammonium oxidation (anammox), and ammonia oxidation within the domain Archaea, have been recognized as two new links in the global nitrogen cycle. All available evidence indicates that these processes and organisms are critically important in the environment, and particularly in the ocean. Here we review what is currently known about the microbial ecology of anaerobic and archaeal ammonia oxidation, highlight relevant unknowns and discuss the implications of these discoveries for the global nitrogen and carbon cycles.}, }
@article {pmid18043609, year = {2007}, author = {Rabaey, K and Rodríguez, J and Blackall, LL and Keller, J and Gross, P and Batstone, D and Verstraete, W and Nealson, KH}, title = {Microbial ecology meets electrochemistry: electricity-driven and driving communities.}, journal = {The ISME journal}, volume = {1}, number = {1}, pages = {9-18}, doi = {10.1038/ismej.2007.4}, pmid = {18043609}, issn = {1751-7362}, mesh = {Bacteria/*metabolism ; Biodegradation, Environmental ; Biofilms ; Biotechnology ; Ecology ; Electricity ; *Electrochemistry ; Electron Transport ; Gram-Positive Bacteria/metabolism ; Sewage/microbiology ; }, abstract = {Bio-electrochemical systems (BESs) have recently emerged as an exciting technology. In a BES, bacteria interact with electrodes using electrons, which are either removed or supplied through an electrical circuit. The most-described type of BES is microbial fuel cells (MFCs), in which useful power is generated from electron donors as, for example, present in wastewater. This form of charge transport, known as extracellular electron transfer, was previously extensively described with respect to metals such as iron and manganese. The importance of these interactions in global biogeochemical cycles is essentially undisputed. A wide variety of bacteria can participate in extracellular electron transfer, and this phenomenon is far more widespread than previously thought. The use of BESs in diverse research projects is helping elucidate the mechanism by which bacteria shuttle electrons externally. New forms of interactions between bacteria have been discovered demonstrating how multiple populations within microbial communities can co-operate to achieve energy generation. New environmental processes that were difficult to observe or study previously can now be simulated and improved via BESs. Whereas pure culture studies make up the majority of the studies performed thus far, even greater contributions of BESs are expected to occur in natural environments and with mixed microbial communities. Owing to their versatility, unmatched level of control and capacity to sustain novel processes, BESs might well serve as the foundation of a new environmental biotechnology. While highlighting some of the major breakthroughs and addressing only recently obtained data, this review points out that despite rapid progress, many questions remain unanswered.}, }
@article {pmid18043608, year = {2007}, author = {Verstraete, W}, title = {Microbial ecology and environmental biotechnology.}, journal = {The ISME journal}, volume = {1}, number = {1}, pages = {4-8}, doi = {10.1038/ismej.2007.7}, pmid = {18043608}, issn = {1751-7362}, mesh = {Animals ; *Biotechnology ; Ecology ; *Environmental Microbiology ; Humans ; Research ; }, }
@article {pmid18043607, year = {2007}, author = {Cohen, Y and Kjelleberg, S and Lappin-Scott, HM}, title = {The ISME journal: a major milestone for the International Society for Microbial Ecology and the microbial ecology community.}, journal = {The ISME journal}, volume = {1}, number = {1}, pages = {3-4}, doi = {10.1038/ismej.2007.14}, pmid = {18043607}, issn = {1751-7362}, mesh = {*Ecology ; *Environmental Microbiology ; *Societies, Scientific ; }, }
@article {pmid18043606, year = {2007}, author = {Kowalchuk, GA and Heidelberg, JF and Bailey, MJ}, title = {The ISME journal: multidisciplinary journal of microbial ecology.}, journal = {The ISME journal}, volume = {1}, number = {1}, pages = {1-3}, doi = {10.1038/ismej.2007.13}, pmid = {18043606}, issn = {1751-7362}, mesh = {*Ecology ; Ecosystem ; *Environmental Microbiology ; Evolution, Molecular ; Genetics, Microbial ; Molecular Biology ; }, }
@article {pmid18040734, year = {2008}, author = {Dell, EA and Bowman, D and Rufty, T and Shi, W}, title = {Intensive management affects composition of betaproteobacterial ammonia oxidizers in turfgrass systems.}, journal = {Microbial ecology}, volume = {56}, number = {1}, pages = {178-190}, pmid = {18040734}, issn = {0095-3628}, mesh = {Ammonia/*metabolism ; Betaproteobacteria/*classification/genetics/growth &amp; development ; Cloning, Molecular ; *Conservation of Natural Resources ; *Ecosystem ; Genetic Variation ; Molecular Sequence Data ; Nitrosomonas/classification/genetics/growth &amp; development ; North Carolina ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; *Poaceae ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Time Factors ; }, abstract = {Turfgrass is a highly managed ecosystem subject to frequent fertilization, mowing, irrigation, and application of pesticides. Turf management practices may create a perturbed environment for ammonia oxidizers, a key microbial group responsible for nitrification. To elucidate the long-term effects of turf management on these bacteria, we assessed the composition of betaproteobacterial ammonia oxidizers in a chronosequence of turfgrass systems (i.e., 1, 6, 23, and 95 years old) and the adjacent native pines by using both 16S rRNA and amoA gene fragments specific to ammonia oxidizers. Based on the Shannon-Wiener diversity index of denaturing gradient gel electrophoresis patterns and the rarefaction curves of amoA clones, turf management did not change the relative diversity and richness of ammonia oxidizers in turf soils as compared to native pine soils. Ammonia oxidizers in turfgrass systems comprised a suite of phylogenetic clusters common to other terrestrial ecosystems. Nitrosospira clusters 0, 2, 3, and 4; Nitrosospira sp. Nsp65-like sequences; and Nitrosomonas clusters 6 and 7 were detected in the turfgrass chronosequence with Nitrosospira clusters 3 and 4 being dominant. However, both turf age and land change (pine to turf) effected minor changes in ammonia oxidizer composition. Nitrosospira cluster 0 was observed only in older turfgrass systems (i.e., 23 and 95 years old); fine-scale differences within Nitrosospira cluster 3 were seen between native pines and turf. Further investigations are needed to elucidate the ecological implications of the compositional differences.}, }
@article {pmid18038213, year = {2008}, author = {Meier, C and Wehrli, B and van der Meer, JR}, title = {Seasonal fluctuations of bacterial community diversity in agricultural soil and experimental validation by laboratory disturbance experiments.}, journal = {Microbial ecology}, volume = {56}, number = {2}, pages = {210-222}, pmid = {18038213}, issn = {0095-3628}, mesh = {2-Methyl-4-chlorophenoxyacetic Acid/analogs &amp; derivatives/pharmacology ; *Agriculture ; Bacteria/classification/drug effects/genetics/*growth &amp; development ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; *Ecosystem ; Genes, rRNA ; Herbicides/pharmacology ; Laboratories ; Polymorphism, Restriction Fragment Length ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; *Seasons ; Sequence Analysis, DNA ; Soil/*analysis ; *Soil Microbiology ; }, abstract = {Natural fluctuations in soil microbial communities are poorly documented because of the inherent difficulty to perform a simultaneous analysis of the relative abundances of multiple populations over a long time period. Yet, it is important to understand the magnitudes of community composition variability as a function of natural influences (e.g., temperature, plant growth, or rainfall) because this forms the reference or baseline against which external disturbances (e.g., anthropogenic emissions) can be judged. Second, definition of baseline fluctuations in complex microbial communities may help to understand at which point the systems become unbalanced and cannot return to their original composition. In this paper, we examined the seasonal fluctuations in the bacterial community of an agricultural soil used for regular plant crop production by using terminal restriction fragment length polymorphism profiling (T-RFLP) of the amplified 16S ribosomal ribonucleic acid (rRNA) gene diversity. Cluster and statistical analysis of T-RFLP data showed that soil bacterial communities fluctuated very little during the seasons (similarity indices between 0.835 and 0.997) with insignificant variations in 16S rRNA gene richness and diversity indices. Despite overall insignificant fluctuations, between 8 and 30% of all terminal restriction fragments changed their relative intensity in a significant manner among consecutive time samples. To determine the magnitude of community variations induced by external factors, soil samples were subjected to either inoculation with a pure bacterial culture, addition of the herbicide mecoprop, or addition of nutrients. All treatments resulted in statistically measurable changes of T-RFLP profiles of the communities. Addition of nutrients or bacteria plus mecoprop resulted in bacteria composition, which did not return to the original profile within 14 days. We propose that at less than 70% similarity in T-RFLP, the bacterial communities risk to drift apart to inherently different states.}, }
@article {pmid18034831, year = {2008}, author = {Liu, Y and Hu, T and Jiang, D and Zhang, J and Zhou, X}, title = {Regulation of urease gene of Actinomyces naeslundii in biofilms in response to environmental factors.}, journal = {FEMS microbiology letters}, volume = {278}, number = {2}, pages = {157-163}, doi = {10.1111/j.1574-6968.2007.00959.x}, pmid = {18034831}, issn = {0378-1097}, mesh = {Actinomyces/enzymology/*genetics/growth &amp; development ; Bacterial Proteins/*genetics/metabolism ; Biofilms/drug effects/*growth &amp; development ; Gene Expression Regulation, Bacterial/drug effects ; Glucose/pharmacology ; Hydrogen-Ion Concentration ; Nitrogen/pharmacology ; Polymerase Chain Reaction/methods ; Urease/*genetics/*metabolism ; }, abstract = {The metabolism of urea by urease enzymes of oral bacteria has a profound influence on oral biofilm pH homeostasis and oral microbial ecology, and Actinomyces naeslundii is an important ureolytic organism in the oral cavity. To gain an insight into the regulation of urease gene expression in cells of A. naeslundii growing in biofilms under different environmental conditions, the behavior of A. naeslundii ATCC12104 was examined in in vitro biofilms. The strain was grown in a chemostat biofilm reactor, and at a quasi-steady state, the urease activity of biofilm cells was measured and transcription of ureC gene was detected with Taqman quantitative PCR. The effect of environmental changes on urease expression was examined by varying the environmental pH, dilution rate, carbohydrate and nitrogen availability of the fluid phase of the culture. The results showed that the conditions of neutral pH, fast dilution rate, increased carbohydrate supply or low nitrogen supply in the medium all resulted in enhancement of urease activity in biofilm cells. But only low nitrogen availability and a fast dilution rate were observed to lead to an increase in ureC mRNA levels. This suggests that nitrogen availability and dilution rate can influence the urease activity of A. naeslundii by modulating ureC gene transcription.}, }
@article {pmid18034358, year = {2008}, author = {Fernández, N and Díaz, EE and Amils, R and Sanz, JL}, title = {Analysis of microbial community during biofilm development in an anaerobic wastewater treatment reactor.}, journal = {Microbial ecology}, volume = {56}, number = {1}, pages = {121-132}, pmid = {18034358}, issn = {0095-3628}, mesh = {Anaerobiosis ; Archaea/classification/genetics/*growth &amp; development/ultrastructure ; Bacteria/classification/genetics/*growth &amp; development/ultrastructure ; Biofilms/*growth &amp; development ; *Bioreactors ; *Ecosystem ; Electrophoresis/methods ; In Situ Hybridization, Fluorescence ; Microscopy, Confocal ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; Phylogeny ; Proteobacteria/classification/genetics/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Waste Disposal, Fluid/*methods ; Water Purification ; }, abstract = {The formation, structure, and biodiversity of a multispecies anaerobic biofilm inside an Upflow Anaerobic Sludge Bed (UASB) reactor fed with brewery wastewater was examined using complementary microbial ecology methods such us fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), and cloning. The biofilm development can be roughly divided into three stages: an initial attachment phase (0-36 h) characterized by random adhesion of the cells to the surface; a consolidation phase (from 36 h to 2 weeks) defined by the appearance of microcolonies; and maturation phase (from 2 weeks to 2 months). During the consolidation period, proteobacteria with broad metabolic capabilities, mainly represented by members of alpha-Proteobacteria class (Oleomonas, Azospirillum), predominated. Beta-, gamma-, delta- (both syntrophobacteria and sulfate-reducing bacteria) and epsilon- (Arcobacter sp.) Proteobacteria were also noticeable. Archaea first appeared during the consolidation period. A Methanospirillum-like methanogen was detected after 36 h, and this was followed by the detection of Methanosarcina, after 4 days of biofilm development. The mature biofilm displayed a hill and valley topography with cells embedded in a matrix of exopolymers where the spatial distribution of the microorganisms became well-established. Compared to the earlier phases, the biodiversity had greatly increased. Although alpha-Proteobacteria remained as predominant, members of the phyla Firmicutes, Bacteroidete, and Thermotogae were also detected. Within the domain Archaea, the acetoclastic methanogen Methanosaeta concilii become dominant. This study provides insights on the trophic web and the shifts in population during biofilm development in an UASB reactor.}, }
@article {pmid18028414, year = {2008}, author = {Fekete, C and Tholander, M and Rajashekar, B and Ahrén, D and Friman, E and Johansson, T and Tunlid, A}, title = {Paralysis of nematodes: shifts in the transcriptome of the nematode-trapping fungus Monacrosporium haptotylum during infection of Caenorhabditis elegans.}, journal = {Environmental microbiology}, volume = {10}, number = {2}, pages = {364-375}, doi = {10.1111/j.1462-2920.2007.01457.x}, pmid = {18028414}, issn = {1462-2920}, mesh = {Animals ; Ascomycota/genetics/metabolism/*pathogenicity ; Caenorhabditis elegans/genetics/metabolism/*microbiology/physiology ; Caenorhabditis elegans Proteins/genetics/*metabolism ; Fungal Proteins/genetics/*metabolism ; *Gene Expression Profiling ; Gene Expression Regulation ; Gene Expression Regulation, Fungal ; Host-Parasite Interactions ; Oligonucleotide Array Sequence Analysis ; }, abstract = {The transcriptional response in the parasitic fungus Monacrosporium haptotylum and its nematode host Caenorhabditis elegans were analysed during infection using cDNA microarrays. The array contained 2684 fungal and 372 worm gene reporters. Dramatic shifts occurred in the transcriptome of M. haptotylum during the different stages of the infection. An initial transcriptional response was recorded after 1 h of infection when the traps adhered to the cuticle, but before immobilization of the captured nematodes. Among the differentially expressed genes were two serine protease genes (spr1 and spr2), and several homologues to genes known to be regulated in other pathogenic fungi. After 4 h, when approximately 40% of the nematodes were paralysed, we identified an upregulated cluster of 372 fungal genes which were not regulated during the other phases of the infection. This cohort contained a large proportion (79%) of genes that appear to be specific for M. haptotylum and closely related species. These genes were of two different classes: those translating into presumably functional peptides and those with no apparent protein coding potential (non-coding RNAs). Among the infection-induced C. elegans genes were those encoding antimicrobial peptides, protease inhibitors and lectins.}, }
@article {pmid18023049, year = {2008}, author = {Hoffmann, RA and Garcia, ML and Veskivar, M and Karim, K and Al-Dahhan, MH and Angenent, LT}, title = {Effect of shear on performance and microbial ecology of continuously stirred anaerobic digesters treating animal manure.}, journal = {Biotechnology and bioengineering}, volume = {100}, number = {1}, pages = {38-48}, doi = {10.1002/bit.21730}, pmid = {18023049}, issn = {1097-0290}, mesh = {Anaerobiosis/physiology ; Animals ; *Bacterial Physiological Phenomena ; *Bioreactors ; Cattle ; Cell Culture Techniques/instrumentation/methods ; Computer Simulation ; Ecosystem ; Equipment Design ; Equipment Failure Analysis ; Manure/*microbiology ; Methane/*metabolism ; Microfluidics/*methods ; *Models, Biological ; Refuse Disposal/*instrumentation/methods ; Rotation ; Shear Strength ; }, abstract = {We determined the effect of different mixing intensities on the performance, methanogenic population dynamics, and juxtaposition of syntrophic microbes in anaerobic digesters treating cow manure from a dairy farm. Computer automated radioactive particle tracking in conjunction with computational fluid dynamics was performed to quantify the shear levels locally. Four continuously stirred anaerobic digesters were operated at different mixing intensities of 1,500, 500, 250, and 50 revolutions per min (RPM) over a 260-day period at a temperature of 34 +/- 1 degrees C. Animal manure at a volatile solids (VS) concentration of 50 g/L was fed into the digesters daily at five different organic loading rates between 0.6 and 3.5 g VS/L day. The different mixing intensities had no effect on the biogas production rates and yields at steady-state conditions. A methane yield of 0.241 +/- 0.007 L CH(4)/g VS fed was obtained by pooling the data of all four digesters during steady-state periods. However, digester performance was affected negatively by mixing intensity during startup of the digesters, with lower biogas production rates and higher volatile fatty acids concentrations observed for the 1,500-RPM digester. Despite similar methane production yields and rates, the acetoclastic methanogenic populations were different for the high- and low-intensity mixed digesters with Methanosarcina spp. and Methanosaeta concilii as the predominant methanogens, respectively. For all four digesters, epifluorescence microscopy revealed decreasing microbial floc sizes beginning at week 4 and continuing through week 26 after which no microbial flocs remained. This decrease in size, and subsequent loss of microbial flocs did not, however, produce any long-term upsets in digester performance.}, }
@article {pmid18008101, year = {2008}, author = {Sedmak, B and Carmeli, S and Elersek, T}, title = {"Non-toxic" cyclic peptides induce lysis of cyanobacteria-an effective cell population density control mechanism in cyanobacterial blooms.}, journal = {Microbial ecology}, volume = {56}, number = {2}, pages = {201-209}, pmid = {18008101}, issn = {0095-3628}, mesh = {*Bacteriolysis ; Bacteriophages/*physiology ; Colony Count, Microbial ; *Eutrophication ; Lysogeny ; *Microcystis/drug effects/physiology/virology ; Peptides, Cyclic/*pharmacology ; Population Density ; }, abstract = {The presence of planktopeptin BL1125, anabaenopeptin B and anabaenopeptin F, two types of "non-toxic" cyclic peptide produced in bloom forming cyanobacteria, can provoke lysis of different non-axenic Microcystis aeruginosa cell lines via the induction of virus-like particles. The resulting particles are also able to infect the axenic M. aeruginosa cell line without lytic effects. Nevertheless, the presence of "non-toxic" cyclic peptides of cyanobacterial origin can induce lysis of these previously infected cells. This effect implies that a possible role of these peptides in the natural environment is the control of cyanobacterial population density. Lysogenic cyanobacteria can consequently act as hot-spots that, in the presence of cyanobacterial cyclic peptides, release numerous infectious particles. The process can be self-augmented with the simultaneous release of additional cyclic peptides from the producing lysogens, starting a forest fire effect that ends in collapse of cyanobacterial blooms.}, }
@article {pmid18005720, year = {2007}, author = {Rawls, JF}, title = {Enteric infection and inflammation alter gut microbial ecology.}, journal = {Cell host &amp; microbe}, volume = {2}, number = {2}, pages = {73-74}, pmid = {18005720}, issn = {1934-6069}, support = {K01 DK073695/DK/NIDDK NIH HHS/United States ; }, mesh = {Ecosystem ; Enterobacteriaceae/pathogenicity/*physiology ; Enterobacteriaceae Infections/*physiopathology ; Humans ; Inflammation/*microbiology/*physiopathology ; Intestinal Diseases/*microbiology/*physiopathology ; }, abstract = {The complex microbial community residing within the intestine plays important roles in host defense. However, the impact of enteric infection and inflammation on this resident community has not been fully explored. In this issue of Cell Host &amp; Microbe, Lupp and coworkers reveal that the composition of the intestinal microbiota changes in distinctive ways in response to infection and inflammation.}, }
@article {pmid17994287, year = {2008}, author = {Damare, S and Raghukumar, C}, title = {Fungi and macroaggregation in deep-sea sediments.}, journal = {Microbial ecology}, volume = {56}, number = {1}, pages = {168-177}, pmid = {17994287}, issn = {0095-3628}, mesh = {Biomass ; Culture Media ; Ecosystem ; Fungi/growth &amp; development/*physiology/ultrastructure ; Geologic Sediments/*chemistry/*microbiology ; Humic Substances/*microbiology ; Hyphae/ultrastructure ; Indian Ocean ; Microscopy, Electron, Scanning ; Microscopy, Fluorescence ; Polymers/chemistry/*metabolism ; Seawater/*microbiology ; }, abstract = {Whereas fungi in terrestrial soils have been well studied, little is known of them in deep-sea sediments. Recent studies have demonstrated the presence of fungal hyphae in such sediments but in low abundance. We present evidence in this study that one of the apparent reasons for the poor detection of fungi in deep-sea sediments is their cryptic presence in macroaggregates. Fungal biomass carbon from different core sections of deep-sea sediments from approximately 5000 m depth in the Central Indian Ocean was estimated based on direct microscopic detection of fungal mycelia. Treatment of sediment samples with ethylenediamine tetra-acetic acid (EDTA) enabled more frequent detection and significantly higher biomass than in samples without such treatment. Treatment with EDTA resulted in detecting various stages of breakdown of aggregates in the sediments, gradually revealing the presence of fungal hyphae within them. Experimental studies of a deep-sea, as well as three terrestrial isolates of fungi, showed that all could grow at 200 bar and 5 degrees C in a nutrient medium and in deep-sea sediment extract. Hyphae of fungi grown in sediment extract under the above conditions showed various stages of accretion of particles around them, leading to the formation of aggregates. Such aggregates showed the presence of humic material, carbohydrate, and proteins. We suggest that fungi in deep-sea sediments may be involved in humic aggregate formation by processes very similar to those in terrestrial sediments. The importance of such a process in carbon sequestration and food web in the deep sea needs to be examined.}, }
@article {pmid17991019, year = {2007}, author = {Rousk, J and Bååth, E}, title = {Fungal and bacterial growth in soil with plant materials of different C/N ratios.}, journal = {FEMS microbiology ecology}, volume = {62}, number = {3}, pages = {258-267}, doi = {10.1111/j.1574-6941.2007.00398.x}, pmid = {17991019}, issn = {0168-6496}, mesh = {Acetates/metabolism ; Bacteria/*growth &amp; development/metabolism ; Biomass ; Carbon/*metabolism ; Carbon Dioxide/metabolism ; Ecosystem ; Fungi/*growth &amp; development/metabolism ; *Hordeum/chemistry/metabolism ; Leucine/metabolism ; *Medicago sativa/chemistry/metabolism ; Nitrogen/*metabolism ; *Soil Microbiology ; }, abstract = {Fungal (acetate-in-ergosterol incorporation) and bacterial (leucine/thymidine incorporation) growth resulting from alfalfa (C/N=15) and barley straw (C/N=75) addition was studied in soil microcosms for 64 days. Nitrogen amendments were used to compensate for the C/N difference between the substrates. Fungal growth increased to a maximum after 3-7 days, at five to eight times the controls, following the addition of straw, and three to four times the controls following the addition of alfalfa. After 20-30 days, the fungal growth rate converged with the controls, resulting in a cumulative fungal growth two to three times the controls following straw addition and about 20% higher than the controls following alfalfa addition. The bacterial growth rate reached rates five times the controls following alfalfa addition and twice that of the controls following straw addition after 3-7 days. It remained elevated after 64 days. The cumulative bacterial growth was two and four times the controls following straw and alfalfa addition, respectively. A negative correlation was found between N addition and bacterial growth, while N stimulated fungal growth. Thus, the C/N ratio of the additions (substrate and extra N) could not entirely explain the different results regarding fungal and bacterial growths. Respiration was not always related to the combined growth of the microorganisms, emphasizing the requirement for a better understanding of growth efficiencies of fungi and bacteria.}, }
@article {pmid17981945, year = {2008}, author = {Fierer, N and Liu, Z and Rodríguez-Hernández, M and Knight, R and Henn, M and Hernandez, MT}, title = {Short-term temporal variability in airborne bacterial and fungal populations.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {1}, pages = {200-207}, pmid = {17981945}, issn = {1098-5336}, mesh = {*Air Microbiology ; Bacteria/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; Colorado ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fungi/*classification/genetics/*isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {Airborne microorganisms have been studied for centuries, but the majority of this research has relied on cultivation-dependent surveys that may not capture all of the microbial diversity in the atmosphere. As a result, our understanding of airborne microbial ecology is limited despite the relevance of airborne microbes to human health, various ecosystem functions, and environmental quality. Cultivation-independent surveys of small-subunit rRNA genes were conducted in order to identify the types of airborne bacteria and fungi found at a single site (Boulder, CO) and the temporal variability in the microbial assemblages over an 8-day period. We found that the air samples were dominated by ascomycete fungi of the Hypocreales order and a diverse array of bacteria, including members of the proteobacterial and Cytophaga-Flavobacterium-Bacteroides groups that are commonly found in comparable culture-independent surveys of airborne bacteria. Bacterium/fungus ratios varied by 2 orders of magnitude over the sampling period, and we observed large shifts in the phylogenetic diversity of bacteria present in the air samples collected on different dates, shifts that were not likely to be related to local meteorological conditions. We observed more phylogenetic similarity between bacteria collected from geographically distant sites than between bacteria collected from the same site on different days. These results suggest that outdoor air may harbor similar types of bacteria regardless of location and that the short-term temporal variability in airborne bacterial assemblages can be very large.}, }
@article {pmid17981943, year = {2008}, author = {Wittebolle, L and Vervaeren, H and Verstraete, W and Boon, N}, title = {Quantifying community dynamics of nitrifiers in functionally stable reactors.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {1}, pages = {286-293}, pmid = {17981943}, issn = {1098-5336}, mesh = {Bacteria/*classification/genetics/*growth &amp; development/metabolism ; Bioreactors/*microbiology ; Colony Count, Microbial/methods ; DNA Fingerprinting/methods ; DNA, Bacterial/chemistry/genetics ; Molecular Sequence Data ; Nitrites/metabolism ; Quaternary Ammonium Compounds/metabolism ; Sequence Analysis, DNA ; Sewage/microbiology ; Time Factors ; *Water Microbiology ; Water Purification/methods ; }, abstract = {A sequential batch reactor (SBR) and a membrane bioreactor (MBR) were inoculated with the same sludge from a municipal wastewater treatment plant, supplemented with ammonium, and operated in parallel for 84 days. It was investigated whether the functional stability of the nitrification process corresponded with a static ammonia-oxidizing bacterial (AOB) community. The SBR provided complete nitrification during nearly the whole experimental run, whereas the MBR showed a buildup of 0 to 2 mg nitrite-N liter(-1) from day 45 until day 84. Based on the denaturing gradient gel electrophoresis profiles, two novel approaches were introduced to characterize and quantify the community dynamics and interspecies abundance ratios: (i) the rate of change [Delta(t)((week))] parameter and (ii) the Pareto-Lorenz curve distribution pattern. During the whole sampling period, it was observed that neither of the reactor types maintained a static microbial community and that the SBR evolved more gradually than the MBR, particularly with respect to AOB (i.e., average weekly community changes of 12.6% +/- 5.2% for the SBR and 24.6% +/- 14.3% for the MBR). Based on the Pareto-Lorenz curves, it was observed that only a small group of AOB species played a numerically dominant role in the nitritation of both reactors, and this was true especially for the MBR. The remaining less dominant species were speculated to constitute a reserve of AOB which can proliferate to replace the dominant species. The value of these parameters in terms of tools to assist the operation of activated-sludge systems is discussed.}, }
@article {pmid17973156, year = {2008}, author = {Bezirtzoglou, E and Voidarou, Ch and Papadaki, A and Tsiotsias, A and Kotsovolou, O and Konstandi, M}, title = {Hormone therapy alters the composition of the vaginal microflora in ovariectomized rats.}, journal = {Microbial ecology}, volume = {55}, number = {4}, pages = {751-759}, pmid = {17973156}, issn = {0095-3628}, mesh = {Animals ; Bacteria/*drug effects ; Estradiol/analogs &amp; derivatives/pharmacology ; Estrogen Receptor Modulators/pharmacology ; *Estrogen Replacement Therapy ; Estrus ; Ethinyl Estradiol/*pharmacology ; Female ; Medroxyprogesterone Acetate/pharmacology ; Norpregnenes/pharmacology ; *Ovariectomy ; Rats ; Rats, Wistar ; Vagina/*microbiology ; Vaginosis, Bacterial/*microbiology ; }, abstract = {The aim of the present study was to evaluate the alterations that may take place in the bacterial genital tract flora in the absence of ovarian hormones. The role of hormone replacement therapy was also assessed. For this purpose, various bacteria were identified from the vaginal flora of ovariectomized and sham operated female rats, following the Bergey's manual criteria. The data of this study showed that substantial differences exist in the vaginal bacterial microflora between ovariectomized and normal cyclic rats. Ovariectomy was associated with a lower total bacterial load that may be due mainly to the absence of Lactobacillus. Anaerobic bacteria were also absent. Streptococcus and Enterococcus were also not favored in an environment lacking the ovarian hormones. In contrast, C. perfringens, Bacteroides, S. epidermidis, and S. aureus were detected in high numbers in ovariectomized rats. In terms of the impact of hormone replacement therapy on vaginal flora, only estradiol (EE2) restored Lactobacillus levels in ovariectomized rats, whereas all hormonal schemes used brought Streptococcus, Clostridium lec (-), and C. perfringens, the spore and vegetative forms, close to those detected in normal cyclic female rats. In conclusion, ovarian hormones appeared to be regulatory factors that favor the presence of a broad variety of bacteria, which are members of the normal genital tract flora. On the other hand, ovariectomy modifies the vaginal microbial profile, and hormone replacement therapy based mainly on schemes containing EE2 could alleviate this disturbance.}, }
@article {pmid17973155, year = {2008}, author = {Bizzarri, MF and Bishop, AH}, title = {The ecology of Bacillus thuringiensis on the Phylloplane: colonization from soil, plasmid transfer, and interaction with larvae of Pieris brassicae.}, journal = {Microbial ecology}, volume = {56}, number = {1}, pages = {133-139}, pmid = {17973155}, issn = {0095-3628}, mesh = {Animals ; Bacillus thuringiensis/genetics/*growth &amp; development ; Brassica/*microbiology ; Conjugation, Genetic ; Ecology ; Larva/growth &amp; development/microbiology ; Lepidoptera/growth &amp; development/*microbiology ; Plant Leaves/microbiology ; Plasmids/*genetics ; *Soil Microbiology ; Spores, Bacterial/growth &amp; development ; Trifolium/growth &amp; development/*microbiology ; }, abstract = {Seedlings of clover (Triflorium hybridum) were colonized by Bacillus thuringiensis when spores and seeds were co-inoculated into soil. Both a strain isolated in the vegetative form from the phylloplane of clover, 2810-S-4, and a laboratory strain, HD-1, were able to colonize clover to a density of about 1000 CFU/g leaf when seeds were sown in sterile soil and to a density of about 300 CFU/g leaf in nonsterile soil. A strain lacking the characteristic insecticidal crystal proteins produced a similar level of colonization over a 5-week period as the wild type strain, indicating that crystal production was not a mitigating factor during colonization. A small plasmid, pBC16, was transferred between strains of B. thuringiensis when donor and recipient strains were sprayed in vegetative form onto leaves of clover and pak choi (Brassica campestris var. chinensis). The rate of transfer was about 0.1 transconjugants/recipient and was dependent on the plant species. The levels of B. thuringiensis that naturally colonized leaves of pak choi produced negligible levels of mortality in third instar larvae of Pieris brassicae feeding on the plants. Considerable multiplication occurred in the excreted frass but not in the guts of living insects. Spores in the frass could be a source of recolonization from the soil and be transferred to other plants. These findings illustrate a possible cycle, not dependent on insect pathology, by which B. thuringiensis diversifies and maintains itself in nature.}, }
@article {pmid17972129, year = {2008}, author = {Wanner, M and Elmer, M and Kazda, M and Xylander, WE}, title = {Community assembly of terrestrial testate amoebae: how is the very first beginning characterized?.}, journal = {Microbial ecology}, volume = {56}, number = {1}, pages = {43-54}, pmid = {17972129}, issn = {0095-3628}, mesh = {Amoeba/*classification/*growth &amp; development/metabolism ; Animals ; Biodiversity ; Cellulose/*metabolism ; Cluster Analysis ; Ecology ; *Ecosystem ; Soil/*parasitology ; Species Specificity ; }, abstract = {Testate amoebae play an important role at the very first beginning of succession on land. We used litterbags buried into four different soils to study the early colonization (which occurred within less than 55 days) and establishment of testate amoebae. The litterbag cellulose exposed at the youngest mining site poor in nitrogen and phosphorus was colonized firstly in high abundances, whereas the substrate introduced into the reference sites of undisturbed soil was colonized slowly and in low densities. Besides the (expected) small-sized r-strategists (e.g., Euglypha rotunda, Tracheleuglypha dentata, and Trinema lineare), large-sized K-strategists (e.g., Centropyxis spp., Phryganella acropodia) occurred in remarkably high densities on all sites. Species that colonized the cellulose in high densities (e.g., P. acropodia and T. dentata) were found extremely rarely in the adjacent source substrate and vice versa, stressing the importance of the target substrate quality. In the course of the experiment, the influencing environmental factors became more complex, as shown by redundancy analysis (RDA). Concerning the amoebal community, there was a change from variability to stability, as visualized by cluster analysis. Adjacent litterbags within an investigation site revealed amoebal species and abundances with an increasing similarity during exposition time, whereas the litterbags between the four investigation sites were colonized differently. These observations point to a stochastic (variable) beginning of community assembly, changing to a more deterministic (stable) course. No species replacement has been observed, which is an essential part of most successional theories. Thus, the more flexible concept of "community assembly" should be considered instead of "succession" for protozoa. The stochastic beginning of community assembly and the lack of species replacement are explained by a neutral community model.}, }
@article {pmid17969627, year = {2007}, author = {Carrasco, E and Pérez-Rodríguez, F and Valero, A and García-Gimeno, RM and Zurera, G}, title = {Survey of temperature and consumption patterns of fresh-cut leafy green salads: risk factors for listeriosis.}, journal = {Journal of food protection}, volume = {70}, number = {10}, pages = {2407-2412}, doi = {10.4315/0362-028x-70.10.2407}, pmid = {17969627}, issn = {0362-028X}, mesh = {Colony Count, Microbial ; Consumer Product Safety ; Food Contamination/analysis/prevention &amp; control ; Food Handling/*methods ; Food Preservation/*methods ; Humans ; Listeria monocytogenes/*growth &amp; development ; Listeriosis/prevention &amp; control ; *Risk Assessment ; Spain ; Surveys and Questionnaires ; Temperature ; Vegetables/*microbiology ; }, abstract = {Increasing demand for fresh-cut or ready-to-eat fruits and vegetables, developed to meet the consumer need for quick and convenient products, has prompted extensive research into their microbiological quality, safety, processing, and packaging. The microbial ecology of Listeria monocytogenes is recognized as a major safety concern for fresh-cut produce. A survey was performed to collect information on consumption patterns of fresh-cut leafy green salads and the temperature of domestic refrigerators. Salad consumption was low-moderate: 24.3% of respondents never purchased fresh-cut leafy green salads; of those who reported buying these products, 7.41% did so more than twice a week, 17.28% once or twice a week, 29.63% once or twice a month, and 45.68% occasionally. Saving time and convenience were the advantages most widely reported by consumers. A total of 9.9% of respondents did not always respect the "use-by" date of fresh-cut salads, a negative practice that could contribute to the risk of listeriosis. Temperatures reported in domestic refrigerators were compatible with the growth of L. monocytogenes on ready-to-eat salads. Variations in average temperature followed a normal distribution, N(6.62, 2.56), while the variability of temperature variance was described by a gamma distribution, G(2.00, 1.00). As expected, when a time of day-temperature profile was plotted over a 24-h period, changes corresponding to the transition between day and night were observed. Knowledge of consumption patterns and consumer hygiene practices is essential, first in assessing the risk of listeriosis (risk assessment) and second in taking measures to manage that risk (risk management).}, }
@article {pmid17968612, year = {2008}, author = {Chauhan, A and Williams, HN}, title = {Biostimulation of estuarine microbiota on substrate coated agar slides: a novel approach to study diversity of autochthonous Bdellovibrio- and like organisms.}, journal = {Microbial ecology}, volume = {55}, number = {4}, pages = {640-650}, pmid = {17968612}, issn = {0095-3628}, mesh = {Agar ; Amino Acids/metabolism ; Bdellovibrio/*genetics/*growth &amp; development ; *Biodiversity ; Biofilms ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Ecology ; Genes, rRNA ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Vibrio parahaemolyticus/growth &amp; development ; *Water Microbiology ; }, abstract = {Characterization of Bdellovibrio- and like organisms (BALOs) from environmental samples involves growing them in the presence of Gram-negative prey bacteria and isolation of BALO plaques. This labor-intensive enrichment and isolation procedure may impede the detection and phylogenetic characterization of uncultivable BALOs. In this article, we describe a simple slide biofilm assay to improve detection and characterization of BALO microbiota. Agar spiked with biostimulants such as yeast extract (YE), casamino acids (CA), or concentrated cells of Vibrio parahaemolyticus P5 (most widely used prey bacteria for isolation of halophilic BALOs) was plated onto buffed glass slides and exposed to water samples collected from Apalachicola Bay, Florida. After incubating for a week, diversity of the biofilm bacterial community was studied by culture-dependent and culture-independent molecular methods. The results revealed that most probable numbers (MPNs) of BALOs and total culturable bacteria recovered from YE agar slide were significantly higher than the numbers on CA- or P5-spiked agar slides. Polymerase chain reaction-restriction fragment length polymorphism followed by 16S rDNA sequencing of clones from different biostimulants resulted in identification of a plethora of Gram-negative bacteria predominantly from the alpha, gamma, delta-proteobacteria, and the Cytophaga-Flavobacterium-Bacteroides group. Corresponding to the higher biomass on the YE agar slide, the BALO clone library from YE was most diverse, consisting of Bacteriovorax spp. and a novel clade representing Peredibacter spp. Microbiota from all three biostimulated biofilms were exclusively Gram-negative, and each bacterial guild represented potential prey for BALOs. We propose the use of this simple yet novel slide biofilm assay to study oligotrophic aquatic bacterial diversity which could also potentially be utilized to isolate marine bacteria with novel traits.}, }
@article {pmid17968538, year = {2008}, author = {Pham, TH and Boon, N and Aelterman, P and Clauwaert, P and De Schamphelaire, L and Vanhaecke, L and De Maeyer, K and Höfte, M and Verstraete, W and Rabaey, K}, title = {Metabolites produced by Pseudomonas sp. enable a Gram-positive bacterium to achieve extracellular electron transfer.}, journal = {Applied microbiology and biotechnology}, volume = {77}, number = {5}, pages = {1119-1129}, doi = {10.1007/s00253-007-1248-6}, pmid = {17968538}, issn = {0175-7598}, mesh = {Acetates ; DNA, Bacterial/chemistry/genetics ; *Electricity ; Electrodes ; Electron Transport ; Glycolipids/metabolism ; Gram-Positive Bacteria/*metabolism ; Iron Compounds/metabolism ; Minerals ; Molecular Sequence Data ; Oxidation-Reduction ; Phenazines/metabolism ; Pseudomonas/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Surface-Active Agents/metabolism ; }, abstract = {Previous studies revealed the abundance of Pseudomonas sp. in the microbial community of a microbial fuel cell (MFC). These bacteria can transfer electrons to the electrode via self-produced phenazine-based mediators. A MFC fed with acetate where several Pseudomonas sp. were present was found to be rich in a Gram-positive bacterium, identified as Brevibacillus sp. PTH1. Remarkably, MFCs operated with only the Brevibacillus strain in their anodes had poor electricity generation. Upon replacement of the anodic aqueous part of Brevibacillus containing MFCs with the cell-free anodic supernatants of MFCs operated with Pseudomonas sp. CMR12a, a strain producing considerable amounts of phenazine-1-carboxamide (PCN) and biosurfactants, the electricity generation was improved significantly. Supernatants of Pseudomonas sp. CMR12a_Reg, a regulatory mutant lacking the ability to produce PCN, had no similar improvement effect. Purified PCN, together with rhamnolipids as biosurfactants (1 mg L(-1)), could clearly improve electricity generation by Brevibacillus sp. PTH1, as well as enable this bacterium to oxidize acetate with concomitant reduction of ferric iron, supplied as goethite (FeOOH). When added alone, PCN had no observable effects on Brevibacillus' electron transfer. This work demonstrates that metabolites produced by Pseudomonas sp. enable Gram-positive bacteria to achieve extracellular electron transfer. Possibly, this bacterial interaction is a key process in the anodic electron transfer of a MFC, enabling Brevibacillus sp. PTH1 to achieve its dominance.}, }
@article {pmid17965957, year = {2008}, author = {López-Cortés, A and Lanz-Landázuri, A and García-Maldonado, JQ}, title = {Screening and isolation of PHB-producing bacteria in a polluted marine microbial mat.}, journal = {Microbial ecology}, volume = {56}, number = {1}, pages = {112-120}, pmid = {17965957}, issn = {0095-3628}, mesh = {*Bacillus/classification/genetics/isolation &amp; purification/metabolism ; DNA, Bacterial/analysis/isolation &amp; purification ; DNA, Ribosomal/analysis ; Ecosystem ; Geologic Sediments/*microbiology ; Hydroxybutyrates/*metabolism ; Industrial Waste ; Mexico ; Molecular Sequence Data ; Phylogeny ; Polyesters/*metabolism ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; Sequence Analysis, DNA ; *Staphylococcus/classification/genetics/isolation &amp; purification/metabolism ; Water Pollution/*analysis ; }, abstract = {The characteristics of microbial mats within the waste stream from a seafood cannery were compared to a microbial community at a pristine site near a sandy beach at Puerto San Carlos, Baja California Sur, Mexico. Isolation of poly-beta-hydroxybutyrate (PHB)-producing bacteria, recognition of brightly refractile cytoplasmatic inclusions, lipophilic stains with Sudan Black and Nile Red, and chemical extraction of PHB were used as a culture-dependent strategy for the detection of PHB-producing bacteria. The culture-independent approach included denaturing gradient gel electrophoresis of phylotypes of 16S rRNA of microbial communities from environmental samples. Significant differences in community structure were found among the polluted and pristine sites. These differences were correlated with the physicochemical characteristics of the seawater column. At the polluted site, the seawater was rich in nutrients (ammonia, phosphates, and organic matter), compared to the pristine location. Partial sequencing of 16S rDNA of cultures of bacteria producing PHB included Bacillus and Staphylococcus at both sites; Paracoccus and Micrococcus were found only at the polluted site and Rhodococcus and Methylobacterium were found only at the pristine site. Bands of the sequences of 16S rDNA from both field samples in the denaturing gradient gel electrophoresis (DGGE) analyses affiliated closely only with bacterial sequences of cultures of Bacillus and Staphylococcus. High concentrations of organic and inorganic nutrients at the polluted site had a clear effect on the composition and diversity of the microbial community compared to the unpolluted site.}, }
@article {pmid17965949, year = {2008}, author = {Ishida, CK and Arnon, S and Peterson, CG and Kelly, JJ and Gray, KA}, title = {Influence of algal community structure on denitrification rates in periphyton cultivated on artificial substrata.}, journal = {Microbial ecology}, volume = {56}, number = {1}, pages = {140-152}, pmid = {17965949}, issn = {0095-3628}, mesh = {Biofilms/*growth &amp; development ; Biomass ; Culture Media ; Cyanobacteria/classification/genetics/*growth &amp; development/metabolism ; Diatoms/classification/genetics/growth &amp; development/metabolism ; *Ecosystem ; Eukaryota/*classification/genetics/*growth &amp; development/metabolism ; Fresh Water/chemistry/*microbiology ; Geologic Sediments/microbiology ; Microbiological Techniques ; Nitrites/*metabolism ; Polymorphism, Restriction Fragment Length ; Seasons ; }, abstract = {We conducted a field survey of periphyton cultivated on benthic mesh installations in freshwater aquatic systems, including two constructed wetlands and a pond, and also studied periphyton grown on a benthic mesh in laboratory mesocosms. The objectives of this study were to (1) determine if periphyton cultivated on benthic mesh denitrifies at higher rates than the underlying sediments and (2) determine if denitrification rates within periphyton vary with characteristics such as algal and bacterial community structure and biomass. We measured denitrification potential rates of field and laboratory periphyton by the acetylene inhibition method. We characterized algal community composition by algal identification and bacterial community composition by terminal restriction fragment length polymorphisms. Periphyton collected on benthic mesh from our field sites denitrified at significantly higher rates than the underlying sediments, regardless of sampling site or season. Results from both our field survey and laboratory studies indicated a significant, positive correlation between diatom presence and denitrification rate. In our laboratory studies, we found that periphyton with the highest diatom abundance showed the highest denitrification rates as well as a distinct bacterial community composition. These results suggest a synergistic relationship between diatoms and denitrifying bacteria that warrants further study.}, }
@article {pmid17960485, year = {2008}, author = {Dominguez, RF and da Silva, ML and McGuire, TM and Adamson, D and Newell, CJ and Alvarez, PJ}, title = {Aerobic bioremediation of chlorobenzene source-zone soil in flow-through columns: performance assessment using quantitative PCR.}, journal = {Biodegradation}, volume = {19}, number = {4}, pages = {545-553}, doi = {10.1007/s10532-007-9160-4}, pmid = {17960485}, issn = {0923-9820}, mesh = {*Aerobiosis ; Base Sequence ; Chlorobenzenes/*metabolism ; DNA Primers ; Environmental Restoration and Remediation/*methods ; Polymerase Chain Reaction/*methods ; }, abstract = {Flow-through aquifer columns were operated for 12 weeks to evaluate the benefits of aerobic biostimulation for the bioremediation of source-zone soil contaminated with chlorobenzenes (CBs). Quantitative Polymerase Chain Reaction (qPCR) was used to measure the concentration of total bacteria (16S rRNA gene) and oxygenase genes involved in the biodegradation of aromatic compounds (i.e., toluene dioxygenase, ring hydroxylating monooxygenase, naphthalene dioxygenase, phenol hydroxylase, and biphenyl dioxygenase). Monochlorobenzene, which is much more soluble than dichlorobenzenes, was primarily removed by flushing, and biostimulation showed little benefit. In contrast, dichlorobenzene removal was primarily due to biodegradation, and the removal efficiency was much higher in oxygen-amended columns compared to a control column. To our knowledge, this is the first report that oxygen addition can enhance CB source-zone soil bioremediation. Analysis by qPCR showed that whereas the biphenyl and toluene dioxygenase biomarkers were most abundant, increases in the concentration of the phenol hydroxylase gene reflected best the higher dichlorobenzene removal due to aerobic biostimulation. This suggests that quantitative molecular microbial ecology techniques could be useful to assess CB source-zone bioremediation performance.}, }
@article {pmid17960375, year = {2007}, author = {Carrigg, C and Rice, O and Kavanagh, S and Collins, G and O'Flaherty, V}, title = {DNA extraction method affects microbial community profiles from soils and sediment.}, journal = {Applied microbiology and biotechnology}, volume = {77}, number = {4}, pages = {955-964}, doi = {10.1007/s00253-007-1219-y}, pmid = {17960375}, issn = {0175-7598}, mesh = {Bacteria/*genetics ; DNA ; DNA, Bacterial/*genetics/isolation &amp; purification ; DNA, Ribosomal/analysis ; Electrophoresis, Polyacrylamide Gel/*methods ; *Environmental Microbiology ; Geologic Sediments/microbiology ; Nucleic Acid Denaturation ; RNA, Ribosomal, 16S/*genetics ; Soil Microbiology ; }, abstract = {To evaluate whether different deoxyribonucleic acid (DNA) extraction procedures can affect estimates of bacterial community composition, based on the 16S ribosomal ribonucleic acid gene denaturing gradient gel electrophoresis (DGGE) profiles, we compared four in situ lysis procedures using three soils and one marine sediment. Analysis of DGGE profiles, generated by polymerase chain reaction of purified DNA extracts, demonstrated that the choice of DNA extraction method significantly influenced the bacterial community profiles generated. This was reflected both in the number of bands or ribotypes detected from each sample and in subsequent principle coordinate analysis and unweighted-pair group method using arithmetic average analyses. The methods also differed significantly in their robustness, i.e. reproducibility across multiple analyses. Two methods, both based on bead beating, were demonstrated to be suitable for comparative studies of a range of soil and sediment types.}, }
@article {pmid17957402, year = {2008}, author = {Lammertyn, E and Vande Voorde, J and Meyen, E and Maes, L and Mast, J and Anné, J}, title = {Evidence for the presence of Legionella bacteriophages in environmental water samples.}, journal = {Microbial ecology}, volume = {56}, number = {1}, pages = {191-197}, pmid = {17957402}, issn = {0095-3628}, mesh = {*Bacteriophages/classification/genetics/isolation &amp; purification/physiology ; Culture Media ; DNA, Viral/analysis/isolation &amp; purification ; Fresh Water/*virology ; Humans ; Legionella/classification/*virology ; Legionella pneumophila/*virology ; Lysogeny ; *Myoviridae/classification/genetics/isolation &amp; purification/physiology ; Species Specificity ; }, abstract = {The existence and preliminary characterization of bacteriophages active against the Gram-negative human pathogen Legionella pneumophila, the causative agent of a very severe form of pneumonia, are reported. Four phages belonging to the family of the Myoviridae were isolated from various fresh water environments, and preliminary characterization showed that these crude preparations infect exclusively bacteria belonging to the genus Legionella. Standard phage amplification, purification, and characterization procedures were, however, not efficiently applicable making more research into these novel phages and their mechanism of infection necessary. The existence of Legionella bacteriophages is very promising for future applications such as the development of novel molecular tools, the design of new detection and typing methods, and the bioremediation of this environmental pathogen.}, }
@article {pmid17955326, year = {2007}, author = {Cavagnaro, TR and Jackson, LE and Scow, KM and Hristova, KR}, title = {Effects of arbuscular mycorrhizas on ammonia oxidizing bacteria in an organic farm soil.}, journal = {Microbial ecology}, volume = {54}, number = {4}, pages = {618-626}, pmid = {17955326}, issn = {0095-3628}, support = {5 P42 ES004699/ES/NIEHS NIH HHS/United States ; }, mesh = {Agriculture/methods ; Ammonia/*metabolism ; Bacteria/*classification/genetics/growth &amp; development/metabolism ; Benzothiazoles ; DNA, Bacterial/analysis/isolation &amp; purification ; Diamines ; Ecosystem ; Solanum lycopersicum/classification/genetics/*microbiology ; Molecular Sequence Data ; Mycorrhizae/*growth &amp; development ; Organic Chemicals ; Oxidation-Reduction ; Plant Roots/*microbiology ; Polymerase Chain Reaction/methods ; Quinolines ; Sequence Analysis, DNA ; *Soil Microbiology ; Taq Polymerase ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) are potentially important in nutrient cycling in agricultural soils and particularly in soils managed for organic production; little is known, however, about the interrelationships between AMF and other members of soil microbial communities. Ammonia oxidizing bacteria (AOB) are a trophic group of bacteria having an enormous impact on nitrogen availability in soils and are expected to be influenced by the presence of AMF. In a field study, we utilized a unique genetic system comprised of a mycorrhiza defective tomato mutant (named rmc) and its mycorrhiza wild-type progenitor (named 76RMYC+). We examined the effect of AMF by comparing AOB community composition and populations in soil containing roots of the two tomato genotypes in an organically managed soil. Responses of AOB to soil N and P amendments were also studied in the same experiment. Phylogenetic analysis of cloned AOB sequences, derived from excised denaturing gradient gel electrophoresis (DGGE) bands, revealed that the organic farm soil supported a diverse yet stable AOB community, which was neither influenced by mycorrhizal colonization of roots nor by N and P addition to the soil. Real-time TaqMan polymerase chain reaction (PCR) was used to quantify AOB population sizes and showed no difference between any of the treatments. An alternative real-time PCR protocol for quantification of AOB utilizing SYBR green yielded similar results as the TaqMan real-time PCR method, although with slightly lower resolution. This alternative method is advantageous in not requiring the detailed background information about AOB community composition required for adaptation of the TaqMan system for a new soil.}, }
@article {pmid17952491, year = {2008}, author = {Fourçans, A and Ranchou-Peyruse, A and Caumette, P and Duran, R}, title = {Molecular analysis of the spatio-temporal distribution of sulfate-reducing bacteria (SRB) in Camargue (France) hypersaline microbial mat.}, journal = {Microbial ecology}, volume = {56}, number = {1}, pages = {90-100}, pmid = {17952491}, issn = {0095-3628}, mesh = {*Biofilms ; DNA, Bacterial/analysis/isolation &amp; purification ; *Deltaproteobacteria/classification/genetics/growth &amp; development/physiology ; Ecosystem ; France ; Fresh Water/*microbiology ; Gene Library ; Molecular Sequence Data ; Oxygen/*pharmacology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Sodium Chloride ; Sulfates/metabolism ; *Sulfur-Reducing Bacteria/classification/genetics/growth &amp; development/physiology ; }, abstract = {The spatio-temporal distribution of sulfate-reducing bacteria (SRB) in the microbial mat of Camargue (Salins-de-Giraud, France) was investigated by molecular approaches at both microscale spatial resolution and different taxonomic organization levels. The vertical distribution of the SRB populations was correlated with oxygen and sulfide microgradient fluctuations. Comparisons of Terminal restriction fragment length polymorphism (T-RFLP) fingerprints showed distinct locations of some operational taxonomic units at daytime and at night (4:00 or 15:00 hours) revealing important differences on the structures of the bacterial communities. When oxygen penetrates the mat, SRB migration was observed either downward to reach deeper anoxic zones to escape oxygen or upward to reach oxic surface zones. When no migration was observed, both metabolism switches and aggregate formations were suspected. These behaviors allowed the aerotolerant SRB to deal with oxygen. The analysis of the Desulfococcus-Desulfonema-Desulfosarcina T-RFLP profiles revealed up-migrating populations related to both Desulfonema sp. and Desulfosarcina variabilis. T-RFLP profiles combined with 16S ribosomal ribonucleic acid gene library analysis of the Desulfobacter group revealed two distinct populations: a population related to the recently described Desulfotignum genus migrating upward during the night and a population of a new species of the Desulfobacter uniformly located throughout the mat independent of the period. Thus, the identification of the new oxygen-tolerant SRB will provide the basis for understanding the physiological adaptations to oxygen.}, }
@article {pmid17949885, year = {2007}, author = {Kurland, CG and Canbäck, B and Berg, OG}, title = {The origins of modern proteomes.}, journal = {Biochimie}, volume = {89}, number = {12}, pages = {1454-1463}, doi = {10.1016/j.biochi.2007.09.004}, pmid = {17949885}, issn = {0300-9084}, mesh = {Amino Acid Sequence ; Archaea/genetics ; Archaeal Proteins/chemistry/genetics ; Bacteria/genetics ; Bacterial Proteins/chemistry/genetics ; Computational Biology ; Databases, Protein ; Eukaryotic Cells/chemistry ; *Evolution, Molecular ; Genes, Archaeal ; Genes, Bacterial ; Genome ; Humans ; Models, Biological ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Proteins ; *Proteome ; Proteomics ; Sequence Homology, Amino Acid ; }, abstract = {Distributions of phylogenetically related protein domains (fold superfamilies), or FSFs, among the three Superkingdoms (trichotomy) are assessed. Very nearly 900 of the 1200 FSFs of the trichotomy are shared by two or three Superkingdoms. Parsimony analysis of FSF distributions suggests that the FSF complement of the last common ancestor to the trichotomy was more like that of modern eukaryotes than that of archaea and bacteria. Studies of length distributions among members of orthologous families of proteins present in all three Superkingdoms reveal that such lengths are significantly longer among eukaryotes than among bacteria and archaea. The data also reveal that proteins lengths of eukaryotes are more broadly distributed than they are within archaeal and bacterial members of the same orthologous families. Accordingly, selective pressure for a minimal size is significantly greater for orthologous protein lengths in archaea and bacteria than in eukaryotes. Alignments of orthologous proteins of archaea, bacteria and eukaryotes are characterized by greater sequence variation at their N-terminal and C-terminal domains, than in their central cores. Length variations tend to be localized in the terminal sequences; the conserved sequences of orthologous families are localized in a central core. These data are consistent with the interpretation that the genomes of the last common ancestor (LUCA) encoded a cohort of FSFs not very different from that of modern eukaryotes. Divergence of bacterial and archaeal genomes from that common ancestor may have been accompanied by more intensive reductive evolution of proteomes than that expressed in eukaryotes. Dollo's Law suggests that the evolution of novel FSFs is a very slow process, while laboratory experiments suggests that novel protein genesis from preexisting FSFs can be relatively rapid. Reassortment of FSFs to create novel proteins may have been mediated by genetic recombination before the advent of more efficient splicing mechanisms.}, }
@article {pmid17943341, year = {2008}, author = {Sullivan, TJ and Faeth, SH}, title = {Local adaptation in Festuca arizonica infected by hybrid and nonhybrid Neotyphodium endophytes.}, journal = {Microbial ecology}, volume = {55}, number = {4}, pages = {697-704}, pmid = {17943341}, issn = {0095-3628}, mesh = {*Adaptation, Physiological ; Analysis of Variance ; Arizona ; Biological Evolution ; Environment ; Festuca/*growth &amp; development/*microbiology ; Gene Flow ; Genetics, Population ; Genotype ; Hybridization, Genetic ; Hypocreales/genetics/*growth &amp; development ; Population Dynamics ; Soil Microbiology ; Symbiosis ; Time Factors ; }, abstract = {Cool-season grasses often harbor obligate fungal symbionts from the genus Neotyphodium, and these symbiota can function as a single ecological unit. Previous studies have shown that gene flow in Neotyphodium in Festuca arizonica is low enough such that populations could diverge and form local adaptations. A reciprocal transplant experiment was performed between two F. arizonica/Neotyphodium populations in Arizona, Clint's Well and Flagstaff, using symbiota with the most common Neotyphodium genotypes in each population, to test for local adaptations. The genetic difference between populations is potentially large as Neotyphodium from Clint's Well are of hybrid origin. Local environmental variation was the most important source of variation for F. arizonica/Neotyphodium symbiota growth, with individuals at Flagstaff growing larger and individuals at Clint's Well not reproducing. Local environment and the source population of the symbiota interacted to affect vegetative growth. Symbiota from Clint's Well, which harbor hybrid Neotyphodium, had higher volume/wet mass and volume/dry mass ratios but only in the marginal Clint's Well habitat. The local environment also affected F. arizonica/Neotyphodium reproduction because only symbiota transplanted to Flagstaff reproduced. Symbiota from Clint's Well produced more panicles, whereas symbiota from Flagstaff with nonhybrid Neotyphodium produced greater seed mass per panicle. Overall seed mass production was not different, suggesting that the two strategies are functionally equivalent. We find that F. arizonica/Neotyphodium symbiota vary geographically, but potential local adaptations are only apparent in marginal habitats and may be related to the evolutionary history of the Neotyphodium part of the symbiota.}, }
@article {pmid17943340, year = {2008}, author = {Korkama-Rajala, T and Müller, MM and Pennanen, T}, title = {Decomposition and fungi of needle litter from slow- and fast-growing Norway spruce (Picea abies) clones.}, journal = {Microbial ecology}, volume = {56}, number = {1}, pages = {76-89}, pmid = {17943340}, issn = {0095-3628}, mesh = {Agaricales/classification/genetics/*isolation &amp; purification ; Ascomycota/classification/genetics/*isolation &amp; purification ; Cloning, Molecular ; Culture Media ; DNA, Fungal/analysis/isolation &amp; purification ; DNA, Ribosomal Spacer/analysis ; Finland ; Molecular Sequence Data ; Picea/genetics/*growth &amp; development/*microbiology ; Plant Leaves/chemistry/*metabolism/microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The fungal species involved in the decomposition of needle litter and their response to intraspecific genetic variation of trees are poorly known. First, we compared the needle decomposition and fungal decomposers underneath eight different Norway spruce clones in situ. This experiment revealed 60-70% loss of needle mass in two years. Although spruce clones differed considerably in growth (twofold height difference) and their needles differed in chemical composition, no significant difference was found for loss of needle mass under the spruce clones. Furthermore, the spruce clones did not affect the community structure of the fungal decomposers. Fungi inhabiting needle litter were identified by extracting ribosomal RNA (rRNA) and sequencing complementary DNA (cDNA) of internal trascribed spacer 1 (ITS1) region. The most frequent identifications were Lophodermium, Pezizales, Mycena, and Marasmius, suggesting that endophytic fungi were involved in the decomposition process. Second, we evaluated the potential of endophytes to decompose needle material in a microcosm experiment in which all other fungi than endophytes were excluded. Within 2 years, the endophytes had decomposed 35-45% of the needle mass. Sequences of Mollisia, Lophodermium, Lachnum, and Phialocephala were most frequently found in rRNA and rDNA extracted from the needles at the end of the microcosm experiment. The dominant needle endophyte in fresh, green needles was Lophodermium piceae, and this species was also found frequently in the needle material after 2 years of decay both in the field and laboratory experiments. Moreover, the relative abundance of Lophodermium-derived denaturing gradient gel electrophoresis (DGGE) bands correlated positively with the decomposition in the microcosm experiment. Hence, our results suggest a significant role of endophytic fungi, and particularly L. piceae, in the process of needle decomposition in boreal forests.}, }
@article {pmid17940820, year = {2008}, author = {Kolarík, M and Kubátová, A and Hulcr, J and Pazoutová, S}, title = {Geosmithia fungi are highly diverse and consistent bark beetle associates: evidence from their community structure in temperate Europe.}, journal = {Microbial ecology}, volume = {55}, number = {1}, pages = {65-80}, pmid = {17940820}, issn = {0095-3628}, mesh = {Animals ; Climate ; Coleoptera/classification/*growth &amp; development ; DNA, Fungal/analysis/isolation &amp; purification ; DNA, Ribosomal Spacer/analysis ; *Ecosystem ; Europe ; Hypocreales/classification/genetics/*growth &amp; development ; *Magnoliopsida/microbiology/parasitology ; Phenotype ; Phylogeny ; *Plant Bark/microbiology/parasitology ; RNA, Ribosomal, 5.8S/genetics ; Random Amplified Polymorphic DNA Technique ; *Tracheophyta/microbiology/parasitology ; }, abstract = {Geosmithia spp. (Ascomycota: Hypocreales) are little-studied, dry-spored fungi that occur in galleries built by many phloeophagous bark beetles. This study mapped the distribution and environmental preferences of Geosmithia species occurring in galleries of temperate European bark beetles. One hundred seven host tree samples of 16 tree species infested with 23 subcortical insect species were collected from across Europe during the years 1997-2005. Over 600 Geosmithia isolates from the beetles were sorted into 17 operational taxonomic units (OTUs) based on their phenotype similarity and phylogeny of internal transcribed spacer (ITS) region of rDNA (ITS1-5.8S-ITS2). The OTUs represent six known species and eight undescribed taxa. Ninety-two samples infested with subcortical insects were characterized by the presence/absence of OTUs and the similarity among the samples was evaluated. Geographically distant populations of the same beetle species host relatively uniform Geosmithia communities across large geographic areas (ranging from southern Bulgaria to the Czech Republic). This suggests effective dispersal of Geosmithia spp. by bark beetles. Clustering of similar samples in ordination analysis is correlated predominantly with the isolation source (bark beetles and their respective feeding plant), but not with their geographical origin. The composition of the Geosmithia OTU community of each bark beetle species depends on the degree of isolation of the species' niches. Thus, Geosmithia communities associated with regularly co-occurring bark beetle species are highly similar. The similarity decreases with decreasing frequency of beetle species' co-occurrence, a pattern resembling that of entomochoric ophiostomatoid fungi. These findings suggest that: 1) communities of Geosmithia spp. are vector-specific; 2) at least in some cases, the association between Geosmithia OTUs and bark beetles may have been very stable and symbioses are likely to be a fundamental factor in the speciation of Geosmithia fungi; and 3) that even nonsticky spores of Geosmithia are suitable for maintaining an insect-fungus association, contrary to previous hypotheses.}, }
@article {pmid17940819, year = {2008}, author = {Koren, O and Rosenberg, E}, title = {Bacteria associated with the bleached and cave coral Oculina patagonica.}, journal = {Microbial ecology}, volume = {55}, number = {3}, pages = {523-529}, pmid = {17940819}, issn = {0095-3628}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Bacteria/*classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Biomass ; Colony Count, Microbial ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; Mediterranean Sea ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {The relative abundance of bacteria in the mucus and tissues of Oculina patagonica taken from bleached and cave (azooxanthellae) corals was determined by analyses of the 16S rRNA genes from cloned libraries of extracted DNA and from isolated colonies. The results were compared to previously published data on healthy O. patagonica. The bacterial community of bleached, cave, and healthy corals were completely different from each other. A tight cluster (>99.5% identity) of bacteria, showing 100% identity to Acinetobacter species, dominated bleached corals, comprising 25% of the 316 clones sequenced. The dominant bacterial cluster found in cave corals, representing 29% of the 97 clones sequenced, showed 98% identity to an uncultured bacterium from the Great Barrier Reef. Vibrio splendidus was the most dominant species in healthy O. patagonica. The culturable bacteria represented 0.1-1.0% of the total bacteria (SYBR Gold staining) of the corals. The most abundant culturable bacteria in bleached, cave, and healthy corals were clusters that most closely matched Microbulbifer sp., an alpha-proteobacterium previously isolated from healthy corals and an alpha-protobacterium (AB026194), respectively. Three generalizations emerge from this study on O. patagonica: (1) More bacteria are associated with coral tissue than mucus; (2) tissue and mucus populations are different; (3) bacterial populations associated with corals change dramatically when corals lack their symbiotic zooxanthellae, either as a result of the bleaching disease or when growing in the absence of light.}, }
@article {pmid17937674, year = {2007}, author = {Woodcock, S and van der Gast, CJ and Bell, T and Lunn, M and Curtis, TP and Head, IM and Sloan, WT}, title = {Neutral assembly of bacterial communities.}, journal = {FEMS microbiology ecology}, volume = {62}, number = {2}, pages = {171-180}, doi = {10.1111/j.1574-6941.2007.00379.x}, pmid = {17937674}, issn = {0168-6496}, mesh = {Bacteria/*growth &amp; development ; Biodiversity ; *Ecosystem ; *Environmental Microbiology ; Fagus/microbiology ; *Models, Biological ; }, abstract = {Two recent, independent advances in ecology have generated interest and controversy: the development of neutral community models (NCMs) and the extension of biogeographical relationships into the microbial world. Here these two advances are linked by predicting an observed microbial taxa-volume relationship using an NCM and provide the strongest evidence so far for neutral community assembly in any group of organisms, macro or micro. Previously, NCMs have only ever been fitted using species-abundance distributions of macroorganisms at a single site or at one scale and parameter values have been calibrated on a case-by-case basis. Because NCMs predict a malleable two-parameter taxa-abundance distribution, this is a weak test of neutral community assembly and, hence, of the predictive power of NCMs. Here the two parameters of an NCM are calibrated using the taxa-abundance distribution observed in a small waterborne bacterial community housed in a bark-lined tree-hole in a beech tree. Using these parameters, unchanged, the taxa-abundance distributions and taxa-volume relationship observed in 26 other beech tree communities whose sizes span three orders of magnitude could be predicted. In doing so, a simple quantitative ecological mechanism to explain observations in microbial ecology is simultaneously offered and the predictive power of NCMs is demonstrated.}, }
@article {pmid17934979, year = {2008}, author = {Nyberg, SD and Meurman, O and Jalava, J and Rantakokko-Jalava, K}, title = {Evaluation of detection of extended-spectrum beta-lactamases among Escherichia coli and Klebsiella spp. isolates by VITEK 2 AST-N029 compared to the agar dilution and disk diffusion methods.}, journal = {Scandinavian journal of infectious diseases}, volume = {40}, number = {5}, pages = {355-362}, doi = {10.1080/00365540701704706}, pmid = {17934979}, issn = {0036-5548}, mesh = {Escherichia coli/*drug effects/*enzymology ; Humans ; Klebsiella/*drug effects/*enzymology ; Microbial Sensitivity Tests/*methods ; Sensitivity and Specificity ; *beta-Lactam Resistance ; beta-Lactamases/*biosynthesis/genetics ; }, abstract = {A total of 123 clinical Escherichia coli and Klebsiella spp. isolates were included in the study in order to evaluate VITEK 2 AST-NO29 (Nordic) card for detection of extended-spectrum beta-lactamases (ESBL) and to compare the results with genotypic ESBL verification. The results were also compared to alternative phenotypic methods, i.e. agar dilution and disk diffusion. The strains that were ESBL-positive according to AST-N029 were further analysed with the ESBL test card, VITEK 2 AST-N041. Using genotype as reference, Vitek 2 AES had the highest accuracy of the tested methods in classifying the strains as ESBL-positive or -negative (91.1%). When VITEK 2 gave ESBL as the only option for E. coli or K. pneumoniae, 44 of 45 (97.8%) strains had an ESBL gene. VITEK 2 achieved an accuracy of 94.9% and disk diffusion 95.9% compared to the agar dilution method as the phenotypic reference method for the E. coli and K. pneumoniae strains. For the K. oxytoca strains VITEK 2 achieved the highest accuracy (84.0%) of the methods used in this work.}, }
@article {pmid17934689, year = {2008}, author = {van Bruggen, AH and Semenov, AM and Zelenev, VV and Semenov, AV and Raaijmakers, JM and Sayler, RJ and de Vos, O}, title = {Wave-like distribution patterns of gfp-marked Pseudomonas fluorescens along roots of wheat plants grown in two soils.}, journal = {Microbial ecology}, volume = {55}, number = {3}, pages = {466-475}, pmid = {17934689}, issn = {0095-3628}, mesh = {Colony Count, Microbial ; Ecosystem ; Green Fluorescent Proteins/genetics/*metabolism ; Meristem/microbiology ; Microbial Viability ; Plant Roots/*microbiology ; Pseudomonas fluorescens/cytology/genetics/*growth &amp; development/metabolism ; Soil/*analysis ; *Soil Microbiology ; Triticum/*microbiology ; }, abstract = {Culturable rhizosphere bacterial communities had been shown to exhibit wave-like distribution patterns along wheat roots. In the current work we show, for the first time, significant wave-like oscillations of an individual bacterial strain, the biocontrol agent Pseudomonas fluorescens 32 marked with gfp, along 3-week-old wheat roots in a conventionally managed and an organically managed soil. Significant wave-like fluctuations were observed for colony forming units (CFUs) on selective media and direct fluorescent counts under the microscope. Densities of fluorescent cells and of CFUs fluctuated in a similar manner along wheat roots in the conventional soil. The frequencies of the first, second, and third harmonics were similar for direct cell counts and CFUs. Survival of P. fluorescens 32-gfp introduced into organically managed soil was lower than that of the same strain added to conventionally managed soil. Thus, when root tips reached a depth of 10-35 cm below soil level, the majority of the introduced cells may have died, so that no cells or CFU"s were detected in this region at the time of sampling. As a result, significant waves in CFUs or direct counts along roots were not found in organically managed soil, except when a sufficiently long series with detectable CFUs were obtained. In this last case the wave-like fluctuation in CFUs was damped toward the root tip. In conclusion, when cells of a single bacterial strain randomly mixed in soil survived until a root tip passed, growth and death cycles after passage of the root tip resulted in oscillating patterns of population densities of this strain along 3-week-old wheat roots.}, }
@article {pmid17932714, year = {2008}, author = {Rose, JM and Vora, NM and Caron, DA}, title = {Effect of temperature and prey type on nutrient regeneration by an antarctic bacterivorous protist.}, journal = {Microbial ecology}, volume = {56}, number = {1}, pages = {101-111}, pmid = {17932714}, issn = {0095-3628}, mesh = {Animals ; Antarctic Regions ; Biomass ; Chrysophyta/growth &amp; development/*metabolism/physiology ; Culture Media ; Halomonas/*growth &amp; development ; Phosphates/*metabolism ; *Predatory Behavior ; Quaternary Ammonium Compounds/*metabolism ; Seawater/microbiology/parasitology ; *Temperature ; }, abstract = {Experimental studies were carried out on an Antarctic isolate of the heterotrophic nanoflagellate Paraphysomonas imperforata to examine the efficiency of incorporation and remineralization of nitrogen and phosphorus from bacterial prey. Experiments were carried out over a temperature range from ambient Antarctic temperature (0 degrees C) to 10 degrees C. Temperature had a marked effect on the maximal growth rate of the phagotrophic nanoflagellate. Growth rate in the presence of high prey abundance ranged from 0.6 day(-1) at 0 degrees C to 2.6 day(-1) at 10 degrees C. In contrast, temperature had no discernable effect on the efficiencies of incorporation and remineralization of major nutrients by P. imperforata. The efficiencies of phosphorus and nitrogen incorporation from prey biomass averaged over the temperature range examined were 58 and 39%, respectively, for the two elements. Ammonium and phosphate were the dominant forms of dissolved nitrogen and phosphorus appearing in the culture medium during the grazing phase of the experiments. Overall, dissolved organic nitrogen and phosphorus constituted minor components of these elements released by the grazing activities of the protist. The results of this study indicated that incorporation/remineralization of nitrogen and phosphorus contained in prey was relatively unaffected by culture temperature in this heterotrophic nanoflagellate, although low temperature significantly depressed its growth rate. This finding has important implications for energy utilization and elemental cycling in perennially cold ecosystems and is at odds with conclusions that have been reached in some previous studies regarding the growth efficiency of phagotrophic Antarctic protists.}, }
@article {pmid17924158, year = {2008}, author = {Tijdens, M and Hoogveld, HL and Kamst-van Agterveld, MP and Simis, SG and Baudoux, AC and Laanbroek, HJ and Gons, HJ}, title = {Population dynamics and diversity of viruses, bacteria and phytoplankton in a shallow eutrophic lake.}, journal = {Microbial ecology}, volume = {56}, number = {1}, pages = {29-42}, pmid = {17924158}, issn = {0095-3628}, mesh = {Animals ; *Bacteria/classification/growth &amp; development ; Colony Count, Microbial ; Cyanobacteria/growth &amp; development ; Ecosystem ; Electrophoresis, Gel, Pulsed-Field ; *Eutrophication ; *Fresh Water/microbiology/virology ; Genetic Variation ; Microscopy, Fluorescence ; Netherlands ; *Phytoplankton/classification/growth &amp; development ; Population Dynamics ; *Viruses/classification/growth &amp; development ; }, abstract = {We have studied the temporal variation in viral abundances and community assemblage in the eutrophic Lake Loosdrecht through epifluorescence microscopy and pulsed field gel electrophoresis (PFGE). The virioplankton community was a dynamic component of the aquatic community, with abundances ranging between 5.5 x 10(7) and 1.3 x 10(8) virus-like particles ml(-1) and viral genome sizes ranging between 30 and 200 kb. Both viral abundances and community composition followed a distinct seasonal cycle, with high viral abundances observed during spring and summer. Due to the selective and parasitic nature of viral infection, it was expected that viral and host community dynamics would covary both in abundances and community composition. The temporal dynamics of the bacterial and cyanobacterial communities, as potential viral hosts, were studied in addition to a range of environmental parameters to relate these to viral community dynamics. Cyanobacterial and bacterial communities were studied applying epifluorescence microscopy, flow cytometry, and denaturing gradient gel electrophoresis (DGGE). Both bacterial and cyanobacterial communities followed a clear seasonal cycle. Contrary to expectations, viral abundances were neither correlated to abundances of the most dominant plankton groups in Lake Loosdrecht, the bacteria and the filamentous cyanobacteria, nor could we detect a correlation between the assemblage of viral and bacterial or cyanobacterial communities during the overall period. Only during short periods of strong fluctuations in microbial communities could we detect viral community assemblages to covary with cyanobacterial and bacterial communities. Methods with a higher specificity and resolution are probably needed to detect the more subtle virus-host interactions. Viral abundances did however relate to cyanobacterial community assemblage and showed a significant positive correlation to Chl-a as well as prochlorophytes, suggesting that a significant proportion of the viruses in Lake Loosdrecht may be phytoplankton and more specific cyanobacterial viruses. Temporal changes in bacterial abundances were significantly related to viral community assemblage, and vice versa, suggesting an interaction between viral and bacterial communities in Lake Loosdrecht.}, }
@article {pmid17915282, year = {2008}, author = {Nerenberg, R and Kawagoshi, Y and Rittmann, BE}, title = {Microbial ecology of a perchlorate-reducing, hydrogen-based membrane biofilm reactor.}, journal = {Water research}, volume = {42}, number = {4-5}, pages = {1151-1159}, doi = {10.1016/j.watres.2007.08.033}, pmid = {17915282}, issn = {0043-1354}, mesh = {Bacteria/classification/genetics/metabolism ; *Bioreactors ; DNA, Bacterial/genetics ; Ecology ; Hydrogen/metabolism ; In Situ Hybridization, Fluorescence ; Nitrates/metabolism ; Oxidation-Reduction ; Oxygen/metabolism ; Perchlorates/*metabolism ; Sequence Analysis, DNA ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The hydrogen-based membrane biofilm reactor (MBfR) has been shown to reduce perchlorate to below 4 microg/L, but little is known about the microbial ecology of this or other hydrogen-based reactors, especially when influent perchlorate concentrations are much lower than the influent oxygen and nitrate concentrations. Dissimilatory (per)chlorate-reducing bacteria (PCRB) can use oxygen as an electron acceptor, and most can also use nitrate. Since oxygen and nitrate can be reduced concurrently with perchlorate, they may serve as primary electron acceptors, sustaining PCRB when the perchlorate concentrations are very low. We studied five identical MBfRs, all seeded with the same inoculum and initially supplied with oxygen, or oxygen plus nitrate, in the influent. After 20 days, perchlorate was added to four MBfRs at influent concentrations of 100-10,000 microg/L, while the fifth was maintained as a control. One day after perchlorate addition, the MBfRs displayed limited perchlorate reduction, suggesting a low initial abundance of PCRB. However, perchlorate reduction improved significantly over time, and denaturing gradient gel electrophoresis (DGGE) analyses suggested an increasing abundance of a single Dechloromonas species. Fluorescence in-situ hybridization (FISH) tests showed that the Dechloromonas species accounted for 14% of the bacterial count in the control MBfR, and 22%, 31%, and 49% in the MBfRs receiving nitrate plus 100, 1000, and 10,000 microg/L perchlorate, respectively. The abundance was 34% in the MBfR receiving oxygen plus 1000 microg/L perchlorate. These results suggest that oxygen is more favorable than nitrate as a primary electron acceptor for PCRB, that PCRB are present at low levels even without perchlorate, and that the presence of perchlorate, even at low levels relative to nitrate or oxygen, significantly enhances selection for PCRB.}, }
@article {pmid17912580, year = {2008}, author = {Lugo, MA and Ferrero, M and Menoyo, E and Estévez, MC and Siñeriz, F and Anton, A}, title = {Arbuscular mycorrhizal fungi and rhizospheric bacteria diversity along an altitudinal gradient in South American Puna grassland.}, journal = {Microbial ecology}, volume = {55}, number = {4}, pages = {705-713}, pmid = {17912580}, issn = {0095-3628}, mesh = {Altitude ; Analysis of Variance ; Bacteria/genetics/*growth &amp; development/isolation &amp; purification ; *Biodiversity ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Molecular Sequence Data ; Mycorrhizae/*growth &amp; development/isolation &amp; purification ; Poaceae/*microbiology ; *Soil Microbiology ; South America ; }, abstract = {Rhizospheric soil samples were taken from Puna native grasses along an altitudinal gradient. Biodiversity of arbuscular mycorrhizal fungi (AMF) and associated bacteria was analyzed considering altitude and grasses photosynthetic pathways (metabolic type C3, C4). Cultivation-dependent approaches were applied to obtain further information about the phylogeny of the dominating cultivable aerobic-heterotrophic bacteria communities present in rhizospheric soil samples. In average, the bacterial count ranged between 1.30 x 10(2) and 8.66 x 10(4) CFU g(-1) of dry weight of soil. Individual bacterial colonies of aerobic heterotrophic bacteria grown on R2A medium were morphologically grouped and identified as typical soil bacteria belonging to the genera Bacillus, Pseudomonas, and Arthrobacter. Ten AMF taxa were found: Acaulospora sp., A. laevis, A. spinosa, Gigaspora sp., Gi. ramisporophora, Glomus sp., Gl. aggregatum, Gl. ambisporum, Gl. sinuosum, and Scutellospora biornata. AMF diversity decreased with altitude.}, }
@article {pmid17912579, year = {2008}, author = {Kao-Kniffin, J and Balser, TC}, title = {Soil fertility and the impact of exotic invasion on microbial communities in Hawaiian forests.}, journal = {Microbial ecology}, volume = {56}, number = {1}, pages = {55-63}, pmid = {17912579}, issn = {0095-3628}, mesh = {*Ecosystem ; Fungi/growth &amp; development ; Gram-Negative Bacteria/growth &amp; development ; Hawaii ; Myrtaceae/classification/*growth &amp; development/microbiology ; Nitrogen/metabolism ; Phosphorus/metabolism ; Plant Roots/microbiology ; Principal Component Analysis ; Soil/*analysis ; *Soil Microbiology ; Zingiberaceae/classification/*growth &amp; development/microbiology ; }, abstract = {Exotic plant invasions into Hawaiian montane forests have altered many important nutrient cycling processes and pools. Across different ecosystems, researchers are uncovering the mechanisms involved in how invasive plants impact the soil microbial community-the primary mediator of soil nutrient cycling. We examined whether the invasive plant, Hedychium gardnerianum, altered microbial community composition in forests dominated by a native tree, Metrosideros polymorpha, under varying soil nutrient limitations and soil fertility properties within forest plots of the Hawaii long-term substrate age gradient (LSAG). Microbial community lipid analysis revealed that when nutrient limitation (as determined by aboveground net primary production [ANPP]) and soil fertility were taken into account, plant species differentially altered soil microbial community composition. Microbial community characteristics differed under invasive and native plants primarily when N or P was added to the older, highly weathered, P-limited soils. Long-term fertilization with N or P at the P-limited site led to a significant increase in the relative abundance of the saprophytic fungal indicator (18:2 omega 6c,9c) under the invasive plant. In the younger, N-limited soils, plant species played a minor role in influencing soil microbial community composition. We found that the general rhizosphere microbial community structure was determined more by soil fertility than by plant species. This study indicates that although the aggressive invasion of a nutrient-demanding, rapidly decomposable, and invasive plant into Hawaiian forests had large impacts on soil microbial decomposers, relatively little impact occurred on the overall soil microbial community structure. Instead, soil nutrient conditions were more important determinants of the overall microbial community structure within Hawaii's montane forests.}, }
@article {pmid17910986, year = {2007}, author = {Ongeng, D and Ryckeboer, J and Vermeulen, A and Devlieghere, F}, title = {The effect of micro-architectural structure of cabbage substratum and or background bacterial flora on the growth of Listeria monocytogenes.}, journal = {International journal of food microbiology}, volume = {119}, number = {3}, pages = {291-299}, doi = {10.1016/j.ijfoodmicro.2007.08.022}, pmid = {17910986}, issn = {0168-1605}, mesh = {Brassica/*microbiology/*ultrastructure ; Colony Count, Microbial ; Consumer Product Safety ; Food Microbiology ; Food Preservation/*methods ; Humans ; Kinetics ; Lactobacillus plantarum/physiology ; Listeria monocytogenes/*growth &amp; development ; *Models, Biological ; Pantoea/physiology ; Pseudomonas fluorescens/physiology ; Temperature ; Time Factors ; }, abstract = {The effect of micro-architectural structure of cabbage (Brassica oleracea var. capitata L.) substratum and or background bacterial flora on the growth of Listeria monocytogenes as a function of incubation temperature was investigated. A cocktail mixture of Pseudomonas fluorescens, Pantoea agglomerans and Lactobacillus plantarum was constituted to a population density of approximately 5 log CFU/ml in order to pseudo-simulate background bacterial flora of fresh-cut cabbage. This mixture was co-inoculated with L. monocytogenes (approximately 3 log CFU/ml) on fresh-cut cabbage or in autoclaved cabbage juice followed by incubation at different temperatures (4-30 degrees C). Data on growth of L. monocytogenes were fitted to the primary growth model of Baranyi in order to generate the growth kinetic parameters of the pathogen. During storage, microbial ecology was dominated by P. fluorescens and L. plantarum at refrigeration and abuse temperature, respectively. At all temperatures investigated, lag duration (lambda, h), maximum specific growth rate (micro(max), h(-1)) and maximum population density (MPD, log CFU/ml) of L. monocytogenes were only affected by medium micro-architectural structure, except at 4 degrees C where it had no effect on the micro(max) of the pathogen. Comparison of observed values of micro(max) with those obtained from the Pathogen Modelling Program (PMP), showed that PMP overestimated the growth rate of L. monocytogenes on fresh-cut cabbage and in cabbage juice, respectively. Temperature dependency of micro(max) of L. monocytogenes, according to the models of Ratkowsky and Arrhenius, showed linearity for temperature range of 4-15 degrees C, discontinuities and linearity again for temperature range of 20-30 degrees C. The results of this experiment have shown that the constituted background bacterial flora had no effect on the growth of L. monocytogenes and that micro-architectural structure of the vegetable was the primary factor that limited the applicability of PMP model for predicting the growth of L. monocytogenes on fresh-cut cabbage. A major limitation of this study however is that nutrient profile of the autoclaved cabbage juice may be different from that of the raw juice thus compromising realistic comparison of the behaviour of L. monocytogenes as affected by micro-architectural structure.}, }
@article {pmid17899248, year = {2008}, author = {Cookson, WR and O'Donnell, AJ and Grant, CD and Grierson, PF and Murphy, DV}, title = {Impact of ecosystem management on microbial community level physiological profiles of postmining forest rehabilitation.}, journal = {Microbial ecology}, volume = {55}, number = {2}, pages = {321-332}, pmid = {17899248}, issn = {0095-3628}, mesh = {Analysis of Variance ; Carbon/analysis ; *Ecosystem ; Fires ; Inorganic Chemicals/analysis/metabolism ; *Mining ; Nitrogen/analysis ; Organic Chemicals/analysis/*metabolism ; Phosphorus/analysis ; Soil/*analysis/standards ; *Soil Microbiology ; Trees/*physiology ; }, abstract = {We investigated the impacts of forest thinning, prescribed fire, and contour ripping on community level physiological profiles (CLPP) of the soil microbial population in postmining forest rehabilitation. We hypothesized that these management practices would affect CLPP via an influence on the quality and quantity of soil organic matter. The study site was an area of Jarrah (Eucalyptus marginata Donn ex Sm.) forest rehabilitation that had been mined for bauxite 12 years previously. Three replicate plots (20 x 20 m) were established in nontreated forest and in forest thinned from 3,000-8,000 stems ha(-1) to 600-800 stems ha(-1) in April (autumn) of 2003, followed either by a prescribed fire in September (spring) of 2003 or left nonburned. Soil samples were collected in August 2004 from two soil depths (0-5 cm and 5-10 cm) and from within mounds and furrows caused by postmining contour ripping. CLPP were not affected by prescribed fire, although the soil pH and organic carbon (C), total C and total nitrogen (N) contents were greater in burned compared with nonburned plots, and the coarse and fine litter mass lower. However, CLPP were affected by forest thinning, as were fine litter mass, soil C/N ratio, and soil pH, which were all higher in thinned than nonthinned plots. Furrow soil had greater coarse and fine litter mass, and inorganic phosphorous (P), organic P, organic C, total C, total N, ammonium, microbial biomass C contents, but lower soil pH and soil C/N ratio than mound soil. Soil pH, inorganic P, organic P, organic C, total C and N, ammonium, and microbial biomass C contents also decreased with depth, whereas soil C/N ratio increased. Differences in CLPP were largely (94%) associated with the relative utilization of gluconic, malic (greater in nonthinned than thinned soil and mound than furrow soil), L-tartaric, succinic, and uric acids (greater in thinned than nonthinned, mound than furrow, and 5-10 cm than 0-5 cm soil). The relative utilization of amino acids also tended to increase with increasing soil total C and organic C contents but decreased with increasing nitrate content, whereas the opposite was true for carboxylic acids. Only 45% of the variance in CLPP was explained using a multivariate multiple regression model, but soil C and N pools and litter mass were significant predictors of CLPP. Differences in soil textural components between treatments were also correlated with CLPP; likely causes of these differences are discussed. Our results suggest that 1 year after treatment, CLPP from this mined forest ecosystem are resilient to a spring prescribed fire but not forest thinning. We conclude that differences in CLPP are likely to result from complex interactions among soil properties that mediate substrate availability, microbial nutrient demand, and microbial community composition.}, }
@article {pmid17899247, year = {2008}, author = {Tuckfield, RC and McArthur, JV}, title = {Spatial analysis of antibiotic resistance along metal contaminated streams.}, journal = {Microbial ecology}, volume = {55}, number = {4}, pages = {595-607}, pmid = {17899247}, issn = {0095-3628}, mesh = {Aminoglycosides/*pharmacology ; Anti-Bacterial Agents/pharmacology ; Bacteria/*drug effects/growth &amp; development ; Colony Count, Microbial ; *Drug Resistance, Bacterial ; Geologic Sediments/microbiology ; Metals, Heavy/*pharmacology ; Microbial Sensitivity Tests ; Multivariate Analysis ; Principal Component Analysis ; Rivers/microbiology ; Selection, Genetic ; *Water Microbiology ; Water Pollutants, Chemical/pharmacology ; }, abstract = {The spatial pattern of antibiotic resistance in culturable sediment bacteria from four freshwater streams was examined. Previous research suggests that the prevalence of antibiotic resistance may increase in populations via indirect or coselection from heavy metal contamination. Sample bacteria from each stream were grown in media containing one of four antibiotics-tetracycline, chloramphenicol, kanamycin, and streptomycin-at concentrations greater than the minimum inhibitory concentration, plus a control. Bacteria showed high susceptibilities to the former two antibiotics. We summarized the latter two more prevalent (aminoglycoside) resistance responses and ten metals concentrations per sediment sample, by Principal Components Analysis. Respectively, 63 and 58% of the variability was explained in the first principal component of each variable set. We used these multivariate summary metrics [i.e., first principal component (PC) scores] as input measures for exploring the spatial correlation between antibiotic resistance and metal concentration for each stream sampled. Results show a significant and negative correlation between metals PC scores versus aminoglycoside resistance scores and suggest that selection for metal tolerance among sediment bacteria may influence selection for antibiotic resistance differently in sediments than in the water column. Our most important finding comes from geostatistical cross-variogram analysis, which shows that increasing metal concentration scores are spatially associated with decreasing aminoglycoside resistance scores--a negative correlation, but holds for contaminated streams only. We suspect our field results are influenced by metal bioavailability in the sediments and by a contaminant promoted interaction or "cocktail effect" from complex combinations of pollution mediated selection agents.}, }
@article {pmid17899246, year = {2008}, author = {Kaufman, MG and Chen, S and Walker, ED}, title = {Leaf-associated bacterial and fungal taxa shifts in response to larvae of the tree hole mosquito, Ochlerotatus triseriatus.}, journal = {Microbial ecology}, volume = {55}, number = {4}, pages = {673-684}, pmid = {17899246}, issn = {0095-3628}, support = {R01 AI021884/AI/NIAID NIH HHS/United States ; R37 AI021884/AI/NIAID NIH HHS/United States ; R56 AI021884/AI/NIAID NIH HHS/United States ; AI21884/AI/NIAID NIH HHS/United States ; }, mesh = {Analysis of Variance ; Animals ; Bacteria/*genetics ; Biodiversity ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; Ergosterol/chemistry ; Fungi/*genetics ; Larva/growth &amp; development ; Ochlerotatus/*growth &amp; development ; Plant Leaves/chemistry/*microbiology ; Population Dynamics ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Alignment ; Species Specificity ; Trees/*microbiology ; }, abstract = {Larvae of the eastern tree hole mosquito, Ochlerotatus triseriatus (Say), and related container-breeding species are known to feed upon substrate-associated microorganisms. Although the importance of these microbial resources to larval growth has been established, almost nothing is known about the taxonomic composition and dynamics of these critical microbial food sources. We examined bacterial and fungal community compositional changes on oak leaves tethered in natural tree hole habitats of O. triseriatus. We eliminated larvae experimentally in a subset of the tree holes and examined 16S rDNA gene sequences for bacteria and ergosterol concentrations and 18S rRNA gene sequences for fungi collected from leaf material subsamples. Leaf ergosterol content varied significantly with time, but not treatment. Principal component analysis (PCA) was used to compare microbial taxonomic patterns found in leaves incubated with or without larvae present, and we found that larval presence affected both bacterial and fungal groups, either from loosely attached or strongly adherent categories. Bacterial communities generally grouped more tightly when larvae were present, and class level taxa proportions changed when larvae were present, suggesting selection by larval feeding or activities for particular taxa such as members of the Bacteroidetes, Alphaproteobacteria, and Betaproteobacteria classes. Fungal taxa composite scores also separated along PC axes related to the presence of larvae and indicated larval feeding effects on several higher taxonomic groups, including Saccharomycetes, Dothideomycetes, and Chytridiomycota. These results support the hypothesis that larval mosquito feeding and activities altered microbial communities associated with substrate surfaces, potentially leading to decreased food value of the resource and affecting decomposition of particulate matter in the system.}, }
@article {pmid17899245, year = {2008}, author = {Rodrigues Marcondes, N and Ledesma Taira, C and Cirena Vandresen, D and Estivalet Svidzinski, TI and Kadowaki, MK and Peralta, RM}, title = {New feather-degrading filamentous fungi.}, journal = {Microbial ecology}, volume = {56}, number = {1}, pages = {13-17}, pmid = {17899245}, issn = {0095-3628}, mesh = {Animal Husbandry/methods ; Animals ; Biotechnology/methods ; Brazil ; *Chickens ; Culture Media ; Feathers/chemistry/*metabolism ; Fungal Proteins/genetics/metabolism ; Fungi/classification/*enzymology/growth &amp; development/physiology ; Keratins/*metabolism ; Peptide Hydrolases/*metabolism ; Poultry ; Spores, Fungal/physiology ; Waste Products ; }, abstract = {Among 106 filamentous fungi isolated from poultry farm waste, 13 species belonging to seven genera (Aspergillus, Acremonium, Alternaria, Beauvaria, Curvularia, Paecilomyces, and Penicillium) were able to grow and produce keratinase in stationary cultures using poultry feather powder as the only substrate. The four most efficient keratinase producers were selected for a comparative study of keratinase production in submerged and stationary conditions. The highest keratinolytic activities were produced after 4-6 days of cultivation in submerged conditions: 53.8 +/- 6.1 U/mL (Alternaria tenuissima), 51.2 +/- 5.4 U/mL (Acremonium hyalinulum), 55.4 +/- 5.2 U/mL (Curvularia brachyspora), and 62.8 +/- 4.8 U/mL (Beauveria bassiana). These novel nondermatophytic keratinolytic fungi have potential use in biotechnological processes involving keratin hydrolysis. The results of this work contribute to show that keratinolytic activity is relatively widespread among common filamentous fungi and may have an important rule in feather decomposition in natural settings.}, }
@article {pmid17894817, year = {2008}, author = {Tyson, GW and Banfield, JF}, title = {Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses.}, journal = {Environmental microbiology}, volume = {10}, number = {1}, pages = {200-207}, doi = {10.1111/j.1462-2920.2007.01444.x}, pmid = {17894817}, issn = {1462-2920}, mesh = {Bacteriophages/*physiology ; Base Composition ; Base Sequence ; Biofilms/growth &amp; development ; Cluster Analysis ; Genome, Bacterial ; Gram-Negative Bacteria/*genetics/*virology ; *Interspersed Repetitive Sequences ; Molecular Sequence Data ; Phylogeny ; Viruses ; }, abstract = {Recent experimental evidence has demonstrated that bacteria acquire resistance to viruses by incorporation of short transcribed nucleotide sequences into regions of clustered regularly interspaced short palindromic repeats (CRISPR). We have analysed community genomic data from acidophilic microbial biofilms and discovered that evolution of the CRISPR regions in two distinct Leptospirillum group II bacteria occurs fast enough to promote individuality in otherwise nearly clonal populations. Comparative genomics strongly indicates very recent lateral transfer of the CRISPR locus between these populations, followed by significant loss of spacer sequences and locus expansion by unidirectional heterogeneous addition of new spacer sequences. Diversification of the CRISPR region is inferred to be a population-level response to the rapidly changing selective pressure of phage predation. Results reinforce the importance of phage-host interactions in shaping microbial ecology and evolution over very short time scales.}, }
@article {pmid17894813, year = {2008}, author = {Mes, TH}, title = {Microbial diversity--insights from population genetics.}, journal = {Environmental microbiology}, volume = {10}, number = {1}, pages = {251-264}, doi = {10.1111/j.1462-2920.2007.01449.x}, pmid = {17894813}, issn = {1462-2920}, mesh = {*Biodiversity ; Carbon/metabolism ; *Ecology ; Genetic Variation ; Genetics, Population/*methods ; Haplotypes ; Models, Biological ; Nitrogen/metabolism ; Population Density ; }, abstract = {Although many environmental microbial populations are large and genetically diverse, both the level of diversity and the extent to which it is ecologically relevant remain enigmatic. Because the effective (or long-term) population size, N(e), is one of the parameters that determines population genetic diversity, tests and simulations that assume selectively neutral mutations may help to identify the processes that have shaped microbial diversity. Using ecologically important genes, tests of selective neutrality suggest that adaptive as well as non-adaptive types of selection act and that departure from neutrality may be widespread or restricted to small groups of genotypes. Population genetic simulations using population sizes between 10(3) and 10(7) suggest extremely high levels of microbial diversity in environments that sustain large populations. However, census and effective population sizes may differ considerably, and because we know nothing of the evolutionary history of environmental microbial populations, we also have no idea what N(e) of environmental populations is. On the one hand, this reflects our ignorance of the microbial world. On the other hand, the tests and simulations illustrate interactions between microbial diversity and microbial population genetics that should inform our thinking in microbial ecology. Because of the different views on microbial diversity across these disciplines, such interactions are crucial if we are to understand the role of genes in microbial communities.}, }
@article {pmid17892477, year = {2007}, author = {Ramette, A}, title = {Multivariate analyses in microbial ecology.}, journal = {FEMS microbiology ecology}, volume = {62}, number = {2}, pages = {142-160}, pmid = {17892477}, issn = {0168-6496}, mesh = {*Data Interpretation, Statistical ; *Ecosystem ; *Environmental Microbiology ; *Multivariate Analysis ; }, abstract = {Environmental microbiology is undergoing a dramatic revolution due to the increasing accumulation of biological information and contextual environmental parameters. This will not only enable a better identification of diversity patterns, but will also shed more light on the associated environmental conditions, spatial locations, and seasonal fluctuations, which could explain such patterns. Complex ecological questions may now be addressed using multivariate statistical analyses, which represent a vast potential of techniques that are still underexploited. Here, well-established exploratory and hypothesis-driven approaches are reviewed, so as to foster their addition to the microbial ecologist toolbox. Because such tools aim at reducing data set complexity, at identifying major patterns and putative causal factors, they will certainly find many applications in microbial ecology.}, }
@article {pmid17885005, year = {2007}, author = {Bolca, S and Possemiers, S and Herregat, A and Huybrechts, I and Heyerick, A and De Vriese, S and Verbruggen, M and Depypere, H and De Keukeleire, D and Bracke, M and De Henauw, S and Verstraete, W and Van de Wiele, T}, title = {Microbial and dietary factors are associated with the equol producer phenotype in healthy postmenopausal women.}, journal = {The Journal of nutrition}, volume = {137}, number = {10}, pages = {2242-2246}, doi = {10.1093/jn/137.10.2242}, pmid = {17885005}, issn = {0022-3166}, mesh = {Adult ; Aged ; *Diet ; Equol ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; *Health ; Humans ; Isoflavones/*metabolism/urine ; Middle Aged ; Phenotype ; Phytoestrogens/metabolism ; Postmenopause/*metabolism ; Soy Milk/*metabolism ; }, abstract = {Equol, a microbial metabolite of daidzein, has been hypothesized as a clue to the effectiveness of soy and its isoflavones but is excreted by only 33% of Caucasians. Microbial and dietary factors associated with the ability to harbor equol-producing bacteria were studied in a randomized dietary intervention trial with 100 healthy postmenopausal women. After a 4-d baseline period, subjects delivered first-void urine, fecal, and breath samples. During the 5-d treatment period, 3 portions of either soymilk or soy germ containing 28.51 and 37.99 mg isoflavone aglycone equivalents/portion, respectively, were administered daily, and on the last day, 24-h urine samples were collected. The urinary recoveries of genistein and daidzein from soymilk were significantly higher than those from soy germ tablets. Because the proportion of equol:(daidzein + metabolites) in the urine did not differ between the treatment groups, subjects were pooled and classified into poor, moderate, and strong equol producers based on this criterion. The strong equol producer phenotype correlated negatively [in vivo, r = -0.478 (-0.256 to -0.893), P = 0.021; in vitro, r = -0.576 (-0.350 to -0.949), P = 0.030] with Clostridium coccoides-Eubacterium rectale counts and positively [in vivo, r = 1.158 (0.971-1.380), P = 0.048; in vitro, r = 1.156 (1.007-1.327), P = 0.039] with the abundance of sulfate-reducing bacteria. Furthermore, persons with a higher PUFA [in vivo, r = 2.150 (1.058-4.371), P = 0.034; in vitro, r = 2.131 (1.144-3.967), P = 0.017] and alcohol [in vivo, r = 1.166 (0.721-1.887), P = 0.050; in vitro, r = 1.850 (1.215-2.817), P = 0.004] intake were more likely to be strong equol producers. Finally, we validated the daidzein metabolism by fecal cultures as screening assay to identify equol producers without dietary intervention.}, }
@article {pmid17878949, year = {2007}, author = {Martín-Cuadrado, AB and López-García, P and Alba, JC and Moreira, D and Monticelli, L and Strittmatter, A and Gottschalk, G and Rodríguez-Valera, F}, title = {Metagenomics of the deep Mediterranean, a warm bathypelagic habitat.}, journal = {PloS one}, volume = {2}, number = {9}, pages = {e914}, pmid = {17878949}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; DNA Primers ; *Genomics ; Mediterranean Sea ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {BACKGROUND: Metagenomics is emerging as a powerful method to study the function and physiology of the unexplored microbial biosphere, and is causing us to re-evaluate basic precepts of microbial ecology and evolution. Most marine metagenomic analyses have been nearly exclusively devoted to photic waters.<br><br>We constructed a metagenomic fosmid library from 3,000 m-deep Mediterranean plankton, which is much warmer (approximately 14 degrees C) than waters of similar depth in open oceans (approximately 2 degrees C). We analyzed the library both by phylogenetic screening based on 16S rRNA gene amplification from clone pools and by sequencing both insert extremities of ca. 5,000 fosmids. Genome recruitment strategies showed that the majority of high scoring pairs corresponded to genomes from Rhizobiales within the Alphaproteobacteria, Cenarchaeum symbiosum, Planctomycetes, Acidobacteria, Chloroflexi and Gammaproteobacteria. We have found a community structure similar to that found in the aphotic zone of the Pacific. However, the similarities were significantly higher to the mesopelagic (500-700 m deep) in the Pacific than to the single 4000 m deep sample studied at this location. Metabolic genes were mostly related to catabolism, transport and degradation of complex organic molecules, in agreement with a prevalent heterotrophic lifestyle for deep-sea microbes. However, we observed a high percentage of genes encoding dehydrogenases and, among them, cox genes, suggesting that aerobic carbon monoxide oxidation may be important in the deep ocean as an additional energy source.<br><br>CONCLUSIONS/SIGNIFICANCE: The comparison of metagenomic libraries from the deep Mediterranean and the Pacific ALOHA water column showed that bathypelagic Mediterranean communities resemble more mesopelagic communities in the Pacific, and suggests that, in the absence of light, temperature is a major stratifying factor in the oceanic water column, overriding pressure at least over 4000 m deep. Several chemolithotrophic metabolic pathways could supplement organic matter degradation in this most depleted habitat.}, }
@article {pmid17878438, year = {2007}, author = {Dunkley, KD and McReynolds, JL and Hume, ME and Dunkley, CS and Callaway, TR and Kubena, LF and Nisbet, DJ and Ricke, SC}, title = {Molting in Salmonella Enteritidis-challenged laying hens fed alfalfa crumbles. II. Fermentation and microbial ecology response.}, journal = {Poultry science}, volume = {86}, number = {10}, pages = {2101-2109}, doi = {10.1093/ps/86.10.2101}, pmid = {17878438}, issn = {0032-5791}, mesh = {Animal Feed ; Animal Nutritional Physiological Phenomena ; Animals ; Cecum ; Chickens/*microbiology/*physiology ; Diet/*veterinary ; Feces/chemistry ; Female ; Fermentation ; Housing, Animal ; Medicago sativa ; Molting/*physiology ; Polymerase Chain Reaction ; Salmonella Infections, Animal/*metabolism/microbiology ; *Salmonella enteritidis ; }, abstract = {The objective of this study was to examine microbial population shifts and short-chain fatty acid (SCFA) responses in the gastrointestinal tract of Salmonella Enteritidis-challenged molted and nonmolted hens fed different dietary regimens. Fifteen Salmonella-free Single Comb Leghorn hens (>50 wk old) were assigned to 3 treatment groups of 5 birds each based on diet in 2 trials: 100% alfalfa crumbles (ALC), full-fed (FF, nonmolted) 100% commercial layer ration, and feed withdrawal (FW). A forced molt was induced by either a 12-d alfalfa diet or FW. In all treatment groups, each hen was challenged by crop gavage orally 4 d after molt induction with a 1-mL inoculum containing 10(6) cfu of Salmonella Enteritidis. Fecal and cecal samples (d 4, 6, 8, 11, and necropsy on d 12) were collected postchallenge. Microbial population shifts were evaluated by PCR-based 16S ribosomal RNA gene amplification and denaturing gradient gel electrophoresis, and SCFA concentrations were measured. Total SCFA in fecal and cecal contents for FW molted hens were generally lower (P < or = 0.05) in the later stages of the molt period when compared to ALC and FF treatment groups. The overall trend of SCFA in cecal and fecal samples exhibited similar patterns. In trials 1 and 2, hens molted with ALC diet generally yielded more similar amplicon band patterns with the FF hens in both fecal and cecal samples by the end of the molting period than with FW hens. The results of these studies suggest that ALC molted hens supported microflora and fermentation activities, which were more comparable to FF hens than FW hens by the end of the molting period.}, }
@article {pmid17878279, year = {2008}, author = {Callaway, TR and Edrington, TS and Anderson, RC and Byrd, JA and Nisbet, DJ}, title = {Gastrointestinal microbial ecology and the safety of our food supply as related to Salmonella.}, journal = {Journal of animal science}, volume = {86}, number = {14 Suppl}, pages = {E163-72}, doi = {10.2527/jas.2007-0457}, pmid = {17878279}, issn = {1525-3163}, mesh = {Adaptation, Physiological ; Animals ; Cattle ; Consumer Product Safety ; Food Contamination/prevention &amp; control ; Humans ; Meat/*microbiology ; Poultry ; Salmonella/classification/genetics/*pathogenicity/physiology ; Salmonella Food Poisoning/*epidemiology/microbiology/prevention &amp; control ; Salmonella Infections, Animal/*epidemiology/microbiology/prevention &amp; control ; Species Specificity ; Swine ; Virulence/genetics ; }, abstract = {Salmonella causes an estimated 1.3 million human foodborne illnesses and more than 500 deaths each year in the United States, representing an annual estimated cost to the economy of approximately $2.4 billion. Salmonella enterica comprises more than 2,500 serotypes. With this genetic and environmental diversity, serotypes are adapted to live in a variety of hosts, which may or may not manifest with clinical illness. Thus, Salmonella presents a multifaceted threat to food production and safety. Salmonella have been isolated from all food animals and can cause morbidity and mortality in swine, cattle, sheep, and poultry. The link between human salmonellosis and host animals is most clear in poultry. During the early part of the 20th century, a successful campaign was waged to eliminate fowl typhoid caused by Salmonella Gallinarum/Pullorum. Microbial ecology is much like macroecology; environmental niches are filled by adapted and specialized species. Elimination of S. Gallinarum cleared a niche in the on-farm and intestinal microbial ecology that was quickly exploited by Salmonella Enteritidis and other serotypes that live in other hosts, such as rodents. In the years since, human salmonellosis cases linked to poultry have increased to the point that uncooked chicken and eggs are regarded as toxic in the zeitgeist. Salmonellosis caused by poultry products have increased significantly in the past 5 yr, leading to a USDA Food Safety and Inspection Service "Salmonella Attack Plan" that aims to reduce the incidence of Salmonella in chickens below the current 19%. The prevalence of Salmonella in swine and cattle is lower, but still poses a threat to food safety and production efficiency. Thus, approaches to reducing Salmonella in animals must take into consideration that the microbial ecology of the animal is a critical factor that should be accounted for when designing intervention strategies. Use of competitive exclusion, sodium chlorate, vaccination, and bacteriophage are all strategies that can reduce Salmonella in the live animal, but it is vital to understand how they function so that we do not invoke the law of unintended consequences.}, }
@article {pmid17876656, year = {2008}, author = {Zhang, XF and Yao, TD and Tian, LD and Xu, SJ and An, LZ}, title = {Phylogenetic and physiological diversity of bacteria isolated from Puruogangri ice core.}, journal = {Microbial ecology}, volume = {55}, number = {3}, pages = {476-488}, pmid = {17876656}, issn = {0095-3628}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification/metabolism ; *Bacterial Physiological Phenomena ; *Biodiversity ; Colony Count, Microbial ; DNA Fingerprinting ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ice Cover/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Tibet ; }, abstract = {The microbial abundance, the percentage of viable bacteria, and the diversity of bacterial isolates from different regions of a 83.45-m ice core from the Puruogangri glacier on the Tibetan Plateau (China) have been investigated. Small subunit 16S rRNA sequences and phylogenetic relationships have been studied for 108 bacterial isolates recovered under aerobic growth conditions from different regions of the ice core. The genomic fingerprints based on ERIC (enterobacterial repetitive intergenic consensus)-polymerase chain reaction and physiological heterogeneity of the closely evolutionary related bacterial strains isolated from different ice core depths were analyzed as well. The results showed that the total microbial cell, percentages of live cells, and the bacterial CFU ranged from 10(4) to 10(5) cell ml(-1) (Mean, 9.47 x 10(4); SD, 5.7 x 10(4), n = 20), 25-81%, and 0-760 cfu ml(-1), respectively. The majority of the isolates had 16S rRNA sequences similar to previously determined sequences, ranging from 92 to 99% identical to database sequences. Based on their 16S rRNA sequences, 42.6% of the isolates were high-G + C-content (HGC) gram-positive bacteria, 35.2% were low-G + C (LGC) gram-positive bacteria, 16.6% were Proteobacteria, and 5.6% were CFB group. There were clear differences in the depth distribution of the bacterial isolates. The isolates tested exhibited unique phenotypic properties and high genetic heterogeneity, which showed no clear correlation with depths of bacterial isolation. This layered distribution and high heterogeneity of bacterial isolates presumably reflect the diverse bacterial sources and the differences in bacteria inhabiting the glacier's surface under different past climate conditions.}, }
@article {pmid17876655, year = {2008}, author = {Vaz-Moreira, I and Silva, ME and Manaia, CM and Nunes, OC}, title = {Diversity of bacterial isolates from commercial and homemade composts.}, journal = {Microbial ecology}, volume = {55}, number = {4}, pages = {714-722}, pmid = {17876655}, issn = {0095-3628}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Biodegradation, Environmental ; *Biodiversity ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Genes, Bacterial ; Genes, rRNA ; Genotype ; Phenotype ; RNA, Ribosomal, 16S/genetics ; Random Amplified Polymorphic DNA Technique ; Refuse Disposal ; Sewage/microbiology ; *Soil ; *Soil Microbiology ; }, abstract = {The diversity of heterotrophic bacterial isolates of three commercial and two homemade composts was studied. The commercial composts were produced from poultry litter (PC), sewage sludge (SC), municipal solid waste (MC), and homemade composts (thermal compost [DC] and vermicompost [VC]) from food wastes. The taxonomic and physiological diversity of the heterotrophic culturable bacteria was assessed using phenotypic and genotypic characterization and the analysis of the partial 16S rRNA gene sequence. Composts DC and SC presented the higher genotypic diversity, as could be inferred from the number of distinct genotypic patterns observed, 28 and 21, respectively. Gram-positive bacteria, mainly Firmicutes, were predominant in all the composts. Some organisms related with taxa rarely reported in composts, as Rhodanobacter spathiphylli, Moraxella osloensis, Lysobacter, Corynebacterium, Pigmentiphaga kullae, and new taxa were also isolated. The highest relative proportion of isolates able to degrade starch was found in compost SC (> 70%), to degrade gelatine in compost DC (> 70%), to degrade Tween 80 in compost PC (> 90%), and to degrade poly-epsilon-caprolactones in compost DC (> 80%). Compost MC presented the lowest relative proportions of isolates able to degrade starch (< 25%), gelatine (< 20%), and poly-epsilon-caprolactone (< 40%). When compared with the others, the homemade composts presented higher relative proportions of Gram-positive isolates able to inhibit the target organisms Staphylococcus aureus, Enterococcus faecalis, Escherichia coli, or Pseudomonas aeruginosa. In compost MC, none of the Gram-positive isolates was able to inhibit those targets.}, }
@article {pmid17876654, year = {2008}, author = {Wieltschnig, C and Fischer, UR and Velimirov, B and Kirschner, AK}, title = {Effects of deposit-feeding macrofauna on benthic bacteria, viruses, and protozoa in a silty freshwater sediment.}, journal = {Microbial ecology}, volume = {56}, number = {1}, pages = {1-12}, pmid = {17876654}, issn = {0095-3628}, mesh = {Animals ; Bacteria/growth &amp; development/metabolism ; Carbon Radioisotopes/metabolism ; Chironomidae/*physiology ; Cladocera/*physiology ; *Ecosystem ; Eukaryota/growth &amp; development/metabolism ; Food Chain ; *Fresh Water/microbiology/parasitology/virology ; *Geologic Sediments/microbiology/parasitology/virology ; Leucine/metabolism ; Oligochaeta/*physiology ; Predatory Behavior ; Thymidine/metabolism ; Tritium/metabolism ; Viruses/growth &amp; development/metabolism ; }, abstract = {In microcosm experiments, we simultaneously tested the effects of increased numbers of deposit-feeding macrofauna (chironomids, oligochaetes and cladocerans) on the standing stock, activities and interactions of heterotrophic bacteria, viruses, and bacterivorous protozoa (heterotrophic nanoflagellates and ciliates) in the aerobic layer of a silty littoral freshwater sediment. On average, bacterial secondary production was stimulated between 11 and 29% by all macrofaunal groups compared to control experiments without macrofauna addition. Bacterial standing stock increased significantly by 8 and 13% in case of chironomids and cladocerans, respectively. Oligochaetes and chironomids produced significant negative effects on viral abundance while the results with cladocerans were inconsistent. The addition of oligochaetes and chironomids resulted in a significant decrease by on average 68 and 32% of viral decay rates, respectively, used as a measure of viral production. The calculated contribution of virus-induced lysis to benthic bacterial mortality was low, with 2.8 to 11.8% of bacterial secondary production, and decreased by 39 to 81% after the addition of macrofauna compared to the control. The abundances of heterotrophic nanoflagellates were significantly reduced by 20% by all tested macrofauna groups, while ciliates showed inconsistent results. The importance of heterotrophic nanoflagellate grazing on benthic bacteria was very low (<1% of bacterial secondary production) and was further reduced by elevated numbers of macrofauna. Thus, the selected deposit feeding macrofauna groups seem to have several direct and indirect and partly antagonistic effects on the benthic bacterial compartment through the enhancement of bacterial production and the reduction of virus-induced cell lysis and protozoan grazing.}, }
@article {pmid17874305, year = {2008}, author = {Süss, J and Herrmann, K and Seidel, M and Cypionka, H and Engelen, B and Sass, H}, title = {Two distinct Photobacterium populations thrive in ancient Mediterranean sapropels.}, journal = {Microbial ecology}, volume = {55}, number = {3}, pages = {371-383}, pmid = {17874305}, issn = {0095-3628}, mesh = {Benzopyrans ; DNA Fingerprinting ; DNA, Bacterial/genetics ; DNA, Intergenic/genetics ; DNA, Ribosomal/genetics ; Fermentation ; Geologic Sediments/*microbiology ; Humic Substances/*microbiology ; Hydrogen-Ion Concentration ; Mediterranean Region ; Molecular Sequence Data ; Phospholipids/metabolism ; Photobacterium/*classification/genetics/*isolation &amp; purification/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; Temperature ; }, abstract = {Eastern Mediterranean sediments are characterized by the periodic occurrence of conspicuous, organic matter-rich sapropel layers. Phylogenetic analysis of a large culture collection isolated from these sediments revealed that about one third of the isolates belonged to the genus Photobacterium. In the present study, 22 of these strains were examined with respect to their phylogenetic and metabolic diversity. The strains belonged to two distinct Photobacterium populations (Mediterranean cluster I and II). Strains of cluster I were isolated almost exclusively from organic-rich sapropel layers and were closely affiliated with P. aplysiae (based on their 16S rRNA gene sequences). They possessed almost identical Enterobacterial Repetitive Intergenic Consensus (ERIC) and substrate utilization patterns, even among strains from different sampling sites or from layers differing up to 100,000 years in age. Strains of cluster II originated from sapropels and from the surface and carbon-lean intermediate layers. They were related to Photobacterium frigidiphilum but differed significantly in their fingerprint patterns and substrate spectra, even when these strains were obtained from the same sampling site and layer. Temperature range for growth (4 to 33 degrees C), salinity tolerance (5 to 100 per thousand), pH requirements (5.5-9.3), and the composition of polar membrane lipids were similar for both clusters. All strains grew by fermentation (glucose, organic acids) and all but five by anaerobic respiration (nitrate, dimethyl sulfoxide, anthraquinone disulfonate, or humic acids). These results indicate that the genus Photobacterium forms subsurface populations well adapted to life in the deep biosphere.}, }
@article {pmid17874304, year = {2008}, author = {Thelaus, J and Forsman, M and Andersson, A}, title = {Role of productivity and protozoan abundance for the occurrence of predation-resistant bacteria in aquatic systems.}, journal = {Microbial ecology}, volume = {56}, number = {1}, pages = {18-28}, pmid = {17874304}, issn = {0095-3628}, mesh = {Animals ; Bacteria/*classification/genetics/*growth &amp; development/isolation &amp; purification ; Ciliophora/growth &amp; development/physiology ; DNA, Bacterial/analysis/isolation &amp; purification ; Ecosystem ; Electrophoresis/methods ; Eukaryota/growth &amp; development/*physiology ; *Fresh Water/chemistry/microbiology/parasitology ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Predatory Behavior/*physiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sweden ; }, abstract = {Top-down control of lower trophic levels, e.g., bacteria, has been suggested to increase along aquatic productivity gradients. The response by the bacterial community may be to become more predation resistant in highly productive environments. To test this hypothesis, samples were taken from 20 aquatic systems along a productivity gradient (dissolved organic carbon from 7 to 71 mg/L), during late summer. The results showed that the biomass of bacteria, phytoplankton, and ciliates increased along the gradient (r2 = 0.532, 0.426, and 0.758, P < 0.01, respectively). However, the organisms did not increase equally, and the ratio of protozoan to bacterial biomass showed a 100-fold increase along the gradient. Ciliates dominated the protozoan biomass in the more nutrient-rich waters. The edibility of colony-forming bacteria was tested using a ciliate predator, Tetrahymena pyriformis. Bacterial edibility was found to decrease with increases in nutrient richness and ciliate biomass in the aquatic systems (r2 = 0.358, P < 0.01; r2 = 0.242, P < 0.05, respectively). Quantile regression analysis indicated that the selection pressures on edible bacteria were increasing along the productivity gradient. Thus, inedible forms of bacteria were selected for in the transition from oligotrophic to eutrophic conditions. Isolated bacteria were distributed among the alpha-, beta-, and gamma- Proteobacteria and the Actinobacteria and Firmicutes taxa. We conclude that bacterial predation resistance increases in nutrient-rich waters with high protozoan predation.}, }
@article {pmid17874261, year = {2008}, author = {Edrington, TS and Callaway, TR and Hallford, DM and Chen, L and Anderson, RC and Nisbet, DJ}, title = {Effects of exogenous melatonin and tryptophan on fecal shedding of E. coli O157:H7 in cattle.}, journal = {Microbial ecology}, volume = {55}, number = {3}, pages = {553-560}, pmid = {17874261}, issn = {0095-3628}, mesh = {Animals ; Cattle/*microbiology ; Colony Count, Microbial ; Dose-Response Relationship, Drug ; Escherichia coli O157/*drug effects/*isolation &amp; purification ; Feces/*microbiology ; Female ; Male ; Melatonin/*administration &amp; dosage/blood ; Tryptophan/*administration &amp; dosage/blood ; }, abstract = {Fecal prevalence of Escherichia coli O157 in ruminants is highest in the summer decreasing to very low levels in the winter. We hypothesize that this seasonal variation is a result of physiological responses within the host animal to changing day-length. To determine the effects of melatonin (MEL) on fecal shedding of E. coli O157:H7 in cattle, eight crossbred beef steers identified as shedding E. coli O157:H7, were allotted to treatment: control or MEL (0.5 mg/kg body weight (BW); 1x) administered orally daily for 7 days. After a 5-day period of no treatment, a second MEL dose (5.0 mg/kg BW; 10x) was administered daily for 4 days. Fecal samples were collected daily for qualification of E. coli O157:H7. No differences (P > 0.10) were observed in the percentage of E. coli O157:H7 positive fecal samples in steers receiving the 1x MEL dose, however the 10x dose decreased (P = 0.05) the percentage of fecal samples E. coli O157:H7 positive. Serum MEL concentrations were higher in the 1x, but not 10x, treated animals compared to control animals. Although it is difficult to explain, this may be a result of decreasing day-length increasing serum melatonin concentrations that may have masked any treatment effect on serum melatonin. In a second similar experiment, a second group of cattle (heifers and steers) were administered tryptophan (TRP) over a 17-day experimental period (5 g/head/day for 10 days followed by 10 g/head/day for 7 days). Tryptophan had no effect (P > 0.20) on the percentage of fecal samples positive for E. coli O157. Serum TRP (P < 0.05), but not MEL (P > 0.20), concentrations were elevated in TRP-treated animals. The decrease in the number of positive fecal samples observed in the first experiment, may be related to gastrointestinal MEL, affected by the 10x, but not 1x MEL dose.}, }
@article {pmid17874260, year = {2008}, author = {Bergmann, I and Geiss-Brunschweiger, U and Hagemann, M and Schoor, A}, title = {Salinity tolerance of the chlorophyll b-synthesizing cyanobacterium Prochlorothrix hollandica strain SAG 10.89.}, journal = {Microbial ecology}, volume = {55}, number = {4}, pages = {685-696}, pmid = {17874260}, issn = {0095-3628}, mesh = {Biomass ; Chlorophyll/*biosynthesis ; Culture Media ; Osmolar Concentration ; Photosynthesis/drug effects ; Prochlorothrix/*drug effects/*growth &amp; development/metabolism ; Salinity ; Sodium Chloride/*pharmacology ; Sucrose/metabolism ; Water Microbiology ; }, abstract = {Ecophysiological investigations on the salinity acclimation of the cyanobacterium Prochlorothrix hollandica SAG 10.89 led to significantly revised salinity tolerance limits. Besides potential effects of cultivation techniques, clear ion composition effects mainly explain formerly described hypersensitivity to NaCl-mediated salinity and lack of osmolyte detection. An extraordinarily broad plasticity of cellular chlorophyll a/b ratios occurred with variations of NaCl-induced salinity. Photosynthesis characteristics, pigment regulation, respiration, and biomass yield in growth medium with field-like ion composition indicated generally reduced acclimation pressure. A simultaneously significant increase in osmolyte (sucrose) accumulation indicated more efficient osmotic acclimation. Minor growth inhibition up to salinities of 10 practical salinity units enlarged the potential habitat of P. hollandica but at the most to about 300,000 km2 in the Baltic Sea. This supports probable observations of Prochlorothrix sp. in phytoplankton assemblages of open waters in Baltic Sea-monitoring studies. Brackish habitats differ from so far known habitats of Prochlorothrix spp. in turbidity, productivity, and plankton composition. Adjusted physiological features dispel fundamental doubts on the establishment of filamentous prochlorophytes in brackish waters.}, }
@article {pmid17874157, year = {2008}, author = {Rusch, A and Amend, JP}, title = {Functional characterization of the microbial community in geothermally heated marine sediments.}, journal = {Microbial ecology}, volume = {55}, number = {4}, pages = {723-736}, pmid = {17874157}, issn = {0095-3628}, mesh = {Archaea/genetics/isolation &amp; purification/*metabolism ; Autotrophic Processes ; Biodiversity ; Chromatography, Gas ; Chromatography, Liquid ; Colony Count, Microbial ; Culture Media ; Geologic Sediments/*microbiology ; Heterotrophic Processes ; Hot Temperature ; In Situ Hybridization, Fluorescence ; Microscopy, Fluorescence ; Phylogeny ; Seawater ; Sulfates/metabolism ; Thermus/genetics/isolation &amp; purification/*metabolism ; *Water Microbiology ; }, abstract = {The microbial population of geothermally heated sediments in a shallow bay of Vulcano Island (Italy) was characterized with respect to metabolic activities and the putatively catalyzing hyperthermophiles. Site-specific anoxic culturing media, most of which were amended with combinations of electron donors (glucose or carboxylic acids) and acceptors (sulfate), were used for selective enrichment of metabolically defined subpopulations. The mostly archaeal chemoautotrophs produced formate at rates of 3.25 and 0.46 fmol cell(-1) day(-1) with and without sulfate, respectively. The glucose fermenting heterotrophs produced acetate (18 fmol cell(-1) day(-1)) and lactate (2.6 fmol cell(-1) day(-1)) and were identified as predominantly Thermus sp. and coccoid archaea. These archaeal cells also metabolized lactate (5.6 fmol cell(-1) day(-1)), but neither formate nor acetate. The heterotrophic culture enriched on formate/ acetate/propionate/sulfate utilized mainly formate (27 fmol cell(-1) day(-1)) and lactate (89-195 fmol cell(-1) day(-1)), and consumed sulfate (38-68 fmol cell(-1) day(-1)). These formate or lactate consuming sulfate reducers were dominated by Archaeoglobales (7% in situ) and unidentified Archaea. The in situ benthic community comprised 15% Crenarchaeota, a significant group only in the autotrophic cultures, and 3% Thermus sp., the putatively predominant group involved in fermentative metabolism. The role of Thermoccales (4% in situ) remained undisclosed in our experiments. This first comprehensive data set established plausible links between several groups of hyperthermophiles in shallow marine hydrothermal systems, their metabolic function within the benthic microbial community, and biogeochemical turnover rates.}, }
@article {pmid17869608, year = {2007}, author = {Kazimierczak, KA and Scott, KP}, title = {Antibiotics and resistance genes: influencing the microbial ecosystem in the gut.}, journal = {Advances in applied microbiology}, volume = {62}, number = {}, pages = {269-292}, doi = {10.1016/S0065-2164(07)62009-7}, pmid = {17869608}, issn = {0065-2164}, mesh = {Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; *Ecosystem ; Intestines/*microbiology ; Probiotics/pharmacology ; Transformation, Bacterial ; }, }
@article {pmid17868363, year = {2007}, author = {Smith, VH}, title = {Microbial diversity-productivity relationships in aquatic ecosystems.}, journal = {FEMS microbiology ecology}, volume = {62}, number = {2}, pages = {181-186}, doi = {10.1111/j.1574-6941.2007.00381.x}, pmid = {17868363}, issn = {0168-6496}, mesh = {*Biodiversity ; *Ecosystem ; *Water Microbiology ; }, abstract = {Thanks to recent advances in molecular biology, one's knowledge of microbial co-occurrence patterns, microbial biogeography and microbial biodiversity is expanding rapidly. This MiniReview explores microbial diversity-productivity relationships in the light of what is known from the general ecology literature. Analyses of microbial diversity-productivity relationships from 70 natural, experimental, and engineered aquatic ecosystems reveal patterns that are strikingly similar to those that have long been documented for communities of macroorganisms. Microbial ecology and the general science of ecology are thus continuing to converge.}, }
@article {pmid17851773, year = {2008}, author = {Icoz, I and Stotzky, G}, title = {Cry3Bb1 protein from Bacillus thuringiensis in root exudates and biomass of transgenic corn does not persist in soil.}, journal = {Transgenic research}, volume = {17}, number = {4}, pages = {609-620}, pmid = {17851773}, issn = {0962-8819}, mesh = {*Biomass ; Electrophoresis, Polyacrylamide Gel ; Endotoxins/genetics/*metabolism ; Enzyme-Linked Immunosorbent Assay ; Plant Roots/*metabolism ; Plants, Genetically Modified/*genetics ; *Soil ; Zea mays/*genetics/*metabolism ; }, abstract = {The Cry3Bb1 protein, insecticidal to the corn rootworm complex (Diabrotica spp.), of Bacillus thuringiensis (Bt) subsp. kumamotoensis was released in root exudates of transgenic Bt corn (event MON863) in sterile hydroponic culture (7.5 +/- 1.12 ng/ml after 28 days of growth) and in nonsterile soil throughout growth of the plants (2.2 +/- 0.62 ng/g after 63 days of growth). Kitchawan soil, which contains predominantly kaolinite (K) but not montmorillonite (M), was amended to 3 or 6% (vol./vol.) with K (3K and 6K soils) or M (3M and 6M soils) and with 1, 3, 5, or 10% (wt./wt.) of ground biomass of Bt corn expressing the Cry3Bb1 protein and incubated at 25 +/- 2 degrees C at the -33-kPa water tension for 60 days. Soils were analyzed for the presence of the protein every 7 to 10 days with a western blot assay (ImmunoStrip) and verified by ELISA. Persistence of the protein varied with the type and amount of clay mineral and the pH of the soils and increased as the concentration of K was increased but decreased as the concentration of M was increased. Persistence decreased when the pH of the K-amended soils was increased from ca. 5 to ca. 7 with CaCO(3): the protein was not detected after 14 and 21 days in the pH-adjusted 3K and 6K soils, respectively, whereas it was detected after 40 days in the 3K and 6K soils not adjusted to pH 7. The protein was detected for only 21 days in the 3M soil and for 14 days in the 6M soil, which were not adjusted in pH. These results indicate that the Cry3Bb1 protein does not persist or accumulate in soil and is degraded rapidly.}, }
@article {pmid17851710, year = {2007}, author = {Adhitya, A and Thomas, FI and Ward, BB}, title = {Diversity of assimilatory nitrate reductase genes from plankton and epiphytes associated with a seagrass bed.}, journal = {Microbial ecology}, volume = {54}, number = {4}, pages = {587-597}, pmid = {17851710}, issn = {0095-3628}, mesh = {Animals ; Bacteria/*enzymology/growth &amp; development ; Bacterial Proteins/genetics/metabolism ; Diatoms/*enzymology/growth &amp; development ; *Ecosystem ; Florida ; *Genetic Variation ; Introns ; Molecular Sequence Data ; Nitrate Reductases/classification/*genetics ; Phylogeny ; Plankton/*enzymology/genetics ; *Plant Development ; Plants/microbiology ; Polymorphism, Restriction Fragment Length ; Seawater ; Sequence Analysis, DNA ; }, abstract = {Assimilatory nitrate reductase gene fragments were isolated from epiphytes and plankton associated with seagrass blades collected from Tampa Bay, Florida, USA. Nitrate reductase genes from diatoms (NR) and heterotrophic bacteria (nasA) were amplified by polymerase chain reaction (PCR) using two sets of degenerate primers. A total of 129 NR and 75 nasA clones from four clone libraries, two from each of epiphytic and planktonic components, were sequenced and aligned. In addition, genomic DNA sequences for the NR fragment were obtained from Skeletonema costatum and Thalassiosira weissflogii diatom cultures. Rarefaction analysis with an operational taxonomic unit cut-off of 6% indicated that diversity of the NR and nasA clone libraries were similar, and that sequencing of the clone libraries was not yet saturated. Phylogenetic analysis indicated that 121 of the 129 NR clones sequenced were similar to diatom sequences. Of the eight non-diatom sequences, four were most closely related to the sequence of Chlorella vulgaris. Introns were found in 8% of the Tampa Bay NR sequences; introns were also observed in S. costatum, but not T. weissflogii. Introns from within the same clone library exhibited close similarity in nucleotide sequence, position and length; the corresponding exon sequences were unique. Introns from within the same component were similar in position and length, but not in nucleotide sequence. These findings raise questions about the function of introns, and mechanisms or time evolution of intron formation. A large cluster of 14 of the 75 nasA sequences was similar to sequences from Vibrio species; other sequences were closely related to sequences from Alteromonas, alpha-proteobacteria and Marinomonas-like species. Biogeographically consistent patterns were observed for the nasA Tampa Bay sequences compared with sequences from other locations: for example, Tampa Bay sequences were similar to those from the South Atlantic Bight, but not the Barents Sea. The Tampa Bay NR clone libraries contained sequences that exhibited phylogenetic similarity with sequences from coastal New Jersey and Monterey Bay, USA. For both NR and nasA, the sequences formed phylogenetic clusters containing nitrate reductase gene fragments that were common to both plankton and epiphyte components, and sequences that were unique to just one component. The implication that some organisms may be differentially represented in epiphytic versus planktonic components of the community suggests that local environmental conditions may have ramifications for regulation of nitrate assimilation processes, community composition, and ecosystem function.}, }
@article {pmid17828570, year = {2008}, author = {Parker, MA}, title = {Symbiotic relationships of legumes and nodule bacteria on Barro Colorado Island, Panama: a review.}, journal = {Microbial ecology}, volume = {55}, number = {4}, pages = {662-672}, pmid = {17828570}, issn = {0095-3628}, mesh = {Bacterial Typing Techniques ; Biodiversity ; Bradyrhizobium/*classification/genetics/isolation &amp; purification ; Burkholderia/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Fabaceae/*microbiology ; Genes, rRNA ; Genetic Variation ; Panama ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Root Nodules, Plant/*microbiology ; Sequence Alignment ; Sequence Analysis, DNA ; Soil Microbiology ; Species Specificity ; *Symbiosis ; }, abstract = {Abstract New data on 129 bacterial isolates were analyzed together with prior samples to characterize community-level patterns of legume-rhizobial symbiosis on Barro Colorado Island (BCI), Panama. Nodules have been sampled from 24 BCI legume species in 18 genera, representing about one quarter of the legume species and one half of the genera on the island. Most BCI legumes associated exclusively with nodule symbionts in the genus Bradyrhizobium, which comprised 86.3% of all isolates (315 of 365). Most of the remaining isolates (44 of 365) belonged to the beta-proteobacterial genus Burkholderia; these were restricted to two genera in the legume subfamily Mimosoideae. Multilocus sequence analysis indicated that BCI Bradyrhizobium strains were differentiated into at least eight lineages with deoxyribonucleic acid divergence of the same magnitude as found among currently recognized species in this bacterial genus. Two of these lineages were widely distributed across BCI legumes. One lineage was utilized by 15 host species of diverse life form (herbs, lianas, and trees) in 12 genera spanning two legume subfamilies. A second common lineage closely related to the taxon B. elkanii was associated with at least five legume genera in four separate tribes. Thus, BCI legume species from diverse clades within the family frequently share interaction with a few common lineages of nodule symbionts. However, certain host species were associated with unique symbiont lineages that have not been found on other coexisting BCI legumes. More comprehensive sampling of host taxa will be needed to characterize the overall diversity of nodule bacteria and the patterns of symbiont sharing among legumes in this community.}, }
@article {pmid17825985, year = {2008}, author = {Khelifi, E and Gannoun, H and Touhami, Y and Bouallagui, H and Hamdi, M}, title = {Aerobic decolourization of the indigo dye-containing textile wastewater using continuous combined bioreactors.}, journal = {Journal of hazardous materials}, volume = {152}, number = {2}, pages = {683-689}, doi = {10.1016/j.jhazmat.2007.07.059}, pmid = {17825985}, issn = {0304-3894}, mesh = {Aerobiosis ; Biodegradation, Environmental ; *Bioreactors ; *Coloring Agents/chemistry/isolation &amp; purification ; Indigo Carmine ; *Indoles/chemistry/isolation &amp; purification ; *Industrial Waste ; *Textile Industry ; *Waste Disposal, Fluid ; Water Pollutants, Chemical/chemistry/*isolation &amp; purification ; }, abstract = {An aerobic bioprocess was applied to Indigo dye-containing textile wastewater treatment aiming at the colour elimination and biodegradation. A combined aerobic system using continuous stirred tank reactor (CSTR) and fixed film bioreactor (FFB) was continuously operated at constant temperature and fed with the textile wastewater (pH: 7.5 and total chemical oxygen demand (COD): 1185 mg l(-1)). The CSTR is a 1l continuous flow stirred tank reactor with a 700 ml working volume, and operated with a variable wastewater loading rate (WLR) from 0.92 to 3.7 g l(-1) d(-1). The FFB is a 1.5l continuous flow with three compartments packed with a rippled cylindrical polyethylene support, operated with a variable WLR between 0.09 and 0.73 g l(-1) d(-1). The combined two bioreactors were inoculated by an acclimated microbial consortium and continuously operated with four total WLR. This system presented high COD elimination and colour removal efficiencies of 97.5% and 97.3%, respectively, obtained with a total hydraulic retention time (HRT) of 4 days and total WLR of 0.29 g l(-1) d(-1). The effects of WLR on absorption phenomena on the yield of conversion of substrate on biomass (R(TSS/COD)) and on the yield of conversion of substrate on active biomass (R(VVS/COD)) are discussed. The increase of WLR and the decrease of HRT diminished the performances of this system in terms of decolourization and COD removal explained by the sloughing of biofilm, and the washout phenomena.}, }
@article {pmid17805918, year = {2008}, author = {Brakstad, OG and Nonstad, I and Faksness, LG and Brandvik, PJ}, title = {Responses of microbial communities in Arctic sea ice after contamination by crude petroleum oil.}, journal = {Microbial ecology}, volume = {55}, number = {3}, pages = {540-552}, pmid = {17805918}, issn = {0095-3628}, mesh = {Arctic Regions ; Bacteria/classification/*drug effects/genetics/*isolation &amp; purification ; Biodegradation, Environmental ; Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ice Cover/*microbiology ; Molecular Sequence Data ; Petroleum/analysis/*metabolism ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Svalbard ; Water Pollutants, Chemical/analysis/*metabolism ; }, abstract = {Microbial communities associated with Arctic fjord ice polluted with petroleum oils were investigated in this study. A winter field experiment was conducted in the Van Mijen Fjord (Svalbard) from February to June 2004, in which the ice was contaminated with a North Sea paraffinic oil. Holes were drilled in the ice and oil samples frozen into the ice at the start of the experiment. Samples, including cores of both oil-contaminated and clean ice, were collected from the field site 33, 74, and 112 days after oil application. The sampled cores were separated into three sections and processed for microbiological and chemical analyses. In the oil-contaminated cores, enumerations of total prokaryotic cells by fluorescence microscopy and colony-forming units (CFU) counts of heterotrophic prokaryotes both showed stimulation of microbial growth, while concentrations of oil-degrading prokaryotes remained at similar levels in contaminated and clean ice. Analysis of polymerase chain reaction (PCR)-amplified bacterial 16S rRNA gene fragments by denaturing gradient gel electrophoresis (DGGE) revealed that bacterial communities in oil-contaminated ice generated fewer bands than communities in clean ice, although banding patterns changed both in contaminated and clean ice during the experimental period. Microbial communities in unpolluted ice and in cores contaminated with the paraffinic oil were examined by cloning and sequence analysis. In the contaminated cores, the communities became predominated by Gammaproteobacteria related to the genera Colwellia, Marinomonas, and Glaciecola, while clean ice included more heterogeneous populations. Chemical analysis of the oil-contaminated ice cores with determinations of n-C17/Pristane and naphthalene/phenanthrene ratios indicated slow oil biodegradation in the ice, primarily in the deeper parts of the ice with low hydrocarbon concentrations.}, }
@article {pmid17803774, year = {2007}, author = {Defoirdt, T and Miyamoto, CM and Wood, TK and Meighen, EA and Sorgeloos, P and Verstraete, W and Bossier, P}, title = {The natural furanone (5Z)-4-bromo-5-(bromomethylene)-3-butyl-2(5H)-furanone disrupts quorum sensing-regulated gene expression in Vibrio harveyi by decreasing the DNA-binding activity of the transcriptional regulator protein luxR.}, journal = {Environmental microbiology}, volume = {9}, number = {10}, pages = {2486-2495}, doi = {10.1111/j.1462-2920.2007.01367.x}, pmid = {17803774}, issn = {1462-2912}, support = {EB003872-01A1/EB/NIBIB NIH HHS/United States ; }, mesh = {DNA, Bacterial/genetics/*metabolism ; Furans/*pharmacology ; Gene Expression Regulation, Bacterial/*drug effects/physiology ; Luminescent Measurements ; Mutation ; Quorum Sensing/*drug effects/physiology ; RNA, Messenger/biosynthesis/genetics/metabolism ; Repressor Proteins/antagonists &amp; inhibitors/biosynthesis/genetics/*metabolism ; Signal Transduction/physiology ; Trans-Activators/antagonists &amp; inhibitors/biosynthesis/genetics/*metabolism ; Vibrio/*drug effects/genetics/metabolism/physiology ; }, abstract = {This study aimed at getting a deeper insight in the molecular mechanism by which the natural furanone (5Z)-4-bromo-5-(bromomethylene)-3-butyl-2(5H)-furanone disrupts quorum sensing in Vibrio harveyi. Bioluminescence experiments with signal molecule receptor double mutants revealed that the furanone blocks all three channels of the V. harveyi quorum sensing system. In further experiments using mutants with mutations in the quorum sensing signal transduction pathway, the compound was found to block quorum sensing-regulated bioluminescence by interacting with a component located downstream of the Hfq protein. Furthermore, reverse transcriptase real-time polymerase chain reaction with specific primers showed that there was no effect of the furanone on luxR(Vh) mRNA levels in wild-type V. harveyi cells. In contrast, mobility shift assays showed that in the presence of the furanone, significantly lower levels of the LuxR(Vh) response regulator protein were able to bind to its target promoter sequences in wild-type V. harveyi. Finally, tests with purified LuxR(Vh) protein also showed less shifts with furanone-treated LuxR(Vh), whereas the LuxR(Vh) concentration was found not to be altered by the furanone (as determined by SDS-PAGE). Therefore, our data indicate that the furanone blocks quorum sensing in V. harveyi by rendering the quorum sensing master regulator protein LuxR(Vh) unable to bind to the promoter sequences of quorum sensing-regulated genes.}, }
@article {pmid17786505, year = {2008}, author = {Chin, KJ and Sharma, ML and Russell, LA and O'Neill, KR and Lovley, DR}, title = {Quantifying expression of a dissimilatory (bi)sulfite reductase gene in petroleum-contaminated marine harbor sediments.}, journal = {Microbial ecology}, volume = {55}, number = {3}, pages = {489-499}, pmid = {17786505}, issn = {0095-3628}, mesh = {Anaerobiosis ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Desulfitobacterium/classification/enzymology/genetics/*isolation &amp; purification ; *Gene Expression ; Geologic Sediments/*chemistry/microbiology ; Hydrogensulfite Reductase/*genetics ; Molecular Sequence Data ; Petroleum/*microbiology ; Phylogeny ; RNA, Bacterial/genetics/isolation &amp; purification/metabolism ; RNA, Messenger/genetics/*isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Temperature ; }, abstract = {The possibility of quantifying in situ levels of transcripts for dissimilatory (bi)sulfite reductase (dsr) genes to track the activity of sulfate-reducing microorganisms in petroleum-contaminated marine harbor sediments was evaluated. Phylogenetic analysis of the cDNA generated from mRNA for a ca. 1.4 kbp portion of the contiguous dsrA and dsrB genes suggested that Desulfosarcina species, closely related to cultures known to anaerobically oxidize aromatic hydrocarbons, were active sulfate reducers in the sediments. The levels of dsrA transcripts (per mug total mRNA) were quantified in sediments incubated anaerobically at the in situ temperature as well as in sediments incubated at higher temperatures and/or with added acetate to increase the rate of sulfate reduction. Levels of dsrA transcripts were low when there was no sulfate reduction because the sediments were depleted of sulfate or if sulfate reduction was inhibited with added molybdate. There was a direct correlation between dsrA transcript levels and rates of sulfate reduction when sulfate was at ca. 10 mM in the various sediment treatments, but it was also apparent that within a given sediment, dsrA levels increased over time as long as sulfate was available, even when sulfate reduction rates did not increase. These results suggest that phylogenetic analysis of dsr transcript sequences may provide insight into the active sulfate reducers in marine sediments and that quantifying levels of dsrA transcripts can indicate whether sulfate reducers are active in particular sediment. Furthermore, it may only be possible to use dsrA transcript levels to compare the relative rates of sulfate reduction in sediments when sulfate concentrations, and possibly other environmental conditions, are comparable.}, }
@article {pmid17786504, year = {2008}, author = {Moore-Kucera, J and Dick, RP}, title = {PLFA profiling of microbial community structure and seasonal shifts in soils of a Douglas-fir chronosequence.}, journal = {Microbial ecology}, volume = {55}, number = {3}, pages = {500-511}, pmid = {17786504}, issn = {0095-3628}, mesh = {Animals ; Bacteria/metabolism ; Biomass ; Eukaryota/metabolism ; Fatty Acids/*analysis/isolation &amp; purification ; Fungi/metabolism ; Phospholipids/*analysis/isolation &amp; purification ; Pseudotsuga/growth &amp; development/*microbiology ; *Seasons ; Soil/*analysis ; *Soil Microbiology ; Temperature ; Time Factors ; Trees ; Washington ; Water/analysis ; }, abstract = {The impact and frequency of forest harvesting could significantly affect soil microbial community (SMC) structure and functioning. The ability of soil microorganisms to perform biogeochemical processes is critical for sustaining forest productivity and has a direct impact on decomposition dynamics and carbon storage potential. The Wind River Canopy Crane Research Forest in SW, WA, provided a unique opportunity to study a forest chronosequence and the residual effects of harvesting on the SMC in comparison to old-growth forests. The objective of this study was to determine the effect of clear-cutting and stand age on temporal dynamics of SMC and physiological stress markers using phospholipid fatty acid (PLFA) profiling. Soil microbial PLFA profiles were determined seven times over 22 months (Nov. 02 to Sep. 04) in old-growth coniferous forest stands (300-500 years) and 8 (CC8)- or 25 (CC25)-year-old replanted clear-cuts. PLFA patterns of the SMC shifted because of clear-cutting, but seasonal temporal changes had greater shifts than differences among stand age. The microbial biomass (total PLFA) and bacterial, fungal, and selected other PLFAs were significantly reduced in CC8 but not in CC25 sites relative to the old-growth sites. An increase in stress indicators [PLFA ratios of saturated/monsaturated and (cy17:0 + cy19:0)/(16:1omega7 + 18:1omega7)] in late summer was related to water stress. Although the canopy and litter input are quite different for a 25-year clear-cut compared to virgin old-growth forest, we conclude that the composition of the microbial communities, 25 years after clear-cutting, has recovered sufficiently to be much more similar to old-growth forests than a recent clear-cut at this Pacific Northwest forest site. The study shows the potential of PLFA analysis for profiling microbial communities and their stress status under field conditions, but wide temporal shifts emphasize the need for sampling over seasons to fully interpret ecosystem management impacts on microbial populations.}, }
@article {pmid17768652, year = {2008}, author = {Bastida, F and Kandeler, E and Hernández, T and García, C}, title = {Long-term effect of municipal solid waste amendment on microbial abundance and humus-associated enzyme activities under semiarid conditions.}, journal = {Microbial ecology}, volume = {55}, number = {4}, pages = {651-661}, pmid = {17768652}, issn = {0095-3628}, mesh = {Analysis of Variance ; Bacteria/chemistry/enzymology ; *Biomass ; Enzymes/metabolism ; Ergosterol/chemistry ; Fatty Acids/chemistry ; Fungi/chemistry/enzymology ; Humic Substances/*microbiology ; Phospholipids/chemistry ; *Refuse Disposal ; Soil/analysis ; *Soil Microbiology ; Time Factors ; }, abstract = {Microbial ecology is the key to understanding the function of soil biota for organic matter cycling after a single amendment of organic waste in semiarid soils. Therefore, in this paper, the long-term effect (17 years) of adding different doses of a solid municipal waste to an arid soil on humus-enzyme complexes, a very stable and long-lasting fraction of soil enzymes, as well as on microbial and plant abundance, was studied. Humic substances were extracted by 0.1 M pH 7 sodium pyrophosphate from soil samples collected in experimental plots amended with different doses of a solid municipal waste (0, 65, 130, 195, and 260 t/ha) 17 years before. The activity of different hydrolases related with the C (beta-glucosidase), N (urease), and P (alkaline phosphatase) cycles and with the formation of humic substances (o-diphenol oxidase) were determined in this extract. The density and diversity of plant cover in the plots, as well as the fungal and bacterial biomass (by analyzing phopholipid fatty acids) were also determined. In general, the amended plots showed greater humic substance-related enzymatic activity than the unamended plots. This activity increased with the dose but only up to a certain level, above which it leveled off or even diminished. Plant diversity and cover density followed the same trend. Fungal and bacterial biomass also benefited in a dose-dependent manner. Different signature molecules representing gram+ and gram- bacteria, and those corresponding to monounsaturated and saturated fatty acids showed a similar behavior. The results demonstrate that organic amendment had a noticeable long-term effect on the vegetal development, humic substances-related enzyme activity and on the development of bacteria and fungi in semiarid conditions.}, }
@article {pmid17766021, year = {2008}, author = {Vanhaecke, L and Knize, MG and Noppe, H and De Brabander, H and Verstraete, W and Van de Wiele, T}, title = {Intestinal bacteria metabolize the dietary carcinogen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine following consumption of a single cooked chicken meal in humans.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {46}, number = {1}, pages = {140-148}, doi = {10.1016/j.fct.2007.07.008}, pmid = {17766021}, issn = {0278-6915}, support = {CA55861/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Animals ; Bacteria/*metabolism ; Biotransformation ; Carcinogens/*metabolism ; Chickens ; Feces/chemistry ; Humans ; Imidazoles/blood/*metabolism/urine ; Meat/*analysis ; Mutagenicity Tests ; Reproducibility of Results ; Salmonella typhimurium/drug effects/genetics ; Spectrophotometry, Ultraviolet ; }, abstract = {2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is a carcinogenic heterocyclic amine formed in meats during cooking. Although the formation of PhIP metabolites by mammalian enzymes has been extensively reported, the involvement of the intestinal bacteria remains unclear. This study examined the urinary and fecal excretion of a newly identified microbial PhIP metabolite 7-hydroxy-5-methyl-3-phenyl-6,7,8,9-tetrahydropyrido[3',2':4,5]imidazo[1,2-a]pyrimidin-5-ium chloride (PhIP-M1) in humans. The subjects were fed 150 g of cooked chicken containing 0.88-4.7 microg PhIP, and urine and feces collections were obtained during 72 h after the meal. PhIP-M1 and its trideuterated derivate were synthesized and a LC/MS/MS method was developed for their quantification. The mutagenic activity of PhIP-M1, as analyzed using the Salmonella strains TA98, TA100 and TA102, yielded no significant response. Of the ingested PhIP dose, volunteers excreted 12-21% as PhIP and 1.2-15% as PhIP-M1 in urine, and 26-42% as PhIP and 0.9-11% as PhIP-M1 in feces. The rate of PhIP-M1 excretion varied among the subjects. Yet, an increase in urinary excretion was observed for successive time increments, whereas for PhIP the majority was excreted in the first 24h. These findings suggest that besides differences in digestion, metabolism and diet, the microbial composition of the gastrointestinal tract also strongly influences individual disposition and carcinogenic risk from PhIP.}, }
@article {pmid17719667, year = {2007}, author = {Defoirdt, T and Boon, N and Sorgeloos, P and Verstraete, W and Bossier, P}, title = {Alternatives to antibiotics to control bacterial infections: luminescent vibriosis in aquaculture as an example.}, journal = {Trends in biotechnology}, volume = {25}, number = {10}, pages = {472-479}, doi = {10.1016/j.tibtech.2007.08.001}, pmid = {17719667}, issn = {0167-7799}, mesh = {Anti-Bacterial Agents/therapeutic use ; *Aquaculture ; Bacterial Vaccines/*therapeutic use ; Communicable Disease Control/*trends ; Drug Resistance, Bacterial/*drug effects ; Vibrio/*drug effects/*virology ; Vibrio Infections/*prevention &amp; control ; }, abstract = {The massive (mis)use of antibiotics to control infections in aquaculture has resulted in the development of resistant strains, which have rendered antibiotic treatments ineffective. Moreover, the horizontal transfer of resistance determinants to human pathogens and the presence of antibiotic residues in aquaculture products for human consumption constitute important threats to public health. Therefore, to make the aquaculture industry more sustainable, new strategies to control infections are urgently needed.}, }
@article {pmid17714481, year = {2007}, author = {Sundin, GW and Weigand, MR}, title = {The microbiology of mutability.}, journal = {FEMS microbiology letters}, volume = {277}, number = {1}, pages = {11-20}, doi = {10.1111/j.1574-6968.2007.00901.x}, pmid = {17714481}, issn = {0378-1097}, mesh = {Animals ; Bacteria/enzymology/*genetics/pathogenicity ; Bacterial Infections/microbiology ; Bacterial Proteins/genetics/metabolism ; *DNA Mismatch Repair ; DNA Repair Enzymes/genetics/metabolism ; DNA-Directed DNA Polymerase/genetics/metabolism ; Humans ; Mice ; *Mutation ; }, abstract = {Bacteria possessing elevated spontaneous mutation rates are prevalent in certain environments, which is a paradox because most mutations are deleterious. For example, cells with defects in the methyl-directed mismatch repair (MMR) system, termed mutators or hypermutators, are overrepresented in populations of bacterial pathogens, with the mutator trait hypothesized to be advantageous in the changing host enviroments faced during colonization and establishment of chronic infections. Error-prone DNA polymerases, such as polIV and polV, function in translesion DNA synthesis, a DNA damage response that ensures genome integrity with a cost of increased mutation. While the biochemical aspects of these mutability pathways are well understood, the biological impacts have received less attention. Here, an examination of bacterial mutability systems and specifically the ecological and evolutionary context resulting in the selection of these systems is carried out.}, }
@article {pmid17714401, year = {2007}, author = {Li, K and Guan, W and Wei, G and Liu, B and Xu, J and Zhao, L and Zhang, Y}, title = {Phylogenetic analysis of intestinal bacteria in the Chinese mitten crab (Eriocheir sinensis).}, journal = {Journal of applied microbiology}, volume = {103}, number = {3}, pages = {675-682}, doi = {10.1111/j.1365-2672.2007.03295.x}, pmid = {17714401}, issn = {1364-5072}, mesh = {Animals ; Bacteria/*genetics/isolation &amp; purification ; Bacteroides/genetics/isolation &amp; purification ; Brachyura/*microbiology ; China ; DNA, Bacterial/genetics ; Electrophoresis, Polyacrylamide Gel/methods ; *Food Microbiology ; Genetic Variation/genetics ; Intestines/*microbiology ; Phylogeny ; Polymerase Chain Reaction/methods ; Proteobacteria/genetics/isolation &amp; purification ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; }, abstract = {AIMS: To identify the dominant intestinal bacteria in the Chinese mitten crab, and to investigate the differences in the intestinal bacteria between pond-raised and wild crabs.<br><br>METHODS AND RESULTS: The diversity of intestinal bacteria in the Chinese mitten crabs was investigated by denaturing gradient gel electrophoresis (DGGE) fingerprinting, 16S rRNA gene clone library analysis and real-time quantitative PCR. The principal component analysis of DGGE profiles indicated that substantial intersubject variations existed in intestinal bacteria in pond-raised crab. The sequencing of 16S rRNA genes revealed that 90-95% of the phylotypes in the clone libraries were affiliated with Proteobacteria and Bacteroidetes. Some genera were identified as unique in wild crabs and in pond-raised crabs, whereas Bacteroidetes was found to be common in all sampled crab groups. Real-time quantitative PCR indicated that the abundance of Bacteroides and the total bacterial load were approximately four-to-10 times higher in pond-raised crabs than in wild crabs. A significant portion of the phylotypes shared low similarity with previously sequenced organisms, indicating that the bacteria in the gut of Chinese mitten crabs are yet to be described.<br><br>CONCLUSIONS: The intestinal bacteria of pond-raised crabs showed higher intersubject variation, total diversity and abundance than that observed in wild crabs. The high proportion of the clones of Proteobacteria and Bacteroidetes in the clone library is an indication that these bacteria may be the dominant population in the gut of the Chinese mitten crab.<br><br>This study demonstrated obvious differences in the intestinal bacterial composition of pond-raised crabs and wild crabs. This knowledge will increase our understanding of the effects of aquaculture operations on bacterial community composition in the crab gut and provide necessary data for the development of probiotic products for crab cultivation.}, }
@article {pmid17712604, year = {2008}, author = {Cho, ST and Tsai, SH and Ravindran, A and Selvam, A and Yang, SS}, title = {Seasonal variation of microbial populations and biomass in Tatachia grassland soils of Taiwan.}, journal = {Environmental geochemistry and health}, volume = {30}, number = {3}, pages = {255-272}, pmid = {17712604}, issn = {0269-4042}, mesh = {Biodiversity ; *Biomass ; Carbon/analysis ; Colony Count, Microbial ; Nitrogen/analysis ; *Poaceae ; RNA, Ribosomal, 16S/analysis ; Seasons ; *Soil Microbiology ; Taiwan ; }, abstract = {To investigate the seasonal variations of microbial ecology in grassland of Tatachia forest, soil properties, microbial populations, microbial biomass, and 16S rDNA clone library analysis were determined. The soil had temperatures 6.6-18.4 degrees C, pH 3.6-5.1, total organic carbon 1.11-10.68%, total nitrogen 0.18-0.78%, and C/N ratios 3.46-20.55. Each gram of dry soil contained bacteria, actinomycetes, fungi, cellulolytic, phosphate-solubilizing microbes, and nitrogen-fixing microbes 4.54 x 10(4) to 3.79 x 10(7), 3.43 x 10(2) to 2.17 x 10(5), 5.74 x 10(3) to 3.76 x 10(6), 1.97 x 10(3) to 1.34 x 10(6), 8.49 x 10(2) to 5.59 x 10(5), and 3.86 x 10(2) to 3.75 x 10(5) CFU, respectively. Each gram of soil contained 117-2,482 microg of microbial biomass carbon, 23-216 microg of microbial biomass nitrogen and 9-29 microg of DNA. The microbial populations, microbial biomass, and DNA decreased stepwise with the depth of soil, and they had low values in winter seasons. The microbial populations, microbial biomass carbon, microbial biomass nitrogen, and DNA at the BW2 horizon were 8.42-17.84, 19.26-64.40, 16.84-61.11, and 31.03-46.26% of those at the O horizon, respectively. When analyzing 16S rDNA library, members of Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, candidate division TMI, candidate division TM7, Gammatimonadetes, and Verrucomicrobia were identified. Members of Proteobacteria (44.4%) and Acidobacteria (33.3%) dominated the clone libraries. Within the phylum Proteobacteria, alpha-, beta-, and gamma-Proteobacteria were most numerous, followed by delta-Proteobacteria.}, }
@article {pmid17704858, year = {2008}, author = {Ballot, A and Dadheech, PK and Haande, S and Krienitz, L}, title = {Morphological and phylogenetic analysis of Anabaenopsis abijatae and Anabaenopsis elenkinii (nostocales, cyanobacteria) from tropical inland water bodies.}, journal = {Microbial ecology}, volume = {55}, number = {4}, pages = {608-618}, pmid = {17704858}, issn = {0095-3628}, mesh = {Cyanobacteria/*classification/cytology/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Genes, Bacterial ; Genes, rRNA ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Tropical Climate ; *Water Microbiology ; }, abstract = {Anabaenopsis spp. are heterocytous cyanobacteria commonly found in tropical, subtropical, and temperate water bodies. So far, the knowledge about the phylogeny of this genus is poor. Therefore, we have isolated 15 Anabaenopsis spp. strains from Kenyan and Mexican alkaline and saline water bodies and from a Ugandan freshwater body and studied the morphology and phylogeny in a polyphasic approach. Morphologically, the investigated strains could be discriminated in two groups. One group was containing six Anabaenopsis abijatae and A. cf. abijatae strains with up to more than 500 vegetative cells in one filament, mostly single intercalary heterocyte formation, and the ability to branch out. The other group comprised nine strains of Anabaenopsis elenkinii with short filaments with up to 38 vegetative cells, intercalary heterocytes in pairs, and no ability to branch out. The morphological differences were reflected in the two distinct clusters, which were found in the phylogenetic trees of 16S rDNA and PC-IGS. While the high 16S rDNA similarity values > 97.5% found between all investigated A. abijatae and A. elenkinii strains support the assignment of these two species to one single genus, the morphological differences and the low similarity values (< 87.3) found in PC-IGS sequences between the two clusters indicate two separate genera. A close morphological and phylogenetic relationship was found for A. abijatae and Anabaenopsis (Cyanospira) rippkae.}, }
@article {pmid17701242, year = {2008}, author = {Srinivasan, V and Nam, HM and Sawant, AA and Headrick, SI and Nguyen, LT and Oliver, SP}, title = {Distribution of tetracycline and streptomycin resistance genes and class 1 integrons in Enterobacteriaceae isolated from dairy and nondairy farm soils.}, journal = {Microbial ecology}, volume = {55}, number = {2}, pages = {184-193}, pmid = {17701242}, issn = {0095-3628}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/growth &amp; development/isolation &amp; purification ; Colony Count, Microbial ; DNA, Bacterial/genetics ; *Drug Resistance, Multiple, Bacterial ; Enterobacteriaceae/drug effects/*genetics/isolation &amp; purification ; Genes, Bacterial/drug effects ; *Integrons ; Microbial Sensitivity Tests ; Polymerase Chain Reaction ; *Soil Microbiology ; Streptomycin/*pharmacology ; Tetracycline/*pharmacology ; }, abstract = {The prevalence of selected tetracycline and streptomycin resistance genes and class 1 integrons in Enterobacteriaceae (n = 80) isolated from dairy farm soil and nondairy soils was evaluated. Among 56 bacteria isolated from dairy farm soils, 36 (64.3%) were resistant to tetracycline, and 17 (30.4%) were resistant to streptomycin. Lower frequencies of tetracycline (9 of 24 or 37.5%) and streptomycin (1 of 24 or 4.2%) resistance were observed in bacteria isolated from nondairy soils. Bacteria (n = 56) isolated from dairy farm soil had a higher frequency of tetracycline resistance genes including tetM (28.6%), tetA (21.4%), tetW (8.9%), tetB (5.4%), tetS (5.4%), tetG (3.6%), and tetO (1.8%). Among 24 bacteria isolated from nondairy soils, four isolates carried tetM, tetO, tetS, and tetW in different combinations; whereas tetA, tetB, and tetG were not detected. Similarly, a higher prevalence of streptomycin resistance genes including strA (12.5%), strB (12.5%), ant(3'') (12.5), aph(6)-1c (12.5%), aph(3'') (10.8%), and addA (5.4%) was detected in bacteria isolated from dairy farm soils than in nondairy soils. None of the nondairy soil isolates carried aadA gene. Other tetracycline (tetC, tetD, tetE, tetK, tetL, tetQ, and tetT) and streptomycin (aph(6)-1c and ant(6)) resistance genes were not detected in both dairy and nondairy soil isolates. A higher distribution of multiple resistance genes was observed in bacteria isolated from dairy farm soil than in nondairy soil. Among 36 tetracycline- and 17 streptomycin-resistant isolates from dairy farm soils, 11 (30.6%) and 9 (52.9%) isolates carried multiple resistance genes encoding resistance to tetracycline and streptomycin, respectively, which was higher than in bacteria isolated from nondairy soils. One strain each of Citrobacter freundii and C. youngae isolated from dairy farm soils carried class 1 integrons with different inserted gene cassettes. Results of this small study suggest that the presence of multiple resistance genes and class 1 integrons in Enterobacteriaceae in dairy farm soil may act as a reservoir of antimicrobial resistance genes and could play a role in the dissemination of these antimicrobial resistance genes to other commensal and indigenous microbial communities in soil. However, additional longer-term studies conducted in more locations are needed to validate this hypothesis.}, }
@article {pmid17694405, year = {2008}, author = {Coppotelli, BM and Ibarrolaza, A and Del Panno, MT and Morelli, IS}, title = {Effects of the inoculant strain Sphingomonas paucimobilis 20006FA on soil bacterial community and biodegradation in phenanthrene-contaminated soil.}, journal = {Microbial ecology}, volume = {55}, number = {2}, pages = {173-183}, pmid = {17694405}, issn = {0095-3628}, mesh = {Bacteria/genetics/*growth &amp; development/metabolism ; Biodegradation, Environmental ; Carbon Dioxide/metabolism ; Chromatography, Gas ; Colony Count, Microbial ; DNA, Bacterial/genetics ; Electrophoresis ; Molecular Sequence Data ; Oxidoreductases/metabolism ; Phenanthrenes/analysis/*metabolism ; Polymerase Chain Reaction ; *Soil Microbiology ; Soil Pollutants/metabolism ; Sphingomonas/genetics/isolation &amp; purification/*metabolism ; }, abstract = {The effects of the inoculant strain Sphingomonas paucimobilis 20006FA (isolated from a phenanthrene-contaminated soil) on the dynamics and structure of microbial communities and phenanthrene elimination rate were studied in soil microcosms artificially contaminated with phenanthrene. The inoculant managed to be established from the first inoculation as it was evidenced by denaturing gradient gel electrophoresis analysis, increasing the number of cultivable heterotrophic and PAH-degrading cells and enhancing phenanthrene degradation. These effects were observed only during the inoculation period. Nevertheless, the soil biological activity (dehydrogenase activity and CO(2) production) showed a late increase. Whereas gradual and successive changes in bacterial community structures were caused by phenanthrene contamination, the inoculation provoked immediate, significant, and stable changes on soil bacterial community. In spite of the long-term establishment of the inoculated strain, at the end of the experiment, the bioaugmentation did not produce significant changes in the residual soil phenanthrene concentration and did not improve the residual effects on the microbial soil community.}, }
@article {pmid17692889, year = {2008}, author = {Zhang, L and De Schryver, P and De Gusseme, B and De Muynck, W and Boon, N and Verstraete, W}, title = {Chemical and biological technologies for hydrogen sulfide emission control in sewer systems: a review.}, journal = {Water research}, volume = {42}, number = {1-2}, pages = {1-12}, doi = {10.1016/j.watres.2007.07.013}, pmid = {17692889}, issn = {0043-1354}, mesh = {*Air Pollutants/chemistry/metabolism ; Air Pollution/*prevention &amp; control ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/metabolism/virology ; Bacteriophages/physiology ; *Drainage, Sanitary ; Energy-Generating Resources ; *Hydrogen Sulfide/chemistry/metabolism ; Oxidation-Reduction ; }, abstract = {Biogenic corrosion of sewers represents a cost of about 10% of total sewage treatment cost in Flanders (Belgium) and is further increasing. In the past, research has resulted in a number of prevention methods, such as injection of air, oxygen, H(2)O(2), NaClO, FeCl(3) and FeSO(4). The possibility of biological oxidation of sulfide using nitrate as the electron acceptor has also been explored in sewer systems. However, all of these methods have a problem with the high cost (euro 1.9-7.2 kg(-1)S removal). In this review, new approaches for hydrogen sulfide emission control in sewer systems are discussed. The control of hydrogen sulfide emission by using a microbial fuel cell (MFC) can be cost-effective while the BOD is removed partially. The use of phages that target sulfate-reducing bacteria (SRB) can possibly inhibit sulfide formation. Novel inhibitors, such as slow release solid-phase oxygen (MgO(2)/CaO(2)) and formaldehyde, warrant further study to control hydrogen sulfide emission in sewer systems.}, }
@article {pmid17690836, year = {2008}, author = {Sun, L and Qiu, F and Zhang, X and Dai, X and Dong, X and Song, W}, title = {Endophytic bacterial diversity in rice (Oryza sativa L.) roots estimated by 16S rDNA sequence analysis.}, journal = {Microbial ecology}, volume = {55}, number = {3}, pages = {415-424}, pmid = {17690836}, issn = {0095-3628}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; *Biodiversity ; China ; DNA, Bacterial/genetics/isolation &amp; purification ; DNA, Ribosomal/genetics/isolation &amp; purification ; Gene Library ; Molecular Sequence Data ; Oryza/*microbiology ; Phylogeny ; Plant Roots/*microbiology/physiology ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics/isolation &amp; purification ; Sequence Analysis, DNA/*methods ; *Soil Microbiology ; Symbiosis ; }, abstract = {The endophytic bacterial diversity in the roots of rice (Oryza sativa L.) growing in the agricultural experimental station in Hebei Province, China was analyzed by 16S rDNA cloning, amplified ribosomal DNA restriction analysis (ARDRA), and sequence homology comparison. To effectively exclude the interference of chloroplast DNA and mitochondrial DNA of rice, a pair of bacterial PCR primers (799f-1492r) was selected to specifically amplify bacterial 16S rDNA sequences directly from rice root tissues. Among 192 positive clones in the 16S rDNA library of endophytes, 52 OTUs (Operational Taxonomic Units) were identified based on the similarity of the ARDRA banding profiles. Sequence analysis revealed diverse phyla of bacteria in the 16S rDNA library, which consisted of alpha, beta, gamma, delta, and epsilon subclasses of the Proteobacteria, Cytophaga/Flexibacter/Bacteroides (CFB) phylum, low G+C gram-positive bacteria, Deinococcus-Thermus, Acidobacteria, and archaea. The dominant group was Betaproteobacteria (27.08% of the total clones), and the most dominant genus was Stenotrophomonas. More than 14.58% of the total clones showed high similarity to uncultured bacteria, suggesting that nonculturable bacteria were detected in rice endophytic bacterial community. To our knowledge, this is the first report that archaea has been identified as endophytes associated with rice by the culture-independent approach. The results suggest that the diversity of endophytic bacteria is abundant in rice roots.}, }
@article {pmid17690835, year = {2008}, author = {Aline, T}, title = {Dissolution of dead corals by euendolithic microorganisms across the northern Great Barrier Reef (Australia).}, journal = {Microbial ecology}, volume = {55}, number = {4}, pages = {569-580}, pmid = {17690835}, issn = {0095-3628}, mesh = {Animals ; Anthozoa/*chemistry/*microbiology ; Australia ; Biodegradation, Environmental ; Biodiversity ; Calcium Carbonate/chemistry ; Chlorophyta/metabolism ; Ecology ; Ecosystem ; Environmental Monitoring ; Fungi/metabolism ; Plectonema/metabolism ; Population Dynamics ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {Spatial and temporal variabilities in species composition, abundance, distribution, and bioeroding activity of euendolithic microorganisms were investigated in experimental blocks of the massive coral Porites along an inshore-offshore transect across the northern Great Barrier Reef (Australia) over a 3-year period. Inshore reefs showed turbid and eutrophic waters, whereas the offshore reefs were characterized by oligotrophic waters. The euendolithic microorganisms and their ecological characteristics were studied using techniques of microscopy, petrographic sections, and image analysis. Results showed that euendolithic communities found in blocks of coral were mature. These communities were dominated by the chlorophyte Ostreobium quekettii, the cyanobacterium Plectonema terebrans, and fungi. O. quekettii was found to be the principal agent of microbioerosion, responsible for 70-90% of carbonate removal. In the offshore reefs, this oligophotic chlorophyte showed extensive systems of filaments that penetrated deep inside coral skeletons (up to 4.1 mm) eroding as much as 1 kg CaCO3 eroded m(-2) year(-1). The percentage of colonization by euendolithic filaments at the surface of blocks did not vary significantly among sites, while their depths of penetration, especially that of O. quekettii (0.6-4.1 mm), increased significantly and gradually with the distance from the shore. Rates of microbioerosion (0.1-1.4 kg m(-2) after 1 year and 0.2-1.3 kg m(-2) after 3 years of exposure) showed a pattern similar to the one found for the depth of penetration of O. quekettii filaments. Accordingly, oligotrophic reefs had the highest rates ofmicrobioerosion ofup to 1.3 kg m(-2) year(-1), whereas the development of euendolithic communities in inshore reefs appeared to be limited by turbidity, high sedimentation rates, and low grazing pressure (rates < 0.5 kg m(-2) after 3 years). Those results suggest that boring microorganisms, including O. quekettii, have a significant impact on the overall calcium carbonate budget of coral reef ecosystems, which varies according to environmental conditions.}, }
@article {pmid17687594, year = {2008}, author = {Meinersmann, RJ and Berrang, ME and Jackson, CR and Fedorka-Cray, P and Ladely, S and Little, E and Frye, JG and Mattsson, B}, title = {Salmonella, Campylobacter and Enterococcus spp.: their antimicrobial resistance profiles and their spatial relationships in a synoptic study of the Upper Oconee River basin.}, journal = {Microbial ecology}, volume = {55}, number = {3}, pages = {444-452}, pmid = {17687594}, issn = {0095-3628}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacterial Typing Techniques ; Campylobacter/classification/*drug effects/isolation &amp; purification ; Cluster Analysis ; Colony Count, Microbial ; *Drug Resistance, Bacterial ; Enterococcus/classification/*drug effects/isolation &amp; purification ; Georgia ; Humans ; Microbial Sensitivity Tests ; Rivers/*microbiology ; Salmonella/classification/*drug effects/isolation &amp; purification ; }, abstract = {Rivers may serve as reservoirs for enteric organisms. Very little is known about the boundaries of microbial communities in moving bodies of water so this study was undertaken to find the limits of distribution of some bacteria, focusing on enteric organisms. The presence of Salmonella, Campylobacter, and Enterococcus spp. and the antimicrobial resistance phenotypes carried by these organisms was evaluated for the Upper Oconee River basin, a small river in the lower Piedmont of northeastern Georgia, USA. Samples were obtained from 83 sites during a 3-h period on a spring day (April 2005) in an approximately 30 x 20 km region. Campylobacter spp. was isolated at 12 sites. The Campylobacter isolates from three sites were resistant to tetracycline. Of the five short-variable region (SVR) subtypes of Campylobacter that were found, three were found at more than one site, two types were found twice, and one subtype was found three times. Enterococcus was isolated at 71 sites. E. casseliflavus was the most common species. Based on species identification and antimicrobial resistance patterns, 24 types of Enterococcus were found. Salmonella was isolated from 62 sites. Of the 19 Salmonella serovars that were isolated, serovar Muenchen accounted for about 20% of the isolates. The next three most common serovars isolated, Rubislaw, Hartford, and Give, accounted for about 44% of the river isolates. Antimicrobial resistance profiling offered limited differentiation of Salmonella isolates because only seven isolates were resistant to any antimicrobial. The sites at which Salmonella, Campylobacter, or Enterococcus were isolated did not correlate with each other or with the total coliform number or Escherichia coli count for the site. However, isolates of some of the same species and type occurred in clusters that were restricted to areas within 5 to 6 km.}, }
@article {pmid17687593, year = {2008}, author = {Manini, E and Luna, GM and Corinaldesi, C and Zeppilli, D and Bortoluzzi, G and Caramanna, G and Raffa, F and Danovaro, R}, title = {Prokaryote diversity and virus abundance in shallow hydrothermal vents of the Mediterranean Sea (Panarea Island) and the Pacific Ocean (north Sulawesi-Indonesia).}, journal = {Microbial ecology}, volume = {55}, number = {4}, pages = {626-639}, pmid = {17687593}, issn = {0095-3628}, mesh = {Archaea/genetics/*growth &amp; development ; Bacteria/genetics/*growth &amp; development ; *Biodiversity ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Ecosystem ; Geologic Sediments/microbiology ; In Situ Hybridization, Fluorescence ; Mediterranean Sea ; Pacific Ocean ; Polymorphism, Restriction Fragment Length ; Population Dynamics ; Viruses/*growth &amp; development ; *Water Microbiology ; }, abstract = {Despite their ubiquitous distribution in tectonically active coastal zones, shallow water hydrothermal vents have been less investigated than deep-sea vents. In the present study, we investigated the role of viral control and fluid emissions on prokaryote abundance, diversity, and community structure (total Archaea, total Bacteria, and sulphate-reducing bacteria) in waters and sediments surrounding the caldera of four different shallow-water hydrothermal vents (three located in the Mediterranean Sea and one in the Pacific Ocean). All vents, independent of their location, generally displayed a significant decrease of benthic prokaryote abundance, as well as its viable fraction, with increasing distance from the vent. Prokaryote assemblages were always dominated by Bacteria. Benthic Archaea accounted for 23-33% of total prokaryote abundance in the Mediterranean Sea and from 13 to 29% in the Pacific Ocean, whereas in the water column they accounted for 25-38%. The highest benthic bacterial ribotype richness was observed in close proximity of the vents (i.e., at 10-cm distance from the emissions), indicating that vent fluids might influence bacterial diversity in surrounding sediments. Virioplankton and viriobenthos abundances were low compared to other marine systems, suggesting that temperature and physical-chemical conditions might influence viral survival in these vent systems. We thus hypothesize that the high bacterial diversity observed in close proximity of the vents is related with the highly variable vent emissions, which could favor the coexistence of several prokaryotic species.}, }
@article {pmid17682816, year = {2008}, author = {Bizzarri, MF and Prabhakar, A and Bishop, AH}, title = {Multiple-locus sequence typing analysis of Bacillus thuringiensis recovered from the phylloplane of clover (Trifolium hybridum) in vegetative form.}, journal = {Microbial ecology}, volume = {55}, number = {4}, pages = {619-625}, pmid = {17682816}, issn = {0095-3628}, mesh = {Bacillus thuringiensis/classification/*genetics ; Bacillus thuringiensis Toxins ; Bacterial Proteins/genetics ; Bacterial Typing Techniques ; Chromosomes, Bacterial/genetics ; Conjugation, Genetic ; DNA, Bacterial/genetics ; *Ecosystem ; Endotoxins/genetics ; Genes, Bacterial ; Genotype ; Hemolysin Proteins/genetics ; Linkage Disequilibrium ; Plant Leaves/*microbiology ; Plasmids ; Trifolium/*microbiology ; }, abstract = {Abstract The chromosomal genotype, as judged by multi locus sequence typing, and the episomal genotype, as judged by plasmid profile and cry gene content, were analyzed for a collection of strains of Bacillus thuringiensis. These had been recovered in vegetative form over a period of several months from the leaves of a small plot of clover (Trifolium hybridum). A clonal population structure was indicated, although greater variation in sequence types (STs) was discovered than in previous collections of B. cereus/B. thuringiensis. Isolates taken at the same time had quite different genotypes, whereas those of identical genotypes were recovered at different times. The profiles of plasmid content and cry genes generally bore no relation to each other nor to the STs. Evidently, although relatively little recombination was occurring in the seven chromosomal genes analyzed, a great deal of conjugal transfer, and perhaps recombination, was occurring involving plasmids. A clinical diarrheal isolate of B. cereus and the commercial biopesticide strain HD-1 of B. thuringiensis, both included as out-groups, were found to have very similar STs. This further emphasizes the role of episomal elements in the characteristics and differentiation of these two species.}, }
@article {pmid17676375, year = {2008}, author = {Zhu, P and Li, Q and Wang, G}, title = {Unique microbial signatures of the alien Hawaiian marine sponge Suberites zeteki.}, journal = {Microbial ecology}, volume = {55}, number = {3}, pages = {406-414}, pmid = {17676375}, issn = {0095-3628}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Cyanobacteria/classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; *Ecosystem ; Gene Library ; Hawaii ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Suberites/*microbiology ; }, abstract = {Invasive species poses a threat to the world's oceans. Alien sponges account for the majority of introduced marine species in the isolated Hawaiian reef ecosystems. In this study, cultivation-dependent and cultivation-independent techniques were applied to investigate microbial consortia associated with the alien Hawaiian marine sponge Suberites zeteki. Its microbial communities were diverse with representatives of Actinobacteria, Firmicutes, alpha- and gamma-Proteobacteria, Bacteroidetes, Chlamydiae, Planctomycetes, and Cyanobacteria. Specifically, the genus Chlamydia was identified for the first time from marine sponges, and two genera (Streptomyces and Rhodococcus) were added to the short list of culturable actinobacteria from sponges. Culturable microbial communities were dominated by Bacillus species (63%) and contained actinobacterial species closely affiliated with those from habitats other than marine sponges. Cyanobacterial clones were clustered with free-living cyanobacteria from water column and other environmental samples; they show no affiliation with other sponge-derived cyanobacteria. The low sequence similarity of Planctomycetes, Chlamydiae, and alpha-Proteobacteria clones to other previously described sequences suggested that S. zeteki may contain new lineages of these bacterial groups. The microbial diversity of S. zeteki was different from that of other studied marine sponges. This is the first report on microbial communities of alien marine invertebrate species. For the first time, it provides an insight into microbial structure within alien marine sponges in the Hawaiian marine ecosystems.}, }
@article {pmid17674087, year = {2008}, author = {Borges, MT and Sousa, A and De Marco, P and Matos, A and Hönigová, P and Castro, PM}, title = {Aerobic and anoxic growth and nitrate removal capacity of a marine denitrifying bacterium isolated from a recirculation aquaculture system.}, journal = {Microbial ecology}, volume = {55}, number = {1}, pages = {107-118}, pmid = {17674087}, issn = {0095-3628}, mesh = {Aerobiosis ; Anaerobiosis ; Animals ; *Aquaculture ; Bioreactors ; Filtration/methods ; Flatfishes/growth &amp; development ; Models, Biological ; Molecular Sequence Data ; Nitrates/*metabolism ; *Pseudomonas fluorescens/genetics/growth &amp; development/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Bacterial biofilters used in marine recirculation aquaculture systems need improvements to enhance nitrogen removal efficiency. Relatively little is known about biofilter autochthonous population structure and function. The present study was aimed at isolating and characterizing an autochthonous denitrifying bacterium from a marine biofilter installed at a recirculation aquaculture system. Colonization of four different media in a marine fish farm was followed by isolation of various denitrifying strains and molecular classification of the most promising one, strain T2, as a novel member of the Pseudomonas fluorescens cluster. This strain exhibits high metabolic versatility regarding N and C source utilization and environmental conditions for growth. It removed nitrate through aerobic assimilatory metabolism at a specific rate of 116.2 mg NO(3)-N g dw(-1) h(-1). Dissimilatory NO(3)-N removal was observed under oxic conditions at a limited rate, where transient NO(2)-N formed represented 22% (0.17 mg L(-1)) of the maximum transient NO(2)-N observed under anoxic conditions. Dissimilatory NO(3)-N removal under anoxic conditions occurred at a specific rate of 53.5 mg NO(3)-N g dw(-1) h(-1). The isolated denitrifying strain was able to colonize different materials, such as granular activated carbon (GAC), Filtralite and Bioflow plastic rings, which allow the development of a prototype bioreactor for strain characterization under dynamic conditions and mimicking fish-farm operating conditions.}, }
@article {pmid17674086, year = {2008}, author = {Abboudi, M and Jeffrey, WH and Ghiglione, JF and Pujo-Pay, M and Oriol, L and Sempéré, R and Charrière, B and Joux, F}, title = {Effects of photochemical transformations of dissolved organic matter on bacterial metabolism and diversity in three contrasting coastal sites in the Northwestern Mediterranean Sea during summer.}, journal = {Microbial ecology}, volume = {55}, number = {2}, pages = {344-357}, pmid = {17674086}, issn = {0095-3628}, mesh = {Bacteria/classification/drug effects/growth &amp; development/*metabolism ; Biodegradation, Environmental/radiation effects ; *Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; Mediterranean Sea ; Organic Chemicals/*metabolism/radiation effects ; Polymorphism, Genetic ; RNA, Ribosomal, 16S/genetics ; Radiation ; Seasons ; Seawater/*chemistry ; Sunlight ; }, abstract = {The effects of phototransformation of dissolved organic matter (DOM) on bacterial growth, production, respiration, growth efficiency, and diversity were investigated during summer in two lagoons and one oligotrophic coastal water samples from the Northwestern Mediterranean Sea, differing widely in DOM and chromophoric DOM concentrations. Exposure of 0.2-microm filtered waters to full sun radiation for 1 d resulted in small changes in optical properties and concentrations of DOM, and no changes in nitrate, nitrite, and phosphate concentrations. After exposure to sunlight or dark (control) treatments, the water samples were inoculated with the original bacterial community. Phototransformation of DOM had contrasting effects on bacterial production and respiration, depending on the water's origin, resulting in an increase of bacterial growth efficiency for the oligotrophic coastal water sample (120%) and a decrease for the lagoon waters (20 to 40%) relative to that observed in dark treatments. We also observed that bacterial growth on DOM irradiated by full sun resulted in changes in community structure of total and metabolically active bacterial cells for the three locations studied when compared to the bacteria growing on un-irradiated DOM, and that changes were mainly caused by phototransformation of DOM by UV radiation for the eutrophic lagoon and the oligotrophic coastal water and by photosynthetically active radiation (PAR) for the mesoeutrophic lagoon. These initial results indicate that phototransformation of DOM significantly alters both bacterial metabolism and community structure in surface water for a variety of coastal ecosystems in the Mediterranean Sea. Further studies will be necessary to elucidate a more detailed appreciation of potential temporal and spatial variations of the effects measured.}, }
@article {pmid17672325, year = {2007}, author = {Li, X and Qin, L and Dai, SK and Jiang, SM and Liu, ZH}, title = {[Marine microbial metagenomics: progress and prospect].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {47}, number = {3}, pages = {548-553}, pmid = {17672325}, issn = {0001-6209}, mesh = {Bacteria/*genetics/isolation &amp; purification ; Biodiversity ; Cloning, Molecular ; *Genome, Bacterial ; Seawater/*microbiology ; }, abstract = {Preliminary statistics showed that there are more than one million species of microbes in marine environments that formed a dynamic genetic reservoir, among which the majority are not revealed and categorized due to barrier in cultivation techniques. However, the situation has changed in recent years because of the rapid development of phylogenetic studies based on small ribosomal RNA and rDNA sequencing independent to standard laboratory cultivation. These changes have significantly altered our understanding about microbial diversity and microbial ecology. In this review, we highlight some of recent progress and innovation in research on microbial diversity, and propose a metagenomic scheme as an alternative to overcome some of the barriers that still remain for exploitation of marine microbial diversity for its enormous potential in pharmaceutical applications. We believe that rapid progress in marine metagenomics allows direct access to the genomes of numerous non-cultivable microorganisms for their associated chemical prosperity.}, }
@article {pmid17669527, year = {2008}, author = {Nichols, PD and Mancuso Nichols, CA}, title = {Microbial signature lipid profiling and exopolysaccharides: experiences initiated with Professor David C White and transported to Tasmania, Australia.}, journal = {Journal of microbiological methods}, volume = {74}, number = {1}, pages = {33-46}, doi = {10.1016/j.mimet.2007.06.017}, pmid = {17669527}, issn = {0167-7012}, mesh = {Animals ; Australia ; Bacteria/chemistry/*metabolism ; Bacterial Adhesion ; Bacterial Physiological Phenomena ; Cell Adhesion ; *Environmental Microbiology ; Eukaryota/chemistry/*metabolism/physiology ; Geologic Sediments/microbiology ; Lipid Metabolism ; Lipids/*chemistry ; Microbiological Techniques/*methods ; Polysaccharides/*chemistry/metabolism ; Research/*education ; }, abstract = {Developments and applications with signature lipid and exopolysaccharide (EPS) methodologies covering a thirty year period in the DC White laboratories at Florida State University and the University of Tennessee at Knoxville are illustrated. These powerful techniques were used to gain new insight into microbial communities, not obtainable by classical approaches. Selected case examples are highlighted and include: use of a specific dimethyl disulphide (DMDS) derivitization procedure with monounsaturated fatty acids (MUFA) to precisely determine double bond position and geometry; application of the DMDS procedure in taxonomic and environmental studies including the degradation of pollutant halogenated hydrocarbons in groundwater and subsurface aquifers; exploiting the ubiquitous nature of uronic acids in microbial EPS to quantify these exopolymers in complex environmental samples; development of rapid and non-destructive approaches including FT-IR to follow biofilm formation in a unique manner not possible with other approaches. The foundations laid in the DC White laboratories have seen a wide suite of applications in modern microbial ecology and associated fields. The training of young scientists by DC White will also ensure that his unique approach and quest for new and or novel methodologies for use in environmental microbiology will continue.}, }
@article {pmid17668262, year = {2008}, author = {Dang, H and Ren, J and Song, L and Sun, S and An, L}, title = {Diverse tetracycline resistant bacteria and resistance genes from coastal waters of Jiaozhou Bay.}, journal = {Microbial ecology}, volume = {55}, number = {2}, pages = {237-246}, pmid = {17668262}, issn = {0095-3628}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Proteins/genetics ; Biodiversity ; China ; Colony Count, Microbial ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Tetracycline/*pharmacology ; *Tetracycline Resistance ; Water Microbiology ; }, abstract = {Environmental microbiology investigation was carried out in Jiaozhou Bay to determine the source and distribution of tetracycline-resistant bacteria and their resistance mechanisms. At least 25 species or the equivalent molecular phylogenetic taxa in 16 genera of resistant bacteria could be identified based on 16S ribosomal deoxyribonucleic acid sequence analysis. Enterobacteriaceae, Pseudomonadaceae, and Vibrionaceae constituted the majority of the typical resistant isolates. Indigenous estuarine and marine Halomonadaceae, Pseudoalteromonadaceae, Rhodobacteraceae, and Shewanellaceae bacteria also harbored tetracycline resistance. All the six resistance determinants screened, tet(A)-(E) and tet(G), could be detected, and the predominant genes were tet(A), tet(B), and tet(G). Both anthropogenic activity-related and indigenous estuarine or coastal bacteria might contribute to the tet gene reservoir, and resistant bacteria and their molecular determinants may serve as bioindicators of coastal environmental quality. Our work probably is the first identification of tet(E) in Proteus, tet(G) in Acinetobacter, tet(C) and tet(D) in Halomonas, tet(D) and tet(G) in Shewanella, and tet(B), tet(C), tet(E), and tet(G) in Roseobacter.}, }
@article {pmid17665240, year = {2008}, author = {Ulrich, A and Klimke, G and Wirth, S}, title = {Diversity and activity of cellulose-decomposing bacteria, isolated from a sandy and a loamy soil after long-term manure application.}, journal = {Microbial ecology}, volume = {55}, number = {3}, pages = {512-522}, pmid = {17665240}, issn = {0095-3628}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Biodiversity ; Biomass ; Cellulose/*metabolism ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Fertilizers/analysis ; Manure/*analysis ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Soil/*analysis ; *Soil Microbiology ; }, abstract = {The community of culturable cellulolytic bacteria was analyzed in two long-term experimental field sites on Albic Luvisol (silty sand) and Haplic Phaeozem (loam), with and without farmyard manure treatment. Against the backdrop of significant differences in soil properties, the bacterial community structure differed clearly between sites and was affected by manure application as analyzed by T-RFLP of 16S rDNA. The population densities of cellulolytic bacteria were significantly increased by manure application in Phaeozem. Cellulose decomposing potentials of 537 isolates were tested on soluble, colloidal, and crystalline cellulose. The results showed some evidence of a greater proportion of isolates with high decomposition activity in Luvisol, but no impact from manure application could be observed in both soils. Restriction analysis and sequencing of 16S rDNA of isolates revealed a rather simple community composition that was dominated by Streptomyces (67%). The composition of the RFLP groups was affected by manure application, which was most evident in Luvisol, whereas an effect of the soil type could not be found. Although abundant RFLP groups were assigned to phylogenetically different bacterial classes (Actinobacteria, Betaproteobacteria, and Gammaproteobacteria), cellulolytic activity could not consistently be differentiated. All in all, cellulolytic capabilities of the isolates were highly variable and did not map to phylogenetic affiliation.}, }
@article {pmid17661180, year = {2008}, author = {Jameson, E and Joint, I and Mann, NH and Mühling, M}, title = {Application of a novel rpoC1-RFLP approach reveals that marine Prochlorococcus populations in the Atlantic gyres are composed of greater microdiversity than previously described.}, journal = {Microbial ecology}, volume = {55}, number = {1}, pages = {141-151}, pmid = {17661180}, issn = {0095-3628}, mesh = {Atlantic Ocean ; Base Sequence ; DNA Primers ; DNA, Bacterial/analysis ; DNA-Directed RNA Polymerases/chemistry/*genetics ; *Genetic Variation ; Molecular Sequence Data ; Phylogeny ; *Polymorphism, Restriction Fragment Length ; Prochlorococcus/*classification/*enzymology/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {To elucidate the degree of microdiversity within the genus Prochlorococcus, novel Prochlorococcus-specific polymerase chain reaction (PCR) primers were developed for the rpoC1 gene, which encodes the ribonucleic acid (RNA) polymerase core subunit. The size of the PCR fragment (925 bp) coupled with high sequence variation within the rpoC1 fragments (70-99% sequence similarity, 16S ribosomal RNA sequences show greater than 97% sequence similarity) meant that it was possible to distinguish Prochlorococcus strains by restriction fragment length polymorphism (RFLP) analysis. Clone libraries were constructed from environmental deoxyribonucleic acid samples from two stations, one in the northern and one in the southern oligotrophic gyre of the Atlantic Ocean. These were screened to determine the microdiversity of Prochlorococcus populations using this high-resolution high-throughput analysis approach. RFLP analysis of the clone libraries from the two gyre sites revealed that the two Prochlorococcus populations had a high degree of microdiversity with 40 and 52 different RFLP-type clones among the 143 clones tested for both the northern and southern gyres, respectively. Phylogenetic analysis of the nucleotide sequences of the RFLP types not only showed that it contained representatives of each of the currently recognized Prochlorococcus clades (based on the internal transcribed spacer region as molecular marker) but also led to the discovery of a previously unseen genetic microdiversity. This level of diversity was greater at the southern gyre site compared to the northern gyre site. Moreover, the high genetic resolution approach also revealed that there are two putative novel lineages within the HL I clade. Analyses of further samples by producing clone libraries from different geographic origins is likely to reveal further diversity and novel lineages within Prochlorococcus.}, }
@article {pmid17661179, year = {2008}, author = {Cassler, M and Peterson, CL and Ledger, A and Pomponi, SA and Wright, AE and Winegar, R and McCarthy, PJ and Lopez, JV}, title = {Use of real-time qPCR to quantify members of the unculturable heterotrophic bacterial community in a deep sea marine sponge, Vetulina sp.}, journal = {Microbial ecology}, volume = {55}, number = {3}, pages = {384-394}, pmid = {17661179}, issn = {0095-3628}, mesh = {Animals ; Bacteria/classification/*genetics/*isolation &amp; purification ; Colony Count, Microbial ; DNA Primers/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Gene Dosage ; *Heterotrophic Processes ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/*methods ; Porifera/*microbiology ; RNA, Ribosomal, 16S/metabolism ; Seawater/*microbiology ; Sensitivity and Specificity ; Sequence Analysis, DNA ; }, abstract = {In this report, real-time quantitative PCR (TaqMan qPCR) of the small subunit (SSU) 16S-like rRNA molecule, a universal phylogenetic marker, was used to quantify the relative abundance of individual bacterial members of a diverse, yet mostly unculturable, microbial community from a marine sponge. Molecular phylogenetic analyses of bacterial communities derived from Caribbean Lithistid sponges have shown a wide diversity of microbes that included at least six major subdivisions; however, very little overlap was observed between the culturable and unculturable microbial communities. Based on sequence data of three culture-independent Lithistid-derived representative bacteria, we designed probe/primer sets for TaqMan qPCR to quantitatively characterize selected microbial residents in a Lithistid sponge, Vetulina, metagenome. TaqMan assays included specificity testing, DNA limit of detection analysis, and quantification of specific microbial rRNA sequences such as Nitrospira-like microbes and Actinobacteria up to 172 million copies per microgram per Lithistid sponge metagenome. By contrast, qPCR amplification with probes designed for common previously cultured sponge-associated bacteria in the genera Rheinheimera and Marinomonas and a representative of the CFB group resulted in only minimal detection of the Rheiheimera in total DNA extracted from the sponge. These data verify that a large portion of the microbial community within Lithistid sponges may consist of currently unculturable microorganisms.}, }
@article {pmid17661128, year = {2008}, author = {Wang, YS and Liu, JC and Chen, WC and Yen, JH}, title = {Characterization of acetanilide herbicides degrading bacteria isolated from tea garden soil.}, journal = {Microbial ecology}, volume = {55}, number = {3}, pages = {435-443}, pmid = {17661128}, issn = {0095-3628}, mesh = {Acetanilides/*metabolism ; Bacillus/cytology/*isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Fatty Acids/metabolism ; Herbicides/*metabolism ; *Soil Microbiology ; Taiwan ; Temperature ; Time Factors ; }, abstract = {Three different green manures were added to the tea garden soils separately and incubated for 40 days. After, incubation, acetanilide herbicides alachlor and metolachlor were spiked into the soils, separately, followed by the isolation of bacteria in each soil at designed intervals. Several bacterial strains were isolated from the soils and identified as Bacillus silvestris, B. niacini, B. pseudomycoides, B. cereus, B. thuringiensis, B. simplex, B. megaterium, and two other Bacillus sp. (Met1 and Met2). Three unique strains with different morphologies were chosen for further investigation. They were B. megaterium, B. niacini, and B. silvestris. The isolated herbicide-degrading bacteria showed optimal performance among three incubation temperatures of 30 degrees C and the best activity in the 10 to 50 microg/ml concentration of the herbicide. Each bacterial strain was able to degrade more than one kind of test herbicides. After incubation for 119 days, B. cereus showed the highest activity to degrade alachlor and propachlor, and B. thuringiensis to degrade metolachlor.}, }
@article {pmid17655911, year = {2007}, author = {Elenter, D and Milferstedt, K and Zhang, W and Hausner, M and Morgenroth, E}, title = {Influence of detachment on substrate removal and microbial ecology in a heterotrophic/autotrophic biofilm.}, journal = {Water research}, volume = {41}, number = {20}, pages = {4657-4671}, doi = {10.1016/j.watres.2007.06.050}, pmid = {17655911}, issn = {0043-1354}, mesh = {Ammonia/metabolism ; Bacterial Physiological Phenomena ; *Biofilms ; *Bioreactors ; Carbon/metabolism ; Ecology ; *Models, Biological ; Nitrates/metabolism ; Nitrites/metabolism ; Quaternary Ammonium Compounds/metabolism ; Stress, Mechanical ; }, abstract = {Competition between heterotrophic bacteria oxidizing organic substrate and autotrophic nitrifying bacteria in a biofilm was evaluated. The biofilm was grown in a tubular reactor under different shear and organic substrate loading conditions. The reactor was initially operated without organic substrate in the influent until stable ammonia oxidation rates of 2.1 gN/(m(2)d) were achieved. A rapid increase of fluid shear in the tubular reactor on day 156 resulted in biofilm sloughing, reducing the biofilm thickness from 330 to 190 microm. This sloughing event did not have a significant effect on ammonia oxidation rates. The addition of acetate to the influent of the reactor resulted in decreased ammonia oxidation rates (1.8 gN/(m(2)d)) for low influent acetate concentrations (17 mg COD/L) and the breakdown of nitrification at high influent acetate concentrations (55 mg COD/L). Rapidly increasing fluid shear triggered biofilm sloughing in some cases--but maintaining constant shear did not prevent sloughing events from occurring. With the addition of acetate to the influent of the reactor, the biofilm thickness increased up to 1350 microm and individual sloughing events removed up to 50% of the biofilm. Biofilm sloughing had no significant influence on organic substrate removal or ammonia oxidation. During 325 days of reactor operation, ammonia was oxidized only to nitrite; no nitrate production was observed. This lack of nitrite oxidation was confirmed by fluorescent in situ hybridization (FISH) analysis, which detected betaproteobacterial ammonia oxidizers but not nitrite oxidizers. Mathematical modeling correctly predicted breakdown of nitrification at high influent acetate concentrations. Model predictions deviated systematically from experimental results, however, for the case of low influent acetate concentrations.}, }
@article {pmid17653786, year = {2008}, author = {Kirkwood, AE and Buchheim, JA and Buchheim, MA and Henley, WJ}, title = {Cyanobacterial diversity and halotolerance in a variable hypersaline environment.}, journal = {Microbial ecology}, volume = {55}, number = {3}, pages = {453-465}, pmid = {17653786}, issn = {0095-3628}, mesh = {*Biodiversity ; Cyanobacteria/classification/genetics/*isolation &amp; purification/*physiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; *Ecosystem ; Geologic Sediments/chemistry/microbiology ; Molecular Sequence Data ; Oklahoma ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; Sequence Alignment ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; Water Microbiology ; }, abstract = {The Great Salt Plains (GSP) in north-central Oklahoma, USA is an expansive salt flat (approximately 65 km(2)) that is part of the federally protected Salt Plains National Wildlife Refuge. The GSP serves as an ideal environment to study the microbial diversity of a terrestrial, hypersaline system that experiences wide fluctuations in freshwater influx and diel temperature. Our study assessed cyanobacterial diversity at the GSP by focusing on the taxonomic and physiological diversity of GSP isolates, and the 16S rRNA phylogenetic diversity of isolates and environmental clones from three sites (north, central, and south). Taxonomic diversity of isolates was limited to a few genera (mostly Phormidium and Geitlerinema), but physiological diversity based on halotolerance ranges was strikingly more diverse, even between strains of the same phylotype. The phylogenetic tree revealed diversity that spanned a number of cyanobacterial lineages, although diversity at each site was dominated by only a few phylotypes. Unlike other hypersaline systems, a number of environmental clones from the GSP were members of the heterocystous lineage. Although a number of cyanobacterial isolates were close matches with prevalent environmental clones, it is not certain if these clones reflect the same halotolerance ranges of their matching isolates. This caveat is based on the notable disparities we found between strains of the same phylotype and their inherent halotolerance. Our findings support the hypothesis that variable or poikilotrophic environments promote diversification, and in particular, select for variation in ecotype more than phylotype.}, }
@article {pmid17647052, year = {2008}, author = {Fuxa, JR}, title = {Threshold concentrations of nucleopolyhedrovirus in soil to initiate infections in Heliothis virescens on cotton plants.}, journal = {Microbial ecology}, volume = {55}, number = {3}, pages = {530-539}, pmid = {17647052}, issn = {0095-3628}, mesh = {Animals ; Gossypium/*virology ; Larva/virology ; Moths/growth &amp; development/*virology ; Nucleopolyhedroviruses/*pathogenicity ; Pest Control, Biological ; Plant Diseases/*virology ; *Soil Microbiology ; }, abstract = {The purpose of the research was to determine threshold concentrations of nucleopolyhedrovirus (NPV) in soil for abiotic transport to cotton plants in the field and under conducive and nonconducive conditions in the greenhouse. Under the assumption that 2% mortality would suffice to initiate foci of infection in Heliothis virescens larvae on the plants, thresholds ranged from 25 to 2,311 viral occlusion bodies (OB)/g soil in the greenhouse. Thresholds generally were smaller for rain on sandy soil and wind on clay soil than for wind on sand or rain on clay. Thresholds generally increased with height of the plant above the soil surface. In field plots, percentage mortality in bioassays of cotton plants was greatest on leaves versus other tissues, and mortality increased with soil dosage and decreased with plant height and over time. Season-long soil-NPV-transport thresholds for 2% plant-bioassay mortality of larvae ranged from 1 OB/g to 7.4 x 10(8) OB/g soil based on the amounts of NPV applied to the soil at planting time, and they ranged from 8 OB/g to 1.2 x 10(5) OB/g soil based on bioassays of soil samples collected concurrently with plant samples throughout the growing season. These results should contribute to NPV epizootiology, biological control, and risk assessment through better understanding of viral soil-to-plant transport.}, }
@article {pmid17638998, year = {2007}, author = {Lee, MR and Huws, SA and Scollan, ND and Dewhurst, RJ}, title = {Effects of fatty acid oxidation products (green odor) on rumen bacterial populations and lipid metabolism in vitro.}, journal = {Journal of dairy science}, volume = {90}, number = {8}, pages = {3874-3882}, doi = {10.3168/jds.2007-0191}, pmid = {17638998}, issn = {1525-3198}, support = {BBS/E/G/00003008/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacteria/*drug effects ; Biodiversity ; Cattle/*metabolism ; Fatty Acids/analysis/*metabolism ; Fatty Acids, Unsaturated/metabolism ; Female ; Hydrogenation ; Lipid Metabolism/*drug effects ; Odorants ; Oxidation-Reduction ; Peroxides/pharmacology ; Poaceae/metabolism ; Rumen/*metabolism/microbiology ; Time Factors ; tert-Butylhydroperoxide/pharmacology ; }, abstract = {This study investigated the effects of green odor fatty acid oxidation products (FAOP) from cut grass on lipid metabolism and microbial ecology using in vitro incubations of rumen microorganisms. These compounds have antimicrobial roles in plant defense, and we hypothesized that they may influence rumen lipid metabolism. Further, they may partially explain the higher levels of conjugated linoleic acid cis-9, trans-11 in milk from cows grazing pasture. The first of 2 batch culture experiments screened 6 FAOP (1 hydroperoxide, 3 aldehydes, 1 ketone, and 1 alcohol) for effects on lipid profile, and in particular C(18) polyunsaturated fatty acid biohydrogenation. Experiment 2 used the most potent FAOP to determine effects of varying concentrations and identify relationships with effects on microbial ecology. Batch cultures contained anaerobic buffer, rumen liquor, and FAOP to a final concentration of 100 microM for experiment 1. Triplicates for each compound and controls (water addition) were incubated at 39 degrees C for 6 h. The hydroperoxide (1,2-dimethylethyl hydroperoxide, 1,2-DMEH) and the long chain aldehyde (trans-2 decenal) had the largest effects on lipid metabolism with significant increases in C(18:0) and C(18:1) trans and reductions in C(12:0), C(14:0), C(16:0), C(18:1) cis, C(18:2n-6), C(18:3n-3), C(20:0) and total branch and odd chain fatty acids compared with the control. This was associated with significantly higher biohydrogenation of C(18) polyunsaturated fatty acid. In experiment 2, 1,2-DMEH was incubated at 50, 100, and 200 microM for 2, 6, and 24 h. Increasing 1,2-DMEH concentration resulted in a significant linear increase in C(18:1) trans-10, trans-11, conjugated linoleic acid, and C(18:0) and a linear decrease in C(18:2n-6) and C(18:3n-3), although the scale of this response declined with time. Microbial profiling techniques showed that 1,2-DMEH at concentrations of 100 and 200 microM changed the microbial community from as early as 2 h after addition, though microbial biomass remained similar. These preliminary studies have shown that FAOP can alter fatty acid biohydrogenation in the rumen. This change was associated with changes in the microbial population that were detected through DNA and branched- and odd-chain fatty acid profiling approaches.}, }
@article {pmid17635536, year = {2007}, author = {Huang, WE and Stoecker, K and Griffiths, R and Newbold, L and Daims, H and Whiteley, AS and Wagner, M}, title = {Raman-FISH: combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function.}, journal = {Environmental microbiology}, volume = {9}, number = {8}, pages = {1878-1889}, doi = {10.1111/j.1462-2920.2007.01352.x}, pmid = {17635536}, issn = {1462-2912}, mesh = {Bacteria/chemistry/genetics/*isolation &amp; purification ; Carbon Isotopes/*metabolism ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; In Situ Hybridization, Fluorescence/*methods ; Naphthalenes/metabolism ; RNA, Ribosomal, 16S/genetics ; Spectrum Analysis, Raman/instrumentation/*methods ; *Water Microbiology ; }, abstract = {We have coupled fluorescence in situ hybridization (FISH) with Raman microscopy for simultaneous cultivation-independent identification and determination of (13)C incorporation into microbial cells. Highly resolved Raman confocal spectra were generated for individual cells which were grown in minimal medium where the ratio of (13)C to (12)C content of the sole carbon source was incrementally varied. Cells which were (13)C-labelled through anabolic incorporation of the isotope exhibited key red-shifted spectral peaks, the calculated 'red shift ratio' (RSR) being highly correlated with the (13)C-content of the cells. Subsequently, Raman instrumentation and FISH protocols were optimized to allow combined epifluorescence and Raman imaging of Fluos, Cy3 and Cy5-labelled microbial populations at the single cell level. Cellular (13)C-content determinations exhibited good congruence between fresh cells and FISH hybridized cells indicating that spectral peaks, including phenylalanine resonance, which were used to determine (13)C-labelling, were preserved during fixation and hybridization. In order to demonstrate the suitability of this technology for structure-function analyses in complex microbial communities, Raman-FISH was deployed to show the importance of Pseudomonas populations during naphthalene degradation in groundwater microcosms. Raman-FISH extends and complements current technologies such as FISH-microautoradiography and stable isotope probing in that it can be applied at the resolution of single cells in complex communities, is quantitative if suitable calibrations are performed, can be used with stable isotopes and has analysis times of typically 1 min per cell.}, }
@article {pmid17632206, year = {2008}, author = {Weber, KP and Gehder, M and Legge, RL}, title = {Assessment of changes in the microbial community of constructed wetland mesocosms in response to acid mine drainage exposure.}, journal = {Water research}, volume = {42}, number = {1-2}, pages = {180-188}, doi = {10.1016/j.watres.2007.06.055}, pmid = {17632206}, issn = {0043-1354}, mesh = {Bacteria/growth &amp; development/metabolism ; Colony Count, Microbial ; Fluoresceins/metabolism ; *Industrial Waste ; Poaceae ; *Water Microbiology ; Water Pollutants, Chemical ; *Wetlands ; }, abstract = {Changes in the bacterial community in the interstitial water of 5 different constructed wetland mesocosms were studied over a 22-day period following exposure to simulated acid mine drainage (AMD). The community-level physiological profile (CLPP) of each mesocosm was assessed using substrate utilization patterns gathered via BIOLOG ECO plates. Principal component analysis (PCA) of the BIOLOG ECO plate data proved feasible and useful in characterizing the interstitial bacterial community in the constructed wetland mesocosms based on mesocosm characteristics such as fixed biological regime development and plant presence, and was also used to successfully track changes in the interstitial bacterial community in response to AMD exposure. Clustering analysis of the BIOLOG ECO plate data was used to characterize the interstitial bacterial community and to validate the mesocosm groupings observed through PCA ordination. The calculation of substrate-based diversity indices from the BIOLOG ECO plate data was used to assess the robustness and the degree of change shown by the metabolic fingerprint of the interstitial bacterial community within the mesocosms. The interstitial bacterial community in the constructed mesocosms was shown to be significantly affected after exposure to AMD. Exposure to AMD caused similar bacterial species to detach from the fixed biotic regime of the mesocosms. It was also shown that mesocosms planted with Phragmites australis did not experience as great an ecological shift in the microbial ecology of the interstitial water after exposure to AMD as did the unplanted mesocosms. The substrate-based diversity indices for the planted mesocosms were also found to be more stable, after exposure to AMD, than those for the unplanted mesocosms. It is possible that the interaction between the plant root system and the substrate biological regime, collectively called the rhizosphere, may create a more ecologically robust and stable treatment system.}, }
@article {pmid17628141, year = {2007}, author = {Taylor, BL and Watts, KJ and Johnson, MS}, title = {Oxygen and redox sensing by two-component systems that regulate behavioral responses: behavioral assays and structural studies of aer using in vivo disulfide cross-linking.}, journal = {Methods in enzymology}, volume = {422}, number = {}, pages = {190-232}, doi = {10.1016/S0076-6879(06)22010-X}, pmid = {17628141}, issn = {0076-6879}, support = {GM29481/GM/NIGMS NIH HHS/United States ; }, mesh = {Azospirillum brasilense/physiology/ultrastructure ; Carrier Proteins/chemistry/genetics/isolation &amp; purification/*physiology ; Cell Movement ; DNA-Directed DNA Polymerase/genetics ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli Proteins/chemistry/genetics/isolation &amp; purification/*physiology ; Intercellular Signaling Peptides and Proteins ; Models, Biological ; Mutagenesis, Site-Directed ; Oxidation-Reduction ; Oxygen/metabolism ; Partial Pressure ; Signal Transduction ; }, abstract = {A remarkable increase in the number of annotated aerotaxis (oxygen-seeking) and redox taxis sensors can be attributed to recent advances in bacterial genomics. However, in silico predictions should be supported by behavioral assays and genetic analyses that confirm an aerotaxis or redox taxis function. This chapter presents a collection of procedures that have been highly successful in characterizing aerotaxis and redox taxis in Escherichia coli. The methods are described in enough detail to enable investigators of other species to adapt the procedures for their use. A gas flow cell is used to quantitate the temporal responses of bacteria to a step increase or decrease in oxygen partial pressure or redox potential. Bacterial behavior in spatial gradients is analyzed using optically flat capillaries and soft agar plates (succinate agar or tryptone agar). We describe two approaches to estimate the preferred partial pressure of oxygen that attracts a bacterial species; this concentration is important for understanding microbial ecology. At the molecular level, we describe procedures used to determine the structure and topology of Aer, a membrane receptor for aerotaxis. Cysteine-scanning mutagenesis and in vivo disulfide cross-linking procedures utilize the oxidant Cu(II)-(1,10-phenanthroline)(3) and bifunctional sulfhydryl-reactive probes. Finally, we describe methods used to determine the boundaries of transmembrane segments of receptors such as Aer. These include 5-iodoacetamidofluorescein, 4-acetamido-4-disulfonic acid, disodium salt (AMS), and methoxy polyethylene glycol maleimide, a 5-kDa molecular mass probe that alters the mobility of Aer on SDS-PAGE.}, }
@article {pmid17628133, year = {2007}, author = {Podar, M}, title = {Two-component systems in microbial communities: approaches and resources for generating and analyzing metagenomic data sets.}, journal = {Methods in enzymology}, volume = {422}, number = {}, pages = {32-46}, doi = {10.1016/S0076-6879(06)22002-0}, pmid = {17628133}, issn = {0076-6879}, mesh = {Bacteria/enzymology/*genetics ; *Bacterial Physiological Phenomena ; Bacterial Proteins/genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; Ecosystem ; Environment ; Gene Expression Regulation, Bacterial ; *Genome, Bacterial ; Genomics/*methods ; Histidine Kinase ; Models, Biological ; Protein Kinases/genetics ; *Signal Transduction ; }, abstract = {Two-component signal transduction represents the main mechanism by which bacterial cells interact with their environment. The functional diversity of two-component systems and their relative importance in the different taxonomic groups and ecotypes of bacteria has become evident with the availability of several hundred genomic sequences. The vast majority of bacteria, including many high rank taxonomic units, while being components of complex microbial communities remain uncultured (i.e., have not been isolated or grown in the laboratory). Environmental genomic data from such communities are becoming available, and in addition to its profound impact on microbial ecology it will propel molecular biological disciplines beyond the traditional model organisms. This chapter describes the general approaches used in generating environmental genomic data and how that data can be used to advance the study of two component-systems and signal transduction in general.}, }
@article {pmid17628130, year = {2007}, author = {Aquilanti, L and Santarelli, S and Silvestri, G and Osimani, A and Petruzzelli, A and Clementi, F}, title = {The microbial ecology of a typical Italian salami during its natural fermentation.}, journal = {International journal of food microbiology}, volume = {120}, number = {1-2}, pages = {136-145}, doi = {10.1016/j.ijfoodmicro.2007.06.010}, pmid = {17628130}, issn = {0168-1605}, mesh = {Colony Count, Microbial ; DNA, Bacterial/analysis ; DNA, Fungal/analysis ; Electrophoresis, Polyacrylamide Gel/methods ; Fermentation ; *Food Microbiology ; Hydrogen-Ion Concentration ; Italy ; Lactobacillus/genetics/*isolation &amp; purification ; Meat Products/*microbiology ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry/genetics ; Sequence Analysis, DNA ; Staphylococcus/genetics/*isolation &amp; purification ; Water/metabolism ; Yeasts/genetics/*isolation &amp; purification ; }, abstract = {We have investigated the bacteria and yeast ecology of the typical Italian Ciauscolo salami that is produced in Central Italy using a polyphasic approach based on culture-dependent and -independent methods. The physico-chemical analyses showed a progressive drop in pH and water activity (aw) during ripening. The viable counts revealed a dominance of lactic acid bacteria (LAB) over coagulase negative cocci (CNC) and yeasts. From the molecular identification of the isolates, the prevalence of Lactobacillus curvatus, Lb. plantarum and Staphylococcus xylosus was shown among the bacteria, while Debaryomyces hansenii was the prevalent species among the yeasts, and it was isolated throughout the whole ripening process. Minority species, namely Rhodotorula mucillaginosa and Trichosporon brassicae, were also recovered from the meat batter. The total microbial community was profiled without cultivation by analyzing the DNA that was directly extracted from the salami samples. Moreover, the cultivable community was profiled by analyzing the DNA recovered from bulk cells that were obtained by harvesting the colonies from serial-dilution agar plates. The 16S rRNA gene V1 and V3 regions were used as targets in the denaturing gradient gel electrophoresis (DGGE) profiling of the LAB and CNC communities, respectively, while the diversity and dynamics of the yeast population were assessed by analyzing a portion of the 28S rRNA gene. Our findings suggest that the microbial diversity of fermented meat products can be successfully investigated by this polyphasic approach that is based on the assessment of both the total and the cultivable community diversity.}, }
@article {pmid17624487, year = {2008}, author = {Wilson, B and Danilowicz, BS and Meijer, WG}, title = {The diversity of bacterial communities associated with Atlantic cod Gadus morhua.}, journal = {Microbial ecology}, volume = {55}, number = {3}, pages = {425-434}, pmid = {17624487}, issn = {0095-3628}, mesh = {Animals ; Atlantic Ocean ; Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Gadus morhua/*microbiology ; Mucous Membrane/microbiology ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Seasons ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {The spatial and temporal changes in the bacterial communities associated with the Atlantic cod Gadus morhua were investigated using terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S recombinant DNA (rDNA). Epidermal mucous was sampled from 366 cod caught in three harvest locations (Baltic, Icelandic, and North Seas) over three seasons (spring 2002, autumn 2002, and spring 2003), and an automated method for the high-throughput processing of environmental samples was developed using a Qiagen BioRobot. The analysis revealed that a diverse consortium of bacteria were found on fish; gamma-proteobacteria and Cytophaga-Flavobacter-Bacteroides (CFB) species were dominant. T-RFLP peak profiles suggested that operational taxonomic units (OTUs) related to Photobacterium sp., Psychrobacter sp., and Bacteroides sp. were common to all sites in all three seasons, but there were intersite variations in community composition. Cod caught from different seas had distinct reproducible bacterial assemblages. Whereas communities from fish caught in the Baltic and Icelandic Seas were relatively stable over the three seasons, those from fish from the North Sea changed significantly over time.}, }
@article {pmid17623231, year = {2008}, author = {Stingl, U and Cho, JC and Foo, W and Vergin, KL and Lanoil, B and Giovannoni, SJ}, title = {Dilution-to-extinction culturing of psychrotolerant planktonic bacteria from permanently ice-covered lakes in the McMurdo Dry Valleys, Antarctica.}, journal = {Microbial ecology}, volume = {55}, number = {3}, pages = {395-405}, pmid = {17623231}, issn = {0095-3628}, mesh = {Actinobacteria/classification/genetics/isolation &amp; purification ; Antarctic Regions ; Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Bacteroidetes/classification/genetics/isolation &amp; purification ; Chemoautotrophic Growth ; Cold Temperature ; Colony Count, Microbial/*methods ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Fresh Water/chemistry/*microbiology ; Ice Cover/*microbiology ; Molecular Sequence Data ; Phylogeny ; Plankton/classification/genetics/isolation &amp; purification/metabolism ; Polymorphism, Restriction Fragment Length ; Proteobacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Lakes in the McMurdo Dry Valleys of Antarctica are characterized by a permanent ice cover and little or no anthropogenic influence. Although bacterial cultures have been obtained from these habitats, recent culture-independent studies indicate that the most abundant microbes in these systems are not yet cultivated. By using dilution-to-extinction cultivation methods with sterilized and nutrient-amended lake water as media, we isolated 148 chemotrophic psychrotolerant bacterial cultures from fresh surface water of Lake Fryxell and the east lobe of Lake Bonney and the hypersaline, suboxic bottom water from the west lobes of Lake Bonney. Screening of the 16S ribosomal ribonucleic acid (rRNA) genes of the cultures by restriction fragment length polymorphism (RFLP) yielded 57 putatively pure psychrotolerant, slow growing cultures grouped into 18 clusters. The sequencing of 16S rRNA genes of randomly selected representatives of each RFLP cluster revealed that the corresponding isolates belong to the Alphaproteobacteria (six RFLP patterns), Betaproteobacteria (six RFLP patterns), Bacteroidetes (four RFLP patterns), and Actinobacteria (two RFLP patterns). Phylogenetic analysis of the sequences showed that the vast majority of the isolates were not closely related to previously described species. Thirteen of 18 RFLP patterns shared a 16S ribosomal deoxyribonucleic acid sequence similarity of 97% or less with the closest described species, and four isolates had a sequence similarity of 93% or less with the nearest described species. Phylogenetic analysis showed that these sequences were representatives of deeply branching organisms in the respective phylum. A comparison of the isolates with 16S rRNA clone libraries prepared from the same environments showed substantial overlap, indicating that dilution-to-extinction culturing in natural lake water media can help isolate some of the most abundant organisms in these perennially ice-covered lakes.}, }
@article {pmid17619214, year = {2008}, author = {Wu, T and Chellemi, DO and Graham, JH and Martin, KJ and Rosskopf, EN}, title = {Comparison of soil bacterial communities under diverse agricultural land management and crop production practices.}, journal = {Microbial ecology}, volume = {55}, number = {2}, pages = {293-310}, pmid = {17619214}, issn = {0095-3628}, mesh = {*Agriculture ; Analysis of Variance ; Bacteria/genetics/*growth &amp; development ; Cloning, Molecular ; Conservation of Natural Resources ; Crops, Agricultural/*growth &amp; development ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Solanum lycopersicum/growth &amp; development ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The composition and structure of bacterial communities were examined in soil subjected to a range of diverse agricultural land management and crop production practices. Length heterogeneity polymerase chain reaction (LH-PCR) of bacterial DNA extracted from soil was used to generate amplicon profiles that were analyzed with univariate and multivariate statistical methods. Five land management programs were initiated in July 2000: conventional, organic, continuous removal of vegetation (disk fallow), undisturbed (weed fallow), and bahiagrass pasture (Paspalum notatum var Argentine). Similar levels in the diversity of bacterial 16S rDNA amplicons were detected in soil samples collected from organically and conventionally managed plots 3 and 4 years after initiation of land management programs, whereas significantly lower levels of diversity were observed in samples collected from bahiagrass pasture. Differences in diversity were attributed to effects on how the relative abundance of individual amplicons were distributed (evenness) and not on the total numbers of bacterial 16S rDNA amplicons detected (richness). Similar levels of diversity were detected among all land management programs in soil samples collected after successive years of tomato (Lycopersicon esculentum) cultivation. A different trend was observed after a multivariate examination of the similarities in genetic composition among soil bacterial communities. After 3 years of land management, similarities in genetic composition of soil bacterial communities were observed in plots where disturbance was minimized (bahiagrass and weed fallow). The genetic compositions in plots managed organically were similar to each other and distinct from bacterial communities in other land management programs. After successive years of tomato cultivation and damage from two major hurricanes, only the composition of soil bacterial communities within organically managed plots continued to maintain a high degree of similarity to each other and remain distinct from other bacterial communities. This study reveals the effects of agricultural land management practices on soil bacterial community composition and diversity in a large-scale, long-term replicated study where the effect of soil type on community attributes was removed.}, }
@article {pmid17619213, year = {2008}, author = {Rich, JJ and Dale, OR and Song, B and Ward, BB}, title = {Anaerobic ammonium oxidation (anammox) in Chesapeake Bay sediments.}, journal = {Microbial ecology}, volume = {55}, number = {2}, pages = {311-320}, pmid = {17619213}, issn = {0095-3628}, mesh = {Bacteria, Anaerobic/classification/genetics/*isolation &amp; purification/metabolism ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Geologic Sediments/*chemistry/microbiology ; Maryland ; Molecular Sequence Data ; Nitrates/analysis ; Nitrites/analysis ; Nitrogen/metabolism ; Nitrogen Isotopes/metabolism ; Oxidation-Reduction ; Phylogeny ; Polymerase Chain Reaction ; Quaternary Ammonium Compounds/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Water Microbiology ; }, abstract = {Anaerobic ammonium oxidation (anammox) has recently been recognized as a pathway for the removal of fixed N from aquatic ecosystems. However, the quantitative significance of anammox in estuarine sediments is variable, and measurements have been limited to a few estuaries. We measured anammox and conventional denitrification activities in sediments along salinity gradients in the Chesapeake Bay and two of its sub-estuaries, the Choptank River and Patuxent River. Homogenized sediments were incubated with (14/15)N amendments of NH4+, NO3-, and NO2- to determine relative activities of anammox and denitrification. The percent of N2 production due to anammox (ra%) ranged from 0 to 22% in the Chesapeake system, with the highest ra% in the freshwater portion of the main stem of upper Chesapeake Bay, where water column NO3- concentrations are consistently high. Intermediate levels of relative anammox (10%) were detected at locations corresponding to tidal freshwater and mesohaline locations in the Choptank River, whereas anammox was not detected in the tidal freshwater location in the Patuxent River. Anammox activity was also not detected in the seaward end of Chesapeake Bay, where water column No3- concentrations are consistently low. The ra% did not correlate with NH4+ accumulation rate in anoxic sediment incubations, but ra% was related to water column NO3- concentrations and salinity. Anammox bacterial communities were also examined by amplifying DNA extracted from the upper Chesapeake Bay sediment with polymerase chain reaction (PCR) primers that are specific for 16S rRNA genes of anammox organisms. A total of 35 anammox-like sequences were detected, and phylogenetic analysis grouped the sequences in two distinct clusters belonging to the Candidatus "Scalindua" genus.}, }
@article {pmid17619212, year = {2008}, author = {Hein, JW and Wolfe, GV and Blee, KA}, title = {Comparison of rhizosphere bacterial communities in Arabidopsis thaliana mutants for systemic acquired resistance.}, journal = {Microbial ecology}, volume = {55}, number = {2}, pages = {333-343}, pmid = {17619212}, issn = {0095-3628}, mesh = {Arabidopsis/genetics/*microbiology/physiology ; Arabidopsis Proteins/genetics/metabolism ; Bacteria/*classification/isolation &amp; purification ; Biodiversity ; Genes, Reporter ; Glucan Endo-1,3-beta-D-Glucosidase/genetics/metabolism ; *Mutation ; Polymorphism, Restriction Fragment Length ; Rhizome/*microbiology ; Seeds/microbiology ; Soil Microbiology ; }, abstract = {Systemic acquired resistance (SAR) is an inducible systemic plant defense against a broad spectrum of plant pathogens, with the potential to secrete antimicrobial compounds into the soil. However, its impact on rhizosphere bacteria is not known. In this study, we examined fingerprints of bacterial communities in the rhizosphere of the model plant Arabidopsis thaliana to determine the effect of SAR on bacterial community structure and diversity. We compared Arabidopsis mutants that are constitutive and non-inducible for SAR and verified SAR activation by measuring pathogenesis-related protein activity via a beta-glucoronidase (GUS) reporter construct driven by the beta-1-3 glucanase promoter. We used terminal restriction fragment length polymorphism (T-RFLP) analysis of MspI- and HaeIII-digested 16S rDNA to estimate bacterial rhizosphere community diversity, with Lactobacillus sp. added as internal controls. T-RFLP analysis showed a clear rhizosphere effect on community structure, and diversity analysis of both rhizosphere and bulk soil operational taxonomic units (as defined by terminal restriction fragments) using richness, Shannon-Weiner, and Simpson's diversity indices and evenness confirmed that the presence of Arabidopsis roots significantly altered bacterial communities. This effect of altered soil microbial community structure by plants was also seen upon multivariate cluster analysis of the terminal restriction fragments. We also found visible differences in the rhizosphere community fingerprints of different Arabidopsis SAR mutants; however, there was no clear decrease of rhizosphere diversity because of constitutive SAR expression. Our study suggests that SAR can alter rhizosphere bacterial communities, opening the door to further understanding and application of inducible plant defense as a driving force in structuring soil bacterial assemblages.}, }
@article {pmid17619096, year = {2008}, author = {Krammer, M and Velimirov, B and Fischer, U and Farnleitner, AH and Herzig, A and Kirschner, AK}, title = {Growth response of soda lake bacterial communities to simulated rainfall.}, journal = {Microbial ecology}, volume = {55}, number = {2}, pages = {194-211}, pmid = {17619096}, issn = {0095-3628}, mesh = {Austria ; Bacteria/*growth &amp; development ; Colony Count, Microbial ; Ecosystem ; Environment ; Leucine/metabolism ; Radioisotopes/metabolism ; Rain/*chemistry ; Salinity ; Seasons ; Tritium/metabolism ; Viruses/growth &amp; development ; Water/analysis ; *Water Microbiology ; }, abstract = {Moderately saline soda lakes harbor extremely abundant and fast growing bacterial communities. An interesting phenomenon of an explosive bacterial growth in shallow soda lakes in Eastern Austria after dilution with rainwater, concomitantly with a significant decrease in temperature was observed in a former study. In the present study, we tried to identify the factors being responsible for this enhanced bacterial growth in laboratory batch cultures. Three experiments were performed with water taken from two different lakes at different seasons. Natural soda lake water was diluted with distilled water, artificial lake water, sterile filtered soda lake water, and grazer-free water to test (1) for the influence of compatible solutes released to the environment and reduced salt stress after osmotic down-shock, (2) for the influence of nutrients, which may be washed in from the dry areas of the lake bottom after rainfall and (3) for the decrease of grazing pressure due to dilution. The potential influence of (4) viruses was indirectly deduced. The response of the bacterial community to the manipulations was measured by changes in bacterial numbers, the incorporation of (3)H-leucine and the concomitant determination of the amount of (3)H-leucine uptaking bacteria by microautoradiography. The influence of the environmental factors enhancing bacterial growth after a simulated rainfall event showed variations between the lakes and over the seasons. The addition of nutrients was, in all experiments, the main factor triggering bacterial growth. The decrease in grazing pressure and viral lysis after dilution was of significant importance in two of three experiments. In the experiment with the highest salinity, we could show that either compatible solutes released after osmotic down-shock and used as a source of nutrients for the soda lake bacterial populations or reduced salt stress were most probably responsible for the observed marked enhancement of bacterial growth.}, }
@article {pmid17616625, year = {2007}, author = {Villani, F and Casaburi, A and Pennacchia, C and Filosa, L and Russo, F and Ercolini, D}, title = {Microbial ecology of the soppressata of Vallo di Diano, a traditional dry fermented sausage from southern Italy, and in vitro and in situ selection of autochthonous starter cultures.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {17}, pages = {5453-5463}, pmid = {17616625}, issn = {0099-2240}, mesh = {Biotechnology/methods ; Colony Count, Microbial ; Culture Media ; *Ecosystem ; Electrophoresis, Gel, Pulsed-Field ; Fermentation ; Italy ; Lactobacillus/*classification/genetics/*isolation &amp; purification/metabolism ; Meat Products/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Saccharomycetales/classification/genetics/isolation &amp; purification ; Staphylococcus/*classification/genetics/*isolation &amp; purification/metabolism ; }, abstract = {The microbial ecology of "soppressata of Vallo di Diano," a traditional dry fermented sausage from southern Italy, was studied by using both culture-dependent and culture-independent approaches. The ripened fermented sausages were characterized by high microbial loads of both staphylococci and lactobacilli. Using PCR-denaturing gradient gel electrophoresis (PCR-DGGE) targeting the variable V3 and V1 regions of the 16S rRNA gene and direct DNA sequencing, it was possible to identify Staphylococcus xylosus, S. succinus, and S. equorum among the staphylococci and Lactobacillus sakei and L. curvatus within the lactobacilli. Moreover, Debaryomyces hansenii was the main yeast species found by targeting the yeast 26S rRNA gene by PCR-DGGE. Selected strains of S. xylosus, L. sakei, and L. curvatus were characterized for their technological properties in the ripening conditions of the fermented sausages so as to select an autochthonous starter formulation. The selection included the determination of nitrate reductase, lipolytic, and antioxidant activity and proteolysis with myofibrillar and sarcoplasmic protein fractions. Such properties were evaluated in both in vitro and in situ assays; the latter were performed by using each strain as a starter in the laboratory-scale manufacture of soppressata of Vallo di Diano and by monitoring the microbiological and chemical changes at the end of ripening. The results show differences between the in vitro and in situ selection results and indicate that in situ evaluation of the technological performance of specific strains is better suited to selecting autochthonous starter cultures for fermented-meat products than in vitro evaluation.}, }
@article {pmid17615316, year = {2007}, author = {Inman, M}, title = {Microbial ecology. The dark and mushy side of a frozen continent.}, journal = {Science (New York, N.Y.)}, volume = {317}, number = {5834}, pages = {35-36}, doi = {10.1126/science.317.5834.35}, pmid = {17615316}, issn = {1095-9203}, mesh = {Antarctic Regions ; Bacteria/classification/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Colony Count, Microbial ; *Ecosystem ; Fresh Water ; Geologic Sediments/*microbiology ; Ice ; Ice Cover/*microbiology ; }, }
@article {pmid17614962, year = {2007}, author = {Röling, WF}, title = {Do microbial numbers count? Quantifying the regulation of biogeochemical fluxes by population size and cellular activity.}, journal = {FEMS microbiology ecology}, volume = {62}, number = {2}, pages = {202-210}, doi = {10.1111/j.1574-6941.2007.00350.x}, pmid = {17614962}, issn = {0168-6496}, mesh = {*Ecosystem ; *Environmental Microbiology ; Halogens/metabolism ; Methane/metabolism ; *Models, Biological ; Nitrites/metabolism ; Sulfates/metabolism ; Water Microbiology ; }, abstract = {In order to enhance understanding of the interrelationships among community members and between them and their environment, the concept of regulation analysis is extended from biochemistry into microbial ecology. Ecological regulation analysis quantifies how biogeochemical fluxes are regulated by the microorganisms performing the process; the degree to which changes in fluxes are due to changes in population size and to changes in activity cell(-1) (cellular activity). Regulation analysis requires data on biogeochemical fluxes and the numbers of cells through which these fluxes run. Its application to five biogeochemical processes (aerobic methane oxidation, aerobic nitrite oxidation, methanogenesis, sulfate reduction and reductive dehalogenation) revealed that in general, but not always, flux was primarily regulated by cellular activity, i.e. by changes in the size and properties of the enzyme pool and in the concentrations of substrates and metabolites. Thus, it is often not sufficient to count the numbers of cells performing a particular step in a biogeochemical process in order to estimate its flux. Ecological regulation analysis can be extended to address which aspects of cellular activity require quantification in order to describe biogeochemical fluxes better. Its application is discussed in the context of the complexity of microbial communities (e.g. functional redundancy) and their functioning.}, }
@article {pmid17614151, year = {2007}, author = {Gálvez, A and Abriouel, H and López, RL and Ben Omar, N}, title = {Bacteriocin-based strategies for food biopreservation.}, journal = {International journal of food microbiology}, volume = {120}, number = {1-2}, pages = {51-70}, doi = {10.1016/j.ijfoodmicro.2007.06.001}, pmid = {17614151}, issn = {0168-1605}, mesh = {Bacteria/*drug effects/growth &amp; development ; Bacteriocins/*pharmacology ; Consumer Behavior ; Consumer Product Safety ; Drug Resistance, Bacterial ; Food Contamination/prevention &amp; control ; Food Handling/*methods ; *Food Microbiology ; Food Preservation/*methods ; Food Preservatives/*pharmacology ; Humans ; }, abstract = {Bacteriocins are ribosomally-synthesized peptides or proteins with antimicrobial activity, produced by different groups of bacteria. Many lactic acid bacteria (LAB) produce bacteriocins with rather broad spectra of inhibition. Several LAB bacteriocins offer potential applications in food preservation, and the use of bacteriocins in the food industry can help to reduce the addition of chemical preservatives as well as the intensity of heat treatments, resulting in foods which are more naturally preserved and richer in organoleptic and nutritional properties. This can be an alternative to satisfy the increasing consumers demands for safe, fresh-tasting, ready-to-eat, minimally-processed foods and also to develop "novel" food products (e.g. less acidic, or with a lower salt content). In addition to the available commercial preparations of nisin and pediocin PA-1/AcH, other bacteriocins (like for example lacticin 3147, enterocin AS-48 or variacin) also offer promising perspectives. Broad-spectrum bacteriocins present potential wider uses, while narrow-spectrum bacteriocins can be used more specifically to selectively inhibit certain high-risk bacteria in foods like Listeria monocytogenes without affecting harmless microbiota. Bacteriocins can be added to foods in the form of concentrated preparations as food preservatives, shelf-life extenders, additives or ingredients, or they can be produced in situ by bacteriocinogenic starters, adjunct or protective cultures. Immobilized bacteriocins can also find application for development of bioactive food packaging. In recent years, application of bacteriocins as part of hurdle technology has gained great attention. Several bacteriocins show additive or synergistic effects when used in combination with other antimicrobial agents, including chemical preservatives, natural phenolic compounds, as well as other antimicrobial proteins. This, as well as the combined use of different bacteriocins may also be an attractive approach to avoid development of resistant strains. The combination of bacteriocins and physical treatments like high pressure processing or pulsed electric fields also offer good opportunities for more effective preservation of foods, providing an additional barrier to more refractile forms like bacterial endospores as well. The effectiveness of bacteriocins is often dictated by environmental factors like pH, temperature, food composition and structure, as well as the food microbiota. Foods must be considered as complex ecosystems in which microbial interactions may have a great influence on the microbial balance and proliferation of beneficial or harmful bacteria. Recent developments in molecular microbial ecology can help to better understand the global effects of bacteriocins in food ecosystems, and the study of bacterial genomes may reveal new sources of bacteriocins.}, }
@article {pmid17609846, year = {2008}, author = {Demir, E and Coyne, KJ and Doblin, MA and Handy, SM and Hutchins, DA}, title = {Assessment of microzooplankton grazing on Heterosigma akashiwo using a species-specific approach combining quantitative real-time PCR (QPCR) and dilution methods.}, journal = {Microbial ecology}, volume = {55}, number = {4}, pages = {583-594}, pmid = {17609846}, issn = {0095-3628}, mesh = {Animals ; Chlorophyll/chemistry ; Chlorophyll A ; DNA, Algal/genetics ; Delaware ; Dinoflagellida/chemistry/genetics/*growth &amp; development ; *Eutrophication ; Polymerase Chain Reaction ; Population Dynamics ; Species Specificity ; Zooplankton/*physiology ; }, abstract = {Delaware's Inland Bays (DIB) are subject to numerous mixed blooms of harmful raphidophytes each year, and Heterosigma akashiwo is one of the consistently occurring species. Often, Chattonella subsalsa, C. cf. verruculosa, and Fibrocapsa japonica co-occur with H. akashiwo, indicating a dynamic consortium of raphidophyte species. In this study, microzooplankton grazing pressure was assessed as a top-down control mechanism on H. akashiwo populations in mixed communities. Quantitative real-time polymerase chain reaction (QPCR) with species-specific primers and probes were used in conjunction with the dilution method to assess grazing pressure on H. akashiwo and other raphidophytes. As a comparison, we measured changes in chlorophyll a (chl a) to determine whole community growth and mortality caused by grazing. We detected grazing on H akashiwo using QPCR in samples where chl a analyses indicated little or no grazing on the total phytoplankton community. Overall, specific microzooplankton grazing pressure on H akashiwo ranged from 0.88 to 1.88 day(-1) at various sites. Experiments conducted on larger sympatric raphidophytes (C. subsalsa, C. cf. verruculosa and F japonica) demonstrated no significant microzooplankton grazing on these species. Grazing pressure on H akashiwo may provide a competitive advantage to other raphidophytes such as Chattonella spp. that are too large to be consumed at high rates by microzooplankton and help to shape the dynamics of this harmful algal bloom consortium. Our results show that QPCR can be used in conjunction with the dilution method for evaluation of microzooplankton grazing pressure on specific phytoplankton species within a mixed community.}, }
@article {pmid17609845, year = {2007}, author = {Kubartová, A and Moukoumi, J and Béguiristain, T and Ranger, J and Berthelin, J}, title = {Microbial diversity during cellulose decomposition in different forest stands: I. microbial communities and environmental conditions.}, journal = {Microbial ecology}, volume = {54}, number = {3}, pages = {393-405}, pmid = {17609845}, issn = {0095-3628}, mesh = {Bacteria/classification/*growth &amp; development ; *Biodiversity ; Biomass ; Cellulose/*metabolism ; Fagus/microbiology ; France ; Fungi/classification/*growth &amp; development ; Picea/microbiology ; Seasons ; Time Factors ; Trees/*microbiology ; }, abstract = {We studied the effect of forest tree species on a community of decomposers that colonize cellulose strips. Both fungal and bacterial communities were targeted in a native forest dominated by beech and oak and 30-year-old beech and spruce plantations, growing in similar ecological conditions in the Breuil-Chenue experimental forest site in Morvan (France). Microbial ingrowths from the 3rd to 10th month of strip decomposition (May to December 2004) were studied. Community composition was assessed using temperature gradient gel electrophoresis with universal fungal (ITS1F, ITS2) and bacterial (1401r, 968f) primers. Soil temperature and moisture as well as fungal biomass were also measured to give additional information on decomposition processes. Changing the dominant tree species had no significant influence in the number of decomposer species. However, decomposer community composition was clearly different. If compared to the native forest, where community composition highly differed, young monocultures displayed similar species structure for fungi and bacteria. Both species numbers and community composition evolved during the decay process. Time effect was found to be more important than tree species. Nevertheless, the actual environmental conditions and seasonal effect seemed to be even more determining factors for the development of microbial communities. The course and correlations of the explored variables often differed between tree species, although certain general trends were identified. Fungal biomass was high in summer, despite that species richness (SR) decreased and conversely, that high SR did not necessarily mean high biomass values. It can be concluded that the growth and development of the microbiological communities that colonized a model material in situ depended on the combination of physical and biological factors acting collectively and interdependently at the forest soil microsite.}, }
@article {pmid17607503, year = {2008}, author = {Hoostal, MJ and Bouzat, JL}, title = {The modulating role of dissolved organic matter on spatial patterns of microbial metabolism in Lake Erie sediments.}, journal = {Microbial ecology}, volume = {55}, number = {2}, pages = {358-368}, pmid = {17607503}, issn = {0095-3628}, mesh = {Bacteria/*enzymology/growth &amp; development/metabolism ; Bacterial Physiological Phenomena ; Carbohydrate Metabolism ; Enzymes/*analysis ; Fresh Water/*microbiology ; Geologic Sediments/*chemistry/microbiology ; Great Lakes Region ; Organic Chemicals/analysis/*metabolism ; Phenols/chemistry ; Water Pollution, Chemical/analysis ; }, abstract = {To evaluate the role of dissolved organic matter (DOM) on microbial community metabolism, we established extracellular enzyme activity (EEA) and substrate-induced respiration (SIR) profiles of sediment samples collected from littoral and profundal regions of the western, central, and eastern basins of Lake Erie. Lake Erie is spatially structured such that the central and western basins receive relatively major inputs of allochthonous DOM in comparison to the eastern basin. Overall, spatial patterns of EEA and SIR profiles suggest both greater metabolic diversity and activity in the littoral regions of the central and western basins. In contrast, the eastern basin demonstrated much less structuring between littoral and profundal areas. To evaluate whether the observed spatial patterns are the result of microbial community adaptations to local DOM availability, we performed three experimental treatments by inoculating sediment samples with polyvinylpyrrolidone, which sequesters large polyphenols, or with either vanillin or catechol, two small phenolic compounds. Our results revealed that esterase and glycosidase EEA from the eastern basin were induced by small phenolics and inhibited by large polyphenols. In contrast, the addition of small phenolics decreased esterase and glycosidase activities from the central basin, while polyphenols had a negligible effect. These results suggest that the source and composition of DOM play a significant role in the local adaptation of microbial communities, determining large-scale spatial patterns of microbial functional diversity in Lake Erie sediments.}, }
@article {pmid17605304, year = {2007}, author = {Neu, J}, title = {Perinatal and neonatal manipulation of the intestinal microbiome: a note of caution.}, journal = {Nutrition reviews}, volume = {65}, number = {6 Pt 1}, pages = {282-285}, doi = {10.1301/nr.2007.jun.282-285}, pmid = {17605304}, issn = {0029-6643}, mesh = {Gastrointestinal Tract/*growth &amp; development/*microbiology ; Humans ; Infant ; Infant Nutritional Physiological Phenomena/*physiology ; Infant, Newborn ; Intestinal Diseases/etiology/prevention &amp; control ; *Probiotics ; Symbiosis ; }, abstract = {As we learn more about interactions between microbes and the developing gastrointestinal (GI) tract, it is becoming clear that the establishment of the intestinal "microbiome" shortly after birth plays a critical role in the early origins of health and disease. Nutrition, mode of delivery, the use of maternal or postnatal antibiotics, and pre- and probiotics are factors that may alter the microbial ecology and affect lifelong gene expression. Because the neonatal period is a critical period of development when microbes become established in the GI tract, the long-term effects of manipulations of the GI microbial ecology during this time are more amplified than the effects of later manipulations. In this paper, recent research findings are reviewed with the intent of providing information about the benefits of early manipulation of the GI microbiome, but also to give a warning about its indiscriminant manipulation during the perinatal and neonatal time periods.}, }
@article {pmid17605067, year = {2008}, author = {He, S and Gu, AZ and McMahon, KD}, title = {Progress toward understanding the distribution of Accumulibacter among full-scale enhanced biological phosphorus removal systems.}, journal = {Microbial ecology}, volume = {55}, number = {2}, pages = {229-236}, pmid = {17605067}, issn = {0095-3628}, mesh = {Acetates/metabolism ; Biodegradation, Environmental ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; In Situ Hybridization, Fluorescence ; Phosphorus/*metabolism ; RNA, Ribosomal, 16S/genetics ; Rhodocyclaceae/genetics/growth &amp; development/*metabolism ; Sewage/chemistry/microbiology ; *Water Microbiology ; *Water Purification ; Wisconsin ; }, abstract = {This study investigated the role of Accumulibacter-related bacterial populations and factors influencing their distribution in enhanced biological phosphorus removal (EBPR) systems in the USA. For this purpose, five full-scale wastewater treatment facilities performing EBPR were surveyed. The facilities had different configurations but were all treating primarily domestic wastewater. Two facilities had history of poor EBPR performance. Batch-scale acetate uptake and inorganic phosphate (P(i)) release and uptake experiments were conducted to evaluate the EBPR activity of each sludge. Typical P(i) and acetate profiles were observed, and EBPR activity was found to be positively correlated to polyphosphate (polyP)-accumulating organism (PAO) abundance, as determined by staining intracellular polyP. The abundance of Accumulibacter-related organisms was investigated using fluorescent in situ hybridization. Accumulibacter-related organisms were present in all full-scale EBPR facilities, at levels ranging from 9 to 24% of total cells. More than 80% of Accumulibacter-related organisms were estimated to have high polyP content, confirming their involvement in EBPR in these five facilities. However, Accumulibacter-related PAOs were only a fraction (40-69%) of the total PAO population. The variation of Accumulibacter-related PAO abundance among these EBPR systems suggests that multiple interacting factors such as wastewater characteristics and operational conditions are structuring PAO communities.}, }
@article {pmid17604989, year = {2008}, author = {Joshi, AA and Kanekar, PP and Kelkar, AS and Shouche, YS and Vani, AA and Borgave, SB and Sarnaik, SS}, title = {Cultivable bacterial diversity of alkaline Lonar lake, India.}, journal = {Microbial ecology}, volume = {55}, number = {2}, pages = {163-172}, pmid = {17604989}, issn = {0095-3628}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Colony Count, Microbial ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Geologic Sediments/*microbiology ; Hydrogen-Ion Concentration ; India ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil Microbiology ; *Water Microbiology ; }, abstract = {Aerobic, alkaliphilic bacteria were isolated and characterized from water and sediment samples collected in the winter season, January 2002 from alkaline Lonar lake, India, having pH 10.5. The total number of microorganisms in the sediment and water samples was found to be 10(2)-10(6) cfu g(-1) and 10(2)-10(4) cfu ml(-1), respectively. One hundred and ninety-six strains were isolated using different enrichment media. To study the bacterial diversity of Lonar lake and to select the bacterial strains for further characterization, screening was done on the basis of pH and salt tolerance of the isolates. Sixty-four isolates were subjected to phenotypic, biochemical characterization and 16S rRNA sequencing. Out of 64, 31 bacterial isolates were selected on the basis of their enzyme profile and further subjected to phylogenetic analysis. Phylogenetic analysis indicated that most of the Lonar lake isolates were related to the phylum Firmicutes, containing Low G+C, Gram-positive bacteria, with different genera: Bacillus, Paenibacillus, Alkalibacillus, Exiguobacterium, Planococcus, Enterococcus and Vagococcus. Seven strains constituted a Gram-negative bacterial group, with different genera: Halomonas, Stenotrophomonas and Providencia affiliated to gamma-Proteobacteria, Alcaligenes to beta-Proteobacteria and Paracoccus to alpha-Proteobacteria. Only five isolates were High G+C, Gram-positive bacteria associated with phylum Actinobacteria, with various genera: Cellulosimicrobium, Dietzia, Arthrobacter and Micrococcus. Despite the alkaline pH of the Lonar lake, most of the strains were alkalitolerant and only two strains were obligate alkaliphilic. Most of the isolates produced biotechnologically important enzymes at alkaline pH, while only two isolates (ARI 351 and ARI 341) showed the presence of polyhydroxyalkcanoate (PHA) and exopolysaccharide (EPS), respectively.}, }
@article {pmid17604988, year = {2008}, author = {Magalhães, C and Bano, N and Wiebe, WJ and Bordalo, AA and Hollibaugh, JT}, title = {Dynamics of nitrous oxide reductase genes (nosZ) in intertidal rocky biofilms and sediments of the Douro River estuary (Portugal), and their relation to N-biogeochemistry.}, journal = {Microbial ecology}, volume = {55}, number = {2}, pages = {259-269}, pmid = {17604988}, issn = {0095-3628}, mesh = {Bacteria/classification/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Biofilms/*growth &amp; development ; Cluster Analysis ; DNA, Bacterial/genetics ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Nitrogen/*metabolism ; Oxidoreductases/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Portugal ; Rivers/*microbiology ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {In this study, temporal variability of nosZ genotypes was evaluated in two intertidal rocky biofilms and two intertidal sediment sites of the Douro River estuary, Portugal. The results were compared to rates of key N-cycle processes and environmental variables to examine possible links between denitrifier community dynamics and N biogeochemistry. Genetic heterogeneity of the nosZ gene was evaluated by terminal restriction fragment length polymorphism analysis (T-RFLP) and by sequencing cloned nosZ gene fragments. Phylogenetic analysis showed that the majority of the nosZ genes detected were most similar to nosZ genes from isolates affiliated with alpha-subclass of the class Proteobacteria. Results revealed low nosZ genotype richness, and hierarchical cluster analysis showed significant differences in the composition of denitrifier communities that inhabit different intertidal environments of the Douro River estuary. Monthly surveys of nosZ genotypes from sandy sediments showed that, while the same T-RFLP peaks were present in all samples, shifts in the relative peak areas of the different nosZ genotypes occurred. Canonical correspondence analysis, based on data from the monthly survey, revealed a strong relationship between the relative peak areas of some T-RFLP operational taxonomic units (OTUs) with denitrification rate and NO3- availability. Results suggest that denitrifiers with specific nosZ genotypes (OTUs) have competitive advantage over others when NO3- fluctuates in the system; these fluctuations reflect, in turn, variability in denitrification rates.}, }
@article {pmid17604934, year = {2007}, author = {Callon, C and Duthoit, F and Delbès, C and Ferrand, M and Le Frileux, Y and De Crémoux, R and Montel, MC}, title = {Stability of microbial communities in goat milk during a lactation year: molecular approaches.}, journal = {Systematic and applied microbiology}, volume = {30}, number = {7}, pages = {547-560}, doi = {10.1016/j.syapm.2007.05.004}, pmid = {17604934}, issn = {0723-2020}, mesh = {Animals ; Bacteria/*classification/isolation &amp; purification ; *Biodiversity ; Colony Count, Microbial ; DNA, Bacterial/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Feeding Methods ; Fungi/*classification/isolation &amp; purification ; Goats ; Lactation ; Milk/*microbiology ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Single-Stranded Conformational ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Seasons ; Sequence Analysis, DNA ; }, abstract = {The microbial communities in milks from one herd were evaluated during 1-year of lactation, using molecular methods to evaluate their stability and the effect of breeding conditions on their composition. The diversity of microbial communities was measured using two approaches: molecular identification by 16S and 18S rDNA sequencing of isolates from counting media (two milks), and direct identification using 16S rDNA from clone libraries (six milks). The stability of these communities was evaluated by counting on selective media and by Single Strand Conformation Polymorphism (SSCP) analysis of variable region V3 of the 16S rRNA gene and variable region V4 of the 18S rRNA gene. One hundred and eighteen milk samples taken throughout the year were analyzed. Wide diversity among bacteria and yeasts in the milk was revealed. In addition to species commonly encountered in milk, such as Lactococcus lactis, Lactococcus garvieae, Enterococcus faecalis, Lactobacillus casei, Leuconostoc mesenteroides, Staphylococcus epidermidis, Staphylococcus simulans, Staphylococcus caprae, Staphylococcus equorum, Micrococcus sp., Kocuria sp., Pantoea agglomerans and Pseudomonas putida, sequences were affiliated to other species only described in cheeses, such as Corynebacterium variabile, Arthrobacter sp., Brachybacterium paraconglomeratum, Clostridium sp. and Rothia sp. Several halophilic species atypical in milk were found, belonging to Jeotgalicoccus psychrophilus, Salinicoccus sp., Dietza maris, Exiguobacterium, Ornithinicoccus sp. and Hahella chejuensis. The yeast community was composed of Debaryomyces hansenii, Kluyveromyces lactis, Trichosporon beigelii, Rhodotorula glutinis, Rhodotorula minuta, Candida pararugosa, Candida intermedia, Candida inconspicua, Cryptococcus curvatus and Cryptococcus magnus. The analyses of microbial counts and microbial SSCP profiles both distinguished four groups of milks corresponding to four periods defined by season and feeding regime. The microbial community was stable within each period. Milks from winter were characterized by Lactococcus and Pseudomonas, those from summer by P. agglomerans and Klebsiella and those from autumn by Chryseobacterium indologenes, Acinetobacter baumanii, Staphylococcus, Corynebacteria and yeasts. However, the composition of the community can vary according to factors other than feeding. This study opens new investigation fields in the field of raw milk microbial ecology.}, }
@article {pmid17603744, year = {2008}, author = {Amalfitano, S and Fazi, S and Zoppini, A and Barra Caracciolo, A and Grenni, P and Puddu, A}, title = {Responses of benthic bacteria to experimental drying in sediments from Mediterranean temporary rivers.}, journal = {Microbial ecology}, volume = {55}, number = {2}, pages = {270-279}, pmid = {17603744}, issn = {0095-3628}, mesh = {Bacteria/growth &amp; development/*isolation &amp; purification/metabolism ; Biomass ; Carbon/metabolism ; Colony Count, Microbial ; Geologic Sediments/chemistry/*microbiology ; In Situ Hybridization, Fluorescence ; Mediterranean Region ; Proteobacteria/growth &amp; development ; Rivers/*microbiology ; Water/*analysis ; }, abstract = {In the semiarid Mediterranean regions, water scarcity represents a common physiological stress for microbial communities residing in river sediments. However, the effect of drying has not yet adequately been evaluated when analyzing riverine microbiological processes. The bacterial community structure (abundance, biomass, composition) and functioning (carbon production, live cell percentage) were assessed during experimental desiccation in microcosms with sediments from different Mediterranean temporary rivers (Tagliamento, Krathis, Mulargia, Pardiela). Our results showed that the overall responses to drying of the bacterial community were independent from sediment origin and strictly related to water content. During desiccation, a prompt decline (up to 100%) of the initial bacterial carbon production was followed by a slower decrease in abundance and biomass, with an overall reduction of 74% and 78%, respectively. By the end of the experiment, live cells were still abundant but depressed in their main metabolic functions, thus resulting in a drastic increase in the community turnover time. Only 14% of the initial live cell biomass was available in dry sediments to immediately start the reactivation of the aquatic microbial food web after the arrival of new water. Community composition analysis showed a relative increase in alpha- and beta-Proteobacteria, when passing from wet to dry conditions. Our results suggest that the occurrence of drought events could affect carbon cycling through the freshwater microbial compartment, by temporarily limiting microbial mineralization and altering bacterial community structure.}, }
@article {pmid17601131, year = {2007}, author = {Schimel, J and Balser, TC and Wallenstein, M}, title = {Microbial stress-response physiology and its implications for ecosystem function.}, journal = {Ecology}, volume = {88}, number = {6}, pages = {1386-1394}, doi = {10.1890/06-0219}, pmid = {17601131}, issn = {0012-9658}, mesh = {*Adaptation, Physiological ; Arctic Regions ; Bacteria/classification/growth &amp; development/metabolism ; *Bacterial Physiological Phenomena ; Carbon/metabolism ; Cold Climate ; *Ecosystem ; Nitrogen/metabolism ; Population Dynamics ; Rain ; *Soil Microbiology ; }, abstract = {Microorganisms have a variety of evolutionary adaptations and physiological acclimation mechanisms that allow them to survive and remain active in the face of environmental stress. Physiological responses to stress have costs at the organismal level that can result in altered ecosystem-level C, energy, and nutrient flows. These large-scale impacts result from direct effects on active microbes' physiology and by controlling the composition of the active microbial community. We first consider some general aspects of how microbes experience environmental stresses and how they respond to them. We then discuss the impacts of two important ecosystem-level stressors, drought and freezing, on microbial physiology and community composition. Even when microbial community response to stress is limited, the physiological costs imposed on soil microbes are large enough that they may cause large shifts in the allocation and fate of C and N. For example, for microbes to synthesize the osmolytes they need to survive a single drought episode they may consume up to 5% of total annual net primary production in grassland ecosystems, while acclimating to freezing conditions switches Arctic tundra soils from immobilizing N during the growing season to mineralizing it during the winter. We suggest that more effectively integrating microbial ecology into ecosystem ecology will require a more complete integration of microbial physiological ecology, population biology, and process ecology.}, }
@article {pmid17597337, year = {2008}, author = {Ongena, M and Jourdan, E and Adam, A and Schäfer, M and Budzikiewicz, H and Thonart, P}, title = {Amino acids, iron, and growth rate as key factors influencing production of the Pseudomonas putida BTP1 benzylamine derivative involved in systemic resistance induction in different plants.}, journal = {Microbial ecology}, volume = {55}, number = {2}, pages = {280-292}, pmid = {17597337}, issn = {0095-3628}, mesh = {Amino Acids/*metabolism ; *Antibiosis ; Benzylamines/chemistry/*metabolism ; Biomass ; Botrytis/pathogenicity ; Carbohydrate Metabolism ; Cucumis sativus/microbiology ; Hydrogen-Ion Concentration ; Iron/*metabolism ; Solanum lycopersicum/microbiology ; Mass Spectrometry ; Oxygen/metabolism ; Phaseolus/microbiology ; Phenylalanine/metabolism ; Plants/*microbiology ; Pseudomonas putida/growth &amp; development/*metabolism/physiology ; }, abstract = {The biological control bacterium Pseudomonas putida BTP1 exerts its protective effect mostly by inducing an enhanced state of resistance in the host plant against pathogen attack [induced systemic resistance (ISR)]. We previously reported that a specific compound derived from benzylamine may be involved in the elicitation of the ISR phenomenon by this Pseudomonas strain. In this article, we provide further information about the N,N-dimethyl-N-tetradecyl-N-benzylammonium structure of this determinant for ISR and show that the benzylamine moiety may be important for perception of the molecule by root cells of different plant species. We also investigated some regulatory aspects of elicitor production with the global aim to better understand how in situ expression of these ISR elicitors can be modulated by physiological and environmental factors. The biosynthesis is clearly related to secondary metabolism, and chemostat experiments showed that the molecule is more efficiently produced at low cell growth rate. Interestingly, the presence of free amino acids in the environment is necessary for optimal production, and a specific positive effect of phenylalanine was evidenced in pulsed continuous cultures. The influence of other abiotic factors, such as mineral content, oxygen concentration, or pH, on elicitor production is also reported and discussed with respect to the specific conditions that the producing strain undergoes in the rhizosphere environment.}, }
@article {pmid17594049, year = {2008}, author = {Batten, KM and Scow, KM and Espeland, EK}, title = {Soil microbial community associated with an invasive grass differentially impacts native plant performance.}, journal = {Microbial ecology}, volume = {55}, number = {2}, pages = {220-228}, pmid = {17594049}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development/metabolism ; *Ecosystem ; Fatty Acids/analysis ; *Plant Development ; Plant Roots/microbiology ; Plants/microbiology ; Poaceae/*growth &amp; development/microbiology ; Soil/analysis ; *Soil Microbiology ; }, abstract = {This study is one of the first to show that invasive plant-induced changes in the soil microbial community can negatively impact native plant performance. This greenhouse experiment tested whether soil microbial communities specific to the rhizospheres of an invasive grass (Aegilops triuncialis) and two native plants (Lasthenia californica and Plantago erecta) affected invasive and/or native plant performance. Each of these species were grown in separate pots for 2 months to prime the soils with plant-specific rhizosphere microbial communities. Each plant species was then planted in native- and invasive-primed soil, and effects on plant performance were monitored. At 5 months, differences in microbial biomarker fatty acids between invaded and native soils mirrored previous differences found in field-collected soil. L. californica performance was significantly reduced when grown in invaded soil compared to native soil (flowering date was delayed, aboveground biomass decreased, specific root length increased, and root mass ratio increased). In contrast, P. erecta and A. triuncialis performance were unaffected when grown in invaded vs native soil. These results suggest that in some cases, invasion-induced changes in the soil microbial community may contribute to a positive feedback loop, leading to the increased dominance of invasive species in an ecosystem.}, }
@article {pmid17594048, year = {2008}, author = {Pringault, O and Duran, R and Jacquet, S and Torréton, JP}, title = {Temporal variations of microbial activity and diversity in marine tropical sediments (New Caledonia lagoon).}, journal = {Microbial ecology}, volume = {55}, number = {2}, pages = {247-258}, pmid = {17594048}, issn = {0095-3628}, mesh = {Bacteria/genetics/*isolation &amp; purification ; *Biodiversity ; Chlorophyll/analysis ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Geologic Sediments/*microbiology ; Metals/analysis ; New Caledonia ; Oxygen/metabolism ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Time Factors ; Water Microbiology ; }, abstract = {Temporal variations of oxygen consumption, sensitivity to metal spiking, and microbial diversity were investigated during a one-year survey at the sediment-water interface in the tropical lagoon of New Caledonia. Sediment oxygen consumption (SOC) exhibited strong variations with time with maximum rates during February (Austral summer) and minimum values during July (cold period). SOC was strongly positively correlated with temperature, with an apparent activation energy (E (a)) of 41 kJ mol(-1), corresponding to an apparent Q (10)(20-30 degrees C) of 1.75. Strong short-term variations of SOC were also observed with ratios between two consecutive samplings reaching up to twofold of magnitude within one week, whereas the maximum/minimum ratio over the whole year was equal to 2.73. In most cases, metal spiking led to a strong decrease of SOC; however, in a third of sampling dates, spiking did not significantly decrease activity. These periods of apparent metal tolerance were not characterized by a particular bacterial community structure. Bacterial community structure estimated from terminal restriction fragment length polymorphism (T-RFLP) analysis exhibited strong variations over the one-year survey, and no seasonality was observed for bacterial richness. However, on average, the Whittaker similarity index between two consecutive T-RFLP profiles was above 60% suggesting a relative stability of the bacterial community structure on the short timescale with prominent T-RFs representing on average more than 67% of relative abundance occurring over most of the year, whereas other T-RFs only occurred during some periods.}, }
@article {pmid17593424, year = {2007}, author = {Burmølle, M and Hansen, LH and Sørensen, SJ}, title = {Establishment and early succession of a multispecies biofilm composed of soil bacteria.}, journal = {Microbial ecology}, volume = {54}, number = {2}, pages = {352-362}, pmid = {17593424}, issn = {0095-3628}, mesh = {Bacteria/*classification ; Bacterial Physiological Phenomena ; *Biofilms ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; Electrophoresis, Polyacrylamide Gel ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Most soil bacteria are likely to be organized in biofilms on roots, litter, or soil particles. Studies of such biofilms are complicated by the many nonculturable species present in soil, as well as the interspecific bacterial interactions affecting biofilm biology. We in this study describe the development of a biofilm flow model and use this system to establish an early (days 1-7) flow biofilm of soil bacteria from agricultural soil. It was possible to follow the succession in the early flow biofilm by denaturing gradient gel electrophoresis (DGGE) analysis, and it was demonstrated that the majority of strains present in the biofilm were culturable. We isolated and identified nine strains, all associated with unique DGGE profiles, and related their intrinsic phenotypes regarding monospecies biofilm formation in microtiter plates and planktonic growth characteristics to the appearance of the strains in the flow biofilm. The ability of the strains to attach to and establish biofilm in microtiter plates was reflected in their flow biofilm appearance, whereas no such reflection of the planktonic growth characteristics in the flow biofilm appearance was observed. One strain-specific synergistic interaction, strongly promoting biofilm formation of two strains when cultured together in a dual-species biofilm, was observed, indicating that some strains promote biofilm formation of others. Thus, the biofilm flow model proved useful for investigations of how intrinsic phenotypic traits of individual species affect the succession in an early soil biofilm consortium.}, }
@article {pmid17593423, year = {2007}, author = {Vieira, RP and Clementino, MM and Cardoso, AM and Oliveira, DN and Albano, RM and Gonzalez, AM and Paranhos, R and Martins, OB}, title = {Archaeal communities in a tropical estuarine ecosystem: Guanabara Bay, Brazil.}, journal = {Microbial ecology}, volume = {54}, number = {3}, pages = {460-468}, pmid = {17593423}, issn = {0095-3628}, mesh = {Archaea/classification/*genetics/growth &amp; development ; Brazil ; DNA, Archaeal/chemistry/genetics ; *Ecosystem ; Geography ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Guanabara Bay is an eutrophic estuarine system located in a humid tropical region surrounded by the second largest metropolitan area of Brazil. This study explores the contrasting environmental chemistry and microbiological parameters that influence the archaeaplankton diversity in a pollution gradient in Guanabara Bay ecosystem. The environments sampled ranged from completely anoxic waters in a polluted inner channel to the adjacent, relatively pristine, coastal Atlantic Ocean. Partial archaeal 16S rDNA sequences in water samples were retrieved by polymerase chain reaction (PCR) and analyzed using denaturing gradient gel electrophoresis (DGGE), cloning, and sequencing. Sequences were subjected to phylogenetic and diversity analyses. Community structure of the free-living archaeal assemblages was different from that of the particle-attached archaea according to DGGE. Gene libraries revealed that phylotype identification was consistent with environmental setting. Archaeal phylotypes found in polluted anoxic waters and in more pristine waters were closely related to organisms that have previously been found in these environments. However, inner bay archaea were related to organisms found in oil, industrial wastes, and sewage, implying that water pollution controls archaea communities in this system. The detection of a substantial number of uncultured phylotypes suggests that Guanabara Bay harbors a pool of novel archaeaplankton taxa.}, }
@article {pmid17587075, year = {2007}, author = {Zinger, L and Gury, J and Giraud, F and Krivobok, S and Gielly, L and Taberlet, P and Geremia, RA}, title = {Improvements of polymerase chain reaction and capillary electrophoresis single-strand conformation polymorphism methods in microbial ecology: toward a high-throughput method for microbial diversity studies in soil.}, journal = {Microbial ecology}, volume = {54}, number = {2}, pages = {203-216}, pmid = {17587075}, issn = {0095-3628}, mesh = {Bacteria/classification/*genetics ; Biodiversity ; DNA Primers/metabolism ; DNA-Directed DNA Polymerase ; Ecosystem ; Electrophoresis, Capillary/*methods ; Polymerase Chain Reaction/*methods ; Polymorphism, Single-Stranded Conformational ; *Soil Microbiology ; }, abstract = {The molecular signature of bacteria from soil ecosystems is an important tool for studying microbial ecology and biogeography. However, a high-throughput technology is needed for such studies. In this article, we tested the suitability of available methods ranging from soil DNA extraction to capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) for high-throughput studies. Our results showed that the extraction method does not dramatically influence CE-SSCP profiles, and that DNA extraction of a 0.25 g soil sample is sufficient to observe overall bacterial diversity in soil matrices. The V3 region of the 16S rRNA gene was amplified by PCR, and the extension time was found to be critical. We have also found that proofreading DNA polymerases generate a better signal in CE-SSCP profiles. Experiments performed with different soil matrices revealed the repeatability, efficiency, and consistency of CE-SSCP. Studies on PCR and CE-SSCP using single-species genomic DNA as a matrix showed that several ribotypes may migrate at the same position, and also that single species can produce double peaks. Thus, the extrapolation between number of peaks and number of species remains difficult. Additionally, peak detection is limited by the analysis software. We conclude that the presented method, including CE-SSCP and the analyzing step, is a simple and effective technique to obtain the molecular signature of a given soil sample.}, }
@article {pmid17587074, year = {2008}, author = {Maduell, P and Armengol, G and Llagostera, M and Orduz, S and Lindow, S}, title = {B. thuringiensis is a poor colonist of leaf surfaces.}, journal = {Microbial ecology}, volume = {55}, number = {2}, pages = {212-219}, pmid = {17587074}, issn = {0095-3628}, mesh = {Antibiosis ; Bacillus thuringiensis/cytology/*growth &amp; development ; Colony Count, Microbial ; Green Fluorescent Proteins/genetics/metabolism ; Microscopy, Fluorescence ; Phaseolus/microbiology ; Plant Leaves/*microbiology ; Plasmids ; Pseudomonas fluorescens ; }, abstract = {The ability of several Bacillus thuringiensis strains to colonize plant surfaces was assessed and compared with that of more common epiphytic bacteria. While all B. thuringiensis strains multiplied to some extent after inoculation on bean plants, their maximum epiphytic population sizes of 10(6) cfu/g of leaf were always much less than that achieved by other resident epiphytic bacteria or an epiphytically fit Pseudomonas fluorescens strain, which attained population sizes of about 10(7) cfu/g of leaf. However B. thuringiensis strains exhibited much less decline in culturable populations upon imposition of desiccation stress than did other resident bacteria or an inoculated P. fluorescens strain, and most cells were in a spore form soon after inoculation onto plants. B. thuringiensis strains produced commercially for insect control were not less epiphytically fit than strains recently isolated from leaf surfaces. The growth of B. thuringiensis was not affected by the presence of Pseudomonas syringae when co-inoculated, and vice versa. B. thuringiensis strains harboring a green fluorescent protein marker gene did not form large cell aggregates, were not associated with other epiphytic bacteria, and were not found associated with leaf structures, such as stomata, trichomes, or veins when directly observed on bean leaves by epifluorescent microscopy. Thus, B. thuringiensis appears unable to grow extensively on leaves and its common isolation from plants may reflect immigration from more abundant reservoirs elsewhere.}, }
@article {pmid17586667, year = {2007}, author = {Nocker, A and Sossa-Fernandez, P and Burr, MD and Camper, AK}, title = {Use of propidium monoazide for live/dead distinction in microbial ecology.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {16}, pages = {5111-5117}, pmid = {17586667}, issn = {0099-2240}, mesh = {2-Propanol/pharmacology ; Bacteria/*drug effects/genetics/growth &amp; development ; DNA, Bacterial/analysis/genetics/isolation &amp; purification ; Ecosystem ; Electrophoresis/methods ; Hot Temperature ; Polymerase Chain Reaction ; Propidium/*pharmacology ; RNA, Ribosomal, 16S/*genetics ; Water Microbiology ; }, abstract = {One of the prerequisites of making ecological conclusions derived from genetic fingerprints is that bacterial community profiles reflect the live portion of the sample of interest. Propidium monoazide is a membrane-impermeant dye that selectively penetrates cells with compromised membranes, which can be considered dead. Once inside the cells, PMA intercalates into the DNA and can be covalently cross-linked to it, which strongly inhibits PCR amplification. By using PCR after PMA treatment, the analysis of bacterial communities can theoretically be limited to cells with intact cell membranes. Four experiments were performed to study the usefulness of PMA treatment of mixed bacterial communities comprising both intact and compromised cells in combination with end-point PCR by generating community profiles from the following samples: (i) defined mixtures of live and isopropanol-killed cells from pure cultures of random environmental isolates, (ii) wastewater treatment plant influent spiked with defined ratios of live and dead cells, (iii) selected environmental communities, and (iv) a water sediment sample exposed to increasing heat stress. Regions of 16S rRNA genes were PCR amplified from extracted genomic DNA, and PCR products were analyzed by using denaturing gradient gel electrophoresis (DGGE). Results from the first two experiments show that PMA treatment can be of value with end-point PCR by suppressing amplification of DNA from killed cells. The last two experiments suggest that PMA treatment can affect banding patterns in DGGE community profiles and their intensities, although the intrinsic limitations of end-point PCR have to be taken into consideration.}, }
@article {pmid17586664, year = {2007}, author = {Wang, Q and Garrity, GM and Tiedje, JM and Cole, JR}, title = {Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {16}, pages = {5261-5267}, pmid = {17586664}, issn = {0099-2240}, mesh = {Algorithms ; Bacteria/*classification/*genetics ; *Bayes Theorem ; Classification/methods ; Databases, Nucleic Acid ; Phylogeny ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The majority of classifications (98%) were of high estimated confidence (> or = 95%) and high accuracy (98%). In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. The results from leave-one-out testing on both corpora show that the overall accuracies at all levels of confidence for near-full-length and 400-base segments were 89% or above down to the genus level, and the majority of the classification errors appear to be due to anomalies in the current taxonomies. For shorter rRNA segments, such as those that might be generated by pyrosequencing, the error rate varied greatly over the length of the 16S rRNA gene, with segments around the V2 and V4 variable regions giving the lowest error rates. The RDP Classifier is suitable both for the analysis of single rRNA sequences and for the analysis of libraries of thousands of sequences. Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. It combines the RDP Classifier with a statistical test to flag taxa differentially represented between samples. The RDP Classifier and RDP Library Compare are available online at http://rdp.cme.msu.edu/.}, }
@article {pmid17583210, year = {2007}, author = {Nikolaev, IuA and Plakunov, VK}, title = {[Biofilm--"City of microbes" or an analogue of multicellular organisms?].}, journal = {Mikrobiologiia}, volume = {76}, number = {2}, pages = {149-163}, pmid = {17583210}, issn = {0026-3656}, mesh = {Bacterial Adhesion/physiology ; *Bacterial Physiological Phenomena ; Biofilms/drug effects/*growth &amp; development ; Biotechnology ; Disinfectants/pharmacology ; Ecosystem ; Genes, Bacterial/genetics ; Regulon ; Time Factors ; }, abstract = {The definition of the term "biofilm" and the validity of the analogy between these structured microbial communities and multicellular organisms are discussed in the review. The mechanisms of biofilm formation, the types of interrelations of the components of biofilms, and the reasons for biofilm resistance to biocides and stress factors are considered in detail. The role of biofilms in microbial ecology and in biotechnology is discussed.}, }
@article {pmid17578635, year = {2007}, author = {Kurtböke, DI and Neller, RJ and Bellgard, SE}, title = {Mesophilic Actinomycetes in the natural and reconstructed sand dune vegetation zones of Fraser Island, Australia.}, journal = {Microbial ecology}, volume = {54}, number = {2}, pages = {332-340}, pmid = {17578635}, issn = {0095-3628}, mesh = {Actinobacteria/classification/*isolation &amp; purification ; *Ecosystem ; Geography ; Mycorrhizae/classification/*isolation &amp; purification ; Plants/*microbiology ; Queensland ; *Soil Microbiology ; }, abstract = {The natural coastal habitat of Fraser Island located in the State of Queensland, Australia, has been disturbed in the past for mining of the mineral sand ilmenite. Currently, there is no information available on whether these past mining disturbances have affected the distribution, diversity, and survival of beneficial soil microorganisms in the sand dunes of the island. This in turn could deleteriously affect the success of the natural regeneration, plant growth, and establishment on the sand dunes. To support ongoing restoration efforts at sites like these mesophilic actinomycetes were isolated using conventional techniques, with particular emphasis on the taxa previously reported to produce plant-growth-promoting substances and providing support to mycorrhizal fungi, were studied at disturbed sites and compared with natural sites. In the natural sites, foredunes contained higher densities of micromonosporae replaced by increasing numbers of streptomycete species in the successional dune and finally leading to complex actinomycete communities in the mature hind dunes. Whereas in the disturbed zones affected by previous mining activities, which are currently being rehabilitated, no culturable actinomycete communities were detected. These findings suggest that the paucity of beneficial microflora in the rehabilitated sand dunes may be limiting the successful colonization by pioneer plant species. Failure to establish a cover of plant species would result in the mature hind dune plants being exposed to harsh salt and climatic conditions. This could exacerbate the incidence of wind erosion, resulting in the destabilization of well-defined and vegetated successional dunal zones.}, }
@article {pmid17578094, year = {2006}, author = {Hernández-Rodríguez, C}, title = {[Different models and a certain methodological unity].}, journal = {Revista latinoamericana de microbiologia}, volume = {48}, number = {2}, pages = {211-225}, pmid = {17578094}, issn = {0187-4640}, mesh = {Animals ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; Benzene/metabolism ; Benzene Derivatives/metabolism ; Biodegradation, Environmental ; Biofilms ; Corrosion ; *Ecosystem ; Metals/metabolism ; Oxidation-Reduction ; Probiotics ; Steel ; Toluene/metabolism ; Triatominae/microbiology ; Xylenes/metabolism ; }, abstract = {The papers included in this section were previously exposed in the Microbial Communities Symposium organized in XXXV Congreso Nacional de Microbiología. The contributions try to understand the diversity associated to different microbial communities from a molecular perspective, regardless of culture or including a cultured based perspective. Thus, natural models, including bacteria associated to insect tissues, biofilms and microbial communities in man-made habitats as oil pipelines, anaerobic digestors and fermented foods are described. The papers explain several questions and exhibit different perspectives, but maintain a methodological unit, illustrating the knowledge and applicative potential of microbial ecology from a molecular point of view.}, }
@article {pmid17577812, year = {2007}, author = {Nyberg, SD and Osterblad, M and Hakanen, AJ and Löfmark, S and Edlund, C and Huovinen, P and Jalava, J}, title = {Long-term antimicrobial resistance in Escherichia coli from human intestinal microbiota after administration of clindamycin.}, journal = {Scandinavian journal of infectious diseases}, volume = {39}, number = {6-7}, pages = {514-520}, doi = {10.1080/00365540701199790}, pmid = {17577812}, issn = {0036-5548}, mesh = {Adult ; Anti-Bacterial Agents/*pharmacology ; Clindamycin/*pharmacology ; Drug Resistance, Multiple, Bacterial ; Electrophoresis, Gel, Pulsed-Field/methods ; Enterobacteriaceae/*drug effects/growth &amp; development/isolation &amp; purification ; Escherichia coli/*drug effects/growth &amp; development/isolation &amp; purification ; Female ; Humans ; Intestines/*microbiology ; Male ; Middle Aged ; }, abstract = {The aim of this study was to gain better knowledge of how the intestinal microbiota are affected over time after administration of an antimicrobial agent. This study monitored the prevalence and frequencies of antibiotic resistance in Enterobacteriaceae against 17 antimicrobial agents, during a 2-y period, in consecutive faecal samples collected from 8 healthy volunteers. Four subjects had received 150 mg clindamycin perorally for 7 d, while 4 non-exposed subjects served as a control group. The samples from both groups were cultured and screened for Enterobacteriaceae. The highest incidence of resistance observed was to ampicillin. The ampicillin resistance is due to production of the beta-lactamase TEM-1. The administration of clindamycin had a prolonged impact on the composition of the microbiota, even though enterobacteria are intrinsically resistant to clindamycin; the level of resistance in Escherichia coli isolates was elevated after administration and persisted up to 9 months after administration. After 9 months the susceptibility levels in the exposed group were similar to those at d 0.}, }
@article {pmid17576098, year = {2007}, author = {Park, JS and Simpson, AG and Lee, WJ and Cho, BC}, title = {Ultrastructure and phylogenetic placement within Heterolobosea of the previously unclassified, extremely halophilic heterotrophic flagellate Pleurostomum flabellatum (Ruinen 1938).}, journal = {Protist}, volume = {158}, number = {3}, pages = {397-413}, doi = {10.1016/j.protis.2007.03.004}, pmid = {17576098}, issn = {1434-4610}, mesh = {Animals ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Eukaryota/*classification/genetics/*isolation &amp; purification/ultrastructure ; Genes, rRNA ; Introns ; Korea ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Organelles/ultrastructure ; Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Sodium Chloride/metabolism ; Temperature ; Water/*parasitology ; }, abstract = {Although Pleurostomum was described almost a century ago, flagellates assigned to this taxon have been recorded only in very occasional faunistic studies of highly saline habitats, and their phylogenetic position has remained uncertain. We report the cultivation, ultrastructure, and phylogenetic relationships of Pleurostomum flabellatum isolated from a Korean saltern pond of 313 per thousand salinity. This isolate is biflagellated with a cytostomal groove, and is not distinguishable from previous accounts of P. flabellatum from saturated brines in India and Australia. Pleurostomum flabellatum shows ultrastructural features characteristic of many Heterolobosea: (1) a striated rhizoplast, (2) an absence of stacked Golgi bodies, (3) parallel basal bodies and flagella, and (4) a large number of peripheral microtubules supporting a rostrum. 18S rRNA gene phylogenies strongly confirm the affinities of P. flabellatum within Heterolobosea. Furthermore, the 18S rRNA gene of P. flabellatum has the heterolobosean-specific helix 17_1, and a group I intron in the same position as in Acrasis rosea. Within Heterolobosea, the 'amoeboflagellate' genera Naegleria and Willaertia were its closest relatives with high bootstrap support and posterior probability. P. flabellatum was observed only as a flagellate, and never as an amoeba. Since light microscopy and electron microscopy observations indicate that P. flabellatum flagellates are capable both of feeding and division, there might be no amoeba stage. Being morphologically distinct from its closest relatives and phylogenetically distant from other flagellate-only Heterolobosea, P. flabellatum cannot be moved into any previously described heterolobosean genus. Instead, we move Pleurostomum into Heterolobosea, and assign as the type species Pleurostomum salinum Namyslowski 1913, a species that closely resembles P. flabellatum. The optimal temperature for growth of P. flabellatum is 40 degrees C. Interestingly, P. flabellatum grows optimally at 300 per thousand salinity and fails to grow below 200 per thousand salinity, indicating that it is an 'extreme halophile'. The optimal salinity for growth is the highest for any eukaryote examined to date.}, }
@article {pmid17574542, year = {2008}, author = {Saravanan, VS and Madhaiyan, M and Osborne, J and Thangaraju, M and Sa, TM}, title = {Ecological occurrence of Gluconacetobacter diazotrophicus and nitrogen-fixing Acetobacteraceae members: their possible role in plant growth promotion.}, journal = {Microbial ecology}, volume = {55}, number = {1}, pages = {130-140}, pmid = {17574542}, issn = {0095-3628}, mesh = {Acetobacteraceae/*growth &amp; development ; Crops, Agricultural/*growth &amp; development/microbiology ; Ecosystem ; Gluconacetobacter/*growth &amp; development ; *Nitrogen Fixation ; Plant Roots/microbiology ; Saccharum/*growth &amp; development/microbiology ; Soil Microbiology ; Symbiosis ; }, abstract = {Gluconacetobacter diazotrophicus has a long-standing history of bacterial-plant interrelationship as a symbiotic endophyte capable of fixing atmospheric nitrogen. In low nitrogen fertilized sugarcane fields it plays a significant role and its occurrence was realised in most of the sugarcane growing countries. In this mini review, the association of G. diazotrophicus with sugarcane, other crop plants and with various hosts is discussed. The factors affecting survival in the rhizosphere and the putative soil mode of transmission are emphasized. In addition, other N(2)-fixing Acetobacteraceae members, including Gluconacetobacter azotocaptans, Gluconacetobacter johannae and Swaminathania salitolerans, occurring in coffee, corn and rice plants are also covered. Lastly, the plant-growth-promoting traits identified in this group of bacteria, including N(2) fixation, phytohormone synthesis, P and Zn solubilization and biocontrol, are analysed.}, }
@article {pmid17564613, year = {2007}, author = {Scupham, AJ}, title = {Examination of the microbial ecology of the avian intestine in vivo using bromodeoxyuridine.}, journal = {Environmental microbiology}, volume = {9}, number = {7}, pages = {1801-1809}, doi = {10.1111/j.1462-2920.2007.01300.x}, pmid = {17564613}, issn = {1462-2912}, mesh = {Animals ; Bacteroides/genetics ; Base Sequence ; Bromodeoxyuridine ; Clostridium/*genetics ; DNA Primers/genetics ; DNA, Ribosomal Spacer/genetics ; Fatty Acids/analysis ; Food Deprivation/*physiology ; Gammaproteobacteria/genetics ; Intestines/*microbiology ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Turkeys/*microbiology/physiology ; }, abstract = {Bromodeoxyuridine, a thymidine analogue that can be incorporated into the DNA of actively dividing cells, has been used in vivo to identify intestinal bacteria that are metabolically active in 3-week-old turkey poults during an acute period of feed withdrawal. Automated ribosomal intergenic spacer analysis was used to identify amplicons unique to animals subjected to feed withdrawal. One amplicon was unique to fasted birds while two amplicons were present in 60% of fasted birds and absent in all fed birds. Sequence analysis of 16S ribosomal genes indicated the caecal communities of all birds were dominated by Clostridiaceae while also harbouring low levels of metabolically active gamma-proteobacteria and Bacteroides. Twenty per cent of clones from the fasted animals were identified as belonging to the genus Papillibacter, suggesting these microbes may be specifically dividing in response to environmental conditions present in the caeca of fasted birds.}, }
@article {pmid17562463, year = {2007}, author = {Lin, Q and Zhao, HM and Chen, YX}, title = {Effects of 2,4-dichlorophenol, pentachlorophenol and vegetation on microbial characteristics in a heavy metal polluted soil.}, journal = {Journal of environmental science and health. Part. B, Pesticides, food contaminants, and agricultural wastes}, volume = {42}, number = {5}, pages = {551-557}, doi = {10.1080/03601230701391658}, pmid = {17562463}, issn = {0360-1234}, mesh = {2,4-Dinitrophenol/toxicity ; Biodegradation, Environmental ; Biomass ; Drug Synergism ; Environmental Monitoring ; Environmental Pollutants/*analysis ; Environmental Pollution/*analysis ; Kinetics ; Lolium/drug effects/*growth &amp; development/metabolism ; Metals, Heavy/*toxicity ; Pentachlorophenol/toxicity ; *Soil Microbiology ; Soil Pollutants ; }, abstract = {The aim of this study was to evaluate the soil microbial characteristics in historically heavy-metal polluted soil, which was also affected by organic co-contaminants, 2,4-dichlorophenol or pentachlorophenol, which often occur due to the conventional use of pesticides. It was observed that the normalized microbial biomass (microbial biomass per unit soil organic C) of the contaminated soil was very low, less than 1% in both non-planted and ryegrass planted soil, and showed a decreasing trend with the treatment of organic co-contaminants. The microbial biomass and substrate-induced respiration (SIR) in the ryegrass planted soil were much larger, as compared with the non-planted soil with or without organic pollutants. The different resistant bacterial community and its physiological diversity in the rhizosphere further suggested that the effect of vegetation on microbial activity was not just a general increase in the mass or activity of pre-existing microorganisms, but rather acted selectively on microbial growth so that the relative abundance of different microbial groups in soil was changed. In sum, high concentrations of organic co-contaminants, especially pentachlorophenol (PCP), could strengthen the deterioration of microbial ecology. The adverse effect of heavy metal-organic pollutants on the soil microbial biomass and activity might be the reason for the slow degradation of PCP that has high chlorinated and high toxicity. Vegetation might be the efficient way to assist in improving and restoring the utilization of agricultural ecosystems. The beneficial microbial effect of vegetation could cause the rapid dissipation of 2,4-dichlorophenol (2,4-DCP) that has less chlorinated and less toxicity in the planted soils.}, }
@article {pmid17557169, year = {2008}, author = {Løvdal, T and Skjoldal, EF and Heldal, M and Norland, S and Thingstad, TF}, title = {Changes in morphology and elemental composition of Vibrio splendidus along a gradient from carbon-limited to phosphate-limited growth.}, journal = {Microbial ecology}, volume = {55}, number = {1}, pages = {152-161}, pmid = {17557169}, issn = {0095-3628}, mesh = {Alkaline Phosphatase/metabolism ; Biomass ; Carbon/metabolism/*pharmacology ; Colony Count, Microbial ; Culture Media ; Electron Probe Microanalysis ; Microscopy, Electron, Transmission ; Nitrogen/metabolism ; Phosphates/metabolism/*pharmacology ; *Vibrio/growth &amp; development/metabolism/ultrastructure ; }, abstract = {We examined morphology, elemental composition (C, N, P), and orthophosphate-uptake efficiency in the marine heterotrophic bacterium Vibrio splendidus grown in continuous cultures. Eight chemostats were arranged along a gradient of increasing glucose concentrations in the reservoirs, shifting the limiting factor from glucose to phosphate. The content of carbon, nitrogen, and phosphorus was measured in individual cells by x-ray microanalysis using a transmission electron microscope (TEM). Cell volumes (V) were estimated from length and width measurements of unfixed, air-dried cells in TEM. There was a transition from coccoid cells in C-limited cultures toward rod-shaped cells in P-limited cultures. Cells in P-limited cultures with free glucose in the media were significantly larger than cells in glucose-depleted cultures (P < 0.0001). We found functional allometry between cellular C-, N-, and P content (in femtograms) and V (in cubic micrometers) in V. splendidus (C = 224 x V(0.89), N = 52.5 x V(0.80), P = 2 x V(0.65)); i.e., larger bacteria had less elemental C, N, and P per V than smaller cells, and also less P relative to C. Biomass-specific affinity for orthophosphate uptake in large P-limited V. splendidus approached theoretical maxima predicted for uptake limited by molecular diffusion toward the cells. Comparing these theoretical values to respective values for the smaller, coccoid, C-limited V. splendidus indicated, contrary to the traditional view, that large size did not represent a trade-off when competing for the non-C-limiting nutrients.}, }
@article {pmid17554047, year = {2007}, author = {Taylor, MW and Radax, R and Steger, D and Wagner, M}, title = {Sponge-associated microorganisms: evolution, ecology, and biotechnological potential.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {71}, number = {2}, pages = {295-347}, pmid = {17554047}, issn = {1092-2172}, mesh = {Animals ; Bacteria/*classification/metabolism ; *Bacterial Physiological Phenomena ; *Biological Evolution ; Biotechnology ; Ecology ; Porifera/*microbiology/physiology ; Social Behavior ; Symbiosis ; }, abstract = {Marine sponges often contain diverse and abundant microbial communities, including bacteria, archaea, microalgae, and fungi. In some cases, these microbial associates comprise as much as 40% of the sponge volume and can contribute significantly to host metabolism (e.g., via photosynthesis or nitrogen fixation). We review in detail the diversity of microbes associated with sponges, including extensive 16S rRNA-based phylogenetic analyses which support the previously suggested existence of a sponge-specific microbiota. These analyses provide a suitable vantage point from which to consider the potential evolutionary and ecological ramifications of these widespread, sponge-specific microorganisms. Subsequently, we examine the ecology of sponge-microbe associations, including the establishment and maintenance of these sometimes intimate partnerships, the varied nature of the interactions (ranging from mutualism to host-pathogen relationships), and the broad-scale patterns of symbiont distribution. The ecological and evolutionary importance of sponge-microbe associations is mirrored by their enormous biotechnological potential: marine sponges are among the animal kingdom's most prolific producers of bioactive metabolites, and in at least some cases, the compounds are of microbial rather than sponge origin. We review the status of this important field, outlining the various approaches (e.g., cultivation, cell separation, and metagenomics) which have been employed to access the chemical wealth of sponge-microbe associations.}, }
@article {pmid17552237, year = {2007}, author = {Yuan, SQ and Xue, YF and Gao, P and Wang, WD and Ma, YH and Li, XM and Xu, GW}, title = {[Microbial diversity in shengli petroleum reservoirs analyzed by T-RFLP].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {47}, number = {2}, pages = {290-294}, pmid = {17552237}, issn = {0001-6209}, mesh = {Bacteria/*classification/genetics ; *Ecology ; Petroleum/*microbiology ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recent investigations on the microbial ecology of oil reservoirs in a variety of locales indicated that these habitats harbor various assemblages. In this study, a cultured-independent molecular technique, Terminal Restriction Fragment Length Polymorphism (T-RFLP), was used to analyze the microbial diversity of an injection well (S12-ZHU) and three related production wells (S12-4, S12-5 and S12-19) in the ShengLi oilfield (Shandong province, China). The 16S rRNA genes were amplified by PCR with the 5'carboxy-fluorescein (5-FAM)-labelled universal forward primers (27F for bacteria and 21F for archaea) and a universal reverse primer (1495R). Then the 16S rRNA genes were digested with restriction enzymes (Hae III and Hha I) and analyzed by using an automated DNA sequencer. The Shannon-Wiener Diversity index, based on the T-RFLP profiles, indicated that the bacterial and archaeal species richness in the injection well was higher than those of the production ones. The similarity coefficient showed the microbial community similarity among the four samples was 22.4%-30.8% (Bacteria) and 20.8%-34.5% (Archaea), respectively. According to the analysis by TAP T-RFLP program, species belonging to Pseudomonas, Marinobacter and Methanosarcina as well as some uncultured archaeon were supposed to be the dominant bacteria in all four samples. Thus, this study indicates that T-RFLP is useful for analysis of the microbial diversity in petroleum reservoirs.}, }
@article {pmid17548239, year = {2007}, author = {Ferrer, M and Golyshina, O and Beloqui, A and Golyshin, PN}, title = {Mining enzymes from extreme environments.}, journal = {Current opinion in microbiology}, volume = {10}, number = {3}, pages = {207-214}, doi = {10.1016/j.mib.2007.05.004}, pmid = {17548239}, issn = {1369-5274}, mesh = {Biotechnology/*methods ; Environmental Microbiology ; Enzymes/genetics/isolation &amp; purification/*metabolism ; Genomics/*methods ; Protein Engineering/methods ; }, abstract = {Current advances in metagenomics have revolutionized the research in fields of microbial ecology and biotechnology, enabling not only a glimpse into the uncultured microbial population and mechanistic understanding of possible biogeochemical cycles and lifestyles of extreme organisms but also the high-throughput discovery of new enzymes for industrial bioconversions. Nowadays, the genetic and enzymatic differences across the gradients from 'neutral and pristine' to 'extreme and polluted' environments are well documented. Yet, extremophilic organisms are possibly the least well understood because our ability to study and understand their metabolic potential has been hampered by our inability to isolate pure cultures. There are at least two obstacles for reaping the fruit of the microbial diversity of extremophiles: first, in spite of the recent progress in development of new culturing techniques most extremophiles cannot be cultured using traditional culturing technologies; and second, the problem of the very low biomass densities often occurs under the conditions hostile for life, which often do not yield enough DNA and reduces the effectiveness of cloning.}, }
@article {pmid17547010, year = {2007}, author = {Zhang, K and Choi, H and Wu, M and Sorial, GA and Dionysiou, D and Oerther, DB}, title = {An ecology-based analysis of irreversible biofouling in membrane bioreactors.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {55}, number = {8-9}, pages = {395-402}, doi = {10.2166/wst.2007.283}, pmid = {17547010}, issn = {0273-1223}, mesh = {Acinetobacter/*physiology ; Biofilms/*growth &amp; development ; Bioreactors/*microbiology ; DNA, Bacterial/genetics ; Ecology ; Escherichia coli/*physiology ; Industrial Waste ; Paper ; RNA, Ribosomal, 16S/genetics ; Ultrafiltration ; Waste Disposal, Fluid ; }, abstract = {To provide the first step towards a microbial ecology-based understanding of irreversible membrane biofouling, four laboratory-scale membrane bioreactors (MBRs) were operated to investigate the identity of bacterial populations highly correlated with irreversible membrane biofouling. The conventional MBR was divided into two separate experimental units. Unit one consisted of four suspended-growth, activated sludge, sequencing batch bioreactors treating a synthetic paper mill wastewater. Unit two consisted of a microfiltration membrane cell. Amplified ribosomal deoxyribonucleic acid restriction analysis (ARDRA) was used to compare the predominant bacterial populations in samples of mixed liquor and irreversibly bound to the membrane surface. The results of ARDRA showed a significant difference between the planktonic and sessile bacterial communities suggesting that irreversible biofouling of microfiltration membranes may be more highly correlated to specific bacterial populations rather than the total, bulk concentration of biomass. A custom-built mini-flow cell and light microscopy were used to visualise the early formation of biofilms by two pure cultures (Escherichia coli and Acinetobacter calcoaceticus) on membrane surfaces. The results confirmed that A. calcoaceticus was able to enhance the initiation of biofilm formation on microfiltration membranes.}, }
@article {pmid17547007, year = {2007}, author = {Collins, G and Mahony, T and Enright, AM and Gieseke, A and de Beer, D and O'Flaherty, V}, title = {Determination and localisation of in situ substrate uptake by anaerobic wastewater treatment granular biofilms.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {55}, number = {8-9}, pages = {369-376}, doi = {10.2166/wst.2007.279}, pmid = {17547007}, issn = {0273-1223}, mesh = {Acetates/metabolism ; Bacteria, Anaerobic/*metabolism ; *Biofilms ; *Bioreactors ; Carbon Radioisotopes ; Glucose/metabolism ; In Situ Hybridization, Fluorescence ; Lactose/metabolism ; Lysine/metabolism ; Tritium ; Waste Disposal, Fluid/methods ; }, abstract = {Radiotracer incubation experiments and beta microimaging, along with fluorescent in situ hybridisation (FISH), are proposed as a complementary approach to specific methanogenic activity testing and measurement of in vitro substrate utilisation rates to understand better the ecophysiology of anaerobic granular biofilms from wastewater treatment reactors.}, }
@article {pmid17547005, year = {2007}, author = {Downing, LS and Nerenberg, R}, title = {Performance and microbial ecology of the hybrid membrane biofilm process for concurrent nitrification and denitrification of wastewater.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {55}, number = {8-9}, pages = {355-362}, doi = {10.2166/wst.2007.277}, pmid = {17547005}, issn = {0273-1223}, mesh = {Bacteria/classification/genetics/metabolism ; Base Sequence ; *Biofilms/classification ; DNA, Bacterial/genetics ; Ecology ; Membranes, Artificial ; Nitrogen/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sewage ; Waste Disposal, Fluid/*methods ; Water Pollutants, Chemical/*metabolism ; }, abstract = {We report on a novel process for total nitrogen (TN) removal, the hybrid membrane biofilm process (HMBP). The HMBP uses air-supplying hollow-fibre membranes inside an activated sludge tank, with suppressed aeration, to allow concurrent nitrification and denitrification. We hypothesised that a nitrifying biofilm would form on the membranes, and that the low bulk-liquid BOD concentrations would encourage heterotrophic denitrifying bacteria to grow in suspension. A nitrifying biofilm was initially established by supplying an influent ammonia concentration of 20 mgN/L. Subsequently, 120 mg/L acetate was added to the influent as BOD. With a bulk-liquid SRT of only 5 days, nitrification rates were 0.85 gN/m(2) per day and the TN removal reached 75%. The biofilm thickness was approximately 500 lim. We used DGGE to obtain a microbial community fingerprint of suspended and attached growth, and prepared a clone library. The DGGE results, along with the clone library and operating data, suggest that nitrifying bacteria were primarily attached to the membranes, while heterotrophic bacteria were predominant in the bulk liquid. Our results demonstrate that the HMBP is effective for TN removal, achieving high levels of nitrification with a low bulk-liquid SRT and concurrently denitrifying with BOD as the sole electron donor.}, }
@article {pmid17546963, year = {2007}, author = {Rittmann, BE}, title = {Where are we with biofilms now? Where are we going?.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {55}, number = {8-9}, pages = {1-7}, doi = {10.2166/wst.2007.235}, pmid = {17546963}, issn = {0273-1223}, mesh = {*Biofilms ; Biotechnology ; Ecology ; Membranes, Artificial ; Models, Biological ; }, abstract = {The IWA's BiofilmVl conference presented a wide range of research on biofilm systems. Particularly popular themes were nitrogen removal, mathematical modelling and microbial ecology. Emerging themes included biofilms with membranes, pathogens in biofilms, biofouling and detachment. Within microbial ecology and mathematical modelling, emphasis was given to N-removal systems, particularly involving nitrifiers and Anammox bacteria. Both themes also recognised the importance of biofilm detachment. Although biofilms on membranes gained attention, little interest was exhibited towards linking biofilms with other advanced materials, such as ceramics, conductors, semi-conductors or nano-materials. Research presented at BiofilmVI marked major advances in improving water sustainability towards removing BOD and N, but did not address many emerging contaminants, such as oxidised contaminants and endocrine disruptors. Attention to energy sustainability, such as with bio-hydrogen or microbial fuel cells, was minimal. Thus, research reported at BiofilmVI was strong towards "improving the expected" with regard to BOD and N removal, but not yet focused on "exploiting the unexpected" to deal with emerging pollutants and bio-energy.}, }
@article {pmid17546693, year = {2008}, author = {Fermoso, FG and Collins, G and Bartacek, J and O'Flaherty, V and Lens, P}, title = {Acidification of methanol-fed anaerobic granular sludge bioreactors by cobalt deprivation: Induction and microbial community dynamics.}, journal = {Biotechnology and bioengineering}, volume = {99}, number = {1}, pages = {49-58}, doi = {10.1002/bit.21528}, pmid = {17546693}, issn = {1097-0290}, mesh = {Bacteria, Anaerobic/*physiology ; Bioreactors/*microbiology ; Cobalt/*metabolism ; Computer Simulation ; Hydrogen-Ion Concentration ; Methanol/*metabolism ; *Models, Biological ; Sewage/*microbiology ; }, abstract = {The acidification of mesophilic (30 degrees C) methanol-fed upflow anaerobic sludge bed (UASB) reactors induced by cobalt deprivation from the influent was investigated by coupling the reactor performance (pH 7.0; organic loading rate 4.5 g COD . L(-1) . d(-1)) to the microbial ecology of the bioreactor sludge. The latter was investigated by specific methanogenic activity (SMA) measurements and fluorescence in situ hybridization (FISH) to quantify the abundance of key organisms over time. This study hypothesized that under cobalt limiting conditions, the SMA on methanol of the sludge gradually decreases, which ultimately results in methanol accumulation in the reactor effluent. Once the methanol accumulation surpasses a threshold value (about 8.5 mM for the sludge investigated), reactor acidification occurs because acetogens outcompete methylothrophic methanogens at these elevated methanol concentrations. Methanogens present in granular sludge at the time of the acidification do not use methanol as the direct substrate and are unable to degrade acetate. Methylotrophic/acetoclastic methanogenic activity was found to be lost within 10 days of reactor operation, coinciding with the disappearance of the Methanosarcina population. The loss of SMA on methanol can thus be used as an accurate parameter to predict reactor acidification of methanol-fed UASB reactors operating under cobalt limiting conditions.}, }
@article {pmid17546519, year = {2007}, author = {Calvaruso, C and Turpault, MP and Leclerc, E and Frey-Klett, P}, title = {Impact of ectomycorrhizosphere on the functional diversity of soil bacterial and fungal communities from a forest stand in relation to nutrient mobilization processes.}, journal = {Microbial ecology}, volume = {54}, number = {3}, pages = {567-577}, pmid = {17546519}, issn = {0095-3628}, mesh = {Analysis of Variance ; Bacteria/*growth &amp; development/isolation &amp; purification/metabolism ; Biodiversity ; Fungi/*growth &amp; development/isolation &amp; purification/metabolism ; Iron/metabolism ; Mycorrhizae ; Phosphorus/metabolism ; Plant Roots/metabolism/microbiology ; Quercus/metabolism/microbiology ; Soil ; *Soil Microbiology ; Trees/*microbiology ; }, abstract = {The ectomycorrhizal symbiosis alters the physicochemical and biological conditions in the surrounding soil, thus creating a particular environment called ectomycorrhizosphere, which selects microbial communities suspected to play a role in gross production and nutrient cycling. To assess the ectomycorrhizosphere effect on the structure of microbial communities potentially involved in the mobilization of nutrients from the soil minerals in a poor-nutrient environment, we compared the functional diversity of soil and ectomycorrhizosphere bacterial communities in a forest stand. Two hundred and sixty-four bacterial strains and 107 fungal strains were isolated from the bulk soil of an oak (Quercus petraea) stand and from oak-Scleroderma citrinum ectomycorrhizosphere and ectomycorrhizae, in two soil organo-mineral horizons (0 to 3 cm and 5 to 10 cm). They were characterized using two in vitro tests related to their capacities to mobilize iron and phosphorus. We demonstrated that the oak-S. citrinum ectomycorrhizosphere significantly structures the culturable bacterial communities in the two soil horizons by selecting very efficient strains for phosphorus and iron mobilization. This effect was also observed on the diversity of the phosphate-solubilizing fungal communities in the lower soil horizon. A previous study already demonstrated that Laccaria bicolor-Douglas fir ectomycorrhizosphere structures the functional diversity of Pseudomonas fluorescens population in a forest nursery soil. Comparing to it, our work highlights the consistency of the mycorrhizosphere effect on the functional diversity of bacterial and fungal communities in relation to the mineral weathering process, no matter the fungal symbiont, the age and species of the host tree, or the environment (nursery vs forest). We also demonstrated that the intensity of phosphorus and iron mobilization by the ectomycorrhizosphere bacteria isolated from the lower soil horizon was significantly higher compared to that which was isolated from the upper horizon. This reveals for the first time a stratification of the functional diversity of the culturable soil bacterial communities as related to phosphorus and iron mobilization.}, }
@article {pmid17542494, year = {2007}, author = {Tsekova, K and Ianis, M and Dencheva, V and Ganeva, S}, title = {Biosorption of binary mixtures of copper and cobalt by Penicillium brevicompactum.}, journal = {Zeitschrift fur Naturforschung. C, Journal of biosciences}, volume = {62}, number = {3-4}, pages = {261-264}, doi = {10.1515/znc-2007-3-417}, pmid = {17542494}, issn = {0939-5075}, mesh = {Adsorption ; Cobalt/*pharmacokinetics ; Copper/*pharmacokinetics ; Kinetics ; Metals, Heavy/pharmacokinetics ; Penicillium/growth &amp; development/*metabolism ; }, abstract = {This work reports on a study of the biosorption of copper and cobalt, both singly and in combination (in equimolar concentrations), by the resting cells of Penicillium brevicompactum. Equilibrium batch sorption studies were carried out at 30 degrees C and pH 5.0 for a contact time of 1 hour to guarantee that equilibrium was reached. The equilibrium data were analyzed using the Langmuir and Freundlich isotherms. The adsorption of binary mixtures of heavy metal solutions on the fungal biomass was found to be of competitive type where the adsorption capacity for any single metal decreased in the presence of the other. The cobalt ions showed a higher affinity for Penicillium brevicompactum than the copper ions.}, }
@article {pmid17542334, year = {2007}, author = {Clavel, T and Haller, D}, title = {Molecular interactions between bacteria, the epithelium, and the mucosal immune system in the intestinal tract: implications for chronic inflammation.}, journal = {Current issues in intestinal microbiology}, volume = {8}, number = {2}, pages = {25-43}, pmid = {17542334}, issn = {1466-531X}, mesh = {Animals ; *Bacteria/genetics/immunology/pathogenicity ; Chronic Disease ; *Epithelium/immunology/microbiology ; Germ-Free Life ; Guinea Pigs ; Humans ; *Immunity, Mucosal ; *Inflammatory Bowel Diseases/immunology/microbiology/physiopathology ; Intestinal Mucosa/immunology/microbiology ; *Intestines/cytology/immunology/microbiology ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Rats ; Rats, Inbred F344 ; }, abstract = {In the last few years, advances in immunology, metabolomics and microbial ecology have shown that the contribution of the intestinal microbiota to the overall health status of the host has been so far underestimated. In this context, intestinal epithelial cells play a crucial role in the maintenance of intestinal homoeostasis. Indeed, at the interface between the luminal content and host tissues, the intestinal epithelium must integrate pro- and anti-inflammatory signals to regulate innate and adaptative immune responses, i.e. to control inflammation. However, under the influence of environmental factors, disturbance of the dialog between enteric bacteria and epithelial cells contributes to the development of chronic inflammation in genetically susceptible hosts. The present review covers the state of knowledge of the host response, especially in intestinal epithelial cells, to enteric bacteria, including colitogenic and probiotic bacteria. It also seeks to give an overview of potential regulatory mechanisms involved in the maintenance of intestinal homeostasis, and discusses the clinical implications for inflammatory bowel diseases.}, }
@article {pmid17541768, year = {2007}, author = {Yan, QY and Yu, YH and Feng, WS and Deng, WN and Song, XH}, title = {Genetic diversity of plankton community as depicted by PCR-DGGE fingerprinting and its relation to morphological composition and environmental factors in Lake Donghu.}, journal = {Microbial ecology}, volume = {54}, number = {2}, pages = {290-297}, pmid = {17541768}, issn = {0095-3628}, mesh = {China ; DNA Fingerprinting ; DNA, Ribosomal/genetics ; Electrophoresis, Polyacrylamide Gel ; Fresh Water/*microbiology ; *Genetic Variation ; Plankton/*classification/*genetics ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; }, abstract = {To collect information about the genetic diversity of the plankton community and to study how plankton respond to environmental conditions, plankton samples were collected from five stations representing different trophic levels in a shallow, eutrophic lake (Lake Donghu), and investigated by PCR-DGGE fingerprinting. A total of 100 bands (61 of 16S rDNA bands and 39 of 18S rDNA bands) were detected. The DGGE bands unique to any single station accounted for 38% of the total bands, whereas common bands detected at all five stations accounted for only 11%. Using UPGMA clustering and MDS ordination of DGGE fingerprints, stations I and II were found to initially group together into one cluster, which was later joined by station V. Stations III and IV were isolated into two separate groups of one station each. Some differences in grouping relationships were found when analysis was completed on the basis of chemical characteristics and morphological composition, with zooplankton composition showing the greatest variability. However, the most similar stations (I and II) were always initially grouped into one cluster. Moreover, stations that exhibited the same or similar trophic level (stations III and IV), but different concentrations of heavy metals, were further differentiated by the DGGE method. Results of the present study indicated that PCR-DGGE fingerprinting was more sensitive than the traditional methods, as other studies suggested. Additionally, PCR-DGGE appears to be more appropriate for diversity characterization of the plankton community, as it is more canonical, systematic, and effective. Most importantly, fingerprinting results are more convenient for the comparative analyses between different studies. Therefore, the use of the described fingerprinting analysis may provide an operable and sensitive biomonitoring approach to identify critical, and potentially negative, stress within an aquatic ecosystem.}, }
@article {pmid17539549, year = {2007}, author = {Clauwaert, P and Rabaey, K and Aelterman, P and de Schamphelaire, L and Pham, TH and Boeckx, P and Boon, N and Verstraete, W}, title = {Biological denitrification in microbial fuel cells.}, journal = {Environmental science &amp; technology}, volume = {41}, number = {9}, pages = {3354-3360}, doi = {10.1021/es062580r}, pmid = {17539549}, issn = {0013-936X}, mesh = {*Bioelectric Energy Sources ; Electrodes ; Graphite/chemistry ; Nitrates/*isolation &amp; purification/metabolism ; Water Pollutants, Chemical/*isolation &amp; purification/metabolism ; }, abstract = {Microbial fuel cells (MFCs) that remove carbon as well as nitrogen compounds out of wastewater are of special interest for practice. We developed a MFC in which microorganisms in the cathode performed a complete denitrification by using electrons supplied by microorganisms oxidizing acetate in the anode. The MFC with a cation exchange membrane was designed as a tubular reactor with an internal cathode and was able to remove up to 0.146 kg NO(3-)-N m(-3) net cathodic compartment (NCC) d(-1) (0.080 kg NO(3-)-N m(-3) total cathodic compartment d(-1) (TCC)) at a current of 58 A m(-3) NCC (32 A m(-3) TCC) and a cell voltage of 0.075 V. The highest power output in the denitrification system was 8 W m(-3) NCC (4 W m(-3) TCC) with a cell voltage of 0.214 V and a current of 35 A m(-3) NCC. The denitrification rate and the power production was limited bythe cathodic microorganisms, which only denitrified significantly at a cathodic electrode potential below 0 V versus standard hydrogen electrode (SHE). This is, to our knowledge, the first study in which a MFC has both a biological anode and cathode performing simultaneous removal of an organic substrate, power production, and complete denitrification without relying on H2-formation or external added power.}, }
@article {pmid17524120, year = {2007}, author = {Ritz, K}, title = {The plate debate: cultivable communities have no utility in contemporary environmental microbial ecology.}, journal = {FEMS microbiology ecology}, volume = {60}, number = {3}, pages = {358-362}, doi = {10.1111/j.1574-6941.2007.00331.x}, pmid = {17524120}, issn = {0168-6496}, mesh = {Bacteria/*cytology/genetics ; Colony Count, Microbial ; Culture Techniques/*methods ; Ecology ; *Environmental Microbiology ; Fungi/cytology/genetics ; }, }
@article {pmid17522847, year = {2007}, author = {Martínez, P and Agulló, L and Hernández, M and Seeger, M}, title = {Chlorobenzoate inhibits growth and induces stress proteins in the PCB-degrading bacterium Burkholderia xenovorans LB400.}, journal = {Archives of microbiology}, volume = {188}, number = {3}, pages = {289-297}, doi = {10.1007/s00203-007-0247-4}, pmid = {17522847}, issn = {0302-8933}, mesh = {Biodegradation, Environmental ; Burkholderia/*drug effects/enzymology/growth &amp; development/metabolism ; Chlorobenzoates/*pharmacology ; Electrophoresis, Gel, Two-Dimensional/methods ; Heat-Shock Proteins/antagonists &amp; inhibitors/*biosynthesis/metabolism ; Microscopy, Electron/methods ; Peptide Elongation Factor G/genetics/metabolism ; Polychlorinated Biphenyls/metabolism/*pharmacokinetics ; Proteome/*metabolism ; Sequence Analysis, Protein ; }, abstract = {Aerobic bacteria, such as Burkholderia xenovorans LB400, are able to degrade a wide range of polychlorobiphenyls (PCBs). Generally, these bacteria are not able to transform chlorobenzoates (CBAs), which accumulate during PCB degradation. In this study, the effects of CBAs on the growth, the morphology and the proteome of Burkholderia xenovorans LB400 were analysed. 4-CBA and 2-CBA were observed to inhibit the growth of strain LB400 on glucose. Strain LB400 exposed to 4-CBA exhibited increased number and size of electron-dense granules in the cytoplasm, which could be polyphosphates. Two-dimensional (2-D) polyacrylamide gel electrophoresis was used to characterise the molecular response of strain LB400 to 4-CBA. This compound induced the enzymes BenD and CatA of benzoate and catechol catabolic pathways. The induction of molecular chaperones DnaK and HtpG by 4-CBA indicated that the exposure to this compound constitutes a stressful condition for this bacterium. Additionally, the induction of some Krebs cycle enzymes was observed, probably as response to cellular energy requirements. This study contributes to the knowledge on the effects of CBA on the PCB-degrader Burkholderia xenovorans LB400.}, }
@article {pmid17517642, year = {2007}, author = {Williams, HT and Lenton, TM}, title = {Artificial selection of simulated microbial ecosystems.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {21}, pages = {8918-8923}, pmid = {17517642}, issn = {0027-8424}, mesh = {Biological Evolution ; *Ecosystem ; *Selection, Genetic ; }, abstract = {Recent work with microbial communities has demonstrated an adaptive response to artificial selection at the level of the ecosystem. The reasons for this response and the level at which adaptation occurs are unclear: does selection act implicitly on traits of individual species, or are higher-level traits genuinely being selected? If the ecosystem response is just the additive combination of the responses of the constituent species, then the ecosystem response could be predicted a priori, and the ecosystem-level selection process is superfluous. However, if the ecosystem response results from ecological interactions among species, then selection at a higher level is necessary. Here we perform artificial ecosystem selection experiments on an individual-based evolutionary simulation model of microbial ecology and observe a similar response to that seen with real ecosystems. We demonstrate that a significant fraction of artificially selected ecosystem responses cannot be accounted for by implicit lower-level selection of a single type of organism within the community, and that interactions among different types of organism contribute significantly to the response in the majority of cases. However, when the ecological problem posed by the artificial ecosystem selection process can be easily solved by a single dominant species, it often is.}, }
@article {pmid17514427, year = {2007}, author = {Ghosh, A and Maity, B and Chakrabarti, K and Chattopadhyay, D}, title = {Bacterial diversity of East Calcutta Wet land area: possible identification of potential bacterial population for different biotechnological uses.}, journal = {Microbial ecology}, volume = {54}, number = {3}, pages = {452-459}, pmid = {17514427}, issn = {0095-3628}, mesh = {Bacteria/classification/*genetics/growth &amp; development ; Biodiversity ; Biotechnology/*methods ; DNA, Bacterial/chemistry/genetics/isolation &amp; purification ; *Genetic Variation ; India ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Wetlands ; }, abstract = {The extent of microbial diversity in nature is still largely unknown, suggesting that there might be many more useful products yet to be identified from soil microorganisms. This insight provides the scientific foundation for a renewed interest in examining soil microorganisms for novel commercially important products. This has led us to access the metabolic potential of soil microorganisms via cultivation strategy. Keeping this in mind, we have performed a culture-dependent survey of important soil bacterial community diversity in East Calcutta Wetland area (Dhapa Landfill Area). We describe isolation of 38 strains, their phenotypic and biochemical characterization, and finally molecular identification by direct sequencing of polymerase chain reaction (PCR)-amplified 16S rRNA gene products. We have isolated and identified strains able to fix nitrogen, produce extracellular enzymes like protease, cellulase, xylanase, and amylase, and solubilize inorganic phosphates. Some isolates can synthesize extracellular insecticidal toxins. We find a good correlation between biochemical and phenotypic behavior and the molecular study using 16S rRNA gene of the isolates. Furthermore, our findings clearly indicate the composition of cultivable soil bacteria in East Calcutta Wetland Area.}, }
@article {pmid17510763, year = {2007}, author = {Lamarche, J and Bradley, RL and Hooper, E and Shipley, B and Simao Beaunoir, AM and Beaulieu, C}, title = {Forest floor bacterial community composition and catabolic profiles in relation to landscape features in Québec's southern boreal forest.}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {10-20}, pmid = {17510763}, issn = {0095-3628}, mesh = {Bacteria/*classification/genetics ; *Biodiversity ; Hydrogen-Ion Concentration ; Polymorphism, Restriction Fragment Length ; Quebec ; RNA, Ribosomal, 16S/chemistry ; *Soil Microbiology ; Time Factors ; Trees/classification/*microbiology ; }, abstract = {Bacterial communities mediate many of the processes in boreal forest floors that determine the functioning of these ecosystems, yet it remains uncertain whether the composition of these communities is distributed nonrandomly across the landscape. In a study performed in the southern boreal mixed wood forest of Québec, Canada, we tested the hypothesis that stand type (spruce/fir, aspen, paper birch), stand age (57, 78-85, and 131 years old), and geologic parent material (clay and till) were correlated with forest floor bacterial community composition. Forest floors in 54 independent forest stands were sampled to comprise a full factorial array of the three predictor variables. Bacterial community structure was examined by terminal restriction fragment (T-RF) length polymorphism analysis of genes encoding for 16S rRNA. Distance-based redundancy analysis of T-RF assemblages revealed that each predictor variable, as well as their interaction terms, had a significant effect on bacterial community composition, geologic parent material being the most discriminating factor. A survey of the 15 T-RFs with the highest percentage fit on the first two ordination axes describing the main effects indicated that each landscape feature correlated to a distinct group of bacteria. A survey of the most discriminant T-RFs describing the effect of stand type within each combination of stand age and geologic parent material indicated a strong dependency of several T-RFs on geologic parent material. Given the possible link between bacterial community composition and forest floor functioning, we also assessed the effects of the same three landscape features on community-level catabolic profiles (CLCP) of the extractable forest floor microbiota. Geologic parent material and stand type had significant effects on CLCPs. On clay plots, the effects of landscape features on T-RF patterns were highly consistent with their effects on CLCPs. In light of our results, we suggest that future research examine whether bacterial community composition or CLCPs can be used to detect latent environmental changes across landscape units.}, }
@article {pmid17509863, year = {2007}, author = {McMahon, KD and Martin, HG and Hugenholtz, P}, title = {Integrating ecology into biotechnology.}, journal = {Current opinion in biotechnology}, volume = {18}, number = {3}, pages = {287-292}, doi = {10.1016/j.copbio.2007.04.007}, pmid = {17509863}, issn = {0958-1669}, mesh = {*Biotechnology ; *Ecology ; Food Chain ; }, abstract = {New high-throughput culture-independent molecular tools are allowing the scientific community to characterize and understand the microbial communities underpinning environmental biotechnology processes in unprecedented ways. By creatively leveraging these new data sources, microbial ecology has the potential to transition from a purely descriptive to a predictive framework, in which ecological principles are integrated and exploited to engineer systems that are biologically optimized for the desired goal. But to achieve this goal, ecology, engineering and microbiology curricula need to be changed from the very root to better promote interdisciplinarity.}, }
@article {pmid17506823, year = {2007}, author = {Possemiers, S and Bolca, S and Eeckhaut, E and Depypere, H and Verstraete, W}, title = {Metabolism of isoflavones, lignans and prenylflavonoids by intestinal bacteria: producer phenotyping and relation with intestinal community.}, journal = {FEMS microbiology ecology}, volume = {61}, number = {2}, pages = {372-383}, doi = {10.1111/j.1574-6941.2007.00330.x}, pmid = {17506823}, issn = {0168-6496}, mesh = {Bacteria/classification/isolation &amp; purification/*metabolism ; Clostridium/classification/isolation &amp; purification/metabolism ; Colony Count, Microbial ; Eubacterium/classification/isolation &amp; purification/metabolism ; Feces/microbiology ; Flavonoids/*metabolism ; Humans ; Intestines/*microbiology ; Isoflavones/*metabolism ; Lignans/*metabolism ; Phenotype ; Phytoestrogens/metabolism ; }, abstract = {Many studies have investigated the importance of the intestinal bacterial activation of individual phytoestrogens. However, human nutrition contains different phytoestrogens and the final exposure depends on the microbial potential to activate all different groups within each individual. In this work, interindividual variations in the bacterial activation of the different phytoestrogens were assessed. Incubation of feces from 100 individuals using SoyLife EXTRA, LinumLife EXTRA and isoxanthohumol suggested that individuals could be separated into high, moderate and low O-desmethylangolensin (O-DMA), equol, enterodiol (END), enterolactone (ENL) or 8-prenylnaringenin producers, but that the metabolism of isoflavones, lignans and prenylflavonoids follows separate, independent pathways. However, O-DMA and equol production correlated negatively, whereas a positive correlation was found between END and ENL production. In addition, END production correlated negatively with Clostridium coccoides-Eubacterium rectale counts. Furthermore, O-DMA production was correlated with the abundance of methanogens, whereas equol production correlated with sulfate-reducing bacteria, indicating that the metabolic fate of daidzein may be related to intestinal H(2) metabolism.}, }
@article {pmid17506683, year = {2007}, author = {Walker, JJ and Pace, NR}, title = {Endolithic microbial ecosystems.}, journal = {Annual review of microbiology}, volume = {61}, number = {}, pages = {331-347}, doi = {10.1146/annurev.micro.61.080706.093302}, pmid = {17506683}, issn = {0066-4227}, mesh = {Archaea/classification/*isolation &amp; purification ; Bacteria/classification/*isolation &amp; purification ; Cyanobacteria/classification/*isolation &amp; purification ; Ecology ; *Ecosystem ; Fungi/classification/*isolation &amp; purification ; Geological Phenomena ; Geology ; Light ; Phylogeny ; Temperature ; }, abstract = {The endolithic environment, the pore space in rocks, is a ubiquitous microbial habitat and an interface between biology and geology. Photosynthesis-based endolithic communities inhabit the outer centimeters of rocks exposed to the surface, and offer model systems for microbial ecology, geobiology, and astrobiology. Endolithic ecosystems are among the simplest microbial ecosystems known and as such provide tractable models for testing ecological hypotheses. Such hypotheses have been difficult to test because microbial ecosystems are extraordinarily diverse. We review here recent culture-independent, ribosomal RNA-based studies that evaluate hypotheses about endolithic ecosystems, and provide insight for understanding general principles in microbial ecology. Comparison of endolithic communities supports the principle that patterns of microbial diversity are governed by similar principles observed in macroecological systems. Recent results also explore geobiological processes that shape the current biosphere and potentially provide clues to life's history on Earth and where to seek life elsewhere in the Solar System.}, }
@article {pmid17504498, year = {2007}, author = {Heinz, E and Kolarov, I and Kästner, C and Toenshoff, ER and Wagner, M and Horn, M}, title = {An Acanthamoeba sp. containing two phylogenetically different bacterial endosymbionts.}, journal = {Environmental microbiology}, volume = {9}, number = {6}, pages = {1604-1609}, pmid = {17504498}, issn = {1462-2912}, mesh = {Acanthamoeba/*microbiology/*ultrastructure ; Animals ; Betaproteobacteria/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/chemistry ; DNA, Protozoan/chemistry ; Molecular Sequence Data ; RNA, Ribosomal, 16S/analysis/chemistry ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Acanthamoebae are ubiquitous free-living amoebae and important predators of microbial communities. They frequently contain obligate intracellular bacterial symbionts, which show a worldwide distribution. All Acanthamoeba spp. described so far harboured no or only a single specific endosymbiont phylotype, and in some cases evidence for coevolution between the symbiotic bacteria and the amoeba host has been reported. In this study we have isolated and characterized an Acanthamoeba sp. (strain OEW1) showing a stable symbiotic relationship with two morphologically different endosymbionts. 16S rRNA sequence analysis assigned these symbionts to the candidate genus Procabacter (Betaproteobacteria) and the genus Parachlamydia (Chlamydiae) respectively. Fluorescence in situ hybridization and transmission electron microscopy confirmed the affiliation of the endosymbionts and showed their co-occurrence in the amoeba host cells and their intracellular location within separate compartments enclosed by host-derived membranes. Further analysis of this stable relationship should provide novel insights into the complex interactions of intracellular multiple-partner associations.}, }
@article {pmid17497228, year = {2008}, author = {Muscholl-Silberhorn, A and Thiel, V and Imhoff, JF}, title = {Abundance and bioactivity of cultured sponge-associated bacteria from the Mediterranean sea.}, journal = {Microbial ecology}, volume = {55}, number = {1}, pages = {94-106}, pmid = {17497228}, issn = {0095-3628}, mesh = {Alphaproteobacteria/classification/genetics/*isolation &amp; purification/metabolism ; Animals ; Anti-Bacterial Agents/*metabolism/*pharmacology ; Bacteria/classification/*drug effects/genetics/*isolation &amp; purification ; Biotechnology/methods ; *Culture Media ; Ecosystem ; Mediterranean Sea ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Phylogeny ; Porifera/*microbiology ; Rhodobacteraceae/classification/genetics/isolation &amp; purification/metabolism ; Seawater/chemistry ; Sequence Analysis, DNA ; }, abstract = {In this study, the search for new antibiotics was combined with quantitative ecological studies. The cultured fraction of the associated bacterial communities from ten different Mediterranean sponge species was investigated. To obtain quantitative and qualitative data of sponge-associated bacterial communities and to expand the cultured diversity, different media were used. The largest morphological diversity and highest yield of isolates was obtained by using oligotrophic media, which consisted of natural habitat seawater amended with (1% additional carbon sources. The dominant bacterial morphotypes were determined and bacterial isolates were tested for antimicrobial activity and identified using 16S rDNA sequencing. The sponge-associated most abundant morphotypes were all affiliated to the Alphaproteobacteria and showed antimicrobial activity against at least one of the tested strains. In contrast, the ambient seawater was dominated by Gammaproteobacteria. One single alphaproteobacterium, which was related to Pseudovibrio denitrificans, was shown to dominate the cultured community of at least six of the sponges. This designated MBIC3368-like alphaproteobacterium has been isolated from sponges before and seems to be restricted to associations with members of the phylum Porifera. It displays a weak and unstable antimicrobial activity, which gets easily lost during cultivation. However, this bioactive bacterium was present in the sponges by up to 10(6) cells per gram wet-weight sponge tissue and dominated the cultured fraction with up to 74%. The association of this alphaproteobacterium with sponges is probably evolutionary young and facultative and possibly involves biologically active secondary metabolites. Besides a demonstrated vertical transfer, additional horizontal transfer between the sponges is assumed. Members of the genus Bacillus displaying antimicrobial activity were found regularly, too. However, actinomycetes, which are known for their production of bioactive substances, were present in very low abundance.}, }
@article {pmid17492474, year = {2007}, author = {Cho, KM and Hong, SY and Lee, SM and Kim, YH and Kahng, GG and Lim, YP and Kim, H and Yun, HD}, title = {Endophytic bacterial communities in ginseng and their antifungal activity against pathogens.}, journal = {Microbial ecology}, volume = {54}, number = {2}, pages = {341-351}, pmid = {17492474}, issn = {0095-3628}, mesh = {Antibiosis ; Bacteria/*classification/genetics/isolation &amp; purification ; Base Composition ; DNA, Bacterial/genetics ; Ecosystem ; Fungi/growth &amp; development ; Genes, rRNA ; Korea ; Panax/*microbiology ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {Plant roots are associated with diverse communities of endophytic bacteria which do not exert adverse effects. The diversity of bacterial endophytes associated with ginseng roots cultivated in three different areas in Korea was investigated. Sixty-three colonies were isolated from the interior of ginseng roots. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates belonged to three major phylogenetic groups: the high G+C Gram-positive bacteria (HGCGPB), low G+C Gram-positive bacteria (LGCGPB), and the Proteobacteria. The dominant species at the three different ginseng growing areas were: HGCGPB at Ganghwa (55.0%), LGCGPB at Geumsan (45.5%), and Proteobacteria at Jinan (61.9%). Most cellulase-, xylanase-, and pectinase-producing colonies among the isolates belong to the LGCGPB group, except for Pectobacterium carotovora which belonged to the Proteobacteria. The 13 isolates belonging to LGCGPB and Proteobacteria were assessed for their antifungal activity against phytopathogenic fungi such as Rhizoctonia solani. Among them, Paenibacillus polymyxa GS01, Bacillus sp. GS07, and Pseudomonas poae JA01 show potential activity as biocontrol agents against phytopathogenic fungi. Finally, most of the low G+C Gram-positive bacteria with antifungal activity against phytopathogenic microorganisms showed cellulolytic enzyme activity while some Proteobacteria with the antifungal activity and the high G+C Gram-positive bacteria did not show any cellulolytic activity.}, }
@article {pmid17487523, year = {2008}, author = {Nix-Stohr, S and Burpee, LL and Buck, JW}, title = {The influence of exogenous nutrients on the abundance of yeasts on the phylloplane of turfgrass.}, journal = {Microbial ecology}, volume = {55}, number = {1}, pages = {15-20}, pmid = {17487523}, issn = {0095-3628}, mesh = {Carbohydrates/pharmacology ; Colony Count, Microbial ; Ecosystem ; Environmental Monitoring ; Festuca/*microbiology ; Nitrogen/*pharmacology ; Organic Chemicals/pharmacology ; Plant Leaves/*microbiology ; Sucrose/pharmacology ; Yeasts/drug effects/*growth &amp; development ; }, abstract = {Four experiments were conducted to assess the effect of foliar applications of various nutrient solutions on the phylloplane yeast community of tall fescue (Festuca arundinacea Schreb.). In the first three experiments, increasing concentrations of sucrose (2-16%), yeast extract (0.5-2.5%), and sucrose plus yeast extract (2.5-18.5% total) were applied and the yeast colony forming units (cfu) enumerated 14 h later by dilution plating. Significant positive linear relationships were observed between the number of yeast cfu and applications of both yeast extract and sucrose plus yeast extract. Foliar applications of sucrose alone had no significant effect on yeast community abundance, indicating that phylloplane yeasts of turfgrass are not limited by the amount or availability of carbohydrates. In the fourth experiment, five different solutions were applied to tall fescue to investigate the response of the yeast community to organic and inorganic nitrogen sources. Tryptone or yeast extract, both with considerable amino acid composition, significantly increased the yeast population, while yeast nitrogen base (with or without amino acids) and ammonium sulfate had no affect on yeast abundance. These results suggest that organic nitrogen stimulate yeast community growth and development on the phylloplane of tall fescue, while carbohydrates, inorganic nitrogen, and non-nitrogenous nutrients have little positive effect.}, }
@article {pmid17483868, year = {2007}, author = {Surakasi, VP and Wani, AA and Shouche, YS and Ranade, DR}, title = {Phylogenetic analysis of methanogenic enrichment cultures obtained from Lonar Lake in India: isolation of Methanocalculus sp. and Methanoculleus sp.}, journal = {Microbial ecology}, volume = {54}, number = {4}, pages = {697-704}, pmid = {17483868}, issn = {0095-3628}, mesh = {*Culture Media ; DNA, Archaeal/analysis/isolation &amp; purification ; DNA, Ribosomal/analysis ; Fresh Water/chemistry/*microbiology ; Geologic Sediments/*microbiology ; Hydrogen-Ion Concentration ; India ; Methanomicrobiales/*classification/genetics/growth &amp; development/*isolation &amp; purification ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sodium Chloride ; }, abstract = {The diversity of methanogenic archaea in enrichment cultures established from the sediments of Lonar Lake (India), a soda lake having pH approximately 10, was investigated using 16S rDNA molecular phylogenetic approach. Methanogenic enrichment cultures were developed in a medium that simulated conditions of soda lake with three different substrates viz., H(2):CO(2), sodium acetate, and trimethylamine (TMA), at alkaline pH. Archaeal 16S rRNA clone libraries were generated from enrichment cultures and 13 RFLP groups were obtained. Representative sequence analysis of each RFLP group indicated that the majority of the 16S rRNA gene sequences were phylogenetically affiliated with uncultured Archaea. Some of the groups may belong to new archaeal genera or families. Three RFLP groups were related to Methanoculleus sp, while two related to Methanocalculus sp. 16S rRNA gene sequences found in Lonar Lake were different from sequences reported from other soda lakes and more similar to those of oil reservoirs, palm oil waste treatment digesters, and paddy fields. In culture-based studies, three isolates were obtained. Two of these were related to Methanoculleus sp. IIE1 and one to Methanocalculus sp. 01F97C. These results clearly show that the Lonar Lake ecosystem harbors unexplored methanogens.}, }
@article {pmid17482237, year = {2007}, author = {Muckian, L and Grant, R and Doyle, E and Clipson, N}, title = {Bacterial community structure in soils contaminated by polycyclic aromatic hydrocarbons.}, journal = {Chemosphere}, volume = {68}, number = {8}, pages = {1535-1541}, doi = {10.1016/j.chemosphere.2007.03.029}, pmid = {17482237}, issn = {0045-6535}, mesh = {*Bacteria/genetics/growth &amp; development ; Biomass ; DNA, Bacterial/genetics ; *Environmental Monitoring ; Ireland ; Polycyclic Aromatic Hydrocarbons/*analysis/chemistry ; Polymorphism, Restriction Fragment Length ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology/*standards ; Soil Pollutants/*analysis/chemistry ; Structure-Activity Relationship ; }, abstract = {Bacterial community structure was examined in polycyclic aromatic hydrocarbon (PAH) contaminated soil taken from a timber treatment facility in southern Ireland. Profiles of soil bacterial communities were generated using a molecular fingerprinting technique, terminal restriction fragment length polymorphism (TRFLP), and results were interpreted using sophisticated multivariate statistical analysis. Findings suggested that there was a correlation between PAH structure and bacterial community composition. Initial characterisation of soil from the timber treatment facility indicated that PAH contamination was unevenly distributed across the site. Bacterial community composition was correlated with the type of PAH present, with microbial community structure associated with soil contaminated with two-ringed PAHs only being distinctly different to communities in soils contaminated with multi-component PAH mixtures. Typically the number of bacterial ribotypes detected in samples did not appear to be adversely affected by the level of contamination.}, }
@article {pmid17481756, year = {2007}, author = {Mummey, DL and Rillig, MC}, title = {Evaluation of LSU rRNA-gene PCR primers for analysis of arbuscular mycorrhizal fungal communities via terminal restriction fragment length polymorphism analysis.}, journal = {Journal of microbiological methods}, volume = {70}, number = {1}, pages = {200-204}, doi = {10.1016/j.mimet.2007.04.002}, pmid = {17481756}, issn = {0167-7012}, mesh = {Biodiversity ; DNA Fingerprinting/*methods ; DNA, Fungal/chemistry/*genetics ; DNA, Ribosomal/chemistry/*genetics ; Fungi/*classification/genetics/isolation &amp; purification ; Genes, rRNA ; Molecular Sequence Data ; *Mycorrhizae ; Polymerase Chain Reaction/*methods ; *Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; }, abstract = {The efficacy of the LSU rDNA PCR primers FLR3 and FLR4 for discrimination of arbuscular mycorrhizal fungi communities via T-RFLP analysis was examined. Analysis of both public database and site-specific derived DNA sequences suggesting LSU rDNA-based T-RFLP analysis represents a valuable alternative for analysis of AMF communities.}, }
@article {pmid17475432, year = {2007}, author = {Enright, AM and Collins, G and O'Flaherty, V}, title = {Temporal microbial diversity changes in solvent-degrading anaerobic granular sludge from low-temperature (15 degrees C) wastewater treatment bioreactors.}, journal = {Systematic and applied microbiology}, volume = {30}, number = {6}, pages = {471-482}, doi = {10.1016/j.syapm.2007.03.005}, pmid = {17475432}, issn = {0723-2020}, mesh = {Anaerobiosis ; Bacteria/classification/genetics/*metabolism ; Bacteria, Anaerobic/metabolism ; Bioreactors/*microbiology ; Cold Temperature ; In Situ Hybridization, Fluorescence/methods ; *Industrial Microbiology ; Industrial Waste ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Temperature ; *Waste Disposal, Fluid ; }, abstract = {Anaerobic sludge granules were obtained from laboratory-scale anaerobic bioreactors used to treat pharmaceutical-like (methanol-, acetone- and propanol-contaminated) wastewater under low-temperature conditions (15 degrees C). The microbial diversity and diversity changes of the sludge samples were ascertained by applying 16S rRNA gene cloning and terminal restriction fragment length polymorphism (TRFLP) analyses, respectively, and using sludge samples from the inoculum, throughout and at the conclusion of the bioreactor trial. Data from genetic fingerprinting correlated well with those from physiological activity assays of the reactor biomass. Specifically, for example, TRFLP profiles indicated the dominance of hydrogenotrophic methanogens within the archaeal community, thus supporting the findings of specific methanogenic activity measurements. TRFLP data supported the hypothesis that the deviation between the replicated reactors, in terms of treatment efficiency, was associated with succession within the microbial communities present, and indicated that community development was linked to both operating temperature and wastewater composition. Fluorescence in situ hybridization (FISH) was also applied, to quantitatively assess the abundance of selected microbial groups, and revealed the underestimation of the abundance Methanosarcina by gene cloning analysis and demonstrated the spatial arrangement of these organisms within the architecture of the low-temperature solvent-degrading anaerobic biofilms.}, }
@article {pmid17473904, year = {2007}, author = {Sundset, MA and Praesteng, KE and Cann, IK and Mathiesen, SD and Mackie, RI}, title = {Novel rumen bacterial diversity in two geographically separated sub-species of reindeer.}, journal = {Microbial ecology}, volume = {54}, number = {3}, pages = {424-438}, pmid = {17473904}, issn = {0095-3628}, mesh = {Animals ; Bacteria/classification/*genetics/growth &amp; development ; Biodiversity ; *Genetic Variation ; Geography ; Molecular Sequence Data ; Norway ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Reindeer/*microbiology ; Rumen/*microbiology ; Sequence Analysis, DNA ; Svalbard ; }, abstract = {Svalbard reindeer (Rangifer tarandus platyrhynchus) live under austere nutritional conditions on the high-arctic archipelago of Svalbard, while semi-domesticated Norwegian reindeer (R. tarandus tarandus) migrate between lush coastal summer pastures and inland winter pastures with lichens on mainland Norway. Svalbard reindeer are known to have high rumen concentrations of cellulolytic bacteria, ranging from 15% of the viable population in summer to 35% in winter, compared to only 2.5% in Norwegian reindeer. Their rumen bacterial diversity was investigated through comparative analyses of 16S rRNA gene sequences (approximately 1.5 kb in length) generated from clone libraries (n = 121) and bacterial isolates (n = 51). LIBSHUFF comparisons of the composition of the two 16S rRNA libraries from Norwegian reindeer showed a significant effect of artificial feeding compared to natural pasture, but failed to yield significant differences between libraries from Norwegian reindeer and Svalbard reindeer. The combined sequences from reindeer were not significantly different from those reported in wild Thompson's gazelle in Kenya but did differ from those reported in domestic cattle in Japan. A total of 90 distinct operational taxonomic units (OTUs) were identified by employing a criterion of 97% similarity, while the Chao1 index estimated the reindeer bacterial rumen population richness at 698 OTUs. The majority of the clone library sequences (92.5%) represented novel strains with <97% identity to any known sequence in the public database, most of them affiliated with the bacterial phylum Firmicutes (low G+C Gram-positives) related to the order Clostridiales (76.7%), while Gram-negative bacteria in the Bacteriodales (Prevotella-Bacteroides group) contributed to 22.5%. Also, six of the isolates were putatively novel strains, possibly representing new species in the Clostridium subphylum (cluster XIVa), Actinomyces and Butyrivibrio.}, }
@article {pmid17472645, year = {2007}, author = {van der Wielen, PW and Heijs, SK}, title = {Sulfate-reducing prokaryotic communities in two deep hypersaline anoxic basins in the Eastern Mediterranean deep sea.}, journal = {Environmental microbiology}, volume = {9}, number = {5}, pages = {1335-1340}, doi = {10.1111/j.1462-2920.2006.01210.x}, pmid = {17472645}, issn = {1462-2912}, mesh = {Bacteria, Anaerobic/*classification/genetics ; Deltaproteobacteria/*classification/genetics ; Mediterranean Sea ; Molecular Sequence Data ; Seawater/chemistry/*microbiology ; Sodium Chloride/chemistry ; Sulfur-Reducing Bacteria/*classification/genetics ; }, abstract = {In the Eastern Mediterranean Sea, deep hypersaline anoxic basins (DHABs) and deep-sea sediment contain anoxic environments where sulfate reduction is an important microbial metabolic process. The objective of this study was to characterize the sulfate-reducing community in the brine and interface of the DHABs L'Atalante and Urania based on a phylogenetic analysis of the dissimilatory sulfite reductase gene (dsrA). Results demonstrated that the sulfate-reducing community was diverse, except for the sulfidogenic brine of the Urania basin. The similarity of the dsrA sequences between different environments was very low demonstrating that each environment had a unique sulfate-reducing community. Sequences had 67.6-93.3% similarity to dsrA sequences from GenBank database and were mostly related to the delta-proteobacteria. Each environment was dominated by a different family within the delta-proteobacteria except for the Urania interface, which was dominated by sequences related to the Gram-positive Peptococcaceae. We conclude that sulfate-reducing communities inhabiting the L'Atalante and Urania basins are highly diverse with low similarities to each other and contain a sulfate-reducing species composition that is very different from sulfate-reducing species compositions in previously studied ecosystems.}, }
@article {pmid17472627, year = {2007}, author = {Flint, HJ and Duncan, SH and Scott, KP and Louis, P}, title = {Interactions and competition within the microbial community of the human colon: links between diet and health.}, journal = {Environmental microbiology}, volume = {9}, number = {5}, pages = {1101-1111}, doi = {10.1111/j.1462-2920.2007.01281.x}, pmid = {17472627}, issn = {1462-2912}, mesh = {Anaerobiosis/physiology ; Colon/*microbiology/physiology ; *Diet ; Dietary Carbohydrates/*metabolism ; *Ecosystem ; Feeding Behavior/physiology ; Health Status ; Phylogeny ; Probiotics ; }, abstract = {The microbiota of the human intestinal tract play an important role in health, in particular by mediating many of the effects of diet upon gut health. Surveys of 16S rRNA sequence diversity in the human colon have emphasized the low proportion of sequences that match cultured bacterial species. This may reflect limited recent effort on cultivation rather than inherent unculturability, however, as anaerobic isolation methods can apparently recover a wide range of the diversity found. A combination of information from representative cultures, molecular tools for enumeration and tracking of bacterial metabolites offers the most powerful route to understanding the roles played by different groups of bacteria in the gut ecosystem. Progress is being made for example in defining key functional groups including primary colonizers of insoluble dietary substrates, and major contributors to metabolites such as butyrate that influence the health of the gut mucosa. There is increasing evidence that bacterial populations in the large intestine respond to changes in diet, in particular to the type and quantity of dietary carbohydrate. A general consequence of increased carbohydrate consumption is to reduce the pH of the gut lumen, which is likely to play a major role in determining bacterial metabolism and competition. Oligosaccharides used as dietary prebiotics must inevitably have complex effects upon the bacterial community that include non-target organisms and the consequences of metabolic cross-feeding and changes in the gut environment.}, }
@article {pmid17468963, year = {2007}, author = {Shinzato, N and Watanabe, I and Meng, XY and Sekiguchi, Y and Tamaki, H and Matsui, T and Kamagata, Y}, title = {Phylogenetic analysis and fluorescence in situ hybridization detection of archaeal and bacterial endosymbionts in the anaerobic ciliate trimyema compressum.}, journal = {Microbial ecology}, volume = {54}, number = {4}, pages = {627-636}, pmid = {17468963}, issn = {0095-3628}, mesh = {Anaerobiosis ; Animals ; Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Ciliophora/growth &amp; development/*microbiology ; DNA, Archaeal/analysis/isolation &amp; purification ; DNA, Bacterial/analysis/isolation &amp; purification ; In Situ Hybridization, Fluorescence ; Methanobrevibacter/classification/genetics/growth &amp; development/*isolation &amp; purification ; Molecular Sequence Data ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {The anaerobic free-living ciliate, Trimyema compressum, is known to harbor both methanogenic archaeal and bacterial symbionts in the cytoplasm. To clarify their phylogenetic belongings, a full-cycle rRNA approach was applied to this symbiosis. Phylogenetic analysis showed that the methanogenic symbiont was related to Methanobrevibacter arboriphilicus, which was distantly related to symbionts found in other Trimyema species. This result suggested that Trimyema species do not require very specific methanogenic symbionts, and symbiont replacement could have occurred in the history of Trimyema species. On the other hand, the bacterial symbiont was located near the lineage of the family Syntrophomonadaceae in the phylum Firmicutes. The sequence similarity between the bacterial symbiont and the nearest species was 85%, indicating that bacterial symbionts may be specific to the Trimyema species. The elimination of bacterial symbionts from the ciliate cell by antibiotic treatment resulted in considerably decreased host growth. However, it was not restored by stigmasterol addition (<2 microg ml(-1)), which was different from the previous report that showed that the symbiont-free strain required exogenous sterols for growth. In addition, the decline of host growth was not accompanied by host metabolism shift toward the formation of more reduced products, which suggested that the contribution of bacterial symbionts to the host ciliate was not a dispose of excessive reducing equivalent arising from the host's fermentative metabolism as methanogenic symbionts do. This study showed that bacterial symbionts make a significant contribution to the host ciliate by an unknown function and suggested that interactions between bacterial symbionts and T. compressum are more complicated than hitherto proposed.}, }
@article {pmid17468962, year = {2007}, author = {Abril, AB and Bucher, EH}, title = {Genetic diversity of fungi occurring in nests of three Acromyrmex leaf-cutting ant species from Córdoba, Argentina.}, journal = {Microbial ecology}, volume = {54}, number = {3}, pages = {417-423}, pmid = {17468962}, issn = {0095-3628}, mesh = {Animals ; Ants/*microbiology/physiology ; Argentina ; DNA, Fungal/analysis/genetics ; Fungi/classification/*genetics/isolation &amp; purification ; *Genetic Variation ; Nesting Behavior ; Phylogeny ; Plant Leaves/parasitology ; Species Specificity ; }, abstract = {It is assumed in current literature that the fungus garden cultivated by leaf-cutting ants consists of a single fungus species, the putative mutualistic fungus. However, most studies report a very high rate of fungi contamination (fungi isolated from fungus gardens that are considered not to be the mutualistic fungus). In this article, we report a genetic similarity analysis of all fungi (regardless of their mutualistic condition) isolated from 16 fungus gardens of three Acromyrmex species in Córdoba, Argentina, using intersimple sequence repeat (ISSR) as genetic markers. We isolated 60 clones, of which the three primers employed yielded 53 loci. The patterns revealed a high interclone polymorphism, with a few bands shared by the clones. Of all possible pairwise comparisons, 99% showed a genetic similarity (S) lower than 0.5, the threshold level assumed for fungus Operational Taxonomy Unit (OTU). We found more than one fungus OTU in all studied nests (range 2-11). Cumulative number of OTUs increased linearly with the number of nests sampled. The number of fungus OTUs common to both ant species and sites was very small. We did not find a core group composed of few very common OTUs, as expected if a set of truly mutualistic OTU was present. A simple explanation for the high number of OTUs found is that they are regular components of the fungus garden, which may be used as food source by the ants.}, }
@article {pmid17468247, year = {2007}, author = {Rincon, MT and Cepeljnik, T and Martin, JC and Barak, Y and Lamed, R and Bayer, EA and Flint, HJ}, title = {A novel cell surface-anchored cellulose-binding protein encoded by the sca gene cluster of Ruminococcus flavefaciens.}, journal = {Journal of bacteriology}, volume = {189}, number = {13}, pages = {4774-4783}, pmid = {17468247}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics/metabolism ; Cellulose/*metabolism ; Electrophoresis, Gel, Two-Dimensional ; Electrophoresis, Polyacrylamide Gel ; Genes, Bacterial ; Models, Biological ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Protein Binding ; Recombinant Proteins/metabolism ; Ruminococcus/*genetics/metabolism ; Sequence Homology, Amino Acid ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {Ruminococcus flavefaciens produces a cellulosomal enzyme complex, based on the structural proteins ScaA, -B, and -C, that was recently shown to attach to the bacterial cell surface via the wall-anchored protein ScaE. ScaA, -B, -C, and -E are all cohesin-bearing proteins encoded by linked genes in the sca cluster. The product of an unknown open reading frame within the sca cluster, herein designated CttA, is similar in sequence at its C terminus to the corresponding region of ScaB, which contains an X module together with a dockerin sequence. The ScaB-XDoc dyad was shown previously to interact tenaciously with the cohesin of ScaE. Likewise, avid binding was confirmed between purified recombinant fragments of the CttA-XDoc dyad and the ScaE cohesin. In addition, the N-terminal regions of CttA were shown to bind to cellulose, thus suggesting that CttA is a cell wall-anchored, cellulose-binding protein. Proteomic analysis showed that the native CttA protein (approximately 130 kDa) corresponds to one of the three most abundant polypeptides binding tightly to insoluble cellulose in cellulose-grown R. flavefaciens 17 cultures. Interestingly, this protein was also detected among cellulose-bound proteins in the related strain R. flavefaciens 007C but not in a mutant derivative, 007S, that was previously shown to have lost the ability to grow on dewaxed cotton fibers. In R. flavefaciens, the presence of CttA on the cell surface is likely to provide an important mechanism for substrate binding, perhaps compensating for the absence of an identified cellulose-binding module in the major cellulosomal scaffolding proteins of this species.}, }
@article {pmid17467280, year = {2007}, author = {Sabharwal, N and Icoz, I and Saxena, D and Stotzky, G}, title = {Release of the recombinant proteins, human serum albumin, beta-glucuronidase, glycoprotein B from human cytomegalovirus, and green fluorescent protein, in root exudates from transgenic tobacco and their effects on microbes and enzymatic activities in soil.}, journal = {Plant physiology and biochemistry : PPB}, volume = {45}, number = {6-7}, pages = {464-469}, doi = {10.1016/j.plaphy.2007.03.009}, pmid = {17467280}, issn = {0981-9428}, mesh = {Animals ; Cytomegalovirus/*metabolism ; Eukaryota/metabolism ; Glucuronidase/*genetics/metabolism ; Green Fluorescent Proteins/*genetics/metabolism ; Humans ; Kinetics ; Plant Roots/*metabolism ; Plants, Genetically Modified ; Recombinant Proteins/metabolism ; Serum Albumin/*genetics/metabolism ; Soil/parasitology ; Nicotiana/enzymology/*genetics/metabolism ; }, abstract = {We determined the release in root exudates of human serum albumin (HSA), beta-glucuronidase (GUS), glycoprotein B (gB) from human cytomegalovirus, and green fluorescent protein (GFP) from genetically modified transgenic tobacco expressing the genes for these proteins in hydroponic culture and non-sterile soil. GUS, gB, and GFP were expressed in the plant but were not released in root exudates, whereas HSA was both expressed in the plant and released in root exudates, as shown by a 66.5-kDa band on SDS-PAGE and Western blot and confirmed by ELISA. Root exudates from GUS and gB plants showed no bands that could be attributed to these proteins on SDS-PAGE, and root exudates from GFP plants showed no fluorescence. The concentration of HSA in root exudates was estimated to be 0.021 ng ml(-1), whereas that in the plant biomass was estimated to be 0.087 ng ml(-1). The concentration of HSA in soil was estimated to be 0.049 ng g(-1). No significant differences in the number of microorganisms and the activity of selected enzymes were observed between rhizosphere soil of non-modified and HSA tobacco.}, }
@article {pmid17464864, year = {2007}, author = {Nyberg, SD and Osterblad, M and Hakanen, AJ and Huovinen, P and Jalava, J and , }, title = {Detection and molecular genetics of extended-spectrum beta-lactamases among cefuroxime-resistant Escherichia coli and Klebsiella spp. isolates from Finland, 2002-2004.}, journal = {Scandinavian journal of infectious diseases}, volume = {39}, number = {5}, pages = {417-424}, doi = {10.1080/00365540601105731}, pmid = {17464864}, issn = {1651-1980}, mesh = {Anti-Bacterial Agents/pharmacology ; Cefuroxime/pharmacology ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/*drug effects/*genetics/isolation &amp; purification ; Finland/epidemiology ; Humans ; Klebsiella/*drug effects/*genetics/isolation &amp; purification ; Microbial Sensitivity Tests ; beta-Lactamases/classification/*genetics ; }, abstract = {Extended-spectrum beta-lactamase (ESBL) producing Escherichia coli and Klebsiella spp. isolates are spreading and becoming an increasing problem concerning treatment, diagnostics and hospital hygiene. We wanted to discover which genotypes are occurring in Finland and to assess the CLSI screening method. The isolates were collected from 26 laboratories during a 3-y period from 2002 to 2004. We studied the zone diameters by disk diffusion according to CLSI recommendations. ESBL genes were detected by PCR and the TEM and SHV genes were sequenced traditionally, while the CTX-M isolates were analysed with pyrosequencing. Of the 402 isolates included in the study, 269 (67%) were confirmed to be ESBL producers according to the CLSI criteria. The CTX-M genes were the most prevalent, especially the combination of a CTX-M-1-group and a TEM-1 gene. In our material there were few isolates that had an ESBL gene but were negative in the CLSI ESBL confirmatory test. During recent y especially the CTX-M producing isolates have increased in Europe and now they are also found in Finland with increasing prevalence.}, }
@article {pmid17457639, year = {2007}, author = {Omelon, CR and Pollard, WH and Ferris, FG}, title = {Inorganic species distribution and microbial diversity within high Arctic cryptoendolithic habitats.}, journal = {Microbial ecology}, volume = {54}, number = {4}, pages = {740-752}, pmid = {17457639}, issn = {0095-3628}, mesh = {Aluminum/analysis ; Arctic Regions ; Biodiversity ; Calcium/analysis ; Cyanobacteria/classification/*isolation &amp; purification ; *Ecosystem ; Eukaryota/classification/*isolation &amp; purification ; Fungi/classification/*isolation &amp; purification ; Geological Phenomena ; Geology ; Hydrogen-Ion Concentration ; Iron/analysis ; Magnesium/analysis ; Quartz/*chemistry ; Silicon/analysis ; }, abstract = {Cryptoendolithic habitats in the Canadian high Arctic are associated with a variety of microbial community assemblages, including cyanobacteria, algae, and fungi. These habitats were analyzed for the presence of metal ions by sequential extraction and evaluated for relationships between these and the various microorganisms found at each site using multivariate statistical methods. Cyanobacteria-dominated communities exist under higher pH conditions with elevated concentrations of calcium and magnesium, whereas communities dominated by fungi and algae are characterized by lower pH conditions and higher concentrations of iron, aluminum, and silicon in the overlying surfaces. These results suggest that the activity of the dominant microorganisms controls the pH of the surrounding environment, which in turn dictates rates of weathering or the possibility for surface crust formation, both ultimately deciding the structure of microbial diversity for each cryptoendolithic habitat.}, }
@article {pmid17450460, year = {2008}, author = {Domozych, DS and Domozych, CR}, title = {Desmids and biofilms of freshwater wetlands: development and microarchitecture.}, journal = {Microbial ecology}, volume = {55}, number = {1}, pages = {81-93}, pmid = {17450460}, issn = {0095-3628}, mesh = {Biofilms/*growth &amp; development ; Chlorophyta/classification/*growth &amp; development/ultrastructure ; Cyanobacteria/*growth &amp; development/ultrastructure ; *Ecosystem ; Fresh Water/chemistry/*microbiology ; Microscopy, Confocal ; New York ; *Wetlands ; }, abstract = {Freshwater wetlands constitute important ecosystems, and their benthic, attached microbial communities, including biofilms, represent key habitats that contribute to primary productivity, nutrient cycling, and substrate stabilization. In many wetland biofilms, algae constitute significant parts of the microbial population, yet little is known about their activities in these communities. An analysis of wetland biofilms from the Adirondack region of New York (USA) was performed with special emphasis on desmids, a group of evolutionarily advanced green algae commonly found in these habitats. Desmids constituted as much as 23.7% of the total algal and cyanobacterial flora of the biofilms during the July and August study periods. These algae represented some of the first eukaryotes to colonize new substrates, and during July their numbers correlated with fluctuations in general biofilm parameters such as biofilm thickness and dry weight as well as total carbohydrate. Significant numbers of bacteria were associated with both the EPS sheaths and cell wall surfaces of the desmids. Colonization of new substrates and development of biofilms were rapid and were followed by various fluctuations in microbial community structure over the short- and long-term observations. In addition to desmids, diatoms, filamentous green algae and transient non-motile phases of flagellates represented the photosynthetic eukaryotes of these biofilms.}, }
@article {pmid17450396, year = {2007}, author = {Wang, CM and Shyu, CL and Ho, SP and Chiou, SH}, title = {Species diversity and substrate utilization patterns of thermophilic bacterial communities in hot aerobic poultry and cattle manure composts.}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {1-9}, pmid = {17450396}, issn = {0095-3628}, mesh = {Animals ; Bacteria/classification/isolation &amp; purification/*metabolism ; *Biodiversity ; Carbon/metabolism ; Cattle/*microbiology ; Hot Temperature ; Manure/*microbiology ; Phylogeny ; Poultry/*microbiology ; *Soil Microbiology ; Taiwan ; }, abstract = {This study investigated the species diversity and substrate utilization patterns of culturable thermophilic bacterial communities in hot aerobic poultry and cattle manure composts by coupling 16S rDNA analysis with Biolog data. Based on the phylogenetic relationships of 16S rDNA sequences, 34 thermophilic (grown at 60 degrees C) bacteria isolated during aerobic composting of poultry manure and cattle manure were classified as Bacillus licheniformis, B. atrophaeus, Geobacillus stearothermophilus, G. thermodenitrificans, Brevibacillus thermoruber, Ureibacillus terrenus, U. thermosphaericus, and Paenibacillus cookii. In this study, B. atrophaeus, Br. thermoruber, and P. cookii were recorded for the first time in hot compost. Physiological profiles of these bacteria, obtained from the Biolog Gram-positive (GP) microplate system, were subjected to principal component analysis (PCA). All isolates were categorized into eight different PCA groups based on their substrate utilization patterns. The bacterial community from poultry manure compost comprised more divergent species (21 isolates, seven species) and utilized more diverse substrates (eight PCA groups) than that from cattle manure compost (13 isolates, five species, and four PCA groups). Many thermophilic bacteria isolated in this study could use a variety of carboxylic acids. Isolate B110 (from poultry manure compost), which is 97.6% similar to U. terrenus in its 16S rDNA sequence, possesses particularly high activity in utilizing a broad spectrum of substrates. This isolate may have potential applications in industry.}, }
@article {pmid17450395, year = {2007}, author = {Mesbah, NM and Abou-El-Ela, SH and Wiegel, J}, title = {Novel and unexpected prokaryotic diversity in water and sediments of the alkaline, hypersaline lakes of the Wadi An Natrun, Egypt.}, journal = {Microbial ecology}, volume = {54}, number = {4}, pages = {598-617}, pmid = {17450395}, issn = {0095-3628}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Archaeal/analysis ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Ecosystem ; Egypt ; Euryarchaeota/*classification/genetics/isolation &amp; purification ; Fresh Water/chemistry/*microbiology ; Genes, rRNA ; Genetic Variation ; Geologic Sediments/*microbiology ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sodium Chloride/*chemistry ; }, abstract = {The phylogenetic diversity of the bacterial and archaeal community in the water and sediments of three large lakes of the Wadi An Natrun was investigated using 16S rRNA clone libraries. The bacterial community was diverse: 769 clones formed 345 operational taxonomic units (OTUs) defined at 99% 16S rRNA sequence identity. The bacterial community in both the water and sediments of the lakes was dominated by clones affiliated with the low G + C Gram-type-positive group, alpha-proteobacteria, and Bacteroidetes, (11-39, 11-30, and 10-37% of OTUs observed, respectively), patterns that have been observed in previously described alkaline, athalassohaline systems. However, a relatively high proportion of Firmicutess-related clones in the water of the lakes and alpha-proteobacteria in the sediments was observed. The bacterial community composition of the water and sediment of the same lake and of different lakes was significantly different (p < 0.05). Operational taxonomic units related to the gamma-proteobacteria were more abundant in the sediment of Lake Fazda, whereas the sediment of Lake UmRisha was dominated by members of the delta-proteobacteria. The proportion of gamma-proteobacterial and Bacteroidetes-affiliated OTUs were predominant in the water of Lake UmRisha and differed significantly from other lake waters (chi-squared analysis, p < or = 0.01). The more oxygenated and dilute nature of Lake Hamra was reflected in its microbial community composition, with the abundance of Bacillales sequences in the water, the absence of Halanaerobiales, Clostridiales, and Archaea in the water, and the presence of representatives of more phyla such as the Actinobacteria, Spirochaetes, and Verrucomicrobia. The archaeal community composition appeared less diverse: 589 clones resulted in 198 OTUs defined at 99% 16S rRNA sequence identity, and all sequences fell into the phylum Euryarchaeota. Phylogenetic analysis showed that many of the sequences were distantly related (83-90% 16S rRNA sequence identity) to cultured and uncultured archaea, with many clones forming clusters that branched deeply within the Euryarchaeota. Forty-two and 53% of the bacterial and archaeal clones had less than 90% 16S rRNA sequence identity to previously described sequences. This indicates that the water and sediments of the Wadi An Natrun harbor a unique and novel prokaryotic diversity that is different from what has been described among other alkaline, athalassohaline lakes.}, }
@article {pmid17450394, year = {2007}, author = {Artz, RR and Anderson, IC and Chapman, SJ and Hagn, A and Schloter, M and Potts, JM and Campbell, CD}, title = {Changes in fungal community composition in response to vegetational succession during the natural regeneration of cutover peatlands.}, journal = {Microbial ecology}, volume = {54}, number = {3}, pages = {508-522}, pmid = {17450394}, issn = {0095-3628}, mesh = {Crops, Agricultural/growth &amp; development ; DNA, Ribosomal Spacer/chemistry/genetics ; *Ecosystem ; Electrophoresis/methods ; Fungi/classification/*genetics/*growth &amp; development ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Soil ; *Soil Microbiology ; Time Factors ; }, abstract = {Despite the importance of peatlands as a major store of sequestered carbon and the role of fungi in releasing sequestered C, we know little about the community structure of fungi in peatlands. We investigated these across a gradient of naturally regenerating peatland vegetation using denaturing gradient gel electrophoresis (DGGE) and clone libraries of fragments of the fungal rRNA internal transcribed spacer (ITS) region. Significant changes in the fungal community structure of peat samples at different stages of regeneration were observed, which relate to the composition of the vegetation recolonizing these sites. Cloning and sequence analysis also demonstrated a potential shift in the relative abundance of the main fungal phyla. Some of the clones identified to genus level were highly related to fungi known to play a role in the degradation of plant litter or wood in similar ecosystems and/or form mycorrhizal associations. In addition, several fungal isolates highly related to peat clones were obtained, and their enzymic capacity to degrade structural plant tissues was assessed. Together, these results suggest that the fungal community composition of peat may be an important indicator of the status of regeneration and potential carbon sequestration of cutover peatlands.}, }
@article {pmid17450393, year = {2007}, author = {Falcón, LI and Cerritos, R and Eguiarte, LE and Souza, V}, title = {Nitrogen fixation in microbial mat and stromatolite communities from Cuatro Cienegas, Mexico.}, journal = {Microbial ecology}, volume = {54}, number = {2}, pages = {363-373}, pmid = {17450393}, issn = {0095-3628}, mesh = {Bacteria/classification/*metabolism ; *Ecosystem ; Mexico ; Molecular Sequence Data ; Nitrogen Fixation ; Phylogeny ; }, abstract = {Nitrogen fixation (nitrogenase activity, NA) of a microbial mat and a living stromatolite from Cuatro Cienegas, Mexico, was examined over spring, summer, and winter of 2004. The goal of the study was to characterize the diazotrophic community through molecular analysis of the nifH gene and using inhibitors of sulfate reduction and oxygenic and anoxygenic photosynthesis. We also evaluated the role of ultraviolet radiation on the diazotrophic activity of the microbial communities. Both microbial communities showed patterns of NA with maximum rates during the day that decreased significantly with 3-3,4-dichlorophenyl-1',1'-dimethylurea, suggesting the potential importance of heterocystous cyanobacteria. There is also evidence of NA by sulfur-reducing bacteria in both microbial communities suggested by the negative effect exerted by the addition of sodium molybdate. Elimination of infrared and ultraviolet radiation had no effect on NA. Both microbial communities had nifH sequences that related to group I, including cyanobacteria and purple sulfur and nonsulfur bacteria, as well as group II nitrogenases, including sulfur reducing and green sulfur bacteria.}, }
@article {pmid17450392, year = {2007}, author = {Batisson, I and Pesce, S and Besse-Hoggan, P and Sancelme, M and Bohatier, J}, title = {Isolation and characterization of diuron-degrading bacteria from lotic surface water.}, journal = {Microbial ecology}, volume = {54}, number = {4}, pages = {761-770}, pmid = {17450392}, issn = {0095-3628}, mesh = {Biodegradation, Environmental ; Culture Media ; DNA, Bacterial/analysis/isolation &amp; purification ; Diuron/*metabolism ; Electrophoresis, Polyacrylamide Gel/methods ; Herbicides/*metabolism ; Molecular Sequence Data ; Phylogeny ; *Pseudomonas/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Sequence Analysis, DNA ; *Stenotrophomonas/classification/genetics/isolation &amp; purification ; Water Pollutants/metabolism ; }, abstract = {The bacterial community structure of a diuron-degrading enrichment culture from lotic surface water samples was analyzed and the diuron-degrading strains were selected using a series of techniques combining temporal temperature gradient gel electrophoresis (TTGE) of 16 S rDNA gene V1-V3 variable regions, isolation of strains on agar plates, colony hybridization methods, and biodegradation assays. The TTGE fingerprints revealed that diuron had a strong impact on bacterial community structure and highlighted both diuron-sensitive and diuron-adapted bacterial strains. Two bacterial strains, designated IB78 and IB93 and identified as belonging to Pseudomonas sp. and Stenotrophomonas sp., were isolated and shown to degrade diuron in pure resting cells in a first-order kinetic reaction during the first 24 h of incubation with no 3,4-DCA detected. The percentages of degradation varied from 25% to 60% for IB78 and 20% to 65% for IB93 and for a diuron concentration range from 20 mg/L to 2 mg/L, respectively. It is interesting to note that diuron was less degraded by single isolates than by mixed resting cells, thereby underlining a cumulative effect between these two strains. To the best of our knowledge, this is the first report of diuron-degrading strains isolated from lotic surface water.}, }
@article {pmid17448158, year = {2007}, author = {Ferguson, AS and Huang, WE and Lawson, KA and Doherty, R and Gibert, O and Dickson, KW and Whiteley, AS and Kulakov, LA and Thompson, IP and Kalin, RM and Larkin, MJ}, title = {Microbial analysis of soil and groundwater from a gasworks site and comparison with a sequenced biological reactive barrier remediation process.}, journal = {Journal of applied microbiology}, volume = {102}, number = {5}, pages = {1227-1238}, doi = {10.1111/j.1365-2672.2007.03398.x}, pmid = {17448158}, issn = {1364-5072}, mesh = {Bacteria/*classification/genetics/growth &amp; development ; Biodegradation, Environmental ; *Ecosystem ; Polycyclic Aromatic Hydrocarbons ; Polymerase Chain Reaction ; *Soil Microbiology ; Soil Pollutants/*metabolism ; *Water Microbiology ; }, abstract = {AIMS: To investigate the distribution of a polymicrobial community of biodegradative bacteria in (i) soil and groundwater at a former manufactured gas plant (FMGP) site and (ii) in a novel SEquential REactive BARrier (SEREBAR) bioremediation process designed to bioremediate the contaminated groundwater.<br><br>METHODS AND RESULTS: Culture-dependent and culture-independent analyses using denaturing gradient gel electrophoresis (DGGE) and polymerase chain reaction (PCR) for the detection of 16S ribosomal RNA gene and naphthalene dioxygenase (NDO) genes of free-living (planktonic groundwater) and attached (soil biofilm) samples from across the site and from the SEREBAR process was applied. Naphthalene arising from groundwater was effectively degraded early in the process and the microbiological analysis indicated a dominant role for Pseudomonas and Comamonas in its degradation. The microbial communities appeared highly complex and diverse across both the sites and in the SEREBAR process. An increased population of naphthalene degraders was associated with naphthalene removal.<br><br>CONCLUSION: The distribution of micro-organisms in general and naphthalene degraders across the site was highly heterogeneous. Comparisons made between areas contaminated with polycyclic aromatic hydrocarbons (PAH) and those not contaminated, revealed differences in the microbial community profile. The likelihood of noncultured bacteria being dominant in mediating naphthalene removal was evident.<br><br>This work further emphasizes the importance of both traditional and molecular-based tools in determining the microbial ecology of contaminated sites and highlights the role of noncultured bacteria in the process.}, }
@article {pmid17448155, year = {2007}, author = {Louis, P and Scott, KP and Duncan, SH and Flint, HJ}, title = {Understanding the effects of diet on bacterial metabolism in the large intestine.}, journal = {Journal of applied microbiology}, volume = {102}, number = {5}, pages = {1197-1208}, doi = {10.1111/j.1365-2672.2007.03322.x}, pmid = {17448155}, issn = {1364-5072}, mesh = {Bacteria, Anaerobic/classification/growth &amp; development/*metabolism ; Butyrates/metabolism ; Colon/metabolism/*microbiology ; Dietary Carbohydrates/*metabolism ; Fermentation ; Humans ; Models, Biological ; Propionates/metabolism ; }, abstract = {Recent analyses of ribosomal RNA sequence diversity have demonstrated the extent of bacterial diversity in the human colon, and have provided new tools for monitoring changes in the composition of the gut microbial community. There is now an excellent opportunity to correlate ecological niches and metabolic activities with particular phylogenetic groups among the microbiota of the human gut. Bacteria that associate closely with particulate material and surfaces in the gut include specialized primary degraders of insoluble substrates, including resistant starch, plant structural polysaccharides and mucin. Butyrate-producing bacteria found in human faeces belong mainly to the clostridial clusters IV and XIVa. In vitro and in vivo evidence indicates that a group related to Roseburia and Eubacterium rectale plays a major role in mediating the butyrogenic effect of fermentable dietary carbohydrates. Additional cluster XIVa species can convert lactate to butyrate, while some members of the clostridial cluster IX convert lactate to propionate. The metabolic outputs of the gut microbial community depend not only on available substrate, but also on the gut environment, with pH playing a major role. Better understanding of the colonic microbial ecosystem will help to explain and predict the effects of dietary additives, including nondigestible carbohydrates, probiotics and prebiotics.}, }
@article {pmid17446886, year = {2007}, author = {Neufeld, JD and Vohra, J and Dumont, MG and Lueders, T and Manefield, M and Friedrich, MW and Murrell, JC}, title = {DNA stable-isotope probing.}, journal = {Nature protocols}, volume = {2}, number = {4}, pages = {860-866}, doi = {10.1038/nprot.2007.109}, pmid = {17446886}, issn = {1750-2799}, mesh = {Carbon Isotopes ; Centrifugation, Density Gradient/*methods ; DNA/analysis/chemistry/*isolation &amp; purification ; DNA, Bacterial/analysis/isolation &amp; purification ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Stable-isotope probing is a method used in microbial ecology that provides a means by which specific functional groups of organisms that incorporate particular substrates are identified without the prerequisite of cultivation. Stable-isotope-labeled carbon (13C) or nitrogen (15N) sources are assimilated into microbial biomass of environmental samples. Separation and molecular analysis of labeled nucleic acids (DNA or RNA) reveals phylogenetic and functional information about the microorganisms responsible for the metabolism of a particular substrate. Here, we highlight general guidelines for incubating environmental samples with labeled substrate and provide a detailed protocol for separating labeled DNA from unlabeled community DNA. The protocol includes a modification of existing published methods, which maximizes the recovery of labeled DNA from CsCl gradients. The separation of DNA and retrieval of unlabeled and labeled fractions can be performed in 4-5 days, with much of the time being committed to the ultracentrifugation step.}, }
@article {pmid17446884, year = {2007}, author = {Whiteley, AS and Thomson, B and Lueders, T and Manefield, M}, title = {RNA stable-isotope probing.}, journal = {Nature protocols}, volume = {2}, number = {4}, pages = {838-844}, doi = {10.1038/nprot.2007.115}, pmid = {17446884}, issn = {1750-2799}, mesh = {Carbon Isotopes ; Centrifugation, Density Gradient/*methods ; RNA, Bacterial/analysis/isolation &amp; purification ; RNA, Ribosomal/analysis/chemistry/*isolation &amp; purification ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {At the heart of microbial ecology lies a true scientific dichotomy. On the one hand, we know microbes are responsible for processes on which all other life on Earth is dependent; their removal would mean the cessation of all known life. However, in opposition, the majority of extant microbial species in natural environments have never been cultured or studied in a laboratory as living organisms. Owing to these factors, the question of "who does what?" has been a major barrier to understanding how microbially mediated ecosystem level events occur. Recently, the use of stable isotopes (13C) to trace carbon from specific substrates into microbes that assimilate carbon from that substrate has significantly advanced our understanding of the relationship between environmental processes and microbial phylogeny.}, }
@article {pmid17436116, year = {2008}, author = {Nix-Stohr, S and Moshe, R and Dighton, J}, title = {Effects of propagule density and survival strategies on establishment and growth: further investigations in the phylloplane fungal model system.}, journal = {Microbial ecology}, volume = {55}, number = {1}, pages = {38-44}, pmid = {17436116}, issn = {0095-3628}, mesh = {Alternaria/*growth &amp; development/physiology ; Ascomycota/*growth &amp; development/physiology ; Ecosystem ; Models, Biological ; Penicillium/*growth &amp; development/physiology ; Plant Diseases/microbiology ; Plant Leaves/microbiology ; Population Density ; Spores, Fungal/growth &amp; development ; Vaccinium macrocarpon/*microbiology ; Xylariales/*growth &amp; development/*pathogenicity/physiology ; }, abstract = {This work builds on an earlier culture study where we determined that species diversity of competing saprotrophic phyllpolane fungi had only a negligible effect on the establishment and coexistence of a target fungus, Pestalotia vaccinii. Here, we explore preliminary evidence suggesting that spore density is a more important contributing factor to colonization and coexistence. We examine the influence of propagule density in vitro on establishment and growth of select members of the phylloplane of Vaccinium macrocarpon (American cranberry). To evaluate the response of the weak pathogen P. vaccinii to changes in competitors spore density, we chose saprotrophs from the previous investigation that had the greatest inhibitory effect on the establishment of P. vaccinii (Curvularia lunata), an intermediate inhibitory effect (Alternaria alternata) and the least inhibitory effect (Penicillium sp.). A constant target spore concentration of 50 viable spores of P. vaccinii was pit against densities of the three individual competitors ranging between 12 and 200 spores. As viable propagule density increased, establishment and coexistence of P. vaccinii significantly decreased, with C. lunata and A. alternata decreasing the growth of P. vaccinii more than Penicillium sp. Concomitantly, both C. lunata and Penicillium sp. were not significantly affected by overall spore density but were significantly affected by the presence of P. vaccinii. A. alternata, on the other hand, was not significantly influenced by the presence of P. vaccinii but was significantly affected by overall spore density. An in vitro investigation into the effect of interspecific competition on mycelial growth suggests how different survival strategies and community assembly rules might influence both growth and development. Growth of P. vaccinii was significantly less when interacting with C. lunata than when interacting with either A. alternata or Penicillium sp. Conversely, P. vaccinii had the greatest effect on the growth of C. lunata, less of an effect on the growth of A. alternata, and the least effect on Penicillium sp.}, }
@article {pmid17436031, year = {2007}, author = {Field, D and Kyrpides, N}, title = {The positive role of the ecological community in the genomic revolution.}, journal = {Microbial ecology}, volume = {53}, number = {3}, pages = {507-511}, pmid = {17436031}, issn = {0095-3628}, mesh = {Base Sequence ; Computational Biology/*trends ; *Ecology/methods/trends ; Environment ; Environmental Microbiology ; Genome/genetics ; *Genomics/trends ; }, abstract = {The exponential increase of genomic and metagenomic data, fueled in part by recent advancements in sequencing technology, are greatly expanding our understanding of the phylogenetic diversity and metabolic capacity present in the environment. Two of the central challenges that bioinformaticians and ecologists alike must face are the design of bioinformatic resources that facilitate the analysis of genomic and metagenomic data in a comparative context and the efficient capture and organization of the plethora of descriptive information required to usefully describe these data sets. In this commentary, we review three initiatives presented in the "new frontiers" session of the second SCOPE meeting on Microbial Environmental Genomics (MicroEnGen-II, Shanghai, June 12-15, 2006). These are (1) the Integrated Microbial Genomes Resources (IMG), (2) the Genomic Standards Consortium (GSC), and (3) the Natural Environment Research Council (NERC) Environmental Bioinformatics Centre (NEBC). These integrative bioinformatics and data management initiatives underscore the increasingly important role ecologists have to play in the genomic (metagenomic) revolution.}, }
@article {pmid17435792, year = {2007}, author = {Prosser, JI and Bohannan, BJ and Curtis, TP and Ellis, RJ and Firestone, MK and Freckleton, RP and Green, JL and Green, LE and Killham, K and Lennon, JJ and Osborn, AM and Solan, M and van der Gast, CJ and Young, JP}, title = {The role of ecological theory in microbial ecology.}, journal = {Nature reviews. Microbiology}, volume = {5}, number = {5}, pages = {384-392}, doi = {10.1038/nrmicro1643}, pmid = {17435792}, issn = {1740-1534}, mesh = {Bacteria/*classification/genetics/*growth &amp; development ; *Ecology ; *Ecosystem ; Geologic Sediments/microbiology ; Species Specificity ; Sulfolobus/growth &amp; development ; *Systems Theory ; Water Microbiology ; }, abstract = {Microbial ecology is currently undergoing a revolution, with repercussions spreading throughout microbiology, ecology and ecosystem science. The rapid accumulation of molecular data is uncovering vast diversity, abundant uncultivated microbial groups and novel microbial functions. This accumulation of data requires the application of theory to provide organization, structure, mechanistic insight and, ultimately, predictive power that is of practical value, but the application of theory in microbial ecology is currently very limited. Here we argue that the full potential of the ongoing revolution will not be realized if research is not directed and driven by theory, and that the generality of established ecological theory must be tested using microbial systems.}, }
@article {pmid17435327, year = {2007}, author = {Harsha, TS and Yamakanamardi, SM and Mahadevaswamy, M}, title = {Heterotrophic free-living and particle-bound bacterial cell size in the river Cauvery and its downstream tributaries.}, journal = {Journal of biosciences}, volume = {32}, number = {2}, pages = {363-374}, pmid = {17435327}, issn = {0250-5991}, mesh = {Bacteria/*cytology ; Chlorides/analysis ; India ; Oxygen/analysis ; Plankton/*cytology ; Regression Analysis ; Rivers/chemistry/*microbiology ; Temperature ; *Water Microbiology ; Water Movements ; }, abstract = {This is the first comprehensive study on planktonic heterotrophic bacterial cell size in the river Cauvery and its important tributaries in Karnataka State, India. The initial hypothesis that the mean cell size of planktonic heterotrophic bacteria in the four tributaries are markedly different from each other and also from that in the main river Cauvery was rejected, because all five watercourses showed similar planktonic heterotrophic bacterial cell size. Examination of the correlation between mean heterotrophic bacterial cell size and environmental variables showed four correlations in the river Arkavathy and two in the river Shimsha. Regression analysis revealed that 18%of the variation in mean heterotrophic free-living bacterial cell size was due to biological oxygen demand (BOD)in the river Arkavathy, 11% due to surface water velocity (SWV)in the river Cauvery and 11% due to temperature in the river Kapila. Heterotrophic particle-bound bacterial cell size variation was 28% due to chloride and BOD in the river Arkavathy, 11% due to conductivity in the river Kapila and 8% due to calcium in the river Cauvery. This type of relationship between heterotrophic bacterial cell size and environmental variables suggests that,though the mean heterotrophic bacterial cell size was similar in all the five water courses, different sets of environmental variables apparently control the heterotrophic bacterial cell size in the various water bodies studied in this investigation. The possible cause for this environmental (bottom -up) control is discussed.}, }
@article {pmid17431711, year = {2007}, author = {Heijs, SK and Haese, RR and van der Wielen, PW and Forney, LJ and van Elsas, JD}, title = {Use of 16S rRNA gene based clone libraries to assess microbial communities potentially involved in anaerobic methane oxidation in a Mediterranean cold seep.}, journal = {Microbial ecology}, volume = {53}, number = {3}, pages = {384-398}, pmid = {17431711}, issn = {0095-3628}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Base Sequence ; *Biodiversity ; DNA Primers/chemistry ; DNA, Archaeal/chemistry/isolation &amp; purification ; DNA, Bacterial/chemistry/isolation &amp; purification ; DNA, Ribosomal/chemistry ; Ecosystem ; *Environmental Microbiology ; Gene Library ; Geologic Sediments/chemistry/*microbiology ; Lipids/analysis ; Mediterranean Sea ; Methane/metabolism ; Methanosarcinales/classification/genetics/isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {This study provides data on the diversities of bacterial and archaeal communities in an active methane seep at the Kazan mud volcano in the deep Eastern Mediterranean sea. Layers of varying depths in the Kazan sediments were investigated in terms of (1) chemical parameters and (2) DNA-based microbial population structures. The latter was accomplished by analyzing the sequences of directly amplified 16S rRNA genes, resulting in the phylogenetic analysis of the prokaryotic communities. Sequences of organisms potentially associated with processes such as anaerobic methane oxidation and sulfate reduction were thus identified. Overall, the sediment layers revealed the presence of sequences of quite diverse bacterial and archaeal communities, which varied considerably with depth. Dominant types revealed in these communities are known as key organisms involved in the following processes: (1) anaerobic methane oxidation and sulfate reduction, (2) sulfide oxidation, and (3) a range of (aerobic) heterotrophic processes. In the communities in the lowest sediment layer sampled (22-34 cm), sulfate-reducing bacteria and archaea of the ANME-2 cluster (likely involved in anaerobic methane oxidation) were prevalent, whereas heterotrophic organisms abounded in the top sediment layer (0-6 cm). Communities in the middle layer (6-22 cm) contained organisms that could be linked to either of the aforementioned processes. We discuss how these phylogeny (sequence)-based findings can support the ongoing molecular work aimed at unraveling both the functioning and the functional diversities of the communities under study.}, }
@article {pmid17431710, year = {2007}, author = {Nicholson, MJ and Evans, PN and Joblin, KN}, title = {Analysis of methanogen diversity in the rumen using temporal temperature gradient gel electrophoresis: identification of uncultured methanogens.}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {141-150}, pmid = {17431710}, issn = {0095-3628}, mesh = {Animals ; Archaea/*classification/genetics/isolation &amp; purification ; Biodiversity ; Cattle ; DNA, Archaeal/chemistry ; Electrophoresis/methods ; Methanobacteriales/classification/genetics/isolation &amp; purification ; Methanosarcinales/classification/genetics/isolation &amp; purification ; Phylogeny ; *Rumen ; Sequence Analysis, DNA ; Sheep ; }, abstract = {A temporal temperature gradient gel electrophoresis (TTGE) method was developed to determine the diversity of methanogen populations in the rumen. Tests with amplicons from genomic DNA from 12 cultured methanogens showed single bands for all strains, with only two showing apparently comigrating bands. Fingerprints of methanogen populations were analyzed from DNA extracted from rumen contents from two cattle and four sheep grazing pasture. For one sheep, dilution cultures selective for methanogens were grown and the culturable methanogens in each successive dilution examined by TTGE. A total of 66 methanogen sequences were retrieved from bands in fingerprints and analyzed to reveal the presence of methanogens belonging to the Methanobacteriales, the Methanosarcinales, and to an uncultured archaeal lineage. Twenty-four sequences were most similar to Methanobrevibacter ruminantium, five to Methanobrevibacter smithii, four to Methanosphaera stadtmanae, and for three, the nearest match was Methanimicrococcus blatticola. The remaining 30 sequences did not cluster with sequences from cultured archaea, but when combined with published novel sequences from clone libraries formed a monophyletic lineage within the Euryarchaeota, which contained two previously unrecognized clusters. The TTGE bands from this lineage showed that the uncultured methanogens had significant population densities in each of the six rumen samples examined. In cultures of dilutions from one rumen sample, TTGE examination revealed these methanogens at a level of at least 10(5)g(-1). Band intensities from low-dilution cultures indicated that these methanogens were present at similar densities to Methanobrevibacter ruminantium-like methanogens, the sole culturable methanogens in high dilutions (10(6)-10(-10) g(-1)). It is suggested that the uncultured methanogens together with Methanobrevibacter spp. may be the predominant methanogens in the rumen. The TTGE method presented in this article provides a new opportunity for characterizing methanogen populations in the rumen microbial ecosystem.}, }
@article {pmid17431709, year = {2007}, author = {Ortega-Retuerta, E and Pulido-Villena, E and Reche, I}, title = {Effects of dissolved organic matter photoproducts and mineral nutrient supply on bacterial growth in Mediterranean inland waters.}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {161-169}, pmid = {17431709}, issn = {0095-3628}, mesh = {Bacteria/*drug effects/growth &amp; development ; Hydrogen-Ion Concentration ; *Light ; Mediterranean Region ; Regression Analysis ; Spain ; Water/*chemistry ; *Water Microbiology ; Water Pollutants/*pharmacology/radiation effects ; }, abstract = {Sunlight reacts with dissolved organic matter (DOM) modifying its availability as bacterial substrate. We assessed the impact of DOM photoproducts and mineral nutrient supply on bacterial growth in seven inland waters from the South of Spain, where DOM is characterized by low chromophoric content and long residence time. Factorial experiments were performed with presence vs absence of DOM photoproducts and mineral nutrient supply. In six of the seven experiments, we found a significant and negative effect of DOM photoproducts on bacterial growth and a significant and positive effect of mineral nutrient supply. The interaction of these two factors leaded to a compensation of negative effects of photoproducts by availability of mineral nutrients. Dissolved organic matter diagenetic status and the ionic environment where organic carbon is dissolved can be influencing bacterial DOM processing.}, }
@article {pmid17431708, year = {2007}, author = {Ude, S and Bailey, MJ and Huang, WE and Spiers, AJ}, title = {The environmental plasmid pQBR103 alters the single-cell Raman spectral profile of Pseudomonas fluorescens SBW25.}, journal = {Microbial ecology}, volume = {53}, number = {3}, pages = {494-497}, pmid = {17431708}, issn = {0095-3628}, mesh = {Bacteriological Techniques/*methods ; Culture Media ; Discriminant Analysis ; Plasmids/genetics/*physiology ; Pseudomonas fluorescens/*chemistry/*genetics/growth &amp; development ; Spectrum Analysis, Raman/*methods ; }, abstract = {Although plasmids are ubiquitous amongst phytosphere pseudomonads, the advantage and costs of plasmids for the bacterial host remain unclear. The application of single-cell Raman spectral analysis to plasmid-bacterial systems under different environmental conditions offers a new means of determining the impact of plasmids on host cell physiology, metabolic status, and response to stress.}, }
@article {pmid17431707, year = {2007}, author = {Maron, PA and Ranjard, L and Mougel, C and Lemanceau, P}, title = {Metaproteomics: a new approach for studying functional microbial ecology.}, journal = {Microbial ecology}, volume = {53}, number = {3}, pages = {486-493}, pmid = {17431707}, issn = {0095-3628}, mesh = {Bacterial Physiological Phenomena ; Ecology/*methods ; *Environmental Microbiology ; Proteomics/*methods ; }, abstract = {In the postgenomic era, there is a clear recognition of the limitations of nucleic acid-based methods for getting information on functions expressed by microbial communities in situ. In this context, the large-scale study of proteins expressed by indigenous microbial communities (metaproteome) should provide information to gain insights into the functioning of the microbial component in ecosystems. Characterization of the metaproteome is expected to provide data linking genetic and functional diversity of microbial communities. Studies on the metaproteome together with those on the metagenome and the metatranscriptome will contribute to progress in our knowledge of microbial communities and their contribution in ecosystem functioning. Effectiveness of the metaproteomic approach will be improved as increasing metagenomic information is made available thanks to the environmental sequencing projects currently running. More specifically, analysis of metaproteome in contrasted environmental situations should allow (1) tracking new functional genes and metabolic pathways and (2) identifying proteins preferentially associated with specific stresses. These proteins considered as functional bioindicators should contribute, in the future, to help policy makers in defining strategies for sustainable management of our environment.}, }
@article {pmid17431706, year = {2007}, author = {Marulanda, A and Porcel, R and Barea, JM and Azcón, R}, title = {Drought tolerance and antioxidant activities in lavender plants colonized by native drought-tolerant or drought-sensitive Glomus Species.}, journal = {Microbial ecology}, volume = {54}, number = {3}, pages = {543-552}, pmid = {17431706}, issn = {0095-3628}, mesh = {Adaptation, Physiological ; Alkaline Phosphatase/metabolism ; Ascorbic Acid/metabolism ; Biomass ; *Disasters ; Glutathione/metabolism ; Hydrogen Peroxide/metabolism ; Lavandula/*growth &amp; development/*metabolism/microbiology ; Mycorrhizae/*growth &amp; development/physiology ; Nitrogen/metabolism ; Plant Roots/growth &amp; development/metabolism/microbiology ; Plant Shoots/growth &amp; development/metabolism/microbiology ; Potassium/metabolism ; Succinate Dehydrogenase/metabolism ; Water/metabolism ; }, abstract = {This study compared the effectiveness of four arbuscular mycorrhizal (AM) fungal isolates (two autochthonous presumably drought-tolerant Glomus sp and two allochthonous presumably drought-sensitive strains) on a drought-adapted plant (Lavandula spica) growing under drought conditions. The autochthonous AM fungal strains produced a higher lavender biomass, specially root biomass, and a more efficient N and K absorption than with the inoculation of similar allochthonous strains under drought conditions. The autochthonous strains of Glomus intraradices and Glomus mosseae increased root growth by 35% and 100%, respectively, when compared to similar allochthonous strains. These effects were concomitant with an increase in water content and a decline in antioxidant compounds: 25% glutathione, 7% ascorbate and 15% H(2)O(2) by G. intraradices, and 108% glutathione, 26% ascorbate and 43% H(2)O(2) by G. mosseae. Glutathione and ascorbate have an important role in plant protection and metabolic function under water deficit; the low cell accumulation of these compounds in plants colonized by autochthonous AM fungal strains is an indication of high drought tolerance. Non-significant differences between antioxidant activities such as glutathione reductase (GR), catalase (CAT) and superoxide dismutase (SOD) in colonized plants were found. Thus, these results do not allow the generalization that GR, CAT and SOD were correlated with the symbiotic efficiency of these AM fungi on lavender drought tolerance. Plants colonized by allochthonous G. mosseae (the less efficient strain under drought conditions) had less N and K content than those colonized by similar autochthonous strain. These ions play a key role in osmoregulation. The AM symbiosis by autochthonous adapted strains also produced the highest intraradical and arbuscular development and extraradical mycelial having the greatest fungal SDH and ALP-ase activities in the root systems. Inoculation of autochthonous drought tolerant fungal strains is an important strategy that assured the greatest tolerance water stress contributing to the best lavender growth under drought.}, }
@article {pmid17416689, year = {2007}, author = {Walker, JJ and Pace, NR}, title = {Phylogenetic composition of Rocky Mountain endolithic microbial ecosystems.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {11}, pages = {3497-3504}, pmid = {17416689}, issn = {0099-2240}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biodiversity ; Chlorophyta/*classification/genetics ; DNA, Ribosomal/chemistry/genetics ; *Ecosystem ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; *Soil Microbiology ; United States ; }, abstract = {The endolithic environment, the pore space in rocks, is a ubiquitous microbial habitat. Photosynthesis-based endolithic communities inhabit the outer few millimeters to centimeters of rocks exposed to the surface. Such endolithic ecosystems have been proposed as simple, tractable models for understanding basic principles in microbial ecology. In order to test previously conceived hypotheses about endolithic ecosystems, we studied selected endolithic communities in the Rocky Mountain region of the United States with culture-independent molecular methods. Community compositions were determined by determining rRNA gene sequence contents, and communities were compared using statistical phylogenetic methods. The results indicate that endolithic ecosystems are seeded from a select, global metacommunity and form true ecological communities that are among the simplest microbial ecosystems known. Statistical analysis showed that biogeographical characteristics that control community composition, such as rock type, are more complex than predicted. Collectively, results of this study support the idea that patterns of microbial diversity found in endolithic communities are governed by principles similar to those observed in macroecological systems.}, }
@article {pmid17415611, year = {2007}, author = {Nelson, KE and Methé, BA and Kowalchuk, GA}, title = {Microbial environmental genomics.}, journal = {Microbial ecology}, volume = {53}, number = {3}, pages = {367-368}, doi = {10.1007/s00248-007-9214-5}, pmid = {17415611}, issn = {0095-3628}, mesh = {Education/organization &amp; administration ; *Environmental Microbiology ; *Genomics ; International Cooperation ; }, }
@article {pmid17410396, year = {2007}, author = {Logares, R and Rengefors, K and Kremp, A and Shalchian-Tabrizi, K and Boltovskoy, A and Tengs, T and Shurtleff, A and Klaveness, D}, title = {Phenotypically different microalgal morphospecies with identical ribosomal DNA: a case of rapid adaptive evolution?.}, journal = {Microbial ecology}, volume = {53}, number = {4}, pages = {549-561}, pmid = {17410396}, issn = {0095-3628}, mesh = {Animals ; DNA, Mitochondrial/chemistry ; DNA, Ribosomal/chemistry ; Dinoflagellida/classification/cytology/*genetics ; Ecosystem ; *Evolution, Molecular ; Genetic Speciation ; Phenotype ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; }, abstract = {The agents driving the divergence and speciation of free-living microbial populations are still largely unknown. We investigated the dinoflagellate morphospecies Scrippsiella hangoei and Peridinium aciculiferum, which abound in the Baltic Sea and in northern temperate lakes, respectively. Electron microscopy analyses showed significant interspecific differences in the external cellular morphology, but a similar plate pattern in the characteristic dinoflagellate armor. Experimentally, S. hangoei grew in a wide range of salinities (0-30), whereas P. aciculiferum only grew in low salinities (0-3). Despite these phenotypic differences and the habitat segregation, molecular analyses showed identical ribosomal DNA sequences (ITS1, ITS2, 5.8S, SSU, and partial LSU) for both morphospecies. Yet, a strong interspecific genetic isolation was indicated by amplified fragment length polymorphism (F (ST) = 0.76) and cytochrome b (cob) sequence divergence (approximately 1.90%). Phylogenetic reconstructions based on ribosomal (SSU, LSU) and mitochondrial (cob) DNA indicated a recent marine ancestor for P. aciculiferum. In conclusion, we suggest that the lacustrine P. aciculiferum and the marine-brackish S. hangoei diverged very recently, after a marine-freshwater transition that exposed the ancestral populations to different selective pressures. This hypothetical scenario agrees with mounting data indicating a significant role of natural selection in the divergence of free-living microbes, despite their virtually unrestricted dispersal capabilities. Finally, our results indicate that identical ITS rDNA sequences do not necessarily imply the same microbial species, as commonly assumed.}, }
@article {pmid17410395, year = {2007}, author = {Hillesland, KL and Lenski, RE and Velicer, GJ}, title = {Ecological variables affecting predatory success in Myxococcus xanthus.}, journal = {Microbial ecology}, volume = {53}, number = {4}, pages = {571-578}, pmid = {17410395}, issn = {0095-3628}, mesh = {Agar/chemistry ; Chemotaxis ; *Ecosystem ; *Food Chain ; Gram-Negative Bacteria/physiology ; Gram-Positive Bacteria/physiology ; Myxococcus xanthus/*physiology ; }, abstract = {The feeding efficiency of microbial predators depends on both the availability of various prey species and abiotic variables. Myxococcus xanthus is a bacterial predator that searches for microbial prey by gliding motility, and then kills and lyses its prey with secreted compounds. We manipulated three ecological variables to examine their effects on the predatory performance of M. xanthus to better understand its behavior and how it affects prey populations. Experiments were designed to determine how surface solidity (hard vs soft agar), density of prey patches (1 vs 2 cm grids), and type of prey (Gram-positive Micrococcus luteus vs Gram-negative Escherichia coli) affect predatory swarming and prey killing by M. xanthus. The prey were dispersed in patches on a buffered agar surface. M. xanthus swarms attacked a greater proportion of prey patches when patches were densely arranged on a hard-agar surface, compared with either soft-agar surfaces or low-patch-density arrangements. These ecological variables did not significantly influence the rate of killing of individual prey within a patch, although a few surviving prey were more likely to be recovered on soft agar than on hard agar. These results indicate that M. xanthus quickly kills most nearby E. coli or M. luteus regardless of the surface. However, the ability of M. xanthus to search out patches of these prey is affected by surface hardness, the density of prey patches, and the prey species.}, }
@article {pmid17410394, year = {2007}, author = {Promputtha, I and Lumyong, S and Dhanasekaran, V and McKenzie, EH and Hyde, KD and Jeewon, R}, title = {A phylogenetic evaluation of whether endophytes become saprotrophs at host senescence.}, journal = {Microbial ecology}, volume = {53}, number = {4}, pages = {579-590}, pmid = {17410394}, issn = {0095-3628}, mesh = {Ascomycota/classification/genetics/growth &amp; development ; Biodiversity ; Colletotrichum/classification/genetics/growth &amp; development ; DNA, Ribosomal/chemistry ; Fungi/*classification/genetics/growth &amp; development ; Fusarium/classification/genetics/growth &amp; development ; Magnolia/growth &amp; development/*microbiology ; Phyllachorales/classification/genetics/growth &amp; development ; *Phylogeny ; Plant Leaves/growth &amp; development/microbiology ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Fungal endophytes and saprotrophs generally play an important ecological role within plant tissues and dead plant material. Several reports based solely on morphological observations have postulated that there is an intimate link between endophytes and saprotrophs. This study aims to provide valuable insight as to whether some endophytic fungi manifest themselves as saprotrophs upon host decay. Ribosomal DNA-based sequence comparison and phylogenetic relationships from 99 fungal isolates (endophytes, mycelia sterilia, and saprotrophs) recovered from leaves and twigs of Magnolia liliifera were investigated in this study. Molecular data suggest there are fungal taxa that possibly exist as endophytes and saprotrophs. Isolates of Colletotrichum, Fusarium, Guignardia, and Phomopsis, which are common plant endophytes, have high sequence similarity and are phylogenetically related to their saprotrophic counterparts. This provides evidence to suggest that some endophytic species change their ecological strategies and adopt a saprotrophic lifestyle. The implication of these findings on fungal biodiversity and host specificity is also discussed.}, }
@article {pmid17410176, year = {2007}, author = {Chait, R and Craney, A and Kishony, R}, title = {Antibiotic interactions that select against resistance.}, journal = {Nature}, volume = {446}, number = {7136}, pages = {668-671}, doi = {10.1038/nature05685}, pmid = {17410176}, issn = {1476-4687}, mesh = {Anti-Bacterial Agents/*pharmacology ; Ciprofloxacin/pharmacology ; Doxycycline/pharmacology ; Drug Interactions ; Drug Resistance, Bacterial/*drug effects/*genetics/physiology ; Drug Therapy, Combination ; Erythromycin/pharmacology ; Escherichia coli/*drug effects/genetics/growth &amp; development/*physiology ; Microbial Sensitivity Tests ; *Selection, Genetic ; }, abstract = {Multidrug combinations are increasingly important in combating the spread of antibiotic-resistance in bacterial pathogens. On a broader scale, such combinations are also important in understanding microbial ecology and evolution. Although the effects of multidrug combinations on bacterial growth have been studied extensively, relatively little is known about their impact on the differential selection between sensitive and resistant bacterial populations. Normally, the presence of a drug confers an advantage on its resistant mutants in competition with the sensitive wild-type population. Here we show, by using a direct competition assay between doxycycline-resistant and doxycycline-sensitive Escherichia coli, that this differential selection can be inverted in a hyper-antagonistic class of drug combinations. Used in such a combination, a drug can render the combined treatment selective against the drug's own resistance allele. Further, this inversion of selection seems largely insensitive to the underlying resistance mechanism and occurs, at sublethal concentrations, while maintaining inhibition of the wild type. These seemingly paradoxical results can be rationalized in terms of a simple geometric argument. Our findings demonstrate a previously unappreciated feature of the fitness landscape for the evolution of resistance and point to a trade-off between the effect of drug interactions on absolute potency and the relative competitive selection that they impose on emerging resistant populations.}, }
@article {pmid17409203, year = {2007}, author = {Flanagan, JL and Brodie, EL and Weng, L and Lynch, SV and Garcia, O and Brown, R and Hugenholtz, P and DeSantis, TZ and Andersen, GL and Wiener-Kronish, JP and Bristow, J}, title = {Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa.}, journal = {Journal of clinical microbiology}, volume = {45}, number = {6}, pages = {1954-1962}, pmid = {17409203}, issn = {0095-1137}, support = {R01 HL069809/HL/NHLBI NIH HHS/United States ; P50 HL074005/HL/NHLBI NIH HHS/United States ; PH50HL74005/HL/NHLBI NIH HHS/United States ; HL69809/HL/NHLBI NIH HHS/United States ; P01 HL024075/HL/NHLBI NIH HHS/United States ; HL024075/HL/NHLBI NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Anti-Bacterial Agents/therapeutic use ; Bacteria/*classification/drug effects/genetics/growth &amp; development ; Cloning, Molecular ; DNA, Bacterial/analysis ; *Ecosystem ; Female ; Gene Library ; *Genetic Variation ; Humans ; Infant ; *Intubation, Intratracheal ; Lung/*microbiology ; Male ; Middle Aged ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Pseudomonas Infections/*drug therapy/microbiology ; Pseudomonas aeruginosa/*drug effects ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Management of airway infections caused by Pseudomonas aeruginosa is a serious clinical challenge, but little is known about the microbial ecology of airway infections in intubated patients. We analyzed bacterial diversity in endotracheal aspirates obtained from intubated patients colonized by P. aeruginosa by using 16S rRNA clone libraries and microarrays (PhyloChip) to determine changes in bacterial community compositions during antibiotic treatment. Bacterial 16S rRNA genes were absent from aspirates obtained from patients briefly intubated for elective surgery but were detected by PCR in samples from all patients intubated for longer periods. Sequencing of 16S rRNA clone libraries demonstrated the presence of many orally, nasally, and gastrointestinally associated bacteria, including known pathogens, in the lungs of patients colonized with P. aeruginosa. PhyloChip analysis detected the same organisms and many additional bacterial groups present at low abundance that were not detected in clone libraries. For each patient, both culture-independent methods showed that bacterial diversity decreased following the administration of antibiotics, and communities became dominated by a pulmonary pathogen. P. aeruginosa became the dominant species in six of seven patients studied, despite treatment of five of these six with antibiotics to which it was sensitive in vitro. Our data demonstrate that the loss of bacterial diversity under antibiotic selection is highly associated with the development of pneumonia in ventilated patients colonized with P. aeruginosa. Interestingly, PhyloChip analysis demonstrated reciprocal changes in abundance between P. aeruginosa and the class Bacilli, suggesting that these groups may compete for a similar ecological niche and suggesting possible mechanisms through which the loss of microbial diversity may directly contribute to pathogen selection and persistence.}, }
@article {pmid17408790, year = {2007}, author = {Lücker, S and Steger, D and Kjeldsen, KU and MacGregor, BJ and Wagner, M and Loy, A}, title = {Improved 16S rRNA-targeted probe set for analysis of sulfate-reducing bacteria by fluorescence in situ hybridization.}, journal = {Journal of microbiological methods}, volume = {69}, number = {3}, pages = {523-528}, doi = {10.1016/j.mimet.2007.02.009}, pmid = {17408790}, issn = {0167-7012}, support = {P 18836/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Databases, Nucleic Acid ; Deltaproteobacteria/genetics/isolation &amp; purification ; In Situ Hybridization, Fluorescence/*methods ; *Oligonucleotide Probes ; RNA, Ribosomal, 16S/*genetics ; Sensitivity and Specificity ; Species Specificity ; Sulfates/*metabolism ; Sulfur-Reducing Bacteria/genetics/*isolation &amp; purification ; }, abstract = {An updated dataset of in silico specificities for 54 previously published 16S rRNA-targeted oligonucleotides was assembled to provide guidance for reliable fluorescence in situ hybridization (FISH) analysis of sulfate-reducing bacteria. Additionally, six new FISH probes were developed for major deltaproteobacterial taxa, including a probe trio targeting most Deltaproteobacteria and Gemmatimonadetes.}, }
@article {pmid17406775, year = {2007}, author = {Shyu, C and Soule, T and Bent, SJ and Foster, JA and Forney, LJ}, title = {MiCA: a web-based tool for the analysis of microbial communities based on terminal-restriction fragment length polymorphisms of 16S and 18S rRNA genes.}, journal = {Microbial ecology}, volume = {53}, number = {4}, pages = {562-570}, pmid = {17406775}, issn = {0095-3628}, support = {IP20 RR16448/RR/NCRR NIH HHS/United States ; }, mesh = {Computational Biology ; Databases, Nucleic Acid ; Internet ; Microbiology ; Polymerase Chain Reaction ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 18S/*genetics ; Restriction Mapping ; Sequence Analysis, DNA ; *Software ; }, abstract = {A web-based resource, Microbial Community Analysis (MiCA), has been developed to facilitate studies on microbial community ecology that use analyses of terminal-restriction fragment length polymorphisms (T-RFLP) of 16S and 18S rRNA genes. MiCA provides an intuitive web interface to access two specialized programs and a specially formatted database of 16S ribosomal RNA sequences. The first program performs virtual polymerase chain reaction (PCR) amplification of rRNA genes and restriction of the amplicons using primer sequences and restriction enzymes chosen by the user. This program, in silico PCR and Restriction (ISPaR), uses a binary encoding of DNA sequences to rapidly scan large numbers of sequences in databases searching for primer annealing and restriction sites while permitting the user to specify the number of mismatches in primer sequences. ISPaR supports multiple digests with up to three enzymes. The number of base pairs between the 5' and 3' primers and the proximal restriction sites can be reported, printed, or exported in various formats. The second program, APLAUS, infers a plausible community structure(s) based on T-RFLP data supplied by a user. APLAUS estimates the relative abundances of populations and reports a listing of phylotypes that are consistent with the empirical data. MiCA is accessible at http://mica.ibest.uidaho.edu/.}, }
@article {pmid17406774, year = {2007}, author = {Borsodi, AK and Rusznyák, A and Molnár, P and Vladár, P and Reskóné, MN and Tóth, EM and Sipos, R and Gedeon, G and Márialigeti, K}, title = {Metabolic activity and phylogenetic diversity of reed (Phragmites australis) periphyton bacterial communities in a hungarian shallow soda lake.}, journal = {Microbial ecology}, volume = {53}, number = {4}, pages = {612-620}, pmid = {17406774}, issn = {0095-3628}, mesh = {Bacteria/*classification/isolation &amp; purification/metabolism ; Biodiversity ; DNA, Ribosomal/chemistry ; Hungary ; *Phylogeny ; Poaceae/*microbiology ; Sequence Analysis, DNA ; Water/chemistry ; *Water Microbiology ; }, abstract = {In the present study, the species composition and potential metabolic activities of bacterial communities of reed Phragmites australis (Cav.) (Trin. ex Steudel) periphyton from Lake Velencei were studied by cultivation-based and metabolic fingerprinting methods. Serially diluted spring biofilm samples were used to test the community-level physiological profiling (CLPP) using BIOLOG microplates, and for plating onto different media. On the basis of their morphological, biochemical, and physiological test results, 173 strains were clustered by numerical analysis. Representatives of amplified ribosomal DNA restriction analysis (ARDRA) groups were identified by their 16S rDNA sequence comparison. Based on the results of the CLPP investigations, regional differences were detected among the utilized substrate numbers and types, parallel with the increase in incubation time. The phenotypic test results of the strains showed considerable variability with respect to the sampling sites and the media used for cultivation. The most frequently isolated strains were identified as members of genera Agrobacterium, Pseudomonas (P. anguilliseptica, P. marginalis, P. alcaligenes, P. fragi) with aerobic or facultative anaerobic respiratory metabolism, and the species Aeromonas sobria and A. veronii with strong facultative fermentative metabolism. Other strains were identified as Gram-positive Arthrobacter, Bacillus, and Kocuria species. The rarely isolated strains were members of beta-Proteobacteria (Acidovorax, Delftia, Hydrogenophaga, and Rhodoferax), gamma-Proteobacteria (Psychrobacter and Shewanella), low G + C Gram-positives (Brevibacillus, Paenibacillus, and Exiguobacterium) and high G + C Gram-positives (Aureobacterium and Microbacterium).}, }
@article {pmid17406773, year = {2007}, author = {Odić, D and Turk, V and Stopar, D}, title = {Environmental stress determines the quality of bacterial lysate and its utilization efficiency in a simple microbial loop.}, journal = {Microbial ecology}, volume = {53}, number = {4}, pages = {639-649}, pmid = {17406773}, issn = {0095-3628}, mesh = {Biomass ; Carbon/metabolism ; *Environment ; Food Chain ; Nitrogen/metabolism ; Phosphorus/metabolism ; Pseudoalteromonas/*growth &amp; development/metabolism ; Sodium Chloride/pharmacology ; Sulfur/metabolism ; Vibrio/drug effects/*metabolism ; }, abstract = {Heterotrophic bacteria provide the critical link in the microbial loop by converting dissolved organic matter (DOM) into particulate form. In this study, DOM was prepared from recently isolated estuarine bacterial strain Vibrio sp. (DSM14379) grown at different salinities [0.2%, 0.5%, 3%, 5%, or 10% (w/v)], washed, concentrated, and lysed by autoclaving. The corresponding lysate-containing media were designated LM(0.2), LM(0.5), LM(3), LM(5), and LM(10). Vibrio sp. cells grown at different salinities had similar C/N/P ratios, but different C/S ratios, different trace element composition, and different 2D gel electrophoresis protein profiles. Pseudoalteromonas sp. (DSM06238) isolated from a similar environment was able to grow on all lysates, and its biomass production was dependent on lysate type. The highest growth rate and biomass production of Pseudoalteromonas sp. at saturation lysate concentrations were observed in LM(3). The biomass production at saturation lysate concentrations was about 3-fold higher as compared to LM(0.2) and LM(10). The initial respiration rate, intracellular adenosine triphosphate (ATP) levels, and (3)H-Leu and (3)H-TdR incorporation rates were lowest in LM(3). On the other hand, in LM(0.2) or LM(10) lysates the situation was reversed, the growth rates and biomass production were lowest, whereas (3)H-Leu and (3)H-TdR incorporation, respiration rates, as well as ATP levels, were highest. These results imply uncoupling of catabolism from growth in either high- or low-salinity lysates. The results also suggest that differences in organic carbon quality generated during Vibrio sp. growth at different NaCl concentrations were propagated through the simple microbial loop, which may have important ecological implications for higher trophic levels that depend on microbial grazing.}, }
@article {pmid17406772, year = {2007}, author = {Diouf, D and Samba-Mbaye, R and Lesueur, D and Ba, AT and Dreyfus, B and de Lajudie, P and Neyra, M}, title = {Genetic diversity of Acacia seyal Del. rhizobial populations indigenous to Senegalese soils in relation to salinity and pH of the sampling sites.}, journal = {Microbial ecology}, volume = {54}, number = {3}, pages = {553-566}, pmid = {17406772}, issn = {0095-3628}, mesh = {Acacia/*microbiology ; *Genetic Variation ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Rhizobiaceae/classification/*genetics/growth &amp; development ; Salinity ; Senegal ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The occurrence and the distribution of rhizobial populations naturally associated to Acacia seyal Del. were characterized in 42 soils from Senegal. The diversity of rhizobial genotypes, as characterized by polymerase chain reaction restriction fragment length polymorphism (RFLP) analysis of 16S-23S rDNA, performed on DNA extracted from 138 nodules resulted in 15 clusters. Results indicated the widespread occurrence of compatible rhizobia associated to A. seyal in various ecogeographic areas. However, the clustering of rhizobial populations based on intergenic spacer (IGS) RFLP profiles did not reflect their geographic origin. Four genera were discriminated on the basis of 16S rRNA gene sequences of the strains representative for the IGS-RFLP profiles. The majority of rhizobia associated to A. seyal were affiliated to Mesorhizobium and Sinorhizobium 64 and 29%, respectively, of the different IGS-RFLP profiles. Our results demonstrate the coexistence inside the nodule of plant-pathogenic non-N(2)-fixing Agrobacterium and Burkholderia strains, which induced the formation of ineffective nodules, with symbiotic rhizobia. Nodulation was recorded in saline soils and/or at low pH values or in alkaline soils, suggesting adaptability of natural rhizobial populations to major ecological environmental stress and their ability to establish symbiotic associations within these soil environments. These results contribute to the progressing research efforts to uncover the biodiversity of rhizobia and to improve nitrogen fixation in agroforestry systems in sub-Saharan Africa.}, }
@article {pmid17406771, year = {2008}, author = {Govindarajan, M and Balandreau, J and Kwon, SW and Weon, HY and Lakshminarasimhan, C}, title = {Effects of the inoculation of Burkholderia vietnamensis and related endophytic diazotrophic bacteria on grain yield of rice.}, journal = {Microbial ecology}, volume = {55}, number = {1}, pages = {21-37}, pmid = {17406771}, issn = {0095-3628}, mesh = {Burkholderia/classification/genetics/*growth &amp; development/isolation &amp; purification ; Colony Count, Microbial ; Crops, Agricultural ; Culture Media ; Genes, rRNA ; Gram-Negative Bacteria/classification/genetics/*growth &amp; development/isolation &amp; purification ; India ; Molecular Sequence Data ; *Nitrogen Fixation ; Oryza/*growth &amp; development/*microbiology ; Phylogeny ; Plant Roots/microbiology ; Plant Shoots/microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {During a survey of endophytic diazotrophic bacteria associated with different rice varieties in Tamilnadu, some "endophytes" were obtained. Thirteen bacterial isolates from surface-sterilized roots and shoots were obtained in pure culture, which produced indole acetic acid (IAA) and reduced acetylene to ethylene. Polymerase chain reaction (PCR) amplification confirmed the presence of nif-H gene in all the isolates. Morphological, biochemical, and molecular characteristics indicated that all of them belonged to the genus Burkholderia One of them, MGK3, was consistently more active in reducing acetylene, and 16S rDNA sequences of isolate MGK3 confirmed its identification as Burkholderia vietnamiensis. Colonization of rice root was confirmed by strain MGK3 marked with gusA gene. The inoculated roots showed a blue color, which was most intense at the points of lateral root emergence and at the root tip. Transverse sections of roots, 15 days after inoculation, revealed beta-glucuronidase (GUS) activity within many of the cortical intercellular spaces next to the stele and within the aerenchyma. Nitrogen fixation was quantified by using (15)N isotope dilution method with two different cultivars grown in pot and field experiments. Higher nitrogen fixation was observed in variety Ponni than in ADT-43, where nearly 42% (field) and 40% (pot) of the nitrogen was derived from the atmosphere (% Ndfa). Isolate MGK3 was used to inoculate rice seedlings in a comparison with four other diazotrophs, viz., Gluconacetobacter diazotrophicus LMG7603, Herbaspirillum seropedicae LMG6513, Azospirillum lipoferum 4B LMG4348, and B. vietnamiensis LMG10929. They were used to conduct two pot and four field inoculation experiments. MGK3 alone, and combined with other diazotrophs, performed best under both pot and field conditions: combined inoculation produced yield increases between 9.5 and 23.6%, while MGK3 alone increased yield by 5.6 to 12.16% over the uninoculated control treatment.}, }
@article {pmid17404788, year = {2007}, author = {Dupuy, C and Ryckaert, M and Le Gall, S and Hartmann, HJ}, title = {Seasonal variations in planktonic community structure and production in an Atlantic coastal pond: the importance of nanoflagellates.}, journal = {Microbial ecology}, volume = {53}, number = {4}, pages = {537-548}, pmid = {17404788}, issn = {0095-3628}, mesh = {Animals ; Atlantic Ocean ; *Biodiversity ; Biomass ; Ciliophora/classification/growth &amp; development/isolation &amp; purification ; Diatoms/classification/growth &amp; development/isolation &amp; purification ; Dinoflagellida/classification/growth &amp; development/isolation &amp; purification ; Plankton/classification/*growth &amp; development/isolation &amp; purification ; *Seasons ; Temperature ; Water/chemistry ; }, abstract = {The structure and summertime production of planktonic communities and the role of nondiatom planktonic cells were studied in coastal ponds, which are areas traditionally used for fattening and greening table-sized oysters. The abundance and biomass of nano-microplanktonic protists were determined at weekly intervals between February 1998 and February 1999 in a coastal pond without oysters in the French Atlantic coast near La Rochelle. The production of these microbiotas was determined in the summer period. The structure of plankton communities revealed the following observations: (1) microphytoplanktonic cells were mostly diatoms and dinoflagellates, (2) microzooplanktonic cells were mainly ciliates, and (3) nanoplanktonic cells were represented by pigmented (80-90% of the nanoplankton biomass) and colorless nanoflagellates. Diatoms were dominated by Naviculiineae. Dinoflagellates were dominated by Peridiniales. Oligotrichida were predominant in the ciliate community. Protist biomass levels were nine times higher from April to August (summer period 1033 microg C L(-1)) than from September to March (winter period 114 microg C L(-1)). Whatever the season, nanoflagellates were dominant in the water column (66 and 53% of the entire protist biomass in the summer and winter periods, respectively). Nanoflagellates represented the highest production of nano-microplanktonic communities (76% of carbon protist production) in the coastal pond in summer and showed the shortest generation time (7.1 h). Dinoflagellates came after nanoflagellates in production (19.5% of carbon protist production). Diatoms represented only a supplementary carbon resource available for higher trophic levels, whereas, until now, they were considered as the principal food of oysters in coastal ponds. Ciliates were a small source of carbon, but their growth rate was high. We suggest, first, that nanoflagellates represented the primary resource available in the pond and could constitute an important food resource for higher trophic levels, such as oysters, farmed in this type of pond. Overall, the system appeared to be more autotrophic than heterotrophic. Because inorganic nutrients are quickly exhausted in a semiclosed pond, pigmented flagellates dominated the carbon biomass, production and biomass of bacteria were high (thus, the microbial food web appeared to be active in this pond), and mixotrophy seemed to be an important trophic mode there.}, }
@article {pmid17404787, year = {2007}, author = {Van Nostrand, JD and Khijniak, TV and Gentry, TJ and Novak, MT and Sowder, AG and Zhou, JZ and Bertsch, PM and Morris, PJ}, title = {Isolation and characterization of four gram-positive nickel-tolerant microorganisms from contaminated sediments.}, journal = {Microbial ecology}, volume = {53}, number = {4}, pages = {670-682}, pmid = {17404787}, issn = {0095-3628}, mesh = {Anti-Bacterial Agents/pharmacology ; Arthrobacter/*drug effects/genetics/isolation &amp; purification ; DNA, Ribosomal/chemistry ; Drug Resistance, Bacterial/genetics ; Geologic Sediments/chemistry/*microbiology ; Metals, Heavy/pharmacology ; Microbial Sensitivity Tests ; Nickel/analysis/*pharmacology ; Phylogeny ; RNA, Ribosomal, 16S/chemistry ; Sequence Analysis, DNA ; Soil Pollutants/*analysis ; Streptomycetaceae/*drug effects/genetics/isolation &amp; purification ; Uranium/pharmacology ; }, abstract = {Microbial communities from riparian sediments contaminated with high levels of Ni and U were examined for metal-tolerant microorganisms. Isolation of four aerobic Ni-tolerant, Gram-positive heterotrophic bacteria indicated selection pressure from Ni. These isolates were identified as Arthrobacter oxydans NR-1, Streptomyces galbus NR-2, Streptomyces aureofaciens NR-3, and Kitasatospora cystarginea NR-4 based on partial 16S rDNA sequences. A functional gene microarray containing gene probes for functions associated with biogeochemical cycling, metal homeostasis, and organic contaminant degradation showed little overlap among the four isolates. Fifteen of the genes were detected in all four isolates with only two of these related to metal resistance, specifically to tellurium. Each of the four isolates also displayed resistance to at least one of six antibiotics tested, with resistance to kanamycin, gentamycin, and ciprofloxacin observed in at least two of the isolates. Further characterization of S. aureofaciens NR-3 and K. cystarginea NR-4 demonstrated that both isolates expressed Ni tolerance constitutively. In addition, both were able to grow in higher concentrations of Ni at pH 6 as compared with pH 7 (42.6 and 8.5 mM Ni at pH 6 and 7, respectively). Tolerance to Cd, Co, and Zn was also examined in these two isolates; a similar pH-dependent metal tolerance was observed when grown with Co and Zn. Neither isolate was tolerant to Cd. These findings suggest that Ni is exerting a selection pressure at this site for metal-resistant actinomycetes.}, }
@article {pmid17404786, year = {2007}, author = {Nelson, K and Methé, BA and Kowalchuk, GA}, title = {Environmental microbial ecology in an "omics" era: summary report of MicroEnGen-II (Shanghai, June 12-15, 2006).}, journal = {Microbial ecology}, volume = {53}, number = {3}, pages = {369-370}, doi = {10.1007/s00248-007-9215-4}, pmid = {17404786}, issn = {0095-3628}, mesh = {*Environmental Microbiology ; Environmental Monitoring ; *Genomics ; Microbiological Techniques ; }, }
@article {pmid17401696, year = {2007}, author = {Queralt, N and Araujo, R}, title = {Analysis of the survival of H. pylori within a laboratory-based aquatic model system using molecular and classical techniques.}, journal = {Microbial ecology}, volume = {54}, number = {4}, pages = {771-777}, pmid = {17401696}, issn = {0095-3628}, mesh = {Bacteriological Techniques ; Colony Count, Microbial ; *Culture Media ; DNA, Bacterial/*analysis/isolation &amp; purification ; Helicobacter pylori/genetics/*growth &amp; development/*isolation &amp; purification/ultrastructure ; Humans ; Laboratories ; Microbial Viability ; Microscopy, Electron, Scanning ; Mineral Waters/*microbiology ; *Polymerase Chain Reaction ; }, abstract = {Despite the significance of Helicobacter pylori infection for man, its transmission is not clearly known. The human stomach is considered the reservoir of this pathogen, and one of the accepted routes is fecal-oral, in which water acts as a vector. However, although H. pylori epidemiology associates its transmission with water, only molecular and not cultural analysis detects the bacteria in water. This study was carried out to understand these data through studying the survival of H. pylori in a laboratory water model using cultural, morphological, and molecular methods. A mineral water system spiked with H. pylori and stored at 7 +/- 1 degrees C in the dark was analyzed by different methods over a period of 3 weeks. The total number of cells observed by DAPI staining and their DNA content remained constant over this study period. In contrast, cells could no longer be cultured after 5 days. Cell viability, which was determined via the LIVE/DEAD BacLight kit, decreased up to day 14, and at day 21 all cell membranes were damaged. In addition, a gradual conversion from spiral to coccal morphology occurred from day 3 onward. However, polymerase chain reaction (PCR) technique detected H. pylori DNA at day 21 and 3 months later. A study of the cell morphology of a young colony demonstrated the coexistence of bacilli and cocci. The results of this study show that H. pylori survives in water but loses its culturability and bacillar morphology rapidly, although it remains viable for longer periods and its DNA is still detectable much later. Thus, interpreting H. pylori's behavior in water differs according to the type of analysis. Consequently, we suggest that the presence of H. pylori infective cells is overestimated by PCR, whereas, in contrast, culture techniques underestimate it. Nevertheless, H. pylori should be considered a waterborne pathogen during its viable period, independently of its shape and culturability, as its presence in water may be risky for human health.}, }
@article {pmid17401597, year = {2007}, author = {Lejon, DP and Sebastia, J and Lamy, I and Chaussod, R and Ranjard, L}, title = {Relationships between soil organic status and microbial community density and genetic structure in two agricultural soils submitted to various types of organic management.}, journal = {Microbial ecology}, volume = {53}, number = {4}, pages = {650-663}, pmid = {17401597}, issn = {0095-3628}, mesh = {Agriculture/methods ; Bacteria/classification/*genetics ; Biodiversity ; Biomass ; DNA Fingerprinting ; DNA, Ribosomal Spacer/chemistry ; Fungi/classification/*genetics ; Humic Substances/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The effects of soil organic management on indigenous microorganisms were studied by comparing mulching straw (S), conifer compost (CC), and conifer bark (CB) as well as grass landing with grass (G), clover (Cl), and fescue (F) in a silty-clay soil (Mâcon), and by incorporating vine shoot (VS) and single and double doses of farmyard manure (FM) and mushroom manure (MM) in a calcareous sandy soil (Chinon). Soil physicochemical and microbial characteristics were assessed at each site at two depths by sampling at 0-5 and 5-20 cm for the Mâcon site and 0-10 and 10-20 cm for the Chinon site. Changes in the quantity of soil organic matter (SOM), through an increase in C(org) and N(org) contents, and in its quality, through modifications in the C/N and humic acid/fulvic acid ratios, were essentially recorded at the surface layer of treated plots with differential magnitudes according to the inputs and soil type. Quantitative modifications in microbial communities were assessed by means of C-biomass measurements and resulted in an increase in microbial densities fitted with the increase of C(org) and N(org) contents. However, the deduced C incorporation in microbial biomass was negatively correlated with the C/N ratio, demonstrating a strong influence of the type of organic management on the rate of microbial processes. Qualitative modifications in microbial communities were evaluated by the characterization of the genetic structure of bacterial and fungal communities from DNA directly extracted from the soil, using bacterial and fungal automated ribosomal intergenic spacer analysis. Organic amendments led to changes in the bacterial and fungal communities of both sites. However, the magnitude and the specificity of these changes were different between sites, organic amendments, and microorganisms targeted, revealing that the impact of organic management is dependent on the soil and organic input types as well as on the particular ecology of microorganisms. A co-inertia analysis was performed to specify the role of the quantity and quality of SOM on the modifications of the genetic structure. A significant costructure was only observed for Mâcon plots at 0-5 cm between the bacterial genetic structure and the SOM characteristics, demonstrating the influence of the relative amount of the different humic substances (humic and fulvic acids) on microbial composition.}, }
@article {pmid17401596, year = {2008}, author = {Basson, A and Flemming, LA and Chenia, HY}, title = {Evaluation of adherence, hydrophobicity, aggregation, and biofilm development of Flavobacterium johnsoniae-like isolates.}, journal = {Microbial ecology}, volume = {55}, number = {1}, pages = {1-14}, pmid = {17401596}, issn = {0095-3628}, mesh = {Animals ; *Aquaculture ; Bacterial Adhesion/*physiology ; Biofilms/*growth &amp; development ; Carps/microbiology ; Congo Red/metabolism ; Eels/microbiology ; Fish Diseases/*microbiology ; Flavobacterium/classification/growth &amp; development/isolation &amp; purification/*physiology ; Hydrophobic and Hydrophilic Interactions ; Oncorhynchus mykiss/microbiology ; Polystyrenes ; South Africa ; }, abstract = {Flavobacterium spp. isolates have been identified in diverse biofilm structures, but the mechanism of adherence has not been elucidated. The absence of conventional biofilm-associated structures such as fimbriae, pili, and flagella suggest that surface hydrophobicity, and/or autoaggregation and coaggregation may play an important role in adherence and biofilm formation. The biofilm-forming capacity of 29 Flavobacterium johnsoniae-like isolates obtained from South African aquaculture systems was assessed using microtiter plate assays. The role of hydrophobicity [salting aggregation test (SAT) and bacterial adherence to hydrocarbons (BATH) assays], autoaggregation, and coaggregation on biofilm formation by Flavobacterium spp. was also investigated, while biofilm structure was examined using flow cells and microscopy. All isolates displayed a hydrophilic nature, but showed varying levels of adherence in microtiter assays. Significant negative correlations were observed between adherence and biofilm-forming capacity in nutrient-poor medium at 26 degrees C and BATH hydrophobicity and motility, respectively. Isolates displayed strain-to-strain variation in their autoaggregation indices and their abilities to coaggregate with various Gram-negative and Gram-positive organisms. Microcolony and/or biofilm development were observed microscopically, and flavobacterial isolates displayed stronger biofilm structures and interaction with a Vibrio spp. isolate than with an Aeromonas hydrophila isolate. The role of extracellular polysaccharides and specific outer membrane proteins will have to be examined to reveal mechanisms of adherence and coaggregation employed by biofilm-forming F. johnsoniae-like strains.}, }
@article {pmid17401560, year = {2007}, author = {Vlaeminck, SE and Dierick, K and Boon, N and Verstraete, W}, title = {Vertical migration of aggregated aerobic and anaerobic ammonium oxidizers enhances oxygen uptake in a stagnant water layer.}, journal = {Applied microbiology and biotechnology}, volume = {75}, number = {6}, pages = {1455-1461}, doi = {10.1007/s00253-007-0944-6}, pmid = {17401560}, issn = {0175-7598}, mesh = {Bacteria, Aerobic/*metabolism ; Bacteria, Anaerobic/*metabolism ; Models, Biological ; Oxygen Consumption/*physiology ; Quaternary Ammonium Compounds/*metabolism ; *Water Microbiology ; }, abstract = {Ammonium can be removed as dinitrogen gas by cooperating aerobic and anaerobic ammonium-oxidizing bacteria (AerAOB and AnAOB). The goal of this study was to verify putative mutual benefits for aggregated AerAOB and AnAOB in a stagnant freshwater environment. In an ammonium fed water column, the biological oxygen consumption rate was, on average, 76 kg O(2) ha(-1) day(-1). As the oxygen transfer rate of an abiotic control column was only 17 kg O(2) ha(-1) day(-1), biomass activity enhanced the oxygen transfer. Increasing the AnAOB gas production increased the oxygen consumption rate with more than 50% as a result of enhanced vertical movement of the biomass. The coupled decrease in dissolved oxygen concentration increased the diffusional oxygen transfer from the atmosphere in the water. Physically preventing the biomass from rising to the upper water layer instantaneously decreased oxygen and ammonium consumption and even led to the occurrence of some sulfate reduction. Floating of the biomass was further confirmed to be beneficial, as this allowed for the development of a higher AerAOB and AnAOB activity, compared to settled biomass. Overall, the results support mutual benefits for aggregated AerAOB and AnAOB, derived from the biomass uplifting effect of AnAOB gas production.}, }
@article {pmid17397470, year = {2007}, author = {Duncan, SH and Louis, P and Flint, HJ}, title = {Cultivable bacterial diversity from the human colon.}, journal = {Letters in applied microbiology}, volume = {44}, number = {4}, pages = {343-350}, doi = {10.1111/j.1472-765X.2007.02129.x}, pmid = {17397470}, issn = {0266-8254}, mesh = {Anaerobiosis ; Archaea/isolation &amp; purification/metabolism ; Bacteria/*classification/growth &amp; development/*isolation &amp; purification/metabolism ; *Biodiversity ; Colon/*microbiology ; Feces/microbiology ; Humans ; }, abstract = {Knowledge of the composition of the colonic microbiota is important for our understanding of how the balance of these microbes is influenced by diet and the environment, and which bacterial groups are important in maintaining gut health or promoting disease. Molecular methodologies have advanced our understanding of the composition and diversity of the colonic microbiota. Importantly, however, it is the continued isolation of bacterial representatives of key groups that offers the best opportunity to conduct detailed metabolic and functional studies. This also permits bacterial genome sequencing which will accelerate the linkage to functionality. Obtaining new human colonic bacterial isolates can be challenging, because most of these are strict anaerobes and many have rather exact nutritional and physical requirements. Despite this many new species are being isolated and described that occupy distinct niches in the colonic microbial community. This review focuses on these under-studied yet important gut anaerobes.}, }
@article {pmid17396253, year = {2007}, author = {Schmeisser, C and Steele, H and Streit, WR}, title = {Metagenomics, biotechnology with non-culturable microbes.}, journal = {Applied microbiology and biotechnology}, volume = {75}, number = {5}, pages = {955-962}, doi = {10.1007/s00253-007-0945-5}, pmid = {17396253}, issn = {0175-7598}, mesh = {Bacteria/*genetics ; *Biotechnology ; *Genomics ; Soil Microbiology ; }, abstract = {Metagenomics as a new field of research has been developed over the past decade to elucidate the genomes of the non-cultured microbes with the goal to better understand global microbial ecology on the one side, and on the other side it has been driven by the increasing biotechnological demands for novel enzymes and biomolecules. Since it is well accepted that the majority of all microbes has not yet been cultured, the not-yet-cultivated microbes represent a shear unlimited and intriguing resource for the development of novel genes, enzymes and chemical compounds for use in biotechnology. However, with respect to biotechnology, metagenomics faces now two major challenges. Firstly, it has to identify truly novel biocatalysts to fulfil the needs of industrial processes and green chemistry. Secondly, the already available genes and enzymes need to be implemented in production processes to further prove the value of metagenome-derived sequences.}, }
@article {pmid17394043, year = {2007}, author = {Edrington, TS and Callaway, TR and Hallford, DM and Anderson, RC and Nisbet, DJ}, title = {Influence of exogenous triiodothyronine (T3) on fecal shedding of Escherichia coli O157 in cattle.}, journal = {Microbial ecology}, volume = {53}, number = {4}, pages = {664-669}, pmid = {17394043}, issn = {0095-3628}, mesh = {Animals ; Cattle/*microbiology ; Escherichia coli O157/*isolation &amp; purification ; Feces/*microbiology ; Seasons ; Triiodothyronine/*pharmacology ; }, abstract = {Fecal prevalence of Escherichia coli O157 in ruminants is highest in the summer months and decreases to low or undetectable levels in the winter. We hypothesize that the seasonal variation of this pathogen is a result of physiological responses within the host animal to changing day length. The thyroid is an endocrine gland known to respond to changing day length. Two experiments were conducted to determine if a hyperthyroid status would initiate fecal shedding of E. coli O157 in cattle during the winter when shedding is virtually nonexistent (winter experiment) or influence cattle actively shedding E. coli O157 (summer experiment). Yearling cattle were group-penned under dry-lot conditions, adjusted to a high concentrate ration, and randomly assigned to treatment: control (1 mL corn oil injected s.c. daily) or triiodothyronine (T(3); 1.5 mg suspended in corn oil injected s.c daily). Cattle were individually processed daily for collection of fecal and blood samples. Treatment with exogenous T(3) produced a significant change in serum thyroid hormone concentrations indicative of a hyperthyroid status in both experiments. No differences (P>0.10) were observed in fecal shedding of E. coli O157 in the winter experiment. In the summer experiment, fecal shedding of E. coli O157 was decreased (P=0.05) by administration of T(3) during the treatment period (days 1-10), tended to be lower (P=0.08) during the following 7-day period of no treatment, and was lower (P=0.01) when examined across the entire experimental period. Results of this research indicate that the thyroid or its hormones may be involved in the seasonal shedding patterns of E. coli O157 in cattle.}, }
@article {pmid17394042, year = {2007}, author = {Labbé, N and Laurin, V and Juteau, P and Parent, S and Villemur, R}, title = {Microbiological community structure of the biofilm of a methanol-fed, marine denitrification system, and identification of the methanol-utilizing microorganisms.}, journal = {Microbial ecology}, volume = {53}, number = {4}, pages = {621-630}, pmid = {17394042}, issn = {0095-3628}, mesh = {Alphaproteobacteria/classification/metabolism/*physiology ; Biofilms/*growth &amp; development ; DNA, Ribosomal/chemistry ; Gammaproteobacteria/classification/metabolism/*physiology ; In Situ Hybridization, Fluorescence ; Methanol/*metabolism ; Nitrates/metabolism ; Quebec ; RNA, Ribosomal, 16S/chemistry ; Sequence Analysis, DNA ; *Water Purification ; }, abstract = {We demonstrated in a previous study that the biofilm of the methanol-fed fluidized marine denitrification reactor at the Montreal Biodome was composed of at least 15 bacterial phylotypes. Among those were 16S ribosomal RNA (rDNA) gene sequences affiliated to Hyphomicrobium spp., and Methylophaga spp.; the latter made up 70% of a clone library. By using fluorescent in situ hybridization (FISH), we investigated the structure of the biofilm during the colonization process in the denitrification reactor by targeting most of the bacterial families that the 16S rDNA gene library suggested would occur in the biofilm. Our results revealed that gamma-Proteobacteria (mostly Methylophaga spp.) accounted for up to 79% of the bacterial population, confirming the abundance of Methylophaga spp. within the biofilm. alpha-Proteobacteria represented 27-57% of the population, which included Hyphomicrobium spp. that appeared after 20 days of colonization and represented 7-8% of the population. We noticed a great abundance and diversity of eukaryotic cells, which made up 20% of the biomass at the beginning of the colonization but decreased to 3-5% in the mature biofilm. We then used FISH combined with microautoradiography (MAR-FISH) to identify the methylotrophs in the biofilm. The results showed that alpha-Proteobacteria used (14)C methanol in the presence of nitrate, suggesting their involvement in denitrification. Despite their abundance, Methylophaga spp. did not assimilate methanol under those conditions.}, }
@article {pmid17394041, year = {2007}, author = {Verma, VC and Gond, SK and Kumar, A and Kharwar, RN and Strobel, G}, title = {The endophytic mycoflora of bark, leaf, and stem tissues of Azadirachta indica A. Juss (neem) from Varanasi (India).}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {119-125}, pmid = {17394041}, issn = {0095-3628}, mesh = {Azadirachta/*microbiology ; Biodiversity ; Fungi/*classification/isolation &amp; purification/physiology ; India ; Plant Bark/microbiology ; Plant Leaves/microbiology ; Plant Stems/microbiology ; }, abstract = {A systematic study was made of the endophytes of Azadirachta indica A. Juss (the neem tree) growing in several of its natural habitats in India. A total of 233 isolates of endophytic fungi representing 18 fungal taxa were obtained from segments of bark, stem, and leaves of this tree. Hyphomycetes (62.2%) were the most prevalent followed by the Coelomycetes (27.4%) and Mycelia Sterilia (7.7%). As mathematically determined, the maximum species richness and frequency of colonization of endophytes appeared in leaf segments rather than stem and bark tissues from each location. Endophytic colonization frequency was also greater in leaves (45.5%) than bark (31.5%). The leaf samples from all locations were nearly constant in their endophytic composition, whereas bark samples showed maximum diversity at different locations. Inter-site comparisons for endophytic diversity, however, were not significantly different with Loc1 and Loc2 having a maximum of 66.67% Jc. The smallest similarity was between Loc2 and Loc3 of 54.17% Jc. The dominant endophytic fungi isolated were Phomopsis oblonga, Cladosporium cladosporioides, Pestalotiopsis sp., Trichoderma sp, and Aspergillus sp. Genera such as Periconia, Stenella, and Drechslera are reported here for the first time as endophytes from this host plant. This report illustrates the value of sampling different tissues of a given plant in several locations to obtain the greatest species diversity of endophytes. The rich and sizeable collection of endophytic fungi from this specific plant may represent a unique source of one or more of the interesting and useful bioactive compounds normally associated with A. indica such as the azadirachtins and related tetranortriterpenoids.}, }
@article {pmid17394040, year = {2007}, author = {Huang, YL and Dobretsov, S and Ki, JS and Yang, LH and Qian, PY}, title = {Presence of acyl-homoserine lactone in subtidal biofilm and the implication in larval behavioral response in the polychaete Hydroides elegans.}, journal = {Microbial ecology}, volume = {54}, number = {2}, pages = {384-392}, pmid = {17394040}, issn = {0095-3628}, mesh = {4-Butyrolactone/*analogs &amp; derivatives/analysis ; Animals ; Bacteria/chemistry ; *Bacterial Physiological Phenomena ; *Biofilms ; Chromatography, Gas ; Larva/physiology ; Mass Spectrometry ; Polychaeta/*microbiology/*physiology ; Quorum Sensing ; Seawater/*microbiology ; }, abstract = {Quorum sensing (QS) signals have been considered to play important roles in biofilm development and in the attractiveness of biofilms to higher organisms in marine ecosystem. In this study, bacterial QS signalsacylated homoserine lactone derivatives (AHLs) were detected in 2-, 4-, and 6-day-old subtidal biofilms by using AHLs reporter strains. N-dodecanoyl-homoserine lactone (C12-HSL) was identified in 6-day-old biofilm at a concentration of 9.04 microg cm(-minus;2) (3.36 mmol l(-minus;1)). To investigate the possible role of AHLs in the consequent eventlarval settlement of the polychaete Hydroides elegans onto subtidal biofilmsseven biofilm-derived bacteria that effectively induced larval settlement of H. elegans, were screened for AHL production. One of them, the Vibrio sp. UST950701-007, produced N-hexanoyl-homoserine lactone (C6-HSL). Larval settlement bioassay showed that C6-HSL, C12-HSL, and 3-oxo-octanoyl-homoserine lactone (3-oxo-C8-HLS) at certain concentrations induced some initial larval settlement behaviors such as reducing swimming speed, crawling on the bottom. However, these AHLs did not effectively induce larval settlement in comparison to the effective settlement inducer 3-isobutyl-1-methylxanthine. The possible chemokinetic mechanism and indirect effects of AHLs on larval settlement are suggested.}, }
@article {pmid17394039, year = {2007}, author = {Wei, G and Lu, H and Zhou, Z and Xie, H and Wang, A and Nelson, K and Zhao, L}, title = {The microbial community in the feces of the giant panda (Ailuropoda melanoleuca) as determined by PCR-TGGE profiling and clone library analysis.}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {194-202}, pmid = {17394039}, issn = {0095-3628}, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Electrophoresis ; Feces/*microbiology ; Female ; Gene Library ; Male ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry ; Ursidae/*microbiology ; }, abstract = {Despite having a typical carnivorous digestive tract, the giant panda has a diet consisting exclusively of bamboo, a low-efficiency food source. Given this paradox, we sought to investigate if the giant panda digestive tract is inhabited by organisms indicative of high cellulose diet or their gastrointestinal tract anatomy. The diversity and dynamics of the predominant bacteria in the fecal flora of two adult (male and female) and one young (male) giant panda reared in two different zoos over a 2-year period was studied using 16S rDNA-based approaches. The temperature gradient gel electrophoresis (TGGE) profiles of the 16S rDNA V3 region of the three individuals were highly similar. The structure of their fecal flora remained relatively stable over the 2-year period. Both the most predominant band in TGGE patterns shared by the three pandas and the biggest operational taxonomic unit (OTU) in the clone library were phylogenetically related to Escherichia coli. Gram-negative, facultative bacteria constituted almost 60% of the whole community in the clone library. All the OTUs were related to previously described phylotypes known to reside in the intestine or rumen. The results of our study indicate that the predominant bacterial populations in the intestine of the three pandas were markedly different from that of herbivores. The unbalanced intestinal community structure may play a role in the inefficient digestion of bamboo by the giant pandas.}, }
@article {pmid17394038, year = {2008}, author = {Braeken, K and Daniels, R and Vos, K and Fauvart, M and Bachaspatimayum, D and Vanderleyden, J and Michiels, J}, title = {Genetic determinants of swarming in Rhizobium etli.}, journal = {Microbial ecology}, volume = {55}, number = {1}, pages = {54-64}, pmid = {17394038}, issn = {0095-3628}, mesh = {Bacterial Proteins/*genetics/metabolism ; DNA Transposable Elements/genetics ; *Gene Expression Regulation, Bacterial ; *Movement ; Mutation ; Phaseolus/microbiology ; Quorum Sensing/genetics ; Rhizobium etli/*genetics/growth &amp; development/*physiology ; Symbiosis ; }, abstract = {Swarming motility is considered to be a social phenomenon that enables groups of bacteria to move coordinately atop solid surfaces. The differentiated swarmer cell population is embedded in an extracellular slime layer, and the phenomenon has previously been linked with biofilm formation and virulence. The gram-negative nitrogen-fixing soil bacterium Rhizobium etli CNPAF512 was previously shown to display swarming behavior on soft agar plates. In a search for novel genetic determinants of swarming, a detailed analysis of the swarming behavior of 700 miniTn5 mutants of R. etli was performed. Twenty-four mutants defective in swarming or displaying abnormal swarming patterns were identified and could be divided into three groups based on their swarming pattern. Fourteen mutants were completely swarming deficient, five mutants showed an atypical swarming pattern with no completely smooth edge and local extrusions, and five mutants displayed an intermediate swarming phenotype. Sequence analysis of the targeted genes indicated that the mutants were likely affected in quorum-sensing, polysaccharide composition or export, motility, and amino acid and polyamines metabolism. Several of the identified mutants displayed a reduced symbiotic nitrogen fixation activity.}, }
@article {pmid17393054, year = {2007}, author = {Voss, JD and Mills, DK and Myers, JL and Remily, ER and Richardson, LL}, title = {Black band disease microbial community variation on corals in three regions of the wider Caribbean.}, journal = {Microbial ecology}, volume = {54}, number = {4}, pages = {730-739}, pmid = {17393054}, issn = {0095-3628}, support = {S06GM8205/GM/NIGMS NIH HHS/United States ; }, mesh = {Alphaproteobacteria/*classification/*genetics/isolation &amp; purification/pathogenicity ; Animals ; Anthozoa/classification/*microbiology ; Caribbean Region ; Cyanobacteria/*classification/*genetics/isolation &amp; purification/pathogenicity ; DNA, Bacterial/analysis/isolation &amp; purification ; DNA, Ribosomal/analysis ; *Ecosystem ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Black band disease (BBD) is a pathogenic consortium of microorganisms that primarily affects massive framework-building scleractinian corals on reefs worldwide. There has been considerable debate concerning the microbial community composition of BBD. The aim of this study was to utilize microbial profiling to assess overall patterns of variation in the BBD bacterial community with respect to geographic location, host coral species, time, and nutrient regime. Length heterogeneity polymerase chain reaction (LH-PCR) was employed to differentiate BBD communities based on the natural variation in the sequence lengths within hypervariable domains of the 16S rRNA gene. Analysis of LH-PCR profiles of 97 BBD samples using multivariate ordination methods and analysis of similarity revealed significant clustering with respect to geographic region when comparing BBD sampled from reefs near Lee Stocking Island in the Bahamas' Exuma Chain, the Northern Florida Keys (NFK), and St. John in the US Virgin Islands. There was much variability in BBD community composition on a regional basis, between sites in the NFK, and in terms of coral host species. The observed differences among BBD microbial community profiles were driven primarily by variation in relative abundance of 313-316-bp amplicons, which correspond to cyanobacteria and alpha-proteobacteria. The results obtained in this study support previous reports of intrinsic variability and complexity of the BBD microbial community but also suggest that this variability has biogeographic patterns.}, }
@article {pmid17393053, year = {2008}, author = {Jahromi, F and Aroca, R and Porcel, R and Ruiz-Lozano, JM}, title = {Influence of salinity on the in vitro development of Glomus intraradices and on the in vivo physiological and molecular responses of mycorrhizal lettuce plants.}, journal = {Microbial ecology}, volume = {55}, number = {1}, pages = {45-53}, pmid = {17393053}, issn = {0095-3628}, mesh = {Fungi/drug effects/*growth &amp; development/physiology ; Lactuca/*drug effects/genetics/*microbiology/physiology ; Mycorrhizae/*drug effects ; Oxygen Consumption/physiology ; Plant Leaves/drug effects/microbiology/physiology ; Plant Proteins/genetics/metabolism ; Proline/metabolism ; Sodium Chloride/*pharmacology ; Spores, Fungal/physiology ; Symbiosis ; }, abstract = {Increased salinization of arable land is expected to have devastating global effects in the coming years. Arbuscular mycorrhizal fungi (AMF) have been shown to improve plant tolerance to abiotic environmental factors such as salinity, but they can be themselves negatively affected by salinity. In this study, the first in vitro experiment analyzed the effects of 0, 50, or 100 mM NaCl on the development and sporulation of Glomus intraradices. In the second experiment, the effects of mycorrhization on the expression of key plant genes expected to be affected by salinity was evaluated. Results showed that the assayed isolate G. intraradices DAOM 197198 can be regarded as a moderately salt-tolerant AMF because it did not significantly decrease hyphal development or formation of branching absorbing structures at 50 mM NaCl. Results also showed that plants colonized by G. intraradices grew more than nonmycorrhizal plants. This effect was concomitant with a higher relative water content in AM plants, lower proline content, and expression of Lsp5cs gene (mainly at 50 mM NaCl), lower expression of the stress marker gene Lslea gene, and lower content of abscisic acid in roots of mycorrhizal plants as compared to nonmycorrhizal plants, which suggest that the AM fungus decreased salt stress injury. In addition, under salinity, AM symbiosis enhanced the expression of LsPIP1. Such enhanced gene expression could contribute to regulating root water permeability to better tolerate the osmotic stress generated by salinity.}, }
@article {pmid17392183, year = {2007}, author = {Laurent, F and Rodríguez-Nava, V and Noussair, L and Couble, A and Nicolas-Chanoine, MH and Boiron, P}, title = {Nocardia ninae sp. nov., isolated from a bronchial aspirate.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {57}, number = {Pt 4}, pages = {661-665}, doi = {10.1099/ijs.0.64476-0}, pmid = {17392183}, issn = {1466-5026}, mesh = {Asthma ; Bronchi/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Humans ; Middle Aged ; Molecular Sequence Data ; Nocardia/*classification/cytology/*isolation &amp; purification/physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A Gram-positive and acid-fast filamentous bacterium (OFN 02.72(T)) was isolated from a bronchial aspirate from a 53-year-old patient. Chemotaxonomic data supported the affiliation of this organism to the genus Nocardia, and the phenotypic characteristics demonstrated that the strain differed from all previously described Nocardia species. Restriction enzyme analysis of the hsp65 gene (encoding the 65 kDa heat-shock protein) and sequencing of the 16S rRNA and hsp65 genes confirmed that this isolate is unique. The most closely related type strains were Nocardia alba YIM 30243(T) (=DSM 44684(T)) and Nocardia jejuensis N3-2(T) (=JCM 13281(T)) (with 16S rRNA gene sequence similarities of 98.3 and 97.2 %, respectively). On the basis of this polyphasic study, strain OFN 02.72(T) represents a novel species within the genus Nocardia, for which the name Nocardia ninae sp. nov. is proposed. The type strain is OFN 02.72(T) (=CIP 108955(T)=DSM 44978(T)).}, }
@article {pmid17391334, year = {2007}, author = {Halet, D and Defoirdt, T and Van Damme, P and Vervaeren, H and Forrez, I and Van de Wiele, T and Boon, N and Sorgeloos, P and Bossier, P and Verstraete, W}, title = {Poly-beta-hydroxybutyrate-accumulating bacteria protect gnotobiotic Artemia franciscana from pathogenic Vibrio campbellii.}, journal = {FEMS microbiology ecology}, volume = {60}, number = {3}, pages = {363-369}, doi = {10.1111/j.1574-6941.2007.00305.x}, pmid = {17391334}, issn = {0168-6496}, mesh = {Animals ; Aquaculture/methods ; Artemia/*microbiology ; Bacteria/growth &amp; development/isolation &amp; purification/*metabolism ; Bioreactors ; *Germ-Free Life ; Hydroxybutyrates/*metabolism ; Polyesters/*metabolism ; Survival Analysis ; Vibrio/*pathogenicity ; Vibrio Infections/microbiology/*prevention &amp; control ; }, abstract = {A poly-beta-hydroxybutyrate (PHB)-accumulating enrichment culture was obtained using activated sludge from a polyphosphate-accumulating reactor as inoculum. PHB accumulated by the enrichment culture significantly enhanced the survival of Artemia nauplii, infected with the virulent pathogen Vibrio campbellii LMG 21363. A strain was isolated from the enrichment culture, based on its ability to accumulate PHB, and 16S rRNA gene sequencing of the isolate revealed 99% sequence similarity to Brachymonas denitrificans AS-P1. The isolate, named PHB2, showed good PHB-accumulating activity (up to 32% of the cell dry weight). PHB accumulated by isolate PHB2 was able to protect Artemia completely from the V. campbellii strain. Our data indicate that PHB-accumulating bacteria, such as B. denitrificans PHB2, could be used as an an effective and economically interesting alternative strategy to control infections in aquaculture.}, }
@article {pmid17388902, year = {2007}, author = {Rajashekar, B and Samson, P and Johansson, T and Tunlid, A}, title = {Evolution of nucleotide sequences and expression patterns of hydrophobin genes in the ectomycorrhizal fungus Paxillus involutus.}, journal = {The New phytologist}, volume = {174}, number = {2}, pages = {399-411}, doi = {10.1111/j.1469-8137.2007.02022.x}, pmid = {17388902}, issn = {0028-646X}, mesh = {Amino Acid Sequence ; Base Sequence ; Basidiomycota/*genetics ; Biological Evolution ; *Evolution, Molecular ; Fungal Proteins/*genetics ; Gene Expression Profiling ; *Gene Expression Regulation, Fungal ; Genes, Fungal ; Molecular Sequence Data ; Mycorrhizae/*genetics ; Oligonucleotide Array Sequence Analysis ; Pseudogenes ; Selection, Genetic ; }, abstract = {Hydrophobins are small, secreted proteins that play important roles in the development of pathogenic and symbiotic fungi. Evolutionary mechanisms generating sequence and expression divergence among members in hydrophobin gene families are largely unknown. Seven hydrophobin (hyd) genes and one hyd pseudogene were isolated from strains of the ectomycorrhizal fungus Paxillus involutus. Sequences were analysed using phylogenetic methods. Expression profiles were inferred from microarray experiments. The hyd genes included both young (recently diverged) and old duplicates. Some young hyd genes exhibited an initial phase of enhanced sequence evolution owing to relaxed or positive selection. There was no significant association between sequence divergence and variation in expression levels. However, three hyd genes displayed a shift in the expression levels or an altered tissue specificity following duplication. The Paxillus hyd genes evolve according to the so-called birth-and-death model in which some duplicates are maintained for a long time, whereas others are inactivated through mutations. The role of subfunctionalization and/or neofunctionalization for preserving the hyd duplicates in the genome is discussed.}, }
@article {pmid17381758, year = {2007}, author = {Wise, MG and Siragusa, GR}, title = {Quantitative analysis of the intestinal bacterial community in one- to three-week-old commercially reared broiler chickens fed conventional or antibiotic-free vegetable-based diets.}, journal = {Journal of applied microbiology}, volume = {102}, number = {4}, pages = {1138-1149}, doi = {10.1111/j.1365-2672.2006.03153.x}, pmid = {17381758}, issn = {1364-5072}, mesh = {Animal Feed/*microbiology ; Animals ; Anti-Bacterial Agents ; Bacteria/*classification/genetics/isolation &amp; purification ; Chickens/*microbiology ; Gastrointestinal Tract/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; Vegetables ; }, abstract = {AIMS: To explore the effect of drug-free poultry production on the intestinal microflora of broiler chickens, the bacterial community of this environment was quantitatively profiled in both conventionally reared birds and birds reared without antibiotic growth promotants (AGPs) on a vegetable-based diet.<br><br>METHODS AND RESULTS: Quantitative, real-time PCR with group-specific 16S rDNA primer sets was used to enumerate the abundance of the following chicken gastrointestinal (GI) tract phylogenetic groups: the Clostridium leptum-Faecalibacterium prausnitzii subgroup (Clostridium genus cluster IV), the Clostridium coccoides - Eubacterium rectale subgroup (Clostridium cluster XIVa and XIVb), the Bacteroides group (including Prevotella and Porphyromonas), Bifidobacterium spp., the Enterobacteriaceae, the Lactobacillus group (including the genera Leuconostoc, Pediococcus, Aerococcus and Weissella), the Clostridium perfringens subgroup (Clostridium cluster I), Enterococcus spp., Veillonella spp., Atopobium spp., Campylobacter spp. and the domain Bacteria. A species-specific 5'-nuclease (Taqman) assay was also employed to specifically assess Cl. perfringens abundance. Ten birds were sampled from each of two commercial chicken houses, one in which feed was supplemented with AGPs and exogenous animal protein, and the other vegetable-based and drug-free, at 7, 14 and 21 days of age. The ileal community was dominated by two large populations, the lactobacilli and the Enterobacteriaceae, with those taxa much more numerous in drug-free vegetable-based diet fed birds than those conventionally reared at the 7- and 14-day time periods. The progressive changes in microflora in both the conventional and drug-free caeca were similar to each other, with the Enterobacteriaceae sequences dominating at day 7, but being replaced by obligate anaerobe signature sequences by day 14. Of note was the finding that all the day 14 and day 21 replicate caecal samples from the drug-free house were positive for Campylobacter spp. averaging >10(8) 16S rDNA gene copies per gram wet weight.<br><br>CONCLUSIONS: Quantitative, real-time PCR indicates that the effects of drug-free rearing on the chicken GI tract microbial community are most pronounced in the ileal region, but AGPs may be important in controlling Campylobacter colonization of the caecum.<br><br>A quantitative taxonomic understanding of the shifting microbial ecology of the broiler chicken gut microbiota is important in the light of AGP withdrawal. AGP withdrawal has occurred in response to concerns over the transfer of antimicrobial-resistant bacteria to humans via the food production chain.}, }
@article {pmid17380356, year = {2007}, author = {Siragusa, AJ and Swenson, JE and Casamatta, DA}, title = {Culturable bacteria present in the fluid of the hooded-pitcher plant Sarracenia minor based on 16S rDNA gene sequence data.}, journal = {Microbial ecology}, volume = {54}, number = {2}, pages = {324-331}, pmid = {17380356}, issn = {0095-3628}, mesh = {Bacteria/classification/*genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sarraceniaceae/*microbiology ; }, abstract = {The culturable microbial community within the pitcher fluid of 93 Sarracenia minor carnivorous plants was examined over a 2-year study. Many aspects of the plant/bacterial/insect interaction within the pitcher fluid are minimally understood because the bacterial taxa present in these pitchers have not been identified. Thirteen isolates were characterized by 16S rDNA sequencing and subsequent phylogenetic analysis. The Proteobacteria were the most abundant taxa and included representatives from Serratia, Achromobacter, and Pantoea. The Actinobacteria Micrococcus was also abundant while Bacillus, Lactococcus, Chryseobacterium, and Rhodococcus were infrequently encountered. Several isolates conformed to species identifiers (>98% rDNA gene sequence similarity) including Serratia marcescens (isolates found in 27.5% of pitchers), Achromobacter xylosoxidans (37.6%), Micrococcus luteus (40.9%), Bacillus cereus (isolates found in 10.2%), Bacillus thuringiensis (5.4%), Lactococcus lactis (17.2%), and Rhodococcus equi (2.2%). Species-area curves suggest that sampling efforts were sufficient to recover a representative culturable bacterial community. The bacteria present represent a diverse community probably as a result of introduction by insect vectors, but the ecological significance remains under explored.}, }
@article {pmid17379702, year = {2007}, author = {Harrison, F}, title = {Microbial ecology of the cystic fibrosis lung.}, journal = {Microbiology (Reading, England)}, volume = {153}, number = {Pt 4}, pages = {917-923}, doi = {10.1099/mic.0.2006/004077-0}, pmid = {17379702}, issn = {1350-0872}, mesh = {Burkholderia cepacia complex/isolation &amp; purification ; Cystic Fibrosis/diagnosis/drug therapy/*microbiology ; Haemophilus influenzae/isolation &amp; purification ; Humans ; Lung/*microbiology/pathology ; Pseudomonas aeruginosa/isolation &amp; purification ; Respiratory Tract Infections/*microbiology ; Staphylococcus aureus/isolation &amp; purification ; }, abstract = {Understanding the microbial flora of the cystic fibrosis (CF) respiratory tract is of considerable importance, as patient morbidity and death are primarily caused by chronic respiratory infections. However, chronically colonized CF airways represent a surprisingly complex and diverse ecosystem. The precise contributions of different microbes to patient morbidity, and in particular the importance of inter-specific interactions, remain largely unelucidated. The importance of within-species genetic and phenotypic variation has similarly received limited explicit attention. While a host of studies provide data on the microbial species recovered from patients, these are often incomparable due to differences in sampling and data reporting, or do not present the data in a way that aids our understanding of the ecosystem within each patient. This review brings together a cross-section of recent research on the CF airways and the microbes which infect them. The results presented suggest that understanding the CF lung in terms of its community and evolutionary ecology could benefit our understanding of disease progression and influence treatment regimens.}, }
@article {pmid17372705, year = {2007}, author = {Palmroth, MR and Koskinen, PE and Kaksonen, AH and Münster, U and Pichtel, J and Puhakka, JA}, title = {Metabolic and phylogenetic analysis of microbial communities during phytoremediation of soil contaminated with weathered hydrocarbons and heavy metals.}, journal = {Biodegradation}, volume = {18}, number = {6}, pages = {769-782}, doi = {10.1007/s10532-007-9105-y}, pmid = {17372705}, issn = {0923-9820}, mesh = {Aminopeptidases/metabolism ; Bacteria/enzymology/genetics ; Biodegradation, Environmental ; Cluster Analysis ; Cytochrome P-450 CYP4A/genetics ; Dioxygenases ; Gas Chromatography-Mass Spectrometry ; Gasoline ; Hydrocarbons/*metabolism ; Metals, Heavy/*metabolism ; Multienzyme Complexes/genetics ; Oxygenases/genetics ; *Phylogeny ; Populus/*metabolism ; *Soil Microbiology ; Soil Pollutants/*metabolism ; Substrate Specificity ; *Weather ; }, abstract = {In the current study, the microbial ecology of weathered hydrocarbon and heavy metal contaminated soil undergoing phytoremediation was studied. The relationship of functional diversity, measured as carbon source utilisation in Biolog plates and extracellular enzymatic activities, and genetic diversity of bacteria was evaluated. Denaturing gradient gel electrophoresis was used for community analyses at the species level. Bulk soil and rhizosphere soil from pine and poplar plantations were analysed separately to determine if the plant rhizosphere impacted hydrocarbon degradation. Prevailing microbial communities in the field site were both genetically and metabolically diverse. Furthermore, both tree rhizosphere and fertilisation affected the compositions of these communities and increased activities of extracellular aminopeptidases. In addition, the abundance of alkane hydroxylase and naphthalene dioxygenase genes in the communities was low, but the prevalence of these genes was increased by the addition of bioavailable hydrocarbons. Tree rhizosphere communities had greater hydrocarbon degradation potential than those of bulk soil. Hydrocarbon utilising communities were dominated generally by the species Ralstonia eutropha and bacteria belonging to the genus Burkholderia. Despite the presence of viable hydrocarbon-degrading microbiota, decomposition of hydrocarbons from weathered hydrocarbon contaminated soil over four years, regardless of the presence of vegetation, was low in unfertilised soil. Compost addition enhanced the removal of hydrocarbons.}, }
@article {pmid17372663, year = {2007}, author = {Giri, B and Kapoor, R and Mukerji, KG}, title = {Improved tolerance of Acacia nilotica to salt stress by Arbuscular mycorrhiza, Glomus fasciculatum may be partly related to elevated K/Na ratios in root and shoot tissues.}, journal = {Microbial ecology}, volume = {54}, number = {4}, pages = {753-760}, pmid = {17372663}, issn = {0095-3628}, mesh = {Acacia/chemistry/drug effects/*growth &amp; development/microbiology ; Fungi/growth &amp; development/*isolation &amp; purification/metabolism ; Heat-Shock Response ; Mycorrhizae ; Plant Roots/*chemistry/microbiology ; Plant Shoots/*chemistry/microbiology ; Potassium/*chemistry ; Seedlings/growth &amp; development ; Sodium/*chemistry ; Sodium Chloride/*pharmacology ; Soil/analysis ; }, abstract = {A pot experiment was conducted to examine the effect of arbuscular mycorrhizal fungus, Glomus fasciculatum, and salinity on the growth of Acacia nilotica. Plants were grown in soil under different salinity levels (1.2, 4.0, 6.5, and 9.5 dS m(-1)). In saline soil, mycorrhizal colonization was higher at 1.2, 4.0, and 6.5 dS m(-1) salinity levels in AM-inoculated plants, which decreased as salinity levels further increased (9.5 dS m(-1)). Mycorrhizal plants maintained greater root and shoot biomass at all salinity levels compared to nonmycorrhizal plants. AM-inoculated plants had higher P, Zn, and Cu concentrations than uninoculated plants. In mycorrhizal plants, nutrient concentrations decreased with the increasing levels of salinity, but were higher than those of the nonmycorrhizal plants. Mycorrhizal plants had greater Na concentration at low salinity levels (1.2, 4.0 dS m(-1)), which lowered as salinity levels increased (6.5, 9.5 dS m(-1)), whereas Na concentration increased in control plants. Mycorrhizal plants accumulated a higher concentration of K at all salinity levels. Unlike Na, the uptake of K increased in shoot tissues of mycorrhizal plants with the increasing levels of salinity. Our results indicate that mycorrhizal fungus alleviates deleterious effects of saline soils on plant growth that could be primarily related to improved P nutrition. The improved K/Na ratios in root and shoot tissues of mycorrhizal plants may help in protecting disruption of K-mediated enzymatic processes under salt stress conditions.}, }
@article {pmid17370029, year = {2007}, author = {Mucciarelli, M and Camusso, W and Maffei, M and Panicco, P and Bicchi, C}, title = {Volatile terpenoids of endophyte-free and infected peppermint (Mentha piperita L.): chemical partitioning of a symbiosis.}, journal = {Microbial ecology}, volume = {54}, number = {4}, pages = {685-696}, pmid = {17370029}, issn = {0095-3628}, mesh = {Fungi/chemistry/growth &amp; development/*isolation &amp; purification ; Mentha/*chemistry/growth &amp; development/*microbiology ; Mycelium/*chemistry ; Plant Leaves/chemistry/microbiology ; Plant Roots/chemistry/microbiology ; *Symbiosis ; Terpenes/*analysis ; Volatilization ; }, abstract = {The study reports the effects on volatiles of an endophytic fungus inhabiting asymptomatically the leaves of peppermint. By means of headspace solid-phase microextraction (HS-SPME) and gaschromatography-mass spectrometry (GC-MS) terpenoids were sampled in time course from the head space of peppermint leaves and roots. After removal of the mycelium from peppermint tissues, fungal volatiles were analyzed and compared with those of pure fungal cultures. In the presence of the endophyte, the relative amount of all main compounds increased in leaves. Starting from the first 14 d of culture, (-)-menthone and (+)-neomenthol were consistently higher than in control plants. On the contrary, (+)-menthofuran increased only by 28 d of culture. Root volatiles were also dramatically altered by the presence of the fungus, with (+)-pulegone accounting for at least 44% of the total volatile emission. (+)-Pulegone was also the main compound of PGP-HSF mycelium isolated from peppermint roots. The sesquiterpenoid cuparene was found as a novel compound of peppermint leaf headspace and was a main volatile of ex planta and pure culture mycelia. The chemical spectrum of terpenoids and their distribution among peppermint roots, leaves, and mycelia are likely to account for a fine regulation of the mutualism in planta and for the acquisition by the fungus of novel metabolic competences.}, }
@article {pmid17370028, year = {2007}, author = {Roeselers, G and van Loosdrecht, MC and Muyzer, G}, title = {Heterotrophic pioneers facilitate phototrophic biofilm development.}, journal = {Microbial ecology}, volume = {54}, number = {3}, pages = {578-585}, pmid = {17370028}, issn = {0095-3628}, mesh = {Biofilms/*growth &amp; development/radiation effects ; Cluster Analysis ; Cyanobacteria/classification/*genetics/*growth &amp; development ; Electrophoresis/methods ; Light ; Molecular Sequence Data ; Phylogeny ; Polycarboxylate Cement/metabolism ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Phototrophic biofilms are matrix-enclosed microbial communities, mainly driven by light energy. In this study, the successional changes in community composition of freshwater phototrophic biofilms growing on polycarbonate slides under different light intensities were investigated. The sequential changes in community composition during different developmental stages were examined by denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rRNA gene fragments in conjugation with sequencing and phylogenetic analysis. Biofilm development was monitored with subsurface light sensors. The development of these biofilms was clearly light dependent. It was shown that under high light conditions the initial colonizers of the substratum predominantly consisted of green algae, whereas at low light intensities, heterotrophic bacteria were the initial colonizers. Cluster analysis of DGGE banding patterns revealed a clear correlation in the community structure with the developmental phases of the biofilms. At all light intensities, filamentous cyanobacteria affiliated to Microcoleus vaginatus became dominant as the biofilms matured. It was shown that the initial colonization phase of the phototrophic biofilms is shorter on polycarbonate surfaces precolonized by heterotrophic bacteria.}, }
@article {pmid17367270, year = {2007}, author = {Sundin, GW}, title = {Genomic insights into the contribution of phytopathogenic bacterial plasmids to the evolutionary history of their hosts.}, journal = {Annual review of phytopathology}, volume = {45}, number = {}, pages = {129-151}, doi = {10.1146/annurev.phyto.45.062806.094317}, pmid = {17367270}, issn = {0066-4286}, mesh = {Bacteria/genetics/*pathogenicity ; Evolution, Molecular ; Plant Diseases/*microbiology ; *Plasmids ; Pseudomonas syringae/pathogenicity ; Xanthomonas/pathogenicity ; }, abstract = {Plasmids are common residents of phytopathogenic bacteria and contribute significantly to host evolution in a multi-faceted manner. Plasmids tend to encode determinants of virulence and ecological fitness that can enhance adaptation to a specific niche or can influence niche expansion. Many of these determinants appear to have been acquired from other bacteria via horizontal transfer, illustrating an important function of plasmids in the acquisition of sequences that enable rapid evolution. These genes can ultimately be delivered to the host chromosome through plasmid integration events, thus stabilizing important acquired determinants within the genome. Most plasmids characterized in phytopathogenic bacteria are self-transmissible and possess suites of genes encoding type IV secretion systems. In addition, the phytopathogenic bacterial plasmid "mobilome" includes insertion sequence and other transposable elements that contribute to the movement of sequences within and between genomes. Possession of mosaic and ever-changing plasmids allows phytopathogenic bacteria to maintain a dynamic, flexible genome and possible advantage in host-pathogen and other environmental interactions that belies the concept of plasmids as apparently selfish genetic elements.}, }
@article {pmid17365326, year = {2007}, author = {Means, NE and Kremer, RJ and Ramsier, C}, title = {Effects of glyphosate and foliar amendments on activity of microorganisms in the soybean rhizosphere.}, journal = {Journal of environmental science and health. Part. B, Pesticides, food contaminants, and agricultural wastes}, volume = {42}, number = {2}, pages = {125-132}, doi = {10.1080/03601230601123227}, pmid = {17365326}, issn = {0360-1234}, mesh = {Bacteria/*drug effects/growth &amp; development ; Biodegradation, Environmental ; Glycine/*analogs &amp; derivatives/analysis/pharmacology ; Herbicides/analysis/*pharmacology ; Oxidoreductases/metabolism ; Soil/analysis ; *Soil Microbiology ; Glycine max/*growth &amp; development ; Time Factors ; Glyphosate ; }, abstract = {A field study was conducted to determine the effects of glyphosate on microbial activity in the rhizosphere of glyphosate-resistant (GR) soybean and to evaluate interactions with foliar amendments. Glyphosate at 0.84 kg ae ha(-1) was applied GR soybean at the V4-V5 development stages. Check treatments included a conventional herbicide tank mix (2003 study only) and no herbicides (hand-weeded). Ten days after herbicide application, a commercially available biostimulant and a urea solution (21.0% N) were applied to soybean foliage at 33.5 mL ha(-1) and 9.2 kg ha(-1), respectively. Soil and plant samples were taken 0, 5, 10, 15, 20 and 25 days after herbicide application then assayed for enzyme and respiration activities. Soil respiration and enzyme activity increased with glyphosate and foliar amendment applications during the 2002 growing season; however, similar increases were not observed in 2003. Contrasting cumulative rainfall between 2002 and 2003 likely accounted for differences in soil microbial activities. Increases in soil microbial activity in 2002 suggest that adequate soil water and glyphosate application acted together to increase microbial activity. Our study suggests that general soil microbial properties including those involving C and N transformations are not sensitive enough to detect effects of glyphosate on rhizosphere microbial activity. Measurements of soil-plant-microbe relationships including specific microbial groups (i.e., root-associated Fusarium spp.) are likely better indicators of impacts of glyphosate on soil microbial ecology.}, }
@article {pmid17364249, year = {2007}, author = {Thiel, V and Leininger, S and Schmaljohann, R and Brümmer, F and Imhoff, JF}, title = {Sponge-specific bacterial associations of the Mediterranean sponge Chondrilla nucula (Demospongiae, Tetractinomorpha).}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {101-111}, pmid = {17364249}, issn = {0095-3628}, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Deltaproteobacteria/classification/genetics/isolation &amp; purification ; Gammaproteobacteria/classification/genetics/isolation &amp; purification ; Gene Library ; Geography ; Mediterranean Sea ; Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S/chemistry ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {A stable and specific bacterial community was shown to be associated with the Mediterranean sponge Chondrilla nucula. The associated bacterial communities were demonstrated to be highly similar for all studied specimens regardless of sampling time and geographical region. In addition, analysis of 16S rDNA clone libraries revealed three constantly C. nucula-associated bacterial phylotypes belonging to the Acidobacteria, the Gamma- and Deltaproteobacteria present in sponge specimens from two Mediterranean regions with distinct water masses (Ligurian Sea and Adriatic Sea). For the first time, candidate division TM7 bacteria were found in marine sponges. A major part (79%) of the C. nucula-derived 16S rDNA sequences were closely related to other sponge-associated bacteria. Phylogenetic analysis identified 14 16S rRNA gene sequence clusters, seven of which consisted of exclusively sponge-derived sequences, whereas the other seven clusters contained additional environmental sequences. This study adds to a growing database on the stability and variability of microbial consortia associated with marine sponges.}, }
@article {pmid17364248, year = {2007}, author = {Aneja, MK and Sharma, S and Fleischmann, F and Stich, S and Heller, W and Bahnweg, G and Munch, JC and Schloter, M}, title = {Influence of ozone on litter quality and its subsequent effects on the initial structure of colonizing microbial communities.}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {151-160}, pmid = {17364248}, issn = {0095-3628}, mesh = {Air Pollutants/*pharmacology ; Bacteria/*classification/growth &amp; development/metabolism ; *Biodiversity ; Fagus/*drug effects/metabolism/microbiology ; Fungi/*classification/growth &amp; development/metabolism ; Genes, rRNA ; Ozone/*pharmacology ; Phylogeny ; Picea/*drug effects/metabolism/microbiology ; *Soil Microbiology ; Trees/microbiology ; }, abstract = {Ozone is considered as the main factor in air pollution related to a decline of forest in North America and Europe. In the present study, the effect of changed litter quality, due to ozone stress to trees, on the microbial communities colonizing the subsequent litter was investigated. Litter bag technique using beech and spruce litter from ozone-stressed and control trees, was combined with 16S and 18S rRNA-based fingerprinting methods and cloning to characterize phylogenetic diversity. Litter bags were incubated for 2 and 8 weeks in a beech-spruce mixed forest. Differences between the structure of microbial communities colonizing control and ozone-exposed litter were evident by fingerprints of 16S and 18S rRNA RT-PCR products. RT-PCR products, from litter degraded for 8 weeks, were cloned to identify the bacterial and fungal groups. Clones similar to members of Actinobacteria dominated the bacterial libraries, whereas effects of changed litter quality were mainly observed for the Proteobacteria. Fungal libraries were dominated by clones similar to Ascomycota members. Reduced proportion of clones similar to Basidiomycota and Zygomycota in library from ozone-stressed spruce trees and Chytridiomycota from ozone-stressed beech trees was observed when compared to their control counterparts. As hypothesized, changed litter quality due to elevated O3 did influence the structure of litter-colonizing microbial communities. However, these differences were not as pronounced as those between the two plant species.}, }
@article {pmid17364247, year = {2007}, author = {Boyd, ES and Cummings, DE and Geesey, GG}, title = {Mineralogy influences structure and diversity of bacterial communities associated with geological substrata in a pristine aquifer.}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {170-182}, pmid = {17364247}, issn = {0095-3628}, mesh = {Bacteria/*classification/genetics/growth &amp; development ; Biodiversity ; Biofilms ; DNA, Bacterial/chemistry ; Ferric Compounds/chemistry ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Quartz/chemistry ; RNA, Ribosomal, 16S/chemistry ; Sequence Analysis, DNA ; Surface Properties ; *Water Microbiology ; }, abstract = {Our understanding of mineralogical influences on subsurface microbial community structure and diversity has been difficult to assess due to difficulties in isolating this variable from others in the subsurface environment. In this study, biofilm coupons were used to isolate specific geological substrata from the surrounding geological matrix during colonization by microorganisms suspended in the surrounding groundwater for an 8-week period. Upon retrieval, the structure and diversity of the microbial community associated with each type of substratum was evaluated using 16S rDNA-based terminal-restriction fragment length polymorphism (T-RFLP). Phylogenetic affiliations of the populations associated with each type of substratum were established based on sequence analysis of near full-length 16S rDNA obtained through construction of a clone library. Hematite, quartz, and saprolite each harbored a community dominated by members of the division Proteobacteria (>67% of community). However, the different substrata selected for different subdivisions of bacteria within the Proteobacteria. After accounting for the influence exerted by substratum type on recovery of DNA from the attached populations, both phylogenetic data and Jaccard and Bray-Curtis similarity indices derived from terminal-restriction fragment (T-RF) profiles suggested a strong mineralogical influence on the structure and composition of the solid phase-associated community. The results suggest that mineralogical heterogeneity influences microbial community structure and diversity in pristine aquifers.}, }
@article {pmid17364246, year = {2007}, author = {Nelson, DM and Ohene-Adjei, S and Hu, FS and Cann, IK and Mackie, RI}, title = {Bacterial diversity and distribution in the holocene sediments of a northern temperate lake.}, journal = {Microbial ecology}, volume = {54}, number = {2}, pages = {252-263}, pmid = {17364246}, issn = {0095-3628}, mesh = {Bacteria/*classification/genetics ; Biodiversity ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Fresh Water/*microbiology ; Geologic Sediments/*microbiology ; Minnesota ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Sediments contain an abundance of microorganisms. However, the diversity and distribution of microorganisms associated with sediments are poorly understood, particularly in lacustrine environments. We used banding patterns from denaturing gradient gel electrophoresis (DGGE) and 16S rDNA sequences to assess the structure of bacterial communities in the Holocene sediments of a meromictic lake in Minnesota. Cluster analysis of the DGGE banding patterns indicates that the early- and middle-Holocene samples group separately from the late-Holocene samples. About 79% of the recovered bacterial sequences cluster with the alpha-, beta-, delta-, epsilon-, and gamma- Proteobacteriaceae and Firmicutes. The remaining approximately 21% lack cultured representatives. The taxonomic lineages of bacteria differ statistically among the early-, middle-, and late-Holocene samples, although the difference is smallest between early- and middle-Holocene samples. Early- and middle-Holocene samples are dominated by epsilon-Proteobacteriaceae, and late-Holocene samples are dominated by sequences from uncultured subphyla. We only recovered delta-Proteobacteriaceae in late-Holocene sediments and alpha- and gamma- Proteobacteriaceae in late- and middle-Holocene sediments. Diversity estimates derived from early-, middle-, and late-Holocene clone libraries indicate that the youngest (late-Holocene) samples had significantly greater bacterial diversity than the oldest (early-Holocene) samples, and the middle-Holocene samples contained intermediate levels of diversity. The observed patterns of diversity may be caused by increased bacterial niche-partitioning in younger sediments that contain a greater abundance of labile organic matter than older sediments.}, }
@article {pmid17364245, year = {2007}, author = {Pankewitz, F and Zöllmer, A and Hilker, M and Gräser, Y}, title = {Presence of Wolbachia in insect eggs containing antimicrobially active anthraquinones.}, journal = {Microbial ecology}, volume = {54}, number = {4}, pages = {713-721}, pmid = {17364245}, issn = {0095-3628}, mesh = {Animals ; Anthraquinones/analysis ; Anti-Bacterial Agents/analysis ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Proteins/genetics ; Coleoptera/chemistry/microbiology/physiology ; Cytoskeletal Proteins/genetics ; DNA, Bacterial/analysis/isolation &amp; purification ; *Hemiptera/chemistry/microbiology/physiology ; Molecular Sequence Data ; Ovum/chemistry/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Wolbachia/classification/genetics/*isolation &amp; purification/physiology ; }, abstract = {Wolbachia are obligatory, cytoplasmatically inherited alpha-proteobacteria, which are common endosymbionts in arthropods where they may cause reproductive abnormalities. Many insects are well known to protect themselves from deleterious microorganisms by antibiotic components. In this study, we addressed the question whether Wolbachia are able to infect insects containing antimicrobial anthraquinones and anthrones, and if so, whether these genotypes of Wolbachia comprise a monophyletic cluster within one of the known supergroups. Leaf beetles of the taxon Galerucini (Galerucinae) are known to contain 1,8-dihydroxylated anthraquinones and anthrones. Also, the scale insect Dactylopius contains an anthraquinone glycoside, carminic acid. Our analyses revealed that a representative of the Galerucini, Galeruca tanaceti and Dactylopius, are indeed infected by endosymbiotic Wolbachia bacteria. Phylogenetic analysis of the wsp and ftsZ genes of these bacteria revealed that strains in G. tanaceti cluster in supergroup A, whereas those present in Dactylopius are distinctive from each other and from those of G. tanaceti. They are clustering in supergroups A and B. Wolbachia strains present in close, but anthraquinone-free relatives of G. tanaceti were shown to belong also to supergroup A. From these results, we can conclude (1) a double infection in Dactylopius, (2) that the presence of antimicrobial compounds such as anthraquinones does not necessarily protect insects from infection by Wolbachia, and (3) that genotypes of Wolbachia-infecting anthraquinone-containing insects most likely do not comprise a unique genotype. These results show that Wolbachia bacteria might be adapted to cope even with conditions usually detrimental to other bacteria and that these adaptations are widespread among Wolbachia supergroups.}, }
@article {pmid17356949, year = {2007}, author = {Enya, J and Shinohara, H and Yoshida, S and Tsukiboshi, T and Negishi, H and Suyama, K and Tsushima, S}, title = {Culturable leaf-associated bacteria on tomato plants and their potential as biological control agents.}, journal = {Microbial ecology}, volume = {53}, number = {4}, pages = {524-536}, pmid = {17356949}, issn = {0095-3628}, mesh = {4-Butyrolactone/analogs &amp; derivatives/biosynthesis ; Alternaria/physiology ; Ascomycota/physiology ; Bacteria/classification/drug effects/*growth &amp; development/metabolism ; Botrytis/physiology ; DNA, Ribosomal/chemistry ; Indoleacetic Acids/metabolism ; Solanum lycopersicum/*microbiology ; Microbial Sensitivity Tests ; Pest Control, Biological ; Plant Diseases/microbiology ; Plant Leaves/microbiology ; Seasons ; Tomatine/analogs &amp; derivatives/pharmacology ; }, abstract = {Culturable leaf-associated bacteria inhabiting a plant have been considered as promising biological control agent (BCA) candidates because they can survive on the plant. We investigated the relationship between bacterial groups of culturable leaf-associated bacteria on greenhouse- and field-grown tomato leaves and their antifungal activities against tomato diseases in vitro and in vivo. In addition, the isolated bacteria were analyzed for N-acyl-homoserine lactone (AHL) and indole-3-acetic acid (IAA) production, which have been reported to associate with bacterial colonization, and resistance to a tomato alkaloid (alpha-tomatine). Leaf washings and subsequent leaf macerates were used to estimate the population size of epiphytic and more internal bacteria. Bacterial population sizes on leaves at the same position increased as the leaves aged under both greenhouse and field conditions. Field-grown tomatoes had significantly larger population sizes than greenhouse-grown tomatoes. Analysis of 16S rRNA gene (rDNA) sequencing using 887 culturable leaf-associated bacteria revealed a predominance of the Bacillus and Pseudomonas culturable leaf-associated bacterial groups on greenhouse- and field-grown tomatoes, respectively. Curtobacterium and Sphingomonas were frequently recovered from both locations. From the 2138 bacterial strains tested, we selected several strains having in vitro antifungal activity against three fungal pathogens of tomato: Botrytis cinerea, Fulvia fulva, and Alternaria solani. Among bacterial strains with strong in vitro antifungal activities, Bacillus and Pantoea tended to show strong antifungal activities, whereas Curtobacterium and Sphingomonas were not effective. The results indicated the differences in antifungal activity among predominant bacterial groups. Analysis of alpha-tomatine resistance revealed that most bacterial strains in the dominant groups exhibited moderate or high resistance to alpha-tomatine in growth medium. Furthermore, some Sphingomonas and Pantoea strains showed AHL and IAA production activities. Strain 125NP12 (Pantoea ananatis) showed particular alpha-tomatine resistance, and AHL and IAA production had the highest protective value (91.7) against gray mold. Thus, the differences of these physiological properties among dominant bacteria may be associated with the disease suppression ability of BCAs on tomato plants.}, }
@article {pmid17356948, year = {2007}, author = {Pradeep Ram, AS and Nair, S and Chandramohan, D}, title = {Bacterial growth efficiency in a tropical estuary: seasonal variability subsidized by allochthonous carbon.}, journal = {Microbial ecology}, volume = {53}, number = {4}, pages = {591-599}, pmid = {17356948}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development/metabolism ; Carbon/*metabolism ; Food Chain ; Oceans and Seas ; Rain ; Rivers/microbiology ; *Seasons ; *Tropical Climate ; Water/chemistry ; *Water Microbiology ; }, abstract = {Bacterial growth efficiency (BGE) is a key factor in understanding bacterial influence on carbon flow in aquatic ecosystems. We report intra-annual variability in BGE, and bacteria-mediated carbon flow in the tropical Mandovi and Zuari estuaries (southwest India) and the adjoining coastal waters (Arabian Sea). BGE ranged from 3% to 61% and showed clear temporal variability with significantly (ANOVA, p < 0.01) higher values in the estuaries (mean, 28 +/- 14%) than coastal waters (mean, 12 +/- 6%). The greater variability of BGE in the estuaries than coastal waters suggest some systematic response to nutrient composition and the variability of dissolved organic matter pools, as BGE was governed by bacterial secondary production (BP). Monsoonal rains and its accompanied changes brought significant variability in BGE and bacterial productivity/primary productivity (BP/PP) ratio when compared to nonmonsoon seasons in the estuaries and coastal waters. High BP/PP ratio (>1) together with high carbon flux through bacteria (>100% of primary productivity) in the estuarine and coastal waters suggests that bacterioplankton consumed dissolved organic carbon in excess of the amount produced in situ by phytoplankton of this region, which led to the mismatch between primary production of carbon and amount of carbon consumed by bacteria. Despite the two systems being subsidized by allochthonous inputs, the low BGE in the coastal waters may be attributable to the nature and time interval in the supply of allochthonous carbon.}, }
@article {pmid17355175, year = {2007}, author = {Seshadri, R and Kravitz, SA and Smarr, L and Gilna, P and Frazier, M}, title = {CAMERA: a community resource for metagenomics.}, journal = {PLoS biology}, volume = {5}, number = {3}, pages = {e75}, pmid = {17355175}, issn = {1545-7885}, mesh = {Bacteria/genetics ; Biological Evolution ; *Genomics ; }, abstract = {The CAMERA (Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis) community database for metagenomic data deposition is an important first step in developing methods for monitoring microbial communities.}, }
@article {pmid17351813, year = {2007}, author = {Martens, T and Gram, L and Grossart, HP and Kessler, D and Müller, R and Simon, M and Wenzel, SC and Brinkhoff, T}, title = {Bacteria of the Roseobacter clade show potential for secondary metabolite production.}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {31-42}, pmid = {17351813}, issn = {0095-3628}, mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; Conserved Sequence ; Peptide Synthases/*genetics/metabolism ; Phylogeny ; Polyketide Synthases/*genetics/metabolism ; Polymerase Chain Reaction ; Roseobacter/classification/enzymology/*metabolism ; Sequence Analysis, DNA ; Sequence Analysis, Protein ; }, abstract = {Members of the Roseobacter clade are abundant and widespread in marine habitats and have very diverse metabolisms. Production of acylated homoserine lactones (AHL) and secondary metabolites, e.g., antibiotics has been described sporadically. This prompted us to screen 22 strains of this group for production of signaling molecules, antagonistic activity against bacteria of different phylogenetic groups, and the presence of genes encoding for nonribosomal peptide synthetases (NRPS) and polyketide synthases (PKS), representing enzymes involved in the synthesis of various pharmaceutically important natural products. The screening approach for NRPS and PKS genes was based on polymerase chain reaction (PCR) with degenerate primers specific for conserved sequence motifs. Additionally, sequences from whole genome sequencing projects of organisms of the Roseobacter clade were considered. Obtained PCR products were cloned, sequenced, and compared with genes of known function. With the PCR approach genes showing similarity to known NRPS and PKS genes were found in seven and five strains, respectively, and three PKS and NRPS sequences from genome sequencing projects were obtained. Three strains exhibited antagonistic activity and also showed production of AHL. Overall production of AHL was found in 10 isolates. Phylogenetic analysis of the 16S rRNA gene sequences of the tested organisms showed that several of the AHL-positive strains clustered together. Three strains were positive for three or four categories tested, and were found to be closely related within the genus Phaeobacter. The presence of a highly similar hybrid PKS/NRPS gene locus of unknown function in sequenced genomes of the Roseobacter clade plus the significant similarity of gene fragments from the strains studied to these genes argues for the functional requirement of the encoded hybrid PKS/NRPS complex. Our screening results therefore suggest that the Roseobacter clade is indeed employing PKS/NRPS biochemistry and should thus be further studied as a potential and largely untapped source of secondary metabolites.}, }
@article {pmid17351812, year = {2007}, author = {Ben-Dov, E and Brenner, A and Kushmaro, A}, title = {Quantification of sulfate-reducing bacteria in industrial wastewater, by real-time polymerase chain reaction (PCR) using dsrA and apsA genes.}, journal = {Microbial ecology}, volume = {54}, number = {3}, pages = {439-451}, pmid = {17351812}, issn = {0095-3628}, mesh = {Bacterial Proteins/genetics/metabolism ; Base Sequence ; Hydrogensulfite Reductase/*genetics/metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases Acting on Sulfur Group Donors/*genetics/metabolism ; Phylogeny ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Sewage/*microbiology ; Sulfur-Reducing Bacteria/classification/enzymology/*genetics ; }, abstract = {Real-time polymerase chain reaction (PCR) is considered a highly sensitive method for the quantification of microbial organisms in environmental samples. This study was conducted to evaluate real-time PCR with SybrGreen detection as a quantification method for sulfate-reducing bacteria (SRB) in industrial wastewater produced by several chemical industries. We designed four sets of primers and developed standard curves based on genomic DNA of Desulfovibrio vulgaris from pure culture and on plasmids containing dissimilatory sulfate reductase (dsrA) or adenosine-5'-phosphosulfate reductase (apsA) genes of SRB. All the standard curves, two for dsrA and two for apsA genes, had a linear range between 0.95 x 10(2) and 9.5 x 10(6) copies/microL and between 1.2 x 10(3) and 1.2 x 10(7) copies/microL, respectively. The theoretical copy numbers of the tenfold dilutions of D. vulgaris genomic DNA were best estimated (between 2.7 to 10.5 times higher than theoretical numbers) by the standard curve with DSR1F and RH3-dsr-R primers. To mimic the effect of foreign DNA in environmental samples, serial dilutions of D. vulgaris genomic DNA were mixed with Escherichia coli chromosomal DNA (40 ng per assay). This influenced neither PCR amplification nor the quantification of target DNA. Industrial wastewater was sampled during a 15-month period and analyzed for the presence of SRB, based on dsrA gene amplification. SRB displayed a higher abundance during the summer (about 10(7)-10(8) targets mL(-1)) and lower during the winter (about 10(4)-10(5) targets mL(-1)). The results indicate that our real-time PCR approach can be used for detection of uncultured SRB and will provide valuable information related to the abundance of SRB in durable environmental samples, such as complex and saline industrial wastewaters.}, }
@article {pmid17351811, year = {2007}, author = {Nocker, A and Lepo, JE and Martin, LL and Snyder, RA}, title = {Response of estuarine biofilm microbial community development to changes in dissolved oxygen and nutrient concentrations.}, journal = {Microbial ecology}, volume = {54}, number = {3}, pages = {532-542}, pmid = {17351811}, issn = {0095-3628}, mesh = {Bacteria/genetics/growth &amp; development/*metabolism ; Biofilms/*growth &amp; development ; Biomass ; Ecosystem ; Florida ; Oxygen/*metabolism ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Seasons ; *Water Microbiology ; }, abstract = {The information content and responsiveness of microbial biofilm community structure, as an integrative indicator of water quality, was assessed against short-term changes in oxygen and nutrient loading in an open-water estuarine setting. Biofilms were grown for 7-day periods on artificial substrates in the Pensacola Bay estuary, Florida, in the vicinity of a wastewater treatment plant (WWTP) outfall and a nearby reference site. Substrates were deployed floating at the surface and near the benthos in 5.4 m of water. Three sampling events covered a 1-month period coincident with declining seasonal WWTP flow and increasing dissolved oxygen (DO) levels in the bottom waters. Biomass accumulation in benthic biofilms appeared to be controlled by oxygen rather than nutrients. The overriding effect of DO was also seen in DNA fingerprints of community structure by terminal restriction fragment length polymorphism (T-RFLP) of amplified 16S rRNA genes. Ribotype diversity in benthic biofilms at both sites dramatically increased during the transition from hypoxic to normoxic. Terminal restriction fragment length polymorphism patterns showed pronounced differences between benthic and surface biofilm communities from the same site in terms of signal type, strength, and diversity, but minor differences between sites. Sequencing of 16S rRNA gene clone libraries from benthic biofilms at the WWTP site suggested that low DO levels favored sulfate-reducing prokaryotes (SRP), which decreased with rising oxygen levels and increasing overall diversity. A 91-bp ribotype in the CfoI-restricted 16S rRNA gene T-RFLP profiles, indicative of SRP, tracked the decrease in relative SRP abundance over time.}, }
@article {pmid17351087, year = {2007}, author = {Allen, JP and Atekwana, EA and Atekwana, EA and Duris, JW and Werkema, DD and Rossbach, S}, title = {The microbial community structure in petroleum-contaminated sediments corresponds to geophysical signatures.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {9}, pages = {2860-2870}, pmid = {17351087}, issn = {0099-2240}, mesh = {Bacteria/*genetics ; Base Sequence ; Cluster Analysis ; DNA Primers ; *Ecosystem ; Electric Conductivity ; Gene Library ; Geologic Sediments/analysis/*microbiology ; Michigan ; Molecular Sequence Data ; Multivariate Analysis ; Petroleum/*microbiology ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The interdependence between geoelectrical signatures at underground petroleum plumes and the structures of subsurface microbial communities was investigated. For sediments contaminated with light non-aqueous-phase liquids, anomalous high conductivity values have been observed. Vertical changes in the geoelectrical properties of the sediments were concomitant with significant changes in the microbial community structures as determined by the construction and evaluation of 16S rRNA gene libraries. DNA sequencing of clones from four 16S rRNA gene libraries from different depths of a contaminated field site and two libraries from an uncontaminated background site revealed spatial heterogeneity in the microbial community structures. Correspondence analysis showed that the presence of distinct microbial populations, including the various hydrocarbon-degrading, syntrophic, sulfate-reducing, and dissimilatory-iron-reducing populations, was a contributing factor to the elevated geoelectrical measurements. Thus, through their growth and metabolic activities, microbial populations that have adapted to the use of petroleum as a carbon source can strongly influence their geophysical surroundings. Since changes in the geophysical properties of contaminated sediments parallel changes in the microbial community compositions, it is suggested that geoelectrical measurements can be a cost-efficient tool to guide microbiological sampling for microbial ecology studies during the monitoring of natural or engineered bioremediation processes.}, }
@article {pmid17347892, year = {2007}, author = {Villanueva, L and Navarrete, A and Urmeneta, J and Geyer, R and White, DC and Guerrero, R}, title = {Monitoring diel variations of physiological status and bacterial diversity in an estuarine microbial mat: an integrated biomarker analysis.}, journal = {Microbial ecology}, volume = {54}, number = {3}, pages = {523-531}, pmid = {17347892}, issn = {0095-3628}, mesh = {Bacteria/growth &amp; development/*metabolism/ultrastructure ; Bacteria, Anaerobic/growth &amp; development/metabolism/ultrastructure ; Bacterial Physiological Phenomena ; *Biodiversity ; Biomarkers/*metabolism ; Biomass ; Ecosystem ; Gram-Positive Bacteria/growth &amp; development/metabolism/ultrastructure ; Lipid Metabolism ; Microscopy, Electron, Transmission ; Oxidation-Reduction ; Oxygen Consumption ; Plasmalogens/metabolism ; Spain ; Sphingolipids/metabolism ; Time Factors ; *Water Microbiology ; }, abstract = {Microbial mats are highly productive microbial systems and a source of not-yet characterized microorganisms and metabolic strategies. In this article, we introduced a lipid biomarker/microbial isolation approach to detect short-term variations of microbial diversity, physiological and redox status, and also characterize lipid biomarkers from specific microbial groups that can be further monitored. Phospholipid fractions (PLFA) were examined for plasmalogens, indicative of certain anaerobes. The glycolipid fraction was processed for polyhydroxyalkanoates (PHA) and the neutral lipid fraction was used to evaluate respiratory quinone content. Data demonstrate an increase in the metabolic stress, unbalanced growth, proportion of anaerobic bacteria and respiratory rate after the maximal photosynthetic activity. Higher accumulation of polyhydroxyalkanoates at the same sampling point also suggested a situation of carbon storage by heterotrophs closely related to photosynthetic microorganisms. Besides, the characterization of lipid biomarkers (plasmalogens, sphingolipids) from specific microbial groups provided clues about the dynamics and diversity of less-characterized mat members. In this case, lipid analyses were complemented by the isolation and characterization of anaerobic spore formers and sulfate reducers to obtain insight into their affiliation and lipid composition. The results revealed that temporal shifts in lipid biomarkers are indicative of an intense change in the physiology, redox condition, and community composition along the diel cycle, and support the hypothesis that interactions between heterotrophs and primary producers play an important role in the carbon flow in microbial mats.}, }
@article {pmid17347891, year = {2007}, author = {Vujanovic, V and Hamelin, RC and Bernier, L and Vujanovic, G and St-Arnaud, M}, title = {Fungal diversity, dominance, and community structure in the rhizosphere of clonal Picea mariana plants throughout nursery production chronosequences.}, journal = {Microbial ecology}, volume = {54}, number = {4}, pages = {672-684}, pmid = {17347891}, issn = {0095-3628}, mesh = {Ascomycota/classification/genetics/isolation &amp; purification ; DNA, Fungal/analysis ; DNA, Ribosomal Spacer/analysis ; *Ecosystem ; Fungi/*classification/*genetics/isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; Picea/growth &amp; development/*microbiology ; Plant Diseases/microbiology ; Plant Roots/*microbiology ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Fungal diversity in the rhizosphere of healthy and diseased clonal black spruce (Picea mariana) plants was analyzed with regard to nursery production chronosequences. The four key production stages were sampled: mother plants (MP), 8-week-old cuttings (B + 0), second-year cuttings (B + 1), and third-year cuttings (B + 2). A total of 45 fungal taxa were isolated and identified based on cultural, phenotypic, and molecular characters. Members of phylum Ascomycota dominated, followed by Basidiomycota and Zygomycota. Diagnosis characters and distance analysis of the internal transcribed spacer rDNA sequences allowed the identification of 39 ascomycetous taxa. Many belong to the order Hypocreales, families Hypocreaceae and Nectriaceae, which contain many clusters of potentially pathogenic taxa (Cylindrocladium, Fusarium, and Neonectria) and are also ecologically associated with antagonistic taxa (Chaetomium, Hypocrea, Microsphaeropsis, Penicillium, Paecilomyces, Verticillium, Trichoderma, and Sporothrix). This is also the first report of a Cylindrocladium canadense association with disease symptoms and relation with Pestalotiopsis, Fusarium, Exserochilum, Rhizoctonia, and Xenochalara fungal consortia. Both production chronosequence and plant health considerably influenced fungal taxa assemblages. Unweighted pair-group arithmetic average clustering showed that isolates from MP, B + 0, and B + 1 plant rhizospheres clustered together within healthy or diseased health classes, whereas isolates from healthy and diseased B + 2 plants clustered together. Canonical correspondence analysis revealed substantial alteration in community assemblages with regard to plant health and yielded a principal axis direction that regrouped taxa associated with diseased plant rhizosphere soil, whereas the opposite axis direction was associated with healthy plants. Two diversity indices were defined and applied to assess the fungal taxa contribution (Tc) and persistence (Pi) throughout the production.}, }
@article {pmid17345141, year = {2007}, author = {Hewson, I and Fuhrman, JA}, title = {Characterization of lysogens in bacterioplankton assemblages of the southern California borderland.}, journal = {Microbial ecology}, volume = {53}, number = {4}, pages = {631-638}, pmid = {17345141}, issn = {0095-3628}, mesh = {Bacteria/growth &amp; development/*virology ; California ; Lysogeny/drug effects ; Mitomycin/pharmacology ; Plankton/growth &amp; development/*virology ; Prophages/drug effects/*physiology ; Seawater/*microbiology/virology ; *Wetlands ; }, abstract = {Viruses cause significant mortality of marine microorganisms; however, their role in shaping the composition of microbial assemblages has not been fully elucidated. Because viruses may form lysogenic relationships with their hosts, temperate viruses may influence bacterial assemblage structures through direct lysis of hosts when induced by environmental stimuli or by homoimmunity (i.e., immunity to closely related viruses). We investigated the components of bacterioplankton assemblages that bore prophage using the lysogenic induction agent mitomycin C. Seawater was collected at two locations (the San Pedro Ocean Time Series Station and in the Santa Barbara Channel) in the Southern California Borderland and amended with mitomycin C. After 24-h incubation, the community structure of bacterioplankton was compared with unamended controls using automated rRNA intergenic spacer analysis. The addition of mitomycin C to seawater had effects on the community structure of bacterioplankton, stimulating detectable overall diversity and richness of fingerprints and causing the assemblages within incubations to become different to control assemblages. Most negatively impacted operational taxonomic units (OTU) in mitomycin C-amended incubations individually comprised a large fraction of total amplified DNA in initial seawater (5.3-23.3% of amplified DNA fluorescence) fingerprints, and data suggest that these include organisms putatively classified as members of the gamma-Proteobacteria, SAR11 cluster, and Synechococcus groups. The stimulation of assemblage richness by induction of lysogens, and the reduction in the contribution to total DNA of common OTU (and concomitant increase in rare OTU), suggests that temperate phage have the potential to strongly influence the diversity of bacterioplankton assemblages. Because lysogenic OTU may also be resistant to closely related lytic (i.e., free-living) viruses, the impact of lytic virioplankton on assemblages may only be pronounced transiently or when conditions causing lysogenic induction arise.}, }
@article {pmid17345140, year = {2007}, author = {Uronen, P and Kuuppo, P and Legrand, C and Tamminen, T}, title = {Allelopathic effects of toxic haptophyte Prymnesium parvum lead to release of dissolved organic carbon and increase in bacterial biomass.}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {183-193}, pmid = {17345140}, issn = {0095-3628}, mesh = {Bacteria/*drug effects/growth &amp; development ; Biological Factors/*pharmacology ; *Biomass ; Carbon/*analysis/metabolism ; Cryptophyta/drug effects/metabolism/physiology ; Eukaryota/drug effects/metabolism/*physiology ; Food Chain ; }, abstract = {The haptophyte Prymnesium parvum has lytic properties, and it affects coexisting phytoplankton species through allelopathy. We studied the effect of P. parvum allelochemicals on the lysis of the nontoxic and nonaxenic cryptomonad Rhodomonas salina and the consequent release of dissolved organic carbon (DOC). Changes in production, cell density, and biomass of associated bacteria were measured over 12 h. Six different combinations of P. parvum and R. salina cultures, their cell- and bacteria-free filtrates, and growth media as controls were used in the experiments. When P. parvum and R. salina cells were mixed, a significant increase in DOC concentration was measured within 30 min. Bacterial biomass increased significantly during the next 6 to 12 h when R. salina was mixed either with the P. parvum culture or the cell-free P. parvum filtrates (allelochemicals only). In contrast, bacterial biomass did not change in the treatments without the allelopathic action (without R. salina cells). Blooms of P. parvum alter the functioning of the planktonic food web by increasing carbon transfer through the microbial loop. In addition, P. parvum may indirectly benefit from the release of DOC as a result of its ability to ingest bacteria, by which it can acquire nutrients during limiting conditions.}, }
@article {pmid17345139, year = {2007}, author = {Ghiglione, JF and Mevel, G and Pujo-Pay, M and Mousseau, L and Lebaron, P and Goutx, M}, title = {Diel and seasonal variations in abundance, activity, and community structure of particle-attached and free-living bacteria in NW Mediterranean Sea.}, journal = {Microbial ecology}, volume = {54}, number = {2}, pages = {217-231}, pmid = {17345139}, issn = {0095-3628}, mesh = {Bacteria/*classification/genetics/metabolism ; Chlorophyll/metabolism ; Chlorophyll A ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; Mediterranean Sea ; Plankton/*classification/genetics ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Seasons ; Seawater/*microbiology ; }, abstract = {Diel and seasonal variations in abundance, activity, and structure of particle-attached vs free-living bacterial communities were investigated in offshore NW Mediterranean Sea (0-1000 m). Attached bacteria were always less abundant and less diverse but generally more active than free-living bacteria. The most important finding of this study was that the activity of attached bacteria showed pronounced diel variations in the upper mixed water column with higher activities at night. Under mesotrophic conditions, the contribution of attached bacteria to total bacterial activity increased from less than 10% at day time to 83% at night time. At high chlorophyll a concentration, the highest cell-specific activities and contribution to total bacterial activity were due to free-living bacteria at day and to attached bacteria at night. Under summer oligotrophic conditions, free-living bacteria dominated and contributed to the most important part of the bacterial activity at both day and night, whereas attached bacteria were much less abundant but presented the highest cell-specific activities. These diel and seasonal variations in activities were concomitant to changes in bacterial community structure, mainly in the upper layer. The number of attached ribotypes was fairly constant suggesting that particles are colonized by a relatively limited number of ubiquitous ribotypes. Most of these ribotypes were also free-living ribotypes suggesting that attached bacteria probably originate from colonization of newly formed particles by free-living bacteria in the upper layer. These results reinforce the biogeochemical role of attached bacteria in the cycling of particulate organic carbon in the NW Mediterranean Sea and the importance of diel variability in these processes.}, }
@article {pmid17345138, year = {2007}, author = {Huang, WE and Ude, S and Spiers, AJ}, title = {Pseudomonas fluorescens SBW25 biofilm and planktonic cells have differentiable Raman spectral profiles.}, journal = {Microbial ecology}, volume = {53}, number = {3}, pages = {471-474}, pmid = {17345138}, issn = {0095-3628}, mesh = {Benzenesulfonates ; *Biofilms ; Discriminant Analysis ; *Environmental Microbiology ; Fluorescent Dyes ; *Plankton ; Principal Component Analysis ; Pseudomonas fluorescens/*chemistry/classification/isolation &amp; purification/physiology ; Spectrum Analysis, Raman/*methods ; }, abstract = {Biofilms, and other bacterial aggregations, are of significance in both environmental microbiology and in plant and human pathogenesis. Comparative single-cell Raman spectral analysis can differentiate between planktonic bacteria and those recovered from biofilms and appears to offer a new means by which to investigate bacterial cell physiology, metabolic status, and stress under different environmental conditions.}, }
@article {pmid17345137, year = {2007}, author = {Nguyen-Viet, H and Gilbert, D and Mitchell, EA and Badot, PM and Bernard, N}, title = {Effects of experimental lead pollution on the microbial communities associated with Sphagnum fallax (Bryophyta).}, journal = {Microbial ecology}, volume = {54}, number = {2}, pages = {232-241}, pmid = {17345137}, issn = {0095-3628}, mesh = {Animals ; Bacteria/drug effects/growth &amp; development ; Ecosystem ; Eukaryota/drug effects/growth &amp; development ; Fungi/drug effects/growth &amp; development ; Lead/*toxicity ; Sphagnopsida/*drug effects/*microbiology ; }, abstract = {Ecotoxicological studies usually focus on single microbial species under controlled conditions. As a result, little is known about the responses of different microbial functional groups or individual species to stresses. In an aim to assess the response of complex microbial communities to pollution in their natural habitat, we studied the effect of a simulated lead pollution on the microbial community (bacteria, cyanobacteria, protists, fungi, and micrometazoa) living on Sphagnum fallax. Mosses were grown in the laboratory with 0 (control), 625, and 2,500 microg L(-1) of Pb(2+) diluted in a standard nutrient solution and were sampled after 0, 6, 12, and 20 weeks. The biomasses of bacteria, microalgae, testate amoebae, and ciliates were dramatically and significantly decreased in both Pb addition treatments after 6, 12, and 20 weeks in comparison with the control. The biomass of cyanobacteria declined after 6 and 12 weeks in the highest Pb treatment. The biomasses of fungi, rotifers, and nematodes decreased along the duration of the experiment but were not significantly affected by lead addition. Consequently, the total microbial biomass was lower for both Pb addition treatments after 12 and 20 weeks than in the controls. The community structure was strongly modified due to changes in the densities of testate amoebae and ciliates, whereas the relative contribution of bacteria to the microbial biomass was stable. Differences in responses among the microbial groups suggest changes in the trophic links among them. The correlation between the biomass of bacteria and that of ciliates or testate amoebae increased with increasing Pb loading. We interpret this result as an effect on the grazing pathways of these predators and by the Pb effect on other potential prey (i.e., smaller protists). The community approach used here complements classical ecotoxicological studies by providing clues to the complex effect of pollutant-affecting organisms both directly and indirectly through trophic effects and could potentially find applications for pollution monitoring.}, }
@article {pmid17345136, year = {2007}, author = {Hypsa, V and Krízek, J}, title = {Molecular evidence for polyphyletic origin of the primary symbionts of sucking lice (phthiraptera, anoplura).}, journal = {Microbial ecology}, volume = {54}, number = {2}, pages = {242-251}, pmid = {17345136}, issn = {0095-3628}, mesh = {Animals ; Bacteria/classification/*genetics ; *Bacterial Physiological Phenomena ; Base Sequence ; DNA, Mitochondrial ; DNA, Ribosomal/genetics ; Phthiraptera/*genetics/*microbiology/physiology ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; }, abstract = {Based on 16S rDNA analyses, the primary symbionts of sucking lice were found to form a polyphyletic assemblage of several distant lineages that have arisen several times within Enterobacteriaceae and at least once within Legionellaceae. Another independent lineage of endosymbiotic enterobacteria inhabits a sister group of the sucking lice, Rhynchophthirina. The inspection of 16S rDNA supports the symbiotic nature of the investigated bacteria; they display a typical trait of degenerative processes, an increased AT content (Adenine-Thymine content) in comparison with free-living bacteria. The calculation of divergence time between the closest anopluran and rhynchophthirine symbionts further support their independent origin. The results shown here, together with evidence from other groups, indicate that the significance of primary symbionts for blood-feeding insects should be reconsidered.}, }
@article {pmid17345135, year = {2007}, author = {Wagner, M and Smidt, H and Loy, A and Zhou, J}, title = {Unravelling microbial communities with DNA-microarrays: challenges and future directions.}, journal = {Microbial ecology}, volume = {53}, number = {3}, pages = {498-506}, pmid = {17345135}, issn = {0095-3628}, mesh = {Biodiversity ; Ecology/*methods ; Ecosystem ; Environmental Microbiology ; Environmental Monitoring/methods ; Genomics ; Oligonucleotide Array Sequence Analysis/*methods/*trends ; }, abstract = {High-throughput technologies are urgently needed for monitoring the formidable biodiversity and functional capabilities of microorganisms in the environment. Ten years ago, DNA microarrays, miniaturized platforms for highly parallel hybridization reactions, found their way into environmental microbiology and raised great expectations among researchers in the field. In this article, we briefly summarize the state-of-the-art of microarray approaches in microbial ecology research and discuss in more detail crucial problems and promising solutions. Finally, we outline scenarios for an innovative combination of microarrays with other molecular tools for structure-function analysis of complex microbial communities.}, }
@article {pmid17345134, year = {2007}, author = {Rattray, RM and Craig, AM}, title = {Molecular characterization of sheep ruminal enrichments that detoxify pyrrolizidine alkaloids by denaturing gradient gel electrophoresis and cloning.}, journal = {Microbial ecology}, volume = {54}, number = {2}, pages = {264-275}, pmid = {17345134}, issn = {0095-3628}, mesh = {Animals ; Bacteria, Anaerobic/*chemistry/genetics/metabolism ; *Cloning, Molecular ; DNA, Bacterial ; DNA, Ribosomal/genetics ; Electrophoresis, Polyacrylamide Gel ; Polymerase Chain Reaction ; Pyrrolizidine Alkaloids/*metabolism ; RNA, Ribosomal, 16S/genetics ; Rumen/metabolism/*microbiology ; Senecio/chemistry/toxicity ; Sheep ; }, abstract = {An enrichment of strictly anaerobic bacteria from ovine rumen fluid, which has previously been named L4M2, is known to detoxify animal hepatotoxins from the pyrrolizidine alkaloid family. These toxins are present in the tansy ragwort plant (Senecio jacobaea). These plants have been described in livestock animals' range forages in regions of the world such as the Northwest United States and South Africa. The bacterial enrichment was characterized by molecular cloning techniques and by the molecular fingerprinting technique of denaturing gradient gel electrophoresis (DGGE). Phylogenetic analysis of the enrichment revealed that the consortium is composed of no more than five putative bacterial species which associated to the Anaerovibrio, Desulfovibrio, Megasphaera, Prevotella, and Synergistes generas. These are all known to exist in the upper gastrointestinal tract of ruminant animals. This work improved upon previous attempts to characterize the consortium by obtaining nearly full-length ribosomal 16S rDNA sequences through cloning. The DGGE results were directly compared to the cloning data by polymerase chain reaction (PCR) amplifying eight phylogenetically representative clones and analyzing them by DGGE. Direct DGGE analysis of the enrichment displayed greater 16S diversity than the clone library used in this study, suggesting that at least one of the organisms present in the enrichment comprises less than 1% of the total cell population. These data will be used to further refine the enrichment in hopes of future use as a probiotic, which could be administered to animals challenged by the presence of tansy ragwort in their forage.}, }
@article {pmid17345133, year = {2007}, author = {Nocker, A and Burr, M and Camper, AK}, title = {Genotypic microbial community profiling: a critical technical review.}, journal = {Microbial ecology}, volume = {54}, number = {2}, pages = {276-289}, pmid = {17345133}, issn = {0095-3628}, mesh = {Archaea/genetics ; Bacteria/genetics ; Biodiversity ; Chromatography, High Pressure Liquid ; Cloning, Molecular ; DNA, Ribosomal/genetics ; Electrophoresis, Polyacrylamide Gel ; Fungi/genetics ; *Genetic Techniques ; Genotype ; Microbiological Techniques/*methods ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Polymorphism, Single-Stranded Conformational ; }, abstract = {Microbial ecology has undergone a profound change in the last two decades with regard to methods employed for the analysis of natural communities. Emphasis has shifted from culturing to the analysis of signature molecules including molecular DNA-based approaches that rely either on direct cloning and sequencing of DNA fragments (shotgun cloning) or often rely on prior amplification of target sequences by use of the polymerase chain reaction (PCR). The pool of PCR products can again be either cloned and sequenced or can be subjected to an increasing variety of genetic profiling methods, including amplified ribosomal DNA restriction analysis, automated ribosomal intergenic spacer analysis, terminal restriction fragment length polymorphism, denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, single strand conformation polymorphism, and denaturing high-performance liquid chromatography. In this document, we present and critically compare these methods commonly used for the study of microbial diversity.}, }
@article {pmid17345132, year = {2007}, author = {Kowalchuk, GA and Speksnijder, AG and Zhang, K and Goodman, RM and van Veen, JA}, title = {Finding the needles in the metagenome haystack.}, journal = {Microbial ecology}, volume = {53}, number = {3}, pages = {475-485}, pmid = {17345132}, issn = {0095-3628}, mesh = {Cloning, Molecular/methods ; Computational Biology/methods ; *Environmental Microbiology ; Environmental Monitoring/*methods ; Genetic Variation ; Genomics/*methods/trends ; Phylogeny ; }, abstract = {In the collective genomes (the metagenome) of the microorganisms inhabiting the Earth's diverse environments is written the history of life on this planet. New molecular tools developed and used for the past 15 years by microbial ecologists are facilitating the extraction, cloning, screening, and sequencing of these genomes. This approach allows microbial ecologists to access and study the full range of microbial diversity, regardless of our ability to culture organisms, and provides an unprecedented access to the breadth of natural products that these genomes encode. However, there is no way that the mere collection of sequences, no matter how expansive, can provide full coverage of the complex world of microbial metagenomes within the foreseeable future. Furthermore, although it is possible to fish out highly informative and useful genes from the sea of gene diversity in the environment, this can be a highly tedious and inefficient procedure. Microbial ecologists must be clever in their pursuit of ecologically relevant, valuable, and niche-defining genomic information within the vast haystack of microbial diversity. In this report, we seek to describe advances and prospects that will help microbial ecologists glean more knowledge from investigations into metagenomes. These include technological advances in sequencing and cloning methodologies, as well as improvements in annotation and comparative sequence analysis. More significant, however, will be ways to focus in on various subsets of the metagenome that may be of particular relevance, either by limiting the target community under study or improving the focus or speed of screening procedures. Lastly, given the cost and infrastructure necessary for large metagenome projects, and the almost inexhaustible amount of data they can produce, trends toward broader use of metagenome data across the research community coupled with the needed investment in bioinformatics infrastructure devoted to metagenomics will no doubt further increase the value of metagenomic studies in various environments.}, }
@article {pmid17345131, year = {2007}, author = {Sonjak, S and Frisvad, JC and Gunde-Cimerman, N}, title = {Genetic variation among Penicillium crustosum isolates from arctic and other ecological niches.}, journal = {Microbial ecology}, volume = {54}, number = {2}, pages = {298-305}, pmid = {17345131}, issn = {0095-3628}, mesh = {Cold Temperature ; *Genetic Variation ; Ice ; Penicillium/*genetics/metabolism ; Phenotype ; Polymorphism, Restriction Fragment Length ; Seawater/microbiology ; Svalbard ; }, abstract = {Penicillium crustosum is an important and panglobal contaminant of lipid- and protein-rich foods and feeds. Although it is infrequent in extremely cold environments, we isolated a high number of P. crustosum strains from Arctic coastal, but particularly, subglacial environments in Svalbard, Norway. P. crustosum is extremely consistent in its phenotypic properties, including morphology, physiology, and secondary metabolite production. However, some Arctic isolates differed from other Arctic and non-Arctic strains in their weak growth on creatine and in the production of the secondary metabolite andrastin A. In this study, we characterized genetic variability of P. crustosum strains originating from different Arctic and non-Arctic environments using amplified fragment length polymorphism (AFLP) and, in addition, M13 minisatellite fingerprinting and partial beta-tubulin gene sequencing. Most of the Arctic strains (85%) showed a relatively low variability and polymorphism level. They produced nine different AFLP genotypes grouped into two clusters in accordance with glacier origin and creatine utilization. The rest of the Arctic isolates and isolates from various non-Arctic environments displayed a much greater degree of genetic variability. It seems that in stressful glacial environment low microbial genetic variation is represented by only a few adapted genotypes that were not recovered from nonpolar environments.}, }
@article {pmid17345130, year = {2007}, author = {Adams, P and De-Leij, FA and Lynch, JM}, title = {Trichoderma harzianum Rifai 1295-22 mediates growth promotion of crack willow (Salix fragilis) saplings in both clean and metal-contaminated soil.}, journal = {Microbial ecology}, volume = {54}, number = {2}, pages = {306-313}, pmid = {17345130}, issn = {0095-3628}, mesh = {Metals/*pharmacology ; Plant Roots/growth &amp; development ; Plant Shoots/growth &amp; development ; Salix/drug effects/*growth &amp; development/*microbiology ; *Soil ; Trichoderma/*physiology ; }, abstract = {We investigated if the plant growth promoting fungus Trichoderma harzianum Rifai 1295-22 (also known as "T22") could be used to enhance the establishment and growth of crack willow (Salix fragilis) in a soil containing no organic or metal pollutants and in a metal-contaminated soil by comparing this fungus with noninoculated controls and an ectomycorrhizal formulation commercially used to enhance the establishment of tree saplings. Crack willow saplings were grown in a temperature-controlled growth room over a period of 5 weeks' in a garden center topsoil and over 12 weeks in a soil which had been used for disposal of building materials and sewage sludge containing elevated levels of heavy metals including cadmium (30 mg kg(-1)), lead (350 mg kg(-1)), manganese (210 mg kg(-1)), nickel (210 mg kg(-1)), and zinc (1,100 mg kg(-1)). After 5 weeks' growth in clean soil, saplings grown with T. harzianum T22 produced shoots and roots that were 40% longer than those of the controls and shoots that were 20% longer than those of saplings grown with ectomycorrhiza (ECM). T. harzianum T22 saplings produced more than double the dry biomass of controls and more than 50% extra biomass than the ECM-treated saplings. After 12 weeks' growth, saplings grown with T. harzianum T22 in the metal-contaminated soil produced 39% more dry weight biomass and were 16% taller than the noninoculated controls. This is the first report of tree growth stimulation by application of Trichoderma to roots, and is especially important as willow is a major source of wood fuel in the quest for renewable energy. These results also suggest willow trees inoculated with T. harzianum T22 could be used to increase the rate of revegetation and phytostabilization of metal-contaminated sites, a property of the fungus never previously demonstrated.}, }
@article {pmid17345129, year = {2007}, author = {Jones, BW and Maruyama, A and Ouverney, CC and Nishiguchi, MK}, title = {Spatial and temporal distribution of the vibrionaceae in coastal waters of Hawaii, Australia, and France.}, journal = {Microbial ecology}, volume = {54}, number = {2}, pages = {314-323}, pmid = {17345129}, issn = {0095-3628}, support = {GM48998/GM/NIGMS NIH HHS/United States ; GM61222-01/GM/NIGMS NIH HHS/United States ; SO6 GM08136-26/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Australia ; Decapodiformes/microbiology ; France ; Hawaii ; In Situ Hybridization, Fluorescence ; Seasons ; Seawater/chemistry/*microbiology ; Temperature ; Vibrionaceae/*isolation &amp; purification ; }, abstract = {Relatively little is known about large-scale spatial and temporal fluctuations in bacterioplankton, especially within the bacterial families. In general, however, a number of abiotic factors (namely, nutrients and temperature) appear to influence distribution. Community dynamics within the Vibrionaceae are of particular interest to biologists because this family contains a number of important pathogenic, commensal, and mutualist species. Of special interest to this study is the mutualism between sepiolid squids and Vibrio fischeri and Vibrio logei, where host squids seed surrounding waters daily with their bacterial partners. This study seeks to examine the spatial and temporal distribution of the Vibrionaceae with respect to V. fischeri and V. logei in Hawaii, southeastern Australia, and southern France sampling sites. In particular, we examine how the presence of sepiolid squid hosts influences community population structure within the Vibrionaceae. We found that abiotic (temperature) and biotic (host distribution) factors both influence population dynamics. In Hawaii, three sites within squid host habitat contained communities of Vibrionaceae with higher proportions of V. fischeri. In Australia, V. fischeri numbers at host collection sites were greater than other populations; however, there were no spatial or temporal patterns seen at other sample sites. In France, host presence did not appear to influence Vibrio communities, although sampled populations were significantly greater in the winter than summer sampling periods. Results of this study demonstrate the importance of understanding how both abiotic and biotic factors interact to influence bacterial community structure within the Vibrionaceae.}, }
@article {pmid17345128, year = {2007}, author = {Gao, L and Chi, Z and Sheng, J and Wang, L and Li, J and Gong, F}, title = {Inulinase-producing marine yeasts: evaluation of their diversity and inulin hydrolysis by their crude enzymes.}, journal = {Microbial ecology}, volume = {54}, number = {4}, pages = {722-729}, pmid = {17345128}, issn = {0095-3628}, mesh = {Animals ; Cryptococcus/*classification/*enzymology/genetics/isolation &amp; purification ; DNA, Fungal/analysis/isolation &amp; purification ; DNA, Ribosomal Spacer/analysis ; Digestive System/microbiology ; Eukaryota/microbiology ; Fishes/microbiology ; Geologic Sediments/microbiology ; Glycoside Hydrolases/*biosynthesis ; Hydrolysis ; Inulin/*metabolism ; Molecular Sequence Data ; RNA, Ribosomal, 18S/genetics ; Saccharomycetales/*classification/*enzymology/genetics/isolation &amp; purification ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Total 427 yeast strains from seawater, sediments, mud of salterns, guts of the marine fish, and marine algae were obtained. After inulinase activity of the yeast cultures was estimated, we found that four strains (OUC1, G7a, OUC2, and G7a1) of the marine yeasts grown in the medium with inulin could secrete a large amount of inulinase into the medium. The results of routine identification and molecular methods show that they belong to Pichia guilliermondii OUC1, Cryptococcus aureus G7a, Yarrowia lipolytica OUC2, and Debaryomyces hansenii G7a1, respectively. The optimal pHs of inulinase activity produced by them were 6.0, 5.0, 5.0, and 5.0, respectively, while the optimal temperatures of inulinase activity produced by them were 60 degrees , 50 degrees , 60 degrees , and 50 degrees C, respectively. A large amount of monosaccharides and a trace amount of oligosaccharides were detected after the hydrolysis by the crude inulinase produced by P. guilliermondii OUC1, indicating that the crude inulinase had a high exoinulinase activity while a large amount of monosaccharides and oligosaccharides were detected after inulin hydrolysis by the crude inulinase produced both by C. aureus G7a and D. hansenii G7a1. However, no monosaccharides and disaccharides were detected after inulin hydrolysis by the crude inulinase produced by Y. lipolytica OUC2, suggesting that the crude inulinase had no exoinulinase activity.}, }
@article {pmid17342529, year = {2007}, author = {Kilbane, JJ and Robbins, J}, title = {Characterization of the dszABC genes of Gordonia amicalis F.5.25.8 and identification of conserved protein and DNA sequences.}, journal = {Applied microbiology and biotechnology}, volume = {75}, number = {4}, pages = {843-851}, doi = {10.1007/s00253-007-0895-y}, pmid = {17342529}, issn = {0175-7598}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; Base Sequence ; *Conserved Sequence ; DNA Primers/genetics ; Gordonia Bacterium/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; Thiophenes/*metabolism ; }, abstract = {Gordonia amicalis F.5.25.8 has the unique ability to desulfurize dibenzothiophene and to metabolize carbazole [Santos et al., Appl Microbiol Biotechnol 71:355-362, 2006]. Efforts to amplify the dsz genes from G. amicalis F.5.25.8 based on polymerase chain reaction (PCR) primers designed using the dsz gene sequences of Rhodococcus erythropolis IGTS8 were mostly unsuccessful. A comparison of the protein sequences of dissimilar desulfurization enzymes (DszABC, BdsABC, and TdsABC) revealed multiple conserved regions. PCR primers targeting some of the most highly conserved regions of the desulfurization genes allowed us to amplify dsz genes from G. amicalis F.5.25.8. DNA sequence data that include nearly the entirety of the desulfurization operon as well as the promoter region were obtained. The most closely related dsz genes are those of G. alkinovorans strain 1B at 85% identity. The PCR primers reported here should be useful in microbial ecology studies and the amplification of desulfurization genes from previously uncharacterized microbial cultures.}, }
@article {pmid17338274, year = {2006}, author = {Siuda, W and Chróst, RJ}, title = {Urea and ureolytic activity in lakes of different trophic status.}, journal = {Polish journal of microbiology}, volume = {55}, number = {3}, pages = {211-225}, pmid = {17338274}, issn = {1733-1331}, mesh = {Colony Count, Microbial ; Environmental Monitoring ; *Eutrophication ; Fresh Water/*chemistry/*microbiology ; *Phytoplankton ; Poland ; Seasons ; Urea/*analysis ; Urease/*analysis ; }, abstract = {Urea and uraease (U-ase) activity were determined in water samples taken from the surface layers of 17 lakes of different trophic status. Urea concentrations were inversely correlated with the trophic status of the studied lakes and varied from below the detection limit to 25 micromol l(-1). Maximal potential ureolytic activity (V(max)) ranged from 0.2 to 7.0 micromol l(-1) h(-1). The highest urea concentrations and the lowest U-ase activities were recorded in the spring, whereas the lowest urea concentrations and the highest rates of urea hydrolysis were observed late in summer, during heavy phytoplankton blooms. Since in the majority of the Great Mazurian Lakes microplankton growth was limited by nitrogen supply, urea was an important N source for both auto- and heterotrophic planktonic microorganisms throughout the growth period. U-ase activity was mainly related to the seston. Only up to 25% of total activity could be attributed to free enzymes dissolved in lake water. In epilimnetic water samples the bulk of the ureolytic activity originated from seston-attached bacteria. However, a positive, statistically significant correlation between ureolytic activity and chlorophyll a (Chl(a)) concentrations suggests that phytoplankton may also be responsible for at least a some of the observed ureolytic activity in the highly eutrophic Great Mazurian Lakes.}, }
@article {pmid17334967, year = {2007}, author = {Bomberg, M and Timonen, S}, title = {Distribution of cren- and euryarchaeota in scots pine mycorrhizospheres and boreal forest humus.}, journal = {Microbial ecology}, volume = {54}, number = {3}, pages = {406-416}, pmid = {17334967}, issn = {0095-3628}, mesh = {Biodiversity ; DNA, Archaeal/chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Euryarchaeota/classification/genetics/*growth &amp; development ; Molecular Sequence Data ; Mycorrhizae/*growth &amp; development ; Phylogeny ; Pinus sylvestris/*microbiology ; Plant Roots/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {Archaeal 16S rRNA gene sequences have been found in a variety of moderate-temperature habitats including soil and rhizospheres. In this study, the differences of archaeal communities associated with Scots pine (Pinus sylvestris L.) short roots, different types of mycorrhizospheric compartments, and uncolonized boreal forest humus were tested by direct DNA extraction, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), and sequencing. The results indicated that mycorrhizal colonization of Scots pine roots substantially influence the archaeal community of pine rhizospheres. Colonization of short roots by most mycorrhizal fungi tested increased both archaeal frequency and diversity. Most of the archaeal sequences encountered in mycorrhizas belonged to the phylum Euryarchaeota, order of Halobacteriales. The difference in archaeal diversity between the mycorrhizospheric compartments and humus was profound. Most compartments with fungal components contained euryarchaeotal 16S rRNA gene sequences, whereas a high diversity of crenarchaeotal sequences and no euryarchaeotal sequences were found in forest humus outside mycorrhizospheres.}, }
@article {pmid17334965, year = {2007}, author = {Miralles, G and Nérini, D and Manté, C and Acquaviva, M and Doumenq, P and Michotey, V and Nazaret, S and Bertrand, JC and Cuny, P}, title = {Effects of spilled oil on bacterial communities of mediterranean coastal anoxic sediments chronically subjected to oil hydrocarbon contamination.}, journal = {Microbial ecology}, volume = {54}, number = {4}, pages = {646-661}, pmid = {17334965}, issn = {0095-3628}, mesh = {Bacteria/*classification/*genetics/growth &amp; development/isolation &amp; purification ; DNA, Bacterial/analysis/isolation &amp; purification ; DNA, Ribosomal Spacer/analysis ; *Ecosystem ; Environmental Monitoring ; Geologic Sediments/chemistry/*microbiology ; *Hydrocarbons/analysis ; Mediterranean Sea ; Molecular Sequence Data ; Oxygen/analysis ; *Petroleum ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Water Pollutants/analysis ; }, abstract = {The effects of spilled oil on sedimentary bacterial communities were examined in situ at 20 m water depth in a Mediterranean coastal area. Sediment collected at an experimental site chronically subjected to hydrocarbon inputs was reworked into PVC cores with or without a massive addition of crude Arabian light oil (approximately 20 g kg(-1) dry weight). Cores were reinserted into the sediment and incubated in situ at the sampling site (20 m water depth) for 135 and 503 days. The massive oil contamination induced significant shifts in the structure of the indigenous bacterial communities as shown by ribosomal intergenic spacer analysis (RISA). The vertical heterogeneity of the bacterial communities within the sediment was more pronounced in the oiled sediments particularly after 503 days of incubation. Response to oil of the deeper depth communities (8-10 cm) was slower than that of superficial depth communities (0-1 and 2-4 cm). Analysis of the oil composition by gas chromatography revealed a typical microbial alteration of n-alkanes during the experiment. Predominant RISA bands in oiled sediments were affiliated to hydrocarbonoclastic bacteria sequences. In particular, a 395-bp RISA band, which was the dominant band in all the oiled sediments for both incubation times, was closely related to hydrocarbonoclastic sulfate-reducing bacteria (SRB). These bacteria may have contributed to the main fingerprint changes and to the observed biodegradation of n-alkanes. This study provides useful information on bacterial dynamics in anoxic contaminated infralittoral sediments and highlights the need to assess more precisely the contribution of SRB to bioremediation in oil anoxic contaminated areas.}, }
@article {pmid17334859, year = {2007}, author = {Van Ryckegem, G and Gessner, MO and Verbeken, A}, title = {Fungi on leaf blades of Phragmites australis in a brackish tidal marsh: diversity, succession, and leaf decomposition.}, journal = {Microbial ecology}, volume = {53}, number = {4}, pages = {600-611}, pmid = {17334859}, issn = {0095-3628}, mesh = {Biodiversity ; Biomass ; Cluster Analysis ; Fungi/*classification/physiology ; Plant Leaves/microbiology/physiology ; Poaceae/*microbiology/physiology ; Spores, Fungal/growth &amp; development ; *Wetlands ; }, abstract = {Although fungi are known to colonize and decompose plant tissues in various environments, there is scanty information on fungal communities on wetland plants, their relation to microhabitat conditions, and their link to plant litter decomposition. We examined fungal diversity and succession on Phragmites australis leaves both attached to standing shoots and decaying in the litter layer of a brackish tidal marsh. Additionally, we followed changes in fungal biomass (ergosterol), leaf nitrogen dynamics, and litter mass loss on the sediment surface of the marsh. Thirty-five fungal taxa were recorded by direct observation of sporulation structures. Detrended correspondence analysis and cluster analysis revealed distinct communities of fungi sporulating in the three microhabitats examined (middle canopy, top canopy, and litter layer), and indicator species analysis identified a total of seven taxa characteristic of the identified subcommunities. High fungal biomass developed in decaying leaf blades attached to standing shoots, with a maximum ergosterol concentration of 548 +/- 83 microg g(-1) ash-free dry mass (AFDM; mean +/- SD). When dead leaves were incorporated in the litter layer on the marsh surface, fungi experienced a sharp decline in biomass (to 191 +/- 60 microg ergosterol g(-1) AFDM) and in the number of sporulation structures. Following a lag phase, species not previously detected began to sporulate. Leaves placed in litter bags on the sediment surface lost 50% of their initial AFDM within 7 months (k = -0.0035 day(-1)) and only 21% of the original AFDM was left after 11 months. Fungal biomass accounted for up to 34 +/- 7% of the total N in dead leaf blades on standing shoots, but to only 10 +/- 4% in the litter layer. These data suggest that fungi are instrumental in N retention and leaf mass loss during leaf senescence and early aerial decay. However, during decomposition on the marsh surface, the importance of living fungal mass appears to diminish, particularly in N retention, although a significant fraction of total detrital N may remain associated with dead hyphae.}, }
@article {pmid17334858, year = {2007}, author = {DeSantis, TZ and Brodie, EL and Moberg, JP and Zubieta, IX and Piceno, YM and Andersen, GL}, title = {High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment.}, journal = {Microbial ecology}, volume = {53}, number = {3}, pages = {371-383}, pmid = {17334858}, issn = {0095-3628}, mesh = {Aerosols ; Bacteria/*classification/genetics ; Base Sequence ; *Biodiversity ; Cloning, Molecular/methods ; DNA Primers/chemistry ; DNA, Bacterial/chemistry ; Environmental Microbiology ; Environmental Monitoring/*methods ; Microarray Analysis/*methods ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; Soil Microbiology ; Water Microbiology ; }, abstract = {Molecular approaches aimed at detection of a broad-range of prokaryotes in the environment routinely rely on classifying heterogeneous 16S rRNA genes amplified by polymerase chain reaction (PCR) using primers with broad specificity. The general method of sampling and categorizing DNA has been to clone then sequence the PCR products. However, the number of clones required to adequately catalog the majority of taxa in a sample is unwieldy. Alternatively, hybridizing target sequences to a universal 16S rRNA gene microarray may provide a more rapid and comprehensive view of prokaryotic community composition. This study investigated the breadth and accuracy of a microarray in detecting diverse 16S rRNA gene sequence types compared to clone-and-sequencing using three environmental samples: urban aerosol, subsurface soil, and subsurface water. PCR products generated from universal 16S rRNA gene-targeted primers were classified by using either the clone-and-sequence method or by hybridization to a novel high-density microarray of 297,851 probes complementary to 842 prokaryotic subfamilies. The three clone libraries comprised 1391 high-quality sequences. Approximately 8% of the clones could not be placed into a known subfamily and were considered novel. The microarray results confirmed the majority of clone-detected subfamilies and additionally demonstrated greater amplicon diversity extending into phyla not observed by the cloning method. Sequences matching operational taxonomic units within the phyla Nitrospira, Planctomycetes, and TM7, which were uniquely detected by the array, were verified with specific primers and subsequent amplicon sequencing. Subfamily richness detected by the array corresponded well with nonparametric richness predictions extrapolated from clone libraries except in the water community where clone-based richness predictions were greatly exceeded. It was concluded that although the microarray is unreliable in identifying novel prokaryotic taxa, it reveals greater diversity in environmental samples than sequencing a typically sized clone library. Furthermore, the microarray allowed samples to be rapidly evaluated with replication, a significant advantage in studies of microbial ecology.}, }
@article {pmid17334857, year = {2007}, author = {Huang, WE and Bailey, MJ and Thompson, IP and Whiteley, AS and Spiers, AJ}, title = {Single-cell Raman spectral profiles of Pseudomonas fluorescens SBW25 reflects in vitro and in planta metabolic history.}, journal = {Microbial ecology}, volume = {53}, number = {3}, pages = {414-425}, pmid = {17334857}, issn = {0095-3628}, mesh = {Amino Acids/chemistry/metabolism ; Beta vulgaris/microbiology ; Carbon/metabolism ; Culture Media ; Discriminant Analysis ; Pseudomonas fluorescens/*chemistry/growth &amp; development/*metabolism ; Spectrum Analysis, Raman/*methods ; }, abstract = {Single-cell Raman microspectroscopy has the potential to report on the whole-cell chemical composition of bacteria, reflecting metabolic status as well as growth history. This potential has been demonstrated through the discriminant functional analysis of Raman spectral profiles (RSP) obtained from the soil and plant-associated bacterium Pseudomonas fluorescens SBW25, grown in vitro using defined media, and in planta using 3-month-old sugar beets (Beta vulgaris var. Roberta). SBW25 in vitro RSP data showed significant variation between those cells grown on different amino acids, sugars, TCA cycle intermediates, rich King's B, and culture media derived from the sugar beet phytosphere. Raman analysis was also able to follow the transition of SBW25 starved of carbon over a period of days, and SBW25 in planta RSP data also showed variation with significant differences between bacteria recovered from soil and the rhizosphere. SBW25 whole-cell chemical composition, and therefore growth and metabolic history, could be interpreted by coanalyzing in vitro and in planta RSP data. SBW25 recovered from the phytosphere was found to be more similar to SBW25 grown in vitro on Fru or Asp, rather than on Glc or Arg, and quite dissimilar to that resulting from carbon starvation. This suggests that SBW25 growth in the phytosphere is generally neither carbon-catabolite-repressed nor carbon-limited. These findings demonstrate that the analysis of single-cell RSP can differentiate between isogenic populations of bacteria with different metabolic histories or after recovery from different parts of their natural environment. In addition, Raman analysis is also capable of providing biologically relevant biochemical inferences, which might then be tested to uncover the mechanistic basis (biochemical-metabolic-genetic) differentiating bacteria growing in complex environments and exposed to different conditions.}, }
@article {pmid17334856, year = {2007}, author = {Tian, X and Cao, L and Tan, H and Han, W and Chen, M and Liu, Y and Zhou, S}, title = {Diversity of cultivated and uncultivated actinobacterial endophytes in the stems and roots of rice.}, journal = {Microbial ecology}, volume = {53}, number = {4}, pages = {700-707}, pmid = {17334856}, issn = {0095-3628}, mesh = {Actinobacteria/*classification/isolation &amp; purification/physiology ; Biodiversity ; Cloning, Molecular ; Gene Library ; Oryza/*microbiology ; Phylogeny ; Plant Roots/microbiology ; Plant Stems/microbiology ; RNA, Ribosomal, 16S/chemistry ; Sequence Analysis, DNA ; }, abstract = {A dual approach consisting of cultivation and molecular retrieval of actinobacterial 16S rRNA genes was used to characterize the diversity of actinobacterial community inhabiting interior of rice stems and roots. Streptomyces is the most frequently isolated genus from rice stems and roots. Forty-five clones chosen randomly among 250 clones in the 16S rRNA gene clone library from roots were affiliated with nine genera of actinobacteria and uncultured actinobacteria (Mycobacterium, Streptomyces, Micromonospora, Actinoplanes, Frankia, Dactylosporangium, Amycolatopsis, Corynebacterium, Rhodococcus, and uncultured actinobacterium). However, 33 clones from stems were affiliated with four genera and uncultured actinobacteria (Streptomyces, Mycobacterium, Nocardiodies, Janibacter, uncultured earthworm cast bacterium, uncultured earthworm intestine bacterium, and uncultured actinobacterium). Species similar to S. cyaneus were isolated from surface-sterilized roots and stems of rice and detected inside rice roots by culture-independent methods. Species similar to S. caviscabies, S. scabies, and S. turgidiscabies were simultaneously detected from the interior of rice stems by the culture-dependent and culture-independent methods. S. galilaeus was detected from the interior of rice stems and roots. These results indicated that some actinobacterial populations in rice stems were correlated with those in roots.}, }
@article {pmid17334855, year = {2007}, author = {Bisson, IA and Marra, PP and Burtt, EH and Sikaroodi, M and Gillevet, PM}, title = {A molecular comparison of plumage and soil bacteria across biogeographic, ecological, and taxonomic scales.}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {65-81}, pmid = {17334855}, issn = {0095-3628}, mesh = {Animals ; Bacteria/*classification/genetics ; Biodiversity ; Birds/*microbiology ; Feathers/*microbiology ; Gene Library ; Geography ; RNA, Ribosomal, 16S/chemistry ; Sequence Analysis, DNA ; *Soil Microbiology ; Species Specificity ; }, abstract = {We used molecular methods to determine the microbial community of soil and avian plumage across biogeographic, ecological, and taxonomic scales. A total of 17 soil and 116 feather samples were collected from five avian species across multiple habitat types within one Neotropical and one temperate locality. Hypotheses regarding patterns of microbial composition relative to acquisition and dispersal of plumage bacteria in the ecosystem were tested by comparing microbial communities within and between soil and plumage. Samples from the plumage of American Redstarts (Setophaga ruticilla) were collected across both habitat types and geographic scales for intraspecific comparisons. The microbial diversity in avian plumage was moderately diverse and was dominated by Pseudomonas species. Despite a highly significant individual bird effect on microbial composition of the plumage, we detected significant biogeographic and type of habitat effects. Pseudomonas species were more abundant on the temperate site when all avian species were included in the analysis, and Bacillus subtilis and Xanthomonas groups were more abundant on the Neotropical site for redstarts alone. However, 16S rDNA sequence libraries were not significantly different between Jamaican and Maryland redstarts. Biogeographic and habitat effects were significant and more pronounced for soil samples indicating lower dispersal of soil microbiota. We detected a significant difference between soil and plumage microbial communities suggesting that soil plays a small role in plumage bacterial acquisition. Our results suggest bacterial communities on the plumage of birds are dynamic and may change at different stages in a bird's annual cycle.}, }
@article {pmid17333428, year = {2007}, author = {van Bodegom, P}, title = {Microbial maintenance: a critical review on its quantification.}, journal = {Microbial ecology}, volume = {53}, number = {4}, pages = {513-523}, pmid = {17333428}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development ; *Biomass ; Kinetics ; *Models, Biological ; }, abstract = {Microbial maintenance is an important concept in microbiology. Its quantification, however, is a subject of continuous debate, which seems to be caused by (1) its definition, which includes nongrowth components other than maintenance; (2) the existence of partly overlapping concepts; (3) the evolution of variables as constants; and (4) the neglect of cell death in microbial dynamics. The two historically most important parameters describing maintenance, the specific maintenance rate and the maintenance coefficient, are based on partly different nongrowth components. There is thus no constant relation between these parameters and previous equations on this subject are wrong. In addition, the partial overlap between these parameters does not allow the use of a simple combination of these parameters. This also applies for combinations of a threshold concentration with one of the other estimates of maintenance. Maintenance estimates should ideally explicitly describe each nongrowth component. A conceptual model is introduced that describes their relative importance and reconciles the various concepts and definitions. The sensitivity of maintenance on underlying components was analyzed and indicated that overall maintenance depends nonlinearly on relative death rates, relative growth rates, growth yield, and endogenous metabolism. This quantitative sensitivity analysis explains the felt need to develop growth-dependent adaptations of existing maintenance parameters, and indicates the importance of distinguishing the various nongrowth components. Future experiments should verify the sensitivity of maintenance components under cellular and environmental conditions.}, }
@article {pmid17333427, year = {2007}, author = {Warner, BG and Asada, T and Quinn, NP}, title = {Seasonal influences on the ecology of testate amoebae (Protozoa) in a small Sphagnum peatland in southern Ontario, Canada.}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {91-100}, pmid = {17333427}, issn = {0095-3628}, mesh = {Amoeba/classification/growth &amp; development/*physiology ; Animals ; Biodiversity ; Ontario ; Population Dynamics ; *Seasons ; Sphagnopsida/*physiology ; }, abstract = {Testate amoebae (Protozoa) were studied in spring, summer, and fall from the same microhabitats in a small Sphagnum-dominated peatland in southern Ontario, Canada. A total of 32 sampling stations were established in two wetland plant communities, 19 in an open Ericaceae low-shrub community and 13 in a closed Picea mariana and Larix laricina swamp community. Sphagnum was collected in each station for analysis of testate amoebae and measurement of soil water content parameters and water table depth in May, August, and October 2001. pH and dissolved oxygen of the groundwater under the Sphagnum were measured also. A total of 52 taxa including the rotifer, Habrotrocha angusticollis, were identified. Soil water content and water table variables emerged as the primary factors separating testate amoebae between the open bog/fen community and swamp community. Testate amoebae in the open bog/fen community showed a clear separation between the May sampling period and the August and October sampling periods. Sampling stations in May had much higher water table and were wetter than those in August and October. Conversely, testate amoebae in the swamp community did not show a clear difference between sampling periods. Soil moisture and water tables appear to be more constant in the swamp communities. Biological factors or other microscale environmental factors may need to be considered to explain seasonal changes in testate amoebae. A greater understanding of relationships between testate amoebae and microenvironmental factors is necessary to track seasonality in testate amoebae distributions.}, }
@article {pmid17333426, year = {2007}, author = {Zhang, HB and Yang, MX and Shi, W and Zheng, Y and Sha, T and Zhao, ZW}, title = {Bacterial diversity in mine tailings compared by cultivation and cultivation-independent methods and their resistance to lead and cadmium.}, journal = {Microbial ecology}, volume = {54}, number = {4}, pages = {705-712}, pmid = {17333426}, issn = {0095-3628}, mesh = {Bacteria/*classification/drug effects/genetics/*isolation &amp; purification ; Bacteriological Techniques ; Cadmium/*pharmacology ; Culture Media ; DNA, Bacterial/analysis/isolation &amp; purification ; *Drug Resistance, Bacterial ; Gene Library ; Lead/*pharmacology ; *Mining ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {To examine bacterial community composition in rhizosphere of plants colonizing on mine tailings and phylogenetic differences between subcommunities resistant to different metals, we constructed four clone libraries of 16S rDNA sequences. One was amplified directly from tailing microbial DNA (named as Ci library) and three from cultures on the plates containing of 0.5 mM CdCl(2) (Cd library), 2 mM Pb (NO(3))(2) (Pb library), and without any metals (Cw library). In total, nine bacterial divisions and two unclassified groups were identified from 352 clones of these libraries. Ci clones covered eight divisions, whereas all cultivable clones only covered four divisions. Thus, Ci library provided more phylogenetic diversity than cultivable libraries. However, the microbes represented by the cultivable clones were more similar to previously described bacteria than those represented by Ci clones. All Ci clones were not found in three cultivable libraries. Cd library were exclusively Gram-negative bacteria of Acinetobacter, Ralstonia, Comamonas, and Chryseobacterium. Meanwhile, dominant Gram-positive bacteria in Pb library, Paenibacillus and Bacillus, were also not found in Cd library. Our data indicate that phylogenetic structure was very different from those in acid mine drainage. Meanwhile, tailings harbored phylogenetically distinct subcommunities resistant to Pb and Cd.}, }
@article {pmid17333172, year = {2007}, author = {Daims, H and Wagner, M}, title = {Quantification of uncultured microorganisms by fluorescence microscopy and digital image analysis.}, journal = {Applied microbiology and biotechnology}, volume = {75}, number = {2}, pages = {237-248}, doi = {10.1007/s00253-007-0886-z}, pmid = {17333172}, issn = {0175-7598}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Colony Count, Microbial ; Ecosystem ; Image Processing, Computer-Assisted/*methods ; Microscopy, Fluorescence/*methods ; Oligonucleotide Probes ; RNA, Bacterial/genetics ; RNA, Ribosomal/genetics ; }, abstract = {Traditional cultivation-based methods to quantify microbial abundance are not suitable for analyses of microbial communities in environmental or medical samples, which consist mainly of uncultured microorganisms. Recently, different cultivation-independent quantification approaches have been developed to overcome this problem. Some of these techniques use specific fluorescence markers, for example ribosomal ribonucleic acid targeted oligonucleotide probes, to label the respective target organisms. Subsequently, the detected cells are visualized by fluorescence microscopy and are quantified by direct visual cell counting or by digital image analysis. This article provides an overview of these methods and some of their applications with emphasis on (semi-)automated image analysis solutions.}, }
@article {pmid17326383, year = {2006}, author = {Pavlova, OA and Severinov, KV}, title = {[Posttranslationally modified microcins].}, journal = {Genetika}, volume = {42}, number = {12}, pages = {1636-1646}, pmid = {17326383}, issn = {0016-6758}, mesh = {Amino Acid Sequence ; Bacteriocins/chemistry/*classification/*metabolism ; Molecular Sequence Data ; *Protein Processing, Post-Translational ; }, abstract = {Microcins are antibacterial compounds that are encoded in the bacterial genome and synthesized via ribosomal translation. Microcins play an important role in microbial ecology and are promising as antibiotics. To exert their effect, most microcins are incorporated in the membrane of sensitive cells to increase its permeability. The review considers the known classes of posttranslationally modified microcins. These microcins are unusual in structure and inhibit the grown of sensitive cells by entering their cytoplasm and affecting intracellular targets, such as DNA gyrase, DNA-dependent RNA polymerase, and aspartyl-tRNA synthase.}, }
@article {pmid17323146, year = {2007}, author = {Aira, M and Monroy, F and Domínguez, J}, title = {Eisenia fetida (Oligochaeta: Lumbricidae) modifies the structure and physiological capabilities of microbial communities improving carbon mineralization during vermicomposting of pig manure.}, journal = {Microbial ecology}, volume = {54}, number = {4}, pages = {662-671}, pmid = {17323146}, issn = {0095-3628}, mesh = {Animals ; Bacteria, Anaerobic/growth &amp; development/metabolism/*physiology ; Biodegradation, Environmental ; Biomass ; Carbon/*metabolism ; Ecosystem ; Fungi/growth &amp; development/metabolism/*physiology ; Manure/*microbiology ; Oligochaeta/*metabolism/physiology ; Spores, Fungal/physiology ; Swine ; }, abstract = {Although microorganisms are largely responsible for organic matter decomposition, earthworms may also affect the rates of decomposition directly by feeding on and digesting organic matter and microorganisms, or indirectly affect them through their interactions with the microorganisms, basically involving stimulation or depression of the microbial populations. We tested the general hypothesis that microbial populations, and especially fungi, are enhanced by earthworm activity, and also whether earthworms are able to modify the biodiversity of microbial populations, and its relation to the function of the system. In addition, we examined the metabolic quotient and the effect of labile organic C to assess the relationships between earthworm and microbes. We found that decomposition of pig manure has two stages characterized by the presence or absence of earthworms. Thus, the presence of earthworms was related with increases in overall microbial biomass and activity, which decreased when earthworms left the substrate; the same pattern was observed for fungi. Furthermore, earthworms modified the physiological profiles of microbial communities of pig manure, increasing the diversity of substrates utilized. In addition, earthworms promoted a more efficient use of energy of microbial communities, as the metabolic quotient showed. The rate of carbon loss was almost twice where earthworms were present, revealing faster decomposition. Our data match with the recent findings that to maintain essential processes the functional properties of present species are at least as important as the number of species per se. This is in accordance with the "insurance hypothesis," which states that a large number of species is probably essential for maintaining stable processes in changing environments, as the presence of earthworms would have promoted in pig manure.}, }
@article {pmid17323118, year = {2007}, author = {Stoeck, T and Bruemmer, F and Foissner, W}, title = {Evidence for local ciliate endemism in an alpine anoxic lake.}, journal = {Microbial ecology}, volume = {54}, number = {3}, pages = {478-486}, pmid = {17323118}, issn = {0095-3628}, mesh = {Animals ; Ciliophora/*genetics/*growth &amp; development/ultrastructure ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal Spacer/genetics ; Fresh Water/*parasitology ; Germany ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 5.8S/genetics ; Sequence Analysis, DNA ; }, abstract = {Despite its long history, biogeography has received relatively little attention within the field of microbial ecology. Consequently, a fierce debate rages whether protists inhabit restricted geographic areas (endemism hypothesis) or are globally dispersed (ubiquitous dispersal hypothesis). The data presented in this article support the endemism hypothesis. We succeeded in isolating an oligohymenophorean ciliate from a microbial mat in a meromictic anoxic alpine lake (Alatsee) in Germany. The ciliary pattern and the morphometry of this isolate are remarkably similar to Urocentrum turbo (Mueller, 1786) Nitzsch, 1827. However, the organism does not possess trichocysts, a conspicuous and characteristic feature of U. turbo. Instead, the U. turbo-like isolate from lake Alatsee displays merely trichocyst anlagen ("ghosts") in the cytoplasm that are only visible after protargol impregnation and which become never attached to the cell's cortex. Despite the distinctness of this difference, such a morphospecies has not been described from any other environment. Thus, we suggest that the U. turbo-like isolate from lake Alatsee is a local endemic ecotype, although the sequences of the 18S rRNA, ITS1, 5.8S rRNA, and ITS2 genes are nearly identical to those of U. turbo (Mueller, 1786) Nitzsch, 1827. This indicates that neither 18S rDNA nor ITS1, ITS2, and 5.8S rDNA sequences are reliable means to conclusively resolve different morphospecies or ecotypes of ciliates. As a consequence, we argue that protist species richness can only be reliably accounted for by considering both molecular and morphological data.}, }
@article {pmid17323117, year = {2007}, author = {Kallistova, AY and Kevbrina, MV and Nekrasova, VK and Shnyrev, NA and Einola, JK and Kulomaa, MS and Rintala, JA and Nozhevnikova, AN}, title = {Enumeration of methanotrophic bacteria in the cover soil of an aged municipal landfill.}, journal = {Microbial ecology}, volume = {54}, number = {4}, pages = {637-645}, pmid = {17323117}, issn = {0095-3628}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Bacteriological Techniques ; Cities ; Colony Count, Microbial ; Culture Media ; In Situ Hybridization, Fluorescence/methods ; Methane/*metabolism ; Oligonucleotide Probes ; *Refuse Disposal ; Seasons ; Soil/analysis ; *Soil Microbiology ; Time Factors ; }, abstract = {The enumeration of methanotrophic bacteria in the cover soil of an aged municipal landfill was carried out using (1) fluorescent in situ hybridization (FISH) with horseradish peroxidase-labeled oligonucleotide probes and tyramide signal amplification, also known as catalyzed reporter deposition-FISH (CARD-FISH), and (2) most probable number (MPN) method. The number of methanotrophs was determined in cover soil samples collected during April-November 2003 from a point with low CH(4) emission. The number of types I and II methanotrophs obtained by CARD-FISH varied from 15 +/- 2 to 56 +/- 7 x 10(8) cells g(-1) absolute dry mass (adm) of soil and methanotrophs of type I dominated over type II. The average number of methanotrophs throughout the cover soil profile was highest during May-September when the cover soil temperature was above 13 degrees C. Methanotrophs accounted for about 50% of the total bacterial population in the deepest cover soil layer owing to higher availability of substrate (CH(4)). A lower number of methanotrophs (7 x 10(2) to 17 x 10(5) cells g(-1) adm of soil) was determined by the MPN method compared to the CARD-FISH counts, thus confirming previous results that the MPN method is limited to the estimation of the culturable species that can be grown under the incubation conditions used. The number of culturable methanotrophs correlated with the methane-oxidizing activity measured in laboratory assays. In comparison to the incubation-based measurements, the number of methanotrophs determined by CARD-FISH better reflected the actual characteristics of the environment, such as release and uptake of CH(4), temperature, and moisture, and availability of substrates.}, }
@article {pmid17322323, year = {2007}, author = {Cámara, B and Seeger, M and González, M and Standfuss-Gabisch, C and Kahl, S and Hofer, B}, title = {Generation by a widely applicable approach of a hybrid dioxygenase showing improved oxidation of polychlorobiphenyls.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {8}, pages = {2682-2689}, pmid = {17322323}, issn = {0099-2240}, mesh = {Biotransformation ; Burkholderia/enzymology/*genetics ; Dioxygenases/*genetics/*metabolism ; Metabolic Networks and Pathways/genetics/physiology ; Oxidation-Reduction ; Polychlorinated Biphenyls/*metabolism ; *Protein Engineering ; Pseudomonas/enzymology/*genetics ; Recombinant Fusion Proteins/metabolism ; Substrate Specificity ; }, abstract = {Recently, a sequence-based approach has been developed for the fast isolation and characterization of class II aryl-hydroxylating dioxygenase activities (S. Kahl and B. Hofer, Microbiology 149:1475-1481, 2003). It comprises the PCR amplification of segments of alpha subunit genes of unknown sequence that encode the catalytic center and their fusion with sequences of the bphA gene cluster of Burkholderia xenovorans LB400. One of the resulting chimeric enzymes, harboring the core segment of a dioxygenase from Pseudomonas sp. strain B4-Magdeburg, has now been characterized with respect to the oxidation of chlorobiphenyls (CBs). Its substrate and product specificities differed favorably from those of the parental dioxygenase of strain LB400. The hybrid possessed a higher regiospecificity and yielded less unproductive dioxygenations at meta and para carbons. It attacked ortho-, meta-, and para-chlorinated rings with comparable efficiencies. It gave significantly higher yields in ortho,meta-dioxygenation of recalcitrant congeners containing a doubly ortho-chlorinated ring. While the parental enzyme yielded mainly unproductive meta, para dioxygenation of 2,5,4'-CB, the hybrid predominantly converted this congener into an ortho,meta-dioxygenated product. The subsequent enzymes of the LB400 catabolic pathway were able to transform most of the metabolites formed by the novel dioxygenase, indicating that the substrate ranges of these biocatalysts are not adapted to that of their initial pathway enzyme. Some of the catabolites, however, were identified as problematic for further degradation. Our results demonstrate that the outlined approach can successfully be applied to obtain novel dioxygenase specificities that favorably complement or supplement known ones.}, }
@article {pmid17320226, year = {2007}, author = {Hoshino, T and Furukawa, K and Tsuneda, S and Inamori, Y}, title = {RNA microarray for estimating relative abundance of 16S rRNA in microbial communities.}, journal = {Journal of microbiological methods}, volume = {69}, number = {2}, pages = {406-410}, doi = {10.1016/j.mimet.2007.01.007}, pmid = {17320226}, issn = {0167-7012}, mesh = {Nitrosomonas/genetics/*isolation &amp; purification ; Nucleic Acid Hybridization/*methods ; Paracoccus denitrificans/genetics/*isolation &amp; purification ; RNA, Bacterial/chemistry/genetics ; RNA, Ribosomal, 16S/chemistry/genetics ; Sewage/*microbiology ; }, abstract = {We developed an RNA microarray protocol in which total RNA from a microbial community was attached to a slide glass, and rRNA was detected by fluorescently labeled oligonucleotide probes. The RNA microarray requires only 4 h for hybridization and enables double staining and estimating relative abundance of rRNA.}, }
@article {pmid17318679, year = {2007}, author = {Liao, PC and Huang, BH and Huang, S}, title = {Microbial community composition of the Danshui river estuary of Northern Taiwan and the practicality of the phylogenetic method in microbial barcoding.}, journal = {Microbial ecology}, volume = {54}, number = {3}, pages = {497-507}, pmid = {17318679}, issn = {0095-3628}, mesh = {Biodiversity ; Comamonadaceae/classification/genetics ; *Ecosystem ; Gammaproteobacteria/classification/genetics ; Genetic Variation ; Geography ; Molecular Sequence Data ; *Phylogeny ; Proteobacteria/classification/*genetics ; RNA, Ribosomal, 16S/genetics ; Rhodobacteraceae/classification/genetics ; Rivers/*microbiology ; Sequence Analysis, DNA ; Taiwan ; Water Microbiology ; }, abstract = {In this study, the microbial community in a mangrove ecosystem was surveyed and used to test the eligibility of 16S rDNA library and neighbor-joining method for the purpose of estimating microbial composition. Genetic diversity (pi) and four other diversity indices (Simpson's unbiased, Shannon-Wiener, Evenness, and Chao1 indices) were applied to estimate the adaptive lineages of microorganisms in the mangrove ecosystem. The results indicated that gamma-Proteobacteria is the most diverse taxon, while the most abundant family is Rhodobacteraceae (alpha-Proteobacteria), followed by Comamonadaceae (beta-Proteobacteria). This result may imply the existence of a graded distribution of microbial diversity across a spectrum of different salinities in the waterbody of this estuary ecosystem. Furthermore, at least 500-1,000 bps of the posterior portion of 16S rDNA is required as a marker to profile the microbial diversity in a microcosm of interest using phylogenetic methods, according to the results of our sliding window analyses for the measurements of pi, consistency index, and retention index.}, }
@article {pmid17309403, year = {2007}, author = {Patel, MS}, title = {Australia's century of meningococcal disease: development and the changing ecology of an accidental pathogen.}, journal = {The Medical journal of Australia}, volume = {186}, number = {3}, pages = {136-141}, doi = {10.5694/j.1326-5377.2007.tb00837.x}, pmid = {17309403}, issn = {0025-729X}, mesh = {Australia/epidemiology ; Cost-Benefit Analysis ; Disease Notification ; History, 20th Century ; History, 21st Century ; Humans ; Meningococcal Infections/*epidemiology/history/prevention &amp; control ; Meningococcal Vaccines/*economics/immunology ; *Neisseria meningitidis/drug effects/pathogenicity ; Vaccines, Conjugate ; }, abstract = {Trends in meningococcal disease (MD) over the 20th century in Australia, as in other industrialised countries, have been characterised by epidemics during the two World Wars, a transient rise in incidence in the 1950s followed by endemic disease, and in the 1980s the emergence of a sustained hypersporadic phase. Epidemics occur at times of social upheaval and among marginalised populations, and resolve when living conditions improve. Periodic serogroup A epidemics have been replaced since the 1950s by endemic disease caused mainly by serogroups B and C meningococci. The current hypersporadic plateau in Australia, as in other industrialised countries, is associated with the intercontinental spread of hypervirulent clones of meningococci. The conjugate serogroup C vaccine has reduced the incidence of MD and carriage rates of serogroup C meningococci. However, the vaccine is expensive and its long-term impact on the emergence of non-vaccine strains and on nasopharyngeal microecology is unknown. A rising incidence of MD should not be viewed as the action of a virulent microbe exploiting a vulnerable population, but as the emergence of an "accidental pathogen" from an evolving host-microbial ecology. While it is essential to monitor the impact of vaccines on this ecology, we must find ways that can optimise our coexistence with microbes.}, }
@article {pmid17308984, year = {2007}, author = {Lohner, RN and Sigler, V and Mayer, CM and Balogh, C}, title = {A comparison of the benthic bacterial communities within and surrounding Dreissena clusters in lakes.}, journal = {Microbial ecology}, volume = {54}, number = {3}, pages = {469-477}, pmid = {17308984}, issn = {0095-3628}, mesh = {Animals ; Bacteria/classification/genetics/*growth &amp; development ; Canada ; DNA, Bacterial/genetics/isolation &amp; purification ; Dreissena/*microbiology ; *Ecosystem ; Electrophoresis, Agar Gel ; Fresh Water/*microbiology ; Geography ; Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; }, abstract = {The impact of Dreissena (Dreissena polymorpha and D. bugensis) on the benthic bacterial community in lakes is largely unknown. Therefore, we quantified differences in the structure and activity of bacterial communities living in sediments (1) associated with Dreissena clusters, and (2) unassociated with established clusters (lake bottom sediments). Dreissena clusters and sediments were collected from locations in Lake Erie, Lake Ontario, and several inland lakes. Denaturing gradient gel electrophoresis (DGGE) analysis of the benthic bacterial community showed that the bacterial populations selected for by Dreissena represent a subset of the bottom communities and are geographically distinct. Community-level physiological profiling (CLPP) showed that overall bacterial activity and metabolic diversity were enhanced by the presence of clusters in all samples, with the exception of those harvested from the two Lake Erie sites. Therefore, Dreissena appears to affect both structure and metabolic function of the benthic bacterial community and may have yet unexplored ecosystem and food web consequences.}, }
@article {pmid17308951, year = {2007}, author = {Rubin, MA and Leff, LG}, title = {Nutrients and other abiotic factors affecting bacterial communities in an Ohio River (USA).}, journal = {Microbial ecology}, volume = {54}, number = {2}, pages = {374-383}, pmid = {17308951}, issn = {0095-3628}, mesh = {Bacteria/*classification/growth &amp; development/isolation &amp; purification ; *Ecosystem ; Nitrogen/analysis ; Ohio ; Phosphorus/analysis ; Rivers/chemistry/*microbiology ; }, abstract = {Nitrogen and phosphorus additions from anthropogenic sources can alter the nutrient pool of aquatic systems, both through increased nutrient concentrations and changes in stoichiometry. Because bacteria are important in nutrient cycling and aquatic food webs, information about how nutrients affect bacterial communities enhances our understanding of how changes in nutrient concentrations and stoichiometry potentially affect aquatic ecosystems as a whole. In this study, bacterial communities were examined in biofilms from cobbles collected across seasons at three sites along the Mahoning River (Ohio) with differing levels of inorganic nutrient inputs. Members of the alpha-, beta-, and gamma-proteobacteria, the Cytophaga-Flavobacteria cluster, and the Domain Bacteria were enumerated using fluorescent in situ hybridization. Detrended canonical correspondence analysis (DCCA) revealed that stoichiometric ratios, especially the dissolved inorganic nitrogen (DIN):soluble reactive phosphorus (SRP) molar ratio (NO(2)/NO(3) + NH(4):soluble reactive phosphorus), were correlated with abundance of the various bacterial taxa. However, the patterns were complicated by correlations with single nutrient concentrations and seasonal changes in temperature. Seasonal cycles appeared to play an important role in structuring the community, as there were distinct winter communities and temperature was negatively correlated with abundance of both alpha-proteobacteria and Cytophaga-Flavobacteria. However, nutrients and stoichiometry also appeared to affect the community. Numbers of cells hybridizing the Domain Bacteria probe were correlated with the DOC:DIN ratio, the beta-proteobacteria had a negative correlation with soluble reactive phosphorus concentrations and a positive correlation with the DIN:SRP ratio, and the Cytophaga-Flavobacteria had a significant negative partial correlation with the DIN:SRP ratio. Abundances of the alpha- or gamma-proteobacteria were not directly correlated to nutrient concentrations or stoichiometry. It appears that nutrient stoichiometry may be an important factor structuring bacterial communities; however, it is one of many factors, such as temperature, that are interlinked and must be considered together when studying environmental bacteria.}, }
@article {pmid17308950, year = {2007}, author = {Fang, Z and Ouyang, Z and Zheng, H and Wang, X and Hu, L}, title = {Culturable airborne bacteria in outdoor environments in Beijing,China.}, journal = {Microbial ecology}, volume = {54}, number = {3}, pages = {487-496}, pmid = {17308950}, issn = {0095-3628}, mesh = {*Air Microbiology ; Bacillus/growth &amp; development/isolation &amp; purification ; Bacteria/classification/*growth &amp; development/*isolation &amp; purification ; Bacterial Typing Techniques ; China ; Colony Count, Microbial ; Environmental Monitoring/methods ; Micrococcus/growth &amp; development/isolation &amp; purification ; Pseudomonas/growth &amp; development/isolation &amp; purification ; Staphylococcus/growth &amp; development/isolation &amp; purification ; }, abstract = {Airborne bacteria are important biological components of bioaerosol and play an important role in ecosystem. Bacteria at a high concentration in the atmosphere can result in biological air pollution and all kinds of diseases. In this study, a systematical survey on the culturable airborne bacteria was carried out for 1 year at three sites in Beijing urban area. Results showed that concentrations of culturable bacteria ranged from 71 colony forming units (CFU)/m(3) to 22,100 CFU/m(3), and the mean was 2,217 CFU/m(3). Bacterial concentrations at the human activity-enriched site (RCEES) and the highly trafficked site (XZM) were virtually the same point. They were significantly higher than those at the greener site (BBG). Significant variation in bacterial concentrations in different seasons was observed at RCEES and XZM with higher concentrations in summer and autumn. In a single day, significantly lower concentrations were detected at 13:00 hours through all sampling sites. In this study, 165 species in 47 genera of culturable bacteria were identified. Micrococcus was one of the most dominant bacterial groups and contributed to approximately 20 approximately 30% of the total bacterial concentration, followed by Staphylococcus, Bacillus, Corynebacterium, and Pseudomonas. The bacterial species with a high concentration percentage included Micrococcus luteus and Micrococcus roseus.}, }
@article {pmid17306857, year = {2007}, author = {Enright, AM and Collins, G and O'Flaherty, V}, title = {Low-temperature anaerobic biological treatment of toluene-containing wastewater.}, journal = {Water research}, volume = {41}, number = {7}, pages = {1465-1472}, doi = {10.1016/j.watres.2007.01.005}, pmid = {17306857}, issn = {0043-1354}, mesh = {Bacteria, Anaerobic/growth &amp; development/*metabolism ; *Bioreactors ; Chromatography, High Pressure Liquid ; Fatty Acids/metabolism ; Methane/analysis ; Spectrophotometry, Ultraviolet ; *Temperature ; Toluene/*metabolism/toxicity ; Toxicity Tests ; Waste Disposal, Fluid/*methods ; Water Pollutants, Chemical/*metabolism ; Water Purification/*methods ; }, abstract = {Two expanded granular sludge bed-anaerobic filter (EGSB-AF) bioreactors, R1 and R2, were operated at 15 degrees C for the treatment of toluene-contaminated volatile fatty acid-based wastewater. The seed inoculum and the R1 reactor were unexposed to toluene, prior to and during the trial, respectively. Both reactors were operated at a hydraulic retention time of 24h at applied organic loading rates of 0.71-1.43kg chemical oxygen demand (COD)m(-3)d(-1). Toluene was supplemented to the R2 influent at concentrations of 5-104 mg toluenel(-1) (solubilised in ethanol). Bioreactor performance was evaluated by COD and toluene removal efficiency, and the methane content of biogas (%). Specific methanogenic activity and toxicity assays were employed to investigate the activity and toluene toxicity thresholds of key trophic groups, respectively, within the seed and reactor biomass samples. COD and toluene removal efficiencies of 70-90% and 55-99%, respectively, were achieved during the 630-d trial. Metabolic assays suggested that a psychrotolerant H(2)/CO(2)-utilizing methanogenic community developed in the toluene-degrading biomass. The results indicate the viability of low-temperature anaerobic digestion for the treatment of wastewater containing toluene.}, }
@article {pmid17306538, year = {2007}, author = {Kuehne, HA and Murphy, HA and Francis, CA and Sniegowski, PD}, title = {Allopatric divergence, secondary contact, and genetic isolation in wild yeast populations.}, journal = {Current biology : CB}, volume = {17}, number = {5}, pages = {407-411}, doi = {10.1016/j.cub.2006.12.047}, pmid = {17306538}, issn = {0960-9822}, mesh = {Asia ; *Biodiversity ; Crosses, Genetic ; Europe ; *Evolution, Molecular ; *Genetic Speciation ; *Genetic Variation ; Geography ; Molecular Sequence Data ; North America ; Phylogeny ; Quercus/microbiology ; Saccharomyces/*classification/*genetics/physiology ; Sequence Analysis, DNA ; Spores, Fungal/genetics/physiology ; }, abstract = {In plants and animals, new biological species clearly have arisen as a byproduct of genetic divergence in allopatry. However, our understanding of the processes that generate new microbial species remains limited [1] despite the large contribution of microbes to the world's biodiversity. A recent hypothesis claims that microbes lack biogeographical divergence because their population sizes are large and their migration rates are presumably high [2, 3]. In recapitulating the classic microbial-ecology dictum that "everything is everywhere, and the environment selects"[4, 5], this hypothesis casts doubt on whether geographic divergence promotes speciation in microbes. To date, its predictions have been tested primarily with data from eubacteria and archaebacteria [6-8]. However, this hypothesis's most important implication is in sexual eukaryotic microbes, where migration and genetic admixture are specifically predicted to inhibit allopatric divergence and speciation [9]. Here, we use nuclear-sequence data from globally distributed natural populations of the yeast Saccharomyces paradoxus to investigate the role of geography in generating diversity in sexual eukaryotic microbes. We show that these populations have undergone allopatric divergence and then secondary contact without genetic admixture. Our data thus support the occurrence of evolutionary processes necessary for allopatric speciation in sexual microbes.}, }
@article {pmid17305122, year = {2007}, author = {Scully, C and Collins, G and O'Flaherty, V}, title = {Granular biofilm-based anaerobic digestion: molecular biomonitoring and high-rate psychrophilic treatment of phenolic wastewater.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {55}, number = {1-2}, pages = {43-49}, doi = {10.2166/wst.2007.027}, pmid = {17305122}, issn = {0273-1223}, mesh = {Bacteria, Anaerobic/*metabolism ; Biodegradation, Environmental ; *Biofilms ; Bioreactors ; *Environmental Monitoring ; Phenol/*metabolism ; Phenols/*metabolism ; Sewage/chemistry/*microbiology ; Time Factors ; *Waste Disposal, Fluid ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Two pairs of expanded granular sludge bed (EGSB) bioreactors, R1/R2 and R3/R4, were designed. R1/R2 were used for mesophilic (37 degrees C) treatment of synthetic wastewater over a 100-day trial. A successful start-up was achieved by R1 and R2, with COD removal over 90%. Both reactors were operated under identical parameters; however, increased organic loading induced a reduction in COD removal by R1, while R2 maintained satisfactory performance throughout the experiment. R3/R4 were operated at 15 degrees C throughout a 422-day trial and were used for the stabilisation of volatile fatty acid-based wastewater. Phenol was introduced to R4 at an applied loading rate of 1 kg phenol m(-3)d(-1), which was increased to 2 kg phenol m(-3)d(-1). No phenol was supplied to R3. Efficient COD conversion was recorded in both R3 and R4, thus demonstrating the feasibility of high-rate phenol degradation under psychrophilic conditions. Terminal restriction fragment length polymorphism analysis was applied to the characterisation of microbial community dynamics within each of the reactors. The results indicated a microbiological basis for the deviation, in terms of operational performance, of R1 and R2. TRFLP analyses indicated stable microbial communities in R3 and R4, but detected changes in the abundance of specific ribotypes in response to phenol mineralisation.}, }
@article {pmid17298376, year = {2007}, author = {Weinbauer, MG and Hornák, K and Jezbera, J and Nedoma, J and Dolan, JR and Simek, K}, title = {Synergistic and antagonistic effects of viral lysis and protistan grazing on bacterial biomass, production and diversity.}, journal = {Environmental microbiology}, volume = {9}, number = {3}, pages = {777-788}, doi = {10.1111/j.1462-2920.2006.01200.x}, pmid = {17298376}, issn = {1462-2912}, mesh = {Animals ; *Bacteria/classification/genetics/growth &amp; development/virology ; Bacteriolysis ; Bacteriophages/*physiology ; *Biomass ; *Ecosystem ; Feeding Behavior ; Flagella/*physiology ; Food Chain ; *Fresh Water/microbiology/parasitology/virology ; Lysogeny ; Plankton/physiology ; }, abstract = {In a mesotrophic reservoir, we examined the effects on the bacterioplankton of distinct consumers of bacteria, viruses and heterotrophic nanoflagellates, both alone and combined in an experiment using natural populations and in situ incubations in dialysis bags. Ribosomal RNA-targeted probes were employed as well as 16S RNA gene based PCR denaturing gradient gel electrophoresis (DGGE) to enumerate bacterial groups and assess bacterial community composition. We employed probes for Actinobacteria (HGC69a probe), Cytophaga-Flavobacterium-Bacteroidetes bacteria (CF319a probe), BET42a probe (Betaproteobacteria) and a subgroup-Betaproteobacteria (R-BT065 probe). We found consumer-specific effects on bacterial activity and diversity (against a background of CF and BET dominating all treatments) suggesting distinct vulnerabilities to the two sources of mortality. For example, growth rate of Actinobacteria was only positive in the presence of flagellates, while towards the end of the experiment (T(72-96 h)) growth rate of R-BT was only positive in the viruses only treatment. More specific data on how viruses and flagellates influenced Flectobacillus are shown in the companion paper. Highest richness (number of DGGE bands) was found in the virus only treatment and lowest when both consumers were present. In addition, we found suggestions of both antagonistic and synergistic interactions between the two sources of bacterial mortality. Notably, bactivory by flagellates was associated with reductions in bacterial diversity and increases in viral production.}, }
@article {pmid17298367, year = {2007}, author = {Leitch, EC and Walker, AW and Duncan, SH and Holtrop, G and Flint, HJ}, title = {Selective colonization of insoluble substrates by human faecal bacteria.}, journal = {Environmental microbiology}, volume = {9}, number = {3}, pages = {667-679}, doi = {10.1111/j.1462-2920.2006.01186.x}, pmid = {17298367}, issn = {1462-2912}, mesh = {*Amylose ; Bacteria/classification/genetics/*growth &amp; development ; Bacterial Adhesion ; Colony Count, Microbial ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; *Dietary Fiber ; Feces/*microbiology ; *Gastric Mucins ; Genes, rRNA ; Humans ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Solubility ; Substrate Specificity ; }, abstract = {Insoluble plant polysaccharides and endogenous mucin are important energy sources for human colonic microorganisms. The object of this study was to determine whether or not specific communities colonize these substrates. Using faecal samples from four individuals as inocula for an anaerobic in vitro continuous flow system, the colonization of wheat bran, high amylose starch and porcine gastric mucin was examined. Recovered substrates were extensively washed and the remaining tightly attached bacterial communities were identified using polymerase chain reaction-amplified 16S rRNA gene sequences and fluorescent in situ hybridization. The substrate had a major influence on the species of attached bacteria detected. Sequences retrieved from bran were dominated by clostridial cluster XIVa bacteria, including uncultured relatives of Clostridium hathewayi, Eubacterium rectale and Roseburia species. Bacteroides species were also detected. The most abundant sequences recovered from starch were related to the cultured species Ruminococcus bromii, Bifidobacterium adolescentis, Bifidobacterium breve and E. rectale. The most commonly recovered sequences from mucin were from Bifidobacterium bifidum and uncultured bacteria related to Ruminococcus lactaris. This study suggests that a specific subset of bacteria is likely to be the primary colonizers of particular insoluble colonic substrates. For a given substrate, however, the primary colonizing species may vary between host individuals.}, }
@article {pmid17298360, year = {2007}, author = {Boenigk, J and Jost, S and Stoeck, T and Garstecki, T}, title = {Differential thermal adaptation of clonal strains of a protist morphospecies originating from different climatic zones.}, journal = {Environmental microbiology}, volume = {9}, number = {3}, pages = {593-602}, doi = {10.1111/j.1462-2920.2006.01175.x}, pmid = {17298360}, issn = {1462-2912}, support = {P 18767/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Adaptation, Physiological ; Chrysophyta/*classification/genetics/growth &amp; development/*physiology ; *Climate ; *Ecosystem ; Fresh Water/microbiology ; Molecular Sequence Data ; Seawater/microbiology ; Sequence Analysis, DNA ; Soil Microbiology ; *Temperature ; }, abstract = {Eco-physiological variation and local adaptation are key issues in microbial ecology. Here, we investigated the thermal adaptation of 19 strains of the same Spumella morphospecies (Chrysophyceae, Heterokonta). In order to test for local adaptation and the existence of specific ecotypes we analysed growth rates of these strains, which originated from different climate regions. We applied temperature-adaptation as an eco-physiological marker and analysed growth rates of the different Spumella strains at temperatures between 0 degrees C and 35 degrees C. The temperatures allowing for maximal growth of strains from temperate and warm climatic zones ranged between 19.9 degrees C and 33.4 degrees C. Phylogenetically, most of these 'warm'-adapted strains fall into two different previously defined 18S rDNA Spumella clusters, one of them consisting of mostly soil organisms and the other one being a freshwater cluster. As a rule, the 'warm'-adapted strains of the soil cluster grew slower than the 'warm'-adapted isolates within the freshwater cluster. This difference most probably reflect different strategies, i.e. the formation of cysts at the expense of lower growth rates in soil organisms. In contrast, as expected, all isolates from Antarctica were cold-adapted and grew already around melting point of freshwater. Surprisingly, optimum temperature for these strains was between 11.8 degrees C and 17.7 degrees C and maximum temperature tolerated was between 14.6 degrees C and 23.5 degrees C. Our data indicate that despite the relatively high optimal temperature of most Antarctic strains, they may have a relative advantage below 5-10 degrees C only. Based on the thermal adaptation of the flagellate strains the Antarctic strains were clearly separated from the other investigated strains. This may indicate a limited dispersal of flagellates to and from Antarctica. Even if the latter assumption needs support from more data, we argue that the high levels of eco-physiological and molecular microdiversity indicate that the current species concepts do not sufficiently reflect protist eco-physiological differentiation.}, }
@article {pmid17296935, year = {2007}, author = {Ramette, A and Tiedje, JM}, title = {Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {8}, pages = {2761-2766}, pmid = {17296935}, issn = {0027-8424}, mesh = {Burkholderia cepacia complex/classification/*physiology ; *Ecosystem ; Genome, Bacterial ; Regression Analysis ; Soil Microbiology ; }, abstract = {Spatial distance (SD) and environmental heterogeneity (EH) are currently thought to represent major factors shaping genetic variation and population abundance, but their relative importance is still poorly understood. Because EH varies at multiple spatial scales, so too are microbial variables expected to vary. The determination of SD x EH interactions at multiple scales is, however, not a trivial exercise, especially when one examines their effects on microbial abundance and genomic similarities. Here we assessed those interactions at all scales perceptible in a patchy environment composed of known plant species and of heterogeneous soil physical and chemical parameters. For free-living, soil-borne Burkholderia ambifaria, genomic similarities responded to most of the spatial scales that the experimental sampling scheme could reveal, despite limited dispersal of the individuals. Species abundance and community composition were, however, responding to much smaller scales more consistent with local responses to EH. Our results suggest that whole-genome similarities may reflect the simultaneous effects of both SD and EH in microbial populations, but the pure effects of each factor only contributed to < 2% of the total genetic variation. The large amount of unexplained variation that remains after considering most environmental, spatial, and biological interactions is then posited to be the result of noise introduced by unmeasured environmental and spatial variability, sampling effects, and neutral ecological drift.}, }
@article {pmid17293459, year = {2007}, author = {Gao, Z and Tseng, CH and Pei, Z and Blaser, MJ}, title = {Molecular analysis of human forearm superficial skin bacterial biota.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {8}, pages = {2927-2932}, pmid = {17293459}, issn = {0027-8424}, support = {M01 RR000096/RR/NCRR NIH HHS/United States ; M01 RR 00096/RR/NCRR NIH HHS/United States ; R01 CA097946/CA/NCI NIH HHS/United States ; R01 GM063270/GM/NIGMS NIH HHS/United States ; CA 97946/CA/NCI NIH HHS/United States ; R01 GM 63270/GM/NIGMS NIH HHS/United States ; AI 063477/AI/NIAID NIH HHS/United States ; R01 AI063477/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Bacteria/classification/*genetics/isolation &amp; purification ; *Biodiversity ; Clone Cells ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal/analysis/genetics ; Female ; Forearm/*microbiology ; Humans ; Male ; Middle Aged ; Molecular Sequence Data ; Phylogeny ; Skin/*microbiology ; }, abstract = {The microbial ecology of human skin is complex, but little is known about its species composition. We examined the diversity of the skin biota from the superficial volar left and right forearms in six healthy subjects using broad-range small subunit rRNA genes (16S rDNA) PCR-based sequencing of randomly selected clones. For the initial 1,221 clones analyzed, 182 species-level operational taxonomic units (SLOTUs) belonging to eight phyla were identified, estimated as 74.0% [95% confidence interval (C.I.), approximately 64.8-77.9%] of the SLOTUs in this ecosystem; 48.0 +/- 12.2 SLOTUs were found in each subject. Three phyla (Actinobacteria, Firmicutes, and Proteobacteria) accounted for 94.6% of the clones. Most (85.3%) of the bacterial sequences corresponded to known and cultivated species, but 98 (8.0%) clones, comprising 30 phylotypes, had <97% similarity to prior database sequences. Only 6 (6.6%) of the 91 genera and 4 (2.2%) of the 182 SLOTUs, respectively, were found in all six subjects. Analysis of 817 clones obtained 8-10 months later from four subjects showed additional phyla (numbering 2), genera (numbering 28), and SLOTUs (numbering 65). Only four (3.4%) of the 119 genera (Propionibacteria, Corynebacteria, Staphylococcus, and Streptococcus) were observed in each subject tested twice, but these genera represented 54.4% of all clones. These results show that the bacterial biota in normal superficial skin is highly diverse, with few well conserved and well represented genera, but otherwise low-level interpersonal consensus.}, }
@article {pmid17277208, year = {2007}, author = {Lenaerts, J and Lappin-Scott, HM and Porter, J}, title = {Improved fluorescent in situ hybridization method for detection of bacteria from activated sludge and river water by using DNA molecular beacons and flow cytometry.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {6}, pages = {2020-2023}, pmid = {17277208}, issn = {0099-2240}, mesh = {*Bacteriological Techniques ; DNA, Bacterial/analysis/genetics ; Flow Cytometry/*methods ; In Situ Hybridization, Fluorescence/*methods ; Pseudomonas putida/genetics/isolation &amp; purification ; Rivers/*microbiology ; Sensitivity and Specificity ; Sewage/*microbiology ; Water Microbiology ; }, abstract = {Fluorescent in situ hybridization (FISH) remains a key technique in microbial ecology. Molecular beacons (MBs) are self-reporting probes that have potential advantages over linear probes for FISH. MB-FISH strategies have been described using both DNA-based and peptide nucleic acid (PNA)-based approaches. Although recent reports have suggested that PNA MBs are superior, DNA MBs have some advantages, most notably cost. The data presented here demonstrate that DNA MBs are suitable for at least some FISH applications in complex samples, providing superior discriminatory power compared to that of corresponding linear DNA-FISH probes. The use of DNA MBs for flow cytometric detection of Pseudomonas putida resulted in approximately double the signal-to-noise ratio of standard linear DNA probes when using laboratory-grown cultures and yielded improved discrimination of target cells in spiked environmental samples, without a need for separate washing steps. DNA MBs were also effective for the detection and cell sorting of both spiked and indigenous P. putida from activated sludge and river water samples. The use of DNA MB-FISH presents another increase in sensitivity, allowing the detection of bacteria in environmental samples without the expense of PNA MBs or multilaser flow cytometry.}, }
@article {pmid17268880, year = {2007}, author = {Aguilera, A and Souza-Egipsy, V and Gómez, F and Amils, R}, title = {Development and structure of eukaryotic biofilms in an extreme acidic environment, rio tinto (SW, Spain).}, journal = {Microbial ecology}, volume = {53}, number = {2}, pages = {294-305}, pmid = {17268880}, issn = {0095-3628}, mesh = {Biofilms/*growth &amp; development ; *Ecosystem ; Eukaryotic Cells/classification/*physiology ; Fresh Water/*analysis ; Hydrogen-Ion Concentration ; Metals, Heavy ; Seasons ; Spain ; Species Specificity ; Water/parasitology ; Water Microbiology ; }, abstract = {An in situ colonization assay was performed to study the early stages of biofilm formation in Rio Tinto (SW, Spain), an extremely acidic environment (pH ca. 2). Eukaryotic assemblages were monitored at monthly intervals for 1 year. Diversity, colonization rates, and seasonal variations were analyzed. Structural features of naturally grown biofilms were explored by light and scanning electron microscopy in backscattered electron mode. A total of 14 taxa were recognized as constituents of the eukaryotic assemblages. The eukaryotic communities were dissimilar at the different sampling sites. The lowest diversity was found at the most extreme locations, in terms of pH and heavy metal concentrations. The biofilms were mainly formed by species from the genera Dunaliella and Cyanidium. Two genera of filamentous algae, Zygnemopsis and Klebsormidium, were principally responsible for the variability in the cell number throughout the year. These species appear in June to decrease almost completely between October and November. In contrast, the number of heterotrophic flagellates and ciliates remained constant throughout the year. The microcolonization sequence showed an initial accumulation of amorphous particles composed of bacteria and inorganic grains of minerals. By the end of the second month, the organic matrix was also populated by fungi, bacteria, and a few eukaryotic heterotrophs such as amoebae and small flagellates. Diatoms only showed significant colonization in regions where mycelial matrices were first established. Flagellated green algae such as Dunaliella or Chlamydomonas as well as Euglena were also present at the very beginning of the biofilm development, although in low numbers (<100 cells cm(-2)). After the flagellated cells, sessile species of algae such Chlorella or Cyanidium appeared. Filamentous algae were the last species to colonize the biofilms. Most of the naturally grown biofilms were found to be structures composed of different species organized in different layers separated, probably by extracellular polymeric substances, although more analysis should be done in this regard. The possible implications of the biofilm structure in the adaptation to this extreme habitat are discussed.}, }
@article {pmid17268879, year = {2007}, author = {Thorén, AK}, title = {Urea transformation of wetland microbial communities.}, journal = {Microbial ecology}, volume = {53}, number = {2}, pages = {221-232}, pmid = {17268879}, issn = {0095-3628}, mesh = {Animals ; Bacteria/metabolism ; Biofilms ; Eukaryota/metabolism ; Fungi/metabolism ; Geologic Sediments/analysis ; Oceans and Seas ; Plankton/metabolism ; Plants/microbiology ; Quaternary Ammonium Compounds/metabolism ; Sweden ; Urea/*metabolism ; Water/*metabolism ; *Water Microbiology ; *Wetlands ; }, abstract = {Transformation of urea to ammonium is an important link in the nitrogen cycle in soil and water. Although microbial nitrogen transformations, such as nitrification and denitrification, are well studied in freshwater sediment and epiphytic biofilm in shallow waters, information about urea transformation in these environments is scarce. In this study, urea transformation of sedimentary, planktonic, and epiphytic microbial communities was quantified and urea transformation of epiphytic biofilms associated with three different common wetland macrophyte species is compared. The microbial communities were collected from a constructed wetland in October 2002 and urea transformation was quantified in the laboratory at in situ temperature (12 degrees C) with the use of the 14C-urea tracer method, which measures the release of 14CO2 as a direct result of urease activity. It was found that the urea transformation was 100 times higher in sediment (12-22 mmol urea-N m(-2) day(-1)) compared with the epiphytic activity on the surfaces of the submerged plant Elodea canadensis (0.1-0.2 mmol urea-N m(-2) day(-1)). The epiphytic activity of leaves of Typha latifolia was lower (0.001-0.03 mmol urea-N m(-2) day(-1)), while urea transformation was negligible in the water column and on the submerged leaves of the emergent plant Phragmites australis. However, because this wetland was dominated by dense beds of the submerged macrophyte E. canadensis, this plant provided a large surface area for epiphytic microbial activity-in the range of 23-33 m2 of plant surfaces per square meter of wetland. Thus, in the wetland system scale at the existing plant distribution and density, the submerged plant community had the potential to transform 2-7 mmol urea-N m(-2) day(-1) and was in the same magnitude as the urea transformation in the sediment.}, }
@article {pmid17267984, year = {2007}, author = {Burns, DG and Janssen, PH and Itoh, T and Kamekura, M and Li, Z and Jensen, G and Rodríguez-Valera, F and Bolhuis, H and Dyall-Smith, ML}, title = {Haloquadratum walsbyi gen. nov., sp. nov., the square haloarchaeon of Walsby, isolated from saltern crystallizers in Australia and Spain.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {57}, number = {Pt 2}, pages = {387-392}, doi = {10.1099/ijs.0.64690-0}, pmid = {17267984}, issn = {1466-5026}, support = {R01 AI067548/AI/NIAID NIH HHS/United States ; }, mesh = {Aerobiosis ; Australia ; Base Composition ; Cell Wall/ultrastructure ; Cytoplasm/ultrastructure ; DNA, Archaeal/chemistry/isolation &amp; purification ; Genes, rRNA ; Halobacteriaceae/*classification/cytology/*isolation &amp; purification/physiology ; Hydrogen-Ion Concentration ; Magnesium/metabolism ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Organelles/ultrastructure ; Phospholipids/analysis/chemistry ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Salts ; Seawater/*microbiology ; Sequence Analysis, DNA ; Spain ; Water Microbiology ; }, abstract = {Strains C23T and HBSQ001 were isolated from solar salterns and are novel square-shaped, aerobic, extremely halophilic members of the domain Archaea and family Halobacteriaceae. Cells stained Gram-negative and grew optimally in media containing 18 % salts at around neutral pH. Mg2+ is not required. The DNA G+C content of both isolates was 46.9 mol% and DNA-DNA cross-hybridization showed a relatedness of 80 %. Their 16S rRNA gene sequences showed only 2 nucleotide differences (99.9 % identity) and phylogenetic tree reconstructions with other recognized members of the Halobacteriaceae indicated that they formed a distinct clade, with the closest relative being Halogeometricum borinquense PR 3T (91.2 % sequence identity). The major polar glycolipid of both isolates was the sulfated diglycosyl diether lipid S-DGD-1. Electron cryomicrosopy of whole cells revealed similar internal structures, such as gas vesicles and polyhydroxyalkanoate granules, but the cell wall of isolate HBSQ001 displayed a more complex S-layer compared with that of isolate C23T. The phenotypic characterization and phylogenetic data support the placement of isolates C23T and HBSQ001 in a novel species in a new genus within the Halobacteriaceae, for which we propose the name Haloquadratum walsbyi gen. nov., sp. nov. The type strain of Haloquadratum walsbyi is C23T (=JCM 12705T=DSM 16854T).}, }
@article {pmid17265004, year = {2007}, author = {Wehrl, M and Steinert, M and Hentschel, U}, title = {Bacterial uptake by the marine sponge Aplysina aerophoba.}, journal = {Microbial ecology}, volume = {53}, number = {2}, pages = {355-365}, pmid = {17265004}, issn = {0095-3628}, mesh = {Animals ; *Bacteria/isolation &amp; purification ; *Feeding Behavior ; Porifera/*microbiology/*physiology ; Seawater/microbiology ; *Symbiosis ; }, abstract = {Sponges (Porifera) are filter feeders that take up microorganisms from seawater and digest them by phagocytosis. At the same time, many sponges are known to harbor massive consortia of symbiotic microorganisms, which are phylogenetically distinct from those in seawater, within the mesohyl matrix. In the present study, feeding experiments were performed to investigate whether phylogenetically different bacterial isolates, hereafter termed "food bacteria," microbial seawater consortia, and sponge symbiont consortia are taken up and processed differently by the host sponge. Aplysina aerophoba retained high numbers of bacterial isolates and microbial seawater consortia with rates of up to 2.76 x 10(6) bacteria (g sponge wet weight)(-1) h(-1), whereas the retention of sponge symbionts was lower by nearly two orders of magnitude [5.37 x 10(4) bacteria (g sponge wet weight)(-1) h(-1)]. In order to visualize the processing of a food bacterium within sponge tissues, the green fluorescent protein-labeled Vibrio strain MMW1, which had originally been isolated from A. aerophoba, was constructed. Incubation of this strain with A. aerophoba and subsequent visualization in tissue cryosections showed its presence in the choanocytes and/or endopinacocytes lining the canals but, unlike latex beads, not in deeper regions of the mesohyl, which suggests digestion of the bacteria upon contact with the host. Denaturing gradient gel electrophoresis (DGGE) was performed on the incubation seawater to monitor the changes in phylogenetic composition after incubation of the sponge with either seawater or sponge symbiont consortia. However, the DGGE experiment provided no evidence for selective processing of individual lineages by the host sponge. In conclusion, this study extends early studies by Wilkinson et al. (Proc R Soc London B 220:519-528, 1984) that sponges, here A. aerophoba, are able to differentiate between food bacteria and their own bacterial symbionts.}, }
@article {pmid17265003, year = {2007}, author = {Inwood, SE and Tank, JL and Bernot, MJ}, title = {Factors controlling sediment denitrification in midwestern streams of varying land use.}, journal = {Microbial ecology}, volume = {53}, number = {2}, pages = {247-258}, pmid = {17265003}, issn = {0095-3628}, mesh = {*Environmental Monitoring ; *Fresh Water/analysis ; *Geologic Sediments/analysis ; Michigan ; Nitrates/analysis/metabolism ; Nitro Compounds/chemistry/*metabolism ; *Rivers ; Water Pollutants/*metabolism ; }, abstract = {We investigated controls on stream sediment denitrification in nine headwater streams in the Kalamazoo River Watershed, Michigan, USA. Factors influencing denitrification were determined by using experimental assays based on the chloramphenicol-amended acetylene inhibition technique. Using a coring technique, we found that sediment denitrification was highest in the top 5 cm of the benthos and was positively related to sediment organic content. To determine the effect of overlying water quality on sediment denitrification, first-order stream sediments were assayed with water from second- and third-order downstream reaches, and often showed higher denitrification rates relative to assays using site-specific water from the first-order stream reach. Denitrification was positively related to nitrate (NO3) concentration, suggesting that sediments may have been nutrient-limited. Using stream-incubated inorganic substrata of varying size classes, we found that finer-grained sand showed higher rates of denitrification compared to large pebbles, likely due to increased surface area per volume of substratum. Denitrification was measurable on both inorganic substrata and fine particulate organic matter loosely associated with inorganic particles, and denitrification rates were related to organic content. Using nutrient-amended denitrification assays, we found that sediment denitrification was limited by NO3- or dissolved organic carbon (DOC, as dextrose) variably throughout the year. The frequency and type of limitation differed with land use in the watershed: forested streams were NO3- -limited or colimited by both NO3- and DOC 92% of the time, urban streams were more often NO3- -limited than DOC-limited, whereas agricultural stream sediments were DOC-limited or co-limited but not frequently limited by NO3- alone.}, }
@article {pmid17265002, year = {2007}, author = {Margesin, R and Hämmerle, M and Tscherko, D}, title = {Microbial activity and community composition during bioremediation of diesel-oil-contaminated soil: effects of hydrocarbon concentration, fertilizers, and incubation time.}, journal = {Microbial ecology}, volume = {53}, number = {2}, pages = {259-269}, pmid = {17265002}, issn = {0095-3628}, mesh = {Biodegradation, Environmental ; Colony Count, Microbial ; Dihydropyridines ; *Environmental Monitoring ; Fatty Acids/metabolism ; Fertilizers/analysis ; *Gasoline/analysis ; Gram-Negative Bacteria/growth &amp; development/isolation &amp; purification/*metabolism ; Hydrocarbons/analysis ; Lipase/metabolism ; Petroleum/analysis/metabolism ; Phospholipids/metabolism ; *Soil Microbiology ; Soil Pollutants/*metabolism ; Species Specificity ; Time Factors ; }, abstract = {We investigated the influence of three factors-diesel oil concentration [2500, 5000, 10,000, 20,000 mg total petroleum hydrocarbons (TPH) kg(-1) soil], biostimulation (unfertilized, inorganic fertilization with NPK nutrients, or oleophilic fertilization with Inipol EAP22), and incubation time-on hydrocarbon removal, enzyme activity (lipase), and microbial community structure [phospholipid fatty acids (PLFA)] in a laboratory soil bioremediation treatment. Fertilization enhanced TPH removal and lipase activity significantly (P < or = 0.001). The higher the initial contamination, the more marked was the effect of fertilization. Differences between the two fertilizers were not significant (P > 0.05). Microbial communities, as assessed by PLFA patterns, were primarily influenced by the TPH content, followed by fertilization, and the interaction of these two factors, whereas incubation time was of minor importance. This was demonstrated by three-factorial analysis of variance and multidimensional scaling analysis. Low TPH content had no significant effect on soil microbial community, independent of the treatment. High TPH content generally resulted in increased PLFA concentrations, whereby a significant increase in microbial biomass with time was only observed with inorganic fertilization, whereas oleophilic fertilization (Inipol EAP22) tended to inhibit microbial activity and to reduce PLFA contents with time. Among bacteria, PLFA indicative of the Gram-negative population were significantly (P < or = 0.05) increased in soil samples containing high amounts of diesel oil and fertilized with NPK after 21-38 days of incubation at 20 degrees C. The Gram-positive population was not significantly influenced by TPH content or biostimulation treatment.}, }
@article {pmid17265001, year = {2007}, author = {Shamir, I and Steinberger, Y}, title = {Vertical distribution and activity of soil microbial population in a sandy desert ecosystem.}, journal = {Microbial ecology}, volume = {53}, number = {2}, pages = {340-347}, pmid = {17265001}, issn = {0095-3628}, mesh = {Bacteria/*isolation &amp; purification ; Biomass ; Carbon Dioxide/metabolism ; Colony Count, Microbial ; Desert Climate ; Fungi/*isolation &amp; purification ; Israel ; *Soil Microbiology ; Species Specificity ; Tamaricaceae ; }, abstract = {The vertical distribution of a microbial community on a temporal and spatial (vertical) scale under the Tamarix aphylla salt-resistant plant was studied. The uniqueness of this plant is in the creation of "islands of salinity" beneath the plant, due to salt excretion and leaf shedding at the plant base. Our working hypothesis was that the activity and biomass of the soil microbial population and the ratio between bacterial biomass and fungal biomass will decrease toward the driest season. Soil samples were collected beneath and between plants under the T. aphylla canopy down to the 0- to 50-cm depth at 10-cm intervals. The substrate-induced respiration method was used to estimate the total soil microbial biomass (MB), CO2 evolution, metabolic quotient (qCO2) index, and MB of both the fungal and bacterial communities. A significant difference was observed (p < 0.05) in MB and qCO2 index between the different soil layers in the control samples, whereas there was no significant difference in the soil samples in the vicinity of the plant (p > 0.05) between the depths, due to the plant rhizosphere effect.}, }
@article {pmid17265000, year = {2007}, author = {Batista, JS and Hungria, M and Barcellos, FG and Ferreira, MC and Mendes, IC}, title = {Variability in Bradyrhizobium japonicum and B. elkanii seven years after introduction of both the exotic microsymbiont and the soybean host in a cerrados soil.}, journal = {Microbial ecology}, volume = {53}, number = {2}, pages = {270-284}, pmid = {17265000}, issn = {0095-3628}, mesh = {Adaptation, Physiological ; Bradyrhizobium/*physiology ; Brazil ; Genetic Variation ; Genome, Bacterial ; Recombination, Genetic ; Glycine max/*microbiology ; Symbiosis ; }, abstract = {The plasticity of rhizobial genomes is far greater than previously thought, with complex genomic recombination events that may be accelerated by the often stressful environmental conditions of the tropics. This study aimed at evaluating changes in soybean rhizobia due to adaptation to inhospitable environmental conditions (high temperatures, drought, and acid soils) in the Brazilian Cerrados. Both the host plant and combinations of four strains of soybean Bradyrhizobium were introduced in an uncropped soil devoid of rhizobia capable of nodulating soybean. After the third year, seeds were not reinoculated. Two hundred and sixty-three isolates were obtained from nodules of field-grown soybean after the seventh year, and their morphological, physiological, serological, and symbiotic properties determined, followed by genetic analysis of conserved and symbiotic genes. B. japonicum strain CPAC 15 (same serogroup as USDA 123) was characterized as having high saprophytic capacity and competitiveness and by the seventh year represented up to 70% of the cultivable population, in contrast to the poor survival and competitiveness of B. japonicum strain CPAC 7 (same serogroup as CB 1809). In general, adapted strains had increased mucoidy, and up to 43% of the isolates showed no serological reaction. High variability, presumably resulting from the adaptation to the harsh environmental conditions, was verified in rep-PCR (polymerase chain reaction) profiles, being lower in strain CPAC 15, intermediate in B. elkanii, and higher in CPAC 7. Restriction fragment length polymorphism (RFLP)-PCR types of the 16S rDNA corresponded to the following: one type for B. elkanii species, two for B. japonicum, associated to CPAC 15 and CPAC 7, and unknown combinations of profiles. However, when nodC sequences and RFLP-PCR of the nifH region data were considered, only two clusters were observed having full congruence with B. japonicum and B. elkanii species. Combining the results, variability was such that even within a genetically more stable group (such as that of CPAC 15), only 6.4% of the isolates showed high similarity to the inoculant strain, whereas none was similar to CPAC 7. The genetic variability in our study seems to result from a variety and combination of events including strain dispersion, genomic recombination, and horizontal gene transfer. Furthermore, the genetic variability appears to be mainly associated with adaptation, saprophytic capacity, and competitiveness, and not with symbiotic effectiveness, as the similarity of symbiotic genes was higher than that of conserved regions of the DNA.}, }
@article {pmid17264999, year = {2007}, author = {Sapp, M and Schwaderer, AS and Wiltshire, KH and Hoppe, HG and Gerdts, G and Wichels, A}, title = {Species-specific bacterial communities in the phycosphere of microalgae?.}, journal = {Microbial ecology}, volume = {53}, number = {4}, pages = {683-699}, pmid = {17264999}, issn = {0095-3628}, mesh = {Animals ; Bacteroidetes/classification/genetics/physiology ; Cluster Analysis ; DNA, Ribosomal Spacer/chemistry ; Diatoms/growth &amp; development/*microbiology ; Dinoflagellida/growth &amp; development/*microbiology ; North Sea ; Photosynthesis/physiology ; Phylogeny ; Proteobacteria/classification/genetics/physiology ; Sequence Analysis, DNA ; Species Specificity ; *Water Microbiology ; }, abstract = {Specific associations of bacteria with phytoplankton have recently been reported in the literature. In our study, we analyzed bacterial communities of microalgal cultures related to algal growth phases. Seven freshly isolated key diatom and dinoflagellate species from Helgoland Roads, North Sea, were investigated. The community composition of associated bacteria as well as the cell numbers, the photosynthetic efficiency of the algae, and the depletion of inorganic nutrients in the medium were recorded over a period of 8 weeks in batch cultures. Diversity and succession of bacterial communities was analyzed by ribosomal intergenic spacer analysis. Phylogenetic analysis of bacterial populations was performed by denaturing gradient gel electrophoresis of 16S rRNA genes followed by DNA sequence analysis. Members of Alphaproteobacteria and Gammaproteobacteria and the Flavobacteria-Sphingobacteria group within the Bacteroidetes phylum predominated in the cultures. Differences in free-living and attached bacterial populations were observed between the phylogenetic groups. Shifts in the bacterial communities could not be correlated to changes of nutrient levels or algal growth phases. Regarding our results, it should not be generalized that the compositions of the bacterial communities are strictly species specific for microalgae. The importance of factors like the composition of exudates is apparent.}, }
@article {pmid17264998, year = {2007}, author = {Barzanti, R and Ozino, F and Bazzicalupo, M and Gabbrielli, R and Galardi, F and Gonnelli, C and Mengoni, A}, title = {Isolation and characterization of endophytic bacteria from the nickel hyperaccumulator plant Alyssum bertolonii.}, journal = {Microbial ecology}, volume = {53}, number = {2}, pages = {306-316}, pmid = {17264998}, issn = {0095-3628}, mesh = {Bacteria ; Brassicaceae/classification/drug effects/*microbiology ; Drug Resistance, Multiple, Bacterial ; Metals, Heavy ; Nickel/*metabolism/pharmacology ; Plant Diseases/*microbiology ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Plant Stems/microbiology ; Siderophores/metabolism ; Species Specificity ; }, abstract = {We report the isolation and characterization of endophytic bacteria, endemic to serpentine outcrops of Central Italy, from a nickel hyperaccumulator plant, Alyssum bertolonii Desv. (Brassicaceae). Eighty-three endophytic bacteria were isolated from roots, stems, and leaves of A. bertolonii and classified by restriction analysis of 16S rDNA (ARDRA) and partial 16S rDNA sequencing in 23 different taxonomic groups. All isolates were then screened for siderophore production and for resistance to heavy metals. One isolate representative of each ARDRA group was then tested for plant tissue colonization ability in sterile culture. Obtained results pointed out that, despite the high concentration of heavy metals present in its tissues, A. bertolonii harbors an endophytic bacterial flora showing a high genetic diversity as well as a high level of resistance to heavy metals that could potentially help plant growth and Ni hyperaccumulation.}, }
@article {pmid17264997, year = {2007}, author = {Stoeck, T and Zuendorf, A and Breiner, HW and Behnke, A}, title = {A molecular approach to identify active microbes in environmental eukaryote clone libraries.}, journal = {Microbial ecology}, volume = {53}, number = {2}, pages = {328-339}, pmid = {17264997}, issn = {0095-3628}, mesh = {Animals ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Denmark ; Eukaryota/genetics/isolation &amp; purification ; Gene Library ; Marine Biology/*methods ; Oceans and Seas ; Plankton/genetics/*isolation &amp; purification ; Polymerase Chain Reaction/*methods ; RNA, Protozoan/genetics ; RNA, Ribosomal/genetics ; Reverse Transcriptase Polymerase Chain Reaction/methods ; *Water Microbiology ; }, abstract = {A rapid method for the simultaneous extraction of RNA and DNA from eukaryote plankton samples was developed in order to discriminate between indigenous active cells and signals from inactive or even dead organisms. The method was tested using samples from below the chemocline of an anoxic Danish fjord. The simple protocol yielded RNA and DNA of a purity suitable for amplification by reverse transcription-polymerase chain reaction (RT-PCR) and PCR, respectively. We constructed an rRNA-derived and an rDNA-derived clone library to assess the composition of the microeukaryote assemblage under study and to identify physiologically active constituents of the community. We retrieved nearly 600 protistan target clones, which grouped into 84 different phylotypes (98% sequence similarity). Of these phylotypes, 27% occurred in both libraries, 25% exclusively in the rRNA library, and 48% exclusively in the rDNA library. Both libraries revealed good correspondence of the general community composition in terms of higher taxonomic ranks. They were dominated by anaerobic ciliates and heterotrophic stramenopile flagellates thriving below the fjord's chemocline. The high abundance of these bacterivore organisms points out their role as a major trophic link in anoxic marine systems. A comparison of the two libraries identified phototrophic dinoflagellates, "uncultured marine alveolates group I," and different parasites, which were exclusively detected with the rDNA-derived library, as nonindigenous members of the anoxic microeukaryote community under study.}, }
@article {pmid17264996, year = {2007}, author = {Manefield, M and Whiteley, A and Curtis, T and Watanabe, K}, title = {Influence of sustainability and immigration in assembling bacterial populations of known size and function.}, journal = {Microbial ecology}, volume = {53}, number = {2}, pages = {348-354}, pmid = {17264996}, issn = {0095-3628}, mesh = {Bioreactors/*microbiology ; Colony Count, Microbial ; Comamonas/*growth &amp; development/metabolism ; Phenol/*metabolism ; Pseudomonas/*growth &amp; development/metabolism ; Sewage/microbiology ; Species Specificity ; }, abstract = {The rational assembly of microbial communities to perform desired functions would be of great practical benefit to society. Broadly speaking, there are two major theoretical foundations for microbial community assembly: one based on island biogeography theory and another based on niche theory. In this study, we compared a parameter from each theory (immigration rate and sustainability, respectively) to ascertain which was more influential in establishing a functional bacterial population in phenol degrading activated sludge over a 30-day period. Two bacterial strains originally isolated from activated sludge, but differing in their ability to sustain a population in this environment, were repeatedly added to activated sludge reactors at different doses. The resulting size of each population was monitored by competitive polymerase chain reaction. Large, unexpected, yet reproducible fluctuations in population sizes were observed. Irrespective of this, difference in the ability to sustain a population in this environment, overshadowed the influence of 100-fold differences in immigration rate.}, }
@article {pmid17264995, year = {2007}, author = {Verma, B and Robarts, RD and Headley, JV}, title = {Impacts of tetracycline on planktonic bacterial production in prairie aquatic systems.}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {52-55}, pmid = {17264995}, issn = {0095-3628}, mesh = {Anti-Bacterial Agents/analysis/*pharmacology ; Bacteria/*drug effects/growth &amp; development/metabolism ; Fresh Water/chemistry/*microbiology ; Microbial Sensitivity Tests ; Plankton/*drug effects/growth &amp; development/metabolism ; Tetracycline/analysis/*pharmacology ; *Wetlands ; }, abstract = {In view of antibiotics being detected in surface waters, experiments were conducted to determine the impacts of tetracycline on planktonic bacteria in wetland and river waters. The minimum inhibitory concentration (MIC) method is often used to measure for resistance or susceptibility of microbes to antibiotics with typical concentrations of antibiotics being mg L(-1). Moreover, there is the belief that antibiotics in the lower microg L(-1) range are unlikely to affect bacteria. We examined this assumption by measuring the effects of a broad range of tetracycline concentrations on bacterial protein production by the incorporation of L-[4,5-3H]leucine method. Tetracycline significantly (P < 0.05) inhibited production in river water bacteria at a "free" concentration of 5 microg L(-1), but the inhibition was significant only at 1000 microg L(-1) in wetland water. The data indicate that planktonic bacteria can be very sensitive to tetracycline at extremely low concentrations and that microbial production is seriously affected.}, }
@article {pmid17264994, year = {2007}, author = {Jiménez-Mercado, A and Cajal-Medrano, R and Maske, H}, title = {Marine heterotrophic bacteria in continuous culture, the bacterial carbon growth efficiency, and mineralization at excess substrate and different temperatures.}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {56-64}, pmid = {17264994}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development/metabolism ; Bacteriological Techniques ; Biomass ; Carbon/*metabolism ; Carbon Dioxide/metabolism ; Food Chain ; Nitrogen/metabolism ; Seawater/*microbiology/virology ; *Temperature ; }, abstract = {To model the physiological potential of marine heterotrophic bacteria, their role in the food web, and in the biogeochemical carbon cycle, we need to know their growth efficiency response within a matrix of different temperatures and degrees of organic substrate limitation. In this work, we present one part of this matrix, the carbon growth efficiencies of marine bacteria under different temperatures and nonlimiting organic and inorganic substrate supply. We ran aerobic turbidostats with glucose enriched seawater, inoculated with natural populations of heterotrophic marine bacteria at 10, 14, 18, 22, and 26 degrees C. The average cell-specific growth rates increased with temperature from 1.17 to 2.6 h-1. At steady-state total CO2 production, biomass production [particulate organic carbon (POC) and nitrogen (PON)], and viruslike particle abundance was measured. CO2 production and specific growth rate increased with increasing temperature. Bacterial carbon growth efficiency (BCGE), the particulate carbon produced per dissolved carbon utilized, varied between 0.12 and 0.70. Maximum BCGE values and decreased specific respiration rates occurred at higher temperatures (22 and 26 degrees C) and growth rates. This trend was largely attributable to an increase in POC per cell abundance; when the BCGE was recalculated, parameterizing the biomass as the product of cell concentration and a constant cellular carbon content, the opposite trend was observed.}, }
@article {pmid17264993, year = {2007}, author = {Chowdhury, SP and Schmid, M and Hartmann, A and Tripathi, AK}, title = {Identification of diazotrophs in the culturable bacterial community associated with roots of Lasiurus sindicus, a perennial grass of Thar Desert, India.}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {82-90}, pmid = {17264993}, issn = {0095-3628}, mesh = {Acetylene/metabolism ; Bacteria/*classification/growth &amp; development/metabolism ; Bacterial Proteins/chemistry/classification ; *Desert Climate ; India ; *Nitrogen Fixation ; Oxidoreductases/chemistry/classification ; Phylogeny ; Plant Roots/microbiology ; Poaceae/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry ; Sequence Analysis, DNA ; }, abstract = {Lasiurus sindicus is a highly nutritive, drought-tolerant, perennial grass that is endemic to the Thar Desert of Rajasthan, India. Analysis of 16S rRNA coding genes of the bacterial isolates enriched in nitrogen-free semisolid medium, from the surface-sterilized roots of L. sindicus, showed predominance of Gram-negative over Gram-positive bacteria. According to comparative sequence analysis of 16S rDNA sequence data, Gram-positive bacteria with low GC content (Staphylococcus warneri and Bacillus sp.) and high GC content (Micrococcus luteus, Microbacterium sp.) were identified. Gram-negative bacteria included Azospirillum sp., Rhizobium sp., Agrobacterium tumefaciens, and Inquilinus limosus (alpha-proteobacteria); Ralstonia sp., Variovorax paradoxus, and Bordetella petrii (beta-proteobacteria); and Pseudomonas pseudoalcaligenes, Stenotrophomonas sp. (gamma-proteobacteria). The occurrence of nifH sequences in Azospirillum sp., Rhizobium sp., and P. pseudoalcaligenes showed the possibility of supplying biologically fixed nitrogen by the root-associated diazotrophs to the host plant.}, }
@article {pmid17264992, year = {2007}, author = {Six, DL and Bentz, BJ}, title = {Temperature determines symbiont abundance in a multipartite bark beetle-fungus ectosymbiosis.}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {112-118}, pmid = {17264992}, issn = {0095-3628}, mesh = {Animals ; Ascomycota/classification/isolation &amp; purification/*physiology ; Coleoptera/*microbiology ; *Symbiosis ; *Temperature ; }, abstract = {In this study, we report evidence that temperature plays a key role in determining the relative abundance of two mutualistic fungi associated with an economically and ecologically important bark beetle, Dendroctonus ponderosae. The symbiotic fungi possess different optimal temperature ranges. These differences determine which fungus is vectored by dispersing host beetles as temperatures fluctuate over a season. Grosmannia clavigera is the predominant fungus carried by dispersing beetles during cool periods but decreases in prevalence as daily maximum temperatures approach 25 degrees C, and becomes extremely rare when temperatures reach or exceed 32 degrees C. In contrast, Ophiostoma montium increases in prevalence as temperatures approach 25 degrees C, and becomes the predominant symbiont dispersed when temperatures reach or exceed 32 degrees C. The possession of different optimal growth temperatures may facilitate the stable coexistence of the two fungi by supporting growth of each fungus at different times, minimizing direct competition. Furthermore, the beetle may reduce its risk of being left aposymbiotic by exploiting not one, but two symbionts, whose combined growth optima span a wide range of environmental conditions. The possession of multiple symbionts with different temperature tolerances may allow the beetle to occupy highly variable habitats over a wide geographic range. Such temperature-driven symbiont shifts are likely to have major consequences for both the host and its symbionts under current temperature regimes and those predicted to occur because of climate change.}, }
@article {pmid17264991, year = {2007}, author = {Labruna, MB and Pacheco, RC and Nava, S and Brandão, PE and Richtzenhain, LJ and Guglielmone, AA}, title = {Infection by Rickettsia bellii and Candidatus "Rickettsia amblyommii" in Amblyomma neumanni ticks from Argentina.}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {126-133}, pmid = {17264991}, issn = {0095-3628}, mesh = {Animals ; Argentina ; DNA, Bacterial/chemistry ; Female ; Genes, Bacterial ; Hemolymph/microbiology ; Ixodidae/*microbiology ; Male ; Phylogeny ; Rickettsia/classification/isolation &amp; purification/*physiology ; Sequence Analysis, DNA ; }, abstract = {The tick species, Amblyomma neumanni (Acari: Ixodidae) is the most frequent tick parasitizing humans in northwestern Argentina. The present study evaluated the rickettsial infection among 55 A. neumanni adult free-living ticks collected in Dean Funes, Córdoba Province. Ticks were individually processed by the hemolymph test with Gimenez staining, isolation of rickettsia in Vero cell culture by the shell vial technique, and polymerase chain reaction (PCR) targeting the citrate synthase rickettsial gene. Through the shell vial technique, rickettsiae were successfully isolated and established in Vero cell culture from two ticks (ticks 4 and 13), which previously showed to contain Rickettsia-like organisms by the hemolymph test. These two Rickettsia isolates were designated as An4 and An13. Molecular characterization (partial DNA sequences of two to three rickettsial genes were determined) of these two isolates and phylogenetic analyses identified them as Rickettsia bellii (isolate An4) and Candidatus "Rickettsia amblyommii" (isolate An13). After testing all A. neumanni ticks by PCR, the prevalence of Candidatus R. amblyommii and R. bellii was 23.6% (13/55) and 3.6% (2/55), respectively. These two rickettsiae have been considered of unknown pathogenicity and appropriate studies to test their pathogenicity to humans or animals need to be conducted. This is the first report of Rickettsia in ticks from Argentina, and also in the species A. neumanni. The results reinforce previous findings that R. bellii (and probably Candidatus R. amblyommii) are widespread among some Neotropical Amblyomma species, suggesting that these ticks gained these bacterial agents from a common ancestor and/or by recent horizontal transmission of rickettsiae between ticks.}, }
@article {pmid17259367, year = {2007}, author = {Louis, P and Flint, HJ}, title = {Development of a semiquantitative degenerate real-time pcr-based assay for estimation of numbers of butyryl-coenzyme A (CoA) CoA transferase genes in complex bacterial samples.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {6}, pages = {2009-2012}, pmid = {17259367}, issn = {0099-2240}, mesh = {Amino Acid Sequence ; Bacteria/*enzymology ; Butyrates/metabolism ; Coenzyme A-Transferases/*genetics ; DNA Primers/*genetics ; Feces/microbiology ; Humans ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; Sequence Homology, Amino Acid ; }, abstract = {We describe a new degenerate real-time PCR approach to simultaneously quantify phylogenetically different butyrate-producing bacteria based on the detection of butyryl-coenzyme A (CoA) CoA transferase genes. This pathway is present in numerically important groups of butyrate producers within the human colon, and thus this assay estimates the butyrate-producing ability of the microbiota.}, }
@article {pmid17259356, year = {2007}, author = {Delbès, C and Ali-Mandjee, L and Montel, MC}, title = {Monitoring bacterial communities in raw milk and cheese by culture-dependent and -independent 16S rRNA gene-based analyses.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {6}, pages = {1882-1891}, pmid = {17259356}, issn = {0099-2240}, mesh = {Animals ; Biodiversity ; Cattle ; Cheese/*microbiology ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gram-Negative Bacteria/*classification/genetics/*isolation &amp; purification ; Gram-Positive Bacteria/*classification/genetics/*isolation &amp; purification ; Milk/*microbiology ; Polymorphism, Single-Stranded Conformational ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {The diversity and dynamics of bacterial populations in Saint-Nectaire, a raw-milk, semihard cheese, were investigated using a dual culture-dependent and direct molecular approach combining single-strand conformation polymorphism (SSCP) fingerprinting and sequencing of 16S rRNA genes. The dominant clones, among 125 16S rRNA genes isolated from milk, belonged to members of the Firmicutes (58% of the total clones) affiliated mainly with the orders Clostridiales and the Lactobacillales, followed by the phyla Proteobacteria (21.6%), Actinobacteria (16.8%), and Bacteroidetes (4%). Sequencing the 16S rRNA genes of 126 milk isolates collected from four culture media revealed the presence of 36 different species showing a wider diversity in the Gammaproteobacteria phylum and Staphylococcus genus than that found among clones. In cheese, a total of 21 species were obtained from 170 isolates, with dominant species belonging to the Lactobacillales and subdominant species affiliated with the Actinobacteria, Bacteroidetes (Chryseobacterium sp.), or Gammaproteobacteria (Stenotrophomonas sp.). Fingerprinting DNA isolated from milk by SSCP analysis yielded complex patterns, whereas analyzing DNA isolated from cheese resulted in patterns composed of a single peak which corresponded to that of lactic acid bacteria. SSCP fingerprinting of mixtures of all colonies harvested from plate count agar supplemented with crystal violet and vancomycin showed good potential for monitoring the subdominant Proteobacteria and Bacteroidetes (Flavobacteria) organisms in milk and cheese. Likewise, analyzing culturable subcommunities from cheese-ripening bacterial medium permitted assessment of the diversity of halotolerant Actinobacteria and Staphylococcus organisms. Direct and culture-dependent approaches produced complementary information, thus generating a more accurate view of milk and cheese microbial ecology.}, }
@article {pmid17256118, year = {2007}, author = {Geets, J and de Cooman, M and Wittebolle, L and Heylen, K and Vanparys, B and De Vos, P and Verstraete, W and Boon, N}, title = {Real-time PCR assay for the simultaneous quantification of nitrifying and denitrifying bacteria in activated sludge.}, journal = {Applied microbiology and biotechnology}, volume = {75}, number = {1}, pages = {211-221}, doi = {10.1007/s00253-006-0805-8}, pmid = {17256118}, issn = {0175-7598}, mesh = {Bacteria/genetics/isolation &amp; purification ; Benzothiazoles ; DNA, Bacterial/analysis/isolation &amp; purification ; Diamines ; Molecular Sequence Data ; Nitrate Reductase/genetics ; Nitrite Reductases/genetics ; Nitrites/*metabolism ; Oligonucleotide Array Sequence Analysis/methods ; Organic Chemicals ; Oxidoreductases/genetics ; Polymerase Chain Reaction/*methods ; Quinolines ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; Waste Disposal, Fluid/*methods ; }, abstract = {In order to improve wastewater treatment processes, a need exists for tools that rapidly give detailed insight into the community structure of activated sludge, supplementary to chemical and physical data. In this study, the advantages of microarrays and quantitative polymerase chin reaction (PCR) methods were combined into a real-time PCR assay that allows the simultaneous quantification of phylogenetic and functional genes involved in nitrification and denitrification processes. Simultaneous quantification was possible along a 5-log dynamic range and with high linear correlation (R (2) > 0.98). The specificity of the assay was confirmed by cloning and sequencing analyses of PCR amplicons obtained from activated sludge. The real-time assay was validated on mixed liquid samples of different treatment plants, which varied in nitrogen removal rate. The abundance of ammonia oxidizers was in the order of magnitude of 10(6) down to 10(4) ml(-1), whereas nitrite oxidizers were less abundant (10(3)-10(1) order of magnitude). The results were in correspondence with the nitrite oxidation rate in the sludge types. As for the nirS, nirK, and nosZ gene copy numbers, their abundance was generally in the order of magnitude of 10(8)-10(5). When sludge samples were subjected to lab-scale perturbations, a decrease in nitrification rate was reflected within 18 h in the copy numbers of nitrifier genes (decrease with 1 to 5 log units), whereas denitrification genes remained rather unaffected. These results demonstrate that the method is a fast and accurate tool for the analysis of the (de)nitrifying community structure and size in both natural and engineered environmental samples.}, }
@article {pmid17245611, year = {2007}, author = {Garnier, M and Labreuche, Y and Garcia, C and Robert, M and Nicolas, JL}, title = {Evidence for the involvement of pathogenic bacteria in summer mortalities of the Pacific oyster Crassostrea gigas.}, journal = {Microbial ecology}, volume = {53}, number = {2}, pages = {187-196}, pmid = {17245611}, issn = {0095-3628}, mesh = {Animals ; Aquaculture ; Crassostrea/*microbiology ; DNA Gyrase/genetics ; Environmental Monitoring ; France ; Hemolymph/microbiology ; Oceans and Seas ; Pseudoalteromonas/classification/genetics/*isolation &amp; purification ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Vibrio/classification/genetics/*isolation &amp; purification ; }, abstract = {A study was conducted to investigate the involvement of bacteria in oyster mortalities during summer. Moribund and apparently healthy oysters were sampled during mortality events along the French coast and in rearing facilities, usually when temperature reached 19 degrees C or higher, and oysters were in the gonadal maturation phase. Hemolymph samples were aseptically withdrawn and submitted to bacteriological analysis. In healthy oysters, bacteria colonized hemolymph at low concentrations depending on the location. In most moribund oysters, bacteria were present in hemolymph and other tissues. These bacterial populations were more often diverse in oysters originating from the open sea than from facilities where animals were generally infected by a single type of bacterium. Only the dominant colonies were identified by phenotypic and genotypic characters (RFLP of GyrB gene and partial sequence of 16S rRNA gene). They belonged to a limited number of species including Vibrio aestuarianus, members of the V. splendidus group, V. natriegens, V. parahaemolyticus, and Pseudoalteromonas sp. The most frequently encountered species was V. aestuarianus (56% of isolates), which was composed of several strains closely related by their 16S rRNA gene but diverse by their phenotypic characters. They appeared intimately linked to oysters. The species within the V. splendidus group were less prevalent (25% of isolates) and more taxonomically dispersed. A majority of the dominant strains of V. aestuarianus and V. splendidus group injected to oysters induced mortality, whereas others belonging to the same species, particularly those found in mixture, appeared innocuous.}, }
@article {pmid17241351, year = {2007}, author = {van de Wiele, T and Boon, N and Possemiers, S and Jacobs, H and Verstraete, W}, title = {Inulin-type fructans of longer degree of polymerization exert more pronounced in vitro prebiotic effects.}, journal = {Journal of applied microbiology}, volume = {102}, number = {2}, pages = {452-460}, doi = {10.1111/j.1365-2672.2006.03084.x}, pmid = {17241351}, issn = {1364-5072}, mesh = {Bifidobacterium/genetics/physiology ; Cichorium intybus ; Colon/metabolism/*microbiology ; Colony Count, Microbial ; DNA Fingerprinting ; Dietary Fiber/*pharmacology ; Fatty Acids, Volatile/analysis ; Fermentation ; Fructans/chemistry/*pharmacology ; Humans ; Inulin/chemistry/pharmacology ; Oligosaccharides/chemistry/pharmacology ; Polymers ; *Probiotics ; }, abstract = {AIMS: We assessed to what extent fructans of different degrees of polymerization (DP) differ in their prebiotic effectiveness towards in vitro microbial communities from the proximal and distal colon.<br><br>METHODS AND RESULTS: Two short chain fructans - oligofructose (DP 2-20) and inulin (DP 3-60) - were administered to the Simulator of the Human Intestinal Microbial Ecosystem (SHIME) at 2.5 g day(-1). The influence of fructan addition towards fermentation activity and microbial community composition from the different SHIME colon compartments were evaluated. Both fructans exerted prebiotic effects with significantly higher butyrate and propionate production and stimulation of lactic acid-producing bacteria. Compared with oligofructose, it was noted that it took more time before significant effects from inulin addition were observed. Yet, the higher short-chain fatty acid production and lower proteolytic activity showed that the prebiotic effects from inulin were more pronounced than oligofructose. Also, the bifidogenic effects from inulin vs oligofructose were higher in the distal colon compartments and this effect was prolonged in the distal colon once the addition was stopped.<br><br>CONCLUSIONS: Inulin has more pronounced prebiotic effects than oligofructose towards both fermentation activity and bacterial community composition in the SHIME model.<br><br>Its slower fermentation rate and higher prebiotic potency makes inulin a more interesting compound than oligofructose to beneficially influence the microbial community from both the proximal and distal colon regions.}, }
@article {pmid17241242, year = {2007}, author = {Louis, P and McCrae, SI and Charrier, C and Flint, HJ}, title = {Organization of butyrate synthetic genes in human colonic bacteria: phylogenetic conservation and horizontal gene transfer.}, journal = {FEMS microbiology letters}, volume = {269}, number = {2}, pages = {240-247}, doi = {10.1111/j.1574-6968.2006.00629.x}, pmid = {17241242}, issn = {0378-1097}, mesh = {Acyl Coenzyme A/metabolism ; Bacteria, Anaerobic/enzymology/*genetics/growth &amp; development ; Base Sequence ; Butyrates/*metabolism ; Coenzyme A-Transferases/chemistry/*genetics ; Colon/*microbiology ; Conserved Sequence ; *Gene Transfer, Horizontal ; Humans ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Substrate Specificity ; }, abstract = {Butyrate producers constitute an important bacterial group in the human large intestine. Butyryl-CoA is formed from two molecules of acetyl-CoA in a process resembling beta-oxidation in reverse. Three different arrangements of the six genes coding for this pathway have been found in low mol% G+C-content gram-positive human colonic bacteria using DNA sequencing and degenerate PCR. Gene arrangements were strongly conserved within phylogenetic groups defined by 16S rRNA gene sequence relationships. In the case of one of the genes, encoding beta-hydroxybutyryl-CoA dehydrogenase, however, sequence relationships were strongly suggestive of horizontal gene transfer between lineages. The newly identified gene for butyryl-CoA CoA-transferase, which performs the final step in butyrate formation in most known human colonic bacteria, was not closely linked to these central pathway genes.}, }
@article {pmid17235561, year = {2007}, author = {Renouf, V and Claisse, O and Lonvaud-Funel, A}, title = {Inventory and monitoring of wine microbial consortia.}, journal = {Applied microbiology and biotechnology}, volume = {75}, number = {1}, pages = {149-164}, doi = {10.1007/s00253-006-0798-3}, pmid = {17235561}, issn = {0175-7598}, mesh = {Colony Count, Microbial ; Culture Media ; DNA, Bacterial/analysis/isolation &amp; purification ; DNA, Fungal/analysis/isolation &amp; purification ; Ecosystem ; Electrophoresis, Polyacrylamide Gel ; Fermentation ; Gram-Negative Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Gram-Positive Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Industrial Microbiology/methods ; Polymerase Chain Reaction ; Vitis/microbiology ; Wine/*microbiology ; Yeasts/classification/genetics/growth &amp; development/*isolation &amp; purification ; }, abstract = {The evolution of the wine microbial ecosystem is generally restricted to Saccharomyces cerevisiae and Oenococcus oeni, which are the two main agents in the transformation of grape must into wine by acting during alcoholic and malolactic fermentation, respectively. But others species like the yeast Brettanomyces bruxellensis and certain ropy strains of Pediococcus parvulus can spoil the wine. The aim of this study was to address the composition of the system more precisely, identifying other components. The advantages of the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach to wine microbial ecology studies are illustrated by bacteria and yeast species identification and their monitoring at each stage of wine production. After direct DNA extraction, PCR-DGGE was used to make the most exhaustive possible inventory of bacteria and yeast species found in a wine environment. Phylogenetic neighbor-joining trees were built to illustrate microbial diversity. PCR-DGGE was also combined with population enumeration in selective media to monitor microbial changes at all stages of production. Moreover, enrichment media helped to detect the appearance of spoilage species. The genetic diversity of the wine microbial community and its dynamics during winemaking were also described. Most importantly, our study provides a better understanding of the complexity and diversity of the wine microbial consortium at all stages of the winemaking process: on grape berries, in must during fermentation, and in wine during aging. On grapes, 52 different yeast species and 40 bacteria could be identified. The diversity was dramatically reduced during winemaking then during aging. Yeast and lactic acid bacteria were also isolated from very old vintages. B. bruxellensis and O. oeni were the most frequent.}, }
@article {pmid17234844, year = {2007}, author = {Mountzouris, KC and Tsirtsikos, P and Kalamara, E and Nitsch, S and Schatzmayr, G and Fegeros, K}, title = {Evaluation of the efficacy of a probiotic containing Lactobacillus, Bifidobacterium, Enterococcus, and Pediococcus strains in promoting broiler performance and modulating cecal microflora composition and metabolic activities.}, journal = {Poultry science}, volume = {86}, number = {2}, pages = {309-317}, doi = {10.1093/ps/86.2.309}, pmid = {17234844}, issn = {0032-5791}, mesh = {Aging ; Animal Feed ; Animal Nutritional Physiological Phenomena ; Animals ; *Bifidobacterium ; Cecum/drug effects/metabolism/*microbiology ; Chickens/*growth &amp; development/metabolism ; Diet/veterinary ; *Enterococcus ; Fatty Acids, Volatile ; Glycolysis ; *Lactobacillus ; Male ; *Pediococcus ; Probiotics/*pharmacology ; Weight Gain/drug effects ; }, abstract = {The aim of this work was to investigate the efficacy of a new multibacterial species probiotic in broiler nutrition. The probiotic contained 2 Lactobacillus strains, 1 Bifidobacterium strain, 1 Enterococcus strain, and 1 Pediococcus strain. Four hundred 1-d-old male Cobb broilers were allocated in 4 experimental treatments for 6 wk. The experimental treatments received a corn-soybean basal diet and were as follows: "control," with no other additions; "probiotic in feed and water," (PFW) with probiotic administered at 1 g/kg of feed for the whole period and in water on scheduled intervals during the first 4 wk; "probiotic in feed," (PF) with probiotic in feed as in PFW; and "antibiotic," (AB) with addition of avilamycin at 2.5 mg/kg of feed. Salinomycin Na was used as a coccidiostat. Each treatment had 5 replicates of 20 broilers. Treatment effects on parameters of broiler performance and cecal microbial ecology were determined. Broiler BW, feed intake, and feed conversion ratio were determined on a weekly and overall basis. Cecal microflora composition, concentration of volatile fatty acids, and activities of 5 bacterial glycolytic enzymes (alpha-galactosidase, beta-galactosidase, alpha-glucosidase, beta-glucosidase, and beta-glucuronidase) were determined at the end of the experiment. Overall, treatment PFW displayed a growth-promoting effect that did not differ from AB. Overall, feed conversion ratio in treatment AB was significantly better (P < or = 0.01) than the control treatment, whereas treatments PFW and PF were intermediate and not different from AB. Concentrations of bacteria belonging to Bifidobacterium spp., Lactobacillus spp., and gram-positive cocci were significantly (P < or = 0.05) higher in treatments PFW and PF compared with the control and AB treatments. Treatments PFW and PF had significantly higher specific activities of alpha-galactosidase and beta-galactosidase compared with the control and AB treatments. In conclusion, probiotic treatment PFW displayed a growth-promoting effect that was comparable to avilamycin treatment. In addition, treatments PFW and PF modulated the composition and, to an extent, the activities of the cecal microflora, resulting in a significant probiotic effect.}, }
@article {pmid17227406, year = {2007}, author = {Rohwer, F}, title = {Real-time microbial ecology.}, journal = {Environmental microbiology}, volume = {9}, number = {1}, pages = {10}, doi = {10.1111/j.1462-2920.2006.01222_9.x}, pmid = {17227406}, issn = {1462-2912}, mesh = {Computational Biology/methods ; Ecology/*trends ; Genomics ; Microbiological Techniques ; Microbiology/*trends ; }, }
@article {pmid17227400, year = {2007}, author = {Ley, RE and Knight, R and Gordon, JI}, title = {The human microbiome: eliminating the biomedical/environmental dichotomy in microbial ecology.}, journal = {Environmental microbiology}, volume = {9}, number = {1}, pages = {3-4}, doi = {10.1111/j.1462-2920.2006.01222_3.x}, pmid = {17227400}, issn = {1462-2912}, mesh = {*Ecosystem ; Genomics ; Humans ; Intestines/microbiology ; Microbiology/*trends ; }, }
@article {pmid17227399, year = {2007}, author = {Dubilier, N}, title = {The searchlight and the bucket of microbial ecology.}, journal = {Environmental microbiology}, volume = {9}, number = {1}, pages = {2-3}, doi = {10.1111/j.1462-2920.2006.01222_2.x}, pmid = {17227399}, issn = {1462-2912}, mesh = {Biodiversity ; Ecology/methods/*trends ; Ecosystem ; *Environmental Microbiology ; Microbiological Techniques ; Microbiology/*trends ; }, }
@article {pmid17222148, year = {2007}, author = {Röling, WF and van Breukelen, BM and Bruggeman, FJ and Westerhoff, HV}, title = {Ecological control analysis: being(s) in control of mass flux and metabolite concentrations in anaerobic degradation processes.}, journal = {Environmental microbiology}, volume = {9}, number = {2}, pages = {500-511}, doi = {10.1111/j.1462-2920.2006.01167.x}, pmid = {17222148}, issn = {1462-2912}, support = {BB/C008219/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria, Anaerobic/*metabolism/physiology ; Biodegradation, Environmental ; *Ecosystem ; Fermentation ; *Humic Substances ; Oxidation-Reduction ; Tetrachloroethylene/metabolism ; Trichloroethylene/metabolism ; }, abstract = {Identification of the functional groups of microorganisms that are predominantly in control of fluxes through, and concentrations in, microbial networks would benefit microbial ecology and environmental biotechnology: the properties of those controlling microorganisms could be studied or monitored specifically or their activity could be modulated in attempts to manipulate the behaviour of such networks. Herein we present ecological control analysis (ECA) as a versatile mathematical framework that allows for the quantification of the control of each functional group in a microbial network on its process rates and concentrations of intermediates. In contrast to current views, we show that rates of flow of matter are not always limited by a single functional group; rather flux control can be distributed over several groups. Also, control over intermediate concentrations is always shared. Because of indirect interactions, through other functional groups, the concentration of an intermediate can also be controlled by functional groups not producing or consuming it. Ecological control analysis is illustrated by a case study on the anaerobic degradation of organic matter, using experimental data obtained from the literature. During anaerobic degradation, fermenting microorganisms interact with terminal electron-accepting microorganisms (e.g. halorespirers, methanogens). The analysis indicates that flux control mainly resides with fermenting microorganisms, but can shift to the terminal electron-accepting microorganisms under less favourable redox conditions. Paradoxically, halorespiring microorganisms do not control the rate of perchloroethylene and trichloroethylene degradation even though they catalyse those processes themselves.}, }
@article {pmid17222142, year = {2007}, author = {Defoirdt, T and Halet, D and Vervaeren, H and Boon, N and Van de Wiele, T and Sorgeloos, P and Bossier, P and Verstraete, W}, title = {The bacterial storage compound poly-beta-hydroxybutyrate protects Artemia franciscana from pathogenic Vibrio campbellii.}, journal = {Environmental microbiology}, volume = {9}, number = {2}, pages = {445-452}, doi = {10.1111/j.1462-2920.2006.01161.x}, pmid = {17222142}, issn = {1462-2912}, mesh = {3-Hydroxybutyric Acid/chemistry/pharmacology ; Animals ; Aquaculture ; Artemia/*microbiology ; Hydroxybutyrates/chemistry/*pharmacology ; Inclusion Bodies/chemistry/metabolism ; Polyesters/chemistry/*pharmacology ; Vibrio/*drug effects/growth &amp; development/physiology ; }, abstract = {Infections caused by antibiotic-resistant luminescent Vibrios can cause dramatic losses in aquaculture. In this study, the short-chain fatty acid beta-hydroxybutyrate and its polymer poly-beta-hydroxybutyrate were investigated as possible new biocontrol agents. beta-Hydroxybutyrate was shown to completely inhibit the growth of pathogenic Vibrio campbelli at 100 mM. Moreover, the addition of 100 mM of this fatty acid to the culture water of Artemia nauplii infected with the V. campbelli strain significantly increased the survival of the nauplii. As Artemia is a non-selective and particle filter feeder, we also investigated whether poly-beta-hydroxybutyrate particles could be used to protect Artemia from the pathogenic V. campbellii. The addition of 100 mg l(-1) poly-beta-hydroxybutyrate or more to the Artemia culture water offered a preventive and curative protection from the pathogen as a significantly enhanced survival was noticed. If added as a preventive treatment, a complete protection of infected nauplii (no significant mortality compared with uninfected nauplii) was observed at 1000 mg l(-1) poly-beta-hydroxybutyrate. Our data indicate that the use of poly-beta-hydroxybutyrate might constitute an ecologically and economically sustainable alternative strategy to fight infections in aquaculture.}, }
@article {pmid17220447, year = {2007}, author = {Goris, J and Konstantinidis, KT and Klappenbach, JA and Coenye, T and Vandamme, P and Tiedje, JM}, title = {DNA-DNA hybridization values and their relationship to whole-genome sequence similarities.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {57}, number = {Pt 1}, pages = {81-91}, doi = {10.1099/ijs.0.64483-0}, pmid = {17220447}, issn = {1466-5026}, mesh = {*Bacterial Typing Techniques ; DNA, Bacterial/analysis/genetics ; Genome, Bacterial/*genetics ; Gram-Negative Bacteria/classification/genetics ; Gram-Positive Bacteria/classification/genetics ; Nucleic Acid Hybridization/*methods ; *Sequence Analysis, DNA ; }, abstract = {DNA-DNA hybridization (DDH) values have been used by bacterial taxonomists since the 1960s to determine relatedness between strains and are still the most important criterion in the delineation of bacterial species. Since the extent of hybridization between a pair of strains is ultimately governed by their respective genomic sequences, we examined the quantitative relationship between DDH values and genome sequence-derived parameters, such as the average nucleotide identity (ANI) of common genes and the percentage of conserved DNA. A total of 124 DDH values were determined for 28 strains for which genome sequences were available. The strains belong to six important and diverse groups of bacteria for which the intra-group 16S rRNA gene sequence identity was greater than 94 %. The results revealed a close relationship between DDH values and ANI and between DNA-DNA hybridization and the percentage of conserved DNA for each pair of strains. The recommended cut-off point of 70 % DDH for species delineation corresponded to 95 % ANI and 69 % conserved DNA. When the analysis was restricted to the protein-coding portion of the genome, 70 % DDH corresponded to 85 % conserved genes for a pair of strains. These results reveal extensive gene diversity within the current concept of "species". Examination of reciprocal values indicated that the level of experimental error associated with the DDH method is too high to reveal the subtle differences in genome size among the strains sampled. It is concluded that ANI can accurately replace DDH values for strains for which genome sequences are available.}, }
@article {pmid17216449, year = {2007}, author = {Vlaeminck, SE and Geets, J and Vervaeren, H and Boon, N and Verstraete, W}, title = {Reactivation of aerobic and anaerobic ammonium oxidizers in OLAND biomass after long-term storage.}, journal = {Applied microbiology and biotechnology}, volume = {74}, number = {6}, pages = {1376-1384}, doi = {10.1007/s00253-006-0770-2}, pmid = {17216449}, issn = {0175-7598}, mesh = {Bacteria, Aerobic/genetics/growth &amp; development/*metabolism ; Bacteria, Anaerobic/genetics/growth &amp; development/*metabolism ; Biofilms ; *Biomass ; Bioreactors/microbiology ; In Situ Hybridization, Fluorescence ; Nitrates/chemistry/metabolism ; Nitrites/chemistry/metabolism ; Nitrogen/chemistry/metabolism ; Oxidation-Reduction ; Polymerase Chain Reaction ; Quaternary Ammonium Compounds/chemistry/*metabolism ; Temperature ; }, abstract = {The biomass of an oxygen-limited autotrophic nitrification/denitrification (OLAND) biofilm reactor was preserved in various ways to find a storage method for both aerobic and anaerobic ammonium-oxidizing bacteria (AerAOB and AnAOB). Storage occurred at -20 degrees C with and without glycerol as cryoprotectant and at 4 and 20 degrees C with and without nitrate as redox buffer. After 2 and 5 months, reactivation of AerAOB and AnAOB was achieved with the biomass stored at 4 degrees C with and without nitrate and at 20 degrees C with nitrate. Moreover, the presence of the AerAOB and AnAOB was confirmed with fluorescent in situ hybridization (FISH). Preservation in a nitrate environment resulted in a lag phase for the AnAOB reactivation. The supplied nitrate was denitrified during storage, and a real-time polymerase chain reaction with nitrifying and denitrifying genes allowed to estimate that at least 1.0 to 6.0% of the OLAND biofilm consisted of denitrifiers. It was concluded that reactivation after long-term storage is possible and that preservation at 4 degrees C without nitrate addition is the recommended storage technique. The possibility to store OLAND biomass will facilitate research on AnAOB and can overcome larger-scale start-up and inhibition problems of novel nitrogen processes involving AnAOB.}, }
@article {pmid17207984, year = {2008}, author = {Niederberger, TD and Ronimus, RS and Morgan, HW}, title = {The microbial ecology of a high-temperature near-neutral spring situated in Rotorua, New Zealand.}, journal = {Microbiological research}, volume = {163}, number = {5}, pages = {594-603}, doi = {10.1016/j.micres.2006.09.001}, pmid = {17207984}, issn = {0944-5013}, mesh = {Adenosine Triphosphate/metabolism ; Archaea/classification/genetics/*isolation &amp; purification/metabolism ; Biofilms/growth &amp; development ; *Ecology ; Hot Springs/*microbiology ; Molecular Sequence Data ; New Zealand ; Phylogeny ; *Water Microbiology ; }, abstract = {A combination of both culture and culture-independent techniques were used to investigate the microbial ecology of a near-neutral, high-temperature hot spring (designated AQ1) in Rotorua, New Zealand. The active microbial members of the community were targeted by analyzing biofilms that developed on surfaces incubated in situ in AQ1. Colonization of surfaces was rapid as indicated by ATP assay and microscopic observation. DNA-based analysis of both colonized surfaces and pool water from AQ1 revealed an exclusively archaeal community. Different colonization patterns were observed on glass slides incubated near the pool surface or at depth. Slides incubated at the surface were colonized exclusively by Pyrobaculum species, while at greater depth a novel coccus was also observed and detected by DGGE. Sequence analysis revealed the coccus was related to Aeropyrum pernix. Two microorganisms were isolated from AQ1 pool water, namely Ignisphaera aggregans AQ1.S1T and a species of Pyrobaculum, isolate AQ1.S2.}, }
@article {pmid17206394, year = {2007}, author = {Khan, NH and Ishii, Y and Kimata-Kino, N and Esaki, H and Nishino, T and Nishimura, M and Kogure, K}, title = {Isolation of Pseudomonas aeruginosa from open ocean and comparison with freshwater, clinical, and animal isolates.}, journal = {Microbial ecology}, volume = {53}, number = {2}, pages = {173-186}, pmid = {17206394}, issn = {0095-3628}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Culture Media ; Drug Resistance, Multiple, Bacterial ; Humans ; Japan ; Pacific Ocean ; Pseudomonas Infections/microbiology/*veterinary ; Pseudomonas aeruginosa/*classification/drug effects/*isolation &amp; purification/*physiology ; Sodium Chloride/pharmacology ; Species Specificity ; *Water Microbiology ; }, abstract = {Pseudomonas aeruginosa is an opportunistic pathogen responsible for morbidity and mortality in humans, animals, and plants. This bacterium has been regarded to be widely present in terrestrial and freshwater environments, but not in open ocean environments. Our purpose was to clarify its presence in open ocean, and their genotypic and physiological characteristics were compared with those of isolates from clinical, animal, and freshwater sources. Water samples were collected from freshwater, bays, and offshore environments in Japan. Sixty-two isolates, including 26 from the open ocean, were identified as P. aeruginosa by phenotypic characteristics and the BD Phoenix System. Pulsed-field gel electrophoresis (PFGE) was performed on all strains, together with 21 clinical and 8 animal strains. The results showed that open ocean strains are composed of a few genotypes, which are separated from other strains. Although some clinical isolates made a cluster, other strains tended to mix together. Different antibiotypes were observed among marine isolates that had similar PFGE and serotyping patterns. Some were multidrug-resistant. Laboratory-based microcosm study were carried out to see the responses of P. aeruginosa toward increased NaCl concentrations in deionized water (DW). Marine strains showed better survival with the increase, whereas river and clinical strains were suppressed by the increase. These findings illustrate the potential significance of open ocean as a possible reservoir of P. aeruginosa, and there may be clones unique to this environment. To our knowledge, this is the first report on the presence and characterization of P. aeruginosa in the open ocean.}, }
@article {pmid17191497, year = {2006}, author = {Grootaert, C and Verstraete, W and Van de Wiele, T}, title = {Arabinoxylan oligosaccharides with different structures exert a bifidogenic effect in a mixed intestinal community.}, journal = {Communications in agricultural and applied biological sciences}, volume = {71}, number = {1}, pages = {159-163}, pmid = {17191497}, issn = {1379-1176}, mesh = {Bifidobacterium/enzymology/*growth &amp; development/metabolism ; Endo-1,4-beta Xylanases/metabolism ; Fermentation ; Glycoside Hydrolases/metabolism ; Humans ; Intestines/*microbiology ; Models, Biological ; Oligosaccharides/*metabolism ; *Probiotics ; Xylans/*metabolism ; }, }
@article {pmid17191479, year = {2006}, author = {Boeckaert, C and Boon, N and Abdulsudi, IZ and Verstraete, W and Fievez, V}, title = {Accumulation of biohydrogenation intermediates and changes in the rumen protozoal population after micro algae feeding to dairy cattle.}, journal = {Communications in agricultural and applied biological sciences}, volume = {71}, number = {1}, pages = {83-86}, pmid = {17191479}, issn = {1379-1176}, mesh = {Animals ; Bacteria, Anaerobic/growth &amp; development/*metabolism ; Cattle ; Eukaryota/growth &amp; development/*metabolism/*physiology ; Female ; Lipid Metabolism/*physiology ; Lipolysis ; Population Dynamics ; Rumen/metabolism/*microbiology/*parasitology ; }, }
@article {pmid17191475, year = {2006}, author = {Aelterman, P and Rabaey, K and The Pham, H and Boon, N and Verstraete, W}, title = {Continuous electricity generation at high voltages and currents using stacked microbial fuel cells.}, journal = {Communications in agricultural and applied biological sciences}, volume = {71}, number = {1}, pages = {63-66}, pmid = {17191475}, issn = {1379-1176}, mesh = {Bacteria/*metabolism ; Bacterial Physiological Phenomena ; Biodegradation, Environmental ; *Bioelectric Energy Sources ; Biofilms/growth &amp; development ; *Bioreactors ; *Electricity ; *Electrochemistry ; Oxidation-Reduction ; Refuse Disposal/methods ; }, }
@article {pmid17189766, year = {2007}, author = {Mercado, L and Dalcero, A and Masuelli, R and Combina, M}, title = {Diversity of Saccharomyces strains on grapes and winery surfaces: analysis of their contribution to fermentative flora of Malbec wine from Mendoza (Argentina) during two consecutive years.}, journal = {Food microbiology}, volume = {24}, number = {4}, pages = {403-412}, doi = {10.1016/j.fm.2006.06.005}, pmid = {17189766}, issn = {0740-0020}, mesh = {Argentina ; Colony Count, Microbial ; Fermentation ; Food Handling/methods ; Food Industry ; *Food Microbiology ; Phylogeny ; *Saccharomyces/classification/growth &amp; development/isolation &amp; purification ; Time Factors ; Vitis/*microbiology ; Wine/*microbiology/standards ; }, abstract = {Spontaneous fermentations are still conducted by several wineries in different regions of Argentina as a common practice. Native Saccharomyces strains associated with winery equipment, grape and spontaneous fermentations of Malbec musts from "Zona Alta del Río Mendoza" region (Argentina) were investigated during 2001 and 2002 in the same cellar. Low occurrence of Saccharomyces on grapes and their limited participation during fermentation were confirmed. Strain sequential substitution during fermentation was observed. Between 30% and 60% of yeast population at the end of fermentation was coming from yeasts already present in the winery. A stable and resident Saccharomyces micro-flora in the winery was confirmed. It exhibited a dynamic behaviour during season and between years. Commercial strains were found during fermentation in different percentages, but their presence on winery equipment was low. The present work represents a first approach to winery yeast and spontaneous fermentation Saccharomyces population dynamics in an important viticultural region from Argentina that has never been characterized before. The results obtained have an important significance for the local industry, showing for the first time the real situation of the microbial ecology of alcoholic fermentation in an industrial winery from Mendoza, Argentina.}, }
@article {pmid17189447, year = {2007}, author = {Duncan, SH and Belenguer, A and Holtrop, G and Johnstone, AM and Flint, HJ and Lobley, GE}, title = {Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {4}, pages = {1073-1078}, pmid = {17189447}, issn = {0099-2240}, mesh = {Adult ; Bacteria/*metabolism ; Butyrates/*metabolism ; Diet, Carbohydrate-Restricted ; *Diet, Reducing ; Feces/*microbiology ; Humans ; Male ; Middle Aged ; Obesity/*diet therapy ; }, abstract = {Weight loss diets for humans that are based on a high intake of protein but low intake of fermentable carbohydrate may alter microbial activity and bacterial populations in the large intestine and thus impact on gut health. In this study, 19 healthy, obese (body mass index range, 30 to 42) volunteers were given in succession three different diets: maintenance (M) for 3 days (399 g carbohydrate/day) and then high protein/medium (164 g/day) carbohydrate (HPMC) and high protein/low (24 g/day) carbohydrate (HPLC) each for 4 weeks. Stool samples were collected at the end of each dietary regimen. Total fecal short-chain fatty acids were 114 mM, 74 mM, and 56 mM (P < 0.001) for M, HPMC, and HPLC diets, respectively, and there was a disproportionate reduction in fecal butyrate (18 mM, 9 mM, and 4 mM, respectively; P < 0.001) with decreasing carbohydrate. Major groups of fecal bacteria were monitored using nine 16S rRNA-targeted fluorescence in situ hybridization probes, relative to counts obtained with the broad probe Eub338. No significant change was seen in the relative counts of the bacteroides (Bac303) (mean, 29.6%) or the clostridial cluster XIVa (Erec482, 23.3%), cluster IX (Prop853, 9.3%), or cluster IV (Fprau645, 11.6%; Rbro730 plus Rfla729, 9.3%) groups. In contrast, the Roseburia spp. and Eubacterium rectale subgroup of cluster XIVa (11%, 8%, and 3% for M, HPMC, and HPLC, respectively; P < 0.001) and bifidobacteria (4%, 2.1%, and 1.9%, respectively; P = 0.026) decreased as carbohydrate intake decreased. The abundance of butyrate-producing bacteria related to Roseburia spp. and E. rectale correlated well with the decline in fecal butyrate.}, }
@article {pmid17186159, year = {2007}, author = {Boëchat, IG and Krüger, A and Adrian, R}, title = {Sterol composition of freshwater algivorous ciliates does not resemble dietary composition.}, journal = {Microbial ecology}, volume = {53}, number = {1}, pages = {74-81}, pmid = {17186159}, issn = {0095-3628}, mesh = {Animals ; Ciliophora/*chemistry/classification/physiology ; Cryptophyta/*chemistry ; Culture Media ; Ergosterol/analysis/metabolism ; *Food Chain ; Fresh Water/*parasitology ; Species Specificity ; Sterols/*analysis/metabolism ; Stigmasterol/analysis/metabolism ; }, abstract = {Algivorous ciliates represent an important link in freshwater food webs, as they transfer energy and biochemical matter from their algal prey to mesozooplankton predators. However, it is still unknown how dietary composition influences the biochemical composition of ciliates. We analyzed the sterol composition of the algivorous ciliates Balanion planctonicum and Urotricha farcta and compared it to the sterol composition of their diet--the cryptomonad Cryptomonas phaseolus. The sterol composition of the ciliates did not resemble that of their algal diet. Ergosterol [(22E)-ergosta-5,7,22-trien-3beta-ol] was the sterol in highest concentration in C. phaseolus, whereas stigmasterol [(24S)-24-ethylcholesta-5,22E-dien-3beta-ol] was dominant in both B. planctonicum and U. farcta. Moreover, the occasionally higher sterol concentrations in the ciliates than in their algal diet suggest sterol accumulation by the ciliates. We conclude that dietary sterol composition influences the composition of the two algivorous ciliates studied, but species-specific differences in metabolism probably determine the ultimate sterol composition of the ciliates.}, }
@article {pmid17186158, year = {2007}, author = {Park, MO and Ikenaga, H and Watanabe, K}, title = {Phage diversity in a methanogenic digester.}, journal = {Microbial ecology}, volume = {53}, number = {1}, pages = {98-103}, pmid = {17186158}, issn = {0095-3628}, mesh = {Anaerobiosis ; *Archaeal Viruses/classification/genetics/isolation &amp; purification/ultrastructure ; *Bacteriophages/classification/genetics/isolation &amp; purification/ultrastructure ; Beer ; Electrophoresis, Agar Gel/methods ; Fluorescence ; Industrial Waste ; Methane/*metabolism ; Organic Chemicals/metabolism ; Sewage/*virology ; *Virion/classification/genetics/isolation &amp; purification/ultrastructure ; Waste Disposal, Fluid/*methods ; }, abstract = {It has been shown that phages are present in natural and engineered ecosystems and influence the structure and performance of prokaryotic communities. However, little has been known about phages occurring in anaerobic ecosystems, including those in methanogenic digesters for waste treatment. This study investigated phages produced in an upflow anaerobic sludge blanket methanogenic digester treating brewery wastes. Phage-like particles (PLPs) in the influent and effluent of the digester were concentrated and purified by sequential filtration and quantified and characterized by transmission electron microscopy (TEM), fluorescence assay, and field inversion gel electrophoresis (FIGE). Results indicate that numbers of PLPs in the effluent of the digester exceeded 1 x 10(9) L-1 and at least 10 times greater than those in the influent, suggesting that substantial amounts of PLPs were produced in the digester. A production rate of the PLPs was estimated at least 5.2 x 10(7) PLPs day-1 L-1. TEM and FIGE showed that a variety of phages were produced in the digester, including those affiliated with Siphoviridae, Myoviridae, and Cystoviridae.}, }
@article {pmid17186157, year = {2007}, author = {Wäli, PR and Ahlholm, JU and Helander, M and Saikkonen, K}, title = {Occurrence and genetic structure of the systemic grass endophyte Epichloë festucae in fine fescue populations.}, journal = {Microbial ecology}, volume = {53}, number = {1}, pages = {20-29}, pmid = {17186157}, issn = {0095-3628}, mesh = {DNA, Fungal/analysis/isolation &amp; purification ; *Ecosystem ; Festuca/growth &amp; development/*microbiology ; Finland ; Genetic Variation ; Genetics, Population ; Genotype ; *Hypocreales/classification/genetics/isolation &amp; purification/pathogenicity ; Linkage Disequilibrium ; Microsatellite Repeats ; Norway ; Plant Diseases/microbiology ; Sequence Analysis, DNA ; }, abstract = {Epichloë species are systemic fungal endophytes that usually specialize in a certain group of related grass species. We examined the infection frequency of Epichloë festucae in populations of two fine fescue species (Festuca rubra and F. ovina) in natural and seminatural habitats at 86 study sites (total=2514 plants) across Finland and northern Norway. Infection incidence varied significantly among grass species and populations. A substantial number of the F. rubra and F. ovina populations (53 out of 77 and 25 out of 30, respectively) were either endophyte-free or had very low (<20%) infection frequencies. The highest infection frequencies were found in subarctic areas. Moreover, infection incidence differed between habitats. In the area with the highest infection frequencies, we used microsatellite markers to study genetic diversity and the rates of gene flow of E. festucae among 12 F. rubra populations. Twenty out of the 25 fungal genotypes detected with four microsatellite markers were carrying multiple alleles in at least one locus, indicating multiple infections or vegetative hybridization of the fungus. One dominant genotype occurred in all 12 populations, representing 63.5% of all isolates. We found a moderate level of average genotypic variation and a low level of genetic differentiation (Fst=0.0814). There was no correlation between infection frequency and genotypic diversity. Although the existence of a dominant genotype and the detected linkage disequilibrium suggest that the fungus is mainly asexual and vertically transmitted, the multiallelic loci and variation of genetic diversity among populations indicate occasional contagious spread and sexual or parasexual recombination of the fungus in some populations. Furthermore, the genotypes carrying multiallelic loci suggest the possibility of multiple infections or hybridization of the endophyte.}, }
@article {pmid17186156, year = {2007}, author = {Halpern, M and Landsberg, O and Raats, D and Rosenberg, E}, title = {Culturable and VBNC Vibrio cholerae: interactions with chironomid egg masses and their bacterial population.}, journal = {Microbial ecology}, volume = {53}, number = {2}, pages = {285-293}, pmid = {17186156}, issn = {0095-3628}, mesh = {Animals ; Chironomidae/metabolism/*microbiology ; *Ecosystem ; Female ; Fresh Water/analysis/*microbiology ; Gram-Negative Bacteria/classification/genetics/isolation &amp; purification ; Ovum/metabolism/*microbiology ; Phylogeny ; Species Specificity ; Vibrio cholerae/classification/genetics/growth &amp; development/*isolation &amp; purification ; Water Microbiology ; }, abstract = {Vibrio cholerae, the etiologic agent of cholera, is autochthonous to various aquatic environments. Recently, it was found that chironomid (nonbiting midges) egg masses serve as a reservoir for the cholera bacterium and that flying chironomid adults are possible windborne carriers of V. cholerae non-O1 non-O139. Chironomids are the most widely distributed insect in freshwater. Females deposit egg masses at the water's edge, and each egg mass contains eggs embedded in a gelatinous matrix. Hemagglutinin/protease, an extracellular enzyme of V. cholerae, was found to degrade chironomid egg masses and to prevent them from hatching. In a yearly survey, chironomid populations and the V. cholerae in their egg masses followed phenological succession and interaction of host-pathogen population dynamics. In this report, it is shown via FISH technique that most of the V. cholerae inhabiting the egg mass are in the viable but nonculturable (VBNC) state. The diversity of culturable bacteria from chironomid egg masses collected from two freshwater habitats was determined. In addition to V. cholerae, representatives of the following genera were isolated: Acinetobacter, Aeromonas, Klebsiella, Shewanella, Pseudomonas, Paracoccus, Exiguobacterium, and unidentified bacteria. Three important human pathogens, Aeromonas veronii, A. caviae, and A. hydrophila, were isolated from chironomid egg masses, indicating that chironomid egg masses may be a natural reservoir for pathogenic Aeromonas species in addition to V. cholerae. All isolates of V. cholerae were capable of degrading chironomid egg masses. This may help explain their host-pathogen relationship with chironomids. In contrast, almost none of the other bacteria that were isolated from the egg masses possessed this ability. Studying the interaction between chironomid egg masses, the bacteria inhabiting them, and V. cholerae could contribute to our understanding of the nature of the V. cholerae-egg mass interactions.}, }
@article {pmid17186155, year = {2007}, author = {Nguyen-Viet, H and Bernard, N and Mitchell, EA and Cortet, J and Badot, PM and Gilbert, D}, title = {Relationship between testate amoeba (protist) communities and atmospheric heavy metals accumulated in Barbula indica (bryophyta) in Vietnam.}, journal = {Microbial ecology}, volume = {53}, number = {1}, pages = {53-65}, pmid = {17186155}, issn = {0095-3628}, mesh = {Air Pollutants/*analysis ; Amoeba/*growth &amp; development ; Animals ; Bryophyta/chemistry/*growth &amp; development/*parasitology ; Environmental Monitoring/*methods ; Lead/analysis ; Metals, Heavy/*analysis ; Urban Health ; Vietnam ; }, abstract = {We studied the relationships between testate amoeba communities and heavy metal (Pb, Cd, Zn, Ni, Cu, Mn, and Fe) concentrations in the moss Barbula indica sampled at 29 sites in and around the city of Hanoi (Vietnam). Our first approach was to compare the heavy metal concentrations and testate amoeba variables between the city (zone 1) and the surrounding (zone 2). Mean moss concentrations of Pb, Cd, Zn, Ni, and Cu were significantly higher and testate amoeba species richness and abundance were significantly lower in zone 1 and the abundance of eight taxa differed significantly between the two zones. We then studied the correlation between heavy metals and testate amoebae. Species richness and abundance were correlated negatively to Pb concentration. Shannon H' was negatively correlated to both Pb and Cd. The abundance of several species was negatively correlated with Pb, Cd, Zn, and Ni; however, at the community level, Pb emerged as the only significant variable in a redundancy analysis. Our results suggest that testate amoebae are sensitive to and may be good bioindicators for heavy metal pollution, especially lead. Further research is needed to understand the causal relationships underlying the observed patterns.}, }
@article {pmid17186154, year = {2007}, author = {Zhang, L and Hurek, T and Reinhold-Hurek, B}, title = {A nifH-based oligonucleotide microarray for functional diagnostics of nitrogen-fixing microorganisms.}, journal = {Microbial ecology}, volume = {53}, number = {3}, pages = {456-470}, pmid = {17186154}, issn = {0095-3628}, mesh = {Azoarcus/genetics ; DNA Probes/chemistry ; DNA, Bacterial/chemistry/isolation &amp; purification ; *Environmental Microbiology ; Environmental Monitoring/methods ; Genetic Variation ; Nitrogen Fixation/genetics/*physiology ; Oligonucleotide Array Sequence Analysis/*methods ; Oxidoreductases/*genetics ; Phylogeny ; RNA, Bacterial/chemistry/isolation &amp; purification ; Reference Standards ; Reproducibility of Results ; Rhodocyclaceae/*classification/enzymology/genetics ; }, abstract = {Nitrogen fixation is an important process in biogeochemical cycles exclusively carried out by prokaryotes, mostly by an evolutionarily conserved nitrogenase protein complex, of which one of the structural genes (nifH) is highly valuable for phylogenetic and diversity analyses. We developed a nifH-based short oligonucleotide microarray (nifH diagnostic microarray) as a rapid tool to effectively monitor nitrogen-fixing diazotrophic populations in a wide range of environments. Taking account of the overwhelming predominance of environmental nifH fragments from uncultivated microorganisms in public databases, our nifH microarray is mainly based on nifH sequences from as yet unidentified prokaryotes. Standard conditions for microarray performance were determined, and criteria for the design of specific oligonucleotides were defined. A primary set of 56 oligonucleotides was validated with fluorescence-labeled single-stranded nifH targets from five reference strains, 26 environmental clones, and artificial mixtures of reference strains. The nifH microarray was applied to analyze the diversity (based on DNA) and activity (based on mRNA) of diazotrophs in roots of wild rice samples from Namibia. Results demonstrated that only a small subset of diazotrophs being present in the sample were actually fixing nitrogen actively. Our data suggest that the developed nifH microarray is a highly reproducible and semiquantitative method for mapping the variability of diazotrophic diversity, allowing rapid comparisons of the relative abundance and activity of diazotrophic prokaryotes in the environment. A further refined nifH microarray comprising of 194 oligonucleotide probes now covers more than 90% of sequences in our nifH database.}, }
@article {pmid17186153, year = {2007}, author = {Ikner, LA and Toomey, RS and Nolan, G and Neilson, JW and Pryor, BM and Maier, RM}, title = {Culturable microbial diversity and the impact of tourism in Kartchner Caverns, Arizona.}, journal = {Microbial ecology}, volume = {53}, number = {1}, pages = {30-42}, pmid = {17186153}, issn = {0095-3628}, mesh = {Actinobacteria/classification/genetics/isolation &amp; purification ; Arizona ; Bacteria/*classification/genetics/isolation &amp; purification ; *Calcium Carbonate ; *Culture Media ; DNA, Bacterial/analysis ; *Genetic Variation ; Geologic Sediments/*microbiology ; Glass/analysis ; Humans ; Molecular Sequence Data ; Paint/microbiology ; Phylogeny ; Proteobacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Kartchner Caverns in Benson, AZ, was opened for tourism in 1999 after a careful development protocol that was designed to maintain predevelopment conditions. As a part of an ongoing effort to determine the impact of humans on this limestone cave, samples were collected from cave rock surfaces along the cave trail traveled daily by tour groups (200,000 visitors year-1) and compared to samples taken from areas designated as having medium (30-40 visitors year-1) and low (2-3 visitors year-1) levels of human exposure. Samples were also taken from fiberglass moldings installed during cave development. Culturable bacteria were recovered from these samples and 90 unique isolates were identified by using 16S rRNA polymerase chain reaction and sequencing. Diversity generally decreased as human impact increased leading to the isolation of 32, 27, and 22 strains from the low, medium, and high impact areas, respectively. The degree of human impact was also reflected in the phylogeny of the isolates recovered. Although most isolates fell into one of three phyla: Actinobacteria, Firmicutes, or Proteobacteria, the Proteobacteria were most abundant along the cave trail (77% of the isolates), while Firmicutes predominated in the low (66%) and medium (52%) impact areas. Although the abundance of Proteobacteria along the cave trail seems to include microbes of environmental rather than of anthropogenic origin, it is likely that their presence is a consequence of increased organic matter availability due to lint and other organics brought in by cave visitors. Monitoring of the cave is still in progress to determine whether these bacterial community changes may impact the future development of cave formations.}, }
@article {pmid17186152, year = {2007}, author = {Shannon, SP and Chrzanowski, TH and Grover, JP}, title = {Prey food quality affects flagellate ingestion rates.}, journal = {Microbial ecology}, volume = {53}, number = {1}, pages = {66-73}, pmid = {17186152}, issn = {0095-3628}, mesh = {Animals ; Carbon/analysis ; Culture Media ; Digestion ; *Feeding Behavior ; Nitrogen/analysis ; Ochromonas/growth &amp; development/*physiology ; Phosphorus/analysis ; *Predatory Behavior ; Pseudomonas fluorescens/*chemistry/cytology/*growth &amp; development ; }, abstract = {Flagellate feeding efficiency appears to depend on morphological characteristics of prey such as cell size and motility, as well as on other characteristics such as digestibility and cell surface characteristics. Bacteria of varying morphological characteristics (cell size) and mineral nutrient characteristics or food quality (as determined by the C:N:P ratio) were obtained by growing Pseudomonas fluorescens in chemostats at four dilution rates (0.03, 0.06, 0.10, and 0.13 h-1) and three temperatures (14 degrees C, 20 degrees C, and 28 degrees C). Cells of a given food quality were heat-killed and used to grow the flagellate Ochromonas danica. Ingestion and digestion rates were determined by using fluorescently labeled bacteria of the same food quality as the bacteria supporting growth. Ingestion rates were affected by both food quality and cell size. Cells of high food quality (low carbon:element ratio) were ingested at higher rates than cells of low food quality. Multiple regression analysis indicated that cell size also influenced ingestion rate but to a much lesser extent than did food quality. Digestion rates were not correlated with either food quality or cell size. Results suggest that flagellates may adjust feeding efficiency based on the quality of food items available.}, }
@article {pmid17186151, year = {2007}, author = {Nugroho, RA and Röling, WF and Laverman, AM and Verhoef, HA}, title = {Low nitrification rates in acid Scots pine forest soils are due to pH-related factors.}, journal = {Microbial ecology}, volume = {53}, number = {1}, pages = {89-97}, pmid = {17186151}, issn = {0095-3628}, mesh = {Bacteria/classification/genetics/*metabolism ; Betaproteobacteria/classification/genetics/metabolism ; DNA, Bacterial/analysis ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Nitrates/*metabolism ; Oxidoreductases ; Pinus sylvestris/*growth &amp; development ; Polymerase Chain Reaction ; Quaternary Ammonium Compounds/metabolism ; Sequence Analysis, DNA ; Soil/*analysis ; *Soil Microbiology ; *Trees ; }, abstract = {In a previous study, ammonia-oxidizing bacteria (AOB)-like sequences were detected in the fragmentation layer of acid Scots pine (Pinus sylvestris L.) forest soils (pH 2.9-3.4) with high nitrification rates (>11.0 microg g-1 dry soil week-1), but were not detected in soils with low nitrification rates (<0.5 microg g-1 dry soil week-1). In the present study, we investigated whether this low nitrification rate has a biotic cause (complete absence of AOB) or an abiotic cause (unfavorable environmental conditions). Therefore, two soils strongly differing in net nitrification were compared: one soil with a low nitrification rate (location Schoorl) and another soil with a high nitrification rate (location Wekerom) were subjected to liming and/or ammonium amendment treatments. Nitrification was assessed by analysis of dynamics in NH4+-N and NO3- -N concentrations, whereas the presence and composition of AOB communities were assessed by polymerase chain reaction-denaturing gradient gel electrophoresis and sequencing of the ammonia monooxygenase (amoA) gene. Liming, rather than ammonium amendment, stimulated the growth of AOB and their nitrifying activity in Schoorl soil. The retrieved amoA sequences from limed (without and with N amendment) Schoorl and Wekerom soils exclusively belong to Nitrosospira cluster 2. Our study suggests that low nitrification rates in acidic Scots pine forest soils are due to pH-related factors. Nitrosospira cluster 2 detected in these soils is presumably a urease-positive cluster type of AOB.}, }
@article {pmid17186150, year = {2007}, author = {Nemergut, DR and Anderson, SP and Cleveland, CC and Martin, AP and Miller, AE and Seimon, A and Schmidt, SK}, title = {Microbial community succession in an unvegetated, recently deglaciated soil.}, journal = {Microbial ecology}, volume = {53}, number = {1}, pages = {110-122}, pmid = {17186150}, issn = {0095-3628}, mesh = {Bacteria/*classification/genetics/*growth &amp; development ; Comamonadaceae/classification/genetics/growth &amp; development ; Cyanobacteria/classification/genetics/growth &amp; development ; DNA, Bacterial/analysis ; *Ecosystem ; Gene Library ; *Ice Cover ; Molecular Sequence Data ; Nitrogen/metabolism ; Peru ; Phylogeny ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; Time Factors ; }, abstract = {Primary succession is a fundamental process in macroecosystems; however, if and how soil development influences microbial community structure is poorly understood. Thus, we investigated changes in the bacterial community along a chronosequence of three unvegetated, early successional soils (approximately 20-year age gradient) from a receding glacier in southeastern Peru using molecular phylogenetic techniques. We found that evenness, phylogenetic diversity, and the number of phylotypes were lowest in the youngest soils, increased in the intermediate aged soils, and plateaued in the oldest soils. This increase in diversity was commensurate with an increase in the number of sequences related to common soil bacteria in the older soils, including members of the divisions Acidobacteria, Bacteroidetes, and Verrucomicrobia. Sequences related to the Comamonadaceae clade of the Betaproteobacteria were dominant in the youngest soil, decreased in abundance in the intermediate age soil, and were not detected in the oldest soil. These sequences are closely related to culturable heterotrophs from rock and ice environments, suggesting that they originated from organisms living within or below the glacier. Sequences related to a variety of nitrogen (N)-fixing clades within the Cyanobacteria were abundant along the chronosequence, comprising 6-40% of phylotypes along the age gradient. Although there was no obvious change in the overall abundance of cyanobacterial sequences along the chronosequence, there was a dramatic shift in the abundance of specific cyanobacterial phylotypes, with the intermediate aged soils containing the greatest diversity of these sequences. Most soil biogeochemical characteristics showed little change along this approximately 20-year soil age gradient; however, soil N pools significantly increased with soil age, perhaps as a result of the activity of the N-fixing Cyanobacteria. Our results suggest that, like macrobial communities, soil microbial communities are structured by substrate age, and that they, too, undergo predictable changes through time.}, }
@article {pmid17186149, year = {2007}, author = {Nakashima, BA and McAllister, TA and Sharma, R and Selinger, LB}, title = {Diversity of phytases in the rumen.}, journal = {Microbial ecology}, volume = {53}, number = {1}, pages = {82-88}, pmid = {17186149}, issn = {0095-3628}, mesh = {6-Phytase/chemistry/*classification/genetics ; Amino Acid Sequence ; Animals ; Bacteria, Anaerobic/chemistry/*enzymology ; DNA Primers ; DNA, Bacterial/analysis/isolation &amp; purification ; Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; Protein Tyrosine Phosphatases/chemistry/*classification/genetics ; Rumen/chemistry/*enzymology/microbiology ; Selenomonas/chemistry/enzymology ; }, abstract = {Examples of a new class of phytase related to protein tyrosine phosphatases (PTP) were recently isolated from several anaerobic bacteria from the rumen of cattle. In this study, the diversity of PTP-like phytase gene sequences in the rumen was surveyed by using the polymerase chain reaction (PCR). Two sets of degenerate primers were used to amplify sequences from rumen fluid total community DNA and genomic DNA from nine bacterial isolates. Four novel PTP-like phytase sequences were retrieved from rumen fluid, whereas all nine of the anaerobic bacterial isolates investigated in this work contained PTP-like phytase sequences. One isolate, Selenomonas lacticifex, contained two distinct PTP-like phytase sequences, suggesting that multiple phytate hydrolyzing enzymes are present in this bacterium. The degenerate primer and PCR conditions described here, as well as novel sequences obtained in this study, will provide a valuable resource for future studies on this new class of phytase. The observed diversity of microbial phytases in the rumen may account for the ability of ruminants to derive a significant proportion of their phosphorus requirements from phytate.}, }
@article {pmid17186148, year = {2007}, author = {Marrero, J and Auling, G and Coto, O and Nies, DH}, title = {High-level resistance to cobalt and nickel but probably no transenvelope efflux: Metal resistance in the Cuban Serratia marcescens strain C-1.}, journal = {Microbial ecology}, volume = {53}, number = {1}, pages = {123-133}, pmid = {17186148}, issn = {0095-3628}, mesh = {Bacterial Proteins/genetics/*metabolism ; Cloning, Molecular ; Cobalt/metabolism/*pharmacology ; Cuba ; DNA Transposable Elements ; *Drug Resistance, Bacterial/genetics ; Escherichia coli/drug effects/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Mutagenesis, Insertional ; Nickel/metabolism/*pharmacology ; Sequence Analysis, DNA ; Serratia marcescens/*drug effects/*genetics/metabolism ; }, abstract = {Molecular mechanisms underlying inducible cobalt and nickel resistance of a bacterial strain isolated from a Cuban serpentine deposit were investigated. This strain C-1 was assigned to Serratia marcescens by 16S rDNA analysis and DNA/DNA hybridization. Genes involved in metal resistance were identified by transposon mutagenesis followed by selection for cobalt- and nickel-sensitive derivatives. The transposon insertion causing the highest decrease in metal resistance was located in the ncrABC determinant. The predicted NcrA product was a NreB ortholog of the major facilitator protein superfamily and central for cobalt/nickel resistance in S. marcescens strain C-1. NcrA also mediated metal resistance in Escherichia coli and caused decreased accumulation of Co(II) and Ni(II) in this heterologous host. NcrB may be a regulatory protein. NcrC was a protein of the nickel-cobalt transport (NiCoT) protein family and necessary for full metal resistance in E. coli, but only when NcrA was also present. Without NcrA, NcrC caused a slight decrease in metal resistance and mediated increased accumulation of Ni(II) and Co(II). Because the cytoplasmic metal concentration can be assumed to be the result of a flow equilibrium of uptake and efflux processes, this interplay between metal uptake system NcrC and metal efflux system NcrA may contribute to nickel and cobalt resistance in this bacterium.}, }
@article {pmid17186147, year = {2007}, author = {Leão, PN and Vasconcelos, MT and Vasconcelos, VM}, title = {Role of marine cyanobacteria in trace metal bioavailability in seawater.}, journal = {Microbial ecology}, volume = {53}, number = {1}, pages = {104-109}, pmid = {17186147}, issn = {0095-3628}, mesh = {Biological Availability ; Copper/analysis/*pharmacokinetics ; Cyanobacteria/*metabolism ; Iron/analysis/*pharmacokinetics ; Seawater/chemistry/*microbiology ; Trace Elements/analysis/*pharmacokinetics ; }, abstract = {In seawater, several trace metals with biological significance are highly complexed with organic matter. Marine cyanobacteria are an important phytoplanktonic group, with the ability to release trace metal-binding compounds to the seawater medium, which in turn modulates their bioavailability and influences their biogeochemical cycles. Such interactions may allow cyanobacteria to more easily access less available trace metals essential for their metabolic processes, or, conversely, keep the toxic forms of the trace metals from reaching intolerable levels. In this minireview, Cu and Fe interactions with cyanobacteria received special attention, although other trace metals (Co, Pb, Zn, and Cd) are also covered. Recent research has shed light on many aspects of trace metal-cyanobacteria ecology in seawater; nevertheless, the biochemical processes behind this dynamics and the structure of the vast majority of the metal binding compounds remain unclear.}, }
@article {pmid17186146, year = {2007}, author = {Jones, PR and Cottrell, MT and Kirchman, DL and Dexter, SC}, title = {Bacterial community structure of biofilms on artificial surfaces in an estuary.}, journal = {Microbial ecology}, volume = {53}, number = {1}, pages = {153-162}, pmid = {17186146}, issn = {0095-3628}, mesh = {Bacteria/*classification/genetics/*growth &amp; development ; Biofilms/*classification/*growth &amp; development ; *Ecosystem ; Electrophoresis, Polyacrylamide Gel/methods ; Gene Library ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Phylogeny ; Polycarboxylate Cement ; RNA, Ribosomal, 16S ; Seawater/*microbiology ; Sequence Analysis, DNA ; Stainless Steel ; }, abstract = {This study examined bacterial community structure of biofilms on stainless steel and polycarbonate in seawater from the Delaware Bay. Free-living bacteria in the surrounding seawater were compared to the attached bacteria during the first few weeks of biofilm growth. Surfaces exposed to seawater were analyzed by using 16S rDNA libraries, fluorescence in situ hybridization (FISH), and denaturing gradient gel electrophoresis (DGGE). Community structure of the free-living bacterial community was different from that of the attached bacteria according to FISH and DGGE. In particular, alpha-proteobacteria dominated the attached communities. Libraries of 16S rRNA genes revealed that representatives of the Rhodobacterales clade were the most abundant members of biofilm communities. Changes in community structure during biofilm growth were also examined by DGGE analysis. We hypothesized that bacterial communities on dissimilar surfaces would initially differ and become more similar over time. In contrast, the compositions of stainless steel and polycarbonate biofilms were initially the same, but differed after about 1 week of biofilm growth. These data suggest that the relationship between surface properties and biofilm community structure changes as biofilms grow on surfaces such as stainless steel and polycarbonate in estuarine water.}, }
@article {pmid17186145, year = {2007}, author = {Zingel, P and Agasild, H and Nõges, T and Kisand, V}, title = {Ciliates are the dominant grazers on pico- and nanoplankton in a shallow, naturally highly eutrophic lake.}, journal = {Microbial ecology}, volume = {53}, number = {1}, pages = {134-142}, pmid = {17186145}, issn = {0095-3628}, mesh = {Animals ; Bacteria/*growth &amp; development ; Biomass ; Ciliophora/*physiology ; Ecosystem ; Eukaryota/growth &amp; development/physiology ; *Eutrophication ; *Food Chain ; Fresh Water/microbiology/*parasitology ; Plankton/*growth &amp; development ; }, abstract = {Abundance and biomass of the microbial loop members [bacteria, heterotrophic nanoflagellates (HNF), and ciliates] were seasonally measured in the naturally eutrophic and shallow (2.8 mean depth) Lake Võrtsjärv, which has a large open surface area (average 270 km2) and highly turbid water (Secchi depth <1 m). Grazing rates (filter feeding rates) on 0.5-, 3-, and 6-microm-diameter particles were measured to estimate pico- and nanoplankton grazing (filter feeding) by micro- and metazooplankton. Among grazers, HNF had a low abundance (<50 cells mL-1) and, due to their low specific filtering rates, they only grazed a minor fraction of the bacterioplankton (<or=4.2% of total grazing). Ciliates were relatively abundant (<or=158 cells mL-1) and, considering their high specific feeding rates, were able to graze more than 100% of the bacterial biomass production in the open part of the lake, whereas the average daily grazing accounted for 9.3% of the bacterial standing stock. Ciliates were potentially important grazers of nanoplanktonic organisms (on average, approximately 20% of the standing stock of 3-microm-size particles was grazed daily). Metazooplankton grazed a minor part of the bacterioplankton, accounting for only 0.1% of standing stock of bacteria. Grazing on nanoplankton (3-6 microm) by metazooplankton was higher (0.4% of standing stock). The hypothesis is proposed that ciliates dominate due to a lack of top-down regulation by predators, and HNF have a low abundance due to strong grazing pressure by ciliates.}, }
@article {pmid17186144, year = {2007}, author = {Yan, X and Xu, Z and Feng, X and Liu, Y and Liu, B and Zhang, X and Zhu, C and Zhao, L}, title = {Cloning of environmental genomic fragments as physical markers for monitoring microbial populations in coking wastewater treatment system.}, journal = {Microbial ecology}, volume = {53}, number = {1}, pages = {163-172}, pmid = {17186144}, issn = {0095-3628}, mesh = {Bacteria/*classification/genetics/growth &amp; development ; Bioreactors ; *Cloning, Molecular ; *Coke ; DNA Fingerprinting/methods ; DNA, Bacterial/analysis/*genetics/isolation &amp; purification ; Ecosystem ; Genome, Bacterial/*genetics ; *Industrial Waste ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Water Microbiology ; Water Purification/*methods ; }, abstract = {The association between community functional shift and dynamics of genomic DNA composition can be used to identify functionally relevant populations as indicator organisms for systems monitoring. In this work, fingerprinting-based community DNA hybridization was used to monitor community structural dynamics and identify genomic fragments whose abundance shifts were concomitant to changes in COD removal capacity in a reactor. A laboratory-scale anaerobic-anoxic-oxic fixed biofilm system treating coking wastewater was operated with (LR mode) or without effluent recirculation (LNR mode). The contribution to total chemical oxygen demand (COD) removal by the anoxic reactor increased from 4% in LNR mode to 26% in LR mode. Long primer RAPD (randomly amplified polymorphic DNA) community fingerprints of the anoxic reactor also changed most significantly from the one similar to the anaerobic reactor to one similar to the oxic reactor. DNA hybridization revealed one signature band of 2.1 kb shared by the anoxic and oxic reactors in LR, but not LNR mode. Clone library profiling of this band resulted in one predominant 2.1-kb genomic fragment (B3) with no homologous sequences in GenBank. Real-time polymerase chain reaction indicated that copy numbers of B3 in the anoxic reactor under LR mode were 69 times higher than that under LNR mode, concomitant to a significant increase in COD removal capacity in this reactor. The different patterns of distribution of B3 in the laboratory system and a comparable malfunctioning industrial system demonstrated the potential of this genomic fragment as physical markers in systems monitoring. In addition, this genomic fragment may allow sequence-guided isolation of the host microbe.}, }
@article {pmid17186143, year = {2007}, author = {Villadas, PJ and Fernández-López, M and Ramírez-Saad, H and Toro, N}, title = {Rhizosphere-bacterial community in Eperua falcata (Caesalpiniaceae) a putative nitrogen-fixing tree from French Guiana rainforest.}, journal = {Microbial ecology}, volume = {53}, number = {2}, pages = {317-327}, pmid = {17186143}, issn = {0095-3628}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Proteins/genetics ; Ecosystem ; French Guiana ; Nitrogen/*metabolism ; Oxidoreductases/genetics ; Phylogeny ; Plant Roots/microbiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Trees/*metabolism/*microbiology ; Tropical Climate ; }, abstract = {The rainforest of French Guiana is still largely unaffected by human activity. Various pristine sites like the Paracou Research Station are devoted to study this tropical ecosystem. We used culture-independent techniques, like polymerase chain reaction-temperature gradient gel electrophoresis, and construction of clone libraries of partial 16S rRNA and nifH genes, to analyze the composition of the bacterial community in the rhizosphere of mature trees of Eperua falcata and Dicorynia guianensis, both species within the Caesalpiniaceae family. E. falcata is one of the more abundant pioneer tree species in this ecosystem and so far, no root nodules have ever been found. However, its nitrogen-fixing status is regarded as "uncertain", whereas D. guianensis is clearly considered a non-nitrogen-fixing plant. The rhizospheres of these mature trees contain specific bacterial communities, including several currently found uncultured microorganisms. In these communities, there are putative nitrogen-fixing bacteria specifically associated to each tree: D. guianensis harbors several Rhizobium spp. and E. falcata members of the genera Burkholderia and Bradyrhizobium. In addition, nifH sequences in the rhizosphere of the latter tree were very diverse. Retrieved sequences were related to bacteria belonging to the alpha-, beta-, and gamma-Proteobacteria in the E. falcata rhizoplane, whereas only two sequences related to gamma-Proteobacteria were found in D. guianensis. Differences in the bacterial communities and the abundance and diversity of nifH sequences in E. falcata rhizosphere suggest that this tree could obtain nitrogen through a nonnodulating bacterial interaction.}, }
@article {pmid17186142, year = {2007}, author = {Boonapatcharoen, N and Meepian, K and Chaiprasert, P and Techkarnjanaruk, S}, title = {Molecular monitoring of microbial population dynamics during operational periods of anaerobic hybrid reactor treating cassava starch wastewater.}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {21-30}, pmid = {17186142}, issn = {0095-3628}, mesh = {Bacteria, Anaerobic/classification/genetics/*metabolism ; Biodegradation, Environmental ; Bioreactors/*microbiology ; In Situ Hybridization, Fluorescence ; *Manihot ; Starch/*metabolism ; Water/chemistry ; *Water Purification ; }, abstract = {This study characterized the microbial community and population dynamics in an anaerobic hybrid reactor (AHR) treating cassava starch wastewater. Methanogens and nonmethanogens were followed during the start-up and operation of the reactor, and linked to operational and performance data. Biomass samples taken from the sludge bed and packed bed zones of the AHR at intervals throughout the operational period were examined by 16S rRNA fluorescence in situ hybridization (FISH). The start-up seed and the reactor biomass were sampled during the feeding of the wastewater with a chemical oxygen demand (COD) value of 8 g L(-1) and a hydraulic retention time (HRT) of 8 days. These samples were characterized by the predominance of cells with long-rod morphology similar to Methanosaeta spp. Following a sharp operational change, accomplished by increasing the COD concentration of the organic influent from 8 to 10 g L(-1) and reducing the HRT from 8 to 5 days, there was a doubling of the organic loading rate, a reduction of the COD removal efficiency, as well as decreased methane content in the biogas and an accumulation of total volatile acids in the reactor. Moreover, this operational change resulted in a significant population shift from long-rod Methanosaeta-like cells to tetrad-forming Methanosarcina-like cells. The distributions of microbial populations involved in different zones of the AHR were determined. The results showed that nonmethanogens became the predominant population in both sludge and the packed bed zone. However, the percentage of methanogens in the packed bed zone was higher than that in the sludge bed zone. This higher percentage of methanogens was likely caused by the fact that the packed bed zone provided a suitable environmental condition with an appropriate nutrient availability for methanogen growth.}, }
@article {pmid17186141, year = {2007}, author = {Wang, B and Hu, W and Liu, H and Zhang, CY and Zhao, JY and Jiang, DM and Wu, ZH and Li, YZ}, title = {Adaptation of salt-tolerant Myxococcus strains and their motility systems to the ocean conditions.}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {43-51}, pmid = {17186141}, issn = {0095-3628}, mesh = {*Adaptation, Physiological ; Morphogenesis ; Myxococcus/classification/growth &amp; development/*physiology ; Oceans and Seas ; Phylogeny ; Seawater/chemistry/*microbiology ; Sodium Chloride/*metabolism ; Spores, Bacterial ; }, abstract = {More and more studies have indicated that myxobacteria are able to live in seawater conditions, which, however, can decrease the fruiting body formation ability and also the adventurous (A) and social (S) motility systems of the myxobacteria. To learn the adaptation mechanism of the salt-tolerant myxobacteria to marine conditions, we analyzed 10 salt-tolerant Myxococcus strains of their fruiting body formation and motility. The isolates were from marine samples and possessed different levels of salt tolerance. They had the dual motility system and formed fruiting bodies in the presence of suitable seawater concentrations. Some high salt-tolerant strains even lost their fruiting abilities in the absence of seawater. In response to the presence of seawater, the S-motility was found to be increased in the high salt-tolerants but decreased in the low salt-tolerants. The A-motility, on the other hand, was observed in all the salt-tolerant Myxococcus strains, but increased or decreased in response to the presence of seawater. Perceived shifts of fruiting body formation abilities and motilities discovered in the salt-tolerant Myxococcus strains suggested an ecological adaptation of myxobacterial social behaviors to the marine environments.}, }
@article {pmid17186140, year = {2007}, author = {Danielsson, J and Reva, O and Meijer, J}, title = {Protection of oilseed rape (Brassica napus) toward fungal pathogens by strains of plant-associated Bacillus amyloliquefaciens.}, journal = {Microbial ecology}, volume = {54}, number = {1}, pages = {134-140}, pmid = {17186140}, issn = {0095-3628}, mesh = {Bacillus/classification/*physiology ; Brassica napus/growth &amp; development/*microbiology ; Fungi/*physiology ; Immunity, Innate/physiology ; Plant Diseases/microbiology ; }, abstract = {In this report, four Bacillus strains were tested for effects on plant fitness and disease protection of oilseed rape (Brassica napus). The strains belonged to newly discovered plant-associated Bacillus amyloliquefaciens and a recently proposed species, Bacillus endophyticus. The fungal pathogens tested represented different infection strategies and included Alternaria brassicae, Botrytis cinerea, Leptosphaeria maculans, and Verticillium longisporum. The B. amyloliquefaciens strains showed no or a weak plant growth promoting activity, whereas the B. endophyticus strain had negative effects on the plant as revealed by phenological analysis. On the other hand, two of the B. amyloliquefaciens strains conferred protection of oilseed rape toward all pathogens tested. In vitro experiments studying the effects of Bacillus exudates on fungal growth showed clear growth inhibition in several but not all cases. The protective effects of Bacillus can therefore, at least in part, be explained by production of antibiotic substances, but other mechanisms must also be involved probably as a result of intricate plant-bacteria interaction. The protective effects observed for certain Bacillus strains make them highly interesting for further studies as biocontrol agents in Brassica cultivation.}, }
@article {pmid17183309, year = {2006}, author = {Ley, RE and Turnbaugh, PJ and Klein, S and Gordon, JI}, title = {Microbial ecology: human gut microbes associated with obesity.}, journal = {Nature}, volume = {444}, number = {7122}, pages = {1022-1023}, doi = {10.1038/4441022a}, pmid = {17183309}, issn = {1476-4687}, support = {P30 DK056341/DK/NIDDK NIH HHS/United States ; }, mesh = {Adiposity/drug effects/physiology ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacteroidetes/classification/genetics/isolation &amp; purification ; *Diet ; Gastrointestinal Tract/*microbiology ; Humans ; Obesity/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Two groups of beneficial bacteria are dominant in the human gut, the Bacteroidetes and the Firmicutes. Here we show that the relative proportion of Bacteroidetes is decreased in obese people by comparison with lean people, and that this proportion increases with weight loss on two types of low-calorie diet. Our findings indicate that obesity has a microbial component, which might have potential therapeutic implications.}, }
@article {pmid17176811, year = {2006}, author = {Pauwels, B and Verstraete, W}, title = {The treatment of hospital wastewater: an appraisal.}, journal = {Journal of water and health}, volume = {4}, number = {4}, pages = {405-416}, pmid = {17176811}, issn = {1477-8920}, mesh = {Anti-Bacterial Agents/adverse effects/analysis ; Disinfectants/adverse effects/analysis ; Drug-Related Side Effects and Adverse Reactions ; *Environmental Monitoring ; Hospitals ; Humans ; Medical Waste/adverse effects/*analysis ; *Medical Waste Disposal ; Pharmaceutical Preparations/analysis ; Risk Assessment ; Sewage/*analysis/chemistry ; *Waste Disposal, Fluid ; }, abstract = {Hospitals discharge considerable amounts of chemicals and microbial agents in their wastewaters. Problem chemicals present in hospital wastewater belong to different groups, such as antibiotics, X-ray contrast agents, disinfectants and pharmaceuticals. Many of these chemical compounds resist normal wastewater treatment. They end up in surface waters where they can influence the aquatic ecosystem and interfere with the food chain. Humans are particularly exposed by the drinking water, produced from surface water. Microbial agents of special concern are multiresistant microbial strains. The latter are suspected to contribute to the spread of antibiotic resistance. In this paper, we will discuss the different approaches towards hospital wastewater treatment. The principle of uncoupling hospitals from public sewers warrants indepth evaluation by technologists and ecotoxicologists as well as public health specialists.}, }
@article {pmid17171461, year = {2007}, author = {Devi, KK and Seth, N and Kothamasi, S and Kothamasi, D}, title = {Hydrogen cyanide-producing rhizobacteria kill subterranean termite Odontotermes obesus (Rambur) by cyanide poisoning under in vitro conditions.}, journal = {Current microbiology}, volume = {54}, number = {1}, pages = {74-78}, pmid = {17171461}, issn = {0343-8651}, mesh = {Alcaligenes/classification/isolation &amp; purification/*metabolism ; Animals ; Gram-Negative Bacteria/classification/isolation &amp; purification/*metabolism ; Hydrogen Cyanide/metabolism/*toxicity ; Insect Control ; Isoptera/*drug effects ; *Pest Control, Biological ; Rhizobium/classification/isolation &amp; purification/*metabolism ; *Soil Microbiology ; }, abstract = {The subterranean termite Odontotermes obesus is an important pest of the Indian subcontinent, causing extensive damage to major agricultural crops and forest plantation trees. Control of termites by strategies employing their parasites has limitations because they have evolved a complex social structure, immune responses, and adaptive behavior toward pathogen-infected individuals. Nonparasitic rhizobacteria that produce harmful metabolites might facilitate the biocontrol of termites. In the present investigation, three different species of hydrogen cyanide-producing rhizobacteria were tested for their potential to kill O. obesus. The three bacterial species were found to be effective in killing the termites under in vitro conditions.}, }
@article {pmid17168847, year = {2006}, author = {Kirkup, BC}, title = {Bacteriocins as oral and gastrointestinal antibiotics: theoretical considerations, applied research, and practical applications.}, journal = {Current medicinal chemistry}, volume = {13}, number = {27}, pages = {3335-3350}, doi = {10.2174/092986706778773068}, pmid = {17168847}, issn = {0929-8673}, mesh = {Animals ; Anti-Bacterial Agents ; Bacteriocins/*therapeutic use ; Drug Resistance ; *Gastrointestinal Agents ; Gastrointestinal Diseases/microbiology/*therapy ; Humans ; Microbiology ; Probiotics/*therapeutic use ; }, abstract = {Bacteriocins, specific and highly potent protein antibiotics, have been long been expected to enter the working pharmacopeia. Despite laboratory experiments demonstrating their effectiveness against a wide range of gastrointestinal pathogens, attempts to reproduce such killing activity by using live bacteriocin-producing bacteria in animal gastrointestinal systems repeatedly failed. This raised doubts about the potential of the bacteriocins as in vivo antibiotics. Thus, though some bacteriocins have been employed in food preservation and processing, none have been applied directly as medicine. Recent experiments, based on an improved theoretical understanding of microbial ecology, demonstrate the in vivo activity of bacteriocins, the potential importance of bacteriocins as antibiotics, and the role that bacteriocins play in antibiotic resistance. Meanwhile, several kinds of bacteriocins have been proposed for applications in gastrointestinal microbiology, as well as for the use of probiotics to reduce dental caries and improve oral hygiene. Unfortunately, much of the probiotic-oriented research appears to be pursued without reference to resistance and the role of the bacteriocins in a community of bacteria. This leads to continued confusion regarding the interpretation of experimental results and mistaken assessments, positive and negative, of bacteriocins' therapeutic potential. A study of microbial ecology should be incorporated in the drug development process in order to apply bacteriocins most effectively.}, }
@article {pmid17165121, year = {2007}, author = {Sloan, WT and Woodcock, S and Lunn, M and Head, IM and Curtis, TP}, title = {Modeling taxa-abundance distributions in microbial communities using environmental sequence data.}, journal = {Microbial ecology}, volume = {53}, number = {3}, pages = {443-455}, pmid = {17165121}, issn = {0095-3628}, mesh = {*Biodiversity ; Ecosystem ; *Environmental Microbiology ; Environmental Monitoring/*methods ; *Models, Biological ; Population Density ; Prokaryotic Cells/*classification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {We show that inferring the taxa-abundance distribution of a microbial community from small environmental samples alone is difficult. The difficulty stems from the disparity in scale between the number of genetic sequences that can be characterized and the number of individuals in communities that microbial ecologists aspire to describe. One solution is to calibrate and validate a mathematical model of microbial community assembly using the small samples and use the model to extrapolate to the taxa-abundance distribution for the population that is deemed to constitute a community. We demonstrate this approach by using a simple neutral community assembly model in which random immigrations, births, and deaths determine the relative abundance of taxa in a community. In doing so, we further develop a neutral theory to produce a taxa-abundance distribution for large communities that are typical of microbial communities. In addition, we highlight that the sampling uncertainties conspire to make the immigration rate calibrated on the basis of small samples very much higher than the true immigration rate. This scale dependence of model parameters is not unique to neutral theories; it is a generic problem in ecology that is particularly acute in microbial ecology. We argue that to overcome this, so that microbial ecologists can characterize large microbial communities from small samples, mathematical models that encapsulate sampling effects are required.}, }
@article {pmid17165120, year = {2007}, author = {Otawa, K and Lee, SH and Yamazoe, A and Onuki, M and Satoh, H and Mino, T}, title = {Abundance, diversity, and dynamics of viruses on microorganisms in activated sludge processes.}, journal = {Microbial ecology}, volume = {53}, number = {1}, pages = {143-152}, pmid = {17165120}, issn = {0095-3628}, mesh = {Animals ; Bacteria/classification/genetics/growth &amp; development/virology ; Bacteriophages/classification/genetics/*growth &amp; development/isolation &amp; purification ; Colony Count, Microbial ; DNA, Viral/analysis/isolation &amp; purification ; Ecosystem ; Electrophoresis, Gel, Pulsed-Field ; Fresh Water/microbiology/virology ; Humans ; Microscopy, Fluorescence ; Sewage/microbiology/*virology ; Waste Disposal, Fluid/*methods ; Water Purification/methods ; }, abstract = {We examined the abundance of viruses on microorganisms in activated sludge and the dynamics of their community structure. Direct counting with epifluorescence microscopy and pulsed-field gel electrophoresis (PFGE) were applied to 20 samples from 14 full-scale wastewater treatment plants (wwtps) treating municipal, industrial, or animal wastewater. Furthermore, to observe the dynamics of viral community structure over time, a laboratory-scale sequencing batch reactor was operated for 58 days. The concentrations of virus particles in the wwtps, as quantified by epifluorescence microscopy, ranged from 4.2 x 10(7) to 3.0 x 10(9) mL-1. PFGE, improved by the introduction of a higher concentration of Tris-EDTA buffer in the DNA extraction step, was successfully used to profile DNA viruses in the activated sludge. Most of the samples from different wwtps commonly had bands in the 40-70 kb range. In the monitoring of viral DNA size distribution in the laboratory-scale reactor, some bands were observed stably throughout the experimental period, some emerged during the operation, and others disappeared. Rapid emergence and disappearance of two intense bands within 6 days was observed. Our data suggest that viruses--especially those associated with microorganisms--are abundant and show dynamic behavior in activated sludge.}, }
@article {pmid17163008, year = {2006}, author = {Aelterman, P and Rabaey, K and Clauwaert, P and Verstraete, W}, title = {Microbial fuel cells for wastewater treatment.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {54}, number = {8}, pages = {9-15}, doi = {10.2166/wst.2006.702}, pmid = {17163008}, issn = {0273-1223}, mesh = {Anaerobiosis ; Biodegradation, Environmental ; *Bioelectric Energy Sources ; Bioreactors ; Conservation of Energy Resources ; Time Factors ; Waste Disposal, Fluid/*instrumentation/methods ; }, abstract = {Microbial fuel cells (MFCs) are emerging as promising technology for the treatment of wastewaters. The potential energy conversion efficiencies are examined. The rates of energy recovery (W/m3 reactor) are reviewed and evaluated. Some recent data relating to potato-processing wastewaters and a hospital wastewater effluent are reported. Finally, a set of process configurations in which MFCs could be useful to treat wastewaters is schematized. Overall, the MFC technology still faces major challenges, particularly in terms of chemical oxygen demand (COD) removal efficiency.}, }
@article {pmid17158990, year = {2006}, author = {Lee, OO and Lau, SCK and Tsoi, MMY and Li, X and Plakhotnikova, I and Dobretsov, S and Wu, MCS and Wong, PK and Weinbauer, M and Qian, PY}, title = {Shewanella irciniae sp. nov., a novel member of the family Shewanellaceae, isolated from the marine sponge Ircinia dendroides in the Bay of Villefranche, Mediterranean Sea.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {56}, number = {Pt 12}, pages = {2871-2877}, doi = {10.1099/ijs.0.64562-0}, pmid = {17158990}, issn = {1466-5026}, mesh = {Animals ; Bacterial Typing Techniques ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Genes, rRNA ; Mediterranean Sea ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Shewanella/chemistry/*classification/genetics/isolation &amp; purification ; }, abstract = {Strain UST040317-058(T), comprising non-pigmented, rod-shaped, facultatively anaerobic, Gram-negative cells that are motile by means of single polar flagella, was isolated from the surface of a marine sponge (Ircinia dendroides) collected from the Mediterranean Sea. Comparative 16S rRNA gene sequence-based phylogenetic analysis placed the strain in a separate cluster with the recognized bacterium Shewanella algae IAM 14159(T), with which it showed a sequence similarity of 95.0 %. The sequence similarity between strain UST040317-058(T) and its other (six) closest relatives ranged from 91.6 to 93.8 %. Strain UST040317-058(T) showed oxidase, catalase and gelatinase activities. The typical respiratory quinones for shewanellas, menaquinone MK-7 and ubiquinones Q-7 and Q-8, were also detected. The predominant fatty acids in strain UST040317-058(T) were i15 : 0, 16 : 0, 17 : 1omega8c and summed feature 3 (comprising i15 : 0 2-OH and/or 16 : 1omega7c), altogether representing 56.9 % of the total. The DNA G+C content was 39.9 mol%. The strain could be differentiated from other Shewanella species by its inability to reduce nitrate or produce H(2)S and by 10-22 additional phenotypic characteristics. On the basis of the phylogenetic and phenotypic data presented in this study, strain UST040317-058(T) represents a novel species in the genus Shewanella, for which the name Shewanella irciniae sp. nov. is proposed. The type strain is UST040317-058(T) (=JCM 13528(T)=NRRL B-41466(T)).}, }
@article {pmid17158971, year = {2006}, author = {Küpfer, M and Kuhnert, P and Korczak, BM and Peduzzi, R and Demarta, A}, title = {Genetic relationships of Aeromonas strains inferred from 16S rRNA, gyrB and rpoB gene sequences.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {56}, number = {Pt 12}, pages = {2743-2751}, doi = {10.1099/ijs.0.63650-0}, pmid = {17158971}, issn = {1466-5026}, mesh = {Aeromonas/*classification/enzymology/*genetics ; Animals ; *Bacterial Typing Techniques ; Cattle ; Child ; DNA Gyrase/*genetics ; DNA, Bacterial/analysis/isolation &amp; purification ; DNA, Ribosomal/analysis ; DNA-Directed RNA Polymerases/*genetics ; Genes, Bacterial ; Humans ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Genetic relationships among bacterial strains belonging to the genus Aeromonas were inferred from 16S rRNA, gyrB and rpoB gene sequences. Twenty-eight type or collection strains of the recognized species or subspecies and 33 Aeromonas strains isolated from human and animal specimens as well as from environmental samples were included in the study. As reported previously, the 16S rRNA gene sequence is highly conserved within the genus Aeromonas, having only limited resolution for this very tight group of species. Analysis of a 1.1 kb gyrB sequence confirmed that this gene has high resolving power, with maximal interspecies divergence of 15.2 %. Similar results were obtained by sequencing only 517 bp of the rpoB gene, which showed maximal interspecies divergence of 13 %. The topologies of the gyrB- and rpoB-derived trees were similar. The results confirm the close relationship of species within the genus Aeromonas and show that a phylogenetic approach including several genes is suitable for improving the complicated taxonomy of the genus.}, }
@article {pmid17158969, year = {2006}, author = {Ramamoorthy, S and Sass, H and Langner, H and Schumann, P and Kroppenstedt, RM and Spring, S and Overmann, J and Rosenzweig, RF}, title = {Desulfosporosinus lacus sp. nov., a sulfate-reducing bacterium isolated from pristine freshwater lake sediments.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {56}, number = {Pt 12}, pages = {2729-2736}, doi = {10.1099/ijs.0.63610-0}, pmid = {17158969}, issn = {1466-5026}, mesh = {Bacterial Typing Techniques ; DNA, Bacterial/analysis ; DNA, Ribosomal/genetics ; Fresh Water/*microbiology ; Genes, rRNA ; Geologic Sediments/*microbiology ; Germany ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Oxidation-Reduction ; Peptococcaceae/*classification/genetics/isolation &amp; purification/physiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Sulfates/metabolism ; Sulfur-Reducing Bacteria ; }, abstract = {A novel sulfate-reducing bacterium was isolated from pristine sediments of Lake Stechlin, Germany. This strain, STP12(T), was found to contain predominantly c-type cytochromes and to reduce sulfate, sulfite and thiosulfate using lactate as an electron donor. Although STP12(T) could not utilize elemental sulfur as an electron acceptor, it could support growth by dissimilatory Fe(III) reduction. In a comparison of 16S rRNA gene sequences, STP12(T) was 96.7 % similar to Desulfosporosinus auripigmenti DSM 13351(T), 96.5 % similar to Desulfosporosinus meridiei DSM 13257(T) and 96.4 % similar to Desulfosporosinus orientis DSM 765(T). DNA-DNA hybridization experiments revealed that strain STP12(T) shows only 32 % reassociation with the type strain of the type species of the genus, D. orientis DSM 765(T). These data, considered in conjunction with strain-specific differences in heavy metal tolerance, cell-wall chemotaxonomy and riboprint patterns, support recognition of strain STP12(T) (=DSM 15449(T)=JCM 12239(T)) as the type strain of a distinct and novel species within the genus Desulfosporosinus, Desulfosporosinus lacus sp. nov.}, }
@article {pmid17156079, year = {2007}, author = {Rodrigues, DF and Tiedje, JM}, title = {Multi-locus real-time PCR for quantitation of bacteria in the environment reveals Exiguobacterium to be prevalent in permafrost.}, journal = {FEMS microbiology ecology}, volume = {59}, number = {2}, pages = {489-499}, doi = {10.1111/j.1574-6941.2006.00233.x}, pmid = {17156079}, issn = {0168-6496}, mesh = {Bacillaceae/classification/genetics/growth &amp; development/*isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Bacterial Proteins/*genetics ; DNA Gyrase/genetics ; DNA Primers ; DNA, Bacterial/analysis ; DNA-Directed RNA Polymerases/*genetics ; Ecosystem ; *Ice ; Phylogeny ; Polymerase Chain Reaction/*methods ; Siberia ; *Soil Microbiology ; Species Specificity ; }, abstract = {We developed a multi-locus quantitative PCR approach to minimize problems of precision, sensitivity and primer specificity for quantifying a targeted microbial group in nature. This approach also avoids a systematic error in population quantitation when 16S rRNA genes are used because of copy number heterogeneity. Specific primers were designed to assess the abundance of psychrotrophic and mesophilic Exiguobacterium spp. that excluded the thermophilic members of the genus. The chosen primers targeted genes for DNA gyrase B (gyrB), the beta subunit of the RNA polymerase gene (rpoB) and a hypothetical gene so far found only in this group. The results demonstrate that the multiple primer approach provides a more reliable estimate of population density; that the targeted Exiguobacterium group is found at a median density of 50,000 gene copies per mug of total community DNA in 27 of 29 permafrost soils but was found in only one of the four temperate and tropical soils tested.}, }
@article {pmid17151201, year = {2007}, author = {Zhang, M and Liu, B and Zhang, Y and Wei, H and Lei, Y and Zhao, L}, title = {Structural shifts of mucosa-associated lactobacilli and Clostridium leptum subgroup in patients with ulcerative colitis.}, journal = {Journal of clinical microbiology}, volume = {45}, number = {2}, pages = {496-500}, pmid = {17151201}, issn = {0095-1137}, mesh = {Bacteroides/genetics/isolation &amp; purification ; Biopsy ; Clostridium/genetics/*isolation &amp; purification ; Colitis, Ulcerative/*microbiology ; DNA, Bacterial/analysis ; Electrophoresis/methods ; Humans ; Intestinal Mucosa/*microbiology ; Lactobacillus/genetics/*isolation &amp; purification ; Polymerase Chain Reaction/methods ; }, abstract = {To understand the role of mucosa-associated microbiota in the pathogenicity of ulcerative colitis (UC), paired biopsies were obtained during colonoscopy from the ulcerated and nonulcerated gut mucosa of 24 patients with UC. Denaturing gradient gel electrophoresis analysis was employed to profile the composition of the dominant bacteria (16S rRNA gene V3 region) and three important groups: lactobacilli, the Clostridium leptum subgroup, and Bacteroides spp. The Pearson coefficient was used to estimate similarities between the bacterial communities of the paired biopsies for each patient. The average similarity values of bacterial composition between the paired samples were 94.8 +/- 3.8% for dominant bacteria, 59.9 +/- 26.1% for lactobacilli, 79.2 +/- 22.6% for the Clostridium leptum subgroup, and 88.7 +/- 16.4% for Bacteroides spp. The data revealed that lactobacilli and the Clostridium leptum subgroup were significantly different between the ulcerated and the nonulcerated regions. It also was noted that for lactobacilli, the composition varied significantly between biopsy sites irrespective of the location of UC in the gut but that the composition of the Clostridium leptum subgroup showed significant differences between paired samples from UC in the rectum and not in the left colon. Localized dysbiosis of the mucosa-associated intestinal microflora, especially for lactobacilli and the Clostridium leptum subgroup, may be closely related to UC.}, }
@article {pmid17135664, year = {2006}, author = {Hume, ME and Clemente-Hernández, S and Oviedo-Rondón, EO}, title = {Effects of feed additives and mixed eimeria species infection on intestinal microbial ecology of broilers.}, journal = {Poultry science}, volume = {85}, number = {12}, pages = {2106-2111}, doi = {10.1093/ps/85.12.2106}, pmid = {17135664}, issn = {0032-5791}, mesh = {*Animal Feed ; Animal Nutritional Physiological Phenomena ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacitracin/pharmacology ; Chickens/*microbiology ; Coccidiostats/pharmacology ; Diet/*veterinary ; *Dietary Supplements ; Eimeria/*physiology ; Gastrointestinal Tract/*drug effects/*microbiology ; Monensin/pharmacology ; Oils, Volatile/pharmacology ; Salicylates/pharmacology ; }, abstract = {Evaluation of digestive microbial ecology is necessary to understand effects of growth-promoting feed. In the current study, the dynamics of intestinal microbial communities (MC) were examined in broilers fed diets supplemented with a combination of antibiotic (bacitracin methylene disalicylate) and ionophore (Coban 60), and diets containing 1 of 2 essential oil (EO) blends, Crina Poultry (CP) and Crina Alternate (CA). Five treatments were analyzed: 1) unmedicated uninfected control; 2) unmedicated infected control; 3) feed additives monensin (bacitracin methylene disalicylate) + monensin (Coban 60; AI); 4) EO blend CP; and 5) EO blend CA. Additives were mixed into a basal feed mixture, and EO were adjusted to 100 ppm. Chicks were infected by oral gavage at 19 d of age with Eimeria acervulina, Eimeria maxima, and Eimeria tenella. Duodenal, ileal, and cecal samples were taken from 12 birds per treatment just before and 7 d after challenge; 2 samples each were pooled to give a final number of 6 samples total; and all pooled samples were frozen until used for DNA extraction. Denaturing gradient gel electrophoresis was used to examine PCR-amplified fragments of the bacterial 16S ribosomal DNA variable region. Results are presented as percentages of similarity coefficients (SC). Dendrograms of PCR amplicon or band patterns indicated MC differences due to intestinal location, feed additives, and cocci challenge. Essential oil blends CP and CA affected MC in all gut sections. Each EO had different effects over MC, and they differed in most instances from the AI group. The cocci challenge caused drastic MC population shifts in duodenal, ileal, and cecal sections (36.7, 55.4, and 36.2% SC, respectively). Diets supplemented with CP supported higher SC between pre- and postchallenge MC (89.9, 83.3, and 76.4%) than AI (81.8., 57.4, and 60.0%). We concluded that mixed coccidia challenge caused drastic shifts in MC. These EO blends modulated MC better than AI, avoiding drastic shifts after a mixed challenge.}, }
@article {pmid17127525, year = {2006}, author = {Salyers, A and Shoemaker, NB}, title = {Reservoirs of antibiotic resistance genes.}, journal = {Animal biotechnology}, volume = {17}, number = {2}, pages = {137-146}, doi = {10.1080/10495390600957076}, pmid = {17127525}, issn = {1049-5398}, mesh = {Animal Husbandry ; Animals ; Anti-Bacterial Agents/*therapeutic use ; Bacteria/*drug effects/*genetics/pathogenicity ; Colon/metabolism/*microbiology ; Conjugation, Genetic ; Drug Resistance, Bacterial/*genetics ; Environmental Microbiology ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; }, abstract = {A potential concern about the use of antibiotics in animal husbundary is that, as antibiotic resistant bacteria move from the farm into the human diet, they may pass antibiotic resistance genes to bacteria that normally reside in a the human intestinal tract and from there to bacteria that cause human disease (reservoir hypothesis). In this article various approaches to evaluating the risk of agricultural use of antibiotics are assessed critically. In addition, the potential benefits of applying new technology and using new insights from the field of microbial ecology are explained.}, }
@article {pmid17123128, year = {2007}, author = {Bakermans, C and Tollaksen, SL and Giometti, CS and Wilkerson, C and Tiedje, JM and Thomashow, MF}, title = {Proteomic analysis of Psychrobacter cryohalolentis K5 during growth at subzero temperatures.}, journal = {Extremophiles : life under extreme conditions}, volume = {11}, number = {2}, pages = {343-354}, pmid = {17123128}, issn = {1431-0651}, mesh = {Adaptation, Physiological/*physiology ; Bacterial Proteins/analysis/*metabolism ; Cold Temperature ; Proteome/analysis/*metabolism ; Psychrobacter/growth &amp; development/*metabolism ; }, abstract = {It is crucial to examine the physiological processes of psychrophiles at temperatures below 4 degrees C, particularly to facilitate extrapolation of laboratory results to in situ activity. Using two dimensional electrophoresis, we examined patterns of protein abundance during growth at 16, 4, and -4 degrees C of the eurypsychrophile Psychrobacter cryohalolentis K5 and report the first identification of cold inducible proteins (CIPs) present during growth at subzero temperatures. Growth temperature substantially reprogrammed the proteome; the relative abundance of 303 of the 618 protein spots detected (approximately 31% of the proteins at each growth temperature) varied significantly with temperature. Five CIPs were detected specifically at -4 degrees C; their identities (AtpF, EF-Ts, TolC, Pcryo_1988, and FecA) suggested specific stress on energy production, protein synthesis, and transport during growth at subzero temperatures. The need for continual relief of low-temperature stress on these cellular processes was confirmed via identification of 22 additional CIPs whose abundance increased during growth at -4 degrees C (relative to higher temperatures). Our data suggested that iron may be limiting during growth at subzero temperatures and that a cold-adapted allele was employed at -4 degrees C for transport of iron. In summary, these data suggest that low-temperature stresses continue to intensify as growth temperatures decrease to -4 degrees C.}, }
@article {pmid17117999, year = {2006}, author = {Vervaeren, H and Temmerman, R and Devos, L and Boon, N and Verstraete, W}, title = {Introduction of a boost of Legionella pneumophila into a stagnant-water model by heat treatment.}, journal = {FEMS microbiology ecology}, volume = {58}, number = {3}, pages = {583-592}, doi = {10.1111/j.1574-6941.2006.00181.x}, pmid = {17117999}, issn = {0168-6496}, mesh = {*Biofilms ; Electrophoresis/methods ; Eukaryotic Cells/physiology ; *Hot Temperature ; Legionella pneumophila/*growth &amp; development/*isolation &amp; purification ; *Models, Biological ; Polymerase Chain Reaction ; Pseudomonas putida/growth &amp; development ; *Water Microbiology ; }, abstract = {An environmentally representative stagnant-water model was developed to monitor the growth dynamics of Legionella pneumophila. This model was evaluated for three distinct water treatments: untreated tap water, heat-treated tap water, and heat-treated tap water supplemented with Pseudomonas putida, a known biofilm-forming bacterium. Bringing heat-treated tap water after subsequent cooling into contact with a densely formed untreated biofilm was found to promote the number of L. pneumophila by 4 log units within the biofilm, while the use of untreated water only sustained the L. pneumophila levels. Subsequent colonization of the water phase by L. pneumophila was noticed in the heat-treated stagnant-water models, with concentrations as high as 1 x 10(10) mip gene copies L(-1) stagnant water. Denaturing gradient gel electrophoresis in combination with clustering analysis of the prokaryotic community in the water phase and in the biofilm phase suggests that the different water treatments induced different communities. Moreover, boosts of L. pneumophila arising from heat treatment of water were accompanied by shifts to a more diverse eukaryotic community. Stimulated growth of L. pneumophila after heating of the water may explain the rapid recolonization of L. pneumophila in water systems. These results highlight the need for additional or alternative measures to heat treatment of water in order to prevent or abate potential outbreaks of L. pneumophila.}, }
@article {pmid17115448, year = {2007}, author = {Paungfoo, C and Prasertsan, P and Burrell, PC and Intrasungkha, N and Blackall, LL}, title = {Nitrifying bacterial communities in an aquaculture wastewater treatment system using fluorescence in situ hybridization (FISH), 16S rRNA gene cloning, and phylogenetic analysis.}, journal = {Biotechnology and bioengineering}, volume = {97}, number = {4}, pages = {985-990}, doi = {10.1002/bit.21270}, pmid = {17115448}, issn = {0006-3592}, mesh = {Animals ; *Aquaculture ; *Cloning, Molecular ; *Ecosystem ; *In Situ Hybridization, Fluorescence ; Nitrogen/*metabolism ; Penaeidae ; *Phylogeny ; Proteobacteria/classification/genetics/*metabolism ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; Waste Disposal, Fluid/*methods ; }, abstract = {Aquaculture, especially shrimp farming, has played a major role in the growth of Thailand's economy in recent years, as well as in many South East Asian countries. However, the nutrient discharges from these activities have caused adverse impacts on the quality of the receiving waterways. In particular nitrogenous compounds, which may accumulate in aquaculture ponds, can be toxic to aquatic animals and cause environmental problems such as eutrophication. The mineralization process is well known, but certain aspects of the microbial ecology of nitrifiers, the microorganisms that convert ammonia to nitrate, are poorly understood. A previously reported enrichment of nitrifying bacteria (ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB)) from a shrimp farm inoculated in a sequencing batch reactor (SBR) was studied by molecular methods. The initial identification and partial quantification of the nitrifying bacteria (AOB and NOB) were carried out by fluorescence in situ hybridization (FISH) using previously published 16S rRNA-targeting oligonucleotide probes. The two dominant bacterial groups detected by FISH were from the Cytophaga-Flavobacterium-Bacteroides and Proteobacteria (beta subdivision) phyla. Published FISH probes for Nitrobacter and Nitrospira did not hybridize to any of the bacterial cells. Therefore it is likely that new communities of NOBs, differing from previously reported ones, exist in the enrichments. Molecular genetic techniques (cloning, sequencing, and phylogenetic analysis) targeting the 16S rRNA genes from the nitrifying enrichments were performed to identify putative AOBs and NOBs.}, }
@article {pmid17115104, year = {2006}, author = {Chauhan, A and Williams, HN}, title = {Response of Bdellovibrio and like organisms (BALOs) to the migration of naturally occurring bacteria to chemoattractants.}, journal = {Current microbiology}, volume = {53}, number = {6}, pages = {516-522}, pmid = {17115104}, issn = {0343-8651}, mesh = {Bacteria/classification/drug effects ; *Bacterial Physiological Phenomena ; Bdellovibrio/*physiology ; Biodiversity ; Biomass ; Chemotactic Factors/pharmacology ; *Chemotaxis ; Colony Count, Microbial ; DNA, Ribosomal/genetics ; Ecology ; Ecosystem ; Florida ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; }, abstract = {A dual culture-based and non-culture-based approach was applied to characterize predator bacterial groups in surface water samples collected from Apalachicola Bay, Florida. Chemotaxis drop assays were performed on concentrated samples in an effort to isolate predator bacteria by their chemotactic ability. Yeast extract (YE) and casamino acids (CA) proved to be strong chemoattractants and resulted in three visibly distinct bands; however, dextrose, succinate, pyruvate, and concentrated cells of Vibrio parahaemolyticus P5 as prey did not elicit any response. The three distinct bands from YE and CA were separately collected to identify the chemotactic microbial assemblages. Plaque-forming unit assays from different chemotaxis bands with P5 as prey indicated 5- (CA) to 10-fold (YE) higher numbers of predator bacteria in the outermost chemotactic bands. Polymerase chain reaction-restriction fragment length polymorphism and 16S rDNA sequencing of clones from different chemotaxis bands resulted in identification of Pseudoalteromonas spp., Marinomonas spp., and Vibrio spp., with their numbers inversely proportional to the numbers of predators-i.e., Bdellovibrio spp. and Bacteriovorax spp-in the chemotaxis bands. This study indicates that predatorial bacteria potentially respond to high densities of microbial biomass in aquatic ecosystems and that chemotaxis drop assay may be an alternate culture-independent method to characterize predatorial bacterial guilds from the environment.}, }
@article {pmid17106807, year = {2007}, author = {Jumpponen, A}, title = {Soil fungal communities underneath willow canopies on a primary successional glacier forefront: rDNA sequence results can be affected by primer selection and chimeric data.}, journal = {Microbial ecology}, volume = {53}, number = {2}, pages = {233-246}, pmid = {17106807}, issn = {0095-3628}, mesh = {Artifacts ; *DNA Primers/genetics ; DNA, Fungal/*genetics ; Ecosystem ; Fungi/*classification/genetics ; *Genetic Variation ; Ice Cover/microbiology ; Mycorrhizae ; Plant Roots/microbiology ; Polymerase Chain Reaction/*methods/standards ; RNA, Ribosomal, 18S/*genetics ; Salix/microbiology ; *Soil Microbiology ; Species Specificity ; Symbiosis ; Trees ; }, abstract = {Soil fungal communities underneath willow canopies that had established on the forefront of a receding glacier were analyzed by cloning the polymerase chain reaction (PCR)-amplified partial small subunit (18S) of the ribosomal (rRNA) genes. Congruence between two sets of fungus-specific primers targeting the same gene region was analyzed by comparisons of inferred neighbor-joining topologies. The importance of chimeric sequences was evaluated by Chimera Check (Ribosomal Database Project) and by data reanalyses after omission of potentially chimeric regions at the 5'- and 3'-ends of the cloned amplicons. Diverse communities of fungi representing Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota were detected. Ectomycorrhizal fungi comprised a major component in the early plant communities in primary successional ecosystems, as both primer sets frequently detected basidiomycetes (Russulaceae and Thelephoraceae) forming mycorrhizal symbioses. Various ascomycetes (Ophiostomatales, Pezizales, and Sordariales) of uncertain function dominated the clone libraries amplified from the willow canopy soil with one set of primers, whereas the clone libraries of the amplicons generated with the second primer set were dominated by basidiomycetes. Accordingly, primer bias is an important factor in fungal community analyses using DNA extracted from environmental samples. A large proportion (>30%) of the cloned sequences were concluded to be chimeric based on their changing positions in inferred phylogenies after omission of possibly chimeric data. Many chimeric sequences were positioned basal to existing classes of fungi, suggesting that PCR artifacts may cause frequent discovery of new, higher level taxa (order, class) in direct PCR analyses. Longer extension times during the PCR amplification and a smaller number of PCR cycles are necessary precautions to allow collection of reliable environmental sequence data.}, }
@article {pmid17106806, year = {2007}, author = {Ramette, A and Tiedje, JM}, title = {Biogeography: an emerging cornerstone for understanding prokaryotic diversity, ecology, and evolution.}, journal = {Microbial ecology}, volume = {53}, number = {2}, pages = {197-207}, pmid = {17106806}, issn = {0095-3628}, mesh = {*Archaea/classification/physiology ; *Bacteria/classification/isolation &amp; purification ; Bacterial Physiological Phenomena ; Biodiversity ; Communicable Diseases/epidemiology/microbiology ; Disease Outbreaks ; Evolution, Molecular ; Genome, Bacterial ; Geography ; }, abstract = {New questions about microbial ecology and diversity combined with significant improvement in the resolving power of molecular tools have helped the reemergence of the field of prokaryotic biogeography. Here, we show that biogeography may constitute a cornerstone approach to study diversity patterns at different taxonomic levels in the prokaryotic world. Fundamental processes leading to the formation of biogeographic patterns are examined in an evolutionary and ecological context. Based on different evolutionary scenarios, biogeographic patterns are thus posited to consist of dramatic range expansion or regression events that would be the results of evolutionary and ecological forces at play at the genotype level. The deterministic or random nature of those underlying processes is, however, questioned in light of recent surveys. Such scenarios led us to predict the existence of particular genes whose presence or polymorphism would be associated with cosmopolitan taxa. Furthermore, several conceptual and methodological pitfalls that could hamper future developments of the field are identified, and future approaches and new lines of investigation are suggested.}, }
@article {pmid17099228, year = {2007}, author = {Loy, A and Maixner, F and Wagner, M and Horn, M}, title = {probeBase--an online resource for rRNA-targeted oligonucleotide probes: new features 2007.}, journal = {Nucleic acids research}, volume = {35}, number = {Database issue}, pages = {D800-4}, pmid = {17099228}, issn = {1362-4962}, support = {P 18836/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bacteria/classification/genetics ; *Databases, Nucleic Acid ; Internet ; Oligonucleotide Array Sequence Analysis ; *Oligonucleotide Probes ; Phylogeny ; RNA, Ribosomal/classification/*genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Software ; User-Computer Interface ; }, abstract = {probeBase is a curated database of annotated rRNA-targeted oligonucleotide probes and supporting information. Rapid access to probe, microarray and reference data is achieved by powerful search tools and via different lists that are based on selected categories such as functional or taxonomic properties of the target organism(s) or the hybridization format (fluorescence in situ hybridization or microarray) in which the probes were applied. Additional information on probe coverage and specificity is available through direct submissions of probe sequences from probeBase to RDP-II and Greengenes, two major rRNA sequence databases. A freely editable user comments field for each probe entry allows any user to add, modify or remove information or to report errors in real-time. probeBase entries increased from 700 to more than 1200 during the past three years. Several options for submission of single probes or entire probe sets, even prior to publication of newly developed probes, should further contribute to keeping probeBase an up-to-date and useful resource. probeBase is freely accessible at http://www.microbial-ecology.net/probebase. Email correspondence can be addressed to probebase@microbial-ecology.net.}, }
@article {pmid17098906, year = {2007}, author = {Cruz-García, C and Murray, AE and Klappenbach, JA and Stewart, V and Tiedje, JM}, title = {Respiratory nitrate ammonification by Shewanella oneidensis MR-1.}, journal = {Journal of bacteriology}, volume = {189}, number = {2}, pages = {656-662}, pmid = {17098906}, issn = {0021-9193}, support = {R01 GM036877/GM/NIGMS NIH HHS/United States ; GM036877/GM/NIGMS NIH HHS/United States ; }, mesh = {Ammonia/*metabolism ; Anaerobiosis ; Genome, Bacterial ; Mutation ; Nitrate Reductase/genetics/metabolism ; Nitrates/*metabolism ; Nitrites/*metabolism ; Oxidation-Reduction ; Shewanella/genetics/*metabolism ; Time Factors ; }, abstract = {Anaerobic cultures of Shewanella oneidensis MR-1 grown with nitrate as the sole electron acceptor exhibited sequential reduction of nitrate to nitrite and then to ammonium. Little dinitrogen and nitrous oxide were detected, and no growth occurred on nitrous oxide. A mutant with the napA gene encoding periplasmic nitrate reductase deleted could not respire or assimilate nitrate and did not express nitrate reductase activity, confirming that the NapA enzyme is the sole nitrate reductase. Hence, S. oneidensis MR-1 conducts respiratory nitrate ammonification, also termed dissimilatory nitrate reduction to ammonium, but not respiratory denitrification.}, }
@article {pmid17093871, year = {2007}, author = {Almeida, MA and Cunha, MA and Dias, JM}, title = {Bacterial productivity distribution during a rainy year in an estuarine system.}, journal = {Microbial ecology}, volume = {53}, number = {2}, pages = {208-220}, pmid = {17093871}, issn = {0095-3628}, mesh = {Bacteria/classification/growth &amp; development/*isolation &amp; purification ; Fresh Water/*microbiology ; Portugal ; *Rain ; Species Specificity ; *Water Microbiology ; }, abstract = {Bacterial density and productivity were investigated along four salinity gradients within the estuary Ria de Aveiro. Bacterial variables and environmental parameters were measured at three to four stations spanning the entire salinity gradient of the four channels. The rather high variation in bacterial productivity (0.16-7.6 microg C L(-1) h(-1)) along the profiles of salinity indicates that bacterial activity shows a reactive behavior to environmental changing. Bacterial density (0.5-11.2 x 10(9) cells L(-1)) with a comparative smaller variation showed a more conservative behavior, mainly reflecting the phytoplankton distribution. Contrary to expectation, minimal values of bacterial productivity were not observed in November-December but in June. In fact, in November-December, the deep zone near the mouth showed the highest values of bacterial activity. At the upper stations, the highest values were observed in October. The relatively high values of bacterial production during the cold rainy season suggest that allochthonous substrates leached out from the surroundings by rain controlled the distribution of bacterial activity in the estuarine system. The substantial decrease in salinity during the rainy season negatively affected bacterial productivity, namely in the marine zone, where water column was highly stratified. Salinity seems to play an indirect role in the regulation of estuarine bacteria because there are different bacterial communities adapted to a wide salinity range.}, }
@article {pmid17091583, year = {2006}, author = {Zavarzin, GA}, title = {[Vinogradskiĭ and modern microbiology].}, journal = {Mikrobiologiia}, volume = {75}, number = {5}, pages = {581-592}, pmid = {17091583}, issn = {0026-3656}, mesh = {Adaptation, Physiological ; Bacteria/classification/isolation &amp; purification/metabolism ; Bacterial Physiological Phenomena ; *Ecology ; Environmental Microbiology ; History, 19th Century ; History, 20th Century ; Inorganic Chemicals/metabolism ; Microbiology/*history/trends ; Research Design ; Substrate Specificity ; }, abstract = {The 150th anniversary of the birth of Sergei N. Winogradsky is a special date for general microbiology. Apart from the discovery of chemosynthesis, the development of the elective method, the application of the direct method, and formulation of microbial ecology problems, Winogradsky, in his pioneering studies, addressed fundamental aspects of the naturalistic Weltanschauung from the position of a microbiologist who studies the role of microorganisms in nature. These problems are still important today. Expanding knowledge throws light on them from different angles of view and highlights them with varying degrees of completeness, but the problems remain beyond time. It may be useful for contemporary microbiologists to realize the extent to which they would recognize their own work in the system of questions and answers stated a hundred years ago.}, }
@article {pmid17090583, year = {2007}, author = {Cole, JR and Chai, B and Farris, RJ and Wang, Q and Kulam-Syed-Mohideen, AS and McGarrell, DM and Bandela, AM and Cardenas, E and Garrity, GM and Tiedje, JM}, title = {The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data.}, journal = {Nucleic acids research}, volume = {35}, number = {Database issue}, pages = {D169-72}, pmid = {17090583}, issn = {1362-4962}, mesh = {*Databases, Nucleic Acid ; Internet ; Quality Control ; RNA, Ribosomal/*chemistry ; Sequence Analysis, RNA/standards ; User-Computer Interface ; }, abstract = {Substantial new features have been implemented at the Ribosomal Database Project in response to the increased importance of high-throughput rRNA sequence analysis in microbial ecology and related disciplines. The most important changes include quality analysis, including chimera detection, for all available rRNA sequences and the introduction of myRDP Space, a new web component designed to help researchers place their own data in context with the RDP's data. In addition, new video tutorials describe how to use RDP features. Details about RDP data and analytical functions can be found at the RDP-II website (http://rdp.cme.msu.edu/).}, }
@article {pmid17088382, year = {2006}, author = {Rooney, D and Kennedy, N and Deering, L and Gleeson, D and Clipson, N}, title = {Effect of sheep urine deposition on the bacterial community structure in an acidic upland grassland soil.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {11}, pages = {7231-7237}, pmid = {17088382}, issn = {0099-2240}, mesh = {Agrostis/*growth &amp; development ; Animals ; Bacteria/classification/*drug effects/genetics/growth &amp; development ; DNA, Bacterial/analysis ; DNA, Ribosomal Spacer/analysis ; *Ecosystem ; Hydrogen-Ion Concentration ; Lolium/*growth &amp; development ; *Sheep ; Soil/analysis ; *Soil Microbiology ; Species Specificity ; Urine/*chemistry ; }, abstract = {The effect of the addition of synthetic sheep urine (SSU) and plant species on the bacterial community composition of upland acidic grasslands was studied using a microcosm approach. Low, medium, and high concentrations of SSU were applied to pots containing plant species typical of both unimproved (Agrostis capillaris) and agriculturally improved (Lolium perenne) grasslands, and harvests were carried out 10 days and 50 days after the addition of SSU. SSU application significantly increased both soil pH (P < 0.005), with pH values ranging from pH 5.4 (zero SSU) to pH 6.4 (high SSU), and microbial activity (P < 0.005), with treatment with medium and high levels of SSU displaying significantly higher microbial activity (triphenylformazan dehydrogenase activity) than treatment of soil with zero or low concentrations of SSU. Microbial biomass, however, was not significantly altered by any of the SSU applications. Plant species alone had no effect on microbial biomass or activity. Bacterial community structure was profiled using bacterial automated ribosomal intergenic spacer analysis. Multidimensional scaling plots indicated that applications of high concentrations of SSU significantly altered the bacterial community composition in the presence of plant species but at different times: 10 days after application of high concentrations of SSU, the bacterial community composition of L. perenne-planted soils differed significantly from those of any other soils, whereas in the case of A. capillaris-planted soils, the bacterial community composition was different 50 days after treatment with high concentrations of SSU. Canonical correspondence analysis also highlighted the importance of interactions between SSU addition, plant species, and time in the bacterial community structure. This study has shown that the response of plants and bacterial communities to sheep urine deposition in grasslands is dependent on both the grass species present and the concentration of SSU applied, which may have important ecological consequences for agricultural grasslands.}, }
@article {pmid17082998, year = {2006}, author = {Robertson, LJ and Gjerde, BK}, title = {Fate of Cryptosporidium oocysts and Giardia cysts in the Norwegian aquatic environment over winter.}, journal = {Microbial ecology}, volume = {52}, number = {4}, pages = {597-602}, pmid = {17082998}, issn = {0095-3628}, mesh = {Animals ; Cryptosporidium/*growth &amp; development/metabolism ; Fresh Water/parasitology ; Giardia/*growth &amp; development/metabolism ; Norway ; Oocysts/*growth &amp; development/metabolism ; Seasons ; Temperature ; Water Pollutants/analysis ; }, abstract = {We investigated the survival of Cryptosporidium oocysts and Giardia cysts during winter in an aquatic environment (approximate temperature measurements between 1 and 7 degrees C) in Norway, using morphology and uptake of dyes as indicators of viability. Previous research has shown that in the terrestrial environment, shear forces caused by freeze and thaw cycles probably cause the parasites to be inactivated. Such forces occurred infrequently in the aquatic environment, as freezing of the water around the parasites was not observed during the study period (although freezing of the water surface did occur). The rate of decline in viability (log(10) N (t)/N (0)) was similar in control and experimental environments for both parasites; no Cryptosporidium oocysts with viable morphology were detected after approximately 20 weeks and no Giardia cysts with apparently viable morphology could be detected after 1 month. These results suggest that infection with these parasites in Norway is not usually from transmission stages that have over-wintered in the Norwegian environment.}, }
@article {pmid17082997, year = {2006}, author = {Francoeur, SN and Schaecher, M and Neely, RK and Kuehn, KA}, title = {Periphytic photosynthetic stimulation of extracellular enzyme activity in aquatic microbial communities associated with decaying typha litter.}, journal = {Microbial ecology}, volume = {52}, number = {4}, pages = {662-669}, pmid = {17082997}, issn = {0095-3628}, mesh = {Bacteria/growth &amp; development/metabolism ; Biomass ; Ecosystem ; Enzyme Activation/radiation effects ; Eukaryota/growth &amp; development/*physiology ; Extracellular Space/enzymology ; Fungi/growth &amp; development/metabolism ; Light ; Michigan ; Phosphoric Monoester Hydrolases/metabolism ; Photosynthesis/*physiology/radiation effects ; Typhaceae/*microbiology ; Wetlands ; beta-Glucosidase/metabolism ; }, abstract = {We examined the effect of light on extracellular enzyme activities of periphytic/endogenous microbial assemblages associated with decomposing litter of an emergent macrophyte Typha angustifolia within a small inland wetland in southeastern Michigan. Standing-dead Typha leaf litter was collected, placed into floating wire mesh litter baskets, and submerged in a wetland pool. Enzyme saturation assays were conducted on three occasions following litter submergence (days 9, 28, and 44) to generate saturation curves for the individual enzymes tested and to examine potential differences in enzyme saturation kinetics during microbial colonization and development. Experimental light manipulations were conducted on two occasions during microbial development (days 10 and 29). Short-term (30 min) light exposure significantly increased extracellular beta-glucosidase activity of litter-associated microbial communities. Activities of beta-xylosidase and leucine-aminopeptidase were not stimulated, and stimulation of phosphatase activity was variable. The exact mechanism for increased enzyme activity remains unknown, but it may have been increased pH arising from periphytic algal photosynthesis. These results suggest that extracellular enzyme activity in microbial communities colonizing natural organic substrata may be influenced by light/photosynthesis, as has previously been demonstrated for periphyton communities grown on artificial, inert substrata. Thus, light/photosynthetic mediated stimulation of extracellular enzyme activities may be a common occurrence in microbial communities associated with natural decaying plant litter in wetlands and might engender diurnal patterns in other microbial decay processes (e.g., production, organic matter decomposition, and mineralization).}, }
@article {pmid17075734, year = {2006}, author = {Marulanda, A and Barea, JM and Azcón, R}, title = {An indigenous drought-tolerant strain of Glomus intraradices associated with a native bacterium improves water transport and root development in Retama sphaerocarpa.}, journal = {Microbial ecology}, volume = {52}, number = {4}, pages = {670-678}, pmid = {17075734}, issn = {0095-3628}, mesh = {Bacillus/growth &amp; development/*physiology ; Biological Transport/physiology ; Fabaceae/growth &amp; development/metabolism/*microbiology ; Mycorrhizae/growth &amp; development/*physiology ; Plant Roots/growth &amp; development/metabolism/*microbiology ; Plant Transpiration/physiology ; Soil Microbiology ; Water/metabolism ; }, abstract = {The effects of interactions between Bacillus thuringiensis, a drought-adapted bacterium, and two isolates of Glomus intraradices, an arbuscular mycorrhizal (AM) fungus, on Retama sphaerocarpa, a drought-adapted legume, were investigated. The fungal isolates were an indigenous drought-tolerant and a nonindigenous drought-sensitive isolate. Shoot length and root growth, symbiotic parameters, water transport (in terms of percent relative plant water uptake), and volumetric soil moisture and soil enzymatic activities in response to microbial inoculations were evaluated. Retama plants colonized by G. intraradices plus Bacillus possessed similar shoot length after 30 days from sowing compared with noninoculated Retama plants after 150 days. Inoculation with drought-adapted bacterium increased root growth by 201%, but maximum root development was obtained by co-inoculation of B. thuringiensis and the indigenous G. intraradices. Nodules were formed only in plants colonized by autochthonous AM fungi. Relative water uptake was higher in inoculated than in noninoculated Retama plants, and these inoculants depleted soil water content concomitantly. G. intraradices-colonized Retama reached similar shoot length irrespective of the fungal origin, but there were strong differences in relative water uptake by plants colonized by each one of the fungi. Indigenous G. intraradices-colonized roots (evaluated as functional alkaline phosphatase staining) showed the highest intensity and arbuscule richness when associated with B. thuringiensis. The interactive microbial effects on Retama plants were more relevant when indigenous microorganisms were involved. Co-inoculation of autochthonous microorganisms reduced by 42% the water required to produce 1 mg of shoot biomass. This is the first evidence of the effectiveness of rhizosphere bacterium, singly or associated with AM fungus, in increasing plant water uptake, which represents a positive microbial effect on plants grown under drought environments.}, }
@article {pmid17075733, year = {2006}, author = {Cook, KL and Garland, JL and Layton, AC and Dionisi, HM and Levine, LH and Sayler, GS}, title = {Effect of microbial species richness on community stability and community function in a model plant-based wastewater processing system.}, journal = {Microbial ecology}, volume = {52}, number = {4}, pages = {725-737}, pmid = {17075733}, issn = {0095-3628}, mesh = {Bacteria/genetics/*growth &amp; development ; Biodiversity ; DNA, Ribosomal/genetics ; Environmental Microbiology ; Plants/*microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Sewage/*microbiology ; Waste Disposal, Fluid/*methods ; }, abstract = {Microorganisms will be an integral part of biologically based waste processing systems used for water purification or nutrient recycling on long-term space missions planned by the National Aeronautics and Space Administration. In this study, the function and stability of microbial inocula of different diversities were evaluated after inoculation into plant-based waste processing systems. The microbial inocula were from a constructed community of plant rhizosphere-associated bacteria and a complexity gradient of communities derived from industrial wastewater treatment plant-activated sludge. Community stability and community function were defined as the ability of the community to resist invasion by a competitor (Pseudomonas fluorescens 5RL) and the ability to degrade surfactant, respectively. Carbon source utilization was evaluated by measuring surfactant degradation and through Biolog and BD oxygen biosensor community level physiological profiling. Community profiles were obtained from a 16S-23S rDNA intergenic spacer region array. A wastewater treatment plant-derived community with the greatest species richness was the least susceptible to invasion and was able to degrade surfactant to a greater extent than the other complexity gradient communities. All communities resisted invasion by a competitor to a greater extent than the plant rhizosphere isolate constructed community. However, the constructed community degraded surfactant to a greater extent than any of the other communities and utilized the same number of carbon sources as many of the other communities. These results demonstrate that community function (carbon source utilization) and community stability (resistance to invasion) are a function of the structural composition of the community irrespective of species richness or functional richness.}, }
@article {pmid17075732, year = {2007}, author = {Säwström, C and Anesio, MA and Granéli, W and Laybourn-Parry, J}, title = {Seasonal viral loop dynamics in two large ultraoligotrophic Antarctic freshwater lakes.}, journal = {Microbial ecology}, volume = {53}, number = {1}, pages = {1-11}, pmid = {17075732}, issn = {0095-3628}, mesh = {Animals ; Antarctic Regions ; Bacteria/growth &amp; development/isolation &amp; purification/*virology ; Bacteriolysis ; Bacteriophages/growth &amp; development/isolation &amp; purification/*physiology ; Carbon/metabolism ; Ecosystem ; Eukaryota/physiology ; Fresh Water/chemistry/microbiology/*virology ; Lysogeny ; *Seasons ; }, abstract = {The effect of viruses on the microbial loop, with particular emphasis on bacteria, was investigated over an annual cycle in 2003-2004 in Lake Druzhby and Crooked Lake, two large ultraoligotrophic freshwater lakes in the Vestfold Hills, Eastern Antarctica. Viral abundance ranged from 0.16 to 1.56 x 10(9) particles L-1 and bacterial abundances ranged from 0.10 to 0.24 x 10(9) cells L-1, with the lowest bacterial abundances noted in the winter months. Virus-to-bacteria ratios (VBR) were consistently low in both lakes throughout the season, ranging from 1.2 to 8.4. lysogenic bacteria, determined by induction with mitomycin C, were detected on three sampling occasions out of 10 in both lakes. In Lake Druzhby and Crooked Lake, lysogenic bacteria made up between 18% and 73% of the total bacteria population during the lysogenic events. Bacterial production ranged from 8.2 to 304.9 x 10(6) cells L-1 day-1 and lytic viral production ranged from 47.5 to 718.4 x 10(6) viruslike particles L-1 day-1. When only considering primary production, heterotrophic nanoflagellate (HNF) grazing and viral lysis as the major contributors to the DOC pool (i.e., autochthonous sources), we estimated a high contribution from viruses during the winter months when >60% of the carbon supplied to the DOC pool originated from viral lysis. In contrast, during the summer <20% originated from viral lysis. Our study shows that viral process in ultraoligotrophic Antarctic lakes may be of quantitative significance with respect to carbon flow especially during the dark winter period.}, }
@article {pmid17072680, year = {2006}, author = {Stabili, L and Gravili, C and Piraino, S and Boero, F and Alifano, P}, title = {Vibrio harveyi associated with Aglaophenia octodonta (Hydrozoa, Cnidaria).}, journal = {Microbial ecology}, volume = {52}, number = {4}, pages = {603-608}, pmid = {17072680}, issn = {0095-3628}, mesh = {Animals ; DNA, Ribosomal/analysis/genetics ; Geography ; Hydrozoa/cytology/growth &amp; development/*microbiology ; Indian Ocean ; Phylogeny ; Vibrio/cytology/genetics/*growth &amp; development ; }, abstract = {A previously unknown association between a luminous bacterium, Vibrio harveyi, and a benthic hydrozoan, Aglaophenia octodonta, is described. Aglaophenia hydrocladia showed a clear fluorescence in the folds along the hydrocaulus and at the base of the hydrotheca, suggesting the presence of luminous bacteria. This hypothesis was confirmed by isolation of luminous bacteria from Aglaophenia homogenates. Phenotypic characterization of bacterial isolates was performed by several morphological, biochemical, and cultural tests, completed with 16S rDNA sequence analysis. All the isolates were referred to a single species: V. harveyi. The association between V. harveyi and A. octodonta has epidemiological as well as ecological significance. Therefore, A. octodonta may function as habitat "islands" providing a unique set of environmental conditions for luminous bacteria colonization, quite different from those already recorded from the plankton for other Vibrio species.}, }
@article {pmid17072679, year = {2006}, author = {Stibal, M and Sabacká, M and Kastovská, K}, title = {Microbial communities on glacier surfaces in Svalbard: impact of physical and chemical properties on abundance and structure of cyanobacteria and algae.}, journal = {Microbial ecology}, volume = {52}, number = {4}, pages = {644-654}, pmid = {17072679}, issn = {0095-3628}, mesh = {Cyanobacteria/*growth &amp; development ; Ecosystem ; Environmental Microbiology ; Eukaryota/*growth &amp; development ; Geography ; Geologic Sediments/microbiology ; Ice Cover/*microbiology ; Svalbard ; }, abstract = {Microbial communities occurring in three types of supraglacial habitats--cryoconite holes, medial moraines, and supraglacial kames--at several glaciers in the Arctic archipelago of Svalbard were investigated. Abundance, biovolume, and community structure were evaluated by using epifluorescence microscopy and culturing methods. Particular emphasis was laid on distinctions in the chemical and physical properties of the supraglacial habitats and their relation to the microbial communities, and quantitative multivariate analyses were used to assess potential relationships. Varying pH (4.8 in cryoconite; 8.5 in a moraine) and texture (the proportion of coarse fraction 2% of dry weight in cryoconite; 99% dw in a kame) were found, and rather low concentrations of organic matter (0.3% of dry weight in a kame; 22% dw in cryoconite) and nutrients (nitrogen up to 0.4% dw, phosphorus up to 0.8% dw) were determined in the samples. In cryoconite sediment, the highest numbers of bacteria, cyanobacteria, and algae were found, whereas relatively low microbial abundances were recorded in moraines and kames. Cyanobacterial cells were significantly more abundant than microalgal ones in cryoconite and supraglacial kames. Different species of the cyanobacterial genus Leptolyngbya were by far the most represented in all samples, and cyanobacteria of the genera Phormidium and Nostoc prevailed in cultures isolated from cryoconite samples. These species are considered opportunistic organisms with wide ecological valency and strong colonizing potential rather than glacial specialists. Statistical analyses suggest that fine sediment with higher water content is the most suitable condition for bacteria, cyanobacteria, and algae. Also, a positive impact of lower pH on microbial growth was found. The fate of a microbial cell deposited on the glacier surface seems therefore predetermined by the physical and chemical factors such as texture of sediment and water content rather than spatial factors or the origin of sediment.}, }
@article {pmid17072678, year = {2006}, author = {Cao, Y and Cherr, GN and Córdova-Kreylos, AL and Fan, TW and Green, PG and Higashi, RM and Lamontagne, MG and Scow, KM and Vines, CA and Yuan, J and Holden, PA}, title = {Relationships between sediment microbial communities and pollutants in two California salt marshes.}, journal = {Microbial ecology}, volume = {52}, number = {4}, pages = {619-633}, pmid = {17072678}, issn = {0095-3628}, mesh = {Animals ; California ; *Ecosystem ; Embryo, Nonmammalian/drug effects/embryology ; Fatty Acids/analysis ; Geography ; Geologic Sediments/*microbiology ; Multivariate Analysis ; Phospholipids/chemistry ; Plants/metabolism ; Polymorphism, Restriction Fragment Length ; Sea Urchins/embryology ; Soil Pollutants/analysis ; *Wetlands ; }, abstract = {Salt marshes are important ecosystems whose plant and microbial communities can alter terrestrially derived pollutants prior to coastal water discharge. However, knowledge regarding relationships between anthropogenic pollutant levels and salt marsh microbial communities is limited, and salt marshes on the West Coast of the United States are rarely examined. In this study, we investigated the relationships between microbial community composition and 24 pollutants (20 metals and 4 organics) in two California salt marshes. Multivariate ordination techniques were used to assess how bacterial community composition, as determined by terminal restriction fragment length polymorphism and phospholipid fatty acid analyses, was related to pollution. Sea urchin embryo toxicity measurements and plant tissue metabolite profiles were considered two other biometrics of pollution. Spatial effects were strongly manifested across marshes and across channel elevations within marshes. Utilizing partial canonical correspondence analysis, an ordination technique new to microbial ecology, we found that several metals were strongly associated with microbial community composition after accounting for spatial effects. The major patterns in plant metabolite profiles were consistent with patterns across microbial community profiles, but sea urchin embryo assays, which are commonly used to evaluate ecological toxicity, had no identifiable relationships with pollution. Whereas salt marshes are generally dynamic and complex habitats, microbial communities in these marshes appear to be relatively sensitive indicators of toxic pollutants.}, }
@article {pmid17072677, year = {2007}, author = {Neufeld, JD and Dumont, MG and Vohra, J and Murrell, JC}, title = {Methodological considerations for the use of stable isotope probing in microbial ecology.}, journal = {Microbial ecology}, volume = {53}, number = {3}, pages = {435-442}, pmid = {17072677}, issn = {0095-3628}, mesh = {Biodiversity ; Carbon Isotopes ; DNA/analysis/isolation &amp; purification ; *Environmental Microbiology ; Fatty Acids/analysis ; Isotope Labeling/*methods ; RNA/analysis ; Sensitivity and Specificity ; }, abstract = {Stable isotope probing (SIP) is a method used for labeling uncultivated microorganisms in environmental samples or directly in field studies using substrate enriched with stable isotope (e.g., (13)C). After consumption of the substrate, the cells of microorganisms that consumed the substrate become enriched in the isotope. Labeled biomarkers, such as phospholipid-derived fatty acid (PLFA), ribosomal RNA, and DNA can be analyzed with a range of molecular and analytical techniques, and used to identify and characterize the organisms that incorporated the substrate. The advantages and disadvantages of PLFA-SIP, RNA-SIP, and DNA-SIP are presented. Using examples from our laboratory and from the literature, we discuss important methodological considerations for a successful SIP experiment.}, }
@article {pmid17071787, year = {2007}, author = {Case, RJ and Boucher, Y and Dahllöf, I and Holmström, C and Doolittle, WF and Kjelleberg, S}, title = {Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies.}, journal = {Applied and environmental microbiology}, volume = {73}, number = {1}, pages = {278-288}, pmid = {17071787}, issn = {0099-2240}, mesh = {Bacteria/*classification/genetics/growth &amp; development ; Base Sequence ; DNA-Directed RNA Polymerases/*genetics ; Ecology/methods ; *Ecosystem ; Evolution, Molecular ; Genes, rRNA ; *Genetic Markers ; Genetic Variation ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {Several characteristics of the 16S rRNA gene, such as its essential function, ubiquity, and evolutionary properties, have allowed it to become the most commonly used molecular marker in microbial ecology. However, one fact that has been overlooked is that multiple copies of this gene are often present in a given bacterium. These intragenomic copies can differ in sequence, leading to identification of multiple ribotypes for a single organism. To evaluate the impact of such intragenomic heterogeneity on the performance of the 16S rRNA gene as a molecular marker, we compared its phylogenetic and evolutionary characteristics to those of the single-copy gene rpoB. Full-length gene sequences and gene fragments commonly used for denaturing gradient gel electrophoresis were compared at various taxonomic levels. Heterogeneity found between intragenomic 16S rRNA gene copies was concentrated in specific regions of rRNA secondary structure. Such "heterogeneity hot spots" occurred within all gene fragments commonly used in molecular microbial ecology. This intragenomic heterogeneity influenced 16S rRNA gene tree topology, phylogenetic resolution, and operational taxonomic unit estimates at the species level or below. rpoB provided comparable phylogenetic resolution to that of the 16S rRNA gene at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution. This is particularly relevant in the context of a growing number of studies focusing on subspecies diversity, in which single-copy protein-encoding genes such as rpoB could complement the information provided by the 16S rRNA gene.}, }
@article {pmid17064753, year = {2006}, author = {Scully, C and Collins, G and O'Flaherty, V}, title = {Anaerobic biological treatment of phenol at 9.5-15 degrees C in an expanded granular sludge bed (EGSB)-based bioreactor.}, journal = {Water research}, volume = {40}, number = {20}, pages = {3737-3744}, doi = {10.1016/j.watres.2006.08.023}, pmid = {17064753}, issn = {0043-1354}, mesh = {Bacteria, Anaerobic/metabolism ; Biodegradation, Environmental ; Bioreactors ; Methane/biosynthesis ; Phenol/*metabolism/toxicity ; Sewage ; Waste Disposal, Fluid/*methods ; Water Pollutants, Chemical/*metabolism/toxicity ; }, abstract = {The aims of this study were to demonstrate the (1) feasibility of psychrophilic, or low-temperature, anaerobic digestion (PAD) of phenolic wastewaters at 10-15 degrees C; (2) economic attractiveness of PAD for the treatment of phenol as measured by daily biogas yields and (3) impact on bioreactor performance of phenol loading rates (PLRs) in excess of those previously documented (1.2 kg phenol m(-3)d(-1)). Two expanded granular sludge bed (EGSB)-based bioreactors, R1 and R2, were employed to mineralise a volatile fatty acid-based wastewater. R2 influent wastewater was supplemented with phenol at an initial concentration of 500 mgl(-1) (PLR, 1 kgm(-3)d(-1)). Reactor performance was measured by chemical oxygen demand (COD) removal efficiency, CH(4) composition of biogas and phenol removal (R2 only). Specific methanogenic activity, biodegradability and toxicity assays were employed to monitor the physiological capacity of reactor biomass samples. The applied PLR was increased to 2 kgm(-3)d(-1) on day 147 and phenol removal by day 415 was 99% efficient, with 4 mgl(-1) present in R2 effluent. The operational temperature of R1 (control) and R2 was reduced by stepwise decrements from 15 degrees C through to a final operating temperature of 9.5 degrees C. COD removal efficiencies of c. 90% were recorded in both bioreactors at the conclusion of the trial (day 673), when the phenol concentration in R2 effluent was below 30 mgl(-1). Daily biogas yields were determined during the final (9.5 degrees C) operating period, when typical daily R2 CH4 yields of c. 3.3lCH4g(-1) COD(removed) d(-1) were recorded. The rate of phenol depletion and methanation by R2 biomass by day 673 were 68 mg phenol gVSS(-1)d(-1) and 12-20 ml CH(4) gVSS(-1)d(-1), respectively.}, }
@article {pmid17064260, year = {2006}, author = {Laverman, AM and Van Cappellen, P and van Rotterdam-Los, D and Pallud, C and Abell, J}, title = {Potential rates and pathways of microbial nitrate reduction in coastal sediments.}, journal = {FEMS microbiology ecology}, volume = {58}, number = {2}, pages = {179-192}, doi = {10.1111/j.1574-6941.2006.00155.x}, pmid = {17064260}, issn = {0168-6496}, mesh = {Bacteria/*metabolism ; Belgium ; Bioreactors ; Geologic Sediments/*microbiology ; Netherlands ; Nitrates/*metabolism ; North Sea ; Oxidation-Reduction ; Quaternary Ammonium Compounds/metabolism ; Seawater/microbiology ; Temperature ; }, abstract = {Nitrate reduction plays a key role in the biogeochemical dynamics and microbial ecology of coastal sediments. Potential rates of nitrate reduction were measured on undisturbed sediment slices from two eutrophic coastal environments using flow-through reactors (FTR). Maximum potential nitrate reduction rates ranged over an order of magnitude, with values of up to 933 nmol cm(-3) h(-1), whereas affinity constants for NO(3) (-) fell mostly between 200 and 600 microM. Homogenized sediment slurries systematically yielded higher rates of nitrate reduction than the FTR experiments. Dentrification was the major nitrate removal pathway in the sediments, although excess ammonium production indicated a contribution of dissimilatory nitrate reduction to ammonium under nitrate-limiting conditions.}, }
@article {pmid17064259, year = {2006}, author = {Roeselers, G and Zippel, B and Staal, M and van Loosdrecht, M and Muyzer, G}, title = {On the reproducibility of microcosm experiments - different community composition in parallel phototrophic biofilm microcosms.}, journal = {FEMS microbiology ecology}, volume = {58}, number = {2}, pages = {169-178}, doi = {10.1111/j.1574-6941.2006.00172.x}, pmid = {17064259}, issn = {0168-6496}, mesh = {Biofilms/*growth &amp; development ; Cluster Analysis ; Cyanobacteria/*classification/genetics/*physiology ; DNA Fingerprinting ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Electrophoresis, Polyacrylamide Gel/methods ; Light ; Molecular Sequence Data ; Nucleic Acid Denaturation ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {Phototrophic biofilms were cultivated simultaneously using the same inoculum in three identical flow-lane microcosms located in different laboratories. The growth rates of the biofilms were similar in the different microcosms, but denaturing gradient gel electrophoresis (DGGE) analysis of both 16S and 18S rRNA gene fragments showed that the communities developed differently in terms of species richness and community composition. One microcosm was dominated by Microcoleus and Phormidium species, the second microcosm was dominated by Synechocystis and Phormidium species, and the third microcosm was dominated by Microcoleus- and Planktothrix- affiliated species. No clear effect of light intensity on the cyanobacterial community composition was observed. In addition, DGGE profiles obtained from the cultivated biofilms showed a low resemblance with the profiles derived from the inoculum. These findings demonstrate that validation of reproducibility is essential for the use of microcosm systems in microbial ecology studies.}, }
@article {pmid17062412, year = {2006}, author = {Konstantinidis, KT and Ramette, A and Tiedje, JM}, title = {The bacterial species definition in the genomic era.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {361}, number = {1475}, pages = {1929-1940}, pmid = {17062412}, issn = {0962-8436}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Classification/*methods ; Genes, Bacterial/genetics ; *Genetic Speciation ; *Phylogeny ; Species Specificity ; *Terminology as Topic ; }, abstract = {The bacterial species definition, despite its eminent practical significance for identification, diagnosis, quarantine and diversity surveys, remains a very difficult issue to advance. Genomics now offers novel insights into intra-species diversity and the potential for emergence of a more soundly based system. Although we share the excitement, we argue that it is premature for a universal change to the definition because current knowledge is based on too few phylogenetic groups and too few samples of natural populations. Our analysis of five important bacterial groups suggests, however, that more stringent standards for species may be justifiable when a solid understanding of gene content and ecological distinctiveness becomes available. Our analysis also reveals what is actually encompassed in a species according to the current standards, in terms of whole-genome sequence and gene-content diversity, and shows that this does not correspond to coherent clusters for the environmental Burkholderia and Shewanella genera examined. In contrast, the obligatory pathogens, which have a very restricted ecological niche, do exhibit clusters. Therefore, the idea of biologically meaningful clusters of diversity that applies to most eukaryotes may not be universally applicable in the microbial world, or if such clusters exist, they may be found at different levels of distinction.}, }
@article {pmid17061212, year = {2006}, author = {Schmidt, TM}, title = {The maturing of microbial ecology.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {9}, number = {3}, pages = {217-223}, pmid = {17061212}, issn = {1139-6709}, mesh = {Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Biodiversity ; Biological Evolution ; *Ecology/education/trends ; Ecosystem ; *Microbiology/education/trends ; Seawater/microbiology ; Soil Microbiology ; Water Microbiology ; }, abstract = {A.J. Kluyver and C.B. van Niel introduced many scientists to the exceptional metabolic capacity of microbes and their remarkable ability to adapt to changing environments in The Microbe's Contribution to Biology. Beyond providing an overview of the physiology and adaptability of microbes, the book outlined many of the basic principles for the emerging discipline of microbial ecology. While the study of pure cultures was highlighted, provided a unifying framework for understanding the vast metabolic potential of microbes and their roles in the global cycling of elements, extrapolation from pure cultures to natural environments has often been overshadowed by microbiologists inability to culture many of the microbes seen in natural environments. A combination of genomic approaches is now providing a culture-independent view of the microbial world, revealing a more diverse and dynamic community of microbes than originally anticipated. As methods for determining the diversity of microbial communities become increasingly accessible, a major challenge to microbial ecologists is to link the structure of natural microbial communities with their functions. This article presents several examples from studies of aquatic and terrestrial microbial communities in which culture and culture-independent methods are providing an enhanced appreciation for the microbe's contribution to the evolution and maintenance of life on Earth, and offers some thoughts about the graduate-level educational programs needed to enhance the maturing field of microbial ecology.}, }
@article {pmid17061209, year = {2006}, author = {Pedrós-Alió, C}, title = {Genomics and marine microbial ecology.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {9}, number = {3}, pages = {191-197}, pmid = {17061209}, issn = {1139-6709}, mesh = {Bacteria/*genetics/isolation &amp; purification/metabolism ; *Bacterial Physiological Phenomena ; Ecology ; *Ecosystem ; *Genomics ; Rhodopsin/genetics ; Rhodopsins, Microbial ; Seawater/*microbiology ; }, abstract = {Genomics has brought about a revolution in all fields of biology. Before the development of microbial ecology in the 1970s, microbes were not even considered in marine ecological studies. Today we know that half of the total primary production of the planet must be credited to microorganisms. This and other discoveries have changed dramatically the perspective and the focus of marine microbial ecology. The application of genomics-based approaches has provided new challenges and has allowed the discovery of novel functions, an appreciation of the great diversity of microorganisms, and the introduction of controversial ideas regarding the concepts of species, genome, and niche. Nevertheless, thorough knowledge of the traditional disciplines of biology is necessary to explore the possibilities arising from these new insights. This work reviews the different genomic techniques that can be applied to marine microbial ecology, including both sequencing of the complete genomes of microorganisms and metagenomics, which, in turn, can be complemented with the study of mRNAs (transcriptomics) and proteins (proteomics). The example of proteorhodopsin illustrates the type of information that can be gained from these approaches. A genomics perspective constitutes a map that will allow microbiologists to focus their research on potentially more productive aspects.}, }
@article {pmid17061172, year = {2006}, author = {Waldrop, MP and Firestone, MK}, title = {Response of microbial community composition and function to soil climate change.}, journal = {Microbial ecology}, volume = {52}, number = {4}, pages = {716-724}, pmid = {17061172}, issn = {0095-3628}, mesh = {Bacteria/growth &amp; development/metabolism ; California ; Carbon/metabolism ; *Climate ; Ecosystem ; Fatty Acids/metabolism ; Fungi/growth &amp; development/metabolism ; Principal Component Analysis ; Soil/*analysis ; *Soil Microbiology ; Temperature ; Time Factors ; Water/metabolism ; }, abstract = {Soil microbial communities mediate critical ecosystem carbon and nutrient cycles. How microbial communities will respond to changes in vegetation and climate, however, are not well understood. We reciprocally transplanted soil cores from under oak canopies and adjacent open grasslands in a California oak-grassland ecosystem to determine how microbial communities respond to changes in the soil environment and the potential consequences for the cycling of carbon. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid analysis (PLFA), microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups by quantifying (13)C uptake from a universal substrate (pyruvate) into PLFA biomarkers. Soil in the open grassland experienced higher maximum temperatures and lower soil water content than soil under the oak canopies. Soil microbial communities in soil under oak canopies were more sensitive to environmental change than those in adjacent soil from the open grassland. Oak canopy soil communities changed rapidly when cores were transplanted into the open grassland soil environment, but grassland soil communities did not change when transplanted into the oak canopy environment. Similarly, microbial biomass, enzyme activities, and microbial respiration decreased when microbial communities were transplanted from the oak canopy soils to the grassland environment, but not when the grassland communities were transplanted to the oak canopy environment. These data support the hypothesis that microbial community composition and function is altered when microbes are exposed to new extremes in environmental conditions; that is, environmental conditions outside of their "life history" envelopes.}, }
@article {pmid17056799, year = {2006}, author = {Ye, Z and Renouf, M and Lee, SO and Hauck, CC and Murphy, PA and Hendrich, S}, title = {High urinary isoflavone excretion phenotype decreases plasma cholesterol in golden Syrian hamsters fed soy protein.}, journal = {The Journal of nutrition}, volume = {136}, number = {11}, pages = {2773-2778}, doi = {10.1093/jn/136.11.2773}, pmid = {17056799}, issn = {0022-3166}, mesh = {Animals ; Cholesterol/*blood ; Cholesterol, HDL/blood ; Cricetinae ; Female ; Genistein/urine ; Isoflavones/*urine ; Mesocricetus ; Phenotype ; Soybean Proteins/*pharmacology ; Triglycerides/blood ; }, abstract = {Apparent absorption of isoflavones varies greatly among individuals but is relatively stable within an individual. We hypothesized that high urinary isoflavone excreters would show less plasma non-HDL cholesterol (non-HDL-C) than low isoflavone excreters after soy protein feeding. Fifty Golden Syrian hamsters were fed a high-fat/casein diet (n = 10) or a high-fat/soy protein diet (n = 40) for 4 wk. We identified 2 distinct urinary isoflavone excretion phenotypes based upon HPLC analysis of urinary glycitein using a pairwise correlation plots analysis, or based upon total urinary isoflavone using a hierarchical cluster test. High isoflavone excreters showed greater urinary isoflavones (P < 0.05) than did low isoflavone excreters at wk 1 and 4. The low urinary glycitein excretion phenotype was more stable than the high urinary glycitein excretion phenotype by McNemar's test. High urinary isoflavone excreters had significantly less non-HDL-C than did the low isoflavone excreters or casein-fed controls (P < 0.05). Plasma total and non-HDL-C were negatively correlated with urinary daidzein, glycitein, and total isoflavone excretion (r = -0.45 to -0.58, P < 0.05). Urinary isoflavone excretion phenotypes predicted the cholesterol-lowering efficacy of soy protein. Isoflavone absorbability, probably due to gut microbial ecology, is an important controllable variable in studies of effects of soy protein on blood lipids.}, }
@article {pmid17051413, year = {2006}, author = {Bottari, B and Ercolini, D and Gatti, M and Neviani, E}, title = {Application of FISH technology for microbiological analysis: current state and prospects.}, journal = {Applied microbiology and biotechnology}, volume = {73}, number = {3}, pages = {485-494}, doi = {10.1007/s00253-006-0615-z}, pmid = {17051413}, issn = {0175-7598}, mesh = {Bacteria ; *Bacterial Typing Techniques ; Biofilms ; Food Microbiology ; In Situ Hybridization, Fluorescence/*methods ; *Molecular Probe Techniques ; *Oligonucleotide Probes ; RNA, Bacterial/genetics ; RNA, Ribosomal/genetics ; }, abstract = {In order to identify and quantify the microorganisms present in a certain ecosystem, it has become necessary to develop molecular methods avoiding cultivation, which allows to characterize only the countable part of the microorganisms in the sample, therefore losing the information related to the microbial component which presents a vitality condition, although it cannot duplicate in culture medium. In this context, one of the most used techniques is fluorescence in situ hybridization (FISH) with ribosomal RNA targeted oligonucleotide probes. Owing to its speed and sensitivity, this technique is considered a powerful tool for phylogenetic, ecological, diagnostic and environmental studies in microbiology. Through the use of species-specific probes, it is possible to identify different microorganisms in complex microbial communities, thus providing a solid support to the understanding of inter-species interaction. The knowledge of the composition and distribution of microorganisms in natural habitats can be interesting for ecological reasons in microbial ecology, and for safety and technological aspects in food microbiology. Methodological aspects, use of different probes and applications of FISH to microbial ecosystems are presented in this review.}, }
@article {pmid17049583, year = {2006}, author = {Boult, S and Hand, VL and Vaughan, DJ}, title = {Microbial controls on metal mobility under the low nutrient fluxes found throughout the subsurface.}, journal = {The Science of the total environment}, volume = {372}, number = {1}, pages = {299-305}, doi = {10.1016/j.scitotenv.2006.08.043}, pmid = {17049583}, issn = {0048-9697}, mesh = {Colony Count, Microbial ; Copper/*analysis ; Polysaccharides/metabolism ; *Water Microbiology ; Water Movements ; Water Pollutants, Chemical/*analysis ; *Water Supply ; }, abstract = {Laboratory simulations and field studies of the shallow subsurface have shown that microbes and their extracellular products can influence the mobility of toxic metals from waste disposal sites. Modelling the transport of contaminants in groundwater may, therefore, require the input of microbial ecology data in addition to geochemical data, thus increasing the costs and the uncertainty of predictions. However, whether microbial effects on contaminant mobility occur extensively in the natural subsurface is unknown because the conditions under which they have been observed hitherto are generally unrepresentative of the average subsurface environment. Here, we show that microbial activity affects the mobility of a toxic trace metal (Cu) under the relatively low nutrient fluxes that dominate subsurface systems. More particularly, we show that under these low nutrient conditions, microbes and microbial products can immobilize metal but may themselves be subject to subsequent mobilization, thus complicating the pattern of metal storage and release. Our results show that the capability of microbes in the subsurface to change both the capacity of porous media to store metal, and the behaviour of metal that is released, is not restricted to the well researched environments close to sites of waste disposal. We anticipate our simulations will be a starting point for generating input data for transport models, and specifying the mechanism of metal remobilisation in environments more representative of the subsurface generally.}, }
@article {pmid17035671, year = {2006}, author = {Barnett, ML}, title = {The rationale for the daily use of an antimicrobial mouthrinse.}, journal = {Journal of the American Dental Association (1939)}, volume = {137 Suppl}, number = {}, pages = {16S-21S}, doi = {10.14219/jada.archive.2006.0408}, pmid = {17035671}, issn = {0002-8177}, mesh = {Clinical Trials as Topic ; Dental Plaque/complications/*prevention &amp; control ; Gingivitis/etiology/*prevention &amp; control ; Humans ; Mouth Mucosa/microbiology ; Mouthwashes/*administration &amp; dosage ; Periodontitis/etiology/*prevention &amp; control ; }, abstract = {BACKGROUND: This article reviews the rationale for incorporating effective antimicrobial mouthrinses into a daily oral hygiene regimen along with mechanical plaque control methods.<br><br>TYPES OF STUDIES REVIEWED: The author reviewed studies demonstrating the essential etiologic role of a pathogenic dental plaque biofilm in the development of gingivitis, as well as studies indicating that most people fail to maintain a level of mechanical plaque control sufficient to prevent disease. In addition, he did a brief review of studies of oral microbial ecology that identified the oral mucosal tissues as a reservoir of bacteria that colonize tooth surfaces, and he summarized six-month clinical studies of marketed antimicrobial mouthrinse ingredients and products.<br><br>CONCLUSIONS: There is a twofold rationale for daily use of antimicrobial mouthrinses: first, given the inadequacy of mechanical plaque control by the majority of people, as a component added to oral hygiene regimens for the control and prevention of periodontal diseases; second, as a method of delivering antimicrobial agents to mucosal sites throughout the mouth that harbor pathogenic bacteria capable of recolonizing supragingival and subgingival tooth surfaces, thereby providing a complementary mechanism of plaque control. The efficacy of several mouthrinse ingredients and products is supported by published six-month clinical trials.<br><br>CLINICAL IMPLICATIONS: The daily use of an effective antiplaque/antigingivitis antimicrobial mouthrinse is well-supported by a scientific rationale and can be a valuable component of oral hygiene regimens.}, }
@article {pmid17033880, year = {2006}, author = {De Windt, W and Boon, N and Van den Bulcke, J and Rubberecht, L and Prata, F and Mast, J and Hennebel, T and Verstraete, W}, title = {Biological control of the size and reactivity of catalytic Pd(0) produced by Shewanella oneidensis.}, journal = {Antonie van Leeuwenhoek}, volume = {90}, number = {4}, pages = {377-389}, doi = {10.1007/s10482-006-9088-4}, pmid = {17033880}, issn = {0003-6072}, mesh = {Biodegradation, Environmental ; Biomass ; Catalysis ; Crystallization ; Environmental Pollutants/metabolism ; Hydrophobic and Hydrophilic Interactions ; Microbial Viability ; Nanoparticles/chemistry ; Palladium/*chemistry/*metabolism/toxicity ; Polychlorinated Biphenyls/metabolism ; Shewanella/cytology/drug effects/*metabolism ; }, abstract = {The interaction between Shewanella oneidensis MR-1 and the soluble metal Pd(II) during the reductive precipitation of Pd(0) determined the size and properties of the precipitated Pd(0) nanoparticles. Assessment of cell viability indicated that the bioreduction of Pd(II) was a detoxification mechanism depending on the Pd(II) concentration and on the presence and properties of the electron donor. The addition of H(2) in the headspace allowed S. oneidensis to resist the toxic effects of Pd(II). Interestingly, 25 mM formate was a less effective electron donor for bioreductive detoxification of Pd(II), since there was a 2 log reduction of culturable cells and a 20% decrease of viable cells within 60 min, followed by a slow recovery. When the ratio of Pd:cell dry weight (CDW) was below 5:2 at a concentration of 50 mg l(-1) Pd(II), most of the cells remained viable. These viable cells precipitated Pd(0) crystals over a relatively larger bacterial surface area and had a particle area that was up to 100 times smaller when compared to Pd(0) crystals formed on non-viable biomass (Pd:CDW ratio of 5:2). The relatively large and densely covering Pd(0) crystals on non-viable biomass exhibited high catalytic reactivity towards hydrophobic molecules such as polychlorinated biphenyls, while the smaller and more dispersed nanocrystals on a viable bacterial carrier exhibited high catalytic reactivity towards the reductive degradation of the anionic pollutant perchlorate.}, }
@article {pmid17033856, year = {2006}, author = {Löhr, AJ and Laverman, AM and Braster, M and van Straalen, NM and Röling, WF}, title = {Microbial communities in the world's largest acidic volcanic lake, Kawah Ijen in Indonesia, and in the Banyupahit river originating from it.}, journal = {Microbial ecology}, volume = {52}, number = {4}, pages = {609-618}, pmid = {17033856}, issn = {0095-3628}, mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; Biodiversity ; Cluster Analysis ; Eukaryotic Cells/classification/metabolism ; Fresh Water/microbiology ; Geography ; Hydrogen-Ion Concentration ; Indonesia ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Rivers ; Sequence Analysis, DNA ; Volcanic Eruptions ; *Water Microbiology ; }, abstract = {A first study was made on the microbial community composition of the Indonesian crater lake Kawah Ijen (pH < 0.3) and the Banyupahit-Banyuputih river (pH 0.4-3.5) originating from it. Culture-independent, rRNA gene-based denaturing gradient gel electrophoresis was used to profile microbial communities in this natural and ancient, extremely acidic environment. Similarity in community profiles of the different sampling locations was low, indicating heterogeneity in community composition. Archaea were present at all sampling locations; archaeal diversity was low at the most acidic locations and increased at pH >2.6. Bacteria were not detected in the water column of the crater lake, but were found at all locations along the acidic river. Bacterial diversity increased with increasing pH. Eukarya were only present at pH >2.6. Retrieved rRNA gene sequences of Bacteria and Archaea were not closely related to known acidophilic species. It is concluded that tolerance to extreme acidity in this system is developed most extensively among Archaea. The acidity gradient of the Banyupahit-Banyuputih river has a clear effect on microbial community composition and biodiversity.}, }
@article {pmid17030797, year = {2006}, author = {Chain, PS and Denef, VJ and Konstantinidis, KT and Vergez, LM and Agulló, L and Reyes, VL and Hauser, L and Córdova, M and Gómez, L and González, M and Land, M and Lao, V and Larimer, F and LiPuma, JJ and Mahenthiralingam, E and Malfatti, SA and Marx, CJ and Parnell, JJ and Ramette, A and Richardson, P and Seeger, M and Smith, D and Spilker, T and Sul, WJ and Tsoi, TV and Ulrich, LE and Zhulin, IB and Tiedje, JM}, title = {Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {42}, pages = {15280-15287}, pmid = {17030797}, issn = {0027-8424}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; P42 ES 04911-12/ES/NIEHS NIH HHS/United States ; }, mesh = {Burkholderia/chemistry/*genetics/metabolism/pathogenicity ; Chromosomes, Bacterial ; Evolution, Molecular ; Gene Expression Profiling ; *Genome, Bacterial ; Molecular Structure ; Oligonucleotide Array Sequence Analysis ; *Replicon ; }, abstract = {Burkholderia xenovorans LB400 (LB400), a well studied, effective polychlorinated biphenyl-degrader, has one of the two largest known bacterial genomes and is the first nonpathogenic Burkholderia isolate sequenced. From an evolutionary perspective, we find significant differences in functional specialization between the three replicons of LB400, as well as a more relaxed selective pressure for genes located on the two smaller vs. the largest replicon. High genomic plasticity, diversity, and specialization within the Burkholderia genus are exemplified by the conservation of only 44% of the genes between LB400 and Burkholderia cepacia complex strain 383. Even among four B. xenovorans strains, genome size varies from 7.4 to 9.73 Mbp. The latter is largely explained by our findings that >20% of the LB400 sequence was recently acquired by means of lateral gene transfer. Although a range of genetic factors associated with in vivo survival and intercellular interactions are present, these genetic factors are likely related to niche breadth rather than determinants of pathogenicity. The presence of at least eleven "central aromatic" and twenty "peripheral aromatic" pathways in LB400, among the highest in any sequenced bacterial genome, supports this hypothesis. Finally, in addition to the experimentally observed redundancy in benzoate degradation and formaldehyde oxidation pathways, the fact that 17.6% of proteins have a better LB400 paralog than an ortholog in a different genome highlights the importance of gene duplication and repeated acquirement, which, coupled with their divergence, raises questions regarding the role of paralogs and potential functional redundancies in large-genome microbes.}, }
@article {pmid17021238, year = {2006}, author = {Penton, CR and Devol, AH and Tiedje, JM}, title = {Molecular evidence for the broad distribution of anaerobic ammonium-oxidizing bacteria in freshwater and marine sediments.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {10}, pages = {6829-6832}, pmid = {17021238}, issn = {0099-2240}, mesh = {Bacteria, Anaerobic/*isolation &amp; purification/metabolism ; Fresh Water/microbiology ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Quaternary Ammonium Compounds/*metabolism ; RNA, Ribosomal, 16S ; Seawater/microbiology ; *Water Microbiology ; }, abstract = {Previously available primer sets for detecting anaerobic ammonium-oxidizing (anammox) bacteria are inefficient, resulting in a very limited database of such sequences, which limits knowledge of their ecology. To overcome this limitation, we designed a new primer set that was 100% specific in the recovery of approximately 700-bp 16S rRNA gene sequences with >96% homology to the "Candidatus Scalindua" group of anammox bacteria, and we detected this group at all sites studied, including a variety of freshwater and marine sediments and permafrost soil. A second primer set was designed that exhibited greater efficiency than previous primers in recovering full-length (1,380-bp) sequences related to "Ca. Scalindua," "Candidatus Brocadia," and "Candidatus Kuenenia." This study provides evidence for the widespread distribution of anammox bacteria in that it detected closely related anammox 16S rRNA gene sequences in 11 geographically and biogeochemically diverse freshwater and marine sediments.}, }
@article {pmid17021230, year = {2006}, author = {Schloss, PD and Handelsman, J}, title = {Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {10}, pages = {6773-6779}, pmid = {17021230}, issn = {0099-2240}, mesh = {*Biodiversity ; Classification ; *Ecology ; Ecosystem ; Environmental Microbiology ; Nuclear Family ; *Software ; }, abstract = {The recent advent of tools enabling statistical inferences to be drawn from comparisons of microbial communities has enabled the focus of microbial ecology to move from characterizing biodiversity to describing the distribution of that biodiversity. Although statistical tools have been developed to compare community structures across a phylogenetic tree, we lack tools to compare the memberships and structures of two communities at a particular operational taxonomic unit (OTU) definition. Furthermore, current tests of community structure do not indicate the similarity of the communities but only report the probability of a statistical hypothesis. Here we present a computer program, SONS, which implements nonparametric estimators for the fraction and richness of OTUs shared between two communities.}, }
@article {pmid17021212, year = {2006}, author = {Parnell, JJ and Park, J and Denef, V and Tsoi, T and Hashsham, S and Quensen, J and Tiedje, JM}, title = {Coping with polychlorinated biphenyl (PCB) toxicity: Physiological and genome-wide responses of Burkholderia xenovorans LB400 to PCB-mediated stress.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {10}, pages = {6607-6614}, pmid = {17021212}, issn = {0099-2240}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; P42 ES 04911-12/ES/NIEHS NIH HHS/United States ; }, mesh = {Aroclors/pharmacology ; Biodegradation, Environmental ; Burkholderia/cytology/*drug effects/physiology ; Environmental Pollutants/metabolism/*pharmacology ; Gene Expression/drug effects ; Genome, Bacterial/*physiology ; Polychlorinated Biphenyls/metabolism/*pharmacology ; }, abstract = {The biodegradation of polychlorinated biphenyls (PCBs) relies on the ability of aerobic microorganisms such as Burkholderia xenovorans sp. LB400 to tolerate two potential modes of toxicity presented by PCB degradation: passive toxicity, as hydrophobic PCBs potentially disrupt membrane and protein function, and degradation-dependent toxicity from intermediates of incomplete degradation. We monitored the physiological characteristics and genome-wide expression patterns of LB400 in response to the presence of Aroclor 1242 (500 ppm) under low expression of the structural biphenyl pathway (succinate and benzoate growth) and under induction by biphenyl. We found no inhibition of growth or change in fatty acid profile due to PCBs under nondegrading conditions. Moreover, we observed no differential gene expression due to PCBs themselves. However, PCBs did have a slight effect on the biosurface area of LB400 cells and caused slight membrane separation. Upon activation of the biphenyl pathway, we found growth inhibition from PCBs beginning after exponential-phase growth suggestive of the accumulation of toxic compounds. Genome-wide expression profiling revealed 47 differentially expressed genes (0.56% of all genes) under these conditions. The biphenyl and catechol pathways were induced as expected, but the quinoprotein methanol metabolic pathway and a putative chloroacetaldehyde dehydrogenase were also highly expressed. As the latter protein is essential to conversion of toxic metabolites in dichloroethane degradation, it may play a similar role in the degradation of chlorinated aliphatic compounds resulting from PCB degradation.}, }
@article {pmid17018406, year = {2006}, author = {Ovez, S and Ors, C and Murat, S and Orhon, D}, title = {Effect of hypochloride on microbial ecology of bulking and foaming activated sludge treatment for tannery wastewater.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances &amp; environmental engineering}, volume = {41}, number = {10}, pages = {2163-2174}, doi = {10.1080/10934520600867813}, pmid = {17018406}, issn = {1093-4529}, mesh = {Actinobacteria/*drug effects/growth &amp; development ; Environmental Monitoring ; Environmental Restoration and Remediation ; Gordonia Bacterium/drug effects/growth &amp; development ; Hypochlorous Acid/*pharmacology ; *Industrial Waste ; Sewage/*microbiology ; *Tanning ; Turkey ; Waste Disposal, Fluid/methods ; *Water Purification/methods ; }, abstract = {This study investigates the effect of hypochloride application for controlling bulking and foaming on the microbial ecology of an activated sludge system treating tannery wastewater. Detailed characterization of the wastewater treatment influent and effluent is also reported for the study period. During the study, bulking and foaming are first monitored with a sudden burst in the sludge volume index over 250 mL g(-1), creating a significant deterioration of the effluent quality. The corresponding upset in the microbial ecology is the combined excessive proliferation of M. parvicella, N. limicola II and Gordona (Nocardia) spp., but mainly triggered by Gordona contamination of the floc structure and the rapid outward growth of this filamentous microorganism extending to adjacent flocs. Chlorine application at an average rate of 3 g Cl(-1)(kg MLSS.day)(-1) for 12 days provide an effective solution for bulking and foaming, restoring the effluent quality. It destroys filamentous texture between the flocs, leaving only a lot of loose and chopped filament fragments and, totally removes the Gordona spp. from solution which retrieves back into the flocs. Therefore, chlorine remediation of bulking and foaming, although temporarily effective, is only superficial as the Gordona seeding inside the floc remains intact and potentially available for excessive growth in the next favorable conditions.}, }
@article {pmid17013554, year = {2006}, author = {Gadanho, M and Libkind, D and Sampaio, JP}, title = {Yeast diversity in the extreme acidic environments of the Iberian Pyrite Belt.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {552-563}, pmid = {17013554}, issn = {0095-3628}, mesh = {*Biodiversity ; Colony Count, Microbial ; Cryptococcus/classification/growth &amp; development/isolation &amp; purification ; DNA, Fungal/*genetics ; DNA, Ribosomal/genetics ; Ecosystem ; Hydrogen-Ion Concentration ; Iron/chemistry ; Mining ; *Phylogeny ; Portugal ; Spain ; Sulfides/chemistry ; *Water Microbiology ; Yeasts/*classification/growth &amp; development/isolation &amp; purification ; }, abstract = {In the Iberian Pyrite Belt (IPB), acid rock drainage gives rise to aquatic habitats with low pH and high concentrations of heavy metals, a situation that causes important environmental problems. We investigated the occurrence and diversity of yeasts in two localities of the IPB: São Domingos (Portugal) and Rio Tinto (Spain). Yeast isolation was performed on conventional culture media (MYP), acidified (pH 3) media (MYP3), and on media prepared with water from the study sites (MYPw). The main goal of the study was to determine the structure of the yeast community; a combination of molecular methods was used for accurate species identifications. Our results showed that the largest fraction of the yeast community was recovered on MYPw rather than on MYP and MYP3. Twenty-seven yeast species were detected, 48% of which might represent undescribed taxa. Among these, an undescribed species of the genus Cryptococcus required low pH for growth, a property that has not been observed before in yeasts. The communities of S. Domingos and R. Tinto showed a considerable resemblance, and eight yeast species were simultaneously found in both localities. Taking into consideration the physicochemical parameters studied, we propose a hierarchic organization of the yeast community in terms of high-, intermediate-, or low-stress conditions of the environment. According to this ranking, the acidophile yeast Cryptococcus sp. 5 is considered the most tolerant species, followed by Cryptococcus sp. 3 and Lecytophora sp. Species occurring in situations of intermediate environmental stress were Candida fluviatilis, Rhodosporidium toruloides, Williopsis californica, and three unidentified yeasts belonging to Rhodotorula and Cryptococcus.}, }
@article {pmid17013553, year = {2006}, author = {Nyyssönen, M and Piskonen, R and Itävaara, M}, title = {A targeted real-time PCR assay for studying naphthalene degradation in the environment.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {533-543}, pmid = {17013553}, issn = {0095-3628}, mesh = {Biodegradation, Environmental ; Dioxygenases ; Environmental Monitoring ; Gene Amplification ; Hydroxylation ; Multienzyme Complexes/*genetics/metabolism ; Naphthalenes/*metabolism ; Oxygenases/*genetics/metabolism ; Phylogeny ; Polymerase Chain Reaction/*methods ; Proteobacteria/classification/*enzymology/genetics/metabolism ; Sensitivity and Specificity ; Sequence Alignment ; Soil Microbiology ; Soil Pollutants/metabolism ; Species Specificity ; }, abstract = {A quantitative real-time polymerase chain reaction (PCR) assay was developed for monitoring naphthalene degradation during bioremediation processes. The phylogenetic affiliations of known naphthalene-hydroxylating dioxygenase genes were determined to target functionally related bacteria, and degenerate primers were designed on the basis of the close relationships among dioxygenase genes identified from naphthalene-degrading Proteobacteria. Evaluation of the amplification specificity demonstrated that the developed real-time PCR assay represents a rapid, precise means for the group-specific enumeration of naphthalene-degrading bacteria. According to validation with bacterial pure cultures, the assay discriminated between the targeted group of naphthalene dioxygenase sequences and genes in other naphthalene or aromatic hydrocarbon-degrading bacterial strains. Specific amplification of gene fragments sharing a high sequence similarity with the genes included in the assay design was also observed in soil samples recovered from large-scale remediation processes. The target genes could be quantified reproducibly at over five orders of magnitude down to 3 x 10(2) gene copies. To investigate the suitability of the assay in monitoring naphthalene biodegradation, the assay was applied in enumerating the naphthalene dioxygenase genes in a soil slurry microcosm. The results were in good agreement with contaminant mineralization and dot blot quantification of nahAc gene copies. Furthermore, the real-time PCR assay was found to be more sensitive than hybridization-based analysis.}, }
@article {pmid17007990, year = {2006}, author = {Favre-Bonté, S and Ranjard, L and Champier, L and Cournoyer, B and Nazaret, S}, title = {Distribution and genetic diversity of bacterial thiopurine methyltransferases in soils emitting dimethyl selenide.}, journal = {Biochimie}, volume = {88}, number = {11}, pages = {1573-1581}, doi = {10.1016/j.biochi.2006.09.005}, pmid = {17007990}, issn = {0300-9084}, mesh = {Bacteria/classification/*enzymology/*genetics ; Base Sequence ; France ; *Genetic Variation ; Methyltransferases/*genetics ; Molecular Sequence Data ; Organoselenium Compounds/*analysis ; Phylogeny ; Polymerase Chain Reaction ; Soil/*analysis ; *Soil Microbiology ; }, abstract = {Dimethyl selenide (DMSe) and dimethyl diselenide (DMDSe) emissions by soil samples spiked with selenite or (methyl)selenocysteine, with or without a supplement of nutrient broth and glucose were measured. DMSe was the main form of volatile Se produced, and was observed for both Se-substrates. DMDSe was only emitted from soils spiked with (methyl)selenocysteine. Two bacterial thiopurine methyltransferases (TPMTs), TPMT-I and TPMT-E, have been reported to be involved in DMSe and DMDSe emissions [J. Bacteriol. 184 (2002) 3146; Appl. Environ. Microbiol. 69 (2003) 3784]. To establish if these TPMTs or other members of their gene family could have contributed to the DMSe emissions observed, the diversity of bTPMT gene (tpm) sequences among the soils of this study was investigated. Total DNAs from these soils were extracted and screened using the tpm PTCF2-PTCR2 consensus primers defined to PCR amplify this gene family. The PCR products obtained from two soils were cloned, analysed by PCR-RFLP, and sequenced. Their analysis showed an important diversity of tpm lineages (around 12) in soils. Phylogenetic analysis of the deduced TPMT sequences of these soils revealed lineages not previously recorded in the databases, sequences closely related or identical to freshwater TPMTs, or sequences encoding TPMTs closely related to those of Pseudomonas fragi TPMT-K, Pseudomonas Hsa.28 TPMT-I, or Colwellia psychrerythraea TPMT-Z. Nested PCRs, allowing detection of about 13 distinct tpm soil and freshwater lineages by PTCF2-PTCR2 PCR screenings, were performed on the soil total DNAs. These PCRs confirmed the sequencing data, and allowed to recover lineages not detected by the cloning strategy. These results indicate that soils, like the freshwater samples, harbour TPMT-I gene sequences but may also have distinct tpm lineages. This study further supports our hypothesis that TPMTs contribute to DMSe soil emissions.}, }
@article {pmid17006744, year = {2006}, author = {Van Ryckegem, G and Van Driessche, G and Van Beeumen, JJ and Verbeken, A}, title = {The estimated impact of fungi on nutrient dynamics during decomposition of Phragmites australis leaf sheaths and stems.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {564-574}, pmid = {17006744}, issn = {0095-3628}, mesh = {*Biodegradation, Environmental ; Biomass ; Carbon/metabolism ; Cellulose/metabolism ; Environmental Monitoring ; Fungi/*growth &amp; development/*metabolism ; Lignin/metabolism ; Nitrogen/metabolism ; Phosphorus/metabolism ; Plant Leaves/microbiology ; Plant Stems/microbiology ; Poaceae/*microbiology ; Population Dynamics ; *Soil Microbiology ; }, abstract = {Decomposition of culms (sheaths and stems) of the emergent macrophyte Phragmites australis (common reed) was followed for 16 months in the litter layer of a brackish tidal marsh along the river Scheldt (the Netherlands). Stems and leaf sheaths were separately analyzed for mass loss, litter-associated fungal biomass (ergosterol), nutrient (N and P), and cell wall polymer concentrations (cellulose and lignin). The role of fungal biomass in litter nutrient dynamics was evaluated by estimating nutrient incorporation within the living fungal mass. After 1 year of standing stem decay, substantial fungal colonization was found. This corresponded to an overall fungal biomass of 49 +/- 8.7 mg g(-1) dry mass. A vertical pattern of fungal colonization on stems in the canopy is suggested. The litter bag experiment showed that mass loss of stems was negligible during the first 6 months, whereas leaf sheaths lost almost 50% of their initial mass during that time. Exponential breakdown rates were -0.0039 +/- 0.0004 and -0.0026 +/- 0.0003 day(-1) for leaf sheaths and stems, respectively (excluding the initial lag period). In contrast to the stem tissue--which had no fungal colonization--leaf sheaths were heavily colonized by fungi (93 +/- 10 mg fungal biomass g(-1) dry mass) prior to placement in the litter layer. Once being on the sediment surface, 30% of leaf sheath's associated fungal biomass was lost, but ergosterol concentrations recovered the following months. In the stems, fungal biomass increased steadily after an initial lag period to reach a maximal biomass of about 120 mg fungal biomass g(-1) dry mass for both plant parts at the end of the experiment. Fungal colonizers are considered to contain an important fraction of nutrients within the decaying plant matter. Fungal N incorporation was estimated to be 64 +/- 13 and 102 +/- 15% of total available N pool during decomposition for leaf sheaths and stems, respectively. Fungal P incorporation was estimated to be 37 +/- 9 and 52 +/- 15% of total available P during decomposition for leaf sheaths and stems, respectively. Furthermore, within the stem tissue, fungi are suggested to be active immobilizers of nutrients from the external environment because fungi were often estimated to contain more than 100% of the original nutrient stock.}, }
@article {pmid18636517, year = {1997}, author = {De Heyder, B and Vanrolleghem, P and Van Langenhove, H and Verstraete, W}, title = {Kinetic characterization of mass transfer limited biodegradation of a low water soluble gas in batch experiments--necessity for multiresponse fitting.}, journal = {Biotechnology and bioengineering}, volume = {55}, number = {3}, pages = {511-519}, doi = {10.1002/(SICI)1097-0290(19970805)55:3&lt;511::AID-BIT7&gt;3.0.CO;2-F}, pmid = {18636517}, issn = {0006-3592}, abstract = {A method was developed to characterize the kinetics of biodegradation of low water soluble gaseous compounds in batch experiments. The degradation of ethene by resting Mycobacterium E3 cells was used as a model system. The batch degradation data were recorded as the progress curve (i.e., the time course of the ethene concentration in the headspace of the batch vessel). The recorded progress curves, however, suffered gas:liquid mass transfer limitation. A new multiresponse fitting method had to be developed to allow unequivocal identification of both the affinity coefficient, K(aff), and the gas:liquid mass transfer coefficient, K(l)a, in the batch vessel from the mass transfer limited data. Simulation showed that the K(aff) estimate obtained is influenced by the dimensionless (volumetric basis) ethene gas:liquid partitioning coefficient (H). In the fitting procedure, Monod, Teissier, and Blackman biokinetics were evaluated for characterization of the ethene biodegradation process. The fits obtained reflected the superiority of the Blackman biokinetic function. Overall, it appears that resting Mycobacterium E3 cells metabolizing ethene at 24 degrees C have, using Blackman biokinetics, a maximum specific degradation rate, v(max), of 10.2 nmol C(2)H(4) mg(-1) CDW min(-1), and an affinity coefficient, K(aff.g), expressed in equilibrium gas concentration units, of 61.9 ppm, when H is assumed equal to 8.309.}, }
@article {pmid18576141, year = {1997}, author = {Duncan, K and Levetin, E and Wells, H and Jennings, E and Hettenbach, S and Bailey, S and Lawlor, K and Sublette, K and Berton Fisher, J}, title = {Managed bioremediation of soil contaminated with crude oil soil chemistry and microbial ecology three years later.}, journal = {Applied biochemistry and biotechnology}, volume = {63-65}, number = {}, pages = {879-889}, doi = {10.1007/BF02920484}, pmid = {18576141}, issn = {0273-2289}, abstract = {Analysis of samples taken from three experimental soil lysimeters demonstrated marked long-term effects of managed bioremediation on soil chemistry and on bacterial and fungal communities 3 yr after the application of crude oil or crude oil and fertilizer. The lysimeters were originally used to evaluate the short-term effectiveness of managed (application of fertilizer and water, one lysimeter) vs unmanaged bioremediation (one lysimeter) of Michigan Silurian crude oil compared to one uncontaminated control lysimeter. Three years following the original experiment, five 2-ft-long soil cores were extracted from each lysimeter, each divided into three sections, and the like sections mixed together to form composited soil samples. All subsequent chemical and microbiological analyses were performed on these nine composited samples. Substantial variation was found among the lysimeters for certain soil chemical characteristics (% moisture, pH, total Kjeldahl nitrogen [TKN], ammonia nitrogen [NH4-N], phosphate phosphorous [PO4-P], and sulfate [SO4 (-2)]). The managed lysimeter had 10% the level of total petroleum hydrocarbons (TPH-IR) found in the unmanaged lysimeter. Assessment of the microbial community was performed for heterotropic bacteria, fungi, and aromatic hydrocarbon-degrading bacteria (toluene, naphthalene, and phenanthrene) by dilution onto solid media. There was little difference in the number of heterotrophic bacteria, in contrast to counts of fungi, which were markedly higher in the contaminated lysimeters. Hydrocarbon-degrading bacteria were elevated in both oil-contaminated lysimeters. In terms of particular hydrocarbons as substrates, phenanthrene degraders were greater in number than naphthalene degraders, which outnumbered toluene degraders. Levels of sulfate-reducing bacteria seem to have been stimulated by hydrocarbon degradation.}, }
@article {pmid19277305, year = {1995}, author = {Ko, MP and Bernard, EC and Schmitt, DP and Sipes, BS}, title = {Occurrence of Pasteuria-like Organisms on Selected Plant-Pamsitic Nematodes of Pineapple in the Hawaiian Islands.}, journal = {Journal of nematology}, volume = {27}, number = {3}, pages = {395-408}, pmid = {19277305}, issn = {0022-300X}, abstract = {Soils from 320 sites representing diverse undisturbed habitats from five Hawaiian Islands were assessed for occurrence of Pasteuria-like organisms. Mean annual rainfall at sites ranged from 125-350 cm, elevation from 69-2,286 m, and annual mean temperature from 12-24 C. Seven different natural communities were represented: wet lowland, mesic lowland, wet montane, mesk montane, dry montane, mesic subalpine, and dry alpine. Pasteuria spp. in a soil sample was detected by baiting with infective stages of Helicotylenchus dihystera, Meloidogyne javanica, Pratylenchus brachyurus, and Rotylenchulus reniformis, followed by cultivation of the nematodes on pineapple plants for 10-11 months. All nematode baits except R. reniformis were readily recovered from the soil samples. A sample was considered Pasteuria-positive if at least 5 % of the nematode specimens showed endospore attachment. Thirteen percent of all samples were positive for Pasteuria-like organisms. The frequencies of association between Pasteuria spp. and Meloidogyne, Helicotylenchus, or Pratylenchus species were 52%, 24%, and 24%, respectively. Positive samples were more prevalent on the older islands of Kauai and Oahu (75%), in lowland communities (61%), and in areas with introduced vegetation (60%). More than 27% of the positive samples were associated with plant species in a few selected families that included Meliaceae and Myrtaceae. Occurrence of Pasteuria spp. seemed to be positively associated with mean annual rainfall or temperature, but negatively associated with elevation.}, }
@article {pmid18618800, year = {1994}, author = {De Heyder, B and Overmeire, A and Van Langenhove, H and Verstraete, W}, title = {Ethene removal from a synthetic waste gas using a dry biobed.}, journal = {Biotechnology and bioengineering}, volume = {44}, number = {5}, pages = {642-648}, doi = {10.1002/bit.260440511}, pmid = {18618800}, issn = {0006-3592}, abstract = {A packed granular activated carbon (GAC) biobed, inoculated with the ethane-degrading strain Mycobacterium E3, was used to study ethene removal from a synthetic waste gas. Ethene, for which the dimensionless partition coefficient for an air-water system at 20 degrees C is about 7.6, was used as a model compound for poorly water soluble gaseous pollutants. In a first mode or operation, the GAC biobed was sprinkled intermittently and the waste gas influent was continuously pre-humidified, establishing relatively moist conditions (water content >40% to 45%). A volumetric ethene removal rate of 0.382 kg COD x m(-3) x d(-1) (0.112 kg ethene x m(-3) x d(-1)) was obtained for an influent concentration of 125 ppm, a superficial waste gas velocity of 3.6E-3 m x s(-1) and a pseudo residence time of 45 s. However, in the second mode of operation, omitting the pre-humidification of the waste gas influent and establishing a "dry" biobed (water content <40% to 45%), and thus obtaining better mass transfer to the biofilm, the ethene removal could be doubled for otherwise comparable operating parameters. Furthermore, under decreased wetting and for the given experimental conditions (influent concentration 125 to 816 ppm, waste gas superficial velocity 3.0E-3 m x s(-1), pseudo waste gas residence time 43 s), the ethene removal was not limited by mass transfer of ethene through the water layer covering the biofilm.}, }
@article {pmid18601290, year = {1993}, author = {Criddle, CS}, title = {The kinetics of cometabolism.}, journal = {Biotechnology and bioengineering}, volume = {41}, number = {11}, pages = {1048-1056}, doi = {10.1002/bit.260411107}, pmid = {18601290}, issn = {0006-3592}, abstract = {Experimental observations indicate that the rates of cometabolic transformation are linked to the consumption of growth substrate during growth and to the consumption of cell mass and/or energy substrate in the absence of growth substrate. Three previously proposed models (models 1 through 3) describing the kinetics of cometabolism by resting cells are compared, and the interrelationships and underlying assumptions for these models are explored. Models 1 to 3 are shown to converge at high concentrations of the nongrowth substrate. An expression describing nongrowth substrate transformation in the presence of growth substrate is proposed, and this expression is integrated with an expression for cell growth to give a single unstructured model (model 4) that encompasses models 1 to 3 and describes cometabolism by both resting and growing cells. Model 4 couples transformation of nongrowth substrate to consumption of growth substrate and biomass, and predicts that cometabolism will result, and decreased specific growth rates for a cometabolizing population. Competitive inhibition can also be incorporated in the model. Experimental aspects of model calibration and verification are discussed. The need for models that distinguish between the exhaustion of cell activity and cell death is emphasized.}, }
@article {pmid17741047, year = {1989}, author = {Nealson, KH}, title = {Microbial ecology: microbial mats.}, journal = {Science (New York, N.Y.)}, volume = {244}, number = {4908}, pages = {1095}, doi = {10.1126/science.244.4908.1095}, pmid = {17741047}, issn = {0036-8075}, }
@article {pmid18964604, year = {1988}, author = {de Beer, D and van den Heuvel, JC}, title = {Response of ammonium-selective microelectrodes based on the neutral carrier nonactin.}, journal = {Talanta}, volume = {35}, number = {9}, pages = {728-730}, doi = {10.1016/0039-9140(88)80171-1}, pmid = {18964604}, issn = {0039-9140}, abstract = {Ammonium-selective microelectrodes made with an ion-exchanger based on nonactin and having a tip diameter of 1 mum have been developed. The response of the electrode is linear from 10(-5) to 10(-1)M NH(+)(4) and the response time is 1 min. Applications of these electrodes can be found in biotechnology and microbial ecology, but the low selectivity with respect to K(+) and Na(+) limits their use to low salt environments. Concentration gradients in gels containing cross-linked urease were measured and found to be in accord with macrokinetic measurements.}, }
@article {pmid19290202, year = {1988}, author = {Rodríguez-Kábana, R and Morgan-Jones, G}, title = {Potential for nematode control by mycofloras endemic in the tropics.}, journal = {Journal of nematology}, volume = {20}, number = {2}, pages = {191-203}, pmid = {19290202}, issn = {0022-300X}, abstract = {Results of mycological surveys of root-knot and cyst nematodes from tropical regions indicate that most fungal species associated with females or cysts of species of Globodera, Heterodera, and Meloidogyne are those found with nematodes from temperate areas. Some fungal species, however, were found in higher frequency in tropical regions than in temperate countries; e.g., Cylindrocarpon destructans and Ulocladium atrum were the most common species associated with G. pallida and G. rostochiensis cysts in Peru. These fungi are not so frequent in nematodes from temperate areas. Fungi associated with diseased nematodes in the tropics vary greatly in nutritional requirements and include thermophilic species as well as cold-tolerant fungi. Multi-cropping systems possible in most tropical regions may be designed to increase the frequency of occurrence of microbial species antagonistic to phytonematodes.}, }
@article {pmid19294153, year = {1986}, author = {Rodríguez-Kábana, R}, title = {Organic and inorganic nitrogen amendments to soil as nematode suppressants.}, journal = {Journal of nematology}, volume = {18}, number = {2}, pages = {129-134}, pmid = {19294153}, issn = {0022-300X}, abstract = {Inorganic fertilizers containing ammoniacal nitrogen or formulations releasing this form of N in the soil are most effective for suppressing nematode populations. Anhydrous ammonia has been shown to reduce soil populations of Tylenchorhynchus claytoni, Helicotylenchus dihystera, and Heterodera glycines. The rates required to obtain significant suppression of nematode populations are generally in excess of 150 kg N/ha. Urea also suppresses several nematode species, including Meloidogyne spp., when applied at rates above 300 kg N/ha. Additional available carbon must be provided with urea to permit soil microorganisms to metabolize excess N and avoid phytotoxic effects. There is a direct relation between the amount of "protein" N in organic amendments and their effectiveness as nematode population suppressants. Most nematicidal amendments are oil cakes, or animal excrements containing 2-7% (w:w) N; these materials are effective at rates of 4-10 t/ha. Organic soil amendments containing mucopolysaccharides (e.g., mycelial wastes, chitinous matter) are also effective nematode suppressants.}, }
@article {pmid18548621, year = {1983}, author = {Segers, L and Verstraete, W}, title = {Conversion of organic acids to h(2) by Rhodospirillaceae grown with glutamate or dinitrogen as nitrogen source.}, journal = {Biotechnology and bioengineering}, volume = {25}, number = {12}, pages = {2843-2853}, doi = {10.1002/bit.260251203}, pmid = {18548621}, issn = {0006-3592}, abstract = {Axenic cultures of Rhodopseudomonas capsulata. Rhodospirillum rubrum, and Rhodomicrobium vannielii grown with glutamate as the nitrogen source converted lactate, acetate, and butyrate to H(2) and CO(2). Conversion rates ranged from 100 to 926 mL H(2) L(r) (-1) day(-1) (where L(r) is the reactor contents), and efficiencies varied from 23 to 100% When grown with N(2), conversion rates up to 760 mL H(2) L(r) (-1) day(-1) and efficiencies up to 100%were achieved. Upon aging, cultures appear to rapidly increase in hydrogen uptake activity and furthermore decrease in nitrogenase activity, both factors leading to a slowdown of hydrogen production. This was particularly the case for diazotrophically grown photobacteria.}, }
@article {pmid17790437, year = {1978}, author = {Dworkin, M}, title = {Microbial ecology.}, journal = {Science (New York, N.Y.)}, volume = {201}, number = {4355}, pages = {520}, doi = {10.1126/science.201.4355.520}, pmid = {17790437}, issn = {0036-8075}, }
@article {pmid17741132, year = {1967}, author = {Silver, WS}, title = {Microbial ecology.}, journal = {Science (New York, N.Y.)}, volume = {156}, number = {3772}, pages = {168}, doi = {10.1126/science.156.3772.168-a}, pmid = {17741132}, issn = {0036-8075}, }
@article {pmid17005975, year = {2006}, author = {Te Poele, EM and Kloosterman, H and Hessels, GI and Bolhuis, H and Dijkhuizen, L}, title = {RepAM of the Amycolatopsis methanolica integrative element pMEA300 belongs to a novel class of replication initiator proteins.}, journal = {Microbiology (Reading, England)}, volume = {152}, number = {Pt 10}, pages = {2943-2950}, doi = {10.1099/mic.0.28746-0}, pmid = {17005975}, issn = {1350-0872}, mesh = {Actinomycetales/*enzymology/genetics ; DNA Helicases/genetics/*isolation &amp; purification/*metabolism ; DNA, Bacterial/chemistry/metabolism ; DNA-Binding Proteins/genetics/*isolation &amp; purification/*metabolism ; Nucleic Acid Conformation ; Open Reading Frames ; Protein Binding ; Repetitive Sequences, Nucleic Acid ; Trans-Activators/genetics/*isolation &amp; purification/*metabolism ; }, abstract = {Accessory genetic elements, such as plasmids and integrative elements, are widespread amongst actinomycetes, but little is known about their functions and mode of replication. The conjugative element pMEA300 from Amycolatopsis methanolica is present mostly in an integrated state at a single specific site in the chromosome, but it can also replicate autonomously. Complete nucleotide sequencing, in combination with deletion studies, has revealed that orfB of pMEA300 is essential for autonomous replication in its host. In this study, it was shown that purified OrfB protein binds specifically to the 3' end of its own coding sequence. Within this short sequence, a putative hairpin structure is located, which contains several direct and inverted repeats, and a nucleotide stretch that resembles the nicking site of the pC194 family of rolling circle replicating plasmids. Additional binding studies revealed that OrfB binds to an 8 bp inverted repeat that occurs three times within the hairpin structure. The data presented show that OrfB is the replication initiator (Rep) protein of pMEA300, and is therefore termed RepAM. Surprisingly, RepAM lacks significant sequence similarity with known prokaryotic Rep proteins, but it is highly similar to a number of yet uncharacterized ORFs that are located on integrative and conjugative elements of other actinomycetes. It is concluded that RepAM and its homologues are members of a novel class of Rep proteins.}, }
@article {pmid17005972, year = {2006}, author = {Laue, H and Schenk, A and Li, H and Lambertsen, L and Neu, TR and Molin, S and Ullrich, MS}, title = {Contribution of alginate and levan production to biofilm formation by Pseudomonas syringae.}, journal = {Microbiology (Reading, England)}, volume = {152}, number = {Pt 10}, pages = {2909-2918}, doi = {10.1099/mic.0.28875-0}, pmid = {17005972}, issn = {1350-0872}, mesh = {Alginates/analysis ; Biofilms/*growth &amp; development ; Fluorescence ; Fructans/analysis/*biosynthesis/genetics ; Gene Deletion ; Glucuronic Acid/analysis/biosynthesis/genetics/physiology ; Hexosyltransferases/analysis ; Hexuronic Acids/analysis ; Lectins/metabolism ; Microscopy, Confocal ; Polysaccharides, Bacterial/analysis/biosynthesis/*physiology ; Pseudomonas syringae/genetics/metabolism/*physiology ; Staining and Labeling ; }, abstract = {Exopolysaccharides (EPSs) play important roles in the attachment of bacterial cells to a surface and/or in building and maintaining the three-dimensional, complex structure of bacterial biofilms. To elucidate the spatial distribution and function of the EPSs levan and alginate during biofilm formation, biofilms of Pseudomonas syringae strains with different EPS patterns were compared. The mucoid strain PG4180.muc, which produces levan and alginate, and its levan- and/or alginate-deficient derivatives all formed biofilms in the wells of microtitre plates and in flow chambers. Confocal laser scanning microscopy with fluorescently labelled lectins was applied to investigate the spatial distribution of levan and an additional as yet unknown EPS in flow-chamber biofilms. Concanavalin A (ConA) bound specifically to levan and accumulated in cell-depleted voids in the centres of microcolonies and in blebs. No binding of ConA was observed in biofilms of the levan-deficient mutants or in wild-type biofilms grown in the absence of sucrose as confirmed by an enzyme-linked lectin-sorbent assay using peroxidase-linked ConA. Time-course studies revealed that expression of the levan-forming enzyme, levansucrase, occurred mainly during early exponential growth of both planktonic and sessile cells. Thus, accumulation of levan in biofilm voids hints to a function as a nutrient storage source for later stages of biofilm development. The presence of a third EPS besides levan and alginate was indicated by binding of the lectin from Naja mossambica to a fibrous structure in biofilms of all P. syringae derivatives. Production of the as yet uncharacterized additional EPS might be more important for biofilm formation than the syntheses of levan and alginate.}, }
@article {pmid16999138, year = {2006}, author = {Maes, A and Van Raemdonck, H and Smith, K and Ossieur, W and Lebbe, L and Verstraete, W}, title = {Transport and activity of Desulfitobacterium dichloroeliminans strain DCA1 during bioaugmentation of 1,2-DCA-contaminated groundwater.}, journal = {Environmental science &amp; technology}, volume = {40}, number = {17}, pages = {5544-5552}, doi = {10.1021/es060953i}, pmid = {16999138}, issn = {0013-936X}, mesh = {Chromatography, Gas ; Desulfitobacterium/genetics/*metabolism ; *Environmental Restoration and Remediation ; Ethylene Dichlorides/*metabolism ; Polymerase Chain Reaction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Water Pollutants, Chemical/*metabolism ; }, abstract = {The transport and activity of Desulfitobacterium dichloroeliminans strain DCA1 in 1,2-dichloroethane (1,2-DCA)-contaminated groundwater have been evaluated through an in situ bioaugmentation test at an industrial site (Belgium). The migration of strain DCA1 was monitored from an injection well toward a monitoring well, and the effect of the imposed groundwater flow on its distribution was assessed by means of transport model MOCDENS3D. The results of the real-time PCR (16S rRNA gene) quantification downstream from the injection point were used to evaluate the bacterial distribution pattern simulated by MOCDENS3D. In the injection well, the 1,2-DCA concentration in the groundwater decreased from 939.8 to 0.9 microM in a 35 day time interval and in the presence of a sodium lactate solution. Moreover, analyses from the monitoring well showed that the cells were still active after transport through the aquifer, although biodegradation occurred to a lesser extent. This study showed that strain DCA1 can be successfully applied for the removal of 1,2-DCA under field conditions and that its limited retardation offers perspectives for large-scale cleanup processes of industrial sites.}, }
@article {pmid16999092, year = {2006}, author = {Rabaey, K and Van de Sompel, K and Maignien, L and Boon, N and Aelterman, P and Clauwaert, P and De Schamphelaire, L and Pham, HT and Vermeulen, J and Verhaege, M and Lens, P and Verstraete, W}, title = {Microbial fuel cells for sulfide removal.}, journal = {Environmental science &amp; technology}, volume = {40}, number = {17}, pages = {5218-5224}, doi = {10.1021/es060382u}, pmid = {16999092}, issn = {0013-936X}, mesh = {Anaerobiosis ; Bacteria/*metabolism ; *Bioelectric Energy Sources ; Microscopy, Electron, Scanning ; Oxidation-Reduction ; Sewage ; Sulfides/*isolation &amp; purification ; }, abstract = {Thus far, microbial fuel cells (MFCs) have been used to convert carbon-based substrates to electricity. However, sulfur compounds are ubiquitously present in organic waste and wastewater. In this study, a MFC with a hexacyanoferrate cathodic electrolyte was used to convert dissolved sulfide to elemental sulfur. Two types of MFCs were used, a square type closed to the air and a tubular type in which the cathode compartment was open to the air. The square-type MFCs demonstrated a potential-dependent conversion of sulfide to sulfur. In the tubular system, up to 514 mg sulfide L(-1) net anodic compartment (NAC) day(-1) (241 mg L(-1) day(-1) total anodic compartment, TAC) was removed. The sulfide oxidation in the anodic compartment resulted in electricity generation with power outputs up to 101 mW L(-1) NAC (47 W m(-3) TAC). Microbial fuel cells were coupled to an anaerobic upflow anaerobic sludge blanket reactor, providing total removals of up to 98% and 46% of the sulfide and acetate, respectively. The MFCs were capable of simultaneously removing sulfate via sulfide. This demonstrates that digester effluents can be polished by a MFC for both residual carbon and sulfur compounds. The recovery of electrons from sulfides implies a recovery of energy otherwise lost in the methane digester.}, }
@article {pmid16980418, year = {2006}, author = {Konstantinidis, KT and Ramette, A and Tiedje, JM}, title = {Toward a more robust assessment of intraspecies diversity, using fewer genetic markers.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {11}, pages = {7286-7293}, pmid = {16980418}, issn = {0099-2240}, mesh = {Bacterial Proteins/*genetics ; Burkholderia/classification/genetics ; Escherichia coli/classification/genetics ; *Genetic Markers ; *Genetic Variation ; *Genome, Bacterial ; *Phylogeny ; Proteobacteria/*classification/genetics ; Reproducibility of Results ; Salmonella/classification/genetics ; Sequence Analysis, DNA ; Shewanella/classification/genetics ; Species Specificity ; }, abstract = {Phylogenetic sequence analysis of single or multiple genes has dominated the study and census of the genetic diversity among closely related bacteria. It remains unclear, however, how the results based on a few genes in the genome correlate with whole-genome-based relatedness and what genes (if any) best reflect whole-genome-level relatedness and hence should be preferentially used to economize on cost and to improve accuracy. We show here that phylogenies of closely related organisms based on the average nucleotide identity (ANI) of their shared genes correspond accurately to phylogenies based on state-of-the-art analysis of their whole-genome sequences. We use ANI to evaluate the phylogenetic robustness of every gene in the genome and show that almost all core genes, regardless of their functions and positions in the genome, offer robust phylogenetic reconstruction among strains that show 80 to 95% ANI (16S rRNA identity, >98.5%). Lack of elapsed time and, to a lesser extent, horizontal transfer and recombination make the selection of genes more critical for applications that target the intraspecies level, i.e., strains that show >95% ANI according to current standards. A much more accurate phylogeny for the Escherichia coli group was obtained based on just three best-performing genes according to our analysis compared to the concatenated alignment of eight genes that are commonly employed for phylogenetic purposes in this group. Our results are reproducible within the Salmonella, Burkholderia, and Shewanella groups and therefore are expected to have general applicability for microevolution studies, including metagenomic surveys.}, }
@article {pmid16971007, year = {2006}, author = {Daims, H and Taylor, MW and Wagner, M}, title = {Wastewater treatment: a model system for microbial ecology.}, journal = {Trends in biotechnology}, volume = {24}, number = {11}, pages = {483-489}, doi = {10.1016/j.tibtech.2006.09.002}, pmid = {16971007}, issn = {0167-7799}, mesh = {Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Ecology ; *Ecosystem ; Genome, Bacterial ; *Water Microbiology ; *Water Purification ; }, abstract = {Biological wastewater treatment is among the most important biotechnological applications and, as drivers of the key processes, microorganisms are central to its success. Therefore, the study of wastewater microorganisms has obvious applied significance; however, the importance of wastewater treatment reactors as model systems for microbial ecology is often overlooked. Modern molecular techniques, including environmental genomics, have identified unexpected microbial key players for nutrient removal and sludge bulking and/or foaming, and provided many exciting insights into the diversity, functions and niche differentiations of these predominantly uncultivated microorganisms. It is now time for wastewater microbiology to be recognized as a mature and dynamic discipline in its own right, offering much toward a deeper understanding of life in complex microbial communities. Here, we consider selected key findings to illustrate the past and future roles of molecular ecophysiology and genomics in the development of wastewater microbiology as an important subdiscipline of microbial ecology.}, }
@article {pmid16958903, year = {2006}, author = {Geets, J and Boon, N and Verstraete, W}, title = {Strategies of aerobic ammonia-oxidizing bacteria for coping with nutrient and oxygen fluctuations.}, journal = {FEMS microbiology ecology}, volume = {58}, number = {1}, pages = {1-13}, doi = {10.1111/j.1574-6941.2006.00170.x}, pmid = {16958903}, issn = {0168-6496}, mesh = {Ammonia/*metabolism ; Models, Biological ; Nitrosomonas/genetics/*metabolism ; Nitrosomonas europaea/genetics/metabolism ; Oxidation-Reduction ; Oxygen/*metabolism ; Phylogeny ; }, abstract = {In most natural environments as well as in engineered environments, such as wastewater treatment plants, ammonia-oxidizing bacteria (AOB) experience fluctuating substrate concentrations. Several physiological traits, such as low maintenance energy demand and decay rate, cell-to-cell communication, cell mobility, stable enzymes and RNAs, could allow AOB to maintain themselves under unfavourable circumstances. This review examines whether AOB possess such traits and how these traits might offer advantages over competing organisms such as heterotrophic bacteria during periods of starvation. In addition, within the AOB groups, differences exist in adaptation to and competitiveness under conditions of high or low ammonia or oxygen concentrations. Because these findings are of importance with regard to the ecology and activity of AOB in natural and engineered environments, concluding remarks are directed towards future research objectives that may clarify unanswered questions, thereby contributing to the general knowledge of the ecology and activity of ammonia oxidizers.}, }
@article {pmid16958856, year = {2006}, author = {Gadkar, V and Rillig, MC}, title = {The arbuscular mycorrhizal fungal protein glomalin is a putative homolog of heat shock protein 60.}, journal = {FEMS microbiology letters}, volume = {263}, number = {1}, pages = {93-101}, doi = {10.1111/j.1574-6968.2006.00412.x}, pmid = {16958856}, issn = {0378-1097}, mesh = {Amino Acid Sequence ; Base Sequence ; Chaperonin 60/chemistry/*genetics ; Chromatography, Liquid ; DNA, Complementary ; Daucus carota/*microbiology ; Fungal Proteins/chemistry/*genetics ; Fungi/*chemistry/*genetics ; Gene Library ; Genes, Fungal ; Genome, Fungal ; Immunoblotting ; Mass Spectrometry ; Molecular Sequence Data ; Mycorrhizae/*chemistry ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {Work on glomalin-related soil protein produced by arbuscular mycorrhizal (AM) fungi (AMF) has been limited because of the unknown identity of the protein. A protein band cross-reactive with the glomalin-specific antibody MAb32B11 from the AM fungus Glomus intraradices was partially sequenced using tandem liquid chromatography-mass spectrometry. A 17 amino acid sequence showing similarity to heat shock protein 60 (hsp 60) was obtained. Based on degenerate PCR, a full-length cDNA of 1773 bp length encoding the hsp 60 gene was isolated from a G. intraradices cDNA library. The ORF was predicted to encode a protein of 590 amino acids. The protein sequence had three N-terminal glycosylation sites and a string of GGM motifs at the C-terminal end. The GiHsp 60 ORF had three introns of 67, 76 and 131 bp length. The GiHsp 60 was expressed using an in vitro translation system, and the protein was purified using the 6xHis-tag system. A dot-blot assay on the purified protein showed that it was highly cross-reactive with the glomalin-specific antibody MAb32B11. The present work provides the first evidence for the identity of the glomalin protein in the model AMF G. intraradices, thus facilitating further characterization of this protein, which is of great interest in soil ecology.}, }
@article {pmid16958758, year = {2006}, author = {Wegley, L and Mosier-Boss, P and Lieberman, S and Andrews, J and Graff-Baker, A and Rohwer, F}, title = {Rapid estimation of microbial numbers in water using bulk fluorescence.}, journal = {Environmental microbiology}, volume = {8}, number = {10}, pages = {1775-1782}, doi = {10.1111/j.1462-2920.2006.01062.x}, pmid = {16958758}, issn = {1462-2912}, mesh = {California ; Deoxyribonuclease I/metabolism ; Fluorescent Dyes/*chemistry ; Fluorometry/*methods ; Fresh Water/microbiology ; Microscopy, Fluorescence ; Organic Chemicals/*chemistry ; Reproducibility of Results ; Seawater/microbiology ; Vibrio parahaemolyticus/*isolation &amp; purification ; *Water Microbiology ; }, abstract = {Enumeration of microbial cells without culturing is an essential technique for microbial ecology and water quality evaluation. Here we show that bulk fluorescence using the SYBR Gold DNA stain can be used to rapidly quantify microbial cells per millilitre in fresh, marine and estuarine waters. The bulk fluorescence method is comparable to estimating cell concentrations in cultures using optical density; however, this enhanced method enables the user to estimate microbial numbers at lower concentration (> 10(5) cells ml(-1)) found in environmental samples. The technique worked in both single-cell and 96-well plate fluorescent spectrophotometers. Differences of approximately 10(5) cells per millilitre were discernible and the precision of the bulk fluorescence was higher than direct counting by epifluorescent microscopy. Treatment with DNase I increased sensitivity by lowering background noise attributed to free DNA. This technique is simple, rapid, inexpensive and adaptable for automatically estimating microbial numbers in water samples.}, }
@article {pmid16957276, year = {2006}, author = {Defoirdt, T and Crab, R and Wood, TK and Sorgeloos, P and Verstraete, W and Bossier, P}, title = {Quorum sensing-disrupting brominated furanones protect the gnotobiotic brine shrimp Artemia franciscana from pathogenic Vibrio harveyi, Vibrio campbellii, and Vibrio parahaemolyticus isolates.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {9}, pages = {6419-6423}, pmid = {16957276}, issn = {0099-2240}, mesh = {Animals ; Artemia/drug effects/*microbiology ; Furans/chemistry/pharmacology ; Germ-Free Life ; Homoserine/analogs &amp; derivatives/metabolism ; Lactones/metabolism ; Species Specificity ; Vibrio/drug effects/growth &amp; development/metabolism/*pathogenicity ; Vibrio parahaemolyticus/drug effects/growth &amp; development/metabolism/*pathogenicity ; }, abstract = {Autoinducer 2 (AI-2) quorum sensing was shown before to regulate the virulence of Vibrio harveyi towards the brine shrimp Artemia franciscana. In this study, several different pathogenic V. harveyi, Vibrio campbellii, and Vibrio parahaemolyticus isolates were shown to produce AI-2. Furthermore, disruption of AI-2 quorum sensing by a natural and a synthetic brominated furanone protected gnotobiotic Artemia from the pathogenic isolates in in vivo challenge tests.}, }
@article {pmid16944347, year = {2006}, author = {Porcel, R and Aroca, R and Cano, C and Bago, A and Ruiz-Lozano, JM}, title = {Identification of a gene from the arbuscular mycorrhizal fungus Glomus intraradices encoding for a 14-3-3 protein that is up-regulated by drought stress during the AM symbiosis.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {575-582}, pmid = {16944347}, issn = {0095-3628}, mesh = {14-3-3 Proteins/chemistry/classification/*genetics/metabolism ; Adaptation, Physiological ; Base Sequence ; Cloning, Molecular ; DNA, Complementary/chemistry/genetics ; Disasters ; Fungal Proteins/*genetics/metabolism ; *Gene Expression Regulation, Fungal/genetics ; Lactuca/microbiology ; Molecular Sequence Data ; Mycorrhizae/*genetics/metabolism ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; *Soil Microbiology ; Glycine max/microbiology ; Symbiosis ; Nicotiana/microbiology ; Up-Regulation ; Zea mays/microbiology ; }, abstract = {In the present study, a 14-3-3 protein-encoding gene from Glomus intraradices has been identified after differential hybridization of a cDNA library constructed from the fungus growing in vitro and subjected to drought stress by addition of 25% PEG 6000. Subsequently, we have studied its expression pattern under drought stress in vitro and also when forming natural symbioses with different host plants. The results obtained suggest that Gi14-3-3 gene may be involved in the protection that the arbuscular mycorrhizal (AM) symbiosis confers to the host plant against drought stress. Our findings provide new evidences that the contribution of AM fungi to the enhanced drought tolerance of the host plant can be mediated by a group of proteins (the 14-3-3) that regulate both signaling pathways and also effector proteins involved in the final plant responses.}, }
@article {pmid16944346, year = {2006}, author = {Aira, M and Monroy, F and Domínguez, J}, title = {Eisenia fetida (Oligochaeta, Lumbricidae) activates fungal growth, triggering cellulose decomposition during vermicomposting.}, journal = {Microbial ecology}, volume = {52}, number = {4}, pages = {738-747}, pmid = {16944346}, issn = {0095-3628}, mesh = {Analysis of Variance ; Animals ; Biodegradation, Environmental ; Biomass ; Bioreactors/microbiology ; Cellulase/metabolism ; Cellulose/analysis/*metabolism ; Ecosystem ; Fungi/*growth &amp; development ; Manure/analysis ; Oligochaeta/growth &amp; development/*physiology ; Polysaccharides/analysis/*metabolism ; Swine ; beta-Glucosidase/metabolism ; }, abstract = {Cellulose is the most abundant polymer in nature and constitutes a large pool of carbon for microorganisms, the main agents responsible for soil organic matter decomposition. Cellulolysis occurs as the result of the combined action of fungi and bacteria with different requirements. Earthworms influence decomposition indirectly by affecting microbial population structure and dynamics and also directly because the guts of some species possess cellulolytic activity. Here we assess whether the earthworm Eisenia fetida (Savigny 1826) digests cellulose directly (i.e., with its associated gut microbiota) and also whether the effects of E. fetida on microbial biomass and activity lead to a change in the equilibrium between fungi and bacteria. By enhancing fungal communities, E. fetida would presumably trigger more efficient cellulose decomposition. To evaluate the role of E. fetida in cellulose decomposition, we carried out an experiment in which pig slurry, a microbial-rich substrate, was treated in small-scale vermireactors with and without earthworms. The presence of earthworms in vermireactors significantly increased the rate of cellulose decomposition (0.43 and 0.26% cellulose loss day(-1), with and without earthworms, respectively). However, the direct contribution of E. fetida to degradation of cellulose was not significant, although its presence increased microbial biomass (C(mic)) and enzyme activity (cellulase and beta-glucosidase). Surprisingly, as fungi may be part of the diet of earthworms, the activity of E. fetida triggered fungal growth during vermicomposting. We suggest that this activation is a key step leading to more intense and efficient cellulolysis during vermicomposting of organic wastes.}, }
@article {pmid16944345, year = {2007}, author = {Hjort, K and Lembke, A and Speksnijder, A and Smalla, K and Jansson, JK}, title = {Community structure of actively growing bacterial populations in plant pathogen suppressive soil.}, journal = {Microbial ecology}, volume = {53}, number = {3}, pages = {399-413}, pmid = {16944345}, issn = {0095-3628}, mesh = {Bacteria/genetics/*growth &amp; development ; Base Sequence ; Biodiversity ; Brassica ; Bromodeoxyuridine/analysis/metabolism ; Chitin/metabolism/pharmacology ; Cluster Analysis ; *Ecosystem ; Electrophoresis, Agar Gel/methods ; Fungi/drug effects/pathogenicity/*physiology ; Molecular Sequence Data ; Plant Diseases/*microbiology ; Plant Roots/microbiology ; Polymorphism, Restriction Fragment Length ; Pseudomonas/drug effects/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Sodium Acetate/pharmacology ; *Soil Microbiology ; Spores, Fungal ; }, abstract = {The bacterial community in soil was screened by using various molecular approaches for bacterial populations that were activated upon addition of different supplements. Plasmodiophora brassicae spores, chitin, sodium acetate, and cabbage plants were added to activate specific bacterial populations as an aid in screening for novel antagonists to plant pathogens. DNA from growing bacteria was specifically extracted from the soil by bromodeoxyuridine immunocapture. The captured DNA was fingerprinted by terminal restriction fragment length polymorphism (T-RFLP). The composition of the dominant bacterial community was also analyzed directly by T-RFLP and by denaturing gradient gel electrophoresis (DGGE). After chitin addition to the soil, some bacterial populations increased dramatically and became dominant both in the total and in the actively growing community. Some of the emerging bands on DGGE gels from chitin-amended soil were sequenced and found to be similar to known chitin-degrading genera such as Oerskovia, Kitasatospora, and Streptomyces species. Some of these sequences could be matched to specific terminal restriction fragments on the T-RFLP output. After addition of Plasmodiophora spores, an increase in specific Pseudomonads could be observed with Pseudomonas-specific primers for DGGE. These results demonstrate the utility of microbiomics, or a combination of molecular approaches, for investigating the composition of complex microbial communities in soil.}, }
@article {pmid16944344, year = {2007}, author = {Pierre-Alain, M and Christophe, M and Séverine, S and Houria, A and Philippe, L and Lionel, R}, title = {Protein extraction and fingerprinting optimization of bacterial communities in natural environment.}, journal = {Microbial ecology}, volume = {53}, number = {3}, pages = {426-434}, pmid = {16944344}, issn = {0095-3628}, mesh = {Bacteria/chemistry/genetics/*isolation &amp; purification ; Bacterial Proteins/drug effects/isolation &amp; purification ; Cadmium/toxicity ; DNA Fingerprinting/*methods ; DNA Primers/chemistry ; DNA, Ribosomal/genetics ; Environmental Monitoring/*methods ; France ; Fresh Water/*microbiology ; Mercury/toxicity ; Peptide Mapping/*methods ; Principal Component Analysis ; Reproducibility of Results ; *Water Microbiology ; Water Pollutants, Chemical/toxicity ; }, abstract = {Recent development in molecular approaches allows access to genetic structure and diversity of indigenous microbial communities. In contrast, the functional analysis of microorganisms in their environment is still hampered by methodological limitations. Analysis of total proteins expressed at the whole community level (metaproteome) has been proposed to characterize the functional structure of microbial communities in their environment. However, developments are still required to perform such analysis. Our aim was to optimize methods to extract and characterize metaproteome of indigenous microbial communities. Experiments were first conducted in monoxenic bacterial cultures, and various methods were examined to define a procedure of protein extraction ensuring an efficient recovery regardless of the taxonomic affiliation of the cells. These developments were next applied to characterize the metaproteome from indigenous bacterial communities in freshwater samples. Bacterial cells were recovered from water using a high-speed density gradient centrifugation method before protein extraction and fingerprinting. The reactivity and sensitivity of this metaproteomic approach were tested by analyzing the variations of protein fingerprints according to perturbations (cadmium or mercury contamination). The genetic structure of the corresponding communities was also characterized by automated ribosomal spacer analysis (ARISA) DNA fingerprinting. Both protein and DNA fingerprints were statistically analyzed. Results obtained showed that the method developed for protein recovery and fingerprinting was efficient, sensitive, and reproducible. Both the functional and genetic structures of the freshwater bacterial community were complex and varied with perturbations. These variations occurred at both population and protein expression levels and were specific to the perturbation applied.}, }
@article {pmid16944343, year = {2006}, author = {Swiecicka, I and Van der Auwera, GA and Mahillon, J}, title = {Hemolytic and nonhemolytic enterotoxin genes are broadly distributed among Bacillus thuringiensis isolated from wild mammals.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {544-551}, pmid = {16944343}, issn = {0095-3628}, mesh = {Animals ; Animals, Wild/*microbiology ; Bacillus thuringiensis/*classification/*genetics/metabolism ; Bacterial Proteins/*genetics ; Blotting, Southern ; DNA, Bacterial/chemistry/genetics ; Diarrhea/microbiology/veterinary ; Enterotoxins/*genetics ; Eulipotyphla ; Hemolysin Proteins/genetics ; Hemolysis ; Phylogeny ; Polymerase Chain Reaction/methods ; Public Health ; Rodentia ; Sequence Alignment ; }, abstract = {The presence of cytotoxin K (cytK), nonhemolytic (NHE), and hemolytic (HBL) enterotoxin genes was investigated in 74 Bacillus thuringiensis strains recovered from the intestines of wild mammals from northeast Poland, using polymerase chain reaction amplification and Southern hybridization. All the isolates harbored genes coding for toxin(s) that could cause diarrhea. The B. thuringiensis strains containing the nhe genes were found more frequently (nheA 100%, nheB 77%, nheC 96%) than those with the hblACD (74%) and cytK (73%) genes. The presence/absence of the nheA, hblA, and cytK genes was confirmed in all of the B. thuringiensis strains by Southern hybridization. Interestingly, these experiments also indicated that the nheA locus is located on a more variable chromosome region compared with hblA and, to a lesser degree, cytK. Detection of the 41-kDa component of NHE enterotoxin by the TECRA assay revealed various protein levels by B. thuringiensis strains. These results indicate the existence of environmental B. thuringiensis strains bearing the potential virulence arsenal for the production of diarrheal toxins, and emphasize the importance of small animals in the spread of B. cereus-like enterotoxin genes in nature. However, further investigation is needed to clarify any possible involvement of environmental B. thuringiensis strains in human health issues.}, }
@article {pmid16944342, year = {2006}, author = {Faeth, SH and Hamilton, CE}, title = {Does an asexual endophyte symbiont alter life stage and long-term survival in a perennial host grass?.}, journal = {Microbial ecology}, volume = {52}, number = {4}, pages = {748-755}, pmid = {16944342}, issn = {0095-3628}, mesh = {Festuca/growth &amp; development/*microbiology ; Hypocreales/*growth &amp; development ; Poaceae/growth &amp; development/*microbiology ; Reproduction ; Seeds/growth &amp; development ; Symbiosis ; }, abstract = {Asexual, seedborne endophytic fungi in perennial grasses are often viewed as strong mutualists because fitness of the symbiont and host grass are closely coupled. However, at least for some native grasses, the asexual endophyte, Neotyphodium, acts parasitically, yet remains at high frequencies in natural populations. Most previous studies of Neotyphodium effects on host survival have been short term relative to the long life span of the perennial grass host. We therefore tested the hypothesis that Neotyphodium alters the survival in various life stages and long-term survival of adult native Arizona fescue (Festuca arizonica). To test the former, we planted 40 infected (E+) and 40 uninfected (E-, endophyte removed) seeds from four different maternal plants in the field under ambient conditions. We followed survival of seeds, seedlings, and adult plants over a 5-year period. To test the latter, we determined the infection of 1633 adult plants and followed their survival over the next 5-7 years. E+ seeds did not differ from uninfected seeds in terms of overall survival from seed germination to seedling to adult. However, the shape of the survival curve differed, with E+ plants showing higher mortality in early life stages. E+ adult plants did not differ from E- plants in long-term survival. Survival was generally very high during the study, which included a severe and prolonged drought. Infection by asexual Neotyphodium does not increase survival in early life stages or that of adult plants. Because asexual, vertically transmitted symbionts are predicted by evolutionary theory to be strong mutualists, the persistence of high infection frequencies in natural populations without long-term benefits to the host remains enigmatic. One possible explanation is that the long life span of the perennial host and low seedling recruitment may obscure either the costs or benefits of endophyte infection.}, }
@article {pmid16944341, year = {2006}, author = {Kojima, H and Koizumi, Y and Fukui, M}, title = {Community structure of bacteria associated with sheaths of freshwater and brackish thioploca species.}, journal = {Microbial ecology}, volume = {52}, number = {4}, pages = {765-773}, pmid = {16944341}, issn = {0095-3628}, mesh = {Animals ; Bacteria/classification/*genetics ; DNA, Ribosomal/chemistry/genetics ; Electrophoresis/methods ; Fresh Water/*microbiology ; Geologic Sediments/microbiology ; Hydrogensulfite Reductase/genetics ; Japan ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Thiotrichaceae/classification/*genetics ; }, abstract = {Bacterial communities associated with sheaths of Thioploca spp. from two freshwater lakes (Lake Biwa, Japan, and Lake Constance, Germany) and one brackish lake (Lake Ogawara, Japan) were analyzed with denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. The comparison between the DGGE band patterns of bulk sediment and Thioploca filaments of Lake Biwa suggested the presence of specific bacterial communities associated with Thioploca sheaths. As members of sheath-associated communities, bacteria belonging to Bacteroidetes were detected from the samples of both freshwater lakes. A DGGE band from Thioploca of Lake Biwa, belonging to candidate division OP8, was quite closely related to another DGGE band detected from that of Lake Constance. In contrast to the case of freshwater lakes, no bacterium of Bacteroidetes or OP8 was detected from Thioploca of Lake Ogawara. However, two DGGE bands from Lake Ogawara, belonging to Chloroflexi, were quite closely related to a DGGE band from Lake Constance. Two DGGE bands obtained from Lake Biwa were closely related to phylogenetically distant dissimilatory Fe(III)-reducing bacteria. Cloning analyses for a dissimilatory sulfite reductase gene were performed on the same samples used for DGGE analysis. The results of the analyses suggest that sheaths of freshwater/brackish Thioploca have little ecological significance for the majority of sulfate reducers.}, }
@article {pmid16944340, year = {2006}, author = {Azanza, MP and Azanza, RV and Vargas, VM and Hedreyda, CT}, title = {Bacterial endosymbionts of Pyrodinium bahamense var. compressum.}, journal = {Microbial ecology}, volume = {52}, number = {4}, pages = {756-764}, pmid = {16944340}, issn = {0095-3628}, mesh = {Animals ; Bacteria/genetics/*isolation &amp; purification/metabolism ; Chromatography, High Pressure Liquid ; Dinoflagellida/*microbiology ; Marine Toxins/analysis/toxicity ; Mice ; Philippines ; RNA, Ribosomal, 16S/genetics ; Saxitoxin/analysis/toxicity ; Symbiosis ; }, abstract = {The study presents evidence in support of the bacterial theory associated with the toxicity of Pyrodinium bahamense var. compressum. Bacterial endosymbionts from Philippine P. bahamense var. compressum strain Pbc MZRVA 042595 were isolated and identified via 16S rDNA sequence analysis. Taxonomic diversity of the identified culturable intracellular microbiota associated with Philippine P. bahamense var. compressum was established to be limited to the Phyla Proteobacteria, Actinobacteria, and Firmicutes. Major endosymbionts identified included Moraxella spp., Erythrobacter spp., and Bacillus spp., whereas Pseudomonas putida, Micrococcus spp., and Dietzia maris were identified as minor isolates. All identified strains except D. maris, P. putida, and Micrococcus spp. were shown to contain either saxitoxin or neo saxitoxin or both at levels < or =73 ng/10(7) bacterial cells based on high-performance liquid chromatography analysis. Paralytic shellfish poisoning-like physiologic reactions in test animals used in the mouse assay were recorded for the endosymbionts except for P. putida. The study is the first to elucidate the possible contribution of bacterial endosymbionts in the toxicity of P. bahamense var. compressum isolated in the Philippines.}, }
@article {pmid16944339, year = {2007}, author = {Castillo, UF and Browne, L and Strobel, G and Hess, WM and Ezra, S and Pacheco, G and Ezra, D}, title = {Biologically active endophytic streptomycetes from Nothofagus spp. and other plants in Patagonia.}, journal = {Microbial ecology}, volume = {53}, number = {1}, pages = {12-19}, pmid = {16944339}, issn = {0095-3628}, mesh = {*Antibiosis ; Asteraceae/microbiology ; Fagaceae/*microbiology ; Fungi/*growth &amp; development ; Loranthaceae/microbiology ; Magnoliopsida/*microbiology ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; Oomycetes/*growth &amp; development ; Phylogeny ; Plant Diseases/microbiology ; Sequence Analysis, DNA ; South America ; Streptomyces/classification/genetics/*growth &amp; development/ultrastructure ; }, abstract = {Endophytic streptomycetes have been isolated and characterized from several species of Nothofagus and other plants growing in the southern reaches of Patagonia. No endophytic streptomycete was obtained from any plant species studied in Northern Patagonia. However, from Southern Patagonia, biologically active Streptomyces spp. from several plant species were isolated. Each isolate, as studied by scanning electron microscopy (SEM), has small hyphae, some produce typical barrel-shaped spores in culture and each has some unique hyphal surface structures. Interestingly, although none has any detectable antibacterial killing properties, each has demonstrable killing activity against one or more pathogenic fungi including representative plant pathogenic organisms such as Phytophthora erythroseptica, Pythium ultimum, Sclerotinia sclerotiorum, Mycosphaerella fijiensis, and Rhizoctonia solani. The 16S rDNA sequences of the isolates were distinct from all other genetic accessions of Streptomyces in GenBank. However, isolate C-2 from Chiliotrichum diffusum (Compositae) is identical, in all respects, to isolate C-4 obtained from Misodendrum punctulatum (Loranthaceae). These results confirm that endophytic streptomycetes represent a novel source of biologically active microorganisms.}, }
@article {pmid16944338, year = {2006}, author = {Tuomainen, J and Hietanen, S and Kuparinen, J and Martikainen, PJ and Servomaa, K}, title = {Community structure of the bacteria associated with Nodularia sp. (Cyanobacteria) aggregates in the Baltic Sea.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {513-522}, pmid = {16944338}, issn = {0095-3628}, mesh = {*Biodiversity ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; Electrophoresis, Agar Gel ; *Nodularia/classification/genetics/growth &amp; development ; Oceans and Seas ; *Phylogeny ; Polymerase Chain Reaction ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; }, abstract = {The community structure of the bacteria associated with Nodularia spumigena (Mertens) cyanobacterial aggregates in the Baltic Sea was studied with temperature gradient gel electrophoresis (TGGE), using a 16S rRNA gene fragment as a target. Various developmental stages of the aggregates and free-floating cyanobacterial filaments were sampled to reveal possible changes in associated microbial community structure during development and senescence of the aggregates. The microbial community structures of all samples differed, and the communities of young and decaying aggregates were separated by cluster analysis of the TGGE fingerprint data. Sequencing of the TGGE fragments indicated the presence of bacteria from the alpha-, beta-, and gamma-proteobacterial groups, as well as members of Cytophaga-Flexibacter-Bacteroides lineages and gram-positive Actinobacteria spp. The majority of the Nodularia-associated sequences were not closely related to previously reported 16S rDNA sequences from the Baltic Sea or any other environment. The structure of the bacterial assemblage reflects the environmental changes associated with the succession and decay of the cyanobacterial aggregates. In addition, the sequence data suggest that the N. spumigena (Mertens) blooms in the Baltic Sea may host thus far uncharacterized bacterial species.}, }
@article {pmid16944337, year = {2006}, author = {Powell, SM and Ferguson, SH and Bowman, JP and Snape, I}, title = {Using real-time PCR to assess changes in the hydrocarbon-degrading microbial community in Antarctic soil during bioremediation.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {523-532}, pmid = {16944337}, issn = {0095-3628}, mesh = {Antarctic Regions ; Bacteria/*enzymology/genetics/growth &amp; development ; *Biodegradation, Environmental ; Colony Count, Microbial/methods ; Cytochrome P-450 CYP4A/analysis/*genetics ; Hydrocarbons/*metabolism ; Polymerase Chain Reaction/methods/*standards ; Reproducibility of Results ; Sensitivity and Specificity ; *Soil Microbiology ; }, abstract = {A real-time polymerase chain reaction (PCR) method to quantify the proportion of microorganisms containing alkane monooxygenase was developed and used to follow changes in the microbial community in hydrocarbon-contaminated Antarctic soil during a bioremediation field trial. Assays for the alkB and rpoB genes were validated and found to be both sensitive and reproducible (less than 2% intrarun variation and 25-38% interrun variation). Results from the real-time PCR analysis were compared to analysis of the microbial population by a culture-based technique [most probable number (MPN) counts]. Both types of analysis indicated that fertilizer addition to hydrocarbon-contaminated soil stimulated the indigenous bacterial population within 1 year. The proportion of alkB containing microorganisms was positively correlated to the concentration of n-alkanes in the soil. After the concentration of n-alkanes in the soil decreased, the proportion of alkane-degrading microorganisms decreased, but the proportion of total hydrocarbon-degrading microorganisms increased, indicating another shift in the microbial community structure and ongoing biodegradation.}, }
@article {pmid16941240, year = {2007}, author = {Icgen, B and Moosa, S and Harrison, ST}, title = {A study of the relative dominance of selected anaerobic sulfate-reducing bacteria in a continuous bioreactor by fluorescence in situ hybridization.}, journal = {Microbial ecology}, volume = {53}, number = {1}, pages = {43-52}, pmid = {16941240}, issn = {0095-3628}, mesh = {*Bacteria, Anaerobic/classification/genetics/growth &amp; development/isolation &amp; purification ; Bioreactors/*microbiology ; Colony Count, Microbial ; Culture Media ; *Deltaproteobacteria/classification/genetics/growth &amp; development/isolation &amp; purification ; In Situ Hybridization, Fluorescence/*methods ; Oligonucleotide Probes ; RNA, Ribosomal, 16S/genetics ; *Sulfur-Reducing Bacteria/classification/genetics/growth &amp; development/isolation &amp; purification ; }, abstract = {The diversity and the community structure of sulfate-reducing bacteria (SRB) in an anaerobic continuous bioreactor used for treatment of a sulfate-containing wastewater were investigated by fluorescence in situ hybridization. Hybridization to the 16S rRNA probe EUB338 for the domain Bacteria was performed, followed by a nonsense probe NON338 as a control for nonspecific staining. Sulfate-reducing consortia were identified by using five nominally genus-specific probes (SRB129 for Desulfobacter, SRB221 for Desulfobacterium, SRB228 for Desulfotomaculum, SRB660 for Desulfobulbus, and SRB657 for Desulfonema) and four group-specific probes (SRB385 as a general SRB probe, SRB687 for Desulfovibrioaceae, SRB814 for Desulfococcus group, and SRB804 for Desulfobacteriaceae). The total prokaryotic population was determined by 4',6-diamidino-2-phenylindole staining. Hybridization analysis using these 16S rRNA-targeted oligonucleotide probes showed that, of those microbial groupings investigated, Desulfonema, Desulfobulbus, spp., and Desulfobacteriaceae group were the main sulfate-reducing bacteria in the bioreactor when operated at steady state at 35 degrees C, pH 7.8, and a 2.5-day residence time with feed stream containing 2.5 kg m-3 sulfate as terminal electron acceptor and 2.3 kg m-3 acetate as carbon source and electron donor.}, }
@article {pmid16939082, year = {2006}, author = {Collins, G and Connaughton, S and Enright, AM and Scully, C and Mahony, T and O'Flaherty, V}, title = {Application and biomolecular monitoring of psychrophilic anaerobic digestion.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {54}, number = {2}, pages = {41-47}, doi = {10.2166/wst.2006.484}, pmid = {16939082}, issn = {0273-1223}, mesh = {Biomass ; Bioreactors ; In Situ Hybridization, Fluorescence ; Polymorphism, Genetic ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; }, abstract = {Thirteen anaerobic hybrid expanded granular sludge bed-anaerobic filter bioreactors were used for psychrophilic (15-18 degrees C) anaerobic digestion of a variety of synthetic and non-synthetic wastewaters, including: food-processing, dairy, aromatic- and aliphatic-containing and brewery discharges. Specific methanogenic activity assays were employed to assess temporal physiological activity dynamics. Terminal restriction fragment length polymorphism genetic fingerprinting and fluorescent in situ hybridization were used to monitor shifts in the structure of the microbial communities in the bioreactors in response to operating conditions. Treatment efficiencies obtained were comparable to previous mesophilic (37 degrees C) trials. Methanogenic activity developed under psychrophilic conditions and putative psychrophilic populations were detected within otherwise psychrotolerant mesophilic communities. Shifts in the population structure of archaeal (methanogenic) communities were more indicative of process disruption than bacterial communities. Biomolecular techniques were demonstrated as valuable tools for anaerobic wastewater treatment plant monitoring.}, }
@article {pmid16924432, year = {2006}, author = {Selbitschka, W and Keller, M and Miethling-Graff, R and Dresing, U and Schwieger, F and Krahn, I and Homann, I and Dammann-Kalinowski, T and Pühler, A and Tebbe, CC}, title = {Long-term field release of bioluminescent Sinorhizobium meliloti strains to assess the influence of a recA mutation on the strains' survival.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {583-595}, pmid = {16924432}, issn = {0095-3628}, mesh = {*Air Microbiology ; Biomass ; Carbon/metabolism ; Colony Count, Microbial ; DNA Fingerprinting ; Ecosystem ; Gene Transfer, Horizontal ; Luminescence ; Medicago sativa/microbiology ; *Mutation ; Nitrogen/metabolism ; Organisms, Genetically Modified ; Phenotype ; Polymerase Chain Reaction ; Random Allocation ; Rec A Recombinases/*genetics ; Seasons ; Sinorhizobium meliloti/*genetics/*growth &amp; development ; *Soil Microbiology ; }, abstract = {A field release experiment was carried out to study the fate of the isogenic, firefly luciferase (luc) gene-tagged Sinorhizobium meliloti strains L1 (RecA-) and L33 (RecA+) in the environment. Both strains were released at concentrations of approximately 10(6) cfu g(-1) soil in replicate and randomized field plots, which had been sown with alfalfa (Medicago sativa). The survival of both strains during the following 7 years could be subdivided into three phases: a sharp decline for more than two orders of magnitude within the first 4 months (phase I), followed by fluctuations around an average number of 10(4) cfu g(-1) soil for nearly 4 years (phase II), and a further decline to approximately 60 cfu g(-1) (phase III). At most sampling dates, no significant differences in the survival of both strains were detected, indicating that the recA gene function was dispensable under these environmental conditions. During the field inoculation, both strains were dispersed accidentally by wind in small numbers to noninoculated field plots. Strain L33 established at a concentration of more than 10(3) cfu g(-1) soil with subsequent seasonal fluctuations. Although strain L1 must have been disseminated to a similar extent, it could never be recovered from noninoculated field plots, indicating that the recA mutation interfered with the strain's capability to establish there. At the beginning of the field experiment, an indigenous alfalfa-nodulating population was below the limit of detection. In the following years, however, an indigenous population arose, which finally outcompeted both strains for saprophytic growth and alfalfa nodulation. RecA- strain L1 was outcompeted for alfalfa nodulation slightly faster than its RecA+ counterpart L33. The diversity of the indigenous population was characterized by employing the Enterobacterial Repetitive Intergenic Consensus polymerase chain reaction fingerprint method. Typing of 2731 root nodule isolates revealed a total of 38 fingerprint groups. More than 80% of the isolates could be grouped into six dominant fingerprint groups, indicating that a few dominant bacterial strain types had outcompeted the released strains.}, }
@article {pmid16917526, year = {2006}, author = {Kennedy, N and Brodie, E and Connolly, J and Clipson, N}, title = {Seasonal influences on fungal community structure in unimproved and improved upland grassland soils.}, journal = {Canadian journal of microbiology}, volume = {52}, number = {7}, pages = {689-694}, doi = {10.1139/w06-015}, pmid = {16917526}, issn = {0008-4166}, mesh = {Analysis of Variance ; DNA, Fungal/analysis ; DNA, Intergenic/classification/genetics ; DNA, Ribosomal/classification/genetics ; Ecosystem ; *Fungi/classification/genetics ; Ireland ; Monte Carlo Method ; Poaceae/*microbiology ; Ribotyping ; Seasons ; *Soil Microbiology ; }, abstract = {Seasonal and management influences on the fungal community structure of two upland grassland soils were investigated. An upland site containing both unimproved floristically diverse (U4a) and improved mesotrophic (MG7b) grassland types was selected. Samples from both grassland types were taken at five times in one year. Soil fungal community structure was assessed using fungal automated ribosomal intergenic spacer analysis (ARISA), a DNA-profiling approach. A grassland management regime was found to strongly affect fungal community structure, with fungal ARISA profiles from unimproved and improved grassland soils differing significantly. The number of fungal ribotypes found was higher in unimproved than improved grassland soils, providing evidence that improvement may reduce the suitability of upland soil as a habitat for specific groups of fungi. Seasonal influences on fungal community structure were also noted, with samples taken in autumn (October) more correlated with change in ribotype profiles than samples from other seasons. However, seasonal variation did not obscure the measurement of differences in the fungal community structure that were due to agricultural improvement, with canonical correspondence analysis indicating grassland type had a stronger influence on fungal profiles than did season.}, }
@article {pmid16913925, year = {2006}, author = {Wu, QL and Hahn, MW}, title = {High predictability of the seasonal dynamics of a species-like Polynucleobacter population in a freshwater lake.}, journal = {Environmental microbiology}, volume = {8}, number = {9}, pages = {1660-1666}, doi = {10.1111/j.1462-2920.2006.01049.x}, pmid = {16913925}, issn = {1462-2912}, mesh = {Austria ; Burkholderiaceae/*growth &amp; development/physiology ; Chlorophyll/chemistry ; Colony Count, Microbial ; Fresh Water/*microbiology ; *Seasons ; Temperature ; }, abstract = {One of the key questions in microbial ecology is if seasonal patterns of bacterial community composition (BCC) observed in one year repeat in the following years. We have investigated if the recorded annual dynamics of a species-like Polynucleobacter (subcluster PnecB) population allowed the prediction of the population dynamics in another year. The abundance of PnecB bacteria in the pelagic of temperate Lake Mondsee was investigated by fluorescence in situ hybridization (FISH) over three consecutive years. The PnecB bacteria formed a persistent population, and were present in the entire water body of the lake. Two of the three investigated years differed strongly in summer temperatures and precipitation, which resulted in markedly different growth conditions. But despite of these different environmental conditions, the PnecB population demonstrated remarkably similar seasonal dynamics in the three investigated years. Water temperature was the best predictor of the population dynamics during the first half of the annual cycles. Statistical analysis also indicated influences of phytoplankton and metazooplankton successions on the PnecB population dynamics. Furthermore, 65 lakes and ponds were investigated for the presence of PnecB bacteria. They were detected in the majority (78%) of circum-neutral and alkaline freshwater habitats, but not in any investigated acidic or saline habitat.}, }
@article {pmid16909924, year = {2006}, author = {Kraus, D and Peschel, A}, title = {Molecular mechanisms of bacterial resistance to antimicrobial peptides.}, journal = {Current topics in microbiology and immunology}, volume = {306}, number = {}, pages = {231-250}, doi = {10.1007/3-540-29916-5_9}, pmid = {16909924}, issn = {0070-217X}, mesh = {Animals ; Antimicrobial Cationic Peptides/*physiology ; Bacterial Infections/*immunology ; Carrier Proteins/metabolism ; Drug Resistance, Bacterial ; Humans ; Static Electricity ; }, abstract = {Cationic antimicrobial peptides (CAMPs) are integral compounds of the antimicrobial arsenals in virtually all kinds of organisms, with important roles in microbial ecology and higher organisms' host defense. Many bacteria have developed countermeasures to limit the efficacy of CAMPs such as defensins, cathelicidins, kinocidins, or bacteriocins. The best-studied bacterial CAMP resistance mechanisms involve electrostatic repulsion of CAMPs by modification of cell envelope molecules, proteolytic cleavage of CAMPs, production of CAMP-trapping proteins, or extrusion of CAMPs by energy-dependent efflux pumps. The repertoire of CAMPs produced by a given host organism and the efficiency of microbial CAMP resistance mechanisms appear to be crucial in host-pathogen interactions, governing the composition of commensal microbial communities and the virulence of bacterial pathogens. However, all CAMP resistance mechanisms have limitations and bacteria have never succeeded in becoming fully insensitive to a broad range of CAMPs. CAMPs or conserved CAMP resistance factors are discussed as new mediators and targets, respectively, of novel and sustainable anti-infective strategies.}, }
@article {pmid16909350, year = {2006}, author = {Cohen, SD}, title = {Host selectivity and genetic variation of Discula umbrinella isolates from two oak species: analyses of intergenic spacer region sequences of ribosomal DNA.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {463-469}, pmid = {16909350}, issn = {0095-3628}, mesh = {Ascomycota/classification/*genetics ; DNA, Fungal/*chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; *Genetic Variation ; Mitosporic Fungi/classification/*genetics ; Molecular Weight ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Quercus/*microbiology ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Discula umbrinella, a fungal endophyte of oak species, colonizes and reproduces on leaves of Quercus alba and Q. rubra in forest ecosystems. Twenty-nine isolates collected from leaves of both oak species (16 from Q. alba and 13 from Q. rubra) were assayed for oak species preference and genetic variation based on primer-specific polymerase chain reactions for the intergenic spacer region (IGS) of ribosomal DNA. DNA sequencing of the polymerase chain reaction products revealed a 10-bp insertion (237-247 bp) at the 3' end of the IGS region present in nine isolates and absent in 20 of the isolates. Phylogenetic analysis of the IGS region using the neighbor-joining method identified IGS groups (groups I-V) based on single nucleotide sequence differences. Host selectivity and geographic origin of isolates were correlated in some instances with the IGS groups. Isolates within each IGS group were further analyzed for nucleotide polymorphisms to confirm genotype identity and genotype diversity. Ten different genotypes (Va-Vj) were identified among the isolates analyzed. Genotype diversity was greatest in IGS groups I, IV, and V. Seventy percent of the genotypes (Vc, Vd, Ve, Vf, Vg,Vi, and Vj) contained isolates with single tree species preferences.}, }
@article {pmid16909349, year = {2006}, author = {Lee, OO and Lau, SC and Qian, PY}, title = {Consistent bacterial community structure associated with the surface of the sponge Mycale adhaerens bowerbank.}, journal = {Microbial ecology}, volume = {52}, number = {4}, pages = {693-707}, pmid = {16909349}, issn = {0095-3628}, mesh = {Animals ; Bacteria/classification/genetics/*growth &amp; development ; DNA, Bacterial/chemistry/genetics ; Ecosystem ; Geography ; Hong Kong ; Molecular Sequence Data ; Phylogeny ; Population Dynamics ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Water Microbiology ; }, abstract = {As a crucial step in the identification of possible association between bacteria and sponges, we investigated if a unique bacterial population community was consistently associated with the surface of the sponge Mycale adhaerens, irrespective of environmental conditions. The composition of bacterial communities associated with the surface of sponges at three geographically distinctive sites in Hong Kong waters over four seasons was examined by analyzing terminal restriction fragment length polymorphism of the bacterial 16S rRNA genes. Statistical analysis indicated that bacterial communities on inanimate reference surfaces (polystyrene dishes deployed in the close vicinity of the sponge colonies for 7 days) had a relatively high degree of both site and seasonal specificities (R statistics of pairwise comparisons approximately 1), which might be attributed to the differences in environmental conditions at different sites and seasons. On the contrary, the sponge-surface-associated bacterial communities from different sites and seasons were hardly distinguishable from each other (lowest R = -0.16) but were rather distinctive from the reference bacterial communities (R approximately 1), suggesting a highly stable and distinctive bacteria-sponge association irrespective of the environmental conditions. The occurrence of some unique bacterial types in the sponge-surface-associated communities over space and time suggests that the associations are consistent and specific.}, }
@article {pmid16909348, year = {2006}, author = {Dang, H and Song, L and Chen, M and Chang, Y}, title = {Concurrence of cat and tet genes in multiple antibiotic-resistant bacteria isolated from a sea cucumber and sea urchin mariculture farm in China.}, journal = {Microbial ecology}, volume = {52}, number = {4}, pages = {634-643}, pmid = {16909348}, issn = {0095-3628}, mesh = {Animals ; Bacteria/classification/*genetics ; China ; Chloramphenicol/pharmacology ; Chloramphenicol O-Acetyltransferase/genetics ; DNA, Bacterial/chemistry/genetics ; Drug Resistance, Bacterial/*genetics ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sea Cucumbers/*microbiology ; Sea Urchins/*microbiology ; Sequence Analysis, DNA ; Tetracycline Resistance/genetics ; Tetracyclines/pharmacology ; }, abstract = {A basic understanding of abundance and diversity of antibiotic-resistant microbes and their genetic determinants is necessary for finding a way to prevent and control the spread of antibiotic resistance. For this purpose, chloramphenicol and multiple antibiotic-resistant bacteria were screened from a mariculture farm in northern China. Both sea cucumber and sea urchin rearing ponds were populated with abundant antibiotic-resistant bacteria, especially marine vibrios. Sixty-five percent chloramphenicol-resistant isolates from sea cucumber harbored a cat gene, either cat IV or cat II, whereas 35% sea urchin isolates harbored a cat gene, actually cat II. The predominant resistance determinant cat IV gene mainly occurred in isolates related to Vibrio tasmaniensis or Pseudoalteromonas atlantica, and the cat II gene mainly occurred in Vibrio splendidus-like isolates. All the cat-positive isolates also harbored one or two of the tet genes, tet(D), tet(B), or tet(A). As no chloramphenicol-related antibiotic was ever used, coselection of the cat genes by other antibiotics, especially oxytetracycline, might be the cause of the high incidence of cat genes in the mariculture farm studied.}, }
@article {pmid16909347, year = {2006}, author = {Findlay, S and Sinsabaugh, RL}, title = {Large-scale variation in subsurface stream biofilms: a cross-regional comparison of metabolic function and community similarity.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {491-500}, pmid = {16909347}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development/*metabolism ; Bacterial Physiological Phenomena ; Biofilms/*growth &amp; development ; Cluster Analysis ; *Ecosystem ; Environmental Monitoring/methods ; Enzymes/metabolism ; Fresh Water/chemistry/*microbiology ; Geologic Sediments ; Oxygen Consumption ; Random Amplified Polymorphic DNA Technique ; *Water Microbiology ; }, abstract = {We examined bacterial metabolic activity and community similarity in shallow subsurface stream sediments distributed across three regions of the eastern United States to assess whether there were parallel changes in functional and structural attributes at this large scale. Bacterial growth, oxygen consumption, and a suite of extracellular enzyme activities were assayed to describe functional variability. Community similarity was assessed using randomly amplified polymorphic DNA (RAPD) patterns. There were significant differences in streamwater chemistry, metabolic activity, and bacterial growth among regions with, for instance, twofold higher bacterial production in streams near Baltimore, MD, compared to Hubbard Brook, NH. Five of eight extracellular enzymes showed significant differences among regions. Cluster analyses of individual streams by metabolic variables showed clear groups with significant differences in representation of sites from different regions among groups. Clustering of sites based on randomly amplified polymorphic DNA banding resulted in groups with generally less internal similarity although there were still differences in distribution of regional sites. There was a marginally significant (p = 0.09) association between patterns based on functional and structural variables. There were statistically significant but weak (r2 approximately 30%) associations between landcover and measures of both structure and function. These patterns imply a large-scale organization of biofilm communities and this structure may be imposed by factor(s) such as landcover and covariates such as nutrient concentrations, which are known to also cause differences in macrobiota of stream ecosystems.}, }
@article {pmid16909346, year = {2006}, author = {Edwards, IP and Bürgmann, H and Miniaci, C and Zeyer, J}, title = {Variation in microbial community composition and culturability in the rhizosphere of Leucanthemopsis alpina (L.) Heywood and adjacent bare soil along an alpine chronosequence.}, journal = {Microbial ecology}, volume = {52}, number = {4}, pages = {679-692}, pmid = {16909346}, issn = {0095-3628}, mesh = {Bacteria/classification/*genetics ; *Biodiversity ; DNA, Bacterial/chemistry/genetics ; Electrophoresis/methods ; Molecular Sequence Data ; Phylogeny ; Plant Roots/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/*analysis ; Soil Microbiology ; Switzerland ; Time Factors ; }, abstract = {We compared the size, culturability, diversity, and dominant species similarity of the bacterial communities of Leucanthemopsis alpina (L.) Heywood rhizosphere and adjacent bare soil (interspace) along a chronosequence of soil development time (5, 50, and 70 years) in the forefield of the Dammaglacier (Switzerland). We found no evidence that the size of the bacterial community was significantly affected by either soil age or the presence of L. alpina. In contrast, the proportion of the bacterial community that could be cultured on nonselective agars, and which was taken as an indication of the proportion of r-selected populations, was significantly higher in the 50- and 70-year-old soils than in the 5-year-old soil, and was also significantly higher in the rhizosphere of L. alpina at all time points. RDA indicated significant correlations between the increased culturability of the bacterial community over time and increasing concentrations of labile N, and between the increased culturability in the rhizosphere and increased concentrations of labile C and N. HaeIII-amplified ribosomal DNA (rDNA) restriction analysis of a library of 120 clones of 16S rDNA revealed 85 distinct phylotypes. Hurlbert's probability of interspecific encounter (PIE) values derived from this library ranged from 0.95 to 1.0, indicating a very high genetic diversity. There was no significant difference in the PIE values of rhizosphere and interspace communities. Detrended correspondence analysis (DCA) of 16S ribosomal RNA (rRNA) denaturing gradient gel electrophoresis (DGGE) community profiles clearly distinguished the rhizosphere from the interspace community in the 5-year-old soils and also clearly distinguished between these communities and the rhizosphere and interspace communities of the 50- and 70-year-old soils. However, 16S rRNA DGGE revealed little difference between rhizosphere and interspace communities in the 50- and 70-year-old soils. The relative similarity of the 16S rRNA profiles strongly reflected labile carbon and nitrogen availability. Overall, our results suggest that improved C and N availability in the rhizosphere of L. alpina increases the size of r-selected bacterial species populations, but that the influence of L. alpina depends on soil age, being maximal in the youngest soils and minimal in the oldest. The reduced influence of L. alpina in the older soils may reflect a feedback between improved nutrient availability and reduced rhizodeposition.}, }
@article {pmid16909345, year = {2006}, author = {Heijs, SK and Aloisi, G and Bouloubassi, I and Pancost, RD and Pierre, C and Sinninghe Damsté, JS and Gottschal, JC and van Elsas, JD and Forney, LJ}, title = {Microbial community structure in three deep-sea carbonate crusts.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {451-462}, pmid = {16909345}, issn = {0095-3628}, mesh = {Anaerobiosis ; Archaea/classification/genetics/metabolism ; Biodiversity ; Carbon Dioxide/metabolism ; Carbonates/*metabolism ; DNA, Bacterial/chemistry ; Geologic Sediments/*analysis/microbiology ; Greenhouse Effect ; Lipids/analysis ; Methane/metabolism ; Phylogeny ; Proteobacteria/*classification/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Volcanic Eruptions ; *Water Microbiology ; }, abstract = {Carbonate crusts in marine environments can act as sinks for carbon dioxide. Therefore, understanding carbonate crust formation could be important for understanding global warming. In the present study, the microbial communities of three carbonate crust samples from deep-sea mud volcanoes in the eastern Mediterranean were characterized by sequencing 16S ribosomal RNA (rRNA) genes amplified from DNA directly retrieved from the samples. In combination with the mineralogical composition of the crusts and lipid analyses, sequence data were used to assess the possible role of prokaryotes in crust formation. Collectively, the obtained data showed the presence of highly diverse communities, which were distinct in each of the carbonate crusts studied. Bacterial 16S rRNA gene sequences were found in all crusts and the majority was classified as alpha-, gamma-, and delta- Proteobacteria. Interestingly, sequences of Proteobacteria related to Halomonas and Halovibrio sp., which can play an active role in carbonate mineral formation, were present in all crusts. Archaeal 16S rRNA gene sequences were retrieved from two of the crusts studied. Several of those were closely related to archaeal sequences of organisms that have previously been linked to the anaerobic oxidation of methane (AOM). However, the majority of archaeal sequences were not related to sequences of organisms known to be involved in AOM. In combination with the strongly negative delta 13C values of archaeal lipids, these results open the possibility that organisms with a role in AOM may be more diverse within the Archaea than previously suggested. Different communities found in the crusts could carry out similar processes that might play a role in carbonate crust formation.}, }
@article {pmid16909344, year = {2006}, author = {Waldrop, MP and Firestone, MK}, title = {Seasonal dynamics of microbial community composition and function in oak canopy and open grassland soils.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {470-479}, pmid = {16909344}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development/*metabolism ; Biomarkers/analysis ; Biomass ; Carbon/metabolism ; Carbon Isotopes/metabolism ; *Ecosystem ; Oxygen Consumption ; Phospholipids/analysis ; Plant Leaves/physiology ; Population Density ; Population Dynamics ; Quercus/*microbiology ; Seasons ; *Soil Microbiology ; Species Specificity ; Temperature ; Water/metabolism ; }, abstract = {Soil microbial communities are closely associated with aboveground plant communities, with multiple potential drivers of this relationship. Plants can affect available soil carbon, temperature, and water content, which each have the potential to affect microbial community composition and function. These same variables change seasonally, and thus plant control on microbial community composition may be modulated or overshadowed by annual climatic patterns. We examined microbial community composition, C cycling processes, and environmental data in California annual grassland soils from beneath oak canopies and in open grassland areas to distinguish factors controlling microbial community composition and function seasonally and in association with the two plant overstory communities. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid (PLFA) analysis, microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups using isotope labeling of PLFA biomarkers (13C-PLFA). Distinct microbial communities were associated with oak canopy soils and open grassland soils and microbial communities displayed seasonal patterns from year to year. The effects of plant species and seasonal climate on microbial community composition were similar in magnitude. In this Mediterranean ecosystem, plant control of microbial community composition was primarily due to effects on soil water content, whereas the changes in microbial community composition seasonally appeared to be due, in large part, to soil temperature. Available soil carbon was not a significant control on microbial community composition. Microbial community composition (PLFA) and 13C-PLFA ordination values were strongly related to intra-annual variability in soil enzyme activities and soil respiration, but microbial biomass was not. In this Mediterranean climate, soil microclimate appeared to be the master variable controlling microbial community composition and function.}, }
@article {pmid16909343, year = {2006}, author = {Oline, DK and Schmidt, SK and Grant, MC}, title = {Biogeography and landscape-scale diversity of the dominant Crenarchaeota of soil.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {480-490}, pmid = {16909343}, issn = {0095-3628}, mesh = {Base Sequence ; Biodiversity ; Biomass ; Cluster Analysis ; Crenarchaeota/*classification/*genetics/growth &amp; development ; DNA, Archaeal/*chemistry/genetics ; *Ecosystem ; Gene Amplification ; Geography ; Likelihood Functions ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction/methods ; *Soil Microbiology ; }, abstract = {We surveyed the diversity of soil Archaea across a large scale elevational gradient of ecosystem types, from foothills forest to alpine tundra in the Front Range of the Rocky Mountains. We used a dilution technique to sequence the single most abundant archaeal 16S rDNA sequence in each of the 40 soil cores distributed across the gradient to compare our results to those of typical 16S clone library studies. We found a greater diversity of sequences than has typically been found in clone library studies from a single site or core, identifying sequences both from the Terrestrial Group and the FFSB Group at several sites. We did not observe any significant environmental correlates with the dominant sequence type, nor was there any relationship between the spatial distance between samples and the phylogenetic similarity of the dominant sequence types. Despite using a very different methodology, our collective results are in remarkably good agreement with other studies of soil Crenarchaeota in terms of the diversity and relative abundance of sequence types identified. We are able to identify two instances of very tightly clustered sequences which we suggest are the results of global selective sweeps-one closely related to SCA1145, an abundant globally distributed group within the Terrestrial Group of Crenarchaeota, and another nested within the more basal FFSB group of sequences. We replicated our sequence results at two levels: first, by repeating the dilution and PCR processes from the same soil core DNA extraction, and second, by performing a replicate DNA extraction from the same homogenized soil core sample. Pairs of sequences produced by the dilution replicates were significantly more similar than the pairs of sequences produced by the extraction replicates, suggesting that soil Crenarchaeota exists in highly localized and discrete clonal populations.}, }
@article {pmid16909342, year = {2006}, author = {Bärlocher, F and Nikolcheva, LG and Wilson, KP and Williams, DD}, title = {Fungi in the hyporheic zone of a springbrook.}, journal = {Microbial ecology}, volume = {52}, number = {4}, pages = {708-715}, pmid = {16909342}, issn = {0095-3628}, mesh = {Canada ; DNA, Fungal/analysis/*genetics ; Electrophoresis/methods ; Geologic Sediments/microbiology ; Mitosporic Fungi/*genetics/isolation &amp; purification/physiology ; Ontario ; Seasons ; Spores, Fungal/genetics/growth &amp; development ; }, abstract = {Eight bimonthly sediment core samples (n = 6) were collected, to a depth of 64 cm, from the hyporheic zone of a springbrook in southern Ontario, Canada. Sediment cores were divided into three to four sections, and organic matter was subdivided into six different categories. Twigs were the most common substrate, followed by roots, cedar leaves, wood, grass, and deciduous leaves. The contributions of deciduous and cedar leaves declined with depth, whereas that of wood increased. On each sampling date and from each section, three randomly chosen substrates >3 cm were examined for conidia of aquatic hyphomycetes. The number of identified species significantly decreased with depth, and was highest on deciduous leaves and lowest on wood. Season had no significant effect on species numbers. DNA from substrates was extracted, amplified with fungal primers, and differentiated into phylotypes with denaturing gradient gel electrophoresis (DGGE). Absence/presence patterns of phylotype were significantly affected by season but not by section level. Both season and section level significantly affected relative densities of the bands of the 10 most common phylotypes. Our data suggest that aquatic hyphomycetes and other fungi readily disperse within the hyporheic zone, and that their relative scarcity in this habitat is due to a lack of suitable substrates.}, }
@article {pmid16907754, year = {2006}, author = {Uz, I and Ogram, AV}, title = {Cellulolytic and fermentative guilds in eutrophic soils of the Florida Everglades.}, journal = {FEMS microbiology ecology}, volume = {57}, number = {3}, pages = {396-408}, doi = {10.1111/j.1574-6941.2006.00120.x}, pmid = {16907754}, issn = {0168-6496}, mesh = {Carbon/chemistry/metabolism ; Cellulose/*metabolism ; Clostridium/genetics ; *Ecosystem ; *Eutrophication ; Fermentation ; Florida ; Fresh Water ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Soil/*analysis ; *Soil Microbiology ; }, abstract = {The northern Florida Everglades has been subject to eutrophication in recent years, resulting in well-documented changes in microbial ecology and a shift in the dominant plant species. This study investigated effects of plant quality and eutrophication on activities and composition of cellulolytic and fermentative guilds in soils. Most probable numbers of cellulolytic bacteria in eutrophic (F1) and transition (F4) soils were 10-fold higher than in oligotrophic soils (U3). Higher potential methanogenesis was observed from cellulose in microcosms with soils from F1 and F4, compared to U3 soils. Nutrient status of soil, rather than plant type, was the major factor controlling methanogenesis rates, although numbers of fermentative bacteria were higher in microcosms supplemented with ground cattail (dominant in F1 and F4) than with sawgrass (dominant component of soil in U3), regardless of soil origin. DNA sequence analysis indicated Clostridium assemblage composition correlates with soil nutrient status.}, }
@article {pmid16907753, year = {2006}, author = {Rillig, MC and Mummey, DL and Ramsey, PW and Klironomos, JN and Gannon, JE}, title = {Phylogeny of arbuscular mycorrhizal fungi predicts community composition of symbiosis-associated bacteria.}, journal = {FEMS microbiology ecology}, volume = {57}, number = {3}, pages = {389-395}, doi = {10.1111/j.1574-6941.2006.00129.x}, pmid = {16907753}, issn = {0168-6496}, mesh = {Bacteria/*growth &amp; development/metabolism ; Cluster Analysis ; Fatty Acids/metabolism ; Mycorrhizae/*genetics/*growth &amp; development/metabolism ; Phospholipids/metabolism ; Phylogeny ; Soil Microbiology ; Symbiosis ; }, abstract = {Many physicochemical and biotic aspects of the soil environment determine the community composition of bacteria. In this study, we examined the effects of arbuscular mycorrhizal fungi, common symbionts of higher plants, on the composition of bacterial communities after long-term (7-8 years) enrichment culture in the presence of a plant host. We showed that the phylogeny of arbuscular mycorrhizal fungal isolates was a highly significant predictor of bacterial community composition, as assessed by cluster analysis, redundancy analysis and linear discriminant analysis of phospholipid fatty acid patterns. Numerous phospholipid fatty acids differed between the phylogenetic groupings; this pattern also held for fungal-origin phospholipid fatty acids and in a combined bacterial/fungal analysis, suggesting that categorizing phospholipid fatty acids into predominantly bacterial and fungal origin did not affect the overall outcome. The mechanisms underlying this observation could include substrate quality (and quantity) effects, interactions mediated by the host plant (e.g. rhizodeposition) and direct biotic interactions between arbuscular mycorrhizal fungi and bacterial populations. Our results suggest that aspects of arbuscular mycorrhizal fungal functions may be partially explained by the symbiosis-accompanying bacterial communities, a possibility that should be explicitly considered in studies examining the roles of arbuscular mycorrhizal fungal species diversity in soil and ecosystem processes.}, }
@article {pmid16902030, year = {2006}, author = {Gao, H and Obraztova, A and Stewart, N and Popa, R and Fredrickson, JK and Tiedje, JM and Nealson, KH and Zhou, J}, title = {Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {56}, number = {Pt 8}, pages = {1911-1916}, doi = {10.1099/ijs.0.64354-0}, pmid = {16902030}, issn = {1466-5026}, mesh = {Base Composition ; Culture Media ; Cyanoacrylates/analysis ; DNA, Bacterial/chemistry ; Fatty Acids/analysis ; Genome, Bacterial ; Iron ; *Marine Biology ; Molecular Sequence Data ; Pacific Ocean ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Homology, Nucleic Acid ; Shewanella/chemistry/*classification/isolation &amp; purification/physiology ; Species Specificity ; Temperature ; Ubiquinone/analysis ; Vitamin K 2/analogs &amp; derivatives ; *Water Microbiology ; }, abstract = {A novel marine bacterial strain, PV-4(T), isolated from a microbial mat located at a hydrothermal vent of Loihi Seamount in the Pacific Ocean, has been characterized. This micro-organism is orangey in colour, Gram-negative, polarly flagellated, facultatively anaerobic and psychrotolerant (temperature range, 0-42 degrees C). No growth was observed with nitrate, nitrite, DMSO or thiosulfate as the electron acceptor and lactate as the electron donor. The major fatty acid detected in strain PV-4(T) was iso-C(15 : 0). Strain PV-4(T) had ubiquinones consisting mainly of Q-7 and Q-8, and possessed menaquinone MK-7. The DNA G+C content of the strain was 53.8 mol% and the genome size was about 4.5 Mbp. Phylogenetic analyses based on 16S rRNA gene sequences placed PV-4(T) within the genus Shewanella. PV-4(T) exhibited 16S rRNA gene sequence similarity levels of 99.6 and 97.5 %, respectively, with respect to the type strains of Shewanella aquimarina and Shewanella marisflavi. DNA from strain PV-4(T) showed low mean levels of relatedness to the DNAs of S. aquimarina (50.5 %) and S. marisflavi (8.5 %). On the basis of phylogenetic and phenotypic characteristics, the bacterium was classified in the genus Shewanella within a distinct novel species, for which the name Shewanella loihica sp. nov. is proposed. The type strain is PV-4(T) (=ATCC BAA-1088(T)=DSM 17748(T)).}, }
@article {pmid16901680, year = {2006}, author = {Verthé, K and Verstraete, W}, title = {Use of flow cytometry for analysis of phage-mediated killing of Enterobacter aerogenes.}, journal = {Research in microbiology}, volume = {157}, number = {7}, pages = {613-618}, doi = {10.1016/j.resmic.2006.02.007}, pmid = {16901680}, issn = {0923-2508}, mesh = {*Bacteriolysis ; Bacteriophages/*physiology ; Colony Count, Microbial ; Culture Media ; Disinfection/methods ; Enterobacter aerogenes/growth &amp; development/pathogenicity/physiology/*virology ; Flow Cytometry/*methods ; Lysogeny ; Polytetrafluoroethylene ; Temperature ; }, abstract = {In this study, the use of flow cytometry to analyze phage-mediated killing of Enterobacter aerogenes under varying conditions of temperature and nutrient availability was assessed. Bacteriophage UZ1, specific for an E. aerogenes strain, was applied at a multiplicity of infection (MOI) of 1 and 1000 to a Teflon surface, artificially infected with its host at a level of 4.5 log cells. After incubation for 20 h, bacteriophages were quantified using the soft agar layer method. For the quantification of bacterial cells, plate counting and flow cytometric analysis of live/dead stained cells were performed in parallel. At an MOI of 1, phage treatment was successful only after incubation under nutrient-rich conditions at 37 degrees C: E. aerogenes cells were not detected and a tenfold increase in phage UZ1 was observed. At a MOI of 1000, no E. aerogenes cells could be cultured after incubation at 37 and 4 degrees C. However, flow cytometric analysis revealed that lysis did not occur at 4 degrees C but was achieved during subsequent plate culture. In conclusion, the use of flow cytometry enabled identification of culture-based bias during plate culture. The flow cytometric assay used in this study proved to be rapid, as this culture-independent method does not require lengthy incubation periods post-sampling. The bacteriophage-mediated killing of E. aerogenes cells on Teflon surfaces indicated that disinfection of E. aerogenes with bacteriophage UZ1 can be successful when high MOIs are achieved, while at low multiplicities of infection conditions favorable for phage replication are required.}, }
@article {pmid16900091, year = {2006}, author = {Gomila, M and Gascó, J and Gil, J and Bernabeu, R and Iñigo, V and Lalucat, J}, title = {A molecular microbial ecology approach to studying hemodialysis water and fluid.}, journal = {Kidney international}, volume = {70}, number = {9}, pages = {1567-1576}, doi = {10.1038/sj.ki.5001756}, pmid = {16900091}, issn = {0085-2538}, mesh = {Alphaproteobacteria/genetics/isolation &amp; purification ; Bacterial Infections/*diagnosis/*etiology/genetics ; Colony Count, Microbial ; Cyanobacteria/genetics/isolation &amp; purification ; DNA Fingerprinting ; DNA, Bacterial/*analysis/genetics ; Gene Library ; Hemodialysis Solutions/*adverse effects ; Herbaspirillum/genetics/isolation &amp; purification ; Humans ; Microbiological Techniques/*methods ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bacteria, or bacteria-derived products, might be responsible for deleterious effects in hemodialysis patients. Most microorganisms in hemodialysis water, including potential pathogens, are difficult to isolate and might subsist in a 'viable but not culturable' state or may need specific culture media. A molecular culture-independent approach based on the analysis of the 16S rDNA obtained from total DNA has been used to better know the diversity of bacteria inhabiting hemodialysis water and fluid, and to address the possible health effects associated with their presence. Four clone libraries from 16S rDNA (274 clones) were analyzed to characterize the species or groups of bacteria present, to assess their distribution in the water circuit, and to compare the results with those previously obtained in culture-dependent analysis. One hundred and ninety-seven clones of four gene libraries were analyzed by sequencing, and were identified phylogenetically. Clones affiliated to the Alphaproteobacteria group led the diversity. The presence in several samples of Alpha-4-proteobacteria, recognized as sphingolipids producers, was to be noted. The most abundant clones were affiliated to the Betaproteobacteria branch, closely related to the genus Herbaspirillum. As known, Alphaproteobacteria and Betaproteobacteria genomes might present a manifest excess in CpG sequences and most of them show a lipopolysaccharide-rich outer membrane, both described as inducers of innate immunity responses. Another abundant group, belonging to the Cyanobacteria class, a possible source of cyanotoxins, was not related to any previously cultured bacterium. Possible risk implications for hemodialysis patients of the bacterial community detected are discussed.}, }
@article {pmid16898133, year = {2006}, author = {Daims, H and Maixner, F and Lücker, S and Stoecker, K and Hace, K and Wagner, M}, title = {Ecophysiology and niche differentiation of Nitrospira-like bacteria, the key nitrite oxidizers in wastewater treatment plants.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {54}, number = {1}, pages = {21-27}, doi = {10.2166/wst.2006.367}, pmid = {16898133}, issn = {0273-1223}, mesh = {Bacteria/classification/*metabolism ; *Ecosystem ; Environmental Restoration and Remediation ; *Industrial Waste ; Microscopy, Confocal ; Nitrites/*metabolism ; Phylogeny ; *Water Microbiology ; }, abstract = {Nitrite-oxidizing bacteria of the genus Nitrospira are key nitrifiers in wastewater treatment plants. Pure cultures of these organisms are unavailable, but cultivation-independent molecular methods make it possible to detect Nitrospira-like bacteria in environmental samples and to investigate their ecophysiology. Comprehensive screening of natural and engineered habitats and of public databases for 16S rRNA sequences of Nitrospira-like bacteria revealed a surprisingly high biodiversity in the genus Nitrospira, which comprises at least four phylogenetic sublineages. All Nitrospira-like bacteria detected in wastewater treatment plants belonged to the sublineages I and II. Subsequently, the population dynamics of different Nitrospira-like bacteria were monitored, by quantitative fluorescence in situ hybridization with rRNA-targeted probes, confocal laser scanning microscopy and digital image analysis, during incubation of nitrifying activated sludge in media containing different nitrite concentrations. These experiments showed that Nitrospira-like bacteria, which were affiliated with the phylogenetic sublineages I or II of the genus Nitrospira, responded differently to nitrite concentration shifts. Previously unknown properties of Nitrospira-like bacteria were discovered in the course of an environmental genomics project. Implications of the obtained results for fundamental understanding of the microbial ecology of nitrite oxidizers as well as for future improvement of nutrient removal in wastewater treatment plants are discussed.}, }
@article {pmid16897311, year = {2006}, author = {Hyun, JH}, title = {Resource-limited heterotrophic prokaryote production and its potential environmental impact associated with Mn nodule exploitation in the northeast equatorial pacific.}, journal = {Microbial ecology}, volume = {52}, number = {2}, pages = {244-252}, pmid = {16897311}, issn = {0095-3628}, mesh = {Biodiversity ; Biomass ; *Conservation of Natural Resources ; Food Chain ; Geologic Sediments/analysis ; *Manganese ; *Mining ; Pacific Ocean ; Prokaryotic Cells/*metabolism ; Water/*analysis ; Water Pollution ; }, abstract = {Shipboard enrichment incubation experiments were performed to elucidate the limiting resources for heterotrophic prokaryotic production and to discuss the potential impact of bottom water and sediment discharges in relation to manganese (Mn) nodule exploitation on the heterotrophic prokaryotes in the oligotrophic northeast equatorial Pacific. Compared to an unamended control, the production of heterotrophic prokaryotes increased 25-fold in water samples supplemented with amino acids (i.e., organic carbon plus nitrogen), whereas the production increased five and two times, respectively, in samples supplemented with either glucose or ammonium alone. These results indicate that heterotrophic prokaryote production in the northeast equatorial Pacific was co-limited by the availability of dissolved organic carbon and inorganic nitrogen. In samples from the nutrient-depleted surface mixed layer (10-m depth), the addition of a slurry of bottom water and sediment doubled heterotrophic prokaryote production compared to an unamended control, whereas sonicating the slurry prior to addition quadrupled the production rate. However, little difference was observed between an unamended control and slurry-amended samples in the subsurface chlorophyll a (Chl a) maximum (SCM) layer. Thus, the impact of slurry discharge is more significant at the nutrient-depleted surface mixed layer than at the high-nutrient SCM layer. The greatly enhanced prokaryote production resulting from the addition of sonicated slurry further suggests that dissociated organic carbon may directly stimulate heterotrophic prokaryote production in the surface mixed layer. Overall, the results suggest that the surface discharge of bottom water and sediments during manganese nodule exploitation could have a significant environmental impact on the production of heterotrophic prokaryotes that are currently resource limited.}, }
@article {pmid16897310, year = {2006}, author = {Franklin, RB and Mills, AL}, title = {Structural and functional responses of a sewage microbial community to dilution-induced reductions in diversity.}, journal = {Microbial ecology}, volume = {52}, number = {2}, pages = {280-288}, pmid = {16897310}, issn = {0095-3628}, mesh = {*Biodiversity ; Carbon/metabolism ; Carbon Radioisotopes ; Colony Count, Microbial ; DNA Fingerprinting ; Polymorphism, Restriction Fragment Length ; Sewage/*microbiology ; }, abstract = {The relationship between functional redundancy and microbial community structure-diversity was examined using laboratory incubations to ensure constant environmental conditions. Serial dilutions of a sewage microbial community were prepared, used to inoculate sterile sewage, and maintained in batch culture. Probability suggests that dilution of the initial community should remove rare organism types, creating mixtures of cells differing in diversity. Regrowth of the diluted mixtures generated communities similar in abundance but differing in community structure and relative diversity (as determined using two DNA fingerprinting techniques and dilution-to-extinction analysis of community-level physiological profiles). The in situ function of each regrown community was examined by monitoring the short-term uptake of five different (14)C-labeled compounds (glucose, acetate, citrate, palmitic acid, and an amino acid mixture). No significant differences were detected between treatments in either the rate of uptake of a substrate or the efficiency with which each community assimilated each compound. The fact that the activity of the original community was the same as that of a community regrown from an inoculum containing fewer that 100 cells (10(-6) dilution) indicates that functional redundancy was quite high in this system. For each organism type eliminated during the dilution process, at least one of the remaining types was able to provide the same function at the same level as the lost one. Further research is necessary to determine what impact this functional redundancy may have on overall ecosystem function and stability.}, }
@article {pmid16897309, year = {2006}, author = {Salles, JF and van Elsas, JD and van Veen, JA}, title = {Effect of agricultural management regime on Burkholderia community structure in soil.}, journal = {Microbial ecology}, volume = {52}, number = {2}, pages = {267-279}, pmid = {16897309}, issn = {0095-3628}, mesh = {*Agriculture ; Basidiomycota ; Biodiversity ; Burkholderia/classification/genetics/*physiology ; Electrophoresis, Agar Gel ; Pest Control, Biological ; Polymerase Chain Reaction ; *Soil Microbiology ; Zea mays/growth &amp; development ; }, abstract = {The main objective of this study was to determine the Burkholderia community structure associated with areas under different agricultural management and to evaluate to which extent this community structure is affected by changes in agricultural management. Two fields with distinct soil history (arable land and permanent grassland) were exposed to three agricultural management regimes (crop rotation, maize monoculture, and grassland). By using a culture-independent approach, based on a Burkholderia-specific polymerase chain reaction-denaturing gradient gel electrophoresis system, it was possible to observe the conversion of Burkholderia communities typical for permanent grassland to those of arable land after four consecutive years. However, the time needed to achieve the reverse transition, i.e., converting the Burkholderia community associated with arable land to that of grassland, was beyond the duration of the field experiment. In addition, by applying principal response curves, the direction and extent of the conversion from grassland to arable land (maize monoculture and to crop rotation) were determined. Hence, the results suggested that agricultural practices, such as fertilization and tillage, were more effective in changing the Burkholderia community structure than agricultural management regime. To determine the effect of agricultural management on the Burkholderia population with biocontrol abilities, the culturable fraction of the Burkholderia community was assessed. The areas under permanent grassland and grassland converted to maize monoculture had the highest percentages of Burkholderia strains with antagonistic activity against Rhizoctonia solani AG-3, mainly Burkholderia pyrrocinia and Burkholderia sp. LMG 22929. The isolation frequency of antagonistic isolates from arable land was extremely low. Our results indicate that (changes in) agricultural management, mainly crop rotation, affect the frequency of isolation of antagonistic Burkholderia strains and that grassland represents a reservoir of Burkholderia species with great potential for agricultural applications.}, }
@article {pmid16897308, year = {2006}, author = {Pereira, SI and Lima, AI and Figueira, EM}, title = {Screening possible mechanisms mediating cadmium resistance in Rhizobium leguminosarum bv. viciae isolated from contaminated Portuguese soils.}, journal = {Microbial ecology}, volume = {52}, number = {2}, pages = {176-186}, pmid = {16897308}, issn = {0095-3628}, mesh = {Bacterial Proteins/metabolism ; Cadmium/*pharmacology ; *Environmental Pollution ; Lipopolysaccharides/biosynthesis ; Plasmids/genetics ; Portugal ; Rhizobium leguminosarum/*drug effects/isolation &amp; purification/metabolism ; Soil/*analysis ; *Soil Microbiology ; }, abstract = {Environment heavy-metal contamination is now widespread. Soils may become contaminated from a variety of anthropogenic sources, such as smelters, mining, industry, and application of metal-containing pesticides and fertilizers. Soil microorganisms are very sensitive to moderate heavy-metal concentrations. Therefore, the present work was designed to screen possible mechanisms involved in Rhizobium's Cd resistance; with this purpose, we determined the tolerance levels of several isolates originated from sites with different heavy-metal contamination. Whole-cell-soluble proteins and plasmid profiles were analyzed. We also determined Cd cell concentrations and lipopolysaccharide (LPS) amounts. Results showed different tolerances among Rhizobium isolates; according to their maximum resistance level, isolates were divided in four groups: sensitive (0-125 microM CdCl(2)), moderately tolerant (125-210 microM CdCl(2)), tolerant (250-500 microM CdCl(2)), and extremely tolerant (> or =750 microM CdCl(2)). Intracellular Cd concentrations were lower when compared to wall-bound Cd. Unexpectedly, extremely tolerant isolates accumulated higher levels of metal, suggesting the presence of intracellular agents that prevent metal interfering with important metabolic pathways. The electrophoretic patterns of whole-cell-soluble proteins evidenced cadmium as an inducer of protein metabolism alterations, which were more evident in some polypeptides. Plasmid profiles also showed differences; most tolerant isolates presented two plasmids with molecular weights of 485 and 415 kb, indicating that extrachromosomal DNA may be involved in cadmium resistance. LPS showed to be a common mechanism of resistance. However, the degree of tolerance conferred by LPS is not enough to support tolerance to the higher levels of stress imposed. Presence of other resistance mechanisms is currently being investigated.}, }
@article {pmid16897307, year = {2006}, author = {Marshall, K and Joint, I and Callow, ME and Callow, JA}, title = {Effect of marine bacterial isolates on the growth and morphology of axenic plantlets of the green alga Ulva linza.}, journal = {Microbial ecology}, volume = {52}, number = {2}, pages = {302-310}, pmid = {16897307}, issn = {0095-3628}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; DNA, Ribosomal/chemistry ; Germ-Free Life/physiology ; Phylogeny ; Sequence Analysis, DNA ; Ulva/cytology/growth &amp; development/*microbiology ; }, abstract = {The green marine macroalga, Ulva linza, adopts an "atypical" form when grown in the absence of bacteria. Twenty unique strains of periphytic bacteria, isolated from three species of Ulva, were identified by 16S rDNA sequencing. These isolates were assessed for their effect on the growth and morphological development of axenic plantlets of U. linza. Results showed that the effect of bacterial strains was strain- but not taxon-specific. Thirteen isolates returned the aberrant morphology to normal and of these, five also significantly increased growth rate. One isolate increased growth, but had no effect on morphology. Biofilms of some of these isolates stimulated the settlement of Ulva zoospores but there was no correlation between bacterial isolates that stimulated zoospore settlement and those that initiated changes in morphology and/or growth of the cultured alga.}, }
@article {pmid16897306, year = {2006}, author = {Joubert, LM and Wolfaardt, GM and Botha, A}, title = {Microbial exopolymers link predator and prey in a model yeast biofilm system.}, journal = {Microbial ecology}, volume = {52}, number = {2}, pages = {187-197}, pmid = {16897306}, issn = {0095-3628}, mesh = {Animals ; *Biofilms ; Cryptococcus/cytology/metabolism/*physiology ; *Food Chain ; Plankton/physiology ; Polymers/*metabolism ; Tetrahymena/cytology/*metabolism/physiology ; }, abstract = {Protistan grazing on biofilms is potentially an important conduit enabling energy flow between microbial trophic levels. Contrary to the widely held assumption that protistan feeding primarily involves ingestion of biofilm cells, with negative consequences for the biofilm, this study demonstrated preferential grazing on the noncellular biofilm matrix by a ciliate, with selective ingestion of yeast and bacterial cells of planktonic origin over attached and biofilm-derived planktonic cells. Introducing a ciliate to two biofilm-forming Cryptococcus species, as well as two bacterial species in a model biofilm system, fluorescent probes were applied to determine ingestion of cellular and noncellular biofilm fractions. Fluoromicroscopy, as well as photometric quantification, confirmed that protistan grazing enhanced yeast biofilm metabolism, and an increase in biofilm biomass and viability. We propose that the extracellular polymeric matrix of biofilms may act as an interface regulating interaction between predator and prey, while serving as source of nutrients and energy for protists.}, }
@article {pmid16897305, year = {2006}, author = {Maddula, VS and Zhang, Z and Pierson, EA and Pierson, LS}, title = {Quorum sensing and phenazines are involved in biofilm formation by Pseudomonas chlororaphis (aureofaciens) strain 30-84.}, journal = {Microbial ecology}, volume = {52}, number = {2}, pages = {289-301}, pmid = {16897305}, issn = {0095-3628}, mesh = {Bacterial Proteins/genetics/metabolism ; Biofilms/*growth &amp; development ; DNA-Binding Proteins/genetics/metabolism ; Mutation ; Phenazines/*metabolism ; Plant Roots/microbiology ; Pseudomonas/genetics/metabolism/*physiology ; Seeds/microbiology ; *Signal Transduction ; Trans-Activators/genetics/metabolism ; Triticum/embryology/microbiology ; }, abstract = {The biological control bacterium Pseudomonas chlororaphis (aureofaciens) strain 30-84 employs two quorum sensing (QS) systems: PhzR/PhzI regulates the production of the antibiotics phenazine-1-carboxylic acid, 2-hydroxy-phenazine-1-carboxylic acid, and 2-hydroxy-phenazine, whereas CsaR/CsaI regulates currently unknown aspects of the cell surface. Previously characterized derivatives of strain 30-84 with mutations in each QS system and in the phenazine biosynthetic genes were screened for their ability to form surface-attached biofilm populations in vitro, using microtiter plate and flow cell biofilm assays, and on seeds and roots. Results from in vitro, seed, and root studies demonstrated that the PhzR/PhzI and the CsaR/CsaI QS regulatory systems contribute to the establishment of biofilms, with mutations in PhzR/PhzI having a significantly greater effect than mutations in CsaR/CsaI. Interestingly, phenazine antibiotic production was necessary for biofilm formation to the same extent as the PhzR/PhzI QS system, suggesting the loss of phenazines was responsible for the majority of the biofilm defect in these mutants. In vitro analysis indicated that genetic complementation or AHL addition to the growth medium restored the ability of the AHL synthase phzI mutant to form biofilms. However, only phenazine addition or genetic complementation of the phenazine biosynthetic mutation in trans restored biofilm formation by mutants defective in the transcriptional activator phzR or the phzB structural mutant. QS and phenazine production were also involved in the establishment of surface-attached populations on wheat seeds and plant roots, and, as observed in vitro, the addition of AHL extracts restored the ability of phzI mutants, but not phzR mutants, to form surface attached populations on seeds. Similarly, the presence of the wild type in mixtures with the mutants restored the ability of the mutants to colonize wheat roots, demonstrating that AHL and/or phenazine production by the wild-type population could complement the AHL- and phenazine-deficient mutants in situ. Together, these data demonstrate that both QS systems are involved in the formation of surface-attached populations required for biofilm formation by P. chlororaphis strain 30-84, and indicate a new role for phenazine antibiotics in rhizosphere community development beyond inhibition of other plant-associated microorganisms.}, }
@article {pmid16897304, year = {2006}, author = {Osaka, T and Yoshie, S and Tsuneda, S and Hirata, A and Iwami, N and Inamori, Y}, title = {Identification of acetate- or methanol-assimilating bacteria under nitrate-reducing conditions by stable-isotope probing.}, journal = {Microbial ecology}, volume = {52}, number = {2}, pages = {253-266}, pmid = {16897304}, issn = {0095-3628}, mesh = {Acetates/*metabolism ; Bacteria/*classification/growth &amp; development/metabolism ; Carbon Isotopes ; Gene Library ; Genetic Markers ; Methanol/*metabolism ; Molecular Probe Techniques ; Molecular Sequence Data ; Nitrates/*metabolism ; Nitrite Reductases/genetics ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/genetics ; Sequence Analysis, DNA/*methods ; Sewage/*microbiology ; Water Purification ; }, abstract = {Stable-isotope probing (SIP) was used to identify acetate- or methanol-assimilating bacteria under nitrate-reducing conditions in activated sludge. A sludge sample obtained from wastewater treatment systems was incubated in a denitrifying batch reactor fed with synthetic wastewater containing [(13)C]acetate or [(13)C]methanol as the main carbon source and nitrate as the electron acceptor. We analyzed how growth of bacterial populations was stimulated by acetate or methanol as the external carbon source in nitrogen-removal systems. Most of the acetate- or methanol-assimilating bacteria identified by SIP have been known as denitrifiers in wastewater treatment systems. When acetate was used as the carbon source, 16S rRNA gene sequences retrieved from (13)C-labeled DNA were closely related to the 16S rRNA genes of Comamonadaceae (e.g., Comamonas and Acidovorax) and Rhodocyclaceae (e.g., Thauera and Dechloromonas) of the Betaproteobacteria, and Rhodobacteraceae (e.g., Paracoccus and Rhodobacter) of the Alphaproteobacteria. When methanol was used as the carbon source, 16S rRNA gene sequences retrieved from (13)C-DNA were affiliated with Methylophilaceae (e.g., Methylophilus, Methylobacillus, and Aminomonas) and Hyphomicrobiaceae. Rarefaction curves for clones retrieved from (13)C-DNA showed that the diversity levels for methanol-assimilating bacteria were considerably lower than those for acetate-assimilating bacteria. Furthermore, we characterized nitrite reductase genes (nirS and nirK) as functional marker genes for denitrifier communities in acetate- or methanol-assimilating populations and detected the nirS or nirK sequence related to that of some known pure cultures, such as Alcaligenes, Hyphomicrobium, and Thauera. However, most of the nirS or nirK sequences retrieved from (13)C-DNA were clustered in some unidentified groups. On the basis of 16S rRNA gene clone libraries retrieved from (13)C-DNA, these unidentified nir sequences might be identified by examining the nir gene in candidates for true denitrifiers (e.g., the families Comamonadaceae, Hyphomicrobiaceae, Methylophilaceae, and Rhodobacteraceae).}, }
@article {pmid16897303, year = {2006}, author = {Gentry, TJ and Wickham, GS and Schadt, CW and He, Z and Zhou, J}, title = {Microarray applications in microbial ecology research.}, journal = {Microbial ecology}, volume = {52}, number = {2}, pages = {159-175}, pmid = {16897303}, issn = {0095-3628}, mesh = {Bacteria/classification/genetics ; Biodiversity ; Ecology/*methods ; Fungi/classification/genetics ; Genetic Markers ; Oligonucleotide Array Sequence Analysis/*methods ; Phylogeny ; RNA, Ribosomal/classification ; *Soil Microbiology ; }, abstract = {Microarray technology has the unparalleled potential to simultaneously determine the dynamics and/or activities of most, if not all, of the microbial populations in complex environments such as soils and sediments. Researchers have developed several types of arrays that characterize the microbial populations in these samples based on their phylogenetic relatedness or functional genomic content. Several recent studies have used these microarrays to investigate ecological issues; however, most have only analyzed a limited number of samples with relatively few experiments utilizing the full high-throughput potential of microarray analysis. This is due in part to the unique analytical challenges that these samples present with regard to sensitivity, specificity, quantitation, and data analysis. This review discusses specific applications of microarrays to microbial ecology research along with some of the latest studies addressing the difficulties encountered during analysis of complex microbial communities within environmental samples. With continued development, microarray technology may ultimately achieve its potential for comprehensive, high-throughput characterization of microbial populations in near real time.}, }
@article {pmid16897302, year = {2006}, author = {Miller, WA and Miller, MA and Gardner, IA and Atwill, ER and Byrne, BA and Jang, S and Harris, M and Ames, J and Jessup, D and Paradies, D and Worcester, K and Melli, A and Conrad, PA}, title = {Salmonella spp., Vibrio spp., Clostridium perfringens, and Plesiomonas shigelloides in marine and freshwater invertebrates from coastal California ecosystems.}, journal = {Microbial ecology}, volume = {52}, number = {2}, pages = {198-206}, pmid = {16897302}, issn = {0095-3628}, mesh = {Animals ; Bacteria/*isolation &amp; purification ; Bivalvia/*microbiology ; California ; Clostridium perfringens/isolation &amp; purification ; *Ecosystem ; Environmental Exposure ; Fresh Water/microbiology ; Oceans and Seas ; Plesiomonas/isolation &amp; purification ; Risk Factors ; Salmonella/isolation &amp; purification ; Sewage/microbiology ; Vibrio/isolation &amp; purification ; *Water Microbiology ; }, abstract = {The coastal ecosystems of California are highly utilized by humans and animals, but the ecology of fecal bacteria at the land-sea interface is not well understood. This study evaluated the distribution of potentially pathogenic bacteria in invertebrates from linked marine, estuarine, and freshwater ecosystems in central California. A variety of filter-feeding clams, mussels, worms, and crab tissues were selectively cultured for Salmonella spp., Campylobacter spp., Escherichia coli-O157, Clostridium perfringens, Plesiomonas shigelloides, and Vibrio spp. A longitudinal study assessed environmental risk factors for detecting these bacterial species in sentinel mussel batches. Putative risk factors included mussel collection near higher risk areas for livestock or human sewage exposure, adjacent human population density, season, recent precipitation, water temperature, water type, bivalve type, and freshwater outflow exposure. Bacteria detected in invertebrates included Salmonella spp., C. perfringens, P. shigelloides, Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio alginolyticus. Overall, 80% of mussel batches were culture positive for at least one of the bacterial species, although the pathogens Campylobacter, E. coli-O157, and Salmonella were not detected. Many of the same bacterial species were also cultured from upstream estuarine and riverine invertebrates. Exposure to human sewage sources, recent precipitation, and water temperature were significant risk factors for bacterial detection in sentinel mussel batches. These findings are consistent with the hypothesis that filter-feeding invertebrates along the coast concentrate fecal bacteria flowing from land to sea and show that the relationships between anthropogenic effects on coastal ecosystems and the environmental niches of fecal bacteria are complex and dynamic.}, }
@article {pmid16897301, year = {2006}, author = {Laguerre, G and Courde, L and Nouaïm, R and Lamy, I and Revellin, C and Breuil, MC and Chaussod, R}, title = {Response of rhizobial populations to moderate copper stress applied to an agricultural soil.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {426-435}, pmid = {16897301}, issn = {0095-3628}, mesh = {Agriculture ; Biodiversity ; Copper/*pharmacology ; Copper Sulfate/pharmacology ; DNA, Ribosomal Spacer ; Dose-Response Relationship, Drug ; Genetic Variation ; Pesticides/adverse effects ; Phaseolus/growth &amp; development/*microbiology ; Phylogeny ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Rhizobiaceae/classification/*drug effects/growth &amp; development/metabolism ; Rhizobium leguminosarum/classification/drug effects/growth &amp; development/metabolism ; Sequence Analysis, DNA ; *Soil Microbiology ; Species Specificity ; }, abstract = {The use of pesticides in agricultural soils may affect the soil microbiota. The effect of repeated application of copper sulfate in soil on indigenous populations of rhizobia was assessed in a medium-term field experiment. Copper sulfate was applied over 8 years at two different rates, 12.5 and 50 kg of CuSO4 ha(-1) year(-1), in the field. The concentrations of total copper in soil varied between 14.0 (control plots that did not receive copper sulfate) and 91.0 mg kg(-1) (the most contaminated plots) at the time of sampling, 3 years after the end of the copper treatments. All the other physicochemical parameters were similar among the plots that also shared the same cropping history. The target rhizobia were monospecific populations of Rhizobium leguminosarum bv. viciae nodulating Vicia sativa and communities of rhizobial species nodulating Phaseolus vulgaris. The size of the vetch rhizobial populations was significantly reduced in the soils with the higher Cu content, whereas the size of the Phaseolus rhizobial populations was not significantly affected. However, the number of nodules formed on both vetches and common beans were reduced for the plants grown in the most contaminated soils, suggesting an additional toxic effect of copper on plant physiology. The diversity (Simpson's indices) of rhizobial genotypes, as characterized by polymerase chain reaction restriction fragment length polymorphism of 16S-23S rDNA intergenic spacer (IGS), was not influenced by copper application. Also, the genetic structure of the R. leguminosarum bv. viciae populations was not modified by copper treatments. By contrast, a shift was observed in the composition of the Phaseolus-nodulating communities in relation to soil copper content. The communities were composed of three 16S rDNA haplotypes: one corresponding to the R. leguminosarum (biovar phaseoli) species, the two others forming a new lineage of Phaseolus rhizobia based on 16S rDNA sequence analysis. The reduced frequency of the R. leguminosarum species in the Phaseolus-nodulating communities from the copper-treated soils was linked to its higher sensitivity to copper as compared to the higher tolerance of isolates belonging to the other rhizobial lineage. The new lineage was functionally efficient for symbiotic nitrogen fixation with P. vulgaris. Our results suggest that functional redundancy among species exhibiting variability for copper tolerance preserved the size of Phaseolus-nodulating communities. In contrast, the abundance of the vetch-nodulating rhizobia, which was a monospecific functional group mainly constituted by copper-sensitive genotypes, was adversely affected by repeated application of copper sulfate.}, }
@article {pmid16897300, year = {2006}, author = {Sonjak, S and Frisvad, JC and Gunde-Cimerman, N}, title = {Penicillium mycobiota in arctic subglacial ice.}, journal = {Microbial ecology}, volume = {52}, number = {2}, pages = {207-216}, pmid = {16897300}, issn = {0095-3628}, mesh = {Arctic Regions ; Biodiversity ; Cold Temperature ; Geologic Sediments/microbiology ; Hydrogen-Ion Concentration ; Ice Cover/*microbiology ; Penicillium/classification/*isolation &amp; purification/metabolism ; }, abstract = {Fungi have been only rarely isolated from glacial ice in extremely cold polar regions and were in these cases considered as random, long-term preserved Aeolian deposits. Fungal presence has so far not been investigated in polar subglacial ice, a recently discovered extreme habitat reported to be inhabited exclusively by heterotrophic bacteria. In this study we report on the very high occurrence (up to 9000 CFU L(-1)) and diversity of filamentous Penicillium spp. in the sediment-rich subglacial ice of three different polythermal Arctic glaciers (Svalbard, Norway). The dominant species was P. crustosum, representing on the average half of all isolated strains from all three glaciers. The other most frequently isolated species were P. bialowiezense, P. chrysogenum, P. thomii, P. solitum, P. palitans, P. echinulatum, P. polonicum, P. commune, P. discolor, P. expansum, and new Penicillium species (sp. 1). Twelve more Penicillium species were occasionally isolated. The fungi isolated produced consistent profiles of secondary metabolites, not different from the same Penicillium species from other habitats. This is the first report on the presence of large populations of Penicillium spp. in subglacial sediment-rich ice.}, }
@article {pmid16897299, year = {2006}, author = {Romaní, AM and Vázquez, E and Butturini, A}, title = {Microbial availability and size fractionation of dissolved organic carbon after drought in an intermittent stream: biogeochemical link across the stream-riparian interface.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {501-512}, pmid = {16897299}, issn = {0095-3628}, mesh = {Bacteria/enzymology/*metabolism ; Biodegradation, Environmental ; Biological Availability ; Biomass ; Carbon/*chemistry/*metabolism ; Chlorides/analysis ; Disasters ; Ecosystem ; Fluorescence ; Leucyl Aminopeptidase/metabolism ; Molecular Weight ; Particle Size ; Rain ; *Rivers/chemistry/microbiology ; Silicon Dioxide/analysis ; Solubility ; Trees/*metabolism ; *Water Microbiology ; Water Movements ; beta-Glucosidase/metabolism ; }, abstract = {The evolution of dissolved organic carbon (DOC) molecular-weight fractions, DOC biodegradability (BDOC), DOC origin [fluorescence index (FI)], and enzyme activities between the stream waters (main and ephemeral channel) and ground waters (riparian and hillslope) were analyzed during the transition from drought to precipitation in a forested Mediterranean stream. After the first rains, DOC content in stream water reached its maximum value (10-18 mg L(-1)), being explained by the leaching of deciduous leaves accumulated on the stream bed during drought. During this period, the largest molecules (>10 kDa), were the most biodegradable, as indicated by high BDOC values measured during storm events and high enzymatic activities (especially for leucine-aminopeptidase). DOC >100 kDa was strongly immobilized (78%) at the stream-riparian interface, whereas the smallest molecules (<1 kDa) were highly mobile and accumulated in ground waters, indicating their greater recalcitrance. Differential enzymatic patterns between compartments showed a fast utilization of polysaccharides in the flowing water but a major protein utilization in the ground water. The results of the FI indicated a more terrestrial origin of the larger molecules in the flowing water, also suggesting that transformation of material occurs through the stream-riparian interface. Microbial immobilization and fast utilization of the most biodegradable fraction at the stream-riparian interface is suggested as a relevant DOC retention mechanism just after initial recharging of the ground water compartment. Large and rapid DOC inputs entering the intermittent river system during the transition from drought to precipitation provide available N and C sources for the heterotrophs. Heterotrophs efficiently utilize these resources that were in limited supply during the period of drought. Such changes in C cycling may highlight possible changes in organic matter dynamics under the prediction of extended drying periods in aquatic ecosystems.}, }
@article {pmid16897298, year = {2006}, author = {Williamson, SJ and Paul, JH}, title = {Environmental factors that influence the transition from lysogenic to lytic existence in the phiHSIC/Listonella pelagia marine phage-host system.}, journal = {Microbial ecology}, volume = {52}, number = {2}, pages = {217-225}, pmid = {16897298}, issn = {0095-3628}, mesh = {Bacteriolysis/*physiology ; Bacteriophages/*pathogenicity/physiology ; *Environment ; Gene Expression Regulation, Viral ; Lysogeny/*physiology ; Open Reading Frames ; Oxygen/metabolism ; Sequence Analysis ; Sodium Chloride ; Temperature ; Vibrionaceae/growth &amp; development/*virology ; Viral Proteins/genetics/metabolism/physiology ; }, abstract = {The marine phage varphiHSIC has been previously reported to enter into a pseudolysogenic-like interaction with its host Listonella pelagia. This phage-host system displays behaviors that are characteristic of both pseudolysogeny and lysogeny including a high rate of spontaneous induction and chromosomal integration of the prophage. To determine what parameters may influence the transition from lysogenic to lytic existence in the varphiHSIC/L. pelagia phage-host system, cultures of this organism were incubated under different environmental conditions, while host cell growth and bacteriophage production were monitored. The environmental parameters tested included salinity, temperature, a rapid temperature shift, and degree of culture aeration. The highest titers of phage were produced by HSIC-1a cells grown in high-salinity nutrient artificial seawater media (67 ppt with a natural salinity equivalent of 57 ppt) or those cultured in highly aerated nutrient artificial seawater media (cultures shaken at 300 rpm). Conversely, the lowest titers of phage were produced under low salinity or rate of aeration. In general, conditions that stimulated growth resulted in greater lytic phage production, whereas slow growth favored lysogeny. These results indicate that elevated salinity and aeration influenced the switch from lysogenic to lytic existence for the phage varphiHSIC. These results may have implications for environmental controls of the lysogenic switch in natural populations of marine bacteria.}, }
@article {pmid16897297, year = {2006}, author = {Carney, KM and Matson, PA}, title = {The influence of tropical plant diversity and composition on soil microbial communities.}, journal = {Microbial ecology}, volume = {52}, number = {2}, pages = {226-238}, pmid = {16897297}, issn = {0095-3628}, mesh = {Bacteria/classification/isolation &amp; purification/metabolism ; *Biodiversity ; Biomarkers/analysis ; Carbon/analysis ; Costa Rica ; Fatty Acids/analysis ; Fungi/classification/isolation &amp; purification/metabolism ; Phospholipids/analysis ; Plants/classification/*microbiology ; Rain ; Seasons ; Soil/analysis ; *Soil Microbiology ; Tropical Climate ; }, abstract = {There is growing interest in understanding the linkages between above- and belowground communities, and very little is known about these linkages in tropical systems. Using an experimental site at La Selva Biological Station, Costa Rica, we examined whether plant diversity, plant community composition, and season influenced microbial communities. We also determined whether soil characteristics were related to differences in microbial communities. Phospholipid fatty acid (PLFA) composition revealed that microbial community composition differed across a plant diversity gradient (plots contained 1, 3, 5, or over 25 species). Plant species identity also was a factor influencing microbial community composition; PLFA composition significantly varied among monocultures, and among three-species combinations that differed in plant species composition. Differences among treatments within each of these comparisons were apparent in all four sampling dates of the study. There was no consistent shift in microbial community composition between wet and dry seasons, although we did see significant changes over time. Of all measured soil characteristics, soil C/N was most often associated with changes in microbial community composition across treatment groups. Our findings provide evidence for human alteration of soil microbial communities via the alteration of plant community composition and diversity and that such changes are mediated in part by changes in soil carbon quality.}, }
@article {pmid16897296, year = {2006}, author = {Wang, LL and Wang, ET and Liu, J and Li, Y and Chen, WX}, title = {Endophytic occupation of root nodules and roots of Melilotus dentatus by Agrobacterium tumefaciens.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {436-443}, pmid = {16897296}, issn = {0095-3628}, mesh = {Agrobacterium tumefaciens/classification/*genetics/*growth &amp; development ; Electrophoresis, Polyacrylamide Gel/methods ; Gene Amplification ; Melilotus/growth &amp; development/*microbiology ; Phylogeny ; Plant Roots/*microbiology ; Plant Tumors/microbiology ; Polymerase Chain Reaction/methods ; *Soil Microbiology ; Symbiosis ; }, abstract = {Agrobacterium strains have been frequently isolated from the root nodules of different legumes. Various possible mechanisms have been proposed to explain the existence of these bacteria in nodules, but there is no sufficient experimental evidence to support the estimations. In this work, we proved that the Agrobacterium strain CCBAU 81181, which was originally isolated from the root nodules of Onobrychis viciaefolia, and a symbiotic strain of Sinorhizobium meliloti CCBAU 10062 could coinhabit the root nodules of Melilotus dentatus. Analyses were performed by using a fluorescence marker, reisolation of bacteria from nodules, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of whole cellular proteins, and polymerase chain reaction amplification of symbiotic genes. The inoculation of A. tumefaciens CCBAU 81181 did not affect the growth and nodulation of plants. CCBAU 81181 and 24 other Agrobacterium strains isolated from nodules were incapable of nodulating on their original or alternative host and 22 strains of these strains were endophytes in the roots and stems of their hosts. Also, the tumor-inducing A. tumefaciens strains IAM 13129(T) and C58 were found capable of entering the roots of Glycyrrhiza pallidiflora, but did not cause pathogenic symptoms. With these results, we conclude that A. tumefaciens strains could be endophytic bacteria in the roots, stems, and root nodules. This finding partially explains why Agrobacterium strains were frequently isolated from the surface-sterilized nodules.}, }
@article {pmid16897295, year = {2006}, author = {Caubet, R and Pedarros-Caubet, F and Quataert, Y and Lescure, A and Moreau, JM and Ellison, WJ}, title = {Assessing the contamination potential of freshly extracted Escherichia coli biofilm cells by impedancemetry.}, journal = {Microbial ecology}, volume = {52}, number = {2}, pages = {239-243}, pmid = {16897295}, issn = {0095-3628}, mesh = {Bacterial Adhesion/physiology ; *Biofilms/growth &amp; development ; Culture Media ; Electric Conductivity ; Escherichia coli/growth &amp; development/pathogenicity/*physiology ; Risk Assessment ; Sonication ; }, abstract = {Planktonic bacteria passing to a sessile state during the formation of a biofilm undergo many gene expression and phenotypic changes. These transformations require a significant time to establish. Inversely, cells extracted from a biofilm should also require a significant time before acquiring the same physiological characteristics as planktonic cells. Relatively few studies have addressed the kinetics of this inverse transformation process. We tested one aspect, namely, the contamination potential of freshly extracted Escherichia coli biofilm cells, precultured in a synthetic medium, in a rich liquid growth medium. We compared the time between inoculation and the beginning of the growth phase of freshly extracted biofilm cells, and suspended exponential and suspended stationary phase cells precultured in the same synthetic medium. Unexpectedly, the lag time for the extracted biofilm cells was the same as the lag time of the suspended exponential phase cells and significantly less than the lag time of the suspended stationary phase cells. The lag times were determined by an impedance technique. Cells extracted from biofilms, i.e., biofilms formed in canalizations and broken up by hydrodynamic forces, are an important source of contamination. Our work shows, in the case of E. coli, the high potential of freshly extracted biofilm cells to reinfect a new medium.}, }
@article {pmid16897294, year = {2006}, author = {Standing, D and Knox, OG and Mullins, CE and Killham, KK and Wilson, MJ}, title = {Influence of nematodes on resource utilization by bacteria--an in vitro study.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {444-450}, pmid = {16897294}, issn = {0095-3628}, mesh = {Animals ; Bacteria/growth &amp; development/*metabolism ; Biomass ; Nematoda/*metabolism/*microbiology ; Nitrogen/*metabolism ; Pseudomonas fluorescens/growth &amp; development/metabolism ; Soil/*parasitology ; *Soil Microbiology ; Time Factors ; }, abstract = {The positive influence of bacterial feeding nematodes on bacterial mediated processes such as organic matter mineralization and nutrient cycling is widely accepted, but the mechanisms of these interactions are not always apparent. Both transport of bacteria by nematodes, and nutritional effects caused by nematode N excretion are thought to be involved, but their relative importance is not known because of the difficulties in studying these interactions in soil. We developed a simple in vitro assay to study complex nematode/bacterial interactions and used it to conduct a series of experiments to determine the potential influence of nematode movement and nutritional effects on bacterial resource use. The system used bacterial feeding and nonfeeding insect parasitic nematodes, and luminescent bacteria marked with metabolic reporter genes. Both nutritional enhancement of bacterial activity and bacterial transport were observed and we hypothesize that in nature, the relative importance of transport is likely to be greater in bulk soil, whereas nematode excretion may have greater impact in the rhizosphere. In both cases, the ability of nematodes to enhance bacterial resource utilization has implications for soil components of biogeochemical cycling.}, }
@article {pmid16893466, year = {2006}, author = {Lozupone, C and Hamady, M and Knight, R}, title = {UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context.}, journal = {BMC bioinformatics}, volume = {7}, number = {}, pages = {371}, pmid = {16893466}, issn = {1471-2105}, support = {T32 GM008759/GM/NIGMS NIH HHS/United States ; T32 GM065103/GM/NIGMS NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; T32 GM08759/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics ; Cluster Analysis ; Computational Biology/*methods ; Ecosystem ; Environmental Microbiology ; Genetic Variation ; *Internet ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Moving beyond pairwise significance tests to compare many microbial communities simultaneously is critical for understanding large-scale trends in microbial ecology and community assembly. Techniques that allow microbial communities to be compared in a phylogenetic context are rapidly gaining acceptance, but the widespread application of these techniques has been hindered by the difficulty of performing the analyses.<br><br>RESULTS: We introduce UniFrac, a web application available at http://bmf.colorado.edu/unifrac, that allows several phylogenetic tests for differences among communities to be easily applied and interpreted. We demonstrate the use of UniFrac to cluster multiple environments, and to test which environments are significantly different. We show that analysis of previously published sequences from the Columbia river, its estuary, and the adjacent coastal ocean using the UniFrac interface provided insights that were not apparent from the initial data analysis, which used other commonly employed techniques to compare the communities.<br><br>CONCLUSION: UniFrac provides easy access to powerful multivariate techniques for comparing microbial communities in a phylogenetic context. We thus expect that it will provide a completely new picture of many microbial interactions and processes in both environmental and medical contexts.}, }
@article {pmid16885296, year = {2006}, author = {Murase, J and Noll, M and Frenzel, P}, title = {Impact of protists on the activity and structure of the bacterial community in a rice field soil.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {8}, pages = {5436-5444}, pmid = {16885296}, issn = {0099-2240}, mesh = {Animals ; Betaproteobacteria/classification/genetics/*growth &amp; development/metabolism ; Biodiversity ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; *Ecosystem ; Eukaryota/growth &amp; development/*physiology ; Genes, rRNA ; Gram-Positive Bacteria/classification/genetics/*growth &amp; development/metabolism ; Molecular Sequence Data ; Oryza/*growth &amp; development ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Flooded rice fields have become a model system for the study of soil microbial ecology. In Italian rice fields, in particular, aspects from biogeochemistry to molecular ecology have been studied, but the impact of protistan grazing on the structure and function of the prokaryotic community has not been examined yet. We compared an untreated control soil with a gamma-radiation-sterilized soil that had been reinoculated with a natural bacterial assemblage. In order to verify that the observed effects were due to protistan grazing and did not result from sterilization, we set up a third set of microcosms containing sterilized soil that had been reinoculated with natural assemblage bacteria plus protists. The spatial and temporal changes in the protistan and prokaryotic communities were examined by denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) analysis, respectively, both based on the small-subunit gene. Sequences retrieved from DGGE bands were preferentially affiliated with Cercozoa and other bacteriovorous flagellates. Without protists, the level of total DNA increased with incubation time, indicating that the level of the microbial biomass was elevated. Betaproteobacteria were preferentially preyed upon, while low-G + C-content gram-positive bacteria became more dominant under grazing pressure. The bacterial diversity detectable by T-RFLP analysis was greater in the presence of protists. The level of extractable NH4+ was lower and the level of extractable SO4(2-) was higher without protists, indicating that nitrogen mineralization and SO4(2-) reduction were stimulated by protists. Most of these effects were more obvious in the partially oxic surface layer (0 to 3 mm), but they could also be detected in the anoxic subsurface layer (10 to 13 mm). Our observations fit well into the overall framework developed for protistan grazing, but with some modifications pertinent to the wetland situation: O2 was a major control, and O2 availability may have limited directly and indirectly the development of protists. Although detectable in the lower anoxic layer, grazing effects were much more obvious in the partially oxic surface layer.}, }
@article {pmid16885270, year = {2006}, author = {Shen, J and Zhang, B and Wei, G and Pang, X and Wei, H and Li, M and Zhang, Y and Jia, W and Zhao, L}, title = {Molecular profiling of the Clostridium leptum subgroup in human fecal microflora by PCR-denaturing gradient gel electrophoresis and clone library analysis.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {8}, pages = {5232-5238}, pmid = {16885270}, issn = {0099-2240}, mesh = {Adult ; Child ; Child, Preschool ; Cloning, Molecular/*methods ; Clostridium/*classification/genetics ; Electrophoresis, Polyacrylamide Gel/*methods ; Feces/*microbiology ; Female ; *Gene Library ; Genetic Variation ; Humans ; Male ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA ; }, abstract = {A group-specific PCR-based denaturing gradient gel electrophoresis (DGGE) method was developed and combined with group-specific clone library analysis to investigate the diversity of the Clostridium leptum subgroup in human feces. PCR products (length, 239 bp) were amplified using C. leptum cluster-specific primers and were well separated by DGGE. The DGGE patterns of fecal amplicons from 11 human individuals revealed host-specific profiles; the patterns for fecal samples collected from a child for 3 years demonstrated the structural succession of the population in the first 2 years and its stability in the third year. A clone library was constructed with 100 clones consisting of 1,143-bp inserts of 16S rRNA gene fragments that were amplified from one adult fecal DNA with one forward universal bacterial primer and one reverse group-specific primer. Eighty-six of the clones produced the 239-bp C. leptum cluster-specific amplicons, and the remaining 14 clones did not produce these amplicons but still phylogenetically belong to the subgroup. Sixty-four percent of the clones were related to Faecalibacterium prausnitzii (similarity, 97 to 99%), 6% were related to Subdoligranulum variabile (similarity, approximately 99%), 2% were related to butyrate-producing bacterium A2-207 (similarity, 99%), and 28% were not identified at the species level. The identities of most bands in the DGGE profiles for the same adult were determined by comigration analysis with the 86 clones that harbored the 239-bp group-specific fragments. Our results suggest that DGGE combined with clone library analysis is an effective technique for monitoring and analyzing the composition of this important population in the human gut flora.}, }
@article {pmid16885260, year = {2006}, author = {Boenigk, J and Pfandl, K and Garstecki, T and Harms, H and Novarino, G and Chatzinotas, A}, title = {Evidence for geographic isolation and signs of endemism within a protistan morphospecies.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {8}, pages = {5159-5164}, pmid = {16885260}, issn = {0099-2240}, support = {P 18767/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Acclimatization ; Animals ; Antarctic Regions ; Chrysophyta/*classification/*growth &amp; development/isolation &amp; purification/physiology ; DNA, Ribosomal/analysis ; *Ecosystem ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; *Soil Microbiology ; Temperature ; Tropical Climate ; *Water Microbiology ; }, abstract = {The possible existence of endemism among microorganisms resulting from and preserved by geographic isolation is one of the most controversial topics in microbial ecology. We isolated 31 strains of "Spumella-like" flagellates from remote sampling sites from all continents, including Antarctica. These and another 23 isolates from a former study were characterized morphologically and by small-subunit rRNA gene sequence analysis and tested for the maximum temperature tolerance. Only a minority of the Spumella morpho- and phylotypes from the geographically isolated Antarctic continent follow the worldwide trend of a linear correlation between ambient (air) temperature during strain isolation and heat tolerance of the isolates. A high percentage of the Antarctic isolates, but none of the isolates from locations on all other continents, were obligate psychrophilic, although some of the latter were isolated at low ambient temperatures. The drastic deviation of Antarctic representatives of Spumella from the global trend of temperature adaptation of this morphospecies provides strong evidence for geographic transport restriction of a microorganism; i.e., Antarctic protistan communities are less influenced by transport of protists to and from the Antarctic continent than by local adaptation, a subtle form of endemism.}, }
@article {pmid16884796, year = {2006}, author = {Birmele, M and Roberts, M and Garland, J}, title = {Characterization of methods for determining sterilization efficacy and reuse efficiency of oxygen biosensor multiwell plates.}, journal = {Journal of microbiological methods}, volume = {67}, number = {3}, pages = {619-623}, doi = {10.1016/j.mimet.2006.06.003}, pmid = {16884796}, issn = {0167-7012}, mesh = {*Biosensing Techniques/economics/instrumentation ; Disinfectants ; Disinfection/*methods ; Equipment Reuse/*economics ; Ethylene Oxide ; Sodium Hypochlorite ; Ultraviolet Rays ; }, abstract = {High-throughput screening (HTS) assays based upon fluorometric detection of oxygen consumption in microtiter plates were primarily developed for applications in drug discovery and ecotoxicology but have recently been adopted for use in microbial community-level physiological profiling assays (CLPP). The widespread use of oxygen biosensor systems for CLPP applications has, however, been hindered by the relatively high cost of oxygen biosensor reagent systems and limited access to microplate fluorometer instrumentation platforms. The ability to recycle and reuse oxygen biosensor system plates would expand their utilization for CLPP assays and other research applications in microbial ecology. Here, the efficacy and cost effectiveness of multiple procedures for sterilization of Oxygen Biosensor System (OBS; BD Biosciences) plates for reuse was evaluated. OBS plates were sterilized using ethylene oxide, ultraviolet radiation, and bleach treatments, then evaluated for biosensor response and plate life-cycle performance. Of the sterilization methods tested, ethylene oxide sterilization was most effective based on its low cost, high sterilization efficacy, and minimal impact upon OBS plate response.}, }
@article {pmid16882654, year = {2006}, author = {Ruan, Q and Dutta, D and Schwalbach, MS and Steele, JA and Fuhrman, JA and Sun, F}, title = {Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors.}, journal = {Bioinformatics (Oxford, England)}, volume = {22}, number = {20}, pages = {2532-2538}, doi = {10.1093/bioinformatics/btl417}, pmid = {16882654}, issn = {1367-4811}, mesh = {Bacteria/*classification ; *Bacterial Physiological Phenomena ; Computer Simulation ; Ecosystem ; *Environment ; *Marine Biology ; *Models, Biological ; Plankton/*classification/*physiology ; }, abstract = {MOTIVATION: Characterizing the diversity of microbial communities and understanding the environmental factors that influence community diversity are central tenets of microbial ecology. The development and application of cultivation independent molecular tools has allowed for rapid surveying of microbial community composition at unprecedented resolutions and frequencies. There is a growing need to discern robust patterns and relationships within these datasets which provide insight into microbial ecology. Pearson correlation coefficient (PCC) analysis is commonly used for identifying the linear relationship between two species, or species and environmental factors. However, this approach may not be able to capture more complex interactions which occur in situ; thus, alternative analyses were explored.<br><br>RESULTS: In this paper we introduced local similarity analysis (LSA), which is a technique that can identify more complex dependence associations among species as well as associations between species and environmental factors without requiring significant data reduction. To illustrate its capability of identifying relationships that may not otherwise be identified by PCC, we first applied LSA to simulated data. We then applied LSA to a marine microbial observatory dataset and identified unique, significant associations that were not detected by PCC analysis. LSA results, combined with results from PCC analysis were used to construct a theoretical ecological network which allows for easy visualization of the most significant associations. Biological implications of the significant associations detected by LSA were discussed. We also identified additional applications where LSA would be beneficial.<br><br>AVAILABILITY: The algorithms are implemented in Splus/R and they are available upon request from the corresponding author.}, }
@article {pmid16874554, year = {2006}, author = {Gentile, M and Yan, T and Tiquia, SM and Fields, MW and Nyman, J and Zhou, J and Criddle, CS}, title = {Stability in a denitrifying fluidized bed reactor.}, journal = {Microbial ecology}, volume = {52}, number = {2}, pages = {311-321}, pmid = {16874554}, issn = {0095-3628}, mesh = {Biodegradation, Environmental ; Biofilms ; Cloning, Molecular ; Gene Library ; Gram-Positive Bacteria/classification/genetics/*physiology ; Nitrates/*metabolism ; Nitrogen/metabolism ; Pilot Projects ; Polymorphism, Restriction Fragment Length ; Proteobacteria/classification/genetics/*physiology ; *Water Purification ; }, abstract = {This study evaluates changes in the microbial community structure and function of a pilot-scale denitrifying fluidized bed reactor during periods of constant operating conditions and periods of perturbation. The perturbations consisted of a shutdown period without feed, two disturbances in which biofilms were mechanically sheared from carrier particles, and a twofold step increase in feed nitrate concentration. In the absence of perturbations, nitrate removal was stable and consistently greater than 99%. The structure and dynamics of the microbial community were studied using cloning and sequencing techniques and terminal restriction fragment length polymorphism (T-RFLP) of the SSU rRNA gene. Under unperturbed operating conditions, stable function was accompanied by high constancy and low variability of community structure with the majority of terminal restriction fragments (T-RFs) appearing throughout operation at consistent relative abundances. Several of the consistently present T-RFs correlated with clone sequences closely related to Acidovorax (98% similarity), Dechloromonas (99% similarity), and Zoogloea (98% similarity), genera recently identified by molecular analyses of similar systems. Significant changes in community structure and function were not observed after the shutdown period. In contrast, following the increase in loading rate and the mechanical disturbances, new T-RFs appeared. After both mechanical disturbances, function and community structure recovered. However, function was much more resilient than community structure. The similarity of response to the mechanical disturbances despite differences in community structure and operating conditions suggests that flexible community structure and potentially the activity of minor members under nonperturbation conditions promotes system recovery.}, }
@article {pmid16874468, year = {2006}, author = {Park, JS and Cho, BC and Simpson, AG}, title = {Halocafeteria seosinensis gen. et sp. nov. (Bicosoecida), a halophilic bacterivorous nanoflagellate isolated from a solar saltern.}, journal = {Extremophiles : life under extreme conditions}, volume = {10}, number = {6}, pages = {493-504}, pmid = {16874468}, issn = {1431-0651}, mesh = {Animals ; *DNA, Protozoan ; Eukaryota/*classification/genetics/growth &amp; development/isolation &amp; purification/metabolism/ultrastructure ; Flagella/ultrastructure ; Korea ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; *Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Ribotyping ; Seawater/chemistry/*parasitology ; Sodium Chloride/analysis/*metabolism ; Temperature ; }, abstract = {Recently, heterotrophic nanoflagellates (HNF) have been reported to actively ingest prokaryotes in high salinity waters. We report the isolation and culture of an HNF from a Korean saltern pond of 300 per thousand salinity. The organism is biflagellated with an acronematic anterior flagellum and never glides on surfaces. The mitochondria have tubular cristae. Neither transitional helix nor spiral fiber were observed in the transition zones of the flagella. The cell has a cytostome supported by an arc of eight microtubules, suggesting that our isolate is a bicosoecid. Our isolate had neither mastigonemes, lorica, body scales, nor cytopharynx and thus could not be placed in any of the presently described bicosoecid genera. Phylogenetic analysis of 18S rRNA gene sequences from stramenopiles confirmed the bicosoecid affinities of our isolate, but did not place it within any established genus or family. Its closest relatives include Caecitellus and Cafeteria. The optimal range of growth temperature was 30-35 degrees C. The isolated HNF grew optimally at 150 per thousand salinity and tolerated up to 363 per thousand salinity, but it failed to grow below 75 per thousand salinity, indicating that it could be a borderline extreme halophile. On the basis of its morphological features and position in 18S rRNA trees we propose a novel genus for our isolate; Halocafeteria, n. gen. The species name Halocafeteria seosinensis sp. nov. is proposed.}, }
@article {pmid16867142, year = {2006}, author = {Engelbrektson, AL and Korzenik, JR and Sanders, ME and Clement, BG and Leyer, G and Klaenhammer, TR and Kitts, CL}, title = {Analysis of treatment effects on the microbial ecology of the human intestine.}, journal = {FEMS microbiology ecology}, volume = {57}, number = {2}, pages = {239-250}, doi = {10.1111/j.1574-6941.2006.00112.x}, pmid = {16867142}, issn = {0168-6496}, mesh = {Adult ; Anti-Bacterial Agents/*administration &amp; dosage ; Bacteria/classification/*drug effects/genetics ; Cluster Analysis ; *DNA Fingerprinting ; DNA, Bacterial/genetics ; Double-Blind Method ; Feces/microbiology ; Humans ; Intestines/*microbiology ; Placebos ; Polymorphism, Restriction Fragment Length ; Principal Component Analysis ; Probiotics/*administration &amp; dosage ; }, abstract = {A large number of studies have investigated gastrointestinal microbiota and changes in the gastrointestinal community. However, a concern in these studies is how best to assess changes in gastrointestinal community structure. This paper presents two different human trials where the fecal terminal restriction fragment length polymorphism data sets were analyzed to search for treatment effects. Principle components analysis and cluster analysis based on grouped data are compared with analysis of data by subject using distance coefficients. Comparison with baseline within an individual before grouping by treatment provided a clearer indication of treatment effects than did an evaluation of data grouped before analysis. In addition, a large within-subject sample size and multiple baseline samples are necessary to accurately analyze treatment effects.}, }
@article {pmid16866931, year = {2006}, author = {Wallander, H}, title = {External mycorrhizal mycelia - the importance of quantification in natural ecosystems.}, journal = {The New phytologist}, volume = {171}, number = {2}, pages = {240-242}, doi = {10.1111/j.1469-8137.2006.01803.x}, pmid = {16866931}, issn = {0028-646X}, mesh = {Carbon ; Cold Climate ; *Ecosystem ; Fertilizers ; Mycelium/*growth &amp; development ; Mycorrhizae/*growth &amp; development ; Soil Microbiology ; Symbiosis ; }, }
@article {pmid16865610, year = {2006}, author = {Warren-Rhodes, KA and Rhodes, KL and Pointing, SB and Ewing, SA and Lacap, DC and Gómez-Silva, B and Amundson, R and Friedmann, EI and McKay, CP}, title = {Hypolithic cyanobacteria, dry limit of photosynthesis, and microbial ecology in the hyperarid Atacama Desert.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {389-398}, pmid = {16865610}, issn = {0095-3628}, mesh = {Biodiversity ; Carbon/*metabolism ; Chile ; Cyanobacteria/*physiology ; *Desert Climate ; Environmental Monitoring ; Mars ; *Photosynthesis ; *Rain ; *Soil Microbiology ; }, abstract = {The occurrence of hypolithic cyanobacteria colonizing translucent stones was quantified along the aridity gradient in the Atacama Desert in Chile, from less arid areas to the hyperarid core where photosynthetic life and thus primary production reach their limits. As mean rainfall declines from 21 to <or=2 mm year(-1), the abundance of hypolithic cyanobacteria drops from 28 to <0.1%, molecular diversity declines threefold, and organic carbon residence times increase by three orders of magnitude. Communities contained a single Chroococcidiopsis morphospecies with heterotrophic associates, yet molecular analysis revealed that each stone supported a number of unique 16S rRNA gene-defined genotypes. A fivefold increase in steady-state residence times for organic carbon within communities in the hyperarid core (3200 years turnover time) indicates a significant decline in biological carbon cycling. Six years of microclimate data suggest that the dry limit corresponds to <or=5 mm year(-1) rainfall and/or decadal periods of no rain, with <75 h year(-1) of liquid water available to cyanobacteria under light conditions suitable for photosynthesis. In the hyperarid core, hypolithic cyanobacteria are rare and exist in small spatially isolated islands amidst a microbially depauperate bare soil. These findings suggest that photosynthetic life is extremely unlikely on the present-day surface of Mars, but may have existed in the past. If so, such microhabitats would probably be widely dispersed, difficult to detect, and millimeters away from virtually lifeless surroundings.}, }
@article {pmid16842349, year = {2006}, author = {Ehling-Schulz, M and Guinebretiere, MH and Monthán, A and Berge, O and Fricker, M and Svensson, B}, title = {Toxin gene profiling of enterotoxic and emetic Bacillus cereus.}, journal = {FEMS microbiology letters}, volume = {260}, number = {2}, pages = {232-240}, doi = {10.1111/j.1574-6968.2006.00320.x}, pmid = {16842349}, issn = {0378-1097}, mesh = {Bacillus cereus/*genetics/metabolism/pathogenicity ; Bacterial Toxins/chemistry/*genetics ; Base Sequence ; DNA, Bacterial/analysis ; Depsipeptides/chemistry/genetics/metabolism ; Emetics/*chemistry/metabolism ; Enterotoxins/chemistry/*genetics ; Food Microbiology ; Foodborne Diseases/*diagnosis/microbiology ; *Genetic Variation ; Humans ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; Sequence Analysis, DNA ; }, abstract = {Very different toxins are responsible for the two types of gastrointestinal diseases caused by Bacillus cereus: the diarrhoeal syndrome is linked to nonhemolytic enterotoxin NHE, hemolytic enterotoxin HBL, and cytotoxin K, whereas emesis is caused by the action of the depsipeptide toxin cereulide. The recently identified cereulide synthetase genes permitted development of a molecular assay that targets all toxins known to be involved in food poisoning in a single reaction, using only four different sets of primers. The enterotoxin genes of 49 strains, belonging to different phylogenetic branches of the B. cereus group, were partially sequenced to encompass the molecular diversity of these genes. The sequence alignments illustrated the high molecular polymorphism of B. cereus enterotoxin genes, which is necessary to consider when establishing PCR systems. Primers directed towards the enterotoxin complex genes were located in different CDSs of the corresponding operons to target two toxin genes with one single set of primers. The specificity of the assay was assessed using a panel of B. cereus strains with known toxin profiles and was successfully applied to characterize strains from food and clinical diagnostic labs as well as for the toxin gene profiling of B. cereus isolated from silo tank populations.}, }
@article {pmid16826322, year = {2006}, author = {Jones, RT and Martin, AP}, title = {Testing for differentiation of microbial communities using phylogenetic methods: accounting for uncertainty of phylogenetic inference and character state mapping.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {408-417}, pmid = {16826322}, issn = {0095-3628}, mesh = {Bacteria/*classification/genetics ; Bayes Theorem ; DNA, Bacterial/chemistry ; DNA, Ribosomal/chemistry ; Gastrointestinal Tract/*microbiology ; Humans ; Mouth/*microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/chemistry/genetics ; *Soil Microbiology ; Stochastic Processes ; }, abstract = {Comparative analyses of microbial communities increasingly involve the assay of 16S rRNA (or other gene) sequences from environmental DNA. Determining whether the composition of two or more communities differ in their phylogenetic composition involves testing for covariation between phylogeny and community type. This approach requires estimating the phylogenetic relationships among all sampled sequences and assessing whether the distribution of sequences among communities differs from the null expectation that sequences are randomly distributed. One method developed for implementing the phylogeny-based test of differentiation, referred to as the Phylogenetic test, relies on a single estimate of the phylogeny. However, for most data sets, many alternative phylogenetic trees provide statistically equivalent descriptions of the data. Because the actual phylogeny is unknown, phylogenetic tests of differentiation among microbial communities must account for phylogenetic uncertainty. In this article, we evaluate bootstrapping and Bayesian phylogenetic methods when implementing the Phylogenetic test using parsimony to map character states, and we investigate the effects of character mapping uncertainty by using a Bayesian approach to stochastically map character states on trees. Our approaches incorporate uncertainty into the tests of two closely related null hypotheses: (1) populations are panmictic, and (2) identical communities existed in both environments over the course of evolutionary history. We use two data sets previously implemented in tests for community differentiation: nitrite reductase genes sampled from marsh and upland soils and 16S rDNA sequences sampled from the human mouth and gut. We show that accounting for phylogenetic and mapping uncertainties can drastically affect results when implementing the Phylogenetic test. Accounting for phylogenetic and character mapping uncertainty provides a more conservative and robust test of covariation between phylogeny and environment when comparing microbial communities using DNA sequences.}, }
@article {pmid16826321, year = {2006}, author = {Trocha, LK and Rudawska, M and Leski, T and Dabert, M}, title = {Genetic diversity of naturally established ectomycorrhizal fungi on Norway spruce seedlings under nursery conditions.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {418-425}, pmid = {16826321}, issn = {0095-3628}, mesh = {Analysis of Variance ; Ascomycota/classification/genetics/growth &amp; development ; Basidiomycota/classification/genetics/growth &amp; development ; DNA, Fungal/chemistry/*genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Fertilizers ; *Genetic Variation ; Genotype ; Molecular Sequence Data ; Mycorrhizae/classification/*genetics/*growth &amp; development ; Norway ; Phylogeny ; Picea/*microbiology ; Plant Roots/microbiology ; Polymorphism, Restriction Fragment Length ; Restriction Mapping ; Seedlings/microbiology ; Sequence Alignment ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {We have assessed ectomycorrhizal fungi colonizing Norway spruce (Picea abies L.) seedlings in nine forest nurseries using restriction fragment length polymorphism (RFLP) and sequencing analyses of the internal transcribed spacers (ITS1-5.8S-ITS2) amplicons. Restriction analysis of the amplified DNA fragments with HinfI, MboI, and TaqI enzymes allowed the definition of 17 RFLP genotypes; five of them could be unambiguously assigned to Thelephora terrestris, Hebeloma longicaudum, H. crustuliniforme, Tricharina ochroleuca, and Cenococcum geophilum species by comparison with the sporocarp RFLP-pattern database. The remaining genotypes have been sequenced and compared with sequences deposited in the GenBank database. The phylogenetic analysis of resulting sequences and their identified matches indicated that isolated genotypes have formed seven clades. The ascomycetes were predominant: we have determined eight species--Wilcoxina mikolae, Phialophora finlandia, Tuber sp., Cenococcum geophilum, Tricharina ochroleuca, Pulvinula constellatio, and two unidentified ascomycetes--whereas the basidiomycetes were less common (four species denoted: Amphinema byssoides, Hebeloma crustuliniforme, H. longicaudum, and Thelephora terrestris). Wilcoxina mikolae and Phialophora finlandia were the most frequent fungi. Analysis of variance revealed that ascomycetes abundance was higher in nurseries that used organic fertilizer.}, }
@article {pmid16820493, year = {2006}, author = {Wilhelm, SW and Carberry, MJ and Eldridge, ML and Poorvin, L and Saxton, MA and Doblin, MA}, title = {Marine and freshwater cyanophages in a Laurentian Great Lake: evidence from infectivity assays and molecular analyses of g20 genes.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {7}, pages = {4957-4963}, pmid = {16820493}, issn = {0099-2240}, mesh = {Bacteriophages/classification/genetics/*physiology/ultrastructure ; Capsid Proteins/*genetics/metabolism ; DNA, Viral/analysis ; Ecosystem ; Fresh Water/*virology ; Molecular Sequence Data ; Myoviridae/classification/genetics/physiology/ultrastructure ; Phylogeny ; Seawater/*virology ; Sequence Analysis, DNA ; Synechococcus/*virology ; }, abstract = {While it is well established that viruses play an important role in the structure of marine microbial food webs, few studies have directly addressed their role in large lake systems. As part of an ongoing study of the microbial ecology of Lake Erie, we have examined the distribution and diversity of viruses in this system. One surprising result has been the pervasive distribution of cyanophages that infect the marine cyanobacterial isolate Synechococcus sp. strain WH7803. Viruses that lytically infect this cyanobacterium were identified throughout the western basin of Lake Erie, as well as in locations within the central and eastern basins. Analyses of the gene encoding the g20 viral capsid assembly protein (a conservative phylogenetic marker for the cyanophage) indicate that these viruses, as well as amplicons from natural populations and the ballast of commercial ships, are related to marine cyanophages but in some cases form a unique clade, leaving questions concerning the native hosts of these viruses. The results suggest that cyanophages may be as important in freshwater systems as they are known to be in marine systems.}, }
@article {pmid16820047, year = {2006}, author = {Bolhuis, H and Palm, P and Wende, A and Falb, M and Rampp, M and Rodriguez-Valera, F and Pfeiffer, F and Oesterhelt, D}, title = {The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity.}, journal = {BMC genomics}, volume = {7}, number = {}, pages = {169}, pmid = {16820047}, issn = {1471-2164}, mesh = {Archaea/*genetics/*physiology ; Bacteriorhodopsins/metabolism ; Body Water ; Dehydration/*genetics ; Dihydroxyacetone/metabolism ; Genetic Structures ; *Genome, Archaeal ; Models, Biological ; Phosphates/metabolism ; Phosphoenolpyruvate/metabolism ; Phosphotransferases/metabolism ; Phylogeny ; Plasmids/chemistry ; }, abstract = {BACKGROUND: The square halophilic archaeon Haloquadratum walsbyi dominates NaCl-saturated and MgCl2 enriched aquatic ecosystems, which imposes a serious desiccation stress, caused by the extremely low water activity. The genome sequence was analyzed and physiological and physical experiments were carried out in order to reveal how H. walsbyi has specialized into its narrow and hostile ecological niche and found ways to cope with the desiccation stress.<br><br>RESULTS: A rich repertoire of proteins involved in phosphate metabolism, phototrophic growth and extracellular protective polymers, including the largest archaeal protein (9159 amino acids), a homolog to eukaryotic mucins, are amongst the most outstanding features. A relatively low GC content (47.9%), 15-20% less than in other halophilic archaea, and one of the lowest coding densities (76.5%) known for prokaryotes might be an indication for the specialization in its unique environment<br><br>CONCLUSION: Although no direct genetic indication was found that can explain how this peculiar organism retains its square shape, the genome revealed several unique adaptive traits that allow this organism to thrive in its specific and extreme niche.}, }
@article {pmid16814840, year = {2006}, author = {Connaughton, S and Collins, G and O'Flaherty, V}, title = {Psychrophilic and mesophilic anaerobic digestion of brewery effluent: a comparative study.}, journal = {Water research}, volume = {40}, number = {13}, pages = {2503-2510}, doi = {10.1016/j.watres.2006.04.044}, pmid = {16814840}, issn = {0043-1354}, mesh = {Bacteria, Anaerobic/*metabolism ; *Biodegradation, Environmental ; Biomass ; Bioreactors/microbiology ; Efficiency ; Industrial Microbiology/*methods ; Waste Disposal, Fluid/*methods ; Water Purification/*methods ; }, abstract = {Two expanded granular sludge bed-anaerobic filter (EGSB-AF) bioreactors (3.38 l active volume) were used to directly compare psychrophilic (15 degrees C), anaerobic digestion (PAD) to mesophilic (37 degrees C) anaerobic digestion (MAD) for the treatment of a brewery wastewater (chemical oxygen demand (COD) concentration of 3,136+/-891 mg l(-1)). Bioreactor performance was evaluated by COD removal efficiency and biogas yields at a range of hydraulic and organic loading rates. Specific methanogenic activity (SMA) assays were also employed to investigate the activity of the biomass in the bioreactors. No significant difference in the COD removal efficiencies (which ranged from 85-93%) were recorded between PAD and MAD during the 194-d trial at maximum organic and hydraulic loading rates of 4.47 kg m(-3) day(-1) and 1.33 m(3) m(-3) day(-1), respectively. In addition, the methane content (%) of the biogas was very similar. The volumetric biogas yield from the PAD bioreactor was approximately 50% of that from the MAD bioreactor at an organic loading rate of 4.47 kg COD m(-3) day(-3) and an applied liquid up-flow velocity (V(up)) of 2.5 m h(-1). Increasing the V(up) in the PAD bioreactor to 5 m h(-1) resulted in a volumetric biogas production rate of approximately 4.1 l d(-1) and a methane yield of 0.28 l CH(4) g(-1) COD d(-1), which were very similar to the MAD bioreactor. Significant and negligible biomass washout was observed in the mesophilic and psychrophilic systems, respectively, thus increasing the sludge loading rate applied to the former and underlining the robustness of the latter, which appeared underloaded. A psychrotolerant mesophilic, but not truly psychrophilic, biomass developed in the PAD bioreactor biomass, with comparable maximum SMA values to the MAD bioreactor biomass. PAD, therefore, was shown to be favourably comparable to MAD for brewery wastewater treatment and biogas generation.}, }
@article {pmid16813010, year = {2006}, author = {Seurinck, S and Verdievel, M and Verstraete, W and Siciliano, SD}, title = {Identification of human fecal pollution sources in a coastal area: a case study at Oostende (Belgium).}, journal = {Journal of water and health}, volume = {4}, number = {2}, pages = {167-175}, pmid = {16813010}, issn = {1477-8920}, mesh = {*Bacteria/genetics ; *Bacteroides/genetics ; Belgium ; Colony Count, Microbial/methods ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; *Environmental Monitoring/methods ; Genetic Markers ; Humans ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sewage/microbiology ; *Water Microbiology ; *Water Pollution ; }, abstract = {From April to June 2001, a monitoring study at Oostende (Belgium) was conducted to obtain an insight into fecal pollution impairing water quality at this coastal area. Eight sampling sites were selected based on the historically low water quality at these sites compared to the remainder of the area. Indicator organisms such as fecal coliforms, Escherichia coli and fecal streptococci were monitored by plating. A real-time PCR assay for quantification of the human-specific HF183 Bacteroides 16S rRNA genetic marker was used to detect human fecal pollution at the sampling sites. Human fecal pollution was detected at all sampling sites. However, the frequency of detection ranged from 30-100% and the amount of human-specific Bacteroides markers recorded varied between the sampling sites. Concentrations of 10(7) human-specific Bacteroides markers per 1 to levels below the detection limit of the real-time PCR assay were recorded. Our results indicate that human fecal pollution is a re-occurring problem in certain areas. Of all the environmental parameters monitored during the study, only rainfall was strongly related to the detection of the indicator organisms and the human-specific Bacteroides marker.}, }
@article {pmid16805696, year = {2006}, author = {Vishnivetskaya, TA and Petrova, MA and Urbance, J and Ponder, M and Moyer, CL and Gilichinsky, DA and Tiedje, JM}, title = {Bacterial community in ancient Siberian permafrost as characterized by culture and culture-independent methods.}, journal = {Astrobiology}, volume = {6}, number = {3}, pages = {400-414}, doi = {10.1089/ast.2006.6.400}, pmid = {16805696}, issn = {1531-1074}, mesh = {*Bacteria/genetics ; Cold Temperature ; Fresh Water/microbiology ; Phylogeny ; *RNA, Ribosomal, 16S ; Seawater/microbiology ; Siberia ; *Soil Microbiology ; }, abstract = {The microbial composition of ancient permafrost sediments from the Kolyma lowland of Northeast Eurasia was examined through culture and culture-independent approaches. These sediments have been continuously frozen for 5,000 to 2-3 million years. A total of 265 Bacteria 16S rRNA gene sequences were amplified from the permafrost total-community genomic DNA and screened by amplified ribosomal 16S rRNA restriction analysis. Members of three major lineages were found: gamma-Proteobacteria (mostly Xanthomonadaceae), Actinobacteria, and Firmicutes. We also determined partial 16S rRNA gene sequences of 49 isolates from a collection of 462 aerobes isolated from these sediments. The bacteria included Actinomycetales (Arthrobacter and Microbacteriaceae); followed by the Firmicutes (Exiguobacterium and Planomicrobium); the Bacteroidetes (Flavobacterium); the gamma-Proteobacteria (Psychrobacter); and the alpha-Proteobacteria (Sphingomonas). Both culture and culture-independent approaches showed the presence of high and low G+C Gram-positive bacteria and gamma-Proteobacteria. Some of the 16S rRNA gene sequences of environmental clones matched those of Arthrobacter isolates. Two-thirds of the isolates grew at -2.5 degrees C, indicating that they are psychroactive, and all are closely related to phylogenetic groups with strains from other cold environments, mostly commonly from Antarctica. The culturable and non-culturable microorganisms found in the terrestrial permafrost provide a prototype for possible life on the cryogenic planets of the Solar System.}, }
@article {pmid16797673, year = {2007}, author = {Mertens, B and Blothe, C and Windey, K and De Windt, W and Verstraete, W}, title = {Biocatalytic dechlorination of lindane by nano-scale particles of Pd(0) deposited on Shewanella oneidensis.}, journal = {Chemosphere}, volume = {66}, number = {1}, pages = {99-105}, doi = {10.1016/j.chemosphere.2006.05.018}, pmid = {16797673}, issn = {0045-6535}, mesh = {Biodegradation, Environmental ; Biomass ; Bioreactors/microbiology ; Catalysis ; Chlorine/chemistry/metabolism ; Hexachlorocyclohexane/*chemistry/metabolism ; Molecular Structure ; Nanostructures/chemistry ; Palladium/*chemistry/metabolism ; Shewanella/growth &amp; development/*metabolism ; }, abstract = {A new approach for the removal of the pesticide lindane (gamma-hexachlorocyclohexane or gamma-HCH) makes use of catalytic reduction of HCH to benzene over a metal catalyst, namely Pd(0). Since specific surface area plays an important role in reactivity of catalysts, this study investigated the use of bioPd(0), i.e. nano-scale Pd(0) particles precipitated on the biomass of Shewanella oneidensis, for the removal of lindane. It was demonstrated that bioPd(0) has catalytic activity towards dechlorination of gamma-HCH, with the addition of formate as electron donor, and that dechlorination with bioPd(0) was more efficient than with commercial powdered Pd(0). The biodegradable compound benzene was formed as reaction product and other HCH isomers could also be dechlorinated. Subsequently bioPd(0) was implemented in a membrane reactor technology for the treatment of gamma-HCH polluted water. In a fed-batch process configuration with formate as electron donor, a removal percentage of 98% of gamma-HCH saturated water (10 mg l(-1)) was achieved within 24h. The measured chloride mass balance approached the theoretical value. The results of this work showed that a complete, efficient and fast removal of lindane was achieved by biocatalysis with bioPd(0).}, }
@article {pmid16791745, year = {2006}, author = {Fukuda, M and Matsuyama, J and Katano, T and Nakano, S and Dazzo, F}, title = {Assessing primary and bacterial production rates in biofilms on pebbles in Ishite stream, Japan.}, journal = {Microbial ecology}, volume = {52}, number = {1}, pages = {1-9}, pmid = {16791745}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development/metabolism ; *Biofilms ; Chlorophyll/analysis ; Chlorophyll A ; Ecosystem ; Food Chain ; Geologic Sediments/*microbiology ; Japan ; Rivers/*microbiology ; }, abstract = {Various measurements of microbial productivity in streambed pebble biofilms were analyzed almost monthly for 1 year to quantify the importance of primary production as an autochthonous source of organic matter utilized to support heterotrophic bacterial production in the dynamic food web within this natural microbial habitat. Bacterial density varied from 0.3x10(8) to 1.4x10(8) cells cm-2, and chlorophyll a concentration ranged from 0.7 to 25.9 microg cm-2, with no coupled oscillation between seasonal changes in these two parameters. In bottle incubation experiments, the instantaneous bacterial growth rate of bacteria was significantly correlated with their production rate [measured by frequency of dividing cells (FDC)] as follows: ln mu=0.138FDC-3.003 (n=15, r2=0.445, p<0.001). FDC values in the pebble biofilms increased with fluctuations during the study period, ranging from 3.6% to 9.2%. Bacterial production rates largely fluctuated between 0.15 to 0.92 microg C cm-2 h-1, and its seasonal pattern was similar to that of bacterial density. Net primary production measured between May 2002 to November 2002 attained minimum level (0.5 microg C cm-2 h-1) in June and maximum level (1.9 microg C cm-2 h-1) in August. Percentages of bacterial production to net primary production ranged between 21% and 120%. Because this ratio extends both below and above 100% for these parameters, it is likely that both autochthonous and allochthonous supplies of organic matter are important for production of bacteria in the pebble biofilms that develop in rapidly flowing fresh water streams.}, }
@article {pmid16783449, year = {2006}, author = {Yang, SS and Tsai, SH and Fan, HY and Yang, CK and Hung, WL and Cho, ST}, title = {Seasonal variation of microbial ecology in hemlock soil of Tatachia Mountain, Taiwan.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {39}, number = {3}, pages = {195-205}, pmid = {16783449}, issn = {1684-1182}, mesh = {Actinobacteria/isolation &amp; purification ; Biomass ; Carbon/analysis ; Carboxylic Acids/analysis ; *Ecology ; Fungi/isolation &amp; purification ; *Hemlock ; Hydrogen-Ion Concentration ; Nitrogen/analysis ; Phosphates/analysis ; Seasons ; Soil/*analysis ; *Soil Microbiology ; Taiwan ; Temperature ; Trees ; }, abstract = {BACKGROUND AND PURPOSE: Forest soil microorganisms and fauna decompose the organic materials, and thus strongly influence the nutrient cycling of the ecosystem. Soil microorganisms also contribute to soil structure and soil fertility. In Taiwan, the microbial distributions of soils have only been determined in acidic soil, inorganic acidic soil, upland soil, alkaline soil and power plant areas. There are few data on the microbial populations of forest soils. Tatachia Mountain is located in the central part of Taiwan and is a typical high altitude protected ecosystem area, designated as a National Park. This study investigated the role of microorganisms in the ecology and nutrient transformation of forest soil in Taiwan.<br><br>METHODS: As part of long-term ecological research in Taiwan, the environmental conditions, seasons, microbial populations, biomass and organic acid contents of hemlock soil were investigated. We also studied the effect of depth on microbial populations and biomass.<br><br>RESULTS: The soil temperatures were between 5.5 and 15.6 degrees C and the soil pH ranged from 3.3 to 4.4. Total organic carbon and total nitrogen contents ranged from 2.3 to 37.1% and from 0.3 to 1.7%, respectively. The carbon/nitrogen ratio was between 8.2 and 24.4. In topsoil, each gram of soil contained 10(5)-10(7) colony-forming units (CFU) culturable bacteria, 10(2)-10(5) CFU actinomycetes, 10(3)-10(5) CFU fungi, 10(4)-10(6) CFU cellulolytic microbes, 10(4)-10(6) CFU phosphate-solubilizing microbes, and 10(3)-10(6) CFU nitrogen-fixing microbes. Microbial populations were higher in topsoil compared with subsoil, but lower in topsoil than in organic layer. Microbial populations also decreased with the depth of soil. Microbial populations at 1E horizon were 0.6% to 9.4% of those at O horizon. The microbial biomass evaluated contained carbon 391-1013 mug, nitrogen 51-146 mug, malic acid 76-557 nM and succinic acid 37-527 nM per gram of soil. Summer season had higher microbial populations, biomass and organic content than winter season, but the differences were not significant.<br><br>CONCLUSION: Heavy coverage of organic matter was found in hemlock and spruce soils and was associated with acidic pH. Microbial populations decreased with increasing soil depth. Microbes play a very important role in organic matter decomposition and nutrition transformation in hemlock soil.}, }
@article {pmid16771981, year = {2006}, author = {Rillig, MC and Mummey, DL}, title = {Mycorrhizas and soil structure.}, journal = {The New phytologist}, volume = {171}, number = {1}, pages = {41-53}, doi = {10.1111/j.1469-8137.2006.01750.x}, pmid = {16771981}, issn = {0028-646X}, mesh = {*Ecosystem ; Food Chain ; Mycelium/physiology ; Mycorrhizae/classification/*physiology ; Plant Roots/microbiology ; Plants/microbiology ; Soil/analysis ; *Soil Microbiology ; Water/metabolism ; Water Microbiology ; }, abstract = {In addition to their well-recognized roles in plant nutrition and communities, mycorrhizas can influence the key ecosystem process of soil aggregation. Here we review the contribution of mycorrhizas, mostly focused on arbuscular mycorrhizal fungi (AMF), to soil structure at various hierarchical levels: plant community; individual root; and the soil mycelium. There are a suite of mechanisms by which mycorrhizal fungi can influence soil aggregation at each of these various scales. By extension of these mechanisms to the question of fungal diversity, it is recognized that different species or communities of fungi can promote soil aggregation to different degrees. We argue that soil aggregation should be included in a more complete 'multifunctional' perspective of mycorrhizal ecology, and that in-depth understanding of mycorrhizas/soil process relationships will require analyses emphasizing feedbacks between soil structure and mycorrhizas, rather than a uni-directional approach simply addressing mycorrhizal effects on soils. We finish the discussion by highlighting new tools, developments and foci that will probably be crucial in further understanding mycorrhizal contributions to soil structure.}, }
@article {pmid16770684, year = {2006}, author = {Boucher, D and Richardot, M and Thénot, A and Debroas, D}, title = {Incorporation of 3H-thymidine by different prokaryotic groups in relation to temperature and nutrients in a lacustrine ecosystem.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {399-407}, pmid = {16770684}, issn = {0095-3628}, mesh = {*Adaptation, Physiological ; Bacteria/*growth &amp; development/*metabolism ; Biomass ; Carbon/metabolism ; Cytophaga/growth &amp; development/metabolism ; Ecosystem ; In Situ Hybridization, Fluorescence ; Nitrogen/metabolism ; Phosphorus/metabolism ; Proteobacteria/growth &amp; development/metabolism ; *Soil Microbiology ; Temperature ; Thymidine/*metabolism ; Tritium ; }, abstract = {The incorporation of [3H-methyl] thymidine (3H-TdR) by Eubacteria, bacterial groups (alpha- and beta-Proteobacteria, Cytophaga-Flavobacter), and Archaea was measured according to temperature (7 and 17 degrees C) and nutrient levels (nitrogen, phosphorus, and carbon) in a lacustrine system (Sep, France). Short-term incubation was performed using a combination of microautoradiography and fluorescent in situ hybridization. Irrespective of the temperatures and nutrients studied, all the major phylogenetic bacterial groups assimilated 3H-TdR, and in most of the treatments studied, the proportion of beta-Proteobacteria taking up 3H-TdR was higher than those in the other bacterial groups. The proportion of Bacteria and different bacterial groups studied incorporating 3H-TdR were significantly increased, approximately 1.5-fold, by temperature except for alpha-Proteobacteria (7.6-fold). The nutrient effect was not the same for the different bacterial groups according to the temperatures studied. The proportions of alpha-Proteobacteria (at both temperatures) and Cytophaga-Flavobacter (at 7 degrees C) taking up 3H-TdR were significantly decreased and increased by adding N and P, respectively. Also, adding N, P, and C increased and decreased the percentage of beta-Proteobacteria incorporating 3H-TdR at 7 and 17 degrees C, respectively. The archaeal community showed a similar proportion of active cells (i.e., 3H-TdR) to the bacterial community, and uptake of 3H-TdR by Archaea was significantly increased (P < 0.05) by both temperature and nutrients. Thus, the assimilation of 3H-TdR by bacterial groups and Archaea in lacustrine system is significantly controlled by both temperature and nutrients.}, }
@article {pmid16767523, year = {2006}, author = {Cotner, JB and Makino, W and Biddanda, BA}, title = {Temperature affects stoichiometry and biochemical composition of Escherichia coli.}, journal = {Microbial ecology}, volume = {52}, number = {1}, pages = {26-33}, pmid = {16767523}, issn = {0095-3628}, mesh = {Biomass ; Carbon/metabolism ; *Ecosystem ; Escherichia coli/*growth &amp; development/*metabolism ; Nitrogen/metabolism ; Phosphorus/metabolism ; RNA, Bacterial/metabolism ; *Temperature ; }, abstract = {Temperature is a master variable controlling biochemical processes in organisms, and its effects are manifested on many organizational levels in organisms and ecosystems. We examined the effects of temperature on the biochemical composition and stoichiometry of a model heterotrophic bacterium, Escherichia coli K-12, held at constant growth rate in chemostats. Increasing temperature led to increased cellular organic carbon (C) and organic nitrogen (N) with decreased phosphorus (P) content, leading to increased C/P and N/P biomass ratios. P content was related to cellular RNA, which is P-rich (9-10% by weight) and nonnucleic acid P (presumably composed of mostly phospholipids, intracellular phosphate, and polyphosphate). These results indicate that E. coli allocates an increased proportion of its P cell quota toward assembly (ribosomes) at low temperatures and an increasing proportion toward resource acquisition machinery (membranes) at higher temperatures. If these results are relevant to the behavior of prokaryotic heterotrophs in natural settings (the gut, soils, lakes, oceans, etc.), it suggests greater nutrient regeneration and less microbial nutrient retention as temperatures increase.}, }
@article {pmid16767522, year = {2006}, author = {James, JB and Sherman, TD and Devereux, R}, title = {Analysis of bacterial communities in seagrass bed sediments by double-gradient denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA genes.}, journal = {Microbial ecology}, volume = {52}, number = {4}, pages = {655-661}, pmid = {16767522}, issn = {0095-3628}, mesh = {Bacteria/classification/*genetics/growth &amp; development ; Ecosystem ; Electrophoresis, Polyacrylamide Gel/*methods ; Florida ; Geography ; Geologic Sediments/*microbiology ; Oceans and Seas ; RNA, Ribosomal, 16S/analysis/*genetics ; Soil Microbiology ; }, abstract = {Bacterial communities associated with seagrass bed sediments are not well studied. The work presented here investigated several factors and their impact on bacterial community diversity, including the presence or absence of vegetation, depth into sediment, and season. Double-gradient denaturing gradient gel electrophoresis (DG-DGGE) was used to generate banding patterns from the amplification products of 16S rRNA genes in 1-cm sediment depth fractions. Bioinformatics software and other statistical analyses were used to generate similarity scores between sections. Jackknife analyses of these similarity coefficients were used to group banding patterns by depth into sediment, presence or absence of vegetation, and by season. The effects of season and vegetation were strong and consistent, leading to correct grouping of banding patterns. The effects of depth were not consistent enough to correctly group banding patterns using this technique. While it is not argued that bacterial communities in sediment are not influenced by depth in sediment, this study suggests that the differences are too fine and inconsistent to be resolved using 1-cm depth fractions and DG-DGGE. The effects of vegetation and season on bacterial communities in sediment were more consistent than the effects of depth in sediment, suggesting they exert stronger controls on microbial community structure.}, }
@article {pmid16767521, year = {2006}, author = {Suehiro, F and Kobayashi, T and Nonaka, L and Tuyen, BC and Suzuki, S}, title = {Degradation of tributyltin in microcosm using Mekong River sediment.}, journal = {Microbial ecology}, volume = {52}, number = {1}, pages = {19-25}, pmid = {16767521}, issn = {0095-3628}, mesh = {Bacteria/growth &amp; development/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Colony Count, Microbial ; Drug Resistance, Bacterial ; Ecosystem ; Environmental Pollutants/analysis/*metabolism/pharmacology ; Geologic Sediments/chemistry/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Trialkyltin Compounds/analysis/*metabolism/pharmacology ; Vietnam ; }, abstract = {The degradation of tributyltin (TBT) and changes of bacterial number and community structures were investigated in microcosms using the sediment collected from the Mekong River, Vietnam. Concentrations of TBT in sediments were less than 0.62 ng/g (dry wt), lower than those reported from other areas. TBT-resistant bacteria were found in the three sampling sites, and the occurrence rates were 11-16% out of the total viable count. In this microcosm experiment, initial concentration of TBT [1.0-1.4 microg/g (dry wt)] decreased to 0.6 microg/g (dry wt) during 150 days, whereas that in the control microcosm with autoclaved sediment did not change, indicating that Mekong River sediment contains high TBT-degrading activity by microorganisms. The occurrence of TBT-resistant bacteria and the bacterial community structures monitored by denaturing gradient gel electrophoresis were almost the same between test and control groups, indicating that the addition of TBT had little influence on microbial community structure. Mekong River sediment seems to have a stable microbial community against TBT pollution.}, }
@article {pmid16767520, year = {2006}, author = {Docherty, KM and Young, KC and Maurice, PA and Bridgham, SD}, title = {Dissolved organic matter concentration and quality influences upon structure and function of freshwater microbial communities.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {378-388}, pmid = {16767520}, issn = {0095-3628}, mesh = {Bacteria/classification/*growth &amp; development/*metabolism ; Biodiversity ; Biomass ; Carbon/chemistry/*metabolism ; Colony Count, Microbial ; *Ecosystem ; Electrophoresis, Agar Gel ; Fresh Water/microbiology ; Molecular Weight ; Organic Chemicals/chemistry/*metabolism ; Species Specificity ; Time Factors ; *Water Microbiology ; }, abstract = {Past studies have suggested that the concentration and quality of dissolved organic matter (DOM) may influence microbial community structure. In this study, we cross-inoculated the bacterial communities from two streams and a dystrophic lake that varied in DOM concentration and chemistry, to yield nine fully crossed treatments. We measured dissolved organic carbon (DOC) concentration and heterotrophic microbial community productivity throughout a 72-h incubation period, characterized DOM quality by molecular weight, and determined microbial community structure at the initial and final time points. Our results indicate that all bacterial inoculate sources had similar effects upon DOC concentration and DOM quality, regardless of the DOM source. These effects included an overall decrease in DOM M (W) and an initial period of DOC concentration variability between 0-24h. In contrast, microbial communities and their metabolic rates converged to profiles that reflected the DOM source upon which they were growing, regardless of the initial bacterial inoculation. The one exception was that the bacterial community from the low-concentration and low-molecular-weight DOM source exhibited a greater denaturing gradient gel electrophoresis (DGGE) band richness when grown in its own DOM source than when grown in the highest concentration and molecular weight DOM source. This treatment also exhibited a higher rate of productivity. In general, our data suggest that microbial communities are selected by the DOM sources to which they are exposed. A microbial community will utilize the low-molecular-weight (or labile) DOM sources as well as parts of the high-molecular-weight (refractory) DOM, until a community develops that can efficiently metabolize the more abundant high-molecular-weight source. This experiment examines some of the complex interactions between microbial community selection and the combined factors of DOM quality and concentration. Our data suggest that the roles of aerobic aquatic heterotrophic bacteria in carbon cycling, as well as the importance of high-molecular-weight DOM as a carbon source, may be more complex than is conventionally recognized.}, }
@article {pmid16767519, year = {2006}, author = {Palumbo, JD and Baker, JL and Mahoney, NE}, title = {Isolation of bacterial antagonists of Aspergillus flavus from almonds.}, journal = {Microbial ecology}, volume = {52}, number = {1}, pages = {45-52}, pmid = {16767519}, issn = {0095-3628}, mesh = {Aflatoxins/antagonists &amp; inhibitors/biosynthesis/genetics ; *Antibiosis ; Aspergillus flavus/genetics/*growth &amp; development/metabolism ; Bacteria/chemistry/*isolation &amp; purification/metabolism ; *Bacterial Physiological Phenomena ; Cell Wall/metabolism ; Chitin/metabolism ; Prunus/*microbiology ; Yeasts/cytology ; }, abstract = {Bacteria were isolated from California almond orchard samples to evaluate their potential antifungal activity against aflatoxin-producing Aspergillus flavus. Fungal populations from the same samples were examined to determine the incidence of aflatoxigenic Aspergillus species. Antagonistic activities of the isolated bacterial strains were screened against a nonaflatoxigenic nor mutant of A. flavus, which accumulates the pigmented aflatoxin precursor norsolorinic acid (NOR) under conditions conducive to aflatoxin production. Using solid and liquid media in coculture assays, 171 bacteria isolated from almond flowers, immature nut fruits, and mature nut fruits showed inhibition of A. flavus growth and/or inhibition of NOR accumulation. Bacterial isolates were further characterized for production of extracellular enzymes capable of hydrolyzing chitin or yeast cell walls. Molecular and physiological identification of the bacterial strains indicated that the predominant genera isolated were Bacillus, Pseudomonas, Ralstonia, and Burkholderia, as well as several plant-associated enteric and nonenteric bacteria. A set of 20 isolates was selected for further study based on their species identification, antifungal phenotypes, and extracellular enzyme production. Quantitative assays using these isolates in liquid coculture with a wild-type, aflatoxin-producing A. flavus strain showed that a number of strains completely inhibited fungal growth in three different media. These results indicate the potential for development of bacterial antagonists as biological control agents against aflatoxigenic aspergilli on almonds.}, }
@article {pmid16767518, year = {2006}, author = {Gil, F and De la Iglesia, R and Mendoza, L and González, B and Wilkens, M}, title = {Soil bacteria are differentially affected by the resin of the medicinal plant Pseudognaphalium vira vira and its main component kaurenoic acid.}, journal = {Microbial ecology}, volume = {52}, number = {1}, pages = {10-18}, pmid = {16767518}, issn = {0095-3628}, mesh = {Anti-Bacterial Agents/analysis/pharmacology ; Asteraceae/*chemistry ; Diterpenes/analysis/*pharmacology ; Gram-Negative Bacteria/*drug effects/isolation &amp; purification ; Gram-Positive Bacteria/*drug effects/isolation &amp; purification ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Resins, Plant/*pharmacology ; Soil/analysis ; *Soil Microbiology ; }, abstract = {The diterpenoid kaurenoic acid is the main component of the resin from the medicinal plant Pseudognaphalium vira vira. As some diterpenoids have antimicrobial properties, the effect of this resin and the kaurenoic acid on soil bacteria was studied. The resin of P. vira vira and purified kaurenoic acid were two to four times more effective as antibacterial agents with Gram-positive than with Gram-negative soil isolates. The chemical stability of kaurenoic acid and the antibacterial activity of both the resin and the diterpenoid were studied in microcosms containing plant-associated soil. After 15 days of incubation, the diterpenoid was stable, as determined by 1H nuclear magnetic resonance and thin-layer chromatography, and soil extracts still exhibited antibacterial activity. However, after 30 days of incubation, loss of antibacterial activity of soil extracts correlated with removal or chemical modification of kaurenoic acid. The effect of the resin or this diterpenoid on the soil bacteria community was analyzed by the terminal restriction fragment length polymorphisms technique. After 15 days of incubation, the resin and the pure compound caused significant changes in the soil bacterial community. The relative abundance of specific bacterial groups was differentially affected by the resin components, being the effects with the resin stronger than with the kaurenoic acid. After 30 days of incubation, these changes mostly reverted. These results indicate that a plant resin containing diterpenoid compounds plays a significant role controlling specific groups of microorganisms in the soil associated with the plant.}, }
@article {pmid16751547, year = {2006}, author = {Temmerman, R and Vervaeren, H and Noseda, B and Boon, N and Verstraete, W}, title = {Necrotrophic growth of Legionella pneumophila.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {6}, pages = {4323-4328}, pmid = {16751547}, issn = {0099-2240}, mesh = {Biofilms ; Kinetics ; Legionella pneumophila/genetics/*growth &amp; development/*pathogenicity ; Polymerase Chain Reaction ; Propidium ; Pseudomonas putida ; Water Microbiology ; Water Supply ; }, abstract = {This study examined whether Legionella pneumophila is able to thrive on heat-killed microbial cells (necrotrophy) present in biofilms or heat-treated water systems. Quantification by means of plate counting, real-time PCR, and flow cytometry demonstrated necrotrophic growth of L. pneumophila in water after 96 h, when at least 100 dead cells are available to one L. pneumophila cell. Compared to the starting concentration of L. pneumophila, the maximum observed necrotrophic growth was 1.89 log units for real-time PCR and 1.49 log units for plate counting. The average growth was 1.57 +/- 0.32 log units (n = 5) for real-time PCR and 1.14 +/- 0.35 log units (n = 5) for plate counting. Viability staining and flow cytometry showed that the fraction of living cells in the L. pneumophila population rose from the initial 54% to 82% after 96 h. Growth was measured on heat-killed Pseudomonas putida, Escherichia coli, Acanthamoeba castellanii, Saccharomyces boulardii, and a biofilm sample. Gram-positive organisms did not result in significant growth of L. pneumophila, probably due to their robust cell wall structure. Although necrotrophy showed lower growth yields compared to replication within protozoan hosts, these findings indicate that it may be of major importance in the environmental persistence of L. pneumophila. Techniques aimed at the elimination of protozoa or biofilm from water systems will not necessarily result in a subsequent removal of L. pneumophila unless the formation of dead microbial cells is minimized.}, }
@article {pmid16751532, year = {2006}, author = {Hamelin, K and Bruant, G and El-Shaarawi, A and Hill, S and Edge, TA and Bekal, S and Fairbrother, JM and Harel, J and Maynard, C and Masson, L and Brousseau, R}, title = {A virulence and antimicrobial resistance DNA microarray detects a high frequency of virulence genes in Escherichia coli isolates from Great Lakes recreational waters.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {6}, pages = {4200-4206}, pmid = {16751532}, issn = {0099-2240}, mesh = {Anti-Bacterial Agents/pharmacology ; DNA, Bacterial/genetics/isolation &amp; purification ; *Drug Resistance, Bacterial ; Escherichia coli/drug effects/*genetics/pathogenicity/*physiology ; Fresh Water/*microbiology ; Microbial Sensitivity Tests ; Oligonucleotide Array Sequence Analysis ; Recreation ; Seasons ; United States ; Virulence/*genetics ; Water Microbiology ; }, abstract = {Escherichia coli is generally described as a commensal species with occasional pathogenic strains. Due to technological limitations, there is currently little information concerning the prevalence of pathogenic E. coli strains in the environment. For the first time, using a DNA microarray capable of detecting all currently described virulence genes and commonly found antimicrobial resistance genes, a survey of environmental E. coli isolates from recreational waters was carried out. A high proportion (29%) of 308 isolates from a beach site in the Great Lakes carried a pathotype set of virulence-related genes, and 14% carried antimicrobial resistance genes, findings consistent with a potential risk for public health. The results also showed that another 8% of the isolates had unusual virulence gene combinations that would be missed by conventional screening. This new application of a DNA microarray to environmental waters will likely have an important impact on public health, epidemiology, and microbial ecology in the future.}, }
@article {pmid16750582, year = {2006}, author = {Van Raemdonck, H and Maes, A and Ossieur, W and Verthé, K and Vercauteren, T and Verstraete, W and Boon, N}, title = {Real time PCR quantification in groundwater of the dehalorespiring Desulfitobacterium dichloroeliminans strain DCA1.}, journal = {Journal of microbiological methods}, volume = {67}, number = {2}, pages = {294-303}, doi = {10.1016/j.mimet.2006.04.001}, pmid = {16750582}, issn = {0167-7012}, mesh = {Benzothiazoles ; Biodegradation, Environmental ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Desulfitobacterium/genetics/*isolation &amp; purification/metabolism ; Diamines ; Ethylene Dichlorides/*metabolism ; Flow Cytometry ; Fresh Water/*microbiology ; Microscopy, Fluorescence ; Organic Chemicals/chemistry ; Phylogeny ; Polymerase Chain Reaction/*methods ; Quinolines ; RNA, Ribosomal, 16S/chemistry/genetics ; Reproducibility of Results ; Sensitivity and Specificity ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Quantifying microorganisms responsible for bioremediation can provide insight in their behavior and can help to obtain a better understanding of the physicochemical parameters monitored during bioremediation. A real time PCR (RTm PCR) assay based on the detection with SYBR Green I was optimized in order to quantify the 1,2-dichloroethane dehalorespiring Desulfitobacterium dichloroeliminans strain DCA1. A primer pair targeting unique regions of the 16 S rRNA gene was designed and tested in silico for its specificity. Selectivity was furthermore evaluated and a Limit of Quantification of 1.5 x 10(4) cells/microL DNA extract was obtained for spiked groundwater. Real time measurements of groundwater samples retrieved from a bioaugmented monitoring well and which had an average concentration lying in the range of the Limit of Quantification were evaluated positively with regards to reproducibility. Validation of the RTm PCR assay on groundwater samples originating from different sites confirmed the specificity of the designed primer pair. This RTm PCR assay can be used to survey the abundance and kinetics of strain DCA1 in in situ bioaugmentation field studies.}, }
@article {pmid16749711, year = {2006}, author = {Aelterman, P and Rabaey, K and Pham, HT and Boon, N and Verstraete, W}, title = {Continuous electricity generation at high voltages and currents using stacked microbial fuel cells.}, journal = {Environmental science &amp; technology}, volume = {40}, number = {10}, pages = {3388-3394}, doi = {10.1021/es0525511}, pmid = {16749711}, issn = {0013-936X}, mesh = {Bacteria/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; *Bioelectric Energy Sources ; *Bioreactors ; *Electricity ; Electrodes ; Ferrocyanides/chemistry ; Sewage/chemistry/*microbiology ; Water Purification/*methods ; }, abstract = {Connecting several microbial fuel cell (MFC) units in series or parallel can increase voltage and current; the effect on the microbial electricity generation was as yet unknown. Six individual continuous MFC units in a stacked configuration produced a maximum hourly averaged power output of 258 W m(-3) using a hexacyanoferrate cathode. The connection of the 6 MFC units in series and parallel enabled an increase of the voltages (2.02 V at 228 W m(-3)) and the currents (255 mA at 248 W m(-3)), while retaining high power outputs. During the connection in series, the individual MFC voltages diverged due to microbial limitations at increasing currents. With time, the initial microbial community decreased in diversity and Gram-positive species became dominant. The shift of the microbial community accompanied a tripling of the short time power output of the individual MFCs from 73 W m(-3) to 275 W m(-3), a decrease of the mass transfer limitations and a lowering of the MFC internal resistance from 6.5 +/- 1.0 to 3.9 +/- 0.5 omega. This study demonstrates a clear relation between the electrochemical performance and the microbial composition of MFCs and further substantiates the potential to generate useful energy by means of MFCs.}, }
@article {pmid16738105, year = {2006}, author = {Bakermans, C and Ayala-Del-Río, HL and Ponder, MA and Vishnivetskaya, T and Gilichinsky, D and Thomashow, MF and Tiedje, JM}, title = {Psychrobacter cryohalolentis sp. nov. and Psychrobacter arcticus sp. nov., isolated from Siberian permafrost.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {56}, number = {Pt 6}, pages = {1285-1291}, doi = {10.1099/ijs.0.64043-0}, pmid = {16738105}, issn = {1466-5026}, mesh = {Cold Climate ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Ice ; Molecular Sequence Data ; Phospholipids/analysis ; Phylogeny ; Psychrobacter/*classification/genetics/isolation &amp; purification ; Siberia ; }, abstract = {Three Gram-negative, non-motile, non-pigmented, oxidase-positive coccobacilli capable of growth at temperatures from -10 to 30 degrees C and salinities of 0 to 1.7 M NaCl were isolated from Siberian permafrost and characterized. Both 16S rRNA and gyrB gene sequencing studies placed the isolates in the Gammaproteobacteria within the genus Psychrobacter. However, with higher bootstrap values and reproducible tree topologies, gyrB represented a more reliable phylogenetic marker for the taxonomy of Psychrobacter species. DNA-DNA hybridization data supported gyrB tree topologies and established two relatedness groups within the three isolates; neither of these groups was related at the species level to any previously described Psychrobacter species. The two groups of isolates could be differentiated phenotypically from 13 previously described Psychrobacter species using API strips. These results support the existence of two novel species of Psychrobacter, for which we propose the names Psychrobacter cryohalolentis sp. nov. (type strain K5(T) = DSM 17306(T) = VKM B-2378(T)) and Psychrobacter arcticus sp. nov. (type strain 273-4(T) = DSM 17307(T) = VKM B-2377(T)).}, }
@article {pmid16737754, year = {2006}, author = {Huang, WE and Hopper, D and Goodacre, R and Beckmann, M and Singer, A and Draper, J}, title = {Rapid characterization of microbial biodegradation pathways by FT-IR spectroscopy.}, journal = {Journal of microbiological methods}, volume = {67}, number = {2}, pages = {273-280}, doi = {10.1016/j.mimet.2006.04.009}, pmid = {16737754}, issn = {0167-7012}, mesh = {Cresols/*metabolism ; Gas Chromatography-Mass Spectrometry ; Principal Component Analysis ; Pseudomonas putida/*metabolism ; Spectroscopy, Fourier Transform Infrared/*methods ; Xylenes/*metabolism ; }, abstract = {Fourier transform-infrared (FT-IR) spectroscopy has become an important tool for rapid analysis of complex biological samples. The infrared absorbance spectrum could be regarded as a "fingerprint" which is characteristic of biochemical substances. In this study, Pseudomonas putida NCIMB 9869 was grown with either 3,5-xylenol or m-cresol as the sole carbon source, each inducing different metabolic pathways for m-cresol biotransformation. FT-IR spectroscopy was capable of differentiating both induced cultures of P. putida NCIMB 9869 as well as the resulting biotransformation product mixtures. FT-IR spectral analysis indicated that carboxylic acids were key chemicals responsible for distinguishing the products of the two catabolic pathways. Gas chromatography-mass spectrometry (GC-MS) was performed to validate the FT-IR analysis, indicating that two carboxylic acids, 3-hydroxybenzoic acid and 2,5-dihydroxybenzoic acid, were present as m-cresol biotransformation products from 3,5-xylenol-grown cells, but were absent in m-cresol-grown cells. The ability to use FT-IR to rapidly distinguish between biotransformation product mixtures as well as differentially induced bacterial strains suggests this approach might be a valuable tool for screening large biotransformation assays for novel products and metabolic mutants.}, }
@article {pmid16734797, year = {2006}, author = {van der Wielen, PW}, title = {Diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes in the MgCl2-dominated deep hypersaline anoxic basin discovery.}, journal = {FEMS microbiology letters}, volume = {259}, number = {2}, pages = {326-331}, doi = {10.1111/j.1574-6968.2006.00284.x}, pmid = {16734797}, issn = {0378-1097}, mesh = {Bacterial Proteins/chemistry/genetics ; Base Sequence ; DNA Primers/genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; Genes, Bacterial ; Genetic Variation ; Magnesium Chloride ; Mediterranean Sea ; Phylogeny ; Piscirickettsiaceae/enzymology/genetics ; Protein Subunits ; Ribulose-Bisphosphate Carboxylase/chemistry/*genetics ; Seawater/microbiology ; Sodium Chloride ; Thiobacillus/enzymology/genetics ; *Water Microbiology ; }, abstract = {Partial sequences of the form I (cbbL) and form II (cbbM) of the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) large subunit genes were obtained from the brine and interface of the MgCl2-dominated deep hypersaline anoxic basin Discovery. CbbL and cbbM genes were found in both brine and interface of the Discovery Basin but were absent in the overlying seawater. The diversity of both genes in the brine and interface was low, which might caused by the extreme saline conditions in Discovery of approximately 5 M MgCl2. None of the retrieved sequences were closely related to sequences deposited in the GenBank database. A phylogenetic analysis demonstrated that the cbbL sequences were affiliated with a Thiobacillus sp. or with one of the RuBisCO genes from Hydrogenovibrio marinus. The cbbM sequences clustered with thiobacilli or formed a new group with no close relatives. The results implicate that bacteria with the potential for carbon dioxide fixation and chemoautotrophy are present in the Discovery Basin. This is the first report demonstrating that RuBisCO genes are present under hypersaline conditions of 5 M MgCl2.}, }
@article {pmid16733620, year = {2006}, author = {Comte, J and Jacquet, S and Viboud, S and Fontvieille, D and Millery, A and Paolini, G and Domaizon, I}, title = {Microbial community structure and dynamics in the largest natural French lake (Lake Bourget).}, journal = {Microbial ecology}, volume = {52}, number = {1}, pages = {72-89}, pmid = {16733620}, issn = {0095-3628}, mesh = {Animals ; *Bacteria/classification/isolation &amp; purification ; Bacterial Physiological Phenomena ; Biodiversity ; Biomass ; Chlorophyll/analysis ; Chlorophyll A ; Colony Count, Microbial ; *Ecosystem ; *Eukaryota/classification/isolation &amp; purification/physiology ; France ; Fresh Water/*microbiology/*parasitology ; In Situ Hybridization, Fluorescence ; Plankton ; }, abstract = {We investigated the dynamics and diversity of heterotrophic bacteria, autotrophic and heterotrophic flagellates, and ciliates from March to July 2002 in the surface waters (0-50 m) of Lake Bourget. The heterotrophic bacteria consisted mainly of "small" cocci, but filaments (>2 microm), commonly considered to be grazing-resistant forms under increased nanoflagellate grazing, were also detected. These elongated cells mainly belonged to the Cytophaga-Flavobacterium (CF) cluster, and were most abundant during spring and early summer, when mixotrophic or heterotrophic flagellates were the main bacterial predators. The CF group strongly dominated fluorescent in situ hybridization-detected cells from March to June, whereas clear changes were observed in early summer when Beta-proteobacteria and Alpha-proteobacteria increased concomitantly with maximal protist grazing pressures. The analysis of protist community structure revealed that the flagellates consisted mainly of cryptomonad forms. The dynamics of Cryptomonas sp. and Dinobryon sp. suggested the potential importance of mixotrophs as consumers of bacteria. This point was verified by an experimental approach based on fluorescent microbeads to assess the potential grazing impact of all protist taxa in the epilimnion. From the results, three distinct periods in the functioning of the epilimnetic microbial loop were identified. In early spring, mixotrophic and heterotrophic flagellates constituted the main bacterivores, and were regulated by the availability of their resources mainly during April (phase 1). Once the "clear water phase" was established, the predation pressure of metazooplankton represented a strong top-down force on all microbial compartments. During this period only mixotrophic flagellates occasionally exerted a significant bacterivory pressure (phase 2). Finally, the early summer was characterized by the highest protozoan grazing impact and by a rapid shift in the carbon pathway transfer, with a fast change-over of the main predators contribution, i.e., mixotrophic, heterotrophic flagellates and ciliates in bacterial mortality. The high abundance of ciliates during this period was consistent with the high densities of resources (heterotrophic nanoflagellates, algae, bacteria) in deep layers containing the most chlorophyll. Bacteria, as ciliates, responded clearly to increasing phytoplankton abundance, and although bacterial grazing impact could vary largely, bacterial abundance seemed to be primarily bottom-up regulated (phase 3).}, }
@article {pmid16729225, year = {2006}, author = {Morales, SE and Mouser, PJ and Ward, N and Hudman, SP and Gotelli, NJ and Ross, DS and Lewis, TA}, title = {Comparison of bacterial communities in New England Sphagnum bogs using terminal restriction fragment length polymorphism (T-RFLP).}, journal = {Microbial ecology}, volume = {52}, number = {1}, pages = {34-44}, pmid = {16729225}, issn = {0095-3628}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Colony Count, Microbial ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; *Ecosystem ; Molecular Sequence Data ; New England ; Phylogeny ; Polymerase Chain Reaction ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sphagnopsida/*microbiology ; }, abstract = {Wetlands are major sources of carbon dioxide, methane, and other greenhouse gases released during microbial degradation. Despite the fact that decomposition is mainly driven by bacteria and fungi, little is known about the taxonomic diversity of bacterial communities in wetlands, particularly Sphagnum bogs. To explore bacterial community composition, 24 bogs in Vermont and Massachusetts were censused for bacterial diversity at the surface (oxic) and 1 m (anoxic) regions. Bacterial diversity was characterized by a terminal restriction fragment length (T-RFLP) fingerprinting technique and a cloning strategy that targeted the 16S rRNA gene. T-RFLP analysis revealed a high level of diversity, and a canonical correspondence analysis demonstrated marked similarity among bogs, but consistent differences between surface and subsurface assemblages. 16S rDNA sequences derived from one of the sites showed high numbers of clones belonging to the Deltaproteobacteria group. Several other phyla were represented, as well as two Candidate Division-level taxonomic groups. These data suggest that bog microbial communities are complex, possibly stratified, and similar among multiple sites.}, }
@article {pmid16716936, year = {2006}, author = {Halet, D and Boon, N and Verstraete, W}, title = {Community dynamics of methanotrophic bacteria during composting of organic matter.}, journal = {Journal of bioscience and bioengineering}, volume = {101}, number = {4}, pages = {297-302}, doi = {10.1263/jbb.101.297}, pmid = {16716936}, issn = {1389-1723}, mesh = {Bacteria/*metabolism ; Biotechnology/*methods ; Cluster Analysis ; Electrophoresis ; Environmental Microbiology ; Models, Statistical ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Soil ; Soil Microbiology ; Time Factors ; }, abstract = {In this study, we describe the effects of composting on the diversity, abundance and activity of the methanotrophic community present in the compost. Composting was allowed to proceed for 10 weeks in an in-vessel reactor. Self-heating capacity (Rottegrad) indicated that compost maturity was reached after 4 weeks. After 6 weeks, a second thermophilic phase was induced by manually increasing temperature to investigate whether or not the methanotrophs shifted back to the thermophilic population. Polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) with primers specific for type I methanotrophs of 16S rDNA and 16S rRNA were used to characterize the composition of the microbial community. Cluster and diversity analyses of RNA DGGE patterns were more sensitive than those of DNA DGGE patterns, and revealed that mesophilic and thermophilic methanotrophic communities could be differentiated. Moreover, it was seen that the diversity of the community was low during the thermophilic phase and increased during the final maturation phase. Real-time PCR analysis was also performed on the DNA and RNA extracts and showed no changes in the abundance of type I methanotrophs during the composting process (10(9) DNA copies/g compost). However, RNA-related activity did change, with the lowest activity (10(7) cDNA copies/g compost) observed during the thermophilic phase, subsequently increasing to its maximum value (10(9) cDNA copies/g compost), and finally decreasing during the maturation phase. This study confirmed the population dynamics, as seen for general groups such as bacteria and fungi during composting, for a very specific and sensitive group of bacteria, it is the type I methanotrophs.}, }
@article {pmid16710792, year = {2006}, author = {Fomina, M and Charnock, JM and Hillier, S and Alexander, IJ and Gadd, GM}, title = {Zinc phosphate transformations by the Paxillus involutus/pine ectomycorrhizal association.}, journal = {Microbial ecology}, volume = {52}, number = {2}, pages = {322-333}, pmid = {16710792}, issn = {0095-3628}, mesh = {Basidiomycota/classification/*metabolism/physiology ; Biodegradation, Environmental ; Biomass ; Mycorrhizae/classification/*metabolism/physiology ; Phosphates/*metabolism ; Phosphorus/metabolism ; Pinus/growth &amp; development/metabolism/*microbiology ; Plant Shoots/growth &amp; development/metabolism/microbiology ; Zinc Compounds/*metabolism ; }, abstract = {In this research, we investigate zinc phosphate transformations by Paxillus involutus/pine ectomycorrhizas using zinc-resistant and zinc-sensitive strains of the ectomycorrhizal fungus under high- and low-phosphorus conditions to further understand fungal roles in the transformation of toxic metal minerals in the mycorrhizosphere. Mesocosm experiments with ectomycorrhizas were performed under sterile conditions with zinc phosphate localized in cellophane bags: zinc and phosphorus mobilization and uptake by the ectomycorrhizal biomass were analyzed. In the presence of a phosphorus source, an ectomycorrhizal association with a zinc-resistant strain accumulated the least zinc compared to a zinc-sensitive ectomycorrhizal association and non-mycorrhizal plants. Under low-phosphorus conditions, mycorrhizal seedlings infected with the zinc-resistant strain increased the dissolution of zinc phosphate and zinc accumulation by the plant. Extended X-ray absorption fine structure analysis of both mycorrhizal and nonmycorrhizal roots showed octahedral coordination of zinc by oxygen-containing ligands such as carboxylates or phosphate. We conclude that zinc phosphate solubilization and zinc and phosphorus uptake by the association depend on ectomycorrhizal infection, strain of the mycobiont, and the phosphorus status of the matrix.}, }
@article {pmid16710791, year = {2006}, author = {Maestre, FT and Martín, N and Díez, B and López-Poma, R and Santos, F and Luque, I and Cortina, J}, title = {Watering, fertilization, and slurry inoculation promote recovery of biological crust function in degraded soils.}, journal = {Microbial ecology}, volume = {52}, number = {3}, pages = {365-377}, pmid = {16710791}, issn = {0095-3628}, mesh = {Acetylene/metabolism ; Analysis of Variance ; Carbon Dioxide/metabolism ; Chlorophyll/*metabolism ; Chlorophyll A ; Conservation of Natural Resources ; Cyanobacteria/classification/genetics/growth &amp; development/*metabolism ; Desert Climate ; *Ecosystem ; Environmental Monitoring ; Fertilizers ; Lichens/growth &amp; development/*metabolism ; Nitrogen/metabolism ; Nitrogen Fixation ; Nitrogenase/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/chemistry ; Sewage ; *Soil Microbiology ; Water ; }, abstract = {Biological soil crusts are very sensitive to human-induced disturbances and are in a degraded state in many areas throughout their range. Given their importance in the functioning of arid and semiarid ecosystems, restoring these crusts may contribute to the recovery of ecosystem functionality in degraded areas. We conducted a factorial microcosm experiment to evaluate the effects of inoculation type (discrete fragments vs slurry), fertilization (control vs addition of composted sewage sludge), and watering frequency (two vs five times per week) on the cyanobacterial composition, nitrogen fixation, chlorophyll content, and net CO2 exchange rate of biological soil crusts inoculated on a semiarid degraded soil from SE Spain. Six months after the inoculation, the highest rates of nitrogen fixation and chlorophyll a content were found when the biological crusts were inoculated as slurry, composted sewage sludge was added, and the microcosms were watered five times per week. Net CO2 exchange rate increased when biological crusts were inoculated as slurry and the microcosms were watered five times per week. Denaturing gradient gel electrophoresis fingerprints and phylogenetic analyses indicated that most of the cyanobacterial species already present in the inoculated crust had the capability to spread and colonize the surface of the surrounding soil. These analyses showed that cyanobacterial communities were less diverse when the microcosms were watered five times per week, and that watering frequency (followed in importance by the addition of composted sewage sludge and inoculation type) was the treatment that most strongly influenced their composition. Our results suggest that the inoculation of biological soil crusts in the form of slurry combined with the addition of composted sewage sludge could be a suitable technique to accelerate the recovery of the composition and functioning of biological soil crusts in drylands.}, }
@article {pmid16709776, year = {2006}, author = {Kurland, CG and Collins, LJ and Penny, D}, title = {Genomics and the irreducible nature of eukaryote cells.}, journal = {Science (New York, N.Y.)}, volume = {312}, number = {5776}, pages = {1011-1014}, doi = {10.1126/science.1121674}, pmid = {16709776}, issn = {1095-9203}, mesh = {*Biological Evolution ; Cell Compartmentation ; *Eukaryotic Cells ; Evolution, Molecular ; *Genomics ; Phagocytosis ; Prokaryotic Cells ; Proteome ; Selection, Genetic ; }, abstract = {Large-scale comparative genomics in harness with proteomics has substantiated fundamental features of eukaryote cellular evolution. The evolutionary trajectory of modern eukaryotes is distinct from that of prokaryotes. Data from many sources give no direct evidence that eukaryotes evolved by genome fusion between archaea and bacteria. Comparative genomics shows that, under certain ecological settings, sequence loss and cellular simplification are common modes of evolution. Subcellular architecture of eukaryote cells is in part a physical-chemical consequence of molecular crowding; subcellular compartmentation with specialized proteomes is required for the efficient functioning of proteins.}, }
@article {pmid16708263, year = {2006}, author = {Yergeau, E and Vujanovic, V and St-Arnaud, M}, title = {Changes in communities of Fusarium and arbuscular mycorrhizal fungi as related to different asparagus cultural factors.}, journal = {Microbial ecology}, volume = {52}, number = {1}, pages = {104-113}, pmid = {16708263}, issn = {0095-3628}, mesh = {Asparagus Plant/*microbiology ; Canada ; DNA Fingerprinting ; Electrophoresis ; Fusarium/classification/*isolation &amp; purification ; Molecular Sequence Data ; Multivariate Analysis ; Mycorrhizae/*isolation &amp; purification ; Plant Diseases ; Plant Roots/microbiology ; }, abstract = {Asparagus (Asparagus officinalis) is a high-value perennial vegetable crop that has shown a marked decline in productivity after many years of continuous harvesting. This decline is caused by an increase in both abiotic (autotoxicity, harvesting pressure) and biotic stresses [fungal infections, mainly Fusarium crown and root rot (FCRR)]. To gain insight into disease development and possible mitigation strategies, we studied the effects of harvesting, time in the growing season, and field age on FCRR development, Fusarium species composition, and arbuscular mycorrhizal fungi (AMF) communities in both a controlled field experiment and an ecological survey of commercial fields. In one experiment, a 3-year-old asparagus field was subdivided into plots that were harvested or not and sampled throughout the growing season to assess short-term dominant Fusarium species shifts. In addition, diseased and healthy asparagus plants sampled from six commercial fields in the same geographical region were used to assess Fusarium and AMF communities in relation to different parameters. Fusarium and AMF communities were described by using a polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) approach, and results were analyzed by mainly correspondence analysis and canonical correspondence analysis. Results showed that dominant Fusarium taxa assemblages changed throughout the growing season. Harvested plots had significantly more FCRR symptomatic plants at the end of the growing season, but this effect was not related with any trend in Fusarium community structure. Sampling site and plant age significantly influenced AMF community structure, whereas only sampling site consistently influenced the Fusarium community. Diseased and healthy plants harbored similar Fusarium and AMF communities. Shifts in Fusarium community might not be responsible for different disease incidence because they are ubiquitous regardless of plant health status or harvesting regime. The different incidence noted might rather be related to plant physiology, antagonist microbial communities, or soil parameters.}, }
@article {pmid16708262, year = {2006}, author = {Vishniac, HS}, title = {A multivariate analysis of soil yeasts isolated from a latitudinal gradient.}, journal = {Microbial ecology}, volume = {52}, number = {1}, pages = {90-103}, pmid = {16708262}, issn = {0095-3628}, mesh = {Biodiversity ; Cryptococcus/classification/isolation &amp; purification/physiology ; DNA, Ribosomal/genetics ; *Ecosystem ; *Environment ; Geography ; Hydrogen-Ion Concentration ; Multivariate Analysis ; *Soil Microbiology ; Yeasts/*classification/*isolation &amp; purification/physiology ; }, abstract = {Yeast isolates from soil samples collected from a latitudinal gradient (>77 degrees S to >64 degrees N) were subjected to multivariate analysis to produce a statistical foundation for observed relationships between habitat characteristics and the distribution of yeast taxa (at various systematic levels) in soil microbial communities. Combinations of temperature, rainfall (highly correlated with net primary productivity), and electrical conductivity (EC) could explain up to ca. 44% of the distribution of the predominant yeast species, rainfall and pH could explain ca. 32% of the distribution of clades in the most common orders (Filobasidiales and Tremellales), whereas vegetation type (trees, forbs, and grass) played the same role for orders. Cryptococcus species with appropriate maximum temperatures for growth predominated in most soils. Cryptococcus species in the Albidus clade of the Filobasidiales predominated in desert soils; Cryptococcus species of other clades in the Filobasidiales and Tremellales predominated in wetter and more-vegetated soils, with Tremellalean species favored in soils of lower pH or higher EC. The predominance of Cryptococcus species in soils has been attributed to their polysaccharide capsules, particularly important when competing with bacteria in arid soils.}, }
@article {pmid16704931, year = {2006}, author = {Wagner, M and Horn, M}, title = {The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance.}, journal = {Current opinion in biotechnology}, volume = {17}, number = {3}, pages = {241-249}, doi = {10.1016/j.copbio.2006.05.005}, pmid = {16704931}, issn = {0958-1669}, mesh = {*Bacterial Physiological Phenomena ; *Biological Evolution ; Biotechnology/*methods ; Chlamydia/physiology ; Environmental Microbiology ; Phylogeny ; Water Microbiology ; }, abstract = {In the rRNA-based tree of life four bacterial phyla, comprising the Planctomycetes, Verrucomicrobia, Chlamydiae and Lentisphaerae, form together with the candidate phyla Poribacteria and OP3 a monophyletic group referred to as the PVC superphylum. This assemblage contains organisms that possess dramatically different lifestyles and which colonize sharply contrasting habitats. Some members of this group are among the most successful human pathogens, others are abundant soil microbes, and others still are of major importance for the marine nitrogen cycle and hold much promise for sustainable wastewater treatment. Recent comparative genomic and metagenomic analyses of a few representatives of this group revealed many unusual features and generated unexpected hypotheses regarding their physiology, some of which have already been confirmed experimentally. Furthermore, the availability of these genome sequences offered new insights into the evolutionary history of this peculiar group of microbes with major medical, ecological and biotechnological relevance.}, }
@article {pmid16704355, year = {2006}, author = {Brandl, MT}, title = {Fitness of human enteric pathogens on plants and implications for food safety.}, journal = {Annual review of phytopathology}, volume = {44}, number = {}, pages = {367-392}, doi = {10.1146/annurev.phyto.44.070505.143359}, pmid = {16704355}, issn = {0066-4286}, mesh = {Food Microbiology/*standards ; Gastrointestinal Diseases/*microbiology ; Humans ; Plants/*microbiology ; Safety/*standards ; }, abstract = {The continuous rise in the number of outbreaks of foodborne illness linked to fresh fruit and vegetables challenges the notion that enteric pathogens are defined mostly by their ability to colonize the intestinal habitat. This review describes the epidemiology of produce-associated outbreaks of foodborne disease and presents recently acquired knowledge about the behavior of enteric pathogens on plants, with an emphasis on Salmonella enterica, Escherichia coli O157:H7, and Listeria monocytogenes. The growth and survival of enteric pathogens on plants are discussed in the light of knowledge and concepts in plant microbial ecology, including epiphytic fitness, the physicochemical nature of plant surfaces, biofilm formation, and microbe-microbe and plant-microbe interactions. Information regarding the various stresses that affect the survival of enteric pathogens and the molecular events that underlie their interactions in the plant environment provides a good foundation for assessing their role in the infectious dose of the pathogens when contaminated fresh produce is the vehicle of illness.}, }
@article {pmid16703447, year = {2006}, author = {Medlin, LK and Metfies, K and Mehl, H and Wiltshire, K and Valentin, K}, title = {Picoeukaryotic plankton diversity at the Helgoland time series site as assessed by three molecular methods.}, journal = {Microbial ecology}, volume = {52}, number = {1}, pages = {53-71}, pmid = {16703447}, issn = {0095-3628}, mesh = {Animals ; *Biodiversity ; DNA Fingerprinting/*methods ; Eukaryota/classification/genetics ; Gene Library ; Germany ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis/*methods ; Oligonucleotide Probes ; Phylogeny ; Plankton/*classification/genetics ; Polymerase Chain Reaction ; *Polymorphism, Single-Stranded Conformational ; RNA, Ribosomal, 18S/genetics ; Seawater/*microbiology/*parasitology ; }, abstract = {We analyzed picoeukaryote assemblages in the German Bight at the Helgoland time series site by sequencing cloned eukaryotic 18S rRNA genes in six genetic libraries plus one library from the Orkney Islands from a cruise of opportunity. The libraries were constructed from environmental samples collected at different periods of the year. The same samples were also analyzed using a fingerprinting technique, single-strand conformational polymorphism (SSCP), and DNA microarrays with class-level oligonucleotide probes. One hundred unique clones were analyzed from each library, thus insuring over 85% coverage of the library. The V4 region of the 18S rRNA gene was sequenced from each of these clones, thus providing the most discrimination among the clones. The nonphotosynthetic picoeukaryotic component dominated over the photosynthetic one and was represented by the ciliates at 45% and group II alveolates at 42%. Prasinophytes dominated the photosynthetic group at 40%, but other picoplankton groups, such as bolidomonads and chrysophytes, were also present. Totally novel groups were found in the cryptomonads and in the dinoflagellates. A new algal group sister to the cryptophyte nuclear gene and the glaucocystophytes was also found. These three groups have been found in other picoeukaryotic planktonic clone libraries. SSCP analyses at closer time intervals suggest that clone libraries should be made at weekly intervals if succession in the picoeukaryotic plankton community is to be monitored accurately. A comparison of annual samples suggests thatthere appears to be an annual cycle with regard to species composition. Microarray analysis supported the clone library data and offered a faster means of community analysis, which can be performed with similar accuracy and with higher throughput for a more in-depth analysis.}, }
@article {pmid16702066, year = {2006}, author = {Collins, G and Kavanagh, S and McHugh, S and Connaughton, S and Kearney, A and Rice, O and Carrigg, C and Scully, C and Bhreathnach, N and Mahony, T and Madden, P and Enright, AM and O'flaherty, V}, title = {Accessing the black box of microbial diversity and ecophysiology: recent advances through polyphasic experiments.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances &amp; environmental engineering}, volume = {41}, number = {5}, pages = {897-922}, doi = {10.1080/10934520600614546}, pmid = {16702066}, issn = {1093-4529}, mesh = {Archaea/classification/genetics/isolation &amp; purification/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Base Sequence ; Biofilms ; Biomass ; Bioreactors/microbiology ; Crenarchaeota/genetics/isolation &amp; purification/metabolism ; DNA, Archaeal/analysis/genetics ; DNA, Bacterial/analysis/genetics ; *Ecosystem ; Electrophoresis, Agar Gel ; Methane/chemistry/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/analysis/*genetics ; Sewage/*microbiology ; *Soil Microbiology ; Waste Disposal, Fluid/*methods ; }, abstract = {The microbial ecology of a range of anaerobic biological assemblages (granular sludge) from full- and laboratory-scale wastewater treatment bioreactors, and of crop-growing and peat soils, was determined using a variety of 16S rRNA gene-based techniques, including clone library, terminal restriction fragment length polymorphism (TRFLP) and denaturing gradient gel electrophoresis (DGGE) analyses. Fluorescent in situ hybridization (FISH) using 16S rRNA gene-targeted probes was employed to complete a "full-cycle rRNA approach" with selected biomass. Genetic fingerprinting (TRFLP and DGGE) was effectively used to elucidate community structure-crop relationships, and to detect and monitor trends in bioreactor sludge and specific enrichment cultures of peat soil. Greater diversity was resolved within bacterial than within archaeal communities, and unexpected reservoirs of uncultured Crenarchaeota were detected in sludge granules. Advanced radiotracer incubations and micro-beta imaging were employed in conjunction with FISH to elucidate the eco-functionalism of these organisms. Crenarchaeota clusters were identified in close associated with methanogenic Archaea and both were localised with acetate uptake in biofilm structure.}, }
@article {pmid16702065, year = {2006}, author = {Collins, G and McHugh, S and Connaughton, S and Enright, AM and Kearney, A and Scully, C and Mahony, T and Madden, P and O'Flaherty, V}, title = {New low-temperature applications of anaerobic wastewater treatment.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances &amp; environmental engineering}, volume = {41}, number = {5}, pages = {881-895}, doi = {10.1080/10934520600614504}, pmid = {16702065}, issn = {1093-4529}, mesh = {Anaerobiosis ; Biodegradation, Environmental ; Biomass ; *Bioreactors ; *Cold Temperature ; Industrial Microbiology/*methods ; Methane/chemistry/metabolism ; Oxygen/chemistry/metabolism ; Sewage/chemistry/*microbiology ; Time Factors ; Waste Disposal, Fluid/*methods ; }, abstract = {Low-temperature or psychrophilic (<20 degrees C) anaerobic biological treatment of simple industrial wastewaters has recently been proven feasible as an alternative to more expensive mesophilic (ca. 37 degrees C) technology. We implemented novel expanded granular sludge bed (EGSB)-based bioreactor designs for 27 psychrophilic anaerobic digestion (PAD) trials for the treatment of a broad range of simple and complex synthetic wastewaters representing dairy, food-processing and pharmaceutical sector effluents. A variety of operating parameters, such as hydraulic retention time, organic and volumetric loading rates and upflow velocity, were tested. Chemical oxygen demand (COD) removal efficiencies were recorded, which were comparable to previous mesophilic trials. Specific methanogenic activity, toxicity and biodegradability batch assays were employed to monitor the metabolic capabilities of microbial consortia in anaerobic reactors. The prevalence of psychrotolerant communities was observed and psychrophilic populations were detected in two of the reactors. The potential of PAD with respect to global sustainable development is discussed.}, }
@article {pmid16701992, year = {2006}, author = {Berry, D and Xi, C and Raskin, L}, title = {Microbial ecology of drinking water distribution systems.}, journal = {Current opinion in biotechnology}, volume = {17}, number = {3}, pages = {297-302}, doi = {10.1016/j.copbio.2006.05.007}, pmid = {16701992}, issn = {0958-1669}, mesh = {Animals ; Bacteria/*pathogenicity ; Biodiversity ; Biofilms ; Drinking ; Eukaryota/microbiology ; Water Microbiology ; Water Supply/*analysis ; }, abstract = {The supply of clean drinking water is a major, and relatively recent, public health milestone. Control of microbial growth in drinking water distribution systems, often achieved through the addition of disinfectants, is essential to limiting waterborne illness, particularly in immunocompromised subpopulations. Recent inquiries into the microbial ecology of distribution systems have found that pathogen resistance to chlorination is affected by microbial community diversity and interspecies relationships. Research indicates that multispecies biofilms are generally more resistant to disinfection than single-species biofilms. Other recent findings are the increased survival of the bacterial pathogen Legionella pneumophila when present inside its protozoan host Hartmannella vermiformis and the depletion of chloramine disinfectant residuals by nitrifying bacteria, leading to increased overall microbial growth. Interactions such as these are unaccounted for in current disinfection models. An understanding of the microbial ecology of distribution systems is necessary to design innovative and effective control strategies that will ensure safe and high-quality drinking water.}, }
@article {pmid16699911, year = {2006}, author = {DeBellis, T and Kernaghan, G and Bradley, R and Widden, P}, title = {Relationships between stand composition and ectomycorrhizal community structure in boreal mixed-wood forests.}, journal = {Microbial ecology}, volume = {52}, number = {1}, pages = {114-126}, pmid = {16699911}, issn = {0095-3628}, mesh = {DNA, Fungal/analysis ; DNA, Ribosomal/genetics ; *Ecosystem ; Molecular Sequence Data ; Mycorrhizae/*classification/cytology/genetics ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Quebec ; Trees/*microbiology ; }, abstract = {We investigated the community structure of ectomycorrhizal fungi under varying overstory tree compositions in the southern mixed-wood boreal forest of Quebec. Sampling took place at two locations of differing postfire ages and nine 100-m2 plots were sampled per location. The dominant overstory tree species in the plots were trembling aspen (Populus tremuloides Michx.), white birch (Betula papyrifera Marsh.) or white spruce [Picea glauca (Moench) Voss], and balsam fir [Abies balsamea (L.) Mill.]. Mycorrhizae were analyzed using morphological as well as molecular methods, employing fungal-specific primers to amplify ribosomal DNA for subsequent cloning and sequencing. A total of 1800 mycorrhizal root tips collected from the 18 plots were morphologically classified into 26 morphotypes, with Cenococcum geophilum dominating (36% of root tips). A second set of root tips, selected from the same 18 samples on which the morphological analysis was based, were analyzed using molecular methods. From this analysis, 576 cloned polymerase chain reaction products were screened by restriction fragment length polymorphism analysis and a total of 207 unique types were found. No one type dominated the system and 159 occurred only once. Sequence analysis of the types that occurred more than once revealed that Piloderma sp., Russula sp., Cortinarius sp., and Lactarius sp. were the most common mycorrhizae. The ectomycorrhizal fungal community structure revealed by the rDNA analysis differed from that observed using morphological methods. Canonical correspondence analyses of the sequenced restriction types and % overstory composition indicate that the distributions of ectomycorrhizal fungi are influenced by the relative proportions of host tree species. The distinct fungal assemblages found in the different plots supported by the different combinations of host tree species provides further support for the need to conserve stand diversity in the southern boreal forest.}, }
@article {pmid16691328, year = {2006}, author = {Aneja, MK and Sharma, S and Fleischmann, F and Stich, S and Heller, W and Bahnweg, G and Munch, JC and Schloter, M}, title = {Microbial colonization of beech and spruce litter--influence of decomposition site and plant litter species on the diversity of microbial community.}, journal = {Microbial ecology}, volume = {52}, number = {1}, pages = {127-135}, pmid = {16691328}, issn = {0095-3628}, mesh = {Bacteria/classification/genetics/*growth &amp; development ; *Biodiversity ; Biomass ; Fagus/*microbiology ; Fungi/classification/genetics/*growth &amp; development ; Lignin/metabolism ; Molecular Sequence Data ; Picea/*microbiology ; Plant Leaves/chemistry/*microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; *Soil Microbiology ; }, abstract = {The present study was conducted to investigate the effect of decomposition site and plant litter species on the colonizing microbial communities. For this, litter bag technique using beech and spruce litter was combined with RNA-based fingerprinting and cloning. Litter bags were incubated for 2 and 8 weeks in the Ah horizon of beech and beech-spruce mixed forest sites. Although sugars and starch were rapidly lost, lignin content increased by more than 40% for beech and more than doubled for spruce litter at both soil sites at the end of the experiment. Denaturing gradient gel electrophoresis analysis of 16S and 18S rRNA RT-PCR products was used for screening of differences between bacterial and fungal communities colonizing the two litter types. Development of the microbial community over time was observed to be specific for each litter type and decomposition site. RT-PCR products from both litter types incubated in beech-spruce mixed forest site were also cloned to identify the bacterial and fungal colonizers. The 16S rRNA clone libraries of beech litter were dominated by gamma-proteobacterial members, whereas spruce libraries were mainly composed of alpha-, beta-, and gamma-proteobacterial members. Ascomycota members dominated the 18S rRNA clone libraries. Clones similar to Zygomycota were absent from spruce, whereas those similar to Basidiomycota and Glomeromycota were absent from beech libraries. Selective effects of litter quality were observed after 8 weeks. The study provides an insight into the bacterial and fungal communities colonizing beech and spruce litter, and the importance of litter quality and decomposition site as key factors in their development and succession.}, }
@article {pmid16691327, year = {2006}, author = {Gundlapally, SR and Garcia-Pichel, F}, title = {The community and phylogenetic diversity of biological soil crusts in the Colorado Plateau studied by molecular fingerprinting and intensive cultivation.}, journal = {Microbial ecology}, volume = {52}, number = {2}, pages = {345-357}, pmid = {16691327}, issn = {0095-3628}, mesh = {Alleles ; Bacteria/*classification/genetics/isolation &amp; purification ; *Biodiversity ; Colorado ; DNA Fingerprinting ; Electrophoresis, Agar Gel ; Molecular Sequence Data ; *Phylogeny ; *Soil Microbiology ; }, abstract = {We studied the bacterial communities in biological soil crusts (BSCs) from the Colorado Plateau by enrichment and cultivation, and by statistically analyzed denaturing gradient gel electrophoresis (DGGE) fingerprinting of environmental 16S rRNA genes, and phylogenetic analyses. Three 500-m-long transects, tens of km apart, consisting of 10 equally spaced samples each, were analyzed. BSC communities consistently displayed less richness (10-32 detectable DGGE bands per sample) and Shannon diversity (2.1-3.3) than typical soil communities, with apparent dominance by few members. In spite of some degree of small-scale patchiness, significant differences in diversity and community structure among transects was detectable, probably related to the degree of crust successional maturity. Phylogenetic surveys indicated that the cyanobacterium Microcoleus vaginatus was dominant, with M. steenstrupii second among phototrophs. Among the 48 genera of nonphototrophs detected, Actinobacteria (particularly Streptomyces spp.) were very common and diverse, with 18 genera and an average contribution to the total 16S rDNA amplificate of 11.8%. beta-Proteobacteria and Bacteriodetes contributed around 10% each; Low-GC Gram-positives, alpha-Proteobacteria, Thermomicrobiales, and Acidobacteria were common (2-5%). However, the second largest contribution was made by deep-branching unaffiliated alleles (12.6%), with some of them representing candidate bacterial divisions. Many of the novel strains isolated are likely new taxa, and some were representatives of the phylotypes detected in the field. The mucoid or filamentous nature of many of these isolates speaks for their role in crust formation.}, }
@article {pmid16691326, year = {2006}, author = {Jansson, M and Bergström, AK and Lymer, D and Vrede, K and Karlsson, J}, title = {Bacterioplankton growth and nutrient use efficiencies under variable organic carbon and inorganic phosphorus ratios.}, journal = {Microbial ecology}, volume = {52}, number = {2}, pages = {358-364}, pmid = {16691326}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development/metabolism ; Carbon/*analysis/metabolism ; Fresh Water/analysis/*microbiology ; Glucose/analysis/metabolism ; Nitrogen/analysis/metabolism ; Phosphorus/*analysis/metabolism ; Plankton/*growth &amp; development/metabolism ; Sweden ; }, abstract = {We carried out enclosure experiments in an unproductive lake in northern Sweden and studied the effects of enrichment with different dissolved organic carbon (glucose)/inorganic phosphorous (DOC/Pi) ratios on bacterioplankton production (BP), growth efficiency (BGE), nutrient use efficiency (BNUE), growth rate, and specific respiration. We found considerable variation in BP, BGE, and BNUE along the tested DOC/Pi gradient. BGE varied between 0.87 and 0.24, with the highest values at low DOC/Pi ratios. BNUE varied between 40 and 9 g C g P(-1), with high values at high DOC/Pi ratios. More DOC was thus allocated to growth when bacteria tended to be C-limited, and to respiration when bacteria were P-limited. Specific respiration was positively correlated with bacterial growth rate throughout the gradient. It is therefore possible that respiration was used to support growth in P-limited bacteria. The results indicated that BP can be limited by Pi when BNUE is at its maximum, by organic C when BGE is at its maximum, and by dual organic C and Pi limitation when BNUE and BGE have suboptimal values.}, }
@article {pmid16691325, year = {2006}, author = {Farjalla, VF and Azevedo, DA and Esteves, FA and Bozelli, RL and Roland, F and Enrich-Prast, A}, title = {Influence of hydrological pulse on bacterial growth and DOC uptake in a clear-water Amazonian lake.}, journal = {Microbial ecology}, volume = {52}, number = {2}, pages = {334-344}, pmid = {16691325}, issn = {0095-3628}, mesh = {Bacteria/drug effects/*growth &amp; development/*metabolism ; Brazil ; Carbon/chemistry/*metabolism ; Disasters ; *Ecosystem ; Fresh Water/*microbiology ; Nitrogen/chemistry/pharmacology ; Phosphorus/chemistry/pharmacology ; }, abstract = {This study was conducted to evaluate: (1) the bacterial growth and the dissolved organic carbon (DOC) uptake in an Amazonian lake (Lake Batata) at high-water and low-water periods of the flood pulse; (2) the influence of nitrogen and phosphorus (NP) additions on bacterial growth and DOC uptake in Lake Batata at two flood pulse periods; and (3) the bioavailability of the main DOC sources in Lake Batata. Lake Batata is a typical clear-water Amazonian lake, located in the watershed of Trombetas River, Central Amazon, Brazil. Bacterial batch cultures were set up with 90% 0.2-microm filtered water and 10% inoculum from Lake Batata. N-NH(4)NO(3) and P-KH(2)PO(4), with final concentrations of 50 and 5 microM, respectively, were added to the cultures, except for controls. Extra sources of DOC (e.g., algal lysate, plant leachates) were added to constitute six distinct treatments. Bacterial response was measured by maximum bacterial abundance and rates of bacterial production, respiration, DOC uptake, and bacterial growth efficiency (BGE). Bacterial growth and DOC uptake were higher in NP treatments than in controls, indicating a consistent nutrient limitation in Lake Batata. The composition of DOC also seems to be an important regulating factor of bacterial growth in Lake Batata. Seasonally, bacterial growth and DOC bioavailability were higher at low-water period, when the phytoplankton is a significant extra source of DOC, than at high-water period, when the forest is the main source of DOC. DOC bioavailability was better estimated based on the diversity and the diagenetic stage of carbon compounds than on single classes of labile compounds. Changes in BGE were better related to CNP stoichiometry in the water, and the "excess" of organic substrates was oxidized in catabolism, despite the quality of these compounds for bacterial growth. Finally, we conclude that bacterial growth and DOC uptake vary throughout the flood pulse in clear-water Amazonian ecosystems as a result of changes in nutrient concentration and in DOC composition.}, }
@article {pmid16691324, year = {2006}, author = {Moorthi, SD and Countway, PD and Stauffer, BA and Caron, DA}, title = {Use of quantitative real-time PCR to investigate the dynamics of the red tide dinoflagellate Lingulodinium polyedrum.}, journal = {Microbial ecology}, volume = {52}, number = {1}, pages = {136-150}, pmid = {16691324}, issn = {0095-3628}, mesh = {Animals ; California ; Dinoflagellida/genetics/*isolation &amp; purification/*physiology ; Molecular Sequence Data ; Phytoplankton/genetics/isolation &amp; purification ; *Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; Seawater/*parasitology ; }, abstract = {A new method based on quantitative real-time polymerase chain reaction (qPCR) was developed and applied to quantify the red tide dinoflagellate Lingulodinium polyedrum in natural seawater samples and in laboratory cultures. The method uses a Molecular Beacontrade mark approach to target a species-specific region of the small subunit ribosomal RNA gene. The accuracy of the method was verified by microscopical counts using cultures of the dinoflagellate isolated from coastal waters near Los Angeles, CA, and with natural water samples spiked with cultured L. polyedrum. The method was applied to document the pattern and timing of vertical migration by the dinoflagellate in a 2-m water column on an 11:13 h light/dark photoperiod established in the laboratory. Positive phototaxis of L. polyedrum resulted in dense aggregations of the dinoflagellate within the top few centimeters of the water column during the light period. This pattern of distribution was readily established by both methods, although abundances of L. polyedrum determined using qPCR were higher than abundances determined by microscopy in the morning and lower in the afternoon and evening. These differences may have been a consequence of variability in the DNA content per cell because of synchrony of cell division. Counts using both methods to analyze natural samples collected from coastal waters in the Long Beach-Los Angeles area and adjacent San Pedro Channel were in close agreement. However, the qPCR method exhibited greater sensitivity than the microscopical method when L. polyedrum was present at low abundances, and qPCR had a much higher rate of sample throughput than microscopy. The development of this new approach for enumerating L. polyedrum provides a useful tool for studying the ecology of this important red tide species.}, }
@article {pmid16689892, year = {2006}, author = {Xu, J}, title = {Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances.}, journal = {Molecular ecology}, volume = {15}, number = {7}, pages = {1713-1731}, doi = {10.1111/j.1365-294X.2006.02882.x}, pmid = {16689892}, issn = {0962-1083}, mesh = {DNA, Ribosomal/analysis ; Ecology/*methods/trends ; Gene Expression Profiling ; Genetics, Microbial/*methods/*trends ; Genomics/*methods/trends ; Microbiological Techniques ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Microbial ecology examines the diversity and activity of micro-organisms in Earth's biosphere. In the last 20 years, the application of genomics tools have revolutionized microbial ecological studies and drastically expanded our view on the previously underappreciated microbial world. This review first introduces the basic concepts in microbial ecology and the main genomics methods that have been used to examine natural microbial populations and communities. In the ensuing three specific sections, the applications of the genomics in microbial ecological research are highlighted. The first describes the widespread application of multilocus sequence typing and representational difference analysis in studying genetic variation within microbial species. Such investigations have identified that migration, horizontal gene transfer and recombination are common in natural microbial populations and that microbial strains can be highly variable in genome size and gene content. The second section highlights and summarizes the use of four specific genomics methods (phylogenetic analysis of ribosomal RNA, DNA-DNA re-association kinetics, metagenomics, and micro-arrays) in analysing the diversity and potential activity of microbial populations and communities from a variety of terrestrial and aquatic environments. Such analyses have identified many unexpected phylogenetic lineages in viruses, bacteria, archaea, and microbial eukaryotes. Functional analyses of environmental DNA also revealed highly prevalent, but previously unknown, metabolic processes in natural microbial communities. In the third section, the ecological implications of sequenced microbial genomes are briefly discussed. Comparative analyses of prokaryotic genomic sequences suggest the importance of ecology in determining microbial genome size and gene content. The significant variability in genome size and gene content among strains and species of prokaryotes indicate the highly fluid nature of prokaryotic genomes, a result consistent with those from multilocus sequence typing and representational difference analyses. The integration of various levels of ecological analyses coupled to the application and further development of high throughput technologies are accelerating the pace of discovery in microbial ecology.}, }
@article {pmid16680512, year = {2006}, author = {Harris, SH and Istok, JD and Suflita, JM}, title = {Changes in organic matter biodegradability influencing sulfate reduction in an aquifer contaminated by landfill leachate.}, journal = {Microbial ecology}, volume = {51}, number = {4}, pages = {535-542}, pmid = {16680512}, issn = {0095-3628}, mesh = {Biodegradation, Environmental ; Geologic Sediments ; Sulfates/*metabolism ; Water Pollutants/*metabolism ; }, abstract = {In situ experiments were conducted to measure sulfate reduction rates and identify rate-limiting factors in a shallow, alluvial aquifer contaminated with municipal landfill leachate. Single-well, push-pull tests conducted in a well adjacent to the landfill with > 8 mM dissolved organic carbon (DOC) exhibited a sulfate reduction rate of 3.2 mumol SO4(-2) (L sediment)(-1) day(-1), a value in close agreement with laboratory-derived estimates. Identical tests conducted in wells located 90 m downgradient where DOC levels remained high (> 3 mM) showed no detectable sulfate consumption, and laboratory assays confirmed this observation. However, the rates of sulfate reduction in sediment samples obtained from this site were three times larger when they were amended with filter-sterilized groundwater from the upgradient location. The effect of various amendments on sulfate reduction rates was further examined in laboratory incubations using sediment collected from the downgradient site amended with 35S sulfate. Unamended sediments showed only weak conversion of the tracer to 35S sulfide (5 to 7 cpm/cm2), whereas the addition of Desulfovibrio cells increased 35S sulfide production to 44 cpm/cm2. However, the application of heat-killed Desulfovibrio had a similar stimulatory effect, as did a lactate amendment. Collectively, these findings indicate that the lack of measurable sulfate reduction at the downgradient site was not due to the absence of the necessary metabolic potential, the presence of lower sulfate concentration, or the quantity of electron donor, but by its biodegradability. The findings also indicate that field bioaugmentation attempts should be interpreted with caution.}, }
@article {pmid16680511, year = {2006}, author = {Feeney, DS and Crawford, JW and Daniell, T and Hallett, PD and Nunan, N and Ritz, K and Rivers, M and Young, IM}, title = {Three-dimensional microorganization of the soil-root-microbe system.}, journal = {Microbial ecology}, volume = {52}, number = {1}, pages = {151-158}, pmid = {16680511}, issn = {0095-3628}, mesh = {*Bacterial Physiological Phenomena ; *Ecosystem ; Fungi/*physiology ; Hydrophobic and Hydrophilic Interactions ; Image Processing, Computer-Assisted ; Lolium/anatomy &amp; histology/growth &amp; development ; Plant Roots/*physiology ; Porosity ; *Soil ; *Soil Microbiology ; }, abstract = {Soils contain the greatest reservoir of biodiversity on Earth, and the functionality of the soil ecosystem sustains the rest of the terrestrial biosphere. This functionality results from complex interactions between biological and physical processes that are strongly modulated by the soil physical structure. Using a novel combination of biochemical and biophysical indicators and synchrotron microtomography, we have discovered that soil microbes and plant roots microengineer their habitats by changing the porosity and clustering properties (i.e., spatial correlation) of the soil pores. Our results indicate that biota act to significantly alter their habitat toward a more porous, ordered, and aggregated structure that has important consequences for functional properties, including transport processes. These observations support the hypothesis that the soil-plant-microbe complex is self-organized.}, }
@article {pmid16680510, year = {2006}, author = {Sabet, S and Chu, W and Jiang, SC}, title = {Isolation and genetic analysis of haloalkaliphilic bacteriophages in a North American Soda Lake.}, journal = {Microbial ecology}, volume = {51}, number = {4}, pages = {543-554}, pmid = {16680510}, issn = {0095-3628}, mesh = {Bacteriophages/*genetics/growth &amp; development/*isolation &amp; purification ; Base Sequence ; Chromosomes, Artificial, Bacterial ; Cloning, Molecular ; DNA Primers ; Electrophoresis, Gel, Pulsed-Field ; Fresh Water ; Nucleic Acid Hybridization ; Seasons ; Viral Plaque Assay ; }, abstract = {Mono Lake is a meromictic, hypersaline, soda lake that harbors a diverse and abundant microbial community. A previous report documented the high viral abundance in Mono Lake, and pulsed-field gel electrophoresis analysis of viral DNA from lake water samples showed a diverse population based on a broad range of viral genome sizes. To better understand the ecology of bacteriophages and their hosts in this unique environment, water samples were collected between February 2001 and July 2004 for isolation of bacteriophages by using four indigenous bacterial hosts. Plaque assay results showed a differential seasonal expression of cultured bacteriophages. To reveal the diversity of uncultured bacteriophages, viral DNA from lake water samples was used to construct clone libraries. Sequence analysis of viral clones revealed homology to viral as well as bacterial proteins. Furthermore, dot blot DNA hybridization analyses showed that the uncultured viruses are more prevalent during most seasons, whereas the viral isolates (Aphi and phi2) were less prevalent, confirming the belief that uncultured viruses represent the dominant members of the community, whereas cultured isolates represent the minority species.}, }
@article {pmid16675292, year = {2006}, author = {Ward, AC and Bora, N}, title = {Diversity and biogeography of marine actinobacteria.}, journal = {Current opinion in microbiology}, volume = {9}, number = {3}, pages = {279-286}, doi = {10.1016/j.mib.2006.04.004}, pmid = {16675292}, issn = {1369-5274}, mesh = {Actinobacteria/*classification/genetics/*growth &amp; development ; Animals ; Culture Media ; Ecosystem ; *Genetic Variation ; Geologic Sediments/microbiology ; *Marine Biology ; Seawater/microbiology ; }, abstract = {The actinomycetes, although not all the Actinobacteria, are easy to isolate from the marine environment. However, their ecological role in the marine ecosystem is largely neglected and various assumptions meant there was little incentive to isolate strains for search and discovery of new drugs. However, the marine environment has become a prime resource in search and discovery for novel natural products and biological diversity, and marine actinomycetes turn out to be important contributors. Similarly, striking advances have been made in marine microbial ecology using molecular techniques and metagenomics, and actinobacteria emerge as an often significant, sometimes even dominant, environmental clade. Both approaches - cultivation methods and molecular techniques - are leading to new insights into marine actinobacterial biodiversity and biogeography. Very different views of actinobacterial diversity emerge from these, however, and the true extent and biogeography of this are still not clear. These are important for developing natural product search and discovery strategies, and biogeography is a hot topic for microbial ecologists.}, }
@article {pmid16673762, year = {2006}, author = {Oviedo-Rondón, EO and Hume, ME and Hernández, C and Clemente-Hernández, S}, title = {Intestinal microbial ecology of broilers vaccinated and challenged with mixed Eimeria species, and supplemented with essential oil blends.}, journal = {Poultry science}, volume = {85}, number = {5}, pages = {854-860}, doi = {10.1093/ps/85.5.854}, pmid = {16673762}, issn = {0032-5791}, mesh = {Animals ; Chickens/*microbiology/parasitology ; Coccidiosis/parasitology/*veterinary ; Dietary Supplements ; Eimeria/*pathogenicity ; Eimeria tenella ; Electrophoresis, Agar Gel/veterinary ; Intestines/microbiology/parasitology ; Male ; Oils, Volatile/*administration &amp; dosage ; Poultry Diseases/microbiology/*parasitology ; *Protozoan Vaccines ; }, abstract = {Intestinal microbiota is an important component in the development of defense mechanisms in the gut mucosa. This project determined the dynamics of intestinal microbial communities (MC) of broilers vaccinated at first day of age with live oocysts of Eimeria species and fed diets supplemented with 2 specific essential oil (EO) blends, Crina Poultry (CP) and Crina Alternate (CA). Five treatments were analyzed: 1) unmedicated-uninfected (UU) control; 2) unmedicated-infected (UI) control; 3) vaccinated with Advent cocci-vaccine and without feed additive (COV) supplements; 4) vaccinated with Advent and supplemented with CP; and 5) vaccinated with Advent and supplemented with CA. The EO blends were added at 100 ppm to the same basal diets. Chicks were gavage-infected at 19 d of age with Eimeria acervulina, Eimeria maxima, and Eimeria tenella. Duodenal, ileal, and cecal samples were taken from 12 birds per treatment just before the infection and 7 d after the challenge, pooled in 6 samples, and frozen. Denaturing gradient gel electrophoresis was used to examine PCR-amplified fragments of the bacterial 16S ribosomal DNA variable region. Results are presented as percentages of similarity coefficients (SC). Dendrograms of amplicon patterns indicated MC differences due to intestinal location, feed additives, and cocci infection. The EO blends CP and CA did affect MC in all gut sections. The cocci-infection caused drastic MC population shifts in duodenal, ileal, and cecal sections (36.7, 55.4, and 36.2% SC, respectively). The CP-supplemented birds had higher SC between pre- and postchallenge MC in duodenal and ileal (73.3, 81.8%) than COV (66.4, 66.5%). However, COV broilers had the smallest changes in cecal MC after infection (79.5% SC). We concluded that cocci-vaccination causes small changes in intestinal MC, but challenge causes drastic shifts. The EO blend supplementation modulates MC in cocci-vaccinated broilers, avoiding drastic shifts after a mixed coccidia infection. Correlations between MC dynamics and host responses are discussed.}, }
@article {pmid16672611, year = {2006}, author = {Reisner, A and Krogfelt, KA and Klein, BM and Zechner, EL and Molin, S}, title = {In vitro biofilm formation of commensal and pathogenic Escherichia coli strains: impact of environmental and genetic factors.}, journal = {Journal of bacteriology}, volume = {188}, number = {10}, pages = {3572-3581}, pmid = {16672611}, issn = {0021-9193}, mesh = {Bacteremia/microbiology ; Base Sequence ; *Biofilms ; DNA Primers ; Environment ; Escherichia coli/classification/genetics/*growth &amp; development/isolation &amp; purification/*pathogenicity ; Escherichia coli Infections/microbiology ; Feces/microbiology ; Humans ; Male ; Plasmids ; Polymerase Chain Reaction ; Reference Values ; Urinary Tract Infections/microbiology ; }, abstract = {Our understanding of Escherichia coli biofilm formation in vitro is based on studies of laboratory K-12 strains grown in standard media. However, pathogenic E. coli isolates differ substantially in their genetic repertoire from E. coli K-12 and are subject to heterogeneous environmental conditions. In this study, in vitro biofilm formation of 331 nondomesticated E. coli strains isolated from healthy (n = 105) and diarrhea-afflicted children (n = 68), bacteremia patients (n = 90), and male patients with urinary tract infections (n = 68) was monitored using a variety of growth conditions and compared to in vitro biofilm formation of prototypic pathogenic and laboratory strains. Our results revealed remarkable variation among the capacities of diverse E. coli isolates to form biofilms in vitro. Notably, we could not identify an association of increased biofilm formation in vitro with a specific strain collection that represented pathogenic E. coli strains. Instead, analysis of biofilm data revealed a significant dependence on growth medium composition (P < 0.05). Poor correlation between biofilm formation in the various media suggests that diverse E. coli isolates respond very differently to changing environmental conditions. The data demonstrate that prevalence and expression of three factors known to strongly promote biofilm formation in E. coli K-12 (F-like conjugative pili, aggregative adherence fimbriae, and curli) cannot adequately account for the increased biofilm formation of nondomesticated E. coli isolates in vitro. This study highlights the complexity of genetic and environmental effectors of the biofilm phenotype within the species E. coli.}, }
@article {pmid16672507, year = {2006}, author = {Belenguer, A and Duncan, SH and Calder, AG and Holtrop, G and Louis, P and Lobley, GE and Flint, HJ}, title = {Two routes of metabolic cross-feeding between Bifidobacterium adolescentis and butyrate-producing anaerobes from the human gut.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {5}, pages = {3593-3599}, pmid = {16672507}, issn = {0099-2240}, mesh = {Acetates/metabolism ; Bacteria, Anaerobic/growth &amp; development/*metabolism ; Bifidobacterium/growth &amp; development/*metabolism ; Butyrates/*metabolism ; Culture Media ; Digestive System/*microbiology ; Ecosystem ; Fatty Acids/metabolism ; Fructose ; Humans ; Lactates/metabolism ; Oligosaccharides/metabolism ; }, abstract = {Dietary carbohydrates have the potential to influence diverse functional groups of bacteria within the human large intestine. Of 12 Bifidobacterium strains of human gut origin from seven species tested, four grew in pure culture on starch and nine on fructo-oligosaccharides. The potential for metabolic cross-feeding between Bifidobacterium adolescentis and lactate-utilizing, butyrate-producing Firmicute bacteria related to Eubacterium hallii and Anaerostipes caccae was investigated in vitro. E. hallii L2-7 and A. caccae L1-92 failed to grow on starch in pure culture, but in coculture with B. adolescentis L2-32 butyrate was formed, indicating cross-feeding of metabolites to the lactate utilizers. Studies with [(13)C]lactate confirmed carbon flow from lactate, via acetyl coenzyme A, to butyrate both in pure cultures of E. hallii and in cocultures with B. adolescentis. Similar results were obtained in cocultures involving B. adolescentis DSM 20083 with fructo-oligosaccharides as the substrate. Butyrate formation was also stimulated, however, in cocultures of B. adolescentis L2-32 grown on starch or fructo-oligosaccharides with Roseburia sp. strain A2-183, which produces butyrate but does not utilize lactate. This is probably a consequence of the release by B. adolescentis of oligosaccharides that are available to Roseburia sp. strain A2-183. We conclude that two distinct mechanisms of metabolic cross-feeding between B. adolescentis and butyrate-forming bacteria may operate in gut ecosystems, one due to consumption of fermentation end products (lactate and acetate) and the other due to cross-feeding of partial breakdown products from complex substrates.}, }
@article {pmid16669299, year = {2006}, author = {Moore, JE and Millar, BC and Goldsmith, CE}, title = {Microbial ecology associated with soft-tissue infections.}, journal = {Journal of wound care}, volume = {15}, number = {1}, pages = {16-17}, doi = {10.12968/jowc.2006.15.1.26856}, pmid = {16669299}, issn = {0969-0700}, mesh = {Ecology ; Humans ; Soft Tissue Infections/*microbiology ; }, }
@article {pmid16650493, year = {2006}, author = {Rittmann, BE}, title = {Microbial ecology to manage processes in environmental biotechnology.}, journal = {Trends in biotechnology}, volume = {24}, number = {6}, pages = {261-266}, doi = {10.1016/j.tibtech.2006.04.003}, pmid = {16650493}, issn = {0167-7799}, mesh = {Biotechnology/methods/*trends ; *Ecosystem ; *Environmental Microbiology ; }, abstract = {Microbial ecology and environmental biotechnology are inherently tied to each other. The concepts and tools of microbial ecology are the basis for managing processes in environmental biotechnology; and these processes provide interesting ecosystems to advance the concepts and tools of microbial ecology. Revolutionary advancements in molecular tools to understand the structure and function of microbial communities are bolstering the power of microbial ecology. A push from advances in modern materials along with a pull from a societal need to become more sustainable is enabling environmental biotechnology to create novel processes. How do these two fields work together? Five principles illuminate the way: (i) aim for big benefits; (ii) develop and apply more powerful tools to understand microbial communities; (iii) follow the electrons; (iv) retain slow-growing biomass; and (v) integrate, integrate, integrate.}, }
@article {pmid16649062, year = {2006}, author = {Gleeson, DB and Kennedy, NM and Clipson, N and Melville, K and Gadd, GM and McDermott, FP}, title = {Characterization of bacterial community structure on a weathered pegmatitic granite.}, journal = {Microbial ecology}, volume = {51}, number = {4}, pages = {526-534}, pmid = {16649062}, issn = {0095-3628}, mesh = {Bacteria/*classification ; Base Sequence ; DNA Primers ; Microscopy, Electron, Scanning ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {This study exploited the contrasting major element chemistry of a pegmatitic granite to investigate mineralogical influences on bacterial community structure. Intact crystals of variably weathered muscovite, plagioclase, K-feldspar, and quartz were extracted, together with whole-rock granite. Environmental scanning electron microscopy revealed a diversity of bacterial structures, with rods and cocci clearly visible on surfaces of all mineral types. Bacterial automated ribosomal intergenic spacer analysis was used to generate a ribotype profile for each mineral. A randomization test revealed that community fingerprints differed between different mineral types, whereas canonical correspondence analysis (CCA) showed that mineral chemistry affected individual bacterial ribotypes. CCA also revealed that Al, Si, and Ca had a significant impact on bacterial community structure within the system, which contrasts with the finding within fungal communities that although Al and Si also had a significant impact, K rather than Ca was important. The bacterial populations associated with different minerals were different. Members of each of these populations were found almost exclusively on a single mineral type, as was previously reported for fungal populations. These results show that bacterial community structure was driven by the chemical composition of minerals, indicating selective pressure by individual chemical elements on bacterial populations in situ.}, }
@article {pmid16649061, year = {2006}, author = {Deslippe, JR and Egger, KN}, title = {Molecular diversity of nifH genes from bacteria associated with high arctic dwarf shrubs.}, journal = {Microbial ecology}, volume = {51}, number = {4}, pages = {516-525}, pmid = {16649061}, issn = {0095-3628}, mesh = {Arctic Regions ; Bacteria/*genetics ; Base Sequence ; DNA Primers ; DNA, Bacterial ; *Genes, Bacterial ; Oxidoreductases/*genetics ; Plants/*microbiology ; Polymorphism, Restriction Fragment Length ; }, abstract = {Biological nitrogen fixation is the primary source of new N in terrestrial arctic ecosystems and is fundamental to the long-term productivity of arctic plant communities. Still, relatively little is known about the nitrogen-fixing microbes that inhabit the soils of many dominant vegetation types. Our objective was to determine which diazotrophs are associated with three common, woody, perennial plants in an arctic glacial lowland. Dryas integrifolia, Salix arctica, and Cassiope tetragona plants in soil were collected at Alexandra Fiord, Ellesmere Island, Canada. DNA was extracted from soil and root samples and a 383-bp fragment of the nifH gene amplified by the polymerase chain reaction. Cloned genotypes were screened for similarity by restriction fragment length polymorphism (RFLP) analysis. Nine primary RFLP phylotypes were identified and 42 representative genotypes selected for sequencing. Majority of sequences (33) were type I nitrogenases, whereas the remaining sequences belonged to the divergent, homologous, type IV group. Within the type I nitrogenases, nifH genes from posited members of the Firmicutes were most abundant, and occurred in root and soil samples from all three plant species. nifH genes from posited Pseudomonads were found to be more closely associated with C. tetragona, whereas nifH genes from putative alpha-Proteobacteria were more commonly associated with D. integrifolia and S. arctica. In addition, 12 clones likely representing a unique clade within the type I nitrogenases were identified. To our knowledge, this study is the first to report on the nifH diversity of arctic plant-associated soil microbes.}, }
@article {pmid16645929, year = {2006}, author = {Thiyagarajan, V and Lau, SC and Cheung, SC and Qian, PY}, title = {Cypris habitat selection facilitated by microbial films influences the vertical distribution of subtidal barnacle Balanus trigonus.}, journal = {Microbial ecology}, volume = {51}, number = {4}, pages = {431-440}, pmid = {16645929}, issn = {0095-3628}, mesh = {Animals ; Electrophoresis, Polyacrylamide Gel ; *Environment ; Species Specificity ; Thoracica ; *Water Microbiology ; }, abstract = {The potential driving force(s) of the vertical distribution of subtidal barnacle Balanus trigonus Darwin were investigated using both field and laboratory experiments. Early juveniles (approximately 24 h old) placed in intertidal [approximately 0.5 m above mean low water level (MLWL)] and subtidal (approximately 3 m below MLWL) habitats survived equally well, indicating that the intertidal absence of B. trigonus in Hong Kong waters was not determined by differential mortality. However, enhanced attachment of cyprids in subtidal habitats indicated the importance of differential larval choice in determining their vertical distribution. In the laboratory, cyprids preferred to attach in response to subtidal microbial films, which may implicate microbial films as a primary cue in driving the adult vertical distribution. Microbial films developed in these two habitats differed in their biomass (= total organic carbon), abundance of bacteria and diatoms (determined by fluorescence microscopy), and bacterial diversity (determined by DNA fingerprinting analysis). For example, 6-day films in subtidal habitat had a significantly higher biomass than in films from intertidal habitat (P < 0.05). There was no difference in the biomass of films from these two habitats in 9-day films (P > 0.05); however, bacterial abundance was greater in subtidal films than in intertidal films, irrespective of the age of the film, although there was no difference in diatom abundance in films from these two habitats. Neither the abundance of bacteria and diatoms nor the biomass correlated with the attachment preferences of cyprids. This study has not provided any data to prove the existence of inductive and inhibitive (to cyprid attachment) bacterial species in subtidal and intertidal films, respectively; however, results indicate that bacterial community provided qualitative information that might explain the preferential attachment of B. trigonus cyprids in subtidal habitat.}, }
@article {pmid16645928, year = {2006}, author = {Izquierdo, JA and Nüsslein, K}, title = {Distribution of extensive nifH gene diversity across physical soil microenvironments.}, journal = {Microbial ecology}, volume = {51}, number = {4}, pages = {441-452}, pmid = {16645928}, issn = {0095-3628}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Base Sequence ; DNA Primers ; *Genes, Bacterial ; Multigene Family ; Oxidoreductases/*genetics ; Phylogeny ; Polymerase Chain Reaction ; *Soil Microbiology ; }, abstract = {The diversity of nitrogen-fixing bacteria is well described for aquatic environments; however, terrestrial analyses remain mostly biased to rhizobial plant-microbe associations. We maximized the level of resolution for this study through the use of nucleotide sequence information extracted from a series of soil microenvironments, ranging from macroaggregates at 2000 microm to the clay fraction at < 75 microm in diameter. In addition, we attempted to create an overview of the distribution of terrestrial nitrogen fixers across such microenvironments by combining culture-independent techniques with a suite of natural soil environments from uniquely different origins. Soil diazotroph diversity was analyzed phylogenetically for 600 terrestrial nifH sequences from 12 midsized clone libraries based on microenvironments of three separate soils across a global scale. Statistical analyses of nifH gene clone libraries were used to estimate coverage, establish degrees of sequence overlap, and compare cluster distributions. These analyses revealed an extensive diversity in a tropical (19 phylotypes) and an arctic soil (17 phylotypes), and moderate diversity in a temperate soil (11 phylotypes). Within each soil, comparisons across aggregate size fractions delineated nifH gene cluster shifts within populations and degrees of sequence overlap that ranged from significantly different (arctic, tropical) to significantly similar (temperate). We suggest that this is due to population separation across aggregates of different size classes, which results from differences in the temporal stability of aggregates as niches for microbial communities. This study not only provides new knowledge of the arrangement of diazotrophic communities at the soil microscale, but it also contributes to the underrepresented knowledge of soil nifH sequences in the public databases.}, }
@article {pmid16645927, year = {2006}, author = {Sedmak, B and Elersek, T}, title = {Microcystins induce morphological and physiological changes in selected representative phytoplanktons.}, journal = {Microbial ecology}, volume = {51}, number = {4}, pages = {508-515}, pmid = {16645927}, issn = {0095-3628}, mesh = {Fluorescence ; Microcystins ; Peptides, Cyclic/*physiology ; Photosynthesis ; Phytoplankton/*cytology/*physiology ; Pigments, Biological ; }, abstract = {Dissolved microcystins (MCs) are regularly present in water dominated by microcystin-producing, bloom-forming cyanobacteria. In vitro experiments with environmentally feasible concentrations (5 x 10(-7) M) of the three most common microcystins, MC-LR, MC-RR, and MC-YR, revealed that they influence the metabolism of different representative phytoplanktons. At light intensities that are close to the cyanobacterial bloom environment (50 micromol m(-2) s(-1)), they produce morphological and physiological changes in both microcystin-producing and -nonproducing Microcystis aeruginosa strains and also have similar effects on the green alga Scenedesmus quadricauda that is frequently present in cyanobacterial blooms. All three microcystin variants tested induce cell aggregation, increase in cell volume, and overproduction of photosynthetic pigments. All three effects appear to be related to each other but are not necessarily caused by the same mechanism. The biological activity of microcystins toward the light-harvesting complex of photobionts can be interpreted as a signal announcing the worsening of light conditions due to the massive proliferation of cyanobacteria. Although the function of microcystins is still unknown, it is evident that they have numerous effects on phytoplankton in nature. These effects depend on the individual organism as well as on the various intracellular and extracellular signaling pathways. The fact that dissolved microcystins also influence the physiology of microcystin-producing cyanobacteria leads us to the conclusion that the role of microcystins in the producing cells differs from the role in the water environment.}, }
@article {pmid16645926, year = {2006}, author = {Hoek, J and Canfield, D and Reysenbach, AL and Iversen, L}, title = {A bioreactor for growth of sulfate-reducing bacteria: online estimation of specific growth rate and biomass for the deep-sea hydrothermal vent thermophile Thermodesulfatator indicus.}, journal = {Microbial ecology}, volume = {51}, number = {4}, pages = {470-478}, pmid = {16645926}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development/metabolism ; Biomass ; *Bioreactors ; Hydrogen/metabolism ; Sulfates/*metabolism ; }, }
@article {pmid16645925, year = {2006}, author = {Burr, MD and Clark, SJ and Spear, CR and Camper, AK}, title = {Denaturing gradient gel electrophoresis can rapidly display the bacterial diversity contained in 16S rDNA clone libraries.}, journal = {Microbial ecology}, volume = {51}, number = {4}, pages = {479-486}, pmid = {16645925}, issn = {0095-3628}, mesh = {Bacteria/*classification/genetics ; Base Sequence ; DNA Primers ; DNA, Ribosomal/*genetics ; Electrophoresis, Polyacrylamide Gel ; RNA, Ribosomal, 16S/*genetics ; Species Specificity ; }, abstract = {Two different strategies for molecular analysis of bacterial diversity, 16S rDNA cloning and denaturing gradient gel electrophoresis (DGGE), were combined into a single protocol that took advantage of the best attributes of each: the ability of cloning to package DNA sequence information and the ability of DGGE to display a community profile. In this combined protocol, polymerase chain reaction products from environmental DNA were cloned, and then DGGE was used to screen the clone libraries. Both individual clones and pools of randomly selected clones were analyzed by DGGE, and these migration patterns were compared to the conventional DGGE profile produced directly from environmental DNA. For two simple bacterial communities (biofilm from a humics-fed laboratory reactor and planktonic bacteria filtered from an urban freshwater pond), pools of 35-50 clones produced DGGE profiles that contained most of the bands visible in the conventional DGGE profiles, indicating that the clone pools were adequate for identifying the dominant genotypes. However, DGGE profiles of two different pools of 50 clones from a lawn soil clone library were distinctly different from each other and from the conventional DGGE profile, indicating that this small number of clones poorly represented the bacterial diversity in soil. Individual clones with the same apparent DGGE mobility as prominent bands in the humics reactor community profiles were sequenced from the clone plasmid DNA rather than from bands excised from the gel. Because a longer fragment was cloned (approximately 1500 bp) than was actually analyzed in DGGE (approximately 350 bp), far more sequence information was available using this approach that could have been recovered from an excised gel band. This clone/DGGE protocol permitted rapid analysis of the microbial diversity in the two moderately complex systems, but was limited in its ability to represent the diversity in the soil microbial community. Nonetheless, clone/DGGE is a promising strategy for fractionating diverse microbial communities into manageable subsets consisting of small pools of clones.}, }
@article {pmid16645924, year = {2006}, author = {Varela, MM and Bode, A and Morán, XA and Valencia, J}, title = {Dissolved organic nitrogen release and bacterial activity in the upper layers of the Atlantic Ocean.}, journal = {Microbial ecology}, volume = {51}, number = {4}, pages = {487-500}, pmid = {16645924}, issn = {0095-3628}, mesh = {Atlantic Ocean ; Bacteria/*metabolism ; Nitrogen/*metabolism ; Solubility ; *Water Microbiology ; }, abstract = {The variability of the percentage of extracellular dissolved organic nitrogen (DON) release (PER), along with the relationship between DON release and bacterioplankton activity, was examined during five oceanographic cruises, carried out in the upwelling region of the NW Iberian Peninsula, the SW Bay of Biscay, and a latitudinal transect in the Atlantic Ocean (50 degrees N-35 degrees S). Rates of nitrogen uptake, DON release, and bacterial production were measured at 66 stations and sampled between August 1998 and October 2000. The percentage of DON release relative to the gross uptake of ammonium (PERNH4+) ranged from 3 to 46%, whereas that relative to total nitrogen (NH4+ + NO3- + urea) gross uptake (PERtotal) varied between 21 and 82%. The highest values for both PERNH4+ and PER(total) were found in oligotrophic oceanic waters (< 0.25 mg chlorophyll a m(-3)). In oceanic environments, a positive relationship was found between nitrogen uptake and DON release rates, with a log-log linear regression slope significantly lower than 1, suggesting an inverse relationship between PER and gross nitrogen uptake rates. In contrast, in areas with higher productivity levels (> 6 mg chlorophyll a m(-3)), such as the continental shelf off the NW Iberian Peninsula, PER held constant as nitrogen uptake increased. These results suggest the dominance of different processes controlling DON release in oceanic and neritic zones. DON release rates accounted for less than 15% of the variability observed in bacterial production rates, suggesting a weak response of bacterioplankton to phytoplankton on short time scales (hours). Furthermore, nitrogen budgets showed an excess of DON release in relation to bacterial requirements.}, }
@article {pmid16645923, year = {2006}, author = {Tso, SF and Taghon, GL}, title = {Protozoan grazing increases mineralization of naphthalene in marine sediment.}, journal = {Microbial ecology}, volume = {51}, number = {4}, pages = {460-469}, pmid = {16645923}, issn = {0095-3628}, mesh = {Animals ; Bacteria/drug effects/growth &amp; development/isolation &amp; purification ; Colony Count, Microbial ; Cytochalasin B/pharmacology ; Eukaryota/*physiology ; Geologic Sediments/*chemistry/parasitology ; Minerals/*chemistry ; Naphthalenes/*chemistry ; }, abstract = {Bacterial decomposition of organic matter is frequently enhanced when protozoa are present. Various mechanisms have been proposed to account for this phenomenon, including effects associated with grazing by protozoa (such as increased recycling of limiting nutrients, removal of senescent cells, or reduction of competition among bacteria) and indirect effects of grazers (such as excretion of bacterial growth factors). Few studies have examined the role of protozoa in bacterial degradation of xenobiotic compounds in sediment containing a natural community of microbes. The effect of protozoa on mineralization of naphthalene was investigated in this study. Laboratory experiments were conducted using field-contaminated estuarine sediment, with the indigenous microbial populations. Mineralization of naphthalene was up to four times greater in treatments with actively grazing protozoa than in treatments containing the grazing inhibitor cytochalasin B. Control experiments confirmed that the grazing inhibitor was not toxic to ciliates but did prevent them from grazing. The grazing inhibitor did not affect growth rates of a mixed culture of sediment bacteria or a pure polycyclic-aromatic-hydrocarbon-degrading strain. Once grazing had been inhibited, supplementing treatments with inorganic N and P, glucose, or additional protozoa failed to stimulate naphthalene mineralization. Naphthalene-degrading bacteria were four to nine times less abundant when protozoan grazing was suppressed. We suggest that protozoa enhance naphthalene mineralization by selectively grazing on those sediment bacteria that ordinarily would outcompete naphthalene-degrading bacteria.}, }
@article {pmid16645922, year = {2006}, author = {Nevot, M and Deroncele, V and López-Iglesias, C and Bozal, N and Guinea, J and Mercade, E}, title = {Ultrastructural analysis of the extracellular matter secreted by the psychrotolerant bacterium Pseudoalteromonas antarctica NF3.}, journal = {Microbial ecology}, volume = {51}, number = {4}, pages = {501-507}, pmid = {16645922}, issn = {0095-3628}, mesh = {Extracellular Space/metabolism ; Microscopy, Electron, Transmission ; Pseudoalteromonas/metabolism/*ultrastructure ; }, abstract = {The psychrotolerant strain Pseudoalteromonas antarctica NF3, a Gram-negative bacterium isolated from muddy soil samples of Antarctica, secretes large amounts of a mucoid exopolymer with a high protein content. It has self-assembly properties and capacity to coat and protect liposomes against surfactants. We examined the ultrastructure of P. antarctica and the extracellular matter it secretes by transmission electron microscopy (TEM) after high-pressure freezing, freeze substitution (HPF-FS), and Epon embedding, and compared this with information obtained by conventional methods. The improvements brought about by HPF-FS to the ultrastructural preservation of the extracellular matter allowed us to establish for the first time, in P. antarctica NF3, the presence of two components: a large amount of cell-derived outer membrane vesicles containing proteins and a capsular polymer around the cells.}, }
@article {pmid16645921, year = {2006}, author = {Acosta-Mercado, D and Lynn, DH}, title = {Contrasting soil ciliate species richness and abundance between two tropical plant species: a test of the plant effect.}, journal = {Microbial ecology}, volume = {51}, number = {4}, pages = {453-459}, pmid = {16645921}, issn = {0095-3628}, mesh = {Plants/*microbiology ; *Soil Microbiology ; Species Specificity ; Tropical Climate ; }, abstract = {We still have a rudimentary understanding about the mechanism by which plant roots may stimulate soil microbial interactions. A biochemical model involving plant-derived biochemical fractions, such as exudates, has been used to explain this "rhizosphere effect" on bacteria. However, the variable response of other soil microbial groups, such as protozoa, to the rhizosphere suggests that other factors could be involved in shaping their communities. Thus, two experiments were designed to: (1) determine whether stimulatory and/or inhibiting factors associated with particular plant species regulate ciliate diversity and abundance and (2) obtain a better understanding about the mechanism by which these plant factors operate in the rhizosphere. Bacterial and chemical slurries were reciprocally exchanged between two plant species known to differ in terms of ciliate species richness and abundance (i.e., Canella winterana and plantation Tectona grandis). Analysis of variance showed that the bacteria plus nutrients and the nutrients only treatment had no significant effect on overall ciliate species richness and abundance when compared to the control treatment. However, the use of only colpodean species increased the taxonomic resolution of treatment effects revealing that bacterial slurries had a significant effect on colpodean ciliate species richness. Thus, for particular rhizosphere ciliates, biological properties, such as bacterial diversity or abundance, may have a strong influence on their diversity and possibly abundance. These results are consistent with a model of soil bacteria-mediated mutualisms between plants and protozoa.}, }
@article {pmid16641460, year = {2006}, author = {Rantala, M and Haanperä-Heikkinen, M and Lindgren, M and Seppälä, H and Huovinen, P and Jalava, J}, title = {Streptococcus pneumoniae isolates resistant to telithromycin.}, journal = {Antimicrobial agents and chemotherapy}, volume = {50}, number = {5}, pages = {1855-1858}, pmid = {16641460}, issn = {0066-4804}, mesh = {Anti-Bacterial Agents/*pharmacology ; Base Sequence ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial ; Humans ; Ketolides/*pharmacology ; Macrolides/*pharmacology ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Promoter Regions, Genetic ; Streptococcus pneumoniae/*drug effects/isolation &amp; purification/physiology ; }, abstract = {The telithromycin susceptibility of 210 erythromycin-resistant pneumococci was tested with the agar diffusion method. Twenty-six erm(B)-positive isolates showed heterogeneous resistance to telithromycin, which was manifested by the presence of colonies inside the inhibition zone. When these cells were cultured and tested, they showed stable, homogeneous, and high-level resistance to telithromycin.}, }
@article {pmid16637707, year = {2006}, author = {Vanhaecke, L and Van Hoof, N and Van Brabandt, W and Soenen, B and Heyerick, A and De Kimpe, N and De Keukeleire, D and Verstraete, W and Van de Wiele, T}, title = {Metabolism of the food-associated carcinogen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine by human intestinal microbiota.}, journal = {Journal of agricultural and food chemistry}, volume = {54}, number = {9}, pages = {3454-3461}, doi = {10.1021/jf053170+}, pmid = {16637707}, issn = {0021-8561}, mesh = {Adult ; Bacteria/*metabolism ; Carcinogens/*metabolism ; Diet ; Feces/microbiology ; Female ; *Food ; Humans ; Imidazoles/*metabolism ; Intestines/*microbiology ; Male ; }, abstract = {2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine is a putative human carcinogenic heterocyclic aromatic amine formed from meat and fish during cooking. Although the formation of hazardous PhIP metabolites by mammalian enzymes is well-documented, nothing is known about the PhIP transformation potency of human intestinal bacteria. In this study, the in vitro metabolism of PhIP by human fecal samples was investigated. Following anaerobic incubation of PhIP with stools freshly collected from six healthy volunteers, we found that PhIP was extensively transformed by the human intestinal bacteria. HPLC analysis showed that the six human fecal microbiota transformed PhIP with efficiencies from 47 to 95% after 72 h incubation, resulting in one major derivative. ESI-MS/MS, HRMS, 1D (1H, 13C, DEPT) and 2D (gCOSY, gTOCSY, gHMBC, gHSQC) NMR, and IC analysis elucidated the complete chemical identity of the microbial PhIP metabolite as 7-hydroxy-5-methyl-3-phenyl-6,7,8,9-tetrahydropyrido[3',2':4,5]imidazo[1,2-a]pyrimidin-5-ium chloride. At present, no information is available about the biological activity of this newly discovered bacterial PhIP metabolite. Our findings however suggest that bacteria derived from the human intestine play a key role in the activation or detoxification of PhIP, a digestive fate ignored so far in risk assessments. Moreover, the variation in transformation efficiency between the human microbiota indicates interindividual differences in the ability to convert PhIP. This may predict individual susceptibility to carcinogenic risk from this suspected dietary carcinogen.}, }
@article {pmid16630008, year = {2006}, author = {Gunasekera, TS and Sundin, GW}, title = {Role of nucleotide excision repair and photoreactivation in the solar UVB radiation survival of Pseudomonas syringae pv. syringae B728a.}, journal = {Journal of applied microbiology}, volume = {100}, number = {5}, pages = {1073-1083}, doi = {10.1111/j.1365-2672.2006.02841.x}, pmid = {16630008}, issn = {1364-5072}, mesh = {Bacteriological Techniques/methods ; DNA Damage ; *DNA Repair ; DNA, Bacterial/genetics ; Dose-Response Relationship, Radiation ; Mutagenesis, Insertional ; Phaseolus/*microbiology ; Plant Diseases/microbiology ; Plant Leaves/microbiology ; Pseudomonas syringae/genetics/metabolism/*radiation effects ; Rec A Recombinases/metabolism ; *Sunlight ; *Ultraviolet Rays ; }, abstract = {AIMS: To assess the role of DNA repair and photoreactivation in the solar radiation survival of the plant pathogen and leaf surface epiphyte Pseudomonas syringae pv. syringae (Pss).<br><br>METHODS AND RESULTS: Mutants of Pss B728a, with insertional mutations within the nucleotide excision repair gene uvrA, photolyase gene phr, or uvrA phr double mutants, were constructed to examine the importance of individual repair mechanisms in solar UV radiation (UVR) survival. The survival of either the uvrA mutant or the phr mutant was reduced by approx. 10(2)-fold following exposure to a dose of 4.5 kJ m(-2) solar UVB (290-320 nm wavelengths) while the uvrA phr double mutant was reduced >10(6)-fold by the same dose. We constructed a transcriptional fusion between the Pss recA promoter and gfp to examine the induction of the SOS response in wild-type and mutant strains. Initiation of the recA mediated SOS response was more rapid and peaked at higher levels in mutant strains suggesting both increased DNA damage in mutant strains and also that photoreactivation and nucleotide excision repair remove DNA damage as it is incurred which is reflected in a delay of recA expression. Visualization of expression of B728a cells containing the recA::gfp reporter on UVB-irradiated bean leaves highlighted the movement of cells to intercellular spaces over time and that SOS induction was detectable when leaves were irradiated 48 h following leaf inoculation.<br><br>CONCLUSIONS: This study indicated that solar UVB is detrimental to Pss B728a, DNA repair mechanisms play an important role in strain survival and expression of the SOS regulon on leaf surfaces contributes to survival of UVR-exposed cells during plant colonization.<br><br>This work links previous laboratory-based UVR analyses with solar UVB dose-response analyses and highlights the role of photoreactivation in delaying induction of the SOS response following solar irradiation. Knowledge of population dynamics following direct solar irradiation will enhance our understanding of the biology of Pss in the phyllosphere.}, }
@article {pmid16629676, year = {2006}, author = {Butcher, BG and Helmann, JD}, title = {Identification of Bacillus subtilis sigma-dependent genes that provide intrinsic resistance to antimicrobial compounds produced by Bacilli.}, journal = {Molecular microbiology}, volume = {60}, number = {3}, pages = {765-782}, doi = {10.1111/j.1365-2958.2006.05131.x}, pmid = {16629676}, issn = {0950-382X}, support = {R01 GM047446/GM/NIGMS NIH HHS/United States ; GM047446/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Anti-Bacterial Agents/metabolism/*pharmacology ; Antibiosis ; Bacillus/classification/*metabolism ; Bacillus subtilis/*drug effects/genetics/growth &amp; development/metabolism ; Bacterial Proteins/chemistry/*genetics/metabolism ; Bacteriocins/metabolism/pharmacology ; Culture Media ; Drug Resistance, Bacterial/*genetics ; *Gene Expression Regulation, Bacterial ; Molecular Sequence Data ; Mutation ; Promoter Regions, Genetic ; Sigma Factor/*metabolism ; }, abstract = {Bacillus subtilis produces many antibiotics of varying structures and specificity. Here we identify a prominent role for sigma(W), an extracytoplasmic function (ECF) sigma factor, in providing intrinsic resistance to antimicrobial compounds produced by other Bacilli. By using a panel of B. subtilis mutants disrupted for each of the 30 known sigma(W)-dependent operons we identified resistance genes for at least three different antimicrobial compounds. The ydbST and fosB genes contribute to resistance to antimicrobial compound(s) produced by B. amyloliquefaciens FZB42, the yqeZyqfAB operon provides resistance to the SPbeta prophage-encoded bacteriocin sublancin, and the yknWXYZ operon and yfhL provide resistance to the antimicrobial peptide SdpC. YfhL encodes a paralogue of SdpI, a membrane protein that provides immunity to SdpC. In competition experiments, we identify sigma(W) as a key factor in allowing B. subtilis to resist antibiotic killing and encroachment by competing strains. Together with the previous observation that sigma(W) provides inducible resistance against the Streptomyces antibiotic fosfomycin, these studies support the notion that sigma(W) controls an antibiosis regulon important in the microbial ecology of soil bacteria.}, }
@article {pmid16623745, year = {2006}, author = {Milinovich, GJ and Trott, DJ and Burrell, PC and van Eps, AW and Thoefner, MB and Blackall, LL and Al Jassim, RA and Morton, JM and Pollitt, CC}, title = {Changes in equine hindgut bacterial populations during oligofructose-induced laminitis.}, journal = {Environmental microbiology}, volume = {8}, number = {5}, pages = {885-898}, doi = {10.1111/j.1462-2920.2005.00975.x}, pmid = {16623745}, issn = {1462-2912}, mesh = {Animal Feed ; Animals ; Bacteria/classification/*isolation &amp; purification ; DNA, Bacterial/analysis ; Disease Models, Animal ; Feces/microbiology ; Foot Diseases/etiology/microbiology/*veterinary ; Horse Diseases/*etiology/metabolism/microbiology ; Horses ; In Situ Hybridization, Fluorescence ; Intestines/*microbiology ; Oligosaccharides/*administration &amp; dosage/*metabolism ; Phylogeny ; Polymerase Chain Reaction ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; }, abstract = {In the horse, carbohydrate overload is thought to play an integral role in the onset of laminitis by drastically altering the profile of bacterial populations in the hindgut. The objectives of this study were to develop and validate microbial ecology methods to monitor changes in bacterial populations throughout the course of experimentally induced laminitis and to identify the predominant oligofructose-utilizing organisms. Laminitis was induced in five horses by administration of oligofructose. Faecal specimens were collected at 8 h intervals from 72 h before to 72 h after the administration of oligofructose. Hindgut microbiota able to utilize oligofructose were enumerated throughout the course of the experiment using habitat-simulating medium. Isolates were collected and representatives identified by 16S rRNA gene sequencing. The majority of these isolates collected belonged to the genus Streptococcus, 91% of which were identified as being most closely related to Streptococcus infantarius ssp. coli. Furthermore, S. infantarius ssp. coli was the predominant oligofructose-utilizing organism isolated before the onset of lameness. Fluorescence in situ hybridization probes developed to specifically target the isolated Streptococcus spp. demonstrated marked population increases between 8 and 16 h post oligofructose administration. This was followed by a rapid population decline which corresponded with a sharp decline in faecal pH and subsequently lameness at 24-32 h post oligofructose administration. This research suggests that streptococci within the Streptococcus bovis/equinus complex may be involved in the series of events which precede the onset of laminitis in the horse.}, }
@article {pmid16607526, year = {2006}, author = {Tiwari, MK and Guha, S and Harendranath, CS and Tripathi, S}, title = {Influence of extrinsic factors on granulation in UASB reactor.}, journal = {Applied microbiology and biotechnology}, volume = {71}, number = {2}, pages = {145-154}, doi = {10.1007/s00253-006-0397-3}, pmid = {16607526}, issn = {0175-7598}, mesh = {Bacteria, Anaerobic/*metabolism ; *Bioreactors ; Hydrogen-Ion Concentration ; Methane/metabolism ; *Sewage/chemistry/microbiology ; Temperature ; }, abstract = {The aim of this mini-review is to synthesize and analyze information on how the process of granulation is affected by environmental and operational conditions in the reactor. The factors reviewed are temperature, pH, alkalinity, organic loading rate, upflow velocity, nature and strength of substrate, nutrients, multivalent cations and heavy metals, microbial ecology of seed sludge, exo-cellular polymer, and addition of natural and synthetic polymers. Careful temperature control and adequate alkalinity is required for generation and maintenance of granules. Nature and strength of substrate in conjunction with intra-granular diffusion to a large extent determines the microstructure of the granules. The divalent cations such as calcium and iron may enhance granulation by ionic bridging and linking exo-cellular polymers. However, their presence in excess may lead to cementation due to precipitation leading to increased ash content and mass transfer limitation. The addition of external additives such as ionic polymers may enhance granulation in the upflow anaerobic sludge blanket reactors.}, }
@article {pmid16598640, year = {2006}, author = {Mummey, D and Holben, W and Six, J and Stahl, P}, title = {Spatial stratification of soil bacterial populations in aggregates of diverse soils.}, journal = {Microbial ecology}, volume = {51}, number = {3}, pages = {404-411}, pmid = {16598640}, issn = {0095-3628}, mesh = {Actinobacteria/genetics/*isolation &amp; purification ; Alphaproteobacteria/genetics/*isolation &amp; purification ; Phylogeny ; Proteobacteria/genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Most soil microbial community studies to date have focused on homogenized bulk soil samples. However, it is likely that many important microbial processes occur in spatially segregated microenvironments in the soil leading to a microscale biogeography. This study attempts to localize specific microbial populations to different fractions or compartments within the soil matrix. Microbial populations associated with macroaggregates and inner- versus total-microaggregates of three diverse soils were characterized using culture-independent, molecular methods. Despite their relative paucity in most surveys of soil diversity, representatives of Gemmatimonadetes and Actinobacteria subdivision Rubrobacteridae were found to be highly abundant in inner-microaggregates of most soils analyzed. By contrast, clones affiliated with Acidobacteria were found to be relatively enriched in libraries derived from macroaggregate fractions of nearly all soils, but poorly represented in inner-microaggregate fractions. Based upon analysis of 16S rRNA, active community members within microaggregates of a Georgian Ultisol were comprised largely of Gemmatimonadetes and Rubrobacteridae, while within microaggregates of a Nebraska Mollisol, Rubrobacteridae and Alphaproteobacteria were the predominant active bacterial lineages. This work suggests that microaggregates represent a unique microenvironment that selects for specific microbial lineages across disparate soils.}, }
@article {pmid16598639, year = {2006}, author = {Zakhia, F and Jeder, H and Willems, A and Gillis, M and Dreyfus, B and de Lajudie, P}, title = {Diverse bacteria associated with root nodules of spontaneous legumes in Tunisia and first report for nifH-like gene within the genera Microbacterium and Starkeya.}, journal = {Microbial ecology}, volume = {51}, number = {3}, pages = {375-393}, pmid = {16598639}, issn = {0095-3628}, mesh = {Burkholderia/enzymology/genetics/isolation &amp; purification ; Electrophoresis, Polyacrylamide Gel/methods ; Fabaceae/metabolism/*microbiology ; Gram-Negative Aerobic Rods and Cocci/enzymology/*genetics/isolation &amp; purification ; Oxidoreductases/*genetics ; Phylogeny ; Plant Roots/metabolism/microbiology ; RNA, Ribosomal, 16S/genetics ; Rhizobiaceae/enzymology/genetics/isolation &amp; purification ; Rhizobium/enzymology/genetics/isolation &amp; purification ; }, abstract = {We characterized 34 endophytic bacterial isolates associated to root nodules collected from spontaneous legumes in the arid zone of Tunisia by 16S rDNA polymerase chain reaction (PCR)-restriction fragment length polymorphism, whole cell protein sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), 16S rDNA and 16S-23S rDNA internal transcribed spacer sequencing. Phylogenetically, these isolates belong to the branches containing the genera Inquilinus, Bosea, Rhodopseudomonas, Paracraurococcus, Phyllobacterium, Ochrobactrum, Starkeya, Sphingomonas, Pseudomonas, Agromyces, Microbacterium, Ornithinicoccus, Bacillus, and Paenibacillus. These strains did not induce any nodule formation when inoculated on the wide host spectrum legume species M. atropurpureum (Siratro) and no nodA gene could be amplified by PCR. However, nifH sequences, most similar to those of Sinorhizobium meliloti, were detected within strains related to the genera Microbacterium, Agromyces, Starkeya and Phyllobacterium.}, }
@article {pmid16598638, year = {2006}, author = {Lemke, MJ and Leff, LG}, title = {Culturability of stream bacteria assessed at the assemblage and population levels.}, journal = {Microbial ecology}, volume = {51}, number = {3}, pages = {365-374}, pmid = {16598638}, issn = {0095-3628}, mesh = {Acinetobacter calcoaceticus/*growth &amp; development/isolation &amp; purification ; Bacteriological Techniques/methods ; Burkholderia cepacia/*growth &amp; development/isolation &amp; purification ; Culture ; In Situ Hybridization, Fluorescence ; *Population ; Pseudomonas putida/*growth &amp; development/isolation &amp; purification ; Rivers/*microbiology ; }, abstract = {Lotic bacterial communities can be examined at multiple levels: from the assemblage level to populations of individual species. In stream environments, as in many other systems, the percentage of bacteria that are culturable is quite low. In this study, the culturability of the overall bacterial assemblage, as well as the culturability of three common species (Acinetobacter calcoaceticus, Burkholderia cepacia, and Pseudomonas putida), was determined in samples collected from four streams on three dates. Colony hybridization (colonies were grown on modified nutrient agar) and fluorescent in situ hybridization were used to calculate the percentage of cells of a given species that were culturable. Approximately half of the overall assemblage was estimated to be viable but nonculturable cells (VBNC). The culturability of two of the species was low (0.29% for A. calcoaceticus and 0.46% for P. putida), whereas the value for B. cepacia (2.48%) exceeded the overall assemblage level culturability (0.90%). Overall, both bacterial assemblages and populations were dominated by VBNC. These results show quantitatively that not all members of a species that has culturable representatives are culturable when retrieved from natural populations, likely because of interspecific phenotypic and genotypic variability. Thus, the large pool of nonculturable cells includes representatives of species that are, under some circumstances, culturable.}, }
@article {pmid16598637, year = {2006}, author = {Weinbauer, MG and Christen, R and Höfle, MG}, title = {The response of Vibrio- and Rhodobacter-related populations of the NW Mediterranean Sea to additions of dissolved organic matter, phages, or dilution.}, journal = {Microbial ecology}, volume = {51}, number = {3}, pages = {336-344}, pmid = {16598637}, issn = {0095-3628}, mesh = {Bacteriophages ; Biological Availability ; Ecology ; Humic Substances ; In Situ Hybridization, Fluorescence ; Mediterranean Sea ; Population Density ; Rhodobacter/*growth &amp; development/isolation &amp; purification ; Vibrio/*growth &amp; development/isolation &amp; purification ; Water Microbiology ; }, abstract = {We investigated the growth response of the heterotrophic prokaryotic community focusing on Vibrio- and Rhodobacter-related populations (SRF3) to variation in the availability of dissolved organic matter (DOM), population density-dependent effects, and prokaryotic virus (phage) infection in coastal and offshore waters of the NW Mediterranean Sea. We tested the response of the prokaryotic community to three different DOM fractions prepared by ultrafiltration. One of the DOM fractions contained phages (<0.2 m), a second was virus-free (<100 kDa), and a third contained only low molecular weight (<1 kDa). The proportion of Vibrio and SRF3 populations as determined by fluorescent in situ hybridization in the community ranged from <1 to 6.2% and from 3.2 to 6.3%, respectively. Based on changes in cell numbers, growth rates ranged from 2.1 to 3.1 day(-1) for Vibrio and from 0.8 to 1.2 day(-1) for SRF3. Growth rates of Vibrio were similar or higher than those of the total prokaryotic community, whereas the ability of Vibrio to use high molecular weight (HMW) DOM and the responses to additions of phage-rich material were lower. Growth rates of SRF3 were lower than that of the community. Susceptibility to infection of SRF3 was sometimes lower than in the community, whereas the growth stimulation of HMW DOM was similar or lower. Reducing the cell concentrations of the prokaryotic community by dilution stimulated the overall growth of the community, including that of its constituent Vibrio and SRF3 populations, but the effect was smaller on the SRF3 and greater on Vibrio populations than for the total community. Comparisons with the community also revealed that life strategy traits of bacterial populations differed between coastal and offshore waters. Overall, our data suggest that Vibrio is an r-strategist or opportunistic population in the NW Mediterranean Sea, whereas SRF3 is a K-strategist or equilibrium population.}, }
@article {pmid16598636, year = {2006}, author = {Remily, ER and Richardson, LL}, title = {Ecological physiology of a coral pathogen and the coral reef environment.}, journal = {Microbial ecology}, volume = {51}, number = {3}, pages = {345-352}, pmid = {16598636}, issn = {0095-3628}, support = {SO6GM8205/GM/NIGMS NIH HHS/United States ; }, mesh = {Alphaproteobacteria/growth &amp; development/metabolism/*physiology ; Animals ; Anthozoa/*microbiology ; Ecology ; Hydrogen-Ion Concentration ; Oxygen/metabolism ; Temperature ; }, abstract = {Laboratory studies on the ecological physiology of a coral pathogen were carried out to investigate growth potential in terms of environmental factors that may control coral diseases on reefs. The disease chosen for this study, white plague type II, is considered to be one of the major diseases of Caribbean scleractinian corals, affecting a wide range of coral hosts and causing rapid and widespread tissue loss. It is caused by a single pathogen, the bacterium Aurantimonas coralicida. A series of laboratory experiments using a pure culture of the pathogen was carried out to examine the roles of temperature, pH, and O(2) concentration on growth rate. Results revealed optimal growth between 30 and 35 degrees Celsius, and between pH values of 6 and 8. There was a distinctive synergistic relationship between pH and temperature. Increasing temperature from 25 to 35 degrees Celsius expanded the range of pH tolerance from a minimum of 6.0 down to 5.0. O(2) concentration directly affected growth rate, which increased with increasing O(2). The combined effects of increasing O(2) and increasing temperature resulted in a synergistic effect of more rapid growth. These laboratory results are discussed in terms of the coral host and the range of the environmental factors that occur on coral reefs. We conclude that changing environmental conditions in the reef environment, in particular observed increases in water temperature, may be promoting coral diseases by allowing coral pathogens to expand their ecological niches. In the case of the white plague type II pathogen, elevated temperature would allow A. coralicida to colonize the low pH environment of the coral surface mucopolysaccharide layer as an initial stage of infection. The synergistic effect between temperature and oxygen concentration appeared to be less environmentally relevant for this coral pathogen.}, }
@article {pmid16598635, year = {2006}, author = {Xinyao, L and Miao, S and Yonghong, L and Yin, G and Zhongkai, Z and Donghui, W and Weizhong, W and Chencai, A}, title = {Feeding characteristics of an amoeba (Lobosea: Naegleria) grazing upon cyanobacteria: food selection, ingestion and digestion progress.}, journal = {Microbial ecology}, volume = {51}, number = {3}, pages = {315-325}, pmid = {16598635}, issn = {0095-3628}, mesh = {Amoeba/metabolism/*physiology ; Animals ; *Cyanobacteria ; Digestion/physiology ; Eating ; *Food Preferences ; Naegleria/metabolism/*physiology ; Phylogeny ; Predatory Behavior ; }, abstract = {Bacterivory by heterotrophic nanoflagellates and ciliates has been widely studied in aquatic environments, but data on the grazing of amoebae, are still scarce. From the water samples of Dianchi Lake (Kunming, Yunnan Province, China), we isolated an amoeba, designated as Naegleria sp. strain W2, which had potent grazing effects on some kind of cyanobacteria. The food selection mechanism and the digestion process of the amoeba were investigated in batch experiments. Predation experiments showed that filamentous cyanobacteria (e.g., Anabaena, Cylindrospermum, Gloeotrichia, and Phormidium) were readily consumed, with clearance rates ranging from 0.332 to 0.513 nL amoeba(-1) h(-1). The tight threads (Oscilltoria) and aggregates (Aphanizomenon) could not be ingested; however, their sonicated fragments were observed inside food vacuoles, suggesting that their morphologies prevent them from being ingested. Live video microscopy noted that unicellular Chroococcaceae (e.g., Synechococcus, Aphanocapsa, and Microcystis) were excreted after ingestion, indicating that food selection takes place inside food vacuoles. To determine whether the tastes or the toxins prevented them from being digested, heat-killed cells were retested for predation. Digestion rates and ingestion rates of the amoebae for filamentous cyanobacteria were estimated from food vacuole content volume. Through a "cold-chase" method, we found that the food vacuole contents declined exponentially in diluted amoebae cells, and digestion rates were relatively constant, averaging about 1.5% food vacuole content min(-1) at 28 degrees Celsius. Ingestion strongly depended on the satiation status of the amoebae, starved amoebae fed at higher rates compared with satiated amoebae. Our results suggest that the food selection and food processing mechanisms of the amoeba are similar to those of interception feeding flagellates; however, filamentous cyanobacteria cannot obtain a refuge under the grazing pressure of phagotrophic amoebae, which may widen our knowledge on the grazing of protists.}, }
@article {pmid16598634, year = {2006}, author = {Lipson, DA and Blair, M and Barron-Gafford, G and Grieve, K and Murthy, R}, title = {Relationships between microbial community structure and soil processes under elevated atmospheric carbon dioxide.}, journal = {Microbial ecology}, volume = {51}, number = {3}, pages = {302-314}, pmid = {16598634}, issn = {0095-3628}, mesh = {Biodiversity ; Biomass ; Carbon Dioxide/*metabolism ; Climate ; *Ecology ; Phylogeny ; Populus/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; *Soil ; *Soil Microbiology ; }, abstract = {There is little current understanding of the relationship between soil microbial community composition and soil processes rates, nor of the effect climate change and elevated CO(2) will have on microbial communities and their functioning. Using the eastern cottonwood (Populus deltoides) plantation at the Biosphere 2 Laboratory, we studied the relationships between microbial community structure and process rates, and the effects of elevated atmospheric CO(2) on microbial biomass, activity, and community structure. Soils were sampled from three treatments (400, 800, and 1200 ppm CO(2)), a variety of microbial biomass and activity parameters were measured, and the bacterial community was described by 16S rRNA libraries. Glucose substrate-induced respiration (SIR) was significantly higher in the 1200 ppm CO(2) treatment. There were also a variety of complex, nonlinear responses to elevated CO(2). There was no consistent effect of elevated CO(2) on bacterial diversity; however, there was extensive variation in microbial community structure within the plantation. The southern ends of the 800 and 1200 ppm CO(2) bays were dominated by beta-Proteobacteria, and had higher fungal biomass, whereas the other areas contained more alpha-Proteobacteria and Acidobacteria. A number of soil process rates, including salicylate, glutamate, and glycine substrate-induced respiration and proteolysis, were significantly related to the relative abundance of the three most frequent bacterial taxa, and to fungal biomass. Overall, variation in microbial activity was better explained by microbial community composition than by CO(2) treatment. However, the altered diversity and activity in the southern bays of the two high CO(2) treatments could indicate an interaction between CO(2) and light.}, }
@article {pmid16598633, year = {2006}, author = {Schmitt, H and Stoob, K and Hamscher, G and Smit, E and Seinen, W}, title = {Tetracyclines and tetracycline resistance in agricultural soils: microcosm and field studies.}, journal = {Microbial ecology}, volume = {51}, number = {3}, pages = {267-276}, pmid = {16598633}, issn = {0095-3628}, mesh = {Agrochemicals/*chemistry ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/*genetics ; Genes, Bacterial ; Manure/*microbiology ; Soil/*analysis ; *Soil Microbiology ; Tetracycline Resistance/*genetics ; Tetracyclines/*pharmacology ; }, abstract = {The influence of the use of antibiotics on the prevalence of resistance genes in the environment is still poorly understood. We studied the diversity of tetracycline and sulfonamide resistance genes as influenced by fertilization with pig manure in soil microcosms and at two field locations. Manure contained a high diversity of resistance genes, regardless of whether it stemmed from a farm operation with low or regular use of antibiotics. In the microcosm soils, the influence of fertilization with manure was clearly shown by an increase in the number of resistance genes in the soil after manuring. Spiking of the tetracycline compounds to the microcosms had only little additional impact on the diversity of resistance genes. Overall, the tetracycline resistance genes tet(T), tet(W), and tet(Z) were ubiquitous in soil and pig slurries, whereas tet(Y), tet(S), tet(C), tet(Q), and tet(H) were introduced to the microcosm soil by manuring. The diversity of tetracycline and sulfonamide [sul(1), sul(2), and sul(3)] resistance genes on a Swiss pasture was very high even before slurry amendment, although manure from intensive farming had not been applied in the previous years. The additional effect of manuring was small, with the tetracycline and sulfonamide resistance diversity staying at high levels for the complete growth season. At an agricultural field site in Germany, the diversity of tetracycline and sulfonamide resistance genes was considerably lower, possibly reflecting regional differences in gene diversity. This study shows that there is a considerable pool of resistance genes in soils. Although it is not possible to conclude whether this diversity is caused by the global spread of resistance genes after 50 years of tetracycline use or is due to the natural background in soil resistance genes, it highlights a role that environmental reservoirs might play in resistance gene capture.}, }
@article {pmid16598632, year = {2006}, author = {Sintupachee, S and Milne, JR and Poonchaisri, S and Baimai, V and Kittayapong, P}, title = {Closely related Wolbachia strains within the pumpkin arthropod community and the potential for horizontal transmission via the plant.}, journal = {Microbial ecology}, volume = {51}, number = {3}, pages = {294-301}, pmid = {16598632}, issn = {0095-3628}, mesh = {Animals ; Coleoptera/microbiology ; Cucurbita/*microbiology/parasitology ; Hemiptera/microbiology ; Insect Vectors/*microbiology ; Luffa/microbiology/parasitology ; Phylogeny ; Plant Diseases/*microbiology/parasitology ; Seasons ; Wolbachia/*classification/genetics/growth &amp; development ; }, abstract = {Phylogenetic studies have implicated frequent horizontal transmission of Wolbachia among arthropod host lineages. However, the ecological routes for such lateral transfer are poorly known. We surveyed the species of two arthropod communities, one on pumpkin and the other on loofah plants, for Wolbachia, constructed wsp gene phylogenies of those Wolbachia strains found to infect community members, and established ecological links among infected members. Four taxonomically diverse insects in the pumpkin arthropod community contained very closely related Wolbachia wsp sequences (<1.5% divergence by Kimura-2-parameter distances). These insects, namely, the whitefly Bemisia tabaci, the planthopper Nisia nervosa, the flea beetle Phyllotreta sp., and the fleahopper Halticus minutus, were all collected from pumpkin leaves. They were ecologically linked through feeding on the same leaf substrate. Unlike other infected leaf insects, the whitefly population appeared to have a permanent breeding relationship with pumpkin plants, and high and stable, but not fixed, monthly Wolbachia infection rates. Our findings suggest potential roles for the plant in Wolbachia transmission and for whiteflies in being an infection source for other pumpkin leaf-feeding insects.}, }
@article {pmid16598631, year = {2006}, author = {Romero, J and Navarrete, P}, title = {16S rDNA-based analysis of dominant bacterial populations associated with early life stages of coho salmon (Oncorhynchus kisutch).}, journal = {Microbial ecology}, volume = {51}, number = {4}, pages = {422-430}, pmid = {16598631}, issn = {0095-3628}, mesh = {Animals ; Bacteria/genetics/*isolation &amp; purification ; Base Sequence ; Colony Count, Microbial ; DNA Primers ; DNA, Ribosomal/*genetics ; Electrophoresis, Polyacrylamide Gel ; Life Cycle Stages ; Oncorhynchus kisutch/*microbiology ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {In this study, we used a 16S rDNA-based approach to determine bacterial populations associated with coho salmon (Oncorhynchus kisutch) in its early life stages, highlighting dominant bacteria in the gastrointestinal tract during growth in freshwater. The present article is the first molecular analysis of bacterial communities of coho salmon. Cultivability of the salmon gastrointestinal microbiota was estimated by comparison of direct microscopic counts (using acridine orange) with colony counts (in tryptone soy agar). In general, a low fraction (about 1%) of the microbiota could be recovered as cultivable bacteria. Using DNA extracted directly from individuals belonging to the same lot, bacterial communities present in eggs and gastrointestinal tract of first-feeding fries and juveniles were monitored by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The DGGE profiles revealed simple communities in all stages and exposed changes in bacterial community during growth. Sequencing and phylogenetic analysis of excised DGGE bands revealed the nature of the main bacteria found in each stage. In eggs, the dominant bacteria belonged to beta-Proteobacteria (Janthinobacterium and Rhodoferax). During the first feeding stage, the most abundant bacteria in the gastrointestinal tract clustered with gamma-Proteobacteria (Shewanella and Aeromonas). In juveniles ranging from 2 to 15 g, prevailing bacteria were Pseudomonas and Aeromonas. To determine the putative origin of dominant Pseudomonas and Aeromonas found in juvenile gastrointestinal tracts, primers for these groups were designed based on sequences retrieved from DGGE gel. Subsequently, samples of the water influent, pelletized feed, and eggs were analyzed by PCR amplification. Only those amplicons obtained from samples of eggs and the water influent presented identical sequences to the dominant bands of DGGE. Overall, our results suggest that a stable microbiota is established after the first feeding stages and its major components could be derived from water and egg epibiota.}, }
@article {pmid16598630, year = {2006}, author = {Mehnaz, S and Lazarovits, G}, title = {Inoculation effects of Pseudomonas putida, Gluconacetobacter azotocaptans, and Azospirillum lipoferum on corn plant growth under greenhouse conditions.}, journal = {Microbial ecology}, volume = {51}, number = {3}, pages = {326-335}, pmid = {16598630}, issn = {0095-3628}, mesh = {Azospirillum lipoferum/genetics/isolation &amp; purification/metabolism/*physiology ; Drug Resistance ; Ethanol/metabolism ; Fatty Acids/metabolism ; Gluconacetobacter/genetics/isolation &amp; purification/metabolism/*physiology ; Indoleacetic Acids/metabolism ; Nitrogen Fixation ; Nitrogenase/metabolism ; Pseudomonas putida/genetics/isolation &amp; purification/metabolism/*physiology ; RNA, Ribosomal, 16S/genetics ; Zea mays/*growth &amp; development/metabolism/*microbiology ; }, abstract = {Alcohol production from corn is gaining importance in Ontario, Canada, and elsewhere. A major cost of corn production is the cost of chemical fertilizers and these continue to increase in price. The competitiveness of alcohol with fossil fuels depends on access to low-cost corn that allows growers to earn a sustainable income. In this study we set out to determine if we can identify root-associated microorganisms from Ontario-grown corn that can enhance the nutrient flow to corn roots, directly or indirectly, and help minimize the use of extraneous fertilizer. Bacteria were isolated from corn rhizosphere and screened for their capacity to enhance corn growth. The bacteria were examined for their ability to fix nitrogen, solubilize phosphate, and produce indole acetic acid (IAA) and antifungal substances on potato dextrose agar. Bacterial suspensions were applied to pregerminated seed of four corn varieties (39D82, 39H84, 39M27, and 39T68) planted in sterilized sand and unsterilized cornfield soil. The plants were grown under greenhouse conditions for 30 days. Three isolates were identified as having growth-promoting effect. These bacteria were identified as to species by biochemical tests, fatty acid profiles, and 16S rDNA sequence analysis. Corn rhizosphere isolates, Gluconacetobacter azotocaptans DS1, Pseudomonas putida CQ179, and Azospirillum lipoferum N7, provided significant plant growth promotion expressed as increased root/shoot weight when compared to uninoculated plants, in sand and/or soil. All strains except P. putida CQ179 were capable of nitrogen fixation and IAA production. Azospirillum brasilense, however, produced significantly more IAA than the other isolates. Although several of the strains were also able to solubilize phosphate and produce metabolites inhibitory to various fungal pathogens, these properties are not considered as contributing to growth promotion under the conditions used in this study. These bacteria will undergo field tests for their effect on corn growth.}, }
@article {pmid16598629, year = {2006}, author = {Horath, T and Neu, TR and Bachofen, R}, title = {An endolithic microbial community in dolomite rock in central Switzerland: characterization by reflection spectroscopy, pigment analyses, scanning electron microscopy, and laser scanning microscopy.}, journal = {Microbial ecology}, volume = {51}, number = {3}, pages = {353-364}, pmid = {16598629}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development ; Calcium Carbonate/*analysis ; Chromatography, High Pressure Liquid/methods ; Magnesium/*analysis ; Microscopy, Confocal ; Microscopy, Electron, Scanning ; Pigmentation ; *Soil Microbiology ; Spectrum Analysis ; Switzerland ; }, abstract = {A community of endolithic microorganisms dominated by phototrophs was found as a distinct band a few millimeters below the surface of bare exposed dolomite rocks in the Piora Valley in the Alps. Using in situ reflectance spectroscopy, we detected chlorophyll a (Chl a), phycobilins, carotenoids, and an unknown type of bacteriochlorophyll-like pigment absorbing in vivo at about 720 nm. In cross sections, the data indicated a defined distribution of different groups of organisms perpendicular to the rock surface. High-performance liquid chromatography analyses of pigments extracted with organic solvents confirmed the presence of two types of bacteriochlorophylls besides chlorophylls and various carotenoids. Spherical organisms of varying sizes and small filaments were observed in situ with scanning electron microscopy and confocal laser scanning microscopy (one- and two-photon technique). The latter allowed visualization of the distribution of phototrophic microorganisms by the autofluorescence of their pigments within the rock. Coccoid cyanobacteria of various sizes predominated over filamentous ones. Application of fluorescence-labeled lectins demonstrated that most cyanobacteria were embedded in an exopolymeric matrix. Nucleic acid stains revealed a wide distribution of small heterotrophs. Some biological structures emitting a green autofluorescence remain to be identified.}, }
@article {pmid16598505, year = {2006}, author = {Wallander, H and Lindahl, BD and Nilsson, LO}, title = {Limited transfer of nitrogen between wood decomposing and ectomycorrhizal mycelia when studied in the field.}, journal = {Mycorrhiza}, volume = {16}, number = {3}, pages = {213-217}, pmid = {16598505}, issn = {0940-6360}, mesh = {Basidiomycota/*metabolism ; Biodegradation, Environmental ; *Ecosystem ; Fagus/*microbiology ; Mycelium/metabolism ; Mycorrhizae/*metabolism ; Nitrogen/*metabolism ; Plant Roots/microbiology ; *Soil Microbiology ; Trees/metabolism/microbiology ; }, abstract = {Transfer of (15)N between interacting mycelia of a wood-decomposing fungus (Hypholoma fasciculare) and an ectomycorrhizal fungus (Tomentellopsis submollis) was studied in a mature beech (Fagus sylvatica) forest. The amount of (15)N transferred from the wood decomposer to the ectomycorrhizal fungus was compared to the amount of (15)N released from the wood-decomposing mycelia into the soil solution as (15)N-NH(4). The study was performed in peat-filled plastic containers placed in forest soil in the field. The wood-decomposing mycelium was growing from an inoculated wood piece and the ectomycorrhizal mycelium from an introduced root from a mature tree. The containers were harvested after 41 weeks when physical contact between the two foraging mycelia was established. At harvest, (15)N content was analyzed in the peat (total N and (15)NH(4) (+)) and in the mycorrhizal roots. A limited amount of (15)N was transferred to the ectomycorrhizal fungus and this transfer could be explained by (15)NH(4) (+) released from the wood-decomposing fungus without involving any antagonistic interactions between the two mycelia. Using our approach, it was possible to study nutritional interactions between basidiomycete mycelia under field conditions and this and earlier studies suggest that the outcomes of such interactions are highly species-specific and depend on environmental conditions such as resource availability.}, }
@article {pmid16597946, year = {2006}, author = {Rodrigues, JL and Kachel, CA and Aiello, MR and Quensen, JF and Maltseva, OV and Tsoi, TV and Tiedje, JM}, title = {Degradation of aroclor 1242 dechlorination products in sediments by Burkholderia xenovorans LB400(ohb) and Rhodococcus sp. strain RHA1(fcb).}, journal = {Applied and environmental microbiology}, volume = {72}, number = {4}, pages = {2476-2482}, pmid = {16597946}, issn = {0099-2240}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; P42 ES 04911/ES/NIEHS NIH HHS/United States ; }, mesh = {Aroclors/*metabolism ; Biodegradation, Environmental ; Burkholderia/genetics/growth &amp; development/*metabolism ; Chlorine/metabolism ; Chlorobenzoates/metabolism ; Environmental Pollutants/*metabolism ; Genetic Engineering/methods ; Geologic Sediments/*microbiology ; Operon ; Polychlorinated Biphenyls/metabolism ; Recombination, Genetic ; Rhodococcus/genetics/growth &amp; development/*metabolism ; Soil Pollutants/metabolism ; }, abstract = {Burkholderia xenovorans strain LB400, which possesses the biphenyl pathway, was engineered to contain the oxygenolytic ortho dehalogenation (ohb) operon, allowing it to grow on 2-chlorobenzoate and to completely mineralize 2-chlorobiphenyl. A two-stage anaerobic/aerobic biotreatment process for Aroclor 1242-contaminated sediment was simulated, and the degradation activities and genetic stabilities of LB400(ohb) and the previously constructed strain RHA1(fcb), capable of growth on 4-chlorobenzoate, were monitored during the aerobic phase. The population dynamics of both strains were also followed by selective plating and real-time PCR, with comparable results; populations of both recombinants increased in the contaminated sediment. Inoculation at different cell densities (10(4) or 10(6) cells g(-1) sediment) did not affect the extent of polychlorinated biphenyl (PCB) biodegradation. After 30 days, PCB removal rates for high and low inoculation densities were 57% and 54%, respectively, during the aerobic phase.}, }
@article {pmid16597927, year = {2006}, author = {Leigh, MB and Prouzová, P and Macková, M and Macek, T and Nagle, DP and Fletcher, JS}, title = {Polychlorinated biphenyl (PCB)-degrading bacteria associated with trees in a PCB-contaminated site.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {4}, pages = {2331-2342}, pmid = {16597927}, issn = {0099-2240}, mesh = {Actinomycetales/classification/genetics/isolation &amp; purification/metabolism ; Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; Biodegradation, Environmental ; Molecular Sequence Data ; Pinus/microbiology ; Plant Roots/microbiology ; Polychlorinated Biphenyls/*metabolism ; Rhodococcus/classification/genetics/isolation &amp; purification/metabolism ; Salix/microbiology ; *Soil Microbiology ; Soil Pollutants/*metabolism ; Trees/*microbiology ; Xanthomonadaceae/classification/genetics/isolation &amp; purification/metabolism ; }, abstract = {The abundance, identities, and degradation abilities of indigenous polychlorinated biphenyl (PCB)-degrading bacteria associated with five species of mature trees growing naturally in a contaminated site were investigated to identify plants that enhance the microbial PCB degradation potential in soil. Culturable PCB degraders were associated with every plant species examined in both the rhizosphere and root zone, which was defined as the bulk soil in which the plant was rooted. Significantly higher numbers of PCB degraders (2.7- to 56.7-fold-higher means) were detected in the root zones of Austrian pine (Pinus nigra) and goat willow (Salix caprea) than in the root zones of other plants or non-root-containing soil in certain seasons and at certain soil depths. The majority of culturable PCB degraders throughout the site and the majority of culturable PCB degraders associated with plants were identified as members of the genus Rhodococcus by 16S rRNA gene sequence analysis. Other taxa of PCB-degrading bacteria included members of the genera Luteibacter and Williamsia, which have not previously been shown to include PCB degraders. PCB degradation assays revealed that some isolates from the site have broad congener specificities; these isolates included one Rhodococcus strain that exhibited degradation abilities similar to those of Burkholderia xenovorans LB400. Isolates with broad congener specificity were widespread at the site, including in the biostimulated root zone of willow. The apparent association of certain plant species with increased abundance of indigenous PCB degraders, including organisms with outstanding degradation abilities, throughout the root zone supports the notion that biostimulation through rhizoremediation is a promising strategy for enhancing PCB degradation in situ.}, }
@article {pmid16596441, year = {2006}, author = {Häubner, N and Schumann, R and Karsten, U}, title = {Aeroterrestrial microalgae growing in biofilms on facades--response to temperature and water stress.}, journal = {Microbial ecology}, volume = {51}, number = {3}, pages = {285-293}, pmid = {16596441}, issn = {0095-3628}, mesh = {Biofilms/*growth &amp; development ; Dehydration ; *Environment ; Eukaryota/growth &amp; development/isolation &amp; purification/metabolism/*physiology ; Humidity ; Photosynthesis ; Temperature ; }, abstract = {The photosynthetic performance of a microalgal biofilm colonizing a building facade was investigated between February and July 2004, with an emphasis on changing water availability and air humidity. The fluorimetric measurements of the quantum efficiency (F (v)/F (m)) indicated diurnal activity patterns. At most sampling dates the algal biofilm photosynthesized particularly in the morning and substantially less in the afternoon. As long as liquid water was present, the microalgae exhibited at least some degree of photosynthesis. However, F (v)/F (m) values never exceeded 0.4, pointing to slight photoinhibition or damage of the cells. Dried cells without photosynthesis could recover within minutes after artificial moistening. Three microalgal strains were isolated from aeroterrestrial biofilms and established as unialgal cultures. Their photosynthesis and growth were characterized under different air humidities and temperatures. Photosynthesis and growth of strain ROS 55/3 (Stichococcus sp.) showed similar patterns with decreasing relative air humidity. Positive growth and optimum photosynthesis were recorded at 100% relative air humidity. At air humidities below 93%, both processes were strongly inhibited. All studied strains grew between 1 and 30 degrees Celsius with optimum rates at 20-23 degrees Celsius, indicating eurythermal features. The data indicate that liquid water or 100% air humidity are the prerequisite for optimum photosynthesis and growth of aeroterrestrial microalgae. However, when dried and consequently inactive, these microorganisms can recover quickly if water is suddenly available, e.g., after rain events. These physiological capabilities explain well the ecological success of aeroterrestrial microalgae in occupying many man-made substrata such as building facades and roof tiles in urban areas.}, }
@article {pmid16596440, year = {2006}, author = {Uchii, K and Matsui, K and Yonekura, R and Tani, K and Kenzaka, T and Nasu, M and Kawabata, Z}, title = {Genetic and physiological characterization of the intestinal bacterial microbiota of Bluegill (Lepomis macrochirus) with three different feeding habits.}, journal = {Microbial ecology}, volume = {51}, number = {3}, pages = {277-284}, pmid = {16596440}, issn = {0095-3628}, mesh = {Animals ; Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Electrophoresis/methods ; *Feeding Behavior ; Intestines/*microbiology ; Perciformes/*microbiology ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Zooplankton ; }, abstract = {Bluegill (Lepomis macrochirus) in Lake Biwa, Japan, feed on benthic invertebrates (benthivorous type), aquatic plants (herbivorous type), and zooplankton (planktivorous type). To evaluate the effect of food on intestinal bacterial microbiota, we characterized and compared the intestinal microbiota of these three types of bluegill in terms of community-level physiological profile (CLPP) and genetic structure. The CLPP was analyzed using Biolog MicroPlates (Biolog, Inc., Hayward, CA, USA), and multivariate analysis of variance revealed that the CLPP of intestinal microbiota differed significantly between any pairs of the three types of bluegill. The genetic profiles were analyzed by temperature gradient gel electrophoresis of polymerase chain reaction (PCR)-amplified 16S rDNA fragments, and multidimensional scaling indicated the existence of specific intestinal bacterial structures for both the benthivorous and the planktivorous types. These results suggest that the host's feeding habit can be one factor controlling the intestinal microbiota of fish in the natural environment.}, }
@article {pmid16596439, year = {2006}, author = {Kiely, PD and Haynes, JM and Higgins, CH and Franks, A and Mark, GL and Morrissey, JP and O'Gara, F}, title = {Exploiting new systems-based strategies to elucidate plant-bacterial interactions in the rhizosphere.}, journal = {Microbial ecology}, volume = {51}, number = {3}, pages = {257-266}, pmid = {16596439}, issn = {0095-3628}, mesh = {*Bacterial Physiological Phenomena ; Genes, Reporter/genetics ; Pest Control, Biological ; Plants/genetics/*microbiology ; Proteomics ; }, abstract = {The rhizosphere is the site of intense interactions between plant, bacterial, and fungal partners. In plant-bacterial interactions, signal molecules exuded by the plant affect both primary initiation and subsequent behavior of the bacteria in complex beneficial associations such as biocontrol. However, despite this general acceptance that plant-root exudates have an effect on the resident bacterial populations, very little is still known about the influence of these signals on bacterial gene expression and the roles of genes found to have altered expression in plant-microbial interactions. Analysis of the rhizospheric communities incorporating both established techniques, and recently developed "omic technologies" can now facilitate investigations into the molecular basis underpinning the establishment of beneficial plant-microbial interactomes in the rhizosphere. The understanding of these signaling processes, and the functions they regulate, is fundamental to understanding the basis of beneficial microbial-plant interactions, to overcoming existing limitations, and to designing improved strategies for the development of novel Pseudomonas biocontrol strains.}, }
@article {pmid16596438, year = {2006}, author = {Smith, JJ and Tow, LA and Stafford, W and Cary, C and Cowan, DA}, title = {Bacterial diversity in three different Antarctic Cold Desert mineral soils.}, journal = {Microbial ecology}, volume = {51}, number = {4}, pages = {413-421}, pmid = {16596438}, issn = {0095-3628}, mesh = {Antarctic Regions ; Bacteria/*classification/genetics/isolation &amp; purification ; Base Sequence ; DNA Primers ; DNA, Ribosomal/genetics ; Electrophoresis, Polyacrylamide Gel ; *Minerals ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil ; *Soil Microbiology ; Species Specificity ; }, abstract = {A bacterial phylogenetic survey of three environmentally distinct Antarctic Dry Valley soil biotopes showed a high proportion of so-called "uncultured" phylotypes, with a relatively low diversity of identifiable phylotypes. Cyanobacterial phylotypic signals were restricted to the high-altitude sample, whereas many of the identifiable phylotypes, such as the members of the Actinobacteria, were found at all sample sites. Although the presence of Cyanobacteria and Actinobacteria is consistent with previous culture-dependent studies of microbial diversity in Antarctic Dry Valley mineral soils, many phylotypes identified by 16S rDNA analysis were of groups that have not hitherto been cultured from Antarctic soils. The general belief that such "extreme" environments harbor a relatively low species diversity was supported by the calculation of diversity indices. The detection of a substantial number of uncultured bacterial phylotypes showing low BLAST identities (< 95%) suggests that Antarctic Dry Valley mineral soils harbor a pool of novel psychrotrophic taxa.}, }
@article {pmid16596437, year = {2006}, author = {Ariosa, Y and Carrasco, D and Quesada, A and Fernández-Valiente, E}, title = {Incorporation of different N sources and light response curves of nitrogenase and photosynthesis by cyanobacterial blooms from rice fields.}, journal = {Microbial ecology}, volume = {51}, number = {3}, pages = {394-403}, pmid = {16596437}, issn = {0095-3628}, mesh = {Anabaena/enzymology/growth &amp; development/metabolism ; Biomass ; Cyanobacteria/enzymology/*growth &amp; development/metabolism ; Light ; Nitrogen/*metabolism ; Nitrogen Fixation ; Nitrogenase/*metabolism ; Oryza/*microbiology ; Photosynthesis ; Spain ; }, abstract = {In this work, we estimate the contributions of the different sources of N incorporated by two N(2)-fixing cyanobacterial blooms (Anabaena sp. and Microchaete sp.) in the rice fields of Valencia (Spain) during the crop cycles of 1999 and 2000, and evaluate the response of nitrogenase and C assimilation activities to changing irradiances. Our results show that, far from the generally assumed idea that the largest part of the N incorporated by N(2)-fixing cyanobacterial blooms in rice fields comes from N(2) fixation, both cyanobacterial blooms incorporated about three times more N from dissolved combined compounds than from N(2) fixation (only about 33-41% of the N incorporated came from N(2) fixation). Our results on the photodependence of C and N(2) fixation indicate that in both cyanobacterial blooms, N(2) fixation showed a steeper initial slope (alpha) and was saturated with less irradiance than C fixation, suggesting that N(2) fixation was more efficient than photosynthesis under conditions of light limitation. At saturating light, N(2) fixation and C fixation differed depending on the bloom and on the environmental conditions created by rice plant growth. Carbon assimilation but not nitrogenase activity appeared photoinhibited in the Anabaena but not in the Microchaete bloom in August 1999, when the plants were tall and the canopy was important, and there was no limitation of dissolved inorganic carbon. The opposite was found in the Microchaete bloom of June 2000, when plants were small and produced little shade, and dissolved inorganic carbon was very low.}, }
@article {pmid16579489, year = {2006}, author = {Duan, ZY and Guo, YQ and Liu, JX}, title = {[Application of modern molecular biology techniques to study micro-ecosystem in the rumen].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {46}, number = {1}, pages = {166-169}, pmid = {16579489}, issn = {0001-6209}, mesh = {Animals ; DNA Fingerprinting ; In Situ Hybridization ; *Nucleic Acid Probes ; Polymerase Chain Reaction/methods ; Rumen/*microbiology ; }, abstract = {The microbial community inhabiting in the rumen is characterized by its high population density, wide diversity and interactive complexity. However, until recently our knowledge of rumen microbiology was primarily based on classical culture based techniques (isolation, enumeration and nutritional characterization) which probably only account for 10% to 20% of the rumen microbial population. Modem molecular biology techniques provide effective methods to study the micro-ecosystem in the rumen. The use of molecular techniques based on nucleic acid probes is likely to revolutionize the approach to microbial ecology in the rumen and provide, not simply a refinement or increased understanding but a complete description of rumen community for the first time. Modem molecular techniques based on sequence comparisons of nucleic acids may be used to explore molecular characterization and provide a classification scheme which predicts natural evolutionary relationships. Genetic fingerprinting techniques that provide a pattern or profile of genetic diversity have been applied in a variety of environmental studies for the analysis of microbial communities. Whole-cell hybridization is a powerful technique which may be used to study the structure and function of microbial communities in situ and describe the expression of key enzymes. Real-time quantitative PCR technique may be conducted to accurately quantify the target microorganisms in the rumen. Development of these procedures and techniques will result in greater insights into community structure and activity of rumen microbial communities in relation to functional interactions, spatial and temporal relationships between different microorganisms and between microorganisms and feed particles. The successful development and application of these methods promise to provide the first opportunity to link distribution and identity of rumen microbes in their natural environment with their genetic potential and in situ activities.}, }
@article {pmid16572761, year = {2006}, author = {Rittmann, BE and Hausner, M and Löffler, F and Love, NG and Muyzer, G and Okabe, S and Oerther, DB and Peccia, J and Raskin, L and Wagner, M}, title = {A vista for microbial ecology and environmental biotechnology.}, journal = {Environmental science &amp; technology}, volume = {40}, number = {4}, pages = {1096-1103}, doi = {10.1021/es062631k}, pmid = {16572761}, issn = {0013-936X}, mesh = {Biodegradation, Environmental ; Bioelectric Energy Sources ; *Biotechnology ; *Ecology ; *Environmental Microbiology ; Genomics ; }, }
@article {pmid16570218, year = {2006}, author = {Seurinck, S and Deschepper, E and Deboch, B and Verstraete, W and Siciliano, S}, title = {Characterization of Escherichia coli isolates from different fecal sources by means of classification tree analysis of fatty acid methyl ester (FAME) profiles.}, journal = {Environmental monitoring and assessment}, volume = {114}, number = {1-3}, pages = {433-445}, pmid = {16570218}, issn = {0167-6369}, mesh = {Animals ; Environmental Monitoring/*methods ; Escherichia coli/classification/*isolation &amp; purification ; Esters/analysis ; Fatty Acids/*analysis ; Feces/*microbiology ; Humans ; Sewage/*microbiology ; Water Supply/*standards ; }, abstract = {Microbial source tracking (MST) methods need to be rapid, inexpensive and accurate. Unfortunately, many MST methods provide a wealth of information that is difficult to interpret by the regulators who use this information to make decisions. This paper describes the use of classification tree analysis to interpret the results of a MST method based on fatty acid methyl ester (FAME) profiles of Escherichia coli isolates, and to present results in a format readily interpretable by water quality managers. Raw sewage E. coli isolates and animal E. coli isolates from cow, dog, gull, and horse were isolated and their FAME profiles collected. Correct classification rates determined with leaveone-out cross-validation resulted in an overall low correct classification rate of 61%. A higher overall correct classification rate of 85% was obtained when the animal isolates were pooled together and compared to the raw sewage isolates. Bootstrap aggregation or adaptive resampling and combining of the FAME profile data increased correct classification rates substantially. Other MST methods may be better suited to differentiate between different fecal sources but classification tree analysis has enabled us to distinguish raw sewage from animal E. coli isolates, which previously had not been possible with other multivariate methods such as principal component analysis and cluster analysis.}, }
@article {pmid16556814, year = {2006}, author = {Pennisi, E}, title = {Microbial ecology. How a marine bacterium adapts to multiple environments.}, journal = {Science (New York, N.Y.)}, volume = {311}, number = {5768}, pages = {1697}, doi = {10.1126/science.311.5768.1697}, pmid = {16556814}, issn = {1095-9203}, mesh = {*Adaptation, Physiological ; Bacteriophages/genetics/*physiology ; *Ecosystem ; Genes, Bacterial ; Genome, Bacterial ; Genomic Islands ; Light ; Oceans and Seas ; Prochlorococcus/classification/genetics/*physiology ; Seawater/*microbiology ; Temperature ; }, }
@article {pmid16552582, year = {2006}, author = {Davies, J}, title = {Are antibiotics naturally antibiotics?.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {33}, number = {7}, pages = {496-499}, pmid = {16552582}, issn = {1367-5435}, mesh = {*Anti-Bacterial Agents/biosynthesis/chemistry/pharmacology ; Bacteria/genetics/*metabolism ; *Environment ; *Evolution, Molecular ; Fungi/genetics/*metabolism ; Transcription, Genetic/drug effects ; }, abstract = {Antibiotics have been used for more than 50 years and are the cornerstone of infectious disease treatment; in addition, these low-molecular-weight bioactive compounds have been applied to many other therapeutic purposes. However, there is almost no information on the evolutionary biology or ecology of naturally occurring low-molecular-weight compounds. The large number of different structural types and the extremely broad range of biological activities of organic molecules produced by microbes raise many questions concerning their roles in nature. Recent evidence for the enormous complexity of microbial populations in the environment favors the notion that the principal roles of small molecules in microbial ecology are cell-cell communication and not antibiosis.}, }
@article {pmid16550305, year = {2006}, author = {Steven, B and Léveillé, R and Pollard, WH and Whyte, LG}, title = {Microbial ecology and biodiversity in permafrost.}, journal = {Extremophiles : life under extreme conditions}, volume = {10}, number = {4}, pages = {259-267}, pmid = {16550305}, issn = {1431-0651}, mesh = {*Acclimatization ; Bacteria/isolation &amp; purification/*metabolism ; *Biodiversity ; *Cold Climate ; Exobiology ; *Soil Microbiology ; }, abstract = {Permafrost represents 26% of terrestrial soil ecosystems; yet its biology, essentially microbiology, remains relatively unexplored. The permafrost environment is considered extreme because indigenous microorganisms must survive prolonged exposure to subzero temperatures and background radiation for geological time scales in a habitat with low water activity and extremely low rates of nutrient and metabolite transfer. Yet considerable numbers and biodiversity of bacteria exist in permafrost, some of which may be among the most ancient viable life on Earth. This review describes the permafrost environment as a microbial habitat and reviews recent studies examining microbial biodiversity found in permafrost as well as microbial growth and activity at ambient in situ subzero temperatures. These investigations suggest that functional microbial ecosystems exist within the permafrost environment and may have important implications on global biogeochemical processes as well as the search for past or extant life in permafrost presumably present on Mars and other bodies in our solar system.}, }
@article {pmid16549455, year = {2006}, author = {Decroos, K and Eeckhaut, E and Possemiers, S and Verstraete, W}, title = {Administration of equol-producing bacteria alters the equol production status in the Simulator of the Gastrointestinal Microbial Ecosystem (SHIME).}, journal = {The Journal of nutrition}, volume = {136}, number = {4}, pages = {946-952}, doi = {10.1093/jn/136.4.946}, pmid = {16549455}, issn = {0022-3166}, mesh = {Bacteria/*metabolism ; Bile ; Colon/microbiology ; DNA, Bacterial/analysis ; *Ecosystem ; Equol ; Feces/microbiology ; Gastrointestinal Tract/*microbiology ; Humans ; Hydrogen-Ion Concentration ; Isoflavones/*biosynthesis/metabolism ; Models, Biological ; Probiotics ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {The intestinal microbial transformation of daidzein, one of the principal isoflavones from soy, into the isoflavan equol is subjected to a high interindividual variability. The latter compound is considered to have a higher biological activity than its precursor; hence, there is interest in dietary applications that modulate this important biotransformation. In 2 separate experiments, we administered a mixed microbial culture (EPC4), which we had isolated previously and which efficiently transforms daidzein into equol, to the Simulator of the Human Intestinal Microbial Ecosystem (SHIME). The SHIME was fed soy germ powder and inoculated with fecal samples from two nonequol-producing individuals. Equol production was induced in the distal colon compartments in both experiments, 5-6 d after the start of the treatment; 2 wk after interrupting the addition of EPC4, equol was still produced in high amounts. There are large interregional differences in daidzein metabolism in the simulated colon. Furthermore, no major shifts in the composition and activity of the microbial communities were caused by the supplementation with the microbial consortium. Although further confirmation in in vivo studies is required, these results validate the concept that administering EPC4 could constitute a novel means for converting a nonequol-producer into a producer.}, }
@article {pmid16549033, year = {2006}, author = {Edwards, RA and Rodriguez-Brito, B and Wegley, L and Haynes, M and Breitbart, M and Peterson, DM and Saar, MO and Alexander, S and Alexander, EC and Rohwer, F}, title = {Using pyrosequencing to shed light on deep mine microbial ecology.}, journal = {BMC genomics}, volume = {7}, number = {}, pages = {57}, pmid = {16549033}, issn = {1471-2164}, mesh = {Bacteria/*genetics/isolation &amp; purification/metabolism ; Ecology ; *Environment ; Genome, Bacterial ; Genomics/*methods ; *Mining ; Minnesota ; RNA, Ribosomal, 16S/genetics ; Water/chemistry ; }, abstract = {BACKGROUND: Contrasting biological, chemical and hydrogeological analyses highlights the fundamental processes that shape different environments. Generating and interpreting the biological sequence data was a costly and time-consuming process in defining an environment. Here we have used pyrosequencing, a rapid and relatively inexpensive sequencing technology, to generate environmental genome sequences from two sites in the Soudan Mine, Minnesota, USA. These sites were adjacent to each other, but differed significantly in chemistry and hydrogeology.<br><br>RESULTS: Comparisons of the microbes and the subsystems identified in the two samples highlighted important differences in metabolic potential in each environment. The microbes were performing distinct biochemistry on the available substrates, and subsystems such as carbon utilization, iron acquisition mechanisms, nitrogen assimilation, and respiratory pathways separated the two communities. Although the correlation between much of the microbial metabolism occurring and the geochemical conditions from which the samples were isolated could be explained, the reason for the presence of many pathways in these environments remains to be determined. Despite being physically close, these two communities were markedly different from each other. In addition, the communities were also completely different from other microbial communities sequenced to date.<br><br>CONCLUSION: We anticipate that pyrosequencing will be widely used to sequence environmental samples because of the speed, cost, and technical advantages. Furthermore, subsystem comparisons rapidly identify the important metabolisms employed by the microbes in different environments.}, }
@article {pmid16539597, year = {2006}, author = {de Boer, W and Kowalchuk, GA and van Veen, JA}, title = {'Root-food' and the rhizosphere microbial community composition.}, journal = {The New phytologist}, volume = {170}, number = {1}, pages = {3-6}, doi = {10.1111/j.1469-8137.2006.01674.x}, pmid = {16539597}, issn = {0028-646X}, mesh = {Bacteria/growth &amp; development ; Bacterial Physiological Phenomena ; *Ecosystem ; Fungi/growth &amp; development/physiology ; Medicago truncatula/metabolism/*microbiology ; Mycorrhizae/physiology ; Plant Roots/metabolism/*microbiology ; Rhizome/microbiology ; Soil/analysis ; }, }
@article {pmid16535717, year = {1997}, author = {Harmsen, H and Prieur, D and Jeanthon, C}, title = {Group-Specific 16S rRNA-Targeted Oligonucleotide Probes To Identify Thermophilic Bacteria in Marine Hydrothermal Vents.}, journal = {Applied and environmental microbiology}, volume = {63}, number = {10}, pages = {4061-4068}, pmid = {16535717}, issn = {0099-2240}, abstract = {Four 16S rRNA-targeted oligonucleotide probes were designed for the detection of thermophilic members of the domain Bacteria known to thrive in marine hydrothermal systems. We developed and characterized probes encompassing most of the thermophilic members of the genus Bacillus, most species of the genus Thermus, the genera Thermotoga and Thermosipho, and the Aquificales order. The temperature of dissociation of each probe was determined. Probe specificities to the target groups were demonstrated by whole-cell and dot blot hybridization against a collection of target and nontarget rRNAs. Whole-cell hybridizations with the specific probes were performed on cells extracted from hydrothermal vent chimneys. One of the samples contained cells that hybridized to the probe specific to genera Thermotoga and Thermosipho. No positive signals could be detected in the samples tested with the probes whose specificities encompassed either the genus Thermus or the thermophilic members of the genus Bacillus. However, when simultaneous hybridizations with the probe specific to the order Aquificales and a probe specific to the domain Bacteria (R. I. Amann, B. Binder, R. J. Olson, S. W. Chisholm, R. Devereux, and D. A. Stahl, Appl. Environ. Microbiol. 56:1919-1925, 1990) were performed on cells extracted from the top and exterior subsamples of chimneys, positive signals were obtained from morphologically diverse bacteria representing about 40% of the bacterial population. Since specificity studies also revealed that the bacterial probe did not hybridize with the members of the order Aquificales, the detected cells may therefore correspond to a new type of bacteria. One of the observed morphotypes was similar to that of a strictly anaerobic autotrophic sulfur-reducing strain that we isolated from the chimney samples. This work demonstrates that application of whole-cell hybridization with probes specific for different phylogenetic levels is a useful tool for detailed studies of hydrothermal vent microbial ecology.}, }
@article {pmid16522539, year = {2005}, author = {McNamara, CJ and Perry, TD and Leard, R and Bearce, K and Dante, J and Mitchell, R}, title = {Corrosion of aluminum alloy 2024 by microorganisms isolated from aircraft fuel tanks.}, journal = {Biofouling}, volume = {21}, number = {5-6}, pages = {257-265}, doi = {10.1080/08927010500389921}, pmid = {16522539}, issn = {0892-7014}, mesh = {*Aircraft ; Alloys/*chemistry ; Aluminum/*chemistry ; Bacillus/growth &amp; development/*isolation &amp; purification ; Corrosion ; *Fossil Fuels ; Fungi/growth &amp; development/*isolation &amp; purification ; Penicillium/isolation &amp; purification ; }, abstract = {Microorganisms frequently contaminate jet fuel and cause corrosion of fuel tank metals. In the past, jet fuel contaminants included a diverse group of bacteria and fungi. The most common contaminant was the fungus Hormoconis resinae. However, the jet fuel community has been altered by changes in the composition of the fuel and is now dominated by bacterial contaminants. The purpose of this research was to determine the composition of the microbial community found in fuel tanks containing jet propellant-8 (JP-8) and to determine the potential of this community to cause corrosion of aluminum alloy 2024 (AA2024). Isolates cultured from fuel tanks containing JP-8 were closely related to the genus Bacillus and the fungi Aureobasidium and Penicillium. Biocidal activity of the fuel system icing inhibitor diethylene glycol monomethyl ether is the most likely cause of the prevalence of endospore forming bacteria. Electrochemical impedance spectroscopy and metallographic analysis of AA2024 exposed to the fuel tank environment indicated that the isolates caused corrosion of AA2024. Despite the limited taxonomic diversity of microorganisms recovered from jet fuel, the community has the potential to corrode fuel tanks.}, }
@article {pmid16517648, year = {2006}, author = {Nocker, A and Camper, AK}, title = {Selective removal of DNA from dead cells of mixed bacterial communities by use of ethidium monoazide.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {3}, pages = {1997-2004}, pmid = {16517648}, issn = {0099-2240}, mesh = {Affinity Labels/*metabolism ; Azides/*metabolism ; Bacteriological Techniques ; Biofilms/*growth &amp; development ; DNA, Bacterial/analysis/*metabolism ; *Ecosystem ; Escherichia coli O157/genetics/*growth &amp; development ; Fresh Water/microbiology ; Heat-Shock Response ; Hot Temperature ; Polymerase Chain Reaction ; Salmonella typhimurium/genetics/*growth &amp; development ; Water Supply ; }, abstract = {The distinction between viable and dead bacterial cells poses a major challenge in microbial diagnostics. Due to the persistence of DNA in the environment after cells have lost viability, DNA-based quantification methods overestimate the number of viable cells in mixed populations or even lead to false-positive results in the absence of viable cells. On the other hand, RNA-based diagnostic methods, which circumvent this problem, are technically demanding and suffer from some drawbacks. A promising and easy-to-use alternative utilizing the DNA-intercalating dye ethidium monoazide bromide (EMA) was published recently. This chemical is known to penetrate only into "dead" cells with compromised cell membrane integrity. Subsequent photoinduced cross-linking was reported to inhibit PCR amplification of DNA from dead cells. We provide evidence here that in addition to inhibition of amplification, most of the DNA from dead cells is actually lost during the DNA extraction procedure, probably together with cell debris which goes into the pellet fraction. Exposure of bacteria to increasing stress and higher proportions of dead cells in defined populations led to increasing loss of genomic DNA. Experiments were performed using Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium as model pathogens and using real-time PCR for their quantification. Results showed that EMA treatment of mixed populations of these two species provides a valuable tool for selective removal of DNA of nonviable cells by using conventional extraction protocols. Furthermore, we provide evidence that prior to denaturing gradient gel electrophoresis, EMA treatment of a mature mixed-population drinking-water biofilm containing a substantial proportion of dead cells can result in community fingerprints dramatically different from those for an untreated biofilm. The interpretation of such fingerprints can have important implications in the field of microbial ecology.}, }
@article {pmid16514153, year = {2006}, author = {Kessi, J}, title = {Enzymic systems proposed to be involved in the dissimilatory reduction of selenite in the purple non-sulfur bacteria Rhodospirillum rubrum and Rhodobacter capsulatus.}, journal = {Microbiology (Reading, England)}, volume = {152}, number = {Pt 3}, pages = {731-743}, doi = {10.1099/mic.0.28240-0}, pmid = {16514153}, issn = {1350-0872}, mesh = {Buthionine Sulfoximine/pharmacology ; Culture Media ; Glutathione/metabolism ; Nitrite Reductases/*metabolism ; Oxidation-Reduction ; Oxidoreductases Acting on Sulfur Group Donors/*metabolism ; Rhodobacter capsulatus/*enzymology/growth &amp; development ; Rhodospirillum rubrum/*enzymology/growth &amp; development ; Sodium Selenite/*metabolism ; }, abstract = {Various enzymic systems, such as nitrite reductase, sulfite reductase and glutathione reductase, have been proposed for, or suspected to be involved in, the reduction of selenite in bacteria. As alphaproteobacteria have been shown to be highly tolerant to transition metal oxyanions, it seemed interesting to investigate the hypothetical involvement of these different enzymes in the reduction of selenite in the purple non-sulfur bacteria Rhodospirillum rubrum and Rhodobacter capsulatus. The hypothetical involvement of nitrite reductase and sulfite reductase in the reduction of selenite in these bacteria was investigated by analysing the effects of nitrite and sulfite amendments on the growth and kinetics of selenite reduction. The reduction of selenite was not concomitant with that of either sulfite or nitrite in Rs. rubrum, suggesting that the reduction pathways operate independently. In Rb. capsulatus, strong interactions were observed between the nitrite reduction and selenite reduction pathways. However, in both organisms, selenite reduction took place during both the growth phase and the stationary phase, indicating that selenite metabolism is constitutively expressed. In contrast, neither nitrite nor sulfite was transformed during stationary phase, suggesting that the metabolism of both ions is induced, which implies that identical reduction pathways for selenite and nitrite or selenite and sulfite are excluded. Buthionine sulfoximine (BSO, S-n-butyl homocysteine sulfoximine), a specific inhibitor of glutathione synthesis, was used to depress the intracellular glutathione level. In stationary-phase cultures of both Rs. rubrum and Rb. capsulatus amended with BSO, the rate of reduction of selenite was slowed, indicating that glutathione may be involved in the dissimilatory reduction of selenite in these organisms. The analysis of the headspace gases of the cultures indicated that the synthesis of methylated selenium compounds was prevented in the presence of 3.0 mM BSO in both organisms, implying that glutathione is also involved in the transformation of selenite to volatile selenium compounds.}, }
@article {pmid16514152, year = {2006}, author = {De Windt, W and Gao, H and Krömer, W and Van Damme, P and Dick, J and Mast, J and Boon, N and Zhou, J and Verstraete, W}, title = {AggA is required for aggregation and increased biofilm formation of a hyper-aggregating mutant of Shewanella oneidensis MR-1.}, journal = {Microbiology (Reading, England)}, volume = {152}, number = {Pt 3}, pages = {721-729}, doi = {10.1099/mic.0.28204-0}, pmid = {16514152}, issn = {1350-0872}, mesh = {*Bacterial Adhesion ; Bacterial Proteins/genetics/*metabolism ; Biofilms/*growth &amp; development ; *Gene Expression Regulation, Bacterial ; *Mutation ; Oligonucleotide Array Sequence Analysis ; Proteomics ; Shewanella/genetics/growth &amp; development/metabolism/*physiology ; }, abstract = {Shewanella oneidensis COAG, a hyper-aggregating mutant of MR-1, was isolated from a rifampicin-challenged culture. Compared to the wild-type, COAG exhibited increased biofilm formation on glass carrier material. The role of surface-located proteins in the process of COAG auto-aggregation was confirmed by different proteolytic treatments of the aggregates. All of the tested proteolytic enzymes resulted in deflocculation within 3 h of incubation. In order to examine the altered expression of outer-membrane proteins in COAG, membrane-enriched cell preparations were analysed by proteomics and the protein pattern was compared to that of MR-1. From the proteomics results, it was hypothesized that the agglutination protein AggA, associated with the secretion of a putative RTX protein, was involved in the hyper-aggregating phenotype. These results were confirmed with a DNA microarray study of COAG versus MR-1. An insertional mutation in the S. oneidensis COAG aggA locus resulted in loss of the hyper-aggregating properties and the increased biofilm-forming capability. The insertional mutation resulted in strongly decreased attachment during the initial stage of biofilm formation. By complementing this mutation with the vector pCM62, expressing the aggA gene, this effect could be nullified and biofilm formation was restored to at least the level of the MR-1 wild-type.}, }
@article {pmid16511969, year = {2005}, author = {Wejse, PL and Ingvorsen, K and Mortensen, KK}, title = {Salinity and temperature effects on accessibility of soluble and cross-linked insoluble xylans to endo-xylanases.}, journal = {IUBMB life}, volume = {57}, number = {11}, pages = {761-763}, doi = {10.1080/15216540500364271}, pmid = {16511969}, issn = {1521-6543}, mesh = {Endo-1,4-beta Xylanases/*physiology ; Gram-Negative Aerobic Bacteria/enzymology ; Sodium Chloride ; Solubility ; Substrate Specificity ; Temperature ; Xylans/*metabolism ; }, abstract = {Different responses to salinity were observed for an extremely halotolerant endo-xylanase when assayed with soluble birchwood glucoronoxylan and cross-linked dyed insoluble birchwood glucoronoxylan. Shrinking of insoluble xylan particles due to increased ionic strength is proposed as the explanation. Temperature affected the xylanase activity measurement on the insoluble xylan greatly, likely due to increased enzyme accessible surface of the substrate at high temperatures.}, }
@article {pmid16491305, year = {2006}, author = {Dick, J and De Windt, W and De Graef, B and Saveyn, H and Van der Meeren, P and De Belie, N and Verstraete, W}, title = {Bio-deposition of a calcium carbonate layer on degraded limestone by Bacillus species.}, journal = {Biodegradation}, volume = {17}, number = {4}, pages = {357-367}, doi = {10.1007/s10532-005-9006-x}, pmid = {16491305}, issn = {0923-9820}, mesh = {Absorption ; Bacillus/chemistry/*metabolism ; *Biodegradation, Environmental ; Biofilms ; Calcium/chemistry ; Calcium Carbonate/*chemistry ; Hydrogen-Ion Concentration ; Microscopy, Electron, Scanning ; Models, Chemical ; Polymers/*chemistry ; Time Factors ; Urea/chemistry ; Water/chemistry ; }, abstract = {To obtain a restoring and protective calcite layer on degraded limestone, five different strains of the Bacillus sphaericus group and one strain of Bacillus lentus were tested for their ureolytic driven calcium carbonate precipitation. Although all the Bacillus strains were capable of depositing calcium carbonate, differences occurred in the amount of precipitated calcium carbonate on agar plate colonies. Seven parameters involved in the process were examined: calcite deposition on limestone cubes, pH increase, urea degrading capacity, extracellular polymeric substances (EPS)-production, biofilm formation, zeta-potential and deposition of dense crystal layers. The strain selection for optimal deposition of a dense CaCO(3) layer on limestone, was based on decrease in water absorption rate by treated limestone. Not all of the bacterial strains were effective in the restoration of deteriorated Euville limestone. The best calcite precipitating strains were characterised by high ureolytic efficiency, homogeneous calcite deposition on limestone cubes and a very negative zeta-potential.}, }
@article {pmid16489412, year = {2006}, author = {Rodrigues, DF and Goris, J and Vishnivetskaya, T and Gilichinsky, D and Thomashow, MF and Tiedje, JM}, title = {Characterization of Exiguobacterium isolates from the Siberian permafrost. Description of Exiguobacterium sibiricum sp. nov.}, journal = {Extremophiles : life under extreme conditions}, volume = {10}, number = {4}, pages = {285-294}, pmid = {16489412}, issn = {1431-0651}, mesh = {Bacillaceae/*classification/*cytology/genetics/isolation &amp; purification ; *Ecosystem ; Phylogeny ; Siberia ; *Soil Microbiology ; }, abstract = {Three Gram-positive bacterial strains, 7-3, 255-15 and 190-11, previously isolated from Siberian permafrost, were characterized and taxonomically classified. These microorganisms are rod-shaped, facultative aerobic, motile with peritrichous flagella and their growth ranges are from -2.5 to 40 degrees C. The chemotaxonomic markers indicated that the three strains belong to the genus Exiguobacterium. Their peptidoglycan type was A3alpha L-Lys-Gly. The predominant menaquinone detected in all three strains was MK7. The polar lipids present were phosphatidyl-glycerol, diphosphatidyl-glycerol and phosphatidyl-ethanolamine. The major fatty acids were iso-C13:0, anteiso-C13:0, iso-C15:0, C16:0 and iso-C17:0. Phylogenetic analysis based on 16S rRNA and six diverse genes, gyrB (gyrase subunit B), rpoB (DNA-directed RNA polymerase beta subunit), recA (homologous recombination), csp (cold shock protein), hsp70 (ClassI-heat shock protein-chaperonin) and citC (isocitrate dehydrogenase), indicated that the strains were closely related to Exiguobacterium undae (DSM 14481(T)) and Exiguobacterium antarcticum (DSM 14480(T)). On the basis of the phenotypic characteristics, phylogenetic data and DNA-DNA reassociation data, strain 190-11 was classified as E. undae, while the other two isolates, 7-3 and 255-15, comprise a novel species, for which the name Exiguobacterium sibiricum sp. nov. is proposed.}, }
@article {pmid16488461, year = {2006}, author = {Connaughton, S and Collins, G and O'Flaherty, V}, title = {Development of microbial community structure and actvity in a high-rate anaerobic bioreactor at 18 degrees C.}, journal = {Water research}, volume = {40}, number = {5}, pages = {1009-1017}, doi = {10.1016/j.watres.2005.12.026}, pmid = {16488461}, issn = {0043-1354}, mesh = {Anaerobiosis ; Archaea/genetics/*metabolism ; Bacteria/genetics/*metabolism ; *Bioreactors ; DNA, Bacterial/genetics ; Methane/metabolism ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sewage ; *Temperature ; Time Factors ; }, abstract = {Anaerobic digestion in the psychrophilic (< 20 degrees C) or sub-mesophilic temperature range has recently been proven as an effective treatment option for the mineralization of a wide variety of problematic wastewaters. In this study, an expanded granular sludge bed-anaerobic filter (EGSB-AF) bioreactor was seeded with a full-scale, mesophilic sludge and employed to evaluate the long-term operational potential, and underlying microbial ecology, of this approach for the treatment of a medium-strength (5 g chemical oxygen demand [COD] l(-1)), synthetic, volatile fatty acid-based wastewater. Throughout the trial period of 625 days, extended intervals of consistently stable and efficient wastewater treatment were sustained. These results were highlighted by a short start-up period (21 d), low hydraulic retention times (4.88h), high organic (up to 24.64kg CODm(-3)d(-1)), and volumetric loading rates (up to 4.92 m3 m(-3) d(-1)). A stable, well-settling granular sludge bed was maintained in the bioreactor for the majority of the trial; however, reduced treatment efficiency and biomass washout were observed at an imposed OLR of 36.96 kg COD m(-3) d(-1). The microbial biomass in the bioreactor was investigated using maximum specific methanogenic activity assays and polymerase chain reaction-denaturing gradient gel electrophoresis. A temporal succession of both the bacterial and archaeal populations was noted during the trial, compared to the seed sludge, in response to bioreactor operation at lower temperatures, loading rate increases and to VFA accumulation in the bioreactor. During the trial, an increased contribution of hydrogenotrophic methanogenesis as a pathway of methane production was observed, along with the overall emergence of a highly active psychrotolerent-though still mesophilic biomass.}, }
@article {pmid16478445, year = {2006}, author = {Gleeson, D and McDermott, F and Clipson, N}, title = {Structural diversity of bacterial communities in a heavy metal mineralized granite outcrop.}, journal = {Environmental microbiology}, volume = {8}, number = {3}, pages = {383-393}, doi = {10.1111/j.1462-2920.2005.00903.x}, pmid = {16478445}, issn = {1462-2912}, mesh = {Bacteria/classification/genetics/*growth &amp; development ; *Biodiversity ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Geologic Sediments/*microbiology ; Metals, Heavy/*analysis ; Microscopy, Electron, Scanning ; Minerals/analysis ; Molecular Sequence Data ; Multivariate Analysis ; Ribotyping ; Sequence Analysis, DNA ; *Silicon Dioxide/chemistry ; *Soil Microbiology ; Statistics as Topic ; }, abstract = {This laboratory study of a variably mineralized and hydrothermally altered granite outcrop investigated the influences of rock-surface chemistry and heavy metal content on resident bacterial populations. Results indicated that elevated heavy metal concentrations had a profound impact on bacterial community structure, with strong relationships found between certain ribotypes and particular chemical/heavy metal elements. Automated ribosomal intergenic sequence analysis (ARISA) was used to assess the nature and extent of bacterial diversity, and this was combined with chemical analysis and multivariate statistics to identify the main geochemical factors influencing bacterial community structure. A randomization test revealed significant changes in bacterial structure between samples, while canonical correspondence analysis (CCA) related each individual ARISA profile to linear combinations of the chemical variables (mineralogy, major element and heavy metal concentrations) revealing the geochemical factors that correlated with changes in the ARISA data. anova was performed to further explore interactions between individual ribotypes and chemical/heavy metal composition, and revealed that a high proportion of ribotypes correlated significantly with heavy metals.}, }
@article {pmid16476182, year = {2006}, author = {Lanciotti, R and Vannini, L and Patrignani, F and Iucci, L and Vallicelli, M and Ndagijimana, M and Guerzoni, ME}, title = {Effect of high pressure homogenisation of milk on cheese yield and microbiology, lipolysis and proteolysis during ripening of Caciotta cheese.}, journal = {The Journal of dairy research}, volume = {73}, number = {2}, pages = {216-226}, doi = {10.1017/S0022029905001640}, pmid = {16476182}, issn = {0022-0299}, mesh = {Animals ; Cattle ; Cheese/*analysis/*microbiology/standards ; Colony Count, Microbial/veterinary ; Fats/metabolism ; Female ; Fermentation ; Food Handling/*methods ; Food Microbiology ; Food Technology ; *Hydrostatic Pressure ; Lipolysis ; Milk/*chemistry/microbiology ; Milk Proteins/metabolism ; Taste ; Time Factors ; }, abstract = {The principal aim of this work was to compare Caciotta cheeses obtained from cow milk previously subjected to high pressure homogenisation (HPH) at 100 MPa with those produced from raw (R) or heat-treated (P) cow milk. HPH had both direct and indirect effects on cheese characteristics and their evolution during ripening. In particular, HPH treatment of milk induced a significant increase of the cheese yield; moreover, it affected the microbial ecology of both curd and cheese. Compared with the thermal treatment, the HPH treatment resulted in a decrease of about one log cfu/g of yeast and lactobacilli cell loads of the curd. The initial milk treatment also affected the evolution over time and the levels attained at the end of ripening of all the microbial groups studied. In fact, lactobacilli, microstaphylococci and yeast cell loads remained at lower levels in the cheeses obtained from HPH milk with respect to the other cheese types over the whole ripening period. Moreover, HPH of milk induced marked and extensive lipolysis. Cheeses from HPH milk showed the presence of high amounts of free fatty acids immediately after brining. The electrophoretic patterns of the different cheese types showed that Caciotta made from HPH-treated milk was characterized by a more extensive and faster proteolysis as well as a significant modification of its volatile molecule profile. The results obtained and the sensory analysis indicated that HPH treatment of milk was able to differentiate Caciotta cheese or to modify its ripening patterns.}, }
@article {pmid16475342, year = {2005}, author = {Yu, CP and Chu, KH}, title = {A quantitative assay for linking microbial community function and structure of a naphthalene-degrading microbial consortium.}, journal = {Environmental science &amp; technology}, volume = {39}, number = {24}, pages = {9611-9619}, doi = {10.1021/es051024e}, pmid = {16475342}, issn = {0013-936X}, mesh = {Bacillus thuringiensis/isolation &amp; purification/metabolism ; Bacteria/classification/*metabolism ; Biodegradation, Environmental ; DNA/chemistry/metabolism ; Environmental Monitoring/methods ; Escherichia coli/isolation &amp; purification/metabolism ; Isotope Labeling/methods ; Naphthalenes/*metabolism ; RNA, Ribosomal, 16S/analysis/genetics ; *Soil Microbiology ; *Water Microbiology ; }, abstract = {A comprehensive culture-independent assay, called Q-FAST, was developed for concurrent identification and quantification of active microorganisms involved a specific function in a given microbial community. The development of Q-FAST was achieved by integrating the concept of stable isotope probing technique into a new quantitative fingerprinting assay called real-time-t-RFLP for microbial community structure analysis. The Q-FAST was successfully validated by using a three-member artificial microbial community containing a known naphthalene-utilizing bacterium (Pseudomonas putida G7) and two nonnaphthalene-degrading bacteria (Escherichia coli and Bacillus thuringiensis). The application of Q-FAST to identify and quantify a guild of naphthalene-utilizing microorganisms in soils revealed the involvement of eight members, with six members relating to several phylogenetic groups of eubacteria (three in beta-proteobacteria, two in gamma-proteobacteria, and one in genera Intrasporangium of Gram-positive bacteria) and two members showing no close phylogenetic affiliation to any known bacterial sequences deposited in GenBank. The quantity of three members belonging to beta-proteobacteria accounted for 34% of total 16S rDNA copies measured from the "heavier" fraction of DNA that was contributed from the DNA of microorganisms capable of incorporating 13C-labeled naphthalene into their genetic biomarkers. The other five members composed 66% of total 16S rDNA copies of active naphthalene-utilizing populations measured. Offering a powerful tool for studying microbial ecology, Q-FAST thus opens a new avenue for deeper exploration of microbial-mediated processes, mainly the quantitative relationship between microbial diversity and microbial activity in a given environment.}, }
@article {pmid16466384, year = {2006}, author = {Collins, G and Mahony, T and O'Flaherty, V}, title = {Stability and reproducibility of low-temperature anaerobic biological wastewater treatment.}, journal = {FEMS microbiology ecology}, volume = {55}, number = {3}, pages = {449-458}, doi = {10.1111/j.1574-6941.2005.00034.x}, pmid = {16466384}, issn = {0168-6496}, mesh = {Anaerobiosis ; Bioreactors ; Citric Acid ; *Cold Temperature ; Crenarchaeota/genetics/*growth &amp; development/isolation &amp; purification ; DNA, Ribosomal/analysis ; Industrial Waste ; Methane/metabolism ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Proteobacteria/genetics/*growth &amp; development/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sewage ; Temperature ; Waste Disposal, Fluid/*methods ; }, abstract = {The reproducibility of low-temperature anaerobic biological wastewater treatment trials was evaluated. Two identical anaerobic expanded granular sludge bed bioreactors were used to treat synthetic volatile fatty acid-based industrial wastewater under ambient conditions (18-20 degrees C) and to investigate the effect of various environmental perturbations on reactor performance and microbial community dynamics, which were assessed by chemical oxygen demand removal or effluent volatile fatty acid determination and terminal restriction fragment length polymorphism analysis, respectively. Methanogenic activity was monitored using specific methanogenic activity assays. Reactor performance and microbial community dynamics were each well replicated between Reactor 1 and Reactor 2. Archaeal dynamics, in particular, were associated with reactor operating parameters. Terminal restriction fragment length polymorphism data suggested dynamic acetoclastic and hydrogenophilic methanogenic populations and were in agreement with temporal specific methanogenic activity data. Putative psychrophilic populations were observed in anaerobic bioreactor sludge for the first time.}, }
@article {pmid16466373, year = {2006}, author = {Ward, N}, title = {New directions and interactions in metagenomics research.}, journal = {FEMS microbiology ecology}, volume = {55}, number = {3}, pages = {331-338}, doi = {10.1111/j.1574-6941.2005.00055.x}, pmid = {16466373}, issn = {0168-6496}, mesh = {Animals ; *Bacteria/genetics/growth &amp; development/isolation &amp; purification/metabolism ; Computational Biology ; *Ecosystem ; *Environmental Microbiology ; Genome, Bacterial ; Genomics/*methods ; Humans ; Mice ; Research ; }, abstract = {Metagenomics, which aims to access the genomic potential of an environmental sample directly, is a burgeoning area that is generating enormous amounts of biological information. An examination of recent metagenomics literature reveals the discipline to be heading in new and interesting directions, including the investigation of the normal flora of mammals, analysis of ancient genomes, and exploration of the distribution of novel pathways. In addition, the development of new bioinformatics approaches and tools is allowing innovative mining of both existing and new data. Finally, there are indications that the integration of metagenomics with complementary approaches in microbial ecology is beginning.}, }
@article {pmid16463134, year = {2006}, author = {Becker, JM and Parkin, T and Nakatsu, CH and Wilbur, JD and Konopka, A}, title = {Bacterial activity, community structure, and centimeter-scale spatial heterogeneity in contaminated soil.}, journal = {Microbial ecology}, volume = {51}, number = {2}, pages = {220-231}, pmid = {16463134}, issn = {0095-3628}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Chromium ; *Ecosystem ; Electrophoresis, Polyacrylamide Gel ; Environmental Monitoring ; Indiana ; Lead ; Polymerase Chain Reaction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Soil Pollutants/*analysis ; }, abstract = {In an anthropogenically disturbed soil (88% sand, 8% silt, 4% clay), 150-mg samples were studied to examine the fine-scale relationship of bacterial activity and community structure to heavy metal contaminants. The soils had been contaminated for over 40 years with aromatic solvents, Pb, and Cr. Samples from distances of <1, 5, 15, and 50 cm over a depth range of 40-90 cm underwent a sequential analysis to determine metabolic potential (from 14C glucose mineralization), bacterial community structure [using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)], and total extractable Pb and Cr levels. Metabolic potential varied by as much as 10,000-fold in samples <1 cm apart; log-log plots of metal concentration and microbial metabolic potential showed no correlation with each other. Overall, metal concentrations ranged from 9 to 29,000 mg kg(-1) for Pb and from 3 to 8500 mg kg(-1) for Cr with small zones of high contamination present. All regions exhibited variable metal concentrations, with some soil samples having 30-fold differences in metal concentration in sites <1 cm apart. Geostatistical analysis revealed a strong spatial dependence for all three parameters tested (metabolic activity, Pb, and Cr levels) with a range up to 30 cm. Kriging maps showed that in zones of high metal, the corresponding metabolic activity was low suggesting that metals negatively impacted the microbial community. PCR-DGGE analysis revealed that diverse communities were present in the soils with a random distribution of phylotypes throughout the sampling zones. These results suggest the presence of spatially isolated microbial communities within the soil profile.}, }
@article {pmid16463133, year = {2006}, author = {Auguet, JC and Montanié, H and Lebaron, P}, title = {Structure of virioplankton in the Charente Estuary (France): transmission electron microscopy versus pulsed field gel electrophoresis.}, journal = {Microbial ecology}, volume = {51}, number = {2}, pages = {197-208}, pmid = {16463133}, issn = {0095-3628}, mesh = {Capsid/chemistry ; *Electrophoresis, Gel, Pulsed-Field ; Environmental Monitoring/methods ; France ; Genome, Viral/genetics ; *Microscopy, Electron ; Plankton ; Rivers/*virology ; Seasons ; Seawater/*microbiology/*virology ; Viruses/genetics/*isolation &amp; purification/ultrastructure ; *Water Microbiology ; }, abstract = {Changes in the composition of viral communities were investigated along a salinity gradient and at different times by means of transmission electron microscopy (TEM) and pulsed field gel electrophoresis (PFGE). Samples were collected in fresh (Charente River), estuarine (Charente Estuary), and coastal (Pertuis d'Antioche, French Atlantic coast) waters. Both methods revealed similar patterns in viral community structure with a dominance of small viral particles (capsid and genome size). Viruses with a head size below 65 nm made up 71 +/- 5% of total virus-like particles, and virus-like genomes (VLG) below 100 kb accounted for 89 +/- 9% of total VLG. Despite this apparent stability of virioplankton composition over spatial scale (salinity gradient), the occurrence of large viruses (capsid and genome size) in estuarine and seawater samples indicated the presence of viral populations specific to a geographical location. Temporal changes in the structure (capsid and genome size) of viral communities were more pronounced than those reported at the spatial scale. From January to May 2003, seasonal changes in viral abundance and bacterial production occurred concomitantly with an increase in viral genomic diversity (richness), suggesting that virioplankton composition was strongly linked to changes in microbial activity and/or in the structure of the host communities. Although PFGE and TEM yielded complementary results in the description of virioplankton structures, it seems that the use of PFGE alone should be enough for the monitoring of community changes.}, }
@article {pmid16463132, year = {2006}, author = {Joynt, J and Bischoff, M and Turco, R and Konopka, A and Nakatsu, CH}, title = {Microbial community analysis of soils contaminated with lead, chromium and petroleum hydrocarbons.}, journal = {Microbial ecology}, volume = {51}, number = {2}, pages = {209-219}, pmid = {16463132}, issn = {0095-3628}, mesh = {Bacteria/chemistry/classification/genetics/*isolation &amp; purification ; Carbon/analysis ; Chromium ; Ecosystem ; Fatty Acids/analysis ; Indiana ; Lead ; Molecular Sequence Data ; Petroleum ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Soil/analysis ; *Soil Microbiology ; *Soil Pollutants ; Species Specificity ; }, abstract = {The impact on the microbial community of long-term environmental exposure to metal and organic contamination was investigated. Twenty-four soil samples were collected along a transect dug in soils contaminated with road paint and paint solvents, mainly toluene. Chemical analysis along the transect revealed a range from high to low concentrations of metals (lead and chromium) and organic solvent compounds. Principal components analysis of microbial community structure based on denaturing gradient gel electrophoresis of the V3 region of the 16S rRNA gene and fatty acid methyl esters derived from phospholipids (phospholipid fatty acid analysis) showing samples with similar fingerprints also had similar contaminant concentrations. There was also a weak positive correlation between microbial biomass and the organic carbon concentration. Results indicated that microbial populations are present despite some extreme contaminant levels in this mixed-waste contaminated site. Nucleotide sequence determination of the 16S rRNA gene indicated the presence of phylogenetically diverse bacteria belonging to the alpha-, beta-, gamma-, and delta-Proteobacteria, the high and low G + C Gram-positive bacteria, green nonsulfur, OP8, and others that did not group within a described division. This indicates that soils contaminated with both heavy metals and hydrocarbons for several decades have undergone changes in community composition, but still contain a phylogenetically diverse group of bacteria (including novel phylotypes) that warrant further investigation.}, }
@article {pmid16463131, year = {2006}, author = {Baeseman, JL and Smith, RL and Silverstein, J}, title = {Denitrification potential in stream sediments impacted by acid mine drainage: effects of pH, various electron donors, and iron.}, journal = {Microbial ecology}, volume = {51}, number = {2}, pages = {232-241}, pmid = {16463131}, issn = {0095-3628}, mesh = {Acids/*adverse effects ; Biodegradation, Environmental ; Colorado ; Ecosystem ; Electrons ; Environmental Monitoring ; Geologic Sediments/analysis/*microbiology ; Hydrogen-Ion Concentration ; Industrial Waste/*adverse effects ; Iron Compounds ; *Mining ; Nitrates/analysis/metabolism ; Nitrogen/*metabolism ; Water Pollutants, Chemical/*adverse effects ; }, abstract = {Acid mine drainage (AMD) contaminates thousands of kilometers of stream in the western United States. At the same time, nitrogen loading to many mountain watersheds is increasing because of atmospheric deposition of nitrate and increased human use. Relatively little is known about nitrogen cycling in acidic, heavy-metal-laden streams; however, it has been reported that one key process, denitrification, is inhibited under low pH conditions. The objective of this research was to investigate the capacity for denitrification in acidified streams. Denitrification potential was assessed in sediments from several Colorado AMD-impacted streams, ranging from pH 2.60 to 4.54, using microcosm incubations with fresh sediment. Added nitrate was immediately reduced to nitrogen gas without a lag period, indicating that denitrification enzymes were expressed and functional in these systems. First-order denitrification potential rate constants varied from 0.046 to 2.964 day(-1). The pH of the microcosm water increased between 0.23 and 1.49 pH units during denitrification. Additional microcosm studies were conducted to examine the effects of initial pH, various electron donors, and iron (added as ferrous and ferric iron). Decreasing initial pH decreased denitrification; however, increasing pH had little effect on denitrification rates. The addition of ferric and ferrous iron decreased observed denitrification potential rate constants. The addition of glucose and natural organic matter stimulated denitrification potential. The addition of hydrogen had little effect, however, and denitrification activity in the microcosms decreased after acetate addition. These results suggest that denitrification can occur in AMD streams, and if stimulated within the environment, denitrification might reduce acidity.}, }
@article {pmid16461883, year = {2006}, author = {Weng, L and Rubin, EM and Bristow, J}, title = {Application of sequence-based methods in human microbial ecology.}, journal = {Genome research}, volume = {16}, number = {3}, pages = {316-322}, doi = {10.1101/gr.3676406}, pmid = {16461883}, issn = {1088-9051}, support = {HL007279F/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/pathogenicity ; Bacterial Infections/diagnosis ; Base Sequence ; Biodiversity ; *Ecology ; Environmental Microbiology/*standards ; Humans ; Models, Biological ; Molecular Sequence Data ; Sequence Analysis, DNA/*methods ; Viruses/pathogenicity ; }, abstract = {Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for many years, and the development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever-greater detail. Despite the widespread application of these new techniques to the characterization of uncultivated microbes and microbial communities in the environment, their application to human health and disease has lagged. Because DNA-based techniques for defining uncultured microbes allow not only cataloging of microbial diversity but also insight into microbial functions, investigators are beginning to apply these tools to the microbial communities that abound on and within us, in what has aptly been called "the second Human Genome Project." In this review we discuss the sequence-based methods for microbial analysis that are currently available and their application to identify novel human pathogens, improve diagnosis of known infectious diseases, and advance understanding of our relationship with microbial communities that normally reside in and on the human body.}, }
@article {pmid16459842, year = {2005}, author = {Chauret, C and Volk, C and Stover, L and Dykstra, TS and Andrews, RC and Gagnon, GA}, title = {Effect of disinfectants on microbial ecology in model distribution systems.}, journal = {Journal of water and health}, volume = {3}, number = {4}, pages = {359-369}, doi = {10.2166/wh.2005.050}, pmid = {16459842}, issn = {1477-8920}, mesh = {Bacteria/*drug effects ; Biofilms/*drug effects ; Chloramines ; Chlorides/*pharmacology ; Chlorine Compounds/*pharmacology ; Colony Count, Microbial ; Disinfectants/*pharmacology ; Oxides ; Water Purification/instrumentation/*methods ; Water Supply ; }, abstract = {This research was conducted to assess the impact of various disinfectants on bacterial water quality within model distribution systems (i.e. annular reactors). After colonization with non-disinfected water, annular reactors were treated with relatively low doses of chlorine (0.4 mg/l), chlorine dioxide (0.15 mg/l), or chloramines (0.9 mg/l). Under the tested conditions, bacterial inactivation varied as a function of disinfectant type (ranking by efficiency per mg of oxidant: ClO2 > Cl2 > ClNH2) and sample type (bulk water vs. biofilm). Depending on the disinfectant, the log inactivation of suspended and attached bacteria were 0.7-1.2 and 0.5-1.0, respectively. The characterization of microbial communities in drinking water can be performed using biochemical and/or molecular methods. In this study, biochemical tests were used, showing that pseudomonad and pseudomonad-like bacteria, as in other studies, were the most predominant micro-organisms (e.g. Pseudomonas fluorescens, Brevundimonas vescularis). The ratio Gram-positive to Gram-negative organisms was 1 to 3. No drastic differences were observed between the non-treated and disinfected pipes. Based on the bacteriological data presented in these experiments, chlorine dioxide represents an alternative to chlorine for certain distribution systems.}, }
@article {pmid16457898, year = {2006}, author = {Leveau, JH and Gerards, S and Fritsche, K and Zondag, G and van Veen, JA}, title = {Genomic flank-sequencing of plasposon insertion sites for rapid identification of functional genes.}, journal = {Journal of microbiological methods}, volume = {66}, number = {2}, pages = {276-285}, doi = {10.1016/j.mimet.2005.12.010}, pmid = {16457898}, issn = {0167-7012}, mesh = {3' Flanking Region/genetics ; Base Sequence ; Cloning, Molecular/*methods ; DNA Transposable Elements/*genetics ; DNA, Bacterial/genetics ; Gene Library ; Gram-Negative Bacteria/*genetics ; Molecular Sequence Data ; Mutagenesis, Insertional/*methods ; Sequence Analysis, DNA ; }, abstract = {Plasposons are modified mini-Tn5 transposons for random mutagenesis of Gram-negative bacteria. Their unique design allows for the rescue cloning and sequencing of DNA that flanks insertion sites in plasposon mutants. However, this process can be laborious and time-consuming, as it involves genomic DNA isolation, restriction endonuclease treatment, subsequent religation, transformation of religated DNA into an Escherichia coli host, and re-isolation as a plasmid, which is then used as a template in sequencing reactions with primers that read from the plasposon ends into the flanking DNA regions. We describe here a method that produces flanking DNA sequences directly from genomic DNA that is isolated from plasposon mutants. By eliminating the need for rescue cloning, our protocol dramatically reduces time and effort, typically by 2 to 3 working days, as well as costs associated with digestion, ligation, transformation, and plasmid isolation. Furthermore, it allows for a high-throughput automated approach to analysis of the plasposome, i.e. the collective set of plasposon insertion sites in a plasposon mutant library. We have tested the utility of genomic flank-sequencing on three plasposon mutants of the soil bacterium Collimonas fungivorans with abolished ability to degrade chitin.}, }
@article {pmid16453201, year = {2006}, author = {Vujanovic, V and Hamel, C and Yergeau, E and St-Arnaud, M}, title = {Biodiversity and biogeography of Fusarium species from northeastern North American asparagus fields based on microbiological and molecular approaches.}, journal = {Microbial ecology}, volume = {51}, number = {2}, pages = {242-255}, pmid = {16453201}, issn = {0095-3628}, mesh = {*Agriculture ; Asparagus Plant/*microbiology ; DNA, Fungal ; Flowering Tops/microbiology ; Fusarium/classification/genetics/*isolation &amp; purification ; Molecular Sequence Data ; Plant Roots/microbiology ; Plant Stems/microbiology ; Quebec ; Soil Microbiology ; Species Specificity ; }, abstract = {Sixteen Fusarium species were recovered from 52 asparagus commercial fields, representing all major ecological (edaphic and climatic) area of asparagus production in the province of Québec, eastern Canada. This study extends our understanding of the geographic range of these species. It also provides climatological and edaphic properties linked to community changes and adaptations. Fusarium oxysporum and F. proliferatum were omnipresent and abundant in all five ecological area under study, whereas F. redolens was less frequently found. Species of Fusarium that produce carmine red pigmentation on potato dextrose agar, i.e., F. acuminatum, F. avenaceum, etc., were common at the northern limit of asparagus production. Abundance of red Fusarium species corresponded with a low isolation frequency of F. proliferatum. Nevertheless, F. proliferatum had a high recovery rate throughout Québec asparagus growing areas, under climatic conditions as cold as those of northern Europe where this species is uncommon in asparagus fields. In the light of these results, redefinition of the geographical distribution of F. proliferatum in asparagus fields is proposed. Intraspecific molecular differences in F. proliferatum and F. oxysporum were detected in the EF-1 alpha sequences and compared with well-characterized strains of North America.}, }
@article {pmid16453200, year = {2006}, author = {Veluci, RM and Neher, DA and Weicht, TR}, title = {Nitrogen fixation and leaching of biological soil crust communities in mesic temperate soils.}, journal = {Microbial ecology}, volume = {51}, number = {2}, pages = {189-196}, pmid = {16453200}, issn = {0095-3628}, mesh = {Biodegradation, Environmental ; *Bryophyta ; *Ecosystem ; *Lichens ; Nitrates/*metabolism ; Nitrogen Fixation ; Ohio ; Quaternary Ammonium Compounds/analysis/metabolism ; *Soil Microbiology ; Temperature ; Water ; }, abstract = {Biological soil crust is composed of lichens, cyanobacteria, green algae, mosses, and fungi. Although crusts are a dominant source of nitrogen (N) in arid ecosystems, this study is among the first to demonstrate their contribution to N availability in xeric temperate habitats. The study site is located in Lucas County of Northwest Ohio. Using an acetylene reduction technique, we demonstrated potential N fixation for these crusts covering sandy, acidic, low N soil. Similar fixation rates were observed for crust whether dominated by moss, lichen, or bare soil. N inputs from biological crusts in northwestern Ohio are comparable to those in arid regions, but contribute substantially less N than by atmospheric deposition. Nitrate and ammonium leaching from the crust layer were quantified using ion exchange resin bags inserted within intact soil cores at 4 cm depth. Leaching of ammonium was greater and nitrate less in lichen than moss crusts or bare soil, and was less than that deposited from atmospheric sources. Therefore, biological crusts in these mesic, temperate soils may be immobilizing excess ammonium and nitrate that would otherwise be leached through the sandy soil. Moreover, automated monitoring of microclimate in the surface 7 cm of soil suggests that moisture and temperature fluctuations in soil are moderated under crust compared to bare soil without crust. We conclude that biological crusts in northwestern Ohio contribute potential N fixation, reduce N leaching, and moderate soil microclimate.}, }
@article {pmid16448419, year = {2006}, author = {Le Quéré, A and Eriksen, KA and Rajashekar, B and Schützendübel, A and Canbäck, B and Johansson, T and Tunlid, A}, title = {Screening for rapidly evolving genes in the ectomycorrhizal fungus Paxillus involutus using cDNA microarrays.}, journal = {Molecular ecology}, volume = {15}, number = {2}, pages = {535-550}, doi = {10.1111/j.1365-294X.2005.02796.x}, pmid = {16448419}, issn = {0962-1083}, mesh = {Analysis of Variance ; Basidiomycota/genetics ; *Evolution, Molecular ; Expressed Sequence Tags ; Fluorescence ; Gene Dosage ; Gene Duplication ; *Genes, Fungal ; Genetic Variation ; In Situ Hybridization, Fluorescence ; Models, Genetic ; Mycorrhizae/*genetics ; Oligonucleotide Array Sequence Analysis/*methods ; }, abstract = {We have examined the variations in gene content and sequence divergence that could be associated with symbiotic adaptations in the ectomycorrhizal fungus Paxillus involutus and the closely related species Paxillus filamentosus. Strains with various abilities to form mycorrhizae were analysed by comparative genomic hybridizations using a cDNA microarray containing 1076 putative unique genes of P. involutus. To screen for genes diverging at an enhanced and presumably non-neutral rate, we implemented a simple rate test using information from both the variations in hybridizations signal and data on sequence divergence of the arrayed genes relative to the genome of Coprinus cinereus. C. cinereus is a free-living saprophyte and is the closest evolutionary relative to P. involutus that has been fully sequenced. Approximately 17% of the genes investigated were detected as rapidly diverging within Paxillus. Furthermore, 6% of the genes varied in copy numbers between the analysed strains. Genome rearrangements associated with this variation including duplications and deletions may also play a role in adaptive evolution. The cohort of divergent and duplicated genes showed an over-representation of either orphans, genes whose products are located at membranes, or genes encoding for components of stress/defence reactions. Some of the identified genomic changes may be associated with the variation in host specificity of ectomycorrhizal fungi. The proposed procedure could be generally applicable to screen for rapidly evolving genes in closely related strains or species where at least one has been sequenced or characterized by expressed sequence tag analysis.}, }
@article {pmid16437710, year = {2005}, author = {Yang, SC and Chen, JY and Shang, HF and Cheng, TY and Tsou, SC and Chen, JR}, title = {Effect of synbiotics on intestinal microflora and digestive enzyme activities in rats.}, journal = {World journal of gastroenterology}, volume = {11}, number = {47}, pages = {7413-7417}, pmid = {16437710}, issn = {1007-9327}, mesh = {Animal Feed ; Animals ; *Bifidobacterium ; Intestines/*enzymology/*microbiology ; *Lactobacillus ; Male ; Probiotics/*pharmacology ; Rats ; Rats, Sprague-Dawley ; }, abstract = {AIM: To investigate the effect of synbiotics, i.e. probiotics and prebiotics mixture, on the gut microbial ecology and digestive enzyme activities in rats.<br><br>METHODS: Forty-eight SD rats weighing about 280 g were used in this study. Rats were divided into three groups according to the contents of probiotics and prebiotics mixture in the feed as control, low and high dose groups. The duration of the experiment was 8 wk.<br><br>RESULTS: Compared with the control group, the fecal Lactobacillus and Bifidobacterium counts were significantly increased and the fecal Coliform organism counts were markedly reduced in the low and high dose groups. Concerning the digestive enzyme activity of jejunum, only lactase activity increased in low dose group. However, significant increase of lipase, lactase, sucrase, and isomaltase activities were observed in high dose group.<br><br>CONCLUSION: Intake of low and high dosages of probiotics and prebiotics mixture significantly improved the ecosystem of the intestinal tract by increasing the probiotics population and digestive enzyme activities in rats.}, }
@article {pmid16437287, year = {2006}, author = {Hewson, I and Fuhrman, JA}, title = {Improved strategy for comparing microbial assemblage fingerprints.}, journal = {Microbial ecology}, volume = {51}, number = {2}, pages = {147-153}, pmid = {16437287}, issn = {0095-3628}, mesh = {Artifacts ; Bacteria/genetics/isolation &amp; purification ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/analysis ; Ecosystem ; Electronic Data Processing/*methods ; Sequence Analysis, DNA ; *Soil Microbiology ; *Water Microbiology ; }, abstract = {Microbial fingerprinting techniques permit the rapid visualization of entire assemblages in single assays, allowing direct comparison of communities in different samples, where the null hypothesis of such analyses is that all samples are the same. The comparison of fingerprints relies upon the precise estimation of all amplified DNA fragment lengths, which correspond to operational taxonomic units (OTU; analogous, but not equal to, a taxon in macroorganism studies). However, computer interpolation of size standards (and consequently OTU size calling) can be imprecise between gel runs, which can lead to imprecise calculation of similarity indices between multiple assemblages. To account for OTU size calling imprecision, all fragments within a range of sizes (a window) can be combined (i.e., "binned") where the window is as wide as the imprecision of OTU size calling. However, artifacts may occur upon binning samples that may cause samples to appear less similar to each other, caused by splitting of OTU between adjacent bin windows. In this work we present an improved binning technique that accounts for OTU size calling imprecision in the comparison of multiple fingerprints. This technique comprises binning all pairwise comparisons in multiple bin window frames, where the starting size of the window (i.e., frame) is shifted by +1 bp for a total of x frames, where x bp is the width of the maximum bin window size in any binning scheme. Pairwise similarity indices between different community fingerprints are calculated for each of the x frames. To best address the null hypothesis of the community comparison, the maximum similarity value of all x frames is then used in downstream analyses to compare the communities. We believe this binning technique provides the most accurate and least biased comparison between different microbial fingerprints.}, }
@article {pmid16436072, year = {2006}, author = {Lievens, B and Claes, L and Vanachter, AC and Cammue, BP and Thomma, BP}, title = {Detecting single nucleotide polymorphisms using DNA arrays for plant pathogen diagnosis.}, journal = {FEMS microbiology letters}, volume = {255}, number = {1}, pages = {129-139}, doi = {10.1111/j.1574-6968.2005.00074.x}, pmid = {16436072}, issn = {0378-1097}, mesh = {DNA, Fungal/*analysis ; Fungi/genetics/*isolation &amp; purification ; Molecular Diagnostic Techniques ; Oligonucleotide Array Sequence Analysis/*methods ; Oligonucleotide Probes ; Plant Diseases/*microbiology ; *Polymorphism, Single Nucleotide ; }, abstract = {The lack of a rapid and reliable means for routine pathogen identification has been one of the main limitations in plant disease management, and has pushed the development of culture-independent, molecular approaches. Currently, DNA array technology is the most suitable technique for high-throughput detection and identification, as well as quantification, of multiple pathogens in a single assay. Closely related pathogens that may have completely different host ranges or pathogenicity often differ in only a single to a few base pairs in genes that may be targeted for identification. Therefore, the ability to discriminate single nucleotide polymorphisms (SNPs) should be pursued in any diagnostic assay. In this paper, we demonstrate the utility of DNA array technology to detect SNPs while accounting for specific criteria such as the position of the mismatch, the sequence of the oligonucleotide, and the length and amount of labeled amplicons that are hybridized. When disregarding mismatches at the extreme ends of the oligonucleotides, cross hybridization to single mismatch oligonucleotides is rare when processing environmental samples that contain genetic material from unknown sources. In addition to plant pathology, this study is relevant for any field of research where DNA arrays are used to detect mutations or polymorphisms, ranging from human diagnostics to environmental microbiology and microbial ecology.}, }
@article {pmid16435170, year = {2006}, author = {Schryver, JC and Brandt, CC and Pfiffner, SM and Palumbo, AV and Peacock, AD and White, DC and McKinley, JP and Long, PE}, title = {Application of nonlinear analysis methods for identifying relationships between microbial community structure and groundwater geochemistry.}, journal = {Microbial ecology}, volume = {51}, number = {2}, pages = {177-188}, pmid = {16435170}, issn = {0095-3628}, mesh = {Bacteria/chemistry/*classification/metabolism ; Biodegradation, Environmental ; Biomarkers/*analysis ; *Ecosystem ; Fatty Acids/analysis ; Industrial Waste/analysis ; Metals/metabolism ; *Neural Networks, Computer ; New Mexico ; Nitrates ; Phospholipids/analysis ; Sensitivity and Specificity ; Species Specificity ; Sulfates ; Tritium/analysis ; Uranium/*analysis ; *Water Microbiology ; Water Pollution, Chemical/analysis ; Water Pollution, Radioactive/*analysis ; }, abstract = {The relationship between groundwater geochemistry and microbial community structure can be complex and difficult to assess. We applied nonlinear and generalized linear data analysis methods to relate microbial biomarkers (phospholipids fatty acids, PLFA) to groundwater geochemical characteristics at the Shiprock uranium mill tailings disposal site that is primarily contaminated by uranium, sulfate, and nitrate. First, predictive models were constructed using feedforward artificial neural networks (NN) to predict PLFA classes from geochemistry. To reduce the danger of overfitting, parsimonious NN architectures were selected based on pruning of hidden nodes and elimination of redundant predictor (geochemical) variables. The resulting NN models greatly outperformed the generalized linear models. Sensitivity analysis indicated that tritium, which was indicative of riverine influences, and uranium were important in predicting the distributions of the PLFA classes. In contrast, nitrate concentration and inorganic carbon were least important, and total ionic strength was of intermediate importance. Second, nonlinear principal components (NPC) were extracted from the PLFA data using a variant of the feedforward NN. The NPC grouped the samples according to similar geochemistry. PLFA indicators of Gram-negative bacteria and eukaryotes were associated with the groups of wells with lower levels of contamination. The more contaminated samples contained microbial communities that were predominated by terminally branched saturates and branched monounsaturates that are indicative of metal reducers, actinomycetes, and Gram-positive bacteria. These results indicate that the microbial community at the site is coupled to the geochemistry and knowledge of the geochemistry allows prediction of the community composition.}, }
@article {pmid16435169, year = {2006}, author = {Ouellette, AJ and Handy, SM and Wilhelm, SW}, title = {Toxic Microcystis is widespread in Lake Erie: PCR detection of toxin genes and molecular characterization of associated cyanobacterial communities.}, journal = {Microbial ecology}, volume = {51}, number = {2}, pages = {154-165}, pmid = {16435169}, issn = {0095-3628}, mesh = {Bacterial Toxins/biosynthesis/genetics ; Cyanobacteria/classification/genetics/*isolation &amp; purification ; Environmental Monitoring ; Fresh Water/microbiology ; Genes, Bacterial ; Microcystis/genetics/isolation &amp; purification ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Synechococcus/genetics/isolation &amp; purification ; United States ; *Water Microbiology ; }, abstract = {During the past decade, algae blooms, which include the toxic cyanobacterium Microcystis, have reoccurred in the Laurentian Great Lakes, most commonly in the western basin of Lake Erie. Whereas the western basin is the most impacted by toxic Microcystis in Lake Erie, there has historically been little effort focused on identifying the spatial distribution of Microcystis throughout this lake. To address this lack of knowledge, we have employed a polymerase-chain-reaction-based detection of genes required for synthesis of the toxin microcystin (mcyD and mcyB), as well as 16S rDNA fragments specific to either all Microcystis or all cyanobacteria. Using a multiplex approach, we tested 21 samples from 13 field stations and found that toxigenic Microcystis were present in the western and eastern basins in the summers of 1999, 2000, and 2002 and the central basin in 1999 and 2002. This is the most extensive distribution of Microcystis reported in Lake Erie. Clone libraries (16S rDNA) of these cyanobacterial communities were generated from 7 of the 13 field stations (representing all three basins) to partially characterize this microbial community. These libraries were shown to be dominated by sequences assigned to the Synechococcus and Cyanobium phylogenetic cluster, indicating the importance of picoplankton in this large lake system.}, }
@article {pmid16435168, year = {2006}, author = {Haukka, K and Kolmonen, E and Hyder, R and Hietala, J and Vakkilainen, K and Kairesalo, T and Haario, H and Sivonen, K}, title = {Effect of nutrient loading on bacterioplankton community composition in lake mesocosms.}, journal = {Microbial ecology}, volume = {51}, number = {2}, pages = {137-146}, pmid = {16435168}, issn = {0095-3628}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; *Ecosystem ; Electrophoresis, Polyacrylamide Gel ; *Environmental Monitoring ; Eutrophication ; Finland ; Fresh Water/*analysis ; Nitrogen/analysis ; Plankton/*isolation &amp; purification ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {Changes in bacterioplankton community composition were followed in mesocosms set up in the littoral of Lake Vesijärvi, southern Finland, over two summers. Increasing nitrogen and phosphorus concentrations in the mesocosms represented different trophic states, from mesotrophic to hypertrophic. In 1998, the mesocosms were in a turbid state with a high biomass of phytoplankton, whereas in 1999, macrophytes proliferated and a clear-water state prevailed. The bacterial communities in the mesocosms also developed differently, as shown by denaturing gradient gel electrophoresis profiling of partial 16S rRNA gene fragments and by nonmetric multidimensional scaling analysis. In 1998, nutrient treatments affected the diversity and clustering of bacterial communities strongly, but in 1999, the bacterial communities were less diversified and not clearly affected by treatments. Canonical correspondence analysis indicated that bacterioplankton communities in the mesocosms were influenced by environmental physicochemical variables linked to the increasing level of eutrophication. Nitrogen concentration correlated directly with the bacterioplankton composition. In addition, the high nutrient levels had indirect effects through changes in the biomass and composition of phyto- and zooplankton. Sequencing analysis showed that the dominant bacterial divisions remained the same, but the dominant phylotypes changed during the 2-year period. The occurrence of Verrucomicrobia correlated with more eutrophic conditions, whereas the occurrence of Actinobacteria correlated with less eutrophic conditions.}, }
@article {pmid16435167, year = {2006}, author = {Calva, E and Oropeza, R}, title = {Two-component signal transduction systems, environmental signals, and virulence.}, journal = {Microbial ecology}, volume = {51}, number = {2}, pages = {166-176}, pmid = {16435167}, issn = {0095-3628}, mesh = {Animals ; Bacteria/genetics/*pathogenicity ; Bacterial Infections/microbiology ; *Bacterial Physiological Phenomena ; Ecosystem ; Humans ; *Signal Transduction ; Virulence ; }, abstract = {The relevance toward virulence of a variety of two-component signal transduction systems is reviewed for 16 pathogenic bacteria, together with the wide array of environmental signals or conditions that have been implicated in their regulation. A series of issues is raised, concerning the need to understand the environmental cues that determine their regulation in the infected host and in the environment outside the laboratory, which shall contribute toward the bridging of bacterial pathogenesis and microbial ecology.}, }
@article {pmid16431089, year = {2006}, author = {Hendrickx, L and De Wever, H and Hermans, V and Mastroleo, F and Morin, N and Wilmotte, A and Janssen, P and Mergeay, M}, title = {Microbial ecology of the closed artificial ecosystem MELiSSA (Micro-Ecological Life Support System Alternative): reinventing and compartmentalizing the Earth's food and oxygen regeneration system for long-haul space exploration missions.}, journal = {Research in microbiology}, volume = {157}, number = {1}, pages = {77-86}, doi = {10.1016/j.resmic.2005.06.014}, pmid = {16431089}, issn = {0923-2508}, mesh = {Bacteria/metabolism ; *Bioreactors ; *Ecological Systems, Closed ; Environmental Microbiology ; *Food ; Humans ; *Life Support Systems ; Medical Waste Disposal ; Oxygen/*metabolism ; Plants/metabolism ; *Space Flight ; }, abstract = {MELiSSA is a bioregenerative life support system designed by the European Space Agency (ESA) for the complete recycling of gas, liquid and solid wastes during long distance space exploration. The system uses the combined activity of different living organisms: microbial cultures in bioreactors, a plant compartment and a human crew. In this minireview, the development of a short-cut ecological system for the biotransformation of organic waste is discussed from a microorganism's perspective. The artificial ecological model--still in full development--that is inspired by Earth's own geomicrobiological ecosystem serves as an ideal study object on microbial ecology and will become an indispensable travel companion in manned space exploration.}, }
@article {pmid16430685, year = {2006}, author = {Imlay, JA}, title = {Iron-sulphur clusters and the problem with oxygen.}, journal = {Molecular microbiology}, volume = {59}, number = {4}, pages = {1073-1082}, doi = {10.1111/j.1365-2958.2006.05028.x}, pmid = {16430685}, issn = {0950-382X}, support = {GM49640/GM/NIGMS NIH HHS/United States ; }, mesh = {Anaerobiosis ; Bacterial Proteins/*chemistry/drug effects ; Evolution, Molecular ; Iron/metabolism ; Iron-Sulfur Proteins/*chemistry/drug effects ; Oxidants/toxicity ; Oxygen/*metabolism ; }, abstract = {During the first billion years of life on the Earth, the environment was anaerobic. Iron and sulphur were plentiful, and they were recruited in the formation of iron-sulphur (Fe-S) clusters within ancient proteins. These clusters provided many enzymes with the ability to transfer electrons; to others they offered a cationic feature that tightly bound oxyanionic and nitrogenous metabolites. Still others acquired a crystallizing surface around which polypeptide could fold to establish a three-dimensional structure. However, the subsequent oxygenation of the Earth's atmosphere by photosynthetic organisms created a threat to cluster-dependent proteins that still has not been fully resolved. By oxidizing environmental iron, oxygen limits its bioavailability, requiring that organisms employ complex schemes with which to satisfy their iron requirement. More directly, oxygen species convert exposed Fe-S clusters to unstable forms that quickly decompose. Some microbes responded to this dilemma by retreating to anaerobic habitats. Others abandoned the use of low-potential electron-transfer pathways, which rely upon the least stable cluster enzymes, and developed antioxidant strategies to protect the remainder. These adjustments were only partially successful: largely because of their reliance upon Fe-S clusters, aerobes remain vulnerable to iron restriction and oxidative stress, features that higher organisms exploit in defending themselves against bacterial pathogens. Thus, the history of Fe-S clusters is an unusual one that has profoundly shaped contemporary microbial ecology.}, }
@article {pmid16430499, year = {2006}, author = {Beer, M and Stratton, HM and Griffiths, PC and Seviour, RJ}, title = {Which are the polyphosphate accumulating organisms in full-scale activated sludge enhanced biological phosphate removal systems in Australia?.}, journal = {Journal of applied microbiology}, volume = {100}, number = {2}, pages = {233-243}, doi = {10.1111/j.1365-2672.2005.02784.x}, pmid = {16430499}, issn = {1364-5072}, mesh = {Actinobacteria/isolation &amp; purification ; Bacteria/*isolation &amp; purification ; Biomass ; Fluorescent Dyes/analysis ; In Situ Hybridization, Fluorescence/methods ; Indoles/analysis ; Polyphosphates/*metabolism ; Proteobacteria/isolation &amp; purification ; Refuse Disposal/*methods ; Rhodocyclaceae/isolation &amp; purification ; Sewage/*microbiology ; }, abstract = {AIMS: To see if the compositions of the microbial communities in full scale enhanced biological phosphorus removal activated sludge systems were the same as those from laboratory scale sequencing batch reactors fed a synthetic sewage.<br><br>METHODS: Biomass samples taken from nine full scale enhanced biological phosphate removal (EBPR) activated sludge plants in the eastern states of Australia were analysed for their populations of polyphosphate (polyP)-accumulating organisms (PAO) using semi-quantitative fluorescence in situ hybridization (FISH) in combination with DAPI (4'-6-diamidino-2-phenylindole) staining for polyP.<br><br>RESULTS: Very few betaproteobacterial Rhodocyclus related organisms could be detected by FISH in most of the plants examined, and even where present, not all these cells even within a single cluster, stained positively for polyP with DAPI. In some plants in samples from aerobic reactors the Actinobacteria dominated populations containing polyP.<br><br>CONCLUSIONS: The PAO populations in full-scale EBPR systems often differ to those seen in laboratory scale reactors fed artificial sewage, and Rhodocyclus related organisms, dominating these latter communities may not be as important in full-scale systems. Instead Actinobacteria may be the major PAO.<br><br>These findings illustrate how little is still known about the microbial ecology of EBPR processes and that more emphasis should now be placed on analysis of full-scale plants if microbiological methods are to be applied to monitoring their performances.}, }
@article {pmid16428429, year = {2006}, author = {Qiu, X and Daly, MJ and Vasilenko, A and Omelchenko, MV and Gaidamakova, EK and Wu, L and Zhou, J and Sundin, GW and Tiedje, JM}, title = {Transcriptome analysis applied to survival of Shewanella oneidensis MR-1 exposed to ionizing radiation.}, journal = {Journal of bacteriology}, volume = {188}, number = {3}, pages = {1199-1204}, pmid = {16428429}, issn = {0021-9193}, mesh = {ATP Binding Cassette Transporter, Subfamily B/genetics ; DNA Damage/*radiation effects ; DNA Repair/radiation effects ; DNA Repair Enzymes/*genetics/radiation effects ; Gene Expression Regulation, Bacterial/*radiation effects ; *Oligonucleotide Array Sequence Analysis ; Oxidative Stress ; Prophages/genetics ; Radiation Tolerance ; *Radiation, Ionizing ; Reactive Oxygen Species/metabolism ; Shewanella/genetics/*radiation effects ; Ultraviolet Rays ; }, abstract = {The ionizing radiation (IR) dose that yields 20% survival (D20) of Shewanella oneidensis MR-1 is lower by factors of 20 and 200 than those for Escherichia coli and Deinococcus radiodurans, respectively. Transcriptome analysis was used to identify the genes of MR-1 responding to 40 Gy (D20). We observed the induction of 170 genes and repression of 87 genes in MR-1 during a 1-h recovery period after irradiation. The genomic response of MR-1 to IR is very similar to its response to UV radiation (254 nm), which included induction of systems involved in DNA repair and prophage synthesis and the absence of differential regulation of tricarboxylic acid cycle activity, which occurs in IR-irradiated D. radiodurans. Furthermore, strong induction of genes encoding antioxidant enzymes in MR-1 was observed. DNA damage may not be the principal cause of high sensitivity to IR, considering that MR-1 carries genes encoding a complex set of DNA repair systems and 40 Gy IR induces less than one double-strand break in its genome. Instead, a combination of oxidative stress, protein damage, and prophage-mediated cell lysis during irradiation and recovery might underlie this organism's great sensitivity to IR.}, }
@article {pmid16423418, year = {2006}, author = {Kang, S and Mills, AL}, title = {The effect of sample size in studies of soil microbial community structure.}, journal = {Journal of microbiological methods}, volume = {66}, number = {2}, pages = {242-250}, doi = {10.1016/j.mimet.2005.11.013}, pmid = {16423418}, issn = {0167-7012}, mesh = {Bacteria/genetics/*isolation &amp; purification ; Colony Count, Microbial ; DNA, Bacterial/chemistry/genetics/isolation &amp; purification ; DNA, Fungal/chemistry/genetics/isolation &amp; purification ; Discriminant Analysis ; Ecosystem ; Electrophoresis, Polyacrylamide Gel ; Fungi/genetics/*isolation &amp; purification ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry/genetics ; Sample Size ; *Soil Microbiology ; Virginia ; }, abstract = {Replicate soil samples of 0.01, 0.1, 0.25, 1.0 and 10.0 g were taken from a single, large, homogenized sample from a field maintained as continuous meadow. The samples were processed for direct enumeration of bacterial cells and community structure assays by DGGE analysis of PCR-amplified 16S-rDNA fragments from whole community extracts. The goal was to determine the sample size or size range that produced the most consistent results (i.e., mean values) and the lowest variance. Enumeration data were analyzed by ANOVA, and the community composition fingerprints were analyzed by discriminant analysis (DA). Acceptable results were obtained for sample sizes from 0.1 to 1.0 g for both enumeration and community fingerprinting, but the size that yielded the best results for both measures was 0.25 g. The results suggest that for well homogenized silt loam soils with moderate organic matter concentrations, this sample size should produce high quality consistent results. For soils that differ in organic concentrations or clay content, a reconnaissance survey similar to the present examination is recommended.}, }
@article {pmid16423009, year = {2006}, author = {Daims, H and Lücker, S and Wagner, M}, title = {daime, a novel image analysis program for microbial ecology and biofilm research.}, journal = {Environmental microbiology}, volume = {8}, number = {2}, pages = {200-213}, doi = {10.1111/j.1462-2920.2005.00880.x}, pmid = {16423009}, issn = {1462-2912}, mesh = {Biofilms/*growth &amp; development ; Imaging, Three-Dimensional/*methods ; In Situ Hybridization, Fluorescence ; RNA Probes ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; Sewage/*microbiology ; *Software ; }, abstract = {Combinations of microscopy and molecular techniques to detect, identify and characterize microorganisms in environmental and medical samples are widely used in microbial ecology and biofilm research. The scope of these methods, which include fluorescence in situ hybridization (FISH) with rRNA-targeted probes, is extended by digital image analysis routines that extract from micrographs important quantitative data. Here we introduce daime (digital image analysis in microbial ecology), a new computer program integrating 2-D and 3-D image analysis and visualization functionality, which has previously not been available in a single open-source software package. For example, daime automatically finds 2-D and 3-D objects in images and confocal image stacks, and offers special functions for quantifying microbial populations and evaluating new FISH probes. A novel feature is the quantification of spatial localization patterns of microorganisms in complex samples like biofilms. In combination with '3D-FISH', which preserves the 3-D structure of samples, this stereological technique was applied in a proof of principle experiment on activated sludge and provided quantitative evidence that functionally linked ammonia and nitrite oxidizers cluster together in their habitat. This image analysis method complements recent molecular techniques for analysing structure-function relationships in microbial communities and will help to characterize symbiotic interactions among microorganisms.}, }
@article {pmid16420635, year = {2006}, author = {Liu, B and Zhang, F and Feng, X and Liu, Y and Yan, X and Zhang, X and Wang, L and Zhao, L}, title = {Thauera and Azoarcus as functionally important genera in a denitrifying quinoline-removal bioreactor as revealed by microbial community structure comparison.}, journal = {FEMS microbiology ecology}, volume = {55}, number = {2}, pages = {274-286}, doi = {10.1111/j.1574-6941.2005.00033.x}, pmid = {16420635}, issn = {0168-6496}, mesh = {Azoarcus/genetics/*isolation &amp; purification/*metabolism ; Biodiversity ; *Bioreactors ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Ecosystem ; Electrophoresis, Polyacrylamide Gel ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Quinolines/*metabolism ; Sequence Analysis, DNA ; Sewage/microbiology ; Thauera/genetics/*isolation &amp; purification/*metabolism ; }, abstract = {Structural shifts associated with functional dynamics in a bacterial community may provide clues for identifying the most valuable members in an ecosystem. A laboratory-scale denitrifying reactor was adapted from use of non-efficient seeding sludge and was utilized to degrade quinoline and remove the chemical oxygen demand. Stable removal efficiencies were achieved after an adaptation period of six weeks. Both denaturing gradient gel electrophoresis profiling of the 16S rRNA gene V3 region and comparison of the 16S rRNA gene sequence clone libraries (LIBSHUFF analysis) demonstrated that microbial communities in the denitrifying reactor and seeding sludge were significantly distinct. The percentage of the clones affiliated with the genera Thauera and Azoarcus was 74% in the denitrifying reactor and 4% in the seeding sludge. Real-time quantitative PCR also indicated that species of the genera Thauera and Azoarcus increased in abundance by about one order of magnitude during the period of adaptation. The greater abundance of Thauera and Azoarcus in association with higher efficiency after adaptation suggested that these phylotypes might play an important role for quinoline and chemical oxygen demand removal under denitrifying conditions.}, }
@article {pmid16420611, year = {2006}, author = {Boon, N and Depuydt, S and Verstraete, W}, title = {Evolutionary algorithms and flow cytometry to examine the parameters influencing transconjugant formation.}, journal = {FEMS microbiology ecology}, volume = {55}, number = {1}, pages = {17-27}, doi = {10.1111/j.1574-6941.2005.00002.x}, pmid = {16420611}, issn = {0168-6496}, mesh = {Algorithms ; Bacteriological Techniques/methods ; *Conjugation, Genetic ; Culture Media ; Environmental Microbiology ; Escherichia coli/*genetics/growth &amp; development ; Flow Cytometry ; Green Fluorescent Proteins ; Plasmids ; Pseudomonas putida/*genetics ; Temperature ; Toluene/metabolism ; }, abstract = {An evolutionary algorithm was used to determine the optimal combination of parameters for transconjugant formation. As a model system, a gfp tagged TOL plasmid pWW0 was chosen to examine transfer from Pseudomonas putida to Escherichia coli. A comparison of flow cytometry results with plating and microscopy showed that the majority of transconjugants were not culturable. The transconjugant ratio therefore was determined by flow cytometry. The evolutionary algorithm showed that the optimal conditions were obtained at 28 degrees C and at the highest nutrient concentrations. This work demonstrates that evolutionary algorithms can be used to find optimal parameter interactions in environmental microbiology.}, }
@article {pmid16411377, year = {2005}, author = {Moore, JE and Shaw, A and Millar, BC and Downey, DG and Murphy, PG and Elborn, JS}, title = {Microbial ecology of the cystic fibrosis lung: does microflora type influence microbial loading?.}, journal = {British journal of biomedical science}, volume = {62}, number = {4}, pages = {175-178}, doi = {10.1080/09674845.2005.11732707}, pmid = {16411377}, issn = {0967-4845}, mesh = {Adult ; Bacteria/*classification/isolation &amp; purification ; Bacterial Infections/*microbiology ; Colony Count, Microbial ; Cystic Fibrosis/*microbiology ; Ecosystem ; Humans ; Lung/*microbiology ; Sputum/microbiology ; }, abstract = {This study aims to examine the association between the numbers of culturable microbial species forming the microflora of the lung in patients with cystic fibrosis (CF) and microbial loading (i.e., type[s] versus numbers). Additionally, it examines qualitative combinations of the microflora present in a large adult CF centre (n=138) in order to ascertain ecological relationships between the taxa present. The culturable microflora of sputum from 34 adults patients with CF are enumerated using a spread plate technique on non-selective agar, and the microflora identified phenotypically employing the API 20NE scheme. Microbiological examination of the 34 adult patients demonstrated that their sputum contained between one and three taxa, with a mean cell density of 8.25 +/- 0.85 log colony-forming units (cfu)/g sputum and a range of 5.91-9.74 log cfu/g sputum. Most colonising patterns demonstrated only Gram-negative infection (22/34), followed by a mixed Gram-positive/Gram-negative infection pattern (10/34). Only 2/34 patients had a single Gram-positive infection. Most patients (53%) were colonised by only one organism, with 38% of patients colonised by two organisms, and the remainder (4%) colonised with three organisms. There was no statistical difference (P>0.05) between microbial cell density and the number of taxa present (i.e., the greater number of taxa present in sputum did not produce a higher cell density). However, there was a significantly higher cell density (log 0.59 cfu/g sputum) noted for those patients who had only Gram-negative infection, compared to those who had a mixed Gram-negative/Gram-positive infection pattern (P=0.02). Relatively little is known about the ecological interactions that exist between the microflora in the CF lung. Further work is required to explore these interactions in order to aid understanding of the succession and dominance of Gram-negatives in chronic chest infections. Ultimately, a greater understanding of such interactions may allow the opportunity to manipulate the ecology of the lung to control otherwise problematic pathogens}, }
@article {pmid16408245, year = {2006}, author = {Gognies, S and Barka, EA and Gainvors-Claisse, A and Belarbi, A}, title = {Interactions between yeasts and grapevines: filamentous growth, endopolygalacturonase and phytopathogenicity of colonizing yeasts.}, journal = {Microbial ecology}, volume = {51}, number = {1}, pages = {109-116}, pmid = {16408245}, issn = {0095-3628}, mesh = {Ecosystem ; Polygalacturonase/*metabolism ; Statistics as Topic ; Vitis/cytology/*microbiology ; Yeasts/cytology/enzymology/*growth &amp; development/*pathogenicity ; }, abstract = {It has been clearly established that phytopathogenic fungi, bacteria, and viruses exert biotic stresses on plants. Much less is known, however, about the interactions between enological species of yeast and their host plants. In a previous study, we described how Saccharomyces cerevisiae, the most common enological yeast, can act as a grapevine (Vitis vinifera L.) pathogen, causing growth retardation or plant death. In the present in vitro study on 11 strains of yeast belonging to different genera, which often occur on the surfaces of vineyard grapes and V. vinifera, a link was found to exist between strain phytopathogenecity and pseudohyphal growth habits and/or endopolygalacturonase activity. The results obtained here are consistent with earlier findings showing that the phytopathogenicity of yeast strains depends on the filamentous growth process, and show that endopolygalacturonase alone is not responsible for the invasion of plants tissues. The mechanisms observed here may be of significant ecological importance and may help to explain the long periods of yeast survival found to occur in vineyards.}, }
@article {pmid16404977, year = {2005}, author = {Shenderov, BA}, title = {[Medical microbial ecology: some of the overall results and research prospects].}, journal = {Vestnik Rossiiskoi akademii meditsinskikh nauk}, volume = {}, number = {12}, pages = {13-17}, pmid = {16404977}, issn = {0869-6047}, mesh = {Bacteria/isolation &amp; purification ; Feces/microbiology ; Gastrointestinal Tract/drug effects/*microbiology ; *Health Status ; Humans ; Probiotics/pharmacology/therapeutic use ; *Research ; }, abstract = {The review discusses data of fundamental and applied research in human microbial ecology. Having analyzed these data, the author concludes that in the natural habitats these is practically no biochemical process or function of a living organism that would not need a direct or indirect participation of symbiotic organisms. The condition of these organisms should be considered one of the main biogenic factors that determine human health and pathology. The author offers a range of measures that would allow development and introduction of fundamentally new approaches to prevention and treatment of the most wide-spread diseases, as well as application of microorganisms of normal intestinal microflora of man in industrial biotechnology.}, }
@article {pmid16402891, year = {2005}, author = {Banfield, JF and Verberkmoes, NC and Hettich, RL and Thelen, MP}, title = {Proteogenomic approaches for the molecular characterization of natural microbial communities.}, journal = {Omics : a journal of integrative biology}, volume = {9}, number = {4}, pages = {301-333}, doi = {10.1089/omi.2005.9.301}, pmid = {16402891}, issn = {1536-2310}, mesh = {Ecosystem ; *Genomics ; Mass Spectrometry ; *Microbiology ; *Proteomics ; }, abstract = {At the present time we know little about how microbial communities function in their natural habitats. For example, how do microorganisms interact with each other and their physical and chemical surroundings and respond to environmental perturbations? We might begin to answer these questions if we could monitor the ways in which metabolic roles are partitioned amongst members as microbial communities assemble, determine how resources such as carbon, nitrogen, and energy are allocated into metabolic pathways, and understand the mechanisms by which organisms and communities respond to changes in their surroundings. Because many organisms cannot be cultivated, and given that the metabolisms of those growing in monoculture are likely to differ from those of organisms growing as part of consortia, it is vital to develop methods to study microbial communities in situ. Chemoautotrophic biofilms growing in mine tunnels hundreds of meters underground drive pyrite (FeS(2)) dissolution and acid and metal release, creating habitats that select for a small number of organism types. The geochemical and microbial simplicity of these systems, the significant biomass, and clearly defined biological-inorganic feedbacks make these ecosystem microcosms ideal for development of methods for the study of uncultivated microbial consortia. Our approach begins with the acquisition of genomic data from biofilms that are sampled over time and in different growth conditions. We have demonstrated that it is possible to assemble shotgun sequence data to reveal the gene complement of the dominant community members and to use these data to confidently identify a significant fraction of proteins from the dominant organisms by mass spectrometry (MS)-based proteomics. However, there are technical obstacles currently restricting this type of "proteogenomic" analysis. Composite genomic sequences assembled from environmental data from natural microbial communities do not capture the full range of genetic potential of the associated populations. Thus, it is necessary to develop bioinformatics approaches to generate relatively comprehensive gene inventories for each organism type. These inventories are critical for expression and functional analyses. In proteomic studies, for example, peptides that differ from those predicted from gene sequences can be measured, but they generally cannot be identified by database matching, even if the difference is only a single amino acid residue. Furthermore, many of the identified proteins have no known function. We propose that these challenges can be addressed by development of proteogenomic, biochemical, and geochemical methods that will be initially deployed in a simple, natural model ecosystem. The resulting approach should be broadly applicable and will enhance the utility and significance of genomic data from isolates and consortia for study of organisms in many habitats. Solutions draining pyrite-rich deposits are referred to as acid mine drainage (AMD). AMD is a very prevalent, international environmental problem associated with energy and metal resources. The biological-mineralogical interactions that define these systems can be harnessed for energy-efficient metal recovery and removal of sulfur from coal. The detailed understanding of microbial ecology and ecosystem dynamics resulting from the proposed work will provide a scientific foundation for dealing with the environmental challenges and technological opportunities, and yield new methods for analysis of more complex natural communities.}, }
@article {pmid16400538, year = {2006}, author = {Chen, R and LaPara, TM}, title = {Aerobic biological treatment of low-strength synthetic wastewater in membrane-coupled bioreactors: the structure and function of bacterial enrichment cultures as the net growth rate approaches zero.}, journal = {Microbial ecology}, volume = {51}, number = {1}, pages = {99-108}, pmid = {16400538}, issn = {0095-3628}, mesh = {Bacteria, Aerobic/*classification/enzymology/genetics/*isolation &amp; purification ; Base Sequence ; Biomass ; Bioreactors/*microbiology ; Culture Media/metabolism ; DNA, Bacterial/chemistry ; Electrophoresis, Polyacrylamide Gel/methods ; Gelatin/metabolism ; Hydrolysis ; Leucyl Aminopeptidase/analysis/metabolism ; Molecular Sequence Data ; RNA, Ribosomal, 16S/chemistry/genetics ; Sequence Analysis, DNA ; Waste Disposal, Fluid/*methods ; }, abstract = {The goal of the current research was to determine if the stringent nutrient limitation imposed by membrane-coupled bioreactors (MBRs) could be used to force mixed bacterial communities to exhibit a zero net growth rate over an extended time period. Mechanistically, this zero net growth rate could be achieved when the amount of energy available for growth is balanced by the maintenance requirements of the bacterial community. Bench-scale MBRs were fed synthetic feed medium containing gelatin as the major organic substrate. Biomass concentrations initially increased rapidly, but subsequently declined until an asymptote was reached. Leucine aminopeptidase activities concomitantly increased by at least 10-fold, suggesting that bacterial catabolic activity remained high even while growth rates became negligible. In contrast, alpha-glucosidase and heptanoate esterase activities decreased, indicating that the bacterial community specifically adapted to the carbon source in the feed medium. Bacterial community analysis by denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments (PCR-DGGE) suggested that the bacterial community structure completely changed from the beginning to the end of each MBR. Excision and nucleotide sequence analysis of prominent PCR-DGGE bands suggested that many of the dominant populations were similar to novel bacterial strains that were previously uncultivated or recently cultivated during studies specifically targeting these novel populations. This research demonstrates that MBRs have substantial practical applications for biological wastewater treatment; in addition, MBRs are a useful tool to study the ecology of slow-growing bacteria.}, }
@article {pmid16400537, year = {2006}, author = {Dong, H and Zhang, G and Jiang, H and Yu, B and Chapman, LR and Lucas, CR and Fields, MW}, title = {Microbial diversity in sediments of saline Qinghai Lake, China: linking geochemical controls to microbial ecology.}, journal = {Microbial ecology}, volume = {51}, number = {1}, pages = {65-82}, pmid = {16400537}, issn = {0095-3628}, mesh = {Acridine Orange/metabolism ; Archaea/*classification/genetics/metabolism ; Bacteria/*classification/genetics/metabolism ; *Biodiversity ; Biomass ; China ; Cloning, Molecular ; Colony Count, Microbial/methods ; *Ecology ; Fatty Acids/analysis ; Fresh Water/chemistry ; Geologic Sediments/*chemistry/*microbiology ; Methane/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Bacterial/genetics ; Water Microbiology ; X-Ray Diffraction/methods ; }, abstract = {Saline lakes at high altitudes represent an important and extreme microbial ecosystem, yet little is known about microbial diversity in such environments. The objective of this study was to examine the change of microbial diversity from the bottom of the lake to sediments of 40 cm in depth in a core from Qinghai Lake. The lake is saline (12.5 g/L salinity) and alkaline (pH 9.4) and is located on the Qinghai-Tibetan Plateau at an altitude of 3196 m above sea level. Pore water chemistry of the core revealed low concentrations of sulfate and iron (<1 mM), but high concentrations of acetate (40-70 mM) and dissolved organic carbon (1596-5443 mg/L). Total organic carbon and total nitrogen contents in the sediments were approximately 2 and <0.5%, respectively. Acridine orange direct count data indicated that cell numbers decreased from 4 x 10(9) cells/g at the water-sediment interface to 6 x 10(7) cells/g wet sediment at the 40-cm depth. This change in biomass was positively correlated with acetate concentration in pore water. Phospholipid fatty acid (PLFA) community structure analyses determined decrease in the proportion of the Proteobacteria and increase in the Firmicutes with increased depth. Characterization of small subunit (SSU) rRNA genes amplified from the sediments indicated a shift in the bacterial community with depth. Whereas the alpha-, beta-, and gamma-Proteobacteria and the Cytophaga/Flavobacterium/Bacteroides (CFB) were dominant at the water-sediment interface, low G + C gram-positive bacteria (a subgroup of Firmicutes) became the predominant group in the anoxic sediments. Both PLFA and the sequence data showed similar trend. The Proteobacteria, CFB, and gram-positive bacteria are present in other saline lakes, but the presence of Actinobacteria and Acidobacteria/Holophaga in significant proportions in the Qinghai Lake sediments appears to be unique. The archaeal diversity was much lower, and clone sequences could be grouped in the Euryarchaeota and Crenarchaeota domains. The archaeal clones were not related to any known cultures but to sequences previously found in methane-rich sediments. Acetate-utilizing methanogens were isolated from sediment incubations, and alpha- and gamma-proteobacterial isolates were obtained from a water sample from the lake-bottom (23 m). Our data collectively showed that the observed diversity and shift in the community structure with depth was correlated with geochemical parameters (the redox state and availability of electron acceptor and donor). Heterotrophic methanogenesis is possibly adominant metabolic process in the Qinghai Lake sediments. These results reinforce the importance of geochemical controls on microbial ecology in saline and alkaline lake environments.}, }
@article {pmid16400536, year = {2006}, author = {Nicomrat, D and Dick, WA and Tuovinen, OH}, title = {Assessment of the microbial community in a constructed wetland that receives acid coal mine drainage.}, journal = {Microbial ecology}, volume = {51}, number = {1}, pages = {83-89}, pmid = {16400536}, issn = {0095-3628}, mesh = {Acidithiobacillus/genetics/isolation &amp; purification ; Alcaligenes/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/*isolation &amp; purification ; Bordetella/genetics/isolation &amp; purification ; *Coal Mining ; DNA, Bacterial/chemistry/isolation &amp; purification ; Electrophoresis, Agar Gel ; Electrophoresis, Polyacrylamide Gel/methods ; Genes, Bacterial ; Geologic Sediments/*microbiology ; Hazardous Waste ; Hydrogen-Ion Concentration ; Polymerase Chain Reaction/methods ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sulfuric Acids/chemistry ; Waste Disposal, Fluid/methods ; *Water Microbiology ; }, abstract = {Constructed wetlands are used to treat acid drainage from surface or underground coal mines. However, little is known about the microbial communities in the receiving wetland cells. The purpose of this work was to characterize the microbial population present in a wetland that was receiving acid coal mine drainage (AMD). Samples were collected from the oxic sediment zone of a constructed wetland cell in southeastern Ohio that was treating acid drainage from an underground coal mine seep. Samples comprised Fe(III) precipitates and were pretreated with ammonium oxalate to remove interfering iron, and the DNA was extracted and purified by agarose gel electrophoresis prior to amplification of portions of the 16S rRNA gene. Amplified products were separated by denaturing gradient gel electrophoresis and DNA from seven distinct bands was excised from the gel and sequenced. The sequences were matched to sequences in the GenBank bacterial 16S rDNA database. The DNA in two of the bands yielded matches with Acidithiobacillus ferrooxidans and the DNA in each of the remaining five bands was consistent with one of the following microorganisms: Acidithiobacillus thiooxidans, strain TRA3-20 (a eubacterium), strain BEN-4 (an arsenite-oxidizing bacterium), an Alcaligenes sp., and a Bordetella sp. Low bacterial diversity in these samples reflects the highly inorganic nature of the oxic sediment layer where high abundance of iron- and sulfur-oxidizing bacteria would be expected. The results we obtained by molecular methods supported our findings, obtained using culture methods, that the dominant microbial species in an acid receiving, oxic wetland are A. thiooxidans and A. ferrooxidans.}, }
@article {pmid16396336, year = {2005}, author = {Wallander, H and Pallon, J}, title = {Temporal changes in the elemental composition of Rhizopogon rhizomorphs during colonization of patches with fresh organic matter or acid-washed sand.}, journal = {Mycologia}, volume = {97}, number = {2}, pages = {295-303}, doi = {10.3852/mycologia.97.2.295}, pmid = {16396336}, issn = {0027-5514}, mesh = {Biomass ; Calcium/analysis ; *Elements ; Iron/analysis ; Manganese/analysis ; Mycorrhizae/*chemistry/growth &amp; development ; Nitrogen ; Organic Chemicals/metabolism ; Phosphorus/analysis ; Potassium/analysis ; *Silicon Dioxide ; Sulfur/analysis ; Zinc/analysis ; }, abstract = {A laboratory experiment was performed to estimate the elemental composition of rhizomorphs of an ectomycorrhizal (EM) fungus growing in a patchy environment. Successive samples of Rhizopogon rhizomorphs, located adjacent to patches with organic matter or patches with acid-washed sand, were taken over a period of 45 d. The mass per unit area was analyzed with scanning transmission ion microscopy (STIM), and the elemental content of elements heavier than Mg were analyzed with particle induced X-ray emission (PIXE). Rhizomorphs associated with the organic matter on average were three times heavier per unit area than rhizomorphs associated with sand. The Ca concentration (mg g(-1)) increased in rhizomorphs adjacent to patches with sand, while it decreased in rhizomorphs adjacent to patches with organic matter. Fe concentration was higher in rhizomorphs adjacent to patches with sand. We concluded that the EM fungus responded to the organic matter by producing larger rhizomorphs, rather than increasing the concentration of elements in the rhizomorphs, to improve the transport of elements to the roots. The elemental composition of rhizomorphs varied considerably over time, and the accumulation of Ca in rhizomorphs in the sand-filled compartments could be the effect of acropetal flow of solutes from the plant roots toward the mycelial front.}, }
@article {pmid16395540, year = {2006}, author = {Freese, HM and Karsten, U and Schumann, R}, title = {Bacterial abundance, activity, and viability in the eutrophic River Warnow, northeast Germany.}, journal = {Microbial ecology}, volume = {51}, number = {1}, pages = {117-127}, pmid = {16395540}, issn = {0095-3628}, mesh = {Bacteria/growth &amp; development/*isolation &amp; purification/metabolism ; *Bacterial Physiological Phenomena ; Carbon/analysis ; Cell Membrane/physiology ; Chlorophyll/analysis ; Chlorophyll A ; *Environment ; Esterases/metabolism ; Eutrophication ; Germany ; *Microbial Viability ; Nitrogen/analysis ; Phosphorus/analysis ; Plankton/microbiology ; Rivers/*microbiology ; Statistics, Nonparametric ; Time Factors ; Water Supply/*standards ; }, abstract = {The River Warnow is the drinking water source for the city of Rostock. Its eutrophic status is accompanied by high amounts of bacteria, which may reach up to 24 x 10(6) cells mL(-1) as recorded during a seasonal study in 2002. Because the river is eutrophic and also heavily loaded with organic matter, this burden is a problem for drinking water purification, as it must be removed completely to not trigger new bacterial growth in the pipeline network. Therefore, restoration measures in the river have to be planned, and bacteria have to be favored as decomposers. That includes the investigation of the physiological state of bacteria in situ. Viable and active cells in the lower reaches of River Warnow were estimated using a broad set of methods. Intact bacteria were investigated by the LIVE/DEAD BacLight bacterial viability kit, containing a mixture of permeant and impermeant nucleic acid stains. Cells with ribosomes were visualized by fluorescence in situ hybridization with the EUB338 oligonucleotide probe. Intact cells and ribosome-containing bacteria represented 24% of total numbers stained by 4'6,-diamidino-2-phenylindole (DAPI) or 66 and 62%, respectively, in relation to all bacteria visualized by the LIVE/DEAD kit. Both fractions were considered as viable, although the fraction of RIB + bacteria is most likely underestimated by the protocol applied. 5-Cyano-2,3-ditolyltetrazolium chloride (CTC) was applied to mark respiring bacteria. The esterase substrate CellTracker Green 5-chloromethylfluorescein diacetate showed cells with intracellular hydrolytic activity. Whereas 1.5% of DAPI-stained bacteria were observed as respiring, 3.8% exhibited intracellular hydrolytic activity on average. If these active fractions were calculated as the percentages of intact cells, much higher fractions of 5.4% were respiring and 16% hydrolytic. Temperature was a main factor influencing total and viable cell numbers simultaneously. The results confirm that there are different states of viable and active cells in natural bacterioplankton communities. However, it remains unclear why fractions of viable and active cells were rather low in this eutrophic river in comparison to similar waters. We recommend to carefully address cells as viable in contrast to nonviable, i.e., dead. As viable cells may be active or inactive with respect to many different activities, e.g., substrate uptake, respiration, hydrolysis, and cell deviation, it is necessary to choose the method to visualize active cells according to the question to be answered.}, }
@article {pmid16395189, year = {2005}, author = {Klossek, JM and Chidiac, C and Serrano, E and Gehanno, P and Naudé, P and Amsellem, J and Dubreuil, C and Ferrand, PA and Jankowski, R and May, T and Bébéar, C and Dubreuil, L and , }, title = {[Community-acquired acute maxillary sinusitis or rhinosinusitis in adults in France: current management].}, journal = {Presse medicale (Paris, France : 1983)}, volume = {34}, number = {22 Pt 2}, pages = {1755-1763}, doi = {10.1016/s0755-4982(05)84269-1}, pmid = {16395189}, issn = {0755-4982}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Bacterial Infections/*diagnosis/*drug therapy ; Community-Acquired Infections/diagnosis/drug therapy ; Diagnosis, Differential ; Drug Resistance, Bacterial ; France ; Humans ; Maxillary Sinusitis/*diagnosis/*drug therapy ; Practice Patterns, Physicians' ; Rhinitis/*diagnosis/*drug therapy ; Risk Factors ; }, abstract = {Sinus infections, often viral, are a common reason for physician visits. The multiplicity of clinical presentations makes its diagnosis difficult. The problem is to recognize bacterial infection without additional testing, except in cases of treatment failures, complications or relapse. Patients with signs suggestive of rhinosinusitis fall into one of four basic clinical situations: common colds, 'doubtful' rhinosinusitis, apparent acute maxillary bacterial rhinosinusitis, and complications. Anterior rhinoscopy may help confirm diagnosis. Current bacterial epidemiology is based on the results of clinical studies, microbial ecology, and samples taken in cases of treatment failure. The two bacteria isolated most frequently are Streptococcus pneumoniae and Haemophilus influenzae, both of which pose resistance problems. Moraxella catarrhalis, Streptococcus pyogenes and Staphylococcus aureus are isolated less often. The dominant issue in management of acute rhinosinusitis is whether to use antibiotic or symptomatic treatment. For viral infections, antibiotic therapy is useless and highly inadvisable. For 'doubtful' infections, symptomatic treatment is likely to lead to recovery. The use of non-recommended antibiotics also increases the risk of selection of resistant bacteria. When bacterial rhinosinusitis is strongly suspected, recourse to antibiotic treatment is recommended in view of the benefits in this situation (AFSSAPS 2005). This treatment is probabilistic, should be decided at the end of the consultation, and follows the AFSSAPS guidelines.}, }
@article {pmid16391878, year = {2006}, author = {McNamara, CJ and Perry, TD and Bearce, KA and Hernandez-Duque, G and Mitchell, R}, title = {Epilithic and endolithic bacterial communities in limestone from a Maya archaeological site.}, journal = {Microbial ecology}, volume = {51}, number = {1}, pages = {51-64}, pmid = {16391878}, issn = {0095-3628}, mesh = {Archaeology ; Bacteria/*classification/*isolation &amp; purification ; *Biodiversity ; Calcium Carbonate/*analysis ; Cloning, Molecular/methods ; DNA Primers/chemistry ; DNA, Ribosomal/chemistry ; Mexico ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Biodeterioration of archaeological sites and historic buildings is a major concern for conservators, archaeologists, and scientists involved in preservation of the world's cultural heritage. The Maya archaeological sites in southern Mexico, some of the most important cultural artifacts in the Western Hemisphere, are constructed of limestone. High temperature and humidity have resulted in substantial microbial growth on stone surfaces at many of the sites. Despite the porous nature of limestone and the common occurrence of endolithic microorganisms in many habitats, little is known about the microbial flora living inside the stone. We found a large endolithic bacterial community in limestone from the interior of the Maya archaeological site Ek' Balam. Analysis of 16S rDNA clones demonstrated disparate communities (endolithic: >80% Actinobacteria, Acidobacteria, and Low GC Firmicutes; epilithic: >50% Proteobacteria). The presence of differing epilithic and endolithic bacterial communities may be a significant factor for conservation of stone cultural heritage materials and quantitative prediction of carbonate weathering.}, }
@article {pmid16391122, year = {2006}, author = {Johnson, MR and Conners, SB and Montero, CI and Chou, CJ and Shockley, KR and Kelly, RM}, title = {The Thermotoga maritima phenotype is impacted by syntrophic interaction with Methanococcus jannaschii in hyperthermophilic coculture.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {1}, pages = {811-818}, pmid = {16391122}, issn = {0099-2240}, mesh = {Bacterial Proteins/genetics/*metabolism ; Coculture Techniques ; DNA, Complementary ; *Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Hot Temperature ; Methanococcus/*growth &amp; development ; Oligonucleotide Array Sequence Analysis ; Phenotype ; Proteome ; Thermotoga maritima/classification/genetics/*growth &amp; development/metabolism ; Transcription, Genetic ; }, abstract = {Significant growth phase-dependent differences were noted in the transcriptome of the hyperthermophilic bacterium Thermotoga maritima when it was cocultured with the hyperthermophilic archaeon Methanococcus jannaschii. For the mid-log-to-early-stationary-phase transition of a T. maritima monoculture, 24 genes (1.3% of the genome) were differentially expressed twofold or more. In contrast, methanogenic coculture gave rise to 292 genes differentially expressed in T. maritima at this level (15.5% of the genome) for the same growth phase transition. Interspecies H2 transfer resulted in three- to fivefold-higher T. maritima cell densities than in the monoculture, with concomitant formation of exopolysaccharide (EPS)-based cell aggregates. Differential expression of specific sigma factors and genes related to the ppGpp-dependent stringent response suggests involvement in the transition into stationary phase and aggregate formation. Cell aggregation was growth phase dependent, such that it was most prominent during mid-log phase and decayed as cells entered stationary phase. The reduction in cell aggregation was coincidental with down-regulation of genes encoding EPS-forming glycosyltranferases and up-regulation of genes encoding beta-specific glycosyl hydrolases; the latter were presumably involved in hydrolysis of beta-linked EPS to release cells from aggregates. Detachment of aggregates may facilitate colonization of new locations in natural environments where T. maritima coexists with other organisms. Taken together, these results demonstrate that syntrophic interactions can impact the transcriptome of heterotrophs in methanogenic coculture, and this factor should be considered in examining the microbial ecology in anaerobic environments.}, }
@article {pmid16391099, year = {2006}, author = {Mertens, B and Boon, N and Verstraete, W}, title = {Slow-release inoculation allows sustained biodegradation of gamma-hexachlorocyclohexane.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {1}, pages = {622-627}, pmid = {16391099}, issn = {0099-2240}, mesh = {Aerobiosis ; Biodegradation, Environmental ; Biotechnology/methods ; Capsules ; Culture Media ; Hexachlorocyclohexane/*metabolism ; Insecticides/*metabolism ; Silicones ; Soil Pollutants/*metabolism ; Sphingomonas/cytology/growth &amp; development/*metabolism ; Time Factors ; }, abstract = {This study investigated the feasibility of a slow-release inoculation approach as a bioaugmentation strategy for the degradation of lindane (gamma-hexachlorocyclohexane [gamma-HCH]). Slow-release inoculation of Sphingomonas sp. gamma 1-7 was established in both liquid and soil slurry microcosms using open-ended silicone tubes in which the bacteria are encapsulated in a protective nutrient-rich matrix. The capacity of the encapsulated cells to degrade lindane under aerobic conditions was evaluated in comparison with inoculation of free-living cells. Encapsulation of cells in tubes caused the removal of lindane by adsorption to the silicone tubes but also ensured prolonged biodegradation activity. Lindane degradation persisted 2.2 and 1.4 times longer for liquid and soil slurry microcosms, respectively, than that for inoculation with free cells. While inoculation of free-living cells led to a loss in lindane-degrading activity in limited time intervals, encapsulation in tubes allowed for a more stable actively degrading community. The loss in degrading activity was linked to the loss of the linA gene, encoding gamma-HCH dehydrochlorinase (LinA), which is involved in the initial steps of the lindane degradation pathway. This work shows that a slow-release inoculation approach using a catabolic strain encapsulated in open-ended tubes is a promising bioaugmentation tool for contaminated sites, as it can enhance pollutant removal and can prolong the degrading activity in comparison with traditional inoculation strategies.}, }
@article {pmid16391095, year = {2006}, author = {Denef, VJ and Klappenbach, JA and Patrauchan, MA and Florizone, C and Rodrigues, JL and Tsoi, TV and Verstraete, W and Eltis, LD and Tiedje, JM}, title = {Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400.}, journal = {Applied and environmental microbiology}, volume = {72}, number = {1}, pages = {585-595}, pmid = {16391095}, issn = {0099-2240}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; P42 ES 04911-12/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; Benzoates/*metabolism ; Biodegradation, Environmental ; Burkholderia/genetics/growth &amp; development/*metabolism/physiology ; Gene Deletion ; *Gene Expression Regulation, Bacterial ; *Genome, Bacterial ; Heat-Shock Response ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; *Oxidative Stress ; *Proteome ; Transcription, Genetic ; }, abstract = {Transcriptomic and proteomic analyses of Burkholderia xenovorans LB400, a potent polychlorinated biphenyl (PCB) degrader, have implicated growth substrate- and phase-dependent expression of three benzoate-catabolizing pathways: a catechol ortho cleavage (ben-cat) pathway and two benzoyl-coenzyme A pathways, encoded by gene clusters on the large chromosome (boxC) and the megaplasmid (boxM). To elucidate the significance of this apparent redundancy, we constructed mutants with deletions of the ben-cat pathway (the DeltabenABCD::kan mutant), the boxC pathway (the DeltaboxABC::kan mutant), and both pathways (the DeltabenABCDDelta boxABC::kan mutant). All three mutants oxidized benzoate in resting-cell assays. However, the DeltabenABCD::kan and DeltabenABCD DeltaboxABC::kan mutants grew at reduced rates on benzoate and displayed increased lag phases. By contrast, growth on succinate, on 4-hydroxybenzoate, and on biphenyl was unaffected. Microarray and proteomic analyses revealed that cells of the DeltabenABCD::kan mutant growing on benzoate expressed both box pathways. Overall, these results indicate that all three pathways catabolize benzoate. Deletion of benABCD abolished the ability of LB400 to grow using 3-chlorobenzoate. None of the benzoate pathways could degrade 2- or 4-chlorobenzoate, indicating that the pathway redundancy does not directly contribute to LB400's PCB-degrading capacities. Finally, an extensive sigmaE-regulated oxidative stress response not present in wild-type LB400 grown on benzoate was detected in these deletion mutants, supporting our earlier suggestion that the box pathways are preferentially active under reduced oxygen tension. Our data further substantiate the expansive network of tightly interconnected and complexly regulated aromatic degradation pathways in LB400.}, }
@article {pmid16389465, year = {2006}, author = {Alexandre, A and Laranjo, M and Oliveira, S}, title = {Natural populations of chickpea rhizobia evaluated by antibiotic resistance profiles and molecular methods.}, journal = {Microbial ecology}, volume = {51}, number = {1}, pages = {128-136}, pmid = {16389465}, issn = {0095-3628}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/*classification/drug effects/genetics/*isolation &amp; purification ; Bacterial Proteins/classification/isolation &amp; purification ; Biodiversity ; Cicer/*microbiology ; Cluster Analysis ; DNA Fingerprinting/methods ; DNA, Ribosomal/chemistry ; Drug Resistance, Bacterial ; Electrophoresis, Polyacrylamide Gel ; Genotype ; Phenotype ; Phylogeny ; Plant Roots/*microbiology ; Polymorphism, Restriction Fragment Length ; Portugal ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {The aims of this study were to investigate the hypothesis that intrinsic antibiotic resistance (IAR) profiles of chickpea rhizobia are correlated with the isolates site of origin, and to compare the discriminating power of IAR profiles with molecular approaches in rhizobial strain identification and differentiation. Rhizobial diversity from five Portuguese soils was assessed by IAR profiles and molecular methods [16S rDNA restriction fragment length polymorphism (RFLP) analysis, direct amplified polymorphic DNA (DAPD) fingerprinting, and SDS-PAGE analysis of protein profiles]. For each analysis, a dendrogram was generated using the software BioNumerics. All three molecular methods generated analogous clustering of the isolates, supporting previous results on 16S rDNA sequence-based phylogeny. Clusters obtained with IAR profile are similar to the species groups generated with the molecular methods used. IAR groups do not correlate significantly with the geographic origin of the isolates. These results may indicate a chromosomal location of antibiotic resistance genes, and suggest that IAR is species related. DAPD and IAR profiles proved to be the most discriminating approaches in strain differentiation and can be used as fast methods to screen diversity in new isolates.}, }
@article {pmid16389464, year = {2006}, author = {Arcate, JM and Karp, MA and Nelson, EB}, title = {Diversity of peronosporomycete (oomycete) communities associated with the rhizosphere of different plant species.}, journal = {Microbial ecology}, volume = {51}, number = {1}, pages = {36-50}, pmid = {16389464}, issn = {0095-3628}, mesh = {*Biodiversity ; DNA Primers/chemistry ; DNA, Fungal/genetics ; Oomycetes/*classification/genetics/*isolation &amp; purification ; Phylogeny ; Plant Roots/*microbiology ; Plants/classification/*microbiology ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Species Specificity ; }, abstract = {Peronosporomycete (oomycete) communities inhabiting the rhizospheres of three plant species were characterized and compared to determine whether communities obtained by direct soil DNA extractions (soil communities) differ from those obtained using baiting techniques (bait communities). Using two sets of Peronosporomycete-specific primers, a portion of the 5' region of the large subunit (28S) rRNA gene was amplified from DNA extracted either directly from rhizosphere soil or from hempseed baits floated for 48 h over rhizosphere soil. Amplicons were cloned, sequenced, and then subjected to phylogenetic and diversity analyses. Both soil and bait communities arising from DNA amplified with a Peronosporomycetidae-biased primer set (Oom1) were dominated by Pythium species. In contrast, communities arising from DNA amplified with a Saprolegniomycetidae-biased primer set (Sap2) were dominated by Aphanomyces species. Neighbor-joining analyses revealed the presence of additional taxa that could not be identified with known Peronosporomycete species represented in GenBank. Sequence diversity and mean sequence divergence (Theta pi) within bait communities were lower than the diversity within soil communities. Furthermore, the composition of Peronosporomycete communities differed among the three fields sampled and between bait and soil communities based on F(st) and parsimony tests. The results of our study represent a significant advance in the study of Peronosporomycetes in terrestrial habitats. Our work has shown the utility of culture-independent approaches using 28S rRNA genes to assess the diversity of Peronosporomycete communities in association with plants. It also reveals the presence of potentially new species of Peronosporomycetes in soils and plant rhizospheres.}, }
@article {pmid16389463, year = {2006}, author = {Stursova, M and Crenshaw, CL and Sinsabaugh, RL}, title = {Microbial responses to long-term N deposition in a semiarid grassland.}, journal = {Microbial ecology}, volume = {51}, number = {1}, pages = {90-98}, pmid = {16389463}, issn = {0095-3628}, mesh = {Carbon/analysis ; Climate ; Ecology ; Enzymes/analysis ; Leucyl Aminopeptidase/analysis ; Nitrogen/analysis/*metabolism ; Nitrous Oxide/analysis/metabolism ; Peroxidase/analysis ; Poaceae/microbiology ; Principal Component Analysis ; Soil/*analysis ; *Soil Microbiology ; Trees/enzymology ; beta-Glucosidase/analysis ; }, abstract = {Nitrogen (N) enrichment of the biosphere is an expanding problem to which arid ecosystems may be particularly sensitive. In semiarid grasslands, scarce precipitation uncouples plant and microbial activities, and creates within the soil a spatial mosaic of rhizosphere and cyanobacterial crust communities. We investigated the impact of elevated N deposition on these soil microbial communities at a grama-dominated study site located incentral New Mexico (USA). The study plots were established in 1995 and receive 10 kg ha(-1) year(-1) of supplemental N in the form of NH(4)NO(3). Soil samples were collected in July 2004, following 2 years of severe drought, and again in March 2005 following a winter of record high precipitation. Soils were assayed for potential activities of 20 extracellular enzymes and N(2)O production. The rhizosphere and crust-associated soils had peptidase and peroxidase potentials that were extreme in relation to those of temperate soils. N addition enhanced glycosidase and phosphatase activities and depressed peptidase. In contrast to temperate forest soils, oxidative enzyme activity did not respond to N treatment. Across sampling dates, extracellular enzyme activity responses correlated with inorganic N concentrations. N(2)O generation did not vary significantly with soil cover or N treatment. Microbial responses to N deposition in this semiarid grassland were distinct from those of forest ecosystems and appear to be modulated by inorganic N accumulation, which is linked to precipitation patterns.}, }
@article {pmid16382284, year = {2006}, author = {Kirkwood, AE and Nalewajko, C and Fulthorpe, RR}, title = {The effects of cyanobacterial exudates on bacterial growth and biodegradation of organic contaminants.}, journal = {Microbial ecology}, volume = {51}, number = {1}, pages = {4-12}, pmid = {16382284}, issn = {0095-3628}, mesh = {2,4-Dichlorophenoxyacetic Acid/metabolism ; Biodegradation, Environmental ; Biomass ; Carbon/analysis ; Culture Media ; Cupriavidus necator/growth &amp; development/*metabolism ; Cyanobacteria/*chemistry/isolation &amp; purification ; Dichloroacetic Acid/*metabolism ; Gram-Negative Aerobic Rods and Cocci/growth &amp; development/*metabolism ; Industrial Waste ; Linear Models ; Paper ; Phenol/*metabolism ; Pseudomonas/growth &amp; development/*metabolism ; Ultraviolet Rays ; }, abstract = {The pulp and paper industry largely depends on the biodegradation activities of heterotrophic bacteria to remove organic contaminants in wastewater prior to discharge. Our recent discovery of extensive cyanobacterial communities in pulp and paper waste treatment systems led us to investigate the potential impacts of cyanobacterial exudates on growth and biodegradation efficiency of three bacterial heterotrophs. Each of the three assessed bacteria represented different taxa commonly found in pulp and paper waste treatment systems: a fluorescent Pseudomonad, an Ancylobacter aquaticus strain, and a Ralstonia eutropha strain. They were capable of utilizing phenol, dichloroacetate (DCA), or 2,4-dichlorophenoxyacetic acid (2,4-D), respectively. Exudates from all 12 cyanobacterial strains studied supported the growth of each bacterial strain to varying degrees. Maximum biomass of two bacterial strains positively correlated with the total organic carbon content of exudate treatments. The combined availability of exudate and a known growth substrate (i.e., phenol, DCA, or 2,4-D) generally had a synergistic affect on the growth of the Ancylobacter strain, whereas mixed effects were seen on the other two strains. Exudates from four representative cyanobacterial strains were assessed for their impacts on phenol and DCA biodegradation by the Pseudomonas and Ancylobacter strains, respectively. Exudates from three of the four cyanobacterial taxa repressed phenol biodegradation, but enhanced DCA biodegradation. These dissimilar impacts of cyanobacterial exudates on bacterial degradation of contaminants suggest a species-specific association, as well as a significant role for cyanobacteria during the biological treatment of wastewaters.}, }
@article {pmid16382283, year = {2006}, author = {Smith, RL and Baumgartner, LK and Miller, DN and Repert, DA and Böhlke, JK}, title = {Assessment of nitrification potential in ground water using short term, single-well injection experiments.}, journal = {Microbial ecology}, volume = {51}, number = {1}, pages = {22-35}, pmid = {16382283}, issn = {0095-3628}, mesh = {Bromides/analysis ; Geologic Sediments/chemistry ; Hydrocarbons, Fluorinated/chemistry ; Nitrites/analysis/chemistry ; Nitrogen/analysis/*chemistry/*metabolism ; Nitrogen Fixation ; Nitrogen Isotopes/analysis/metabolism ; Oxygen/chemistry ; Quaternary Ammonium Compounds/chemistry ; Time Factors ; Waste Disposal, Fluid ; Water/*analysis ; }, abstract = {Nitrification was measured within a sand and gravel aquifer on Cape Cod, MA, using a series of single-well injection tests. The aquifer contained a wastewater-derived contaminant plume, the core of which was anoxic and contained ammonium. The study was conducted near the downgradient end of the ammonium zone, which was characterized by inversely trending vertical gradients of oxygen (270 to 0 microM) and ammonium (19 to 625 microM) and appeared to be a potentially active zone for nitrification. The tests were conducted by injecting a tracer solution (ambient ground water + added constituents) into selected locations within the gradients using multilevel samplers. After injection, the tracers moved by natural ground water flow and were sampled with time from the injection port. Rates of nitrification were determined from changes in nitrate and nitrite concentration relative to bromide. Initial tests were conducted with (15)N-enriched ammonium; subsequent tests examined the effect of adding ammonium, nitrite, or oxygen above background concentrations and of adding difluoromethane, a nitrification inhibitor. In situ net nitrate production exceeded net nitrite production by 3- to 6- fold and production rates of both decreased in the presence of difluoromethane. Nitrification rates were 0.02-0.28 mumol (L aquifer)(-1) h(-1) with in situ oxygen concentrations and up to 0.81 mumol (L aquifer)(-1) h(-1) with non-limiting substrate concentrations. Geochemical considerations indicate that the rates derived from single-well injection tests yielded overestimates of in situ rates, possibly because the injections promoted small-scale mixing within a transport-limited reaction zone. Nonetheless, these tests were useful for characterizing ground water nitrification in situ and for comparing potential rates of activity when the tracer cloud included non-limiting ammonium and oxygen concentrations.}, }
@article {pmid16382282, year = {2006}, author = {Tóth, EM and Hell, E and Kovács, G and Borsodi, AK and Márialigeti, K}, title = {Bacteria isolated from the different developmental stages and larval organs of the obligate parasitic fly, Wohlfahrtia magnifica (Diptera: Sarcophagidae).}, journal = {Microbial ecology}, volume = {51}, number = {1}, pages = {13-21}, pmid = {16382282}, issn = {0095-3628}, mesh = {Animal Structures/microbiology ; Animals ; Antibiosis ; Bacteria/classification/*isolation &amp; purification ; DNA, Ribosomal/chemistry ; Diptera/growth &amp; development/*microbiology ; Enterobacteriaceae/classification/*isolation &amp; purification ; Exudates and Transudates/microbiology ; Fat Body/microbiology ; Gram-Negative Bacteria/isolation &amp; purification ; Gram-Positive Bacteria/isolation &amp; purification ; Larva/microbiology ; *Life Cycle Stages ; Phenotype ; RNA, Ribosomal, 16S/genetics ; Salivary Glands/microbiology ; Sheep ; }, abstract = {Wohlfahrtia magnifica (Diptera: Sarcophagidae) is the major myiasis-causing fly species in the whole of Eurasia for most important domestic animals. The aim of the present work was to obtain data on the culturable bacteria isolated under aerobic conditions from this fly: bacteria were isolated from all developmental stages (larvae, pupa, and imago) of Wohlfahrtia magnifica, and the third-stage larval organs were also sampled. To determine the possible antagonistic effects between the dominant bacterial groups, an antibiosis assay was carried out. Plating and isolation of bacteria was performed by classical microbiological methods. Characterization of the isolated strains was carried out via a polyphasic approach; classical phenotypic tests, chemotaxonomical examinations, and 16S rDNA sequence analyses were also applied. In the case of maggot macerate samples, members of the family Enterobacteriaceae were characteristic. Members of a new genus (Schineria) belonging to the gamma subdivision of proteobacteria were also isolated. According to our data, the shifts in the Schineria and Proteus populations within the larvae are strongly influenced by their interactions with each other and among the members of the family Enterobacteriaceae. The pupa and imago samples contained several other Gram-negative bacteria (Stenotrophomonas, Brevundimonas, etc.). Among Gram-positive bacteria, in all maggot macerate samples, members of the genus Bacillus and the Arthrobacter-Micrococcus group of actinobacteria were dominant (neither of them was a producer or sensitive to the compounds of other microorganisms), and bacteria related to the genus Corynebacterium were also found. From the larvae Aureobacterium liquefaciens and Enterococcus faecalis were isolated, and from the pupae Dietzia maris and Enterococcus faecalis. In the samples of third-stage larval organs, the dominant groups were the same as in the third-stage larval macerate sample; however, several additional genera/species were observed (Rhodococcus fascians, Streptomyces sp., Rathayibacter sp., Bacillus thuringiensis/cereus).}, }
@article {pmid16377170, year = {2006}, author = {Wagner, M and Nielsen, PH and Loy, A and Nielsen, JL and Daims, H}, title = {Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays.}, journal = {Current opinion in biotechnology}, volume = {17}, number = {1}, pages = {83-91}, doi = {10.1016/j.copbio.2005.12.006}, pmid = {16377170}, issn = {0958-1669}, mesh = {Archaea/genetics/metabolism ; Autoradiography ; Bacteria/genetics/metabolism ; DNA, Bacterial/analysis ; *Environmental Microbiology ; In Situ Hybridization, Fluorescence/*methods ; Isotopes ; Oligonucleotide Array Sequence Analysis ; Plankton/genetics/metabolism ; RNA, Bacterial/analysis ; RNA, Ribosomal/analysis ; Radioisotopes ; }, abstract = {The ecophysiology of microorganisms has been at the heart of microbial ecology since its early days, but only during the past decade have methods become available for cultivation-independent, direct identification of microorganisms in complex communities and for the simultaneous investigation of their activity and substrate uptake patterns. The combination of fluorescence in situ hybridization (FISH) and microautoradiography (MAR) is currently the most widely applied tool for revealing physiological properties of microorganisms in their natural environment with single-cell resolution. For example, this technique has been used in wastewater treatment and marine systems to describe the functional properties of newly discovered species, and to identify microorganisms responsible for key physiological processes. Recently, the scope of FISH-MAR was extended by rendering it quantitative and by combining it with microelectrode measurements or stable isotope probing. Isotope arrays have also been developed that exploit the parallel detection offered by DNA microarrays to measure incorporation of labelled substrate into the rRNA of many community members in a single experiment.}, }
@article {pmid16349535, year = {1998}, author = {Smalla, K and Wachtendorf, U and Heuer, H and Liu, WT and Forney, L}, title = {Analysis of BIOLOG GN Substrate Utilization Patterns by Microbial Communities.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {4}, pages = {1220-1225}, pmid = {16349535}, issn = {0099-2240}, abstract = {BIOLOG GN plates are increasingly used to characterize microbial communities by determining the ability of the communities to oxidize various carbon sources. Studies were done to determine whether the BIOLOG GN plate assay accurately reflects the catabolic potential of the inoculum used. To gain insight into which populations of microbial communities contribute to the BIOLOG patterns, denaturing gradient gel electrophoresis and temperature gradient gel electrophoresis (TGGE) were used to assess the diversity of ribotypes in the inocula and individual wells of BIOLOG plates following incubation. These studies were done with microbial communities from the rhizosphere of potatoes and an activated sludge reactor fed with glucose and peptone. TGGE analyses of BIOLOG wells inoculated with cell suspensions from the potato rhizosphere revealed that, compared with the inoculum, there was a decrease in the number of 16S rRNA gene fragments obtained from various wells, as well as a concomitant loss of populations that had been numerically dominant in the inoculum. The dominant fragments in TGGE gels could be assigned to the gamma subclass of the class Proteobacteria, suggesting that fast-growing bacteria adapted to high substrate concentrations were numerically dominant in the wells and may have been primarily responsible for the patterns of substrate use that were observed. Similarly, the community structure changed in wells inoculated with cells from activated sludge; one or more populations were enriched, but all dominant populations of the inoculum could be detected in at least one well. This study showed that carbon source utilization profiles obtained with BIOLOG GN plates do not necessarily reflect the functional potential of the numerically dominant members of the microbial community used as the inoculum.}, }
@article {pmid16349527, year = {1998}, author = {Damgaard, LR and Revsbech, NP and Reichardt, W}, title = {Use of an oxygen-insensitive microscale biosensor for methane to measure methane concentration profiles in a rice paddy.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {3}, pages = {864-870}, pmid = {16349527}, issn = {0099-2240}, abstract = {An oxygen-insensitive microscale biosensor for methane was constructed by furnishing a previously described biosensor with an oxygen guard. The guard consisted of a glass capillary containing heterotrophic bacteria, which consumed oxygen diffusing through the tip membrane, thus preventing it from diffusing into the methane-sensing unit. Oxygen microprofiles were measured through the oxygen guard capillary, demonstrating the principle and limitations of the method. When the tip of the guard capillary was exposed to 100% oxygen at 21 degrees C, heterotrophic oxygen consumption prevented oxygen from diffusing further than 170 mum into the capillary, whereas atmospheric levels of oxygen were consumed within 50 mum. The capacity of the oxygen guard for scavenging oxygen decreased with decreasing temperature, and atmospheric levels of oxygen caused oxygen penetration to 200 mum at 5 degrees C. The sensors could be manufactured with tip diameters as small as 25 mum, and response times were about 1 min at room temperature. Pore water profiles of methane concentrations in a rice paddy soil were measured, and a strong correlation between the depths of oxygen penetration and methane appearance was observed as a function of the light regimen; this finding confirmed the role of microbenthic photosynthesis in limiting methane emissions from surfaces of waterlogged sediments and soils.}, }
@article {pmid16349506, year = {1998}, author = {Santo Domingo, JW and Kaufman, MG and Klug, MJ and Tiedje, JM}, title = {Characterization of the Cricket Hindgut Microbiota with Fluorescently Labeled rRNA-Targeted Oligonucleotide Probes.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {2}, pages = {752-755}, pmid = {16349506}, issn = {0099-2240}, abstract = {Most cricket hindgut microorganisms (60 to 80%) were detected with a universal fluorescent rRNA-targeted probe and found to be eubacteria. Group-specific probes showed that the hindguts of five different cricket species harbor similar bacterial groups, although in different proportions, and that different diets shifted the structure of the hindgut microbial community. The Bacteroides-Prevotella probe, of the eight eubacterial probes tested, stained the largest percentage of cells in all crickets.}, }
@article {pmid16349497, year = {1998}, author = {Weinbauer, MG and Höfle, MG}, title = {Significance of viral lysis and flagellate grazing as factors controlling bacterioplankton production in a eutrophic lake.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {2}, pages = {431-438}, pmid = {16349497}, issn = {0099-2240}, abstract = {The effects of viral lysis and heterotrophic nanoflagellate (HNF) grazing on bacterial mortality were estimated in a eutrophic lake (Lake Plusssee in northern Germany) which was separated by a steep temperature and oxygen gradient into a warm and oxic epilimnion and a cold and anoxic hypolimnion. Two transmission electron microscopy-based methods (whole-cell examination and thin sections) were used to determine the frequency of visibly infected cells, and a model was used to estimate bacterial mortality due to viral lysis. Examination of thin sections also showed that between 20.2 and 29.2% (average, 26.1%) of the bacterial cells were empty (ghosts) and thus could not contribute to viral production. The most important finding was that the mechanism for regulating bacterial production shifted with depth from grazing control in the epilimnion to control due to viral lysis in the hypolimnion. We estimated that in the epilimnion viral lysis accounted on average for 8.4 to 41.8% of the summed mortality (calculated by determining the sum of the mortalities due to lysis and grazing), compared to 51.3 to 91.0% of the summed mortality in the metalimninon and 88.5 to 94.2% of the summed mortality in the hypolimnion. Estimates of summed mortality values indicated that bacterial production was controlled completely or almost completely in the epilimnion (summed mortality, 66.6 to 128.5%) and the hypolimnion (summed mortality, 43.4 to 103.3%), whereas in the metalimnion viral lysis and HNF grazing were not sufficient to control bacterial production (summed mortality, 22.4 to 56.7%). The estimated contribution of organic matter released by viral lysis of cells into the pool of dissolved organic matter (DOM) was low; however, since cell lysis products are very likely labile compared to the bulk DOM, they might stimulate bacterial production. The high mortality of bacterioplankton due to viral lysis in anoxic water indicates that a significant portion of bacterial production in the metalimnion and hypolimnion is cycled in the bacterium-virus-DOM loop. This finding has major implications for the fate and cycling of organic nutrients in lakes.}, }
@article {pmid16349483, year = {1998}, author = {Bååth, E and Díaz-Raviña, M and Frostegård, S and Campbell, CD}, title = {Effect of metal-rich sludge amendments on the soil microbial community.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {1}, pages = {238-245}, pmid = {16349483}, issn = {0099-2240}, abstract = {The effects of heavy-metal-containing sewage sludge on the soil microbial community were studied in two agricultural soils of different textures, which had been contaminated separately with three predominantly single metals (Cu, Zn, and Ni) at two different levels more than 20 years ago. We compared three community-based microbiological measurements, namely, phospholipid fatty acid (PLFA) analysis to reveal changes in species composition, the Biolog system to indicate metabolic fingerprints of microbial communities, and the thymidine incorporation technique to measure bacterial community tolerance. In the Luddington soil, bacterial community tolerance increased in all metal treatments compared to an unpolluted-sludge-treated control soil. Community tolerance to specific metals increased the most when the same metal was added to the soil; for example, tolerance to Cu increased most in Cu-polluted treatments. A dose-response effect was also evident. There were also indications of cotolerance to metals whose concentration had not been elevated by the sludge treatment. The PLFA pattern changed in all metal treatments, but the interpretation was complicated by the soil moisture content, which also affected the results. The Biolog measurements indicated similar effects of metals and moisture to the PLFA measurements, but due to high variation between replicates, no significant differences compared to the uncontaminated control were found. In the Lee Valley soil, significant increases in community tolerance were found for the high levels of Cu and Zn, while the PLFA pattern was significantly altered for the soils with high levels of Cu, Ni, and Zn. No effects on the Biolog measurements were found in this soil.}, }
@article {pmid16343329, year = {2006}, author = {Kovacik, WP and Takai, K and Mormile, MR and McKinley, JP and Brockman, FJ and Fredrickson, JK and Holben, WE}, title = {Molecular analysis of deep subsurface Cretaceous rock indicates abundant Fe(III)- and S(zero)-reducing bacteria in a sulfate-rich environment.}, journal = {Environmental microbiology}, volume = {8}, number = {1}, pages = {141-155}, doi = {10.1111/j.1462-2920.2005.00876.x}, pmid = {16343329}, issn = {1462-2912}, mesh = {Base Sequence ; *Biodiversity ; Blotting, Northern ; DNA Primers ; Deltaproteobacteria/*genetics/metabolism ; Electrophoresis ; Geologic Sediments/*microbiology ; Geological Phenomena ; Geology ; Iron/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; *Phylogeny ; Sequence Analysis, DNA ; Sulfur/*metabolism ; }, abstract = {A multilevel sampler (MLS) was emplaced in a borehole straddling anaerobic, sulfate-rich Cretaceous-era shale and sandstone rock formations approximately 200 m below ground surface at Cerro Negro, New Mexico. Sterile quartzite sand contained in chambers in the sampler allowed in situ colonization and recovery of nucleic acids for molecular analyses. Denaturing gradient gel electrophoresis and 16S rRNA gene cloning results indicated a homogeneously distributed bacterial community across the shale-sandstone interface. delta-Proteobacteria sequences were common at all depths, and were dominated by members of the Geobacteraceae family (Pelobacter, Desulphuromonas and Geobacter). Other members of this group are capable of dissimilatory Fe(III) and/or S degrees reduction, but not sulfate reduction. RNA hybridization data also suggested that Fe(III)-/S degrees -reducing bacteria were predominant. These findings are striking considering the lack of significant concentrations of these electron acceptors in this environment. The next most abundant bacterial group indicated was the sulfate reducers, including Desulfobacterium, Desulfocapsa and Desulfobulbus. Sequences related to fermenters, denitrifiers and acetogens were also recovered. The presence of a phylogenetically and functionally diverse microbial community in this deep subsurface environment likely reflects the complex nature of the primary energy and carbon sources, kerogen associated with the shale.}, }
@article {pmid16341831, year = {2005}, author = {Luis, P and Kellner, H and Zimdars, B and Langer, U and Martin, F and Buscot, F}, title = {Patchiness and spatial distribution of laccase genes of ectomycorrhizal, saprotrophic, and unknown basidiomycetes in the upper horizons of a mixed forest cambisol.}, journal = {Microbial ecology}, volume = {50}, number = {4}, pages = {570-579}, pmid = {16341831}, issn = {0095-3628}, mesh = {Base Sequence ; Basidiomycota/classification/*enzymology/*genetics ; DNA, Fungal/chemistry ; Demography ; Genetic Variation ; Germany ; Laccase/classification/*genetics ; Molecular Sequence Data ; Mycorrhizae/genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; Trees/*microbiology ; }, abstract = {Decomposition of plant litter by the soil microbial community is an important process of controlling nutrient cycling and soil humus formation. Fungal laccases are key players in litter-associated polyphenol degradation, but little is known about the diversity and spatial distribution of fungal species with laccase genes in soils. Diversity of basidiomycete laccase genes was assessed in a cambisolic forest soil, and the spatial distribution of the sequences was mapped in a 100-m(2) plot by using polymerase chain reaction (PCR) on soil DNA extracts. Diversity of laccase sequences was higher in the organic horizon and decreased with the depth. A total of 167 different sequences sharing 44-96% oligonucleotide similarity was found in 13 soil cores harvested in the 100-m(2) plot. Dissimilarity in laccase sequence content was 67% between adjacent cores; 45.5%, 35.5% and 19% of laccase sequences were attributed to ectomycorrhizal, unknown and saprotrophic basidiomycetes, respectively. Most dominant sequences were attributed to the extramatrical hyphae of known ectomycorrhizal taxa (e.g., Russulaceae) and restricted to small patches (<0.77 m(2)) in a specific soil horizon. Soil fungi with laccase genes occupied different niches and showed strikingly variable distribution patterns. The distribution of laccase sequences, and corresponding fungi, likely reflected a part of the oxidative potential in soils.}, }
@article {pmid16341642, year = {2005}, author = {Algesten, G and Sobek, S and Bergström, AK and Jonsson, A and Tranvik, LJ and Jansson, M}, title = {Contribution of sediment respiration to summer CO2 emission from low productive boreal and subarctic lakes.}, journal = {Microbial ecology}, volume = {50}, number = {4}, pages = {529-535}, pmid = {16341642}, issn = {0095-3628}, mesh = {Carbon/analysis/metabolism ; Carbon Dioxide/*analysis/metabolism ; Ecosystem ; Fresh Water/*chemistry ; Geologic Sediments/*chemistry ; Methane/analysis/metabolism ; Seasons ; Sweden ; }, abstract = {We measured sediment production of carbon dioxide (CO(2)) and methane (CH(4)) and the net flux of CO(2) across the surfaces of 15 boreal and subarctic lakes of different humic contents. Sediment respiration measurements were made in situ under ambient light conditions. The flux of CO(2) between sediment and water varied between an uptake of 53 and an efflux of 182 mg C m(-2) day(-1) from the sediments. The mean respiration rate for sediments in contact with the upper mixed layer (SedR) was positively correlated to dissolved organic carbon (DOC) concentration in the water (r(2) = 0.61). The net flux of CO(2) across the lake surface [net ecosystem exchange (NEE)] was also closely correlated to DOC concentration in the upper mixed layer (r(2) = 0.73). The respiration in the water column was generally 10-fold higher per unit lake area compared to sediment respiration. Lakes with DOC concentrations <5.6 mg L(-1) had net consumption of CO(2) in the sediments, which we ascribe to benthic primary production. Only lakes with very low DOC concentrations were net autotrophic (<2.6 mg L(-1)) due to the dominance of dissolved allochthonous organic carbon in the water as an energy source for aquatic organisms. In addition to previous findings of allochthonous organic matter as an important driver of heterotrophic metabolism in the water column of lakes, this study suggests that sediment metabolism is also highly dependent on allochthonous carbon sources.}, }
@article {pmid16341641, year = {2005}, author = {Franco, AR and Calheiros, CS and Pacheco, CC and De Marco, P and Manaia, CM and Castro, PM}, title = {Isolation and characterization of polymeric galloyl-ester-degrading bacteria from a tannery discharge place.}, journal = {Microbial ecology}, volume = {50}, number = {4}, pages = {550-556}, pmid = {16341641}, issn = {0095-3628}, mesh = {Bacteria/classification/growth &amp; development/isolation &amp; purification/*metabolism ; Bacteria, Aerobic/classification/isolation &amp; purification/metabolism ; Biodegradation, Environmental ; Chromatography, High Pressure Liquid/methods ; Culture Media/chemistry ; Flavonoids/*metabolism ; Hydrolyzable Tannins/metabolism ; *Industrial Waste ; Phenols/*metabolism ; Plant Roots/*microbiology ; Poaceae/microbiology ; Polyphenols ; Proanthocyanidins/metabolism ; *Soil Microbiology ; Typhaceae/microbiology ; Zingiberales/microbiology ; }, abstract = {The culturable bacteria colonizing the rhizosphere of plants growing in the area of discharge of a tannery effluent were characterized. Relative proportions of aerobic, denitrifying, and sulfate-reducing bacteria were determined in the rhizosphere of Typha latifolia, Canna indica, and Phragmites australis. Aerobic bacteria were observed to be the most abundant group in the rhizosphere, and plant type did not seem to influence the abundance of the bacterial types analyzed. To isolate bacteria able to degrade polyphenols used in the tannery industry, enrichments were conducted under different conditions. Bacterial cultures were enriched with individual polyphenols (tannins Tara, Quebracho, or Mimosa) or with an undefined mixture of tannins present in the tannery effluent as carbon source. Cultures enriched with the effluent or Tara tannin were able to degrade tannic acid. Six bacterial isolates purified from these mixed cultures were able to use tannic acid as a sole carbon source in axenic culture. On the basis of 16S ribosomal DNA sequence analysis, these isolates were closely related to organisms belonging to the taxa Serratia, Stenotrophomonas maltophilia, Klebsiella oxytoca, Herbaspirillum chlorophenolicum, and Pseudomonas putida.}, }
@article {pmid16341640, year = {2005}, author = {Jardillier, L and Bettarel, Y and Richardot, M and Bardot, C and Amblard, C and Sime-Ngando, T and Debroas, D}, title = {Effects of viruses and predators on prokaryotic community composition.}, journal = {Microbial ecology}, volume = {50}, number = {4}, pages = {557-569}, pmid = {16341640}, issn = {0095-3628}, mesh = {Animals ; Bacteria/genetics/*virology ; Biodiversity ; Ecosystem ; Lysogeny ; Mortality ; Polymorphism, Restriction Fragment Length ; Population Dynamics ; Predatory Behavior ; Prokaryotic Cells/classification/*virology ; RNA, Ribosomal, 16S/genetics ; Time Factors ; Viruses/genetics/*pathogenicity ; *Water Microbiology ; }, abstract = {Dialysis bags were used to examine the impact of predation and viral lysis on prokaryotic community composition (PCC) over a 5-day experiment in the oligomesotrophic Lake Pavin (France). The impact of the different predator communities (protists and metazoans) of prokaryotes was estimated by water fractionation (<5 microm: treatment filtered on 5 microm, without ciliates and metazoans; UNF: unfiltered treatment with all planktonic communities). Enrichments of natural viruses (<1.2 microm: with a natural virus concentration; <1.2 mum V and VV: with enrichment leading to a double or triple concentration of viruses, respectively) were used to indirectly assess the control of virioplankton. Viral activity was estimated from the frequency of visibly infected cells (FVIC). PCC was determined by fluorescence in situ hybridization (FISH) and terminal restriction fragment length polymorphism (T-RFLP). In this study, PCC was affected by the eukaryote communities (especially flagellates), and viruses to a lesser extent. Cyanobacteria declined significantly during the experiment and were highly correlated with the FVIC. In addition, the 503-bp terminal restriction fragment (T-RF) disappeared in treatments with virus enrichments, suggesting possible viral-associated mortality processes, whereas the 506-bp T-RF was not affected in these treatments. On one hand, these results suggest a control of the PCC: first, by viral lysis of some dominant phylotypes and second, by interspecific competition between resistant strains for the uptake of substrates released by this lysis. The increase of Archaea may suggest that these cells benefit such resources. On the other hand, the disappearance and the stable proportion of some dominant phylotypes suggested a selection pressure due to the predatory activity on prokaryotes. In conclusion, prokaryotic abundance appears to be mainly controlled by flagellate protists, which also affected PCC, whereas viruses seemed to be essentially responsible for profound changes in PCC via direct and indirect actions.}, }
@article {pmid16341639, year = {2005}, author = {Lyautey, E and Jackson, CR and Cayrou, J and Rols, JL and Garabétian, F}, title = {Bacterial community succession in natural river biofilm assemblages.}, journal = {Microbial ecology}, volume = {50}, number = {4}, pages = {589-601}, pmid = {16341639}, issn = {0095-3628}, mesh = {Bacteria/*classification/genetics/growth &amp; development ; *Biodiversity ; Biofilms/*classification/growth &amp; development ; Biomass ; Chlorophyll/analysis ; Chlorophyll A ; DNA, Bacterial/analysis/chemistry ; *Ecosystem ; Electrophoresis, Polyacrylamide Gel ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Rivers/*microbiology ; Species Specificity ; }, abstract = {Temporal bacterial community changes in river biofilms were studied using 16S rRNA gene-based polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) followed by sequence analysis. Naturally occurring biofilms were sampled in 2001 during an undisturbed 7-month low-water period in the River Garonne (SW France). During the sampling period epilithic biomass exhibited a particular pattern: two 3-month periods of accumulation that resulted in two peaks in summer and fall, each at about 25 g ash-free dry mass per square meter. Bacterial community DGGE profiles differed between the summer and fall biomass peaks and shared only 30% common operational taxonomic units (OTUs), suggesting the influence of seasonal factors on these communities. During the second biomass accrual phase, bacterial richness and the appearance of new OTUs fitted a conceptual model of bacterial biofilm succession. During succession, five OTUs (corresponding to Dechloromonas sp., Nitrospira sp., and three different Spirosoma spp.) exhibited particular patterns and were present only during clearly defined successional stages, suggesting differences in life-history strategies for epilithic bacteria. Co-inertia analysis of DGGE banding patterns and physical-chemical data showed a significant relationship between community structure and environmental conditions suggesting that bacterial communities were mainly influenced by seasonal changes (temperature, light) and hydrodynamic stability. Within the periods of stability, analysis of environmental variables and community patterns showed the dominant influence of time and maturation on bacterial community structure. Thus, succession in these naturally occurring epilithic biofilm assemblages appears to occur through a combination of allogenic (seasonal) and autogenic changes.}, }
@article {pmid16341638, year = {2005}, author = {Pusceddu, A and Fiordelmondo, C and Danovaro, R}, title = {Sediment resuspension effects on the benthic microbial loop in experimental microcosms.}, journal = {Microbial ecology}, volume = {50}, number = {4}, pages = {602-613}, pmid = {16341638}, issn = {0095-3628}, mesh = {Aminopeptidases/metabolism ; Analysis of Variance ; Bacteria/enzymology/*growth &amp; development ; Biomass ; Biopolymers/metabolism ; Carbohydrates/analysis ; Carbon/metabolism ; *Ecosystem ; Geologic Sediments/*chemistry/microbiology ; Proteins/analysis ; Time Factors ; *Water Microbiology ; beta-Glucosidase/metabolism ; }, abstract = {Sediment resuspension induced by anthropogenic disturbance is becoming a major threat of marine coastal ecosystems worldwide. The effects of sediment resuspension on the pelagic domain and on macro- and meiobenthos are well documented in the literature, whereas the effects on the benthic microbial components are nearly neglected. We have investigated the effects of sediment resuspension at two different disturbance levels on benthic bacterial abundance, biomass, and activities and on heterotrophic nanobenthos abundance in experimental microcosms. The results of our experiments pointed out that, independently from the amount of involved energy, sediment resuspension determined a general decrease of all benthic microbial components. The main effects consisted of a decreased abundance of the metabolically active bacterial fraction and of heterotrophic nanobenthos abundance. However, the amount of energy involved in sediment resuspension had differential effects on the structure and functioning of the benthic microbial loop, but only in the short term (i.e., within 36 h). Sediment resuspension had a stimulatory effect on activities of surviving bacterial cells, which, in turn, resulted in increased sediment organic C turnover rates. We hypothesize that such an effect, enhancing nutrient availability, might have relevant consequences on the trophic state of coastal marine ecosystem.}, }
@article {pmid16341637, year = {2005}, author = {Sánchez, O and Diestra, E and Esteve, I and Mas, J}, title = {Molecular characterization of an oil-degrading cyanobacterial consortium.}, journal = {Microbial ecology}, volume = {50}, number = {4}, pages = {580-588}, pmid = {16341637}, issn = {0095-3628}, mesh = {Biodegradation, Environmental ; Biodiversity ; Cloning, Molecular ; Cyanobacteria/*classification/*genetics/metabolism ; DNA, Bacterial/analysis/isolation &amp; purification ; Electrophoresis, Polyacrylamide Gel/methods ; Petroleum/*metabolism ; Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/chemistry/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Recent studies have shown that the cyanobacterium Microcoleus chthonoplastes forms a consortium with heterotrophic bacteria present within the cyanobacterial sheath. These studies also show that this consortium is able to grow in the presence of crude oil, degrading aliphatic heterocyclic organo-sulfur compounds as well as alkylated monocyclic and polycyclic aromatic hydrocarbons. In this work, we characterize this oil-degrading consortium through the analysis of the 16S rRNA gene sequences. We performed the study in cultures of Microcoleus grown in mineral medium and in cultures of the cyanobacterium grown in mineral medium supplemented with crude oil. The results indicate that most of the clones found in the polluted culture correspond to well-known oil-degrading and nitrogen-fixing microorganisms, and belong to different phylogenetic groups, such as the Alpha, Beta, and Gamma subclasses of Proteobacteria, and the Cytophaga/Flavobacteria/Bacteroides group. The control is dominated by one predominant organism (88% of the clones) closely affiliated to Pseudoxanthomonas mexicana (similarity of 99.8%). The presence of organisms closely related to well-known nitrogen fixers such as Rhizobium and Agrobacterium suggests that at least some of the cyanobacteria-associated heterotrophic bacteria are responsible for nitrogen fixation and degradation of hydrocarbon compounds inside the polysaccharidic sheath, whereas Microcoleus provides a habitat and a source of oxygen and organic matter.}, }
@article {pmid16341636, year = {2005}, author = {Declerck, P and Behets, J and Delaedt, Y and Margineanu, A and Lammertyn, E and Ollevier, F}, title = {Impact of non-Legionella bacteria on the uptake and intracellular replication of Legionella pneumophila in Acanthamoeba castellanii and Naegleria lovaniensis.}, journal = {Microbial ecology}, volume = {50}, number = {4}, pages = {536-549}, pmid = {16341636}, issn = {0095-3628}, mesh = {Acanthamoeba castellanii/cytology/metabolism/*microbiology ; Aeromonas hydrophila/physiology/radiation effects ; Analysis of Variance ; Animals ; Bacteria/classification/metabolism/radiation effects ; *Bacterial Physiological Phenomena/radiation effects ; Escherichia coli/physiology/radiation effects ; Flavobacterium/physiology/radiation effects ; Legionella pneumophila/*growth &amp; development ; Microscopy, Confocal/methods ; Microscopy, Fluorescence ; Naegleria/metabolism/*microbiology ; Pseudomonas aeruginosa/physiology/radiation effects ; Ultraviolet Rays ; }, abstract = {In aquatic environments, Legionella pneumophila survives, in association with other bacteria, within biofilms by multiplying in free-living amoebae. The precise mechanisms underlying several aspects of the uptake and intracellular replication of L. pneumophila in amoebae, especially in the presence of other bacteria, remain unknown. In the present study, we examined the competitive effect of selected non-Legionella bacteria (Escherichia coli, Aeromonas hydrophila, Flavobacterium breve, and Pseudomonas aeruginosa) on the uptake of L. pneumophila serogroup 1 by the amoebae Acanthamoeba castellanii and Naegleria lovaniensis. We also investigated their possible influence on the intracellular replication of L. pneumophila in both amoeba species. Our results showed that the non-Legionella bacteria did not compete with L. pneumophila for uptake, suggesting that the amoeba hosts took in L. pneumophila through a specific and presumably highly efficient uptake mechanism. Living and heat-inactivated P. aeruginosa best supported the replication of L. pneumophila in N. lovaniensis and A. castellanii, respectively, whereas for both amoeba species, E. coli yielded the lowest number of replicated L. pneumophila. Furthermore, microscopic examination showed that 100% of the A. castellanii and only 2% of the N. lovaniensis population were infected with L. pneumophila at the end of the experiment. This study clearly shows the influence of some non-Legionella bacteria on the intracellular replication of L. pneumophila in A. castellanii and N. lovaniensis. It also demonstrates the different abilities of the two tested amoeba species to serve as a proper host for the replication and distribution of the human pathogen in man-made aquatic environments such as cooling towers, shower heads, and air conditioning systems with potential serious consequences for human health.}, }
@article {pmid16333718, year = {2005}, author = {Renker, C and Otto, P and Schneider, K and Zimdars, B and Maraun, M and Buscot, F}, title = {Oribatid mites as potential vectors for soil microfungi: study of mite-associated fungal species.}, journal = {Microbial ecology}, volume = {50}, number = {4}, pages = {518-528}, pmid = {16333718}, issn = {0095-3628}, mesh = {Animals ; Arachnid Vectors/*microbiology ; Base Sequence ; Cloning, Molecular ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Ecosystem ; Fungi/*classification/genetics/isolation &amp; purification/ultrastructure ; Genes, rRNA/genetics ; Mites/*microbiology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Soil Microbiology ; Species Specificity ; }, abstract = {The ability of soil-living oribatid mites to disperse fungal propagules on their bodies was investigated. Classical plating methods were applied to cultivate these fungi and to study their morphology. Molecular markers were used for further determination. The nuclear ribosomal large subunit and the nuclear ribosomal internal transcribed spacer of DNA extracts of the cultured fungi as well as total DNA extracts of the mites themselves, also containing fungal DNA, were amplified and sequenced. Based on phylogenetic analysis, a total of 31 fungal species from major fungal groups were found to be associated with oribatid mites, indicating that mites do not selectively disperse specific species or species groups. The detected taxa were mainly saprobiontic, cosmopolitan (e.g., Alternaria tenuissima), but also parasitic fungi (Beauveria bassiana) for whose dispersal oribatid mites might play an important role. In contrast, no mycorrhizal fungi were detected in association with oribatid mites, indicating that their propagules are dispersed in a different way. In addition, fungi that are known to be a preferred food for oribatid mites such as the Dematiacea were not detected in high numbers. Results of this study point to the potential of oribatid mites to disperse fungal taxa in soil and indicate that co-evolutionary patterns between oribatid mites and their associated fungi might be rare or even missing in most cases, since we only detected ubiquitous taxa attached to the mites.}, }
@article {pmid16333717, year = {2005}, author = {Lejon, DP and Chaussod, R and Ranger, J and Ranjard, L}, title = {Microbial community structure and density under different tree species in an acid forest soil (Morvan, France).}, journal = {Microbial ecology}, volume = {50}, number = {4}, pages = {614-625}, pmid = {16333717}, issn = {0095-3628}, mesh = {Bacteria/classification/genetics/*growth &amp; development ; *Biodiversity ; Biomass ; Carbon/analysis ; DNA, Ribosomal Spacer/genetics ; France ; Fungi/classification/genetics/*growth &amp; development ; Genetic Variation ; Principal Component Analysis ; Soil/analysis ; *Soil Microbiology ; Species Specificity ; *Trees ; }, abstract = {Overexploitation of forests to increase wood production has led to the replacement of native forest by large areas of monospecific tree plantations. In the present study, the effects of different monospecific tree cover plantations on density and composition of the indigenous soil microbial community are described. The experimental site of "Breuil-Chenue" in the Morvan (France) was the site of a comparison of a similar mineral soil under Norway spruce (Picea abies), Douglas fir (Pseudotuga menziesii), oak (Quercus sessiflora), and native forest [mixed stand dominated by oak and beech (Fagus sylvatica)]. Sampling was performed during winter (February) at three depths (0-5, 5-10, and 10-15 cm). Abundance of microorganisms was estimated via microbial biomass measurements, using the fumigation-extraction method. The genetic structure of microbial communities was investigated using the bacterial- and fungal-automated ribosomal intergenic spacer analysis (B-ARISA and F-ARISA, respectively) DNA fingerprint. Only small differences in microbial biomass were observed between tree species, the highest values being recorded under oak forest and the lowest under Douglas fir. B- and F-ARISA community profiles of the different tree covers clustered separately, but noticeable similarities were observed for soils under Douglas fir and oak. A significant stratification was revealed under each tree species by a decrease in microbial biomass with increasing depths and by distinct microbial communities for each soil layer. Differences in density and community composition according to tree species and depth were related to soil physicochemical characteristics and organic matter composition.}, }
@article {pmid16333331, year = {2005}, author = {Morgan-Sagastume, F and Boon, N and Dobbelaere, S and Defoirdt, T and Verstraete, W}, title = {Production of acylated homoserine lactones by Aeromonas and Pseudomonas strains isolated from municipal activated sludge.}, journal = {Canadian journal of microbiology}, volume = {51}, number = {11}, pages = {924-933}, doi = {10.1139/w05-077}, pmid = {16333331}, issn = {0008-4166}, mesh = {4-Butyrolactone/*analogs &amp; derivatives/biosynthesis/chemistry ; Aeromonas/*classification/isolation &amp; purification/*metabolism ; Agrobacterium tumefaciens/growth &amp; development ; Bacterial Typing Techniques/methods ; Chromatography, Thin Layer ; Chromobacterium/growth &amp; development ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/methods ; Pseudomonas/*classification/isolation &amp; purification/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Sewage/*microbiology ; Waste Disposal, Fluid ; }, abstract = {Up to now, the production and role of N-acyl homoserine lactones (AHLs) in activated sludge have been poorly understood. In this study, cross-feeding assays with the reporter strains Agrobacterium tumefaciens NTL4 and Chromobacterium violaceum CV026 were used to investigate AHL signal production by municipal activated sludge samples. AHL signal production was consistently detected from municipal activated sludge when different samples were incubated on nutrient media. From one municipal activated sludge sample, 10 strains producing AHL-like auto inducers were isolated by an overlay technique. 16S rDNA-based phylogenetic analysis showed that eight of the isolates belonged to Aeromonas spp. and two to Pseudomonas spp. Box-PCR indicated that six of these Aeromonas isolates were different strains and the two Pseudomonas strains were identical. The production of AHL or AHL-like compounds by these strains was confirmed by thin layer chromatography and biosensor overlays. The six different Aeromonas strains were found to produce the same set of AHLs, including N-hexanoyl-L-homoserine lactone. These results may indicate the possible presence of AHLs in municipal activated sludge. The potential roles of AHL in this eco system are briefly discussed.}, }
@article {pmid16332868, year = {2005}, author = {Coolen, MJ and Post, E and Davis, CC and Forney, LJ}, title = {Characterization of microbial communities found in the human vagina by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {12}, pages = {8729-8737}, pmid = {16332868}, issn = {0099-2240}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; P20 RR16448/RR/NCRR NIH HHS/United States ; }, mesh = {Base Sequence ; DNA Primers ; Female ; Humans ; Lactobacillus/*genetics/isolation &amp; purification ; *Polymorphism, Restriction Fragment Length ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; Staphylococcus/genetics/isolation &amp; purification ; Streptococcus/genetics/isolation &amp; purification ; Vagina/*microbiology ; }, abstract = {To define and monitor the structure of microbial communities found in the human vagina, a cultivation-independent approach based on analyses of terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes was developed and validated. Sixteen bacterial strains commonly found in the human vagina were used to construct model communities that were subsequently used to develop efficient means for the isolation of genomic DNA and an optimal strategy for T-RFLP analyses. The various genera in the model community could best be resolved by digesting amplicons made using bacterial primers 8f and 926r with HaeIII; fewer strains could be resolved using other primer-enzyme combinations, and no combination successfully distinguished certain species of the same genus. To demonstrate the utility of the approach, samples from five women that had been collected over a 2-month period were analyzed. Differences and similarities among the vaginal microbial communities of the women were readily apparent. The T-RFLP data suggest that the communities of three women were dominated by a single phylotype, most likely species of Lactobacillus. In contrast, the communities of two other women included numerically abundant populations that differed from Lactobacillus strains whose 16S rRNA genes had been previously determined. The T-RFLP profiles of samples from all the women were largely invariant over time, indicating that the kinds and abundances of the numerically dominant populations were relatively stable throughout two menstrual cycles. These findings show that T-RFLP of 16S rRNA genes can be used to compare vaginal microbial communities and gain information about the numerically dominant populations that are present.}, }
@article {pmid16329955, year = {2005}, author = {Coci, M and Riechmann, D and Bodelier, PL and Stefani, S and Zwart, G and Laanbroek, HJ}, title = {Effect of salinity on temporal and spatial dynamics of ammonia-oxidising bacteria from intertidal freshwater sediment.}, journal = {FEMS microbiology ecology}, volume = {53}, number = {3}, pages = {359-368}, doi = {10.1016/j.femsec.2005.01.016}, pmid = {16329955}, issn = {0168-6496}, mesh = {Ammonia/metabolism ; Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/analysis/genetics ; Electrophoresis/methods ; Fresh Water/chemistry/microbiology ; Geologic Sediments/chemistry/*microbiology ; Oxidation-Reduction ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sodium Chloride/*pharmacology ; Time Factors ; }, abstract = {Temporal and spatial dynamics within an ammonia-oxidising community from intertidal, freshwater sediments were studied in microcosms simulating flooding twice a day with fresh, brackish and marine waters. The microcosms had been filled with the upper 5 cm of intertidal freshwater sediment from the river Scheldt. Changes in community composition were examined by denaturing gradient gel electrophoresis of amplified DNA from the community. In the first week of incubation the initially present members of the Nitrosomonas oligotropha lineage were replaced by other members of the same lineage in the top layer of the sediment subjected to flooding with freshwater. Prolonged incubation extended niche differentiation to a depth of 5 cm. In the microcosms flooded with saline media, the initially present members of the N. oligotropha lineage were replaced by strains belonging to the Nitrosomonas marina lineage, but only in the top 1cm. Shift in community composition occurred earlier in the marine microcosms than in the brackish microcosms and was slower than the change in the freshwater microcosms. Irrespective of the nature of the flooding medium, shifts in community composition were always consistent among replicate microcosms. We conclude that salinity is an important steering factor in niche differentiation among ammonia-oxidising bacteria and also that changes within the community of this functional group of bacteria may occur at different rates.}, }
@article {pmid16329952, year = {2005}, author = {Kennedy, NM and Gleeson, DE and Connolly, J and Clipson, NJ}, title = {Seasonal and management influences on bacterial community structure in an upland grassland soil.}, journal = {FEMS microbiology ecology}, volume = {53}, number = {3}, pages = {329-337}, doi = {10.1016/j.femsec.2005.01.013}, pmid = {16329952}, issn = {0168-6496}, mesh = {Bacteria/*genetics ; DNA Fingerprinting ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal Spacer/analysis ; Hydrogen-Ion Concentration ; Ireland ; Nitrogen/analysis ; Phosphorus/analysis ; *Poaceae ; Potassium/analysis ; Seasons ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Floristically diverse Nardo-Galion upland grasslands are common in Ireland and the UK and are valuable in agricultural, environmental and ecological terms. Under improvement (inputs of lime, fertiliser and re-seeding), they convert to mesotrophic grassland containing very few plant species. The effects of upland grassland improvement and seasonality on soil microbial communities were investigated at an upland site. Samples were taken at five times in one year in order to observe seasonal trends, and bacterial community structure was monitored using automated ribosomal intergenic spacer analysis (ARISA), a DNA-fingerprinting approach. Differences in soil chemistry and bacterial community structure between unimproved and improved grassland soils were noted. Season was also found to cause mild fluctuations in bacterial community structure, with soil samples from colder months (October and December) more correlated with change in ribotype profiles than samples from warmer months. However, for the majority of seasons clear differences in bacterial community structures from unimproved and improved soils could be seen, indicating seasonal influences did not obscure effects associated with improvement.}, }
@article {pmid16329938, year = {2005}, author = {Collins, G and Foy, C and McHugh, S and O'Flaherty, V}, title = {Anaerobic treatment of 2,4,6-trichlorophenol in an expanded granular sludge bed-anaerobic filter (EGSB-AF) bioreactor at 15 degrees C.}, journal = {FEMS microbiology ecology}, volume = {53}, number = {1}, pages = {167-178}, doi = {10.1016/j.femsec.2004.10.008}, pmid = {16329938}, issn = {0168-6496}, mesh = {Bacteria, Anaerobic/*metabolism ; Biodegradation, Environmental ; *Bioreactors ; Chlorophenols/*metabolism ; Chromatography, High Pressure Liquid ; Methane/analysis ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; Species Specificity ; Spectrophotometry, Ultraviolet ; Temperature ; Time Factors ; Waste Disposal, Fluid/*methods ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Expanded granular sludge bed-anaerobic filter (EGSB-AF) bioreactors were operated at 15 degrees C for the treatment of 2,4,6-trichlorophenol (TCP)-containing volatile fatty acid (VFA)-based wastewaters. The seed sludge used as inoculum for the control (no TCP) and test reactor was unexposed to chlorophenols (CPs) prior to the 425-day trial. TCP supplementation to the feed at 50 mg TCPl(-1) partially inhibited the anaerobic degradation of the VFA feed measured as COD removal efficiency. However, the withdrawal and subsequent application of stepwise increments to the TCP loading resulted in steady COD removal. Terminal restriction fragment length polymorphism analysis showed Methanosaeta-like Archaea in the control reactor over the experimental period. Different methanogenic populations were detected in the test reactor and responded to the changes in feed composition. Bacterial community analyses indicated changes in the community structure over time and suggested the presence of Campylobacter-like, Acidimicrobium-like and Heliophilum-like organisms in the samples. TCP mineralisation was by a reductive dechlorination pathway through 2,4-dichlorophenol (DCP) and 4-chlorophenol (4-CP) or 2-chlorophenol (2-CP). CP degradation rates in sludge granules from the lower chamber of the hybrid EGSB-AF reactor was in the order TCP > DCP > 4-CP > 2-CP. However, a biodegradability order of lower CPs > TCP was observed in fixed-film biomass taken from the upper reactor chamber, thus reflecting the role of this reactor section in the metabolism of residual lower CPs from the lower sludge-bed stage of operation.}, }
@article {pmid16329903, year = {2005}, author = {Bodelier, PL and Meima-Franke, M and Zwart, G and Laanbroek, HJ}, title = {New DGGE strategies for the analyses of methanotrophic microbial communities using different combinations of existing 16S rRNA-based primers.}, journal = {FEMS microbiology ecology}, volume = {52}, number = {2}, pages = {163-174}, doi = {10.1016/j.femsec.2004.11.004}, pmid = {16329903}, issn = {0168-6496}, mesh = {DNA Primers/*genetics ; Ecosystem ; Electrophoresis, Gel, Two-Dimensional/*methods ; Fresh Water ; Genetic Variation ; Methane/metabolism ; Methylobacteriaceae/*genetics/*isolation &amp; purification/metabolism ; Nucleic Acid Denaturation ; Phylogeny ; RNA, Bacterial/analysis/*genetics ; RNA, Ribosomal, 16S/*genetics ; Soil Microbiology ; }, abstract = {Methane-oxidising microbial communities are studied intensively because of their importance for global methane cycling. A suite of molecular microbial techniques has been applied to the study of these communities. Denaturing gradient gel electrophoresis (DGGE) is a diversity screening tool combining high sample throughput with phylogenetic information of high resolution. The existing 16S rRNA-based DGGE assays available for methane-oxidising bacteria suffer from low-specificity, low phylogentic information due to the length of the amplified fragments and/or from lack of resolving power. In the present study we developed new combinations of existing primers and applied these on methane-oxidising microbial communities in a freshwater wetland marsh. The designed strategies comprised nested as well as direct amplification of environmental DNA. Successful application of direct amplification using combinations of universal and specific primers circumvents the nested designs currently used. All developed assays resulted in identical community profiles in wetland soil cores with Methylobacter sp. and Methylocystis sp.-related sequences. Changes in the occurrence of Methylobacter-related sequences with depth in the soil profile may be related to the decrease in methane-oxidizing activity.}, }
@article {pmid16329901, year = {2005}, author = {Rastall, RA and Gibson, GR and Gill, HS and Guarner, F and Klaenhammer, TR and Pot, B and Reid, G and Rowland, IR and Sanders, ME}, title = {Modulation of the microbial ecology of the human colon by probiotics, prebiotics and synbiotics to enhance human health: an overview of enabling science and potential applications.}, journal = {FEMS microbiology ecology}, volume = {52}, number = {2}, pages = {145-152}, doi = {10.1016/j.femsec.2005.01.003}, pmid = {16329901}, issn = {0168-6496}, mesh = {Colon/*drug effects/immunology/*microbiology ; Developing Countries ; Drug and Narcotic Control ; Humans ; Probiotics/chemistry/economics/*pharmacology/therapeutic use ; }, abstract = {The application of probiotics and prebiotics to the manipulation of the microbial ecology of the human colon has recently seen many scientific advances. The sequencing of probiotic genomes is providing a wealth of new information on the biology of these microorganisms. In addition, we are learning more about the interactions of probiotics with human cells and with pathogenic bacteria. An alternative means of modulating the colonic microbial community is by the use of prebiotic oligosaccharides. Increasing knowledge of the metabolism of prebiotics by probiotics is allowing us to consider specifically targeting such dietary intervention tools at specific population groups and specific disease states.}, }
@article {pmid16329892, year = {2005}, author = {Pietikäinen, J and Pettersson, M and Bååth, E}, title = {Comparison of temperature effects on soil respiration and bacterial and fungal growth rates.}, journal = {FEMS microbiology ecology}, volume = {52}, number = {1}, pages = {49-58}, doi = {10.1016/j.femsec.2004.10.002}, pmid = {16329892}, issn = {0168-6496}, mesh = {Acetates/metabolism ; Bacteria/*growth &amp; development/metabolism ; Carbon Dioxide/metabolism ; Chromatography, Gas ; Fungi/*growth &amp; development/metabolism ; Hydrogen-Ion Concentration ; *Models, Biological ; *Soil Microbiology ; *Temperature ; Thymidine/metabolism ; }, abstract = {Temperature is an important factor regulating microbial activity and shaping the soil microbial community. Little is known, however, on how temperature affects the most important groups of the soil microorganisms, the bacteria and the fungi, in situ. We have therefore measured the instantaneous total activity (respiration rate), bacterial activity (growth rate as thymidine incorporation rate) and fungal activity (growth rate as acetate-in-ergosterol incorporation rate) in soil at different temperatures (0-45 degrees C). Two soils were compared: one was an agricultural soil low in organic matter and with high pH, and the other was a forest humus soil with high organic matter content and low pH. Fungal and bacterial growth rates had optimum temperatures around 25-30 degrees C, while at higher temperatures lower values were found. This decrease was more drastic for fungi than for bacteria, resulting in an increase in the ratio of bacterial to fungal growth rate at higher temperatures. A tendency towards the opposite effect was observed at low temperatures, indicating that fungi were more adapted to low-temperature conditions than bacteria. The temperature dependence of all three activities was well modelled by the square root (Ratkowsky) model below the optimum temperature for fungal and bacterial growth. The respiration rate increased over almost the whole temperature range, showing the highest value at around 45 degrees C. Thus, at temperatures above 30 degrees C there was an uncoupling between the instantaneous respiration rate and bacterial and fungal activity. At these high temperatures, the respiration rate closely followed the Arrhenius temperature relationship.}, }
@article {pmid16329887, year = {2005}, author = {Grommen, R and Dauw, L and Verstraete, W}, title = {Elevated salinity selects for a less diverse ammonia-oxidizing population in aquarium biofilters.}, journal = {FEMS microbiology ecology}, volume = {52}, number = {1}, pages = {1-11}, doi = {10.1016/j.femsec.2004.10.001}, pmid = {16329887}, issn = {0168-6496}, mesh = {Ammonia/metabolism ; Base Sequence ; Betaproteobacteria/*drug effects/genetics/physiology ; Cluster Analysis ; Filtration/instrumentation ; Fresh Water/*microbiology ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Nitrogen/analysis ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; *Selection, Genetic ; Sequence Analysis, DNA ; Sodium Chloride/*pharmacology ; Time Factors ; }, abstract = {The activity and changes in the structure of the community of the ammonia-oxidizing bacteria belonging to the Betaproteobacteria were monitored in freshwater and artificial seawater biofilters for two months after inoculation with a commercial nitrifying consortium. Both in freshwater and artificial seawater, ammonium oxidation proceeded immediately after addition of the inoculum, although initial activity in artificial seawater was lower than in freshwater. Denaturing gradient gel electrophoresis of the ammonia-oxidizing bacterial community of the inoculum and the freshwater and the artificial seawater aquaria as a function of time showed that initially only one dominant ammonia-oxidizer, closely related to Nitrosomonas marina, was detectable in all the systems. The fingerprint of the ammonia-oxidizing bacterial community in the artificial seawater biofilters continued to be dominated by this single band. In the freshwater aquaria, in contrast, the composition of the ammonia-oxidizer community became more diverse after one month, with 4-7 new bands appearing in the denaturing gradient gel fingerprint. Since the inoculum is cultivated at an average salinity of 11 gl(-1), it is argued that the elevated salinity selects for a less diverse ammonia-oxidizer community in the inoculum and the artificial seawater aquaria.}, }
@article {pmid16329877, year = {2005}, author = {Ikeda, K and Nakamura, H and Arakawa, M and Toshiyuki Koiwa,  and Matsumoto, N}, title = {Dynamics of double-stranded RNA segments in a Helicobasidium mompa clone from a tulip tree plantation.}, journal = {FEMS microbiology ecology}, volume = {51}, number = {2}, pages = {293-301}, doi = {10.1016/j.femsec.2004.09.011}, pmid = {16329877}, issn = {0168-6496}, mesh = {*Agriculture ; Basidiomycota/*genetics/*isolation &amp; purification/pathogenicity ; Liriodendron/*microbiology ; Plant Diseases/microbiology ; RNA, Double-Stranded/*genetics ; RNA, Fungal/*genetics ; Virulence ; }, abstract = {Eighty-three isolates of the violet root rot fungus, Helicobasidium mompa, were collected in a tulip tree plantation and analyzed for the dynamics of double-stranded (ds) RNA for five years. They were divided into eight mycelial compatibility groups (MCGs). Prevalent MCGs 60 and 68 included 61 and 11 isolates, respectively. Electrophoretic profiles of dsRNA in the first year collection of MCG 60 contained no or a single large dsRNA (more than 10 kb) with or without small dsRNAs (ca. 2.0-2.5 kb). Additional dsRNA fragments, i.e., a middle dsRNA (ca. 8.0 kb) or another type of small dsRNAs, became evident within MCG 60 isolates with time. Northern hybridization revealed the relatedness of all large and middle dsRNA fragments within MCG 60 but small fragments of dsRNA were variable. Large dsRNA fragment differed from that in other MCGs even in the same field. Correlation between specific dsRNA fragments and hypovirulence was not observed. Possible explanations for the accumulation of dsRNA fragments during the growth of disease patch by MCG 60 are discussed in terms of their internal changes such as evolution of novel dsRNA fragments from pre-existing viruses or fungal genomic DNA and horizontal transmissions.}, }
@article {pmid16329863, year = {2004}, author = {de Wiele, TV and Boon, N and Possemiers, S and Jacobs, H and Verstraete, W}, title = {Prebiotic effects of chicory inulin in the simulator of the human intestinal microbial ecosystem.}, journal = {FEMS microbiology ecology}, volume = {51}, number = {1}, pages = {143-153}, doi = {10.1016/j.femsec.2004.07.014}, pmid = {16329863}, issn = {0168-6496}, mesh = {Bifidobacterium/drug effects/genetics/*physiology ; Cichorium intybus/chemistry ; Colon/*microbiology ; Electrophoresis, Gel, Two-Dimensional ; Fermentation ; Humans ; Inulin/*pharmacology ; Lactobacillaceae/drug effects/genetics/*physiology ; Polymerase Chain Reaction ; Population Dynamics ; }, abstract = {The prebiotic potential of native chicory inulin was assessed in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME) by monitoring microbial community from the colon compartments, its metabolic activity and community structure. Inulin addition selected for a higher short chain fatty acid production with shifts towards propionic and butyric acid. Conventional culture-based techniques and PCR-denaturing gradient gel electrophoresis analysis showed no remarkable changes in the overall microbial community from the colon compartments of the SHIME, whereas selective effects were seen for lactic acid bacteria. Quantitative PCR with bifidobacteria-specific primers revealed a significant increase with more than 1 log CFU ml(-1) from the proximal to distal colon, in contrast to culture-based techniques, which only showed a minor bifidogenic effect in the ascending colon. Our results indicate that inulin purports prebiotic effects from the proximal to distal colon and that real-time PCR is a more precise technique to detect differences in bifidobacterial populations whereas conventional culturing techniques are much more variable.}, }
@article {pmid16328662, year = {2005}, author = {Polymenakou, PN and Bertilsson, S and Tselepides, A and Stephanou, EG}, title = {Bacterial community composition in different sediments from the Eastern Mediterranean Sea: a comparison of four 16S ribosomal DNA clone libraries.}, journal = {Microbial ecology}, volume = {50}, number = {3}, pages = {447-462}, pmid = {16328662}, issn = {0095-3628}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Geologic Sediments/*microbiology ; Mediterranean Region ; Molecular Sequence Data ; Oceans and Seas ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Bacterial/analysis/genetics ; RNA, Ribosomal, 16S/analysis/genetics ; Species Specificity ; }, abstract = {The regional variability of sediment bacterial community composition and diversity was studied by comparative analysis of four large 16S ribosomal DNA (rDNA) clone libraries from sediments in different regions of the Eastern Mediterranean Sea (Thermaikos Gulf, Cretan Sea, and South lonian Sea). Amplified rDNA restriction analysis of 664 clones from the libraries indicate that the rDNA richness and evenness was high: for example, a near-1:1 relationship among screened clones and number of unique restriction patterns when up to 190 clones were screened for each library. Phylogenetic analysis of 207 bacterial 16S rDNA sequences from the sediment libraries demonstrated that Gamma-, Delta-, and Alphaproteobacteria, Holophaga/Acidobacteria, Planctomycetales, Actinobacteria, Bacteroidetes, and Verrucomicrobia were represented in all four libraries. A few clones also grouped with the Betaproteobacteria, Nitrospirae, Spirochaetales, Chlamydiae, Firmicutes, and candidate division OPl 1. The abundance of sequences affiliated with Gammaproteobacteria was higher in libraries from shallow sediments in the Thermaikos Gulf (30 m) and the Cretan Sea (100 m) compared to the deeper South Ionian station (2790 m). Most sequences in the four sediment libraries clustered with uncultured 16S rDNA phylotypes from marine habitats, and many of the closest matches were clones from hydrocarbon seeps, benzene-mineralizing consortia, sulfate reducers, sulk oxidizers, and ammonia oxidizers. LIBSHUFF statistics of 16S rDNA gene sequences from the four libraries revealed major differences, indicating either a very high richness in the sediment bacterial communities or considerable variability in bacterial community composition among regions, or both.}, }
@article {pmid16328661, year = {2005}, author = {Bååth, E and Díaz-Raviña, M and Bakken, LR}, title = {Microbial biomass, community structure and metal tolerance of a naturally Pb-enriched forest soil.}, journal = {Microbial ecology}, volume = {50}, number = {4}, pages = {496-505}, pmid = {16328661}, issn = {0095-3628}, mesh = {Bacteria/classification/drug effects/growth &amp; development ; *Biomass ; Colony Count, Microbial ; *Ecosystem ; Fatty Acids/analysis ; Fungi/classification/drug effects/growth &amp; development ; Hypocreales/drug effects/growth &amp; development ; Lead/*analysis/toxicity ; Leucine/metabolism ; Phospholipids/chemistry ; Soil/*analysis ; *Soil Microbiology ; Soil Pollutants/analysis/toxicity ; Statistics as Topic ; Trees ; }, abstract = {The effect of long-term elevated soil Pb levels on soil microbiota was studied at a forest site in Norway, where the soil has been severely contaminated with Pb since the last period of glaciation (several thousand years). Up to 10% Pb (total amount, w/w) has been found in the top layer. The microbial community was drastically affected, as judged from changes in the phospholipid fatty acid (PLFA) pattern. Specific PLFAs that were high in Pb-enriched soil were branched (especially br17:0 and br18:0), whereas PLFAs common in eukaryotic organisms such as fungi (18:2omega6,9 and 20:4) were low compared with levels at adjacent, uncontaminated sites. Congruent changes in the PLFA pattern were found upon analyzing the culturable part of the bacterial community. The high Pb concentrations in the soil resulted in increased tolerance to Pb of the bacterial community, measured using both thymidine incorporation and plate counts. Furthermore, changes in tolerance were correlated to changes in the community structure. The bacterial community of the most contaminated soils showed higher specific activity (thymidine and leucine incorporation rates) and higher culturability than that of control soils. Fungal colony forming units (CFUs) were 10 times lower in the most Pb-enriched soils, the species composition was widely different from that in control soils, and the isolated fungi had high Pb tolerance. The most commonly isolated fungus in Pb-enriched soils was Tolypocladium inflatum. Comparison of isolates from Pb-enriched soil and isolates from unpolluted soils showed that T. inflatum was intrinsically Pb-tolerant, and that the prolonged conditions with high Pb had not selected for any increased tolerance.}, }
@article {pmid16328660, year = {2005}, author = {Johnsen, AR and Karlson, U}, title = {PAH degradation capacity of soil microbial communities--does it depend on PAH exposure?.}, journal = {Microbial ecology}, volume = {50}, number = {4}, pages = {488-495}, pmid = {16328660}, issn = {0095-3628}, mesh = {Bacteria/growth &amp; development/*metabolism ; Biodegradation, Environmental ; Colony Count, Microbial ; Environmental Exposure ; Phenanthrenes/metabolism ; Polycyclic Aromatic Hydrocarbons/analysis/*metabolism ; Pyrenes/metabolism ; Soil/analysis ; *Soil Microbiology ; Statistics as Topic ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous pollutants of the environment. But is their microbial degradation equally wide in distribution? We estimated the PAH degradation capacity of 13 soils ranging from pristine locations (total PAHs approximately 0.1 mg kg(-1)) to heavily polluted industrial sites (total PAHs approximately 400 mg kg(-1)). The size of the pyrene- and phenanthrene-degrading bacterial populations was determined by most probable number (MPN) enumeration. Densities of phenanthrene degraders reflected previous PAH exposure, whereas pyrene degraders were detected only in the most polluted soils. The potentials for phenanthrene and pyrene degradation were measured as the mineralization of (14)C-labeled spikes. The time to 10% mineralization of added (14)C phenanthrene and (14)C pyrene was inversely correlated with the PAH content of the soils. Substantial (14)C phenanthrene mineralization in all soils tested, including seven unpolluted soils, demonstrated that phenanthrene is not a suitable model compound for predicting PAH degradation in soils. (14)C pyrene was mineralized by all Danish soil samples tested, regardless of whether they were from contaminated sites or not, suggesting that in industrialized areas the background level of pyrene is sufficient to maintain pyrene degradation traits in the gene pool of soil microorganisms. In contrast, two pristine forest soils from northern Norway and Ghana mineralized little (14)C pyrene within the 140-day test period. Mineralization of phenanthrene and pyrene by all Danish soils suggests that soil microbial communities of inhabited areas possess a sufficiently high PAH degradation capacity to question the value of bioaugmentation with specific PAH degraders for bioremediation.}, }
@article {pmid16328659, year = {2005}, author = {Goberna, M and Insam, H and Klammer, S and Pascual, JA and Sánchez, J}, title = {Microbial community structure at different depths in disturbed and undisturbed semiarid Mediterranean forest soils.}, journal = {Microbial ecology}, volume = {50}, number = {3}, pages = {315-326}, pmid = {16328659}, issn = {0095-3628}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Ecosystem ; Electrophoresis, Gel, Two-Dimensional ; Mediterranean Region ; Pinus ; Poaceae ; Polymerase Chain Reaction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Soil/analysis ; *Soil Microbiology ; Spain ; Species Specificity ; Trees/*microbiology ; }, abstract = {Metabolic abilities and micrfiobial community structure were investigated through three semiarid Mediterranean soils of SE Spain. The soils were (1) a Typic Calcixerept under an adult pine plantation (PP), growing on abandoned agricultural terraces; (2) a Typic Calcixeroll under a native pinewood (NP); and (3) a Typic Haploxerept covered with a grass steppe (GS). PP and NP were similar as regards their genesis, but the former used to be tilled. NP and GS were undisturbed and supported natural and seminatural vegetation, respectively. Seven samples in 10-cm depth increments were taken in triplicate along each soil profile. Community-level physiological profiles based on sole-C-source use were determined to characterize the metabolic abilities. A 16S rDNA polymerase chain reaction-denaturing gradient gel electrophoresis analysis was performed to investigate the microbial genetic structure. Plant cover and land-use history were major determinants of microbial community structure. Microbial communities residing in soils under a native pinewood, the most diverse and stable plant cover, were the most complex both metabolically and genetically. The microbial community structure distinctly changed with depth, related to the quantity and quality of total organic carbon. Both undisturbed soils showed falling gradients of metabolic and genetic complexity, which were invariably of a greater magnitude in the mature woodland than in the grass steppe. In the planted pinewood, however, the substrate-use diversity increased with depth, apparently a response to the depleted metabolic abilities within its upper layer (0-30 cm). Tilling and plant cover removal might be responsible for such a perturbation. In the same profile, molecular fingerprint patterns of the topsoil layer (0-10 cm) indicated a disturbed genetic structure that might underlie the loss of metabolic abilities. However, the genetic structure of the deeper layers of the planted and native pinewoods was not dissimilar, revealing that equivalent genetic resources perform different environmental functions under changing soil scenarios.}, }
@article {pmid16328658, year = {2005}, author = {Auguet, JC and Montanié, H and Delmas, D and Hartmann, HJ and Huet, V}, title = {Dynamic of virioplankton abundance and its environmental control in the Charente estuary (France).}, journal = {Microbial ecology}, volume = {50}, number = {3}, pages = {337-349}, pmid = {16328658}, issn = {0095-3628}, mesh = {Bacteria/isolation &amp; purification ; Ecosystem ; *Environment, Controlled ; France ; Plankton/*isolation &amp; purification ; Rivers/chemistry/*microbiology ; Seasons ; Viruses/*isolation &amp; purification ; Water Microbiology ; }, abstract = {The Charente River provides nutrient- and virus-rich freshwater input to the Marennes Oléron Basin, the largest oyster-producing region in Europe. To evaluate virioplankton distribution in the Charente Estuary and identify which environmental variables control dynamic of virioplankton abundance, five stations defined by a salinity gradient (0-0.5, 0.6-5, 13-17, 20-24, and higher than 30 PSU) were surveyed over a year. Viral abundance was related to bacterioplankton abundance and activities, photosynthetic pigments, nutrient concentration, and physical parameters (temperature and salinity). On a spatial scale, virus displayed a decreasing pattern seaward with abundance ranging over the sampling period from 1.4x10(7) to 20.8x10(7) viruses mL-1 making virioplankton the most abundant component of planktonic microorganisms in the Charente Estuary. A good correlation was found between viral and bacterial abundance (rs=0.85). Furthermore, bacterial abundance was the most important predictor of viral abundance explaining alone between 66% (winter) and 76% (summer) of viral variability. However, no relation existed between viral abundance and chlorophyll a. Temporal variations in viral distributions were mainly controlled by temperature through the control of bacterial dynamics. Spatial variations of viral abundance were influenced by hydrodynamic conditions especially during the winter season where virioplankton distribution was entirely driven by mixing processes.}, }
@article {pmid16328657, year = {2005}, author = {Briand, JF and Jacquet, S and Flinois, C and Avois-Jacquet, C and Maisonnette, C and Leberre, B and Humbert, JF}, title = {Variations in the microcystin production of Planktothrix rubescens (cyanobacteria) assessed from a four-year survey of Lac du Bourget (France) and from laboratory experiments.}, journal = {Microbial ecology}, volume = {50}, number = {3}, pages = {418-428}, pmid = {16328657}, issn = {0095-3628}, mesh = {Bacterial Toxins/*biosynthesis ; Culture Media ; Cyanobacteria/growth &amp; development/*metabolism ; *Environmental Monitoring ; *Fresh Water ; Microcystins ; Peptides, Cyclic/*biosynthesis ; Phosphorus ; *Water Microbiology ; Water Pollutants/analysis ; }, abstract = {Between 1999 and 2002, a routine survey of water quality in the Lac du Bourget was performed to study the dynamics and microcystin (MC) production of Planktothrix rubescens. Using liquid chromatography coupled to diode array detection and mass spectrometry, we found that two main variants ([D-Asp3] and [D-Asp3, Dhb7] microcystin-RR) were produced. The proportion of these two variants was not influenced by the depth or season of sampling. Expressed in microcystin-LR equivalents, high microcystin concentrations were recorded from August to December each year, reaching values of up to 6.7 microg L-1. A significant correlation was found between the microcystin cell content and the cell densities of P. rubescens. Cellular quotas of microcystins ranged from 0.1 to 0.3 pg cell-1. Simultaneously, laboratory experiments were performed on a strain of P. rubescens isolated from the lake to assess the potential impact of various P-PO4 (3-) concentrations on intra- and extracellular microcystin production. Unlike natural populations, this strain only produced [D-Asp3] MC-RR. The intracellular microcystin content was similarly correlated to the cell density, but the cellular quota was slightly higher (0.3-0.7 pg cell-1) than in the natural population. Again, as in the natural population, a linear relationship was found between growth rate and microcystin production rate. These findings support the hypothesis that environmental factors, such as phosphate concentrations, have no direct impact on microcystin production by P. rubescens, but act indirectly by affecting growth rate.}, }
@article {pmid16328656, year = {2005}, author = {Earl, J and Pickup, RW and Ritchie, DA and Edwards, C}, title = {Development of temporal temperature gradient electrophoresis for characterising methanogen diversity.}, journal = {Microbial ecology}, volume = {50}, number = {3}, pages = {327-336}, pmid = {16328656}, issn = {0095-3628}, mesh = {DNA Primers ; DNA, Archaeal/*analysis/genetics ; Electrophoresis, Gel, Two-Dimensional/*methods ; Environmental Monitoring ; Fresh Water/analysis/*microbiology ; Geologic Sediments/analysis/*microbiology ; Methane/analysis ; Methanomicrobiales/*classification/genetics/isolation &amp; purification ; Methanosarcinales/*classification/genetics/isolation &amp; purification ; Molecular Sequence Data ; Polyethylene Glycols ; Polymerase Chain Reaction ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Seasons ; Species Specificity ; Temperature ; United Kingdom ; *Water Microbiology ; }, abstract = {Temporal temperature gradient electrophoretic (TTGE) analysis of 16S rDNA sequences was optimized to monitor the methanogen population present in water and sediments of a small eutrophic lake, Priest Pot, in the English Lake district. The production of nonrepresentative TTGE profiles due to the generation of polymerase chain reaction (PCR) artifacts initially proved problematical. The use of a proofreading polymerase in the PCR was found to be essential and fully optimized protocols were established and tested to ensure confidence that the TTGE profiles truly reflected sequence diversity. TTGE analysis revealed the methanogen population to be less diverse in water than in sediment. The most genetic diversity was observed in TTGE profiles of sediment DNA isolated in winter and the least was in sediment DNA isolated in summer. DNA sequencing analysis of bands recovered from TTGE gels revealed the presence of two methanogen communities. One clustered with Methanosaeta species and the other with the Methanomicrobiales. Many sequences showed low DNA sequence similarity to known methanogens, suggesting that Priest Pot harbors previously undescribed methanogen species.}, }
@article {pmid16328655, year = {2005}, author = {Gadanho, M and Sampaio, JP}, title = {Occurrence and diversity of yeasts in the mid-atlantic ridge hydrothermal fields near the Azores Archipelago.}, journal = {Microbial ecology}, volume = {50}, number = {3}, pages = {408-417}, pmid = {16328655}, issn = {0095-3628}, mesh = {Azores ; Biodiversity ; Culture Media/chemistry ; DNA Primers ; Microsatellite Repeats ; Oceans and Seas ; Polymerase Chain Reaction/methods ; RNA, Fungal/genetics ; RNA, Ribosomal/genetics ; Species Specificity ; Water Microbiology ; Yeasts/classification/genetics/growth &amp; development/*isolation &amp; purification ; }, abstract = {The yeast community associated with deep-sea hydrothermal systems of the Mid-Atlantic Rift was surveyed for the first time. This study relied on a culture-based approach using two different growth media: a conventional culture medium for yeasts supplemented with sea salts (MYPss) and the same medium additionally supplemented with sulfur (MYPssS). For the evaluation of species diversity, a molecular approach involving minisatellite-primed polymerase chain reaction (MSP-PCR) strain typing and sequence analysis of the D1/D2 domains of the 26S rDNA was followed. In the seven water samples that were studied, the number of colony-forming units per liter (cfu/L) ranged from 0 to 5940. The nonpigmented yeasts were much more abundant than the pink-pigmented ones. This disproportion was not observed in studies of other marine systems and may be due to the unique conditions of hydrothermal vents, characterized by a rich animal and microbial diversity and therefore by the availability of organic compounds utilizable by yeasts. Higher counts of nonpigmented yeast were obtained using MYPss, whereas for pink yeasts, higher counts were obtained using MYPssS. Moreover, among pink yeasts, some of the MSP-PCR classes obtained were composed of isolates obtained only on MYPssS, which might be an indication that these isolates are adapted to the ecosystems of the hydrothermal vents. Twelve phylotypes belonged to the Ascomycota and seven phylotypes belonged to the Basidiomycota. The nonpigmented yeasts were identified as Candida atlantica, C. atmosphaerica, C. lodderae, C. parapsilosis, Exophiala dermatitidis, Pichia guilliermondii, and Trichosporon dermatis, whereas the pigmented yeasts were identified as Rhodosporidium diobovatum, R. sphaerocarpum, R. toruloides, and Rhodotorula mucilaginosa. Some of the yeasts that were found belong to phylogenetic groups that include species reported from other marine environments, and eight phylotypes represent undescribed species. The new phylotypes found at Mid-Atlantic Ridge hydrothermal fields represent 33% of the total number of yeast taxa that were found.}, }
@article {pmid16328654, year = {2005}, author = {Gleeson, DB and Clipson, N and Melville, K and Gadd, GM and McDermott, FP}, title = {Characterization of fungal community structure on a weathered pegmatitic granite.}, journal = {Microbial ecology}, volume = {50}, number = {3}, pages = {360-368}, pmid = {16328654}, issn = {0095-3628}, mesh = {Aluminum ; Calcium ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Ecosystem ; Fungi/*classification/genetics/isolation &amp; purification/ultrastructure ; Geologic Sediments/chemistry/*microbiology ; Microscopy, Electron, Scanning ; Ribotyping ; Silicon ; Silicon Dioxide/chemistry ; Species Specificity ; }, abstract = {This study exploited the contrasting major element chemistry of adjacent, physically separable crystals of framework and sheet silicates in a pegmatitic granite to investigate the mineralogical influences of fungal community structure on mineral surfaces. Large intact crystals of variably weathered muscovite, plagioclase, K-feldspar, and quartz were individually extracted, together with whole-rock granite. Environmental scanning electron microscopy (ESEM) revealed a diversity of fungal structures, with microcolonial fungi and fungal hyphae clearly visible on surfaces of all mineral types. Fungal automated ribosomal intergenic spacer analysis (FARISA) was used to generate a ribotype profile for each mineral sample and a randomization test revealed that ribotype profiles, or community fingerprints, differed between different mineral types. Canonical correspondence analysis (CCA) revealed that mineral chemistry affected individual fungal ribotypes, and strong relationships were found between certain ribotypes and particular chemical elements. This finding was further supported by analysis of variance (ANOVA) of the 16 most abundant ribotypes within the community. Significantly, individual ribotypes were largely restricted to single mineral types and ribotypes clustered strongly on the basis of mineral type. CCA also revealed that Al, Si, and Ca had a significant impact on fungal community structure within this system. These results show that fungal community structure was driven by the chemical composition of mineral substrates, indicating selective pressure by individual chemical elements on fungal populations in situ.}, }
@article {pmid16328653, year = {2005}, author = {Alisi, C and Lasinio, GJ and Dalmastri, C and Sprocati, A and Tabacchioni, S and Bevivino, A and Chiarini, L}, title = {Metabolic profiling of Burkholderia cenocepacia, Burkholderia ambifaria, and Burkholderia pyrrocinia isolates from maize rhizosphere.}, journal = {Microbial ecology}, volume = {50}, number = {3}, pages = {385-395}, pmid = {16328653}, issn = {0095-3628}, mesh = {Burkholderia cepacia/*classification/metabolism ; Gardening ; Plant Roots/microbiology ; Reagent Kits, Diagnostic ; Sensitivity and Specificity ; Species Specificity ; Substrate Specificity ; Zea mays/*microbiology ; }, abstract = {Burkholderia cenocepacia, Burkholderia ambifaria, and Burkholderia pyrrocinia are the Burkholderia cepacia complex (Bcc) species most frequently associated with roots of crop plants. To investigate the ecophysiological diversity of these species, metabolic profiling of maize rhizosphere isolates was carried out by means of the Biolog system, using GN2 and SFN2 plates and different parameters related to optical density (OD). The metabolic profiles produced by the SFN2 and GN2 plates were identical, but the SFN2's narrower range of OD values and significantly longer reaction times made these plates less suitable for differentiation of isolates. Principal component analysis of maximum OD (ODM) and maximum substrate oxidation rate (muM) data generated by GN2 plates allowed the selection of a reduced number of carbon sources. Statistical analysis of ODM values highlighted marked differences between the metabolic profiles of B. cenocepacia and B. ambifaria, whereas metabolic profiles of B. pyrrocinia clustered very often with those of B. cenocepacia. Analysis of the mu(M) parameter resulted in a slightly lower differentiation among the three Bcc species and a higher metabolic diversity within the single species, in particular within B. cenocepacia. Finally, B. cenocepacia and B. pyrrocinia showed generally higher oxidation rates than B. ambifaria on those GN2 substrates that commonly occur in maize root exudates.}, }
@article {pmid16328652, year = {2005}, author = {Roest, K and Altinbas, M and Paulo, PL and Heilig, HG and Akkermans, AD and Smidt, H and de Vos, WM and Stams, AJ}, title = {Enrichment and detection of microorganisms involved in direct and indirect methanogenesis from methanol in an anaerobic thermophilic bioreactor.}, journal = {Microbial ecology}, volume = {50}, number = {3}, pages = {440-446}, pmid = {16328652}, issn = {0095-3628}, mesh = {Acetates ; Anaerobiosis ; Archaea/classification/genetics/growth &amp; development/*isolation &amp; purification ; Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Biodegradation, Environmental ; Bioreactors/*microbiology ; Carbon Dioxide ; Culture Media ; Hydrogen ; Methane/*metabolism ; Methanobacteriaceae/genetics/growth &amp; development/isolation &amp; purification ; Methanol/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sewage ; Species Specificity ; }, abstract = {To gain insight into the microorganisms involved in direct and indirect methane formation from methanol in a laboratory-scale thermophilic (55 degrees C) methanogenic bioreactor, reactor sludge was disrupted and serial dilutions were incubated in specific growth media containing methanol and possible intermediates of methanol degradation as substrates. With methanol, growth was observed up to a dilution of 10(8). However, when Methanothermobacter thermoautotrophicus strain Z245 was added for H2 removal, growth was observed up to a 10(10)-fold dilution. With H2/CO2 and acetate, growth was observed up to dilutions of 10(9) and 10(4), respectively. Dominant microorganisms in the different dilutions were identified by 16S rRNA-gene diversity and sequence analysis. Furthermore, dilution polymerase chain reaction (PCR) revealed a similar relative abundance of Archaea and Bacteria in all investigated samples, except in enrichment with acetate, which contained 100 times less archaeal DNA than bacterial DNA. The most abundant bacteria in the culture with methanol and strain Z245 were most closely related to Moorella glycerini. Thermodesulfovibrio relatives were found with high sequence similarity in the H2/CO2 enrichment, but also in the original laboratory-scale bioreactor sludge. Methanothermobacter thermoautotrophicus strains were the most abundant hydrogenotrophic archaea in the H2/CO2 enrichment. The dominant methanol-utilizing methanogen, which was present in the 10(8)-dilution, was most closely related to Methanomethylovorans hollandica. Compared to direct methanogenesis, results of this study indicate that syntrophic, interspecies hydrogen transfer-dependent methanol conversion is equally important in the thermophilic bioreactor, confirming previous findings with labeled substrates and specific inhibitors.}, }
@article {pmid16328651, year = {2005}, author = {Kastovská, K and Elster, J and Stibal, M and Santrůcková, H}, title = {Microbial assemblages in soil microbial succession after glacial retreat in Svalbard (high arctic).}, journal = {Microbial ecology}, volume = {50}, number = {3}, pages = {396-407}, pmid = {16328651}, issn = {0095-3628}, mesh = {Arctic Regions ; Chlorophyta/isolation &amp; purification ; Colony Count, Microbial ; Cyanobacteria/classification/*isolation &amp; purification ; Ecosystem ; Eukaryota/classification/*isolation &amp; purification ; Ice ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Microbial community composition (cyanobacteria and eukaryotic microalgae abundance and diversity, bacterial abundance, and soil respiration) was studied in subglacial and periglacial habitats on five glaciers near Ny-Alesund, Svalbard (79 degrees N). Soil microbial communities from nonvegetated sites (subglacial, recently deglaciated, and cryoconite sediments) and sites with plant cover (deglaciated some hundreds of years ago) were analyzed. Physicochemical analyses (pH, texture, water content, organic matter, total C and N content) were also performed on the samples. In total, 57 taxa of 23 genera of cyanobacteriaand algae were identified. Algae from the class Chlorophyceae (25 species) and cyanobacteria (23 species) were richest in biodiversity. The numbers of identified species in single habitat types were 23 in subglacial, 39 inbarren, 22 in cryoconite, and 24 in vegetated soils. The highest cyanobacterial and algal biovolume and cell numbers, respectively, were present in cryoconite (13x10(4) microm3 mg-1 soil and 508 cells per mg of soil), followed by barren (5.7x10(4) and 188), vegetated (2.6x10(4) and 120), and subglacial (0.1x10(4) and 5) soils. Cyanobacteria prevailed in all soil samples. Algae (mainly green algae) were present only as accessory organisms. The density of bacteria showed a slightly different trend to that of the cyanobacterial and algal assemblages. The highest number of bacteria was present in vegetated (mean: 13,722x10(8) cells per mg of soil dry wt.), followed by cryoconite (3802x10(8)), barren (654x10(8)), and subglacial (78x10(8)) soils. Response of cyanobacteria and algae to physical parameters showed that soil texture and water content are important for biomass development. In addition, it is shown that nitrogen and water content are the main factors affecting bacterial abundance and overall soil respiration. Redundancy analysis (RDA) with forward selection was used to create a model explaining variability in cyanobacterial, algal, and bacterial abundance. Cryoconites accounted for most of the variation in cyanobacteria and algae biovolume, followed by barren soils. Oscillatoriales, desmids, and green coccoid algae preferred cryoconites, whereas Nostocales and Chroococcales occurred mostly in barren soils. From the data obtained, it is evident that of the studied habitats cryoconite sediments are the most suitable ones for the development of microbial assemblages. Although subglacial sediments do not provide as good conditions as cryoconites, they support the survival of microbial communities. Both mentioned habitats are potential sources for the microbial recolonization of freshly deglaciated soil after the glacier retreat.}, }
@article {pmid16328650, year = {2005}, author = {Hajaij, M and Carron, A and Deleuze, J and Gaven, B and Setier-Rio, ML and Vigo, G and Thiéry, I and Nielsen-LeRoux, C and Lagneau, C}, title = {Low persistence of Bacillus thuringiensis serovar israelensis spores in four mosquito biotopes of a salt marsh in southern France.}, journal = {Microbial ecology}, volume = {50}, number = {4}, pages = {475-487}, pmid = {16328650}, issn = {0095-3628}, mesh = {Animals ; Bacillus thuringiensis/classification/isolation &amp; purification/*physiology ; *Ecosystem ; France ; Larva ; Ochlerotatus ; Pest Control, Biological/*standards ; Plants/microbiology ; Soil Microbiology ; Spores, Bacterial/classification/isolation &amp; purification/physiology ; Time Factors ; Water Microbiology ; }, abstract = {We studied the persistence of Bacillus thuringiensis serovar israelensis (Bti) in a typical breeding site of the mosquito Ochlerotatus caspius in a particularly sensitive salt marsh ecosystem following two Bti-based larvicidal applications (Vectobac 12AS, 1.95 L/ha). The treated area was composed of four larval biotopes that differed in terms of the most representative plant species (Sarcocornia fruticosa, Bolboschoenus maritimus, Phragmites australis, and Juncus maritimus) and the physical and chemical characteristics of the soil. We sampled water, soil, and plants at various times before and after the applications (from spring to autumn, 2001) and quantified the spores of B. thuringiensis (Bt) and Bacillus species. The B. cereus group accounted for between 0% and 20% of all Bacillus spp. before application depending on the larval biotope. No Bti were found before application. The variation in the quantity of bacilli during the mosquito breeding season depended more on the larval biotope than on the season or the larvicidal application. More bacilli were found in soil (10(4)-10(6) spores/g) than on plant samples (10(2)-10(4) spores/g). The abundance in water (10(5) to 10(7) spores/L) appeared to be correlated to the water level of the breeding site. The number of Bti spores increased just after application, after declining; no spores were detected in soil or water 3 months after application. However, low numbers of Bti spores were present on foliage from three of the four studied plant strata. In conclusion, the larvicidal application has very little impact on Bacillus spp. flora after one breeding season (two applications).}, }
@article {pmid16328649, year = {2005}, author = {Kennedy, N and Edwards, S and Clipson, N}, title = {Soil bacterial and fungal community structure across a range of unimproved and semi-improved upland grasslands.}, journal = {Microbial ecology}, volume = {50}, number = {3}, pages = {463-473}, pmid = {16328649}, issn = {0095-3628}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer ; Fungi/classification/genetics/*isolation &amp; purification ; Ireland ; Plants ; Poaceae ; Polymorphism, Restriction Fragment Length ; Soil/analysis ; *Soil Microbiology ; Species Specificity ; }, abstract = {Changes in soil microbial community structure due to improvement are often attributed to concurrent shifts in floristic community composition. The bacterial and fungal communities of unimproved and semi-improved (as determined by floristic classification) grassland soils were studied at five upland sites on similar geological substrata using both broad-scale (microbial activity and fungal biomass) and molecular [terminal restriction fragment length polymorphism (TRFLP), automated ribosomal intergenic spacer analysis (ARISA)] approaches. It was hypothesized that microbial community structure would be similar in soils from the same grassland type, and that grassland vegetation classifications could thus be used as predictors of microbial community structure. Microbial community measurements varied widely according to both site and grassland type, and trends in the effect of grassland improvement differed between sites. These results were consistent with those from similar studies, and indicated that floristic community composition was not a stable predictor of microbial community structure across sites. This may indicate a lack of correlation between grassland plant composition and soil microbial community structure, or that differences in soil chemistry between sites had larger impacts on soil microbial populations than plant-related effects.}, }
@article {pmid16320814, year = {2005}, author = {Spears, JK and Karr-Lilienthal, LK and Fahey, GC}, title = {Influence of supplemental high molecular weight pullulan or gamma-cyclodextrin on ileal and total tract nutrient digestibility, fecal characteristics, and microbial populations in the dog.}, journal = {Archives of animal nutrition}, volume = {59}, number = {4}, pages = {257-270}, doi = {10.1080/17450390500216993}, pmid = {16320814}, issn = {1745-039X}, mesh = {Animals ; Bifidobacterium/*growth &amp; development/metabolism ; Clostridium perfringens/growth &amp; development ; *Digestion ; Dogs/*metabolism ; Dose-Response Relationship, Drug ; Feces/microbiology ; Female ; Glucans/*administration &amp; dosage/metabolism ; Ileum/microbiology ; Lactobacillus/*growth &amp; development/metabolism ; Molecular Weight ; Probiotics ; Random Allocation ; gamma-Cyclodextrins/*administration &amp; dosage/metabolism ; }, abstract = {This study was conducted to determine if supplemental pullulan and gamma-cyclodextrin affect canine nutrient digestibility, microbial populations, and fecal characteristics. Ileal cannulated dogs were fed a commercial diet, and treatments were administered daily in a 5 x 5 Latin square design: (i) no supplement; (ii) 2 g pullulan; (iii) 4 g pullulan; (iv) 2 g gamma-cyclodextrin; (v) 4 g gamma-cyclodextrin. Ileal and fecal samples were collected the last 4 d of each 14-d period. Increasing pullulan tended (p < 0.10) to linearly increase ileal bifidobacteria and lactobacilli and quadratically increase fecal lactobacilli. A similar response was noted in ileal bifidobacteria and lactobacilli with gamma-cyclodextrin. Gamma-Cyclodextrin resulted in a quadratic decrease (p < 0.05) in fecal Clostridium perfringens. Increasing pullulan linearly increased (p < 0.05) fecal score, while gamma-cyclodextrin resulted in a linear decrease (p < 0.05). Pullulan and gamma-cyclodextrin supplementation may have beneficial effects on the microbial ecology of dogs.}, }
@article {pmid16313649, year = {2005}, author = {Olsson, PA and Burleigh, SH and van Aarle, IM}, title = {The influence of external nitrogen on carbon allocation to Glomus intraradices in monoxenic arbuscular mycorrhiza.}, journal = {The New phytologist}, volume = {168}, number = {3}, pages = {677-686}, doi = {10.1111/j.1469-8137.2005.01532.x}, pmid = {16313649}, issn = {0028-646X}, mesh = {Base Sequence ; Carbon/*metabolism ; Cells, Cultured ; Chitinases/metabolism ; DNA Primers ; Daucus carota/*microbiology ; Mycorrhizae/*metabolism ; Nitrogen/*pharmacology ; Phosphoric Monoester Hydrolases/metabolism ; Plant Roots/microbiology ; Polyphosphates/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {The influence of external nitrogen (N) on carbon (C) allocation and processes related to phosphorus (P) metabolism were studied in monoxenic arbuscular mycorrhiza (AM) cultures of Daucus carota. Fungal hyphae of Glomus intraradices proliferated from colonized roots growing on solid medium into C-free liquid minimal medium with two different N and P levels. Furthermore, we exposed the colonized roots to high or low N availability and then studied the mycelial development. Roots were provided with (13)C-glucose in order to follow the C allocation. The mycelium was analysed for phosphatase activity and transcription levels of two nutrient regulated genes. High N availability to the monoxenic AM root reduced the C allocation to the AM fungus while N availability to the mycelium was important for the upregulation of the fungal inorganic phosphorus (Pi)-transporter GiPT. We found that N availability can regulate nutritional processes in arbuscular mycorrhiza. We conclude that negative impacts of N on AM abundance are caused by reduced C allocation from the plant. Upregulation of the fungal Pi-transporter GiPT indicated that increased N availability might induce P limitation in the mycelium.}, }
@article {pmid16313419, year = {2005}, author = {Scully, C and Collins, G and O'Flaherty, V}, title = {Assessment of anaerobic wastewater treatment failure using terminal restriction fragment length polymorphism analysis.}, journal = {Journal of applied microbiology}, volume = {99}, number = {6}, pages = {1463-1471}, doi = {10.1111/j.1365-2672.2005.02743.x}, pmid = {16313419}, issn = {1364-5072}, mesh = {Anaerobiosis ; Bacteria/*metabolism ; Biodegradation, Environmental ; Bioreactors ; *Genes, Bacterial ; Hydrogen/metabolism ; Industrial Microbiology/*methods ; *Industrial Waste ; Methane/metabolism ; *Polymorphism, Restriction Fragment Length ; Sewage ; *Waste Disposal, Fluid ; }, abstract = {AIMS: The suitability of genetic fingerprinting to study the microbiological basis of anaerobic bioreactor failure is investigated.<br><br>METHODS AND RESULTS: Two laboratory-scale anaerobic expanded granular sludge bed bioreactors, R1 and R2, were used for the mesophilic (37 degrees C) treatment of high-strength [10 g chemical oxygen demand (COD) l(-1)] synthetic industrial-like wastewater over a 100-day trial period. A successful start up was achieved by both bioreactors with COD removal over 90%. Both reactors were operated under identical parameters; however, increased organic loading during the trial induced a reduction in the COD removal of R1, while R2 maintained satisfactory performance (COD removal >90%) throughout the experiment. Specific methanogenic activity measurements of biomass from both reactors indicated that the main route of methane production was hydrogenotrophic methanogenesis. Terminal restriction fragment length polymorphism (TRFLP) analysis was applied to the characterization of microbial community dynamics within the system during the trial. The principal differences between the two consortia analysed included an increased abundance of Thiovulum- and Methanococcus-like organisms and uncultured Crenarchaeota in R1.<br><br>CONCLUSIONS: The results indicated that there was a microbiological basis for the deviation, in terms of operational performance, of R1 and R2.<br><br>High-throughput fingerprinting techniques, such as TRFLP, have been demonstrated as practically relevant for biomonitoring of anaerobic reactor communities.}, }
@article {pmid16308673, year = {2005}, author = {Leloup, J and Petit, F and Boust, D and Deloffre, J and Bally, G and Clarisse, O and Quillet, L}, title = {Dynamics of sulfate-reducing microorganisms (dsrAB genes) in two contrasting mudflats of the Seine estuary (France).}, journal = {Microbial ecology}, volume = {50}, number = {3}, pages = {307-314}, pmid = {16308673}, issn = {0095-3628}, mesh = {Bacteria/genetics/*isolation &amp; purification/metabolism ; Carbon/analysis ; Colony Count, Microbial ; Ecosystem ; Environmental Monitoring ; France ; Genes, Bacterial/genetics ; Hydrogensulfite Reductase/genetics ; Organic Chemicals/analysis ; Polymerase Chain Reaction ; Rivers/chemistry/*microbiology ; Seasons ; Sulfates/analysis/metabolism ; Sulfuric Acid Esters/analysis/metabolism ; *Water Microbiology ; }, abstract = {By combining molecular biology and biochemical approaches, the dynamics of sulfate-reducing microorganisms (SRM) was investigated in the sediments of the Seine estuary (France). Both intertidal mixing-zone and freshwater mudflats were sampled during a 1-year period; the quantification of SRM was realized by using competitive polymerase chain reaction (PCR) based on dsrAB gene amplification, previously described by Leloup et al. (2004), and sulfate reduction rate (SRR) was determined via the SO4(2-) radiotracer method. Throughout the year, abundance of dsrAB genes and SRR were predominantly high in the top 15 cm of the sediment. A seasonal dynamic was observed; a predominance of activity was noted during the early summer, and seems to be mainly controlled by physical-chemical parameters (temperature and dissolved organic carbon concentration) and topographic evolution of the mudflat (erosion/deposit erosion).}, }
@article {pmid16307384, year = {2005}, author = {van Diepeningen, AD and de Vos, OJ and Zelenev, VV and Semenov, AM and van Bruggen, AH}, title = {DGGE fragments oscillate with or counter to fluctuations in cultivable bacteria along wheat roots.}, journal = {Microbial ecology}, volume = {50}, number = {4}, pages = {506-517}, pmid = {16307384}, issn = {0095-3628}, mesh = {Bacteria/genetics/*growth &amp; development ; *Biodiversity ; DNA, Bacterial/*analysis/genetics ; DNA, Ribosomal/analysis ; Discriminant Analysis ; Electrophoresis, Polyacrylamide Gel/methods ; Plant Roots/genetics/growth &amp; development/microbiology ; Population Density ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Statistics as Topic ; Stem Cells/microbiology ; Triticum/genetics/*microbiology ; }, abstract = {Previously, we showed that bacterial populations oscillate in response to a moving substrate source such as a root tip, resulting in moving wavelike distributions along roots. For this article, we investigated if bacterial communities fluctuate as a whole or if there is a succession in bacterial composition from peak to peak or within peaks. Rhizosphere microbial communities along roots of wheat Triticum aestivum L. were studied in detail (20-25 rhizosphere and bulk soil samples along the total root length) in two related soils by colony enumeration and culture-independent DNA analysis. Similar to our previous findings, the numbers of copiotrophic and oligotrophic bacteria oscillated with significant harmonics along each root, independent of soil moisture or lateral roots. Shifts in amplified eubacterial 16S rDNA fragments from denaturing gradient gel electrophoresis (DGGE) analysis were detected along the roots. The most abundant and intensively amplified fragments fluctuated in phase with colony-forming unit (CFU) oscillations; fewer amplified fragments with less intensive bands fluctuated out of phase or were restricted to certain root zones. The bacterial species richness along the root was negatively correlated with the numbers of oligotrophic bacterial CFUs. Discriminant analyses on DGGE patterns distinguished between soil types, rhizosphere and bulk soil, and waxing and waning phases in the oscillations along roots. Bacterial compositions shifted within oscillations but were repeated from oscillation to oscillation, supporting the idea that the most abundant bacterial taxa were growing and dying over time and consequently in space, whereas other taxa counterfluctuated or hardly responded to the substrate supplied by the passing root tip.}, }
@article {pmid16295878, year = {2005}, author = {Rabaey, K and Clauwaert, P and Aelterman, P and Verstraete, W}, title = {Tubular microbial fuel cells for efficient electricity generation.}, journal = {Environmental science &amp; technology}, volume = {39}, number = {20}, pages = {8077-8082}, doi = {10.1021/es050986i}, pmid = {16295878}, issn = {0013-936X}, mesh = {Acetates/chemistry ; Bacteria/*metabolism ; Biodegradation, Environmental ; *Bioelectric Energy Sources ; *Bioreactors ; Electrochemistry/instrumentation/*methods ; Fatty Acids/analysis ; Glucose/chemistry ; Water Purification/*methods ; }, abstract = {A tubular, single-chambered, continuous microbial fuel cell (MFC) that generates high power outputs using a granular graphite matrix as the anode and a ferricyanide solution as the cathode is described. The maximal power outputs obtained were 90 and 66 W m(-3) net anodic compartment (NAC) (48 and 38 W m(-3) total anodic compartment (TAC)) for feed streams based on acetate and glucose, respectively, and 59 and 48 W m(-3) NAC for digester effluent and domestic wastewater, respectively. For acetate and glucose, the total Coulombic conversion efficiencies were 75 +/- 5% and 59 +/- 4%, respectively, at loading rates of 1.1 kg chemical oxygen demand m(-3) NAC volume day(-1). When wastewater was used, of the organic matter effectively removed (i.e., 22% at a loading of 2 kg organic matter m(-3) NAC day(-1)), up to 96% was converted to electricity on a Coulombic basis. The lower overall efficiency of the wastewater-treating reactors is related to the presence of nonreadily biodegradable organics and the interference of alternative electron acceptors such as sulfate present in the wastewater. To further improve MFCs, focus has to be placed on the enhanced conversion of nonrapidly biodegradable material and the better directing of the anode flow toward the electrode instead of to alternative electron acceptors. Also the use of sustainable, open-air cathodes is a critical issue for practical implementation.}, }
@article {pmid16291673, year = {2005}, author = {Denef, VJ and Patrauchan, MA and Florizone, C and Park, J and Tsoi, TV and Verstraete, W and Tiedje, JM and Eltis, LD}, title = {Growth substrate- and phase-specific expression of biphenyl, benzoate, and C1 metabolic pathways in Burkholderia xenovorans LB400.}, journal = {Journal of bacteriology}, volume = {187}, number = {23}, pages = {7996-8005}, pmid = {16291673}, issn = {0021-9193}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; P42 ES 04911-12/ES/NIEHS NIH HHS/United States ; }, mesh = {Aerobiosis ; Bacterial Proteins/analysis/biosynthesis ; Benzoates/chemistry/*metabolism ; Biphenyl Compounds/chemistry/*metabolism ; Burkholderia/growth &amp; development/*metabolism ; Carbon/*metabolism ; Culture Media ; Cytosol/metabolism ; Electrophoresis, Gel, Two-Dimensional ; Substrate Specificity ; }, abstract = {Recent microarray experiments suggested that Burkholderia xenovorans LB400, a potent polychlorinated biphenyl (PCB)-degrading bacterium, utilizes up to three apparently redundant benzoate pathways and a C(1) metabolic pathway during biphenyl and benzoate metabolism. To better characterize the roles of these pathways, we performed quantitative proteome profiling of cells grown on succinate, benzoate, or biphenyl and harvested during either mid-logarithmic growth or the transition between the logarithmic and stationary growth phases. The Bph enzymes, catabolizing biphenyl, were approximately 16-fold more abundant in biphenyl- versus succinate-grown cells. Moreover, the upper and lower bph pathways were independently regulated. Expression of each benzoate pathway depended on growth substrate and phase. Proteins specifying catabolism via benzoate dihydroxylation and catechol ortho-cleavage (ben-cat pathway) were approximately an order of magnitude more abundant in benzoate- versus biphenyl-grown cells at the same growth phase. The chromosomal copy of the benzoyl-coenzyme A (CoA) (box(C)) pathway was also expressed during growth on biphenyl: Box(C) proteins were approximately twice as abundant as Ben and Cat proteins under these conditions. By contrast, proteins of the megaplasmid copy of the benzoyl-CoA (box(M)) pathway were only detected in transition-phase benzoate-grown cells. Other proteins detected at increased levels in benzoate- and biphenyl-grown cells included general stress response proteins potentially induced by reactive oxygen species formed during aerobic aromatic catabolism. Finally, C(1) metabolic enzymes were present in biphenyl-grown cells during transition phase. This study provides insights into the physiological roles and integration of apparently redundant catabolic pathways in large-genome bacteria and establishes a basis for investigating the PCB-degrading abilities of this strain.}, }
@article {pmid16283115, year = {2005}, author = {Jaatinen, K and Tuittila, ES and Laine, J and Yrjälä, K and Fritze, H}, title = {Methane-oxidizing bacteria in a Finnish raised mire complex: effects of site fertility and drainage.}, journal = {Microbial ecology}, volume = {50}, number = {3}, pages = {429-439}, pmid = {16283115}, issn = {0095-3628}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; *Ecosystem ; Electrophoresis, Gel, Two-Dimensional ; Finland ; Genes, Bacterial ; Methane/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Polymerase Chain Reaction ; *Soil Microbiology ; Species Specificity ; }, abstract = {Methane-oxidizing bacteria (MOB) are the only biological sinks for methane (CH4). Drainage of peatlands is known to decrease overall CH4 emission, but the effect on MOB is unknown. The objective of this work was to characterize the MOB community and activity in two ecohydrologically different pristine peatland ecosystems, a fen and a bog, and their counterparts that were drained in 1961. Oligotrophic fens are groundwater-fed peatlands, but ombrotrophic bogs receive additional water and nutrients only from rainwater. The sites were sampled in August 2003 down to 10 cm below the water table (WT), and cores were divided into 10-cm subsamples. CH4 oxidation was measured by gas chromatography (GC) to characterize MOB activity. The MOB community structure was characterized by polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) and sequencing methods using partial pmoA and mmoX genes. The highest CH4 oxidation rates were measured from the subsamples 20-30 and 30-40 cm above WT at the pristine oligotrophic fen (12.7 and 10.5 micromol CH4 dm-3 h-1, respectively), but the rates decreased to almost zero in the vicinity of WT. In the pristine ombrotrophic bog, the highest oxidation rate at 0-10 cm was lower than in the fen (8.10 micromol CH4 dm-3 h-1), but in contrast to the fen, oxidation rates of 4.5 micromol CH4 dm-3 h-1 were observed at WT and 10 cm below WT. Drainage reduced the CH4 oxidation rates to maximum values of 1.67 and 5.77 micromol CH4 dm-3 h-1 at 30-40 and 20-30 cm of the fen and bog site, respectively. From the total of 13 pmoA-derived DGGE bands found in the study, 11, 3, 6, and 2 were observed in the pristine fen and bog and their drained counterparts, respectively. According to the nonmetric multidimensional scaling of the DGGE banding pattern, the MOB community of the pristine fen differed from the other sites. The majority of partial pmoA sequences belonged to type I MOB, whereas the partial mmoX bands that were observed only in the bog sites formed a distinct group relating more to type II MOB. This study indicates that fen and bog ecosystems differ in MOB activity and community structure, and both these factors are affected by drainage.}, }
@article {pmid16269794, year = {2005}, author = {Collins, G and O'Connor, L and Mahony, T and Gieseke, A and de Beer, D and O'Flaherty, V}, title = {Distribution, localization, and phylogeny of abundant populations of Crenarchaeota in anaerobic granular sludge.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {11}, pages = {7523-7527}, pmid = {16269794}, issn = {0099-2240}, mesh = {Anaerobiosis ; Crenarchaeota/*genetics/growth &amp; development/*isolation &amp; purification/metabolism ; DNA, Archaeal/analysis ; DNA, Ribosomal/analysis ; Genes, rRNA ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Waste Disposal, Fluid/*methods ; }, abstract = {Eight anaerobic granular sludges were surveyed for Crenarchaeota using rRNA gene cloning. Microbial arrangement and substrate uptake patterns were elucidated by fluorescent in situ hybridization and beta imaging. Group 1.3 Crenarchaeota represented up to 50% of Archaea and 25% of the total microbiota in five sludges. Crenarchaeota were localized in close association with methanogenic Archaea.}, }
@article {pmid16267281, year = {2005}, author = {Rincon, MT and Cepeljnik, T and Martin, JC and Lamed, R and Barak, Y and Bayer, EA and Flint, HJ}, title = {Unconventional mode of attachment of the Ruminococcus flavefaciens cellulosome to the cell surface.}, journal = {Journal of bacteriology}, volume = {187}, number = {22}, pages = {7569-7578}, pmid = {16267281}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics/metabolism ; Base Sequence ; Cell Cycle Proteins/genetics ; Cellulosomes/*metabolism ; Chromosomal Proteins, Non-Histone ; DNA, Bacterial/chemistry/genetics ; Escherichia coli/genetics ; Fungal Proteins/genetics ; Genes, Bacterial ; Molecular Sequence Data ; Multigene Family/genetics ; Nuclear Proteins/genetics ; Phylogeny ; Protein Binding ; Protein Structure, Tertiary/genetics ; Recombinant Proteins/genetics ; Ruminococcus/*genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Cohesins ; }, abstract = {Sequence extension of the scaffoldin gene cluster from Ruminococcus flavefaciens revealed a new gene (scaE) that encodes a protein with an N-terminal cohesin domain and a C terminus with a typical gram-positive anchoring signal for sortase-mediated attachment to the bacterial cell wall. The recombinant cohesin of ScaE was recovered after expression in Escherichia coli and was shown to bind to the C-terminal domain of the cellulosomal structural protein ScaB, as well as to three unknown polypeptides derived from native cellulose-bound Ruminococcus flavefaciens protein extracts. The ScaB C terminus includes a cryptic dockerin domain that is unusual in its sequence, and considerably larger than conventional dockerins. The ScaB dockerin binds to ScaE, suggesting that this interaction occurs through a novel cohesin-dockerin pairing. The novel ScaB dockerin was expressed as a xylanase fusion protein, which was shown to bind tenaciously and selectively to a recombinant form of the ScaE cohesin. Thus, ScaE appears to play a role in anchoring the cellulosomal complex to the bacterial cell envelope via its interaction with ScaB. This sortase-mediated mechanism for covalent cell-wall anchoring of the cellulosome in R. flavefaciens differs from those reported thus far for any other cellulosome system.}, }
@article {pmid16260310, year = {2005}, author = {Wagner, M and Loy, A and Klein, M and Lee, N and Ramsing, NB and Stahl, DA and Friedrich, MW}, title = {Functional marker genes for identification of sulfate-reducing prokaryotes.}, journal = {Methods in enzymology}, volume = {397}, number = {}, pages = {469-489}, doi = {10.1016/S0076-6879(05)97029-8}, pmid = {16260310}, issn = {0076-6879}, mesh = {Bacteria, Anaerobic/*genetics/metabolism ; DNA, Bacterial/isolation &amp; purification ; Electrophoresis, Agar Gel ; Environmental Microbiology ; Genes, Bacterial/*genetics ; Hydrogensulfite Reductase/*chemistry/genetics ; Oxidation-Reduction ; Phylogeny ; Polymerase Chain Reaction ; Seawater/microbiology ; Sequence Analysis, Protein ; Sulfates/*metabolism ; }, abstract = {Sulfate-reducing prokaryotes (SRPs) exploit sulfate as an electron acceptor for anaerobic respiration and exclusively catalyze this essential step of the world's sulfur cycle. Because SRPs are found in many prokaryotic phyla and are often closely related to non-SRPs, 16S rRNA gene-based analyses are inadequate to identify novel lineages of this guild in a cultivation-independent manner. This problem can be solved by comparative sequence analysis of environmentally retrieved gene fragments of the dissimilatory (bi)sulfite (dsrAB) and adenosine-5'-phosphosulfate reductases (apsA), which encode key enzymes of the SRP energy metabolism. This chapter provides detailed protocols for the application of these functional marker molecules for SRP diversity surveys in the environment. Data from the analysis of dsrAB sequence diversity in water samples from the Mariager Fjord in northeast Denmark are presented to illustrate the different steps of the protocols. Furthermore, this chapter describes a novel gel retardation-based technique, suitable for fingerprinting of the approximately 1.9-kb-large dsrAB polymerase chain reaction amplification products, which efficiently increases the chance of retrieving rare and novel dsrAB sequence types from environmental samples.}, }
@article {pmid16260301, year = {2005}, author = {Zwirglmaier, K and Fichtl, K and Ludwig, W}, title = {In situ functional gene analysis: recognition of individual genes by fluorescence in situ hybridization.}, journal = {Methods in enzymology}, volume = {397}, number = {}, pages = {338-351}, doi = {10.1016/S0076-6879(05)97020-1}, pmid = {16260301}, issn = {0076-6879}, mesh = {Escherichia coli/genetics ; Genes, Bacterial/*genetics ; In Situ Hybridization, Fluorescence/*methods ; Polymerase Chain Reaction/methods ; RNA Probes/chemical synthesis ; Sensitivity and Specificity ; Synechococcus/genetics ; }, abstract = {Fluorescence in situ hybridization (FISH) using specific probes certainly is one of the most commonly applied molecular techniques in microbial ecology. Monitoring of community composition and dynamics can be combined with localization and identification of individual cells in situ. However, the resolution power of the method is limited by the need for high target numbers per cell. Apart from standard targets (ribosomal RNAs), mRNAs could be used successfully for in situ visualization in some cases. A new promising variant of in situ hybridization could be established that should provide access to any low copy number nucleic acid targets, such as chromosomal genes. The recognition of individual genes by FISH (RING-FISH) technology is based on target visualization mediated by polynucleotide probe network formation. The specificity of the approach is provided by intracellular probe-target hybridization. This initial hybridization apparently acts as a focal point for inter-probe hybridization within and mainly in the periphery of the cells. Probe-conferred fluorescence typically appears halo-like around the cells. RING-FISH can be used in combination with conventional oligonucleotide FISH. Thus, genetic potential can be assigned to in situ identified cells.}, }
@article {pmid16260298, year = {2005}, author = {Hughes, JB and Hellmann, JJ}, title = {The application of rarefaction techniques to molecular inventories of microbial diversity.}, journal = {Methods in enzymology}, volume = {397}, number = {}, pages = {292-308}, doi = {10.1016/S0076-6879(05)97017-1}, pmid = {16260298}, issn = {0076-6879}, mesh = {Bacteria/genetics ; Ecology/*methods ; Environmental Microbiology ; Statistics as Topic/*methods ; }, abstract = {With the growing capacity to inventory microbial community diversity, the need for statistical methods to compare community inventories is also growing. Several approaches have been proposed for comparing the diversity of microbial communities: some adapted from traditional ecology and others designed specifically for molecular inventories of microbes. Rarefaction is one statistical method that is commonly applied in microbial studies, and this chapter discusses the procedure and its advantages and disadvantages. Rarefaction compares observed taxon richness at a standardized sampling effort using confidence intervals. Special emphasis is placed here on the need for precise, rather than unbiased, estimation methods in microbial ecology, but precision can be judged only with a very large sample or with multiple samples drawn from a single community. With low sample sizes, rarefaction curves also have the potential to lead to incorrect rankings of relative species richness, but this chapter discusses a new method with the potential to address this problem. Finally, this chapter shows how rarefaction can be applied to the comparison of the taxonomic similarity of microbial communities.}, }
@article {pmid16260292, year = {2005}, author = {Brune, A and Pester, M}, title = {In situ measurements of metabolite fluxes: microinjection of radiotracers into insect guts and other small compartments.}, journal = {Methods in enzymology}, volume = {397}, number = {}, pages = {200-212}, doi = {10.1016/S0076-6879(05)97011-0}, pmid = {16260292}, issn = {0076-6879}, mesh = {Animals ; Carbon Radioisotopes ; Intestines/*microbiology ; Isoptera/*metabolism ; Isotope Labeling/methods ; *Metabolism ; Microinjections/instrumentation/*methods ; Radioisotope Dilution Technique ; }, abstract = {In microbial ecology, it is of great interest to determine metabolic activities under in situ conditions, i.e., without disturbing the structure of the community and the spatial arrangement of individual populations by experimental manipulation. Microinjection of radiotracers and subsequent analysis using the isotope dilution technique has proven to be a powerful method to measure metabolic fluxes in small biological systems, e.g., the intestinal tract of termites. The large variety of commercially available radiolabeled substrates and the identification and quantitation of radiolabeled products by chromatographic methods allow for investigation of the complete metabolic network in a given system.}, }
@article {pmid16260290, year = {2005}, author = {Revsbech, NP}, title = {Analysis of microbial communities with electrochemical microsensors and microscale biosensors.}, journal = {Methods in enzymology}, volume = {397}, number = {}, pages = {147-166}, doi = {10.1016/S0076-6879(05)97009-2}, pmid = {16260290}, issn = {0076-6879}, mesh = {Bacteria/metabolism ; Biosensing Techniques/*instrumentation ; Cells, Immobilized ; Diffusion ; Electrochemistry/*instrumentation ; Hydrogen/analysis ; Hydrogen Sulfide/analysis ; Hydrogen-Ion Concentration ; Microchemistry/instrumentation/methods ; Microelectrodes ; Nitrates/analysis ; Nitrous Oxide/analysis ; Rheology ; }, abstract = {Electrochemical microsensors for O2, pH, H2S, H2, and N2O are now available commercially, thus it has become a relatively simple task to analyze the microenvironment in stratified microbial communities for several chemical species. In addition, sensors are available for the physical parameters diffusivity and flow, and based on knowledge about both transport processes and microdistribution of chemistry, it becomes possible to calculate the spatial distribution and local rates of transformations, such as aerobic respiration or denitrification. As compared to other advanced techniques, microsensor equipment is inexpensive. For example, it is possible to start working with oxygen microsensors with an investment of only about 5000 dollars. Construction of one's own microsensors is only recommended for the very dedicated user, but the investment here is mainly in terms of man-hours as the equipment is simple and inexpensive. By establishing a microsensor construction facility, it is possible to work with short-lived sensors such as ion-selective microsensors for H+, NO2(-), NO3(-), Ca2+, and CO3(-) based on ion exchangers and with microscale biosensors for NO(x)-, NO2(-), CH4, and volatile fatty acids based on immobilized bacteria.}, }
@article {pmid16254762, year = {2005}, author = {Forsgren, E and Lundhagen, AC and Imdorf, A and Fries, I}, title = {Distribution of Melissococcus plutonius in honeybee colonies with and without symptoms of European foulbrood.}, journal = {Microbial ecology}, volume = {50}, number = {3}, pages = {369-374}, pmid = {16254762}, issn = {0095-3628}, mesh = {Animal Husbandry ; Animals ; Bees/*microbiology ; DNA, Bacterial/genetics ; Gram-Positive Bacteria/genetics/*isolation &amp; purification ; Honey/microbiology ; Larva/microbiology ; Polymerase Chain Reaction ; Pupa/microbiology ; Switzerland ; }, abstract = {A sensitive hemi-nested polymerase chain reaction (PCR) was used for detection of Melissococcus plutonius, the causative agent of European foulbrood (EFB). Sampling was made in Switzerland, where EFB is a widespread disease and incidences have increased in recent years. Larvae from brood samples with and without clinical signs of disease (n=92) and honey (n=92) from the same colonies were investigated. Individual larvae (n=60) and pupae (n=30) from diseased brood in single colonies were also investigated to study the distribution of the bacterium within the brood between larvae. M. plutonius was detected in larvae in all apiaries where symptoms of EFB could be seen, but not in all colonies judged as cases of EFB in the field, when healthy-looking larvae from such colonies were tested. The occurrence of the bacterium within the brood was not limited to larvae with symptoms only, but was mainly found in diseased larvae. The bacterium was also found in pupae. Healthy-looking larvae-even from heavily diseased combs-failed, in a number of cases, to amplify product in the PCR. M. plutonius could only be detected in 35% of the brood nest honey from clinically diseased colonies.}, }
@article {pmid16254761, year = {2005}, author = {Mengoni, A and Tatti, E and Decorosi, F and Viti, C and Bazzicalupo, M and Giovannetti, L}, title = {Comparison of 16S rRNA and 16S rDNA T-RFLP approaches to study bacterial communities in soil microcosms treated with chromate as perturbing agent.}, journal = {Microbial ecology}, volume = {50}, number = {3}, pages = {375-384}, pmid = {16254761}, issn = {0095-3628}, mesh = {Agriculture ; Asbestos, Serpentine ; Bacteria/classification/genetics/*isolation &amp; purification ; Chromates ; DNA, Bacterial/genetics ; *Polymorphism, Restriction Fragment Length ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; Soil/analysis ; *Soil Microbiology ; Soil Pollutants ; Species Specificity ; }, abstract = {Transcripts of ribosomal RNA have been used for assessing the structure and dynamics of active bacterial populations; however, it remains unclear whether the information provided by community profiling derived from RNA is different from that derived from DNA, particularly when a selective pressure is applied on the bacterial community. In the present work, terminal-restriction fragment length polymorphism (T-RFLP) community profiles based on DNA and RNA extracted from soil microcosms treated with a toxic concentration of chromate were compared. Microcosms of a nonpolluted agricultural soil and of a heavy-metal-rich soil (serpentine) were treated with chromate and DNA and RNA were extracted. T-RFLP analysis was performed on amplified and retro-amplified 16SrRNA gene sequences, and band profiles obtained from samples of DNA and of RNA were compared. Some of the T-RFLP bands, identified as peculiar peaks in the profiles, were cloned and sequenced for taxonomic interpretation. Results indicated that: (1) community profiles derived from RNA and DNA were partly overlapping; (2) there was a strong correlation between the dynamics shown by RNA- and DNA-based T-RFLP profiles; (3) chromate addition exerted a clear effect on both agricultural and serpentine soil bacterial communities, either at the DNA and at the RNA level; however, the profiles derived from RNA showed sharper differences between treated and control samples than that of DNA-based profiles.}, }
@article {pmid16254760, year = {2005}, author = {Assigbetse, K and Gueye, M and Thioulouse, J and Duponnois, R}, title = {Soil bacterial diversity responses to root colonization by an ectomycorrhizal fungus are not root-growth-dependent.}, journal = {Microbial ecology}, volume = {50}, number = {3}, pages = {350-359}, pmid = {16254760}, issn = {0095-3628}, mesh = {Acacia/growth &amp; development/*microbiology ; Actinobacteria/classification/isolation &amp; purification ; Bacteria/classification/*isolation &amp; purification ; *Basidiomycota ; Colony Count, Microbial ; Fertilizers ; Gardening/methods ; Plant Roots/growth &amp; development/microbiology ; Pseudomonas/classification/isolation &amp; purification ; *Soil Microbiology ; }, abstract = {The hypothesis tested in this present study was that the ectomycorrhizosphere effect on the bacterial community was not root-growth-dependent. The impacts of ectomycorrhizal infection (Pisolithus albus COI007) and a chemical fertilization to reproduce the fungal effect on root growth were examined on (1) the structure of bacterial community and (2) fluorescent pseudomonad and actinomycete populations in the mycorrhizosphere of Acacia auriculiformis using both culture-independent and culture-dependent methods. A. auriculiformis plants were grown in disinfested soil in pots with or without addition of the ectomycorrhizal fungus or N/P/K fertilization (to reproduce the fungal effect on root growth) for 4 months and then transferred to 20-L pots filled with nondisinfested sandy soil. The fungal and fertilizer applications significantly improved the plant growth after 4-month culture in the disinfested soil. In the nondisinfested cultural substrate, these positive effects on plant growth were maintained. The total soil microbiota was significantly different within the treatments as revealed from DNA analysis [denaturing gradient gel electrophoresis (DGGE)]. The structure of fluorescent pseudomonad populations was also affected by fungal and fertilizer applications. In contrast, no qualitative effect was observed for the actinomycete communities within each treatment, but fungal inoculation significantly decreased the number of actinomycetes compared to the fertilizer application treatment. These results show that the mycorrhizosphere effect is not root-growth-dependent but is mainly due to the presence of the ectomycorrhizal fungus and more particularly to the extramatrical mycelium.}, }
@article {pmid16245827, year = {2005}, author = {Mouser, PJ and Rizzo, DM and Röling, WF and Van Breukelen, BM}, title = {A multivariate statistical approach to spatial representation of groundwater contamination using hydrochemistry and microbial community profiles.}, journal = {Environmental science &amp; technology}, volume = {39}, number = {19}, pages = {7551-7559}, doi = {10.1021/es0502627}, pmid = {16245827}, issn = {0013-936X}, mesh = {Archaea/genetics ; Bacteria/genetics ; Chemistry Techniques, Analytical/methods ; Environmental Monitoring/*methods ; Fresh Water/*chemistry/microbiology ; Multivariate Analysis ; Netherlands ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Refuse Disposal/*methods ; *Soil Microbiology ; Water Pollution, Chemical/*analysis ; }, abstract = {Managers of landfill sites are faced with enormous challenges when attempting to detect and delineate leachate plumes with a limited number of monitoring wells, assess spatial and temporal trends for hundreds of contaminants, and design long-term monitoring (LTM) strategies. Subsurface microbial ecology is a unique source of data that has been historically underutilized in LTM groundwater designs. This paper provides a methodology for utilizing qualitative and quantitative information (specifically, multiple water quality measurements and genome-based data) from a landfill leachate contaminated aquifer in Banisveld, The Netherlands, to improve the estimation of parameters of concern. We used a principal component analysis (PCA) to reduce nonindependent hydrochemistry data, Bacteria and Archaea community profiles from 16S rDNA denaturing gradient gel electrophoresis (DGGE), into six statistically independent variables, representing the majority of the original dataset variances. The PCA scores grouped samples based on the degree or class of contamination and were similar over considerable horizontal distances. Incorporation of the principal component scores with traditional subsurface information using cokriging improved the understanding of the contaminated area by reducing error variances and increasing detection efficiency. Combining these multiple types of data (e.g., genome-based information, hydrochemistry, borings) may be extremely useful at landfill or other LTM sites for designing cost-effective strategies to detect and monitor contaminants.}, }
@article {pmid16242171, year = {2005}, author = {Enright, AM and McHugh, S and Collins, G and O'FLaherty, V}, title = {Low-temperature anaerobic biological treatment of solvent-containing pharmaceutical wastewater.}, journal = {Water research}, volume = {39}, number = {19}, pages = {4587-4596}, doi = {10.1016/j.watres.2005.08.037}, pmid = {16242171}, issn = {0043-1354}, mesh = {Anaerobiosis ; Biodegradation, Environmental ; Biomass ; *Bioreactors ; Biotechnology ; Cold Temperature ; *Drug Industry ; Industrial Microbiology/economics/*methods ; *Industrial Waste ; Methane/metabolism ; Sewage/chemistry/microbiology ; Solvents/chemistry/metabolism ; Temperature ; Waste Disposal, Fluid/economics/*methods ; }, abstract = {Low-temperature or psychrophilic (<20 degrees C) anaerobic digestion (PAD) has recently been demonstrated as a cost-effective option for the treatment of a range of wastewater categories. The aim of this work was 2-fold: (1) to screen three anaerobic sludges, obtained from full-scale reactors, with respect to suitability for PAD of pharmaceutical-like, solvent-contaminated wastewater; (2) to assess the feasibility of PAD of this wastewater category. Toxicity thresholds of key trophic groups within three candidate biomass samples were assessed against solvents prevalent in pharmaceutical wastewaters (propanol, methanol and acetone). Specific methanogenic activity (SMA) assays indicated that the metabolic optimum of each candidate biomass was within the mesophilic range. One biomass sample exhibited higher SMA assays than the other candidate samples and was also the sample least methanogenically inhibited by the addition of solvents to batch cultures. This sludge was selected as the biomass of choice for laboratory-scale trials. Two identical expanded granular sludge bed (EGSB)-based anaerobic reactors were used for the treatment of solvent-contaminated wastewater at 15 degrees C, and at applied organic loading rates (OLRs) of 5-20 kg chemical oxygen demand (COD) m(-3)d(-1). COD removal efficiencies of 60-70% were achieved during the 450 day trial. In addition, SMA assays carried out at the conclusion of the trial indicated the development of a putatively psychrophilic hydrogenotrophic methanogenic community.}, }
@article {pmid16238731, year = {2005}, author = {Wittebolle, L and Boon, N and Vanparys, B and Heylen, K and De Vos, P and Verstraete, W}, title = {Failure of the ammonia oxidation process in two pharmaceutical wastewater treatment plants is linked to shifts in the bacterial communities.}, journal = {Journal of applied microbiology}, volume = {99}, number = {5}, pages = {997-1006}, doi = {10.1111/j.1365-2672.2005.02731.x}, pmid = {16238731}, issn = {1364-5072}, mesh = {Ammonia/*chemistry ; Cluster Analysis ; DNA, Bacterial/analysis ; Electrophoresis/methods ; Nitrates/chemistry ; Nitrosomonas/isolation &amp; purification/metabolism ; Oxidation-Reduction ; Polymerase Chain Reaction ; RNA, Bacterial/analysis ; *Water Microbiology ; Water Purification/*methods ; }, abstract = {AIMS: To investigate whether two different wastewater treatment plants (WWTPs) -- treating the same pharmaceutical influent -- select for a different bacterial and/or ammonia oxidizing bacterial (AOB) community.<br><br>METHODS AND RESULTS: Molecular fingerprinting demonstrated that each WWTP had its own total bacterial and AOB community structure, but Nitrosomonas eutropha and N. europea were dominant in both WWTP A and B. The DNA and RNA analysis of the AOB communities revealed different patterns; so the most abundant species may not necessarily be the most active ones. Nitritation failures, monitored by chemical parameter analysis, were reflected as AOB community shifts and visualized by denaturing gradient gel electrophoresis (DGGE)-based moving window analysis.<br><br>CONCLUSIONS: This research demonstrated the link between functional performance (nitritation parameters) and the presence and activity of a specific microbial ecology (AOB). Clustering and moving window analysis based on DGGE showed to be valuable to monitor community shifts in both WWTPs.<br><br>This study of specific community shifts together with functional parameter analysis has potential as a tool for relating functional instability (such as operational failures) to specific-bacterial community shifts.}, }
@article {pmid16233349, year = {2002}, author = {Aoi, Y}, title = {In situ identification of microorganisms in biofilm communities.}, journal = {Journal of bioscience and bioengineering}, volume = {94}, number = {6}, pages = {552-556}, pmid = {16233349}, issn = {1389-1723}, abstract = {Diverse microorganisms form complex microbial communities and usually exist in biofilm communities in both natural environments and engineered systems such as a wastewater treatment process. However, the conventional approach to investigate microbial ecology has not contributed to the understanding and clarification of the structure and function of biofilm communities. Some effective methods have been developed to investigate phylogenetic affiliations, metabolic activities and genetic activities in biofilm communities at the single-cell level. These techniques have been contributing to a better understanding of the spatial organization of biofilm communities and activities in engineered systems. However, further effort is needed to set out the general rules governing community development in biofilm communities and to advance the process performance of engineered systems. This review describes advances and limitations in methodology, particularly focusing on fluorescence in situ hybridization (FISH) and related techniques and the application of these methods to nitrifying biofilms in wastewater treatment processes.}, }
@article {pmid16233066, year = {2001}, author = {Egli, T}, title = {Biodegradation of metal-complexing aminopolycarboxylic acids.}, journal = {Journal of bioscience and bioengineering}, volume = {92}, number = {2}, pages = {89-97}, doi = {10.1263/jbb.92.89}, pmid = {16233066}, issn = {1389-1723}, abstract = {Aminopolycarboxylic acids (APCAs) are used in a broad range of household products and industrial applications to control the solubility and precipitation of metal ions. The two most widely used APCAs are ethylenediaminetetraacetate (EDTA) and nitrilotriacetate (NTA). Because their application is mostly water-based APCAs are disposed off in wastewater from where they reach the environment if not sufficiently well eliminated. A number of NTA and EDTA-degrading bacterial strains have been isolated. Many of them are strictly aerobic members of the alpha-2 subgroup of Proteobacteria. The two newly established NTA-degrading genera Chelatobacter and Chelatococcus appear to be well represented in most aerobic environments. The biochemistry of NTA and EDTA catabolism has been studied in considerable detail and recently, also information on the degradation of ethylenediaminedisuccinate [S,S]-EDDS, a structural isomer of EDTA of natural origin, was reported. For both, NTA and EDTA, a specific monooxygenase/NADH2:FMN oxidoreductase enzyme system has been purified and characterised and their regulation under environmentally relevant growth conditions has been studied. The genes for NTA MO and EDTA MO have been cloned and sequenced and they share many similarities. In addition, an oxygen-independent NTA dehydrogenase has been isolated from a denitrifying NTA-degrading bacterium and the breakdown of [S,S]-EDDS was found to be initiated by a lyase. Information on the transport of APCAs is presently limited to EDTA, where there is strong evidence for an energy-dependent carrier that can transport free and Ca2+-complexed EDTA. Metal speciation of APCAs strongly influences both transport and subsequent metabolism. However, from the data available for the intracellular metabolism of APCAs no generalising pattern with respect to influence of metal speciation on degradation can be deduced yet.}, }
@article {pmid16232850, year = {2000}, author = {Aoi, Y and Miyoshi, T and Okamoto, T and Tsuneda, S and Hirata, A and Kitayama, A and Nagamune, T}, title = {Microbial ecology of nitrifying bacteria in wastewater treatment process examined by fluorescence in situ hybridization.}, journal = {Journal of bioscience and bioengineering}, volume = {90}, number = {3}, pages = {234-240}, pmid = {16232850}, issn = {1389-1723}, abstract = {The microbial ecology of nitrifying bacteria in various types of wastewater treatment processes and the dynamic response of the microbial ecology in biofilms were investigated using fluorescence in situ hybridization (FISH) with 16S rRNA-targeted oligonucleotide probes. Nitrifying bacteria were found to exhibit various organizational forms under different conditions of substrate composition and concentration. Ammonia-oxidizing bacteria were dominant in ammonia-rich inorganic wastewater, while heterotrophic bacteria and ammonia-oxidizing bacteria were localized at different positions in the biofilm in organic wastewater. The dynamics of the microbial ecology in the biofilm with regard to the spatial distribution of ammonia-oxidizing bacteria and heterotrophic bacteria caused by a gradual change in substrate composition was successfully monitored by FISH analysis.}, }
@article {pmid16232691, year = {2000}, author = {Watanabe, K and Baker, PW}, title = {Environmentally relevant microorganisms.}, journal = {Journal of bioscience and bioengineering}, volume = {89}, number = {1}, pages = {1-11}, doi = {10.1016/s1389-1723(00)88043-3}, pmid = {16232691}, issn = {1389-1723}, abstract = {The development of molecular microbial ecology in the 1990s has allowed scientists to realize that microbial populations in the natural environment are much more diverse than microorganisms so far isolated in the laboratory. This finding has exerted a significant impact on environmental biotechnology, since knowledge in this field has been largely dependent on studies with pollutant-degrading bacteria isolated by conventional culture methods. Researchers have thus started to use molecular ecological methods to analyze microbial populations relevant to pollutant degradation in the environment (called environmentally relevant microorganisms, ERMs), although further effort is needed to gain practical benefits from these studies. This review highlights the utility and limitations of molecular ecological methods for understanding and advancing environmental biotechnology processes. The importance of the combined use of molecular ecological and physiological methods for identifying ERMs is stressed.}, }
@article {pmid16232296, year = {2005}, author = {Dandie, CE and Larrainzar, E and Mark, GL and O'gara, F and Morrissey, JP}, title = {Establishment of DsRed.T3_S4T as an improved autofluorescent marker for microbial ecology applications.}, journal = {Environmental microbiology}, volume = {7}, number = {11}, pages = {1818-1825}, doi = {10.1111/j.1462-2920.2005.00925.x}, pmid = {16232296}, issn = {1462-2912}, mesh = {Cloning, Molecular ; Ecology/*methods ; Genetic Vectors/genetics ; Luminescent Proteins/*genetics/*metabolism ; Microbiological Techniques/*methods ; Microscopy, Fluorescence ; Pseudomonas fluorescens/growth &amp; development/metabolism ; }, abstract = {Autofluorescent proteins (AFPs), such as green fluorescent protein (GFP) and DsRed, are valuable tools for studying plant-microbe interactions. Nevertheless, because of some limitations, efforts are ongoing to generate improved AFP variants. Several groups have generated variants of GFP with altered spectral characteristics, and faster maturing and brighter variants of DsRed. In this study we used plasmid and chromosomal constructs to test the efficacy of a new variant of DsRed, DsRed.T3_S4T, in Pseudomonas fluorescens F113rif. In addition, we compared the ecological fitness of strains carrying chromosomal copies of EGFP, DsRed or DsRed.T3_S4T. Strains expressing DsRed.T3_S4T fluoresced significantly brighter than strains expressing DsRed. Furthermore, it was found that although all strains grew equally well in vitro, only strains carrying DsRed.T3_S4T functioned as well as wild type in a competitive rhizosphere colonization assay. In particular, it was observed that DsRed.T3_S4T is an improved marker over DsRed for microbial ecology studies in this strain.}, }
@article {pmid16225902, year = {2005}, author = {Windey, K and De Bo, I and Verstraete, W}, title = {Oxygen-limited autotrophic nitrification-denitrification (OLAND) in a rotating biological contactor treating high-salinity wastewater.}, journal = {Water research}, volume = {39}, number = {18}, pages = {4512-4520}, doi = {10.1016/j.watres.2005.09.002}, pmid = {16225902}, issn = {0043-1354}, mesh = {Biodegradation, Environmental ; Biomass ; Nitrogen/*chemistry ; Oxygen/chemistry ; Sodium Chloride/*chemistry ; Water Purification/*instrumentation/methods ; }, abstract = {A lab-scale rotating biological contactor (RBC) reactor operated under OLAND conditions was slowly adapted during 178 days to increasing salt concentrations going up to 30 g NaCl L(-1). The reactor performed well during this experimental period. However, the removal capacity of the reactor was lower under high-salinity conditions. A removal efficiency of 84% was achieved at a N loading rate of 725 mg N L(-1) d(-1) and a salt concentration of 30 g L(-1). The effect of salt shock loading and adaptation to 30 g NaCl L(-1) on the specific nitritation and anammox activity of the biomass was investigated in short-term batch experiments. A salt shock loading of 30 g L(-1) caused a 43% decrease in specific nitritation activity and 96% loss of specific anammox activity compared to reference biomass (not exposed to salt). The salt-adapted biomass (3-4 weeks) showed a specific nitritation activity that was 23% lower, and a specific anammox activity that was 58% lower, compared to the reference biomass. Overall, these results demonstrate that the OLAND process can have the potential to treat ammonium-rich brines after adaptation to high salinity.}, }
@article {pmid16222487, year = {2005}, author = {Smith, AH and Zoetendal, E and Mackie, RI}, title = {Bacterial mechanisms to overcome inhibitory effects of dietary tannins.}, journal = {Microbial ecology}, volume = {50}, number = {2}, pages = {197-205}, pmid = {16222487}, issn = {0095-3628}, mesh = {Animal Feed ; Animals ; Bacteria/drug effects/*metabolism ; Drug Resistance, Bacterial ; Plants/chemistry ; Rats ; Rumen/*microbiology ; Tannins/chemistry/metabolism/*pharmacology ; }, abstract = {High concentrations of tannins in fodder plants inhibit gastrointestinal bacteria and reduce ruminant performance. Increasing the proportion of tannin-resistant bacteria in the rumen protects ruminants from anti-nutritional effects. The reason for the protective effect is unclear, but could be elucidated if the mechanism(s) by which tannins inhibit bacteria and the mechanisms of tannin resistance were understood. A review of the literature indicates that the ability of tannins to complex with polymers and minerals is the basis of the inhibitory effect on gastrointestinal bacteria. Mechanisms by which bacteria can overcome inhibition include tannin modification/degradation, dissociation of tannin-substrate complexes, tannin inactivation by high-affinity binders, and membrane modification/repair and metal ion sequestration. Understanding the mechanism of action of tannins and the mechanism(s) bacteria use to overcome the inhibitory effects will allow better management of the rumen ecosystem to reduce the anti-nutritional effects of tannin-rich fodder plants and thereby improve ruminant production.}, }
@article {pmid16219069, year = {2005}, author = {Hinsinger, P and Gobran, GR and Gregory, PJ and Wenzel, WW}, title = {Rhizosphere geometry and heterogeneity arising from root-mediated physical and chemical processes.}, journal = {The New phytologist}, volume = {168}, number = {2}, pages = {293-303}, doi = {10.1111/j.1469-8137.2005.01512.x}, pmid = {16219069}, issn = {0028-646X}, mesh = {Ecosystem ; Microscopy, Electron, Scanning ; Models, Biological ; Mycorrhizae/cytology/*physiology ; Phosphates/metabolism ; Plant Roots/*microbiology/*physiology ; Soil/analysis ; Soil Microbiology ; Symbiosis ; }, abstract = {The rhizosphere differs from the bulk soil in a range of biochemical, chemical and physical processes that occur as a consequence of root growth, water and nutrient uptake, respiration and rhizodeposition. These processes also affect microbial ecology and plant physiology to a considerable extent. This review concentrates on two features of this unique environment: rhizosphere geometry and heterogeneity in both space and time. Although it is often depicted as a soil cylinder of a given radius around the root, drawing a boundary between the rhizosphere and bulk soil is an impossible task because rhizosphere processes result in gradients of different sizes. For instance, because of diffusional constraints, root uptake can result in a depletion zone extending <1 mm for phosphate to several centimetres for nitrate, while respiration may affect the bulk of the soil. Rhizosphere processes are responsible for spatial and temporal heterogeneities in the soil, although these are sometimes difficult to distinguish from intrinsic soil heterogeneity. A further complexity is that these processes are regulated by plants, microbial communities and soil constituents, and their many interactions. Novel in situ techniques and modelling will help in providing a holistic view of rhizosphere functioning, which is a prerequisite for its management and manipulation.}, }
@article {pmid16215646, year = {2005}, author = {Yadav, RK and Karamanoli, K and Vokou, D}, title = {Bacterial colonization of the phyllosphere of mediterranean perennial species as influenced by leaf structural and chemical features.}, journal = {Microbial ecology}, volume = {50}, number = {2}, pages = {185-196}, pmid = {16215646}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development ; Cistus/microbiology ; *Ecosystem ; Greece ; Lavandula/microbiology ; Myrtus/microbiology ; Phosphorus/analysis ; Pistacia/microbiology ; *Plant Leaves/chemistry/microbiology/ultrastructure ; Plants/*microbiology ; Quercus/microbiology ; Trees/microbiology ; Water/analysis ; }, abstract = {In this study, we assessed various leaf structural and chemical features as possible predictors of the size of the phyllosphere bacterial population in the Mediterranean environment. We examined eight perennial species, naturally occurring and coexisting in the same area, in Halkidiki (northern Greece). They are Arbutus unedo, Quercus coccifera, Pistacia lentiscus, and Myrtus communis (evergreen sclerophyllous species), Lavandula stoechas and Cistus incanus (drought semi-deciduous species), and Calamintha nepeta and Melissa officinalis (non-woody perennial species). M. communis, L. stoechas, C. nepeta, and M. officinalis produce essential oil in substantial quantities. We sampled summer leaves from these species and (1) estimated the size of the bacterial population of their phyllosphere, (2) estimated the concentration of different leaf constituents, and (3) studied leaf morphological and anatomical features and expressed them in a quantitative way. The aromatic plants are on average more highly colonized than the other species, whereas the non-woody perennials are more highly colonized than the woody species. The population size of epiphytic bacteria is positively correlated with glandular and non-glandular trichome densities, and with water and phosphorus contents; it is negatively correlated with total phenolics content and the thickness of the leaf, of the mesophyll, and of the abaxial epidermis. No correlation was found with the density of stomata, the nitrogen, and the soluble sugar contents. By regression tree analysis, we found that the leaf-microbe system can be effectively described by three leaf attributes with leaf water content being the primary explanatory attribute. Leaves with water content >73% are the most highly colonized. For leaves with water content <73%, the phosphorus content, with a critical value of 1.34 mg g(-1) d.w., is the next explanatory leaf attribute, followed by the thickness of the adaxial epidermis. Leaves higher in phosphorus (>1.34 mg g(-1) d.w.) are more colonized, and leaves with the adaxial epidermis thicker than 20.77 microm are the least colonized. Although these critical attributes and values hold true only within the Mediterranean ecosystem studied and the range of observations taken, they are important because they provide a hypothesis to be tested in other Mediterranean ecosystems and other biomes. Such comparative studies may give insight as to the general properties governing the leaf-microbe system.}, }
@article {pmid16215645, year = {2005}, author = {Sedmak, B and Elersek, T}, title = {Microcystins induce morphological and physiological changes in selected representative phytoplanktons.}, journal = {Microbial ecology}, volume = {50}, number = {2}, pages = {298-305}, pmid = {16215645}, issn = {0095-3628}, mesh = {Eutrophication ; Light-Harvesting Protein Complexes/metabolism ; Marine Toxins ; Microcystins ; Microcystis/drug effects/growth &amp; development/*metabolism ; Peptides, Cyclic/metabolism/*pharmacology ; Photosynthesis ; Phycocyanin/metabolism ; *Phytoplankton/drug effects/growth &amp; development/physiology/ultrastructure ; *Scenedesmus/drug effects/growth &amp; development/metabolism/physiology ; }, abstract = {Dissolved microcystins (MC) are regularly present in water dominated by microcystin-producing, bloom-forming cyanobacteria. In vitro experiments with environmentally feasible concentrations (5 x 10(-7) M) of the three most common microcystins, MC-LR, -RR, and -YR, revealed that they influence the metabolism of different representative phytoplanktons. At light intensities close to the cyanobacterial bloom environment (50 mumol m(-2) s(-1)), they produce morphological and physiological changes in both microcystin-producing and nonproducing Microcystis aeruginosa strains, and also have similar effects on the green alga Scenedesmus quadricauda that is frequently present in cyanobacterial blooms. All three microcystin variants tested induce cell aggregation, increase in cell volume, and overproduction of photosynthetic pigments. All three effects appear to be related to each other, but are not necessarily caused by the same mechanism. The biological activity of microcystins toward the light-harvesting complex of photobionts can be interpreted as a signal announcing the worsening of light conditions due to the massive proliferation of cyanobacteria. Although the function of microcystins is still unknown, it is evident that they have numerous effects on phytoplankton organisms in nature. These effects depend on the individual organism as well as on the various intracellular and extracellular signaling pathways. The fact that dissolved microcystins also influence the physiology of microcystin-producing cyanobacteria leads us to the conclusion that the role of microcystins in the producing cells differs from their role in the water environment.}, }
@article {pmid16215644, year = {2005}, author = {Lafi, FF and Garson, MJ and Fuerst, JA}, title = {Culturable bacterial symbionts isolated from two distinct sponge species (Pseudoceratina clavata and Rhabdastrella globostellata) from the Great Barrier Reef display similar phylogenetic diversity.}, journal = {Microbial ecology}, volume = {50}, number = {2}, pages = {213-220}, pmid = {16215644}, issn = {0095-3628}, mesh = {Animals ; Bacteria/*classification/genetics/*growth &amp; development/isolation &amp; purification ; Culture Media ; Genes, rRNA ; Molecular Sequence Data ; *Phylogeny ; Porifera/classification/*microbiology ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {The diversity of the culturable microbial communities was examined in two sponge species-Pseudoceratina clavata and Rhabdastrella globostellata. Isolates were characterized by 16S rRNA gene sequencing and phylogenetic analysis. The bacterial community structures represented in both sponges were found to be similar at the phylum level by the same four phyla in this study and also at a finer scale at the species level in both Firmicutes and Alphaproteobacteria. The majority of the Alphaproteobacteria isolates were most closely related to isolates from other sponge species including alpha proteobacterium NW001 sp. and alpha proteobacterium MBIC3368. Members of the low %G + C gram-positive (phylum Firmicutes), high %G + C gram-positive (phylum Actinobacteria), and Cytophaga-Flavobacterium-Bacteroides (phylum Bacteroidetes) phyla of domain Bacteria were also represented in both sponges. In terms of culturable organisms, taxonomic diversity of the microbial community in the two sponge species displays similar structure at phylum level. Within phyla, isolates often belonged to the same genus-level monophyletic group. Community structure and taxonomic composition in the two sponge species P. clavata and Rha. globostellata share significant features with those of other sponge species including those from widely separated geographical and climatic regions of the sea.}, }
@article {pmid16211328, year = {2005}, author = {Harris, MJ and Boddy, L}, title = {Nutrient movement and mycelial reorganization in established systems of Phanerochaete velutina, following arrival of colonized wood resources.}, journal = {Microbial ecology}, volume = {50}, number = {2}, pages = {141-151}, pmid = {16211328}, issn = {0095-3628}, mesh = {Biomass ; Ecosystem ; Mycelium/*growth &amp; development ; Phanerochaete/*growth &amp; development/metabolism ; Phosphorus/*metabolism ; Soil Microbiology ; Trees/microbiology ; Wood ; }, abstract = {The effect of arrival of wood resources, pre-colonized by Coriolus versicolor, Phlebia radiata, Stereum hirsutum, and Vuilleminia comedens, on mycelial systems of Phanerochaete velutina was studied in trays of nonsterile soil in the laboratory over 5 months. Morphological responses were quantified non-destructively using image analysis. In a parallel series of experiments, nutrient movement was also quantified non-destructively using (32)P monitoring with a scintillation probe and subsequently by destructively harvesting after 155 days. The presence of a fungus occupying a newly arriving resource had major effects on deployment of biomass and on the uptake and allocation of phosphorus in the established Pha. velutina system. The effects varied depending on the species occupying the new resource. Hyphal coverage was greater in the half of the system to which new resources were added. Following addition of new resources, there was massive redeployment of biomass away from regions with no new resource when the new resource was (1) uncolonized, (2) colonized by V. comedens, or (3) colonized by S. hirsutum (although to a lesser extent with the latter), but not with others. (32)P was taken up by Pha. velutina both in the vicinity of the inoculum and the new resource and was translocated to the new resource from both sites of uptake; however, the local supply contributed most. Bidirectional translocation also occurred. The results are discussed in relation to mycelial foraging strategies, nutrient translocation, and partitioning within mycelial cord systems.}, }
@article {pmid16211327, year = {2005}, author = {Herschkovitz, Y and Lerner, A and Davidov, Y and Rothballer, M and Hartmann, A and Okon, Y and Jurkevitch, E}, title = {Inoculation with the plant-growth-promoting rhizobacterium Azospirillum brasilense causes little disturbance in the rhizosphere and rhizoplane of maize (Zea mays).}, journal = {Microbial ecology}, volume = {50}, number = {2}, pages = {277-288}, pmid = {16211327}, issn = {0095-3628}, mesh = {Azospirillum brasilense/genetics/*growth &amp; development ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Electrophoresis/methods ; Genes, rRNA ; Molecular Sequence Data ; Plant Roots/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Zea mays/*microbiology ; }, abstract = {Inoculation with Azospirillum brasilense exerts beneficial effects on plant growth and crop yields. In this study, a comparative analysis of maize (Zea mays) root inoculated or not inoculated with A. brasilense strains was performed in two soils. Colonization dynamics of the rhizobacteria were tracked in various root compartments using 16S rRNA-targeted probes and 4',6'diamidino-2-phenylindole staining, and the structure of bacterial populations in the same samples was analyzed by denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction products of the 16S rRNA gene. Based on whole cell hybridization, a large fraction of the bacterial community was found to be active in both the rhizoplane-endorhizosphere and rhizosphere soil compartments, in both soil types. A DGGE fingerprint analysis revealed that plant inoculation with A. brasilense had no effect on the structural composition of the bacterial communities, which were also found to be very similar at the root tip and at zones of root branching. However, rhizobacterial populations were strongly influenced by plant age, and their complexity decreased in the rhizoplane-endorhizosphere in comparison to rhizosphere soil. A clone library generated from rhizosphere DNA revealed a highly diverse community of soil and rhizosphere bacteria, including an indigenous Azospirillum-like organism. A large proportion of these clones was only distantly related to known species.}, }
@article {pmid16211326, year = {2005}, author = {Gamalero, E and Lingua, G and Tombolini, R and Avidano, L and Pivato, B and Berta, G}, title = {Colonization of tomato root seedling by Pseudomonas fluorescens 92 rkG5: spatio-temporal dynamics, localization, organization, viability, and culturability.}, journal = {Microbial ecology}, volume = {50}, number = {2}, pages = {289-297}, pmid = {16211326}, issn = {0095-3628}, mesh = {Culture Media ; Solanum lycopersicum/growth &amp; development/*microbiology ; Microscopy, Confocal ; Plant Roots/growth &amp; development/*microbiology/ultrastructure ; Pseudomonas fluorescens/*growth &amp; development ; Seedlings/*microbiology ; }, abstract = {The localization, viability, and culturability of Pseudomonas fluorescens 92 rkG5 were analyzed on three morphological root zones (root tip + elongation, root hair, and collar) of 3-, 5-, and 7-day-old tomato plants. Qualitative information about the localization and viability was collected by confocal laser scanning microscopy. Quantitative data concerning the distribution, viability, and culturability were obtained through combined dilution plating and flow cytometry. Colonization by P. fluorescens affected root development in a complex way, causing a general increase in the length of the collar and early stimulation of the primary root growth (3rd day), followed by a reduction in length (7th day). The three root zones showed different distribution, organization, and viability of the bacterial cells, but the distribution pattern within each zone did not change with time. Root tips were always devoid of bacteria, whereas with increasing distance from the apex, microcolonies or strings of cells became more and more prominent. Viability was high in the elongation zone, but it declined in the older parts of the roots. The so-called viable but not culturable cells were observed on the root, and their proportion in the distal (root tip + elongation) zone dramatically increased with time. These results suggest the existence of a specific temporal and spatial pattern of root colonization, related to cell viability and culturability, expressed by the plant-beneficial strain P. fluorescens 92 rkG5.}, }
@article {pmid16211325, year = {2005}, author = {Camacho, A and Rochera, C and Silvestre, JJ and Vicente, E and Hahn, MW}, title = {Spatial dominance and inorganic carbon assimilation by conspicuous autotrophic biofilms in a physical and chemical gradient of a cold sulfurous spring: the role of differential ecological strategies.}, journal = {Microbial ecology}, volume = {50}, number = {2}, pages = {172-184}, pmid = {16211325}, issn = {0095-3628}, mesh = {Biofilms/*growth &amp; development ; Carbon/*metabolism ; *Cold Temperature ; Cyanobacteria/classification/genetics/*growth &amp; development ; Ecosystem ; Fresh Water/chemistry/*microbiology ; Inorganic Chemicals/metabolism ; Molecular Sequence Data ; Photosynthesis ; Proteobacteria/classification/genetics/*growth &amp; development ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; Sulfur ; }, abstract = {The community composition and ecophysiological features of microbial autotrophic biofilms were studied in Fuente Podrida, a cold sulfur spring located in East Spain. We demonstrated how different ecophysiological strategies, such as resistance and/or utilization of sulfide and oxygen, light adaptation, or resistance to high water flow, allow each of the microorganisms described to efficiently colonize several areas within the environmental gradient. In the zone of the spring constantly influenced by sulfide-rich waters, biofilms were formed by purple bacteria, cyanobacteria, and filamentous colorless sulfur bacteria. Purple bacteria showed higher photosynthetic efficiency per pigment unit than cyanobacteria, although they were dominant only in anoxic areas. Two filamentous cyanobacteria, strain UVFP1 and strain UVFP2, were also abundant in the sulfide-rich area. Whereas the cyanobacterial strain UVFP2 shows a strategy based on the resistance to sulfide of oxygenic photosynthesis, strain UVFP1, additionally, has the capacity for sulfide-driven anoxygenic photosynthesis. Molecular phylogenetic analyses cluster the benthic strain UVFP1 with genus Planktothrix, but with no particular species, whereas UVFP2 does not closely cluster with any known cyanobacterial species. The colorless sulfur bacterium Thiothrix sp. extended throughout the zone in which both sulfide and oxygen were present, exhibiting its capacity for chemolithoautotrophic dark carbon fixation. Downstream from the source, where springwater mixes with well-oxygenated stream water and sulfide disappears, autotrophic biofilms were dominated by diatoms showing higher photosynthetic rates than cyanobacteria and, by a lesser extent, by a sulfide-sensitive cyanobacterium (strain UVFP3) well adapted to low light availability, although in the areas of higher water velocity far from the river shore, the dominance shifted to crust-forming cyanobacteria. Both types of microorganisms were highly sensitive to sulfide impeding them from occupying sulfide-rich areas of the spring. Sulfide, oxygen, light availability, and water velocity appear as the main factors structuring the autotrophic community of Fuente Podrida spring.}, }
@article {pmid16211324, year = {2005}, author = {Gernert, C and Glöckner, FO and Krohne, G and Hentschel, U}, title = {Microbial diversity of the freshwater sponge Spongilla lacustris.}, journal = {Microbial ecology}, volume = {50}, number = {2}, pages = {206-212}, pmid = {16211324}, issn = {0095-3628}, mesh = {Animals ; Bacteria/*classification/genetics ; Fresh Water ; Gene Library ; Genes, rRNA ; *Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {To provide insight into the phylogenetic bacterial diversity of the freshwater sponge Spongilla lacustris, a 16S rRNA gene libraries were constructed from sponge tissues and from lake water. Restriction fragment length polymorphism (RFLP) analysis of >190 freshwater sponge-derived clones resulted in six major restriction patterns, from which 45 clones were chosen for sequencing. The resulting sequences were affiliated with the Alpha proteobacteria (n=19), the Actinobacteria (n=15), the Beta proteobacteria (n=2), and the Chloroflexi (n=2) lineages. About half of the sequences belonged to previously described actinobacterial (hgc-I) and beta proteobacterial (beta-II) sequence clusters of freshwater bacteria that were also present in the lake water 16S rRNA gene library. At least two novel, deeply rooting alpha proteobacterial lineages were recovered from S. lacustris that showed <89% sequence similarity to known phylogenetic groups. Electron microscopical observations revealed that digested bacterial remnants were contained within food vacuoles of sponge archaeocytes, whereas the extracellular matrix was virtually free of bacteria. This study is the first molecular diversity study of a freshwater sponge and adds to a growing database on the diversity and community composition of sponge-associated microbial consortia.}, }
@article {pmid16205847, year = {2005}, author = {Wilczek, S and Fischer, H and Pusch, MT}, title = {Regulation and seasonal dynamics of extracellular enzyme activities in the sediments of a large lowland river.}, journal = {Microbial ecology}, volume = {50}, number = {2}, pages = {253-267}, pmid = {16205847}, issn = {0095-3628}, mesh = {Enzymes/*metabolism ; Eukaryota/enzymology/growth &amp; development ; Gene Expression Regulation ; Geologic Sediments/*microbiology ; Glucan 1,4-beta-Glucosidase/metabolism ; Leucyl Aminopeptidase/metabolism ; Organic Chemicals/*metabolism ; Phosphoric Monoester Hydrolases/metabolism ; Plankton/enzymology/growth &amp; development ; Rivers/*microbiology ; Seasons ; beta-Glucosidase/metabolism ; }, abstract = {We tested whether seasonal changes in the sources of organic substances for microbial metabolism were reflected changes in the activities of five extracellular enzymes in the eighth order lowland River Elbe, Germany. Leucine aminopeptidase showed the highest activities in the water column and the sediments, followed by phosphatase > beta-glucosidase > alpha-glucosidase > exo-1,4-beta-glucanase. Individual enzymes exhibited characteristic seasonal dynamics, as indicated by their relative contribution to cumulative enzyme activity. Leucine aminopeptidase was significantly more active in spring and summer. In contrast, the carbohydrate-degrading enzymes peaked in autumn, and beta-glucosidase activity peaked once again in winter. Thus, in sediments, the ratio of leucine aminopeptidase/beta-glucosidase reached significant higher medians in spring and summer (5-cm depth: ratio 7.7; 20-cm depth: ratio 10.1) than in autumn and winter (5-cm depth: ratio 3.7, 20-cm depth: ratio 6.3). The relative activity of phosphatase in the sediments was seasonally related to both the biomass of planktonic algae as well as to the high content of total particulate phosphorus in autumn and winter. Due to temporal shifts in organic matter supply and changes in the storage capacity of sediments, the seasonal peaks of enzyme activities in sediments exhibited a time lag of 2-3 months compared to that in the water column, along with a significant extension of peak width. Hence, our data show that the seasonal pattern of extracellular enzyme activities provides a sensitive approach to infer seasonal or temporary availability of organic matter in rivers from autochthonous and allochthonous sources. From the dynamics of individual enzyme activities, a consistent synoptic pattern of heterotrophic functioning in the studied river ecosystem could be derived. Our data support the revised riverine productivity model predicting that the metabolism of organic matter in high-order rivers is mainly fuelled by autochthonous production occurring in these reaches and riparian inputs.}, }
@article {pmid16200494, year = {2005}, author = {Beech, IB and Sunner, JA and Hiraoka, K}, title = {Microbe-surface interactions in biofouling and biocorrosion processes.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {8}, number = {3}, pages = {157-168}, pmid = {16200494}, issn = {1139-6709}, mesh = {*Bacterial Physiological Phenomena ; Biofilms/*growth &amp; development ; Corrosion ; Electron Transport ; *Environmental Microbiology ; Extracellular Matrix/metabolism ; Mass Spectrometry ; Metals/chemistry ; Microscopy, Atomic Force ; Polymers/metabolism ; }, abstract = {The presence of microorganisms on material surfaces can have a profound effect on materials performance. Surface-associated microbial growth, i.e. a biofilm, is known to instigate biofouling. The presence of biofilms may promote interfacial physico-chemical reactions that are not favored under abiotic conditions. In the case of metallic materials, undesirable changes in material properties due to a biofilm (or a biofouling layer) are referred to as biocorrosion or microbially influenced corrosion (MIC). Biofouling and biocorrosion occur in aquatic and terrestrial habitats varying in nutrient content, temperature, pressure and pH. Interfacial chemistry in such systems reflects a wide variety of physiological activities carried out by diverse microbial populations thriving within biofilms. Biocorrosion can be viewed as a consequence of coupled biological and abiotic electron-transfer reactions, i.e. redox reactions of metals, enabled by microbial ecology. Microbially produced extracellular polymeric substances (EPS), which comprise different macromolecules, mediate initial cell adhesion to the material surface and constitute a biofilm matrix. Despite their unquestionable importance in biofilm development, the extent to which EPS contribute to biocorrosion is not well-understood. This review offers a current perspective on material/microbe interactions pertinent to biocorrosion and biofouling, with EPS as a focal point, while emphasizing the role atomic force spectroscopy and mass spectrometry techniques can play in elucidating such interactions.}, }
@article {pmid16198103, year = {2006}, author = {Dubey, SK and Tripathi, AK and Upadhyay, SN}, title = {Exploration of soil bacterial communities for their potential as bioresource.}, journal = {Bioresource technology}, volume = {97}, number = {17}, pages = {2217-2224}, doi = {10.1016/j.biortech.2005.06.008}, pmid = {16198103}, issn = {0960-8524}, mesh = {Bacteria/*classification/genetics ; Bacterial Physiological Phenomena ; Biotechnology ; DNA Fingerprinting ; Ecosystem ; Fatty Acids/analysis ; Nucleic Acid Hybridization ; Phospholipids/analysis ; Phylogeny ; Polymerase Chain Reaction ; *Soil Microbiology ; }, abstract = {Soil is a repository of diverse microorganisms, which has frequently been used to isolate and exploit microbes for industrial, environmental and agricultural applications. Knowledge about the structure and dynamics of bacterial communities in soil has been limited as only a small fraction of bacterial diversity is accessible to culture methods. Traditional enrichment techniques and the pure culture approach for microbiological studies have offered only a narrow portal for examining the soil microbial flora due to their limited selectivity. Therefore, the morphological and nutritional criteria used to describe bacterial community failed to provide a natural taxonomic order according to evolutionary relationship. Molecular methods under an emerging discipline of biology "molecular microbial ecology" are now helping in getting these constraints removed to some extent. Nucleic acid extraction from soil is the first crucial step in the application of most of the molecular techniques, which have largely been dominated by diverse variations of PCR. Due to its rapidity, sensitivity and specificity, PCR-based finger printing techniques have proved extremely useful in assessing the changes in microbial community structure. Such techniques can yield complex community profiles and can also provide useful phylogenetic information. Fluorescent in situ hybridization (FISH) can be used to evaluate the distribution and function of bacterial population in situ. DNA microarray techniques have also been developed and being frequently used for the evaluation of ecological role and phylogenetic affiliations of bacterial populations in the soil.}, }
@article {pmid16195831, year = {2005}, author = {Burmølle, M and Hansen, LH and Sørensen, SJ}, title = {Use of a whole-cell biosensor and flow cytometry to detect AHL production by an indigenous soil community during decomposition of litter.}, journal = {Microbial ecology}, volume = {50}, number = {2}, pages = {221-229}, pmid = {16195831}, issn = {0095-3628}, mesh = {4-Butyrolactone/*analogs &amp; derivatives/biosynthesis ; Biodegradation, Environmental ; *Biosensing Techniques ; Enterobacteriaceae/cytology/genetics/growth &amp; development/metabolism ; Flow Cytometry/*methods ; Green Fluorescent Proteins/genetics/metabolism ; Sequence Analysis, DNA ; Soil/*analysis ; *Soil Microbiology ; }, abstract = {Quorum sensing, mediated by acylated homoserine lactones (AHLs), is well described for pure culture bacteria, but few studies report detection of AHL compounds in natural bacterial habitats. In this study, we detect AHL production during a degradation process in soil by use of whole-cell biosensor technology and flow cytometry analysis. An indigenous soil bacterium, belonging to the family of Enterobacteriaceae, was isolated and transformed with a low-copy plasmid harboring a gene encoding an unstable variant of the green fluorescent protein (gfpASV) fused to the AHL-regulated P(luxI) promoter originating from Vibrio fischeri. This resulted in a whole-cell biosensor, responding to the presence of AHL compounds. The biosensor was introduced to compost soil microcosms amended with nettle leaves. After 3 days of incubation, cells were extracted and analyzed by flow cytometry. All microcosms contained induced biosensors. From these microcosms, AHL producers were isolated and further identified as species previously shown to produce AHLs. The results demonstrate that AHL compounds are produced during degradation of litter in soil, indicating the presence of AHL-mediated quorum sensing in this environment.}, }
@article {pmid16195830, year = {2005}, author = {Bongiorni, L and Mirto, S and Pusceddu, A and Danovaro, R}, title = {Response of benthic protozoa and thraustochytrid protists to fish farm impact in seagrass (Posidonia oceanica) and soft-bottom sediments.}, journal = {Microbial ecology}, volume = {50}, number = {2}, pages = {268-276}, pmid = {16195830}, issn = {0095-3628}, mesh = {*Alismatales/growth &amp; development/microbiology/parasitology ; Animals ; *Aquaculture ; Bacteria/growth &amp; development/metabolism ; Ecosystem ; Eukaryota/classification/*growth &amp; development/metabolism ; Fishes/growth &amp; development ; *Geologic Sediments/chemistry/microbiology/parasitology ; Mediterranean Sea ; *Seawater/chemistry/microbiology/parasitology ; }, abstract = {We investigated the impact of fish farm biodeposition on benthic bacteria, thraustochytrid protists, and heterotrophic protozoa (nanoflagellates and ciliates) in an oligotrophic area of the Mediterranean Sea. The fish farm impact was investigated both on a seagrass (Posidonia oceanica) bed and on soft bottom sediments. In both systems, sediment samples were collected with a multicontrol sampling strategy (i.e., beneath the fish farm and at three control sites per system). The uneaten food pellets supplied to the fish determined the accumulation of sediment organic matter and the enhancement of protein content in impacted sediments (both seagrass bed and soft sediments). In both systems, the abundance and biomass of heterotrophic protists increased significantly beneath the fish farm, but the structure of the protist assemblages responded differently in vegetated and unvegetated sediments. Thraustochytrid abundance increased significantly in impacted seagrass. These results provide evidence that the structure of protist assemblages respond significantly to fish farm biodeposition and indicate that the monitoring of these benthic components provides complementary information for the assessment of the fish farm impact on the benthic systems.}, }
@article {pmid16184338, year = {2005}, author = {Sarr, A and Neyra, M and Houeibib, MA and Ndoye, I and Oihabi, A and Lesueur, D}, title = {Rhizobial populations in soils from natural Acacia senegal and Acacia nilotica forests in Mauritania and the Senegal river valley.}, journal = {Microbial ecology}, volume = {50}, number = {2}, pages = {152-162}, pmid = {16184338}, issn = {0095-3628}, mesh = {Acacia/*growth &amp; development ; DNA, Bacterial/analysis ; DNA, Ribosomal Spacer/analysis ; Mauritania ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Rhizobium/*classification/genetics/growth &amp; development ; Rivers ; Senegal ; Sequence Analysis, DNA ; *Soil Microbiology ; *Trees ; }, abstract = {Eighty-two strains of rhizobia were isolated from soils taken from several sites in Mauritania and Senegal. These soil samples were collected from natural stands of Acacia nilotica and Acacia senegal. The soils from Mauritania were less rich in native rhizobia than the soils from Senegal. The strains were characterized using polymerase chain reaction-restriction fragment length polymorphism and by sequencing the rDNA 16S-23S intergenic spacer region (IGS). They were sorted into seven IGS groups. These groups were not associated with the geographical origin of the strains or with the host-plant species at the site where the soils were collected. Most of the strains were in three of the IGS groups (I, IV, and V). One representative strain from each IGS group was sequenced and showed that the strains were from the genus Mesorhizobium. IGS groups I, IV, and VI were close to the species M. plurifarium (AF34563), IGS groups IIand III were close to the species Mesorhizobium sp. (AF510360), IGS group V was close to the species Mesorhizobium sp. (AF510366), and IGS group VII was close to Mesorhizobium sp. (AF510346).}, }
@article {pmid16184337, year = {2005}, author = {Steger, K and Eklind, Y and Olsson, J and Sundh, I}, title = {Microbial community growth and utilization of carbon constituents during thermophilic composting at different oxygen levels.}, journal = {Microbial ecology}, volume = {50}, number = {2}, pages = {163-171}, pmid = {16184337}, issn = {0095-3628}, mesh = {Actinobacteria/chemistry/growth &amp; development/metabolism ; Bacteria/chemistry/*growth &amp; development/metabolism ; Biomass ; Carbon/chemistry/*metabolism ; Ecosystem ; Fatty Acids/analysis ; Gram-Negative Bacteria/chemistry/growth &amp; development/metabolism ; *Hot Temperature ; Oxygen/*pharmacology ; *Soil/analysis ; *Soil Microbiology ; }, abstract = {Composting is characterized by dramatic changes in microbial community structure, to a high extent driven by changes in temperature and in the composition of the organic substrate. This study focuses on the interrelationships between decomposition of major classes in the organic material and dynamics in microbial populations during thermophilic composting of source-separated organic household waste. Experiments were performed in a 200-L laboratory reactor at 16, 2.5, and 1% O(2) in the compost atmosphere. Major classes of carbon constituents were analyzed by chemical methods, and the microbial biomass and community structure determined by fatty acid analyses with phospholipid fatty acids (PLFA) and total ester-linked fatty acids (EL) methods. At all three O(2) levels, the process was characterized by a rapid increase in microbial activity and biomass in the early thermophilic phase, although this period was delayed at the lower O(2) concentrations. Starch and fat were the main substrates utilized at all three O(2) levels during this period. The depletion of the starch fraction coincided with the beginning of a microbial biomass decrease, suggesting that starch is an important carbon substrate for the growth of thermophilic microorganisms during composting. Growth yields in the microbial community based on consumption of major carbon constituent classes in the high-activity period fell between 22 and 28%. Multivariate statistical analysis of changes in fatty acid composition revealed small, but statistically significant differences in the microbial community succession. At 16% O(2), 10 Me fatty acids from Actinomycetes and cyclopropyl fatty acids (from Gram-negative bacteria) became more important with time, whereas 18:1 omega 7t was characteristic at 2.5 and 1% O(2), indicating a more stressed bacterial community at the lower O(2) concentrations. Although adequate composting was achieved at O(2) levels as low as 2.5 and 1%, it is not recommended to compost at such low levels in large-scale systems, because the heterogeneous gas transport through the material in these systems might lead to anaerobic conditions and inefficient composting.}, }
@article {pmid16184336, year = {2005}, author = {García-Cantizano, J and Casamayor, EO and Gasol, JM and Guerrero, R and Pedrós-Alió, C}, title = {Partitioning of CO(2) incorporation among planktonic microbial guilds and estimation of in situ specific growth rates.}, journal = {Microbial ecology}, volume = {50}, number = {2}, pages = {230-241}, pmid = {16184336}, issn = {0095-3628}, mesh = {Carbon Dioxide/*metabolism ; Chromatiaceae/*growth &amp; development/metabolism ; Cryptophyta/*growth &amp; development/metabolism ; *Ecosystem ; Fresh Water/*microbiology ; Oxygen/metabolism/pharmacology ; Plankton/*growth &amp; development/metabolism ; Seasons ; Spain ; }, abstract = {Partitioning of CO(2) incorporation into oxygenic phototrophic, anoxygenic phototrophic, and chemolithoautotrophic guilds was determined in a freshwater lake (Lake Cisó, Banyoles, Spain). CO(2) incorporation into the different types of microorganisms was studied at different depths, during diel cycles, and throughout the year. During winter holomixis, the whole lake became anoxic and both the anoxygenic and chemolithoautotrophic guilds were more active at the surface of the lake, whereas the activity of the oxygenic guild was negligible. During stratification, the latter guild was more active in the upper metalimnion, whereas the anoxygenic guild was more active in the lower metalimnion. Specific growth rates and doubling times were estimated for the most conspicuous phototrophic microorganisms. Doubling times for Cryptomonas phaseolus ranged between 0.5 and 192 days, whereas purple sulfur bacteria (Chromatiaceae-like) ranged between 1.5 and 238 days. These growth rates were similar to those calculated with a different approach in previous papers and indicate slow-growing populations with very large biomass. Overall, the annual total CO(2) incorporation in Lake Cisó was 220 g C m(-2). Most of the CO(2) incorporation, however, was due to the chemolithoautotrophic guild (61% during holomixis and 56% during stratification), followed by the anoxygenic phototrophic guild (35 and 19%, respectively) and the oxygenic phototrophs (4 and 25%, respectively), making dark carbon fixation the key process in the autotrophic metabolism of the lake.}, }
@article {pmid16184335, year = {2005}, author = {Dionisio Pires, LM and Ibelings, BW and Brehm, M and Van Donk, E}, title = {Comparing grazing on lake seston by Dreissena and Daphnia: lessons for biomanipulation.}, journal = {Microbial ecology}, volume = {50}, number = {2}, pages = {242-252}, pmid = {16184335}, issn = {0095-3628}, mesh = {Animals ; Daphnia/growth &amp; development/*physiology ; Dreissena/growth &amp; development/*physiology ; Environmental Monitoring/methods ; Feeding Behavior ; *Fresh Water/microbiology ; Microcystins ; Microcystis/growth &amp; development ; Peptides, Cyclic/metabolism ; Phytoplankton/growth &amp; development ; }, abstract = {Biomanipulation measures in lakes, taken to diminish algal blooms, have mainly been restricted to the reduction of zooplanktivorous fish with the aim to stimulate the grazing pressure by native filter feeders such as Daphnia. However, larger filter feeders like the exotic zebra mussel, Dreissena polymorpha, have been suggested as an optional tool because of their high filtering capacity. We compared grazing by two filter feeders, D. polymorpha and Daphnia galeata, offered seston from Lake IJsselmeer, the Netherlands in two consecutive years: 2002 and 2003. The seston in both years was dominated by the colony-forming cyanobacterium Microcystis aeruginosa. The grazing studies were performed under controlled conditions in the laboratory and samples were analyzed on a flow cytometer, making it possible to quantify grazing on different seston components and size fractions, including cyanobacteria, other phytoplankton (green algae, diatoms, etc.), and detritus. No differences in clearance rates, on a per weight basis, were found between the two grazer species. The clearance rate on cyanobacteria (especially <20 microm) was lower in 2003 than in 2002. In 2003, the microcystin concentration of cyanobacteria was higher than in 2002, suggesting that the observed lower clearance rate in 2003 was due to the enhanced toxin content of the cyanobacteria. Zebra mussels, although indiscriminately filtering all seston groups out of the water, positively selected for phytoplankton in their mantle cavity, irrespective of its toxicity, and rejected detritus. Since no differences in clearance rates were found between the two grazer species, we conclude that for biomanipulation purposes of shallow lakes, native species like the daphnids should be preferred over exotic species like zebra mussels. When the seston is dominated by phytoplankton that cannot be filtered out of the water column by Daphnia, however, the use of zebra mussels may be considered. Care should be taken, however, in the choice of the lakes since the mussels may have severe ecological and economic impacts.}, }
@article {pmid16180472, year = {2005}, author = {Rabaey, I and Ossieur, W and Verhaege, M and Verstraete, W}, title = {Continuous microbial fuel cells convert carbohydrates to electricity.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {52}, number = {1-2}, pages = {515-523}, pmid = {16180472}, issn = {0273-1223}, mesh = {Acer/chemistry ; Acetates/metabolism ; Bacteria, Anaerobic/*metabolism ; *Bioelectric Energy Sources ; Electricity ; Electrodes ; Glucose/*metabolism ; Indicators and Reagents ; Indigo Carmine ; Methylene Blue/analogs &amp; derivatives ; Oxazines ; Phenazines ; Plant Extracts/metabolism ; Sucrose/*metabolism ; Waste Disposal, Fluid/*methods ; }, abstract = {Microbial fuel cells which are operated in continuous mode are more suitable for practical applications than fed batch ones. Three influent types containing carbohydrates were tested, i.e. a glucose medium, a plant extract and artificial wastewater. The anode reactor compartment yielding the best results was a packed bed reactor containing graphite granules. While in non-mediated batch systems power outputs up to 479 W m(-3) of anode compartment could be attained; in continuous mode the power outputs were limited to 49W m(-3). Cyclic voltammetry was performed to determine the potential of the in-situ synthesized bacterial redox mediators. Addition of mediators with a potential similar to the bacterial potential did not significantly alter the MFC power output, indicating a limited influence of soluble mediators for continuous microbial fuel cells. Maximum coulombic and energy conversion efficiencies were, for the continuous microbial fuel cell operating on plant extract at a loading rate of 1 kg COD m(-3) of anode compartment per day, 50.3% and 26.0% respectively.}, }
@article {pmid16180409, year = {2005}, author = {Verstraete, W and Morgan-Sagastume, F and Aiyuk, S and Waweru, M and Rabaey, K and Lissens, G}, title = {Anaerobic digestion as a core technology in sustainable management of organic matter.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {52}, number = {1-2}, pages = {59-66}, pmid = {16180409}, issn = {0273-1223}, mesh = {Bacteria, Anaerobic/*metabolism ; Bioelectric Energy Sources ; Bioreactors ; Chlorine/chemistry ; *Conservation of Energy Resources ; Nitrogen/isolation &amp; purification ; Phosphorus/isolation &amp; purification ; Refuse Disposal ; Waste Disposal, Fluid ; Water Purification ; }, abstract = {In the past decades, anaerobic digestion (AD) has steadily gained importance. However, the technology is not regarded as a top priority in science policy and in industrial development at present. In order for AD to further develop, it is crucial that AD profits from the current fuel issues emerging in the international arena. AD can provide low-cost treatment of sewage and solid domestic wastes, which represents a vast application potential that should be promoted in the developing world. Furthermore, the developments in the last decades in the domain of anaerobic microbiology and technology have generated some interesting niches for the application of AD, such as anaerobic nitrogen removal and the treatment of chlorinated organics. Recently, AD has also generated some serendipities, such as the use of AD in processes for sulphur and calcium removal and the coupling of AD with microbial fuel cells. The international developments in terms of bio-refineries and CO2-emission abatement are of crucial importance with respect to the impetus that AD will receive in the coming decade. There should be little doubt that by placing the focus of AD on the production of green energy and clean nutrients, the future of AD will be assured.}, }
@article {pmid16179797, year = {2004}, author = {Wright, CA and Beattie, GA}, title = {Bacterial species specificity in proU osmoinducibility and nptII and lacZ expression.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {8}, number = {4}, pages = {201-208}, doi = {10.1159/000086701}, pmid = {16179797}, issn = {1464-1801}, mesh = {Amino Acid Transport Systems/*genetics ; Bacteria/*genetics/metabolism ; Bacterial Proteins/*genetics ; DNA Transposable Elements/genetics ; *Gene Expression ; *Gene Expression Regulation, Bacterial ; Genes, Reporter ; Green Fluorescent Proteins/genetics/metabolism ; *Lac Operon ; Osmolar Concentration ; Promoter Regions, Genetic/*physiology ; }, abstract = {Reporter gene-based transcriptional fusions are increasingly being used to address questions in microbial ecology, with constitutively expressed fusions enabling microbe tracking and inducible fusions reporting the presence of environmental signals. To more readily apply this technology to a variety of bacterial species, we examined species specificity in the expression of three promoters of interest. A comparison of two potentially constitutive promoters, each fused to the reporter gene gfp, showed that the nptII promoter (P(nptII)) was expressed in a broader range of species (100% of 11 tested) than the lacZ promoter (P(lacZ)) (75% of 11 tested), and thus has broader applicability for marking bacteria than P(lacZ). For the species that expressed P(lacZ), however,P(lacZ) was expressed 3-fold more than P(nptII), on average. The Escherichia coli proU promoter, which is induced by low water potential in E. coli, Salmonella typhimurium, Pantoea agglomerans, and Pseudomonas syringae, was shown to be similarly responsive to water potential in strains of Clavibacter michiganensis, Enterobacter aerogenes, Pseudomonas fluorescens, Pseudomonas putida, and Sinorhizobium meliloti, as well as mildly osmoresponsive in Agrobacterium tumefaciens, supporting its broad use as a reporter of water potential. Surprisingly, this promoter was not regulated by water potential in strains of Staphylococcus aureus and Erwinia amylovora, illustrating heretofore unrecognized species specificity in proU inducibility, as well as potential limitations in the species that can serve as bioreporters of water potential.}, }
@article {pmid16176592, year = {2005}, author = {DasSarma, S}, title = {Saline Systems: a research journal bridging gene systems and ecosystems.}, journal = {Saline systems}, volume = {1}, number = {}, pages = {1}, pmid = {16176592}, issn = {1746-1448}, abstract = {Saline Systems addresses the publication needs of scientists conducting basic and applied research on coastal and inland saline environments and their flora and fauna. The journal covers research at all levels, from individual genes to whole genomes and entire ecosystems. Rapid progress in the molecular biology and microbial ecology of halotolerant and halophilic organisms and the sensitivity of many saline environments warrants an online journal with fast turnaround times. Many saline environments are threatened and the need for an Open Access journal to address the dissemination and sharing of knowledge on their conservation and management is compelling. Saline Systems provides an interdisciplinary forum for scientists working within all of the relevant fields.}, }
@article {pmid16168638, year = {2006}, author = {McHugh, S and Collins, G and O'Flaherty, V}, title = {Long-term, high-rate anaerobic biological treatment of whey wastewaters at psychrophilic temperatures.}, journal = {Bioresource technology}, volume = {97}, number = {14}, pages = {1669-1678}, doi = {10.1016/j.biortech.2005.07.020}, pmid = {16168638}, issn = {0960-8524}, mesh = {Anaerobiosis ; Bacteria, Anaerobic/genetics/*metabolism ; Biomass ; Bioreactors/microbiology ; *Cold Temperature ; Feasibility Studies ; Methane/analysis/metabolism ; Milk Proteins/*metabolism ; Sewage/chemistry/*microbiology ; Temperature ; Time Factors ; Waste Disposal, Fluid/*methods ; Whey Proteins ; }, abstract = {Two laboratory-scale anaerobic hybrid reactors, R1 and R2, treated low- (1 kg COD m-3) and high-strength (10 kg COD m-3) whey-based wastewaters, respectively, in a 500-day trial. The chemical oxygen demand (COD) removal efficiencies of R1 averaged 70-80%, at organic loading rates of 0.5-1.3 kg COD m-3 day-1, between 20 and 12 degrees C. The COD removal efficiencies of R2 exceeded 90%, at organic loading rates up to 13.3 kg COD m-3 day-1, between 20 and 14 degrees C. Lowering the operating temperature of R2 to 12 degrees C resulted in a decrease in COD removal efficiency, to between 50% and 60%, and a disintegration of granular sludge. The decline in performance, and granule disintegration, was reversed by decreasing the organic loading rate of R2 to 6.6 kg m-3 day-1. Specific methanogenic activity profiles revealed mesophilic (37 degrees C) temperature optima for biomass in both reactors, even after 500 days of psychrophilic operation, although the development of psychrotolerance in the biomass was noted.}, }
@article {pmid16166679, year = {2005}, author = {Collingro, A and Toenshoff, ER and Taylor, MW and Fritsche, TR and Wagner, M and Horn, M}, title = {'Candidatus Protochlamydia amoebophila', an endosymbiont of Acanthamoeba spp.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {55}, number = {Pt 5}, pages = {1863-1866}, doi = {10.1099/ijs.0.63572-0}, pmid = {16166679}, issn = {1466-5026}, mesh = {Acanthamoeba/*microbiology ; Animals ; Chlamydiales/*classification/*genetics/growth &amp; development ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Genes, rRNA ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Ribonuclease P/genetics ; Ribosomal Proteins/genetics ; *Symbiosis ; }, abstract = {The obligately intracellular coccoid bacterium UWE25, a symbiont of Acanthamoeba spp., was previously identified as being related to chlamydiae based upon the presence of a chlamydia-like developmental cycle and its 16S rRNA gene sequence. Analysis of its complete genome sequence demonstrated that UWE25 shows many characteristic features of chlamydiae, including dependency on host-derived metabolites, composition of the cell envelope and the ability to thrive as an energy parasite within the cells of its eukaryotic host. Phylogenetic analysis of 44 ribosomal proteins further confirmed the affiliation of UWE25 to the 'Chlamydiae'. Within this phylum, UWE25 could be assigned to the family Parachlamydiaceae based on comparative analyses of the 16S rRNA, 23S rRNA and endoribonuclease P RNA genes. The distinct dissimilarities from its closest relative, Parachlamydia acanthamoebae Bn(9)(T) (7.1, 9.7 and 28.8%, respectively), observed in this analysis justify its classification in a new genus. Therefore, the name 'Candidatus Protochlamydia amoebophila' is proposed for the designation of the Acanthamoeba sp. symbiont UWE25 (=ATCC PRA-7).}, }
@article {pmid16166549, year = {2005}, author = {Beaumont, HJ and Lens, SI and Westerhoff, HV and van Spanning, RJ}, title = {Novel nirK cluster genes in Nitrosomonas europaea are required for NirK-dependent tolerance to nitrite.}, journal = {Journal of bacteriology}, volume = {187}, number = {19}, pages = {6849-6851}, pmid = {16166549}, issn = {0021-9193}, mesh = {Genes, Bacterial/physiology ; Multigene Family/*physiology ; Mutation ; Nitric Oxide/metabolism ; Nitrite Reductases/*genetics/metabolism ; Nitrites/*metabolism ; Nitrosomonas europaea/*genetics/*metabolism ; Operon/physiology ; Oxidoreductases/genetics/metabolism ; }, abstract = {Nitrite reductase (NirK) of Nitrosomonas europaea confers tolerance to nitrite (NO2-). The nirK gene is clustered with three genes of unknown physiological function: ncgABC. At present, this organization is unique to nitrifying bacteria. Here we report that the ncgABC gene products facilitate NirK-dependent NO2- tolerance by reversing the negative physiological effect that is associated with the activity of NirK in their absence. We hypothesize that the ncg gene products are involved in the detoxification of nitric oxide that is produced by NirK.}, }
@article {pmid16162244, year = {2005}, author = {Devos, L and Clymans, K and Boon, N and Verstraete, W}, title = {Evaluation of nested PCR assays for the detection of Legionella pneumophila in a wide range of aquatic samples.}, journal = {Journal of applied microbiology}, volume = {99}, number = {4}, pages = {916-925}, doi = {10.1111/j.1365-2672.2005.02668.x}, pmid = {16162244}, issn = {1364-5072}, mesh = {Base Sequence ; Colony Count, Microbial/methods ; Culture Media ; DNA Primers/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Electrophoresis/methods ; Flow Cytometry/methods ; Legionella pneumophila/*isolation &amp; purification ; Phylogeny ; Polymerase Chain Reaction/*methods ; *Water Microbiology ; }, abstract = {AIMS: To compare the sensitivities of two nested PCR assays for the detection of Legionella pneumophila to each other and to the plate counting technique (ISO 11731) in a wide range of aquatic samples.<br><br>METHODS AND RESULTS: The nested PCR assay with the primer set LEG 225-LEG 858 revealed 56% of the 46 analysed aquatic samples as being positive for Legionella spp., while the primer set JFP-JRP yielded 98% positive samples. The detection was confirmed by sequencing the PCR products. These results are considerably higher than the result obtained with the plate counting technique (41%), indicating the higher sensitivity of PCR-based diagnostic methods. As the PCR assay with the LEG 225-LEG 858 primer set resulted in a lower number of positive samples, it is considered not sensitive enough for aquatic samples. Similar results for the respective primer sets were obtained for the detection of the species L. pneumophila, responsible for 90% of all human Legionella infections, in the aquatic samples analysed. Both microbial community analysis by PCR-denaturing gradient gel electrophoresis and the analysis of biotic and abiotic water quality parameters revealed no relation between L. pneumophila-positive and -negative samples and the physico-chemical and bacteriological characteristics of the aquatic samples.<br><br>CONCLUSIONS: The results show the additional value of the PCR assay with the JFP-JRP primer set compared with the plate counting technique, as well as its applicability in a wide range of aquatic samples.<br><br>This study shows the importance of comparing different primer sets for nested PCR assays for the detection of L. pneumophila in aquatic samples, as well as the lower sensitivity of the widely accepted plate counting technique (ISO 11731).}, }
@article {pmid16159916, year = {2005}, author = {Chung, WH and Rhee, SK and Wan, XF and Bae, JW and Quan, ZX and Park, YH}, title = {Design of long oligonucleotide probes for functional gene detection in a microbial community.}, journal = {Bioinformatics (Oxford, England)}, volume = {21}, number = {22}, pages = {4092-4100}, doi = {10.1093/bioinformatics/bti673}, pmid = {16159916}, issn = {1367-4803}, mesh = {Algorithms ; Cluster Analysis ; Computational Biology/*methods ; Conserved Sequence ; DNA Primers/*chemistry ; DNA Probes/chemistry ; Ecology/methods ; Gene Expression Profiling/*methods ; *Genes, Bacterial ; *Genetic Techniques ; Genetic Variation ; *Genome, Bacterial ; Internet ; *Models, Genetic ; Models, Theoretical ; Oligonucleotide Array Sequence Analysis/methods ; Oligonucleotide Probes/genetics ; Programming Languages ; Software ; }, abstract = {MOTIVATION: Analysis of the functions of microorganisms and their dynamics in the environment is essential for understanding microbial ecology. For analysis of highly similar sequences of a functional gene family using microarrays, the previous long oligonucleotide probe design strategies have not been useful in generating probes.<br><br>RESULTS: We developed a Hierarchical Probe Design (HPD) program that designs both sequence-specific probes and hierarchical cluster-specific probes from sequences of a conserved functional gene based on the clustering tree of the genes, specifically for analyses of functional gene diversity in environmental samples. HPD was tested on datasets for the nirS and pmoA genes. Our results showed that HPD generated more sequence-specific probes than several popular oligonucleotide design programs. With a combination of sequence-specific and cluster-specific probes, HPD generated a probe set covering all the sequences of each test set.<br><br>AVAILABILITY: http://brcapp.kribb.re.kr/HPD/}, }
@article {pmid16159757, year = {2005}, author = {Konstantinidis, KT and Tiedje, JM}, title = {Towards a genome-based taxonomy for prokaryotes.}, journal = {Journal of bacteriology}, volume = {187}, number = {18}, pages = {6258-6264}, pmid = {16159757}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Bacteria/*classification/genetics ; Classification/*methods ; Genetic Markers ; *Genome, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S/*analysis/genetics ; Sequence Analysis, DNA ; }, abstract = {The ranks higher than the species in the prokaryotic taxonomy are primarily designated based on phylogenetic analysis of the 16S rRNA gene sequences, but no definite standards exist for the absolute relatedness (measured by 16S rRNA or other means) between the ranks. Accordingly, it remains unknown how comparable the ranks are between different organisms. To gain insights into this question, we studied the relationship between shared gene content and genetic relatedness for 175 fully sequenced strains, using as a robust measure of relatedness the average amino acid identity (AAI) of the shared genes. Our results reveal that adjacent ranks (e.g., phylum versus class) frequently show extensive overlap in terms of genetic and gene content relatedness of the grouped organisms, and hence, the current system is of limited predictive power in this respect. The overlap between nonadjacent ranks (e.g., phylum versus family) is generally limited and attributable to clear inconsistencies of the taxonomy. In addition to providing means for standardizing taxonomy, our AAI-based approach provides a means to evaluate the robustness of alternative genetic markers for phylogenetic purposes. For instance, the 23S rRNA gene was found to be as good a marker as the 16S rRNA gene, while several of the widely distributed protein-coding genes, such as the RNA polymerase and gyrase subunits, show a strong phylogenetic signal, albeit less strong than the rRNA genes (0.78 > R2 > 0.69 for the protein-coding genes versus R2 = 0.84 for the rRNA genes). The AAI approach outlined here could contribute significantly to a genome-based taxonomy for all microbial organisms.}, }
@article {pmid16153732, year = {2005}, author = {Possemiers, S and Van Camp, J and Bolca, S and Verstraete, W}, title = {Characterization of the bactericidal effect of dietary sphingosine and its activity under intestinal conditions.}, journal = {International journal of food microbiology}, volume = {105}, number = {1}, pages = {59-70}, doi = {10.1016/j.ijfoodmicro.2005.05.007}, pmid = {16153732}, issn = {0168-1605}, mesh = {Anti-Bacterial Agents/administration &amp; dosage/isolation &amp; purification/*pharmacology ; Bifidobacterium/*drug effects/growth &amp; development ; Colony Count, Microbial ; *Diet ; Flow Cytometry ; Food Microbiology ; Intestines/microbiology ; Lactobacillus/*drug effects/growth &amp; development ; Models, Biological ; Sphingosine/administration &amp; dosage/isolation &amp; purification/*pharmacology ; }, abstract = {Sphingosine is known as a natural antimicrobial agent, protecting the human skin from bacterial colonization and possibly affecting the intestinal microbial community after ingestion. In this study we further investigated the antibacterial spectrum of dietary d-eythro-sphingosine in saline towards three intestinal pathogens and to the health promoting lactobacilli and bifidobacteria. The degree of bactericidal effect was studied using plate counts and Live/Dead analysis combined with flow cytometry. To assess activity under complex intestinal conditions, sphingosine was dosed to the Simulator of the Human Intestinal Microbial Ecosystem (SHIME) for a period of 11 days. Finally, we tried to elucidate the factors influencing the activity and the mode of action of sphingosine. In all performed experiments, high correlation occurred between plate counts and Live/Dead analysis. In saline a strong antibacterial effect was seen to all tested species, Gram-negative and Gram-positive, and sphingosine not selectively acted against pathogens, as health promoting bacteria were also affected. Under simulated intestinal conditions however, no shifts in bacterial concentrations were detected. Experiments with individual medium components thought that the effect of sphingosine is very easily neutralized by BSA, stearic acid and surfactants. Based on our results, d-erythro-sphingosine would only be active when protonated and its mode of action would imply electrostatic attraction to the bacteria and disruption of membrane integrity. In conclusion, the application of sphingosine is limited to specific environments, as activity was very sensitive to inhibition. Yet, because of its broad spectrum membrane disrupting activity, it could be very useful under controlled conditions.}, }
@article {pmid16153170, year = {2005}, author = {Larrainzar, E and O'Gara, F and Morrissey, JP}, title = {Applications of autofluorescent proteins for in situ studies in microbial ecology.}, journal = {Annual review of microbiology}, volume = {59}, number = {}, pages = {257-277}, doi = {10.1146/annurev.micro.59.030804.121350}, pmid = {16153170}, issn = {0066-4227}, mesh = {*Bacteria/genetics/growth &amp; development/metabolism ; Biofilms/*growth &amp; development ; Biosensing Techniques/*methods ; *Ecosystem ; Luminescent Proteins/genetics/*metabolism ; Plants/*microbiology ; }, abstract = {When autofluorescent proteins (AFPs), such as green fluorescent protein (GFP) and Discosoma striata red fluorescent protein (DsRed), are excited with light of a specific wavelength, they emit light of a longer wavelength, without the further addition of substrates. A range of AFPs have been identified and cloned from marine organisms, and mutagenesis techniques have been employed to develop improved variant AFPs for applications in biological research. In recent years, AFP technology has become an important tool for microbiologists and microbial ecologists studying processes such as microbe-plant interactions, biosensors, biofilm formation, and horizontal gene transfer. The ability to use AFPs with differing fluorescent spectra within a single cell has allowed simultaneous monitoring of several aspects of microbial physiology and gene expression in situ in real time. This provides a tremendous insight into microbial function and behavior in natural environments. Furthermore, the integration of AFP reporters with other markers and technologies is facilitating a systems approach to research in microbial ecology.}, }
@article {pmid16132428, year = {2005}, author = {Kim, YH and Engesser, KH and Cerniglia, CE}, title = {Numerical and genetic analysis of polycyclic aromatic hydrocarbon-degrading mycobacteria.}, journal = {Microbial ecology}, volume = {50}, number = {1}, pages = {110-119}, pmid = {16132428}, issn = {0095-3628}, mesh = {Base Sequence ; DNA, Bacterial/analysis ; Germany ; Molecular Sequence Data ; Mycobacteriaceae/classification/*genetics/*physiology ; Phylogeny ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Population Dynamics ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Ability to degrade high molecular weight polycyclic aromatic hydrocarbons (PAHs) has been found in diverse species of fast-growing mycobacteria. This study included several PAH-degrading mycobacteria from heavily contaminated sites and an uncontaminated humus soil in the Natural Park, Schwäbische Alb, Germany. The numerical analysis with a total of 131 tests showed that isolates from humus soil and contaminated sites had similar substrate utilization patterns for primary alcohols from ethanol to pentanol, 1,4-butanediol, benzyl alcohol, hexadecane, ethyl acetate, fluoranthene, phenanthrene, and pyrene as the sole carbon and energy (C/E) sources. Significant differences between the two subgroups isolated from humus soil and contaminated sites were observed in the utilization of polyalcoholic sugars, including adonitol, D: -arabitol, L: -arabitol, erythritol, inositol, rhamnose, sorbitol, and xylitol. Among isolates from humus soil, strain PYR100 showed high similarity in 16S rDNA sequence with M. vanbaalenii strain PYR-1 (=DSM 7251, 100%) and M. austroafricanum ATCC 33464 (99.9%). In addition to the numerical analysis, the 16S-23S intergenic spacer sequence was useful for discriminating between the closely related strains PYR100 and PYR-1 (98% similarity). The patterns of the variable V2 and V3 regions in the ribosomal RNA gene corresponding to Escherichia coli positions 179 to 197 and 1006 to 1023, respectively, were useful for dividing fast-growing and thermosensitive PAH-degrading mycobacteria into ten subgroups consistent with the phylogenetic positions.}, }
@article {pmid16132427, year = {2005}, author = {Satokari, RM and Kataja, K and Söderlund, H}, title = {Multiplexed quantification of bacterial 16S rRNA by solution hybridization with oligonucleotide probes and affinity capture.}, journal = {Microbial ecology}, volume = {50}, number = {1}, pages = {120-127}, pmid = {16132427}, issn = {0095-3628}, mesh = {Bacteria/*genetics ; Base Sequence ; DNA, Bacterial/*analysis ; In Situ Hybridization ; *Oligonucleotide Array Sequence Analysis ; Oligonucleotide Probes ; RNA, Ribosomal, 16S/*analysis/*genetics ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Analysis, DNA ; }, abstract = {Multiplexed and quantitative analysis of nucleic acid sequences in complex mixtures is essential in various applications of microbiological research. We have developed a method based on solution hybridization between biotinylated nucleic acid targets and multiple fluorophore-labeled oligonucleotide probes of distinct sizes. The biotin-nucleic acid-probe complexes are captured on magnetic streptavidin-coated microparticles and washed. The hybridized probes are eluted and their identity and quantity are determined by capillary electrophoresis. The signal intensities of the recorded probes correspond to the amount of target nucleic acid in the mixture, and the size indicates the target. Based on this principle and 16S rRNA-specific oligonucleotide probes, we set up an application for the relative quantification of different groups of clostridia and related organisms in a mixed bacterial population. The lower detection limit is 0.05 ng of total RNA and the linear range of measurement is 10(2). The method allowed accurate and highly repeatable quantification of the proportion of clostridia in human feces. Further, we discuss other applications of the method such as quantitative transcriptional analysis of eukaryotic microorganisms, which can be performed without conversion of mRNA to cDNA.}, }
@article {pmid16132426, year = {2005}, author = {Santamaría, J and Bayman, P}, title = {Fungal epiphytes and endophytes of coffee leaves (Coffea arabica).}, journal = {Microbial ecology}, volume = {50}, number = {1}, pages = {1-8}, pmid = {16132426}, issn = {0095-3628}, mesh = {Classification ; Coffea/*microbiology ; DNA, Fungal/analysis ; Environmental Monitoring ; Fungi/*growth &amp; development ; Plant Leaves/microbiology ; Population Dynamics ; }, abstract = {Plants harbor diverse communities of fungi and other microorganisms. Fungi are known to occur both on plant surfaces (epiphytes) and inside plant tissues (endophytes), but the two communities have rarely been compared. We compared epiphytic and endophytic fungal communities associated with leaves of coffee (Coffea arabica) in Puerto Rico. We asked whether the dominant fungi are the same in both communities, whether endophyte and epiphyte communities are equally diverse, and whether epiphytes and endophytes exhibit similar patterns of spatial heterogeneity among sites. Leaves of naturalized coffee plants were collected from six sites in Puerto Rico. Epiphytic and endophytic fungi were isolated by placing leaf pieces on potato dextrose agar without and with surface sterilization, respectively. A total of 821 colonies were isolated and grouped into 131 morphospecies. The taxonomic affinities of the four most common nonsporulating fungi were determined by sequencing the nuclear ribosomal internal transcribed spacer (ITS) region: two grouped with Xylaria and one each with Botryosphaeria and Guignardia. Of the most common genera, Pestalotia and Botryosphaeria were significantly more common as epiphytes; Colletotrichum, Xylaria, and Guignardia were significantly more common as endophytes. Suprisingly, more morphospecies occurred as endophytes than as epiphytes. Differences among sites in number of fungi per plant were significant. Thus epiphytic and endophytic communities differed greatly on a single leaf, despite living only millimeters apart, and both communities differed from site to site. Significant correlations between occurrence of fungal morphospecies suggested that fungi may have positive or negative effects on their neighbors. This is the first quantitative comparison of epiphytic and endophytic fungal floras in any plant, and the first to examine endophytic fungi or epiphytic fungi in leaves of coffee, one of the world's most valuable crops.}, }
@article {pmid16132425, year = {2005}, author = {Borsodi, AK and Micsinai, A and Rusznyák, A and Vladár, P and Kovács, G and Tóth, EM and Márialigeti, K}, title = {Diversity of alkaliphilic and alkalitolerant bacteria cultivated from decomposing reed rhizomes in a Hungarian soda lake.}, journal = {Microbial ecology}, volume = {50}, number = {1}, pages = {9-18}, pmid = {16132425}, issn = {0095-3628}, mesh = {Bacteria, Aerobic/*physiology ; Biodegradation, Environmental ; Hungary ; Hydrogen-Ion Concentration ; Plant Roots ; Poaceae/metabolism/*microbiology ; Population Dynamics ; Water/chemistry ; *Water Microbiology ; }, abstract = {Bacterial communities associated with decomposing rhizomes of Phragmites australis were investigated in Lake Ferto (Neusiedlersee, Hungary). Alkaliphilic and alkalitolerant strains were isolated on cellulose-containing alkaline medium spread with dilutions of scrapings taken from the surface of the decaying plant material. Fifty-one strains were grouped by numerical analysis based on physiological tests and BIOLOG sole carbon source utilization data. The strains identified by 16S rDNA sequence comparisons included members of low G+C Gram positives (Marinibacillus marinus, Bacillus cereus, and Exiguobacterium aurantiacum), high G+C Gram positives (Nesterenkonia halobia and Dietzia natronolimnea), alpha-proteobacteria (Pannonibacter phragmitetus), and gamma-proteobacteria (Pseudomonas pseudoalcaligenes and Halomonas venusta). Most of the strains were characterized by aerobic chemoorganotrophic respiratory metabolism and utilized several different carbon sources, although no direct cellulolytic activity was observed. Results of the pH and salt tolerance tests revealed optimuma in most cases at pH 11 and at the presence of 2.5-5% NaCl. These bacteria probably occupy niches in the aerobic, alkaline, water-influenced environments on the decomposing reed surfaces.}, }
@article {pmid16132424, year = {2005}, author = {Maul, JD and Gandhi, JP and Farris, JL}, title = {Community-level physiological profiles of cloacal microbes in songbirds (order: Passeriformes): variation due to host species, host diet, and habitat.}, journal = {Microbial ecology}, volume = {50}, number = {1}, pages = {19-28}, pmid = {16132424}, issn = {0095-3628}, mesh = {Animals ; *Bacteria ; Carbon/*metabolism ; Classification ; Cloaca/*microbiology ; Diet ; Environment ; Female ; Male ; Population Dynamics ; Seasons ; Songbirds/*microbiology ; }, abstract = {The relationship between microorganisms and birds has received increased attention recently. The state of knowledge of this relationship, however, is based largely on examination of sick or dead birds, and knowledge of the prevalence and community structure and function of microbes in healthy wild populations is limited. Using carbon substrate utilization profiles, microbial communities were examined in 91 cloacal samples from 14 species within apparently healthy summer and winter passerine populations. Within each season, gradient lengths and eigenvalues from ordination analyses suggested that many samples differed in their carbon substrate utilization and several had very different communities. Cloacal microbe carbon utilization profiles were distinguishable among host species, season-specific diet, and study site in the ordination analyses. However, these patterns were only observed for the analysis of the summer data set. The results of this study support the idea that the avian host's microbial community, relative to carbon substrate utilization, is related to host diet. Previously, this pattern had only been reported for potential pathogens isolated from the avian cloaca. Study site-specific patterns in the ordination analysis suggest that environmental conditions at a particular study site may influence cloacal microbial communities in birds. Results of this study indicate that examination of community-level physiological profiles may be a useful technique for distinguishing among avian cloacal samples, similar to that already established for discriminating aqueous and soil samples. Future studies that correlate microbe physiological profiles to condition-based indices of avian hosts may be most useful for eventually using the profile as an indicator of environmental conditions experienced by hosts.}, }
@article {pmid16132423, year = {2005}, author = {Scholten, JC and Joye, SB and Hollibaugh, JT and Murrell, JC}, title = {Molecular analysis of the sulfate reducing and archaeal community in a meromictic soda lake (Mono Lake, California) by targeting 16S rRNA, mcrA, apsA, and dsrAB genes.}, journal = {Microbial ecology}, volume = {50}, number = {1}, pages = {29-39}, pmid = {16132423}, issn = {0095-3628}, mesh = {Archaea/classification/*genetics/*physiology ; Bacterial Proteins/analysis/*genetics ; Base Sequence ; California ; Carbon/metabolism ; Gene Amplification ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Population Dynamics ; RNA, Ribosomal, 16S/analysis/genetics ; Sulfates/*metabolism ; Water/chemistry ; Water Microbiology ; Water Supply ; }, abstract = {Sulfate reduction is the most important process involved in the mineralization of carbon in the anoxic bottom waters of Mono Lake, an alkaline, hypersaline, meromictic Lake in California. Another important biogeochemical process in Mono Lake is thought to be sulfate-dependent methane oxidation (SDMO). However little is known about what types of organisms are involved in these processes in Mono Lake. Therefore, the sulfate-reducing and archaeal microbial community in Mono Lake was analyzed by targeting 16S rRNA, methyl-coenzyme M reductase (mcrA), adenosine-5'-phosphosulfate (apsA), and dissimilatory sulfite reductase (dsrAB) genes to investigate the sulfate-reducing and archaeal community with depth. Most of the 16S rRNA gene sequences retrieved from the samples fell into the delta-subdivision of the Proteobacteria. Phylogenetic analyses suggested that the clones obtained represented sulfate-reducing bacteria, which are probably involved in the mineralization of carbon in Mono Lake, many of them belonging to a novel line of descent in the delta-Proteobacteria. Only 6% of the sequences retrieved from the samples affiliated to the domain Euryarchaeota but did not represent Archaea, which is considered to be responsible for SDMO [Orphan et al. 2001: Appl Environ Microbiol 67:1922-1934; Teske et al.: Appl Environ Microbiol 68:1994-2007]. On the basis of our results and thermodynamic arguments, we proposed that SDMO in hypersaline environments is presumably carried out by SRB alone. Polymerase chain reaction (PCR) amplifications of the mcrA-, apsA-, and dsrAB genes in Mono Lake samples were, in most cases, not successful. Only the PCR amplification of the apsA gene was partially successful. The amplification of these functional genes was not successful because there was either insufficient "target" DNA in the samples, or the microorganisms in Mono Lake have divergent functional genes.}, }
@article {pmid16132422, year = {2005}, author = {Shawkey, MD and Mills, KL and Dale, C and Hill, GE}, title = {Microbial diversity of wild bird feathers revealed through culture-based and culture-independent techniques.}, journal = {Microbial ecology}, volume = {50}, number = {1}, pages = {40-47}, pmid = {16132422}, issn = {0095-3628}, mesh = {Animals ; Animals, Wild ; Bacillus/*genetics/growth &amp; development/isolation &amp; purification ; Classification ; DNA, Bacterial/analysis ; Data Collection ; Feathers/*microbiology ; Female ; Male ; Phylogeny ; Polymerase Chain Reaction ; Population Dynamics ; Proteobacteria/*genetics/growth &amp; development/isolation &amp; purification ; Songbirds/*microbiology ; }, abstract = {Despite recent interest in the interactions between birds and environmental microbes, the identities of the bacteria that inhabit the feathers of wild birds remain largely unknown. We used culture-based and culture-independent surveys of the feathers of eastern bluebirds (Sialis sialis) to examine bacterial flora. When used to analyze feathers taken from the same birds, the two survey techniques produced different results. Species of the poorly defined genus Pseudomonas were most common in the molecular survey, whereas species of the genus Bacillus were predominant in the culture-based survey. This difference may have been caused by biases in both the culture and polymerase chain reaction techniques that we used. The pooled results from both techniques indicate that the overall community is diverse and composed largely of members of the Firmicutes and beta- and gamma- subdivisions of the Proteobacteria. For the most part, bacterial sequences isolated from birds were closely related to sequences of soil-borne and water-borne bacteria in the GenBank database, suggesting that birds may have acquired many of these bacteria from the environment. However, the metabolic properties and optimal growth requirements of several isolates suggest that some of the bacteria may have a specialized association with feathers.}, }
@article {pmid16126187, year = {2006}, author = {Loy, A and Bodrossy, L}, title = {Highly parallel microbial diagnostics using oligonucleotide microarrays.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {363}, number = {1-2}, pages = {106-119}, doi = {10.1016/j.cccn.2005.05.041}, pmid = {16126187}, issn = {0009-8981}, mesh = {Bacteria/*isolation &amp; purification ; *Environmental Microbiology ; Genetic Markers ; Genome ; Humans ; Infections/diagnosis/microbiology/virology ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis/*methods ; Oligonucleotide Probes ; Sensitivity and Specificity ; Viruses/*isolation &amp; purification ; }, abstract = {Oligonucleotide microarrays are highly parallel hybridization platforms, allowing rapid and simultaneous identification of many different microorganisms and viruses in a single assay. In the past few years, researchers have been confronted with a dramatic increase in the number of studies reporting development and/or improvement of oligonucleotide microarrays for microbial diagnostics, but use of the technology in routine diagnostics is still constrained by a variety of factors. Careful development of microarray essentials (such as oligonucleotide probes, protocols for target preparation and hybridization, etc.) combined with extensive performance testing are thus mandatory requirements for the maturation of diagnostic microarrays from fancy technological gimmicks to robust and routinely applicable tools.}, }
@article {pmid16118479, year = {2005}, author = {Yamashita, M and Ishikawa, Y and Oshima, T and , }, title = {[Engineering issues of microbial ecology in space agriculture].}, journal = {Uchu Seibutsu Kagaku}, volume = {19}, number = {1}, pages = {25-36}, doi = {10.2187/bss.19.25}, pmid = {16118479}, issn = {0914-9201}, mesh = {Agriculture/methods ; *Biodegradation, Environmental ; *Ecological Systems, Closed ; Ecology ; Extraterrestrial Environment ; Humans ; *Life Support Systems ; Mars ; Moon ; Plant Roots/microbiology ; Soil Microbiology ; *Space Flight ; Waste Management/*methods ; }, abstract = {Closure of the materials recycle loop for water-foods-oxygen is the primary purpose of space agriculture on Mars and Moon. A microbial ecological system takes a part of agriculture to process our metabolic excreta and inedible biomass and convert them to nutrients and soil substrate for cultivating plants. If we extend the purpose of space agriculture to the creation and control of a healthy and pleasant living environment, we should realize that our human body should not be sterilized but exposed to the appropriate microbial environment. We are proposing a use of hyper-thermophilic aerobic composting microbial ecology in space agriculture. Japan has a broad historical and cultural background on this subject. There had been agriculture that drove a closed loop of materials between consuming cities and farming villages in vicinity. Recent environmental problems regarding garbage collection and processing in towns have motivated home electronics companies to innovate "garbage composting" machines with bacterial technology. Based on those matured technology, together with new insights on microbiology and microbial ecology, we have been developing a conceptual design of space agriculture on Moon and Mars. There are several issues to be answered in order to prove effectiveness of the use of microbial systems in space. 1) Can the recycled nutrients, processed by the hyper-thermal aerobic composting microbial ecology, be formed in the physical and chemical state or configuration, with which plants can uptake those nutrients? A possibility of removing any major components of fertilizer from its recycle loop is another item to be evaluated. 2) What are the merits of forming soil microbial ecology around the root system of plants? This might be the most crucial question. Recent researches exhibit various mutually beneficial relationships among soil microbiota and plants, and symbiotic ecology in composting bacteria. It is essential to understand those features, and define how to conduct preventive maintenance for keeping cultivating soil healthy and productive. 3) Does microbial ecology contribute to building sustainable and expandable human habitation by utilizing the on site extraterrestrial resources? We are assessing technical feasibility of converting regolith to farming soil and structural materials for space agriculture. In the case of Mars habitation, carbon dioxide and a trace amount of nitrogen in atmosphere, and potassium and phosphor in minerals are the sources we consider. Excess oxygen can be accumulated by woods cultivation and their use for lumber. 4) Is the operation of space agriculture robust and safe, if it adopts hyper-thermophilic aerobic microbial ecology? Any ecological system is complex and non-linear, and shows latency and memory effects in its response. It is highly important to understand those features to design and operate space agriculture without falling into the fatal failure. Assessment should be made on the microbial safety and preparation of the preventive measures to eliminate negative elements that would either retard agricultural production or harm the healthy environment. It is worth to mention that such space agriculture would be an effective engineering testbed to solve the global problem on energy and environment. Mars and Moon exploration itself is a good advocate of healthy curiosity expressed by the sustainable civilization of our humankind. We propose to work together towards Mars and Moon with microbial ecology to assure pleasant habitation there.}, }
@article {pmid16108803, year = {2005}, author = {Corte, L and Lattanzi, M and Buzzini, P and Bolano, A and Fatichenti, F and Cardinali, G}, title = {Use of RAPD and killer toxin sensitivity in Saccharomyces cerevisiae strain typing.}, journal = {Journal of applied microbiology}, volume = {99}, number = {3}, pages = {609-617}, doi = {10.1111/j.1365-2672.2005.02631.x}, pmid = {16108803}, issn = {1364-5072}, mesh = {DNA, Fungal/genetics ; Electrophoresis, Agar Gel/methods ; Genetic Markers/genetics ; Killer Factors, Yeast ; Mycological Typing Techniques/*methods ; Phylogeny ; Proteins/*analysis ; Random Amplified Polymorphic DNA Technique/*methods ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/*analysis ; }, abstract = {AIMS: Two different strain characterization techniques, random amplified polymorphic DNA (RAPD) and killer toxin sensitivity (KTS), were compared to assess their typing performance using a set of 30 certified Saccharomyces cerevisiae strains.<br><br>METHODS AND RESULTS: A sequential random resampling procedure was employed to subdivide the 32 descriptors in eight sets, in order to compare the differential performances of the two techniques with diverse number of characters. Results showed that RAPD performs better than killer, although the complete differentiation of the strains under study could be obtained only by combining profiles from the two techniques.<br><br>CONCLUSIONS: The combination of different typing techniques was useful when discriminating similar organisms. In such cases, the introduction of a second typing technique can be more advantageous than increasing the number of characters obtained with a single method.<br><br>The distribution of among-strains pairwise distances and the relative performance of the two techniques has implications for the study of biodiversity, taxonomy and microbial ecology.}, }
@article {pmid16104857, year = {2005}, author = {Huang, WE and Wang, H and Zheng, H and Huang, L and Singer, AC and Thompson, I and Whiteley, AS}, title = {Chromosomally located gene fusions constructed in Acinetobacter sp. ADP1 for the detection of salicylate.}, journal = {Environmental microbiology}, volume = {7}, number = {9}, pages = {1339-1348}, doi = {10.1111/j.1462-5822.2005.00821.x}, pmid = {16104857}, issn = {1462-2912}, mesh = {Acinetobacter/*genetics/growth &amp; development ; *Artificial Gene Fusion ; Bacterial Proteins/genetics ; Base Sequence ; Biodegradation, Environmental ; Biosensing Techniques ; Chromosomes, Bacterial/*genetics ; Environmental Pollutants/*analysis ; Genes, Bacterial/*genetics ; Genetic Engineering ; Green Fluorescent Proteins/genetics ; Molecular Sequence Data ; Mutation ; Salicylates/*analysis ; }, abstract = {Acinetobacter sp. ADP1 is a common soil-associated bacterium with high natural competency, allowing it to efficiently integrate foreign DNA fragments into its chromosome. This property was exploited to engineer salicylate-inducible luxCDABE and green fluorescent protein (GFP) variants of Acinetobacter sp. ADP1. Specifically, Acinetobacter sp. ADPWH_lux displayed the higher sensitivity when comparing the two variants (minimum detection c. 0.5-1 microM salicylate) and a faster turnover of the lux marker gene, making it suitable for whole-cell luminescence assays of salicylate concentration. In contrast, the longer maturation and turnover times of the GFP protein make the Acinetobacter sp. ADPWH_gfp variant more suited to applications involving whole-cell imaging of the presence of salicylate. The sensitivity of the luxCDABE variant was demonstrated by assaying salicylate production in naphthalene-degrading cultures. Assays using ADPWH_lux specifically mapped the kinetics of salicylate production from naphthalene and were similar to that observed by high-performance liquid chromatography (HPLC) data. However, ADPWH_lux exhibited the higher sensitivity, when compared with HPLC, for detecting salicylate production during the first 24 h of naphthalene metabolism. These data demonstrate that the engineered Acinetobacter variants have significant potential for salicylate detection strategies in laboratory and field studies, especially in scenarios where genetic stability of the construct is required for in situ monitoring.}, }
@article {pmid16088717, year = {2000}, author = {Chalfine, A and Timsit, JF and Acar, J}, title = {Antibiotic resistance in nosocomial pulmonary pathogens.}, journal = {Seminars in respiratory and critical care medicine}, volume = {21}, number = {1}, pages = {45-51}, doi = {10.1055/s-2000-9929}, pmid = {16088717}, issn = {1069-3424}, abstract = {Nosocomial pneumonia is the second most common hospital-acquired infection and are associated with antibiotic-resistant microorganisms. In nosocomial pneumonia, both the diagnosis of the disease and the identification of the pathogen agent are controversial. The lack of standard diagnostic criteria can lead to the inappropriate use of broad-spectrum antibiotic therapy and the emergence of multiresistant bacteria. Moreover, empirical antibiotic treatment must be prescribed after bacteriological sample but before culture results because the majority of nosocomial pneumonias require an urgent antibiotic therapy. Most nosocomial pneumonias are of an endogenous origin, particularly in mechanically ventilated patients, and this is associated with a higher rate of multiresistant methicillin-resistant Staphylococcus aureus, Acinetobacter baumanii, Klebsiella pneumoniae with extended spectrum b-lactamases, and Pseudomonadaceae. Multiple factors influence the frequency of pathogens associated with antibiotic resistance, such as duration of hospital stay, time of onset, prior antibiotic therapy, and local microbial ecology.}, }
@article {pmid16086530, year = {2005}, author = {Lesitevuo, J and Huikko, S and Rautakorpi, UM and Leistevuo, T and Honkanen, PO and Klaukka, T and Mäkelä, M and Palva, E and Roine, R and Sarkkinen, H and Varonen, H and Huovinen, P and , }, title = {Prescription rates and diagnostic patterns are stable: a comparison of high-, medium- and low-prescribing primary care physicians treating community-acquired respiratory tract infections.}, journal = {Scandinavian journal of infectious diseases}, volume = {37}, number = {6-7}, pages = {465-470}, doi = {10.1080/00365540510037975}, pmid = {16086530}, issn = {0036-5548}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Community-Acquired Infections/diagnosis/drug therapy ; Drug Prescriptions/*statistics &amp; numerical data ; Drug Utilization ; Humans ; Odds Ratio ; Practice Patterns, Physicians'/*standards ; Respiratory Tract Infections/*diagnosis/*drug therapy ; }, abstract = {The objective was to study prescription practices of primary care physicians in prescribing antibiotics for community-acquired respiratory tract infections. Design was time series analysis and cross-sectional survey. The setting was 30 community primary health care centres. A case report form was completed for 3478 patient consultations treated by 198 office-based primary care physicians. Main outcome measures were: classification of diagnoses of respiratory tract infections made by each physician; number of antibiotic prescriptions related to these diagnoses; each physician's mean weekly number of antibiotic prescriptions during 6 months before and after the survey. Patients' risk (odds ratio: OR) to receive an antibiotic prescription from the high and medium prescribers was 5.81 (95% confidence interval [CI] 4.85-6.96) and 2.41 (95% CI 2.04-2.86), compared to low prescribers. High and medium prescribers made more diagnoses of otitis media (OR 2.07, 95% CI 1.70-2.53 and 1.85, 95% CI 1.51-2.26, respectively) and fewer diagnoses of unspecified upper respiratory tract infection (OR 0.32, 95% CI 0.26-0.38 and 0.57, 95% CI 0.48-0.68, respectively) than low prescribers. The rank of the prescription rate of high, medium and low prescriber groups remained the same for all diagnoses except pneumonia. In addition, the annual rank between high, medium and low prescriber groups remained stable; high group prescribed more antibiotics during the year than medium group, which prescribed more than low prescriber group.}, }
@article {pmid16085891, year = {2005}, author = {Neufeld, JD and Mohn, WW}, title = {Fluorophore-labeled primers improve the sensitivity, versatility, and normalization of denaturing gradient gel electrophoresis.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {8}, pages = {4893-4896}, pmid = {16085891}, issn = {0099-2240}, mesh = {Bacteria/*genetics/isolation &amp; purification ; Carbocyanines ; DNA Fingerprinting/methods ; *DNA Primers ; DNA, Bacterial/*analysis/isolation &amp; purification ; Electrophoresis, Polyacrylamide Gel/*methods/standards ; *Fluorescent Dyes ; Sensitivity and Specificity ; Soil Microbiology ; }, abstract = {Denaturing gradient gel electrophoresis (DGGE) is widely used in microbial ecology. We tested the effect of fluorophore-labeled primers on DGGE band migration, sensitivity, and normalization. The fluorophores Cy5 and Cy3 did not visibly alter DGGE fingerprints; however, 6-carboxyfluorescein retarded band migration. Fluorophore modification improved the sensitivity of DGGE fingerprint detection and facilitated normalization of samples from multiple gels by the application of intralane standards.}, }
@article {pmid16081938, year = {2005}, author = {Gafan, GP and Lucas, VS and Roberts, GJ and Petrie, A and Wilson, M and Spratt, DA}, title = {Statistical analyses of complex denaturing gradient gel electrophoresis profiles.}, journal = {Journal of clinical microbiology}, volume = {43}, number = {8}, pages = {3971-3978}, pmid = {16081938}, issn = {0095-1137}, mesh = {Child ; Child, Preschool ; DNA, Bacterial/*analysis ; Dental Plaque/*microbiology ; Electrophoresis, Polyacrylamide Gel ; Gingivitis/*microbiology ; Humans ; Logistic Models ; }, abstract = {Studies using molecular techniques have demonstrated that a culture-based approach can severely underestimate the bacterial diversity in most environments. One of the molecular techniques that has been applied in microbial ecology is denaturing gradient gel electrophoresis (DGGE). The purpose of this study was to investigate differences in the microbiota of plaque, using a number of analysis techniques, from children without gingivitis (n = 30) and from those with gingivitis (n = 30). Extracted DNA from gingival margin plaque was subjected to PCR targeting the 16S rRNA gene using universal primers. DGGE profiles were analyzed in three ways. (i) Bacterial diversity was compared between cohorts by using the Shannon-Wiener index (also known as the Shannon-Weaver index). (ii) A hierarchical cluster analysis of the banding patterns was calculated and expressed as a dendrogram. (iii) Individual DGGE bands and their intensities for both cohorts were compared using a logistic regression analysis. The Shannon-Wiener indices demonstrated a greater bacterial diversity associated with no-gingivitis plaque (P = 0.009). Dendrograms demonstrated that seven clades associated with gingivitis and five clades associated with no gingivitis. The logistic regression demonstrated that one band was significantly associated with no gingivitis (P = 0.001), while two bands were significantly associated with gingivitis (P = 0.005 and P = 0.042). In conclusion, this study demonstrates that the development of gingivitis might be accompanied by a decrease in bacterial diversity. Furthermore, we have demonstrated that logistic regression is a good statistical method for analyzing and characterizing DGGE profiles.}, }
@article {pmid16076107, year = {2005}, author = {Possemiers, S and Heyerick, A and Robbens, V and De Keukeleire, D and Verstraete, W}, title = {Activation of proestrogens from hops (Humulus lupulus L.) by intestinal microbiota; conversion of isoxanthohumol into 8-prenylnaringenin.}, journal = {Journal of agricultural and food chemistry}, volume = {53}, number = {16}, pages = {6281-6288}, doi = {10.1021/jf0509714}, pmid = {16076107}, issn = {0021-8561}, mesh = {Adult ; Bacteria/*metabolism ; Eubacterium/metabolism ; Feces/microbiology ; Fermentation ; Flavanones/*metabolism ; Flavonoids/metabolism ; Humans ; Humulus/*chemistry ; Intestines/*microbiology ; Phytoestrogens/*metabolism ; Propiophenones/*metabolism ; }, abstract = {Hop, an essential ingredient in most beers, contains a number of prenylflavonoids, among which 8-prenylnaringenin (8-PN) would be the most potent phytoestrogen currently known. Although a number of health effects are attributed to these compounds, only a few reports are available about the bioavailability of prenylflavonoids and the transformation potency of the intestinal microbial community. To test these transformations, four fecal samples were incubated with xanthohumol, isoxanthohumol (IX), and 8-PN. Upon incubation with IX, present in strong ales up to 4 mg/L, 36% was converted into 8-PN in one fecal sample and the estrogenic properties of the sample drastically increased. In an experiment with 12 fecal cultures, this conversion was observed in one-third of the samples, indicating the importance of interindividual variability in the intestinal microbial community. Eubacterium limosum was identified to be capable of this conversion (O-demethylation) of IX into 8-PN, and after strain selection, a conversion efficiency of 90% was achieved. Finally, strain supplementation to a nonconverting fecal sample led to rapid and high 8-PN production at only 1% (v/v) addition. Up to now, the concentration of 8-PN in beer was considered too low to affect human health. However, these results show that the activity of the intestinal microbial community could more than 10-fold increase the exposure concentration. Because prenylflavonoids are present in many beers with IX being the major constituent, the results raise the question whether moderate beer consumption might contribute to increased in vivo levels of 8-PN and even influence human health.}, }
@article {pmid16059660, year = {2005}, author = {Lamentowicz, M and Mitchell, EA}, title = {The ecology of testate amoebae (Protists) in sphagnum in North-western Poland in relation to peatland ecology.}, journal = {Microbial ecology}, volume = {50}, number = {1}, pages = {48-63}, pmid = {16059660}, issn = {0095-3628}, mesh = {Adaptation, Physiological ; Amoeba/*growth &amp; development ; Animals ; Ecology ; Environmental Monitoring ; Hydrogen-Ion Concentration ; Poland ; Population Dynamics ; Sphagnopsida/microbiology ; Water/chemistry ; *Water Microbiology ; }, abstract = {We studied the relationship between testate amoebae (Protozoa) communities and the depth to the water table (DWT), pH, conductivity, and microhabitat type in Sphagnum dominated peatlands of north-western Poland and built predictive (transfer function) models for inferring DWT and pH based on the testate amoebae community structure. Such models can be used for peatland monitoring and paleoecology. A total of 52 testate amoebae taxa were recorded. In a redundancy analysis, DWT and pH explained 20.1% of the variation in the species data and allowed us to identify three groups of taxa: species that are associated with (1) high DWT and low pH, (2) low DWT and low pH, and (3) high pH and mid-range DWT. Our transfer function models allow DWT and pH to be estimated with mean errors of 9.89 cm and 0.71 pH units. The prediction error of the DWT model and the tolerance of the species both increase with increasing dryness. This pattern mirrors the ecology of Sphagnum mosses: Species growing in wet habitats are more sensitive to change in water table depth than the species growing in drier microhabitats. Our results are consistent with studies of testate amoeba ecology in other regions, and they provide additional support for the use of these organisms in paleoecological and biomonitoring contexts.}, }
@article {pmid16055329, year = {2006}, author = {Demirel, B and Yenigün, O}, title = {Changes in microbial ecology in an anaerobic reactor.}, journal = {Bioresource technology}, volume = {97}, number = {10}, pages = {1201-1208}, doi = {10.1016/j.biortech.2005.05.009}, pmid = {16055329}, issn = {0960-8524}, mesh = {Bacteria, Anaerobic/*physiology ; Bioreactors/*microbiology ; Colony Count, Microbial ; Dairying ; *Ecology ; Fatty Acids, Volatile/analysis ; Industrial Microbiology ; Methanobacteriales/physiology ; Sewage/*microbiology ; Waste Disposal, Fluid/*methods ; }, abstract = {This study examined the behaviour of the microbial population in an anaerobic reactor, in terms of changes in numbers of total bacterial community, autofluorescent methanogens, non-methanogens and morphology of the autofluorescent methanogens, using epifluorescence microscopy and microbiological enumeration techniques. A laboratory-scale, continuous flow-completely mixed anaerobic reactor, coupled with a conventional gravity settling tank and a continuous recycling system, was operated at an HRT range between 24 and 12 h, using dairy wastewater as the substrate. The numbers of the total bacterial community and autofluorescent methanogens both decreased during start-up. Also, the proportion of the number of autofluorescent methanogens in the total bacterial community varied from 5% to 16% during operation. In particular, the activity of the methane-forming bacteria decreased significantly at HRTs of 16 and 12 h. A membrane module, instead of a conventional settling tank, would obviously have been a more effective method if recycling were required in the anaerobic treatment system.}, }
@article {pmid16055328, year = {2006}, author = {Aiyuk, S and Forrez, I and Lieven, de K and van Haandel, A and Verstraete, W}, title = {Anaerobic and complementary treatment of domestic sewage in regions with hot climates--a review.}, journal = {Bioresource technology}, volume = {97}, number = {17}, pages = {2225-2241}, doi = {10.1016/j.biortech.2005.05.015}, pmid = {16055328}, issn = {0960-8524}, mesh = {Bacteria, Anaerobic/growth &amp; development/*physiology ; Biodegradation, Environmental ; Bioreactors ; *Climate ; *Hot Temperature ; Sewage/chemistry/*microbiology ; Waste Disposal, Fluid ; *Water Purification ; }, abstract = {This study presents a literature review on the treatment of domestic sewage in controlled environments having the anaerobic process and specifically the upflow anaerobic sludge blanket (UASB) concept as the core, under natural hot conditions. The UASB process application is however beset by the preponderance of suspended solids, and the paper looks at its optimization via pre- and post-treatments to curb the prevailing problems, in the light of possible discharge and re-use/recycling/resource recovery, leading to efficient environmental protection. Pre-treatment clarification could be done with ferric chloride/polyelectrolyte, so that phosphate precipitates during the process. The pre-treated liquid phase can be submitted to a high rate anaerobic process, using the simple and robust UASB technology. In a subsequent post-treatment step, ammonium can be removed by ion exchange using a zeolite column through which the wastewater percolates after leaving the anaerobic digester. The various stages can also eliminate a large fraction of the pathogens present in the raw wastewater, mainly through the pre-treatment sedimentation and the ion exchange filtration. The sludge produced in the precipitation stage can be stabilized in a conventional anaerobic digester. Integration of the different treatment steps provides a sustainable technology to treat domestic sewage under hot climate conditions.}, }
@article {pmid16052383, year = {2005}, author = {Bjelland, T and Ekman, S}, title = {Fungal diversity in rock beneath a crustose lichen as revealed by molecular markers.}, journal = {Microbial ecology}, volume = {49}, number = {4}, pages = {598-603}, pmid = {16052383}, issn = {0095-3628}, mesh = {Base Sequence ; *Biodiversity ; Computational Biology ; DNA Primers ; DNA, Ribosomal Spacer/genetics ; Fungi/*genetics ; *Lichens ; Molecular Sequence Data ; Norway ; Sequence Analysis, DNA ; }, abstract = {Lichen-forming fungi have been assumed to be more or less restricted to the surface of the substrate on which they grow, Conclusive identification of hyphae or an assessment of the fungal diversity inside lichen-covered rock has not been possible using methods based on direct observation. We circumvented this problem by using a DNA sequencing approach. Cores were drilled from a Devonian arcosic sandstone rock harboring the crustose lichen Ophioparma ventosa (L.) Norman on the surface. The cores were cut vertically, and DNA was extracted from the pulverized rock slices. A series of polymerase chain reactions using fungal-specific primers as well as Ophioparma ventosa specific primers were employed to amplify the internal transcribed spacer region of the nuclear ribosomal DNA. The results show that hyphae of O. ventosa penetrate approximately 10-12 mm into the rock. Consequently, the hyphal layer formed by the lichen fungus inside the rock could be 7-12 times as thick as the symbiotic thallus at the surface of the rock. In addition, eight non-lichenized fungal taxa and five that could not be identified to species were encountered. One fungal species in the order Helotiales occurs in six of the eight cores. The significance of these results to the colonization and weathering of rock by lichenized fungi is discussed.}, }
@article {pmid16052382, year = {2005}, author = {Pringault, O and de Wit, R and Camoin, G}, title = {Irradiance regulation of photosynthesis and respiration in modern marine microbialites built by benthic cyanobacteria in a tropical lagoon (New Caledonia).}, journal = {Microbial ecology}, volume = {49}, number = {4}, pages = {604-616}, pmid = {16052382}, issn = {0095-3628}, mesh = {Chromatography, High Pressure Liquid ; Cyanobacteria/cytology/*physiology ; Geologic Sediments/*microbiology ; *Light ; New Caledonia ; Oxygen Consumption/physiology/*radiation effects ; Photosynthesis/physiology/*radiation effects ; Pigments, Biological/analysis ; Tropical Climate ; }, abstract = {Microbialites are organosedimentary deposits that have built up as a result of the growth and binding of detrital sediment by a benthic microbial community. This study focuses on microbialites built by monospecific populations of cyanobacteria in the south-west lagoon of New Caledonia, where they have been observed down to 20-25 m depth. The aim was to study their photosynthetic and respiratory responses to various light intensities. The Phormidium sp. TK1 microbialite was collected at 19 m depth and the P. crosbyanum (Tilden) microbialite was collected at 0.5 and 13 m depth. Phormidium sp. TK1 showed all the characteristic features of a low-light adapted species. The initial slope of the Photosynthesis versus Irradiance curve for this microbialite was close to the maximum quantum yield indicating an efficient light absorption and utilization at low light. The photosynthesis maximum was located 0.2-0.4 mm below the surface and did not shift with changing light intensity. Respiration rates were low and not enhanced by light; photoinhibition was observed at higher light intensities. In Phormidium crosbyanum (Tilden) microbialites, the photosynthesis maximum shifted downward to lower depths with increasing light, probably as a result of phototactic migration of cyanobacterial filaments, and light-enhanced respiration was observed at light intensities above light saturation. The photosynthetic para- meters measured in P. crosbyanum indicate that P. crosbyanum is capable of photo-acclimation at high light intensities. The gross productivity of the different microbialites was comparable to values measured in cyanobacterial stromatolites observed in other shallow environments. However, the microbialites studied here were characterized by a lower respiration / production ratio which indicates a higher growth efficiency.}, }
@article {pmid16052381, year = {2005}, author = {Pradeep Ram, AS and Boucher, D and Sime-Ngando, T and Debroas, D and Romagoux, JC}, title = {Phage bacteriolysis, protistan bacterivory potential, and bacterial production in a freshwater reservoir: coupling with temperature.}, journal = {Microbial ecology}, volume = {50}, number = {1}, pages = {64-72}, pmid = {16052381}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development ; Bacteriolysis ; Bacteriophages/*pathogenicity ; Biomass ; Chlorophyll/analysis ; Molecular Sequence Data ; Population Dynamics ; Regression Analysis ; Seasons ; Temperature ; *Water Microbiology ; Water Supply ; }, abstract = {Phage abundance and infection of bacterioplankton were studied from March to November 2003 in the Sep Reservoir (Massif Central, France), together with temperature, chlorophyll, bacteria (abundance and production), and heterotrophic nanoflagellates (abundance and potential bacterivory). Virus abundance (VA) ranged from 0.6 to 13 x 10(10) viruses l(-1), exceeding bacterial abundance (BA) approximately sixfold on average. In terms of carbon, viruses corresponded to up to 25% of bacterial biomass. A multiple regression model indicated that BA was the best predictor for VA (R(2) = 0.75). The frequency of infected bacteria (estimated from the percentage of visibly infected cells) varied from 1% to 32% and was best explained by a combination of temperature (R(2) = 0.20) and bacterial production (R(2) = 0.25). Viruses and flagellates contributed about equally to bacterial mortality. Both factors destroyed 55% of bacterial production, with a shift from phage bacteriolysis in early spring to protistan bacterivory in late summer. The vertical differences in most of the biological variables were not significant, contrasting with the seasonal differences (i.e., spring vs. summer-autumn). All biological variables under study were indeed significantly coupled to temperature. We regarded this to be the consequence of the enhanced discharge of the reservoir in 2003 (compared to previous years). This substantially weakened the stability and the thermal inertia of the water column, thereby establishing temperature as a stronger forcing factor in setting the conditions for optimal metabolic activity of microbial communities.}, }
@article {pmid16052380, year = {2005}, author = {Inbar, E and Green, SJ and Hadar, Y and Minz, D}, title = {Competing factors of compost concentration and proximity to root affect the distribution of streptomycetes.}, journal = {Microbial ecology}, volume = {50}, number = {1}, pages = {73-81}, pmid = {16052380}, issn = {0095-3628}, mesh = {Biodegradation, Environmental ; Cucumis sativus/microbiology ; Electrophoresis, Gel, Two-Dimensional ; Fertilizers ; Plant Roots/microbiology ; Polymerase Chain Reaction ; Streptomycetaceae/*growth &amp; development ; }, abstract = {Streptomycetes are important members of soil microbial communities and are particularly active in the degradation of recalcitrant macromolecules and have been implicated in biological control of plant disease. Using a streptomycetes-specific polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (PCR-DGGE) methodology coupled with band excision and sequence analysis, we examined the effect of grape marc compost amendment to soil on cucumber plant-associated streptomycetes community composition. We observed that both compost amendment and proximity to the root surface influenced the streptomycetes community composition. A strong root selection for a soil-derived Streptomycete, most closely related to Streptomyces thermotolerans, S. iakyrus, and S. thermocarboxydus, was independent of compost amendment rate. However, while the impact of compost amendment was mitigated with increasing proximity to the root, high levels of compost amendment resulted in the detection of compost-derived species on the root surface. Conversely, in rhizosphere and non-rhizosphere soils, the community composition of streptomycetes was affected strongly even by modest compost amendment. The application of a streptomycetes-specific PCR primer set combined with DGGE analysis provided a rapid means of examining the distribution and ecology of streptomycetes in soils and plant-associated environments.}, }
@article {pmid16052379, year = {2005}, author = {Rosenstock, B and Zwisler, W and Simon, M}, title = {Bacterial consumption of humic and non-humic low and high molecular weight DOM and the effect of solar irradiation on the turnover of labile DOM in the Southern Ocean.}, journal = {Microbial ecology}, volume = {50}, number = {1}, pages = {90-101}, pmid = {16052379}, issn = {0095-3628}, mesh = {*Bacterial Physiological Phenomena ; Biodegradation, Environmental ; Ecosystem ; Humic Substances/*analysis ; Molecular Weight ; Organic Chemicals/*metabolism ; Seawater ; Solubility ; Sunlight ; *Water Microbiology ; }, abstract = {The decomposition of dissolved organic matter (DOM) in pelagic ecosystems is mediated primarily by heterotrophic bacteria, but transformation by short-wave solar radiation may play an important role in surface waters, in particular when humic substances constitute a substantial fraction of the DOM pool. Most of the studies examining bacterial decomposition and photochemical transformation of DOM stem from limnetic and coastal marine systems and much less information is available from oceanic environments. To examine the bacterial decomposition of humic and non-humic DOM in the Southern Ocean we carried out microcosm experiments in which we measured bacterial growth on isolated fractions of humic and non-humic DOM of the size classes <3 kDa and >3 kDa. Experiments carried out at the Polar Front showed a preferential bacterial growth on non-humic DOM and in particular on the size fraction <3 kDa. Bacterial growth, measured as bacterial biomass production, on non-humic DOM accounted for 74% to 88% of the total growth on all four DOM fractions. In experiments in the Antarctic circumpolar current and the coastal current under pack ice, bacterial growth was 6x lower than at the Polar Front, and humic and non-humic DOM was consumed to equal amounts. The size fraction <3 kDa was always preferred. Experiments examining the effect of solar radiation on the release of dissolved amino acids (DAA) and carbohydrates (DCHO) and their subsequent bacterial utilization showed a stimulating effect on glucose uptake and the release of DAA at the Polar Front but an inhibition in the eastern Weddell Sea. Ultraviolet-B was the most effective component of the solar radiation spectrum tested. Effects of UV-B on glucose uptake and release of DAA were positively correlated with concentrations of humic-bound DAA. The data imply that at low concentrations, e.g., <100 nM (amino acid equivalent), UV-irradiation reduces, whereas at concentrations >100 nM UV-irradiation stimulates glucose uptake and release of DAA as compared to dark conditions.}, }
@article {pmid16052378, year = {2005}, author = {Janus, LR and Angeloni, NL and McCormack, J and Rier, ST and Tuchman, NC and Kelly, JJ}, title = {Elevated atmospheric CO2 alters soil microbial communities associated with trembling aspen (Populus tremuloides) roots.}, journal = {Microbial ecology}, volume = {50}, number = {1}, pages = {102-109}, pmid = {16052378}, issn = {0095-3628}, mesh = {Carbon Dioxide/*pharmacology ; DNA, Bacterial/analysis ; Ecosystem ; Greenhouse Effect ; Plant Roots/*microbiology ; Polymorphism, Restriction Fragment Length ; Population Dynamics ; Populus/*microbiology ; *Soil Microbiology ; }, abstract = {Global atmospheric CO(2) levels are expected to double within the next 50 years. To assess the effects of increased atmospheric CO(2) on soil ecosystems, cloned trembling aspen (Populus tremuloides) seedlings were grown individually in 1 m(3) open bottom root boxes under either elevated (720 ppm, ELEV) or ambient CO(2) (360 ppm, AMB). After 5 years, soil cores (40 cm depth) were collected from the root boxes and divided into 0-20 cm and 20-40 cm fractions. ELEV treatment resulted in significant decreases in both soil nitrate and total soil nitrogen in both the 0-20 cm and 20-40 cm soil fractions, with a 47% decrease in soil nitrate and a 50% decrease in total soil nitrogen occurring in the 0-20 cm fraction. ELEV treatment did not result in a significant change in the amount of soil microbial biomass. However, analysis of indicator phospholipid fatty acids (PLFA) indicated that ELEV treatment did result in significant increases in PLFA indicators for fungi and Gram-negative bacteria in the 0-20 cm fraction. Terminal restriction fragment length polymorphism (T-RFLP) analysis was used to analyze the composition of the soil bacterial communities (using primers targeting the 16SrRNA gene) and the soil fungal communities (using primers targeting the intergenic transcribed spacer region). T-RFLP analysis revealed shifts in both bacterial and fungal community structure, as well as increases in both bacterial and fungal species richness with ELEV treatment. These results indicated that increased atmospheric CO(2) had significant effects on both soil nutrient availability and the community composition of soil microbes associated with aspen roots.}, }
@article {pmid16052377, year = {2005}, author = {Ibelings, BW and Bruning, K and de Jonge, J and Wolfstein, K and Pires, LM and Postma, J and Burger, T}, title = {Distribution of microcystins in a lake foodweb: no evidence for biomagnification.}, journal = {Microbial ecology}, volume = {49}, number = {4}, pages = {487-500}, pmid = {16052377}, issn = {0095-3628}, mesh = {Animals ; Bivalvia/metabolism ; Cyanobacteria/*chemistry ; *Ecosystem ; Environmental Monitoring/*statistics &amp; numerical data ; Fishes/metabolism ; *Food Chain ; Fresh Water ; Liver/metabolism ; Microcystins ; Netherlands ; Peptides, Cyclic/*analysis/pharmacokinetics ; Zooplankton/metabolism ; }, abstract = {Microcystins, toxins produced by cyanobacteria, may play a role in fish kills, although their specific contribution remains unclear. A better understanding of the eco-toxicological effects of microcystins is hampered by a lack of analyses at different trophic levels in lake foodwebs. We present 3 years of monitoring data, and directly compare the transfer of microcystin in the foodweb starting with the uptake of (toxic) cyanobacteria by two different filter feeders: the cladoceran Daphnia galeata and the zebra mussel Dreissena polymorpha. Furthermore foodwebs are compared in years in which the colonial cyanobacterium Microcystis aeruginosa or the filamentous cyanobacterium Planktothrix agardhii dominated; there are implications in terms of the types and amount of microcystins produced and in the ingestion of cyanobacteria. Microcystin concentrations in the seston commonly reached levels where harmful effects on zooplankton are to be expected. Likewise, concentrations in zooplankton reached levels where intoxication of fish is likely. The food chain starting with Dreissena (consumed by roach and diving ducks) remained relatively free from microcystins. Liver damage, typical for exposure to microcystins, was observed in a large fraction of the populations of different fish species, although no relation with the amount of microcystin could be established. Microcystin levels were especially high in the livers of planktivorous fish, mainly smelt. This puts piscivorous birds at risk. We found no evidence for biomagnification of microcystins. Concentrations in filter feeders were always much below those in the seston, and yet vectorial transport to higher trophic levels took place. Concentrations of microcystin in smelt liver exceeded those in the diet of these fish, but it is incorrect to compare levels in a selected organ to those in a whole organism (zooplankton). The discussion focuses on the implications of detoxication and covalent binding of microcystin for the transfer of the toxin in the foodweb. It seems likely that microcystins are one, but not the sole, factor involved in fish kills during blooms of cyanobacteria.}, }
@article {pmid16052376, year = {2005}, author = {de Brouwer, JF and Wolfstein, K and Ruddy, GK and Jones, TE and Stal, LJ}, title = {Biogenic stabilization of intertidal sediments: the importance of extracellular polymeric substances produced by benthic diatoms.}, journal = {Microbial ecology}, volume = {49}, number = {4}, pages = {501-512}, pmid = {16052376}, issn = {0095-3628}, mesh = {Adsorption ; Analysis of Variance ; *Carbohydrate Metabolism ; Carbohydrates/chemistry ; Chlorophyll/analysis ; Chlorophyll A ; Diatoms/*chemistry/metabolism ; Fluorescence ; Geologic Sediments/*analysis/microbiology ; Microscopy, Confocal ; Rheology ; Uronic Acids/analysis ; }, abstract = {The sediment-stabilizing effect of benthic diatoms was investigated in a laboratory setting. Axenic cultures of the benthic diatoms Nitzschia cf. brevissima and Cylindrotheca closterium were inoculated in Petri dishes containing sand and incubated under axenic conditions. By ensuring aseptic routines throughout the experiments, interference from other organisms occurring with diatoms in natural photothrophic biofilms was avoided. This allowed the examination of the role of benthic diatoms in sediment stabilization. Increases in the critical erosion shear stress of the sediment were observed in the presence of both diatom taxa relative to sterile sediment. However, N. cf. brevissima was more effective than C. closterium. Values of critical shear stress in the experimental system were in the same range as those observed in natural biofilms, which indicates that diatoms are important agents for biogenic stabilization. Extracellular carbohydrate contents in the microcosms were similar for both diatom species. However, in the presence of N cf. brevissima, extracellular carbohydrate correlated significantly to critical shear stress, explaining up to 80% of the variation, whereas this was not the case for C. closterium. Therefore, it was concluded that the quantity of extracellular polymeric substances (EPS) alone did not explain the biogenic stabilization. Observed adsorption of EPS to sediment particles depended on the relative amount of uronic acids in the exopolymers. Using fluorescently labeled lectins, confocal laser scanning microscopy showed that EPS secretion by N. cf. brevissima resulted in ordered three-dimensional matrix structures. It is suggested that the structuring of EPS plays an prominent role in the process of biostabilization, and that diatoms such as N. cf. brevissima are actively involved in producing the structure of EPS, whereas others such as C. closterium do not do so to the same extent.}, }
@article {pmid16052375, year = {2005}, author = {Misic, C and Fabiano, M}, title = {Enzymatic activity on sandy beaches of the Ligurian Sea (NW Mediterranean).}, journal = {Microbial ecology}, volume = {49}, number = {4}, pages = {513-522}, pmid = {16052375}, issn = {0095-3628}, mesh = {Acetylglucosaminidase/*metabolism ; Chlorophyll/metabolism ; Chlorophyll A ; Colony Count, Microbial ; Geologic Sediments/*analysis/*microbiology ; Italy ; Leucyl Aminopeptidase/*metabolism ; Mediterranean Sea ; Microscopy, Fluorescence ; *Silicon Dioxide ; alpha-Glucosidases/*metabolism ; beta-Glucosidase/*metabolism ; }, abstract = {Enzymatic activity was measured on two beaches of the Ligurian Sea (NW Mediterranean) during late spring and summer 2003. The detected activities (leucine aminopeptidase, beta-glucosidase, alpha-glucosidase, and beta-N-acetylglucosaminidase) were related to the available organic substrates (proteins and carbohydrates) and to the bacterial community (expressed in terms of abundance, biomass, and frequency of cell division). The very low chlorophyll a concentrations (never higher than 40 ng g(-1)) suggested that heterotrophic microorganisms play a major role in the beach ecosystem. Enzymatic activities devoted to organic matter degradation were lower in the emerged part of the beaches and higher in the sites covered, permanently or temporarily, by seawater, suggesting that sea action enlivens the degradation processes. Leucine aminopeptidase ranged from 0.26 to 13.02 nmol g(-1)h(-1), and beta-glucosidase (the most expressed glycolytic enzyme) from 0.03 to 4.51 nmol g(-1)h(-1). Strong changes in the proteolytic/glycolytic activity ratio were observed, with a sudden rise in glycolysis during summer, leading to ratio values from about 30 down to 1. Thus, beaches were identified as preferential degradation sites, where very refractory compounds such as cellulose may also be efficiently processed.}, }
@article {pmid16052374, year = {2005}, author = {Wright, MS and Covich, AP}, title = {Relative importance of bacteria and fungi in a tropical headwater stream: leaf decomposition and invertebrate feeding preference.}, journal = {Microbial ecology}, volume = {49}, number = {4}, pages = {536-546}, pmid = {16052374}, issn = {0095-3628}, mesh = {Animals ; Bacteria/*metabolism ; Cecropia Plant ; Decapoda/*physiology ; Feeding Behavior/physiology ; *Food Chain ; Fungi/*metabolism ; Plant Leaves/*metabolism/microbiology ; Puerto Rico ; Rivers/*microbiology ; Time Factors ; Tropical Climate ; }, abstract = {Bacteria and fungi provide critical links between leaf detritus and higher trophic levels in forested headwater food webs, but these links in tropical streams are not well understood. We compared the roles of bacteria and fungi in the leaf decomposition process and determining feeding preference for two species of freshwater shrimp found in the Luquillo Experimental Forest, Puerto Rico, using experimental microcosms. We first tested the effects of four treatments on decomposition rates for leaves from two common riparian species, Cecropia scheberiana (Moraceae) and Dacryodes excelsa (Burseraceae), in laboratory microcosms. Treatments were designed to alter the microbial community by minimizing the presence of bacteria or fungi. The fastest decay rate was the control treatment for D. excelsa where both bacteria and fungi were present (k = -0.0073 day(-1)) compared to the next fastest rate of k = -0.0063 day(-1) for the bacterial-conditioned D. excelsa leaves. The fastest decay rate for C. scheberiana was also the control treatment (k = -0.0035 day(-1)), while the next fastest rate was for fungal-conditioned leaves (k = -0.0029 day(-1)). The nonadditive effect for leaf decomposition rates observed in the control treatments where both fungi and bacteria were present indicate that bacteria and fungi perform different functions in processing leaf litter. Additionally, leaf types differed in microbial colonization patterns. We next tested feeding preference for leaf type and microbe treatment in microcosms using two species of freshwater shrimp: Xiphocaris elongata, a shredder, and Atya lanipes, a scraper/filterer. To estimate feeding preferences of individual shrimp, we measured change in leaf surface area and the amount of particles generated during 5-day trials in 16 different two-choice combinations. X. elongata preferred D. excelsa over C. scheberiana, and leaves with microbial conditioning over leaves without conditioning. There was no clear preference for fungal-conditioned leaves over bacterial-conditioned leaves. This lack of preference for which microbes were responsible for the conditioning demonstrates the importance of both bacterial and fungal resources in these tropical stream food web studies.}, }
@article {pmid16052373, year = {2005}, author = {Hillesland, KL and Velicer, GJ}, title = {Resource level affects relative performance of the two motility systems of Myxococcus xanthus.}, journal = {Microbial ecology}, volume = {49}, number = {4}, pages = {558-566}, pmid = {16052373}, issn = {0095-3628}, mesh = {Agar ; Caseins/metabolism ; Cell Surface Extensions/physiology ; Movement/*physiology ; Myxococcus xanthus/metabolism/*physiology ; }, abstract = {The adventurous (A) and social (S) motility systems of the microbial predator Myxococcus xanthus show differential swarming performance on distinct surface types. Under standard laboratory conditions, A-motility performs well on hard agar but poorly on soft agar, whereas the inverse pattern is shown by S-motility. These properties may allow M. xanthus to swarm effectively across a greater diversity of natural surfaces than would be possible with one motility system alone. Nonetheless, the range of ecological conditions under which dual motility enhances effective swarming across distinct surfaces and how ecological parameters affect the complementarity of A-motility and S-motility remain unclear. Here we have examined the role of nutrient concentration in determining swarming patterns driven by dual motility on distinct agar surfaces, as well as the relative contributions of A-motility and S-motility to these patterns. Swarm expansion rates of dually motile (A+S+), solely A-motile (A+S-), and solely S-motile (A-S+) strains were compared on hard and soft agar across a wide range of casitone concentrations. At low casitone concentrations (0-0.1%), swarming on soft agar driven by S-motility is very poor, and is significantly slower than swarming on hard agar driven by A-motility. This reverses at high casitone concentration (1-3.2%) such that swarming on soft agar is much faster than swarming on hard agar. This pattern greatly constrained the ability of M. xanthus to encounter patches of prey bacteria on a soft agar surface when nutrient levels between the patches were low. The swarming patterns of a strain that is unable to produce extracellular fibrils indicate that these appendages are responsible for the elevated swarming of S-motility at high resource levels. Together, these data suggest that large contributions by S-motility to predatory swarming in natural soils may be limited to soft, wet, high-nutrient conditions that may be uncommon. Several likely benefits of S-motility to the M. xanthus life cycle are discussed, including synergistic interactions with A-motility across a wide variety of conditions.}, }
@article {pmid16052372, year = {2005}, author = {Nichols, CM and Lardière, SG and Bowman, JP and Nichols, PD and A E Gibson, J and Guézennec, J}, title = {Chemical characterization of exopolysaccharides from Antarctic marine bacteria.}, journal = {Microbial ecology}, volume = {49}, number = {4}, pages = {578-589}, pmid = {16052372}, issn = {0095-3628}, mesh = {Antarctic Regions ; Bacteroidetes/chemistry/*genetics ; Base Sequence ; Colorimetry ; Fatty Acids/analysis ; Gammaproteobacteria/chemistry/*genetics ; Gas Chromatography-Mass Spectrometry ; Ice Cover/*microbiology ; Molecular Sequence Data ; Monosaccharides/analysis ; Polysaccharides, Bacterial/*analysis ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; Spectroscopy, Fourier Transform Infrared ; Uronic Acids/analysis ; }, abstract = {Exopolysaccharides (EPS) may have an important role in the Antarctic marine environment, possibly acting as ligands for trace metal nutrients such as iron or providing cryoprotection for growth at low temperature and high salinity. Ten bacterial strains, isolated from Southern Ocean particulate material or from sea ice, were characterized. Whole cell fatty acid profiles and 16S rRNA gene sequences showed that the isolates included representatives of the genera Pseudoalteromonas, Shewanella, Polaribacter, and Flavobacterium as well as one strain, which constituted a new bacterial genus in the family Flavobacteriaceae. The isolates are, therefore, members of the "Gammaproteobacteria" and Cytophaga-Flexibacter-Bacteroides, the taxonomic groups that have been shown to dominate polar sea ice and seawater microbial communities. Exopolysaccharides produced by Antarctic isolates were characterized. Chemical composition and molecular weight data revealed that these EPS were very diverse, even among six closely related Pseudoalteromonas isolates. Most of the EPS contained charged uronic acid residues; several also contained sulfate groups. Some strain produced unusually large polymers (molecular weight up to 5.7 MDa) including one strain in which EPS synthesis is stimulated by low temperature. This study represents a first step in the understanding of the role of bacterial EPS in the Antarctic marine environment.}, }
@article {pmid16047099, year = {2005}, author = {Huguet, V and Land, EO and Casanova, JG and Zimpfer, JF and Fernandez, MP}, title = {Genetic diversity of Frankia microsymbionts from the relict species Myrica faya (Ait.) and Myrica rivas-martinezii (S.) in Canary Islands and Hawaii.}, journal = {Microbial ecology}, volume = {49}, number = {4}, pages = {617-625}, pmid = {16047099}, issn = {0095-3628}, mesh = {Atlantic Islands ; Cluster Analysis ; DNA Primers ; DNA, Ribosomal Spacer/genetics ; Frankia/*genetics ; *Genetic Variation ; Hawaii ; Myrica/*microbiology ; Plant Roots/*microbiology ; Polymorphism, Restriction Fragment Length ; Species Specificity ; }, abstract = {In the Western Canary Islands, Myrica faya and Myrica rivas-martinezii (Myricaceae) are phylogenetically close, endemic, actinorhizal species presumed to be remnants either of the European or the African Tertiary floras. Unisolated Frankia strains from field-collected nodules on Tenerife, Gomera, and La Palma Islands were compared by their rrs gene and 16S-23S intergenic spacer (IGS) restriction patterns. To compare the genetic diversity of Frankia strains from within and outside the host's native range, nodules of M. faya field plants were collected both in Canary Islands and in Hawaii, where this species is an exotic invasive. Myrica rivas-martinezii, endemic to the Canary Islands, was sparsely nodulated in the field. Frankia strains harbored in field-collected nodules of M. faya and M. rivas-martinezii belonged to the Elaeagnaceae strains' genetic cluster and exhibited a high degree of diversity. Frankia genotypes were specific to each host species. In the Canary archipelago, we found no relationship between site of collection and Frankia genotype for M. faya. The only exceptions were strains from site 2 in Tenerife, a location with a geological history different from the other sites sampled. Hawaiian and Canarian M. faya strains had no genotypes in common, raising questions concerning the origin of M. faya-infective Frankia in Hawaii. Nodular strains of M. rivas-martinezii from nursery plants were genetically characterized and shown to be divergent from the strains of field-collected nodules and belong to the Alnus-Casuarina strains cluster. This suggests Myrica may have the potential to nodulate with a broader range of Frankia genotypes under artificial conditions than has been detected in field-collected nodules.}, }
@article {pmid16047098, year = {2005}, author = {Barriuso, J and Pereyra, MT and Lucas García, JA and Megías, M and Gutierrez Mañero, FJ and Ramos, B}, title = {Screening for putative PGPR to improve establishment of the symbiosis Lactarius deliciosus-Pinus sp.}, journal = {Microbial ecology}, volume = {50}, number = {1}, pages = {82-89}, pmid = {16047098}, issn = {0095-3628}, mesh = {Classification ; DNA, Bacterial/analysis ; Pinus/*microbiology ; Plant Roots/growth &amp; development/microbiology ; Polymerase Chain Reaction ; Random Amplified Polymorphic DNA Technique ; Rhizobiaceae/genetics/*growth &amp; development/*physiology ; Symbiosis/*physiology ; }, abstract = {A screening for plant growth promoting rhizobacteria (PGPR) was carried out in the mycorrhizosphere of wild populations of Pinus pinea and P. pinaster, and in the mycosphere of associated Lactarius deliciosus. A total of 720 bacteria were isolated, purified, and grouped by morphological criteria. Fifty percent of the isolates were selected and tested for aminocyclopropanecarboxylic acid (ACC) degradation, auxin and siderophore production, and phosphate solubilization. Thirty eight percent of the isolates showed at least one of the evaluated activities. Nutrient-related traits were associated with P. pinaster, whereas hormone production traits predominated in P. pinea. These activities were found mostly in Gram positive isolates. After PCR-RAPDs (random amplified polymorphic DNA) analysis, 10 groups appeared with 85% similiarity when considering all isolates, indicating the low diversity in the system. One strain of each group was identified by 16S rDNA sequencing. Our results suggest that P. pinaster selects for mycorrhizosphere bacteria that mobilize nutrients, whereas P. pinea selects for bacteria that have the capacity to increase root growth via production of plant growth regulators.}, }
@article {pmid16047097, year = {2005}, author = {Franke-Whittle, IH and O'Shea, MG and Leonard, GJ and Sly, LI}, title = {Design, development, and use of molecular primers and probes for the detection of Gluconacetobacter species in the pink sugarcane mealybug.}, journal = {Microbial ecology}, volume = {50}, number = {1}, pages = {128-139}, pmid = {16047097}, issn = {0095-3628}, mesh = {Animals ; Classification ; DNA Primers ; DNA, Bacterial/analysis ; Gluconacetobacter/classification/*genetics/*isolation &amp; purification ; In Situ Hybridization, Fluorescence ; Insecta/*microbiology ; Larva ; Molecular Probes ; New South Wales ; Polymerase Chain Reaction ; Population Dynamics ; Saccharum ; }, abstract = {Molecular tools for the species-specific detection of Gluconacetobacter sacchari, Gluconacetobacter diazotrophicus, and Gluconacetobacter liquefaciens from the pink sugarcane mealybug (PSMB) Saccharicoccus sacchari Cockerell (Homiptera: Pseudococcidae) were developed and used in polymerase chain reactions (PCR) and in fluorescence in situ hybridizations (FISH) to better understand the microbial diversity and the numerical significance of the acetic acid bacteria in the PSMB microenvironment. The presence of these species in the PSMB occurred over a wide range of sites, but not in all sites in sugarcane-growing areas of Queensland, Australia, and was variable over time. Molecular probes for use in FISH were also designed for the three acetic acid bacterial species, and shown to be specific only for the target species. Use of these probes in FISH of "squashed" whole mealybugs indicated that these acetic acid bacteria species represent only a small proportion of the microbial population of the PSMB. Despite the detection of Glac. sacchari, Glac. diazotrophicus, and Glac. liquefaciens by PCR from different mealybugs isolated at various times and from various sugarcane-growing areas in Queensland, Australia, these bacteria do not appear to be significant commensals in the PSMB environment.}, }
@article {pmid16047096, year = {2005}, author = {Amachi, S and Muramatsu, Y and Akiyama, Y and Miyazaki, K and Yoshiki, S and Hanada, S and Kamagata, Y and Ban-nai, T and Shinoyama, H and Fujii, T}, title = {Isolation of iodide-oxidizing bacteria from iodide-rich natural gas brines and seawaters.}, journal = {Microbial ecology}, volume = {49}, number = {4}, pages = {547-557}, pmid = {16047096}, issn = {0095-3628}, mesh = {Alphaproteobacteria/*genetics/*metabolism ; Base Sequence ; Cluster Analysis ; DNA Primers ; Fossil Fuels/*microbiology ; Gas Chromatography-Mass Spectrometry ; Iodides/analysis/*metabolism ; Japan ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/analysis/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Iodide-oxidizing bacteria (IOB), which oxidize iodide (I-) to molecular iodine (I2), were isolated from iodide-rich (63 microM to 1.2 mM) natural gas brine waters collected from several locations. Agar media containing iodide and starch were prepared, and brine waters were spread directly on the media. The IOB, which appeared as purple colonies, were obtained from 28 of the 44 brine waters. The population sizes of IOB in the brines were 10(2) to 10(5) colony-forming units (CFU) mL(-1). However, IOB were not detected in natural seawaters and terrestrial soils (fewer than 10 CFU mL(-1) and 10(2) CFU g wet weight of soils(-1), respectively). Interestingly, after the enrichment with 1 mM iodide, IOB were found in 6 of the 8 seawaters with population sizes of 10(3) to 10(5) CFU mL(-1). 16S rDNA sequencing and phylogenetic analyses showed that the IOB strains are divided into two groups within the alpha-subclass of the Proteobacteria. One of the groups was phylogenetically most closely related to Roseovarius tolerans with sequence similarities between 94% and 98%. The other group was most closely related to Rhodothalassium salexigens, although the sequence similarities were relatively low (89% to 91%). The iodide-oxidizing reaction by IOB was mediated by an extracellular enzyme protein that requires oxygen. Radiotracer experiments showed that IOB produce not only I2 but also volatile organic iodine, which were identified as diiodomethane (CH2I2) and chloroiodomethane (CH2ClI). These results indicate that at least two types of IOB are distributed in the environment, and that they are preferentially isolated in environments in which iodide levels are very high. It is possible that IOB oxidize iodide in the natural environment, and they could significantly contribute to the biogeochemical cycling of iodine.}, }
@article {pmid16047095, year = {2005}, author = {Koschorreck, M}, title = {Nitrogen turnover in drying sediments of an Amazon floodplain lake.}, journal = {Microbial ecology}, volume = {49}, number = {4}, pages = {567-577}, pmid = {16047095}, issn = {0095-3628}, mesh = {Bacteria/*metabolism ; Brazil ; Carbon Dioxide/metabolism ; Chromatography, Gas ; Colony Count, Microbial ; Fresh Water ; Geologic Sediments/*analysis/*microbiology ; Nitrates/analysis ; Nitrogen/analysis/*metabolism ; Nitrous Oxide/analysis ; Quaternary Ammonium Compounds/analysis ; }, abstract = {In the Amazon floodplain large areas are subject to annual cycles of drying and rewetting. The turnover of nitrogen in the periodically drying sediments is an important regulator of floodplain fertility. In the present study the transition of a lake sediment from flooded to dry conditions was studied with respect to microbial nitrogen turnover. Soil nitrogen pools, as well as the activity and abundance of denitrifying and nitrifying bacteria, were investigated during one dry season. During the first weeks after drying, most of the inorganic nitrogen vanished from the sediment. The process was inhibited by a nitrification inhibitor, showing that coupled nitrification-denitrification was responsible for the nitrogen loss. Assimilation by plants or microbes, as well as leaching, were not important mechanisms of nitrogen loss. During a period of only 10 days, 59% of the total denitrification and 94% of the total N2O emission during the dry period occurred. Cell numbers of denitrifiers were not correlated with activities. Denitrification was not correlated with other sediment variables but was regulated by the patchy distribution of reduced and oxidized zones in the uppermost centimeters of the sediment. This heterogeneity was probably introduced by the bioturbation of small insects, which was restricted to a rather short time period shortly after drying.}, }
@article {pmid16042012, year = {2005}, author = {Le Quéré, A and Wright, DP and Söderström, B and Tunlid, A and Johansson, T}, title = {Global patterns of gene regulation associated with the development of ectomycorrhiza between birch (Betula pendula Roth.) and Paxillus involutus (Batsch) Fr.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {18}, number = {7}, pages = {659-673}, doi = {10.1094/MPMI-18-0659}, pmid = {16042012}, issn = {0894-0282}, mesh = {Base Sequence ; Basidiomycota/*genetics/*growth &amp; development/metabolism ; Betula/*genetics/growth &amp; development/metabolism/*microbiology ; Carbon/metabolism ; DNA, Fungal/genetics ; DNA, Plant/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Gene Expression Regulation, Plant ; Genes, Fungal ; Genes, Plant ; Mycorrhizae/*genetics/*growth &amp; development/metabolism ; Oligonucleotide Array Sequence Analysis ; Symbiosis ; Water/metabolism ; }, abstract = {The formation of ectomycorrhizal (ECM) root tissue is characterized by distinct morphological and developmental stages, such as preinfection and adhesion, mantle, and Hartig net formation. The global pattern of gene expression during these stages in the birch (Betula pendula)-Paxillus involutus ECM association was analyzed using cDNA microarrays. In comparison with nonsymbiotic conditions, 251 fungal (from a total of 1,075) and 138 plant (1,074 in total) genes were found to be differentially regulated during the ECM development. For instance, during mantle and Hartig net development, there were several plant genes upregulated that are normally involved in defense responses during pathogenic fungal challenges. These responses were, at later stages of ECM development, found to be repressed. Other birch genes that showed differential regulation involved several homologs that usually are implicated in water permeability (aquaporins) and water stress tolerance (dehydrins). Among fungal genes differentially upregulated during stages of mantle and Hartig net formation were homologs putatively involved in mitochondrial respiration. In fully developed ECM tissue, there was an upregulation of fungal genes related to protein synthesis and the cytoskeleton assembly machinery. This study highlights complex molecular interactions between two symbionts during the development of an ECM association.}, }
@article {pmid16041474, year = {2005}, author = {Moran, D and Turner, SJ and Clements, KD}, title = {Ontogenetic development of the gastrointestinal microbiota in the marine herbivorous fish Kyphosus sydneyanus.}, journal = {Microbial ecology}, volume = {49}, number = {4}, pages = {590-597}, pmid = {16041474}, issn = {0095-3628}, mesh = {Age Factors ; *Animal Nutritional Physiological Phenomena ; Animals ; Base Sequence ; Body Size ; Chromatography, Gas ; Clostridium/*genetics ; Cluster Analysis ; DNA Primers ; Fatty Acids/analysis ; Gastrointestinal Tract/*microbiology ; Molecular Sequence Data ; New Zealand ; Perciformes/*microbiology ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Molecular techniques were used to investigate the composition and ontogenetic development of the intestinal bacterial community in the marine herbivorous fish Kyphosus sydneyanus from the north eastern coast of New Zealand. Previous work showed that K. sydneyanus maintains an exclusively algivorous diet throughout post-settlement life and passes through an ontogenetic diet shift from a juvenile diet which is readily digestible to an adult diet high in refractory algal metabolites. Terminal restriction fragment length polymorphism (T-RFLP) analysis was used to investigate the relationship between bacterial community structure and fish size. Bacterial diversity was higher in posterior gut sections than anterior gut sections, and in larger fish than in smaller fish. Partial sequencing of bacterial 16S rDNA genes PCR amplified and cloned from intestine content samples was used to identify the phylogenetic affiliation of dominant gastrointestinal bacteria. Phylogenetic analysis of clones showed that most formed a clade within the genus Clostridium, with one clone associated with the parasitic mycoplasmas. No bacteria were specific to a particular intestinal section or size class of host, though some appeared more dominant than others and were established in smaller fishes. Clones closely related to C. lituseburense were particularly dominant in most intestine content samples. All bacteria identified in the intestinal samples were phylogenetically related to those possessing fermentative type metabolism. Short-chain fatty acids in intestinal fluid samples increased from 15.6 +/- 2.1 mM in fish <100 mm to 51.6 +/- 5.5 mM in fish >300 mm. The findings of this study support the hypothesis that the ontogenetic diet shift of K. sydneyanus is accompanied by an increase in the diversity of intestinal microbial symbionts capable of degrading refractory algal metabolites into short-chain fatty acids, which can then be assimilated by the host.}, }
@article {pmid16033867, year = {2005}, author = {Ley, RE and Bäckhed, F and Turnbaugh, P and Lozupone, CA and Knight, RD and Gordon, JI}, title = {Obesity alters gut microbial ecology.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {31}, pages = {11070-11075}, pmid = {16033867}, issn = {0027-8424}, support = {T32 DK007130/DK/NIDDK NIH HHS/United States ; DK 070977/DK/NIDDK NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; DK 007130/DK/NIDDK NIH HHS/United States ; R01 DK070977/DK/NIDDK NIH HHS/United States ; T32 GM008759/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Base Sequence ; Cyanobacteria/classification/genetics/isolation &amp; purification ; DNA/genetics ; Ecosystem ; Female ; Genes, Bacterial ; Humans ; Intestines/*microbiology ; Mice ; Mice, Inbred C57BL ; Mice, Obese ; Molecular Sequence Data ; Obesity/etiology/*microbiology ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {We have analyzed 5,088 bacterial 16S rRNA gene sequences from the distal intestinal (cecal) microbiota of genetically obese ob/ob mice, lean ob/+ and wild-type siblings, and their ob/+ mothers, all fed the same polysaccharide-rich diet. Although the majority of mouse gut species are unique, the mouse and human microbiota(s) are similar at the division (superkingdom) level, with Firmicutes and Bacteroidetes dominating. Microbial-community composition is inherited from mothers. However, compared with lean mice and regardless of kinship, ob/ob animals have a 50% reduction in the abundance of Bacteroidetes and a proportional increase in Firmicutes. These changes, which are division-wide, indicate that, in this model, obesity affects the diversity of the gut microbiota and suggest that intentional manipulation of community structure may be useful for regulating energy balance in obese individuals. The sequences reported in this paper have been deposited in the GenBank database [accession nos. DQ 014552--DQ 015671 (mothers) and AY 989911--AY 993908 (offspring)].}, }
@article {pmid16033523, year = {2005}, author = {Keith, JE and Boyer, JG and de los Reyes, FL}, title = {Changes in the rRNA levels of specific microbial groups in activated sludge during sample handling and storage.}, journal = {Letters in applied microbiology}, volume = {41}, number = {2}, pages = {208-215}, doi = {10.1111/j.1472-765X.2005.01745.x}, pmid = {16033523}, issn = {0266-8254}, mesh = {Actinobacteria/isolation &amp; purification ; *Environmental Microbiology ; Flavobacterium/isolation &amp; purification ; Nucleic Acid Hybridization ; Preservation, Biological ; Proteobacteria/isolation &amp; purification ; RNA, Bacterial/*analysis ; RNA, Fungal/*analysis ; RNA, Ribosomal/*analysis ; Sewage/*microbiology ; Time Factors ; }, abstract = {AIMS: To quantitatively analyse the changes in group-specific rRNA levels in activated sludge as a function of sample handling and storage procedure.<br><br>METHODS AND RESULTS: Quantitative membrane hybridizations with (32)P-labelled oligonucleotide probes were used to analyse the effects of different sample handling and storage conditions on the relative rRNA levels of the alpha, beta, and gamma-Proteobacteria, the Cytophaga-Flavobacteria group, and the mycolic acid-containing actinomycetes in activated sludge. Group-specific rRNA levels, expressed as percentages of total 16S rRNA detected with a universal probe, in samples maintained at room temperature significantly changed after 48 h. Group-specific rRNA levels in samples treated with chloramphenicol showed significant change after 72 h.<br><br>CONCLUSIONS: Sample storage at room temperature is a viable option if freezing or analysis can be performed within 24 h, while treatment with chlorampenicol can extend that time to at least 48 h.<br><br>Handling, shipping, and storage of environmental samples under several conditions may result in inaccurate determination of the microbial populations in microbial ecology studies.}, }
@article {pmid16022560, year = {2005}, author = {Qiu, X and Tiedje, JM and Sundin, GW}, title = {Genome-wide examination of the natural solar radiation response in Shewanella oneidensis MR-1.}, journal = {Photochemistry and photobiology}, volume = {81}, number = {6}, pages = {1559-1568}, doi = {10.1562/2005-04-15-RA-490}, pmid = {16022560}, issn = {0031-8655}, mesh = {Down-Regulation ; Gene Expression Regulation, Bacterial/*radiation effects ; Genome/*radiation effects ; Reverse Transcriptase Polymerase Chain Reaction ; Shewanella/*genetics/*radiation effects ; *Ultraviolet Rays ; Up-Regulation ; }, abstract = {We previously reported that Shewanella oneidensis MR-1 is extremely sensitive to natural solar radiation (NSR). Here we analyzed the global transcriptional profile of MR-1 during a 1-h recovering period after exposure to ambient solar light at a dose that yields about 20% survival rate on a Luria-Bertani (LB) plate. We observed the induction of DNA damage-repair genes, the SOS response as well as detoxification strategies that we previously observed in MR-1 following artificial UV-A irradiation. Few prophage-related genes were induced by natural solar UV radiation, however, in contrast to what was observed following artificial UV-B irradiation. Overall, the cellular response to NSR in MR-1 was more similar to that of UV-A than that of UV-B, but additional genes involved in detoxification were induced compared with induction by either UV-B or UV-A or their sum. Thus, oxidative stress appeared to contribute greatly to the NSR-induced cytotoxic effects in MR-1. A total of 29.1% of genome showed differential expression following NSR exposure, which is much greater than following exposure by UV-B (4.0%), UV-A (8.2%) or their sum (10.7%). Our data suggest that NSR may impact biological processes in a much more complex manner than previously thought.}, }
@article {pmid16021479, year = {2005}, author = {Hagerberg, D and Pallon, J and Wallander, H}, title = {The elemental content in the mycelium of the ectomycorrhizal fungus Piloderma sp. during the colonization of hardened wood ash.}, journal = {Mycorrhiza}, volume = {15}, number = {6}, pages = {387-392}, pmid = {16021479}, issn = {0940-6360}, mesh = {Basidiomycota/*chemistry/growth &amp; development ; Calcium/analysis ; Lead/analysis ; Mycelium/*chemistry/growth &amp; development ; Phosphorus/analysis ; Picea/microbiology ; Potassium/analysis ; Spectrometry, X-Ray Emission ; Wood/*microbiology ; }, abstract = {Piloderma sp., a wood ash-colonizing ectomycorrhizal (EM) fungus, was grown symbiotically with Norway spruce in microcosms which contained granules of hardened wood ash. Mycelium close to the granules was sampled 3 times over a period of 11 weeks and the elemental content was investigated with particle induced X-ray emission. Mycelium from microcosms without wood ash was used as controls. The contents of P and K were similar in mycelium growing close to wood ash granules to those in control mycelium, while the Ca content increased from 23+/-21 mg g(-1) in controls to 63+/-8 mg g(-1) in mycelium growing close to wood ash granules. The Ca content was also increased in other parts of the mycelium more distant from the wood ash. Piloderma sp. may have a role in the short-term storage of Ca released from wood ash, rather than in releasing and storing P.}, }
@article {pmid16014485, year = {2005}, author = {Everett, KDE and Thao, M and Horn, M and Dyszynski, GE and Baumann, P}, title = {Novel chlamydiae in whiteflies and scale insects: endosymbionts 'Candidatus Fritschea bemisiae' strain Falk and 'Candidatus Fritschea eriococci' strain Elm.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {55}, number = {Pt 4}, pages = {1581-1587}, doi = {10.1099/ijs.0.63454-0}, pmid = {16014485}, issn = {1466-5026}, mesh = {Animals ; Base Composition ; Chlamydiales/*classification/*genetics/isolation &amp; purification ; Hemiptera/*microbiology ; Microscopy, Electron ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; rRNA Operon ; }, abstract = {Bacteria called 'Fritschea' are endosymbionts of the plant-feeding whitefly Bemisia tabaci and scale insect Eriococcus spurius. In the gut of B. tabaci, these bacteria live within bacteriocyte cells that are transmitted directly from the parent to oocytes. Whiteflies cause serious economic damage to many agricultural crops; B. tabaci fecundity and host range are less than those of Bemisia argentifolii, possibly due to the presence of this endosymbiont. The B. tabaci endosymbiont has been characterized using electron microscopy and DNA analysis but has not been isolated or propagated outside of insects. The present study compared sequences for 11 endosymbiont genes to genomic data for chlamydial families Parachlamydiaceae, Chlamydiaceae and Simkaniaceae and to 16S rRNA gene signature sequences from 330 chlamydiae. We concluded that it was appropriate to propose 'Candidatus Fritschea bemisiae' strain Falk and 'Candidatus Fritschea eriococci' strain Elm as members of the family Simkaniaceae in the Chlamydiales.}, }
@article {pmid16014294, year = {2005}, author = {Vadasz, P and Vadasz, AS}, title = {Predictive modeling of microorganisms: LAG and LIP in monotonic growth.}, journal = {International journal of food microbiology}, volume = {102}, number = {3}, pages = {257-275}, doi = {10.1016/j.ijfoodmicro.2004.12.018}, pmid = {16014294}, issn = {0168-1605}, mesh = {Bacteria/*growth &amp; development ; Colony Count, Microbial ; *Food Microbiology ; Kinetics ; *Models, Biological ; Predictive Value of Tests ; }, abstract = {The variety of models that are currently being used in "Predictive Microbiology" or "Microbial Ecology" aiming at reproducing the growth curve of microorganisms motivates this study. It is widely agreed that no model can reproduce generically and consistently the "LAG Phase" of microorganism growth. To promote the objective of "predictive modeling", we present here a model that was derived from first biological and physical principles, which is shown to reproduce qualitatively as well as quantitatively all typical features captured experimentally in microorganism growth. In particular, this paper focuses on capturing and controlling of the "LAG Phase" a typical phase in microorganisms growth, at the initial growth stages, as well as the inflection point on the "ln curve" of the cell concentration, i.e. a Logarithmic Inflection Point referred here as "LIP". The proposed model also captures the Logistic Growth curve as a special case. Comparison of the solutions obtained from the proposed model with experimental data confirms its quantitative validity, as well as its ability to recover a wide range of qualitative features captured in experiments.}, }
@article {pmid16013217, year = {2002}, author = {Papapanou, PN}, title = {Population studies of microbial ecology in periodontal health and disease.}, journal = {Annals of periodontology}, volume = {7}, number = {1}, pages = {54-61}, doi = {10.1902/annals.2002.7.1.54}, pmid = {16013217}, issn = {1553-0841}, mesh = {Asia/epidemiology ; Bacterial Typing Techniques ; Carrier State ; Case-Control Studies ; Clone Cells ; Ecosystem ; Genetic Variation ; Humans ; Odds Ratio ; Opportunistic Infections/epidemiology/microbiology ; Pacific Islands/epidemiology ; Periodontal Diseases/epidemiology/ethnology/*microbiology ; Periodontitis/epidemiology/ethnology/microbiology ; Periodontium/*microbiology ; Prevalence ; United States/epidemiology ; Virulence ; }, abstract = {It has been established that the bacterial diversity in any given environment is severely underestimated when assessed by means of culture-based techniques. Yet, almost all currently available knowledge related to the periodontal microbiota in health and disease has been generated either by culture-based surveys or by methods that require prior species identification by culture. A handful of recent studies using culture-independent molecular methods providing 16S rRNA sequences for both cultivable and not yet cultivated species of human periodontal bacteria demonstrated a high bacterial diversity in the oral cavity. It has been estimated that approximately 500 species may colonize the human oral cavity, half of which have been cultivated to date. A review of the available epidemiological data on the prevalence of certain periodontal microbiota on a population level reveals considerable variation in estimates with respect to 1) sampling strategy, 2) mode of bacterial identification, and 3) race/ethnicity of the studied population. Nevertheless, specific bacterial profiles appear to confer high odds ratios for pathological periodontal conditions and/or progressive periodontal disease. However, the currently recognized periodontal pathogens are commonly recovered from periodontally healthy children, and their carrier rate in adults is substantial. Virulent clones, such as a highly leukotoxic strain of Actinobacillus actinomycetemcomitans, have been found to be closely associated with aggressive forms of periodontitis. In conclusion, while the majority of the periodontal microbiota are commensals, a subset of likely opportunistic pathogens fulfills the epidemiologic requirements needed in order to be ascribed as risk/causative factors. Given the large proportion of the periodontal microbial habitat that is currently insufficiently explored, and assuming that the hitherto uncultivated segment of the bacterial community will include similar levels of pathogenic species, the list of periodontal pathogens should be expected to expand.}, }
@article {pmid16011761, year = {2005}, author = {Defoirdt, T and Bossier, P and Sorgeloos, P and Verstraete, W}, title = {The impact of mutations in the quorum sensing systems of Aeromonas hydrophila, Vibrio anguillarum and Vibrio harveyi on their virulence towards gnotobiotically cultured Artemia franciscana.}, journal = {Environmental microbiology}, volume = {7}, number = {8}, pages = {1239-1247}, doi = {10.1111/j.1462-2920.2005.00807.x}, pmid = {16011761}, issn = {1462-2912}, mesh = {Aeromonas hydrophila/genetics/growth &amp; development/*pathogenicity ; Animals ; Aquaculture ; Artemia/growth &amp; development/*microbiology ; Bacterial Proteins/genetics/metabolism ; Carbon-Sulfur Lyases ; *Germ-Free Life ; Homoserine/analogs &amp; derivatives/genetics/metabolism ; Lactones/metabolism ; *Mutation ; *Signal Transduction ; Vibrio/classification/genetics/growth &amp; development/*pathogenicity ; Virulence ; }, abstract = {Disruption of quorum sensing, bacterial cell-to-cell communication by means of small signal molecules, has been suggested as a new anti-infective strategy for aquaculture. However, data about the impact of quorum sensing on the virulence of aquatic pathogens are scarce. In this study, a model system using gnotobiotically cultured Artemia franciscana was developed in order to determine the impact of mutations in the quorum sensing systems of Aeromonas hydrophila, Vibrio anguillarum and V. harveyi on their virulence. Mutations in the autoinducer 2 (AI-2) synthase gene luxS, the AI-2 receptor gene luxP or the response regulator gene luxO of the dual channel quorum sensing system of V. harveyi abolished virulence of the strain towards Artemia. Moreover, the addition of an exogenous source of AI-2 could restore the virulence of an AI-2 non-producing mutant. In contrast, none of the mutations in either the acylated homoserine lactone (AHL)-mediated component of the V. harveyi system or the quorum sensing systems of Ae. hydrophila and V. anguillarum had an impact on virulence of these bacteria towards Artemia. Our results indicate that disruption of quorum sensing could be a good alternative strategy to combat infections caused by V. harveyi.}, }
@article {pmid16003481, year = {2005}, author = {Leys, NM and Ryngaert, A and Bastiaens, L and Top, EM and Verstraete, W and Springael, D}, title = {Culture independent detection of Sphingomonas sp. EPA 505 related strains in soils contaminated with polycyclic aromatic hydrocarbons (PAHs).}, journal = {Microbial ecology}, volume = {49}, number = {3}, pages = {443-450}, pmid = {16003481}, issn = {0095-3628}, mesh = {Biodegradation, Environmental ; DNA Primers ; Environmental Monitoring ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Polymerase Chain Reaction ; Population Dynamics ; RNA, Ribosomal, 16S/*analysis ; Soil Microbiology ; Soil Pollutants/*metabolism ; Sphingomonas/*genetics/*physiology ; }, abstract = {The Sphingomonas genus hosts many interesting pollutant-degrading strains. Sphingomonas sp. EPA505 is the best studied polycyclic aromatic hydrocarbon (PAH)-degrading Sphingomonas strain. Based on 16S rRNA gene sequence analysis, Sphingomonas sp. strain EPA505 forms a separate branch in the Sphingomonas phylogenetic tree grouping exclusively PAH-degrading isolates. For specific PCR detection and monitoring of Sphingomonas sp. EPA505 and related strains in PAH-contaminated soils, a new 16S rRNA gene-based primer set was designed. The new primer set was shown to be highly selective for Sphingomonas sp. strain EPA505 as it only amplified DNA from strain EPA505 and not from other tested Sphingomonas strains or soil bacteria not belonging to the Sphingomonas genus. Using DNA extracts of a variety of inoculated PAH-contaminated soils, the primer pair was able to detect EPA505 in concentrations as low as 10(2) cells per gram of soil. Applying the new primer set, 16S rRNA gene fragments which were 99-100% similar to the corresponding gene of strain EPA505 were amplified from four of five PAH-contaminated soils. On the other hand, no PCR products were obtained from any of five tested uncontaminated soils. The preferential presence of EPA505 related Sphingomonas strains in PAH-contaminated soils with very different contamination profiles and different origin suggests an important role of this type of Sphingomonas in the natural Sphingomonas community colonizing PAH-contaminated sites.}, }
@article {pmid16003480, year = {2005}, author = {McCluskey, C and Quinn, JP and McGrath, JW}, title = {An evaluation of three new-generation tetrazolium salts for the measurement of respiratory activity in activated sludge microorganisms.}, journal = {Microbial ecology}, volume = {49}, number = {3}, pages = {379-387}, pmid = {16003480}, issn = {0095-3628}, mesh = {*Bacterial Physiological Phenomena ; Biomass ; Environmental Monitoring/methods ; *Indicators and Reagents ; Oxygen/*metabolism ; Sewage/*microbiology ; *Tetrazolium Salts ; Waste Disposal, Fluid ; }, abstract = {XTT (3'-[1-[(phenylamino)-carbonyl]-3,4-tetrazolium]-bis(4-methoxy-6-nitro)benzenesulfonic acid hydrate), MTS (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium, inner salt), and WST-1 (4-(3-4-iodophenyl)-2-(4-nitrophenyl)-2H-5-tetrazolio)-1,3-benzenedisulfonate) are tetrazolium salts that have become commercially available only in relatively recent years; they differ from earlier such compounds in that their reduction gives rise to a formazan product that is water soluble. We have established the sites in the prokaryotic respiratory chain at which each of the dyes is reduced to its corresponding formazan and have evaluated the suitability of each for the colorimetric estimation of electron transport system activity in populations of activated sludge microorganisms. Reduction of all three tetrazolium salts was shown to be proportional to cell biomass and oxygen uptake and to be susceptible to low levels of the reference toxicant 3,5-dichlorophenol. XTT, which was not inhibitory at concentrations of up to 2 mM and was reduced by 91% of isolates from a sample of culturable activated sludge bacteria, was chosen for further assay development. XTT-formazan production was found to be stimulated by the availability of an exogenous carbon and energy source, and by the presence of the electron-coupling agent phenazine methosulfate. Less than 3% of XTT reduction by an activated sludge sample was abiotic. An assay based on this compound could be a valuable and simple tool for the routine monitoring of the performance of wastewater treatment systems.}, }
@article {pmid16003479, year = {2005}, author = {Heilmann-Clausen, J and Boddy, L}, title = {Inhibition and stimulation effects in communities of wood decay fungi: exudates from colonized wood influence growth by other species.}, journal = {Microbial ecology}, volume = {49}, number = {3}, pages = {399-406}, pmid = {16003479}, issn = {0095-3628}, mesh = {Ecology ; Fagus ; Fungi/*chemistry/*growth &amp; development ; Population Dynamics ; *Wood ; }, abstract = {The effects of exudates from uncolonized and from partly decayed beech wood on the extension rates of 16 later stage decay fungi were investigated. The partly decayed wood had been colonized by the pyrenomycete Eutypa spinosa, or the basidiomycetes Fomes fomentarius, Stereum hirsutum, and Trametes versicolor, all known as common early decay agents in European beech forests. Sterilized wood pieces were placed onto 0.5% malt agar, opposite to small agar plugs containing the test fungi. The latter showed very variable and species-specific growth responses to the various wood types. The presence of uncolonized wood stimulated extension rates in many species, whereas the four previously decayed wood types had variable stimulatory or inhibitory effects. Wood decayed by S. hirsutum resulted in reduced extension rate, delayed growth, or total inhibition in the majority of species, thus it is suggested that this species uses secondary metabolites in a defensive strategy. A single species was, however, stimulated in the presence of S. hirsutum-decayed wood. In contrast, the presence of wood decayed by F. fomentarius was stimulatory to 45% of the species. The other previously decayed wood types generally resulted in more variable responses, depending upon species. The results are discussed in an ecological context and it is suggested that the exudates from the partly decayed wood that are responsible for the reported effects may function as infochemicals, structuring microbial communities in wood.}, }
@article {pmid16003478, year = {2005}, author = {Kamjunke, N and Tittel, J and Krumbeck, H and Beulker, C and Poerschmann, J}, title = {High heterotrophic bacterial production in acidic, iron-rich mining lakes.}, journal = {Microbial ecology}, volume = {49}, number = {3}, pages = {425-433}, pmid = {16003478}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development ; Biomass ; Environmental Monitoring ; Food Chain ; Germany ; Hydrogen-Ion Concentration ; Iron ; *Mining ; Phytoplankton/*growth &amp; development ; Population Dynamics ; Water/chemistry ; }, abstract = {The acidic mining lakes of Eastern Germany are characterized by their extremely low pH and high iron concentrations. Low concentrations of CO2 in the epilimnion due to the low pH and reduced light transmission due to dissolved ferric iron potentially limit phytoplankton primary production (PP), whereas dissolved organic carbon (DOC) may promote heterotrophic production of bacteria (HP). We, therefore, tested whether HP exceeds PP in three lakes differing in pH and iron concentration (mean pH 2.3-3.0, 23-500 mg Fe L(-1)). Bacterial biomass and HP achieved highest values in the most acidic, most iron-rich lake, whereas PP was highest in the least acidic lake. HP was often higher than PP (ratio HP/PP up to 11), indicating that planktonic PP was not the main carbon source for the bacteria. HP was not related to PP and DOC, but HP as well as bacterial biomass increased with decreasing pH. Light stimulated the formation of ferrous iron, changed the DOC composition, and increased the HP in laboratory experiments, suggesting that iron photoreduction caused DOC degradation. This may explain why we found the highest HP in the most acidic and most rich lake. Overall, the importance of bacteria in the cycling of matter and as a basis for the whole food web seemed to increase in more acidic lakes with higher iron concentrations.}, }
@article {pmid16003477, year = {2005}, author = {Zhang, H and Logan, BE and Regan, JM and Achenbach, LA and Bruns, MA}, title = {Molecular assessment of inoculated and indigenous bacteria in biofilms from a pilot-scale perchlorate-reducing bioreactor.}, journal = {Microbial ecology}, volume = {49}, number = {3}, pages = {388-398}, pmid = {16003477}, issn = {0095-3628}, mesh = {Bacteria/*genetics/*growth &amp; development ; Biofilms/*growth &amp; development ; *Bioreactors ; DNA, Bacterial/analysis ; Oxidation-Reduction ; Perchlorates/*metabolism ; Survival ; Water Pollutants, Chemical/*metabolism ; Water Purification/methods ; }, abstract = {Bioremediation of perchlorate-contaminated groundwater can occur via bacterial reduction of perchlorate to chloride. Although perchlorate reduction has been demonstrated in bacterial pure cultures, little is known about the efficacy of using perchlorate-reducing bacteria as inoculants for bioremediation in the field. A pilot-scale, fixed-bed bioreactor containing plastic support medium was used to treat perchlorate-contaminated groundwater at a site in Southern California. The bioreactor was inoculated with a field-grown suspension of the perchlorate-respiring bacterium Dechlorosoma sp. strain KJ and fed groundwater containing indigenous bacteria and a carbon source amendment. Because the reactor was flushed weekly to remove accumulated biomass, only bacteria capable of growing in biofilms in the reactor were expected to survive. After 26 days of operation, perchlorate was not detected in bioreactor effluent. Perchlorate remained undetected by ion chromatography (detection limit 4 mug L(-1)) during 6 months of operation, after which the reactor was drained. Plastic medium was subsampled from top, middle, and bottom locations of the reactor for shipment on blue ice and storage at -80 degrees C prior to analysis. Microbial community DNA was extracted from successive washes of thawed biofilm material for PCR-based community profiling by 16S-23S ribosomal intergenic spacer analysis (RISA). No DNA sequences characteristic of strain KJ were recovered from any RISA bands. The most intense bands yielded DNA sequences with high similarities to Dechloromonas spp., a closely related but different genus of perchlorate-respiring bacteria. Additional sequences from RISA profiles indicated presence of representatives of the low G+C gram-positive bacteria and the Cytophaga-Flavobacterium-Bacteroides group. Confocal scanning laser microscopy and fluorescence in situ hybridization (FISH) were also used to examine biofilms using genus-specific 16S ribosomal RNA probes. FISH was more sensitive than RISA profiling in detecting possible survivors from the initial inoculum. FISH revealed that bacteria hybridizing to Dechlorosoma probes constituted <1% of all cells in the biofilms examined, except in the deepest portions where they represented 3-5%. Numbers of bacteria hybridizing to Dechloromonas probes decreased as biofilm depth increased, and they were most abundant at the biofilm surface (23% of all cells). These spatial distribution differences suggested persistence of low numbers of the inoculated strain Dechlorosoma sp. KJ in parts of the biofilm nearest to the plastic medium, concomitant with active colonization or growth by indigenous Dechloromonas spp. in the biofilm exterior. This study demonstrated the feasibility of post hoc analysis of frozen biofilms following completion of field remediation studies.}, }
@article {pmid16003476, year = {2005}, author = {Polymenakou, PN and Bertilsson, S and Tselepides, A and Stephanou, EG}, title = {Links between geographic location, environmental factors, and microbial community composition in sediments of the Eastern Mediterranean Sea.}, journal = {Microbial ecology}, volume = {49}, number = {3}, pages = {367-378}, pmid = {16003476}, issn = {0095-3628}, mesh = {Bacteria/genetics/*growth &amp; development ; Chlorophyll/analysis ; Chlorophyll A ; Environmental Monitoring ; Fatty Acids/analysis ; Geography ; Geologic Sediments/*chemistry/*microbiology ; Mediterranean Sea ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/analysis ; *Water Microbiology ; }, abstract = {The bacterial community composition of marine surface sediments originating from various regions of the Eastern Mediterranean Sea (12 sampling sites) was compared by parallel use of three fingerprinting methods: analysis of 16S rRNA gene fragment heterogeneity by denaturing gradient electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP), and analysis of phospholipid-linked fatty acid composition (PLFA). Sampling sites were located at variable depths (30-2860 m; water column depth above the sediments) and the sediments differed greatly also in their degree of petroleum contamination (0.4-18 microg g(-1)), organic carbon (0.38-1.5%), and chlorophyll a content (0.01-7.7 microg g(-1)). Despite a high degree of correlation between the three different community fingerprint methods, some major differences were observed. DGGE banding patterns showed a significant separation of sediment communities from the northern, more productive waters of the Thermaikos Gulf and the oligotrophic waters of the Cretan, S. Ionian, and Levantine Sea. T-RFLP analysis clearly separated the communities of deep sediments (>1494 m depth) from their shallow (<617 m) counterparts. PLFA analysis grouped a shallow station from the productive waters of the north with the deep oligotrophic sediments from the Ionian and Levantine Sea, with low concentrations of PLFAs, and hence low microbial biomass, as the common denominator. The degree of petroleum contamination was not significantly correlated to the apparent composition of the microbial communities for any of the three methods, whereas organic carbon content and sediment chlorophyll a were important in this regard.}, }
@article {pmid16003475, year = {2005}, author = {Olapade, OA and Gao, X and Leff, LG}, title = {Abundance of three bacterial populations in selected streams.}, journal = {Microbial ecology}, volume = {49}, number = {3}, pages = {461-467}, pmid = {16003475}, issn = {0095-3628}, mesh = {Acinetobacter/genetics/*growth &amp; development ; Burkholderia cepacia/genetics/*growth &amp; development ; DNA, Bacterial/analysis ; Geologic Sediments/microbiology ; In Situ Hybridization, Fluorescence ; Population Density ; Pseudomonas putida/genetics/*growth &amp; development ; Rivers ; Water Microbiology ; }, abstract = {The population sizes of three bacterial species, Acinetobacter calcoaceticus, Burkholderia cepacia, and Pseudomonas putida, were examined in water and sediment from nine streams in different parts of the United States using fluorescent in situ hybridization (FISH). Population sizes were determined from three sites (upstream, midstream, and downstream) in each stream to compare differences in the occurrence and distribution of the species within each stream and among streams. Physical and chemical variables measured reflected differences in environmental conditions among the streams. In the water, B. cepacia numbers were highest in the agricultural, Iowa stream. P. putida numbers were highest in the southern coastal plain streams, Black Creek (GA) and Meyers Branch (SC). Compared to the other two species, the abundance of A. calcoaceticus was similar in all the streams. In sediment, the greatest abundance of all three species was found in the Iowa stream, while the lowest was in Hugh White Creek (NC). Detrended correspondence analysis (DCA) explained 95.8% and 83.9% of the total variation in bacterial numbers in water and sediment of the streams, respectively. In sediments and water, B. cepacia numbers were related to nitrate concentrations. A. calcoaceticus in water clustered with several environmental variables (i.e., SRP, pH, and conductivity) but benthic populations were less well correlated with these variables. This study reveals the potential influence of various environmental conditions on different bacterial populations in stream communities.}, }
@article {pmid16003474, year = {2005}, author = {Vázquez-Domínguez, E and Casamayor, EO and Català, P and Lebaron, P}, title = {Different marine heterotrophic nanoflagellates affect differentially the composition of enriched bacterial communities.}, journal = {Microbial ecology}, volume = {49}, number = {3}, pages = {474-485}, pmid = {16003474}, issn = {0095-3628}, mesh = {Animals ; Bacteria/classification/*growth &amp; development ; *Eukaryota ; Fluorescence ; Food Chain ; *Phylogeny ; Population Dynamics ; Seawater/microbiology ; Water Microbiology ; }, abstract = {We studied the effects of predation on the cytometric and phylogenetic features of two enriched bacterial communities obtained from two cultures of marine heterotrophic nanoflagellates: Jakoba libera and a mixed culture of Cafeteria sp. and Monosiga sp. Protists were harvested by flow cytometric cell sorting and eight different treatments were prepared. Each bacterial community was incubated with and without protists, and we added two treatments with protists and the bacteria present after the sorting procedure (cosorted bacteria). The bacterial community derived from the culture of Jakoba libera had higher green fluorescence per cell (FL1) than that derived from the mixed culture of Cafeteria sp. and Monosiga sp. When the experiment began all treatments presented bacterial communities that increase in fluorescence per bacterium (FL1); after that the FL1 decreased when bacteria attained maximal concentrations; and, finally, there was a new increase in FL1 toward the end of the experiment. Cosorted bacteria of Jakoba libera had the same fluorescence as the bacterial community derived from this protist, while the bacteria derived from the mixed culture of Cafeteria sp. and Monosiga sp. was nearly twice as fluorescent than that of the parental community. All treatments presented a general decline of SSC along the incubation. Therefore, there was a small influence of protists on the cytometric signature of each bacterial community. However, each bacterial community preyed by Jakoba libera or the mixed culture of Cafeteria sp. and Monosiga sp. led to four different phylogenetic fingerprint. Besides, the final Communities were different from the fingerprint of controls without protists, and most of them diverge from the fingerprint of cosorted bacteria. Our results confirm that changes in the phylogenetic composition of marine bacterial communities may depend on the initial communities of both bacteria and protists.}, }
@article {pmid16003473, year = {2005}, author = {Sharma, S and Aneja, MK and Mayer, J and Munch, JC and Schloter, M}, title = {Characterization of bacterial community structure in rhizosphere soil of grain legumes.}, journal = {Microbial ecology}, volume = {49}, number = {3}, pages = {407-415}, pmid = {16003473}, issn = {0095-3628}, mesh = {DNA, Bacterial ; Lupinus/*microbiology ; Pisum sativum/*microbiology ; Plant Roots/*microbiology ; Population Dynamics ; RNA, Ribosomal, 16S/analysis ; Reverse Transcriptase Polymerase Chain Reaction ; Soil Microbiology ; }, abstract = {Molecular techniques were used to characterize bacterial community structure, diversity (16S rDNA), and activity (16S rRNA) in rhizospheres of three grain legumes: faba beans (Vicia faba L., cv. Scirocco), peas (Pisum sativum L., cv. Duel) and white lupin (Lupinus albus L., cv. Amiga). All plants were grown in the same soil under controlled conditions in a greenhouse and sampled after fruiting. Amplified 16S rDNA and rRNA products (using universal bacterial primers) were resolved by denaturing gradient gel electrophoresis (DGGE). Distinct profiles were observed for the three legumes with most of the bands derived from RNA being a subset of those derived from DNA. Comparing the total bacterial profiles with actinomycete-specific ones (using actinomycete-specific primers) highlighted the dominance of this group in the three rhizospheres. 16S PCR and RT-PCR products were cloned to construct libraries and 100 clones from each library were sequenced. Actinomycetes and proteobacteria dominated the clone libraries with differences in the groups of proteobacteria. Absence of beta-subdivision members in pea and gamma-subdivision members of proteobacteria in faba bean rhizosphere was observed. Plant-dependent rhizosphere effects were evident from significant differences in the bacterial community structure of the legume rhizospheres under study. The study gives a detailed picture of both residing and "active" bacterial community in the three rhizospheres. The high abundance of actinomycetes in the rhizospheres of mature legumes indicates their possible role in soil enrichment after the legumes are plowed into the soil as biofertilizers.}, }
@article {pmid16003472, year = {2005}, author = {Vivas, A and Barea, JM and Azcón, R}, title = {Brevibacillus brevis isolated from cadmium- or zinc-contaminated soils improves in vitro spore germination and growth of Glomus mosseae under high Cd or Zn concentrations.}, journal = {Microbial ecology}, volume = {49}, number = {3}, pages = {416-424}, pmid = {16003472}, issn = {0095-3628}, mesh = {Biodegradation, Environmental ; Brevibacterium/*chemistry ; Cadmium/*isolation &amp; purification/*metabolism ; Fungi/*growth &amp; development ; Soil Pollutants/*isolation &amp; purification/*metabolism ; Spores ; Tissue Distribution ; Zinc/*isolation &amp; purification/*metabolism ; }, abstract = {In this study we investigated the saprophyte growth of two arbuscular-mycorrhizal fungi (Glomus mosseae isolate) under increasing Cd or Zn levels and the influence of a selected bacterial strain of Brevibacillus brevis. Microorganisms here assayed were isolated from Cd or Zn polluted soils. B. brevis increased the presymbiotic growth (germination rate growth and mycelial development) of Glomus mosseae. Spore germination and mycelial development of both G. mosseae isolate were reduced as much as the amount of Cd or Zn increased in the growth medium. In medium supplemented with 20 microg Cd mL(-1), the spore germination was only 12% after 20 days of incubation, but the coinoculation with B. brevis increased this value to 40% after only 15 days. The addition of 20 microg Cd mL(-1) to the growth medium drastically inhibited hyphal development, but the presence of the bacterium increased hyphal growth of G. mosseae from 195% (without Cd) until 254% (with 20 microg Cd mL(-1)). The corresponding bacterial effect increasing micelial growth ranged from 125% (without Zn) to 232% (200 microg Zn mL(-1)) in the case of G. mosseae isolated from Zn-polluted soil. Mycelial growth under 5 microg Cd mL(-1) (without bacterium) was similarly reduced from that produced at 15 microg Cd mL(-1) in the presence of the bacteria. As well, 50 microg Zn mL(-1) (without bacterium) reduced hyphal growth as much as 200 microg Zn mL(-1) did in the presence of B. brevis. The bacterial effect on the saprophytic growth of G. mosseae in absence of metal may be due to the involvement of indole acetic acid (IAA) produced by these bacteria. The Cd bioaccumulation ability exhibited (76%) by Cd-adapted B. brevis reduced the Cd damage on G. mosseae in Cd-contaminated medium. These capabilities of B. brevis isolates partially alleviate the inhibitory effects of Cd or Zn on the axenic growth of G. mosseae.}, }
@article {pmid16003471, year = {2005}, author = {Downing, TG and Sember, CS and Gehringer, MM and Leukes, W}, title = {Medium N:P ratios and specific growth rate comodulate microcystin and protein content in Microcystis aeruginosa PCC7806 and M. aeruginosa UV027.}, journal = {Microbial ecology}, volume = {49}, number = {3}, pages = {468-473}, pmid = {16003471}, issn = {0095-3628}, mesh = {Carcinogens/*analysis ; Microcystins ; Microcystis/*chemistry/*growth &amp; development ; Nitrogen/analysis/*metabolism ; Peptides, Cyclic/*analysis ; Phosphorus/analysis/*metabolism ; Population Dynamics ; Proteins/analysis ; }, abstract = {Hepatotoxin production in cyanobacteria has been shown to correlate to external stimuli such as light and nutrient concentrations and ratios, although conflicting results have been reported. Specific growth rates and protein and microcystin content of M. aeruginosa PCC7806 and M. aeruginosa UV027 were determined under nonlimiting batch culture conditions for a range of medium nitrogen and phosphorous atomic ratios. Both strains exhibited a similar optimal medium N:P ratio for increased cellular microcystin levels. Additionally, total cellular protein content and intracellular microcystin content were significantly correlated to each other (r2 = 0.81, p < 0.001). Microcystin and protein content increased considerably as the maximum specific growth rate for the experimental conditions was reached. The significant correlation of cellular protein and microcystin content and their relative increase with increasing specific growth rate, within defined ranges of medium N:P ratios, suggest a close association between microcystin production and N:P ratio-dependent assimilation of nitrogen, and resulting total cellular protein levels, which may be further modulated by specific growth rate.}, }
@article {pmid16003470, year = {2005}, author = {Vannini, C and Petroni, G and Verni, F and Rosati, G}, title = {A bacterium belonging to the Rickettsiaceae family inhabits the cytoplasm of the marine ciliate Diophrys appendiculata (Ciliophora, Hypotrichia).}, journal = {Microbial ecology}, volume = {49}, number = {3}, pages = {434-442}, pmid = {16003470}, issn = {0095-3628}, mesh = {Animals ; Ciliophora/*microbiology ; Ecology ; Phylogeny ; RNA, Ribosomal, 16S/analysis ; Rickettsiaceae/*growth &amp; development ; Seawater ; Symbiosis ; Water Microbiology ; }, abstract = {Bacteria of the family Rickettsiaceae (order Rickettsiales, alpha-Proteobacteria) are mainly known to be endosymbionts of arthropods with the capability to infect also vertebrate cells. Recently, they have also been found as leech endocytobionts. In the present paper, we report the first finding of a bacterium belonging to the family Rickettsiaceae in a natural population of a marine ciliate protozoan, namely Diophrys appendiculata, collected in the Baltic Sea. Bacteria were unambiguously identified through morphological characterization and the "full-cycle rRNA approach" (i.e., 16S rRNA gene characterization and use of specifically designed oligonucleotide probes for in situ detection). Symbionts are rod-shaped bacteria that grow freely in the cytoplasm of the host cell. They present two different morphotypes, similar in size, but different in cytoplasmic density. These are typical morphological features of members of the family Rickettsiaceae. 16S rRNA gene sequence showed that Diophrys symbionts share a high similarity value (>92%) with bacteria belonging to the genus Rickettsia. Phylogenetic analysis revealed that these new endosymbionts are clearly included in the clade of the family Rickettsiaceae, but they occupy an independent phylogenetic position with respect to members of the genus Rickettsia. This is the first report of a member of this family from a host protozoan and from a marine habitat. This result shows that this bacterial group is more diversified and widespread than supposed so far, and that its ecological relevance could until now have been underestimated. In light of these considerations, the two 16S rRNA oligonucleotide probes here presented, specific for members of the Rickettsiaceae, can represent useful tools for further researches on the presence and the spread of these microorganisms in the natural environment.}, }
@article {pmid16003469, year = {2005}, author = {Monier, JM and Lindow, SE}, title = {Aggregates of resident bacteria facilitate survival of immigrant bacteria on leaf surfaces.}, journal = {Microbial ecology}, volume = {49}, number = {3}, pages = {343-352}, pmid = {16003469}, issn = {0095-3628}, mesh = {Micronutrients/metabolism ; Pantoea/*growth &amp; development ; *Plant Leaves ; Population Dynamics ; Pseudomonas fluorescens/*growth &amp; development ; Pseudomonas syringae/*growth &amp; development ; Survival ; Water ; }, abstract = {The fate of immigrant bacterial cells on leaves under stressful conditions was determined as a function of the anatomical features and the local spatial density of resident cells at their landing site. Pantoea agglomerans 299R was established on bean leaves and the survival of immigrant cells of Pseudomonas fluorescens A506 and Pseudomonas syringae B728a, as well as P. agglomerans itself, was determined by epifluorescence microscopy following subsequent exposure of plants to desiccation stress. Resident and immigrant bacterial strains constitutively expressed the cyan and the green fluorescent protein, respectively, and the viability of individual cells was assessed directly on leaf surfaces following propidium iodide staining. Although only a small fraction of the immigrant cells landed on established bacterial aggregates, their fate was usually strongly influenced by the presence of indigenous bacteria at the site at which they landed. Immigrants of P. agglomerans 299R or P. fluorescens A506 that arrived as solitary cells had about double the probability of survival when landing on aggregates formed by P. agglomerans 299R than when landing on uncolonized areas of the leaf surface. In contrast, the survival of P. syringae B728a was similar irrespective of whether it landed on colonized or uncolonized parts of a leaf. The nature of plant anatomical features at which immigrant bacteria landed also strongly influenced the fate of immigrant bacteria. The fraction of immigrant cells of each species tested that landed on veins, glandular trichomes, or epidermal cells altered by P. agglomerans that died was always less than when they landed on normal epidermal cells or at the base of hooked trichomes. Depending on the process by which immigrants arrive at a leaf, only a small fraction of cells may be deposited on existing bacterial aggregates. Although uncolonized sites differed greatly in their ability to influence the survival of immigrant cells, the fate of an immigrant bacterium will depend on the nature of the leaf structure on which it is deposited, and apparently indirectly on the amount of nutrients and water available at that site to support the development of bacterial aggregates.}, }
@article {pmid16003468, year = {2005}, author = {Bowman, JP and McCammon, SA and Dann, AL}, title = {Biogeographic and quantitative analyses of abundant uncultivated gamma-proteobacterial clades from marine sediment.}, journal = {Microbial ecology}, volume = {49}, number = {3}, pages = {451-460}, pmid = {16003468}, issn = {0095-3628}, mesh = {Climate ; Geologic Sediments/*microbiology ; *Phylogeny ; Proteobacteria/classification/*genetics ; RNA, Ribosomal, 16S/analysis ; }, abstract = {16S rRNA gene-based molecular analyses revealed the presence of several large and so far uncultivated clades within class gamma-Proteobacteria, designated gamma-proteobacterial marine sediment (GMS) clades 1 to 4, in marine sediment. The GMS clades appear only indigenous to marine sediment and so far have an unknown functionality. SYBR Green-based real-time PCR analyses using GMS clade-specific primers indicated GMS clades were a significant part of the bacterial community (0.3-8.7% of total 16S rRNA genes) in both polar and temperate marine sediment samples. Univariate statistical analyses indicated that GMS clade communities were indistinguishable in two temperate coastal sediment samples even though these possessed very different mean grain sizes, organic contents, and organic loading rates. GMS clade communities were slightly different (p < 0.05) between polar and temperate sites, suggesting that psychrophilic adaptation among GMS clade taxa corresponds only to subtle phylogenetic differences. Similar levels of difference were also observed through a sediment core reflecting that through the sediment core history, which spanned approximately 3000 years, GMS clonal diversity shifted only marginally.}, }
@article {pmid16000770, year = {2005}, author = {Loy, A and Beisker, W and Meier, H}, title = {Diversity of bacteria growing in natural mineral water after bottling.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {7}, pages = {3624-3632}, pmid = {16000770}, issn = {0099-2240}, mesh = {Bacteria/*classification/genetics/*growth &amp; development ; Betaproteobacteria/classification/genetics/growth &amp; development ; Colony Count, Microbial ; Ecosystem ; Food Packaging/methods ; Gene Library ; Genes, rRNA ; *Genetic Variation ; In Situ Hybridization, Fluorescence ; Indoles/metabolism ; Mineral Waters/*microbiology ; Molecular Sequence Data ; Oligonucleotide Probes ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Staining and Labeling ; }, abstract = {Bacterial growth occurs in noncarbonated natural mineral waters a few days after filling and storage at room temperature, a phenomenon known for more than 40 years. Using the full-cycle rRNA approach, we monitored the development of the planktonic bacterial community in a noncarbonated natural mineral water after bottling. Seven 16S rRNA gene libraries, comprising 108 clones in total, were constructed from water samples taken at various days after bottling and from two different bottle sizes. Sequence analyses identified 11 operational taxonomic units (OTUs), all but one affiliated with the betaproteobacterial order Burkholderiales (6 OTUs) or the class Alphaproteobacteria (4 OTUs). Fluorescence in situ hybridization (FISH) was applied in combination with DAPI (4',6'-diamidino-2-phenylindole) staining, viability staining, and microscopic counting to quantitatively monitor changes in bacterial community composition. A growth curve similar to that of a bacterium grown in a batch culture was recorded. In contrast to the current perception that Gammaproteobacteria are the most important bacterial components of natural mineral water in bottles, Betaproteobacteria dominated the growing bacterial community and accounted for 80 to 98% of all bacteria detected by FISH in the late-exponential and stationary-growth phases. Using previously published and newly designed genus-specific probes, members of the betaproteobacterial genera Hydrogenophaga, Aquabacterium, and Polaromonas were found to constitute a significant proportion of the bacterial flora (21 to 86% of all bacteria detected by FISH). For the first time, key genera responsible for bacterial growth in a natural mineral water were identified by applying molecular cultivation-independent techniques.}, }
@article {pmid15998408, year = {2005}, author = {Wright, DP and Johansson, T and Le Quéré, A and Söderström, B and Tunlid, A}, title = {Spatial patterns of gene expression in the extramatrical mycelium and mycorrhizal root tips formed by the ectomycorrhizal fungus Paxillus involutus in association with birch (Betula pendula) seedlings in soil microcosms.}, journal = {The New phytologist}, volume = {167}, number = {2}, pages = {579-596}, doi = {10.1111/j.1469-8137.2005.01441.x}, pmid = {15998408}, issn = {0028-646X}, mesh = {Ammonium Sulfate/metabolism ; Base Sequence ; Betula/metabolism/*microbiology ; Cytoskeleton/metabolism ; DNA, Fungal/genetics ; Ecosystem ; Fungal Proteins/genetics/metabolism ; Gene Expression ; Gene Expression Profiling ; Genes, Fungal ; Models, Biological ; Mycorrhizae/*genetics/growth &amp; development/metabolism ; Nitrogen/metabolism ; Oligonucleotide Array Sequence Analysis ; Plant Roots/metabolism/microbiology ; Seedlings/metabolism/microbiology ; Signal Transduction ; Soil/analysis ; Symbiosis ; }, abstract = {Functional compartmentation of the extramatrical mycelium of ectomycorrhizal (ECM) fungi is considered important for the operation of ECM associations, although the molecular basis is poorly characterized. Global gene expression profiles of mycelium colonizing an ammonium sulphate ((NH4)2SO4) nutrient patch, rhizomorphs and ECM root tips of the Betula pendula-Paxillus involutus association were compared by cDNA microarray analysis. The expression profiles of rhizomorphs and nutrient patch mycelium were similar to each other but distinctly different from that of mycorrhizal tips. Statistical analyses revealed 337 of 1075 fungal genes differentially regulated among these three tissues. Clusters of genes exhibiting distinct expression patterns within specific tissues were identified. Genes implicated in the glutamine synthetase/glutamate synthase (GS/GOGAT) and urea cycles, and the provision of carbon skeletons for ammonium assimilation via beta-oxidation and the glyoxylate cycle, were highly expressed in rhizomorph and nutrient patch mycelium. Genes implicated in vesicular transport, cytoskeleton organization and morphogenesis and protein degradation were also differentially expressed. Differential expression of genes among the extramatrical mycelium and mycorrhizal tips indicates functional specialization of tissues forming ECM associations.}, }
@article {pmid15986831, year = {2005}, author = {Kadouri, D and Jurkevitch, E and Okon, Y and Castro-Sowinski, S}, title = {Ecological and agricultural significance of bacterial polyhydroxyalkanoates.}, journal = {Critical reviews in microbiology}, volume = {31}, number = {2}, pages = {55-67}, doi = {10.1080/10408410590899228}, pmid = {15986831}, issn = {1040-841X}, mesh = {Acyltransferases/genetics ; *Adaptation, Physiological ; Bacteria/classification/genetics/*metabolism ; *Bacterial Physiological Phenomena ; Biopolymers/*metabolism ; Carboxylic Ester Hydrolases/genetics ; *Ecosystem ; Phylogeny ; }, abstract = {Polyhydroxyalkanoates (PHAs) are a group of carbon andenergy storage compounds that are accumulated during suboptimal growth by many bacteria, and intracellularly deposited in the form of inclusion bodies. Accumulation of PHAs is thought to be used by bacteria to increase survival and stress tolerance in changing environments, and in competitive settings where carbon and energy sources may be limited, such as those encountered in the soil and the rhizosphere. Understanding the role that PHAs play as internal storage polymers is of fundamental importance in microbial ecology, and holds great potential for the improvement of bacterial inoculants for plants and soils. This review summarizes the current knowledge on the ecological function of PHAs, and their strategic role as survival factors in microorganisms under varying environmental stress is emphasized. It also explores the phylogeny of the PHA cycle enzymes, PHA synthase, and PHA depolymerase, suggesting that PHA accumulation was earlier acquired and maintained during evolution, thus contributing to microbial survival in the environment.}, }
@article {pmid15976296, year = {2005}, author = {Bell, T and Ager, D and Song, JI and Newman, JA and Thompson, IP and Lilley, AK and van der Gast, CJ}, title = {Larger islands house more bacterial taxa.}, journal = {Science (New York, N.Y.)}, volume = {308}, number = {5730}, pages = {1884}, doi = {10.1126/science.1111318}, pmid = {15976296}, issn = {1095-9203}, mesh = {Bacteria/classification/genetics/*growth &amp; development ; *Biodiversity ; *Ecosystem ; Environment ; Fagus/microbiology ; Genetic Variation ; Water Microbiology ; }, abstract = {The power law that describes the relationship between species richness and area size is one of the few generalizations in ecology, but recent studies show that this relationship differs for microbes. We demonstrate that the natural bacterial communities inhabiting small aquatic islands (treeholes) do indeed follow the species-area law. The result requires a re-evaluation of the current understanding of how natural microbial communities operate and implies that analogous processes structure both microbial communities and communities of larger organisms.}, }
@article {pmid15970996, year = {2005}, author = {Steppe, TF and Paerl, HW}, title = {Nitrogenase activity and nifH expression in a marine intertidal microbial mat.}, journal = {Microbial ecology}, volume = {49}, number = {2}, pages = {315-324}, pmid = {15970996}, issn = {0095-3628}, mesh = {Bacteria/*enzymology ; Biodiversity ; Circadian Rhythm ; Gene Expression Regulation, Bacterial ; Nitrogenase/*metabolism ; Oxidoreductases/*metabolism ; Phylogeny ; Seawater/*microbiology ; }, abstract = {N(2) fixation, diazotrophic community composition, and organisms actively expressing genes for N(2) fixation were examined over at 3-year period (1997-1999) for intertidal microbial mats on a sand flat located in the Rachel Carson National Estuarine Research Reserve (RCNERR) (Beaufort, NC, USA). Specifically, diel variations of N(2) fixation in the mats from the RCNERR were examined. Three distinct diel patterns of nitrogenase activity (NA) were observed. NA responses to short-term inhibitions of photosynthesis corresponded to one of the three patterns. High rates of NA were observed during peak O(2) production periods for diel experiments during summer months. Different types of NA diel variations correspond to different stages of mat development. Chloramphenicol treatments indicated that the mechanism of protein synthesis supporting NA changed throughout the day. Analysis of mat DNA and RNA gave further evidence suggesting that in addition to cyanobacteria, other functional groups were responsible for the NA observed in the RCNERR mats. The role of microbial diversity in the N(2) fixation dynamics of these mats is discussed.}, }
@article {pmid15968499, year = {2005}, author = {Raviraja, NS and Nikolcheva, LG and Bärlocher, F}, title = {Diversity of conidia of aquatic hyphomycetes assessed by microscopy and by DGGE.}, journal = {Microbial ecology}, volume = {49}, number = {2}, pages = {301-307}, pmid = {15968499}, issn = {0095-3628}, mesh = {Biodiversity ; DNA, Fungal/analysis ; Electrophoresis/methods ; Fresh Water/*microbiology ; Microscopy ; Mitosporic Fungi/genetics/*isolation &amp; purification ; Nucleic Acid Denaturation ; Seasons ; Spores, Fungal/*genetics ; Temperature ; }, abstract = {Water samples from a Canadian stream were passed through membrane filters between 22 July 2002 and 19 May 2003. Filters with trapped conidia of aquatic hyphomycetes were cut in half. One half was examined under a light microscope, and conidia were counted and identified. From the second half, DNA was extracted and amplified with fungal primers. The number of different ITS sequences (phylotypes) in the amplified DNA was assessed with DGGE. On average, the number of visually identified species per sample (12.4) was higher than the number of phylotypes (11.7), but the difference was nonsignificant (P = 0.36). However, the difference between species and phylotype numbers increased significantly with the number of species or conidia present on the filter, indicating that the sensitivity of DGGE decreases with sample size. When few conidia were present, phylotype numbers often exceeded species numbers, suggesting insufficient resolution of visual identification or the presence of DNA from nonconidial sources. A modification of the described method may be useful to check the accuracy of taxonomy and identification based on conidial morphology.}, }
@article {pmid15965728, year = {2005}, author = {Koch, AL}, title = {Bacterial choices for the consumption of multiple resources for current and future needs.}, journal = {Microbial ecology}, volume = {49}, number = {2}, pages = {183-197}, pmid = {15965728}, issn = {0095-3628}, mesh = {Bacteria/*metabolism ; Biological Evolution ; Biological Transport ; *Computer Simulation ; Ecosystem ; *Models, Biological ; Substrate Specificity ; }, abstract = {Microorganisms differ in their effectiveness in uptake and selection of substances that they bring in from the environment. They also differ in how they balance the allocation of nutrients for immediate and for delayed use. Moreover, they may not take up resources as fast as they seemingly could, and they may extrude derivatives of substances just pumped in. A good deal of these apparent choices must reside in the uptake systems and the linkage of these with the cell's intermediate metabolism. An important feature is that a resource may vary in concentration from time to time, nutrient to nutrient, and habitat to habitat. This variation must have been critical to the evolution of regulatory processes. Some possibilities for the combined uptake and consumption are considered for substrates serving the same (homologous) and different (heterologous) roles for the bacterium. From the membrane transport processes diagrammed in Fig. 1c and Fig. 2 and corresponding computer program given in Appendix A, the combined effect of uptake processes and cell growth can be studied. The model can be modified for various alternate models to study the possible control of cellular uptake and metabolism for the range of ecological roles of the bacterium.}, }
@article {pmid15965727, year = {2005}, author = {Galand, PE and Juottonen, H and Fritze, H and Yrjälä, K}, title = {Methanogen communities in a drained bog: effect of ash fertilization.}, journal = {Microbial ecology}, volume = {49}, number = {2}, pages = {209-217}, pmid = {15965727}, issn = {0095-3628}, mesh = {Bacteria/*genetics/*metabolism ; Biodiversity ; Ecosystem ; *Fertilizers ; Genes, Bacterial ; Methane/*metabolism ; Phylogeny ; Polymorphism, Restriction Fragment Length ; }, abstract = {Forestry practises such has drainage have been shown to decrease emissions of the greenhouse gas methane (CH(4)) from peatlands. The aim of the study was to examine the methanogen populations in a drained bog in northern Finland, and to assess the possible effect of ash fertilization on potential methane production and methanogen communities. Peat samples were collected from control and ash fertilized (15,000 kg/ha) plots 5 years after ash application, and potential CH(4) production was measured. The methanogen community structure was studied by DNA isolation, PCR amplification of the methyl coenzyme-M reductase (mcr) gene, denaturing gradient gel electrophoresis (DGGE), and restriction fragment length polymorphism (RFLP) analysis. The drained peatland showed low potential methane production and methanogen diversity in both control and ash-fertilized plots. Samples from both upper and deeper layers of peat were dominated by three groups of sequences related to Rice cluster-I hydrogenotroph methanogens. Even though pH was marginally greater in the ash-treated site, the occurrence of those sequences was not affected by ash fertilization. Interestingly, a less common group of sequences, related to the Fen cluster, were found only in the fertilized plots. The study confirmed the depth related change of methanogen populations in peatland.}, }
@article {pmid15965726, year = {2005}, author = {Johansen, A and Olsson, S}, title = {Using phospholipid fatty acid technique to study short-term effects of the biological control agent Pseudomonas fluorescens DR54 on the microbial microbiota in barley rhizosphere.}, journal = {Microbial ecology}, volume = {49}, number = {2}, pages = {272-281}, pmid = {15965726}, issn = {0095-3628}, mesh = {Fatty Acids/*analysis ; Fungi/enzymology ; Hordeum/*microbiology ; Laccase/metabolism ; Oxygen Consumption ; *Pest Control, Biological ; Phospholipids/analysis ; Plant Roots/*microbiology ; Pseudomonas fluorescens/*physiology ; *Soil Microbiology ; Substrate Specificity ; Time Factors ; }, abstract = {The biological control agent (BCA) Pseudomonas fluorescens DR54 was applied to seeds (experiment 1) or roots (experiment 2) of barley growing in microcosms, while noninoculated plants served as controls. The fate of the BCA and its effects on the rhizosphere microbial community was evaluated in microcosms destructively sampled at days 2, 4, 6, and 9 after inoculation. In both experiments the number of P. fluorescens DR54 cells decreased immediately after application as enumerated by immunostaining and microscope direct counting. Substrate-induced respiration (SIR) was taken as a measurement of the active microbial biomass, while indicators of the total microbiota (and main taxonomic groups) were obtained using the phospholipid fatty acid (PLFA) technique. In experiment 1, these parameters were unaffected by the relatively small number of BCA cells applied, whereas in experiment 2, the larger BCA input resulted in an enhanced level of both SIR and PLFAs from Gram-negative bacteria (which included the BCA itself). However, at day 9 after inoculation, treatments with P. fluorescens DR54 and controls were similar in all measured parameters in both experiments. This was also illustrated very clearly by principal component analysis of the PLFA data, which in both experiments were able to discriminate between treatments in the first days after BCA inoculation, thus confirming the sensitivity of this method. Laccase activity has a potential as an indicator of fungal stress, e.g., when challenged with an antifungal BCA. This seemed to be supported in experiment 2, where the activity of this enzyme was enhanced four-fold in the BCA treatment at day 2. Our study shows that under the present conditions, P. fluorescens DR54 disappears from the soil and causes only transient effects on the soil microbiota. It also shows that the PLFA technique is a sensitive and reliable monitoring tool in in situ assessment of BCA nontarget effect on indigenous microorganisms in soil.}, }
@article {pmid15965725, year = {2005}, author = {Kikuchi, Y and Fukatsu, T}, title = {Rickettsia infection in natural leech populations.}, journal = {Microbial ecology}, volume = {49}, number = {2}, pages = {265-271}, pmid = {15965725}, issn = {0095-3628}, mesh = {Animals ; Body Size ; Disease Reservoirs ; Leeches/*microbiology ; Ovum ; Phylogeny ; Rickettsia/genetics/*isolation &amp; purification ; }, abstract = {Field-collected specimens of glossiphoniid leeches, Torix tagoi, Torix tukubana, Hemiclepsis marginata, and Hemiclepsis japonica, were surveyed for Rickettsia infection by using a diagnostic PCR assay. Rickettsia was detected in 96% (69/72) of T. tagoi, 83% (24/29) of T. tukubana, 29% (33/113) of H. marginata, and 0% (0/30) of H. japonica. The frequencies of Rickettsia infection were stably maintained in different seasons. In H. marginata and T. tukubana, distant local populations exhibited remarkably different frequencies of Rickettsia infection. Eggs carried by infected females of T. tagoi and H. marginata were all Rickettsia-positive, indicating nearly 100% vertical transmission. Analysis of 16S rDNA sequences revealed that phylogenetic relationship of the leech-associated Rickettsia reflected the specific and populational divisions of the host leeches. However, circumstantial lines of evidence strongly suggested that horizontal transmission of Rickettsia must have occurred in the ancestors of these leeches. In T. tagoi and T. tukubana, infected individuals were remarkably larger in size than uninfected individuals, wheras in H. marginata, infected and uninfected individuals were almost comparable in size. This study first provides information on ecological aspects of leech-bone endocellular bacteria of the genus Rickettsia. On the basis of these data, we discuss possible mechanisms whereby Rickettsia infection is maintained in natural populations of these leeches in the freshwater ecosystem.}, }
@article {pmid15965724, year = {2005}, author = {Santrůcková, H and Bird, MI and Elhottová, D and Novák, J and Picek, T and Simek, M and Tykva, R}, title = {Heterotrophic fixation of CO(2) in soil.}, journal = {Microbial ecology}, volume = {49}, number = {2}, pages = {218-225}, pmid = {15965724}, issn = {0095-3628}, mesh = {Bacteria/*metabolism ; Biomass ; Carbon Dioxide/*metabolism ; Carbon Isotopes ; Ecosystem ; Hydrogen-Ion Concentration ; Oxygen Consumption ; *Soil Microbiology ; }, abstract = {The occurrence of heterotrophic CO(2) fixation by soil microorganisms was tested in several mineral soils differing in pH and two artificial soils (a mixture of silica sand, alfalfa powder, and nutrient medium inoculated with a soil suspension). Soils were incubated at ambient (approximately 0.05 vol%) and elevated (approximately 5 vol%) CO(2) concentrations under aerobic conditions for up to 21 days. CO(2) fixation was detected using either a technique for determining the natural abundance of (13)C or by measuring the distribution of labeled (14)C-CO(2) in soil and bacteria. The effects of elevated CO(2) on microbial biomass (direct counts, chloroform fumigation extraction method), composition of microbial community (phospholipid fatty acids), microbial activity (respiration, dehydrogenase activity), and turnover rate were also measured. Heterotrophic CO(2) fixation was proven in all soils under study, being higher in neutral soils. The main portion of the fixed CO(2) (98-99%) was found in extracellular metabolites while only approximately 1% CO(2) was incorporated into microbial cells. High CO(2) concentration always induced an increase in microbial activity, changes in the composition of the microbial community, and a decrease in microbial turnover. The results suggest that heterotrophic CO(2) fixation could be a widespread process in soils.}, }
@article {pmid15965723, year = {2005}, author = {Matos, A and Kerkhof, L and Garland, JL}, title = {Effects of microbial community diversity on the survival of Pseudomonas aeruginosa in the wheat rhizosphere.}, journal = {Microbial ecology}, volume = {49}, number = {2}, pages = {257-264}, pmid = {15965723}, issn = {0095-3628}, mesh = {*Biodiversity ; Plant Roots/*microbiology ; Pseudomonas aeruginosa/*physiology ; *Soil Microbiology ; Triticum/*microbiology ; }, abstract = {Ecological theory suggests that microbial communities with greater microbial diversity would be less susceptible to invasion by potential opportunistic pathogens. We investigated whether the survival of the opportunistic pathogen Pseudomonas aeruginosa in the wheat rhizosphere would be affected by the presence of natural and constructed microbial communities of various diversity levels. Three levels of microbial community diversity were derived from wheat roots by a dilution/extinction approach. These wheat rhizosphere inocula, as well as a gnotobiotic microbial community consisting of seven culturable wheat rhizobacterial isolates, were introduced into the nutrient solution of hydroponically grown wheat plants on the day of planting. Phenotypic characterization of the culturable microbial communities on R2A medium, Shannon microbial diversity index, community-level physiological profiles, and terminal restriction fragment length polymorphisms were used to assess the varying microbial diversity levels. At day 7 the roots were invaded with P. aeruginosa and the number of P. aeruginosa colony forming units per root were measured at day 14. The average number of surviving P. aeruginosa cells was 3.52, 4.90, 7.18, 6.65 log(10) cfu/root in the high, medium, low, and gnotobiotic microbial community diversity level treatments, respectively. The invasibility of the rhizosphere communities by P. aeruginosa was inversely related to the level of diversity from the dilution extinction gradient. The gnotobiotic community did not confer protection against P. aeruginosa invasion. Although these data indicate that invasibility is inversely related to diversity, further study is needed to both reproduce these findings and define the specific mechanisms of the diversity effect.}, }
@article {pmid15965722, year = {2005}, author = {Tadonléké, RD and Planas, D and Lucotte, M}, title = {Microbial food webs in boreal humic lakes and reservoirs: ciliates as a major factor related to the dynamics of the most active bacteria.}, journal = {Microbial ecology}, volume = {49}, number = {2}, pages = {325-341}, pmid = {15965722}, issn = {0095-3628}, mesh = {Animals ; Arctic Regions ; Bacteria/*metabolism ; Chlorophyll ; Chlorophyll A ; Ciliophora/*physiology ; *Food Chain ; Fresh Water/chemistry/*microbiology ; Humic Substances/analysis ; Seasons ; Temperature ; Water Microbiology ; }, abstract = {In order to assess the factors that determine the dynamics of bacteria with high nucleic acid content in aquatic systems, we (i) conducted 24-h in situ dialysis experiments, involving different fractions of plankton and unfiltered water and (ii) examined empirical relationships between bacteria and both abiotic factors and protists, in boreal humic freshwaters (reservoir and lakes) in the James Bay region (Québec, Canada). Bacteria were subdivided into two subgroups on the basis of their nucleic acid content assessed by flow cytometry. The abundance of bacteria with the highest nucleic acid content and high light scatter (HNA-hs) was significantly correlated, across sites, to bacterial production, whereas bacteria with lower nucleic acid content (LNA) and total bacteria were not. In addition, HNA-hs growth was higher and more variable than LNA growth, indicating that HNA-hs were the most dynamic bacteria. Heterotrophic nanoflagellate and ciliate biomass represented, on average, 5 and 13% of bacterial biomass, respectively. Both in ambient waters and in experiments, ciliates were significantly and negatively correlated with bacteria, whereas heterotrophic nanoflagellates, likely under the grazing pressure from ciliates and metazooplankton, were not. Among ciliates, Cyclidium glaucoma appeared to play an important role. Its growth was significantly and negatively correlated to that of HNA-hs but not to that of LNA. In ambient waters, the abundance of this species explained 56% of the variations in HNA-hs abundance and only 27% of those for LNA. The abundances of total bacteria and LNA significantly increased with chlorophyll a, whereas those of HNA-hs did not. In addition, during the experiments, the estimated potential losses of HNA-hs significantly increased with the initial abundance of C. glaucoma. These results suggest selective removal of the most dynamic bacteria by C. glaucoma and indicate that ciliates may play an important role in the dynamics of active bacteria in natural waters. These findings suggest the existence, within the aquatic microbial food webs, of keystone species that are very important in regulating the activity structure of bacteria.}, }
@article {pmid15965721, year = {2005}, author = {Granados, DP and Castañeda, E}, title = {Isolation and characterization of Cryptococcus neoformans varieties recovered from natural sources in Bogotá, Colombia, and study of ecological conditions in the area.}, journal = {Microbial ecology}, volume = {49}, number = {2}, pages = {282-290}, pmid = {15965721}, issn = {0095-3628}, mesh = {Animals ; Birds/microbiology ; Colombia ; Cryptococcus neoformans/*classification/*isolation &amp; purification ; Ecosystem ; Feces/microbiology ; Phenotype ; Plants/microbiology ; Seasons ; }, abstract = {Cryptococcus neoformans, the etiological agent of cryptococcosis, has been associated with avian droppings and certain trees in different countries, including Colombia. C neoformans environmental isolates were obtained in urban areas in Bogotá, Colombia, and the strains recovered were phenotypically characterized. Attempts to determine the ecological conditions (micro- and macroclimatic) possibly related to their habitat were also undertaken. Four hundred and eighty samples from bark, soil around trunk bases, and detritus inside hollows of 32 trees were collected in three urban areas during a 5-month period, as well as 89 avian droppings samples from different places. Of plant samples, 6.7% collected from nine tree species yielded C. neoformans var. gattii, serotype B strains in 99% of the cases, and C. neoformans var. grubii, serotype A in 1%. The yeast was more frequently recovered from bark than from soil or detritus inside hollows, and from trees with hollows or rotted wood rather than from trees in which birds nest. C. neoformans was present with higher frequency and density in the rainy season than in the dry season; we found that slightly higher temperature and humidity values of the microhabitat, as compared to those of the environment, favored fungal occurrence, but the phenological state of the tree did not. Of dropping samples, 7.9% yielded C. neoformans strains, all of them C. neoformans var. grubii, serotype A. The yeast was obtained more frequently from dry droppings than from moist ones, but neither the sunlight exposure nor the site of collection of samples was correlated with this occurrence. Population density was significantly higher in droppings than in tree samples. Under laboratory conditions, isolates of different serotype showed similar capsular sizes. Water content and pH ranges were wide and did not show any significant difference between positive and negative samples.}, }
@article {pmid15965720, year = {2005}, author = {Vrede, K}, title = {Nutrient and temperature limitation of bacterioplankton growth in temperate lakes.}, journal = {Microbial ecology}, volume = {49}, number = {2}, pages = {245-256}, pmid = {15965720}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development/metabolism ; Carbon/*physiology ; Ecosystem ; Fresh Water/*microbiology ; Nitrogen/*physiology ; Phosphorus/*physiology ; Plankton/*growth &amp; development/metabolism ; Seasons ; Temperature ; Water Microbiology ; }, abstract = {Limitation of bacterioplankton production by nutrients and temperature was investigated in eight temperate lakes in summer. Six of the lakes were resampled in autumn. The lakes differ in nutrient content, water color, and concentration of dissolved organic carbon. Nutrients (phosphorus, nitrogen, and organic carbon) were added alone and in all possible combinations to filtered lake water inoculated with bacteria from the lake. After incubation for 36-40 h at in situ temperatures (ranging from 7 to 20 degrees C), the response in bacterioplankton production was determined. The effect of increased temperature on bacterioplankton growth was also tested. Bacterioplankton production was often limited by phosphorus alone, organic carbon alone, or the two in combination. Phosphorus limitation of bacterioplankton production was more common in the summer, whereas limitation by organic carbon was more frequently observed in the autumn. There was a close balance between limitation by phosphorus and organic carbon in the epilimnion in the summer. In the hypolimnion in the summer, bacterioplankton growth was primarily phosphorus-limited. The effect of phosphorus additions decreased with increasing phosphorus concentrations in the lakes. However, there were no correlations between the effect of added organic carbon and water color, dissolved organic carbon concentration, or phosphorus concentration. When temperature was low (in the hypolimnion in the summer, and throughout the water column in the autumn) temperature also limited bacterioplankton production. Thus, temperature and inorganic nutrients or organic compounds can limit bacterioplankton growth both alone and simultaneously. However, at low temperatures, temperature is the most important factor influencing bacterioplankton growth.}, }
@article {pmid15965719, year = {2005}, author = {Jonkers, HM and Koh, IO and Behrend, P and Muyzer, G and de Beer, D}, title = {Aerobic organic carbon mineralization by sulfate-reducing bacteria in the oxygen-saturated photic zone of a hypersaline microbial mat.}, journal = {Microbial ecology}, volume = {49}, number = {2}, pages = {291-300}, pmid = {15965719}, issn = {0095-3628}, mesh = {Aerobiosis ; Carbon/*metabolism ; Oxygen Consumption ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sodium Chloride/*chemistry ; Substrate Specificity ; Sulfur-Reducing Bacteria/classification/genetics/*metabolism ; }, abstract = {The sulfate-reducing bacterium strain SRB D2 isolated from the photic zone of a hypersaline microbial mat, from Lake Chiprana, NE Spain, respired pyruvate, alanine, and alpha-ketoglutarate but not formate, lactate, malate, succinate, and serine at significant rates under fully oxic conditions. Dehydrogenase enzymes of only the former substrates are likely oxygen-tolerant as all substrates supported anaerobic sulfate reduction. No indications were found, however, that aerobic respiration supported growth. Although strain SRB D2 appeared phylogenetically closely related to the oxygen-tolerant sulfate-reducing bacterium Desulfovibrio oxyclinae, substrate spectra were markedly different. Most-probable-number (MPN) estimates of sulfate-reducing bacteria and aerobic heterotrophic bacteria indicated that the latter were numerically dominant in both the photic and aphotic zones of the mat. Moreover, substrate spectra of representative isolates showed that the aerobic heterotrophic bacteria are metabolically more diverse. These findings indicate that sulfate-reducing bacteria in the fully oxic photic zone of mats have to compete with aerobic heterotrophic bacteria for organic substrates. Porewater analysis revealed that total carbohydrates and low-molecular-weight carbon compounds (LMWC) made up substantial fractions of the total dissolved organic carbon (DOC) pool and that nighttime degradation of the former was concomitant with increased concentration of the latter. Our findings indicate that aerobic respiration by sulfate-reducing bacteria contributes to organic carbon mineralization in the oxic zone of microbial mats as daytime porewater LMWC concentrations are above typical half-saturation constants.}, }
@article {pmid15965718, year = {2005}, author = {Boyd, TJ and Montgomery, MT and Steele, JK and Pohlman, JW and Reatherford, SR and Spargo, BJ and Smith, DC}, title = {Dissolved oxygen saturation controls PAH biodegradation in freshwater estuary sediments.}, journal = {Microbial ecology}, volume = {49}, number = {2}, pages = {226-235}, pmid = {15965718}, issn = {0095-3628}, mesh = {Bacteria/*metabolism ; Biodegradation, Environmental ; Geologic Sediments/*microbiology ; Oxygen/*analysis ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Regression Analysis ; Rivers/*chemistry ; Temperature ; Time Factors ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are common contaminants in terrestrial and aquatic environments and can represent a significant constituent of the carbon pool in coastal sediments. We report here the results of an 18-month seasonal study of PAH biodegradation and heterotrophic bacterial production and their controlling biogeochemical factors from 186 sediment samples taken in a tidally influenced freshwater estuary. For each sampling event, measurements were averaged from 25-45 stations covering approximately 250 km(2). There was a clear relationship between bacterial production and ambient temperature, but none between production and bottom water dissolved oxygen (DO) % saturation or PAH concentrations. In contrast with other studies, we found no effect of temperature on the biodegradation of naphthalene, phenanthrene, or fluoranthene. PAH mineralization correlated with bottom water DO saturation above 70% (r(2) > 0.99). These results suggest that the proportional utilization of PAH carbon to natural organic carbon is as much as three orders of magnitude higher during cooler months, when water temperatures are lower and DO % saturation is higher. Infusion of cooler, well-oxygenated water to the water column overlying contaminated sediments during the summer months may stimulate PAH metabolism preferentially over non-PAH organic matter.}, }
@article {pmid15965717, year = {2005}, author = {Humbert, JF and Duris-Latour, D and Berre, BL and Giraudet, H and Salençon, MJ}, title = {Genetic diversity in Microcystis populations of a French storage reservoir assessed by sequencing of the 16S-23S rRNA intergenic spacer.}, journal = {Microbial ecology}, volume = {49}, number = {2}, pages = {308-314}, pmid = {15965717}, issn = {0095-3628}, mesh = {Biodiversity ; DNA, Ribosomal Spacer ; France ; *Genetic Variation ; Geologic Sediments/*microbiology ; Microcystis/*genetics ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 23S/*genetics ; Water Microbiology ; }, abstract = {We compared the genetic diversity of the 16S-23S spacer of the rRNA gene (ITS1) in benthic and pelagic colonies of the Microcystis genus isolated from two different sampling stations with different depths and at two different sampling times (winter and summer) in the French storage reservoir of Grangent. In all, 66 ITS1 sequences were found in the different clone libraries. The nucleotide diversity of all the sampled isolates were in the same range (average number = 0.022) regardless of their origin, showing that several clones are involved in the summer bloom event and contribute to the high biomass production. Phylogenetic study and analysis of molecular variance (AMOVA) revealed no obvious genetic differentiation between the benthic and pelagic isolates. This finding confirms that the Microcystis genus in this lake is characterized by having both a benthic phase in winter and spring allowing this organism to survive in unfavorable environmental conditions, and a pelagic phase in summer and autumn when environmental conditions allow them to grow in the water column. Finally, comparing these sequences with those available in the GenBank database showed that some highly conserved genotypes are found throughout the world.}, }
@article {pmid15954622, year = {2001}, author = {Seghers, D and Reheul, D and Bulcke, R and Verstraete, W and Top, EM}, title = {Do conventionally and biologically cultivated soils differ in bacterial diversity and community structure?.}, journal = {Mededelingen (Rijksuniversiteit te Gent. Fakulteit van de Landbouwkundige en Toegepaste Biologische Wetenschappen)}, volume = {66}, number = {3b}, pages = {381-388}, pmid = {15954622}, issn = {1373-7503}, mesh = {Bacteria/*drug effects/*genetics/isolation &amp; purification/metabolism ; Biodegradation, Environmental ; *Biodiversity ; Cluster Analysis ; Colony Count, Microbial ; DNA Fingerprinting ; DNA, Bacterial/genetics ; Electrophoresis, Polyacrylamide Gel/methods ; Herbicides/*pharmacology ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/*genetics ; Sensitivity and Specificity ; *Soil Microbiology ; }, abstract = {The effects of a long-term herbicide treatment on the microbial community of an agricultural soil were investigated. Therefor, molecular techniques were used to evaluate the structure and diversity of the soil microbial community. Eubacterial and group-specific primers for methanotrophs type I and II were used to amplify 16S rRNA gene fragments from total soil DNA. These fragments were subsequently separated by denaturing gradient gel electrophoresis (DGGE). The structure of the methanotrophic community was affected by the herbicides as the patterns obtained from a herbicide treated soil (conventional) clustered separately from the control soil (biological). It seems that group-specific PCR followed by DGGE is a very powerful and sensitive technique to differentiate fields, which have received a herbicide treatment from those who did not. The diversity of the methanotrophic community was quantified by calculating the Shannon-Weaver index of biodiversity. The type I methanotrophs showed a significant decreased biodiversity due to the herbicide treatment but the diversity of the methanotrophs type II was slightly higher in the herbicide treated soil.}, }
@article {pmid15954588, year = {2001}, author = {Van Tomme, I and Pieters, J and Verstraete, W}, title = {Individual wastewater treatment in Flanders (Belgium).}, journal = {Mededelingen (Rijksuniversiteit te Gent. Fakulteit van de Landbouwkundige en Toegepaste Biologische Wetenschappen)}, volume = {66}, number = {3a}, pages = {205-209}, pmid = {15954588}, issn = {1373-7503}, mesh = {Belgium ; Costs and Cost Analysis ; *Sewage ; Technology ; Waste Disposal, Fluid/economics/*methods ; }, abstract = {In Flanders, it is not possible to centralise the infrastructure for handling all wastewater. Decentralised treatment should be considered an essential part of an overall regional policy. Decentralised wastewater treatment can be small-scale (20 to 2,200 Inhabitant Equivalent (IE)) or individual (less than 20 IE). This paper deals with the operation, performances, technological aspects and costs of Individual Wastewater Treatment Plants (IWTPs) in Flanders. Different treatment systems are described and tentatively evaluated. The total costs (capital and operation) can be of the same order of those of centralised systems, i.e. 100 EURO/IE.year. In terms of overall performance, most of the systems tested in Flanders, i.e. aerobic biological filter, activated sludge system, submerged aerated filter, biorotor and percolation reed bed, appear capable to perform well in principle. However, there remain problems to be solved. The effluent quality differs 'in situ' considerably, depending on the care and attention given by the owner. Hence, the legislator should not only focus on certification of installations as such, but foremost give attention to regular validation of the performance at the household. In this respect, there is an urgent need for the design and the logistic management of proper performance control systems.}, }
@article {pmid15954580, year = {2001}, author = {Hammes, F and Verstraete, W}, title = {Bacterial Ca2+ metabolism as the key to microbial carbonate precipitation.}, journal = {Mededelingen (Rijksuniversiteit te Gent. Fakulteit van de Landbouwkundige en Toegepaste Biologische Wetenschappen)}, volume = {66}, number = {3a}, pages = {169-172}, pmid = {15954580}, issn = {1373-7503}, mesh = {Bacteria/*metabolism ; Calcium/*metabolism ; Calcium Carbonate/isolation &amp; purification/metabolism ; Carbonates/isolation &amp; purification/*metabolism ; Crystallization ; Delftia/metabolism ; Flavobacteriaceae/metabolism ; Hydrogen-Ion Concentration ; Kinetics ; }, abstract = {Ca2+ -ATPase enzymes facilitate active trans-membrane transport of Ca2+ in micro-organisms. This study investigates the hypothesis that active calcium metabolism under conditions of alkaline stress is a key element of microbial carbonate precipitation, and that the latter plays an integral part in survival of bacteria under alkaline conditions.}, }
@article {pmid15954579, year = {2001}, author = {Hammes, F and de Knijf, S and Verstraete, W}, title = {First steps in microbiological calcium removal from calcium-rich industrial wastewater.}, journal = {Mededelingen (Rijksuniversiteit te Gent. Fakulteit van de Landbouwkundige en Toegepaste Biologische Wetenschappen)}, volume = {66}, number = {3a}, pages = {165-168}, pmid = {15954579}, issn = {1373-7503}, mesh = {Bacteria/*metabolism ; Belgium ; Bioreactors ; Calcium/isolation &amp; purification/*metabolism ; Hydrolysis ; *Industrial Waste ; Urea/metabolism ; Waste Disposal, Fluid/*methods ; }, abstract = {A novel application for the process of microbial carbonate precipitation (MCP) was developed. It facilitates the removal of soluble calcium from calcium-rich industrial wastewater. It was shown that via the urea hydrolysis pathway, mediated by autochthonous bacteria, calcium removal exceeding 90% could be maintained in a semi-continuous reactor system.}, }
@article {pmid15954575, year = {2001}, author = {De Rudder, J and Van Hege, K and Verstraete, W}, title = {Assessment of the fouling potential of wastewater treatment plant effluent using a modified capillary suction time measurement.}, journal = {Mededelingen (Rijksuniversiteit te Gent. Fakulteit van de Landbouwkundige en Toegepaste Biologische Wetenschappen)}, volume = {66}, number = {3a}, pages = {145-148}, pmid = {15954575}, issn = {1373-7503}, mesh = {Capillary Action ; Environmental Monitoring ; Humic Substances/analysis ; Membranes, Artificial ; Suction/methods ; Ultrafiltration/methods ; *Waste Disposal, Fluid/methods ; }, abstract = {A new technique was developed to measure membrane fouling, which is derived from the capillary suction time (CST)--a parameter often used to indicate the dewaterability of sludge--and which is called the modified CST (CSTm). The results indicate a good repeatability and reproducibility of the test. Spiking tests with suspended solids and humic acid, which have a high fouling potential, resulted in a significant rise of the CSTm value, indicating a sensitive assessment of these fouling components. However, the CSTm measurement is mainly indicative for the colloidal fouling of the sample.}, }
@article {pmid15954566, year = {2001}, author = {Grommen, R and Van Hauteghem, I and Van Wambeke, M and Verstraete, W}, title = {Use of a nitrifying culture to shorten the activation time of biofilters for the removal of ammonium and nitrite in freshwater aquaria.}, journal = {Mededelingen (Rijksuniversiteit te Gent. Fakulteit van de Landbouwkundige en Toegepaste Biologische Wetenschappen)}, volume = {66}, number = {3a}, pages = {79-86}, pmid = {15954566}, issn = {1373-7503}, mesh = {Ammonia/*isolation &amp; purification ; Animals ; Filtration/*methods ; Fishes ; Fresh Water/*chemistry ; Models, Theoretical ; Nitrites ; }, abstract = {The removal of ammonia (NH3) through nitrification in intensive aquaculture systems is an important process as the total ammonia nitrogen (TAN, compromising NH4+ and NH3) concentration often is the key limiting water quality parameter in these intensive aquaculture systems. In this study, the performance characteristics of a suspension of nitrifying cells (named ABIL) have been explored This aqueous suspension contains a highly active, nitrifying microbial consortium and is stable for several months when preserved at 4 degrees C. Tests were performed in freshwater at lab scale (70 L, 20 - 24 degrees C). Results showed that the application of the consortium at a dose of 5 mg Volatile Suspended Solids (VSS) L(-1) assures a total removal of ammonium and nitrite species from 10 mg N L(-1) to below the detection limit within a period of four days. Experimentally, at a substrate level of 10 mg TAN L(-1), a rate of biological ammonium and nitrite conversion of the order of 0.3 - 0.5 g TAN g(-1) VSS(-1) d(-1) could be achieved by the consortium in the freshwater aquaria systems tested Provided adequate aeration and dissolved oxygen levels of 6 mg per L or more, no important intermediary nitrite concentrations were noticed Only a small amount of TAN was not found back as nitrate and might have been lost due to ammonia stripping After 12 months preservation of the inoculum at 4 degrees C, no important decrease in ammonium removal activity and only a minor decrease in the nitrite removal rate of the consortium were noticed.}, }
@article {pmid15954563, year = {2001}, author = {Seka, MA and Van De Wiele, T and Verstraete, W}, title = {Efficient control of activated sludge filamentous bulking by means of a multi-component additive.}, journal = {Mededelingen (Rijksuniversiteit te Gent. Fakulteit van de Landbouwkundige en Toegepaste Biologische Wetenschappen)}, volume = {66}, number = {3a}, pages = {57-62}, pmid = {15954563}, issn = {1373-7503}, mesh = {Food Industry ; Indicators and Reagents ; Industrial Waste ; *Sewage ; Waste Management/*methods ; }, abstract = {A multi-component additive formulated for a more efficient control of activated sludge filamentous bulking was evaluated at a full-scale treatment plant experiencing a severe filamentous bulking. It was found that, besides offering an immediate improvement of sludge settling, the multi-component additive was able to eliminate the filamentous bacteria causing the bulking. Hence, contrarily to ordinary additives, this novel additive yielded immediate as well as long-term improvement of sludge sedimentation upon a few additions.}, }
@article {pmid15954274, year = {2001}, author = {Van Hege, K and Verstraete, W}, title = {Biological membrane assisted carbon filtration for reuse of wastewater treatment plant effluent.}, journal = {Mededelingen (Rijksuniversiteit te Gent. Fakulteit van de Landbouwkundige en Toegepaste Biologische Wetenschappen)}, volume = {66}, number = {4}, pages = {113-117}, pmid = {15954274}, issn = {1373-7503}, mesh = {Adsorption ; Belgium ; Charcoal ; *Conservation of Natural Resources ; Filtration ; Membranes, Artificial ; Waste Disposal, Fluid/*methods ; Water Purification/*methods ; }, }
@article {pmid15954272, year = {2001}, author = {Lissens, G and Verstraete, W and Verhaege, M}, title = {Electrochemical post-treatment of anaerobic digested slurries: removal of refractory compounds in a closed nutrient cycle (LSS).}, journal = {Mededelingen (Rijksuniversiteit te Gent. Fakulteit van de Landbouwkundige en Toegepaste Biologische Wetenschappen)}, volume = {66}, number = {4}, pages = {101-106}, pmid = {15954272}, issn = {1373-7503}, mesh = {Ammonia ; Bacteria, Anaerobic/*metabolism/physiology ; Biodegradation, Environmental ; *Bioreactors ; Electrochemistry/*methods ; Environmental Pollution/*prevention &amp; control ; Manure/analysis/microbiology ; Oxidation-Reduction ; Soil Pollutants/metabolism ; Solubility ; Waste Management/*methods ; }, }
@article {pmid15954271, year = {2001}, author = {Dejonghe, W and Maertens, S and Verstraete, W and Top, EM}, title = {Rhizoremediation of a 3,4-dichloroaniline contaminated soil.}, journal = {Mededelingen (Rijksuniversiteit te Gent. Fakulteit van de Landbouwkundige en Toegepaste Biologische Wetenschappen)}, volume = {66}, number = {4}, pages = {97-99}, pmid = {15954271}, issn = {1373-7503}, mesh = {Aniline Compounds/*metabolism ; *Biodegradation, Environmental ; Comamonas testosteroni/*physiology ; Dose-Response Relationship, Drug ; Sinapis/*growth &amp; development/metabolism ; Soil Microbiology ; Soil Pollutants/*metabolism ; }, }
@article {pmid15954269, year = {2001}, author = {Boon, N and Lievens, H and Verstraete, W and Top, EM}, title = {Aniline and 3-chloroaniline degrading bacteria: genetics and possible applications.}, journal = {Mededelingen (Rijksuniversiteit te Gent. Fakulteit van de Landbouwkundige en Toegepaste Biologische Wetenschappen)}, volume = {66}, number = {4}, pages = {87-91}, pmid = {15954269}, issn = {1373-7503}, mesh = {Aniline Compounds/*metabolism ; Biodegradation, Environmental ; Bioreactors ; Carcinogens/metabolism ; Comamonas testosteroni/genetics/*metabolism ; Cupriavidus necator/genetics/*metabolism ; Organisms, Genetically Modified ; *Sewage/chemistry/microbiology ; Waste Disposal, Fluid ; Water Pollutants, Chemical/metabolism ; }, }
@article {pmid15954258, year = {2001}, author = {Muthumbi, W and De Boever, P and Pieters, JG and Van Langenhove, H and Comhaire, F and Verstraete, W}, title = {Screening for the presence of estrogenic compounds and polycyclic aromatic hydrocarbons in experimental flue gas matrices.}, journal = {Mededelingen (Rijksuniversiteit te Gent. Fakulteit van de Landbouwkundige en Toegepaste Biologische Wetenschappen)}, volume = {66}, number = {4}, pages = {21-28}, pmid = {15954258}, issn = {1373-7503}, mesh = {Air Pollutants/*analysis ; Biological Assay ; Estrogens/*analysis ; Gases ; Humans ; Incineration ; Plants, Edible/metabolism ; Polycyclic Aromatic Hydrocarbons/*analysis ; Receptors, Estrogen/physiology ; *Refuse Disposal ; }, }
@article {pmid15954096, year = {2005}, author = {Kurland, CG}, title = {What tangled web: barriers to rampant horizontal gene transfer.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {27}, number = {7}, pages = {741-747}, doi = {10.1002/bies.20258}, pmid = {15954096}, issn = {0265-9247}, mesh = {Animals ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome ; Humans ; *Models, Genetic ; Models, Theoretical ; Mutation ; Phylogeny ; }, abstract = {Dawkins in his The Selfish Gene(1) quite aptly applies the term "selfish" to parasitic repetitive DNA sequences endemic to eukaryotic genomes, especially vertebrates. Doolittle and Sapienza(2) as well as Orgel and Crick(3) enlivened this notion of selfish DNA with the identification of such repetitive sequences as remnants of mobile elements such as transposons. In addition, Orgel and Crick(3) associated parasitic DNA with a potential to outgrow their host genomes by propagating both vertically via conventional genome replication as well as infectiously by horizontal gene transfer (HGT) to other genomes. Still later, Doolittle(4) speculated that unchecked HGT between unrelated genomes so complicates phylogeny that the conventional representation of a tree of life would have to be replaced by a thicket or a web of life.(4) In contrast, considerable data now show that reconstructions based on whole genome sequences are consistent with the conventional "tree of life".(5-10) Here, we identify natural barriers that protect modern genome populations from the inroads of rampant HGT.}, }
@article {pmid15953928, year = {2005}, author = {Oremland, RS and Capone, DG and Stolz, JF and Fuhrman, J}, title = {Whither or wither geomicrobiology in the era of 'community metagenomics'.}, journal = {Nature reviews. Microbiology}, volume = {3}, number = {7}, pages = {572-578}, doi = {10.1038/nrmicro1182}, pmid = {15953928}, issn = {1740-1526}, mesh = {Bacteria/genetics/metabolism ; Ecosystem ; *Environmental Microbiology ; *Genome, Bacterial ; Genomics/*methods ; }, abstract = {Molecular techniques are valuable tools that can improve our understanding of the structure of microbial communities. They provide the ability to probe for life in all niches of the biosphere, perhaps even supplanting the need to cultivate microorganisms or to conduct ecophysiological investigations. However, an overemphasis and strict dependence on such large information-driven endeavours as environmental metagenomics could overwhelm the field, to the detriment of microbial ecology. We now call for more balanced, hypothesis-driven research efforts that couple metagenomics with classic approaches.}, }
@article {pmid15952424, year = {2001}, author = {Wouters, R and Lardenoit, R and De Boever, P and Verstraete, W}, title = {Probiotic removal of herbicides with endocrine disrupting potential from aqueous matrices.}, journal = {Mededelingen (Rijksuniversiteit te Gent. Fakulteit van de Landbouwkundige en Toegepaste Biologische Wetenschappen)}, volume = {66}, number = {1}, pages = {5-13}, pmid = {15952424}, issn = {1373-7503}, mesh = {2,4-Dichlorophenoxyacetic Acid/adverse effects/isolation &amp; purification ; Adsorption ; Atrazine/adverse effects/isolation &amp; purification ; Charcoal/*chemistry ; Chromatography, High Pressure Liquid ; Cultured Milk Products ; Dose-Response Relationship, Drug ; Endocrine Glands/*drug effects ; Fresh Water ; Herbicides/adverse effects/*isolation &amp; purification ; *Probiotics ; Water Pollutants, Chemical/*isolation &amp; purification ; Water Purification/methods ; }, abstract = {Water dosed with 50 mg/L of 2,4-D and atrazine was treated to remove the herbicides which both are reported to have endocrine disrupting potential. Both chemicals could be removed effectively with activated carbon. Yet, traces of endocrine disrupter remained in the water and are able to enter the food chain. The further biological elimination of these compounds was investigated. Milk alone did not decrease the amount of chemicals present in the aqueous supernatant. Yet, the probiotic products Bifidus yoghurt (GB), Actimel (Danone) and Yakult (Yakult Honsha) appeared to bind a substantial amount of the endocrine disrupting chemicals to the particulate fraction and thus render them potentially less bio-available in the aqueous phase.}, }
@article {pmid15947174, year = {2005}, author = {Quinn, TC and Overbaugh, J}, title = {HIV/AIDS in women: an expanding epidemic.}, journal = {Science (New York, N.Y.)}, volume = {308}, number = {5728}, pages = {1582-1583}, doi = {10.1126/science.1112489}, pmid = {15947174}, issn = {1095-9203}, mesh = {Acquired Immunodeficiency Syndrome/*epidemiology ; Contraceptive Agents, Female/adverse effects ; *Disease Outbreaks ; Disease Susceptibility ; Female ; Gonadal Steroid Hormones/physiology ; HIV Infections/*epidemiology/*etiology/prevention &amp; control/transmission ; *HIV-1 ; Humans ; Pregnancy ; Pregnancy Complications, Infectious/epidemiology ; Risk Factors ; Sex Characteristics ; Sex Distribution ; Sexually Transmitted Diseases/complications/epidemiology ; }, abstract = {More than 20 years into the human immunodeficiency virus-type 1 (HIV-1) epidemic, women account for nearly half of the 40 million people living with HIV-1 worldwide, with an even higher proportion existing in developing countries. Social determinants of female vulnerability to HIV-1 include gender disparities, poverty, cultural and sexual norms, lack of education, and violence. Women are also more susceptible to HIV-1 because of hormonal changes, vaginal microbial ecology and physiology, and a higher prevalence of sexually transmitted diseases. Prevention strategies must address the wide range of gender inequalities that promote the dissemination of HIV-1.}, }
@article {pmid15938406, year = {2005}, author = {Medvedeva, SE and Boiandin, AN and Lankin, IuP and Kotov, DA and Kargatova, TV and Rodicheva, EK and Popova, LIu}, title = {[Database on natural and transgenic luminous microorganisms: "BiolumBase"].}, journal = {Mikrobiologiia}, volume = {74}, number = {2}, pages = {278-286}, pmid = {15938406}, issn = {0026-3656}, mesh = {Bacteria/chemistry/*genetics ; Biotechnology ; *Databases, Factual ; Ecology ; *Genes, Bacterial ; Luminescence ; Luminescent Proteins/chemistry/*genetics ; Transgenes ; }, abstract = {The database "BiolumBase" is designed for the selection and systematization of available world information on microorganisms containing bioluminescent systems; it includes two sections: "natural" and "transgenic" luminous microorganisms. At present, logic schemes of divisions, classification of the objects, presentation of characteristics, and the inputs of relative information, as well as the necessary program modules including links to the database, are developed. The database is constructed on the basis of published data and our own experimental results; the subsequent linkage of the database to the Internet is envisaged. Users will be able to obtain not only the catalogues of strains but also information concerning the properties and functions of the known species of luminous bacteria, the structure, regulatory mechanisms, and application of bioluminescent systems and genetically engineered constructions with lux genes, as well as to find references and to search strains by using any set of attributes. The database will provide information that is of interest for the development of microbial ecology and biotechnology, in particular, for the prediction of biological hazard from the application of transgenic strains.}, }
@article {pmid15936100, year = {2005}, author = {Gadkar, V and Rillig, MC}, title = {Suitability of genomic DNA synthesized by strand displacement amplification (SDA) for AFLP analysis: genotyping single spores of arbuscular mycorrhizal (AM) fungi.}, journal = {Journal of microbiological methods}, volume = {63}, number = {2}, pages = {157-164}, doi = {10.1016/j.mimet.2005.03.009}, pmid = {15936100}, issn = {0167-7012}, mesh = {*DNA Replication ; DNA, Fungal/genetics/metabolism ; Fungi/*classification/genetics/metabolism/physiology ; *Genome, Fungal ; Genotype ; Mycology/methods ; *Mycorrhizae ; Nucleic Acid Amplification Techniques/*methods ; *Polymorphism, Restriction Fragment Length ; Spores, Fungal/classification/genetics ; }, abstract = {Limited biological samples of microbial origin often yield insufficient amounts of genomic DNA, making application of standard techniques of genetic analysis, like amplified fragment length polymorphism (AFLP), virtually impossible. The Phi29 DNA polymerase based whole genome amplification (WGA) method has the potential to alleviate this technical bottleneck. In the present work, we have sought to investigate the suitability of genomic DNA synthesized using Phi29 based WGA for AFLP analysis. We first used genomic DNA from Saccharomyces cerevisiae to optimize the protocol for the use of SDA-amplified DNA for AFLP analysis. Based on the optimized protocol we obtained AFLP fingerprints which were indistinguishable from the non-amplified genomic DNA. Finally, AFLP analysis was performed using SDA synthesized genomic DNA from single spores of various species of arbuscular mycorrhizal (AM) fungi. Unique and highly reproducible fingerprints for each species were obtained. The present study introduces the application of WGA-mediated AFLP to AM fungal biology; similarly, our protocol could be useful for other microbial genomes currently not amenable to genetic analysis owing to the paucity of starting template.}, }
@article {pmid15935676, year = {2005}, author = {Matz, C and Kjelleberg, S}, title = {Off the hook--how bacteria survive protozoan grazing.}, journal = {Trends in microbiology}, volume = {13}, number = {7}, pages = {302-307}, doi = {10.1016/j.tim.2005.05.009}, pmid = {15935676}, issn = {0966-842X}, mesh = {*Adaptation, Biological ; Animals ; *Bacterial Physiological Phenomena ; Biological Evolution ; Ecology ; Eukaryota/microbiology/*physiology ; Food Chain ; }, abstract = {Bacterial growth and survival in numerous environments are constrained by the action of bacteria-consuming protozoa. Recent findings suggest that bacterial adaptations against protozoan predation might have a significant role in bacterial persistence and diversification. We argue that selective predation has given rise to diverse routes of bacterial defense, including adaptive mechanisms in bacterial biofilms, and has promoted major transitions in bacterial evolution, such as multicellularity and pathogenesis. We propose that studying predation-driven adaptations will provide an exciting frontier for microbial ecology and evolution at the interface of prokaryotes and eukaryotes.}, }
@article {pmid15933010, year = {2005}, author = {Williamson, KE and Radosevich, M and Wommack, KE}, title = {Abundance and diversity of viruses in six Delaware soils.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {6}, pages = {3119-3125}, pmid = {15933010}, issn = {0099-2240}, mesh = {Agriculture ; Bacteria/isolation &amp; purification/virology ; Bacteriophages/classification/*isolation &amp; purification ; Delaware ; Ecosystem ; Microscopy, Electron, Transmission ; Microscopy, Fluorescence ; Soil/*analysis ; *Soil Microbiology ; Trees ; Virion/classification/*isolation &amp; purification ; }, abstract = {The importance of viruses in marine microbial ecology has been established over the past decade. Specifically, viruses influence bacterial abundance and community composition through lysis and alter bacterial genetic diversity through transduction and lysogenic conversion. By contrast, the abundance and distribution of viruses in soils are almost completely unknown. This study describes the abundance and diversity of autochthonous viruses in six Delaware soils: two agricultural soils, two coastal plain forest soils, and two piedmont forest soils. Viral abundance was measured using epifluorescence microscopy, while viral diversity was assessed from morphological data obtained through transmission electron microscopy. Extracted soil virus communities were dominated by bacteriophages that demonstrated a wide range of capsid diameters (20 nm to 160 nm) and morphologies, including filamentous forms and phages with elongated capsids. The reciprocal Simpson's index suggests that forest soils harbor more diverse assemblages of viruses, particularly in terms of morphological distribution. Repeated extractions of virus-like particles (VLPs) from soils indicated that the initial round of extraction removes approximately 70% of extractable viruses. Higher VLP abundances were observed in forest soils (1.31 x 10(9) to 4.17 x 10(9) g(-1) dry weight) than in agricultural soils (8.7 x 10(8) to 1.1 x 10(9) g(-1) dry weight). Soil VLP abundance was significantly correlated to moisture content (r = 0.988) but not to soil texture. Land use (agricultural or forested) was significantly correlated to both bacterial (r = 0.885) and viral (r = 0.812) abundances, as were soil organic matter and water content. Thus, land use is a significant factor influencing viral abundance and diversity in soils.}, }
@article {pmid15931167, year = {2005}, author = {Allen, EE and Banfield, JF}, title = {Community genomics in microbial ecology and evolution.}, journal = {Nature reviews. Microbiology}, volume = {3}, number = {6}, pages = {489-498}, doi = {10.1038/nrmicro1157}, pmid = {15931167}, issn = {1740-1526}, mesh = {DNA/genetics/isolation &amp; purification ; *Ecosystem ; Environment ; *Evolution, Molecular ; Gene Transfer Techniques ; *Genomics ; Proteomics ; }, abstract = {It is possible to reconstruct near-complete, and possibly complete, genomes of the dominant members of microbial communities from DNA that is extracted directly from the environment. Genome sequences from environmental samples capture the aggregate characteristics of the strain population from which they were derived. Comparison of the sequence data within and among natural populations can reveal the evolutionary processes that lead to genome diversification and speciation. Community genomic datasets can also enable subsequent gene expression and proteomic studies to determine how resources are invested and functions are distributed among community members. Ultimately, genomics can reveal how individual species and strains contribute to the net activity of the community.}, }
@article {pmid15926596, year = {2005}, author = {Rabaey, K and Boon, N and Höfte, M and Verstraete, W}, title = {Microbial phenazine production enhances electron transfer in biofuel cells.}, journal = {Environmental science &amp; technology}, volume = {39}, number = {9}, pages = {3401-3408}, doi = {10.1021/es048563o}, pmid = {15926596}, issn = {0013-936X}, mesh = {*Bioelectric Energy Sources ; Electrons ; Phenazines/*chemistry ; Pseudomonas aeruginosa/*physiology ; Pyocyanine/metabolism ; }, abstract = {High-rate electron transfer toward an anode in microbial fuel cells (MFCs) has thus far not been described for bacteria-producing soluble redox mediators. To studythe mechanism of electron transfer, we used a MFC isolate, Pseudomonas aeruginosa strain KRP1. Bacterial electron transfer toward the MFC anode was enabled through pyocyanin and phenazine-1-carboxamide. The presence of the anode stimulated pyocyanin production. Mutant strains, deficient in the synthesis of pyocyanin and phenazine-1-carboxamide, were unable to achieve substantial electron transfer and reached only 5% of the wild type's power output. Upon pyocyanin addition, the power output was restored to 50%. Pyocyanin was not only used by P. aeruginosa to improve electron transfer but as well enhanced electron transfer by other bacterial species. The finding that one bacterium can produce electron shuttles, which can be used also by other bacteria, to enhance electron-transfer rate and growth, has not been shown before. These findings have considerable implications with respect to the power output attainable in MFCs.}, }
@article {pmid15922081, year = {2005}, author = {Rabaey, K and Verstraete, W}, title = {Microbial fuel cells: novel biotechnology for energy generation.}, journal = {Trends in biotechnology}, volume = {23}, number = {6}, pages = {291-298}, doi = {10.1016/j.tibtech.2005.04.008}, pmid = {15922081}, issn = {0167-7799}, mesh = {Biodegradation, Environmental ; Bioelectric Energy Sources/microbiology/*trends ; Bioreactors/microbiology ; Biotechnology/instrumentation/methods/*trends ; Oxidation-Reduction ; *Waste Disposal, Fluid/methods ; }, abstract = {Microbial fuel cells (MFCs) provide new opportunities for the sustainable production of energy from biodegradable, reduced compounds. MFCs function on different carbohydrates but also on complex substrates present in wastewaters. As yet there is limited information available about the energy metabolism and nature of the bacteria using the anode as electron acceptor; few electron transfer mechanisms have been established unequivocally. To optimize and develop energy production by MFCs fully this knowledge is essential. Depending on the operational parameters of the MFC, different metabolic pathways are used by the bacteria. This determines the selection and performance of specific organisms. Here we discuss how bacteria use an anode as an electron acceptor and to what extent they generate electrical output. The MFC technology is evaluated relative to current alternatives for energy generation.}, }
@article {pmid15910530, year = {2005}, author = {Nevalainen, A and Seuri, M}, title = {Of microbes and men.}, journal = {Indoor air}, volume = {15 Suppl 9}, number = {}, pages = {58-64}, doi = {10.1111/j.1600-0668.2005.00344.x}, pmid = {15910530}, issn = {0905-6947}, mesh = {*Air Microbiology ; Air Pollution, Indoor/*adverse effects ; Arthritis, Rheumatoid/etiology/microbiology ; Bacteria/*pathogenicity ; *Environmental Exposure ; Fungi/*pathogenicity ; Humans ; Humidity ; Hypersensitivity ; Male ; Nervous System Diseases/etiology/microbiology ; Occupational Diseases/etiology/microbiology ; Respiratory Tract Diseases/etiology/microbiology ; Risk Factors ; }, abstract = {UNLABELLED: Moisture accumulation in building structures, the microbial ecology of water-damaged sites and human exposure to biological contaminants are complex phenomena and may result in various types of indoor air pollution and adverse health outcomes. Commonly reported are building-related irritation symptoms, respiratory infections and non-specific symptoms and occasionally neurological impairment. Various diseases have been associated with mold exposure, e.g. an increased risk of asthma development and exacerbation as well as clusters of hypersensitivity pneumonitis, pulmonary hemorrhage in infants and rheumatic diseases. The causal agents of these illnesses, still poorly understood, may be linked to the complex interactions between bacteria and fungi with environmental growth substrates and other microorganisms which lead to a wide diversity of exposures. Fungi and bacteria growing on building materials may produce toxic secondary metabolites, and the material appears to be a key determinant of metabolite production. Modern building technology has provided new ecological niches for microbes which readily exploit faults in moisture control. To better describe microbial exposures in buildings, current method development focuses on chemical markers of biomass and assays for specific genetic sequences.<br><br>PRACTICAL IMPLICATIONS: Dampness and moisture phenomena in buildings, resulting microbial and chemical exposures and individual human responses are complex phenomena. While the causative links between exposing agents and health responses are still not well understood, the essential issue is to prevent the problems with good design, construction and maintenance.}, }
@article {pmid15906089, year = {2005}, author = {Vallet, S and Gagneur, A and Legrand, MC and Chomel, JJ and Picard, B}, title = {Enteroviral infection mimicking primary herpetic stomatitis in four children.}, journal = {European journal of pediatrics}, volume = {164}, number = {9}, pages = {594-595}, pmid = {15906089}, issn = {0340-6199}, mesh = {Antibodies, Monoclonal ; Antibodies, Viral/isolation &amp; purification ; Child, Preschool ; Coxsackievirus Infections/*diagnosis/immunology/*virology ; Diagnosis, Differential ; Enterovirus/immunology/*isolation &amp; purification ; Enterovirus Infections/*diagnosis/immunology/*virology ; Herpesviridae/immunology/isolation &amp; purification ; Humans ; Reverse Transcriptase Polymerase Chain Reaction ; Stomatitis, Herpetic/*diagnosis/virology ; }, }
@article {pmid15900775, year = {2005}, author = {Xue, K and Luo, HF and Qi, HY and Zhang, HX}, title = {Changes in soil microbial community structure associated with two types of genetically engineered plants analyzing by PLFA.}, journal = {Journal of environmental sciences (China)}, volume = {17}, number = {1}, pages = {130-134}, pmid = {15900775}, issn = {1001-0742}, mesh = {Bacterial Physiological Phenomena ; China ; *Ecosystem ; Fatty Acids/*chemistry ; Fungi/physiology ; Phospholipids/*chemistry ; Plants, Genetically Modified/*growth &amp; development ; Principal Component Analysis ; *Soil Microbiology ; Solanum tuberosum/chemistry/genetics/*growth &amp; development ; Zea mays/chemistry/genetics/*growth &amp; development ; }, abstract = {With the rapid expansion of GEPs(genetically engineered plants), people are more and more concerned about the ecological risks brought by their release. Assessing the effect of GEPs on soil microbial ecology is indispensable to study their ecological risks. In our study, the phospholipids fatty acid (PLFA) method was used to analyze the microbial community of soil samples collected from fields with two types of GEPs-Bt transgenic corn and PVY (potato virus Y) cell protein gene transgenic potato. The principal components analysis (PCA) showed all controls were on the right of related GEPs samples along the PC1 (the first principal component) axis, which means a decrease of fungi in soils with genetically engineered crop since most of PLFAs that are strongly positively correlated with PC1 represent fungi. For samples collected from Bt transgenic cornfield, the ratios of gram-positive to gram-negative bacteria were less than those of controls. For samples of transgenic potato field, these ratios were lower than those of controls when soils were collected from deep layer (20-40 cm), but were higher when soils collected from surface layer(0-20 cm). For soils collected from 0-20 cm, the ratios of fungi to bacteria for all GEPs samples were at the same level. So were such rations for all controls. Changes of soil microbial community in two types of GEPs fields were detected in our study, but the causes and more information still needs further study.}, }
@article {pmid15900395, year = {2005}, author = {Sun, HJ and Friedmann, EI}, title = {Communities adjust their temperature optima by shifting producer-to-consumer ratio, shown in lichens as models: II. Experimental verification.}, journal = {Microbial ecology}, volume = {49}, number = {4}, pages = {528-535}, pmid = {15900395}, issn = {0095-3628}, mesh = {Adaptation, Physiological/*physiology ; Antarctic Regions ; Ascomycota/cytology/*growth &amp; development ; Chlorophyta/*growth &amp; development ; Lichens/*physiology ; Photosynthesis/*physiology ; *Symbiosis ; *Temperature ; }, abstract = {The community adaptation hypothesis [7] predicts that lichens, simple communities of microorganisms, can adapt to a wide range of thermal regimes by regulating the ratio of primary producers (algae) and consumers (fungi): R(p/c). To test this hypothesis, we determined R(p/c) values by image analysis of cross sections of herbarium specimens of the lichen Cladina rangiferina, which is widely distributed between the Arctic and the tropics. We found that R(p/c) for C. rangiferina increases with summer temperature by more than one order of magnitude, consistent with the hypothesis. To assess the ecological significance of community adaptation (R(p/c) regulation), other adaptive mechanisms (e.g., photobiont substitution, genetic adaptation, and photosynthetic acclimation in North American Cladina spp.) were studied. Laboratory investigations with algae and fungi isolated in culture from live specimens suggested that the role of these mechanisms is relatively minor and cannot account for the high degree of lichen adaptability.}, }
@article {pmid15893390, year = {2005}, author = {Gérard, E and Guyot, F and Philippot, P and López-García, P}, title = {Fluorescence in situ hybridisation coupled to ultra small immunogold detection to identify prokaryotic cells using transmission and scanning electron microscopy.}, journal = {Journal of microbiological methods}, volume = {63}, number = {1}, pages = {20-28}, doi = {10.1016/j.mimet.2005.02.018}, pmid = {15893390}, issn = {0167-7012}, mesh = {Deinococcus/isolation &amp; purification ; Escherichia coli/isolation &amp; purification ; Fluorescence ; Image Enhancement/methods ; Immunohistochemistry ; In Situ Hybridization ; Microbiological Techniques/*methods ; Microscopy ; Microscopy, Electron/*methods ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Oligonucleotide Probes ; RNA, Ribosomal/metabolism ; Species Specificity ; }, abstract = {We describe a method based on fluorescence in situ hybridisation (FISH) that allows the identification of individual cells by electron microscopy. We hybridised universal and specific fluorescein-labelled oligonucleotide probes to the ribosomal RNA of prokaryotic microorganisms in heterogeneous cell mixtures. We then used antibodies against fluorescein coupled to sub-nanometer gold particles to label the hybridised probes in the ribosome. After increasing the diameter of the metal particles by silver enhancement, the specific gold-silver signal was visualised by optical microscopy, transmission electron microscopy (TEM) and scanning electron microscopy (SEM). It is the first time that SEM is applied to the detection of gold nanoparticles hybridised to an intracellular target, such as the ribosome. The possibility to couple phylogenetic identification by FISH to cell surface and ultrastructure observation at electron microscopy resolution has promising potential applications in microbial ecology.}, }
@article {pmid15892708, year = {2005}, author = {Gjermansen, M and Ragas, P and Sternberg, C and Molin, S and Tolker-Nielsen, T}, title = {Characterization of starvation-induced dispersion in Pseudomonas putida biofilms.}, journal = {Environmental microbiology}, volume = {7}, number = {6}, pages = {894-906}, doi = {10.1111/j.1462-2920.2005.00775.x}, pmid = {15892708}, issn = {1462-2912}, mesh = {Bacterial Proteins/genetics/*metabolism ; Biofilms/*growth &amp; development ; Carbon/*metabolism ; Gene Expression Regulation, Bacterial ; Pseudomonas putida/chemistry/*physiology ; Starvation/*metabolism ; }, abstract = {The biofilm lifestyle, where microbial cells are aggregated because of expression of cell-to-cell interconnecting compounds, is believed to be of paramount importance to microbes in the environment. Because microbes must be able to alternate between sessile and planktonic states, it is anticipated that they must be able to regulate their ability to form biofilm and to dissolve biofilm. We present an investigation of a biofilm dissolution process occurring in flow-chamber-grown Pseudomonas putida biofilms. Local starvation-induced biofilm dissolution appears to be an integrated part of P. putida biofilm development that causes characteristic structural rearrangements. Rapid global dissolution of entire P. putida biofilms was shown to occur in response to carbon starvation. Genetic analysis suggested that the adjacent P. putida genes PP0164 and PP0165 play a role in P. putida biofilm formation and dissolution. PP0164 encodes a putative periplasmic protein of previously unknown function, and PP0164 mutant bacteria are sticky, and unable to reduce their adhesiveness and dissolve their biofilm in response to carbon starvation. PP0165 encodes a putative transmembrane protein containing GGDEF and EAL domains, and PP0165 mutant bacteria are unable to increase their adhesiveness and form biofilm. We suggest that the PP0164 and PP0165 proteins are involved in the regulation of the adhesiveness of the bacteria; the PP0165 protein through c-di-GMP signalling, and the PP0164 protein as a transducer of the signal.}, }
@article {pmid15892697, year = {2005}, author = {Kennedy, N and Connolly, J and Clipson, N}, title = {Impact of lime, nitrogen and plant species on fungal community structure in grassland microcosms.}, journal = {Environmental microbiology}, volume = {7}, number = {6}, pages = {780-788}, doi = {10.1111/j.1462-2920.2005.00748.x}, pmid = {15892697}, issn = {1462-2912}, mesh = {Calcium Compounds/*pharmacology ; DNA Fingerprinting ; DNA, Fungal/analysis ; Fungi/*drug effects/genetics/physiology ; Nitrogen/*pharmacology ; Oxides/*pharmacology ; Poaceae/physiology ; RNA, Fungal/analysis/isolation &amp; purification ; Soil/analysis ; *Soil Microbiology ; }, abstract = {A microcosm-based approach was used to study impacts of plant and chemical factors on the fungal community structure of an upland acidic grassland soil. Seven plant species typical of both unimproved and fertilized grasslands were either left unamended or treated with lime, nitrogen or lime plus nitrogen. Fungal community structure was assessed by a molecular approach, fungal automated ribosomal intergenic spacer analysis (FARISA), while fungal biomass was estimated by measuring soil ergosterol content. Addition of nitrogen (with or without lime) had the largest effect, decreasing soil pH, fungal biomass and fungal ribotype number, but there was little corresponding change in fungal community structure. Although different plant species were associated with some changes in fungal biomass, this did not result in significant differences in fungal community structure between plant species. Addition of lime alone caused no changes in fungal biomass, ribotype number or community structure. Overall, fungal community structure appeared to be more significantly affected through interactions between plant species and chemical treatments, as opposed to being directly affected by changes in individual improvement factors. These results were in contrast to those found for the bacterial communities of the same soils, which changed substantially in response to chemical (lime and nitrogen) additions.}, }
@article {pmid15891938, year = {2005}, author = {Friedmann, EI and Sun, HJ}, title = {Communities adjust their temperature optima by shifting producer-to-consumer ratio, shown in lichens as models: I. Hypothesis.}, journal = {Microbial ecology}, volume = {49}, number = {4}, pages = {523-527}, pmid = {15891938}, issn = {0095-3628}, mesh = {Adaptation, Physiological/*physiology ; Antarctic Regions ; Lichens/*physiology ; Oxygen Consumption/physiology ; Photosynthesis/*physiology ; *Symbiosis ; *Temperature ; }, abstract = {An apparent paradox exists in the ecology of Antarctic lichens: their net photosynthetic temperature optimum (around 0 degrees C) lies far below the temperature optima of their constituent algae and fungi (around 20 degrees C). To address this paradox, we consider lichens as microbial communities and propose the "community adaptation" hypothesis, which posits that in each thermal regime there is an equilibrium between photosynthetic primary producers (photobionts), and heterotrophic consumers (mycobiont and parasymbiont fungi). This equilibrium, expressed as the producer/consumer ratio (R(p/c)), maximizes the fitness of the community. As respiration increases with temperature, more rapidly than does photosynthesis, R(p/c)will shift accordingly in warm habitats, resulting in a high-growth temperature optimum for the community (the lichen). This lends lichens an adaptive flexibility that enables them to function optimally at any thermal regime within the tolerance limits of the constituent organisms. The variable equilibrium of producers and consumers may have a similar role in thermal adaptation of more complex communities and ecosystems.}, }
@article {pmid15888102, year = {2005}, author = {Caglar, E and Kargul, B and Tanboga, I}, title = {Bacteriotherapy and probiotics' role on oral health.}, journal = {Oral diseases}, volume = {11}, number = {3}, pages = {131-137}, doi = {10.1111/j.1601-0825.2005.01109.x}, pmid = {15888102}, issn = {1354-523X}, mesh = {Animals ; Bifidobacterium ; Cariostatic Agents/*therapeutic use ; Cheese/microbiology ; Dental Caries/*prevention &amp; control ; Gastrointestinal Tract/microbiology ; Humans ; Lactobacillus acidophilus ; Lacticaseibacillus casei ; Milk/microbiology ; Mouth/microbiology ; Probiotics/*therapeutic use ; Yogurt/microbiology ; }, abstract = {Oral infections constitute some of the most common and costly forms of infections in humans. The concept of microbial ecological change as a mechanism for preventing dental disease is an important one while altered microbial ecology may lead to dental disease. New methods such as probiotic approaches (i.e. whole bacteria replacement therapy) to eliminate pathogenic members of the microbiota can be investigated. Bacteriotherapy is an alternative and promising way to combat infections by using harmless bacteria to displace pathogenic microorganisms. Probiotics are one of these new agents which are widely used for their therapeutic action. Limited research is available showing that some probiotic cultures may help dental improvement. Present paper focuses on possible oral benefits of probiotics.}, }
@article {pmid15887487, year = {2005}, author = {Decroos, K and Vincken, JP and Heng, L and Bakker, R and Gruppen, H and Verstraete, W}, title = {Simultaneous quantification of differently glycosylated, acetylated, and 2,3-dihydro-2,5-dihydroxy-6-methyl-4H-pyran-4-one-conjugated soyasaponins using reversed-phase high-performance liquid chromatography with evaporative light scattering detection.}, journal = {Journal of chromatography. A}, volume = {1072}, number = {2}, pages = {185-193}, doi = {10.1016/j.chroma.2005.03.021}, pmid = {15887487}, issn = {0021-9673}, mesh = {Acetylation ; Chromatography, High Pressure Liquid/*methods ; Glycosylation ; Light ; Mass Spectrometry ; Reproducibility of Results ; Saponins/*analysis ; Scattering, Radiation ; }, abstract = {A novel method utilizing high-performance liquid chromatography (HPLC) with evaporative light scattering detection (ELSD) and electrospray ionisation mass spectrometry (ESI-MS) was developed for the analysis of soyasaponins, a divers group of triterpenic compounds with one or two sugar side chains, occurring in soy. Group A soyasaponins in different degrees of acetylation, as well as group B soyasaponins in both their 2,3-dihydro-2,5-dihydroxy-6-methyl-4H-pyran-4-one (DDMP)-conjugated and non-conjugated forms could be separated and quantified using authentic soyasaponin standards, in one single run. The method was tested by the determination of the soyasaponin content and composition of eight soygerm samples of different origin. Differences in the composition and the degree of acetylation of the group A soyasaponins were observed among these samples. The group B soyasaponins showed much less variability and they were mainly present in their DDMP-conjugated form.}, }
@article {pmid15883866, year = {2005}, author = {Lee, TH and Kurata, S and Nakatsu, CH and Kamagata, Y}, title = {Molecular analysis of bacterial community based on 16S rDNA and functional genes in activated sludge enriched with 2,4-dichlorophenoxyacetic acid (2,4-D) under different cultural conditions.}, journal = {Microbial ecology}, volume = {49}, number = {1}, pages = {151-162}, pmid = {15883866}, issn = {0095-3628}, mesh = {2,4-Dichlorophenoxyacetic Acid/*metabolism ; Bacteria/*genetics/metabolism ; Base Sequence ; Biodegradation, Environmental ; *Biodiversity ; *Bioreactors ; Cluster Analysis ; Culture Media/metabolism ; DNA Primers ; Electrophoresis ; Molecular Sequence Data ; Oxygenases/genetics ; *Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/chemistry/*microbiology ; }, abstract = {Differential emergence and diversity of bacterial communities from activated sludge in response to varied cultural conditions using 2,4-dichlorophenoxyacetic acid (2,4-D) were investigated by coupling molecular analyses based on 16S rDNA with functional genes. We employed three different cultural conditions: (1) a culture sequentially fed a high concentration (300 mg/L) of 2,4-D (HS); (2) a culture continuously fed a low concentration (10 mg/L) of 2,4-D (LC); and (3) a serial batch culture in which 1% (v/v) of culture was transferred to a fresh medium containing a high concentration (300 mg/L) of 2,4-D (HB). The HS and LC bioreactors were operated for 3 months and HB was repeatedly transferred for 1 month. The 2,4-D was stably degraded under all the cultural conditions tested. PCR amplification and cloning-based analysis of functional genes using community DNAs from the cultures revealed five different oxygenase genes that may be involved in the initial step of 2,4-D degradation. All five gene-types were present in HS, while one of the five genes, type V (tftA) was not detected in LC. Quantitative PCR analysis showed that in HS, Ralstonia eutropha JMP 134 type-tfdA4 (type I) was the most abundant in copy number (2.0 +/- 0.1 x 10(7) copies/microg DNA) followed by RASC type-tfdA (type II) (1.8 +/- 1.0 x 10(6) copies/microg DNA), putative cadA-like gene (type IV) (2.6 +/- 0.8 x 10(5) copies/microg DNA), cadA gene (type III) (1.3 +/- 1.0 x 10(4) copies/microg DNA), and tftA gene (type V) (3.5 +/- 1.1 x 10(3) copies/microg DNA). Similar results were obtained in LC. In contrast, HB contained only type I and type III genes, and the type I gene was five orders of magnitude greater in copy number than the type III gene. Denaturing gel gradient electrophoresis (DGGE) analysis of PCR, amplified 16S rDNA fragments of bacterial communities in the three different cultures showed low similarity coefficient values (< or =0.35) when compared to the original activated sludge, suggesting that 2,4-D amendment caused a drastic change in the bacterial community. Particularly, HB showed only six bands (16-18 bands in the other cultures) and very low similarity coefficient values when compared to the other communities (0.10 to HS, 0.17 to LC, and 0.0 to original sludge). These results indicated that serial batch culturing (HB) resulted in a phylogenetically limited number of 2,4-D degrading bacteria carrying limited catabolic genes whereas more diverse 2,4-D degraders and catabolic genes were present in HS and LC. Therefore, the approach used for monitoring should be taken into account when one evaluates the population dynamics of contaminant-degrading bacteria at bioremediation sites.}, }
@article {pmid15883865, year = {2005}, author = {Jacobs, JL and Carroll, TL and Sundin, GW}, title = {The role of pigmentation, ultraviolet radiation tolerance, and leaf colonization strategies in the epiphytic survival of phyllosphere bacteria.}, journal = {Microbial ecology}, volume = {49}, number = {1}, pages = {104-113}, pmid = {15883865}, issn = {0095-3628}, mesh = {Actinomycetales/genetics/*physiology/*radiation effects ; Arachis/microbiology ; Dose-Response Relationship, Radiation ; Mutation/genetics ; Pigmentation/*physiology ; Plant Leaves/microbiology ; Population Dynamics ; Pseudomonas/radiation effects ; Rifampin ; Time Factors ; *Ultraviolet Rays ; }, abstract = {Phenotypic mechanisms that enhance bacterial UVR survival typically include pigmentation and DNA repair mechanisms which provide protection from UVA and UVB wavelengths, respectively. In this study, we examined the contribution of pigmentation to field survival in Clavibacter michiganensis and evaluated differences in population dynamics and leaf colonization strategies. Two C. michiganensis pigment-deficient mutants were significantly reduced in UVA radiation survival in vitro; one of these mutants also exhibited reduced field populations on peanut when compared to the wild-type strain over the course of replicate 25-day experiments. The UVR-tolerant C. michiganensis strains G7.1 and G11.1 maintained larger epiphytic field populations on peanut compared to the UVR-sensitive C. michiganensis T5.1. Epiphytic field populations of C. michiganensis utilized the strategy of solar UVR avoidance during leaf colonization resulting in increased strain survival on leaves after UVC irradiation. These results further demonstrate the importance of UVR tolerance in the ability of bacterial strains to maintain population size in the phyllosphere. However, an examination of several bacterial species from the peanut phyllosphere and a collection of environmental Pseudomonas spp. revealed that sensitivity to UVA and UVC radiation was correlated in some but not all of these bacteria. These results underscore a need to further understand the biological effects of different solar wavelength groups on microbial ecology.}, }
@article {pmid15883864, year = {2005}, author = {Brakstad, OG and Lødeng, AG}, title = {Microbial diversity during biodegradation of crude oil in seawater from the North Sea.}, journal = {Microbial ecology}, volume = {49}, number = {1}, pages = {94-103}, pmid = {15883864}, issn = {0095-3628}, mesh = {Alkanes/metabolism ; Alphaproteobacteria/genetics/*metabolism ; Biodegradation, Environmental ; *Biodiversity ; Chromatography, Gas ; Cloning, Molecular ; Cluster Analysis ; DNA Primers ; Microscopy, Fluorescence ; North Sea ; Petroleum/*metabolism/*microbiology ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Regression Analysis ; Seawater/analysis/*microbiology ; Sequence Analysis, DNA ; Time Factors ; *Water Microbiology ; }, abstract = {Microbial communities were characterized during biodegradation of immobilized oil in seawater from the Statfjord field and the German Bight in the North Sea. Seawater samples were collected at different distances from pollution sources at the two locations. A Statfjord oil was immobilized on hydrophobic synthetic Fluortex fabrics and submerged in closed flasks (no headspace) with natural or sterile seawater and incubated at 13 degrees C for 56 days. Biodegradation of immobilized n-alkanes was measured by gas chromatography, total microbes were enumerated by epifluorescence microscopy, and culturable heterotrophic and oil-degrading microorganisms were quantified by most probable number (MPN) analysis. Polymerase chain reaction (PCR) amplification of bacterial 16S rDNA in water samples was conducted during biodegradation experiments. The amplified 16S rDNA fragments were characterized by denaturing gradient gel electrophoresis (DGGE), and by sequence analysis of cloned inserts. Biodegradation rates of alkanes in seawater collected at different distances from the pollution sources did not differ significantly (P > 0.05). Concentrations of oil-degrading microorganisms showed a temporary peak after 7 days of degradation, with a subsequent decline later in the period. DGGE analysis of 16S rRNA genes showed that community diversity decreased during the first 2-3 weeks of biodegradation, with the emergence of a few dominant bands. Cloning, restriction analysis, and sequence analysis of the 16S rDNA fragments revealed >30 different phylotypes. Abundant types during biodegradation belonged to the alpha-Proteobacteria, in waters from both Statfjord and the German Bight. Cloning and sequencing studies indicated that the most abundant bacteria during biodegradation belonged to the family Rhodobacteraceae, with the closest relationship to the genera Sulfitobacter and Roseobacter.}, }
@article {pmid15883863, year = {2005}, author = {Crispim, CA and Gaylarde, CC}, title = {Cyanobacteria and biodeterioration of cultural heritage: a review.}, journal = {Microbial ecology}, volume = {49}, number = {1}, pages = {1-9}, pmid = {15883863}, issn = {0095-3628}, mesh = {*Architecture ; Biofilms/*growth &amp; development ; *Culture ; Cyanobacteria/*genetics/growth &amp; development ; Genetic Techniques ; }, abstract = {Growing concern for the preservation of cultural heritage has led to a greater interest in the biological attack on these buildings. The importance of cyanobacteria as deteriogens is emphasized and the traditional and more modern molecular methods used to detect these microorganisms are discussed. The development of molecular techniques for the rapid identification of cyanobacteria without need for culture and isolation is fundamental if our knowledge of these communities in biofilms on the surfaces of historic buildings is to be extended.}, }
@article {pmid15879253, year = {2005}, author = {Sessitsch, A and Coenye, T and Sturz, AV and Vandamme, P and Barka, EA and Salles, JF and Van Elsas, JD and Faure, D and Reiter, B and Glick, BR and Wang-Pruski, G and Nowak, J}, title = {Burkholderia phytofirmans sp. nov., a novel plant-associated bacterium with plant-beneficial properties.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {55}, number = {Pt 3}, pages = {1187-1192}, doi = {10.1099/ijs.0.63149-0}, pmid = {15879253}, issn = {1466-5026}, mesh = {4-Butyrolactone/analogs &amp; derivatives/analysis/isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; Burkholderia/*classification/cytology/*isolation &amp; purification/physiology ; Carbon-Carbon Lyases/analysis ; DNA, Bacterial/chemistry/isolation &amp; purification ; DNA, Ribosomal/chemistry/isolation &amp; purification ; Fatty Acids/analysis/isolation &amp; purification ; Flagella/physiology ; Genes, rRNA ; Gentian Violet ; Molecular Sequence Data ; Movement ; Nucleic Acid Hybridization ; Onions/*microbiology ; Phenazines ; Phylogeny ; Plant Roots/*microbiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {A Gram-negative, non-sporulating, rod-shaped, motile bacterium, with a single polar flagellum, designated strain PsJN(T), was isolated from surface-sterilized onion roots. This isolate proved to be a highly effective plant-beneficial bacterium, and was able to establish rhizosphere and endophytic populations associated with various plants. Seven related strains were recovered from Dutch soils. Based on 16S rRNA gene sequence data, strain PsJN(T) and the Dutch strains were identified as representing a member of the genus Burkholderia, as they were closely related to Burkholderia fungorum (98.7 %) and Burkholderia phenazinium (98.5 %). Analysis of whole-cell protein profiles and DNA-DNA hybridization experiments confirmed that all eight strains belonged to a single species. Strain PsJN(T) had a DNA G+C content of 61.0 mol%. Only low levels of DNA-DNA hybridization to closely related species were found. Qualitative and quantitative differences in fatty acid composition between strain PsJN(T) and closely related species were identified. The predominant fatty acids in strain PsJN(T) were 16 : 0, 18 : 1omega7c and summed feature 3 (comprising 16 : 1omega7c and/or iso-15 : 0 2-OH). Isolate PsJN(T) showed high 1-aminocyclopropane-1-carboxylate deaminase activity and is therefore able to lower the ethylene level in a developing or stressed plant. Production of the quorum-sensing signal compound 3-hydroxy-C8-homoserine lactone was detected. Based on the results of this polyphasic taxonomic study, strain PsJN(T) and the seven Dutch isolates are considered to represent a single, novel species, for which the name Burkholderia phytofirmans sp. nov. is proposed. The type strain is strain PsJN(T) (=LMG 22146(T) = CCUG 49060(T)).}, }
@article {pmid15878034, year = {2005}, author = {Collins, G and Foy, C and McHugh, S and Mahony, T and O'Flaherty, V}, title = {Anaerobic biological treatment of phenolic wastewater at 15-18 degrees C.}, journal = {Water research}, volume = {39}, number = {8}, pages = {1614-1620}, doi = {10.1016/j.watres.2005.01.017}, pmid = {15878034}, issn = {0043-1354}, mesh = {Bacteria, Anaerobic/*physiology ; Phenols/*metabolism ; Sewage/chemistry ; Temperature ; Waste Disposal, Fluid/*methods ; Water Pollutants, Chemical/metabolism ; }, abstract = {Low-temperature, or psychrophilic (<20 degrees C) anaerobic digestion has been proven feasible for the mineralisation of simple wastewaters. In this study, hybrid expanded granular sludge bed-anaerobic filter (EGSB-AF) bioreactors were used to evaluate the feasibility of psychrophilic digestion for the treatment of phenol-containing wastewater. Efficient chemical oxygen demand and phenol removal were observed at organic and phenol loading rates of 5 kg COD m(-3)d(-1) and 0.4-1.2 kg phenol m(-3)d(-1) (400-1200 mg phenol [l wastewater](-1)), respectively. There was no long-term accumulation of volatile fatty acids in the reactor systems. Methanogenic activity was developed under psychrophilic conditions but anaerobic methane-producing populations remained mesophilic throughout the trial of 415 days.}, }
@article {pmid15870372, year = {2005}, author = {Hobel, CF and Marteinsson, VT and Hreggvidsson, GO and Kristjánsson, JK}, title = {Investigation of the microbial ecology of intertidal hot springs by using diversity analysis of 16S rRNA and chitinase genes.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {5}, pages = {2771-2776}, pmid = {15870372}, issn = {0099-2240}, mesh = {Bacteria/classification/*genetics ; Base Sequence ; Chitinases/*genetics ; *Ecology ; Gene Dosage ; Genetic Variation ; Hot Springs/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Temperature ; }, abstract = {The microbial diversity of intertidal hot springs on the seashore of northwest Iceland was examined by combining directed in situ enrichments, artificial support colonization, and mat sampling. Analysis of 16S rRNA genes revealed the presence of clones related to both marine and terrestrial, thermophilic, mesophilic, and psychrophilic microorganisms scattered among 11 bacterial divisions. No archaea were found. The species composition of the enrichments was affected by the length of the hot periods experienced at low tide and was very different from those found in the biomass. A total of 36 chitinase genes were detected by molecular screening of the samples with degenerate primers for glycoside hydrolase family 18. The chitinase gene diversity was at least twofold higher in the enrichment samples than in the controls, indicating that a much higher diversity of hydrolytic genes can be accessed with this approach.}, }
@article {pmid15870322, year = {2005}, author = {Ponciano, JM and Vandecasteele, FP and Hess, TF and Forney, LJ and Crawford, RL and Joyce, P}, title = {Use of stochastic models to assess the effect of environmental factors on microbial growth.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {5}, pages = {2355-2364}, pmid = {15870322}, issn = {0099-2240}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; P20 RR 16448/RR/NCRR NIH HHS/United States ; }, mesh = {Edetic Acid/pharmacology ; Escherichia coli/*growth &amp; development ; Models, Biological ; Sodium Chloride/pharmacology ; *Stochastic Processes ; }, abstract = {We present a novel application of a stochastic ecological model to the study and analysis of microbial growth dynamics as influenced by environmental conditions in an extensive experimental data set. The model proved to be useful in bridging the gap between theoretical ideas in ecology and an applied problem in microbiology. The data consisted of recorded growth curves of Escherichia coli grown in triplicate in a base medium with all 32 possible combinations of five supplements: glucose, NH(4)Cl, HCl, EDTA, and NaCl. The potential complexity of 2(5) experimental treatments and their effects was reduced to 2(2) as just the metal chelator EDTA, the presumed osmotic pressure imposed by NaCl, and the interaction between these two factors were enough to explain the variability seen in the data. The statistical analysis showed that the positive and negative effects of the five chemical supplements and their combinations were directly translated into an increase or decrease in time required to attain stationary phase and the population size at which the stationary phase started. The stochastic ecological model proved to be useful, as it effectively explained and summarized the uncertainty seen in the recorded growth curves. Our findings have broad implications for both basic and applied research and illustrate how stochastic mathematical modeling coupled with rigorous statistical methods can be of great assistance in understanding basic processes in microbial ecology.}, }
@article {pmid15866945, year = {2005}, author = {Qiu, X and Sundin, GW and Wu, L and Zhou, J and Tiedje, JM}, title = {Comparative analysis of differentially expressed genes in Shewanella oneidensis MR-1 following exposure to UVC, UVB, and UVA radiation.}, journal = {Journal of bacteriology}, volume = {187}, number = {10}, pages = {3556-3564}, pmid = {15866945}, issn = {0021-9193}, mesh = {ATP Binding Cassette Transporter, Subfamily B/genetics ; Bacterial Toxins/genetics ; Carrier Proteins/genetics/metabolism ; DNA Damage/genetics ; DNA Repair Enzymes/*genetics/radiation effects ; Gene Expression Regulation, Bacterial/*radiation effects ; Metals, Heavy/metabolism ; Oligonucleotide Array Sequence Analysis ; Prophages/genetics ; Reactive Oxygen Species/metabolism ; Shewanella/*genetics/*radiation effects ; *Ultraviolet Rays ; }, abstract = {We previously reported that Shewanella oneidensis MR-1 is highly sensitive to UVC (254 nm), UVB (290 to 320 nm), and UVA (320 to 400 nm). Here we delineated the cellular response of MR-1 to UV radiation damage by analyzing the transcriptional profile during a 1-h recovering period after UVC, UVB, and UVA exposure at a dose that yields about a 20% survival rate. Although the SOS response was observed with all three treatments, the induction was more robust in response to short-wavelength UV radiation (UVB and UVC). Similarly, more prophage-related genes were induced by short-wavelength UV radiation. MR-1 showed an active detoxification mechanism in response to UVA, which included the induction of antioxidant enzymes and iron-sequestering proteins to scavenge reactive oxygen species. In addition, a great number of genes encoding multidrug and heavy metal efflux pumps were induced following UVA irradiation. Our data suggested that activation of prophages appears the major lethal factor in MR-1 following UVC or UVB irradiation, whereas oxidative damage contributes greatly to the high UVA sensitivity in MR-1.}, }
@article {pmid15864265, year = {2005}, author = {Madsen, EL}, title = {Identifying microorganisms responsible for ecologically significant biogeochemical processes.}, journal = {Nature reviews. Microbiology}, volume = {3}, number = {5}, pages = {439-446}, doi = {10.1038/nrmicro1151}, pmid = {15864265}, issn = {1740-1526}, mesh = {Anaerobiosis ; Bacteria/metabolism ; Bacterial Physiological Phenomena ; Earth, Planet ; Ecosystem ; Environment ; Microbiology/*trends ; }, abstract = {Throughout evolutionary time, and each day in every habitat throughout the globe, microorganisms have been responsible for maintaining the biosphere. Despite the crucial part that they play in the cycling of nutrients in habitats such as soils, sediments and waters, only rarely have the microorganisms actually responsible for key processes been identified. Obstacles that have traditionally impeded fundamental microbial ecology inquiries are now yielding to technical advancements that have important parallels in medical microbiology. The pace of new discoveries that document ecological processes and their causative agents will no doubt accelerate in the near future, and might assist in ecosystem management.}, }
@article {pmid15853975, year = {2005}, author = {Sakamoto, M and Umeda, M and Benno, Y}, title = {Molecular analysis of human oral microbiota.}, journal = {Journal of periodontal research}, volume = {40}, number = {3}, pages = {277-285}, doi = {10.1111/j.1600-0765.2005.00793.x}, pmid = {15853975}, issn = {0022-3484}, mesh = {DNA Probes ; Humans ; *Molecular Diagnostic Techniques ; Mouth/*microbiology ; Periodontal Diseases/genetics/*microbiology ; Polymerase Chain Reaction/methods ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/*analysis ; }, abstract = {OBJECTIVES: The application of molecular, mainly 16S ribosomal RNA (rRNA)-based approaches enables researchers to bypass the cultivation step and has proven its usefulness in studying the microbial composition in a variety of ecosystems, including the human oral cavity. In this mini-review, we describe the impact of these culture-independent approaches on our knowledge of the ecology of the human oral cavity and provide directions for future studies that should emphasize the role of specific strains, species and groups of microbes in periodontal disease.<br><br>MATERIALS AND METHODS: Recent findings are summarized to elucidate the relationship between periodontal disease and human oral microbiota, including as-yet-to-be-cultured organisms.<br><br>RESULTS: The real-time polymerase chain reaction (PCR) method was developed to detect and quantify periodontopathic bacteria, such as Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Tannerella forsythensis (formerly Bacteroides forsythus) and Treponema denticola. The checkerboard DNA-DNA hybridization technique allowed enumeration of large numbers of species in very large numbers of samples. 16S rRNA gene clone library analysis revealed the diversity of human oral microbiota and the existence of as-yet-to-be-cultured organisms that are presumed periodontal pathogens. In addition, terminal restriction fragment length polymorphism (T-RFLP) analysis was applied for assessment of diversity of human oral microbiota.<br><br>CONCLUSION: Culture-independent approaches are useful for studying the microbial ecology in the human oral cavity and should be useful in the future to elucidate the etiology of periodontal disease.}, }
@article {pmid15853940, year = {2005}, author = {Socransky, SS and Haffajee, AD}, title = {Periodontal microbial ecology.}, journal = {Periodontology 2000}, volume = {38}, number = {}, pages = {135-187}, doi = {10.1111/j.1600-0757.2005.00107.x}, pmid = {15853940}, issn = {0906-6713}, support = {DE 10977/DE/NIDCR NIH HHS/United States ; DE 12108/DE/NIDCR NIH HHS/United States ; DE 12861/DE/NIDCR NIH HHS/United States ; DE 13232/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacterial Physiological Phenomena ; Biofilms/growth &amp; development ; Dental Plaque/genetics/*microbiology ; *Ecosystem ; Gingival Crevicular Fluid/microbiology ; Humans ; Mouth/*microbiology ; Obesity/microbiology ; Periodontitis/*microbiology ; Saliva/microbiology ; Smoking/immunology ; }, }
@article {pmid15837240, year = {2005}, author = {He, Q and Viljanen, MK and Hinkkanen, AE and Arvilommi, H and Mertsola, J and Viander, M}, title = {No evidence of cross-reactivity of human antibodies to a 33-mer peptide of the alpha-gliadin component of gluten with Bordetella pertussis pertactin.}, journal = {Vaccine}, volume = {23}, number = {25}, pages = {3336-3340}, doi = {10.1016/j.vaccine.2005.01.078}, pmid = {15837240}, issn = {0264-410X}, mesh = {Adolescent ; Adult ; Antibodies, Bacterial/analysis/*biosynthesis ; Antibody Specificity ; Bacterial Outer Membrane Proteins/chemistry/*immunology ; Bordetella pertussis/chemistry/*immunology ; Child ; Child, Preschool ; Cross Reactions ; Enzyme-Linked Immunosorbent Assay ; Female ; Finland ; Gliadin/*immunology ; Glutens/*immunology ; Humans ; Immunoglobulin A/analysis/immunology ; Immunoglobulin G/analysis/immunology ; Male ; Middle Aged ; Virulence Factors, Bordetella/chemistry/*immunology ; Whooping Cough/immunology ; }, abstract = {A 33-mer peptide of the alpha-gliadin component of gluten was recently identified as primary initiator of the inflammatory response to gluten in coeliac disease (CD) patients. This proline-glutamine-rich peptide (PG-peptide) is highly homologous to internal sequence of pertactin, an immunogenic protein of Bordetella pertussis. Using enzyme immunoassays, we measured serum antibodies to pertactin and to PG-peptide in 167 Finnish subjects including pertussis vaccine recipients and pertussis patients, CD and non-CD patients and healthy individuals. We found no cross-reactivity between human antibodies to the two different components, suggesting that neither pertussis immunization nor disease contributes to the pathogenesis of CD.}, }
@article {pmid15836490, year = {2005}, author = {Duthoit, F and Tessier, L and Montel, MC}, title = {Diversity, dynamics and activity of bacterial populations in 'Registered Designation of Origin' Salers cheese by single-strand conformation polymorphism analysis of 16S rRNA genes.}, journal = {Journal of applied microbiology}, volume = {98}, number = {5}, pages = {1198-1208}, doi = {10.1111/j.1365-2672.2005.02575.x}, pmid = {15836490}, issn = {1364-5072}, mesh = {*Cheese ; Ecosystem ; Fermentation ; *Food Microbiology ; *Genes, Bacterial ; Genetic Variation ; Polymorphism, Single-Stranded Conformational ; RNA, Ribosomal, 16S/*analysis ; }, abstract = {AIMS: The aim of this work was to measure the dynamic global metabolic activities of the microbial community during ripening of RDO Salers cheese by using a direct molecular approach.<br><br>METHODS AND RESULTS: A culture-independent approach including PCR, reverse transcriptase PCR (RT-PCR) and single strand conformation polymorphism (SSCP) analysis of 16S rRNA genes was applied on 'Registered Designation of Origin' Salers cheese samples collected in three farms. The evolution of the global structure of the microbial community in terms of structure or global activities was assessed using ecological indices. The diversity of the global population was higher on RNA patterns than on DNA patterns, because of less dominance and greater richness. Comparison of the SSCP patterns derived from RNA and DNA analysis indicated that the dominant population was not necessarily the most active. The metabolic activities of each bacterial group changed significantly during ripening. Besides lactic acid bacteria that were dominant on both DNA and RNA patterns, the dynamics of the presence and activity of microbial groups rarely studied in the core of cheese, such as corynebacteria, or of unidentified peaks were reported.<br><br>CONCLUSIONS: By using SSCP RNA analysis, we were able to obtain information about the activity of bacterial population in cheese, which varied a lot between cheeses and was changing perpetually during ripening.<br><br>Double DNA-RNA SSCP analysis opens up future prospects in the microbial ecology of cheeses. It will have many applications for controlling of microbial community during cheese processing.}, }
@article {pmid15827833, year = {2005}, author = {Boyd, TJ and Wolgast, DM and Rivera-Duarte, I and Holm-Hansen, O and Hewes, CD and Zirino, A and Chadwick, DB}, title = {Effects of dissolved and complexed copper on heterotrophic bacterial production in San Diego bay.}, journal = {Microbial ecology}, volume = {49}, number = {3}, pages = {353-366}, pmid = {15827833}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development ; California ; Copper/*chemistry ; Population Dynamics ; Seawater/chemistry ; Solubility ; *Water Microbiology ; }, abstract = {Bacterial abundance and production, free (uncomplexed) copper ion concentration, total dissolved copper concentration, dissolved organic carbon (DOC), total suspended solids (TSS), and chlorophyll a were measured over the course of 1 year in a series of 27 sample "Boxes" established within San Diego Bay. Water was collected through a trace metal-clean system so that each Box's sample was a composite of all the surface water in that Box. Bacterial production, chlorophyll a, TSS, DOC, and dissolved copper all generally increased from Box 1 at the mouth of the Bay to Box 27 in the South or back Bay. Free copper ion concentration generally decreased from Box 1 to Box 27 presumably due to increasing complexation capacity within natural waters. Based on correlations between TSS, chlorophyll a, bacterial production or DOC and the ratio of dissolved to free Cu ion, both DOC and particulate (bacteria and algae) fractions were potentially responsible for copper complexation, each at different times of the year. CuCl2 was added to bacterial production assays from 0 to 10 microg L(-1) to assess acute copper toxicity to the natural microbial assemblage. Interestingly, copper toxicity appeared to increase with decreases in free copper from the mouth of the Bay to the back Bay. This contrasts the free-ion activity model in which higher complexation capacity should afford greater copper protection. When cell-specific growth rates were calculated, faster growing bacteria (i.e. toward the back Bay) appeared to be more susceptible to free copper toxicity. The protecting effect of natural dissolved organic material (DOM) concentrated by tangential flow ultrafiltration (>1 kDa), illite and kaolinite minerals, and glutathione (a metal chelator excreted by algae under copper stress) was assessed in bacterial production assays. Only DOM concentrate offered any significant protection to bacterial production under increased copper concentrations. Although the potential copper protecting agents were allowed to interact with added copper before natural bacteria were added to production assays, there may be a temporal dose-response relationship that accounts for higher toxicity in short production assays. Regardless, it appears that effective natural complexation of copper in the back portions of San Diego Bay limits exposure of native bacterial assemblages to free copper ion, resulting in higher bacterial production.}, }
@article {pmid15825640, year = {2003}, author = {Hentschel, U and Fieseler, L and Wehrl, M and Gernert, C and Steinert, M and Hacker, J and Horn, M}, title = {Microbial diversity of marine sponges.}, journal = {Progress in molecular and subcellular biology}, volume = {37}, number = {}, pages = {59-88}, doi = {10.1007/978-3-642-55519-0_3}, pmid = {15825640}, issn = {0079-6484}, mesh = {Animals ; Bacteria/*metabolism ; Biotechnology/methods ; Cell Culture Techniques ; Ecology ; Gene Library ; Genetic Techniques ; In Situ Hybridization, Fluorescence ; Models, Biological ; Models, Chemical ; Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S/metabolism ; }, abstract = {The recent application of molecular microbial ecology tools to sponge-microbe associations has revealed a glimpse into the biodiversity of these microbial communities, that is considered just 'the tip of the iceberg'. This chapter provides an overview over these new findings with regard to identity, diversity and distribution patterns of sponge-associated microbial consortia. The sponges Aplysina aerophoba (Verongida), Rhopaloeides odorabile (Dicytoceratida) and Theonella swinhoei (Lithistida) were chosen as model systems for this review because they have been subject to both, cultivation-dependent and cultivation-independent approaches. A discussion of the microbial assemblages of Halichondriapanicea is presented in the accompanying chapter by Imhoff and Stöhr. Considering that a large fraction of sponge-associated microbes is not yet amenable to cultivation, an emphasis has been placed on the techniques centering around the 16S rRNA gene. A section has been included that covers the potential of sponge microbial communities for drug discovery. Finally, a 'sponge-microbe interaction model' is presented that summarizes our current understanding of the processes that might have shaped the community structure of the microbial assemblages within sponges.}, }
@article {pmid15819923, year = {2005}, author = {van Aarle, IM and Cavagnaro, TR and Smith, SE and Smith, FA and Dickson, S}, title = {Metabolic activity of Glomus intraradices in Arum- and Paris-type arbuscular mycorrhizal colonization.}, journal = {The New phytologist}, volume = {166}, number = {2}, pages = {611-618}, doi = {10.1111/j.1469-8137.2005.01340.x}, pmid = {15819923}, issn = {0028-646X}, mesh = {Acid Phosphatase/metabolism ; Alkaline Phosphatase/metabolism ; Allium/*microbiology ; Magnoliopsida/*microbiology ; Mycorrhizae/classification/*enzymology ; Plant Roots/microbiology ; Succinate Dehydrogenase/metabolism ; }, abstract = {Colonization of two plant species by Glomus intraradices was studied to investigate the two morphological types (Arum and Paris), their symbiotic interfaces and metabolic activities. Root pieces and sections were stained to observe the colonization and metabolic activity of all mycorrhizal structures. There were no growth responses observed in the plants caused by mycorrhizal symbiosis. The two morphological types had a similar percentage of root colonized, but the Arum-type had higher metabolic activity. Most of the mycorrhizal structures (88%) showed succinate dehydrogenase activity; about half showed acid phosphatase activity; and a small percentage showed alkaline phosphatase activity. Phosphatase activity was highest in arbuscules and low in intercellular hyphae in the Arum-type colonization. In the Paris-type, hyphal coils and arbusculate coils showed a similar intermediate percentage of phosphatase activity. We conclude that acid phosphatase is more important than alkaline phosphatase in both colonization types. We discuss the possibility that, whereas arbuscules in Arum-type are the main site for phosphorus release to the host plant, both the hyphal and arbusculate coils may be involved in the Paris-type.}, }
@article {pmid15819848, year = {2005}, author = {Mertens, B and Boon, N and Verstraete, W}, title = {Stereospecific effect of hexachlorocyclohexane on activity and structure of soil methanotrophic communities.}, journal = {Environmental microbiology}, volume = {7}, number = {5}, pages = {660-669}, doi = {10.1111/j.1462-2920.2005.00735.x}, pmid = {15819848}, issn = {1462-2912}, mesh = {DNA, Bacterial/chemistry/genetics ; Electrophoresis ; Euryarchaeota/*drug effects/*metabolism ; Genetic Variation ; Hexachlorocyclohexane/chemistry/*pharmacology ; Methane/*metabolism ; Oxidation-Reduction ; Polymerase Chain Reaction ; *Soil Microbiology ; Stereoisomerism ; }, abstract = {In the past decades, large amounts of non-insecticidal hexachlorocyclohexane (HCH) isomers (alpha-, beta-, delta- and epsilon-HCH) have been dumped as side-products of the insecticide gamma-HCH (lindane). This study investigates the effect of HCH isomers on methane oxidation, an important soil function performed by methanotrophic bacteria. Both activity and structure of the methanotrophic community were assessed, using methane oxidation assays and PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) respectively. Methane oxidation assays with historically polluted soils revealed that on the long-term methane oxidation was inhibited by HCH pollution. PCR-DGGE and diversity analysis based on Lorenz curves showed that the type I methanotrophic community was less evenly distributed in historically HCH-polluted soils compared with less polluted reference soils. Short-term experiments with methane-enriched consortia further demonstrated that only gamma- and delta-isomers inhibited methane oxidation. Type I methanotrophs of methane-enriched microbial consortia that received gamma- or delta-HCH evolved towards higher species richness. Apparently, for historically HCH-polluted soils, a narrow community remained after long-term exposure while in case of short-term exposures, methane-enriched consortia were converted into less active, but richer communities when they were stressed by the presence of gamma- or delta-HCH. This work demonstrates the importance of incorporating all isomers and possible other side-products in risk assessment studies of persistent organic pollutants and the use of structural analysis of type I methanotrophic communities as evaluating tool.}, }
@article {pmid15818476, year = {2005}, author = {Vervaeren, H and De Wilde, K and Matthys, J and Boon, N and Raskin, L and Verstraete, W}, title = {Quantification of an Eikelboom type 021N bulking event with fluorescence in situ hybridization and real-time PCR.}, journal = {Applied microbiology and biotechnology}, volume = {68}, number = {5}, pages = {695-704}, doi = {10.1007/s00253-005-1963-9}, pmid = {15818476}, issn = {0175-7598}, mesh = {Gammaproteobacteria/classification/genetics/*physiology ; In Situ Hybridization, Fluorescence ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/analysis/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; *Waste Disposal, Fluid ; }, abstract = {Primers targeting 16S rRNA genes were designed to detect and quantify Eikelboom type 021N organisms by real-time PCR. Eikelboom type 021N filamentous bulking was induced in a laboratory-scale sequencing batch reactor and the evolution of Eikelboom type 021N 16S rRNA and 16S rRNA genes was monitored. A significant correlation was found between the sludge volume index and the amount of these filamentous organisms present in the sludge (r (2)=94.6%, n=10, P<0.01), as measured by real-time PCR. The amount of Eikelboom type 021N 16S rRNA genes increased by a factor of 21 during the experiment, while the 16S rRNA increased by a factor of 33. Moreover, Eikelboom type 021N 16S rRNA increased with increased feeding frequency. It was observed that the RNA:DNA ratio peaked before the sludge volume index increased. In parallel, a fluorescence in situ hybridization study indicated a factor of four increase in the length of Eikelboom type 021N filaments, due to a factor of two increase in both length and number of Eikelboom type 021N filaments. Further, an increase in the fraction of filaments extending outside the activated sludge flocs was observed (19-55%). Monitoring of 16S rRNA genes and 16S rRNA of Eikelboom type 021N was shown to be valuable in evaluating activated sludge settling characteristics; and measuring RNA:DNA ratios may be used as an early warning tool for sludge bulking.}, }
@article {pmid15816925, year = {2005}, author = {Wagner, M}, title = {Crystal ball. The community level: physiology and interactions of prokaryotes in the wilderness.}, journal = {Environmental microbiology}, volume = {7}, number = {4}, pages = {483-485}, doi = {10.1111/j.1462-2920.2005.803_13.x}, pmid = {15816925}, issn = {1462-2912}, mesh = {Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Biodiversity ; Biofilms ; Ecology ; *Ecosystem ; Gene Expression Regulation, Bacterial ; Oligonucleotide Array Sequence Analysis ; Proteome/analysis ; }, }
@article {pmid15815019, year = {2005}, author = {Couble, A and Rodríguez-Nava, V and de Montclos, MP and Boiron, P and Laurent, F}, title = {Direct detection of Nocardia spp. in clinical samples by a rapid molecular method.}, journal = {Journal of clinical microbiology}, volume = {43}, number = {4}, pages = {1921-1924}, pmid = {15815019}, issn = {0095-1137}, mesh = {Biopsy ; Bronchoalveolar Lavage Fluid/microbiology ; Culture Media ; DNA, Bacterial/*analysis ; DNA, Ribosomal/analysis ; Humans ; Nocardia/genetics/*isolation &amp; purification ; Nocardia Infections/*diagnosis/microbiology ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/*genetics ; Sensitivity and Specificity ; Skin/microbiology ; Sputum/microbiology ; Suppuration/microbiology ; Time Factors ; }, abstract = {We developed a 16S PCR-based assay for the rapid detection of Nocardia spp. directly from human clinical samples. The applicability of the assay was confirmed by using 18 samples from patients with nocardiosis as diagnosed by conventional cultures and 20 clinical samples from patients with confirmed tuberculosis used as negative controls.}, }
@article {pmid15812029, year = {2005}, author = {Rantsiou, K and Urso, R and Iacumin, L and Cantoni, C and Cattaneo, P and Comi, G and Cocolin, L}, title = {Culture-dependent and -independent methods to investigate the microbial ecology of Italian fermented sausages.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {4}, pages = {1977-1986}, pmid = {15812029}, issn = {0099-2240}, mesh = {Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Colony Count, Microbial ; Culture Media ; DNA, Bacterial/analysis ; DNA, Fungal/analysis ; *Ecosystem ; Electrophoresis/methods ; Fermentation ; Italy ; Meat Products/*microbiology ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Yeasts/classification/genetics/growth &amp; development/*isolation &amp; purification ; }, abstract = {In this study, the microbial ecology of three naturally fermented sausages produced in northeast Italy was studied by culture-dependent and -independent methods. By plating analysis, the predominance of lactic acid bacteria populations was pointed out, as well as the importance of coagulase-negative cocci. Also in the case of one fermentation, the fecal enterocci reached significant counts, highlighting their contribution to the particular transformation process. Yeast counts were higher than the detection limit (> 100 CFU/g) in only one fermented sausage. Analysis of the denaturing gradient gel electrophoresis (DGGE) patterns and sequencing of the bands allowed profiling of the microbial populations present in the sausages during fermentation. The bacterial ecology was mainly characterized by the stable presence of Lactobacillus curvatus and Lactobacillus sakei, but Lactobacillus paracasei was also repeatedly detected. An important piece of evidence was the presence of Lactococcus garvieae, which clearly contributed in two fermentations. Several species of Staphylococcus were also detected. Regarding other bacterial groups, Bacillus sp., Ruminococcus sp., and Macrococcus caseolyticus were also identified at the beginning of the transformations. In addition, yeast species belonging to Debaryomyces hansenii, several Candida species, and Willopsis saturnus were observed in the DGGE gels. Finally, cluster analysis of the bacterial and yeast DGGE profiles highlighted the uniqueness of the fermentation processes studied.}, }
@article {pmid15812016, year = {2005}, author = {Graber, JR and Breznak, JA}, title = {Folate cross-feeding supports symbiotic homoacetogenic spirochetes.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {4}, pages = {1883-1889}, pmid = {15812016}, issn = {0099-2240}, mesh = {Animals ; DNA, Bacterial/analysis ; Digestive System/microbiology ; Genes, rRNA ; Isoptera/*microbiology ; Lactococcus lactis/classification/genetics/growth &amp; development/metabolism ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Serratia/classification/genetics/growth &amp; development/metabolism ; *Symbiosis ; Tetrahydrofolates/*metabolism ; Treponema/*growth &amp; development/metabolism ; }, abstract = {Treponema primitia, an H2-consuming CO2-reducing homoacetogenic spirochete in termite hindguts, requires an exogenous source of folate for growth. Tetrahydrofolate (THF) acts as a C1 carrier in CO2-reductive acetogenesis, a microbially mediated process important to the carbon and energy requirements of termites. To examine the hypothesis that other termite gut microbes probably supply some form of folate to T. primitia in situ, we used a bioassay to screen for and isolate folate-secreting bacteria from hindguts of Zootermopsis angusticollis, which is the host of T. primitia. Based on morphology, physiology, and 16S rRNA gene sequences, the major folate secretors were identified as strains of Lactococcus lactis and Serratia grimesii. During growth, these isolates secreted 5-formyl-THF at levels up to 146 ng/ml, and their cell-free culture fluids satisfied the folate requirement of T. primitia strains in vitro. Analysis of Z. angusticollis hindgut fluid revealed that 5-formyl-THF was the only detectable folate compound and occurred at an in situ concentration (1.3 mug/ml) which was more than sufficient to support the growth of T. primitia. These results imply that cross-feeding of 5-formyl-THF by other community members is important for growth of symbiotic hindgut spirochetes and thus termite nutrition and survival.}, }
@article {pmid15803311, year = {2005}, author = {Malhautier, L and Khammar, N and Bayle, S and Fanlo, JL}, title = {Biofiltration of volatile organic compounds.}, journal = {Applied microbiology and biotechnology}, volume = {68}, number = {1}, pages = {16-22}, doi = {10.1007/s00253-005-1960-z}, pmid = {15803311}, issn = {0175-7598}, mesh = {Aerobiosis ; *Air Pollutants/metabolism ; Air Pollution/*prevention &amp; control ; Anaerobiosis ; Biodegradation, Environmental ; *Bioreactors ; Volatilization ; }, abstract = {The removal of volatile organic compounds (VOCs) from contaminated airstreams has become a major air pollution concern. Improvement of the biofiltration process commonly used for the removal of odorous compounds has led to a better control of key parameters, enabling the application of biofiltration to be extended also to the removal of VOCs. Moreover, biofiltration, which is based on the ability of micro-organisms to degrade a large variety of compounds, proves to be economical and environmentally viable. In a biofilter, the waste gas is forced to rise through a layer of packed porous material. Thus, pollutants contained in the gaseous effluent are oxidised or converted into biomass by the action of microorganisms previously fixed on the packing material. The biofiltration process is then based on two principal phenomena: (1) transfer of contaminants from the air to the water phase or support medium, (2) bioconversion of pollutants to biomass, metabolic end-products, or carbon dioxide and water. The diversity of biofiltration mechanisms and their interaction with the microflora mean that the biofilter is defined as a complex and structured ecosystem. As a result, in addition to operating conditions, research into the microbial ecology of biofilters is required in order better to optimise the management of such biological treatment systems.}, }
@article {pmid15780708, year = {2005}, author = {Liu, WT and Zhu, L}, title = {Environmental microbiology-on-a-chip and its future impacts.}, journal = {Trends in biotechnology}, volume = {23}, number = {4}, pages = {174-179}, doi = {10.1016/j.tibtech.2005.02.004}, pmid = {15780708}, issn = {0167-7799}, mesh = {*Environmental Microbiology ; Environmental Monitoring/instrumentation/*methods ; Lab-On-A-Chip Devices ; Microchip Analytical Procedures/methods/*trends ; }, abstract = {Rapid advances in microfabrication, DNA and protein microarray and microfluidic technologies have enabled the development of fully-integrated, miniaturized systems. These so called 'laboratory-on-a-chip' (LOC) devices perform sample preparation (i.e. concentration, separation and purification) together with biochemical reactions and detection steps in a simple and automated manner. We believe LOC technology for environmental microbiology studies will have immediate impacts on microbial monitoring by achieving detection and identification within minutes at the single-cell level, and on microbial ecology by deepening the understanding of microbial community structure and diversity and correlating these with niche-specific functions within a micro space. In the long run, significant impacts are anticipated on environmental metagenomics and proteomics.}, }
@article {pmid15767017, year = {2005}, author = {Pang, X and Ding, D and Wei, G and Zhang, M and Wang, L and Zhao, L}, title = {Molecular profiling of Bacteroides spp. in human feces by PCR-temperature gradient gel electrophoresis.}, journal = {Journal of microbiological methods}, volume = {61}, number = {3}, pages = {413-417}, doi = {10.1016/j.mimet.2004.12.012}, pmid = {15767017}, issn = {0167-7012}, mesh = {Bacterial Typing Techniques ; Bacteroides/classification/*genetics/*isolation &amp; purification ; Base Sequence ; Child ; DNA, Bacterial/genetics/isolation &amp; purification ; Electrophoresis, Polyacrylamide Gel/methods ; Feces/*microbiology ; Humans ; Male ; Polymerase Chain Reaction/*methods ; Species Specificity ; }, abstract = {A group-specific PCR-based temperature gradient gel electrophoresis (TGGE) method was developed to study the population composition of genus Bacteroides in human gut. Highly reproducible and well-separated bands in TGGE fingerprints of ten unrelated human fecal samples showed complex and host-specific Bacteroides species composition. Dynamic monitoring over 22 months of samples from one healthy 10-year-old boy indicated a relatively stable population profile of Bacteroides. The species identity of each band in TGGE gel of this boy was also resolved via comigration analysis of sequenced inserts in a Bacteroides group-specific clone library. This work provides a rapid and effective technique for analyzing the species composition of Bacteroides in human gut.}, }
@article {pmid15758225, year = {2005}, author = {Ahrén, D and Tholander, M and Fekete, C and Rajashekar, B and Friman, E and Johansson, T and Tunlid, A}, title = {Comparison of gene expression in trap cells and vegetative hyphae of the nematophagous fungus Monacrosporium haptotylum.}, journal = {Microbiology (Reading, England)}, volume = {151}, number = {Pt 3}, pages = {789-803}, doi = {10.1099/mic.0.27485-0}, pmid = {15758225}, issn = {1350-0872}, mesh = {Animals ; Ascomycota/genetics/growth &amp; development/metabolism/*ultrastructure ; Caenorhabditis elegans/*microbiology ; Expressed Sequence Tags ; Fungal Proteins/genetics/*metabolism ; *Gene Expression Regulation, Fungal ; Hyphae/genetics/growth &amp; development/*metabolism ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; }, abstract = {Nematode-trapping fungi enter the parasitic stage by developing specific morphological structures called traps. The global patterns of gene expression in traps and mycelium of the fungus Monacrosporium haptotylum were compared. The trap of this fungus is a unicellular spherical structure called the knob, which develops on the apex of a hyphal branch. RNA was isolated from knobs and mycelium and hybridized to a cDNA array containing probes of 2822 EST clones of M. haptotylum. Despite the fact that the knobs and mycelium were grown in the same medium, there were substantial differences in the patterns of genes expressed in the two cell types. In total, 23.3 % (657 of 2822) of the putative genes were differentially expressed in knobs versus mycelium. Several of these genes displayed sequence similarities to genes known to be involved in regulating morphogenesis and cell polarity in fungi. Among them were several putative homologues for small GTPases, such as rho1, rac1 and ras1, and a rho GDP dissociation inhibitor (rdi1). Several homologues to genes involved in stress response, protein synthesis and protein degradation, transcription, and carbon metabolism were also differentially expressed. In the last category, a glycogen phosphorylase (gph1) gene homologue, one of the most upregulated genes in the knobs as compared to mycelium, was characterized. A number of the genes that were differentially expressed in trap cells are also known to be regulated during the development of infection structures in plant-pathogenic fungi. Among them, a gas1 (mas3) gene homologue (designated gks1), which is specifically expressed in appressoria of the rice blast fungus, was characterized.}, }
@article {pmid15746340, year = {2005}, author = {Loy, A and Schulz, C and Lücker, S and Schöpfer-Wendels, A and Stoecker, K and Baranyi, C and Lehner, A and Wagner, M}, title = {16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order "Rhodocyclales".}, journal = {Applied and environmental microbiology}, volume = {71}, number = {3}, pages = {1373-1386}, pmid = {15746340}, issn = {0099-2240}, mesh = {Base Sequence ; Betaproteobacteria/classification/*genetics/*isolation &amp; purification ; DNA Probes/genetics ; DNA, Bacterial/genetics ; *Environmental Microbiology ; Environmental Monitoring ; Genes, Bacterial ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis/*methods/statistics &amp; numerical data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sensitivity and Specificity ; Sewage/microbiology ; }, abstract = {For simultaneous identification of members of the betaproteobacterial order "Rhodocyclales" in environmental samples, a 16S rRNA gene-targeted oligonucleotide microarray (RHC-PhyloChip) consisting of 79 probes was developed. Probe design was based on phylogenetic analysis of available 16S rRNA sequences from all cultured and as yet uncultured members of the "Rhodocyclales." The multiple nested probe set was evaluated for microarray hybridization with 16S rRNA gene PCR amplicons from 29 reference organisms. Subsequently, the RHC-PhyloChip was successfully used for cultivation-independent "Rhodocyclales" diversity analysis in activated sludge from an industrial wastewater treatment plant. The implementation of a newly designed "Rhodocyclales"-selective PCR amplification system prior to microarray hybridization greatly enhanced the sensitivity of the RHC-PhyloChip and thus enabled the detection of "Rhodocyclales" populations with relative abundances of less than 1% of all bacteria (as determined by fluorescence in situ hybridization) in the activated sludge. The presence of as yet uncultured Zoogloea-, Ferribacterium/Dechloromonas-, and Sterolibacterium-related bacteria in the industrial activated sludge, as indicated by the RHC-PhyloChip analysis, was confirmed by retrieval of their 16S rRNA gene sequences and subsequent phylogenetic analysis, demonstrating the suitability of the RHC-PhyloChip as a novel monitoring tool for environmental microbiology.}, }
@article {pmid15746329, year = {2005}, author = {Bollmann, A and Schmidt, I and Saunders, AM and Nicolaisen, MH}, title = {Influence of starvation on potential ammonia-oxidizing activity and amoA mRNA levels of Nitrosospira briensis.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {3}, pages = {1276-1282}, pmid = {15746329}, issn = {0099-2240}, mesh = {Acetylene/pharmacology ; Ammonia/*metabolism ; Base Sequence ; Culture Media ; DNA, Bacterial/genetics ; Enzyme Inhibitors/pharmacology ; Genes, Bacterial ; Kinetics ; Nitrosomonadaceae/drug effects/*genetics/*metabolism ; Oxidation-Reduction ; Oxidoreductases/antagonists &amp; inhibitors/genetics/metabolism ; RNA, Bacterial/*genetics/*metabolism ; RNA, Messenger/*genetics/*metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {The effect of short-term ammonia starvation on Nitrosospira briensis was investigated. The ammonia-oxidizing activity was determined in a concentrated cell suspension with a NOx biosensor. The apparent half-saturation constant [Km(app)] value of the NH3 oxidation of N. briensis was 3 microM NH3 for cultures grown both in continuous and batch cultures as determined by a NOx biosensor. Cells grown on the wall of the vessel had a lower Km(app) value of 1.8 microM NH3. Nonstarving cultures of N. briensis showed potential ammonia-oxidizing activities of between 200 to 250 microM N h(-1), and this activity decreased only slowly during starvation up to 10 days. Within 10 min after the addition of fresh NH4+, 100% activity was regained. Parallel with activity measurements, amoA mRNA and 16S rRNA were investigated. No changes were observed in the 16S rRNA, but a relative decrease of amoA mRNA was observed during the starvation period. During resuscitation, an increase in amoA mRNA expression was detected simultaneously. The patterns of the soluble protein fraction of a 2-week-starved culture of N. briensis showed only small differences in comparison to a nonstarved control. From these results we conclude that N. briensis cells remain in a state allowing fast recovery of ammonia-oxidizing activity after addition of NH4+ to a starved culture. Maintaining cells in this kind of active state could be the survival strategy of ammonia-oxidizing bacteria in nature under fluctuating NH4+ availability.}, }
@article {pmid15746318, year = {2005}, author = {Ramette, A and LiPuma, JJ and Tiedje, JM}, title = {Species abundance and diversity of Burkholderia cepacia complex in the environment.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {3}, pages = {1193-1201}, pmid = {15746318}, issn = {0099-2240}, mesh = {Base Sequence ; Burkholderia cepacia complex/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Ecosystem ; *Environmental Microbiology ; Genes, Bacterial ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/methods/statistics &amp; numerical data ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rec A Recombinases/genetics ; Sensitivity and Specificity ; Species Specificity ; Zea mays/microbiology ; }, abstract = {Despite considerable interest in studying Burkholderia cepacia complex in the environment, we still do not have efficient methods to detect, isolate, and screen large numbers of B. cepacia isolates. To better describe the ecology and diversity of B. cepacia complex, a colony hybridization assay was developed to detect specifically all species of the complex based on polymorphism of the variable V3 region of the 16S rRNA sequence. The sensitivity of the assay was dramatically enhanced by using a probe consisting of three repeats of a B. cepacia complex-specific probe, each separated by a phosphoramidite spacer. In addition, a duplex PCR targeting B. cepacia complex-specific recA and 16S rRNA sequences was developed to enable a fast and reliable diagnostic assay for members of the complex. When applied to maize rhizosphere samples, colony hybridization results were in good agreement with those of most-probable-number duplex PCR, both indicating a >100-fold fluctuation of abundance between individual plants. Using restriction analysis of recA for a total of 285 confirmed isolates of the B. cepacia complex, up to seven B. cepacia complex species were identified; however, their diversity and abundance were not evenly distributed among individual plants, and several allelic variants were commonly found from the same rhizosphere sample. These results indicate that not only complex communities of B. cepacia complex species and closely related strains of the same species may coexist at high population levels but also species composition and abundance may dramatically vary between individual plants.}, }
@article {pmid15736879, year = {2005}, author = {Roels, J and Vanhaecke, F and Verstraete, W}, title = {Combustive approach for measuring total volatile phosphorus content in landfill gas.}, journal = {Environmental monitoring and assessment}, volume = {101}, number = {1-3}, pages = {103-116}, pmid = {15736879}, issn = {0167-6369}, mesh = {Chromatography, Gas ; Environmental Monitoring/methods ; Gases ; Phosphorus/*analysis ; *Refuse Disposal ; Volatilization ; }, abstract = {A technique was developed to measure the total gaseous phosphorus content in biogas. The amount of air needed for a neutral to oxidising flame was mixed with the biogas. The gas mixture was burnt in a closed quartz burner and the combustion gasses were bubbled through a nitric acid solution. The phosphate content in the bubbling liquid was determined with sector field ICP-MS. The technique was validated in the lab with phosphine. Afterwards the set-up was installed on a landfill. The total gaseous phosphorus content in the landfill gas, measured with the combustive technique, ranged from 1.65 to 4.44 microg P/m3. At the same time the phosphine concentration in the landfill gas was determined gas chromatographically (GC). The phosphine (PH3) content measured with GC ranged from 7.6 to 16.7 microg PH3-P/m3. Since the phosphine-P content (GC) was consistently higher than the total gaseous phosphorus content (burner/ICP-MS), the hypothesised presence of highly toxic gaseous phosphorus compounds other than phosphine could not be demonstrated.}, }
@article {pmid15735941, year = {2005}, author = {Third, KA and Paxman, J and Schmid, M and Strous, M and Jetten, MS and Cord-Ruwisch, R}, title = {Enrichment of anammox from activated sludge and its application in the CANON process.}, journal = {Microbial ecology}, volume = {49}, number = {2}, pages = {236-244}, pmid = {15735941}, issn = {0095-3628}, mesh = {Aerobiosis ; Ammonia/*metabolism ; Anaerobiosis ; Bacteria, Anaerobic/*metabolism ; Bioreactors ; Nitrogen/*metabolism ; Oxidation-Reduction ; *Sewage ; Time Factors ; }, abstract = {A microbial culture capable of actively oxidizing ammonium to dinitrogen gas in the absence of oxygen, using nitrite as the electron acceptor, was enriched from local activated sludge (Western Australia) in <14 weeks. The maximum anaerobic ammonium oxidation (i.e., anammox) activity achieved by the anaerobic culture was 0.26 mmol NH (4) (+) (g biomass)(-1) h(-1) (0.58 kg total-N m(-3) day(-1)). Qualitative FISH analysis (fluorescence in situ hybridization) confirmed the phylogenetic position of the enriched microorganism as belonging to the order Planctomycetales, in which all currently identified anammox strains fall. Preliminary FISH analysis suggests the anammox strain belongs to the same phylogenetic group as the Candidatus 'Brocadia anammoxidans' strain discovered in the Netherlands. However, there are quite a few differences in the target sites for the more specific probes of these organisms and it is therefore likely to represent a new species of anammox bacteria. A small amount of aerobic ammonium-oxidizing biomass was inoculated into the anammox reactor (10% v/v) to initiate completely autotrophic nitrogen removal over nitrite (the CANON process) in chemostat culture. The culture was always under oxygen limitation and no organic carbon was added. The CANON reactor was operated as an intermittently aerated system with 20 min aerobiosis and 30 min anaerobiosis, during which aerobic and anaerobic ammonium oxidation were performed in sequential fashion, respectively. Anammox was not inhibited by repeated intermittent exposure to oxygen, allowing sustained, completely autotrophic ammonium removal (0.08 kg N m(-3) day(-1)) for an extended period of time.}, }
@article {pmid15735940, year = {2005}, author = {Goregues, CM and Michotey, VD and Bonin, PC}, title = {Molecular, biochemical, and physiological approaches for understanding the ecology of denitrification.}, journal = {Microbial ecology}, volume = {49}, number = {2}, pages = {198-208}, pmid = {15735940}, issn = {0095-3628}, mesh = {Bacteria/*genetics/*metabolism ; *Biodiversity ; Ecosystem ; Genes, Bacterial ; Genetic Variation ; Nitrogen/*metabolism ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {One of the major challenges in microbial ecology for the future is to establish links between structural and functional biodiversity. This is particularly difficult when one is interested in a phylogenetically diversified function such as denitrification. The data banks are very rich in functional gene sequences (nirS in this study), but most of them were obtained from not yet cultivated bacteria, and thus must be supplemented by sequences of organisms from the environment for which we could associate a taxonomic position and physiological characteristics. Combined analysis including molecular (16S-rRNA or nirS genes), physiological, and biochemical approaches was carried out on a bacterial set of 89 strains isolated from marine sediment. The denaturing gradient gel electrophoresis (DGGE) technique was successfully applied on unclamped polymerase chain reaction (PCR) products of nirS genes to compare the picture of the biodiversity obtained with 16S rRNA and nirS genes. The diversity of nirS genes and denitrifier characteristics were found within several of the 16S rDNA phylotypes. In contrast, the nirS phylotypes were no diverse both with respect to 16S rDNA and to physiology and biochemistry of denitrification. Sequences of the nirS PCR products were very close to marine environmental clones and were analyzed within the same phylogenetic tree.}, }
@article {pmid15722151, year = {2005}, author = {McNamara, CJ and Perry, TD and Bearce, K and Hernandez-Duque, G and Mitchell, R}, title = {Measurement of limestone biodeterioration using the Ca2+ binding fluorochrome Rhod-5N.}, journal = {Journal of microbiological methods}, volume = {61}, number = {2}, pages = {245-250}, doi = {10.1016/j.mimet.2004.12.004}, pmid = {15722151}, issn = {0167-7012}, mesh = {Biodegradation, Environmental ; Calcium/*metabolism ; Calcium Carbonate/*chemistry ; Fluorescent Dyes/*chemistry ; Gram-Positive Endospore-Forming Rods/*metabolism ; Spectrometry, Fluorescence ; }, abstract = {Limestone and marble have been used extensively in the construction of modern and historic buildings. Microbial colonization and growth on these stone structures is common. Microbial deterioration of stone has been assessed by measuring Ca2+ released from the stone, using ion selective electrodes and titration with EDTA. In this study, the calcium binding fluorochrome Rhod-5N was used to measure Ca2+ released from limestone by endolithic bacteria as an indicator of biodeterioration. In a 17 d flask experiment, Ca2+ released by endolithic bacteria was twice that of uninoculated controls. Rhod-5N is a rapid and accurate method for measuring microbial biodeterioration of stone.}, }
@article {pmid15720671, year = {2005}, author = {Nilsson, LO and Giesler, R and Bååth, E and Wallander, H}, title = {Growth and biomass of mycorrhizal mycelia in coniferous forests along short natural nutrient gradients.}, journal = {The New phytologist}, volume = {165}, number = {2}, pages = {613-622}, doi = {10.1111/j.1469-8137.2004.01223.x}, pmid = {15720671}, issn = {0028-646X}, mesh = {Biomass ; Fatty Acids/chemistry/physiology ; Mycelium/growth &amp; development/*physiology ; Mycorrhizae/growth &amp; development/*physiology ; Soil/analysis ; Soil Microbiology ; *Trees ; }, abstract = {Total fungal biomass, the biomass of ectomycorrhizal and ericoid mycorrhizal (EM + ErM), and arbuscular mycorrhizal (AM) fungi, as well as the production of EM and AM fungi, were estimated in coniferous forest soils along four natural nutrient gradients. Plant community changes, forest productivity, soil pH and N availability increase over relatively short distances (< 100 m) along the gradients. The amounts of the phospholipid fatty acid (PLFA) 18 : 2omega6,9 were used to estimate total fungi (not including AM), and the PLFA 16 : 1omega5 to estimate AM fungi in soil samples. The decrease in the PLFA 18 : 2omega6,9 during incubation of soils was used to estimate EM + ErM biomass. Production of AM and EM mycorrhiza was estimated using ingrowth mesh bags. Total fungal biomass was highest in soils with the lowest nutrient availability and tree productivity. Biomass of ErM + EM was also highest in these soils. We found tendencies that EM mycelial production was lowest in the soils with the highest nutrient availability and tree productivity. Production of AM fungi was highest in nutrient-rich soils with high pH. Our results suggest that mycorrhizal communities change from being ErM-, to EM- and finally to AM-dominated along these gradients. The observed changes in mycorrhizal type in the short nutrient gradients follow similar patterns to those suggested for altitudinal or latitudinal gradients over longer distances.}, }
@article {pmid15717784, year = {2005}, author = {Ovez, S and Orhon, D}, title = {Microbial ecology of bulking and foaming activated sludge treating tannery wastewater.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances &amp; environmental engineering}, volume = {40}, number = {2}, pages = {409-422}, doi = {10.1081/ese-200045635}, pmid = {15717784}, issn = {1093-4529}, mesh = {Data Collection ; Flocculation ; Gordonia Bacterium/*growth &amp; development ; Industrial Waste ; *Tanning ; Waste Disposal, Fluid/*methods ; Water Purification/*methods ; }, abstract = {This study involves a comprehensive survey of the microbial ecology of the activated sludge process treating tannery wastewater, emphasizing evaluation during periods of bulking and foaming. The survey also includes a detailed characterization of process influent and effluent. Observations always associate bulking with significant increase in protozoa species and rotifers, but decrease or disappearance of nematodes. Activated sludge sustained under normal conditions with a sludge volume index lower than 80 ml g(-1), exhibits all the properties of a compact and healthy zoogleal floc structure. Three types of filamentous bacteria prevail in the microscopic examinations. Two of the filamentous bacteria, Microthrix parvicella and Nostocoida limicola II, always appear as components of the floc structure under normal conditions and abundant or even excessive levels. The study identifies Gordona spp. as the main microorganism responsible for bulking and foaming, which starts by a Gordona contamination process inside the floc, later branching out and extending through adjacent flocs. When completed, this process increases sludge volume index values to over 200 ml g(-1). Microscopic examinations indicate significant morphological differences between filamentous microorganisms observed in this study and reported in the literature mostly for domestic sewage treatment.}, }
@article {pmid15713333, year = {2005}, author = {Roels, J and Huyghe, G and Verstraete, W}, title = {Microbially mediated phosphine emission.}, journal = {The Science of the total environment}, volume = {338}, number = {3}, pages = {253-265}, doi = {10.1016/j.scitotenv.2004.07.016}, pmid = {15713333}, issn = {0048-9697}, mesh = {Bacteria, Anaerobic ; Insecticides/*analysis ; Oxidation-Reduction ; Phosphates/*metabolism ; Phosphines/*analysis ; *Refuse Disposal ; Soil Microbiology ; Volatilization ; }, abstract = {There is still a lot of controversy in literature concerning the question whether a biochemical system exists enabling micro-organisms to reduce phosphate to phosphine gas. The search for so-called 'de novo synthesised' phosphine is complicated by the fact that soils, slurries, sludges, etc., which are often used as inocula, usually contain matrix bound phosphine (MBP). Matrix bound phosphine is a general term used to indicate non-gaseous reduced phosphorus compounds that are transformed into phosphine gas upon reaction with bases or acids. A study was carried out to compare the different digestion methods, used to transform matrix bound phosphine into phosphine gas. It was demonstrated that caustic and acidic digestion methods should be used to measure the matrix bound phosphine of the inoculum prior to inoculation to avoid false positive results concerning de novo synthesis. This is especially true if anthropogenically influenced inocula possibly containing minute steel or aluminium particles are used. The comparative study on different digestion methods also revealed that the fraction of phosphorus in mild steel, converted to phosphine during acid corrosion depended on the temperature. Following these preliminary studies, anaerobic growth experiments were set up using different inocula and media to study the emission of phosphine gas. Phosphine was detected in the headspace gases and its quantity and timeframe of emission depended on the medium composition, suggesting microbially mediated formation of the gas. The amount of phosphine emitted during the growth experiments never exceeded the bound phosphine present in inocula, prior to inoculation. Hence, de novo synthesis of phosphine from phosphate could not be demonstrated. Yet, microbially mediated conversion to phosphine of hitherto unknown reduced phosphorus compounds in the inoculum was evidenced.}, }
@article {pmid15705557, year = {2005}, author = {Cooper, TF and Lenski, RE and Elena, SF}, title = {Parasites and mutational load: an experimental test of a pluralistic theory for the evolution of sex.}, journal = {Proceedings. Biological sciences}, volume = {272}, number = {1560}, pages = {311-317}, pmid = {15705557}, issn = {0962-8452}, mesh = {Analysis of Variance ; Animals ; *Biological Evolution ; *Epistasis, Genetic ; Escherichia coli/genetics/growth &amp; development ; Genotype ; Host-Parasite Interactions ; *Models, Biological ; Mutagenesis, Insertional ; Mutation/*genetics ; Parasites/*genetics ; Plasmids/genetics ; *Sex ; }, abstract = {Ecological and mutational explanations for the evolution of sexual reproduction have usually been considered independently. Although many of these explanations have yielded promising theoretical results,experimental support for their ability to overcome a twofold cost of sex has been limited. For this reason, it has recently been argued that a pluralistic approach, combining effects from multiple models, may be necessary to explain the apparent advantage of sex. One such pluralistic model proposes that parasite load and synergistic epistasis between deleterious mutations might interact to create an advantage for recombination.Here, we test this proposal by comparing the fitness functions of parasitized and parasite-free genotypes of Escherichia coli bearing known numbers of transposon-insertion mutations. In both classes, we failed to detect any evidence for synergistic epistasis. However, the average effect of deleterious mutations was greater in parasitized than parasite-free genotypes. This effect might broaden the conditions under which another proposed model combining parasite-host coevolutionary dynamics and mutation accumulation can explain the maintenance of sex. These results suggest that, on average, deleterious mutations act multiplicatively with each other but in synergy with infection in determining fitness.}, }
@article {pmid15701695, year = {2005}, author = {Konstantinidis, KT and Tiedje, JM}, title = {Genomic insights that advance the species definition for prokaryotes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {7}, pages = {2567-2572}, pmid = {15701695}, issn = {0027-8424}, mesh = {Bacteria/*classification/*genetics ; Conserved Sequence ; DNA, Bacterial/genetics ; Ecosystem ; Evolution, Molecular ; Genetic Variation ; *Genome, Bacterial ; *Genomics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {To help advance the species definition for prokaryotes, we have compared the gene content of 70 closely related and fully sequenced bacterial genomes to identify whether species boundaries exist, and to determine the role of the organism's ecology on its shared gene content. We found the average nucleotide identity (ANI) of the shared genes between two strains to be a robust means to compare genetic relatedness among strains, and that ANI values of approximately 94% corresponded to the traditional 70% DNA-DNA reassociation standard of the current species definition. At the 94% ANI cutoff, current species includes only moderately homogeneous strains, e.g., most of the >4-Mb genomes share only 65-90% of their genes, apparently as a result of the strains having evolved in different ecological settings. Furthermore, diagnostic genetic signatures (boundaries) are evident between groups of strains of the same species, and the intergroup genetic similarity can be as high as 98-99% ANI, indicating that justifiable species might be found even among organisms that are nearly identical at the nucleotide level. Notably, a large fraction, e.g., up to 65%, of the differences in gene content within species is associated with bacteriophage and transposase elements, revealing an important role of these elements during bacterial speciation. Our findings are consistent with a definition for species that would include a more homogeneous set of strains than provided by the current definition and one that considers the ecology of the strains in addition to their evolutionary distance.}, }
@article {pmid15696393, year = {2004}, author = {Davelos, AL and Xiao, K and Samac, DA and Martin, AP and Kinkel, LL}, title = {Spatial variation in Streptomyces genetic composition and diversity in a prairie soil.}, journal = {Microbial ecology}, volume = {48}, number = {4}, pages = {601-612}, pmid = {15696393}, issn = {0095-3628}, mesh = {DNA Fingerprinting ; DNA, Bacterial ; DNA, Ribosomal ; Ecosystem ; Genetic Variation/*genetics ; Minnesota ; Phylogeny ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Streptomyces/classification/*genetics ; }, abstract = {Understanding how microbial genotypes are arrayed in space is crucial for identifying local factors that may influence the spatial distribution of genetic diversity. In this study we investigated variation in 16S rDNA sequences and rep-PCR fingerprints of Streptomyces stains isolated from prairie soil among three locations and four soil depths. Substantial variation in Streptomyces OTU (operational taxonomic unit) and BOX-PCR fingerprint diversity was found among locations within a limited spatial area (1 m2). Further, phylogenetic lineages at each location were distinct. However, there was little variation in genetic diversity among isolates from different soil depths and similar phylogenetic lineages were found at each depth. Some clones were found at a localized scale while other clones had a relatively widespread distribution. There was poor correspondence between 16S rDNA groupings and rep-PCR fingerprint groupings. The finding of distinct phylogenetic lineages and the variation in spatial distribution of clones suggests that selection pressures may vary over the soil landscape.}, }
@article {pmid15696392, year = {2004}, author = {Feris, KP and Hristova, K and Gebreyesus, B and Mackay, D and Scow, KM}, title = {A shallow BTEX and MTBE contaminated aquifer supports a diverse microbial community.}, journal = {Microbial ecology}, volume = {48}, number = {4}, pages = {589-600}, pmid = {15696392}, issn = {0095-3628}, support = {1R21ES012812-01/ES/NIEHS NIH HHS/United States ; 2P42 ESO 4699/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics/metabolism ; Benzene/analysis ; Benzene Derivatives/analysis ; Biodiversity ; California ; DNA, Bacterial ; DNA, Intergenic ; Hydrocarbons, Aromatic/*analysis ; Methyl Ethers/*analysis ; Petroleum/*analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Toluene/analysis ; *Water Microbiology ; Water Pollutants, Chemical/*analysis ; Xylenes/analysis ; }, abstract = {Microbial communities in subsurface environments are poorly characterized and the impacts of anthropogenic contamination on their structure and function have not been adequately addressed. The release of contaminant(s) to a previously unexposed environment is often hypothesized to decrease the diversity of the affected community. We characterized the structure of microbial communities along a gradient of benzene, toluene, ethylbenzene, and xylene (BTEX) and methyl-tert-butyl-ether (MTBE) contamination, resulting from a petroleum spill, within a shallow sandy aquifer at Vandenberg Air Force Base (VAFB) in Lompoc, CA. Differences in microbial community composition along the contaminant plume were assessed via a combinatorial approach utilizing denaturing gradient gel electrophoresis (DGGE), cloning and sequencing, intergenic transcribed spacer analysis (ITS), and comparative phylogenetic analysis of partial 16S rDNA sequences. Substantial bacterial sequence diversity, similar levels of species richness, and similar phylo-groups (including the Cytophaga-Flavobacterium-Bacteroidetes group and numerous members of the alpha-, beta-, gamma-, delta-, and epsilon-groups of the proteobacteria) were observed in both uncontaminated and contaminated regions of the aquifer. High-resolution measures (ITS fingerprinting and phylogenetic inference) readily separated communities impacted by the original petroleum spill (in source zone) from those in other parts of the aquifer and indicated that communities exposed to MTBE only were similar to communities in uncontaminated regions. Collectively, these data suggest that petroleum contamination alters microbial community structure at the species and subspecies level. Further study is required to determine whether these changes have an impact on the functioning of this subsurface ecosystem.}, }
@article {pmid15696391, year = {2004}, author = {Magnuson, TS and Neal, AL and Geesey, GG}, title = {Combining in situ reverse transcriptase polymerase chain reaction, optical microscopy, and X-ray photoelectron spectroscopy to investigate mineral surface-associated microbial activities.}, journal = {Microbial ecology}, volume = {48}, number = {4}, pages = {578-588}, pmid = {15696391}, issn = {0095-3628}, mesh = {Bacterial Proteins/genetics ; Cytochromes c/genetics ; *Environmental Microbiology ; Ferric Compounds/chemistry ; Ferritins/chemistry ; Gene Expression ; Geobacter/genetics/*metabolism ; In Situ Hybridization/*methods ; *Microscopy, Fluorescence ; Minerals/*chemistry ; Reverse Transcriptase Polymerase Chain Reaction/*methods ; Spectrometry, X-Ray Emission/*methods ; Time Factors ; }, abstract = {A study was undertaken to investigate expression of a gene encoding a c-type cytochrome in cells of the dissimilatory metal reducing bacterium (DMRB) Geobacter sulfurreducens during association with poorly crystalline and crystalline solid-phase Fe(III)-oxides. The gene encoding OmcC (outer membrane c-type cytochrome) was used as a target for PCR-based molecular detection and visualization of omcC gene expression by individual cells and aggregates of cells of G. sulfurreducens associated with ferrihydrite and hematite mineral particles. Expression of omcC was demonstrated in individual bacterial cells associated with these Fe-oxide surfaces by in situ RT-PCR (IS-RT PCR) and epifluorescence microscopy. Epifluorescence microscopy also permitted visualization of total DAPI-stained cells in the same field of view to assess the fraction of the cell population expressing omcC. By combining reflected differential interference contrast (DIC) microscopy and epifluorescence microscopy, it was possible to determine the spatial relationship between cells expressing omcC and the mineral surface. Introduction of the fluorescently labeled lectin concanavalin A revealed extracellular polymeric substances (EPS) extending between aggregations of bacterial cells and the mineral surface. The results indicate that EPS mediates an association between cells of G. sulfurreducens and ferrihydrite particles, but that direct cell contact with the mineral surface is not required for expression of omcC. XPS analysis revealed forms of reduced Fe associated with areas of the mineral surface where EPS-mediated bacterial associations occurred. The results demonstrate that by combining molecular biology, reflectance microscopy, and XPS, chemical transformations at a mineral surface can be related to the expression of specific genes by individual bacterial cells and cell aggregates associated with the mineral surface. The approach should be useful in establishing involvement of specific gene products in a wide variety of surface chemical processes.}, }
@article {pmid15696390, year = {2004}, author = {Lavrentyev, PJ and McCarthy, MJ and Klarer, DM and Jochem, F and Gardner, WS}, title = {Estuarine microbial food web patterns in a Lake Erie coastal wetland.}, journal = {Microbial ecology}, volume = {48}, number = {4}, pages = {567-577}, pmid = {15696390}, issn = {0095-3628}, mesh = {Bacteria/metabolism ; Bacterial Physiological Phenomena ; Biomass ; Ecosystem ; *Food Chain ; Fresh Water/microbiology/*parasitology ; Nitrogen/metabolism ; Ohio ; Plankton/*physiology ; Population Dynamics ; *Water Microbiology ; }, abstract = {Composition and distribution of planktonic protists were examined relative to microbial food web dynamics (growth, grazing, and nitrogen cycling rates) at the Old Woman Creek (OWC) National Estuarine Research Reserve during an episodic storm event in July 2003. More than 150 protistan taxa were identified based on morphology. Species richness and microbial biomass measured via microscopy and flow cytometry increased along a stream-lake (Lake Erie) transect and peaked at the confluence. Water column ammonium (NH4+) uptake (0.06 to 1.82 microM N h(-1)) and regeneration (0.04 to 0.55 microM N h(-1)) rates, measured using 15NH4+ isotope dilution, followed the same pattern. Large light/dark NH4+ uptake differences were observed in the hypereutrophic OWC interior, but not at the phosphorus-limited Lake Erie site, reflecting the microbial community structural shift from net autotrophic to net heterotrophic. Despite this shift, microbial grazers (mostly choreotrich ciliates, taxon-specific growth rates up to 2.9 d(-1)) controlled nanophytoplankton and bacteria at all sites by consuming 76 to 110% and 56 to 97% of their daily production, respectively, in dilution experiments. Overall, distribution patterns and dynamics of microbial communities in OWC resemble those in marine estuaries, where plankton productivity increases along the river-sea gradient and reaches its maximum at the confluence.}, }
@article {pmid15696389, year = {2004}, author = {Snyder, JC and Spuhler, J and Wiedenheft, B and Roberto, FF and Douglas, T and Young, MJ}, title = {Effects of culturing on the population structure of a hyperthermophilic virus.}, journal = {Microbial ecology}, volume = {48}, number = {4}, pages = {561-566}, pmid = {15696389}, issn = {0095-3628}, mesh = {Archaeal Viruses/*genetics ; Genetic Markers ; Genetic Variation/*genetics ; Genome, Viral ; Hot Temperature ; Northwestern United States ; Phylogeny ; Sulfolobus/virology ; Virus Cultivation/*methods ; Water Microbiology ; }, abstract = {The existence of a culturing bias has long been known when sampling organisms from the environment. This bias underestimates microbial diversity and does not accurately reflect the most ecologically relevant species. Until now no study has examined the effects of culture bias on viral populations. We have employed culture-independent methods to assess the diversity of Sulfolobus spindle-shaped viruses (SSVs) from extremely hyperthermal environments. This diversity is then compared to the viral diversity of cultured samples. We detected a clear culturing bias between environmental samples and cultured isolates. This is the first study identifying a culture bias in a viral population.}, }
@article {pmid15696388, year = {2004}, author = {Kent, AD and Jones, SE and Yannarell, AC and Graham, JM and Lauster, GH and Kratz, TK and Triplett, EW}, title = {Annual patterns in bacterioplankton community variability in a humic lake.}, journal = {Microbial ecology}, volume = {48}, number = {4}, pages = {550-560}, pmid = {15696388}, issn = {0095-3628}, mesh = {*Bacterial Physiological Phenomena ; Biodiversity ; Ecosystem ; Fresh Water/chemistry ; Hydrocarbons/analysis ; Hydrogen-Ion Concentration ; Nitrogen/analysis ; Phosphorus/analysis ; Plankton/*physiology ; Population Dynamics ; Time Factors ; *Water Microbiology ; Wisconsin ; }, abstract = {Bacterioplankton community composition (BCC) was monitored in a shallow humic lake in northern Wisconsin, USA, over 3 years using automated ribosomal intergenic spacer analysis (ARISA). Comparison of ARISA profiles of bacterial communities over time indicated that BCC was highly variable on a seasonal and annual scale. Nonmetric multidimensional scaling (MDS) analysis indicated little similarity in BCC from year to year. Nevertheless, annual patterns in bacterioplankton community diversity were observed. Trends in bacterioplankton community diversity were correlated to annual patterns in community succession observed for phytoplankton and zooplankton populations, consistent with the notion that food web interactions affect bacterioplankton community structure in this humic lake. Bacterioplankton communities experience a dramatic drop in richness and abundance each year in early summer, concurrent with an increase in the abundance of both mixotrophic and heterotrophic flagellates. A second drop in richness, but not abundance, is observed each year in late summer, coinciding with an intense bloom of the nonphagotrophic dinoflagellate Peridinium limbatum. A relationship between bacterial community composition, size, and abundance and the population dynamics of Daphnia was also observed. The noted synchrony between these major population and species shifts suggests that linkages across trophic levels play a role in determining the annual time course of events for the microbial and metazoan components of the plankton.}, }
@article {pmid15696387, year = {2004}, author = {Wilson, C and Caton, TM and Buchheim, JA and Buchheim, MA and Schneegurt, MA and Miller, RV}, title = {DNA-repair potential of Halomonas spp. from the Salt Plains Microbial Observatory of Oklahoma.}, journal = {Microbial ecology}, volume = {48}, number = {4}, pages = {541-549}, pmid = {15696387}, issn = {0095-3628}, mesh = {Adaptation, Physiological ; DNA Repair/*physiology/radiation effects ; Escherichia coli/genetics/radiation effects ; Halomonas/*genetics/*radiation effects ; Oklahoma ; Phylogeny ; Pseudomonas aeruginosa/genetics/radiation effects ; Sodium Chloride ; *Soil Microbiology ; Ultraviolet Rays ; }, abstract = {The Great Salt Plains (GSP), an unvegetated, barren salt flat that is part of the Salt Plains National Wildlife Refuge near Cherokee, Oklahoma, is the site of the Salt Plains Microbial Observatory. At the GSP the briny remains of an ancient sea rise to the surface, evaporate under dry conditions, and leave crusts of white salt. Adaptation to this environment requires development of coping mechanisms providing tolerance to desiccating conditions due to the high salinity, extreme temperatures, alkaline pH, unrelenting exposure to solar UV radiation, and prevailing winds. Several lines of evidence suggest that the same DNA repair mechanisms that are usually associated with UV light or chemically induced DNA damage are also important in protecting microbes from desiccation. Because little is known about the DNA repair capacity of microorganisms from hypersaline terrestrial environments, we explored the DNA repair capacity of microbial isolates from the GSP. We used survival following exposure to UV light as a convenient tool to assess DNA repair capacity. Two species of Halomonas (H. salina and H. venusta) that have been isolated repeatedly from the GSP were chosen for analysis. The survival profiles were compared to those of Escherichia coli, Pseudomonas aeruginosa, and Halomonas spp. from aquatic saline environments. Survival of GSP organisms exceeded that of the freshwater organism P. aeruginosa, although they survived no better than E. coli. The GSP isolates were much more resistance to killing by UV than were the aquatic species of Halomonas reported in the literature [Martin et al. (2000) Can J Microbiol 46:180-187]. Unlike E. coli, the GSP isolates did not appear to have an inducible, error-prone repair mechanism. However, they demonstrated high levels of spontaneous mutation.}, }
@article {pmid15696386, year = {2004}, author = {Graham, JM and Kent, AD and Lauster, GH and Yannarell, AC and Graham, LE and Triplett, EW}, title = {Seasonal dynamics of phytoplankton and planktonic protozoan communities in a northern temperate humic lake: diversity in a dinoflagellate dominated system.}, journal = {Microbial ecology}, volume = {48}, number = {4}, pages = {528-540}, pmid = {15696386}, issn = {0095-3628}, mesh = {Animals ; Bacterial Physiological Phenomena ; Biodiversity ; Dinoflagellida/*physiology ; Ecosystem ; Eukaryota/*physiology ; Fresh Water/microbiology/*parasitology ; Hydrogen-Ion Concentration ; Phytoplankton/*physiology ; Population Dynamics ; Seasons ; Wisconsin ; }, abstract = {Species diversity and richness, and seasonal population dynamics of phytoplankton, planktonic protozoa, and bacterioplankton sampled from the epilimnion of Crystal Bog in 2000, were examined in order to test the hypothesis that these groups' diversity and abundance patterns might be linked. Crystal Bog, a humic lake in Vilas County, Wisconsin, is part of the North Temperate Lakes Long-Term Ecological Research Site. Phytoplankton and planktonic protozoa were identified and enumerated in a settling chamber with an inverted microscope. Bacterial cells were enumerated with the use of fluorescence 4', 6'-diamidino-2-phenylindole (DAPI)-staining procedures, and automated ribosomal intergenic spacer analysis (ARISA) was used to assess bacterioplankton diversity. Bacterial cell counts showed little seasonal variation and averaged 2.6 x 10(6) cells/mL over the ice-free season. Phytoplankton and planktonic protozoan numbers varied by up to two orders of magnitude and were most numerous in late spring and summer. Dinoflagellates largely dominated Crystal Bog throughout the ice-free period, specifically Peridiniopsis quadridens in the spring, Peridinium limbatum in summer, and Gymnodinium fuscum and P. quadridens in fall. Brief blooms of Cryptomonas, Dinobryon, and Synura occurred between periods of dinoflagellate domination. The dominant dinoflagellate, Peridinium limbatum, was calculated to have a growth rate of 0.065 day(-1) and a doubling time of 10.7 days. Heterotrophic nanoflagellates (HNFs) were a consistent component of the planktonic protozoa; seasonal patterns were determined for three genera of HNFs (Monosiga, Bicosoeca, and Desmarella moniliformis). Three genera of ciliates (Coleps, Strobilidium, and Strombidium) comprised the greater part of the planktonic protozoa in Crystal Bog. The number of species of planktonic protozoa was too low to calculate a diversity index. Shannon-Weaver diversity indices for phytoplankton and bacterioplankton in the epilimnion followed very similar seasonal patterns in this lake, supporting the hypothesis that in freshwaters, diversity patterns of these groups are linked.}, }
@article {pmid15696385, year = {2004}, author = {Kim, E and Wilcox, L and Graham, L and Graham, J}, title = {Genetically distinct populations of the dinoflagellate Peridinium limbatum in neighboring Northern Wisconsin lakes.}, journal = {Microbial ecology}, volume = {48}, number = {4}, pages = {521-527}, pmid = {15696385}, issn = {0095-3628}, mesh = {Animals ; Base Sequence ; DNA, Ribosomal ; Dinoflagellida/classification/*genetics ; Fresh Water/*parasitology ; *Genetic Variation ; Molecular Sequence Data ; Phenotype ; RNA, Ribosomal, 18S ; Sequence Homology, Nucleic Acid ; Wisconsin ; }, abstract = {The extent to which free-living microorganisms exist in geographically isolated, genetically distinct populations is a subject of continuing debate. Some authorities contend that many microorganisms have cosmopolitan distributions, while others provide evidence that more limited geographical distribution of genetically distinct populations can occur. We report the occurrence of two morphologically similar, but genetically distinct, populations of the microbial eukaryote Peridinium limbatum (Stokes) Lemmermann from neighboring Northern Wisconsin freshwater bodies. Five strains of P. limbatum were cultured by single-cell isolation from both Crystal Lake and Crystal Bog (Oneida Co., WI). Genetic variation between the two populations encompassed 8.9% (mean of 35.4 of 397 nucleotides) of the nuclear ribosomal DNA internal transcribed spacer (ITS1 and ITS2) region. In contrast, 0.5% (mean of 2.25 of 397 nucleotides) variation was observed within the Crystal Lake population and 0.3% (mean of 1.21 of 397 nucleotides), within the Crystal Bog population. This difference between the two populations was highly statistically significant (p-value << 0.001). The extent of genetic variation between the two P. limbatum populations was greater than that reported in the literature for some morphologically distinguishable microalgal species, suggesting the occurrence of cryptic sister species. On the other hand, hybrid sequences obtained from one of the Crystal Lake strains suggest that the two populations may still be members of a single sexually compatible biological species. Our data suggest that the two neighboring P. limbatum populations may be diverging genetically under conditions of limited gene flow, suggesting a mechanism for the origin of geographically isolated, genetically distinct populations of microbial eukaryotes.}, }
@article {pmid15696384, year = {2004}, author = {Donachie, SP and Hou, S and Lee, KS and Riley, CW and Pikina, A and Belisle, C and Kempe, S and Gregory, TS and Bossuyt, A and Boerema, J and Liu, J and Freitas, TA and Malahoff, A and Alam, M}, title = {The Hawaiian Archipelago: a microbial diversity hotspot.}, journal = {Microbial ecology}, volume = {48}, number = {4}, pages = {509-520}, pmid = {15696384}, issn = {0095-3628}, mesh = {Bacteria/*classification/*genetics ; *Biodiversity ; Ecosystem ; Fresh Water ; Geologic Sediments/microbiology ; Hawaii ; Phylogeny ; *Water Microbiology ; }, abstract = {The Hawaiian Archipelago is a "biodiversity hotspot" where significant endemism among eukaryotes has evolved through geographic isolation and local topography. To address the absence of corresponding region-wide data on Hawaii's microbiota, we compiled the first 16S SSU rDNA clone libraries and cultivated bacteria from five Hawaiian lakes, an anchialine pool, and the Lō'ihi submarine volcano. These sites offer diverse niches over approximately 5000 m elevation and approximately 1150 nautical miles. Each site hosted a distinct prokaryotic community dominated by Bacteria. Cloned sequences fell into 158 groups from 18 Bacteria phyla, while seven were unassigned and two belonged in the Euryarchaeota. Only seven operational taxonomic units (each OTU comprised sequences that shared > or =97% sequence identity) occurred in more than one site. Pure bacterial cultures from all sites fell into 155 groups (each group comprised pure cultures that shared > or =97% 16S SSU rDNA sequence identity) from 10 Bacteria phyla; 15 Proteobacteria and Firmicutes were cultivated from more than one site. One hundred OTUs (60%) and 52 (33.3%) cultures shared <97% 16S SSU rDNA sequence identity with published sequences. Community structure reflected habitat chemistry; most delta-Proteobacteria occurred in anoxic and sulfidic waters of one lake, while beta-Proteobacteria were cultivated exclusively from fresh or brackish waters. Novel sequences that affiliate with an Antarctic-specific clade of Deinococci, and Candidate Divisions TM7 and BRC1, extend the geographic ranges of these phyla. Globally and locally remote, as well as physically and chemically diverse, Hawaiian aquatic habitats provide unique niches for the evolution of novel communities and microorganisms.}, }
@article {pmid15696383, year = {2004}, author = {Bottomley, PJ and Taylor, AE and Boyle, SA and McMahon, SK and Rich, JJ and Cromack, K and Myrold, DD}, title = {Responses of nitrification and ammonia-oxidizing bacteria to reciprocal transfers of soil between adjacent coniferous forest and meadow vegetation in the Cascade Mountains of Oregon.}, journal = {Microbial ecology}, volume = {48}, number = {4}, pages = {500-508}, pmid = {15696383}, issn = {0095-3628}, mesh = {Ammonia/*metabolism ; Bacteria/*metabolism ; Ecosystem ; Nitrogen/*metabolism ; Oregon ; Oxidation-Reduction ; *Soil Microbiology ; }, abstract = {Despite the critical position of nitrification in N cycling in coniferous forest soils of western North America, little information exists on the composition of ammonia-oxidizing bacteria (AOB) in these soils, or their response to treatments that promote or reduce nitrification. To this end, an experiment was conducted in which a set of soil cores was reciprocally transplanted between adjacent forest (low nitrification potential) and meadow (high nitrification potential) environments, at two high-elevation (approximately 1500 m) sites in the H.J. Andrews Experimental Forest located in the Cascade Mountains of Oregon. Half of the cores were placed in screened PVC pipe (closed) to prevent new root colonization, large litter debris inputs, and animal disturbance; the other cores were placed in open mesh bags. A duplicate set of open and closed soil cores was not transferred between sites and was incubated in place. Over the 2-year experiment, net nitrification increased in both open and closed cores transferred from forest to meadow, and to a lesser extent in cores remaining in the forest. In three of four forest soil treatments, net nitrification increases were accompanied by increases in nitrification potential rates (NPR) and 10- to 100-fold increases in AOB populations. In open cores remaining in the forests, however, increases in net nitrification were not accompanied by significant increases in either NPR or AOB populations. Although some meadow soil treatments reduced both net nitrification and nitrification potential rates, significant changes were not detected in most probable number (MPN)-based estimates of AOB population densities. Terminal restriction fragment profiles (T-RFs) of a PCR-amplified 491-bp fragment of the ammonia monooxygenase subunit A gene (amoA) changed significantly in response to some soil treatments, and treatment effects differed among locations and between years. A T-RF previously shown to be a specific biomarker of Nitrosospira cluster 4 (Alu390) was widespread and dominant in the majority of soil samples. Despite some treatments causing substantial increases in AOB population densities and nitrification potential rates, nitrosomonads remained undetectable, and the nitrosospirad AOB community composition did not change radically following treatment.}, }
@article {pmid15696382, year = {2004}, author = {Fawley, MW and Fawley, KP and Buchheim, MA}, title = {Molecular diversity among communities of freshwater microchlorophytes.}, journal = {Microbial ecology}, volume = {48}, number = {4}, pages = {489-499}, pmid = {15696382}, issn = {0095-3628}, mesh = {Base Sequence ; Chlorophyta/classification/*genetics ; DNA, Bacterial ; DNA, Ribosomal ; Fresh Water ; Genetic Variation/*genetics ; Minnesota ; North Dakota ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; *Water Microbiology ; }, abstract = {Current hypotheses on the distribution of freshwater microchlorophytes lead to predictions of low diversity and wide environmental tolerances. Thus, the same few species should be found worldwide in many different habitats. However, these hypotheses are based on a morphospecies concept, which precludes the possibility of numerous cryptic species among these organisms. In this study, we examined the diversity of coccoid green microalgae and chlamydomonads (Chlorophyta) isolated from sites in Minnesota and North Dakota (USA) using techniques of 18S rDNA sequence analysis. Of 93 distinct 18S rDNA sequences identified from among 273 isolates examined by molecular techniques, all but four are new to science. The spatial distribution of organisms represented by these 18S rDNA sequences was not uniform, because some lakes and ponds yielded distinct 18S rDNA types not found at other sites. In addition, organisms generally considered to be cosmopolitan, such as Chlamydomonas reinhardtii and Chlorella vulgaris, were not found. These results challenge predictions of low species number and wide environmental tolerances among these eukaryotic microorganisms.}, }
@article {pmid15696381, year = {2004}, author = {Suzuki, MT and Preston, CM and Béjà, O and de la Torre, JR and Steward, GF and DeLong, EF}, title = {Phylogenetic screening of ribosomal RNA gene-containing clones in Bacterial Artificial Chromosome (BAC) libraries from different depths in Monterey Bay.}, journal = {Microbial ecology}, volume = {48}, number = {4}, pages = {473-488}, pmid = {15696381}, issn = {0095-3628}, mesh = {Bacteria/*classification/genetics ; California ; Chromosomes, Artificial, Bacterial/*genetics ; DNA, Intergenic ; Gene Library ; Genes, Bacterial ; Molecular Sequence Data ; Pacific Ocean ; Phylogeny ; RNA, Bacterial/*genetics ; RNA, Ribosomal/*genetics ; *Water Microbiology ; }, abstract = {Marine picoplankton are central mediators of many oceanic biogeochemical processes, but much of their biology and ecology remains ill defined. One approach to better defining these environmentally significant microbes involves the acquisition of genomic data that can provide information about genome content, metabolic capabilities, and population variability in picoplankton assemblages. Previously, we constructed and phylogenetically screened a Bacterial Artificial Chromosome (BAC) library from surface water picoplankton of Monterey Bay. To further describe niche partitioning, metabolic variability, and population structure in coastal picoplankton populations, we constructed and compared several picoplankton BAC libraries recovered from different depths in Monterey Bay. To facilitate library screening, a rapid technique was developed (ITS-LH-PCR) to identify and quantify ribosomal RNA (rRNA) gene-containing BAC clones in BAC libraries. The approach exploited natural length variations in the internal transcribed spacer (ITS) located between SSU and LSU rRNA genes, as well as the presence and location of tRNA-alanine coding genes within the ITS. The correspondence between ITS-LH-PCR fragment sizes and 16S rRNA gene phylogenies facilitated rapid identification of rRNA genes in BAC clones without requiring direct DNA sequencing. Using this approach, 35 phylogenetic groups (previously identified by cultivation or PCR-based rRNA gene surveys) were detected and quantified among the BAC clones. Since the probability of recovering chimeric rRNA gene sequences in large insert BAC clones was low, we used these sequences to identify potentially chimeric sequences from previous PCR amplified clones deposited in public databases. Full-length SSU rRNA gene sequences from picoplankton BAC libraries, cultivated bacterioplankton, and nonchimeric RNA genes were then used to refine phylogenetic analyses of planktonic marine gamma Proteobacteria, Roseobacter, and Rhodospirillales species.}, }
@article {pmid15696380, year = {2004}, author = {Kalyuzhnaya, MG and Lidstrom, ME and Chistoserdova, L}, title = {Utility of environmental primers targeting ancient enzymes: methylotroph detection in Lake Washington.}, journal = {Microbial ecology}, volume = {48}, number = {4}, pages = {463-472}, pmid = {15696380}, issn = {0095-3628}, mesh = {Bacteria/classification/*enzymology/genetics ; Bacterial Proteins/classification/genetics ; Base Sequence ; DNA Primers ; Euryarchaeota/classification/*enzymology/genetics ; Genetic Variation ; Geologic Sediments/*microbiology ; Methylobacteriaceae/classification/*enzymology/genetics ; Molecular Sequence Data ; Proteobacteria/classification/*enzymology/genetics ; Washington ; Water Microbiology ; }, abstract = {Methods have been explored for detection of methylotrophs in natural samples, using environmental primers based on genes involved in the tetrahydromethanopterin (H4MPT)-linked C1 transfer pathway. The underlying hypotheses were that the H4MPT-linked pathway is an ancient methylotrophy pathway, based on gene divergence, and that primers targeting more divergent genes will detect a broader variety of methylotrophs compared to the variety uncovered using probes and primers targeting highly conserved genes. Three groups of novel primer sets were developed targeting mch, mtdB, and fae, key genes in the H4MPT-linked pathway, and these were used to assess the variety of microorganisms possessing these genes in sediments from Lake Washington in Seattle, WA. Environmental clone libraries were constructed for each of the genes and were analyzed by RFLP, and representatives of different RFLP groups were sequenced and subjected to phylogenetic analysis. A combination of all three sets of novel primers allowed detection of the two previously characterized groups of methylotrophs in the site: methanotrophs of the (alpha- and the gamma-proteobacterial groups, belonghg to genera Methylosinus, Methylocystis, Methylomonas, Methylobacter, Methylomicrobium, and Methylococcus. In addition to the genes belonging to known methanotroph populations, novel genes were identified, suggesting existence of previously undetected microbial groups possessing C1 transfer functions in this site. These included sequences clustering with the well-characterized methylotrophic phyla, Methylobacterium, Hyphomicrobium, and Xanthobacter. In addition, sequences divergent from those known for any groups of methylotrophs or methanogens were obtained, suggesting the presence of a yet unidentified microbial group possessing this H4MPT-linked C1 transfer pathway.}, }
@article {pmid15696379, year = {2004}, author = {Caton, TM and Witte, LR and Ngyuen, HD and Buchheim, JA and Buchheim, MA and Schneegurt, MA}, title = {Halotolerant aerobic heterotrophic bacteria from the Great Salt Plains of Oklahoma.}, journal = {Microbial ecology}, volume = {48}, number = {4}, pages = {449-462}, pmid = {15696379}, issn = {0095-3628}, support = {P20 RR16475/RR/NCRR NIH HHS/United States ; }, mesh = {Bacteria, Aerobic/*classification/drug effects/physiology ; Oklahoma ; Phenotype ; Phylogeny ; *Sodium Chloride/pharmacology ; *Soil Microbiology ; }, abstract = {The Salt Plains National Wildlife Refuge (SPNWR) near Cherokee, Oklahoma, contains a barren salt flat where Permian brine rises to the surface and evaporates under dry conditions to leave a crust of white salt. Rainfall events dissolve the salt crust and create ephemeral streams and ponds. The rapidly changing salinity and high surface temperatures, salinity, and UV exposure make this an extreme environment. The Salt Plains Microbial Observatory (SPMO) examined the soil microbial community of this habitat using classic enrichment and isolation techniques and phylogenetic rDNA studies. Rich growth media have been emphasized that differ in total salt concentration and composition. Aerobic heterotrophic enrichments were performed under a variety of conditions. Heterotrophic enrichments and dilution plates have generated 105 bacterial isolates, representing 46 phylotypes. The bacterial isolates have been characterized phenotypically and subjected to rDNA sequencing and phylogenetic analyses. Fast-growing isolates obtained from enrichments with 10% salt are predominantly from the gamma subgroup of the Proteobacteria and from the low GC Gram-positive cluster. Several different areas on the salt flats have yielded a variety of isolates from the Gram-negative genera Halomonas, Idiomarina, Salinivibrio, and Bacteroidetes. Gram-positive bacteria are well represented in the culture collection including members of the Bacillus, Salibacillus, Oceanobacillus, and Halobacillus.}, }
@article {pmid15696378, year = {2004}, author = {Kane, MD}, title = {Microbial observatories: exploring and discovering microbial diversity in the 21st century.}, journal = {Microbial ecology}, volume = {48}, number = {4}, pages = {447-448}, doi = {10.1007/s00248-004-9953-5}, pmid = {15696378}, issn = {0095-3628}, mesh = {*Biodiversity ; Ecosystem ; *Environmental Microbiology ; }, }
@article {pmid15692864, year = {2004}, author = {Treton, C and Chauvet, E and Charcosset, JY}, title = {Competitive interaction between two aquatic hyphomycete species and increase in leaf litter breakdown.}, journal = {Microbial ecology}, volume = {48}, number = {3}, pages = {439-446}, pmid = {15692864}, issn = {0095-3628}, mesh = {Alnus/microbiology ; Ascomycota/physiology ; Ecosystem ; Environmental Microbiology ; Mitosporic Fungi/growth &amp; development/*physiology ; Plant Leaves/*microbiology ; }, abstract = {Aquatic hyphomycete species produce large numbers of conidia which rapidly colonize the leaf litter that falls into rivers during autumn. Our objective was to understand how a species which produces many fewer conidia than another in laboratory conditions can nevertheless be codominant in a natural setting. In microcosm studies with two pioneer dominant species, Flagellospora curvula and Tetrachaetum elegans, inoculated on alder leaves, we first verified that the ratio of the conidium production of both species (6 to 7:1) was inverse to that of individual conidial masses (1:7) as previously described. Calculating the percentage of leaf mass loss that corresponds to 1A mg of conidial mass produced, the combination of the two species produced 2.9-fold more loss than the mean of each species. By contrast, the reproductive biomasses of F. curvula and T. elegans were 5.2- and 2.6-fold lower, respectively. As a result, the conidium production of F. curvula in the combination was only 3.2-fold that of T. elegans instead of 6- to 7-fold in pure culture. In a mixed culture of the two species, T. elegans conidia had a high germination potential (>90%) whereas the proportion of germinated F. curvula conidia was only 50%. Moreover, T. elegans reduced the area on which F. curvula could grow on poor and rich solid media. These results indicate that the dominance of F. curvula conidia in the river may be partly controlled by T. elegans and suggest that a negative interaction between microfungi may have a positive effect on the ecosystem functioning.}, }
@article {pmid15692863, year = {2004}, author = {Stohr, SN and Dighton, J}, title = {Effects of species diversity on establishment and coexistence: a phylloplane fungal community model system.}, journal = {Microbial ecology}, volume = {48}, number = {3}, pages = {431-438}, pmid = {15692863}, issn = {0095-3628}, mesh = {Ascomycota/physiology ; *Biodiversity ; Culture Techniques ; Fungi/*physiology ; Models, Biological ; Plant Components, Aerial/*microbiology ; Vaccinium macrocarpon/microbiology ; }, abstract = {A model system was devised, evaluating the influence that species diversity (species richness) has on fungal establishment and coexistence. Seven members of the fungal phylloplane community of Vaccinium macrocarpon (American cranberry) were selected to assess how species diversity affected development and coexistence of another community member, Pestalotia vaccinii. Pestalotia was engaged in competitive interactions on 1% Malt Extract Agar (MEA) petri dishes with each of the seven individual saprotrophs (two-way interaction), in random combinations with three of the seven saprotrophs (four-way interaction), and in random combinations with five of the seven saprotrophs (six-way interaction). The saprotrophic fungi used in this study were Aspergillus sp., Alternaria alternata, Cladosporium cladosporoides, Curvularia lunata, Epicoccum purpuracens, Penicillium sp., and Pithomyces chartarum. We hypothesized that species diversity would have a significant impact on the establishment and coexistence of Pestalotia vaccinii in culture. In an effort to minimize density-dependent effects, the number of viable spores employed in the three types of interactions was kept constant. Target spore concentrations of 50 viable spores of P. vaccinii and 50 saprotroph spores were used, regardless of the number of species involved in the interaction. This proved to be a very important factor in the experiment. As our results show, species diversity had little or no effect on the establishment and coexistence of Pestalotia vaccinii; however, spore density played an extremely important role in the establishment and development of fungal propagules in our model.}, }
@article {pmid15692862, year = {2004}, author = {Drenovsky, RE and Vo, D and Graham, KJ and Scow, KM}, title = {Soil water content and organic carbon availability are major determinants of soil microbial community composition.}, journal = {Microbial ecology}, volume = {48}, number = {3}, pages = {424-430}, pmid = {15692862}, issn = {0095-3628}, support = {2P42 ESO4699/ES/NIEHS NIH HHS/United States ; }, mesh = {Agriculture ; Bacteria ; Carbon/*physiology ; Fatty Acids/analysis ; Fungi ; Solanum lycopersicum ; Oryza ; Phospholipids/analysis ; Soil/*analysis ; *Soil Microbiology ; Water/*analysis ; }, abstract = {Exploration of environmental factors governing soil microbial community composition is long overdue and now possible with improved methods for characterizing microbial communities. Previously, we observed that rice soil microbial communities were distinctly different from tomato soil microbial communities, despite management and seasonal variations within soil type. Potential contributing factors included types and amounts of organic inputs, organic carbon content, and timing and amounts of water inputs. Of these, both soil water content and organic carbon availability were highly correlated with observed differences in composition. We examined how organic carbon amendment (compost, vetch, or no amendment) and water additions (from air dry to flooded) affect microbial community composition. Using canonical correspondence analysis of phospholipid fatty acid data, we determined flooded, carbon-amended (+C) microcosm samples were distinctly different from other +C samples and unamended (-C) samples. Although flooding without organic carbon addition influenced composition some, organic carbon addition was necessary to substantially alter community composition. Organic carbon availability had the same general effects on microbial communities regardless of whether it was compost or vetch in origin. In addition, flooded samples, regardless of organic carbon inputs, had significantly lower ratios of fungal to bacterial biomarkers, whereas under drier conditions and increased organic carbon availability the microbial communities had higher proportions of fungal biomass. When comparing field and microcosm soil, flooded +C microcosm samples were most similar to field-collected rice soil, whereas all other treatments were more similar to field-collected tomato soil. Overall, manipulating water and carbon content selected for microbial communities similar to those observed when the same factors were manipulated at the field scale.}, }
@article {pmid15692861, year = {2004}, author = {Enright, MR and Griffin, CT}, title = {Specificity of association between Paenibacillus spp. and the entomopathogenic nematodes, Heterorhabditis spp.}, journal = {Microbial ecology}, volume = {48}, number = {3}, pages = {414-423}, pmid = {15692861}, issn = {0095-3628}, mesh = {Animals ; Bacterial Adhesion ; Endospore-Forming Bacteria/genetics/*physiology ; Host-Parasite Interactions ; Insecta/parasitology ; Photorhabdus/physiology ; Phylogeny ; Rhabditoidea/*microbiology ; Species Specificity ; }, abstract = {Endospore-forming bacteria, Paenibacillus spp., have recently been isolated in association with insect pathogenic nematodes Heterorhabditis spp. Sporangia adhere to nematode infective juveniles (J3) and are carried with them into insects. Paenibacillus proliferates in the killed insect along with Heterorhabditis and its obligate bacterial symbiont, Photorhabdus, despite the antibiotic production of the latter. Nematode infective juveniles leave the insect cadaver with Paenibacillus sporangia attached. The specificity of the relationship between Paenibacillus and Heterorhabditis was investigated. Sporangia of nematode-associated Paenibacillus adhered to infective juveniles (but not other stages) of all Heterorhabditis species tested, and to infective juveniles of vertebrate parasitic Strongylida species, but not to a variety of other soil nematodes tested. Paenibacillus species that were not isolated from nematodes, but were phylogenetically close to the nematode-associated strains, did not adhere to Heterorhabditis, and they were also sensitive to Photorhabdus antibiotics in vitro, whereas the nematode-associated strains were not. Unusual longevity of the sporangium and resistance to Photorhabdus antibiotics may represent specific adaptations of the nematode-associated Paenibacillus strains to allow them to coexist with and be transported by Heterorhabditis. Adaptation to specific Heterorhabditis-Photorhabdus strains is evident among the three nematode-associated Paenibacillus strains (each from a different nematode strain). Paenibacillus NEM1a and NEM3 each developed best in cadavers with the nematode from which it was isolated and not at all with the nematode associate of the other strain. Differences between nematode-associated Paenibacillus strains in cross-compatibility with the various Heterorhabditis strains in cadavers could not be explained by differential sensitivity to antibiotics produced by the nematodes' Photorhabdus symbionts in vitro.}, }
@article {pmid15692860, year = {2004}, author = {Nicolas, JL and Corre, S and Cochard, JC}, title = {Bacterial population association with phytoplankton cultured in a bivalve hatchery.}, journal = {Microbial ecology}, volume = {48}, number = {3}, pages = {400-413}, pmid = {15692860}, issn = {0095-3628}, mesh = {Animals ; Aquaculture/*methods ; Bacteria/classification/*isolation &amp; purification ; Eukaryota/microbiology ; Larva/growth &amp; development ; Mollusca/*growth &amp; development ; Phylogeny ; Phytoplankton/*microbiology ; }, abstract = {Bacterial populations association with phytoplankton cultures used as food for bivalve larvae were enumerated and identified from their partial 16S rDNA gene sequences. Microalgae were provided from different European hatcheries during the larval production season. Average concentration (direct counts) of bacteria ranged from 1.3 x 10(5) to 5.3 x 10(8) mL(-1) while culturable bacteria represented from 10% to >60% of total bacteria. In most cases, three to six representatives of each type of colony were collected on solid medium. The identity of isolates from the same colony type was checked by two different randomly amplified polymorphic DNA (RAPD) typing methods, after which the 16S rDNA gene of one to three isolates by colony type were partially sequenced. Algae harbored a large spectrum of bacteria belonging to the alpha-Proteobacteria, beta-Proteobacteria, gamma-Proteobacteria, Cytophaga- Flavobacterium- Bacteroides (CFB) group, Actinobacteria, and Bacillus. Members of the Roseobacter clade and CFB group were the most abundant. In the majority of cases one strain constituted 50% or more of the culturable bacterial flora. About half of the isolates were common to two hatcheries or at least two microalgal cultures. Several isolates were closely related to bacteria associated with harmful dinoflagellates in culture. Thus, the algal cultures seemed to favor certain bacterial species which belonged to distantly separated groups. As some of them could disturb the development of bivalve larvae, the control of bacterial populations would undoubtedly make it possible to reduce larval losses in bivalve rearing.}, }
@article {pmid15692859, year = {2004}, author = {Glissman, K and Chin, KJ and Casper, P and Conrad, R}, title = {Methanogenic pathway and archaeal community structure in the sediment of eutrophic Lake Dagow: effect of temperature.}, journal = {Microbial ecology}, volume = {48}, number = {3}, pages = {389-399}, pmid = {15692859}, issn = {0095-3628}, mesh = {Archaea/genetics/*physiology ; Carbon Dioxide ; Environmental Microbiology ; *Eutrophication ; Fresh Water ; Geologic Sediments/*microbiology ; Germany ; Hydrogen ; Methane/*metabolism ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Temperature ; }, abstract = {Methanogenic degradation of organic matter is an important microbial process in lake sediments. Temperature may affect not only the rate but also the pathway of CH4 production by changing the activity and the abundance of individual microorganisms. Therefore, we studied the function and structure of a methanogenic community in anoxic sediment of Lake Dagow, a eutrophic lake in north-eastern Germany. Incubation of sediment samples (in situ 7.5 degrees C) at increasing temperatures (4, 10, 15, 25, 30 degrees C) resulted in increasing production rates of CH4 and CO2 and in increasing steady-state concentrations of H2. Thermodynamic conditions for H2/CO2 -dependent methanogenesis were only exergonic at 25 and 30 degrees C. Inhibition of methanogenesis with chloroform resulted in the accumulation of methanogenic precursors, i.e., acetate, propionate, and isobutyrate. Mass balance calculations indicated that less CH4 was formed via H2 at 4 degrees C than at 30 degrees C. Conversion of 14CO2 to 14CH4 also showed that H2/CO2 -dependent methanogenesis contributed less to total CH4 production at 4 degrees C than at 30 degrees C. [2-14 C]Acetate turnover rates at 4 degrees C accounted for a higher percentage of total CH4 production than at 30 degrees C. Collectively, these results showed a higher contribution of H2-dependent methanogenesis and a lower contribution of acetate-dependent methanogenesis at high versus low temperature. The archaeal community was characterized by cloning, sequencing, and phylogenetic analysis of the 16S rRNA genes retrieved from the sediment. Sequences were affiliated with Methanosaetaceae, Methanomicrobiaceae, and three deeply branching euryarchaeotal clusters, i.e., group III, Rice cluster V, and a novel euryarchaeotal cluster, the LDS cluster. Terminal restriction fragment length polymorphism (T-RFLP) analysis showed that 16S rRNA genes affiliated to Methanosaetaceae (20-30%), Methanomicrobiaceae (35-55%), and group III (10-25%) contributed most to the archaeal community. Incubation of the sediment at different temperatures (4-30 degrees C) did not result in a systematic change of the archaeal community composition, indicating that change of temperature primarily affected the activity rather than the structure of the methanogenic community.}, }
@article {pmid15692858, year = {2004}, author = {Blum, LK and Roberts, MS and Garland, JL and Mills, AL}, title = {Distribution of microbial communities associated with the dominant high marsh plants and sediments of the United States East Coast.}, journal = {Microbial ecology}, volume = {48}, number = {3}, pages = {375-388}, pmid = {15692858}, issn = {0095-3628}, mesh = {Bacteria ; Ecosystem ; *Environmental Microbiology ; Fungi ; Geography ; Geologic Sediments/*microbiology ; Plants/*microbiology ; Polymorphism, Restriction Fragment Length ; Seawater ; Species Specificity ; United States ; }, abstract = {Microbial communities in the sediment and associated with the dominant type of standing dead plant were collected from the high marsh zones of 10 sites along the eastern coast of the United States from Maine to Florida. Microbial community composition was examined using T-RFLP, and bacterial and fungal abundance was determined microscopically. Within the sediment, community composition was strongly correlated with latitude, indicating that biogeographical factors are important determinants of sediment community composition, whereas abundance was positively and strongly correlated with sediment organic matter content. A strong biogeographical effect was observed for both bacterial and fungal abundance on standing dead plants, but there was no clear relationship between community composition and latitude. Microbial community composition was more similar among plants of the same type (i.e., related plant species) suggesting that plant type (i.e., substrate quality) is primarily responsible for the determining community composition on standing dead plants.}, }
@article {pmid15692857, year = {2004}, author = {Duarte, S and Pascoal, C and Cássio, F}, title = {Effects of zinc on leaf decomposition by fungi in streams: studies in microcosms.}, journal = {Microbial ecology}, volume = {48}, number = {3}, pages = {366-374}, pmid = {15692857}, issn = {0095-3628}, mesh = {Alnus ; Dose-Response Relationship, Drug ; Ecosystem ; Fresh Water/chemistry/*microbiology ; Fungi/*drug effects/physiology ; Plant Leaves/*chemistry ; Time Factors ; Water Pollutants, Chemical/*pharmacology ; Zinc/*pharmacology ; }, abstract = {The effect of zinc on leaf decomposition by aquatic fungi was studied in microcosms. Alder leaf disks were precolonized for 15 days at the source of the Este River and exposed to different zinc concentrations during 25 days. Leaf mass loss, fungal biomass (based on ergosterol concentration), fungal production (rates of [1-14C]acetate incorporation into ergosterol), sporulation rates, and species richness of aquatic hyphomycetes were determined. At the source of the Este River decomposition of alder leaves was fast and 50% of the initial mass was lost in 25 days. A total of 18 aquatic hyphomycete species were recorded during 42 days of leaf immersion. Articulospora tetracladia was the dominant species, followed by Lunulospora curvula and two unidentified species with sigmoid conidia. Cluster analysis suggested that zinc concentration and exposure time affected the structure of aquatic hyphomycete assemblages, even though richness had not been severely affected. Both zinc concentration and exposure time significantly affected leaf mass loss, fungal production and sporulation, but not fungal biomass. Zinc exposure reduced leaf mass loss, inhibited fungal production and affected fungal reproduction by either stimulating or inhibiting sporulation rates. The results of this work suggested zinc pollution might depress leaf decomposition in streams due to changes in the structure and activity of aquatic fungi.}, }
@article {pmid15692856, year = {2004}, author = {Rodger, S and Griffiths, BS and McNicol, JW and Wheatley, RW and Young, IM}, title = {The impact of bacterial diet on the migration and navigation of Caenorhabditis elegans.}, journal = {Microbial ecology}, volume = {48}, number = {3}, pages = {358-365}, pmid = {15692856}, issn = {0095-3628}, mesh = {Acinetobacter calcoaceticus/*physiology ; Animals ; Bacillus megaterium/*physiology ; Behavior, Animal ; Caenorhabditis elegans/*physiology ; Escherichia coli/*physiology ; Feeding Behavior ; Movement ; Rhabditoidea/physiology ; Serratia liquefaciens/*physiology ; }, abstract = {Can diet have a significant impact on the ability of organisms to sense and locate food? Focusing on the bacterial feeder Caenorhabditis elegans, we investigated what effect preconditioning on a range of bacterial substrates had on the subsequent chemotaxis process involved in the nematode locating other bacterial populations. Remarkably, we found that C. elegans, initially fed on a diet of Escherichia coli OP50, was significantly impaired in finding E. coli OP50 populations, compared to other available bacterial populations (P <0.001). We found similar results for another bacterial feeding nematode species, suggesting that a general "substrate legacy" may operate across a wide range of organisms. We discuss this important finding with respect to the variation in response exhibited within a given nematode population, and the impact nematode migration has on bacterial dispersal in the environment.}, }
@article {pmid15692855, year = {2004}, author = {Bainton, NJ and Lynch, JM and Naseby, D and Way, JA}, title = {Survival and ecological fitness of Pseudomonas fluorescens genetically engineered with dual biocontrol mechanisms.}, journal = {Microbial ecology}, volume = {48}, number = {3}, pages = {349-357}, pmid = {15692855}, issn = {0095-3628}, mesh = {Biodiversity ; Ecosystem ; Genetic Engineering ; Organisms, Genetically Modified ; Pisum sativum/growth &amp; development/microbiology ; Pest Control, Biological/*methods ; Plant Roots/microbiology ; Pseudomonas fluorescens/*genetics/*physiology ; }, abstract = {The antibiotic 2,4-diacetylphloroglucinol (Phl) is produced by a range of naturally occurring fluorescent pseudomonads. One isolate, Pseudomonas fluorescens F113, protects pea plants from the pathogenic fungus Pythium ultimum by reducing the number of pathogenic lesions on plant roots, but with a concurrent reduction in the emergence of plants such as pea. The genes responsible for Phl production have been shown to be functionally conserved between the wild-type (wt) P. fluorescens strains F113 and Q2-87. In this study the genes from F113 were isolated using an optimized long PCR method and a 6.7-kb gene cluster inserted into the chromosome of the non-Phl-producing P. fluorescens strain SBW25 EeZY6KX. This strain is a lacZY, km(R) marked derivative of the wt SBW25 which effects biological control against the plant pathogen Pythium ultimum by competitive exclusion as a result of its strong rhizosphere-colonizing ability. We describe here the integration of the Phl antifungal and competitive exclusion mechanisms into a single strain, and the impact this has on survival and plant emergence in microcosms. The insertion of the Phl biosynthetic genes from the F113 into the SBW25 chromosome gave a Phl-producing transformant (strain Pa21) able to suppress P. ultimum through antibiotic production. The growth of Pa21 was not reduced in flask culture at 20 degrees C compared with its parent strain. When inoculated on pea seedlings, the strain containing the Phl operon behaved similarly to the SBW25 EeZY6KX parent but did not show the tendency of the wt Phl producer F113 to cause lower pea seed emergence. Pea roots inoculated with SBW25 EeZY6KX have significantly lower indigenous populations than with F113 and the control. This is indicative of this strain's strong colonising presence. Pa21, the Phl-modified strain, is able to exclude the resident population from roots to the same degree as the SBW25 EeZY6KX from which it is derived. This suggests that it has maintained its competitiveness around the root systems of plants even with the introduction of the Phl locus. Thus, strain Pa21 possesses the qualities necessary to provide effective integrated biocontrol, through maintaining both its wt trait of competitive exclusion on the plant roots, while also expressing the genes from the F113 biocontrol strain for Phl production. Interestingly, however, an additional beneficial trait appears to emerge with the strain Pa21's lowered survival competence compared with SBW25 EeZY6KX in the rhizosphere soil. With fears of the spread of genetically modified organisms and persistence in the soil, this trait may be of some ecological and commercial benefit and becomes a candidate for further investigation and possible exploitation.}, }
@article {pmid15692854, year = {2004}, author = {Mazzola, M and Funnell, DL and Raaijmakers, JM}, title = {Wheat cultivar-specific selection of 2,4-diacetylphloroglucinol-producing fluorescent Pseudomonas species from resident soil populations.}, journal = {Microbial ecology}, volume = {48}, number = {3}, pages = {338-348}, pmid = {15692854}, issn = {0095-3628}, mesh = {Bacterial Proteins/genetics/physiology ; Biodiversity ; Fluorescence ; Genetic Variation ; Genotype ; Phloroglucinol/analogs &amp; derivatives/*metabolism ; Phylogeny ; Population Density ; Pseudomonas/genetics/metabolism/*physiology ; Pseudomonas fluorescens/physiology ; Soil Microbiology ; Triticum/genetics/*microbiology ; }, abstract = {An emerging body of evidence indicates a role for plant genotype as a determinant of the species and genetic composition of the saprophytic microbial community resident to the rhizosphere. In this study, experiments were conducted to determine the capacity of five different wheat cultivars to enhance resident populations and support introduced strains of 2,4-diacetylphloroglucinol (2,4-DAPG)-producing fluorescent pseudomonads, a group of bacteria known to provide biological control of several soilborne diseases. When soils were cropped with three successive 28-day growth cycles of wheat, the 2,4-DAPG-producing strains were consistently recovered from the rhizosphere of the cultivar Lewjain, and commonly were present at populations higher than those recovered from other wheat cultivars. Based on restriction fragment length polymorphism and sequence analyses of phlD, a key gene involved in 2,4-DAPG production, two previously undefined phlD+ genotypes, referred to as genotypes PfZ and PfY, were discovered. Wheat cultivar Lewjain was the primary source of genotype PfY while cultivar Penawawa yielded the majority of genotype PfZ. Based on 16S rDNA sequence analysis, both new phlD genotypes were classified as P. fluorescens. Comparison of the rhizosphere competence of 2,4-DAPG-producing P. fluorescens Q2-87 (genotype B) and P. fluorescens LR3-A28 (genotype PfY) showed that both strains persisted at similar populations in the rhizosphere of all cultivars tested over a 30 day period when introduced as a seed inoculant. However, when strain LR3-A28 was applied as a soil inoculant, this strain was recovered at higher populations from the rhizosphere of wheat cultivar Lewjain than from the rhizospheres of two other cultivars. No cultivar effects were shown for strain Q2-87. Collectively, these results add further to evidence indicating a degree of specificity in interactions between plant cultivars and specific members of the saprophytic microbial community. Furthermore, as 2,4-DAPG-producing fluorescent Pseudomonas spp. have a central role in the spontaneous reduction in severity of take-all disease of wheat in response to continuous wheat monoculture, we postulate that the use of specific cultivars, such as Lewjain, which possess a superior capacity to enhance resident soil populations of these bacteria may have potential to reduce the length of the monoculture period required to induce natural suppressiveness of soils toward this disease.}, }
@article {pmid15692853, year = {2004}, author = {Bucher, VV and Pointing, SB and Hyde, KD and Reddy, CA}, title = {Production of wood decay enzymes, loss of mass, and lignin solubilization in wood by diverse tropical freshwater fungi.}, journal = {Microbial ecology}, volume = {48}, number = {3}, pages = {331-337}, pmid = {15692853}, issn = {0095-3628}, mesh = {Cellulase/metabolism ; Fresh Water/*microbiology ; Fungi/classification/*enzymology ; Laccase/metabolism ; Lignin/*metabolism ; Peroxidases/metabolism ; Solubility ; Tropical Climate ; *Wood ; Xylosidases/metabolism ; }, abstract = {In vitro production of cellulase and xylanase was common among diverse freshwater ascomycetes and their hyphomycetous anamorphs. Production of enzymes involved in lignin degradation was rare. Most isolates were capable of causing mass loss in angiosperm wood, although values were low, at approximately 10% during a 24-week period. A few isolates caused higher mass loss of up to 26.5%, and five of these were shown to solubilize significant amounts of lignin. This is the first report of lignin solubilization by freshwater fungi. Torula herbarum (hyphomycete) and Ophioceras dolichostomum (ascomycete) produced indices of lignin solubilization equivalent to those of terrestrial white-rot basidiomycetes. In all cases wood decay was 2.2- to 3-fold higher in exposed rather than submerged conditions.}, }
@article {pmid15692852, year = {2004}, author = {McNamara, CJ and Leff, LG}, title = {Response of biofilm bacteria to dissolved organic matter from decomposing maple leaves.}, journal = {Microbial ecology}, volume = {48}, number = {3}, pages = {324-330}, pmid = {15692852}, issn = {0095-3628}, mesh = {Acer/*chemistry ; Acinetobacter calcoaceticus/physiology ; Biofilms/*growth &amp; development ; Burkholderia cepacia/physiology ; Fresh Water/*chemistry ; Plant Leaves/*chemistry ; Pseudomonas putida/physiology ; Time Factors ; }, abstract = {Stream bacteria play an important role in the utilization of dissolved organic matter (DOM) leached from leaves, and in transfer of this DOM to other trophic levels. Leaf leachate is a mixture of labile, recalcitrant, and inhibitory compounds, and bacterial communities vary in their ability to utilize leachate. The purpose of this study was to determine the effects of DOM from sugar maple leaves on bacterial populations in biofilms on decomposing leaf surfaces. Populations of Acinetobacter calcoaceticus, Burkholderia cepacia, and Pseudomonas putida were enumerated on decomposing maple leaves in a northeast Ohio stream using fluorescence in situ hybridization. Additionally, artificial substrata consisting of PVC-end caps filled with agar supplemented with leaf leachate and covered with cellulose filters were used to determine bacterial response to leachate from leaves at different stages of decomposition. Population sizes of bacterial species exhibited different responses. Leachate did not affect A. calcoaceticus. B. cepacia was tolerant of phenolic compounds released from leaves and the population size increased when DOM concentrations were greatest. In contrast, P. putida was inhibited by phenolic components of leachate when total DOM concentrations were greatest. Differences in response of the bacterial species to components of leaf leachate indicate the complexity of microbial population dynamics and interactions with DOM. Differences among species in response to DOM have the potential to influence transport and retention of organic matter in stream ecosystems.}, }
@article {pmid15692851, year = {2004}, author = {Sigler, WV and Zeyer, J}, title = {Colony-forming analysis of bacterial community succession in deglaciated soils indicates pioneer stress-tolerant opportunists.}, journal = {Microbial ecology}, volume = {48}, number = {3}, pages = {316-323}, pmid = {15692851}, issn = {0095-3628}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/growth &amp; development ; *Bacterial Physiological Phenomena ; Colony Count, Microbial ; Drug Resistance, Bacterial ; Ecosystem ; Greenhouse Effect ; Ice Cover ; Population Dynamics ; *Soil Microbiology ; }, abstract = {We investigated the response of bacterial communities inhabiting two deglaciated soils (10 and 100 years post-deglaciation) to two stimuli: (i) physical disruption (mixing), and (ii) disruption plus nutrient addition. PCR/DGGE analysis of 16S rRNA genes extracted from soil during a 168-h incubation period following the stimuli revealed that more bacterial phylotypes were stimulated in the 10-y soil than in the 100-y soil. In addition to 10-y and 100-y soils, two additional soils (46 and 70 y) were further differentiated using colony-forming curve (CFC) analysis during a 168-h incubation period, which revealed that younger soils contained a higher proportion of rapidly colonizing bacteria than successively older soils. "Eco-collections" of CFC isolates that represented colonies that formed "fast" (during the first 24 h) and "slow" (final 36 h) were harvested from 10-y and 100-y soils and differentiated according to response to three stress parameters: (i) tolerance to nutrient limitation, (ii) tolerance to temperature change, and (iii) resistance to antibiotics. The tested parameters distinguished "fast" from "slow" bacteria regardless of the age of the soil from which they were isolated. Specifically, eco-collections of "fast" bacteria exhibited greater nutrient- and temperature-stress tolerance as well as more frequent antibiotic resistance than "slow" bacteria. Further DGGE analysis showed that several eco-collection phylotype bands matched (electrophoretically) those of soil phylotypes enriched by mixing and nutrient stimulus. Overall, the results of this study indicated that the succession of colony-forming bacteria was differentiated by bacterial opportunism and temporal response to stimuli. Furthermore, although stress tolerance strategies are associated with opportunistic bacteria regardless of successional age, it appears that the proportion of opportunistic bacteria distinguishes early vs late succession forefield bacterial populations.}, }
@article {pmid15692850, year = {2004}, author = {Ben-David, EA and Holden, PJ and Stone, DJ and Harch, BD and Foster, LJ}, title = {The use of phospholipid fatty acid analysis to measure impact of acid rock drainage on microbial communities in sediments.}, journal = {Microbial ecology}, volume = {48}, number = {3}, pages = {300-315}, pmid = {15692850}, issn = {0095-3628}, mesh = {Bacteria/*metabolism ; Environment ; Fatty Acids/*analysis ; Fresh Water ; Hydrogen-Ion Concentration ; Mining ; Phospholipids/*analysis ; South Australia ; *Water Pollution, Chemical ; }, abstract = {The impact of acid rock drainage (ARD) and eutrophication on microbial communities in stream sediments above and below an abandoned mine site in the Adelaide Hills, South Australia, was quantified by PLFA analysis. Multivariate analysis of water quality parameters, including anions, soluble heavy metals, pH, and conductivity, as well as total extractable metal concentrations in sediments, produced clustering of sample sites into three distinct groups. These groups corresponded with levels of nutrient enrichment and/or concentration of pollutants associated with ARD. Total PLFA concentration, which is indicative of microbial biomass, was reduced by >70% at sites along the stream between the mine site and as far as 18 km downstream. Further downstream, however, recovery of the microbial abundance was apparent, possibly reflecting dilution effect by downstream tributaries. Total PLFA was >40% higher at, and immediately below, the mine site (0-0.1 km), compared with sites further downstream (2.5-18 km), even after accounting for differences in specific surface area of different sediment samples. The increased microbial population in the proximity of the mine source may be associated with the presence of a thriving iron-oxidizing bacteria community as a consequence of optimal conditions for these organisms while the lower microbial population further downstream corresponded with greater sediments' metal concentrations. PCA of relative abundance revealed a number of PLFAs which were most influential in discriminating between ARD-polluted sites and the rest of the sites. These PLFA included the hydroxy fatty acids: 2OH12:0, 3OH12:0, 2OH16:0; the fungal marker: 18:2omega6; the sulfate-reducing bacteria marker 10Me16:1omega7; and the saturated fatty acids 12:0, 16:0, 18:0. Partial constrained ordination revealed that the environmental parameters with the greatest bearing on the PLFA profiles included pH, soluble aluminum, total extractable iron, and zinc. The study demonstrated the successful application of PLFA analysis to rapidly assess the toxicity of ARD-affected waters and sediments and to differentiate this response from the effects of other pollutants, such as increased nutrients and salinity.}, }
@article {pmid15692849, year = {2004}, author = {Malits, A and Peters, F and Bayer-Giraldi, M and Marrasé, C and Zoppini, A and Guadayol, O and Alcaraz, M}, title = {Effects of small-scale turbulence on bacteria: a matter of size.}, journal = {Microbial ecology}, volume = {48}, number = {3}, pages = {287-299}, pmid = {15692849}, issn = {0095-3628}, mesh = {Bacteria/cytology/*growth &amp; development ; *Bacterial Physiological Phenomena ; Cell Division ; Chlorophyll ; Chlorophyll A ; Flagella ; Plankton/physiology ; Time Factors ; *Water Movements ; }, abstract = {We examined the influence of small-scale turbulence and its associated shear on bacterioplankton abundance and cell size. We incubated natural microbial assemblages and bacteria-only fractions and subjected them to treatments with turbulence and additions of mineral nutrients and/or organic carbon. Bacterial abundance was not affected directly by turbulence in bacteria-only incubations. In natural microbial assemblage incubations, bacterial concentrations were higher under turbulence than in still-water controls when nutrients were added. In general, in the turbulence treatments bacteria increased significantly in size, mainly due to elongation of cells. The addition of inorganic nutrients had a negative effect on bacterial size, but a significantly positive effect on abundance independently of other factors such as turbulence and the presence of predators. Flagellate grazing did not trigger an increase in bacterial size as a grazing resistance response in unmixed containers. With the addition of organic carbon, bacteria elongated and partly settled to the bottom of the containers, in both the turbulent and still treatment, but bacterial abundance did not further increase. Furthermore, bacteria aggregated in the turbulence treatments after the second day of incubation even in the absence of other components of the microbial community. We found that turbulence and the associated shear increase bacterial size and change bacterial morphology, at least under certain nutrient conditions. This might be due to a physiological response (enhanced growth rate and/or unbalanced growth) or due to the selection of opportunistic strains when organic carbon is in excess compared to mineral nutrients. We suggest that shear associated with turbulent flow enhances the DOM flux to bacteria directly as well as indirectly through enhanced grazing activity and photosynthetic release. The formation of bacterial aggregates and filaments under turbulence might give selective advantage to bacteria in terms of nutrient uptake and grazing resistance.}, }
@article {pmid15690230, year = {2005}, author = {Zelenev, VV and van Bruggen, AH and Semenov, AM}, title = {Short-term wavelike dynamics of bacterial populations in response to nutrient input from fresh plant residues.}, journal = {Microbial ecology}, volume = {49}, number = {1}, pages = {83-93}, pmid = {15690230}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development/metabolism ; Colony Count, Microbial ; Hydrogen-Ion Concentration ; Linear Models ; Lolium ; Nitrates/metabolism ; Plant Stems/metabolism ; Population Dynamics ; Quaternary Ammonium Compounds/metabolism ; Soil/*analysis ; *Soil Microbiology ; Trifolium ; }, abstract = {The objectives of the research were to investigate short-term dynamics of bacterial populations in soil after a disturbance in the form of fresh organic matter incorporation and to investigate how these dynamics are linked to those of some environmental parameters. To reach these objectives, soil bacterial populations, mineral nitrogen, pH, and redox potential (ROP) were monitored daily for 1 month after incorporation of clover-grass (CG) plant material in microcosm experiments. Colony-forming units (CFUs) and direct microscopic counts of FDA-stained and FTTC-stained bacteria increased immediately after incorporation of the plant material, dropped within 2 days, and fluctuated thereafter. Harmonics analysis demonstrated that there were significant wavelike fluctuations with three or four significant peaks within 1 month after incorporation of clover-grass material. Peaks in CFUs were 1-2 days ahead of those in direct counts. Ammonium (NH4) concentrations increased from the start of the experiments until nitrification commenced. Nitrate (NO3) concentrations dropped immediately after plant incorporation, and then rose monotonically until the end of the experiments. There were no wavelike fluctuations in NH4 and NO3 concentrations, so that bacterial fluctuations could not be attributed to alternating mineral N shortages and sufficiencies. pH levels rose and declined with NH4 levels. ROP dropped shortly before NH4 concentrations rose, and increased before NH4 concentrations decreased; there were no regular fluctuations in ROP, so that temporary oxygen shortages may not have been responsible for the observed fluctuations in bacterial populations. Thus, for the first time, regular wavelike dynamics were demonstrated for bacterial populations after perturbation by addition of fresh organic matter to soil, and several potential reasons for the death phase of the fluctuations could be excluded from further consideration.}, }
@article {pmid15690229, year = {2005}, author = {Rodriguez Zaragoza, S and Mayzlish, E and Steinberger, Y}, title = {Seasonal changes in free-living amoeba species in the root canopy of Zygophyllum dumosum in the Negev Desert, Israel.}, journal = {Microbial ecology}, volume = {49}, number = {1}, pages = {134-141}, pmid = {15690229}, issn = {0095-3628}, mesh = {*Amoebida ; Analysis of Variance ; Animals ; *Biodiversity ; Cluster Analysis ; Israel ; Plant Roots/*microbiology ; *Seasons ; *Soil Microbiology ; Zygophyllum/*microbiology ; }, abstract = {The influence of seasonality and Zygophyllum dumosum root canopy on the species diversity of free-living amoebae at two soil depths (0-10 and 10-20 cm) was studied in a Negev Desert ecosystem in Israel. Free-living amoebae were extracted and identified after cultivation in non-nutritive agar plates. A total of 90 amoeba species were identified in the soil during the study period, with the most common genera present being Hartmannella, Platyamoeba, Vahlkampfia, Acanthamoeba, and Echinamoeba. Differences between the control soil and the soil under Z. dumosum were found mainly during the dry seasons, when 97% similarity was found between the two soil layers, which could be due to the effect of the shrub on the soil microenvironment. The amoeba community exhibited more species diversity in spring (reaching a value of 34 species) than in the winter (18 species) or summer and autumn (20 species), since the community has a time lag for becoming stabilized after the dry summer and autumn. This is one of the first studies on the amoeba population in the Negev Desert and elucidates the importance and the need for taking trophic and functional groups into consideration in order to understand biomineralization processes.}, }
@article {pmid15690228, year = {2005}, author = {Caravaca, F and Alguacil, MM and Azcón, R and Parladé, J and Torres, P and Roldán, A}, title = {Establishment of two ectomycorrhizal shrub species in a semiarid site after in situ amendment with sugar beet, rock phosphate, and Aspergillus niger.}, journal = {Microbial ecology}, volume = {49}, number = {1}, pages = {73-82}, pmid = {15690228}, issn = {0095-3628}, mesh = {Analysis of Variance ; Aspergillus niger/metabolism ; Beta vulgaris/metabolism ; Carbon/metabolism ; Cistus/*growth &amp; development/metabolism/microbiology ; Electric Conductivity ; Enzymes/metabolism ; Hydrogen-Ion Concentration ; *Mycorrhizae ; Phosphates/metabolism ; Quercus/*growth &amp; development/metabolism/microbiology ; Soil/*analysis ; *Soil Microbiology ; Spain ; }, abstract = {A field experiment was carried out to assess the effectiveness of the addition of sugar beet, rock phosphate, and Aspergillus niger directly into the planting hole, and the mycorrhizal inoculation of seedlings with Scleroderma verrucosum, for promotion of plant growth of Cistus albidus L. and Quercus coccifera L. and enhancement of soil physicochemical, biochemical, and biological properties, in a degraded semiarid Mediterranean area. One year after planting, the available phosphorus content in the amended soils of both species was about fourfold higher than in the nonamended soil. Amendment addition increased the aggregate stability of the rhizosphere of C. albidus (by 56% with respect to control soil) while the mycorrhizal inoculation increased only the aggregate stability of the rhizosphere of Q. coccifera (by 13% with respect to control soil). Biomass C content and enzyme activities (dehydrogenase, urease, protease-BAA, acid phosphatase, and beta-glucosidase) of the rhizosphere of C. albidus were increased by amendment addition but not by mycorrhizal inoculation. Both treatments increased enzyme activities of the rhizosphere of Q. coccifera. The mycorrhizal inoculation of the seedlings with S. verrucosum was the most effective treatment for stimulating the growth of C. albidus (by 469% with respect to control plants) and Q. coccifera (by 74% with respect to control plants). The combined treatment, involving mycorrhizal inoculation of seedlings and addition of the amendment directly into soil, had no additive effect on the growth of either shrub species.}, }
@article {pmid15690227, year = {2005}, author = {Bossio, DA and Girvan, MS and Verchot, L and Bullimore, J and Borelli, T and Albrecht, A and Scow, KM and Ball, AS and Pretty, JN and Osborn, AM}, title = {Soil microbial community response to land use change in an agricultural landscape of western Kenya.}, journal = {Microbial ecology}, volume = {49}, number = {1}, pages = {50-62}, pmid = {15690227}, issn = {0095-3628}, mesh = {*Agriculture ; Bacteria/genetics/*metabolism ; Biomass ; Carbon/metabolism ; Cluster Analysis ; *Ecosystem ; Electrophoresis ; Fatty Acids/metabolism ; Kenya ; Multivariate Analysis ; Nitrogen/metabolism ; Phospholipids/metabolism ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; *Trees ; Tropical Climate ; }, abstract = {Tropical agroecosystems are subject to degradation processes such as losses in soil carbon, nutrient depletion, and reduced water holding capacity that occur rapidly resulting in a reduction in soil fertility that can be difficult to reverse. In this research, a polyphasic methodology has been used to investigate changes in microbial community structure and function in a series of tropical soils in western Kenya. These soils have different land usage with both wooded and agricultural soils at Kakamega and Ochinga, whereas at Ochinga, Leuro, Teso, and Ugunja a replicated field experiment compared traditional continuous maize cropping against an improved N-fixing fallow system. For all sites, principal component analysis of 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) profiles revealed that soil type was the key determinant of total bacterial community structure, with secondary variation found between wooded and agricultural soils. Similarly, phospholipid fatty acid (PLFA) analysis also separated wooded from agricultural soils, primarily on the basis of higher abundance of monounsaturated fatty acids, anteiso- and iso-branched fatty acids, and methyl-branched fatty acids in the wooded soils. At Kakamega and Ochinga wooded soils had between five 5 and 10-fold higher levels of soil carbon and microbial biomass carbon than agricultural soils from the same location, whereas total enzyme activities were also lower in the agricultural sites. Soils with woody vegetation had a lower percentage of phosphatase activity and higher cellulase and chitinase activities than the agricultural soils. BIOLOG analysis showed woodland soils to have the greatest substrate diversity. Throughout the study the two functional indicators (enzyme activity and BIOLOG), however, showed lower specificity with respect to soil type and land usage than did the compositional indicators (DGGE and PLFA). In the field experiment comparing two types of maize cropping, both the maize yields and total microbial biomass were found to increase with the fallow system. Moreover, 16S rRNA gene and PLFA analyses revealed shifts in the total microbial community in response to the different management regimes, indicating that deliberate management of soils can have considerable impact on microbial community structure and function in tropical soils.}, }
@article {pmid15690226, year = {2005}, author = {Mattison, RG and Taki, H and Harayama, S}, title = {The soil flagellate Heteromita globosa accelerates bacterial degradation of alkylbenzenes through grazing and acetate excretion in batch culture.}, journal = {Microbial ecology}, volume = {49}, number = {1}, pages = {142-150}, pmid = {15690226}, issn = {0095-3628}, mesh = {Acetates/*metabolism ; Analysis of Variance ; Animals ; Benzene/*metabolism/toxicity ; Benzene Derivatives/metabolism/toxicity ; Biodegradation, Environmental ; Carbon Radioisotopes/metabolism ; Chromatography, Gas ; Eukaryota/drug effects/growth &amp; development/*metabolism ; Inhibitory Concentration 50 ; Nitrates/metabolism ; Oxygen/metabolism ; Pseudomonas/drug effects/*metabolism ; Soil/*parasitology ; Toluene/metabolism/toxicity ; }, abstract = {The impact of grazing by soil flagellates Heteromita globosa on aerobic biodegradation of benzene by Pseudomonas strain PS+ was examined in batch culture. Growth of H. globosa on these bacteria obeyed Monod kinetics (mu(max), 0.17 +/- 0.03 h(-1); K(s), 1.1 +/- 0.2 x 10(7) bacteria mL(-1)) and was optimal at a bacteria/ flagellate ratio of 2000. Carbon mass balance showed that 5.2% of total [ring-U-(14)C]benzene fed to bacteria was subsequently incorporated into flagellate biomass. Growth-inhibiting concentrations (IC50) of alkylbenzenes (benzene, toluene, ethylbenzene) were inversely related with their octanol/ water partitioning coefficients, and benzene was least toxic for bacteria and flagellates with IC50 values of 4392 (+/- 167) microM and 2770 (+/- 653) microM, respectively. The first-order rate constant for benzene degradation (k1, 0.48 +/- 0.12 day(-1)) was unaffected by the presence or absence of flagellates in cultures. However, the rate of benzene degradation by individual bacteria averaged three times higher in the presence of flagellates (0.73 +/- 0.13 fmol cell(-1) h(-1)) than in their absence (0.26 +/- 0.03 fmol cell(-1) h(-1)). Benzene degradation also coincided with higher levels of dissolved oxygen and a higher rate of nitrate reduction in the presence of flagellates (p < 0.02). Grazing by flagellates may have increased the availability of dissolved oxygen to a smaller surviving population of bacteria engaged in the aerobic reactions initiating benzene degradation. In addition, flagellates may also have increased the rate of nitrate reduction through the excretion of acetate as an additional electron donor for these bacteria. Indeed, acetate was shown to progressively accumulate in cultures where flagellates grazed on heat-killed bacteria. This study provided evidence that grazing flagellates stimulate bacterial degradation of alkylbenzenes and provide a link for carbon cycling to consumers at higher trophic levels. This may have important implications for bioremediation processes.}, }
@article {pmid15690225, year = {2005}, author = {Tsuchida, T and Koga, R and Meng, XY and Matsumoto, T and Fukatsu, T}, title = {Characterization of a facultative endosymbiotic bacterium of the pea aphid Acyrthosiphon pisum.}, journal = {Microbial ecology}, volume = {49}, number = {1}, pages = {126-133}, pmid = {15690225}, issn = {0095-3628}, mesh = {Animals ; Aphids/*microbiology/ultrastructure ; Bacteria/*genetics ; Base Sequence ; DNA Primers ; DNA, Mitochondrial/genetics ; In Situ Hybridization, Fluorescence ; Japan ; Microscopy, Electron ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; }, abstract = {The pea aphid U-type symbiont (PAUS) was investigated to characterize its microbiological properties. Fluorescence in situ hybridization (FISH) and electron microscopy revealed that PAUS was a rod-shaped bacterium found in three different locations in the body of the pea aphid Acyrthosiphon pisum: sheath cells, secondary mycetocytes, and hemolymph. Artificial transfer experiments revealed that PAUS could establish stable infection and vertical transmission when introduced into uninfected pea aphids. When 28 aphid species collected in Japan were subjected to a diagnostic PCR assay, four species of the subfamily Aphidinae (Aphis citricola, Aphis nerii, Macrosiphum avenae, and Uroleucon giganteus) and a species of the subfamily Pemphiginae (Colopha kansugei) were identified to be PAUS-positive. The sporadic incidences of PAUS infection without reflecting the aphid phylogeny can be best explained by occasional horizontal transfers of the symbiont across aphid lineages.}, }
@article {pmid15688258, year = {2005}, author = {Rooney-Varga, JN and Giewat, MW and Savin, MC and Sood, S and LeGresley, M and Martin, JL}, title = {Links between phytoplankton and bacterial community dynamics in a coastal marine environment.}, journal = {Microbial ecology}, volume = {49}, number = {1}, pages = {163-175}, pmid = {15688258}, issn = {0095-3628}, mesh = {Atlantic Ocean ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; Base Sequence ; Diatoms/genetics/*physiology ; *Ecosystem ; Electrophoresis ; Likelihood Functions ; *Marine Biology ; Models, Genetic ; Molecular Sequence Data ; New Brunswick ; *Phylogeny ; Phytoplankton/genetics/*physiology ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Bacteria and phytoplankton dynamics are thought to be closely linked in coastal marine environments, with correlations frequently observed between bacterial and phytoplankton biomass. In contrast, little is known about how these communities interact with each other at the species composition level. The purpose of the current study was to analyze bacterial community dynamics in a productive, coastal ecosystem and to determine whether they were related to phytoplankton community dynamics. Near-surface seawater samples were collected in February, May, July, and September 2000 from several stations in the Bay of Fundy. Savin et al. (M.C. Savin et al., Microb Ecol 48: 51-65) analyzed the phytoplankton community in simultaneously collected samples. The attached and free-living bacterial communities were collected by successive filtration onto 5 microm and 0.22 microm pore-size filters, respectively. DNA was extracted from filters and bacterial 16S rRNA gene fragments were amplified and analyzed by denaturing gradient gel electrophoresis (DGGE). DGGE revealed that diversity and temporal variability were lower in the free-living than the attached bacterial community. Both attached and free-living communities were dominated by members of the Roseobacter and Cytophaga groups. Correspondence analysis (CA) ordination diagrams showed similar patterns for the phytoplankton and attached bacterial communities, indicating that shifts in the species composition of these communities were linked. Similarly, canonical CA revealed that the diversity, abundance, and percentage of diatoms in the phytoplankton community accounted for a significant amount of the variability in the attached bacterial community composition. In contrast, ordination analyses did not reveal an association between free-living bacteria and phytoplankton. These results suggest that there are specific interactions between phytoplankton and the bacteria attached to them, and that these interactions influence the composition of both communities.}, }
@article {pmid15688257, year = {2005}, author = {Komlos, J and Cunningham, AB and Camper, AK and Sharp, RR}, title = {Interaction of Klebsiella oxytoca and Burkholderia cepacia in dual-species batch cultures and biofilms as a function of growth rate and substrate concentration.}, journal = {Microbial ecology}, volume = {49}, number = {1}, pages = {114-125}, pmid = {15688257}, issn = {0095-3628}, mesh = {Biodegradation, Environmental ; *Biofilms ; Burkholderia cepacia/growth &amp; development/metabolism/*physiology ; Carbon/metabolism ; *Culture Media ; Klebsiella oxytoca/growth &amp; development/metabolism/*physiology ; Population Density ; Population Dynamics ; Species Specificity ; }, abstract = {Dual-species microbial interactions have been extensively reported for batch and continuous culture environments. However, little research has been performed on dual-species interaction in a biofilm. This research examined the effects of growth rate and substrate concentration on dual-species population densities in batch and biofilm reactors. In addition, the feasibility of using batch reactor kinetics to describe dual-species biofilm interactions was explored. The scope of the research was directed toward creating a dual-species biofilm for the biodegradation of trichloroethylene, but the findings are a significant contribution to the study of dual-species interactions in general. The two bacterial species used were Burkholderia cepacia PR1-pTOM(31c), an aerobic organism capable of constitutively mineralizing trichloroethylene (TCE), and Klebsiella oxytoca, a highly mucoid, facultative anaerobic organism. The substrate concentrations used were different dilutions of a nutrient-rich medium resulting in dissolved organic carbon (DOC) concentrations on the order of 30, 70, and 700 mg/L. Presented herein are single- and dual-species population densities and growth rates for these two organisms grown in batch and continuous-flow biofilm reactors. In batch reactors, planktonic growth rates predicted dual-species planktonic species dominance, with the faster-growing organism (K. oxytoca) outcompeting the slower-growing organism (B. cepacia). In a dual-species biofilm, however, dual-species planktonic growth rates did not predict which organism would have the higher dual-species biofilm population density. The relative fraction of each organism in a dual-species biofilm did correlate with substrate concentration, with B. cepacia having a greater proportional density in the dual-species culture with K. oxytoca at low (30 and 70 mg/L DOC) substrate concentrations and K. oxytoca having a greater dual-species population density at a high (700 mg/L DOC) substrate concentration. Results from this research demonstrate the effectiveness of using substrate concentration to control population density in this dual-species biofilm.}, }
@article {pmid15688256, year = {2005}, author = {Rubio, MB and Hermosa, MR and Keck, E and Monte, E}, title = {Specific PCR assays for the detection and quantification of DNA from the biocontrol strain Trichoderma harzianum 2413 in soil.}, journal = {Microbial ecology}, volume = {49}, number = {1}, pages = {25-33}, pmid = {15688256}, issn = {0095-3628}, mesh = {DNA/*genetics ; DNA Primers ; Genetic Markers/genetics ; Nucleic Acid Amplification Techniques/methods ; Polymerase Chain Reaction/*methods ; *Soil Microbiology ; Spectrometry, Fluorescence ; Trichoderma/*genetics ; }, abstract = {Strain identification in situ is an important factor in the monitoring of microorganisms used in the field. In this study, we demonstrated the use of sequence-characterized amplified region (SCAR) markers to detect genomic DNA from Trichoderma harzianum 2413 from soil. Two primers (SCAR A1/SCAR A1c) were tested against DNA of 27 isolates of Trichoderma spp. and amplified a 990-bp fragment from T. atroviride 11 and a 1.5-kb fragment from T. harzianum 2413, using an annealing temperature of 68 degrees C. These fragments showed no significant homology to any sequence deposited in the databases. The primer pair, BR1 and BR2, was designed to the 1.5-kb fragment amplified from T. harzianum 2413, generating a SCAR marker. To test the specificity of these primers, experiments were conducted using the DNA from 27 Trichoderma spp. strains and 22 field soil samples obtained from four different countries. PCR results showed that BR1 and BR2 amplified an 837-bp fragment unique to T. harzianum 2413. Assays in which total DNA was extracted from sterile and nonsterile soil samples, inoculated with spore or mycelium combinations of Trichoderma spp. strains, indicated that the BR1 and BR2 primers could specifically detect T. harzianum 2413 in a pool of mixed DNA. No other soil-microorganisms containing these sequences were amplified using these primers. To test whether the 837-bp SCAR marker of T. harzianum 2413 could be used in real-time PCR experiments, new primers (Q2413f and Q2413r) conjugated with a TaqMan fluorogenic probe were designed. Real-time PCR assays were applied using DNA from sterile and nonsterile soil samples inoculated with a known quantity of spores of Trichoderma spp. strains.}, }
@article {pmid15688255, year = {2005}, author = {Gkelis, S and Rajaniemi, P and Vardaka, E and Moustaka-Gouni, M and Lanaras, T and Sivonen, K}, title = {Limnothrix redekei (Van Goor) Meffert (Cyanobacteria) strains from Lake Kastoria, Greece form a separate phylogenetic group.}, journal = {Microbial ecology}, volume = {49}, number = {1}, pages = {176-182}, pmid = {15688255}, issn = {0095-3628}, mesh = {Analysis of Variance ; Base Sequence ; Cluster Analysis ; Cyanobacteria/*genetics/*ultrastructure ; DNA Primers ; Fresh Water ; Greece ; Likelihood Functions ; Microscopy, Electron ; Microscopy, Fluorescence ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; *Water Microbiology ; }, abstract = {Three strains of Limnothrix (Cyanobacteria) isolated from Lake Kastoria, Greece, were characterized based on their morphological features and 16S rRNA gene sequences. The Limnothrix isolates 007a, 165a, and 165c can morphologically be assigned to Limnothrix redekei (Van Goor) Meffert. The 16S rRNA gene of the Limnothrix strains showed a 99% similarity to the 16S rRNA gene of Planktothrix sp. FP1. Limnothrix redekei strains 165a, 165c, 007a and Planktothrix sp. FP1 formed a separate cluster in the cyanobacterial 16S rRNA gene tree. It was distinct from the Pseudanabaena cluster, which included the other Limnothrix strains isolated from northern temperate lakes. This is the first report on the phylogeny of L. redekei strains originating from a Mediterranean lake (southern Europe) and provides new data about the genus Limnothrix.}, }
@article {pmid15683402, year = {2005}, author = {Taylor, MW and Schupp, PJ and de Nys, R and Kjelleberg, S and Steinberg, PD}, title = {Biogeography of bacteria associated with the marine sponge Cymbastela concentrica.}, journal = {Environmental microbiology}, volume = {7}, number = {3}, pages = {419-433}, doi = {10.1111/j.1462-2920.2004.00711.x}, pmid = {15683402}, issn = {1462-2912}, mesh = {Animals ; Biodiversity ; *Ecosystem ; Electrophoresis, Polyacrylamide Gel ; Oceans and Seas ; Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {Recent debate regarding microbial biogeography has focused largely on free-living microbes, yet those microbes associated with host organisms are also of interest from a biogeographical perspective. Marine eukaryotes and associated bacteria should provide ideal systems in which to consider microbial biogeography, as (i) bacteria in seawater should be able to disperse among individuals of the same host species, yet (ii) potential for adaptation to particular hosts (and thus speciation) also exists. We used 16S rDNA-DGGE (denaturing gradient gel electrophoresis) to examine geographic variability in bacterial community composition in the marine sponge Cymbastela concentrica. Denaturing gradient gel electrophoresis banding patterns (and phylogenetic analysis of excised DGGE bands) indicated different communities in Cymbastela concentrica from tropical versus temperate Australia. In contrast, communities were very similar over a 500-km portion of the sponge's temperate range. Variation in bacterial community composition was also considered with respect to ocean current patterns. We speculate that the divergent communities in different parts of the sponge's range provide evidence of endemism attributed to host association, although variation in environmental factors such as light and temperature could also explain the observed results. Interestingly, bacterial communities in seawater varied much less between tropical and temperate locations than did those in C. concentrica, supporting the concept of widespread dispersal among these free-living microbes.}, }
@article {pmid15683392, year = {2005}, author = {De Windt, W and Aelterman, P and Verstraete, W}, title = {Bioreductive deposition of palladium (0) nanoparticles on Shewanella oneidensis with catalytic activity towards reductive dechlorination of polychlorinated biphenyls.}, journal = {Environmental microbiology}, volume = {7}, number = {3}, pages = {314-325}, doi = {10.1111/j.1462-2920.2005.00696.x}, pmid = {15683392}, issn = {1462-2912}, mesh = {Biodegradation, Environmental ; Chlorine/metabolism ; Environmental Pollutants/metabolism/pharmacokinetics ; Nanostructures ; Oxidation-Reduction ; Palladium/*pharmacokinetics ; Polychlorinated Biphenyls/*metabolism/toxicity ; Shewanella/classification/*metabolism/ultrastructure ; }, abstract = {Microbial reduction of soluble Pd(II) by cells of Shewanella oneidensis MR-1 and of an autoaggregating mutant (COAG) resulted in precipitation of palladium Pd(0) nanoparticles on the cell wall and inside the periplasmic space (bioPd). As a result of biosorption and subsequent bioreduction of Pd(II) with H2, formate, lactate, pyruvate or ethanol as electron donors, recoveries higher than 90% of Pd associated with biomass could be obtained. The bioPd(0) nanoparticles thus obtained had the ability to reductively dehalogenate polychlorinated biphenyl (PCB) congeners in aqueous and sediment matrices. Bioreduction was observed in assays with concentrations up to 1000 mg Pd(II) l(-1) with depletion of soluble Pd(II) of 77.4% and higher. More than 90% decrease of PCB 21 (2,3,4-chloro biphenyl) coupled to formation of its dechlorination products PCB 5 (2,3-chloro biphenyl) and PCB 1 (2-chloro biphenyl) was obtained at a concentration of 1 mg l(-1) within 5 h at 28 degrees C. Bioreductive precipitation of bioPd by S. oneidensis cells mixed with sediment samples contaminated with a mixture of PCB congeners, resulted in dechlorination of both highly and lightly chlorinated PCB congeners adsorbed to the contaminated sediment matrix within 48 h at 28 degrees C. Fifty milligrams per litre of bioPd resulted in a catalytic activity that was comparable to 500 mg l(-1) commercial Pd(0) powder. The high reactivity of 50 mg l(-1) bioPd in the soil suspension was reflected in the reduction of the sum of seven most toxic PCBs to 27% of their initial concentration.}, }
@article {pmid15676203, year = {2005}, author = {Cohen, SD}, title = {A protocol for direct sequencing of multiple gene specific PCR products from Discula umbrinella, a fungal endophyte, utilizing bufferless precast electrophoresis.}, journal = {Journal of microbiological methods}, volume = {61}, number = {1}, pages = {131-135}, doi = {10.1016/j.mimet.2004.11.004}, pmid = {15676203}, issn = {0167-7012}, mesh = {Chitin Synthase/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Electrophoresis, Agar Gel ; Mitosporic Fungi/*genetics ; Peptide Elongation Factor 1/chemistry/genetics ; Polymerase Chain Reaction/*methods ; Quercus/*microbiology ; Sequence Analysis, DNA ; }, abstract = {A protocol for direct sequencing of polymerase chain reaction (PCR) products from mycelia of Discula umbrinella, a fungal endophyte, using bufferless electrophoresis is described. This improved method allows researchers to conduct high-capacity screening of multiple gene regions for fungal endophytes applicable to microbial ecology and population genetic studies.}, }
@article {pmid15674247, year = {2005}, author = {Dolan, JR}, title = {Marine ecology: different measures of biodiversity.}, journal = {Nature}, volume = {433}, number = {7024}, pages = {E9; discussion E9}, doi = {10.1038/nature03320}, pmid = {15674247}, issn = {1476-4687}, mesh = {Animals ; *Biodiversity ; Biomass ; Classification ; *Ecology ; Food Chain ; Marine Biology ; Oceans and Seas ; Phytoplankton/classification/*physiology ; Population Density ; Zooplankton/classification/*physiology ; }, abstract = {In their analysis of global trends of diversity in marine plankton, Irigoien et al. find that taxonomic diversity of zooplankton (consumer) is a unimodal function of community biomass that is unrelated to phytoplankton (producer) diversity. Their results are unexpected because in terrestrial organisms primary-producer diversity is a good predictor of consumer diversity. I contend that this apparent uncoupling of producer and consumer diversity in marine plankton is likely to be an artefact due to the authors' use of different measures of diversity for producers and for consumers.}, }
@article {pmid15660994, year = {2005}, author = {Johnson, MR and Montero, CI and Conners, SB and Shockley, KR and Bridger, SL and Kelly, RM}, title = {Population density-dependent regulation of exopolysaccharide formation in the hyperthermophilic bacterium Thermotoga maritima.}, journal = {Molecular microbiology}, volume = {55}, number = {3}, pages = {664-674}, doi = {10.1111/j.1365-2958.2004.04419.x}, pmid = {15660994}, issn = {0950-382X}, mesh = {Bacterial Proteins/genetics/*metabolism ; Culture Media ; Ecosystem ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Genome, Archaeal ; Genome, Bacterial ; Methanococcus/genetics/*growth &amp; development/metabolism ; Oligonucleotide Array Sequence Analysis ; Polysaccharides, Bacterial/*metabolism ; *Signal Transduction ; Temperature ; Thermotoga maritima/*growth &amp; development/metabolism ; Transcription, Genetic ; }, abstract = {Co-cultivation of the hyperthermophiles Thermotoga maritima and Methanococcus jannaschii resulted in fivefold higher T. maritima cell densities when compared with monoculture as well as concomitant formation of exopolysaccharide and flocculation of heterotroph-methanogen cellular aggregates. Transcriptional analysis of T. maritima cells from these aggregates using a whole genome cDNA microarray revealed the induction of a putative exopolysaccharide synthesis pathway, regulated by intracellular levels of cyclic diguanosine 3',5'-(cyclic)phosphate (cyclic di-GMP) and mediated by the action of several GGDEF proteins, including a putative diguanylate cyclase (TM1163) and a putative phosphodiesterase (TM1184). Transcriptional analysis also showed that TM0504, which encodes a polypeptide containing a motif common to known peptide-signalling molecules in mesophilic bacteria, was strongly upregulated in the co-culture. Indeed, when a synthetically produced peptide based on TM0504 was dosed into the culture at ecologically relevant levels, the production of exopolysaccharide was induced at significantly lower cell densities than was observed in cultures lacking added peptide. In addition to identifying a pathway for polysaccharide formation in T. maritima, these results point to the existence of peptide-based quorum sensing in hyperthermophilic bacteria and indicate that cellular communication should be considered as a component of the microbial ecology within hydrothermal habitats.}, }
@article {pmid15659198, year = {2005}, author = {Tresse, O and Mounien, F and Lévesque, MJ and Guiot, S}, title = {Comparison of the microbial population dynamics and phylogenetic characterization of a CANOXIS reactor and a UASB reactor degrading trichloroethene.}, journal = {Journal of applied microbiology}, volume = {98}, number = {2}, pages = {440-449}, doi = {10.1111/j.1365-2672.2004.02475.x}, pmid = {15659198}, issn = {1364-5072}, mesh = {*Bacteria, Aerobic ; *Bacteria, Anaerobic ; Biodegradation, Environmental ; *Bioreactors ; Population Dynamics ; *Soil Pollutants ; *Trichloroethylene ; }, abstract = {AIMS: To understand the microbial ecology underlying trichloethene (TCE) degradation in a coupled anaerobic/aerobic single stage (CANOXIS) reactor oxygenated with hydrogen peroxide (H2O2) and in an upflow anaerobic sludge bed (UASB) reactor.<br><br>METHODS AND RESULTS: The molecular study of the microbial population dynamics and a phylogenetic characterization were conducted using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). In both reactors, TCE had a toxic effect on two uncultured bacterial populations whereas oxygen favoured the growth of aerobic species belonging to Rhizobiaceae and Dechloromonas. No methanotrophic bacteria were detected when targeting 16S rRNA gene with universal primers. Alternatively, pmo gene encoding the particulate methane monooxygenase of Methylomonas sp. LW21 could be detected in the coupled reactor when H2O2 was supplied at 0.7 g O2 l day(-1).<br><br>CONCLUSIONS: Methylomonas sp. LW21 that could be responsible for the aerobic degradation of the TCE by-products is not among the predominant bacterial populations in the coupled reactor. It seems to have been outcompeted by heterotrophic bacteria (Rhizobiaceae and Dechloromonas sp.) for oxygen.<br><br>The results obtained show the limitations of the coupled reactor examined in this study. Further investigations should focus on the operating conditions of this reactor in order to favour the growth of the methanotrophs.}, }
@article {pmid15658993, year = {2005}, author = {Wiles, S and Lilley, AK and Philp, JC and Bailey, MJ and Whiteley, AS}, title = {Calibration and deployment of custom-designed bioreporters for protecting biological remediation consortia from toxic shock.}, journal = {Environmental microbiology}, volume = {7}, number = {2}, pages = {260-269}, doi = {10.1111/j.1462-2920.2004.00703.x}, pmid = {15658993}, issn = {1462-2912}, mesh = {Biodegradation, Environmental ; Biosensing Techniques/*methods ; Genes, Reporter ; Genetic Engineering ; Luminescent Measurements ; Luminescent Proteins/genetics/*metabolism ; Phenol/*analysis/*toxicity ; Photorhabdus/genetics ; Pseudomonadaceae/*drug effects/genetics/growth &amp; development/metabolism ; Waste Disposal, Fluid/methods ; Water Pollutants, Chemical/metabolism ; Water Pollution, Chemical ; Water Purification/methods ; }, abstract = {We have previously described the development of a panel of site-specific lux-based bioreporters from an industrial wastewater treatment system remediating coking effluents. The Pseudomonad strains carry a stable chromosomal copy of the luxCDABE operon from Photorhabdus luminescens and display proportional responses in bioluminescence decay with increasing phenol concentration up to 800 mg l-1. In this work we describe their deployment to provide a strategic sensing network for protecting bacterial communities involved in the biological breakdown of coking effluents. This evaluation demonstrated the utility of strategic placement of reporters around heavy industry treatment systems and the reliability of the reporter strains under normal operational conditions. Mono-phenol or total phenolic variation within the treatment system accounted for>65-80% of the luminescence response. The reporters exhibited stable luminescence output during normal operations with maximum standard deviations of luminescence over time of c. 5-15% depending on the treatment compartment. Furthermore, deployment of the bioreporters over a 5-month period allowed the determination of an operational range (OR) for each reporter for effluent samples from each compartment. The OR allowed a convenient measure of toxicity effects between treatment compartments and accurately reflected a specific pollution event occurring within compartments of the treatment system. This work demonstrates the utility of genetic modification to provide ecologically relevant bioreporters, extends the sensing capabilities currently obtained through marine derived biosensors and significantly enhances the potential for in situ deployment of reporting agents.}, }
@article {pmid15658992, year = {2005}, author = {Seurinck, S and Defoirdt, T and Verstraete, W and Siciliano, SD}, title = {Detection and quantification of the human-specific HF183 Bacteroides 16S rRNA genetic marker with real-time PCR for assessment of human faecal pollution in freshwater.}, journal = {Environmental microbiology}, volume = {7}, number = {2}, pages = {249-259}, doi = {10.1111/j.1462-2920.2004.00702.x}, pmid = {15658992}, issn = {1462-2912}, mesh = {Bacteroides/*genetics/*isolation &amp; purification ; Benzothiazoles ; Colony Count, Microbial ; DNA, Bacterial/analysis ; DNA, Ribosomal/*analysis ; Diamines ; Feces/microbiology ; Fresh Water/*microbiology ; Genes, rRNA ; Genetic Markers ; Humans ; Molecular Sequence Data ; Organic Chemicals/metabolism ; *Polymerase Chain Reaction ; Quinolines ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/*genetics ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Temperature ; Time Factors ; Water Microbiology ; }, abstract = {The human-specific HF183 Bacteriodes 16S rRNA genetic marker can be used to detect human faecal pollution in water environments. However, there is currently no method to quantify the prevalence of this marker in environmental samples. We developed a real-time polymerase chain reaction (PCR) assay using SYBR Green I detection to quantify this marker in faecal and environmental samples. To decrease the amplicon length to a suitable size for real-time PCR detection, a new reverse primer was designed and validated on human and animal faecal samples. The use of the newly developed reverse primer in combination with the human-specific HF183 primer did not decrease the specificity of the real-time PCR assay but a melting curve analysis must always be included. This new assay was more sensitive than conventional PCR and highly reproducible with a coefficient of variation of less than 1% within an assay and 3% between assays. As the Bacteroides species that carries this human-specific marker has never been isolated, a bacteria real-time assay was used to determine the detection efficiency. The estimated detection efficiency in freshwater ranged from 78% to 91% of the true value with an average detection efficiency of 83+/-4% of the true value. Using a simple filtration method, the limit of quantification was 4.7+/-0.3x10(5) human-specific Bacteroides markers per litre of freshwater. The aerobic incubation of the human-specific Bacteroides marker in freshwater for up to 24 days at 4 and 12 degrees C, and up to 8 days at 28 degrees C, indicated that the marker persisted up to the end of the incubation period for all incubation temperatures.}, }
@article {pmid15658983, year = {2005}, author = {Favre-Bonté, S and Ranjard, L and Colinon, C and Prigent-Combaret, C and Nazaret, S and Cournoyer, B}, title = {Freshwater selenium-methylating bacterial thiopurine methyltransferases: diversity and molecular phylogeny.}, journal = {Environmental microbiology}, volume = {7}, number = {2}, pages = {153-164}, doi = {10.1111/j.1462-2920.2004.00670.x}, pmid = {15658983}, issn = {1462-2912}, mesh = {Aeromonas ; Bacteria/*enzymology/genetics ; Base Sequence ; Bordetella ; Consensus Sequence ; DNA, Bacterial/chemistry/isolation &amp; purification ; Escherichia coli Proteins/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genetic Variation ; Methyltransferases/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary/genetics ; Selenium/*metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology ; Water Microbiology ; }, abstract = {The diversity of bacterial thiopurine methyltransferases (bTPMT) among five natural Se-methylating freshwaters was investigated by polymerase chain reaction (PCR) screenings and sequencings. DNA sequence analyses confirmed the cloned products' identity and revealed a broad diversity of freshwater TPMTs. Neighbour-joining (NJ) phylogenetic analyses combining these sequences, all GenBank entries closely related to these sequences and deduced TPMTs obtained in this work from selected gamma-proteobacteria showed TPMTs to form a distinct radiation, closely related to UbiG methyltransferases. Inside the TPMT phylogenetic cluster, eukaryote sequences diverged early from the bacterial ones, and all the bacterial database entries belonged to a subgroup of gamma-proteobacteria, with an apparent lateral transfer of a particular allele to beta-proteobacteria of Bordetella. The NJ phylogenetic tree revealed 22 bTPMT lineages, 10 of which harboured freshwater sequences. All lineages showed deep and long branches indicative of major genetic drifts outside regions encoding highly conserved domains. Selected residues among these highly variable domains could reflect adaptations for particular ecological niches. PCR lineage-specific primers differentiated Se-methylating freshwaters according to their 'tpm lineage' signatures. Most freshwater tpm alleles were found to be distinct from those available in the databases, but a group of tpm was found encoding TPMTs identical to an Aeromonas veronii TPMT characterized in this work.}, }
@article {pmid15650915, year = {2005}, author = {Roussel-Delif, L and Tarnawski, S and Hamelin, J and Philippot, L and Aragno, M and Fromin, N}, title = {Frequency and diversity of nitrate reductase genes among nitrate-dissimilating Pseudomonas in the rhizosphere of perennial grasses grown in field conditions.}, journal = {Microbial ecology}, volume = {49}, number = {1}, pages = {63-72}, pmid = {15650915}, issn = {0095-3628}, mesh = {Carbon Dioxide/metabolism ; Colony Count, Microbial ; DNA Primers ; *Genetic Variation ; Membrane Proteins/metabolism ; Nitrate Reductases/*genetics ; Periplasmic Proteins/metabolism ; Plant Roots/*microbiology ; Poaceae/*microbiology ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Pseudomonas/enzymology/*genetics ; *Soil Microbiology ; Switzerland ; }, abstract = {A total of 1246 Pseudomonas strains were isolated from the rhizosphere of two perennial grasses (Lolium perenne and Molinia coerulea) with different nitrogen requirements. The plants were grown in their native soil under ambient and elevated atmospheric CO2 content (pCO2) at the Swiss FACE (Free Air CO2 Enrichment) facility. Root-, rhizosphere-, and non-rhizospheric soil-associated strains were characterized in terms of their ability to reduce nitrate during an in vitro assay and with respect to the genes encoding the membrane-bound (named NAR) and periplasmic (NAP) nitrate reductases so far described in the genus Pseudomonas. The diversity of corresponding genes was assessed by PCR-RFLP on narG and napA genes, which encode the catalytic subunit of nitrate reductases. The frequency of nitrate-dissimilating strains decreased with root proximity for both plants and was enhanced under elevated pCO2 in the rhizosphere of L. perenne. NAR (54% of strains) as well as NAP (49%) forms were present in nitrate-reducing strains, 15.5% of the 439 strains tested harbouring both genes. The relative proportions of narG and napA detected in Pseudomonas strains were different according to root proximity and for both pCO2 treatments: the NAR form was more abundant close to the root surface and for plants grown under elevated pCO2. Putative denitrifiers harbored mainly the membrane-bound (NAR) form of nitrate reductase. Finally, both narG and napA sequences displayed a high level of diversity. Anyway, this diversity was correlated neither with the root proximity nor with the pCO2 treatment.}, }
@article {pmid15644909, year = {2004}, author = {López-Archilla, AI and González, AE and Terrón, MC and Amils, R}, title = {Ecological study of the fungal populations of the acidic Tinto River in southwestern Spain.}, journal = {Canadian journal of microbiology}, volume = {50}, number = {11}, pages = {923-934}, doi = {10.1139/w04-089}, pmid = {15644909}, issn = {0008-4166}, mesh = {Culture Media ; *Ecosystem ; Fungi/*classification/growth &amp; development/isolation &amp; purification ; Hydrogen-Ion Concentration ; Metals ; *Metals, Heavy ; Mining ; Rivers/chemistry/*microbiology ; Spain ; *Water Pollution, Chemical ; }, abstract = {The characterization of the microbial ecology of the Tinto River, an extreme habitat with an extremely low pH and a high concentration of heavy metals, revealed an unexpected level of microbial richness. A variety of microbial eukaryotes was isolated, among them several fungal strains that were identified and their physiological characteristics studied. Ninety strains of yeast were isolated from the Tinto River. Fifty-two percent of them were capable of growth in vitro using medium amended with river water. They belong to 6 genera of basidiomycetes (Rhodotorula, Cryptococcus, Tremella, Holtermannia, Leucosporidium, and Mrakia) and 2 of ascomycetes (Candida and Williopsis). In addition, 349 strains of hyphomycetes belonging to 17 genera (most of them ascomycetes) were isolated and studied. Forty-four percent of the isolated filamentous fungi (154 strains) were capable of growing in vitro using medium amended with Tinto River water. Of this percentage, 19% (29 strains) belonged to the genus Penicillium (16 species) and 66% (102 strains) were included in the genera Scytalidium, Bahusakala, Phoma, and Heteroconium or showed dark sterile mycelia, which probably are of dematiaceous hyphomycetes. In addition, we characterized strains of the ascomycete genera Lecythophora and Acremonium and of the zygomycete genus Mortierella, all of them capable of growing in medium amended with river water. Statistical correlation of biological and physicochemical variables suggested a positive relationship between the dematiaceous hyphomycetes and the most extreme physicochemical conditions found in the Tinto River. Principal components analysis confirmed this relationship and also showed that the Acremonium and Lecythophora groups had environmental preferences similar to those of dematiaceous fungi. The spatial positions of the sampling sites were grouped in 2 main clusters: (i) sampling sites in the mine zone in which most of the dematiaceous, Acremonium, and Lecythophora strains were isolated and (ii) sites that were not in the mine zone and sampling station 5 from which were isolated mainly strains of fungi that were not capable of growing in the medium amended with river water and species of the Penicillium genus.}, }
@article {pmid15640177, year = {2005}, author = {Ehling-Schulz, M and Vukov, N and Schulz, A and Shaheen, R and Andersson, M and Märtlbauer, E and Scherer, S}, title = {Identification and partial characterization of the nonribosomal peptide synthetase gene responsible for cereulide production in emetic Bacillus cereus.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {1}, pages = {105-113}, pmid = {15640177}, issn = {0099-2240}, mesh = {Amino Acid Sequence ; Bacillus cereus/*enzymology ; Cluster Analysis ; DNA Primers ; Gram-Positive Bacterial Infections/*microbiology ; Humans ; Molecular Sequence Data ; *Peptide Synthases/chemistry/genetics/metabolism ; Polymerase Chain Reaction/methods ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Vomiting/*microbiology ; }, abstract = {Cereulide, a depsipeptide structurally related to valinomycin, is responsible for the emetic type of gastrointestinal disease caused by Bacillus cereus. Due to its chemical structure, (D-O-Leu-D-Ala-L-O-Val-L-Val)(3), cereulide might be synthesized nonribosomally. Therefore, degenerate PCR primers targeted to conserved sequence motifs of known nonribosomal peptide synthetase (NRPS) genes were used to amplify gene fragments from a cereulide-producing B. cereus strain. Sequence analysis of one of the amplicons revealed a DNA fragment whose putative gene product showed significant homology to valine activation NRPS modules. The sequences of the flanking regions of this DNA fragment revealed a complete module that is predicted to activate valine, as well as a putative carboxyl-terminal thioesterase domain of the NRPS gene. Disruption of the peptide synthetase gene by insertion of a kanamycin cassette through homologous recombination produced cereulide-deficient mutants. The valine-activating module was highly conserved when sequences from nine emetic B. cereus strains isolated from diverse geographical locations were compared. Primers were designed based on the NRPS sequence, and the resulting PCR assay, targeting the ces gene, was tested by using a panel of 143 B. cereus group strains and 40 strains of other bacterial species showing PCR bands specific for only the cereulide-producing B. cereus strains.}, }
@article {pmid15638840, year = {2004}, author = {Jalava, J and Marttila, H}, title = {Application of molecular genetic methods in macrolide, lincosamide and streptogramin resistance diagnostics and in detection of drug-resistant Mycobacterium tuberculosis.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {112}, number = {11-12}, pages = {838-855}, doi = {10.1111/j.1600-0463.2004.apm11211-1209.x}, pmid = {15638840}, issn = {0903-4641}, mesh = {ATP-Binding Cassette Transporters/genetics ; Bacterial Proteins/genetics ; Base Sequence ; DNA Primers/genetics ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Genotype ; Humans ; Lincosamides ; Macrolides/pharmacology ; Molecular Biology/*methods ; Mutation ; Mycobacterium tuberculosis/*drug effects/*genetics/isolation &amp; purification ; Polymerase Chain Reaction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 23S/genetics ; Streptogramins/pharmacology ; Tuberculosis, Pulmonary/diagnosis/drug therapy/microbiology ; }, abstract = {Antimicrobial susceptibility testing has traditionally been based on measurements of minimal inhibitory concentrations of antimicrobials. Molecular genetic studies on antimicrobial resistance have produced a great deal of genetic information which can be used for diagnosis of antimicrobial resistance determinants. Bacteria can acquire resistance to macrolides, lincosamides and streptogramin antibiotics by modification of the target site of the drugs, by active efflux of the drugs, and by inactivation of the drugs. The genetic backgrounds of these resistance mechanisms are well known and several molecular methods for detection of resistance determinants have been developed. Outbreaks of multidrug-resistant tuberculosis have focused international attention on the emergence of Mycobacterium tuberculosis strains that are resistant to antimycobacterial agents. Knowledge of the antimycobacterial resistance genetics and progress in molecular methods has made it possible to develop rapid molecular methods for susceptibility testing. This review presents the genetic background of drug resistance and introduces some methods for genotypic susceptibility testing.}, }
@article {pmid15637281, year = {2005}, author = {van der Wielen, PW and Bolhuis, H and Borin, S and Daffonchio, D and Corselli, C and Giuliano, L and D'Auria, G and de Lange, GJ and Huebner, A and Varnavas, SP and Thomson, J and Tamburini, C and Marty, D and McGenity, TJ and Timmis, KN and , }, title = {The enigma of prokaryotic life in deep hypersaline anoxic basins.}, journal = {Science (New York, N.Y.)}, volume = {307}, number = {5706}, pages = {121-123}, doi = {10.1126/science.1103569}, pmid = {15637281}, issn = {1095-9203}, mesh = {Anaerobiosis ; Archaea/classification/isolation &amp; purification/*physiology ; Bacteria/classification/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Biodiversity ; Cluster Analysis ; *Ecosystem ; Euryarchaeota/classification/isolation &amp; purification/physiology ; Genes, Archaeal ; Genes, Bacterial ; Genes, rRNA ; Magnesium Chloride/analysis ; Mediterranean Sea ; Methane/metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; *Sodium Chloride ; Sulfates/metabolism ; }, abstract = {Deep hypersaline anoxic basins in the Mediterranean Sea are a legacy of dissolution of ancient subterranean salt deposits from the Miocene period. Our study revealed that these hypersaline basins are not biogeochemical dead ends, but support in situ sulfate reduction, methanogenesis, and heterotrophic activity. A wide diversity of prokaryotes was observed, including a new, abundant, deeply branching order within the Euryarchaeota. Furthermore, we demonstrated the presence of a unique, metabolically active microbial community in the Discovery basin, which is one of the most extreme terrestrial saline environments known, as it is almost saturated with MgCl2 (5 M).}, }
@article {pmid15632447, year = {2005}, author = {Collingro, A and Poppert, S and Heinz, E and Schmitz-Esser, S and Essig, A and Schweikert, M and Wagner, M and Horn, M}, title = {Recovery of an environmental Chlamydia strain from activated sludge by co-cultivation with Acanthamoeba sp.}, journal = {Microbiology (Reading, England)}, volume = {151}, number = {Pt 1}, pages = {301-309}, doi = {10.1099/mic.0.27406-0}, pmid = {15632447}, issn = {1350-0872}, mesh = {Acanthamoeba/*growth &amp; development/*microbiology ; Animals ; Chlamydiales/*classification/genetics/*isolation &amp; purification/pathogenicity ; Chlorocebus aethiops ; Coculture Techniques ; DNA, Ribosomal/analysis ; Genes, rRNA ; HeLa Cells ; Humans ; In Situ Hybridization, Fluorescence ; Microscopy, Confocal ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; Sewage/*microbiology ; Vero Cells ; }, abstract = {Chlamydiae are a unique group of obligate intracellular bacteria comprising important pathogens of vertebrates as well as symbionts of free-living amoebae. Although there is ample molecular evidence for a huge diversity and wide distribution of chlamydiae in nature, environmental chlamydiae are currently represented by only few isolates. This paper reports the recovery of a novel environmental chlamydia strain from activated sludge by co-cultivation with Acanthamoeba sp. The recovered environmental chlamydia strain UV-7 showed the characteristic morphology of chlamydial developmental stages as revealed by electron microscopy and was identified as a new member of the family Parachlamydiaceae (98.7 % 16S rRNA sequence similarity to Parachlamydia acanthamoebae). Infection studies suggested that Parachlamydia sp. UV-7 is not confined to amoeba hosts but is also able to invade mammalian cells. These findings outline a new straightforward approach to retrieving environmental chlamydiae from nature without prior, tedious isolation and cultivation of their natural host cells, and lend further support to suggested implications of environmental chlamydiae for public health.}, }
@article {pmid15626640, year = {2005}, author = {Van de Wiele, T and Vanhaecke, L and Boeckaert, C and Peru, K and Headley, J and Verstraete, W and Siciliano, S}, title = {Human colon microbiota transform polycyclic aromatic hydrocarbons to estrogenic metabolites.}, journal = {Environmental health perspectives}, volume = {113}, number = {1}, pages = {6-10}, pmid = {15626640}, issn = {0091-6765}, mesh = {Administration, Oral ; Biological Availability ; Biotransformation ; Colon/*microbiology ; Estrogens/*metabolism ; Humans ; In Vitro Techniques ; *Models, Theoretical ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Risk Assessment ; Soil ; Soil Pollutants/*metabolism ; }, abstract = {Ingestion is an important exposure route for polycyclic aromatic hydrocarbons (PAHs) to enter the human body. Although the formation of hazardous PAH metabolites by human biotransformation enzymes is well documented, nothing is known about the PAH transformation potency of human intestinal microbiota. Using a gastrointestinal simulator, we show that human intestinal microbiota can also bioactivate PAHs, more in particular to estrogenic metabolites. PAH compounds are not estrogenic, and indeed, stomach and small intestine digestions of 62.5 nmol naphthalene, phenanthrene, pyrene, and benzo(a)pyrene showed no estrogenic effects in the human estrogen receptor bioassay. In contrast, colon digests of these PAH compounds displayed estrogenicity, equivalent to 0.31, 2.14, 2.70, and 1.48 nmol 17alpha-ethynylestradiol (EE2), respectively. Inactivating the colon microbiota eliminated these estrogenic effects. Liquid chromatography-mass spectrometry analysis confirmed the microbial PAH transformation by the detection of PAH metabolites 1-hydroxypyrene and 7-hydroxybenzo(a)pyrene in colon digests of pyrene and benzo(a)pyrene. Furthermore, we show that colon digests of a PAH-contaminated soil (simulated ingestion dose of 5 g/day) displayed estrogenic activity equivalent to 0.58 nmol EE2, whereas stomach or small intestine digests did not. Although the matrix in which PAHs are ingested may result in lower exposure concentrations in the gut, our results imply that the PAH bioactivation potency of colon microbiota is not eliminated by the presence of soil. Moreover, because PAH toxicity is also linked to estrogenicity of the compounds, the PAH bioactivation potency of colon microbiota suggests that current risk assessment may underestimate the risk from ingested PAHs.}, }
@article {pmid15621429, year = {2005}, author = {Bundy, JG and Willey, TL and Castell, RS and Ellar, DJ and Brindle, KM}, title = {Discrimination of pathogenic clinical isolates and laboratory strains of Bacillus cereus by NMR-based metabolomic profiling.}, journal = {FEMS microbiology letters}, volume = {242}, number = {1}, pages = {127-136}, doi = {10.1016/j.femsle.2004.10.048}, pmid = {15621429}, issn = {0378-1097}, support = {E17880/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacillus cereus/classification/isolation &amp; purification/*metabolism/*pathogenicity ; Bacterial Toxins/genetics ; Genome, Bacterial ; Gram-Positive Bacterial Infections/microbiology ; Humans ; *Magnetic Resonance Spectroscopy ; Meningitis, Bacterial/microbiology ; Multivariate Analysis ; Pattern Recognition, Automated ; Virulence ; Virulence Factors/genetics ; }, abstract = {Six different Bacillus cereus strains were selected from two different ecotypes: (1) three commonly used laboratory strains that are considered avirulent, and (2) three clinical isolates from meningitis patients. Screening of genomic DNA for the presence of genes encoding known toxins gave no candidate genes that were unambiguously able to distinguish between the two groups. However, the application of multivariate pattern-recognition methods to metabolite profiles derived from the different strains using 1H nuclear magnetic resonance spectroscopy (metabolomics) was able to classify the different profiles. The two different ecotypes were clearly separated on the basis of their metabolite profiles, showing that it is possible to use metabolomic methods to classify pathogens on the basis of their expressed physiology, even when it is not possible to infer a direct mechanistic link to specific virulence factors. This metabolomic approach could also have a wide range of possible applications in both general microbiology and microbial ecology for distinguishing and identifying different functional/physiological ecotypes of bacterial strains or species.}, }
@article {pmid15621421, year = {2005}, author = {Gadkar, V and Rillig, MC}, title = {Application of Phi29 DNA polymerase mediated whole genome amplification on single spores of arbuscular mycorrhizal (AM) fungi.}, journal = {FEMS microbiology letters}, volume = {242}, number = {1}, pages = {65-71}, doi = {10.1016/j.femsle.2004.10.041}, pmid = {15621421}, issn = {0378-1097}, mesh = {Bacillus Phages/*enzymology ; Base Sequence ; *DNA Replication ; DNA, Fungal/chemistry/*metabolism ; DNA, Ribosomal/genetics ; DNA-Directed DNA Polymerase/*metabolism ; Genes, Fungal/genetics ; *Genome, Fungal ; Molecular Sequence Data ; Mycorrhizae/*genetics ; *Nucleic Acid Amplification Techniques ; Sequence Analysis, DNA ; Spores, Fungal/genetics ; Tubulin/genetics ; }, abstract = {Genetic analysis of arbuscular mycorrhizal (AM) fungi relies on analysis of single spores. The low DNA content makes it difficult to perform large scale molecular analysis. We present the application of Phi29 DNA polymerase mediated strand displacement amplification (SDA) to genomic DNA extracted from single spores of Glomus and Gigaspora species to address this problem. The genome coverage of the SDA process was evaluated by PCR amplification of the beta-tubulin1 gene and part of the rDNA cluster present in AM fungi. The fidelity of SDA was evaluated further by sequencing the Glomus intraradices ITS1 variants to detect the four ITS1 variants previously identified for this fungus.}, }
@article {pmid15617446, year = {2004}, author = {Aiyuk, S and Xu, H and van Haandel, A and Verstraete, W}, title = {Removal of ammonium nitrogen from pretreated domestic sewage using a natural ion exchanger.}, journal = {Environmental technology}, volume = {25}, number = {11}, pages = {1321-1330}, doi = {10.1080/09593332508618377}, pmid = {15617446}, issn = {0959-3330}, mesh = {Ion Exchange ; Nitrogen/*chemistry/*isolation &amp; purification ; Quaternary Ammonium Compounds/*chemistry/*isolation &amp; purification ; Sewage/*chemistry ; Waste Disposal, Fluid/*methods ; Water Movements ; Zeolites/chemistry ; }, abstract = {Ammonium nitrogen was removed from pretreated domestic sewage using a natural zeolite-clinoptilolite, applying a column with downflow regime. The pretreated wastewater had an average total ammonium nitrogen (TAN) of 23 mg l(-1). Ion exchange was allowed to take place under normal sewage treatment plant conditions and tropical temperature setting. The sorption capacity of the natural clinoptilolite was studied with the column fitted to a chemically enhanced primary treatment (CEPT)-upflow anaerobic sludge blanket (UASB) system, operating at 33 degrees C. Optimal operational cation exchange capacity (CEC) of 14 g TAN kg(-1) zeolite was obtained for the zeolite granulometry of 1-2.5 mm in a reversible way. The treatment was done at 3.9 bed volumes (BV) per day, and breakthrough was attained after about 560 BV. Regeneration of exhausted zeolite was effected with a 25 g NaCl l(-1) salt solution, rendering the column amenable to reuse. Employing a 3-column test and bed contact times of 6, 2.6 and 1.1 minutes, the use of pretreated wastewater with average concentration of 38 mg NH4(+)-N l(-1) showed that the operational cation exchange capacity also depended on flow rate, with the removal efficiency decreasing from 95 to 47% with increase in the flow rate. Overall, the approach of removing TAN from digested sewage offers potential to recover the TAN from the domestic wastewater, thus minimizing the need for subsequent nitrification-denitrification of the whole water volume.}, }
@article {pmid15616841, year = {2005}, author = {Vallet, S and Nousbaum, JB and Gouriou, S and Legrand-Quillien, MC and Goudeau, A and Picard, B}, title = {A particular hepatitis C virus protease NS3 gene pattern in a patient not responding to interferon-ribavirin therapy.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {24}, number = {1}, pages = {79-80}, pmid = {15616841}, issn = {0934-9723}, mesh = {Biopsy, Needle ; DNA, Viral/analysis ; Drug Therapy, Combination ; Follow-Up Studies ; Hepacivirus/*genetics/isolation &amp; purification ; Hepatitis C, Chronic/diagnosis/*drug therapy ; Humans ; Immunohistochemistry ; Interferon-alpha/*therapeutic use ; Liver Function Tests ; Male ; Middle Aged ; Polymerase Chain Reaction/methods ; Ribavirin/*therapeutic use ; Severity of Illness Index ; Treatment Failure ; Viral Load ; Viral Nonstructural Proteins/*genetics ; }, }
@article {pmid15616336, year = {2005}, author = {Haanperä, M and Huovinen, P and Jalava, J}, title = {Detection and quantification of macrolide resistance mutations at positions 2058 and 2059 of the 23S rRNA gene by pyrosequencing.}, journal = {Antimicrobial agents and chemotherapy}, volume = {49}, number = {1}, pages = {457-460}, pmid = {15616336}, issn = {0066-4804}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects ; Base Sequence ; DNA, Ribosomal/analysis/genetics ; Diphosphates/*metabolism ; Drug Resistance, Bacterial/*genetics ; Genes, rRNA ; Humans ; Macrolides/*pharmacology ; Microbial Sensitivity Tests/methods ; Molecular Sequence Data ; *Mutation ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 23S/*genetics ; Sequence Analysis, DNA ; }, abstract = {A pyrosequencing method for detection and quantification of macrolide resistance mutations at positions 2058 and 2059 (Escherichia coli numbering) of the 23S rRNA gene is described. The method was developed and tested for Streptococcus pneumoniae, Streptococcus pyogenes, Mycobacterium avium, Campylobacter jejuni, and Haemophilus influenzae.}, }
@article {pmid15614465, year = {2005}, author = {Wieland, A and Zopfi, J and Benthien, M and Kühl, M}, title = {Biogeochemistry of an iron-rich hypersaline microbial mat (Camargue, France).}, journal = {Microbial ecology}, volume = {49}, number = {1}, pages = {34-49}, pmid = {15614465}, issn = {0095-3628}, mesh = {Biochemical Phenomena ; Biochemistry ; Carbon/*metabolism ; Cyanobacteria/*metabolism/physiology ; France ; Geological Phenomena ; Geology ; Hydrogen-Ion Concentration ; Iron/metabolism ; Oxidation-Reduction ; Oxygen/*metabolism ; Photosynthesis/physiology ; Seawater/*microbiology ; Sulfur/*metabolism ; Temperature ; }, abstract = {In situ microsensor measurements were combined with biogeochemical methods to determine oxygen, sulfur, and carbon cycling in microbial mats growing in a solar saltern (Salin-de-Giraud, France). Sulfate reduction rates closely followed the daily temperature changes and were highest during the day at 25 degrees C and lowest during the night at 11 degrees C, most probably fueled by direct substrate interactions between cyanobacteria and sulfate-reducing bacteria. Sulfate reduction was the major mineralization process during the night and the contribution of aerobic respiration to nighttime DIC production decreased. This decrease of aerobic respiration led to an increasing contribution of sulfide (and iron) oxidation to nighttime O2 consumption. A peak of elemental sulfur in a layer of high sulfate reduction at low sulfide concentration underneath the oxic zone indicated anoxygenic photosynthesis and/or sulfide oxidation by iron, which strongly contributed to sulfide consumption. We found a significant internal carbon cycling in the mat, and sulfate reduction directly supplied DIC for photosynthesis. The mats were characterized by a high iron content of 56 micromol Fe cm(-3), and iron cycling strongly controlled the sulfur cycle in the mat. This included sulfide precipitation resulting in high FeS contents with depth, and reactions of iron oxides with sulfide, especially after sunset, leading to a pronounced gap between oxygen and sulfide gradients and an unusual persistence of a pH peak in the uppermost mat layer until midnight.}, }
@article {pmid15614464, year = {2005}, author = {Ayuso-Sacido, A and Genilloud, O}, title = {New PCR primers for the screening of NRPS and PKS-I systems in actinomycetes: detection and distribution of these biosynthetic gene sequences in major taxonomic groups.}, journal = {Microbial ecology}, volume = {49}, number = {1}, pages = {10-24}, pmid = {15614464}, issn = {0095-3628}, mesh = {Actinobacteria/*genetics ; Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; Computational Biology ; Conserved Sequence/genetics ; DNA Primers/*genetics ; Electrophoresis, Agar Gel ; *Genome, Bacterial ; Molecular Sequence Data ; Peptide Synthases/*genetics ; Polyketide Synthases/*genetics ; Sequence Analysis, DNA ; }, abstract = {Nonribosomal peptide synthetases (NRPS) and type I polyketide synthases (PKS-I) are biosynthetic systems involved in the synthesis of a large number of important biologically active compounds produced by microorganisms, among others by actinomycetes. In order to assess the occurrence of these biosynthetic systems in this metabolically active bacterial group, we designed new PCR primers targeted to specifically amplify NRPS and PKS-I gene sequences from actinomycetes. The sequence analysis of amplified products cloned from two model systems and used to validate these molecular tools has shown the extreme richness of NRPS or PKS-I-like sequences in the actinomycete genome. When these PCR primers were tested on a large collection of 210 reference strains encompassing all major families and genera in actinomycetes, we observed that the wide distribution of these genes in the well-known productive Streptomyces species is also extended to other minor lineages where in some cases very few bioactive compounds have been identified to date.}, }
@article {pmid15608200, year = {2005}, author = {Cole, JR and Chai, B and Farris, RJ and Wang, Q and Kulam, SA and McGarrell, DM and Garrity, GM and Tiedje, JM}, title = {The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis.}, journal = {Nucleic acids research}, volume = {33}, number = {Database issue}, pages = {D294-6}, pmid = {15608200}, issn = {1362-4962}, mesh = {DNA Probes ; DNA, Ribosomal/*chemistry/classification ; *Databases, Nucleic Acid ; *Genes, rRNA ; RNA, Bacterial/genetics ; RNA, Ribosomal/chemistry/classification ; Sequence Alignment ; *Sequence Analysis, DNA ; *Software ; }, abstract = {The Ribosomal Database Project (RDP-II) provides the research community with aligned and annotated rRNA gene sequences, along with analysis services and a phylogenetically consistent taxonomic framework for these data. Updated monthly, these services are made available through the RDP-II website (http://rdp.cme.msu.edu/). RDP-II release 9.21 (August 2004) contains 101,632 bacterial small subunit rRNA gene sequences in aligned and annotated format. High-throughput tools for initial taxonomic placement, identification of related sequences, probe and primer testing, data navigation and subalignment download are provided. The RDP-II email address for questions or comments is rdpstaff@msu.edu.}, }
@article {pmid15581933, year = {2005}, author = {Nollet, H and Van de Putte, I and Raskin, L and Verstraete, W}, title = {Carbon/electron source dependence of polychlorinated biphenyl dechlorination pathways for anaerobic granules.}, journal = {Chemosphere}, volume = {58}, number = {3}, pages = {299-310}, doi = {10.1016/j.chemosphere.2004.07.036}, pmid = {15581933}, issn = {0045-6535}, mesh = {Bacteria, Anaerobic/*physiology ; *Bioreactors ; Carbon/chemistry ; Catalysis ; Chlorine Compounds/metabolism ; Electrons ; Environmental Pollutants/*metabolism ; Polychlorinated Biphenyls/*metabolism ; }, abstract = {The effect of acclimating anaerobic granules from commercial bioreactors with different carbon/electron sources on their ability to reductively dechlorinate a tri-(2,3,4-CB) and heptachlorobiphenyl (2,2',3,3',4,5,6-CB) was studied. The anaerobic granules were first grown in upflow anaerobic sludge blanket (UASB) reactors fed with two different mixtures of carbon/electron sources, i.e., propionate/butyrate/methanol and formate/methanol. Differences in dechlorination patterns for 2,2',3,3',4,5,6-CB were observed in batch experiments inoculated with granules from these two sets of UASB reactors. Variation of the carbon/electron source, during the dechlorination process, had no effect on the dechlorination pathway, but the extents and rates of dechlorination were highest for ethanol and formate and lowest for pyruvate fed batches. Pre-acclimation of different anaerobic sludges to polychlorinated biphenyls (PCBs) shortened the lag period, but did not influence the PCB dechlorination pathway. This is the first time that similar acclimation conditions for several anaerobic microbial communities prior to inoculation were reported to yield similar substrate specificities for the reductive dechlorination of specific PCB congeners. This research demonstrates a successful strategy for the development of biocatalysts to serve as the inoculum of partially decontaminated sites in order to provide microorganisms with specificities complementary to those of naturally occurring dechlorinators.}, }
@article {pmid15578160, year = {2005}, author = {Decroos, K and Vanhemmens, S and Cattoir, S and Boon, N and Verstraete, W}, title = {Isolation and characterisation of an equol-producing mixed microbial culture from a human faecal sample and its activity under gastrointestinal conditions.}, journal = {Archives of microbiology}, volume = {183}, number = {1}, pages = {45-55}, doi = {10.1007/s00203-004-0747-4}, pmid = {15578160}, issn = {0302-8933}, mesh = {Bacteria/*classification/isolation &amp; purification/*metabolism ; Butyrates/metabolism ; DNA Fingerprinting ; DNA, Bacterial/analysis/chemistry/isolation &amp; purification ; DNA, Ribosomal/chemistry/isolation &amp; purification ; Enterococcus faecium/classification/isolation &amp; purification/metabolism ; Equol ; Feces/*microbiology ; Genes, rRNA ; Humans ; Hydrogen/metabolism ; Isoflavones/*metabolism ; Lactobacillus/classification/isolation &amp; purification/metabolism ; Molecular Sequence Data ; Oligosaccharides/metabolism ; Phylogeny ; Propionates/metabolism ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Veillonella/classification/isolation &amp; purification/metabolism ; }, abstract = {Only about one third of humans possess a microbiota capable of transforming the dietary isoflavone daidzein into equol. Little is known about the dietary and physiological factors determining this ecological feature. In this study, the in vitro metabolism of daidzein by faecal samples from four human individuals was investigated. One culture produced the metabolites dihydrodaidzein and O-desmethylangolensin, another produced dihydrodaidzein and equol. From the latter, a stable and transferable mixed culture transforming daidzein into equol was obtained. Molecular fingerprinting analysis (denaturing gradient gel electrophoresis) showed the presence of four bacterial species of which only the first three strains could be brought into pure culture. These strains were identified as Lactobacillus mucosae EPI2, Enterococcus faecium EPI1 and Finegoldia magna EPI3, and did not produce equol in pure culture. The fourth species was tentatively identified as Veillonella sp strain EP. It was found that hydrogen gas in particular, but also butyrate and propionate, which are all colonic fermentation products from poorly digestible carbohydrates, stimulated equol production by the mixed culture. However, when fructo-oligosaccharides were added, equol production was inhibited. Furthermore, the equol-producing capacity of the isolated culture was maintained upon its addition to a faecal culture originating from a non-equol-producing individual.}, }
@article {pmid15574893, year = {2004}, author = {Loy, A and Küsel, K and Lehner, A and Drake, HL and Wagner, M}, title = {Microarray and functional gene analyses of sulfate-reducing prokaryotes in low-sulfate, acidic fens reveal cooccurrence of recognized genera and novel lineages.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {12}, pages = {6998-7009}, pmid = {15574893}, issn = {0099-2240}, mesh = {Bacterial Proteins/genetics/*metabolism ; DNA, Bacterial/analysis ; Gene Expression Profiling ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis/*methods ; Oxidoreductases Acting on Sulfur Group Donors/genetics/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; Sulfates/metabolism ; Sulfur/metabolism ; Sulfur-Reducing Bacteria/*classification/genetics/metabolism ; }, abstract = {Low-sulfate, acidic (approximately pH 4) fens in the Lehstenbach catchment in the Fichtelgebirge mountains in Germany are unusual habitats for sulfate-reducing prokaryotes (SRPs) that have been postulated to facilitate the retention of sulfur and protons in these ecosystems. Despite the low in situ availability of sulfate (concentration in the soil solution, 20 to 200 microM) and the acidic conditions (soil and soil solution pHs, approximately 4 and 5, respectively), the upper peat layers of the soils from two fens (Schlöppnerbrunnen I and II) of this catchment displayed significant sulfate-reducing capacities. 16S rRNA gene-based oligonucleotide microarray analyses revealed stable diversity patterns for recognized SRPs in the upper 30 cm of both fens. Members of the family "Syntrophobacteraceae" were detected in both fens, while signals specific for the genus Desulfomonile were observed only in soils from Schlöppnerbrunnen I. These results were confirmed and extended by comparative analyses of environmentally retrieved 16S rRNA and dissimilatory (bi)sulfite reductase (dsrAB) gene sequences; dsrAB sequences from Desulfobacca-like SRPs, which were not identified by microarray analysis, were obtained from both fens. Hypotheses concerning the ecophysiological role of these three SRP groups in the fens were formulated based on the known physiological properties of their cultured relatives. In addition to these recognized SRP lineages, six novel dsrAB types that were phylogenetically unrelated to all known SRPs were detected in the fens. These dsrAB sequences had no features indicative of pseudogenes and likely represent novel, deeply branching, sulfate- or sulfite-reducing prokaryotes that are specialized colonists of low-sulfate habitats.}, }
@article {pmid15572449, year = {2004}, author = {Costerton, B}, title = {Microbial ecology comes of age and joins the general ecology community.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {49}, pages = {16983-16984}, pmid = {15572449}, issn = {0027-8424}, mesh = {Biofilms/*growth &amp; development ; Ecology/*methods ; Ecosystem ; Microbiology/*trends ; }, }
@article {pmid15568985, year = {2004}, author = {Riesenfeld, CS and Schloss, PD and Handelsman, J}, title = {Metagenomics: genomic analysis of microbial communities.}, journal = {Annual review of genetics}, volume = {38}, number = {}, pages = {525-552}, doi = {10.1146/annurev.genet.38.072902.091216}, pmid = {15568985}, issn = {0066-4197}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Bacteriophages/*genetics ; Biodiversity ; *Environmental Microbiology ; Gene Library ; Genome, Archaeal ; *Genome, Bacterial ; Genomic Library ; Microscopy ; Phylogeny ; Rhodopsin/genetics ; Rhodopsins, Microbial ; Sequence Analysis ; }, abstract = {Uncultured microorganisms comprise the majority of the planet's biological diversity. Microorganisms represent two of the three domains of life and contain vast diversity that is the product of an estimated 3.8 billion years of evolution. In many environments, as many as 99% of the microorganisms cannot be cultured by standard techniques, and the uncultured fraction includes diverse organisms that are only distantly related to the cultured ones. Therefore, culture-independent methods are essential to understand the genetic diversity, population structure, and ecological roles of the majority of microorganisms. Metagenomics, or the culture-independent genomic analysis of an assemblage of microorganisms, has potential to answer fundamental questions in microbial ecology. This review describes progress toward understanding the biology of uncultured Bacteria, Archaea, and viruses through metagenomic analyses.}, }
@article {pmid15567219, year = {2005}, author = {Zhang, X and Yan, X and Gao, P and Wang, L and Zhou, Z and Zhao, L}, title = {Optimized sequence retrieval from single bands of temperature gradient gel electrophoresis profiles of the amplified 16S rDNA fragments from an activated sludge system.}, journal = {Journal of microbiological methods}, volume = {60}, number = {1}, pages = {1-11}, doi = {10.1016/j.mimet.2004.08.015}, pmid = {15567219}, issn = {0167-7012}, mesh = {Alphaproteobacteria/*genetics/isolation &amp; purification ; Base Sequence ; Betaproteobacteria/*genetics/isolation &amp; purification ; DNA, Bacterial/chemistry/*genetics ; DNA, Single-Stranded/metabolism ; Electrophoresis, Polyacrylamide Gel/*methods ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sewage/*microbiology ; Single-Strand Specific DNA and RNA Endonucleases/metabolism ; }, abstract = {Sequence retrieval from single bands of polymerase chain reaction (PCR)-denaturing gel electrophoresis (DGE) profiles is an important but often difficult step for molecular diversity analysis of complex microbial communities such as activated sludge systems. We analyzed the temperature gradient gel electrophoresis (TGGE) profiles of PCR-amplified 16S rDNA fragments from an activated sludge sample of a coking wastewater treatment plant. Single bands were excised, and a clone library was constructed for each. Sequence heterogeneity in each single band was found to be significantly overestimated due to single-stranded DNA (ssDNA) contamination formed during the PCR amplification, since only 10-60% of library clones of each single TGGE band had identical migration behavior compared with the parent band. Three methods, digestion with mung bean nuclease, optimization of PCR amplification, and purification via denatured polyacrylamide gel electrophoresis (d-PAGE), were compared for their ability to minimize ssDNA contamination, with the last one being the most efficient. After using d-PAGE to minimize ssDNA to a nearly nondetectable level, 70-100% of library clones for each single TGGE band had identical migration compared with the parent band. Several sequences were found in each of six single bands, and this co-migration could be predicted with the Poland software. The predominant bacteria of the activated sludge were assessed via a combination of sequence retrieval from each single TGGE band and band intensity analysis. Only beta and alpha subclasses of the Proteobacteria were detected, 93.8% and 6.2%, respectively. Our work suggests that prior to constructing a clone library to retrieve the actual sequence diversity of a single DGE band, it is advisable to minimize ssDNA contamination to a nondetectable level.}, }
@article {pmid15560825, year = {2004}, author = {Bolhuis, H and Poele, EM and Rodriguez-Valera, F}, title = {Isolation and cultivation of Walsby's square archaeon.}, journal = {Environmental microbiology}, volume = {6}, number = {12}, pages = {1287-1291}, doi = {10.1111/j.1462-2920.2004.00692.x}, pmid = {15560825}, issn = {1462-2912}, mesh = {Archaea/cytology/*growth &amp; development/*isolation &amp; purification/ultrastructure ; Culture Media/chemistry ; Genome, Archaeal ; Geologic Sediments/microbiology ; Hypertonic Solutions ; Magnesium Chloride ; Microscopy ; Microscopy, Electron ; Seawater/microbiology ; Sodium Chloride ; Water Microbiology ; }, abstract = {In 1980, A. E. Walsby described a square halophilic archaeon. This archaeon is of specific interest because of its unique shape and its abundance in hypersaline ecosystems, which suggests an important ecophysiological role. Ever since its discovery, the isolation and cultivation of 'Walsby's square archaeon' has been a holy grail for many microbiologists working on halophiles. Despite their abundance and easy recognition by microscopy, all cultivation attempts have failed up to now, marking the organism as one of the unculturables. Cultivation of the square archaeon is essential to understand their ecophysiological role and the nature of their unique morphologically features. Here, we report the isolation and cultivation of the enigmatic square archaeon that we propose to name Haloquadratum walsbyi. Pure cultures are easily maintained in simple artificial hypersaline media. Initial growth experiments revealed a tolerance to high concentrations of MgCl(2) (>2 M) in the presence of 3.3 M NaCl. Fresh cultures contained extraordinary large cells (>40 x 40 microm) without any visible division structures, ranking them among the largest prokaryotes known to date. The genome was estimated to contain approximately three million basepairs.}, }
@article {pmid15558328, year = {2005}, author = {Kytöviita, MM}, title = {Role of nutrient level and defoliation on symbiotic function: experimental evidence by tracing 14C/15N exchange in mycorrhizal birch seedlings.}, journal = {Mycorrhiza}, volume = {15}, number = {1}, pages = {65-70}, pmid = {15558328}, issn = {0940-6360}, mesh = {Betula/*microbiology/physiology ; Carbon Radioisotopes/metabolism ; Mycorrhizae/*physiology ; Nitrogen Isotopes/metabolism ; Plant Leaves/physiology ; Plant Roots/microbiology/physiology ; Seedlings/microbiology/physiology ; Symbiosis/*physiology ; }, abstract = {High nutrient availability and defoliation generally reduce ectomycorrhizal colonization levels in trees, but it is not known how this affects the functional aspects of mycorrhizal symbiosis. It was therefore investigated whether (1) defoliation or increasing substrate N availability reduce C allocation from the plant to the fungus and N allocation from the fungus to the plant (symbiotic resource exchange), (2) symbiotic resource exchange depends on relative N and P availability, and (3) fungal N translocation to plant and plant C allocation to fungus are interdependent. Birch (Betula pendula) seedlings were grown in symbiosis with the ectomycorrhizal fungus Paxillus involutus at five times excess N, or at five times excess N and P for 6 weeks. One-half of the plants were defoliated and the plant shoots were allowed to photosynthesize 14CO2 while the fungal compartment was exposed to 14NH4. After 3 days, the 14C of plant origin in fungal tissues and 15N of fungal origin in plant tissues were quantified. Nutrient availability had no observable effect on symbiotic resource exchange in non-defoliated systems. Defoliation reduced symbiotic N acquisition by plants at all levels of nutrient availability, with the reduction being most marked at higher N availability, indicating an increased tendency in the symbiotic system to discontinue resource exchange after defoliation at higher fertility levels. The concentration of 14C in extramatrical mycelium correlated significantly with the concentration of 15N in birch shoots. The results support the assumption that N delivery to the host by the mycorrhizal fungus is dependent on C flow from the plant to the fungus, and that exchanges between the partners are reciprocal. No significant reductions in root 14C content as a response to defoliation were observed, indicating that defoliation specifically reduced allocation to fungus, but not markedly to roots.}, }
@article {pmid15548293, year = {2004}, author = {Le Quéré, A and Schützendübel, A and Rajashekar, B and Canbäck, B and Hedh, J and Erland, S and Johansson, T and Tunlid, A}, title = {Divergence in gene expression related to variation in host specificity of an ectomycorrhizal fungus.}, journal = {Molecular ecology}, volume = {13}, number = {12}, pages = {3809-3819}, doi = {10.1111/j.1365-294X.2004.02369.x}, pmid = {15548293}, issn = {0962-1083}, mesh = {Base Sequence ; Basidiomycota/*genetics/metabolism ; DNA Primers ; DNA, Ribosomal Spacer/genetics ; *Evolution, Molecular ; Gene Expression Regulation, Fungal/*genetics ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Mycorrhizae/*genetics/metabolism ; Oligonucleotide Array Sequence Analysis ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; }, abstract = {Ectomycorrhizae are formed by mutualistic interactions between fungi and the roots of woody plants. During symbiosis the two organisms exchange carbon and nutrients in a specific tissue that is formed at the contact between a compatible fungus and plant. There is considerable variation in the degree of host specificity among species and strains of ectomycorrhizal fungi. In this study, we have for the first time shown that this variation is associated with quantitative differences in gene expression, and with divergence in nucleotide sequences of symbiosis-regulated genes. Gene expression and sequence evolution were compared in different strains of the ectomycorrhizal fungus Paxillus involutus; the strains included Nau, which is not compatible with birch and poplar, and the two compatible strains Maj and ATCC200175. On a genomic level, Nau and Maj were very similar. The sequence identity was 98.9% in the 16 loci analysed, and only three out of 1075 genes analysed by microarray-based hybridizations had signals indicating differences in gene copy numbers. In contrast, 66 out of the 1075 genes were differentially expressed in Maj compared to Nau after contact with birch roots. Thirty-seven of these symbiosis-regulated genes were also differentially expressed in the ATCC strain. Comparative analysis of DNA sequences of the symbiosis-regulated genes in different strains showed that two of them have evolved at an enhanced rate in Nau. The sequence divergence can be explained by a decreased selection pressure, which in turn is determined by lower functional constraints on these proteins in Nau as compared to the compatible strains.}, }
@article {pmid15546044, year = {2004}, author = {Grötzschel, S and Köster, J and de Beer, D}, title = {Degradation of 2,4-dichlorophenoxyacetic acid (2,4-d) by a hypersaline microbial mat and related functional changes in the mat community.}, journal = {Microbial ecology}, volume = {48}, number = {2}, pages = {254-262}, pmid = {15546044}, issn = {0095-3628}, mesh = {2,4-Dichlorophenoxyacetic Acid/*metabolism ; Biodegradation, Environmental ; Cyanobacteria/growth &amp; development/*metabolism ; *Ecosystem ; Herbicides/*metabolism ; Hydrogen-Ion Concentration ; Mexico ; Sulfides/metabolism ; }, abstract = {Microbial mats possibly possess degradation capacities for haloorganic pollutants because of their wide range of different functional groups of microorganisms combined with extreme diurnal changes in pH, oxygen, and sulfide gradients. In this study, 20 mg/l of the chlorinated herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) was applied to a pristine hypersaline cyanobacterial mat from Guerrero Negro, Mexico, under a light regime of 12 h dark/12 h light (600 mumol photons/m(2)s). The loss of 2,4-D was followed by chemical GC analysis; functional changes within the mat were determined with microelectrodes for oxygen, photosynthesis, pH, and sulfide. The depletion of 2,4-D due to photooxidation or sorption processes was checked in control experiments. Within 13 days, the light/dark incubated mats degraded 97% of the herbicide, while in permanent darkness only 35% were degraded. Adsorption of 2,4-D to the mat material, agar, or glass walls was negligible (4.6%), whereas 21% of the herbicide was degraded photochemically. The 2,4-D removal rate in the light/dark incubations was comparable to values reported for soils. The phototrophic community of the mat was permanently inhibited by the 2,4-D addition by 17% on average. The sulfate reduction in the entire mat and the respiration in the photic zone were inhibited more strongly but returned to original levels. Since at the end of the experiment the photosynthetic and respiratory activity of the mats were almost as high as in the beginning and 2,4-D almost completely disappeared, we conclude that the examined mats represent a robust and effective system for the degradation of the herbicide where probably the aerobic heterotrophic population is a major player in the degradation process.}, }
@article {pmid15546043, year = {2004}, author = {Backman, A and Jansson, JK}, title = {Degradation of 4-chlorophenol at low temperature and during extreme temperature fluctuations by Arthrobacter chlorophenolicus A6.}, journal = {Microbial ecology}, volume = {48}, number = {2}, pages = {246-253}, pmid = {15546043}, issn = {0095-3628}, mesh = {Arthrobacter/growth &amp; development/*metabolism ; Biodegradation, Environmental ; Chlorophenols/*metabolism ; Chromatography, Gas ; Colony Count, Microbial ; Luciferases/metabolism ; *Soil Microbiology ; *Temperature ; }, abstract = {Low average temperatures and temperature fluctuations in temperate soils challenge the efficacy of microbial strains used for clean up of pollutants. In this study, we investigated the cold tolerance of Arthrobacter chlorophenolicus A6, a microorganism previously shown to degrade high concentrations of 4-chlorophenol at 28 degrees C. Luciferase activity from a luc-tagged derivative of the strain (A6L) was used to monitor the metabolic status of the population during 4-chlorophenol degradation. The A6L strain could degrade 200-300 mug mL(-1) 4-chlorophenol in pure cultures incubated at 5 degrees C, although rates of degradation, growth and the metabolic status of the cells were lower at 5 degrees C compared to 28 degrees C. When subjected to temperature fluctuations between 5 and 28 degrees C, A6L continued to degrade 4-chlorophenol and remained active. In soil microcosm experiments, the degradation rates were significantly faster the first week at 28 degrees C, compared to 5 degrees C. However, this difference was no longer seen after 7 days, and equally low 4-chlorophenol concentrations were reached after 17 days at both temperatures. During 4-chlorophenol degradation in soil, CFU and luciferase activity values remained constant at both 5 and 28 degrees C. However, once most of the 4-chlorophenol was degraded, both values decreased by 1-1.5 logarithmic values at 28 degrees C, whereas they remained constant at 5 degrees C, indicating a high survival of the cells at low temperatures. Because of the ability of A. chlorophenolicus A6 to degrade high concentrations of 4-chlorophenol at 5 degrees C, together with its tolerance to temperature fluctuations and stress conditions found in soil, this strain is a promising candidate for bioaugmentation of chlorophenol-contaminated soil in temperate climates.}, }
@article {pmid15546042, year = {2004}, author = {Gallo, M and Amonette, R and Lauber, C and Sinsabaugh, RL and Zak, DR}, title = {Microbial community structure and oxidative enzyme activity in nitrogen-amended north temperate forest soils.}, journal = {Microbial ecology}, volume = {48}, number = {2}, pages = {218-229}, pmid = {15546042}, issn = {0095-3628}, mesh = {Analysis of Variance ; *Ecosystem ; Enzymes/*metabolism ; Michigan ; Nitrogen/*analysis ; Phospholipids/analysis ; Principal Component Analysis ; Soil/*analysis ; *Soil Microbiology ; *Trees ; }, abstract = {Large regions of temperate forest are subject to elevated atmospheric nitrogen (N) deposition which can affect soil organic matter dynamics by altering mass loss rates, soil respiration, and dissolved organic matter production. At present there is no general model that links these responses to changes in the organization and operation of microbial decomposer communities. Toward that end, we studied the response of litter and soil microbial communities to high levels of N amendment (30 and 80 kg ha(-1) yr(-1)) in three types of northern temperate forest: sugar maple/basswood (SMBW), sugar maple/red oak (SMRO), and white oak/black oak (WOBO). We measured the activity of extracellular enzymes (EEA) involved directly in the oxidation of lignin and humus (phenol oxidase, peroxidase), and indirectly, through the production of hydrogen peroxide (glucose oxidase, glyoxal oxidase). Community composition was analyzed by extracting and quantifying phospholipid fatty acids (PLFA) from soils. Litter EEA responses at SMBW sites diverged from those at oak-bearing sites (SMRO, BOWO), but the changes were not statistically significant. For soil, EEA responses were consistent across forests types: phenol oxidase and peroxidase activities declined as a function of N dose (33-73% and 5-41%, respectively, depending on forest type); glucose oxidase and glyoxal oxidase activities increased (200-400% and 150-300%, respectively, depending on forest type). Principal component analysis (PCA) ordinated forest types and treatment responses along two axes; factor 1 (44% of variance) was associated with phenol oxidase and peroxidase activities, factor 2 (31%) with glucose oxidase. Microbial biomass did not respond to N treatment, but nine of the 23 PLFA that formed >1 mol% of total biomass showed statistically significant treatment responses. PCA ordinated forest types and treatment responses along three axes (36%, 26%, 12% of variance). EEA factors 1 and 2 correlated negatively with PLFA factor 1 (r = -0.20 and -0.35, respectively, n = 108) and positively with PLFA factor 3 (r = +0.36 and +0.20, respectively, n = 108). In general, EEA responses were more strongly tied to changes in bacterial PLFA than to changes in fungal PLFA. Collectively, our data suggests that N inhibition of oxidative activity involves more than the repression of ligninase expression by white-rot basidiomycetes.}, }
@article {pmid15546041, year = {2004}, author = {Mengoni, A and Grassi, E and Barzanti, R and Biondi, EG and Gonnelli, C and Kim, CK and Bazzicalupo, M}, title = {Genetic diversity of bacterial communities of serpentine soil and of rhizosphere of the nickel-hyperaccumulator plant Alyssum bertolonii.}, journal = {Microbial ecology}, volume = {48}, number = {2}, pages = {209-217}, pmid = {15546041}, issn = {0095-3628}, mesh = {Bacteria/*genetics ; Base Sequence ; Brassicaceae/*microbiology ; Cloning, Molecular/methods ; Cluster Analysis ; DNA Primers ; DNA Restriction Enzymes/genetics ; DNA, Ribosomal/genetics ; *Genetic Variation ; Italy ; Metals, Heavy/analysis ; Molecular Sequence Data ; Plant Roots/*microbiology ; Polymorphism, Restriction Fragment Length ; Principal Component Analysis ; Sequence Analysis, DNA ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Serpentine soils are characterized by high levels of heavy metals (Ni, Co, Cr), and low levels of important plant nutrients (P, Ca, N). Because of these inhospitable edaphic conditions, serpentine soils are typically home to a very specialized flora including endemic species as the nickel hyperaccumulator Alyssum bertolonii. Although much is known about the serpentine flora, few researches have investigated the bacterial communities of serpentine areas. In the present study bacterial communities were sampled at various distances from A. bertolonii roots in three different serpentine areas and their genetic diversity was assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis. The obtained results indicated the occurrence of a high genetic diversity and heterogeneity of the bacterial communities present in the different serpentine areas. Moreover, TRFs (terminal restriction fragments) common to all the investigated A. bertolonii rhizosphere samples were found. A new cloning strategy was applied to 27 TRFs that were sequenced and taxonomically interpreted as mainly belonging to Gram-positive and alpha-Proteobacteria representatives. In particular, cloned TRFs which discriminated between rhizosphere and soil samples were mainly interpreted as belonging to Proteobacteria representatives.}, }
@article {pmid15546040, year = {2004}, author = {Smith, SM and Abed, RM and Gercia-Pichel, F}, title = {Biological soil crusts of sand dunes in Cape Cod National Seashore, Massachusetts, USA.}, journal = {Microbial ecology}, volume = {48}, number = {2}, pages = {200-208}, pmid = {15546040}, issn = {0095-3628}, mesh = {Bacteria/*genetics ; Base Sequence ; *Biodiversity ; Chlorophyta/*genetics ; Cluster Analysis ; DNA, Ribosomal/genetics ; Databases, Nucleic Acid ; Electrophoresis ; Likelihood Functions ; Massachusetts ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Silicon Dioxide/analysis ; *Soil Microbiology ; }, abstract = {Biological soil crusts cover hundreds of hectares of sand dunes at the northern tip of Cape Cod National Seashore (Massachusetts, USA). Although the presence of crusts in this habitat has long been recognized, neither the organisms nor their ecological roles have been described. In this study, we report on the microbial community composition of crusts from this region and describe several of their physical and chemical attributes that bear on their environmental role. Microscopic and molecular analyses revealed that eukaryotic green algae belonging to the genera Klebsormidium or Geminella formed the bulk of the material sampled. Phylogenetic reconstruction of partial 16S rDNA sequences obtained from denaturing gradient gel electrophoresis (DGGE) fingerprints also revealed the presence of bacterial populations related to the subclass of the Proteobacteria, the newly described phylum Geothrix/ Holophaga/ Acidobacterium, the Cytophaga/ Flavobacterium/ Bacteroides group, and spirochetes. The presence of these crusts had significant effects on the hydric properties and nutrient status of the natural substrate. Although biological soil crusts are known to occur in dune environments around the world, this study enhances our knowledge of their geographic distribution and suggests a potential ecological role for crust communities in this landscape.}, }
@article {pmid15546039, year = {2004}, author = {Fall, S and Nazaret, S and Chotte, JL and Brauman, A}, title = {Bacterial density and community structure associated with aggregate size fractions of soil-feeding termite mounds.}, journal = {Microbial ecology}, volume = {48}, number = {2}, pages = {191-199}, pmid = {15546039}, issn = {0095-3628}, mesh = {Acridine Orange ; Analysis of Variance ; Animals ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; Colony Count, Microbial ; DNA Primers ; DNA, Ribosomal Spacer/genetics ; *Ecosystem ; *Environment ; Isoptera/*physiology ; Multivariate Analysis ; Population Density ; Principal Component Analysis ; Soil/*analysis ; *Soil Microbiology ; Species Specificity ; }, abstract = {The building and foraging activities of termites are known to modify soil characteristics such as the heterogeneity. In tropical savannas the impact of the activity of soil-feeding termites (Cubitermes niokoloensis) has been shown to affect the properties of the soil at the aggregate level by creating new soil microenvironments (aggregate size fractions) [13]. These changes were investigated in greater depth by looking at the microbial density (AODC) and the genetic structure (automated rRNA intergenic spacer analysis: ARISA) of the communities in the different aggregate size fractions (i.e., coarse sand, fine sand, coarse silt, fine silt, and dispersible clays) separated from compartments (internal and external wall) of three Cubitermes niokoloensis mounds. The bacterial density of the mounds was significantly higher (1.5 to 3 times) than that of the surrounding soil. Within the aggregate size fractions, the termite building activity resulted in a significant increase in bacterial density within the coarser fractions (>20 mum). Multivariate analysis of the ARISA profiles revealed that the bacterial genetic structures of unfractionated soil and soil aggregate size fractions of the three mounds was noticeably different from the savanna soil used as a reference. Moreover, the microbial community associated with the different microenvironments in the three termite mounds revealed three distinct clusters formed by the aggregate size fractions of each mound. Except for the 2-20 mum fraction, these results suggest that the mound microbial genetic structure is more dependent upon microbial pool affiliation (the termite mound) than on the soil location (aggregate size fraction). The causes of the specificity of the microbial community structure of termite mound aggregate size fractions are discussed.}, }
@article {pmid15546038, year = {2004}, author = {Holmes, DE and Bond, DR and O'Neil, RA and Reimers, CE and Tender, LR and Lovley, DR}, title = {Microbial communities associated with electrodes harvesting electricity from a variety of aquatic sediments.}, journal = {Microbial ecology}, volume = {48}, number = {2}, pages = {178-190}, pmid = {15546038}, issn = {0095-3628}, mesh = {Base Sequence ; *Biodiversity ; Bioelectric Energy Sources/*microbiology ; Cloning, Molecular ; DNA Primers ; Electrodes/microbiology ; Gammaproteobacteria/*genetics ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Restriction Mapping ; Sequence Analysis, DNA ; }, abstract = {The microbial communities associated with electrodes from underwater fuel cells harvesting electricity from five different aquatic sediments were investigated. Three fuel cells were constructed with marine, salt-marsh, or freshwater sediments incubated in the laboratory. Fuel cells were also deployed in the field in salt marsh sediments in New Jersey and estuarine sediments in Oregon, USA. All of the sediments produced comparable amounts of power. Analysis of 16S rRNA gene sequences after 3-7 months of incubation demonstrated that all of the energy-harvesting anodes were highly enriched in microorganisms in the delta-Proteobacteria when compared with control electrodes not connected to a cathode. Geobacteraceae accounted for the majority of delta-Proteobacterial sequences or all of the energy-harvesting anodes, except the one deployed at the Oregon estuarine site. Quantitative PCR analysis of 16S rRNA genes and culturing studies indicated that Geobacteraceae were 100-fold more abundant on the marine-deployed anodes versus controls. Sequences most similar to microorganisms in the family Desulfobulbaceae predominated on the anode deployed in the estuarine sediments, and a significant proportion of the sequences recovered from the freshwater anodes were closely related to the Fe(III)-reducing isolate, Geothrix fermentans. There was also a specific enrichment of microorganisms on energy harvesting cathodes, but the enriched populations varied with the sediment/water source. Thus, future studies designed to help optimize the harvesting of electricity from aquatic sediments or waste organic matter should focus on the electrode interactions of these microorganisms which are most competitive in colonizing anodes and cathodes.}, }
@article {pmid15546037, year = {2004}, author = {Usher, KM and Fromont, J and Sutton, DC and Toze, S}, title = {The biogeography and phylogeny of unicellular cyanobacterial symbionts in sponges from Australia and the Mediterranean.}, journal = {Microbial ecology}, volume = {48}, number = {2}, pages = {167-177}, pmid = {15546037}, issn = {0095-3628}, mesh = {Animals ; Australia ; Base Sequence ; Bayes Theorem ; Cyanobacteria/*genetics ; DNA Primers ; DNA, Ribosomal/genetics ; *Demography ; Electrophoresis ; Geography ; Likelihood Functions ; Mediterranean Sea ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Porifera/*microbiology ; Sequence Analysis, DNA ; Sequence Homology ; *Symbiosis ; }, abstract = {The distribution, host associations, and phylogenetic relationships of the unicellular cyanobacterial symbionts of selected marine sponges were investigated with direct 16s rDNA sequencing. The results indicate that the symbionts of the marine sponges Aplysina aerophoba, Ircinia variabilis, and Petrosia ficiformis from the Mediterranean, four Chondrilla species from Australia and the Mediterranean, and Haliclona sp. from Australia support a diversity of symbionts comprising at least four closely related species of Synechococcus. These include the symbionts presently described as Aphanocapsa feldmannii from P. ficiformis and Chondrilla nucula. A fifth symbiont from Cymbastela marshae in Australia is an undescribed symbiont of sponges, related to Oscillatoria rosea. One symbiont, Candidatus Synechococcus spongiarum, was found in diverse sponge genera in the Mediterranean Sea and the Indian, Pacific, and Southern oceans, whereas others were apparently more restricted in host association and distribution. These results are discussed in terms of the biodiversity and biogeographic distributions of cyanobacterial symbionts.}, }
@article {pmid15545436, year = {2004}, author = {Margesin, R and Schumann, P and Spröer, C and Gounot, AM}, title = {Arthrobacter psychrophenolicus sp. nov., isolated from an alpine ice cave.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {54}, number = {Pt 6}, pages = {2067-2072}, doi = {10.1099/ijs.0.63124-0}, pmid = {15545436}, issn = {1466-5026}, mesh = {Aerobiosis ; Arthrobacter/*classification/cytology/*isolation &amp; purification/physiology ; Austria ; Bacterial Typing Techniques ; Biodegradation, Environmental ; Cell Wall/chemistry ; Cold Temperature ; DNA, Bacterial/chemistry/isolation &amp; purification ; DNA, Ribosomal/chemistry/isolation &amp; purification ; Fatty Acids/analysis/isolation &amp; purification ; Genes, rRNA ; Gentian Violet ; Geologic Sediments/*microbiology ; Glucose/metabolism ; *Ice ; Molecular Sequence Data ; Movement ; Nucleic Acid Hybridization ; Peptidoglycan/chemistry/isolation &amp; purification ; Phenazines ; Phenol/metabolism ; Phospholipids/analysis/isolation &amp; purification ; Phylogeny ; Pigments, Biological/biosynthesis ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Spores, Bacterial ; Vitamin K 2/analysis/isolation &amp; purification ; }, abstract = {On the basis of phenotypic, genotypic and chemotaxonomic characteristics, a novel species belonging to the genus Arthrobacter is described. A facultatively psychrophilic bacterium, strain AG31(T), was isolated from an alpine ice cave. The aerobic, Gram-positive, non-spore-forming, non-motile strain exhibited a rod-coccus growth cycle and produced a yellow pigment. Good growth and phenol biodegradation occurred at a temperature range of 1-25 degrees C. Up to 10 mM phenol was utilized as a sole carbon source. Glucose was not assimilated. Analysis of the 16S rRNA gene revealed that strain AG31(T) represents a distinct lineage within the genus Arthrobacter, being most closely related to Arthrobacter sulfureus. The level of DNA-DNA relatedness to the type strain of A. sulfureus was 29.9 %. Anteiso-C(15 : 0) was the predominant fatty acid (72 %). Strain AG31(T) exhibited A4alpha l-lys-l-Glu-type peptidoglycan and contained glucose as the only cell-wall sugar. MK-10 was the predominant menaquinone, and the polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. Strain AG31(T) (=DSM 15454(T)=LMG 21914(T)) is assigned as the type strain of a novel Arthrobacter species, Arthrobacter psychrophenolicus sp. nov.}, }
@article {pmid15537477, year = {2004}, author = {German-Fattal, M and Mösges, R}, title = {How to improve current therapeutic standards in upper respiratory infections: value of fusafungine.}, journal = {Current medical research and opinion}, volume = {20}, number = {11}, pages = {1769-1776}, doi = {10.1185/030079904X5535}, pmid = {15537477}, issn = {0300-7995}, mesh = {Administration, Topical ; Aerosols/administration &amp; dosage/*therapeutic use ; Anti-Bacterial Agents/administration &amp; dosage/*therapeutic use ; Anti-Inflammatory Agents, Non-Steroidal/administration &amp; dosage/*therapeutic use ; Depsipeptides ; Fusarium ; Humans ; Respiratory Tract Infections/*drug therapy ; }, abstract = {Despite guidelines and educational programs, systemic antibiotics and anti-inflammatory drugs are often inappropriately prescribed in upper respiratory tract infections (URTIs), although they are most often of viral origin, generally benign, and self-limiting with spontaneous recovery in more than 80% of cases. Reduced use of systemic antibiotics is crucial in the current context of concern about emerging antibiotic resistance and reducing unnecessary costs associated both with drug over-consumption and with the management of the consequences of antibiotic resistance. Local bacterial or viral infection of the airways induces an early inflammatory reaction. Although this inflammatory reaction has a beneficial effect in the capture and destruction of the pathogens, it can be responsible for deleterious tissue damage and vascular alterations leading to a self-perpetuating cycle of events. A wide array of medicines is available for symptomatic relief of URTIs: many of them are partially effective in reducing symptoms, but none is curative. Local administration of antibiotics and anti-inflammatory drugs allows drug delivery directly to the target site of infection and inflammation, i.e., the respiratory mucosa, thus enabling a higher concentration of the drug, which results in smaller doses to be given, decreased potential for systemic toxicity, fewer side effects, protection of other flora, and rapid relief. Fusafungine is a naturally occurring peptide antibiotic with anti-inflammatory properties, which selectively targets the tissue reaction and preserves the natural antibacterial and antiviral defences. It is indicated for topical use in nose and throat infections. A recent analysis of French general practitioners' (GPs) prescribing pattern in the field of URTIs has demonstrated that prescription of fusafungine has achieved what many educational programs have failed to do: a significant reduction in the 'real life' prescription of systemic antibiotics and antiinflammatory drugs, without the side effects of corticosteroids and vasoconstrictive agents, and without impact on microbial ecology.}, }
@article {pmid15537084, year = {2004}, author = {Horn, M and Wagner, M}, title = {Bacterial endosymbionts of free-living amoebae.}, journal = {The Journal of eukaryotic microbiology}, volume = {51}, number = {5}, pages = {509-514}, doi = {10.1111/j.1550-7408.2004.tb00278.x}, pmid = {15537084}, issn = {1066-5234}, mesh = {Amoeba/genetics/*microbiology ; Animals ; Chlamydia/genetics/metabolism/physiology ; Phylogeny ; RNA, Bacterial/analysis ; Rickettsieae/genetics/metabolism/physiology ; Symbiosis/*physiology ; }, abstract = {The occurrence of bacterial endosymbionts in free-living amoebae has been known for decades, but their obligate intracellular lifestyle hampered their identification. Application of the full cycle rRNA approach, including 16S rRNA gene sequencing and fluorescence in-situ hybridization with 16S rRNA-targeted oligonucleotide probes, assigned the symbionts of Acanthamoeba spp. and Hartmannella sp. to five different evolutionary lineages within the Proteobacteria, the Bacteroidetes, and the Chlamydiae, respectively. Some of these bacterial symbionts are most closely related to bacterial pathogens of humans, and it has been suggested that they should be considered potential emerging pathogens. Complete genome sequence analysis of a chlamydia-related symbiont of Acanthamoeba sp. showed that this endosymbiont uses similar mechanisms for interaction with its eukaryotic host cell as do the well-known bacterial pathogens of humans. Furthermore, phylogenetic analysis suggested that these mechanisms have been evolved by the ancestor of these amoeba symbionts in interplay with ancient unicellular eukaryotes.}, }
@article {pmid15535071, year = {2004}, author = {Ahren, D and Faedo, M and Rajashekar, B and Tunlid, A}, title = {Low genetic diversity among isolates of the nematode-trapping fungus Duddingtonia flagrans: evidence for recent worldwide dispersion from a single common ancestor.}, journal = {Mycological research}, volume = {108}, number = {Pt 10}, pages = {1205-1214}, doi = {10.1017/s0953756204000942}, pmid = {15535071}, issn = {0953-7562}, mesh = {Ascomycota/*genetics ; Calmodulin/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; Evolution, Molecular ; Genetic Variation ; Peptide Elongation Factor 1/chemistry/genetics ; Phylogeny ; Polymerase Chain Reaction ; Restriction Mapping ; Tubulin/chemistry/genetics ; }, abstract = {The genetic variation of Duddingtonia flagrans, which has become a promising biocontrol agent of animal parasitic nematodes, was investigated in a worldwide collection of 22 isolates. We analysed the sequence variation in four nuclear genes, tubA (beta-tubulin), CMD1 (calmodulin), EF1alpha (translation elongation factor 1alpha), and PII (extracellular serine protease). 1428 aligned base pairs (bp) were analysed from the four genes, including 709 bp of introns. In addition, the variations in three anonymous genomic regions comprising 1155 bp were examined. Three single nucleotide polymorphisms (SNPs) were detected in the seven loci, none of them in the protein encoding genes. The genetic variation was significantly higher in the nematode-trapping fungus Arthrobotrys oligospora, the closest evolutionary relative to D. flagrans. Analysis of 12 isolates of A. oligospora revealed 30 SNPs in tubA, CMD1, EF1alpha and PII. The genetic variation in the isolates of D. flagrans was further examined using AFLP analysis. Five primer combinations were used to detect 159 bands, of which 94 (59.1%) were polymorphic. A neighbour-joining tree based on the AFLP data showed no clear association between genotype and geographical origin. Furthermore, the AFLP data suggest that D. flagrans is mainly clonal and no recombination could be detected, not even within the same country. The low genetic variation in D. flagrans suggests that this fungus has recently diverged from a single progenitor. Based on estimations of mutation rates, it was calculated that this most recent common ancestor lived about 16,000-23,000 years ago.}, }
@article {pmid15528503, year = {2004}, author = {Qiu, X and Sundin, GW and Chai, B and Tiedje, JM}, title = {Survival of Shewanella oneidensis MR-1 after UV radiation exposure.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {11}, pages = {6435-6443}, pmid = {15528503}, issn = {0099-2240}, mesh = {Adenosine Triphosphatases/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Base Sequence ; Culture Media ; DNA Damage ; DNA Repair ; DNA, Complementary/genetics ; DNA-Binding Proteins/genetics/metabolism ; Escherichia coli Proteins/genetics/metabolism ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Shewanella/genetics/*growth &amp; development/*radiation effects ; *Sunlight ; *Ultraviolet Rays ; }, abstract = {We systematically investigated the physiological response as well as DNA damage repair and damage tolerance in Shewanella oneidensis MR-1 following UVC, UVB, UVA, and solar light exposure. MR-1 showed the highest UVC sensitivity among Shewanella strains examined, with D37 and D10 values of 5.6 and 16.5% of Escherichia coli K-12 values. Stationary cells did not show an increased UVA resistance compared to exponential-phase cells; instead, they were more sensitive at high UVA dose. UVA-irradiated MR-1 survived better on tryptic soy agar than Luria-Bertani plates regardless of the growth stage. A 20% survival rate of MR-1 was observed following doses of 3.3 J of UVC m(-2), 568 J of UVB m(-2), 25 kJ of UVA m(-2), and 558 J of solar UVB m(-2), respectively. Photoreactivation conferred an increased survival rate to MR-1 of as much as 177- to 365-fold, 11- to 23-fold, and 3- to 10-fold following UVC, UVB, and solar light irradiation, respectively. A significant UV mutability to rifampin resistance was detected in both UVC- and UVB-treated samples, with the mutation frequency in the range of 10(-5) to 10(-6). Unlike in E. coli, the expression levels of the nucleotide excision repair (NER) component genes uvrA, uvrB, and uvrD were not damage inducible in MR-1. Complementation of Pseudomonas aeruginosa UA11079 (uvrA deficient) with uvrA of MR-1 increased the UVC survival of this strain by more than 3 orders of magnitude. Loss of damage inducibility of the NER system appears to contribute to the high sensitivity of this bacterium to UVR as well as to other DNA-damaging agents.}, }
@article {pmid15527918, year = {2004}, author = {Holley, RA and Peirson, MD and Lam, J and Tan, KB}, title = {Microbial profiles of commercial, vacuum-packaged, fresh pork of normal or short storage life.}, journal = {International journal of food microbiology}, volume = {97}, number = {1}, pages = {53-62}, doi = {10.1016/j.ijfoodmicro.2004.03.029}, pmid = {15527918}, issn = {0168-1605}, mesh = {Animals ; Bacteria/*growth &amp; development/isolation &amp; purification ; Food Contamination/*analysis/prevention &amp; control ; Food Microbiology ; Food Packaging ; Food Preservation/*methods ; Food-Processing Industry/*standards ; Hydrogen-Ion Concentration ; Hygiene ; Meat/*microbiology ; Odorants/analysis ; Quality Control ; Swine ; Time Factors ; Vacuum ; }, abstract = {The microbial ecology of fresh vacuum-packed pork cuts during storage at -1.5 degrees C for up to 45 days was examined to characterize rates of microbial growth and pH changes in commercially prepared products of normal storage quality. Pork loins in commercial distribution with odour defects were also studied to determine a possible cause of the defects and avoid future problems. In addition, microbial profiles of pork cuts from two plants were compared, after storage for 25 days at -1.5 degrees C, to identify possible reasons for differences in the storage life of product from the plants. The effects of a change in sanitation procedures on the microbial populations of products stored for 25 days were also studied. With normal product, microbial growth in different packages progressed at different rates, reflecting differences in initial levels of bacterial contamination. All samples in the study reached 8 weeks without apparent organoleptic change and samples carried 5.8+/-1.2 log bacteria cm(-2) (mean+/-S.D.). The flora of loins with the odour defect were predominately lactic acid bacteria (LAB) and carnobacteria, but they contained large fractions of Enterobacteriaceae <35 days after packaging. Aeromonas spp. and Shewanella spp. were likely responsible for the sulfide-putrid smell of these spoiled products, but species of Enterobacteriaceae and lactic acid bacteria could have contributed to spoilage. Comparison of microbial groups present in 16 other cuts, half from each of two commercial plants, which were stored for 25 days at -1.5 degrees C, showed that larger fractions of Enterobacteriaceae were present in samples from the plant having difficulty achieving the desired storage life. Additional bacterial samples from 12 cuts supplied by the latter plant obtained after adoption of an acid sanitizer step in the plant cleaning regimen, and also stored for 25 days at -1.5 degrees C, yielded few Enterobacteriaceae, Aeromonas or Shewanella. Use of an acid sanitizer in plant cleaning may be a means of controlling alkali-tolerant bacteria such as Aeromonas or Shewanella which can contaminate pork cuts and spoil vacuum-packaged product. The fraction of Enterobacteriaceae in bacteria populations on fresh pork stored for 25 days at -1.5 degrees C may be a useful indicator of the effectiveness of plant sanitation.}, }
@article {pmid15518874, year = {2004}, author = {Lambertsen, LM and Molin, S and Kroer, N and Thomas, CM}, title = {Transcriptional regulation of pWW0 transfer genes in Pseudomonas putida KT2440.}, journal = {Plasmid}, volume = {52}, number = {3}, pages = {169-181}, doi = {10.1016/j.plasmid.2004.06.005}, pmid = {15518874}, issn = {0147-619X}, mesh = {Base Sequence ; DNA Primers ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; *Gene Expression Regulation, Bacterial ; Gene Transfer Techniques ; Plasmids/*genetics ; Polymerase Chain Reaction ; Pseudomonas putida/*genetics ; Restriction Mapping ; *Transcription, Genetic ; }, abstract = {The conjugative IncP-9 plasmid pWW0 (TOL) carries transfer genes, many of whose functions can be predicted from sequence similarities to the well-studied IncW and IncP-1 plasmids, and that are clustered with the replication and maintenance genes of the plasmid core. In this study we show that the IncP-9 transfer genes are transcribed from at least three promoter regions. The promoters for traA and traD act divergently from the region found to encode the origin of transfer, oriT. These promoters regulate expression of traA, B, and perhaps traC in one direction and traD in the other, all of whose gene products are predicted to be involved in relaxasome formation and DNA processing during transfer, and they are repressed by TraA. The third promoter region, upstream of mpfR, is responsible for transcription of mpfR and mpfA to mpfJ, encoding proteins involved in mating pair formation. Transcription from this region is negatively autoregulated by MpfR. Thus the pWW0 transfer genes, like those of the IncP-1 plasmids, are expressed at all times, but kept in control by a negative feed back loop to limit the metabolic burden on the host. Although many of the related mating pair formation systems are, as in pWW0, transcribed divergently from an operon for replication and/or stable inheritance functions, MpfR is not related to the known regulatory proteins of these other transfer systems outside those of the IncP-9 family and indeed the regulators tend to be specific for each plasmid family. This suggests that the general pattern of genetic organisation exhibited by these systems has arisen a number of times independently and must therefore be highly favourable to plasmid survival and spread.}, }
@article {pmid15472305, year = {2004}, author = {Rodríguez-Nava, V and Couble, A and Molinard, C and Sandoval, H and Boiron, P and Laurent, F}, title = {Nocardia mexicana sp. nov., a new pathogen isolated from human mycetomas.}, journal = {Journal of clinical microbiology}, volume = {42}, number = {10}, pages = {4530-4535}, pmid = {15472305}, issn = {0095-1137}, mesh = {Bacterial Typing Techniques ; Base Sequence ; DNA, Ribosomal/analysis ; Genes, rRNA ; Humans ; Molecular Sequence Data ; Mycetoma/*microbiology ; *Nocardia/*classification/genetics/isolation &amp; purification/pathogenicity ; Nocardia Infections/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Three isolates collected from human mycetomas and showing an unusual brownish purple pigmentation on Bennett agar plates were analyzed by a polyphasic taxonomic approach, including morphological, biochemical, physiological, and chemotaxonomic properties coupled with genomic and phylogenetic analysis. It clearly appeared that these microorganisms were distinct from their closest phenotypic and genetic match, the most related species according to 16S rRNA gene sequence analysis being Nocardia pseudobrasiliensis. The data obtained indicated that the three clinical strains should be recognized as a new species for which the name Nocardia mexicana sp. nov. is proposed.}, }
@article {pmid15469063, year = {2004}, author = {Salvat, G and Fravalo, P}, title = {Risk assessment strategies for Europe: integrated safety strategy or final product control: Example of Listeria monocytogenes in processed products from pork meat industry.}, journal = {DTW. Deutsche tierarztliche Wochenschrift}, volume = {111}, number = {8}, pages = {331-334}, pmid = {15469063}, issn = {0341-6593}, mesh = {Animals ; Consumer Product Safety ; Disease Outbreaks/prevention &amp; control ; Europe ; Food Handling ; *Food Microbiology ; France/epidemiology ; Humans ; *Listeria monocytogenes ; Listeriosis/*epidemiology/prevention &amp; control ; Meat/*microbiology ; Quality Control ; *Risk Assessment ; Swine ; }, abstract = {The European regulation 2160/2003 of November 17th, 2003 clearly shows the European strategy of zoonosis monitoring and control as an integrated approach, including the entire food production chain with a first application to Salmonella control in different animal species. This regulation is the consequence of a risk assessment performed with a "farm to fork" philosophy. European strategy is scarcely different from the American strategy, despite the fact that both were achieved by a quantitative risk assessment, as for instance, in the USA the control of Salmonella in eggs is supposed to be completed by refrigeration. Nevertheless, the EU will still have a final product control approach towards future regulations on microbiological criteria for foodstuffs. The final production monitoring and control with HACCP (93/43/EC) and microbiological criteria is the only one available for L. monocytogenes in foodstuffs. The purpose of this paper is to discuss alternative control strategies for L. monocytogenes in pig production including integrated risk assessment. In France, most of the food-borne outbreaks associated with L. monocytogenes in delicatessen were due to one particular group of strains belonging to serovar 4b and presenting a particular RFLP/PFGE (Restriction Fragment Length Polymorphism/Pulsed Field Gel Electrophoresis) profile. The outbreak itself is always associated with the initial contamination of a RTE ("ready to eat") product and re-contamination by inappropriate handling after cooking. Consequently, in most cases the RTE product is subject to inadequate refrigeration during an excessive shelf-life. The responsibility of the food industry and the consumer is clearly engaged during this scenario of foodborne diseases. The question is how to avoid the introduction of this particular strain of L. monocytogenes in the food chain. In a study we tried to evaluate the risk of pig carcass contamination at slaughterhouse level and to identify the main risk factors associated with the infection of live pigs. In most cases inappropriate cleaning and disinfection of surfaces were associated with the contamination of raw meat, but in some cases the introduction of epidemic strains in the food chain was also associated with primary production. Feeding with soup in piggeries seemed to select a particular microbial ecology associated to L. monocytogenes contamination of live pigs. The possible strategies that may be used to control L. monocytogenes in live pig production are not yet developed sufficiently to be included in the EC regulation but should be discussed in more detail.}, }
@article {pmid15466556, year = {2004}, author = {Pysz, MA and Conners, SB and Montero, CI and Shockley, KR and Johnson, MR and Ward, DE and Kelly, RM}, title = {Transcriptional analysis of biofilm formation processes in the anaerobic, hyperthermophilic bacterium Thermotoga maritima.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {10}, pages = {6098-6112}, pmid = {15466556}, issn = {0099-2240}, mesh = {ATP-Binding Cassette Transporters/genetics/metabolism ; Base Sequence ; Biofilms/*growth &amp; development ; Bioreactors ; DNA, Bacterial/genetics ; Gene Expression Profiling ; Genes, Bacterial ; Iron/metabolism ; Models, Biological ; Oligonucleotide Array Sequence Analysis ; Oxidative Stress ; Polysaccharides, Bacterial/genetics/metabolism ; Sulfur/metabolism ; Temperature ; Thermotoga maritima/*genetics/*physiology/ultrastructure ; Transcription, Genetic ; }, abstract = {Thermotoga maritima, a fermentative, anaerobic, hyperthermophilic bacterium, was found to attach to bioreactor glass walls, nylon mesh, and polycarbonate filters during chemostat cultivation on maltose-based media at 80 degrees C. A whole-genome cDNA microarray was used to examine differential expression patterns between biofilm and planktonic populations. Mixed-model statistical analysis revealed differential expression (twofold or more) of 114 open reading frames in sessile cells (6% of the genome), over a third of which were initially annotated as hypothetical proteins in the T. maritima genome. Among the previously annotated genes in the T. maritima genome, which showed expression changes during biofilm growth, were several that corresponded to biofilm formation genes identified in mesophilic bacteria (i.e., Pseudomonas species, Escherichia coli, and Staphylococcus epidermidis). Most notably, T. maritima biofilm-bound cells exhibited increased transcription of genes involved in iron and sulfur transport, as well as in biosynthesis of cysteine, thiamine, NAD, and isoprenoid side chains of quinones. These findings were all consistent with the up-regulation of iron-sulfur cluster assembly and repair functions in biofilm cells. Significant up-regulation of several beta-specific glycosidases was also noted in biofilm cells, despite the fact that maltose was the primary carbon source fed to the chemostat. The reasons for increased beta-glycosidase levels are unclear but are likely related to the processing of biofilm-based polysaccharides. In addition to revealing insights into the phenotype of sessile T. maritima communities, the methodology developed here can be extended to study other anaerobic biofilm formation processes as well as to examine aspects of microbial ecology in hydrothermal environments.}, }
@article {pmid15460065, year = {2004}, author = {Zoetendal, EG and Cheng, B and Koike, S and Mackie, RI}, title = {Molecular microbial ecology of the gastrointestinal tract: from phylogeny to function.}, journal = {Current issues in intestinal microbiology}, volume = {5}, number = {2}, pages = {31-47}, pmid = {15460065}, issn = {1466-531X}, mesh = {Bacteria/*classification/genetics/growth &amp; development/*metabolism ; DNA, Ribosomal/analysis ; *Ecosystem ; Gastrointestinal Tract/*microbiology ; Humans ; Molecular Biology/*methods ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {During the past decade it became evident that anaerobic cultivation-based approaches provides an incomplete picture of the microbial diversity in the GI tract, since at present only a minority of microbes can be obtained in culture. The application of molecular, mainly 16S ribosomal RNA (rRNA)-based approaches enables researchers to bypass the cultivation step and has proven its usefulness in studying the microbial composition in a variety of ecosystems, including the gastrointestinal (GI) tract. This critical review summarizes the impact of these culture-independent approaches on our knowledge of the ecology of the GI tract and provides directions for future studies which should emphasize function of specific strains, species and groups of microbes.}, }
@article {pmid15451504, year = {2004}, author = {Streit, WR and Schmitz, RA}, title = {Metagenomics--the key to the uncultured microbes.}, journal = {Current opinion in microbiology}, volume = {7}, number = {5}, pages = {492-498}, doi = {10.1016/j.mib.2004.08.002}, pmid = {15451504}, issn = {1369-5274}, mesh = {Bacteria/*genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; DNA, Bacterial/chemistry/isolation &amp; purification ; DNA, Ribosomal/chemistry/isolation &amp; purification ; Ecosystem ; *Environmental Microbiology ; Genes, Bacterial ; *Genome, Bacterial ; *Genomics ; RNA, Ribosomal, 16S/genetics ; *Sequence Analysis, DNA ; }, abstract = {It is widely accepted that up to 99.8% of the microbes present in many environments are not readily culturable. 'Metagenome technology' tries to overcome this bottleneck by developing and using culture-independent approaches. From the outset, metagenome-based approaches have led to the accumulation of an increasing number of DNA sequences, but until this time the sequences retrieved have been those of uncultured microbes. These genomic sequences are currently exploited for novel biotechnological and pharmaceutical applications and to increase our knowledge on microbial ecology and physiology of these microbes. Using the metagenome sequences to fully understand how complex microbial communities function and how microbes interact within these niches represents a major challenge for microbiologists today.}, }
@article {pmid15388727, year = {2004}, author = {Goris, J and De Vos, P and Caballero-Mellado, J and Park, J and Falsen, E and Quensen, JF and Tiedje, JM and Vandamme, P}, title = {Classification of the biphenyl- and polychlorinated biphenyl-degrading strain LB400T and relatives as Burkholderia xenovorans sp. nov.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {54}, number = {Pt 5}, pages = {1677-1681}, doi = {10.1099/ijs.0.63101-0}, pmid = {15388727}, issn = {1466-5026}, support = {P42ES04911/ES/NIEHS NIH HHS/United States ; }, mesh = {Arabinose/metabolism ; Base Composition ; Biodegradation, Environmental ; Biphenyl Compounds/*metabolism ; Blood/microbiology ; Burkholderia/*classification/genetics/isolation &amp; purification/*metabolism ; Burkholderia Infections/microbiology ; DNA, Bacterial/chemistry/isolation &amp; purification ; Fatty Acids/analysis ; Genes, rRNA ; Humans ; Nucleic Acid Hybridization ; Phylogeny ; Polychlorinated Biphenyls/*metabolism ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {Strain LB400T is the best-studied polychlorinated biphenyl (PCB) degrader. This organism has previously been allocated in the genus Burkholderia, since its 16S rRNA gene sequence shows 98.6 % sequence similarity to the type strains of Burkholderia graminis and Burkholderia terricola. A polyphasic study was undertaken to clarify the actual taxonomic position of this biotechnologically important organism and of two strains, one recovered from a blood culture vial and one from a coffee plant rhizosphere, both of which resembled strain LB400T in their whole-cell protein patterns. DNA-DNA hybridization experiments revealed that the three strains represented a single novel species, for which the name Burkholderia xenovorans sp. nov. is proposed. Strains of this novel species can be differentiated phenotypically from nearly all other Burkholderia species by their inability to assimilate L-arabinose. The whole-cell fatty acid profile of B. xenovorans strains is consistent with their classification in the genus Burkholderia, with 18 : 1omega7c, 16 : 1omega7c, 16 : 0, 14 : 0 3OH, 16 : 0 3OH, 17 : 0 cyclo and 14 : 0 being the most abundant fatty acids. The G + C content of the species varies between 62.4 and 62.9 mol%. The type strain of B. xenovorans is LB400T (= LMG 21463T = CCUG 46959T = NRRL B-18064T).}, }
@article {pmid15382856, year = {2004}, author = {Griffin, BM and Tiedje, JM and Löffler, FE}, title = {Anaerobic microbial reductive dechlorination of tetrachloroethene to predominately trans-1,2-dichloroethene.}, journal = {Environmental science &amp; technology}, volume = {38}, number = {16}, pages = {4300-4303}, doi = {10.1021/es035439g}, pmid = {15382856}, issn = {0013-936X}, mesh = {Bacteria, Anaerobic ; Dichloroethylenes/chemistry ; Solvents/*metabolism ; Tetrachloroethylene/*metabolism ; }, abstract = {While most sites and all characterized PCE and TCE dechlorinating anaerobic bacteria produce cis-DCE as the major DCE isomer, significant amounts of trans-DCE are found in the environment. We have obtained microcosms from some sites and enrichment cultures that produce more trans-DCE than cis-DCE. These cultures reductively dechlorinated PCE and TCE to trans-DCE and cis-DCE simultaneously and in a ratio of 3(+/-0.5):1 that was stable through serial transfers with a variety of electron donors and occurred in both methanogenic and nonmethanogenic enrichments. Two sediment-free, nonmethanogenic enrichment cultures produced trans-DCE at rates of up to 2.5 micromol L(-1) day(-1). Dehalococcoides populations were detected in both trans-DCE producing cultures by their 16S rRNA gene sequences, and trans-DCE was produced in the presence of ampicillin. Because trans-DCE can be the major product from PCE and TCE microbial dechlorination, high fractions of trans-DCE at chloroethene-contaminated sites are not necessarily from source contamination.}, }
@article {pmid15371444, year = {2004}, author = {Kessi, J and Hanselmann, KW}, title = {Similarities between the abiotic reduction of selenite with glutathione and the dissimilatory reaction mediated by Rhodospirillum rubrum and Escherichia coli.}, journal = {The Journal of biological chemistry}, volume = {279}, number = {49}, pages = {50662-50669}, doi = {10.1074/jbc.M405887200}, pmid = {15371444}, issn = {0021-9258}, mesh = {Cytochromes c/metabolism ; Escherichia coli/*metabolism ; Glutathione/*analogs &amp; derivatives/chemistry/*metabolism ; Glutathione Reductase/metabolism ; Hydrogen Peroxide/chemistry ; Kinetics ; Light ; Microscopy, Electron ; Microscopy, Electron, Transmission ; Models, Chemical ; Organoselenium Compounds/chemistry ; Oxygen/chemistry ; Rhodospirillum rubrum/*metabolism ; Selenium/chemistry ; Sodium Selenite/*chemistry/metabolism ; Superoxide Dismutase/chemistry/metabolism ; Time Factors ; }, abstract = {Various mechanisms have been proposed to explain the biological dissimilatory reduction of selenite (SeO3(2-)) to elemental selenium (Se(o)), although none is without controversy. Glutathione, the most abundant thiol in the eukaryotic cells, the cyanobacteria, and the alpha, beta, and gamma groups of the proteobacteria, has long been suspected to be involved in selenium metabolism. Experiments with the phototrophic alpha proteobacterium Rhodospirillum rubrum showed that the rate of selenite reduction was decreased when bacteria synthesized lower than normal levels of glutathione, and in Rhodobacter sphaeroides and Escherichia coli the reaction was reported to induce glutathione reductase. In the latter organism superoxide dismutase was also induced in cells grown in the presence of selenite, indicating that superoxide anions (O2-) were produced. These observations led us to investigate the abiotic (chemical) reduction of selenite by glutathione and to compare the features of this reaction with those of the reaction mediated by R. rubrum and E. coli. Our findings imply that selenite was first reduced to selenodiglutathione, which reached its maximum concentration within the 1st min of the reaction. Formation of selenodiglutathione was paralleled by a rapid reduction of cytochrome c, a known oxidant for superoxide anions. Cytochrome c reduction was inhibited by superoxide dismutase, indicating that O2- was the source of electrons for the reduction. These results demonstrated that superoxide was produced in the abiotic reduction of selenite with glutathione, thus lending support to the hypothesis that glutathione may be involved in the reaction mediated by R. rubrum and E. coli. The second phase of the reaction, which led to the formation of elemental selenium (Se(o)), developed more slowly. Se(o) precipitation reached a maximum within 2 h after the beginning of the reaction. Secondary reactions leading to the degradation of the superoxide significantly decreased the yield of Se(o) in the abiotic reaction compared with that of the bacterially mediated selenite reduction. Abiotically formed selenium particles showed the same characteristic orange-red color, spherical structure, and size as particles produced by R. rubrum, again providing support for the hypothesis that glutathione is involved in the reduction of selenite to elemental selenium in this organism.}, }
@article {pmid15369484, year = {2004}, author = {Wierzchos, J and De Los Ríos, A and Sancho, LG and Ascaso, C}, title = {Viability of endolithic micro-organisms in rocks from the McMurdo Dry Valleys of Antarctica established by confocal and fluorescence microscopy.}, journal = {Journal of microscopy}, volume = {216}, number = {Pt 1}, pages = {57-61}, doi = {10.1111/j.0022-2720.2004.01386.x}, pmid = {15369484}, issn = {0022-2720}, mesh = {Antarctic Regions ; Cold Climate ; Cyanobacteria/isolation &amp; purification/ultrastructure ; Ecology ; Fluorescent Dyes ; Fungi/*isolation &amp; purification/ultrastructure ; Microscopy, Confocal ; Microscopy, Fluorescence ; *Soil Microbiology ; }, abstract = {The rocks of the McMurdo Dry Valleys desert in Antarctica harbour endolithic communities of micro-organisms such as lichens, fungi, cyanobacteria and bacteria. Establishing the physiological status and viability of these microbial colonies in their natural microhabitat has far-reaching implications for understanding the microbial ecology of the harsh environment of this polar desert. Here we describe the use of confocal microscopy and a specific fluorescent probe (FUN-1) to evaluate the metabolic activity of fungal cells. Application of confocal microscopy also served to identify living and dead bacteria or cyanobacteria using the fluorescent assay reagents Live/Dead SYTO 9 and propidium iodide or SYTOX Green, respectively. In addition, through the use of epifluorescence microscopy, live/dead bacteria and cyanobacteria could be detected by estimating fluorescence from their cell components provoked by simultaneously staining with nucleic acids stains such as DAPI and SYTOX Green.}, }
@article {pmid15358434, year = {2004}, author = {Burns, DG and Camakaris, HM and Janssen, PH and Dyall-Smith, ML}, title = {Cultivation of Walsby's square haloarchaeon.}, journal = {FEMS microbiology letters}, volume = {238}, number = {2}, pages = {469-473}, doi = {10.1016/j.femsle.2004.08.016}, pmid = {15358434}, issn = {0378-1097}, mesh = {Culture Techniques/*methods ; Halobacteriales/genetics/*growth &amp; development/isolation &amp; purification/physiology ; RNA, Ribosomal, 16S/genetics ; Sodium Chloride/metabolism ; }, abstract = {The square haloarchaea of Walsby (SHOW group) dominate hypersaline microbial communities but have not been cultured since their discovery 25 years ago. We show that natural water dilution cultures can be used to isolate members of this group and, once in pure culture, they can be grown in standard halobacterial media. Cells display a square morphology and contain gas vesicles and poly-beta-hydroxybutyrate (PHB) granules. The 16S rRNA gene sequence was >99% identical to other SHOW group sequences. They prefer high salinities (23-30%), and can grow with a doubling time of 1-2 days in rich media. The ability to culture SHOW group organisms makes it possible to study, in a comprehensive way, the microbial ecology of salt lakes.}, }
@article {pmid15357285, year = {2004}, author = {Hur, I and Chun, J}, title = {A method for comparing multiple bacterial community structures from 16S rDNA clone library sequences.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {42}, number = {1}, pages = {9-13}, pmid = {15357285}, issn = {1225-8873}, mesh = {Algorithms ; Bacteria/*genetics/*growth &amp; development ; Cluster Analysis ; Computational Biology ; DNA, Bacterial/analysis/isolation &amp; purification ; DNA, Ribosomal/*chemistry/isolation &amp; purification ; Ecosystem ; *Environmental Microbiology ; *Gene Library ; Genes, rRNA ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; *Sequence Analysis, DNA ; Software ; }, abstract = {Culture-independent approaches, based on 16S rDNA sequences, are extensively used in modern microbial ecology. Sequencing of the clone library generated from environmental DNA has advantages over fingerprint-based methods, such as denaturing gradient gel electrophoresis, as it provides precise identification and quantification of the phylotypes present in samples. However, to date, no method exists for comparing multiple bacterial community structures using clone library sequences. In this study, an automated method to achieve this has been developed, by applying pair wise alignment, hierarchical clustering and principle component analysis. The method has been demonstrated to be successful in comparing samples from various environments. The program, named CommCluster, was written in JAVA, and is now freely available, at http://chunlab.snu.ac.kr/commcluster/.}, }
@article {pmid15345436, year = {2004}, author = {Schloss, PD and Larget, BR and Handelsman, J}, title = {Integration of microbial ecology and statistics: a test to compare gene libraries.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {9}, pages = {5485-5492}, pmid = {15345436}, issn = {0099-2240}, mesh = {Aeromonas/genetics ; Animals ; Ecosystem ; Evolution, Molecular ; *Gene Library ; Pseudomonas/genetics ; RNA, Ribosomal, 16S/*genetics ; Reproducibility of Results ; Soil ; Zebrafish/genetics ; }, abstract = {Libraries of 16S rRNA genes provide insight into the membership of microbial communities. Statistical methods help to determine whether differences in library composition are artifacts of sampling or are due to underlying differences in the communities from which they are derived. To contribute to a growing statistical framework for comparing 16S rRNA libraries, we present a computer program, integral -LIBSHUFF, which calculates the integral form of the Cramér-von Mises statistic. This implementation builds upon the LIBSHUFF program, which uses an approximation of the statistic and makes a number of modifications that improve precision and accuracy. Once integral -LIBSHUFF calculates the P values, when pairwise comparisons are tested at the 0.05 level, the probability of falsely identifying a significant P value is 0.098 for a study with two libraries, 0.265 for three libraries, and 0.460 for four libraries. The potential negative effects of making the multiple pairwise comparisons necessitate correcting for the increased likelihood that differences between treatments are due to chance and do not reflect biological differences. Using integral -LIBSHUFF, we found that previously published 16S rRNA gene libraries constructed from Scottish and Wisconsin soils contained different bacterial lineages. We also analyzed the published libraries constructed for the zebrafish gut microflora and found statistically significant changes in the community during development of the host. These analyses illustrate the power of integral -LIBSHUFF to detect differences between communities, providing the basis for ecological inference about the association of soil productivity or host gene expression and microbial community composition.}, }
@article {pmid15345423, year = {2004}, author = {Rabaey, K and Boon, N and Siciliano, SD and Verhaege, M and Verstraete, W}, title = {Biofuel cells select for microbial consortia that self-mediate electron transfer.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {9}, pages = {5373-5382}, pmid = {15345423}, issn = {0099-2240}, mesh = {Animals ; Bacteria/classification/*isolation &amp; purification ; Electrochemistry ; Fuel Oils/*microbiology ; Manure/microbiology ; Molecular Sequence Data ; Oligochaeta/microbiology ; Swine ; }, abstract = {Microbial fuel cells hold great promise as a sustainable biotechnological solution to future energy needs. Current efforts to improve the efficiency of such fuel cells are limited by the lack of knowledge about the microbial ecology of these systems. The purposes of this study were (i) to elucidate whether a bacterial community, either suspended or attached to an electrode, can evolve in a microbial fuel cell to bring about higher power output, and (ii) to identify species responsible for the electricity generation. Enrichment by repeated transfer of a bacterial consortium harvested from the anode compartment of a biofuel cell in which glucose was used increased the output from an initial level of 0.6 W m(-2) of electrode surface to a maximal level of 4.31 W m(-2) (664 mV, 30.9 mA) when plain graphite electrodes were used. This result was obtained with an average loading rate of 1 g of glucose liter(-1) day(-1) and corresponded to 81% efficiency for electron transfer from glucose to electricity. Cyclic voltammetry indicated that the enhanced microbial consortium had either membrane-bound or excreted redox components that were not initially detected in the community. Dominant species of the enhanced culture were identified by denaturing gradient gel electrophoresis and culturing. The community consisted mainly of facultative anaerobic bacteria, such as Alcaligenes faecalis and Enterococcus gallinarum, which are capable of hydrogen production. Pseudomonas aeruginosa and other Pseudomonas species were also isolated. For several isolates, electrochemical activity was mainly due to excreted redox mediators, and one of these mediators, pyocyanin produced by P. aeruginosa, could be characterized. Overall, the enrichment procedure, irrespective of whether only attached or suspended bacteria were examined, selected for organisms capable of mediating the electron transfer either by direct bacterial transfer or by excretion of redox components.}, }
@article {pmid15344932, year = {2004}, author = {Kennedy, N and Brodie, E and Connolly, J and Clipson, N}, title = {Impact of lime, nitrogen and plant species on bacterial community structure in grassland microcosms.}, journal = {Environmental microbiology}, volume = {6}, number = {10}, pages = {1070-1080}, doi = {10.1111/j.1462-2920.2004.00638.x}, pmid = {15344932}, issn = {1462-2912}, mesh = {Analysis of Variance ; Bacteria/*drug effects/genetics ; *Bacterial Physiological Phenomena ; Biomass ; Calcium Compounds/*pharmacology ; DNA Primers ; *Ecosystem ; Hydrogen-Ion Concentration ; Multivariate Analysis ; Nitrogen/*pharmacology ; Oxides/*pharmacology ; Poaceae/physiology ; Polymorphism, Restriction Fragment Length ; Soil/analysis ; }, abstract = {A microcosm-based approach was used to study impacts of plant and chemical factors on the bacterial community structure of an upland acidic grassland soil. Seven perennial plant species typical of both natural, unimproved (Nardus stricta, Agrostis capillaris, Festuca ovina and F. rubra) and fertilized, improved (Holcus lanatus, Lolium perenne and Trifolium repens) grasslands were either left unamended or treated with lime, nitrogen, or lime plus nitrogen in a 75-day glasshouse experiment. Lime and nitrogen amendment were shown to have a greater effect on microbial activity, biomass and bacterial ribotype number than plant species. Liming increased soil pH, microbial activity and biomass, while decreasing ribotype number. Nitrogen addition decreased soil pH, microbial activity and ribotype number. Addition of lime plus nitrogen had intermediate effects, which appeared to be driven more by lime than nitrogen. Terminal restriction fragment length polymorphism (TRFLP) analysis revealed that lime and nitrogen addition altered soil bacterial community structure, while plant species had little effect. These results were further confirmed by multivariate redundancy analysis, and suggest that soil lime and nitrogen status are more important controllers of bacterial community structure than plant rhizosphere effects.}, }
@article {pmid15341639, year = {2004}, author = {Zhang, LH and Dong, YH}, title = {Quorum sensing and signal interference: diverse implications.}, journal = {Molecular microbiology}, volume = {53}, number = {6}, pages = {1563-1571}, doi = {10.1111/j.1365-2958.2004.04234.x}, pmid = {15341639}, issn = {0950-382X}, mesh = {Animals ; Bacterial Physiological Phenomena ; Candida albicans/physiology ; Cell Communication/*physiology ; Gene Expression Regulation, Bacterial ; Humans ; Signal Transduction/*physiology ; }, abstract = {Quorum sensing (QS) is a community genetic regulation mechanism that controls microbiological functions of medical, agricultural and industrial importance. Discovery of microbial QS signals and the signalling mechanisms led to identification of numerous enzymatic and non-enzymatic signal interference mechanisms that quench microbial QS signalling. Evidence is accumulating that such signal interference mechanisms can be developed as promising approaches to control microbial infection and biofilm formation. In addition, these mechanisms exist not only in microorganisms but also in the host organisms of bacterial pathogens, highlighting their potential implications in microbial ecology and in host-pathogen interactions. Investigation of QS and signal interference mechanisms might significantly broaden the scope of research in microbiology.}, }
@article {pmid15325756, year = {2004}, author = {Wei, G and Pan, L and Du, H and Chen, J and Zhao, L}, title = {ERIC-PCR fingerprinting-based community DNA hybridization to pinpoint genome-specific fragments as molecular markers to identify and track populations common to healthy human guts.}, journal = {Journal of microbiological methods}, volume = {59}, number = {1}, pages = {91-108}, doi = {10.1016/j.mimet.2004.06.007}, pmid = {15325756}, issn = {0167-7012}, mesh = {Adult ; Animals ; Base Sequence ; Child ; Cluster Analysis ; DNA Fingerprinting/methods ; DNA, Bacterial/chemistry/genetics ; Diarrhea/microbiology ; Digestive System/*microbiology ; Enterobacteriaceae/classification/*genetics/growth &amp; development ; Failure to Thrive/microbiology ; Feces/microbiology ; Female ; Humans ; Infant ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Polymerase Chain Reaction/*methods ; Swine ; }, abstract = {Bacterial populations common to healthy human guts may play important roles in human health. A new strategy for discovering genomic sequences as markers for these bacteria was developed using Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR fingerprinting. Structural features within microbial communities are compared with ERIC-PCR followed by DNA hybridization to identify genomic fragments shared by samples from healthy human individuals. ERIC-PCR profiles of fecal samples from 12 diseased or healthy human and piglet subjects demonstrated stable, unique banding patterns for each individual tested. Sequence homology of DNA fragments in bands of identical size was examined between samples by hybridization under high stringency conditions with DIG-labeled ERIC-PCR products derived from the fecal sample of one healthy child. Comparative analysis of the hybridization profiles with the original agarose fingerprints identified three predominant bands as signatures for populations associated with healthy human guts with sizes of 500, 800 and 1000 bp. Clone library profiling of the three bands produced 17 genome fragments, three of which showed high similarity only with regions of the Bacteroides thetaiotaomicron genome, while the remainder were orphan sequences. Association of these sequences with healthy guts was validated by sequence-selective PCR experiments, which showed that a single fragment was present in all 32 healthy humans and 13 healthy piglets tested. Two fragments were present in the healthy human group and in 18 children with non-infectious diarrhea but not in eight children with infectious diarrhea. Genome fragments identified with this novel strategy may be used as genome-specific markers for dynamic monitoring and sequence-guided isolation of functionally important bacterial populations in complex communities such as human gut microflora.}, }
@article {pmid15325534, year = {2004}, author = {Hammerman, C and Bin-Nun, A and Kaplan, M}, title = {Germ warfare: probiotics in defense of the premature gut.}, journal = {Clinics in perinatology}, volume = {31}, number = {3}, pages = {489-500}, doi = {10.1016/j.clp.2004.04.015}, pmid = {15325534}, issn = {0095-5108}, mesh = {Animals ; Bacterial Translocation ; Enterocolitis, Necrotizing/diet therapy ; Humans ; Infant, Newborn ; Infant, Premature ; Infant, Premature, Diseases/*diet therapy ; Intestinal Diseases/*diet therapy ; Intestines/*microbiology ; Probiotics/*therapeutic use ; }, abstract = {The potential benefits of a predominantly lactic acid bacterial flora include an improved balance of gut microbial ecology and decreased susceptibility of the gut mucosa to bacterial translocation via adherence to the intestinal mucosa, strengthening mucosal barrier function. These properties should be especially beneficial to the premature neonate with (1) delayed establishment of nor-mal flora, increasing the potential for proliferation of pathogenic bacteria and (2) immature development of the intestinal mucosa, rendering it more susceptible to the translocation of these pathogenic bacteria and leading to extra-intestinal spread and systemic disease. Early probiotic supplementation in preterm infants is theoretically sound and associated with minimal risk. Clinical data remain preliminary but are supportive of a reduction in feeding intolerance and NEC in this high-risk group.}, }
@article {pmid15321685, year = {2004}, author = {Zhang, X and Gao, P and Chao, Q and Wang, L and Senior, E and Zhao, L}, title = {Microdiversity of phenol hydroxylase genes among phenol-degrading isolates of Alcaligenes sp. from an activated sludge system.}, journal = {FEMS microbiology letters}, volume = {237}, number = {2}, pages = {369-375}, doi = {10.1016/j.femsle.2004.06.057}, pmid = {15321685}, issn = {0378-1097}, mesh = {Alcaligenes/*enzymology/genetics/isolation &amp; purification ; DNA Fingerprinting ; DNA, Bacterial/analysis ; *Genes, Bacterial ; Genes, rRNA ; Genetic Variation ; Mixed Function Oxygenases/classification/*genetics/metabolism ; Nucleic Acid Hybridization ; Phenol/*metabolism ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; }, abstract = {Enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting classified 97 phenol-degrading isolates with identical amplified ribosomal DNA restriction analysis (ARDRA) patterns into six genotypic groups. The 16S rRNA gene of the representative isolate of each group had higher than 99.47% common identity with each other and higher than 98% identity with the type strain of Alcaligenes faecalis. PCR-TGGE (temperature gradient gel electrophoresis) analysis of the genes of the largest subunit of the multi-component phenol hydroxylase (LmPH) in each isolate followed with sequencing showed that isolates within each ERIC-PCR group had identical LmPH gene sequences. Among the six different ERIC-PCR groups, two were found to harbor two different LmPH genes encoding low- and high-Ks (affinity constants) phenol hydroxylases, and the low-Ks type LmPH was identical in sequence with one predominant LmPH of the parental activated sludge. Three ERIC-PCR groups had only the high-Ks type and one had no sequence similar to the known LmPHs. Our work suggests that there is no correlation between the phylogenetic groupings of phenol-degrading bacteria and their LmPH genotypes possibly due to extensive horizontal gene transfer of this functional gene.}, }
@article {pmid15314221, year = {2004}, author = {Schimel, J}, title = {Playing scales in the methane cycle: from microbial ecology to the globe.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {34}, pages = {12400-12401}, pmid = {15314221}, issn = {0027-8424}, mesh = {Climate ; *Ecology ; Methane/*metabolism ; Oceans and Seas ; Sulfur-Reducing Bacteria/metabolism ; *Water Microbiology ; }, }
@article {pmid15305919, year = {2004}, author = {Teeling, H and Meyerdierks, A and Bauer, M and Amann, R and Glöckner, FO}, title = {Application of tetranucleotide frequencies for the assignment of genomic fragments.}, journal = {Environmental microbiology}, volume = {6}, number = {9}, pages = {938-947}, doi = {10.1111/j.1462-2920.2004.00624.x}, pmid = {15305919}, issn = {1462-2912}, mesh = {Bacteria/*genetics ; Base Composition ; Databases, Genetic ; *Genome, Bacterial ; Genomics/*methods ; Likelihood Functions ; Nucleotides/*genetics ; Species Specificity ; }, abstract = {A basic problem of the metagenomic approach in microbial ecology is the assignment of genomic fragments to a certain species or taxonomic group, when suitable marker genes are absent. Currently, the (G + C)-content together with phylogenetic information and codon adaptation for functional genes is mostly used to assess the relationship of different fragments. These methods, however, can produce ambiguous results. In order to evaluate sequence-based methods for fragment identification, we extensively compared (G + C)-contents and tetranucleotide usage patterns of 9054 fosmid-sized genomic fragments generated in silico from 118 completely sequenced bacterial genomes (40 982 931 fragment pairs were compared in total). The results of this systematic study show that the discriminatory power of correlations of tetranucleotide-derived z-scores is by far superior to that of differences in (G + C)-content and provides reasonable assignment probabilities when applied to metagenome libraries of small diversity. Using six fully sequenced fosmid inserts from a metagenomic analysis of microbial consortia mediating the anaerobic oxidation of methane (AOM), we demonstrate that discrimination based on tetranucleotide-derived z-score correlations was consistent with corresponding data from 16S ribosomal RNA sequence analysis and allowed us to discriminate between fosmid inserts that were indistinguishable with respect to their (G + C)-contents.}, }
@article {pmid15296160, year = {2003}, author = {Roels, J and Verstraete, W}, title = {Occurrence and origin of phosphine in landfill gas.}, journal = {Communications in agricultural and applied biological sciences}, volume = {68}, number = {2 Pt A}, pages = {191-194}, pmid = {15296160}, issn = {1379-1176}, mesh = {Air Pollutants/*analysis ; Anaerobiosis ; Belgium ; Fermentation ; Gases/analysis ; Insecticides/analysis ; Phosphines/*analysis ; Refuse Disposal/*methods ; }, abstract = {A landfill (Hooge Maey, Flanders, Belgium) was subjected to an in-depth study in order to explain the origin of phosphine detected in high amounts in landfill gas during a previous study. The spatial and temporal variability of the phosphine concentration in landfill gas was assessed. Twenty four wells were monitored and differences in phosphine concentration up to one log unit were observed (3.2-32.4 microg/m3). The phosphine concentration in each well was constant in time over a period of 4 months. No correlation was found between the phosphine concentration and methane, carbon dioxide, hydrogen sulphide, ethene or ethane concentration. In a series of laboratory tests, it was shown that phosphine was emitted during batch fermentation tests inoculated with landfill leachate when Fe0 or Al0 specimens were added. Conditions favouring corrosion of iron gave rise to higher emissions of phosphine. The phosphine concentration in the headspace of a batch test rose to 1.43 mg/m3 after 27 days of incubation. Weight loss of corroding steel coupons correlated with phosphine emission. Calculations showed that all phosphine emitted from the 0.005 km3 landfill (160 g/year) could be attributed to corrosion of metals. No evidence of de novo synthesis could be established}, }
@article {pmid15296159, year = {2003}, author = {Nollet, H and Verstraete, W}, title = {Development of microbial granules for PCB dechlorination.}, journal = {Communications in agricultural and applied biological sciences}, volume = {68}, number = {2 Pt A}, pages = {185-189}, pmid = {15296159}, issn = {1379-1176}, mesh = {Anaerobiosis ; Bacteria, Anaerobic/*metabolism ; Biodegradation, Environmental ; Biomass ; Chlorine/isolation &amp; purification ; Kinetics ; Polychlorinated Biphenyls/*pharmacokinetics ; Waste Management/methods ; }, abstract = {The effect of acclimating anaerobic granules from commercial bioreactors with different carbon/electron sources on their ability to reductively dechlorinate a tri- (2,3,4-CB) and heptachlorobiphenyl (2,2',3,3',4,5,6-CB) was studied. The anaerobic granules were first grown in upflow anaerobic sludge blanket (UASB) reactors fed with two different mixtures of carbon/electron sources, i.e., propionate/butyrate/methanol and formate/methanol. Differences in dechlorination patterns for 2,2',3,3',4,5,6-CB were observed in batch experiments inoculated with granules from these two sets of UASB reactors. The reductive dechlorination of 2,2',3,3',4,5,6-CB for propionate/butyrate/methanol acclimated granules proceeded via 2,2',3,3',4,5-CB for all 2,2',3,3',4,5-CB for all 2,2',3',4,5-CB + 2,2',3',4-CB for all 2,4-CB + 2,3-CB + 2,4'-CB and 2,2',3,3',5,6-CB for all 2,2',3,5,6-CB for all 2,2',3,5-CB for all 2',3,5-CB. The dechlorination pathway for formate/methanol acclimated granules followed: 2,2',3,3',4,5-CB + 2,2',3,3',5,6-CB for all 2,2',3,3',4-CB + 2,2',3,3',6-CB for all 2,2',3,3'-CB for all 2,2',3-CB for all 2,2'-CB. This research demonstrates a successful strategy for the development of biocatalysts to serve as the inoculum of partially decontaminated sites in order to provide microorganisms with specificities complementary to those of naturally occuring dechlorinators.}, }
@article {pmid15296155, year = {2003}, author = {Lissens, G and Verstraete, W and Albrecht, T and Brunner, G and Lasseur, C}, title = {Anaerobic bioconversion of organic waste into biogas by hot water treatment at near-critical conditions: application in bioregenerative life support.}, journal = {Communications in agricultural and applied biological sciences}, volume = {68}, number = {2 Pt A}, pages = {171-174}, pmid = {15296155}, issn = {1379-1176}, mesh = {Anaerobiosis ; *Cellulose ; Equipment Design ; Kinetics ; *Lignin ; *Organic Chemicals ; Refuse Disposal/instrumentation/*methods ; }, abstract = {The feasibility of nearly-complete conversion of lignocellulosic waste (70% food crops, 20% faecal matter and 10% green algae) into biogas was investigated in the context of a Life Support Project. The treatment comprised a series of processes, i.e. a mesophilic laboratory scale CSTR (continuously stirred tank reactor), an upflow biofilm reactor and a hydrothermolysis system in near-critical water. By the one-stage CSTR, a biogas yield of 75% with a specific biogas production of 0.37 l biogas g(-1) VSS (volatile suspended solids) added at a HRT (hydraulic retention time) of 20 d was obtained. Biogas yields further increased with 10-15% at HRT > 20 d, indicating the hydrolysis of lignocellulose to be the rate-limiting conversion step. The solids present in the CSTR-effluent were subsequently treated by hot water treatment (T approximately 310-350 degrees C, p approximately 240 bar), resulting in effective carbon liquefaction (50-60% without and 83% with carbon dioxide saturation) and complete hygienisation of the residue. Subsequent anaerobic digestion of the hydrolysate allowed further conversion of 48-60% on COD (chemical oxygen demand) basis. Thus, the total process yielded biogas corresponding with a COD conversion up to 90% of the original organic matter. It appears that mesophilic digestion in conjunction with hydrothermolysis at near-critical conditions offers interesting features for (nearly) complete, non-toxic and hygienic carbon and energy recovery from human waste in a bioregenerative life support context.}, }
@article {pmid15296152, year = {2003}, author = {Grommen, R and Verstraete, W}, title = {Nitrate removal in aquaria systems: use of electrochemically generated hydrogen gas as electron donor for denitrification.}, journal = {Communications in agricultural and applied biological sciences}, volume = {68}, number = {2 Pt A}, pages = {159-162}, pmid = {15296152}, issn = {1379-1176}, mesh = {Electrochemistry/methods ; Hydrogen ; Kinetics ; Nitrates/*isolation &amp; purification ; Waste Management/methods ; *Water ; }, abstract = {Nitrate, the end product of the nitrification process, tends to accumulate in aquaria systems. Removal of nitrate in these systems by means of biological denitrification requires the addition of an external electron donor. In this study, the possibilities for using hydrogen gas in aquaria systems as a harmless alternative to other electron donors such as sulphur or reduced organic carbon was investigated. To circumvent safety issues regarding the storage of large volumes of hydrogen gas, in situ generation of hydrogen gas by means of a separate electrochemical cell was chosen. A plug flow reactor filled with polyester cotton wool as carrier material for denitrifying bacteria received hydrogen gas in the headspace. Removal rates of 15 +/- 6 mg N per day were achieved with a hydraulic residence time of 3.3 hours. During the start-up phase nitrite peaks up to 3 mg N per liter were measured in the effluent of the reactor.}, }
@article {pmid15296149, year = {2003}, author = {De Windt, W and Verstraete, W}, title = {Engineering the interaction between micro-organisms and construction materials.}, journal = {Communications in agricultural and applied biological sciences}, volume = {68}, number = {2 Pt A}, pages = {147-150}, pmid = {15296149}, issn = {1379-1176}, mesh = {Biodegradation, Environmental ; Construction Materials/*microbiology/standards ; Corrosion ; Shewanella/isolation &amp; purification/*metabolism/ultrastructure ; }, abstract = {The influence of micro-organisms on degradation of mineral materials, cement bound systems, wood and steel is a rather new subject of research slowly becoming recognised by the 'classical' technical disciplines. An increasing amount of literature appears on biodeterioration of construction materials and microbial activity can not be neglected as a determining factor in the deterioration process. Microbial communities interact in many different ways with mineral materials and their external environment. They can be present on the surface or in crevices and fissures within the material and often their actions become organized in a biofilm. The interaction with the material and its environment can give rise to biodeterioration. Yet recent findings show that in some cases the microbial interaction can lead to protection of materials. It is our mission for the future to engineer the microbiological processes with positive impact on construction materials with a view to practical applications.}, }
@article {pmid15296147, year = {2003}, author = {Aiyuk, S and Raskin, L and van Haandel, A and Verstraete, W}, title = {Development of a sustainable treatment technology for domestic sewage.}, journal = {Communications in agricultural and applied biological sciences}, volume = {68}, number = {2 Pt A}, pages = {135-139}, pmid = {15296147}, issn = {1379-1176}, mesh = {Animals ; Animals, Domestic ; Equipment Design ; Hydrogen-Ion Concentration ; Sewage/*analysis ; Waste Management/instrumentation/*methods ; }, abstract = {We propose an integrated chemical-physical-biological treatment concept for the low-cost treatment of domestic wastewater. Domestic wastewater was subjected to a chemically enhanced primary sedimentation (CEPS), followed by treatment in an upflow anaerobic sludge blanket (UASB) reactor. In addition, a regenerable zeolite was used to remove NH4+, either after CEPS pretreatment or after biological treatment in the UASB reactor. The CEPS pretreatment consisted of the addition of a coagulant (FeCl3) and an anionic organic flocculant and removed on average 73% of the total chemical oxygen demand (CODt), 85% of the total suspended solids, and 80% of PO4(3-) present in the wastewater. The UASB system, which consequently received a low CODt input of approximately 140 mg/L, was operated using a volumetric loading rate of 0.4 g CODt/L.d (hydraulic retention time [HRT] = 10 h) and 0.7 g CODt/L.d (HRT = 5 h). For these conditions, the system removed about 55% of the CODt in its influent, thus producing an effluent with a low CODt of approximately 50 mg/L. The zeolite, when applied in batch mode before the UASB reactor, removed approximately 45% of the NH4+, whereas its application as a post-treatment cartridge resulted in almost 100% NH4+ removal. The simple design and relatively low operating costs, due to low costs of added chemicals and low energy input (estimated at Euro 0.07-0.1 per m3 wastewater treated), combined with excellent treatment performance, suggest that this system can be used as a novel domestic wastewater treatment system for developing countries. Therefore, the system is called a Low-cost, Integrated Sewage Treatment (LIST) system.}, }
@article {pmid15294836, year = {2004}, author = {Denef, VJ and Park, J and Tsoi, TV and Rouillard, JM and Zhang, H and Wibbenmeyer, JA and Verstraete, W and Gulari, E and Hashsham, SA and Tiedje, JM}, title = {Biphenyl and benzoate metabolism in a genomic context: outlining genome-wide metabolic networks in Burkholderia xenovorans LB400.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {8}, pages = {4961-4970}, pmid = {15294836}, issn = {0099-2240}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/*metabolism ; Benzoates/*metabolism ; Burkholderia/genetics/growth &amp; development/*metabolism ; Culture Media ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; *Genome, Bacterial ; Oligonucleotide Array Sequence Analysis/*methods ; Polychlorinated Biphenyls/*metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {We designed and successfully implemented the use of in situ-synthesized 45-mer oligonucleotide DNA microarrays (XeoChips) for genome-wide expression profiling of Burkholderia xenovorans LB400, which is among the best aerobic polychlorinated biphenyl degraders known so far. We conducted differential gene expression profiling during exponential growth on succinate, benzoate, and biphenyl as sole carbon sources and investigated the transcriptome of early-stationary-phase cells grown on biphenyl. Based on these experiments, we outlined metabolic pathways and summarized other cellular functions in the organism relevant for biphenyl and benzoate degradation. All genes previously identified as being directly involved in biphenyl degradation were up-regulated when cells were grown on biphenyl compared to expression in succinate-grown cells. For benzoate degradation, however, genes for an aerobic coenzyme A activation pathway were up-regulated in biphenyl-grown cells, while the pathway for benzoate degradation via hydroxylation was up-regulated in benzoate-grown cells. The early-stationary-phase biphenyl-grown cells showed similar expression of biphenyl pathway genes, but a surprising up-regulation of C(1) metabolic pathway genes was observed. The microarray results were validated by quantitative reverse transcription PCR with a subset of genes of interest. The XeoChips showed a chip-to-chip variation of 13.9%, compared to the 21.6% variation for spotted oligonucleotide microarrays, which is less variation than that typically reported for PCR product microarrays.}, }
@article {pmid15294835, year = {2004}, author = {Ayala-Del-Río, HL and Callister, SJ and Criddle, CS and Tiedje, JM}, title = {Correspondence between community structure and function during succession in phenol- and phenol-plus-trichloroethene-fed sequencing batch reactors.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {8}, pages = {4950-4960}, pmid = {15294835}, issn = {0099-2240}, mesh = {Bacteria/*classification/*enzymology/genetics/growth &amp; development ; *Bioreactors ; DNA, Bacterial/analysis/isolation &amp; purification ; *Ecosystem ; Mixed Function Oxygenases/genetics ; Phenol/*metabolism ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Trichloroethylene/*metabolism ; }, abstract = {The effects of more than 2 years of trichloroethene (TCE) application on community succession and function were studied in two aerobic sequencing batch reactors. One reactor was fed phenol, and the second reactor was fed both phenol and TCE in sequence twice per day. After initiation of TCE loading in the second reactor, the TCE transformation rates initially decreased, but they stabilized with an average second-order rate coefficient of 0.044 liter mg(-1) day(-1) for 2 years. In contrast, the phenol-fed reactor showed higher and unstable TCE transformation rates, with an average rate coefficient of 0.093 liter mg(-1) day(-1). Community analysis by terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes showed that the phenol-plus-TCE-fed reactor had marked changes in community structure during the first 100 days and remained relatively stable afterwards, corresponding to the period of stable function. In contrast, the community structure of the phenol-fed reactor changed periodically, and the changes coincided with the periodicity observed in the TCE transformation rates. Correspondence analysis of each reactor community showed that different community structures corresponded with function (TCE degradation rate). Furthermore, the phenol hydroxylase genotypes, as determined by restriction fragment length polymorphism analysis, corresponded to community structure patterns identified by T-RFLP analysis and to periods when the TCE transformation rates were high. Long-term TCE stress appeared to select for a different and stable community structure, with lower but stable TCE degradation rates. In contrast, the community under no stress exhibited a dynamic structure and dynamic function.}, }
@article {pmid15294812, year = {2004}, author = {Feris, KP and Ramsey, PW and Rillig, M and Moore, JN and Gannon, JE and Holben, WE}, title = {Determining rates of change and evaluating group-level resiliency differences in hyporheic microbial communities in response to fluvial heavy-metal deposition.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {8}, pages = {4756-4765}, pmid = {15294812}, issn = {0099-2240}, mesh = {DNA, Bacterial/analysis ; *Ecosystem ; Electrophoresis/methods ; Fresh Water/*microbiology ; Geologic Sediments/*microbiology ; Metals, Heavy/*pharmacology ; Polymerase Chain Reaction ; Proteobacteria/classification/*drug effects/genetics/growth &amp; development ; Water Pollution, Chemical ; }, abstract = {Prior field studies by our group have demonstrated a relationship between fluvial deposition of heavy metals and hyporheic-zone microbial community structure. Here, we determined the rates of change in hyporheic microbial communities in response to heavy-metal contamination and assessed group-level differences in resiliency in response to heavy metals. A controlled laboratory study was performed using 20 flowthrough river mesocosms and a repeated-measurement factorial design. A single hyporheic microbial community was exposed to five different levels of an environmentally relevant metal treatment (0, 4, 8, 16, and 30% sterilized contaminated sediments). Community-level responses were monitored at 1, 2, 4, 8, and 12 weeks via denaturing gradient gel electrophoresis and quantitative PCR using group-specific primer sets for indigenous populations most closely related to the alpha-, beta-, and gamma-proteobacteria. There was a consistent, strong curvilinear relationship between community composition and heavy-metal contamination (R(2) = 0.83; P < 0.001), which was evident after only 7 days of metal exposure (i.e., short-term response). The abundance of each phylogenetic group was negatively affected by the heavy-metal treatments; however, each group recovered from the metal treatments to a different extent and at a unique rate during the course of the experiment. The structure of hyporheic microbial communities responded rapidly and at contamination levels an order of magnitude lower than those shown to elicit a response in aquatic macroinvertebrate assemblages. These studies indicate that hyporheic microbial communities are a sensitive and useful indicator of heavy-metal contamination in streams.}, }
@article {pmid15289485, year = {2004}, author = {Hill, JE and Penny, SL and Crowell, KG and Goh, SH and Hemmingsen, SM}, title = {cpnDB: a chaperonin sequence database.}, journal = {Genome research}, volume = {14}, number = {8}, pages = {1669-1675}, pmid = {15289485}, issn = {1088-9051}, mesh = {Animals ; Bacteria/genetics ; Base Sequence ; Chaperonin 60/*genetics ; Computational Biology ; Databases, Genetic ; Molecular Sequence Data ; Sequence Homology, Nucleic Acid ; }, abstract = {Type I chaperonins are molecular chaperones present in virtually all bacteria, some archaea and the plastids and mitochondria of eukaryotes. Sequences of cpn60 genes, encoding 60-kDa chaperonin protein subunits (CPN60, also known as GroEL or HSP60), are useful for phylogenetic studies and as targets for detection and identification of organisms. Conveniently, a 549-567-bp segment of the cpn60 coding region can be amplified with universal PCR primers. Here, we introduce cpnDB, a curated collection of cpn60 sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic, and microbial ecology studies. The growing database currently contains approximately 2000 records covering over 240 genera of bacteria, eukaryotes, and archaea. The database also contains over 60 sequences for the archaeal Type II chaperonin (thermosome, a homolog of eukaryotic cytoplasmic chaperonin) from 19 archaeal genera. As the largest curated collection of sequences available for a protein-encoding gene, cpnDB provides a resource for researchers interested in exploiting the power of cpn60 as a diagnostic or as a target for phylogenetic or microbial ecology studies, as well as those interested in broader subjects such as lateral gene transfer and codon usage. We built cpnDB from open source tools and it is available at http://cpndb.cbr.nrc.ca.}, }
@article {pmid15285499, year = {2004}, author = {Poole, TL and Genovese, KJ and Callaway, TR and Bischoff, KM and Donskey, CJ and Nisbet, DJ}, title = {Competitive exclusion of a glycopeptide-resistant Enterococcus faecium in the presence of vancomycin but not equivalent concentrations of tylosin or gentamicin.}, journal = {Poultry science}, volume = {83}, number = {7}, pages = {1099-1105}, doi = {10.1093/ps/83.7.1099}, pmid = {15285499}, issn = {0032-5791}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Chickens/*microbiology ; Dose-Response Relationship, Drug ; *Drug Resistance, Microbial ; Enterococcus faecium/*drug effects ; Fatty Acids, Volatile/metabolism ; Gentamicins/pharmacology ; Intestinal Mucosa/metabolism ; Intestines/microbiology ; Tylosin/pharmacology ; Vancomycin/pharmacology ; }, abstract = {The effect of subtherapeutic concentrations of antibiotics (10.0 and 40.0 microg/mL of vancomycin, gentamicin, and tylosin) on the efficacy of a mixed anaerobe culture of chicken microflora (CCF) was studied in a continuous-flow fermentation system. Efficacy of CCF posttreatment was assessed by challenge with glycopeptide-resistant Enterococcus faecium (GRE) at 6.0 log10 cfu/mL. Bacterial enumeration of endogenous CCF isolates, volatile fatty acid (VFA) analysis, and challenge with GRE indicated that CCF efficacy was affected by all antibiotic treatments. Although CCF treated with 10.0 microg/mL of vancomycin eliminated GRE13 at a rate of 0.61 log10 cfu/ mL per day, it was unable to eliminate E. coli, a gram-negative challenge organism. All other antibiotic treatments allowed GRE persistence at approximately 2.0 to 6.5 log10 cfu/mL. All antibiotic-treated cultures had decreased concentrations of acetic and propionic acids. Our data suggest that low concentrations of antimicrobials may adversely affect the microbial ecology of gut microflora with respect to its ability to exclude exogenous bacteria. Moreover, gentamicin had an adverse effect on the inhibitory stringency of CCF even though it showed little anti-anaerobic activity against CCF strict anaerobes in pure culture. Verification of the results in live animals will be necessary to determine if antimicrobial treatment could compromise the effectiveness of normal microflora to serve as a natural host defense against infection.}, }
@article {pmid15283668, year = {2004}, author = {Nelson, EB}, title = {Microbial dynamics and interactions in the spermosphere.}, journal = {Annual review of phytopathology}, volume = {42}, number = {}, pages = {271-309}, doi = {10.1146/annurev.phyto.42.121603.131041}, pmid = {15283668}, issn = {0066-4286}, mesh = {Animals ; Bacteria/metabolism/pathogenicity ; Ecosystem ; Fungi/metabolism/pathogenicity ; Host-Parasite Interactions ; Seeds/*microbiology/*physiology ; Soil Microbiology ; }, abstract = {The spermosphere represents a short-lived, rapidly changing, and microbiologically dynamic zone of soil surrounding a germinating seed. It is analogous to the rhizosphere, being established largely by the carbon compounds released into the soil once the seed begins to hydrate. These seed exudations drive the microbial activities that take place in the spermosphere, many of which can have long-lasting impacts on plant growth and development as well as on plant health. In this review, I discuss the nature of the spermosphere habitat and the factors that give rise to its character, with emphasis on the types of microbial activities in the spermosphere that have important implications for disease development and biological disease control. This review, which represents the first comprehensive synthesis of the literature on spermosphere biology, is meant to illustrate the unique nature of the spermosphere and how studies of interactions in this habitat may serve as useful experimental models for testing hypotheses about plant-microbe associations and microbial ecology.}, }
@article {pmid15283587, year = {2004}, author = {Huang, WE and Griffiths, RI and Thompson, IP and Bailey, MJ and Whiteley, AS}, title = {Raman microscopic analysis of single microbial cells.}, journal = {Analytical chemistry}, volume = {76}, number = {15}, pages = {4452-4458}, doi = {10.1021/ac049753k}, pmid = {15283587}, issn = {0003-2700}, mesh = {Bacteria/*cytology/growth &amp; development/ultrastructure ; Fungi/*cytology/growth &amp; development/ultrastructure ; Microscopy, Confocal/methods ; Multivariate Analysis ; Sensitivity and Specificity ; Spectrum Analysis, Raman/methods ; }, abstract = {We demonstrate the utility of the Raman confocal microscope to generate a spectral profile from a single microbial cell and the use of this approach to differentiate bacterial species. In general, profiles from different bacterial taxa shared similar peaks, but the relative abundances of these components varied between different species. The use of multivariate methods subsequently allowed taxa discrimination. Further investigations revealed that the single-cell spectra could be used to differentiate between growth phases of a single species, but these differences did not obscure the overall interspecies discrimination. Finally, we tested the efficacy of the method as a means to identify cells responsible for the uptake of a specific substrate. A single strain was grown in media containing incrementally varying ratios of (13)C(6) to (12)C(6) glucose, and it was found that (13)C incorporation shifted characteristic peaks to lower wavenumbers. These findings suggest that Raman microscopy has significant potential for studies requiring the taxonomic identity and functioning of single microbial cells to be determined.}, }
@article {pmid15261541, year = {2004}, author = {Aiyuk, S and Amoako, J and Raskin, L and van Haandel, A and Verstraete, W}, title = {Removal of carbon and nutrients from domestic wastewater using a low investment, integrated treatment concept.}, journal = {Water research}, volume = {38}, number = {13}, pages = {3031-3042}, doi = {10.1016/j.watres.2004.04.040}, pmid = {15261541}, issn = {0043-1354}, mesh = {*Bioreactors ; Carbon/*isolation &amp; purification ; Flocculation ; Nitrogen/*isolation &amp; purification ; Phosphorus/*isolation &amp; purification ; Sewage/chemistry ; Waste Disposal, Fluid/*methods ; Zeolites/chemistry ; }, abstract = {An integrated chemical-physical-biological treatment concept for the low-cost treatment of domestic wastewater is proposed. Domestic wastewater was subjected to a chemically enhanced primary treatment (CEPT), followed by treatment in an upflow anaerobic sludge blanket (UASB) reactor. In addition, a regenerable zeolite was used to remove NH4+, either after CEPT pretreatment or after biological treatment in the UASB reactor. The CEPT pretreatment consisted of the addition of a coagulant (FeCl3) and an anionic organic flocculant and removed on average 73% of the total chemical oxygen demand (COD(t)), 85% of the total suspended solids, and 80% of PO4(3-) present in the wastewater. The UASB system, which consequently received a low COD(t) input of approximately 140 mg/L, was operated using a volumetric loading rate of 0.4 g COD(t)/L. d (hydraulic retention time [HRT]=10 h) and 0.7 g COD(t)/L. d (HRT=5 h). For these conditions, the system removed about 55% of the COD(t) in its influent, thus producing an effluent with a low COD(t) of approximately 50 mg/L. The zeolite, when applied in batch mode before the UASB reactor, removed approximately 45% of the NH4+, whereas its application as a post-treatment cartridge resulted in almost 100% NH4+ removal. The simple design and relatively low operating costs, due to low costs of added chemicals and low energy input (estimated at Euro 0.07-0.1 per m3 wastewater treated), combined with excellent treatment performance, means that this system can be used as a novel domestic wastewater treatment system for developing countries. Therefore, the system is called a Low Investment Sewage Treatment (LIST) system.}, }
@article {pmid15259275, year = {2004}, author = {Griffiths, BS and Kuan, HL and Ritz, K and Glover, LA and McCaig, AE and Fenwick, C}, title = {The relationship between microbial community structure and functional stability, tested experimentally in an upland pasture soil.}, journal = {Microbial ecology}, volume = {47}, number = {1}, pages = {104-113}, pmid = {15259275}, issn = {0095-3628}, mesh = {Analysis of Variance ; Bacteria/*genetics/*growth &amp; development ; Bacterial Physiological Phenomena/drug effects/radiation effects ; Carbon Dioxide/metabolism ; Chloroform/toxicity ; Copper/toxicity ; *Ecosystem ; Gamma Rays ; Hot Temperature ; Nitrates/analysis ; Principal Component Analysis ; Quaternary Ammonium Compounds/analysis ; Reverse Transcriptase Polymerase Chain Reaction ; Scotland ; *Soil Microbiology ; }, abstract = {Soil collected from an upland pasture was manipulated experimentally in ways shown previously to alter microbial community structure. One set of soil was subjected to chloroform fumigation for 0, 0.5, 2, or 24 h and the other was sterilised by gamma-irradiation and inoculated with a 10(-2), 10(-4), 10(-6), or 10(-8) dilution of a soil suspension prepared from unsterilized soil. Following incubation for 8 months, to allow for the stabilization of microbial biomass and activity, the resulting microbial community structure (determined by PCR-DGGE of bacterial specific amplification products of total soil DNA) was assessed. In addition, the functional stability (defined here as the resistance and resilience of short-term decomposition of plant residues to a transient heat or a persistent copper perturbation) was determined. Changes in the active bacterial population following perturbation (determined by RT-PCR-DGGE of total soil RNA) were also monitored. The manipulations resulted in distinct shifts in microbial community structure as shown by PCR-DGGE profiles, but no significant decreases in the number of bands. These shifts in microbial community structure were associated with a reduction in functional stability. The clear correlation between altered microbial community structure and functional stability observed in this upland pasture soil was not evident when the same protocols were applied to soils in other studies. RT-PCR-DGGE profiles only detected a shift in the active bacterial population following heat, but not copper, perturbation. We conclude that the functional stability of decomposition is related to specific components of the microbial community.}, }
@article {pmid15259274, year = {2004}, author = {Oger, PM and Mansouri, H and Nesme, X and Dessaux, Y}, title = {Engineering root exudation of Lotus toward the production of two novel carbon compounds leads to the selection of distinct microbial populations in the rhizosphere.}, journal = {Microbial ecology}, volume = {47}, number = {1}, pages = {96-103}, pmid = {15259274}, issn = {0095-3628}, mesh = {Arginine/*analogs &amp; derivatives/biosynthesis/chemistry ; Bacteria/genetics/*isolation &amp; purification/metabolism ; Cluster Analysis ; France ; *Genetic Variation ; Lotus/*microbiology ; Mannitol/*analogs &amp; derivatives/chemistry ; *Phylogeny ; Plant Roots/*metabolism/microbiology ; Plants, Genetically Modified ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {The culture of opine-producing transgenic Lotus plants induces the increase in the rhizosphere of bacterial communities that are able to utilize these molecules as sole carbon source. We used transgenic Lotus plants producing two opines, namely mannopine and nopaline, to characterize the microbial communities directly influenced by the modification of root exudation. We showed that opine-utilizers represent a large community in the rhizosphere of opine-producing transgenic Lotus. This community is composed of at least 12 different bacterial species, one third of which are able to utilize the opine mannopine and two thirds the opine nopaline. Opine utilizers are diverse, belonging to the Gram-positive and -negative bacteria. We described two novel mannopine-utilizing species, Rhizobium and Duganella spp., and five novel nopaline-utilizing species, Duganella, Afipia, Phyllobacterium, Arthrobacter, and Bosea spp. Although opine utilizers mostly belong to the alpha-Proteobacteria, Rhizobiaceae family, there is little overlap between the populations able to utilize each of the two opines produced by the plants. Noticeably, in the rhizosphere of transgenic Lotus, only the opine mannopine favors the growth of Agrobacterium tumefaciens, the bacterium from which opines have been characterized. The diversity of opine utilizers from the rhizosphere of Lotus plants is greater than that observed from any other environment. Therefore, transgenic plants with engineered exudation constitute an excellent tool to isolate and characterize specific microbial populations.}, }
@article {pmid15259273, year = {2004}, author = {Boureau, T and Jacques, MA and Berruyer, R and Dessaux, Y and Dominguez, H and Morris, CE}, title = {Comparison of the phenotypes and genotypes of biofilm and solitary epiphytic bacterial populations on broad-leaved endive.}, journal = {Microbial ecology}, volume = {47}, number = {1}, pages = {87-95}, pmid = {15259273}, issn = {0095-3628}, mesh = {*Asteraceae ; *Biofilms ; Biological Assay ; Electrophoresis, Agar Gel ; France ; Genotype ; *Phenotype ; Plant Leaves/*microbiology ; Polymerase Chain Reaction ; Pseudomonas fluorescens/*isolation &amp; purification/metabolism ; Species Specificity ; }, abstract = {The discovery that biofilms are ubiquitous among the epiphytic microflora of leaves has prompted research about the impact of biofilms on the ecology of epiphytic microorganisms and on the efficiency of strategies to manage these populations for disease control and to ensure food safety. Biofilms are likely to influence the microenvironment and phenotype of the microorganisms they harbor. However, it is also important to determine whether there are differences in the types of bacteria within biofilms compared to those outside of biofilms so as to better target microorganisms via disease control strategies. Broad-leaved endive (Cichorium endivia var. latifolia) harbors biofilms containing fluorescent pseudomonads. These bacteria can cause considerable post-harvest losses when this plant is used for manufacturing minimally processed salads. To determine whether the population structure of the fluorescent pseudomonads in biofilms is different from that outside of biofilms on the same leaves, bacteria were isolated quantitatively from the biofilm and solitary components of the epiphytic population on leaves of field-grown broad-leaved endive. Population structure was determined in terms of taxonomic identities of the bacteria isolated, in terms of genotypic profiles, and in terms of phenotypic traits related to surface colonization and biofilm formation. The results illustrate that there are no systematic differences in the composition and structure of biofilm and solitary populations of fluorescent pseudomonads, in terms of either genotypic profiles or phenotypic profiles of the strains. However, Gram-positive bacteria tended to occur more frequently within biofilms than outside of biofilms. We suggest that leaf colonization by fluorescent pseudomonads involves a flux of cells between biofilm and solitary states. This would allow bacteria to exploit the advantages of these two types of existence; biofilms would favor resistance to stressful conditions, whereas solitary cells could foster spread of bacteria to newly colonizable sites on leaves as environmental conditions fluctuate.}, }
@article {pmid15259272, year = {2004}, author = {Wong, D and Suflita, JM and McKinley, JP and Krumholz, LR}, title = {Impact of clay minerals on sulfate-reducing activity in aquifers.}, journal = {Microbial ecology}, volume = {47}, number = {1}, pages = {80-86}, pmid = {15259272}, issn = {0095-3628}, mesh = {Aluminum Oxide/chemistry/toxicity ; Bentonite/*chemistry/toxicity ; Desulfovibrio/*metabolism/ultrastructure ; Fresh Water ; Geologic Sediments/*microbiology ; Kaolin/*chemistry/toxicity ; Microscopy, Electron, Scanning ; Oklahoma ; Oxidation-Reduction/*drug effects ; Sulfates/*metabolism ; }, abstract = {Previous studies have shown that sulfate-reduction activity occurs in a heterogeneous manner throughout the terrestrial subsurface. Low-activity regions are often observed in the presence of clay minerals. Here we report that clays inhibit sulfate reduction activity in sediments and in a pure culture of Desulfovibrio vulgaris. Clay minerals including bentonite and kaolinite inhibited sulfate reduction by 70-90% in sediments. Intact clays and clay colloids or soluble components, capable of passing through a 0.2-microm filter, were also inhibitory to sulfate-reducing bacteria. Other adsorbent materials, including anion or cation exchangers and a zeolite, did not inhibit sulfate reduction in sediments, suggesting that the effect of clays was not due to their cation-exchange capacity. We observed a strong correlation between the Al2O3 content of clays and their relative ability to inhibit sulfate reduction in sediments (r2 = 0.82). This suggested that inhibition might be a direct effect of Al3+ (aq) on the bacteria. We then tested pure aluminum oxide (Al2O3) and showed it to act in a similar manner to clay. As dissolved aluminum is known to be toxic to a variety of organisms at low concentrations, our results suggest that the effects of clay on sulfate-reducing bacteria may be directly due to aluminum. Thus, our experiments provide an explanation for the lack of sulfate-reduction activity in clay-rich regions and presents a mechanism for the effect.}, }
@article {pmid15259271, year = {2004}, author = {Oda, Y and Meijer, WG and Gibson, JL and Gottschal, JC and Forney, LJ}, title = {Analysis of diversity among 3-chlorobenzoate-degrading strains of Rhodopseudomonas palustris.}, journal = {Microbial ecology}, volume = {47}, number = {1}, pages = {68-79}, pmid = {15259271}, issn = {0095-3628}, support = {GM45404/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Blotting, Southern ; Chlorobenzoates/metabolism ; Cluster Analysis ; Coenzyme A Ligases/genetics ; DNA Fingerprinting ; DNA Primers ; *Genetic Variation ; Molecular Sequence Data ; *Phenotype ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhodopseudomonas/*genetics/metabolism ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The phenotypic and genetic characteristics of 14 strains of the purple nonsulfur bacterium Rhodopseudomonas palustris were studied to assess diversity within this species. While all strains had certain phenotypic characteristics in common, including the ability to metabolize benzoate and degrade 2- and 3-chlorobenzoate, there were also significant differences among the strains such as the rate of growth in media containing benzoate as a carbon source. Genetic characterization of the strains revealed there were three divergent lineages in the species. Based on 16S rRNA gene sequences, the 14 strains could be grouped into three distinct clusters (A, B, and C), and this clustering was congruent with that based on gene sequences of form II ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). Although BOX-PCR genomic DNA fingerprints of all 14 strains exhibited differences, analysis of the fingerprint images and UPGMA/product-moment analysis of similarities showed there were three groupings that were entirely consistent with clusters based on other characteristics of the strains. Thus, regardless of the method of analysis used, strains in groups A and B consistently clustered together and were separate from those of group C. These results suggest that strains in groups A-B and C represent phylogenetically related clones that have diverged from one another. This indicates that at least three lineages of Rhodopseudomonas palustris exist among the strains included in this study, and that each may be particularly well adapted to a distinct ecological niche.}, }
@article {pmid15259270, year = {2004}, author = {Chin, KJ and Lueders, T and Friedrich, MW and Klose, M and Conrad, R}, title = {Archaeal community structure and pathway of methane formation on rice roots.}, journal = {Microbial ecology}, volume = {47}, number = {1}, pages = {59-67}, pmid = {15259270}, issn = {0095-3628}, mesh = {Acetates ; Base Sequence ; Carbon Isotopes ; Chromatography, Gas ; Chromatography, High Pressure Liquid ; Euryarchaeota/*genetics ; Likelihood Functions ; Methane/*metabolism ; Models, Genetic ; Molecular Sequence Data ; Oryza/metabolism/*microbiology ; *Phylogeny ; Plant Roots/metabolism/*microbiology ; Polymorphism, Restriction Fragment Length ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {The community structure of methanogenic Archaea on anoxically incubated rice roots was investigated by amplification, sequencing, and phylogenetic analysis of 16S rRNA and methyl-coenzyme M reductase (mcrA) genes. Both genes demonstrated the presence of Methanomicrobiaceae, Methanobacteriaceae, Methanosarcinaceae, Methanosaetaceae, and Rice cluster I, an uncultured methanogenic lineage. The pathway of CH4 formation was determined from the 13C-isotopic signatures of the produced CH4, CO2 and acetate. Conditions and duration of incubation clearly affected the methanogenic community structure and the pathway of CH4 formation. Methane was initially produced from reduction of CO2 exclusively, resulting in accumulation of millimolar concentrations of acetate. Simultaneously, the relative abundance of the acetoclastic methanogens (Methanosarcinaceae, Methanosaetaceae), as determined by T-RFLP analysis of 16S rRNA genes, was low during the initial phase of CH4 production. Later on, however, acetate was converted to CH4 so that about 40% of the produced CH4 originated from acetate. Most striking was the observed relative increase of a population of Methanosarcina spp. (but not of Methanosaeta spp.) briefly before acetate concentrations started to decrease. Both acetoclastic methanogenesis and Methanosarcina populations were suppressed by high phosphate concentrations, as observed under application of different buffer systems. Our results demonstrate the parallel change of microbial community structure and function in a complex environment, i.e., the increase of acetoclastic Methanosarcina spp. when high acetate concentrations become available.}, }
@article {pmid15259269, year = {2004}, author = {Alavi, MR}, title = {Predator/prey interaction between Pfiesteria piscicida and Rhodomonas mediated by a marine alpha proteobacterium.}, journal = {Microbial ecology}, volume = {47}, number = {1}, pages = {48-58}, pmid = {15259269}, issn = {0095-3628}, mesh = {Alphaproteobacteria/genetics/*physiology ; Base Sequence ; Cluster Analysis ; *Cryptophyta ; DNA Primers ; DNA, Ribosomal/genetics ; *Food Chain ; Molecular Sequence Data ; Pfiesteria piscicida/*growth &amp; development/microbiology ; *Phylogeny ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {The dinoflagellate Pfiesteria piscicida coexists with bacteria in aquatic environments and as such, may interact with them at the physiological level. This study was designed to investigate the influence of bacteria, present in a clonal culture of Pfiesteria piscicida, on the predator/prey relationship of this dinoflagellate with the alga Rhodomonas. A series of replenishment experiments with bacteria isolated from P. piscicida clonal culture and the bacteria-free P. piscicida derived from the same culture were carried out. In the presence of bacteria, the number of P. piscicida increased significantly when incubated with alga Rhodomonas. This enhanced growth was almost entirely due to the increased consumption rate of Rhodomonas by P. piscicida since in bacteria-free (axenic) cultures Rhodomonas were consumed at significantly reduced rates relative to cultures with bacteria. Subsequent replenishment experiments with individual bacterial isolates showed that a single isolate was responsible for the increased predation rate of P. piscicida. The presence or absence of this specific bacterium determined the outcome of the interaction between P. piscicida and Rhodomonas. Partial sequence analysis of the 16S rDNA of this isolate indicated that it was a novel marine alpha proteobacterium with sequence similarities to a Roseobacter sp. and a bacterium recently isolated from a toxic dinoflagellate Alexandrium sp.}, }
@article {pmid15259268, year = {2004}, author = {Kimata, N and Nishino, T and Suzuki, S and Kogure, K}, title = {Pseudomonas aeruginosa isolated from marine environments in Tokyo Bay.}, journal = {Microbial ecology}, volume = {47}, number = {1}, pages = {41-47}, pmid = {15259268}, issn = {0095-3628}, mesh = {Bacterial Outer Membrane Proteins/isolation &amp; purification ; Bacterial Proteins/isolation &amp; purification ; Blotting, Western ; DNA Primers ; DNA, Ribosomal/genetics ; Escherichia coli Proteins ; Fluorescent Antibody Technique, Direct ; Japan ; Lipoproteins/isolation &amp; purification ; Pacific Ocean ; Peptidoglycan/isolation &amp; purification ; Polymerase Chain Reaction/methods ; Pseudomonas aeruginosa/genetics/*isolation &amp; purification ; Seawater/analysis/*microbiology ; Sequence Analysis, DNA ; Sodium Chloride/analysis ; }, abstract = {Pseudomonas aeruginosa is a pathogenic bacterium that has been thoroughly investigated since the 19th century and is generally regarded as a freshwater or terrestrial organism. In 1995, it was reported that the OprP porin, an outer membrane protein corresponding to that of this bacterium, was widely distributed as a dissolved component in seawater. This finding led us to investigate the presence of P. aeruginosa in marine environments. Both culture-independent and -dependent methods were applied to seawater samples obtained in Tokyo Bay during four cruises. The DVC-FA (direct viable count-fluorescent antibody) technique showed that cells reactive to an antibody against P. aeruginosa were widely present in the bay, i.e., 10(3) to 10(4) cells/mL in the inner bay, and 10(2) to 10(3) cells/mL at the mouth. Bacterial cells isolated by selective medium were identified by three methods: the presence of oprI and oprL, two outer membrane lipoprotein genes specific to P. aeruginosa; the API20 NE kit; and 16S rDNA sequence analysis. The results confirmed that the majority of isolates from the bay were P. aeruginosa. Immuno-chemical analyses of the seawater results indicate that P. aeruginosa is commonly present in coastal marine environments and sheds OprP.}, }
@article {pmid15259267, year = {2004}, author = {Steward, GF and Zehr, JP and Jellison, R and Montoya, JP and Hollibaugh, JT}, title = {Vertical distribution of nitrogen-fixing phylotypes in a meromictic, hypersaline lake.}, journal = {Microbial ecology}, volume = {47}, number = {1}, pages = {30-40}, pmid = {15259267}, issn = {0095-3628}, mesh = {Bacteria/*genetics/metabolism ; Base Sequence ; California ; Cloning, Molecular ; Cluster Analysis ; DNA Primers ; Electric Conductivity ; Fresh Water/*chemistry/*microbiology ; Molecular Sequence Data ; Nitrogen Isotopes/metabolism ; Nitrogenase/analysis/*genetics ; Oxygen/analysis ; *Phylogeny ; Plankton/*genetics ; Polymerase Chain Reaction ; Quaternary Ammonium Compounds/analysis ; Sequence Analysis, DNA ; Temperature ; }, abstract = {We investigated the diversity of nitrogenase genes in the alkaline, moderately hypersaline Mono Lake, California to determine (1) whether nitrogen-fixing (diazotrophic) populations were similar to those in other aquatic environments and (2) if there was a pattern of distribution of phylotypes that reflected redox conditions, as well as (3) to identify populations that could be important in N dynamics in this nitrogen-limited lake. Mono Lake has been meromictic for almost a decade and has steep gradients in oxygen and reduced compounds that provide a wide range of aerobic and anaerobic habitats. We amplified a fragment of the nitrogenase gene (nifH) from planktonic DNA samples collected at three depths representing oxygenated surface waters, the oxycline, and anoxic, ammonium-rich deep waters. Forty-three percent of the 90 sequences grouped in nifH Cluster I. The majority of clones (57%) grouped in Cluster III, which contains many known anaerobic bacteria. Cluster I and Cluster III sequences were retrieved at every depth indicating little vertical zonation in sequence types related to the prominent gradients in oxygen and ammonia. One group in Cluster I was found most often at every depth and accounted for 29% of all the clones. These sequences formed a subcluster that contained other environmental clones, but no cultivated representatives. No significant nitrogen fixation was detected by the 15N2 method after 48 h of incubation of surface, oxycline, or deep waters, suggesting that pelagic diazotrophs were contributing little to nitrogen fluxes in the lake. The failure to measure any significant nitrogen fixation, despite the detection of diverse and novel nitrogenase genes throughout the water column, raises interesting questions about the ecological controls on diazotrophy in Mono Lake and the distribution of functional genes in the environment.}, }
@article {pmid15259266, year = {2004}, author = {Hamels, I and Sabbe, K and Muylaert, K and Vyverman, W}, title = {Quantitative importance, composition, and seasonal dynamics of protozoan communities in polyhaline versus freshwater intertidal sediments.}, journal = {Microbial ecology}, volume = {47}, number = {1}, pages = {18-29}, pmid = {15259266}, issn = {0095-3628}, mesh = {Analysis of Variance ; Animals ; *Bacteria ; Belgium ; Biomass ; Eukaryota/*physiology ; Fresh Water ; Geologic Sediments/analysis/microbiology/*parasitology ; Nitrates/analysis ; Particle Size ; Quaternary Ammonium Compounds/analysis ; *Seasons ; Seawater ; Species Specificity ; }, abstract = {The quantitative importance and composition of protozoan communities was investigated in sandy and silty intertidal sediments of a polyhaline and a freshwater site in the Schelde estuary. Total biomass of the protozoans studied, integrated over the upper 4 cm of the sediment, ranged from 41 to 597 mg C m(-2) and was in the same order of magnitude at the polyhaline and the freshwater intertidal site. Nanoheterotrophs were the dominant protozoans, in terms of both abundance and biomass. Ciliate abundances appeared to be largely determined by physical constraints, namely, the amount of interstitial space and hydrodynamic disturbances. It remains unclear which factors control nanoheterotrophic abundances and biomasses, which showed comparatively little seasonal and between-site fluctuations. Salinity differences were clearly reflected in the protozoan community composition. The dominant role of sessile ciliates is a unique feature of sediments in the freshwater tidal reaches, which can be attributed to the dynamic nature of sedimentation and resuspension processes associated with the maximum turbidity zone. Based on biomass ratios and estimated weight-specific metabolic rates, protozoa possibly accounted for approximately 29 to 96% of the estimated combined metabolic rate of protozoan and metazoan consumers at our sampling stations in late spring/early autumn. The contribution of protozoa to this combined metabolic rate was higher at the sandy than at the silty stations and was mainly accounted for by the nanoheterotrophs. These data emphasize the potential importance of small protozoa in sediments and suggest that protozoa are important components of benthic food webs.}, }
@article {pmid15259265, year = {2004}, author = {Jiang, S and Steward, G and Jellison, R and Chu, W and Choi, S}, title = {Abundance, distribution, and diversity of viruses in alkaline, hypersaline Mono Lake, California.}, journal = {Microbial ecology}, volume = {47}, number = {1}, pages = {9-17}, pmid = {15259265}, issn = {0095-3628}, mesh = {Ammonia/analysis ; Bacteriophages/*isolation &amp; purification ; Base Sequence ; California ; Cluster Analysis ; DNA Probes ; Electric Conductivity ; Electrophoresis, Gel, Pulsed-Field ; Fresh Water/*microbiology/*virology ; *Genome, Viral ; Microscopy, Fluorescence ; Molecular Sequence Data ; Oxygen/analysis ; Proteobacteria/genetics/*virology ; Regression Analysis ; Sequence Analysis, DNA ; Sodium Chloride/*analysis ; Sulfides/analysis ; Temperature ; }, abstract = {Mono Lake is a large (180 km2), alkaline (pH approximately 10), moderately hypersaline (70-85 g kg(-1)) lake lying at the western edge of the Great Basin. An episode of persistent chemical stratification (meromixis) was initiated in 1995 and has resulted in depletion of oxygen and accumulation of ammonia and sulfide beneath the chemocline. Although previous studies have documented high bacterial abundances and marked seasonal changes in phytoplankton abundance and community composition, there have been no previous reports on the occurrence of viruses in this unique lake. Based on the high concentrations and diversity of microbial life in this lake, we hypothesized that planktonic viruses are also abundant and diverse. To examine the abundance and distribution of viruses and bacteria, water samples were collected from four stations along 5 to 15 vertical depths at each station. Viral abundance ranged from 1 x 10(8) to 1 x 10(9) mL(-1), among the highest observed in any natural aquatic system examined so far. Increases (p < 0.1) in viral densities were observed in the anoxic bottom water at multiple stations. However, regression analysis indicated that viral abundance could not be predicted by any single environmental parameter. Pulsed field gel electrophoresis revealed a diverse viral community in Mono Lake with genome sizes ranging from approximately 14 to >400 kb with most of the DNA in the 30 to 60 kb size range. Cluster analysis grouped the anoxic bottom-water viral community into a unique cluster differentiating it from surface and mid-water viral communities. A hybridization study using an indigenous viral isolate as a probe revealed an episodic pattern of temporal phage distribution with strong niche stratification between oxic and anoxic waters.}, }
@article {pmid15259264, year = {2004}, author = {Stopar, D and Cerne, A and Zigman, M and Poljsak-Prijatelj, M and Turk, V}, title = {Viral abundance and a high proportion of lysogens suggest that viruses are important members of the microbial community in the Gulf of Trieste.}, journal = {Microbial ecology}, volume = {47}, number = {1}, pages = {1-8}, pmid = {15259264}, issn = {0095-3628}, mesh = {Bacteriophages/*physiology ; Enterobacteriaceae/*virology ; Italy ; *Lysogeny ; Microscopy, Electron ; Microscopy, Fluorescence ; Mitomycin ; Oceans and Seas ; Quaternary Ammonium Compounds/analysis ; Seawater/analysis/microbiology/*virology ; Time Factors ; Virus Activation/*physiology ; }, abstract = {Epifluorescence microscopy and transmission electron microscopy were applied to study virioplankton community in the Gulf of Trieste (northern Adriatic Sea). The total viral abundance was in a range between 2.5 x 10(9)/L and 2.9 x 10(10)/L and was positively correlated with trophic status of the environment. Viruslike particles were significantly correlated with bacterial abundance in all samples studied. Correlations with other physicochemical or biological parameters were not significant. The data suggest that, because of the substantial fraction of tailed viruses present (26%), bacteriophages are an important component of the virioplankton community in the Gulf of Trieste. The abundance of viruslike particles in the seawater changed at hour intervals in a range from 1.3 x 10(9)/L to 5.1 x 10(9)/L. A significant fraction (71%) of the bacterial isolates was inducible in vitro by mitomycin C, and a high occurrence (51%) of lysogenic isolates with more than one phage morphotype present in the lysate was detected. The presence of lysogenic bacteria in the seawater was confirmed in situ with a mitomycin C induction experiment on the natural bacterial population. Results suggest that virioplankton is an abundant component of the microbial community in the Gulf of Trieste.}, }
@article {pmid15254116, year = {2004}, author = {Van de Wiele, TR and Verstraete, W and Siciliano, SD}, title = {Polycyclic aromatic hydrocarbon release from a soil matrix in the in vitro gastrointestinal tract.}, journal = {Journal of environmental quality}, volume = {33}, number = {4}, pages = {1343-1353}, doi = {10.2134/jeq2004.1343}, pmid = {15254116}, issn = {0047-2425}, mesh = {Absorption ; Bacillus subtilis ; Biological Availability ; Bioreactors ; Colon/chemistry/physiology ; Duodenum/chemistry/physiology ; Humans ; In Vitro Techniques ; *Models, Biological ; Polycyclic Aromatic Hydrocarbons/*pharmacokinetics ; Soil Pollutants/*pharmacokinetics ; Stomach/chemistry/physiology ; }, abstract = {Soil ingestion is an important exposure route by which immobile soil contaminants enter the human body. We assessed polycyclic aromatic hydrocarbon (PAH) release from a contaminated soil, containing 49 mg PAH kg(-1), using a SHIME (Simulator of the Human Intestinal Microbial Ecosystem) reactor comprising the stomach, duodenal, and colon compartments. Polycyclic aromatic hydrocarbon release was defined as that fraction remaining in the digest supernatant after centrifugation for 5 min at 1500 x g. The PAH release in the stomach digest was only 0.44% of the total PAH present in soil, resulting in PAH concentrations of 23 micrograms PAH L(-1) chyme. The lower PAH releases in duodenum (0.13%) and colon (0.30%) digests, compared with the stomach digest, were thought to be attributed to combined complexation and precipitation with bile salts, dissolved organic matter, or colon microbiota. We studied these complexation processes in an intestinal suspension more in depth by preparing mixtures of 9-anthracenepropionic acid, a Bacillus subtilis culture, and cholin as model compounds for PAHs, organic matter, and bile salts, respectively. Bile salts or organic matter in the aqueous phase initially enhance PAH desorption from soil. However, desorbed PAHs may form large aggregates with bile and organic matter, lowering the freely dissolved PAH fraction in the supernatant. Using the model compounds, mathematical equations were developed and validated to predict PAH complexation processes in the gastrointestinal tract. Contaminant release and subsequent complexation in the gut is an important prerequisite to intestinal absorption and thus bioavailability of that contaminant. The data from this research may help in understanding the processes to which PAHs are subjected in the gastrointestinal tract, before intestinal absorption.}, }
@article {pmid15248225, year = {2004}, author = {Penttinen, MA and Heiskanen, KM and Mohapatra, R and DeLay, ML and Colbert, RA and Sistonen, L and Granfors, K}, title = {Enhanced intracellular replication of Salmonella enteritidis in HLA-B27-expressing human monocytic cells: dependency on glutamic acid at position 45 in the B pocket of HLA-B27.}, journal = {Arthritis and rheumatism}, volume = {50}, number = {7}, pages = {2255-2263}, doi = {10.1002/art.20336}, pmid = {15248225}, issn = {0004-3591}, support = {AR-46177/AR/NIAMS NIH HHS/United States ; AR-48372/AR/NIAMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Amino Acid Substitution ; Cell Line ; Cell Membrane/metabolism ; Endoplasmic Reticulum/metabolism ; Gene Transfer Techniques ; Green Fluorescent Proteins ; HLA-B27 Antigen/chemistry/genetics/*metabolism ; Histocompatibility Antigens Class I/genetics/metabolism ; Humans ; Intracellular Membranes/*microbiology ; Luminescent Proteins/genetics ; Methionine ; Monocytes/*immunology/*microbiology ; Phenotype ; Protein Folding ; Salmonella Infections/microbiology ; Salmonella enteritidis/*growth &amp; development ; Time Factors ; Transfection ; }, abstract = {OBJECTIVE: To reveal the cause of the impaired elimination of Salmonella enteritidis in HLA-B27-transfected human monocytic cells and to study whether the B pocket of HLA-B27 contributes to these modulatory effects.<br><br>METHODS: Stable U937 cell transfectants expressing HLA-A2, B27, or different forms of B27 with amino acid substitutions in the B pocket were prepared. Mock-transfected cells were prepared using the antibiotic resistance vector (pSV2neo) alone. Cells were differentiated, infected with S enteritidis, and the number of live intracellular S enteritidis organisms was determined using the colony-forming unit method. To visualize intracellular S enteritidis, the bacteria were transformed with green fluorescent protein (GFP), and studied by confocal microscopy.<br><br>RESULTS: Cells expressing wild-type HLA-B27 were more permissive of intracellular replication of S enteritidis compared with mock-transfected or A2-transfected controls. Cells expressing B27 with an altered B pocket composition having either 6 amino acid substitutions (B27.A2B; substitutions H9F, T24A, E45M, I66K, C67V, and K70H) or a single substitution (B27.E45M) were no longer permissive of S enteritidis replication. In contrast, cells expressing B27 with the single substitution of F for H at position 9 (B27.H9F) retained their permissiveness. Studies using GFP-transformed S enteritidis confirmed that the increase in the amount of intracellular bacteria in B27-expressing cells was due to replication of the bacteria.<br><br>CONCLUSION: Our data indicate that HLA-B27 expression modulates the host-microbe interaction that results in an impaired capacity of monocytes to resist intracellular replication of S enteritidis. The phenotype is dependent on glutamic acid at position 45 in the B pocket and, thus, may be due to properties of the B27 heavy chain that are related to this residue. The ability of HLA-B27 to confer susceptibility to Salmonella-triggered reactive arthritis may occur, at least in part, through these modulatory effects.}, }
@article {pmid15245920, year = {2004}, author = {Ranjard, L and Prigent-Combaret, C and Favre-Bonté, S and Monnez, C and Nazaret, S and Cournoyer, B}, title = {Characterization of a novel selenium methyltransferase from freshwater bacteria showing strong similarities with the calicheamicin methyltransferase.}, journal = {Biochimica et biophysica acta}, volume = {1679}, number = {1}, pages = {80-85}, doi = {10.1016/j.bbaexp.2004.05.001}, pmid = {15245920}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Bacteria/*enzymology ; Base Sequence ; DNA Primers ; Gas Chromatography-Mass Spectrometry ; Methyltransferases/chemistry/*metabolism ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; Water Microbiology ; }, abstract = {A novel group of Se-methyltransferases is presented. The genetic determinant, named mmtA, which revealed this group was isolated from selenite and selenate-resistant freshwater bacteria. E. coli expressing mmtA and grown with a Se supplement emitted dimethyl selenide (DMSe) and dimethyl diselenide (DMDSe). Phylogenetic analysis divided MmtA-like bacterial sequences into two clusters, one grouping MmtA with S- and O-methyltransferases, and one grouping UbiE C-methyltransferases. Se methylation by some of these MmtA phyletic neighbours was investigated.}, }
@article {pmid15228075, year = {2004}, author = {Lissens, G and Verstraete, W and Albrecht, T and Brunner, G and Creuly, C and Seon, J and Dussap, G and Lasseur, C}, title = {Advanced anaerobic bioconversion of lignocellulosic waste for bioregenerative life support following thermal water treatment and biodegradation by Fibrobacter succinogenes.}, journal = {Biodegradation}, volume = {15}, number = {3}, pages = {173-183}, doi = {10.1023/b:biod.0000026515.16311.4a}, pmid = {15228075}, issn = {0923-9820}, mesh = {*Anaerobiosis ; Biodegradation, Environmental ; Cellulose/*metabolism ; Fermentation ; Fibrobacter/*metabolism ; Hot Temperature ; Lignin/*metabolism ; Pressure ; Water Microbiology ; }, abstract = {The feasibility of nearly-complete conversion of lignocellulosic waste (70% food crops, 20% faecal matter and 10% green algae) into biogas was investigated in the context of a life support project. The treatment comprised a series of processes, i.e., a mesophilic laboratory scale CSTR (continuously stirred tank reactor), an upflow biofilm reactor, a fiber liquefaction reactor employing the rumen bacterium Fibrobacter succinogenes and a hydrothermolysis system in near-critical water. By the one-stage CSTR, a biogas yield of 75% with a specific biogas production of 0.37 l biogas g(-1) VSS (volatile suspended solids) added at a RT (hydraulic retention time) of 20-25 d was obtained. Biogas yields could not be increased considerably at higher RT, indicating the depletion of readily available substrate after 25 d. The solids present in the CSTR-effluent were subsequently treated in two ways. Hydrothermal treatment (T approximately 310-350 degrees C, p approximately 240 bar) resulted in effective carbon liquefaction (50-60% without and 83% with carbon dioxide saturation) and complete sanitation of the residue. Application of the cellulolytic Fibrobacter succinogenes converted remaining cellulose contained in the CSTR-effluent into acetate and propionate mainly. Subsequent anaerobic digestion of the hydrothermolysis and the Fibrobacter hydrolysates allowed conversion of 48-60% and 30%, respectively. Thus, the total process yielded biogas corresponding with conversions up to 90% of the original organic matter. It appears that particularly mesophilic digestion in conjunction with hydrothermolysis at near-critical conditions offers interesting features for (nearly) complete and hygienic carbon and energy recovery from human waste in a bioregenerative life support context.}, }
@article {pmid15221578, year = {2005}, author = {Wallander, H and Fossum, A and Rosengren, U and Jones, H}, title = {Ectomycorrhizal fungal biomass in roots and uptake of P from apatite by Pinus sylvestris seedlings growing in forest soil with and without wood ash amendment.}, journal = {Mycorrhiza}, volume = {15}, number = {2}, pages = {143-148}, pmid = {15221578}, issn = {0940-6360}, mesh = {Apatites/metabolism ; Biomass ; Mycorrhizae/*physiology ; Phosphorus/metabolism ; Pinus sylvestris/*microbiology/physiology ; Plant Roots/*microbiology/physiology ; Seedlings/microbiology/physiology ; Soil Microbiology ; Trees/*microbiology/physiology ; Wood ; }, abstract = {Forest soil from an experimental Norway spruce forest with four levels of wood ash addition (0, 1, 3 and 6 tonnes ha(-1)) was used to inoculate pine (Pinus sylvestris) seedlings with indigenous ectomycorrhizal (EM) fungi. Uptake of 32P and 86Rb in a root bioassay was used to estimate the demand for P and K by seedlings grown in the different soils. Utilisation of P from apatite was tested in a laboratory system where uptake by the ectomycorrhizal mycelium was separated from uptake by roots. The demand for P and K in the seedlings was similar regardless of the ash treatment. Variation in EM levels, estimated as fungal biomass (ergosterol) in roots, was large in the different soils, but not related to ash addition. Uptake of P from apatite was, on average, 23% of total seedling P and was not related to EM levels. It was concluded that the improved P uptake from apatite by EM fungi found in earlier studies is probably not a general phenomenon among EM fungi. The small effect of ash addition on EM levels and P uptake suggests that addition of granulated wood ash is a forest management treatment that will have only minor influence on ectomycorrhizal symbiosis.}, }
@article {pmid15196491, year = {2004}, author = {Bodrossy, L and Sessitsch, A}, title = {Oligonucleotide microarrays in microbial diagnostics.}, journal = {Current opinion in microbiology}, volume = {7}, number = {3}, pages = {245-254}, doi = {10.1016/j.mib.2004.04.005}, pmid = {15196491}, issn = {1369-5274}, mesh = {Ecosystem ; *Environmental Microbiology ; Gene Expression Profiling ; Humans ; Infections/*diagnosis/etiology ; Oligonucleotide Array Sequence Analysis/*methods ; }, abstract = {Oligonucleotide microarrays offer a fast, high-throughput alternative for the parallel detection of microbes from virtually any sample. The application potential spreads across most sectors of life sciences, including environmental microbiology and microbial ecology; human, veterinary, food and plant diagnostics; water quality control; industrial microbiology, and so on. The past two years have witnessed a rapid increase of research in this field. Many alternative techniques were developed and validated as seen in 'proof-of-concept' articles. Publications reporting on the application of oligonucleotide microarray technology for microbial diagnostics in microbiology driven projects have just started to appear. Current and future technical and bioinformatics developments will inevitably improve the potential of this technology further.}, }
@article {pmid15196488, year = {2004}, author = {Curtis, TP and Sloan, WT}, title = {Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology.}, journal = {Current opinion in microbiology}, volume = {7}, number = {3}, pages = {221-226}, doi = {10.1016/j.mib.2004.04.010}, pmid = {15196488}, issn = {1369-5274}, mesh = {Ecology ; *Ecosystem ; *Genetic Variation ; Prokaryotic Cells/*classification ; }, abstract = {Recent advances in the estimation of prokaryotic diversity have brought us insight into two questions: what is the extent of prokaryotic diversity, and perhaps more importantly, why bother finding out. In this review, we highlight the insights about the extent of diversity that may be gained by considering patterns that occur, or are likely to occur, in the relative abundance of prokaryotic taxa. We posit that global reservoirs of diversity are an important driving force behind patterns in localised diversity seen in leaves, intestines and wastewater treatment reactors. Thus, where the reservoir community is very large and relatively even, chance alone will prevent physically identical communities from having the same, or sometimes even stable, communities. By contrast, communities that tend to be similar (even when not physically identical) and stable are observed where the source diversity is low. Thus the relationship between structure and function in a community can only be understood, predicted and engineered through an understanding of the source of diversity from which the community is drawn.}, }
@article {pmid15196487, year = {2004}, author = {Forney, LJ and Zhou, X and Brown, CJ}, title = {Molecular microbial ecology: land of the one-eyed king.}, journal = {Current opinion in microbiology}, volume = {7}, number = {3}, pages = {210-220}, doi = {10.1016/j.mib.2004.04.015}, pmid = {15196487}, issn = {1369-5274}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Base Sequence ; DNA, Ribosomal/analysis ; *Ecosystem ; Electrophoresis ; Lactobacillus/genetics ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/*genetics ; Sequence Alignment ; }, abstract = {Studies of microbial biodiversity have made astounding discoveries of late due to the use of methodologies based on phylogenetic analyses of small subunit ribosomal RNA sequences. Although there are limitations to these methods, they can nonetheless be very useful if these limitations are kept in mind. These limitations range from technical problems such as obtaining representative genomic DNA and suitable primers, to conceptual problems such as defining and using meaningful taxonomic units of diversity (species). Here we discuss several of the limitations inherent in studies of microbial diversity that must be considered when interpreting the results obtained using these approaches.}, }
@article {pmid15191740, year = {2004}, author = {Saxena, D and Stewart, CN and Altosaar, I and Shu, Q and Stotzky, G}, title = {Larvicidal Cry proteins from Bacillus thuringiensis are released in root exudates of transgenic B. thuringiensis corn, potato, and rice but not of B. thuringiensis canola, cotton, and tobacco.}, journal = {Plant physiology and biochemistry : PPB}, volume = {42}, number = {5}, pages = {383-387}, doi = {10.1016/j.plaphy.2004.03.004}, pmid = {15191740}, issn = {0981-9428}, mesh = {Bacterial Proteins ; Biodegradation, Environmental ; Biological Assay ; Gossypium/microbiology ; Green Fluorescent Proteins ; Insect Proteins/*chemistry/metabolism ; Luminescent Proteins/metabolism ; Oryza/microbiology ; *Pest Control, Biological ; Plant Roots/*microbiology ; Plants, Genetically Modified/*microbiology ; Promoter Regions, Genetic ; Protein Binding ; Receptors, Cell Surface/*chemistry/metabolism ; Soil ; Solanum tuberosum/microbiology ; Surface-Active Agents/pharmacology ; Nicotiana/microbiology ; Zea mays/microbiology ; }, abstract = {Larvicidal proteins encoded by cry genes from Bacillus thuringiensis were released in root exudates from transgenic B. thuringiensis corn, rice, and potato but not from B. thuringiensis canola, cotton, and tobacco. Nonsterile soil and sterile hydroponic solution in which B. thuringiensis corn, rice, or potato had been grown were immunologically positive for the presence of the Cry proteins; from B. thuringiensis corn and rice, the soil and solution were toxic to the larva of the tobacco hornworm (Manduca sexta), and from potato, to the larva of the Colorado potato beetle (Leptinotarsa decemlineata), representative lepidoptera and coleoptera, respectively. No toxin was detected immunologically or by larvicidal assay in soil or hydroponic solution in which B. thuringiensis canola, cotton, or tobacco, as well as all near-isogenic non-B. thuringiensis plant counterparts or no plants, had been grown. All plant species had the cauliflower mosaic virus (CaMV) 35S promoter, except rice, which had the ubiquitin promoter from maize. The reasons for the differences between species in the exudation from roots of the toxins are not known. The released toxins persisted in soil as the result of their binding on surface-active particles (e.g. clay minerals, humic substances), which reduced their biodegradation. The release of the toxins in root exudates could enhance the control of target insect pests, constitute a hazard to nontarget organisms, and/or increase the selection of toxin-resistant target insects.}, }
@article {pmid15188567, year = {2004}, author = {Gracheva, NM and Kolganova, NA and Shcherbakov, IT and Abakov, AA and Solov'eva, AI}, title = {[Microbial ecology and the state of the gastrointestinal mucosa in patients with allergic diseases].}, journal = {Zhurnal mikrobiologii, epidemiologii i immunobiologii}, volume = {}, number = {2}, pages = {79-81}, pmid = {15188567}, issn = {0372-9311}, mesh = {Adult ; Bacteria/isolation &amp; purification ; Campylobacter/isolation &amp; purification ; Dermatitis, Allergic Contact/complications ; Humans ; Hypersensitivity/*complications/microbiology ; Intestinal Diseases/*complications/microbiology/pathology ; Intestinal Mucosa/*microbiology ; Respiratory Hypersensitivity/complications ; }, abstract = {Patients with allergic diseases of the skin and the respiratory system were found to have a high rate of disturbances in the microbial ecology of the gastrointestinal tract and the involvement of all its sections into the pathological process. On the mucous membrane of different sections of the digestive tract spiral-like bacteria were detected in a large percentage of cases. The possibility of the fact that the development and maintenance of the allergic process were evidently linked with the detected changes in the microbial ecology and pathomorphological features of the gastrointestinal mucosa could hardly be excluded, which made it necessary to make corrections in the therapeutic process.}, }
@article {pmid15186443, year = {2004}, author = {Holah, JT and Bird, J and Hall, KE}, title = {The microbial ecology of high-risk, chilled food factories; evidence for persistent Listeria spp. and Escherichia coli strains.}, journal = {Journal of applied microbiology}, volume = {97}, number = {1}, pages = {68-77}, doi = {10.1111/j.1365-2672.2004.02272.x}, pmid = {15186443}, issn = {1364-5072}, mesh = {*Cold Temperature ; Environmental Monitoring/methods ; Escherichia coli/*isolation &amp; purification ; *Food Contamination ; *Food Industry ; *Food Preservation ; Humans ; Hygiene ; Listeria/*isolation &amp; purification ; Risk ; Time Factors ; }, abstract = {AIMS: The intention of this study was to provide evidence of any Listeria spp. or Escherichia coli strain persistence, and to identify whether strains of these organisms adapt to specific environmental or product niches in food factories.<br><br>METHODS AND RESULTS: A 3-year assessment of the microbial ecology of four, ready-to-eat food-processing factories was undertaken in which approx. 196 000 and 75 000 product and environmental samples were examined for Escherichia coli and Listeria spp. respectively. A total of 152 E. coli isolates (44 environmental and 108 product in 62 ribogroups) and 260 Listeria spp. isolates (174 environmental and 86 product in 30 ribogroups) were identified and ribotyped. The overall prevalence of E. coli (0.08%), all Listeria spp. (0.35%) and L. monocytogenes (0.23%) was very low. Some 10 E. coli ribogroups and 14 Listeria spp. ribogroups showed evidence for persistence, defined as the isolation of the same strain, from the same site, over a prolonged time period. The majority of E. coli strains were product niche oriented whilst the majority of Listeria spp. strains were environmental niche oriented.<br><br>CONCLUSION: Current UK high-risk food factory designs, personnel hygiene and cleaning and disinfection regimes are sufficient to control Listeria spp. and E. coli to very low levels.<br><br>Persistent strains of these organisms, however, can remain within factory high-risk production areas over considerable time periods, warranting an examination of the strain persistence mechanisms and alternative hygiene controls.}, }
@article {pmid15186351, year = {2004}, author = {Lambertsen, L and Sternberg, C and Molin, S}, title = {Mini-Tn7 transposons for site-specific tagging of bacteria with fluorescent proteins.}, journal = {Environmental microbiology}, volume = {6}, number = {7}, pages = {726-732}, doi = {10.1111/j.1462-2920.2004.00605.x}, pmid = {15186351}, issn = {1462-2912}, mesh = {Artificial Gene Fusion ; Blotting, Southern ; Chromosomes, Bacterial ; *DNA Transposable Elements ; DNA, Bacterial/analysis/isolation &amp; purification ; Escherichia coli/genetics ; Genes, Reporter ; Lac Operon ; Luminescent Proteins/genetics/*metabolism ; Plasmids ; Polymerase Chain Reaction ; Promoter Regions, Genetic ; Pseudomonas putida/*genetics/growth &amp; development/metabolism ; Recombinant Proteins/genetics/metabolism ; Recombination, Genetic ; Staining and Labeling ; rRNA Operon ; }, abstract = {The mini-Tn7 transposon system is a convenient tool for site-specific tagging of bacteria in which the tagging DNA is inserted at a unique and neutral chromosomal site. We have expanded the panel of mini-Tn7 delivery plasmids expressing different fluorescent proteins (stable and unstable) from the Escherichia coli lac derived promoter, P(A1/04/03), or from the growth-rate-dependent Escherichia coli promoter PrrnB P1. The mini-Tn7 transposons were inserted and tested in the soil bacterium, Pseudomonas putida KT2440. Successful and site-specific tagging was verified by Southern blots as well as by PCR. Furthermore, the effect of fluorescent protein expression on the cellular growth rate was tested by growth competition assays.}, }
@article {pmid15184147, year = {2004}, author = {Mikkelsen, LL and Naughton, PJ and Hedemann, MS and Jensen, BB}, title = {Effects of physical properties of feed on microbial ecology and survival of Salmonella enterica serovar Typhimurium in the pig gastrointestinal tract.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {6}, pages = {3485-3492}, pmid = {15184147}, issn = {0099-2240}, mesh = {*Animal Feed ; Animals ; Bacteria/isolation &amp; purification ; Cecum/microbiology ; Digestive System/*microbiology ; *Ecosystem ; Salmonella typhimurium/*growth &amp; development ; Stomach/microbiology ; Swine/*microbiology ; Yeasts/isolation &amp; purification ; }, abstract = {A two-by-two factorial experiment with pigs was conducted to study the effect of feed grinding (fine and coarse) and feed processing (pelleted and nonpelleted) on physicochemical properties, microbial populations, and survival of Salmonella enterica serovar Typhimurium DT12 in the gastrointestinal tracts of pigs. Results demonstrated a strong effect of diet on parameters measured in the stomachs of the pigs, whereas the effect was less in the other parts of the gastrointestinal tract. Pigs fed the coarse nonpelleted (C-NP) diet showed more solid gastric content with higher dry matter content than pigs fed the fine nonpelleted (F-NP), coarse pelleted (C-P), or fine pelleted (F-P) diet. Pigs fed the C-NP diet also showed significantly increased number of anaerobic bacteria (P < 0.05), increased concentrations of organic acids, and reduced pH in the stomach. In addition, pigs fed the C-NP diet showed increased in vitro death rate of S. enterica serovar Typhimurium DT12 in content from the stomach (P < 0.001). Pigs fed the C-NP diet had a significantly higher concentration of undissociated lactic acid in gastric content than pigs fed the other diets (P < 0.001). A strong correlation between the concentration of undissociated lactic acid and the death rate of S. enterica serovar Typhimurium DT12 was found. In the distal small intestine, cecum, and midcolon, significantly lower numbers of coliform bacteria were observed in pigs fed the coarse diets than in pigs fed the fine diets (P < 0.01). Pigs fed the C-NP diet showed the lowest number of coliform bacteria in these segments of the gastrointestinal tract. Pigs fed the coarse diets showed increased concentration of butyric acid in the cecum (P < 0.05) and colon (P < 0.10) compared with pigs fed the fine diets. It was concluded that feeding a coarsely ground meal feed to pigs changes the physicochemical and microbial properties of content in the stomach, which decreases the survival of Salmonella during passage through the stomach. In this way the stomach acts as a barrier preventing harmful bacteria from entering and proliferating in the lower part of the gastrointestinal tract.}, }
@article {pmid15177910, year = {2004}, author = {Griffiths, RI and Manefield, M and Ostle, N and McNamara, N and O'Donnell, AG and Bailey, MJ and Whiteley, AS}, title = {13CO2 pulse labelling of plants in tandem with stable isotope probing: methodological considerations for examining microbial function in the rhizosphere.}, journal = {Journal of microbiological methods}, volume = {58}, number = {1}, pages = {119-129}, doi = {10.1016/j.mimet.2004.03.011}, pmid = {15177910}, issn = {0167-7012}, mesh = {Carbon Dioxide/*metabolism ; Carbon Isotopes ; Mass Spectrometry ; Photosynthesis/physiology ; Plant Roots ; Poaceae/*metabolism ; RNA/chemistry/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; *Soil Microbiology ; Water/metabolism ; }, abstract = {Recently developed 13CO2 pulse labelling and stable isotope probing (SIP) methods offer the potential to track 13C-labelled plant photosynthate into phylogenetic groups of microbial taxa in the rhizosphere, permitting an examination of the link between soil microbial diversity and carbon flow in situ. We tested the feasibility of this approach to detect functional differences in microbial communities utilising recently fixed plant photosynthate in moisture perturbed grassland turfs. Specifically, we addressed two questions: (1) How does moisture perturbation (three treatments; continual wetting, drying, and drying followed by rewetting) affect the assimilation of 13C-labelled exudates carbon into the soil microbial community?; (2) Can 13C deposited in soil from pulse-labelled plants be used to identify microbes utilising plant exudates using SIP methodologies? Net CO2 fluxes showed that prior to 13CO2 pulse labelling, all treatments were photosynthetically active, but differences were observed in night time respiration, indicating moisture treatments had impacted on net CO2 efflux. Measurements of pulse-derived 13C incorporated into soil RNA over 2 months showed that there was only evidence of 13C enrichment in the continuously wetted treatments. However, isotopic values represented only a 0.1-0.2 13C at.% increase over natural abundance levels and were found to be insufficient for the application of RNA-SIP. These findings reveal that in this experimental system, the microbial uptake of labelled carbon from plant exudates is low, and further optimisation of methodologies may be required for application of SIP to natural plant-soil systems where 13C tracer dilution is a consideration.}, }
@article {pmid15172581, year = {2004}, author = {Roels, J and Verstraete, W}, title = {Occurrence and origin of phosphine in landfill gas.}, journal = {The Science of the total environment}, volume = {327}, number = {1-3}, pages = {185-196}, doi = {10.1016/j.scitotenv.2003.11.016}, pmid = {15172581}, issn = {0048-9697}, mesh = {Aluminum/metabolism ; Bacteria, Anaerobic/*metabolism ; Belgium ; Biodegradation, Environmental ; Corrosion ; Environmental Monitoring/*statistics &amp; numerical data ; Gases/*analysis ; Iron/metabolism ; Phosphines/*analysis/chemistry/metabolism ; *Refuse Disposal ; Time Factors ; }, abstract = {A landfill (Hooge Maey, Flanders, Belgium) was subjected to an in-depth study in order to explain the origin of phosphine detected in high amounts in landfill gas, in comparison with biogas from other sources, during a previous study. The spatial and temporal variability of the phosphine concentration in landfill gas was assessed. Twenty-four wells were monitored and differences in phosphine concentration up to one log unit were observed (3.2-32.4 microg/m(3)). The phosphine concentration in each well was constant in time over a period of 4 months. No correlation was found between the phosphine concentration and methane, carbon dioxide, hydrogen sulfide, ethene or ethane concentration. In a series of laboratory tests, it was shown that phosphine was emitted during batch fermentation tests inoculated with landfill leachate when Fe(0) or Al(0) specimens were added. Conditions favouring corrosion of iron gave rise to higher emissions of phosphine. The phosphine concentration in the headspace of a batch test rose to 1.43 mg/m(3) after 27 days of incubation. Weight loss of corroding steel coupons correlated with phosphine emission. Calculations showed that all phosphine emitted from the 0.005 km(3) landfill (160 g/year) could be attributed to corrosion of metals. No evidence of de novo synthesis could be established.}, }
@article {pmid15171935, year = {2004}, author = {Van de Wiele, TR and Peru, KM and Verstraete, W and Siciliano, SD and Headley, JV}, title = {Liquid chromatography-mass spectrometry analysis of hydroxylated polycyclic aromatic hydrocarbons, formed in a simulator of the human gastrointestinal tract.}, journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences}, volume = {806}, number = {2}, pages = {245-253}, doi = {10.1016/j.jchromb.2004.04.001}, pmid = {15171935}, issn = {1570-0232}, mesh = {Calibration ; Chromatography, High Pressure Liquid/*methods ; Gastrointestinal Tract/*chemistry ; Humans ; Hydroxylation ; Mass Spectrometry/*methods ; Polycyclic Compounds/*analysis ; Sensitivity and Specificity ; }, abstract = {Described is a liquid chromatography-mass spectrometry (LC-MS) procedure for the determination of hydroxylated biotransformation products of polycyclic aromatic hydrocarbons (PAH) in the human gastrointestinal tract. The formation of hydroxylated PAHs was monitored upon incubation of PAHs with colon microbiota from the Simulator of the Human Intestinal Microbial Ecosystem (SHIME). The analytical method consisted of a biomass removal step followed by a solid phase extraction (SPE) step using C18 packed columns to remove non-digested food compounds and microbial metabolites that interfere with the detection of the target compounds. For quantification, 9-hydroxyphenanthrene (13)C(6)was used as the internal standard. The detection limits of the hydroxylated PAHs were generally in the range 0.36-14.09 microg x l(-1), based on a signal/noise ratio of 3:1. The recovery of hydroxylated PAHs in intestinal suspension was variable ranging from 45 to 107%, with relative standard deviation (R.S.D.) between 5 and 17%. The analytical procedure was used to show the microbial production of 1-hydroxypyrene and 7-hydroxybenzo(a)pyrene, metabolites that may give colon incubated PAHs bioactive properties.}, }
@article {pmid15164242, year = {2004}, author = {Montagnes, DJ and Berges, JA}, title = {Determining parameters of the numerical response.}, journal = {Microbial ecology}, volume = {48}, number = {1}, pages = {139-144}, pmid = {15164242}, issn = {0095-3628}, mesh = {Animals ; Cell Division/physiology ; Ciliophora/*growth &amp; development/*metabolism ; Computer Simulation ; *Food Chain ; *Models, Biological ; Monte Carlo Method ; *Numerical Analysis, Computer-Assisted ; }, abstract = {The numerical response, the change in specific growth rate with food concentration, is a fundamental component of many aquatic microbial studies. Accurately and precisely determining the parameters of this response is essential to obtain useful data for both aut- and synec-ological studies. In this work we emphasize four points that are often ignored in designing numerical response experiments: (1) the inclusion of subthreshold concentrations (i.e., where growth rate is negative) in the experimental design; (2) an appropriate allocation of effort, i.e., the superiority of choosing more individual prey concentrations rather than replicating fewer; (3) the potential superiority of replicating experiments rather than simply replicating treatment in a single experiment; and (4) the placement of most measurements near the lower end of the concentration gradient, well below the asymptote, possibly following a geometric progression. We illustrate the first point by examining a small subset of published data on planktonic oligotrich ciliates and then, using a Monte Carlo simulation, rigorously evaluate the experimental design, supporting the remaining points.}, }
@article {pmid15164241, year = {2004}, author = {Teyssier-Cuvelle, S and Oger, P and Mougel, C and Groud, K and Farrand, SK and Nesme, X}, title = {A highly selectable and highly transferable Ti plasmid to study conjugal host range and Ti plasmid dissemination in complex ecosystems.}, journal = {Microbial ecology}, volume = {48}, number = {1}, pages = {10-18}, pmid = {15164241}, issn = {0095-3628}, support = {GM52465/GM/NIGMS NIH HHS/United States ; }, mesh = {Chromosome Mapping ; Conjugation, Genetic/*genetics ; DNA, Recombinant/genetics ; Drug Resistance, Bacterial/genetics ; *Ecosystem ; Plant Tumor-Inducing Plasmids/*genetics ; Rhizobium/*genetics/*pathogenicity ; Species Specificity ; }, abstract = {A conjugal donor system, ST2, was constructed to study the conjugal dissemination of a Ti plasmid to wild-type recipient bacteria in vitro and in situ. The system consisted of a polyauxotrophic derivative of C58 harboring a hyperconjugative and highly selectable Ti plasmid, pSTiEGK, which was constructed by inserting a multiple antibiotic resistance cassette in the traM- mcpA region of pTiC58Delta accR. ST2 transfers pSTiEGK constitutively at frequencies up to 10(-1) to plasmidless Agrobacterium recipients. The host range of pSTiEGK includes all the known genomic species of Agrobacterium, indigenous soil agrobacteria and some Rhizobium and Phyllobacterium spp. All transconjugants became pathogenic upon acquisition of the Ti plasmid and were also able to transfer pSTiEGK by conjugation. This host range was indistinguishable from that of its wild-type parent pTiC58, and therefore pSTiEGK constitute a valid proxy to study the dissemination of Ti plasmids directly in the environment. Transconjugants can be selected on a combination of four antibiotics, which efficiently prevents the growth of the indigenous microbiota present in complex environments. The transfer of pSTiEGK to members of the genus Agrobacterium was affected primarily by the plasmid content of the recipient strain (10(3)- to 10(5)-fold reduction), e.g., the presence of incompatible plasmids. As a consequence, a species should be considered permissive to Ti transfer whenever one permissive isolate is found.}, }
@article {pmid15164240, year = {2004}, author = {Greenblatt, CL and Baum, J and Klein, BY and Nachshon, S and Koltunov, V and Cano, RJ}, title = {Micrococcus luteus -- survival in amber.}, journal = {Microbial ecology}, volume = {48}, number = {1}, pages = {120-127}, pmid = {15164240}, issn = {0095-3628}, mesh = {Amber ; Base Sequence ; Cluster Analysis ; Culture Media ; Evolution, Molecular ; Fatty Acids/metabolism ; Fluorescence ; *Fossils ; Israel ; Methyl Ethers/metabolism ; Micrococcus luteus/*genetics/isolation &amp; purification/*metabolism/ultrastructure ; Microscopy, Electron ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {A growing body of evidence now supports the isolation of microorganisms from ancient materials. However, questions about the stringency of extraction methods and the genetic relatedness of isolated organisms to their closest living relatives continue to challenge the authenticity of these ancient life forms. Previous studies have successfully isolated a number of spore-forming bacteria from organic and inorganic deposits of considerable age whose survival is explained by their ability to enter suspended animation for extended periods of time. However, despite a number of putative reports, the isolation of non-spore-forming bacteria and an explanation for their survival have remained enigmatic. Here we describe the isolation of non-spore-forming cocci from a 120-million-year-old block of amber, which by genetic, morphological, and biochemical analyses are identified as belonging to the bacterial species Micrococcus luteus. Although comparison of 16S rRNA sequences from the ancient isolates with their modern counterparts is unable to confirm the precise age of these bacteria, we demonstrate, using complementary molecular and cell biological techniques, evidence supporting the view that these (and related modern members of the genus) have numerous adaptations for survival in extreme, nutrient-poor environments, traits that will assist in this bacteria's persistence and dispersal in the environment. The bacteria's ability to utilize succinic acid and process terpine-related compounds, both major components of natural amber, support its survival in this oligotrophic environment.}, }
@article {pmid15164239, year = {2004}, author = {Ferrari, BC and Oregaard, G and Sørensen, SJ}, title = {Recovery of GFP-labeled bacteria for culturing and molecular analysis after cell sorting using a benchtop flow cytometer.}, journal = {Microbial ecology}, volume = {48}, number = {2}, pages = {239-245}, pmid = {15164239}, issn = {0095-3628}, mesh = {Cell Separation/instrumentation/*methods ; DNA Primers ; DNA, Ribosomal/genetics ; Erwinia/genetics/metabolism ; Escherichia coli/metabolism ; Flow Cytometry/instrumentation/*methods ; Green Fluorescent Proteins/metabolism ; Microscopy, Fluorescence ; Polymerase Chain Reaction ; }, abstract = {Exciting opportunities exist for the application of simple fluorescence-activated cell sorting (FACS) to microbiology. The technology is widely available, but critical reports on the efficiency of cell sorting using benchtop instruments are lacking. It is vital that single cell sorting be of the highest purity possible. If purity is compromised detrital material or unwanted cells will be captured along with target cells of interest. Here, the isolation of fluorescent bacteria using a benchtop FACSCalibur-sort flow cytometer is described. The efficiency and purity of isolated cells was determined using fluorescence microscopy, culturing, and molecular analysis. To achieve high purity it was essential that the total event rate did not exceed 300 cells per second. This instrument was capable of recovering >55% sorted Escherichia coli cells, coupled with a purity exceeding 99%. However, the purity of recovered cells was substantially reduced (<25%) when the event rate increased. Cell sorting onto polycarbonate membranes did not reduce the ability of E. coli to form colonies, and sorting of ~1000 E. coli cells was sufficient for 16S rDNA amplification. Additionally, as few as 100 isolated Erwinia sp. carrying the gfp gene were amplified using seminested PCR targeting the single copy gfp gene. With such low numbers of bacteria being required for molecular identification, FACS can be achieved without the requirement for high-speed droplet cell sorters.}, }
@article {pmid15164238, year = {2004}, author = {Lepp, PW and Schmidt, TM}, title = {Changes in Synechococcus population size and cellular ribosomal RNA content in response to predation and nutrient limitation.}, journal = {Microbial ecology}, volume = {48}, number = {1}, pages = {1-9}, pmid = {15164238}, issn = {0095-3628}, mesh = {Animals ; Cyanobacteria/*genetics/growth &amp; development/*physiology ; Fluorescence ; *Food Chain ; Louisiana ; *Models, Biological ; Oligonucleotide Probes ; Population Density ; RNA, Ribosomal/*genetics ; Seawater/microbiology ; Tetrahymena/physiology ; }, abstract = {A mathematical model of predator-prey interactions was used to predict the relationship between population size and cellular growth rate in a two-tiered trophic system consisting of Synechococcus PCC 6301 and Tetrahymena pyriformis. As predicted, axenic chemostat cultures of Synechococcus responded to increased nutrient availability by expanding the equilibrium population size without a concurrent change in growth rate. Likewise, the addition of the predator Tetrahymena pyriformis decreased the Synechococcus population size by 85% and increased the Synechococcus growth rate. Synechococcus populations in the surface waters of the Gulf of Mexico were sampled to ascertain whether the relationship between population size and cellular 16S rRNA concentration conformed to that predicted by the model. Direct counts of autofluorescent cells in size-fractionated seawater samples provided an estimate of Synechococcus population size. The growth rate of in situ populations was estimated by measuring the extent of hybridization of an oligonucleotide probes complementary to Synechococcus 16S rRNA, based on evidence that ribosomal RNA content increases concurrently with growth rate. The comparison of in situ population sizes and specific growth rates revealed that relatively large Synechococcus populations were growing slowly, indicative of nutrient limitation, and that quickly growing populations were relatively small, as predicted for predator-limited populations.}, }
@article {pmid15164237, year = {2004}, author = {Savin, MC and Martin, JL and LeGresley, M and Giewat, M and Rooney-Varga, J}, title = {Plankton diversity in the Bay of Fundy as measured by morphological and molecular methods.}, journal = {Microbial ecology}, volume = {48}, number = {1}, pages = {51-65}, pmid = {15164237}, issn = {0095-3628}, mesh = {Atlantic Ocean ; Base Sequence ; *Biodiversity ; Electrophoresis ; Molecular Sequence Data ; New Brunswick ; *Phylogeny ; Plankton/*cytology/*genetics ; RNA, Ribosomal, 18S/genetics ; Seasons ; Sequence Analysis, DNA ; }, abstract = {Phytoplankton have traditionally been identified based on morphological characteristics. However, identifications based on morphology are time-consuming, require expertise in taxonomy, and often fail to distinguish differences among the multitudes of minute, nondescript planktonic organisms. Molecular techniques, which have revealed new insights into bacterial and picoplankton communities, may also enhance our knowledge of the diversity among communities of larger plankton. We compared plankton identifications and community assessments based on the two types of techniques (morphological vs molecular) for surface seawater samples collected on 2 May, 31 July and 25 September 2000 from several sampling stations in the Bay of Fundy. Phytoplankton captured in surface bucket samples were quantified and identified based on morphology. DNA was extracted from plankton communities (5-100 microm in diameter) collected by filtration, and 18S rRNA gene fragments were amplified with primers specific for eukaryotes. Denaturing gradient gel electrophoresis (DGGE) was used to develop DNA profiles of eukaryotic phylogenetic diversity and to select cloned 18S rDNA fragments for sequencing. Both morphological and molecular methods showed great community diversity. However, the communities identified with the two different types of techniques were starkly different. Morphological abundances and taxon richness were lowest in the May samples, whereas the number of DGGE bands was highest in May and July. Morphological identifications showed a succession of dominant organisms through time. Whereas neither diatoms nor dinoflagellates were dominant in May, diatoms and a few dinoflagellates were dominant in July and September. In contrast, few 18S rDNA sequences were related to rDNA sequences of known identity, and furthermore, few diatoms were identified in the molecular analyses. Molecular phylogenetic analysis indicated the presence of many novel organisms, several of which were most closely related to other unidentified sequences from diverse marine environments representing new lineages. Our results support the ideas that we are just beginning to uncover the diversity of eukaryotic marine organisms and that there may be many more ubiquitous, microeukaryotic plankton than previously realized. Our results suggest that both types of methods capture only a portion of the community. Morphological methods may be more adept at capturing the phototrophic organisms within the community. However, just as for bacteria and picoplankton, molecular techniques can enhance our understanding of plankton diversity, particularly by detecting previously unidentified organisms.}, }
@article {pmid15151278, year = {2003}, author = {Maes, M and Baeyen, S}, title = {Experiences and perspectives for the use of a Paenibacillus strain as a plant protectant.}, journal = {Communications in agricultural and applied biological sciences}, volume = {68}, number = {4 Pt B}, pages = {457-462}, pmid = {15151278}, issn = {1379-1176}, mesh = {Araceae/microbiology ; Bacillus/genetics/pathogenicity/*physiology ; DNA, Bacterial/analysis/isolation &amp; purification ; Ficus/microbiology ; Magnoliopsida/microbiology ; Plant Roots/*microbiology ; Polymerase Chain Reaction ; Robinia/*microbiology ; Seeds/microbiology ; *Soil Microbiology ; Water Microbiology ; }, abstract = {A study on the microbial ecology in an active slow sand filter, used for disinfecting the circulating plant nutrient solutions, showed that spore-forming plant-associated bacteria belonging to the Bacillus-Paenibacillus complex are well adapted for transmission in the solutions and passage through the filter. Therefore, strains from this bacterial group were suitable candidates for biological control in irrigated and closed plant growth systems. The spore-forming Paenibacillus polymyxa strain PpDGB was selected in in vitro tests as a potent pathogen-antagonist and was tested as a prophylactic protection agent in the plant rhizosphere, especially for cultures stages that are highly susceptible to stress and disease. Plant cuttings, in vitro plants and seeds of different plant types were bacterized and planted in their typical disease-conducive environment where nutrient solutions or water irrigation was applied and further plant development was monitored. Observed plant parameters were plant survival, weight, chlorophyll concentration in the leaf mesophyl, root health and root hair formation. The PpDGB treatment initially induced stress in the plants, which was observed as a transient stop in plant transpiration. This effect caused some necrosis in the most stress-sensitive in vitro plant species. In the other plants this stress period was followed by a significant enhancement in plant growth. In case of seed treatment, more seeds germinated and seedling growth was faster. In the tested formulation, PpDGB enhanced growth but not disease resistance, probably due to simultaneous activation of the residual plant pathogens. Therefore variant formulations have to be tested. The influence of PpDGB on the composition of the bacterial communities in the rhizosphere was assessed by DGGE profiling. In soilless plant cultures, PpDGB-driven profile changes could be observed from the 5th day after the initial treatment. P. polymyxa bacteria were shown to be widely present in association with plants and specific PpDGB detection in plant and rhizosphere was only possible with newly developed strain-specific PCR primers based on Nif H gene sequences. Quantitative PCR based on SYBR Green fluorescence enabled detection of low PpDGB concentrations in the plant rhizosphere.}, }
@article {pmid15134880, year = {2004}, author = {Sys, K and Boon, N and Verstraete, W}, title = {Development and validation of evolutionary algorithm software as an optimization tool for biological and environmental applications.}, journal = {Journal of microbiological methods}, volume = {57}, number = {3}, pages = {309-322}, doi = {10.1016/j.mimet.2004.01.004}, pmid = {15134880}, issn = {0167-7012}, mesh = {*Algorithms ; Ecology/*methods ; *Models, Biological ; *Software ; }, abstract = {A flexible, extendable tool for the optimization of (micro)biological processes and protocols using evolutionary algorithms was developed. It has been tested using three different theoretical optimization problems: 2 two-dimensional problems, one with three maxima and one with five maxima and a river autopurification optimization problem with boundary conditions. For each problem, different evolutionary parameter settings were used for the optimization. For each combination of evolutionary parameters, 15 generations were run 20 times. It has been shown that in all cases, the evolutionary algorithm gave rise to valuable results. Generally, the algorithms were able to detect the more stable sub-maximum even if there existed less stable maxima. The latter is, from a practical point of view, generally more desired. The most important factors influencing the convergence process were the parameter value randomization rate and distribution. The developed software, described in this work, is available for free.}, }
@article {pmid15134838, year = {2004}, author = {Vermeirssen, V and van der Bent, A and Van Camp, J and van Amerongen, A and Verstraete, W}, title = {A quantitative in silico analysis calculates the angiotensin I converting enzyme (ACE) inhibitory activity in pea and whey protein digests.}, journal = {Biochimie}, volume = {86}, number = {3}, pages = {231-239}, doi = {10.1016/j.biochi.2004.01.003}, pmid = {15134838}, issn = {0300-9084}, mesh = {Amino Acid Sequence ; Angiotensin-Converting Enzyme Inhibitors/chemistry/*isolation &amp; purification/metabolism ; Animals ; Cattle ; *Computational Biology ; Milk Proteins/*chemistry ; Molecular Sequence Data ; Pisum sativum/*chemistry ; Peptide Fragments/chemistry/metabolism ; Peptidyl-Dipeptidase A/*metabolism ; Time Factors ; Whey Proteins ; }, abstract = {Angiotensin I converting enzyme (ACE) inhibitory peptides can induce antihypertensive effects after oral administration. By means of an ACE inhibitory peptide database, containing about 500 reported sequences and their IC(50) values, the different proteins in pea and whey were quantitatively evaluated as precursors for ACE inhibitory peptides. This analysis was combined with experimental data from the evolution in ACE inhibitory activity and protein degradation during in vitro gastrointestinal digestion. Pea proteins produced similar in silico scores and were degraded early in the in vitro digestion. High ACE inhibitory activity was observed after the simulated stomach phase and augmented slightly in the simulated small intestine phase. The major whey protein beta-lactoglobulin obtained the highest in silico scores, which corresponded with the fact that degradation of this protein in vitro only occurred from the simulated small intestine phase on and resulted in a 10-fold increase in the ACE inhibitory activity. Whey protein obtained total in silico scores of about 124 ml/mg, compared to 46 ml/mg for pea protein, indicating that whey protein would be a richer source of ACE inhibitory peptides than pea protein. Although beta-lactoglobulin is only partially digested, a higher ACE inhibitory activity was indeed found in the whey (IC(50) = 0.048 mg/ml) compared to the pea digest (IC(50) = 0.076 mg/ml). In silico gastrointestinal digestion of the highest scoring proteins in pea and whey, vicilin and albumin PA2, and beta-lactoglobulin, respectively, directly released a number of potent ACE inhibitory peptides. Several other ACE inhibitory sequences resisted in silico digestion by gastrointestinal proteases. Briefly, the quantitative in silico analysis will facilitate the study of precursor proteins on a large scale and the specific release of bioactive peptides.}, }
@article {pmid15128558, year = {2004}, author = {Rajapaksha, RM and Tobor-Kapłon, MA and Bååth, E}, title = {Metal toxicity affects fungal and bacterial activities in soil differently.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {5}, pages = {2966-2973}, pmid = {15128558}, issn = {0099-2240}, mesh = {Bacteria/drug effects/growth &amp; development/*metabolism ; Biomass ; Copper/*toxicity ; Ecosystem ; Fungi/drug effects/growth &amp; development/*metabolism ; Hydrogen-Ion Concentration ; Metals, Heavy/*toxicity ; *Soil Microbiology ; Soil Pollutants/toxicity ; Trees ; Zinc/*toxicity ; }, abstract = {Although the toxic effect of heavy metals on soil microorganism activity is well known, little is known about the effects on different organism groups. The influence of heavy metal addition on total, bacterial, and fungal activities was therefore studied for up to 60 days in a laboratory experiment using forest soil contaminated with different concentrations of Zn or Cu. The effects of the metals differed between the different activity measurements. During the first week after metal addition, the total activity (respiration rate) decreased by 30% at the highest level of contamination and then remained stable during the 60 days of incubation. The bacterial activity (thymidine incorporation rate) decreased during the first days with the level of metal contamination, resulting in a 90% decrease at the highest level of contamination. Bacterial activity then slowly recovered to values similar to those of the control soil. The recovery was faster when soil pH, which had decreased due to metal addition, was restored to control values by liming. Fungal activity (acetate-in-ergosterol incorporation rate) initially increased with the level of metal contamination, being up to 3 and 7 times higher than that in the control samples during the first week at the highest levels of Zn and Cu addition, respectively. The positive effect of metal addition on fungal activity then decreased, but fungal activity was still higher in contaminated than in control soil after 35 days. This is the first direct evidence that fungal and bacterial activities in soil are differently affected by heavy metals. The different responses of bacteria and fungi to heavy metals were reflected in an increase in the relative fungal/bacterial ratio (estimated using phospholipid fatty acid analysis) with increased metal load.}, }
@article {pmid15128522, year = {2004}, author = {Pallud, C and Dechesne, A and Gaudet, JP and Debouzie, D and Grundmann, GL}, title = {Modification of spatial distribution of 2,4-dichlorophenoxyacetic acid degrader microhabitats during growth in soil columns.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {5}, pages = {2709-2716}, pmid = {15128522}, issn = {0099-2240}, mesh = {2,4-Dichlorophenoxyacetic Acid/*metabolism ; Bacteria/*growth &amp; development/metabolism ; Bacteriological Techniques/instrumentation ; Biodegradation, Environmental ; Colony Count, Microbial ; *Ecosystem ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Bacterial processes in soil, including biodegradation, require contact between bacteria and substrates. Knowledge of the three-dimensional spatial distribution of bacteria at the microscale is necessary to understand and predict such processes. Using a soil microsampling strategy combined with a mathematical spatial analysis, we studied the spatial distribution of 2,4-dichlorophenoxyacetic acid (2,4-D) degrader microhabitats as a function of 2,4-D degrader abundance. Soil columns that allowed natural flow were percolated with 2,4-D to increase the 2,4-D degrader abundance. Hundreds of soil microsamples (minimum diameter, 125 microm) were collected and transferred to culture medium to check for the presence of 2,4-D degraders. Spatial distributions of bacterial microhabitats were characterized by determining the average size of colonized soil patches and the average number of patches per gram of soil. The spatial distribution of 2,4-D degrader microhabitats was not affected by water flow, but there was an overall increase in colonized patch sizes after 2,4-D amendment; colonized microsamples were dispersed in the soil at low 2,4-D degrader densities and clustered in patches that were more than 0.5 mm in diameter at higher densities. During growth, spreading of 2,4-D degraders within the soil and an increase in 2,4-D degradation were observed. We hypothesized that spreading of the bacteria increased the probability of encounters with 2,4-D and resulted in better interception of the degradable substrate. This work showed that characterization of bacterial microscale spatial distribution is relevant to microbial ecology studies. It improved quantitative bacterial microhabitat description and suggested that sporadic movement of cells occurs. Furthermore, it offered perspectives for linking microbial function to the soil physicochemical environment.}, }
@article {pmid15128458, year = {2004}, author = {Jalava, J and Vaara, M and Huovinen, P}, title = {Mutation at the position 2058 of the 23S rRNA as a cause of macrolide resistance in Streptococcus pyogenes.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {3}, number = {}, pages = {5}, pmid = {15128458}, issn = {1476-0711}, abstract = {BACKGROUND: In streptococci, three macrolide resistance determinants (erm(B), erm(TR) and mef(A)) have been found. In addition, certain mutations at the ribosomal 23S RNA can cause resistance to macrolides. Mutation at the position 2058 of the 23S rRNA of the Streptococcus pyogenes as a cause of macrolide resistance has not been described before.<br><br>METHODS: Antibiotic resistance determinations for the clinical S. pyogenes strain ni4277 were done using the agar dilution technique. Macrolide resistance mechanisms were studied by PCR and sequencing. All six rRNA operons were amplified using operon-specific PCR. The PCR products were partially sequenced in order to resolve the sequences of different 23S rRNA genes.<br><br>RESULTS: One clinical isolate of S. pyogenes carrying an adenine to guanine mutation at the position 2058 of the 23S rRNA in five of the six possible rRNA genes but having no other known macrolide resistance determinants is described. The strain was highly resistant to macrolides and azalides, having erythromycin and azithromycin MICs > 256 microgram/ml. It was resistant to lincosamides (clindamycin MIC 16 microgram/ml) and also MIC values for ketolides were clearly elevated. The MIC for telithromycin was 16 microgram/ml.<br><br>CONCLUSION: In this clinical S. pyogenes strain, a mutation at the position 2058 was detected. No other macrolide resistance-causing determinants were detected. This mutation is known to cause macrolide resistance in other bacteria. We can conclude that this mutation was the most probable cause of macrolide, lincosamide and ketolide resistance in this strain.}, }
@article {pmid15116280, year = {2004}, author = {Plante, CJ and Wilde, SB}, title = {Biotic disturbance, recolonization, and early succession of bacterial assemblages in intertidal sediments.}, journal = {Microbial ecology}, volume = {48}, number = {2}, pages = {154-166}, pmid = {15116280}, issn = {0095-3628}, mesh = {Analysis of Variance ; Animals ; Bacteria/*metabolism ; DNA Primers ; DNA, Ribosomal/genetics ; *Ecosystem ; Electrophoresis ; Feces/chemistry ; Feeding Behavior/*physiology ; Geologic Sediments/*microbiology ; Invertebrates/*physiology ; Microscopy, Fluorescence ; Polymerase Chain Reaction ; Population Dynamics ; South Carolina ; }, abstract = {The role of disturbance in structuring natural microbial communities has been largely unexplored. Disturbance associated with invertebrate ingestion can reduce bacterial biomass and alter metabolic activities and compositions of bacterial assemblages in marine sediments. The primary objectives of the research presented here were to test whether ingestion by a taxonomically diverse group of deposit feeders constituted a disturbance, and to determine the mechanisms by which bacterial assemblages recover following deposit-feeder ingestion. To test the question of disturbance, we compared fresh egesta vs surficial sediments with respect to bacterial assemblage structure. In emersed intertidal sediments, microbial recovery could be due to regrowth of bacterial populations surviving gut passage or to immigration from adjacent sediments. To differentiate between these modes of recolonization we used field manipulative experiments to exclude migration by isolating freshly extruded fecal coils of three deposit-feeding species from surrounding sediments. We then followed the quantitative and qualitative recovery in egesta and sediments through time using epifluorescence microscopy and PCR-DGGE analysis of 16S rDNA. Our findings indicate that (1) the degree and nature of the disturbance to bacterial assemblages from deposit feeding varies among invertebrate taxa, (2) recovery was significant but incomplete over 3 h, and (3) recolonization of biotically disturbed sediments is dominated by immigration.}, }
@article {pmid15116279, year = {2004}, author = {Saikaly, PE and Oerther, DB}, title = {Bacterial competition in activated sludge: theoretical analysis of varying solids retention times on diversity.}, journal = {Microbial ecology}, volume = {48}, number = {2}, pages = {274-284}, pmid = {15116279}, issn = {0095-3628}, mesh = {*Bacterial Physiological Phenomena ; Biodiversity ; Competitive Behavior/*physiology ; Computer Simulation ; *Ecosystem ; *Models, Biological ; Population Dynamics ; Sewage/*microbiology ; Species Specificity ; }, abstract = {A mechanistic model for activated sludge sewage treatment was developed to predict exploitative competition of six aerobic heterotrophic bacterial species competing for three essential resources. The central hypothesis of the model is that in a multispecies/limiting resource system the number of coexisting bacterial species, N, exceeds the number of limiting resources, K, available for them. The explanation for this is that for certain species combinations, the dynamics of the competition process generate oscillations in the abundances of species, and these oscillations allow the coexistence of greater number of species than the number of limiting resources (N > K). This result is a direct contradiction of an existing activated sludge steady state competition theory, "the principle of competitive exclusion," which states that the competition process proceeds to equilibrium, allowing only N </= K species to coexist. The model was used to investigate the effect of varying solids retention times on the diversity of species using the conventional, completely mixed activated sludge configuration. The results of model simulations showed that for a certain range of solids retention times (2.28-5.66 days) the competition of six species for three essential resources produces oscillations within the structure of the bacterial community allowing for the sustained growth of more than three species on three resources.}, }
@article {pmid15107957, year = {2004}, author = {Selosse, MA and Faccio, A and Scappaticci, G and Bonfante, P}, title = {Chlorophyllous and achlorophyllous specimens of Epipactis microphylla,(Neottieae, Orchidaceae) are associated with ectomycorrhizal septomycetes, including truffles.}, journal = {Microbial ecology}, volume = {47}, number = {4}, pages = {416-426}, pmid = {15107957}, issn = {0095-3628}, mesh = {Ascomycota/genetics/*physiology/ultrastructure ; Base Sequence ; Chlorophyll/physiology ; DNA Primers ; DNA, Ribosomal/genetics ; *Ecosystem ; France ; Immunohistochemistry ; Microscopy, Electron ; Molecular Sequence Data ; Mycorrhizae/genetics/*physiology/ultrastructure ; Orchidaceae/*microbiology ; Plant Roots/cytology/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Mycoheterotrophic species (i.e., achlorophyllous plants obtaining carbon from their mycorrhizal fungi) arose many times in evolution of the Neottieae, an orchid tribe growing in forests. Moreover, chlorophyllous Neottieae species show naturally occurring achlorophyllous individuals. We investigated the fungal associates of such a member of the Neottieae, Epipactis microphylla, to understand whether their mycorrhizal fungi predispose the Neottieae to mycoheterotrophy. Root symbionts were identified by sequencing the fungal ITS of 18 individuals from three orchid populations, including achlorophyllous and young, subterranean individuals. No rhizoctonias (the usual orchid symbionts) were recovered, but 78% of investigated root pieces were colonized by Tuber spp. Other Pezizales and some Basidiomycetes were also found. Using electron microscopy, we demonstrated for the first time that ascomycetes, especially truffles, form typical orchid mycorrhizae. All identified fungi (but one) belonged to taxa forming ectomycorrhizae on tree roots, and four of them were even shown to colonize surrounding trees. This is reminiscent of mycoheterotrophic orchid species that also associate with ectomycorrhizal fungi, although with higher specificity. Subterranean and achlorophyllous E. microphylla individuals thus likely rely on tree photosynthates, and a partial mycoheterotrophy in individuals plants can be predicted. We hypothesize that replacement of rhizoctonias by ectomycorrhizal symbionts in Neottieae entails a predisposition to achlorophylly.}, }
@article {pmid15107956, year = {2004}, author = {Altmann, D and Stief, P and Amann, R and de Beer, D}, title = {Nitrification in freshwater sediments as influenced by insect larvae: quantification by microsensors and fluorescence in situ hybridization.}, journal = {Microbial ecology}, volume = {48}, number = {2}, pages = {145-153}, pmid = {15107956}, issn = {0095-3628}, mesh = {Animals ; Bacteria/*metabolism ; Chironomidae/*physiology ; Colony Count, Microbial ; Feeding Behavior/physiology ; Fresh Water ; Geologic Sediments/*analysis/*microbiology ; Germany ; In Situ Hybridization, Fluorescence ; Larva/physiology ; Nitrogen/*chemistry ; }, abstract = {Sediment-reworking macrofauna can stimulate nitrification by increasing the O(2) penetration into sediments or it can reduce nitrification by grazing on nitrifying bacteria. We investigated the influence of Chironomus riparius larvae (Insecta: Diptera) on the in situ activity, abundance, and distribution of NH4+-oxidizing (AOB) and NO2--oxidizing bacteria (NOB) in two freshwater sediments with microsensors and fluorescence in situ hybridization. In organic-poor sediment, nitrification activity was reduced by the presence of C. riparius larvae, whereas no such effect was detected in organic-rich sediment. We explain this difference with the variable larval burrowing and grazing behavior in the two sediment types: In organic-poor sediment larval activities were intense and evenly distributed across the whole sediment surface, whereas in organic-rich sediment larval activities were locally restricted to the microenvironment of animal burrows. Surprisingly, the animals did not cause any significant change of the abundance of AOB and NOB. This implies that the observed reduction of nitrification activity was not density-regulated, but rather was due to the lowered metabolic activity of the nitrifiers. Partial digestion and redeposition of particle-associated bacteria by C. riparius larvae are believed to have caused this loss of metabolic activity.}, }
@article {pmid15107955, year = {2004}, author = {Lydell, C and Dowell, L and Sikaroodi, M and Gillevet, P and Emerson, D}, title = {A population survey of members of the phylum Bacteroidetes isolated from salt marsh sediments along the east coast of the United States.}, journal = {Microbial ecology}, volume = {48}, number = {2}, pages = {263-273}, pmid = {15107955}, issn = {0095-3628}, mesh = {Bacteroidetes/enzymology/*genetics/metabolism ; Base Sequence ; *Biodiversity ; Blotting, Southern ; Cluster Analysis ; Fatty Acids/metabolism ; Genotype ; Geologic Sediments/*microbiology ; Mid-Atlantic Region ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The population diversity of cultured isolates of the phylum Bacteroidetes was investigated from salt-marsh sediments. A total of 44 isolates that belonged to this phylum were isolated either from high-dilution plates or from end-dilution most-probable-number (MPN) tubes. The majority of the isolates came from Virginia, with others isolated from salt marshes in Delaware and North Carolina. All the isolates were aerobic Gram-negative, catalase positive small rods that formed uniform colonies; most had either yellow or orange pigmentation. Riboprinting of 40 isolates revealed they were genotypically diverse, consisting of 33 different riboprint patterns; there were four riboprint groups with two or more members. The isolates could be divided into 23 different fatty acid methyl ester (FAME) profiles at the species level with 14 of the profiles being unique to single isolates. One group of 10 isolates was closely related, suggesting this group may be well adapted for life in salt marshes. Thirteen of the isolates were selected for sequencing of the small-subunit ribosomal RNA gene representing a diverse group of isolates that fell within the classes Sphingobacteria and Flavobacteria. Only one of the isolates was >97% similar at the 16S rDNA to a described species of Cytophaga marinoflava; the other isolates were 94 to 96.5% related to undescribed isolates mostly within the class Flavobacteria. There was good concordance between the FAME dendrogram and a phylogenetic tree based on comparison of 16S sequences. There were no obvious temporal or spatial distribution patterns to the isolates, suggesting that this group of bacteria is inherently diverse.}, }
@article {pmid15107954, year = {2004}, author = {Miller, CD and Hall, K and Liang, YN and Nieman, K and Sorensen, D and Issa, B and Anderson, AJ and Sims, RC}, title = {Isolation and characterization of polycyclic aromatic hydrocarbon-degrading Mycobacterium isolates from soil.}, journal = {Microbial ecology}, volume = {48}, number = {2}, pages = {230-238}, pmid = {15107954}, issn = {0095-3628}, mesh = {Base Sequence ; Biodegradation, Environmental ; Carbon Radioisotopes ; Catalase/metabolism ; Cluster Analysis ; DNA Primers ; DNA, Ribosomal/genetics ; Isoenzymes ; Microscopy, Electron ; Molecular Sequence Data ; Montana ; Mycobacterium/genetics/*metabolism/ultrastructure ; *Phylogeny ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Sequence Analysis, DNA ; *Soil Microbiology ; Species Specificity ; Superoxide Dismutase/metabolism ; }, abstract = {Bioremediation of soils contaminated with wood preservatives containing polycyclic aromatic hydrocarbons (PAHs) is desired because of their toxic, mutagenic, and carcinogenic properties. Creosote wood preservative-contaminated soils at the Champion International Superfund Site in Libby, Montana currently undergo bioremediation in a prepared-bed land treatment unit (LTU) process. Microbes isolated from these LTU soils rapidly mineralized the (14)C-labeled PAH pyrene in the LTU soil. Gram staining, electron microscopy, and 16S rDNA-sequencing revealed that three of these bacteria, JLS, KMS, and MCS, were Mycobacterium strains. The phylogeny of the 16S rDNA showed that they were distinct from other Mycobacterium isolates with PAH-degrading activities. Catalase and superoxide dismutase (SOD) isozyme profiles confirmed that each isolate was distinct from each other and from the PAH-degrading mycobacterium, Mycobacterium vanbaalenii sp. nov, isolated from a petroleum-contaminated soil. We find that dioxygenase genes nidA and nidB are present in each of the Libby Mycobacterium isolates and are adjacent to each other in the sequence nidB-nidA, an order that is unique to the PAH-degrading mycobacteria.}, }
@article {pmid15107953, year = {2004}, author = {Poerschmann, J and Spijkerman, E and Langer, U}, title = {Fatty acid patterns in Chlamydomonas sp. as a marker for nutritional regimes and temperature under extremely acidic conditions.}, journal = {Microbial ecology}, volume = {48}, number = {1}, pages = {78-89}, pmid = {15107953}, issn = {0095-3628}, mesh = {Animals ; Benzopyrans/metabolism ; Chlamydomonas/*isolation &amp; purification/*metabolism ; Chromatography, Ion Exchange ; Cold Temperature ; Culture Media ; Fatty Acids/*metabolism ; Fresh Water/analysis ; Gas Chromatography-Mass Spectrometry ; Hydrogen-Ion Concentration ; Mining ; Principal Component Analysis ; }, abstract = {Fatty acid profiles were used to characterize nutritional pathways in Chlamydomonas sp. isolated from an acidic mining lake (pH 2.7). Surprisingly, profiles of Chlamydomonas sp. grown in the lab under photoautotrophic, mixotrophic, and heterotrophic conditions at in situ deep strata lake water temperatures (8 degrees C) were very similar, polyunsaturated fatty acids including alpha-linolenic acid (18:3omega3) and 16:4omega3 along with palmitic acid (16:0) being most abundant. Therefore, heterotrophic growth of Chlamydomonas sp. at low temperatures can result in high concentrations of polyunsaturated fatty acids, as previously only described for some psychrophilic bacteria. By contrast, the cultivation of isolated Chlamydomonas sp. at 20 degrees C, reflecting surface water temperatures, provided fatty acid patterns characteristic of the nutrition strategy applied: the concentration of polyunsaturated fatty acids decreased when the growth pathway changed from photoautotrophic via mixotrophic to heterotrophic. Total fatty acid concentration also diminished in this order. Principal component analysis confirmed the significance of FA profiling to mirror nutritional pathways. Lake-water analysis revealed low concentrations of dissolved organic carbon, mainly consisting of polymeric fulvic acids that are unable to support heterotrophic growth of Chlamydomonas sp. Polymeric fulvic acids present in the deeper strata of the lake turned out to be formed in situ on the basis of organic monomers including reduced sulfur-containing ones, as revealed by thermochemolysis and pyrolysis. Growth of Chlamydomonas sp. in the deep chlorophyll maximum is therefore assumed to mainly result from photosynthesis, despite very low photon densities. Phytol-including metabolites proved to be significant biomarkers to indicate the nutritional pathway of Chlamydomonas sp. alpha, omega-Dicarboxylic acids-light-induced degradation products of unsaturated fatty acids-appeared to be good indicators of photooxidative alterations to the algal species under study.}, }
@article {pmid15105885, year = {2004}, author = {Keinänen, MM and Martikainen, PJ and Kontro, MH}, title = {Microbial community structure and biomass in developing drinking water biofilms.}, journal = {Canadian journal of microbiology}, volume = {50}, number = {3}, pages = {183-191}, doi = {10.1139/w04-005}, pmid = {15105885}, issn = {0008-4166}, mesh = {Bacteria/*growth &amp; development ; *Biodiversity ; Biofilms/*growth &amp; development ; Biomass ; *Ecosystem ; Fatty Acids/analysis/chemistry ; Fresh Water/*microbiology ; Lipopolysaccharides/analysis/chemistry ; Phospholipids/analysis/chemistry ; Time Factors ; Water Microbiology ; Water Purification/methods ; *Water Supply ; }, abstract = {Traditional techniques to study microbes, such as culturable counts, microbial biomass, or microbial activity, do not give information on the microbial ecology of drinking water systems. The aim of this study was to analyze whether the microbial community structure and biomass differed in biofilms collected from two Finnish drinking water distribution systems (A and B) receiving conventionally treated (coagulation, filtration, disinfection) surface water. Phospholipid fatty acid methyl esters (PLFAs) and lipopolysaccharide 3-hydroxy fatty acid methyl esters (LPS 3-OH-FAs) were analyzed from biofilms as a function of water residence time and development time. The microbial communities were rather stabile through the distribution systems, as water residence time had minor effects on PLFA profiles. In distribution system A, the microbial community structure in biofilms, which had developed in 6 weeks, was more complex than those grown for 23 or 40 weeks. The microbial communities between the studied distribution systems differed, possibly reflecting the differences in raw water, water purification processes, and distribution systems. The viable microbial biomass, estimated on the basis of PLFAs, increased with increasing water residence time in both distribution systems. The quantitative amount of LPS 3-OH-FAs increased with increasing development time of biofilms of distribution system B. In distribution system A, LPS 3-OH-FAs were below the detection limit.}, }
@article {pmid15094087, year = {2004}, author = {Vincent, WF and Mueller, DR and Bonilla, S}, title = {Ecosystems on ice: the microbial ecology of Markham Ice Shelf in the high Arctic.}, journal = {Cryobiology}, volume = {48}, number = {2}, pages = {103-112}, doi = {10.1016/j.cryobiol.2004.01.006}, pmid = {15094087}, issn = {0011-2240}, mesh = {Arctic Regions ; Biomass ; Chromatography, High Pressure Liquid ; Cyanobacteria/cytology/ultrastructure ; *Ecosystem ; Eukaryota/cytology/ultrastructure ; Geologic Sediments ; *Ice/analysis ; Nunavut ; Pigments, Biological/analysis ; Seawater/chemistry/*microbiology ; Temperature ; *Water Microbiology ; }, abstract = {Microbial communities occur throughout the cryosphere in a diverse range of ice-dominated habitats including snow, sea ice, glaciers, permafrost, and ice clouds. In each of these environments, organisms must be capable of surviving freeze-thaw cycles, persistent low temperatures for growth, extremes of solar radiation, and prolonged dormancy. These constraints may have been especially important during global cooling events in the past, including the Precambrian glaciations. One analogue of these early Earth conditions is the thick, landfast sea ice that occurs today at certain locations in the Arctic and Antarctic. These ice shelves contain liquid water for a brief period each summer, and support luxuriant microbial mat communities. Our recent studies of these mats on the Markham Ice Shelf (Canadian high Arctic) by high performance liquid chromatography (HPLC) showed that they contain high concentrations of chlorophylls a and b, and several carotenoids notably lutein, echinenone and beta-carotene. The largest peaks in the HPLC chromatograms were two UV-screening compounds known to be produced by cyanobacteria, scytonemin, and its decomposition product scytonemin-red. Microscopic analyses of the mats showed that they were dominated by the chlorophyte genera cf. Chlorosarcinopsis, Pleurastrum, Palmellopsis, and Bracteococcus, and cyanobacteria of the genera Nostoc, Phormidium, Leptolyngbya, and Gloeocapsa. From point transects and localized sampling we estimated a total standing stock on this ice shelf of up to 11,200 tonnes of organic matter. These observations underscore the ability of microbial communities to flourish despite the severe constraints imposed by the cryo-ecosystem environment.}, }
@article {pmid15092994, year = {2000}, author = {Romantschuk, M and Sarand, I and Petänen, T and Peltola, R and Jonsson-Vihanne, M and Koivula, T and Yrjälä, K and Haahtela, K}, title = {Means to improve the effect of in situ bioremediation of contaminated soil: an overview of novel approaches.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {107}, number = {2}, pages = {179-185}, doi = {10.1016/s0269-7491(99)00136-0}, pmid = {15092994}, issn = {0269-7491}, abstract = {Different aspects of bacterial degradation of organic contaminants in soil, and how to improve the efficiency and reproducibility is discussed in this review. Although bioremediation in principle includes the use of any type of organism in improving the condition of a contaminated site, most commonly bacteria are the degraders and other organisms, such as soil animals or plant roots, play a role in dissemination of bacteria and, indirectly, plasmids between bacteria, and in providing nutrients and co-substrates for the bacteria active in the degradation process. There are a number of different procedures that have been tested more-or-less successfully in attempts to improve reliability, cost efficiency and speed of bioremediation. The methods range from minimal intervention, such as mere monitoring of intrinsic bioremediation, through in situ introduction of nutrients and/or bacterial inocula or improvement of physico-chemical conditions, all the way to excavation followed by on site or ex situ composting in its different varieties. In the past the rule has been that more intervention (leading to higher costs) has been more reliable, but novel ideas are continuously tried out, both as a means to come up with new truly functional applications and also as a line of studies in basic soil microbial ecology. Both approaches generate valuable information needed when predicting outcome of remediation activities, evaluating environmental risks, deciding on cleaning-up approaches, etc. The emphasis of this review is to discuss some of the novel methods for which the value has not been clearly shown, but that in our view merit continued studies and efforts to make them work, separately or in combination.}, }
@article {pmid15085304, year = {2004}, author = {Detmers, J and Strauss, H and Schulte, U and Bergmann, A and Knittel, K and Kuever, J}, title = {FISH shows that Desulfotomaculum spp. are the dominating sulfate-reducing bacteria in a pristine aquifer.}, journal = {Microbial ecology}, volume = {47}, number = {3}, pages = {236-242}, pmid = {15085304}, issn = {0095-3628}, mesh = {Archaea/genetics/physiology ; Desulfotomaculum/genetics/*physiology ; *Ecosystem ; Fresh Water/chemistry/*microbiology ; Germany ; In Situ Hybridization, Fluorescence ; Likelihood Functions ; Models, Genetic ; Oligonucleotides ; *Phylogeny ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {The hydrochemistry and the microbial diversity of a pristine aquifer system near Garzweiler, Germany, were characterized. Hydrogeochemical and isotopic data indicate a recent activity of sulfate-reducing bacteria in the Tertiary marine sands. The community structure in the aquifer was studied by fluorescence in situ hybridization (FISH). Up to 7.3 x 10(5) cells/mL were detected by DAPI-staining. Bacteria (identified by the probe EUB338) were dominant, representing 51.9% of the total cell number (DAPI). Another 25.7% of total cell were affiliated with the domain Archaea as identified by the probe ARCH915. Within the domain Bacteria, the beta-Proteobacteria were most abundant (21.0% of total cell counts). Using genus-specific probes for sulfate-reducing bacteria (SRB), 2.5% of the total cells were identified as members of the genus Desulfotomaculum. This reflects the predominant role these microorganisms have been found to play in sulfate-reducing zones of aquifers at other sites. Previously, all SRB cultured from this site were from the spore-forming genera Desulfotomaculum and Desulfosporosinus.}, }
@article {pmid15085303, year = {2004}, author = {Dopson, M and Lindström, EB}, title = {Analysis of community composition during moderately thermophilic bioleaching of pyrite, arsenical pyrite, and chalcopyrite.}, journal = {Microbial ecology}, volume = {48}, number = {1}, pages = {19-28}, pmid = {15085303}, issn = {0095-3628}, mesh = {Arsenicals/metabolism ; Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Base Sequence ; Cluster Analysis ; *Coal Mining ; Copper/metabolism ; DNA Primers ; *Ecosystem ; Hot Temperature ; Iron/metabolism ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfides/metabolism ; }, abstract = {An analysis of the community composition of three previously undefined mixed cultures of moderately thermophilic bioleaching bacteria grown at 45 degrees C on pyrite, arsenical pyrite, and chalcopyrite has been carried out. The bacterial species present were identified by comparative sequence analysis of the 16S rRNA gene isolated from the bioleaching vessels and analyzed by denaturing gradient gel electrophoresis, cloning, and sequencing. The mixed cultures leached all three minerals, as shown by the increase in iron released from the mineral concentrates. The species identified from the mixed cultures during bioleaching of pyrite, arsenical pyrite, and chalcopyrite were clones closely related to Acidithiobacillus caldus C-SH12, Sulfobacillus thermosulfidooxidans AT-1, " Sulfobacillus montserratensis" L15, and an uncultured thermal soil bacterium YNP. It was also found that the same mixed culture maintained for over a year on chalcopyrite mineral selected approximately the same consortia of bacteria as the original mixed culture grown on chalcopyrite.}, }
@article {pmid15085302, year = {2004}, author = {Cinquin, C and Le Blay, G and Fliss, I and Lacroix, C}, title = {Immobilization of infant fecal microbiota and utilization in an in vitro colonic fermentation model.}, journal = {Microbial ecology}, volume = {48}, number = {1}, pages = {128-138}, pmid = {15085302}, issn = {0095-3628}, mesh = {Analysis of Variance ; Bacteria/*metabolism ; Carboxylic Acids/metabolism ; Cells, Immobilized/physiology ; Chromatography, High Pressure Liquid ; Colon/microbiology/*physiology ; Culture Media ; Feces/*microbiology ; Fermentation/physiology ; Humans ; Hydrogen-Ion Concentration ; Infant ; *Models, Biological ; }, abstract = {Bacteria isolated from infant feces were immobilized in polysaccharide gel beads (2.5% gellan gum, 0.25% xanthan gum) using a two-phase dispersion process. A 52-day continuous culture was carried out in a single-stage chemostat containing precolonized beads and fed with a medium formulated to approximate the composition of infant chyme. Different dilution rates and pH conditions were tested to simulate the proximal (PCS), transverse (TCS), and distal (DCS) colons. Immobilization preserved all nine bacterial groups tested with survival rates between 3 and 56%. After 1 week fermentation, beads were highly colonized with all populations tested (excepted Staphylococcus spp. present in low numbers), which remained stable throughout the 7.5 weeks of fermentation, with variations below 1 log unit. However, free-cell populations in the circulating liquid medium, produced by immobilized cell growth, cell-release activity from gel beads, and free-cell growth, were altered considerably by culture conditions. Compared to the stabilization period, PCS was characterized by a considerable and rapid increase in Bifidobacterium spp. concentrations (7.4 to 9.6 log CFU/mL), whereas Bifidobacterium spp., Lactobacillus spp., and Clostridium spp. concentrations decreased and Staphylococcus spp. and coliforms increased during TCS and DCS. Under pseudo-steady-state conditions, the community structure developed in the chemostat reflected the relative proportions of viable bacterial numbers and metabolites generally encountered in infant feces. This work showed that a complex microbiota such as infant fecal bacteria can be immobilized and used in a continuous in vitro intestinal fermentation model to reproduce the high bacterial concentration and bacterial diversity of the feces inoculum, at least at the genera level, with a high stability during long-term experiment.}, }
@article {pmid15085301, year = {2004}, author = {Mallet, C and Basset, M and Fonty, G and Desvilettes, C and Bourdier, G and Debroas, D}, title = {Microbial population dynamics in the sediments of a eutrophic lake (Aydat, France) and characterization of some heterotrophic bacterial isolates.}, journal = {Microbial ecology}, volume = {48}, number = {1}, pages = {66-77}, pmid = {15085301}, issn = {0095-3628}, mesh = {Anaerobiosis ; Base Sequence ; Biomass ; Carbon/metabolism ; Clostridium/cytology/*genetics/*physiology ; DNA Primers ; Fatty Acids/metabolism ; France ; Fresh Water ; Geologic Sediments/*microbiology ; Microscopy, Fluorescence ; Molecular Sequence Data ; Phospholipids/metabolism ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Temperature ; }, abstract = {The bacterial populations of anoxic sediments in a eutrophic lake (Aydat, Puy-de-Dôme-France) were studied by phospholipid fatty acid analysis (PLFA) and also by culturing heterotrophic bacteria under strictly anaerobic conditions. The mean PLFA concentrations of prokaryotes and microeukaryotes were 5.7 +/- 2.9 mgC g(-1) DS and 9.6 +/- 6.7 mgC g(-1) DS, respectively. The analysis of bacterial PLFA markers was used to determine the dynamics of the Gram-positive and Gram-negative species of anaerobic bacteria, Clostridiae, and sulfate-reducing bacteria. Throughout the sampling period the concentrations of i15:0 (from 20 nmol g(-1) DS to 130 nmol g(-1) DS), markers of Gram-positive bacteria, were higher than those for Gram-negative bacteria. The dynamics of Clostridiae (Cy15:0) paralleled those of sulfate-reducing bacteria that were marked by i17:1omega7. Partial 16S rDNA sequencing and the physiological study of the various fermenting strains, whose abundance in the superficial sediment layer was 1.1 +/- 0.4 x 10(6) cells mL(-1), showed that all the isolates belonged to the Clostridiae and related taxa (Lactosphaera pasteurii, Clostridium vincentii, C. butyricum, C. algidixylanolyticum, C. puniceum, C. lituseburense, and C. gasigenes). All the isolates were capable of metabolizing a wide range of organic substrates.}, }
@article {pmid15085300, year = {2004}, author = {Gentry, TJ and Wang, G and Rensing, C and Pepper, IL}, title = {Chlorobenzoate-degrading bacteria in similar pristine soils exhibit different community structures and population dynamics in response to anthropogenic 2-, 3-, and 4-chlorobenzoate levels.}, journal = {Microbial ecology}, volume = {48}, number = {1}, pages = {90-102}, pmid = {15085300}, issn = {0095-3628}, support = {5 P42 ES04940-09/ES/NIEHS NIH HHS/United States ; }, mesh = {Arizona ; Bacteria/genetics/*metabolism ; Base Sequence ; Biodegradation, Environmental ; Blotting, Southern ; Chlorobenzoates/*metabolism ; Cluster Analysis ; DNA Fingerprinting ; DNA Primers ; *Ecosystem ; Molecular Sequence Data ; *Phylogeny ; Plasmids/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {A study was conducted to determine the diversity of 2-, 3-, and 4-chlorobenzoate (CB) degraders in two pristine soils with similar physical and chemical characteristics. Surface soils were collected from forested sites and amended with 500 microg of 2-, 3-, or 4-CB g(-1) soil. The CB levels and degrader numbers were monitored throughout the study. Degraders were isolated, grouped by DNA fingerprints, identified via 16S rDNA sequences, and screened for plasmids. The CB genes in selected degraders were isolated and/or sequenced. In the Madera soil, 2-CB and 4-CB degraded within 11 and 42 d, respectively, but 3-CB did not degrade. In contrast, 3-CB and 4-CB degraded in the Oversite soil within 14 and 28 d, respectively, while 2-CB did not degrade. Approximately 10(7) CFU g(-1) of degraders were detected in the Madera soil with 2-CB, and the Oversite soil with 3- and 4-CB. No degraders were detected in the Madera soil with 4-CB even though the 4-CB degraded. Nearly all of the 2-CB degraders isolated from the Madera soil were identified as a Burkholderia sp. containing chromosomally encoded degradative genes. In contrast, several different 3- and 4-CB degraders were isolated from the Oversite soil, and their populations changed as CB degradation progressed. Most of these 3-CB degraders were identified as Burkholderia spp. while the majority of 4-CB degraders were identified as Bradyrhizobium spp. Several of the 3-CB degraders contained the degradative genes on large plasmids, and there was variation between the plasmids in different isolates. When a fresh sample of Madera soil was amended with 50, 100, or 200 microg 3-CB g(-1), 3-CB degradation occurred, suggesting that 500 microg 3-CB g(-1) was toxic to the degraders. Also, different 3-CB degraders were isolated from the Madera soil at each of the three lower levels of 3-CB. No 2-CB degradation was detected in the Oversite soil even at lower 2-CB levels. These results indicate that the development of 2-, 3-, and 4-CB degrader populations is site-specific and that 2-, 3-, and 4-CB are degraded by different bacterial populations in pristine soils. These results also imply that the microbial ecology of two soils that develop under similar biotic and abiotic environments can be quite different.}, }
@article {pmid15085299, year = {2004}, author = {Leckie, SE and Prescott, CE and Grayston, SJ and Neufeld, JD and Mohn, WW}, title = {Characterization of humus microbial communities in adjacent forest types that differ in nitrogen availability.}, journal = {Microbial ecology}, volume = {48}, number = {1}, pages = {29-40}, pmid = {15085299}, issn = {0095-3628}, mesh = {Bacteria/genetics ; Biomass ; British Columbia ; Carbon/metabolism ; DNA Primers ; DNA, Ribosomal Spacer/genetics ; *Ecosystem ; Electrophoresis ; Fungi/genetics ; Nitrogen/*metabolism ; Phospholipids/metabolism ; *Soil ; *Soil Microbiology ; Trees/*microbiology ; }, abstract = {To address the link between soil microbial community composition and soil processes, we investigated the microbial communities in forest floors of two forest types that differ substantially in nitrogen availability. Cedar-hemlock (CH) and hemlock-amabilis fir (HA) forests are both common on northern Vancouver Island, B.C., occurring adjacently across the landscape. CH forest floors have low nitrogen availability and HA high nitrogen availability. Total microbial biomass was assessed using chloroform fumigation-extraction and community composition was assessed using several cultivation-independent approaches: denaturing gradient gel electrophoresis (DGGE) of the bacterial communities, ribosomal intergenic spacer analysis (RISA) of the bacterial and fungal communities, and phospholipid fatty acid (PLFA) profiles of the whole microbial community. We did not detect differences in the bacterial communities of each forest type using DGGE and RISA, but differences in the fungal communities were detected using RISA. PLFA analysis detected subtle differences in overall composition of the microbial community between the forest types, as well as in particular groups of organisms. Fungal PLFAs were more abundant in the nitrogen-poor CH forests. Bacteria were proportionally more abundant in HA forests than CH in the lower humus layer, and Gram-positive bacteria were proportionally more abundant in HA forests irrespective of layer. Bacterial and fungal communities were distinct in the F, upper humus, and lower humus layers of the forest floor and total biomass decreased in deeper layers. These results indicate that there are distinct patterns in forest floor microbial community composition at the landscape scale, which may be important for understanding nutrient availability to forest vegetation.}, }
@article {pmid15085298, year = {2004}, author = {Mummey, DL and Stahl, PD}, title = {Analysis of soil whole- and inner-microaggregate bacterial communities.}, journal = {Microbial ecology}, volume = {48}, number = {1}, pages = {41-50}, pmid = {15085298}, issn = {0095-3628}, mesh = {Actinobacteria/*genetics ; Base Sequence ; Cluster Analysis ; Coal Mining ; DNA Primers ; *Ecosystem ; Evolution, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Photochemistry ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/*analysis ; *Soil Microbiology ; Ultraviolet Rays ; Wyoming ; }, abstract = {Although soil structure largely determines energy flows and the distribution and composition of soil microhabitats, little is known about how microbial community composition is influenced by soil structural characteristics and organic matter compartmentalization dynamics. A UV irradiation-based procedure was developed to specifically isolate inner-microaggregate microbial communities, thus providing the means to analyze these communities in relation to their environment. Whole- and inner-microaggregate fractions of undisturbed soil and soils reclaimed after disturbance by surface coal mining were analyzed using 16S rDNA terminal restriction fragment polymorphism (T-RFLP) and sequence analyses to determine salient bacterial community structural characteristics. We hypothesized that inner-microaggregate environments select for definable microbial communities and that, due to their sequestered environment, inner-microaggregate communities would not be significantly impacted by disturbance. However, T-RFLP analysis indicated distinct differences between bacterial populations of inner-microaggregates of undisturbed and reclaimed soils. While both undisturbed and reclaimed inner-microaggregate bacterial communities were found dominated by Actinobacteria, undisturbed soils contained only Actinobacteridae, while in inner-microaggregates of reclaimed soils Rubrobacteridae predominate. Spatial stratification of division-level lineages within microaggregates was also evidenced, with Proteobacteria clones being prevalent in libraries derived from whole microaggregates. The fractionation methods employed in this study therefore represent a valuable tool for defining relationships between biodiversity and soil structure.}, }
@article {pmid15073324, year = {2004}, author = {Horn, M and Collingro, A and Schmitz-Esser, S and Beier, CL and Purkhold, U and Fartmann, B and Brandt, P and Nyakatura, GJ and Droege, M and Frishman, D and Rattei, T and Mewes, HW and Wagner, M}, title = {Illuminating the evolutionary history of chlamydiae.}, journal = {Science (New York, N.Y.)}, volume = {304}, number = {5671}, pages = {728-730}, doi = {10.1126/science.1096330}, pmid = {15073324}, issn = {1095-9203}, mesh = {Acanthamoeba/microbiology ; Animals ; Bacterial Proteins/analysis/genetics/metabolism ; *Biological Evolution ; Cell Membrane/chemistry ; Cell Wall/chemistry ; Chlamydia/classification/genetics/metabolism/pathogenicity ; Chlamydiales/*classification/*genetics/metabolism/pathogenicity ; Chlamydophila/classification/genetics/metabolism/pathogenicity ; Electron Transport ; Gene Order ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Bacterial ; Molecular Sequence Data ; Nucleotide Transport Proteins/metabolism ; Phylogeny ; Symbiosis ; Virulence ; Virulence Factors/genetics/metabolism ; }, abstract = {Chlamydiae are the major cause of preventable blindness and sexually transmitted disease. Genome analysis of a chlamydia-related symbiont of free-living amoebae revealed that it is twice as large as any of the pathogenic chlamydiae and had few signs of recent lateral gene acquisition. We showed that about 700 million years ago the last common ancestor of pathogenic and symbiotic chlamydiae was already adapted to intracellular survival in early eukaryotes and contained many virulence factors found in modern pathogenic chlamydiae, including a type III secretion system. Ancient chlamydiae appear to be the originators of mechanisms for the exploitation of eukaryotic cells.}, }
@article {pmid15072075, year = {2004}, author = {Remold, SK and Lenski, RE}, title = {Pervasive joint influence of epistasis and plasticity on mutational effects in Escherichia coli.}, journal = {Nature genetics}, volume = {36}, number = {4}, pages = {423-426}, doi = {10.1038/ng1324}, pmid = {15072075}, issn = {1061-4036}, mesh = {*Epistasis, Genetic ; Escherichia coli/*genetics ; Mutagenesis, Insertional ; }, abstract = {The effects of mutations on phenotype and fitness may depend on the environment (phenotypic plasticity), other mutations (genetic epistasis) or both. Here we examine the fitness effects of 18 random insertion mutations in E. coli in two resource environments and five genetic backgrounds. We tested each mutation for plasticity and epistasis by comparing its fitness effects across these ecological and genetic contexts. Some mutations had no measurable effect in any of these contexts. None of the mutations had effects on phenotypic plasticity that were independent of genetic background. However, half the mutations had epistatic interactions such that their effects differed among genetic backgrounds, usually in an environment-dependent manner. Also, the pattern of mutational effects across backgrounds indicated that epistasis had been shaped primarily by unique events in the evolutionary history of a population rather than by repeatable events associated with shared environmental history.}, }
@article {pmid15070763, year = {2004}, author = {Rawls, JF and Samuel, BS and Gordon, JI}, title = {Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {13}, pages = {4596-4601}, pmid = {15070763}, issn = {0027-8424}, support = {DK62675/DK/NIDDK NIH HHS/United States ; R01 DK030292/DK/NIDDK NIH HHS/United States ; DK30292/DK/NIDDK NIH HHS/United States ; F32 DK062675/DK/NIDDK NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; }, mesh = {Air Sacs/microbiology ; Animals ; *Biological Evolution ; Digestive System/*microbiology ; Epithelial Cells/cytology/immunology ; Fisheries ; Germ-Free Life ; Intestinal Mucosa/microbiology ; Intestines/*microbiology ; Mammals/microbiology ; Molecular Sequence Data ; Transcription, Genetic ; Zebrafish/*microbiology ; }, abstract = {Animals have developed the means for supporting complex and dynamic consortia of microorganisms during their life cycle. A transcendent view of vertebrate biology therefore requires an understanding of the contributions of these indigenous microbial communities to host development and adult physiology. These contributions are most obvious in the gut, where studies of gnotobiotic mice have disclosed that the microbiota affects a wide range of biological processes, including nutrient processing and absorption, development of the mucosal immune system, angiogenesis, and epithelial renewal. The zebrafish (Danio rerio) provides an opportunity to investigate the molecular mechanisms underlying these interactions through genetic and chemical screens that take advantage of its transparency during larval and juvenile stages. Therefore, we developed methods for producing and rearing germ-free zebrafish through late juvenile stages. DNA microarray comparisons of gene expression in the digestive tracts of 6 days post fertilization germ-free, conventionalized, and conventionally raised zebrafish revealed 212 genes regulated by the microbiota, and 59 responses that are conserved in the mouse intestine, including those involved in stimulation of epithelial proliferation, promotion of nutrient metabolism, and innate immune responses. The microbial ecology of the digestive tracts of conventionally raised and conventionalized zebrafish was characterized by sequencing libraries of bacterial 16S rDNA amplicons. Colonization of germ-free zebrafish with individual members of its microbiota revealed the bacterial species specificity of selected host responses. Together, these studies establish gnotobiotic zebrafish as a useful model for dissecting the molecular foundations of host-microbial interactions in the vertebrate digestive tract.}, }
@article {pmid15068024, year = {2004}, author = {Zechner, EL and Bailey, MJ}, title = {The Horizontal Gene Pool: an ESF workshop summary.}, journal = {Plasmid}, volume = {51}, number = {2}, pages = {67-74}, doi = {10.1016/j.plasmid.2004.01.002}, pmid = {15068024}, issn = {0147-619X}, mesh = {Bacteria/*genetics ; Gene Pool ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Interspersed Repetitive Sequences/*genetics ; Selection, Genetic ; }, abstract = {The European Science Foundation (ESF) funds a limited number of exploratory workshops each year that enable scientists to meet and develop plans for a program of integrated research which would benefit from a coordinated European effort. In summer 2003, the Standing Committee for Life and Environmental Sciences (LESC) sponsored such a workshop called The Horizontal Gene Pool: The Functional Role of Mobile Genetic Information--How Bacteria Perceive, Sample, and Utilize Genetic Elements in evolution and Local Adaptation. The workshop took place at St. Catherine's College, Oxford, UK. Its purpose was to identify how recent advances in the application of genomics and microbial ecology can be harnessed to determine the genetic mechanisms that underpin the biological role of the horizontal gene pool. Scientific excellence at the workshop was contributed by senior scientists and young investigators from research institutes located in nine European countries.}, }
@article {pmid15066834, year = {2004}, author = {Skovhus, TL and Ramsing, NB and Holmström, C and Kjelleberg, S and Dahllöf, I}, title = {Real-time quantitative PCR for assessment of abundance of Pseudoalteromonas species in marine samples.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {4}, pages = {2373-2382}, pmid = {15066834}, issn = {0099-2240}, mesh = {Animals ; Base Sequence ; Chlorophyta/microbiology ; Ciona intestinalis/microbiology ; DNA Primers/genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; Denmark ; Fresh Water/microbiology ; Genes, Bacterial ; *Marine Biology ; Phylogeny ; Polymerase Chain Reaction/*methods ; Pseudoalteromonas/classification/*genetics/*isolation &amp; purification ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Ulva/microbiology ; }, abstract = {A real-time quantitative PCR (RTQ-PCR) method for measuring the abundance of Pseudoalteromonas species in marine samples is presented. PCR primers targeting a Pseudoalteromonas-specific region of the 16S rRNA gene were tested at three different levels using database searches (in silico), a selection of pure cultures (in vitro), and a combined denaturing gradient gel electrophoresis and cloning approach on environmental DNA (in situ). The RTQ-PCR method allowed for the detection of SYBR Green fluorescence from double-stranded DNA over a linear range spanning six orders of magnitude. The detection limit was determined as 1.4 fg of target DNA (1,000 gene copies) measured in the presence of 20 ng of nontarget DNA from salmon testes. In this study, we discuss the importance of robust post-PCR analyses to overcome pitfalls in RTQ-PCR when samples from different complex marine habitats are analyzed and compared on a nonroutine basis. Representatives of the genus Pseudoalteromonas were detected in samples from all investigated habitats, suggesting a widespread distribution of this genus across many marine habitats (e.g., seawater, rocks, macroalgae, and marine animals). Three sample types were analyzed by RTQ-PCR to determine the relative abundance of Pseudoalteromonas ribosomal DNA (rDNA) compared to the total abundance of eubacterial rDNA. The rDNA fractions of Pseudoalteromonas compared to all Eubacteria were 1.55% on the green alga Ulva lactuca, 0.10% on the tunicate Ciona intestinalis, and 0.06% on the green alga Ulvaria fusca.}, }
@article {pmid15066828, year = {2004}, author = {Feris, KP and Ramsey, PW and Frazar, C and Rillig, M and Moore, JN and Gannon, JE and Holben, WE}, title = {Seasonal dynamics of shallow-hyporheic-zone microbial community structure along a heavy-metal contamination gradient.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {4}, pages = {2323-2331}, pmid = {15066828}, issn = {0099-2240}, mesh = {Base Sequence ; DNA Primers/genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; *Ecosystem ; Fresh Water/*microbiology ; Geologic Sediments/analysis/microbiology ; Metals, Heavy/*analysis ; Montana ; Polymerase Chain Reaction ; Seasons ; Water Pollutants, Chemical/*analysis ; }, abstract = {Heavy metals contaminate numerous freshwater streams and rivers worldwide. Previous work by this group demonstrated a relationship between the structure of hyporheic microbial communities and the fluvial deposition of heavy metals along a contamination gradient during the fall season. Seasonal variation has been documented in microbial communities in numerous terrestrial and aquatic environments, including the hyporheic zone. The current study was designed to assess whether relationships between hyporheic microbial community structure and heavy-metal contamination vary seasonally by monitoring community structure along a heavy-metal contamination gradient for more than a year. No relationship between total bacterial abundance and heavy metals was observed (R(2) = 0.02, P = 0.83). However, denaturing gradient gel electrophoresis pattern analysis indicated a strong and consistent linear relationship between the difference in microbial community composition (populations present) and the difference in the heavy metal content of hyporheic sediments throughout the year (R(2) = 0.58, P < 0.001). Correlations between heavy-metal contamination and the abundance of four specific phylogenetic groups (most closely related to the alpha, beta, and gamma-proteobacteria and cyanobacteria) were apparent only during the fall and early winter, when the majority of organic matter is deposited into regional streams. These seasonal data suggest that the abundance of susceptible populations responds to heavy metals primarily during seasons when the potential for growth is highest.}, }
@article {pmid15066821, year = {2004}, author = {Holben, WE and Feris, KP and Kettunen, A and Apajalahti, JH}, title = {GC fractionation enhances microbial community diversity assessment and detection of minority populations of bacteria by denaturing gradient gel electrophoresis.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {4}, pages = {2263-2270}, pmid = {15066821}, issn = {0099-2240}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacteriological Techniques ; Chickens ; Cloning, Molecular ; DNA, Bacterial/genetics/isolation &amp; purification ; Ecology/methods ; *Ecosystem ; Electrophoresis, Polyacrylamide Gel/*methods ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Effectively and accurately assessing total microbial community diversity is one of the primary challenges in modern microbial ecology. This is particularly true with regard to the detection and characterization of unculturable populations and those present only in low abundance. We report a novel strategy, GC fractionation combined with denaturing gradient gel electrophoresis (GC-DGGE), which combines mechanistically different community analysis approaches to enhance assessment of microbial community diversity and detection of minority populations of microbes. This approach employs GC fractionation as an initial step to reduce the complexity of the community in each fraction. This reduced complexity facilitates subsequent detection of diversity in individual fractions. DGGE analysis of individual fractions revealed bands that were undetected or only poorly represented when total bacterial community DNA was analyzed. Also, directed cloning and sequencing of individual bands from DGGE lanes corresponding to individual G+C fractions allowed detection of numerous phylotypes that were not recovered using a traditional random cloning and sequencing approach.}, }
@article {pmid15063069, year = {2004}, author = {Flood, JA and Tripp, TJ and Davis, CC and Hill, DR and Schlievert, PM}, title = {A toroid model for in vitro investigations of toxic shock syndrome toxin-1 production.}, journal = {Journal of microbiological methods}, volume = {57}, number = {2}, pages = {283-288}, doi = {10.1016/j.mimet.2004.01.005}, pmid = {15063069}, issn = {0167-7012}, mesh = {Bacterial Toxins/*biosynthesis ; Enterotoxins/*biosynthesis ; Female ; Humans ; Menstruation ; *Models, Biological ; Staphylococcus aureus/*growth &amp; development/*metabolism ; Superantigens/*biosynthesis ; Tampons, Surgical/microbiology ; Vagina/microbiology ; }, abstract = {Human behaviours and consumer products may affect vaginal microbial ecology, thereby influencing women's health. Relevant experimentation systems are needed to understand such possible links. Here, we describe the development of a practical semi-solid in vitro model to assess the effects of interactions between vaginal environment and the presence of tampons, on bacterial communities, including the production of toxic shock syndrome toxin-1 (TSST-1) by Staphylococcus aureus.}, }
@article {pmid15063068, year = {2004}, author = {Janse, I and Bok, J and Zwart, G}, title = {A simple remedy against artifactual double bands in denaturing gradient gel electrophoresis.}, journal = {Journal of microbiological methods}, volume = {57}, number = {2}, pages = {279-281}, doi = {10.1016/j.mimet.2003.12.006}, pmid = {15063068}, issn = {0167-7012}, mesh = {Artifacts ; Cyanobacteria/genetics/isolation &amp; purification ; DNA Fingerprinting/*methods ; DNA, Bacterial/*analysis ; Electrophoresis, Polyacrylamide Gel/*methods ; False Positive Reactions ; Nucleic Acid Denaturation ; Polymerase Chain Reaction/*methods ; *Water Microbiology ; }, abstract = {Denaturant gradient gel electrophoresis (DGGE) is a widely used method for mutation analysis and for studies of microbial diversity. Particular combinations of target gene fragments and primers may give rise to erroneous DGGE profiles. We report on a very straightforward means to eliminate the artifactual 'double bands' that can be encountered in several applications.}, }
@article {pmid15063066, year = {2004}, author = {Mumy, KL and Findlay, RH}, title = {Convenient determination of DNA extraction efficiency using an external DNA recovery standard and quantitative-competitive PCR.}, journal = {Journal of microbiological methods}, volume = {57}, number = {2}, pages = {259-268}, doi = {10.1016/j.mimet.2004.01.013}, pmid = {15063066}, issn = {0167-7012}, mesh = {Bacteriophage lambda/genetics ; DNA/analysis/*isolation &amp; purification ; DNA, Bacterial/analysis/isolation &amp; purification ; DNA, Viral/analysis/isolation &amp; purification ; Electrophoresis, Agar Gel ; Environmental Microbiology ; Geologic Sediments/chemistry/*microbiology ; Plasmids ; Polycyclic Aromatic Hydrocarbons ; *Polymerase Chain Reaction/methods/standards ; Reference Standards ; Sensitivity and Specificity ; Water Pollution, Chemical ; }, abstract = {Molecular biology techniques have advanced the field of microbial ecology through the analysis of nucleic acids. Most techniques that use DNA or RNA require their extraction from environmental matrices, which can be tedious and inefficient. While a number of extraction methods, both laboratory-based and commercially available, have been developed, none of these include a convenient method to determine extraction efficiency. We have developed an external DNA recovery standard, Lambda DNA (target DNA) contained within pBR322, allowing routine determinations of DNA recovery efficiency. Target DNA was added to sediments as whole cells, total DNA extracted using commercial DNA extraction/purification kits and the amount of target DNA recovered quantified by quantitative-competitive PCR (QC-PCR). Three commercially available kits (UltraClean Soil DNA, FastDNA SPIN and Soil Master DNA Extraction) were evaluated for recovery efficiency. Recoveries for the three kits ranged from undetectable to 43.3% with average recoveries of 14.9+/-16.0%, 28.3+/-10.5% and 2.4+/-0.1% (UltraClean, FastDNA and Soil Master, respectively). Quantification of target DNA proved robust in sediments heavily polluted with polycyclic aromatic hydrocarbons and the external recovery standard could be detected following extraction and amplification from as few as 1 x 10(3) cells added to 0.5 g sediment (wet weight). The external DNA recovery standard was also added directly to the sediment as purified plasmid DNA prior to extraction. It was recovered with similar efficiency as when added as whole cells, suggesting its usefulness in estimating DNA recovery in ribosomal DNA studies. These results show that, while the commercial kits offer expedited sample processing, the extraction efficiencies vary on a sample-by-sample basis and were <100%. Therefore, quantitative DNA studies require an estimation of DNA recovery.}, }
@article {pmid15062822, year = {2004}, author = {Aiyuk, S and Verstraete, W}, title = {Sedimentological evolution in an UASB treating SYNTHES, a new representative synthetic sewage, at low loading rates.}, journal = {Bioresource technology}, volume = {93}, number = {3}, pages = {269-278}, doi = {10.1016/j.biortech.2003.11.006}, pmid = {15062822}, issn = {0960-8524}, mesh = {Bacteria, Anaerobic/*metabolism ; Biomass ; *Bioreactors ; Hydrogen-Ion Concentration ; Kinetics ; Methane/metabolism ; Oxygen/metabolism ; Particle Size ; Refuse Disposal/*methods ; Sewage/*chemistry ; Temperature ; Time Factors ; }, abstract = {The changes in the sedimentological attributes of the sludge bed in an upflow anaerobic sludge blanket (UASB) reactor fed with a low-strength wastewater mimicking raw domestic sewage were assessed in this study. The reactor was inoculated with 250 ml of granular sludge from a full-scale UASB reactor. The organic loading rate (OLR) varied from 1 to 2 g COD/ld. During the half-year long study, the reactor was operated at hydraulic retention times (HRTs) of 4.8 and 10 h, at 33 degrees C. Sludge sedimentology showed that the original granular sludge experienced serious instability and disintegration, leading to a much finer final grain assemblage, mainly due to substrate transfer limitation and cell starvation at the interior of larger granules. With time, the size uniformity tended to decrease, sphericity tended to increase, the skewness of the granule size distribution became negative, and the kurtosis became peaked and leptokurtic. In spite of the observed size reduction, reactor efficiency increased to a CODtotal removal of 96%. Biomass (sludge) yield was 0.012 g VS/g COD removed. The CH4 content of the biogas was high (up to 96%). This study thus highlights the treatment of a new type of wastewater with the deployment of the UASB reactor. It also reports the evolutionary trend of the biomass particle size distribution, making reference to a classic sedimentological appraisal.}, }
@article {pmid15060036, year = {2004}, author = {Bakermans, C and Nealson, KH}, title = {Relationship of critical temperature to macromolecular synthesis and growth yield in Psychrobacter cryopegella.}, journal = {Journal of bacteriology}, volume = {186}, number = {8}, pages = {2340-2345}, pmid = {15060036}, issn = {0021-9193}, mesh = {Bacterial Proteins/biosynthesis ; DNA, Bacterial/biosynthesis ; Psychrobacter/*growth &amp; development/*metabolism ; RNA, Bacterial/biosynthesis ; *Temperature ; }, abstract = {Most microorganisms isolated from low-temperature environments (below 4 degrees C) are eury-, not steno-, psychrophiles. While psychrophiles maximize or maintain growth yield at low temperatures to compensate for low growth rate, the mechanisms involved remain unknown, as does the strategy used by eurypsychrophiles to survive wide ranges of temperatures that include subzero temperatures. Our studies involve the eurypsychrophilic bacterium Psychrobacter cryopegella, which was isolated from a briny water lens within Siberian permafrost, where the temperature is -12 degrees C. P. cryopegella is capable of reproducing from -10 to 28 degrees C, with its maximum growth rate at 22 degrees C. We examined the temperature dependence of growth rate, growth yield, and macromolecular (DNA, RNA, and protein) synthesis rates for P. cryopegella. Below 22 degrees C, the growth of P. cryopegella was separated into two domains at the critical temperature (T(critical) = 4 degrees C). RNA, protein, and DNA synthesis rates decreased exponentially with decreasing temperatures. Only the temperature dependence of the DNA synthesis rate changed at T(critical). When normalized to growth rate, RNA and protein synthesis reached a minimum at T(critical), while DNA synthesis remained constant over the entire temperature range. Growth yield peaked at about T(critical) and declined rapidly as temperature decreased further. Similar to some stenopsychrophiles, P. cryopegella maximized growth yield at low temperatures and did so by streamlining growth processes at T(critical). Identifying the specific processes which result in T(critical) will be vital to understanding both low-temperature growth and growth over a wide range of temperatures.}, }
@article {pmid15054677, year = {2004}, author = {Pladdies, T and Babenzien, HD and Cypionka, H}, title = {Distribution of Nevskia ramosa and other rosette-forming neustonic bacteria.}, journal = {Microbial ecology}, volume = {47}, number = {3}, pages = {218-223}, pmid = {15054677}, issn = {0095-3628}, mesh = {*Biofilms ; DNA Fingerprinting ; Demography ; Europe ; In Situ Hybridization, Fluorescence ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology ; Species Specificity ; *Water Microbiology ; Weather ; Xanthomonadaceae/*cytology/*genetics ; }, abstract = {Samples from 27 natural and artificial aquatic environments were analyzed for the presence of rosette-forming bacteria by a combined cultivation and molecular biological approach. Rosette-forming bacteria developed in 20 enrichment cultures with ammonia-free medium under air. Three morphotypes could be distinguished. The most abundant type I resembled Nevskia ramosa and formed hydrophobic, flat, and dichotomously branching rosettes. Type II rosettes were three-dimensional and were observed in 10 enrichments, often together with those of type I. These rosettes were hydrophilic indicating life in the hyponeuston underneath the air-water interface. Rosettes of a third type consisted of hydrophilic slime stalks that were excreted at the cell poles and were observed in only one sample. Using fluorescence in situ hybridization (FISH) with the Nevskia-specific probes NEV177 and NEV656, the presence of Nevskia ramosa was demonstrated in exactly those samples that showed type I rosettes. In a series of most-probable-number experiments, during a calm and sunny weather period 430,000 Nevskia-like bacteria per mL were found in surface samples, while during rainy weather and within the water body the numbers were lower by several orders of magnitude. Five pure cultures isolated from various enrichments were characterized in detail. The two isolates forming type I rosettes were identified as Nevskia ramosa by 16S rDNA analysis. However, comparison by genomic fingerprinting (ERIC-PCR) revealed differences between the two isolates and previously characterized strains. The 16S rDNA of two isolates forming type II rosettes showed 97.6% similarity to that of Pseudomonas fluorescens. The closest relative of the isolate forming type III rosettes was Sphingomonas parapaucimobilis (96.4% sequence similarity of the 16S rRNA sequence). All isolates grew homogeneously submersed if ammonia was added to the medium. Our results indicate that Nevskia ramosa is a widely distributed epineustonic bacterium, which can specifically be deleted by its flat and hydrophobic rosettes on ammonia-free media.}, }
@article {pmid15054676, year = {2004}, author = {Tindall, BJ}, title = {Prokaryotic diversity in the Antarctic: the tip of the iceberg.}, journal = {Microbial ecology}, volume = {47}, number = {3}, pages = {271-283}, pmid = {15054676}, issn = {0095-3628}, mesh = {Antarctic Regions ; Bacteria/*genetics/*growth &amp; development ; *Biodiversity ; *Environment ; Geography ; Species Specificity ; }, abstract = {In contrast to the rather limited diversity of plants and animals to be found in the Antarctic, the microbial diversity of this continent has been shown to be "surprisingly" diverse. Apparently barren soil and rock landscapes, as well as the numerous and diverse lakes found at the edges of the continent, harbor a range of prokaryotes which indicate that the extremely low temperatures which prevail seasonally are no obstacle to microbial colonization. Both direct cultivation methods and modern molecular genetic methods have contributed to our understanding of the range of organisms to be found. Cultivation based studies are often hampered by constraints inherent in the methods selected for the isolation of organisms. Molecular-based approaches do not suffer from the same cultivation-based biases, but other problems need to be taken into consideration. It has rarely been possible to combine both techniques in a single study, nor has it usually been possible to take the results and conclusions drawn from the study of one environment and apply this knowledge to a further series of experiments on the same environment. The Antarctic may be considered to be a geographically well isolated area to study. Comparison with other environments that may also be "isolated" from their surroundings (i.e., hot springs or highly saline lakes) allows parallels to be drawn. The conclusions drawn provide important insights into the way the Antarctic may have been colonized and the microbiota diversified. Much work still needs to be done beyond the simple task of making an inventory. The functioning of complex communities, such as mat systems, requires an understanding of the ecology of the systems, not only at the level of the whole system, but also the role of localized environments within that system. Perhaps these ecosystems have, in the absence of plant and animal communities, a role to play in the monitoring of polar climate change. The information available at present clearly indicates that the Antarctic is deserving of further study at the microbial level.}, }
@article {pmid15054675, year = {2004}, author = {Labrenz, M}, title = {Living Science: Peter Hirsch Celebrates his 75(th) Birthday.}, journal = {Microbial ecology}, volume = {47}, number = {3}, pages = {197-199}, doi = {10.1007/s00248-003-1049-0}, pmid = {15054675}, issn = {1432-184X}, }
@article {pmid15052572, year = {2004}, author = {Sturt, HF and Summons, RE and Smith, K and Elvert, M and Hinrichs, KU}, title = {Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry--new biomarkers for biogeochemistry and microbial ecology.}, journal = {Rapid communications in mass spectrometry : RCM}, volume = {18}, number = {6}, pages = {617-628}, doi = {10.1002/rcm.1378}, pmid = {15052572}, issn = {0951-4198}, mesh = {Biomarkers/analysis ; Chromatography, High Pressure Liquid/*methods ; Ecology ; *Ecosystem ; Environmental Monitoring ; Geologic Sediments/*chemistry ; Geology/methods ; Membrane Lipids/*analysis ; Microbiology ; Spectrometry, Mass, Electrospray Ionization/*methods ; Sulfolobales/*chemistry/metabolism ; }, abstract = {Lipids from prokaryotic cell membranes can serve as sources of information on the biogeochemistry and microbial ecology of natural ecosystems. Traditionally, apolar derivatives of the intact polar membrane molecules, e.g., fatty acids, have been the major target of lipid-based biogeochemical studies. However, when still intact, i.e., as glycerol esters and ethers with attached polar headgroups, membrane lipids are diagnostic for living prokaryotes, which makes them excellent biomarkers for the study of in situ microbial processes in geological systems such as sediments or soils. Intact polar lipids (IPLs) are attractive analytical targets because they are taxonomically more specific than their apolar derivatives and avoid exclusion of signals from prokaryotes that primarily build their membranes with ether-bound lipids such as archaea and some bacteria. Here we report results from analyses of IPLs in pure cultures of biogeochemically relevant prokaryotes and marine sediments by high-performance liquid chromatography/electrospray ionization ion-trap mass spectrometry (HPLC/ESI-IT-MSn). This technique is suitable for screening of biomass and environmental samples for distinctive taxonomic structural features such as distribution of polar lipid headgroups, types of bonds between alkyl moiety and glycerol backbone, and the chain length and degree of unsaturation in the alkyl moieties. We present analytical protocols to decipher structural information from mass spectral data. The IPL contents in selected archaeal and bacterial species are diverse and qualify as molecular fingerprints. Applied to marine sediments, the approach provided detailed information on the dominant microbial groups. The IPLs from bacterial members of anaerobic methanotrophic communities in surface sediments at Hydrate Ridge resemble those found in Desulfosarcina variabilis. The presence of dietherglycerophospholipids, however, suggests the presence of other bacteria possibly affiliated with the deepest phylogenetic branches in the tree of life. Sediments from approximately 90 m below the seafloor on the Peruvian continental margin are dominated by intact archaeal tetraethers with glycosidically bound hexoses as headgroups, consistent with a significant fraction of the community being archaea. Additional calditol-based tetraethers imply that the sedimentary archaea are taxonomically linked to the crenarchaeal Sulfolobales.}, }
@article {pmid15049919, year = {2004}, author = {Roose-Amsaleg, C and Brygoo, Y and Harry, M}, title = {Ascomycete diversity in soil-feeding termite nests and soils from a tropical rainforest.}, journal = {Environmental microbiology}, volume = {6}, number = {5}, pages = {462-469}, doi = {10.1111/j.1462-2920.2004.00579.x}, pmid = {15049919}, issn = {1462-2912}, mesh = {Animals ; Ascomycota/classification/*genetics/metabolism ; DNA, Ribosomal/analysis ; Gabon ; *Genetic Variation ; Isoptera/*physiology ; Molecular Sequence Data ; Phylogeny ; Soil ; *Soil Microbiology ; *Tropical Climate ; }, abstract = {Molecular microbial ecology has revealed remarkable biodiversity - prokaryotic and eukaryotic - in numerous soil environments. However, no culture-independent surveys of the termitosphere exists, although termites dominate tropical rainforests. Here, we focused on soil feeders, building nests with their soil-born faeces, enriched with clay-organic complexes, thus contributing to the improvement of soil fertility. In order to assess the fungal community composition of these termitaries compared with soils not foraged by termites, samples of the two types were collected in the Lopé rainforest, Gabon, and processed for generation of fungal internal transcribed spacer (ITS) clone libraries. Although primers were universal, most of the recovered sequences represented Ascomycete that were previously uncharacterized and the proportions of which reached 72.5% in soils and 80% in termitaries. Their affiliation with identified fungi was analysed in performing a phylogenetic tree based on 5.8S rDNA. Furthermore, the ascomycete communities of soil-feeding termitaries and soils shared only 6.3% of sequences. This discrepancy of composition between soil and nest may result from the building behaviour of termites, as the organic matter in the nest is chemically modified, and some vacant ecological microniches are available for more specialized fungi.}, }
@article {pmid15046569, year = {2004}, author = {Johnson, MR and Montero, CI and Conners, SB and Shockley, KR and Pysz, MA and Kelly, RM}, title = {Functional genomics-based studies of the microbial ecology of hyperthermophilic micro-organisms.}, journal = {Biochemical Society transactions}, volume = {32}, number = {Pt 2}, pages = {188-192}, doi = {10.1042/bst0320188}, pmid = {15046569}, issn = {0300-5127}, mesh = {Biofilms ; DNA, Complementary/metabolism ; Ecology ; Gene Transfer Techniques ; Genes, Archaeal ; Genome ; *Genome, Archaeal ; Microscopy, Fluorescence ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Temperature ; }, abstract = {Although much attention has been paid to the genetic, biochemical and physiological aspects of individual hyperthermophiles, how these unique micro-organisms relate to each other and to their natural habitats must be addressed in order to develop a comprehensive understanding of life at high temperatures. Phylogenetic 16 S rRNA-based profiling of samples from various geothermal sites has provided insights into community structure, but this must be complemented with efforts to relate metabolic strategies to biotic and abiotic characteristics in high-temperature habitats. Described here are functional genomics-based approaches, using cDNA microarrays, to gain insight into how ecological features such as biofilm formation, species interaction, and possibly even gene transfer may occur in native environments, as well as to determine what genes or sets of genes may be tied to environmental functionality.}, }
@article {pmid15037968, year = {2004}, author = {Matsumiya, H and Garland, J}, title = {Editorial: microbial ecology.}, journal = {Microbial ecology}, volume = {47}, number = {2}, pages = {117-118}, doi = {10.1007/s00248-004-9951-7}, pmid = {15037968}, issn = {0095-3628}, mesh = {*Bacteria ; Biodiversity ; *Ecology ; Education ; *Extraterrestrial Environment ; International Cooperation ; }, }
@article {pmid15037966, year = {2004}, author = {Fouilland, E and Descolas-Gros, C and Courties, C and Collos, Y and Vaquer, A and Gasc, A}, title = {Productivity and growth of a natural population of the smallest free-living eukaryote under nitrogen deficiency and sufficiency.}, journal = {Microbial ecology}, volume = {48}, number = {1}, pages = {103-110}, pmid = {15037966}, issn = {0095-3628}, mesh = {Carbon/*metabolism ; Carbonates/metabolism ; Cell Division/drug effects ; Chlorophyta/drug effects/growth &amp; development/*metabolism ; Flow Cytometry ; France ; Mediterranean Sea ; Nitrogen Compounds/metabolism/*pharmacology ; Phytoplankton/drug effects/*metabolism ; }, abstract = {The influence of dissolved inorganic nitrogen (DIN) enrichments on cell-normalized carbon uptake rate, chlorophyll a content, and apparent cell size of a picoeukaryote (<1 microm) (Ostreococcus tauri, the smallest eukaryotic cell) from a natural summer phytoplanktonic assemblage (<200 microm) in a northern Mediterranean Lagoon (Thau Lagoon) was studied in 20-L enclosures in June 1995. The natural planktonic community was incubated in situ for 24 h with initial ammonium and nitrate enrichments and compared to a control without enrichment. O. tauri cell-normalized productivity was estimated from the combination of flow cytometric (FCM) enumeration and 2-h (radioactive) carbonate incorporation measured on post-incubation size fractions (<1microm). No difference between the effects of the two DIN sources of enrichment on the studied biological parameters was measured during this experiment. Growth of natural O. tauri was perturbed by the low DIN availability in the control with drastic changes in cell productivity, chlorophyll content, and cell cycle (from the variations in apparent cell size) as compared to the DIN sufficiency conditions. On the other hand, a very high specific growth rate for natural O. tauri, up to 8 day(-1) under DIN enrichments, has been estimated from production and abundance data obtained during this experiment. This supports values measured in culture and suggests that the yearly high contribution of picophytoplankton to the total primary production in Thau Lagoon is likely to be due to their high growth rate rather than the previously suggested lack of grazing pressure.}, }
@article {pmid15037965, year = {2004}, author = {Felske, AD and Tzeneva, V and Heyrman, J and Langeveld, MA and Akkermans, AD and De Vos, P}, title = {Isolation and biodiversity of hitherto undescribed soil bacteria related to Bacillus niacini.}, journal = {Microbial ecology}, volume = {48}, number = {1}, pages = {111-119}, pmid = {15037965}, issn = {0095-3628}, mesh = {Bacillus/*genetics ; Base Pairing ; Base Sequence ; *Biodiversity ; DNA Fingerprinting ; Genetic Variation ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Netherlands ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {The hitherto largely not described phylogenetic neighborhood of Bacillus niacini has been explored by a comprehensive cultivation experiment and genomic variety studies. Previous culture-independent studies demonstrated that approximately 15% of all Bacillus 16S rDNA directly extracted from soils worldwide was affiliated to B. niacini. Seven different media were inoculated with soil suspensions in serial dilutions and incubated at different temperatures. Then, bacterial colonies were picked and analyzed by sequencing. A mineral medium with acetate as carbon source yielded a B. niacini rate of >3% of all picked colonies. Other media were less efficient but also successful. Applying this culturing approach, we succeeded in obtaining 64 isolates from different Dutch soils. The isolates turned out to be diverse, although closely related to B. niacini as revealed by 16S rDNA sequencing. Close matches with environmental clones were also found, thus demonstrating much more diversity beyond previously known 16S rDNA sequences. The rep-PCR fingerprinting method revealed a high genomic variety, redundancy could not be observed among our isolates. Hence, the hitherto neglected B. niacini lineage, apparently among the most abundant soil Bacillus, was accessible to our cultivation approach.}, }
@article {pmid15037964, year = {2004}, author = {Klein, DA and Paschke, MW}, title = {Filamentous fungi: the indeterminate lifestyle and microbial ecology.}, journal = {Microbial ecology}, volume = {47}, number = {3}, pages = {224-235}, pmid = {15037964}, issn = {0095-3628}, mesh = {Cytoplasm/physiology ; *Ecosystem ; Fungi/*cytology/genetics/growth &amp; development/*physiology ; Phylogeny ; Soil/analysis ; *Soil Microbiology ; }, abstract = {The filamentous fungi have dynamic and variable hyphal structures within which cytoplasm can be moved, synthesized, and degraded, in response to changes in environmental conditions, resource availability, and resource distribution. Their study has gone through several phases. In the first phase, direct observation was emphasized without undue concern for interior structures or in the presence of cytoplasm. By the mid-1970s, single biochemical proxies (ergosterol, marker fatty acids, chitin derivatives, etc.) were being used increasingly. The use of these surrogate single measurements continues, in spite of their inability to provide information on the physical structure of the filamentous fungi. Molecular approaches also are being used, primarily through the use of bulk nucleic acid extraction and cloning. Because the sources of the nucleic acids used in such studies usually are not known, taxonomic and phylogenetic information derived by this approach cannot be linked to specific fungal structures. Recently, a greater emphasis has been placed on assessing physical aspects of indeterminate fungal growth, involving the assessment of cytoplasm-filled and evacuated (empty) hyphae. Both of these parameters are important for describing filamentous fungal growth and function. The use of phase contrast microscopy and varied general stains, as well as fluorogenic substrates with observation by epifluorescence microscopy, has made it possible to provide estimates of cytoplasm-filled hyphal lengths. Using this approach, it has been possible to evaluate the responses of the indeterminate fungal community to changes in environmental conditions, including soil management. It is now possible to obtain molecular information from individual bacteria and fungal structures (hyphae, spores, fruiting bodies) recovered from environments, making it possible to link individual fungal structures with their taxonomic and phylogenetic information. In addition, this information can be considered in the context of the indeterminate filamentous fungal lifestyle, involving the dynamics of resource allocation to hyphal structural development and synthesis of cytoplasm. Use of this approach should make it possible to gain a greater appreciation of the indeterminate filamentous fungal lifestyle, particularly in the context of microbial ecology.}, }
@article {pmid15037963, year = {2004}, author = {Huss, AA and Wehr, JD}, title = {Strong indirect effects of a submersed aquatic macrophyte, Vallisneria americana, on bacterioplankton densities in a mesotrophic lake.}, journal = {Microbial ecology}, volume = {47}, number = {4}, pages = {305-315}, pmid = {15037963}, issn = {0095-3628}, mesh = {Ammonia/analysis ; Analysis of Variance ; Bacteria/*growth &amp; development ; Carbon/analysis ; *Ecosystem ; Fresh Water/analysis ; Hydrocharitaceae/*physiology ; Indoles ; Microscopy, Fluorescence ; New York ; Phosphorus/analysis ; Plankton/*growth &amp; development ; }, abstract = {Phytoplankton and allochthonous matter are important sources of dissolved organic carbon (DOC) for planktonic bacteria in aquatic ecosystems. But in small temperate lakes, aquatic macrophytes may also be an important source of DOC, as well as a source or sink for inorganic nutrients. We conducted micro- and mesocosm studies to investigate the possible effects of an actively growing macrophyte, Vallisneria americana, on bacterial growth and water chemistry in mesotrophic Calder Lake. A first microcosm (1 L) study conducted under high ambient NH4+ levels (NH4+ > or = 10 microM) demonstrated that macrophytes had a positive effect on bacterial densities through release of DOC and P. A second microcosm experiment, conducted under NH4+-depleted conditions (NH4+ < 10 microM), examined inter- active effects of macrophytes and their sediments on bacterial growth and water chemistry. Non-rooted macrophytes had negative effects on bacterial numbers, while rooted macrophytes had no significant effects, despite significant increases in DOC and P. A 70-L mesocosm experiment manipulated macrophytes, as well as N and P supply under surplus NH4-+conditions (NH4+ > or = 10 gmicro), and measured effects on bacterial growth, Chl a concentrations, and water chemistry. Bacterial growth and Chl a concentrations declined with macrophyte additions, while bacterial densities increased with P addition (with or without N). Results suggest that the submersed macrophyte Vallisneria exerts a strong but indirect effect on bacteria by modifying nutrient conditions and/or suppressing phytoplankton. Effects of living macrophytes differed with ambient nutrient conditions: under NH4+-surplus conditions, submersed macrophytes stimulated bacterioplankton through release of DOC or P, but in NH4-+depleted conditions, the influence of Vallisneria was negative or neutral. Effects of living macrophytes on planktonic bacteria were apparently mediated by the macrophytes use and/or release of nutrients, as well as through possible effects on phytoplankton production.}, }
@article {pmid15037962, year = {2004}, author = {Brubaker, RR}, title = {The recent emergence of plague: a process of felonious evolution.}, journal = {Microbial ecology}, volume = {47}, number = {3}, pages = {293-299}, pmid = {15037962}, issn = {0095-3628}, mesh = {Animals ; *Biological Evolution ; Environment ; *Genome, Bacterial ; Mutation/genetics ; *Phenotype ; Plague/epidemiology/*genetics/pathology ; Selection, Genetic ; Siphonaptera/microbiology ; Yersinia pestis/classification/*genetics/pathogenicity ; }, abstract = {Yersinia pestis, the causative agent of bubonic plague, evolved from closely related Yersinia pseudotuberculosis within the past 20,000 years, an event that corresponds to the end of the last ice age and distribution of Homo sapiens throughout the world. Y. pseudotuberculosis causes chronic but generally mild enteropathogenic infections whereas plague is the most devastating acute disease experienced by mankind. The very recent evolution of plague from its progenitor assures close genomic homogeneity between the two species and thus high probability that disparities in DNA sequence mediate dramatic differences in symptoms of infection. The purpose of this minireview is to define salient distinctions between the genomes of Y. pestis and Y. pseudotuberculosis and to equate unique functions to respective acute and chronic mechanisms of virulence. The significance of these processes is then related to the procedures the organisms use to survive when between hosts (i.e., the flea vector colonized by Y. pestis and natural environments including soil and water in the case of Y. pseudotuberculosis). Next, an attempt is made to order the various mutational events that caused the recent emergence of Y. pestis as a distinct species. Finally, selective pressures such as predatory soil nematodes are considered that possibly influenced the early evolution of those yersiniae now pathogenic to humans.}, }
@article {pmid15037961, year = {2004}, author = {Caldwell, DE and Caldwell, SJ}, title = {The calculative nature of microbe-mineral interactions.}, journal = {Microbial ecology}, volume = {47}, number = {3}, pages = {252-265}, pmid = {15037961}, issn = {0095-3628}, mesh = {Bacteria/*genetics/metabolism ; Carbonates/chemistry ; *Ecosystem ; Environment ; Geological Phenomena ; Geology ; Ice ; Minerals/*metabolism ; *Models, Biological ; Silicates/chemistry ; *Systems Theory ; }, abstract = {Microorganisms continually redefine themselves at many levels, including the molecule, cell, and community. Although it was initially assumed that this resulted from the genesis of information within DNA alone, it has since been shown that innovation originates at multiple levels. This occurs through calculative units, each unit consisting of two proliferating structures, one nested within the other and each undergoing changes in structural geometry that affect the proliferation rate of the other. For example, the recombination of genetic structures affects the proliferation of community structures, and the recombination of community structures affects the proliferation of genetic structures. The proliferation of a nested series of structures (e.g., genes proliferating within cells, cells proliferating within communities, communities proliferating within ecosystems) results in a logic circuit that calculates the form and function of each structural element in the series. In this situation each element functions as both a habitat and an inhabitant (environment and organism), and it is this dichotomy that determines the balance of nature. Nested geological structures, such as minerals and continents, also proliferate and redefine themselves in much the same way. Microbe-mineral interactions thus link nested biological calculations to an analogous set of nested geological calculations. Examples include the microorganisms involved in the nucleation (proliferation) of ferric hydroxides, carbonates, silicates, and ice crystals.}, }
@article {pmid15037960, year = {2004}, author = {Lisle, JT and Priscu, JC}, title = {The occurrence of lysogenic bacteria and microbial aggregates in the lakes of the McMurdo Dry Valleys, Antarctica.}, journal = {Microbial ecology}, volume = {47}, number = {4}, pages = {427-439}, pmid = {15037960}, issn = {0095-3628}, mesh = {Alkaline Phosphatase/metabolism ; Antarctic Regions ; Bacteria/metabolism/*virology ; *Bacteriophages ; Chlorophyll/analysis ; Chlorophyll A ; Colony Count, Microbial ; *Ecosystem ; Fluorescence ; Fresh Water/analysis/*microbiology ; *Lysogeny ; Mitomycin/metabolism ; Phosphorus/analysis ; Staining and Labeling ; *Water Microbiology ; }, abstract = {The McMurdo Dry Valleys of Antarctica form the coldest and driest ecosystem on Earth. Within this region there are a number of perennially ice-covered (3-6 m thick) lakes that support active microbial assemblages and have a paucity of metazoans. These lakes receive limited allochthonous input of carbon and nutrients, and primary productivity is limited to only 6 months per year owing to an absence of sunlight during the austral winters. In an effort to establish the role that bacteria and their associated viruses play in carbon and nutrient cycling in these lakes, indigenous bacteria, free bacteriophage, and lysogen abundances were determined. Total bacterial abundances (TDC) ranged from 3.80 x 10(4) to 2.58 x 10(7) cells mL(-1) and virus-like particle (VLP) abundances ranged from 2.26 x 10(5) to 5.56 x 10(7) VLP mL(-1). VLP abundances were significantly correlated (P < 0.05) with TDC, bacterial productivity (TdR), chlorophyll a (Chl a), and soluble reactive phosphorus (SRP). Lysogenic bacteria, determined by induction with mitomycin C, made up between 2.0% and 62.5% of the total population of bacteria when using significant decreases and increases in TDC and VLP abundances, respectively, and 89.5% when using increases in VLP abundances as the sole criterion for a successful induction event. The contribution of viruses released from induced lysogens contributed <0.015% to the total viral production rate. Carbohydrate and protein based organic aggregates were abundant within the water column of the lakes and were heavily colonized by bacteria and VLPs. Alkaline phosphatase activity was detected within the matrix of the aggregates, implying phosphorus deficiency and consortial nutrient exchanges among microorganisms.}, }
@article {pmid15028874, year = {2004}, author = {Frederiksen, TM and Finster, K}, title = {The transformation of inorganic sulfur compounds and the assimilation of organic and inorganic carbon by the sulfur disproportionating bacterium Desulfocapsa sulfoexigens.}, journal = {Antonie van Leeuwenhoek}, volume = {85}, number = {2}, pages = {141-149}, doi = {10.1023/B:ANTO.0000020153.82679.f4}, pmid = {15028874}, issn = {0003-6072}, mesh = {Acetates/metabolism ; Bicarbonates/metabolism ; Carbon/metabolism ; Desulfitobacterium/growth &amp; development/*metabolism ; Fermentation ; Hydrogen-Ion Concentration ; Kinetics ; Sulfur Compounds/*pharmacokinetics ; Thiosulfates/metabolism ; }, abstract = {The physiology of the sulfur disproportionator Desulfocapsa sulfoexigens was investigated in batch cultures and in a pH-regulated continuously flushed fermentor system. It was shown that a sulphide scavanger in the form of ferric iron was not obligatory and that the control of pH allowed production of more biomass than was possible in carbonate buffered but unregulated batch cultures. Small amounts of sulphite were produced during disproportionation of elemental sulfur and thiosulphate. In addition, it was shown that in the presence of hydrogen, a respiratory type of process is favored before the disproportionation of sulphite, thiosulphate and elemental sulfur. Sulphate reduction was not observed. D. sulfoexigens assimilated inorganic carbon even in the presence of organic carbon sources. Inorganic carbon assimilation was probably catalyzed by the reverse CO-dehydrogenase pathway, which was supported by the constitutive expression of the gene encoding CO-dehydrogenase in cultures grown in the presence of acetate and by the high carbon fractionation values that are indicative of this pathway.}, }
@article {pmid15027428, year = {2004}, author = {Rodríguez-Valera, F}, title = {Environmental genomics, the big picture?.}, journal = {FEMS microbiology letters}, volume = {231}, number = {2}, pages = {153-158}, doi = {10.1016/S0378-1097(04)00006-0}, pmid = {15027428}, issn = {0378-1097}, mesh = {*Ecology ; *Environmental Microbiology ; *Evolution, Molecular ; Genomics/*trends ; }, abstract = {The enormous sequencing capabilities of our times might be reaching the point of overflowing the possibilities to analyse data and allow for a feedback on where to focus the available resources. We have now a foreseeable future in which most bacterial species will have an annotated genome. However, we know also that most prokaryotic diversity would not be included there. On the one hand, there is the problem of many groups not being easily amenable to culture and hence not represented in culture-centred microbial taxonomy. On the other hand, the gene pools present in one species can be orders of magnitude larger than the genome of one strain (selected for genome sequencing). Contrasting with eukaryotic genomes, the repertoire of genes present in one prokaryotic cell genome does not correlate stringently with its taxonomic identity. Hence gene catalogues from one environment might provide more meaningful information than the classical species catalogues. Metagenomics or microbial environmental genomics provide a different tool that gravitates around the habitat rather than the species. Such a tool could be just the right way to complement "organismal genomics". Its potential to advance our understanding of microbial ecology and prokaryotic diversity and evolution is discussed.}, }
@article {pmid15023950, year = {2004}, author = {Abildgaard, L and Ramsing, NB and Finster, K}, title = {Characterization of the marine propionate-degrading, sulfate-reducing bacterium Desulfofaba fastidiosa sp. nov. and reclassification of Desulfomusa hansenii as Desulfofaba hansenii comb. nov.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {54}, number = {Pt 2}, pages = {393-399}, doi = {10.1099/ijs.0.02820-0}, pmid = {15023950}, issn = {1466-5026}, mesh = {DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Deltaproteobacteria/*classification/genetics/growth &amp; development/isolation &amp; purification ; Fermentation ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Polymerase Chain Reaction ; Propionates/metabolism ; Seawater/*microbiology ; }, abstract = {A rod-shaped, slightly curved sulfate reducer, designated strain P2(T), was isolated from the sulfate-methane transition zone of a marine sediment. Cells were motile by means of a single polar flagellum. The strain reduced sulfate, thiosulfate and sulfite to sulfide and used propionate, lactate and 1-propanol as electron donors. Strain P2(T) also grew by fermentation of lactate. Propionate was oxidized incompletely to acetate and CO(2). The DNA G+C content was 48.8 mol%. Sequence analysis of the small-subunit rDNA and the dissimilatory sulfite reductase gene revealed that strain P2(T) was related to the genera Desulfonema, Desulfococcus, Desulfosarcina, 'Desulfobotulus', Desulfofaba, Desulfomusa and Desulfofrigus. These genera include incomplete as well as complete oxidizers of substrates. Strain P2(T) shared important morphological and physiological traits with Desulfofaba gelida and Desulfomusa hansenii, including the ability to oxidize propionate incompletely to acetate. The 16S rRNA gene similarities of P2(T) to Desulfofaba gelida and Desulfomusa hansenii were respectively 92.9 and 91.5 %. Combining phenotypic and genotypic traits, we propose strain P2(T) to be a member of the genus Desulfofaba. The name Desulfofaba fastidiosa sp. nov. (type strain P2(T)=DSM 15249(T)=ATCC BAA-815(T)) is proposed, reflecting the limited number of substrates consumed by the strain. In addition, the reclassification of Desulfomusa hansenii as a member of the genus Desulfofaba, Desulfofaba hansenii comb. nov., is proposed. A common line of descent and a number of shared phenotypic traits support this reclassification.}, }
@article {pmid15016532, year = {2004}, author = {Van Hege, K and Verhaege, M and Verstraete, W}, title = {Electro-oxidative abatement of low-salinity reverse osmosis membrane concentrates.}, journal = {Water research}, volume = {38}, number = {6}, pages = {1550-1558}, doi = {10.1016/j.watres.2003.12.023}, pmid = {15016532}, issn = {0043-1354}, mesh = {Electrolysis/*methods ; Filtration ; Membranes, Artificial ; *Models, Theoretical ; Osmosis ; Oxidation-Reduction ; Sodium Chloride/chemistry ; Water Purification/*methods ; }, abstract = {The present study encompasses the application of electrolysis as novel treatment technique for the abatement of low-salinity concentrates generated from the filtrative treatment of water and wastewater. Four different materials have been tested as anode for a number of brine samples in a one-compartment electrolytic cell in galvanostatic mode. It was found that PbO(2) and SnO(2) anodes initiated electrochemical precipitation through an increase of the pH. Boron-doped diamond (BDD) and RuO(2) anodes successfully oxidised the pollutants in the brine and a linear removal of total ammonia nitrogen (TAN) and chemical oxygen demand (COD) was observed during the first phase of oxidation. Oxidation was predominantly achieved through indirect hypochlorite bulk oxidation; the higher oxidation rate and extent for the BDD anode was attributed to the higher selectivity and activity of the latter. Overall performance of the BDD electrode was higher than for RuO(2): higher rates for TAN (17.9 vs. 13.5mg/Ah) and COD (74.5 vs. 20.0mg/Ah) removal as well as higher overall current efficiencies (35.2% vs. 14.5%). Extensive colour removal was observed for both anodes (>90% decrease in absorbency at 455 nm).}, }
@article {pmid15012499, year = {1998}, author = {Johnson, KB and Stockwell, VO}, title = {Management of fire blight: a case study in microbial ecology.}, journal = {Annual review of phytopathology}, volume = {36}, number = {}, pages = {227-248}, doi = {10.1146/annurev.phyto.36.1.227}, pmid = {15012499}, issn = {0066-4286}, abstract = {Suppression of the blossom-blight phase of fire blight is a key point in the management of this destructive and increasingly important disease of apple and pear. For blossom infection to occur, the causal bacterium, Erwinia amylovora, needs to increase its population size through an epiphytic phase that occurs on stigmatic surfaces. Knowledge of the ecology of the pathogen on stigmas has been key to the development of predictive models for infection and optimal timing of antibiotic sprays. Other bacterial epiphytes also colonize stigmas where they can interact with and suppress epiphytic growth of the pathogen. A commercially available bacterial antagonist of E. amylovora (BlightBan, Pseudomonas fluorescens A506) can be included in antibiotic spray programs. Integration of bacterial antagonists with chemical methods suppresses populations of the pathogen and concomitantly, fills the ecological niche provided by the stigma with a nonpathogenic, competing microorganism. Further integration of biologically based methods with conventional management of blossom blight may be achievable by increasing the diversity of applied antagonists, by refining predictive models to incorporate antagonist use, and by gaining an improved understanding of the interactions that occur among indigenous and applied bacterial epiphytes, antibiotics, and the physical environment.}, }
@article {pmid15011958, year = {2004}, author = {Penttinen, MA and Ekman, P and Granfors, K}, title = {Non-antigen presenting effects of HLA-B27.}, journal = {Current molecular medicine}, volume = {4}, number = {1}, pages = {41-49}, doi = {10.2174/1566524043479275}, pmid = {15011958}, issn = {1566-5240}, mesh = {Antigen Presentation/immunology ; Disease Susceptibility/immunology/microbiology ; Environmental Exposure/adverse effects ; Gram-Negative Bacterial Infections/complications/*immunology/metabolism ; HLA-B27 Antigen/*immunology ; Histocompatibility Antigens Class I/immunology/metabolism ; Humans ; Lipopolysaccharides/pharmacology ; Molecular Mimicry/immunology ; Prohibitins ; Rheumatic Diseases/etiology/*immunology/metabolism ; Signal Transduction/drug effects ; beta 2-Microglobulin/immunology/metabolism ; }, abstract = {Spondyloarthropathies (SpA) are a group of chronic rheumatic diseases, which show a strong asoociation with human leukocyte antigen (HLA)-B27. Although the association between HLA-B27 and the susceptibility to SpA was discovered thirty years ago, the exact mechanism by which HLA-B27 predisposes to disease development remains unclear. The classical role of MHC class I molecules is to present peptides for CD8+ T cells. Therefore, it has been proposed that the antigen presenting function of HLA-B27 is somehow altered in the patients developing SpA. However, despite extensive research, the attempts to create a comprehensive theory that would explain the role of HLA-B27 as an antigen presenting molecule in the development of SpA have been unsuccessful. Reactive arthritis (ReA) belongs to the group of SpA. It is a joint inflammation developing after certain bacterial infections e.g. Salmonella, Yersinia, and Chlamydia. Several unrelated observations indicate that HLA-B27 modulates the interaction between ReA-triggering bacteria and host cell. These findings suggest that HLA-B27 may possess functions, which are unrelated to antigen presentation. In this paper, we summarize these findings and discuss their potential impact in the development of SpA.}, }
@article {pmid15008819, year = {2004}, author = {Valle, A and Bailey, MJ and Whiteley, AS and Manefield, M}, title = {N-acyl-l-homoserine lactones (AHLs) affect microbial community composition and function in activated sludge.}, journal = {Environmental microbiology}, volume = {6}, number = {4}, pages = {424-433}, doi = {10.1111/j.1462-2920.2004.00581.x}, pmid = {15008819}, issn = {1462-2912}, mesh = {4-Butyrolactone/analogs &amp; derivatives/chemistry/*metabolism ; Bioreactors ; *Gene Expression Regulation, Bacterial ; Phylogeny ; Proteobacteria/classification/genetics/*metabolism ; Sewage/*microbiology ; Waste Disposal, Fluid ; }, abstract = {The role of intercellular signalling in the regulation of genes and phenotypes in a broad range of bacterial species is now firmly established. In contrast, the impact of intercellular signalling on microbial community parameters, such as species diversity and function, is less well understood. In this study the role of N-acyl-l-homoserine lactones (AHLs) in microbial community dynamics in an industrial wastewater treatment system is addressed. Seven proteobacterial strains producing compounds with AHL-like activity were isolated from the treatment plant. Three of these belong to genera with no previously identified AHL producing species. Addition of AHLs at 2 micro M to sludge samples generated changes in both community function (phenol degradation) and composition as determined by length heterogeneity PCR and denaturing gradient gel electrophoresis. Phenol degradation was more stable as a result of the AHL augmentation. A dominant functional member of the Thauera genus was transiently supplanted by a member of the Comomonas genus in response to AHL addition. This suggests that AHLs can play a role in mediating microbial community parameters and has implications for ecosystem function and industrial wastewater treatment.}, }
@article {pmid15006793, year = {2004}, author = {Fuller, ME and Mailloux, BJ and Streger, SH and Hall, JA and Zhang, P and Kovacik, WP and Vainberg, S and Johnson, WP and Onstott, TC and DeFlaun, MF}, title = {Application of a vital fluorescent staining method for simultaneous, near-real-time concentration monitoring of two bacterial strains in an Atlantic coastal plain aquifer in Oyster, Virginia.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {3}, pages = {1680-1687}, pmid = {15006793}, issn = {0099-2240}, mesh = {Biodegradation, Environmental ; Colony Count, Microbial/*methods ; Comamonadaceae/isolation &amp; purification/metabolism ; Comamonas/isolation &amp; purification/metabolism ; Ecosystem ; Environmental Monitoring ; Environmental Pollutants/metabolism ; Fluoresceins ; *Fluorescent Dyes ; Geologic Sediments/microbiology ; Rhodamines ; Seawater/microbiology ; Staining and Labeling/*methods ; Succinimides ; Virginia ; *Water Microbiology ; }, abstract = {Two differentially labeled bacterial strains were monitored in near-real time during two field-scale bacterial transport experiments in a shallow aquifer in July 2000 and July 2001. Comamonas sp. strain DA001 and Acidovorax sp. strain OY-107 were grown and labeled with the vital fluorescent stain TAMRA/SE (5 [and -6]-carboxytetramethylrhodamine, succinimidyl ester) or CFDA/SE (5 [and -6]-carboxyfluorescein diacetate, succinimidyl ester). Fluorescently labeled cells and a conservative bromide tracer were introduced into a suboxic superficial aquifer, followed by groundwater collection from down-gradient multilevel samplers. Cells were enumerated in the field by microplate spectrofluorometry, with confirmatory analyses for selected samples done in the laboratory by epifluorescence microscopy, flow cytometry, and ferrographic capture. There was general agreement in the results from all of the vital-stain-based enumeration methods, with differences ranging from <10% up to 40% for the analysis of identical samples between different tracking methods. Field analysis by microplate spectrofluorometry was robust and efficient, allowing thousands of samples to be analyzed in quadruplicate for both of the injected strains. The near-real-time data acquisition allowed adjustments to the predetermined sampling schedule to be made. The microplate spectrofluorometry data sets for the July 2000 and July 2001 experiments allowed the transport of the injected cells to be related to the site hydrogeology and injection conditions and enabled the assessment of differences in the transport of the two strains. This near-real-time method should prove effective for a number of microbial ecology applications.}, }
@article {pmid15006768, year = {2004}, author = {Seghers, D and Wittebolle, L and Top, EM and Verstraete, W and Siciliano, SD}, title = {Impact of agricultural practices on the Zea mays L. endophytic community.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {3}, pages = {1475-1482}, pmid = {15006768}, issn = {0099-2240}, mesh = {Agriculture/methods ; DNA Fingerprinting ; DNA, Bacterial/genetics/isolation &amp; purification ; DNA, Fungal/genetics/isolation &amp; purification ; Ecosystem ; Fertilizers ; Herbicides ; Plant Roots/microbiology ; Polymerase Chain Reaction ; Soil Microbiology ; Zea mays/*microbiology ; }, abstract = {Agricultural practices are known to alter bulk soil microbial communities, but little is known about the effect of such practices on the plant endophytic community. We assessed the influence of long-term applications (20 years) of herbicides and different fertilizer types on the endophytic community of maize plants grown in different field experiments. Nested PCR-denaturing gradient gel electrophoresis (DGGE) analyses targeting general bacteria, type I or II methanotrophs, actinomycetes, and general fungi were used to fingerprint the endophytic community in the roots of Zea mays L. Low intraplant variability (reproducible DGGE patterns) was observed for the bacterial, type I methanotroph, and fungal communities, whereas the patterns for endophytic actinomycetes exhibited high intraplant variability. No endophytic amplification product was obtained for type II methanotrophs. Cluster and stability analysis of the endophytic type I methanotroph patterns differentiated maize plants cultivated by using mineral fertilizer from plants cultivated by using organic fertilizer with a 100% success rate. In addition, lower methanotroph richness was observed for mineral-fertilized plants than for organically fertilized plants. The use of herbicides could not be traced by fingerprinting the endophytic type I methanotrophs or by evaluating any other endophytic microbial group. Our results indicate that the effect of agrochemicals is not limited to the bulk microbial community but also includes the root endophytic community. It is not clear if this effect is due to a direct effect on the root endophytic community or is due to changes in the bulk community, which are then reflected in the root endophytic community.}, }
@article {pmid15006749, year = {2004}, author = {Griswold, A and Chen, YY and Snyder, JA and Burne, RA}, title = {Characterization of the arginine deiminase operon of Streptococcus rattus FA-1.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {3}, pages = {1321-1327}, pmid = {15006749}, issn = {0099-2240}, support = {R01 DE010362/DE/NIDCR NIH HHS/United States ; DE13062/DE/NIDCR NIH HHS/United States ; }, mesh = {Base Sequence ; DNA, Bacterial/genetics ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Enzymologic ; Genes, Bacterial ; Genes, Reporter ; Hydrolases/*genetics ; Molecular Sequence Data ; *Operon ; Streptococcus/*enzymology/*genetics ; Streptococcus mutans/enzymology/genetics ; }, abstract = {The arginine deiminase system (ADS) is of critical importance in oral biofilm pH homeostasis and microbial ecology. The ADS consists of three enzymes. Arginine is hydrolyzed by AD (ArcA) to generate citrulline and ammonia. Citrulline is then converted to ornithine and carbamoylphosphate via ornithine carbamoyltransferase (ArcB). Finally, carbamate kinase (ArcC) transfers a phosphate from carbamoylphosphate to ADP, yielding ATP. Ammonia production from this pathway protects bacteria from lethal acidification, and ATP production provides a source of energy for the cells. The purpose of this study was to initiate a characterization of the arc operon of Streptococcus rattus, the least cariogenic and sole ADS-positive member of the mutans streptococci. Using an arcB gene fragment obtained by degenerate PCRs, the FA-1 arc operon was identified in subgenomic DNA libraries and sequence analysis was performed. Results showed that the genes encoding the AD pathway in S. rattus FA-1 are organized as an arcABCDT-adiR operon gene cluster, including the enzymes of the pathway, an arginine-ornithine antiporter (ArcD) and a putative regulatory protein (AdiR). The arcA transcriptional start site was identified by primer extension, and a sigma(70)-like promoter was mapped 5' to arcA. Reverse transcriptase PCR was used to establish that arcABCDT could be cotranscribed. Reporter gene fusions and AD assays demonstrated that the operon is regulated by substrate induction and catabolite repression, the latter apparently through a CcpA-dependent pathway.}, }
@article {pmid15006748, year = {2004}, author = {Graber, JR and Leadbetter, JR and Breznak, JA}, title = {Description of Treponema azotonutricium sp. nov. and Treponema primitia sp. nov., the first spirochetes isolated from termite guts.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {3}, pages = {1315-1320}, pmid = {15006748}, issn = {0099-2240}, mesh = {Animals ; Base Composition ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/genetics ; Digestive System/microbiology ; Fermentation ; Genome, Bacterial ; Isoptera/*microbiology ; Microscopy, Electron ; Molecular Sequence Data ; Phenotype ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Treponema/classification/genetics/*isolation &amp; purification/metabolism ; }, abstract = {Long after their original discovery, termite gut spirochetes were recently isolated in pure culture for the first time. They revealed metabolic capabilities hitherto unknown in the Spirochaetes division of the Bacteria, i.e., H(2) plus CO(2) acetogenesis (J. R. Leadbetter, T. M. Schmidt, J. R. Graber, and J. A. Breznak, Science 283:686-689, 1999) and dinitrogen fixation (T. G. Lilburn, K. S. Kim, N. E. Ostrom, K. R. Byzek, J. R. Leadbetter, and J. A. Breznak, Science 292:2495-2498, 2001). However, application of specific epithets to the strains isolated (Treponema strains ZAS-1, ZAS-2, and ZAS-9) was postponed pending a more complete characterization of their phenotypic properties. Here we describe the major properties of strain ZAS-9, which is readily distinguished from strains ZAS-1 and ZAS-2 by its shorter mean cell wavelength or body pitch (1.1 versus 2.3 micro m), by its nonhomoacetogenic fermentation of carbohydrates to acetate, ethanol, H(2), and CO(2), and by 7 to 8% dissimilarity between its 16S rRNA sequence and those of ZAS-1 and ZAS-2. Strain ZAS-9 is proposed as the type strain of the new species, Treponema azotonutricium. Strains ZAS-1 and ZAS-2, which are H(2)-consuming, CO(2)-reducing homoacetogens, are proposed here to be two strains of the new species Treponema primitia. Apart from the salient differences mentioned above, the genomes of all three strains were similar in size (3,461 to 3,901 kb), in G+C content (50.0 to 51.0 mol%), and in possession of 2 copies of the gene encoding 16S rRNA (rrs). For comparison, the genome of the free-living spirochete Spirochaeta aurantia strain J1 was analyzed by the same methods and found to have a size of 3,719 kb, to contain 65.6 mol% G+C, and also to possess 2 copies of the rrs gene.}, }
@article {pmid15006747, year = {2004}, author = {Graber, JR and Breznak, JA}, title = {Physiology and nutrition of Treponema primitia, an H2/CO2-acetogenic spirochete from termite hindguts.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {3}, pages = {1307-1314}, pmid = {15006747}, issn = {0099-2240}, mesh = {Acetic Acid/metabolism ; Animals ; Carbon Dioxide/metabolism ; Digestive System/microbiology ; Hydrogen/metabolism ; Isoptera/*microbiology ; Oxidative Stress ; Oxygen/metabolism ; Treponema/growth &amp; development/*isolation &amp; purification/*physiology ; }, abstract = {Treponema primitia strains ZAS-1 and ZAS-2, the first spirochetes to be isolated from termite hindguts (J. R. Leadbetter, T. M. Schmidt, J. R. Graber, and J. A. Breznak, Science 283:686-689, 1999), were examined for nutritional, physiological, and biochemical properties relevant to growth and survival in their natural habitat. In addition to using H(2) plus CO(2) as substrates, these strains were capable of homoacetogenic growth on mono- and disaccharides and (in the case of ZAS-2) methoxylated benzenoids. Cells were also capable of mixotrophic growth (i.e., simultaneous utilization of H(2) and organic substrates). Cell extracts of T. primitia possessed enzyme activities of the Wood/Ljungdahl (acetyl coenzyme A) pathway of acetogenesis, including tetrahydrofolate-dependent enzymes of the methyl group-forming branch. However, a folate compound was required in the medium for growth. ZAS-1 and ZAS-2 growing on H(2) plus CO(2) displayed H(2) thresholds of 650 and 490 ppmv, respectively. Anoxic cultures of ZAS-1 and ZAS-2 maintained growth after the addition of as much as 0.5% (vol/vol) O(2) to the headspace atmosphere. Cell extracts exhibited NADH and NADPH peroxidase and NADH oxidase activities but neither catalase nor superoxide dismutase activity. Results indicate that (i) T. primitia is able to exploit a variety of substrates derived from the food of its termite hosts and in so doing contributes to termite nutrition via acetogenesis, (ii) in situ growth of T. primitia is likely dependent on secretion of a folate compound(s) by other members of the gut microbiota, and (iii) cells possess enzymatic adaptations to oxidative stress, which is likely to be encountered in peripheral regions of the termite hindgut.}, }
@article {pmid15003690, year = {2004}, author = {Calvó, L and Garcia-Gil, LJ}, title = {Use of amoB as a new molecular marker for ammonia-oxidizing bacteria.}, journal = {Journal of microbiological methods}, volume = {57}, number = {1}, pages = {69-78}, doi = {10.1016/j.mimet.2003.11.019}, pmid = {15003690}, issn = {0167-7012}, mesh = {Amino Acid Sequence ; Base Sequence ; DNA, Bacterial/chemistry/genetics ; Genetic Markers/genetics ; Molecular Sequence Data ; Nitrosomonadaceae/enzymology/*genetics ; Oxidoreductases/chemistry/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; }, abstract = {Specific molecular determination and classification of ammonia-oxidizing bacteria have relied on the use of conventional markers such as 16S rDNA. However, this gene does not satisfactorily provide a wide vision of all phylogenetic lineages. Despite the initial expectations, the use of functional genes as for example amoA has only been useful to corroborate the established taxonomy. Ammonia-oxidizing bacteria constitute a physiological group that crosses over principal phylogenetic radiations. Therefore, it is necessary to look for novel functional markers, which are needed for both diversity and taxonomic studies. In this work, the available amoB sequences have been used to design a new degenerate set of primers flanking a ca. 500-bp region. Partial amoB gene sequences of up to 16 AOB strains (5 Nitrosomonas, 10 Nitrosospira, and 1 Nitrosococcus) belonging to both the beta- and the gamma-Proteobacteria have been obtained. Comparison of both DNA and deduced amino acid sequences results in three subgroups, two of them of the beta-Proteobacteria and a third one of the gamma-Proteobacteria displaying 75% and 35% homology in their deduced amino acid sequences, respectively. This gene has proven to be a suitable molecular marker to study AOB, as well as providing a new insight into the classification of this group.}, }
@article {pmid14998042, year = {2004}, author = {Pynaert, K and Smets, BF and Beheydt, D and Verstraete, W}, title = {Start-up of autotrophic nitrogen removal reactors via sequential biocatalyst addition.}, journal = {Environmental science &amp; technology}, volume = {38}, number = {4}, pages = {1228-1235}, doi = {10.1021/es030081+}, pmid = {14998042}, issn = {0013-936X}, mesh = {Bacteria, Aerobic/physiology ; *Bioreactors ; Catalysis ; Nitrogen/*isolation &amp; purification ; Oxygen ; Population Dynamics ; Waste Disposal, Fluid/*methods ; }, abstract = {A procedure for start-up of oxygen-limited autotrophic nitrification-denitrification (OLAND) in a lab-scale rotating biological contactor (RBC) is presented. In this one-step process, NH4+ is directly converted to N2 without the need for an organic carbon source. The approach is based on a sequential addition of two types of easily available biocatalyst to the reactor during start-up: aerobic nitrifying and anaerobic, granular methanogenic sludge. The first is added as a source of aerobic ammonia-oxidizing bacteria (AAOB), the second as a possible source of planctomycetes including anaerobic ammonia-oxidizing bacteria (AnAOB). The initial nitrifying biofilm serves as a matrix for anaerobic cell incorporation. By subsequently imposing oxygen limitation, one can create an optimal environment for autotrophic N removal. In this way, N removal of about 250 mg of N L(-1) d(-1) was achieved after 100 d treating a synthetic NH4+-rich wastewater. By gradually imposing higher loads on the reactor, the N elimination could be increased to about 1.8 g of N L(-1) d(-1) at 250 d. The resulting microbial community was compared with that of the inocula using general bacterial and AAOB- and planctomycete-specific PCR primers. Subsequently, the RBC reactor was shown to treat a sludge digestor effluent under suboptimal and strongly varying conditions. The RBC biocatalyst was also submitted to complete absence of oxygen in a fixed-film bioreactor (FFBR) and proved able to remove NH4+ with NO2- as electron acceptor (maximal 434 mg of NH4+-N (g of VSS)(-1) d(-1) on day 136). DGGE and real-time PCR analysis demonstrated that the RBC biofilm was dominated by members of the genus Nitrosomonas and close relatives of Kuenenia stuttgartiensis, a known AnAOB. The latter was enriched during FFBR operation, but AAOB were still present and the ratio planctomycetes/AAOB rRNA gene copies was about 4.3 after 136 d of reactor operation. Whether this relates to an active role of AAOB in the anoxic N removal process remains to be solved.}, }
@article {pmid14994180, year = {2004}, author = {Hunt, J and Boddy, L and Randerson, PF and Rogers, HJ}, title = {An evaluation of 18S rDNA approaches for the study of fungal diversity in grassland soils.}, journal = {Microbial ecology}, volume = {47}, number = {4}, pages = {385-395}, pmid = {14994180}, issn = {0095-3628}, mesh = {Base Sequence ; *Biodiversity ; Cluster Analysis ; DNA, Ribosomal/genetics ; Fungi/*genetics ; Molecular Sequence Data ; Phylogeny ; Poaceae/*microbiology ; Restriction Mapping/methods ; Sequence Analysis, DNA/methods ; *Soil Microbiology ; United Kingdom ; }, abstract = {Fungal community structure and diversity in two types of agricultural grassland soil were investigated by amplified 18S ribosomal DNA restriction analysis (ARDRA) and 18S ribosomal DNA sequence analysis. These two grassland sites represent a species-rich old hay meadow and an agriculturally improved site with low floristic diversity. Two primer sets were used in combination to amplify approximately 550 bp of rDNA from three major fungal groups, the zygomycetes, basidiomycetes, and ascomycetes, and clone libraries were created for each site. 18S ARDRA was used to analyze 170 rDNA clones, and three diversity indices were calculated. A small-scale culturing analysis was also carried out and the most common isolates analyzed using ARDRA and sequence analysis. The soil fungal community revealed by the rDNA approaches was significantly different from that produced by this limited culture-based analysis. Twenty-eight soil-derived clones were sequenced, and many represented fungal taxa rarely reported in culture-based studies. The PCR-based techniques detected differences in diversity between the two fungal communities and changes in patterns of dominance that paralleled higher plant diversity. The results suggest that 18S rDNA-based approaches are a useful tool for initial screening of fungal communities, and that they represent a more comprehensive picture of the community than plate culturing.}, }
@article {pmid14994179, year = {2004}, author = {Roberts, MS and Garland, JL and Mills, AL}, title = {Microbial astronauts: assembling microbial communities for advanced life support systems.}, journal = {Microbial ecology}, volume = {47}, number = {2}, pages = {137-149}, pmid = {14994179}, issn = {0095-3628}, mesh = {Bacteria/genetics ; Biodiversity ; Biological Evolution ; *Ecosystem ; Environment ; *Environment, Controlled ; *Extraterrestrial Environment ; Fungi/genetics ; *Life Support Systems ; Models, Genetic ; Principal Component Analysis ; *Spacecraft ; }, abstract = {Extension of human habitation into space requires that humans carry with them many of the microorganisms with which they coexist on Earth. The ubiquity of microorganisms in close association with all living things and biogeochemical processes on Earth predicates that they must also play a critical role in maintaining the viability of human life in space. Even though bacterial populations exist as locally adapted ecotypes, the abundance of individuals in microbial species is so large that dispersal is unlikely to be limited by geographical barriers on Earth (i.e., for most environments "everything is everywhere" given enough time). This will not be true for microbial communities in space where local species richness will be relatively low because of sterilization protocols prior to launch and physical barriers between Earth and spacecraft after launch. Although community diversity will be sufficient to sustain ecosystem function at the onset, richness and evenness may decline over time such that biological systems either lose functional potential (e.g., bioreactors may fail to reduce BOD or nitrogen load) or become susceptible to invasion by human-associated microorganisms (pathogens) over time. Research at the John F. Kennedy Space Center has evaluated fundamental properties of microbial diversity and community assembly in prototype bioregenerative systems for NASA Advanced Life Support. Successional trends related to increased niche specialization, including an apparent increase in the proportion of nonculturable types of organisms, have been consistently observed. In addition, the stability of the microbial communities, as defined by their resistance to invasion by human-associated microorganisms, has been correlated to their diversity. Overall, these results reflect the significant challenges ahead for the assembly of stable, functional communities using gnotobiotic approaches, and the need to better define the basic biological principles that define ecosystem processes in the space environment.}, }
@article {pmid14994178, year = {2004}, author = {Novikova, ND}, title = {Review of the knowledge of microbial contamination of the Russian manned spacecraft.}, journal = {Microbial ecology}, volume = {47}, number = {2}, pages = {127-132}, pmid = {14994178}, issn = {0095-3628}, mesh = {*Air Microbiology ; Bacteria/genetics ; *Environment, Controlled ; *Environmental Monitoring ; *Extraterrestrial Environment ; Fungi/genetics ; *Spacecraft ; }, abstract = {The 15-year experience of orbital station Mir service demonstrated that specifically modified space vehicle environments allows for the consideration of spaceship habitats as a certain ecological niche of microbial community development and functioning, which was formed from the organisms of different physiological and taxonomical groups. The base unit of the orbital station (OS) Mir was launched on February 20, 1986, and on March 13 the first crew arrived to it. From that moment a unique microbiocenosis started forming in the closed environment of the space station, and vital activity of the microorganisms continued for the next 15 years in a specifically changed environment, in conditions of continuous influence of a set of factors intrinsic to space flight. A total of 234 species of bacteria and fungi were found onboard orbital station Mir, among which microorganisms capable of resident colonization of the environment of space objects as a unique anthropotechnological niche were revealed. In such conditions the evolution of microflora is followed by the rise of medical and technical risks that can affect both sanitary-microbiological conditions of the environment and the safety and reliability characteristics of space equipment. The latter is caused by progressing biological damage to the structural materials. The microbial loading dynamic does not have linearly progressing character, but it is a wavy process of alternation of the microflora activation and stabilization phases; on this background there is a change of the dominating species by quantity and prevalence. The accumulated data is evidence of the necessity of the constant control of the microbial environmental factors to maintain their sanitary and microbiological optimum condition and to prevent the processes of constructional materials biodestruction.}, }
@article {pmid14994177, year = {2004}, author = {Breezee, J and Cady, N and Staley, JT}, title = {Subfreezing growth of the sea ice bacterium "Psychromonas ingrahamii".}, journal = {Microbial ecology}, volume = {47}, number = {3}, pages = {300-304}, pmid = {14994177}, issn = {0095-3628}, mesh = {Alaska ; Base Sequence ; Chromatography, High Pressure Liquid ; Cluster Analysis ; Gammaproteobacteria/*genetics/growth &amp; development ; *Ice ; Models, Genetic ; Molecular Sequence Data ; *Phenotype ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {"Psychromonas ingrahamii," named for John L. Ingraham, was isolated from sea ice from off Point Barrow, Alaska. This large rod-shaped bacterium belongs to the gamma-Proteobacteria. "P. ingrahamii" is a psychrophilic, heterotrophic bacterium that is gas vacuolate and nonmotile. "P. ingrahamii" is notable in that it grows at a temperature of -12 degrees C with a generation time of 240 h. This is the lowest growth temperature of any organism authenticated by a growth curve.}, }
@article {pmid14994176, year = {2004}, author = {Foght, J and Aislabie, J and Turner, S and Brown, CE and Ryburn, J and Saul, DJ and Lawson, W}, title = {Culturable bacteria in subglacial sediments and ice from two Southern Hemisphere glaciers.}, journal = {Microbial ecology}, volume = {47}, number = {4}, pages = {329-340}, pmid = {14994176}, issn = {0095-3628}, mesh = {Bacteria/*genetics/metabolism ; Base Sequence ; Carbon/analysis ; Carbon Radioisotopes ; Colony Count, Microbial ; DNA Primers ; DNA, Ribosomal/genetics ; Geologic Sediments/*microbiology ; Ice Cover/*microbiology ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; New Zealand ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; }, abstract = {Viable prokaryotes have been detected in basal sediments beneath the few Northern Hemisphere glaciers that have been sampled for microbial communities. However, parallel studies have not previously been conducted in the Southern Hemisphere, and subglacial environments in general are a new and underexplored niche for microbes. Unfrozen subglacial sediments and overlying glacier ice samples collected aseptically from the Fox Glacier and Franz Josef Glacier in the Southern Alps of New Zealand now have been shown to harbor viable microbial populations. Total direct counts of 2-7 x 10(6) cells g(-1) dry weight sediment were observed, whereas culturable aerobic heterotrophs ranged from 6-9 x 10(5) colony-forming units g(-1) dry weight. Viable counts in the glacier ice typically were 3-4 orders of magnitude smaller than in sediment. Nitrate-reducing and ferric iron-reducing bacteria were detected in sediment samples from both glaciers, but were few or below detection limits in the ice samples. Nitrogen-fixing bacteria were detected only in the Fox Glacier sediment. Restriction fragment analysis of 16S rDNA amplified from 37 pure cultures of aerobic heterotrophs capable of growth at 4 degrees C yielded 23 distinct groups, of which 11 were identified as beta-Proteobacteria. 16S rDNA sequences from representatives of these 11 groups were analyzed phylogenetically and shown to cluster with bacteria such as Polaromonas vacuolata and Rhodoferax antarcticus, or with clones obtained from permanently cold environments. Chemical analysis of sediment and ice samples revealed a dilute environment for microbial life. Nevertheless, both the sediment samples and one ice sample demonstrated substantial aerobic mineralization of 14C-acetate at 8 degrees C, indicating that sufficient nutrients and viable psychrotolerant microbes were present to support metabolism. Unfrozen subglacial sediments may represent a significant global reservoir of biological activity with the potential to influence glacier meltwater chemistry.}, }
@article {pmid14994175, year = {2004}, author = {Labrenz, M and Banfield, JF}, title = {Sulfate-reducing bacteria-dominated biofilms that precipitate ZnS in a subsurface circumneutral-pH mine drainage system.}, journal = {Microbial ecology}, volume = {47}, number = {3}, pages = {205-217}, pmid = {14994175}, issn = {0095-3628}, mesh = {Bacteria/genetics ; Base Sequence ; Biodegradation, Environmental ; *Biofilms ; Clostridium/metabolism ; Cluster Analysis ; DNA Primers ; Hydrogen-Ion Concentration ; In Situ Hybridization, Fluorescence ; Microscopy, Electron ; *Mining ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Sulfides/*metabolism ; Sulfur-Reducing Bacteria/growth &amp; development/*metabolism/ultrastructure ; Symbiosis ; *Water Microbiology ; Water Purification/methods ; Wisconsin ; Zinc Compounds/*metabolism ; }, abstract = {The microbial diversity of ZnS-forming biofilms in 8 degrees C, circumneutral-pH groundwater in tunnels within the abandoned Piquette Zn, Pb mine (Tennyson, Wisconsin, USA) has been investigated by molecular methods, fluorescence in situ hybridization (FISH), and cultivation techniques. These biofilms are growing on old mine timbers that generate locally anaerobic zones within the mine drainage system. Sulfate-reducing bacteria (SRB) exclusively of the family Desulfobacteriaceae comprise a significant fraction of the active microbiota. Desulfosporosinus strains were isolated, but could not be detected by molecular methods. Other important microbial clusters belonged to the beta-, gamma-, and epsilon-Proteobacteria, the Cytophaga/Flexibacter/Bacteroides-group (CFB), Planctomycetales, Spirochaetales, Clostridia, and green nonsulfur bacteria. Our investigations indicated a growth dependence of SRB on fermentative, cellulolytic, and organic acid-producing Clostridia. A few clones related to sulfur-oxidizing bacteria were detected, suggesting a sulfur cycle related to redox gradients within the biofilm. Sulfur oxidation prevents sulfide accumulation that would lead to precipitation of other sulfide phases. FISH analyses indicated that Desulfobacteriaceae populations were not early colonizers in freshly grown and ZnS-poor biofilms, whereas they were abundant in older, naturally established, and ZnS-rich biofilms. Gram-negative SRB have been detected in situ over a period of 6 months, supporting the important role of these organisms in selective ZnS precipitation in Tennyson mine. Results demonstrate the complex nature of biofilms responsible for in situ bioremediation of toxic metals in a subsurface mine drainage system.}, }
@article {pmid14994174, year = {2004}, author = {Peacock, AD and Chang, YJ and Istok, JD and Krumholz, L and Geyer, R and Kinsall, B and Watson, D and Sublette, KL and White, DC}, title = {Utilization of microbial biofilms as monitors of bioremediation.}, journal = {Microbial ecology}, volume = {47}, number = {3}, pages = {284-292}, pmid = {14994174}, issn = {0095-3628}, mesh = {Acetates ; Bacteria/genetics/metabolism ; Base Sequence ; Benzoquinones/metabolism ; Biodegradation, Environmental ; *Biofilms ; Cluster Analysis ; Environmental Monitoring/*instrumentation/*methods ; Ethanol ; Glucose ; Molecular Sequence Data ; Phospholipids/metabolism ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Tennessee ; *Water Microbiology ; }, abstract = {A down-well aquifer microbial sampling system was developed using glass wool or Bio-Sep beads as a solid-phase support matrix. Here we describe the use of these devices to monitor the groundwater microbial community dynamics during field bioremediation experiments at the U.S. Department of Energy Natural and Accelerated Bioremediation Research Program's Field Research Center at the Oak Ridge National Laboratory. During the 6-week deployment, microbial biofilms colonized glass wool and bead internal surfaces. Changes in viable biomass, community composition, metabolic status, and respiratory state were reflected in sampler composition, type of donor, and groundwater pH. Biofilms that formed on Bio-Sep beads had 2-13 times greater viable biomass; however, the bead communities were less metabolically active [higher cyclopropane/monoenoic phospholipid fatty acid (PLFA) ratios] and had a lower aerobic respiratory state (lower total respiratory quinone/ PLFA ratio and ubiquinone/menaquinone ratio) than the biofilms formed on glass wool. Anaerobic growth in these systems was characterized by plasmalogen phospholipids and was greater in the wells that received electron donor additions. Partial 16S rDNA sequences indicated that Geobacter and nitrate-reducing organisms were induced by the acetate, ethanol, or glucose additions. DNA and lipid biomarkers were extracted and recovered without the complications that commonly plague sediment samples due to the presence of clay or dissolved organic matter. Although microbial community composition in the groundwater or adjacent sediments may differ from those formed on down-well biofilm samplers, the metabolic activity responses of the biofilms to modifications in groundwater geochemistry record the responses of the microbial community to biostimulation while providing integrative sampling and ease of recovery for biomarker analysis.}, }
@article {pmid14994173, year = {2004}, author = {Gade, D and Schlesner, H and Glöckner, FO and Amann, R and Pfeiffer, S and Thomm, M}, title = {Identification of planctomycetes with order-, genus-, and strain-specific 16S rRNA-targeted probes.}, journal = {Microbial ecology}, volume = {47}, number = {3}, pages = {243-251}, pmid = {14994173}, issn = {0095-3628}, mesh = {Animals ; Bacteria/*genetics/ultrastructure ; Base Composition ; Base Sequence ; DNA/*genetics ; Germany ; Mediterranean Sea ; Microscopy, Electron ; Nucleic Acid Hybridization ; *Oligonucleotide Probes ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; *Water Microbiology ; }, abstract = {A specific 16S rRNA-targeted oligonucleotide probe (PIR1223) for the genus Pirellula and a species-specific probe (RB454) for Pirellula sp. strain SH1 have been designed and optimized. Together with the already existing order-specific probe PLA886, the two newly designed probes were used to detect and identify planctomycetes, pirellulae, and close relatives of Pirellula sp. strain SH1 in different habitats. With the help of these probes for detection and identification, bacteria of the genus Pirellula were detected and cultivated from tissue of the Mediterranean sponge Aplysina aerophoba and from the water column of the Kiel Fjord. An unexpected result was the close phylogenetic relationship of the isolate from the sponge and the brackish water habitat Kiel Fjord as revealed by DNA/DNA hybridization.}, }
@article {pmid14994172, year = {2004}, author = {Fiencke, C and Bock, E}, title = {Genera-specific immunofluorescence labeling of ammonia oxidizers with polyclonal antibodies recognizing both subunits of the ammonia monooxygenase.}, journal = {Microbial ecology}, volume = {47}, number = {4}, pages = {374-384}, pmid = {14994172}, issn = {0095-3628}, mesh = {Antibodies, Bacterial/*metabolism ; Betaproteobacteria/*immunology/*metabolism/ultrastructure ; Fluorescent Antibody Technique, Direct/methods ; Germany ; Immunoblotting ; In Situ Hybridization, Fluorescence ; Microscopy, Confocal ; Microscopy, Electron, Transmission ; Microscopy, Fluorescence ; Oxidoreductases/*metabolism ; Sewage/microbiology ; *Soil Microbiology ; Species Specificity ; }, abstract = {Polyclonal antibodies that recognize the two subunits AmoA and AmoB of the ammonia monooxygenase (AMO) were applied to identify ammonia-oxidizing bacteria by immunofluorescence (IF) labeling in pure, mixed, and enriched cultures. The antibodies against the AmoA were produced using a synthetic peptide of the AmoA of Nitrosomonas eutropha, whereas the antibodies against the AmoB had been developed previously is against the whole B-subunit of the AMO [Pinck et al. (2001) Appl Environ Microbiol 67:118-124]. Using IF labeling, the AmoA antibodies were specific for the detection of all species of the genus Nitrosomonas. In contrast, the antiserum against AmoB labeled all genera of ammonia oxidizers of the beta-subclass of Proteobacteria (Nitrosomonas, Nitrosospira, Nitrosolobus, and Nitrosovibrio). The fluorescence signals of the AmoA antibodies were spread all over the cells, whereas the signals of the AmoB antibodies were associated with the cytoplasmic membranes. The specificity of the reactions of the antisera with ammonia oxidizers were proven in pure and mixed cultures, and the characteristic IF labeling and the morphology of the cells enabled their identification at the genus level. The genus-specific IF labeling could be used to identify ammonia oxidizers enriched from various habitats. In enrichment cultures of natural sandstone, cells of the genera Nitrosomonas, Nitrosovibrio, and Nitrosospira were detected. Members of the genus Nitrosovibrio and Nitrosolobus were most prominent in enriched garden soil samples, whereas members of the genus Nitrosomonas dominated in enriched activated sludge. The antibodies caused only slight background fluorescence on sandstone and soil particles compared to oligonucleotide probes, which could not be used to detect ammonia oxidizers on these materials because of strong nonspecific fluorescence.}, }
@article {pmid14987816, year = {2004}, author = {Wilshusen, JH and Hettiaratchi, JP and De Visscher, A and Saint-Fort, R}, title = {Methane oxidation and formation of EPS in compost: effect of oxygen concentration.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {129}, number = {2}, pages = {305-314}, doi = {10.1016/j.envpol.2003.10.015}, pmid = {14987816}, issn = {0269-7491}, mesh = {Animals ; Biodegradation, Environmental ; Ecosystem ; Methane/*chemistry ; Oxidation-Reduction ; *Soil Microbiology ; *Soil Pollutants ; *Waste Management ; }, abstract = {Oxygen concentration plays an important role in the regulation of methane oxidation and the microbial ecology of methanotrophs. However, this effect is still poorly quantified in soil and compost ecosystems. The effect of oxygen on the formation of exopolymeric substances (EPS) is as yet unknown. We studied the effect of oxygen on the evolution of methanotrophic activity. At both high and low oxygen concentrations, peak activity was observed twice within a period of 6 months. Phospholipid fatty acid analysis showed that there was a shift from type I to type II methanotrophs during this period. At high oxygen concentration, EPS production was about 250% of the amount at low oxygen concentration. It is hypothesized that EPS serves as a carbon cycling mechanism for type I methanotrophs when inorganic nitrogen is limiting. Simultaneously, EPS stimulates nitrogenase activity in type II methanotrophs by creating oxygen-depleted zones. The kinetic results were incorporated in a simulation model for gas transport and methane oxidation in a passively aerated biofilter. Comparison between the model and experimental data showed that, besides acting as a micro-scale diffusion barrier, EPS can act as a barrier to macro-scale diffusion, reducing the performance of such biofilters.}, }
@article {pmid14987487, year = {2003}, author = {Prieto-Ballesteros, O and Rodríguez, N and Kargel, JS and Kessler, CG and Amils, R and Remolar, DF}, title = {Tírez lake as a terrestrial analog of Europa.}, journal = {Astrobiology}, volume = {3}, number = {4}, pages = {863-877}, doi = {10.1089/153110703322736141}, pmid = {14987487}, issn = {1531-1074}, mesh = {Chemical Phenomena ; Chemistry ; *Earth, Planet ; *Environment ; Evolution, Planetary ; Exobiology ; Extraterrestrial Environment ; Geological Phenomena ; Geology ; Ice ; In Situ Hybridization, Fluorescence ; *Jupiter ; Magnesium Sulfate/chemistry ; Models, Chemical ; Oxygen/chemistry ; Salts ; Sodium Chloride/chemistry ; Spacecraft ; Spectrophotometry, Infrared ; Spectroscopy, Fourier Transform Infrared ; Sulfates ; Temperature ; *Water ; *Water Microbiology ; }, abstract = {Tírez Lake (La Mancha, central Spain) is proposed as a terrestrial analogue of Europa's ocean. The proposal is based on the comparison of the hydrogeochemistry of Tírez Lake with the geochemical features of the alteration mineralogy of meteoritic precursors and with Galileo's Near Infrared Mapping Spectrometer data on Europa's surface. To validate the astrobiological potential of Tírez Lake as an analog of Europa, different hydrogeochemical, mineral, and microbial analyses were performed. Experimental and theoretical modeling helped to understand the crystallization pathways that may occur in Europa's crust. Calculations about the oxidation state of the hypothetical Europan ocean were estimated to support the sulfate-rich neutral liquid model as the origin of Europa's observed hydrated minerals and to facilitate their comparison with Tírez's hydrogeochemistry. Hydrogeochemical and mineralogical analyses showed that Tírez waters corresponded to Mg-Na-SO(4)-Cl brines with epsomite, hexahydrite, and halite as end members. A preliminary microbial ecology characterization identified two different microbial domains: a photosynthetically sustained community represented by planktonic/benthonic forms and microbial mat communities, and a subsurficial anaerobic realm in which chemolithotrophy predominates. Fluorescence in situ hybridization has been used to characterize the prokaryotic diversity of the system. The subsurficial community seemed to be dominated by sulfate-reducing bacteria and methanogens. Frozen Tírez brines were analyzed by Fourier-transform infrared techniques providing spectra similar to those reported previously using pure components and to the Galileo spectral data. Calorimetric measurements of Tírez brines showed pathways and phase metastability for magnesium sulfate and sodium chloride crystallization that may aid in understanding the processes involved in the formation of Europa's icy crust. The use of fluorescence hybridization techniques for microbial detection and characterization in hypersaline environments makes this methodology strongly advisable for future Europa astrobiological missions.}, }
@article {pmid14975667, year = {2004}, author = {Alexandrino, M and Grohmann, E and Szewzyk, U}, title = {Optimization of PCR-based methods for rapid detection of Campylobacter jejuni, Campylobacter coli and Yersinia enterocolitica serovar 0:3 in wastewater samples.}, journal = {Water research}, volume = {38}, number = {5}, pages = {1340-1346}, doi = {10.1016/j.watres.2003.10.036}, pmid = {14975667}, issn = {0043-1354}, mesh = {Campylobacter coli/*isolation &amp; purification ; Campylobacter jejuni/*isolation &amp; purification ; DNA, Bacterial/*analysis ; Environmental Monitoring/*methods ; Polymerase Chain Reaction/methods ; Reproducibility of Results ; Sensitivity and Specificity ; Waste Disposal, Fluid ; Yersinia enterocolitica/*isolation &amp; purification ; }, abstract = {PCR-based methods were evaluated for their adequacy to assess the removal of pathogens from wastewater samples. For the development and optimization of the methods, samples were taken at two different sites from two different constructed wetlands. Campylobacter jejuni/coli and Yersinia enterocolitica serogroup 0:3 were selected as model pathogens and Enterococcus faecalis as a standard microbiological indicator. The chosen PCR protocols were optimized for wastewater DNA extracts in order to obtain high sensitivity and reproducibility independently of the background flora. All PCR protocols were successfully performed and reproducible with a background of up to 10(10) nontarget cells per reaction. Five cells of Y. enterocolitica, 50 cells of C. jejuni/coli, and 500 cells of E. faecalis per 100ml treated water could be detected. The method detection limit in the settled wastewater was higher: 200 cells per 100ml for Y. enterocolitica, 2000 cells per 100ml for C. jejuni/coli, and 20,000 cells per 100ml for E. faecalis. C. jejuni/coli and Y. enterocolitica PCRs were adapted to municipal wastewater, with higher loads of potential PCR inhibitors. Sensitivity was lower for this type of wastewater: 200 cells of Y. enterocolitica and 2000 cells of C. jejuni/coli were detected per 100ml treated wastewater, 2500 cells of Y. enterocolitica and 25,000 cells of C. jejuni/coli per 100ml settled wastewater. The developed PCR methods enable the detection of C. jejuni/coli, Y. enterocolitica serogroup 0:3 and E. faecalis within 12h. They show specificity, reproducibility and low detection limits for the investigated pathogens.}, }
@article {pmid14973198, year = {2004}, author = {Konstantinidis, KT and Tiedje, JM}, title = {Trends between gene content and genome size in prokaryotic species with larger genomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {9}, pages = {3160-3165}, pmid = {14973198}, issn = {0027-8424}, mesh = {Animals ; Cell Division/genetics ; Cell Physiological Phenomena ; DNA/genetics ; DNA Replication/genetics ; Energy Metabolism/genetics ; *Genome ; Genome, Bacterial ; Metabolism/genetics ; Models, Genetic ; Nucleotides/metabolism ; Open Reading Frames ; Protein Biosynthesis ; }, abstract = {Although the evolution process and ecological benefits of symbiotic species with small genomes are well understood, these issues remain poorly elucidated for free-living species with large genomes. We have compared 115 completed prokaryotic genomes by using the Clusters of Orthologous Groups database to determine whether there are changes with genome size in the proportion of the genome attributable to particular cellular processes, because this may reflect both cellular and ecological strategies associated with genome expansion. We found that large genomes are disproportionately enriched in regulation and secondary metabolism genes and depleted in protein translation, DNA replication, cell division, and nucleotide metabolism genes compared to medium- and small-sized genomes. Furthermore, large genomes do not accumulate noncoding DNA or hypothetical ORFs, because the portion of the genome devoted to these functions remained constant with genome size. Traits other than genome size or strain-specific processes are reflected by the dispersion around the mean for cell functions that showed no correlation with genome size. For example, Archaea had significantly more genes in energy production, coenzyme metabolism, and the poorly characterized category, and fewer in cell membrane biogenesis and carbohydrate metabolism than Bacteria. The trends we noted with genome size by using Clusters of Orthologous Groups were confirmed by our independent analysis with The Institute for Genomic Research's Comprehensive Microbial Resource and Kyoto Encyclopedia of Genes and Genomes' Orthology annotation databases. These trends suggest that larger genome-sized species may dominate in environments where resources are scarce but diverse and where there is little penalty for slow growth, such as soil.}, }
@article {pmid14964534, year = {2004}, author = {Johansson, T and Le Quéré, A and Ahren, D and Söderström, B and Erlandsson, R and Lundeberg, J and Uhlén, M and Tunlid, A}, title = {Transcriptional responses of Paxillus involutus and Betula pendula during formation of ectomycorrhizal root tissue.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {17}, number = {2}, pages = {202-215}, doi = {10.1094/MPMI.2004.17.2.202}, pmid = {14964534}, issn = {0894-0282}, mesh = {Amino Acid Sequence ; Arabidopsis/classification/genetics ; Basidiomycota/*genetics ; Betula/*microbiology ; DNA, Complementary/chemistry/genetics ; Enzymes/genetics ; Expressed Sequence Tags ; Fungal Proteins/genetics ; Gene Library ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Plant Proteins/genetics ; Plant Roots/*microbiology ; Sequence Alignment ; Sequence Homology, Amino Acid ; Symbiosis ; Transcription, Genetic ; }, abstract = {In order to obtain information on genes specifically expressed in the ectomycorrhizal symbiosis, 3,555 expressed sequence tags (ESTs) were analyzed from a cDNA library constructed from ectomycorrhiza formed between the basidiomycete Paxillus involutus and birch (Betula pendula). cDNA libraries from saprophytically growing fungus (3,964 ESTs) and from axenic plants (2,532 ESTs) were analyzed in parallel. By clustering all the EST obtained, a nonredundant set of 2,284 unique transcripts of either fungal or plant origin were identified. The expression pattern of these genes was analyzed using cDNA microarrays. The analyses showed that the plant and fungus responded to the symbiosis by altering the expression levels of a number of enzymes involved in carbon metabolism. Several plant transcripts with sequence similarities to genes encoding enzymes in the tricarboxylic cycle and electron transport chain were down regulated as compared with the levels in free-living roots. In the fungal partner, a number of genes encoding enzymes in the lipid and secondary metabolism were down regulated in mycorrhiza as compared with the saprophytically growing mycelium. A substantial number of the ESTs analyzed displayed significant sequence similarities to proteins involved in biotic stress responses, but only a few of them showed differential expression in the mycorrhizal tissue, including plant and fungal metallothioneins and a plant defensin homologue. Several of the genes that were differentially expressed in the mycorrhizal root tissue displayed sequence similarity to genes that are known to regulate growth and development of plant roots and fungal hyphae, including transcription factors and Rho-like GTPases.}, }
@article {pmid14766581, year = {2004}, author = {Lavire, C and Blaha, D and Cournoyer, B}, title = {Selection of unusual actinomycetal primary sigma70 factors by plant-colonizing Frankia strains.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {2}, pages = {991-998}, pmid = {14766581}, issn = {0099-2240}, mesh = {Base Sequence ; DNA-Directed RNA Polymerases/chemistry/*genetics/metabolism ; Elaeagnaceae/*microbiology ; Frankia/*genetics/metabolism ; Gene Expression Regulation, Bacterial ; Molecular Sequence Data ; Phylogeny ; Plant Diseases/*microbiology ; *Selection, Genetic ; Sequence Analysis, DNA ; Sigma Factor/chemistry/*genetics/metabolism ; }, abstract = {Functional adaptations of sigma70 transcriptional factors led to the emergence of several paralogous lineages, each one being specialized for gene transcription under particular growth conditions. Screening of a Frankia strain EaI-12 gene library by sigma70 DNA probing allowed the detection and characterization of a novel actinomycetal primary (housekeeping) sigma70 factor. Phylogenetic analysis positioned this factor in the RpoD cluster of proteobacterial and low-G+C-content gram-positive factors, a cluster previously free of any actinobacterial sequences. sigma70 DNA probing of Frankia total DNA blots and PCR screening detected one or two rpoD-like DNA regions per species. rpoD matched the conserved region in all of the species tested. The other region was found to contain sigA, an alternative primary factor. sigA appeared to be strictly distributed among Frankia species infecting plants by the root hair infection process. Both genes were transcribed by Frankia strain ACN14a grown in liquid cultures. The molecular phylogeny of the sigma70 family determined with Frankia sequences showed that the alternative actinomycetal factors and the essential ones belonged to the same radiation. At least seven distinct paralogous lineages were observed among this radiation, and gene transfers were detected in the HrdB actinomycetal lineage.}, }
@article {pmid14765282, year = {2004}, author = {Taitt, CR and Golden, JP and Shubin, YS and Shriver-Lake, LC and Sapsford, KE and Rasooly, A and Ligler, FS}, title = {A portable array biosensor for detecting multiple analytes in complex samples.}, journal = {Microbial ecology}, volume = {47}, number = {2}, pages = {175-185}, pmid = {14765282}, issn = {0095-3628}, mesh = {Antibodies ; Biosensing Techniques/*instrumentation/*methods ; Biotinylation ; *Environmental Microbiology ; Environmental Monitoring/*methods ; *Extraterrestrial Environment ; Fluorescence ; Immunohistochemistry ; *Spacecraft ; Time Factors ; Toxins, Biological/*analysis ; }, abstract = {The Multi-Analyte Array Biosensor (MAAB) has been developed at the Naval Research Laboratory (NRL) with the goal of simultaneously detecting and identifying multiple target agents in complex samples with minimal user manipulation. This paper will focus on recent improvements in the biochemical and engineering aspects of this instrument. These improvements have enabled the expansion of the repertoire of analytes detected to include Salmonella typhimurium and Listeria monocytogenes, and also expanded the different sample matrices tested. Furthermore, all components of the biochemical assays could be prepared well in advance of sample testing, resulting in a "plug-and-play" methodology. Simultaneous detection of three toxins (ricin, staphylococcal enterotoxin B, and cholera toxin) was demonstrated using a novel fluidics cube module that limits the number of manipulations to only the initial sample loading. This work demonstrates the utility of the MAAB for rapid analysis of complex samples with multianalyte capability, with a minimum of operator manipulations required for either sample preparation or final analysis.}, }
@article {pmid14749909, year = {2004}, author = {Katoh, H and Asthana, RK and Ohmori, M}, title = {Gene expression in the cyanobacterium Anabaena sp. PCC7120 under desiccation.}, journal = {Microbial ecology}, volume = {47}, number = {2}, pages = {164-174}, pmid = {14749909}, issn = {0095-3628}, mesh = {Anabaena/*genetics/*metabolism/physiology ; Biological Transport, Active/physiology ; DNA Primers ; DNA-Directed RNA Polymerases/metabolism ; Dehydration/*metabolism ; Fluorescence ; *Gene Expression Regulation ; Heat-Shock Proteins/metabolism ; Oligonucleotide Array Sequence Analysis ; Potassium/metabolism ; RNA, Messenger/*metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Water-Electrolyte Balance/physiology ; }, abstract = {The N2-fixing cyanobacterium Anabaena sp. PCC7120 showed an inherent capacity for desiccation tolerance. A DNA microarray covering almost the entire genome of Anabaena was used to determine the genome-wide gene expression under desiccation. RNA was extracted from cells at intervals starting from early to late desiccation. The pattern of gene expression in DNA fragments was categorized into seven types, which include four types of up-regulated and three types of down-regulated fragments. Validation of the data was carried out by RT-PCR on selected up-regulated DNA fragments and was consistent with the changes in mRNA levels. Our conclusions regarding desiccation tolerance for Anabaena sp. PCC7120 are as follows: (i) Genes for osmoprotectant metabolisms and the K+ transporting system are up-regulated from early to mid-desiccation; (ii) genes induced by osmotic, salt, and low-temperature stress are up-regulated under desiccation; (iii) genes for heat shock proteins are up-regulated after mid-desiccation; (iv) genes for photosynthesis and the nitrogen-transporting system are down-regulated during early desiccation; and (v) genes for RNA polymerase and ribosomal protein are down-regulated between the early and the middle phase of desiccation. Profiles of gene expression are discussed in relation to desiccation acclimation.}, }
@article {pmid14749908, year = {2004}, author = {Castro, VA and Thrasher, AN and Healy, M and Ott, CM and Pierson, DL}, title = {Microbial characterization during the early habitation of the International Space Station.}, journal = {Microbial ecology}, volume = {47}, number = {2}, pages = {119-126}, pmid = {14749908}, issn = {0095-3628}, mesh = {Bacteria/*genetics ; Cluster Analysis ; DNA Fingerprinting ; *Environment, Controlled ; *Environmental Monitoring ; *Extraterrestrial Environment ; Fungi/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Spacecraft ; }, abstract = {An evaluation of the microbiota from air, water, and surface samples provided a baseline of microbial characterization onboard the International Space Station (ISS) to gain insight into bacterial and fungal contamination during the initial stages of construction and habitation. Using 16S genetic sequencing and rep-PCR, 63 bacterial strains were isolated for identification and fingerprinted for microbial tracking. Of the bacterial strains that were isolated and fingerprinted, 19 displayed similarity to each other. The use of these molecular tools allowed for the identification of bacteria not previously identified using automated biochemical analysis and provided a clear indication of the source of several ISS contaminants. Strains of Bradyrhizobium and Sphingomonas unable to be identified using sequencing were identified by comparison of rep-PCR DNA fingerprints. Distinct DNA fingerprints for several strains of Methylobacterium provided a clear indication of the source of an ISS water supply contaminant. Fungal and bacterial data acquired during monitoring do not suggest there is a current microbial hazard to the spacecraft, nor does any trend indicate a potential health risk. Previous spacecraft environmental analysis indicated that microbial contamination will increase with time and will require continued surveillance.}, }
@article {pmid14749907, year = {2004}, author = {Suzuki, Y and Inagaki, F and Takai, K and Nealson, KH and Horikoshi, K}, title = {Microbial diversity in inactive chimney structures from deep-sea hydrothermal systems.}, journal = {Microbial ecology}, volume = {47}, number = {2}, pages = {186-196}, pmid = {14749907}, issn = {0095-3628}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Barium Sulfate ; Base Sequence ; *Biodiversity ; Colony Count, Microbial ; Copper ; DNA Primers ; DNA, Ribosomal/genetics ; *Ecosystem ; Geologic Sediments/analysis/*microbiology ; In Situ Hybridization, Fluorescence ; Indoles ; Molecular Sequence Data ; Oceans and Seas ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Spectrum Analysis ; X-Ray Diffraction ; }, abstract = {Massive chimney structures, which are characteristic of many hydrothermally active zones, harbor diverse microbial communities containing both thermophilic and hyperthermophilic microbes. However, vent chimneys ultimately become hydrothermally inactive, and the changes that occur in the microbial communities upon becoming inactive have not been documented. We thus collected inactive chimneys from two geologically and geographically distinct hydrothermal fields, Iheya North in the western Pacific Ocean and the Kairei field in the Indian Ocean. The chimneys displayed easily distinguishable strata, which were analyzed with regard to both mineralogical and microbiological properties. X-ray diffraction pattern and energy-dispersive spectroscopic analyses revealed that the main mineral components of the chimney substructures from Iheya North and the Kairei field were barite (BaSO4) and chalcopyrite (CuFeS2), respectively. Microbial cell densities in the substructures determined by DAPI counting ranged from 1.7 x 10(7) cells g(-1) to 3.0 x 10(8) cells g(-1). The proportions of archaeal rDNA in the whole microbial rDNA assemblages in all substructures were, at most, a few percent as determined by quantitative fluorogenic PCR. The microbial rDNA clone analysis and whole-cell fluorescence in situ hybridization revealed a community that was decidedly different from any communities previously reported in active chimneys. Curiously, both samples revealed the abundant presence of a group of Bacteria related to a magnetosome-bearing bacterium, " Magnetobacterium bavaricum" of the Nitrospirae division. These results suggest that inactive chimneys provide a distinct microbial habitat.}, }
@article {pmid14749906, year = {2004}, author = {La Duc, MT and Kern, R and Venkateswaran, K}, title = {Microbial monitoring of spacecraft and associated environments.}, journal = {Microbial ecology}, volume = {47}, number = {2}, pages = {150-158}, pmid = {14749906}, issn = {0095-3628}, mesh = {Adenosine Triphosphate/analysis ; Bacteria/genetics ; Biological Assay/methods ; Colony Count, Microbial ; DNA/genetics/isolation &amp; purification ; *Environment, Controlled ; *Environmental Microbiology ; Environmental Monitoring/*methods ; *Extraterrestrial Environment ; Phylogeny ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; *Spacecraft ; }, abstract = {Rapid microbial monitoring technologies are invaluable in assessing contamination of spacecraft and associated environments. Universal and widespread elements of microbial structure and chemistry are logical targets for assessing microbial burden. Several biomarkers such as ATP, LPS, and DNA (ribosomal or spore-specific), were targeted to quantify either total bioburden or specific types of microbial contamination. The findings of these assays were compared with conventional, culture-dependent methods. This review evaluates the applicability and efficacy of some of these methods in monitoring the microbial burden of spacecraft and associated environments. Samples were collected from the surfaces of spacecraft, from surfaces of assembly facilities, and from drinking water reservoirs aboard the International Space Station (ISS). Culture-dependent techniques found species of Bacillus to be dominant on these surfaces. In contrast, rapid, culture-independent techniques revealed the presence of many Gram-positive and Gram-negative microorganisms, as well as actinomycetes and fungi. These included both cultivable and noncultivable microbes, findings further confirmed by DNA-based microbial detection techniques. Although the ISS drinking water was devoid of cultivable microbes, molecular-based techniques retrieved DNA sequences of numerous opportunistic pathogens. Each of the methods tested in this study has its advantages, and by coupling two or more of these techniques even more reliable information as to microbial burden is rapidly obtained.}, }
@article {pmid14749905, year = {2004}, author = {Robertson, LJ and Gjerde, BK}, title = {Effects of the Norwegian winter environment on Giardia cysts and Cryptosporidium oocysts.}, journal = {Microbial ecology}, volume = {47}, number = {4}, pages = {359-365}, pmid = {14749905}, issn = {0095-3628}, mesh = {Animals ; Cattle/parasitology ; *Climate ; Cryptosporidium/cytology/metabolism/*physiology ; Dogs/parasitology ; *Environment ; Feces/parasitology ; Fluorescent Dyes/metabolism ; Giardia/cytology/metabolism/*physiology ; Indoles ; Norway ; Oocysts/*physiology ; *Seasons ; }, abstract = {The structural integrity of Cryptosporidium oocysts and Giardia cysts in the Norwegian winter environment was investigated. During winter 2001/2002, Cryptosporidium oocysts and Giardia cysts were placed in the upper layers of soil in different matrices contained in chambers and exposed to the Norwegian climate. Morphological characteristics and inclusion/exclusion of vital dyes were monitored and compared to refrigerated controls. Reduction in parasite numbers was recorded for all parasites, geographical locations, and matrices. Shear forces generated during freeze-thaw cycles are postulated to have disintegrated the parasites exposed to the Norwegian winter and retrospective laboratory studies support this theory. Increased dye inclusion, possibly indicative of viability loss, was also noted. The refrigerated control parasites exhibited no decline in numbers, and alteration in dye inclusion characteristics for refrigerated parasites was slower. Cryptosporidium oocysts were apparently more robust than Giardia cysts; differences between isolates were also noted. These results suggest Cryptosporidium oocysts and Giardia cysts do not persist in the Norwegian terrestrial environment over winter, and when detected, will have been excreted since the previous winter. Differences in the morphological characteristics, matrix effects, and the possible relationship of the dye data to parasite survival are discussed in relation to further studies.}, }
@article {pmid14735216, year = {2003}, author = {Lemriss, S and Laurent, F and Couble, A and Casoli, E and Lancelin, JM and Saintpierre-Bonaccio, D and Rifai, S and Fassouane, A and Boiron, P}, title = {Screening of nonpolyenic antifungal metabolites produced by clinical isolates of actinomycetes.}, journal = {Canadian journal of microbiology}, volume = {49}, number = {11}, pages = {669-674}, doi = {10.1139/w03-088}, pmid = {14735216}, issn = {0008-4166}, mesh = {Anti-Bacterial Agents/pharmacology ; Antifungal Agents/*pharmacology ; Aspergillus/drug effects ; Candida/drug effects ; *Drug Evaluation, Preclinical ; Ergosterol ; Gram-Negative Bacteria/drug effects ; Gram-Positive Bacteria/drug effects ; Humans ; Microbial Sensitivity Tests ; Mitosporic Fungi/*drug effects ; Polyenes/chemistry ; Streptomyces/*metabolism ; Trichophyton/drug effects ; }, abstract = {The purpose of this work was to screen clinical isolates of actinomycetes producing nonpolyenic antifungals. This choice was made to limit the problem of rediscovery of well-known antifungal families, especially polyenic antifungals. One hundred and ten strains were tested, using two diffusion methods and two test media, against three yeast species and three filamentous fungi. Among 54 strains (49%) showing antifungal activity, five strains belonging to the genus Streptomyces were active against all test organisms and appeared promising. These results indicate that clinical and environmental isolates of actinomycetes could be an interesting source of antifungal bioactive substances. The production of nonpolyenic antifungal substances by these five active isolates was investigated using several criteria: antibacterial activity, ergosterol inhibition, and UV-visible spectra of active extracts. One active strain responded to all three selection criteria and produced potentially nonpolyenic antifungal metabolites. This strain was retained for further investigation, in particular, purification, structure elucidation, and mechanism of action of the active product.}, }
@article {pmid14727173, year = {2004}, author = {Wallander, H and Göransson, H and Rosengren, U}, title = {Production, standing biomass and natural abundance of 15N and 13C in ectomycorrhizal mycelia collected at different soil depths in two forest types.}, journal = {Oecologia}, volume = {139}, number = {1}, pages = {89-97}, pmid = {14727173}, issn = {0029-8549}, mesh = {Biomass ; Carbon Isotopes/analysis ; Mycorrhizae/*chemistry/*growth &amp; development ; Nitrogen Isotopes/analysis ; Picea/growth &amp; development/physiology ; Plant Roots/*microbiology ; Quercus/growth &amp; development/physiology ; *Trees ; }, abstract = {Nutrient uptake by forest trees is dependent on ectomycorrhizal (EM) mycelia that grow out into the soil from the mycorrhizal root tips. We estimated the production of EM mycelia in root free samples of pure spruce and mixed spruce-oak stands in southern Sweden as mycelia grown into sand-filled mesh bags placed at three different soil depths (0-10, 10-20 and 20-30 cm). The mesh bags were collected after 12 months and we found that 590+/-70 kg ha(-1) year(-1) of pure mycelia was produced in spruce stands and 420+/-160 kg ha(-1) year(-1) in mixed stands. The production of EM mycelia in the mesh bags decreased with soil depth in both stand types but tended to be more concentrated in the top soil in the mixed stands compared to the spruce stands. The fungal biomass was also determined in soil samples taken from different depths by using phospholipid fatty acids as markers for fungal biomass. Subsamples were incubated at 20 degrees C for 5 months and the amount of fungal biomass that degraded during the incubation period was used as an estimate of EM fungal biomass. The EM biomass in the soil profile decreased with soil depth and did not differ significantly between the two stand types. The total EM biomass in the pure spruce stands was estimated to be 4.8+/-0.9 x 10(3) kg ha(-1) and in the mixed stands 5.8+/-1.1 x 10(3) kg ha(-1) down to 70 cm depth. The biomass and production estimates of EM mycelia suggest a very long turnover time or that necromass has been included in the biomass estimates. The amount of N present in EM mycelia was estimated to be 121 kg N ha(-1) in spruce stands and 187 kg N ha(-1) in mixed stands. The delta13C value for mycelia in mesh bags was not influenced by soil depth, indicating that the fungi obtained all their carbon from the tree roots. The delta13C values in mycelia collected from mixed stands were intermediate to values from pure spruce and pure oak stands suggesting that the EM mycelia received carbon from both spruce and oak trees in the mixed stands. The delta15N value for the EM mycelia and the surrounding soil increased with soil depth suggesting that they obtained their entire N from the surrounding soil.}, }
@article {pmid14723944, year = {2004}, author = {Långmark, J and Storey, MV and Ashbolt, NJ and Stenström, TA}, title = {Artificial groundwater treatment: biofilm activity and organic carbon removal performance.}, journal = {Water research}, volume = {38}, number = {3}, pages = {740-748}, doi = {10.1016/j.watres.2003.10.021}, pmid = {14723944}, issn = {0043-1354}, mesh = {Biodegradation, Environmental ; *Biofilms ; Carbon/*isolation &amp; purification/*metabolism ; DNA, Bacterial ; Filtration ; In Situ Hybridization, Fluorescence ; Organic Chemicals/metabolism ; Population Dynamics ; Silicon Dioxide ; *Soil Microbiology ; Waste Disposal, Fluid/*methods ; Water Purification/*methods ; }, abstract = {The artificial recharge of sand aquifers with raw source waters is a means both explored and utilised by many water utilities to meet the future potable water demands for increasing urban populations. The microbial ecology within these systems is however, poorly understood, as is the role that microbial biofilms play in the quality of finished water. Knowledge of the ability of biofilm bacteria to metabolise natural organic matter (NOM) is limited, particularly in respect to the degradation of normally recalcitrant hydrophilic and hydrophobic humic acid fractions by sessile and planktonic microbial consortia within sand aquifer systems. To simulate the artificial recharge of sand aquifers that were proposed for the Greater Stockholm Area, four separate 4 m deep sand columns were fed raw lake water and examined over a 45-week study period. The simulated aquifer system (hydraulic retention time 9-16 h) demonstrated the removal of total organic carbon (TOC) (10+/-5%), direct total counts (DTC) of bacteria (74+/-11%), heterotrophic plate count (HPC) bacteria (87+/-5%) and assimilable organic carbon (AOC) (87+/-5%), thereby fulfilling an important barrier function, except for the removal of TOC. Hydrophilic humic acid fractions were more readily metabolised by microbiota (HPC and EUB338-positive cells) harvested from the raw source water (SSM-W), whilst hydrophobic humic acid fractions promoted higher activity by microbiota harvested from the sand matrix (SSM-S). The apparent low activity demonstrated by biofilm microbiota (approximately 40% and 25% of DTC were positive to EUB338 probing for sand matrix and slide biofilms, respectively) could be attributed to the highly recalcitrant nature of the organic loads, whilst at the same time explain the poor removal of TOC. Following nutrient activation (by the PAC assay) nonetheless, a 3-fold increase in the percentage of EUB-positive bacteria was observed on glass slides. Furthermore, the incubation of SSM-S with R2A increased probe-active cells from 57+/-8% to 75+/-7% of DTC and at the same time increased SSM-W from 38+/-8% to 50+/-10%. Whilst these results may imply a good potential for the biological treatment of water by shallow sand aquifers, further work should address the poor removal of TOC observed in this study.}, }
@article {pmid14722690, year = {2003}, author = {Muñoz-Rojas, J and Caballero-Mellado, J}, title = {Population dynamics of Gluconacetobacter diazotrophicus in sugarcane cultivars and its effect on plant growth.}, journal = {Microbial ecology}, volume = {46}, number = {4}, pages = {454-464}, pmid = {14722690}, issn = {0095-3628}, mesh = {Gluconacetobacter/*physiology ; Nitrogen Fixation/*physiology ; Population Dynamics ; Saccharum/chemistry/*growth &amp; development/*microbiology ; Species Specificity ; *Symbiosis ; }, abstract = {Different experiments have estimated that the contribution of biological nitrogen fixation (BNF) is largely variable among sugarcane cultivars. Which bacteria are the most important in sugarcane-associated BNF is unknown. However, Gluconacetobacter diazotrophicus has been suggested as a strong candidate responsible for the BNF observed. In the present study, bacteria-free micropropagated plantlets of five sugarcane cultivars were inoculated with three G. diazotrophicus strains belonging to different genotypes. Bacterial colonization was monitored under different nitrogen fertilization levels and at different stages of plant growth. Analysis of the population dynamics of G. diazotrophicus strains in the different sugarcane varieties showed that the bacterial populations decreased drastically in relation to plant age, regardless of the nitrogen fertilization level, bacterial genotype or sugarcane cultivars. However, the persistence of the three strains was significantly longer in some cultivars (e.g., MEX 57-473) than in others (e.g., MY 55-14). In addition, some strains (e.g., PAl 5(T)) persisted for longer periods in higher numbers than other strains (e.g., PAl 3) inside plants of all the cultivars tested. Indeed, the study showed that the inoculation of G. diazotrophicus may be beneficial for sugarcane plant growth, but this response is dependent both on the G. diazotrophicus genotype and the sugarcane variety. The most positive response to inoculation was observed with the combination of strain PAl 5(T) and the variety MEX 57-473. Although the positive effect on sugarcane growth apparently occurred by mechanisms other than nitrogen fixation, the results show the importance of the sugarcane variety for the persistence of the plant-bacteria interaction, and it could explain the different rates of BNF estimated among sugarcane cultivars.}, }
@article {pmid14717449, year = {2003}, author = {Müller, T and Müller, M and Behrendt, U and Stadler, B}, title = {Diversity of culturable phyllosphere bacteria on beech and oak: the effects of lepidopterous larvae.}, journal = {Microbiological research}, volume = {158}, number = {4}, pages = {291-297}, doi = {10.1078/0944-5013-00207}, pmid = {14717449}, issn = {0944-5013}, mesh = {Ammonia/metabolism ; Animals ; Bacteria/classification/*isolation &amp; purification ; Culture Media ; Ecosystem ; Fagus/*microbiology ; Larva/microbiology ; Lepidoptera/growth &amp; development/*microbiology ; Nitrates/metabolism ; Plant Leaves/*microbiology ; Quercus/*microbiology ; }, abstract = {The community composition of epiphytic heterotrophic bacteria on leaves of beech and oak, which were either damaged by lepidopterous larvae or remained undamaged, was investigated. In addition, the ability of these bacteria to utilize inorganic nitrogen was studied. The bacteria were isolated on nutrient agar and systematically identified with biochemical and physiological tests. Rarefaction plots and the Shannon-Wiener function revealed that species diversity was significantly higher on leaves of damaged beech compared to undamaged leaves, but no differences were found on leaves of oak. The portion of bacterial isolates showing a strong response to ammonia and nitrate was significantly larger on leaves of oak than on those of beech. Furthermore, significantly more isolates with a high capability to assimilate both nitrogen compounds were found on leaves attacked by the folivorous larvae compared to those not attacked on oak. It is suggested that the changes in the microbial community in response to folivorous insects might affect the extent of nutrient cycling exceeding eventually the scale of a leaf.}, }
@article {pmid14711656, year = {2004}, author = {Stres, B and Mahne, I and Avgustin, G and Tiedje, JM}, title = {Nitrous oxide reductase (nosZ) gene fragments differ between native and cultivated Michigan soils.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {1}, pages = {301-309}, pmid = {14711656}, issn = {0099-2240}, mesh = {*Agriculture ; Alphaproteobacteria/classification/*enzymology/genetics ; DNA, Bacterial/analysis/genetics ; Gammaproteobacteria/classification/*enzymology/genetics ; Genetic Variation ; Michigan ; Molecular Sequence Data ; Oxidoreductases/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Soil/*analysis ; Soil Microbiology ; }, abstract = {The effect of standard agricultural management on the genetic heterogeneity of nitrous oxide reductase (nosZ) fragments from denitrifying prokaryotes in native and cultivated soil was explored. Thirty-six soil cores were composited from each of the two soil management conditions. nosZ gene fragments were amplified from triplicate samples, and PCR products were cloned and screened by restriction fragment length polymorphism (RFLP). The total nosZ RFLP profiles increased in similarity with soil sample size until triplicate 3-g samples produced visually identical RFLP profiles for each treatment. Large differences in total nosZ profiles were observed between the native and cultivated soils. The fragments representing major groups of clones encountered at least twice and four randomly selected clones with unique RFLP patterns were sequenced to verify nosZ identity. The sequence diversity of nosZ clones from the cultivated field was higher, and only eight patterns were found in clone libraries from both soils among the 182 distinct nosZ RFLP patterns identified from the two soils. A group of clones that comprised 32% of all clones dominated the gene library of native soil, whereas many minor groups were observed in the gene library of cultivated soil. The 95% confidence intervals of the Chao1 nonparametric richness estimator for nosZ RFLP data did not overlap, indicating that the levels of species richness are significantly different in the two soils, the cultivated soil having higher diversity. Phylogenetic analysis of deduced amino acid sequences grouped the majority of nosZ clones into an interleaved Michigan soil cluster whose cultured members are alpha-Proteobacteria. Only four nosZ sequences from cultivated soil and one from the native soil were related to sequences found in gamma-Proteobacteria. Sequences from the native field formed a distinct, closely related cluster (D(mean) = 0.16) containing 91.6% of the native clones. Clones from the cultivated field were more distantly related to each other (D(mean) = 0.26), and 65% were found outside of the cluster from the native soil, further indicating a difference in the two communities. Overall, there appears to be a relationship between use and richness, diversity, and the phylogenetic position of nosZ sequences, indicating that agricultural use of soil caused a shift to a more diverse denitrifying community.}, }
@article {pmid14708752, year = {2003}, author = {Maruyama, T and Kato, K and Yokoyama, A and Tanaka, T and Hiraishi, A and Park, HD}, title = {Dynamics of microcystin-degrading bacteria in mucilage of Microcystis.}, journal = {Microbial ecology}, volume = {46}, number = {2}, pages = {279-288}, pmid = {14708752}, issn = {0095-3628}, mesh = {Adhesives ; Carcinogens/*metabolism ; Ecology ; In Situ Hybridization, Fluorescence ; Microcystins ; Microcystis/genetics/*physiology ; Peptides, Cyclic/*metabolism ; Population Dynamics ; *Water Microbiology ; Water Supply ; }, abstract = {To reveal the process of degradation of hepatotoxic microcystin produced in Microcystis cells during the Microcystis bloom period, we used fluorescence in situ hybridization (FISH) to analyze the population dynamics of microcystin-degrading bacteria in Microcystis mucilage. We designed and applied an oligonucleotide probe targeted to the 16S rRNA sequence of strain Y2 of a microcystin-degrading bacterium (MCD-bacterium), which was isolated from Lake Suwa, Japan. In both the 1998 and 1999 tests, FISH clearly showed that MCD-bacteria existed in the mucilage and that, when a high concentration of cell-bound microcystin was detected, MCD-bacteria exceeded 10% of the sum of bacteria hybridized with group-specific probes. The concentration of MCD-bacteria was highest in summer 1998, when a toxic species, M. viridis, was dominant. There was a high correlation between the number of MCD-bacteria in the mucilage and the concentration of cell-bound microcystin in the lake. Our results suggest that MCD-bacteria responded to changes in the concentration of microcystin and degraded the microcystin when it was released from Microcystis cells. We also analyzed changes in the bacterial community structure associated with the Microcystis colonies by using domain- and group-specific oligonucleotide probes. Changes in the concentrations of the Cytophaga/Flavobacterium group and delta-Proteobacteria, which can degrade macromolecules derived from Microcystis cells, were synchronized with changes in the concentration of Microcystis. The results not only suggest the significant role of MCD-bacteria in detoxification, but also demonstrate a possible sequence of degradation from Microcystis cells to microcystin maintained in the cell, which is then carried out by bacterial consortia in the mucilage.}, }
@article {pmid14708751, year = {2003}, author = {Earl, J and Hall, G and Pickup, RW and Ritchie, DA and Edwards, C}, title = {Analysis of methanogen diversity in a hypereutrophic lake using PCR-RFLP analysis of mcr sequences.}, journal = {Microbial ecology}, volume = {46}, number = {2}, pages = {270-278}, pmid = {14708751}, issn = {0095-3628}, mesh = {*Bacteria ; DNA, Bacterial/*analysis ; Ecology ; Environmental Monitoring/methods ; *Eutrophication ; Methane/*metabolism ; Oxidoreductases/analysis/*genetics ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Population Dynamics ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {The incidence and diversity of methanogens in Priest Pot, a dynamic and active lake, were monitored by analysing mcrA gene sequences generated from total DNA samples obtained at different times of the year and amplified using the polymerase chain reaction. A number of mcrA clones were analysed by developing an RFLP-based protocol to generate a number of restriction patterns that were assigned to a number of classes. The RFLP patterns for each class were compared with published sequence information for mcrA from cultured methanogens as well as with those from other experimental studies. They could be used to assign tentative identification for some of the Priest Pot clones and also revealed the presence of a number of clones that could not be affiliated to any known methanogens. The limitations of using RFLP profiles of mcrA gene sequences for studying methanogen ecology are discussed.}, }
@article {pmid14708750, year = {2003}, author = {Cummings, DE and Snoeyenbos-West, OL and Newby, DT and Niggemyer, AM and Lovley, DR and Achenbach, LA and Rosenzweig, RF}, title = {Diversity of Geobacteraceae species inhabiting metal-polluted freshwater lake sediments ascertained by 16S rDNA analyses.}, journal = {Microbial ecology}, volume = {46}, number = {2}, pages = {257-269}, pmid = {14708750}, issn = {0095-3628}, mesh = {Cloning, Molecular ; Geobacter/*genetics ; Geologic Sediments/*microbiology ; *Phylogeny ; Polymerase Chain Reaction ; Population Dynamics ; RNA, Ribosomal, 16S/*genetics ; Water Pollutants/*poisoning ; Water Supply ; }, abstract = {The abundance, distribution, and phylogenetic diversity of members of the Fe(III)-reducing family Geobacteraceae were studied along a gradient of metal contaminants in Lake Coeur d'Alene, Idaho. Partial 16S rRNA gene fragments were amplified by PCR using primers directed toward conserved regions of the gene within the family Geobacteraceae. Analysis of amplicons separated by denaturing gradient gel electrophoresis (DGGE) suggested within-site variation was as great as between-site variation. Amplicons were cloned and grouped by RFLP type and DGGE migration distance and representatives were sequenced. Grouping clones with 3% or less sequence dissimilarity, 15 distinct phylotypes were identified compared to 16 distinct DGGE bands. Only 1 phylotype was recovered from all sites. This clone, B14, is most closely related to Geobacter metallireducens and constituted a greater portion of the pristine community than of the contaminated communities. A second phylotype, Q2, predominated in the contaminated communities and was notably absent from the pristine libraries. Clone Q2 presents a high degree of sequence similarity to two Geobacter spp. previously isolated from this region of Lake Coeur d'Alene. Six phylotypes were unique to the contaminated sediments, whereas two were found only in the pristine sediments. Indices of diversity (Shannon and Simpson) were consistently higher when calculated with DGGE data than when clone library data were used. Most-probable-number PCR and real-time PCR suggested that the Geobacteraceae phylotypes were spread relatively evenly across all three sites along the gradient. Our data indicate that the Geobacteraceae are diverse and abundant in Lake Coeur d'Alene sediments, regardless of metals content. These results provide insight into the ability of dissimilatory Fe(III)-reducing bacteria to colonize habitats with elevated metal concentrations, and they have important implications for the management and remediation of metal-contaminated sites.}, }
@article {pmid14708749, year = {2003}, author = {Stopar, D and Cerne, A and Zigman, M and Poljsak-Prijatelj, M and Turk, V}, title = {Viral abundance and a high proportion of lysogens suggest that viruses are important members of the microbial community in the Gulf of Trieste.}, journal = {Microbial ecology}, volume = {46}, number = {2}, pages = {249-256}, pmid = {14708749}, issn = {0095-3628}, mesh = {Bacteria ; Bacteriophages ; Italy ; Microscopy, Electron ; Plankton ; Population Dynamics ; *Viruses ; *Water Microbiology ; }, abstract = {Epifluorescence microscopy and transmission electron microscopy were applied to study virioplankton community in the Gulf of Trieste (northern Adriatic Sea). The total viral abundance was in a range between 2.5 x 10(9)/L and 2.9 x 10(10)/L and was positively correlated with trophic status of the environment. Viruslike particles were significantly correlated with bacterial abundance in all samples studied. Correlations with other physicochemical or biological parameters were not significant. The data suggest that, because of the substantial fraction of tailed viruses present (26%), bacteriophages are an important component of the virioplankton community in the Gulf of Trieste. The abundance of viruslike particles in the seawater changed at hour intervals in a range from 1.3 x 10(9)/L to 5.1 x 10(9)/L. A significant fraction (71%) of the bacterial isolates was inducible in vitro by mitomycin C, and a high occurrence (51%) of lysogenic isolates with more than one phage morphotype present in the lysate was detected. The presence of lysogenic bacteria in the seawater was confirmed in situ with a mitomycin C induction experiment on the natural bacterial population. Results suggest that virioplankton is an abundant component of the microbial community in the Gulf of Trieste.}, }
@article {pmid14708748, year = {2003}, author = {Keough, BP and Schmidt, TM and Hicks, RE}, title = {Archaeal nucleic acids in picoplankton from great lakes on three continents.}, journal = {Microbial ecology}, volume = {46}, number = {2}, pages = {238-248}, pmid = {14708748}, issn = {0095-3628}, mesh = {Africa ; Archaea/*genetics ; Asia ; Cloning, Molecular ; Europe ; Great Lakes Region ; Nucleic Acids/*analysis ; *Phylogeny ; *Plankton ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Phylogenetic analysis of PCR-amplified 16S rRNA genes revealed the presence of archaea in picoplankton collected from the Laurentian Great Lakes in North America, Africa's Lake Victoria, and Lakes Ladoga and Onega in northeastern Eurasia. From 1 to 10% of the rRNA extracted from size-fractionated picoplankton (>0.2 microm but <1.2 microm) collected in the epilimnion and hypolimnion of these lakes was specific to the Archaea, whereas the majority of rRNA was derived from Bacteria. Analysis of the 16S rRNA genes cloned from these samples indicated they were closely related to crenarchaeal sequences that have been widely characterized from marine environments. The presence of nearly identical 16S rDNA clones in several of these geographically disparate lakes suggests a cosmopolitan distribution of specific subgroups of these Archaea in freshwater environments. Despite their abundance in the water column of freshwater lakes, we have no representatives of these crenarchaea in pure culture, and so their physiological characteristics and ecological role remain unknown.}, }
@article {pmid14708747, year = {2003}, author = {LaMontagne, MG and Holden, PA}, title = {Comparison of free-living and particle-associated bacterial communities in a coastal lagoon.}, journal = {Microbial ecology}, volume = {46}, number = {2}, pages = {228-237}, pmid = {14708747}, issn = {0095-3628}, mesh = {*Bacteria ; *Ecosystem ; Particle Size ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Population Dynamics ; Principal Component Analysis ; RNA, Ribosomal, 16S/analysis ; Rain ; Seasons ; Soil ; *Water Microbiology ; Water Supply ; }, abstract = {We analyzed, by terminal restriction fragment length polymorphisms (T-RFLPs) of PCR-amplified 16S rDNA, microbial diversity in water collected during the dry and wet seasons in a human-impacted coastal lagoon. Water samples were fractionated by prefiltration to differentiate particle-associated and free-living microbes. From a sample collected during the dry season, prefiltration removed 23 to 44% of bacteria, as assessed by direct counts and MPN, and 99% of phytoplankton, as assessed by chlorophyll a. Restriction with RsaI yielded fewer peaks than restriction with HhaI. Diversity indices calculated from T-RFLPs were higher in the lagoon than adjoining coastal waters and higher in the particle-associated than the free-living fraction. In the dry season, peaks found only in bulk and particle-associated T-RFLPs were consistent with plastid and cyanobacterial ribotypes. These peaks matched those observed in the sequence of a clone generated from the bulk fraction with plastid and cyanobacterial specific primers. This clone appeared related to plastids found in the diatom genus Skeletonema. Principal component analysis of T-RFLPs suggested that the difference between the free-living and particle-associated fractions in the dry season was less than temporal variability in this lagoon and that these fractions varied significantly only in the wet season. This fractionation of microbial populations into particle-associated and free-living guilds during the wet season, when water residence time in the lagoon is relatively low, suggests an external source of particle-associated bacteria such as erosion of upland soils by runoff.}, }
@article {pmid14708746, year = {2003}, author = {LaMontagne, MG and Schimel, JP and Holden, PA}, title = {Comparison of subsurface and surface soil bacterial communities in California grassland as assessed by terminal restriction fragment length polymorphisms of PCR-amplified 16S rRNA genes.}, journal = {Microbial ecology}, volume = {46}, number = {2}, pages = {216-227}, pmid = {14708746}, issn = {0095-3628}, mesh = {Biomass ; California ; Carbon/metabolism ; Cloning, Organism ; DNA, Bacterial/*analysis ; *Ecosystem ; *Poaceae ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Population Dynamics ; RNA, Ribosomal, 16S/analysis ; *Soil Microbiology ; Water ; }, abstract = {The integrated biomass beneath the surface horizon in unsaturated soils is large and potentially important in nutrient and carbon cycling. Compared to surface soils, the ecology of these subsurface soils is weakly understood, particularly in terms of the composition of bacterial communities. We compared soil bacterial communities along two vertical transects by terminal restriction fragment length polymorphisms (TRFLPs) of PCR-amplified 16S rRNA genes to determine how surface and deep bacterial communities differ. DNA yield from soils collected from two Mediterranean grassland transects decreased exponentially from the surface to 4 m deep. Richness, as assessed by the number of peaks obtained after restriction with HhaI, MspI, RsaI, or HaeIII, and diversity, as assessed by the Shannon diversity indices, were lowest in the deepest sample. Lower diversity at depth is consistent with species-energy theory, which would predict relatively low diversity in the low organic matter horizons. Principal components analysis suggested that, in terms of HhaI and HaeIII generated TRFLPs, bacterial communities differed between depths. The most abundant amplicons cloned from the deepest sample contained sequences with restriction sites consistent with the largest peaks observed in TRFLPs generated from deep samples. These more abundant operational taxonomic units (OTUs) appeared related to Pseudomonas and Variovorax. Several OTUs were more related to each other than any previously described ribotypes. These OTUs showed similarity to bacteria from the divisions Actinobacteria and Firmicutes.}, }
@article {pmid14708745, year = {2003}, author = {Feris, KP and Ramsey, PW and Frazar, C and Rillig, MC and Gannon, JE and Holben, WE}, title = {Structure and seasonal dynamics of hyporheic zone microbial communities in free-stone rivers of the western United States.}, journal = {Microbial ecology}, volume = {46}, number = {2}, pages = {200-215}, pmid = {14708745}, issn = {0095-3628}, mesh = {DNA, Bacterial/analysis ; *Food Chain ; *Hyphomicrobium ; Phylogeny ; Polymerase Chain Reaction ; Population Dynamics ; RNA, Ribosomal, 16S/analysis ; *Rhizobium ; Rivers ; Seasons ; United States ; *Water Microbiology ; }, abstract = {The hyporheic zone of a river is characterized by being nonphotic, exhibiting chemical/redox gradients, and having a heterotrophic food web based on the consumption of organic carbon entrained from surface waters. Hyporheic microbial communities constitute the base of food webs in these environments and are important for maintaining a functioning lotic ecosystem. While microbial communities of rivers dominated by fine-grained sediments are relatively well studied, little is known about the structure and seasonal dynamics of microbial communities inhabiting the predominantly gravel and cobble hyporheic zones of rivers of the western United States. Here, we present the first molecular analysis of hyporheic microbial communities of three different stream types (based on mean base discharge, substratum type, and drainage area), in Montana. Utilizing 16S rDNA phylogeny, DGGE pattern analysis, and qPCR, we have analyzed the prokaryotic communities living on the 1.7 to 2.36 mm grain-size fraction of hyporheic sediments from three separate riffles in each stream. DGGE analysis showed clear seasonal community patterns, indicated similar community composition between different riffles within a stream (95.6-96.6% similarity), and allowed differentiation between communities in different streams. Each river supported a unique complement of species; however, several phylogenetic groups were conserved between all three streams including Pseudomonads and members of the genera Aquabacterium, Rhodoferax, Hyphomicrobium, and Pirellula. Each group showed pronounced seasonal trends in abundance, with peaks during the Fall. The Hyphomicrobium group was numerically dominant throughout the year in all three streams. This work provides a framework for investigating the effects of various environmental factors and anthropogenic effects on microbial communities inhabiting the hyporheic zone.}, }
@article {pmid14708744, year = {2003}, author = {Mitchell, EA and Gilbert, D and Buttler, A and Amblard, C and Grosvernier, P and Gobat, JM}, title = {Structure of microbial communities in Sphagnum peatlands and effect of atmospheric carbon dioxide enrichment.}, journal = {Microbial ecology}, volume = {46}, number = {2}, pages = {187-199}, pmid = {14708744}, issn = {0095-3628}, mesh = {Amoeba ; Animals ; Biomass ; Carbon Dioxide/*pharmacology ; *Greenhouse Effect ; Methane/analysis ; Population Dynamics ; *Soil Microbiology ; *Sphagnopsida ; }, abstract = {Little is known about the structure of microbial communities in Sphagnum peatlands, and the potential effects of the increasing atmospheric CO2 concentration on these communities are not known. We analyzed the structure of microbial communities in five Sphagnum-dominated peatlands across Europe and their response to CO2 enrichment using miniFACE systems. After three growing seasons, Sphagnum samples were analyzed for heterotrophic bacteria, cyanobacteria, microalgae, heterotrophic flagellates, ciliates, testate amoebae, fungi, nematodes, and rotifers. Heterotrophic organisms dominated the microbial communities and together represented 78% to 97% of the total microbial biomass. Testate amoebae dominated the protozoan biomass. A canonical correspondence analysis revealed a significant correlation between the microbial community data and four environmental variables (Na+, DOC, water table depth, and DIN), reflecting continentality, hydrology, and nitrogen deposition gradients. Carbon dioxide enrichment modified the structure of microbial communities, but total microbial biomass was unaffected. The biomass of heterotrophic bacteria increased by 48%, and the biomass of testate amoebae decreased by 13%. These results contrast with the absence of overall effect on methane production or on the vegetation, but are in line with an increased below-ground vascular plant biomass at the same sites. We interpret the increase in bacterial biomass as a response to a CO2-induced enhancement of Sphagnum exudation. The causes for the decrease of testate amoebae are unclear but could indicate a top-down rather than a bottom-up control on their density.}, }
@article {pmid14708743, year = {2003}, author = {Pettersson, M and Bååth, E}, title = {The rate of change of a soil bacterial community after liming as a function of temperature.}, journal = {Microbial ecology}, volume = {46}, number = {2}, pages = {177-186}, pmid = {14708743}, issn = {0095-3628}, mesh = {*Adaptation, Physiological ; Bacteria ; Calcium Compounds ; Fatty Acids/analysis/metabolism ; Hydrogen-Ion Concentration ; Oxides ; Phospholipids/analysis/metabolism ; Population Dynamics ; *Soil Microbiology ; Temperature ; Trees ; }, abstract = {The response of a bacterial community to liming of a forest humus soil (pH 4.9 increased to pH 7.5) was studied in the laboratory at three temperatures (5, 20, and 30 degrees C). As a comparison an unlimed soil (pH 4.9) and a soil limed in the field 15 years ago (pH around 6) were also included. The bacterial community tolerance of pH was measured using TdR incorporation. The pH of the bacterial suspensions (bacteria directly extracted from soil) was altered to 3.6 and 8.3 using different buffers before measuring TdR incorporation. The logarithmic ratio between TdR incorporation at 8.3 and 3.6 was then used as an indicator of the community pH tolerance. The rate of changes in the community tolerance to pH after liming was fastest for the soil incubated at 30 degrees C, but only minor differences in rate of change could be seen between samples incubated at 5 and 20 degrees C. Changes in phospholipid fatty acid (PLFA) pattern after increasing the pH were most rapid for the bacterial community in the soil incubated at 30 degrees C followed by the soil incubated at 20 degrees C, whereas no changes could be seen in the PLFA pattern of the soil incubated at 5 degrees C, even after 82 days' incubation. Thus, the changes in the PLFA pattern were considerably slower than the changes in bacterial community tolerance to pH measured using TdR incorporation.}, }
@article {pmid14708742, year = {2003}, author = {Wenderoth, DF and Rosenbrock, P and Abraham, WR and Pieper, DH and Höfle, MG}, title = {Bacterial community dynamics during biostimulation and bioaugmentation experiments aiming at chlorobenzene degradation in groundwater.}, journal = {Microbial ecology}, volume = {46}, number = {2}, pages = {161-176}, pmid = {14708742}, issn = {0095-3628}, mesh = {Bacteria, Aerobic/*physiology ; Bacteria, Anaerobic/*physiology ; Biodegradation, Environmental ; Chlorobenzenes/*metabolism ; DNA, Bacterial/analysis ; In Situ Hybridization, Fluorescence ; Population Dynamics ; RNA, Ribosomal, 16S ; Soil ; *Soil Microbiology ; Soil Pollutants/*metabolism ; Water Pollutants, Chemical/*metabolism ; Water Supply ; }, abstract = {A set of microcosm experiments was performed to assess different bioremediation strategies, i.e., biostimulation and bioaugmentation, for groundwater contaminated with chlorobenzenes. The biodegradative potential was stimulated either by the supply of electron acceptors (air, (NO3-), to increase the activity of the indigenous bacterial community, or by the addition of aerobic chlorobenzene-degrading bacteria (Pseudomonas putida GJ31, Pseudomonas aeruginosa RHO1, Pseudomonas putida F1deltaCC). Experiments were performed with natural groundwater of the aquifer of Bitterfeld, which had been contaminated with 1,2-dichlorobenzene (1,2-DCB), 1,4-dichlorobenzene (1,4-DCB), and chlorobenzene (CB). The microcosms consisted of airtight glass bottles with 800 mL of natural groundwater and were incubated under in situ temperature (13 degrees C). Behavior of the introduced strains within the indigenous bacterial community was monitored by fluorescent in situ hybridization (FISH) with species-specific oligonucleotides. Dynamics of the indigenous community and the introduced strains within the microcosms were followed by single-strand conformation polymorphism (SSCP) analysis of 16S rDNA amplicons obtained from total DNA of the microbial community. An indigenous biodegradation potential under aerobic as well as anaerobic denitrifying conditions was observed accompanied by fast and specific changes in the natural bacterial community composition. Augmentation with P. aeruginosa RHO1 did not enhance bio-degradation. In contrast, both P. putida GJ31 as well as P. putida F1deltaCC were capable of growing in groundwater, even in the presence of the natural microbial community, and thereby stimulating chlorobenzene depletion. P. putida GJ31 disappeared when the xenobiotics were depleted and P. putida F1deltaCC persisted even in the absence of CB. Detailed statistical analyses revealed that community dynamics of the groundwater microbiota were highly reproducible but specific to the introduced strain, its inoculum size, and the imposed physicochemical conditions. These findings could contribute to the design of better in situ bioremediation strategies for contaminated groundwater.}, }
@article {pmid14708741, year = {2003}, author = {Rhine, ED and Fuhrmann, JJ and Radosevich, M}, title = {Microbial community responses to atrazine exposure and nutrient availability: linking degradation capacity to community structure.}, journal = {Microbial ecology}, volume = {46}, number = {2}, pages = {145-160}, pmid = {14708741}, issn = {0095-3628}, mesh = {Atrazine/*metabolism ; Biodegradation, Environmental ; Carbon/metabolism ; Herbicides/*metabolism ; Nitrogen/metabolism ; Population Dynamics ; *Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {Repeated pesticide exposure may enhance biodegradation through selective enrichment of pesticide-metabolizing microorganisms, particularly when the compound is used as a C and energy source. The relationship between pesticide application history and degradation rate is unclear when the chemical is utilized as a nutrient source other than C. Atrazine, a poor source of C and energy, was chosen as a model compound because it can serve as an N source for some microorganisms. Soils with (H-soil) and without (NH-soil) prior s-triazine treatment history were repeatedly exposed to atrazine and a variety of C and N source amendments. Exposure to atrazine and inorganic-N availability were the dominant factors leading to the development of microbial communities with an enhanced capacity to degrade atrazine. The density of the atrazine-degrading microorganisms increased immediately, up to 1000-fold, with atrazine exposure in the H-soil, but comparable increases were not observed in the NH-soil until 12 weeks following laboratory acclimation, despite high rates of atrazine mineralization in these soils immediately following the acclimation period. Whole-soil fatty acid methyl ester (FAME) analysis showed that the application of alternative C and N sources in addition to atrazine resulted in a microbial community composition that was distinctly different from that in either the atrazinealone treatment or water controls for both the H- and NH-soils. These data suggest that the microbial communities in both soils were altered differently in response to the treatments but developed a similar enhanced capacity to mineralize atrazine.}, }
@article {pmid14702649, year = {2003}, author = {Van de Wiele, T and Boeckaert, C and Verstraete, W and Siciliano, S}, title = {Oral exposure to PAH: bioactivation processes in the human gut.}, journal = {Communications in agricultural and applied biological sciences}, volume = {68}, number = {3}, pages = {3-6}, pmid = {14702649}, issn = {1379-1176}, mesh = {Administration, Oral ; Biological Assay ; Chromatography, High Pressure Liquid ; Colon/*metabolism/microbiology ; Dose-Response Relationship, Drug ; Environmental Exposure ; Humans ; Models, Biological ; Polycyclic Aromatic Hydrocarbons/administration &amp; dosage/*metabolism/toxicity ; Risk Assessment ; Soil Pollutants/administration &amp; dosage/*metabolism/toxicity ; }, }
@article {pmid14696235, year = {2003}, author = {Vande Sijpe, T and Verstraete, W}, title = {Evaluation of a synthetic wastewater with variable COD soluble/COD total and its use in a lab scale clarigester.}, journal = {Communications in agricultural and applied biological sciences}, volume = {68}, number = {1}, pages = {33-41}, pmid = {14696235}, issn = {1379-1176}, mesh = {Anaerobiosis ; Animals ; Bacteria, Anaerobic/physiology ; Biodegradation, Environmental ; Bioreactors ; *Dietary Fiber ; Hydrogen-Ion Concentration ; Milk/*chemistry ; Nitrogen/*analysis ; Oxygen/*chemistry ; Refuse Disposal/methods ; Solubility ; Water/*chemistry ; }, }
@article {pmid14686936, year = {2004}, author = {Weinbauer, MG and Rassoulzadegan, F}, title = {Are viruses driving microbial diversification and diversity?.}, journal = {Environmental microbiology}, volume = {6}, number = {1}, pages = {1-11}, doi = {10.1046/j.1462-2920.2003.00539.x}, pmid = {14686936}, issn = {1462-2912}, mesh = {Bacteria/*genetics/*virology ; Bacteriophages/*genetics/growth &amp; development/*physiology ; Biodiversity ; *Biological Evolution ; Ecosystem ; Gene Transfer, Horizontal ; *Genetic Variation ; Lysogeny ; Transduction, Genetic ; Water Microbiology ; }, abstract = {Viruses can influence the genetic diversity of prokaryotes in various ways. They can affect the community composition of prokaryotes by 'killing the winner' and keeping in check competitive dominants. This may sustain species richness and the amount of information encoded in genomes. Viruses can also transfer (viral and host) genes between species. Such mechanisms have probably influenced the speciation of prokaryotes. Whole-genome sequencing has clearly revealed the importance of (virus-mediated) gene transfer. However, its significance for the ecological performance of aquatic microbial communities is only poorly studied, although the few available reports indicate a large potential. Here, we present data supporting the hypothesis that viral genes and viral activity generate genetic variability of prokaryotes and are a driving force for ecological functioning and evolutionary change.}, }
@article {pmid14681739, year = {2004}, author = {Delille, D and Coulon, F and Pelletier, E}, title = {Biostimulation of natural microbial assemblages in oil-amended vegetated and desert sub-Antarctic soils.}, journal = {Microbial ecology}, volume = {47}, number = {4}, pages = {407-415}, pmid = {14681739}, issn = {0095-3628}, mesh = {Acridine Orange ; Antarctic Regions ; Bacteria/*metabolism ; Biodegradation, Environmental ; Biological Assay ; *Ecosystem ; Fertilizers/*microbiology ; Petroleum/*metabolism/toxicity ; Soil/analysis ; *Soil Microbiology ; Soil Pollutants/*metabolism/toxicity ; Time Factors ; Vibrio ; }, abstract = {A field study was initiated in December 2000 in two selected soils of The Grande Terre (Kerguelen Archipelago) with the objective of determining the long-term effects of fertilizer addition on the biodegradation rate and the toxicity of oil residues under severe sub-Antarctic conditions. Two soils were selected. The first site supports an abundant vegetal cover; the second one was desert soil, devoid of plant material. These two soils were located in the vicinity of the permanent station of Port-aux-Français (69 degrees 42'E; 49 degrees 19'S). A series of five experimental plots (0.75 x 0.75 m) were settled firmly into each of the studied soils. Each plot received 500 mL of diesel or Arabian light crude oil, and some of them were treated with a bioremediation agent: slow-release fertilizer Inipol EAP-22 (Elf Atochem). All the plots were sampled on a regular basis over a 1 year period. Heterotrophic and hydrocarbon-degrading microorganisms increased by two orders of magnitude during the first month of the experimentation in all treated enclosures, but differences appeared between the different plots. The microbial response was improved by bioremediation treatments. However, fertilizer addition had a greater impact on the desert soil when compared to the vegetated one. All chemical indices show a reduction of alkanes and light aromatics. Toxicity results show a high variability between treatments and environmental conditions. As a conclusion, it is clear that the microbial response was rapid and efficient in spite of the severe weather conditions, and the rate of degradation was improved by bioremediation treatments. However, after 1 year of treatment, the signal of a relatively high toxicity of oiled residues remained present in the two studied soils.}, }
@article {pmid14681738, year = {2004}, author = {Romaní, AM and Guasch, H and Muñoz, I and Ruana, J and Vilalta, E and Schwartz, T and Emtiazi, F and Sabater, S}, title = {Biofilm structure and function and possible implications for riverine DOC dynamics.}, journal = {Microbial ecology}, volume = {47}, number = {4}, pages = {316-328}, pmid = {14681738}, issn = {0095-3628}, mesh = {Analysis of Variance ; Bacteria/enzymology/*metabolism ; *Biofilms ; Carbon/*metabolism ; Carbon Radioisotopes ; Ecosystem ; Electrophoresis ; Eukaryota/enzymology/*metabolism ; Glucose/metabolism ; Regression Analysis ; Rivers/chemistry/*microbiology ; Spain ; }, abstract = {Biofilms are major sites of carbon cycling in streams and rivers. Here we elucidate the relationship between biofilm structure and function and river DOC dynamics. Metabolism (extracellular enzymatic activity) and structure (algae, bacteria, C/N content) of light-grown (in an open channel) and dark-grown (in a dark pipe) biofilms were studied over a year, and variations in dissolved organic carbon (DOC) and biodegradable DOC (BDOC) were also recorded. A laboratory experiment on 14C-glucose uptake and DOC dynamics was also performed by incubating natural biofilms in microcosms. On the basis of our field (annual DOC budget) and laboratory results, we conclude that light-grown biofilm is, on annual average, a net DOC consumer. This biofilm showed a high monthly variability in DOC uptake/release rates, but, on average, the annual uptake rate was greater than that of the dark-grown biofilm. The higher algal biomass and greater structure of the light-grown biofilm may enhance the development of the bacterial community (bacterial biomass and activity) and microbial heterotrophic activity. In addition, the light-grown biofilm may promote abiotic adsorption because of the development of a polysaccharide matrix. In contrast, the dark-grown biofilm is highly dependent on the amount and quality of organic matter that enters the system and is more efficient in the uptake of labile molecules (higher 14C-glucose uptake rate per mgC). The positive relationships between the extracellular enzymatic activity of biofilm and DOC and BDOC content in flowing water indicate that biofilm metabolism contributes to DOC dynamics in fluvial systems. Our results show that short-term fluvial DOC dynamics is mainly due to the use and recycling of the more labile molecules. At the river ecosystem level, the potential surface area for biofilm formation and the quantity and quality of available organic carbon might determine the effects of biofilm function on DOC dynamics.}, }
@article {pmid14681737, year = {2004}, author = {Repka, S and Meyerhöfer, M and von Bröckel, K and Sivonen, K}, title = {Associations of cyanobacterial toxin, nodularin, with environmental factors and zooplankton in the Baltic Sea.}, journal = {Microbial ecology}, volume = {47}, number = {4}, pages = {350-358}, pmid = {14681737}, issn = {0095-3628}, mesh = {Animals ; Chromatography, High Pressure Liquid ; Cyanobacteria/*metabolism ; *Environment ; Enzyme-Linked Immunosorbent Assay ; Fluorescence ; Marine Toxins/*analysis ; North Sea ; Peptides, Cyclic/*analysis ; Regression Analysis ; Zooplankton/*metabolism ; }, abstract = {Concentrations of a cyanobacterial toxin, nodularin, were measured in the Baltic Sea in 1998 and 1999. Statistical associations of nodularin concentrations with environmental factors were tested by multiple regression analysis. To reveal the toxin-producing organism, colonies of Aphanizomenon and filaments of Nodularia were picked and analyzed for peptide toxins. It was also investigated whether there was an association with zooplankton and Nodularia. All the measured seston samples contained nodularin, but other toxins were not detected by the HPLC analysis. In both years, the highest nodularin concentrations were found at the surface water layer. The nodularin concentrations were positively correlated with silicate concentrations in water. High concentrations of silica in surface water may indicate recent upwelling, which in turn renders surface water rich in nutrients. This upwelling is likely to intensify cyanobacterial growth and toxin production, which may explain this rather unexpected result. The picked Aphanizomenon colonies did not contain nodularin and the dissolved nodularin concentrations were below detection limit. Thus it was concluded that most of the nodularin was bound to Nodularia cells. The abundances of zooplankton (copepods, rotifers, and cladocerans) were unrelated to Nodularia, but were positively associated with Aphanizomenon.}, }
@article {pmid14681736, year = {2004}, author = {Halpern, M and Broza, YB and Mittler, S and Arakawa, E and Broza, M}, title = {Chironomid egg masses as a natural reservoir of Vibrio cholerae non-O1 and non-O139 in freshwater habitats.}, journal = {Microbial ecology}, volume = {47}, number = {4}, pages = {341-349}, pmid = {14681736}, issn = {0095-3628}, mesh = {Africa ; Animals ; Chironomidae/*microbiology ; *Disease Reservoirs ; *Environment ; Fresh Water/analysis/microbiology ; India ; Israel ; Ovum/*microbiology ; Seasons ; Species Specificity ; Temperature ; *Vibrio cholerae ; }, abstract = {Cholera is a diarrheal disease caused by the gram-negative bacterium Vibrio cholerae, and an estimated 120,000 deaths from cholera occur globally every year. The natural reservoir of the bacterium is environmental. A recent report indicated an association between V. cholerae and chironomid egg masses. Chironomids, the "non-biting midges" (Diptera; Chironomidae), are the most widely distributed and frequently the most abundant insects in freshwater. Females attach egg masses, each containing hundreds of eggs encased in a layer of gelatin, to the water's edge where bacteria are abundant and may encounter the nutrient-rich substrate. Here we report the isolation of non-O1 and non-O139 V. cholerae from chironomid egg masses from different freshwater bodies in Israel, India, and Africa. In a yearly survey in Israel, chironomid populations were found to peak biannually, and it seemed that those peaks were followed by subsequent bacterial growth and disappearance during the winter in the Mediterranean region. The bacterial population rose as water temperature surpassed 25 degrees C. Thirty-five different serogroups of V. cholerae were identified among the bacteria isolated from chironomids, demonstrating population heterogeneity. Two strains of V. cholerae O37 and O201 that were isolated from chironomid egg masses in Zanzibar Island were NAG-ST positive. Our findings support the hypothesis that the association found between chironomids and the cholera bacteria is not a rare coincidence, indicating that chironomid egg masses may serve as yet another potential reservoir for V. cholerae.}, }
@article {pmid14679195, year = {2004}, author = {Perron, K and Caille, O and Rossier, C and Van Delden, C and Dumas, JL and Köhler, T}, title = {CzcR-CzcS, a two-component system involved in heavy metal and carbapenem resistance in Pseudomonas aeruginosa.}, journal = {The Journal of biological chemistry}, volume = {279}, number = {10}, pages = {8761-8768}, doi = {10.1074/jbc.M312080200}, pmid = {14679195}, issn = {0021-9258}, mesh = {Carbapenems/*pharmacology ; *Drug Resistance, Bacterial/genetics ; Metals, Heavy/*pharmacology ; Mutation ; Pseudomonas aeruginosa/*drug effects/genetics/metabolism ; }, abstract = {Pseudomonas aeruginosa is an environmental bacterium involved in mineralization of organic matter. It is also an opportunistic pathogen able to cause serious infections in immunocompromised hosts. As such, it is exposed to xenobiotics including solvents, heavy metals, and antimicrobials. We studied the response of P. aeruginosa upon exposure to heavy metals or antibiotics to investigate whether common regulatory mechanisms govern resistance to both types of compounds. We showed that sublethal zinc concentrations induced resistance to zinc, cadmium, and cobalt, while lethal zinc concentrations selected mutants constitutively resistant to these heavy metals. Both zinc-induced and stable zinc-resistant strains were also resistant to the carbapenem antibiotic imipenem. On the other hand, only 20% of clones selected on imipenem were also resistant to zinc. Heavy metal resistance in the mutants could be correlated by quantitative real time PCR with increased expression of the heavy metal efflux pump CzcCBA and its cognate two-component regulator genes czcR-czcS. Western blot analysis revealed reduced expression of the basic amino acid and carbapenem-specific OprD porin in all imipenem-resistant mutants. Sequencing of the czcR-czcS DNA region in eight independent zinc- and imipenem-resistant mutants revealed the presence of the same V194L mutation in the CzcS sensor protein. Overexpression in a susceptible wild type strain of the mutated CzsS protein, but not of the wild type form, resulted in decreased oprD and increased czcC expression. We further show that zinc is released from latex urinary catheters into urine in amounts sufficient to induce carbapenem resistance in P. aeruginosa, possibly compromising treatment of urinary tract infections by this class of antibiotics.}, }
@article {pmid14672833, year = {2004}, author = {Cocolin, L and Innocente, N and Biasutti, M and Comi, G}, title = {The late blowing in cheese: a new molecular approach based on PCR and DGGE to study the microbial ecology of the alteration process.}, journal = {International journal of food microbiology}, volume = {90}, number = {1}, pages = {83-91}, doi = {10.1016/s0168-1605(03)00296-4}, pmid = {14672833}, issn = {0168-1605}, mesh = {Cheese/*microbiology ; Clostridium/*isolation &amp; purification ; Colony Count, Microbial ; DNA, Bacterial/analysis ; Electrophoresis, Agar Gel/*methods ; Fatty Acids, Volatile/analysis ; Food Contamination/analysis ; Food Microbiology ; Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; }, abstract = {A molecular biology method based on polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) was developed to detect Clostridium spp. in cheese samples suspected of late blowing. Strains of Clostridium spp. and different Lactic Acid Bacteria species, obtained from international collections, were used to determine the experimental conditions for the PCR amplification and DGGE differentiation. DNA extracted directly from cheeses with late blowing symptoms was subjected to PCR and DGGE analysis and traditional agar plating was performed for samples pasteurized and enriched overnight. Moreover, volatile fatty acids were determined for comparison purposes. The PCR-DGGE results were in agreement with the plating performed, and only samples presenting DGGE bands migrating at the same position as Clostridium spp. bands, showed the presence of Clostridium colonies on Reinforced Clostridial Medium plates. Butyric acid contents were high (>100 mg/kg) in the cases of positive DGGE results, underlining the suitability of the protocol for the study of cheese spoilage. The sensitivity of the method is estimated to be 10(4) CFU/g.}, }
@article {pmid14660337, year = {2003}, author = {Griffiths, RI and Whiteley, AS and O'Donnell, AG and Bailey, MJ}, title = {Physiological and community responses of established grassland bacterial populations to water stress.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {12}, pages = {6961-6968}, pmid = {14660337}, issn = {0099-2240}, mesh = {Bacteria/classification/genetics/*growth &amp; development/metabolism ; Colony Count, Microbial ; Culture Media/chemistry ; DNA, Ribosomal/analysis ; *Ecosystem ; Electrophoresis/methods ; Genetic Variation ; Plant Roots/*microbiology ; *Poaceae ; RNA, Ribosomal, 16S ; *Soil Microbiology ; *Water ; }, abstract = {The effects of water stress upon the diversity and culturable activity of bacterial communities in the rhizosphere of an established upland grassland soil have been investigated. Intact monoliths were subjected to different watering regimens over a 2-month period to study community adaptation to moisture limitation and subsequent response to stress alleviation following rewetting. Genetic diversity was analyzed with 16S-based denaturing gradient gel electrophoresis (DGGE) of total soil-extracted DNA (rRNA genes) and RNA (rRNA transcripts) in an attempt to discriminate between total and active communities. Physiological response was monitored by plate counts, total counts, and BIOLOG-GN2 substrate utilization analyses. Controlled soil drying decreased the total number of CFU on all the media tested and also decreased the substrate utilization response. Following rewetting of dried soil, culture-based analyses indicated physiological recovery of the microbial population by the end of the experiment. In contrast, DGGE analyses of community 16S rRNA genes, rRNA transcripts and cultured communities did not reveal any changes relating to the moisture regimens, despite the observed physiological effects. We conclude that the imposed moisture regimen modulated the physiological status of the bacterial community and that bacterial communities in this soil are resistant to water stress. Further, we highlight the need for a reexamination of rRNA transcript-based molecular profiling techniques as a means of describing the active component of soil bacterial communities.}, }
@article {pmid14655000, year = {2004}, author = {Klappenbach, JA and Pierson, BK}, title = {Phylogenetic and physiological characterization of a filamentous anoxygenic photoautotrophic bacterium ' Candidatus Chlorothrix halophila' gen. nov., sp. nov., recovered from hypersaline microbial mats.}, journal = {Archives of microbiology}, volume = {181}, number = {1}, pages = {17-25}, doi = {10.1007/s00203-003-0615-7}, pmid = {14655000}, issn = {0302-8933}, mesh = {Bacterial Physiological Phenomena ; Bicarbonates/metabolism ; Chloroflexi/*classification/growth &amp; development/isolation &amp; purification/ultrastructure ; Chloroflexus/genetics ; Coenzyme A Ligases/physiology ; DNA, Bacterial/chemistry/isolation &amp; purification ; DNA, Ribosomal/chemistry/isolation &amp; purification ; Geologic Sediments/microbiology ; Lactic Acid/*analogs &amp; derivatives/metabolism ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfides/metabolism ; *Water Microbiology ; }, abstract = {We report the phylogenetic and physiological characterization of a mesophilic and halophilic member of the filamentous anoxygenic phototrophic (FAP) bacteria, provisionally named ' Candidatus Chorothrix halophila' gen. nov. sp. nov., that has been maintained in a highly enriched culture in our laboratory for over a decade. Phylogenetic analysis of small-subunit RNA-encoding sequences places ' Candidatus Chlorothrix halophila' in a clade that includes cultivated members of the genera Chloroflexus and Oscillochloris. Physiological studies demonstrated sulfide-dependent photosynthetic uptake of (14)C-labeled bicarbonate. Enzymatic assays for the activity of propionyl-coenzyme A synthase indicated that ' Candidatus Chlorothrix halophila' does not use the 3-hydroxypropionate cycle of Chloroflexus aurantiacus OK-70-fl for autotrophic carbon assimilation. New concepts regarding the taxonomy and phylogeny of FAP bacteria have emerged from this work.}, }
@article {pmid14645846, year = {2003}, author = {Loewe, L and Textor, V and Scherer, S}, title = {High deleterious genomic mutation rate in stationary phase of Escherichia coli.}, journal = {Science (New York, N.Y.)}, volume = {302}, number = {5650}, pages = {1558-1560}, doi = {10.1126/science.1087911}, pmid = {14645846}, issn = {1095-9203}, mesh = {Biological Evolution ; Escherichia coli/*genetics/*growth &amp; development ; *Genome, Bacterial ; Likelihood Functions ; *Mutation ; Phenotype ; Selection, Genetic ; Temperature ; Time Factors ; }, abstract = {In natural habitats, bacteria spend most of their time in some form of growth arrest. Little is known about deleterious mutations in such stages, and consequently there is limited understanding of what evolutionary events occur. In a deleterious mutation accumulation experiment in prolonged stationary phase of Escherichia coli, about 0.03 slightly deleterious mutations were observed per genome per day. This is over an order of magnitude higher than extrapolations from fast-growing cells, but in line with inferences from observations in adaptive stationary phase mutation experiments. These findings may affect understanding of bacterial evolution and the emergence of bacterial pathogenicity.}, }
@article {pmid14641597, year = {2003}, author = {De Windt, W and Boon, N and Siciliano, SD and Verstraete, W}, title = {Cell density related H2 consumption in relation to anoxic Fe(0) corrosion and precipitation of corrosion products by Shewanella oneidensis MR-1.}, journal = {Environmental microbiology}, volume = {5}, number = {11}, pages = {1192-1202}, doi = {10.1046/j.1462-2920.2003.00527.x}, pmid = {14641597}, issn = {1462-2912}, mesh = {4-Butyrolactone/analogs &amp; derivatives/analysis/biosynthesis ; Anaerobiosis ; Chemical Precipitation ; Colony Count, Microbial ; Corrosion ; Escherichia coli/genetics/metabolism ; Ferrous Compounds/analysis/metabolism ; Gene Expression Regulation, Bacterial/physiology ; Genes, Reporter/genetics/physiology ; Green Fluorescent Proteins ; Hydrogen/*metabolism ; Iron/*chemistry ; Luminescent Proteins/genetics/metabolism ; Nitrates/*metabolism ; Shewanella/cytology/*metabolism ; }, abstract = {In the absence of oxygen, a protective H2 film is formed around an Fe(0) surface, inhibiting the electron flow from this surface. Our study of anoxic corrosion of Fe(0) beads revealed that, in the presence of Shewanella oneidensis MR-1, H2 removal and precipitation of Fe mineral particles on the cell surface are determining processes for corrosion. These two biologically mediated processes were governed by cell density. H2 removal by Shewanella oneidensis was detected at cell concentrations of 1.0 x 10(6) live cells ml-1 and higher and H2 was electron donor for denitrification of NO3-. The removal of the protective H2 layer from Fe(0) beads by Shewanella oneidensis, resulted in an increase of Fe release out of the Fe(0) beads from 153 +/- 25 mg l(-1) to 196 +/- 7 mg l-1 after 20 h. When the cell concentration exceeded 1.0 x 10(8) live cells ml-1, precipitation of iron minerals on the cell surface was characteristic for the greatest percentage of MR-1 cells, whereas micrometre-scale iron precipitates not associated with culturable cell biomass significantly decreased in number. Addition of supernatant of a corrosion assay with high cell concentration induced metabolic activity in a corrosion assay with low cell concentration, resulting in increased H2 consumption and Fe release from Fe(0) beads. Homoserine lactone-like molecules were detected in the supernatant by a bio-assay, suggesting the involvement of a quorum-sensing regulatory mechanism.}, }
@article {pmid14641591, year = {2003}, author = {Ranjard, L and Lejon, DP and Mougel, C and Schehrer, L and Merdinoglu, D and Chaussod, R}, title = {Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities.}, journal = {Environmental microbiology}, volume = {5}, number = {11}, pages = {1111-1120}, doi = {10.1046/j.1462-2920.2003.00521.x}, pmid = {14641591}, issn = {1462-2912}, mesh = {Bacteria/genetics ; Biomass ; DNA/analysis/isolation &amp; purification ; DNA Fingerprinting/methods ; DNA, Ribosomal Spacer/analysis/isolation &amp; purification ; Ecology/*methods ; Electrophoresis, Polyacrylamide Gel ; Fungi/genetics ; Polymerase Chain Reaction/methods ; Polymorphism, Genetic ; Principal Component Analysis ; Soil/analysis ; Soil Microbiology/*standards ; }, abstract = {Assessing soil microbial community structure by the use of molecular techniques requires a satisfactory sampling strategy that takes into account the high microbial diversity and the heterogeneous distribution of microorganisms in the soil matrix. The influence of the sample size of three different soil types (sand, silt and clay soils) on the DNA yield and analysis of bacterial and fungal community structure were investigated. Six sample sizes from 0.125 g to 4 g were evaluated. The genetic community structure was assessed by automated ribosomal intergenic spacer analysis (A-RISA fingerprint). Variations between bacterial (B-ARISA) and fungal (F-ARISA) community structure were quantified by using principal component analysis (PCA). DNA yields were positively correlated with the sample size for the sandy and silty soils, suggesting an influence of the sample size on DNA recovery, whereas no correlation was observed in the clay soil. B-ARISA was shown to be consistent between the different sample sizes for each soil type indicating that the sampling procedure has no influence on the assessment of bacterial community structure. On the contrary for F-ARISA profiles, strong variations were observed between replicates of the smaller samples (<1 g). Principal component analysis analysis revealed that sampling aliquots of soil > or =1 g are required to obtain robust and reproducible fingerprinting analysis of the genetic structure of fungal communities. However, the smallest samples could be adequate for the detection of minor populations masked by dominant ones in larger samples. The sampling strategy should therefore be different according to the objectives: rather large soil samples (> or =1 g) for a global description of the genetic community structure, or a large number of small soil samples for a more complete inventory of microbial diversity.}, }
@article {pmid14634868, year = {2004}, author = {Sundin, GW and Mayfield, CT and Zhao, Y and Gunasekera, TS and Foster, GL and Ullrich, MS}, title = {Complete nucleotide sequence and analysis of pPSR1 (72,601 bp), a pPT23A-family plasmid from Pseudomonas syringae pv. syringae A2.}, journal = {Molecular genetics and genomics : MGG}, volume = {270}, number = {6}, pages = {462-476}, pmid = {14634868}, issn = {1617-4615}, mesh = {Bacterial Proteins/chemistry/*genetics ; Chromosome Mapping ; Conjugation, Genetic ; Gene Library ; Genes, Fungal/genetics ; Open Reading Frames ; Plasmids/*genetics ; Pseudomonas syringae/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {Plasmid pPSR1 is a conjugative plasmid originally isolated from Pseudomonas syringae pv. syringae A2, and is a member of the recently described pPT23A plasmid family. We have determined the complete sequence of pPSR1 and found the plasmid to be 72,601 bp in length, encoding 55 ORFs. Putative functions were assigned to 49 ORFs; of these, 24 (49.0%) are involved in plasmid replication, maintenance or conjugation, 17 (34.7%) have roles in virulence or ecological fitness, and eight (16.3%) encode transposase functions as part of mobile elements. pPSR1 carries the effector gene orf34, the mutagenic DNA repair operon rulAB which confers tolerance to ultraviolet radiation, and two genes for methyl-accepting chemotaxis proteins, one of which was located within the novel transposon Tn 5395. The streptomycin resistance transposon Tn 5393a, which carries a strA-strB determinant, was found inserted immediately downstream of the pPSR1 repA gene. Functional analysis of the replication region of pPSR1 indicated that the repA gene and flanking upstream and downstream sequences are required for autonomous replication in P. syringae. Hybridization analyses of the distribution of 11 of the pPSR1 ORFs indicated that many of the ecologically important ORFs were confined to the pathovar P. syringae pv. syringae -either to strains from the local population from which pPSR1 was originally isolated, or strains from a worldwide collection. Conjugative transfer genes and a gene encoding a transcriptional regulator were more widely distributed among several P. syringae pathovars. The sequence analysis of pPSR1 suggests that pPT23A-family plasmids evolve by accumulating genes that are important for host-pathogen interactions or growth on plant hosts, which are incorporated onto a conserved backbone encoding conjugation and stability determinants.}, }
@article {pmid14629389, year = {2003}, author = {Lilley, AK and Bailey, MJ and Barr, M and Kilshaw, K and Timms-Wilson, TM and Day, MJ and Norris, SJ and Jones, TH and Godfray, HC}, title = {Population dynamics and gene transfer in genetically modified bacteria in a model microcosm.}, journal = {Molecular ecology}, volume = {12}, number = {11}, pages = {3097-3107}, doi = {10.1046/j.1365-294x.2003.01960.x}, pmid = {14629389}, issn = {0962-1083}, mesh = {Bacteriophages/genetics ; Chromosomes, Bacterial/*genetics ; Cluster Analysis ; DNA Primers ; *Ecosystem ; Gene Transfer Techniques ; *Gene Transfer, Horizontal ; Genes, Reporter/genetics ; Phylogeny ; Plasmids/genetics ; Population Dynamics ; Pseudomonas fluorescens/*genetics/physiology ; Sequence Analysis, DNA ; Stellaria/*microbiology ; *Transformation, Bacterial ; }, abstract = {The horizontal transfer and effects on host fitness of a neutral gene cassette inserted into three different genomic loci of a plant-colonizing pseudomonad was assessed in a model ecosystem. The KX reporter cassette (kanamycin resistance, aph, and catechol 2, 3, dioxygenase, xylE) was introduced on the disarmed transposon mini-Tn5 into: (I) the chromosome of a spontaneous rifampicin resistant mutant Pseudomonas fluorescens SBW25R; (II) the chromosome of SBW25R in the presence of a naturally occurring lysogenic-phage (phage Phi101); and (III) a naturally occurring plasmid pQBR11 (330 kbp, tra+, Hgr) introduced into SBW25R. These bacteria were applied to Stellaria media (chickweed) plants as seed dressings [c. 5 x 104 colony-forming units (cfu)/seed] and the seedlings planted in 16 microcosm chambers containing model plant and animal communities. Gene transfer to pseudomonads in the phyllosphere and rhizosphere was found only in the plasmid treatment (III). Bacteria in the phage treatment (II) initially declined in density and free phage was detected, but populations partly recovered as the plants matured. Surprisingly, bacteria in the chromosome insertion treatment (I) consistently achieved higher population densities than the unmanipulated control and other treatments. Plasmids were acquired from indigenous bacterial populations in the control and chromosome insertion treatments. Plasmid acquisition, plasmid transfer from inocula and selection for plasmid carrying inocula coincided with plant maturation.}, }
@article {pmid14624318, year = {2004}, author = {Calvó, L and Vila, X and Abella, CA and Garcia-Gil, LJ}, title = {Use of the ammonia-oxidizing bacterial-specific phylogenetic probe Nso1225 as a primer for fingerprint analysis of ammonia-oxidizer communities.}, journal = {Applied microbiology and biotechnology}, volume = {63}, number = {6}, pages = {715-721}, doi = {10.1007/s00253-003-1433-1}, pmid = {14624318}, issn = {0175-7598}, mesh = {Ammonia/*metabolism ; Bacteria/*classification/*genetics/isolation &amp; purification/metabolism ; Cluster Analysis ; *DNA Fingerprinting ; DNA Primers ; DNA Probes ; DNA, Bacterial/chemistry/isolation &amp; purification ; DNA, Ribosomal/chemistry/isolation &amp; purification ; Electrophoresis, Polyacrylamide Gel ; Environmental Microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {Autotrophic ammonia-oxidizing bacteria (AOB) are an essential component of nitrifying wastewater treatment systems. The molecular tools used in group-specific studies are mostly based on the sequence of the 16S rRNA gene, but they have not proved to be fully specific. In this study, the sequence of the FISH probe Nso1225R was used as a reverse primer in order to analyze the AOB composition of several environmental samples by denaturing gradient gel electrophoresis (DGGE). For this purpose, samples from several environments, including aerated reactors, water treatment wetlands, and pilot plants, both aerobic and anaerobic, were analyzed. PCR fragments displayed a DGGE pattern consisting of bands melting between 30 and 40% denaturant, and a series of unresolved bands above 45%, mostly corresponding to AOB and beta-non-AOB, respectively. This second set of bands corresponded to environments subjected to severe oxygen restrictions. AOB sequences showed similarity percentages higher than 92% with those of known beta-AOB. Nso1225R, therefore, proved to be a good molecular phylogenetic marker for AOB samples from well-aerated systems, showing a higher specificity than the group-specific primers used previously.}, }
@article {pmid14614063, year = {2003}, author = {Mäkinen, J and Mertsola, J and Soini, H and Arvilommi, H and Viljanen, MK and Guiso, N and He, Q}, title = {PFGE and pertactin gene sequencing suggest limited genetic variability within the Finnish Bordetella parapertussis population.}, journal = {Journal of medical microbiology}, volume = {52}, number = {Pt 12}, pages = {1059-1063}, doi = {10.1099/jmm.0.05434-0}, pmid = {14614063}, issn = {0022-2615}, mesh = {Bacterial Outer Membrane Proteins/*genetics ; Base Sequence ; Bordetella parapertussis/*genetics ; Electrophoresis, Gel, Pulsed-Field ; *Genetic Variation ; Molecular Sequence Data ; Virulence Factors, Bordetella/*genetics ; }, abstract = {The outer-membrane protein pertactin (Prn) of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica is believed to function as an adhesin and is an important immunogen. The emergence of B. pertussis and B. bronchiseptica Prn variants has been reported. The aim of this study was to determine whether similar variation is found in B. parapertussis Prn and to characterize Finnish clinical B. parapertussis isolates that were collected in 1982-2000. Of 76 B. parapertussis isolates studied, seven (9 %) were found to have silent and non-silent nucleotide changes. In addition, one (1 %) had eight PQP repeats instead of nine. Three closely related B. parapertussis XbaI PFGE patterns were found. Genetic variation of B. parapertussis was found to be very limited, suggesting that B. parapertussis is a stable organism that is well-adapted to its own ecological niche.}, }
@article {pmid14609263, year = {2003}, author = {Collinder, E and Cardona, ME and Berge, GN and Norin, E and Stern, S and Midtvedt, T}, title = {Influence of zinc bacitracin and Bacillus licheniformis on microbial intestinal functions in weaned piglets.}, journal = {Veterinary research communications}, volume = {27}, number = {7}, pages = {513-526}, pmid = {14609263}, issn = {0165-7380}, mesh = {Animals ; Animals, Suckling/microbiology ; Anti-Bacterial Agents/*pharmacology ; *Bacillus ; Bacitracin/*pharmacology ; Bilirubin/metabolism ; Cholestanol/metabolism ; Cholesterol/metabolism ; Dipeptides/metabolism ; Fatty Acids, Volatile/metabolism ; Feces/chemistry ; Intestines/*microbiology ; Mucins/metabolism ; Probiotics/*pharmacology ; Random Allocation ; Swine/*microbiology ; Trypsin/metabolism ; Urobilin/metabolism ; }, abstract = {The influence of zinc bacitracin (ZB) and of Bacillus licheniformis on host microbial-related functions in young piglets was investigated by applying the concept of microflora-associated characteristics. Six biochemical parameters were determined before and after weaning in faecal samples from piglets in four litters having access to a diet containing ZB, to a diet containing B. licheniformis, to a diet with both additives, or to a diet with no additives, from 3 weeks of age. Statistically significant differences were found in three of the intestinal functions investigated: formation of short-chain fatty acids (at 7 and 10 weeks of age). degradation of mucin (at 7 and 10 weeks of age) and conversion of bilirubin to urobilins (at 7 weeks of age). We also found age-dependent influences on the formation of short-chain fatty acids, on conversion of cholesterol to coprostanol and on conversion of bilirubin to urobilins. We conclude that a functional approach is appropriate for measuring exogenous influence(s) on the microbial intestinal metabolisms in weaned piglets.}, }
@article {pmid14607409, year = {2003}, author = {Wiles, S and Whiteley, AS and Philp, JC and Bailey, MJ}, title = {Development of bespoke bioluminescent reporters with the potential for in situ deployment within a phenolic-remediating wastewater treatment system.}, journal = {Journal of microbiological methods}, volume = {55}, number = {3}, pages = {667-677}, doi = {10.1016/s0167-7012(03)00203-3}, pmid = {14607409}, issn = {0167-7012}, mesh = {Biodegradation, Environmental ; Genes, Reporter ; Genetic Engineering ; Luminescent Measurements ; Mutagenesis, Insertional ; Phenols/chemistry/*metabolism ; Photorhabdus/genetics/*metabolism ; Pseudomonas/genetics/*metabolism ; Waste Disposal, Fluid/methods ; Water Pollutants, Chemical/*metabolism ; }, abstract = {A suite of ecologically relevant, site-specific bioreporters was constructed by transposon mutagenesis of microorganisms isolated from a polluted phenolic-remediating wastewater treatment system. Four Pseudomonad species were engineered to carry a stable chromosomal copy of the lux operon (luxCDABE) derived from Photorhabdus luminescens. These recombinant reporter microorganisms were tested for bioluminescence response to relevant phenol concentrations in the laboratory and to phenolic-containing effluents generated by an industrial wastewater treatment plant. The reporters displayed proportional responses of bioluminescence decay with increasing phenol concentrations up to 800 mg l(-1) of phenol. When deployed against samples from the treatment system, they showed superior operational range and sensing capabilities to that observed for industry standard microorganisms such as Vibrio fischeri. Specifically, the engineered strains accurately predicted toxicity shifts in all the treatment compartments under study (with phenolic concentrations ranging from approximately 10 to 600 mg l(-1)) with a low coefficient of variation of replicate determinations (between 1.16% and 8.32%). This work highlights the utility of genetic modification of native microorganisms from sites of interest to provide robust and ecologically relevant organism-based reagents for toxicity monitoring with the potential for in situ deployment.}, }
@article {pmid14605778, year = {2004}, author = {Narang, R and Dunbar, J}, title = {Modeling bacterial species abundance from small community surveys.}, journal = {Microbial ecology}, volume = {47}, number = {4}, pages = {396-406}, pmid = {14605778}, issn = {0095-3628}, mesh = {*Bacteria ; *Biodiversity ; Computer Simulation ; *Models, Biological ; Population Dynamics ; Sample Size ; }, abstract = {Taxon abundance patterns are a central focus in evolution and ecology, providing the basic architecture of natural assemblages and potential clues to their formative processes. To better interpret species abundance patterns in natural microbial communities, we examined the consequences of three fundamental types of abundance patterns--uniform, geometric, and lognormal distributions. Theoretical communities were constructed based on the three pattern types with 2000 to 20,000 species and 10(7) to 10(10) individuals. The "dominant" species (species 1) among models that differed only in pattern type generally varied in abundance by 1 to 3 orders of magnitude. At the extremes among all the models examined, the dominant species comprised as much as 16% and as little as 0.005% of the total community. Analysis of the models and comparison with seven published surveys suggests that entire soil bacterial communities do not routinely exhibit Preston's cannonical subset of lognormal distributions. Use of the models to evaluate survey limitations showed that common diversity indices are generally sensitive to sample size over the range (50 to 200 clones) commonly used for microbial communities, emphasizing the need to compare surveys of similar size. The results collectively demonstrate that uniform, geometric, and lognormal distributions have profoundly different experimental and ecological consequences. Further, defined abundance models provide a simple quantitative tool for evaluating abundance patterns in clone libraries (even small ones) from natural communities.}, }
@article {pmid14605777, year = {2004}, author = {Pringault, O and Garcia-Pichel, F}, title = {Hydrotaxis of cyanobacteria in desert crusts.}, journal = {Microbial ecology}, volume = {47}, number = {4}, pages = {366-373}, pmid = {14605777}, issn = {0095-3628}, mesh = {Cyanobacteria/*physiology ; *Desert Climate ; Movement/*physiology ; *Soil Microbiology ; Spain ; Time Factors ; *Water ; }, abstract = {We studied the migration of cyanobacteria in desert crusts from Las Bárdenas Reales (Spain). The crusts were almost exclusively colonized by the filamentous cyanobacterium Oscillatoria, which formed a dense layer approximately 600 microm thick located between 1.5 and 2.1 mm deep. Laboratory and field experiments showed that saturation of the crust with liquid water induced a migration of the cyanobacteria leading to a significant greening of the surface within a few minutes. Under light and rapid evaporation, the green color rapidly disappeared and the crust surface was completely devoid of filaments within 60 min. In contrast, 260 min was required to recover the original white color of the crust when slow evaporation was experimentally imposed. The up and down migration following wetting and drying occurred also in the dark. This demonstrates that light was not a required stimulus. Addition of ATP synthesis inhibitors prevented the cyanobacterium from migrating down into the crust, with filaments remaining on the surface. Therefore, the disappearance of the green color observed during desiccation can only be attributed to an active cyanobacterial motility response to the decrease in the water content. The simplest explanation that can account for the evidence gathered is the presence of a mechanism that links, directly or indirectly, these motility responses to gradients in water content, namely a form of hydrotaxis.}, }
@article {pmid14602638, year = {2003}, author = {van Aarle, IM and Olsson, PA}, title = {Fungal lipid accumulation and development of mycelial structures by two arbuscular mycorrhizal fungi.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {11}, pages = {6762-6767}, pmid = {14602638}, issn = {0099-2240}, mesh = {Fatty Acids/analysis ; Fungi/*growth &amp; development/metabolism ; *Lipid Metabolism ; Mycelium/*growth &amp; development ; *Mycorrhizae ; Plant Roots/*microbiology ; Plantago/*microbiology ; Symbiosis ; }, abstract = {We monitored the development of intraradical and extraradical mycelia of the arbuscular mycorrhizal (AM) fungi Scutellospora calospora and Glomus intraradices when colonizing Plantago lanceolata. The occurrence of arbuscules (branched hyphal structures) and vesicles (lipid storage organs) was compared with the amounts of signature fatty acids. The fatty acid 16:1omega5 was used as a signature for both AM fungal phospholipids (membrane constituents) and neutral lipids (energy storage) in roots (intraradical mycelium) and in soil (extraradical mycelium). The formation of arbuscules and the accumulation of AM fungal phospholipids in intraradical mycelium followed each other closely in both fungal species. In contrast, the neutral lipids of G. intraradices increased continuously in the intraradical mycelium, while vesicle occurrence decreased after initial rapid root colonization by the fungus. S. calospora does not form vesicles and accumulated more neutral lipids in extraradical than in intraradical mycelium, while the opposite pattern was found for G. intraradices. G. intraradices allocated more of its lipids to storage than did S. calospora. Thus, within a species, the fatty acid 16:1omega5 is a good indicator for AM fungal development. The phospholipid fatty acid 16:1omega5 is especially suitable for indicating the frequency of arbuscules in the symbiosis. We propose that the ratio of neutral lipids to phospholipids is more important than is the presence of vesicles in determining the storage status of AM fungi.}, }
@article {pmid14602623, year = {2003}, author = {Janse, I and Meima, M and Kardinaal, WE and Zwart, G}, title = {High-resolution differentiation of Cyanobacteria by using rRNA-internal transcribed spacer denaturing gradient gel electrophoresis.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {11}, pages = {6634-6643}, pmid = {14602623}, issn = {0099-2240}, mesh = {Bacterial Typing Techniques ; Cyanobacteria/*classification/genetics ; DNA Primers ; DNA, Bacterial/analysis ; DNA, Ribosomal Spacer/*analysis ; Electrophoresis, Polyacrylamide Gel/methods ; Fresh Water/microbiology ; Molecular Sequence Data ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 23S/*genetics ; Sequence Analysis, DNA ; }, abstract = {For many ecological studies of cyanobacteria, it is essential that closely related species or strains can be discriminated. Since this is often not possible by using morphological features, cyanobacteria are frequently studied by using DNA-based methods. A powerful method for analysis of the diversity and dynamics of microbial populations and for checking the purity and affiliation of cultivated strains is denaturing gradient gel electrophoresis (DGGE). We realized high-resolution discrimination of a variety of cyanobacteria by means of DGGE analysis of sections of the internal transcribed spacer between the 16S and 23S rRNA genes (rRNA-ITS). A forward primer specific for cyanobacteria, targeted at the 3' end of the 16S rRNA gene, was designed. The combination of this primer and three different reverse primers targeted to the rRNA-ITS or to the 23S rRNA gene yielded PCR products of different sizes from cultures of all 16 cyanobacterial genera that were tested but not from other bacteria. DGGE profiles produced from the shortest section of rRNA-ITS consisted of one band for all but one cyanobacterial genera, and those generated from longer stretches of rRNA-ITS yielded DGGE profiles containing one to four bands. The suitability of DGGE for detecting intrageneric and intraspecific variation was tested by using strains of the genus Microcystis: Many strains could be discriminated by means of rRNA-ITS DGGE, and the resolution of this method was strikingly higher than that obtained with previously described methods. The applicability of the developed DGGE assays for analysis of cyanobacteria in field samples was demonstrated by using samples from freshwater lakes. The advantages and disadvantages associated with the use of each developed primer set are discussed.}, }
@article {pmid14602586, year = {2003}, author = {Hopkins, MJ and Englyst, HN and Macfarlane, S and Furrie, E and Macfarlane, GT and McBain, AJ}, title = {Degradation of cross-linked and non-cross-linked arabinoxylans by the intestinal microbiota in children.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {11}, pages = {6354-6360}, pmid = {14602586}, issn = {0099-2240}, mesh = {Anaerobiosis ; Bacteria, Anaerobic/classification/genetics/isolation &amp; purification/metabolism ; Bacteroides/classification/genetics/isolation &amp; purification/metabolism ; Child, Preschool ; Colon/*microbiology ; Coumaric Acids/chemistry/*metabolism ; Cross-Linking Reagents/*metabolism ; DNA, Ribosomal/analysis ; Dietary Carbohydrates/metabolism ; Feces/microbiology ; Female ; Fermentation ; Humans ; Male ; Molecular Sequence Data ; Porphyromonas/classification/genetics/isolation &amp; purification/metabolism ; Prevotella/classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Starch ; Xylans/chemistry/*metabolism ; }, abstract = {In humans, nonstarch polysaccharides (NSP), such as arabinoxylans (AX), are not digested in the upper gut and provide fermentable carbon sources for bacteria growing in the large bowel. Despite the ubiquity of AX in nature, the microbiologic and physiologic consequences of AX digestion in the gut are poorly understood. In this study, we investigated the breakdown of ferulic acid-cross-linked AX (AXF) and non-cross-linked AX in children's intestinal microbiotas, using starch as a readily fermentable polysaccharide for comparative purposes. The experiments were performed using pH-controlled fermentation vessels under anaerobic conditions. The results demonstrated that there was variation in the metabolism of these polysaccharides by colonic microbiotas. AX was always degraded more slowly than starch, while ferulic acid cross-linking reduced the rate of AX fermentation, as shown by fermentation product measurements. Starch digestion was associated with significant acetate and butyrate production, whereas AX breakdown resulted in increased propionate formation. In general, the presence of fermentable carbohydrate significantly increased the total anaerobe counts and eubacterial rRNA concentrations (P < 0.01), while non-cross-linked AX digestion was principally associated with increased viable counts of Bacteroides fragilis group organisms, which was supported by increases in Bacteroides-Porphyromonas-Prevotella group rRNA (P < 0.01). Starch was considerably more bifidogenic than AX in these fermentations. In conclusion, in this study we found that the effects of AX and AXF on the microbial ecology and metabolism of intestinal microbiotas are similar in children and adults.}, }
@article {pmid14599043, year = {2003}, author = {Chierici, R and Fanaro, S and Saccomandi, D and Vigi, V}, title = {Advances in the modulation of the microbial ecology of the gut in early infancy.}, journal = {Acta paediatrica (Oslo, Norway : 1992). Supplement}, volume = {91}, number = {441}, pages = {56-63}, doi = {10.1111/j.1651-2227.2003.tb00647.x}, pmid = {14599043}, issn = {0803-5326}, mesh = {Bacterial Physiological Phenomena ; Bifidobacterium/physiology ; Humans ; Infant, Newborn ; Intestines/*microbiology ; }, abstract = {It is now generally accepted that the microbiota of the human gut may influence health and well-being. Lactic acid bacteria are the most important microorganisms associated with these beneficial effects and the elevated bifidobacterial count may be one of the greatest advantages that breastfed infants have over infants fed with milk formulas. Several studies relative to the selective growth stimulation of bifidobacteria, both in vitro and in vivo, are reported in this review. Over the years, diverse human milk components have been identified as the specific factors able to modulate the growth of bifidobacteria. Even if there is a certain agreement that the bifidogenic activity of human milk may be based not on single growth substances, but on a complex set of interacting factors, the present state of knowledge indicates that the use of non-digestible but fermentable carbohydrates may be an easy and reliable method to influence the growth of lactic acid bacteria. In this context, some of the characteristics of the major physiological effects of inulin-type fructans, of galacto-oligosaccharides, but also of lactoferrin, a milk whey protein fraction with purported bifidogenic activity, are briefly examined.}, }
@article {pmid14583827, year = {2004}, author = {Palmer, RJ}, title = {Peter Hirsch and biofilms: microbial ecology's role in a "new" field.}, journal = {Microbial ecology}, volume = {47}, number = {3}, pages = {200-204}, pmid = {14583827}, issn = {0095-3628}, mesh = {Bacteriology/*history ; *Biofilms ; Ecology/*history ; Germany ; History, 20th Century ; History, 21st Century ; }, }
@article {pmid14582496, year = {2003}, author = {Pulido-Villena, E and Reche, I}, title = {Exploring bacteriplankton growth and protein synthesis to determine conversion factors across a gradient of dissolved organic matter.}, journal = {Microbial ecology}, volume = {46}, number = {1}, pages = {33-42}, pmid = {14582496}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development/*metabolism ; Connecticut ; *Ecosystem ; Fresh Water/*analysis ; *Models, Biological ; Organic Chemicals/chemistry ; Plankton/growth &amp; development/metabolism ; Protein Biosynthesis ; Spain ; *Water Microbiology ; }, abstract = {The effect of bacterial specific growth rates of abundance (micro) and protein synthesis (b) on conversion factor (CF) variability was explored in order to provide an alternative approach to the controversial application of just one universal CF to field data. Nine regrowth cultures (RCs) were set up from very diverse aquatic ecosystems, controlling temperature and adding N and P to avoid mineral limitation and force organic carbon limitation. The values of micro varied one order of magnitude from 0.26 to 3.34 d(-1), whereas b values varied two orders of magnitude from 0.28 to 34.87 d(-1). We found no relationships between micro or b values and the dissolved organic carbon (DOC) concentration or the dissolved organic matter (DOM) quality indexes assayed. Abundance and protein synthesis increased exponentially and synchronously in four RCs, leading to balanced growth (micro = b). In contrast, abundance and protein synthesis increased logistically in the other five RCs and b values were significantly higher than g values, leading to unbalanced growth (micro not equal b). CFs ranged from 0.0062 to 0.0576 x 10(18) cells mol leucine(-1) with an average of 0.0305 x 10(18) cells mol leucine(-1). CFs obtained in RCs with balanced growth were generally higher than CFs obtained in RCs with unbalanced growth and were not alike, impeding the establishment of an upper limit for CFs. A positive and significant relationship (n = 8, p < 0.0 1, r2 = 0.71) was found between CFs and DOC concentration (CF (x10(18) cells mol leucine(-1)) = 0.0104 + 0.0094 DOC (mM)) when the value for the most productive system was excluded. This function permits the estimation of site-specific CFs based on DOC concentration instead of the controversial use of a single CF for different systems.}, }
@article {pmid14582492, year = {2003}, author = {Dollhopf, SL and Pariseau, ML and Hashsham, SA and Tiedje, JM}, title = {Competitive and interactions affecting a fermentative spirochete in anaerobic chemostats.}, journal = {Microbial ecology}, volume = {46}, number = {1}, pages = {1-11}, pmid = {14582492}, issn = {0095-3628}, mesh = {Base Sequence ; Bioreactors/microbiology ; Clostridium/*genetics/*physiology ; Colony Count, Microbial ; DNA Primers ; *Ecosystem ; Fermentation ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Pantothenic Acid/chemistry ; Polymorphism, Restriction Fragment Length ; Population Dynamics ; Treponema/*physiology ; }, abstract = {Terminal restriction fragment length polymorphism and fluorescent in situ hybridization revealed that spirochete-related populations dominated two glucose-fed methanogenic bioreactor communities at dilution rates of 0.06, 0.13, and 0.17 day(-1). At dilution rates of 0.25 and 0.50 day(-1), spirochete-related populations decreased while Clostridium-related populations increased. Isolates representing both dominant populations were obtained (Treponema R8 and Clostridium S9) and competed against each other in continuous culture. Treponema R8 out-competed Clostridium S9 at all dilution rates applied (0.17 to 1.0 day(-1)) when sufficient pantothenate was supplied in the medium. Without sufficient pantothenate, the population size of Treponema R8 was limited to 40% of the total cells. Coculture of Treponema R8 with Methanobacterium bryantii increased the cell yield of Treponema R8 and relieved the pantothenate requirement. Triculture of Treponema R8, Clostridium S9, and M. bryantii in pantothenate-deficient medium allowed Treponema R8 to outcompete Clostridium S9 in continuous culture upto a dilution rate of 0.50 day(-1). These experiments demonstrate that cofactor and vitamin requirements can affect the competitive success of a microbial species.}, }
@article {pmid14580749, year = {2003}, author = {Costalos, C and Skouteri, V and Gounaris, A and Sevastiadou, S and Triandafilidou, A and Ekonomidou, C and Kontaxaki, F and Petrochilou, V}, title = {Enteral feeding of premature infants with Saccharomyces boulardii.}, journal = {Early human development}, volume = {74}, number = {2}, pages = {89-96}, doi = {10.1016/s0378-3782(03)00090-2}, pmid = {14580749}, issn = {0378-3782}, mesh = {Colony Count, Microbial ; *Enteral Nutrition ; Feces/microbiology ; Female ; Gestational Age ; Humans ; *Infant Food ; Infant, Newborn ; *Infant, Premature ; Intestinal Absorption ; Intestinal Mucosa/metabolism ; Intestines/microbiology ; Male ; Polysaccharides/administration &amp; dosage ; Probiotics/*therapeutic use ; Saccharomyces/isolation &amp; purification/*physiology ; Weight Gain ; Xylose/metabolism ; }, abstract = {BACKGROUND: Saccharomyces boulardii (SB) is a yeast that acts both as a probiotic and as a polyamine producer. Probiotics prevent the overgrowth of pathogens in the gut while polyamines enhance intestinal maturation. The aim of this randomized study was to investigate the ability of SB to modify the gut microbial ecology and its function.<br><br>METHODS: A total of 87 healthy babies with gestational age 28-32 weeks were studied. They were randomly assigned to receive a preterm formula to which SB or maltodextrins was added for 30 days. Evaluations were made on the following: SB tolerance and weight gain, faecal flora analysis, intestinal D-xylose absorption and faecal lipid excretion.<br><br>RESULTS: SB was well tolerated by the infants. There was no difference in weight gain between the two groups. Median log of colony forming units per gram of faeces for Escherichia coli and enterococci was significantly lower in the SB group [E. coli: 2.67 (0.045) vs. 2.75 (0.058), P<0.001; enterococci: 2.14 (0.359) vs. 2.19 (0.138), P<0.05]. On the other hand, the number of bifidobacteria and staphylococci in the stools was significantly higher in the SB group [bifidobacteria: 2.65 (0.083) vs. 2.27 (0.075), P<0.001; staphylococci: 1.23 (0.869) vs. 0.6 (0.281), P<0.001]. D-Xylose and lipid absorption was not improved by SB [median blood D-xylose: 1.5 (0.4) mmol/l vs. 1.35 (0.3) mmol/l, P>0.1; median stool steatocrit: 64% (3.05%) vs. 65% (2.72%) P>0.5].<br><br>CONCLUSIONS: An SB-supplemented formula is well tolerated by preterm infants, it has a beneficial effect on stool flora bringing it closer to that of breast fed babies but it does not improve D-xylose or lipid gut absorption.}, }
@article {pmid14574526, year = {2004}, author = {Eaglesham, BS and Lion, LW and Ghiorse, WC}, title = {An aufwuchs chamber slide for high-resolution confocal laser scanning microscopy and stereo imaging of microbial communities in natural biofilms.}, journal = {Microbial ecology}, volume = {47}, number = {3}, pages = {266-270}, pmid = {14574526}, issn = {0095-3628}, mesh = {Acridine Orange ; *Biofilms ; *Ecosystem ; Image Processing, Computer-Assisted ; Microscopy, Confocal/*instrumentation/*methods ; Microscopy, Fluorescence ; New York ; }, abstract = {Aufwuchs chamber slides were constructed by attaching a silicone rubber gasket to a glass slide with epoxy cement. For biofilm growth, the slides were suspended in Cayuga Lake near Ithaca, NY, for 27 days. Biofilms in the chamber were stained with 0.05% acridine orange. After rinsing, the chamber was filled with molten 1% agarose to stabilize filaments and delicate polymer structures at the biofilm surface. Areas of biofilm approximately 0.5 mm thick on the inner face of the wall of the chamber were selected for side-on optical sectioning in a confocal laser scanning microscope (CLSM). Stacks of high-resolution optical images captured by the CLSM z-sectioning software, were used to create left-right stereo image pairs. At low magnification the stereo pairs showed 3-D details of the microbial landscape in the mature biofilms. Channels, pores, and other structural features of the biofilm matrix were observed in peripheral regions. Higher magnification images revealed the 3-D distribution of specific biofilm components such as filaments of sheathed bacteria projecting outward into the liquid milieu, and organic coatings, including bacterial cells on the surfaces of mineral particles.}, }
@article {pmid14571978, year = {2003}, author = {Rabaey, K and Lissens, G and Siciliano, SD and Verstraete, W}, title = {A microbial fuel cell capable of converting glucose to electricity at high rate and efficiency.}, journal = {Biotechnology letters}, volume = {25}, number = {18}, pages = {1531-1535}, doi = {10.1023/a:1025484009367}, pmid = {14571978}, issn = {0141-5492}, mesh = {Bacteria, Anaerobic/*physiology ; Bioelectric Energy Sources/*microbiology ; Cell Culture Techniques/*instrumentation/methods ; Coculture Techniques/instrumentation/methods ; Electrochemistry/*instrumentation/methods ; *Electrodes ; Energy Transfer/*physiology ; Equipment Design ; Equipment Failure Analysis ; Glucose/*metabolism ; Oxygen Consumption/*physiology ; }, abstract = {A microbial fuel cell containing a mixed bacterial culture utilizing glucose as carbon source was enriched to investigate power output in relation to glucose dosage. Electron recovery in terms of electricity up to 89% occurred for glucose feeding rates in the range 0.5-3 g l(-1) d(-1), at powers up to 3.6 W m(-2) of electrode surface, a five fold higher power output than reported thus far. This research indicates that microbial electricity generation offers perspectives for optimization.}, }
@article {pmid14569419, year = {2004}, author = {Ott, CM and Bruce, RJ and Pierson, DL}, title = {Microbial characterization of free floating condensate aboard the Mir space station.}, journal = {Microbial ecology}, volume = {47}, number = {2}, pages = {133-136}, pmid = {14569419}, issn = {0095-3628}, mesh = {Animals ; Bacteria/genetics ; *Environment, Controlled ; *Environmental Monitoring ; Eukaryota/genetics ; *Extraterrestrial Environment ; Fungi/genetics ; Humidity ; Pyroglyphidae/genetics ; *Spacecraft ; *Water Microbiology ; }, abstract = {Three samples of humidity condensate that had accumulated behind panels aboard the Russian space station Mir were collected and returned to earth for analysis. As these floating masses of liquid come into contact with the astronauts and the engineering systems, they have the potential to affect both crew health and systems performance. Using a combination of culturing techniques, a wide variety of organisms were isolated included Escherichia coli, Serratia marcescens, and a presumed Legionella species. In addition, microscopic analysis indicated the presence of protozoa, dust mites, and spirochetes. These findings suggest the need for more comprehensive microbial analysis of the environment through the use of new methodologies to allow a more thorough risk assessment of spacecraft.}, }
@article {pmid14569287, year = {2003}, author = {Lee, DH and Cha, IH and Woo, DS and Ohba, M}, title = {Microbial ecology of Bacillus thuringiensis: fecal populations recovered from wildlife in Korea.}, journal = {Canadian journal of microbiology}, volume = {49}, number = {7}, pages = {465-471}, doi = {10.1139/w03-063}, pmid = {14569287}, issn = {0008-4166}, mesh = {Aedes/growth &amp; development ; Animals ; Animals, Wild/*microbiology ; Bacillus thuringiensis/classification/growth &amp; development/*isolation &amp; purification ; Behavior, Animal ; Feces/*microbiology ; Feeding Behavior ; Insecta/*growth &amp; development ; Korea ; Larva/growth &amp; development ; Lepidoptera/growth &amp; development ; Mammals/*microbiology ; *Pest Control, Biological ; Plants ; Serotyping ; }, abstract = {A total of 34 fecal samples, collected from 14 species of wild mammals in Korea, were examined for the occurrence of Bacillus thuringiensis. The organism was detected in 18 (53%) samples. Among the three food-habit groups, herbivorous animals yielded the highest frequency (69%) of samples positive for B. thuringiensis, followed by omnivorous animals (50%). Of the six fecal samples from carnivorous animals, only one sample contained B. thurin giensis. Among 527 isolates belonging to the Bacillus cereus - B. thuringiensis group, 43 (8%) were assigned to B. thurin giensis on the basis of the formation of parasporal inclusions. Of the 43 isolates, 13 were serologically allocated to the nine H-antigenic serotypes: H3ad (serovar sumiyoshiensis), H15 (dakota), H17/27 (tohokuensis/ mexicanensis), H19 (tochigiensis), H21 (colmeri), H29 (amagiensis), H31/49 (toguchini/muju), H42 (jinghongiensis), and H44 (higo). Other isolates were untestable or untypable by the 55 reference H antisera available. Insecticidal activity was associated with 23% of the fecal populations: three isolates killed larvae of the silkworm, Bombyx mori (Lepidoptera), and seven exhibited larvicidal activity against the mosquito, Aedes aegypti (Diptera). There was no larvicidal activity against the three lepidopterous insects: Plutella xylostella, Spodoptera exigua, and Spodoptera litura. The overall results suggest that wild animals in Korea are in contact with naturally occurring B. thuringiensis at high frequencies through the daily food intake of plants.}, }
@article {pmid14566429, year = {2004}, author = {De Wildeman, S and Linthout, G and Van Langenhove, H and Verstraete, W}, title = {Complete lab-scale detoxification of groundwater containing 1,2-dichloroethane.}, journal = {Applied microbiology and biotechnology}, volume = {63}, number = {5}, pages = {609-612}, doi = {10.1007/s00253-003-1363-y}, pmid = {14566429}, issn = {0175-7598}, mesh = {Biodegradation, Environmental ; Chlorides/metabolism ; Desulfitobacterium/*growth &amp; development/*metabolism ; Ethylene Dichlorides/*metabolism ; Ethylenes/metabolism ; Kinetics ; Time Factors ; Water Pollutants, Chemical/*metabolism ; Water Pollution, Chemical ; }, abstract = {The suspected carcinogenic solvent 1,2-dichloroethane (1,2-DCA) is the most abundant chlorinated C(2) groundwater pollutant on earth. However, an efficient reductive in situ detoxification technology for this compound is not known. Detoxification results of 1,2-DCA with the recently isolated anaerobic bacterium Desulfitobacterium dichloroeliminans strain DCA1 are presented. First, it was verified that strain DCA1 could compete for nutrients in the presence of fast-growing Enterococcus faecalis; the latter was observed in the enrichment culture from which strain DCA1 was isolated. Subsequently, lab-scale bioaugmentation of the strain to groundwater containing 40 mg 1,2-DCA/l indicated that the bacterium has strong metabolic activity under prevailing environmental conditions, converting the pollutant into ethene. During exponential growth, the maximum 1,2-DCA dechlorination rate exceeded 350 nmol chloride released per min per mg total bacterial protein. Growth and dechlorination within the community with autochthonous bacteria indicated a high competitive strength of strain DCA1. Interestingly this dechlorination process does not produce any toxic byproducts, such as vinyl chloride. Furthermore, complete groundwater detoxification happens within a short time-frame (days) and is robust in terms of bacterial competition, oxygen tolerance, high ionic strength, and pH range.}, }
@article {pmid14532039, year = {2003}, author = {Zwart, G and van Hannen, EJ and Kamst-van Agterveld, MP and Van der Gucht, K and Lindström, ES and Van Wichelen, J and Lauridsen, T and Crump, BC and Han, SK and Declerck, S}, title = {Rapid screening for freshwater bacterial groups by using reverse line blot hybridization.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {10}, pages = {5875-5883}, pmid = {14532039}, issn = {0099-2240}, mesh = {Animals ; Bacteria/*classification/genetics ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Europe ; Fresh Water/*microbiology ; Genes, rRNA ; *Multigene Family ; Nucleic Acid Hybridization/*methods ; Oligonucleotide Probes/*genetics ; Plankton/classification/genetics ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; Time Factors ; }, abstract = {The identification of phylogenetic clusters of bacteria that are common in freshwater has provided a basis for probe design to target important freshwater groups. We present a set of 16S ribosomal RNA gene-based oligonucleotide probes specific for 15 of these freshwater clusters. The probes were applied in reverse line blot hybridization, a simple method that enables the rapid screening of PCR products from many samples against an array of probes. The optimized assay was made stringent to discriminate at approximately the single-mismatch level. This made 10 of the probes highly specific, with at least two mismatches to the closest noncluster member in the global database. Screening of PCR products from bacterioplankton of 81 diverse lakes from Belgium, The Netherlands, Denmark, Sweden, and Norway showed that the respective probes were reactive against 5 to 100% of the lake samples. Positive reactivity of six highly specific probes showed that bacteria from actinobacterial clusters ACK-M1 and Sta2-30 and from verrucomicrobial cluster CLO-14 occurred in at least 90% of the investigated lakes. Furthermore, bacteria from alpha-proteobacterial cluster LD12 (closely related to the marine SAR11 cluster), beta-proteobacterial cluster LD28 and cyanobacterial cluster Synechococcus 6b occurred in more than 70% of the lakes. Reverse line blot hybridization is a new tool in microbial ecology that will facilitate research on distribution and habitat specificity of target species at relatively low costs.}, }
@article {pmid14531429, year = {2003}, author = {Raizada, N and Sonakya, V and Dalhoff, R and Hausner, M and Wilderer, PA}, title = {Population dynamics of rumen microbes using modern techniques in rumen enhanced solid incubation.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {48}, number = {4}, pages = {113-119}, pmid = {14531429}, issn = {0273-1223}, mesh = {Animals ; *Archaea ; *Bioreactors ; Hydrolysis ; *Methanosarcinales ; Poaceae/metabolism ; Population Dynamics ; Rumen/*microbiology ; }, abstract = {The microbial ecology of the rumen is very complex. Different species of bacteria, protozoa, and fungi are involved in digestion of plant material in ruminants. In spite of complicated interrelationships among the various groups of microorganisms in the rumen ecosystem, Bacteria and Archaea are believed to play a major role because of their numerical predominance and metabolic diversity. In this work we are presenting the results for microbial population dynamics of rumen microbes during two-stage anaerobic digestion of grass. The reactors were inoculated with fresh rumen content. Fluorescent in situ hybridization, confocal laser scanning microscopy and epifluorescence microscopy were employed for microbial investigation. It was observed that Bacteria dominated in the hydrolytic reactor (1st stage) whereas Archaea were predominant in the methanogenic reactor (2nd stage). The stability of the methanogenic reactor was result of the dominance of Methanosaeta species (mainly the filamentous type).}, }
@article {pmid14527796, year = {2003}, author = {Bagge-Ravn, D and Ng, Y and Hjelm, M and Christiansen, JN and Johansen, C and Gram, L}, title = {The microbial ecology of processing equipment in different fish industries-analysis of the microflora during processing and following cleaning and disinfection.}, journal = {International journal of food microbiology}, volume = {87}, number = {3}, pages = {239-250}, doi = {10.1016/s0168-1605(03)00067-9}, pmid = {14527796}, issn = {0168-1605}, mesh = {Animals ; Bacteria/*isolation &amp; purification ; Colony Count, Microbial ; Disinfection/methods/*standards ; *Equipment Contamination ; Food Handling/instrumentation/*methods ; Food Microbiology ; Food-Processing Industry/*standards ; Humans ; Seafood/microbiology ; Yeasts/isolation &amp; purification ; }, abstract = {The microflora adhering to the processing equipment during production and after cleaning and disinfecting procedures was identified in four different processing plants. A total of 1009 microorganisms was isolated from various-agar plates and identified. A stepwise procedure using simple phenotypic tests was used to identify the isolates and proved a fast way to group a large collection of microorganisms. Pseudomonas, Neisseriaceae, Enterobactericeae, Coryneform, Acinetobacter and lactic acid bacteria dominated the microflora of cold-smoked salmon plants, whereas the microflora in a plant processing semi-preserved herring consisted of Pseudomonas, Alcaligenes and Enterobactericeae. Psychrobacter, Staphylococcus and yeasts were found in a caviar processing plant. Overall, many microorganisms that are often isolated from fish were also isolated from the fish processing plants. However, some selection depending on processing parameters occurred, since halo- and osmo-tolerant organisms dominated in the caviar processing. After cleaning and disinfection, yeasts, Pseudomonas, Neisseriaceae and Alcaligenes remained in smokehouses, yeasts and Pseudomonas in the herring plant and Pseudomonas, Staphylococcus and yeasts in the caviar plant. The dominant adhering organisms after cleaning and disinfection were pseudomonads and yeasts independently of the microflora during processing. Knowledge of the adhering microflora is essential in the Good Hygienic Practises programme of food processing plants, as the development and design of improved cleaning and disinfecting procedures should target the microorganisms persisting and potentially contaminating the product.}, }
@article {pmid14510847, year = {2003}, author = {Denef, VJ and Park, J and Rodrigues, JL and Tsoi, TV and Hashsham, SA and Tiedje, JM}, title = {Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities.}, journal = {Environmental microbiology}, volume = {5}, number = {10}, pages = {933-943}, doi = {10.1046/j.1462-2920.2003.00490.x}, pmid = {14510847}, issn = {1462-2912}, support = {P42 ES 04911-12/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Biodegradation, Environmental ; Genome, Bacterial ; *Genomics ; Oligonucleotide Array Sequence Analysis/*methods ; Sensitivity and Specificity ; Soil Microbiology ; }, abstract = {Spotted oligonucleotide microarrays potentially offer a wide scope of applications for microbial ecology, especially as they improve the flexibility of design and the specificity of detection compared to PCR product based microarrays. Sensitivity, however, was expected to be problematic, as studies with the more sensitive PCR-based cDNA microarrays indicate that only genes from populations contributing to more than 5% of the community DNA can be detected. We evaluated several parameters to increase sensitivity and then tested applicability for bacterial functional genomics. The optimal parameters were the use of 5'-C6-amino-modified 70-mers printed on CMT-GAPS II substrates at a 40 micro M concentration combined with the use of Tyramide Signal Amplification labelling. This protocol allowed detection of single copy genes belonging to an organism contributing to 1% or more of the total community. To demonstrate its application, we detected the specific aromatic oxygenase genes in a soil community degrading polychlorinated biphenyls (PCBs). This increase in sensitivity is important if oligonucleotide microarrays are to be used for simultaneous monitoring of a range of functions performed by different microorganisms in the environment.}, }
@article {pmid14510840, year = {2003}, author = {Seghers, D and Top, EM and Reheul, D and Bulcke, R and Boeckx, P and Verstraete, W and Siciliano, SD}, title = {Long-term effects of mineral versus organic fertilizers on activity and structure of the methanotrophic community in agricultural soils.}, journal = {Environmental microbiology}, volume = {5}, number = {10}, pages = {867-877}, doi = {10.1046/j.1462-2920.2003.00477.x}, pmid = {14510840}, issn = {1462-2912}, mesh = {Alphaproteobacteria/classification/*metabolism ; Crops, Agricultural ; Fatty Acids/chemistry/metabolism ; *Fertilizers ; Gammaproteobacteria/classification/*metabolism ; Manure/*microbiology ; Methane/*metabolism ; Methylococcaceae/*metabolism ; Minerals/chemistry/metabolism ; Nitrates/metabolism ; Oxidation-Reduction ; Phylogeny ; Quaternary Ammonium Compounds/metabolism ; RNA, Ribosomal, 16S/analysis ; Soil ; Soil Microbiology ; }, abstract = {Agricultural practices, such as mineral nitrogen fertilization, have an impact on the soil's ability to oxidize methane, but little is known about the shifts in the methanotrophic community composition associated with these practices. Therefore, the long-term effect of both mineral (NH4NO3) and organic (manure and GFT-compost) fertilizer applications on the soil methanotrophic community activity and structure were investigated. Both high and low affinity methane oxidation rates were lower in the soil treated with mineral fertilizer compared to the other soils. An enhanced nitrate concentration was observed in the mineral fertilized soil but nitrate did not show a direct affect on the high affinity methane oxidation. In contrast, the low affinity methane oxidation was slowed down by increased nitrate concentrations, which suggests a direct effect of nitrate on low affinity methane oxidation. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments specific for methanotrophs revealed a distinct community between the mineral and organic fertilized soils as extra Type I methanotrophic bands (phylotypes) became visible in the organic fertilized soils. These phylotypes were not visible in the patterns of the added organic fertilizers suggesting an indirect effect of the organic fertilizers on the methanotrophic community. Additionally, a molecular analysis was performed after the low affinity methane oxidation test. The enhanced methane concentrations used in the test enriched certain low affinity methanotrophs in the organic fertilized soils but not in the mineral fertilized soil. Supporting the molecular and functional observations, fatty acids characteristic for methanotrophs were less abundant in the soil treated with mineral fertilizer compared to the soil treated with compost. In conclusion, the function and molecular and chemical composition of the methanotrophic community are all altered in soil fertilized with mineral fertilizer.}, }
@article {pmid14509706, year = {2003}, author = {Hashsham, SA and Freedman, DL}, title = {Adsorption of vitamin B12 to alumina, kaolinite, sand and sandy soil.}, journal = {Water research}, volume = {37}, number = {13}, pages = {3189-3193}, doi = {10.1016/S0043-1354(03)00131-3}, pmid = {14509706}, issn = {0043-1354}, mesh = {Adsorption ; Aluminum/*chemistry ; Bacteria, Anaerobic/*physiology ; Biodegradation, Environmental ; Kaolin/*chemistry ; Population Dynamics ; Silicon Dioxide/*chemistry ; Soil ; Vitamin B 12/*chemistry ; Water Movements ; }, abstract = {Vitamin B12 is an important component of media used to stimulate the growth of many anaerobic microbes that dechlorinate aliphatic compounds. Its delivery to the subsurface is therefore a concern for enhanced in situ bioremediation and bioaugmentation. In situ circulation of vitamin B12 and a chemical reductant has also been field tested for treatment of chlorinated methanes, ethanes, and ethenes. The objective of this study was to determine the extent of B12 (added as cyanocobalamin) adsorption to aquifer solids. Batch studies indicated a minor amount of adsorption to kaolinite clay (Freundlich Kf = 1.5 (microgram/g) (mL/microgram)1/n and 1/n = 0.39) and sand (Kf = 0.70 (microgram/g) (mL/microgram)1/n and 1/n = 0.84), and no detectable adsorption to alumina. Column studies using a 3H2O tracer and vitamin B12 in distilled water (10 microM) resulted in a B12 retardation factor (R) of approximately 2 for both sand (0.14% organic carbon) and a sandy soil (2.5% organic carbon). Using groundwater containing organic carbon (2.8 mg/L) in place of distilled water did not significantly change R. The relatively low value for R indicates vitamin B12 can be distributed throughout a contaminated aquifer without experiencing significant losses to adsorption.}, }
@article {pmid14507363, year = {2003}, author = {Klausen, M and Aaes-Jørgensen, A and Molin, S and Tolker-Nielsen, T}, title = {Involvement of bacterial migration in the development of complex multicellular structures in Pseudomonas aeruginosa biofilms.}, journal = {Molecular microbiology}, volume = {50}, number = {1}, pages = {61-68}, doi = {10.1046/j.1365-2958.2003.03677.x}, pmid = {14507363}, issn = {0950-382X}, mesh = {Biofilms/*growth &amp; development ; Fimbriae, Bacterial/genetics/physiology ; Gene Deletion ; Genes, Bacterial/genetics ; Microscopy, Confocal ; Movement ; Pseudomonas aeruginosa/*cytology/genetics/*physiology ; }, abstract = {Detailed knowledge of the developmental process from single cells scattered on a surface to complex multicellular biofilm structures is essential in order to create strategies to control biofilm development. In order to study bacterial migration patterns during Pseudomonas aeruginosa biofilm development, we have performed an investigation with time-lapse confocal laser scanning microscopy of biofilms formed by various combinations of colour-coded P. aeruginosa wild type and motility mutants. We show that mushroom-shaped multicellular structures in P. aeruginosa biofilms can form in a sequential process involving a non-motile bacterial subpopulation and a migrating bacterial subpopulation. The non-motile bacteria form the mushroom stalks by growth in certain foci of the biofilm. The migrating bacteria form the mushroom caps by climbing the stalks and aggregating on the tops in a process which is driven by type-IV pili. These results lead to a new model for biofilm formation by P. aeruginosa.}, }
@article {pmid14503688, year = {2003}, author = {Callaway, TR and Edrington, TS and Rychlik, JL and Genovese, KJ and Poole, TL and Jung, YS and Bischoff, KM and Anderson, RC and Nisbet, DJ}, title = {Ionophores: their use as ruminant growth promotants and impact on food safety.}, journal = {Current issues in intestinal microbiology}, volume = {4}, number = {2}, pages = {43-51}, pmid = {14503688}, issn = {1466-531X}, mesh = {Animals ; Animals, Domestic/growth &amp; development/microbiology ; Cattle ; Drug Resistance ; Drug Resistance, Bacterial ; Food/adverse effects ; Food Additives/adverse effects/therapeutic use ; Growth Substances/adverse effects/*therapeutic use ; Ionophores/adverse effects/*therapeutic use ; Ruminants/*growth &amp; development/microbiology ; Safety ; }, abstract = {Ionophores (such as monensin, lasalocid, laidlomycin, salinomycin and narasin) are antimicrobial compounds that are commonly fed to ruminant animals to improve feed efficiency. These antimicrobials specifically target the ruminal bacterial population and alter the microbial ecology of the intestinal microbial consortium, resulting in increased carbon and nitrogen retention by the animal, increasing production efficiency. Ionophores transport ions across cell membranes of susceptible bacteria, dissipating ion gradients and uncoupling energy expenditures from growth, killing these bacteria. Not all bacteria are susceptible to ionophores, and several species have been shown to develop several mechanisms of ionophore resistance. The prophylactic use of antimicrobials as growth promotants in food animals has fallen under greater scrutiny due to fears of the spread of antibiotic resistance. Because of the complexity and high degree of specificity of ionophore resistance, it appears that ionophores do not contribute to the development of antibiotic resistance to important human drugs. Therefore it appears that ionophores will continue to play a significant role in improving the efficiency of animal production in the future.}, }
@article {pmid14502419, year = {2003}, author = {Vrede, K and Stensdotter, U and Lindström, ES}, title = {Viral and bacterioplankton dynamics in two lakes with different humic contents.}, journal = {Microbial ecology}, volume = {46}, number = {4}, pages = {406-415}, pmid = {14502419}, issn = {0095-3628}, mesh = {Analysis of Variance ; *Bacterial Physiological Phenomena ; Chlorophyll/*analysis ; Chlorophyll A ; Fresh Water/analysis ; Microscopy, Electron ; Microscopy, Fluorescence ; Phytoplankton/*physiology/virology ; Plankton/*physiology/virology ; Soil/*analysis ; Sweden ; Virion/*ultrastructure ; }, abstract = {Viral and bacterioplankton dynamics were investigated, together with the temporal variation of phage-infected bacterioplankton in two oligotrophic lakes, one humic and the other clearwater. Bacterial abundance was significantly higher in the humic lake, while the abundance of virus-like particles (VLP) was significantly higher in the clearwater lake. There were no differences in either the frequency of infected bacterial cells (FIC), or in burst size between the lakes. Because of the higher bacterial abundance in the humic lake, a larger number of bacteria were lyzed in this lake. FIC showed large seasonal changes, varying between 9 and 43%, which covers almost the entire range of previously published data from both lacustrine and marine environments. The temporal changes in VLP abundance and FIC were slow in both the humic and clearwater lakes. The burst size was low in both lakes (average value, nine in each case), probably because of the oligotrophic status of the lakes. The chlorophyll a concentrations were higher and positively correlated with VLP numbers in the clearwater lake, indicating that a significant proportion of the viruses in this lake may be phytoplankton viruses.}, }
@article {pmid14502418, year = {2003}, author = {Ekendahl, S and O'Neill, AH and Thomsson, E and Pedersen, K}, title = {Characterisation of yeasts isolated from deep igneous rock aquifers of the Fennoscandian Shield.}, journal = {Microbial ecology}, volume = {46}, number = {4}, pages = {416-428}, pmid = {14502418}, issn = {0095-3628}, mesh = {Adaptation, Physiological ; *Biodiversity ; Environment ; Fresh Water/*analysis ; Hydrogen-Ion Concentration ; Microscopy, Electron ; Models, Genetic ; *Phylogeny ; RNA, Ribosomal/genetics ; Sequence Analysis, RNA ; Sodium Chloride ; Sweden ; Temperature ; *Water Microbiology ; Yeasts/*genetics/ultrastructure ; }, abstract = {The diversity of prokaryotes in the groundwater deep below the surface of the Baltic Sea at the Aspö Hard Rock Laboratory (HRL) in southeast Sweden is well documented. In addition, there is some evidence that eukaryotes, too, are present in the deep groundwater at this site, although their origins are uncertain. To extend the knowledge of eukaryotic life in this environment, five yeast, three yeastlike, and 17 mold strains were isolated from Aspö HRL groundwater between 201 and 444 m below sea level. Phenotypic testing and phylogenetic analysis of 18S rDNA sequences of the five yeast isolates revealed their relationships to Rhodotorula minuta and Cryptococcus spp. Scanning and transmission electron microscopy demonstrated that the strains possessed morphological characteristics typical for yeast, although they were relatively small, with an average length of 3 micro m. Enumeration through direct counting and most probable number methods showed low numbers of fungi, between 0.01 and 1 cells mL(-1), at some sites. Five of the strains were characterized physiologically to determine whether they were adapted to life in the deep biosphere. These studies revealed that the strains grew within a pH range of 4-10, between temperatures of 4 degrees C and 25-30 degrees C, and in NaCl concentrations from 0 to 70 g L(-1). These growth parameters suggest a degree of adaptation to the groundwater at Aspö HRL. Despite the fact that these eukaryotic microorganisms may be transient members of the deep biosphere microbial community, many of the observations of this study suggest that they are capable of growing in this extreme environment.}, }
@article {pmid14502417, year = {2004}, author = {Link, L and Sawyer, J and Venkateswaran, K and Nicholson, W}, title = {Extreme spore UV resistance of Bacillus pumilus isolates obtained from an ultraclean Spacecraft Assembly Facility.}, journal = {Microbial ecology}, volume = {47}, number = {2}, pages = {159-163}, pmid = {14502417}, issn = {0095-3628}, mesh = {Analysis of Variance ; Bacillus/*physiology ; *Environment, Controlled ; *Environmental Microbiology ; Radiation Tolerance/*physiology ; *Spacecraft ; Spores, Bacterial ; *Ultraviolet Rays ; }, abstract = {Recent environmental microbial sampling of the ultraclean Spacecraft Assembly Facility at NASA Jet Propulsion Laboratory (JPL-SAF) identified spores of Bacillus pumilus as major culturable bacterial contaminants found on and around spacecraft. As part of an effort to assess the efficacy of various spacecraft sterilants, purified spores of 10 JPL-SAF B. pumilus isolates were subjected to 254-nm UV and their UV resistance was compared to spores of standard B. subtilis biodosimetry strains. Spores of six of the 10 JPL-SAF isolates were significantly more resistant to UV than the B. subtilis biodosimetry strain, and one of the JPL-SAF isolates, B. pumilus SAFR-032, exhibited the highest degree of spore UV resistance observed by any Bacillus spp. encountered to date.}, }
@article {pmid14502416, year = {2003}, author = {Frederickson, CM and Short, SM and Suttle, CA}, title = {The physical environment affects cyanophage communities in British Columbia inlets.}, journal = {Microbial ecology}, volume = {46}, number = {3}, pages = {348-357}, pmid = {14502416}, issn = {0095-3628}, mesh = {Bacteriophages/*genetics ; British Columbia ; Chlorophyll/analysis ; *Cyanobacteria ; Ecosystem ; Fluorescence ; Polymerase Chain Reaction ; Population Dynamics ; Water Microbiology ; Water Movements ; }, abstract = {Little is known about the natural distribution of viruses that infect the photosynthetically important group of marine prokaryotes, the cyanobacteria. The current investigation reveals that the structure of cyanophage communities is dependent on water column structure. PCR was used to amplify a fragment of the cyanomyovirus gene (g) 20, which codes for the portal vertex protein. Denaturing gradient gel electrophoresis (DGGE) of PCR amplified g20 gene fragments was used to examine variations in cyanophage community structure in three inlets in British Columbia, Canada. Qualitative examination of denaturing gradient gels revealed cyanophage community patterns that reflected the physical structure of the water column as indicated by temperature and salinity. Based on mobility of PCR fragments in the DGGE gels, some cyanophages appeared to be widespread, while others were observed only at specific depths. Cyanophage communities within Salmon Inlet were more related to one another than to communities from either Malaspina Inlet or Pendrell Sound. As well, surface communities in Malaspina Inlet and Pendrell Sound were different when compared to communities at depth. In the same two locations, distinct differences in community composition were observed in communities that coincided with depths of high chlorophyll fluorescence. The observed community shifts over small distances (only a few meters in depth or inlets separated by less than 100 km) support the idea that cyanophage communities separated by small spatial scales develop independently of each other as a result isolation by water column stratification or land mass separation, which may ultimately lead to changes in the distribution or composition of the host community.}, }
@article {pmid14502415, year = {2003}, author = {Batten, KM and Scow, KM}, title = {Sediment microbial community composition and methylmercury pollution at four mercury mine-impacted sites.}, journal = {Microbial ecology}, volume = {46}, number = {4}, pages = {429-441}, pmid = {14502415}, issn = {0095-3628}, support = {2P42 ES04699/ES/NIEHS NIH HHS/United States ; }, mesh = {California ; Desulfovibrio/*chemistry ; Geologic Sediments/analysis/*microbiology ; Mercury/analysis ; Methylmercury Compounds/*analysis ; *Mining ; Phospholipids/analysis ; *Soil Microbiology ; Soil Pollutants/*analysis ; Sulfur-Reducing Bacteria/*chemistry ; }, abstract = {Mercury pollution presents a globally significant threat to human and ecosystem health. An important transformation in the mercury cycle is the conversion of inorganic mercury to methylmercury, a toxic substance that negatively affects neurological function and bioaccumulates in food chains. This transformation is primarily bacterially mediated, and sulfate-reducing bacteria (SRB) have been specifically implicated as key mercury methylators in lake and estuarine sediments. This study used phospholipid fatty acid (PLFA) analysis to investigate sediment microbial community composition at four abandoned mercury mine-impacted sites in the California Coast Range: the Abbott, Reed, Sulphur Bank, and Mt. Diablo mines. Differences in watershed and hydrology among these sites were related to differences in microbial community composition. The Abbott and Sulphur Bank mines had the highest levels of methylmercury. Floc (a type of precipitate that forms when acid mine drainage contacts lake or river water) and sediment samples differed in terms of several important environmental variables and microbial community composition, but did not have statistically different methylmercury concentrations. Quantification of PLFA biomarkers for SRB (10Mel6:0 for Desulfobacter and i17:1 for Desulfovibrio) revealed that Desulfobacter and Desulfovibrio organisms made up higher percentages of overall microbial biomass at the Sulphur Bank and Mt. Diablo mines than at the Abbott and Reed mines. Correlations between these SRB biomarker fatty acids and methylmercury concentrations suggest that Desulfobacter and Desulfovibrio organisms may contribute to methylmercury production in the Abbott, Reed, and Sulphur Bank mines but may not be important contributors to methylmercury in the Mt. Diablo Mine.}, }
@article {pmid14502414, year = {2003}, author = {Garcia-Pichel, F and Johnson, SL and Youngkin, D and Belnap, J}, title = {Small-scale vertical distribution of bacterial biomass and diversity in biological soil crusts from arid lands in the Colorado plateau.}, journal = {Microbial ecology}, volume = {46}, number = {3}, pages = {312-321}, pmid = {14502414}, issn = {0095-3628}, mesh = {Biomass ; Climate ; Colorado ; DNA Fingerprinting ; DNA, Bacterial/analysis ; Micronutrients ; Population Dynamics ; RNA, Ribosomal, 16S/analysis ; *Soil Microbiology ; }, abstract = {We characterized, at millimeter resolution, bacterial biomass, diversity, and vertical stratification of biological soil crusts in arid lands from the Colorado Plateau. Microscopic counts, extractable DNA, and plate counts of viable aerobic copiotrophs (VAC) revealed that the top centimeter of crusted soils contained atypically large bacterial populations, tenfold larger than those in uncrusted, deeper soils. The plate counts were not always consistent with more direct estimates of microbial biomass. Bacterial populations peaked at the immediate subsurface (1-2 mm) in light-appearing, young crusts, and at the surface (0-1 mm) in well-developed, dark crusts, which corresponds to the location of cyanobacterial populations. Bacterial abundance decreased with depth below these horizons. Spatially resolved DGGE fingerprints of Bacterial 16S rRNA genes demonstrated the presence of highly diverse natural communities, but we could detect neither trends with depth in bacterial richness or diversity, nor a difference in diversity indices between crust types. Fingerprints, however, revealed the presence of marked stratification in the structure of the microbial communities, probably a result of vertical gradients in physicochemical parameters. Sequencing and phylogenetic analyses indicated that most of the naturally occurring bacteria are novel types, with low sequence similarity (83-93%) to those available in public databases. DGGE analyses of the VAC populations indicated communities of lower diversity, with most types having sequences more than 94% similar to those in public databases. Our study indicates that soil crusts represent small-scale mantles of fertility in arid ecosystems, harboring vertically structured, little-known bacterial populations that are not well represented by standard cultivation methods.}, }
@article {pmid14502413, year = {2003}, author = {Gaze, WH and Burroughs, N and Gallagher, MP and Wellington, EM}, title = {Interactions between Salmonella typhimurium and Acanthamoeba polyphaga, and observation of a new mode of intracellular growth within contractile vacuoles.}, journal = {Microbial ecology}, volume = {46}, number = {3}, pages = {358-369}, pmid = {14502413}, issn = {0095-3628}, mesh = {Acanthamoeba/*growth &amp; development ; Animals ; Biofilms ; Ecology ; Feeding Behavior ; Genes, Reporter ; Intracellular Space ; Microscopy ; Population Dynamics ; *Salmonella typhimurium ; Survival Analysis ; Vacuoles ; }, abstract = {Acanthamoeba polyphaga feeding on Salmonella typhimurium in a simple model biofilm were observed by light microscopy and a detailed record of interactions kept by digital image capture and image analysis. A strain of S. typhimurium SL1344 carrying a fis: gfp reporter construct (pPDT105) was used to assess intracellular growth in A. polyphaga on non-nutrient agar (NNA) plates. Invasion of the contractile vacuole (CV) was observed at a frequency of 1:100-1000 acanthamoebae at 35 degrees C. The salmonellae contained in CVs illustrated significant up-regulation of fis relative to extracellular bacteria, indicating that they were in the early stages of logarithmic growth, and reached numbers of 100-200 cells per vacuole after 4 days. This is the first report of this mode of intracellular growth. Up-regulation of fis was also observed in a proportion of S. typhimurium cells contained within food vacuoles. Filamentation of S. typhimurium and E. coli cells was frequently observed in coculture with A. polyphaga on NNA plates, with bacterial cells reaching lengths of up to 500 microm after 10 days' incubation at 35 degrees C. A. polyphaga was also seen to mediate bacterial translocation over the agar surface; egested salmonellae subsequently formed microcolonies along amoebal tracks. This illustrated intracellular survival of a fraction of the S. typhimurium population. These phenomena suggest that protozoa such as A. polyhaga may play an important role in the ecology of S. typhimurium in soil and aquatic environments.}, }
@article {pmid14502411, year = {2003}, author = {Hewson, I and Vargo, GA and Fuhrman, JA}, title = {Bacterial diversity in shallow oligotrophic marine benthos and overlying waters: effects of virus infection, containment, and nutrient enrichment.}, journal = {Microbial ecology}, volume = {46}, number = {3}, pages = {322-336}, pmid = {14502411}, issn = {0095-3628}, mesh = {*Bacteria ; Classification ; Cluster Analysis ; DNA, Bacterial/analysis ; *Ecosystem ; Geologic Sediments/*microbiology ; Micronutrients ; Population Dynamics ; *Viruses ; *Water Microbiology ; }, abstract = {Little is known of the factors shaping sediment bacterial communities, despite their high abundance and reports of high diversity. Two factors hypothesized to shape bacterial communities in the water column are nutrient (resource) availability and virus infection. The role these factors play in benthic bacterial diversity was assessed in oligotrophic carbonate-based sediments of Florida Bay (USA). Sediment-water mesocosm enclosures were made from 1-m diameter clear polycarbonate cylinders which were pushed into sediments to approximately 201 cm sediment depth enclosing approximately 80 L of water. Mesocosms were amended each day for 14 d with 10 microM NH4+ and 1 microM PO4(3-). In a second experiment, viruses from a benthic flocculent layer were concentrated and added back to flocculent layer samples which were collected near the mesocosm enclosures. Photosynthesis by microalgae in virus-amended incubations was monitored by pulse-amplitude modulated (PAM) fluorescence. In both experiments, bacterial diversity was estimated using automated rRNA intergenic spacer analysis (ARISA), a high-resolution fingerprinting approach. Initial sediment bacterial operational taxonomic unit (OTU) richness (236 +/- 3) was higher than in the water column (148 +/- 9), where an OTU was detectable when its amplified DNA represented >0.09% of the total amplified DNA. Effects on bacterial diversity and operational taxonomic unit (OTU) richness in nutrient-amended mesocosms may have been masked by the effects of containment, which stimulated OTU richness in the water column, but depressed OTU richness and diversity in sediments. Nutrient addition significantly elevated virus abundance and the ratio of viruses to bacteria (p < 0.05 for both) in the sediments, concomitant with elevated bacterial diversity. However, water column bacterial diversity (in unamended controls) was not affected by nutrient amendments, which may be due to rapid nutrient uptake by sediment organisms or adsorption of P to carbonate sediments. Addition of live viruses to benthic flocculent layer samples increased bacterial OTU diversity and richness compared with heat-killed controls; however, cluster analyses showed that the community structure in the virus-amended mesocosms varied greatly between replicates. Despite the strong effects upon eubacterial communities, photosynthesis of co-occurring protists and cyanobacteria was not significantly altered by the presence of virus concentrates. This study supports the hypothesis that nutrient availability plays a key role in shaping sediment bacterial communities, and also that viruses may regulate the abundance of the dominant competitors and allow less dominant organisms to maintain or increase their abundance in a community due to decreased competition for resources.}, }
@article {pmid14502410, year = {2003}, author = {Küsel, K and Chabbi, A and Trinkwalter, T}, title = {Microbial processes associated with roots of bulbous rush coated with iron plaques.}, journal = {Microbial ecology}, volume = {46}, number = {3}, pages = {302-311}, pmid = {14502410}, issn = {0095-3628}, mesh = {Carbon Dioxide/analysis ; Coal ; Fermentation ; Hydrogen-Ion Concentration ; Iron/*metabolism ; Magnoliopsida/growth &amp; development/*microbiology ; Mining ; Oxidation-Reduction ; Plant Roots/*microbiology ; *Soil Microbiology ; }, abstract = {Bulbous rush (Juncus bulbosus) is a pioneer species in acidic, iron-rich, coal mining lakes in the eastern part of Germany. Juncus roots are coated with iron plaques, and it has been suggested that microbial processes under the iron plaques might be supportive for Juncus plant growth. The objectives of this work were to enumerate the microbes involved in the turnover of iron and organic root exudates in the rhizoplane, to investigate the effect of oxygen and pH on the utilization of these exudates by the rhizobacteria, and to study the ability of the root-colonizing microbiota to reduce sulfate. Enumeration studies done at pH 3 demonstrated that 10(6) Fe(III) reducers and 10(7) Fe(II) oxidizers g (fresh wt root)(-1) were associated with Juncus roots. When roots were incubated in goethite-containing medium without and with supplemental glucose, Fe(II) was formed at rates approximating 1.1 mmol g (fresh wt root) (-1) d(-1) and 3.6 mmol g (fresh wt root)(-1) d(-1) under anoxic conditions, respectively. These results suggest that a rapid microbially mediated cycling of iron occurs in the rhizosphere of Juncus roots under changing redox conditions. Most-probable-number estimates of aerobes and anaerobes capable of consuming root exudates at pH 3 were similar in the rhizosphere sediment and in Juncus roots, but numbers of aerobes were significantly higher than those of anaerobes. At pH 3, supplemental organic exudates were primarily subject to aerobic oxidation to CO2 and not subject to fermentation. However, at pH 4.5, root exudates were also rapidly utilized under anoxic conditions. Root-associated sulfate reduction was not observed at pH 3 to 4.5 but was observed at pH 4.9. The pH increased during all root-incubation studies both under oxic and anoxic conditions. Thus, as result of the microbial turnover of organic root exudates, pH and CO2 levels might be elevated at the root surface and favor Juncus plants to colonize acidic habitats.}, }
@article {pmid14502409, year = {2003}, author = {Hewson, I and Fuhrman, JA}, title = {Viriobenthos production and virioplankton sorptive scavenging by suspended sediment particles in coastal and pelagic waters.}, journal = {Microbial ecology}, volume = {46}, number = {3}, pages = {337-347}, pmid = {14502409}, issn = {0095-3628}, mesh = {Adsorption ; Bacteria ; California ; Carbon/*metabolism ; Geologic Sediments/*microbiology ; Particle Size ; *Plankton ; Population Dynamics ; Survival Analysis ; *Viruses ; *Water Microbiology ; }, abstract = {Virus production in oxic surface sediments and virioplankton sorption to suspended particles was estimated across three stations in the Southern California region (33.4 degrees N, 118.6 degrees W). Viriobenthos production was estimated using a sterile sediment and filtered porewater dilution technique that targeted production from both attached bacteria and bacteria living free in the porewater, and attached bacteria alone. Potential virus production rates by bacteria free in the porewater ranged from 1.7 to 4.6 x 10(8) VLP cm(-3) h(-1), while attached bacteria had slower potential production rates of between 0.4 and 1.1 x 10(8) VLP cm(-3) h(-1), suggesting turnover rates of viruses in sediments (1-5 h) which are significantly higher than those of virioplankton (approximately 24-48 h). Virioplankton adsorbed to small (<150 microm) suspended sediments at stations with high ambient suspended solid concentrations. Virioplankton scavenging rates combined with published sedimentation rates demonstrate that this mechanism of virus arrival could only account for 0.01% of daily benthic virus production. Calculated mortality rates of benthic bacteria (4-14% h(-1)) suggest viruses may play an important role in sediment carbon cycling.}, }
@article {pmid14500011, year = {2003}, author = {Böckelmann, U and Szewzyk, U and Grohmann, E}, title = {A new enzymatic method for the detachment of particle associated soil bacteria.}, journal = {Journal of microbiological methods}, volume = {55}, number = {1}, pages = {201-211}, doi = {10.1016/s0167-7012(03)00144-1}, pmid = {14500011}, issn = {0167-7012}, mesh = {Bacteria/growth &amp; development/*isolation &amp; purification ; Bacteriological Techniques/*methods ; Lectins/metabolism ; Lipase/pharmacology ; *Soil Microbiology ; Sonication ; alpha-Glucosidases/pharmacology ; beta-Galactosidase/pharmacology ; }, abstract = {A new enzymatic technique for the detachment of bacteria from soil particles was developed and applied to different soil samples taken at various sampling sites and depths. Many soil microorganisms are closely associated with the organic matrix of soil particles. They produce extracellular polymeric substances (EPS), which promote the irreversible adhesion of cells to soil particulates. To characterize the EPS, a prestaining of the soil samples with different lectins was performed. Samples from a sewage field, an urban park, a farmland, a mixed forest and garden mold were stained with a set of FITC-labelled lectins from Triticum vulgaris, Ulex europaeus, Concanavalin A and Pseudomonas aeruginosa. Based on the results, a combination of alpha-glucosidase, beta-galactosidase and a lipase was chosen for degradation of the EPS structures, followed by gentle mechanical and chemical dispersion in a modified sodium pyrophosphate buffer. The samples were fixed with formaldehyde and total cell counts were determined by DAPI staining. With the exception of the wheat field sample, this technique revealed up to 22-fold higher total cell counts for all investigated soil samples compared to the conventional detachment method, a simple dispersion with sodium pyrophosphate buffer. Efficiency of the technique was assessed by scanning electron microscopy. These images showed convincingly that the enzymatic treatment followed by sonication efficiently detached the bacteria and left the soil particles almost blank.}, }
@article {pmid13130034, year = {2003}, author = {Behrendt, U and Ulrich, A and Schumann, P}, title = {Fluorescent pseudomonads associated with the phyllosphere of grasses; Pseudomonas trivialis sp. nov., Pseudomonas poae sp. nov. and Pseudomonas congelans sp. nov.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {53}, number = {Pt 5}, pages = {1461-1469}, doi = {10.1099/ijs.0.02567-0}, pmid = {13130034}, issn = {1466-5026}, mesh = {DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Fluorescence ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Poaceae/*microbiology ; Pseudomonas/classification/genetics/*isolation &amp; purification/metabolism ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {Strains of fluorescent pseudomonads, isolated from the phyllosphere of grasses, were analysed by a polyphasic approach in order to clarify their interspecific position. Classification on the basis of ribotyping revealed six genotypes; four of these, which could be differentiated clearly from each other and from Pseudomonas species with validly published names on the basis of phenotypic features, were chosen for detailed phylogenetic analysis. DNA-DNA hybridization studies among representative strains of the four genotypes and closely related Pseudomonas species, determined by comparison of 16S rDNA sequences, showed that three of the studied ribotypes represented novel species. Two of them were related to mainly saprophytic fluorescent pseudomonads and could be easily distinguished by a negative arginine dihydrolase reaction. One ribotype, also characterized by a negative arginine dihydrolase reaction, was closely related to potentially plant-pathogenic fluorescent pseudomonads and differed in certain phenotypic features from its phylogenetic neighbours. As a consequence of the phenotypic and phylogenetic analyses, Pseudomonas trivialis sp. nov. (type strain: P 513/19(T)=DSM 14937(T)=LMG 21464(T)), Pseudomonas poae sp. nov. (type strain: P 527/13(T)=DSM 14936(T)=LMG 21465(T)) and Pseudomonas congelans sp. nov. (type strain: P 538/23(T)=DSM 14939(T)=LMG 21466(T)) are proposed.}, }
@article {pmid13130029, year = {2003}, author = {Dorofeeva, LV and Krausova, VI and Evtushenko, LI and Tiedje, JM}, title = {Agromyces albus sp. nov., isolated from a plant (Androsace sp.).}, journal = {International journal of systematic and evolutionary microbiology}, volume = {53}, number = {Pt 5}, pages = {1435-1438}, doi = {10.1099/ijs.0.02428-0}, pmid = {13130029}, issn = {1466-5026}, mesh = {Actinomycetales/classification/genetics/*isolation &amp; purification/metabolism ; Base Composition ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/genetics ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Primulaceae/*microbiology ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Agromyces albus sp. nov. is proposed for an aerobic, oxidase- and catalase-positive actinomycete that was isolated from the above-ground part of a plant (Androsace sp., in the family Primulaceae). The strain is characterized by white colonies, fragmenting hyphae that penetrate into agar media and chemotaxonomic properties that are typical of the genus AGROMYCES: Analysis of 16S rDNA sequences confirmed that the strain belongs to the genus Agromyces and revealed its close phylogenetic relationship with Agromyces ramosus. DNA-DNA pairing studies showed that the strain belongs to a separate genomic species; this is consistent with its distinction from other Agromyces species at the phenotypic level. The G+C content of the DNA was 69.0 mol%. The type strain is VKM Ac-1800(T) (=UCM Ac-623(T)).}, }
@article {pmid12973164, year = {2003}, author = {Leone, M and Albanese, J and Antonini, F and Nguyen-Michel, A and Martin, C}, title = {Long-term (6-year) effect of selective digestive decontamination on antimicrobial resistance in intensive care, multiple-trauma patients.}, journal = {Critical care medicine}, volume = {31}, number = {8}, pages = {2090-2095}, doi = {10.1097/01.CCM.0000079606.16776.C5}, pmid = {12973164}, issn = {0090-3493}, mesh = {APACHE ; Administration, Cutaneous ; Administration, Oral ; Adult ; Amphotericin B/administration &amp; dosage/pharmacology ; Anti-Bacterial Agents/administration &amp; dosage/*pharmacology ; *Antibiotic Prophylaxis ; Case-Control Studies ; Colistin/administration &amp; dosage/pharmacology ; Cross Infection/complications/*microbiology/prevention &amp; control ; *Drug Resistance, Bacterial ; Female ; France ; Gentamicins/administration &amp; dosage/pharmacology ; Gram-Negative Bacteria/drug effects/physiology ; Gram-Positive Bacteria/drug effects/physiology ; Hospitals, University ; Humans ; Intensive Care Units ; Male ; Methicillin Resistance ; Microbial Sensitivity Tests ; Middle Aged ; Multiple Trauma/*complications/microbiology/pathology ; Retrospective Studies ; Staphylococcus epidermidis/*drug effects/physiology ; }, abstract = {OBJECTIVE: To determine whether selective digestive decontamination (SDD) had some negative impact on the bacterial resistance observed in strains isolated from samples from patients receiving nonabsorbable antibiotics and cefazolin.<br><br>DESIGN: Case-control study.<br><br>SETTING: Intensive care unit of a university tertiary-care hospital.<br><br>PATIENTS: Over a 6-yr period, 360 multiple trauma patients (case patients) submitted to SDD were compared with 360 patients not receiving SDD (controls).<br><br>INTERVENTIONS: SDD consisted of polymyxin E, gentamicin, and amphotericin B and was applied on the buccal mucosa and provided in the nares and the stomach. For the first 3 days, systemic cefazolin (1 g three times a day) was provided. Resistance analysis was performed in case patients and controls on samples collected at predetermined intervals.<br><br>MEASUREMENTS AND MAIN RESULTS: SDD was used in a small subset of patients admitted to the intensive care unit (360 of 5987 over the 6-yr study period). A relative overgrowth of gram-positive cocci was observed. Methicillin resistance of Staphylococcus epidermidis was increased (SDD 76%, controls 63%, p <.05) but not that of Staphylococcus aureus (SDD 20%, controls 18%). Resistance of Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter to beta-lactamines and aminoglycosides was the same in SDD patients and controls.<br><br>CONCLUSIONS: When used in a small subset of patients who have been shown to derive benefit from it (patients who have experienced multiple trauma), SDD has a moderate impact on microbial ecology. However, surveillance cultures are indispensable because the absence of resistance to SDD antibiotics determines the long-term safety of the SDD prophylaxis.}, }
@article {pmid12962715, year = {2003}, author = {Nollet, H and Roels, M and Lutgen, P and Van der Meeren, P and Verstraete, W}, title = {Removal of PCBs from wastewater using fly ash.}, journal = {Chemosphere}, volume = {53}, number = {6}, pages = {655-665}, doi = {10.1016/S0045-6535(03)00517-4}, pmid = {12962715}, issn = {0045-6535}, mesh = {Adsorption ; Carbon/*chemistry ; Coal ; Coal Ash ; Hydrogen-Ion Concentration ; Industrial Waste ; Ions/chemistry ; Kinetics ; Particulate Matter ; Polychlorinated Biphenyls/chemistry/*isolation &amp; purification ; Temperature ; Thermodynamics ; *Waste Disposal, Fluid ; Water Pollutants/*isolation &amp; purification ; Water Purification/*methods ; }, abstract = {Liquids and sludges containing polychlorinated biphenyls (PCBs) can be treated to concentrate the PCBs in a solid residue. The latter can then be handled to destroy the PCBs. A study on sorption kinetics of PCBs on fly ash was conducted in controlled batch systems. TCB and HeCB are removed at 25 degrees C by adsorption on fly ash up to 97% at pH 7, with an adsorbent dose of 5 g/l. An examination of the thermodynamic parameters shows that the adsorption of TCB and HeCB by fly ash is a process occurring spontaneously at ambient conditions. Activation energies for the sorption process ranged between 5.6 and 49.1 kJ/mol. It was observed that the rate at which TCB and HeCB are adsorbed onto fly ash showed a diffusion limitation. The uptake rate of TCB and HeCB increases with increasing initial concentration and gradually tends to a constant value. A decrease in the adsorption of TCB and HeCB was observed when interfering ions and other PCB congeners were present. Changing the pH in the aqueous solution from 2 to 10 had no effect on the adsorption process. Overall, fly ash can be used for an efficient removal of PCBs from several aqueous solutions.}, }
@article {pmid12957957, year = {2003}, author = {Stoeck, T and Taylor, GT and Epstein, SS}, title = {Novel eukaryotes from the permanently anoxic Cariaco Basin (Caribbean Sea).}, journal = {Applied and environmental microbiology}, volume = {69}, number = {9}, pages = {5656-5663}, pmid = {12957957}, issn = {0099-2240}, mesh = {Animals ; Archaea/classification/isolation &amp; purification ; Bacteria/classification/genetics/*isolation &amp; purification ; Caribbean Region ; Evolution, Molecular ; Microsporidia/classification/isolation &amp; purification ; Oxygen Consumption ; Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 18S/genetics ; Seawater/analysis/microbiology ; }, abstract = {Present knowledge of microbial diversity is decidedly incomplete (S. J. Giovannoni and M. S. Rappé, p. 47-84, in D. Kirchman, ed., Microbial Ecology of the Oceans, 2000; E. Stackebrandt and T. M. Embley, p. 57-75, in R. R. Colwell and D. J. Grimes, ed., Nonculturable Microorganisms in the Environment, 2000). Protistan phylogenies are particularly deficient and undoubtedly exclude clades of principal ecological and evolutionary importance (S. L. Baldauf, Science 300:1703-1706, 2003). The rRNA approach has been extraordinarily successful in expanding the global prokaryotic record (S. J. Giovannoni and M. S. Rappé, p. 47-84, in D. Kirchman, ed., Microbial Ecology of the Oceans, 2000; E. Stackebrandt and T. M. Embley, p. 57-75, in R. R. Colwell and D. J. Grimes, ed., Nonculturable Microorganisms in the Environment, 2000) but has rarely been used in protistan discovery. Here we report the first application of the 18S rRNA approach to a permanently anoxic environment, the Cariaco Basin off the Venezuelan coast. On the basis of rRNA sequences, we uncovered a substantial number of novel protistan lineages. These included new clades of the highest taxonomic level unrelated to any known eukaryote as well as deep branches within established protistan groups. Three novel lineages branch at the base of the eukaryotic evolutionary tree preceding, contemporary with, or immediately following the earliest eukaryotic branches. These newly discovered protists may retain traits reminiscent of an early eukaryotic ancestor(s).}, }
@article {pmid12957955, year = {2003}, author = {De Wildeman, S and Diekert, G and Van Langenhove, H and Verstraete, W}, title = {Stereoselective microbial dehalorespiration with vicinal dichlorinated alkanes.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {9}, pages = {5643-5647}, pmid = {12957955}, issn = {0099-2240}, mesh = {Alkanes/chemistry/*metabolism ; Anaerobiosis ; DNA, Ribosomal/genetics/isolation &amp; purification ; Desulfitobacterium/classification/isolation &amp; purification/*metabolism ; Electron Transport ; Ethylene Dichlorides/*metabolism ; Hydrolases/metabolism ; Kinetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Substrate Specificity ; }, abstract = {The suspected carcinogen 1,2-dichloroethane (1,2-DCA) is the most abundant chlorinated C(2) groundwater pollutant on earth. However, a reductive in situ detoxification technology for this compound does not exist. Although anaerobic dehalorespiring bacteria are known to catalyze several dechlorination steps in the reductive-degradation pathway of chlorinated ethenes and ethanes, no appropriate isolates that selectively and metabolically convert them into completely dechlorinated end products in defined growth media have been reported. Here we report on the isolation of Desulfitobacterium dichloroeliminans strain DCA1, a nutritionally defined anaerobic dehalorespiring bacterium that selectively converts 1,2-dichloroethane and all possible vicinal dichloropropanes and -butanes into completely dechlorinated end products. Menaquinone was identified as an essential cofactor for growth of strain DCA1 in pure culture. Strain DCA1 converts chiral chlorosubstrates, revealing the presence of a stereoselective dehalogenase that exclusively catalyzes an energy-conserving anti mechanistic dichloroelimination. Unlike any known dehalorespiring isolate, strain DCA1 does not carry out reductive hydrogenolysis reactions but rather exclusively dichloroeliminates its substrates. This unique dehalorespiratory biochemistry has shown promising application possibilities for bioremediation purposes and fine-chemical synthesis.}, }
@article {pmid12957946, year = {2003}, author = {Feris, K and Ramsey, P and Frazar, C and Moore, JN and Gannon, JE and Holben, WE}, title = {Differences in hyporheic-zone microbial community structure along a heavy-metal contamination gradient.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {9}, pages = {5563-5573}, pmid = {12957946}, issn = {0099-2240}, mesh = {Alphaproteobacteria/drug effects/genetics/isolation &amp; purification ; Bacteria/drug effects/genetics/*isolation &amp; purification ; Base Sequence ; Betaproteobacteria/drug effects/genetics/isolation &amp; purification ; Cyanobacteria/drug effects/genetics/isolation &amp; purification ; DNA Primers ; Gammaproteobacteria/drug effects/genetics/isolation &amp; purification ; Geography ; Metals, Heavy/*analysis/pharmacology ; Montana ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics/isolation &amp; purification ; *Water Microbiology ; Water Pollutants, Chemical/*analysis/pharmacology ; }, abstract = {The hyporheic zone of a river is nonphotic, has steep chemical and redox gradients, and has a heterotrophic food web based on the consumption of organic carbon entrained from downwelling surface water or from upwelling groundwater. The microbial communities in the hyporheic zone are an important component of these heterotrophic food webs and perform essential functions in lotic ecosystems. Using a suite of methods (denaturing gradient gel electrophoresis, 16S rRNA phylogeny, phospholipid fatty acid analysis, direct microscopic enumeration, and quantitative PCR), we compared the microbial communities inhabiting the hyporheic zone of six different river sites that encompass a wide range of sediment metal loads resulting from large base-metal mining activity in the region. There was no correlation between sediment metal content and the total hyporheic microbial biomass present within each site. However, microbial community structure showed a significant linear relationship with the sediment metal loads. The abundances of four phylogenetic groups (groups I, II, III, and IV) most closely related to alpha-, beta-, and gamma-proteobacteria and the cyanobacteria, respectively, were determined. The sediment metal content gradient was positively correlated with group III abundance and negatively correlated with group II abundance. No correlation was apparent with regard to group I or IV abundance. This is the first documentation of a relationship between fluvially deposited heavy-metal contamination and hyporheic microbial community structure. The information presented here may be useful in predicting long-term effects of heavy-metal contamination in streams and provides a basis for further studies of metal effects on hyporheic microbial communities.}, }
@article {pmid12957923, year = {2003}, author = {Zhu, XY and Lubeck, J and Kilbane, JJ}, title = {Characterization of microbial communities in gas industry pipelines.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {9}, pages = {5354-5363}, pmid = {12957923}, issn = {0099-2240}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification/ultrastructure ; Base Sequence ; Cloning, Molecular ; DNA Primers ; DNA, Ribosomal/genetics ; *Gasoline ; Gene Amplification ; Microscopy, Electron, Scanning ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Culture-independent techniques, denaturing gradient gel electrophoresis (DGGE) analysis, and random cloning of 16S rRNA gene sequences amplified from community DNA were used to determine the diversity of microbial communities in gas industry pipelines. Samples obtained from natural gas pipelines were used directly for DNA extraction, inoculated into sulfate-reducing bacterium medium, or used to inoculate a reactor that simulated a natural gas pipeline environment. The variable V2-V3 (average size, 384 bp) and V3-V6 (average size, 648 bp) regions of bacterial and archaeal 16S rRNA genes, respectively, were amplified from genomic DNA isolated from nine natural gas pipeline samples and analyzed. A total of 106 bacterial 16S rDNA sequences were derived from DGGE bands, and these formed three major clusters: beta and gamma subdivisions of Proteobacteria and gram-positive bacteria. The most frequently encountered bacterial species was Comamonas denitrificans, which was not previously reported to be associated with microbial communities found in gas pipelines or with microbially influenced corrosion. The 31 archaeal 16S rDNA sequences obtained in this study were all related to those of methanogens and phylogenetically fall into three clusters: order I, Methanobacteriales; order III, Methanomicrobiales; and order IV, Methanosarcinales: Further microbial ecology studies are needed to better understand the relationship among bacterial and archaeal groups and the involvement of these groups in the process of microbially influenced corrosion in order to develop improved ways of monitoring and controlling microbially influenced corrosion.}, }
@article {pmid12957900, year = {2003}, author = {Oda, Y and Star, B and Huisman, LA and Gottschal, JC and Forney, LJ}, title = {Biogeography of the purple nonsulfur bacterium Rhodopseudomonas palustris.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {9}, pages = {5186-5191}, pmid = {12957900}, issn = {0099-2240}, mesh = {Cluster Analysis ; DNA Fingerprinting/methods ; DNA, Bacterial/genetics/isolation &amp; purification ; Ecosystem ; Environment ; Genotype ; Geography ; Phenotype ; Phylogeny ; Rhodopseudomonas/*classification/*genetics/isolation &amp; purification ; }, abstract = {The biogeography of the purple nonsulfur bacterium Rhodopseudomonas palustris on a local scale was investigated. Thirty clones of phototrophic bacteria were isolated from each of five unevenly spaced sampling locations in freshwater marsh sediments along a linear 10-m transect, and a total of 150 clones were characterized by BOX-PCR genomic DNA fingerprinting. Cluster analysis of 150 genomic fingerprints yielded 26 distinct genotypes, and 106 clones constituted four major genotypes that were repeatedly isolated. Representatives of these four major genotypes were tentatively identified as R. palustris based on phylogentic analyses of 16S rRNA gene sequences. The differences in the genomic fingerprint patterns among the four major genotypes were accompanied by differences in phenotypic characteristics. These phenotypic differences included differences in the kinetics of carbon source use, suggesting that there may be functional differences with possible ecological significance among these clonal linages. Morisita-Horn similarity coefficients (C(MH)), which were used to compare the numbers of common genotypes found at pairs of sampling locations, showed that there was substantial similarity between locations that were 1 cm apart (C(MH), >/=0.95) but there was almost no similarity between locations that were >/=9 m apart (C(MH), </=0.25). These calculations showed there was a gradual decrease in similarity among the five locations as a function of distance and that clones of R. palustris were lognormally distributed along the linear 10-m transect. These data indicate that natural populations of R. palustris are assemblages of genetically distinct ecotypes and that the distribution of each ecotype is patchy.}, }
@article {pmid12952419, year = {2003}, author = {Vermeirssen, V and Van Camp, J and Devos, L and Verstraete, W}, title = {Release of angiotensin I converting enzyme (ACE) inhibitory activity during in vitro gastrointestinal digestion: from batch experiment to semicontinuous model.}, journal = {Journal of agricultural and food chemistry}, volume = {51}, number = {19}, pages = {5680-5687}, doi = {10.1021/jf034097v}, pmid = {12952419}, issn = {0021-8561}, mesh = {Angiotensin-Converting Enzyme Inhibitors/*metabolism ; *Digestion ; Digestive System/enzymology/*metabolism ; Endopeptidases/metabolism ; Hydrolysis ; In Vitro Techniques ; Milk Proteins/metabolism ; Pisum sativum/chemistry ; Peptides/metabolism ; Plant Proteins/metabolism ; Whey Proteins ; }, abstract = {Gastrointestinal digestion is of major importance in the bioavailability of angiotensin I converting enzyme (ACE) inhibitory peptides, bioactive peptides with possible antihypertensive effects. In this study, the conditions of in vitro gastrointestinal digestion leading to the formation and degradation of ACE inhibitory peptides were investigated for pea and whey protein. In batch experiments, the digestion simulating the physiological conditions sufficed to achieve the highest ACE inhibitory activity, with IC(50) values of 0.076 mg/mL for pea and 0.048 mg/mL for whey protein. The degree of proteolysis did not correlate with the ACE inhibitory activity and was always higher for pea than whey. In a semicontinuous model of gastrointestinal digestion, response surface methodology studied the influence of temperature and incubation time in both the stomach and small intestine phases on the ACE inhibitory activity and degree of proteolysis. For pea protein, a linear model for the degree of proteolysis and a quadratic model for the ACE inhibitory activity could be constituted. Within the model, a maximal degree of proteolysis was observed at the highest temperature and the longest incubation time in the small intestine phase, while maximal ACE inhibitory activity was obtained at the longest incubation times in the stomach and small intestine phase. These results show that ACE inhibitory activity of pea and whey hydrolysates can be controlled by the conditions of in vitro gastrointestinal digestion.}, }
@article {pmid12948054, year = {2003}, author = {De Wildeman, S and Neumann, A and Diekert, G and Verstraete, W}, title = {Growth-substrate dependent dechlorination of 1,2-dichloroethane by a homoacetogenic bacterium.}, journal = {Biodegradation}, volume = {14}, number = {4}, pages = {241-247}, doi = {10.1023/a:1024781722670}, pmid = {12948054}, issn = {0923-9820}, mesh = {Acetobacterium/genetics/growth &amp; development/*metabolism ; Bacteria, Anaerobic/metabolism ; Biodegradation, Environmental ; Culture Media, Conditioned ; Ethylene Dichlorides/*metabolism ; Formates/metabolism ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/analysis ; }, abstract = {A rod shaped, gram positive, non sporulating Acetobacterium strain was isolated that dechlorinated 1,2dichloroethane (1,2-DCA) to ethene at a dechlorination rate of up to 2 nmol Cl- min(-1) mg(-1) of protein in the exponential growth phase with formate (40 mM) as the substrate. Although with other growth substrates such as pyruvate, lactate, H2/CO2, and ethanol higher biomass productions were obtained, the dechlorination rate with these substrates was more than 10-fold lower compared with formate growing cells. Neither cell extracts nor autoclaved cells of the isolated Acetobacterium strain mediated the dechlorination of 1,2-DCA at significant rates. The addition of 1,2-DCA to the media did not result in increased cell production. No significant differences in corrinoid concentrations could be measured in cells growing on several growth-substrates. However, these measurements indicated that differences in corrinoid structure might cause the different dechlorination activity. The Acetobacterium sp. strain gradually lost its dechlorination ability during about 10 transfers in pure culture, probably due to undefined nutritional requirements. 16S rDNA analysis of the isolate revealed a 99.7% similarity with Acetobacterium wieringae. However, the type strains of A. wieringae and A. woodii did not dechlorinate 1,2-DCA.}, }
@article {pmid12942357, year = {2004}, author = {Münzenberger, B and Golldack, J and Ullrich, A and Schmincke, B and Hüttl, RF}, title = {Abundance, diversity, and vitality of mycorrhizae of Scots pine (Pinus sylvestris L.) in lignite recultivation sites.}, journal = {Mycorrhiza}, volume = {14}, number = {3}, pages = {193-202}, pmid = {12942357}, issn = {0940-6360}, mesh = {Biodiversity ; *Coal Mining ; Germany ; Mycorrhizae/*physiology ; Pinus/*microbiology ; Soil ; }, abstract = {Scots pine (Pinus sylvestris L.) stands cover large areas in the Lusatian and the Middle German lignite mining districts. Due to adverse chemical substrate conditions, the root systems of the trees are restricted to the ameliorated top-spoil and the organic forest floor layers. To investigate functioning of fine root systems under the prevailing site factors, we studied mycorrhizal colonization rate and frequency as well as mycorrhizal diversity, vitality and growth phases in Scots pine ecosystems along a chronosequence in both mining districts. Mycorrhizal rate was close to 100% in both districts. Mycorrhizal abundance was higher in the organic forest floor layer than the mineral soil layer. In total, 25 morphotypes were recorded. Diversity differed between the districts. The mycorrhizae of Amphinema byssoides, Tuber puberulum, Pinirhiza discolor, Pinirhiza cf. bicolorata and E-type were present in both mining areas. These morphotypes are typical of nutrient-rich soils with high pH values. Compared with the undisturbed sites, vitality of mycorrhizae was very high at the test sites on spoil substrate, correlating with the high growth dynamics of mycorrhizae at recultivation sites. A relatively high carbon flow to the mycorrhizal root systems at these sites seems likely. Thus, mycorrhizal root systems are able to cope with the ameliorated top-spoil and the organic layer. The main reason for the adaptation is the large number of ectomycorrhizal fungal species available in this area where Pinus sylvestris is indigenous.}, }
@article {pmid12934933, year = {2003}, author = {Johri, BN and Sharma, A and Virdi, JS}, title = {Rhizobacterial diversity in India and its influence on soil and plant health.}, journal = {Advances in biochemical engineering/biotechnology}, volume = {84}, number = {}, pages = {49-89}, doi = {10.1007/3-540-36488-9_2}, pmid = {12934933}, issn = {0724-6145}, mesh = {Agriculture/methods ; Biotechnology/methods ; Ecosystem ; Genetic Variation/genetics/*physiology ; India ; Pest Control, Biological/methods ; Plant Diseases/microbiology ; Plant Roots/genetics/*microbiology/*physiology ; Population Dynamics ; Rhizobiaceae/classification/genetics/*physiology ; *Soil Microbiology ; Species Specificity ; }, abstract = {The rhizosphere or the zone of influence around roots harbors a multitude of microorganisms that are affected by both abiotic and biotic stresses. Among these are the dominant rhizobacteria that prefer living in close vicinity to the root or on its surface and play a crucial role in soil health and plant growth. Both free-living and symbiotic bacteria are involved in such specific ecological niches and help in plant matter degradation, nutrient mobilization and biocontrol of plant disease. While the rhizosphere as a domain of fierce microbial activity has been studied for over a century, the availability of modern tools in microbial ecology has now permitted the study of microbial communities associated with plant growth and development, in situ localization of important forms, as well as the monitoring of introduced bacteria as they spread in the soil and root environment. This interest is linked to environmental concerns for reduced use of chemicals for disease control as well as an appreciation for utilization of biologicals and organics in agriculture. Indian researchers have studied the diversity of rhizobacteria in a variety of plants, cereals, legumes and others along with assessment of their functionality based on the release of enzymes (soil dehydrogenase, phosphatase, nitrogenase, etc.), metabolites (siderophores, antifungals, HCN, etc.), growth promoters (IAA, ethylene) and as inducers of systemic disease resistance (ISR). Based on such primary screening protocols, effective rhizobacteria have been field tested with success stories from various agroecological zones of the country, as reflected in the control of root- and soil-borne diseases, improved soil health and increased crop yields. Several commercial formulations, mostly based on dry powder (charcoal, lignite, farmyard manure, etc.) have been prepared and field tested, however, problems of appropriate shelf-life and cell viability are still to be solved. Also, inherent in such low cost technologies are the problems of variability in field performance and successful establishment of introduced inoculants in the root zone. In addition, most products available in the market are not properly monitored for quality before they reach the farmer. As a consequence, the acceptance of rhizobacterial formulations in the country is limited. However, several laboratories have now developed protocols for the rapid characterization of effective isolates based on molecular fingerprinting and other similar tools. Also, the use of molecular markers (gus, lux, gfp, etc.) makes it easy to monitor introduced inoculants in situ in soil and rhizosphere environments. The government initiative in integrated nutrient management and pest management systems has provided additional incentives to relate rhizobacterial science to other ongoing activities so that the benefit of this research leads to technologies that are environmentally and socially acceptable.}, }
@article {pmid12926783, year = {2003}, author = {Flickinger, EA and Schreijen, EM and Patil, AR and Hussein, HS and Grieshop, CM and Merchen, NR and Fahey, GC}, title = {Nutrient digestibilities, microbial populations, and protein catabolites as affected by fructan supplementation of dog diets.}, journal = {Journal of animal science}, volume = {81}, number = {8}, pages = {2008-2018}, doi = {10.2527/2003.8182008x}, pmid = {12926783}, issn = {0021-8812}, mesh = {Ammonia/analysis ; *Animal Feed ; Animal Nutritional Physiological Phenomena ; Animals ; *Digestion ; Dogs ; Dose-Response Relationship, Drug ; Fatty Acids, Volatile/analysis ; Feces/*chemistry/microbiology ; Female ; Fermentation ; Fructans/*administration &amp; dosage/metabolism ; Ileum/metabolism/microbiology ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Male ; Odorants/analysis ; Random Allocation ; }, abstract = {Fructans are fermentable carbohydrates and include short-chain fructooligosaccharides (scFOS), inulin, and hydrolyzed inulin (oligofructose, OF). Two studies with dogs were designed to examine the effects of low concentrations of fructans on nutrient digestibilities, fecal microbial populations, and endproducts of protein fermentation, and fecal characteristics. In Exp. 1, 11 adult male beagles were fed corn-based, kibbled diets supplemented with or without OF to provide 1.9 +/- 0.6 g/d. Dietary inclusion of OF decreased (P < 0.05) nutrient digestibilities, but did not affect fecal characteristics. Increasing OF concentration tended (P < 0.06) to linearly decrease fecal ammonia concentrations, but not those of branched-chain fatty acids (BCFA), amines, indole, or phenols. Fecal concentrations of total short-chain fatty acids (SCFA) and butyrate tended to be higher in OF-supplemented dogs (P < 0.10), as was the ratio of bifidobacteria to total anaerobes (P = 0.15). In Exp. 2, ileally cannulated adult female hounds were fed a meat-based kibbled diet and were assigned to four scFOS treatments (0, 1, 2, or 3 g/d) in a 4 x 4 Latin square design. Ileal nutrient digestibilities tended to increase (P < 0.15) with increasing concentrations of scFOS. On a DMI basis, fecal output tended to decrease linearly (P < 0.10) in response to increasing scFOS supplementation, whereas fecal score tended to exhibit a quadratic response (P = 0.12). In general, fecal concentrations of SCFA, BCFA, ammonia, phenols, and indoles were not altered by supplemental scFOS. Supplementation of scFOS increased fecal concentrations of total aerobes (P < 0.05) and decreased concentrations of Clostridium perfringens (P < 0.05). From these data, it seems that low levels of supplemental fructans have divergent effects on nutrient digestibility and fermentative endproducts, but do not adversely affect nutrient digestibility or fecal characteristics and may improve colonic microbial ecology in dogs.}, }
@article {pmid12916428, year = {2003}, author = {Bilev, AE}, title = {[Epidemiological analysis of microbial ecology damage in bronchial asthma].}, journal = {Voenno-meditsinskii zhurnal}, volume = {324}, number = {6}, pages = {72-75}, pmid = {12916428}, issn = {0026-9050}, mesh = {Asthma/*epidemiology/*microbiology/pathology ; Candida/pathogenicity ; Ecology ; Escherichia/pathogenicity ; Humans ; Pulmonary Disease, Chronic Obstructive/microbiology/pathology ; Risk Factors ; Russia/epidemiology ; Staphylococcus/pathogenicity ; }, }
@article {pmid12910328, year = {2004}, author = {De Kempeneer, L and Sercu, B and Vanbrabant, W and Van Langenhove, H and Verstraete, W}, title = {Bioaugmentation of the phyllosphere for the removal of toluene from indoor air.}, journal = {Applied microbiology and biotechnology}, volume = {64}, number = {2}, pages = {284-288}, doi = {10.1007/s00253-003-1415-3}, pmid = {12910328}, issn = {0175-7598}, mesh = {Air Pollutants/*metabolism ; *Air Pollution, Indoor ; Biodegradation, Environmental ; Biotechnology/methods ; Plant Leaves/microbiology ; Pseudomonas putida/*growth &amp; development/*metabolism ; Rhododendron/*microbiology ; Toluene/analysis/*metabolism ; }, abstract = {The removal of airborne toluene by means of the phyllosphere of Azalea indica augmented with a toluene-degrading enrichment culture of Pseudomonas putida TVA8 was studied. The 95% disappearance time [DT95%; the time in which an initial toluene concentration of 90 ppmv (339 mg.m(3)) was removed in a batch experiment] was 75 h for Azalea plants. Under the same experimental conditions, DT95% of inoculated Azalea plants decreased remarkably to about 27 h. Subsequent additions of toluene further increased the removal efficiency of the bioaugmented system (DT95% decreased by a factor of four). A decrease in DT95% was also recorded after repeated incubations of non-inoculated plants, but the toluene-removal rate was remarkably low, compared with the inoculated plants. Hence, inoculation of the leaf surface appeared essential for obtaining rapid removal rates. It was not possible to obtain comparable and sustained removal of airborne toluene by inoculating artificial plant surfaces. This is, to our knowledge, the first report on bioaugmentation of the leaf surface of plants to remove gaseous pollutants from air. The results presented are promising and could be of great practical importance in the field of indoor air pollution control.}, }
@article {pmid12904916, year = {2003}, author = {Øvreås, L and Daae, FL and Torsvik, V and Rodríguez-Valera, F}, title = {Characterization of microbial diversity in hypersaline environments by melting profiles and reassociation kinetics in combination with terminal restriction fragment length polymorphism (T-RFLP).}, journal = {Microbial ecology}, volume = {46}, number = {3}, pages = {291-301}, pmid = {12904916}, issn = {0095-3628}, mesh = {*Bacteria ; Biomass ; *DNA Fingerprinting ; DNA Primers ; DNA, Bacterial/*analysis ; *Genetic Variation ; Kinetics ; Microscopy, Electron ; Polymorphism, Restriction Fragment Length ; Population Dynamics ; Sodium Chloride/*pharmacology ; *Water Microbiology ; }, abstract = {The diversity of prokaryotes inhabiting solar saltern ponds was determined by thermal melting and reassociation of community DNA. These measurements were compared with fingerprinting techniques such as terminal restriction fragment length polymorphisms (T-RFLP) analysis, denaturant gradient gel electrophoresis (DGGE), and cloning and sequencing approaches. Three ponds with salinities of 22, 32, and 37% (NaCl saturation) were studied. The combination of independent molecular techniques to estimate the total genetic diversity provided a realistic assessment to reveal the microbial diversity in these environments. The changes in the prokaryotic communities at different salinity (22, 32, and 37% salt) were significant and revealed that the total genetic diversity increased from 22% to 32% salinity. At 37% salinity the diversity was reduced again to nearly half that at 22% salinity. Our results revealed that the community "genome" had a DNA complexity that was 7 (in 22% salinity pond), 13 (in 32% salinity pond), and 4 (in 37% salinity pond) times the complexity of an Escherichia coli genome. The base composition profiles showed two abundant populations, which changed in relative amount between the three ponds. They indicated an uneven taxon distribution at 22% and 37% salinity and a more even distribution at 32% salinity. The results indicated a large predominating population at 37% salinity, which might correspond to the abundance of square archaea (SPhT) observed by transmission electron microscopy (TEM) and also indicated by the same T-RFLP fragment as the SPhT. The SPhT phylotype has also been reported to be the most frequently retrieved phylotype from this environment by culture independent techniques. In addition, two different operational taxonomic units (OTU) were detected at 37% salinity based on PCR with bacterial specific primers and T-RFLP. One of these predominant phylotypes is the extreme halophilic bacterium belonging to the bacteroidetes group, Salinibacter ruber.}, }
@article {pmid12904915, year = {2003}, author = {Yannarell, AC and Kent, AD and Lauster, GH and Kratz, TK and Triplett, EW}, title = {Temporal patterns in bacterial communities in three temperate lakes of different trophic status.}, journal = {Microbial ecology}, volume = {46}, number = {4}, pages = {391-405}, pmid = {12904915}, issn = {0095-3628}, mesh = {Bacteria/*genetics ; *Biodiversity ; DNA Primers ; DNA, Ribosomal Spacer/genetics ; Electrophoresis ; Eutrophication/*physiology ; Fluorescence ; Fresh Water/analysis ; *Seasons ; Time Factors ; *Water Microbiology ; Wisconsin ; }, abstract = {Despite considerable attention in recent years, the composition and dynamics of lake bacterial communities over annual time scales are poorly understood. This study used automated ribosomal intergenic spacer analysis (ARISA) to explore the patterns of change in lake bacterial communities in three temperate lakes over 2 consecutive years. The study lakes included a humic lake, an oligotrophic lake, and a eutrophic lake, and the epilimnetic bacterial communities were sampled every 2 weeks. The patterns of change in bacterial communities indicated that seasonal forces were important in structuring the behavior of the bacterial communities in each lake. All three lakes had relatively stable community composition in spring and fall, but summer changes were dramatic. Summertime variability was often characterized by recurrent drops in bacterial diversity. Specific ARISA fragments derived from these lakes were not constant among lakes or from year to year, and those fragments that did recur in lakes in different years did not exhibit the same seasonal pattern of recurrence. Nonetheless, seasonal patterns observed in 2000 were fairly successful predictors of the rate of change in bacterial communities and in the degree of autocorrelation of bacterial communities in 2001. Thus, seasonal forces may be important structuring elements of these systems as a whole even if they are uncoupled from the dynamics of the individual system components.}, }
@article {pmid12904913, year = {2003}, author = {Maruyama, A and Ishiwata, H and Kitamura, K and Sunamura, M and Fujita, T and Matsuo, M and Higashihara, T}, title = {Dynamics of microbial populations and strong selection for Cycloclasticus pugetii following the Nakhodka oil spill.}, journal = {Microbial ecology}, volume = {46}, number = {4}, pages = {442-453}, pmid = {12904913}, issn = {0095-3628}, mesh = {Base Sequence ; Cluster Analysis ; DNA, Ribosomal/genetics ; Disasters ; *Environmental Pollution ; Japan ; Microscopy, Fluorescence ; Molecular Probe Techniques ; Molecular Sequence Data ; Petroleum/*microbiology ; *Phylogeny ; Piscirickettsiaceae/*genetics ; Population Dynamics ; *Selection, Genetic ; Sequence Analysis, DNA ; Ships ; }, abstract = {Microbial population changes were monitored immediately after the Nakhodka oil spill accident in January 1997 at the heavily oil-contaminated Mikuni coast along the Sea of Japan. The total cell number was almost stable for one year at 2-5 x 10(5) cells mL(-1), while the relative occurrence of culturable heterotrophs and degraders of oil components such as C-heavy oil, kerosene, and n-tetradecane varied, showing a maximum (>50% of the total) immediately following the accident. Gene amplification and phylogenetic analysis of a dilution culture using C-heavy oil as the sole carbon and energy source revealed that one of the predominant oil degraders at the oil-contaminated coast in 2 weeks after the accident closely resembled the aromatic hydrocarbon decomposer Cycloclasticus pugetii. Microbial community composition in oil-contaminated seawater was estimated at the molecular level using newly developed oligonucleotide probes, probe wash-off curve estimation, and quantitative fluorescence dot-blot hybridization techniques. At two different oil-polluted sites, harbor and intertidal regions, the C. pugetii group was estimated to make up 23-25% of the total Bacteria population, followed by the aliphatic hydrocarbon decomposer Alcanivorax borkumensis, which formed 4-7% of the Bacteria. In incubation experiments using floated oil slick and indigenous microbes collected at the harbor, oil degradation activities were enhanced by the addition of both organic and inorganic nutrients. Significant decreases were found in aromatic and aliphatic hydrocarbon fractions: 54-60% and 22-24% in 2 weeks to 68-77% and 23-32% in 2 months, respectively.}, }
@article {pmid12904912, year = {2003}, author = {Wieland, A and Kühl, M and McGowan, L and Fourçans, A and Duran, R and Caumette, P and García de Oteyza, T and Grimalt, JO and Solé, A and Diestra, E and Esteve, I and Herbert, RA}, title = {Microbial mats on the Orkney Islands revisited: microenvironment and microbial community composition.}, journal = {Microbial ecology}, volume = {46}, number = {4}, pages = {371-390}, pmid = {12904912}, issn = {0095-3628}, mesh = {Bacteria/*chemistry ; *Biodiversity ; Chromatography, Gas ; Cluster Analysis ; DNA Primers ; *Environmental Microbiology ; Eukaryota/*chemistry ; Euryarchaeota/*chemistry ; Geography ; Microscopy, Confocal ; Photosynthesis ; Polymorphism, Restriction Fragment Length ; Scotland ; Spectrophotometry ; }, abstract = {The microenvironment and community composition of microbial mats developing on beaches in Scapa Flow (Orkney Islands) were investigated. Analysis of characteristic biomarkers (major fatty acids, hydrocarbons, alcohols, and alkenones) revealed the presence of different groups of bacteria and microalgae in mats from Waulkmill and Swanbister beach, including diatoms, Haptophyceae, cyanobacteria, and sulfate-reducing bacteria. These analyses also indicated the presence of methanogens, especially in Swanbister beach mats, and therefore a possible role of methanogenesis for the carbon cycle of these sediments. High amounts of algal lipids and slightly higher numbers (genera, abundances) of cyanobacteria were found in Waulkmill Bay mats. However, overall only a few genera and low numbers of unicellular and filamentous cyanobacteria were present in mats from Waulkmill and Swanbister beach, as deduced from CLSM (confocal laser scanning microscopy) analysis. Spectral scalar irradiance measurements with fiber-optic microprobes indicated a pronounced heterogeneity concerning zonation and density of mainly anoxygenic phototrophs in Swanbister Bay mats. By microsensor and T-RFLP (terminal restriction fragment length polymorphism) analysis in Swanbister beach mats, the depth distribution of different populations of purple and sulfate-reducing bacteria could be related to the microenvironmental conditions. Oxygen, but also sulfide and other (inorganic and organic) sulfur compounds, seems to play an important role in the stratification and diversity of these two major bacterial groups involved in sulfur cycling in Swanbister beach mats.}, }
@article {pmid12902290, year = {2003}, author = {Seurinck, S and Verstraete, W and Siciliano, SD}, title = {Use of 16S-23S rRNA intergenic spacer region PCR and repetitive extragenic palindromic PCR analyses of Escherichia coli isolates to identify nonpoint fecal sources.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {8}, pages = {4942-4950}, pmid = {12902290}, issn = {0099-2240}, mesh = {Animals ; DNA Fingerprinting ; DNA, Ribosomal Spacer/*genetics ; Escherichia coli/genetics/*isolation &amp; purification ; Feces/*microbiology ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 23S/*genetics ; Sewage/microbiology ; }, abstract = {Despite efforts to minimize fecal input into waterways, this kind of pollution continues to be a problem due to an inability to reliably identify nonpoint sources. Our objective was to find candidate source-specific Escherichia coli fingerprints as potential genotypic markers for raw sewage, horses, dogs, gulls, and cows. We evaluated 16S-23S rRNA intergenic spacer region (ISR)-PCR and repetitive extragenic palindromic (rep)-PCR analyses of E. coli isolates as tools to identify nonpoint fecal sources. The BOXA1R primer was used for rep-PCR analysis. A total of 267 E. coli isolates from different fecal sources were typed with both techniques. E. coli was found to be highly diverse. Only two candidate source-specific E. coli fingerprints, one for cow and one for raw sewage, were identified out of 87 ISR fingerprints. Similarly, there was only one candidate source-specific E. coli fingerprint for horse out of 59 BOX fingerprints. Jackknife analysis resulted in an average rate of correct classification (ARCC) of 83% for BOX-PCR analysis and 67% for ISR-PCR analysis for the five source categories of this study. When nonhuman sources were pooled so that each isolate was classified as animal or human derived (raw sewage), ARCCs of 82% for BOX-PCR analysis and 72% for ISR-PCR analysis were obtained. Critical factors affecting the utility of these methods, namely sample size and fingerprint stability, were also assessed. Chao1 estimation showed that generally 32 isolates per fecal source individual were sufficient to characterize the richness of the E. coli population of that source. The results of a fingerprint stability experiment indicated that BOX and ISR fingerprints were stable in natural waters at 4, 12, and 28 degrees C for 150 days. In conclusion, 16S-23S rRNA ISR-PCR and rep-PCR analyses of E. coli isolates have the potential to identify nonpoint fecal sources. A fairly small number of isolates was needed to find candidate source-specific E. coli fingerprints that were stable under the simulated environmental conditions.}, }
@article {pmid12902285, year = {2003}, author = {Hammes, F and Boon, N and de Villiers, J and Verstraete, W and Siciliano, SD}, title = {Strain-specific ureolytic microbial calcium carbonate precipitation.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {8}, pages = {4901-4909}, pmid = {12902285}, issn = {0099-2240}, mesh = {Bacteria/*enzymology/genetics ; Calcium/pharmacology ; Calcium Carbonate/*chemistry ; Chemical Precipitation ; Crystallization ; Genetic Variation ; Species Specificity ; Urease/analysis/genetics/*metabolism ; }, abstract = {During a study of ureolytic microbial calcium carbonate (CaCO(3)) precipitation by bacterial isolates collected from different environmental samples, morphological differences were observed in the large CaCO(3) crystal aggregates precipitated within bacterial colonies grown on agar. Based on these differences, 12 isolates were selected for further study. We hypothesized that the striking differences in crystal morphology were the result of different microbial species or, alternatively, differences in the functional attributes of the isolates selected. Sequencing of 16S rRNA genes showed that all of the isolates were phylogenetically closely related to the Bacillus sphaericus group. Urease gene diversity among the isolates was examined by using a novel application of PCR-denaturing gradient gel electrophoresis (DGGE). This approach revealed significant differences between the isolates. Moreover, for several isolates, multiple bands appeared on the DGGE gels, suggesting the apparent presence of different urease genes in these isolates. The substrate affinities (K(m)) and maximum hydrolysis rates (V(max)) of crude enzyme extracts differed considerably for the different strains. For certain isolates, the urease activity increased up to 10-fold in the presence of 30 mM calcium, and apparently this contributed to the characteristic crystal formation by these isolates. We show that strain-specific calcification occurred during ureolytic microbial carbonate precipitation. The specificity was mainly due to differences in urease expression and the response to calcium.}, }
@article {pmid12902280, year = {2003}, author = {González-Toril, E and Llobet-Brossa, E and Casamayor, EO and Amann, R and Amils, R}, title = {Microbial ecology of an extreme acidic environment, the Tinto River.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {8}, pages = {4853-4865}, pmid = {12902280}, issn = {0099-2240}, mesh = {DNA Fingerprinting ; *Ecology ; Ecosystem ; Fresh Water/*microbiology ; Hydrogen-Ion Concentration ; In Situ Hybridization, Fluorescence ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; *Water Microbiology ; }, abstract = {The Tinto River (Huelva, southwestern Spain) is an extreme environment with a rather constant acidic pH along the entire river and a high concentration of heavy metals. The extreme conditions of the Tinto ecosystem are generated by the metabolic activity of chemolithotrophic microorganisms thriving in the rich complex sulfides of the Iberian Pyrite Belt. Molecular ecology techniques were used to analyze the diversity of this microbial community. The community's composition was studied by denaturing gradient gel electrophoresis (DGGE) using 16S rRNA and by 16S rRNA gene amplification. A good correlation between the two approaches was found. Comparative sequence analysis of DGGE bands showed the presence of organisms related to Leptospirillum spp., Acidithiobacillus ferrooxidans, Acidiphilium spp., "Ferrimicrobium acidiphilum," Ferroplasma acidiphilum, and Thermoplasma acidophilum. The different phylogenetic groups were quantified by fluorescent in situ hybridization with a set of rRNA-targeted oligonucleotide probes. More than 80% of the cells were affiliated with the domain Bacteria, with only a minor fraction corresponding to Archaea. Members of Leptospirillum ferrooxidans, Acidithiobacillus ferrooxidans, and Acidiphilium spp., all related to the iron cycle, accounted for most of the prokaryotic microorganisms detected. Different isolates of these microorganisms were obtained from the Tinto ecosystem, and their physiological properties were determined. Given the physicochemical characteristics of the habitat and the physiological properties and relative concentrations of the different prokaryotes found in the river, a model for the Tinto ecosystem based on the iron cycle is suggested.}, }
@article {pmid12892924, year = {2003}, author = {Ardhana, MM and Fleet, GH}, title = {The microbial ecology of cocoa bean fermentations in Indonesia.}, journal = {International journal of food microbiology}, volume = {86}, number = {1-2}, pages = {87-99}, doi = {10.1016/s0168-1605(03)00081-3}, pmid = {12892924}, issn = {0168-1605}, mesh = {Bacillus/*growth &amp; development/isolation &amp; purification/metabolism ; Cacao/*microbiology ; Ethanol/metabolism ; Fermentation ; *Food Microbiology ; Food Technology ; Fungi/*growth &amp; development/isolation &amp; purification/metabolism ; Indonesia ; Lactobacillus/*growth &amp; development/isolation &amp; purification/metabolism ; Yeasts/*growth &amp; development/isolation &amp; purification/metabolism ; }, abstract = {Cocoa beans are the principal raw material of chocolate manufacture. The beans are subject to a microbial fermentation as the first stage in chocolate production. The microbial ecology of bean fermentation (Forastero and Trinitario cultivars) was investigated at three commercial fermentaries in East Java, Indonesia by determining the populations of individual species at 12-h intervals throughout the process. The first 2-3 days of fermentation were characterised by the successional growth of various species of filamentous fungi, yeasts, lactic acid bacteria and acetic acid bacteria. The principal species found were Penicillium citrinum, an unidentified basidiomycete, Kloeckera apis, Saccharomyces cerevisiae, Candida tropicalis, Lactobacillus cellobiosus, Lactobacillus plantarum and Acetobacter pasteurianus. The later stages of fermentation were dominated by the presence of Bacillus species, mostly, Bacillus pumilus and Bacillus licheniformis. Glucose, fructose, sucrose and citric acid of the bean pulp were utilised during fermentation, with the production of ethanol, acetic acid and lactic acid that diffused into the beans. The filamentous fungi were notable for their production of polygalacturonase activity and probably contributed to the degradation of bean pulp.}, }
@article {pmid12889609, year = {2003}, author = {Frederiksen, TM and Finster, K}, title = {Sulfite-oxido-reductase is involved in the oxidation of sulfite in Desulfocapsa sulfoexigens during disproportionation of thiosulfate and elemental sulfur.}, journal = {Biodegradation}, volume = {14}, number = {3}, pages = {189-198}, doi = {10.1023/a:1024255830925}, pmid = {12889609}, issn = {0923-9820}, mesh = {Gram-Negative Anaerobic Bacteria/cytology/enzymology/metabolism ; Oxidation-Reduction/drug effects ; Oxidoreductases Acting on Sulfur Group Donors/antagonists &amp; inhibitors/*metabolism ; Sulfites/*metabolism ; Sulfur-Reducing Bacteria/cytology/*enzymology/metabolism ; Thiosulfates/metabolism ; Uncoupling Agents/pharmacology ; }, abstract = {The enzymatic pathways of elemental sulfur and thiosulfate disproportionation were investigated using cell-free extract of Desulfocapsa sulfoexigens. Sulfite was observed to be an intermediate in the metabolism of both compounds. Two distinct pathways for the oxidation of sulfite have been identified. One pathway involves APS reductase and ATP sulfurylase and can be described as the reversion of the initial steps of the dissimilatory sulfate reduction pathway. The second pathway is the direct oxidation of sulfite to sulfate by sulfite oxidoreductase. This enzyme has not been reported from sulfate reducers before. Thiosulfate reductase, which cleaves thiosulfate into sulfite and sulfide, was only present in cell-free extract from thiosulfate disproportionating cultures. We propose that this enzyme catalyzes the first step in thiosulfate disproportionation. The initial step in sulfur disproportionation was not identified. Dissimilatory sulfite reductase was present in sulfur and thiosulfate disproportionating cultures. The metabolic function of this enzyme in relation to elemental sulfur or thiosulfate disproportionation was not identified. The presence of the uncouplers HQNO and CCCP in growing cultures had negative effects on both thiosulfate and sulfur disproportionation. CCCP totally inhibited sulfur disproportionation and reduced thiosulfate disproportionation by 80% compared to an unamended control. HQNO reduced thiosulfate disproportionation by 80% and sulfur disproportionation by 90%.}, }
@article {pmid12884087, year = {2003}, author = {Wejse, PL and Ingvorsen, K and Mortensen, KK}, title = {Purification and characterisation of two extremely halotolerant xylanases from a novel halophilic bacterium.}, journal = {Extremophiles : life under extreme conditions}, volume = {7}, number = {5}, pages = {423-431}, pmid = {12884087}, issn = {1431-0651}, mesh = {Bacteria/*enzymology ; Chromatography, Gel ; Chromatography, Ion Exchange ; Electrophoresis, Polyacrylamide Gel ; Enzyme Stability ; Half-Life ; Hydrogen-Ion Concentration ; Hydrolysis ; Isoelectric Focusing ; Molecular Weight ; Potassium Chloride/chemistry ; Sodium Chloride/chemistry ; Substrate Specificity ; Temperature ; Xylosidases/chemistry/*isolation &amp; purification/metabolism ; }, abstract = {The present work reports for the first time the purification and characterisation of two extremely halotolerant endo-xylanases from a novel halophilic bacterium, strain CL8. Purification of the two xylanases, Xyl 1 and 2, was achieved by anion exchange and hydrophobic interaction chromatography. The enzymes had relative molecular masses of 43 kDa and 62 kDa and pI of 5.0 and 3.4 respectively. Stimulation of activity by Ca(2+), Mn(2+), Mg(2+), Ba(2+), Li(2+), NaN(3) and isopropanol was observed. The K(m) and V(max) values determined for Xyl 1 with 4- O-methyl- d-glucuronoxylan are 5 mg/ml and 125,000 nkat/mg respectively. The corresponding values for Xyl 2 were 1 mg/ml and 143,000 nkat/mg protein. Xylobiose and xylotriose were the major end products for both endoxylanases. The xylanases were stable at pH 4-11 showing pH optima around pH 6. Xyl 1 shows maximal activity at 60 degrees C, Xyl 2 at 65 degrees C (at 4 M NaCl). The xylanases showed high temperature stability with half-lives at 60 degrees C of 97 min and 192 min respectively. Both xylanases showed optimal activity at 1 M NaCl, but substantial activity remained for both enzymes at 5 M NaCl.}, }
@article {pmid12883864, year = {2003}, author = {Hammes, F and Boon, N and Clement, G and de Villiers, J and Siciliano, SD and Verstraete, W}, title = {Molecular, biochemical and ecological characterisation of a bio-catalytic calcification reactor.}, journal = {Applied microbiology and biotechnology}, volume = {62}, number = {2-3}, pages = {191-201}, doi = {10.1007/s00253-003-1287-6}, pmid = {12883864}, issn = {0175-7598}, mesh = {Base Sequence ; Bioreactors/*microbiology ; Calcium/*isolation &amp; purification/*metabolism ; Calcium Carbonate/isolation &amp; purification/metabolism ; Catalysis ; Chemical Precipitation ; DNA, Bacterial/genetics ; Ecosystem ; Genes, Bacterial ; Kinetics ; Microscopy, Electron, Scanning ; Models, Biological ; Molecular Sequence Data ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Urea/metabolism ; Urease/genetics/metabolism ; Water Pollutants, Chemical/*isolation &amp; purification/*metabolism ; }, abstract = {Bio-catalytic calcification (BCC) reactors utilise microbial urea hydrolysis by autochthonous bacteria for the precipitation-removal of calcium, as calcite, from industrial wastewater. Due to the limited knowledge available concerning natural ureolytic microbial calcium carbonate (CaCO(3)) precipitation, the microbial ecology of BCC reactors has remained a black box to date. This paper characterises BCC reactor evolution from initialisation to optimisation over a 6-week period. Three key parameters were studied: (1) microbial evolution, (2) the (bio)chemical CaCO(3) precipitation pathway, and (3) crystal nucleation site development. Six weeks were required to establish optimal reactor performance, which coincided with an increase in urease activity from an initial 7 mg urea l(-1) reactor h(-1) to about 100 mg urea l(-1) reactor h(-1). Urease activity in the optimal period was directly proportional to Ca(2+) removal, but urease gene diversity was seemingly limited to a single gene. Denaturing gradient gel electrophoresis of 16S rRNA genes revealed the dynamic evolution of the microbial community structure of the calcareous sludge, which was eventually dominated by a few species including Porphyromonas sp., Arcobacter sp. and Bacteroides sp. Epi-fluorescence and scanning electron microscopy showed that the calcareous sludge was colonised with living bacteria, as well as the calcified remains of organisms. It appears that the precipitation event is localised in a micro-environment, due to colonisation of crystal nucleation sites (calcareous sludge) by the precipitating organisms.}, }
@article {pmid12877467, year = {2003}, author = {Nicholas, DR and Ramamoorthy, S and Palace, V and Spring, S and Moore, JN and Rosenzweig, RF}, title = {Biogeochemical transformations of arsenic in circumneutral freshwater sediments.}, journal = {Biodegradation}, volume = {14}, number = {2}, pages = {123-137}, doi = {10.1023/a:1024031700533}, pmid = {12877467}, issn = {0923-9820}, mesh = {Arsenic/*chemistry ; Arsenicals/*chemistry ; Bacteria/chemistry/metabolism ; Biodegradation, Environmental ; Fresh Water/*analysis ; Indicators and Reagents ; Iron/chemistry ; Methylation ; Oxidation-Reduction ; Sulfates/chemistry ; Water Microbiology ; Water Pollutants/*analysis ; }, abstract = {Arsenic is a wide-spread contaminant of soils and sediments, and many watersheds worldwide regularly experience severe arsenic loading. While the toxicity of arsenic to plants and animals is well recognized, the geochemical and biological transformations that alter its bioavailability in the environment are multifaceted and remain poorly understood. This communication provides a brief overview of our current understanding of the biogeochemistry of arsenic in circumneutral freshwater sediments, placing special emphasis on microbial transformations. Arsenic can reside in a number of oxidation states and complex ions. The common inorganic aqueous species at circumneutral pH are the negatively charged arsenates (H2As(V)O4(-) and Has(V)O4(2-)) and zero-charged arsenite (H3As(III)O3(0)). Arsenic undergoes diagenesis in response to both physical and biogeochemical processes. It accumulates in oxic sediments by adsorption on and/or co-precipitation with hydrous iron and manganese oxides. Burial of such sediments in anoxic/suboxic environments favors their reduction, releasing Fe(II), Mn(II) and associated adsorbed/coprecipitated As. Upward advection can translocate these cations and As into the overlying oxic zone where they may reprecipitate. Alternatively, As may be repartitioned to the sulfidic phase, forming precipitates such as arsenopyrite and orpiment. Soluble and adsorbed As species undergo biotic transformations. As(V) can serve as the terminal electron acceptor in the biological oxidation of organic matter, and the limited number of microbes capable of this transformations are diverse in their phylogeny and physiology. Fe(III)-respiring bacteria can mobilize both As(V) and As(III) bound to ferric oxides by the reductive dissolution of iron-arsenate minerals. SO4(2-)-reducing bacteria can promote deposition of As(III) as sulfide minerals via their production of sulfide. A limited number of As(III)-oxidizing bacteria have been identified, some of which couple this reaction to growth. Lastly, prokaryotic and eukaryotic microbes can alter arsenic toxicity either by coupling cellular export to its reduction or by converting inorganic As to organo-arsenical compounds. The degree to which each of these metabolic transformations influences As mobilization or sequestration in different sedimentary matrices remains to be established.}, }
@article {pmid12855166, year = {2003}, author = {Park, J and Malinverni, J and Adriaens, P and Kukor, JJ}, title = {Quantitative structure-activity relationship (QSAR) analysis of aromatic effector specificity in NtrC-like transcriptional activators from aromatic oxidizing bacteria.}, journal = {FEMS microbiology letters}, volume = {224}, number = {1}, pages = {45-52}, doi = {10.1016/S0378-1097(03)00400-2}, pmid = {12855166}, issn = {0378-1097}, mesh = {*Bacterial Proteins ; Base Sequence ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Gram-Negative Aerobic Rods and Cocci/*genetics/*metabolism ; Hydrocarbons, Aromatic/*metabolism ; Molecular Sequence Data ; Operon/genetics ; Oxidation-Reduction ; PII Nitrogen Regulatory Proteins ; Promoter Regions, Genetic/physiology ; Quantitative Structure-Activity Relationship ; Toluene/metabolism ; Trans-Activators/metabolism ; *Transcription Factors ; Transcriptional Activation/physiology ; Trichloroethylene/metabolism ; }, abstract = {A quantitative structure-activity relationship (QSAR) approach was taken to provide mechanistic insights into the interaction between the chemical structure of inducing compounds and the transcriptional activation of aromatic monooxygenase operons among the XylR/DmpR subclass of bacterial NtrC-like transcriptional regulators. Compared to XylR and DmpR, a broader spectrum of effector compounds was observed for the TbuT system from Ralstonia pickettii PKO1. The results of QSAR analysis for TbuT suggested that a steric effect, rather than hydrophobic or electronic effects, may be the predominant factor in determining aromatic effector specificity, and the active site of the regulator may positively interact not only with the methyl moiety but also with the most electron-rich aryl side of an aromatic effector.}, }
@article {pmid12849777, year = {2003}, author = {Molin, S and Tolker-Nielsen, T}, title = {Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure.}, journal = {Current opinion in biotechnology}, volume = {14}, number = {3}, pages = {255-261}, doi = {10.1016/s0958-1669(03)00036-3}, pmid = {12849777}, issn = {0958-1669}, mesh = {Bacteria/*genetics ; Biodegradation, Environmental ; Biofilms/*growth &amp; development ; *Conjugation, Genetic ; Environmental Pollutants/*metabolism ; Environmental Pollution/prevention &amp; control ; Gene Expression Regulation, Bacterial/*genetics ; *Gene Transfer Techniques ; Genetic Engineering/*methods ; Plasmids/*genetics ; Transformation, Bacterial/physiology ; }, abstract = {There has been much interest in bioremediation based on the introduction of bacteria able to catabolise recalcitrant compounds deposited in the environment. In particular, the delivery of catabolic information in the form of conjugative plasmids to bacterial populations in situ has great potential. As most bacteria in the environment live in surface-associated communities (biofilms), the gene transfer systems within these communities need to be better characterised for bio-enhancement strategies to be developed. Recent findings suggest that gene transfer does take place within biofilms, but studies also identified limitations and bottlenecks of the process. The dense population structure in biofilms increases plasmid dispersal by conjugation, and the conjugation mechanism itself may stimulate biofilm development. Moreover, DNA release and transformation seem to be part of a biofilm-related life cycle and released DNA stabilises the biofilm structure. Both of these gene-transfer mechanisms may be autocatalytically promoted in biofilms, presenting new possibilities for efficient bio-enhancement strategies.}, }
@article {pmid12839788, year = {2003}, author = {Lee, L and Saxena, D and Stotzky, G}, title = {Activity of free and clay-bound insecticidal proteins from Bacillus thuringiensis subsp. israelensis against the mosquito Culex pipiens.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {7}, pages = {4111-4115}, pmid = {12839788}, issn = {0099-2240}, mesh = {Adsorption ; Aluminum Silicates/*chemistry ; Animals ; Bacillus thuringiensis/*metabolism ; Bacillus thuringiensis Toxins ; Bacterial Proteins/chemistry/isolation &amp; purification/*pharmacology ; *Bacterial Toxins ; Bentonite/chemistry ; Clay ; Culex/*drug effects/growth &amp; development ; Endotoxins/chemistry/isolation &amp; purification/*pharmacology ; Hemolysin Proteins ; Hydrogen-Ion Concentration ; Kaolin/chemistry ; Larva/drug effects ; *Pest Control, Biological ; }, abstract = {Bacillus thuringiensis subsp. israelensis produces parasporal insecticidal crystal proteins (ICPs) that have larvicidal activity against some members of the order Diptera, such as blackflies and mosquitoes. Hydrolysis of the ICPs in the larval gut results in four major proteins with a molecular mass of 27, 65, 128, and 135 kDa. Toxicity is caused by synergistic interaction between the 25-kDa protein (proteolytic product of the 27-kDa protein) and one or more of the higher-molecular-mass proteins. Equilibrium adsorption of the proteins on the clay minerals montmorillonite and kaolinite, which are homoionic to various cations, was rapid (<30 min for maximal adsorption), increased with protein concentration and then reached a plateau (68 to 96% of the proteins was adsorbed), was significantly lower on kaolinite than on montmorillonite, and was not significantly affected by the valence of the cation to which the clays were homoionic. Binding of the toxins decreased as the pH was increased from 6 to 11, and there was 35 to 66% more binding in phosphate buffer at pH 6 than in distilled water at pH 6 or 7.2. Only 2 to 12% of the adsorbed proteins was desorbed by two washes with water; additional washings desorbed no more toxins, indicating that they were tightly bound. Formation of clay-toxin complexes did not alter the structure of the proteins, as indicated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the equilibrium supernatants and desorption washes and by dot blot enzyme-linked immunosorbent assay of the complexes, which was confirmed by enhanced chemiluminescence Western blot analysis. Free and clay-bound toxins resulted in 85 to 100% mortality of the mosquito Culex pipiens. Persistence of the bound toxins in nonsterile water after 45 days was significantly greater (mortality of 63% +/- 12.7%) than that of the free toxins (mortality of 25% +/- 12.5%).}, }
@article {pmid12839745, year = {2003}, author = {Ranjard, L and Nazaret, S and Cournoyer, B}, title = {Freshwater bacteria can methylate selenium through the thiopurine methyltransferase pathway.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {7}, pages = {3784-3790}, pmid = {12839745}, issn = {0099-2240}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/classification/genetics/*metabolism ; DNA, Bacterial/analysis ; Escherichia coli/metabolism ; Fresh Water/*microbiology ; Humans ; Methylation ; Methyltransferases/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Phylogeny ; Pseudomonas/metabolism ; Rats ; Selenium/*metabolism ; Sequence Analysis, DNA ; }, abstract = {Involvement of the bacterial thiopurine methyltransferase (bTPMT) in natural selenium methylation by freshwater was investigated. A freshwater environment that had no known selenium contamination but exhibited reproducible emission of dimethyl selenide (DMSe) or dimethyl diselenide (DMDSe) when it was supplemented with an organic form of selenium [(methyl)selenocysteine] or an inorganic form of selenium (sodium selenite) was used. The distribution of the bTPMT gene (tpm) in the microflora was studied. Freshwater bacteria growing on 10 micro M sodium selenite and 10 micro M sodium selenate were isolated, and 4.5 and 10% of the strains, respectively, were shown by colony blot hybridization to hybridize with a Pseudomonas syringae tpm DNA probe. Ribotyping showed that these strains are closely related. The complete rrs sequence of one of the strains, designated Hsa.28, was obtained and analyzed. Its closest phyletic neighbor was found to be the Pseudomonas anguilliseptica rrs sequence. The Hsa.28 strain grown with sodium selenite or (methyl)selenocysteine produced significant amounts of DMSe and DMDSe. The Hsa.28 tpm gene was isolated by genomic DNA library screening and sequencing. BLASTP comparisons of the deduced Hsa.28 bTPMT sequence with P. syringae, Pseudomonas aeruginosa, Vibrio cholerae, rat, and human thiopurine methyltransferase sequences revealed that the levels of similarity were 52 to 71%. PCR-generated Escherichia coli subclones containing the Hsa.28 tpm open reading frame were constructed. E. coli cells harboring the constructs and grown with sodium selenite or (methyl)selenocysteine produced significant levels of DMSe and DMDSe, confirming that the gene plays a role in selenium methylation. The effect of strain Hsa.28 population levels on freshwater DMSe and DMDSe emission was investigated. An increase in the size of the Hsa.28 population was found to enhance significantly the emission of methyl selenides by freshwater samples supplemented with sodium selenite or (methyl)selenocysteine. These data suggest that bTPMT can play a role in natural freshwater selenium methylation processes.}, }
@article {pmid12836921, year = {2003}, author = {Wiedmann, M and , }, title = {ADSA Foundation Scholar Award--An integrated science-based approach to dairy food safety: Listeria monocytogenes as a model system.}, journal = {Journal of dairy science}, volume = {86}, number = {6}, pages = {1865-1875}, doi = {10.3168/jds.s0022-0302(03)73774-6}, pmid = {12836921}, issn = {0022-0302}, support = {R01GM63259/GM/NIGMS NIH HHS/United States ; }, mesh = {Agriculture ; Animals ; Cattle ; Dairy Products/*microbiology ; Ecology ; *Food Microbiology ; Genotype ; Humans ; *Listeria monocytogenes/genetics/pathogenicity/physiology ; Listeriosis/transmission ; Milk/microbiology ; Models, Biological ; Phylogeny ; Zoonoses ; }, abstract = {Transmission of food- and milkborne pathogens often involves complex interactions among the pathogen, the environment, and one or multiple host species. A complete understanding of these interactions is critical to allow the development of science-based, effective intervention strategies for foodborne infectious diseases. This article summarizes our studies on the transmission, ecology, pathogenesis and population genetics of Listeria monocytogenes, which we have used as model for a food- and milkborne pathogen that infects multiple hosts and also has considerable ability to survive and multiply in nonhost environments. Application of molecular subtyping tools in conjunction with phenotypic characterization of selected strains has allowed us to define distinct L. monocytogenes subtypes and clonal groups that appear to differ in relevant phenotypic characteristics that may affect their abilities to be transmitted through food systems. For example, a genetic group designated as lineage I has been shown to be not only more common among human listeriosis cases than among animal cases, but lineage I strains also appear to show an increased in vitro ability to spread intracellularly from host cell to host cell. These findings are consistent with the fact that while genetically diverse strains may be classified to one bacterial species, these strains often differ from one another in important genetic and phenotypic characteristics. I thus propose that evolutionary- and molecular subtyping-based definitions of bacterial subtypes and clonal groups will provide critical insight into the microbial ecology of dairy food systems, including not only foodborne pathogens, but also organisms important for dairy fermentation and spoilage.}, }
@article {pmid12836560, year = {2003}, author = {Xiang, W and Wu, J and Xiao, H and Li, X}, title = {[Advances in extraction and purification of soil microorganism].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {14}, number = {3}, pages = {453-456}, pmid = {12836560}, issn = {1001-9332}, mesh = {Bacteria/*isolation &amp; purification ; Fungi/*isolation &amp; purification ; *Soil Microbiology ; }, abstract = {For the studies on soil microbial ecology and bio-diversity as well as on the dynamics of C, N, S and P in soil, it is necessary to quantitatively extract microorganism from soil. The recent advances on extraction and purification of microorganism from soil were reviewed in this paper. The procedure for extracting microorganism from soil was comprised of three steps, i.e., soil dispersion, separation and purification. Most bacteria in soil could be successively extracted from soil particles by present techniques such as filtration, centrifugation and elutriation. However, filamentous fungi seem more difficult to be extracted than bacteria, because it is tangled with soil particles. Rotating wire frame, aqueous extraction and membrane filter technique, and low-speed centrifugation were used for extracting filamentous fungi from soil, but the extraction efficiency was rather low and needed to be raised. Aqueous two-phase partitioning system was successfully adopted as a technique for bacteria purification, and it would possibly become a technique suitable for fungi purification. The potential area of research on soil microbial ecology as well as on soil and plant nutrition by using microbial extraction technique was also discussed.}, }
@article {pmid12836550, year = {2003}, author = {Huang, L and Chen, Y and Zhou, H and Qu, L}, title = {[Characterization of several synthetic and environmental microbial samples by quantitative hybridization].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {14}, number = {3}, pages = {405-408}, pmid = {12836550}, issn = {1001-9332}, mesh = {Ecology ; *Environmental Microbiology ; Nucleic Acid Hybridization/*methods ; Oligonucleotide Probes ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Limitations of traditional techniques based on selective enrichment and pure-culture isolation make it difficult to precisely characterize the natural microbial ecosystems. Molecular techniques are now being developed and used to address these limitations. Group-specific 16S rRNAs-targeted oligonucleotide probes of different phylogenetic levels are increasingly used to identify and quantify the microbial members in complex environmental samples. Two domain-specific probes were used in this study to elementarily characterize the defined mixtures of RNAs extracted from pure culture (synthetic samples) and a RNA sample obtained from landfill leachate (environmental sample). The results demonstrated that 16S rRNA quantitative hybridization provided an excellent estimation of domain level community composition of these samples, and thus, had a huge potential of usefulness in microbial ecology studies.}, }
@article {pmid12834725, year = {2003}, author = {Seka, MA and Verstraete, W}, title = {Test for assessing shear sensitivity of activated sludge flocs: a feasibility study.}, journal = {Water research}, volume = {37}, number = {14}, pages = {3327-3334}, doi = {10.1016/S0043-1354(02)00558-4}, pmid = {12834725}, issn = {0043-1354}, mesh = {Feasibility Studies ; Flocculation ; Forecasting ; Mechanics ; *Models, Theoretical ; Reproducibility of Results ; Sewage/*microbiology ; *Waste Disposal, Fluid ; }, abstract = {Sludge deflocculation can cause, like excessive growth of filamentous bacteria, activated sludge wastewater treatment failure. Yet, unlike the latter cause, there exists no widely accepted tool to assess the flocculation level of activated sludge and to predict sludge deflocculation. In this study, a test procedure is proposed to assess the sensitivity of activated sludge flocs to shear. The test consists in subjecting sludge sample to a shear treatment followed by a sludge volume measurement (SV(30)), with reference to a control. The ratio (%) obtained by dividing the SV(30) of the sheared sample by the SV(30) of the control is used to express the shear sensitivity. In a first series of experiments using two types of sludge, the test was shown to be able of ranging sludge samples in a correct order of shear sensitivity. Applying this so-called shear-SV test procedure to a series of sludge samples allowed to distinguish amorphous sludges (SV(30) ratio> or =100%) from normal sludges (SV(30) ratio<100%). The test was shown to be repeatable and simple. It requires only basic laboratory equipment and implies minimum cost. It can be used as framework for the assessment of activated sludge shear sensitivity in practice.}, }
@article {pmid12831908, year = {2003}, author = {Wagner, M and Horn, M and Daims, H}, title = {Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes.}, journal = {Current opinion in microbiology}, volume = {6}, number = {3}, pages = {302-309}, doi = {10.1016/s1369-5274(03)00054-7}, pmid = {12831908}, issn = {1369-5274}, mesh = {Bacteria/*genetics/*isolation &amp; purification ; In Situ Hybridization, Fluorescence/*trends ; Microbiology/*trends ; Prokaryotic Cells ; }, abstract = {Fluorescence in situ hybridisation with rRNA-targeted nucleic acid probes can be used to directly identify microorganisms within complex samples in a few hours and therefore has widespread application in environmental and medical microbiology. The past year has seen significant methodological improvements in fluorescence in situ hybridisation, as well as in the combination of this method with other techniques for inferring functional traits of microorganisms within their environment.}, }
@article {pmid12831907, year = {2003}, author = {Wellington, EM and Berry, A and Krsek, M}, title = {Resolving functional diversity in relation to microbial community structure in soil: exploiting genomics and stable isotope probing.}, journal = {Current opinion in microbiology}, volume = {6}, number = {3}, pages = {295-301}, doi = {10.1016/s1369-5274(03)00066-3}, pmid = {12831907}, issn = {1369-5274}, mesh = {Bacteria/genetics/*metabolism ; Ecology ; *Ecosystem ; Microbiology/*trends ; *Soil Microbiology ; }, abstract = {The microbial ecology of soil still presents a challenge to microbiologists attempting to establish the ways in which bacteria and fungi actively metabolise substrates, link into food webs and recycle plant and animal remains and provide essential nutrients for plants. Extraction and in situ analysis of rRNA has enabled identification of active taxa, and detection of mRNA has provided an insight into the expression of key functional genes in soil. Recent advances in genomic analysis and stable isotope probing are the first steps in resolving the linkage between structure and function in microbial communities.}, }
@article {pmid12830827, year = {2003}, author = {Franklin, RB and Mills, AL}, title = {Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field.}, journal = {FEMS microbiology ecology}, volume = {44}, number = {3}, pages = {335-346}, doi = {10.1016/S0168-6496(03)00074-6}, pmid = {12830827}, issn = {0168-6496}, mesh = {Bacteria/growth &amp; development ; DNA, Bacterial/analysis ; *Ecology ; Geography/statistics &amp; numerical data ; Geology/statistics &amp; numerical data ; *Models, Statistical ; Soil/*analysis ; *Soil Microbiology ; Virginia ; }, abstract = {To better understand the distribution of soil microbial communities at multiple spatial scales, a survey was conducted to examine the spatial organization of community structure in a wheat field in eastern Virginia (USA). Nearly 200 soil samples were collected at a variety of separation distances ranging from 2.5 cm to 11 m. Whole-community DNA was extracted from each sample, and community structure was compared using amplified fragment length polymorphism (AFLP) DNA fingerprinting. Relative similarity was calculated between each pair of samples and compared using geostatistical variogram analysis to study autocorrelation as a function of separation distance. Spatial autocorrelation was found at scales ranging from 30 cm to more than 6 m, depending on the sampling extent considered. In some locations, up to four different correlation length scales were detected. The presence of nested scales of variability suggests that the environmental factors regulating the development of the communities in this soil may operate at different scales. Kriging was used to generate maps of the spatial organization of communities across the plot, and the results demonstrated that bacterial distributions can be highly structured, even within a habitat that appears relatively homogeneous at the plot and field scale. Different subsets of the microbial community were distributed differently across the plot, and this is thought to be due to the variable response of individual populations to spatial heterogeneity associated with soil properties.}, }
@article {pmid12829276, year = {2003}, author = {Mergeay, M and Monchy, S and Vallaeys, T and Auquier, V and Benotmane, A and Bertin, P and Taghavi, S and Dunn, J and van der Lelie, D and Wattiez, R}, title = {Ralstonia metallidurans, a bacterium specifically adapted to toxic metals: towards a catalogue of metal-responsive genes.}, journal = {FEMS microbiology reviews}, volume = {27}, number = {2-3}, pages = {385-410}, doi = {10.1016/S0168-6445(03)00045-7}, pmid = {12829276}, issn = {0168-6445}, mesh = {Adenosine Triphosphatases/classification/metabolism ; Amino Acid Sequence ; Drug Resistance, Bacterial/*genetics ; Genes, Bacterial/genetics ; Genomics ; Metals/metabolism/*pharmacology/toxicity ; Models, Genetic ; Multigene Family ; Phylogeny ; Plasmids/genetics ; Proteobacteria/drug effects/*genetics/metabolism ; Sequence Alignment ; }, abstract = {Ralstonia metallidurans, formerly known as Alcaligenes eutrophus and thereafter as Ralstonia eutropha, is a beta-Proteobacterium colonizing industrial sediments, soils or wastes with a high content of heavy metals. The type strain CH34 carries two large plasmids (pMOL28 and pMOL30) bearing a variety of genes for metal resistance. A chronological overview describes the progress made in the knowledge of the plasmid-borne metal resistance mechanisms, the genetics of R. metallidurans CH34 and its taxonomy, and the applications of this strain in the fields of environmental remediation and microbial ecology. Recently, the sequence draft of the genome of R. metallidurans has become available. This allowed a comparison of these preliminary data with the published genome data of the plant pathogen Ralstonia solanacearum, which harbors a megaplasmid (of 2.1 Mb) carrying some metal resistance genes that are similar to those found in R. metallidurans CH34. In addition, a first inventory of metal resistance genes and operons across these two organisms could be made. This inventory, which partly relied on the use of proteomic approaches, revealed the presence of numerous loci not only on the large plasmids pMOL28 and pMOL30 but also on the chromosome. It suggests that metal-resistant Ralstonia, through evolution, are particularly well adapted to the harsh environments typically created by extreme anthropogenic situations or biotopes.}, }
@article {pmid12827889, year = {2003}, author = {Zhang, H and Zhang, Q and Zhou, Q and Zhang, C}, title = {[Introduction and progress of molecular microbial ecology].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {14}, number = {2}, pages = {286-292}, pmid = {12827889}, issn = {1001-9332}, mesh = {*Ecology ; *Environmental Microbiology ; In Situ Hybridization, Fluorescence ; *Molecular Biology ; Polymerase Chain Reaction ; }, abstract = {Molecular microbial ecology is an interdisciplinary field of molecular biological techniques and microbial ecology, which deals with microbial population, diversity, function, and relationships between microorganisms and biotic and abotic environments in microbial ecosystem. All the progress in molecular microbial ecology, especially in microbial diversity, phylogeny and communities of some microoganisms, indicate the renovation in traditional microbial ecology by the introduction of molecular techniques and strategies. This article reviewed the ideation, development, key domains, main methods and the future hot fields in molecular microbial ecology.}, }
@article {pmid12826062, year = {2003}, author = {Kurenbach, B and Bohn, C and Prabhu, J and Abudukerim, M and Szewzyk, U and Grohmann, E}, title = {Intergeneric transfer of the Enterococcus faecalis plasmid pIP501 to Escherichia coli and Streptomyces lividans and sequence analysis of its tra region.}, journal = {Plasmid}, volume = {50}, number = {1}, pages = {86-93}, doi = {10.1016/s0147-619x(03)00044-1}, pmid = {12826062}, issn = {0147-619X}, mesh = {Base Sequence/genetics ; Conjugation, Genetic/*genetics ; Enterococcus faecalis/genetics ; Escherichia coli/genetics ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Molecular Sequence Data ; Open Reading Frames ; Plasmids/*genetics ; Streptomyces/genetics ; }, abstract = {The nucleotide sequence of the transfer (tra) region of the multiresistance broad-host-range Inc18 plasmid pIP501 was completed. The 8629-bp DNA sequence encodes 10 open reading frames (orf), 9 of them are possibly involved in pIP501 conjugative transfer. The putative pIP501 tra gene products show highest similarity to the respective ORFs of the conjugative Enterococcus faecalis plasmids pRE25 and pAMbeta1, and the Streptococcus pyogenes plasmid pSM19035, respectively. ORF7 and ORF10 encode putative homologues of type IV secretion systems involved in transport of effector molecules from pathogens to host cells and in conjugative plasmid transfer in Gram-negative (G-) bacteria. pIP501 mobilized non-selftransmissible plasmids such as pMV158 between different E. faecalis strains and from E. faecalis to Bacillus subtilis. Evidence for the very broad-host-range of pIP501 was obtained by intergeneric conjugative transfer of pIP501 to a multicellular Gram-positive (G+) bacterium, Streptomyces lividans, and to G- Escherichia coli. We proved for the first time pIP501 replication, expression of its antibiotic resistance genes as well as functionality of the pIP501 tra genes in S. lividans and E. coli.}, }
@article {pmid12814560, year = {2003}, author = {Lenski, R}, title = {The ecology, genetics and evolution of bacteria in an experimental setting.}, journal = {Current biology : CB}, volume = {13}, number = {12}, pages = {R466-7}, doi = {10.1016/s0960-9822(03)00401-9}, pmid = {12814560}, issn = {0960-9822}, mesh = {Bacteria/*genetics ; *Biological Evolution ; Genetics, Microbial/*trends ; }, abstract = {Richard Lenski is the John Hannah Distinguished Professor of Microbial Ecology at Michigan State University. He studies the ecology, genetics and evolution of bacteria in an experimental setting that enables him to observe the dynamical processes and outcomes across many generations. One of his experiments with Escherichia coli has passed 30,000 generations and is still on-going. A few years ago, he also began studying artificial life in the form of 'digital organisms' - computer programs that replicate, mutate, compete, and therefore evolve and adapt.}, }
@article {pmid12794193, year = {2003}, author = {Grohmann, E and Muth, G and Espinosa, M}, title = {Conjugative plasmid transfer in gram-positive bacteria.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {67}, number = {2}, pages = {277-301, table of contents}, pmid = {12794193}, issn = {1092-2172}, mesh = {Amino Acid Sequence ; Base Sequence ; Conjugation, Genetic/*genetics ; DNA, Bacterial/genetics ; Gram-Negative Bacteria/genetics ; Gram-Positive Bacteria/*genetics ; Molecular Sequence Data ; Plasmids/*genetics ; R Factors/genetics ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; }, abstract = {Conjugative transfer of bacterial plasmids is the most efficient way of horizontal gene spread, and it is therefore considered one of the major reasons for the increase in the number of bacteria exhibiting multiple-antibiotic resistance. Thus, conjugation and spread of antibiotic resistance represents a severe problem in antibiotic treatment, especially of immunosuppressed patients and in intensive care units. While conjugation in gram-negative bacteria has been studied in great detail over the last decades, the transfer mechanisms of antibiotic resistance plasmids in gram-positive bacteria remained obscure. In the last few years, the entire nucleotide sequences of several large conjugative plasmids from gram-positive bacteria have been determined. Sequence analyses and data bank comparisons of their putative transfer (tra) regions have revealed significant similarities to tra regions of plasmids from gram-negative bacteria with regard to the respective DNA relaxases and their targets, the origins of transfer (oriT), and putative nucleoside triphosphatases NTP-ases with homologies to type IV secretion systems. In contrast, a single gene encoding a septal DNA translocator protein is involved in plasmid transfer between micelle-forming streptomycetes. Based on these clues, we propose the existence of two fundamentally different plasmid-mediated conjugative mechanisms in gram-positive microorganisms, namely, the mechanism taking place in unicellular gram-positive bacteria, which is functionally similar to that in gram-negative bacteria, and a second type that occurs in multicellular gram-positive bacteria, which seems to be characterized by double-stranded DNA transfer.}, }
@article {pmid12791135, year = {2003}, author = {Klausen, M and Heydorn, A and Ragas, P and Lambertsen, L and Aaes-Jørgensen, A and Molin, S and Tolker-Nielsen, T}, title = {Biofilm formation by Pseudomonas aeruginosa wild type, flagella and type IV pili mutants.}, journal = {Molecular microbiology}, volume = {48}, number = {6}, pages = {1511-1524}, doi = {10.1046/j.1365-2958.2003.03525.x}, pmid = {12791135}, issn = {0950-382X}, mesh = {Biofilms/*growth &amp; development ; Citrates/metabolism ; Culture Media ; Fimbriae, Bacterial/genetics/*metabolism ; Flagella/genetics/*metabolism ; Green Fluorescent Proteins ; Image Processing, Computer-Assisted ; Luminescent Proteins/genetics/metabolism ; Microscopy, Confocal ; *Mutation ; Pseudomonas aeruginosa/genetics/metabolism/*physiology ; Software ; }, abstract = {Biofilm formation by Gfp-tagged Pseudomonas aeruginosa PAO1 wild type, flagella and type IV pili mutants in flow chambers irrigated with citrate minimal medium was characterized by the use of confocal laser scanning microscopy and comstat image analysis. Flagella and type IV pili were not necessary for P. aeruginosa initial attachment or biofilm formation, but the cell appendages had roles in biofilm development, as wild type, flagella and type IV pili mutants formed biofilms with different structures. Dynamics and selection during biofilm formation were investigated by tagging the wild type and flagella/type IV mutants with Yfp and Cfp and performing time-lapse confocal laser scanning microscopy in mixed colour biofilms. The initial microcolony formation occurred by clonal growth, after which wild-type P. aeruginosa bacteria spread over the substratum by means of twitching motility. The wild-type biofilms were dynamic compositions with extensive motility, competition and selection occurring during development. Bacterial migration prevented the formation of larger microcolonial structures in the wild-type biofilms. The results are discussed in relation to the current model for P. aeruginosa biofilm development.}, }
@article {pmid12788771, year = {2003}, author = {Pynaert, K and Smets, BF and Wyffels, S and Beheydt, D and Siciliano, SD and Verstraete, W}, title = {Characterization of an autotrophic nitrogen-removing biofilm from a highly loaded lab-scale rotating biological contactor.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {6}, pages = {3626-3635}, pmid = {12788771}, issn = {0099-2240}, mesh = {Anaerobiosis ; Bacteria/*classification/genetics/metabolism ; Biofilms/*classification/growth &amp; development ; *Bioreactors ; DNA, Ribosomal/analysis ; In Situ Hybridization, Fluorescence ; Microscopy, Confocal ; Molecular Sequence Data ; Nitrogen/*metabolism ; Nitrosomonas/classification/genetics/metabolism ; Oxidation-Reduction ; Polymerase Chain Reaction ; Quaternary Ammonium Compounds/metabolism ; RNA, Ribosomal, 16S ; Waste Disposal, Fluid/*methods ; }, abstract = {In this study, a lab-scale rotating biological contactor (RBC) treating a synthetic NH(4)(+) wastewater devoid of organic carbon and showing high N losses was examined for several important physiological and microbial characteristics. The RBC biofilm removed 89% +/- 5% of the influent N at the highest surface load of approximately 8.3 g of N m(-2) day(-1), with N(2) as the main end product. In batch tests, the RBC biomass showed good aerobic and anoxic ammonium oxidation (147.8 +/- 7.6 and 76.5 +/- 6.4 mg of NH(4)(+)-N g of volatile suspended solids [VSS](-1) day(-1), respectively) and almost no nitrite oxidation (< 1 mg of N g of VSS(-1) day(-1)). The diversity of aerobic ammonia-oxidizing bacteria (AAOB) and planctomycetes in the biofilm was characterized by cloning and sequencing of PCR-amplified partial 16S rRNA genes. Phylogenetic analysis of the clones revealed that the AAOB community was fairly homogeneous and was dominated by Nitrosomonas-like species. Close relatives of the known anaerobic ammonia-oxidizing bacterium (AnAOB) Kuenenia stuttgartiensis dominated the planctomycete community and were most probably responsible for anoxic ammonium oxidation in the RBC. Use of a less specific planctomycete primer set, not amplifying the AnAOB, showed a high diversity among other planctomycetes, with representatives of all known groups present in the biofilm. The spatial organization of the biofilm was characterized using fluorescence in situ hybridization (FISH) with confocal scanning laser microscopy (CSLM). The latter showed that AAOB occurred side by side with putative AnAOB (cells hybridizing with probe PLA46 and AMX820/KST1275) throughout the biofilm, while other planctomycetes hybridizing with probe PLA886 (not detecting the known AnAOB) were present as very conspicuous spherical structures. This study reveals that long-term operation of a lab-scale RBC on a synthetic NH(4)(+) wastewater devoid of organic carbon yields a stable biofilm in which two bacterial groups, thought to be jointly responsible for the high autotrophic N removal, occur side by side throughout the biofilm.}, }
@article {pmid12788766, year = {2003}, author = {Schrenk, MO and Kelley, DS and Delaney, JR and Baross, JA}, title = {Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {6}, pages = {3580-3592}, pmid = {12788766}, issn = {0099-2240}, mesh = {Archaea/*classification/genetics/growth &amp; development ; Bacteria/*classification/genetics/growth &amp; development ; Colony Count, Microbial ; DNA, Ribosomal/analysis ; *Ecosystem ; *Hot Temperature ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal/genetics ; Seawater/chemistry/*microbiology ; Sequence Analysis, DNA ; *Sulfides ; }, abstract = {A large, intact sulfide chimney, designated Finn, was recovered from the Mothra Vent Field on the Juan de Fuca Ridge in 1998. Finn was venting 302 degrees C fluids on the seafloor and contained complex mineralogical zones surrounding a large open central conduit. Examination of microorganisms within these zones, followed by community analysis with oligonucleotide probes, showed that there were variations in the abundance and diversity of eubacteria and archaea from the exterior to the interior of the chimney. The microbial abundance based upon epifluorescence microscopy and quantitative fatty acid analyses varied from >10(8) cells/g of sulfide 2 to 10 cm within the chimney wall to <10(5) cells/g in interior zones. Direct microscopic observation indicated that microorganisms were attached to mineral surfaces throughout the structure. Whole-cell hybridization results revealed that there was a transition from a mixed community of eubacteria and archaea near the cool exterior of the chimney to primarily archaea near the warm interior. Archaeal diversity was examined in three zones of Finn by cloning and sequencing of the 16S rRNA gene. The majority of sequences from the exterior of the chimney were related to marine group I of the Crenarchaeota and uncultured Euryarchaeota from benthic marine environments. In contrast, clone libraries from interior regions of the chimney contained sequences closely related to methanogens, Thermococcales, and Archaeoglobales, in addition to uncultured crenarchaeal phylotypes obtained from deep subsurface sites. These observations of microbial communities within an active hydrothermal chimney provide insight into the microbial ecology within such structures and may facilitate follow-up exploration into expanding the known upper temperature limits of life.}, }
@article {pmid12788753, year = {2003}, author = {Braker, G and Tiedje, JM}, title = {Nitric oxide reductase (norB) genes from pure cultures and environmental samples.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {6}, pages = {3476-3483}, pmid = {12788753}, issn = {0099-2240}, mesh = {Culture Media ; Fresh Water/*microbiology ; Genetic Variation ; Geologic Sediments/*microbiology ; Gram-Negative Bacteria/classification/*enzymology/genetics/growth &amp; development ; Molecular Sequence Data ; Nitrites/metabolism ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {A PCR-based approach was developed to recover nitric oxide (NO) reductase (norB) genes as a functional marker gene for denitrifying bacteria. norB database sequences grouped in two very distinct branches. One encodes the quinol-oxidizing single-subunit class (qNorB), while the other class is a cytochrome bc-type complex (cNorB). The latter oxidizes cytochrome c, and the gene is localized adjacent to norC. While both norB types occur in denitrifying strains, the qnorB type was also found in a variety of nondenitrifying strains, suggesting a function in detoxifying NO. Branch-specific degenerate primer sets detected the two norB types in our denitrifier cultures. Specificity was confirmed by sequence analysis of the norB amplicons and failure to amplify norB from nondenitrifying strains. These primer sets also specifically amplified norB from freshwater and marine sediments. Pairwise comparison of amplified norB sequences indicated minimum levels of amino acid identity of 43.9% for qnorB and 38% for cnorB. Phylogenetic analysis confirmed the existence of two classes of norB genes, which clustered according to the respective primer set. Within the qnorB cluster, the majority of genes from isolates and a few environmental clones formed a separate subcluster. Most environmental qnorB clones originating from both habitats clustered into two distinct subclusters of novel sequences from presumably as yet uncultivated organisms. cnorB clones were located on separate branches within subclusters of genes from known organisms, suggesting an origin from similar organisms.}, }
@article {pmid12788716, year = {2003}, author = {Lu, Z and Breidt, F and Plengvidhya, V and Fleming, HP}, title = {Bacteriophage ecology in commercial sauerkraut fermentations.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {6}, pages = {3192-3202}, pmid = {12788716}, issn = {0099-2240}, mesh = {Bacteriophages/classification/isolation &amp; purification/*physiology ; Brassica/*microbiology ; Colony Count, Microbial ; *Ecosystem ; Fermentation ; Food-Processing Industry/methods ; Lactobacillus/classification/isolation &amp; purification/*virology ; Leuconostoc/classification/isolation &amp; purification/*virology ; Microscopy, Electron ; Myoviridae/classification/genetics/isolation &amp; purification/physiology ; Siphoviridae/classification/genetics/isolation &amp; purification/physiology ; }, abstract = {Knowledge of bacteriophage ecology in vegetable fermentations is essential for developing phage control strategies for consistent and high quality of fermented vegetable products. The ecology of phages infecting lactic acid bacteria (LAB) in commercial sauerkraut fermentations was investigated. Brine samples were taken from four commercial sauerkraut fermentation tanks over a 60- or 100-day period in 2000 and 2001. A total of 171 phage isolates, including at least 26 distinct phages, were obtained. In addition, 28 distinct host strains were isolated and identified as LAB by restriction analysis of the intergenic transcribed spacer region and 16S rRNA sequence analysis. These host strains included Leuconostoc, Weissella, and Lactobacillus species. It was found that there were two phage-host systems in the fermentations corresponding to the population shift from heterofermentative to homofermentative LAB between 3 and 7 days after the start of the fermentations. The data suggested that phages may play an important role in the microbial ecology and succession of LAB species in vegetable fermentations. Eight phage isolates, which were independently obtained two or more times, were further characterized. They belonged to the family Myoviridae or Siphoviridae and showed distinct host ranges and DNA fingerprints. Two of the phage isolates were found to be capable of infecting two Lactobacillus species. The results from this study demonstrated for the first time the complex phage ecology present in commercial sauerkraut fermentations, providing new insights into the bioprocess of vegetable fermentations.}, }
@article {pmid12782381, year = {2003}, author = {Whiteley, AS and Griffiths, RI and Bailey, MJ}, title = {Analysis of the microbial functional diversity within water-stressed soil communities by flow cytometric analysis and CTC+ cell sorting.}, journal = {Journal of microbiological methods}, volume = {54}, number = {2}, pages = {257-267}, doi = {10.1016/s0167-7012(03)00066-6}, pmid = {12782381}, issn = {0167-7012}, mesh = {Bacteria/genetics/isolation &amp; purification/metabolism ; Cell Count/methods ; *Flow Cytometry ; Osmotic Pressure ; *Soil Microbiology ; Tetrazolium Salts/*analysis ; Titrimetry/methods ; Water Microbiology ; }, abstract = {Total and active cell counts within soil samples were determined by culture-independent methods using flow cytometry and preparative Nycodenz gradient centrifugation. Whole cells were purified from soil cores and total extractable cell counts assessed by SYBR Green II fluorescence, while active cell counts were determined by 5-cyano-2,3-ditolyl tetrazolium chloride reduction (CTC+ cells). Parallel microcosms, maintained at either field water capacity or subjected to drying, indicated that the total extractable cell count remained between 10(8) and 10(9) g(-1) (dry weight). In contrast, the CTC+ active count fell threefold in dried microcosms (6% of total cell count) when compared to wetted microcosms (18% of total cell count). Specifically, these data highlighted an overall deactivation of microbial biomass during water stress, with 16S rDNA analyses of flow-sorted CTC+ cells demonstrating shifts within the active diversity. Flow cytometry coupled with cell purification techniques represents a significant tool for operationally defining an active and redundant microbial component within soil communities and is demonstrated during water stress.}, }
@article {pmid12781671, year = {2003}, author = {Balogh, J and Tunlid, A and Rosén, S}, title = {Deletion of a lectin gene does not affect the phenotype of the nematode-trapping fungus Arthrobotrys oligospora.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {39}, number = {2}, pages = {128-135}, doi = {10.1016/s1087-1845(03)00023-9}, pmid = {12781671}, issn = {1087-1845}, mesh = {Amino Acid Sequence ; Animals ; Fungal Proteins/biosynthesis/*genetics ; Gene Deletion ; Lectins/biosynthesis/*genetics ; Mitosporic Fungi/*genetics/pathogenicity ; Molecular Sequence Data ; Nematoda/growth &amp; development/*microbiology ; Phenotype ; Sequence Alignment ; Spores, Fungal/growth &amp; development ; Time Factors ; }, abstract = {A number of filamentous fungi are known to produce high levels of saline-soluble and low-molecular-mass lectins. The function of these proteins are not clear but it has been proposed that they are involved in storage of nutrients, development, recognition of other organisms, and defense reactions. A gene encoding such a lectin (AOL) was deleted in the nematode-trapping fungus Arthrobotrys oligospora by homologous recombination. The deletion mutants did not express any hemagglutinating activity or protein cross-reacting with AOL antibodies. There were no significant differences between the DeltaAOL and wild-type strains in spore (conidia) germination, saprophytic growth, and pathogenicity. Furthermore, there was no significant difference in the growth and reproduction of collembolan feeding on the various strains of A. oligospora. Thus either the previous proposed functions of AOL are not correct, or the fungus can compensate for the absence of the lectin by expressing other proteins with similar function(s) as AOL.}, }
@article {pmid12764574, year = {2003}, author = {Séka, MA and Hammes, F and Verstraete, W}, title = {Predicting the effects of chlorine on the micro-organisms of filamentous bulking activated sludges.}, journal = {Applied microbiology and biotechnology}, volume = {61}, number = {5-6}, pages = {562-568}, doi = {10.1007/s00253-003-1237-3}, pmid = {12764574}, issn = {0175-7598}, mesh = {Bacteria/drug effects/metabolism ; Chlorine/*pharmacology ; Disinfectants/*pharmacology ; Flocculation Tests ; Sewage/*microbiology ; Waste Disposal, Fluid/methods ; }, abstract = {Rapid and definite assessment of the effect that a specific biocide has on a specific case of filamentous bulking sludge is a much-needed tool in activated sludge wastewater treatment. The Live/Dead stain (LIVE/DEAD BacLight) distinguishing "living" and "non-living" cells, a nitrifying activity (NA) test and the oxygen uptake rate (OUR) measurement were examined for their appropriateness to predict the effects of chlorine on filamentous bulking sludges. The study showed the live/dead stain to be relevant for revealing the specific effect of chlorine on the filamentous bacteria of a bulking sludge. However, using live/dead stain alone for the determination of the appropriate chlorine dose against bulking may lead to an underestimation of the damage caused by chlorine to the useful microorganisms in the flocs. Indeed, using the live/dead stain, it was not easy to distinguish dead cells caused by chlorination from those originally present in the flocs The NA test was the most sensitive in detecting damage caused by chlorine to the floc-forming microorganisms. Therefore, for a safer determination of the chlorine dose effective against bulking and protective of the microbial activity of the sludge, the results of this study suggest coupling of the live/dead stain with the NA test and/or the OUR test.}, }
@article {pmid12755711, year = {2003}, author = {Buckley, DH and Schmidt, TM}, title = {Diversity and dynamics of microbial communities in soils from agro-ecosystems.}, journal = {Environmental microbiology}, volume = {5}, number = {6}, pages = {441-452}, doi = {10.1046/j.1462-2920.2003.00404.x}, pmid = {12755711}, issn = {1462-2912}, mesh = {*Agriculture ; Bacteria/*genetics/metabolism ; *Ecosystem ; Genes, rRNA ; RNA, Bacterial/analysis ; RNA, Ribosomal/analysis ; *Soil Microbiology ; }, abstract = {Soil microbial communities are integrally involved in biogeochemical cycles and their activities are crucial to the productivity of terrestrial ecosystems. Despite the importance of soil microorganisms, little is known about the distribution of microorganisms in the soil or the manner in which microbial community structure responds to changes in land management. We investigated the structure of microbial communities in the soil over two years in a series of replicated plots, that included, cultivated fields, fields abandoned from cultivation and fields with no history of cultivation. Microbial community structure was examined by monitoring the relative abundance of ribosomal RNA (rRNA) from seven of the most common bacterial groups in soil (the Alpha and Beta Proteobacteria, Actinobacteria, Cytophagales, Planctomycetes, Verrucomicrobia and the Acidobacteria) and the Eukarya. These data reveal that soil microbial communities are dynamic, capable of significant change at temporal scales relative to seasonal events. However, despite temporal change in microbial community structure, the rRNA relative abundance of particular microbial groups is affected by the local environment such that recognizable patterns of community structure exist in relation to field management.}, }
@article {pmid12754661, year = {2003}, author = {Sigmund, JM and Clark, DC and Rainey, FA and Anderson, AS}, title = {Detection of eubacterial 3-hydroxy-3-methylglutaryl coenzyme a reductases from natural populations of actinomycetes.}, journal = {Microbial ecology}, volume = {46}, number = {1}, pages = {106-112}, pmid = {12754661}, issn = {0095-3628}, mesh = {Actinobacteria/*chemistry/*genetics ; Amino Acid Sequence ; DNA Primers ; *Environment ; Hydroxymethylglutaryl CoA Reductases/*genetics ; Molecular Sequence Data ; *Phylogeny ; }, abstract = {Three natural populations of actinomycetes were investigated by PCR for the presence of type I 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG CoA), a gene associated with isoprenoid biosynthesis. The populations were obtained from an agricultural site (69 isolates), a coastal salt marsh (220 isolates), and a desert soil (96 isolates). A set (34) of standard actinomycete reference strains were also investigated. The target gene was only detected in 5 of the 419 actinomycetes screened, which represented 4 from the coastal salt marsh and one reference strain. The isolates that contained the gene were taxonomically diverse (4 Streptomyces spp. and 1 Nocardia sp.). These results suggest that type I HMG CoA containing pathways are rare in actinomycetes and their distribution within actinomycetes populations is not random.}, }
@article {pmid12754660, year = {2003}, author = {Hirst, CN and Cyr, H and Jordan, IA}, title = {Distribution of exopolymeric substances in the littoral sediments of an oligotrophic lake.}, journal = {Microbial ecology}, volume = {46}, number = {1}, pages = {22-32}, pmid = {12754660}, issn = {0095-3628}, mesh = {Bacteria/*chemistry ; Carbohydrates/*chemistry ; Eukaryota/*chemistry ; Fresh Water ; Geologic Sediments/*analysis ; Ontario ; Oxidoreductases/chemistry ; Proteins/*chemistry ; Seasons ; *Water Microbiology ; }, abstract = {Bacteria and algae release exopolymeric substances (EPS) that perform a wide range of important functions in aquatic and terrestrial systems. In this study we measured EPS in sediments at nine littoral sites around a shallow oligotrophic basin, and tested whether the concentration and composition of EPS was related to sediment characteristics. The concentrations of both loosely bound (colloidal) and tightly bound (capsular) EPS carbohydrates ranged up to ~800 micro g glucose equiv. cm(-2) and were well within the range of concentrations reported from marine intertidal flats, where EPS play an important role in stabilizing sediments, affecting nutrient exchanges between sediments and the water column, feeding benthic invertebrates, and sequestering and increasing the transfer of contaminants to food webs. Proteins were an important component of the EPS in these littoral sediments, with protein:carbohydrate ratios of approximately 0.4. In summer, the concentrations of most EPS fractions were positively related (P < 0.05) to the porewater and organic matter content of the sediments. Capsular EPS concentrations were lower in the fall, with a simultaneous increase in colloidal proteins but not in colloidal carbohydrates. This suggests that the carbohydrates in this colloidal EPS may be more labile than the proteins. Our results suggest that exopolymeric substances could be an important, but neglected, component of littoral sediments in lakes.}, }
@article {pmid12754659, year = {2003}, author = {Elias, DA and Krumholz, LR and Wong, D and Long, PE and Suflita, JM}, title = {Characterization of microbial activities and U reduction in a shallow aquifer contaminated by uranium mill tailings.}, journal = {Microbial ecology}, volume = {46}, number = {1}, pages = {83-91}, pmid = {12754659}, issn = {0095-3628}, mesh = {Bacteria/*metabolism ; Biodegradation, Environmental ; Chromatography ; Fresh Water/*chemistry/*microbiology ; Geologic Sediments/*chemistry/*microbiology ; New Mexico ; Nitrates/chemistry ; Uranium/*chemistry/metabolism ; Water Pollutants, Radioactive/metabolism ; }, abstract = {A characterization of the Shiprock, NM, uranium mill tailing site focused on the geochemical and microbiological factors governing in-situ uranium-redox reactions. Groundwater and aqueous extracts of sediment samples contained a wide concentration range of sulfate, nitrate, and U(VI) with median values of 21.2 mM, 16.1 micro M, and 2.7 micro M, respectively. Iron(III) was not detected in groundwater, but a median value of 0.3 mM in sediment extracts was measured. Bacterial diversity down gradient from the disposal pile reflected the predominant geochemistry with relatively high numbers of sulfate- and nitrate-reducing microorganisms, and smaller numbers of acetogenic, methanogenic, nitrate-dependent Fe(II)-oxidizing, Fe(III)-reducing, and sulfide-oxidizing bacteria. In aquifer slurry incubations, nitrate reduction was always preferred and had a negative impact on sulfate-, Fe(III)-, and U-reduction rates. We also found that sulfate-reduction rates decreased sharply in the presence of clay, while Fe(III)-reduction increased with no clear impact on U reduction. In the absence of clay, iron and sulfate reduction correlated with concentrations of Fe(III) and sulfate, respectively. Rates of U(VI) loss did not correlate with the concentration of any electron acceptor. With the exception of Fe(III), electron donor amendment was largely unsuccessful in stimulating electron acceptor loss over a 2-week incubation period, suggesting that endogenous forms of organic matter were sufficient to support microbial activity. Our findings suggest that efforts to accelerate biological U reduction should initially focus on stimulating nitrate removal.}, }
@article {pmid12747563, year = {2003}, author = {Hofman-Bang, J and Zheng, D and Westermann, P and Ahring, BK and Raskin, L}, title = {Molecular ecology of anaerobic reactor systems.}, journal = {Advances in biochemical engineering/biotechnology}, volume = {81}, number = {}, pages = {151-203}, doi = {10.1007/3-540-45839-5_5}, pmid = {12747563}, issn = {0724-6145}, mesh = {Anaerobiosis/genetics ; Archaea/*classification/*genetics ; Bacteria, Anaerobic/*classification/*genetics ; Bioreactors/*microbiology ; DNA/analysis/genetics ; Gene Expression Profiling/methods ; Gene Expression Regulation, Archaeal/genetics ; Gene Expression Regulation, Bacterial ; RNA/analysis/genetics ; Sewage/analysis/microbiology ; Species Specificity ; }, abstract = {Anaerobic reactor systems are essential for the treatment of solid and liquid wastes and constitute a core facility in many waste treatment plants. Although much is known about the basic metabolism in different types of anaerobic reactors, little is known about the microbes responsible for these processes. Only a few percent of Bacteria and Archaea have so far been isolated, and almost nothing is known about the dynamics and interactions between these and other microorganisms. This lack of knowledge is most clearly exemplified by the sometimes unpredictable and unexplainable failures and malfunctions of anaerobic digesters occasionally experienced, leading to sub-optimal methane production and wastewater treatment. Using a variety of molecular techniques, we are able to determine which microorganisms are active, where they are active, and when they are active, but we still need to determine why and what they are doing. As genetic manipulations of anaerobes have been shown in only a few species permitting in-situ gene expression studies, the only way to elucidate the function of different microbes is to correlate the metabolic capabilities of isolated microbes in pure culture to the abundance of each microbe in anaerobic reactor systems by rRNA probing. This chapter focuses on various molecular techniques employed and problems encountered when elucidating the microbial ecology of anaerobic reactor systems. Methods such as quantitative dot blot/fluorescence in-situ probing using various specific nucleic acid probes are discussed and exemplified by studies of anaerobic granular sludge, biofilm and digester systems.}, }
@article {pmid12739081, year = {2003}, author = {Chèneby, D and Hallet, S and Mondon, M and Martin-Laurent, F and Germon, JC and Philippot, L}, title = {Genetic characterization of the nitrate reducing community based on narG nucleotide sequence analysis.}, journal = {Microbial ecology}, volume = {46}, number = {1}, pages = {113-121}, pmid = {12739081}, issn = {0095-3628}, mesh = {Bacteria, Anaerobic/*genetics ; *Ecosystem ; France ; Nitrate Reductase ; Nitrate Reductases/*genetics ; Nitrates/*metabolism ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; *Soil Microbiology ; Zea mays/microbiology ; }, abstract = {The ability of facultative anerobes to respire nitrate has been ascribed mainly to the activity of a membrane-bound nitrate reductase encoded by the narGHJI operon. Respiratory nitrate reduction is the first step of the denitrification pathway, which is considered as an important soil process since it contributes to the global cycling of nitrogen. In this study, we employed direct PCR, cloning, and sequencing of narG gene fragments to determine the diversity of nitrate-reducing bacteria occurring in soil and in the maize rhizosphere. Libraries containing 727 clones in total were screened by restriction fragment analysis. Phylogenetic analysis of 128 narG sequences separated the clone families into two main groups that represent the Gram-positive and Gram-negative nitrate-reducing bacteria. Novel narG lineages that branch distinctly from all currently known membrane bound nitrate-reductase encoding genes were detected within the Gram-negative branch. All together, our results revealed a more complex nitrate-reducing community than did previous culture-based studies. A significant and consistent shift in the relative abundance of the nitrate-reducing groups within this functional community was detected in the maize rhizosphere. Thus a substantially higher abundance of the dominant clone family and a lower diversity index were observed in the rhizosphere compared to the unplanted soil, suggesting that a bacterial group has been specifically selected within the nitrate-reducing community. Furthermore, restriction fragment length polymorphism analysis of cloned narG gene fragments proved to be a powerful tool in evaluating the structure and the diversity of the nitrate-reducing community and community shifts therein.}, }
@article {pmid12739080, year = {2003}, author = {Eiler, A and Farnleitner, AH and Zechmeister, TC and Herzig, A and Hurban, C and Wesner, W and Krachler, R and Velimirov, B and Kirschner, AK}, title = {Factors controlling extremely productive heterotrophic bacterial communities in shallow soda pools.}, journal = {Microbial ecology}, volume = {46}, number = {1}, pages = {43-54}, pmid = {12739080}, issn = {0095-3628}, mesh = {Austria ; Bacteria/*growth &amp; development/*metabolism ; Colony Count, Microbial ; *Ecosystem ; *Environment ; Fresh Water/chemistry ; Plankton/metabolism ; Principal Component Analysis ; Seasons ; *Water Microbiology ; }, abstract = {Dilute soda lakes are among the world's most productive environments and are usually dominated by dense blooms of cyanobacteria. Up to now, there has been little information available on heterotrophic bacterial abundance, production, and their controlling factors in these ecosystems. In the present study the main environmental factors responsible for the control of the heterotrophic bacterial community in five shallow soda pools in Eastern Austria were investigated during an annual cycle. Extremely high cyanobacterial numbers and heterotrophic bacterial numbers up to 307 x 10(9) L(-1) and 268 x 10(9) L(-1) were found, respectively. Bacterial secondary production rates up to 738 micro g C L(-1) h(-1) and specific growth rates up to 1.65 h(-1) were recorded in summer and represent the highest reported values for natural aquatic ecosystems. The combination of dense phytoplankton blooms, high temperature, high turbidity, and nutrient concentration due to evaporation is supposed to enable the development of such extremely productive microbial populations. By principal component analysis containing the data set of all five investigated pools, two factors were extracted which explained 62.5% of the total variation of the systems. The first factor could be interpreted as a turbidity factor; the second was assigned to as concentration factor. From this it was deduced that bacterial and cyanobacterial abundance were mainly controlled by wind-induced sediment resuspension and turbidity stabilized by the high pH and salinity and less by evaporative concentration of salinity and dissolved organic carbon. Bacterial production was clustered with temperature in factor 3, showing that bacterial growth was mainly controlled by temperature. The concept of describing the turbid water columns of the shallow soda pools as "fluid sediment" is discussed.}, }
@article {pmid12739079, year = {2003}, author = {Wieltschnig, C and Fischer, UR and Kirschner, AK and Velimirov, B}, title = {Benthic bacterial production and protozoan predation in a silty freshwater environment.}, journal = {Microbial ecology}, volume = {46}, number = {1}, pages = {62-72}, pmid = {12739079}, issn = {0095-3628}, mesh = {Animals ; Austria ; Bacteria/*growth &amp; development/metabolism ; Biomass ; Carbon Radioisotopes ; Eukaryota/*physiology ; *Food Chain ; Fresh Water ; Geologic Sediments/*microbiology ; Leucine/metabolism ; Population Dynamics ; Seasons ; Thymidine/metabolism ; Tritium ; }, abstract = {The interrelation of heterotrophic bacteria with bacterivorous protists has been widely studied in pelagic environments, but data on benthic habitats, especially in freshwater systems, are still scarce. We present a seasonal study focusing on bacterivory by heterotrophic nanoflagellates (HNF) and ciliates in the silty sediment of a temperate macrophyte-dominated oxbow lake. From January 2001 to February 2002 we monitored the standing stock of bacteria and protozoa, bacterial secondary production (BSP, (3)H-thymidine, and (14)C-leucine incorporation), and grazing rates of HNF and ciliates on bacteria (FLB uptake) in the oxic sediment of the investigated system. BSP ranged from 470 to 4050 micro g C L(-1) wet sediment h(-1). The bacterial compartment turned out to be highly dynamic, indicated by population doubling times (0.6-10.0 d), which were comparable to those in the water column of the investigated system. Yet, the control mechanisms acting upon the bacterial population led to a relative constancy of bacterial standing stock during a year. Ingestion rates of protozoan grazers were 0-20.0 bacteria HNF(-1) h(-1) and 0-97.6 bacteria ciliate(-1) h(-1). HNF and ciliates together cropped 0-14 (mean 4)% of BSP, indicating that they did not significantly contribute to benthic bacterial mortality during any period of the year. The low impact of protozoan grazing was due to the low numbers of HNF and ciliates in relation to bacteria (1.8-3.5 x 10(4) bacteria HNF(-1), 0.9-3.1 x 10(6) bacteria ciliate(-1)). Thus, grazing by HNF and ciliates could be ruled out as a parameter regulating bacterial standing stock or production in the sediment of the investigated system, but the factors responsible for the limitation of benthic protistan densities and the fate of benthic BSP remained unclear.}, }
@article {pmid12739078, year = {2003}, author = {Pearce, DA}, title = {Bacterioplankton community structure in a maritime antarctic oligotrophic lake during a period of holomixis, as determined by denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH).}, journal = {Microbial ecology}, volume = {46}, number = {1}, pages = {92-105}, pmid = {12739078}, issn = {0095-3628}, mesh = {Antarctic Regions ; *Bacterial Physiological Phenomena ; Colony Count, Microbial ; DNA Primers ; *Ecosystem ; Electrophoresis, Polyacrylamide Gel ; Fresh Water/*microbiology ; In Situ Hybridization, Fluorescence ; Plankton/*physiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The bacterioplankton community structure in Moss Lake, a maritime Antarctic oligotrophic lake, was determined with vertical depth in the water column, during the ice-free period on Signy Island in the South Orkney Islands. Bacterioplankton community structure was determined using a combination of direct counting of 4',6-diamidino-2-phenylindole (DAPI) stained cells, PCR amplification of 16S rRNA gene fragments, denaturing gradient gel electrophoresis (DGGE) and in situ hybridization with group-specific, fluorescently labeled oligonucleotide probes. Using PCR amplification of 16S rRNA gene fragments and DGGE, the bacterioplankton community composition was shown to be constant with vertical depth in the water column. Specific bacterioplankton species identified through cloning and sequencing the DGGE products obtained were Flavobacterium xinjiangensis (a Flavobacterium), Leptothrix discophora (a beta-Proteobacterium), and a number of uncultured groups: two beta-Proteobacteria, an unclassified Proteobacterium, three sequences from Actinobacteria, and a Cyanobacterium. Fluorescence in situ hybridization (FISH), however, demonstrated that there were minor but significant fluctuations in different groups of bacteria with vertical depth in the water column. It showed that the beta-Proteobacteria accounted for between 26.4 and 71.5%, the alpha-Proteobacteria 2.3-10.6%, the gamma-Proteobacteria 0-29.6%, and the Cytophaga-Flavobacterium group 1.8-23.5% of cells hybridizing to a universal probe. This study reports the first description of the community structure of an oligotrophic Antarctic freshwater lake as determined by PCR-dependent and PCR-independent molecular techniques. It also suggests that the bacterioplankton community of Moss Lake contains classes of bacteria known to be important in freshwater systems elsewhere in the world.}, }
@article {pmid12739077, year = {2003}, author = {Johnson, JE and Hill, RT}, title = {Sediment microbes of deep-sea bioherms on the northwest shelf of Australia.}, journal = {Microbial ecology}, volume = {46}, number = {1}, pages = {55-61}, pmid = {12739077}, issn = {0095-3628}, mesh = {Australia ; Bacteria/*genetics/*metabolism ; Biodegradation, Environmental ; Cluster Analysis ; DNA Primers ; Fatty Acids/isolation &amp; purification ; Fermentation ; Gas Chromatography-Mass Spectrometry ; Geologic Sediments/*microbiology ; Hydrocarbons/*metabolism ; Oceans and Seas ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater ; Sequence Analysis, DNA ; }, abstract = {The northwest shelf of Australia is a region with known petroleum reserves. Recent geological investigations have revealed carbonate knolls postulated to be of biological origin. Sediment microbial populations at three sites on the northwest shelf, Pee Shoal, Mermaid Reef, and Scott Reef, were investigated for the presence of hydrocarbon-degrading bacteria. From two sampling trips, 246 bacterial strains were purified, and 182 of these strains displayed preferential growth on hydrocarbon-selective media. Strains were tested for nutrient specificity using single hydrocarbon fermentations. Metabolic profiles were constructed using biochemical testing, fatty acid analysis, and metabolic rate experiments. 16S rRNA gene sequence analysis of four strains identified these strains as members of the genera Sphingomonas, Bacillus, and Microbacterium, and one strain as a member of the alpha-Proteobacteria. The potential of these strains as bioindicators of hydrocarbon pollutants or for bioremediation in marine environments is discussed.}, }
@article {pmid12739076, year = {2003}, author = {Tu, C and Koenning, SR and Hu, S}, title = {Root-parasitic nematodes enhance soil microbial activities and nitrogen mineralization.}, journal = {Microbial ecology}, volume = {46}, number = {1}, pages = {134-144}, pmid = {12739076}, issn = {0095-3628}, mesh = {Animals ; Biomass ; Carbon Dioxide/metabolism ; Gossypium/physiology ; Nematoda/*metabolism ; Nitrogen/*metabolism ; North Carolina ; Plant Roots/parasitology ; Soil/*analysis ; *Soil Microbiology ; }, abstract = {Obligate root-parasitic nematodes can affect soil microbes positively by enhancing C and nutrient leakage from roots but negatively by restricting total root growth. However, it is unclear how the resulting changes in C availability affect soil microbial activities and N cycling. In a microplot experiment, effects of root-parasitic reniform nematodes (Rotylenchulus reniformis) on soil microbial biomass and activities were examined in six different soils planted with cotton. Rotylenchulus reniformis was introduced at 900 nematodes kg(-1) soil in May 2000 prior to seeding cotton. In 2001, soil samples were collected in May before cotton was seeded and in November at the final harvest. Extractable C and N were consistently higher in the R. reniformis treatments than in the non-nematode controls across the six different soils. Nematode inoculation significantly reduced microbial biomass C, but increased microbial biomass N, leading to marked decreases in microbial biomass C:N ratios. Soil microbial respiration and net N mineralization rates were also consistently higher in the nematode treatments than in the controls. However, soil types did not have a significant impact on the effects of nematodes on these microbial parameters. These findings indicate that nematode infection of plant roots may enhance microbial activities and the turnover of soil microbial biomass, facilitating soil N cycling. The present study provides the first evidence about the direct role of root-feeding nematodes in enhancing soil N mineralization.}, }
@article {pmid12739075, year = {2003}, author = {Bastviken, D and Olsson, M and Tranvik, L}, title = {Simultaneous measurements of organic carbon mineralization and bacterial production in oxic and anoxic lake sediments.}, journal = {Microbial ecology}, volume = {46}, number = {1}, pages = {73-82}, pmid = {12739075}, issn = {0095-3628}, mesh = {*Bacterial Physiological Phenomena ; Fresh Water ; Geologic Sediments/*analysis/*microbiology ; Hydrogen-Ion Concentration ; Leucine/metabolism ; Methane/metabolism ; Organic Chemicals/*chemistry ; Oxygen/*chemistry ; Sweden ; Tritium ; }, abstract = {Based on work in marine sediments it can be hypothesized that (i) overall OM mineralization depends on the enzymatic capacity and is largely independent from the energy yield, (ii) similar oxic and anoxic rates are expected for fresh OM, while oxic rates should be faster for old OM that is partially degraded or adsorbed to particles, and (iii) that the thermodynamic energy yield does not regulate mineralization, but primarily determines the energy fraction allocated to bacterial production (BP). We addressed these hypotheses by simultaneous measurements of mineralization rates (MR) and BP in sediments from a eutrophic lake, along with MR measurements in sediments of a dystrophic lake. Anoxic MR were 44 and 78% of oxic MR in the eutrophic and dystrophic lake, respectively, which was always higher than expected given the theoretical energy yields. The BP:MR ratio was 0.94 and 0.24 in the oxic and anoxic treatments, respectively, in accordance with the expected energy yields. Thus, the results support all three hypotheses above. We also critically discuss BP measurements in sediments and suggest that bacterial growth efficiency values from simultaneous MR and BP measurements can be used to evaluate the reliability of BP estimates.}, }
@article {pmid12739074, year = {2003}, author = {Labbé, N and Juteau, P and Parent, S and Villemur, R}, title = {Bacterial diversity in a marine methanol-fed denitrification reactor at the montreal biodome, Canada.}, journal = {Microbial ecology}, volume = {46}, number = {1}, pages = {12-21}, pmid = {12739074}, issn = {0095-3628}, mesh = {Alphaproteobacteria/*genetics/*isolation &amp; purification ; *Biodiversity ; Cluster Analysis ; DNA Primers ; DNA, Ribosomal/genetics ; Electrophoresis ; Environment, Controlled ; Methanol/chemistry ; *Phylogeny ; Quebec ; Restriction Mapping ; Seawater ; Sequence Analysis, DNA ; *Water Microbiology ; Water Purification ; }, abstract = {The bacterial biota of a methanol-fed denitrification reactor used to treat seawater at the Montreal Biodome were investigated using culture-dependent and molecular biology methods. The microbiota extracted from the reactor carriers were cultivated on three media. Three isolate types were recovered and their 16S ribosomal DNA (rDNA) genes were determined. The analysis showed that the isolate types were related to alpha-Proteobacteria. They are members of the Hyphomicrobium and Paracoccus genera and the Phyllobacteriaceae family. Uncultured bacteria were identified through a 16S rDNA library generated from total DNA extracted from the microbiota. Clones were screened for different restriction profiles and for different DGGE (denaturing gradient gel electrophoresis) migration profiles. More than 70% of clones have the same restriction profile, and the sequence of representative clones showed a relation with the Methylophaga members of the Piscirickettsia family (gamma-Proteobacteria). Sequences from other profiles were related to bacterial species involved in denitrification. The number of species in the denitrification reactor was estimated at 15. Bacterial colonization on newly added carriers in the denitrification reactor was monitored by PCR-DGGE. The DGGE migration profiles evolved during the first 5 weeks and then remained essentially unchanged. PCR-DGGE was also used to monitor the microbial profiles in various aquarium locations. As expected, bacterial populations differed from one location to another, except for the sand and trickling filters which presented similar DGGE migration profiles.}, }
@article {pmid12739073, year = {2003}, author = {Holguin, G and Glick, BR}, title = {Transformation of Azospirillum brasilense Cd with an ACC deaminase gene from enterobacter cloacae UW4 fused to the Tet r gene promoter improves its fitness and plant growth promoting ability.}, journal = {Microbial ecology}, volume = {46}, number = {1}, pages = {122-133}, pmid = {12739073}, issn = {0095-3628}, mesh = {Azospirillum brasilense/*genetics/*physiology/ultrastructure ; Carbon-Carbon Lyases/*genetics ; Colony Count, Microbial ; DNA Primers ; Enterobacter cloacae/genetics ; Solanum lycopersicum/physiology ; Microscopy, Electron, Scanning ; Promoter Regions, Genetic/*genetics ; Repressor Proteins/genetics ; Soil Microbiology ; *Transformation, Bacterial ; }, abstract = {It has been reported that PGPB, containing ACC deaminase, can cleave the plant ethylene precursor ACC and thereby lower ethylene concentration in a developing or stressed plant, protecting it against the deleterious effects of stress ethylene and facilitating the formation of longer roots. In a previous work we have demonstrated expression of the ACC deaminase gene (acdS) from Enterobacter cloacae UW4 under the control of the lac promoter in Azospirillum brasilense Cd. With the inference that a construct including the ACC deaminase gene under the control of a constitutive promoter weaker than the lac promoter might impose less metabolic load on Azospirillum and improve its fitness, it was decided to clone acdS under the control of a tetracycline resistance gene promoter. The ACC deaminase structural gene was fused to the Tet(r) gene promoter by overlap extension using PCR, cloned in pRK415, and transferred into A. brasilense Cd. The resulting transformants showed lower ACC deaminase activity than those with the lac promoter controlled acdS gene. However, acdS under the control of the Tet(r) gene promoter imposed lesser metabolic load on Azospirillum brasilense Cd. The result was significantly increased IAA synthesis and greater bacterial growth rate, as well as increased ability to survive on the surface of tomato leaves and to promote the growth of tomato seedlings.}, }
@article {pmid12732521, year = {2003}, author = {Egert, M and Friedrich, MW}, title = {Formation of pseudo-terminal restriction fragments, a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {5}, pages = {2555-2562}, pmid = {12732521}, issn = {0099-2240}, mesh = {Animals ; Archaea/genetics/isolation &amp; purification ; Bacteria/genetics/isolation &amp; purification ; Base Sequence ; Coleoptera/microbiology ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Ecosystem ; Genes, Archaeal ; Genes, Bacterial ; *Genetics, Microbial ; Models, Genetic ; Nucleic Acid Conformation ; *Polymerase Chain Reaction ; *Polymorphism, Restriction Fragment Length ; }, abstract = {Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified genes is a widely used fingerprinting technique in molecular microbial ecology. In this study, we show that besides expected terminal restriction fragments (T-RFs), additional secondary T-RFs occur in T-RFLP analysis of amplicons from cloned 16S rRNA genes at high frequency. A total of 50% of 109 bacterial and 78% of 68 archaeal clones from the guts of cetoniid beetle larvae, using MspI and AluI as restriction enzymes, respectively, were affected by the presence of these additional T-RFs. These peaks were called "pseudo-T-RFs" since they can be detected as terminal fluorescently labeled fragments in T-RFLP analysis but do not represent the primary terminal restriction site as indicated by sequence data analysis. Pseudo-T-RFs were also identified in T-RFLP profiles of pure culture and environmental DNA extracts. Digestion of amplicons with the single-strand-specific mung bean nuclease prior to T-RFLP analysis completely eliminated pseudo-T-RFs. This clearly indicates that single-stranded amplicons are the reason for the formation of pseudo-T-RFs, most probably because single-stranded restriction sites cannot be cleaved by restriction enzymes. The strong dependence of pseudo-T-RF formation on the number of cycles used in PCR indicates that (partly) single-stranded amplicons can be formed during amplification of 16S rRNA genes. In a model, we explain how transiently formed secondary structures of single-stranded amplicons may render single-stranded amplicons accessible to restriction enzymes. The occurrence of pseudo-T-RFs has consequences for the interpretation of T-RFLP profiles from environmental samples, since pseudo-T-RFs may lead to an overestimation of microbial diversity. Therefore, it is advisable to establish 16S rRNA gene sequence clone libraries in parallel with T-RFLP analysis from the same sample and to check clones for their in vitro digestion T-RF pattern to facilitate the detection of pseudo-T-RFs.}, }
@article {pmid12732417, year = {2003}, author = {Li, M and Gong, J and Cottrill, M and Yu, H and de Lange, C and Burton, J and Topp, E}, title = {Evaluation of QIAamp DNA Stool Mini Kit for ecological studies of gut microbiota.}, journal = {Journal of microbiological methods}, volume = {54}, number = {1}, pages = {13-20}, doi = {10.1016/s0167-7012(02)00260-9}, pmid = {12732417}, issn = {0167-7012}, mesh = {Animals ; Bacteria/genetics/*isolation &amp; purification ; DNA, Bacterial/*analysis/isolation &amp; purification ; DNA, Ribosomal/analysis ; *Ecosystem ; Electrophoresis/methods ; Feces/*microbiology ; Intestinal Mucosa/chemistry/microbiology ; Intestines/*microbiology ; Microspheres ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Reagent Kits, Diagnostic ; Sequence Analysis, DNA ; Swine ; }, abstract = {Cell lysis efficiency and the quality of DNA extracts from complex bacterial ecosystems are two major concerns in molecular ecological studies of gut microbiota. In this study, we use PCR-denaturing gradient gel electrophoresis (DGGE) DNA profiling, random cloning and sequence analysis of 16S rRNA genes to compare the QIAamp DNA Stool Mini Kit with the bead beating technique in the preparation of DNA extracts from gut microbiota of pigs. We also developed a washing procedure that can release more than 93% of bacterial cells attached to the gut mucosa. Both the QIAamp kit and bead beating method lysed approximately 95% of bacterial cells. PCR-DGGE DNA profiles of ileal and cecal microbiota from both digesta and mucosa that were generated from the DNA extracts using the two methods were nearly identical. Random cloning and sequence analysis also demonstrated the high quality of DNA extracts using the two methods. Two random clone sets of 16S rRNA genes generated from the DNA extracts had a similar degree of bacterial diversity. Different preparations of DNA extract from a single sample using the QIAamp kit consistently produced similar PCR-DGGE DNA profiles with similarity indexes higher than 99%. Our data suggest the appropriateness of the QIAamp DNA Stool Mini Kit for the studies of gut microbial ecology and the effectiveness of the QIAamp kit in processing multiple samples for cell lysis and DNA extraction.}, }
@article {pmid12712341, year = {2003}, author = {Bothin, C and Midtvedt, T and Perbeck, L}, title = {Orally delivered antibiotics which lower bacterial numbers decrease experimental intra-abdominal adhesions.}, journal = {Langenbeck's archives of surgery}, volume = {388}, number = {2}, pages = {112-115}, pmid = {12712341}, issn = {1435-2443}, mesh = {Abdomen ; Amoxicillin-Potassium Clavulanate Combination/*therapeutic use ; Animals ; Drug Therapy, Combination/*therapeutic use ; Female ; Male ; Peritoneal Diseases/*prevention &amp; control ; Postoperative Complications/*prevention &amp; control ; Random Allocation ; Rats ; Rats, Inbred Strains ; Tissue Adhesions/prevention &amp; control ; }, abstract = {BACKGROUND: Postsurgical adhesion formation is a common occurrence after most surgical procedures and is still a major cause of postoperative morbidity because no satisfactory treatment or prophylaxis has yet been developed. Further elucidation of the basic mechanisms of postsurgical adhesion formation is needed. Recent studies using germfree rats have found the indigenous bowel flora to be important in the adhesive response. The present study examined whether antibiotic treatment affects intra-abdominal adhesion formation.<br><br>METHODS: Using the cecal crush model to inflict adhesions, groups of rats (n=12) were treated with placebo or amoxicillin/clavulanic acid in the drinking water. Treatment started 3 days before operation and continued until evaluation. Adhesion scores were recorded after 7 days. Bacterial counts were made from cultures of fecal samples on operation day and at termination.<br><br>RESULTS: Amoxicillin/clavulanic acid decreased adhesion score compared to placebo. Adhesion incidence was 50% in the treatment group and 92% in the placebo group. Bacterial numbers were lower in the treatment group.<br><br>CONCLUSIONS: Antibiotic treatment which lowers bacterial numbers can decrease adhesions.}, }
@article {pmid12708663, year = {2003}, author = {Muthumbi, W and De Boever, P and Pieters, JG and Siciliano, S and D'Hooge, W and Verstraete, W}, title = {Polycyclic aromatic hydrocarbons (PAHs) and estrogenic compounds in experimental flue gas streams.}, journal = {Journal of environmental quality}, volume = {32}, number = {2}, pages = {417-422}, doi = {10.2134/jeq2003.4170}, pmid = {12708663}, issn = {0047-2425}, mesh = {Air Pollutants/*analysis ; Biological Assay ; Estrogens/*analysis ; Gases ; Humans ; Incineration ; Polycyclic Aromatic Hydrocarbons/*analysis ; Receptors, Estrogen/*physiology ; *Refuse Disposal ; }, abstract = {The importance of combustion processes as a source of substances with estrogenic activity in the environment was investigated. Wood (nontreated and treated with wood preservatives), barbecue charcoal, meat, and kitchen waste were combusted in a laboratory-scale incinerator. Flue gas emissions (particulates and gaseous pollutants) were trapped in polyurethane foam cartridges. The cartridges were subjected to Soxhlet extraction and part of the extracts redissolved in dimethylsulfoxide (DMSO) for analyses of estrogenic activity by means of the yeast-based human estrogen receptor (hER) bioassay. A synthetic estrogen, 17-alpha-ethinylestradiol (EE2), was used as the reference estrogenic compound. Part of the extracts was analyzed for the 16 USEPA priority polycyclic aromatic hydrocarbons (PAHs). Estrogenic compounds in the flue gas (wood) were as high as 234 +/- 25 ng m(-3) EE2 equivalent compared with 27 to 81 ng m(-3) EE2 equivalent in flue gas from combustion of barbecue charcoal. Concentrations of polycyclic aromatic hydrocarbons in both flue gas streams were in the range of 21,000 +/- 2000 and 240 +/- 110 ng m(-3), respectively. In general, the concentrations of EE2 equivalent in the flue gas samples were at least a factor of 1000 lower than total PAH concentration. The EE2 levels were not related to the concentration of PAHs in any flue gas sample.}, }
@article {pmid12704564, year = {2003}, author = {Alfreider, A and Vogt, C and Hoffmann, D and Babel, W}, title = {Diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes from groundwater and aquifer microorganisms.}, journal = {Microbial ecology}, volume = {45}, number = {4}, pages = {317-328}, doi = {10.1007/s00248-003-2004-9}, pmid = {12704564}, issn = {0095-3628}, mesh = {Adaptation, Physiological ; Carbon Dioxide/*metabolism ; DNA, Bacterial/*analysis ; *Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Polymorphism, Restriction Fragment Length ; Ribulose-Bisphosphate Carboxylase/*genetics ; Sequence Analysis, DNA ; Soil Microbiology ; *Water Microbiology ; Water Supply ; }, abstract = {To test our hypothesis that microbial autotrophic CO2 fixation plays an important role in subsurface systems of two large groundwater remediation projects, several anaerobic/microaerobic aquifer and groundwater samples were taken and used to investigate the distribution and phylogenetic diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large-subunit genes. Two primer sets were designed for amplifying partial-subunit genes of RubisCO forms I and II from the DNA, directly extracted from the samples. PCR products were used to construct five clone libraries with putative RubisCO form I sequences, and two libraries of DNA amplified by form II primers. Selected clones were screened for variation by restriction fragment length polymorphism analysis, and a total of 28 clone inserts were sequenced and further analyzed. The phylogenies constructed from amino acid sequences derived from the partial RubisCO large-subunit sequences showed a distinct pattern. Diverse sequences affiliated to the cluster of green-like type IA RubisCO sequences were found, representing various obligate and facultative chemolithoautotrophic Proteobacteria, whereas type II RubisCO sequences detected were most closely related to those of thiobacilli species. An isolate obtained from aquifer enrichment culture, which has been provisionally named Halothiobacillus sp. RA13 on the basis of its 16S rDNA sequence, was found to contain both types of RubisCO genes, i.e., forms I and II. Physiological and ecological considerations are discussed in the context of additional microbial data and physicochemical properties.}, }
@article {pmid12704563, year = {2003}, author = {Kadivar, H and Stapleton, AE}, title = {Ultraviolet radiation alters maize phyllosphere bacterial diversity.}, journal = {Microbial ecology}, volume = {45}, number = {4}, pages = {353-361}, doi = {10.1007/s00248-002-1065-5}, pmid = {12704563}, issn = {0095-3628}, mesh = {*Bacteria/genetics ; DNA, Bacterial/analysis ; Ecosystem ; Plant Leaves/*microbiology ; Population Dynamics ; RNA, Ribosomal, 16S/analysis ; Ultraviolet Rays/*adverse effects ; Zea mays ; }, abstract = {Epiphytic bacteria are subjected to very stressful environments, including UV radiation. Bacterial assemblages on Zea mays (maize) leaves exposure were examined with and without UV-B radiation. Culture-independent molecular techniques were utilized for bacterial identification, diversity analysis and selection of putative UV exposure marker sequences. Few sequences corresponded to previously characterized phyllosphere bacteria. There was a strong tendency toward increased 16S rDNA sequence diversity in UV samples. Overall community structure was assessed using denaturing gel gradient electrophoresis; significant alterations in community structure were found in comparisons of phyllosphere bacterial samples from control and solar UV-B exposed plants.}, }
@article {pmid12704562, year = {2003}, author = {Kuske, CR and Ticknor, LO and Busch, JD and Gehring, CA and Whitham, TG}, title = {The pinyon rhizosphere, plant stress, and herbivory affect the abundance of microbial decomposers in soils.}, journal = {Microbial ecology}, volume = {45}, number = {4}, pages = {340-352}, doi = {10.1007/s00248-002-1042-z}, pmid = {12704562}, issn = {0095-3628}, mesh = {Animals ; Ecosystem ; Fungi ; Humic Substances/*metabolism ; Insecta ; *Pinus ; Plant Roots/*microbiology ; Population Dynamics ; Pseudomonadaceae ; Seasons ; *Soil Microbiology ; }, abstract = {In terrestrial ecosystems, changes in environmental conditions that affect plant performance cause a cascade of effects through many trophic levels. In a 2-year field study, seasonal abundance measurements were conducted for fast-growing bacterial heterotrophs, humate-degrading actinomycetes, fungal heterotrophs, and fluorescent pseudomonads that represent the decomposers in soil. Links between plant health and soil microbiota abundance in pinyon rhizospheres were documented across two soil types: a dry, nutrient-poor volcanic cinder field and a sandy-loam soil. On the stressful cinder fields, we identified relationships between soil decomposer abundance, pinyon age, and stress due to insect herbivory. Across seasonal variation, consistent differences in microbial decomposer abundance were identified between the cinders and sandy-loam soil. Abundance of bacterial heterotrophs and humate-degrading actinomycetes was affected by both soil nutritional status and the pinyon rhizosphere. In contrast, abundance of the fungal heterotrophs and fluorescent pseudomonads was affected primarily by the pinyon rhizosphere. On the cinder field, the three bacterial groups were more abundant on 150-year-old trees than on 60-year-old trees, whereas fungal heterotrophs were unaffected by tree age. Fungal heterotrophs and actinomycetes were more abundant on insect-resistant trees than on susceptible trees, but the opposite was true for the fluorescent pseudomonads. Although all four groups were present in all the environments, the four microbial groups were affected differently by the pinyon rhizosphere, by tree age, and by tree stress caused by the cinder soil and insect herbivory.}, }
@article {pmid12704561, year = {2003}, author = {Schlickeisen, E and Tietjen, TE and Arsuffi, TL and Groeger, AW}, title = {Detritus processing and microbial dynamics of an aquatic macrophyte and terrestrial leaf in a thermally constant, spring-fed stream.}, journal = {Microbial ecology}, volume = {45}, number = {4}, pages = {411-418}, doi = {10.1007/s00248-002-1062-8}, pmid = {12704561}, issn = {0095-3628}, mesh = {Bacteria ; Biomass ; Carbon/metabolism ; *Ecosystem ; Fungi/physiology ; Organic Chemicals/metabolism ; *Plant Leaves ; *Populus ; *Sagittaria ; Trees ; *Water Microbiology ; *Water Supply ; }, abstract = {Past studies of organic matter processing in stream ecosystems have focused on the fate of allochthonous terrestrial leaf detritus. In streams with a reduced canopy, submerged macrophytes may provide a significant source of organic matter to the microbial community and higher trophic levels. We compared mass loss patterns and microbial dynamics between a submerged macrophyte, Sagittaria platyphylla, and a deciduous leaf, Populus deltoides. Mass loss rates were higher for the submerged macrophyte, though exponential decay values indicated that both are "fast" decomposers. Bacterial abundance was not significantly different between plant types, but bacterial productivity was significantly higher in Sagittaria. Although fungal biomass was higher overall for Populus, it was not significantly different from that of Sagittaria until day 30. Relative to fungi, bacteria made up 4% and 7% of the peak microbial biomass on Populus and Sagittaria, respectively. Aquatic hyphomycete sporulation was detected only on Populus. These results suggest that in systems where submerged macrophytes are abundant, they can provide a carbon source quantitatively comparable to that of riparian leaf detritus, but that qualitative differences in leaf structural composition cause a shift toward a more significant role for bacterial decomposers.}, }
@article {pmid12704560, year = {2003}, author = {Jiang, S and Fu, W and Chu, W and Fuhrman, JA}, title = {The vertical distribution and diversity of marine bacteriophage at a station off Southern California.}, journal = {Microbial ecology}, volume = {45}, number = {4}, pages = {399-410}, doi = {10.1007/s00248-002-1059-3}, pmid = {12704560}, issn = {0095-3628}, mesh = {Bacteriophages/*genetics ; California ; DNA, Viral/*analysis ; Environmental Monitoring ; *Genetic Variation ; Population Dynamics ; RNA, Ribosomal, 16S/analysis ; Vibrio ; }, abstract = {Sixty-two bacteriophages were isolated on eight indigenous bacteria from a Pacific Ocean station spanning 887-m vertical depth, on two occasions between 1999 and 2000. On the basis of 16S rRNA sequences, six hosts were tentatively identified to be in the genus Vibrio and the other two were closely related to Altermonas macleodii (W9a) and Pseudoalteromonas spp. (W13a). Restriction fragment length polymorphism (RFLP) analysis of phage genomes using AccI and HapI showed that 16 phages infecting host C4a (Vibrio) displayed 14 unique RFLP patterns. However, identical phages infecting host C4b, C6a, and C6b (all Vibrio) were obtained from both the surface layer and the hypoxic zone at 850 m. Most phage isolates from the second year had a different RFLP pattern but shared genetic similarity to the phages infecting the same host from the previous year based on a hybridization study using phage genome probes. Cluster analysis of RFLP patterns and hybridization results also indicated that phages infecting the same or genetically related hosts, in general, shared higher degrees of homology in spite of the diverse RFLP patterns. Pulsed field gel electrophoresis (PFGE) analysis of native viral genomes indicated a range in genome size from less than 40 to 200 kb, and the dominant band shifted up by about 5-10 kb in the deep samples compared to the shallow ones. Hybridization of phage genome probes with total viral community DNA from various depths suggests these isolates, or at least some of their genes, represent a detectable portion of the natural viral community and were distributed throughout the water column. Thus, the results of this study demonstrated that the genetic diversity of bacteriophage in the ocean is far greater than that of their bacterial hosts. However, host range may have contributed to the evolution of the diverse phage population in the marine environment.}, }
@article {pmid12704559, year = {2003}, author = {Rosenstock, B and Simon, M}, title = {Consumption of dissolved amino acids and carbohydrates by limnetic bacterioplankton according to molecular weight fractions and proportions bound to humic matter.}, journal = {Microbial ecology}, volume = {45}, number = {4}, pages = {433-443}, doi = {10.1007/s00248-003-3001-8}, pmid = {12704559}, issn = {0095-3628}, mesh = {Amino Acids/*metabolism ; Animals ; *Bacteria ; *Carbohydrate Metabolism ; Environmental Monitoring ; Humic Substances/chemistry ; Molecular Weight ; *Plankton ; Solubility ; *Water Microbiology ; }, abstract = {We investigated the bacterial decomposition of dissolved amino acids (DAA) and carbohydrates (DCHO) bound to humic substances and in the nonhumic fraction, and of low (< 3 KDA) AND HIGH (> 3 kDa) molecular weight (MW). Experiments were conducted in mesotrophic Lake Constance, Germany, in October and November 1997 and June 1998 during periods of low phytoplankton biomass. Dilution cultures, inoculated with bacterioplankton of the < 1 mm size fraction from 3 m, were run over 5 to 8 days to determine bacterial consumption of the various fractions of DAA and DCHO. In all experiments consumption rates of DCHO were higher than that of DAA. On average, 70% of the DAA and DCHO consumed were associated with the humic fraction, which, however, also consisted of a substantial recalcitrant component. In contrast, there was no preferential consumption of DAA and DCHO in either of the two MW fractions. Overall, we found a highly significant positive correlation between the consumption of the various fractions of DAA and DCHO and their initial concentrations. The consumed DAA, i.e, their labile pool, was dominated by serine and glutamate and that of DCHO by arabinose. In contrast, the residual DAA, i.e., the recalcitrant pool, comprised highest proportions of glycine + threonine and that of DCHO of mannose + xylose. These results indicate that the bacterial consumption of DAA and DCHO was mainly a function of their concentrations, irrespective of the molecular weight and whether they are bound to humic substances or not and despite the fact that they consist of a more labile and a more refractory pool.}, }
@article {pmid12704558, year = {2003}, author = {Bååth, E}, title = {The use of neutral lipid fatty acids to indicate the physiological conditions of soil fungi.}, journal = {Microbial ecology}, volume = {45}, number = {4}, pages = {373-383}, doi = {10.1007/s00248-003-2002-y}, pmid = {12704558}, issn = {0095-3628}, mesh = {Biomarkers/*analysis ; Carbon/metabolism ; Environmental Monitoring/*methods ; Fatty Acids/*analysis ; Fungi/chemistry/*physiology ; Glucose/metabolism ; Phosphorus/metabolism ; Population Dynamics ; *Soil Microbiology ; }, abstract = {The usefulness of measuring neutral lipid fatty acids (NLFAs) and phospholipid fatty acids (PLFAs) separately in order to interpret perturbation effects on soil and compost microorganisms has been studied. Initially the NLFA/PLFA ratios were studied in different soils. Low ratios were found for fatty acids common in bacteria, especially for cyclopropane fatty acids. Higher ratios were found for fatty acids common in eukaryotic organisms such as fungi (18:1omega9 and 18:2omega6,9) or in saturated fatty acids, common to many types of organisms. Adding glucose to a forest soil increased the amounts of the fungal NLFAs 18:1omega9 and 18:2 omega6,9 up to 60 and 10 times, respectively, after 10 days, followed by a gradual decrease. After 3 months incubation, higher levels of these NLFAs were still found compared with the control samples. Adding glucose together with nitrogen (N) and phosphorus (P) resulted in no increase in NLFAs but a 10-fold increase in the PLFAs 18:1omega9 and 18:2omega6,9. Thus, the NLFA/PLFA ratios for these fatty acids were lower than in the no-addition control when glucose was added together with N and P, but higher when glucose was added alone, even 3 months after the addition. Adding N+P without glucose did not affect the NLFA/PLFA ratio for any fatty acid. Increasing NLFA/PLFA ratios for the fungal fatty acids were also found with time after the thermophilic phase in a compost, indicating increased availability of easily available carbon.}, }
@article {pmid12704557, year = {2003}, author = {Dal Bello, F and Walter, J and Hammes, WP and Hertel, C}, title = {Increased complexity of the species composition of lactic acid bacteria in human feces revealed by alternative incubation condition.}, journal = {Microbial ecology}, volume = {45}, number = {4}, pages = {455-463}, doi = {10.1007/s00248-003-2001-z}, pmid = {12704557}, issn = {0095-3628}, mesh = {DNA, Bacterial/*analysis ; Digestive System/microbiology ; Electrophoresis ; Feces/microbiology ; Humans ; Lactobacillus/genetics/*isolation &amp; purification ; Leuconostoc/genetics/*isolation &amp; purification ; Polymerase Chain Reaction ; Reproducibility of Results ; Specimen Handling ; }, abstract = {Denaturing gradient gel electrophoresis (DGGE) of DNA fragments generated by PCR with primers specific for lactic acid bacteria (LAB) was applied to investigate various media and incubation conditions to recover LAB from human feces. Samples were plated on selective and nonselective media and incubated under standard condition (37 degrees C, anaerobiosis) for fecal LAB as well as alternative condition (30 degrees C, 2% O2). PCR-DGGE analyses of resuspended bacterial biomass (RBB) obtained from agar plates revealed that the species composition of the recovered LAB was affected more strongly by the incubation condition than by the used medium. It was observed that food-associated LAB, such as Lactobacillus sakei and Leuconostoc mesenteroides, hitherto not described as intestinal inhabitants, are more easily selected when the alternative incubation condition is used. Identification of randomly picked colonies grown under the alternative condition showed that L. sakei is one of the predominant food-associated LAB species, reaching counts of up to 106 CFU/g feces. Comparison of the results of bacteriological culture with those obtained by PCR-DGGE analysis of the RBB showed that investigation of RBB is a fast and reliable method to gain insight into the species composition of culturable LAB in feces.}, }
@article {pmid12704556, year = {2003}, author = {Matz, C and Jürgens, K}, title = {Interaction of nutrient limitation and protozoan grazing determines the phenotypic structure of a bacterial community.}, journal = {Microbial ecology}, volume = {45}, number = {4}, pages = {384-398}, doi = {10.1007/s00248-003-2000-0}, pmid = {12704556}, issn = {0095-3628}, mesh = {Animals ; *Bacteria ; Carbon/metabolism ; DNA, Bacterial ; Ecosystem ; *Eukaryota ; *Food Chain ; Genotype ; Phenotype ; Phosphorus/metabolism ; Polymorphism, Restriction Fragment Length ; Population Dynamics ; *Water Microbiology ; }, abstract = {We examined the impact of nutrient conditions (carbon and phosphorus limitation) and grazing by protozoans on the phenotypic community structure of freshwater bacteria in continuous culture systems. Lakewater bacteria were grown on mineral medium, which was supplemented with glucose and amino acids and adjusted by different phosphorus concentrations to achieve either carbon or phosphorus limitation. Each nutrient treatment was inoculated with the same bacterial community and consisted of a nongrazing and a grazing treatment, to which the heterotrophic nanoflagellates Spumella sp. and Ochromonas sp. were added. We found that nutrient conditions alone resulted in differences in the phenotypic structure of the bacterial community: small and motile bacteria dominated under C limitation while large, elongated, and capsulated bacteria were characteristic for P limitation. The genotypic community composition as measured by T-RFLP (terminal restriction fragment length polymorphism) was not severely influenced by the two nutrient treatments. In the presence of flagellate predators, grazing-resistant bacteria developed under both nutrient conditions, but with different survival mechanisms: highly motile bacteria prevailed under C limitation, whereas the P-limited grazing treatment was dominated by filamentous forms. T-RFLP analysis revealed only moderate changes in bacterial community composition due to grazing, which were most pronounced under P limitation. Analysis by video microscopy revealed that high swimming speed is an efficient nonmorphological survival mechanism for bacteria to reduce the capture success of the flagellate predator. The rejection of optimal-sized, nonmotile bacteria under P limitation suggests the importance of other nonmorphological, surface-located cell properties. Our results illustrate that the realized mechanisms of grazing resistance are linked to the actual limitation conditions, and that the combined effects of nutrient limitation and grazing are major determinants of bacterial community structure.}, }
@article {pmid12704555, year = {2003}, author = {Krauss, G and Sridhar, KR and Jung, K and Wennrich, R and Ehrman, J and Bärlocher, F}, title = {Aquatic hyphomycetes in polluted groundwater habitats of central Germany.}, journal = {Microbial ecology}, volume = {45}, number = {4}, pages = {329-339}, doi = {10.1007/s00248-003-0001-7}, pmid = {12704555}, issn = {0095-3628}, mesh = {*Copper ; Environmental Monitoring ; Germany ; Mining ; *Mitosporic Fungi/isolation &amp; purification/physiology ; Oxygen/analysis ; Population Dynamics ; Soil ; Water Microbiology ; *Water Pollutants ; *Water Supply ; }, abstract = {Polluted groundwater wells located in a former copper shale mining district (11 sites; Mansfelder Land, Central Germany) and in meadows of the Mulde and Elbe rivers (2 sites) were assessed for occurrence and species richness of aquatic hyphomycetes. Water temperatures at all sites were relatively low and fluctuated less than in surface waters. Oxygen concentrations were always below saturation, whereas sulfate, nitrate, and phosphate levels reached extremely high values in several of the wells. Relatively high levels of Pb, Mn, and Fe were found in some of the wells, but overall few concentrations of individual metals and metalloids exceeded European guidelines for drinking water. Pollen tube growth inhibition, used to assess cytotoxicity of the water, ranged between 4 and 50%. Between 1 and 10 distinct species of aquatic hyphomycetes colonized sterile Alnus glutinosa leaves exposed at the Mansfelder Land sites; for the meadow sites, 8-20 species were found. Heliscus lugdunensis and Anguillospora sp. were the two most widespread species. Fungal colonization occurred much more slowly than in surface water, as demonstrated by scanning electron microscopy and the release of conidia from recovered leaves. The conidial output from exposed alder leaves ranged from 0.2 to 95 conidia mg (-1) dry mass, corresponding to 10% of the values for contaminated surface waters in the same region. Overall, groundwater appears to be a marginal habitat for aquatic hyphomycetes, but may nevertheless play a vital role as long-term reservoir facilitating rapid recolonization following a collapse in fungal communities in surface waters.}, }
@article {pmid12704554, year = {2003}, author = {Mazza, P and Monciardini, P and Cavaletti, L and Sosio, M and Donadio, S}, title = {Diversity of Actinoplanes and related genera isolated from an Italian soil.}, journal = {Microbial ecology}, volume = {45}, number = {4}, pages = {362-372}, doi = {10.1007/s00248-002-2038-4}, pmid = {12704554}, issn = {0095-3628}, mesh = {DNA, Bacterial/*analysis ; Italy ; Micromonosporaceae/*genetics/*isolation &amp; purification ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Population Dynamics ; RNA, Ribosomal, 23S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Actinoplanes and related genera are good producers of bioactive secondary metabolites. However, many strains within these genera present similar morphological characteristics, and this prevents an effective discrimination of replicate strains during industrial isolation and screening programs. Using PCR-RFLP analysis of the 23S rDNA gene and of the 16S-23S intergenic spacer, we have analyzed 182 strains of Actinoplanes and related genera obtained through a selective isolation method from a single Italian soil. Combining the 23S and IGS data, 99 unique profiles were observed, and morphologically undistinguishable strains were discriminated. Further analyses on a restricted number of strains through 16S sequencing and hybridization to a probe for secondary metabolism established a good correlation between strain diversity seen by PCR-RFLP and that seen by the other methods. Overall, the data indicate the presence of a high diversity of Actinoplanes and related genera isolated from a single Italian soil.}, }
@article {pmid12704553, year = {2003}, author = {Egli, K and Bosshard, F and Werlen, C and Lais, P and Siegrist, H and Zehnder, AJ and Van der Meer, JR}, title = {Microbial composition and structure of a rotating biological contactor biofilm treating ammonium-rich wastewater without organic carbon.}, journal = {Microbial ecology}, volume = {45}, number = {4}, pages = {419-432}, doi = {10.1007/s00248-002-2037-5}, pmid = {12704553}, issn = {0095-3628}, mesh = {Bacteria, Aerobic/genetics/*physiology ; *Biofilms ; DNA, Bacterial ; Environmental Monitoring ; In Situ Hybridization, Fluorescence ; Nitrogen/*metabolism ; Oxidation-Reduction ; Population Dynamics ; Quaternary Ammonium Compounds/*metabolism ; RNA, Ribosomal, 16S/analysis ; *Waste Disposal, Fluid ; }, abstract = {High nitrogen losses were observed in a rotating biological contactor (RBC) treating ammonium-rich (up to 500 mg NH4(+)-N/L) but organic-carbon-poor leachate from a hazardous waste landfill in Kölliken, Switzerland. The composition and spatial structure of the microbial community in the biofilm on the RBC was analyzed with specific attention for the presence of aerobic ammonium and nitrite oxidizing bacteria and anaerobic ammonium oxidizers. Anaerobic ammonium oxidation (anammox) involves the oxidation of ammonium with nitrite to N2. First the diversity of the biofilm community was determined from sequencing cloned PCR-amplified 16S rDNA fragments. This revealed the presence of a number of very unusual 16S rDNA sequences, but very few sequences related to known ammonium or nitrite oxidizing bacteria. From analysis of biofilm samples by fluorescence in situ hybridization with known phylogenetic probes and by dot-blot hybridization of the same probes to total RNA purified from biofilm samples, the main groups of microorganisms constituting the biofilm were found to be ammonium-oxidizing bacteria from the Nitrosomonas europaea/eutropha group, anaerobic ammonium-oxidizing bacteria of the "Candidatus Kuenenia stuttgartiensis" type, filamentous bacteria from the phylum Bacteroidetes, and nitrite-oxidizing bacteria from the genus Nitrospira. Aerobic and anaerobic ammonium-oxidizing bacteria were present in similar amounts of around 20 to 30% of the biomass, whereas members of the CFB phylum were present at around 7%. Nitrite oxidizing bacteria were only present in relatively low amounts (less than 5% determined with fluorescence in situ hybridization). Data from 16S rRNA dot-blot and in situ hybridization were not in all cases congruent. FISH analysis of thin-sliced and fixed biofilm samples clearly showed that the aerobic nitrifiers were located at the top of the biofilm in an extremely high density and in alternating clusters. Anammox bacteria were exclusively present in the lower half of the biofilm, whereas CFB-type filamentous bacteria were present throughout the biofilm. The structure and composition of these biofilms correlated very nicely with the proposed physiological functional separations in ammonium conversion.}, }
@article {pmid12704552, year = {2003}, author = {Ramaiah, N and De, J}, title = {Unusual rise in mercury-resistant bacteria in coastal environs.}, journal = {Microbial ecology}, volume = {45}, number = {4}, pages = {444-454}, doi = {10.1007/s00248-001-1068-7}, pmid = {12704552}, issn = {0095-3628}, mesh = {Bacteria/*drug effects/genetics ; Drug Resistance ; India ; Mercury/*pharmacology ; Plasmids ; Population Dynamics ; Selection, Genetic ; *Water Microbiology ; }, abstract = {A sharp rise in mercury-resistant bacteria (MRB) capable of tolerating very high concentration of Hg was observed over the last 3-4 years in the coastal environs of India. While none or negligible colony-forming units (CFU) of bacteria were counted on seawater nutrient agar with 0.5 ppm (2.5 microM) Hg (II) as HgCl2 until 1997, from 13 to over 75% of the CFU grew on 20 times higher, 50 microM, Hg concentrations from almost every recently examined marine sample. Although exceptionally high counts of MRB (96% of CFU) were recorded from samples collected from the polluted zones off Mumbai, the MRB capable of growth on seawater nutrient agar with 50 microM Hg were quite abundant in most samples collected from many locations with few or no pollution effects. We noticed for the first time the occurrence of aerobic heterotrophic bacterial isolates capable of growth with 250 microM Hg. Such MRB grew with higher concentrations of many other toxic xenobiotics than the Hg sensitive ones. Based on the unusually high populations of viable MRB and some simple experiments, we propose that many marine bacterial species are selected, possibly through acquisition of plasmids and/or transposable elements and modifying Hg, whose concentration, according to recent studies, is on the rise in marine habitats.}, }
@article {pmid12703861, year = {2003}, author = {Baloch, MI and Akunna, JC}, title = {Effect of rapid hydraulic shock loads on the performance of granular bed baffled reactor.}, journal = {Environmental technology}, volume = {24}, number = {3}, pages = {361-368}, doi = {10.1080/09593330309385568}, pmid = {12703861}, issn = {0959-3330}, mesh = {Biomass ; *Bioreactors ; Euryarchaeota/*physiology ; Glucose/metabolism ; Organic Chemicals/analysis ; Oxygen/analysis ; Particle Size ; Population Dynamics ; Pressure ; Waste Disposal, Fluid/*methods ; Water Movements ; }, abstract = {This paper describes the performance of a granular bed baffled reactor when receiving unpredictable hydraulic shock loads, which is a frequent occurrence in industrial wastewater treatment plants. Shock loads were created by rapidly increasing volumetric organic loading rates from 2.5 to 20 kg COD m(-3) d(-1), by decreasing (in a stepwise fashion) hydraulic retention time from 48 hrs to 6 hrs. Synthetic wastewater containing glucose as the main organic compound was used in this study. High effluent quality was observed, with soluble COD removal efficiencies of 94% to 97%, during all shock loading conditions at steady state. The reactor appeared to possess high tolerance to rapid hydraulic changes with fast recovery time. Marked phase separation between different microorganisms occurred at high organic loading rate, with acidogenesis and methanogenesis being the respective dominant activities in the upstream and downstream compartments of the reactor. The compartmentalised nature of the reactor and the granular bed structure were believed to be responsible for high reactor stability during overloading conditions. Microbial ecology in the system appeared to favour acetate and butyrate production at high organic loading rate. Granular biomass possessed good settling characteristics, hence encouraging high biomass retention within the system. The dense granular bed in the methanogenic zone acted as a filtration bed for lighter floating non-granular biomass, thus further reducing overall effluent solids concentration. This study demonstrated that the granular bed baffled reactor is a suitable system for treating industrial wastewaters with highly varying rates.}, }
@article {pmid12697344, year = {2003}, author = {Seviour, RJ and Mino, T and Onuki, M}, title = {The microbiology of biological phosphorus removal in activated sludge systems.}, journal = {FEMS microbiology reviews}, volume = {27}, number = {1}, pages = {99-127}, doi = {10.1016/S0168-6445(03)00021-4}, pmid = {12697344}, issn = {0168-6445}, mesh = {Aerobiosis ; Anaerobiosis ; Bacteria/classification/growth &amp; development/metabolism ; Biodegradation, Environmental ; Models, Biological ; Phosphorus/chemistry/*metabolism ; Phylogeny ; Polyphosphates/chemistry/metabolism ; Sewage/*microbiology ; *Waste Disposal, Fluid ; Water Microbiology ; }, abstract = {Activated sludge systems are designed and operated globally to remove phosphorus microbiologically, a process called enhanced biological phosphorus removal (EBPR). Yet little is still known about the ecology of EBPR processes, the microbes involved, their functions there and the possible reasons why they often perform unreliably. The application of rRNA-based methods to analyze EBPR community structure has changed dramatically our understanding of the microbial populations responsible for EBPR, but many substantial gaps in our knowledge of the population dynamics of EBPR and its underlying mechanisms remain. This review critically examines what we once thought we knew about the microbial ecology of EBPR, what we think we now know, and what still needs to be elucidated before these processes can be operated and controlled more reliably than is currently possible. It looks at the history of EBPR, the currently available biochemical models, the structure of the microbial communities found in EBPR systems, possible identities of the bacteria responsible, and the evidence why these systems might operate suboptimally. The review stresses the need to extend what have been predominantly laboratory-based studies to full-scale operating plants. It aims to encourage microbiologists and process engineers to collaborate more closely and to bring an interdisciplinary approach to bear on this complex ecosystem.}, }
@article {pmid12696699, year = {2003}, author = {Erickson, MC and Kornacki, JL}, title = {Bacillus anthracis: current knowledge in relation to contamination of food.}, journal = {Journal of food protection}, volume = {66}, number = {4}, pages = {691-699}, doi = {10.4315/0362-028x-66.4.691}, pmid = {12696699}, issn = {0362-028X}, mesh = {Animals ; Anthrax/diagnosis/*prevention &amp; control ; *Anthrax Vaccines ; Bacillus anthracis/immunology/*isolation &amp; purification/pathogenicity ; Biological Warfare/prevention &amp; control ; Bioterrorism/prevention &amp; control ; Ecology ; Food Contamination/*analysis/prevention &amp; control ; Food Microbiology ; Humans ; }, abstract = {In this article, information related to anthrax and its etiologic agent, Bacillus anthracis, in food is reviewed. The major topics discussed include the taxonomic relationship of B. anthracis to other Bacillus species, methods used for the recovery of the organism from surfaces and foods, routes of infection, the pathogenesis of the organism, the microbial ecology of the vegetative cell and spore in foods and the environment, chemical and physical treatments for spore inactivation, and the control of the disease in animals.}, }
@article {pmid12695998, year = {2003}, author = {He, Q and Mäkinen, J and Berbers, G and Mooi, FR and Viljanen, MK and Arvilommi, H and Mertsola, J}, title = {Bordetella pertussis protein pertactin induces type-specific antibodies: one possible explanation for the emergence of antigenic variants?.}, journal = {The Journal of infectious diseases}, volume = {187}, number = {8}, pages = {1200-1205}, doi = {10.1086/368412}, pmid = {12695998}, issn = {0022-1899}, mesh = {Adolescent ; Amino Acid Sequence ; Antibodies, Bacterial/*immunology ; Antibody Specificity/immunology ; *Antigenic Variation ; Antigens, Bacterial/*genetics/*immunology ; Bacterial Outer Membrane Proteins/genetics/*immunology ; Bordetella pertussis/genetics/*immunology ; Diphtheria-Tetanus-Pertussis Vaccine/immunology ; Female ; Genes, Bacterial/genetics ; Humans ; Infant ; Male ; Virulence Factors, Bordetella/genetics/*immunology ; }, abstract = {Divergence has been found between Bordetella pertussis vaccine strains and circulating strains. Polymorphism in pertactin (Prn) is essentially limited to region 1, which is made up of repeats. Today, the 3 most prevalent Prn variants are Prn1-3. Vaccine strains produce Prn1, whereas Prn2 is the predominant type found in circulating strains. We investigated how variation in region 1 affects the production of human serum antibodies. Individuals infected by Prn2 strains had significantly fewer antibodies to Prn1 did than those infected by Prn3 strains and those immunized with a booster dose of acellular vaccines containing Prn1. Moreover, in contrast to vaccine recipients and subjects infected by Prn3 strains, individuals infected by Prn2 strains had hardly any antibodies specific to the variable region of Prn1. These results indicate that conformational changes have occurred in the variable region of Prn, which may offer a possible explanation for the emergence of Prn2 strains in certain countries.}, }
@article {pmid12694914, year = {2003}, author = {Mahmood, S}, title = {Colonisation of spruce roots by two interacting ectomycorrhizal fungi in wood ash amended substrates.}, journal = {FEMS microbiology letters}, volume = {221}, number = {1}, pages = {81-87}, doi = {10.1016/S0378-1097(03)00166-6}, pmid = {12694914}, issn = {0378-1097}, mesh = {Basidiomycota/*classification/genetics/*growth &amp; development ; Culture Media ; DNA, Fungal/analysis ; Nitrogen/metabolism ; Picea/*microbiology ; Plant Roots/*microbiology ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Seedlings/microbiology ; Soil/analysis ; Wood ; }, abstract = {Interactions between two ectomycorrhizal fungal species, Piloderma croceum Erikss. and Hjortst. and Piloderma sp. 1 (found to colonise spruce roots and wood ash granules in the field), were investigated in wood ash amended substrates. The comparative ability of these fungi to colonise roots of non-mycorrhizal spruce (Picea abies (L.) Karst.) seedlings was studied in relation to factorial combinations of wood ash and N fertilisation. Non-mycorrhizal spruce seedlings (bait seedlings) were planted together with spruce seedlings colonised by P. croceum or Piloderma sp. 1. The growth substrate was a sand-peat mixture with wood ash or no ash and supplied with two levels of N, so that four substrate combinations were obtained. Piloderma sp. 1 mycelia colonised around 60% of the fine roots of bait seedlings in ash treatments regardless of N level and around 20-26% in treatments without ash. P. croceum only colonised 8% of the root tips in the presence of ash but 56% of the root tips in the low-N treatment without ash. However, in the high-N treatment without ash the colonisation level was reduced to around 30%. Total numbers of root tips per seedling did not vary significantly between the treatments. Possible reasons for the competitive advantage of Piloderma sp. 1 in wood ash fertilised substrate are discussed.}, }
@article {pmid12689714, year = {2003}, author = {Acosta-Mercado, D and Lynn, DH}, title = {The edaphic quantitative protargol stain: a sampling protocol for assessing soil ciliate abundance and diversity.}, journal = {Journal of microbiological methods}, volume = {53}, number = {3}, pages = {365-375}, doi = {10.1016/s0167-7012(03)00042-3}, pmid = {12689714}, issn = {0167-7012}, mesh = {Animals ; Ciliophora/classification/*isolation &amp; purification ; Coloring Agents/*chemistry ; Population Dynamics ; Silver Proteins/*chemistry ; Silver Staining/*methods ; Soil/*parasitology ; Time Factors ; }, abstract = {It has been suggested that species loss from microbial groups low in diversity that occupy trophic positions close to the base of the detrital food web could be critical for terrestrial ecosystem functioning. Among the protozoans within the soil microbial loop, ciliates are presumably the least abundant and of low diversity. However, the lack of a standardized method to quantitatively enumerate and identify them has hampered our knowledge about the magnitude of their active and potential diversity, and about the interactions in which they are involved. Thus, the Edaphic Quantitative Protargol Staining (EQPS) method is provided to simultaneously account for ciliate species richness and abundance in a quantitative and qualitative way. This direct method allows this rapid and simultaneous assessment by merging the Non-flooded Petri Dish (NFPD) method [Prog. Protistol. 2 (1987) 69] and the Quantitative Protargol Stain (QPS) method [Montagnes, D.J.S., Lynn, D.H., 1993. A quantitative protargol stain (QPS) for ciliates and other protists. In: Kemp, P.F., Sherr, B.F., Sherr, E.B., Cole, J.J. (Eds.), Handbook of Methods in Aquatic Microbial Ecology. Lewis Publishers, Boca Raton, FL, pp. 229-240]. The abovementioned protocols were refined by experiments examining the spatial distribution of ciliates under natural field conditions, sampling intensity, the effect of storage, and the use of cytological preparations versus live observations. The EQPS could be useful in ecological studies since it provides both a "snapshot" of the active and effective diversity and a robust estimate of the potential diversity.}, }
@article {pmid12688705, year = {2003}, author = {Hammes, F and Seka, A and de Knijf, S and Verstraete, W}, title = {A novel approach to calcium removal from calcium-rich industrial wastewater.}, journal = {Water research}, volume = {37}, number = {3}, pages = {699-704}, doi = {10.1016/s0043-1354(02)00308-1}, pmid = {12688705}, issn = {0043-1354}, mesh = {Calcium/chemistry/*isolation &amp; purification ; Chemical Precipitation ; Hydrogen-Ion Concentration ; *Industrial Waste ; Urea/chemistry ; Water Purification/*methods ; }, abstract = {Calcium-rich wastewater is a problem for industries due to calcification during downstream processing. The potential for Ca2+ removal from industrial wastewater through ureolytic microbiological carbonate precipitation was investigated for the first time. Batch experiments were used to determine feasible urea concentrations and hydraulic retention times. These results were applied in a semi-continuous reactor system, where the emphasis was placed on the development of a calcifying sludge. Calcium removal in excess of 90% was achieved throughout the experimental period, while the effluent pH remained at a reasonable level.}, }
@article {pmid12682834, year = {2003}, author = {Münzenberger, B and Hammer, E and Wray, V and Schauer, F and Schmidt, J and Strack, D}, title = {Detoxification of ferulic acid by ectomycorrhizal fungi.}, journal = {Mycorrhiza}, volume = {13}, number = {2}, pages = {117-121}, pmid = {12682834}, issn = {0940-6360}, mesh = {Agaricales/*metabolism ; Coumaric Acids/*metabolism ; Mycorrhizae/*metabolism ; Vanillic Acid/metabolism ; }, abstract = {The ectomycorrhizal fungi Laccaria amethystina and Lactarius deterrimus grown in liquid culture were used to study the fate of added ferulic acid. Laccaria amethystina degraded ferulic acid to the major metabolite vanillic acid. The intermediate vanillin was not detected. Lactarius deterrimus showed a completely different detoxification pattern. Two dimers and one trimer of ferulic acid could be identified as polymerization products of this fungus. A bioassay of the possible biological activities of ferulic acid and vanillic acid on these fungi revealed that vanillic acid was less toxic than ferulic acid for Laccaria amethystina but that both phenolic acids were toxic for Lactarius deterrimus. The results are discussed with respect to ectomycorrhizal fungal growth in the organic layer of forest soils and between living root cells of ectomycorrhizas.}, }
@article {pmid12685705, year = {2003}, author = {Jensen, AM and Finster, KW and Karlson, U}, title = {Degradation of carbazole, dibenzothiophene, and dibenzofuran at low temperature by Pseudomonas sp. strain C3211.}, journal = {Environmental toxicology and chemistry}, volume = {22}, number = {4}, pages = {730-735}, pmid = {12685705}, issn = {0730-7268}, mesh = {Benzofurans/chemistry/*metabolism ; Biodegradation, Environmental ; Carbazoles/chemistry/*metabolism ; Carcinogens/chemistry/*metabolism ; Molecular Structure ; Pseudomonas/classification/*metabolism ; Temperature ; Thiophenes/chemistry/*metabolism ; Time Factors ; }, abstract = {Pseudomonas sp. strain C3211 was isolated from a temperate climate soil contaminated with creosote. This strain was able to degrade carbazole, dibenzothiophene and dibenzofuran at 10 degrees C with acetone as a co-substrate. When dibenzothiophene was degraded by strain C3211, an orange compound, which absorbed at 472 nm, accumulated in the medium. Degradation of dibenzofuran was followed by accumulation of a yellowish compound, absorbing at 462 nm. The temperature optimum of strain C3211 for degradation of dibenzothiophene and dibenzofuran was at 20 to 21 degrees C, while the maximum temperature for degradation was at 27 degrees C. Both compounds were degraded at 4 degrees C. Degradation at 10 degrees C was faster than degradation at 25 degrees C. This indicates that strain C3211 is adapted to life at low temperatures.}, }
@article {pmid12676551, year = {2003}, author = {Nakabachi, A and Ishikawa, H and Kudo, T}, title = {Extraordinary proliferation of microorganisms in aposymbiotic pea aphids, Acyrthosiphon pisum.}, journal = {Journal of invertebrate pathology}, volume = {82}, number = {3}, pages = {152-161}, doi = {10.1016/s0022-2011(03)00020-x}, pmid = {12676551}, issn = {0022-2011}, mesh = {Animals ; Aphids/metabolism/*microbiology ; Bacteria/*genetics/isolation &amp; purification ; Buchnera/genetics/isolation &amp; purification ; Chromatography, High Pressure Liquid ; DNA, Ribosomal/analysis ; Diet ; Fungi/*genetics/isolation &amp; purification ; Histamine/analysis ; *Phylogeny ; Polymerase Chain Reaction ; Symbiosis/physiology ; Vicia faba/*microbiology ; }, abstract = {Aposymbiotic pea aphids, which were deprived of their intracellular symbiotic bacterium, Buchnera, exhibit growth retardation and no fecundity. High performance liquid chromatographic (HPLC) analysis revealed that these aposymbiotic aphids, when reared on broad bean plants, accumulated a large amount of histamine. To assess the possibility of extraordinary proliferation of microorganisms other than Buchnera, we enumerated eubacteria and fungi in aphids using the real-time quantitative PCR method that targets genes encoding small-subunit rRNAs. The result showed that these microorganisms were extremely abundant in the aposymbiotic aphids reared on plants. Microbial communities in aposymbiotic aphids were further profiled by phylogenetic analysis of small-subunit rDNAs. Of 172 nonchimeric sequences of fungal 18S rDNAs, 138 (80.2%) belonged to the phylum Ascomycota. Among them, 21 clustered within a monophyletic group consisting of insect-pathogenic fungi and yeast-like symbionts of homopteran insects. Thirty-one (18.0%), two (1.2%), and one (0.6%) clones were clustered within the Basidiomycota, Zygomycota, and Oomycota, respectively. Of 167 nonchimeric sequences of eubacterial 16S rDNAs, 84 (50.3%) belonged to the gamma-subdivision of Proteobacteria to which most primary endosymbionts of insects and prolific histamine producers belong. Forty (24.0%), 25 (15.0%), 10 (6.0%), and five (3.0%) clones were clustered within alpha-Proteobacteria, Cytophaga-Flavobacterium-Bacteroides (CFB) group, Actinobacteria, and beta-Proteobacteria, respectively. Three had no phylogenetic association with known taxonomic divisions. None of the sequences studied in this study coincided exactly with those deposited in GenBank.}, }
@article {pmid12658525, year = {2003}, author = {Buesing, N and Gessner, MO}, title = {Incorporation of radiolabeled leucine into protein to estimate bacterial production in plant litter, sediment, epiphytic biofilms, and water samples.}, journal = {Microbial ecology}, volume = {45}, number = {3}, pages = {291-301}, doi = {10.1007/s00248-002-2036-6}, pmid = {12658525}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development/metabolism ; Bacterial Proteins/*metabolism ; Biofilms/*growth &amp; development ; Fresh Water ; Geologic Sediments/microbiology ; Leucine/*metabolism ; Plants/metabolism/microbiology ; Protein Synthesis Inhibitors/*pharmacology ; Tritium ; Water Microbiology ; }, abstract = {The present study assessed the application of tritiated leucine incorporation into protein, as a measure of bacterial biomass production, within four benthic habitats of a littoral freshwater wetland dominated by emergent vegetation. Basic assumptions underlying the method, such as linearity of leucine incorporation, saturation level of incorporation rates, and specificity of incorporation for bacterial assemblages, were tested, and two procedures for extracting radiolabeled protein were compared. TCA precipitation followed by ultrasonication, and subsequent alkaline dissolution in 0.5 M NaOH, 25 mM EDTA, and 0.1% w/v SDS, gave best results in terms of both extraction efficiency and signal-to-noise ratio. Incorporation of leucine was linear for all habitats for up to 1 h. Saturation concentrations of leucine incorporation into protein were 150 nM for littoral surface waters, >960 nM for biofilms on plant surfaces, and 50 mM for aerobic sediment and submerged plant litter. An experiment with prokaryotic and eukaryotic inhibitors designed to examine specificity of leucine incorporation into bacterial protein showed no significant leucine incorporation into eukaryotes during short-term incubations. Calculations based on kinetic parameters of fungal leucine uptake suggest, nevertheless, that significant leucine incorporation cannot be ruled out in all situations. Thus, the leucine methodology can be used for estimating bacterial production in benthic aquatic habitats, provided that substrate saturation and isotope dilution are determined and that the active biomass of eukaryotes, such as fungi, does not greatly exceed bacterial biomass.}, }
@article {pmid12658524, year = {2003}, author = {Nazaret, S and Brothier, E and Ranjard, L}, title = {Shifts in diversity and microscale distribution of the adapted bacterial phenotypes due to Hg(II) spiking in soil.}, journal = {Microbial ecology}, volume = {45}, number = {3}, pages = {259-269}, doi = {10.1007/s00248-002-2035-7}, pmid = {12658524}, issn = {0095-3628}, mesh = {Adaptation, Biological ; Base Sequence ; DNA, Bacterial/chemistry/*genetics ; DNA, Intergenic/chemistry/genetics ; Ecosystem ; Mercury/metabolism/*pharmacology ; Molecular Sequence Data ; Polymerase Chain Reaction ; Pseudomonas/*drug effects/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/chemistry/genetics ; *Soil Microbiology ; }, abstract = {In a previous experiment [Ranjard et al. (2000) FEMS Microbiol Ecol 31:107-115], the spatial heterogeneity of a mercury impact on soil bacterial community was revealed by an increase of mercury-resistant (HgR) bacterial numbers in the outer fraction and the sand fractions when compared to those in the silt fractions. The objectives of the present study were (i) to investigate whether mercury exposure affects the diversity and the distribution within the various fractions of the HgR populations and (ii) to evaluate the contribution of the HgR populations to the overall community adaptation. A total of 236 strains isolated before (104 isolates) and 30 days (132 isolates) after spiking were characterized by an amplified ribosomal DNA restriction analysis (ARDRA) and grouped into 30 different genotypes. Whereas almost the same numbers of different genotypes were observed at both sampling times when considering all microenvironments, important changes in their evenness were observed. At the microscale level, we also noticed a heterogeneous distribution of the genotypes. Partial 16S rDNA sequences of each genotype were determined to permit phylogenetic affiliation. Whereas Pseudomonas-like species were dominant in all microenvironments at T = 0, genotypes not detected before spiking such as genotypes closely related to Xanthomonas, Pseudoaminobacter, and Sphingomonas-like species became dominant at T = 30. Similarly, several genotypes close to Bacillus, Streptomyces, and Rhodococcus species were only detected in the sand fractions at T = 0 and could not be detected in these fractions at T = 30. Probes defined within the intergenic spacer between the rrs and rrl genes were designed for the dominant genotypes and were hybridized toward the RISA (Ribosomal Intergenic Spacer Analysis) profiles derived from the T = 0 and T = 30 bacterial communities associated to the unfractionated soil. Results showed that the culturable dominant HgR genotypes partially contributed to the adaptation of the whole bacterial community.}, }
@article {pmid12658523, year = {2003}, author = {Lucas, FS and Broennimann, O and Febbraro, I and Heeb, P}, title = {High diversity among feather-degrading bacteria from a dry meadow soil.}, journal = {Microbial ecology}, volume = {45}, number = {3}, pages = {282-290}, doi = {10.1007/s00248-002-2032-x}, pmid = {12658523}, issn = {0095-3628}, mesh = {Animals ; Bacteria, Aerobic/genetics/isolation &amp; purification/*metabolism ; Base Sequence ; Columbidae ; DNA, Bacterial/chemistry/genetics ; Feathers/*metabolism ; Genetic Variation ; Keratins/metabolism ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry/genetics ; *Soil Microbiology ; }, abstract = {The aim of this study was to determine the diversity of cultivable bacteria able to degrade feathers and present in soil under temperate climate. We obtained 33 isolates from soil samples, which clustered in 13 ARDRA groups. These isolates were able to grow on solid medium with pigeon feathers as sole carbon and nitrogen source. One representative isolate of each ARDRA group was selected for identification and feather degradation tests. The phylogenetic analysis of 16S rDNA gene fragments revealed that only 4 isolates were gram positives. Two other isolates belonged to the Cytophaga-Flavobacterium group, and the remaining to Proteobacteria. High keratinolysis activity was found for strains related to Bacillus, Cytophagales, Actinomycetales, and Proteobacteria. The 13 selected strains showed variable efficiency in degrading whole feathers and 5 strains were able to degrade maximum 40% to 98% of the whole feathers. After 4 weeks incubation, five strains grown on milled feathers produced more than 0.5 U keratinase per mL. Keratinase activities across the 13 strains were positively correlated with the percentage of feather fragmentation and protein concentration.}, }
@article {pmid12658522, year = {2003}, author = {Burmølle, M and Hansen, LH and Oregaard, G and Sørensen, SJ}, title = {Presence of N-acyl homoserine lactones in soil detected by a whole-cell biosensor and flow cytometry.}, journal = {Microbial ecology}, volume = {45}, number = {3}, pages = {226-236}, doi = {10.1007/s00248-002-2028-6}, pmid = {12658522}, issn = {0095-3628}, mesh = {4-Butyrolactone/*analogs &amp; derivatives/analysis/*metabolism ; Biosensing Techniques/*methods ; Escherichia coli/genetics/metabolism ; Flow Cytometry ; Green Fluorescent Proteins ; Luminescent Proteins/genetics/metabolism ; Recombinant Proteins/genetics/metabolism ; Serratia/metabolism ; *Soil Microbiology ; }, abstract = {Quorum sensing enables bacteria to regulate expression of certain genes according to population density. N-acyl homoserine lactone (AHL)-based quorum sensing is known to be widespread among gram-negative bacteria. Several bacterial whole-cell biosensors for AHL detection have been developed and some were used in in situ studies of AHL production. From these studies our knowledge of the significance of quorum sensing in various environments has been improved. However, very little is known about production of AHLs in soil environments. In the present study, an approach for detecting AHL production in bulk soil was developed. A whole-cell biosensor based on the regulatory region of the lux-operon from Vibrio fischeri fused to gfp was constructed, resulting in a luxR-PluxI-gfpmut3*-fusion in the high copy plasmid, pAHL-GFP. Escherichia coli MC4100 harboring pAHL-GFP responded to the AHL-compound N-octanoyl homoserine lactone (OHL) by expressing green fluorescence. In situ application of E. coli MC4100/pAHL-GFP was tested by adding OHL in different concentrations to sterile soil microcosms. E. coli MC4100/pAHL-GFP were incubated in the soil microcosms and extracted by an improved Nycodenz-extraction method optimized for flow cytometry. The presence of induced cells was then verified by single-cell analysis by flow cytometry. OHL concentrations between 0.5 and 50 nmol per g soil were detected. When introducing the AHL-producing Serratia liquefaciens to soil microcosms, expression of green fluorescent protein was induced in E. coli MC4100/pAHL-GFP. Thereby, the ability of this strain to detect excretion of AHLs by S. liquefaciens in sterile soil was shown. The use of an improved extraction method and a whole-cell biosensor combined with flow cytometry analysis proved to be promising tools in future studies of AHL production by microbial populations in soil environments.}, }
@article {pmid12658521, year = {2003}, author = {Orvain, F and Galois, R and Barnard, C and Sylvestre, A and Blanchard, G and Sauriau, PG}, title = {Carbohydrate production in relation to microphytobenthic biofilm development: an integrated approach in a tidal mesocosm.}, journal = {Microbial ecology}, volume = {45}, number = {3}, pages = {237-251}, doi = {10.1007/s00248-002-2027-7}, pmid = {12658521}, issn = {0095-3628}, mesh = {Biofilms/*growth &amp; development ; Carbohydrate Metabolism ; Carbohydrates/*biosynthesis ; Chlorophyll/metabolism ; Chlorophyll A ; Diatoms/growth &amp; development/*metabolism ; Ecosystem ; Geologic Sediments/*microbiology ; Photosynthesis ; Seawater ; *Water Microbiology ; }, abstract = {Experiments were performed to evaluate short-term changes in sediment extracellular carbohydrates for a multispecific assemblage of benthic diatoms in relation to physiological status, endogenous migratory rhythms, and environmental conditions. For this purpose, a mesocosm was used, which simulated both tidal and dark: light alternating cycles under controlled conditions. Scanning electronic microscopy in combination with picture analyses indicated that natural diatom migration patterns were reproduced in the mesocosm. Two EPS fractions were operationally separated in colloidal carbohydrate measurements: alcohol-soluble EPS (termed "soluble EPS") and alcohol-insoluble EPS (termed "bound EPS"). Microphytobenthic biomass followed a logistic-type curve and converged toward a maximal value termed the "biotic capacity of the local environment." Both EPS fractions showed oscillations with production during photosynthetic periods and sharp decreases during night immersion periods. Productions of both EPS fractions increased with Chl a production during light periods suggesting a light dependence in relation to migratory patterns. The decreases in both EPS fractions, which occurred during night immersion periods suggest that carbohydrate hydrolysis and/or washaway affected both EPS fractions similarly in benthic environments. Our results confirm the theory according to which the two distinct fractions are under different metabolic controls. No change in soluble EPS release was obtained during the transition from logarithmic to stationary phase. On the other hand, a metabolism modification of microalgae, probably related to ammonium depletion, occurred when cells entered the stationary phase, since there was a high enhancement in bound EPS production. Mesocosm results can serve as a system of reference useful to characterize biofilm development in field investigations and to revisit the effective implication of each EPS fraction in sediment stability.}, }
@article {pmid12658520, year = {2003}, author = {Delaney, MP}, title = {Effects of temperature and turbulence on the predator-prey interactions between a heterotrophic flagellate and a marine bacterium.}, journal = {Microbial ecology}, volume = {45}, number = {3}, pages = {218-225}, doi = {10.1007/s00248-002-1058-4}, pmid = {12658520}, issn = {0095-3628}, mesh = {Animals ; Eukaryota/*growth &amp; development ; Linear Models ; Population Dynamics ; *Predatory Behavior ; Temperature ; Vibrio/*growth &amp; development ; *Water Microbiology ; }, abstract = {Biotic and abiotic factors can influence interactions between microbial grazers and their prey, thus impacting both the cycling of biogenic carbon within the surface layer of the ocean and the export of carbon to the deep ocean and higher trophic levels. In this study, microcosm experiments were used to evaluate the combined effect of temperature and turbulence on the growth rate of a marine bacterium (Vibrio splendidus), a protistan predator (Paraphysomonas sp.), and the community grazing impact of Paraphysomonas sp. on V. splendidus. It was found that the artificial turbulence generated (1.35 x 10-1 cm2 s-3) significantly increased the rates of growth of Paraphysomonas sp. at high (>10 degrees C), but not low (<5 degrees C) temperatures, and that turbulence had no effect on the growth of V. splendidus. Both flagellate and bacterial growth were temperature dependent and decreased 4- to 6-fold as temperatures decreased from 15 to 0 degrees C. Bacterial grazing mortality by Paraphysomonas sp. was 1.3- to 2.5-fold greater in the turbulent than static treatments among all four temperatures, and the rates of cell-specific ingestion of bacteria by Paraphysomonas sp. was 2-fold greater at 15 and 10 degrees C in the turbulent than in the static treatment. Hence, this study shows that turbulence can influence nanoflagellate grazing at temperatures >5 degrees C and suggests that at low temperatures, increased viscosity may limit the size of organisms that can be affected by small-scale turbulence.}, }
@article {pmid12658519, year = {2003}, author = {Roden, EE and Wetzel, RG}, title = {Competition between Fe(III)-reducing and methanogenic bacteria for acetate in iron-rich freshwater sediments.}, journal = {Microbial ecology}, volume = {45}, number = {3}, pages = {252-258}, doi = {10.1007/s00248-002-1037-9}, pmid = {12658519}, issn = {0095-3628}, mesh = {Acetates/*metabolism ; Anaerobiosis ; Euryarchaeota/*metabolism ; Ferric Compounds/*metabolism ; Fresh Water/microbiology ; Geologic Sediments/*microbiology ; Kinetics ; *Soil Microbiology ; }, abstract = {The kinetics of acetate uptake and the depth distribution of [2-14C]acetate metabolism were examined in iron-rich sediments from a beaver impoundment in northcentral Alabama. The half-saturation constant (Km) determined for acetate uptake in slurries of Fe(III)-reducing sediment (0.8 mM) was more than 10-fold lower than that measured in methanogenic slurries (12 mM) which supported comparable rates of bulk organic carbon metabolism and Vmax values for acetate uptake. The endogenous acetate concentration (Sn) was also substantially lower (1.7 mM) in Fe(III)-reducing vs methanogenic (9.0 mM) slurries. The proportion of [2-14C]acetate converted to 14CH4 increased with depth from ca 0.1 in the upper 0.5 cm to ca 0.8 below 2 cm and was inversely correlated (r2 = 0.99) to a decline in amorphous Fe(III) oxide concentration. The results of the acetate uptake kinetics experiments suggest that differences in the affinity of Fe(III)-reducing bacteria vs methanogens for acetate can account for the preferential conversion of [2-14C]acetate to 14CO2 in Fe(III) oxide-rich surface sediments, and that the downcore increase in conversion of [2-14C]acetate to 14CH4 can be attributed to progressive liberation of methanogens from competition with Fe(III) reducers as Fe(III) oxides are depleted with depth.}, }
@article {pmid12658509, year = {2003}, author = {Ohkuma, M}, title = {Termite symbiotic systems: efficient bio-recycling of lignocellulose.}, journal = {Applied microbiology and biotechnology}, volume = {61}, number = {1}, pages = {1-9}, doi = {10.1007/s00253-002-1189-z}, pmid = {12658509}, issn = {0175-7598}, mesh = {Animals ; Cellulose/*metabolism ; Fungi/metabolism ; Isoptera/*metabolism/*microbiology/physiology ; Lignin/*metabolism ; Models, Biological ; Prokaryotic Cells/metabolism ; Soil ; Spirochaetales/growth &amp; development/metabolism ; *Symbiosis ; }, abstract = {Termites thrive in great abundance in terrestrial ecosystems and play important roles in biorecycling of lignocellulose. Together with their microbial symbionts, they efficiently decompose lignocellulose. In so-called lower termites, a dual decomposing system, consisting of the termite's own cellulases and those of its gut protists, was elucidated at the molecular level. Higher termites degrade cellulose apparently using only their own enzymes, because of the absence of symbiotic protists. Termite gut prokaryotes efficiently support lignocellulose degradation. However, culture-independent molecular studies have revealed that the majority of these gut symbionts have not yet been cultivated, and that the gut symbiotic community shows a highly structured spatial organization. In situ localization of individual populations and their functional interactions are important to understand the nature of symbioses in the gut. In contrast to cellulose, lignin degradation does not appear to be important in the gut of wood-feeding termites. Soil-feeding termites decompose humic substances in soil at least partly, but little is known about the decomposition. Fungus-growing termites are successful in the almost complete decomposition of lignocellulose in a sophisticated cooperation with basidiomycete fungi cultivated in their nest. A detailed understanding of efficient biorecycling systems, such as that for lignocellulose, and the symbioses that provide this efficiency will benefit applied microbiology and biotechnology.}, }
@article {pmid12655450, year = {2003}, author = {De Wildeman, S and Verstraete, W}, title = {The quest for microbial reductive dechlorination of C (2) to C (4) chloroalkanes is warranted.}, journal = {Applied microbiology and biotechnology}, volume = {61}, number = {2}, pages = {94-102}, doi = {10.1007/s00253-002-1174-6}, pmid = {12655450}, issn = {0175-7598}, mesh = {Alkanes/*metabolism ; Anaerobiosis ; Bacteria/growth &amp; development/*metabolism ; Biodegradation, Environmental ; Chlorine/*metabolism ; Hydrocarbons, Chlorinated/*metabolism ; Oxidation-Reduction ; }, abstract = {C (2) to C (4) chloroalkanes have been used for a wide range of industrial applications. Consequently, numerous leaks to the environment have occurred. It is generally observed that the lower chlorinated members of the group, containing 1-3 chlorine atoms, accumulate in environments where reductive conditions prevail. Their half-lives under these conditions often exceed several decades. To date, successes in rapid and complete in situ reductive dechlorination have only been obtained with tetrachloroethene (PCE) and trichloroethene (TCE), but not with chloroalkanes. Since the key-player PCE- and TCE-dechlorinating bacteria involved have been studied, these organisms could be used as very efficient tools for low-cost in situ bioremediation. Except for one 1,2-dichloroethane-dehalorespiring bacterium with limited application possibilities and a recent isolate which partly dechlorinates some polychloroethanes, all bacterial reductive conversions of C (2) to C (4) chloroalkanes are based on slow, mostly incomplete and poorly controllable cometabolic dechlorinations. Furthermore, metals such as Fe(0) cannot dechlorinate most lower-chlorinated C (2) to C (4) alkanes. Hence, pump and treat, or aerobic degradation are the applied technologies, although they are expensive and time-intensive. However, energetic consideration of chloroalkane dechlorination suggests that metabolizing anaerobes may exist. Isolation and characterization of these organisms is warranted in order to develop cost-efficient, controlled, fast and complete in situ remediation technologies.}, }
@article {pmid12642141, year = {2003}, author = {Kupferberg, ED}, title = {A field of great promise: soil bacteriology in America, 1900-1925.}, journal = {Endeavour}, volume = {27}, number = {1}, pages = {16-21}, doi = {10.1016/s0160-9327(03)00002-4}, pmid = {12642141}, issn = {0160-9327}, mesh = {Agriculture/history ; Agrochemicals/history ; Bacteriology/*history ; History, 20th Century ; *Soil Microbiology ; United States ; }, abstract = {In the first decades of the 20th century, soil bacteriologists promised to revolutionize farming practice, much in the same way that medical bacteriologists, in the previous century, had transformed pathology, public health and sanitary engineering. Following the isolation of the microorganisms responsible for nitrification and nitrogen fixation, American soil scientists anticipated the time when farmers could 'seed' their crops and lands with these beneficial bacteria. Soil bacteriologists, during the early 20th century, never fulfilled the promise of supplying a biological source of unending soil fertility. However, in their search for productive microbes, these same researchers directed attention to the underappreciated dimensions of bacterial metabolism and microbial ecology.}, }
@article {pmid12638659, year = {2003}, author = {Schneegurt, MA and Dore, SY and Kulpa, CF}, title = {Direct extraction of DNA from soils for studies in microbial ecology.}, journal = {Current issues in molecular biology}, volume = {5}, number = {1}, pages = {1-8}, pmid = {12638659}, issn = {1467-3037}, mesh = {DNA/*isolation &amp; purification ; DNA, Ribosomal/analysis/isolation &amp; purification ; *Ecology ; Electrophoresis ; *Genetic Techniques ; Soil/*analysis ; *Soil Microbiology ; }, abstract = {Molecular analyses for the study of soil microbial communities often depend on the extraction of DNA directly from soils. These extractions are by no means trivial, being complicated by humic substances that are inhibitory to PCR and restriction enzymes or being too highly colored for blot hybridization protocols. Many different published protocols exist, but none have been found to be suitable enough to be generally accepted as a standard. Most direct extraction protocols start with relatively harsh cell breakage steps such as bead-beating and freeze-thaw cycles, followed by the addition of detergents and high salt buffers and/or enzymic digestion with lysozyme and proteases. After typical organic extraction and alcohol precipitation, further purification is usually needed to remove inhibitory substances from the extract. The purification steps include size-exclusion chromatography, ion-exchange chromatography, silica gel spin columns, and cesium chloride gradients, among others. A direct DNA extraction protocol is described that has been shown to be effective in a wide variety of soil types. This protocol is experimentally compared to several published protocols.}, }
@article {pmid12636267, year = {2003}, author = {Smiejan, A and Wilkinson, KJ and Rossier, C}, title = {Cd bioaccumulation by a freshwater bacterium, Rhodospirillum rubrum.}, journal = {Environmental science &amp; technology}, volume = {37}, number = {4}, pages = {701-706}, doi = {10.1021/es025901h}, pmid = {12636267}, issn = {0013-936X}, mesh = {Cadmium/*pharmacokinetics ; Kinetics ; Rhodospirillum rubrum/*chemistry ; Water Pollutants/*pharmacokinetics ; }, abstract = {Cd bioaccumulation by Rhodospirillum rubrum, a Gram-negative freshwater bacterium, was studied in a synthetic medium. The free ion (Cd2+) was the best predictor of the Cd internalization fluxes. Representation of the short-term uptake fluxes as a function of [Cd2+] in the medium demonstrated a linear relationship, as would be expected for a rate-limiting, first-order internalization with a single transporter. Nonetheless, several different accumulation profiles were observed, depending on the Cd concentration. Cd uptake was regulated differently for concentrations above and below 10(-6) M (or was regulated only above [Cd2+] = 10(-6) M). Short-and long-term studies revealed that regulation was rapidly initiated for the highest Cd concentrations examined, effectively decreasing both adsorbed and internalized Cd. Anodic stripping voltammetry demonstrated that a Cd complexing ligand was produced within minutes upon exposure to 5 x 10(-6) M Cd2+ and that an extracellular sequestration of Cd was one mechanism regulating Cd uptake. Competition studies with other cations revealed a competitive inhibition of Cd uptake by Zn and an uptake enhancement in the presence of Mn and Cu.}, }
@article {pmid12635734, year = {2003}, author = {Coleman, ME and Sandberg, S and Anderson, SA}, title = {Impact of microbial ecology of meat and poultry products on predictions from exposure assessment scenarios for refrigerated storage.}, journal = {Risk analysis : an official publication of the Society for Risk Analysis}, volume = {23}, number = {1}, pages = {215-228}, doi = {10.1111/1539-6924.00301}, pmid = {12635734}, issn = {0272-4332}, mesh = {Animals ; Colony Count, Microbial ; Escherichia coli O157/growth &amp; development ; *Food Microbiology ; Humans ; Listeria monocytogenes/growth &amp; development ; Meat/*microbiology ; Models, Biological ; Poultry/*microbiology ; Refrigeration ; Risk Assessment ; Safety ; Salmonella/growth &amp; development ; }, abstract = {A novel extension of traditional growth models for exposure assessment of food-borne microbial pathogens was developed to address the complex interactions of competing microbial populations in foods. Scenarios were designed for baseline refrigeration and mild abuse of servings of chicken broiler and ground beef Our approach employed high-quality data for microbiology of foods at production, refrigerated storage temperatures, and growth kinetics of microbial populations in culture media. Simple parallel models were developed for exponential growth of multiple pathogens and the abundant and ubiquitous nonpathogenic indigenous microbiota. Monte Carlo simulations were run for unconstrained growth and growth with the density-dependent constraint based on the "Jameson effect," inhibition of pathogen growth when the indigenous microbiota reached 10(9) counts per serving. The modes for unconstrained growth of the indigenous microbiota were 10(8), 10(10), and 10(11) counts per serving for chicken broilers, and 10(7), 10(9) and 10(11) counts per serving for ground beef at respective sites for backroom, meat case, and home refrigeration. Contamination rates and likelihoods of reaching temperatures supporting growth of the pathogens in the baseline refrigeration scenario were rare events. The unconstrained exponential growth models appeared to overestimate L. monocytogenes growth maxima for the baseline refrigeration scenario by 1500-7233% (10(6)-10(7) counts/serving) when the inhibitory effects of the indigenous microbiota are ignored. The extreme tails of the distributions for the constrained models appeared to overestimate growth maxima 110% (10(4)-10(5) counts/serving) for Salmonella spp. and 108% (6 x 10(3) counts/serving) for E. coli O157:H7 relative to the extremes of the unconstrained models. The approach of incorporating parallel models for pathogens and the indigenous microbiota into exposure assessment modeling motivates the design of validation studies to test the modeling assumptions, consistent with the analytical-deliberative process of risk analysis.}, }
@article {pmid12635732, year = {2003}, author = {Ross, T and McMeekin, TA}, title = {Modeling microbial growth within food safety risk assessments.}, journal = {Risk analysis : an official publication of the Society for Risk Analysis}, volume = {23}, number = {1}, pages = {179-197}, doi = {10.1111/1539-6924.00299}, pmid = {12635732}, issn = {0272-4332}, mesh = {Bacteria/growth &amp; development/pathogenicity ; Ecosystem ; *Food Microbiology ; Fungi/growth &amp; development/pathogenicity ; Humans ; Models, Biological ; Risk Assessment ; Safety ; Time Factors ; }, abstract = {Risk estimates for food-borne infection will usually depend heavily on numbers of microorganisms present on the food at the time of consumption. As these data are seldom available directly, attention has turned to predictive microbiology as a means of inferring exposure at consumption. Codex guidelines recommend that microbiological risk assessment should explicitly consider the dynamics of microbiological growth, survival, and death in foods. This article describes predictive models and resources for modeling microbial growth in foods, and their utility and limitations in food safety risk assessment. We also aim to identify tools, data, and knowledge sources, and to provide an understanding of the microbial ecology of foods so that users can recognize model limits, avoid modeling unrealistic scenarios, and thus be able to appreciate the levels of confidence they can have in the outputs of predictive microbiology models. The microbial ecology of foods is complex. Developing reliable risk assessments involving microbial growth in foods will require the skills of both microbial ecologists and mathematical modelers. Simplifying assumptions will need to be made, but because of the potential for apparently small errors in growth rate to translate into very large errors in the estimate of risk, the validity of those assumptions should be carefully assessed. Quantitative estimates of absolute microbial risk within narrow confidence intervals do not yet appear to be possible. Nevertheless, the expression of microbial ecology knowledge in "predictive microbiology" models does allow decision support using the tools of risk assessment.}, }
@article {pmid12632213, year = {2003}, author = {Cavicchioli, R and Ostrowski, M and Fegatella, F and Goodchild, A and Guixa-Boixereu, N}, title = {Life under nutrient limitation in oligotrophic marine environments: an eco/physiological perspective of Sphingopyxis alaskensis (formerly Sphingomonas alaskensis).}, journal = {Microbial ecology}, volume = {45}, number = {3}, pages = {203-217}, doi = {10.1007/s00248-002-3008-6}, pmid = {12632213}, issn = {0095-3628}, mesh = {Alaska ; DNA, Bacterial/genetics ; *Ecosystem ; North Sea ; Pacific Ocean ; Sphingomonas/genetics/*physiology/ultrastructure ; *Water Microbiology ; }, abstract = {The oceans of the world are nutrient-limited environments that support a dynamic diversity of microbial life. Heterotrophic prokaryotes proliferate in oligotrophic regions and affect nutrient transformation and remineralization thereby impacting directly on the all marine biota. An important challenge in studying the microbial ecology of oligotrophic environments has been the isolation of ecologically important species. This goal has been recognized not only for its relevance in defining the dynamics of community composition, but for enabling physiological studies of competitive species and inferring their impact on the microbial food web. This review describes the successful isolation attempts of the ultramicrobacterium, Sphingopyxis alaskensis (formerly described as Sphingomonas alaskensis) using extinction dilution culturing methods. It then provides a comprehensive perspective of the unique physiological and genetic properties that have been identified that distinguish it from typical copiotrophic species. These properties are described through studies of the growth phase and growth rate control of macromolecular synthesis, stress resistance and global gene expression (proteomics). We also discuss the importance of integrating ecological and physiological approaches for studying microorganisms in marine environments.}, }
@article {pmid12632212, year = {2003}, author = {Garbeva, P and van Veen, JA and van Elsas, JD}, title = {Predominant Bacillus spp. in agricultural soil under different management regimes detected via PCR-DGGE.}, journal = {Microbial ecology}, volume = {45}, number = {3}, pages = {302-316}, doi = {10.1007/s00248-002-2034-8}, pmid = {12632212}, issn = {0095-3628}, mesh = {Bacillus/*classification/genetics ; Base Sequence ; Cloning, Molecular ; DNA, Bacterial/chemistry/genetics ; Electrophoresis ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; *Soil Microbiology ; }, abstract = {A PCR system for studying the diversity of species of Bacillus and related taxa directly from soil was developed. For this purpose, a specific 24-bp forward primer located around position 110 of the 16S ribosomal RNA gene was designed and combined with a reverse bacterial primer located at the end of the gene. The specificity of this PCR system for bacilli and related taxons was confirmed on the basis of tests with diverse strains as well as with soil DNA. Analysis of a soil DNA derived clone library showed that the amplified fragments affiliated exclusively with sequences of gram-positive bacteria, with up to 95% of the sequences originating from putative Bacillus species. In particular, sequences affiliated to those of B. mycoides, B. pumilus, B. megaterium, B. thuringiensis, and B. firmus, as well as to related taxa such as Paenibacillus, were obtained. A minority, i.e., less than 6%, of the clones affiliated with other gram-positive bacteria, such as Arthrobacter spp., Frankia spp., and uncultured gram-positives. The amplified fragments were used as templates for a second PCR using bacterial 16S rDNA primers, yielding PCR products of about 410 bp, which were separated by denaturing gradient gel electrophoresis (DGGE). Amplicons indicating Bacillus spp. were found in the gel between 45% and roughly 60% denaturant, whereas those representing other, high-G+C% bacteria, were localized in gel regions with denaturant concentrations exceeding about 60%, thus allowing the distinction between these two groups of sequences. We applied this system to compare the group-specific diversity in bacterial communities in an agricultural soil under different regimes, i.e., permanent grassland, grassland recently turned to arable land, and arable land under agricultural rotation. Differences in the Bacillus-related community structures between the treatments were clearly detected. Higher diversities, as judged by Shannon-Weaver indices calculated on the basis of the molecular profiles, were consistently observed in the permanent grassland and the grassland turned into arable land, as compared to the arable land.}, }
@article {pmid12632211, year = {2003}, author = {Lyons, JI and Newell, SY and Buchan, A and Moran, MA}, title = {Diversity of ascomycete laccase gene sequences in a southeastern US salt marsh.}, journal = {Microbial ecology}, volume = {45}, number = {3}, pages = {270-281}, doi = {10.1007/s00248-002-1055-7}, pmid = {12632211}, issn = {0095-3628}, mesh = {Amino Acid Sequence ; Ascomycota/*enzymology/genetics ; Base Sequence ; DNA, Fungal/chemistry/*genetics ; Ecosystem ; Genetic Variation ; Georgia ; Laccase ; Molecular Sequence Data ; Oxidoreductases/chemistry/*genetics ; Phylogeny ; Poaceae/microbiology ; Sequence Alignment ; }, abstract = {The diversity of ascomycete laccase sequences was surveyed in a southeastern US salt marsh using a degenerate primer set designed around copper binding sites conserved in fungal laccases. This gene was targeted for diversity analysis because of its potential function in lignin degradation in the salt marsh ecosystem and because few studies have assessed functional gene diversity in natural fungal communities. Laccase sequences were amplified from genomic DNA extracted from 24 isolates (representing 10 ascomycete species) cultured from decaying blades of Spartina alterniflora, and from DNA extracted directly from the decaying blades. Among the ascomycete isolates, 21 yielded a PCR product of expected size (900 bp) that was tentatively identified as laccase based on sequence similarities to previously published laccase sequences from related organisms. Overall, 13 distinct sequence types, containing 39 distinct sequences, were identified among the isolates, with several species yielding multiple distinct laccase types. PCR amplifications from early and late decay blades of S. alterniflora yielded seven laccase types. Of these, five were composed of sequences >96% similar at the amino acid level to sequences from three cultured ascomycetes previously found to be dominant members of the fungal communities on decaying S. alterniflora blades. Two of the laccase types from the natural-decay clone library were novel and did not match any of the sequences obtained from the cultured ascomycetes. The 39 distinct sequences and 15 distinct laccase sequence types retrieved from the S. alterniflora decay system demonstrate high sequence diversity of this functional gene in a natural fungal community.}, }
@article {pmid12620840, year = {2003}, author = {Dejonghe, W and Berteloot, E and Goris, J and Boon, N and Crul, K and Maertens, S and Höfte, M and De Vos, P and Verstraete, W and Top, EM}, title = {Synergistic degradation of linuron by a bacterial consortium and isolation of a single linuron-degrading variovorax strain.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {3}, pages = {1532-1541}, pmid = {12620840}, issn = {0099-2240}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; P20 RR 16448-01/RR/NCRR NIH HHS/United States ; }, mesh = {Betaproteobacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Culture Media ; *Ecosystem ; Herbicides/*metabolism ; Linuron/*metabolism ; Molecular Sequence Data ; Pseudomonas/*metabolism ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {The bacterial community composition of a linuron-degrading enrichment culture and the role of the individual strains in linuron degradation have been determined by a combination of methods, such as denaturing gradient gel electrophoresis of the total 16S rRNA gene pool, isolation and identification of strains, and biodegradation assays. Three strains, Variovorax sp. strain WDL1, Delftia acidovorans WDL34, and Pseudomonas sp. strain WDL5, were isolated directly from the linuron-degrading culture. In addition, subculture of this enrichment culture on potential intermediates in the degradation pathway of linuron (i.e., N,O-dimethylhydroxylamine and 3-chloroaniline) resulted in the isolation of, respectively, Hyphomicrobium sulfonivorans WDL6 and Comamonas testosteroni WDL7. Of these five strains, only Variovorax sp. strain WDL1 was able to use linuron as the sole source of C, N, and energy. WDL1 first converted linuron to 3,4-dichloroaniline (3,4-DCA), which transiently accumulated in the medium but was subsequently degraded. To the best of our knowledge, this is the first report of a strain that degrades linuron further than the aromatic intermediates. Interestingly, the rate of linuron degradation by strain WDL1 was lower than that for the consortium, but was clearly increased when WDL1 was coinoculated with each of the other four strains. D. acidovorans WDL34 and C. testosteroni WDL7 were found to be responsible for degradation of the intermediate 3,4-DCA, and H. sulfonivorans WDL6 was the only strain able to degrade N,O-dimethylhydroxylamine. The role of Pseudomonas sp. strain WDL5 needs to be further elucidated. The degradation of linuron can thus be performed by a single isolate, Variovorax sp. strain WDL1, but is stimulated by a synergistic interaction with the other strains isolated from the same linuron-degrading culture.}, }
@article {pmid12620837, year = {2003}, author = {Boon, N and Top, EM and Verstraete, W and Siciliano, SD}, title = {Bioaugmentation as a tool to protect the structure and function of an activated-sludge microbial community against a 3-chloroaniline shock load.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {3}, pages = {1511-1520}, pmid = {12620837}, issn = {0099-2240}, mesh = {Ammonia/*metabolism ; Aniline Compounds/*metabolism ; Bacteria/classification/genetics/*growth &amp; development/*metabolism ; *Bioreactors ; Cluster Analysis ; Comamonas testosteroni/*metabolism ; DNA, Ribosomal/analysis ; Electrophoresis/methods ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Oxidation-Reduction ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; Waste Disposal, Fluid ; }, abstract = {Bioaugmentation of bioreactors focuses on the removal of xenobiotics, with little attention typically paid to the recovery of disrupted reactor functions such as ammonium-nitrogen removal. Chloroanilines are widely used in industry as a precursor to a variety of products and are occasionally released into wastewater streams. This work evaluated the effects on activated-sludge reactor functions of a 3-chloroaniline (3-CA) pulse and bioaugmentation by inoculation with the 3-CA-degrading strain Comamonas testosteroni I2 gfp. Changes in functions such as nitrification, carbon removal, and sludge compaction were studied in relation to the sludge community structure, in particular the nitrifying populations. Denaturing gradient gel electrophoresis (DGGE), real-time PCR, and fluorescent in situ hybridization (FISH) were used to characterize and enumerate the ammonia-oxidizing microbial community immediately after a 3-CA shock load. Two days after the 3-CA shock, ammonium accumulated, and the nitrification activity did not recover over a 12-day period in the nonbioaugmented reactors. In contrast, nitrification in the bioaugmented reactor started to recover on day 4. The DGGE patterns and the FISH and real-time PCR data showed that the ammonia-oxidizing microbial community of the bioaugmented reactor recovered in structure, activity, and abundance, while the number of ribosomes of the ammonia oxidizers in the nonbioaugmented reactor decreased drastically and the community composition changed and did not recover. The settleability of the activated sludge was negatively influenced by the 3-CA addition, with the sludge volume index increasing by a factor of 2.3. Two days after the 3-CA shock in the nonbioaugmented reactor, chemical oxygen demand (COD) removal efficiency decreased by 36% but recovered fully by day 4. In contrast, in the bioaugmented reactor, no decrease of the COD removal efficiency was observed. This study demonstrates that bioaugmentation of wastewater reactors to accelerate the degradation of toxic chlorinated organics such as 3-CA protected the nitrifying bacterial community, thereby allowing faster recovery from toxic shocks.}, }
@article {pmid12620635, year = {2003}, author = {McHugh, S and Carton, M and Mahony, T and O'Flaherty, V}, title = {Methanogenic population structure in a variety of anaerobic bioreactors.}, journal = {FEMS microbiology letters}, volume = {219}, number = {2}, pages = {297-304}, doi = {10.1016/S0378-1097(03)00055-7}, pmid = {12620635}, issn = {0378-1097}, mesh = {Anaerobiosis ; Bacteria, Anaerobic/classification/genetics/isolation &amp; purification ; Biomass ; *Bioreactors ; Euryarchaeota/classification/genetics/growth &amp; development/*isolation &amp; purification ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sewage/*microbiology ; }, abstract = {The methanogenic community structures of six anaerobic sludges were examined using culture-independent techniques. The sludges were obtained from full-scale and laboratory-scale bioreactors, treating a variety of low- and high-strength, simple and complex wastewaters at psychrophilic (10-14 degrees C), mesophilic (37 degrees C) and thermophilic (55 degrees C) temperatures. Amplified rDNA restriction analysis identified 18 methanogenic operational taxonomic units in the six samples. 16S rRNA gene sequencing and phylogenetic reconstruction demonstrated that five separate groups of methanogens were represented with Methanosaeta-like species dominant in all sludges, but particularly in samples from a psychrophilic bioreactor treating low-strength synthetic sewage (75% of all clones detected).}, }
@article {pmid12618045, year = {2003}, author = {Philips, S and Rabaey, K and Verstraete, W}, title = {Impact of iron salts on activated sludge and interaction with nitrite or nitrate.}, journal = {Bioresource technology}, volume = {88}, number = {3}, pages = {229-239}, doi = {10.1016/s0960-8524(02)00314-0}, pmid = {12618045}, issn = {0960-8524}, mesh = {Biodegradation, Environmental ; Bioreactors ; Chemical Precipitation ; Hydrogen-Ion Concentration ; Iron/*chemistry/metabolism ; Nitrates/*chemistry/metabolism ; Nitrites/*chemistry/metabolism ; Phosphates/metabolism ; Sewage/*chemistry/microbiology ; Water Pollutants/metabolism ; }, abstract = {Iron salts are often used in activated sludge treatment plants as coagulants or to improve reactor performance. Previous studies have indicated that iron itself has an impact on the activated sludge process. However, the interaction of iron with nitrite or nitrate present in the sludge has received little attention. In this research, the influence of addition of Fe(II) or Fe(III), alone or together with NO(2)(-) or NO(3)(-) on bench-scale activated sludge reactors was examined. Large differences were established between the distinct treatments, regarding reactor performance, sludge characteristics as well as microbial community. Ferric iron was more detrimental than ferrous iron. In some cases, nitrite was found to enhance inhibitory effects of the added iron, whereas nitrate had more a neutralizing effect. It was found that precipitation of phosphate by the iron was not responsible for the observed inhibition. Decrease in pH upon formation of iron hydroxides and the impairment of the floc structure could partially explain the toxicity of the iron dosages. The formation of toxic nitrogen oxides, such as nitric oxide, can also be of importance. The observed positive effect of nitrate on the floc activity is of interest and warrants further elucidation.}, }
@article {pmid12604982, year = {2003}, author = {Agarwal, R and Sharma, N and Chaudhry, R and Deorari, A and Paul, VK and Gewolb, IH and Panigrahi, P}, title = {Effects of oral Lactobacillus GG on enteric microflora in low-birth-weight neonates.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {36}, number = {3}, pages = {397-402}, doi = {10.1097/00005176-200303000-00019}, pmid = {12604982}, issn = {0277-2116}, support = {TW-00601/TW/FIC NIH HHS/United States ; }, mesh = {Administration, Oral ; Age Factors ; Colony Count, Microbial ; Digestive System/*microbiology ; Female ; Gestational Age ; Gram-Negative Bacteria/*growth &amp; development ; Gram-Positive Bacteria/*growth &amp; development ; Humans ; Infant, Low Birth Weight ; Infant, Newborn ; *Infant, Very Low Birth Weight ; Lactobacillus/growth &amp; development/*physiology ; Male ; *Probiotics ; Prospective Studies ; }, abstract = {BACKGROUND: Colonization patterns, especially by anaerobic flora, may play an important role in neonatal gut function. Probiotics could affect disease risk either directly through colonization or indirectly by promoting changes in gut microbial ecology.<br><br>METHODS: To study the ability of Lactobacillus GG(LGG) to colonize the neonatal gut and modify its microbial ecology, a prospective, randomized study was performed in 71 preterm infants of less than 2000 g birth weight. Infants less than 1500 g (24 treated, 15 control) received 10(9) LGG orally twice daily for 21 days. Those infants weighing 1500 to 1999 g (23 treated, 9 control) were treated for 8 days. Stools were collected before treatment and on day 7 to 8 (and day 14 and 21, in the infants weighing less than 1500 g) for quantitative aerobic and anaerobic cultures.<br><br>RESULTS: Colonization with LGG occurred in 5 of 24 (21%) infants who weighed less than 1500 g versus 11 of 23 (47%) in larger infants. Colonization was limited to infants who were not on antibiotics within 7 days of treatment with LGG. There was a paucity of bacterial species at baseline, although larger infants had more bacterial species (1.59 +/- 0.13 (SEM) vs 1.11 +/- 0.12; P < 0.03) and higher mean log colony forming units (CFU) (8.79 +/- 0.43 vs 7.22 +/- 0.63; P < 0.05) compared with infants weighing less than 1500 g LGG. Treatment in infants weighing less than 1500 g resulted in a significant increase in species number by day 7, with further increases by day 21. This increase was mainly the result of increased Gram (+) and anaerobic species. No difference in species number was noted in controls. Mean log CFU of Gram (-) bacteria did not change in treated infants weighing less than 1500 g. However, Gram (+) mean log CFU showed a significant increase on day 21 (6.1 +/- 0.9) compared with day 0 (3.5 +/- 0.9) (P < 0.05). No significant changes in species number or quantitative counts were noted after LGG treatment in the infants weighing 1500 to 1999 g LGG was well tolerated in all infants.<br><br>CONCLUSION: The neonatal response to a probiotic preparation is dependent on gestational and post-natal age and prior antibiotic exposure. Although LGG is a relatively poor colonizer in infants, especially those infants weighing less than 1500 g at birth, it does appear to affect neonatal intestinal colonization patterns.}, }
@article {pmid12583719, year = {2002}, author = {Wirth, S and Ulrich, A}, title = {Cellulose-degrading potentials and phylogenetic classification of carboxymethyl-cellulose decomposing bacteria isolated from soil.}, journal = {Systematic and applied microbiology}, volume = {25}, number = {4}, pages = {584-591}, doi = {10.1078/07232020260517724}, pmid = {12583719}, issn = {0723-2020}, mesh = {Base Sequence ; Biodegradation, Environmental ; Carboxymethylcellulose Sodium/*metabolism ; Cellulose/chemistry/classification/*metabolism ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S ; *Soil Microbiology ; Streptomyces/*classification/genetics/isolation &amp; purification/metabolism ; }, abstract = {In a previous study, culturable carboxymethyl-cellulose (CMC) decomposing soil bacteria isolated from different sampling positions across an agricultural encatchment have been classified into 31 pattern groups by digestion of amplified 16S rDNA using a single restriction enzyme (Ulrich and Wirth: Microb. Ecol. 37, 238-247, 1999). In order to reveal relationships between phylogenetic diversity and phenotypic functions, a further differentiation of two selected site-specific pattern groups (I and H) was performed, resulting in a sub-classification of four and three ARDRA groups, respectively. Based on sequencing a representative isolate of each ARDRA group, the isolates were assigned to the genus Streptomyces. The ARDRA groups were dispersed across various clades of the genus with a direct affiliation to species known for cellulolytic activity in one group, only. The isolates differed in potentials to degrade colloidal, native or highly crystalline cellulose derivatives. Out of 39 isolates, 11 were capable of degrading all substrates, 17 were restricted to degrade CMC only, and 11 were active decomposers of exclusively both CMC and colloidal cellulose. In most cases, the genetic classification of the isolates corresponded with groupings based on cellulose degrading capabilities. Thus, isolates of four ARDRA groups were restricted to the degradation of CMC, while two further isolates which efficiently degraded all cellulose derivatives formed two separate ARDRA groups. The major ARDRA group, however; displayed a high variability of degradation capabilities. The study of additional phenotypic features revealed a broad potential to decompose a set of various carbon substrates, which matched the phylogenetic classification in several cases.}, }
@article {pmid12571043, year = {2003}, author = {Taroncher-Oldenburg, G and Griner, EM and Francis, CA and Ward, BB}, title = {Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {2}, pages = {1159-1171}, pmid = {12571043}, issn = {0099-2240}, mesh = {Bacteria/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; DNA, Bacterial/analysis ; Ecosystem ; Fresh Water/*microbiology ; *Gene Expression Profiling ; Nitrite Reductases/genetics/metabolism ; Nitrogen/*metabolism ; *Oligonucleotide Array Sequence Analysis ; Oligonucleotide Probes ; Seawater/*microbiology ; }, abstract = {The analysis of functional diversity and its dynamics in the environment is essential for understanding the microbial ecology and biogeochemistry of aquatic systems. Here we describe the development and optimization of a DNA microarray method for the detection and quantification of functional genes in the environment and report on their preliminary application to the study of the denitrification gene nirS in the Choptank River-Chesapeake Bay system. Intergenic and intragenic resolution constraints were determined by an oligonucleotide (70-mer) microarray approach. Complete signal separation was achieved when comparing unrelated genes within the nitrogen cycle (amoA, nifH, nirK, and nirS) and detecting different variants of the same gene, nirK, corresponding to organisms with two different physiological modes, ammonia oxidizers and denitrifying halobenzoate degraders. The limits of intragenic resolution were investigated with a microarray containing 64 nirS sequences comprising 14 cultured organisms and 50 clones obtained from the Choptank River in Maryland. The nirS oligonucleotides covered a range of sequence identities from approximately 40 to 100%. The threshold values for specificity were determined to be 87% sequence identity and a target-to-probe perfect match-to-mismatch binding free-energy ratio of 0.56. The lower detection limit was 10 pg of DNA (equivalent to approximately 10(7) copies) per target per microarray. Hybridization patterns on the microarray differed between sediment samples from two stations in the Choptank River, implying important differences in the composition of the denitirifer community along an environmental gradient of salinity, inorganic nitrogen, and dissolved organic carbon. This work establishes a useful set of design constraints (independent of the target gene) for the implementation of functional gene microarrays for environmental applications.}, }
@article {pmid12571013, year = {2003}, author = {Blackwood, CB and Marsh, T and Kim, SH and Paul, EA}, title = {Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {2}, pages = {926-932}, pmid = {12571013}, issn = {0099-2240}, mesh = {Bacteria/*classification/genetics ; *Bioreactors ; Cluster Analysis ; Crops, Agricultural ; *Data Interpretation, Statistical ; Medicago sativa/growth &amp; development ; *Polymorphism, Restriction Fragment Length ; Sensitivity and Specificity ; *Soil Microbiology ; Statistics as Topic/methods ; Zea mays/growth &amp; development ; }, abstract = {Terminal restriction fragment length polymorphism (T-RFLP) is a culture-independent method of obtaining a genetic fingerprint of the composition of a microbial community. Comparisons of the utility of different methods of (i) including peaks, (ii) computing the difference (or distance) between profiles, and (iii) performing statistical analysis were made by using replicated profiles of eubacterial communities. These samples included soil collected from three regions of the United States, soil fractions derived from three agronomic field treatments, soil samples taken from within one meter of each other in an alfalfa field, and replicate laboratory bioreactors. Cluster analysis by Ward's method and by the unweighted-pair group method using arithmetic averages (UPGMA) were compared. Ward's method was more effective at differentiating major groups within sets of profiles; UPGMA had a slightly reduced error rate in clustering of replicate profiles and was more sensitive to outliers. Most replicate profiles were clustered together when relative peak height or Hellinger-transformed peak height was used, in contrast to raw peak height. Redundancy analysis was more effective than cluster analysis at detecting differences between similar samples. Redundancy analysis using Hellinger distance was more sensitive than that using Euclidean distance between relative peak height profiles. Analysis of Jaccard distance between profiles, which considers only the presence or absence of a terminal restriction fragment, was the most sensitive in redundancy analysis, and was equally sensitive in cluster analysis, if all profiles had cumulative peak heights greater than 10,000 fluorescence units. It is concluded that T-RFLP is a sensitive method of differentiating between microbial communities when the optimal statistical method is used for the situation at hand. It is recommended that hypothesis testing be performed by redundancy analysis of Hellinger-transformed data and that exploratory data analysis be performed by cluster analysis using Ward's method to find natural groups or by UPGMA to identify potential outliers. Analyses can also be based on Jaccard distance if all profiles have cumulative peak heights greater than 10,000 fluorescence units.}, }
@article {pmid12568064, year = {2002}, author = {Guerrero, R}, title = {Microbial ecology comes of age.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {5}, number = {4}, pages = {157-159}, doi = {10.1007/s10123-002-0093-9}, pmid = {12568064}, issn = {1139-6709}, mesh = {Bacterial Physiological Phenomena ; Bioterrorism/trends ; *Ecology ; *Environmental Microbiology ; }, }
@article {pmid12560989, year = {2003}, author = {Garcia-Gil, LJ and Gich, FB and Fuentes-Garcia, X}, title = {A comparative study of bchG from green photosynthetic bacteria.}, journal = {Archives of microbiology}, volume = {179}, number = {2}, pages = {108-115}, doi = {10.1007/s00203-002-0506-3}, pmid = {12560989}, issn = {0302-8933}, mesh = {Amino Acid Sequence ; Bacteria/*classification/*enzymology/genetics ; Bacteriochlorophylls/analysis/biosynthesis/genetics ; Carbon-Oxygen Ligases/*genetics ; Chlorobi/*classification/*enzymology/genetics ; Esterases/genetics ; Evolution, Molecular ; Genes, Bacterial ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; }, abstract = {The gene bchG, coding for bacteriochlorophyll a synthase from a variety of green sulfur bacteria and the filamentous anoxygenic phototrophic bacteria, Chloroflexus aurantiacus, Chloronema sp., and Roseiflexus castenholzii HL08, was partially sequenced and compared. The deduced amino acid consensus sequences for green sulfur bacteria and green filamentous anoxygenic phototrophic bacteria were found to belong to the UbiA enzyme family of polyprenyltransferases with the most similar sequences being those of photosynthetic organisms. All deduced amino acid sequences showed a highly conserved region, which includes the motif DRXXD, characteristic of polyprenyltransferases, which was extended to DREVDAINEP for green sulfur bacteria. Neighbor-joining analysis of a protein similitude matrix displayed a relatively high distance between green sulfur bacteria and the other groups. Sequences from green sulfur bacteria were more closely related to those of purple bacteria than to those of filamentous anoxygenic phototrophic bacteria. In addition, internal grouping within green sulfur bacteria was congruent regarding taxonomic features including cell shape, presence of gas vacuoles and NaCl requirement. In addition to bchlG, another gene encoding for a second chlorophyll synthetase, previously tentatively identified as chlG, was also found in Chlorobium tepidum, showing the highest similarities with polyprenyltransferases from chlorophyll- a-containing organisms.}, }
@article {pmid12548285, year = {2003}, author = {Hooper, LV and Stappenbeck, TS and Hong, CV and Gordon, JI}, title = {Angiogenins: a new class of microbicidal proteins involved in innate immunity.}, journal = {Nature immunology}, volume = {4}, number = {3}, pages = {269-273}, doi = {10.1038/ni888}, pmid = {12548285}, issn = {1529-2908}, support = {DK02954/DK/NIDDK NIH HHS/United States ; DK30292/DK/NIDDK NIH HHS/United States ; P30 DK52574/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteroides/immunology ; Humans ; Immunity, Innate/*physiology ; Mice ; Molecular Sequence Data ; Organ Specificity ; Paneth Cells/metabolism/physiology ; Ribonuclease, Pancreatic/*immunology/physiology ; }, abstract = {Although angiogenins have been implicated in tumor-associated angiogenesis, their normal physiologic function remains unclear. We show that a previously uncharacterized angiogenin, Ang4, is produced by mouse Paneth cells, is secreted into the gut lumen and has bactericidal activity against intestinal microbes. Ang4 expression is induced by Bacteroides thetaiotaomicron, a predominant member of the gut microflora, revealing a mechanism whereby intestinal commensal bacteria influence gut microbial ecology and shape innate immunity. Furthermore, mouse Ang1 and human angiogenin, circulating proteins induced during inflammation, exhibit microbicidal activity against systemic bacterial and fungal pathogens, suggesting that they contribute to systemic responses to infection. These results establish angiogenins as a family of endogenous antimicrobial proteins.}, }
@article {pmid12545316, year = {2003}, author = {Kis-Papo, T and Oren, A and Wasser, SP and Nevo, E}, title = {Survival of filamentous fungi in hypersaline Dead Sea water.}, journal = {Microbial ecology}, volume = {45}, number = {2}, pages = {183-190}, doi = {10.1007/s00248-002-3006-8}, pmid = {12545316}, issn = {0095-3628}, mesh = {Fungi/*growth &amp; development ; Israel ; Mycelium/growth &amp; development/metabolism ; Oceans and Seas ; Seawater/*microbiology ; Spores, Fungal/growth &amp; development/metabolism ; Water Microbiology ; }, abstract = {A variety of filamentous fungi have recently been isolated from the Dead Sea (340 g/L total dissolved salts). To assess the extent to which such fungi can survive for prolonged periods in Dead Sea water, we examined the survival of both spores and mycelia in undiluted Dead Sea water and in Dead Sea water diluted to different degrees with distilled water. Mycelia of Aspergillus versicolor and Chaetomium globosum strains isolated from the Dead Sea remained viable for up to 8 weeks in undiluted Dead Sea water. Four Dead Sea isolates (A. versicolor, Eurotium herbariorum, Gymnascella marismortui, and C. globosum) retained their viability in Dead Sea water diluted to 80% during the 12 weeks of the experiment. Mycelia of all species survived for the full term of the experiment in Dead Sea water diluted to 50% and 10% of its original salinity. Comparison of the survival of Dead Sea species and closely related isolates obtained from other locations showed prolonged viability of the strains obtained from the Dead Sea. Spores of isolates obtained from the terrestrial shore of the Dead Sea generally proved less tolerant to suspension in undiluted Dead Sea water than spores of species isolated from the water column. Spores of the species isolated from the control sites had lost their viability in undiluted Dead Sea water within 12 weeks. However, with the exception of Emericella spores, which showed poor survival, a substantial fraction of the spores of Dead Sea fungal isolates remained viable for that period. The difference in survival rate between spores and mycelia of isolates of the same species points to the existence of adapted halotolerant and/or halophilic fungi in the Dead Sea.}, }
@article {pmid12545315, year = {2003}, author = {Mille-Lindblom, C and Tranvik, LJ}, title = {Antagonism between bacteria and fungi on decomposing aquatic plant litter.}, journal = {Microbial ecology}, volume = {45}, number = {2}, pages = {173-182}, doi = {10.1007/s00248-002-2030-z}, pmid = {12545315}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development/metabolism ; Biomass ; Fungi/*growth &amp; development/metabolism ; Poaceae/metabolism/*microbiology ; Water Microbiology ; }, abstract = {Bacterial and fungal decomposers of aquatic plant litter may exhibit either synergistic or antagonistic interactions, which are likely to influence microbial growth as well as the decomposition of litter and, eventually, the carbon metabolism of aquatic systems. To elucidate such interactions, we inoculated decomposing Phragmites culms in microcosms with fungal isolates and with natural communities of bacteria and fungi in different combinations. The development of fungal and bacterial biomass and the carbon dynamics were studied during several months of degradation. The results show a bilateral antagonistic relationship between bacteria and fungi. After 3 months, fungal biomass accumulation was approximately 12 times higher in the absence than in the presence of bacteria. Bacterial biomass accumulation was about double in the absence of fungi compared to when fungi were present. Similar interactions developed between a natural assemblage of bacteria and five different fungal strains isolated from Phragmites litter (three identified hyphomycetes and two unidentified strains). Despite the great difference in biomass development between the treatments, the carbon metabolism was similar regardless of whether fungi and/or bacteria were present alone or in coexistence. We suggest that the antagonism between bacteria and fungi is an important controlling factor for microbial colonization and growth on aquatic plant litter.}, }
@article {pmid12545314, year = {2003}, author = {Walsh, UF and Moënne-Loccoz, Y and Tichy, HV and Gardner, A and Corkery, DM and Lorkhe, S and O'Gara, F}, title = {Residual impact of the biocontrol inoculant Pseudomonas fluorescens F113 on the resident population of rhizobia nodulating a red clover rotation crop.}, journal = {Microbial ecology}, volume = {45}, number = {2}, pages = {145-155}, doi = {10.1007/s00248-002-2026-8}, pmid = {12545314}, issn = {0095-3628}, mesh = {DNA, Bacterial/chemistry/genetics ; Fungicides, Industrial/metabolism ; Genetic Variation ; Ireland ; Pest Control, Biological/*methods ; Phloroglucinol/analogs &amp; derivatives/metabolism ; Plant Roots/growth &amp; development/microbiology ; Pseudomonas fluorescens/*growth &amp; development/metabolism ; Random Amplified Polymorphic DNA Technique ; Rhizobium leguminosarum/genetics/*growth &amp; development/metabolism ; Soil Microbiology ; Trifolium/*growth &amp; development/microbiology ; }, abstract = {A field trial was previously conducted in which sugarbeet seeds were either untreated, inoculated with the biocontrol strain Pseudomonas fluorescens F113Rif, or treated with chemical fungicides. Following harvest of sugarbeet, the field site was sown with uninoculated red clover. The aim of this study was to assess the residual impact of the microbial inoculant (and the fungicide treatment) on the diversity of resident rhizobia nodulating the red clover rotation crop. The percentage of nodules yielding rhizobial isolates after surface disinfection was 67% in the control and 70% in the P. fluorescens F113Rif treatment, but only 23% in the chemical treatment. Isolates were characterized by RAPD analysis. The main RAPD cluster (arbitrarily defined at 70% similarity) was prevalent in all three treatments. In addition, the distribution of RAPD clusters followed a log series model, regardless of the treatment applied, indicating that neither the microbial inoculant nor the fungicide treatment had caused a strong perturbation of the rhizobial population. When the P. fluorescens F113Rif and control treatments were compared using diversity indices, however, it appeared that the genetic diversity of rhizobia was significantly less in the inoculated treatment. The percentage of rhizobia sensitive to 2,4-diacetylphloroglucinol (Phl; the antimicrobial metabolite produced by P. fluorescens F113Rif) fluctuated according to field site heterogeneity, and treatments had no effect on this percentage. Yet, the proportion of Phl-sensitive isolates in the main RAPD cluster was lower in the P. fluorescens F113Rif treatment compared with the control, raising the possibility that the residual impact of the inoculant could have been partly mediated by production of Phl. This impact on the rhizobial population took place without affecting the functioning of the Rhizobium-clover symbiosis.}, }
@article {pmid12545313, year = {2003}, author = {Konstantinidis, KT and Isaacs, N and Fett, J and Simpson, S and Long, DT and Marsh, TL}, title = {Microbial diversity and resistance to copper in metal-contaminated lake sediment.}, journal = {Microbial ecology}, volume = {45}, number = {2}, pages = {191-202}, doi = {10.1007/s00248-002-1035-y}, pmid = {12545313}, issn = {0095-3628}, mesh = {Arthrobacter/drug effects/*growth &amp; development/metabolism ; Base Sequence ; Copper/*analysis/toxicity ; Cupriavidus necator/drug effects/genetics/*growth &amp; development/metabolism ; DNA, Bacterial/chemistry/genetics ; Fresh Water/*microbiology ; Geologic Sediments/chemistry/*microbiology ; Microscopy, Electron, Scanning ; Microscopy, Phase-Contrast ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/chemistry/genetics ; Sequence Alignment ; Water Microbiology ; Water Pollutants, Chemical/*analysis/toxicity ; }, abstract = {Contamination of habitats with heavy metals has become a worldwide problem. We describe herein the analysis of lake sediment contaminated with high concentrations of copper as a consequence of mine milling disposal over a 100-year period. Copper concentrations in the sediment were found to vary with depth and ranged from 200 to 5500 ppm. Analysis of the microbial community with T-RFLP identified a minimum of 20 operational taxonomic units (OTU). T-RFLP analysis along a depth profile detected as many as nine shared OTUs across 15 centimeters, suggesting a conservation of community structure over this range. Only two genera, Arthrobacter and Ralstonia, were detected among 50 aerobic copper-resistant isolates cultivated on R2A, one of which (Ralstonia sp.) was characterized by the sequestration of copper, identified by electron diffraction scanning, in growing colonies. Scanning electron microscopy showed changes to the outer envelope of the cells when grown in the presence of copper. The copper-resistant Ralstonia isolates were also resistant to Ni, Cd, and Zn, showing two patterns of phenotypic resistant to these three metals in which either resistance to Zn or Ni was expressed in an isolate but never both.}, }
@article {pmid12545312, year = {2003}, author = {Danovaro, R and Corinaldesi, C}, title = {Sunscreen products increase virus production through prophage induction in marine bacterioplankton.}, journal = {Microbial ecology}, volume = {45}, number = {2}, pages = {109-118}, doi = {10.1007/s00248-002-1033-0}, pmid = {12545312}, issn = {0095-3628}, mesh = {Aminopeptidases/metabolism ; Animals ; Ecosystem ; Glucosidases/metabolism ; Phosphoric Monoester Hydrolases/metabolism ; Plankton/drug effects/enzymology/*microbiology/*virology ; Prophages/drug effects/*growth &amp; development ; Seawater/microbiology ; Sunscreening Agents/*adverse effects/chemistry ; Water Microbiology ; Water Pollutants, Chemical/*adverse effects ; }, abstract = {Classical pollutants (e.g., hydrocarbon, pesticides) have been recently recognized to induce lytic cycle in lysogenic bacteria, but information on micro-pollutants is almost completely lacking. We investigated the effects of cosmetic sun products (sunscreen and solar oil) on viral abundance and bacterial activity. We found that both sunscreen and solar oil acted as pollutants, inducing viral development and controlling bacterial abundance and production, thus leading to an increase of the virus to bacterium ratio. Short-term experiments revealed that sunscreen supplementation induced the lytic cycle in a large fraction of total bacterial abundance (13-24% of bacteria, at low and high concentrations, respectively), whereas solar oil had a lower impact (6-9%). A synchronized development of the phage-host system was observed only after sunscreen addition. The addition of sunscreen, even at low concentrations, had a significant impact on all enzymatic activities (aminopeptidase, glucosidase, and phosphatase), which increased significantly. However, when enzymatic activities were normalized per cell, a selective enhancement was observed for certain enzymes (e.g., aminopeptidase) and inhibition for others (e.g., glucosidase). These results indicate that sunscreen products can modify C, N, and P biogeochemical cycling in seawater and increase virus abundance through prophage induction in marine bacterioplankton.}, }
@article {pmid12545311, year = {2003}, author = {Kernaghan, G and Sigler, L and Khasa, D}, title = {Mycorrhizal and root endophytic fungi of containerized Picea glauca seedlings assessed by rDNA sequence analysis.}, journal = {Microbial ecology}, volume = {45}, number = {2}, pages = {128-136}, doi = {10.1007/s00248-002-1024-1}, pmid = {12545311}, issn = {0095-3628}, mesh = {Base Sequence ; DNA, Fungal/chemistry/*genetics ; DNA, Ribosomal/chemistry/*genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Fungi/chemistry/classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Picea/*microbiology ; Plant Roots/microbiology ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Fungi colonizing fine roots of containerized Picea glauca seedlings were assessed in four large conifer nurseries in northern Alberta. PCR amplification of fungal rDNA (internal transcribed spacer and a portion of the 5' end of the large subunit gene) from random samples of fine feeder roots gave between 1 and 4 amplicons per seedling. Amplicons were either separated by electrophoresis and sequenced directly, or cloned and sequenced. The resulting sequences were compared to sequences obtained from cultures established from seedling roots and from GenBank by maximum parsimony analysis. ITS sequences formed 11 distinct clades, each including at least one reference sequence. The ectomycorrhizal basidiomycetes Thelephora americana and Amphinema byssoides were dominant, whereas ascomycetes were less common. Fungi with sequences similar to members of the Heleotiales which form ericoid mycorrhizas were also present. Correspondence analysis revealed strong positive and negative associations among fungal taxa as well as an influence of applied fertilizer level on fungal diversity and species composition.}, }
@article {pmid12545310, year = {2003}, author = {André, S and Neyra, M and Duponnois, R}, title = {Arbuscular mycorrhizal symbiosis changes the colonization pattern of Acacia tortilis spp. Raddiana rhizosphere by two strains of rhizobia.}, journal = {Microbial ecology}, volume = {45}, number = {2}, pages = {137-144}, doi = {10.1007/s00248-002-1022-3}, pmid = {12545310}, issn = {0095-3628}, mesh = {Acacia/*growth &amp; development/*microbiology ; DNA, Bacterial/chemistry/genetics ; Fungi/*growth &amp; development/metabolism ; Mycorrhizae/growth &amp; development ; Plant Roots/growth &amp; development/microbiology ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Rhizobiaceae/*growth &amp; development/metabolism ; Sequence Analysis, DNA ; Silicon Dioxide ; Sinorhizobium/growth &amp; development ; Soil ; Soil Microbiology ; Symbiosis ; }, abstract = {The aim of the study was to assess the effect of the mycorrhizosphere of A. tortillis spp. raddiana mycorrhized with Glomus intraradices on the root nodulation by Sinorhizobium terangae (ORS 1009) and/or Mesorhizobium plurifarium (ORS 1096) in two different culture substrates (sandy soil and sand). The endomycorrhizal fungus only stimulated plant growth in the sandy soil. Moreover, arbuscular mycorrhizal infection enhanced the nodulation process in both culture substrates. Beside the stimulatory effects of the mycorrhizosphere on both rhizobia development, fungal symbiosis induces two different dynamics of each bacterial strains in the sand-grown plants. These results suggest specific relationships could occur during the development of the tripartite symbiosis, at physiological and molecular level. From a practical point of view, the role of arbuscular mycorrhizas in improving nodulation and N2 fixation is universally recognized. The fungal symbiosis could modify the development of bacterial inoculants along the root systems. This effect is of particular interest in the controlled inoculation of selected rhizobia.}, }
@article {pmid12545309, year = {2003}, author = {Bettarel, Y and Amblard, C and Sime-Ngando, T and Carrias, JF and Sargos, D and Garabétian, F and Lavandier, P}, title = {Viral lysis, flagellate grazing potential, and bacterial production in Lake Pavin.}, journal = {Microbial ecology}, volume = {45}, number = {2}, pages = {119-127}, doi = {10.1007/s00248-002-1016-1}, pmid = {12545309}, issn = {0095-3628}, mesh = {Animals ; Bacteria/*growth &amp; development/virology ; Cell Count ; *Ecosystem ; Eukaryota/*growth &amp; development ; France ; Fresh Water ; Microscopy, Electron ; Viruses/*growth &amp; development ; *Water Microbiology ; }, abstract = {Abundances of different compartments of the microbial loop (i.e., viruses, heterotrophic bacteria, nonpigmented nanoflagellates, and pigmented nanoflagellates), bacterial heterotrophic production (BHP), viral lysis, and potential flagellate grazing impacts on the bacterial assemblages were estimated during a short-term study (24 h) conducted in June 1998 in the epilimnion (5 m) and metalimnion (10 m) of a moderate-altitude oligomesotrophic lake (Lake Pavin, France). Viral and bacterial abundances were higher in the metalimnion than in the epilimnion, whereas pigmented and nonpigmented nanoflagellates were more numerous in the epilimnion. The control of the BHP due to viral lysis (determined by examination of viral-containing bacteria using a transmission electron microscope) was significantly higher in the meta- (range = 6.0-33.7%, mean = 15.6%) than in the epilimnion (3.5-10.3%, 6.4%). The same was for the losses of BHP from the potential predation by nanoflagellates which ranged from 0.5 to 115.4% (mean = 38.7%) in the epilimnion, and from 0.7 to 97.5% (mean = 66.7%) in the metalimnion. Finally, estimated viral mediated mortality rates from the percentage of visibly infected cells and potential nanoflagellate grazing rates based on assumed clearance rates suggest that flagellates consumed a larger proportion of bacterial production than was lost to viral lysis.}, }
@article {pmid12542639, year = {2003}, author = {Reeson, AF and Jankovic, T and Kasper, ML and Rogers, S and Austin, AD}, title = {Application of 16S rDNA-DGGE to examine the microbial ecology associated with a social wasp Vespula germanica.}, journal = {Insect molecular biology}, volume = {12}, number = {1}, pages = {85-91}, doi = {10.1046/j.1365-2583.2003.00390.x}, pmid = {12542639}, issn = {0962-1075}, mesh = {Animals ; DNA Fingerprinting ; DNA, Bacterial/chemistry/genetics ; Ecosystem ; Electrophoresis, Polyacrylamide Gel ; Lactobacillus/genetics/isolation &amp; purification ; Lactococcus/genetics/isolation &amp; purification ; Leuconostoc/genetics/isolation &amp; purification ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry/genetics ; Rickettsia/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; South Australia ; Wasps/*microbiology ; }, abstract = {Invertebrates host numerous bacteria, with interactions ranging from pathogenesis to symbiosis. While certain symbiotic relationships have been well studied, little is known about the dynamics of these bacterial communities. Denaturing gradient gel electrophoresis (DGGE) was used to examine the bacterial microflora associated with the eusocial wasp Vespula germanica. DGGE profiles of larval guts revealed a variable microflora, suggesting that V. germanica is not dependent on a particular suite of mutualists. The variation in profiles was not related to season, nest size or macrohabitat. Sequences corresponding to Lactococcus, Lactobacillus, a novel Leuconostoc and two Rickettsiella grylli strains were obtained. DGGE proved to be a useful technique for characterizing the wasp microflora. Given the importance of microbial communities to invertebrates, there is much to be gained from the application of such techniques.}, }
@article {pmid12542032, year = {2002}, author = {Franklin, RB and Blum, LK and McComb, AC and Mills, AL}, title = {A geostatistical analysis of small-scale spatial variability in bacterial abundance and community structure in salt marsh creek bank sediments.}, journal = {FEMS microbiology ecology}, volume = {42}, number = {1}, pages = {71-80}, doi = {10.1111/j.1574-6941.2002.tb00996.x}, pmid = {12542032}, issn = {0168-6496}, mesh = {Bacteria/genetics/growth &amp; development/*isolation &amp; purification ; Colony Count, Microbial ; DNA, Bacterial/analysis/genetics ; *Ecosystem ; Environmental Microbiology ; Geologic Sediments/*microbiology ; *Models, Statistical ; Sampling Studies ; Seawater/*microbiology ; Specimen Handling ; Virginia ; *Water Microbiology ; }, abstract = {Small-scale variations in bacterial abundance and community structure were examined in salt marsh sediments from Virginia's eastern shore. Samples were collected at 5 cm intervals (horizontally) along a 50 cm elevation gradient, over a 215 cm horizontal transect. For each sample, bacterial abundance was determined using acridine orange direct counts and community structure was analyzed using randomly amplified polymorphic DNA fingerprinting of whole-community DNA extracts. A geostatistical analysis was used to determine the degree of spatial autocorrelation among the samples, for each variable and each direction (horizontal and vertical). The proportion of variance in bacterial abundance that could be accounted for by the spatial model was quite high (vertical: 60%, horizontal: 73%); significant autocorrelation was found among samples separated by 25 cm in the vertical direction and up to 115 cm horizontally. In contrast, most of the variability in community structure was not accounted for by simply considering the spatial separation of samples (vertical: 11%, horizontal: 22%), and must reflect variability from other parameters (e.g., variation at other spatial scales, experimental error, or environmental heterogeneity). Microbial community patch size based upon overall similarity in community structure varied between 17 cm (vertical) and 35 cm (horizontal). Overall, variability due to horizontal position (distance from the creek bank) was much smaller than that due to vertical position (elevation) for both community properties assayed. This suggests that processes more correlated with elevation (e.g., drainage and redox potential) vary at a smaller scale (therefore producing smaller patch sizes) than processes controlled by distance from the creek bank.}, }
@article {pmid12538876, year = {2003}, author = {Cooper, TF and Rozen, DE and Lenski, RE}, title = {Parallel changes in gene expression after 20,000 generations of evolution in Escherichiacoli.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {3}, pages = {1072-1077}, pmid = {12538876}, issn = {0027-8424}, mesh = {Biological Evolution ; Carrier Proteins ; Cyclic AMP Receptor Protein/genetics ; Escherichia coli/*genetics/*physiology ; *Evolution, Molecular ; Guanosine/metabolism ; Mutation ; Oligonucleotide Array Sequence Analysis ; Pyrophosphatases/genetics ; Time Factors ; }, abstract = {Twelve populations of Escherichia coli, derived from a common ancestor, evolved in a glucose-limited medium for 20,000 generations. Here we use DNA expression arrays to examine whether gene-expression profiles in two populations evolved in parallel, which would indicate adaptation, and to gain insight into the mechanisms underlying their adaptation. We compared the expression profile of the ancestor to that of clones sampled from both populations after 20,000 generations. The expression of 59 genes had changed significantly in both populations. Remarkably, all 59 were changed in the same direction relative to the ancestor. Many of these genes were members of the cAMP-cAMP receptor protein (CRP) and guanosine tetraphosphate (ppGpp) regulons. Sequencing of several genes controlling the effectors of these regulons found a nonsynonymous mutation in spoT in one population. Moving this mutation into the ancestral background showed that it increased fitness and produced many of the expression changes manifest after 20,000 generations. The same mutation had no effect on fitness when introduced into the other evolved population, indicating that a mutation of similar effect was present already. Our study demonstrates the utility of expression arrays for addressing evolutionary issues including the quantitative measurement of parallel evolution in independent lineages and the identification of beneficial mutations.}, }
@article {pmid12530416, year = {2002}, author = {}, title = {Interactions in the microbial world. Proceedings of the 9th International Symposium on Microbial Ecology.}, journal = {Antonie van Leeuwenhoek}, volume = {81}, number = {1-4}, pages = {1-702}, pmid = {12530416}, issn = {0003-6072}, mesh = {*Microbiology ; }, }
@article {pmid12530237, year = {2002}, author = {Neilan, BA and Burns, BP and Relman, DA and Lowe, DR}, title = {Molecular identification of cyanobacteria associated with stromatolites from distinct geographical locations.}, journal = {Astrobiology}, volume = {2}, number = {3}, pages = {271-280}, doi = {10.1089/153110702762027853}, pmid = {12530237}, issn = {1531-1074}, mesh = {Base Sequence ; Cyanobacteria/*classification/genetics ; DNA Primers ; Geography ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Modern stromatolites represent a significant resource for studying microbial ecology and evolution. A preliminary investigation was undertaken employing specific genetic probes to characterize the cyanobacteria responsible for stromatolite construction in a range of environments, including microbial mats found in Australia not previously examined with molecular methods. Isolates of cyanobacteria were collected from stromatolites in thermal springs, hypersaline lakes, and oceanic fringes on two continents. A polymerase chain reaction specific for DNA of cyanobacterial 16S rRNA was developed, the resulting products of the DNA amplification reaction were sequenced, and the data were used to infer relatedness between the isolates studied and other members of the cyanobacterial radiation. Complete sequence was generated for the region from position 27 to 408 for 13 strains of cyanobacteria associated with stromatolites. All stromatolite-derived sequences were most closely related to cyanobacteria, as indicated by local sequence alignment. It was possible to correlate genetic identity with morphological nomenclatures and to expand the phylogeny of benthic cyanobacteria. These inferences were also expanded to temporal variation in the dominant resident cyanobacterial species based on sampling of surface and core sinter laminations. Under the methods employed, only one cyanobacterial strain was detected in each sample, suggesting the possible dominance of a specific clonal population of cyanobacteria at any one time in the biota of the samples tested. The data indicate that internal core samples of a stromatolite at least 10 years old can be successfully analyzed by DNA-based methods to identify preserved cyanobacteria.}, }
@article {pmid12521151, year = {2002}, author = {Simpson, JM and Santo Domingo, JW and Reasoner, DJ}, title = {Microbial source tracking: state of the science.}, journal = {Environmental science &amp; technology}, volume = {36}, number = {24}, pages = {5279-5288}, doi = {10.1021/es026000b}, pmid = {12521151}, issn = {0013-936X}, mesh = {Electrophoresis, Gel, Pulsed-Field/methods ; Enterobacteriaceae/genetics/growth &amp; development ; Escherichia coli/genetics/growth &amp; development ; Polymerase Chain Reaction/methods ; Polymorphism, Restriction Fragment Length ; Ribotyping/methods ; Water/chemistry ; Water Microbiology/*standards ; Water Pollutants/analysis ; Water Pollution/analysis ; Water Supply/*standards ; }, abstract = {Although water quality of the Nation's lakes, rivers and streams has been monitored for many decades and especially since the passage of the Clean Water Act in 1972, many still do not meet the Act's goal of "fishable and swimmable". While waterways can be impaired in numerous ways, the protection from pathogenic microbe contamination is most important for waters used for human recreation, drinking water and aquaculture. Typically, monitoring methods used for detecting potential pathogenic microorganisms in environmental waters are based upon cultivation and enumeration of fecal indicator bacteria (i.e. fecal coliforms, E. coli, and fecal enterococci). Currently, there is increasing interest in the potential for molecular fingerprinting methods to be used not only for detection but also for identification of fecal contamination sources. Molecular methods have been applied to study the microbial ecology of environmental systems for years and are now being applied to help improve our waters by identifying problem sources and determining the effect of implemented remedial solutions. Management and remediation of water pollution would be more cost-effective if the correct sources could be identified. This review provides an outline of the main methods that either have been used or have been suggested for use in microbial source tracking and some of the limitations associated with those methods.}, }
@article {pmid12520046, year = {2003}, author = {Cole, JR and Chai, B and Marsh, TL and Farris, RJ and Wang, Q and Kulam, SA and Chandra, S and McGarrell, DM and Schmidt, TM and Garrity, GM and Tiedje, JM and , }, title = {The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy.}, journal = {Nucleic acids research}, volume = {31}, number = {1}, pages = {442-443}, pmid = {12520046}, issn = {1362-4962}, mesh = {Animals ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Databases, Nucleic Acid ; Eukaryotic Cells/classification ; Phylogeny ; Prokaryotic Cells/classification ; RNA, Archaeal/chemistry/classification ; RNA, Bacterial/chemistry/classification ; RNA, Ribosomal/*chemistry/classification ; Sequence Alignment ; Sequence Analysis, RNA ; Software ; }, abstract = {The Ribosomal Database Project-II (RDP-II) pro-vides data, tools and services related to ribosomal RNA sequences to the research community. Through its website (http://rdp.cme.msu.edu), RDP-II offers aligned and annotated rRNA sequence data, analysis services, and phylogenetic inferences (trees) derived from these data. RDP-II release 8.1 contains 16 277 prokaryotic, 5201 eukaryotic, and 1503 mitochondrial small subunit rRNA sequences in aligned and annotated format. The current public beta release of 9.0 debuts a new regularly updated alignment of over 50 000 annotated (eu)bacterial sequences. New analysis services include a sequence search and selection tool (Hierarchy Browser) and a phylogenetic tree building and visualization tool (Phylip Interface). A new interactive tutorial guides users through the basics of rRNA sequence analysis. Other services include probe checking, phylogenetic placement of user sequences, screening of users' sequences for chimeric rRNA sequences, automated alignment, production of similarity matrices, and services to plan and analyze terminal restriction fragment polymorphism (T-RFLP) experiments. The RDP-II email address for questions or comments is rdpstaff@msu.edu.}, }
@article {pmid12519970, year = {2003}, author = {Urbance, JW and Cole, J and Saxman, P and Tiedje, JM}, title = {BSD: the Biodegradative Strain Database.}, journal = {Nucleic acids research}, volume = {31}, number = {1}, pages = {152-155}, pmid = {12519970}, issn = {1362-4962}, mesh = {Bacteria/genetics/*metabolism ; Biodegradation, Environmental ; *Databases, Factual ; Hazardous Substances/*metabolism ; Information Storage and Retrieval ; Internet ; Phylogeny ; }, abstract = {The Biodegradative Strain Database (BSD) is a freely-accessible, web-based database providing detailed information on degradative bacteria and the hazardous substances that they degrade, including corresponding literature citations, relevant patents and links to additional web-based biological and chemical data. The BSD (http://bsd.cme.msu.edu) is being developed within the phylogenetic framework of the Ribosomal Database Project II (RDPII: http://rdp.cme.msu.edu/html) to provide a biological complement to the chemical and degradative pathway data of the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD: http://umbbd.ahc.umn.edu). Data is accessible through a series of strain, chemical and reference lists or by keyword search. The web site also includes on-line data submission and user survey forms to solicit user contributions and suggestions. The current release contains information on over 250 degradative bacterial strains and 150 hazardous substances. The transformation of xenobiotics and other environmentally toxic compounds by microorganisms is central to strategies for biocatalysis and the bioremediation of contaminated environments. However, practical, comprehensive, strain-level information on biocatalytic/biodegradative microbes is not readily available and is often difficult to compile. Similarly, for any given environmental contaminant, there is no single resource that can provide comparative information on the array of identified microbes capable of degrading the chemical. A web site that consolidates and cross-references strain, chemical and reference data related to biocatalysis, biotransformation, biodegradation and bioremediation would be an invaluable tool for academic and industrial researchers and environmental engineers.}, }
@article {pmid12514050, year = {2003}, author = {Noda, S and Ohkuma, M and Yamada, A and Hongoh, Y and Kudo, T}, title = {Phylogenetic position and in situ identification of ectosymbiotic spirochetes on protists in the termite gut.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {1}, pages = {625-633}, pmid = {12514050}, issn = {0099-2240}, mesh = {Animals ; DNA, Ribosomal/analysis ; Eukaryota/*microbiology ; In Situ Hybridization ; Isoptera/microbiology/*parasitology ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spirochaetaceae/*classification/genetics ; Stomach/*parasitology ; *Symbiosis ; Treponema/classification/genetics ; }, abstract = {Phylogenetic relationships, diversity, and in situ identification of spirochetes in the gut of the termite Neotermes koshunensis were examined without cultivation, with an emphasis on ectosymbionts attached to flagellated protists. Spirochetes in the gut microbial community investigated so far are related to the genus Treponema and divided into two phylogenetic clusters. In situ hybridizations with a 16S rRNA-targeting consensus oligonucleotide probe for one cluster (known as termite Treponema cluster I) detected both the ectosymbiotic spirochetes on gut protists and the free-swimming spirochetes in the gut fluid of N. koshunensis. The probe for the other cluster (cluster II), which has been identified as ectosymbionts on gut protists of two other termite species, Reticulitermes speratus and Hodotermopsis sjoestedti, failed to detect any spirochete population. The absence of cluster II spirochetes in N. koshunensis was confirmed by intensive 16S ribosomal DNA (rDNA) clone analysis, in which remarkably diverse spirochetes of 45 phylotypes were identified, almost all belonging to cluster I. Ectosymbiotic spirochetes of the three gut protist species Devescovina sp., Stephanonympha sp., and Oxymonas sp. in N. koshunensis were identified by their 16S rDNA and by in situ hybridizations using specific probes. The probes specific for these ectosymbionts did not receive a signal from the free-swimming spirochetes. The ectosymbionts were dispersed in cluster I of the phylogeny, and they formed distinct phylogenetic lineages, suggesting multiple origins of the spirochete attachment. Each single protist cell harbored multiple spirochete species, and some of the spirochetes were common among protist species. The results indicate complex relationships of the ectosymbiotic spirochetes with the gut protists.}, }
@article {pmid16887593, year = {1997}, author = {Chung, KT and Bryant, MP}, title = {Robert E. Hungate: pioneer of anaerobic microbial ecology.}, journal = {Anaerobe}, volume = {3}, number = {4}, pages = {213-217}, doi = {10.1006/anae.1997.0109}, pmid = {16887593}, issn = {1075-9964}, }
@article {pmid16887579, year = {1997}, author = {Norin, KE}, title = {Influence of antibiotics on some intestinal microflora associated characteristics.}, journal = {Anaerobe}, volume = {3}, number = {2-3}, pages = {145-148}, doi = {10.1006/anae.1997.0091}, pmid = {16887579}, issn = {1075-9964}, abstract = {Intestinal functions related to the presence of microbes in host organisms are normally heavily influenced by administration of antimicrobial drugs. We have investigated the effect of several antibiotics in man and rat, on some MACs (Microflora Associated Characteristics). A MAC is defined as the recording of any anatomical structure, biochemical or physiological function in the host organism which is influenced by microflora. When functional, active microbes are absent as in germfree animals, healthy newborns, or in relation to antimicrobial therapies, a MAC defined as a GAC (Germfree Animal Characteristic). Faecal samples have been collected prior to, during and up to several weeks after the antimicrobial administration in order to investigate different MAC/GAC patterns. Microbial conversion of cholesterol to coprostanol, bilirubin to urobilinogen and 7-alpha-dehydroxylation of cholic acid have been investigated to evaluate hepatic/intestinal co-functions, and degradation of intestinal mucin in order to evaluate the integrity in the intestinal mucosa. Furthermore, degradation of the dietary derived beta-aspartylglycine, the level of faecal trypsin and production of short chain fatty acids were investigated to evaluate dietary/intestinal co-functions. It is concluded that each antimicrobial drug creates its own profile, both with regard to duration and function.}, }
@article {pmid15093372, year = {1997}, author = {Carnol, M and Ineson, P and Dickinson, AL}, title = {Soil solution nitrogen and cations influenced by (NH4)2SO4 deposition in a coniferous forest.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {97}, number = {1-2}, pages = {1-10}, doi = {10.1016/s0269-7491(97)00088-2}, pmid = {15093372}, issn = {0269-7491}, abstract = {The effects of chronically enhanced (NH(4))(2)SO(4) deposition on ion concentrations in soil solution and ionic fluxes were investigated in a Picea abies plot at Grizedale forest, NW England. Soil cores closed at the base and containing a ceramic suction cup sampler were 'roofed' and watered every 2 weeks with bulk throughfall collected in the field. Treatments consisted of the inclusion of living roots from mature trees in the lysimeters and increasing (NH(4))(2)SO(4) deposition (NS treatment) to ambient + 75 kg N ha(-1) a(-1). Rainfall, throughfall and soil solutions were collected every 2 weeks during 18 months, and analysed for major cations and anions. NO(3)(-) fluxes significantly increased following NS treatment, and were balanced by increased Al(3+) losses. Increased SO(4)(2-) concentrations played a minor role in controlling soil solution cation concentrations. The soil exchange complex was dominated by Al and, during the experimental period, cores of all treatments 'switched' from Ca(2+) to Al(3+) leaching, leading to mean [Formula: see text] molar ratios in soil solution of NS treated cores of 0.24. The experiment confirmed that the most sensitive soils to acidification (through deposition or changing environmental conditions) are those with low base saturation, and with a pH in the lower Ca, or Al buffer ranges.}, }
@article {pmid16534951, year = {1995}, author = {Assmus, B and Hutzler, P and Kirchhof, G and Amann, R and Lawrence, JR and Hartmann, A}, title = {In Situ Localization of Azospirillum brasilense in the Rhizosphere of Wheat with Fluorescently Labeled, rRNA-Targeted Oligonucleotide Probes and Scanning Confocal Laser Microscopy.}, journal = {Applied and environmental microbiology}, volume = {61}, number = {3}, pages = {1013-1019}, pmid = {16534951}, issn = {0099-2240}, abstract = {The colonization of wheat roots by Azospirillum brasilense was used as a model system to evaluate the utility of whole-cell hybridization with fluorescently labeled, rRNA-targeted oligonucleotide probes for the in situ monitoring of rhizosphere microbial communities. Root samples of agar- or soil-grown 10- and 30-day-old wheat seedlings inoculated with different strains of A. brasilense were hybridized with a species-specific probe for A. brasilense, a probe hybridizing to alpha subclass proteobacteria, and a probe specific for the domain Bacteria to identify and localize the target bacteria. After hybridization, about 10 to 25% of the rhizosphere bacteria as visualized with 4(prm1),6-diamidino-2-phenylindole (DAPI) gave sufficient fluorescence signals to be detected with rRNA-targeted probes. Scanning confocal laser microscopy was used to overcome disturbing effects arising from autofluorescence of the object or narrow depth of focus in thick specimens. This technique also allowed high-resolution analysis of the spatial distribution of bacteria in the rhizosphere. Occurrence of cells of A. brasilense Sp7 and Wa3 was restricted to the rhizosphere soil, mainly to the root hair zone. C-forms of A. brasilense were demonstrated to be physiologically active forms in the rhizosphere. Strain Sp245 also was found repeatedly at high density in the interior of root hair cells. In general, the combination of fluorescently labeled oligonucleotide probes and scanning confocal laser microscopy provided a very suitable strategy for detailed studies of rhizosphere microbial ecology.}, }
@article {pmid16534914, year = {1995}, author = {Hennes, KP and Simon, M}, title = {Significance of bacteriophages for controlling bacterioplankton growth in a mesotrophic lake.}, journal = {Applied and environmental microbiology}, volume = {61}, number = {1}, pages = {333-340}, pmid = {16534914}, issn = {0099-2240}, abstract = {Bacterium-specific viruses have attracted much interest in aquatic microbial ecology because they have been shown to be about 10 times more abundant than planktonic bacteria. So far most of the studies of interactions of planktonic bacteria and viruses have been done in marine environments, and very little is known about these interactions in lakes. Therefore, we studied phage proliferation in Lake Constance, a large mesotrophic lake in Germany. We enumerated bacteria and quantified the fraction of bacteria with mature intracellular phage particles and the number of free viruses by transmission electron microscopy. Between the end of March and early August 1992, peaks of bacterial abundance were followed in 1 to 2 weeks by peaks in the fraction of bacteria containing visible phage particles (0 to 1.7%) and in the number of free viruses (1 x 10(sup7) to 4 x 10(sup7) ml(sup-1)). We estimated that 1 to 17% +/- 12% of all bacteria were phage infected, implying that phage-induced mortality was <34% +/- 24% of total mortality. A direct comparison between phage-induced mortality, the net decrease of bacterial numbers, and bacterial growth rates indicated that phage-induced mortality accounted for <11% of total bacterial mortality during the phytoplankton spring bloom and 18 to 21% following the bloom. Estimated burst sizes ranged from 21 to 121 phages. Phage production rates of 0.5 x 10(sup6) to 2.5 x 10(sup6) ml(sup-1) day(sup-1) accounted for 70 to 380% of the observed net increase rates of free phages, implying high rates of simultaneous phage decay. The cyclic dynamics between bacteria and phages and the varying size structure of the intracellular mature phage particles suggested that phage infection was important in structuring the bacterial host assemblage during the study period.}, }
@article {pmid14537146, year = {1995}, author = {Schloter, M and Assmus, B and Hartmann, A}, title = {The use of immunological methods to detect and identify bacteria in the environment.}, journal = {Biotechnology advances}, volume = {13}, number = {1}, pages = {75-90}, doi = {10.1016/0734-9750(94)00023-6}, pmid = {14537146}, issn = {0734-9750}, abstract = {Immunological detection methods have become increasingly important in microbial ecology for the tracking of specific microorganisms and for community analysis. For a reliable application of these techniques, the monoclonal antibodies or polyclonal antisera used have to fulfill several quality criteria. Cross reactivity, cellular localization of the antigenic determinant, affinity characteristics and the expression of the antigenic determinant at environmental conditions have to be determined. Immunological methods can be used for the identification, quantification and enrichment of specific bacteria in extracts as well as for the visualization of cells in situ. The sensitivity of advanced immunological methods can be compared to PCR techniques. Using image processing of epifluorescence micrographs or confocal laser scanning microscopy, the immunofluorescence approach can now be applied to study complex environmental samples.}, }
@article {pmid16349434, year = {1994}, author = {Emerson, D and Revsbech, NP}, title = {Investigation of an Iron-Oxidizing Microbial Mat Community Located near Aarhus, Denmark: Laboratory Studies.}, journal = {Applied and environmental microbiology}, volume = {60}, number = {11}, pages = {4032-4038}, pmid = {16349434}, issn = {0099-2240}, abstract = {We constructed a small flow chamber in which suboxic medium containing 60 to 120 muM FeCl(2) flowed up through a sample well into an aerated reservoir, thereby creating an suboxic-oxic interface similar to the physicochemical conditions that exist in natural iron seeps. When microbial mat material from the Marselisborg iron seep that contained up to 10 bacterial cells per cm (D. Emerson and N. P. Revsbech, Appl. Environ. Microbiol. 60:4022-4031, 1994) was placed in the sample well of the chamber, essentially all of the Fe flowing through the sample well was oxidized at rates of up to 1,200 nmol of Fe oxidized per h per cm of mat material. The oxidation rates of samples of the mat that were pasteurized prior to inoculation were only about 20 to 50% of the oxidation rates of unpasteurized samples. Sodium azide also significantly inhibited oxidation. These results suggest that at least 50% and up to 80% of the Fe oxidation in the chamber were actively mediated by the microbes in the mat. It also appeared that Fe stimulated the growth of the community since chambers fed with FeCl(2) accumulated masses of either filamentous or particulate growth, both in the sample well and attached to the walls of the chamber. Control chambers that did not receive FeCl(2) showed no sign of such growth. Furthermore, after 4 to 5 days the chambers fed with FeCl(2) contained 35 to 75% more protein than chambers not supplemented with FeCl(2). Leptothrix ochracea and, to a lesser extent, Gallionella spp. were responsible for the filamentous growth, and the sheaths and stalks, respectively, of these two organisms harbored large numbers of Fe-encrusted, nonappendaged unicellular bacteria. In chambers where particulate growth predominated, the unicellular bacteria alone appeared to be the primary agents of iron oxidation. These results provide the first clear evidence that the "iron bacteria" commonly found associated with neutral-pH iron seeps are responsible for most of the iron oxidation and that the presence of ferrous iron appears to stimulate the growth of these organisms.}, }
@article {pmid16349433, year = {1994}, author = {Emerson, D and Revsbech, NP}, title = {Investigation of an Iron-Oxidizing Microbial Mat Community Located near Aarhus, Denmark: Field Studies.}, journal = {Applied and environmental microbiology}, volume = {60}, number = {11}, pages = {4022-4031}, pmid = {16349433}, issn = {0099-2240}, abstract = {We investigated the microbial community that developed at an iron seep where anoxic groundwater containing up to 250 muM Fe flowed out of a rock wall and dense, mat-like aggregations of ferric hydroxides formed at the oxic-anoxic interface. In situ analysis with oxygen microelectrodes revealed that the oxygen concentrations in the mat were rarely more than 50% of air saturation and that the oxygen penetration depth was quite variable, ranging from <0.05 cm to several centimeters. The bulk pH of the mat ranged from 7.1 to 7.6. There appeared to be a correlation between the flow rates at different subsites of the mat and the morphotypes of the microorganisms and Fe oxides that developed. In subsites with low flow rates (<2 ml/s), the iron-encrusted sheaths of Leptothrix ochracea predominated. Miniature cores revealed that the top few millimeters of the mat consisted primarily of L. ochracea sheaths, only about 7% of which contained filaments of cells. Deeper in the mat, large particulate oxides developed, which were often heavily colonized by unicellular bacteria that were made visible by staining with acridine orange. Direct cell counts revealed that the number of bacteria increased from approximately 10 to 10 cells per cm and the total iron concentration increased from approximately 0.5 to 3 mmol/cm with depth in the mat. Primarily because of the growth of L. ochracea, the mat could accrete at rates of up to 3.1 mm/day at these subsites. The iron-encrusted stalks of Gallionella spp. prevailed in localized zones of the same low-flow-rate subsites, usually close to where the source water emanated from the wall. These latter zones had the lowest O(2) concentrations (<10% of the ambient concentration), confirming the microaerobic nature of Gallionella spp. In subsites with high flow rates (>6 ml/s) particulate Fe oxides were dominant; direct counts revealed that up to 10 cells of primarily unicellular bacteria per cm were associated with these particulate oxides. These zones exhibited little vertical stratification in either the number of cells or iron concentration. Finally, mat samples incubated anaerobically in the presence of acetate or succinate exhibited significant potential for iron reduction, suggesting the possibility that a localized iron cycle could occur within the mat community.}, }
@article {pmid16349370, year = {1994}, author = {Blackburn, TH and Blackburn, ND and Jensen, K and Risgaard-Petersen, N}, title = {Simulation Model of the Coupling between Nitrification and Denitrification in a Freshwater Sediment.}, journal = {Applied and environmental microbiology}, volume = {60}, number = {9}, pages = {3089-3095}, pmid = {16349370}, issn = {0099-2240}, abstract = {A model was constructed to simulate the results of experiments which investigated nitrification and denitrification in the freshwater sediment of Lake Vilhelmsborg, Denmark (K. Jensen, N. P. Sloth, N. Risgaard-Petersen, S. Rysgaard, and N. P. Revsbech, Appl. Environ. Microbiol. 60:2094-2100, 1994). The model output faithfully represented the profiles of O(2) and NO(3) and rates of nitrification, denitrification, and O(2) consumption as the O(2) concentration in the overlying water was increased from 10 to 600 muM. The model also accurately predicted the response, to increasing O(2) concentrations, of the integrated (micromoles per square meter per hour) rates of nitrification and denitrification. The simulated rates of denitrification of NO(3) diffusing from the overlying water (D(w)) and of NO(3) generated by nitrification within the sediment (D(n)) corresponded to the experimental rates as the O(2) concentration in the overlying water was altered. The predicted D(w) and D(n) rates, as NO(3) concentration in the overlying water was changed, closely resembled those determined experimentally. The model was composed of 41 layers 0.1 mm thick, of which 3 represented the diffusive boundary layer in the water. Large first-order rate constants for nitrification and denitrification were required to completely oxidize all NH(4) diffusing from the lower sediment layers and to remove much of the NO(3) produced. In addition to the flux of NH(4) from below, the model required a flux of an electron donor, possibly methane. Close coupling between nitrification and denitrification, achieved by allowing denitrification to tolerate some O(2) (approximately 10 muM), was necessary to reproduce the real data. Spatial separation of the two processes (no toleration by denitrification of O(2)) resulted in too high NO(3) concentrations and too low rates of denitrification.}, }
@article {pmid16349327, year = {1994}, author = {Haack, SK and Garchow, H and Odelson, DA and Forney, LJ and Klug, MJ}, title = {Accuracy, reproducibility, and interpretation of Fatty Acid methyl ester profiles of model bacterial communities.}, journal = {Applied and environmental microbiology}, volume = {60}, number = {7}, pages = {2483-2493}, pmid = {16349327}, issn = {0099-2240}, abstract = {We determined the accuracy and reproducibility of whole-community fatty acid methyl ester (FAME) analysis with two model bacterial communities differing in composition by using the Microbial ID, Inc. (MIDI), system. The biomass, taxonomic structure, and expected MIDI-FAME profiles under a variety of environmental conditions were known for these model communities a priori. Not all members of each community could be detected in the composite profile because of lack of fatty acid "signatures" in some isolates or because of variations (approximately fivefold) in fatty acid yield across taxa. MIDI-FAME profiles of replicate subsamples of a given community were similar in terms of fatty acid yield per unit of community dry weight and relative proportions of specific fatty acids. Principal-components analysis (PCA) of MIDI-FAME profiles resulted in a clear separation of the two different communities and a clustering of replicates of each community from two separate experiments on the first PCA axis. The first PCA axis accounted for 57.1% of the variance in the data and was correlated with fatty acids that varied significantly between communities and reflected the underlying community taxonomic structure. On the basis of our data, community fatty acid profiles can be used to assess the relative similarities and differences of microbial communities that differ in taxonomic composition. However, detailed interpretation of community fatty acid profiles in terms of biomass or community taxonomic composition must be viewed with caution until our knowledge of the quantitative and qualitative distribution of fatty acids over a wide variety of taxa and the effects of growth conditions on fatty acid profiles is more extensive.}, }
@article {pmid16349314, year = {1994}, author = {Díaz-Raviña, M and Bååth, E and Frostegård, A}, title = {Multiple heavy metal tolerance of soil bacterial communities and its measurement by a thymidine incorporation technique.}, journal = {Applied and environmental microbiology}, volume = {60}, number = {7}, pages = {2238-2247}, pmid = {16349314}, issn = {0099-2240}, abstract = {A thymidine incorporation technique was used to determine the tolerance of a soil bacterial community to Cu, Cd, Zn, Ni, and Pb. An agricultural soil was artificially contaminated in our laboratory with individual metals at three different concentrations, and the results were compared with the results obtained by using the plate count technique. Thymidine incorporation was found to be a simple and rapid method for measuring tolerance. Data obtained by this technique were very reproducible. A linear relationship was found between changes in community tolerance levels obtained by the thymidine incorporation and plate count techniques (r = 0.732, P < 0.001). An increase in tolerance to the metal added to soil was observed for the bacterial community obtained from each polluted soil compared with the community obtained from unpolluted soil. The only exception was when Pb was added; no indication of Pb tolerance was found. An increase in the tolerance to metals other than the metal originally added to soil was also observed, indicating that there was multiple heavy metal tolerance at the community level. Thus, Cu pollution, in addition to increasing tolerance to Cu, also induced tolerance to Zn, Cd, and Ni. Zn and Cd pollution increased community tolerance to all five metals. Ni amendment increased tolerance to Ni the most but also increased community tolerance to Zn and, to lesser degrees, increased community tolerance to Pb and Cd. In soils polluted with Pb increased tolerance to other metals was found in the following order: Ni > Cd > Zn > Cu. We found significant positive relationships between changes in Cd, Zn, and Pb tolerance and, to a lesser degree, between changes in Pb and Ni tolerance when all metals and amendment levels were compared. The magnitude of the increase in heavy metal tolerance was found to be linearly related to the logarithm of the metal concentration added to the soil. Threshold tolerance concentrations were estimated from these linear relationships, and changes in tolerance could be detected at levels of soil contamination similar to those reported previously to result in changes in the phospholipid fatty acid pattern (A. Frostegård, A. Tunlid, and E. Bååth, Appl. Environ. Microbiol. 59: 3605-3617, 1993).}, }
@article {pmid16349295, year = {1994}, author = {Jensen, K and Sloth, NP and Risgaard-Petersen, N and Rysgaard, S and Revsbech, NP}, title = {Estimation of nitrification and denitrification from microprofiles of oxygen and nitrate in model sediment systems.}, journal = {Applied and environmental microbiology}, volume = {60}, number = {6}, pages = {2094-2100}, pmid = {16349295}, issn = {0099-2240}, abstract = {The coupling between nitrification and denitrification and the regulation of these processes by oxygen were studied in freshwater sediment microcosms with O(2) and NO(3) microsensors. Depth profiles of nitrification (indicated as NO(3) production), denitrification (indicated as NO(3) consumption), and O(2) consumption activities within the sediment were calculated from the measured concentration profiles. From the concentration profiles, it was furthermore possible to distinguish between the rate of denitrification based on the diffusional supply of NO(3) from the overlying water and the rate based on NO(3) supplied by benthic nitrification (D(w) and D(n), respectively). An increase in O(2) concentration caused a deeper O(2) penetration while a decrease in D(w) and an increase in D(n) were observed. The relative importance for total denitrification of NO(3) produced by nitrification thus increased compared with NO(3) supplied from the water phase. The decrease in D(w) at high oxygen was due to an increase in diffusion path for NO(3) from the overlying water to the denitrifying layers in the anoxic sediment. At high O(2) concentrations, nitrifying activity was restricted to the lower part of the oxic zone where there was a continuous diffusional supply of NH(4) from deeper mineralization processes, and the long diffusion path from the nitrification zone to the overlying water compared with the path to the denitrifying layers led to a stimulation in D(n).}, }
@article {pmid16349216, year = {1994}, author = {Top, E and De Smet, I and Verstraete, W and Dijkmans, R and Mergeay, M}, title = {Exogenous isolation of mobilizing plasmids from polluted soils and sludges.}, journal = {Applied and environmental microbiology}, volume = {60}, number = {3}, pages = {831-839}, pmid = {16349216}, issn = {0099-2240}, abstract = {Exogenous plasmid isolation was used to assess the presence of mobilizing plasmids in several soils and activated sludges. Triparental matings were performed with Escherichia coli (a member of the gamma subgroup of the Proteobacteria) as the donor of an IncQ plasmid (pMOL155, containing the heavy metal resistance genes czc: Co, Zn, and Cd), Alcaligenes eutrophus (a member of the beta subgroup of the Proteobacteria) as the recipient, and indigenous microorganisms from soil and sludge samples as helper strains. We developed an assay to assess the plasmid mobilization potential of a soil ecosystem on the basis of the number of transconjugants obtained after exogenous isolations. After inoculation into soil of several concentrations of a helper strain (E. coli CM120 harboring IncP [IncP1] mobilizing plasmid RP4), the log numbers of transconjugants obtained from exogenous isolations with different soil samples were a linear function of the log numbers of helper strain CM120(RP4) present in the soils. Four soils were analyzed for the presence of mobilizing elements, and mobilizing plasmids were isolated from two of these soils. Several sludge samples from different wastewater treatment plants yielded much higher numbers of transconjugants than the soil samples, indicating that higher numbers of mobilizing strains were present. The mobilizing plasmids isolated from Gent-O sludge and one plasmid isolated from Eislingen soil hybridized to the repP probe, whereas the plasmids isolated from Essen soil did not hybridize to a large number of rep probes (repFIC, repHI1, repH12, repL/M, repN, repP, repT, repU, repW, repX). This indicates that in Essen soil, broad-host-range mobilizing plasmids belonging to other incompatibility groups may be present.}, }
@article {pmid16349091, year = {1993}, author = {Lens, PN and De Beer, D and Cronenberg, CC and Houwen, FP and Ottengraf, SP and Verstraete, WH}, title = {Heterogeneous Distribution of Microbial Activity in Methanogenic Aggregates: pH and Glucose Microprofiles.}, journal = {Applied and environmental microbiology}, volume = {59}, number = {11}, pages = {3803-3815}, pmid = {16349091}, issn = {0099-2240}, abstract = {Methanogenic aggregates, harvested from an upflow anaerobic sludge blanket reactor treating potato starch wastewater, were acclimatized to either glucose or a mixture of sugars and organic nitrogen compounds (i.e., diluted molasses). Both types of granules exhibited internal pH and substrate concentration gradients in mineral medium (pH 7.0, 30 degrees C) as was measured with microelectrodes. Glucose-acclimatized granules suspended in a mineral medium lacking glucose exhibited a distinct internal pH decrease of about 1 U within the granule, suggesting strong metabolism by the acidogenic bacteria. Molasses-acclimatized and aged granules suspended in mineral medium did not exhibit such a pH decrease, suggesting the importance of the metabolic state of these acidogens. The pH gradient did not occur in deactivated granules and was not observable in strongly buffered media (mineral medium containing 33 mM phosphate or reactor liquid). When glucose (0.5 to 5.0 mM) was added to the mineral medium, granules exhibited a convex pH profile. Glucose consumption was located exclusively in the outer 200 to 300 mum of the aggregates (mean diameter = 1.5 mm). The addition of 20 mM 2-bromoethanesulfonic acid to the mineral medium indicated that the higher pH levels in the centre of the granule appeared to be related to the activity of methanogens. It is suggested that acidogenic activity occurs predominantly in the outer 200 to 300 mum of the aggregate and methanogenic activity occurs predominantly in the center of the investigated granules.}, }
@article {pmid16349080, year = {1993}, author = {Frostegård, A and Tunlid, A and Bååth, E}, title = {Phospholipid Fatty Acid composition, biomass, and activity of microbial communities from two soil types experimentally exposed to different heavy metals.}, journal = {Applied and environmental microbiology}, volume = {59}, number = {11}, pages = {3605-3617}, pmid = {16349080}, issn = {0099-2240}, abstract = {The phospholipid fatty acid (PLFA) pattern was analyzed in a forest humus and in an arable soil experimentally polluted with Cd, Cu, Ni, Pb, or Zn at different concentrations. In both soil types, there were gradual changes in the PLFA patterns for the different levels of metal contamination. The changes in the forest soil were similar irrespective of which metal was used, while in the arable soil the changes due to Cu contamination differed from those due to the other metals. Several PLFAs reacted similarly to the metal amendments in the two soil types, while others showed different responses. In both soils, the metal pollution resulted in a decrease in the iso-branched PLFAs i15:0 and i17:0 and in the monounsaturated 16:1omega5 and 16:1omega7c fatty acids, while increases were found for i16:0, the branched br17:0 and br18:0, and the cyclopropane cy17:0 fatty acids. In the forest soil, the methyl branched PLFAs 10Me16:0, 10Me17:0, and 10Me18:0 increased in metal-polluted soils, indicating an increase in actinomycetes, while in the arable soil a decrease was found for 10Me16:0 and 10Me18:0 in response to most metals. The bacterial PLFAs 15:0 and 17:0 increased in all metal-contaminated samples in the arable soil, while they were unaffected in the forest soil. Fatty acid 18:2omega6, which is considered to be predominantly of fungal origin, increased in the arable soil, except in the Cu-amended samples, in which it decreased instead. Effects on the PLFA patterns were found at levels of metal contamination similar to or lower than those at which effects on ATP content, soil respiration, or total amount of PLFAs had occurred.}, }
@article {pmid16349065, year = {1993}, author = {Jensen, K and Revsbech, NP and Nielsen, LP}, title = {Microscale distribution of nitrification activity in sediment determined with a shielded microsensor for nitrate.}, journal = {Applied and environmental microbiology}, volume = {59}, number = {10}, pages = {3287-3296}, pmid = {16349065}, issn = {0099-2240}, abstract = {Microprofiles of O(2) and NO(3) were measured simultaneously in freshwater sediment with microsensors which were completely free from electrical interference because of coaxial designs. Depth profiles of nitrification (NO(3) production) and denitrification (NO(3) consumption) were subsequently determined by computer simulation of the measured microprofiles. The nitrifying bacterial community responded very quickly to changes in environmental conditions, and new steady-state microprofiles of O(2) and NO(3) were usually approached within a few hours after perturbation. Nitrification started quickly after introduction of O(2) in previously anoxic layers, suggesting prolonged survival of the nitrifiers during anaerobiosis. Changes in the availability of O(2) and NH(4) greatly affected the nitrification profile, and there was a high rate of coupled nitrification-denitrification under conditions in which nitrification occurred right above the oxic-anoxic interface. Addition of C(2)H(2) rapidly removed the NO(3) peaks, indicating that NO(3) production was due mainly to autotrophic nitrification.}, }
@article {pmid16349039, year = {1993}, author = {Yadav, JS and Reddy, CA}, title = {Mineralization of 2,4-Dichlorophenoxyacetic Acid (2,4-D) and Mixtures of 2,4-D and 2,4,5-Trichlorophenoxyacetic Acid by Phanerochaete chrysosporium.}, journal = {Applied and environmental microbiology}, volume = {59}, number = {9}, pages = {2904-2908}, pmid = {16349039}, issn = {0099-2240}, abstract = {Evidence is presented for mineralization of 2,4-dichlorophenoxyacetic acid (2,4-D) in nutrient-rich media (high-nitrogen and malt extract media) by wild-type Phanerochaete chrysosporium and by a peroxidase-negative mutant of this organism. Mass balance analysis of [U-ring-C]2,4-D mineralization in malt extract cultures showed 82.7% recovery of radioactivity. Of this, 38.6% was released as CO(2) and 27.0, 11.2, and 5.9% were present in the aqueous, methylene chloride, and mycelial fractions, respectively. 2,4-D and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) were simultaneously mineralized when presented as a mixture, and mutual inhibition of degradation was not observed. In contrast, a relatively higher rate of mineralization of 2,4-D and 2,4,5-T was observed when these compounds were tested as mixtures than when they were tested alone.}, }
@article {pmid16348987, year = {1993}, author = {Rysgaard, S and Risgaard-Petersen, N and Nielsen, LP and Revsbech, NP}, title = {Nitrification and denitrification in lake and estuarine sediments measured by the N dilution technique and isotope pairing.}, journal = {Applied and environmental microbiology}, volume = {59}, number = {7}, pages = {2093-2098}, pmid = {16348987}, issn = {0099-2240}, abstract = {The transformation of nitrogen compounds in lake and estuarine sediments incubated in the dark was analyzed in a continuous-flowthrough system. The inflowing water contained NO(3), and by determination of the isotopic composition of the N(2), NO(3), and NH(4) pools in the outflowing water, it was possible to quantify the following reactions: total NO(3) uptake, denitrification based on NO(3) from the overlying water, nitrification, coupled nitrification-denitrification, and N mineralization. In sediment cores from both lake and estuarine environments, benthic microphytes assimilated NO(3) and NH(4) for a period of 25 to 60 h after darkening. Under steady-state conditions in the dark, denitrification of NO(3) originating from the overlying water accounted for 91 to 171 mumol m h in the lake sediments and for 131 to 182 mumol m h in the estuarine sediments, corresponding to approximately 100% of the total NO(3) uptake for both sediments. It seems that high NO(3) uptake by benthic microphytes in the initial dark period may have been misinterpreted in earlier investigations as dissimilatory reduction to ammonium. The rates of coupled nitrification-denitrification within the sediments contributed to 10% of the total denitrification at steady state in the dark, and total nitrification was only twice as high as the coupled process.}, }
@article {pmid16348964, year = {1993}, author = {Sharma, RV and Edwards, RT and Beckett, R}, title = {Physical characterization and quantification of bacteria by sedimentation field-flow fractionation.}, journal = {Applied and environmental microbiology}, volume = {59}, number = {6}, pages = {1864-1875}, pmid = {16348964}, issn = {0099-2240}, abstract = {Studies in microbial ecology require accurate measures of cell number and biomass. Although epifluorescence microscopy is an accepted and dependable method for determining cell numbers, current methods of converting biovolume to biomass are error prone, tedious, and labor-intensive. This paper describes a technique with sedimentation field-flow fractionation to enumerate bacteria and determine their density, size, and mass. Using cultured cells of different shapes and sizes, we determined optimum values for separation run parameters and sample-handling procedures. The technique described can separate and detect 4', 6-diamidino-2-phenylindole-stained cells and generate a fractogram from which cell numbers and their size or mass distribution can be calculated. A direct method for estimating bacterial biomass (dry organic matter content) which offers distinct advantages over present methods for calculating biomass has been developed.}, }
@article {pmid16348934, year = {1993}, author = {Finster, K and Bak, F}, title = {Complete oxidation of propionate, valerate, succinate, and other organic compounds by newly isolated types of marine, anaerobic, mesophilic, gram-negative, sulfur-reducing eubacteria.}, journal = {Applied and environmental microbiology}, volume = {59}, number = {5}, pages = {1452-1460}, pmid = {16348934}, issn = {0099-2240}, abstract = {Anaerobic enrichment cultures with either propionate, succinate, lactate, or valerate and elemental sulfur and inocula from shallow marine or deep-sea sediments were dominated by rod-shaped motile bacteria after three transfers. By application of deep-agar dilutions, five eubacterial strains were obtained in pure culture and designated Kyprop, Gyprop, Kysw2, Gylac, and Kyval. All strains were gram negative and grew by complete oxidation of the electron donors and concomitant stoichiometric reduction of elemental sulfur to hydrogen sulfide. The isolates used acetate, propionate, succinate, lactate, pyruvate, oxaloacetate, maleate, glutamate, alanine, aspartate, and yeast extract. All isolates, except strain Gylac, used citrate as an electron donor but valerate was oxidized only by strain Kyval. Fumarate and malate were degraded by all strains without an additional electron donor or acceptor. Kyprop, Gyprop, and Gylac utilized elemental sulfur as the sole inorganic electron acceptor, while Kysw2 and Kyval also utilized nitrate, dimethyl sulfoxide, or Fe(III)-citrate as an electron acceptor.}, }
@article {pmid16348931, year = {1993}, author = {Prufert-Bebout, L and Paerl, HW and Lassen, C}, title = {Growth, nitrogen fixation, and spectral attenuation in cultivated trichodesmium species.}, journal = {Applied and environmental microbiology}, volume = {59}, number = {5}, pages = {1367-1375}, pmid = {16348931}, issn = {0099-2240}, abstract = {Physiological studies of Trichodesmium species have been hindered by difficulties in maintaining actively growing, nitrogen-fixing cultures. Previous cultivation successes have not been widely duplicated. We present here a simple modified seawater medium and handling techniques which have been used to maintain actively growing Trichodesmium thiebautii in laboratory culture for over 1 year. The cultured population, isolated from coastal Atlantic waters, has a growth rate of 0.23 division day and exhibits light-dependent nitrogen fixation during exponential growth. Various morphologies, including solitary trichomes, and aggregates (spherical puffs and fusiform tufts) are present during growth. Spectral and scalar irradiance were measured within naturally occurring (coastal Atlantic) aggregates with small (diameter, 50 to 70 mum) spherical fiber-optic sensors. In contrast to naturally occurring puffs, cultivated Trichodesmium aggregates exhibited spectral properties consistent with low-light adaptation. Cultivated puff-type aggregates were also examined by using oxygen microelectrodes. The simple medium and approach used for cultivation should be easily reproducible and amenable to further manipulations and modifications useful for physiological studies of Trichodesmium spp. in culture.}, }
@article {pmid16348891, year = {1993}, author = {Barkay, T and Liebert, C and Gillman, M}, title = {Conjugal gene transfer to aquatic bacteria detected by the generation of a new phenotype.}, journal = {Applied and environmental microbiology}, volume = {59}, number = {3}, pages = {807-814}, pmid = {16348891}, issn = {0099-2240}, abstract = {An experimental approach based on the assembly of genes of a catabolic pathway was used to detect transconjugants in aquatic communities. Resistance to phenylmercury acetate was established in transconjugants when wide-host-range conjugal plasmids containing merB, the gene encoding organomercurial lyase, were transferred to strains from aquatic communities that had been acclimated to inorganic mercury and thus enriched for populations containing merA, the gene encoding mercuric reductase (T. Barkay, Appl. Environ. Microbiol. 53:2725-2732, 1987). Conjugation was confirmed by using the plasmids' encoded antibiotic resistance patterns and by hybridization with a eukaryotic gene. Three merB-conjugal plasmids, belonging to incompatibility groups W (pGTE16), P1 (pGTE26), and N (pGTE25), were prepared. Transfers by filter matings of pGTE16 and pGTE26 from Pseudomonas aeruginosa PA01 to indigenous strains were at efficiencies of 4.5 x 10 and 4.8 x 10 transconjugant per potential recipient, respectively. These efficiencies were from 1 to 2 orders of magnitude below those observed for intraspecies matings with genetically marked recipients. The third plasmid, pGTE25, was not stably maintained in P. aeruginosa donors, and its transfer from Escherichia coli donors was below the level of detection. Characterized transconjugant strains were shown to be Pseudomonas spp. Potential applications of the described experimental approach in the creation of bacterial populations with new catabolic capabilities in hazardous waste sites and in the detection of transfer of recombinant DNA from engineered microorganisms to indigenous bacteria are discussed.}, }
@article {pmid16348872, year = {1993}, author = {Adamsen, AP and King, GM}, title = {Methane consumption in temperate and subarctic forest soils: rates, vertical zonation, and responses to water and nitrogen.}, journal = {Applied and environmental microbiology}, volume = {59}, number = {2}, pages = {485-490}, pmid = {16348872}, issn = {0099-2240}, abstract = {Rates of methane consumption were measured in subarctic coniferous and temperate mixed-hardwood forest soils, using static chambers and intact soil cores. Rates at both sites were generally between 1 and 3 mg of CH(4) m day and decreased with increasing soil water contents above 20%. Addition of ammonium (1 mumol g of soil) strongly inhibited methane oxidation in the subarctic soils; a lesser inhibition was observed for temperate forest samples. The response to nitrogen additions occurred within a few hours and was probably due to physiological changes in the active methane-consuming populations. Methane consumption in soils from both sites was stratified vertically, with a pronounced subsurface maximum. This maximum was coincident with low levels of both nitrate and ammonium in the mixed-hardwood forest soil.}, }
@article {pmid15335810, year = {1993}, author = {Lenski, RE}, title = {Evolution: a lac of interest in evolution.}, journal = {Current biology : CB}, volume = {3}, number = {2}, pages = {121-123}, doi = {10.1016/0960-9822(93)90171-j}, pmid = {15335810}, issn = {0960-9822}, }
@article {pmid16348835, year = {1993}, author = {Thamdrup, B and Finster, K and Hansen, JW and Bak, F}, title = {Bacterial disproportionation of elemental sulfur coupled to chemical reduction of iron or manganese.}, journal = {Applied and environmental microbiology}, volume = {59}, number = {1}, pages = {101-108}, pmid = {16348835}, issn = {0099-2240}, abstract = {A new chemolithotrophic bacterial metabolism was discovered in anaerobic marine enrichment cultures. Cultures in defined medium with elemental sulfur (S) and amorphous ferric hydroxide (FeOOH) as sole substrates showed intense formation of sulfate. Furthermore, precipitation of ferrous sulfide and pyrite was observed. The transformations were accompanied by growth of slightly curved, rod-shaped bacteria. The quantification of the products revealed that S was microbially disproportionated to sulfate and sulfide, as follows: 4S + 4H(2)O --> SO(4) + 3H(2)S + 2H. Subsequent chemical reactions between the formed sulfide and the added FeOOH led to the observed precipitation of iron sulfides. Sulfate and iron sulfides were also produced when FeOOH was replaced by FeCO(3). Further enrichment with manganese oxide, MnO(2), instead of FeOOH yielded stable cultures which formed sulfate during concomitant reduction of MnO(2) to Mn. Growth of small rod-shaped bacteria was observed. When incubated without MnO(2), the culture did not grow but produced small amounts of SO(4) and H(2)S at a ratio of 1:3, indicating again a disproportionation of S. The observed microbial disproportionation of S only proceeds significantly in the presence of sulfide-scavenging agents such as iron and manganese compounds. The population density of bacteria capable of S disproportionation in the presence of FeOOH or MnO(2) was high, > 10 cm in coastal sediments. The metabolism offers an explanation for recent observations of anaerobic sulfide oxidation to sulfate in anoxic sediments.}, }
@article {pmid16348828, year = {1992}, author = {Bååth, E and Frostegård, A and Fritze, H}, title = {Soil Bacterial Biomass, Activity, Phospholipid Fatty Acid Pattern, and pH Tolerance in an Area Polluted with Alkaline Dust Deposition.}, journal = {Applied and environmental microbiology}, volume = {58}, number = {12}, pages = {4026-4031}, pmid = {16348828}, issn = {0099-2240}, abstract = {Soil bacterial biomass, phospholipid fatty acid pattern, pH tolerance, and growth rate were studied in a forest area in Finland that is polluted with alkaline dust from an iron and steel works. The pollution raised the pH of the humus layer from 4.1 to 6.6. Total bacterial numbers and the total amounts of bacterial phospholipid fatty acids in the humus layer did not differ between the unpolluted control sites and the polluted ones. The number of CFU increased by a factor of 6.4 in the polluted sites compared with the controls, while the bacterial growth rate, measured by the thymidine incorporation technique, increased about 1.8-fold in the polluted sites. A shift in the pattern of phospholipid fatty acids indicated a shift in the bacterial species composition. The largest proportional increase was found for the fatty acid 10Me18:0, which indicated an increase in the number of actinomycetes in the polluted sites. The levels of the fatty acids i14:0, 16:1omega5, cy17:0, 18:1omega7, and 19:1 also increased in the polluted sites while those of fatty acids 15:0, i15:0, 10Me16:0, 16:1omega7t, 18:1omega9, and cy19:0 decreased compared with the unpolluted sites. An altered pH tolerance of the bacterial assemblage was detected either as a decrease in acid-tolerant CFU in the polluted sites or as altered bacterial growth rates at different pHs. The latter was estimated by measuring the thymidine incorporation rate of bacteria extracted from soil by homogenization-centrifugation at different pHs.}, }
@article {pmid16348766, year = {1992}, author = {King, GM and Adamsen, AP}, title = {Effects of Temperature on Methane Consumption in a Forest Soil and in Pure Cultures of the Methanotroph Methylomonas rubra.}, journal = {Applied and environmental microbiology}, volume = {58}, number = {9}, pages = {2758-2763}, pmid = {16348766}, issn = {0099-2240}, abstract = {Methane oxidation in soil cores from a mixed hardwood-coniferous forest varied relatively little as a function of incubation temperatures from -1 to 30 degrees C. The increase in oxidation rate was proportional to T (in kelvins). This relationship was consistent with limitation of methane transport through a soil gas phase to a subsurface zone of consumption by diffusion. The Q(10) for CO(2) production, 3.4, was substantially higher than that for methane oxidation, 1.1, and indicated that the response of soil respiration to temperature was limited by enzymatic processes and not diffusion of either organic substrates or molecular oxygen. When grown under conditions of phase-transfer limitation, cultures of Methylomonas rubra showed a minimal response to temperature changes between 19 and 38 degrees C, as indicated by methane oxidation rates; in the absence of phase-transfer limitations, M. rubra oxidized methane at rates strongly dependent on temperature.}, }
@article {pmid16348759, year = {1992}, author = {Natarajan, MR and Oriel, P}, title = {Transfer of Transposon Tn916 from Bacillus subtilis into a Natural Soil Population.}, journal = {Applied and environmental microbiology}, volume = {58}, number = {8}, pages = {2701-2703}, pmid = {16348759}, issn = {0099-2240}, abstract = {A Bacillus subtilis transconjugant with a Tn916 chromosomal insert was obtained through mating with Escherichia coli carrying the transposon as a plasmid insert. Actinomycetes were identified as frequent transposon recipients following the introduction of the B. subtilis transconjugant into a soil microcosm.}, }
@article {pmid16348584, year = {1991}, author = {Jones, RA and Broder, MW and Stotzky, G}, title = {Effects of genetically engineered microorganisms on nitrogen transformations and nitrogen-transforming microbial populations in soil.}, journal = {Applied and environmental microbiology}, volume = {57}, number = {11}, pages = {3212-3219}, pmid = {16348584}, issn = {0099-2240}, abstract = {The principal concern about releasing genetically engineered microorganisms (GEMs) into the environment is their potential adverse effects on the environment, whether caused directly or indirectly by the GEMs. The effects of five GEMs on ammonification, nitrification, and denitrification in soil were studied. With the possible exception of a strain of Enterobacter cloacae carrying a plasmid, no consistent statistically or ecologically significant differences in effects on these processes or on the population dynamics of the microorganisms responsible for the processes were observed between soils inoculated with the GEMs or their homologous plasmidless hosts and those that were not inoculated. Increasing the concentration of montmorillonite in the soil enhanced the rate of nitrification, regardless of the inoculum, indicating that the perfusion technique used was sensitive enough to detect changes in nitrification rates when they occurred.}, }
@article {pmid16348473, year = {1991}, author = {Vande Woestyne, M and Bruyneel, B and Mergeay, M and Verstraete, W}, title = {The Fe Chelator Proferrorosamine A Is Essential for the Siderophore-Mediated Uptake of Iron by Pseudomonas roseus fluorescens.}, journal = {Applied and environmental microbiology}, volume = {57}, number = {4}, pages = {949-954}, pmid = {16348473}, issn = {0099-2240}, abstract = {Pseudomonas roseus fluorescens produces, besides the Fe chelator proferrorosamine A, Fe -chelating compounds, called siderophores. The production of proferrorosamine A and siderophores by P. roseus fluorescens appears to be controlled in a similar way by the concentration of available iron and by the concentration of dissolved oxygen. The higher the concentration of iron available for the microorganism, the lower the production of both chelating compounds. However, the production of siderophores was much more sensitive to iron availability than was proferrorosamine A production. Proferrorosamine A and siderophores were only produced in minimal medium C if the concentration of dissolved oxygen ranged from 4.5 to 2.0 ppm. At higher or lower concentrations, none of the iron-chelating compounds were produced. Furthermore, it has been shown that proferrorosamine-negative Tn5 mutants of P. roseus fluorescens were able to form siderophores only under iron-limiting conditions when proferrorosamine A was added to the medium. Our data suggest that proferrorosamine A production is essential for siderophore synthesis by P. roseus fluorescens; the production of siderophores occurred only when proferrorosamine A was present.}, }
@article {pmid16837349, year = {1990}, author = {Leijonmarck, CE and Carlstedt-Duke, B and Gustafsson, A and Midtvedt, AC and Norin, KE and Saxerholt, H and Midtvedt, T}, title = {Enteral nutrition and the function of the intestinal microflora in healthy adults.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {9}, number = {3}, pages = {163-167}, doi = {10.1016/0261-5614(90)90049-x}, pmid = {16837349}, issn = {0261-5614}, abstract = {An oral feeding formula was given to 5 healthy volunteers for 8 days. Faecal samples were collected before, during and after the feeding period. The effect of enteral nutrition (EN) on the following seven intestinal microflora-associated characteristics (MACs) was studied: formation of urobilinogen, coprostanol and deoxycholic acid, degradation of mucin and beta-aspartylglycine, faecal tryptic activity, and production of short-chain fatty acids (SCFAs). None of the microbial functions studied were lost during the study. The urobilinogen level increased during EN (P < 0.05) but it seems reasonable to assume that this was a concentration effect due to a decrease in stool mass. The concentration of SCFAs decreased during EN (P < 0.05) and this reflects the absence of dietary fibre in the feed used.}, }
@article {pmid16348212, year = {1990}, author = {Orvos, DR and Lacy, GH and Cairns, J}, title = {Genetically Engineered Erwinia carotovora: Survival, Intraspecific Competition, and Effects upon Selected Bacterial Genera.}, journal = {Applied and environmental microbiology}, volume = {56}, number = {6}, pages = {1689-1694}, pmid = {16348212}, issn = {0099-2240}, abstract = {Environmental use of genetically engineered microorganisms has raised concerns about potential ecological impact. This research evaluated the survival, competitiveness, and effects upon selected bacterial genera of wild-type and genetically engineered Erwinia carotovora subsp. carotovora to ascertain if differences between the wild-type and genetically engineered strains exist in soil microcosms. The engineered strain contained a chromosomally inserted gene for kanamycin resistance. No significant differences in survival in nonsterile soil over 2 months or in the competitiveness of either strain were observed when the strains were added concurrently to microcosms. For reasons that remain unclear, the engineered strain did survive longer in sterilized soil. The effects of both strains on total bacteria, Pseudomonas and Staphylococcus strains, and actinomycetes were observed. While some apparent differences were observed, they were not statistically significant. A better understanding of the microbial ecology of engineered bacteria, especially pathogens genetically altered for use as biological control agents, is essential before commercial applications can be accomplished.}, }
@article {pmid16348197, year = {1990}, author = {Armstrong, JL and Wood, ND and Porteous, LA}, title = {Transconjugation between Bacteria in the Digestive Tract of the Cutworm Peridroma saucia.}, journal = {Applied and environmental microbiology}, volume = {56}, number = {5}, pages = {1492-1493}, pmid = {16348197}, issn = {0099-2240}, abstract = {Transconjugants arising from transfer of plasmid R388::Tn1721 between donor and recipient strains of Enterobacter cloacae were detected in samples from the digestive tracts and fecal pellets of variegated cutworms (Peridroma saucia).}, }
@article {pmid16348069, year = {1989}, author = {Mueller, JG and Chapman, PJ and Pritchard, PH}, title = {Action of a fluoranthene-utilizing bacterial community on polycyclic aromatic hydrocarbon components of creosote.}, journal = {Applied and environmental microbiology}, volume = {55}, number = {12}, pages = {3085-3090}, pmid = {16348069}, issn = {0099-2240}, abstract = {Cultures enriched by serial transfer through a mineral salts medium containing fluoranthene were used to establish a stable, seven-member bacterial community from a sandy soil highly contaminated with coal tar creosote. This community exhibited an ability to utilize fluoranthene as the sole carbon source for growth, as demonstrated by increases in protein concentration and changes in absorption spectra when grown on fluoranthene in liquid culture. Biotransformation of other polycyclic aromatic hydrocarbons (PAHs) was verified by demonstrating their disappearance from an artificial PAH mixture by capillary gas chromatography. When grown on fluoranthene as the sole carbon source and subsequently exposed to fluoranthene plus 16 additional PAHs typical of those found in creosote, this community transformed all PAHs present in this defined mixture. After 3 days of incubation, 13 of the original 17 PAH components were degraded to levels below the limit of detection (10 ng/liter). Continued incubation resulted in extensive degradation of the remaining four compounds. The ability of this community to utilize a high-molecular-weight PAH as the sole carbon source, in conjunction with its ability to transform a diverse array of PAHs, suggests that it may be of value in the bioremediation of environments contaminated with PAHs, such as those impacted by creosote.}, }
@article {pmid16348015, year = {1989}, author = {Lighthart, B and Kim, J}, title = {Simulation of airborne microbial droplet transport.}, journal = {Applied and environmental microbiology}, volume = {55}, number = {9}, pages = {2349-2355}, pmid = {16348015}, issn = {0099-2240}, abstract = {The framework for a simulation model which describes the dispersion of individual droplets of water containing viable microbes is presented. The model accounts for physical, chemical, biological, and measured meteorological parameters of each droplet at each of many short time steps. Repeating the modeling process for many droplets will simulate a cloud of droplets. The model is compared with the Tulelake, Calif., release in 1988 and found to show very similar patterns of deposition within 30 m (the maximum observation distance of the source. A hypothesis for the survival sequence in the microbe-containing droplets is discussed.}, }
@article {pmid16347941, year = {1989}, author = {Genthner, BR and Price, WA and Pritchard, PH}, title = {Characterization of anaerobic dechlorinating consortia derived from aquatic sediments.}, journal = {Applied and environmental microbiology}, volume = {55}, number = {6}, pages = {1472-1476}, pmid = {16347941}, issn = {0099-2240}, abstract = {Four methanogenic consortia which degraded 2-chlorophenol, 3-chlorophenol, 2-chlorobenzoate, and 3-chlorobenzoate, respectively, and one nitrate-reducing consortium which degraded 3-chlorobenzoate were characterized. Degradative activity in these consortia was maintained by laboratory transfer for over 2 years. In the methanogenic consortia, the aromatic ring was dechlorinated before mineralization to methane and carbon dioxide. After dechlorination, the chlorophenol consortia converted phenol to benzoate before mineralization. All methanogenic consortia degraded both phenol and benzoate. The 3-chlorophenol and 3-chlorobenzoate consortia also degraded 2-chlorophenol. No other cross-acclimation to monochlorophenols or monochlorobenzoates was detected in the methanogenic consortia. The consortium which required nitrate for the degradation of 3-chlorobenzoate degraded benzoate and 4-chlorobenzoate anaerobically in the presence of KNO(3), but not in its absence. This consortium also degraded benzoate, but not 3-chlorobenzoate, aerobically.}, }
@article {pmid16347940, year = {1989}, author = {Genthner, BR and Price, WA and Pritchard, PH}, title = {Anaerobic Degradation of Chloroaromatic Compounds in Aquatic Sediments under a Variety of Enrichment Conditions.}, journal = {Applied and environmental microbiology}, volume = {55}, number = {6}, pages = {1466-1471}, pmid = {16347940}, issn = {0099-2240}, abstract = {Anaerobic degradation of monochlorophenols and monochlorobenzoates in a variety of aquatic sediments was compared under four enrichment conditions. A broader range of compounds was degraded in enrichments inoculated with sediment exposed to industrial effluents. Degradation of chloroaromatic compounds was observed most often in methanogenic enrichments and in enrichments amended with 1 mM bromoethane sulfonic acid. Degradation was observed least often in enrichments with added nitrate or sulfate. The presence of 10 mM bromoethane sulfonic acid prevented or inhibited degradation of most compounds tested. Primary enrichments in which KNO(3) was periodically replenished to maintain enrichment characteristics degraded chlorobenzoates, but not chlorophenols. In contrast, primary enrichments in which Na(2)SO(4) was periodically replenished failed to degrade any chloroaromatic compounds. Upon transfer to fresh medium, none of the sulfate enrichments required the presence of Na(2)SO(4) for degradation, while only two nitrate enrichments required the presence of KNO(3) for degradation. As a class of compounds, chlorophenols were degraded more readily than chlorobenzoates. However, as individual compounds 3-chlorobenzoate, 2-chlorophenol, and 3-chlorophenol degradation was observed most often and with an equal frequency. Within the chlorophenol class, the relative order of degradability was ortho > meta > para, while that of chlorobenzoates was meta > ortho > para, In laboratory transfers, 2-chlorobenzoate, 3-chlorobenzoate, and 2-chlorophenol degradation was most easily maintained, while degradation of para-chlorinated compounds was very difficult to maintain.}, }
@article {pmid16347937, year = {1989}, author = {Hansen, GH and Olafsen, JA}, title = {Bacterial Colonization of Cod (Gadus morhua L.) and Halibut (Hippoglossus hippoglossus) Eggs in Marine Aquaculture.}, journal = {Applied and environmental microbiology}, volume = {55}, number = {6}, pages = {1435-1446}, pmid = {16347937}, issn = {0099-2240}, abstract = {Aquaculture has brought about increased interest in mass production of marine fish larvae. Problems such as poor egg quality and mass mortality of fish larvae have been prevalent. The intensive incubation techniques that often result in bacterial overgrowth on fish eggs could affect the commensal relationship between the indigenous microflora and opportunistic pathogens and subsequently hamper egg development, hatching, larval health, and ongrowth. Little information about the adherent microflora on fish eggs is available, and the present study was undertaken to describe the microbial ecology during egg development and hatching of two fish species of potential commercial importance in marine aquaculture. Attachment and development of the bacterial flora on cod (Gadus morhua L.) eggs from fertilization until hatching was studied by scanning electron microscopy. The adherent microflora on cod (G. morhua L.) and halibut (Hippoglossus hippoglossus) eggs during incubation was characterized and grouped by cluster analysis. Marked bacterial growth could be demonstrated 2 h after fertilization, and at hatching eggs were heavily overgrown. Members of the genera Pseudomonas, Alteromonas, Aeromonas, and Flavobacterium were found to dominate on the surface of both cod and halibut eggs. The filamentous bacterium Leucothrix mucor was found on eggs from both species. While growth of L. mucor on halibut eggs was sparse, cod eggs with a hairy appearance due to overgrowth by this bacterium close to hatching were frequently observed. Vibrio fischeri could be detected on cod eggs only, and pathogenic vibrios were not detected. Members of the genera Moraxella and Alcaligenes were found only on halibut eggs. Caulobacter and Seliberia spp. were observed attached to eggs dissected from cod ovaries under sterile conditions, indicating the presence of these bacteria in ovaries before spawning. Adherent strains did not demonstrate antibiotic resistance above a normal level. Attempts to regulate the egg microflora by incubation of gnotobiotic eggs with defined antibiotic-producing strains did not result in persistent protection against subsequent colonization by the microflora of the incubator.}, }
@article {pmid15092468, year = {1989}, author = {Santo Domingo, JW and Fuentes, FA and Hazen, TC}, title = {Survival and activity of Streptococcus faecalis and Escherichia coli in petroleum-contaminated tropical marine waters.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {56}, number = {4}, pages = {263-281}, doi = {10.1016/0269-7491(89)90073-0}, pmid = {15092468}, issn = {0269-7491}, abstract = {The in situ survival and activity of Streptococcus faecalis and Escherichia coli were studied using membrane diffusion chambers in tropical marine waters receiving oil refinery effluents. Protein synthesis, DNA synthesis, respiration or fermentation, INT reduced per cell, and ATP per cell were used to measure physiological activity. Cell densities decreased significantly over time at both sites for both S. faecalis and E. coli; however, no significant differences in survival pattern were observed between S. faecalis and E. coli. Differences in protein synthesis between the two were only observed at a study site which was not heavily oiled. E. coli was more active in protein synthesis and respiration than S. faecalis at both oiled and unoiled sites, and the percentage of the E. coli population that was respiring was significantly higher than S. faecalis fermenting cells at both sites. However, S. faecalis cells were more active in DNA synthesis and higher in ATP content than E. coli cells at both sites. Although fecal streptococci have been suggested as a better indicator of fecal contamination than fecal coliforms in marine waters, in this study both E. coli and S. faecalis survived and remained physiologically active for extended periods of time. These results suggest that the fecal streptococci group is not a better indicator of fecal contamination in tropical marine waters than the fecal coliform group, especially when that environment is high in long-chained hydrocarbons.}, }
@article {pmid16347791, year = {1988}, author = {Tomei, FA and Rouse, D and Maki, JS and Mitchell, R}, title = {Presence of an unusual methanogenic bacterium in coal gasification waste.}, journal = {Applied and environmental microbiology}, volume = {54}, number = {12}, pages = {2964-2970}, pmid = {16347791}, issn = {0099-2240}, abstract = {Methanogenic bacteria growing on a pilot-scale, anaerobic filter processing coal gasification waste were enriched in a mineral salts medium containing hydrogen and acetate as potential energy sources. Transfer of the enrichments to methanol medium resulted in the initial growth of a strain of Methanosarcina barkeri, but eventually small cocci became dominant. The cocci growing on methanol produced methane and exhibited the typical fluorescence of methanogenic bacteria. They grew in the presence of the cell wall synthesis-inhibiting antibiotics d-cycloserine, fosfomycin, penicillin G, and vancomycin as well as in the presence of kanamycin, an inhibitor of protein synthesis in eubacteria. The optimal growth temperature was 37 degrees C, and the doubling time was 7.5 h. The strain lysed after reaching stationary phase. The bacterium grew poorly with hydrogen as the energy source and failed to grow on acetate. Morphologically, the coccus shared similarities with Methanosarcina sp. Cells were 1 mum wide, exhibited the typical thick cell wall and cross-wall formation, and formed tetrads. Packets and cysts were not formed.}, }
@article {pmid16347703, year = {1988}, author = {Lighthart, B}, title = {Some Changes in Gut Bacterial Flora of Field-Grown Peridroma saucia (Lepidoptera: Noctuidae) When Brought into the Laboratory.}, journal = {Applied and environmental microbiology}, volume = {54}, number = {7}, pages = {1896-1898}, pmid = {16347703}, issn = {0099-2240}, abstract = {Removal of Peridroma saucia from the field to the laboratory caused little change in the quantity of facultative and aerobic bacteria in the gut but produced significant qualitative and quantitative changes in distinguishable groups of the family Enterobacteriaceae in the gut.}, }
@article {pmid16347630, year = {1988}, author = {Mead, LJ and Khachatourians, GG and Jones, GA}, title = {Microbial Ecology of the Gut in Laboratory Stocks of the Migratory Grasshopper, Melanoplus sanguinipes (Fab.) (Orthoptera: Acrididae).}, journal = {Applied and environmental microbiology}, volume = {54}, number = {5}, pages = {1174-1181}, pmid = {16347630}, issn = {0099-2240}, abstract = {Mean pH values in pooled samples of foregut, midgut, and hindgut from adult Melanoplus sanguinipes, which had been raised in the laboratory on barley shoots and wheat bran, were 5.15, 6.39, and 5.98, respectively. Homogenates of midgut/hindgut sections and frass (feces) yielded colony counts of bacteria by the spread plate method of 5.7 to 5.9 and 5.3 to 5.5 log(10) colonies per mg, respectively; there were no significant differences (P > 0.05) between counts obtained on several media or on media incubated aerobically or anaerobically. There was no evidence of significant populations of protozoa, fungi, or obligately anaerobic bacteria associated with the gut. A total of 168 pure strains of bacteria isolated from the gut sections were characterized and assigned to 11 taxonomic groups, including Enterococcus spp., Serratia liquefaciens, Pseudomonas spp., and Enterobacter spp. Numbers of Enterococcus spp. in the gut were 2 to 3 orders of magnitude higher than those of the other genera. Strains representing only four of the groups were recovered from bran fed to the grasshoppers; the barley shoots, which were raised in sterile soil, appeared virtually sterile. Examination of the gut wall by scanning electron microscopy revealed the presence of epimural bacteria in the foregut and hindgut but not in the midgut. The distribution of epimural cocci and bacilli differed with the gut section examined. Numerous spherical to ovoid structures up to 10 mum in diameter, which were not identified, were associated with the microvillous surface of the midgut epithelium. Acetate was present in gut, hemolymph, and frass, and it was shown that representative isolates of Enterococcus spp. and Enterobacter agglomerans produced acetate when incubated in an aqueous suspension of bran. The egestion time of solid digesta, as measured with methylene blue-stained barley shoots, was 3.0 to 5.7 h. The results show that M. sanguinipes supported extensive indigenous populations of luminal and epimural bacteria in the gut which were composed predominantly of facultatively anaerobic species; the relatively short egestion time, indicating rapid passage of digesta through the gut, was consistent with the microscopic appearance of digesta residues in frass and could account, at least in part, for the absence of a significant population of obligately anaerobic bacteria from the gut.}, }
@article {pmid16347488, year = {1987}, author = {Barkay, T}, title = {Adaptation of aquatic microbial communities to hg stress.}, journal = {Applied and environmental microbiology}, volume = {53}, number = {12}, pages = {2725-2732}, pmid = {16347488}, issn = {0099-2240}, abstract = {The mechanism of adaptation to Hg in four aquatic habitats was studied by correlating microbially mediated Hg volatilization with the adaptive state of the exposed communities. Community diversity, heterotrophic activity, and Hg resistance measurements indicated that adaptation of all four communities was stimulated by preexposure to Hg. In saline water communities, adaptation was associated with rapid volatilization after an initial lag period. This mechanism, however, did not promote adaptation in a freshwater sample, in which Hg was volatilized slowly, regardless of the resistance level of the microbial community. Distribution of the mer operon among representative colonies of the communities was not related to adaptation to Hg. Thus, although volatilization enabled some microbial communities to sustain their functions in Hg-stressed environments, it was not mediated by the genes that serve as a model system in molecular studies of bacterial resistance to mercurials.}, }
@article {pmid16347389, year = {1987}, author = {Belay, N and Daniels, L}, title = {Production of ethane, ethylene, and acetylene from halogenated hydrocarbons by methanogenic bacteria.}, journal = {Applied and environmental microbiology}, volume = {53}, number = {7}, pages = {1604-1610}, pmid = {16347389}, issn = {0099-2240}, abstract = {Several methanogenic bacteria were shown to produce ethane, ethylene, and acetylene when exposed to the halogenated hydrocarbons bromoethane, dibromo- or dichloroethane, and 1,2-dibromoethylene, respectively. They also produced ethylene when exposed to the coenzyme M analog and specific methanogenic inhibitor bromoethanesulfonic acid. The production of these gases from halogenated hydrocarbons has a variety of implications concerning microbial ecology, agriculture, and toxic waste treatment. All halogenated aliphatic compounds tested were inhibitory to methanogens. Methanococcus thermolithotrophicus, Methanococcus deltae, and Methanobacterium thermoautotrophicum DeltaH and Marburg were completely inhibited by 7 muM 1,2-dibromoethane and, to various degrees, by 51 to 1,084 muM 1,2-dichloroethane, 1,2-dibromoethylene, 1,2-dichloroethylene, and trichloroethylene. In general, the brominated compounds were more inhibitory. The two Methanococcus species were fully inhibited by 1 muM bromoethanesulfonic acid, whereas both Methanobacterium strains were only partly inhibited by 2,124 muM. Coenzyme M protected cells from bromoethanesulfonic acid but not from any of the other inhibitors.}, }
@article {pmid16347019, year = {1986}, author = {Isa, Z and Grusenmeyer, S and Verstraete, W}, title = {Sulfate reduction relative to methane production in high-rate anaerobic digestion: microbiological aspects.}, journal = {Applied and environmental microbiology}, volume = {51}, number = {3}, pages = {580-587}, pmid = {16347019}, issn = {0099-2240}, abstract = {In the high-rate anaerobic reactors studied (ca. 10 g of chemical oxygen demand [COD] removed per liter of reactor per day), the sulfate-reducing bacteria (SRB) were poor competitors of methane-producing bacteria (MPB), scavenging only on the order of 10 to 20% of the total electron flow. The relatively noncompetitive nature of the SRB in this type of reactor is in sharp contrast to the tendency of the SRB to dominate in natural environments and in other types of anaerobic digesters. Various factors such as the feedback inhibition of H(2)S on the SRB, iron limitation, the origin of the SRB inocula, biokinetics, and thermodynamics were investigated. The outcome of the SRB-MPB competition under the reactor conditions studied appeared to be particularly determined by two factors. The SRB, as predicted by the V(max)-K(m) kinetics, competed most effectively at low substrate levels (<0.5 g of COD per liter). The MPB, however, appeared to colonize and adhere much more effectively to the polyurethane carrier matrix present in the reactor, thus compensating for the apparent lower growth rates. Even if the reactor was initially allowed to be predominantly colonized by SRB, the MPB could regain dominance.}, }
@article {pmid16347018, year = {1986}, author = {Isa, Z and Grusenmeyer, S and Verstraete, W}, title = {Sulfate reduction relative to methane production in high-rate anaerobic digestion: technical aspects.}, journal = {Applied and environmental microbiology}, volume = {51}, number = {3}, pages = {572-579}, pmid = {16347018}, issn = {0099-2240}, abstract = {The effect of different substrates and different levels of sulfate and sulfide on methane production relative to sulfate reduction in high-rate anaerobic digestion was evaluated. Reactors could be acclimated so that sulfate up to a concentration of 5 g of sulfate S per liter did not significantly affect methanogenesis. Higher levels gave inhibition because of salt toxicity. Sulfate reduction was optimal at a relatively low level of sulfate, i.e., 0.5 g of sulfate S per liter, but was also not significantly affected by higher levels. Both acetoclastic and hydrogenotrophic methane-producing bacteria adapted to much higher levels of free H(2)S than the values reported in the literature (50% inhibition occurred only at free H(2)S levels of more than 1,000 mg/liter). High levels of free H(2)S affected the sulfate-reducing bacteria only slightly. Formate and acetate supported the sulfate-reducing bacteria very poorly. In the high-rate reactors studied, intensive H(2)S formation occurred only when H(2) gas or an H(2) precursor such as ethanol was supplied.}, }
@article {pmid16346977, year = {1986}, author = {Frazer, AC and Bossert, I and Young, LY}, title = {Enzymatic aryl-o-methyl-C labeling of model lignin monomers.}, journal = {Applied and environmental microbiology}, volume = {51}, number = {1}, pages = {80-83}, pmid = {16346977}, issn = {0099-2240}, abstract = {Aryl-O-methyl ethers are abundant in aerobic and anaerobic environments. In particular, lignin is composed of units of this type. Lignin monomers specifically radiolabeled in methoxy, side chain, and ring carbons have been synthesized by chemical procedures and are important in studies of lignin synthesis and degradation, humus formation, and microbial O-demethylation. In this paper attention is drawn to an enzymatic procedure for preparing O-methyl-C-labeled aromatic lignin monomers which has not previously been exploited in microbial ecology and physiology studies and which has several advantages compared with chemical synthesis procedures. O-[methyl-C]vanillic and O-[methyl-C]ferulic acids were prepared with S-[methyl-C]adenosyl-l-methionine as the methyl donor, using commercially obtained porcine liver catechol-O-methyltransferase (EC 2.1.1.6). The specific activity of the methylated products was the same as that of the methyl donor, a maximum of about 58 muCi/mumol, and the yields were 42% (vanillate) and 35% (ferulate). Thus lignin monomers are readily prepared as O-methylated products of the catechol-O-methyltransferase reaction and, with this enzyme method of preparation, would be more widely available than labeled compounds which require chemical synthesis.}, }
@article {pmid16346930, year = {1985}, author = {Tomei, FA and Maki, JS and Mitchell, R}, title = {Interactions in syntrophic associations of endospore-forming, butyrate-degrading bacteria and h(2)-consuming bacteria.}, journal = {Applied and environmental microbiology}, volume = {50}, number = {5}, pages = {1244-1250}, pmid = {16346930}, issn = {0099-2240}, abstract = {Butyrate is an important intermediate in the anaerobic degradation of organic matter. In sulfate-depleted environments butyrate is oxidized to acetate and hydrogen by obligate proton reducers, in syntrophic association with hydrogen-consuming methanogens. This paper describes two enrichments of endospore-forming bacteria degrading butyrate in consortia with methanogens. The isolates are readily established in coculture with H(2)-consuming, sulfate-reducing bacteria by pasteurizing the culture. The two original enrichments differed in that one grew to an optically dense culture while the second grew in clumps. Examination by scanning electron microscopy showed that clumping resulted from the production of large amounts of extracellular polymer. Several H(2)-consuming methanogens were identified in the enrichments. Some of them grew closely associated to the butyrate degraders. This attachment to the hydrogen producer may permit some methanogens to compete for the growth substrate against other bacteria having higher substrate affinity.}, }
@article {pmid16346569, year = {1984}, author = {Blomquist, GK and Ström, GB and Söderström, B}, title = {Separation of fungal propagules by partition in aqueous polymer two-phase systems.}, journal = {Applied and environmental microbiology}, volume = {47}, number = {6}, pages = {1316-1318}, pmid = {16346569}, issn = {0099-2240}, abstract = {Conidia of Penicillium chrysogenum and Penicillium frequentans and sporangiospores of Rhizopus rhizopodiformis, Rhizomucor pusillus, and Mucor racemosus were subjected to partition in aqueous polymer two-phase systems. The partition behavior differed drastically between the conidia of the two Penicillium species and the sporangiospores of the three species of phycomycetes. This difference in partition behavior can be used for purification of fungi belonging to different taxonomical groups. P. frequentans was completely separated from M. racemosus by two extractions, whereas four extractions were needed to purify M. racemosus. This method was used on an air sample from a locality where wood fuel chips are handled. The conidia of the fungi Trichoderma viride and Rhizopus rhizopodiformis were removed completely by only two extractions.}, }
@article {pmid16346545, year = {1984}, author = {Houba, C and Remacle, J}, title = {Removal of cadmium by microorganisms in a two-stage chemostat.}, journal = {Applied and environmental microbiology}, volume = {47}, number = {5}, pages = {1158-1160}, pmid = {16346545}, issn = {0099-2240}, abstract = {A two-stage chemostat was used to study removal of cadmium by microorganisms in continuous culture. The medium was contaminated with 0.8 mg of Cd per liter. At 20 degrees C, most of the microbial biomass formed aggregates which settled in the second stage of the chemostat. Effluent was free of bacteria. Up to 80% of the metal contained in the inlet flux was removed by the biomass, with 20% remaining in solution. At 10 degrees C and with a shorter retention time, flocculation was poorer and metal removal by settling biomass did not exceed 35%.}, }
@article {pmid16346417, year = {1983}, author = {Rosenzweig, WD and Ackroyd, D}, title = {Binding characteristics of lectins involved in the trapping of nematodes by fungi.}, journal = {Applied and environmental microbiology}, volume = {46}, number = {5}, pages = {1093-1096}, pmid = {16346417}, issn = {0099-2240}, abstract = {Seventeen saccharides were tested for their ability to bind to the trap lectins of three species of nematode-trapping fungi and prevent nematode capture. The lectin of Arthrobotrys conoides was found to be inhibited by alpha-d-glucose/d-mannose and similar saccharides. The lectins of Monacrosporium eudermatum and Monacrosporium rutgeriensis were inhibited by alpha-l-fucose and 2-deoxy-d-glucose, respectively. Human group O(H) erythrocytes agglutinated to traps of M. eudermatum but not A. conoides or M. rutgeriensis. There was no agglutination of group A or B to traps formed by all three fungi. Exposure of the traps to trypsin eliminated the ability to capture nematodes. The presence of d-glucose/d-mannose and l-fucose residues on the nematode cuticle was suggested through the use of commercially prepared lectin-peroxidase conjugates.}, }
@article {pmid16346316, year = {1983}, author = {Nordgren, A and Bååth, E and Söderström, B}, title = {Microfungi and microbial activity along a heavy metal gradient.}, journal = {Applied and environmental microbiology}, volume = {45}, number = {6}, pages = {1829-1837}, pmid = {16346316}, issn = {0099-2240}, abstract = {Soil fungal biomass, microfungal species composition, and soil respiration rate of conifer mor soil were studied along a steep copper and zinc gradient (up to 20,000 mug of Cu and 20,000 mug of Zn g dry soil) around a brass mill near the town of Gusum in South Sweden. Fungal biomass and soil respiration rate decreased by about 75% along the metal gradient. Above 1,000 mug of Cu g, the decrease was clearly evident; below 1,000 mug of Cu g, no obvious effects were observed, but there was a tendency for a decrease in total mycelial length. No decrease in CFU was found along the gradient, but fungal species composition was drastically changed. The frequency of the genera Penicillium and Oidiodendron decreased from about 30 and 20%, respectively, at the control sites to only a few percent close to the mill. Mortierella was most frequently isolated in moderately polluted sites, but at the highest pollution levels, a decrease in isolation frequency was evident. Some fungal taxa increased in abundance towards the mill, e.g., Geomyces (from 1 to 10%), Paecilomyces (0 to 10%), and sterile forms (from 10 to 20%). Analyses with a multivariate statistical method (partial least squares) showed that organic matter content and soil moisture had little influence on the fungal community compared with the heavy metal pollution.}, }
@article {pmid16346172, year = {1983}, author = {Nordbring-Hertz, B}, title = {Dialysis membrane technique for studying microbial interaction.}, journal = {Applied and environmental microbiology}, volume = {45}, number = {1}, pages = {290-293}, doi = {10.1128/aem.45.1.290-293.1983}, pmid = {16346172}, issn = {0099-2240}, abstract = {A dialysis membrane method is described which allows (i) cultivation of fungi on an agar support, (ii) observation of growth and development by direct light microscopy, (iii) transfer of cultures from agar surfaces for subsequent treatments or for biochemical analysis, and (iv) preparation for scanning electron microscopy. The method is used routinely in studies of fungus-nematode and fungus-fungus interactions.}, }
@article {pmid16346114, year = {1982}, author = {Karl, DM}, title = {Selected nucleic Acid precursors in studies of aquatic microbial ecology.}, journal = {Applied and environmental microbiology}, volume = {44}, number = {4}, pages = {891-902}, pmid = {16346114}, issn = {0099-2240}, abstract = {The use of radiolabeled nucleosides and nucleic acid bases to estimate the rates of RNA and DNA synthesis in naturally occurring microbial assemblages requires numerous assumptions, several of which are evaluated herein. Comparative time series analyses of the uptake and incorporation, labeling specificity, and extent of catabolism of [2-H]adenine, [methyl-H]thymidine, and [5-H]uridine were performed with pure bacterial and algal cultures, as well as with environmental samples. [H]thymidine yielded the most variable results, especially with regard to the extent of nonspecific macromolecular labeling. The pathways of [H]thymidine and [H]adenine metabolism were further evaluated by isotope dilution methods and by comparing incorporation patterns of thymidine labeled at different sites of the molecule. The advantages, uncertainties, and limitations of the use of radiolabeled nucleic acid precursors in studies of aquatic microbial ecology are discussed and a prospectus for future studies presented.}, }
@article {pmid16345871, year = {1981}, author = {Boyle, PJ and Mitchell, R}, title = {External microflora of a marine wood-boring isopod.}, journal = {Applied and environmental microbiology}, volume = {42}, number = {4}, pages = {720-729}, pmid = {16345871}, issn = {0099-2240}, abstract = {Bacteria associated with the marine wood-boring isopod Limnoria lignorum were enumerated by acridine orange epifluorescence microscopy and by plate counts on several media; the plate-viable bacteria were isolated and identified. Similar procedures were followed to enumerate and identify bacteria associated with the wood substrate from which the isopods were collected and with the surrounding water from the isopod habitat. Approximately 1.4 x 10 bacterial cells were associated with each individual L. lignorum. Aeromonas hydrophila, Pseudomonas, and Vibrio were the most common genera in the isopod microflora. Wood from L. lignorum burrows had an associated bacterial flora of 1.6 x 10 cells per mg (damp weight). A. hydrophila also predominated in the wood microflora. The water from which the isopod population was collected contained 2.3 x 10 bacteria per ml. Pseudomonas and Vibrio species were very common in the water microflora, but A. hydrophila was not detected. Interactions between the isopod, its associated microorganisms, and the microorganisms within the wood substrate are discussed in the light of the known absence of a resident digestive tract microflora in these animals.}, }
@article {pmid16345509, year = {1980}, author = {Rosenzweig, WD and Stotzky, G}, title = {Influence of environmental factors on antagonism of fungi by bacteria in soil: nutrient levels.}, journal = {Applied and environmental microbiology}, volume = {39}, number = {2}, pages = {354-360}, pmid = {16345509}, issn = {0099-2240}, abstract = {The addition of 0.25, 0.5, or 1.0% glucose to a soil (K) amended with either 6% kaolinite (K6K) or montmorillonite (K6M) or the adjustment of the C/N ratio of the soils from 23/1 to 10/1 with NH(4)NO(3) eliminated the inhibition of Aspergillus niger by Serratia marcescens, regardless of whether the fungus and bacterium were inoculated into the same or separate sites in the soils. The adjustment of the C/N ratio to 15/1 or of the C/P ratio from 1,000/1 to 100/1 with KH(2)PO(4) did not eliminate the antagonism. However, with the higher glucose and NH(4)NO(3) amendments, S. marcescens died out in the K and K6K (but not in the K6M) soils, apparently due to reductions in pH that resulted from the increased metabolism induced by added nutrients. In soils amended with CaCO(3), S. marcescens did not die out, but the inhibition of A. niger by S. marcescens or Agrobacterium radiobacter was eliminated or reduced by the addition of glucose, but not of NH(4)NO(3), and was influenced by the clay mineralogy and pH of the soils. When NH(4)NO(3) was added to the soils adjusted with CaCO(3) to pH values above 6.0, growth of A. niger was inhibited, regardless of whether bacteria were present or not, as a result of the volatilization of NH(3). Bacillus cereus and another species of Bacillus did not inhibit A. niger under any of the environmental conditions. There was a direct correlation between the degree of inhibition and the rate of glucose utilization by the various bacteria, indicating that the antagonism of A. niger by some bacteria in soil was the result primarily of a competition for carbon and that this competition was influenced by other environmental factors, such as pH and clay mineralogy.}, }
@article {pmid16345477, year = {1979}, author = {Rosenzweig, WD and Stotzky, G}, title = {Influence of Environmental Factors on Antagonism of Fungi by Bacteria in Soil: Clay Minerals and pH.}, journal = {Applied and environmental microbiology}, volume = {38}, number = {6}, pages = {1120-1126}, pmid = {16345477}, issn = {0099-2240}, abstract = {The soil replica plating technique was used to evaluate the influence of clay minerals and pH on antagonistic interactions between fungi and bacteria in soil. In general, the antagonistic activity of bacteria towards filamentous fungi was greater in soil than on agar. The spread of Aspergillus niger through soil was inhibited by Serratia marcescens when the organisms were inoculated into separate sites in soil, and this antagonistic effect was maintained when the soil was amended with 3, 6, 9, or 12% (vol/vol) montmorillonite, whereas the addition of kaolinite at a concentration of 3% reduced the antagonism and at 6, 9, or 12% totally eliminated it. Similar results were obtained with the inhibition of A. niger by Agrobacterium radiobacter and of Penicillium vermiculatum by either S. marcescens or Nocardia paraffinae. When A. niger and S. marcescens were inoculated into the same soil site, A. niger was inhibited in all soils, regardless of clay content, although the extent of inhibition was greater as the concentration of montmorillonite, but not of kaolinite, increased. A. niger was inhibited more when inoculated as spores than as mycelial fragments and when inoculated 96 h after S. marcescens, but a 1% glucose solution reduced the amount of inhibition when the fungus was inoculated 96 h after the bacterium. When the pH of the soil-clay mixtures was altered, the amount of antagonism usually increased as the pH increased. Antagonism appeared to be related to the cation-exchange capacity and the pH of the soil-clay mixtures. Bacillus cereus and another species of Bacillus showed no activity in soil towards A. niger under any of the environmental conditions tested, even though the Bacillus sp. significantly inhibited A. niger and seven other fungi on agar.}, }
@article {pmid16345228, year = {1977}, author = {Babich, H and Stotzky, G}, title = {Reductions in the toxicity of cadmium to microorganisms by clay minerals.}, journal = {Applied and environmental microbiology}, volume = {33}, number = {3}, pages = {696-705}, pmid = {16345228}, issn = {0099-2240}, abstract = {The clay minerals montmorillonite and kaolinite protected bacteria, including actinomycetes, and filamentous fungi from the inhibitory effects of cadmium (Cd). Montmorillonite provided greater protection than did equivalent concentrations of kaolinite. The protective ability of the clays was correlated with their cation exchange capacity (CEC). The greater the CEC, the greater the absorbancy of exogenous Cd by the exchange complex and the greater the protection. The greater protection afforded by montmorillonite, as compared to kaolinite, was correlated with its higher CEC. Clays homoionic to Cd did not protect against exogenous Cd, as the exchange complex was already saturated with Cd. Montmorillonite homoionic to Cd was more detrimental to microbial growth than was kaolinite homoionic to Cd, as more Cd was present on and apparently desorbed from the montmorillonite.}, }
@article {pmid16345227, year = {1977}, author = {Babich, H and Stotzky, G}, title = {Sensitivity of Various Bacteria, Including Actinomycetes, and Fungi to Cadmium and the Influence of pH on Sensitivity.}, journal = {Applied and environmental microbiology}, volume = {33}, number = {3}, pages = {681-695}, pmid = {16345227}, issn = {0099-2240}, abstract = {A variety of microorganisms, including gram-negative and gram-positive eubacteria, actinomycetes, yeasts, and filamentous fungi, were tested for their sensitivity to cadmium (Cd). In general, the actinomycetes were more tolerant to Cd than were the eubacteria; gram-negative eubacteria were more tolerant to Cd than were gram-positive eubacteria. The period of exponential growth of the eubacteria and actinomycetes was extended in the presence of Cd. Wide extremes in sensitivity to Cd were noted among the fungi; there was no correlation between the class of fungus and tolerance to Cd. Fungal sporulation was more sensitive to Cd than was mycelial growth, as spore formation was inhibited at Cd concentrations that were noninhibitory to mycelial proliferation. The toxicity of Cd to the eubacteria, actinomycetes, and fungi appeared to be pH dependent, as toxicity was generally potentiated at pH 8 or 9.}, }
@article {pmid16345214, year = {1977}, author = {McBride, ME and Duncan, WC and Knox, JM}, title = {The environment and the microbial ecology of human skin.}, journal = {Applied and environmental microbiology}, volume = {33}, number = {3}, pages = {603-608}, pmid = {16345214}, issn = {0099-2240}, abstract = {Microbial flora of the skin of three human population groups representing different natural environments was examined quantitatively and qualitatively to determine whether environmental differences in temperature and humidity can influence the microbial flora of normal skin. Five anatomical skin sites - hands, back, axillae, groin, and feet - were sampled from 10 subjects working in a high-humidity, high-temperature environment, 10 subjects from a low-temperature, high-humidity environment, and 10 subjects working in a moderate-temperature and low-humidity environment. Bacterial populations were significantly larger from the back, axillae, and feet in individuals from the high-temperature and high-humidity environment as compared to the moderate-temperature, low-humidity environment. High humidity and low temperature had no significant effect on total populations, but this group showed a higher frequency of isolation of fungi, and gram-negative bacteria from the back and feet. Although there was an indication that increase in the environmental humidity could result in an increased frequency of isolation of gram-negative bacteria, there was no evidence that an increase in either temperature or humidity altered the relative proportions of gram-negative bacteria in the predominantly gram-positive microbial flora found on normal skin. It was concluded that, although climatic changes may cause fluctation in microbial populations from certain sites, they are not a major influence on the ecology of the microbial flora of normal skin in the natural environment. The variables introduced by studying individuals in their natural environment and the influence of these on the results are discussed.}, }
@article {pmid15825303, year = {1974}, author = {Rogers, AH}, title = {Bacteriocin production and susceptibility among strains of Streptococcus mutans grown in the presence of sucrose.}, journal = {Antimicrobial agents and chemotherapy}, volume = {6}, number = {5}, pages = {547-550}, pmid = {15825303}, issn = {0066-4804}, mesh = {Bacteriocins/*biosynthesis/pharmacology ; Dextrans/pharmacology ; Streptococcus mutans/*drug effects/*metabolism ; Sucrose/*pharmacology ; }, abstract = {Whereas the bacteriocin activity of eight strains of Streptococcus mutans was unaffected by growth in the presence of sucrose, such a medium rendered five S. mutans and one S. salivarius indicator strains unsusceptible to the bacteriocins. In contrast, the susceptibility of three S. faecalis and one S. pyogenes strains was unaltered when these indicators were grown in the presence of sucrose. Since the S. mutans and S. salivarius strains produced extracellular polysaccharides from sucrose whereas the S. faecalis and S. pyogenes strains did not, it was concluded that a coating of extracellular polysaccharides rendered normally susceptible organisms unsusceptible to bacteriocin action. This supports previous suggestions that such bacteriocins are not active in vivo and therefore play no role in regulating the microbial ecology in dental plaque.}, }
@article {pmid14325890, year = {1965}, author = {DIAS, FF and BHAT, JV}, title = {MICROBIAL ECOLOGY OF ACTIVATED SLUDGE. II. BACTERIOPHAGES, BDELLOVIBRIO, COLIFORMS, AND OTHER ORGANISMS.}, journal = {Applied microbiology}, volume = {13}, number = {2}, pages = {257-261}, pmid = {14325890}, issn = {0003-6919}, mesh = {*Achromobacter ; *Azotobacter ; *Bacteriophages ; *Bdellovibrio ; *Corynebacterium ; *Culture Media ; *Ecology ; *Enterobacter aerogenes ; *Escherichia coli ; *Nitrogen ; *Research ; *Sewage ; }, abstract = {A comparative estimation of the coliform population of raw sewage, activated sludge, and the effluent derived therefrom revealed that raw sewage had a preponderance of Escherichia coli (75%), as compared with 25 and 30%, respectively, in sludge and effluent. Nitrogen-free mannitol-sucrose enrichments of activated sludge resulted in the isolation of Azotobacter agilis, Aerobacter aerogenes, Corynebacterium laevaniformans, and an Achromabacter species. Sludge had a large population of C. laevaniformans and A. aerogenes but not of Azotobacter. The bacterial parasites, Bdellovibrio and bacteriophages, were not active during activated-sludge treatment. A 10-fold reduction in phage content occurred after 2 hr of aeration, but the Bdellovibrio population was unaffected.}, }
@article {pmid14215970, year = {1964}, author = {DIAS, FF and BHAT, JV}, title = {MICROBIAL ECOLOGY OF ACTIVATED SLUDGE. I. DOMINANT BACTERIA.}, journal = {Applied microbiology}, volume = {12}, number = {5}, pages = {412-417}, pmid = {14215970}, issn = {0003-6919}, mesh = {*Achromobacter ; *Alcaligenes ; *Amino Acids ; *Bacillus ; *Bacteria ; *Brevibacterium ; *Corynebacterium ; *Enterobacter ; *Flavobacterium ; *Hydroxybutyrates ; *Metabolism ; *Micrococcus ; *Polyesters ; *Pseudomonas ; *Research ; *Sewage ; *Spirillum ; *Vitamins ; *Yeasts ; *Zoogloea ; }, abstract = {Over 300 bacterial strains were isolated from seven samples of activated sludge by plating on sewage agar. Gram-negative bacteria of the genera Zoogloea and Comamonas predominated. Many isolates (51%) showed sudanophilic inclusions of poly-beta-hydroxybutyric acid, whereas 34% accumulated iodophilic material on media containing starch. A large number required either vitamins or amino acids, or both, for growth. None of the isolates tested for their ability to bring about changes in autoclaved sewage produced an effluent comparable in quality to the activated sludge control, although the Zoogloea did produce activated sludgelike flocs. A study of 150 bacterial strains isolated from raw sewage revealed that they differed from the sludge isolates in several respects. Coliforms, which constitute nearly a quarter of the sewage isolates, were rarely encountered in sludge.}, }
@article {pmid14000909, year = {1963}, author = {WILLIAMS, NB}, title = {Microbial ecology of the oral cavity.}, journal = {Journal of dental research}, volume = {42(1)Pt 2}, number = {}, pages = {509-520}, doi = {10.1177/00220345630420016101}, pmid = {14000909}, issn = {0022-0345}, mesh = {*Enterobacter ; *Lactobacillus ; *Mouth ; *Streptococcus ; *Yeasts ; }, }
@article {pmid13898350, year = {1962}, author = {GIBBONS, RJ and SOCRANSKY, SS}, title = {Intracellular polysaccharide storage by organisms in dental plaques. Its relation to dental caries and microbial ecology of the oral cavity.}, journal = {Archives of oral biology}, volume = {7}, number = {}, pages = {73-79}, doi = {10.1016/0003-9969(62)90050-x}, pmid = {13898350}, issn = {0003-9969}, mesh = {Dental Caries/*chemistry ; *Dental Plaque ; Humans ; Mouth/*microbiology ; Polysaccharides/*chemistry ; }, }
@article {pmid13716827, year = {1960}, author = {HUNGATE, RE}, title = {Symposium: selected topics in microbial ecology. I. Microbial ecology of the rumen.}, journal = {Bacteriological reviews}, volume = {24}, number = {4}, pages = {353-364}, pmid = {13716827}, issn = {0005-3678}, mesh = {Animals ; *Ecology ; *Rumen ; Stomach/*microbiology ; }, }
@article {pmid12514043, year = {2003}, author = {Long, RA and Qureshi, A and Faulkner, DJ and Azam, F}, title = {2-n-Pentyl-4-quinolinol produced by a marine Alteromonas sp. and its potential ecological and biogeochemical roles.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {1}, pages = {568-576}, pmid = {12514043}, issn = {0099-2240}, support = {AI46600/AI/NIAID NIH HHS/United States ; CA-49084/CA/NCI NIH HHS/United States ; }, mesh = {Alteromonas/*metabolism ; Animals ; *Antibiosis ; Cyanobacteria/drug effects/growth &amp; development ; Diatoms/drug effects/growth &amp; development ; *Ecosystem ; Hydroxyquinolines/chemistry/*metabolism/pharmacology ; Plankton/drug effects/growth &amp; development ; Proteobacteria/drug effects/growth &amp; development ; Seawater/*microbiology ; }, abstract = {Bacterium-bacterium interactions occur at intimate spatial scales on the order of micrometers, but our knowledge of interactions at this level is rudimentary. Antagonism is a potential interaction in such microenvironments. To study the ecological role of antibiosis, we developed a model system involving an antibiotic-producing isolate (SWAT5) derived from a marine particle and its dominant antibiotic product, 2-n-pentyl-4-quinolinol (PQ). This system was used to address questions about the significance of this antibiotic for microbial ecology and carbon cycling on particles. We characterized the chemical and inhibitory properties of PQ in relation to the mechanisms used by particle-associated bacteria in interacting with particles and with other attached bacteria. PQ was produced by SWAT5 only on surfaces. When SWAT5 was grown in polysaccharide matrices, PQ diffused within the matrices but not into the surrounding seawater. SWAT5 might thus be able to generate a localized zone of high antibiotic concentration on particles suspended or sinking through seawater. Target bacterial respiration was most sensitive to PQ (75 nM), while inhibition of DNA synthesis, protein synthesis, and bacterial motility required higher (micromolar) PQ levels. The presence of PQ altered the composition of the bacterial community that colonized and developed in a model particle system. PQ also inhibited Synechococcus and phytoplankton growth. Our results suggest that antibiosis may significantly influence community composition and activities of attached bacterial and thus regulate the biogeochemical fate of particulate organic matter in the ocean.}, }
@article {pmid12511066, year = {2002}, author = {Loewe, L}, title = {Global computing for bioinformatics.}, journal = {Briefings in bioinformatics}, volume = {3}, number = {4}, pages = {377-388}, doi = {10.1093/bib/3.4.377}, pmid = {12511066}, issn = {1467-5463}, mesh = {*Computational Biology ; *Computer Communication Networks/economics ; Databases, Factual ; Humans ; *Information Storage and Retrieval ; Software ; Systems Integration ; User-Computer Interface ; }, abstract = {Global computing, the collaboration of idle PCs via the Internet in a SETI@home style, emerges as a new way of massive parallel multiprocessing with potentially enormous CPU power. Its relations to the broader, fast-moving field of Grid computing are discussed without attempting a review of the latter. This review (i) includes a short table of milestones in global computing history, (ii) lists opportunities global computing offers for bioinformatics, (iii) describes the structure of problems well suited for such an approach, (iv) analyses the anatomy of successful projects and (v) points to existing software frameworks. Finally, an evaluation of the various costs shows that global computing indeed has merit, if the problem to be solved is already coded appropriately and a suitable global computing framework can be found. Then, either significant amounts of computing power can be recruited from the general public, or--if employed in an enterprise-wide Intranet for security reasons--idle desktop PCs can substitute for an expensive dedicated cluster.}, }
@article {pmid12506639, year = {2002}, author = {Kafarskaia, LI and Korshunova, OV and Efimov, BA and Volodin, NN and Korshunov, VM}, title = {[Microbial ecology of the vagina].}, journal = {Zhurnal mikrobiologii, epidemiologii i immunobiologii}, volume = {}, number = {6}, pages = {91-99}, pmid = {12506639}, issn = {0372-9311}, mesh = {Bacteria, Anaerobic/classification/growth &amp; development/isolation &amp; purification/pathogenicity ; Bacterial Infections/microbiology ; Drug Resistance, Microbial ; Female ; Gram-Negative Bacteria/growth &amp; development ; Gram-Positive Bacteria/growth &amp; development ; Humans ; Pregnancy ; Pregnancy Complications, Infectious ; Vagina/metabolism/*microbiology ; Vaginosis, Bacterial/complications ; }, abstract = {In this review recent information on relationships between the vaginal environment and microflora, including new taxonomic groups of microorganisms, is updated. The role of normal microflora in formation of vaginal colonization resistance and possible participation of some representatives of normal microflora, mainly nonsporulating anaerobic organisms, in the development of perinatal, neonatal and gynecological infectious complications are considered.}, }
@article {pmid12501425, year = {1998}, author = {Cabirol, N and Jacob, F and Perrier, J and Fouillet, B and Chambon, P}, title = {Interaction between methanogenic and sulfate-reducing microorganisms during dechlorination of a high concentration of tetrachloroethylene.}, journal = {The Journal of general and applied microbiology}, volume = {44}, number = {4}, pages = {297-301}, doi = {10.2323/jgam.44.297}, pmid = {12501425}, issn = {1349-8037}, abstract = {A methanogenic and sulfate-reducing consortium, which was enriched on medium containing tetrachloroethylene (PCE), had the ability to dechlorinate high concentrations of PCE. Dehalogenation was due to the direct activity of methanogens. However, interactions between methanogenic and sulfate-reducing bacteria involved modification of the dechlorination process according to culture conditions. In the absence of sulfate, the relative percentage of electrons used in PCE dehalogenation increased after an addition of lactate in batch conditions. The sulfate reducers would produce further reductant from lactate catabolism. This reductant might be used by methanogenic bacteria in PCE dechlorination. A mutualistic interaction was observed in the absence of sulfate. However in the presence of sulfate, methanogenesis and dechlorination decreased because of interspecific competition, probably between the H(2)-oxydizing methanogenic and sulfate-reducing bacteria in batch conditions. In the semicontinuous fixed-bed reactor, the presence of sulfate did not affect dechlorination and methanogenesis. The sulfate-reducing bacteria may not be competitors of H(2)-consuming methanogens in the reactor because of the existence of microbial biofilm. The presence of the fixed film may be an advantage for bioremediation and industrial treatment of effluent charged in sulfate and PCE. This is the first report on the microbial ecology of a methanogenic and sulfate-reducing PCE-enrichment consortium.}, }
@article {pmid12501278, year = {1998}, author = {Santo Domingo, JW}, title = {Use of 16S rDNA community fingerprints to study cricket hindgut microbial communities.}, journal = {The Journal of general and applied microbiology}, volume = {44}, number = {2}, pages = {119-127}, doi = {10.2323/jgam.44.119}, pmid = {12501278}, issn = {1349-8037}, abstract = {A nucleic acid-based method was evaluated in the course of a study of microbial community structure in the cricket hindgut. Genomic DNA was extracted from the hindgut microbial community of Acheta domesticus and used as a template in the polymerase chain reaction (PCR) method, using primers that align to well conserved regions of the 16S rRNA gene. The rDNA-PCR product was used as a community probe to generate restriction fragment length polymorphisms (RFLPs) of hindgut bacterial isolates and gut microbial communities of insects fed different diets. Fingerprints of the bacterial isolates consisted of several bands suggesting multiple rRNA operons. In contrast with soil communities, hindgut community RFLP contained distinguishable band patterns. However, community rDNA fingerprints were complex and varied among insects fed similar diets, suggesting considerable intrinsic variability in the hindgut microbial community structure between crickets regardless of dietary regime. These results suggest that community RFLP methods using broad-specific phylogenetic probes do not have the resolution or specificity required to ascertain the effect of diet on the cricket hindgut microbial community structure.}, }
@article {pmid12497186, year = {2002}, author = {Stolz, JF and Basu, P and Oremland, RS}, title = {Microbial transformation of elements: the case of arsenic and selenium.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {5}, number = {4}, pages = {201-207}, doi = {10.1007/s10123-002-0091-y}, pmid = {12497186}, issn = {1139-6709}, mesh = {Adenosine Triphosphatases/metabolism ; Arsenic/*metabolism ; Arsenite Transporting ATPases ; Bacteria/classification/enzymology/*metabolism ; Biotransformation ; Ion Pumps/metabolism ; Multienzyme Complexes/metabolism ; Oxidoreductases/metabolism ; Phylogeny ; Selenium/*metabolism ; }, abstract = {Microbial activity is responsible for the transformation of at least one third of the elements in the periodic table. These transformations are the result of assimilatory, dissimilatory, or detoxification processes and form the cornerstones of many biogeochemical cycles. Arsenic and selenium are two elements whose roles in microbial ecology have only recently been recognized. Known as "essential toxins", they are required in trace amounts for growth and metabolism but are toxic at elevated concentrations. Arsenic is used as an osmolite in some marine organisms while selenium is required as selenocysteine (i.e. the twenty-first amino acid) or as a ligand to metal in some enzymes (e.g. FeNiSe hydrogenase). Arsenic resistance involves a small-molecular-weight arsenate reductase (ArsC). The use of arsenic and selenium oxyanions for energy is widespread in prokaryotes with representative organisms from the Crenarchaeota, thermophilic bacteria, low and high G+C gram-positive bacteria, and Proteobacteria. Recent studies have shown that both elements are actively cycled and play a significant role in carbon mineralization in certain environments. The occurrence of multiple mechanisms involving different enzymes for arsenic and selenium transformation indicates several different evolutionary pathways (e.g. convergence and lateral gene transfer) and underscores the environmental significance and selective impact in microbial evolution of these two elements.}, }
@article {pmid12497182, year = {2002}, author = {Montesinos, E and Bonaterra, A and Badosa, E and Francés, J and Alemany, J and Llorente, I and Moragrega, C}, title = {Plant-microbe interactions and the new biotechnological methods of plant disease control.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {5}, number = {4}, pages = {169-175}, doi = {10.1007/s10123-002-0085-9}, pmid = {12497182}, issn = {1139-6709}, mesh = {Bacteria/growth &amp; development/pathogenicity ; *Bacterial Physiological Phenomena ; Biotechnology/*methods ; Pest Control, Biological ; Plant Diseases/*microbiology ; Plant Physiological Phenomena ; Plant Roots/microbiology/physiology ; Plants/immunology ; Rhizobiaceae/growth &amp; development ; Signal Transduction ; Soil Microbiology ; Virulence/genetics ; }, abstract = {Plants constitute an excellent ecosystem for microorganisms. The environmental conditions offered differ considerably between the highly variable aerial plant part and the more stable root system. Microbes interact with plant tissues and cells with different degrees of dependence. The most interesting from the microbial ecology point of view, however, are specific interactions developed by plant-beneficial (either non-symbiotic or symbiotic) and pathogenic microorganisms. Plants, like humans and other animals, also become sick, but they have evolved a sophisticated defense response against microbes, based on a combination of constitutive and inducible responses which can be localized or spread throughout plant organs and tissues. The response is mediated by several messenger molecules that activate pathogen-responsive genes coding for enzymes or antimicrobial compounds, and produces less sophisticated and specific compounds than immunoglobulins in animals. However, the response specifically detects intracellularly a type of protein of the pathogen based on a gene-for-gene interaction recognition system, triggering a biochemical attack and programmed cell death. Several implications for the management of plant diseases are derived from knowledge of the basis of the specificity of plant-bacteria interactions. New biotechnological products are currently being developed based on stimulation of the plant defense response, and on the use of plant-beneficial bacteria for biological control of plant diseases (biopesticides) and for plant growth promotion (biofertilizers).}, }
@article {pmid12497181, year = {2002}, author = {Atlas, RM}, title = {Responding to the threat of bioterrorism: a microbial ecology perspective--the case of anthrax.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {5}, number = {4}, pages = {161-167}, doi = {10.1007/s10123-002-0084-x}, pmid = {12497181}, issn = {1139-6709}, mesh = {Anthrax/diagnosis/pathology/*prevention &amp; control ; Anthrax Vaccines ; Bacillus anthracis/physiology/ultrastructure ; Biological Warfare/prevention &amp; control ; Bioterrorism/*prevention &amp; control ; Disaster Planning/methods ; Ecology ; Humans ; Spores, Bacterial/growth &amp; development/ultrastructure ; }, abstract = {Anthrax is a disease of herbivores caused by the gram-positive bacterium Bacillus anthracis. It can affect cattle, sheep, swine, horses and various species of wildlife. The routes for the spread among wildlife are reviewed. There are three kinds of human anthrax--inhalation, cutaneous, and intestinal anthrax--which differ in their routes of infection and outcomes. In the United States, confirmation of cases is made by the isolation of B. anthracis and by biochemical tests. Vaccination is not recommended for the general public; civilians who should be vaccinated include those who, in their work places, come in contact with products potentially contaminated with B. anthracis spores, and people engaged in research or diagnostic activities. After September 11, 2001, there were bioterrorism anthrax attacks in the United States: anthrax-laced letters sent to multiple locations were the source of infectious B. anthracis. The US Postal Service issued recommendations to prevent the danger of hazardous exposure to the bacterium. B. anthracis spores can spread easily and persist for very long times, which makes decontamination of buildings very difficult. Early detection, rapid diagnosis, and well-coordinated public health response are the key to minimizing casualties. The US Government is seeking new ways to deter bioterrorism, including a tighter control of research on infectious agents, even though pathogens such as B. anthracis are widely spread in nature and easy to grow. It is necessary to define the boundary between defensive and offensive biological weapons research. Deterring bioterrorism should not restrict critical scientific research.}, }
@article {pmid12491968, year = {2002}, author = {Philips, S and Verstraete, W}, title = {Changes in the microbiology of activated sludge upon the addition of iron salts with or without nitrite or nitrate.}, journal = {Mededelingen (Rijksuniversiteit te Gent. Fakulteit van de Landbouwkundige en Toegepaste Biologische Wetenschappen)}, volume = {67}, number = {1}, pages = {35-50}, pmid = {12491968}, issn = {1373-7503}, mesh = {Bacteria/genetics/growth &amp; development/isolation &amp; purification/metabolism ; Biomass ; *Bioreactors ; Ferric Compounds/metabolism ; Ferrous Compounds/metabolism ; Iron/*metabolism ; Nitrates/*metabolism ; Nitrites/*metabolism ; Population Dynamics ; Quaternary Ammonium Compounds/metabolism ; RNA, Ribosomal, 16S/analysis ; Sewage/*microbiology ; }, abstract = {Iron salts are frequently used in activated sludge treatment as coagulants or to improve reactor performance. However, the effect of the iron salts on the microbiology has received little attention. Furthermore, the interaction of iron ions with nitrite or nitrate present in the sludge has not been considered. In this research, the influence of ferrous and ferric iron additions, and their possible interactions with nitrite or nitrate at levels of a few mM, on the activated sludge microbiology of semi-continuous bench-scale reactors were examined. Conventional as well as molecular techniques have been used to investigate the microbial communities. Microscopic investigations showed that repeated addition of ferric iron at 2 mM gave rise to breaking of the sludge flocs, resulting in massive growth of sessile-protozoa and lowering of the numbers of nitrifiers. Ferrous iron at the same dosage resulted in large coherent flocs. Nitrite hereby seemed to enhance the detrimental effect of the ferric iron on the floc structure, whereas nitrate had a neutralizing character. 16S rRNA gene analysis showed a clear impact of the different iron respectively nitrogen treatments on the composition of bacterial communities. Cloning the sludge samples revealed the increased presence of denitrifying Feoxidizing bacteria in both the Fe(II) and Fe(III) reactors, suggesting a redox-state cycling between Fe(II) and Fe(III) in the mixed liquor.}, }
@article {pmid12491024, year = {2003}, author = {Petroni, G and Rosati, G and Vannini, C and Modeo, L and Dini, F and Verni, F}, title = {In situ identification by fluorescently labeled oligonucleotide probes of morphologically similar, closely related ciliate species.}, journal = {Microbial ecology}, volume = {45}, number = {2}, pages = {156-162}, doi = {10.1007/s00248-002-2016-x}, pmid = {12491024}, issn = {0095-3628}, mesh = {Animals ; DNA Probes/chemistry/genetics ; DNA, Protozoan/chemistry/*genetics ; Euplotes/chemistry/classification/*genetics ; Fluorescent Dyes/chemistry ; Genetic Variation ; In Situ Hybridization, Fluorescence/*methods ; }, abstract = {Ciliate protozoa are important members of microbial communities in which they play specific ecological roles. The determination of single species distribution is fundamental for food web analysis, but species recognition, which is mainly based on morphological characters, is often difficult between closely related species. The use of species-specific, purposely designed, fluorescently labeled probes for in situ hybridization is here presented as an easy and fast identification method for three closely related species belonging to the widespread genus Euplotes, namely E. crassus, E. vannus, and E. minuta, that in spite of their remarkable morphological similarity have significant metabolic and ecological differences. These three species can be detected simultaneously, provided the probes employed are bound to different fluorescent dyes: in this way their relative abundance and their population dynamics in the natural environment can be evaluated. As more ciliate sequences become available in databases, species-specific probes can be designed for other ciliates, thus rendering the application of the method of more general importance. The probes used in this study may also provide a tool to prevent erroneous species identification in future studies.}, }
@article {pmid12491023, year = {2003}, author = {Rice, AR and Hamilton, MA and Camper, AK}, title = {Movement, replication, and emigration rates of individual bacteria in a biofilm.}, journal = {Microbial ecology}, volume = {45}, number = {2}, pages = {163-172}, doi = {10.1007/s00248-002-1028-x}, pmid = {12491023}, issn = {0095-3628}, mesh = {Biofilms/*growth &amp; development ; Bioreactors ; Green Fluorescent Proteins ; Luminescent Proteins/chemistry ; Microscopy, Confocal ; Pseudomonas aeruginosa/cytology/growth &amp; development/*physiology ; Statistics, Nonparametric ; }, abstract = {Single-cell behavior within a biofilm was observed over a period of several hours. The observations were converted into quantitative stochastic rules governing the behavior of individual cells within a biofilm. Such a quantitative summary provides not only a concise description of the results but also information helpful when constructing computer models of dynamic biofilm systems. The time to division, emigration, and rate of motility of individual green fluorescent protein labeled Pseudomonas aeruginosa PAO1 cells in a 3-10 microm thick biofilm containing predominantly non-GFP labeled cells were calculated based on images of individual cells collected at 15-min time intervals. The biofilms were grown in flow cells and the images captured with a confocal laser microscope. Cells destined to emigrate are more active than those that remain; the geometric means for velocities in the biofilm are 1.0 microm/h for remaining cells and 1.5 microm/h for emigrating cells. The median time to emigration was 2.0 h. During the experimental observation period, the estimated probability for emigration is 0.44, illustrating that a substantial number of bacteria leave the field of view. Cells emigrate at a median time one-third that of the median time to replication. Specifically, the median time for cells to divide was 6.9 h, and it was estimated that 10% of the cells had a time to division greater than 10 h.}, }
@article {pmid12481234, year = {2003}, author = {Pirttilä, AM and Pospiech, H and Laukkanen, H and Myllylä, R and Hohtola, A}, title = {Two endophytic fungi in different tissues of scots pine buds (Pinus sylvestris L.).}, journal = {Microbial ecology}, volume = {45}, number = {1}, pages = {53-62}, doi = {10.1007/s00248-002-1038-8}, pmid = {12481234}, issn = {0095-3628}, mesh = {Ascomycota/genetics/*isolation &amp; purification/physiology ; DNA, Fungal/*analysis ; In Situ Hybridization ; Pinus/*microbiology ; Pinus sylvestris ; Polymerase Chain Reaction ; Population Dynamics ; RNA, Ribosomal, 18S/analysis ; Rhodotorula/genetics/*isolation &amp; purification/physiology ; Tissue Distribution ; }, abstract = {Two fungal species were isolated with different frequencies from pine tissue cultures originating from buds. One species was detected in 33.1% of the cultures initiated in March, and another was present in 1.7% of cultures initiated in June. Based on analyses of phylogenetic and physiological characteristics these fungi were identified as Hormonema dematioides (isolated in March) and Rhodotorula minuta (isolated in June). Probes targeted towards the 18S rRNA of H. dematioides and R. minuta were made. When in situ hybridizations were performed on pine bud tissue, R. minuta was detected inside the cells of meristematic tissue in 40% of the samples, in contrast to H. dematioides, which was not found in this tissue. Using light microscopy, H. dematioides was found to be localized in the scale tissues of the buds. Fungal endophytes have previously been detected in scale tissues, but not in the meristematic tissues of buds. The habitats of these fungi may reflect their different roles in the plant.}, }
@article {pmid12481233, year = {2003}, author = {Villareal, TA and Carpenter, EJ}, title = {Buoyancy regulation and the potential for vertical migration in the oceanic cyanobacterium trichodesmium.}, journal = {Microbial ecology}, volume = {45}, number = {1}, pages = {1-10}, doi = {10.1007/s00248-002-1012-5}, pmid = {12481233}, issn = {0095-3628}, mesh = {*Cyanobacteria ; Light ; *Movement ; Nitrogen/analysis ; Phosphorus/analysis ; Population Dynamics ; Pressure ; Water Microbiology ; }, abstract = {Diel protein and carbohydrate content in Trichodesmium thiebautii was measured to evaluate the relationship to buoyancy status. Carbohydrate:protein ratio was the best predictor of buoyancy and fit a cosine curve with increasing values during the day and decreasing values at night in cycles that paralleled observed diel buoyancy patterns. This ratio also increased in short-term experiments as a function of light and increased in parallel with decreasing positive buoyancy. We used changes in this ratio to estimate the potential for vertical migration. Whereas limited vertical excursions in the upper 70 m are possible, deeper migrations appear unlikely unless respiration rates decrease significantly. N:P ratios in sinking and floating colonies were used to test for the P acquisition at depth (vertical migration). We noted that pooled N:P ratios were not significantly different between sinking and ascending colonies (N:P = 65.6 and 66.3, respectively) collected along the northern Australian coast, much like published results from north of Hawaii. Highly significant differences (p <0.0001) were observed in the western Gulf of Mexico between sinking and ascending colonies (N:P = 87.0 and 43.5, respectively) and provide the best direct evidence to date of vertical migration for P acquisition. Our physiological data on compositional changes during buoyancy reversals suggest a complex relationship between light and nutrients. It appears likely that light and P metabolism interact to regulate the vertical extent of migrations, with deep vertical migration regulated by P metabolism superimposed on a mixed-layer light-driven migration. The variability in N:P ratios suggests that care should be taken in assuming buoyancy reversals always result in P acquisition in this oceanic cyanobacterium.}, }
@article {pmid12480879, year = {2002}, author = {Manefield, M and Turner, SL}, title = {Quorum sensing in context: out of molecular biology and into microbial ecology.}, journal = {Microbiology (Reading, England)}, volume = {148}, number = {Pt 12}, pages = {3762-3764}, doi = {10.1099/00221287-148-12-3762}, pmid = {12480879}, issn = {1350-0872}, mesh = {4-Butyrolactone/*analogs &amp; derivatives/metabolism ; Bacterial Proteins/genetics/metabolism ; Biological Evolution ; *Ecosystem ; *Gene Expression Regulation, Bacterial ; Molecular Biology ; Proteobacteria/classification/*genetics/*growth &amp; development ; *Signal Transduction ; }, }
@article {pmid12480096, year = {2002}, author = {Pryde, SE and Duncan, SH and Hold, GL and Stewart, CS and Flint, HJ}, title = {The microbiology of butyrate formation in the human colon.}, journal = {FEMS microbiology letters}, volume = {217}, number = {2}, pages = {133-139}, doi = {10.1111/j.1574-6968.2002.tb11467.x}, pmid = {12480096}, issn = {0378-1097}, mesh = {Anaerobiosis/physiology ; Bacteria, Anaerobic/classification/growth &amp; development/*metabolism ; Butyrates/*metabolism ; Colon/metabolism/*microbiology ; Culture Media ; Feces/microbiology ; Fermentation ; Humans ; Models, Biological ; Phylogeny ; }, abstract = {Butyrate arising from microbial fermentation is important for the energy metabolism and normal development of colonic epithelial cells and has a mainly protective role in relation to colonic disease. While certain dietary substrates such as resistant starch appear to be butyrogenic in the colon, it is not known to what extent these stimulate butyrate production directly, e.g. by promoting amylolytic species, or indirectly, e.g. through cross-feeding of fermentation products. Cultural and molecular studies indicate that the most numerous butyrate-producing bacteria found in human faeces are highly oxygen-sensitive anaerobes belonging to the Clostridial clusters IV and XIVa. These include many previously undescribed species related to Eubacterium, Roseburia, Faecalibacterium and Coprococcus whose distribution and metabolic characteristics are under investigation. A better understanding of the microbial ecology of colonic butyrate-producing bacteria will help to explain the influence of diet upon butyrate supply, and to suggest new approaches for optimising microbial activity in the large intestine.}, }
@article {pmid12469947, year = {2002}, author = {Zilles, JL and Peccia, J and Noguera, DR}, title = {Microbiology of enhanced biological phosphorus removal in aerated-anoxic Orbal processes.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {74}, number = {5}, pages = {428-436}, doi = {10.2175/106143002x140224}, pmid = {12469947}, issn = {1061-4303}, mesh = {Bacteria, Anaerobic/genetics/*physiology ; *Bioreactors ; Flow Cytometry ; In Situ Hybridization, Fluorescence ; Phosphorus/*isolation &amp; purification ; Waste Disposal, Fluid/*methods ; }, abstract = {The traditional process for enhanced biological phosphorus removal (EBPR) in wastewater treatment involves an anaerobic zone followed by an aerobic zone. Although there is no strict anaerobic zone in aerated-anoxic Orbal processes, phosphorus removal in excess of that required for cell growth does occur. The microbial ecology of polyphosphate-accumulating organisms (PAO) in two full-scale Orbal wastewater treatment plants was investigated using flow cytometry to physically separate PAO from non-PAO and fluorescent in situ hybridization (FISH) to identify organisms. Although Candidatus Accumulibacter phosphatis, an uncultured organism associated with EBPR in acetate-fed laboratory-scale reactors, was detected, it did not seem to be the dominant PAO in these processes. Comparative FISH analyses of the activated sludge and the PAO-rich subpopulation did not reveal the presence of a dominant group of PAO in these full-scale plants. Rather, the analysis suggested that the operational characteristics of aerated-anoxic processes might select for a diverse PAO community that is significantly different from that observed in acetate-fed laboratory reactors or in traditional EBPR configurations.}, }
@article {pmid12469859, year = {2002}, author = {Merrill, L and Halverson, LJ}, title = {Seasonal variation in microbial communities and organic malodor indicator compound concentrations in various types of swine manure storage systems.}, journal = {Journal of environmental quality}, volume = {31}, number = {6}, pages = {2074-2085}, doi = {10.2134/jeq2002.2074}, pmid = {12469859}, issn = {0047-2425}, mesh = {Air Pollutants ; Animals ; *Bacteria ; Environmental Monitoring ; Fatty Acids/analysis ; *Manure ; *Odorants ; Population Dynamics ; *Refuse Disposal ; Seasons ; Swine ; Water Supply ; }, abstract = {Anaerobic manure storage systems are one of the major contributors to the odor and environmental pollution associated with swine (Sus scrofa) production systems. The microbial ecology of manure storage systems and the relationships between microbial communities and odor production are largely unknown. In this study, we used community fatty acid methyl ester (FAME) analysis to generate lipid profiles to assess seasonal differences among microbial communities inhabiting various types of outdoor swine manure storage systems. Concurrently, we measured manure concentrations of several malodor indicator compounds as well as pH, temperature, and solids content. Principal components analysis (PCA) showed that there are differences in FAME profiles among the swine manure storage systems examined and most of the variation was in the relative abundance of 18:0, 18:1omega7t, 18:1omega7c/omega9t/omega12t, and 16:1omega7t/i15:0 2OH FAMEs. The PCA of the FAME profiles revealed that the phototrophic systems were more similar to each other and that the nonphototrophic systems were more similar to each other than they were to phototrophic lagoons. There were seasonal changes in the FAME profiles in the phototrophic systems and the concrete nonphototrophic basin (CNPB), and in one phototrophic system, the FAME profiles more closely resembled a CNPB FAME profile during the winter than the other phototrophic lagoons. In the phototrophic lagoon systems, there was a direct correlation between the abundance of the FAMEs identified in the PCA and manure concentrations of phenol, p-cresol, and 4-ethyl phenol. In the CNPB, there was a negative correlation between the total phenolics concentration and the 18:1omega7t FAME. Our results indicate that community FAME profiles could be used as a diagnostic tool for obtaining preliminary evidence that management practices are altering the system's microbial community to one that favors less air pollution potential.}, }
@article {pmid12469247, year = {2003}, author = {Ram, AS and Nair, S and Chandramohan, D}, title = {Bacterial growth efficiency in the tropical estuarine and coastal waters of Goa, southwest coast of India.}, journal = {Microbial ecology}, volume = {45}, number = {1}, pages = {88-96}, doi = {10.1007/s00248-002-3005-9}, pmid = {12469247}, issn = {0095-3628}, mesh = {Bacteria/*growth &amp; development ; Carbon/analysis/*metabolism ; Ecosystem ; Environmental Monitoring ; India ; Nitrogen/analysis/metabolism ; Tropical Climate ; *Water Supply ; }, abstract = {Bacterial growth efficiency (BGE) is an index of organic carbon passing through bacteria in an aquatic system. BGE values of natural bacterioplankton assemblages were measured in tropical estuarine and adjacent coastal waters in Goa along the southwest coast of India. The BGE values for estuarine and coastal waters were 18 (+/-7.84%) and 11 (+/-4.19%), respectively. BGE in these waters were at the lower end of what is usually found in productive systems. This may be due to the high respiration rates. Further, it was observed that grazers also influenced BGE. As BGE was positively correlated with bacterial productivity, the observed variation in BGE was attributed to bacterial productivity. BGE was inversely related to C:N ratio, indicating a close coupling between the nature of the substrates and BGE. Being system-dependent, the variations in BGE at the two locations were dynamic and were regulated by the quality of the substrates. Therefore, a constant value for BGE would lead to error in carbon budgets in these waters.}, }
@article {pmid12469246, year = {2003}, author = {Folman, LB and Postma, J and van Veen, JA}, title = {Inability to find consistent bacterial biocontrol agents of Pythium aphanidermatum in cucumber using screens based on ecophysiological traits.}, journal = {Microbial ecology}, volume = {45}, number = {1}, pages = {72-87}, doi = {10.1007/s00248-002-2013-0}, pmid = {12469246}, issn = {0095-3628}, mesh = {Bacteria/*pathogenicity ; Biomass ; Carbon/metabolism ; Cucumis sativus/*microbiology ; Drug Evaluation, Preclinical ; *Pest Control, Biological ; Plant Roots/microbiology ; Pythium/*microbiology/*pathogenicity ; }, abstract = {A collection of 821 rhizobacteria from cucumber, originating from different root locations and stages of plant development, was screened for potential biocontrol agents of Pythium aphanidermatum (Edson) Fitzp. The screening procedure exploited carbon source utilization profiles and growth rates of bacteria as indicators of a partial niche overlap with the pathogen. The bacteria were tested for growth on nine carbon sources (glucose, fucose, sucrose, maltose, asparagine, alanine, galacturonic acid, succinic acid, and linoleic acid), most of which are reported to be used by the zoospores of P. aphanidermatum in the infection process. The isolates were classified as fast- or slow-growing, depending on their growth rate in 1/10 strength TSB. By nonhierarchical cluster analysis, 20 clusters were generated of bacteria with similar profiles of carbon source utilization. Redundancy analysis showed that the type of root sample explained 47% of the variance found in the relative abundance of bacteria from the clusters. Bacteria from clusters using none or few of the carbon sources, e.g., maltose and linoleic acid, with many slow-growing isolates, showed a preference for plants in the vegetative or generative stage, or for old root regions (root base). Bacteria from clusters with fast-growing isolates, using many carbon sources, were relatively abundant in the seedling stage. A selection of 127 bacteria from the different clusters was tested for disease suppressive capabilities in bioassays on young cucumber plants in nutrient solution, inoculated with zoospores of P. aphanidermatum. Nine of these bacteria produced biosurfactants, and 27 showed antibiosis against mycelial growth in plate assays. For 31 isolates, significant positive effects on plant biomass were shown, as analyzed with a general linear regression model. For most isolates, these effects occurred only in one of two replicate assays and no reductions in the degree of root and crown rot were found. Of the isolates that used many of the tested carbon sources, only four had positive effects on plant biomass. The majority of the isolates that positively affected plant biomass used few to moderate numbers of carbon sources and did not produce antibiotics or biosurfactants. In conclusion, competition for the tested carbon sources with the zoospores did not play a decisive role in disease suppression, and no clear relation was found between ecophysiological traits and disease suppression. Only isolate 3.1T8, isolated from root tips in the generative stage of plant growth, significantly increased plant biomass and suppressed root and crown rot symptoms in five out of six bioassays. The isolate produced an antifungal substance in plate assays and showed biosurfactant production in several (cucumber-derived) media.}, }
@article {pmid12469245, year = {2003}, author = {Fierer, N and Schimel, JP and Holden, PA}, title = {Influence of drying-rewetting frequency on soil bacterial community structure.}, journal = {Microbial ecology}, volume = {45}, number = {1}, pages = {63-71}, doi = {10.1007/s00248-002-1007-2}, pmid = {12469245}, issn = {0095-3628}, mesh = {Classification ; DNA, Bacterial/analysis ; Disasters ; *Ecosystem ; Poaceae ; Polymorphism, Restriction Fragment Length ; Population Dynamics ; Seasons ; *Soil Microbiology ; Trees ; Water ; }, abstract = {Soil drying and rewetting represents a common physiological stress for the microbial communities residing in surface soils. A drying-rewetting cycle may induce lysis in a significant proportion of the microbial biomass and, for a number of reasons, may directly or indirectly influence microbial community composition. Few studies have explicitly examined the role of drying-rewetting frequency in shaping soil microbial community structure. In this experiment, we manipulated soil water stress in the laboratory by exposing two different soil types to 0, 1, 2, 4, 6, 9, or 15 drying-rewetting cycles over a 2-month period. The two soils used for the experiment were both collected from the Sedgwick Ranch Natural Reserve in Santa Ynez, CA, one from an annual grassland, the other from underneath an oak canopy. The average soil moisture content over the course of the incubation was the same for all samples, compensating for the number of drying-rewetting cycles. At the end of the 2-month incubation we extracted DNA from soil samples and characterized the soil bacterial communities using the terminal restriction fragment length polymorphism (T-RFLP) method. We found that drying-rewetting regimes can influence bacterial community composition in oak but not in grass soils. The two soils have inherently different bacterial communities; only the bacteria residing in the oak soil, which are less frequently exposed to moisture stress in their natural environment, were significantly affected by drying-rewetting cycles. The community indices of taxonomic diversity and richness were relatively insensitive to drying-rewetting frequency. We hypothesize that drying-rewetting induced shifts in bacterial community composition may partly explain the changes in C mineralization rates that are commonly observed following exposure to numerous drying-rewetting cycles. Microbial community composition may influence soil processes, particularly in soils exposed to a significant level of environmental stress.}, }
@article {pmid12468613, year = {2002}, author = {Swanson, KS and Grieshop, CM and Flickinger, EA and Bauer, LL and Chow, J and Wolf, BW and Garleb, KA and Fahey, GC}, title = {Fructooligosaccharides and Lactobacillus acidophilus modify gut microbial populations, total tract nutrient digestibilities and fecal protein catabolite concentrations in healthy adult dogs.}, journal = {The Journal of nutrition}, volume = {132}, number = {12}, pages = {3721-3731}, doi = {10.1093/jn/132.12.3721}, pmid = {12468613}, issn = {0022-3166}, mesh = {Animals ; *Digestion ; Dogs ; Feces/*chemistry ; Female ; Intestines/*microbiology ; *Lactobacillus acidophilus ; Male ; Oligosaccharides/*administration &amp; dosage ; Proteins/*metabolism ; }, abstract = {The objective of this research was to determine whether fructooligosaccharides (FOS) and (or) Lactobacillus acidophilus (LAC) affected concentrations of gut microbial populations, fermentative end products and nutrient digestibilities in healthy adult dogs. Two experiments were performed using 40 adult dogs (20 dogs/experiment). Dogs in each experiment were randomly assigned to one of 4 treatments. Twice daily, treatments were given orally via gelatin capsules: 1) 2 g sucrose + 80 mg cellulose; 2) 2 g FOS + 80 mg cellulose; 3) 2 g sucrose + 1 x 10(9) colony forming units (cfu) LAC; or 4) 2 g FOS + 1 x 10(9) cfu LAC. Data were analyzed by the General Linear Models procedure of SAS. In Experiment 1, FOS resulted in lower (P = 0.08) Clostridium perfringens and greater fecal butyrate (P = 0.06) and lactate (P < 0.05) concentrations. In Experiment 2, FOS supplementation increased (P < 0.05) bifidobacteria, increased lactobacilli (P = 0.08), increased fecal lactate (P = 0.06) and butyrate (P < 0.05), and decreased (P < 0.05) fecal ammonia, isobutyrate, isovalerate and total branched-chain fatty acid concentrations. Dogs fed LAC had the highest fecal concentrations of hydrogen sulfide and methanethiol in Experiment 1 and dimethyl sulfide in Experiment 2, whereas dogs fed FOS had the lowest concentrations of these compounds. Overall, FOS appeared to enhance indices of gut health by positively altering gut microbial ecology and fecal protein catabolites, whereas LAC was more effective when fed in combination with FOS rather than fed alone.}, }
@article {pmid12462915, year = {2002}, author = {Swanson, KS and Grieshop, CM and Flickinger, EA and Healy, HP and Dawson, KA and Merchen, NR and Fahey, GC}, title = {Effects of supplemental fructooligosaccharides plus mannanoligosaccharides on immune function and ileal and fecal microbial populations in adult dogs.}, journal = {Archiv fur Tierernahrung}, volume = {56}, number = {4}, pages = {309-318}, doi = {10.1080/00039420214344}, pmid = {12462915}, issn = {0003-942X}, mesh = {Animals ; Bacteria ; Cross-Over Studies ; Dietary Supplements ; Dogs/immunology/*metabolism/microbiology ; Feces/chemistry/*microbiology ; Female ; Fermentation ; Ileum/chemistry/*microbiology ; Immunity/*drug effects ; Mannans/*administration &amp; dosage/metabolism ; Oligosaccharides/*administration &amp; dosage/metabolism ; Random Allocation ; }, abstract = {The goal of this study was to examine whether supplemental fructooligosaccharides (FOS) plus mannanoligosaccharides (MOS) influenced immune function and ileal and fecal microbial populations of adult dogs. Eight adult dogs surgically fitted with ileal cannulas were used in a crossover design. Dogs were fed 200 g of a dry, extruded, kibble diet twice daily. At each feeding, dogs were dosed with either 1 g sucrose (placebo) or 2 g FOS plus 1 g MOS orally via gelatin capsule. Fecal, ileal, and blood samples were collected at the end of each 14-d period to measure microbial populations and immune characteristics. Treatment least squares means were compared using the GLM procedure of SAS. Supplementation of FOS plus MOS increased fecal bifidobacteria and fecal and ileal lactobacilli concentrations. Dogs fed FOS plus MOS also tended to have lower blood neutrophils and greater blood lymphocytes vs placebo. Serum, fecal, and ileal immunoglobulin concentrations were unchanged by treatment. Supplementation of FOS plus MOS beneficially altered indices of gut health by improving ileal and fecal microbial ecology. Supplementation of FOS plus MOS also altered immune function by causing a shift in blood immune cells.}, }
@article {pmid12462273, year = {2002}, author = {Van Kessel, JS and Nedoluha, PC and Williams-Campbell, A and Baldwin, RL and McLeod, KR}, title = {Effects of ruminal and postruminal infusion of starch hydrolysate or glucose on the microbial ecology of the gastrointestinal tract in growing steers.}, journal = {Journal of animal science}, volume = {80}, number = {11}, pages = {3027-3034}, pmid = {12462273}, issn = {0021-8812}, mesh = {Abomasum/*metabolism ; Animals ; Bacteria/drug effects/*growth &amp; development/isolation &amp; purification ; Carbohydrate Metabolism ; Carbohydrates/*administration &amp; dosage/pharmacology ; Catheterization/veterinary ; Cattle/*growth &amp; development/metabolism ; Cecum/chemistry/microbiology ; Colony Count, Microbial/veterinary ; Digestive System/chemistry/*microbiology ; Feces/chemistry/microbiology ; Glucose/administration &amp; dosage/metabolism/pharmacology ; Hydrogen-Ion Concentration ; Infusions, Parenteral/veterinary ; Male ; Random Allocation ; Rumen/*metabolism/microbiology ; Starch/administration &amp; dosage/metabolism/pharmacology ; }, abstract = {Forty crossbred steers were used to determine the effects of carbohydrate supply site on the indigenous bacteria of the gastrointestinal tract. Steers were fitted with ruminal and abomasal infusion catheters and assigned randomly to one of eight groups in a complete randomized block design. The experimental period was 36 d. Treatments included: 1) a pelleted basal diet fed at 0.163 Mcal ME x (kg BW(0.75)) x 1 x d(-1) (LE); 2) the basal diet fed at 0.215 Mcal ME x (kg BW(0.75)) (-1) x d(-1) (HE); 3) the basal diet fed at 0.163 Mcal ME x (kg BW(0.75))(-1) x d(-1) with ruminal infusion of starch hydrolysate (SH) (RSH); 4) the basal diet fed at 0.163 Mcal ME x (kg BW(0.75))(-1) x d(-1) with abomasal infusion of SH (ASH); and 5) the basal diet fed at 0.163 Mcal ME x (kg BW(0.75))(-1) x d(-1) with abomasal infusion of glucose (AG). The total volume ofinfusate (5 kg x site(-1) x d(-1)) was equalized across treatments and infusion sites by infusion of water. Glucose and SH were infused at rates of 14.35 and 12.64 g x (kg BW(0.75)) x d(-1), respectively. Ruminal, cecal, and fecal samples were obtained on d 36. Ruminal pH was low (5.79) in LE steers and unaffected (P > 0.10) by increased energy intake or carbohydrate infusion. Cecal and fecal pH were 6.93 and 7.00, respectively, for LE steers. Increasing energy intake (P < 0.10) and the rate of carbohydrate infusion (P < 0.01) significantly decreased cecal and fecal pH compared with LE. Ruminal counts of anaerobic bacteria in LE steers were 8.99 log10 cells/g and abomasal carbohydrate infusion had no affect (P > 0.10) on these numbers. However, ASH and AG steers had approximately 1.5 log10 cells/g more (P < 0.01) cecal and fecal anaerobic populations. Ruminal, cecal, and fecal aerobic bacterial counts were 40, 22, and 23%, respectively, lower than anaerobic counts. Generally, aerobic counts responded similarly to the anaerobic counts. Less than 1% of the anaerobic bacteria enumerated in the rumen, cecum, and feces were coliforms, and 97% of the coliforms were Escherichia coli. Carbohydrate infusions resulted in only numerical increases in fecal coliform and E. coli concentrations (P > 0.10). Fecal E. coli were highly acid sensitive in all steers, with less than 1% surviving a 1-h exposure to low pH (2.0). This suggests that cecal or fecal pH is not a good indicator of acid resistance, and it supports the concept that there are other factors that may induce acid resistance.}, }
@article {pmid12460271, year = {2002}, author = {Fromin, N and Hamelin, J and Tarnawski, S and Roesti, D and Jourdain-Miserez, K and Forestier, N and Teyssier-Cuvelle, S and Gillet, F and Aragno, M and Rossi, P}, title = {Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns.}, journal = {Environmental microbiology}, volume = {4}, number = {11}, pages = {634-643}, doi = {10.1046/j.1462-2920.2002.00358.x}, pmid = {12460271}, issn = {1462-2912}, mesh = {Bacteria/*genetics ; DNA Fingerprinting/*methods ; Data Interpretation, Statistical ; Electrophoresis ; Nucleic Acid Denaturation ; }, abstract = {Technical developments in molecular biology have found extensive applications in the field of microbial ecology. Among these techniques, fingerprinting methods such as denaturing gel electrophoresis (DGE, including the three options: DGGE, TGGE and TTGE) has been applied to environmental samples over this last decade. Microbial ecologists took advantage of this technique, originally developed for the detection of single mutations, for the analysis of whole bacterial communities. However, until recently, the results of these high quality fingerprinting patterns were restricted to a visual interpretation, neglecting the analytical potential of the method in terms of statistical significance and ecological interpretation. A brief recall is presented here about the principles and limitations of DGE fingerprinting analysis, with an emphasis on the need of standardization of the whole analytical process. The main content focuses on statistical strategies for analysing the gel patterns, from single band examination to the analysis of whole fingerprinting profiles. Applying statistical method make the DGE fingerprinting technique a promising tool. Numerous samples can be analysed simultaneously, permitting the monitoring of microbial communities or simply bacterial groups for which occurrence and relative frequency are affected by any environmental parameter. As previously applied in the fields of plant and animal ecology, the use of statistics provides a significant advantage for the non-ambiguous interpretation of the spatial and temporal functioning of microbial communities.}, }
@article {pmid12455614, year = {2002}, author = {Gustafson, AM and O'Connell, KP and Thomashow, MF}, title = {Regulation of Sinorhizobium meliloti 1021 rrnA-reporter gene fusions in response to cold shock.}, journal = {Canadian journal of microbiology}, volume = {48}, number = {9}, pages = {821-830}, doi = {10.1139/w02-078}, pmid = {12455614}, issn = {0008-4166}, mesh = {Base Sequence ; *Cold Temperature ; *Gene Expression Regulation, Bacterial ; Genes, Reporter/*genetics ; Genes, rRNA/*genetics ; Heat-Shock Response ; Luciferases/genetics/metabolism ; Luminescent Measurements ; Molecular Sequence Data ; Promoter Regions, Genetic ; RNA, Ribosomal, 16S/genetics ; Recombinant Fusion Proteins/genetics/*metabolism ; Sinorhizobium meliloti/genetics/*growth &amp; development/metabolism ; Transcription, Genetic ; }, abstract = {We previously reported that mutants of Sinorhizobium meliloti 1021 carrying luxAB insertions in each of the three 16S rRNA genes exhibited a dramatic (> or = 28-fold) increase in luminescence following a temperature downshift from 30 to 15 degrees C. These results raised the possibility that the rRNA operons (rrn) of S. meliloti were cold shock loci. In testing this possibility, we found that fusion of the S. meliloti 1021 rrnA promoter to two different reporter genes, luxAB and uidA, resulted in hybrid genes that were transiently upregulated (as measured by transcript accumulation) about four- to sixfold in response to a temperature downshift. These results are consistent with the hypothesis that the rrn promoters are transiently upregulated in response to cold shock. However, much of the apparent cold shock regulation of the initial luxAB insertions was due to an unexpected mechanism: an apparent temperature-dependent inhibition of translation. Specifically, the rrnA sequences from +1 to +172 (relative to the start of transcription) were found to greatly decrease the ability of S. meliloti to translate hybrid rrn-luxAB transcripts into active protein at 30 degrees C. This effect, however, was largely eliminated at 15 degrees C. Possible mechanisms for the apparent transient increase in rrnA promoter activity and temperature-dependent inhibition of translation are discussed.}, }
@article {pmid12448764, year = {2002}, author = {Strous, M and Kuenen, JG and Fuerst, JA and Wagner, M and Jetten, MS}, title = {The anammox case-a new experimental manifesto for microbiological eco-physiology.}, journal = {Antonie van Leeuwenhoek}, volume = {81}, number = {1-4}, pages = {693-702}, doi = {10.1023/a:1020590413079}, pmid = {12448764}, issn = {0003-6072}, mesh = {Bacteria, Anaerobic/*classification/genetics/*growth &amp; development/metabolism ; Bacteriological Techniques ; Bioreactors ; Culture Media ; *Ecosystem ; In Situ Hybridization, Fluorescence ; Oxidation-Reduction ; Quaternary Ammonium Compounds/*metabolism ; Waste Disposal, Fluid/*methods ; Water Pollutants, Chemical/metabolism ; }, abstract = {The anaerobic ammonium oxidation process is a new process for ammonia removal from wastewater. It is also a new microbial physiology that was previously believed to be impossible. The identification of Candidatus Brocadia anammoxidans and its relatives as the responsible bacteria was only possible with the development of a new experimental approach. That approach is the focus of this paper. The approach is a modernisation of the Winogradsky/Beyerinck strategy of selective enrichment and is based on the introduction of the molecular toolbox and modern bioreactor engineering to microbial ecology. It consists of five steps: (1) postulation of an ecological niche based on thermodynamic considerations and macro-ecological field data; (2) engineering of this niche into a laboratory bioreactor for enrichment culture; (3) black-box physiological characterisation of the enrichment culture as a whole; (4) phylogenetic characterisation of the enriched community using molecular tools; (5) physical separation of the dominant members of the enrichment culture using gradient centrifugation and the identification of the species of interest in accordance with Koch's postulates; (6) verification of the in situ importance of these species in the actual ecosystems. The power of this approach is illustrated with a case study: the identification of the planctomycetes responsible for anaerobic ammonium oxidation. We argue that this was impossible using molecular ecology or conventional 'cultivation based techniques' alone. We suggest that the approach might also be used for the microbiological study of many interesting microbes such as anaerobic methane oxidisers.}, }
@article {pmid12448763, year = {2002}, author = {Blackall, LL and Crocetti, GR and Saunders, AM and Bond, PL}, title = {A review and update of the microbiology of enhanced biological phosphorus removal in wastewater treatment plants.}, journal = {Antonie van Leeuwenhoek}, volume = {81}, number = {1-4}, pages = {681-691}, doi = {10.1023/a:1020538429009}, pmid = {12448763}, issn = {0003-6072}, mesh = {Betaproteobacteria/classification/growth &amp; development/*metabolism ; Biodegradation, Environmental ; Phosphorus/*metabolism ; Sewage/*microbiology ; *Waste Disposal, Fluid ; *Water Microbiology ; }, abstract = {Enhanced biological phosphorus removal (EBPR) from wastewater can be more-or-less practically achieved but the microbiological and biochemical components are not completely understood. EBPR involves cycling microbial biomass and influent wastewater through anaerobic and aerobic zones to achieve a selection of microorganisms with high capacity to accumulate polyphosphate intracellularly in the aerobic period. Biochemical or metabolic modelling of the process has been used to explain the types of carbon and phosphorus transformations in sludge biomass. There are essentially two broad-groupings of microorganisms involved in EBPR. They are polyphosphate accumulating organisms (PAOs) and their supposed carbon-competitors called glycogen accumulating organisms (GAOs). The morphological appearance of microorganisms in EBPR sludges has attracted attention. For example, GAOs as tetrad-arranged cocci and clusters of coccobacillus-shaped PAOs have been much commented upon and the use of simple cellular staining methods has contributed to EBPR knowledge. Acinetobacter and other bacteria were regularly isolated in pure culture from EBPR sludges and were initially thought to be PAOs. However, when contemporary molecular microbial ecology methods in concert with detailed process performance data and simple intracellular polymer staining methods were used, a betaproteobacteria called 'Candidatus Accumulibacter phosphatis' was confirmed as a PAO and organisms from a novel gammaproteobacteria lineage were GAOs. To preclude making the mistakes of previous researchers, it is recommended that the sludge 'biography' be well understood--i.e. details of phenotype (process performance and biochemistry) and microbial community structure should be linked.}, }
@article {pmid12448762, year = {2002}, author = {Wagner, M and Loy, A and Nogueira, R and Purkhold, U and Lee, N and Daims, H}, title = {Microbial community composition and function in wastewater treatment plants.}, journal = {Antonie van Leeuwenhoek}, volume = {81}, number = {1-4}, pages = {665-680}, doi = {10.1023/a:1020586312170}, pmid = {12448762}, issn = {0003-6072}, mesh = {Bacteria/*classification/genetics/growth &amp; development/*metabolism ; Biofilms ; DNA, Ribosomal/analysis ; Ecosystem ; In Situ Hybridization, Fluorescence ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Radiography ; Sewage/*microbiology ; Waste Disposal, Fluid/*methods ; *Water Microbiology ; }, abstract = {Biological wastewater treatment has been applied for more than a century to ameliorate anthropogenic damage to the environment. But only during the last decade the use of molecular tools allowed to accurately determine the composition, and dynamics of activated sludge and biofilm microbial communities. Novel, in many cases yet not cultured bacteria were identified to be responsible for filamentous bulking and foaming as well as phosphorus and nitrogen removal in these systems. Now, methods are developed to infer the in situ physiology of these bacteria. Here we provide an overview of what is currently known about the identity and physiology of some of the microbial key players in activated sludge and biofilm systems.}, }
@article {pmid12448759, year = {2002}, author = {Vogel, RF and Ehrmann, MA and Gänzle, MG}, title = {Development and potential of starter lactobacilli resulting from exploration of the sourdough ecosystem.}, journal = {Antonie van Leeuwenhoek}, volume = {81}, number = {1-4}, pages = {631-638}, doi = {10.1023/a:1020530227192}, pmid = {12448759}, issn = {0003-6072}, mesh = {Bread/*microbiology ; *Ecosystem ; Fermentation ; Lactobacillus/*growth &amp; development/metabolism ; Maltose/metabolism ; }, abstract = {Lactic acid bacteria are widely used as starter organisms in food fermentations. The development of such cultures as organisms fulfilling all metabolic, technical and handling requirements is the result of a multidisciplinary approach, i.e. to analyse, follow and direct the microbial ecology in food fermentations by molecular biology tools, gene cloning, biochemical and physiological analyses, pilot trials and modelling of behaviour and metabolism. The possibilities and restrictions of such an approach is given for cereal fermentations, namely sourdoughs. In this environment highly adapted lactobacilli are predominant, sharing the environment with yeasts present in traditional preparations. The competitiveness of these lactobacilli and their contribution to flavour, machineability and prebiosis of doughs and bread relies on their maltose and amino acid metabolism, use of electron acceptors and EPS formation. Their reactions on environmental stresses can be used to embed these recalcitrant organisms into starter culture preparations. Beyond the cereal environment the described strategy can be generally applied to understand ecosystems in food fermentations and finally control them.}, }
@article {pmid12448726, year = {2002}, author = {Valentine, DL}, title = {Biogeochemistry and microbial ecology of methane oxidation in anoxic environments: a review.}, journal = {Antonie van Leeuwenhoek}, volume = {81}, number = {1-4}, pages = {271-282}, doi = {10.1023/a:1020587206351}, pmid = {12448726}, issn = {0003-6072}, mesh = {Anaerobiosis ; Archaea/*growth &amp; development/metabolism ; *Ecosystem ; Geologic Sediments/*microbiology ; Methane/*metabolism ; Oxidation-Reduction ; Seawater/*microbiology ; }, abstract = {Evidence supporting a key role for anaerobic methane oxidation in the global methane cycle is reviewed. Emphasis is on recent microbiological advances. The driving force for research on this process continues to be the fact that microbial communities intercept and consume methane from anoxic environments, methane that would otherwise enter the atmosphere. Anaerobic methane oxidation is biogeochemically important because methane is a potent greenhouse gas in the atmosphere and is abundant in anoxic environments. Geochemical evidence for this process has been observed in numerous marine sediments along the continental margins, in methane seeps and vents, around methane hydrate deposits, and in anoxic waters. The anaerobic oxidation of methane is performed by at least two phylogenetically distinct groups of archaea, the ANME-1 and ANME-2. These archaea are frequently observed as consortia with sulfate-reducing bacteria, and the metabolism of these consortia presumably involves a syntrophic association based on interspecies electron transfer. The archaeal member of a consortium apparently oxidizes methane and shuttles reduced compounds to the sulfate-reducing bacteria. Despite recent advances in understanding anaerobic methane oxidation, uncertainties still remain regarding the nature and necessity of the syntrophic association, the biochemical pathway of methane oxidation, and the interaction of the process with the local chemical and physical environment. This review will consider the microbial ecology and biogeochemistry of anaerobic methane oxidation with a special emphasis on the interactions between the responsible organisms and their environment.}, }
@article {pmid12448721, year = {2002}, author = {Whitehead, NA and Byers, JT and Commander, P and Corbett, MJ and Coulthurst, SJ and Everson, L and Harris, AK and Pemberton, CL and Simpson, NJ and Slater, H and Smith, DS and Welch, M and Williamson, N and Salmond, GP}, title = {The regulation of virulence in phytopathogenic Erwinia species: quorum sensing, antibiotics and ecological considerations.}, journal = {Antonie van Leeuwenhoek}, volume = {81}, number = {1-4}, pages = {223-231}, doi = {10.1023/a:1020570802717}, pmid = {12448721}, issn = {0003-6072}, mesh = {Bacterial Proteins/genetics/metabolism ; Carbapenems/*biosynthesis ; Ecosystem ; Erwinia/genetics/growth &amp; development/*pathogenicity ; *Gene Expression Regulation, Bacterial ; Plant Diseases/*microbiology ; *Signal Transduction ; Virulence ; }, abstract = {Erwinia carotovora is a Gram-negative bacterial phytopathogen that causes soft-rot disease and potato blackleg. The organism is environmentally widespread and exhibits an opportunistic plant pathogenesis. The ability to secrete multiple plant cell wall-degrading enzymes is a key virulence trait and exoenzyme production is responsive to multiple environmental and physiological cues. One important cue is the cell population density of the pathogen. Cell density is monitored via an acylated homoserine lactone (acyl HSL) signalling molecule, which is thought to diffuse between Erwinia cells in a process now commonly known as 'quorum sensing'. This molecule also acts as the chemical communication signal controlling production of a broad-spectrum beta-lactam antibiotic (1-carbapen-2-em-3-carboxylic acid; carbapenem) synthesised in concert with exoenzyme elaboration, possibly for niche defence. In antibiotic production control, quorum sensing acts at the level of transcriptional activation of the antibiotic biosynthetic cluster. This is achieved via a dedicated LuxR-type protein, CarR that is bound to the signalling molecule. The molecular relay connecting acyl HSL production and exoenzyme induction is not clear, despite the identification of a multitude of global regulatory genes, including those of the RsmA/rsmB system, impinging on enzyme synthesis. Quorum sensing control mediated by acyl HSLs is widespread in Gram-negative bacteria and is responsible for the regulation of diverse phenotypes. Although there is still a paucity of meaningful information on acyl HSL availability and in-situ biological function, there is growing evidence that such molecules play significant roles in microbial ecology.}, }
@article {pmid12448716, year = {2002}, author = {Purdy, KJ and Embley, TM and Nedwell, DB}, title = {The distribution and activity of sulphate reducing bacteria in estuarine and coastal marine sediments.}, journal = {Antonie van Leeuwenhoek}, volume = {81}, number = {1-4}, pages = {181-187}, doi = {10.1023/a:1020550215012}, pmid = {12448716}, issn = {0003-6072}, mesh = {DNA, Ribosomal/analysis ; Ecosystem ; Fresh Water/*microbiology ; Geologic Sediments/*microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sulfates/*metabolism ; Sulfur-Reducing Bacteria/classification/genetics/*isolation &amp; purification ; }, abstract = {Sulphate-reducing bacteria (SRB) play a vital role both the carbon and sulphur cycles and thus are extremely important components of the global microbial community. However, it is clear that the ecology, the distribution and activity of different SRB groups is poorly understood. Probing of rRNA suggests that different sediments have distinctly different patterns of SRB with complex factors controlling the activity of these organisms. The linking of community structure and function using sediment slurry microcosms suggests that certain groups of SRB, e.g., Desulfobacter and Desulfobulbus, can be linked to the use of specific substrates in situ. However, it is still unclear what environmental substrates are utilised by the majority of known SRBs. The work to date has greatly enhanced our understanding of the ecology of these organisms and is beginning to suggest patterns in their distribution and activity that may be relevant to understanding microbial ecology in general.}, }
@article {pmid12447585, year = {2003}, author = {Björklöf, K and Sen, R and Jørgensen, KS}, title = {Maintenance and impacts of an inoculated mer/luc-tagged Pseudomonas fluorescens on microbial communities in birch rhizospheres developed on humus and peat.}, journal = {Microbial ecology}, volume = {45}, number = {1}, pages = {39-52}, doi = {10.1007/s00248-002-2018-8}, pmid = {12447585}, issn = {0095-3628}, mesh = {Betula/*growth &amp; development ; DNA Fingerprinting ; DNA, Bacterial/analysis ; Forestry ; *Genetic Engineering ; Genetic Markers ; Plant Roots/microbiology ; Polymerase Chain Reaction ; Population Dynamics ; Pseudomonas fluorescens/genetics/*physiology ; Seedlings/growth &amp; development ; Soil ; Survival ; }, abstract = {Antagonistic bacteria represent promising biocontrol agents for improving forest production in seedling nurseries or forest soils. The fate of an introduced mer/luc-tagged antagonistic Pseudomonas fluorescens 31K3 was monitored in the rhizosphere of silver birch (Betula pendula) seedlings grown in microcosms containing forest humus or nursery peat. The inoculated strain (10(8) cfu g(-1) soil) was unable to establish in significant numbers in either soil type and turned nonculturable in humus. Detection in both soils was possible only via luminescence of enrichment cultures 80 days post-inoculation. Despite low P. fluorescens survival, inoculation had a positive effect on seedling growth. Limited impact of inoculation on the indigenous microbial communities was identified following analyses of respiration and denitrification potential, community-level physiological profiles and molecular fingerprinting of fungi and eubacteria, and Pseudomonas community structures. The minor changes observed in the indigenous microbial communities, including mycorrhiza development, were not consistent between humus and peat growth substrates. It was concluded that the rhizosphere-related microbial communities developed in both of these highly organic soil systems are highly buffered against introduction of foreign bacteria.}, }
@article {pmid12447584, year = {2003}, author = {Gulis, V and Suberkropp, K}, title = {Effect of inorganic nutrients on relative contributions of fungi and bacteria to carbon flow from submerged decomposing leaf litter.}, journal = {Microbial ecology}, volume = {45}, number = {1}, pages = {11-19}, doi = {10.1007/s00248-002-1032-1}, pmid = {12447584}, issn = {0095-3628}, mesh = {*Bacteria ; Biodegradation, Environmental ; Carbon/*metabolism ; *Fungi ; Nitrogen/analysis/metabolism ; Phosphorus/analysis/metabolism ; Plant Leaves/*metabolism ; Population Dynamics ; Soil Microbiology ; }, abstract = {The relative contributions of fungi and bacteria to carbon flow from submerged decaying plant litter at different levels of inorganic nutrients (N and P) were studied. We estimated leaf mass loss, fungal and bacterial biomass and production, and microbial respiration and constructed partial carbon budgets for red maple leaf disks precolonized in a stream and then incubated in laboratory microcosms at two levels of nutrients. Patterns of carbon flow for leaf disks colonized with the full microbial assemblage were compared with those colonized by bacteria but in which fungi were greatly reduced by placing leaf disks in colonization chambers sealed with membrane filters to exclude aquatic hyphomycete conidia but not bacterial cells. On leaves colonized by the full microbial assemblage, elevated nutrient concentrations stimulated fungi and bacteria to a similar degree. Peak fungal and bacterial biomass increased by factors of 3.9 and 4.0; cumulative production was 3.9 and 5.1 times higher in the high nutrient in comparison with the low nutrient treatment, respectively. Fungi dominated the total microbial biomass (98.4 to 99.8%) and cumulative production (97.3 and 96.5%), and the fungal yield coefficient exceeded that of bacteria by a factor of 36 and 27 in low- and high-nutrient treatments, respectively. Consequently, the dominant role of fungi in leaf decomposition did not change as a result of nutrient manipulation. Carbon budgets indicated that 8% of leaf carbon loss in the low-nutrient treatment and 17% in the high-nutrient treatment were channeled to microbial (essentially fungal) production. Nutrient enrichment had a positive effect on rate of leaf decomposition only in microcosms with full microbial assemblages. In treatments where fungal colonization was reduced, cumulative bacterial production did not change significantly at either nutrient level and leaf decomposition rate was negatively affected (high nutrients), suggesting that bacterial participation in carbon flow from decaying leaf litter is low regardless of the presence of fungi and nutrient availability. Moreover, 1.5 and 2.3 times higher yield coefficients of bacteria in the reduced fungal treatments at low and high nutrients, respectively (percentage of leaf carbon loss channeled to bacterial production), suggest that bacteria are subjected to strong competition with fungi for resources available in leaf litter.}, }
@article {pmid12447583, year = {2003}, author = {Arana, I and Irizar, A and Seco, C and Muela, A and Fernández-Astorga, A and Barcina, I}, title = {gfp-Tagged cells as a useful tool to study the survival of Escherichia coli in the presence of the river microbial community.}, journal = {Microbial ecology}, volume = {45}, number = {1}, pages = {29-38}, doi = {10.1007/s00248-002-1029-9}, pmid = {12447583}, issn = {0095-3628}, mesh = {Biomarkers/analysis ; Environmental Monitoring/*methods ; *Escherichia coli ; Food Chain ; Green Fluorescent Proteins ; Hot Temperature ; Indicators and Reagents/*analysis ; Luminescent Proteins/*analysis ; Survival ; *Water Microbiology ; }, abstract = {We have used an Escherichia coli strain DH5a containing pGreenTIR to study the survival of this bacterium in river water. As green fluorescence was maintained throughout survival both in dark and illuminated conditions, gfp-tagged E. coli cells were clearly distinguished from the microbial community of the river Butrón. gfp-tagged E. coli cells were monitored to estimate total density as well as the density of the culturable and viable (active electron transport system, CTC+) cells. Our results indicate that autochthonous bacteria and introduced E. coli are predated by flagellates. The autochthonous bacterial community behaves as predation-escaping prey, showing a tendency to cellular miniaturization and so maintaining the density of the population. In contrast, introduced E. coli behaves as predation-non-escaping prey, so E. coli was eliminated from the system. When comparing the elimination by predation of heat-treated and non-heated gfp-tagged E. coli cells we deduce that the flagellates do not discriminate between live and heat-treated cells. Finally, in the presence of the river microbial community, the E. coli cells appeared to be ingested before cellular deterioration could occur. Thus predation reduces the quantitative importance of the viable but nonculturable (VBNC) population of E. coli in the aquatic systems.}, }
@article {pmid12442292, year = {2002}, author = {Manefield, M and Whiteley, AS and Ostle, N and Ineson, P and Bailey, MJ}, title = {Technical considerations for RNA-based stable isotope probing: an approach to associating microbial diversity with microbial community function.}, journal = {Rapid communications in mass spectrometry : RCM}, volume = {16}, number = {23}, pages = {2179-2183}, doi = {10.1002/rcm.782}, pmid = {12442292}, issn = {0951-4198}, mesh = {Biomarkers/analysis ; Carbon Isotopes/metabolism ; Mass Spectrometry ; Phenol/metabolism ; Pseudomonas putida/classification/*genetics/metabolism ; *RNA Probes ; RNA, Bacterial/*analysis ; Reverse Transcriptase Polymerase Chain Reaction ; *Soil Microbiology ; }, abstract = {An ongoing challenge within microbial ecology is the development of methodologies that attribute microbial community functions to microbial diversity. One approach, involving the incorporation of stable isotopes from labelled tracer compounds into biological signature molecules (biomarkers), may overcome this current limitation. To examine the potential of RNA as the biomarker in stable isotope probing we have generated a series of atom % (13)C-enriched RNA samples through exploitation of the anabolic abilities of a phenol-degrading environmental isolate. Isotope ratio mass spectrometry was used to determine the atom % (13)C of each RNA sample (ca. 1-100%). The corresponding buoyant density (1.755-1.795 g mL(-1)) was determined by equilibrium density gradient centrifugation and agarose gel electrophoresis. This empirically defined relationship between the atom % (13)C of RNA and its buoyant density suggests ribonucleic acids with atom % (13)C enrichments greater than 10% can be isolated by equilibrium density centrifugation. The processing and analysis of isolated RNA by reverse transcription polymerase chain reaction, denaturing gradient gel electrophoresis, cloning and sequencing are discussed. The RNA-based stable isotope probing protocol presented here will find particular utility in assessing the roles of microbial community members in the biodegradation of natural and anthropogenic xenobiotic compounds.}, }
@article {pmid12432102, year = {2002}, author = {Stappenbeck, TS and Hooper, LV and Gordon, JI}, title = {Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {24}, pages = {15451-15455}, pmid = {12432102}, issn = {0027-8424}, support = {R01 DK030292/DK/NIDDK NIH HHS/United States ; DK30292/DK/NIDDK NIH HHS/United States ; DK52574/DK/NIDDK NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteroides/*physiology ; Cell Differentiation ; Cell Lineage ; Defensins ; Diphtheria Toxin/pharmacology ; Germ-Free Life ; Imaging, Three-Dimensional ; Intestinal Mucosa/cytology/growth &amp; development ; Intestine, Small/*blood supply/growth &amp; development/microbiology/ultrastructure ; Mice ; Mice, Transgenic ; Microvilli ; Neovascularization, Physiologic/*physiology ; Paneth Cells/cytology/drug effects/*metabolism ; Peptide Fragments/pharmacology ; Proteins/genetics/*metabolism ; Specific Pathogen-Free Organisms ; alpha-Defensins/*metabolism ; }, abstract = {The adult mouse intestine contains an intricate vascular network. The factors that control development of this network are poorly understood. Quantitative three-dimensional imaging studies revealed that a plexus of branched interconnected vessels developed in small intestinal villi during the period of postnatal development that coincides with assembly of a complex society of indigenous gut microorganisms (microbiota). To investigate the impact of this environmental transition on vascular development, we compared the capillary networks of germ-free mice with those of ex-germ-free animals colonized during or after completion of postnatal gut development. Adult germ-free mice had arrested capillary network formation. The developmental program can be restarted and completed within 10 days after colonization with a complete microbiota harvested from conventionally raised mice, or with Bacteroides thetaiotaomicron, a prominent inhabitant of the normal mouse/human gut. Paneth cells in the intestinal epithelium secrete antibacterial peptides that affect luminal microbial ecology. Comparisons of germ-free and B. thetaiotaomicron-colonized transgenic mice lacking Paneth cells established that microbial regulation of angiogenesis depends on this lineage. These findings reveal a previously unappreciated mechanism of postnatal animal development, where microbes colonizing a mucosal surface are assigned responsibility for regulating elaboration of the underlying microvasculature by signaling through a bacteria-sensing epithelial cell.}, }
@article {pmid12427983, year = {2002}, author = {Olsson, PA and van Aarle, IM and Allaway, WG and Ashford, AE and Rouhier, H}, title = {Phosphorus effects on metabolic processes in monoxenic arbuscular mycorrhiza cultures.}, journal = {Plant physiology}, volume = {130}, number = {3}, pages = {1162-1171}, pmid = {12427983}, issn = {0032-0889}, mesh = {Acid Phosphatase/metabolism ; Alkaline Phosphatase/metabolism ; Biomass ; Carbon/metabolism ; Carbon Isotopes/metabolism ; Culture Techniques ; Daucus carota/growth &amp; development ; Fatty Acids/metabolism ; Glucose/metabolism ; Mycelium/drug effects/growth &amp; development ; Mycorrhizae/drug effects/growth &amp; development/*metabolism ; Phosphorus/*pharmacology ; Plant Roots/drug effects/growth &amp; development ; Vacuoles/metabolism ; }, abstract = {The influence of external phosphorus (P) on carbon (C) allocation and metabolism as well as processes related to P metabolism was studied in monoxenic arbuscular mycorrhiza cultures of carrot (Daucus carota). Fungal hyphae of Glomus intraradices proliferated from the solid minimal medium containing the colonized roots into C-free liquid minimal medium with different P treatments. The fungus formed around three times higher biomass in P-free liquid medium than in medium with 2.5 mM inorganic P (high-P). Mycelium in the second experiment was harvested at an earlier growth stage to study metabolic processes when the mycelium was actively growing. P treatment influenced the root P content and [(13)C]glucose administered to the roots 7 d before harvest gave a negative correlation between root P content and (13)C enrichment in arbuscular mycorrhiza fungal storage lipids in the extraradical hyphae. Eighteen percent of the enriched (13)C in extraradical hyphae was recovered in the fatty acid 16:1omega5 from neutral lipids. Polyphosphate accumulated in hyphae even in P-free medium. No influence of P treatment on fungal acid phosphatase activity was observed, whereas the proportion of alkaline-phosphatase-active hyphae was highest in high-P medium. We demonstrated the presence of a motile tubular vacuolar system in G. intraradices. This system was rarely seen in hyphae subjected to the highest P treatment. We concluded that the direct responses of the extraradical hyphae to the P concentration in the medium are limited. The effects found in hyphae seemed instead to be related to increased availability of P to the host root.}, }
@article {pmid12420111, year = {2002}, author = {Blaut, M}, title = {Relationship of prebiotics and food to intestinal microflora.}, journal = {European journal of nutrition}, volume = {41 Suppl 1}, number = {}, pages = {I11-6}, doi = {10.1007/s00394-002-1102-7}, pmid = {12420111}, issn = {1436-6207}, mesh = {Bacteria/*growth &amp; development/metabolism ; Bifidobacterium/growth &amp; development/metabolism ; Colon/metabolism/*microbiology ; Dietary Fiber/administration &amp; dosage/metabolism ; Digestion ; Fermentation ; Humans ; Lactobacillus/growth &amp; development/metabolism ; Oligosaccharides/*administration &amp; dosage/*metabolism ; }, abstract = {Dietary carbohydrates that escape digestion in the small intestine, undergo bacterial fermentation in the colon. This process affects the microbial ecology of the gastrointestinal tract and influences gut metabolism and function. Prebiotics are non-digestible but fermentable oligosaccharides that are specifically designed to change the composition and activity of the intestinal microbiota with the prospect to promote the health of the host. Dietary fiber and non-digestible oligosaccharides are the main growth substrates of gut microorganisms. Their fermentation results in the acidification of the colonic contents and the formation of short chain fatty acids which serve as fuels in different tissues and may play a role in the regulation of cellular processes. Prebiotics specifically stimulate the growth of endogenous microbial population groups such as bifidobacteria and lactobacilli which are perceived as being beneficial to human health. In spite of the interesting nutritional properties of prebiotics it is questionable whether a wholesome diet rich in fruit and vegetables needs to be supplemented with prebiotics for optimal health effects.}, }
@article {pmid12415420, year = {2003}, author = {Dinkla, IJ and Janssen, DB}, title = {Simultaneous growth on citrate reduces the effects of iron limitation during toluene degradation in Pseudomonas.}, journal = {Microbial ecology}, volume = {45}, number = {1}, pages = {97-107}, doi = {10.1007/s00248-002-2023-y}, pmid = {12415420}, issn = {0095-3628}, mesh = {Amino Acids ; Biodegradation, Environmental ; Biomass ; Citric Acid/chemistry ; Iron/*metabolism ; Plant Roots ; Population Dynamics ; Pseudomonas putida/*physiology ; Soil Pollutants/*metabolism ; Toluene/*metabolism ; Yeasts ; }, abstract = {Rhizoremediation has been suggested as an attractive bioremediation strategy for the effective breakdown of pollutants in soil. The presence of plant root exudates such as organic acids, sugars, and amino acids that may serve as carbon sources or biosynthetic building blocks and the limited bioavailability of iron may influence the degradation of pollutants in the rhizosphere. To test the effect of such compounds on hydrocarbon degradation, trace concentrations of yeast extract or mixtures of organic acids and amino acids were added to continuous cultures of Pseudomonas putida mt2 and P. putida WCS358 (TOL) growing on toluene. By addition of these compounds increased growth yields and higher specific growth rates on toluene were obtained. The effects of iron limitation on the substrate utilization pattern of both strains were tested by growing the strains on a mixture of toluene and the readily degradable carbon source citrate while the iron concentration was varied. Simultaneous use of both substrates under carbon-limited as well as iron-limited conditions was observed. Growth yields were less reduced and iron requirement was lower during iron-limited growth in the toluene + citrate grown cultures compared to cultures in which toluene was used as the sole carbon source. The kinetic properties of the cells for toluene degradation were less hampered by the lack of iron when citrate was used as an additional carbon source. The results indicate that the availability of low concentrations of natural organic compounds, such as produced in the rhizosphere, may positively influence the degradative performance of hydrocarbon-degrading bacteria.}, }
@article {pmid12415419, year = {2003}, author = {Treves, DS and Xia, B and Zhou, J and Tiedje, JM}, title = {A two-species test of the hypothesis that spatial isolation influences microbial diversity in soil.}, journal = {Microbial ecology}, volume = {45}, number = {1}, pages = {20-28}, doi = {10.1007/s00248-002-1044-x}, pmid = {12415419}, issn = {0095-3628}, mesh = {*Cupriavidus necator ; *Ecosystem ; Population Dynamics ; Silicon Dioxide ; *Soil Microbiology ; *Sphingomonas ; Water ; }, abstract = {The hypothesis that spatial isolation is a key determinant of microbial community structure in soils was evaluated by examining the competitive dynamics of two species growing on a single resource in a uniform sand matrix under varied moisture content. One species dominated the community under highly connected, saturated treatments, suggesting that these conditions allow competitive interactions to structure the community. As moisture content decreased, however, the less competitive species became established in the community. This effect was most pronounced at a matric water potential of -0.14 MPa where estimates of final population density and species fitness were equal. A second but more closely related species pair exhibited a similar response to decreasing moisture, suggesting that the effects of spatial isolation we observed are not simply a species-pair-specific phenomenon. These findings indicate that spatial isolation, created by low moisture content, plays an important role in structuring soil microbial communities.}, }
@article {pmid12411705, year = {2002}, author = {Sun, B and Griffin, BM and Ayala-del-Río, HL and Hashsham, SA and Tiedje, JM}, title = {Microbial dehalorespiration with 1,1,1-trichloroethane.}, journal = {Science (New York, N.Y.)}, volume = {298}, number = {5595}, pages = {1023-1025}, doi = {10.1126/science.1074675}, pmid = {12411705}, issn = {1095-9203}, mesh = {Anaerobiosis ; Bacteria, Anaerobic/classification/cytology/isolation &amp; purification/metabolism ; Base Composition ; Biodegradation, Environmental ; Culture Media ; DNA, Ribosomal/genetics ; Electron Transport ; Energy Metabolism ; Environmental Pollutants/*metabolism ; Ethyl Chloride/metabolism ; Formates/metabolism ; Geologic Sediments/*microbiology ; Hydrogen/metabolism ; Oxidation-Reduction ; Peptococcaceae/classification/cytology/growth &amp; development/*isolation &amp; purification/*metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Temperature ; Trichloroethanes/*metabolism ; }, abstract = {1,1,1-Trichloroethane (TCA) is a ubiquitous environmental pollutant because of its widespread use as an industrial solvent, its improper disposal, and its substantial emission to the atmosphere. We report the isolation of an anaerobic bacterium, strain TCA1, that reductively dechlorinates TCA to 1,1-dichloroethane and chloroethane. Strain TCA1 required H2 as an electron donor and TCA as an electron acceptor for growth, indicating that dechlorination is a respiratory process. Phylogenetic analysis indicated that strain TCA1 is related to gram-positive bacteria with low DNA G+C content and that its closest relative is Dehalobacter restrictus, an obligate H2-oxidizing, chloroethene-respiring bacterium.}, }
@article {pmid12410839, year = {2002}, author = {Ehling-Schulz, M and Schulz, S and Wait, R and Görg, A and Scherer, S}, title = {The UV-B stimulon of the terrestrial cyanobacterium Nostoc commune comprises early shock proteins and late acclimation proteins.}, journal = {Molecular microbiology}, volume = {46}, number = {3}, pages = {827-843}, doi = {10.1046/j.1365-2958.2002.03209.x}, pmid = {12410839}, issn = {0950-382X}, mesh = {*Adaptation, Physiological ; Amino Acid Sequence ; Bacterial Proteins/chemistry/*metabolism ; Cyanobacteria/growth &amp; development/physiology/*radiation effects ; Heat-Shock Proteins/chemistry/*metabolism ; *Heat-Shock Response ; Molecular Sequence Data ; Proteome ; Spectrometry, Mass, Electrospray Ionization ; Ultraviolet Rays/*adverse effects ; }, abstract = {The UV-B and desiccation-tolerant terrestrial cyanobacterium Nostoc commune was grown under defined UV irradiation. Proteome changes were monitored in the membrane and the cytosolic and the extracellular fractions. Tools were developed to separate stress-triggered from growth stage-dependent changes. UV-B changed the relative cellular concentration of 493 out of 1,350 protein spots at least by a factor of three, rendering the UV-B stimulon of N. commune the most complex one described so far. It comprises two different parts: an early shock response influencing 214 proteins and a late acclimation response involving 279 proteins. The shock response comprised many membrane or membrane-associated proteins, whereas the acclimation response mainly changed cytosolic proteins. Most of the shock-induced changes were transient and did not overlap with the acclimation response. In the extracellular fraction, UV irradiation induced superoxide dismutase and the water stress protein. In total, 27 intracellular, UV-B-induced proteins were partially sequenced by electrospray ionization tandem mass spectrometry. Three functional classes were identified: proteins involved in lipid metabolism, in carbohydrate metabolism and in regulatory pathways. About 50% of the sequenced proteins were homologous to cyanobacterial database entries with un-known function. Interestingly, all of these proteins belong to the UV-B acclimation response. We conclude that the UV-B shock response and the UV-B acclimation response represent two completely different and remarkably complex strategies of N. commune to protect itself against UV-B radiation in its natural environment.}, }
@article {pmid12406737, year = {2002}, author = {Barrangou, R and Yoon, SS and Breidt, F and Fleming, HP and Klaenhammer, TR}, title = {Characterization of six Leuconostoc fallax bacteriophages isolated from an industrial sauerkraut fermentation.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {11}, pages = {5452-5458}, pmid = {12406737}, issn = {0099-2240}, mesh = {Bacteriophages/genetics/growth &amp; development/*isolation &amp; purification/metabolism/ultrastructure ; DNA Fingerprinting ; DNA, Viral/analysis ; Fermentation ; *Genome, Viral ; Leuconostoc/*virology ; Polymorphism, Restriction Fragment Length ; Random Amplified Polymorphic DNA Technique ; Viral Proteins/analysis ; }, abstract = {Six bacteriophages active against Leuconostoc fallax strains were isolated from industrial sauerkraut fermentation brines. These phages were characterized as to host range, morphology, structural proteins, and genome fingerprint. They were exclusively lytic against the species L. fallax and had different host ranges among the strains of this species tested. Morphologically, three of the phages were assigned to the family Siphoviridae, and the three others were assigned to the family Myovidae: Major capsid proteins detected by electrophoresis were distinct for each of the two morphotypes. Restriction fragment length polymorphism analysis and randomly amplified polymorphic DNA fingerprinting showed that all six phages were genetically distinct. These results revealed for the first time the existence of bacteriophages that are active against L. fallax and confirmed the presence and diversity of bacteriophages in a sauerkraut fermentation. Since a variety of L. fallax strains have been shown to be present in sauerkraut fermentation, bacteriophages active against L. fallax are likely to contribute to the microbial ecology of sauerkraut fermentation and could be responsible for some of the variability observed in this type of fermentation.}, }
@article {pmid12406726, year = {2002}, author = {Manefield, M and Whiteley, AS and Griffiths, RI and Bailey, MJ}, title = {RNA stable isotope probing, a novel means of linking microbial community function to phylogeny.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {11}, pages = {5367-5373}, pmid = {12406726}, issn = {0099-2240}, mesh = {Carbon Isotopes ; Phenol/metabolism ; *Phylogeny ; RNA Probes ; RNA, Bacterial/analysis ; Thauera/*classification/physiology ; }, abstract = {Identifying microorganisms responsible for recognized environmental processes remains a great challenge in contemporary microbial ecology. Only in the last few years have methodological innovations provided access to the relationship between the function of a microbial community and the phylogeny of the organisms accountable for it. In this study stable-isotope-labeled [13C]phenol was fed into a phenol-degrading community from an aerobic industrial bioreactor, and the 13C-labeled RNA produced was used to identify the bacteria responsible for the process. Stable-isotope-labeled RNA was analyzed by equilibrium density centrifugation in concert with reverse transcription-PCR and denaturing gradient gel electrophoresis. In contradiction with findings from conventional methodologies, this unique approach revealed that phenol degradation in the microbial community under investigation is dominated by a member of the Thauera genus. Our results suggest that this organism is important for the function of this bioreactor.}, }
@article {pmid12406709, year = {2002}, author = {Park, J and Kukor, JJ and Abriola, LM}, title = {Characterization of the adaptive response to trichloroethylene-mediated stresses in Ralstonia pickettii PKO1.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {11}, pages = {5231-5240}, pmid = {12406709}, issn = {0099-2240}, support = {P42 ES004911/ES/NIEHS NIH HHS/United States ; P42-ES-04911/ES/NIEHS NIH HHS/United States ; }, mesh = {Betaproteobacteria/*drug effects/metabolism ; Kinetics ; Toluene/metabolism ; Trichloroethylene/*pharmacology ; }, abstract = {In Ralstonia pickettii PKO1, a denitrifying toluene oxidizer that carries a toluene-3-monooxygenase (T3MO) pathway, the biodegradation of toluene and trichloroethylene (TCE) by the organism is induced by TCE at high concentrations. In this study, the effect of TCE preexposure was studied in the context of bacterial protective response to TCE-mediated toxicity in this organism. The results of TCE degradation experiments showed that cells induced by TCE at 110 mg/liter were more tolerant to TCE-mediated stress than were those induced by TCE at lower concentrations, indicating an ability of PKO1 to adapt to TCE-mediated stress. To characterize the bacterial protective response to TCE-mediated stress, the effect of TCE itself (solvent stress) was isolated from TCE degradation-dependent stress (toxic intermediate stress) in the subsequent chlorinated ethylene toxicity assays with both nondegradable tetrachloroethylene and degradable TCE. The results of the toxicity assays showed that TCE preexposure led to an increase in tolerance to TCE degradation-dependent stress rather than to solvent stress. The possibility that such tolerance was selected by TCE degradation-dependent stress during TCE preexposure was ruled out because a similar extent of tolerance was observed in cells that were induced by toluene, whose metabolism does not produce any toxic products. These findings suggest that the adaptation of TCE-induced cells to TCE degradation-dependent stress was caused by the combined effects of solvent stress response and T3MO pathway expression.}, }
@article {pmid12399899, year = {2002}, author = {Sigler, WV and Crivii, S and Zeyer, J}, title = {Bacterial succession in glacial forefield soils characterized by community structure, activity and opportunistic growth dynamics.}, journal = {Microbial ecology}, volume = {44}, number = {4}, pages = {306-316}, doi = {10.1007/s00248-002-2025-9}, pmid = {12399899}, issn = {0095-3628}, mesh = {*Bacteria ; Ecosystem ; Fluoresceins/chemistry ; Hydrolysis ; Population Dynamics ; Ribosomes ; *Soil Microbiology ; *Trees ; }, abstract = {The succession of bacterial communities inhabiting the forefield of the Dammaglacier (Switzerland) was investigated in soils ranging in successional age from 0 to 100 years since deglaciation. Overall activity per bacterial cell was estimated by the amount of fluorescein diacetate (FDA) hydrolyzed per DAPI-stained cell, and an index of "opportunism" was determined from the ratio of culturable to total cells (C:T ratio). Ribosomal intergenic spacer analysis (RISA) was used to estimate the richness of dominant phylotypes and to construct rank-abundance plots of the dominant populations. We observed a biphasic trend in specific cellular activity, which exhibited minima in the 0- and 100-year-old soils while a maximum activity per cell was reached in the 70-y soil. On average, the C:T ratio showed the same trend as the specific activity, although we observed some differences between the two sampling transects. RISA revealed a decrease in dominant phylotype richness as successional age increased, and rank-abundance plots indicated that the evenness of the dominant bacterial phylotypes significantly decreased with successional age. The combination of specific cellular activity and C:T ratio results suggested the presence of an r-K continuum of bacteria while RISA showed that richness and evenness of dominant phylotypes decreased with successional age. We conclude that bacterial succession in the glacier forefield was a dynamic process with adaptation to the differing stages of succession occurring on both the individual and community levels.}, }
@article {pmid12399898, year = {2002}, author = {Romero, J and García-Varela, M and Laclette, JP and Espejo, RT}, title = {Bacterial 16S rRNA gene analysis revealed that bacteria related to Arcobacter spp. constitute an abundant and common component of the oyster microbiota (Tiostrea chilensis).}, journal = {Microbial ecology}, volume = {44}, number = {4}, pages = {365-371}, doi = {10.1007/s00248-002-1063-7}, pmid = {12399898}, issn = {0095-3628}, mesh = {Animals ; Arcobacter/*genetics/physiology ; Classification ; DNA, Bacterial/analysis/genetics ; Ostreidae/*microbiology ; Polymerase Chain Reaction ; Population Dynamics ; RNA, Ribosomal, 16S/analysis/*genetics ; }, abstract = {To explore the bacterial microbiota in Chilean oyster (Tiostrea chilensis), a molecular approach that permits detection of different bacteria, independently of their capacity to grow in culture media, was used. Bacterial diversity was assessed by analysis of both the 16S rDNA and the 16S-23S intergenic region, obtained by PCR amplifications of DNA extracted from depurated oysters. RFLP of the PCR amplified 16S rDNA showed a prevailing pattern in most of the individuals analyzed, indicating that a few bacterial species were relatively abundant and common in oysters. Cloning and sequencing of the 16S rDNA with the prevailing RFLP pattern indicated that this rRNA was most closely related to Arcobacter spp. However, analysis by the size of the amplified 16S-23S rRNA intergenic regions revealed not Arcobacter spp. but Staphylococcus spp. related bacteria as a major and common component in oyster. These different results may be caused by the absence of target for one of the primers employed for amplification of the intergenic region. Neither of the two bacteria species found in large abundance was recovered after culturing under aerobic, anaerobic, or microaerophilic conditions. This result, however, is expected because the number of bacteria recovered after cultivation was less than 0.01% of the total. All together, these observations suggest that Arcobacter-related strains are probably abundant and common in the Chilean oyster bacterial microbiota.}, }
@article {pmid12399897, year = {2002}, author = {LaPara, TM and Zakharova, T and Nakatsu, CH and Konopka, A}, title = {Functional and structural adaptations of bacterial communities growing on particulate substrates under stringent nutrient limitation.}, journal = {Microbial ecology}, volume = {44}, number = {4}, pages = {317-326}, doi = {10.1007/s00248-002-1046-8}, pmid = {12399897}, issn = {0095-3628}, mesh = {*Bacteria ; Biomass ; *Bioreactors ; DNA, Bacterial ; Ecosystem ; *Phylogeny ; Polymerase Chain Reaction ; Population Dynamics ; RNA, Ribosomal, 16S/analysis ; *Soil Microbiology ; Yeasts ; }, abstract = {Biomass recycle reactors (BRRs) were used as a model system to study the functional and structural adaptations of mixed bacterial communities in response to the imposition of increasingly severe nutrient limitation. BRRs were fed synthetic media containing either spinach homogenate or autoclaved yeast cells to simulate the complex mixtures of particulate carbon sources that are often present in nature. In the BRRs fed spinach homogenate, the biomass (measured as particulate protein) exhibited a physiological response similar to previous studies as detected by 40-80% reductions in respiratory potential and by relatively stable catabolic ectoenzyme activities. Concomitant adaptations in bacterial community structure were detected by PCR-DGGE and RT-PCR-DGGE of 16S rDNA and 16S rRNA fragments, respectively. The microbial community structure was dynamic even after the biomass had reached a quasi-steady state with respect to physiological measurements. In the BRRs fed yeast cells, respiratory potentials increased 2- to 5-fold during the initial portion of the BRR run and alpha-glucosidase and beta-glucosidase activities increased 2- to 4-fold. Substantial bacterial community shifts were also detected in both the rDNA and rRNA profiles, indicating that this community was also structurally dynamic. These experiments suggest that phylogenetically different bacteria sustained the functional activities in these ecosystems in response to increasingly stringent nutrient limitation.}, }
@article {pmid12399896, year = {2002}, author = {Drakare, S}, title = {Competition between picoplanktonic cyanobacteria and heterotrophic bacteria along crossed gradients of glucose and phosphate.}, journal = {Microbial ecology}, volume = {44}, number = {4}, pages = {327-335}, doi = {10.1007/s00248-002-1013-4}, pmid = {12399896}, issn = {0095-3628}, mesh = {*Bacterial Physiological Phenomena ; Biomass ; *Cyanobacteria ; Glucose/metabolism ; Phosphates/metabolism ; *Phytoplankton ; Population Dynamics ; *Water Microbiology ; }, abstract = {A laboratory experiment was performed to test whether differences in nutrient and energy demands between picophytoplankton and heterotrophic bacteria can explain the apparent inverse biomass relationship between these organisms in lakes along gradients of organic carbon and nutrients. Growth rates and final yield of cells were analyzed in crossed gradients of glucose and phosphate. Concentrations of phosphate (10, 25, and 60 microg P L(-1)) and glucose (0, 0.3, and 3 mg C L(-1)) were used in all possible combinations giving 9 different treatments. Heterotrophic bacteria had higher maximum growth rates in all treatments and became larger than picophytoplankton in many treatments. The variance in abundance of heterotrophic bacteria between treatments could almost completely be explained by the combined effects of glucose and P. In treatments where carbon limitation slowed down the growth of heterotrophic bacteria, picophytoplankton became abundant and these organisms showed a positive response to P in combination with a negative response to glucose. The negative effect of glucose on picophytoplankton is suggested to be indirect and caused by competition with bacteria that are favored by organic C. The results suggest that competition for phosphate between phytoplankton and bacteria is not size-dependent, that heterotrophic bacteria are superior competitors for P, and that organic C produced by picophytoplankton was of minor importance for heterotrophic bacteria.}, }
@article {pmid12396461, year = {2002}, author = {Sanni, AI and Sefa-Dedeh, S and Sakyi-Dawson, E and Asiedu, M}, title = {Microbiological evaluation of ghanaian maize dough co-fermented with cowpea.}, journal = {International journal of food sciences and nutrition}, volume = {53}, number = {5}, pages = {367-373}, doi = {10.1080/0963748021000044705}, pmid = {12396461}, issn = {0963-7486}, mesh = {Colony Count, Microbial ; Developing Countries ; Fabaceae/*microbiology ; Fermentation ; Food Handling/*methods ; *Food Microbiology ; Food, Fortified/*microbiology ; Ghana ; Humans ; Zea mays/*microbiology ; }, abstract = {Fermented maize dough meals form a large proportion of people's diet in Ghana. To enhance the nutritive value of these carbohydrate-rich foods, protein complementation was introduced. In this study, microbial ecology of fermenting maize dough fortified with 20% cowpea was investigated. A total of 106 microbial strains were isolated from different batches of the fermenting dough at periodic intervals. Ten genera of microorganisms namely Lactobacillus, Leuconostoc, Saccharomyces, Debaryomyces, Candida, Bacillus, Micrococcus, Klebsiella, Escherichia and Aspergillus were identified, with lactic acid bacteria species being predominant. A lactic count of log 9.9 cfu/g was obtained at the end of 72 h fermentation relative to log 6.6 cfu/g recorded for aerobic mesophiles. At the 12 h fermentation period, the population of yeasts was less than log 1.0 cfu/g, but gradually rose to log 5.36 cfu/g by 48 h followed a slight decline at the end of 72 h fermentation period (log 4.08 cfu/g). Enteric microorganisms that were isolated from the raw cowpea were less than log 1.0 cfu/g at 12 h of fermentation, while the Aspergillus species were isolated from the raw maize and the dough subjected to drying treatment. The growth of inoculated enteropathogenic E. coli and S. typhimurium was inhibited in the cooked, fermented maize-cowpea dough, and at 72 h, they were not within detectable limit. The study concluded that addition of cowpea at 20% level did not affect the natural fermentation characteristics of the maize dough.}, }
@article {pmid12386516, year = {2002}, author = {Bengmark, S}, title = {Gut microbial ecology in critical illness: is there a role for prebiotics, probiotics, and synbiotics?.}, journal = {Current opinion in critical care}, volume = {8}, number = {2}, pages = {145-151}, doi = {10.1097/00075198-200204000-00010}, pmid = {12386516}, issn = {1070-5295}, mesh = {Critical Care/standards ; Critical Illness ; Diarrhea/therapy ; Diet ; Dietary Fiber/*therapeutic use ; Dietary Supplements ; Digestive System/*immunology/*microbiology ; Food ; Food Additives ; Humans ; Immune System/physiology ; Lactobacillus ; Life Style ; Pancreatitis/therapy ; Probiotics/*therapeutic use ; }, abstract = {Approximately 70% of the immune system is localized in the gastrointestinal tract: its glands, mucosa, and mucosa-associated lymphoid system. The system influences health conditions because it produces large amounts of important gastrointestinal secretions as rich as breast milk in health-supporting and disease-preventing factors, and because of its rich gastrointestinal flora. The intestine normally contains 10 times more microbes than there are eukaryotic cells in the entire body. The optimal function of these microbes depends on the supply of food destined for the colonic bacteria (fermentable fibers, complex proteins, gastrointestinal secretions). The consideration of these functions influences outcome. Unfortunately, the conditions (supply of drugs-especially antibiotics, and reduced supply of food-especially fruits and vegetables) in the modern ICU are extremely poor both for optimal gastrointestinal secretion and for flora and need more attention. To improve treatment, a supply of new and effective flora (probiotics) and food for the flora (prebiotics) is needed, from which numerous health-supporting products (synbiotics) will be produced and absorbed at the level of the mucosa, mainly in the lower gastrointestinal tract.}, }
@article {pmid12379032, year = {2002}, author = {Bilev, AE}, title = {[Interactions in the parasite-host system in chronic obstructive lung diseases].}, journal = {Voenno-meditsinskii zhurnal}, volume = {323}, number = {8}, pages = {50-4, 96}, pmid = {12379032}, issn = {0026-9050}, mesh = {Asthma/complications/epidemiology/*microbiology ; Bacteria/classification/immunology ; Bacterial Physiological Phenomena ; Bronchitis, Chronic/complications/epidemiology/*microbiology ; Chronic Disease ; Fungi/classification/physiology ; Humans ; Intestines/microbiology ; Lung/microbiology ; Male ; Microbiological Techniques ; Opportunistic Infections/complications/epidemiology/*microbiology ; Russia/epidemiology ; Serologic Tests ; }, abstract = {The interactions in "parasite-host" system were studied in 120 patients with chronic obstructive pulmonary diseases (COPD) living in Samara. The significant interrelation between the composition of intestinal and pneumotropic microflora was revealed. It is conditioned both by the mechanisms of cooperation between some types of bacteria and by their translocation from one organs to another. The data obtained demonstrate the complex influence of abnormal microbial ecology in lungs and intestine on formation of "parasite-host" system and the significance of its function in COPD pathogenesis. The results of investigation show the necessity to include the measures for correction of microbial ecology disorders into the general complex of COPD therapy.}, }
@article {pmid12376421, year = {2002}, author = {Yang, R and Gallo, DJ and Baust, JJ and Watkins, SK and Delude, RL and Fink, MP}, title = {Effect of hemorrhagic shock on gut barrier function and expression of stress-related genes in normal and gnotobiotic mice.}, journal = {American journal of physiology. Regulatory, integrative and comparative physiology}, volume = {283}, number = {5}, pages = {R1263-74}, doi = {10.1152/ajpregu.00278.2002}, pmid = {12376421}, issn = {0363-6119}, support = {GM-37631/GM/NIGMS NIH HHS/United States ; GM-53789/GM/NIGMS NIH HHS/United States ; GM-58484/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cyclooxygenase 2 ; Digestive System/immunology/pathology/*physiopathology ; Fluorescein ; Gastric Mucosa/physiology ; Gene Expression Regulation/*physiology ; Germ-Free Life/*physiology ; Gram-Negative Bacteria ; Immunohistochemistry ; Interleukin-6/biosynthesis ; Intestinal Absorption/physiology ; Intestinal Mucosa/physiology ; Isoenzymes/biosynthesis ; Liver/metabolism/pathology ; Male ; Mice ; NF-kappa B/biosynthesis/genetics ; Nitric Oxide Synthase/biosynthesis/genetics ; Nitric Oxide Synthase Type II ; Pilot Projects ; Prostaglandin-Endoperoxide Synthases/biosynthesis ; RNA, Messenger/biosynthesis/genetics ; Resuscitation ; Reverse Transcriptase Polymerase Chain Reaction ; Shock, Hemorrhagic/*genetics/pathology/*physiopathology ; Stress, Physiological/*genetics/*physiopathology ; }, abstract = {We sought to determine whether gut-derived microbial factors influence the hepatic or intestinal inflammatory response to hemorrhagic shock and resuscitation (HS/R). Conventional and gnotobiotic mice contaminated with a defined microbiota without gram-negative bacteria were subjected to either a sham procedure or HS/R. Tissue samples were obtained 4 h later for assessing ileal mucosal permeability to FITC dextran and hepatic and ileal mucosal steady-state IL-6, inducible nitric oxide synthase (iNOS), cyclooxygenase (COX)-2, and TNF mRNA levels. Whereas HS/R significantly increased ileal mucosal permeability in conventional mice, this effect was not apparent in gnotobiotic animals. HS/R markedly increased hepatic mRNA levels for several proinflammatory genes in both conventional and gnotobiotic mice. HS/R increased ileal mucosal IL-6 and COX-2 mRNA expression in conventional but not gnotobiotic mice. If gnotobiotic mice were contaminated with Escherichia coli C25, HS/R increased ileal mucosal permeability and upregulated expression of IL-6 and COX-2. These data support the view that the hepatic inflammatory response to HS/R is largely independent of the presence of potentially pathogenic gram-negative bacteria colonizing the gut, whereas the local mucosal response to HS/R is profoundly influenced by the microbial ecology within the lumen during and shortly after the period of hemorrhage.}, }
@article {pmid12375097, year = {2002}, author = {Dorigo, U and Bérard, A and Humbert, JF}, title = {Comparison of eukaryotic phytobenthic community composition in a polluted river by partial 18S rRNA gene cloning and sequencing.}, journal = {Microbial ecology}, volume = {44}, number = {4}, pages = {372-380}, doi = {10.1007/s00248-002-2024-x}, pmid = {12375097}, issn = {0095-3628}, mesh = {Chlorophyta/*genetics ; DNA Primers ; DNA, Plant/analysis ; Diatoms/*genetics ; Environmental Monitoring ; France ; *Phylogeny ; Polymerase Chain Reaction ; Population Dynamics ; RNA, Ribosomal, 16S/analysis/*genetics ; Water Pollutants/*adverse effects ; }, abstract = {We compared the species composition in phytobenthic communities at different sampling sites in a small French river presenting polluted and unpolluted areas. For each sampling point, the total DNA was extracted and used to construct an 18S rRNA gene clone library after PCR amplification of a ca 400 bp fragment. Phytobenthic community composition was estimated by random sequencing of several clones per library. Most of the sequences corresponded to the Bacillariophyceae and Chlorophyceae groups. By combining phylogenetic and correspondence analyses, we showed that our molecular approach is able to estimate and compare the species composition at different sampling sites in order to assess the environmental impact of xenobiotics on phytobenthic communities. Changes in species composition of these communities were found, but no evident decrease in the diversity. We discuss the significance of these changes with regard to the existing level of pollution and their impact on the functionality of the ecosystem. Our findings suggest that it is now possible to use faster molecular methods (DGGE, ARISA.) to test large numbers of samples in the context of ecotoxicological studies, and thus to assess the impact of pollution in an aquatic ecosystem.}, }
@article {pmid12375096, year = {2002}, author = {Inácio, J and Pereira, P and de Carvalho, M and Fonseca, A and Amaral-Collaço, MT and Spencer-Martins, I}, title = {Estimation and diversity of phylloplane mycobiota on selected plants in a Mediterranean-type ecosystem in Portugal.}, journal = {Microbial ecology}, volume = {44}, number = {4}, pages = {344-353}, doi = {10.1007/s00248-002-2022-z}, pmid = {12375096}, issn = {0095-3628}, mesh = {*Ecosystem ; Environmental Monitoring ; *Fungi ; Humidity ; Plant Leaves/microbiology ; Population Dynamics ; Portugal ; *Yeasts ; }, abstract = {Mediterranean ecosystems have not been consistently investigated as natural habitats for microbes in general, and fungi in particular. Here we present the results of a survey of epiphytic mycobiota (filamentous fungi and yeasts) on the phylloplane of selected plants in the Arrábida Natural Park, an ecosystem of Mediterranean characteristics in Portugal, using conventional culture-dependent isolation methods. Leaves from the species Acer monspessulanum and Quercus faginea (deciduous trees) and Cistus albidus, Pistacia lentiscus, and Osyris quadripartita (evergreen shrubs) were collected twice a year for two consecutive years, at two distinct locations of Serra da Arrábida: the more humid northern slope and the drier southern slope. A total of 1029 strains of filamentous fungi and 540 strains of yeasts were isolated, which represented at least 36 and 46 distinct species, respectively. Total counts were higher on the plants from the northern slope and there was a general increase from spring to autumn, notably on the deciduous trees for the yeasts. Plant species that had higher numbers of leaf colonists (A. monspessulanum, C. albidus, and Q. faginea) also yielded a wider range of species. Among the filamentous fungi there was a predominance of species of ascomycetous affinity, whereas basidiomycetous species dominated among yeast isolates. Some of the taxa recovered were common to other phylloplane studies (e.g., ubiquitous molds and yeasts such as Cladosporium spp. and Cryptococcus spp., respectively), but less common species were also found, some of which appeared to represent undescribed taxa. Interestingly, a few species seemed to be associated with a particular plant, notably in the case of the evergreen shrub C. albidus. However, for a considerable number of fungi and yeasts the same taxon was recovered throughout the year from more than one plant and at both sites, suggesting that such species might be genuine phylloplane inhabitants (or at least of aerial plant surfaces) even though they appeared not to display host specificity.}, }
@article {pmid12375095, year = {2002}, author = {Nunan, N and Wu, K and Young, IM and Crawford, JW and Ritz, K}, title = {In situ spatial patterns of soil bacterial populations, mapped at multiple scales, in an arable soil.}, journal = {Microbial ecology}, volume = {44}, number = {4}, pages = {296-305}, doi = {10.1007/s00248-002-2021-0}, pmid = {12375095}, issn = {0095-3628}, mesh = {Agriculture ; Bacteria ; Environmental Monitoring/*methods/statistics &amp; numerical data ; Population Dynamics ; *Soil Microbiology ; }, abstract = {Very little is known about the spatial organization of soil microbes across scales that are relevant both to microbial function and to field-based processes. The spatial distributions of microbes and microbially mediated activity have a high intrinsic variability. This can present problems when trying to quantify the effects of disturbance, management practices, or climate change on soil microbial systems and attendant function. A spatial sampling regime was implemented in an arable field. Cores of undisturbed soil were sampled from a 3 x 3 x 0.9 m volume of soil (topsoil and subsoil) and a biological thin section, in which the in situ distribution of bacteria could be quantified, prepared from each core. Geostatistical analysis was used to quantify the nature of spatial structure from micrometers to meters and spatial point pattern analysis to test for deviations from complete spatial randomness of mapped bacteria. Spatial structure in the topsoil was only found at the microscale (micrometers), whereas evidence for nested scales of spatial structure was found in the subsoil (at the microscale, and at the centimeter to meter scale). Geostatistical ranges of spatial structure at the micro scale were greater in the topsoil and tended to decrease with depth in the subsoil. Evidence for spatial aggregation in bacteria was stronger in the topsoil and also decreased with depth in the subsoil, though extremely high degrees of aggregation were found at very short distances in the deep subsoil. The data suggest that factors that regulate the distribution of bacteria in the subsoil operate at two scales, in contrast to one scale in the topsoil, and that bacterial patches are larger and more prevalent in the topsoil.}, }
@article {pmid12375094, year = {2002}, author = {Muela, A and García-Bringas, JM and Seco, C and Arana, I and Barcina, I}, title = {Participation of oxygen and role of exogenous and endogenous sensitizers in the photoinactivation of Escherichia coli by photosynthetically active radiation, UV-A and UV-B.}, journal = {Microbial ecology}, volume = {44}, number = {4}, pages = {354-364}, doi = {10.1007/s00248-002-1027-y}, pmid = {12375094}, issn = {0095-3628}, mesh = {Adsorption ; Cell Division ; Electron Transport ; Escherichia coli/pathogenicity/*physiology ; Organic Chemicals ; Oxygen/metabolism ; Photochemistry ; *Photosynthesis ; Ultraviolet Rays/*adverse effects ; }, abstract = {We studied the mechanisms by which photosynthetically active radiation (PAR) and ultraviolet (UV-A and UV-B) radiation damage Escherichia coli suspended in water. The roles played by oxygen and exogenous and endogenous sensitizers were analyzed by monitoring changes in the physiological state of irradiated cells. Impairment of the cellular functions was more severe in the case of UV radiations. Radiation caused cellular damage in the absence of oxygen. PAR, UV-A, and UV-B radiation induced photobiological and photodynamic reactions mediated by endogenous sensitizers, which significantly shortened the T90 (time needed to reduce a cellular parameter by 90%) based on the growth ability of the cells. In addition, when exogenous sensitizers were present, the photodynamic reactions also had a negative effect on the operation of the electron transport chains. The presence of oxygen might enhance photoinactivation, affecting both the growth ability and the electron transport chains. Endogenous sensitizers were responsible for the noxious action of oxygen. The presence of dissolved organic material played a protective role against the oxygen by absorbing the incident radiation, thereby reducing the energy that reached the endogenous sensitizers.}, }
@article {pmid12375093, year = {2002}, author = {Burns, JA and Zehr, JP and Capone, DG}, title = {Nitrogen-fixing phylotypes of Chesapeake Bay and Neuse River estuary sediments.}, journal = {Microbial ecology}, volume = {44}, number = {4}, pages = {336-343}, doi = {10.1007/s00248-002-1000-9}, pmid = {12375093}, issn = {0095-3628}, mesh = {Bacteria, Aerobic/*genetics/physiology ; DNA Primers ; DNA, Bacterial/*analysis ; Ecosystem ; Gene Amplification ; *Genes, Bacterial ; Geologic Sediments/*microbiology ; Maryland ; Nitrogen Fixation/*genetics ; *Phylogeny ; Plant Roots ; Poaceae ; Water Microbiology ; }, abstract = {Sediments often exhibit low rates of nitrogen fixation, despite the presence of elevated concentrations of inorganic nitrogen. The organisms that potentially fix nitrogen in sediments have not previously been identified. Amplification of nifH genes with degenerate primers was used to assess the diversity of diazotrophs in two distinct sediment systems, anoxic muds of Chesapeake Bay and shallow surficial sediments of the Neuse River. Phylogenetic analysis revealed that sequences obtained from mid-Chesapeake Bay, which receive high organic loading and are highly reducing, clustered closely with each other and with known anaerobic microorganisms, suggesting a low abundance of aerobic or facultative diazotrophs in these sediments. Sulfate reduction dominates in the surface, but methanogenesis becomes more important with depth. A thin (<1 cm) oxidized layer is present only in the spring. No archaeal nifH sequences were obtained from Chesapeake Bay. Sequences of nifH amplified from surficial sediments of the Neuse River were distant from Chesapeake Bay sequences and included nif phylotypes related to sequences previously reported from marine mats and the Spartina rhizosphere. Differences in environmental site characteristics appear to select for different types of sediment diazotrophs, which is reflected in the phylogenetic composition of amplified nifH sequences.}, }
@article {pmid12361382, year = {2002}, author = {Van Hege, K and Dewettinck, T and Claeys, T and De Smedt, G and Verstraete, W}, title = {Reclamation of treated domestic wastewater using biological membrane assisted carbon filtration (BioMAC).}, journal = {Environmental technology}, volume = {23}, number = {9}, pages = {971-980}, doi = {10.1080/09593332308618350}, pmid = {12361382}, issn = {0959-3330}, mesh = {*Bioreactors ; *Conservation of Natural Resources ; Escherichia coli/isolation &amp; purification ; Filtration ; Membranes, Artificial ; Nitrogen/analysis/isolation &amp; purification ; Odorants ; *Waste Disposal, Fluid ; Water Movements ; Water Purification/*methods ; }, abstract = {Membrane processes are increasingly used as an advanced treatment technique for the reclamation of treated domestic wastewater. Despite their inherent advantages, fouling remains an operational problem, while the removal of dissolved organic components such as volatile organic compounds is negligible. In the present work, the addition of a partially non-submerged biological granular activated carbon filtration to a microfiltration lab-scale reactor was investigated. It was observed that the reactor could be operated under stable flux conditions although regular hydraulic backwashing was necessary. Preferential attached growth of nitrifiers on the activated carbon particles allowed for a complete and very stable nitrification, with permeate total ammonium nitrogen and nitrite levels below 0.2 mg l(-1) regardless of influent concentrations. Chemical oxygen demand of the permeate averaged 5.26 mg O2 l(-1) which is below the Environmental Protection Agency guideline for wastewater reuse. Using an electronic nose, elimination of volatile compounds was assessed. The combined process resulted in complete odour removal, with the permeate odour levels equaling the reference samples (tap water), even during periods of increased reactor load (shock load experiment). A 4.2 log10 CFU and 3.7 log10 CFU removal were observed for total coliforms and E. coli, respectively.}, }
@article {pmid12354560, year = {2002}, author = {Tunlid, A and Talbot, NJ}, title = {Genomics of parasitic and symbiotic fungi.}, journal = {Current opinion in microbiology}, volume = {5}, number = {5}, pages = {513-519}, doi = {10.1016/s1369-5274(02)00355-7}, pmid = {12354560}, issn = {1369-5274}, mesh = {DNA, Fungal/analysis/chemistry ; Evolution, Molecular ; Fungi/*genetics/pathogenicity ; *Genome, Fungal ; Genomics/*methods ; Symbiosis/*genetics ; }, abstract = {Complete and partial genome sequence information is underway in several parasitic and symbiotic fungi that infect humans, other animals and plants. Comparative analyses of these sequences will provide new insights into the genomic plasticity and evolution of parasitism and mutualism in fungi.}, }
@article {pmid12324402, year = {2002}, author = {Jin, Q and Bethke, CM}, title = {Kinetics of electron transfer through the respiratory chain.}, journal = {Biophysical journal}, volume = {83}, number = {4}, pages = {1797-1808}, pmid = {12324402}, issn = {0006-3495}, mesh = {Animals ; Biophysical Phenomena ; Biophysics ; Dose-Response Relationship, Drug ; *Electron Transport ; *Electrons ; Kinetics ; Mitochondria/physiology ; Models, Chemical ; Models, Statistical ; Oxidation-Reduction ; Thermodynamics ; }, abstract = {We show that the rate at which electrons pass through the respiratory chain in mitochondria and respiring prokaryotic cells is described by the product of three terms, one describing electron donation, one acceptance, and a third, the thermodynamic drive. We apply the theory of nonequilibrium thermodynamics in the context of the chemiosmotic model of proton translocation and energy conservation. This approach leads to a closed-form expression that predicts steady-state electron flux as a function of chemical conditions and the proton motive force across the mitochondrial inner membrane or prokaryotic cytoplasmic membrane. The rate expression, derived considering reverse and forward electron flow, is the first to account for both thermodynamic and kinetic controls on the respiration rate. The expression can be simplified under specific conditions to give rate laws of various forms familiar in cellular physiology and microbial ecology. The expression explains the nonlinear dependence of flux on electrical potential gradient, its hyperbolic dependence on substrate concentration, and the inhibiting effects of reaction products. It provides a theoretical basis for investigating life under unusual conditions, such as microbial respiration in alkaline waters.}, }
@article {pmid12324335, year = {2002}, author = {Mills, DA and Johannsen, EA and Cocolin, L}, title = {Yeast diversity and persistence in botrytis-affected wine fermentations.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {10}, pages = {4884-4893}, pmid = {12324335}, issn = {0099-2240}, mesh = {Botrytis/*growth &amp; development ; Ecosystem ; Electrophoresis, Polyacrylamide Gel/methods ; Fermentation ; Fructose/metabolism ; Glucose/metabolism ; Polymerase Chain Reaction ; RNA, Ribosomal/analysis/genetics ; Wine/*microbiology ; Yeasts/*classification/genetics/growth &amp; development/isolation &amp; purification ; }, abstract = {Culture-dependent and -independent methods were used to examine the yeast diversity present in botrytis-affected ("botrytized") wine fermentations carried out at high (approximately 30 degrees C) and ambient (approximately 20 degrees C) temperatures. Fermentations at both temperatures possessed similar populations of Saccharomyces, Hanseniaspora, Pichia, Metschnikowia, Kluyveromyces, and Candida species. However, higher populations of non-Saccharomyces yeasts persisted in ambient-temperature fermentations, with Candida and, to a lesser extent, Kluyveromyces species remaining long after the fermentation was dominated by Saccharomyces. In general, denaturing gradient gel electrophoresis profiles of yeast ribosomal DNA or rRNA amplified from the fermentation samples correlated well with the plating data. The direct molecular methods also revealed a Hanseniaspora osmophila population not identified in the plating analysis. rRNA analysis also indicated a large population (>10(6) cells per ml) of a nonculturable Candida strain in the high-temperature fermentation. Monoculture analysis of the Candida isolate indicated an extreme fructophilic phenotype and correlated with an increased glucose/fructose ratio in fermentations containing higher populations of Candida. Analysis of wine fermentation microbial ecology by using both culture-dependent and -independent methods reveals the complexity of yeast interactions enriched during spontaneous fermentations.}, }
@article {pmid12324316, year = {2002}, author = {Bollmann, A and Bär-Gilissen, MJ and Laanbroek, HJ}, title = {Growth at low ammonium concentrations and starvation response as potential factors involved in niche differentiation among ammonia-oxidizing bacteria.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {10}, pages = {4751-4757}, pmid = {12324316}, issn = {0099-2240}, mesh = {Ammonia/*metabolism ; Biofilms/*growth &amp; development ; Fresh Water/*microbiology ; Geologic Sediments ; Nitrosomonas/genetics/metabolism/*physiology ; Oxidation-Reduction ; Polymerase Chain Reaction ; }, abstract = {In nature, ammonia-oxidizing bacteria have to compete with heterotrophic bacteria and plants for limiting amounts of ammonium. Previous laboratory experiments conducted with Nitrosomonas europaea suggested that ammonia-oxidizing bacteria are weak competitors for ammonium. To obtain a better insight into possible methods of niche differentiation among ammonia-oxidizing bacteria, we carried out a growth experiment at low ammonium concentrations with N. europaea and the ammonia oxidizer G5-7, a close relative of Nitrosomonas oligotropha belonging to Nitrosomonas cluster 6a, enriched from a freshwater sediment. Additionally, we compared the starvation behavior of the newly enriched ammonia oxidizer G5-7 to that of N. europaea. The growth experiment at low ammonium concentrations showed that strain G5-7 was able to outcompete N. europaea at growth-limiting substrate concentrations of about 10 micro M ammonium, suggesting better growth abilities of the ammonia oxidizer G5-7 at low ammonium concentrations. However, N. europaea displayed a more favorable starvation response. After 1 to 10 weeks of ammonium deprivation, N. europaea became almost immediately active after the addition of fresh ammonium and converted the added ammonium within 48 to 96 h. In contrast, the regeneration time of the ammonia oxidizer G5-7 increased with increasing starvation time. Taken together, these results provide insight into possible mechanisms of niche differentiation for the ammonia-oxidizing bacteria studied. The Nitrosomonas cluster 6a member, G5-7, is able to grow at ammonium concentrations at which the growth of N. europaea, belonging to Nitrosomonas cluster 7, has already ceased, providing an advantage in habitats with continuously low ammonium concentrations. On the other hand, the ability of N. europaea to become active again after longer periods of starvation for ammonium may allow better exploitation of irregular pulses of ammonium in the environment.}, }
@article {pmid12324312, year = {2002}, author = {Wenning, M and Seiler, H and Scherer, S}, title = {Fourier-transform infrared microspectroscopy, a novel and rapid tool for identification of yeasts.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {10}, pages = {4717-4721}, pmid = {12324312}, issn = {0099-2240}, mesh = {*Microbiological Techniques ; Phylogeny ; Saccharomyces cerevisiae/classification/isolation &amp; purification/metabolism ; Spectroscopy, Fourier Transform Infrared/economics/*methods ; Yeasts/*classification/*isolation &amp; purification/metabolism ; }, abstract = {Fourier-transform infrared (FT-IR) microspectroscopy was used in this study to identify yeasts. Cells were grown to microcolonies of 70 to 250 micro m in diameter and transferred from the agar plate by replica stamping to an IR-transparent ZnSe carrier. IR spectra of the replicas on the carrier were recorded using an IR microscope coupled to an IR spectrometer, and identification was performed by comparison to reference spectra. The method was tested by using small model libraries comprising reference spectra of 45 strains from 9 genera and 13 species, recorded with both FT-IR microspectroscopy and FT-IR macrospectroscopy. The results show that identification by FT-IR microspectroscopy is equivalent to that achieved by FT-IR macrospectroscopy but the time-consuming isolation of the organisms prior to identification is not necessary. Therefore, this method also provides a rapid tool to analyze mixed populations. Furthermore, identification of 21 Debaryomyces hansenii and 9 Saccharomyces cerevisiae strains resulted in 92% correct identification at the strain level for S. cerevisiae and 91% for D. hansenii, which demonstrates that the resolution power of FT-IR microspectroscopy may also be used for yeast typing at the strain level.}, }
@article {pmid12240988, year = {2002}, author = {Tsekova, K and Petrov, G}, title = {Removal of heavy metals from aqueous solution using Rhizopus delemar mycelia in free and polyurethane-bound form.}, journal = {Zeitschrift fur Naturforschung. C, Journal of biosciences}, volume = {57}, number = {7-8}, pages = {629-633}, doi = {10.1515/znc-2002-7-814}, pmid = {12240988}, issn = {0939-5075}, mesh = {Absorption ; Cells, Immobilized ; Cobalt/isolation &amp; purification ; Metals, Heavy/*isolation &amp; purification ; *Polyurethanes ; *Rhizopus ; Water Pollutants, Chemical/*isolation &amp; purification ; }, abstract = {This study assesses the ability of mycelia of Rhizopus delemar (both free and immobilized on polyurethane foam) to remove heavy metals from single-ion solutions as well as from a mixture of them. All experiments were conducted using 0.5-5 mm solutions of CuSO4 x 5H2O, CoCl2-6H2O and FeSO4 7H2O. Mycelia immobilized on polyurethane foam cells showed some times increase in uptake compared with that of free cells. Metal ions accumulation from a mixed solution was decreased slightly for cobalt and iron and considerable for copper ions. Heavy metal uptake was examined in the immobilized column experiments and more than 92% heavy metal removal (mg heavy metals removed/mg heavy metals added) from a mixed solution was achieved during the 5 cycles. During these experiments, the dry weight of the immobilized cells was decreased by only 2%. These results showed that immobilized mycelia of Rhizopus delemar can be used repeatedly for removal of heavy metals from aqueous solutions.}, }
@article {pmid12226662, year = {2002}, author = {Li, WK}, title = {Macroecological patterns of phytoplankton in the northwestern North Atlantic Ocean.}, journal = {Nature}, volume = {419}, number = {6903}, pages = {154-157}, doi = {10.1038/nature00994}, pmid = {12226662}, issn = {0028-0836}, mesh = {Animals ; Atlantic Ocean ; Biomass ; Cell Size ; Chlorophyll/analysis ; Chlorophyll A ; *Ecosystem ; Flow Cytometry ; Phytoplankton/classification/*cytology/*isolation &amp; purification/metabolism ; Water Movements ; }, abstract = {Many issues in biological oceanography are regional or global in scope; however, there are not many data sets of extensive areal coverage for marine plankton. In microbial ecology, a fruitful approach to large-scale questions is comparative analysis wherein statistical data patterns are sought from different ecosystems, frequently assembled from unrelated studies. A more recent approach termed macroecology characterizes phenomena emerging from large numbers of biological units by emphasizing the shapes and boundaries of statistical distributions, because these reflect the constraints on variation. Here, I use a set of flow cytometric measurements to provide macroecological perspectives on North Atlantic phytoplankton communities. Distinct trends of abundance in picophytoplankton and both small and large nanophytoplankton underlaid two patterns. First, total abundance of the three groups was related to assemblage mean-cell size according to the 3/4 power law of allometric scaling in biology. Second, cytometric diversity (an ataxonomic measure of assemblage entropy) was maximal at intermediate levels of water column stratification. Here, intermediate disturbance shapes diversity through an equitable distribution of cells in size classes, from which arises a high overall biomass. By subsuming local fluctuations, macroecology reveals meaningful patterns of phytoplankton at large scales.}, }
@article {pmid12222955, year = {2002}, author = {Röling, WF and van Verseveld, HW}, title = {Natural attenuation: what does the subsurface have in store?.}, journal = {Biodegradation}, volume = {13}, number = {1}, pages = {53-64}, doi = {10.1023/a:1016310519957}, pmid = {12222955}, issn = {0923-9820}, mesh = {Biological Specimen Banks ; Containment of Biohazards ; DNA/analysis ; Environmental Monitoring/methods ; Environmental Pollutants/*analysis ; Environmental Pollution/*analysis ; Hazardous Waste/analysis ; Humans ; RNA/analysis ; Reverse Transcriptase Polymerase Chain Reaction ; Soil Microbiology ; }, abstract = {Throughout the world, organic and inorganic substances leach into the subsurface as a result of human activities and accidents. There, the chemicals pose direct or indirect threats to the environment and to increasingly scarce drinking water resources. At many contaminated sites the subsurface is able to attenuate pollutants which, potentially, lowers the costs of remediation. Natural attenuation comprises a wide range of processes of which the microbiological component, which is responsible for intrinsic bioremediation, can decrease the mass and toxicity of the contaminants and is, therefore, the most important. Reliance on intrinsic bioremediation requires methods to monitor the process. The subject of this review is how knowledge of subsurface geology and hydrology, microbial ecology and degradation processes is used and can be used to monitor the potential and capacity for intrinsic bioremediation in the subsurface and to verify degradation in situ. As research on natural attenuation in the subsurface has been rather fragmented and limited and often allows only conclusions to be drawn of the site under investigation, we provide a concept based on Environmental Specimen Banking which will contribute to further understanding subsurface natural attenuation processes and will help to develop and implement new monitoring techniques.}, }
@article {pmid12219266, year = {2002}, author = {Tay, ST and Ivanov, V and Yi, S and Zhuang, WQ and Tay, JH}, title = {Presence of anaerobic bacteroides in aerobically grown microbial granules.}, journal = {Microbial ecology}, volume = {44}, number = {3}, pages = {278-285}, doi = {10.1007/s00248-002-2014-z}, pmid = {12219266}, issn = {0095-3628}, mesh = {Aerobiosis ; Bacteria, Anaerobic/genetics/*growth &amp; development ; Bacteroides/genetics/*growth &amp; development ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Flow Cytometry ; In Situ Hybridization, Fluorescence ; Microscopy, Confocal ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Microbial granules were grown in a column-type sequential aerobic sludge blanket reactor inoculated with activated sludge flocs taken from a wastewater treatment plant and containing a medium with glucose as the main carbon source. The reactor selected for granules that could settle rapidly by employing a short settling time of 2 min. Matured granules with diameters between 2 and 3 micro m were examined for anaerobic bacteria as their presence can signal the onset of diffusion limitation problems that can potentially diminish granule stability due to the bacterial production of fermentation gases and organic acids under anaerobic conditions. To detect the anaerobes in the granules, clones were constructed from 16S rRNA PCR amplicons. Two sequence types associated with a strict anaerobe Bacteroides spp. were identified from these clones. Fluorescence in situ hybridization (FISH) followed by confocal laser scanning microscopy (CLSM) demonstrated that cells of Bacteroides spp. were concentrated at a depth of approximately 800 micro m below the surface of the granule. Cell enumeration using flow cytometry showed that the percentage of labeled cells of Bacteroides spp. compared to total bacterial cells in the granules was 0.56%. This is the first study to use a suite of culture-independent techniques to report the presence of a defined species of anaerobic bacteria in aerobically grown microbial granules.}, }
@article {pmid12219265, year = {2002}, author = {van der Wielen, PW and Keuzenkamp, DA and Lipman, LJ and van Knapen, F and Biesterveld, S}, title = {Spatial and temporal variation of the intestinal bacterial community in commercially raised broiler chickens during growth.}, journal = {Microbial ecology}, volume = {44}, number = {3}, pages = {286-293}, doi = {10.1007/s00248-002-2015-y}, pmid = {12219265}, issn = {0095-3628}, mesh = {Animals ; Bacteria/genetics/*growth &amp; development ; Chickens/growth &amp; development/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Electrophoresis, Polyacrylamide Gel ; Genetic Variation ; Intestines/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; Time Factors ; }, abstract = {The objective of this study was to determine whether host, compartment, or environmental specific factors play an important role in the establishment of the intestinal microflora in broiler chickens during growth. This objective was addressed using a 16S rDNA approach. PCR-amplicons from the V6 to V8 regions of the 16S rDNA of intestinal samples were separated by denaturing gradient gel electrophoresis (DGGE). The number of bands in all intestinal compartments increased when broilers grew older, indicating that the dominant bacterial community becomes more complex when chickens age. Each chicken had a unique banding pattern for all locations in the intestinal tract, irrespective of the age of chickens. This suggests that host-related factors affect the establishment of the dominant bacterial community. Banding patterns of intestinal compartments within one chicken were different from each other for broilers older than 4 days, except for both ceca which were highly similar. In 4-day-old broilers, banding patterns from crop, duodenum, and ileum were very similar. We conclude that (unknown) host specific factors play an important role in the development of the intestinal bacterial community in each broiler chicken. Furthermore, compartment-specific factors play an important role in the bacterial development of each intestinal compartment within one chicken.}, }
@article {pmid12219264, year = {2002}, author = {Danovaro, R and Manini, E and Fabiano, M}, title = {Exoenzymatic activity and organic matter composition in sediments of the Northern Adriatic Sea: response to a river plume.}, journal = {Microbial ecology}, volume = {44}, number = {3}, pages = {235-251}, doi = {10.1007/s00248-002-1023-2}, pmid = {12219264}, issn = {0095-3628}, mesh = {Aminopeptidases/metabolism ; Carbohydrates/*analysis ; Chlorophyll/analysis ; Chlorophyll A ; Environmental Monitoring/methods ; Enzymes/*metabolism ; Fresh Water/analysis ; Geologic Sediments/*analysis ; Italy ; Lipids/analysis ; Oceans and Seas ; Proteins/analysis ; Seasons ; Seawater/analysis ; beta-Glucosidase/metabolism ; }, abstract = {Exoenzymatic activities (aminopeptidase and b-glucosidase) and organic matter composition were investigated in June 1996 and February 1997 in the sediment of two areas of the Adriatic Sea differently influenced by the Po river. Protein, carbohydrate, and lipid concentrations were comparable to those reported in most productive systems. Sediment chlorophyll a and biopolymeric carbon concentrations in June were twice as high as in February, but highest exoenzymatic activities and organic matter turnover rates were observed in February (with aminopeptidase activities 10 times higher than in June). The accumulation of organic matter and lower protein and carbohydrate turnover rates observed in June were the result of a different biochemical composition of organic matter in the two sampling periods. In June, organic matter was characterized by a more refractory composition. The consequent reduction of available organic substrate was associated with a decrease in the exoenzymatic substrate affinity. Lower organic matter turnover rates were also observed in deeper sediment layers. In February, the freshwater plume was almost completely confined to the northern area, whereas in June it was extended to the southern area. The results suggest that river inputs influence the biochemical composition and distribution of the sediment organic matter and exoenzymatic activities in coastal marine sediments.}, }
@article {pmid12216618, year = {2002}, author = {Lee, N and Jansen, Jl and Aspegren, H and Henze, M and Nielsen, PH and Wagner, M}, title = {Population dynamics in wastewater treatment plants with enhanced biological phosphorus removal operated with and without nitrogen removal.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {46}, number = {1-2}, pages = {163-170}, pmid = {12216618}, issn = {0273-1223}, mesh = {Autoradiography ; *Bioreactors ; Gram-Negative Bacteria ; In Situ Hybridization, Fluorescence ; Nitrogen/metabolism ; Phosphorus/*metabolism ; Population Dynamics ; *Waste Disposal, Fluid ; }, abstract = {The population dynamics of activated sludge in a pilot plant with two activated sludge systems, both designed for enhanced biological phosphorus removal (EBPR), but one of them with (BNP) and the other without (BP) nitrogen removal, was monitored during a period of 2.5 years. The influent water to the pilot plant was periodically manipulated by external addition of phosphorus (P), acetate and glucose, respectively. The population dynamics and the in situ physiology were monitored by quantitative fluorescence in situ hybridization (FISH) and microautoradiography. Significant P removal was observed in both systems throughout the whole period, with significant increases of the P removal when substrates were dosed. The activated sludge in both systems contained large amounts of dense clusters of gram-negative, methylene-blue staining coccoid rods during the whole period. A large part of the clusters belonged to the beta Proteobacteria, whereas the rest of the clusters belonged either to the Actinobacteria or to the alpha Proteobacteria. The relative abundance of Rhodocyclus-related bacteria in the activated sludge varied significantly in both systems during the whole period (from 6 to 18% in BNP, and from 4 to 28% in BP). However, no statistically significant correlation of the Rhodocyclus-related nor any of the other investigated bacterial groups to the P content of the activated sludge (correlation for all groups investigated was always < 0.5) was observed. A significant 33Pi uptake was observed by the beta Proteobacteria (part of them Rhodocyclus-related, the identity of the rest unknown) and the Actinobacteria. However, not all of the Rhodocyclus-related bacteria showed 33Pi uptake. The P removal in the investigated plants is thus believed to be mediated by a mixed population consisting of a part of the Rhodocyclus-related bacteria, the Actinobacteria and other, yet unidentified bacteria.}, }
@article {pmid12214659, year = {2002}, author = {Dybas, MJ and Hyndman, DW and Heine, R and Tiedje, J and Linning, K and Wiggert, D and Voice, T and Zhao, X and Dybas, L and Criddle, CS}, title = {Development, operation, and long-term performance of a full-scale biocurtain utilizing bioaugmentation.}, journal = {Environmental science &amp; technology}, volume = {36}, number = {16}, pages = {3635-3644}, doi = {10.1021/es0114557}, pmid = {12214659}, issn = {0013-936X}, support = {ES04911/ES/NIEHS NIH HHS/United States ; }, mesh = {Biodegradation, Environmental ; Carbon Tetrachloride/analysis/*metabolism ; Engineering ; Nitrates/analysis/*metabolism ; Pseudomonas/*physiology ; Soil Pollutants/*metabolism ; Water Pollution/*prevention &amp; control ; }, abstract = {A full-scale field evaluation of bioaugmentation was conducted in a carbon tetrachloride (CT)- and nitrate-impacted aquifer at Schoolcraft, MI. The added organism was Pseudomonas stutzeri KC (strain KC), a denitrifying bacterium that cometabolically degrades CT without producing chloroform (CF). To introduce and maintain strain KC in the aquifer, a row of closely spaced (1-m) injection/extraction wells were installed normal to the direction of groundwater flow near the leading edge of the CT plume. The resulting system of wells was used to establish and maintain a "biocurtain" for CT degradation through the intermittent addition of base to create favorable pH conditions; inoculation; and weekly addition of acetate (electron donor), alkali, and phosphorus. Although half of the test zone was inoculated twice, the long-term performance of both sections was indistinguishable: both had high CT removal efficiencies (median of 98-99.9%) and similar levels of strain KC colonization (>10(5) strain KC/g). Sustained and efficient (98%) removal of CT has now been observed over 4 yr. Transient low levels of CF (<20 ppb) and H2S (<2 ppm) were observed, but both disappeared when the concentration of acetate in the weekly feed was reduced. Nitrate removal efficiencies ranged from 60% at low acetate concentrations to nearly 100% at high acetate concentrations. We conclude that closely spaced wells and intermittent substrate addition are effective means of delivering organisms and substrates to subsurface environments. At the Schoolcraft site, we achieved uniform removal efficiencies over a significant vertical depth (15 m), despite significant variability in hydraulic conductivity. This was accomplished by pumping 65% (v/v) of the natural gradient flow passing through the biocurtain during a given week in a single 6-h pumping event. Approximately 18,600 m3 of contaminated groundwater was treated during the project.}, }
@article {pmid12209255, year = {2002}, author = {Brodie, E and Edwards, S and Clipson, N}, title = {Bacterial community dynamics across a floristic gradient in a temperate upland grassland ecosystem.}, journal = {Microbial ecology}, volume = {44}, number = {3}, pages = {260-270}, doi = {10.1007/s00248-002-2012-1}, pmid = {12209255}, issn = {0095-3628}, mesh = {Bacteria/genetics/*growth &amp; development ; *Biomass ; Calcium/analysis ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; *Ecosystem ; Hydrogen-Ion Concentration ; Nitrates/analysis ; Phosphorus/analysis ; *Plant Development ; Polymorphism, Restriction Fragment Length ; Potassium/analysis ; Quaternary Ammonium Compounds/metabolism ; RNA, Ribosomal, 16S/*genetics ; Soil/analysis ; Soil Microbiology ; }, abstract = {Alterations in soil bacterial communities across a transect between a semi natural upland grassland and an agriculturally improved enclosure were assessed using culture-based methods and a nucleic-acid-based method, terminal restriction fragment length polymorphism (TRFLP). While plant diversity decreased across the transect towards the improved area, numbers of 16S rDNA terminal restriction fragments increased, indicating an increase in numbers of bacterial ribotypes. Bacterial numbers, microbial activity, and potential functional diversity also followed a similar trend, increasing with decreasing plant diversity. Alterations in bacterial community structure were coincident with changes in soil physicochemical properties which also changed across the transect. Increases in soil pH, nitrate, phosphorus, potassium, and calcium occurred toward the improved grassland, while organic matter and ammonium declined. The inverse relationship between floristic diversity and bacterial ribotype numbers suggests that soil physicochemical factors may be as influential in determining bacterial diversity in soils of upland grassland communities as floristic diversity.}, }
@article {pmid12209254, year = {2002}, author = {Morán, XA and Estrada, M and Gasol, JM and Pedrós-Alió, C}, title = {Dissolved primary production and the strength of phytoplankton- bacterioplankton coupling in contrasting marine regions.}, journal = {Microbial ecology}, volume = {44}, number = {3}, pages = {217-223}, doi = {10.1007/s00248-002-1026-z}, pmid = {12209254}, issn = {0095-3628}, mesh = {Algorithms ; Antarctic Regions ; Atlantic Ocean ; Bacteria/*growth &amp; development/metabolism ; Carbon Dioxide/metabolism ; Eukaryota/growth &amp; development/metabolism ; Mediterranean Sea ; Phytoplankton/*growth &amp; development/metabolism ; Seawater/*analysis ; }, abstract = {We analyzed the strength of phytoplankton-bacterioplankton coupling by comparing the rate of particulate (PPP) and dissolved primary production (DPP) with bacterial carbon demand (BCD) in four contrasting marine regions: offshore and coastal waters of the Southern Ocean, a coastal area of the NE Atlantic, and a coastal-offshore transect in the NW Mediterranean. We measured bacterial heterotrophic production (BHP) and estimated BCD from a literature model. Average phytoplanktonic percent extracellular release [PER = DPP/(DPP + PPP)] was 18-20% in the Antarctic (offshore and coastal, respectively), 16% in the NW Mediterranean, and 7% in the NE Atlantic. A significant inverse relationship was found between PER and total system productivity with pooled data. On average BHP amounted to <5% of total primary production in all regions. However, the strength of phytoplankton-bacterioplankton coupling, estimated as the potential importance of DPP in meeting BCD, differed greatly in the four regions. DPP was highly correlated to BCD in offshore Antarctic waters and was sufficient to meet BCD. In contrast, BCD exceeded DPP and bore no significant relationship in the remaining regions. The data suggest that a strong dependence of bacteria on algal extracellular production is only expected in open-ocean environments isolated from coastal inputs of DOC.}, }
@article {pmid12209253, year = {2002}, author = {Trusova, MY and Gladyshev, MI}, title = {Phylogenetic diversity of winter bacterioplankton of eutrophic siberian reservoirs as revealed by 16S rRNA gene sequence.}, journal = {Microbial ecology}, volume = {44}, number = {3}, pages = {252-259}, doi = {10.1007/s00248-002-2020-1}, pmid = {12209253}, issn = {0095-3628}, mesh = {Animals ; Bacteria/*genetics ; DNA, Bacterial/chemistry/genetics ; Fresh Water/microbiology ; Genetic Variation ; Molecular Sequence Data ; *Phylogeny ; Plankton/*genetics ; RNA, Ribosomal, 16S/*genetics ; Seasons ; Sequence Analysis, DNA ; Siberia ; }, abstract = {Using 16S rRNA gene sequence analyses we investigated the bacterial diversity of winter bacterioplankton of two eutrophic Siberian reservoirs. These reservoirs show similarity in phytoplankton community composition in spring and autumn but tend to differ in summer in exhibiting cyanobacterial bloom. Forty-eight unique partial 16S RNA gene sequences retrieved from two libraries were mostly affiliated with the class Actinobacteria, b subdivision of the class Proteobacteria, and the phylum Cytophaga-Flavobacterium-Bacteroides. The clone library of the pond exhibiting summer cyanobacterial bloom showed more diversity in sequence composition. A significant number of bacterial 16S rRNA gene clones were closely related to freshwater bacteria previously found in different aquatic ecosystems. This finding confirms the assumption that some bacterial clades are globally distributed.}, }
@article {pmid12209252, year = {2002}, author = {Saleena, LM and Rangarajan, S and Nair, S}, title = {Diversity of azospirillum strains isolated from rice plants grown in saline and nonsaline sites of coastal agricultural ecosystem.}, journal = {Microbial ecology}, volume = {44}, number = {3}, pages = {271-277}, doi = {10.1007/s00248-002-2019-7}, pmid = {12209252}, issn = {0095-3628}, mesh = {Agriculture ; Azospirillum/genetics/*growth &amp; development/isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; Fresh Water/*microbiology ; Genetic Variation ; Genotype ; India ; Oryza/*microbiology ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/*genetics ; Seawater/*microbiology ; Species Specificity ; }, abstract = {The diversity of indigenous Azospirillum spp. associated with rice cultivated along the coastline of Tamil Nadu was analyzed. Twelve sites with varying soil characteristics such as salinity, texture, and the host variety were chosen. Of the 402 strains isolated using NFB media, 302 were confirmed to be Azospirillum spp. and subjected to DNA polymorphism analysis using PCR-RFLP of 16S rDNA. They were also screened for their salt tolerance and microaerobic N2-fixing-dependent growth. On species identification, all the strains were found to be A. brasilense, A. lipoferum, or unidentified. On comparing the influence of the previously noted variability on the indigenous population, soil salinity was found to play a dominant role. This was revealed by PCR-RFLP studies and salt tolerance studies. A high association between soil salinity and the distribution of Azospirillum genotypes reveals that soil salinity should be taken into consideration while developing biofertilizers specifically for the coastal agricultural ecosystem.}, }
@article {pmid12209251, year = {2002}, author = {Misic, C and Povero, P and Fabiano, M}, title = {Ectoenzymatic ratios in relation to particulate organic matter distribution (Ross Sea, Antarctica).}, journal = {Microbial ecology}, volume = {44}, number = {3}, pages = {224-234}, doi = {10.1007/s00248-002-2017-9}, pmid = {12209251}, issn = {0095-3628}, mesh = {Antarctic Regions ; *Carbohydrate Metabolism ; Enzymes/*metabolism ; Hexosaminidases/metabolism ; Leucyl Aminopeptidase/metabolism ; Particle Size ; Proteins/metabolism ; Seawater/*analysis ; beta-Glucosidase/metabolism ; }, abstract = {The results of a study on ectoenzymatic activity (the enzyme activity bound to particles larger than 0.2 micro m) and its relation to organic particle concentration are reported here. The sampling was carried out during the 1994 Antarctic spring, at a fixed station (Station 11) in the polynya of the Ross Sea, an area characterized by quick changes in sea ice cover. The sampling was repeated 4 times over a 20-day time period. The particulate organic matter distribution followed the physical structure of the water column, which depends on ice dynamics and is mainly determined by salinity. In the mixed-water surface layer (0-50 m) the concentrations were higher (on average 65.6 micro gC/L) than in the deeper water layer (50 m-bottom) (on average 19.1 micro gC/L). This distribution and quality, expressed by the protein:carbohydrate ratio, linked the particulate organic matter to the phytoplanktonic bloom which was in progress in the area. We determined the kinetic parameters of the glycolytic and proteolytic ectoenzymes and also the total activity for the proteolytic enzyme, in order to evaluate the contribution of the particle-bound activity. We observed higher values in the surface layer than in the deeper layer. b-Glucosidase activity ranged between 0.03 and 0.92 nmol L(-1) h(-1); b-N-acetylglucosaminidase activity was in the range of 0.04-0.58 nmol (L-1) (h-1). The total proteolytic activity (leucine aminopeptidase) ranged between 0.85 and 33.71 nmol L(-1) (h-1). The ectoproteolytic activity was about 35-60% of the total. The Km values were slightly higher for the proteolytic activity (on average 0.43 micro M for ectoproteolytic activity and 0.58 micro M for total proteolytic activity) than for the b-glucosidase (on average 0.36 micro M) and b-N-acetylglucosaminidase (on average 0.17 micro M), showing no remarkable variations in the water column. The ectoenzymatic ratios and their relationship with particulate organic substrates confirm the close link between organic substrate availability and degradation system response. The significant and positive correlations are not specific and suggest a prompt and efficient systemic response to the input of trophic resources. Nevertheless, changes in ectoenzyme activity and synthesis may act as adaptive responses to changing features of the ecosystem. In particular, variations in the proteolysis:glycolysis ratio depend on the functional features of the ecological system. In our study area this ratio is higher (about 10 or more) during production (particularly autotrophic) and lower (about 5 or less) during degradation/consumption events. The analysis of previous data, collected over a larger area characterized by different environmental conditions due to the changes of the pack ice cover, during the same cruise, confirms the existence of a significant relationship. Furthermore, the analysis of enzyme-uptake systems, expressed as Vmax:Km ratio, suggests that glycolytic ectoenzymes, although poorly expressed, may encourage microconsumers to grow rapidly on a wide range of organic substrates, including the refractory ones such as cellulose and chitin. However, low ectoenzyme potential exploitation rates of available organic substrates (on average about 5% for glycolytic and 12% for proteolytic ectoenzymes) would suggest that, during spring, zooplankton grazing or vertical and lateral transport are likely to play an important role in the removal of organic materials from the system.}, }
@article {pmid12197947, year = {2002}, author = {Watanabe, K and Kodama, Y and Kaku, N}, title = {Diversity and abundance of bacteria in an underground oil-storage cavity.}, journal = {BMC microbiology}, volume = {2}, number = {}, pages = {23}, pmid = {12197947}, issn = {1471-2180}, mesh = {Bacteria/*classification/genetics ; DNA, Bacterial/*analysis ; Ecology ; Genetic Variation ; In Situ Hybridization, Fluorescence ; Industrial Oils/microbiology ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*analysis/genetics ; Water Microbiology ; }, abstract = {BACKGROUND: Microorganisms inhabiting subterranean oil fields have recently attracted much attention. Since intact groundwater can easily be obtained from the bottom of underground oil-storage cavities without contamination by surface water, studies on such oil-storage cavities are expected to provide valuable information to understand microbial ecology of subterranean oil fields.<br><br>RESULTS: DNA was extracted from the groundwater obtained from an oil-storage cavity situated at Kuji in Iwate, Japan, and 16S rRNA gene (16S rDNA) fragments were amplified by PCR using combinations of universal and Bacteria-specific primers. The sequence analysis of 154 clones produced 31 different bacterial sequence types (a unique clone or group of clones with sequence similarity of > 98). Major sequence types were related to Desulfotomaculum, Acetobacterium, Desulfovibrio, Desulfobacula, Zoogloea and Thiomicrospira denitrificans. The abundance in the groundwater of bacterial populations represented by these major sequence types was assessed by quantitative competitive PCR using specific primers, showing that five rDNA types except for that related to Desulfobacula shared significant proportions (more than 1%) of the total bacterial rDNA.<br><br>CONCLUSIONS: Bacteria inhabiting the oil-storage cavity were unexpectedly diverse. A phylogenetic affiliation of cloned 16S rDNA sequences suggests that bacteria exhibiting different types of energy metabolism coexist in the cavity.}, }
@article {pmid12188575, year = {2002}, author = {De Wildeman, S and Nollet, H and Van Langenhove, H and Diekert, G and Verstraete, W}, title = {Reductive biodegradation of 1,2-dichloroethane by methanogenic granular sludge: perspectives for in situ remediation.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {45}, number = {10}, pages = {43-48}, pmid = {12188575}, issn = {0273-1223}, mesh = {Acetobacteraceae/*physiology ; Biodegradation, Environmental ; *Bioreactors ; Ethylene Dichlorides/*metabolism ; RNA, Ribosomal, 16S/analysis ; Water Pollutants/*metabolism ; Water Supply ; }, abstract = {Granular methanogenic sludge was able to dechlorinate 1,2-dichloroethane (1,2-DCA) to ethene in UASB reactors. Ethanol served as the sole carbon and energy source. The average dechlorination rate measured on the basis of ethene production varied between 1.7 and 2.1 micromol 1,2-DCA/(h.gVSS) (46.7 and 57.4 mg/L.d). In order to elucidate the microbial origin of this bioconversion, enrichment cultures of the methanogenic sludge were prepared with different carbon and electron sources: pyruvate, lactate, H2/CO2, ethanol and formate. Dithiothreitol (DTT) was the strong reductant in order to increase the negative redox potential in the media. A homo-acetogenic gram-positive strain could be isolated in the presence of formate. 16S rRNA of the isolated strain showed that the bacterium was closely related (99.7%) to Acetobacterium wieringae. The strain also grew on pyruvate, lactate, H2/CO2 and ethanol, although dechlorination rates of 1,2-DCA were at least 5 times higher when formate was the (only) electron source. Average conversion rates reached 3 micromol/(h.g(dry cells)) and appeared t relate to cometabolic biocatalysis on the corrinoid centers of the homo-acetogenic strain. Some perspectives of anaerobic in situ bioremediation of groundwater polluted with chloroethanes are presented.}, }
@article {pmid12188571, year = {2002}, author = {Pynaert, K and Wyffels, S and Sprengers, R and Boeckx, P and Van Cleemput, O and Verstraete, W}, title = {Oxygen-limited nitrogen removal in a lab-scale rotating biological contactor treating an ammonium-rich wastewater.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {45}, number = {10}, pages = {357-363}, pmid = {12188571}, issn = {0273-1223}, mesh = {Bacteria, Anaerobic/*physiology ; Biofilms ; *Bioreactors ; Carbon/metabolism ; Nitrites/chemistry ; Nitrogen/*metabolism ; Quaternary Ammonium Compounds/*chemistry ; Waste Disposal, Fluid/*methods ; }, abstract = {A lab-scale Rotating Biological Contactor (RBC) was operated with the purpose of oxygen-limited (autotrophic) nitrification-denitrification of an ammonium-rich synthetic wastewater without Chemical Oxygen Demand (COD). Based on the field observations that RBCs receiving anaerobic effluents come to anoxic ammonium removal, the RBC was inoculated with methanogenic sludge. Some 100 days after the addition of the anaerobic sludge to the reactor as a possible means of a rapid initiation of the nitrogen (N) removal process, a maximum ammonium removal of 1,550 mg N m(-2) d(-1) was achieved. Batch tests with 15N labeled ammonium and nitrite indicated that a large part of that N was removed via oxygen-limited oxidation of ammonium with nitrite as the electron acceptor. The other part was removed via conventional denitrification, presumably with COD released from lysis of cells. Species identification of the most abundant microorganisms revealed that Nitrosomonas spp. were the dominant ammonium-oxidizers in the sludge. Thus far, the molecular characterization of the sludge could not show the presence of Planctomycetes among the most dominant species. Overall this experiment confirms the property of the RBC system to remove ammonium to nitrogen gas without the use of heterotrophic carbon source.}, }
@article {pmid12187377, year = {2002}, author = {Mullan, A and Quinn, JP and McGrath, JW}, title = {Enhanced phosphate uptake and polyphosphate accumulation in Burkholderia cepacia grown under low pH conditions.}, journal = {Microbial ecology}, volume = {44}, number = {1}, pages = {69-77}, pmid = {12187377}, issn = {0095-3628}, mesh = {Burkholderia cepacia/enzymology/growth &amp; development/*metabolism/ultrastructure ; Culture Media ; Environment ; Hydrogen-Ion Concentration ; Organophosphates/*metabolism ; Phosphotransferases (Phosphate Group Acceptor)/metabolism ; Polyphosphates/*metabolism ; Sewage/microbiology ; Time Factors ; }, abstract = {Of bacterial cells in a sample of activated sludge, 34% contained detectable intracellular polyphosphate inclusions following Neisser staining, when grown on glucose/mineral salts medium at pH 5.5; at pH 7.5 only 7% of cells visibly accumulated polyphosphate. In a sludge isolate of Burkholderia cepacia chosen for further study, maximal removal of phosphate and accumulation of polyphosphate occurred at pH 5.5; levels were up to 220% and 330% higher, respectively, than in cells grown at pH 7.5. During the early stationary phase of growth at pH 5.5 a maximum level of intracellular polyphosphate that comprised 13.6% of cellular dry weight was reached. Polyphosphate kinase activity was detected in actively growing cells only when cultured at pH 5.5. The phenomenon of acid-stimulated phosphate uptake and polyphosphate accumulation in this environmental bacterial population parallels observations previously made by us in the yeast Candida humicola and may thus represent a widespread microbial response to low external pH values.}, }
@article {pmid12187376, year = {2002}, author = {Pascual, JA and Garcia, C and Hernandez, T and Lerma, S and Lynch, JM}, title = {Effectiveness of municipal waste compost and its humic fraction in suppressing Pythium ultimum.}, journal = {Microbial ecology}, volume = {44}, number = {1}, pages = {59-68}, pmid = {12187376}, issn = {0095-3628}, mesh = {Agriculture/methods ; Alanine/*analogs &amp; derivatives/pharmacology ; Germination/drug effects ; Humic Substances/analysis/*pharmacology ; Pisum sativum/microbiology/*parasitology ; Pest Control/*methods ; Pesticides/pharmacology ; Plant Diseases/microbiology/parasitology ; Plant Roots/microbiology/parasitology ; Plant Structures/microbiology/parasitology ; Pythium/*drug effects/*growth &amp; development ; *Refuse Disposal ; Seeds/drug effects/growth &amp; development ; Soil Microbiology ; Sterilization ; Time Factors ; }, abstract = {The effect of addition of a municipal solid waste (MSW) compost and its water-soluble and humic fraction to suppress the effect of Pythium ultimum on pea plants was studied and compared with that of a chemical pesticide (metalaxyl). The biotic and abiotic characteristics of compost involved in the biocontrol effects of these materials were also evaluated. The addition into soil of whole composts and their humic fractions reduced the effect of the pathogen on pea plants, significantly reducing the number of root lesions and Pythium populations and avoiding reductions of plant growth. The greatest pathogen suppression was achieved with the chemical pesticide. However, it also caused a significant decrease in the number of nontarget bacteria and fungi and on beneficial soil microorganisms such as Trichoderma and Pseudomonas. Addition of organic amendments increased population size of nontarget and specific biocontrol microorganisms. The humic fraction showed similar results to compost. All this suggests that metalaxyl has a nonspecific effect, producing adverse effects on aspects of soil quality. This was avoided if the chemical pesticide was reduced and replaced by organic amendments such as an MSW compost or its humic fraction.}, }
@article {pmid12181912, year = {2002}, author = {Cao, Y}, title = {[Application of continuous-flow culture in microecological research].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {13}, number = {5}, pages = {629-631}, pmid = {12181912}, issn = {1001-9332}, mesh = {Animals ; Bacteria/*growth &amp; development ; Culture Media ; *Ecology ; Humans ; }, abstract = {The application of continuous-flow culture in microbial ecology and its advances were reviewed. Continuous-flow culture can be used to build in vitro models simulating ecosystems composed of normal bacteria such as human or animals intestinal and buccal bacteria, to examine the interactions between normal bacteria and pathogens, to investigate the physiological and biochemical traits of bacteria and their metabolic products, and to develop microecological preparations.}, }
@article {pmid12180103, year = {2002}, author = {Gram, L and Dalgaard, P}, title = {Fish spoilage bacteria--problems and solutions.}, journal = {Current opinion in biotechnology}, volume = {13}, number = {3}, pages = {262-266}, doi = {10.1016/s0958-1669(02)00309-9}, pmid = {12180103}, issn = {0958-1669}, mesh = {Animals ; Bacteria/*classification/*metabolism ; Bacterial Physiological Phenomena ; Ecosystem ; Fishes/*microbiology ; *Food Microbiology ; Food Preservation/*methods ; Models, Biological ; Seafood/*microbiology ; }, abstract = {Microorganisms are the major cause of spoilage of most seafood products. However, only a few members of the microbial community, the specific spoilage organisms (SSOs), give rise to the offensive off-flavours associated with seafood spoilage. Combining microbial ecology, molecular techniques, analytical chemistry, sensory analysis and mathematical modelling allows us to characterise the SSOs and to develop methods to determine, predict and extend the shelf life of products.}, }
@article {pmid12180099, year = {2002}, author = {Lindow, SE and Leveau, JH}, title = {Phyllosphere microbiology.}, journal = {Current opinion in biotechnology}, volume = {13}, number = {3}, pages = {238-243}, doi = {10.1016/s0958-1669(02)00313-0}, pmid = {12180099}, issn = {0958-1669}, mesh = {Bacteria/*genetics/*pathogenicity ; *Bacterial Physiological Phenomena ; *Ecosystem ; *Environmental Microbiology ; Genetic Variation ; Plant Components, Aerial/*microbiology ; Plant Leaves/microbiology ; }, abstract = {Aerial plant surfaces harbor large numbers of microbes, some of which are deleterious to plants whereas others are benign or beneficial. Commercial formulations of bacteria antagonistic to plant pathogenic microbes and ice nucleation active bacteria have been utilized as an environmentally safe method to manage plant disease and to prevent frost damage. Molecular genetic tools, microscopic examination and whole-cell bacterial biosensors have provided extensive information on these microbes, their complex associations and their habitat. The aerial habitat influenced by plants, termed the phyllosphere, is particularly amenable to studies of microbial ecology and the information gained should lead to more effective means of plant protection.}, }
@article {pmid12180096, year = {2002}, author = {Wagner, M and Loy, A}, title = {Bacterial community composition and function in sewage treatment systems.}, journal = {Current opinion in biotechnology}, volume = {13}, number = {3}, pages = {218-227}, doi = {10.1016/s0958-1669(02)00315-4}, pmid = {12180096}, issn = {0958-1669}, mesh = {Bacteria/*classification/*genetics/metabolism ; Bioreactors ; Ecosystem ; *Gene Expression Regulation, Bacterial ; *Genetic Variation ; Nitrogen/metabolism ; Phosphorus/metabolism ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; *Waste Disposal, Fluid ; }, abstract = {The application of modern molecular techniques has led to the identification, in situ quantification, and partial ecophysiological characterisation of bacteria responsible for bulking and foaming or for nutrient removal in sewage treatment systems. Unexpectedly, previously unrecognised, yet uncultured bacteria were demonstrated to catalyse nitrogen and phosphorous removal in activated-sludge and biofilm reactors. These findings provide the basis for the development of novel concepts for improving the efficiency and functional stability of waste water treatment systems.}, }
@article {pmid12180095, year = {2002}, author = {Dahllöf, I}, title = {Molecular community analysis of microbial diversity.}, journal = {Current opinion in biotechnology}, volume = {13}, number = {3}, pages = {213-217}, doi = {10.1016/s0958-1669(02)00314-2}, pmid = {12180095}, issn = {0958-1669}, mesh = {*Ecosystem ; *Environmental Microbiology ; *Genetic Variation ; Microbiological Techniques/*methods ; Molecular Biology/methods ; *Oligonucleotide Array Sequence Analysis ; *Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {New technologies that avoid the need for either gene amplification (e.g. microarrays) or nucleic acid extraction (e.g. in situ PCR) have recently been implemented in microbial ecology. Together with new approaches for culturing microorganisms and an increased understanding of the biases of molecular methods, these techniques form the most exciting advances in this field during the past year.}, }
@article {pmid12174041, year = {2002}, author = {Coskuner, G and Curtis, TP}, title = {In situ characterization of nitrifiers in an activated sludge plant: detection of Nitrobacter Spp.}, journal = {Journal of applied microbiology}, volume = {93}, number = {3}, pages = {431-437}, doi = {10.1046/j.1365-2672.2002.01715.x}, pmid = {12174041}, issn = {1364-5072}, mesh = {Ammonia/metabolism ; Betaproteobacteria/classification/genetics/isolation &amp; purification/metabolism ; Ecosystem ; *In Situ Hybridization, Fluorescence ; Microscopy, Confocal ; Nitrites/*metabolism ; Nitrobacter/*classification/*genetics/isolation &amp; purification/metabolism ; Nitrogen/metabolism ; Oligonucleotide Probes ; Oxidation-Reduction ; Sewage/*microbiology ; Species Specificity ; }, abstract = {AIMS: The purpose of this work was to investigate microbial ecology of nitrifiers at the genus level in a typical full-scale activated sludge plant.<br><br>METHODS AND RESULTS: Grab samples of mixed liquor were collected from a plug-flow reactor receiving domestic wastewater. Fluorescent in situ hybridization technique (FISH) was used to characterize both ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) in combination with Confocal Scanning Laser Microscope (CSLM). Fluorescently labelled, 16S rRNA-targeted oligonucleotide probes were used in this study. Both Nitrosomonas and Nitrosospira genera as AOB and Nitrobacter and Nitrospira genera as NOB were sought with genus specific probes Nsm156, Nsv443 and NIT3 and NSR1156, respectively.<br><br>CONCLUSIONS: It was shown that Nitrosospira genus was dominant in the activated sludge system studied, although Nitrosomonas is usually assumed to be the dominant genus. At the same time, Nitrobacter genus was detected in activated sludge samples.<br><br>Previous studies based on laboratory scale pilot plants employing synthetic wastewater suggested that only Nitrospira are found in wastewater treatment plants. We have shown that Nitrobacter genus might also be present. We think that these kinds of studies may not give a valid indication of the microbial diversity of the real full-scale plants fed with domestic wastewater.}, }
@article {pmid12173119, year = {2002}, author = {Edmiston, CE and Krepel, CJ and Seabrook, GR and Jochimsen, WG}, title = {Anaerobic infections in the surgical patient: microbial etiology and therapy.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {35}, number = {Suppl 1}, pages = {S112-8}, doi = {10.1086/341931}, pmid = {12173119}, issn = {1537-6591}, mesh = {*Bacteria, Anaerobic ; Bacterial Infections/metabolism/*physiopathology ; Bacteroides Infections/physiopathology ; Bacteroides fragilis/isolation &amp; purification ; General Surgery ; Humans ; Oxidation-Reduction ; Postoperative Complications/metabolism/*microbiology ; Treatment Failure ; }, abstract = {Anaerobic infections occur in surgical patients in part because of structural or functional defects in the host that (1) cause a breech in the normal mucosal barriers, (2) create localized vascular insufficiencies, or (3) produce an obstruction. Any or all of these events may compromise the oxidation-reduction potential within the tissues, encouraging rapid anaerobic growth. Although diverse anaerobic populations are spread throughout the gastrointestinal tract, a relatively limited number of organisms are responsible for clinical infection in the surgical patient. Many of these offending organisms express overt virulence factors that enhance microbial adherence, tissue destruction, and, in the case of Bacteroides fragilis, facilitate abscess formation. The selection of an appropriate perioperative or therapeutic agent requires a fundamental knowledge of the microbial ecology of this microbial population. The failure to consider the anaerobic flora as a component in the etiology of mixed surgical infections is associated with a high rate of perioperative and therapeutic failures.}, }
@article {pmid12172626, year = {2002}, author = {Philips, S and Wyffels, S and Sprengers, R and Verstraete, W}, title = {Oxygen-limited autotrophic nitrification/denitrification by ammonia oxidisers enables upward motion towards more favourable conditions.}, journal = {Applied microbiology and biotechnology}, volume = {59}, number = {4-5}, pages = {557-566}, doi = {10.1007/s00253-002-1059-8}, pmid = {12172626}, issn = {0175-7598}, mesh = {Anaerobiosis ; Biomass ; Bioreactors ; Colony Count, Microbial ; Culture Media ; DNA, Ribosomal/analysis ; Gammaproteobacteria/classification/genetics/isolation &amp; purification/*metabolism ; Geologic Sediments/*microbiology ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Nitrates/*metabolism ; Nitrogen/metabolism ; Nitrosomonas/classification/genetics/isolation &amp; purification/*metabolism ; Oxidation-Reduction ; Oxygen/*pharmacology ; Polymerase Chain Reaction ; Quaternary Ammonium Compounds/*metabolism ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; }, abstract = {The hypothesis is formulated that in case of oxygen limitation in the sediment, nitrifiers switch from nitrification to oxygen-limited autotrophic nitrification-denitrification (OLAND) in order to survive and maintain activity. During OLAND, ammonium is oxidised using nitrite as e-acceptor to form dinitrogen gas. As an additional advantage they benefit from the gaseous N(2) formed as a means of transport. In this way, the nitrifiers can move out of the sediment and rise through the water column towards more favourable conditions. At the surface, the bacteria could take up oxygen, and recommence nitrification. In order to test this hypothesis, nitrifying sediment with an overlaying water column was simulated in lab-scale columns. Nitrogen transformations and material transport through the water column were followed after addition of different forms of nitrogen under oxygen-limited conditions. (15)N-labelling experiments showed a large contribution of OLAND to the observed nitrogen deficits. Nitrifier enumerations, fluorescent in situ hybridisation and 16S rRNA gene analysis revealed increased populations of ammonia oxidising nitrifiers in the upper water layers. The results presented support the proposed hypothesis of transport using OLAND. Nitrifying activity in the sediment immediately recovered almost completely from prolonged oxygen-limited incubation when oxygen concentrations were increased.}, }
@article {pmid12154389, year = {2002}, author = {Grötzschel, S and de Beer, D}, title = {Effect of oxygen concentration on photosynthesis and respiration in two hypersaline microbial mats.}, journal = {Microbial ecology}, volume = {44}, number = {3}, pages = {208-216}, doi = {10.1007/s00248-002-2011-2}, pmid = {12154389}, issn = {0095-3628}, mesh = {Algorithms ; Biofilms/drug effects/*growth &amp; development ; Carbon Dioxide/metabolism ; Cyanobacteria/drug effects/growth &amp; development/metabolism ; Hydrogen-Ion Concentration ; Oxygen/metabolism/*pharmacology ; Oxygen Consumption/*drug effects ; Photosynthesis/*drug effects ; Ribulose-Bisphosphate Carboxylase/metabolism ; Seawater/microbiology ; Sodium Chloride/pharmacology ; }, abstract = {The effects of oxygen concentration on photosynthesis and respiration in two hypersaline cyanobacterial mats were investigated. Experiments were carried out on mats from Eilat, Israel, with moderate photosynthetic activity, and mats from Mallorca, Spain, with high photosynthetic activity. The oxygen concentration in the overlying water above the mats was increased stepwise from 0% to 100% O2. Subsequent changes in oxygen concentration, gross photosynthetic rates, and pH values inside the mats were measured with microelectrodes. According to published reports on the regulation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), the key enzyme in the CO2-fixation pathway of phototrophs, we expected photosynthetic activity to decrease with increasing oxygen concentration. Gross photosynthetic and total respiration rates in both mats were highest when the O2 concentration was at 0% in the overlying water. Net oxygen production rates under these conditions were the same as under air saturation (21% O2), while gross photosynthetic and respiration rates were lowest at air saturation. In both mats, gross photosynthetic and respiration rates increased upon gradually increasing the oxygen concentration in the overlying water from 21% to 100%. These results contradict the expectation that photosynthesis decreases with increasing oxygen concentration. Increased photosynthetic rates at oxygen concentrations above 21% were probably caused by enhanced oxidation of organic matter and concomitant CO2 production due to the increased oxygen availability. The cause of the high respiration rates at 0% O2 in the overlying water was presumably the enhanced excretion of photosynthetic products during increased photosynthesis. We conclude that the effect of the O2/CO2 concentration ratio on the activity of Rubisco as demonstrated in vitro on enzyme extracts cannot be extrapolated to the situation in intact microbial mats, because the close coupling of the activity of primary producers and heterotrophic bacteria plays a major role in this ecosystem.}, }
@article {pmid12154388, year = {2002}, author = {Lawrence, JR and Scharf, B and Packroff, G and Neu, TR}, title = {Microscale evaluation of the effects of grazing by invertebrates with contrasting feeding modes on river biofilm architecture and composition.}, journal = {Microbial ecology}, volume = {44}, number = {3}, pages = {199-207}, doi = {10.1007/s00248-001-1064-y}, pmid = {12154388}, issn = {0095-3628}, mesh = {Animals ; Bacteria/growth &amp; development ; Biofilms/*growth &amp; development ; Crustacea/physiology ; Ecology ; Eukaryota/growth &amp; development ; Feeding Behavior/*physiology ; Fresh Water/*analysis/microbiology/parasitology ; Insecta/physiology ; Invertebrates/*physiology ; Polymers/analysis ; Snails/physiology ; }, abstract = {River biofilms are a valuable food resource for many invertebrates. In the present study biofilms were cultivated in a rotating annular bioreactor with river water as sole source of inoculum. The resulting biofilms were then presented to starved snails, ostracods, and mayflies as sole food source. The biofilms were then removed and microscopically examined to determine areas that had been grazed. The grazed and ungrazed areas were marked and analyzed for the effects of grazing using confocal laser scanning microscopy and image analyses. Samples were treated with fluorescent probes for nucleic acids to quantify bacterial biomass and fluor-conjugated lectins to quantify exopolymer, and far red autofluorescence was imaged to quantify algal or photosynthetic biomass. Grazing by snails significantly reduced algal biomass (1.1 +/- 0.6 micro m 3 micro m 2 to 0.02 +/- 0.04 micro m 3 micro m 2), exopolymer (5.3 +/- 3.4 micro m 3 micro m 2 to 0.18 +/- 0.18 micro m 3 micro m 2), and biofilm thickness (154 micro m +/- 50 to 11 micro m +/- 5.2; ANOVA, p < or= 0.05). Although bacterial biomass was influenced by grazing snails the impact was not statistically significant (p <or= 0.05). Ostracods had a significant (p <or= 0.05) impact on the algal biomass and exopolymer but not on bacteria. Mayfly grazing resulted in reduction of biofilm thickness to approximately 40 mm and reductions in all biofilm components with little evidence of selectivity. Thus grazing consistently resulted in a significant reduction in autotrophic biomass and exopolymer with a resultant increased importance of bacterial biomass within the grazed regions. Examination of grazed biofilms after a recovery period in the absence of grazing indicated that grazed regions remained predominantly bacterial after 28 days. A comparison of grazing in diclofop methyl and atrazine contaminated (1 ppb and 10 ppb) versus control biofilms indicated no significant influence of the contaminants on grazing patterns.}, }
@article {pmid12147723, year = {2002}, author = {Novák, K and Chovanec, P and Skrdleta, V and Kropácová, M and Lisá, L and Nemcová, M}, title = {Effect of exogenous flavonoids on nodulation of pea (Pisum sativum L.).}, journal = {Journal of experimental botany}, volume = {53}, number = {375}, pages = {1735-1745}, doi = {10.1093/jxb/erf016}, pmid = {12147723}, issn = {0022-0957}, mesh = {*Flavanones ; Flavonoids/chemistry/*pharmacology ; Hesperidin/chemistry/pharmacology ; Hydroponics ; Nitrogenase/metabolism ; Pisum sativum/drug effects/*growth &amp; development/microbiology ; Plant Roots/drug effects/*growth &amp; development/microbiology ; Quercetin/chemistry/pharmacology ; Rhizobium leguminosarum/drug effects/genetics/*growth &amp; development ; Symbiosis/drug effects ; beta-Galactosidase/metabolism ; }, abstract = {Selected flavonoids that are known as inducers and a suppressor of nodulation (nod) genes of the symbiotic bacterium Rhizobium leguminosarum bv. viciae were tested for their effect on symbiosis formation with garden pea as the host. A solid substrate was omitted from the hydroponic growing system in order to prevent losses of flavonoids due to adsorption and degradation. The presumed interaction of the tested flavonoids with nod genes has been verified for the genetic background of strain 128C30. A stimulatory effect of a nod gene inducer naringenin on symbiotic nodule number formed per plant 14 d after inoculation was detected at concentrations of 0.1 and 1 micro g ml(-1) nutrient solution. At 10 micro g ml(-1), the highest concentration tested, naringenin was already inhibitory. By contrast, nodulation was negatively affected by a nod gene suppressor, quercetin, at concentrations above 1 micro g ml(-1), as well as by another tested nod gene inducer, hesperetin. The deleterious effect of hesperetin might be due to its toxicity or to the toxicity of its degradation product(s) as indicated by the inhibition of root growth. Both the stimulatory effect of naringenin and the inhibitory effect of quercetin on nodule number were more pronounced at earlier stages of nodule development as revealed with specific staining of initial nodules. The lessening of the flavonoid impact during nodule development was ascribed to the plant autoregulatory mechanisms. Feedback regulation of nodule metabolism might also be responsible for the fact that the naringenin-conditioned increase in nodule number was not accompanied by any increase in nitrogenase activity. By contrast, the inhibitory action of quercetin and hesperetin on nodule number was associated with decreases in total nitrogenase activity. Naringenin also stimulated root hair curling (RHC) as one of the earliest nodulation responses at concentrations of 1 and 10 microg ml(-1), however, the same effect was exerted by the nod gene suppressor, quercetin, suggesting that feedback regulatory mechanisms control RHC in the range of nodulation-inhibiting high flavonoid concentrations. The comparison of the effect of the tested flavonoids in planta with nod gene activity response showed a two orders of magnitude shift to higher concentrations. This shift is explained by the absorption and degradation of flavonoids by both the symbionts during 3 d intervals between hydroponic solution changes. The losses were 99, 96.4, and 90% of the initial concentration of 10 micro g ml(-1) for naringenin, hesperetin, and quercetin, respectively.}, }
@article {pmid12135598, year = {2002}, author = {Rakwal, R and Tamogami, S and Agrawal, GK and Iwahashi, H}, title = {Octadecanoid signaling component "burst" in rice (Oryza sativa L.) seedling leaves upon wounding by cut and treatment with fungal elicitor chitosan.}, journal = {Biochemical and biophysical research communications}, volume = {295}, number = {5}, pages = {1041-1045}, doi = {10.1016/s0006-291x(02)00779-9}, pmid = {12135598}, issn = {0006-291X}, mesh = {Antigens, Fungal/pharmacology ; Chitin/analogs &amp; derivatives/*pharmacology ; Chitosan ; Cyclopentanes/*metabolism ; Diazonium Compounds/*metabolism ; Oryza/*drug effects/metabolism ; Oxylipins ; Plant Leaves/drug effects/metabolism ; Pyridines/*metabolism ; Signal Transduction/physiology ; Wound Healing/physiology ; Wounds and Injuries/*metabolism ; }, abstract = {Octadecanoid pathway components, 12-oxo-phytodieonic acid (OPDA) and jasmonic acid (JA), are key biologically active regulators of plant self-defense response(s). However, to date these compounds have been studied mostly in dicots, and used large (1-10 g fresh weight, FW) samples for quantification, even when examined in mature rice plants, which is a drawback considering their rapid responsiveness to stress. Focusing on rice--a monocot cereal crop research model--this work describes an efficient and simultaneous quantification of both OPDA and JA using a minimum amount of 200mg FW seedling leaf tissue upon wounding (by cut) and treatment with fungal elicitor, chitosan (CT) by high-pressure liquid chromatography-turboionspray tandem mass spectrometry. Transient OPDA/JA "burst" was consistently and reproducibly detected within 3 min in wounded and CT treated leaves. OPDA peaked dramatically around 5 min and returned to its basal level within 15 min, whereas JA induction upon wounding and CT treatment were in parallel to OPDA production, peaking at 30 and 60 min, respectively. Present results mark a major advance in our understanding of key inducible octadecanoid pathway components in rice, and strongly suggest a role for the octadecanoid pathway downstream of perception of at least these two fundamentally different extracellular stimuli.}, }
@article {pmid12135579, year = {2002}, author = {Le Quéré, A and Johansson, T and Tunlid, A}, title = {Size and complexity of the nuclear genome of the ectomycorrhizal fungus Paxillus involutus.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {36}, number = {3}, pages = {234-241}, doi = {10.1016/s1087-1845(02)00024-5}, pmid = {12135579}, issn = {1087-1845}, mesh = {Amino Acid Sequence ; Basidiomycota/*genetics ; Cosmids/genetics ; DNA, Fungal/chemistry/isolation &amp; purification ; *Genes, Fungal ; Genetic Variation ; *Genome, Fungal ; Genomic Library ; Molecular Sequence Data ; Open Reading Frames ; Sequence Homology, Amino Acid ; }, abstract = {The basidiomycete Paxillus involutus is forming ectomycorrhizal symbiosis with a broad range of forest trees. Reassociation kinetics on P. involutus nuclear DNA indicated a haploid genome size of 23 Mb including 11% of repetitive DNA. A similar genome size (20 Mb) was estimated by genomic reconstruction analysis using three single copy genes. To assess the gene density in the P. involutus genome, a cosmid containing a 33-kb fragment of genomic DNA was sequenced and used to identify putative open reading frames (ORFs). Twelve potential ORFs were predicted, eight displayed significant sequence similarities to known proteins found in other organisms and notably, several homologues to the Podospora anserina vegetative incompatibility protein (HetE1) were found. By extrapolation, we estimate the total number of genes in the P. involutus haploid genome to approximately 7700.}, }
@article {pmid12133615, year = {2002}, author = {Bjerrum, L and Kjaer, T and Ramsing, NB}, title = {Enumerating ammonia-oxidizing bacteria in environmental samples using competitive PCR.}, journal = {Journal of microbiological methods}, volume = {51}, number = {2}, pages = {227-239}, doi = {10.1016/s0167-7012(02)00077-5}, pmid = {12133615}, issn = {0167-7012}, mesh = {Ammonia/*metabolism ; Calibration ; Colony Count, Microbial/*methods ; DNA, Bacterial/analysis ; *Environmental Microbiology ; Oxidation-Reduction ; Polymerase Chain Reaction/*methods ; Soil Microbiology ; }, abstract = {Primers targeting part of the ammonia-monooxygenase gene (amoA) have been used to detect and characterize ammonia-oxidizing bacteria (AOB) in different environments. In this study, a quantitative polymerase chain reaction (PCR) technique using a competitive template for the amoA primer pair is described and evaluated. The method is based on addition of an internal standard to the PCR, a competitive template, which is amplified together with the template in the environmental sample. By adding different amounts of competitive template to the sample and observing the relative intensity of environmental amplificate and competitive amplificate, the number of amoA gene copies can be determined. Different tests were made to evaluate the competitive PCR method (cPCR) with respect to equal amplification efficiency of the two templates, degeneracy of the priming site and the importance of flanking regions surrounding the competitive template. Calibration curves made by addition of known amounts of Nitrosomonas europaea to soil samples revealed a detection limit for this technique of less than 1000 cells g(-1) soil and a linear response over a wide range of cell additions. Cloning and sequencing of amoA amplificates have confirmed the specificity of the primers, as we have not detected any false positives among the more than 200 clones investigated. The vertical distribution of ammonia-oxidizers in the upper cm of a waterlogged rice paddy soil was compared to nitrate and oxygen concentration profiles determined with microsensors and to net process rates derived from these profiles.}, }
@article {pmid12133610, year = {2002}, author = {Rodrigues, JL and Aiello, MR and Urbance, JW and Tsoi, TV and Tiedje, JM}, title = {Use of both 16S rRNA and engineered functional genes with real-time PCR to quantify an engineered, PCB-degrading Rhodococcus in soil.}, journal = {Journal of microbiological methods}, volume = {51}, number = {2}, pages = {181-189}, doi = {10.1016/s0167-7012(02)00067-2}, pmid = {12133610}, issn = {0167-7012}, support = {P42 ES04911-13/ES/NIEHS NIH HHS/United States ; }, mesh = {Biodegradation, Environmental ; Colony Count, Microbial/*methods ; DNA Primers ; DNA Probes ; Genetic Engineering ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/*genetics ; Rhodococcus/*isolation &amp; purification ; Sensitivity and Specificity ; *Soil Microbiology ; }, abstract = {A real-time PCR (RTm-PCR) assay using fluorescently labeled oligonucleotides (TaqMan probes) was used to detect and quantify the recombinant Rhodococcus sp. strain RHA1(fcb) in soil. One primer and probe set targeted a hypervariable region of the 16S rRNA gene unique to strain RHA1(fcb) and its phylogenetic relatives, and the other set targeted the recombinant 4-chlorobenzoate (4-CBA) degradation operon (fcb) and was strain-specific. The method had a 6-log dynamic range of detection (10(2)-10(7) cells ml(-1)) for both probes when DNA from pure cultures was used. Although the method was less sensitive in soil, the estimated number of cells in soil by real-time PCR corresponded to the measured number of RHA1(fcb) cells determined by colony-forming units.}, }
@article {pmid12126810, year = {2002}, author = {Grommen, R and Verstraete, W}, title = {Environmental biotechnology: the ongoing quest.}, journal = {Journal of biotechnology}, volume = {98}, number = {1}, pages = {113-123}, doi = {10.1016/s0168-1656(02)00090-1}, pmid = {12126810}, issn = {0168-1656}, mesh = {Air Pollution/prevention &amp; control ; Aquaculture/methods ; *Biotechnology/methods/standards ; Environmental Monitoring/instrumentation/*methods ; *Environmental Pollution/prevention &amp; control ; Gases/analysis/isolation &amp; purification ; Quality Control ; Refuse Disposal/instrumentation/methods ; Risk Assessment ; Waste Disposal, Fluid/instrumentation/methods ; *Waste Management/instrumentation/methods ; *Water Supply/analysis ; }, abstract = {Environmental biotechnology, until now, has primarily focused on the development of technologies to treat aqueous, solid and gaseous wastes. At present, the basic knowledge on how biotechnology can handle these wastes has been acquired and the focus is now on the implementation of these processes as 'best available technology not entailing excessive costs' (BATNEEC) in the framework of strict and transparent environmental legislation. New environmental challenges continue to evolve, as it becomes clear that waste streams should be tackled in an overall holistic way. New technologies to reach this goal are currently under development. Novel aspects with respect to the domain of water treatment are, for example, the biomembrane reactor technology and the newly discovered processes to remove nitrogen by means of anaerobic ammonium oxidation. Also, most challenging is the continuing strive for re-use of treated wastewater. Indeed, water shortage is emerging in an increasing number of countries all over the world and necessitates the short cycling of water. Finally, biotechnology has a key role to play in the novel approaches to design wastewater treatment based on decentralised sanitation and reuse (DESAR). Solid waste is a major challenge worldwide. The implementation of anaerobic digestion to treat biowastes has become a grown-up technology. New approaches in which biotechnological processes are linked to physical processes, such as plasma technology, certainly deserve special attention for the coming decades. Soil and sediment clean up by means of biostimulation/remediation/augmentation is now well established. Certainly, a number of prospects need to be further explored, such as the use of special energy sources to stimulate in situ the microbial community and the seeding of knowledge to the in situ community by means of horizontal gene transfer mechanisms. A number of waste gases can be handled by biofilter systems. Biological treatment of wastegases is also evolving, inasmuch as that besides conventional chemical pollutants, now also highly problematic chemicals (even dioxins) can be dealt with through proper biotechnological approaches. A remarkable new potential is the use of well designed probiotics to upgrade aquaculture and together with conventional biological water treatment processes, to guarantee the overall water quality of this domain of food production.}, }
@article {pmid12123580, year = {2002}, author = {Rozen, DE and de Visser, JA and Gerrish, PJ}, title = {Fitness effects of fixed beneficial mutations in microbial populations.}, journal = {Current biology : CB}, volume = {12}, number = {12}, pages = {1040-1045}, doi = {10.1016/s0960-9822(02)00896-5}, pmid = {12123580}, issn = {0960-9822}, mesh = {Adaptation, Physiological ; *Directed Molecular Evolution ; Escherichia coli/*genetics/physiology ; Genotype ; *Models, Genetic ; *Mutation ; }, abstract = {Beneficial mutations are intuitively relevant to understanding adaptation, yet not all beneficial mutations are of consequence to the long-term evolutionary outcome of adaptation. Many beneficial mutations-mostly those of small effect-are lost due either to (1) genetic drift or to (2) competition among clones carrying different beneficial mutations, a phenomenon called the "Hill-Robertson effect" for sexual populations and "clonal interference" for asexual populations. Competition among clones becomes more prevalent with increasing genetic linkage and increasing population size, and it is thus generally characteristic of microbial populations. Together, these two phenomena suggest that only those beneficial mutations of large fitness effect should achieve fixation, despite the fact that most beneficial mutations produced are predicted to have very small fitness effects. Here, we confirm this prediction-both empirically and theoretically-by showing that fitness effects of fixed beneficial mutations follow a distribution whose mode is positive.}, }
@article {pmid12089030, year = {2002}, author = {Oda, Y and Wanders, W and Huisman, LA and Meijer, WG and Gottschal, JC and Forney, LJ}, title = {Genotypic and phenotypic diversity within species of purple nonsulfur bacteria isolated from aquatic sediments.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {7}, pages = {3467-3477}, pmid = {12089030}, issn = {0099-2240}, mesh = {Benzoates/metabolism ; Blotting, Southern ; DNA Fingerprinting ; DNA, Bacterial/analysis ; Genetic Variation ; *Genotype ; Geologic Sediments/microbiology ; Molecular Sequence Data ; *Phenotype ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/analysis/*genetics ; Rhodopseudomonas/classification/*genetics/metabolism ; }, abstract = {To assess the extent of genotypic and phenotypic diversity within species of purple nonsulfur bacteria found in aquatic sediments, a total of 128 strains were directly isolated from agar plates that had been inoculated with sediment samples from Haren and De Biesbosch in The Netherlands. All isolates were initially characterized by BOX-PCR genomic DNA fingerprinting, and 60 distinct genotypes were identified. Analyses of 16S rRNA gene sequences of representatives of each genotype showed that five and eight different phylotypes of purple nonsulfur bacteria were obtained from the Haren and De Biesbosch sites, respectively. At the Haren site, 80.5% of the clones were Rhodopseudomonas palustris, whereas Rhodoferax fermentans and Rhodopseudomonas palustris were numerically dominant at the De Biesbosch site and constituted 45.9 and 34.4% of the isolates obtained, respectively. BOX-PCR genomic fingerprints showed that there was a high level of genotypic diversity within each of these species. The genomic fingerprints of Rhodopseudomonas palustris isolates were significantly different for isolates from the two sampling sites, suggesting that certain strains may be endemic to each sampling site. Not all Rhodopseudomonas palustris isolates could degrade benzoate, a feature that has previously been thought to be characteristic of the species. There were differences in the BOX-PCR genomic fingerprints and restriction fragment length polymorphisms of benzoate-coenzyme A ligase genes and form I and form II ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) genes between benzoate-degrading and non-benzoate-degrading genotypes. The ability to distinguish these two Rhodopseudomonas palustris groups based on multiple genetic differences may reflect an incipient speciation event resulting from adaptive evolution to local environmental conditions.}, }
@article {pmid12089022, year = {2002}, author = {Ahman, J and Johansson, T and Olsson, M and Punt, PJ and van den Hondel, CA and Tunlid, A}, title = {Improving the pathogenicity of a nematode-trapping fungus by genetic engineering of a subtilisin with nematotoxic activity.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {7}, pages = {3408-3415}, pmid = {12089022}, issn = {0099-2240}, mesh = {Animals ; Ascomycota/genetics/*physiology ; Genetic Engineering ; Hydrolysis ; Mutation ; Nematoda/drug effects/*microbiology/physiology ; Recombinant Proteins/metabolism ; *Soil Microbiology ; Subtilisin/genetics/pharmacology/*physiology ; }, abstract = {Nematophagous fungi are soil-living fungi that are used as biological control agents of plant and animal parasitic nematodes. Their potential could be improved by genetic engineering, but the lack of information about the molecular background of the infection has precluded this development. In this paper we report that a subtilisin-like extracellular serine protease designated PII is an important pathogenicity factor in the common nematode-trapping fungus Arthrobotrys oligospora. The transcript of PII was not detected during the early stages of infection (adhesion and penetration), but high levels were expressed concurrent with the killing and colonization of the nematode. Disruption of the PII gene by homologous recombination had a limited effect on the pathogenicity of the fungus. However, mutants containing additional copies of the PII gene developed a higher number of infection structures and had an increased speed of capturing and killing nematodes compared to the wild type. The paralyzing activity of PII was verified by demonstrating that a heterologous-produced PII (in Aspergillus niger) had a nematotoxic activity when added to free-living nematodes. The toxic activity of PII was significantly higher than that of other commercially available serine proteases. This is the first report showing that genetic engineering can be used to improve the pathogenicity of a nematode-trapping fungus. In the future it should be possible to express recombinant subtilisins with nematicidal activity in other organisms that are present in the habitat of parasitic nematodes (e.g., host plant).}, }
@article {pmid12088533, year = {2002}, author = {Flickinger, EA and Fahey, GC}, title = {Pet food and feed applications of inulin, oligofructose and other oligosaccharides.}, journal = {The British journal of nutrition}, volume = {87 Suppl 2}, number = {}, pages = {S297-300}, doi = {10.1079/BJNBJN/2002552}, pmid = {12088533}, issn = {0007-1145}, mesh = {*Animal Feed ; Animals ; *Animals, Domestic ; *Fructans ; Gastroenteritis/prevention &amp; control/veterinary ; Intestines/microbiology ; Inulin ; Oligosaccharides ; }, abstract = {Prebiotics may be considered as functional food ingredients. They are attracting considerable interest from pet owners, pet food manufacturers, livestock producers and feed manufacturers. The most common forms of prebiotics are nondigestible oligosaccharides (NDO), including inulin, oligofructose mannanoligosaccharides, gluco-oligosaccharides, and galacto-oligosaccharides. These NDO are nondigestible by enzymes present in the mammalian small intestine, but are fermented by bacteria present in the hindgut of nonruminants. Inulin and oligofructose are present in measurable quantities in feed ingredients like wheat, wheat by-products, barley, and peanut hulls. Consumption of prebiotic oligosaccharides elicits several purported health benefits. In companion animals, prebiotics have been shown to improve gut microbial ecology and enhance stool quality. In production livestock and poultry, prebiotics are employed to control pathogenic bacteria, reduce faecal odour, and enhance growth performance. Research to date indicates positive effects of prebiotics on health status and performance of companion animals, livestock, and poultry.}, }
@article {pmid12087428, year = {2002}, author = {Simpson, JM and Martineau, B and Jones, WE and Ballam, JM and Mackie, RI}, title = {Characterization of fecal bacterial populations in canines: effects of age, breed and dietary fiber.}, journal = {Microbial ecology}, volume = {44}, number = {2}, pages = {186-197}, doi = {10.1007/s00248-002-0001-z}, pmid = {12087428}, issn = {0095-3628}, mesh = {Age Factors ; Animal Feed ; Animals ; *Bacteria/genetics/isolation &amp; purification ; DNA, Bacterial/analysis ; Diet ; Dogs/*microbiology ; Electrophoresis, Gel, Two-Dimensional ; Feces/*microbiology ; Pedigree ; Polymerase Chain Reaction ; Population Dynamics ; }, abstract = {The effects of age, breed, and diet on fecal chemistry, enzyme activity, and bacterial populations of dogs were studied. Eighteen dogs from two age groups (young: 2.5 +/- 0.5 years, old: 10.9 +/-0.7 years) and three different breeds (German shepherds, miniature schnauzers, and English setters) were rotated through a Latin Square design such that every dog was fed each of the diets. The test diets included a low-fiber (control) diet and a 10% fiber diet which contained 5% soybean hulls and 5% beet pulp. Inclusion of 10% fiber in the diet decreased the fecal concentration of ammonia, sulfide, and indole. Fiber inclusion significantly increased acetic, propionic, and butyric acid concentrations, while fecal pH decreased by 0.4 units. Fresh fecal samples were plated on selected aerobic and anaerobic culture media and DNA extracted for denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S ribosomal DNA fragments. Plate counts showed significant effects of breed (p < or = 0.05) and age (p < or = 0.01) on selected aerobic and anaerobic bacterial counts, while no significant effect of diet was found. Analysis of PCR-DGGE banding patterns showed there was a tendency for individual dogs to cluster together according to age (young or old dogs) and also for size (large or small dogs). However, the outstanding conclusion obtained from the DGGE analysis of fecal bacterial profiles was that individual dogs had their own characteristic banding pattern which was unique and stable. The relative stability and individuality of the patterns indicates that each individual harbored a characteristic fecal bacterial community which was independent of diet.}, }
@article {pmid12087427, year = {2002}, author = {Maduell, P and Callejas, R and Cabrera, KR and Armengol, G and Orduz, S}, title = {Distribution and characterization of Bacillus thuringiensis on the phylloplane of species of piper (Piperaceae) in three altitudinal levels.}, journal = {Microbial ecology}, volume = {44}, number = {2}, pages = {144-153}, doi = {10.1007/s00248-002-1018-z}, pmid = {12087427}, issn = {0095-3628}, mesh = {Adaptation, Physiological ; *Altitude ; Animals ; Bacillus thuringiensis/*genetics/pathogenicity ; *Culex ; DNA, Bacterial/analysis/*genetics ; Genotype ; Piperaceae/*microbiology ; Polymerase Chain Reaction ; Population Dynamics ; Toxicity Tests ; }, abstract = {Bacillus thuringiensis is found naturally on the phylloplane. In this study 35 samples from 13 species of the genus Piper (Piperaceae) were collected from three altitudinal levels located between 1800 and 2900 m above sea level in the Colombian Andean forest of Central Cordillera. Two hundred and fifty-six isolates of B. thuringiensis were obtained from 74% of the samples studied. B. thuringiensis index (number of isolates of B. thuringiensis/number of isolates of sporulated bacilli) was 0.2. The isolates were characterized by crystal morphology, the presence of cry genes by PCR, and toxicity against insects. Fifty-five percent of the isolates found presented bipyramidal-crystal morphology, and 42% had round-crystal morphology. Seventy percent of the isolates amplified cry1 [cry one] genes (generally toxic to lepidopterans); 41.4% amplified cry4 and/or cry11 [cry eleven] genes (generally toxic to dipterans), and none of the isolates amplified cry3 genes (generally toxic to coleopterans). The most abundant genotype of cry genes (54.7% of the total) was cry1Aa, cry1Ab, cry1Ac, cry1Ad, and cry1B. From the total isolates found, 7.8% presented both cry1 and cry11 genes, and five isolates (2.0%) harbored cry1, cry4, and cry11 genes; all these isolates were toxic to Culex quinquefasciatus (Diptera) but not to Spodoptera frugiperda (Lepidoptera). To our knowledge, these genotypes have not been previously reported. Overall, almost 60% of the isolates were toxic to S. frugiperda, and a little more than 40% of the isolates were toxic to C. quinquefasciatus. The populations of viable vegetative cells and spores per unit area were estimated and studied statistically. No significant differences in the number of B. thuringiensis isolates per cm2 of leaf among the three altitudinal levels were found, nor were they found among the different Piper species evaluated. This study increases the knowledge of the ecology of B. thuringiensis.}, }
@article {pmid12087426, year = {2002}, author = {Mira, A and Moran, NA}, title = {Estimating population size and transmission bottlenecks in maternally transmitted endosymbiotic bacteria.}, journal = {Microbial ecology}, volume = {44}, number = {2}, pages = {137-143}, doi = {10.1007/s00248-002-0012-9}, pmid = {12087426}, issn = {0095-3628}, mesh = {Animals ; Aphids/*microbiology ; *Buchnera ; Eggs/microbiology ; Embryo, Nonmammalian/microbiology ; *Infectious Disease Transmission, Vertical ; Larva ; Microscopy, Electron ; Population Dynamics ; Symbiosis/*physiology ; }, abstract = {Many species of bacterial endosymbionts are acquired by animal hosts before birth, through direct transmission from mothers to eggs or embryos. This vertical transmission imposes a reduction in numbers or "bottleneck," and the size of this bottleneck affects the population structure and evolution of symbiotic lineages. We have estimated the size of the transmission bottleneck in Buchnera, the bacterial symbiont of aphids, using basic light and electron microscopy techniques. By serial-sectioning whole aphid abdomens, their eggs, and embryos, we determined the following parameters: (i) The average size of a Buchnera cell is 2.9 mm in diameter. (ii) The total number of Buchnera in an Acyrthosiphon pisum embryo was around 36700 whereas a first instar nymph contained more than 119000. (iii) The number of symbionts per bacteriocyte was around 800 in an embryo and 3200 in a first instar nymph. (iv) The total number of Buchnera transmitted to each sexual egg ranged from 850 in Nasonovia to 1800 in A. pisum to more than 8000 in Uroleucon ambrosiae. (v) The total number of secondary endosymbionts in A. pisum was 12170 for an embryo and 18360 for a first instar nymph. Secondary symbionts were arranged both extracellularly and in clusters of 2000-8000 bacteria inside bacteriocytes. These numbers are consistent with the few previous estimates of symbiont population sizes based on counts of gene copies.}, }
@article {pmid12087425, year = {2002}, author = {Bakermans, C and Madsen, EL}, title = {Diversity of 16S rDNA and naphthalene dioxygenase genes from coal-tar-waste-contaminated aquifer waters.}, journal = {Microbial ecology}, volume = {44}, number = {2}, pages = {95-106}, doi = {10.1007/s00248-002-0005-8}, pmid = {12087425}, issn = {0095-3628}, mesh = {Bacteria, Aerobic/*genetics/physiology ; *Coal ; DNA, Bacterial/*analysis ; Dioxygenases ; *Genetic Variation ; Multienzyme Complexes/*genetics/pharmacology ; Oxygenases/*genetics/pharmacology ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Population Dynamics ; Waste Disposal, Fluid ; Water Microbiology ; *Water Supply ; }, abstract = {Microbial diversity in four wells along a groundwater flowpath in a coal-tar-waste-contaminated aquifer was examined using RFLP analysis of both 16S rDNA and naphthalene dioxygenase (NDO) genes. Amplified ribosomal DNA restriction analysis (ARDRA) relied upon eubacteria-specific primers to generate four clone libraries. From each library, 100 clones were randomly picked for analysis. Sixty percent of 400 clones contained unique ARDRA patterns. Diversity indices calculated for each community were high (Shannon-Weaver, H = 3.53 to 3.69). Clones representing ARDRA patterns found in the highest abundance were sequenced (31 total). Sequences related to aerobic bacteria (e.g., Nitrospira, Methylomonas, and Gallionella) predominated among those retrieved from the uncontaminated area of the site, whereas sequences related to facultatively aerobic and anaerobic bacteria (e.g. Azoarcus, Syntrophus, and Desulfotomaculum) predominated among those retrieved from contaminated areas of the site. Using NDO-specific primers and low-stringency PCR conditions, variability in RFLP patterns was only detected in community-derived DNA (3 of 4 wells) and not in 5 newly isolated naphthalene-degrading pure cultures. The ARDRA patterns of the pure culture isolates were not found in the clone libraries. Polymorphisms in community 16S rDNA and NDO genes found in well-water microorganisms reflected distinctive geochemical conditions across the site. Sequences related to sulfate-reducing bacteria were found in groundwater that contained sulfide, while sequences related to Gallionella, Syntrophus, and nitrate-reducing aromatic hydrocarbon-degrading bacteria were found in groundwater that contained ferrous iron, methane, and naphthalene, respectively.}, }
@article {pmid12087424, year = {2002}, author = {Bakermans, C and Hohnstock-Ashe, AM and Padmanabhan, S and Padmanabhan, P and Madsen, EL}, title = {Geochemical and physiological evidence for mixed aerobic and anaerobic field biodegradation of coal tar waste by subsurface microbial communities.}, journal = {Microbial ecology}, volume = {44}, number = {2}, pages = {107-117}, doi = {10.1007/s00248-002-3011-y}, pmid = {12087424}, issn = {0095-3628}, mesh = {Bacteria, Aerobic/*physiology ; Bacteria, Anaerobic/*physiology ; Biodegradation, Environmental ; *Coal ; Ecosystem ; Models, Theoretical ; *Refuse Disposal ; Soil Pollutants/*metabolism ; Water Pollutants/*metabolism ; *Water Supply ; }, abstract = {We used geochemical analyses of groundwater and laboratory-incubated microcosms to investigate the physiological responses of naturally occurring microorganisms to coal-tar-waste constituents in a contaminated aquifer. Waters were sampled from wells along a natural hydrologic gradient extending from uncontaminated (1 well) into contaminated (3 wells) zones. Groundwater analyses determined the concentrations of carbon and energy sources (pollutants or total organic carbon), final electron acceptors (oxygen, nitrate, sulfate), and metabolic byproducts (dissolved inorganic carbon [DIC], alkalinity, methane, ferrous iron, sulfide, Mn2+). In the contaminated zone of the study site, concentrations of methane, hydrogen, alkalinity, and DIC were enhanced, while dissolved oxygen and nitrate were depleted. Field-initiated biodegradation assays using headspace-free serum bottle microcosms filled with groundwater examined metabolism of the ambient organic contaminants (naphthalene, 2-methylnaphthalene, benzothiophene, and indene) by the native microbial communities. Unamended microcosms from the contaminated zone demonstrated the simultaneous degradation of several coal-tar-waste constituents at the in situ temperature (10 degrees C). Lag phases prior to the onset of biodegradation indicated the prevalence of both aerobic and anaerobic conditions in situ. Electron acceptor-amended microcosms from the most contaminated well waters demonstrated only aerobic naphthalene degradation. Collectively, the geochemical and microbial evidence show that biodegradation of coal-tar-waste constituents occurs via both aerobic and anaerobic terminal electron accepting processes at this site.}, }
@article {pmid12087423, year = {2002}, author = {Guevara, R and Armesto, JJ and Caru, M}, title = {Genetic diversity of Nostoc microsymbionts from Gunnera tinctoria revealed by PCR-STRR fingerprinting.}, journal = {Microbial ecology}, volume = {44}, number = {2}, pages = {127-136}, doi = {10.1007/s00248-002-1019-y}, pmid = {12087423}, issn = {0095-3628}, mesh = {Cyanobacteria/*genetics/physiology ; *DNA Fingerprinting ; DNA, Bacterial/analysis/genetics ; *Genetic Variation ; *Plants ; Polymerase Chain Reaction ; Symbiosis/*physiology ; Tandem Repeat Sequences/*genetics ; }, abstract = {The cyanobacteria belonging to the genus Nostoc fix atmospheric nitrogen, both as free-living organisms and in symbiotic associations with a wide range of hosts, including bryophytes, gymnosperms (cycads), the small water fern Azolla (Pteridophyte), the angiosperm genus Gunnera, and fungi (lichens). The Gunnera-Nostoc symbiosis is the only one that involves a flowering plant. In Chile, 12 species of Gunnera have been described with a broad distribution in the temperate region. We examined the genetic diversity of Nostoc symbionts from three populations of Gunnera tinctoria from Abtao, Chiloé Island, southern Chile, and microsymbionts from other two species of Gunnera from southern Chile, using PCR amplification of STRR (short tandemly repeated repetitive) sequences of the Nostoc infected tissue. To our knowledge, this is the first report of PCR fingerprinting obtained directly from symbiotic tissue of Gunnera. Genetic analyses revealed that Nostoc symbionts exhibit important genetic diversity among host plants, both within and between Gunnera populations. It was also found that only one Nostoc strain, or closely related strains, established symbiosis with an individual plant host.}, }
@article {pmid12082454, year = {2002}, author = {Stoderegger, KE and Herndl, GJ}, title = {Distribution of capsulated bacterioplankton in the North Atlantic and North Sea.}, journal = {Microbial ecology}, volume = {44}, number = {2}, pages = {154-163}, doi = {10.1007/s00248-002-0008-5}, pmid = {12082454}, issn = {0095-3628}, mesh = {Animals ; Atlantic Ocean ; *Bacteria ; Environmental Monitoring ; *Eutrophication ; North Sea ; *Plankton ; Polysaccharides/analysis/chemistry ; Population Dynamics ; }, abstract = {In laboratory experiments, bacterioplankton were incubated under different nutrient conditions, and the percentage of bacteria exhibiting a polysaccharidic capsule (capsulated bacteria) and that of CTC (cyanotetrazolium chloride)-positive and therefore metabolically highly active bacteria were determined. In these seawater cultures amended with nutrients more than 95% of the CTC-positive cells exhibited a capsule. During two cruises, one to the North Atlantic and one to the North Sea, we investigated the distribution of capsulated bacteria throughout the water column. Capsulated bacteria were generally more abundant in eutrophic surface waters than in deeper layers or more oligotrophic regions. In the upper 100 m of the North Atlantic, about 6-14% of the total bacterioplankton community was capsulated, while in the layers below 100 m depth, 97% of the bacteria lacked a visible capsule. The percentage of capsulated bacteria correlated with bacterial abundance and production, and chlorophyll a concentration. Also, the bioavailability of DOC (dissolved organic carbon), estimated by the ratio between bacterial production and DOC concentration, significantly correlated with the percentage of capsulated bacteria. In the North Sea, the contribution of capsulated bacteria to the total number of bacteria decreased from the surface (3 m depth) to the near-bottom (25-35 m) layers from 20% to 14% capsulated bacteria. In the nearshore area of the North Sea, about 27% of the bacteria exhibited a capsule. Overall, a pronounced decrease in the contribution of capsulated bacteria to the total bacterial abundance was detectable from the eutrophic coastal environment to the open North Atlantic. Using this epifluorescence-based technique to enumerate capsulated bacterioplankton thus allowed us to routinely assess the number of capsulated bacteria even in the oceanic water column. Based on the data obtained in this study we conclude that almost all metabolically highly active bacteria exhibit a capsule, but also some of the metabolically less active cells express a polysaccharide capsule detectable with this method.}, }
@article {pmid12082453, year = {2002}, author = {Holben, WE and Williams, P and Gilbert, M and Saarinen, M and Särkilahti, LK and Apajalahti, JH}, title = {Phylogenetic analysis of intestinal microflora indicates a novel Mycoplasma phylotype in farmed and wild salmon.}, journal = {Microbial ecology}, volume = {44}, number = {2}, pages = {175-185}, doi = {10.1007/s00248-002-1011-6}, pmid = {12082453}, issn = {0095-3628}, mesh = {Animals ; Animals, Wild ; *Aquaculture ; DNA, Bacterial/analysis/*genetics ; Digestive System/microbiology ; Mycoplasma/*genetics/physiology ; *Phylogeny ; Population Dynamics ; Salmon/*microbiology ; }, abstract = {All studies of the microbial community of the gastrointestinal tract of salmon to date have employed culture-based approaches, typically on pond- or tank-raised, freshwater animals. We present a phylogenetic survey of the bacterial populations present in the distal intestine of salmon from three different marine locations in Europe. This was accomplished through PCR amplification, cloning, and sequencing of partial 16S rDNA genes from microbial community DNA isolated from the contents of the GI tract distal to the pyloric ceca. Using this approach, the intestinal microbial communities of wild salmon from Scotland and pen-raised salmon from Scotland and Norway were compared. The predominating bacterial populations detected were Acinetobacter junii and a novel Mycoplasma phylotype. This Mycoplasma phylotype apparently comprised approximately 96% of the total microbes in the distal intestine of wild salmon. Substantial differences in intestinal microbial community composition and diversity were observed between the two groups of pen-raised salmon, which, in addition to geographical separation, were raised on different feeds. The microbial profiles found in this study were substantially different from those indicated in earlier culture-based studies for several species of fish, presumably because of the culture-independent techniques employed. Further, analysis of short-chain fatty acids in the digestive tract indicated that the decreasing redox gradient from proximal to distal reaches common to homeothermic animals was absent in salmon, and that the bacterial fermentation levels were much lower than are reported in homeothermic animals.}, }
@article {pmid12071981, year = {2002}, author = {Krave, AS and Lin, B and Braster, M and Laverman, AM and van Straalen, NM and Röling, WF and van Verseveld, HW}, title = {Stratification and seasonal stability of diverse bacterial communities in a Pinus merkusii (pine) forest soil in central Java, Indonesia.}, journal = {Environmental microbiology}, volume = {4}, number = {6}, pages = {361-373}, doi = {10.1046/j.1462-2920.2002.00304.x}, pmid = {12071981}, issn = {1462-2912}, mesh = {Bacteria/*classification/genetics/metabolism ; *Ecosystem ; Electrophoresis ; Indonesia ; Phylogeny ; *Pinus ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics/metabolism ; *Seasons ; *Soil Microbiology ; }, abstract = {In Java, Indonesia, many nutrient-poor soils are intensively reforested with Pinus merkusii (pine). Information on nutrient cycles and microorganisms involved in these cycles will benefit the management of these important forests. Here, seasonal effects on the stratification of bacterial community structure in the soil profile of a tropical pine forest are described, and differences in bacterial communities are related to chemical and physical soil parameters. Culture-independent community profiles of litter, fragmented litter and mineral soil layers were made by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA-specific polymerase chain reaction (PCR) fragments. The community profiles of the different soil layers clustered separately, correlating with significant differences in organic matter content between the three layers. The bacterial communities appeared to be stable during the wet season of 1998. The drought in 1997, caused by the El Niño climatic effect, did not influence the bacterial communities in fragmentation and mineral soil, although moisture content and other soil parameters were markedly lower than in the wet season. However, communities in litter were influenced by drought. In the litter layer, the moisture content was significantly lower than in the fragmentation and mineral layers during the dry season. A clone library was made from a litter sample taken during the wet season. Partial sequencing of 74 clones and linking the DGGE banding positions of these clones to bands in the DGGE profile of the sample from which the clone library was derived showed considerable bacterial diversity. Alpha-proteobacteria (40.5% of the clones, of which 57% belonged to the Rhizobium-Agrobacterium group) and high-G+C content, Gram-positive bacteria (36.5%) dominated the clone library.}, }
@article {pmid12071980, year = {2002}, author = {Benlloch, S and López-López, A and Casamayor, EO and Øvreås, L and Goddard, V and Daae, FL and Smerdon, G and Massana, R and Joint, I and Thingstad, F and Pedrós-Alió, C and Rodríguez-Valera, F}, title = {Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern.}, journal = {Environmental microbiology}, volume = {4}, number = {6}, pages = {349-360}, doi = {10.1046/j.1462-2920.2002.00306.x}, pmid = {12071980}, issn = {1462-2912}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; *Ecosystem ; Electrophoresis ; Gene Library ; *Genetic Variation ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; *Sodium Chloride ; Water Microbiology ; }, abstract = {Bacterial and archaeal assemblages have been studied in a multipond solar saltern using a range of microbial ecology techniques by four laboratories simultaneously. These include 16S rDNA sequencing from both denaturing gradient gel electrophoresis (DGGE) and clone libraries, and culturing methods. Water samples from eight ponds were analysed, covering a salinity range from near sea water (4% salt) to saturated sodium chloride (37% salt; ponds called crystallizers). Clone libraries focused on ponds with salinity of 8%, 22% and 32%. Although different cloning strategies were able to retrieve the same type of dominant sequences, there were differing degrees of success with less abundant sequences. Thus, the use of two sets of primers recovered a higher number of phylotypes. Bacterial and archaeal isolates were, however, different from any of the retrieved environmental sequences. For Bacteria, most sequences in the 8% salt pond were related to organisms of marine origin. Thus, representatives of the alpha-, beta-, gamma- and epsilon-subdivisions of Proteobacteria, the Cytophaga-Flavobacterium-Bacteroides group (CFB), high-G+C Gram-positive bacteria and cyanobacteria were found. In the 22% salt pond, alpha- and gamma-Proteobacteria, cyanobacteria and CFB were the only groups found, and most of them were related to specialized halophilic bacteria. From the 32% salt pond, only CFB were found, and most of the sequences retrieved clustered with Salinibacter ruber, an extremely halophilic bacterium. A decrease in the richness of bacterial genera was therefore apparent along the gradient. Archaea behaved quite similarly. In the lowest salinity ponds, sequences were related to environmental clones of Marine Archaea Group III (Thermoplasmales relatives) and to unclassified branches of Euryarchaeaota. In the 8%, 22% and 32% ponds, most of the clones were related to different cultured strains of Halobacteriaceae. Finally, most sequences from the crystallizers clustered with the uncultured square archaeon SPhT. Crenarchaeaota were not detected. Despite the fact that higher prokaryotic richness was apparent in the lower salinity ponds than in the crystallizers, the diversity index from clone libraries calculated according to Shannon and Weaver did not show this trend. This was because diversity in the crystallizers can be considered as 'microdiversity', the co-existence of several closely related clones of Bacteria (the S. ruber cluster) and Archaea (the SPhT cluster). Regardless of the changes in abundance, both Bacteria and Archaea showed the same pattern; as salinity increased, the number of different clusters decreased, and only one cluster became dominant. Both clusters, however, showed a considerable degree of microdiversity. The meaning of such microdiversity remains to be determined.}, }
@article {pmid12071977, year = {2002}, author = {Rosenberg, E and Ben-Haim, Y}, title = {Microbial diseases of corals and global warming.}, journal = {Environmental microbiology}, volume = {4}, number = {6}, pages = {318-326}, doi = {10.1046/j.1462-2920.2002.00302.x}, pmid = {12071977}, issn = {1462-2912}, mesh = {Animals ; *Bacteria ; Bacterial Physiological Phenomena ; Cnidaria/cytology/*microbiology/physiology ; *Fungi ; *Greenhouse Effect ; Seawater ; Symbiosis ; Temperature ; }, abstract = {Coral bleaching and other diseases of corals have increased dramatically during the last few decades. As outbreaks of these diseases are highly correlated with increased sea-water temperature, one of the consequences of global warming will probably be mass destruction of coral reefs. The causative agent(s) of a few of these diseases have been reported: bleaching of Oculina patagonica by Vibrio shiloi; black band disease by a microbial consortium; sea-fan disease (aspergillosis) by Aspergillus sydowii; and coral white plague possibly by Sphingomonas sp. In addition, we have recently discovered that Vibrio coralyticus is the aetiological agent for bleaching the coral Pocillopora damicornis in the Red Sea. In the case of coral bleaching by V. shiloi, the major effect of increasing temperature is the expression of virulence genes by the pathogen. At high summer sea-water temperatures, V. shiloi produces an adhesin that allows it to adhere to a beta-galactoside-containing receptor in the coral mucus, penetrate into the coral epidermis, multiply intracellularly, differentiate into a viable-but-not-culturable (VBNC) state and produce toxins that inhibit photosynthesis and lyse the symbiotic zooxanthellae. In black band disease, sulphide is produced at the coral-microbial biofilm interface, which is probably responsible for tissue death. Reports of newly emerging coral diseases and the lack of epidemiological and biochemical information on the known diseases indicate that this will become a fertile area of research in the interface between microbial ecology and infectious disease.}, }
@article {pmid12064734, year = {2002}, author = {Tsekova, K and Todorova, D}, title = {Copper (II) accumulation and superoxide dismutase activity during growth of Aspergillus niger B-77.}, journal = {Zeitschrift fur Naturforschung. C, Journal of biosciences}, volume = {57}, number = {3-4}, pages = {319-322}, doi = {10.1515/znc-2002-3-421}, pmid = {12064734}, issn = {0939-5075}, mesh = {Aspergillus niger/drug effects/growth &amp; development/*metabolism ; Copper/*metabolism/pharmacology ; Culture Media ; Kinetics ; Superoxide Dismutase/*metabolism ; }, abstract = {The influence of copper (II) ions on the growth, accumulation properties and superoxide dismutase (SOD) activity of a growing culture of Aspergillus niger B-77 were studied. Microbial growth, the level of copper (II) accumulation and SOD activity depended on the initial copper (II) concentration. Aspergillus niger is able to accumulate large amounts of copper (II) from the nutrient medium with 200 mg x l(-1) copper (II) ions without loosing its biological activities. Addition of copper (II) ions increased the SOD activity in the growing cell cultures. The changes in enzyme activity induced by heavy metal ions might be used as an indicator of intracellular oxy-intermediate generation in a cell culture growing under stress conditions.}, }
@article {pmid12064534, year = {2002}, author = {Roels, J and Van Langenhove, H and Verstraete, W}, title = {Determination of phosphine in biogas and sludge at ppt-levels with gas chromatography-thermionic specific detection.}, journal = {Journal of chromatography. A}, volume = {952}, number = {1-2}, pages = {229-237}, doi = {10.1016/s0021-9673(02)00084-5}, pmid = {12064534}, issn = {0021-9673}, mesh = {Chromatography, Gas/*methods ; Phosphines/*analysis ; Sensitivity and Specificity ; Sewage/*chemistry ; }, abstract = {A gas chromatographic (GC) system to measure free phosphine in biogas and matrix bound phosphine in manure and sludge is presented. The system consists of a sample preconcentration trap filled with glass beads, connected with a capillary GC equipped with a thermionic specific detector. With a trap temperature as low as -155 degrees C, a sampling flow of 20 ml/min and a typical total sample volume of 100 ml, free phosphine concentrations in the low ng/m3 range and matrix bound phosphine in the low ng/kg dry matter range, can be accurately and reproducibly determined.}, }
@article {pmid12060962, year = {2002}, author = {Enwonwu, CO and Phillips, RS and Falkler, WA}, title = {Nutrition and oral infectious diseases: state of the science.}, journal = {Compendium of continuing education in dentistry (Jamesburg, N.J. : 1995)}, volume = {23}, number = {5}, pages = {431-4, 436, 438 passim; quiz 448}, pmid = {12060962}, issn = {1548-8578}, support = {D43TW00907A/TW/FIC NIH HHS/United States ; }, mesh = {Acute-Phase Proteins/physiology ; Bacteria, Anaerobic/pathogenicity ; Cytokines/physiology ; Gingivitis, Necrotizing Ulcerative/etiology ; Gram-Negative Bacterial Infections/etiology/*immunology/microbiology ; Herpesviridae Infections/etiology/immunology ; Humans ; *Immunocompromised Host ; Mouth Diseases/*etiology/*immunology/microbiology ; Nutrition Disorders/*complications/immunology ; Periodontitis/etiology/immunology/microbiology ; }, abstract = {Immunological competence and nutritional status are two of the most important determinants of morbidity and mortality. Oral diseases, particularly inflammatory periodontal lesions, are caused by viruses and specific periodontopathic bacteria. Paradoxically, the production of cytokines and oxidant molecules, which are supposed to be part of a highly effective mechanism for combating the periodontal pathogens, may damage the host. Malnutrition consistently impairs innate and adaptive defenses of the host, including phagocytic function, cell-mediated immunity, complement system, secretory antibody, and cytokine production and function. In protein-energy malnutrition, there are marked changes in the oral microbial ecology resulting in a preponderance of pathogenic anaerobic organisms, increased propensity of bacteria to bind to oral mucosal cells, attenuation of acute phase protein response, and dysfunction of the cytokine system. Cellular depletion of antioxidant nutrients promotes immunosuppression, accelerated replication rate of ribonucleic acid viruses, and increased disease progression. Therefore, malnutrition can intensify the severity of oral infections and may lead to their evolution into life-threatening diseases.}, }
@article {pmid12060864, year = {2002}, author = {Boelen, P and Post, AF and Veldhuis, MJ and Buma, AG}, title = {Diel patterns of UVBR-induced DNA damage in picoplankton size fractions from the Gulf of Aqaba, Red Sea.}, journal = {Microbial ecology}, volume = {44}, number = {2}, pages = {164-174}, doi = {10.1007/s00248-002-1002-7}, pmid = {12060864}, issn = {0095-3628}, mesh = {Antibodies/analysis ; Bacteria/*genetics ; *DNA Damage ; DNA Repair ; Environmental Monitoring ; Indian Ocean ; Particle Size ; Periodicity ; Phytoplankton/*genetics ; Population Dynamics ; Pyrimidine Dimers/*analysis ; Ultraviolet Rays/*adverse effects ; }, abstract = {This study focuses on the impact of natural levels of UVBR (ultraviolet-B radiation: 280 to 315 nm) on bacterio- and phytoplankton (<10 microm) from the Gulf of Aqaba, Red Sea. Incident biologically effective doses (BEDs) and attenuation of biologically effective radiation in the water column were measured using a DNA biodosimeter. UVBR-induced DNA damage was measured as cyclobutane pyrimidine dimers (CPDs), using an antibody directed to CPDs followed by chemiluminescent detection. Depth profiles of DNA damage were determined in two plankton size fractions (0.2 to 0.8 microm and 0.8 to 10 microm) collected down to 50 m depth. Furthermore, accumulation and removal of CPDs were monitored in surface plankton samples during several daily cycles. Small plankton (plankton <10 microm) composition was determined by flow cytometry. The plankton community in the Gulf of Aqaba was dominated by nonphototrophic bacteria and the free-living prochlorophyte Prochlorococcus spp. (<0.8 microm). In general, no DNA damage could be detected in dosimeter DNA below 15 m. In contrast, DNA damage (up to 124 CPD Mnucl-1) could be detected in all bacterio- and phytoplankton samples. DNA damage accumulated throughout the day, indicating that plankton in the Gulf of Aqaba undergo UVBR stress via CPD induction. Although the numbers of CPDs decreased during darkness, both size fractions showed some residual DNA damage at the end of the night. This suggests that dark repair processes did not remove all CPDs, or that part of the plankton community was incapable of repair at all. CPD levels in the two size fractions showed no significant differences in situ. During full solar radiation exposures (samples incubated in bags), more CPDs were detected in the smaller (0.2 to 0.8 microm) size fraction as compared to the larger (0.8 to 10 microm) size fraction. In these experiments, initial plankton composition was significantly different from the field samples. This implies that a shift in the population structure or irradiance conditions can lead to a significant change in UVBR sensitivity. In conclusion, the results show that the picoplankton-dominated phyto- and bacterioplankton communities in the clear surface waters from the Gulf of Aqaba undergo UVBR stress. Repair pathways are not sufficient to eliminate damage during or after UVBR exposure hours, suggesting photomortality as a potential loss parameter of the plankton community.}, }
@article {pmid12060863, year = {2002}, author = {Delille, D and Delille, B and Pelletier, E}, title = {Effectiveness of bioremediation of crude oil contaminated subantarctic intertidal sediment: the microbial response.}, journal = {Microbial ecology}, volume = {44}, number = {2}, pages = {118-126}, doi = {10.1007/s00248-001-1047-z}, pmid = {12060863}, issn = {0095-3628}, mesh = {Animals ; Bacteria ; Biodegradation, Environmental ; Fertilizers ; Fishes ; Geologic Sediments/*chemistry ; Hydrocarbons/metabolism ; Petroleum/*metabolism/toxicity ; Population Dynamics ; Refuse Disposal ; Toxicity Tests ; Vibrio ; }, abstract = {A field study was initiated in February 1996 in a remote sandy beach of The Grande Terre (Kerguelen Archipelago, 69 degrees 42 degrees E, 49 degrees 19 degrees S) with the objective of determining the long-term effects of some bioremediation agents on the biodegradation rate and the toxicity of oil residues under severe subantarctic conditions. A series of 10 experimental plots were settled firmly into sediment. Each plot received 2L of Arabian light crude oil and some of them were treated with bioremediation agents: slow release fertilizer Inipol EAP-22 (Elf Atochem) or fish composts. Plots were sampled on a regular basis over a 3-year period. A two-order of magnitude increase of saprophytic and hydrocarbon-utilizing microorganisms occurred during the first month of the experiment in all treated enclosures, but no clear differences appeared between the plots. Very high microbial populations were present during the experiment. Biodegradation within treated spots was faster than within the untreated ones and appeared almost complete after 6 months as indicated by the degradation index of aliphatic hydrocarbons within all plots. The analysis of interstitial water collected below the oily residues presented no toxicity. However, a high toxicity signal, using Microtox solid phase, appeared for all oiled sand samples with a noticeable reduction with time even if the toxicity signal remained present and strong after 311 days of oil exposition. As a conclusion, it is clear that the microbial response was rapid and efficient in spite of the severe weather conditions, and the rate of degradation was improved in presence of bioremediation agents. However, the remaining residues had a relatively high toxicity.}, }
@article {pmid12057679, year = {2002}, author = {Leveau, JH and Lindow, SE}, title = {Bioreporters in microbial ecology.}, journal = {Current opinion in microbiology}, volume = {5}, number = {3}, pages = {259-265}, doi = {10.1016/s1369-5274(02)00321-1}, pmid = {12057679}, issn = {1369-5274}, mesh = {Bacteria/*genetics ; *Ecology ; *Environmental Microbiology ; Genes, Reporter/*physiology ; }, abstract = {Bioreporters are effective research tools for gaining an understanding of a microbe's perception of the world. Fitted with a fusion of an environmentally responsive promoter to a suitable reporter gene, a bacterial or fungal bioreporter is able to communicate its metabolic or transcriptional behavior in a habitat, and furnish us with information on the chemical, physical or biological properties of its immediate surroundings. This review details recent developments in the use of such bioreporters in microbial ecology. Emphasis is placed on reporter genes that allow detection in individual microbial cells, as they provide a high-resolution description of the habitat under investigation. In an outlook on the future of bioreporter technology, this review stresses the need to interpret the activity of a bioreporter within the context of its biology.}, }
@article {pmid12057676, year = {2002}, author = {Torsvik, V and Øvreås, L}, title = {Microbial diversity and function in soil: from genes to ecosystems.}, journal = {Current opinion in microbiology}, volume = {5}, number = {3}, pages = {240-245}, doi = {10.1016/s1369-5274(02)00324-7}, pmid = {12057676}, issn = {1369-5274}, mesh = {Bacteria/*genetics ; *Ecosystem ; Genes, Bacterial ; *Genetic Variation ; *Soil Microbiology ; }, abstract = {Soils sustain an immense diversity of microbes, which, to a large extent, remains unexplored. A range of novel methods, most of which are based on rRNA and rDNA analyses, have uncovered part of the soil microbial diversity. The next step in the era of microbial ecology is to extract genomic, evolutionary and functional information from bacterial artificial chromosome libraries of the soil community genomes (the metagenome). Sophisticated analyses that apply molecular phylogenetics, DNA microarrays, functional genomics and in situ activity measurements will provide huge amounts of new data, potentially increasing our understanding of the structure and function of soil microbial ecosystems, and the interactions that occur within them. This review summarizes the recent progress in studies of soil microbial communities with focus on novel methods and approaches that provide new insight into the relationship between phylogenetic and functional diversity.}, }
@article {pmid12051650, year = {2001}, author = {Yadav, JS and Lawrence, DL and Nuck, BA and Federle, TW and Reddy, CA}, title = {Biotransformation of linear alkylbenzene sulfonate (LAS) by Phanerochaete chrysosporium: oxidation of alkyl side-chain.}, journal = {Biodegradation}, volume = {12}, number = {6}, pages = {443-453}, doi = {10.1023/a:1015056530264}, pmid = {12051650}, issn = {0923-9820}, mesh = {Biotransformation ; Oxidation-Reduction ; Phanerochaete/*metabolism ; Spectrometry, Mass, Electrospray Ionization ; Sulfonic Acids/*metabolism ; }, abstract = {The white rot fungus Phanerochaete chrysosporium, which generally mineralizes substituted aromatics to CO2, transformed linear alkylbenzene sulfonate (LAS) surfactants mainly at their alkyl side chain. Degradation of LAS was evidenced by a zone of clearing on LAS-containing agar plates and colorimetric analysis of liquid cultures. Disappearance of LAS was virtually complete within 10 days in low nitrogen (2.4 mM N), high nitrogen (24 mM N) and malt extract (ME) liquid media. After 5 days of incubation in ME medium, transformation of LAS was complete at concentrations < or = 4 mg l(-1), but decreased at higher concentrations. The LAS degradation was not dependent on lignin peroxidases (LiPs) and manganese-dependent peroxidases (MnPs). Mineralization of 14C-ring-LAS to 14CO2 by P. chrysosporium was < 1% regardless of the culture conditions used. Thin layer chromatography and mass spectral analyses indicated that P. chrysosporium transformed LAS to sulfophenyl carboxylates (SPCs) through oxidative shortening of the alkyl side-chains. While LAS disappearance in the cultures was not dependent on LiPs and MnPs, transformation of the parent LAS moieties to SPCs was more extensive in low N medium that favors expression of these enzymes. The SPCs produced in LN cultures were shorter in chain- length than those produced in ME cultures. Also there was a notable shift in the relative abundance of odd and even chain length metabolites compared to the starting LAS particularly in the low N cultures suggesting the possible involvement of processes other than or in addition to beta-oxidation in the chain-shortening process.}, }
@article {pmid12051567, year = {2001}, author = {López-Cortés, A and García-Pichel, F and Nübel, U and Vázquez-Juárez, R}, title = {Cyanobacterial diversity in extreme environments in Baja California, Mexico: a polyphasic study.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {4}, number = {4}, pages = {227-236}, doi = {10.1007/s10123-001-0042-z}, pmid = {12051567}, issn = {1139-6709}, mesh = {Animals ; Cyanobacteria/*classification/genetics ; Decapoda ; Ecosystem ; *Environmental Microbiology ; Fresh Water ; Mexico ; Molecular Sequence Data ; Oceans and Seas ; Phylogeny ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Cyanobacterial diversity from two geographical areas of Baja California Sur, Mexico, were studied: Bahia Concepcion, and Ensenada de Aripez. The sites included hypersaline ecosystems, sea bottom, hydrothermal springs, and a shrimp farm. In this report we describe four new morphotypes, two are marine epilithic from Bahia Concepcion, Dermocarpa sp. and Hyella sp. The third, Geitlerinema sp., occurs in thermal springs and in shrimp ponds, and the fourth, Tychonema sp., is from a shrimp pond. The partial sequences of the 16S rRNA genes and the phylogenetic relationship of four cyanobacterial strains (Synechococcus cf. elongatus, Leptolyngbya cf. thermalis, Leptolyngbya sp., and Geitlerinema sp.) are also presented. Polyphasic studies that include the combination of light microscopy, cultures and the comparative analysis of 16S rRNA gene sequences provide the most powerful approach currently available to establish the diversity of these oxygenic photosynthetic microorganisms in culture and in nature.}, }
@article {pmid12043004, year = {2002}, author = {}, title = {Erratum.}, journal = {Microbial ecology}, volume = {43}, number = {4}, pages = {482}, doi = {10.1007/s00248-002-0010-7}, pmid = {12043004}, issn = {1432-184X}, }
@article {pmid12043003, year = {2002}, author = {Lau, WW and Jumars, PA and Armbrust, EV}, title = {Genetic diversity of attached bacteria in the hindgut of the deposit-feeding shrimp Neotrypaea (formerly Callianassa) californiensis (decapoda: thalassinidae).}, journal = {Microbial ecology}, volume = {43}, number = {4}, pages = {455-466}, doi = {10.1007/s00248-001-1043-3}, pmid = {12043003}, issn = {0095-3628}, mesh = {Animals ; Bacteria/*genetics/*isolation &amp; purification ; DNA, Ribosomal/genetics ; Decapoda/*microbiology ; Diet ; Digestive System/microbiology ; Genes, Bacterial/genetics ; Genetic Variation ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbial colonization of marine invertebrate guts is widespread, but in general the roles that these bacteria play in the nutrition of their hosts are unknown. To examine the diversity and potential nutritional roles of hindgut microbiota in a deposit feeder, PCR-amplified 16S rRNA genes were cloned from the bacterial community attached to the hindguts of the thalassinid shrimp Neotrypaea californiensis exposed to different feeding treatments. Partial 16S rDNA sequences were analyzed for 30 clones for three shrimp per treatment for a total of 270 clones. No effects of host starvation or high-protein diets were apparent on hindgut bacterial community composition. Diversity analyses indicated high variability between bacterial communities in individual shrimp hindguts, but partial 16S rDNA sequences revealed remarkable species-level similarity (>98%) within clusters of sequences from the different shrimp hindguts, and many sequences from different shrimp hindguts were identical. Sequences belonged to three main groups of bacteria: Cytophaga-Flavobacteria-Bacteroides (CFB), proteobacteria, and gram-positives. Of the 270 sequences, 40% belonged to the alpha-proteobacteria, > or = 5% each to the gamma- and epsilon -proteobacteria, and > or =20% each to the gram-positive and CFB groups. All except one sequence are novel with < or = 95% sequence similarity to known genes. Despite weak similarity to known taxa,about 75% of the sequences were most closely related to known symbiotic and sedimentary bacteria. The bacteria in shrimp hindguts represent new species that have not yet been en-countered in other environments, and gut environments may be a rich source of the difficult-to-culture and novel components of marine bacterial diversity.}, }
@article {pmid12043002, year = {2002}, author = {Moisander, PH and McClinton, E and Paerl, HW}, title = {Salinity effects on growth, photosynthetic parameters, and nitrogenase activity in estuarine planktonic cyanobacteria.}, journal = {Microbial ecology}, volume = {43}, number = {4}, pages = {432-442}, doi = {10.1007/s00248-001-1044-2}, pmid = {12043002}, issn = {0095-3628}, mesh = {Adaptation, Physiological ; Animals ; Carbon Dioxide/metabolism ; Cyanobacteria/*drug effects/enzymology/*growth &amp; development/metabolism ; Fresh Water/*chemistry ; Nitrogen Fixation/drug effects ; Nitrogenase/*metabolism ; Photosynthesis/*drug effects ; Plankton/drug effects/*microbiology ; Seawater/chemistry ; Sodium Chloride/*pharmacology ; Time Factors ; Water Microbiology ; }, abstract = {Salinity has been suggested as being a controlling factor for blooms of N2-fixing cyanobacteria in estuaries. We tested the effect of salinity on the growth, N2 fixation, and photosynthetic activities of estuarine and freshwater isolates of heterocystous bloom-forming cyanobacteria. Anabaena aphanizomenoides and Anabaenopsis sp. were isolated from the Neuse River Estuary, North Carolina, and Cylindrospermopsis raciborskii from Lakes Dora and Griffin, central Florida. Salinity tolerance of these cyanobacteria was compared with that of two Nodularia strains from the Baltic Sea. We measured growth rates, N2 fixation (nitrogenase activity), and CO2 fixation at salinities between 0 and 20 g L(-1) NaCl. We also examined photosynthesis-irradiance relation-ships in response to salinity. Anabaenopsis maintained similar growth rates in the full range of salinities from 2 to 20 g L(-1) NaCl. Anabaena grew at up to 15 g L-', but the maximum salinity 20 g L(-1) NaCl was inhibitory. The upper limit for salinity tolerance of Cylindrospermopsis was 4 g L(-1) NaCl. Nodularia spp. maintained similar growth rates in the full range of salinities from 0 to 20 g L(-1) . Between 0 and 10 g L(-1), the growth rate of Nodularia spumigena was slower than that of the Neuse Estuary strains. In most strains, the sensitivity of nitrogenase activity and CO2 fixation to salinity appeared similar. Anabaenopsis, Anabaena, and the two Nodularia strains rapidly responded to NaCl by increasing their maximum photosynthetic rates (Pmn). Overall, both Neuse River Estuary and Baltic Sea strains showed an ability to acclimate to salt stress over short-(24 h) and long-term (several days to weeks) exposures. The study suggested that direct effect of salinity (as NaCl in these experiments) on cyanobacterial physiology does not alone explain the low frequency and magnitude of blooms of N2-fixing cyanobacteria in estuaries.}, }
@article {pmid12043001, year = {2002}, author = {Steinberger, RE and Allen, AR and Hansa, HG and Holden, PA}, title = {Elongation correlates with nutrient deprivation in Pseudomonas aeruginosa-unsaturates biofilms.}, journal = {Microbial ecology}, volume = {43}, number = {4}, pages = {416-423}, doi = {10.1007/s00248-001-1063-z}, pmid = {12043001}, issn = {0095-3628}, mesh = {Adaptation, Biological ; Biofilms/*growth &amp; development ; Culture Media ; Diffusion ; Microscopy, Atomic Force ; Pseudomonas aeruginosa/cytology/*growth &amp; development/*metabolism ; }, abstract = {Bacteria in nature frequently grow as biofilms, yet little is known regarding how biofilm bacteria morphologically adapt to low nutrient availability, which is common in unsaturated environments such as the terrestrial subsurface or on plant leaves. For unsaturated biofilms, in which the substratum may provide all nutrients, what are the relationships between nutrition and cell size and shape-the simplest metrics of cellular morphology? To address this question, we cultured Pseudomonas aeruginosa, a ubiquitous gram-negative bacterium that is environmentally and medically important, on membranes overlaying solid media, and then measured cellular dimensions using atomic force microscopy (AFM). Nutrition was controlled chemically by media composition and physically by stacking membranes to increase the path length for nutrient diffusion. Under conditions of carbon-nitrogen imbalance, low carbon bioavailability, or increased nutrient diffusional path length, cells elongated while maintaining constant width. A mathematical relationship suggests that, by elongating, biofilm bacteria strategically enlarge their nutrient collection surface without substantially changing the ratio of surface area to volume (SA/V). We conclude that P. aeruginosa growing as unsaturated biofilm with a planar nutrient source morphologically adapt to starvation by elongating. This adaptation, if generalizable, differs from a better-understood starvation response (i.e., cell size decreases; thus SA/V in-creases) for planktonic bacteria in well-mixed environments.}, }
@article {pmid12043000, year = {2002}, author = {West, AE and Schimdt, SK}, title = {Endogenous methanogenesis stimulates oxidation of atmospheric CH(4) in alpine tundra soil.}, journal = {Microbial ecology}, volume = {43}, number = {4}, pages = {408-415}, doi = {10.1007/s00248-001-1049-x}, pmid = {12043000}, issn = {0095-3628}, mesh = {Aerobiosis ; Anaerobiosis ; Atmosphere/*chemistry ; Bacteria/drug effects/*metabolism ; Carbon Dioxide/pharmacology ; Hydrogen/pharmacology ; Methane/*metabolism ; Oxidation-Reduction/drug effects ; Pteridines/pharmacology ; Soil/*analysis ; *Soil Microbiology ; Time Factors ; }, abstract = {Experiments were done to test the hypothesis that atmospheric CH(4) oxidizers in a well-drained alpine tundra soil are supported by CH(4) production from anaerobic microsites in the soil. Soil was subjected to 22 days of anaerobic conditions with elevated H(2) and CO(2) in order to stimulate methanogenesis. This treatment stimulated subsequent atmospheric CH(4) consumption, probably by increasing soil methanogenesis. After removal from anaerobic conditions, soils emitted CH(4) for up to 6 h, then oxidized atmospheric CH(4) at 111 (+/- 5.7) pmol (g dry weight)(-1) h(-1), which was more than 3 times the rate of control soils. Further supporting our hypothesis, additions of lumazine, a highly specific inhibitor of methanogenesis, prevented the stimulation of atmospheric CH(4) oxidation by the anaerobic treatment. The method used to create anaerobic conditions with elevated H(2) and CO(2) also elevated headspace CH(4) concentrations. However, elevated CH(4) concentrations under aerobic conditions did not stimulate CH(4) oxidation as much as preexposure to H(2) and CO(2) under anaerobic conditions. Anaerobic conditions created by N(2) flushing did not stimulate atmospheric CH4 oxidation, probably because N2 flushing inhibited methanogenesis by removing necessary precursors for methane production. We conclude that anaerobic conditions with elevated H(2) and CO(2) stimulate atmospheric CH(4) oxidation in this dry alpine tundra soil by increasing endogenous CH(4) production. This effect was prevented by inhibiting methanogenesis, indicating the importance of endogenous CH(4) production in a CH(4-) consuming soil.}, }
@article {pmid12039764, year = {2002}, author = {Banasaz, M and Norin, E and Holma, R and Midtvedt, T}, title = {Increased enterocyte production in gnotobiotic rats mono-associated with Lactobacillus rhamnosus GG.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {6}, pages = {3031-3034}, pmid = {12039764}, issn = {0099-2240}, mesh = {Animals ; Cecum/cytology/physiology ; Colon/cytology/physiology ; Enterocytes/*physiology ; *Germ-Free Life ; Ileum/cytology/physiology ; Jejunum/cytology/physiology ; Lactobacillus/*physiology ; Male ; Rats ; }, abstract = {There is increasing scientific and commercial interest in using beneficial microorganisms (i.e., probiotics) to enhance intestinal health. Of the numerous microbial strains examined, Lactobacillus rhamnosus GG has been most extensively studied. Daily intake of L. rhamnosus GG shortens the course of rotavirus infection by mechanisms that have not been fully elucidated. Comparative studies with germfree and conventional rats have shown that the microbial status of an animal influences the intestinal cell kinetics and morphology. The present study was undertaken to study whether establishment of L. rhamnosus GG as a mono-associate in germfree rats influences intestinal cell kinetics and morphology. L. rhamnosus GG was easily established in germfree rats. After 3 days of mono-association, the rate of mitoses in the upper part of the small intestine (jejunum 1) increased as much as 14 and 22% compared to the rates in germfree and conventional counterparts, respectively. The most striking alteration in morphology was an increase in the number of cells in the villi. We hypothesis that the compartmentalized effects of L. rhamnosus GG may represent a reparative event for the mucosa.}, }
@article {pmid12039745, year = {2002}, author = {Barrangou, R and Yoon, SS and Breidt, F and Fleming, HP and Klaenhammer, TR}, title = {Identification and characterization of Leuconostoc fallax strains isolated from an industrial sauerkraut fermentation.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {6}, pages = {2877-2884}, pmid = {12039745}, issn = {0099-2240}, mesh = {Brassica/*microbiology ; Cell Culture Techniques ; DNA, Intergenic/analysis ; Fermentation ; Industry ; Leuconostoc/genetics/*isolation &amp; purification ; Plant Extracts ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*analysis/genetics ; Random Amplified Polymorphic DNA Technique ; }, abstract = {Lactic acid bacterial strains were isolated from brines sampled after 7 days of an industrial sauerkraut fermentation, and six strains were selected on the basis of susceptibility to bacteriophages. Bacterial growth in cabbage juice was monitored, and the fermentation end products were identified, quantified, and compared to those of Leuconostoc mesenteroides. Identification by biochemical fingerprinting, endonuclease digestion of the 16S-23S intergenic transcribed spacer region, and sequencing of variable regions V1 and V2 of the 16S rRNA gene indicated that the six selected sauerkraut isolates were Leuconostoc fallax strains. Random amplification of polymorphic DNA fingerprints indicated that the strains were distinct from one another. The growth and fermentation patterns of the L. fallax isolates were highly similar to those of L. mesenteroides. The final pH of cabbage juice fermentation was 3.6, and the main fermentation end products were lactic acid, acetic acid, and mannitol for both species. However, none of the L. fallax strains exhibited the malolactic reaction, which is characteristic of most L. mesenteroides strains. These results indicated that in addition to L. mesenteroides, a variety of L. fallax strains may be present in the heterofermentative stage of sauerkraut fermentation. The microbial ecology of sauerkraut fermentation appears to be more complex than previously indicated, and the prevalence and roles of L. fallax require further investigation.}, }
@article {pmid12039720, year = {2002}, author = {Johnsen, AR and Bendixen, K and Karlson, U}, title = {Detection of microbial growth on polycyclic aromatic hydrocarbons in microtiter plates by using the respiration indicator WST-1.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {6}, pages = {2683-2689}, pmid = {12039720}, issn = {0099-2240}, mesh = {Bacteria/growth &amp; development/*metabolism ; Carbon Radioisotopes ; Electrons ; Minerals ; Oxidation-Reduction ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Sodium Azide/chemistry ; Tetrazolium Salts/*chemistry ; }, abstract = {We have developed a microtiter plate method for screening a large number of bacterial isolates for the ability to grow on different crystalline polycyclic aromatic hydrocarbons (PAHs). Growth on PAHs cannot easily be determined with standard growth assays because of the very low aqueous solubility and bioavailability of the PAHs. Our microtiter plate assay utilizes a new water-soluble respiration indicator, WST-1 [4-[3-(4-iodophenyl)-2-(4-nitrophenyl)-2H-5-tetrazolio]-1,3-benzene disulfonate], in combination with easily degradable carbon sources. PAH-mineralizing strains were grown on PAHs in microtiter plates for 7 to 10 days. The tetrazolium dye WST-1 was added after incubation. Dehydrogenases in growing cells reduced WST-1 to a water-soluble colored formazan, and the intensity of the color was a measure of the respiration rate. Addition of easily degradable carbon to the wells along with WST-1 resulted in a 3- to 40-fold increase in the absorbance of positive wells within 90 min, which made it possible to detect growth on fluorene, phenanthrene, anthracene, fluoranthene, and pyrene. Addition of the electron transport blocker sodium azide unexpectedly decreased formazan formation. The method was adapted for most-probable-number enumeration of PAH degraders in soil.}, }
@article {pmid12037616, year = {2002}, author = {Lahav, R and Fareleira, P and Nejidat, A and Abeliovich, A}, title = {The identification and characterization of osmotolerant yeast isolates from chemical wastewater evaporation ponds.}, journal = {Microbial ecology}, volume = {43}, number = {3}, pages = {388-396}, doi = {10.1007/s00248-002-2001-4}, pmid = {12037616}, issn = {0095-3628}, mesh = {*Adaptation, Physiological ; Carbon/metabolism ; Chemical Industry ; DNA, Ribosomal/genetics ; Glycerol/analysis ; Hydrocarbons/metabolism ; Hydrogen-Ion Concentration ; Industrial Waste ; *Osmosis ; Pichia/genetics/isolation &amp; purification/*physiology ; Rhodotorula/genetics/isolation &amp; purification/*physiology ; Sodium Chloride ; *Waste Disposal, Fluid ; }, abstract = {Ramat Hovav is a major chemical industrial park manufacturing pharmaceuticals, pesticides, and various aliphatic and aromatic halogens. All wastewater streams are collected in large evaporation ponds. Salinity in the evaporation ponds fluctuates between 3% (w/v) and saturation and pH values range between 2.0 and 10.0. We looked for microorganisms surviving in these extreme environmental conditions and found that 2 yeast strains dominate this biotope. 18S rDNA sequence analysis identified the isolates as Pichia guilliermondii and Rhodotorula mucilaginosa. Both isolates grew in NaCl concentrations ranging up to 3.5 M and 2.5 M, respectively, and at a pH range of 2-10. There was a distinct difference between the Rhodotorula and Pichia strains and S. cerevisiae RS16 that served as a control strain with respect to accumulation of osmoregulators and internal ion concentrations when exposed to osmotic stress. The Pichia and Rhodotorula strains maintained high glycerol concentration also in media low in NaCl. Utilization of various carbon sources was examined. Using a tetrazolium-based assay we show that the Rhodotorula and Pichia strains are capable of utilizing a wide range of different carbon sources including anthracene, phenanthrene, and other cyclic aromatic hydrocarbons.}, }
@article {pmid12037615, year = {2002}, author = {Plugge, CM and Stams, AJ}, title = {Enrichment of thermophilic syntrophic anaerobic glutamate-degrading consortia using a dialysis membrane reactor.}, journal = {Microbial ecology}, volume = {43}, number = {3}, pages = {378-387}, doi = {10.1007/s00248-001-0047-3}, pmid = {12037615}, issn = {0095-3628}, mesh = {Bacteria, Anaerobic/*growth &amp; development/physiology ; Ecosystem ; Euryarchaeota ; Glutamic Acid/*biosynthesis ; *Membranes, Artificial ; Population Dynamics ; Water Microbiology ; }, abstract = {A dialysis cultivation system was used to enrich slow-growing moderately thermophilic anaerobic bacteria at high cell densities. Bicarbonate buffered mineral salts medium with 5 mM glutamate as the sole carbon and energy source was used and the incubation temperature was 55 degrees C. The reactor inoculum originated from anaerobic methanogenic granular sludge bed reactors. The microbial population was monitored over a period of 2 years using the most probable number (MPN) technique. In the reactor glutamate was readily degraded to ammonium, methane, and carbon dioxide. Cell numbers of glutamate-degrading organisms increased 400-fold over the first year. In medium supplemented with bromoethane sulfonic acid (BES, an inhibitor of methanogenesis), tenfold lower cell numbers were counted, indicating the syntrophic nature of glutamate degradation. After 2 years of reactor operation the predominant organisms were isolated and characterized. Methanobacterium thermoautotrophicum (strain R43) and a Methanosaeta thermophila strain (strain A) were the predominant hydrogenotrophic and acetoclastic methanogens, respectively. The numbers in which the organisms were present in the reactor after 24 months of incubation were 8.6 x 10(9) and 3.8 x 10(7) mL(-1) sludge, respectively. The most predominant glutamate-degrading organism (8.6 x 10(7) mL(-1) sludge), strain Z, was identified as a new species, Caloramator coolhaasii. It converted glutamate to hydrogen, acetate, some propionate, ammonium, and carbon dioxide. Growth of this syntrophic organism on glutamate was strongly enhanced by the presence of methanogens.}, }
@article {pmid12037614, year = {2002}, author = {Stief, P and De Beer, D and Neumann, D}, title = {Small-scale distribution of interstitial nitrite in freshwater sediment microcosms: the role of nitrate and oxygen availability, and sediment permeability.}, journal = {Microbial ecology}, volume = {43}, number = {3}, pages = {367-378}, doi = {10.1007/s00248-002-2008-x}, pmid = {12037614}, issn = {0095-3628}, mesh = {Biological Availability ; *Environmental Monitoring ; Geologic Sediments/*chemistry ; Nitrates/analysis ; Nitrites/*analysis ; Nitrogen/*metabolism ; Organic Chemicals/metabolism ; Oxygen/analysis ; Permeability ; *Water Microbiology ; }, abstract = {The spatial distribution of interstitial NO2(-) concentrations was studied in NO3(-)-exposed freshwater sediment microcosms, using pore water extractions as well as ion-selective microsensors. Porewater extractions revealed ecotoxicologically critical NO2(-) concentrations in hypoxic and anoxic sediment layers in which significant NO3(-) consumption took place. In contrast, the use of ion-selective microsensors demonstrated the high capacity of the thin oxic surface layer of the sediments to consume NO2(-) and to produce NO3(-). Two modes of NO3(-) supply to the sediments were compared: In treatments with NO3(-) supply to the overlying water, a subsurface maximum of NO2(-) concentration was observed, coinciding with the site of maximum NO3(-) consumption. When NO3(-) was perfused up through the sediment cores, however, NO2(-) accumulated throughout the entire sediment column. Such spatially extensive NO2(-) accumulations were only observed in sediments poor in organic matter with a relatively high permeability. By manipulating the O2 content of the overlying water, the release of NO2(-) from the sediments could be influenced: In treatments with air-saturated overlying water, the sediments did not release detectable amounts of NO2(-) into the water phase. When kept hypoxic (25% air saturation) instead, significant NO2(-) accumulations were recorded in the overlying water. These findings suggest that in treatments with air-saturated overlying water, NO2(-) that was produced in deeper sediment layers (denitrifying conditions) was completely consumed at the oxic sediment surface (nitrifying conditions) before it could reach the overlying water.}, }
@article {pmid12037613, year = {2002}, author = {Olsen, LM and Reinertsen, H and Vadstein, O}, title = {Can phosphorus limitation inhibit dissolved organic carbon consumption in aquatic microbial food webs? A study of three food web structures in microcosms.}, journal = {Microbial ecology}, volume = {43}, number = {3}, pages = {353-366}, doi = {10.1007/s00248-002-2009-9}, pmid = {12037613}, issn = {0095-3628}, mesh = {Animals ; Bacteria ; Carbon/*metabolism ; Eukaryota/*growth &amp; development ; Eutrophication ; *Food Chain ; Phosphorus/*analysis ; Population Dynamics ; *Water Microbiology ; }, abstract = {Microcosms with three different food web structures and phosphorus (P) limited growth medium were used to study the interactions between P and organic carbon (C) fractions in pelagic food webs. The cultures were run with low dilution to allow the biological processes to determine the outcome. A double isotope technique was used to follow the C and P compartments. In all systems the primary production was P limited. The measured P:C ratios and the observed accumulation of degradable dissolved organic carbon (DOC) indicated that the growth of heterotrophic bacteria was also P limited. The presence of neither algal grazers nor flagellates feeding on bacteria altered the limitation pattern. A net loss of P from the bacterial fraction was observed after the bloom. Different strategies for nutrient aquisition and growth are proposed as mechanisms enabling simultaneous P limitation of algae and bacteria, and a concomitant accumulation of degradable DOC. The ability of the algae to grow with low P:C ratio keeps the regeneration of P through grazers low enough to cause sustained P limitation of both algae and bacteria. The grazers were important producers of DOC when present. This implies that the usual assumption of carbon limited bacterial growth may lead to wrong conclusions regarding the dynamics of plankton communities and the DOC pool.}, }
@article {pmid12037612, year = {2002}, author = {Christaki, U and Courties, C and Karayanni, H and Giannakourou, A and Maravelias, C and Kormas, KA and Lebaron, P}, title = {Dynamic characteristics of Prochlorococcus and Synechococcus consumption by bacterivorous nanoflagellates.}, journal = {Microbial ecology}, volume = {43}, number = {3}, pages = {341-352}, doi = {10.1007/s00248-002-2002-3}, pmid = {12037612}, issn = {0095-3628}, mesh = {Animals ; *Cyanobacteria ; *Eating ; *Eukaryota ; Periodicity ; Population Dynamics ; Water Microbiology ; }, abstract = {We compared the characteristics of ingestion of Prochlorococcus and Synechococcus by the marine heterotrophic nanoflagellate Pseudobodo sp. and by a mixed nanoflagellate culture (around 3 microm in size) obtained from an open sea oligotrophic area. Maximum ingestion rate on Synechococcus (2.7 Syn flagellate(-1) h(-1)) was reached at concentrations of 5 x 10(5) Syn mL(-1) and decreased between 6 x 10(5) and 1.5 x 10(6) Syn mL(-1). In order to validate laboratory data, one set of data on Synechococcus grazing was obtained during a field study in the oligotrophic northeastern Mediterranean Sea. Ingestion rates by heterotrophic nanoflagellates were related to Synechococcus abundance in the water, and the feeding rate showed a clear diel rhythm with consumption being highest during the night, declining during the day hours, and being lowest at dusk. Ingestion rates on Prochlorococcus increased linearly for the whole range of prey density used (i.e., from 1 x 10(3) to 3 x 10(6) Proc mL(-1)), with maximum ingestion of 6.7 Proc flagellate(-1) h(-1). However, for prey concentrations in the range of 10(3)-10(5), which are usually encountered in aquatic systems, ingestion rates were significantly less than on Synechococcus. In our experiments, both Prochlorococcus and Synechococcus proved to be poor food items for support of nanoflagellate growth.}, }
@article {pmid12037611, year = {2002}, author = {Buchan, A and Newell, SY and Moreta, JI and Moran, MA}, title = {Analysis of internal transcribed spacer (ITS) regions of rRNA genes in fungal communities in a southeastern U.S. salt marsh.}, journal = {Microbial ecology}, volume = {43}, number = {3}, pages = {329-340}, doi = {10.1007/s00248-001-1062-0}, pmid = {12037611}, issn = {0095-3628}, mesh = {Ascomycota/*genetics/physiology ; Biological Assay ; *Ecosystem ; Poaceae/microbiology ; Polymorphism, Restriction Fragment Length ; *RNA Processing, Post-Transcriptional ; RNA, Ribosomal/*genetics ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {The ascomycete community colonizing decaying Spartina alterniflora blades in a southeastern U.S. salt marsh was characterized by analysis of internal transcribed spacer (ITS) regions of fungal rRNA genes. ITS sequences were amplified with ascomycete-specific primers from DNA extracted from S. alterniflora blades at two stages of decay (early and late) and were identified based on sequence analysis of a companion ascomycete culture collection. The S. alterniflora ITS libraries were dominated by clones from three species of ascomycetes: Mycosphaerella sp. 2, Phaeosphaeria spartinicola, and Phaeosphaeria halima. ITS sequences from five other less abundant ascomycete species were also found in the clone libraries, only two of which could be identified based on the culture collection, Hydropisphaera erubescens and a new species nicknamed '4clt'. Ascospore expulsion assays indicated dominance by the same three species as the ITS analysis, although this non-molecular approach differed from the molecular method in relative ranking of the dominant species and in characterization of minor species. Analysis of ITS amplicons from three replicate plots by terminal restriction fragment length polymorphism (T-RFLP) analysis showed significant spatial homogeneity in ascomycete community composition for both early- and late-stage decay. ITS sequence analysis identified morphologically cryptic subgroups for two of the three dominant salt marsh ascomycetes.}, }
@article {pmid12037610, year = {2002}, author = {Junge, K and Imhoff, F and Staley, T and Deming, JW}, title = {Phylogenetic diversity of numerically important Arctic sea-ice bacteria cultured at subzero temperature.}, journal = {Microbial ecology}, volume = {43}, number = {3}, pages = {315-328}, doi = {10.1007/s00248-001-1026-4}, pmid = {12037610}, issn = {0095-3628}, mesh = {Arctic Regions ; Biological Evolution ; Cytophaga/genetics/*isolation &amp; purification/physiology ; DNA, Bacterial/analysis ; *Ice ; *Phylogeny ; Population Dynamics ; Proteobacteria/genetics/*isolation &amp; purification/physiology ; RNA, Ribosomal, 16S/analysis ; Temperature ; *Water Microbiology ; }, abstract = {Heterotrophic bacteria in sea ice play a key role in carbon cycling, but little is known about the predominant players at the phylogenetic level. In a study of both algal bands and clear ice habitats within summertime Arctic pack ice from the Chukchi Sea, we determined the abundance of total bacteria and actively respiring cells in melted ice samples using epifluorescence microscopy and the stains 4', 6'-diamidino-2-phenylindole 2HCl (DAPI) and 5-cyano-2,3-ditolyl tetrazolium chloride (CTC), respectively. Organic-rich and -poor culturing media were used to determine culturable members by plating (at 0 degrees C and 5 degrees C) and most-probable-number (MPN) analyses (at -1 degrees C). Total bacterial counts ranged from 5.44 x 10(4) ml(-1) in clear ice to 2.41 x 10(6) ml(-1) in algal-band ice samples, with 2-27% metabolically active by CTC stain. Plating and MPN results revealed a high degree of culturability in both types of media, but greater success in oligotrophic media (to 62% of total abundance) and from clear ice samples. The bacterial enumeration anomaly, commonly held to mean <or= 0.01% cultured, was not demonstrated in any of our samples. Denaturing gradient gel electrophoresis was used to check the purity of 44 isolates and select representatives for subsequent sequencing. Phylogenetic analyses based on 16S rRNA sequences indicated close relationships exclusively to known marine psychrophiles within two bacterial divisions, Proteobacteria (in the genera Alteromonas, Colwellia, Glaciecola, Octadecabacter, Pseudoaltermonas and Shewanella) and Cytophaga-Flexibacter-Bacteroides (Cytophaga, Flavobacterium, Gelidibacter and Polaribacter). All cultures from the clear ice sample with highest (62%) culturability were closely related to each other or to psychrophilic Cytophaga-Flexibacter-Bacteroides (94.9-99.6% sequence similarities). Overall, these findings suggest limited, heterotrophic bacterial diversity at cold temperatures and may provide insight into the recent evolution of psychrophilic bacteria.}, }
@article {pmid12037609, year = {2002}, author = {Lipson, DA and Schadt, CW and Schmidt, SK}, title = {Changes in soil microbial community structure and function in an alpine dry meadow following spring snow melt.}, journal = {Microbial ecology}, volume = {43}, number = {3}, pages = {307-314}, doi = {10.1007/s00248-001-1057-x}, pmid = {12037609}, issn = {0095-3628}, mesh = {Biomass ; Cellulase/analysis/pharmacology ; DNA, Bacterial/analysis ; *Ecosystem ; *Environmental Monitoring ; Fungi ; Glycine/analysis ; Phenols/metabolism ; Plant Roots/microbiology ; Poaceae/microbiology ; Population Dynamics ; Seasons ; Snow ; *Soil Microbiology ; Temperature ; Water Movements ; }, abstract = {Previous work in an alpine dry meadow in the Front Range of the Rocky Mountains has shown that microbial biomass is high during winter and declines rapidly as snow melts in the spring, and that this decline is associated with changes in temperature regime and substrate availability. In this study we tested the hypothesis that the summer and winter microbial communities differ in function and composition. Shifts in species composition between pre- and post-snowmelt communities were detected using reciprocal hybridization of community DNA; DNA extracted from soils sampled at different times was significantly less homologous relative to spatial replicates sampled at the same time. Fungal/bacterial ratios, as measured by direct microscopic counts and by substrate-induced respiration experiments with specific inhibitors, were higher in winter soils. Specific activity of cellulase (absolute cellulase activity per unit microbial biomass C) was higher in the winter soils than in summer soils, while specific amylase activity was not different between winter and summer. Based on most-probable number measurements, the use of the phenolic compound vanillic acid was highest in the winter, while the use of the amino acid glycine was lowest in the winter. Winter and summer soil respiration responded differently to temperature; at 0 degrees C, winter soils respired at a higher proportion of the 22 degrees C rate than did summer soils.}, }
@article {pmid12037608, year = {2002}, author = {Johansen, JE and Binnerup, SJ}, title = {Contribution of cytophaga-like bacteria to the potential of turnover of carbon, nitrogen, and phosphorus by bacteria in the rhizosphere of barley (Hordeum vulgare L.).}, journal = {Microbial ecology}, volume = {43}, number = {3}, pages = {298-306}, doi = {10.1007/s00248-002-2006-z}, pmid = {12037608}, issn = {0095-3628}, mesh = {Carbon/*metabolism ; Classification ; Cytophaga/*physiology ; Enzyme Induction ; Hordeum/*microbiology ; Nitrogen/*metabolism ; Phosphorus/*metabolism ; Plant Roots/microbiology ; Population Dynamics ; Seasons ; Soil Microbiology ; }, abstract = {The functional potential of bacteria isolated from the rhizosphere of barley (Hordeum vulgare L.) in May, July, and August and cultivated on nutrient-rich substrate (1/10 TSBA) and nutrient-poor substrate (cold soil extract agar) was determined. There was no significant difference in numbers of CFU when counted on nutrient rich or poor substrate. Bacterial numbers increased approximately 3-fold in the rhizosphere soil from May to August but was unchanged in bulk soil over the same period. A total of 4474 randomly isolated bacteria were screened for enzymatic activities involved in carbon turnover (amylase, cellulase, mannanase, xylanase, and chitinase), nitrogen turnover (protease, nitrate and nitrite reductase), and phosphate turnover (phosphatase). In the rhizosphere soil, bacteria carrying C and P turnover enzymes were not stimulated by the growing plant whereas protease and nitrate and nitrite reductase were stimulated by the growing plant. No changes were observed in the bulk soil. Two taxonomic groups were followed: Cytophaga-like bacteria (CLB) and fluorescent pseudomonads, the latter being abundant in the rhizosphere and important contributors to the cycling of organic matter in soil. Unexpectedly in the spring samples, CLB were around 25% of all bacteria isolated, whereas fluorescent pseudomonads made up less than 10%. The relative proportion of these bacterial groups then decreased during the plant growth season but at all times showing a clear rhizosphere effect. Furthermore, up to 70% of the isolates carrying enzymes involved in the turnover of carbon, in the May sample, were identified as CLB, indicating the importance of this group in early colonization of the rhizosphere. The fluorescent pseudomonad group contributed less than 3%.}, }
@article {pmid12037607, year = {2002}, author = {Kay, E and Bertolla, F and Vogel, TM and Simonet, P}, title = {Opportunistic colonization of Ralstonia solanacearum-infected plants by Acinetobacter sp. and its natural competence development.}, journal = {Microbial ecology}, volume = {43}, number = {3}, pages = {291-297}, doi = {10.1007/s00248-002-2007-y}, pmid = {12037607}, issn = {0095-3628}, mesh = {*Acinetobacter ; *Alcaligenes ; Solanum lycopersicum/microbiology ; Plant Roots/microbiology ; Population Dynamics ; Soil Microbiology ; }, abstract = {The behavior of the soil bacterium Acinetobacter sp. BD413 was monitored in Ralstonia solanacearum-infected and non-infected tomato plants after direct injection into the stem or natural infection by roots. In healthy plants, Acinetobacter sp. BD413 failed to colonize plant tissue. In plants infected simultaneously by the pathogen R. solanacearum,the Acinetobacter population increased linearly to about 3.1 x 10(7) cells per gram plant material and was maintained at a high level until the death of the plant. Moreover, Acinetobacter sp. BD413 was found to develop a competent state when multiplying in planta, indicating it could possibly be transformed by bacterial or plant DNA.}, }
@article {pmid12035101, year = {2000}, author = {Zheng, D and Raskin, L}, title = {Quantification of Methanosaeta Species in Anaerobic Bioreactors Using Genus- and Species-Specific Hybridization Probes.}, journal = {Microbial ecology}, volume = {39}, number = {3}, pages = {246-262}, doi = {10.1007/s002480000003}, pmid = {12035101}, issn = {1432-184X}, abstract = {A BSTRACTTo evaluate the role of Methanosaeta spp. in a variety of anaerobic environments, small-subunit rRNA targeted oligonucleotide hybridization probes were developed and experimentally characterized. The probes were designed to be genus specific for Methanosaeta and species specific for Methanosaeta concilii and Methanosaeta thermophila. The temperature of dissociation was determined for each probe. Probe specificities were determined using a diverse collection of Archaea and through an evaluation of probe nesting using samples from a variety of anaerobic bioreactors. Cell fixation and hybridization conditions for fluorescence in situ hybridizations were also evaluated. Although permeability of methanogens was variable, M. concilii cells could be permeabilized using a range of paraformaldehyde and ethanol based fixation conditions. Using the newly designed probes together with previously designed probes for methanogens, it was determined that Methanosaeta spp. were the dominant aceticlastic methanogens in a variety of anaerobic bioreactors when acetate concentrations were low. Their levels were higher in bioreactors with granular sludge than in those with flocculent sludge. In lab-scale upflow anaerobic sludge blanket reactors, the levels of M. concilii rRNA were as high as 30% of the total rRNA.}, }
@article {pmid12035100, year = {2000}, author = {Iakovlev, A and Stenlid, J}, title = {Spatiotemporal Patterns of Laccase Activity in Interacting Mycelia of Wood-Decaying Basidiomycete Fungi.}, journal = {Microbial ecology}, volume = {39}, number = {3}, pages = {236-245}, doi = {10.1007/s002480000022}, pmid = {12035100}, issn = {1432-184X}, abstract = {A BSTRACTInterspecific fungal interactions are important ecological processes, whereas their physiological mechanisms are little understood. The aim of this work was to study how activity of fungal extracellular laccase was changed across mycelia during interactions between white- and brown-rot basidiomycetes from different wood decay stages. Qualitative assay of eight species interacting with each other in all combinations showed four spatial patterns of laccase activity: (I) laccase activity present both in contact zone and mycelium, (II) laccase activity only in contact zone, (III) laccase activity in mycelium but not in contact zone, (IV) no laccase activity. Presence of laccase activity only in the contact zone was more frequent than expected from random samples associated with mycelia that replaced other ones. On the other hand, the presence of laccase activity in the mycelium but not in the contact zone was only attributed to fungal species that were replaced by their antagonists. After one month, laccase activity was distributed over mycelia more homogeneously than after 6 days of interactions. In interacting mycelia, laccase activity was higher than in control and increasing with time. Saprotrophic fungi from late successional stages of wood decay generally had higher laccase activity than early succession saprotrophic and pathogenic fungi. The qualitative assays were confirmed by quantitative assay of total laccase activity. Significance of the results in antagonistic fungal interactions as well as in the processes of hyphal tip growth and mycelium senescence is discussed.}, }
@article {pmid12035099, year = {2000}, author = {Aakra, A and Hesselsøe, M and Bakken, LR}, title = {Surface Attachment of Ammonia-Oxidizing Bacteria in Soil.}, journal = {Microbial ecology}, volume = {39}, number = {3}, pages = {222-235}, doi = {10.1007/s002480000006}, pmid = {12035099}, issn = {1432-184X}, abstract = {A BSTRACTIndigenous ammonia-oxidizing bacteria (AOB) in a clay loam soil were extremely difficult to release from soil particles compared to most heterotrophic bacteria; less than 1% of indigenous AOB (estimated as potential ammonia oxidation rate) were extractable by the dispersion-density-gradient centrifugation technique. This is at least 10-fold less than the extractability of heterotrophic bacteria. Urea applications to the same soil induced a 5-fold increase in the potential ammonia oxidation rate, and this resulted in a much higher percentage (8%) extractability of AOB. Thus, the newly grown AOB in the urea-treated soil were less strongly attached to the soil particles. The contrast suggests that the strong attachment of indigenous AOB is a gradual process taking place due to a long residence time (infrequent/slow cell division) compared to heterotrophic organisms. However, the contrast could also reflect differences in species composition of the original AOB community and those growing in response to urea inputs. Specific detection of AOB in extinction dilution cultures was done by PCR and sequencing of the products. Considerable diversity was found within the genus Nitrosospira, but severe problems with the specificity of the primers were observed. Two allegedly AOB specific PCR primers pairs were used: one specific for Nitrosospira (SPIRA) and one which should encompass all AOB within the beta- Proteobacteria (GAOB). Only 33% of the cultures that gave PCR products with GAOB also gave products with the SPIRA primer pair, suggesting the presence of AOB other than Nitrosospira. However, the phylogeny based on the sequencing placed all the cultures in various clusters of the Nitrosospira clade, suggesting that the SPIRA primers do not match all members of the Nitrosospira genus. The cultures obtained from the urea-treated soil were different from the others in giving PCR products only with the SPIRA primers and not with the GAOB. Since sequencing also here confirmed the presence of Nitrosospira, these observations suggest that the GAOB primers do not match all AOB species.}, }
@article {pmid12035098, year = {2000}, author = {Stapleton, RD and Bright, NG and Sayler, GS}, title = {Catabolic and Genetic Diversity of Degradative Bacteria from Fuel-Hydrocarbon Contaminated Aquifers.}, journal = {Microbial ecology}, volume = {39}, number = {3}, pages = {211-221}, doi = {10.1007/s002480000002}, pmid = {12035098}, issn = {1432-184X}, abstract = {A BSTRACTSubsurface sediments were recovered from two aquifers contaminated with petroleum hydrocarbons in order to isolate and characterize indigenous microorganisms capable of biodegrading fuel-related compounds. These sediments had been previously studied using catabolic gene probes providing putative demonstration of significant biodegradation potential. Based on 16S rDNA sequence analysis, the isolates were phylogenetically similar to common soil microorganisms, including members of the genera Pseudomonas, Ralstonia, Burkholderia, Sphingomonas, Flavobacterium, and Bacillus. A total of 26 isolates were obtained using a vapor-plate enrichment technique with the volatile aromatic hydrocarbons toluene, ethylbenzene, p-xylene, naphthalene, and JP-4 jet fuel. JP-4, toluene, and ethylbenzene served as growth substrates for more than 80% of the isolates, while less than 10% of the organisms grew on the aromatic compounds benzene and o-xylene. Subsequent assays monitoring the evolution of (14)CO(2) indicated that only seven isolates were able to completely mineralize target compounds. One isolate, designated CAFB-naph-5, was able to completely mineralize the monoaromatic compounds salicylate and toluene, as well as the polyaromatic compound naphthalene. Molecular probing of the isolates showed four isolates hybridized with DNA probes targeting genes commonly associated with hydrocarbon-degrading bacteria. The isolates also demonstrated broad ability to grow in the presence of the antimicrobial agents streptomycin, tetracycline rifampicin, carbenicillin, nalidixic acid, kanamycin, and ampicillin. The results of the study demonstrate the biochemical and biodegradative capabilities of microorganisms isolated from contaminated aquifer systems and provide closure for indirect molecular monitoring of degradative potential in contaminated environments.}, }
@article {pmid12035097, year = {2000}, author = {Wikström, P and Hägglund, L and Forsman, M}, title = {Structure of a Natural Microbial Community in a Nitroaromatic Contaminated Groundwater Is Altered during Biodegradation of Extrinsic, but Not Intrinsic Substrates.}, journal = {Microbial ecology}, volume = {39}, number = {3}, pages = {203-210}, doi = {10.1007/s002480000001}, pmid = {12035097}, issn = {1432-184X}, abstract = {A BSTRACTThis study demonstrates microbial community changes over time in a nitroaromatic-contaminated groundwater upon amendment with hydrocarbons previously unknown to the microbial community (extrinsic) and hydrocarbons previously known to the microbial community (intrinsic). Sealed flasks, shaken and incubated at 25 degrees C, containing contaminated groundwater and salts were amended twice with extrinsic hydrocarbons including phenol, benzoic acid, and naphthalene, and intrinsic hydrocarbons including 2,4-dinitrotoluene (2,4-DNT) and para-nitrotoluene (p-NT). Microbial growth, biodegradation, and community structure changes measured by random amplified polymorphic DNA (RAPD) and quantitative PCR (qPCR) targeting catechol-2,3-dioxygenase (C23O) genes were monitored over time. All amended substrates were biodegraded after both substrate amendments except for 2,4-DNT, which was only partially degraded after the second amendment. Unique microbial communities were developed in flasks amended with phenol, benzoic acid, and naphthalene. However, in the flasks amended with intrinsic hydrocarbons the microbial community remained similar to the unamended control flasks. The relative amount of C23O genes detected by qPCR correlated with the biodegradation of phenol and naphthalene but not with 2,4-DNT. The results showed that a selection for microorganisms capable of catabolizing extrinsic hydrocarbons naturally and initially present in the nitroaromatic-contaminated groundwater occurred. However, growth-linked biodegradation of added intrinsic hydrocarbons was not selective.}, }
@article {pmid12035096, year = {2000}, author = {Gordon, DA and Priscu, J and Giovannoni, S}, title = {Origin and Phylogeny of Microbes Living in Permanent Antarctic Lake Ice.}, journal = {Microbial ecology}, volume = {39}, number = {3}, pages = {197-202}, doi = {10.1007/s002480000016}, pmid = {12035096}, issn = {1432-184X}, abstract = {A BSTRACTThe phylogenetic diversity of bacteria and cyanobacteria colonizing sediment particles in the permanent ice cover of an Antarctic lake was characterized by analyses of 16S rRNA genes amplified from environmental DNA. Samples of mineral particles were collected from a depth of 2.5 m in the 4-m-thick ice cover of Lake Bonney, McMurdo Dry Valleys, Antarctica. A rRNA gene clone library of 198 clones was made and characterized by sequencing and oligonucleotide probe hybridization. The library was dominated by representatives of the cyanobacteria, proteobacteria, and Planctomycetales, but also contained diverse clones representing many other microbial groups, including the Acidobacterium/Holophaga division, the Green Non-Sulfur division, and the Actinobacteria. Six oligonucleotide probes were made for the most abundant clades recovered in the library. To determine whether the ice microbial community might originate from wind dispersal of the algal mats found elsewhere in Taylor Valley, the probes were hybridized to 16S rDNAs amplified from three samples of terrestrial cyanobacterial mats collected at nearby sites, as well as to bacterial 16S rDNAs from the lake ice community. The results demonstrate the presence of a diverse microbial community dominated by cyanobacteria in the lake ice, and also show that the dominant members of the lake ice microbial community are found in terrestrial mats elsewhere in the area. The lake ice microbial community appears to be dominated by organisms that are not uniquely adapted to the lake ice ecosystem, but instead are species that originate elsewhere in the surrounding region and opportunistically colonize the unusual habitat provided by the sediments suspended in lake ice.}, }
@article {pmid12035095, year = {2000}, author = {Groben, R and Doucette, GJ and Kopp, M and Kodama, M and Amann, R and Medlin, LK}, title = {16S rRNA Targeted Probes for the Identification of Bacterial Strains Isolated from Cultures of the Toxic Dinoflagellate Alexandrium tamarense.}, journal = {Microbial ecology}, volume = {39}, number = {3}, pages = {186-196}, doi = {10.1007/s002480000025}, pmid = {12035095}, issn = {1432-184X}, abstract = {A BSTRACTBacteria have been implicated in the production of paralytic shellfish poison (PSP) toxins, which are normally associated with bloom-forming algal species, specifically toxic dinoflagellate algae. To clarify the role that these bacteria may play in the production of PSP toxins, it is desirable to identify and localize the bacteria associated with the dinoflagellates. 16S rRNA-targeted probes offer the possibility for both, and thus, probes have been made to putatively toxigenic bacteria isolated from the PSP-related dinoflagellate Alexandrium tamarense and tested for their specificity in dot blot and in situ hybridization experiments.}, }
@article {pmid12035094, year = {2000}, author = {Hahn, MW and Moore, ER and Höfle, MG}, title = {Role of Microcolony Formation in the Protistan Grazing Defense of the Aquatic Bacterium Pseudomonas sp. MWH1.}, journal = {Microbial ecology}, volume = {39}, number = {3}, pages = {175-185}, doi = {10.1007/s002480000026}, pmid = {12035094}, issn = {1432-184X}, abstract = {A BSTRACTThe defense strategy of the aquatic bacterium Pseudomonas sp. MWH1 against flagellate grazing was investigated in chemostat and batch experiments. The influence of predation on the Pseudomonas population was studied in the absence and presence of a potential competitor (Vibrio sp. CB5), as well as under starvation conditions and in a situation of unlimited growth. In the competition experiment the two bacterial strains were distinguished by immunofluorescence microscopy. When the Pseudomonas strain was cultured in the absence of the predator Ochromonas sp. DS, only mobile single cells were detectable. Grazing by this bacterivorous flagellate resulted in all experiments in the occurrence of a Pseudomonas subpopulation, which grew as floclike, suspended microcolonies. These microcolonies consisted of up to approximately 1,000 cells and were, because of their large size, protected against flagellate grazing. The microcolony subpopulation dominated the total Pseudomonas population in situations of high grazing pressure at a wide range of bacterial growth conditions. Thus, the formation of the microcolonies is interpreted as a successful grazing-defense strategy, which is effective under several growth conditions, allowing for the survival of the strain even when substrate depletion is combined with strong grazing pressure. Batch culture experiments demonstrated that the change in morphology of Pseudomonas sp. MWH1 is not controlled by growth rate, although no formation of microcolonies was observed after the addition of 0.2-&amp;mgr;m-filtered flagellate cultures to Pseudomonas cultures, indicating that a chemical trigger released by the flagellate is not involved in the control of this defense mechanism.}, }
@article {pmid12035093, year = {2000}, author = {Beaulieu, M and Bécaert, V and Deschênes, L and Villemur, R}, title = {Evolution of Bacterial Diversity during Enrichment of PCP-Degrading Activated Soils.}, journal = {Microbial ecology}, volume = {40}, number = {4}, pages = {345-356}, pmid = {12035093}, issn = {1432-184X}, abstract = {The microbiota of completely mixed soil slurry was acclimated with pentachlorophenol (PCP) or with a wood preservative mixture (WPM) containing several pollutants such as PCP and petroleum hydrocarbons. The impact of these compounds on the bacterial diversity was studied by using molecular tools. PCR amplifications of the 16S ribosomal RNA gene sequences (rDNA) were carried out with total DNA extracted from soil slurry samples taken at different time points during the enrichment process of the PCP and WPM reactors. The composition of these PCR products, reflecting the bacterial diversity, was monitored by the single-strand-conformation polymorphism (SSCP) method. Our results showed that the complexity of the SSCP profiles in the PCP reactor decreased significantly during the enrichment process, whereas they remained complex in the WPM reactor. PCR-amplified 16S rDNA libraries were generated from each reactor. The SSCP method was used to rapidly screen several clones of these libraries to find specific single-strand DNA migration profiles. In the PCP-activated soil, 96% of examined clones had the same SSCP profile, and sequences of representative clones were related to the genus Sphingomonas, suggesting that the enrichment with PCP resulted in a selection of little phylogenetic diversity. Four different SSCP profiles were observed with the 68 examined clones from the WPM reactor. Representative clones of these profiles were related to Methylocystaceae or Rhizobiaceae, to sulfur-oxidizing symbionts, to the genus Acinetobacter, and to the genus Sphingomonas. We also cloned and sequenced PCR-amplified DNA related to the pcpB gene, coding for the Sphingomonas PCP-4-monooxygenase and detected in both reactors after two weeks of enrichment. Of the 16 examined clones, deduced amino acid sequences of 13 clones were highly related to the Sphingomonas sp. strain UG30 pcpB. The three remaining pcpB clones were not closely related to the three known Sphingomonas pcpB.}, }
@article {pmid12035092, year = {2000}, author = {Muela, A and García-Bringas, JM and Arana, I and Barcina, I}, title = {Humic Materials Offer Photoprotective Effect to Escherichia coli Exposed to Damaging Luminous Radiation.}, journal = {Microbial ecology}, volume = {40}, number = {4}, pages = {336-344}, pmid = {12035092}, issn = {1432-184X}, abstract = {The behavior of Escherichia coli immersed in aqueous systems amended with humic acids, under PAR, UV-A, UV-B, and simulated solar radiation was examined. Culturability, ability to elongate, functioning of the electron transport systems, and glucose uptake were assessed. Humic substances in the range from 1 to 50 mg L-1 protected cells from photoinactivation. Decrease in culturability and cellular activities was significantly (p <0.05) less in the presence of humic material. However, humic acids were not used as nutrients. Neither irradiated nor nonirradiated humic solutions (50 mg L-1) supported the growth of 105 cells ml-1. However, humic acids dissolved in 0.9% NaC1 efficiently absorbed light over wavelengths from 270 to 500 nm. Also, a photoprotective effect against simulated sunlight was observed when humic acids were not in contact with but rather enveloped the cellular suspensions in double-wall microcosms. The protection afforded by humic acids against luminous radiation likely derives from their ability to absorb these radiations and hence reduces the amount of energy reaching the cells.}, }
@article {pmid12035091, year = {2000}, author = {Kusch, J and Stremmel, M and Breiner, HW and Adams, V and Schweikert, M and Schmidt, HJ}, title = {The Toxic Symbiont Caedibacter caryophila in the Cytoplasm of Paramecium novaurelia.}, journal = {Microbial ecology}, volume = {40}, number = {4}, pages = {330-335}, pmid = {12035091}, issn = {1432-184X}, abstract = {Endosymbiotic bacteria were observed to inhabit the cytoplasm of the freshwater ciliate Paramecium novaurelia. Transmission electron microscopy and toxicity tests with sensitive paramecia showed that the endosymbionts belong to the genus Caedibacter. The bacteria conferred a killer trait to their host paramecia. The production of a proteinaceous inclusion body ("R-body") in the bacterial cell makes them toxic to other paramecia after they become enclosed in food vacuoles. R-bodies of Caedibacter sp were associated with phages, which are known in most other Caedibacter species to code for the R-body proteins. The killer-effect of P. novaurelia on sensitive P. caudatum strains was of the "paralysis" type, which is a characteristic of the symbiont species Caedibacter caryophila. Until now C. caryophila was known to inhabit the macronucleus of Paramecium caudatum only. Sequencing of the 16S rRNA-gene proved that Caedibacter sp from the cytoplasm of P. novaurelia belongs to the species C. caryophila as well. The rDNA-sequence of 1695 bp length differed in a total of only 1 bp from the corresponding gene in C. caryophila from the macronucleus of P. caudatum. The results indicate that the infection of specific host cell compartments may depend on host genes, but not on different traits of the infecting symbiont species. The occurrence of killer and sensitive paramecia strains together in one pond is discussed with respect to the competitive advantage of the killer trait.}, }
@article {pmid12035090, year = {2000}, author = {Jugnia, LB and Tadonléké, RD and Sime-Ngando, T and Devaux, J}, title = {The Microbial Food Web in the Recently Flooded Sep Reservoir: Diel Fluctuations in Bacterial Biomass and Metabolic Activity in Relation to Phytoplankton and Flagellate Grazers.}, journal = {Microbial ecology}, volume = {40}, number = {4}, pages = {317-329}, pmid = {12035090}, issn = {1432-184X}, abstract = {The spatial distribution of the bacterial biomass and production and of potential heterotrophic activity (PHA) were measured every 4 h between 23 July (10:00 h) and 25 July (10:00 h) 1997 in a recently flooded oligo-mesotrophic reservoir (the Sep Reservoir, Puy-de-Dôme, France), in relation to temperature, the phytoplankton biomass and production, and the abundance of heterotrophic flagellates. The temperature varied slightly with time during the study, but the well-established thermal stratification agreed well with vertical distribution of the biological variables that were measured. Only the bacterial production and the PHA showed significant diel changes (t-test, p <0.05), with maxima at 18:00 h and minima at 02:00 h. A significant positive relation was found between bacterial abundance and that of heterotrophic flagellates, which, rather than being an association related to the thermal stratification of the water column, was considered to reflect a trophic relation between these two communities. A carbon balance analysis suggested that at least 30% of the C from primary production measured during the sampling period was used by bacteria, and that 42% of this secondary production, or 6% of the primary production, would be used for the development of the heterotrophic flagellates present. We conclude that the bacterioplankton forms, at least occasionally, an important source of carbon for higher trophic levels, and reject the hypothesis that bacterial production in the Sep Reservoir depends exclusively on organic matter of allochthonous origin.}, }
@article {pmid12035089, year = {2000}, author = {Schallmach, E and Minz, D and Jurkevitch, E}, title = {Culture-Independent Detection of Changes in Root-Associated Bacterial Populations of Common Bean (Phaseolus vulgaris L.) Following Nitrogen Depletion.}, journal = {Microbial ecology}, volume = {40}, number = {4}, pages = {309-316}, pmid = {12035089}, issn = {1432-184X}, abstract = {The structure of root-associated bacterial populations in the legume common bean (Phaseolus vulgaris L.), was studied in plants grown under nitrogen sufficiency and under conditions inducing nitrogen deficiency. Similar cell numbers were obtained in the rhizosphere of nitrogen-amended plants as compared to nitrogen-deficient plants and between various root parts-tip, elongation and branching zones-using DAPI staining. In contrast, a higher proportion of DAPI-stained cells from the nitrogen-amended plants hybridized with a fluorescence-labeled EUB338 probe for the Bacteria domain than cells originating from nitrogen-deficient plants. Shifts in the percentages of EUB338-reactive cells-as well as in absolute cell number-hybridizing to fluorescent rRNA-directed probes specific for the a and g Proteobacteria and for high GC content gram-positive bacteria in separated root segments were detected between the treatments. No such differences were found using b and d Proteobacteria or rRNA group I pseudomonad targeted probes. Denaturating gradient gel electrophoresis profiles of PCR products obtained from the same samples and amplified with Bacteria-domain targeted primers supported the results obtained with the whole cell hybridizations. The advantages and drawbacks of the techniques applied are discussed.}, }
@article {pmid12035088, year = {2000}, author = {Jurkevitch, EJ and Shapira, G}, title = {Structure and Colonization Dynamics of Epiphytic Bacterial Communities and of Selected Component Strains on Tomato (Lycopersicon esculentum) Leaves.}, journal = {Microbial ecology}, volume = {40}, number = {4}, pages = {300-308}, pmid = {12035088}, issn = {1432-184X}, abstract = {The sizes and compositions of bacterial populations found on leaves of greenhouse and field grown tomato plants were studied by dilution plating, fatty acid methyl ester analysis (FAME), and BIOLOG plates of isolates in pure cultures. In the greenhouse, overhead-irrigated plants sustained higher microbial populations (up to 105 cfu g-1) than soil-irrigated plants (103 cfu g-1). Strains isolated from overhead-irrigated plants grown in a vegetable garden (n = 216) and from greenhouse-grown plants (n = 114) were subjected to FAME analysis. Similarly, strains from soil-irrigated field-grown plants (n = 83) were identified using BIOLOG plates. In each case, populations were dominated by a few genera. When concentrated phyllosphere washes (CPW) were sprayed on greenhouse-grown, soil-irrigated plants, leaf bacterial populations of more than 105 CFU g-1 were sustained for 4 days; sterile buffer-sprayed leaves sustained less than 104 CFU g-1. No significant enrichment of any strain isolated from the sprayed leaves could be detected by FAME identification of randomly selected colonies. However, when recurring leaf saprophytic species (both Gram-positive and Gram-negative) isolated from these experiments and from plants grown outdoors were tested for epiphytic colonization under stressful conditions, all could still be detected at various levels up to 4 days after inoculation, indicating differential epiphytic fitness. The non-epiphytic bacteria Escherichia coli and Azospirillum brasilense disappeared from the leaf surface within the same experimental period.}, }
@article {pmid12035087, year = {2000}, author = {Scholten, JC and Stams, AJ}, title = {Isolation and Characterization of Acetate-Utilizing Anaerobes from a Freshwater Sediment.}, journal = {Microbial ecology}, volume = {40}, number = {4}, pages = {292-299}, pmid = {12035087}, issn = {1432-184X}, abstract = {Acetate-degrading anaerobic microorganisms in freshwater sediment were quantified by the most probable number technique. From the highest dilutions a methanogenic, a sulfate-reducing, and a nitrate-reducing microorganism were isolated with acetate as substrate. The methanogen (culture AMPB-Zg) was non-motile and rod-shaped with blunted ends (0.5-1 mm x 3-4 mm long). Doubling times with acetate at 30-35 degrees C were 5.6-8.1 days. The methanogen grew only on acetate. Analysis of the 16S rRNA sequence showed that AMPB-Zg is closely related to Methanosaeta concilii. The isolated sulfate-reducing bacterium (strain ASRB-Zg) was rod-shaped with pointed ends (0.5-0.7 mm x 1.5-3.5 mm long), weakly motile, spore forming, and gram positive. At the optimum growth temperature of 30 degrees C the doubling times with acetate were 3.9-5.3 days. The bacterium grew on a range of organic acids, such as acetate, butyrate, fumarate, and benzoate, but did not grow autotrophically with H2, CO2, and sulfate. The closest relative of strain ASRB-Zg is Desulfotomaculum acetoxidans. The nitrate-reducing bacterium (strain ANRB-Zg) was rod-shaped (0.5-0.7 mm x 0.7-1 mm long), weakly motile, and gram negative. Optimum growth with acetate occurred at 20-25 degrees C. The bacterium grew on a range of organic substrates, such as acetate, butyrate, lactate, and glucose, and did grow autotrophically with H2, CO2, and oxygen but not with nitrate. In the presence of acetate and nitrate, thiosulfate was oxidized to sulfate. Phylogenetically, the closest relative of strain ANRB-Zg is Variovorax paradoxus.}, }
@article {pmid12035086, year = {2000}, author = {Lawrence, JR and Hendry, MJ and Wassenaar, LI and Germida, JJ and Wolfaardt, GM and Fortin, N and Greer, CW}, title = {Distribution and Biogeochemical Importance of Bacterial Populations in a Thick Clay-Rich Aquitard System.}, journal = {Microbial ecology}, volume = {40}, number = {4}, pages = {273-291}, pmid = {12035086}, issn = {1432-184X}, abstract = {To investigate the distribution of microbial biomass, populations and activities within a clay-rich, low hydraulic conductivity (10-11 to 10-12 m s-1) aquitard complex, cores were aseptically obtained from a series of overlying clayey deposits; a fractured till, unfractured till (20-30 ka BP), a disturbed interfacial zone (20-30 ka BP), and a Cretaceous clay aquitard (71-72 Ma BP). The results of confocal microscopy studies, culture methods, molecular approaches, and extractive fatty acid analyses all indicated low bacterial numbers that were non-homogeneously distributed within the sediments. Various primers for catabolic genes were used to amplify extracted DNA. Results indicated the presence of eubacterial 23S rDNA, and the narH gene for nitrate reductase and ribulose-1,5-biphosphate carboxylase (RuBP carboxylase). Although there was no evidence of limitation by electron acceptors or donors, sulfate-reducing bacteria were not detected below the fractured till zone, using PCR, enrichment, or culture techniques. Denaturing gradient gel electrophoresis (DGGE) analyses indicated differences in community composition and abundance between the various geologic units. Results of FAME analyses of sediments yielded detectable extractable fatty acids throughout the aquitard complex. Bacterial activities were demonstrated by measuring mineralization of (14C) glucose. Porewater chemistry and stable isotope data were in keeping with an environment in which extremely slow growing, low populations of bacteria exert little impact. The observations also support the contention that in low permeability sediments bacteria may survive for geologic time periods.}, }
@article {pmid12035085, year = {2001}, author = {Hassen, A and Jerboui, Z and Chérif, M and Saidi, N and Gharbi, S and Boudabous, A}, title = {Impact of Heavy Metals on the Selective Phenotypical Markers of Pseudomonas aeruginosa.}, journal = {Microbial ecology}, volume = {42}, number = {1}, pages = {99-107}, pmid = {12035085}, issn = {1432-184X}, abstract = {The aim of this study was to characterize the impact of heavy metals on phenotypical markers of Pseudomonas aeruginosa. Twenty-two isolates of P. aeruginosa, either clinical (20) or secondary treated wastewater (2), were used to inoculate micro-ecosystems of sterile distilled water or secondary waste effluent in the presence of subminimal inhibitory concentrations of a variety of heavy metals commonly encountered in the aquatic naturally habitat (Ca2+, Co2+, Cr3+, Cu2+, Hg2+, Ni2+, Zn2+). Micro-ecosystems were exposed to visible light at laboratory temperature and individual strains were reisolated after a 1-, 3-, or 6-month period. The re-isolates (129) were characterized using hierarchical classification analysis in order to define affinities among variants of P. aeruginosa. Subsequently, discriminant analysis was used to detect eventual relationships among the different phenotypical markers studied. Results of the hierarchical classification, based on qualitative or quantitative approaches, showed clearly that incubation of P. aeruginosa in the presence of heavy metals altered the studied phenotypical markers, namely serotype, phage type, MIC of metals, and pyocin type. Discriminant analysis showed that the studied phenotypical markers could be classified into four clusters: C1 (L1 and L2 phage types, Hg tolerance and/or resistance, S2 serotype), C2 (P2 pyocin type, Cd tolerance and/or resistance, S1 serotype), C3 (Co and Cr tolerance and/or resistance) and C4 (P1 pyocin type, Ni, Zn, and Cu tolerance and/or resistance).}, }
@article {pmid12035084, year = {2001}, author = {Gimmler, H and Jesus, J and Greiser, A}, title = {Heavy Metal Resistance of the Extreme Acidotolerant Filamentous Fungus Bispora sp.}, journal = {Microbial ecology}, volume = {42}, number = {1}, pages = {87-98}, pmid = {12035084}, issn = {1432-184X}, abstract = {To obtain information on the importance of membrane and zeta potentials as repelling or facilitating forces during the uptake of cationic trace elements, the heavy metal content and the growth resistance of the acidotolerant fungus Bispora. sp. to heavy metals were compared at pH 1.0 and pH 7.0. Cu, Co, Ni, Cd, Cr, and La contents of the fungus were significantly lower at pH 1.0 than at pH 7.0. A similar pH effect occurred with cationic macro elements such as Na, Mg, Ca, Fe, and Mn. Only K and Zn exhibited higher levels at pH 1.0 in the fungus than at pH 7.0. Macro and micro elements present in the medium in anionic form (sulfate, chloride) showed the opposite pattern to cations: Contents were higher at pH 1.0 than at pH 7.0. Minerals present at pH 1.0 predominantly in the electrical neutral, protonated form (phosphate, borate) exhibited a similar cell content at both acid and neutral pH (P) or a higher content at neutral pH than at acid pH (B). The resistance of fungal growth to the cations Cu, Zn, Ni, Co, Cr, and Cd was significantly higher at pH 1.0 than at pH 7.0. Such a difference was not observed with Hg, present in the medium at both pH values as electrically silent HgCl2. The anionic tungstate exhibited the opposite pattern to cationic heavy metals: The resistance of growth was higher at pH 7.0 than at pH 1.0. A greater growth resistance to heavy metals was correlated with a lower uptake of these elements, and vice versa; Uptake of heavy metals correlated with a lower resistance of fungal growth to these elements. The results are in agreement with the hypothesis that membrane and zeta potentials of the fungus are important factors controlling the uptake of heavy metals and thereby the resistance of growth to these elements: At pH 1.0 positive potentials of fungal hyphae impede the uptake of cationic heavy metals, but facilitate the uptake of anionic species. At neutral pH values the negative potentials facilitate the uptake of cations, but impede the uptake of anions.}, }
@article {pmid12035083, year = {2001}, author = {Kearns, KD and Hunter, MD}, title = {Toxin-Producing Anabaena flos-aquae Induces Settling of Chlamydomonas reinhardtii, a Competing Motile Alga.}, journal = {Microbial ecology}, volume = {42}, number = {1}, pages = {80-86}, pmid = {12035083}, issn = {1432-184X}, abstract = {Toxin production is an adaptation that allows cyanobacteria in resource-limiting environments to ameliorate the effects of herbivory and competition with other phototrophs. We demonstrate that the cyanobacterial toxins anatoxin-a and microcystin-LR paralyze the motile green alga Chlamydomonas reinhardtii. In addition, both purified toxins and cyanobacterial extracellular products containing these toxins cause the alga to settle faster than in nontoxic media. In microcosm experiments, the presence of either the cyanobacterium or its extracellular products induce settling in the alga, similar to the response observed with the addition of both anatoxin-a and microcystin-LR. The cyanobacterial production of paralyzing toxins represents a novel mechanism for phytoplankton settling. This prokaryotic/eukaryotic chemical interaction may create a competitor-free zone for cyanobacteria in lake environments, predicating optimal conditions for a toxic cyanobacterial bloom.}, }
@article {pmid12035082, year = {2001}, author = {Cunha, MA and Almeida, MA and Alcântara, F}, title = {Short-Term Responses of the Natural Planktonic Bacterial Community to the Changing Water Properties in an Estuarine Environment: Ectoenzymatic Activity, Glucose Incorporation, and BiomassProduction.}, journal = {Microbial ecology}, volume = {42}, number = {1}, pages = {69-79}, pmid = {12035082}, issn = {1432-184X}, abstract = {The possibility that two principal bacterial communities expressing different levels of heterotrophic activity might coexist in an estuarine ecosystem (Ria de Aveiro, Portugal) and could quickly respond to tidal fluctuations of environmental factors was experimentally tested in diffusion chambers by swapping the dissolved components of the natural water between the two communities and comparing their reactivity against the unaltered controls. The results for ectoenzymatic activity (Leu-aminopeptidase and b-glucosidase), glucose incorporation and biomass production after transference of the marine bacterial community to brackish water showed maxima in the range of 241-384% of the control values. The opposite transference of the brackish-water bacterial community to marine water produced maximal decreases to 0.14-0.58% of the control values. In a reverse experiment, designed as the return to the initial conditions after 2 hours of the first exposure, the marine community rapidly re-acquired the characteristic low profile of activity. Contrastingly, the negative effects of 2 hours of exposure to marine water on the activity of the brackish water bacteria persisted, at least for 4 hours, after return to their own water. The apparent short-term irreversibility of the decline in activity of the brackish water bacteria when exposed to marine water, in parallel with the quick and reversible positive response of the marine water bacteria to the brackish water, suggests the development of two distinct bacterioplankton communities adapted to the environmental conditions prevailing at distinct sections of the estuary. The reactivity to environmental changes demonstrated by the two communities allows the prediction of estuarine profiles of bacterial activity steeper than those expected from the conservative transport of bacterial cells associated with tidal currents.}, }
@article {pmid12035081, year = {2001}, author = {Ross, N and Villemur, R and Marcandella, E and Deschênes, L}, title = {Assessment of Changes in Biodiversity when a Community of Ultramicrobacteria Isolated from Groundwater Is Stimulated to Form a Biofilm.}, journal = {Microbial ecology}, volume = {42}, number = {1}, pages = {56-68}, pmid = {12035081}, issn = {1432-184X}, abstract = {The stimulation of groundwater bacteria to form biofilms, for the remediation of polluted aquifers, is subjected to environmental regulations that include measurement of effects on microbial biodiversity. Groundwater microorganisms contain a proportion of unidentified and uncharacterized ultramicrobacteria (UMB) that might play a major role in the bioclogging of geological materials. This study aimed to assess the changes in genetic and metabolic biodiversity when a community of UMB, isolated from groundwater, is stimulated to form biofilms on a ceramic surface. UMB were stimulated with aerobic conditions and injection of molasses, in reactors reproducing groundwater composition and temperature. Concentration of planktonic viable UMB, secretion of extracellular polymeric substances (EPS), and biofilm thickness were monitored. The assessment of changes in biodiversity was achieved by comparing the initial UMB community to the biofilm community, using the single strand conformational polymorphism (SSCP) method, the cloning and sequencing of 16S rRNA gene (16S rDNA) sequences, and the Biolog microplate system. The hypothesis stating that indigenous UMB would play a significant role of in the biofilm development was corroborated. Within 13 days of stimulation, the UMB produced 700 mg L?1 of planktonic EPS and formed a biofilm up to a thickness of 1100 mm. This stimulation led to a decrease in genetic diversity and an increase in metabolic diversity. The decrease in genetic diversity was shown by a reduced number of single strand DNA fragments in the SSCP profiles. As such, 16S rDNA sequences from the biofilm revealed the predominance of four bacterial groups: Zoogloea, Bacillus/Paenibacillus, Enterobacteriaceae, and Pseudomonads. A significant increase in metabolic diversity was shown by a highest substrate richness profile and a lower substrate evenness profile of the biofilm bacterial population (p = 0.0 and p = 0.09, respectively). This higher metabolic diversity might be a consequence of the stimulation that seemed to favor the growth of bacteria having a high nutritional versatility. Stimulation of UMB, isolated from groundwater, was effective to form a biofilm having a high metabolic biodiversity. This combination of molecular-based and metabolic-based methods expanded the insight into monitoring the changes in bacterial biodiversity.}, }
@article {pmid12035080, year = {2001}, author = {Berthe-Corti, L and Bruns, A}, title = {Composition and Activity of Marine Alkane-Degrading Bacterial Communities in the Transition from Suboxic to Anoxic Conditions.}, journal = {Microbial ecology}, volume = {42}, number = {1}, pages = {46-55}, pmid = {12035080}, issn = {1432-184X}, abstract = {The impact of the oxygen supply rate (OSR) on the metabolic activity and on the composition of hexadecane-degrading bacterial communities in a quasi-anoxic milieu (nominal DOT = 0%) was studied in continuous cultures containing intertidal sediment. The dilution rate was kept constant at 0.035 h-1. The OSR was stepwise reduced from 3.5 mmol O2 L-1 h-1 to 0.06 mmol O2 L-1 h-1. Activity was determined by analyzing the respiration quotient (RQ) and the rates of hexadecane degradation (QHex), of hexadecane mineralization, and of protein production (PPR). The community composition and size were investigated by fluorescence in situ hybridization (FISH), by dilution plating (colony forming units or CFU), and by most probable number (MPN). The culture showed an aerobic hexadecane metabolism down to an OSR of 0.35 mmol O2 L-1 h-1. Below this OSR, anaerobic metabolism was initiated. The relationship among the RQ, PPR, QHex, and the OSR can be approximated by hyperbola (Michaelis-Menten kinetics). We suggest that the metabolic adaptation of the culture to low OSRs is due to regulation of protein expression and enzyme activity. Reducing the OSR resulted in minor but significant changes in the concentration of different physiological and phylogenetic groups. This means that, in addition to protein expression and activity regulation, the adaptation of the population to low OSRs is due to changes in the community composition.}, }
@article {pmid12035079, year = {2001}, author = {Laverman, AM and Speksnijder, AG and Braster, M and Kowalchuk, GA and Verhoef, HA and Van Verseveld, HW}, title = {Spatiotemporal Stability of an Ammonia-Oxidizing Community in a Nitrogen-Saturated Forest Soil.}, journal = {Microbial ecology}, volume = {42}, number = {1}, pages = {35-45}, pmid = {12035079}, issn = {1432-184X}, abstract = {Elevated levels of nitrogen input into various terrestrial environments in recent decades have led to increases in soil nitrate production and leaching. However, nitrifying potential and nitrifying activity tend to be highly variable over space and time, making broad-scale estimates of nitrate production difficult. This study investigates whether the high spatiotemporal variation in nitrate production might be explained by differences in the structure of ammonia-oxidizing bacterial communities in nitrogen-saturated coniferous forest soils. The diversity of ammonia-oxidizing bacteria of the b-subgroup Proteobacteria was therefore investigated using two different PCR-based approaches. The first targeted the 16S rRNA gene and involved temporal temperature gradient electrophoresis (TTGE) of specifically amplified PCR products, with subsequent band excision and nucleotide sequence determination. The second approach involved the cloning and sequencing of PCR-amplified amoA gene fragments. All recovered 16S rDNA sequences were closely related to the culture strain Nitrosospira sp. AHB1, which was isolated from an acid soil and is affiliated with Nitrosospira cluster 2, a sequence group previously shown to be associated with acid environments. All amoA-like sequences also showed a close affinity with this acid-tolerant Nitrosospira strain, although greater sequence variation could be detected in the amoA analysis. The ammonia-oxidizing bacterial community in the nitrogen-saturated coniferous forest soil was determined to be very stable, showing little variation between different organic layers and throughout the year, despite large differences in the total Bacterial community structure as determined by 16S rDNA DGGE community fingerprinting. These results suggest that environmental heterogeneity affecting ammonia oxidizer numbers and activity, and not ammonia oxidizer community structure, is chiefly responsible for spatial and temporal variation in nitrate production in these acid forest soils.}, }
@article {pmid12035078, year = {2001}, author = {Golet, DS and Ward, BB}, title = {Vertical Distribution of Denitrification Potential, Denitrifying Bacteria, and Benzoate Utilization in Intertidal Microbial Mat Communities.}, journal = {Microbial ecology}, volume = {42}, number = {1}, pages = {22-34}, pmid = {12035078}, issn = {1432-184X}, abstract = {Aspects of denitrification and benzoate degradation were studied in two estuarine microbial mat communities on the California coast by measuring the depth distributions of potential denitrification rates, genetic potential for denitrification, nitrate concentration, benzoate mineralization rates, total bacterial abundance, and abundance of a denitrifying strain (TBD-8b) isolated from one of the sites. Potential denitrification was detected in microbial mat cores from both Elkhorn Slough and Tomales Bay. Maximum denitrification rates were more than two orders of magnitude higher at Elkhorn Slough (3.14 mmol N m -2 d -1) than at Tomales Bay (0.02 mmol N m -2 d -1), and at both sites, the maximum rates occurred in the 0-2 mm depth interval. Ambient pore [NO 3 + NO 2] was substantially higher at Elkhorn Slough than at Tomales Bay. Incorporation and mineralization of benzoate was maximal near the mat surface at Elkhorn Slough. The areal rate of benzoate utilization was 1045 nmol C m -2 d -1, which represented utilization of 70% of the added substrate in 24 h. Total bacterial and TBD-8b abundances were greatest near the surface at both Tomales Bay and Elkhorn Slough, and TBD-8b represented less than 0.2% of the total. Genetic potential for denitrification, quantified by hybridization with a nitrite reductase gene fragment, was present below the mat surface at average levels representing presence of the gene in approximately 10% of the total cells.}, }
@article {pmid12035077, year = {2001}, author = {Buckley, DH and Schmidt, TM}, title = {The Structure of Microbial Communities in Soil and the Lasting Impact of Cultivation.}, journal = {Microbial ecology}, volume = {42}, number = {1}, pages = {11-21}, pmid = {12035077}, issn = {1432-184X}, abstract = {The structure of microbial communities was examined as a function of community composition and the relative abundance of specific microbial groups to examine the effects that plant community composition and land-use history have on microbial communities in the soil. The sites sampled were part of the Long Term Ecological Research (LTER) project in agricultural ecology at the W.K. Kellogg Biological Station of Michigan State University (Hickory Corners, MI) and included both active and abandoned agricultural fields as well as nearby fields that had never been cultivated. Microbial community structure was assessed by extracting total RNA from soil samples and using 16S rRNA-targeted oligonucleotide probes to quantify the abundance of rRNA from the alpha, beta, and gamma Proteobacteria, the Actinobacteria (Gram positive bacteria with a high mol % G+C genome), the Bacteria, and the Eukarya. In addition, soil microbial communities were characterized by examining fluorescently tagged terminal restriction fragment length polymorphisms (T-RFLP) in PCR amplified 16S rDNA. Microbial community structure was observed to be remarkably similar among plots that shared a long-term history of agricultural management despite differences in plant community composition and land management that have been maintained on the plots in recent years. In contrast, microbial community structure differed significantly between fields that had never been cultivated and those having a long-term history of cultivation.}, }
@article {pmid12035076, year = {2001}, author = {Sørensen, KB and Finster, K and Ramsing, NB}, title = {Thermodynamic and Kinetic Requirements in Anaerobic Methane Oxidizing Consortia Exclude Hydrogen, Acetate, and Methanol as Possible Electron Shuttles.}, journal = {Microbial ecology}, volume = {42}, number = {1}, pages = {1-10}, pmid = {12035076}, issn = {1432-184X}, abstract = {Anaerobic methane oxidation (AMO) has long remained an enigma in microbial ecology. In the process the net reaction appears to be an oxidation of methane with sulfate as electron acceptor. In order to explain experimental data such as effects of inhibitors and isotopic signals in biomarkers it has been suggested that the process is carried out by a consortium of bacteria using an unknown compound to shuttle electrons between the participants. The overall change in free energy during AMO with sulfate is very small (?22 kJ mol-1) at in situ concentrations of methane and sulfate. In order to share the available free energy between the members of the consortium, the concentration of the intermediate electron shuttle compound becomes crucial. Diffusive flux of a substrate (i.e, the electron shuttle) between bacteria requires a stable concentration gradient where the concentration is higher in the producing organism than in the consuming organism. Since changes in concentrations cause changes in reaction free energies, the diffusive flux of a catabolic product/substrate between bacteria is associated with a net loss of available energy. This restricts maximal inter-bacterial distances in consortia composed of stationary bacteria. A simple theoretical model was used to describe the relationship between inter-bacterial distances and the energy lost due to concentration differences in consortia. Key parameters turned out to be the permissible concentration range of the electron shuttle in the consortium (i.e., the concentration range that allows both participants to gain sufficient energy) and the stoichiometry of the partial reactions. The model was applied to two known consortia degrading ethanol and butyrate and to four hypothetical methane-oxidizing consortia (MOC) based on interspecies transfer of hydrogen, methanol, acetate, or formate, respectively. In the first three MOCs the permissible distances between producers and consumers of the transferred compounds were less than two times prokaryotic cell wall diameters. Consequently, it is not possible that a MOC can be based on inter-species transfer of hydrogen, methanol, or acetate. Formate, on the other hand, is a possible shuttle candidate provided the bacteria are attached to one another. In general the model predicts that members of consortia thriving on low energy such as the MOC must adhere to each other and utilize a compound for the exchange of electrons that has a high permissible concentration range and a high diffusion coefficient and transfers as many electrons as possible per molecule.}, }
@article {pmid12032621, year = {2001}, author = {Pozárová, E and Herben, T and Gryndler, M}, title = {Soil Saprotrophic Microfungi Associated with Roots of Calamagrostis epigeios on an Abandoned Deposit of Toxic Waste from Smelter Factory Processing Pyrite Raw Materials.}, journal = {Microbial ecology}, volume = {41}, number = {2}, pages = {162-171}, pmid = {12032621}, issn = {1432-184X}, abstract = {Saprotrophic microfungi associated with roots of Calamagrostis epigeios growing in industrial waste contaminated with high concentrations of heavy metals (manganese, iron, zinc) were isolated on three different media. The isolates were obtained from three plots colonized by plant cenoses, representing three different succession series of plant cover: initial, intermediate, and advanced. A total of 60 species of saprotrophic microfungi were found in the roots during three samplings. In addition, unidentified dark and white sterile mycelia were frequently isolated. Trichoderma koningii was frequent in the roots formed under the advanced phytocenose. The abundance of dark sterile mycelium gradually decreased with progressing succession of the plant cover. Chrysosporium merdarium was rarely observed in the roots under the intermediate and advanced plant cenoses. Multivariate redundancy analysis showed that the effect of succession stage of phytocenoses on incidence of saprotrophic microfungi in mycocenoses present in roots was statistically significant. When the similarity of root mycocenoses of the three plots was studied using the similarity coefficients, the results proved that the similarities between the initial and intermediate or intermediate and advanced mycocenoses were higher than that between the initial and advanced mycocenoses. This corresponds to a different speed of succession of the mycocenoses. The results suggest that the dark sterile mycelia, abundant at slowly developing plots, play a dominant role during the first stages of succession where the plant cover is poor.}, }
@article {pmid12032620, year = {2001}, author = {Bond, PL and Banfield, JF}, title = {Design and Performance of rRNA Targeted Oligonucleotide Probes for in Situ Detection and Phylogenetic Identification of Microorganisms Inhabiting Acid Mine Drainage Environments.}, journal = {Microbial ecology}, volume = {41}, number = {2}, pages = {149-161}, pmid = {12032620}, issn = {1432-184X}, abstract = {At Iron Mountain, CA, there is an extreme occurrence of acid mine drainage (AMD). This is a result of past mining activity that has exposed a sulfide ore body to weathering and microbial activity. This study presents seven new oligonucleotide probes for the detection of microorganisms at this AMD site by fluorescent in situ hybridization. In the design of these probes we have accounted for a large body of 16S rRNA sequence data recently compiled by us. This was obtained by PCR and cloning directly from environmental DNA and was mostly represented by novel sequences. The probes were developed to include detection of novel and uncultivated organisms. This includes detection for the Thermoplasmales group, a new group of Leptospirillum, the genus Sulfobacillus, the Acidiphilium genus, Acidimicrobium and relatives, and for organisms within the delta Proteobacteria. These probes have been used to examine the abundance and distribution of organisms, including novel and uncultivated taxa, and to clarify their potential contributions to AMD production at the site. We anticipate that these probes will be useful tools for exploration of the microbiology of other natural acidic environments and bioleaching systems.}, }
@article {pmid12032619, year = {2001}, author = {Probanza, A and Mateos, JL and Lucas García, JA and Ramos, B and De Felipe, MR and Gutierrez Mañero, FJ}, title = {Effects of Inoculation with PGPR Bacillus and Pisolithus tinctorius on Pinus pinea L. Growth, Bacterial rhizosphere Colonization, and Mycorrhizal Infection.}, journal = {Microbial ecology}, volume = {41}, number = {2}, pages = {140-148}, pmid = {12032619}, issn = {1432-184X}, abstract = {The effect of co-inoculation with Pisolithus tinctorius and a PGPR belonging to the genus Bacillus (Bacillus licheniformis CECT 5106 and Bacillus pumilus CECT 5105) in enhancing growth of Pinus pinea plants and the changes that occurred in rhizosphere microbial communities and the degree of mycorrhization were evaluated. Both bacterial strains of Bacillus promote the growth of Pinus pinea seedlings, but this biological effect does not imply a synergic effect with mycorrhizal infection. However, the positive response to mycorrhiza in a longer-term experiment it could be expected. The introduction of both inocula causes an alteration in the microbial rhizosphere composition, despite the low levels of inocula that were found at the end of the assay.}, }
@article {pmid12032618, year = {2001}, author = {Völksch, B and May, R}, title = {Biological Control of Pseudomonas syringae pv. glycinea by Epiphytic Bacteria under Field Conditions.}, journal = {Microbial ecology}, volume = {41}, number = {2}, pages = {132-139}, pmid = {12032618}, issn = {1432-184X}, abstract = {The efficacy of a bacterial strain as a biocontrol agent in the field may be related to the ecological similarity between the biocontrol agent and the target pathogen. Therefore, a number of different Pseudomonas syringae strains were evaluated for their antagonistic activities in vitro (agar-diffusion assay) and in planta (greenhouse assay) against the target pathogen, Pseudomonas syringae pv. glycinea. Six strains of five different pathovars were found to be antagonistic in vitro as well as in planta. The epiphytic fitness of the antagonistic Pseudomonas syringae strain 22d/93 and its two antibiotic-resistant mutants were examined on soybean plants in the fields. After adaptation the parental strain and its mutants had the ability to establish and maintain large epiphytic populations (about 106 cfu/g FW) over the whole growing season after a single spray inoculation. The epiphytic behaviors of the mutants and the parent were not significantly different. The introduced bacteria did not influence the total bacterial population size. When the antagonist was coinoculated with the pathogen, the development of the pathogen was significantly reduced during the whole growing season. When the antagonistic strain was inoculated 4 weeks in advance of the pathogen, this antagonistic effect could be markedly enhanced. The final population size of the pathogen reached just 104 cfu/g FW and was significantly reduced to 0.12% compared to the pathogen alone. This study demonstrates that biological control of foliar pathogens through colonization of the host plants with near isogenic or ecologically similar antagonistical strains seems to be a realistic goal.}, }
@article {pmid12032617, year = {2001}, author = {Tay, ST and Hemond, FH and Krumholz, LR and Cavanaugh, CM and Polz, MF}, title = {Population Dynamics of Two Toluene Degrading Bacterial Species in a Contaminated Stream.}, journal = {Microbial ecology}, volume = {41}, number = {2}, pages = {124-131}, pmid = {12032617}, issn = {1432-184X}, abstract = {Toluene uptake by a benthic biofilm community was previously shown to vary seasonally from 0.03 m hr?1 in winter to 0.2 m hr?1 in summer in a solvent-contaminated stream of the Aberjona watershed. We used quantitative PCR to estimate the population dynamics of previously isolated species of toluene-degrading Xanthobacter autotrophicus and Mycobacterium sp. in both toluene-contaminated and uncontaminated reaches of the stream, and to estimate their relative roles in overall biodegradation rate. Quantification using specific 16S rDNA primers forX. autotrophicus and Mycobacterium sp. showed that populations of both species were much larger in the toluene-contaminated than the toluene-free reach, in agreement with earlier culture-based investigations. A relatively brief bloom of X. autotrophicus occurred in the contaminated reach in the summer, while Mycobacterium sp. populations occurred at elevated densities for more than 5 months. Calculations showed that Mycobacterium, previously thought to be less important than Xanthobacter in annual toluene degradation based on single time-point CFU estimates, appears actually more important because of this longer persistence.}, }
@article {pmid12032616, year = {2001}, author = {Affourtit, J and Zehr, JP and Paerl, HW}, title = {Distribution of Nitrogen-Fixing Microorganisms along the Neuse River Estuary, North Carolina.}, journal = {Microbial ecology}, volume = {41}, number = {2}, pages = {114-123}, pmid = {12032616}, issn = {1432-184X}, abstract = {Nitrogen fixation genes (nifH) were amplified and sequenced from DNA extracted from surface water samples collected from six stations along the length of the Neuse River Estuary, North Carolina, in order to determine the distribution of nitrogen-fixing organisms in the transition from fresh- to saltwater. Nitrogenase genes were detected in all samples by a nested polymerase chain reaction method, and the amplification products from the upriver, midriver, and downriver stations were cloned, sequenced, and used for phylogenetic analysis. The composition of nifH clone libraries from upriver, midriver, and downriver stations (each composed of 14 randomly selected clones) were very diverse (samples from upriver and midriver stations were composed of 14 unique sequences, downriver station composed of 7 unique sequences) and differed among the stations. Some phylotypes were found at more than one station, but were usually found in the upriver and midriver stations or in the midriver and downriver stations, indicating that the phylotypes were probably transported along the river. Cyanobacterial nifH were not found at the most upriver site, but were a large fraction of sequences (50%) recovered from the downriver station, where nitrate concentration was an order of magnitude lower and salinity was higher. In contrast, g proteobacteria nifH sequences were much more common at the midriver and upriver sites (58% and 64%, respectively), compared to the downriver site (14%). Results indicate that substantially different nitrogen-fixing assemblages are present along the river, reflecting differential watershed hydrological inputs, sedimentation, and environmental selection pressures, along the salinity gradient.}, }
@article {pmid12032615, year = {2001}, author = {Mallet, C and Debroas, D}, title = {Regulation of b- and a-Glycolytic Activities in the Sediments of a Eutrophic Lake.}, journal = {Microbial ecology}, volume = {41}, number = {2}, pages = {106-113}, pmid = {12032615}, issn = {1432-184X}, abstract = {Temporal changes in a- and b-glucosidase activities, dissolved organic matter content, and bacterial biomass were studied in the superficial sediment layer of a eutrophic lake during the period of anoxia. The mean a- and b-glucosidase activities were 30.7 +/- 11.0 and 15.1 +/- 6.2 nmol h-1 g-1 of dry sediment, respectively. The specifc b-glucosidase activity seemed to be stimulated by carbohydrates (r = 0.80, P <0.05), whereas the specifc a-glucosidase activity was negatively correlated with the dissolved protein concentration (r = -0.72, P <0.10). To test the effect of organic matter on hydrolytic activities under controlled conditions, changes in specific activities were studied in relation to the concentrations of different types of organic matter: phytoplankton, polymers (proteins, cellobiose, and starch) and monomers (glucose and amino acids). The specifc a- and b-glucosidase activities were strongly induced by their natural substrates (starch and cellobiose, respectively) (P <0.05) and were not inhibited by glucose. Proteins inhibited these activities (P <0.05), whereas supplementation with amino acids had no effect on specifc glycolytic activities.}, }
@article {pmid12032614, year = {2001}, author = {Rashidan, KK and Bird, DF}, title = {Role of Predatory Bacteria in the Termination of a Cyanobacterial Bloom.}, journal = {Microbial ecology}, volume = {41}, number = {2}, pages = {97-105}, pmid = {12032614}, issn = {1432-184X}, abstract = {Changes in cyanobacterial abundance and in the occurrence of bacteria capable of lysing cyanobacteria were monitored over a period of 6 months (May to October 1998) in eutrophic Brome Lake (Quebec, Canada), in which dense cyanobacterial blooms recur regularly. By screening lake water, we isolated two strains of lytic bacteria from the family Cytophagaceae. When tested on 12 cyanobacteria and 6 heterotrophic bacteria, strain 1 lysed only Anabaena flos-aquae and strain 2 lysed only Synechococcus cedorum, Synechococcus leopoliensis, Synechococcus elongatus, and Anacystis nidulans: both liquid and agar-grown cultures of these cyanobacteria were lysed. The number of plaque-forming units of bacteria increased dramatically during the decline of the bloom. The results are consistent with an important role for these host-specific lytic bacteria in control and elimination of cyanobacterial blooms in this lake.}, }
@article {pmid12032613, year = {2001}, author = {Slattery, M and Rajbhandari, I and Wesson, K}, title = {Competition-Mediated Antibiotic Induction in the Marine Bacterium Streptomyces tenjimariensis.}, journal = {Microbial ecology}, volume = {41}, number = {2}, pages = {90-96}, pmid = {12032613}, issn = {1432-184X}, abstract = {Microbial competition for limiting natural resources within a community is thought to be the selective force that promotes biosynthesis of antimicrobial compounds. The marine bacterium Streptomyces tenjimariensis produces the antibiotics istamycin A and B under select laboratory culture conditions; presumably these compounds serve an ecological role under natural conditions. Here we report results of a novel marine microbial competition experiment that examined the impact of co-culture of marine bacteria on istamycin production by S. tenjimariensis. Twelve of the 53 bacterial species tested (i.e., 22.6%) induced Istamycin production; this antibiotic also inhibited growth of the competitor colonies. These results suggest that marine bacterial metabolites serve an ecological role in countering competitive species.}, }
@article {pmid12032612, year = {2001}, author = {Dolfing, J}, title = {The Microbial Logic behind the Prevalence of Incomplete Oxidation of Organic Compounds by Acetogenic Bacteria in Methanogenic Environments.}, journal = {Microbial ecology}, volume = {41}, number = {2}, pages = {83-89}, pmid = {12032612}, issn = {1432-184X}, abstract = {Microbial degradation of organic material in methanogenic ecosystems is a multistep process in which subsequent groups use the products of the first groups of organisms in the chain as substrates. The acetogenic bacteria in these systems produce both H2 and acetate. In the present minireview a thermodynamic approach is taken to evaluate the logic behind this duality. The evaluation shows that at the H2 partial pressures that usually occur in methanogenic ecosystems the acetogenic oxidation of known acetogenic substrates such as propionate, butyrate, and benzoate yields more energy than their complete oxidation to H2/CO2. Also, H2 partial pressures needed to achieve complete hydrogenogenic oxidation of these acetogenic substrates would have to be so low that H2 would be virtually unavailable to the hydrogenotrophic bacteria, in casu the methanogens.}, }
@article {pmid12032611, year = {2001}, author = {Garbeva, P and Overbeek, LS and Vuurde, JW and Elsas, JD}, title = {Analysis of Endophytic Bacterial Communities of Potato by Plating and Denaturing Gradient Gel Electrophoresis (DGGE) of 16S rDNA Based PCR Fragments.}, journal = {Microbial ecology}, volume = {41}, number = {4}, pages = {369-383}, pmid = {12032611}, issn = {1432-184X}, abstract = {The diversity of endophytic bacterial populations of potato (Solanum tuberosum cv Desirée) was assessed using a combination of dilution plating of plant macerates followed by isolation and characterization of isolates, and direct PCR-DGGE on the basis of DNA extracted from plants. The culturable endophytic bacterial communities detected in potato stem bases as well as in roots were in most cases on the order 103 to 105 CFU g?1 of fresh plant tissue. Dilution plating revealed that a range of bacterial types dominated these populations. Dominant isolates fell into the a and g subgroups of the Proteobacteria, as well as in the Flavobacterium/Cytophaga group. Different representatives of the Firmicutes were also found. The most frequently isolated strains (>5% of the total) were characterized as different Pseudomonas spp. (including P. aureofaciens, P. corrugata, and P. putida), Agrobacterium radiobacter, Stenotrophomonas maltophilia, and Flavobacterium resinovorans, using fatty acid methyl ester (FAME) analysis and/or sequencing of their partial 16S ribosomal RNA genes. Other Proteobacteria or Firmicutes were also found, albeit infrequently, and mainly in potato stem tissue. The fate of three putative potato endophytes, Stenotrophomonas maltophilia, Bacillus sp., and Sphingomonas paucimobilis, was monitored following their release into potato plants via injection, via root dipping, or via the soil. Following stem injection, the S. maltophilia and Bacillus inoculants could be tracked over time periods of, respectively, 22 and 1 day(s) by dilution plating as well as via PCR-DGGE. However, only S. maltophilia was able to colonize, and persist in, plant tissue from soil or dipped roots. S. paucimobilis was never recovered from the plant irrespective of the mode of introduction. The diversity of the indigenous bacterial flora associated with potato was then monitored via PCR-DGGE. The patterns obtained revealed the existence of bacterial communities of limited complexity, with communities from potato stems typically differing from those from stem peel and roots. Evidence was obtained for the endophytic occurrence of a range of organisms falling into the a, b, and g subgroups of the Proteobacteria as well as in the Firmicutes. Several of the sequences found matched those from isolates, suggesting that the molecular evidence reported culturable organisms. However, a number of sequences did not have matching sequences from isolates, suggesting that non-culturable or as-yet-uncultured endophytic organisms were being detected.}, }
@article {pmid12032610, year = {2001}, author = {Petänen, T and Virta, M and Karp, M and Romantschuk, M}, title = {Construction and Use of Broad Host Range Mercury and Arsenite Sensor Plasmids in the Soil Bacterium Pseudomonas fluorescens OS8.}, journal = {Microbial ecology}, volume = {41}, number = {4}, pages = {360-368}, pmid = {12032610}, issn = {1432-184X}, abstract = {We have generated new sensors for the specific detection and studies of bioavailability of metals by engineering Pseudomonas fluorescens with reporter gene systems. One broad host range mercury (pTPT11) and two arsenite (pTPT21 and pTPT31) sensor plasmids that express metal presence by luminescence phenotype were constructed and transferred into Escherichia coli DH5a and Pseudomonas fluorescens OS8. The maximal induction was reached after 2 h of incubation in metal solutions at room temperature (22 degrees C). In optimized conditions the half maximal velocity of reaction was achieved at acidic pH using a d-luciferin substrate concentration that was nearly sixfold lower for P. fluorescens OS8 than for E. coli DH5a. When using a luciferin concentration (150 mM) that was optimal for E. coli the luminescence declined rapidly in the case of Pseudomonas, for which the substrate level 25 mM gave a stable reading between about 20 min and 3 h. The ability of the strain OS8 to quantitatively detect specific heavy metals in spiked soil and soil extracts is as good, or even better in being a real-time reporter system, than that of a traditional chemical analysis. The Pseudomonas strain used is an isolate from pine rhizosphere in oil and heavy metal contaminated soil. It is also a good humus soil colonizer and is therefore a good candidate for measuring soil heavy metal bioavailability.}, }
@article {pmid12032609, year = {2001}, author = {Palomares, AJ and Vázquez, ME and Rodríguez-Llorente, ID and Dary, M and Caviedes, MA}, title = {Plasmid Transfer Detection in Soil using the Inducible lPR System Fused to Eukaryotic Luciferase Genes.}, journal = {Microbial ecology}, volume = {41}, number = {4}, pages = {352-359}, pmid = {12032609}, issn = {1432-184X}, abstract = {We report a model system for plasmid transfer analysis using the regulated lambda phage right promoter, lPR, fused to luc and lucOR as reporter genes. We have demonstrated that the systems cI857-lPR::luc and cI857-lPR::lucOR are temperature-inducible in Escherichia coli but not in other Gram-negative bacteria analyzed, enabling detection of luminescence when plasmids were mobilized from E. coli to those Gram-negative backgrounds. Using light for the detection, we have observed plasmid transfer from E. coli harboring RK2 and R388 derived plasmids to Pseudomonas putida KT2440 (co-introduced with donors) and to indigenous microorganisms, in vitro and in nonsterile soil microcosms. The importance of nutrients for an efficient plasmid transfer in nonsterile soil microcosms has been confirmed. When plasmid transfer experiments were carried out into nonsterile soil microcosms, significant populations of indigenous transconjugants arose. This system provides efficient marker genes and avoids the use of antibiotics for the selection of transconjugants.}, }
@article {pmid12032608, year = {2001}, author = {Thimm, T and Hoffmann, A and Fritz, I and Tebbe, CC}, title = {Contribution of the Earthworm Lumbricus rubellus (Annelida, Oligochaeta) to the Establishment of Plasmids in Soil Bacterial Communities.}, journal = {Microbial ecology}, volume = {41}, number = {4}, pages = {341-351}, pmid = {12032608}, issn = {1432-184X}, abstract = {The contribution of the earthworm Lumbricus rubellus in spreading plasmids from a nonindigenous bacterial species to the soil microbial community was studied with Escherichia coli strains as donor organisms. The selected donor strains harbored marker-gene tagged plasmids with different transfer properties and host ranges. Prototrophic benzoate degrading indigenous bacteria were analyzed as potential recipients. In filter-mating experiments, donor strains were mixed with bacterial cell consortia extracted from earthworm casts (feces) and incubated on nutrient agar at 28 degrees C. Transfer was detected with the broad host range IncP plasmid pRP4luc; with the IncQ plasmid, pSUP104luc, but only when it was present in a mobilizing donor strain; and with the transposon delivery vector pUTlux. No transfer was detected with the nonmobilizable pUCluc and the mobilizable pSUP202luc, both of narrow host range. In microcosm studies with E. coli inoculated soil incubated at 12 degrees C, transconjugants were only detected in casts of L. rubellus but not in bulk soil, indicating that the gut passage was a precondition for plasmid transfer. Plasmid pRP4luc was transferred at higher frequencies than detected in filter mating. Results of the filter matings were confirmed except that transfer of pUTlux could not be detected. The majority of transconjugants isolated in this study lost their acquired plasmid upon further cultivation. Stable transconjugants, however, were obtained and identified at the 16S rRNA gene level as members of the b- and g-subgroups of Proteobacteria. Incubation of E. coli and selected transconjugants in soil microcosms with L. rubellus demonstrated that the gut passage resulted in a slight but significant reduction of ingested cells. In contrast to the donor strains, however, the population sizes of transconjugants in bulk soil and in casts did not decrease over time. This demonstrated that the transferred plasmids had established themselves in the soil microbial community.}, }
@article {pmid12032607, year = {2001}, author = {Corich, V and Giacomini, A and Vian, P and Vendramin, E and Carlot, M and Basaglia, M and Squartini, A and Casella, S and Nuti, MP}, title = {Aspects of Marker/Reporter Stability and Selectivity in Soil Microbiology.}, journal = {Microbial ecology}, volume = {41}, number = {4}, pages = {333-340}, pmid = {12032607}, issn = {1432-184X}, abstract = {Based on several experiences of microbial release using genetically modified Rhizobium leguminosarum, we have highlighted a number of aspects related to the suitability of introduced markers such as resistance to mercury and b-galactosidase activity, the latter serving the function of high-expression level reporter gene obtained by the introduction of a synthetic promoter conferring strong inducible expression in Gram-negative bacteria. In vitro expression and in vivo performances of the chosen examples have been followed in model strains comparing gene dosage and expression levels. The technical possibility of unambiguously monitoring the marked GMM has been evaluated in medium- and long-term experiments carried out both in microcosms and soil, also including the presence of the plant symbiotic host. Marker stability, regardless the nature of the gene, was shown to be dependent on the location of the genetic modification and on its degree of gene expression regulation. Reporter strength was found to be an advantage allowing the distinction of marker-bearing bacteria while negatively affecting their genetic stability. Plasmid-borne regulated reporters were found to be stable up to the stages of rhizosphere colonization, but were more critically selected against upon symbiotic host invasion.}, }
@article {pmid12032606, year = {2001}, author = {Xi, C and Dirix, G and Hofkens, J and Schryver, FC and Vanderleyden, J and Michiels, J}, title = {Use of Dual Marker Transposons to Identify New Symbiosis Genes in Rhizobium.}, journal = {Microbial ecology}, volume = {41}, number = {4}, pages = {325-332}, pmid = {12032606}, issn = {1432-184X}, abstract = {Rhizobium etli elicits nitrogen-fixing nodules on the roots of Phaseolus vulgaris. Using a composite dual-marker mini-Tn5 transposon carrying combinations of a constitutively expressed gfp gene and a promoterless gusA gene, we identified novel genes required for an efficient symbiosis. The induction of the gusA gene was used to determine the expression level of the different target genes under conditions partly mimicking the symbiotic environment ex planta. The green fluorescence was used to localize the bacteria in infection threads or inside the plant cells. Among the identified R. etli mutants, several produced a Nod- phenotype, whereas others were Fix- or displayed a reduced acetylene reduction activity during symbiosis. Partial sequence analysis of the mutated genes allowed us to classify them as nodulation genes, nitrogen fixation genes, genes possessing various enzymatic functions previously not yet associated with symbiosis, and genes displaying no similarity to any other sequence in the database. This methodology can be used to screen large numbers of mutants in the search for novel genes important for Rhizobium-legume symbiosis, and may be adapted to study other plant-bacterium interactions.}, }
@article {pmid12032605, year = {2001}, author = {Séveno, NA and Morgan, JA and Wellington, EM}, title = {Growth of Pseudomonas aureofaciens PGS12 and the Dynamics of HHL and Phenazine Production in Liquid Culture, on Nutrient Agar, and on Plant Roots.}, journal = {Microbial ecology}, volume = {41}, number = {4}, pages = {314-324}, pmid = {12032605}, issn = {1432-184X}, abstract = {The growth of Pseudomonas aureofaciens PGS12 was followed in nutrient broth (NB), on nutrient agar (NA), and on plant roots by monitoring cell numbers, the production of the autoinducer hexanoyl-homoserine lactone (HHL), and the antibiotic phenazine-1-carboxylic acid (PCA). In NB, as the growth rate declined in transition phase, HHL synthesis increased rapidly, shortly followed by PCA production. During stationary phase, HHL concentration declined rapidly while PCA concentration continued to increase slowly. The luxAB reporter genes were inserted in the phzB gene of the phenazine operon and phenazine transcriptional activity was monitored using measurement of luminescence. Levels and pattern of light output were similar to HHL accumulation and indicated that gene expression was maximal in transition phase and silenced in stationary phase. PCA production continued in stationary phase, suggesting that the protein products of the phenazine operon were maintained in the cell after down regulation. HHL accumulation was 60 times higher on NA than in NB per equivalent volume because of a 60-fold increase in cell density on NA. Higher levels of PCA per cell (6.8 times) and per equivalent volume (360-fold) accumulated in a colony compared to that found in broth. HHL remained at a high concentration in a colony for a longer period compared to a short burst in NB, and this may explain the increased PCA production. In contrast, on wheat seedlings and bean plant roots, bacterial growth was observed, but neither HHL nor PCA was detected; however, transcriptional activity of the phzB::luxAB reporter occurred on the bean plant roots.}, }
@article {pmid12032604, year = {2001}, author = {Lowder, M and Oliver, JD}, title = {The Use of Modified GFP as a Reporter for Metabolic Activity in Pseudomonas putida.}, journal = {Microbial ecology}, volume = {41}, number = {4}, pages = {310-313}, pmid = {12032604}, issn = {1432-184X}, abstract = {Many bacteria are now known to enter into a "viable but nonculturable" (VBNC) state in response to various environmental stresses. In this state, the cells are no longer culturable on routine media, but retain viability and in many cases have been shown to be capable of resuscitating to the metabolically active and culturable state. There have been no simple means of measuring the metabolic activity of cells in the VBNC state. The use of green fluorescent protein (GFP) variants with short half-lives was examined in cells intended for environmental release to examine the potential of GFP as a reporter of metabolic activity. Unlike strains with the native (stable) GFP, Pseudomonas putida strains tagged with unstable GFP rapidly lost GFP fluorescence following exposure to starvation and VBNC-inducing conditions. Our results suggest that tagging cells with the modified GFP provides a method for determining metabolic activity in these cells.}, }
@article {pmid12032603, year = {2001}, author = {Qazi, SN and Rees, CE and Mellits, KH and Hill, PJ}, title = {Development of gfp Vectors for Expression in Listeria monocytogenes and Other Low G+C Gram Positive Bacteria.}, journal = {Microbial ecology}, volume = {41}, number = {4}, pages = {301-309}, pmid = {12032603}, issn = {1432-184X}, abstract = {The gfp (green fluorescent protein) gene has previously been used to construct a variety of reporter plasmids for Gram-positive bacteria for bacterial localization and gene expression studies. When a native red-shifted gfp variant (gfp3) was cloned into an expression vector using the Pxyn promoter and used to transform the soil-borne pathogen Listeria monocytogenes, only a small proportion of the population was seen to fluoresce when examined by epifluorescence microscopy. When the Pxyn promoter was replaced with the PxylA promoter, with accompanying modification of the translation initiation region of the gfp3 gene, a homogeneously fluorescent population of cells was obtained. When expressed in other Gram-positive organisms, such as Staphylococcus aureus and Bacillus subtilis, the translationally enhanced gene also resulted in high-level and homogeneous GFP production within the bacterial population. High-level expression of these reporter constructs in L. monocytogenes was evaluated to determine if it had any detrimental biological effect during intracellular infection of eukaryotic cell lines. The gfp3+ Listeria were found to invade equally as well as the wild-type cells; showing that these expression systems can be used to monitor the bacterium in natural environments. Based on these results, similar translationally enhanced vectors were also developed using unstable GFP3 variants, which retain their short-half life characteristics in L. monocytogenes and therefore can be used as a sensitive monitor of gene expression.}, }
@article {pmid12032602, year = {2001}, author = {Unge, A and Jansson, J}, title = {Monitoring Population Size, Activity, and Distribution of gfp-luxAB-Tagged Pseudomonas fluorescens SBW25 during Colonization of Wheat.}, journal = {Microbial ecology}, volume = {41}, number = {4}, pages = {290-300}, pmid = {12032602}, issn = {1432-184X}, abstract = {Increasingly, focus has been directed towards the use of microorganisms as biological control agents to combat fungal disease, as an alternative to chemical fungicides. Pseudomonas fluorescens SBW25 is one bacterial strain that has been demonstrated to promote plant growth by biocontrol of pathogenic fungi. To understand the mode of action of this bacterium, information regarding its localization and metabolic activity on plants is important. In this study, a gfp/luxAB-tagged derivative of P. fluorescens SBW25, expressing the green fluorescent protein (GFP) and bacterial luciferase, was monitored during colonization of wheat starting from seed inoculation. Since bacterial luciferase is dependent on cellular energy reserves for phenotypic expression, metabolically active cells were detected using this marker. In contrast, the stable GFP fluorescence phenotype was used to detect the cells independently of their metabolic status. The combination of these two markers enabled P. fluorescens SBW25 cells to be monitored on wheat plants to determine their specific location and metabolic activity. Studies on homogenized wheat plant parts demonstrated that the seed was the preferred location of P. fluorescens SBW25 during the 65-day time period studied, but the leaves and roots were also colonized. Interestingly, the bacteria were also found to be metabolically active on all plant parts examined. In situ localization of P. fluorescens SBW25 using a combination of different microscopic techniques confirmed the preference for the cells to colonize specific regions of the seed. We speculate that the colonization pattern of P. fluorescens SBW25 can be linked to the mechanism of protection of plants from fungal infection.}, }
@article {pmid12032601, year = {2001}, author = {Wellington, EM and Jansson, JK}, title = {Preface.}, journal = {Microbial ecology}, volume = {41}, number = {4}, pages = {289}, doi = {10.1007/s002480000113}, pmid = {12032601}, issn = {1432-184X}, }
@article {pmid12032339, year = {2002}, author = {Edgcomb, VP and Kysela, DT and Teske, A and de Vera Gomez, A and Sogin, ML}, title = {Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {11}, pages = {7658-7662}, pmid = {12032339}, issn = {0027-8424}, mesh = {Animals ; Ciliophora/classification/genetics ; DNA Primers ; Ecosystem ; Fungi/classification/genetics ; *Genetic Variation ; Geologic Sediments/*analysis/microbiology ; Molecular Sequence Data ; *Phylogeny ; Plants/classification/genetics ; Polymerase Chain Reaction ; RNA, Ribosomal/chemistry/*genetics ; }, abstract = {Molecular microbial ecology studies have revealed remarkable prokaryotic diversity in extreme hydrothermal marine environments. There are no comparable reports of culture-independent surveys of eukaryotic life in warm, anoxic marine sediments. By using sequence comparisons of PCR-amplified small subunit ribosomal RNAs, we characterized eukaryotic diversity in hydrothermal vent environments of Guaymas Basin in the Gulf of California. Many sequences from these anoxic sediments and the overlaying seawater represent previously uncharacterized protists, including early branching eukaryotic lineages or extended diversity within described taxa. At least two mechanisms, with overlapping consequences, account for the eukaryotic community structure of this environment. The adaptation to anoxic environments is evidenced by specific affinity of environmental sequences to aerotolerant anaerobic species in molecular trees. This pattern is superimposed against a background of widely distributed aerophilic and aerotolerant protists, some of which may migrate into and survive in the sediment whereas others (e.g., phototrophs) are simply deposited by sedimentary processes. In contrast, bacterial populations in these sediments are primarily characteristic of anoxic, reduced, hydrocarbon-rich sedimentary habitats.}, }
@article {pmid12024285, year = {2001}, author = {}, title = {Erratum.}, journal = {Microbial ecology}, volume = {42}, number = {2}, pages = {215}, doi = {10.1007/s00248-001-0030-z}, pmid = {12024285}, issn = {1432-184X}, }
@article {pmid12024284, year = {2001}, author = {Ohtomo, R and Saito, M}, title = {Increase in the Culturable Cell Number of Escherichia coli during Recovery from Saline Stress: Possible Implication for Resuscitation from the VBNC State.}, journal = {Microbial ecology}, volume = {42}, number = {2}, pages = {208-214}, doi = {10.1007/s002480000103}, pmid = {12024284}, issn = {1432-184X}, abstract = {The change in colony-forming units (CFUs) in saline-stressed Escherichia coli cultures was examined. Exposure of E. coli cells to high saline stress decreased the number of CFUs significantly. When the culture was relieved from the stressful condition, the number of CFUs returned within 2 hr to the same level as before the stress. This recovery in the number of CFUs seemed to be independent of DNA synthesis and cell division, because the same phenomenon was also observed in the presence of nalidixic acid. However, the total cell number enumerated by microscopy was the same before and after relief from saline stress. This phenomenon was considered to be the result of the resuscitation of cells that had been in the VBNC state during saline stress. Our method, in which we examined CFU recovery in the presence of a DNA synthesis inhibitor, might be useful for further VBNC study.}, }
@article {pmid12024283, year = {2001}, author = {Jager, ES and Wehner, FC and Korsten, L}, title = {Microbial Ecology of the Mango Phylloplane.}, journal = {Microbial ecology}, volume = {42}, number = {2}, pages = {201-207}, doi = {10.1007/s002480000106}, pmid = {12024283}, issn = {1432-184X}, abstract = {Bacteria, filamentous fungi, and yeasts were enumerated on the mango phylloplane by indirect leaf impression and washing- and dilution plating. The phylloplane microbial community was qualitatively and quantitatively related to leaf age, position in the tree canopy, seasonality, and chemical spraying. Filamentous fungi and yeasts were more abundant during winter and spring, whereas bacterial population densities increased during autumn. Community density and diversity increased progressively with leaf age. The western tree aspect sustained the least diverse bacterial, filamentous fungal, and yeast communities. Chemical sprays reduced bacterial, filamentous fungal, and yeast community diversities. Gram-positive bacteria (Bacillus spp. and coryneform spp.) exceeded gram-negative bacteria. The most common fungal genera isolated were Cladosporium and Alternaria. Yeasts prevalent in the mango phylloplane were of the genera Aureobasidium, Cryptococcus, and Sporobolomyces.}, }
@article {pmid12024282, year = {2001}, author = {Naseby, DC and Lynch, JM}, title = {Effect of 2,4-Diacetylphloroglucinol Producing, Overproducing, and Nonproducing Pseudomonas fluorescens F113 in the Rhizosphere of Pea.}, journal = {Microbial ecology}, volume = {42}, number = {2}, pages = {193-200}, doi = {10.1007/s002480000105}, pmid = {12024282}, issn = {1432-184X}, abstract = {Pseudomonas fluorescens F113lacZY and modified strains carrying different function modifications were assessed for their impact in the rhizosphere of pea. Strain F113lacZY naturally produces the anti-fungal metabolite 2,4-diacetylphloroglucinol (Phl) useful in plant disease control. The first modified strain of F113 was repressed in production of Phl, creating the Phl negative strain F113G22. The second was a plasmid based overproducer of Phl (F113Rif (pCUGP)). Both the F113lacZY and the F113Rif (pCUGP) strains increased the rhizoplane fungal populations, whereas the same strains reduced the rhizosphere soil fungal populations with respect to the control. Similar results were found with the rhizoplane and rhizosphere soil bacterial populations. The F113G22 treatment resulted in a significantly greater indigenous fluorescent Pseudomonas population than the F113lacZY and F113Rif (pCUGP) treatments and a greater total Pseudomonas population than the control, F113lacZY, and F113Rif (pCUGP) treatments. Overproduction of Phl did not affect the establishment of the introduced Pseudomonas population. None of the inocula displaced the indigenous populations, but the F113G22 inocula had an additive effect on the total Pseudomonas population. P (phosphatase), S (sulphatase), and N (urease) cycle enzyme activities were increased while C (glucosidase, NAGase) cycle activities were decreased by the F113lacZY and F113Rif (pCUGP) treatments, suggesting C leakage from the roots. Overall, most effects of inoculation compared to the wild type were found with the non-Phl-producing strain. Overproduction of Phl had little environmental effect in relation to wild-type inocula.}, }
@article {pmid12024281, year = {2001}, author = {Abranches, J and Starmer, WT and Hagler, AN}, title = {Yeast-Yeast Interactions in Guava and Tomato Fruits.}, journal = {Microbial ecology}, volume = {42}, number = {2}, pages = {186-192}, doi = {10.1007/s002480000111}, pmid = {12024281}, issn = {1432-184X}, abstract = {The host specificity of yeast-yeast interactions was investigated for two yeast types, represented by six pairs of Pichia membranifaciens clade yeasts (Pichia membranifaciens or Issatchenkia occidentalis) with apiculate yeasts (Kloeckera apis, Kloeckera africana, or Saccharomycodes ludwigii), commonly found in fruits. Competitive interactions between the two types were detected in both ripe tomato and guava fruit pulp. The differences in growth rates and carrying capacities depended on fruit type (host) and culture conditions (monocultures versus bicultures). These differences were probably due to nutrient composition of each fruit. Pichia membranifaciens did not show host dependent responses, but the apiculate yeasts and Issatchenkia occidentalis did. Depending on yeast strain and culture conditions (i.e., monoculture or biculture), carbon, nitrogen, and vitamins were investigated as potential limiting growth factors in guava fruit. Both singular and multiple limiting nutrients were implicated.}, }
@article {pmid12024280, year = {2001}, author = {Danovaro, R and Armeni, M and Dell'Anno, A and Fabiano, M and Manini, E and Marrale, D and Pusceddu, A and Vanucci, S}, title = {Small-Scale Distribution of Bacteria, Enzymatic Activities, and Organic Matter in Coastal Sediments.}, journal = {Microbial ecology}, volume = {42}, number = {2}, pages = {177-185}, doi = {10.1007/s002480000109}, pmid = {12024280}, issn = {1432-184X}, abstract = {The small-scale distribution of several structural (bacterial abundance, phytopigment, total and soluble protein, and carbohydrate content) and functional ecological variables (enzymatic activities, frequency of dividing cells) was investigated in coastal sediments during a spring bloom. For bacterial abundance, enzymatic activity, and organic matter determinations, samples were collected at 5-m depth from a sediment surface delimited by a 42 x 42-cm frame, divided into 49 squares. In order to test the influence of the bottom microtopography on the investigated variables, the size of this frame was defined to cover the distance between two subsequent ripples. As indicated by Fisher's index, benthic bacteria, enzymatic activities, proteins, carbohydrates, and their soluble fractions exhibited an aggregate distribution. Sampling size (i.e., sample unit of 36 cm2) was appropriate for all variables, except for chlorophyll a and frequency of dividing cells that displayed a contagious distribution. To estimate the reliability of the current sampling strategy, we compared the mean values from three randomly selected sample units with the average value of the entire sediment surface (i.e., 49 samples). For all variables reported in this study, the use of three replicates was representative of the mean values of the sampled area with a confidence limit within +/-20%. Bacterial population sizes did not correlate with their potential food sources (e.g., phytopigments, proteins, and carbohydrates), or with enzymatic activities, suggesting the presence of possible time lags between organic inputs and microbial response. Chlorophyll a during the spring bloom displayed much higher concentrations than phaeopigments and correlated with carbohydrates. Chlorophyll a distribution was autocorrelated and displayed a large patch size (1,134 cm2). Phaeopigments and proteins accumulated in the central depression of the ripple-mark structure, apparently depending upon a passive accumulation due to the reduced current action. In contrast, microphytobenthic biomass and bacterial numbers were highest in the two opposite ripples, suggesting that different driving forces operate selectively on the living components.}, }
@article {pmid12024279, year = {2001}, author = {Boenigk, J and Matz, C and Jürgens, K and Arndt, H}, title = {The Influence of Preculture Conditions and Food Quality on the Ingestion and Digestion Process of Three Species of Heterotrophic Nanoflagellates.}, journal = {Microbial ecology}, volume = {42}, number = {2}, pages = {168-176}, doi = {10.1007/s002480000116}, pmid = {12024279}, issn = {1432-184X}, abstract = {The influence of prey characteristics such as motility and size as well as of predator characteristics such as satiation and preculturing diet on the feeding process of interception feeding heterotrophic nanoflagellates was investigated. Three species of gram-negative bacteria, one species of gram-positive bacteria, two species of cyanobacteria (Synechococcus) and inert latex particles were fed as prey particles for three species of heterotrophic nanoflagellates (Spumella, Ochromonas, Cafeteria). Ingestion rates depended on the satiation of the flagellates and especially on the filling status of the food vacuoles. In addition, the ingestion rates depended on the characteristics of the food particle and were modified by pre-culturing the flagellates on either Pseudomonas putida or Bacillus subtilis. Digestion was found to be particle-specific. Cyanobacteria were excreted a few minutes after ingestion whereas heterotrophic bacteria were stored and digested in the food vacuoles. The spectrum of ingested particles is not identical to that of digested particles and thus neither the diet of the flagellates nor their impact on bacterial communities can be calculated simply from food vacuole content. "Selective digestion" could be shown to be an important selection mechanism concerning natural food particles. The digestion strategies of Cafeteria on the one hand and Spumella and Ochromonas on the other hand may be an important factor to explain protozoan species composition and succession in the field. In addition to bacterial abundance and grazing pressure by metazooplankton, the bacterial speciescomposition as well as biochemical variations within bacterial species may influence protozoan species composition and abundance.}, }
@article {pmid12024278, year = {2001}, author = {Wieltschnig, C and Kirschner, AK and Steitz, A and Velimirov, B}, title = {Weak Coupling between Heterotrophic Nanoflagellates and Bacteria in a Eutrophic Freshwater Environment.}, journal = {Microbial ecology}, volume = {42}, number = {2}, pages = {159-167}, doi = {10.1007/s002480000107}, pmid = {12024278}, issn = {1432-184X}, abstract = {In a study on the dynamics and trophic role of the heterotrophic nanoflagellate (HNAN) assemblage in the microbial food web of a eutrophic oxbow lake abundances, biomass, and production rates of HNAN and their potential prey organisms, namely heterotrophic bacteria and autotrophic picoplankton, were monitored for a period of 2 years. No coupling between HNAN abundance and biomass and the abundance and biomass of their picoplanktonic prey was observed for the investigation period. The ratio of heterotrophic bacterial to HNAN abundance ranged from 2.2 x 103 to 8.6 x 103 (mean: 4.2 x 103 +/- 1.8 x 103). HNAN carbon consumption could account for only 10% to 40% of bacterial secondary production. The lack of coupling between HNAN and their potential prey and the low HNAN abundance relative to bacterial abundance suggested (a) that HNAN grazing was an insignificant factor in the regulation of bacterial abundance and (b) that HNAN abundance was regulated by predation rather than by prey abundance. This hypothesis was supported by the fact that HNAN growth rates were high (in the range of 0.45 d-1 to 1.00 d-1 during spring and summer, yearly mean: 0.52 d-1), and only weakly correlated with prey abundance and biomass. The results indicated strong top-down control of HNAN and consequently a weak coupling of HNAN and picoplankton in the investigated eutrophic freshwater environment.}, }
@article {pmid12024277, year = {2001}, author = {Kaiser, O and Pühler, A and Selbitschka, W}, title = {Phylogenetic Analysis of Microbial Diversity in the Rhizoplane of Oilseed Rape (Brassica napus cv. Westar) Employing Cultivation-Dependent and Cultivation-Independent Approaches.}, journal = {Microbial ecology}, volume = {42}, number = {2}, pages = {136-149}, doi = {10.1007/s002480000121}, pmid = {12024277}, issn = {1432-184X}, abstract = {The structure of the microbial rhizoplane community of the important crop plant oilseed rape was studied by using a culture-dependent as well as a culture-independent approach based on 16S rDNA amplification. After isolation of the microbial community from the rhizoplane of oilseed rape (Brassica napus cv. Westar), the collected suspension was divided into two parts. One part was used for cultivation of bacteria onto three different growth media to establish a culture collection. From the other part of the rhizoplane suspension, genomic DNA was isolated and purified. Thereafter, 16S rDNA was amplified by PCR and cloned to obtain a library of 16S rDNA genes representative for the bacterial communities of this habitat. Phylogenetic 16S rDNA sequence analysis of 103 clones of this library revealed considerable differences from the corresponding nucleotide sequences of 111 cultured bacteria. Whereas the 16S rDNA clone library was dominated by a-Proteobacteria and bacteria of the Cytophaga-Flavobacterium-Bacteroides (CFB) phylum (51% and 30%, respectively), less than 17% of the cultured bacteria belonged to these two groups. More than 64% of the cultivated isolates were allocated to the b- and g-subclasses of the Proteobacteria, which were present in the clone library at about 14%. Most of the clones of the a-Proteobacteria of the library showed highest similarity to Bradyrhizobium sp. No such bacteria were found in the culture collection. Similarly, the second dominant group of the clone library comprising members of the CFB phylum was represented in the culture collection by a single isolate. The phylogenetic analysis of isolates of the culture collection clearly emphasized the need to use different growth media for recovery of rhizoplane bacteria. Whereas most of the a-Proteobacteria were recovered on complex medium, most of the b-Proteobacteria were isolated onto minimal media. Our results demonstrate that the combined approach pursued in this paper is necessary to explore the biodiversity of bacterial rhizoplane communities.}, }
@article {pmid12024276, year = {2001}, author = {Wiemken, V and Laczko, E and Ineichen, K and Boller, T}, title = {Effects of Elevated Carbon Dioxide and Nitrogen Fertilization on Mycorrhizal Fine Roots and the Soil Microbial Community in Beech-Spruce Ecosystems on Siliceous and Calcareous Soil.}, journal = {Microbial ecology}, volume = {42}, number = {2}, pages = {126-135}, doi = {10.1007/s002480000080}, pmid = {12024276}, issn = {1432-184X}, abstract = {To study the responses of forests to global change, model ecosystems consisting of beech and spruce trees were maintained in open top chambers for 4 years under four conditions, namely with normal and elevated CO2 and with low and high nitrogen input, each replicated four times. Each open top chamber (height 3 m, diameter 3 m, soil depth 1.5 m) contained two separate soil compartments containing nutrient-poor siliceous and nutrient-rich calcareous soil. Here, we focus on the fine roots and the soil microbial community in these model ecosystems. At the time of planting, the fine roots were cut back according to forestry practice, and the newly formed roots were colonized by the indigenous soil microflora. After 4 years, the total biomass of fine roots, when averaged over all treatments, was almost the same in each of the two soil types; it was highest in the top 100 mm of soil (60%) and decreased sharply in deeper soil layers. Fungal biomass associated with the fine roots, consisting mainly of ectomycorrhizal fungi, was estimated using the ergosterol content as a marker. It was much higher in fine roots in the siliceous than in the calcareous soil, indicating considerably enhanced ectomycorrhiza formation in the nutrient-poor siliceous soil. Elevated atmospheric CO2 stimulated fine root production by ca. 85% and 43% in the top 100 mm of calcareous and siliceous soils respectively. Increased nitrogen input caused a slightly reduced production of fine root biomass in the calcareous soil but increased it by 33% in the siliceous soil. Marker substances for microorganisms were analyzed in the root-free soil. The amounts of carbon released by fumigation/extraction (a general marker for microbial biomass) and chitin (a marker for fungal biomass) were significantly higher in the top layer of the siliceous than of the calcareous soil, but they did not respond significantly to the treatments with elevated CO2 or the nitrogen fertilizer. The total concentration of the phospholipid fatty acids (PLFAs) and the number of the PLFAs did not differ between the two soil types. However, four of the eight most abundant PLFAs differed significantly between the two soil types. Principal component analysis revealed clearly separated clusters for the two soil types. Although analysis did not reveal any significant changes in response to the treatments, the concentration of the PLFA typical for ectomycorrhizal fungi was significantly higher under conditions of elevated CO2 in the nutrient-rich calcareous soil.}, }
@article {pmid12024275, year = {2001}, author = {Hjorleifsdottir, S and Skirnisdottir, S and Hreggvidsson, GO and Holst, O and Kristjansson, JK}, title = {Species Composition of Cultivated and Noncultivated Bacteria from Short Filaments in an Icelandic Hot Spring at 88 degrees C.}, journal = {Microbial ecology}, volume = {42}, number = {2}, pages = {117-125}, doi = {10.1007/s002480000110}, pmid = {12024275}, issn = {1432-184X}, abstract = {Samples of short pink-grayish filaments were collected from a hot spring in the Hengill area in southwestern Iceland at 85-88 degrees C, pH 6.9 and 1.7 mg/L sulfide. The species composition was studied by cloning and sequencing small subunit rRNA genes obtained by PCR amplifications from mat DNA. Using 98% sequence similarity as a cutoff value, a total of 5 bacterial operational taxonomic units (OTUs) and 6 archaeal OTUs were detected among 68 bacterial clones and 97 archaeal clones. Database matching showed that 80.5% of the archaeal sequences were 99% similar to Pyrobaculum islandicum and 14.5% were closest to the Korarchaeota clone sequence SRI306. About 87% of the bacterial sequences had the closest database match (99%) to the clone sequence SRI48 but were also found to be 99% identical with hydrogen-oxidizing strains previously isolated in this laboratory from hot springs in the same region. Out of 7 Thermus sequences, 4 were 100% identical to T. scotoductus NMX2 A.1 but 3 represented a new uncultivated Thermus species. Four different media, varying in organic nutrients and phosphate composition were used to isolate 81 aerobic thermophilic heterotrophs. Four isolates were Bacillus spp; but out of 77 Thermus isolates, 42 belonged to T. scotoductus and 35 to T. brockianus. T. scotoductus seemed to be preferably isolated on media low in nutrients and phosphate, whereas for T. brockianus it was the opposite. The T. scotoductus clones and isolates had 99-100% sequence similarity to each other. No T. brockianus sequences were found in the bacterial clone library.}, }
@article {pmid12024274, year = {2001}, author = {}, title = {Erratum.}, journal = {Microbial ecology}, volume = {42}, number = {2}, pages = {116}, doi = {10.1007/s00248-001-0019-7}, pmid = {12024274}, issn = {1432-184X}, }
@article {pmid12024273, year = {2001}, author = {Rasmussen, LD and Ekelund, F and Hansen, LH and Sørensen, SJ and Johnsen, K}, title = {Group-Specific PCR Primers to Amplify 24S a-Subunit rRNA Genes from Kinetoplastida (Protozoa) Used in Denaturing Gradient Gel Electrophoresis.}, journal = {Microbial ecology}, volume = {42}, number = {2}, pages = {109-115}, doi = {10.1007/s002480000120}, pmid = {12024273}, issn = {1432-184X}, abstract = {We developed and tested a set of primers for amplification of a region of the 24S a-subunit rRNA genes (24S rDNA) specific to Kinetoplastida (Protozoa). The reverse primer was supplied with a GC rich region in the 5? end in order to make the PCR product suitable for analysis by denaturing gradient gel electrophoresis (DGGE). PCR product was obtained from all the kinetoplastids tested and no PCR product was obtained from any other Eukaryotes or Prokaryotes tested. It was possible to distinguish between all pure cultures of kinetoplastids by denaturing gradient gel electrophoresis in gels ranging from 20% to 60% denaturants. PCR-DGGE analysis of DNA purified from lake sediment revealed approximately 20 bands indicating high kinetoplastid diversity. Direct cloning and sequencing of 24S rDNA sequences retrieved from the lake sediment by PCR also showed high kinetoplastid diversity. Of 43 clones, 27 different sequences were found. Alignments and phylogenetic analysis showed that a majority of the sequences were most closely related to the Bodonidae. Four sequences were closer to the Trypanosomatidae, whereas three sequences fell outside both groups. The PCR-DGGE procedure developed in this study has been shown to be useful for distinguishing between different kinetoplastid species. Thus, it may be a useful tool for evaluating the genetic diversity of this group in environmental samples, e.g., as a result of perturbation. Another possible application of this method is in fast and accurate screening for the presence and identification of pathological parasitic Kinetoplastida from environmental samples and for diagnostics of human and animal infections.}, }
@article {pmid12024272, year = {2001}, author = {Anderson, OR and Gorrell, T and Bergen, A and Kruzansky, R and Levandowsky, M}, title = {Naked Amoebas and Bacteria in an Oil-Impacted Salt Marsh Community.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {474-481}, doi = {10.1007/s00248-001-0008-x}, pmid = {12024272}, issn = {1432-184X}, abstract = {Populations of soil amoebas were monitored in two salt marshes in Staten Island, NY for 2 years. One site, Gulfport Reach on the Arthur Kill, has been highly impacted by numerous oil spills. In particular, in 1990 a massive no. 2 fuel oil spill from a ruptured pipe flooded the area; its sediments had total petroleum hydrocarbon (TPH) concentrations in the range 800-46,000 ppm. A reference site 11 km away, on the Atlantic coast, had low TPH levels. Amoeba population densities were in general higher in the impacted sediments. In laboratory microcosm experiments, sediment samples from unimpacted sites were treated with added fresh (unweathered) hydrocarbons (no. 2 fuel oil) and cultured; these also yielded higher amoeba numbers than untreated controls. Four distinct amoeba morphotypes were monitored. Changes in population levels of total amoebas were correlated in the two sites, particularly for morphotype 2 (r = 0.83). The ratios of total amoebas to total bacterial numbers were also correlated (r = 0.85) between the sites. This suggests the amoebas may function as generalists, and that their trophic relation to bacterial prey is not much affected by the presence of petroleum hydrocarbons, but rather may reflect regional parameters such as ambient temperature or other physical factors.}, }
@article {pmid12024271, year = {2001}, author = {Bergholz, PW and Bagwell, CE and Lovell, CR}, title = {Physiological Diversity of Rhizoplane Diazotrophs of the Saltmeadow Cordgrass, Spartina patens: Implications for Host Specific Ecotypes.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {466-473}, doi = {10.1007/s002480000118}, pmid = {12024271}, issn = {1432-184X}, abstract = {Diazotrophic bacteria are important contributors to salt marsh productivity, but the biotic and abiotic factors that influence their distributions and function and the extent of their diversity cannot be understood in the absence of physiological information. Here we examine the physiological diversity and distribution patterns of diazotrophic bacteria associated with the rhizoplane of the saltmeadow cordgrass, Spartina patens, in comparison with diazotrophs from other intertidal grasses (tall and short form Spartina alterniflora and Juncus roemerianus) from the same salt marsh. S. patens plants were collected from two distinct habitats, and a total of 115 strains (111 Gram negative and 4 Gram positive strains) were isolated into pure culture by stab inoculating roots and rhizomes into combined nitrogen-free semisolid media. Most strains were microaerophilic and approximately one-half were motile. API test strips were used to eliminate redundancy within the culture collection, resulting in 21 physiologically different API groups (17 Gram negative and 4 Gram positive groups). A representative strain from each API group was selected for dot blot hybridization with a nifH specific probe and 16 strains (13 Gram negative and 3 Gram positive) were scored as positive. The nifH positive API group representative strains were characterized further using BIOLOG test plates. Substrate utilization potentials defined two S. patens strain clusters, and only one S. patens strain was physiologically similar to any other strain from a different host plant origin. No distinctions could be made based on the different S. patens habitats, suggesting that the host plant may have a greater impact than abiotic environmental conditions on the distributions of the rhizoplane diazotrophs recovered.}, }
@article {pmid12024270, year = {2001}, author = {Schwaner, NE and Kroer, N}, title = {Effect of Plant Species on the Kinetics of Conjugal Transfer in the Rhizosphere and Relation to Bacterial Metabolic Activity.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {458-465}, doi = {10.1007/s00248-001-0001-4}, pmid = {12024270}, issn = {1432-184X}, abstract = {Conjugal transfer of a derivative of the RP4 plasmid between Pseudomonas fluorescens AS12 and Serratia plymuthica RF7 was compared in the rhizosphere of pea, wheat, and barley and related to the metabolic activity of the bacteria. To obtain a reliable measure of transfer, which allowed comparison of results between experiments, mathematical mass-action models were used to determine plasmid intrinsic kinetic coefficients. The data showed that not only were the rhizospheres highly conducive of transfer, with rates up to six orders of magnitude higher than in bulk soil, but differences between rhizospheres were also observed. Highest intrinsic kinetic coefficients were found in the pea rhizosphere (1.1-4.1 x 10-11), followed by the barley rhizosphere (2.4-7.2 x 10-12) and the wheat rhizosphere (2.2-2.9 x 10-13). It was further shown that the metabolic activity of the cells in the rhizosphere of the three plants was not significantly different, and that activity and transfer were not correlated. Thus, the data demonstrated species specific rhizosphere effects on the conjugal transfer process that could not be attributed to different metabolic activities of the bacteria.}, }
@article {pmid12024269, year = {2001}, author = {Wohl, DL and McArthur, JV}, title = {Aquatic Actinomycete-Fungal Interactions and Their Effects on Organic Matter Decomposition: A Microcosm Study.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {446-457}, doi = {10.1007/s00248-001-0005-0}, pmid = {12024269}, issn = {1432-184X}, abstract = {The role of fungi in the decomposition of organic matter in streams has been well examined, although the role of bacterial antagonists in such processes has gained little attention. To examine bacterial-fungal interactions, experiments involving pairwise combinations of four actinomycete isolates (A1+ and A2+ could remove chitin from chitin-containing media, and A1? and A2? could not) and two fungal isolates (F+ a true fungus, F? an oomycote) were conducted. For each bacterial-fungal combination, 250-ml microcosms were sampled at 8 day intervals for 32 days. Microbial biomass and organic matter, as well as the activities of five extracellular enzymes, were measured. Each experiment consisted of a control group and four treatment groups. Controls comprised sterilized stream water and macrophytes. The first treatment was inoculated with only actinomycetes (~103 cells ml-1), the second treatment was inoculated with only fungi (~102 cells ml-1), the third group was inoculated simultaneously with actinomycetes and fungi, and the fourth group was inoculated with actinomycetes 2 days after fungal establishment. For all combinations, the lowest rates of organic matter decomposition were expected in the controls, as a result of only physical degradation. In contrast, the greatest rates of organic matter decomposition were predicted in treatments inoculated with F+ 2 days prior to A1? or A2?. Greater than 50% of the organic matter was decomposed in each of the fungal treatments. Fungal-actinomycete interactions resulted in reduced fungal biomass relative to the fungal-only treatments. However, when inoculated 2 days apart, combinations of F? and actinomycetes resulted in enhanced rates of organic matter decomposition, as well as greater levels of extracellular enzyme activities. These results demonstrate that actinomycete-fungal interactions and their colonization dynamics affect the accumulation of biomass, extracellular enzyme activities, and rates of organic matter decomposition.}, }
@article {pmid12024268, year = {2001}, author = {Thrane, C and Nielsen, MN and Sørensen, J and Olsson, S}, title = {Pseudomonas fluorescens DR54 Reduces Sclerotia Formation, Biomass Development, and Disease Incidence of Rhizoctonia solani Causing Damping-Off in Sugar Beet.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {438-445}, doi = {10.1007/s00248-001-0007-y}, pmid = {12024268}, issn = {1432-184X}, abstract = {Effects of the biocontrol strain, Pseudomonas fluorescens DR54, on growth and disease development by Rhizoctonia solani causing damping-off in sugar beet were studied in soil microcosms and in pot experiments with natural, clay-type soil. In pot experiments with P. fluorescens DR54-treated seeds, significantly fewer Rhizoctonia-challenged seedlings showed damping-off symptoms than when not inoculated with the biocontrol agent. In the rhizosphere of P. fluorescens DR54 inoculated seeds, the bacterial inoculant was present in high numbers as shown by dilution plating and immunoblotting. By the ELISA antibody technique and direct microscopy of the fungal pathogen grown in soil microcosms, it was shown that the presence of P. fluorescens DR54 on the inoculated seeds had a strong inhibitory effect on development of both mycelium biomass and sclerotia formation by R. solani. In the field experiment, plant emergence was increased by treatment with P. fluorescens DR54 and the inoculant was found to be the dominating rhizosphere colonizing pseudomonad immediately after seedling emergence.}, }
@article {pmid12024267, year = {2001}, author = {Casamayor, EO and Mas, J and Pedrós-Alió, C}, title = {In Situ Assessment on the Physiological State of Purple and Green Sulfur Bacteria through the Analyses of Pigment and 5S rRNA Content.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {427-437}, doi = {10.1007/s002480000068}, pmid = {12024267}, issn = {1432-184X}, abstract = {Time-depth distribution of the microbial anaerobic assemblage of Lake Cisó was analyzed by microscopy, pigment composition, and electrophoretic analysis of 5S rRNAs. Purple (Amoebobacter-like and Thiocystis minor-like cells) and green (Chlorobium-like) sulfur bacteria were very abundant. Both groups coexisted in depth and in time despite the fact that they compete for the same natural resources (e.g., light and sulfide). Cell abundance, group-specific pigment content, and group-specific 5S rRNA content did not change in parallel with depth. This was due to variations in the specific content of both RNA and pigments. Specific content of RNA was systematically higher in purple than in green sulfur bacteria. The latter, in turn, displayed a much higher pigment content. Specific content of both RNA and pigments changed with depth and time. Analysis of tRNA band patterns indicated no changes in the populations forming the assemblage. Changes in specific contents, therefore, were the result of physiological adaptations of the populations already present in the system. We concluded that each group of bacteria showed differential adaptations in both RNA and pigment content, and that the specific contents measured were good indicators of the physiological status of these bacteria in situ. The higher content of RNA in purple sulfur bacteria indicates that these organisms are the main contributors to anaerobic carbon fixation and sulfide oxidation processes in Lake Cisó.}, }
@article {pmid12024266, year = {2001}, author = {Almeida, MA and Cunha, MA and Alcântara, F}, title = {Factors Influencing Bacterial Production in a Shallow Estuarine System.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {416-426}, doi = {10.1007/s002480000119}, pmid = {12024266}, issn = {1432-184X}, abstract = {The bacterioplankton of the marine and brackish water zones of the complex system Ria de Aveiro was characterized as profiles of bacterial abundance and biomass productivity. During the warm season, total bacteria ranged from 0.2 to 8.5 x 109 cells L-1 and active bacteria number from 0.1 to 3.1 x 109 cells L-1. Total and active bacterial numbers were, on average, three times higher in brackish than in marine water. Bacterial productivity on different dates and different tides in the marine zone varied from 0.05 to 4.5 mg C L-1 h-1. Here the average productivity (1.1 mg C L-1 h-1) was 3.5 times less than in brackish water (average 3.8 mg C L-1 h-1; range 0.7-14.2 mg C L-1 h-1). Specific productivity varied from 0.05 to 2.61 fg C cell-1 h-1, a range that was similar throughout the ecosystem. However, specific productivity per active cell was 19% higher in brackish water. Bacterial production variation was best explained by the number of active bacteria, which, in turn, was highly associated with total bacterial number, temperature, and particulate organic carbon. In the marine zone, bacterial production was also influenced by depth and salinity. In the brackish zone, the set of independent variables explained a smaller percentage of bacterial production variation than in marine zone, suggesting greater importance of other variables. In the marine zone, and mainly near low tide, productivity was significantly higher (average 3.3 times) at the surface (down to 0.5 m) than in the deeper layers of the water column. This stratification of bacterial productivity was linked to the increased specific productivity per active cell, as no modification in the proportion of active cells in the population could be detected. The vertical profile of bacterial production in the deeper zone of this estuarine ecosystem, in which no clear salinity or thermal stratification occurs throughout the tidal cycle, seemed to reflect a biochemical stratification generated by increased phytoplankton exudation and/or by photochemical transformation of semilabile or recalcitrant organic compounds. Shallower water masses tend to blur this surface effect. The relative importance of photochemical transformation in the pattern of estuarine bacterial production will therefore tend to vary with the bathymetry of the system.}, }
@article {pmid12024265, year = {2001}, author = {Alonso, MC and Jimenez-Gomez, F and Rodriguez, J and Borrego, JJ}, title = {Distribution of virus-like Particles in an Oligotrophic Marine Environment (Alboran Sea, Western Mediterranean).}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {407-415}, doi = {10.1007/s00248-001-0015-y}, pmid = {12024265}, issn = {1432-184X}, abstract = {Viruses are abundant in a variety of aquatic environments, often exceeding bacterial abundance by one order of magnitude. In the present study, the spatial distribution of viruses in offshore waters of the Alboran Sea (Western Mediterranean) have been studied to determine the relationships between viruses and host communities in this oligotrophic marine environment. Viral abundance was determined using two methods: (i) epifluorescence light microscopy using the dsDNA binding fluorochrome DAPI, and (ii) direct counts by transmission electron microscopy (TEM). The results obtained were significantly different; the highest viral counts were obtained by mean of TEM analyses. In all the samples tested the number of viruses was exceeded by the bacterial concentrations, with a ratio between viral and bacterial titers varying between 1.4 and 20. VLP (virus-like particle) counts were not significantly correlated (p > 0.001) with chlorophyll a concentration or the abundance of cyanobacteria. However, there was a positive and significant correlation with bacterial abundance (p <0.001). THE ANALYSIS OF SIZE AND MORPHOLOGY OF VIRAL PARTICLES BY TEM AND THE CORRELATION OBTAINED BETWEEN THE NUMBERS OF VLP AND BACTERIA SUGGEST THAT THE MAJORITY OF THE VIRAL PARTICLES IN THE ALBORAN SEA ARE BACTERIOPHAGES. NONE OF THE INDIRECT EVIDENCE SUGGESTED THAT EUKARYOTIC ALGAE OR CYANOBACTERIA WERE IMPORTANT HOST ORGANISMS IN THESE WATERS.}, }
@article {pmid12024264, year = {2001}, author = {Middelboe, M and Hagström, A and Blackburn, N and Sinn, B and Fischer, U and Borch, NH and Pinhassi, J and Simu, K and Lorenz, MG}, title = {Effects of Bacteriophages on the Population Dynamics of Four Strains of Pelagic Marine Bacteria.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {395-406}, doi = {10.1007/s00248-001-0012-1}, pmid = {12024264}, issn = {1432-184X}, abstract = {Viral lysis of specific bacterial populations has been suggested to be an important factor for structuring marine bacterioplankton communities. In the present study, the influence of bacteriophages on the diversity and population dynamics of four marine bacterial phage-host systems was studied experimentally in continuous cultures and theoretically by a mathematical model. By use of whole genome DNA hybridization toward community DNA, we analyzed the dynamics of individual bacterial host populations in response to the addition of their specific phage in continuous cultures of mixed bacterial assemblages. In these experiments, viral lysis had only temporary effects on the dynamics and diversity of the individual bacterial host species. Following the initial lysis of sensitive host cells, growth of phage-resistant clones of the added bacteria resulted in a distribution of bacterial strains in the phage-enriched culture that was similar to that in the control culture without phages after about 50-60 h incubation. Consequently, after a time frame of 5-10 generations after lysis, it was the interspecies competition rather than viral lysis of specific bacterial strains that was the driving force in the regulation of bacterial species composition in these experiments. The clonal diversity, on the other hand, was strongly influenced by viral activity, since the clonal composition of the four species in the phage-enriched culture changed completely from phage-sensitive to phage-resistant clones. The model simulation predicted that viral lysis had a strong impact on the population dynamics, the species composition, and the clonal composition of the bacterial community over longer time scales (weeks). However, according to the model, the overall density of bacteria in the system was not affected by phages, since resistant clones complemented the fluctuations caused by viral lysis. Based on the model analysis, we therefore suggest that viral lysis can have a strong influence on the dynamics of bacterial populations in planktonic marine systems.}, }
@article {pmid12024263, year = {2001}, author = {Blomqvist, P and Jansson, M and Drakare, S and Bergström, AK and Brydsten, L}, title = {Effects of Additions of DOC on Pelagic Biota in a Clearwater System: Results from a Whole Lake Experiment in Northern Sweden.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {383-394}, doi = {10.1007/s002480000101}, pmid = {12024263}, issn = {1432-184X}, abstract = {An oligotrophic clearwater lake, initially characterized by a pronounced dominance of autotrophic phytoplankton and mostly by one species, the green alga Botryococcus, was subject to additions of dissolved organic carbon in the form of white sugar (sucrose) during two consecutive years. The hypothesis tested was that it is organic carbon per se, and not other possible effects of humic substances, that determines the differences in structure of the planktonic ecosystem between humic and clearwater lakes. The additions of DOC resulted in a significant increase in bacterial biomass and a decrease in the biomass of autotrophic phytoplankton. The biomass of mixotrophic and heterotrophic flagellates instead increased significantly, whereas no effects were found to propagate to higher trophic levels. As a result of the changes among biota, total planktonic biomass also decreased to a level typical of nearby humic lakes. We suggest that it is the carbon component of humic material and its utilization by bacterioplankton that determines the structure and function of the pelagic food web in humic lakes.}, }
@article {pmid12024262, year = {2001}, author = {Karlsson, J and Jonsson, A and Jansson, M}, title = {Bacterioplankton Production in Lakes along an Altitude Gradient in the Subarctic North of Sweden.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {372-382}, doi = {10.1007/s00248-001-0009-9}, pmid = {12024262}, issn = {1432-184X}, abstract = {We examined changes in bacterioplankton standing stock and production in subarctic lakes in the north of Sweden to elucidate their coupling to lake physical, chemical, and biological characteristics. Sixteen lakes situated along an altitude gradient extending from the coniferous forest to the high-alpine belt were studied during 1998 and 1999. The summer mean bacterial numbers and production varied substantially between the lakes, with a general trend toward decreasing values with increasing altitude. The results demonstrate that P probably restricted bacterial utilization of DOC in the coniferous forest lakes, while low DOC concentrations limited bacterial growth during the summer in the alpine lakes. The primary production of plankton was insufficient to support bacterial production in the lakes. High input of allochthonous DOC to the alpine lakes in spring was sufficient both to increase the bacterial production and to induce P-limitation. As a consequence, there was a tendency toward higher bacterial activity in the spring compared to the summer in the alpine lakes. The results indicate that most of the bacterial standing stock and production are supported by allochthonous DOC plus DOC from benthic production, and more or less limited by the phosphorus supply. We therefore suggest that bacteria populations in subarctic lakes may be indirectly affected by climate variations through its impact on the input of DOC and nutrients from the lake catchments.}, }
@article {pmid12024261, year = {2001}, author = {Simek, K and Armengol, J and Comerma, M and Garcia, JC and Kojecka, P and Nedoma, J and Hejzlar, J}, title = {Changes in the Epilimnetic Bacterial Community Composition, Production, and Protist-Induced Mortality along the Longitudinal Axis of a Highly Eutrophic Reservoir.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {359-371}, doi = {10.1007/s00248-001-0014-z}, pmid = {12024261}, issn = {1432-184X}, abstract = {We studied changes in the epilimnetic bacterial community composition (BCC), bacterial biomass and production, and protistan succession and bacterivory along the longitudinal axis of the canyon-shaped, highly eutrophic Sau Reservoir (NE Spain) during two sampling campaigns, in April and July 1997. Longitudinal changes in BCC from the river inflow to the dam area of the reservoir were detected by using oligonucleotide probes targeted to the kingdom Bacteria, to the alpha, beta, and gamma subclasses (ALFA, BETA, and GAMA) of the class Proteobacteria, and to the Cytophaga/Flavobacterium (CF) cluster. In general, the inflow of the organically loaded Ter river, with highly abundant allochthonous bacterial populations, induced a clearly distinguishable longitudinal succession of the structure of the microbial food web. The most dynamic changes in microbial parameters occurred at the plunge point, the mixing area of river water and the reservoir epilimnion. Changes within members of BETA and CF were the most important in determining changes in BCC, bacterial abundance and biomass. Much less relevant changes occurred within the less abundant ALFA and GAMA bacteria. From the plunge point downstream, we described a significant shift in BCC in the form of decreased proportions of BETA and CF. This shift spatially coincided with the highest values of heterotrophic nanoflagellate bacterivory (roughly doubled the bacterial production). CF numerically dominated throughout the reservoir without any marked longitudinal changes in their mean cell volume. In contrast, very large cells affiliated to BETA clearly dominated in the allochthonous bacterial biomass brought by the river. BETA showed a marked downstream trend of decreasing mean cell volume. We conclude that the observed BCC shift and the longitudinal shift in food web structure (bacteria-heterotrophic nanoflagellates-ciliates) resulted from highly complex interactions brought about by several major factors: varying hydrology, the high localized allochthonous input of organic matter brought by the river, downstream changing substrate availability, and selective protistan bacterivory.}, }
@article {pmid12024260, year = {2001}, author = {Smoot, JC and Findlay, RH}, title = {Spatial and Seasonal Variation in a Reservoir Sedimentary Microbial Community as Determined by Phospholipid Analysis.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {350-358}, doi = {10.1007/s002480000102}, pmid = {12024260}, issn = {1432-184X}, abstract = {Sediment samples were collected monthly from Acton Lake, a eutrophic reservoir located in an agricultural region of southwestern Ohio, from three stations (River, Middle, and Dam) during the period May 1995 through January 1997. Sedimentary microbial biomass and community structures from these stations were studied using phospholipid analysis. At the River and Middle stations, the water column remained aerobic throughout the year, whereas the water overlying the Dam station sediments became anaerobic during summer stratification. Sedimentary microbial biomass at the River and Middle stations, as measured by the phospholipid phosphate (PLP) method, ranged from 225 to 450 nmol PLP g?1 d.w. (dry weight). Sedimentary microbial biomass at the Dam station was typically greater and ranged from 500 to 1,500 nmol PLP g?1 d.w. Principal component analysis of phospholipid fatty acid (PLFA) profiles indicated that the sedimentary microbial communities at all three stations displayed seasonal patterns of change. Among these patterns of change was a shift from aerobic microorganisms during times of cold water to anaerobic microorganisms during times of warm water. The Dam station differed from the River and Middle stations in that sediments from this station had disproportionately more polyenoic fatty acids, whereas sediments from the River and Middle stations had disproportionately more bacterial fatty acids. These data suggest that the Dam station may be a depositional zone for microeukaryotic phytoplankton produced in the overlying water column. These findings have implications for the understanding of carbon flux in reservoirs and preservation of organic matter in aquatic systems.}, }
@article {pmid12024259, year = {2001}, author = {Fernández-Valiente, E and Quesada, A and Howard-Williams, C and Hawes, I}, title = {N2-Fixation in Cyanobacterial Mats from Ponds on the McMurdo Ice Shelf, Antarctica.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {338-349}, doi = {10.1007/s00248-001-1010-z}, pmid = {12024259}, issn = {1432-184X}, abstract = {We have investigated the ecological importance of N2-fixation in cyanobacterial mats, dominated by oscillatorean species, in ponds of the Bratina Island area of the McMurdo Ice Shelf, Antarctica (78 degrees S, 166 degrees E). Nitrogenase activity, estimated as acetylene reducing activity (ARA), was found in all the mats investigated (n = 16). The average ARA was 75.9 mmol ethylene m-2 h-1, ranging from 6 to 201 mmol ethylene m-2 h-1. Nitrogenase activity was positively correlated with dissolved reactive phosphorus concentration in pondwater and the C/N ratio of the mat, and was negatively correlated with pondwater NH4+-N concentrations and natural abundance of 15N in the mats. ARA was restricted to the upper, oxic layer of the mats. Experiments conducted to ascribe ARA to different groups of prokaryotes suggested that ARA was mainly conducted by heterocystous cyanobacteria, since no activity was found in the dark and the activity was inhibited by the photosystem II inhibitor DCMU (3-[3,4-dichlorophenyl]-1,1-dimethyl urea). In spite of 24 h of daylight, nitrogenase activity showed a diel cycle with maximum activity at midday (10-18 h) and minimal activity at early morning (6-10 h) when pond temperatures were at their minima. Light dependency of nitrogenase activity for three cyanobacterial communities showed that the irradiance required for saturating ARA was low, in every case lower than 100 mmol photon m-2s-1. Irradiance rarely fell below 100 mmol photon m-2s-1 during Antarctic summer days and ARA was likely to be light saturated for much of the time. We estimate that N2 fixation represented on average a N input into the ponds of over 1 g m-2y-1. This value appears to be the highest N input to this Antarctic ecosystem.}, }
@article {pmid12024258, year = {2001}, author = {Espeland, EM and Wetzel, RG}, title = {Effects of Photosynthesis on Bacterial Phosphatase Production in Biofilms.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {328-337}, doi = {10.1007/s002480000117}, pmid = {12024258}, issn = {1432-184X}, abstract = {The fraction of bacteria displaying phosphatase activity within natural photosynthetic biofilms was examined in relation to phosphorus limitation and algal photosynthesis. An artificial substrate that forms a fluorescent precipitate was used in conjunction with the nucleic acid stain DAPI to enumerate extracellular phosphatase expression by biofilm bacteria exposed to different photosynthetic activities and phosphorus supplies. The proportion of bacteria displaying phosphatase activity changed in response to the presence or absence of algal photosynthesis. In general, phosphate-deprived biofilms had positive linear trends in bacterial phosphatase activity (p <0.001), with greater proportions of bacteria displaying phosphatase under photosynthetic inhibition compared to active photosynthesis. Under sufficient phosphate supplies, biofilms had negative linear trends (p <0.05) or were lower in the proportion of bacteria displaying phosphatase activity in the presence of algal photosynthesis, whereas bacterial phosphatase activity was generally maintained when photosynthesis was inhibited. it is suggested that the amount of extracellular organic carbon released within the biofilm matrix during photosynthesis indirectly affected bacterial phosphatase synthesis.}, }
@article {pmid12024257, year = {2001}, author = {DeLorenzo, ME and Lewitus, AJ and Scott, GI and Ross, PE}, title = {Use of Metabolic Inhibitors to Characterize Ecological Interactions in an Estuarine Microbial Food Web.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {317-327}, doi = {10.1007/s00248-001-0004-1}, pmid = {12024257}, issn = {1432-184X}, abstract = {Understanding microbial food web dynamics is complicated by the multitude of competitive or interdependent trophic interactions involved in material and energy flow. Metabolic inhibitors can be used to gain information on the relative importance of trophic pathways by uncoupling selected microbial components and examining the net effect on ecosystem structure and function. A eukaryotic growth inhibitor (cycloheximide), a prokaryotic growth inhibitor (antibiotic mixture), and an inhibitor of photosynthesis (DCMU) were used to examine the trophodynamics of microbial communities from the tidal creek in North Inlet, a salt marsh estuary near Georgetown, South Carolina. Natural microbial communities were collected in the spring, summer, and fall after colonization onto polyurethane foam substrates deployed in the tidal creek. Bacterial abundance and productivity, heterotrophic ciliate and flagellate abundance, and phototrophic productivity, biomass, and biovolume were measured at five time points after inhibitor additions. The trophic responses of the estuarine microbial food web to metabolic inhibitors varied with season. In the summer, a close interdependency among phototrophs, bacteria, and protozoa was indicated, and the important influence of microzooplanktonic nutrient recycling was evident (i.e., a positive feedback loop). In the fall, phototroph and bacteria interactions were competitive rather than interdependent, and grazer nutrient regeneration did not appear to be an important regulatory factor for bacterial or phototrophic activities. The results indicate a seasonal shift in microbial food web structure and function in North Inlet, from a summer community characterized by microbial loop dynamics to a more linear trophic system in the fall. This study stresses the important role of microbial loops in driving primary and secondary production in estuaries such as North Inlet that are tidally dominated by fluctuations in nutrient supply and a summer phytoplankton bloom.}, }
@article {pmid12024256, year = {2001}, author = {Satish, N and Krugman, T and Vinogradova, ON and Nevo, E and Kashi, Y}, title = {Genome Evolution of the Cyanobacterium Nostoc linckia under Sharp Microclimatic Divergence at "Evolution Canyon," Israel.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {306-316}, doi = {10.1007/s00248-001-0013-0}, pmid = {12024256}, issn = {1432-184X}, abstract = {We describe the genomic DNA diversity and divergence of the cyanobacterium Nostoc linckia from "Evolution Canyon," a microsite consisting of ecologically contrasting slopes, south-facing slope (SFS) and north-facing slope (NFS), at lower Nahal Oren, Mt. Carmel, Israel. The opposing slopes share their limestone lithology but vary greatly in their ecology, primarily because of different levels of solar radiation (which is six times higher on the SFS than on the NFS). The warm and xeric SFS displays a tropical African savanna, whereas the cool and mesic NFS displays a temperate South European Mediterranean live-oak maquis shrub forest. The cyanobacterium Nostoc linckia tested here is a sessile microorganism, growing as a carpet on rock surfaces and constantly exposed to environmental fluctuations of solar radiation, temperature, and desiccation. We demonstrate remarkable interslope and intraslope genetic divergence of the genome (including both coding and noncoding regions) of Nostoc linckia, by using 211 AFLP (amplified fragment length polymorphism) DNA molecular marker loci. Genetic polymorphism of N. linckia subpopulations on the ecologically harsher SFS was significantly (p <0.05) higher (p = 99.53%) than was that of the subpopulations on the climatically milder nfs (p = 85.78%). genetic polymorphism (p) and gene diversity (he) were significantly correlated with variables influencing aridity stress: solar radiation (sr) (rp = 0.956; p = 0.046), temperature (tm) (rp = 0.993; p = 0.0068), and day-night temperature difference (tdd) (rp = 0.975; p = 0.025). as in other tested organisms from "evolution canyon", but even more exceptionally because of its completely sedentary nature, we suggest that the climatically stressed sfs environment is responsible for this marked increase of genetic polymorphism, which is maintained by the combined evolutionary forces of diversifying and balancing selection. This could highlight the importance of ecological stress and selection in evolution and its remarkable effect on the genetic system across the prokaryotic genome.}, }
@article {pmid12024255, year = {2001}, author = {Brettar, I and Moore, ER and Höfle, MG}, title = {Phylogeny and Abundance of Novel Denitrifying Bacteria Isolated from the Water Column of the Central Baltic Sea.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {295-305}, doi = {10.1007/s00248-001-0011-2}, pmid = {12024255}, issn = {1432-184X}, abstract = {The Baltic Sea is an estuarine ecosystem where denitrification in the low oxic and anoxic parts of the deep water contributes significantly to the nitrogen budget. Seventy-six heterotrophic, denitrifying, strains have been isolated by four cultivation procedures from the water column of the Gotland Deep, the main anoxic basin of the Central Baltic. Phylogenetic positions of representative strains of 10 different genotypes, grouped beforehand by low molecular weight (LMW) RNA profiling, were estimated by 16S rRNA sequence analysis. The 10 genotypes consisted of two members of the alpha subclass of the Proteobacteria and eight members of the gamma subclass. The major fraction of the genotypes was considered to be novel species or even genera. The gamma-Proteobacteria were the most abundant of the denitrifying isolates (96% of the total isolates) with a predominance of Shewanella baltica (77%), whereas the alpha-Proteobacteria were represented by single isolates. The diversity spectrum of Baltic sea denitrifying isolates was rather distinct from that previously described for marine and freshwater environments. Denitrifying bacteria could be isolated from all depths of the water column with the highest diversity and abundance of genotypes detected in samples of the oxic-anoxic interface, the layer of high in situ denitrification. For success of isolation of phylogenetically divers denitrifiers, both sample origin and cultivation procedure were observed to have an impact.}, }
@article {pmid12024254, year = {2001}, author = {Halda-Alija, L and Hendricks, SP and Johnston, TC}, title = {Spatial and Temporal Variation of Enterobacter Genotypes in Sediments and the Underlying Hyporheic Zone of an Agricultural Stream.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {286-294}, doi = {10.1007/s00248-001-0021-0}, pmid = {12024254}, issn = {1432-184X}, abstract = {Population studies of enteric bacteria in an agriculturally impacted stream (Ledbetter Creek, Murray, Kentucky, USA) were conducted over a period of 2 years. Total number of bacteria, cultivated heterotrophic aerobic bacteria, and enteric bacteria showed significant differences between winter and summer. The cultivated numbers of heterotrophic aerobic bacteria and enteric bacteria were significantly more abundant in summer than in winter. The abundance of enteric bacteria was 12.9% in an upwelling zone and 9.8% in a downwelling zone in summer. Most of the enteric bacterial strains isolated on MacConkey agar were assigned to Enterobacter cloacae and E. agglomerans by API 20E and an analysis of the restriction patterns produced by amplified DNA coding for 16S rRNA (ARDRA) with the enzyme Hpa II. E. cloacae and E. agglomerans genotypes isolated from three hyporheic and gravel bar depth intervals (0-10 cm, 15-25 cm, and 30-40 cm) in summer and fall showed significant spatial variation and were heterogeneously distributed along the stream. Temperature, inorganic nutrients, and occurrence of anoxic zones affected the distribution of enteric bacteria. These techniques can be used as a model to monitor shifts among different species in the stream ecosystem.}, }
@article {pmid12024253, year = {2001}, author = {Riemann, L and Winding, A}, title = {Community Dynamics of Free-living and Particle-associated Bacterial Assemblages during a Freshwater Phytoplankton Bloom.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {274-285}, doi = {10.1007/s00248-001-0018-8}, pmid = {12024253}, issn = {1432-184X}, abstract = {Bacterial community dynamics were followed in a 19-day period during an induced diatom bloom in two freshwater mesocosms. The main goal was to compare diversity and succession among free-living (<10 mm) and particle-associated (>10 mm) bacteria. Denaturing gradient gel electrophoresis (DGGE) of PCR amplified 16S rDNA showed the highest number of bands among free-living bacteria, but with a significant phylogenetic overlap in the two size fractions indicating that free-living bacteria were also important members of the particle-associated bacterial assemblage. Whereas the number of bands in the free-living fraction decreased during the course of the bloom, several phylotypes unique to particles appeared towards the end of the experiment. Besides the primer set targeting Bacteria, a primer set targeting most members of the Cytophaga-Flavobacterium (CF)-cluster of the Cytophaga-Flavobacterium-Bacteroides group and a primer set mainly targeting a-Proteobacteria were applied. PCR-DGGE analyses revealed that a number of phylotypes targeted by those primer sets were found solely on particles. Almost all sequenced bands from the bacterial DGGE gel were related to phylogenetic groups commonly found in freshwater: a-Proteobacteria, CF, and Firmicutes. Despite the use of primers intended to be specific mainly for a-Proteobacteria most bands sequenced from the a-proteobacterial DGGE gel formed a cluster within the Verrucomicrobiales subdivision of the Verrucomicrobia division and were not related to a-Proteobacteria. Bands sequenced from the CF DGGE gel were related to members of the CF cluster. From the present study, we suggest that free-living and particle-associated bacterial communities should not be perceived as separate entities, but rather as interacting assemblages, where the extent of phylogenetic overlap is dependent on the nature of the particulate matter.}, }
@article {pmid12024252, year = {2001}, author = {Ka, JO and Yu, Z and Mohn, WW}, title = {Monitoring the Size and Metabolic Activity of the Bacterial Community during Biostimulation of Fuel-Contaminated Soil using Competitive PCR and RT-PCR.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {267-273}, doi = {10.1007/s00248-001-0003-2}, pmid = {12024252}, issn = {1432-184X}, abstract = {Efforts to understand and improve soil bioremediation are limited by our ability to determine how treatment variables affect microbial communities. A method was developed to monitor the density and metabolic activity of the total bacterial community in soil. This method was used to monitor the bacterial community in microcosms of Arctic soil after addition of N plus P to stimulate biodegradation of hydrocarbon contaminants. During 29 days of incubation, the total petroleum hydrocarbon level in the soil was reduced from 850 to 360 mg/g of soil. DNA and RNA were extracted from soil using a bead beating method, purified by ammonium acetate precipitation, and assayed by competitive PCR and RT-PCR assays with universal bacterial primers. The copy number of 16S rDNA in the soil microbial community was relatively stable and ranged from 1.7 x 109 to 4.5 x 109/g of soil throughout the incubation. The copy number of 16S rRNA changed substantially and ranged from 5.6 x 1010 to 1.0 x 1012/g of soil. The rRNA:rDNA ratio was highest during the phase of fastest hydrocarbon biodegradation. These results suggest that the treatment to stimulate hydrocarbon biodegradation did not substantially change the density of the bacterial community but did transiently increase its overall metabolic activity.}, }
@article {pmid12024251, year = {2001}, author = {Holden, PA and Hersman, LE and Firestone, MK}, title = {Water Content Mediated Microaerophilic Toluene Biodegradation in Arid Vadose Zone Materials.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {256-266}, doi = {10.1007/s00248-001-0010-3}, pmid = {12024251}, issn = {1432-184X}, abstract = {We investigated the conditions promoting toluene biodegradation for gasoline-contaminated near-surface (0.6 m depth) and subsurface (4.7 to 5.0 m depth) vadose zone soils sampled from an arid environment. At both depths, water addition was required for toluene biodegradation to occur. In near-surface samples, no inorganic nutrient addition was necessary and (i) biodegradation was fastest at 0.0 MPa, (ii) biodegradation rates decreased with decreasing water potential down to ?1.0 MPa, and (iii) biodegradation was undetectable at ?1.5 MPa. For subsurface material, toluene depletion was stimulated either by slurrying with a nutrient solution or by adjusting the moisture content to 20% (0.0 MPa) with nutrient solution and lowering the oxygen concentration (to effectively 1 mg L-1 in the aqueous phase). Thus, in the subsurface material, toluene depletion was microaerobic and nutrient-limited, occurring only under low oxygen and with inorganic nutrient addition. Our studies implicate microaerophily as an important characteristic of the toluene-degrading communities in these dry soils, with soil water as a primary controller of oxygen availability.}, }
@article {pmid12024250, year = {2001}, author = {Wilkinson, SC and Anderson, JM}, title = {Spatial Patterns of Soil Microbial Communities in a Norway Spruce (Picea abies) Plantation.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {248-255}, doi = {10.1007/s00248-001-0006-z}, pmid = {12024250}, issn = {1432-184X}, abstract = {The phospholipid fatty acid (PLFA) profiles of soil microbial communities were determined in relation to the patterns of tree cover in a mature Norway spruce plantation. Replicate samples of the surface organic layers were taken close to the trunk, at 1 m and at 2 m (under the edge of the canopy) beneath five trees. Samples were analyzed for standard PLFAs to assess the initial composition of the microbial communities. Replicate samples were then incubated under constant or fluctuating moisture conditions for 30 d to test the hypothesis that the patterns of microbial community structure (or its physiological state) might be determined by biophysical conditions under the tree canopies. The PLFA profiles near the trunks and at 2 m were similar, but samples taken 1 m from the bases of the trees contained lower concentrations of polyunsaturated (fungal) and monounsaturated PLFAs, and higher concentrations of saturated PLFAs. These differences in PLFA profiles were maintained during laboratory incubation under a regime of drying and wetting cycles, but there was some evidence of convergence in community structure under constant moisture conditions resulting from significant increases and decreases in specific bacterial PLFA concentrations. There were no effects of either moisture treatment on fungal PLFA concentrations. It is concluded that variation in the soil biophysical environment beneath the tree canopies resulted in the differentiation of spatially defined bacterial communities that were tolerant of moisture stress. The anomaly that differences in community structure were largest at an intermediate position of 1 m between the trunk and below the canopy edge was not explained but may relate to tree root distribution.}, }
@article {pmid12024249, year = {2001}, author = {Detmers, J and Schulte, U and Strauss, H and Kuever, J}, title = {Sulfate Reduction at a Lignite Seam: Microbial Abundance and Activity.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {238-247}, doi = {10.1007/s00248-001-1014-8}, pmid = {12024249}, issn = {1432-184X}, abstract = {In a combined isotope geochemical and microbiological investigation, a setting of multiple aquifers was characterized. Biologically mediated redox processes were observed in the aquifers situated in marine sands of Tertiary age and overlying Quaternary gravel deposits. Intercalated lignite seams define the aquitards, which separate the aquifers. Bacterial oxidation of organic matter is evident from dissolved inorganic carbon characterized by average carbon isotope values between ?18.4 per thousand and ?15.7 per thousand (PDB). Strongly positive sulfur isotope values of up to +50 per thousand (CTD) for residual sulfate indicate sulfate reduction under closed system conditions with respect to sulfate availability. Both, hydrochemical and isotope data are thus consistent with the recent activity of sulfate-reducing bacteria (SRB). Microbiological investigations revealed the presence of an anaerobic food chain in the aquifers. Most-probable-number (MPN) determinations for SRB and fermenting microorganisms reached highest values at the interface between aquifer and lignite seam (1.5 x 103 cells/g sediment dry mass). Five strains of SRB were isolated from highest MPN dilutions. Spore-forming bacteria appeared to dominate the SRB population. Sulfate reduction rates were determined by the 35S-radiotracer method. A detailed assessment indicates an increase in the reduction rate in proximity to the lignite seam, with a maximum turnover of 8.4 mM sulfate/a, suggesting that lignite-drived compounds represent the substrate for sulfate reduction.}, }
@article {pmid12024248, year = {2001}, author = {Smith, Z and McCaig, AE and Stephen, JR and Embley, TM and Prosser, JI}, title = {Species Diversity of Uncultured and Cultured Populations of Soil and Marine Ammonia Oxidizing Bacteria.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {228-237}, doi = {10.1007/s00248-001-0016-x}, pmid = {12024248}, issn = {1432-184X}, abstract = {Although molecular techniques are considered to provide a more comprehensive view of species diversity of natural microbial populations, few studies have compared diversity assessed by molecular and cultivation-based approaches using the same samples. To achieve this, the diversity of natural populations of ammonia oxidising bacteria in arable soil and marine sediments was determined by analysis of 16S rDNA sequences from enrichment cultures, prepared using standard methods for this group, and from 16S rDNA cloned from DNA extracted directly from the same environmental samples. Soil and marine samples yielded 31 and 18 enrichment cultures, respectively, which were compared with 50 and 40 environmental clones. There was no evidence for selection for particular ammonia oxidizer clusters by different procedures employed for enrichment from soil samples, although no culture was obtained in medium at acid pH. In soil enrichment cultures, Nitrosospira cluster 3 sequences were most abundant, whereas clones were distributed more evenly between Nitrosospira clusters 2, 3, and 4. In marine samples, the majority of enrichment cultures contained Nitrosomonas, whereas Nitrosospira sequences were most abundant among environmental clones. Soil enrichments contained a higher proportion of identical sequences than clones, suggesting laboratory selection for particular strains, but the converse was found in marine samples. In addition, 16% of soil enrichment culture sequences were identical to those in environmental clones, but only 1 of 40 marine enrichments was found among clones, indicating poorer culturability of marine strains represented in the clone library, under the conditions employed. The study demonstrates significant differences in species composition assessed by molecular and culture-based approaches but indicates also that, employing only a limited range of cultivation conditions, 7% of the observed sequence diversity in clones of ammonia oxidizers from these environments could be obtained in laboratory enrichment culture. Further studies and experimental approaches are required to determine which approach provides better representation of the natural community.}, }
@article {pmid12024247, year = {2001}, author = {Posch, T and Jezbera, J and Vrba, J and Simek, K and Pernthaler, J and Andreatta, S and Sonntag, B}, title = {Size Selective Feeding in Cyclidium glaucoma (Ciliophora, Scuticociliatida) and Its Effects on Bacterial Community Structure: A Study from a Continuous Cultivation System.}, journal = {Microbial ecology}, volume = {42}, number = {3}, pages = {217-227}, doi = {10.1007/s002480000114}, pmid = {12024247}, issn = {1432-184X}, abstract = {Three aspects of size selective feeding by the scuticociliate Cyclidium glaucoma were studied in continuous cultivation systems. Firstly, grazing-induced changes in abundance, biomass, and size structure of a bacterial community were investigated. Secondly, we studied possible grazing-protection mechanisms of bacteria as a response to permanent presence of the predator. And finally, we were looking for potential feedback mechanisms within this predator-prey relationship, i.e., how the ciliate population reacted to a changed, more grazing-protected bacterial community. The first stage of the cultivation system consisted of the alga Cryptomonas sp. and the accompanying mixed bacterial community. These organisms were transferred to two second stage vessels, a control stage without ciliates and a second one inoculated with C. glaucoma. After the first week, the abundance of bacteria in the latter decreased by 60% and remained stable until the end of the experiment (65 d), whereas bacterial biomass was less affected (393 mg C L-1 during days 0-7, 281 mg C L-1 afterwards). The mean bacterial cell volume doubled from 0.089 mm3 to 0.167 mm3, which was mainly due to increasing cell widths. During the whole investigation period formation of colonies or filaments was not observed, but we found a clear feedback of ciliates on bacterial size. An increase in bacterial cell volume was always followed by a decline of the predator population, resulting in a yet undescribed type of microbial predator-prey relation. Literature and our own data on the optimal food size range grazed by C. glaucoma showed that bacterial cell width rather than length was responsible for that observed phenomenon. Finally, we suggest that uptake rates of spherical latex beads give only limited information on truly ingestible prey volumes and that prey geometry should be considered in future studies on size selective feeding of protists.}, }
@article {pmid12024246, year = {2001}, author = {Rozen, Y and Dyk, TK and LaRossa, RA and Belkin, S}, title = {Seawater Activation of Escherichia coli Gene Promoter Elements: Dominance of rpoS Control.}, journal = {Microbial ecology}, volume = {42}, number = {4}, pages = {635-643}, doi = {10.1007/s00248-001-1012-x}, pmid = {12024246}, issn = {1432-184X}, abstract = {The release of non-disinfected wastewater into the marine environment is a common practice in many countries; nevertheless, the molecular mechanisms involved in determining the survival of enteric bacteria in seawater are poorly understood, in spite of the obvious public health implications. In a methodological attempt to address this issue, a plasmid-based collection of 687 Escherichia coli distinct promoter::luxCDABE fusions was screened to identify promoters that are induced upon exposure to seawater. The luminescence driven by 22 out of these promoters reproducibly increased at least two-fold in an artificial seawater medium; only 9 of the corresponding genes have previously been assigned a function. The most prominent characteristic of the induced genes was that most (18 out of 22) were under rpoS control. The induction of these seawater-responsive promoters was evaluated in different media to identify the cause of the increased transcription. Salinity or osmolarity was instrumental in only four cases, and in three promoters, increased pH also seemed to play a role; however, the most significant environmental effector in inducing the majority of the seawater-induced promoters appeared to be nutrient limitation.}, }
@article {pmid12024245, year = {2001}, author = {Canstein, HF and Li, Y and Felske, A and Wagner-Döbler, I}, title = {Long-Term Stability of Mercury-Reducing Microbial Biofilm Communities Analyzed by 16S-23S rDNA Interspacer Region Polymorphism.}, journal = {Microbial ecology}, volume = {42}, number = {4}, pages = {624-634}, doi = {10.1007/s00248-001-0028-6}, pmid = {12024245}, issn = {1432-184X}, abstract = {The composition of mercury-reducing communities in two bioreactors retaining Hg(II) from chloralkali electrolysis wastewater for 485 days was analyzed based on effluent community DNA. Packed bed bioreactors with lava chips as carrier of the biofilm were inoculated with nine Hg(II)-resistant isolates that belonged to the alpha and gamma subdivisions of the proteobacteria. A rapid DNA-fingerprinting method was applied, using the intergenic spacer region (ISR) of the 16S-23S rDNA for analysis of the community composition. This allowed discrimination of the inoculum strains down to subspecies level. A merA specific PCR permitted the discrimination of the community's merA genes. During the 485 days of operation, the bioreactors were exposed to various physical stresses (mixing, gas bubbles, temperature increase up to 41 degrees C, increased flow velocity) and repeated high mercury inflow concentrations, resulting in reduced bioreactor performance and decreased culturable cell numbers in the reactor effluent. Nevertheless, the composition of the microbial community remained rather stable throughout the investigated time period. Of the inoculum strains, two could be detected throughout, whereas three were sometimes present with varying periods of nondetection. Two inoculum strains were only detected within the first month. Two strains of gamma-proteobacteria that were able to reduce ionic mercury invaded the bioreactor community. They did not outcompete established strains and had no negative effect on the Hg(II)-retention activity of the bioreactors. The community comprised diverse merA genes. The abundance of merA genes matched the abundance of their respective strains as confirmed by ISR community analysis. The continuously high selection pressure for mercury resistance maintained a stable and highly active mercury-reducing microbial community within the bioreactors.}, }
@article {pmid12024244, year = {2001}, author = {Ahn, YB and Beaudette, LA and Lee, H and Trevors, JT}, title = {Survival of a GFP-Labeled Polychlorinated Biphenyl Degrading Psychrotolerant Pseudomonas spp. in 4 and 22 degrees C Soil Microcosms.}, journal = {Microbial ecology}, volume = {42}, number = {4}, pages = {614-623}, doi = {10.1007/s00248-001-0023-y}, pmid = {12024244}, issn = {1432-184X}, abstract = {The green fluorescent protein gene (gfp) was inserted into the chromosome of Pseudomonas spp. Cam-1 and Sag-50G, two psychrotolerant polychlorinated biphenyl (PCB)-degrading bacteria. The gfp-transformed microorganisms, designated Cam-1-gfp1, Cam-1-gfp2, Sag-50G-gfp1, and Sag-50G-gfp2, exhibited green fluorescence under an epifluorescent microscope. The gfp was inserted into the chromosome of each psychrotolerant strain and was stable with no apparent adverse affects on the metabolism and growth of each organism. Activity of gfp-transformed microorganisms against biphenyl and 2,3-dichlorobiphenyl was determined by assaying for BphC activity and by resting cell assays. The patterns of BphC activity at two different growth temperatures in batch cultures were similar for each of the gfp-transformed microorganisms. Resting cell assays of both the parent strains (Cam-1, Sag-50G) and the gfp-transformed strains (Cam-1-gfp1, Cam-1-gfp2, Sag-50G-gfp1, Sag-50G-gfp2), grown on glycerol or glucose, exhibited BphC activity to a lesser extent and at a slower rate than those observed for biphenyl grown cells. In addition, all gfp-transformed microorganisms degraded 2,3-dichlorobiphenyl (2,3-DCB) in broth to the same extent as the parent strains. When Cam-1-gfp1 and Sag-50G-gfp1 were used as a bioremediation amendment in soil microcosms spiked with 2,3-DCB, both strains survived in high numbers (5.6 to 7.9 log cfu g?1 and 5.6 to 8.0 log cfu g?1) when inoculated into nonsterilized soil over 16 weeks at 22 degrees C and 18 weeks at 4 degrees C, respectively. Biodegradation of 2,3-DCB was enhanced with the microbial amendment; however, the addition of sunflower oil did not help the PCB degrading bacteria and may have enhanced the growth of the indigenous population, thereby decreasing the amended PCB-degrading population.}, }
@article {pmid12024243, year = {2001}, author = {Repka, S and Mehtonen, J and Vaitomaa, J and Saari, L and Sivonen, K}, title = {Effects of Nutrients on Growth and Nodularin Production of Nodularia Strain GR8b.}, journal = {Microbial ecology}, volume = {42}, number = {4}, pages = {606-613}, doi = {10.1007/s00248-001-0026-8}, pmid = {12024243}, issn = {1432-184X}, abstract = {To determine the effects of nutrients on growth and toxin production of Nodularia strain GR8b, several nutrient concentrations were tested in batch and chemostat cultures. In batch cultures, phosphate (55-5,500 mg L-1) and nitrate (100-30,000 mg L-1) concentrations were applied, whereas in chemostat cultures, phosphate concentrations (5-315 mg L-1) were tested. Intra- and extracellular toxin concentrations, together with biomass parameters, were measured. In the batch cultures with low phosphate concentrations, chlorophyll a and protein contents were reduced, but dry weights and cell numbers were not significantly affected. The highest nitrate concentrations resulted in reduced dry weight concentrations. Nodularin concentration per dry weight, nodularin to protein ratio, and dissolved nodularin were highest at the end of the experiment, but were not influenced by the nutrient concentrations. Nodularin concentration per cell was also rather constant under the varying nutrient concentrations. In the chemostat cultures, the biomass increased with high phosphate concentrations. However, the phosphate concentrations did not have statistically significant effects on nodularin production rates.}, }
@article {pmid12024242, year = {2001}, author = {Lindström, ES}, title = {Investigating Influential Factors on Bacterioplankton Community Composition: Results from a Field Study of Five Mesotrophic Lakes.}, journal = {Microbial ecology}, volume = {42}, number = {4}, pages = {598-605}, doi = {10.1007/s00248-001-0031-y}, pmid = {12024242}, issn = {1432-184X}, abstract = {In order to investigate which biotic and abiotic factors may have an impact on the community composition of bacterioplankton, five mesotrophic lakes were studied. The composition of the bacterioplankton communities was determined by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA. Multivariate statistical analyses of the gel patterns, in relation to each other and to the chemical, biological, and physical parameters of the lakes, were performed. The analyses showed that the import of allochthonous bacteria and the interaction with other plankton organisms (for example, grazing) in the lakes probably had an impact on the composition of the communities.}, }
@article {pmid12024241, year = {2001}, author = {Folman, LB and Postma, J and Veen, JA}, title = {Ecophysiological Characterization of Rhizosphere Bacterial Communities at Different Root Locations and Plant Developmental Stages of Cucumber Grown on Rockwool.}, journal = {Microbial ecology}, volume = {42}, number = {4}, pages = {586-597}, doi = {10.1007/s00248-001-0032-x}, pmid = {12024241}, issn = {1432-184X}, abstract = {Bacterial communities from the rhizosphere of cucumber were characterized with respect to growth rates and carbon source utilization, in order to develop a selection strategy for biocontrol agents against Pythium aphanidermatum. Rhizosphere samples were collected from different root regions (root tips, the root base, and the intermediate region where lateral roots emerge) and developmental stages (the seedling, vegetative, and generative stage) from plants cultivated on reused rockwool. By colony counts on 1/10 strength TSA on subsequent days after plating, percentages of fast- and slow-growing isolates (i.e., forming visible colonies within 2 days, or after 3 or more days, respectively) were determined for each rhizosphere sample. At all plant developmental stages, root tips had the highest percentages of fast growing isolates, and root bases the lowest. During plant growth, the relative amounts of slowly growing bacteria increased. Community-level carbon source utilization was determined for the different rhizosphere samples with Biolog GN plates. Principal component analysis showed that rhizosphere samples from different developmental stages and root locations had distinct carbon source utilization patterns. Communities from root tips of seedlings showed the highest utilization of several monosaccharides. Communities from tips and intermediate regions of plants in the vegetative stage utilized relatively many amino acids and several organic acids, and in the generative stage, more di- and polysaccharides were used. Root base samples scored low with respect to carbon source utilization, except for some disaccharides. From the different rhizosphere samples, 826 bacteria, randomly collected from 1/10 strength TSA plates, were screened on the utilization of 9 carbon sources. The 9 selected carbon sources were chosen because they are reported to occur in the rhizosphere, to be used by the zoospores of Pythium in the infection process, or appeared to be discriminant in the analysis of community-level carbon source utilization performed in this study. It appeared that monosaccharides (glucose and fucose), amino acids (alanine and asparagine), and organic acids (galacturonic, succinic, and linoleic acid) were used for growth mainly by bacteria from the root tips, and to a lesser extent from the intermediate region, of young plants. Disaccharides were predominantly utilized by isolates from plants in the vegetative stage. Overall, the results indicated that growth rates and carbon source utilization reflect the adaptation of bacteria to the rhizosphere environment. The possibility of using these characteristics to screen for rhizosphere competent biocontrol agents that compete for substrates with P. aphanidermatum is discussed.}, }
@article {pmid12024240, year = {2001}, author = {Espeland, EM and Wetzel, RG}, title = {Complexation, Stabilization, and UV Photolysis of Extracellular and Surface-Bound Glucosidase and Alkaline Phosphatase: Implications for Biofilm Microbiota.}, journal = {Microbial ecology}, volume = {42}, number = {4}, pages = {572-585}, doi = {10.1007/s00248-001-1023-7}, pmid = {12024240}, issn = {1432-184X}, abstract = {Biofilm-produced and commercially-purified a- and b-glucosidase and alkaline phosphatase were subjected to different spectral portions of natural and artificial light and exposed to various humic substances to elucidate their impact on enzyme activities. Photochemical degradation of all enzymes occurred under different portions of the light spectrum. UVB irradiance produced the greatest overall photochemical degradation of enzymes, with significant rates occurring with UVA and PAR irradiance. The complexation of enzymes with humic substances resulted in inhibition, stabilization, and photochemical protection of the enzyme. Inhibition of enzyme activity occurred via reductions in overall enzyme activity in the presence of humic substances. However, humic-enzyme complexation also resulted in stabilization by restricting enzyme degradation while retaining high activities. Enzymes exposed to natural and artificial light sources had significantly lower reductions in enzyme activities in the presence of humic substances, which indicates that humic-enzyme complexes may protect enzymes from light-induced photochemical degradation. Bacterial surface-bound a- and b-glucosidase activities were significantly reduced in the presence of humic substances. Photosynthetically induced pH changes within biofilm communities can cause large reductions in a- and b-glucosidase activities while enhancing the hydrolytic activity of alkaline phosphatase.}, }
@article {pmid12024239, year = {2001}, author = {Almeida, MA and Cunha, MA and Alcântara, F}, title = {Loss of Estuarine Bacteria by Viral Infection and Predation in Microcosm Conditions.}, journal = {Microbial ecology}, volume = {42}, number = {4}, pages = {562-571}, doi = {10.1007/s00248-001-0020-1}, pmid = {12024239}, issn = {1432-184X}, abstract = {The bacterioplankton density in Ria de Aveiro, a shallow estuarine ecosystem, varied in the broad range of 1.9-10.6 x 109 cells L-1. The range of values was about 2 times higher in brackish water than in marine water. At high tide bacterial abundance was 2-3 times lower than at low tide. The overall variation in virioplankton was in the range of 2.4-25.0 x 1010 particles L-1. Brackish water was about 2 times richer in viral particles than the marine water. Near low tide the virioplankton was 2-3 times higher that at high tide. Viral density followed the pattern of bacterial abundance (it explained 40% of virioplankton variation). The viruses to bacterium ratio varied, throughout tidal cycles, by a factor of about 10 establishing the range 4.7-55.6 (average 17.6). This ratio was rather similar in the two estuarine zones. We compared the effects of infection and predation on the control of bacterioplankton size in the two zones of the estuary. The approach to this question was conducted in experimental microcosms, set up in six combinations of plankton variables affecting the presence/absence of predators, virus-to-bacterium ratio (10-fold increase), virus-to-bacterium distance (2.2-fold increase), and bacterial growth rate. The results showed that predation was similar, in a percent basis, in marine (69%) and brackish water (73%). Viral infection was, however, higher in brackish water (59%) than in the marine water (36%). We conclude that the bacterioplankton along the salinity gradient evolves under biological pressures that are in different balance in the marine and brackish water zones. The effect of viral lysis on bacterial communities with enhanced growth (after yeast extract addition) was masked even when the initial ratio was 10-fold greater than in the natural samples. The high density of the virioplankton did not preclude the large and rapid increase in bacterial density. We suggest that the dynamics of the equilibrium between bacteria and viruses in the environment is driven to higher numerical levels during periods of intensive bacterial growth. On the contrary, at low bacterial growth rates the temporarily increased virus-to-bacterium ratio may drive the equilibrium to its lowest levels.}, }
@article {pmid12024238, year = {2001}, author = {Dixon, JL and Turley, CM}, title = {Measuring Bacterial Production in Deep-Sea Sediments using 3H-Thymidine Incorporation: Ecological Significance.}, journal = {Microbial ecology}, volume = {42}, number = {4}, pages = {549-561}, doi = {10.1007/s00248-001-0022-z}, pmid = {12024238}, issn = {1432-184X}, abstract = {Bacteria play a major role in the decomposition of organic matter arriving at the deep-sea floor, and hence there is a need to determine accurate rates of bacterial production associated with sediment particles. However, sediment-based procedures are not well defined and sampling deep-sea sediments is technically difficult, time consuming, and expensive, often only producing relatively small amounts of undisturbed sediment for analysis. We describe and test a small-scale method (requiring 0.25 ml sediment) for the examination of bacterial production in deep-sea calcium carbonate rich sediments. Time course experiments showed variation in the period of linear [3H]thymidine uptake between 1 and 3 hr depending on station depth. The average concentration of natural thymidine in deep-sea sediments was 0.61 nmol per 0.5 ml slurry sample. Isotope dilution was significant, ranging between 26 and 51%. There was substantial small-scale (0.2-1.0 m) variation in deep-sea benthic bacterial [3H]thymidine incorporation rates (39%). Deep-sea surficial sediment bacterial production (assuming zero isotope dilution due to its potential high variability) in surficial sediments of the deep NE Atlantic varied between 0.014 and 0.48 mg C g-1 d-1 (mean = 0.23 mg C g-1 d-1) over 3 locations of depths between 1,092 and 3,572 m and at 3 times. Bacterial biomass varied between 1.1 and 12 mg C g-1 (mean = 6.1 mg C g-1). Bacterial growth rate estimates in these deep-sea sediments varied between 0.003 and 0.13 d-1 (mean = 0.050 d-1) giving doubling times of 5.3-216 d (mean = 44.5 d); which are similar to those of bacteria inhabiting waters in the upper mixed layer (2-<40 m) of the water column (2.6-57.8 d). comparison with shallow and coastal sea sediments (0.13-116 d) indicates that deep-sea sediment bacteria in the NE Atlantic are able to grow at rates similar to those in shallow sediment systems given sufficient food. However, the range is broader for deep-sea sediment bacteria, which may indicate a more "feast" and "fast" life than their counterparts in shallower environments. waters >2,000 m cover 60% of the Earth's surface; thus bacterial production in deep-sea sediments must contribute an important fraction of oceanic and global bacterial production. It is therefore important to establish an accurate method of measuring bacterial production so that the full roles and controls of bacteria from this environment can be determined.}, }
@article {pmid12024237, year = {2001}, author = {Jiang, SC and Fu, W}, title = {Seasonal Abundance and Distribution of Vibrio cholerae in Coastal Waters Quantified by a 16S-23S Intergenic Spacer Probe.}, journal = {Microbial ecology}, volume = {42}, number = {4}, pages = {540-548}, doi = {10.1007/s00248-001-0029-5}, pmid = {12024237}, issn = {1432-184X}, abstract = {Vibrio cholerae is the causative agent of the severe diarrheal disease cholera and is indigenous to brackish waters. To advance our understanding of the ecology of this bacterium, we have developed a molecular probing method for detection of V. cholerae in coastal waters. Water samples from 7 locations in the Newport Bay watershed, California were sampled monthly for a whole year. V. cholerae concentrations were determined by membrane filtration-colony hybridization using an oligonucleotide probe targeting the 16S-23S intergenic spacer (ITS) region. In addition to V. cholerae concentrations, environmental parameters, including temperature, salinity, total bacterial direct counts, total viable counts, and chlorophyll a concentrations, were determined for each site. V. cholerae was detected year-round throughout the watershed. Regression analysis indicated that the concentration of V. cholerae inversely correlated with salinity (p <0.001). The sampling sites located nearest to the Pacific Ocean had lower concentrations, whereas sites located along the brackish San Diego Creek (salinity 0-12 per thousand) routinely had higher concentrations. V. cholerae concentrations also correlated with temperature (p <0.01) in the watershed, with concentrations ranging from less than 1 CFU mL-1 to 2,930 CFU mL-1 of water. The results of this study indicate that the dynamics of V. cholerae is mainly influenced, out of the parameters measured, by the temperature and salinity of the environment. This information is valuable for understanding the ecology of V. cholerae.}, }
@article {pmid12024236, year = {2001}, author = {Booth, MG and Jeffrey, WH and Miller, RV}, title = {RecA Expression in Response to Solar UVR in the Marine Bacterium Vibrio natriegens.}, journal = {Microbial ecology}, volume = {42}, number = {4}, pages = {531-539}, doi = {10.1007/s00248-001-1009-5}, pmid = {12024236}, issn = {1432-184X}, abstract = {Solar ultraviolet radiation may produce daily stress on marine and estuarine communities as cells are damaged and repair that damage. Reduction in the earth's stratospheric ozone layer has increased awareness of the potential effects that ultraviolet radiation may have in the environment, including how marine bacteria respond to changes in solar radiation. We examined the use of the bacterial RecA protein as an indicator of the potential of bacteria to repair DNA damage caused by solar UV irradiation using the marine bacterium Vibrio natriegens as a model. RecA is universally present in bacteria and is a regulator protein for the so-called Dark Repair Systems, which include excision repair, postreplication recombinational repair, and mutagenic or SOS repair. Solar UVB and UVA both reduced V. natriegens viability in seawater microcosms. After exposure to unfiltered solar radiation or radiation in which UVB was blocked, survival dropped below 1%, whereas visible light from which UVA and UVB had been filtered had no effect on survival. Using a RecA-specific antibody for detection, RecA protein was induced by solar radiation in a diel pattern in marine microcosms conducted in the Gulf of Mexico. Peak induction was observed at dusk each day. Although RecA expression was correlated with the formation of UVB-induced cyclobutyl pyrimidine dimers, longer wavelength UVA radiation also induced recA gene expression. Our results demonstrate that RecA-regulated, light-independent repair is an important component in the ability of marine bacteria to survive exposure to solar ultraviolet radiation and that RecA expression is a useful monitor of bacterial repair after exposure to solar UVR.}, }
@article {pmid12024235, year = {2001}, author = {Espeland, EM and Francoeur, SN and Wetzel, RG}, title = {Influence of Algal Photosynthesis on Biofilm Bacterial Production and Associated Glucosidase and Xylosidase Activities.}, journal = {Microbial ecology}, volume = {42}, number = {4}, pages = {524-530}, doi = {10.1007/s00248-001-1022-8}, pmid = {12024235}, issn = {1432-184X}, abstract = {Natural photosynthetic biofilms were incubated under light (100 mmol m-2 s-1) and dark conditions to elucidate the impact of photosynthesis on bacterial production, abundance, biovolume, biomass, and enzyme activities over 24 h. Use of organic carbon-free media limited carbon sources to algal photosynthesis and possibly the polysaccharides of the biofilm matrix. Bacterial production of biofilm communities was significantly higher in light incubations (p <0.001). The greatest differences in production rates between light and dark incubations occurred between 8 and 24 h. Biomass-specific a- and b-glucosidase and b-xylosidase activities were stimulated by photosynthesis, with significantly greater activities occurring at hours 16 and 24 in the light treatment (p <0.01). The results indicate that algal photosynthesis can have a significant impact on bacterial productivity, biomass, biovolume, and enzyme production over longer time periods at low photon flux densities (?100 mmol m-2 s-1).}, }
@article {pmid12024234, year = {2001}, author = {Sanders, RW and Caron, DA and Davidson, JM and Dennett, MR and Moran, DM}, title = {Nutrient Acquisition and Population Growth of a Mixotrophic Alga in Axenic and Bacterized Cultures.}, journal = {Microbial ecology}, volume = {42}, number = {4}, pages = {513-523}, doi = {10.1007/s00248-001-1024-6}, pmid = {12024234}, issn = {1432-184X}, abstract = {Axenic growth of a mixotrophic alga, Ochromonas sp., was compared in several inorganic and organic media, and in the presence of live bacteria under nutrient-replete and low-nutrient conditions. Axenic growth in the light was negligible in inorganic media with or without the addition of glucose. Addition of vitamins increased growth rate, but average cell size declined, resulting in no net increase in biomass. Supplementing axenic cultures with a more complex organic substrate resulted in moderate growth and higher maximal abundance (and biomass) than in the inorganic media with added vitamins. The absence of light did not greatly affect population growth rate in the presence of complex dissolved organic compounds, although cell size was significantly greater in the light than in the dark. The highest growth rates for the alga (up to 2.6 d-1) were measured in treatments containing live bacteria. Increases in cell number of Ochromonas sp. in the presence of bacterial prey were similar in the light and dark, although chloroplast and cell sizes differed. Bacterial abundance was reduced and dissolved phosphorus and ammonia were rapidly released in bacterized cultures in the light and dark, indicating high rates of bacterial ingestion and suggesting an inability of the alga to store or utilize N and P in excess of the quantities required for heterotrophic growth. Low-nutrient conditions in the presence of bacteria were promoted by adding glucose to stimulate bacterial growth and the uptake of N and P released by algal phagotrophy. Subsequent decreases in dissolved N and P following the addition of glucose corresponded to a second period of rapid growth of the alga in both light and dark. This result, combined with evidence for slow axenic growth of this strain, indicated that nutrient acquisition for this species in the presence of bacteria was accomplished primarily via ingestion of bacteria.}, }
@article {pmid12024233, year = {2001}, author = {Bermingham, S and Dewey, FM and Fisher, PJ and Maltby, L}, title = {Use of a Monoclonal Antibody-Based Immunoassay for the Detection and Quantification of Heliscus lugdunensis Colonizing Alder Leaves and Roots.}, journal = {Microbial ecology}, volume = {42}, number = {4}, pages = {506-512}, doi = {10.1007/s00248-001-0017-9}, pmid = {12024233}, issn = {1432-184X}, abstract = {A genus-specific monoclonal antibody, NG-CF10, raised in a previous study to the fungal pathogen Nectria galligena, was found to recognize the aquatic hyphomycete Heliscus lugdunensis (anamorph) and its teleomorph Nectria lugdunensis. Using this MAb in a plate trapped antigen- ELISA we could detect and determine the biomass of Heliscus lugdunensis in mixed assemblages in both naturally occurring and artificially inoculated leaves and roots of Alnus glutinosa trees. Initial studies indicate that the biomass associated with naturally occurring leaf material is significantly lower than that recorded with laboratory inoculated leaves, suggesting that biomass production is limited in the natural environment. Significantly lower biomass was associated with roots when compared with leaf material, which supports the proposition that rather than a major substrate for the growth of aquatic hyphomycetes, roots act as a refugium for fungal growth.}, }
@article {pmid12024232, year = {2001}, author = {Dollhopf, SL and Hashsham, SA and Tiedje, JM}, title = {Interpreting 16S rDNA T-RFLP Data: Application of Self-Organizing Maps and Principal Component Analysis to Describe Community Dynamics and Convergence.}, journal = {Microbial ecology}, volume = {42}, number = {4}, pages = {495-505}, doi = {10.1007/s00248-001-0027-7}, pmid = {12024232}, issn = {1432-184X}, abstract = {Interpreting the large amount of data generated by rapid profiling techniques, such as T-RFLP, DGGE, and DNA arrays, is a difficult problem facing microbial ecologists. This study compares the ability of two very different ordination methods, principal component analysis (PCA) and self-organizing map neural networks (SOMs), to analyze 16S-DNA terminal restriction-fragment length polymorphism (T-RFLP) profiles from microbial communities in glucose-fed methanogenic bioreactors during startup and changes in operational parameters. Our goal was not only to identify which samples were similar, but also to decipher community dynamics and describe specific phylotypes, i.e., phylogenetically similar organisms, that behaved similarly in different reactors. Fifteen samples were taken over 56 volume changes from each of two bioreactors inoculated from river sediment (S2) and anaerobic digester sludge (M3) and from a well-established control reactor (R1). PCA of bacterial T-RFLP profiles indicated that both the S2 and M3 communities changed rapidly during the first nine volume changes, and then became relatively stable. PCA also showed that an HRT of 8 or 6 days had no effect on either reactor communtity, while an HRT of 2 days changed community structure significantly in both reactors. The SOM clustered the terminal restriction fragments according to when each fragment was most abundant in a reactor community, resulting in four clearly discernible groups. Thirteen fragments behaved similarly in both reactors, eight of which composed a significant proportion of the microbial community as judged by the relative abundance of the fragment in the T-RFLP profiles. Six Bacteria terminal restriction fragments shared between the two communities matched cloned 16S rDNA sequences from the reactors related to Spirochaeta, Aminobacterium, Thermotoga, and Clostridium species. Convergence also occurred within the acetoclastic methanogen community, resulting in a predominance of Methanosarcina siciliae-related organisms. The results demonstrate that both PCA and SOM analysis are useful in the analysis of T-RFLP data; however, the SOM was better at resolving patterns in more complex and variable data than PCA ordination.}, }
@article {pmid12024231, year = {2001}, author = {Hansen, LH and Sørensen, SJ}, title = {The Use of Whole-Cell Biosensors to Detect and Quantify Compounds or Conditions Affecting Biological Systems.}, journal = {Microbial ecology}, volume = {42}, number = {4}, pages = {483-494}, doi = {10.1007/s00248-001-0025-9}, pmid = {12024231}, issn = {1432-184X}, abstract = {A new and promising technique in microbial ecology and environmental biology is the use of whole-cell bacterial biosensors. This minireview describes the use of such biosensors for detection and quantification of various compounds and other conditions affecting bacterial expression of different genes. Three types of biosensors (nonspecific, stress-induced, and specific biosensors) are described including their use in different environments. We present tables of published biosensors, including gene fusions, host organisms, and environments in which they are used. We here describe the use of different reporter genes in the construction of biosensors and discuss their use as tools for monitoring the bioavailability of pollutants and their potential use in studying microbial ecology in general.}, }
@article {pmid12023735, year = {2002}, author = {Rangarajan, S and Saleena, LM and Nair, S}, title = {Diversity of Pseudomonas spp. isolated from rice rhizosphere populations grown along a salinity gradient.}, journal = {Microbial ecology}, volume = {43}, number = {2}, pages = {280-289}, doi = {10.1007/s00248-002-2004-1}, pmid = {12023735}, issn = {0095-3628}, mesh = {*Adaptation, Physiological ; Agriculture ; Drug Resistance, Microbial ; Oryza/microbiology ; Phenotype ; Plant Roots/microbiology ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Population Dynamics ; Pseudomonas/*genetics/isolation &amp; purification ; Sodium Chloride ; }, abstract = {Along the coastline of Tamil Nadu, five sites were chosen to assess the diversity of Pseudomonas populations isolated from rice (Oryza sativa) cultivated along a salinity gradient. One of these sites was under organic farming while the other four were under inorganic farming. A total of 256 Pseudomonas strains isolated from these five sites were analyzed using both phenotypic (substrate utilization patterns and antibiotic resistance assay) and genotypic (PCR-RFLP of 16S rDNA) characteristics. The results derived from this study indicate that soil salinity affects rhizosphere Pseudomonas populations. It was observed that increasing salinity led to decreasing diversity. Fluorescent pseudomonads were the dominant species found in the non-saline site, while in the saline sites they were replaced by salt-tolerant species, in particular Pseudomonas alcaligenes and P. pseudoalcaligenes. An interesting observation was the increase in diversity found in the saline site under organic farming. Organic farming was found to be capable of mitigating the harmful effects of saline stress to a large extent, and restoring the Pseudomonas diversity, thereby making it comparable with the diversity encountered in the non-saline site.}, }
@article {pmid12023734, year = {2002}, author = {Desvaux, M and Petitdemange, H}, title = {Sporulation of Clostridium cellulolyticum while grown in cellulose-batch and cellulose-fed continuous cultures on a mineral-salt based medium.}, journal = {Microbial ecology}, volume = {43}, number = {2}, pages = {271-279}, doi = {10.1007/s00248-001-0043-7}, pmid = {12023734}, issn = {0095-3628}, mesh = {Adaptation, Physiological ; Cellulose/*metabolism ; Clostridium/growth &amp; development/*physiology ; Culture Media ; Hydrogen-Ion Concentration ; Hypoxia ; Quaternary Ammonium Compounds ; Spores ; Survival Analysis ; }, abstract = {Clostridium cellulolyticum sporulation was investigated during growth on cellulose fibers in a mineral-salt based medium which corresponds to conditions linked to its natural ecological niche. At steady state of the continuous cultures under limitation and with an excess of cellulose and/or ammonium, bacterial cells mainly sporulated at low dilution rates (D), at least 10% sporulation being observed at the lowest D tested. Increasing the cellulose concentration in the feed-medium reservoir increased the percentage of spores in the bioreactor. It appeared that the remaining undigested cellulose could serve as an exogenous carbon source supply at a continuous but limited rate throughout the sporulation process. In addition to the proportion of carbon and nitrogen, the influence of the environmental pH on spore formation was studied. In cellulose-fed continuous cultures at a constant D and a pH decreasing from 7.2 to 6.4, the percentage of spores increased to 14% at the lowest pH tested. When C. cellulolyticum was grown in batch culture, the level of sporulation was dramatically higher in unregulated-pH fermentation compared to pH-controlled growth conditions at pH 7.2 since in the former it reached 45% within 5 days of cultivation. It then appeared that a low specific growth rate and a low environmental pH in the presence of an insoluble carbon substrate were the major factors inducing sporulation in C. cellulolyticum. Furthermore, since the spores adhere to the carbon substrate (the cellulose) the bacteria gain advantages when the environment allows germination thanks to the recovery of suitable growth conditions. By allowing the maintenance and the integrity of the bacteria in the microbiota, spore formation could then explain the successful survival of C. cellulolyticum in cellulosic anaerobic habitats where low environmental pH conditions are often found.}, }
@article {pmid12023733, year = {2002}, author = {Reilly, K and Carruthers, VR and Attwood, GT}, title = {Design and use of 16S ribosomal DNA-directed primers in competitive PCRs to enumerate proteolytic bacteria in the rumen.}, journal = {Microbial ecology}, volume = {43}, number = {2}, pages = {259-270}, doi = {10.1007/s00248-001-1052-2}, pmid = {12023733}, issn = {0095-3628}, mesh = {Animal Feed ; Animals ; Cattle ; DNA Primers ; DNA, Bacterial/analysis/*genetics ; Dietary Carbohydrates ; Eubacterium/genetics/isolation &amp; purification ; Female ; Nitrogen ; Polymerase Chain Reaction/*methods ; Prevotella/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Streptococcus/genetics/isolation &amp; purification ; }, abstract = {Competitive Polymerase Chain Reaction primers were designed for Streptococcus, B. fibrisolvens, P. bryantii, Eubacterium sp., Prevotella, and a universal primer for the eubacteria. DNA was extracted from rumen contents collected from eight dairy cows fed four diets: adequate nitrogen, adequate nitrogen plus carbohydrate, low nitrogen, and low nitrogen plus carbohydrate. B. fibrisolvens was significantly higher on the adequate nitrogen plus carbohydrate and the low nitrogen plus carbohydrate diets compared with the other diets, while P. bryantii was significantly higher on the low nitrogen plus carbohydrate diet compared with the adequate nitrogen diet. The population of Eubacterium sp. was significantly lower on both the adequate nitrogen plus carbohydrate and low nitrogen plus carbohydrate diets. Streptococcus populations were significantly lower on the low nitrogen plus carbohydrate diet compared with all three other diets, whereas there were no significant differences in populations of Prevotella or total eubacteria on any of the diets.}, }
@article {pmid12023732, year = {2002}, author = {Mary, P and Chihib, NE and Charafeddine, O and Defives, C and Hornez, JP}, title = {Starvation survival and viable but nonculturable states in Aeromonas hydrophila.}, journal = {Microbial ecology}, volume = {43}, number = {2}, pages = {250-258}, doi = {10.1007/s00248-001-0046-4}, pmid = {12023732}, issn = {0095-3628}, mesh = {Aeromonas hydrophila/*physiology ; Cell Culture Techniques ; Population Dynamics ; Seasons ; Starvation/*physiopathology ; Survival Analysis ; Temperature ; }, abstract = {The behavior of Aeromonas hydrophila stored at 4 degrees C and 25 degrees C in nutrient-poor filtered sterilized distilled water was investigated. At 4 degrees C, the A. hydrophila population declined below the detection level (0.1 cell mL(-1)) after 7 weeks, whereas the number of cells with intact membrane as determined by the LIVE/DEAD method decreased only by 1 log unit. Although, this response is reminiscent of the so-called VBNC state, the cells could not be resuscitated by an upshift to 25 degrees C. A mixture of rods with normal size and elongated cells was observed in this state. At 25 degrees C, viable cells and cells with intact membrane declined only by 0.8 log unit over the 10-week storage period, and thus A. hydrophila entered the classical starvation survival state. During this state, a mixture of rods and cocci was observed. Prestarvation at 25 degrees C for 24 h and especially 49 days delayed significantly the rate of entry into the VBNC state. However, stationary phase cells were not significantly more tolerant than exponential phase cells. No significant improvements in recovery yield were obtained on LB agar plates amended with catalase or sodium pyruvate. During cold incubation, high variability in responses was observed. Intermittent cryptic regrowth might be responsible for this variability in responses.}, }
@article {pmid12023731, year = {2002}, author = {Ivanova, EP and Bakunina, IY and Sawabe, T and Hayashi, K and Alexeeva, YV and Zhukova, NV and Nicolau, DV and Zvaygintseva, TN and Mikhailov, VV}, title = {Two species of culturable bacteria associated with degradation of brown algae Fucus evanescens.}, journal = {Microbial ecology}, volume = {43}, number = {2}, pages = {242-249}, doi = {10.1007/s00248-001-1011-y}, pmid = {12023731}, issn = {0095-3628}, mesh = {Biodegradation, Environmental ; Halomonas/*isolation &amp; purification/physiology ; Molecular Weight ; Organic Chemicals/metabolism ; Phaeophyceae/*metabolism ; Polysaccharides/metabolism ; Population Dynamics ; Proteobacteria/*isolation &amp; purification/physiology ; Water Microbiology ; }, abstract = {The heterotrophic microbial enrichment community established during degradation of brown algae Fucus evanescens was characterized. A two-species bacterial community of marine culturable gamma-proteobacteria consisted of Pseudoalteromonas and Halomonas. The first member of the community, Pseudoalteromonas sp., was highly metabolically active, had bacteriolytic and hemolytic activities, produced proteinases (gelatinase and caseinase), lipases, DNases, and fucoidanhydrolases, laminaranases, alginases, pustulanases, beta-glucosidases, beta-galactosidases, beta-N-acetylglucosaminidases, and beta-xylosidases. The second member of the community, Halomonas marina, produced only caseinase and DNase, and it did not hydrolyze algal polysaccharides. Both members of the studied bacterial community utilized a range of easily assimilable monosaccharides and other low molecular weight organic substances. The results provide an evidence of the complex metabolic interrelations between two members of this culturable community. One of them Pseudoalteromonas sp., most likely plays the major role in the initial stages of algal degradation; the other one, H. marina, resistant to the bacteriolytic activity of the former, is able to utilize the products of degradation of polysaccharides.}, }
@article {pmid12023730, year = {2002}, author = {Haglund, AL and Törnblom, E and Boström, B and Tranvik, L}, title = {Large differences in the fraction of active bacteria in plankton, sediments, and biofilm.}, journal = {Microbial ecology}, volume = {43}, number = {2}, pages = {232-241}, doi = {10.1007/s00248-002-2005-0}, pmid = {12023730}, issn = {0095-3628}, mesh = {Animals ; Bacteria/*isolation &amp; purification ; *Biofilms ; *Environmental Monitoring ; Fluorescent Dyes/chemistry ; Geologic Sediments/microbiology ; Oxidation-Reduction ; *Plankton ; Population Dynamics ; Tetrazolium Salts/chemistry ; Water Microbiology ; }, abstract = {Generally, only a small fraction of free-living pelagic bacteria are metabolically active, while particle-associated bacteria usually exhibit a larger proportion of active bacteria. Most previous studies on the active fraction of bacteria focus on planktonic communities, and there are only a few studies on sediment and epiphytic biofilm bacteria. We compared the active fraction of the total number of bacteria in three different habitats of the littoral zone of Lake Erken, Sweden, including the sediments, the epiphytic biofilm on the submerged macrophyte Ranunculus circinatus, and the water column. Active bacteria were detected as those with an active electron transport system, identified by the capacity to reduce the tetrazolium salt CTC (5-cyano-2,3-ditolyltetrazolium chloride) into its fluorescent, water insoluble state. There were large differences between habitats. The active fraction of the total number of bacteria detected by fluorescence microscopy (annual mean +/- SD) in the sediments was 46 +/- 10%, on R. circinatus 37 +/- 18%, and in the water column 4 +/- 4%. The abundance of CTC-reducing cells was correlated with total bacterial abundance, and the fraction of CTC-reducing bacteria generally increased with total bacterial abundance, for all the habitats. Consequently, the difference in the fraction of CTC-reducing bacteria between the habitats could be attributed to different densities of bacteria, with a larger proportion of active bacteria at higher bacterial densities.}, }
@article {pmid12023729, year = {2002}, author = {Ortmann, AC and Lawrence, JE and Suttle, CA}, title = {Lysogeny and lytic viral production during a bloom of the cyanobacterium Synechococcus spp.}, journal = {Microbial ecology}, volume = {43}, number = {2}, pages = {225-231}, doi = {10.1007/s00248-001-1058-9}, pmid = {12023729}, issn = {0095-3628}, mesh = {British Columbia ; Cyanobacteria/*virology ; *Environmental Monitoring ; *Eutrophication ; *Lysogeny ; Mitomycin/pharmacology ; Population Dynamics ; *Viruses ; Water Microbiology ; }, abstract = {Lytic viral production and lysogeny were investigated in cyanobacteria and heterotrophic bacteria during a bloom of Synechococcus spp. in a pristine fjord in British Columbia, Canada. Triplicate seawater samples were incubated with and without mitomycin C and the abundances of heterotrophic bacteria, cyanobacteria, total viruses and infectious cyanophage were followed over 24 h. Addition of mitomycin C led to increases in total viral abundance as well as the abundance of cyanophages infecting Synechococcus strain DC2. Given typical estimates of burst size, these increases were consistent with 80% of the heterotrophic bacteria and 0.6% of Synechococcus cells being inducible by the addition of mitomycin C. This is the highest percentage of lysogens reported for a natural microbial community and demonstrates induction in a marine Synechococcus population. It is likely that the cyanophage production following the addition of mitomycin C was much higher than that titered against a single strain of Synechococcus; hence this estimate is a minimum. In untreated seawater samples, lytic viral production was estimated to remove ca. 27% of the gross heterotrophic bacterial production, and a minimum of 1.0% of the gross cyanobacterial production. Our results demonstrate very high levels of lysogeny in the heterotrophic bacterial community, outside of an oligotrophic environment, and the presence of inducible lysogens in Synechococcus spp. during a naturally occurring bloom. These data emphasize the need for further examination of the factors influencing lytic and lysogenic viral infection in natural microbial communities.}, }
@article {pmid12023728, year = {2002}, author = {Abd-El-Haleem, D and Moawad, H and Zaki, EA and Zaki, S}, title = {Molecular characterization of phenol-degrading bacteria isolated from different Egyptian ecosystems.}, journal = {Microbial ecology}, volume = {43}, number = {2}, pages = {217-224}, doi = {10.1007/s00248-002-2003-2}, pmid = {12023728}, issn = {0095-3628}, mesh = {Acinetobacter/*genetics/isolation &amp; purification ; *DNA Fingerprinting ; Disinfectants/*metabolism ; Ecosystem ; Egypt ; Phenol/*metabolism ; Polymerase Chain Reaction ; Proteobacteria/*genetics/isolation &amp; purification ; RNA, Ribosomal, 16S ; Soil Microbiology ; }, abstract = {Twelve selected phenol-degrading bacterial isolates were obtained on phenol agar plates using culture enrichment technique. Molecular identification of the isolates was performed using eubacterial 16S rRNA PCR specific primers. Based on 16S rDNA sequence analysis, the results revealed that the majority of the isolates (8 out of 12) are affiliated to the g-subdivision of Proteobacteria. Four out of the eight isolates are closely related to the genus Acinetobacter. Molecular heterogeneity among the phenol-degrading isolates was further investigated by using rep-PCR chromosomal fingerprinting and correlated with plasmid and antibiotic profile analysis. Rep-PCR results strongly confirmed that the bacterial isolates from different environmental sites produced different fingerprinting patterns. The mineralization of phenol by all isolates was evaluated using 14C-labeled phenol assay. Phenol mineralization ranged from 55% (W-17) to 0.4% (Sea-9). This was further confirmed by the detection of several monoaromatic and polyaromatic degrading genes, e.g., pheA, MopR, XylE, and NahA. In addition, catalytic enzymes such as catalase and dioxygenase were also monitored.}, }
@article {pmid12023727, year = {2002}, author = {Bott, TL and Kaplan, LA}, title = {Autecological properties of 3-chlorobenzoate-degrading bacteria and their population dynamics when introduced into sediments.}, journal = {Microbial ecology}, volume = {43}, number = {2}, pages = {199-216}, doi = {10.1007/s00248-001-1034-4}, pmid = {12023727}, issn = {0095-3628}, mesh = {Alcaligenes/*physiology ; Biodegradation, Environmental ; Chlorobenzoates/*metabolism ; Geologic Sediments ; Organisms, Genetically Modified ; Population Dynamics ; Pseudomonas/*physiology ; Survival Analysis ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Ecologically significant properties of wild-type and genetically engineered bacteria capable of degrading 3-chlorobenzoate (3-CB) were compared in the laboratory, and isolates were introduced into streambed sediments in microcosms to observe their population dynamics. 3-CB metabolism, growth on algal extract, temperature optima, and ingestion by protozoa were ecological properties considered relevant to the persistence of these bacteria if introduced into nature. Cell-specific Vmax for 3-CB metabolism and cell-specific mineralization rates each spanned approximately 2 orders of magnitude, but isolates did not rank consistently. The Ks for 3-CB metabolism for Alcaligenes sp. BR60 was approximately 40-fold lower than the mean value for the other isolates, which differed only approximately 4-fold among themselves. All isolates grew on an algal extract nearly as well as on tryptone-yeast extract, implying potential for survival on natural metabolic substrates in situ. Most isolates had temperature optima that were 3-15 degrees C higher than maximum stream water temperature (22 degrees C). Ciliates preferentially ingested P. acidovorans M3GY, and either P. putida RC-4(pSI30) or its parent strain were least preferred, but microflagellates did not exhibit consistent preferences. Fluorescent antibodies were prepared against isolates to permit detection of target cells in natural communities. In three different microcosm experiments the cell densities of introduced isolates declined over a period of days. In one experiment, 3-CB additions (100 mg/L) led to increases of P. alcaligenes C-0 and P. acidovorans M3GY cell densities within 1 day, although P. putida RC-4(pSI30) took 4 days. In a second experiment, the persistence of P. putida RC-4(pSI30) and its parent strain P. putida RC-4 were compared and rates of initial population decline were not statistically different. 3-CB addition stimulated the growth of other organisms while densities of the P. putida strains further declined. In a third experiment exposure to 100 mg 3-CB/L slowed the rate of decline of P. acidovorans M3GY densities compared to a 10 mg/L concentration or unamended control. Competition with the native flora was a significant factor affecting the persistence of introduced 3-CB degraders.}, }
@article {pmid12023726, year = {2002}, author = {Langworthy, DE and Stapleton, RD and Sayler, GS and Findlay, RH}, title = {Lipid analysis of the response of a sedimentary microbial community to polycyclic aromatic hydrocarbons.}, journal = {Microbial ecology}, volume = {43}, number = {2}, pages = {189-198}, doi = {10.1007/s00248-001-1040-6}, pmid = {12023726}, issn = {0095-3628}, mesh = {Biomass ; Ecosystem ; *Environmental Monitoring ; Geologic Sediments/*microbiology ; Lipids/*analysis ; Polycyclic Aromatic Hydrocarbons/*adverse effects ; Population Dynamics ; *Water Microbiology ; Water Pollutants, Chemical/*adverse effects ; }, abstract = {Polycyclic aromatic hydrocarbons (PAH) are widespread environmental contaminants that can, under proper conditions, be degraded by microorganisms. The responses of a riverine sedimentary microbial community to PAH contamination were examined using an integrated biochemical assay that yielded data on PAH concentration, total microbial biomass, and microbial community structure and were interpreted using perturbation theory and the subsidy-stress gradient. Microbial mineralization of naphthalene, anthracene, fluorene, and phenanthrene was observed 24 h after their addition to all sediments sampled and ranged from 0.9 to 16.3% in ambient sediments and from 14.8 to 35.8% in contaminated sediments. Total microbial biomass, determined by phospholipid phosphate, increased in response to intermediate PAH concentration and decreased at sites with the highest PAH concentration (p < 0.05) during seven out of nine (78%) seasonal sampling periods. The two sampling periods that were not statistically different followed periods of high water and cold temperatures. Phospholipid fatty acid analysis of microbial community structure analysis indicated that increases in the relative abundance of gram-negative aerobes and heterotrophic eukaryotes were responsible, in part, for these observed increases in total microbial biomass. These findings (increased degradation rates, increased biomass at intermediate PAH concentrations, and altered community structure) indicate that a component of the microbial community responded to PAH as a usable input and are consistent with the predictions of perturbation theory and a subsidy-stress gradient.}, }
@article {pmid12019464, year = {2002}, author = {Weitere, M and Arndt, H}, title = {Water discharge-regulated bacteria/heterotrophic nanoflagellate (HNF) interactions in the water column of the river Rhine.}, journal = {Microbial ecology}, volume = {44}, number = {1}, pages = {19-29}, pmid = {12019464}, issn = {0095-3628}, mesh = {Animals ; Bacteria/*growth &amp; development ; Biomass ; Carbon/metabolism ; Eating ; Fresh Water/*microbiology ; Germany ; Seasons ; Temperature ; *Water Movements ; Zooplankton/growth &amp; development/*physiology ; }, abstract = {Heterotrophic nanoflagellates (HNF) make up a large fraction of the zooplankton biomass of rivers. Their abundance can be strongly affected by water discharge, but the consequences of this highly dynamic factor for their main prey, the bacteria, is still unknown. The focus of this study was on bacterial/HNF interactions in the Lower River Rhine (Germany) with respect to the discharge-dependent dynamics. The bacterial and HNF abundances and biomasses were determined over the course of 17 months. The potential consumption of bacteria by HNF was calculated based on the biomass data and on data on the HNF production. The mean bacterial abundance in the Rhine at Cologne ranged from 0.3 x 10(6) to 3.5 x 10(6) cells mL(-1), with lowest abundances in winter and highest in late spring. No significant changes in abundance during the downstream passage were found. Neither could a significant correlation be found between bacterial and HNF abundance. The ratio of bacterial to HNF abundance showed high variations which lay between 166 and 19,055 and was negatively dependent on water discharge. Monthly routine calculations on the potential bacterial consumption by HNF revealed a clearance of between 2 and 82% of the bacterial standing stock d(-1). The values increased greatly with water discharge and could exceed 100% d(-1) at times of high water flow. The presented data suggests a change in the top-down control of the planktonic bacteria due to the water discharge: The importance of benthic predation at low water flow (high contact probability to benthic predators) gives way to an increased importance in predation by planktonic HNF at high water flow.}, }
@article {pmid12019463, year = {2002}, author = {Nishiguchi, MK}, title = {Host-symbiont recognition in the environmentally transmitted sepiolid squid-Vibrio mutualism.}, journal = {Microbial ecology}, volume = {44}, number = {1}, pages = {10-18}, pmid = {12019463}, issn = {0095-3628}, support = {SO6-GM08136-26/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Decapodiformes/classification/genetics/*microbiology ; Environment ; Luminescent Measurements ; Photobacterium/genetics/*physiology ; Species Specificity ; *Symbiosis ; Time Factors ; Vibrio/genetics/*physiology ; }, abstract = {Associations between environmentally transmitted symbionts and their hosts provide a unique opportunity to study the evolution of specificity and subsequent radiation of tightly coupled host-symbiont assemblages [3, 8, 24]. The evidence provided here from the environmentally transmitted bacterial symbiont Vibrio fischeri and its sepiolid squid host (Sepiolidae: Euprymna) demonstrates how host-symbiont specificity can still evolve without vertical transmission of the symbiont [1]. Infection by intraspecific V. fischeri symbionts exhibited preferential colonization over interspecific V. fischeri symbionts, indicating a high degree of specificity for the native symbiotic strains. Inoculation with symbiotic bacteria from other taxa (monocentrid fish and loliginid squids) produced little or no colonization in two species of Euprymna, despite their presence in the same or similar habitats as these squids. These findings of host specificity between native Vibrios and sepiolid squids provides evidence that the presence of multiple strains of symbionts does not dictate the composition of bacterial symbionts in the host.}, }
@article {pmid12019462, year = {2002}, author = {Reed, DL and Hafner, MS}, title = {Phylogenetic analysis of bacterial communities associated with ectoparasitic chewing lice of pocket gophers: a culture-independent approach.}, journal = {Microbial ecology}, volume = {44}, number = {1}, pages = {78-93}, pmid = {12019462}, issn = {0095-3628}, mesh = {Animals ; Bacteria/*classification/*genetics ; Base Sequence ; DNA, Bacterial/genetics ; Gammaproteobacteria/classification/genetics ; Host-Parasite Interactions ; Phthiraptera/*microbiology ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; Rodent Diseases/parasitology ; Rodentia/*parasitology ; Staphylococcus/classification/genetics ; }, abstract = {This study identifies the bacteria associated with ectoparasitic chewing lice that live in the fur of pocket gophers. Samples of chewing lice were collected from pocket gopher hosts in Florida, Missouri, New Mexico, and Costa Rica. We used a molecular sampling method whereby total community DNA was extracted from samples of chewing lice, and PCR was used to selectively amplify small-subunit rRNA genes from bacteria. This culture-independent method yielded ca. 35 distinct lineages representing eight widely divergent groups within the domain Bacteria. Phylogenetic analysis of two lineages (Acinetobacter and Staphylococcus) provides evidence that multiple species of each group are found in chewing lice. Phylogenetic analysis also demonstrated that diversification within chewing lice may be evident in both Acinetobacter and Staphylococcus. Some clones amplified from chewing louse hosts appeared to be distinct from known species of Acinetobacter and Staphylococcus. This diversification may be the result of the extreme isolation of populations of both chewing lice and their pocket gopher hosts.}, }
@article {pmid12019461, year = {2002}, author = {van Bruggen, AH and Semenov, AM and Zelenev, VV}, title = {Wavelike distributions of infections by an introduced and naturally occurring root pathogen along wheat roots.}, journal = {Microbial ecology}, volume = {44}, number = {1}, pages = {30-38}, pmid = {12019461}, issn = {0095-3628}, mesh = {Colony Count, Microbial ; Plant Diseases/microbiology/parasitology ; Plant Roots/*microbiology/*parasitology ; Pythium/growth &amp; development/*isolation &amp; purification ; Rhizoctonia/growth &amp; development/*isolation &amp; purification ; Soil Microbiology ; Time Factors ; Triticum/*microbiology/*parasitology ; }, abstract = {Previously, we showed that copiotrophic and oligotrophic bacteria fluctuate as moving waves along roots. These waves probably originate as a result of growth and death cycles at any location where a moving nutrient source passed. In this study, we placed sclerotia of Rhizoctonia solani AG8 along growing roots of wheat and showed that the proportions of root sections from which R. solani was isolated fluctuated with distance from the root tip. Similarly, proportions of root sections from which naturally occurring Pythium spp. were isolated fluctuated with distance from the root tip. Fourier analysis showed that these fluctuations constituted significant waves. Cross-correlation analyses demonstrated that there were negative correlations between R. solani infections and colony forming units of copiotrophic bacteria at the time of inoculation at the same locations on the root (lag = 0 cm), indicating that infection by R. solani could have been inhibited by these bacteria. There was a positive correlation between Pythium infections and copiotrophic bacteria at a lag of 6 cm along the roots. It therefore appears that Pythium infection took place shortly after the initial peak in copiotrophic bacteria following the passage of the root tip.}, }
@article {pmid12019460, year = {2002}, author = {Reyes, I and Bernier, L and Antoun, H}, title = {Rock phosphate solubilization and colonization of maize rhizosphere by wild and genetically modified strains of Penicillium rugulosum.}, journal = {Microbial ecology}, volume = {44}, number = {1}, pages = {39-48}, pmid = {12019460}, issn = {0095-3628}, mesh = {Biological Transport ; Colony Count, Microbial ; Electroporation ; *Genetic Engineering ; Geologic Sediments/*chemistry ; Hygromycin B/pharmacology ; Mitosis ; Mutation/genetics ; Penicillium/enzymology/*genetics/*metabolism ; Phosphates/*metabolism ; Phosphotransferases (Alcohol Group Acceptor)/genetics ; Plant Roots/cytology/microbiology ; Soil Microbiology ; Solubility ; Zea mays/cytology/*microbiology ; }, abstract = {Maize root colonization and phosphate solubilizing activity of the fungus Penicillium rugulosum were assessed in a greenhouse trial using soil-plant microcosms. The bacterial gene hph conferring resistance to hygromicin B was introduced by electroporation in the wild-type strain IR-94MF1 of P. rugulosum and one transformant, w-T3, was selected. Maize plants were grown for 5 weeks in a P-poor soil and fertilized with a Florida apatite mineral, with Navay, an apatite rock deposit from Venezuela, or with simple superphosphate. Inoculation treatments included strain IR-94MF1, transformant w-T3 and two IR-94MF1 UV-induced mutants with enhanced (Mps++) or reduced (Mps-) in vitro mineral phosphate solubilizing activity. In the absence of P fertilization, inoculation with any P. rugulosum isolate significantly reduced the size of the total and P-solubilizing bacterial community present in maize rhizosphere. The bacterial community significantly increased in maize inoculated with IR-94MF1 and w-T3 when P was added as apatites Navay or Florida. All P. rugulosum strains were able to stimulate the growth of maize plants as indicated by 3.6 to 28.6% increases in dry matter yields. In the presence of rock phosphate, P uptake by maize plants inoculated with the two mutants Mps++ and Mps- was not always in agreement with their P-solubilizing phenotypes. Strain IR-94MF1 and transformant w-T3 increased P assimilation by the plants fertilized with Navay rock phosphate by 26 and 38%, respectively. In this treatment, w-T3 showed its highest significant maize rhizosphere colonization. With the simple superphosphate treatment, w-T3 increased P uptake in plants by 8% over the uninoculated control and also decreased significantly the community size of total bacteria, total fungi, and P-solubilizing fungi in the rhizosphere.}, }
@article {pmid12016460, year = {2002}, author = {Lindström, ES and Leskinen, E}, title = {Do neighboring lakes share common taxa of bacterioplankton? Comparison of 16S rDNA fingerprints and sequences from three geographic regions.}, journal = {Microbial ecology}, volume = {44}, number = {1}, pages = {1-9}, pmid = {12016460}, issn = {0095-3628}, mesh = {Actinobacteria/*classification/*genetics ; Alphaproteobacteria/*classification/*genetics ; Animals ; DNA Fingerprinting ; Ecosystem ; Electrophoresis ; Fresh Water/*microbiology ; Genes, Bacterial/genetics ; Genes, rRNA/genetics ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Scandinavian and Nordic Countries ; }, abstract = {Bacterioplankton community composition was studied in 12 lakes in three different geographic regions in Scandinavia using denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rDNA. Area-specific abundant taxa were found in the lakes in two of the regions. In the region of Uppland the lakes had an alpha-proteobacterium, belonging to the subgroup Alpha V in common. The Alpha V bacteria appeared to be favored by neutral or higher pH values. The lakes in Lappland were found to harbor Actinobacteria, which appeared to be favored in bog lakes. No abundant taxon was found to be in common for the lakes in Svalbard, the third region studied.}, }
@article {pmid12003960, year = {2002}, author = {Ranjard, L and Prigent-Combaret, C and Nazaret, S and Cournoyer, B}, title = {Methylation of inorganic and organic selenium by the bacterial thiopurine methyltransferase.}, journal = {Journal of bacteriology}, volume = {184}, number = {11}, pages = {3146-3149}, pmid = {12003960}, issn = {0021-9193}, mesh = {Escherichia coli/genetics/*metabolism ; Genetic Vectors ; Methylation ; Methyltransferases/*metabolism ; Selenium/chemistry/*metabolism ; Thauera/*enzymology ; }, abstract = {Escherichia coli cells expressing the tpm gene encoding the bacterial thiopurine methyltransferase (bTPMT) are shown to methylate selenite and (methyl)selenocysteine into dimethylselenide (DMSe) and dimethyldiselenide (DMDSe). E. coli cells expressing tpm from a gene library cosmid clone (harboring a Pseudomonas syringae insert of about 20 kb) also methylated selenate into DMSe and DMDSe. bTPMT is the first methyltransferase shown to be involved in the methylation of these selenium derivatives.}, }
@article {pmid12000318, year = {2002}, author = {Barclay, M and Day, JC and Thompson, IP and Knowles, CJ and Bailey, MJ}, title = {Substrate-regulated cyanide hydratase (chy) gene expression in Fusarium solani: the potential of a transcription-based assay for monitoring the biotransformation of cyanide complexes.}, journal = {Environmental microbiology}, volume = {4}, number = {3}, pages = {183-189}, doi = {10.1046/j.1462-2920.2002.00284.x}, pmid = {12000318}, issn = {1462-2912}, mesh = {Amino Acid Sequence ; Base Sequence ; Biodegradation, Environmental ; Cyanides/*metabolism ; DNA, Complementary/chemistry ; DNA, Intergenic/chemistry/genetics ; Formamides/analysis/metabolism ; Fusarium/*enzymology/genetics ; Gene Expression Regulation, Enzymologic/physiology ; Hydro-Lyases/biosynthesis/genetics/*metabolism ; Molecular Sequence Data ; RNA, Fungal/chemistry/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Substrate Specificity ; }, abstract = {The fungus Fusarium solani detoxifies cyanide through induction of the cyanide hydratase gene activity (chy) in the presence of either KCN or the metal-complexed cyanides, K2Ni(CN)4 or K4Fe(CN)6, at pH 7.0 and 4.0 respectively. Sequence analysis of the chy gene identified primers for reverse transcriptase-polymerase chain reaction (RT-PCR)-directed analysis of mRNA transcripts, which demonstrated that activity correlated to the substrate-specific induction of gene expression. chy transcription was initiated 30-60 min after exposure of F. solani cultures to cyanide complexes. Maximum expression was detected within 4.5 h, after which chy mRNA synthesis declined below the limits of detection within 26 h. A lag period of approximately 2 h, following initial transcription, was recorded before cyanide complexes were converted to formamide. mRNA transcripts of chy were not detected in the absence of cyanide or cyanide complexes. The presence of introns within the gene resulted in a difference in size of 100 bp for DNA compared with mRNA of the corresponding 5' region. This size difference facilitated PCR detection of gene and transcript respectively. Comparisons of the predicted amino acid sequence of the F. solani chy gene and those of Gloeocerospora sorghi, Fusarium lateritium and Leptosphaeria maculans demonstrate that cyanide hydratase genes are highly conserved and of a similar evolutionary origin. These data predict that the functional assay described here to monitor the induction of chy gene expression and, potentially, cyanide degradation would be applicable to a variety of polluted environments.}, }
@article {pmid11999997, year = {2002}, author = {Pynaert, K and Sprengers, R and Laenen, J and Verstraete, W}, title = {Oxygen-limited nitrification and denitrification in a lab-scale rotating biological contactor.}, journal = {Environmental technology}, volume = {23}, number = {3}, pages = {353-362}, doi = {10.1080/09593332508618419}, pmid = {11999997}, issn = {0959-3330}, mesh = {*Bioreactors ; Nitrogen/*metabolism ; Oxygen/metabolism ; Quaternary Ammonium Compounds/analysis ; Waste Disposal, Fluid/*methods ; }, abstract = {Rotating Biological Contactors (RBC) treating highly nitrogenous wastewaters are known to give rise to nitrogen losses, generally assumed to be due to concomitant nitrification and denitrification. In this study, a lab-scale nitrifying RBC reactor was shown to bring about losses of nitrogen of the order of 10 to 20% at ammonium loading rates of up to 2129 mg N m(-2) d(-1), when no extra carbon source was added. These higher removal values could be due to Oxygen-Limited Autotrophic Nitrification and Denitrification (OLAND), because the reactor was operated at oxygen limitation. When methanol was added as a soluble organic carbon source to further diminish oxygen transfer into the deeper parts of the biofilm, the RBC achieved 84% nitrogen removal (loading rate 2300 mg N m(-2) d(-1)) at a COD/N ratio of 3.1. The latter also suggests that the process was occurring parallel to conventional denitrification.}, }
@article {pmid11999990, year = {2002}, author = {Muthumbi, W and De Boever, P and D'Haese, I and D'Hooge, W and Top, EM and Pieters, JG and Comhaire, F and Verstraete, W}, title = {Assessment of the estrogenic activity of flue gases from burning processes by means of the yeast based human estrogen receptor (hER) bioassay.}, journal = {Environmental technology}, volume = {23}, number = {3}, pages = {287-291}, doi = {10.1080/09593332508618415}, pmid = {11999990}, issn = {0959-3330}, mesh = {Air Pollutants/*adverse effects/analysis ; Biological Assay ; Calibration ; Environmental Monitoring/methods ; Gases ; Humans ; Incineration ; Receptors, Estrogen/*drug effects/physiology ; *Refuse Disposal ; Wood ; Yeasts ; }, abstract = {Combustion processes are known to produce organic micro-pollutants in the flue gas at concentrations ranging over several orders of magnitude. Some organic micro-pollutants are suspected of being pseudo-estrogens and as such they can affect the public health. In this study, the possible application of the yeast based human estrogen receptor (hER) bioassay to screen flue gas streams for the presence of estrogenic active micro-pollutants was explored. Specifically, the protocol was modified to allow the detection and quantification of the potential estrogenic active non-polar organic micro-pollutants contained in the flue gas matrix. The modified assay was calibrated using a model estrogenic compound (17-alpha-ethinylestradiol (EE2)) dissolved in methylene chloride at concentrations ranging from 3 ng l(-1) to 3000 ng l(-1). The effective concentration to elucidate a 50% response (EC50) was 87 ng l(-1) of equivalent dissolved in methylene chloride. Samples of methylene chloride used to trap non-polar micro-pollutants in flue gas from combustion of pine wood were found to clearly register estrogenic activity by the bioassay under certain conditions. The combustion tests were performed with pinewood alone and with pine wood in the presence of both Copper-naphthenate and copper(II)chloride at 600 degrees C and 1000 degrees C. These conditions must be considered as experimental rather than practical. Overall, the results suggest that, by means of this modified assay, it is possible and warranted to screen systematically for estrogens in flue gas combustion processes.}, }
@article {pmid11997169, year = {2002}, author = {Nicolaisen, MH and Ramsing, NB}, title = {Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteria.}, journal = {Journal of microbiological methods}, volume = {50}, number = {2}, pages = {189-203}, doi = {10.1016/s0167-7012(02)00026-x}, pmid = {11997169}, issn = {0167-7012}, mesh = {Ammonia/*metabolism ; Culture Media ; DNA Primers/genetics ; Electrophoresis, Agar Gel ; Environmental Microbiology ; *Genetic Variation ; Molecular Sequence Data ; Nitrosomonas/*classification/genetics/isolation &amp; purification ; Oxidation-Reduction ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Denaturing gradient gel electrophoresis (DGGE) of PCR amplicons of the ammonia monooxygenase gene (amoA) was developed and employed to investigate the diversity of ammonia-oxidizing bacteria (AOB) in four different habitats. The results were compared to DGGE of PCR-amplified partial 16S rDNA sequences made with primers specific for ammonia-oxidizing bacteria. Potential problems, such as primer degeneracy and multiple gene copies of the amoA gene, were investigated to evaluate and minimize their possible impact on the outcome of a DGGE analysis. amoA and 16S rDNA amplicons were cloned, and a number of clones screened by DGGE to determine the abundance of different motility types in the clone library. The abundance of clones was compared to the relative intensity of bands emerging in the band pattern produced by direct amplification of the genes from the environmental sample. Selected clones were sequenced to evaluate the specificity of the respective primers. The 16S rDNA primer pair, reported to be specific for ammonia-oxidizing bacteria (AOB), generated several sequences that were not related to the known Nitrosospira-Nitrosomonas group and, thus, not likely to be ammonia oxidizers. However, no false positives were found among the sequences retrieved with the modified amoA primers. Some phylogenetic information could be deduced from the position of amoA bands in DGGE gels. The Nitrosomonas-like sequences were found within a denaturant range from 30% to 46%, whereas the Nitrosospira-like sequences migrated to 50% to 60% denaturant. The majority of retrieved sequences from all four habitats with high ammonia loads were Nitrosomonas-like and only few Nitrosospira-like sequences were detected.}, }
@article {pmid11990037, year = {2002}, author = {Donnelly, CW}, title = {Detection and isolation of Listeria monocytogenes from food samples: implications of sublethal injury.}, journal = {Journal of AOAC International}, volume = {85}, number = {2}, pages = {495-500}, pmid = {11990037}, issn = {1060-3271}, mesh = {Culture Media ; *Food Microbiology ; Listeria monocytogenes/classification/growth &amp; development/*isolation &amp; purification ; *Microbiological Techniques ; Ribotyping ; }, abstract = {Detection of L. monocytogenes is often limited by the performance of the enrichment media used to support bacterial growth to detectable levels. Because Listeria may exist at extremely low levels in foods, sample enrichment protocols must amplify these low initial populations to detectable limits. Listeria may also exist in an injured state in food products as a result of processing treatments such as heating, freezing, exposure to acids, or exposure to sanitizing compounds. Selective agents in enrichment media normally used for recovery of Listeria may inhibit repair and detection of sublethally injured Listeria, which may go on to repair, grow, and regain pathogenicity. Simple modifications to existing regulatory protocols, such as those that use more than one enrichment broth, raise sensitivity of detection to 90%. This review shows the efficacy of repair/enrichment strategies, which increase sensitivity of detection to 97.5-98.8% compared with 65-70% by standard regulatory protocols. Ribotype analysis of isolates obtained from meat samples reveals a complex microbial ecology, with striking differences in both number and distribution of distinct genetic types of Listeria, depending upon whether samples are enriched in selective or repair/enrichment media. In studies on enrichment of dairy environmental samples in University of Vermont medium and Listeria repair broth (UVM and LRB), combining these 2 primary enrichment media into a single tube of Fraser broth for dual secondary enrichment yielded a significantly higher percentage (p < 0.05) of Listeria-positive samples than did use of either LRB or UVM alone. Refinement of conventional Listeria recovery methods should consider the importance of the enrichment step, the nutritional needs of specific genetic types, and the physiological condition of Listeria isolates in foods.}, }
@article {pmid11988527, year = {2002}, author = {Oberreuter, H and Charzinski, J and Scherer, S}, title = {Intraspecific diversity of Brevibacterium linens, Corynebacterium glutamicum and Rhodococcus erythropolis based on partial 16S rDNA sequence analysis and Fourier-transform infrared (FT-IR) spectroscopy.}, journal = {Microbiology (Reading, England)}, volume = {148}, number = {Pt 5}, pages = {1523-1532}, doi = {10.1099/00221287-148-5-1523}, pmid = {11988527}, issn = {1350-0872}, mesh = {Bacterial Typing Techniques/*methods ; Brevibacterium/classification/*genetics/isolation &amp; purification ; Corynebacterium/classification/*genetics/isolation &amp; purification ; DNA, Bacterial/*genetics ; DNA, Ribosomal/*genetics ; Evolution, Molecular ; Genetic Variation/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Reference Standards ; Rhodococcus/classification/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Species Specificity ; Spectroscopy, Fourier Transform Infrared/methods ; }, abstract = {The intraspecific diversity of 31 strains of Brevibacterium linens, 27 strains of Corynebacterium glutamicum and 29 strains of Rhodococcus erythropolis was determined by partial 16S rDNA sequence analysis and Fourier-transform infrared (FT-IR) spectroscopy. As a prerequisite for the analyses, 27 strains derived from culture collections which had carried invalid or wrong species designations were reclassified in accordance with polyphasic taxonomical data. FT-IR spectroscopy proved to be a rapid and reliable method for screening for similar isolates and for identifying these actinomycetes at the species level. Two main conclusions emerged from the analyses. (1) Comparison of intraspecific 16S rDNA similarities suggested that R. erythropolis strains have a very low diversity, B. linens displays high diversity and C. glutamicum occupies an intermediate position. (2) No correlation of FT-IR spectral similarity and 16S rDNA sequence similarity below the species level (i.e. between strains of one species) was observed. Therefore, diversification of 16S rDNA sequences and microevolutionary change of the cellular components detected by FT-IR spectroscopy appear to be de-coupled.}, }
@article {pmid11984640, year = {2002}, author = {de los Ríos, A and Wierzchos, J and Ascaso, C}, title = {Microhabitats and chemical microenvironments under saxicolous lichens growing on granite.}, journal = {Microbial ecology}, volume = {43}, number = {1}, pages = {181-188}, doi = {10.1007/s00248-001-1028-2}, pmid = {11984640}, issn = {0095-3628}, mesh = {*Biofilms ; Ecosystem ; *Environment ; Lichens/*growth &amp; development ; Population Dynamics ; Silicon Dioxide ; }, abstract = {Lasallia hispanica, Parmelia omphalodes, and Cornicularia normoerica, saxicolous thalli growing on granite, show a close relationship with other lichens and microorganisms living in the lithic substrate beneath them. The lithobiontic community is an accumulation of microorganisms at an interface forming a biofilm, which interacts with the lithic substrate both geophysically and geochemically. Because of their fruticose and foliose morphology, the saxicolous species examined here are mainly involved in geophysical processes, but in the proximity of their attachment structures, geochemical processes may also be observed. On the other hand, fungi, algae and cyanobacteria forming crustose lichens, as well as free-living lithobiontic microorganisms, are known to show combined geophysical and geochemical action, mainly on laminar minerals. The substrate zone where the saxicolous lichens are attached is most affected by weathering reactions and shows the highest co-occurrence of lithobiontic microorganisms. The physical and chemical properties of the substrate, along with lichen and microorganism activity, determine different microenvironments and microhabitats. The ecological functioning of these lithobiontic communities is not yet fully understood, and research efforts similar to the present are needed to confirm that their development is influenced by interrelations between different community members and the substrate, as suggested here.}, }
@article {pmid11984639, year = {2002}, author = {Kearns, KD and Hunter, MD}, title = {Algal extracellular products suppress Anabaena flos-aquae heterocyst spacing.}, journal = {Microbial ecology}, volume = {43}, number = {1}, pages = {174-180}, doi = {10.1007/s00248-001-1039-z}, pmid = {11984639}, issn = {0095-3628}, mesh = {Anabaena/*growth &amp; development ; Animals ; Chlamydomonas reinhardtii/*chemistry ; Phenotype ; Phytoplankton ; Plant Extracts/*pharmacology ; Population Dynamics ; Water Microbiology ; }, abstract = {Intra- and interspecific chemical signals allow bacteria to respond to environmental conditions by regulating gene transcription. In cyanobacteria, gene products and the presence of fixed nitrogen regulate heterocyst frequency. In this paper, we describe a chemical made by a green alga, Chlamydomonas reinhardtii, that suppresses heterocyst formation in the co-occurring cyanobacterium, Anabaena flos-aquae. Cyanobacterial heterocyst frequencies were reduced in the presence of water-soluble, proteinase- and heat-resistant molecules greater than 15 kDa in molecular size. Green algal cells in all phases of growth made the suppressor. Ammonium and nitrate concentrations in the medium did not correlate with this change in phenotype. In addition, growth rate was not enhanced by the extracellular products. Therefore, C. reinhardtii extracellular products acted as a heterocyst inhibitor, not as a fixed nitrogen source. Chemical interactions between green algae and cyanobacteria influence heterocyst formation, an important consideration in understanding the outcome of competition between these organisms and the dynamics of phytoplankton communities.}, }
@article {pmid11984638, year = {2002}, author = {Wilhelm, SW and Brigden, SM and Suttle, CA}, title = {A dilution technique for the direct measurement of viral production: a comparison in stratified and tidally mixed coastal waters.}, journal = {Microbial ecology}, volume = {43}, number = {1}, pages = {168-173}, doi = {10.1007/s00248-001-1021-9}, pmid = {11984638}, issn = {0095-3628}, mesh = {*Bacteria ; Population Dynamics ; *Viruses ; *Water Microbiology ; Water Movements ; }, abstract = {The abundance of heterotrophic bacteria and viruses, as well as rates of viral production and virus-mediated mortality, were measured in Discovery Passage and the Strait of Georgia (British Columbia, Canada) along a gradient of tidal mixing ranging from well mixed to stratified. The abundances of bacteria and viruses were approximately 10(6) and 10(7) mL(-1), respectively, independent of mixing regime. Viral production estimates, monitored by a dilution technique, demonstrated that new viruses were produced at rates of 10(6) and 10(7) mL(-1)h(-1) across the different mixing regimes. Using an estimated burst size of 50 viruses per lytic event, ca. 19 to 27% of the standing stock of bacteria at the stratified stations and 46 to 137% at the deep-mixed stations were removed by viruses. The results suggest that mixing of stratified waters during tidal exchange enhances virus-mediated bacterial lysis. Consequently, viral lysis recycled a greater proportion of the organic carbon required for bacterial growth under non-steady-state compared to steady-state conditions.}, }
@article {pmid11984637, year = {2002}, author = {Toh, SK and Webb, RI and Ashbolt, NJ}, title = {Enrichment of autotrophic anaerobic ammonium-oxidizing consortia from various wastewaters.}, journal = {Microbial ecology}, volume = {43}, number = {1}, pages = {154-167}, doi = {10.1007/s00248-001-0033-9}, pmid = {11984637}, issn = {0095-3628}, mesh = {Bacteria, Anaerobic/*physiology ; Biodegradation, Environmental ; Bioreactors ; Coke ; Incineration ; Industrial Waste ; Nitrogen/*metabolism ; Quaternary Ammonium Compounds/*chemistry ; *Waste Disposal, Fluid ; *Water Microbiology ; }, abstract = {The option for biological nitrogen removal has recently been broadened with the description of simultaneous nitrification/denitrification, anaerobic ammonium oxidation (ANAMMOX) and the concept of CANON (completely autotrophic nitrogen removal over nitrite). An autotrophic anaerobic ammonium oxidation (AAAO) consortium was successfully selected and enriched from municipal treatment plant sludges in Sydney, Australia, but not from industrial coke-oven wastewater sludges. Chemolithoautotrophic basic salt (CLABS) medium was used in the selection of AAAO organisms and chloramphenicol was added to the initial stage of selection to eliminate denitrifiers. Two different temperatures, 37 degrees C and 55 degrees C, were used in the selection of mesophilic and thermophilic consortia, respectively. Thermophilic AAAO organisms were not selected at 55 degrees C. Mesophilic AAAO activities, however, were evident in both batch and continuous cultures, whereby ammonium was consumed concurrently with a decrease of nitrite, giving a ratio of 1:1-1:1.3 in ammonium removal rate over nitrite consumption rate. A continuous-mode mesophilic fixed-bed reactor was established to enrich the AAAO consortium. After 1 year, biofilms, pinkish in color, had developed on the support media and side wall of the feed-line tubing. Ammonium and nitrite consumption increased from approximately 15 mg to 60 mg d(-1) L(-1) over a period of 243 days. Later, transmission electron microscopy (TEM) and fluorescence in situ hybridization (FISH) techniques revealed that the dominant cell type in the AAAO consortium had a similar morphology and 16S rDNA sequence homology to that of the recently described ANAMMOX organism, "Brocadia anammoxidans".}, }
@article {pmid11984636, year = {2002}, author = {Teixeira, H and Gonçalves, MG and Rozès, N and Ramos, A and San Romão, MV}, title = {Lactobacillic acid accumulation in the plasma membrane of Oenococcus oeni: a response to ethanol stress?.}, journal = {Microbial ecology}, volume = {43}, number = {1}, pages = {146-153}, doi = {10.1007/s00248-001-0036-6}, pmid = {11984636}, issn = {0095-3628}, mesh = {Adaptation, Physiological ; Cell Membrane/physiology ; Central Nervous System Depressants/*pharmacology ; Ethanol/*pharmacology ; Fatty Acids/*analysis ; Fermentation ; Gram-Positive Cocci/*physiology ; Leuconostoc/physiology ; Population Dynamics ; Survival Analysis ; Wine ; }, abstract = {It is known that ethanol strongly interferes with the development and activity of lactic acid bacteria in wine. In this work, it was observed that membrane composition was dependent of ethanol concentration and cell physiological state. The protein electrophoretic profile was modified in the membranes of Oenococcus oeni cultured in presence of 8 and 10% ethanol. Concerning the membrane lipid composition, it was observed that O. oeni maintained a high level of phospholipid biosynthesis via the relative increased biosynthesis of phosphoethanolamine and sphingomyelin in presence of ethanol. On the other hand, ethanol induced an increase in the membrane lactobacillic acid percentage at the expense of cis-vaccenic acid. This increased synthesis of lactobacillic acid appears as the more significant change induced by ethanol in O. oeni membrane. The increase of lactobacillic acid in the membrane of O. oeni clearly appears as a factor that provides protection against the toxic effect of ethanol, balancing the increase of membrane fluidity normally attributed to ethanol. The results presented in this paper constitute evidence that lactobacillic acid may have a part in the survival and or adaptive mechanisms developed by O. oeni under culture adverse conditions, allowing these bacteria to maintain their activity in the presence of ethanol, namely performing malolactic fermentation in wine.}, }
@article {pmid11984635, year = {2002}, author = {Hayes, LA and Lovley, DR}, title = {Specific 16S rDNA sequences associated with naphthalene degradation under sulfate-reducing conditions in harbor sediments.}, journal = {Microbial ecology}, volume = {43}, number = {1}, pages = {134-145}, doi = {10.1007/s00248-001-1055-z}, pmid = {11984635}, issn = {0095-3628}, mesh = {Biodegradation, Environmental ; DNA Primers ; DNA, Bacterial/*genetics ; Geologic Sediments/*microbiology ; Naphthalenes/*metabolism ; Oxidation-Reduction ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Sulfur-Reducing Bacteria/classification/*genetics/physiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Previous studies have demonstrated that naphthalene and other polycyclic aromatic hydrocarbons (PAHs) can be anaerobically oxidized with the reduction of sulfate in PAH-contaminated marine harbor sediments, including those in San Diego Bay. In order to learn more about the microorganisms that might be involved in anaerobic naphthalene degradation, the microorganisms associated with naphthalene degradation in San Diego Bay sediments were evaluated. A dilution-to-extinction enrichment culture strategy, designed to recover the most numerous culturable naphthalene-degrading sulfate reducers, resulted in the enrichment of microorganisms with 16S rDNA sequences in the d-Proteobacteria, which were closely related to a previously described pure culture of a naphthalene-degrading sulfate reducer, NaphS2, isolated from sediments in Germany. A more traditional enrichment culture approach, expected to enrich for the fastest-growing naphthalene-degrading sulfate reducers, yielded 16S rDNA sequences closely related to those found in the dilution-to-extinction enrichments and NaphS2. Analysis of 16S rDNA sequences in sediments from two sites in San Diego Bay that had been adapted for rapid naphthalene degradation by continual amendment with low levels of naphthalene suggested that the microbial community composition in the amended sediments differed from that present in the unamended sediments from the same sites. Most significantly, 6-8% of the sequences recovered from 100 clones of each of the naphthalene-amended sediments were closely related to the 16S rDNA sequences in the enrichment cultures as well as the sequence of the pure culture, NaphS2. No sequences in this NaphS2 phylotype were recovered from the sediments that were not continually exposed to naphthalene. A PCR primer, which was designed based on these phylotype sequences, was used to amplify additional 16S rDNA sequences belonging to the NaphS2 phylotype from PAH-degrading sediments from Island End River (Boston), MA, and Liepaja Harbor, Latvia. Closely related sequences were also recovered from highly contaminated sediment from Tampa Bay, FL. These results suggest that microorganisms closely related to NaphS2 might be involved in naphthalene degradation in harbor sediments. This finding contrasts with the frequent observation that the environmentally relevant microorganisms cannot be readily recovered in pure culture and suggests that further study of the physiology of NaphS2 may provide insights into factors controlling the rate and extent of naphthalene degradation in marine harbor sediments.}, }
@article {pmid11984634, year = {2002}, author = {Van Wambeke, F and Christaki, U and Giannakourou, A and Moutin, T and Souvemerzoglou, K}, title = {Longitudinal and vertical trends of bacterial limitation by phosphorus and carbon in the Mediterranean Sea.}, journal = {Microbial ecology}, volume = {43}, number = {1}, pages = {119-133}, doi = {10.1007/s00248-001-0038-4}, pmid = {11984634}, issn = {0095-3628}, mesh = {Alkaline Phosphatase/metabolism/*pharmacology ; *Bacteria ; Carbon/analysis/*metabolism ; Mediterranean Sea ; Oxygen Consumption ; Phosphorus/analysis/*metabolism ; Population Dynamics ; *Water Microbiology ; }, abstract = {The effect of phosphate (P), nitrate (N), and organic carbon (C, glucose) enrichment on heterotrophic bacterial production was examined along two longitudinal transects covering the whole Mediterranean Sea during June and September 1999. During these cruises, integrated bacterial production ranged from 11 to 349 mgC m(-2) d(-1) for the 0-150 m layer. P was found to stimulate bacterial production (BP) in 13 out of 18 experiments, in the eastern and in the western Mediterranean Sea. Organic carbon stimulation of bacterial production was observed at two stations in the Alboran Sea, where the highest bacterial production was recorded (216 and 349 mg C m(-2) d(-1)) and in the Sicily Strait. Maximum rates of alkaline phosphatase (AP) increased from the Alboran to the Levantine Sea whereas AP turnover time decreased. Moreover, alkaline phosphatase activity was not systematically reduced following additions of P. In cases of P limitation, however, the alkaline phosphatase activity to bacterial production ratio was severely reduced in the P and NPC enrichments. Generally, the addition of the limiting factor--whether P or C--had a synchronous stimulating effect on bacterial production and ectoaminopeptidase activity and induced a decline in the amino acid respiration percentage. At two selected stations in the eastern and northwestern Mediterranean, response to enrichment was tested on vertical profiles. Bacteria shifted from P to C limitation at a depth where soluble reactive phosphorus was still undetectable, but corresponding to a strong increase in alkaline phosphatase turnover time. Our results showed that values of AP turnover time lower than 100 h corresponded to situations of P limitation of bacterial production.}, }
@article {pmid11984633, year = {2002}, author = {Kurmayer, R and Dittmann, E and Fastner, J and Chorus, I}, title = {Diversity of microcystin genes within a population of the toxic cyanobacterium Microcystis spp. in Lake Wannsee (Berlin, Germany).}, journal = {Microbial ecology}, volume = {43}, number = {1}, pages = {107-118}, doi = {10.1007/s00248-001-0039-3}, pmid = {11984633}, issn = {0095-3628}, mesh = {Amino Acid Sequence ; DNA Primers ; DNA, Bacterial/*genetics ; *Genetic Variation ; Genotype ; Germany ; Marine Toxins ; Mass Spectrometry ; Microcystins ; Microcystis/*genetics ; Molecular Sequence Data ; Peptides, Cyclic/chemistry/*genetics ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Population Dynamics ; }, abstract = {In order to find out how many genotypes determine microcystin production of Microcystis spp. in field populations, single colonies (clones) were sampled from Lake Wannsee (Berlin, Germany), characterized morphologically, and subsequently analyzed by PCR for a region within the mcyB gene encoding the activation of one amino acid during microcystin biosynthesis. The different morphospecies varied considerably in the proportion of microcystin-producing genotypes. Most colonies (73%) of M. aeruginosa contained this gene whereas only 16% of the colonies assigned to M. ichthyoblabe and no colonies of M. wesenbergii gave a PCR product of the mcyB gene. Restriction fragment length polymorphism revealed seven restriction profiles showing low variability in nucleotide sequence within each restriction type (0.4-4%) and a low to high variability (1.6-38%) between restriction types. In addition, the sequences of amino acids within the mcyB gene were analyzed to compare the specificity of the amino acid activation during microcystin biosynthesis between restriction types and with the occurrence of amino acids in microcystin variants as detected by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Most of the microcystin-producing colonies showed high similarity in the sequence of amino acids and contained microcystin-LR (LR refers to leucine and arginine in the variable positions of the heptapeptide), microcystin-RR, and microcystin-YR, as well as other variants in minor concentrations. It is concluded that the gene product found for most of the microcystin-producing colonies in the lake is rather unspecific and the diversity of microcystin variants in the lake results from activation of various amino acids during microcystin biosynthesis in the same genotypes.}, }
@article {pmid11984632, year = {2002}, author = {Wendt-Potthoff, K and Koschorreck, M}, title = {Functional groups and activities of bacteria in a highly acidic volcanic mountain stream and lake in Patagonia, Argentina.}, journal = {Microbial ecology}, volume = {43}, number = {1}, pages = {92-106}, doi = {10.1007/s00248-001-1030-8}, pmid = {11984632}, issn = {0095-3628}, mesh = {Argentina ; *Bacteria ; Biomass ; *Environmental Monitoring ; Euryarchaeota ; Fermentation ; Geologic Sediments/microbiology ; Hydrogen-Ion Concentration ; Iron/chemistry ; Oxygen Consumption ; Population Dynamics ; Sulfur/chemistry ; *Volcanic Eruptions ; *Water Microbiology ; }, abstract = {Acidic volcanic waters are naturally occurring extreme habitats that are subject of worldwide geochemical research but have been little investigated with respect to their biology. To fill this gap, the microbial ecology of a volcanic acidic river (pH approximately equal to 0-1.6), Rio Agrio, and the recipient lake Caviahue in Patagonia, Argentina, was studied. Water and sediment samples were investigated for Fe(II), Fe(III), methane, bacterial abundances, biomass, and activities (oxygen consumption, iron oxidation and reduction). The extremely acidic river showed a strong gradient of microbial life with increasing values downstream and few signs of life near the source. Only sulfide-oxidizing and fermentative bacteria could be cultured from the upper part of Rio Agrio. However, in the lower part of the system, microbial biomass and oxygen penetration and consumption in the sediment were comparable to non-extreme aquatic habitats. To characterize similarities and differences of chemically similar natural and man-made acidic waters, our findings were compared to those from acidic mining lakes in Germany. In the lower part of the river and the lake, numbers of iron and sulfur bacteria and total biomass in sediments were comparable to those known from acidic mining lakes. Bacterial abundance in water samples was also very similar for both types of acidic water (around 10(5) mL(-1)). In contrast, Fe(II) oxidation and Fe(III) reduction potentials appeared to be lower despite higher biogenic oxygen consumption and higher photosynthetic activity at the sediment-water interface. Surprisingly, methanogenesis was detected in the presence of high sulfate concentrations in the profundal sediment of Lake Caviahue. In addition to supplementing microbiological knowledge on acidic volcanic waters, our study provides a new view of these extreme sites in the general context of aquatic habitats.}, }
@article {pmid11984631, year = {2002}, author = {Sekiguchi, H and Koshikawa, H and Hiroki, M and Murakami, S and Xu, K and Watanabe, M and Nakahara, T and Zhu, M and Uchiyama, H}, title = {Bacterial distribution and phylogenetic diversity in the Changjiang estuary before the construction of the Three Gorges Dam.}, journal = {Microbial ecology}, volume = {43}, number = {1}, pages = {82-91}, doi = {10.1007/s00248-001-0034-8}, pmid = {11984631}, issn = {0095-3628}, mesh = {*Bacteria/classification/genetics/isolation &amp; purification ; China ; Conservation of Natural Resources ; DNA, Bacterial/analysis ; *Ecosystem ; *Environmental Monitoring ; Genotype ; Phenotype ; *Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Population Dynamics ; Water Microbiology ; Water Supply ; }, abstract = {The bacterial community structure in the Changjiang estuary was studied for comparison with future changes, related to the construction of the Three Gorges Dam. Population densities of bacteria in the surface water at station C1 estimated by CFU on marine agar plates and by DAPI direct count, were 2.8 x 10(4) ml(-1) and 4.2 x 10(5) ml(-1), respectively. Physicochemical properties of water, such as temperature and salinity, suggested that station C1 was affected by freshwater from the Changjiang River. Cluster analysis of the PCR-RFLP patterns obtained from 9 samples showed that the bacterial community structure at station C1 was different from the structure at the other stations. Bacterial diversity in the surface water at station C1 was studied based on the genotypes of the 250 clones of 16S rRNA, and on the phenotypes generated on Biolog GN plates for 70 isolates. Sequences of bacteria from two common marine groups, alpha- and gamma-Proteobacteria, were frequently observed. Some other divisions, including the beta-Proteobacteria, C/F/B group, low G+C gram positive, high G+C gram positive, chloroplasts, and relatives of Verrucomicrobia were also observed. The putative dominant species based on both genotype and phenotype analyses were close relatives of Alteromonas macleodii or Roseobacter spp. These results reflected the nutrient-rich environment at station C1.}, }
@article {pmid11984630, year = {2002}, author = {Tadonléké, RD and Jugnia, LB and Sime-Ngando, T and Devaux, J and Romagoux, JC}, title = {Food web structure in the recently flooded Sep Reservoir as inferred from phytoplankton population dynamics and living microbial biomass.}, journal = {Microbial ecology}, volume = {43}, number = {1}, pages = {67-81}, doi = {10.1007/s00248-001-1015-7}, pmid = {11984630}, issn = {0095-3628}, mesh = {*Bacteria ; Biomass ; Disasters ; *Environmental Monitoring ; *Eutrophication ; *Food Chain ; Phosphorus/*metabolism ; *Phytoplankton ; Population Dynamics ; Seasons ; Survival Analysis ; Water Supply ; }, abstract = {Phytoplankton dynamics, bacterial standing stocks and living microbial biomass (derived from ATP measurements, 0.7-200 mm size class) were examined in 1996 in the newly flooded (1995) Sep Reservoir ('Massif Central,' France), for evidence of the importance of the microbial food web relative to the traditional food chain. Phosphate concentrations were low, N:P ratios were high, and phosphate losses converted into carbon accounted for <50% of phytoplankton biomass and production, indicating that P was limiting phytoplankton development during the study. The observed low availability of P contrasts with the high release of "directly" assimilable P often reported in newly flooded reservoirs, suggesting that factors determining nutrient dynamics in such ecosystems are complex. The phosphate availability, but also the water column stability, seemed to be among the major factors determining phytoplankton dynamics, as (i) large-size phytoplankton species were prominent during the period of increasing water column stability, whereas small-size species dominated phytoplankton assemblages during the period of decreasing stability, and (ii) a Dinobryon divergens bloom occurred during a period when inorganic P was undetectable, coinciding with the lowest values of bacterial standing stocks. Indication of grazing limitation of bacterial populations by the mixotrophic chrysophyte D. divergens (in late spring) and by other potential grazers (mainly rotifers in summer) seemed to be confirmed by the Model II or functional slopes of the bacterial vs phytoplankton regressions, which were always <0.63. Phytoplankton biomass was not correlated with phosphorus sources and its contribution was remarkably low relative to the living microbial biomass which, in contrast, was positively correlated with total phosphorus in summer. We conclude that planktonic microheterotrophs are strongly implicated in the phosphorus dynamics in the Sep Reservoir, and thus support the idea that an important amount of matter and energy flows through the "microbial loop" and food web, shortly after the flooding of a reservoir.}, }
@article {pmid11984629, year = {2002}, author = {Findlay, S and Tank, J and Dye, S and Valett, HM and Mulholland, PJ and McDowell, WH and Johnson, SL and Hamilton, SK and Edmonds, J and Dodds, WK and Bowden, WB}, title = {A cross-system comparison of bacterial and fungal biomass in detritus pools of headwater streams.}, journal = {Microbial ecology}, volume = {43}, number = {1}, pages = {55-66}, doi = {10.1007/s00248-001-1020-x}, pmid = {11984629}, issn = {0095-3628}, mesh = {*Bacteria ; Biodegradation, Environmental ; Biomass ; Carbon/metabolism ; *Ecosystem ; *Fungi ; Nitrogen/metabolism ; Organic Chemicals ; Particle Size ; Phosphorus/metabolism ; Plant Leaves/metabolism ; *Water Microbiology ; Water Movements ; Wood ; }, abstract = {The absolute amount of microbial biomass and relative contribution of fungi and bacteria are expected to vary among types of organic matter (OM) within a stream and will vary among streams because of differences in organic matter quality and quantity. Common types of benthic detritus [leaves, small wood, and fine benthic organic matter (FBOM)] were sampled in 9 small (1st-3rd order) streams selected to represent a range of important controlling factors such as surrounding vegetation, detritus standing stocks, and water chemistry. Direct counts of bacteria and measurements of ergosterol (a fungal sterol) were used to describe variation in bacterial and fungal biomass. There were significant differences in bacterial abundance among types of organic matter with higher densities per unit mass of organic matter on fine particles relative to either leaves or wood surfaces. In contrast, ergosterol concentrations were significantly greater on leaves and wood, confirming the predominance of fungal biomass in these larger size classes. In general, bacterial abundance per unit organic matter was less variable than fungal biomass, suggesting bacteria will be a more predictable component of stream microbial communities. For 7 of the 9 streams, the standing stock of fine benthic organic matter was large enough that habitat-weighted reach-scale bacterial biomass was equal to or greater than fungal biomass. The quantities of leaves and small wood varied among streams such that the relative contribution of reach-scale fungal biomass ranged from 10% to as much as 90% of microbial biomass. Ergosterol concentrations were positively associated with substrate C:N ratio while bacterial abundance was negatively correlated with C:N. Both these relationships are confounded by particle size, i.e., leaves and wood had higher C:N than fine benthic organic matter. There was a weak positive relationship between bacterial abundance and streamwater soluble reactive phosphorus concentration, but no apparent pattern between either bacteria or fungi and streamwater dissolved inorganic nitrogen. The variation in microbial biomass per unit organic matter and the relative abundance of different types of organic matter contributed equally to driving differences in total microbial biomass at the reach scale.}, }
@article {pmid11984628, year = {2002}, author = {Baraniecki, CA and Aislabie, J and Foght, JM}, title = {Characterization of Sphingomonas sp. Ant 17, an aromatic hydrocarbon-degrading bacterium isolated from Antarctic soil.}, journal = {Microbial ecology}, volume = {43}, number = {1}, pages = {44-54}, doi = {10.1007/s00248-001-1019-3}, pmid = {11984628}, issn = {0095-3628}, mesh = {Antarctic Regions ; Biodegradation, Environmental ; Cold Temperature ; Hydrocarbons, Aromatic/*metabolism ; Hydrogen-Ion Concentration ; Kinetics ; Population Dynamics ; Soil Microbiology ; Sphingomonas/isolation &amp; purification/*physiology ; Survival Analysis ; }, abstract = {Sphingomonas sp. strain Ant 17 was isolated from fuel-contaminated soil collected at Scott Base, Ross Island, Antarctica. We anticipated that Ant 17 would be a good model organism for studying cold climate bioremediation, and therefore determined its biodegradation capabilities and tolerance of potentially growth-limiting environmental conditions. Sphingomonas sp. Ant 17 degrades the aromatic fraction of several different crude oils, jet fuel, and diesel fuel at low temperatures and without nutrient amendment. It utilizes or transforms a broad range of pure aromatic substrates, including hydrocarbons, heterocycles, and aromatic acids and alcohols. Ant 17 grows at temperatures of 1 degree C to 35 degrees C and mineralizes radiolabeled phenanthrene over a range of more than 24 degrees C. This psychrotolerant isolate appears to utilize hydrocarbons more efficiently at low temperatures than would be predicted by mesophilic enzyme kinetics. The optimum pH for growth was 6.4 at 22 degrees C, with extended lag phases observed in more alkaline media. However, there was less effect of pH on lag phase at lower temperatures. Ant 17 displayed greater tolerance to UV irradiation and freeze-thaw cycles than the hydrocarbon-degrading isolate Sphingomonas sp. WPO-1, which may reflect adaptation to its Antarctic soil environment. However, it was more sensitive than expected to desiccation and to low concentrations of NaCl and CaCl(2). Ant 17 was phenotypically stable and lacked detectable plasmids, suggesting a chromosomal location for genes encoding aromatic degradation enzymes. Its broad aromatic substrate range and tolerance of low and fluctuating temperature and low nutrients make Sphingomonas sp. Ant 17 a valuable microbe for examining fuel spill bioremediation in cold soils.}, }
@article {pmid11984627, year = {2002}, author = {Di Mattia, E and Grego, S and Cacciari, I}, title = {Eco-physiological characterization of soil bacterial populations in different states of growth.}, journal = {Microbial ecology}, volume = {43}, number = {1}, pages = {34-43}, doi = {10.1007/s00248-001-1035-3}, pmid = {11984627}, issn = {0095-3628}, mesh = {*Ecology ; Environment ; *Environmental Monitoring ; Population Dynamics ; Reproduction ; *Soil Microbiology ; Survival Analysis ; }, abstract = {The method based on characterization of microbial populations in terms of their growth rate in agar plates has been used for testing the prediction of the theory of r- and K-selection in a microbial community from a tropical soil. Conditions which could lead bacterial populations to grow exponentially or to enter into a stationary phase were obtained by growing soil microbial populations in a chemostat and in a chemostat with recycle, respectively. Significant differences in population distribution patterns were observed by comparing results from the two growth systems. When soil community was grown in a chemostat and subjected specifically to well-defined r- and K-conditions, stable associations of organisms with r- and K-type characteristics developed as a consequence of environmental pressure. In contrast, when cultivated in chemostat with recycle under the same r- and K-conditions imposed on chemostat cultures, distribution patterns of r- and K-selected populations appeared very little affected by changes in substrate availability.}, }
@article {pmid11984626, year = {2002}, author = {Bartosch, S and Hartwig, C and Spieck, E and Bock, E}, title = {Immunological detection of Nitrospira-like bacteria in various soils.}, journal = {Microbial ecology}, volume = {43}, number = {1}, pages = {26-33}, doi = {10.1007/s00248-001-0037-5}, pmid = {11984626}, issn = {0095-3628}, mesh = {Antibodies, Monoclonal ; Classification ; Gram-Negative Chemolithotrophic Bacteria/*immunology/isolation &amp; purification/ultrastructure ; Immunoblotting ; Microscopy, Fluorescence ; Nitrites/chemistry ; Oxidation-Reduction ; Population Dynamics ; *Soil Microbiology ; }, abstract = {Chemolithotrophic nitrite oxidizers were enriched from five different soils including freshwater marsh, permafrost, garden, agricultural, and desert soils and monitored during the cultivation procedure. Immunoblot analysis was used to identify the nitrite oxidizing organisms with monoclonal antibodies, which recognize the key enzyme of nitrite oxidation in a genus-specific reaction [Bartosch et al. (1999) Appl Environ Microbiol 65:4126-4133]. The morphological characteristics of the enriched nitrite oxidizers were additionally studied using transmission electron microscopy (TEM) and fluorescence microscopy. By means of the antibodies and TEM analysis Nitrospira could be clearly identified in enrichment cultures derived from freshwater marsh and from permafrost soil. Nitrospira cells were enriched simultaneously with cells of the genus Nitrobacter when nitrite concentrations of 0.2 g of NaNO2 L(-1) were used. However, in enrichment cultures containing 2 g of NaNO2 L(-1) Nitrobacter was exclusively detected. During fluorescence microscopic observations of DAPI stained samples microcolonies were found in enrichment cultures from freshwater marsh, permafrost, garden, and agricultural soil. They had a similar morphology to Nitrospira-like microcolonies from activated sludge. In conclusion, Nitrospira seems to be not only a common aquatic but also a usual soil bacterium.}, }
@article {pmid11984625, year = {2002}, author = {Bowker, MA and Reed, SC and Belnap, J and Phillips, SL}, title = {Temporal variation in community composition, pigmentation, and F(v)/F(m) of desert cyanobacterial soil crusts.}, journal = {Microbial ecology}, volume = {43}, number = {1}, pages = {13-25}, doi = {10.1007/s00248-001-1013-9}, pmid = {11984625}, issn = {0095-3628}, mesh = {Climate ; *Cyanobacteria ; *Environmental Monitoring ; Pigmentation ; Population Dynamics ; Seasons ; *Soil Microbiology ; Temperature ; Ultraviolet Rays ; Utah ; Water ; }, abstract = {Summers on the Colorado Plateau (USA) are typified by harsh conditions such as high temperatures, brief soil hydration periods, and high UV and visible radiation. We investigated whether community composition, physiological status, and pigmentation might vary in biological soil crusts as a result of such conditions. Representative surface cores were sampled at the ENE, WSW, and top microaspects of 20 individual soil crust pedicels at a single site in Canyonlands National Park, Utah, in spring and fall of 1999. Frequency of cyanobacterial taxa, pigment concentrations, and dark adapted quantum yield [F(v)/F(m)] were measured for each core. The frequency of major cyanobacterial taxa was lower in the fall compared to spring. The less-pigmented cyanobacterium Microcoleus vaginatus showed significant mortality when not in the presence of Nostoc spp. and Scytonema myochrous (Dillw.) Agardh. (both synthesizers of UV radiation-linked pigments) but had little or no mortality when these species were abundant. We hypothesize that the sunscreen pigments produced by Nostoc and Scytonema in the surface of crusts protect other, less-pigmented taxa. When fall and spring samples were compared, overall cyanobacterial frequency was lower in fall, while sunscreen pigment concentrations, chlorophyll a concentration, and F(v)/F(m) were higher in fall. The ratio of cyanobacterial frequency/chlorophyll a concentrations was 2-3 times lower in fall than spring. Because chlorophyll a is commonly used as a surrogate measure of soil cyanobacterial biomass, these results indicate that seasonality needs to be taken into consideration. In the fall sample, most pigments associated with UV radiation protection or repair were at their highest concentrations on pedicel tops and WSW microaspects, and at their lowest concentrations on ENE microaspects. We suggest that differential pigment concentrations between microaspects are induced by varying UV radiation dosage at the soil surface on these different microaspects.}, }
@article {pmid11984624, year = {2002}, author = {Hawkes, CV and Flechtner, VR}, title = {Biological soil crusts in a xeric Florida shrubland: composition, abundance, and spatial heterogeneity of crusts with different disturbance histories.}, journal = {Microbial ecology}, volume = {43}, number = {1}, pages = {1-12}, doi = {10.1007/s00248-001-1017-5}, pmid = {11984624}, issn = {0095-3628}, mesh = {Climate ; Data Collection ; *Ecosystem ; Florida ; Plants ; Population Dynamics ; *Soil Microbiology ; }, abstract = {Biological soil crusts consisting of algae, cyanobacteria, lichens, fungi, bacteria, and mosses are common in habitats where water and nutrients are limited and vascular plant cover is discontinuous. Crusts alter soil factors including water availability, nutrient content, and erosion susceptibility, and thus are likely to both directly and indirectly affect plants. To establish this link, we must first understand the crust landscape. We described the composition, abundance, and distribution of microalgae in crusts from a periodically burned, xeric Florida shrubland, with the goal of understanding the underlying variability they create for vascular plants, as well as the scale of that variability. This is the first comprehensive study of crusts in the southeastern United States, where the climate is mesic but sandy soils create xeric conditions. We found that crusts were both temporally and spatially heterogeneous in depth and species composition. For example, cyanobacteria and algae increased in abundance 10-15 years after fire and away from dominant shrubs. Chlorophyll a levels recovered rapidly from small-scale disturbance relative to intact crusts, but these disturbances added to crust patchiness. Plants less than 1 m apart can experience different crust environments that may alter plant fitness, plant interactions, and plant community composition.}, }
@article {pmid11976785, year = {2002}, author = {Müller, AK and Westergaard, K and Christensen, S and Sørensen, SJ}, title = {The diversity and function of soil microbial communities exposed to different disturbances.}, journal = {Microbial ecology}, volume = {44}, number = {1}, pages = {49-58}, pmid = {11976785}, issn = {0095-3628}, mesh = {Bacteria/*drug effects/genetics/growth &amp; development/metabolism ; Cell Respiration ; Colony Count, Microbial ; DNA Fingerprinting ; DNA, Bacterial/genetics ; *Ecosystem ; Mercury/analysis/pharmacology ; RNA, Ribosomal, 16S/genetics ; Soil/analysis ; *Soil Microbiology ; Soil Pollutants/analysis/pharmacology ; Substrate Specificity ; Time Factors ; Tylosin/analysis/pharmacology ; }, abstract = {To improve understanding of the relationship between the diversity and function of the soil ecosystem, we investigated the effect of two different disturbances on soil bacterial communities -- long-term exposure to the heavy metal mercury and transient exposure to the antibiotic tylosin. In the mercury-contaminated soil the diversity (Shannon index) was reduced as assessed from denaturing gradient gel electrophoresis (DGGE) of amplified 16S rDNA sequences from the soil community DNA and from colony morphology typing of the culturable bacterial population. However, analysis of the substrate utilization profiles did not reveal any differences in diversity. In the tylosin-treated soil, DGGE revealed a small difference in the diversity of 16S rDNA compared to the control soil, whereas analysis of the colony morphology typing or substrate utilization results did not reveal any differences in diversity. Soil function was also affected by mercury contamination. The lag time before soil respiration increased following addition of glucose or alfalfa substrate was longer in the mercury-contaminated soil than in the control soil. Moreover, it was markedly prolonged in mercury-contaminated soil subjected to heat treatment prior to substrate addition, thus indicating reduced resistance to a new disturbance in the mercury-contaminated soil as compared to the control soil. Tylosin treatment did not have any significant effect on any of the respiration parameters measured, either with or without prior heat treatment of the soil.}, }
@article {pmid11976126, year = {2002}, author = {Christensen, BB and Haagensen, JA and Heydorn, A and Molin, S}, title = {Metabolic commensalism and competition in a two-species microbial consortium.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {5}, pages = {2495-2502}, pmid = {11976126}, issn = {0099-2240}, mesh = {Acinetobacter/*physiology ; *Antibiosis ; *Biofilms/growth &amp; development ; Pseudomonas putida/*physiology ; }, abstract = {We analyzed metabolic interactions and the importance of specific structural relationships in a benzyl alcohol-degrading microbial consortium comprising two species, Pseudomonas putida strain R1 and Acinetobacter strain C6, both of which are able to utilize benzyl alcohol as their sole carbon and energy source. The organisms were grown either as surface-attached organisms (biofilms) in flow chambers or as suspended cultures in chemostats. The numbers of CFU of P. putida R1 and Acinetobacter strain C6 were determined in chemostats and from the effluents of the flow chambers. When the two species were grown together in chemostats with limiting concentrations of benzyl alcohol, Acinetobacter strain C6 outnumbered P. putida R1 (500:1), whereas under similar growth conditions in biofilms, P. putida R1 was present in higher numbers than Acinetobacter strain C6 (5:1). In order to explain this difference, investigations of microbial activities and structural relationships were carried out in the biofilms. Insertion into P. putida R1 of a fusion between the growth rate-regulated rRNA promoter rrnBP1 and a gfp gene encoding an unstable variant of the green fluorescent protein made it possible to monitor the physiological activity of P. putida R1 cells at different positions in the biofilms. Combining this with fluorescent in situ hybridization and scanning confocal laser microscopy showed that the two organisms compete or display commensal interactions depending on their relative physical positioning in the biofilm. In the initial phase of biofilm development, the growth activity of P. putida R1 was shown to be higher near microcolonies of Acinetobacter strain C6. High-pressure liquid chromatography analysis showed that in the effluent of the Acinetobacter strain C6 monoculture biofilm the metabolic intermediate benzoate accumulated, whereas in the biculture biofilms this was not the case, suggesting that in these biofilms the excess benzoate produced by Acinetobacter strain C6 leaks into the surrounding environment, from where it is metabolized by P. putida R1. After a few days, Acinetobacter strain C6 colonies were overgrown by P. putida R1 cells and new structures developed, in which microcolonies of Acinetobacter strain C6 cells were established in the upper layer of the biofilm. In this way the two organisms developed structural relationships allowing Acinetobacter strain C6 to be close to the bulk liquid with high concentrations of benzyl alcohol and allowing P. putida R1 to benefit from the benzoate leaking from Acinetobacter strain C6. We conclude that in chemostats, where the organisms cannot establish in fixed positions, the two strains will compete for the primary carbon source, benzyl alcohol, which apparently gives Acinetobacter strain C6 a growth advantage, probably because it converts benzyl alcohol to benzoate with a higher yield per time unit than P. putida R1. In biofilms, however, the organisms establish structured, surface-attached consortia, in which heterogeneous ecological niches develop, and under these conditions competition for the primary carbon source is not the only determinant of biomass and population structure.}, }
@article {pmid11975741, year = {2002}, author = {Olsson, PA and Kjellbom, P and Rosendahl, L}, title = {Rhizobium colonization induced changes in membrane-bound and soluble hydroxyproline-rich glycoprotein composition in pea.}, journal = {Physiologia plantarum}, volume = {114}, number = {4}, pages = {652-660}, doi = {10.1034/j.1399-3054.2002.1140420.x}, pmid = {11975741}, issn = {1399-3054}, abstract = {Abundance and distribution of plant cell surface proteins of the hydroxyproline-rich glycoprotein (HRGP) class were studied in the pea-Rhizobium symbiosis using immunoblot analysis. The MAC 265-epitope was especially abundant in pea root nodules containing nitrogen-fixing Rhizobium bacteria. A 180-kDa MAC 265-HRGP dominated in pea shoot plasma membranes, while almost no MAC 265-HRGP was detected in root plasma membranes. We show here that a major difference between the plant-derived peribacteroid membrane of the symbiosomes and the root plasma membrane was the presence of a 100-kDa MAC 265-HRGP in the former. Arabinogalactan proteins (AGPs), as recognized by the monoclonal antibodies MAC 207 and JIM 8, were not detected in the peribacteroid membrane, while two isoforms (100 and 220 kDa) were detected in shoot and root plasma membranes. Specific MAC 265-HRGP isoforms were found in the peribacteroid space fraction of the symbiosomes and thus as soluble proteins in the interface between the symbionts. The abundance of the MAC 265-epitope was much reduced in non-nitrogen-fixing nodules when this phenotype resulted from a dicarboxylate transport mutation in Rhizobium. There was no reduction in the abundance of the MAC 265-epitope in non-fixing phenotypes resulting from a mutation in the plant. The results suggest that bacterial signals related to the bacterial ability to fix nitrogen, might be responsible for the regulation of HRGP expression in root nodules.}, }
@article {pmid11969087, year = {2002}, author = {Kovalevskaia, NP}, title = {[Mobile gene cassettes and DNA integration elements ].}, journal = {Molekuliarnaia biologiia}, volume = {36}, number = {2}, pages = {261-267}, pmid = {11969087}, issn = {0026-8984}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/*genetics ; *Gene Expression Regulation, Bacterial ; Gram-Negative Bacteria/drug effects/*genetics ; Operon ; Recombination, Genetic ; }, abstract = {Integrons are unique natural systems for capturing and spreading the antibiotic resistance genes among Gram-negative bacteria. Gene transfer into small genomes and into plasmids is via site-specific recombination. Integrons act as receptors of antibiotic resistance cassettes. There are known more than 50 cassettes conferring resistance to beta-lactams, aminoglycosides, trimethoprim, chloramphenicol, streptomycin, and other antibiotics. The structure of integrons and of gene cassettes are described and the mechanisms of capture, mobilization, and expression of cassettes considered.}, }
@article {pmid11966821, year = {2002}, author = {Smets, BF and Verstraete, WH and Siciliano, SD}, title = {Microbial imprints as forensic tools in food production.}, journal = {Environmental microbiology}, volume = {4}, number = {1}, pages = {16-17}, doi = {10.1046/j.1462-2920.2002.t01-5-00257.x}, pmid = {11966821}, issn = {1462-2912}, mesh = {*Environmental Microbiology ; Food Microbiology/*standards ; }, }
@article {pmid11963851, year = {2001}, author = {Weekers, F and Rodriguez, C and Jacques, P and Mergeay, M and Thonart, P}, title = {Dissemination of catabolic plasmids among desiccation-tolerant bacteria in soil microcosms.}, journal = {Applied biochemistry and biotechnology}, volume = {91-93}, number = {}, pages = {219-232}, doi = {10.1385/abab:91-93:1-9:219}, pmid = {11963851}, issn = {0273-2289}, mesh = {Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Biotechnology ; Conjugation, Genetic ; Desiccation ; Ecosystem ; Models, Genetic ; Plasmids/*genetics ; Pseudomonas putida/genetics/physiology ; Rhodococcus/genetics/physiology ; *Soil Microbiology ; Soil Pollutants/isolation &amp; purification/metabolism ; }, abstract = {The dissemination of catabolic plasmids was compared to bioaugmentation by strain inoculation in microcosm experiments. When Rhodococcus erythropolis strain T902, bearing a plasmid with trichloroethene and isopropylbenzene degradation pathways, was used as the inoculum, no transconjugant was isolated but the strain remained in the soil. This plasmid had a narrow host range. Pseudomonas putida strain C8S3 was used as the inoculum in a second approach. It bore a broad host range conjugative plasmid harboring a natural transposon, RP4::Tn4371, responsible for biphenyl and 4-chlorobiphenyl degradation pathways. The inoculating population slowly decreased from its original level (10(6) colony-forming units [CFU]/g of dry soil) to approx 3 x 10(2) CFU/g of dry soil after 3 wk. Transconjugant populations degrading biphenyl appeared in constant humidity soil (up to 2 x 10(3) CFU/g) and desiccating soil (up to 10(4) CFU/g). The feasibility of plasmid dissemination as a bioaugmentation technique was demonstrated in desiccating soils. The ecologic significance of desiccation in bioaugmentation was demonstrated: it upset the microbial ecology and the development of transconjugants.}, }
@article {pmid11953812, year = {2002}, author = {Lack, JG and Chaudhuri, SK and Chakraborty, R and Achenbach, LA and Coates, JD}, title = {Anaerobic biooxidation of Fe(II) by Dechlorosoma suillum.}, journal = {Microbial ecology}, volume = {43}, number = {4}, pages = {424-431}, doi = {10.1007/s00248-001-1061-1}, pmid = {11953812}, issn = {0095-3628}, mesh = {Aerobiosis ; Anaerobiosis ; Culture Media ; Geologic Sediments/chemistry ; Iron/*metabolism ; Nitrates/metabolism ; Oxidation-Reduction ; Oxygen/metabolism ; Perchlorates/metabolism ; Proteobacteria/*metabolism ; Sodium Compounds/metabolism ; Time Factors ; Water Microbiology ; }, abstract = {Anaerobic microbial oxidation of Fe(II) was only recently discovered and very little is known about this metabolism. We recently demonstrated that several dissimilatory perchlorate-reducing bacteria could utilize Fe(II) as an electron donor under anaerobic conditions. Here we report on a more in-depth analysis of Fe(II) oxidation by one of these organisms, Dechlorosoma suillum. Similarly to most known nitrate-dependent Fe(II) oxidizers, D. suillum did not grow heterotrophically or lithoautotrophically by anaerobic Fe(II) oxidation. In the absence of a suitable organic carbon source, cells rapidly lysed even though nitrate-dependent Fe(II) oxidation was still occurring. The coupling of Fe(II) oxidation to a particular electron acceptor was dependent on the growth conditions of cells of D. suillum. As such, anaerobically grown cultures of D. suillum did not mediate Fe(II) oxidation with oxygen as the electron acceptor, while conversely, aerobically grown cultures did not mediate Fe(II) oxidation with nitrate as the electron acceptor. Anaerobic washed cell suspensions of D. suillum rapidly produced an orange/brown precipitate which X-ray diffraction analysis identified as amorphous ferric oxyhydroxide or ferrihydrite. This is similar to all other identified nitrate-dependent Fe(II) oxidizers but is in contrast to what is observed for growth cultures of D. suillum, which produced a mixed-valence Fe(II)-Fe(III) precipitate known as green rust. D. suillum rapidly oxidized the Fe(II) content of natural sediments. Although the form of ferrous iron in these sediments is unknown, it is probably a component of an insoluble mineral, as previous studies indicated that soluble Fe(II) is a relatively minor form of the total Fe(II) content of anoxic environments. The results of this study further enhance our knowledge of a poorly understood form of microbial metabolism and indicate that anaerobic Fe(II) oxidation by D. suillum is significantly different from previously described forms of nitrate-dependent microbial Fe(II) oxidation.}, }
@article {pmid11953810, year = {2002}, author = {Lee, WJ and Patterson, DJ}, title = {Abundance and biomass of heterotrophic flagellates, and factors controlling their abundance and distribution in sediments of Botany Bay.}, journal = {Microbial ecology}, volume = {43}, number = {4}, pages = {467-481}, doi = {10.1007/s00248-002-2000-5}, pmid = {11953810}, issn = {0095-3628}, mesh = {Animals ; Australia ; Bacteria/growth &amp; development/*isolation &amp; purification ; *Biomass ; Carbon/analysis ; Chlorophyll/analysis ; Chlorophyll A ; Cilia/physiology ; Diatoms/growth &amp; development/isolation &amp; purification ; Ecosystem ; Eukaryota/growth &amp; development/*isolation &amp; purification ; Flagella/*physiology ; Geologic Sediments/chemistry/*microbiology/*parasitology ; Hydrogen-Ion Concentration ; Phytoplankton/growth &amp; development/isolation &amp; purification ; Population Density ; Population Dynamics ; Seasons ; Seawater/chemistry ; Sodium Chloride/analysis ; Temperature ; Water Microbiology ; }, abstract = {The abundance and biomass of heterotrophic flagellates were estimated monthly in sediments of Botany Bay during March 1999-February 2000. The annual abundance and biomass were in the ranges of 0.46-4.70 x 10(5) cells/cm(3) and of 0.30-8.61 micro g C/cm(3), respectively. The majority of heterotrophic flagellates (93-100%) were less than 10 mm in length and few flagellates were larger than 10 mm. Of the total microbial carbon biomass, heterotrophic flagellates made up about 5% (but at times up to 35%). The contribution of heterotrophic flagellates varied from month to month, and among the sites. The abundance of heterotrophic flagellates was negatively correlated with sediment grain size and positively correlated with the abundance of bacteria, algae (autotrophic flagellates and diatoms), and their probable grazers. A best subsets regression analysis showed that bacterial and algal abundance are the most important factors controlling the abundance of heterotrophic flagellates. When the previously reported grazing rates on bacteria were applied, heterotrophic flagellates would consume a maximum of 64% of bacterial standing stock daily in Botany Bay, suggesting that heterotrophic flagellates are important as bacterivores. However, the importance of heterotrophic flagellate grazing probably varies significantly among the sites and from month to month.}, }
@article {pmid11953809, year = {2002}, author = {Vézie, C and Rapala, J and Vaitomaa, J and Seitsonen, J and Sivonen, K}, title = {Effect of nitrogen and phosphorus on growth of toxic and nontoxic Microcystis strains and on intracellular microcystin concentrations.}, journal = {Microbial ecology}, volume = {43}, number = {4}, pages = {443-454}, doi = {10.1007/s00248-001-0041-9}, pmid = {11953809}, issn = {0095-3628}, mesh = {Adaptation, Physiological/drug effects ; Chromatography, High Pressure Liquid ; Culture Media ; Microcystins ; Microcystis/classification/*drug effects/*growth &amp; development/metabolism ; Nitrogen/*pharmacology ; Peptides, Cyclic/biosynthesis/*metabolism ; Phosphorus/*pharmacology ; Time Factors ; Water Microbiology ; }, abstract = {The growth and intracellular microcystin concentration of two hepatotoxic and two nontoxic axenic Microcystis strains were measured in batch cultures with variable nitrogen (0.84-84 mg L(-1)) and phosphorus (0.05-5.5 mg L(-1)) concentrations. Growth was estimated by measuring dry weight, optical density, chlorophyll a, and cellular protein concentration. Microcystin concentrations in cells and in culture medium were measured by HPLC analysis. Both nontoxic strains needed less nutrients for their growth at low nutrient concentrations. With high nutrient concentrations the toxic strains grew better than the nontoxic strains. Growth and intracellular microcystin concentration did not correlate in the hepatotoxic strains. Multivariate regression analysis together with mathematical modeling revealed a significant interactive effect of nitrogen and phosphorus, which partly explains the controversial results obtained in previous studies. In this study we have shown that variation of nitrogen and phosphorus concentrations influence the growth and the microcystin production of Microcystis strains and that the strains differ in their response to nutrients. High levels of nitrogen and phosphorus in freshwaters may favor the growth of toxic Microcystis strains over nontoxic ones.}, }
@article {pmid11953808, year = {2002}, author = {Sigler, WV and Zeyer, J}, title = {Microbial diversity and activity along the forefields of two receding glaciers.}, journal = {Microbial ecology}, volume = {43}, number = {4}, pages = {397-407}, doi = {10.1007/s00248-001-0045-5}, pmid = {11953808}, issn = {0095-3628}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Biomass ; Colony Count, Microbial ; DNA Fingerprinting ; DNA, Bacterial/genetics/isolation &amp; purification ; *Ecosystem ; Geological Phenomena ; Geology ; *Ice ; Indoles ; Population Density ; Radioimmunoassay ; Soil/analysis ; *Soil Microbiology ; }, abstract = {Forefields of two receding glaciers were sampled along either a 150 or 200 m long transect at identical spatial intervals for assessment of soil microbial activity and community diversity trends. The forefields belonged to the Dammaglacier (forefield area is 157 ha, 2000 m above sea level) and Rotfirnglacier (100 ha, 2200 m) and at the time of sampling were receding at an estimated rate of 8 and 10 m yr(-1) over the past 5 years, respectively. Direct counting of bacteria (DAPI staining), assessment of dehydrogenase activity (DH), and fluorescein diacetate hydrolysis activity (FDA) were performed to estimate bacteria number and soil microbial activity. Along the Dammaglacier forefield (from youngest to oldest soil), bacteria number (8.21 x 10(7) to 1.49 x 10(9) cells g(-1) soil), DH activity (0 to 61 mg TTC reduced g(-1) soil h(-1)), and FDA activity (0 to 100 mg fluorescein produced g-1 soil h-1) increased, suggesting the development of microbial populations increasing in number and activity. The Rotfirn forefield exhibited similar trends per gram of soil in bacteria number (1.13 x 10(8) to 5.93 x 10(9) cells), DH activity (0 to 36 mg TTC reduced), and FDA activity (2 to 70 mg fluorescein produced), but with more variability among samples than the Damma forefield samples. Molecular assessment of bacterial diversity included denaturing gradient gel electrophoresis (DGGE) and ribosomal intergenic spacer analysis (RISA) of soil DNA. DGGE and RISA revealed that the composition and succession of bacterial populations were different in both forefields. Comparison of Shannon diversity index values indicated that all populations sampled from the Damma forefield were significantly different (p < 0.05). Conversely, similar populations existed in the Rotfirn forefield succession. Overall, the results indicate that diverse bacterial assemblages increasing in number and activity characterize these glacier forefield soils with both forefield successions exhibiting differing modes of bacterial community establishment.}, }
@article {pmid11936677, year = {2002}, author = {Nielsen, M and Revsbech, NP and Larsen, LH and Lynggaard-Jensen, A}, title = {On-line determination of nitrite in wastewater treatment by use of a biosensor.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {45}, number = {4-5}, pages = {69-76}, pmid = {11936677}, issn = {0273-1223}, mesh = {Biosensing Techniques/*instrumentation/*methods ; Nitrates/*analysis ; Pilot Projects ; Sterilization ; Water/chemistry ; Water Pollutants, Chemical/analysis ; Water Purification/instrumentation/*methods ; }, abstract = {A newly developed biosensor for nitrite having a 90% response time of about 1 min was used to monitor nitrite concentration in activated sludge exposed to oxic/anoxic cycles. The NO2- biosensor contains bacteria that reduce NO2-, but not NO3-, to N2O that is subsequently monitored by a built-in electrochemical sensor. Nitrite plus nitrate (NOx-) was simultaneously monitored by a NOx- biosensor. The maximum operational lifetime of the NO2- biosensor was 6 weeks, but much longer lifetimes can be expected as malfunctioning by the 3 sensors used for longer periods was due to either mechanical damage or ineffective internal sterilization during the construction. Insufficiently sterilized sensors became sensitive also to NO3- after some time due to development of NO3(-)-reducing bacterial populations within the sensor. The fraction of NO2- as compared to NO3- in the activated sludge was very dependent on prehistory, actual loading, and aeration. During balanced operation with NH4+ being exhausted during the later parts of the aerobic cycle, NO2- increased in concentration up to about 50 microM during the early part of the aeration cycle until NH4+ became limiting. At that time the NO2- concentration decreased to low levels. Under some operating conditions a peak of NO2- also appeared in the beginning of the anoxic period. NO2- and NO3- were depleted simultaneously during the anoxic period.}, }
@article {pmid11931586, year = {2002}, author = {Vermeirssen, V and Deplancke, B and Tappenden, KA and Van Camp, J and Gaskins, HR and Verstraete, W}, title = {Intestinal transport of the lactokinin Ala-Leu-Pro-Met-His-Ile-Arg through a Caco-2 Bbe monolayer.}, journal = {Journal of peptide science : an official publication of the European Peptide Society}, volume = {8}, number = {3}, pages = {95-100}, doi = {10.1002/psc.371}, pmid = {11931586}, issn = {1075-2617}, mesh = {Amino Acids/*metabolism ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Biological Transport ; Caco-2 Cells ; Cell Line ; Chromatography, High Pressure Liquid ; Electrophysiology ; Humans ; Kinetics ; Mass Spectrometry ; Milk Proteins/*metabolism ; Peptides/*chemistry ; Peptidyl-Dipeptidase A/*metabolism ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Whey Proteins ; }, abstract = {ACE inhibitory peptides are biologically active peptides that play a role in blood pressure regulation. When derived from food proteins during food processing or gastrointestinal digestion, these peptides could function as efficient agents in treating and preventing hypertension. However, in order to exert an antihypertensive effect by inhibition of the ACE enzyme, they have to reach the bloodstream intact. The aim of this research was to assess if the known ACE inhibitory peptide Ala-Leu-Pro-Met-His-Ile-Arg, derived from a tryptic digest of beta-lactoglobulin, could be absorbed through a Caco-2 Bbe cell monolayer in an Ussing chamber and reach the serosal side undegraded. Samples of the mucosal compartment showed high ACE inhibitory activity. No or only little ACE inhibitory activity was detected in the serosal compartment. However, when the serosal sample was concentrated three-fold, a substantial ACE inhibitory activity was registered. Concomitantly, HPLC and MS clearly showed the presence of Ala-Leu-Pro-Met-His-Ile-Arg in the mucosal compartment, whereas in the serosal compartment only MS was able to detect the heptapeptide. In conclusion. under the observed experimental conditions, the ACE inhibitory peptide Ala-Leu-Pro-Met-His-Ile-Arg was transported intact through the Caco-2 Bbe monolayer, but in concentrations too low to exert an ACE inhibitory activity.}, }
@article {pmid11930989, year = {2001}, author = {Płaza, G and Ulfig, K and Hazen, TC and Brigmon, RL}, title = {Use of molecular techniques in bioremediation.}, journal = {Acta microbiologica Polonica}, volume = {50}, number = {3-4}, pages = {205-218}, pmid = {11930989}, issn = {0137-1320}, mesh = {Bacteria/genetics/*metabolism ; *Biodegradation, Environmental ; Biotechnology/methods ; DNA, Bacterial/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Soil Pollutants/*metabolism ; Water Pollutants, Chemical/*metabolism ; }, abstract = {In a practical sense, biotechnology is concerned with the production of commercial products generated by biological processes. More formally, biotechnology may be defined as "the application of scientific and engineering principles to the processing of material by biological agents to provide goods and services" (Cantor, 2000). From a historical perspective, biotechnology dates back to the time when yeast was first used for beer or wine fermentation, and bacteria were used to make yogurt. In 1972, the birth of recombinant DNA technology moved biotechnology to new heights and led to the establishment of a new industry. Progress in biotechnology has been truly remarkable. Within four years of the discovery of recombinant DNA technology, genetically modified organisms (GMOs) were making human insulin, interferon, and human growth hormone. Now, recombinant DNA technology and its products--GMOs are widely used in environmental biotechnology (Glick and Pasternak, 1988; Cowan, 2000). Bioremediation is one of the most rapidly growing areas of environmental biotechnology. Use of bioremediation for environmental clean up is popular due to low costs and its public acceptability. Indeed, bioremediation stands to benefit greatly and advance even more rapidly with the adoption of molecular techniques developed originally for other areas of biotechnology. The 1990s was the decade of molecular microbial ecology (time of using molecular techniques in environmental biotechnology). Adoption of these molecular techniques made scientists realize that microbial populations in the natural environments are much more diverse than previously thought using traditional culture methods. Using molecular ecological methods, such as direct DNA isolation from environmental samples, denaturing gradient gel electrophoresis (DGGE), PCR methods, nucleic acid hybridization etc., we can now study microbial consortia relevant to pollutant degradation in the environment. These techniques promise to provide a better understanding and better control of environmental biotechnology processes, thus enabling more cost effective and efficient bioremediation of our toxic waste and contaminated environments.}, }
@article {pmid11924822, year = {2001}, author = {Fredricks, DN}, title = {Microbial ecology of human skin in health and disease.}, journal = {The journal of investigative dermatology. Symposium proceedings}, volume = {6}, number = {3}, pages = {167-169}, doi = {10.1046/j.0022-202x.2001.00039.x}, pmid = {11924822}, issn = {1087-0024}, mesh = {Acne Vulgaris/*microbiology ; *Ecosystem ; Humans ; Skin/*microbiology ; }, abstract = {Cultivation of human skin reveals numerous bacteria and at least one fungus to be normal inhabitants of this ecosystem; however, most of our knowledge about the microbiology of human skin was acquired decades ago. Modern techniques employing nucleic acid-based microbial identification methods demonstrate the limitations of cultivation for appreciating microbial diversity in many ecosystems. The application of modern molecular methods to the study of skin may offer new perspectives on the resident microfora, and new insights into the causes of antibiotic responsive dermatologic conditions, such as acne and rosacea.}, }
@article {pmid11918402, year = {2002}, author = {Seka, MA and Van DeWiele, T and Verstraete, W}, title = {Full-scale evaluation of a multi-component additive for efficient control of activated sludge filamentous bulking.}, journal = {Environmental technology}, volume = {23}, number = {1}, pages = {67-72}, doi = {10.1080/09593332508618434}, pmid = {11918402}, issn = {0959-3330}, mesh = {Animals ; *Daphnia ; Flocculation ; Polymers ; Quaternary Ammonium Compounds ; Sewage/chemistry/*microbiology ; Talc/chemistry ; Toxicity Tests ; }, abstract = {A multi-component additive formulated for a more efficient control of activated sludge filamentous bulking was evaluated at a full-scale treatment plant experiencing severe filamentous bulking. It was found that, besides offering an immediate improvement of sludge settling, the multi-component additive was able to eliminate the filamentous bacteria causing the bulking. Hence, contrary to ordinary additives, this novel additive yielded immediate as well as long-term improvements in sludge sedimentation upon a few additions. Preliminary lab-scale toxicity tests showed that the treatment of the sludge by the additive should not impart any toxicity to the resulting effluent.}, }
@article {pmid11916709, year = {2002}, author = {Priemé, A and Braker, G and Tiedje, JM}, title = {Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {4}, pages = {1893-1900}, pmid = {11916709}, issn = {0099-2240}, mesh = {Bacteria/*classification/*enzymology/genetics ; Bacterial Proteins/genetics/metabolism ; Cloning, Molecular ; Genetic Markers ; *Genetic Variation ; Nitrite Reductases/*genetics/metabolism ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; *Soil Microbiology ; *Trees ; }, abstract = {The genetic heterogeneity of nitrite reductase gene (nirK and nirS) fragments from denitrifying prokaryotes in forested upland and marsh soil was investigated using molecular methods. nirK gene fragments could be amplified from both soils, whereas nirS gene fragments could be amplified only from the marsh soil. PCR products were cloned and screened by restriction fragment length polymorphism (RFLP), and representative fragments were sequenced. The diversity of nirK clones was lower than the diversity of nirS clones. Among the 54 distinct nirK RFLP patterns identified in the two soils, only one pattern was found in both soils and in each soil two dominant groups comprised >35% of all clones. No dominance and few redundant patterns were seen among the nirS clones. Phylogenetic analysis of deduced amino acids grouped the nirK sequences into five major clusters, with one cluster encompassing most marsh clones and all upland clones. Only a few of the nirK clone sequences branched with those of known denitrifying bacteria. The nirS clones formed two major clusters with several subclusters, but all nirS clones showed less than 80% identity to nirS sequences from known denitrifying bacteria. Overall, the data indicated that the denitrifying communities in the two soils have many members and that the soils have a high richness of different nir genes, especially of the nirS gene, most of which have not yet been found in cultivated denitrifiers.}, }
@article {pmid11913248, year = {2001}, author = {Enwonwu, CO and Sanders, C}, title = {Nutrition: impact on oral and systemic health.}, journal = {Compendium of continuing education in dentistry (Jamesburg, N.J. : 1995)}, volume = {22}, number = {3 Spec No}, pages = {12-18}, pmid = {11913248}, issn = {1548-8578}, mesh = {Acute-Phase Reaction/etiology ; Bacteria, Anaerobic/growth &amp; development ; Cytokines/physiology ; DNA Damage ; DNA Methylation ; Feeding Behavior ; Folic Acid Deficiency/genetics ; Growth/physiology ; *Health Status ; Humans ; Immune System Diseases/etiology ; Immune Tolerance ; Mouth Neoplasms/etiology/genetics ; Noma/etiology ; Nutrition Disorders/complications ; Nutritional Physiological Phenomena/*physiology ; Nutritional Status ; *Oral Health ; Periodontitis/etiology ; Protein-Energy Malnutrition/complications ; Salivary Gland Diseases/etiology ; }, abstract = {Good dietary practices and optimal nutritional status promote growth and tissue development, as well as feature prominently in the prevention of diseases. Malnutrition (particularly protein-energy malnutrition, which invariably involves concurrent deficiencies of the antioxidant micronutrients) promotes salivary gland hypofunction, impaired immunity, and an early shift in the oral microbial ecology toward a preponderance of anaerobic organisms. The immune suppression, which includes impaired cytokine function as well as diminished acute-phase response to infections, impacts negatively on the natural history of inflammatory periodontal diseases. The pathogenesis of oral cancer is influenced by deficiencies of antioxidant nutrients, and there is evidence for diminished DNA methylation, disruption of DNA integrity, and increased DNA damage in folate deficiency.}, }
@article {pmid11879921, year = {2002}, author = {Vermeirssen, V and Van Camp, J and Verstraete, W}, title = {Optimisation and validation of an angiotensin-converting enzyme inhibition assay for the screening of bioactive peptides.}, journal = {Journal of biochemical and biophysical methods}, volume = {51}, number = {1}, pages = {75-87}, doi = {10.1016/s0165-022x(02)00006-4}, pmid = {11879921}, issn = {0165-022X}, mesh = {Acetone/metabolism ; Angiotensin-Converting Enzyme Inhibitors/*pharmacology ; Animals ; Biochemistry/*methods ; Calibration ; Cattle ; Inhibitory Concentration 50 ; Lactoglobulins/metabolism ; Lung/metabolism ; Peptides/*chemistry ; Peptidyl-Dipeptidase A/*metabolism ; Rabbits ; Sensitivity and Specificity ; }, abstract = {Angiotensin-converting enzyme (ACE) plays a major role in the regulation of blood pressure. A diagnostic assay to measure angiotensin-converting enzyme (ACE) activity was transformed into an enzyme inhibition assay and optimised, which led to a more sensitive and less expensive assay. By this spectrophotometric method, ACE inhibition is measured using the substrate furanacryloyl-Phe-Gly-Gly and as ACE source rabbit lung acetone extract. The optimised as well as the original ACE inhibition assay were used to verify the ACE inhibitory activity of captopril. The ACE inhibition assay was further validated by enalapril, its active derivative enalaprilat and the ACE-inhibitory peptide Ala-Leu-Pro-Met-His-Ile-Arg, corresponding to a tryptic fragment of bovine beta-lactoglobulin. Sigmoid curves could be fit adequately to the data points representing ACE inhibition in function of inhibitor concentration. IC(50) values for these compounds corresponded well with literature data. Furthermore, pea and whey protein hydrolysates obtained by digestion with trypsin showed ACE inhibitory activity in the ACE inhibition assay. Hence, this optimised assay is suitable to screen for ACE inhibitory peptides derived from food proteins with a possible antihypertensive effect in vivo.}, }
@article {pmid11873910, year = {2002}, author = {Sepúlveda-Torre, L and Huang, A and Kim, H and Criddle, CS}, title = {Analysis of regulatory elements and genes required for carbon tetrachloride degradation in Pseudomonas stutzeri strain KC.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {4}, number = {2}, pages = {151-161}, pmid = {11873910}, issn = {1464-1801}, support = {ES04911/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacterial Proteins/*genetics/metabolism ; Base Sequence ; Biodegradation, Environmental ; Carbon Tetrachloride/*metabolism ; DNA Transposable Elements ; *Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Molecular Sequence Data ; Mutagenesis, Insertional ; Promoter Regions, Genetic ; Pseudomonas/genetics/growth &amp; development/*metabolism ; Pyridines/metabolism ; *Regulatory Sequences, Nucleic Acid ; Sequence Analysis, DNA ; }, abstract = {Previously, we described the generation and initial characterization of four Tn5 mutants of Pseudomonas stutzeri strain KC with impaired ability to degrade carbon tetrachloride (Sepúlveda-Torres et al., 1999). In this study, we show cloning and sequencing of an 8.3 kbp region in which all four transposons were located. This fragment encodes eight potential genes and is located in the central part of the 25 kbp fragment recently identified by Lewis et al. (2000) and shown by them to be sufficient to confer carbon tetrachloride transformation capability upon other pseudomonads. The four transposon insertion mutants mapped in ORF's F and I designated by Lewis et al. (2000). This is consistent with the results by Lewis et al. (2000) that orfFis required for carbon tetrachloride degradation. We further established that orfl is required for CCl4 degradation since the three mutants in this ORF were unable to degrade carbon tetrachloride. We present our analysis of the gene and protein sequences from the 8.3 kbp region and propose a tentative model for the role of different genes in the synthesis and activity of pyridine-2,6-bis(thiocarboxylate) (PDTC), the secreted factor responsible for carbon tetrachloride dechlorination. We also found a putative promoter that overlaps with a Fur-box-like sequence in the region upstream of mutated genes. To test this putative promoter region and Fur-box, we generated and ligated DNA fragments containing wild-type and mutant Fur-boxes to a lacZ reporter. The wild-type fragment showed promoter activity that is regulated by the concentration of iron in the medium. Finally, we screened a selection of Pseudomonas strains, including P. putida DSMZ 3601--a strain known to produce PDTC--for the presence of the genes characterized in this study. None of the strains tested positive, suggesting that Pseudomonas stutzeri strain KC may possess a distinct biosynthetic pathway for PDTC production.}, }
@article {pmid11872501, year = {2002}, author = {Laanbroek, HJ and Bär-Gilissen, MJ and Hoogveld, HL}, title = {Nitrite as a stimulus for ammonia-starved Nitrosomonas europaea.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {3}, pages = {1454-1457}, pmid = {11872501}, issn = {0099-2240}, mesh = {Ammonia/*metabolism ; Culture Media/chemistry ; Nitrites/*metabolism ; Nitrosomonas/*growth &amp; development/*physiology ; Oxidation-Reduction ; }, abstract = {Ammonia-starved cells of Nitrosomonas europaea are able to preserve a high level of ammonia-oxidizing activity in the absence of ammonium. However, when the nitrite-oxidizing cells that form part of the natural nitrifying community do not keep pace with the ammonia-oxidizing cells, nitrite accumulates and may subsequently inhibit ammonia oxidation. The maintenance of a high ammonia-oxidizing capacity during starvation is then nullified. In this study we demonstrated that cells of N. europaea starved for ammonia were not sensitive to nitrite, either when they were starved in the presence of nitrite or when nitrite was supplied simultaneously with fresh ammonium. In the latter case, the initial ammonia-oxidizing activity of starved cells was stimulated at least fivefold.}, }
@article {pmid11872496, year = {2002}, author = {Cho, JC and Tiedje, JM}, title = {Quantitative detection of microbial genes by using DNA microarrays.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {3}, pages = {1425-1430}, pmid = {11872496}, issn = {0099-2240}, mesh = {Dioxygenases ; *Gene Expression Profiling ; Gram-Negative Bacteria/enzymology/*genetics/immunology ; Multienzyme Complexes/genetics ; Nitrate Reductase ; Nitrate Reductases/genetics ; O Antigens/genetics ; *Oligonucleotide Array Sequence Analysis ; Oxygenases/genetics ; }, abstract = {To quantify target genes in biological samples using DNA microarrays, we employed reference DNA to normalize variations in spot size and hybridization. This method was tested using nitrate reductase (nirS), naphthalene dioxygenase (nahA), and Escherichia coli O157 O-antigen biosynthesis genes as model genes and lambda DNA as the reference DNA. We observed a good linearity between the log signal ratio and log DNA concentration ratio at DNA concentrations above the method's detection limit, which was approximately 10 pg. This approach for designing quantitative microarrays and the inferred equation from this study provide a simple and convenient way to estimate the target gene concentration from the hybridization signal ratio.}, }
@article {pmid11872469, year = {2002}, author = {Meyer, RL and Larsen, LH and Revsbech, NP}, title = {Microscale biosensor for measurement of volatile fatty acids in anoxic environments.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {3}, pages = {1204-1210}, pmid = {11872469}, issn = {0099-2240}, mesh = {Anaerobiosis ; *Biosensing Techniques ; Electrochemistry/instrumentation ; Fatty Acids, Volatile/*metabolism ; Hydrogen-Ion Concentration ; Nitrates/metabolism ; Nitrous Oxide/*metabolism ; Sodium Chloride ; Stenotrophomonas/classification/genetics/*growth &amp; development ; Substrate Specificity ; Temperature ; }, abstract = {A microscale biosensor for acetate, propionate, isobutyrate, and lactate is described. The sensor is based on the bacterial respiration of low-molecular-weight, negatively charged species with a concomitant reduction of NO(-)(3) to N(2)O. A culture of denitrifying bacteria deficient in N(2)O reductase was immobilized in front of the tip of an electrochemical N(2)O microsensor. The bacteria were separated from the outside environment by an ion-permeable membrane and supplied with nutrients (except for electron donors) from a medium reservoir behind the N(2)O sensor. The signal of the sensor, which corresponded to the rate of N(2)O production, was proportional to the supply of the electron donor to the bacterial mass. The selectivity for volatile fatty acids compared to other organic compounds was increased by selectively enhancing the transport of negatively charged compounds into the sensor by electrophoretic migration (electrophoretic sensitivity control). The sensor was susceptible to interference from O(2), N(2)O, NO(2)(-), H(2)S, and NO(-)(3). Interference from NO(-)(3) was low and could be quantified and accounted for. The detection limit was equivalent to about 1 microM acetate, and the 90% response time was 30 to 90 s. The response of the sensor was not affected by changes in pH between 5.5 and 9 and was also unaffected by changes in salinity in the range of 2 to 32 per thousand. The functioning of the sensor over a temperature span of 7 to 30 degrees C was investigated. The concentration range for a linear response was increased five times by increasing the temperature from 7 to 19.5 degrees C. The life span of the biosensor varied between 1 and 3 weeks after manufacturing.}, }
@article {pmid11872453, year = {2002}, author = {Weinbauer, MG and Fritz, I and Wenderoth, DF and Höfle, MG}, title = {Simultaneous extraction from bacterioplankton of total RNA and DNA suitable for quantitative structure and function analyses.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {3}, pages = {1082-1087}, pmid = {11872453}, issn = {0099-2240}, mesh = {Animals ; Bacteria/*genetics ; DNA Fingerprinting ; DNA, Bacterial/analysis/*isolation &amp; purification ; DNA, Ribosomal/analysis ; Ecosystem ; Fresh Water/microbiology ; Genes, rRNA ; Plankton ; Polymerase Chain Reaction ; Polymorphism, Single-Stranded Conformational ; RNA, Bacterial/analysis/*isolation &amp; purification ; RNA, Messenger/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {The aim of this study was to develop a protocol for the simultaneous extraction from bacterioplankton of RNA and DNA suitable for quantitative molecular analysis. By using a combined mechanical and chemical extraction method, the highest RNA and DNA yield was obtained with sodium lauryl sarcosinate-phenol or DivoLab-phenol as the extraction mix. The efficiency of extraction of nucleic acids was comparatively high and varied only moderately in gram-negative bacterial isolates and bacterioplankton (RNA, 52 to 66%; DNA, 43 to 61%); significant amounts of nucleic acids were also obtained for a gram-positive bacterial isolate (RNA, 20 to 30%; DNA, 20 to 25%). Reverse transcription-PCR and PCR amplification products of fragments of 16S rRNA and its genes were obtained from all isolates and communities, indicating that the extracted nucleic acids were intact and pure enough for community structure analyses. By using single-strand conformation polymorphism of fragments of 16S rRNA and its gene, community fingerprints were obtained from pond bacterioplankton. mRNA transcripts encoding fragments of the enzyme nitrite reductase gene (nir gene) could be detected in a pond water sample, indicating that the extraction method is also suitable for studying gene expression. The extraction method presented yields nucleic acids that can be used to perform structural and functional studies of bacterioplankton communities from a single sample.}, }
@article {pmid11869790, year = {2002}, author = {LaMontagne, MG and Michel, FC and Holden, PA and Reddy, CA}, title = {Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis.}, journal = {Journal of microbiological methods}, volume = {49}, number = {3}, pages = {255-264}, doi = {10.1016/s0167-7012(01)00377-3}, pmid = {11869790}, issn = {0167-7012}, mesh = {Bacteria/genetics/*isolation &amp; purification ; Biodegradation, Environmental ; Chromatography, Gel ; DNA, Bacterial/genetics/*isolation &amp; purification ; Electrophoresis, Agar Gel ; *Environmental Microbiology ; Evaluation Studies as Topic ; Humic Substances/analysis ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Principal Component Analysis ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/analysis ; *Refuse Disposal ; }, abstract = {Analysis of microbial community structure in complex environmental samples using nucleic acid techniques requires efficient unbiased DNA extraction procedures; however, humic acids and other contaminants complicate the isolation of PCR-amplifiable DNA from compost and other organic-rich samples. In this study, combinations of DNA extraction and purification methods were compared based on DNA yield, humic acid contamination, PCR amplifiability, and microbial community structure assessed by terminal restriction fragment length polymorphisms (TRFLP) of amplified 16S rRNA genes. DNA yield and humic acid contamination, determined by A230, varied significantly between extraction methods. Humic acid contamination of DNA obtained from compost decreased with increasing salt concentration in the lysis buffer. DNA purified by gel permeation chromatography (Sepharose 4B columns) gave satisfactory PCR amplification with universal eubacterial 16S rRNA gene primers only when A260/A280 ratios exceeded 1.5. DNA purified with affinity chromatography (hydroxyapatite columns), and showing A260/A280 ratios as high as 1.8, did not show consistently satisfactory PCR amplification using the same 16S rRNA primers. Almost all DNA samples purified by agarose gel electrophoresis showed satisfactory PCR amplification. Principal components analysis (PCA) of TRFLP patterns differentiated compost types based on the presence/absence of peaks and on the height of the peaks, but differences in TRFLP patterns were not appreciable between extraction methods that yielded relatively pure DNA. High levels of humic acid contamination in extracted DNA resulted in TRFLP patterns that were not consistent and introduced a bias towards lower estimates of diversity.}, }
@article {pmid11864249, year = {1998}, author = {Gustafsson, A and Norin, E and Midtvedt, T}, title = {Effect of clindamycin given alone or with Lactobacillus delbrueckii and Streptococcus thermophilus on 7alpha-dehydroxylation of bile acids in rats.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {4}, number = {10}, pages = {594-598}, doi = {10.1111/j.1469-0691.1998.tb00043.x}, pmid = {11864249}, issn = {1469-0691}, abstract = {OBJECTIVES: To evaluate the influence of clindamycin, given alone or with Lactobacillus delbrueckii and Streptococcus thermophilus to conventional rats, on 7alpha-dehydroxylation of cholic acid to deoxycholic acid. METHODS: The presence of deoxycholic acid was determined by gas-liquid chromatography. The fecal concentration of clindamycin was determined on PDM antibiotic sensitivity medium. Colony-forming units of L. delbrueckii and S. thermophilus were counted on lactic acid bacteria agar, and their ability to deconjugate was determined by thin-layer chromatography. RESULTS: Clindamycin significantly reduced the formation of deoxycholic acid, while the administration of lactobacilli-streptococci at the same time significantly reduced the effect of the antibiotic (p<0.05). CONCLUSIONS: Clindamycin reduced the formation of deoxycholic acid in rats and this effect was diminished by concomitant administration of L. delbrueckii and S. thermophilus. As the given microbes could not 7alpha-dehydroxylate, it seems reasonable to assume that they stimulate microbial species already present in the intestine.}, }
@article {pmid11848415, year = {2002}, author = {Davison, J}, title = {Genetic tools for pseudomonads, rhizobia, and other gram-negative bacteria.}, journal = {BioTechniques}, volume = {32}, number = {2}, pages = {386-8, 390, 392-4, passim}, doi = {10.2144/02322rv02}, pmid = {11848415}, issn = {0736-6205}, mesh = {Cloning, Molecular ; DNA Probes ; DNA Transposable Elements ; DNA, Bacterial ; DNA, Recombinant ; Escherichia coli/genetics ; Genes, Reporter ; *Genetic Techniques ; Genetic Vectors ; Gram-Negative Bacteria/*genetics ; Mutagenesis ; Promoter Regions, Genetic ; Pseudomonadaceae/*genetics ; Rhizobiaceae/*genetics ; }, abstract = {Gram-negative bacteria are extraordinarily diverse microorganisms that present a wide variety of characteristics worthy of genetic investigation. For historical reasons, the application of recombinant DNA technology to gram-negative bacteria in general has always lagged behind that of E. coli and its close relatives. However, the past 10 years have seen dramatic advances in the development of new tools and vectors for genetic analysis in non-E. coli hosts. Applications include various kinds of genetic manipulation, conjugation, transposition, site-specific recombination, protein secretion, protein purification, cell suicide, microbial ecology, biodegradation, and plant and animal pathogenicity.}, }
@article {pmid11848365, year = {2002}, author = {Uyanik, S and Sallis, PJ and Anderson, GK}, title = {The effect of polymer addition on granulation in an anaerobic baffled reactor (ABR). Part II: compartmentalization of bacterial populations.}, journal = {Water research}, volume = {36}, number = {4}, pages = {944-955}, doi = {10.1016/s0043-1354(01)00316-5}, pmid = {11848365}, issn = {0043-1354}, mesh = {*Bacteria, Anaerobic ; Biomass ; *Bioreactors ; Food Industry ; Industrial Waste ; Microscopy, Electron, Scanning ; Polymers/*chemistry ; Population Dynamics ; Waste Disposal, Fluid ; Water Purification/*methods ; }, abstract = {The microbial ecology of wastewater treatment plants remains one of the least understood aspects in both aerobic and anaerobic systems, despite the fact that both processes are ultimately dependent on an active biomass for operational efficiency. Ultimately, future developments in anaerobic treatment processes will require a much greater understanding of the fundamental relationships between bacterial populations within the biomass if optimum process efficiency is to be fully realised. This study assesses the influence of polymer addition on granule formation within an ABR and compares the ecology of the biomass in each compartment of two ABRs treating ice-cream wastewater. To our knowledge, this is the first reported characterisation of the microbiology of acidogenic and methanogenic bacteria in the individual compartments of an ABR. The polymer-amended reactor contained sludge that had a greater density of anaerobic bacteria and larger and denser granules than the control reactor, indicating that polymer addition possibly contributed to the retention of active biomass within the ABR. The average fraction of autofluorescent methanogens was lower, with 1.5% being in the initial compartments of the ABRs, compared to the last compartment which had 15%, showing that each compartment of an ABR had a unique microbial composition. Partial spatial separation of anaerobic bacteria appeared to have taken place with acidogenic bacteria predominating in the initial compartments and methanogenic bacteria predominating in the final compartments. Scanning electron micrographs have revealed that the dominant bacteria in the initial compartments of the ABR (Compartments 1 and 2) were those which could consume H2/CO2 and formate as substrate, i.e. Methanobrevibacter, Methanococcus, with populations shifting to acetate utilisers, i.e. Methanosaeta, Methanosarcina, in the final compartments (Compartments 3 and 4). In addition, there appeared to be a stratified structure to the bacterial genera present within the granules.}, }
@article {pmid11846772, year = {2001}, author = {Timms-Wilson, TM and Bryant, K and Bailey, MJ}, title = {Strain characterization and 16S-23S probe development for differentiating geographically dispersed isolates of the phytopathogen Ralstonia solanacearum.}, journal = {Environmental microbiology}, volume = {3}, number = {12}, pages = {785-797}, doi = {10.1046/j.1462-2920.2001.00250.x}, pmid = {11846772}, issn = {1462-2912}, mesh = {Betaproteobacteria/chemistry/classification/cytology/*genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Electrophoresis, Polyacrylamide Gel ; Fatty Acids/analysis ; Genotype ; In Situ Hybridization, Fluorescence ; Microscopy, Fluorescence ; Molecular Sequence Data ; Oligonucleotide Probes ; Phenotype ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 23S/*genetics ; Solanaceae/microbiology ; Statistics as Topic ; }, abstract = {The causative agent of potato brown rot and bacterial wilt, Ralstonia solanacearum, results in serious world-wide economic losses, particularly in the tropics. In the last decade, however, the incidence of bacterial wilt in potatoes grown in Northern Europe has increased, presenting an interesting epidemiological puzzle. Its occurrence may be as a result of changes in agricultural practice or the emergence of a novel bacterial variety, better adapted to cooler conditions. To understand the distribution and genetic diversity of this phytopathogen, we have analysed a collection of 82 isolates from Europe and tropical regions. Both phenotypic [SDS-PAGE (sodium dodecyl sulphate polyacrylamide gel electrophoresis) profiling, FAME (fatty acid methyl esters) analysis, growth profiles and EPS (exopolysaccharide) production] and genotypic [16S rRNA RFLP (restriction fragment length polymorphism), ARDRA (amplified ribosomal DNA restriction analysis) and sequence analysis of 16S-23S rRNA ITS and flanking regions] methods were compared. Principal component analysis of FAME profiles clustered isolates into three groups and ARDRA of a 0.85 kb amplified fragment from the 16S-23S ITS region differentiated isolates into four groups. Using sequence analysis, specific primers were designed within the variable region 147-170 of the 23S rRNA. These primers, RsolT2 and RsolT3, respectively, differentiated isolates into two distinct clusters as described previously by Wullings and colleagues (Wullings et al., 1998). The European strains (Biovar 2, race 3) analysed in this study specifically hybridized with RsolT3, and showed considerable genetic homogeneity when compared with strains of other races from 'the rest of the world'. These data indicate the possible selection and proliferation of a 'European'-adapted variant.}, }
@article {pmid11827345, year = {2002}, author = {Witzig, R and Manz, W and Rosenbergerb, S and Krügerb, U and Kraumeb, M and Szewzyk, U}, title = {Microbiological aspects of a bioreactor with submerged membranes for aerobic treatment of municipal wastewater.}, journal = {Water research}, volume = {36}, number = {2}, pages = {394-402}, doi = {10.1016/s0043-1354(01)00221-4}, pmid = {11827345}, issn = {0043-1354}, mesh = {*Bacteria ; Biomass ; *Bioreactors ; In Situ Hybridization, Fluorescence ; *Membranes, Artificial ; Oxygen Consumption ; Sewage ; Waste Disposal, Fluid/*methods ; Water Purification/*methods ; }, abstract = {An aerobic membrane bioreactor treating municipal wastewater at complete biomass retention was studied in respect of microbiological parameters over a period of 380 days. The results were compared to those obtained from a conventional activated sludge wastewater treatment plant (WWTP) treating the same wastewater. Microscopically, significant changes in the structure of the flocs and of the ratio between free suspended and aggregated cells could be observed. The presence of filamentous bacteria varied from almost not present to very high numbers. With the exception of short periods after changes in operating conditions, protozoa and metazoa were rarely present in the sludge community. The rate of oxygen consumption and the cell detectability by fluorescence in situ hybridizatio (FISH) with rRNA-targeted oligonucleotide probes were used to assess the physiological state of the bacterial cells Oxygen consumption rates of sludge samples obtained from both the conventional and membrane filtration plant wer determined without and after addition of different energy and carbon sources. In contrast to the conventional activate sludge, a pronounced increase in respiration activity upon the addition of organic substrates could be observed in th membrane filtration sludge. In situ probing with the Bacteria-specific probe EUB338 visualized 40-50% of all DAPI stainable bacteria in the membrane bioreactor, compared to 80% cells detectable by FISH in the conventional activate sludge. These results suggest that bacteria present in the highly concentrated biomass of the membrane reactor use the energy supplied for their maintenance metabolism and were not in a physiological state characteristic for growth This assumption could explain the zero net biomass production observed in the reactor.}, }
@article {pmid11823550, year = {2002}, author = {Wade, W}, title = {Unculturable bacteria--the uncharacterized organisms that cause oral infections.}, journal = {Journal of the Royal Society of Medicine}, volume = {95}, number = {2}, pages = {81-83}, pmid = {11823550}, issn = {0141-0768}, mesh = {Bacterial Infections/*microbiology ; DNA, Bacterial/isolation &amp; purification ; Gram-Positive Bacteria/isolation &amp; purification ; Gram-Positive Bacterial Infections/microbiology ; Humans ; Mouth Diseases/*microbiology ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; }, }
@article {pmid11823234, year = {2002}, author = {Neu, TR and Kuhlicke, U and Lawrence, JR}, title = {Assessment of fluorochromes for two-photon laser scanning microscopy of biofilms.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {2}, pages = {901-909}, pmid = {11823234}, issn = {0099-2240}, mesh = {Biofilms/*growth &amp; development ; Cyanobacteria/*growth &amp; development/metabolism ; Fluorescent Dyes/*metabolism ; Fungi/growth &amp; development/*metabolism ; Microscopy, Confocal/*methods ; *Photons ; Staining and Labeling/methods ; }, abstract = {A major limitation for the use of two-proton laser scanning microscopy (2P-LSM) in biofilm and other studies is the lack of a thorough understanding of the excitation-emission responses of potential fluorochromes. In order to use 2P-LSM, the utility of various fluorochromes and probes specific for a range of biofilm constituents must be evaluated. The fluorochromes tested in this study included classical nucleic acid-specific stains, such as acridine orange (AO) and 4",6"-diamidino-2-phenylindole (DAPI), as well as recently developed stains. In addition, stains specific for biofilm extracellular polymeric substances (EPS matrix components) were tested. Two-photon excitation with a Ti/Sapphire laser was carried out at wavelengths from 760 to 900 nm in 10-nm steps. It was found that autofluorescence of phototrophic organisms (cyanobacteria and green algae) resulted in strong signals for the entire excitation range. In addition, the coenzyme F(420)-related autofluorescence of methanogenic bacteria could be used to obtain images of dense aggregates (excitation wavelength, 780 nm). The intensities of the emission signals for the nucleic acid-specific fluorochromes varied. For example, the intensities were similar for excitation wavelengths ranging from 780 to 900 nm for AO but were higher for a narrower range, 780 to 810 nm, for DAPI. In selective excitation, fading, multiple staining, and combined single-photon-two-photon studies, the recently developed nucleic acid-specific fluorochromes proved to be more suitable regardless of whether they are intended for living or fixed samples. Probes specific for proteins and glycoconjugates allowed two-photon imaging of polymeric biofilm constituents. Selective excitation-emission was observed for Calcofluor White M2R (780 to 800 nm) and SyproOrange (880 to 900 nm). In addition, fluor-conjugated concanavalin A lectins were examined and provided acceptable two-photon emission signals at wavelengths ranging from 780 to 800 nm. Finally, CellTracker, a fluorochrome suitable for long-term labeling of microbial eucaryote cells, was found to give strong emission at wavelengths ranging from 770 to 810 nm. If fluorochromes have the same two-photon excitation cross section, they are suitable for multiple staining and multichannel recording. Generally, if an appropriate excitation wavelength and fluorochrome were used, it was possible to obtain more highly resolved images for thick biofilm samples with two-photon laser microscopy than with conventional single-photon laser microscopy. Due to its potential for higher resolution in light-scattering tissue-like material, such as biofilms, and extremely localized excitation, 2P-LSM is a valuable addition to conventional confocal laser scanning microscopy with single-photon excitation. However, further development of the method and basic research are necessary to take full advantage of nonlinear excitation in studies of interfacial microbial ecology.}, }
@article {pmid11812343, year = {2001}, author = {Wang, C and Li, Z and Wu, K}, title = {[Preliminary study on the rules of streptococcus mutans reactive oxygen species metabolism].}, journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology}, volume = {36}, number = {3}, pages = {202-205}, pmid = {11812343}, issn = {1002-0098}, mesh = {Electron Spin Resonance Spectroscopy ; Multienzyme Complexes/metabolism ; NADH, NADPH Oxidoreductases/metabolism ; *Reactive Oxygen Species ; Streptococcus mutans/*metabolism ; Superoxides/metabolism ; }, abstract = {OBJECTIVE: To study the rules of Streptococcus mutans reactive oxygen species metabolism and its enzymatic basis, and to investigate its significance intermediate to plaque microbial ecology.<br><br>METHODS: Electron spin trapping method was used to measure reactive oxygen species produced by Streptococcus mutans in the different incubation conditions, and evaluate the efficicay of NADH to hypoxanthine-xanthine oxidase and Fe(2+)-H2O2 system.<br><br>RESULTS: Electron spin resonance (ESR) spectrum of DMPO-O2- and DMPO-OH. and superoxide dismutase were obtained in Streptococcus mutans culture fluid, these spectrum were strengthened by exogenous sugar, and disappeared when methylene blue was added to culture fluid, but that spectrum was not significantly changed by NADH. ESR spectrum of hypoxanthine-xanthine oxidase and Fe(2+)-H2O2 system were significantly reduced or disappeared by NADH.<br><br>CONCLUSION: These results suggest that there are O2- and OH in Streptococcus mutans metabolism, and they may come mainly from the reaction catalyzed by NADH oxidase.}, }
@article {pmid11808803, year = {2002}, author = {Samelis, J and Sofos, JN and Kendall, PA and Smith, GC}, title = {Effect of acid adaptation on survival of Escherichia coli O157:H7 in meat decontamination washing fluids and potential effects of organic acid interventions on the microbial ecology of the meat plant environment.}, journal = {Journal of food protection}, volume = {65}, number = {1}, pages = {33-40}, doi = {10.4315/0362-028x-65.1.33}, pmid = {11808803}, issn = {0362-028X}, mesh = {Acetic Acid/*pharmacology ; Adaptation, Physiological ; Animals ; Cattle ; Disinfection/*methods ; Escherichia coli O157/growth &amp; development/*physiology ; Food Handling/*methods ; Hydrogen-Ion Concentration ; Meat/*microbiology ; }, abstract = {The acid tolerance of Escherichia coli O157:H7 may be pH inducible. Correspondingly, organic acid meat decontamination washing fluids may enhance the establishment of acid-adapted E. coli O157:H7 strains in packing plants, especially in mixtures with water washings from meat that may be of sublethal pH. Acid-adapted and nonadapted cultures of a rifampin-resistant derivative of the acid-resistant E. coli O157:H7 strain ATCC 43895 were tested to evaluate their survival in meat-washing fluids over a wide pH range. The cultures were exposed (10(5) CFU/ml) to acidic (2% lactic acid. 2% acetic acid, or a mixture of the two with water washings at ratios of 1/1, 1/9, or 1/99 [vol/vol]) or nonacid (water) meat washings for up to 14 days at 4 or 10 degrees C storage. E. coli O157:H7 survived in water washings, but the low storage temperatures and predominant natural microbiota synergistically inhibited its growth. Compared with acid-adapted populations, nonadapted populations displayed greater potential for survival and a tendency to initiate growth in water meat washings at 10 degrees C. The pathogen survived in most of the acid washings throughout storage (14 days), sometimes with minimal population reductions. Overall. nonadapted populations declined faster than acid-adapted populations, while the declines increased as the acid concentration and temperature of storage increased and were more dramatic in lactate, compared to acetate, washings. Acid-containing washings were selective for growth of lactic acid bacteria and yeasts. indicating that organic acid treatments may alter the microbial ecology of meat plant environments and potentially that of the meat. These results should be considered when selecting decontamination technologies for meat.}, }
@article {pmid11805313, year = {2002}, author = {Lenski, RE and Riley, MA}, title = {Chemical warfare from an ecological perspective.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {2}, pages = {556-558}, pmid = {11805313}, issn = {0027-8424}, mesh = {Bacterial Toxins/toxicity ; *Ecosystem ; Microbiology ; Models, Biological ; Mycotoxins/toxicity ; }, }
@article {pmid11792454, year = {2002}, author = {Verstraete, W}, title = {Environmental biotechnology for sustainability.}, journal = {Journal of biotechnology}, volume = {94}, number = {1}, pages = {93-100}, doi = {10.1016/s0168-1656(01)00421-7}, pmid = {11792454}, issn = {0168-1656}, mesh = {*Biotechnology ; *Environment ; Environmental Monitoring ; Thermodynamics ; *Waste Management ; }, abstract = {In the post-industrial society, waste management is integrated in the concepts of responsibility, reliability and continuity. Therefore industry and public office are obliged to implement the concepts of structured environmental management systems more and more strictly. The endpoints are dependent on the type of wastes and on the priorities set by society. They will with time evolve towards more restriction of all kinds of emissions. This will require increasing inputs of labour, information technology and energy into waste treatment and overall waste management. Particularly for aqueous and gaseous wastes that are not contained, continuously improving treatment with maximum re-use and minimum dissipation in the ecosphere will be the trend of the future. Moreover, the public in general and the individual citizen in particular will request to have (bio)assays to monitor regularly and autonomously the quality of his environment. Such advanced waste management requires considerable energy input. It thus may come in conflict with current concerns about CO2-emissions and the Kyoto agreements. Innovative approaches to combine waste management and the International Climate Change Partnership (ICCP) directives, for instance by implementing biological carbon sequestration, are therefore warranted. Biotechnology has a major role to play particularly in terms of advanced treatment down to ng/l-levels and in terms of validating the quality of the environment by means of powerful and intelligent bio-monitoring devices.}, }
@article {pmid11778893, year = {2001}, author = {Vincke, E and Boon, N and Verstraete, W}, title = {Analysis of the microbial communities on corroded concrete sewer pipes--a case study.}, journal = {Applied microbiology and biotechnology}, volume = {57}, number = {5-6}, pages = {776-785}, doi = {10.1007/s002530100826}, pmid = {11778893}, issn = {0175-7598}, mesh = {Bacteria/genetics/isolation &amp; purification ; Base Sequence ; Biofilms ; Cloning, Molecular ; Corrosion ; DNA, Bacterial/genetics/isolation &amp; purification ; DNA, Ribosomal/genetics/isolation &amp; purification ; Environmental Microbiology ; Fungi/genetics/isolation &amp; purification ; Molecular Sequence Data ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Sanitary Engineering ; Sewage/*microbiology ; Waste Management ; }, abstract = {Conventional as well as molecular techniques have been used to determine the microbial communities present on the concrete walls of sewer pipes. The genetic fingerprint of the microbiota on corroded concrete sewer pipes was obtained by means of denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. The DGGE profiles of the bacterial communities present on the concrete surface changed as observed by shifts occurring at the level of the dominance of bands from non-corroded places to the most severely corroded places. By means of statistical tools, it was possible to distinguish two different groups, corresponding to the microbial communities on corroded and non-corroded surfaces, respectively. Characterization of the microbial communities indicated that the sequences of typical bands showed the highest level of identity to sequences from the bacterial strains Thiobacillus thiooxidans, Acidithiobacillus sp., Mycobacterium sp. and different heterotrophs belonging to the alpha-, beta- and gamma-Proteobacteria, Acidobacteria and Actinobacteria. In addition, the presence of N-acyl-homoserine lactone signal molecules was shown by two bio-assays of the biofilm on the concrete under the water level and at the most severely corroded places on the concrete surface of the sewer pipe.}, }
@article {pmid11777585, year = {2002}, author = {Böckelmann, U and Manz, W and Neu, TR and Szewzyk, U}, title = {Investigation of lotic microbial aggregates by a combined technique of fluorescent in situ hybridization and lectin-binding-analysis.}, journal = {Journal of microbiological methods}, volume = {49}, number = {1}, pages = {75-87}, doi = {10.1016/s0167-7012(01)00354-2}, pmid = {11777585}, issn = {0167-7012}, mesh = {Animals ; Betaproteobacteria/genetics/growth &amp; development/*isolation &amp; purification/metabolism ; *Ecosystem ; Fresh Water/*microbiology ; Glycoconjugates/metabolism ; *In Situ Hybridization, Fluorescence ; Lectins/*metabolism ; Microscopy, Confocal ; Polymers/metabolism ; *Snow ; }, abstract = {A technique combining fluorescent in situ hybridization and lectin-binding-analysis (FISH-LBA) was developed and applied for the simultaneous detection of cellular components and glycoconjugates in lotic microbial aggregates (river snow). River snow aggregates were directly collected from the bulk water phase into coverslip chambers, in which the complete procedure including fixation, fluorescent in situ hybridization, lectin-binding and optical analysis by confocal laser scanning microscopy was performed. Neither autofluorescence originating from phyotosynthetic organisms nor inorganic particles did negatively interfere with the FISH-LBA technique. In river snow samples obtained from the river Elbe, Germany, distinct compartments of the river snow structure could be visualized with FITC-labelled lectins from Triticum vulgaris, Limulus polyphemus, Arachis hypogaea, Phaseolus vulgaris and Pseudomonas aeruginosa, binding to frequently occurring saccharide residues in the river snow matrix. The analysis could be performed on different levels of complexity. The combined technique visualized bacteria of different phylogenetic groups in the entire river snow structure as well as glycoconjugate components linked with various microcolonies. Different lectins stained slime layers and cell-envelopes of individual eukaryotic and prokaryotic cells. Consequently, application of the FISH-LBA technique allows the linkage between cellular and glycoconjugate identity in complex microbial communities.}, }
@article {pmid11772638, year = {2002}, author = {Baxter, NJ and Scanlan, J and De Marco, P and Wood, AP and Murrell, JC}, title = {Duplicate copies of genes encoding methanesulfonate monooxygenase in Marinosulfonomonas methylotropha strain TR3 and detection of methanesulfonate utilizers in the environment.}, journal = {Applied and environmental microbiology}, volume = {68}, number = {1}, pages = {289-296}, pmid = {11772638}, issn = {0099-2240}, mesh = {Alphaproteobacteria/classification/enzymology/*genetics/isolation &amp; purification ; Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; DNA Probes/genetics ; *Electron Transport Complex III ; Environmental Microbiology ; *Genes, Duplicate ; Iron-Sulfur Proteins/genetics ; Mesylates/*metabolism ; Mixed Function Oxygenases/chemistry/*genetics/metabolism ; Molecular Sequence Data ; *Multigene Family ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Marinosulfonomonas methylotropha strain TR3 is a marine methylotroph that uses methanesulfonic acid (MSA) as a sole carbon and energy source. The genes from M. methylotropha strain TR3 encoding methanesulfonate monooxygenase, the enzyme responsible for the initial oxidation of MSA to formaldehyde and sulfite, were cloned and sequenced. They were located on two gene clusters on the chromosome of this bacterium. A 5.0-kbp HindIII fragment contained msmA, msmB, and msmC, encoding the large and small subunits of the hydroxylase component and the ferredoxin component, respectively, of the methanesulfonate monooxygenase, while a 6.5-kbp HindIII fragment contained duplicate copies of msmA and msmB, as well as msmD, encoding the reductase component of methanesulfonate. Both sets of msmA and msmB genes were virtually identical, and the derived msmA and msmB sequences of M. methylotropha strain TR3, compared with the corresponding hydroxylase from the terrestrial MSA utilizer Methylosulfonomonas methylovora strain M2 were found to be 82 and 69% identical. The msmA gene was investigated as a functional gene probe for detection of MSA-utilizing bacteria. PCR primers spanning a region of msmA which encoded a unique Rieske [2Fe-2S] binding region were designed. These primers were used to amplify the corresponding msmA genes from newly isolated Hyphomicrobium, Methylobacterium, and Pedomicrobium species that utilized MSA, from MSA enrichment cultures, and from DNA samples extracted directly from the environment. The high degree of identity of these msmA gene fragments, compared to msmA sequences from extant MSA utilizers, indicated the effectiveness of these PCR primers in molecular microbial ecology.}, }
@article {pmid11770814, year = {2001}, author = {Monte, E}, title = {Understanding Trichoderma: between biotechnology and microbial ecology.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {4}, number = {1}, pages = {1-4}, doi = {10.1007/s101230100001}, pmid = {11770814}, issn = {1139-6709}, mesh = {Biotechnology ; Ecology ; *Pest Control, Biological ; Plant Diseases/*microbiology ; *Trichoderma/genetics ; }, }
@article {pmid11759695, year = {2001}, author = {Dewettinck, T and Hulsbosch, W and Van Hege, K and Top, EM and Verstraete, W}, title = {Molecular fingerprinting of bacterial populations in groundwater and bottled mineral water.}, journal = {Applied microbiology and biotechnology}, volume = {57}, number = {3}, pages = {412-418}, doi = {10.1007/s002530100797}, pmid = {11759695}, issn = {0175-7598}, mesh = {Beverages ; Cluster Analysis ; Colony Count, Microbial ; DNA, Bacterial/chemistry/isolation &amp; purification ; DNA, Ribosomal/chemistry/isolation &amp; purification ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/genetics/*growth &amp; development ; Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; *Water Microbiology ; }, abstract = {Monitoring the hygienic quality of drinking waters by determining the concentration of fecal indicators with traditional plate count techniques suffers from important drawbacks. In this work, the potential of PCR-DGGE (polymerase chain reaction - denaturing gradient gel electrophoresis) analysis of 16S rDNA genes to fingerprint the bacterial populations of mineral water and groundwater was investigated. A rapid and simple pretreatment to concentrate and release bacterial DNA prior to PCR was explored. This pretreatment was successful for commercially bottled mineral water. For groundwater, an additional resuscitation step was required to obtain a PCR signal. It was clear that the groundwater under scrutiny contained a more diverse bacterial community than the mineral water. A comparison was made between four kinds of mineral waters and one sample of groundwater using the developed procedures. For each kind of water, bacterial populations cultured on R2A plates were also subjected to PCR-DGGE. Comparison of the fingerprints of the plated samples and the original samples suggested the presence of viable but nonculturable bacteria in the waters. The obtained cluster dendrogram indicated that each kind of water was characterized by a specific molecular fingerprint. The sensitivity of the whole of the procedure was between 10(4) and 10(5) cfu ml(-1) as determined using a pure culture of Escherichia coli. The described PCR-DGGE method can constitute the basis of a new and interesting strategy to monitor in a relatively rapid way (less than 24 h) the bacterial quality of waters such as mineral water, groundwater and certain types of reclaimed water.}, }
@article {pmid11751763, year = {2002}, author = {Levy, SB}, title = {The 2000 Garrod lecture. Factors impacting on the problem of antibiotic resistance.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {49}, number = {1}, pages = {25-30}, doi = {10.1093/jac/49.1.25}, pmid = {11751763}, issn = {0305-7453}, mesh = {Animals ; Anti-Bacterial Agents/adverse effects/chemistry ; Bacterial Infections/epidemiology/prevention &amp; control ; Community-Acquired Infections/epidemiology/prevention &amp; control ; *Drug Resistance, Bacterial/physiology ; Humans ; }, abstract = {Antibiotic resistance has become a major clinical and public health problem within the lifetime of most people living today. Confronted by increasing amounts of antibiotics over the past 60 years, bacteria have responded to the deluge with the propagation of progeny no longer susceptible to them. While it is clear that antibiotics are pivotal in the selection of bacterial resistance, the spread of resistance genes and of resistant bacteria also contributes to the problem. Selection of resistant forms can occur during or after antimicrobial treatment; antibiotic residues can be found in the environment for long periods of time after treatment. Besides antibiotics, there is the mounting use of other agents aimed at destroying bacteria, namely the surface antibacterials now available in many household products. These too enter the environment. The stage is thus set for an altered microbial ecology, not only in terms of resistant versus susceptible bacteria, but also in terms of the kinds of microorganisms surviving in the treated environment. We currently face multiresistant infectious disease organisms that are difficult and, sometimes, impossible to treat successfully. In order to curb the resistance problem, we must encourage the return of the susceptible commensal flora. They are our best allies in reversing antibiotic resistance.}, }
@article {pmid11737624, year = {2001}, author = {De Boever, P and Wouters, R and Verstraete, W}, title = {Combined use of Lactobacillus reuteri and soygerm powder as food supplement.}, journal = {Letters in applied microbiology}, volume = {33}, number = {6}, pages = {420-424}, doi = {10.1046/j.1472-765x.2001.01023.x}, pmid = {11737624}, issn = {0266-8254}, mesh = {Animals ; Deoxycholic Acid/*pharmacology ; Detergents/*pharmacology ; Fermentation ; Glycodeoxycholic Acid/*pharmacology ; Hemolysis ; Isoflavones/isolation &amp; purification ; Lactobacillus/drug effects/*growth &amp; development/metabolism ; Milk/*microbiology ; Probiotics ; Glycine max ; }, abstract = {AIMS: The survival of Lactobacillus reuteri when challenged with glycodeoxycholic acid (GDCA), deoxycholic acid (DCA) and soygerm powder was investigated. Moreover, the impact of Lact. reuteri on the bioavailability of isoflavones present in soygerm powder was examined.<br><br>METHODS AND RESULTS: The strain experienced a die-off when adding 2 or 3 mmol l-1 bile salts, with more pronounced effects in the case of DCA. By means of a haemolysis test it was shown that toxicity could be due to membrane damage. When 4 g l-1 soygerm powder was added, the Lactobacillus strain survived the bile salt burden better (P < or = 0.05) and the membrane damage in the haemolysis test decreased (P < or = 0.05). The Lact. strain cleaved beta-glycosidic isoflavones during fermentation of milk supplemented with soygerm powder.<br><br>The interactions between the Lactobacillus strain and soygerm powder suggest that combining both in fermented milk can exhibit advantageous probiotic effects. The relevance of the combination of the strain and the soygerm powder should be studied under more relevant physiological conditions.}, }
@article {pmid11730142, year = {2001}, author = {Lissens, G and Vandevivere, P and De Baere, L and Biey, EM and Verstrae, W}, title = {Solid waste digestors: process performance and practice for municipal solid waste digestion.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {44}, number = {8}, pages = {91-102}, pmid = {11730142}, issn = {0273-1223}, mesh = {Bacteria, Anaerobic/*physiology ; Biomass ; *Bioreactors ; *Developing Countries ; Facility Design and Construction ; Refuse Disposal/*methods ; Waste Disposal, Fluid ; }, abstract = {The most common types of anaerobic digesters for solid wastes have been compared based on biological and technical performance and reliability. Batch systems have the most simple designs and are the least expensive solid waste digesters. They have high potential for application in developing countries. Two-stage systems are the most complex and most expensive systems. Their greatest advantage lies in the equalisation of the organic loading rate in the first stage, allowing a more constant feeding rate of the methanogenic second stage. Two-stage systems with biomass accumulation devices in the second stage display a larger resistance toward toxicants and inhibiting substances such as ammonia. However, the large majority of industrial applications use one-stage systems and these are evenly split between "dry" systems (wastes are digested as received) and "wet" systems (wastes are slurried to about 12% total solids). Regarding biological performance, this study compares the different digester systems in terms of organic loading rates and biogas yields considering differences in input waste composition. As a whole, "dry" designs have proven reliable due to their higher biomass concentration, controlled feeding and spatial niches. Moreover, from a technical viewpoint the "dry" systems are more robust and flexible than "wet' systems.}, }
@article {pmid11724385, year = {2001}, author = {Tsekova, K and Dentcheva, V and Ianis, M}, title = {Copper uptake by Penicillium brevicompactum.}, journal = {Zeitschrift fur Naturforschung. C, Journal of biosciences}, volume = {56}, number = {9-10}, pages = {803-805}, doi = {10.1515/znc-2001-9-1019}, pmid = {11724385}, issn = {0939-5075}, mesh = {Biological Transport ; Biomass ; Copper/*pharmacokinetics ; Kinetics ; Penicillium/growth &amp; development/*metabolism ; Time Factors ; }, abstract = {The copper binding properties of Penicillium brevicompactum biomass were influenced by growth phase of mycelium and concentration of copper in reaction mixtures. The efficiency of copper uptake increased with growth time and was largest at the mid-logarithmic growth phase. The time course of copper uptake was biphasic. Double reciprocal plots of absorption velocity of copper vs. copper concentration gave straight lines at concentration between 0.5 to 4 mM. The apparent affinity of copper to the biomass of the stationary growth phase was the same as that of logarithmic growth phase and Km values were about 1.4 mM. Pretreatment of the mycelium with glucose increased the amount of metal uptake about five times in comparison with the controls.}, }
@article {pmid11722545, year = {2001}, author = {Dejonghe, W and Boon, N and Seghers, D and Top, EM and Verstraete, W}, title = {Bioaugmentation of soils by increasing microbial richness: missing links.}, journal = {Environmental microbiology}, volume = {3}, number = {10}, pages = {649-657}, doi = {10.1046/j.1462-2920.2001.00236.x}, pmid = {11722545}, issn = {1462-2912}, mesh = {Bacteria/chemistry/*classification/genetics ; Biodegradation, Environmental ; Ecosystem ; Environment ; Environmental Monitoring ; *Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {It is generally assumed that increased microbial diversity corresponds to increased catabolic potential and, hence, to better removal of metabolites and pollutants. Yet, microbial diversity, more specifically richness of species in environmental samples and sites, is difficult to assess. It is proposed to interpret this diversity more in the framework of Pareto's law, i.e. 20% of the species govern 80% of the energy flux of the ecosystem. Ecological studies should attempt to delineate the main energy fluxes and that group of species playing quantitative key roles in the system. Consequently, bioaugmentation should aim at the rearrangement of the group of organisms dominantly involved in the overall energy flux, so that specific catabolic traits necessary for the clean up of pollutants are part of that active group. For soil ecosystems, the capacity of plant roots as creators of physical and chemical discontinuity should be used more strategically to bring about such rearrangements. Overall, this paper identifies a number of ecological concepts, such as the Pareto law, the Gompertz model and plant community-induced microbial competence, which may, given careful underpinning, open new perspectives for microbial ecology and biodegradation.}, }
@article {pmid11699590, year = {2001}, author = {Downes, J and Munson, MA and Spratt, DA and Kononen, E and Tarkka, E and Jousimies-Somer, H and Wade, WG}, title = {Characterisation of Eubacterium-like strains isolated from oral infections.}, journal = {Journal of medical microbiology}, volume = {50}, number = {11}, pages = {947-951}, doi = {10.1099/0022-1317-50-11-947}, pmid = {11699590}, issn = {0022-2615}, mesh = {Actinomycetales Infections/*microbiology ; Bacterial Typing Techniques ; DNA, Bacterial/analysis/genetics ; Dental Implants/microbiology ; Eubacterium/*classification/genetics/isolation &amp; purification ; Genes, rRNA ; Genotype ; Humans ; Mouth Diseases/*microbiology ; Phenotype ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; Sequence Analysis, DNA ; }, abstract = {The genus Eubacterium currently includes a heterogeneous group of gram-positive, non-spore-forming anaerobic bacilli, many of which are slow growing, fastidious and generally unreactive in biochemical tests. As a consequence, cultivation and identification of isolates are difficult and the taxonomy of the group remains indifferent. In this study, 105 isolates from odontogenic infections, infections associated with dental implants or saliva from healthy subjects and provisionally assigned to the genus Eubacterium were subjected to phenotypic and genotypic analysis. Ninety-one of the isolates were identified as belonging to one of 14 previously described species: Atopobium parvulum (5 isolates), A. rimae (29), Bulleidia extructa (2), Cryptobacterium curtum (1), Dialister pneumosintes (1), Eubacterium saburreum (2), E. sulci (8), E. yurii subsp. yurii (1), Filifactor alocis (3), Lactobacillus uli (1), Mogibacterium timidum (13), M. vescum (6), Pseudoramibacter alactolyticus (6) and Slackia exigua (13). The remaining 14 isolates did not correspond to existing species. This study confirms the diversity of organisms provisionally assigned to the genus Eubacterium by conventional identification methods. This group of organisms is frequently isolated from oral infections but their role in the aetiology of these conditions has yet to be determined.}, }
@article {pmid11695619, year = {2001}, author = {Kümmerer, K}, title = {Drugs in the environment: emission of drugs, diagnostic aids and disinfectants into wastewater by hospitals in relation to other sources--a review.}, journal = {Chemosphere}, volume = {45}, number = {6-7}, pages = {957-969}, doi = {10.1016/s0045-6535(01)00144-8}, pmid = {11695619}, issn = {0045-6535}, mesh = {Anesthetics ; Anti-Bacterial Agents/analysis ; Antineoplastic Agents ; Contrast Media ; Disinfectants/*analysis ; Hospitals ; Humans ; Medical Waste/*analysis ; *Medical Waste Disposal ; Pharmaceutical Preparations/analysis ; Risk Assessment ; Sewage ; Waste Disposal, Fluid/*methods ; *Water Purification ; *Water Supply ; }, abstract = {After administration, pharmaceuticals are excreted by the patients into wastewater. Unused medications are sometimes disposed of in drains. The drugs enter the aquatic environment and eventually reach drinking water if they are not biodegraded or eliminated during sewage treatment. Additionally, antibiotics and disinfectants are supposed to disturb the wastewater treatment process and the microbial ecology in surface waters. Furthermore, resistant bacteria may be selected in the aeration tanks of STPs by the antibiotic substances present. Recently, pharmaceuticals have been detected in surface water, ground water and drinking water. However, only little is known about the significance of emissions from households and hospitals. A brief summary of input by different sources, occurrence, and elimination of different pharmaceutical groups such as antibiotics, anti-tumour drugs, anaesthetics and contrast media as well as AOX resulting from hospital effluent input into sewage water and surface water will be presented.}, }
@article {pmid11682181, year = {2001}, author = {Horn, M and Wagner, M}, title = {Evidence for additional genus-level diversity of Chlamydiales in the environment.}, journal = {FEMS microbiology letters}, volume = {204}, number = {1}, pages = {71-74}, doi = {10.1111/j.1574-6968.2001.tb10865.x}, pmid = {11682181}, issn = {0378-1097}, mesh = {Chlamydiales/*classification/*genetics ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal/analysis/genetics ; Industrial Waste ; Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Sewage/*microbiology ; Waste Disposal, Fluid ; }, abstract = {The medically important order Chlamydiales has long been considered to contain a few closely related bacteria which occur exclusively in animals and humans. This perception of diversity and habitat had to be revised with the recent identification of the genera Simkania, Waddlia, Parachlamydia, and Neochlamydia with the latter two comprising endosymbionts of amoebae. Application of a newly developed PCR assay for the specific amplification of a near full length 16S rDNA fragment of these novel Chlamydia-related bacteria on activated sludge samples revealed the existence of at least four additional, previously unknown evolutionary lineages of Chlamydiales (each showing less than 92% 16S rRNA sequence similarity with all recognized members of this order). These findings suggest that some waste water treatment plants represent reservoirs for a diverse assemblage of environmental chlamydiae, a discovery which might also be of relevance from the viewpoint of human public health.}, }
@article {pmid11680502, year = {2001}, author = {Garland, JL and Cook, KL and Adams, JL and Kerkhof, L}, title = {Culturability as an indicator of succession in microbial communities.}, journal = {Microbial ecology}, volume = {42}, number = {2}, pages = {150-158}, doi = {10.1007/s00248-001-0002-3}, pmid = {11680502}, issn = {0095-3628}, mesh = {Amino Acids/pharmacokinetics ; Bacteria/growth &amp; development/metabolism ; Biomass ; Bioreactors ; Colony Count, Microbial ; Ecology ; *Ecosystem ; *Environment, Controlled ; Hydroponics ; Plant Roots/growth &amp; development/metabolism/*microbiology ; Time Factors ; Triticum/growth &amp; development/metabolism/*microbiology ; *Water Microbiology ; }, abstract = {Successional theory predicts that opportunistic species with high investment of energy in reproduction and wide niche width will be replaced by equilibrium species with relatively higher investment of energy in maintenance and narrower niche width as communities develop. Since the ability to rapidly grow into a detectable colony on nonselective agar medium could be considered as characteristic of opportunistic types of bacteria, the percentage of culturable cells may be an indicator of successional state in microbial communities. The ratios of culturable cells (colony forming units on R2A agar) to total cells (acridine orange direct microscopic counts) and culturable cells to active cells (reduction of 5-cyano-2,3-ditolyl tetrazolium chloride) were measured over time in two types of laboratory microcosms (the rhizosphere of hydroponically grown wheat and aerobic, continuously stirred tank reactors containing plant biomass) to determine the effectiveness of culturabilty as an index of successional state. The culturable cell:total cell ratio in the rhizosphere decreased from approximately 0.25 to less than 0.05 during the first 30-50 days of plant growth, and from 0.65 to 0.14 during the first 7 days of operation of the bioreactor. The culturable cell:active cell ratio followed similar trends, but the values were consistently greater than the culturable cell:total cell ratio, and even exceeded I in early samples. Follow-up studies used a cultivation-independent method, terminal restriction fragment length polymorphisms (TRFLP) from whole community DNA, to assess community structure. The number of TRFLP peaks increased with time, while the number of culturable types did not, indicating that the general decrease in culturability is associated with a shift in community structure. The ratio of respired to assimilated C-14-labeled amino acids increased with the age of rhizosphere communities, supporting the hypothesis that a shift in resource allocation from growth to maintenance occurs with time. Results from this work indicate that the percentage of culturable cells may be a useful method for assessing the successional state of microbial communities.}, }
@article {pmid11679359, year = {2001}, author = {Séka, MA and Kalogo, Y and Hammes, F and Kielemoes, J and Verstraete, W}, title = {Chlorine-susceptible and chlorine-resistant type 021N bacteria occurring in bulking activated sludges.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {11}, pages = {5303-5307}, pmid = {11679359}, issn = {0099-2240}, mesh = {Chlorine/*pharmacology ; Disinfectants/*pharmacology ; *Drug Resistance, Bacterial ; Gram-Negative Bacteria/classification/*drug effects/genetics/isolation &amp; purification ; In Situ Hybridization, Fluorescence ; Sewage/*microbiology ; Staining and Labeling/methods ; Waste Disposal, Fluid ; }, abstract = {Two filamentous bacteria causing bulking in two activated sludges were examined. Investigations using morphological features, staining techniques, and fluorescent in situ hybridization identified both filaments as type 021N. However, an examination of the effect of chlorine on the sludges revealed a chlorine-susceptible type 021N in one sludge and a chlorine-resistant type 021N in the other.}, }
@article {pmid11641486, year = {2001}, author = {Lenski, RE}, title = {Genetics and evolution. Come fly, and leave the baggage behind.}, journal = {Science (New York, N.Y.)}, volume = {294}, number = {5542}, pages = {533-534}, doi = {10.1126/science.1066241}, pmid = {11641486}, issn = {0036-8075}, mesh = {Adaptation, Physiological ; Animals ; Biological Evolution ; Drosophila melanogaster/*genetics/physiology ; Female ; Genes, Insect ; Genetic Variation ; Male ; *Mutation ; *Recombination, Genetic ; *Reproduction ; Reproduction, Asexual ; *Selection, Genetic ; }, }
@article {pmid11601634, year = {2001}, author = {Dewettinck, T and Van Hege, K and Verstraete, W}, title = {Development of a rapid pH-based biosensor to monitor and control the hygienic quality of reclaimed domestic wastewater.}, journal = {Applied microbiology and biotechnology}, volume = {56}, number = {5-6}, pages = {809-815}, doi = {10.1007/s002530100705}, pmid = {11601634}, issn = {0175-7598}, mesh = {Biosensing Techniques/*methods ; Colony Count, Microbial ; Enterobacteriaceae/isolation &amp; purification ; Hydrogen-Ion Concentration ; Quality Control ; Waste Disposal, Fluid/methods/*standards ; Water Supply/*standards ; }, abstract = {The re-use of treated domestic wastewater necessitates a rigorous control and rapid monitoring of the hygienic quality of the reclaimed water. For this purpose, a new pH-based biosensor was developed. The essence of the methodology of the sensor is the monitoring of the acidification due to bacterial metabolism of added glucose. To improve the sensitivity, the alkalinity of the water sample is reduced prior to monitoring the acidification. This is done by stripping CO2 at a neutral or acidic pH value. The hygienic aspect of the sensor lies in the applied temperature (37 degrees C) and the use of N2 as decarbonizing gas, thus creating conditions favorable for enteric bacteria. The developed sensor could be used onsite at an advanced stage of treatment, as an endpoint or intake quality control device. For both applications, a useful correlation was obtained between log total plate count and lag time or acidification rate, respectively. Absolute detection limits lay in the ranges of either 10(3) colony-forming units (CFU)/ml in 6 h (endpoint quality control), or less than 10(5) CFU/ml in 1 h (intake quality control).}, }
@article {pmid11583845, year = {2001}, author = {Heinfling-Weidtmann, A and Reemtsma, T and Storm, T and Szewzyk, U}, title = {Sulfophthalimide as major metabolite formed from sulfonated phthalocyanine dyes by the white-rot fungus Bjerkandera adusta.}, journal = {FEMS microbiology letters}, volume = {203}, number = {2}, pages = {179-183}, doi = {10.1111/j.1574-6968.2001.tb10838.x}, pmid = {11583845}, issn = {0378-1097}, mesh = {Basidiomycota/growth &amp; development/*metabolism ; Biodegradation, Environmental ; Coloring Agents/chemistry/*metabolism ; Indoles/chemistry/*metabolism ; Isoindoles ; Peroxidases/metabolism ; Phthalimides/chemistry/*metabolism ; Sulfur Compounds/chemistry/*metabolism ; Textiles ; }, abstract = {The reaction products formed during the decolorization of the sulfophthalocyanine textile dyes Reactive blue 15 (RB15) and Reactive blue 38 (RB38) by the white-rot fungus Bjerkandera adusta were analyzed by high-performance liquid chromatography with diode array detection and with liquid chromatography-electrospray ionization-tandem mass spectrometry. Sulfophthalimides (SPI; 3 and 4) were identified as major metabolites by comparison with synthesized reference compounds. SPI was formed from both dyes in fungal cultures and by incubation with its purified manganese peroxidase and lignin peroxidase. Quantitative assessment of the SPI formed from RB15 accounted for approximately 60% of the theoretical amount.}, }
@article {pmid11577154, year = {2001}, author = {Inoue, T and Tanimoto, I and Tada, T and Ohashi, T and Fukui, K and Ohta, H}, title = {Fermentable-sugar-level-dependent regulation of leukotoxin synthesis in a variably toxic strain of Actinobacillus actinomycetemcomitans.}, journal = {Microbiology (Reading, England)}, volume = {147}, number = {Pt 10}, pages = {2749-2756}, doi = {10.1099/00221287-147-10-2749}, pmid = {11577154}, issn = {1350-0872}, mesh = {Aggregatibacter actinomycetemcomitans/genetics/growth &amp; development/*metabolism ; Anaerobiosis ; Culture Media ; Cyclic AMP/metabolism ; Exotoxins/*biosynthesis/genetics ; Fermentation ; Fructose/*metabolism ; *Gene Expression Regulation, Bacterial ; Humans ; Molecular Sequence Data ; Promoter Regions, Genetic/genetics ; Sequence Analysis, DNA ; Transcription, Genetic ; }, abstract = {Actinobacillus actinomycetemcomitans, a Gram-negative periodontopathic bacterium, produces a leukotoxin belonging to the RTX family. The production of leukotoxin varies greatly among different strains of this species and under different culture conditions. A toxin-production-variable strain, 301-b, stably produces significant amounts of leukotoxin in anaerobic fructose-limited chemostat cultures, but does not do so in the presence of excess fructose. This communication describes the cloning and sequencing of the leukotoxin promoter region from 301-b, showing that this strain has a promoter region similar to that from strain 652, a moderately toxic strain. Northern blot analysis using a leukotoxin gene probe demonstrated that change in toxin production in response to the level of external fructose was due to alteration in the transcriptional level of the leukotoxin gene. Pulsing of fructose into the fructose-limited chemostat culture remarkably reduced the intracellular cAMP level from 40 pmol (mg dry wt cells)(-1) to 3.1 pmol (mg dry wt cells)(-1), which was restored when the culture was returned to fructose-limited conditions. Further, it was found that addition of external cAMP to the culture with excess fructose resulted in an apparent recovery of leukotoxin production. Taken together, these findings indicate that a cAMP-dependent mechanism, possibly a catabolite-repression-like system, may be involved in the regulation of leukotoxin production in this bacterium.}, }
@article {pmid11576680, year = {2001}, author = {Björkman, KM and Karl, DM}, title = {A novel method for the measurement of dissolved adenosine and guanosine triphosphate in aquatic habitats: applications to marine microbial ecology.}, journal = {Journal of microbiological methods}, volume = {47}, number = {2}, pages = {159-167}, doi = {10.1016/s0167-7012(01)00301-3}, pmid = {11576680}, issn = {0167-7012}, mesh = {Adenosine Triphosphate/*analysis/metabolism ; Ecology ; Firefly Luciferin/metabolism ; Fresh Water/*chemistry ; Guanosine Triphosphate/*analysis/metabolism ; Hydrolysis ; Kinetics ; Luciferases/metabolism ; Luminescent Measurements ; Marine Biology/methods ; Pacific Ocean ; Reproducibility of Results ; Seawater/*chemistry ; Solubility ; Water Microbiology ; }, abstract = {A novel method for the measurement of dissolved adenosine-5'-triphosphate and guanosine-5'-triphosphate (D-ATP and D-GTP, respectively) in marine and freshwater habitats was developed and applied to samples collected from the oligotrophic North Pacific Ocean. Both D-ATP and D-GTP are co-precipitated by authigenically formed Mg(OH)(2) and can be concentrated by factors greater than 200-fold, for subsequent measurement by the firefly luciferin-luciferase bioluminescence reaction. The detection limit for this method was 2-3 pmol ml(-1) of concentrated sample (equivalent to an in situ concentration of 10 pM) with a 5% precision at concentrations of 10 pmol ml(-1) or above.A significant positive correlation (P<0.001) was observed between particulate ATP (P-ATP) and D-ATP in water samples collected from Station ALOHA (22.75 degrees N, 158 degrees W; depth profiles 0-1000 m). The highest concentrations of dissolved nucleotides were found in the euphotic zone (0-175 m) below which the concentrations were low and relatively invariant. The dissolved nucleotide pools generally exceeded their corresponding particulate pools.Using radioisotopic tracer techniques and the new concentration method, turnover times for both particulate and dissolved nucleotides can be determined. The ability to measure concentrations and follow nucleotide tracers accurately in a very dilute environment provides a unique opportunity to address questions on microbial community metabolism, nutrient dynamics and energy flux.}, }
@article {pmid11572987, year = {2001}, author = {Remold, SK and Lenski, RE}, title = {Contribution of individual random mutations to genotype-by-environment interactions in Escherichia coli.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {20}, pages = {11388-11393}, pmid = {11572987}, issn = {0027-8424}, mesh = {Biological Evolution ; DNA Transposable Elements ; *Environment ; Escherichia coli/*genetics/growth &amp; development ; Genotype ; Glucose/metabolism ; Maltose/metabolism ; Models, Genetic ; *Mutation ; Selection, Genetic ; Temperature ; }, abstract = {Numerous studies have shown genotype-by-environment (GxE) interactions for traits related to organismal fitness. However, the genetic architecture of the interaction is usually unknown because these studies used genotypes that differ from one another by many unknown mutations. These mutations were also present as standing variation in populations and hence had been subject to prior selection. Based on such studies, it is therefore impossible to say what fraction of new, random mutations contributes to GxE interactions. In this study, we measured the fitness in four environments of 26 genotypes of Escherichia coli, each containing a single random insertion mutation. Fitness was measured relative to their common progenitor, which had evolved on glucose at 37 degrees C for the preceding 10,000 generations. The four assay environments differed in limiting resource and temperature (glucose, 28 degrees C; maltose, 28 degrees C; glucose, 37 degrees C; and maltose, 37 degrees C). A highly significant interaction between mutation and resource was found. In contrast, there was no interaction involving temperature. The resource interaction reflected much higher among mutation variation for fitness in maltose than in glucose. At least 11 mutations (42%) contributed to this GxE interaction through their differential fitness effects across resources. Beneficial mutations are generally thought to be rare but, surprisingly, at least three mutations (12%) significantly improved fitness in maltose, a resource novel to the progenitor. More generally, our findings demonstrate that GxE interactions can be quite common, even for genotypes that differ by only one mutation and in environments differing by only a single factor.}, }
@article {pmid11571165, year = {2001}, author = {Röling, WF and van Breukelen, BM and Braster, M and Lin, B and van Verseveld, HW}, title = {Relationships between microbial community structure and hydrochemistry in a landfill leachate-polluted aquifer.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {10}, pages = {4619-4629}, pmid = {11571165}, issn = {0099-2240}, mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Cloning, Molecular ; DNA, Ribosomal/analysis ; *Ecosystem ; Electrophoresis, Polyacrylamide Gel/methods ; Fresh Water/*chemistry/*microbiology ; Geologic Sediments/chemistry/microbiology ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; *Refuse Disposal ; Sequence Analysis, DNA ; *Water Pollution, Chemical ; }, abstract = {Knowledge about the relationship between microbial community structure and hydrogeochemistry (e.g., pollution, redox and degradation processes) in landfill leachate-polluted aquifers is required to develop tools for predicting and monitoring natural attenuation. In this study analyses of pollutant and redox chemistry were conducted in parallel with culture-independent profiling of microbial communities present in a well-defined aquifer (Banisveld, The Netherlands). Degradation of organic contaminants occurred under iron-reducing conditions in the plume of pollution, while upstream of the landfill and above the plume denitrification was the dominant redox process. Beneath the plume iron reduction occurred. Numerical comparison of 16S ribosomal DNA (rDNA)-based denaturing gradient gel electrophoresis (DGGE) profiles of Bacteria and Archaea in 29 groundwater samples revealed a clear difference between the microbial community structures inside and outside the contaminant plume. A similar relationship was not evident in sediment samples. DGGE data were supported by sequencing cloned 16S rDNA. Upstream of the landfill members of the beta subclass of the class Proteobacteria (beta-proteobacteria) dominated. This group was not encountered beneath the landfill, where gram-positive bacteria dominated. Further downstream the contribution of gram-positive bacteria to the clone library decreased, while the contribution of delta-proteobacteria strongly increased and beta-proteobacteria reappeared. The beta-proteobacteria (Acidovorax, Rhodoferax) differed considerably from those found upstream (Gallionella, Azoarcus). Direct comparisons of cloned 16S rDNA with bands in DGGE profiles revealed that the data from each analysis were comparable. A relationship was observed between the dominant redox processes and the bacteria identified. In the iron-reducing plume members of the family Geobacteraceae made a strong contribution to the microbial communities. Because the only known aromatic hydrocarbon-degrading, iron-reducing bacteria are Geobacter spp., their occurrence in landfill leachate-contaminated aquifers deserves more detailed consideration.}, }
@article {pmid11563384, year = {2001}, author = {Séka, MA and Cabooter, S and Verstraete, W}, title = {A test for predicting propensity of activated sludge to acute filamentous bulking.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {73}, number = {2}, pages = {237-242}, doi = {10.2175/106143001x139227}, pmid = {11563384}, issn = {1061-4303}, mesh = {Bacteria ; Cytoskeleton ; Particle Size ; Population Dynamics ; *Refuse Disposal ; *Sewage ; Water Movements ; }, abstract = {Filamentous bulking is a solid-liquid separation problem well known to activated-sludge plant operators. The use of curative additives is a rather delicate solution and the tools developed to anticipate it seem limited. To complement existing sludge sedimentation monitoring tools, a new test to assess the propensity of activated sludge for filamentous bulking was developed. It consists of challenging the sludges by feeding them under conditions favoring filamentous bacteria for 24 hours. The effects of such an acute treatment on sludge settleability is subsequently assessed through a simple sludge volume (SV30) measurement with reference to a control. The sludge can then be evaluated as prone to bulking (unstable sludge) or not (stable sludge). Such a test can be used to predict the occurrence of filamentous bulking in activated-sludge treatment plants. This so-called acute bulking test requires simple equipment and can be done by any wastewater treatment plant operator.}, }
@article {pmid11554604, year = {2001}, author = {Philips, S and Verstraete, W}, title = {Effect of repeated addition of nitrite to semi-continuous activated sludge reactors.}, journal = {Bioresource technology}, volume = {80}, number = {1}, pages = {73-82}, doi = {10.1016/s0960-8524(01)00066-9}, pmid = {11554604}, issn = {0960-8524}, mesh = {Bioreactors ; Diatoms ; Nitrites/*chemistry ; *Sewage ; }, abstract = {To a semi-continuous lab-scale activated sludge system (SCAS), nitrite was dosed discontinuously, i.e. together with the feed. The nitrite was added at a concentration (50 mg N/l) which had been found earlier not to cause acute inhibition of the general running of the reactors. Repeated nitrite addition, however, exerted an inhibitory effect which was reflected in decreased removal efficiencies and was also expressed in decreases in total respiratory and nitrifying activity of 20% and 40%, respectively. The inhibition by nitrite was reversible as removal efficiencies improved after ceasing nitrite addition. The two consecutive test runs revealed that addition of nitrite gave rise to high amounts of dispersed cells and free-swimming protozoa. Moreover, DGGE patterns confirmed a shift in microbial community structure upon application of nitrite.}, }
@article {pmid11549034, year = {2001}, author = {Willumsen, PA and Nielsen, JK and Karlson, U}, title = {Degradation of phenanthrene-analogue azaarenes by Mycobacterium gilvum strain LB307T under aerobic conditions.}, journal = {Applied microbiology and biotechnology}, volume = {56}, number = {3-4}, pages = {539-544}, doi = {10.1007/s002530100640}, pmid = {11549034}, issn = {0175-7598}, mesh = {Aerobiosis ; Biodegradation, Environmental ; Culture Media ; Mycobacterium/*growth &amp; development/*metabolism ; Phenanthrenes/*chemistry/*metabolism ; Phenanthridines/chemistry/metabolism ; Quinolines/chemistry/metabolism ; }, abstract = {A polycyclic aromatic hydrocarbon degrading Mycobacterium gilvum, strain LB307T, was able to degrade the azaarenes 5,6-benzoquinoline, 7,8-benzoquinoline, and phenanthridine (nitrogen-containing heterocyclic aromatic hydrocarbons) under aerobic conditions. The strain was able to use 5,6-benzoquinoline as sole sources of carbon, nitrogen, and energy. However, inhibition of degradation and growth was observed with increasing substrate concentration. During degradation, metabolites built up transiently. One of the metabolites detected during 5,6-benzoquinoline degradation is suggested to be 2-oxo-5,6-benzoquinoline. This is the first report on bacterial degradation of phenanthrene-analogue azaarenes.}, }
@article {pmid11549033, year = {2001}, author = {Dollhopf, SL and Hashsham, SA and Dazzo, FB and Hickey, RF and Criddle, CS and Tiedje, JM}, title = {The impact of fermentative organisms on carbon flow in methanogenic systems under constant low-substrate conditions.}, journal = {Applied microbiology and biotechnology}, volume = {56}, number = {3-4}, pages = {531-538}, doi = {10.1007/s002530100612}, pmid = {11549033}, issn = {0175-7598}, mesh = {Acetates/metabolism ; *Bioreactors ; Carbon/*metabolism ; DNA, Ribosomal/analysis ; Ecosystem ; Ethanol/metabolism ; Fermentation ; Glucose/metabolism ; Methane/*metabolism ; Molecular Sequence Data ; Polymorphism, Restriction Fragment Length ; Propionates/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Spirochaetaceae/classification/genetics/*isolation &amp; purification/metabolism ; Streptococcus/classification/genetics/*isolation &amp; purification/metabolism ; }, abstract = {We compared carbon flow under constant low-substrate conditions (below 20 microM glucose in situ) in laboratory-scale glucose-fed methanogenic bioreactors containing two very different microbial communities that removed chemical oxygen demand at similar rates. One community contained approximately equal proportions of spiral and cocci morphologies, while the other community was dominated by cocci. In the former bioreactor, over 50% of the cloned SSU rRNA genes and the most common SSU rDNA terminal restriction fragment corresponded to Spirochaetaceae-related sequences, while in the latter bioreactor over 50% of the cloned SSU rRNA genes and the most common SSU rDNA terminal restriction fragment corresponded to Streptococcus-related sequences. Carbon flow was assessed by measuring 14C-labeled metabolites derived from a feeding of [U-14C]glucose that did not alter the concentration of glucose in the bioreactors. Acetate and ethanol were detected in the Spirochaetaceae-dominated reactor, whereas acetate and propionate were detected in the Streptococcus-dominated reactor. A spirochete isolated from a Spirochaetaceae-dominated reactor fermented glucose to acetate, ethanol, and small amounts of lactate. Maximum substrate utilization assays carried out on fluid from the same reactor indicated that acetate and ethanol were rapidly utilized by this community. These data indicate that an acetate- and ethanol-based food chain was present in the Spirochaetaceae-dominated bioreactor, while the typical acetate- and propionate-based food chain was prevalent in the Streptococcus-dominated bioreactor.}, }
@article {pmid11549028, year = {2001}, author = {Xu, J and Verstraete, W}, title = {Evaluation of nitric oxide production by lactobacilli.}, journal = {Applied microbiology and biotechnology}, volume = {56}, number = {3-4}, pages = {504-507}, doi = {10.1007/s002530100616}, pmid = {11549028}, issn = {0175-7598}, mesh = {Arginine/metabolism ; Culture Media ; Lactobacillus/enzymology/growth &amp; development/*metabolism ; Nitrates/metabolism ; Nitric Oxide/*biosynthesis ; Nitric Oxide Synthase/metabolism ; Nitrite Reductases/metabolism ; Oxidation-Reduction ; }, abstract = {Six strains of Lactobacillus fermentum and Lactobacillus plantarum were investigated for nitric oxide (NO) production. First, the potential presence of NO synthase was examined. None of the strains of L. fermentum and L. plantarum examined produced NO from L-arginine under aerobic conditions. Interestingly, all L. fermentum strains expressed strong L-arginine deiminase activity. All L. fermentum strains produced NO in MRS broth, but the NO was found to be chemically derived from nitrite, which was produced by L. fermentum from nitrate present in the medium. Indeed all L. fermentum strains express nitrate reductase under anaerobic conditions. Moreover, one strain, L. fermentum LF1, had nitrate reductase activity under aerobic conditions. It was also found that L. fermentum strains JCM1173 and LF1 possessed ammonifying nitrite reductase. The latter strain also had denitrifying nitrite reductase activity at neutral pH under both anaerobic and aerobic conditions. The LF1 strain is thus capable of biochemically converting nitrate to NO. NO and nitrite produced from nitrate by lactobacilli may constitute a potential antimicrobial mechanism. studied in a rat acute liver injury model (Adawi et al. 1997). The results indicate that Lactobacillus plantarum DSM 9842 may possess NOS (Adawi et al. 1997). However, NO production from L-arginine has not been investigated in pure cultures of L. plantarum. According to the results of a 15N enrichment experiment, traces of (NO2-+NO3-)-N (total oxidised nitrogen: TON), which seemed to be formed by the resting cells of Lactobacillus fermentum IFO3956, appeared to be derived from L-arginine (Morita et al. 1997). Therefore, it was suggested that L. fermentum may possess a NOS. However, NO produced from L-arginine was not directly measured and a NOS inhibitor test was not performed by Morita et al. (1997). It is known that L-arginine deiminase (ADI) in bacteria may convert L-arginine to NH4+ (Cunin et al. 1986), which may be further oxidised to TON via nitrification by bacteria. Therefore, 15N enrichment experiments could not definitely conclude that L. fermentum possess NOS to convert L-arginine directly to NO. In this study, six Lactobacillus strains belonging to L. plantarum and L. fermentum were measured for NO production in MRS broth. The metabolism of nitrate and L-arginine by the Lactobacillus cell suspensions was also studied. The possibility that NO and nitrite production by lactobacilli may be a potential probiotic trait is also discussed.}, }
@article {pmid11548250, year = {2001}, author = {Beliavskaia, VA and Kashperova, TA and Bondarenko, VM and Il'ichev, AA and Sorokulova, IB and Malik, NI}, title = {[Experimental evaluation of the biological safety of gene-engineered bacteria using a model strain Bacillus subtilis interferon-producing strain].}, journal = {Zhurnal mikrobiologii, epidemiologii i immunobiologii}, volume = {}, number = {2}, pages = {16-20}, pmid = {11548250}, issn = {0372-9311}, mesh = {Animals ; Bacillus subtilis/*genetics/growth &amp; development/metabolism ; Bacteriological Techniques ; Cattle ; Chickens ; Gene Transfer, Horizontal ; Humans ; Interferon-alpha/*biosynthesis ; Intestines/microbiology ; Mice ; Polymerase Chain Reaction ; Probiotics/*adverse effects ; Salmonella typhimurium/growth &amp; development ; }, abstract = {The in vitro and in vivo evaluation of the biological and ecological safety of genetically modified bacteria (GMB) was carried out on B. subtilis recombinant strain 2335/105, capable of producing human interferon alpha-2, used as experimental model. As shown in this investigation made with the use of bacteriological analysis and polymerase chain reaction, the oral administration of GMB to calves, chickens and white mice produced no disturbances in the microbial ecology of the gastrointestinal tract of warm-blooded animals and did not lead to the appearance of spontaneous transformants. The present work is the first experimental evaluation of the biological safety of genetically modified microorganisms, used as the component of Subalin, a probiotic preparation intended for use in veterinary practice.}, }
@article {pmid11547879, year = {2001}, author = {Långmark, J and Ashbolt, NJ and Szewzyk, U and Stenström, TA}, title = {Adequacy of in situ glass slides and direct sand extractions to assess the microbiota within sand columns used for drinking water treatment.}, journal = {Canadian journal of microbiology}, volume = {47}, number = {7}, pages = {601-607}, pmid = {11547879}, issn = {0008-4166}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biofilms ; Colony Count, Microbial ; Filtration/instrumentation/methods ; Fresh Water/*microbiology ; Glass ; In Situ Hybridization, Fluorescence ; Indoles/metabolism ; Silicon Dioxide ; *Water Purification ; *Water Supply ; }, abstract = {Historically, Cholodny-Rossi buried glass slide techniques have been used to study the microbiota of subsurface environments, yet the bias of such a technique has not been compared against direct sand extraction using modern in situ probing. Over a period of 34 wk, four separate 4-m-deep sand columns receiving raw lake water were examined to compare direct extraction of sand filter biofilm material against in situ glass slide biofilms. Significantly different DAPI direct counts and fluorescent in situ hybridization signals for major phylogenetic groups were observed. Not only were lower proportions (P < 0.001) of EUB338-probed DAPI cells observed on in situ glass slides, but also fewer gamma-Proteobacteria (12%-21%) and more alpha-Proteobacteria (16%-33%) when compared to direct sand extracts. Hence, investigators of the microbial ecology of even simple sand biofilms must consider the inherent biases from "accepted" methods and seek further independent methods to identify those which may be most accurate.}, }
@article {pmid11544365, year = {2001}, author = {Kowalchuk, GA and Stephen, JR}, title = {Ammonia-oxidizing bacteria: a model for molecular microbial ecology.}, journal = {Annual review of microbiology}, volume = {55}, number = {}, pages = {485-529}, doi = {10.1146/annurev.micro.55.1.485}, pmid = {11544365}, issn = {0066-4227}, mesh = {Ammonia/economics/*metabolism ; Betaproteobacteria/metabolism ; Ecology ; *Environmental Microbiology ; Gram-Negative Chemolithotrophic Bacteria/genetics/isolation &amp; purification/*metabolism ; Nitrobacter/metabolism ; Nitrosomonas/metabolism ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/analysis ; }, abstract = {The eutrophication of many ecosystems in recent decades has led to an increased interest in the ecology of nitrogen transformation. Chemolitho-autotrophic ammonia-oxidizing bacteria are responsible for the rate-limiting step of nitrification in a wide variety of environments, making them important in the global cycling of nitrogen. These organisms are unique in their ability to use the conversion of ammonia to nitrite as their sole energy source. Because of the importance of this functional group of bacteria, understanding of their ecology and physiology has become a subject of intense research over recent years. The monophyletic nature of these bacteria in terrestrial environments has facilitated molecular biological approaches in studying their ecology, and progress in this field has been rapid. The ammonia-oxidizing bacteria of the beta-subclass Proteobacteria have become somewhat of a model system within molecular microbial ecology, and this chapter reviews recent progress in our knowledge of their distribution, diversity, and ecology.}, }
@article {pmid11542540, year = {1999}, author = {Smernoff, DT and Mancinelli, RL}, title = {Development of autonomous control in a closed microbial bioreactor.}, journal = {Advances in space research : the official journal of the Committee on Space Research (COSPAR)}, volume = {24}, number = {3}, pages = {319-328}, doi = {10.1016/s0273-1177(99)00318-x}, pmid = {11542540}, issn = {0273-1177}, mesh = {*Artificial Intelligence ; *Bioreactors ; Colony Count, Microbial ; Computers ; *Ecological Systems, Closed ; *Environmental Microbiology ; Equipment Design ; Life Support Systems/*instrumentation ; Nephelometry and Turbidimetry ; Nitrogen/chemistry/metabolism ; Pseudomonas fluorescens/growth &amp; development/metabolism ; Robotics ; Software ; Systems Integration ; Temperature ; }, abstract = {Space-based life support systems which include ecological components will rely on sophisticated hardware and software to monitor and control key system parameters. Autonomous closed artificial ecosystems are useful for research in numerous fields. We are developing a bioreactor designed to study both microbe-environment interactions and autonomous control systems. Currently we are investigating N-cycling and N-mass balance in closed microbial systems. The design features of the system involve real-time monitoring of physical parameters (e.g. temperature, light), growth solution composition (e.g. pH, NOx, CO2), cell density and the status of important hardware components. Control of key system parameters is achieved by incorporation of artificial intelligence software tools that permit autonomous decision-making by the instrument. These developments provide a valuable research tool for terrestrial microbial ecology, as well as a testbed for implementation of artificial intelligence concepts. Autonomous instrumentation will be necessary for robust operation of space-based life support systems, and for use on robotic spacecraft. Sample data acquired from the system, important features of software components, and potential applications for terrestrial and space research will be presented.}, }
@article {pmid11541393, year = {1998}, author = {Gu, JD and Roman, M and Esselman, T and Mitchell, R}, title = {The role of microbial biofilms in deterioration of space station candidate materials.}, journal = {International biodeterioration &amp; biodegradation}, volume = {41}, number = {1}, pages = {25-33}, pmid = {11541393}, issn = {0964-8305}, mesh = {*Bacterial Physiological Phenomena ; Biodegradation, Environmental ; *Biofilms ; Corrosion ; Environmental Microbiology ; Humidity ; *Materials Testing ; *Polymers ; Spacecraft/*instrumentation ; Temperature ; }, abstract = {Formation of microbial biofilms on surfaces of a wide range of materials being considered as candidates for use on the International Space Station was investigated. The materials included a fibre-reinforced polymeric composite, an adhesive sealant, a polyimide insulation foam, teflon cable insulation, titanium, and an aliphatic polyurethane coating. They were exposed to a natural mixed population of bacteria under controlled conditions of temperature and relative humidity (RH). Biofilms formed on the surfaces of the materials at a wide range of temperatures and RHs. The biofilm population was dominated by Pseudomonas aeruginosa, Ochrobactrum anthropi, Alcaligenes denitrificans, Xanthomonas maltophila, and Vibrio harveyi. The biocide, diiodomethyl-p-tolyl sulfone, impregnated in the polyurethane coating, was ineffective against microbial colonization and growth. Degradation of the polyurethane coatings was monitored with electrochemical impedance spectroscopy (EIS). The impedance spectra indicated that microbial degradation of the coating occurred in several stages. The initial decreases in impedance were due to the transport of water and solutes into the polymeric matrices. Further decreases were a result of polymer degradation by microorganisms. Our data showed that these candidate materials for space application are susceptible to biofilm formation and subsequent degradation. Our study suggests that candidate materials for use in space missions need to be carefully evaluated for their susceptibility to microbial biofilm formation and biodegradation.}, }
@article {pmid11525630, year = {2001}, author = {Muthumbi, W and Boon, N and Boterdaele, R and De Vreese, I and Top, EM and Verstraete, W}, title = {Microbial sulfate reduction with acetate: process performance and composition of the bacterial communities in the reactor at different salinity levels.}, journal = {Applied microbiology and biotechnology}, volume = {55}, number = {6}, pages = {787-793}, doi = {10.1007/s002530100623}, pmid = {11525630}, issn = {0175-7598}, mesh = {Acetates/*metabolism ; Anaerobiosis ; Bacteria/classification/genetics/growth &amp; development/*metabolism ; *Bioreactors ; Clostridium/classification/genetics/growth &amp; development/metabolism ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal/analysis/genetics ; Electrophoresis, Polyacrylamide Gel ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Oxidation-Reduction ; Pseudomonas/classification/genetics/growth &amp; development/metabolism ; RNA, Ribosomal, 16S/genetics ; Sodium Chloride/metabolism ; Sulfates/*metabolism ; Temperature ; }, abstract = {Microbial sulfate reduction with acetate as carbon source and electron donor was investigated at salinity levels between 0.53 and 1.48%. The experiment was carried out in a 2.3-1 upflow anaerobic sludge blanket reactor inoculated with granular methanogenic sludge. A pH of 8.3, a temperature of 32 +/- 1 degrees C and a chemical oxygen demand (COD)/SO4(2-)-S ratio of 2 were maintained in the reactor throughout the experiment. Sulfate reduction and the composition of the dominant bacterial communities in the reactor were monitored. The results showed that a maximal conversion rate for SO4(2-)-S of 14 g l(-1) day(-1) and a conversion efficiency of more than 90% were obtained at a salinity level of 1.26-1.39%. A further increase in the salinity level led to reactor instability. Denaturant gradient gel electrophoresis of 16S rDNA fragments amplified by PCR from total bacterial DNA extracted from the inoculum and reactor sludge showed that salinity level had an impact on the composition of the bacterial communities in the reactor. However, no clear relationship was found between reactor performance and the composition of the dominant bacterial communities in the reactor.}, }
@article {pmid11520616, year = {2001}, author = {Hansen, BM and Leser, TD and Hendriksen, NB}, title = {Polymerase chain reaction assay for the detection of Bacillus cereus group cells.}, journal = {FEMS microbiology letters}, volume = {202}, number = {2}, pages = {209-213}, doi = {10.1111/j.1574-6968.2001.tb10805.x}, pmid = {11520616}, issn = {0378-1097}, mesh = {Bacillus cereus/genetics/*isolation &amp; purification ; DNA Primers ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Food Microbiology ; Gram-Positive Bacterial Infections/microbiology ; Oryza/microbiology ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Recent investigations have shown that members of the Bacillus cereus group carry genes which have the potential to cause gastrointestinal and somatic diseases. Although most cases of diseases caused by the B. cereus group bacteria are relatively mild, it is desirable to be able to detect members of the B. cereus group in food and in the environment. Using 16S rDNA as target, a PCR assay for the detection of B. cereus group cells has been developed. Primers specific for the 16S rDNA of the B. cereus group bacteria were selected and used in combination with consensus primers for 16S rDNA as internal PCR procedure control. The PCR procedure was optimized with respect to annealing temperature. When DNA from the B. cereus group bacteria was present, the PCR assay yielded a B. cereus specific fragment, while when non-B. cereus prokaryotic DNA was present, the consensus 16S rDNA primers directed synthesis of the PCR products. The PCR analyses with DNA from a number of non-B. cereus confirmed the specificity of the PCR assay.}, }
@article {pmid11506276, year = {2001}, author = {Singleton, S and Cahill, JG and Watson, GK and Allison, C and Cummins, D and Thurnheer, T and Guggenheim, B and Gmür, R}, title = {A fully automated microscope bacterial enumeration system for studies of oral microbial ecology.}, journal = {Journal of immunoassay &amp; immunochemistry}, volume = {22}, number = {3}, pages = {253-274}, doi = {10.1081/IAS-100104710}, pmid = {11506276}, issn = {1532-1819}, mesh = {*Automation ; Bacteria/classification/isolation &amp; purification ; Colony Count, Microbial/*methods ; Evaluation Studies as Topic ; Humans ; Image Processing, Computer-Assisted ; Microscopy, Fluorescence/*instrumentation ; Mouth/*microbiology ; }, abstract = {A fast and fully automated image analysis technique for the enumeration of fluorescence-labeled bacteria in oral sampleswas developed. This paper describes the system configuration, application strategy, automated operation, and initial validation experiments using fluorescent microspheres, bacterial cultures, in vitro grown biofilms and human dental plaque. Following a series of brief operator-controlled calibration steps, the technique automatically performs all necessary microscope operations (stage translation, focus, sampling and analysis) on slides with up to 48 wells for as many different samples. It quantifies bacteria from differential interference contrast images, images showing cells that had been labeled by immunofluorescence with monoclonal antibodies, or images with cells labeled by a fluorescent DNA stain. With all evaluated samples, close agreement between the automated system and the assessor's visual counts was observed. This novel automated image grabbing and analysis procedure is applicable to the enumeration of specific taxa in clinical samples by both immunofluorescence and fluorescent in situ hybridization.}, }
@article {pmid11502244, year = {2001}, author = {Kleessen, B and Hartmann, L and Blaut, M}, title = {Oligofructose and long-chain inulin: influence on the gut microbial ecology of rats associated with a human faecal flora.}, journal = {The British journal of nutrition}, volume = {86}, number = {2}, pages = {291-300}, doi = {10.1079/bjn2001403}, pmid = {11502244}, issn = {0007-1145}, mesh = {Analysis of Variance ; Animals ; Butyrates/analysis/metabolism ; Cecum/microbiology ; Clostridium/isolation &amp; purification/metabolism ; Colon/microbiology ; Eubacterium/isolation &amp; purification/metabolism ; Fatty Acids, Volatile/analysis ; Feces/chemistry/*microbiology ; Germ-Free Life ; Humans ; Hydrogen-Ion Concentration ; Intestines/anatomy &amp; histology/*microbiology ; Inulin/*administration &amp; dosage ; Lactic Acid/analysis ; Lactobacillus/isolation &amp; purification/metabolism ; Male ; Oligosaccharides/*administration &amp; dosage ; Organ Size ; Random Allocation ; Rats ; Rats, Wistar ; }, abstract = {Dietary incorporation of fermentable, indigestible fructans may be of benefit to gastrointestinal health by providing short-chain fatty acids, stimulating the proliferation of bifidobacteria or lactobacilli and suppressing potential pathogenic organisms in the gut. We tested the hypothesis that the effects of fructans on caecal, colonic and faecal short-chain fatty acid concentration and microflora composition depend on their chain length. Germ-free rats associated with a human faecal flora were randomly assigned to one of four treatments as follows: (1) commercial standard diet as a control (Con); (2) Con+50 g short-chain oligofructose/kg (OF); (3) C+50 g long-chain inulin/kg (lcIN); or (4) Con+50 g OF-lcIN/kg (Mix OF-lcIN). Changes in bacterial population groups in response to feeding these diets were investigated with 16S rRNA-targeted probes applied in in situ hybridization. Mix OF-lcIN- and lcIN-containing diets resulted in larger numbers of caecal, colonic and faecal bacteria of the Clostridium coccoides-Eubacterium rectale cluster than Con (10.6 and 10.3 v. 9.5 log10/g wet wt), whereas OF alone did not affect this bacterial group in caecum, colon or faeces. A bifidogenic effect was only observed in the colon and faeces of OF-treated rats. More lactobacilli were found in caecal and colonic contents of Mix OF-lcIN-fed rats and in faeces of OF-fed rats compared with Con. Mix OF-lcIN and OF led to significantly smaller numbers of caecal, colonic and faecal bacteria belonging to the Clostridium histolyticum and C. lituseburense groups than Con (6.8 and 6.9 v. 7.9 log10/g wet wt). Counts of total bacteria, Bacteroides-Prevotella and Enterobacteriaceae did not differ between the groups. OF and/or lcIN-containing diets significantly increased the caecal and colonic concentration of butyrate and its relative molar proportion. Only lcIN-containing diets resulted in a higher faecal concentration of butyrate than Con. Higher molar proportions of faecal butyrate were observed with all diets that had been supplemented with OF and/or lcIN. Stimulation of butyrate production could be of interest for the prevention of ulcerative colitis and colon cancer.}, }
@article {pmid11499578, year = {2001}, author = {Roels, J and Verstraete, W}, title = {Biological formation of volatile phosphorus compounds.}, journal = {Bioresource technology}, volume = {79}, number = {3}, pages = {243-250}, doi = {10.1016/s0960-8524(01)00032-3}, pmid = {11499578}, issn = {0960-8524}, mesh = {Chromatography, Gas ; Environmental Monitoring ; Insecticides/analysis/*chemistry ; Iron/*metabolism ; Methane/chemistry ; Oxidation-Reduction ; Phosphines/analysis/*chemistry ; Phosphorus Compounds/*chemistry ; Thermodynamics ; Volatilization ; Water Microbiology ; }, abstract = {Phosphine and phosphides are reported to occur at numerous environmental sites such as fresh and marine sediments, landfills, faecal matter, biogas digesters and soils. The concentrations are several log units lower than the time-weighted average exposure standard, i.e. in the order of ng per m3 of gas or ng per kg material. Research about the biological formation of highly reduced gaseous phosphorus compounds dates back more than a hundred years. The early reports had to deal with a lot of scepticism. Thanks to new analytical tools (gas chromatography) it has become clear, during the last decade, that phosphine is a global constituent of the atmosphere. Pure strains of micro-organisms cultivated under highly anaerobic conditions were shown to produce phosphine. Thermodynamic considerations indicate that it is very improbable that the reduction of phosphate to phosphine is endergonic. Therefore the generation of phosphine cannot be compared with sulphidogenesis and methanogenesis. There seems to be a link between the existence of highly reactive gaseous phosphorus compounds and increased levels of metal corrosion. The reactive compounds could be formed by micro-organisms or they are liberated from phosphorus-containing impurities in the iron by the action of bacterial metabolites. The biochemical pathways responsible for the production of gaseous phosphorus compounds have not been characterised yet.}, }
@article {pmid11485867, year = {2001}, author = {De Boever, P and Demaré, W and Vanderperren, E and Cooreman, K and Bossier, P and Verstraete, W}, title = {Optimization of a yeast estrogen screen and its applicability to study the release of estrogenic isoflavones from a soygerm powder.}, journal = {Environmental health perspectives}, volume = {109}, number = {7}, pages = {691-697}, pmid = {11485867}, issn = {0091-6765}, mesh = {Biological Assay/methods ; Chlorophenols/chemistry ; Culture Techniques ; Cycloheximide/chemistry ; Digestive System/drug effects ; Estrogens, Non-Steroidal/adverse effects/*analysis ; Galactosides/chemistry ; Humans ; Isoflavones/*analysis ; Time Factors ; Yeasts/*physiology ; beta-Galactosidase/*biosynthesis/metabolism ; }, abstract = {Here we describe a redesigned protocol of the yeast estrogen screen developed by Routledge and Sumpter. The redesigned test comprises two steps. First, a large amount of yeast with estrogenic compounds is incubated for 24 hr. Subsequently, a mixture of cycloheximide and the chromogenic substrate chlorophenol red-beta-d-galactopyranoside (CPRG) is added. The cycloheximide stops protein synthesis and allows for an end-point measurement of beta-galactosidase activity generated during the first 24 hr. CPRG is converted to chlorophenol red and reflects beta-galactosidase activity, which is indicative of the estrogenic activity. The modifications shorten the duration of the assay at least 1 day and avoid interference of the estrogenic CPRG or chlorophenol red. The redesigned and the original protocol were used to study the estrogenic activity of bisphenol A, methoxychlor, p,p'-DDT, and isoflavones (genistein, daidzein, and glycitein). Bisphenol A, methoxychlor, and genistein triggered higher levels of beta-galactosidase activity in the redesigned protocol. Estrogenic activity of p,p'-DDT could only be demonstrated with the redesigned protocol. Glycitein and daidzein failed to give a response with both protocols. We also studied deconjugation of beta-glycosidic isoflavones present in soygerm powder. Treatment of the soygerm powder with beta-glycosidase released isoflavones. The estrogenic response of the samples was confirmed with the redesigned protocol and correlated with the amount of genistein present. The release of isoflavones under conditions prevailing in the intestines was studied. Bacterial beta-glycosidase present in the large intestine released isoflavones, and moderate estrogenic activity could be demonstrated.}, }
@article {pmid11473591, year = {2001}, author = {Müller, T and Ulrich, A and Ott, EM and Müller, M}, title = {Identification of plant-associated enterococci.}, journal = {Journal of applied microbiology}, volume = {91}, number = {2}, pages = {268-278}, doi = {10.1046/j.1365-2672.2001.01373.x}, pmid = {11473591}, issn = {1364-5072}, mesh = {Bacterial Typing Techniques ; DNA, Bacterial/analysis/genetics ; Drug Resistance, Bacterial ; Electrophoresis, Polyacrylamide Gel/methods ; Enterococcus/classification/genetics/*isolation &amp; purification ; Phylogeny ; Poaceae/genetics/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {AIMS: Enterococcus isolates from forage grass were subjected to taxonomical investigations and tested for antibiotic resistance.<br><br>METHODS AND RESULTS: The identification procedure included phenotypic characterizations, restriction analyses of polymerase chain reaction-amplified 16S rDNA, whole-cell protein profile analyses and 16S rDNA sequence analyses. Agar diffusion tests were performed to detect antibiotic resistance.<br><br>CONCLUSION: The isolates were identified as belonging to the species Enterococcus faecium, Ent. mundtii, Ent. casseliflavus, Ent. faecalis and Ent. sulfureus. However, the majority of isolates differed distinctly in their restriction patterns from those of known species. They formed a group of a homogeneous 16S rDNA genotype (VI). The 16S rDNA sequence of a representative isolate revealed the closest relationship to the species Ent. faecalis (similarity of 97.4%). All isolates were sensitive to vancomycin, but almost all were resistant to gentamycin and streptomycin.<br><br>The taxonomical investigations suggest that the isolates of the 16S rDNA genotype VI represent a new plant-associated Enterococcus species.}, }
@article {pmid11472948, year = {2001}, author = {Gonzalez-Gil, G and Lens, PN and Van Aelst, A and Van As, H and Versprille, AI and Lettinga, G}, title = {Cluster structure of anaerobic aggregates of an expanded granular sludge bed reactor.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {8}, pages = {3683-3692}, pmid = {11472948}, issn = {0099-2240}, mesh = {Acetates/metabolism ; Bacteria, Anaerobic/classification/genetics/*physiology ; *Bacterial Adhesion ; Biomass ; *Bioreactors ; Deltaproteobacteria/classification/genetics/physiology ; Euryarchaeota/classification/genetics/physiology ; In Situ Hybridization, Fluorescence ; Magnetic Resonance Spectroscopy ; Methane/metabolism ; Microscopy, Electron, Scanning ; Sewage/*microbiology ; *Waste Disposal, Fluid/instrumentation/methods ; }, abstract = {The metabolic properties and ultrastructure of mesophilic aggregates from a full-scale expanded granular sludge bed reactor treating brewery wastewater are described. The aggregates had a very high methanogenic activity on acetate (17.19 mmol of CH(4)/g of volatile suspended solids [VSS].day or 1.1 g of CH(4) chemical oxygen demand/g of VSS.day). Fluorescent in situ hybridization using 16S rRNA probes of crushed granules showed that 70 and 30% of the cells belonged to the archaebacterial and eubacterial domains, respectively. The spherical aggregates were black but contained numerous whitish spots on their surfaces. Cross-sectioning these aggregates revealed that the white spots appeared to be white clusters embedded in a black matrix. The white clusters were found to develop simultaneously with the increase in diameter. Energy-dispersed X-ray analysis and back-scattered electron microscopy showed that the whitish clusters contained mainly organic matter and no inorganic calcium precipitates. The white clusters had a higher density than the black matrix, as evidenced by the denser cell arrangement observed by high-magnification electron microscopy and the significantly higher effective diffusion coefficient determined by nuclear magnetic resonance imaging. High-magnification electron microscopy indicated a segregation of acetate-utilizing methanogens (Methanosaeta spp.) in the white clusters from syntrophic species and hydrogenotrophic methanogens (Methanobacterium-like and Methanospirillum-like organisms) in the black matrix. A number of physical and microbial ecology reasons for the observed structure are proposed, including the advantage of segregation for high-rate degradation of syntrophic substrates.}, }
@article {pmid11472947, year = {2001}, author = {Cho, JC and Tiedje, JM}, title = {Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {8}, pages = {3677-3682}, pmid = {11472947}, issn = {0099-2240}, mesh = {DNA, Bacterial/analysis/genetics ; *Genome, Bacterial ; Nucleic Acid Hybridization/methods ; Oligonucleotide Array Sequence Analysis/*methods ; Pseudomonas/*classification/*genetics ; Reproducibility of Results ; }, abstract = {Whole genomic DNA-DNA hybridization has been a cornerstone of bacterial species determination but is not widely used because it is not easily implemented. We have developed a method based on random genome fragments and DNA microarray technology that overcomes the disadvantages of whole-genome DNA-DNA hybridization. Reference genomes of four fluorescent Pseudomonas species were fragmented, and 60 to 96 genome fragments of approximately 1 kb from each strain were spotted on microarrays. Genomes from 12 well-characterized fluorescent Pseudomonas strains were labeled with Cy dyes and hybridized to the arrays. Cluster analysis of the hybridization profiles revealed taxonomic relationships between bacterial strains tested at species to strain level resolution, suggesting that this approach is useful for the identification of bacteria as well as determining the genetic distance among bacteria. Since arrays can contain thousands of DNA spots, a single array has the potential for broad identification capacity. In addition, the method does not require laborious cross-hybridizations and can provide an open database of hybridization profiles, avoiding the limitations of traditional DNA-DNA hybridization.}, }
@article {pmid11472944, year = {2001}, author = {Tan, Z and Hurek, T and Vinuesa, P and Müller, P and Ladha, JK and Reinhold-Hurek, B}, title = {Specific detection of Bradyrhizobium and Rhizobium strains colonizing rice (Oryza sativa) roots by 16S-23S ribosomal DNA intergenic spacer-targeted PCR.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {8}, pages = {3655-3664}, pmid = {11472944}, issn = {0099-2240}, mesh = {Bradyrhizobium/classification/genetics/growth &amp; development/*isolation &amp; purification ; DNA Primers ; DNA, Ribosomal Spacer/*analysis ; Molecular Sequence Data ; Oryza/growth &amp; development/*microbiology ; Phylogeny ; Plant Roots/*microbiology ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Rhizobium/classification/genetics/growth &amp; development/*isolation &amp; purification ; Sequence Analysis, DNA ; }, abstract = {In addition to forming symbiotic nodules on legumes, rhizobial strains are members of soil or rhizosphere communities or occur as endophytes, e.g., in rice. Two rhizobial strains which have been isolated from root nodules of the aquatic legumes Aeschynomene fluminensis (IRBG271) and Sesbania aculeata (IRBG74) were previously found to promote rice growth. In addition to analyzing their phylogenetic positions, we assessed the suitability of the 16S-23S ribosomal DNA (rDNA) intergenic spacer (IGS) sequences for the differentiation of closely related rhizobial taxa and for the development of PCR protocols allowing the specific detection of strains in the environment. 16S rDNA sequence analysis (sequence identity, 99%) and phylogenetic analysis of IGS sequences showed that strain IRBG271 was related to but distinct from Bradyrhizobium elkanii. Rhizobium sp. (Sesbania) strain IRBG74 was located in the Rhizobium-Agrobacterium cluster as a novel lineage according to phylogenetic 16S rDNA analysis (96.8 to 98.9% sequence identity with Agrobacterium tumefaciens; emended name, Rhizobium radiobacter). Strain IRBG74 harbored four copies of rRNA operons whose IGS sequences varied only slightly (2 to 9 nucleotides). The IGS sequence analyses allowed intraspecies differentiation, especially in the genus Bradyrhizobium, as illustrated here for strains of Bradyrhizobium japonicum, B. elkanii, Bradyrhizobium liaoningense, and Bradyrhizobium sp. (Chamaecytisus) strain BTA-1. It also clearly differentiated fast-growing rhizobial species and strains, albeit with lower statistical significance. Moreover, the high sequence variability allowed the development of highly specific IGS-targeted nested-PCR assays. Strains IRBG74 and IRBG271 were specifically detected in complex DNA mixtures of numerous related bacteria and in the DNA of roots of gnotobiotically cultured or even of soil-grown rice plants after inoculation. Thus, IGS sequence analysis is an attractive technique for both microbial ecology and systematics.}, }
@article {pmid11472524, year = {2001}, author = {Kielemoes, J and Verstraete, W}, title = {Influence of copper-alloying of austenitic stainless steel on multi-species biofilm development.}, journal = {Letters in applied microbiology}, volume = {33}, number = {2}, pages = {148-152}, doi = {10.1046/j.1472-765x.2001.00967.x}, pmid = {11472524}, issn = {0266-8254}, mesh = {Bacteria/*growth &amp; development ; *Bacterial Adhesion ; Biofilms/*growth &amp; development ; Colony Count, Microbial ; Copper/*chemistry ; Microscopy, Fluorescence ; Stainless Steel/*chemistry/standards ; }, abstract = {AIMS: To investigate the bactericidal influence of copper-alloying of stainless steel on microbial colonization.<br><br>METHODS AND RESULTS: Inhibition of bacterial adherence was investigated by monitoring (192 h) the development of a multi-species biofilm on Cu-alloyed (3.72 wt%) stainless steel in a natural surface water. During the first 120 h of exposure, lower numbers of viable bacteria in the water in contact with copper-containing steel relative to ordinary stainless steel were observed. Moreover, during the first 48 h of exposure, lower colony counts were found in the biofilm adhering to the Cu-alloyed steel. No lower colony or viable counts were found throughout the remainder of the experimental period.<br><br>CONCLUSION: The presence of Cu in the steel matrix impedes the adhesion of micro-organisms during an initial period (48 h), while this bactericidal effect disappears after longer incubation periods.<br><br>The application of Cu-alloyed stainless steels for bactericidal purposes should be restricted to regularly-cleaned surfaces.}, }
@article {pmid11471700, year = {2001}, author = {Seka, AM and Van De Wiele, T and Verstraete, W}, title = {Feasibility of a multi-component additive for efficient control of activated sludge filamentous bulking.}, journal = {Water research}, volume = {35}, number = {12}, pages = {2995-3003}, doi = {10.1016/s0043-1354(00)00589-3}, pmid = {11471700}, issn = {0043-1354}, mesh = {Bacteria/growth &amp; development ; Biodegradation, Environmental ; Coagulants/pharmacology ; Feasibility Studies ; Flocculation ; Macromolecular Substances ; Microscopy ; Oxygen/metabolism ; Polymers/*pharmacology ; Quaternary Ammonium Compounds/*pharmacology ; Sewage/*chemistry/*microbiology ; Talc/*pharmacology ; Water Microbiology ; Water Purification/*methods ; }, abstract = {Instantaneous improvement of the settling of bulking filamentous activated sludge can be achieved by the addition of a polymer or a large amount (up to 100% of the MLSS concentration) of talc powder to the sludge. Long-term improvement relies on repeated additions, as these additives have no adverse effects on the causative filaments. A multi-component additive was compared to the traditional additives in lab-scale activated sludge units using three highly filamentous sludges from different industrial treatment plants. The study demonstrated that the multi-component additive was superior to the traditional remedies. It was shown that, in the case of severe filamentous bulking, a single addition of the new additive immediately improved sludge settling and exerted a destructive effect on the causative filamentous bacteria. Thus, the latter additive also ensured a long-term sludge sedimentation improvement. The traditional additives exhibited an immediate and short-term effect. The novel additive also retarded sludge rising due to denitrification and it improved sludge dewaterability. The study revealed Nostocoido limicola II, with slightly hydrophobic cell wall, to be somewhat resistant to the quaternary ammonium salt present as biocide in the additive.}, }
@article {pmid11464766, year = {2001}, author = {Dewettinck, T and Van Houtte, E and Geenens, D and Van Hege, K and Verstraete, W}, title = {HACCP (Hazard Analysis and Critical Control Points) to guarantee safe water reuse and drinking water production--a case study.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {43}, number = {12}, pages = {31-38}, pmid = {11464766}, issn = {0273-1223}, mesh = {Conservation of Natural Resources ; Environmental Monitoring ; Humans ; *Models, Theoretical ; *Public Health ; Risk Assessment ; Viruses ; *Waste Disposal, Fluid ; *Water Supply ; }, abstract = {To obtain a sustainable water catchment in the dune area of the Flemish west coast, the integration of treated domestic wastewater in the existing potable water production process is planned. The hygienic hazards associated with the introduction of treated domestic wastewater into the water cycle are well recognised. Therefore, the concept of HACCP (Hazard Analysis and Critical Control Points) was used to guarantee hygienically safe drinking water production. Taking into account the literature data on the removal efficiencies of the proposed advanced treatment steps with regard to enteric viruses and protozoa and after setting high quality limits based on the recent progress in quantitative risk assessment, the critical control points (CCPs) and points of attention (POAs) were identified. Based on the HACCP analysis a specific monitoring strategy was developed which focused on the control of these CCPs and POAs.}, }
@article {pmid11452367, year = {2000}, author = {Kuiarov, AV and Vorob'ev, AA and Nesvizhskiĭ, IuV}, title = {[Possibility of participation of bacterial factor in the correction of histamine metabolism in the body].}, journal = {Voprosy pitaniia}, volume = {69}, number = {6}, pages = {22-24}, pmid = {11452367}, issn = {0042-8833}, mesh = {Adult ; Amine Oxidase (Copper-Containing)/metabolism ; Animals ; Antigens, Bacterial/immunology ; Bacteria/*immunology/isolation &amp; purification/metabolism ; Basophils/immunology/metabolism ; Birds ; Cells, Cultured ; Child ; Colitis, Ulcerative/etiology/immunology/metabolism ; Crohn Disease/etiology/immunology/metabolism ; Digestive System/metabolism/microbiology ; Duodenal Ulcer/etiology/immunology/metabolism ; Ecology ; Food Hypersensitivity/immunology/metabolism ; Gastric Mucosa/immunology/metabolism ; Germ-Free Life ; Histamine/biosynthesis/*metabolism/physiology ; Humans ; Hypersensitivity/etiology/*immunology/metabolism ; Immunoglobulin E/immunology ; Inflammation Mediators/physiology ; Lectins/immunology/physiology ; Mast Cells/immunology/metabolism ; Rats ; }, abstract = {Microbial factor belongs a significant role in mechanisms of regulation of contents free histamine in the organism. Magnified amounts this mediator connected with the condition of microbial ecology, can stimulate a number of pathophysiological effects. This dictates need of further studying dug autoflora master in processes of accumulation free histamine in the organism and their correction.}, }
@article {pmid11451518, year = {2001}, author = {Stach, JE and Bathe, S and Clapp, JP and Burns, RG}, title = {PCR-SSCP comparison of 16S rDNA sequence diversity in soil DNA obtained using different isolation and purification methods.}, journal = {FEMS microbiology ecology}, volume = {36}, number = {2-3}, pages = {139-151}, doi = {10.1111/j.1574-6941.2001.tb00834.x}, pmid = {11451518}, issn = {1574-6941}, abstract = {This study compared different methods of direct DNA extraction and purification from a silt loam soil and investigated the relationship between DNA quantity and sequence diversity. Five extraction methods and four purification techniques were investigated. Quantities of DNA extracted were between 3.4+/-0.55 and 54.3+/-8.18 &amp;mgr;g g(-1) (dry wt) of soil with OD(260)/OD(230) purity ratios between 0.80 and 1.15. Analysis of sequence diversity in all extracts was conducted using PCR-single strand conformation polymorphism (SSCP). Profiles generated using universal 16S rDNA primers (Com1/Com2) were found to be identical when used to amplify 16S rDNA extracted directly from soil. The genus Pseudomonas was targeted in order to reduce profile complexity, which was apparent when using universal 16S rDNA primers, and which hindered direct comparison of sequence diversity. A Pseudomonas culture library and non-cultured Pseudomonas 16S rDNA genes were used to provide a background count of Pseudomonas operational taxonomic units present in the soil. Cloning and sequencing of amplicons generated using a Pseudomonas-specific (Ps-for) and a universal 16S rDNA (Com2) primer, coupled with nested amplification (Com1/Com2 amplification from Ps-for/Ps-rev amplicons), used in conjunction with SSCP, revealed that environmental contaminants co-extracted with DNA, such as humic acid, significantly reduced primer specificity. SSCP was sensitive enough to reveal template bias in different primer sets. PCR-restriction fragment length-SSCP of Pseudomonas 16S rDNA amplified from soil-extracted DNA revealed distinct differences in sequence representation between extraction methods and showed that greater DNA yield is not synonymous with higher sequence diversity. We, therefore, suggest that DNA extractions from soil should be evaluated not only in terms of quantity and purity, but also in terms of the sequence diversity present. SSCP proved to be a valuable tool for the assessment of the methodologies commonly used in PCR-mediated microbial ecology studies.}, }
@article {pmid11450854, year = {2001}, author = {Rasmussen, MA and Casey, TA}, title = {Environmental and food safety aspects of Escherichia coli O157:H7 infections in cattle.}, journal = {Critical reviews in microbiology}, volume = {27}, number = {2}, pages = {57-73}, doi = {10.1080/20014091096701}, pmid = {11450854}, issn = {1040-841X}, mesh = {Animals ; Cattle ; Cattle Diseases/*microbiology ; Disease Reservoirs ; Ecosystem ; Environmental Microbiology ; Escherichia coli Infections/microbiology/*veterinary ; Escherichia coli O157/*pathogenicity ; Eukaryota/microbiology ; Food Microbiology ; Humans ; Safety ; United States ; Virulence ; }, abstract = {The presence of E. coli O157:H7 in cattle illustrates the complex, interrelated nature of the environment, livestock production practices, food safety, and the science of microbiology, particularly microbial ecology. Enterohemorrhagic E. coli, including E. coli O157:H7, can cause severe human diseases that can be debilitating and life threatening. Cattle are currently considered to be the definitive source for E. coli O157:H7 in the food supply, but this view may be simplistic and incomplete. E. coli O157:H7, appears widespread among U.S. cattle herds, while individual animal prevalence is low and transient. Most individual animals appear to be a transient reservoir for E. coli O157:H7 although the issue of carrier animals still remains unresolved. Epidemiological studies of the cattle production system have not clearly identified risk factors or management practices that affect E. coli O157:H7 prevalence in cattle feces. The problem of E. coli O157:H7 increases during the summer and fall months, but the environmental factors that contribute to this increase are poorly understood. Possible environmental factors that may influence E. coli O157:H7 shedding in cattle include livestock feed and waste handling practices as well as insects and microbial interactions in soil and water. Studies of E. coli O157:H7 ecology in cattle and the environment have been limited, but they suggest that a consideration of other independent, environmental sources of this microbe seems appropriate. The natural ecology of cholera may serve as a useful environmental model for pursuing additional environmental research on the occurrence and transmission of E. coli O157:H7 in nature.}, }
@article {pmid11439993, year = {2001}, author = {Cantekin, EI}, title = {alpha Streptococci and recurrences of otitis media. Tampering with microbial ecology is risky.}, journal = {BMJ (Clinical research ed.)}, volume = {322}, number = {7301}, pages = {1543; author reply 1543-4}, pmid = {11439993}, issn = {0959-8138}, mesh = {Acute Disease ; Anti-Bacterial Agents/*adverse effects ; Antibiosis/*drug effects ; Child ; Humans ; Otitis Media/*drug therapy/microbiology ; Recurrence ; Research Design ; }, }
@article {pmid11431569, year = {2001}, author = {Lilburn, TG and Kim, KS and Ostrom, NE and Byzek, KR and Leadbetter, JR and Breznak, JA}, title = {Nitrogen fixation by symbiotic and free-living spirochetes.}, journal = {Science (New York, N.Y.)}, volume = {292}, number = {5526}, pages = {2495-2498}, doi = {10.1126/science.1060281}, pmid = {11431569}, issn = {0036-8075}, mesh = {Acetylene/metabolism ; Animals ; Cattle ; Culture Media ; Digestive System/microbiology ; Genes, Bacterial ; Geologic Sediments/microbiology ; Humans ; Hydrogen/pharmacology ; Isoptera/*microbiology ; Nitrogen/metabolism ; Nitrogen Fixation/*genetics ; Nitrogenase/chemistry/genetics/metabolism ; Oxidation-Reduction ; Oxidoreductases/chemistry/genetics/metabolism ; Oxygen/pharmacology ; Spirochaeta/classification/genetics/growth &amp; development/*metabolism ; Spirochaetaceae/genetics/metabolism ; *Symbiosis ; Treponema/classification/genetics/growth &amp; development/*metabolism ; }, abstract = {Spirochetes from termite hindguts and freshwater sediments possessed homologs of a nitrogenase gene (nifH) and exhibited nitrogenase activity, a previously unrecognized metabolic capability in spirochetes. Fixation of 15-dinitrogen was demonstrated with termite gut Treponema ZAS-9 and free-living Spirochaeta aurantia. Homologs of nifH were also present in human oral and bovine ruminal treponemes. Results implicate spirochetes in the nitrogen nutrition of termites, whose food is typically low in nitrogen, and in global nitrogen cycling. These results also proffer spirochetes as a likely origin of certain nifHs observed in termite guts and other environments that were not previously attributable to known microbes.}, }
@article {pmid11430649, year = {2001}, author = {Cooper, VS and Bennett, AF and Lenski, RE}, title = {Evolution of thermal dependence of growth rate of Escherichia coli populations during 20,000 generations in a constant environment.}, journal = {Evolution; international journal of organic evolution}, volume = {55}, number = {5}, pages = {889-896}, doi = {10.1554/0014-3820(2001)055[0889:eotdog]2.0.co;2}, pmid = {11430649}, issn = {0014-3820}, mesh = {Adaptation, Physiological ; *Biological Evolution ; Environment, Controlled ; Escherichia coli/*genetics/*growth &amp; development/physiology ; Kinetics ; Models, Genetic ; Mutation ; Temperature ; }, abstract = {Twelve experimental populations of the bacterium Escherichia coli evolved for 20,000 generations in a defined medium at 37 degrees C. We measured their maximum growth rates across a broad range of temperatures and at several evolutionary time points to quantify the extent to which they became thermal specialists with diminished performance at other temperatures. We also sought to determine whether antagonistic pleiotropy (genetic trade-offs) or mutation accumulation (drift decay) was primarily responsible for any thermal specialization. Populations showed consistent improvement in growth rate at moderate temperatures (27-39 degrees C), but tended to have decreased growth rate at both low (20 degrees C) and high (41-42 degrees C) temperatures. Most loss occurred early in the experiment, when adaptation was most rapid. This dynamic is predicted by antagonistic pleiotropy but not by mutation accumulation. Several populations evolved high mutation rates due to defects in their DNA repair, but they did not subsequently undergo a greater decrease in growth rate at thermal extremes than populations that retained low mutation rates, contrary to the acceleration of decay predicted by mutation accumulation. Antagonistic pleiotropy therefore is more likely to be responsible for the evolution of thermal specialization observed in maximum growth rate.}, }
@article {pmid11429772, year = {2001}, author = {Andreatta, S and Wallinger, MM and Posch, T and Psenner, R}, title = {Detection of subgroups from flow cytometry measurements of heterotrophic bacterioplankton by image analysis.}, journal = {Cytometry}, volume = {44}, number = {3}, pages = {218-225}, doi = {10.1002/1097-0320(20010701)44:3&lt;218::aid-cyto1114&gt;3.0.co;2-7}, pmid = {11429772}, issn = {0196-4763}, mesh = {Animals ; Bacteria/*classification ; Flow Cytometry/methods ; Image Processing, Computer-Assisted/methods ; Plankton/classification ; *Water Microbiology ; }, abstract = {BACKGROUND: Flow cytometry is an invaluable tool for the analysis of large series of samples in aquatic microbial ecology. However, analysis of the resulting data is often inefficient or does not reflect the complexity of natural communities. Because bacterioplankton assemblages frequently fall into several clusters with respect to their cellular properties, these subgroups seem to be a promising level of abstraction. Image analysis was used to detect clusters from flow cytometry data. The method was tested on a bacterial community under heavy protozoan grazing pressure.<br><br>METHODS: A bivariate histogram of flow cytometry data was transformed into a gray-scale image for image analysis. After low-pass filtration, regional maxima were delimited by a watershed algorithm. The resulting areas were then used as gates on the original measurements.<br><br>RESULTS: Three clusters could be detected from the bacterial assemblage. Protozoan grazing had a strong impact on the bacterial community, which could be analyzed in detail at the level of individual subgroups.<br><br>CONCLUSIONS: Investigation at the level of bacterial subgroups allowed a more detailed analysis than whole-community statistics and delivered essential and ecologically meaningful information. Image analysis proved to be an adequate tool to detect the subgroups without a priori knowledge.}, }
@article {pmid11425760, year = {2001}, author = {Joulian, C and Ramsing, NB and Ingvorsen, K}, title = {Congruent phylogenies of most common small-subunit rRNA and dissimilatory sulfite reductase gene sequences retrieved from estuarine sediments.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {7}, pages = {3314-3318}, pmid = {11425760}, issn = {0099-2240}, mesh = {DNA, Bacterial/analysis/genetics ; Deltaproteobacteria/*classification/enzymology/genetics ; Electrophoresis/methods ; Genes, Bacterial ; *Genes, rRNA ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Oxidoreductases Acting on Sulfur Group Donors/*genetics ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Sulfur-Reducing Bacteria/*classification/enzymology/genetics ; }, abstract = {The diversity of sulfate-reducing bacteria (SRB) in brackish sediment was investigated using small-subunit rRNA and dissimilatory sulfite reductase (DSR) gene clone libraries and cultivation. The phylogenetic affiliation of the most commonly retrieved clones for both genes was strikingly similar and produced Desulfosarcina variabilis-like sequences from the inoculum but Desulfomicrobium baculatum-like sequences from a high dilution in natural media. Related organisms were subsequently cultivated from the site. PCR bias appear to be limited (or very similar) for the two primersets and target genes. However, the DSR primers showed a much higher phylogenetic specificity. DSR gene analysis is thus a promising and specific approach for investigating SRB diversity in complex habitats.}, }
@article {pmid11424729, year = {2001}, author = {Van Hege, K and Dewettinck, T and Verstraete, W}, title = {Pre-evaporative fenton remediation of treated municipal wastewater for reuse purposes.}, journal = {Environmental technology}, volume = {22}, number = {5}, pages = {523-532}, doi = {10.1080/09593332208618256}, pmid = {11424729}, issn = {0959-3330}, mesh = {*Conservation of Natural Resources ; Electronics ; Odorants/analysis ; Organic Chemicals ; Oxidation-Reduction ; Sodium Chloride/*chemistry ; Volatilization ; Waste Disposal, Fluid/*methods ; Water Pollutants, Chemical/*analysis ; }, abstract = {The present study explored the application of evaporative technology as an alternative desalination technique for wastewater treatment plant effluent. In the experiments carried out, it was shown that evaporation allowed for extensive decontamination of wastewater treatment plant effluent as most inorganic and organic contaminants were completely removed. Ammonia could be retained in the concentrate when pH was adjusted to values lower than 4; however this led to increased nitrite volatility due to the formation of nitric oxide. Using an electronic nose, it was observed that evaporation gave rise to a change in odour quality and quantity due to volatilisation of the volatile organic compounds present in the effluent. Remediation of these components was carried out by Fenton oxidation prior to evaporation. A high removal was observed under the applied conditions of Fe2+ = 25 mg l-1, H2O2 = 50 mg l-1, pH = 3 and a reaction time of 2 hours.}, }
@article {pmid11423943, year = {1999}, author = {Cavicchioli, R and Fegatella, F and Ostrowski, M and Eguchi, M and Gottschal, J}, title = {Sphingomonads from marine environments.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {23}, number = {4-5}, pages = {268-272}, doi = {10.1038/sj.jim.2900732}, pmid = {11423943}, issn = {1476-5535}, abstract = {Sphingomonas species play an important role in the ecology of a range of marine habitats. Isolates and 16S-rRNA clones have been obtained from corals, natural and artificial sources of marine hydrocarbons and eutrophic and oligotrophic waters, and have been isolated as hosts for marine phages. In addition they are found in oceans spanning temperature ranges from polar to temperate waters. While less is known about marine sphingomonads in comparison to their terrestrial counterparts, their importance in microbial ecology is evident. This is illustrated by, for example, the numerical dominance of strain RB2256 in oligotrophic waters. Furthermore, the known marine sphingomonads represent a phylogenetic cross-section of the Sphingomonas genus. This review focuses on our present knowledge of cultured isolates and 16S-rDNA clones from marine environments.}, }
@article {pmid11414335, year = {2001}, author = {Kalogo, Y and M'Bassiguié Séka, A and Verstraete, W}, title = {Enhancing the start-up of a UASB reactor treating domestic wastewater by adding a water extract of Moringa oleifera seeds.}, journal = {Applied microbiology and biotechnology}, volume = {55}, number = {5}, pages = {644-651}, doi = {10.1007/s002530000544}, pmid = {11414335}, issn = {0175-7598}, mesh = {Anaerobiosis ; Biomass ; *Bioreactors/microbiology ; Euryarchaeota/metabolism ; Flocculation ; Microscopy, Electron, Scanning ; Moringa oleifera/chemistry ; Plant Extracts/chemistry ; Seeds/chemistry ; Sewage ; *Waste Disposal, Fluid/instrumentation ; Water Microbiology ; }, abstract = {Water extract of Moringa oleifera seeds (WEMOS) was used to enhance the start-up of a self-inoculated upflow anaerobic sludge blanket (UASB) reactor treating raw domestic wastewater. Two reactors labelled control (RC) and WEMOS addition (RM) were started without special inoculum. Both reactors were fed continuously for 22 weeks with domestic wastewater containing an average total chemical oxygen demand (COD) of 320 mg O2/l and suspended solid (SS) of 165 mg/l. The reactors operated during the entire experimental period at 29 degrees C and at a hydraulic retention time (HRT) of 4 h. The RM reactor received 2 ml WEMOS per litre of influent. WEMOS solution was prepared on the basis of 2.5% (w/v) ground M. oleifera seeds in water. The results of 22 weeks' operation showed an improvement in the performance of the RM compared to that of the RC. The dosage of WEMOS in the feed (1) shortened the biological start-up period by 20%, (2) increased acidogenic and methanogenic activity by a factor of 2.4 and 2.2 respectively, (3) increased the specific biogas production by a factor of 1.6, (4) favoured fast growth of the sludge bed, and (5) allowed the aggregation of coccoid bacteria and growth of microbial nuclei, which are precursors of anaerobic granulation.}, }
@article {pmid11412916, year = {2001}, author = {Timms-Wilson, TM and Bailey, MJ}, title = {Reliable use of green fluorescent protein in fluorescent pseudomonads.}, journal = {Journal of microbiological methods}, volume = {46}, number = {1}, pages = {77-80}, doi = {10.1016/s0167-7012(01)00262-7}, pmid = {11412916}, issn = {0167-7012}, mesh = {Culture Media ; DNA Transposable Elements ; Escherichia coli/genetics/metabolism ; Ferric Compounds/pharmacology ; Fluorescence ; Green Fluorescent Proteins ; Luminescent Proteins/genetics/*metabolism ; Mutagenesis, Insertional ; Plasmids ; Pseudomonas fluorescens/genetics/isolation &amp; purification/*metabolism ; Siderophores/metabolism ; }, abstract = {When fluorescent pseudomonads are cultured on standard solid media under iron limiting conditions, they produce fluorescent, pigmented iron collating agents (siderophores). Siderophores can be readily identified by strong fluorescence seen under UV/blue light. The application of the eukaryotic green fluorescent protein (GFP) as a bacterial marker in microbial ecology is increasingly being used, particularly as it is a powerful method for non-destructive monitoring in situ. As gfp expressing bacteria have to be detected under UV/blue light, the fluorescence of siderophore-producing Pseudomonas spp. masks normal levels of GFP fluorescence when colonies are viewed on standard bacterial agar. Here, we describe a simple but effective way of identifying gfp-expressing Pseudomonas fluorescens using media supplemented with 0.45 mM FeSO(4).7H(2)O. This is of relevance for the screening of insertion libraries and in the application of GFP transposons as promoter probes.}, }
@article {pmid11412913, year = {2001}, author = {Edenborn, HM and Brickett, LA}, title = {Bacteria in gel probes: comparison of the activity of immobilized sulfate-reducing bacteria with in situ sulfate reduction in a wetland sediment.}, journal = {Journal of microbiological methods}, volume = {46}, number = {1}, pages = {51-62}, doi = {10.1016/s0167-7012(01)00261-5}, pmid = {11412913}, issn = {0167-7012}, mesh = {Acrylic Resins ; Cells, Immobilized ; Ferric Compounds/metabolism ; Gels ; Geologic Sediments/*microbiology ; Oxidation-Reduction ; *Soil Microbiology ; Sulfur-Reducing Bacteria/growth &amp; development/*metabolism ; }, abstract = {A novel method was used to examine the microbial ecology of iron-rich wetland sediments receiving neutral-pH coal mine drainage. Gel probes inserted into the sediments allowed analysis of the distribution and activity of bacterial sulfate reduction (BSR). A mixed population of sulfate-reducing bacteria enriched from anoxic wetland sediments was immobilized in low temperature-gelling agarose held in grooved rods or probes. The probes were inserted vertically into sediments and were allowed to incubate in situ for 48 h. After their retrieval, the gels were sectioned and analyzed for residual BSR activity and were compared to in situ BSR rates and chemical porewater profiles. The depth distribution of residual BSR activity in the immobilized cell gel probes differed significantly from the BSR measured in situ. Approximately 51% of the total integrated residual sulfate reduction activity measured in the gel probes occurred between 0 and 7 cm of the upper 20 cm of sediment. In contrast, ca. 99% of the integrated in situ BSR occurred between 7- and 20-cm depth, and only 1% of the total integrated rate occurred between 0- and 7-cm depth. Lactate-enriched bacteria immobilized in the gel may have been atypical of the majority of sulfate-reducing bacteria in the sediment. Agarose-immobilized sulfate-reducing bacteria might also be able to proliferate in the otherwise inhospitable zone of iron reduction, where sulfate and labile carbon compounds for which they are usually outcompeted can diffuse freely into the gel matrix. Gel probes containing particulate iron monosulfide (FeS) indicated that FeS remained stable in sediments at depths greater than 2 to 3 cm below the sediment-water interface, consistent with the shallow penetration of oxygen into surface sediments.}, }
@article {pmid11404100, year = {2001}, author = {Watanabe, K}, title = {Microorganisms relevant to bioremediation.}, journal = {Current opinion in biotechnology}, volume = {12}, number = {3}, pages = {237-241}, doi = {10.1016/s0958-1669(00)00205-6}, pmid = {11404100}, issn = {0958-1669}, mesh = {Anaerobiosis/physiology ; *Bacteria ; *Biodegradation, Environmental ; *Environmental Microbiology ; Hazardous Waste/analysis ; In Situ Hybridization, Fluorescence/methods ; Methane/chemistry/*metabolism ; Polycyclic Aromatic Hydrocarbons/metabolism ; Proteobacteria/metabolism ; RNA, Ribosomal, 16S/metabolism ; Trichloroethylene/metabolism ; Water Purification/methods ; }, abstract = {Naturally occurring microbial consortia have been utilized in a variety of bioremediation processes. Recent developments in molecular microbial ecology offer new tools that facilitate molecular analyses of microbial populations at contaminated and bioremediated sites. Information provided by such analyses aids in the evaluation of the effectiveness of bioremediation and the formulation of strategies that might accelerate bioremediation.}, }
@article {pmid11404099, year = {2001}, author = {Amann, R and Fuchs, BM and Behrens, S}, title = {The identification of microorganisms by fluorescence in situ hybridisation.}, journal = {Current opinion in biotechnology}, volume = {12}, number = {3}, pages = {231-236}, doi = {10.1016/s0958-1669(00)00204-4}, pmid = {11404099}, issn = {0958-1669}, mesh = {Bacteria/genetics/*isolation &amp; purification ; Environmental Microbiology ; Geologic Sediments/chemistry/microbiology ; In Situ Hybridization, Fluorescence/*methods ; Molecular Probes/chemistry ; RNA, Ribosomal, 16S/genetics/*physiology ; Sensitivity and Specificity ; Sewage/microbiology ; Symbiosis ; }, abstract = {Fluorescence in situ hybridisation (FISH) with rRNA-targeted oligonucleotide probes facilitates the rapid and specific identification of individual microbial cells in their natural environments. Over the past year there have been a number of methodological developments in this area and new applications of FISH in microbial ecology and biotechnology have been reported.}, }
@article {pmid11398430, year = {2001}, author = {Ramos, C and Licht, TR and Sternberg, C and Krogfelt, KA and Molin, S}, title = {Monitoring bacterial growth activity in biofilms from laboratory flow chambers, plant rhizosphere, and animal intestine.}, journal = {Methods in enzymology}, volume = {337}, number = {}, pages = {21-42}, doi = {10.1016/s0076-6879(01)37004-0}, pmid = {11398430}, issn = {0076-6879}, mesh = {Animals ; Biofilms/*growth &amp; development ; Intestines/microbiology ; Microbiological Techniques/instrumentation/methods ; Plants/microbiology ; }, }
@article {pmid11398404, year = {2001}, author = {Manz, W and Wagner, M and Kalmbach, S}, title = {Assessment of metabolic potential of biofilm-associated bacteria.}, journal = {Methods in enzymology}, volume = {336}, number = {}, pages = {265-276}, doi = {10.1016/s0076-6879(01)36595-3}, pmid = {11398404}, issn = {0076-6879}, mesh = {Autoradiography ; Bacteria/*metabolism ; Bacterial Physiological Phenomena ; *Biofilms/growth &amp; development ; Colony Count, Microbial ; Ecosystem ; Fluorescent Dyes ; In Situ Hybridization, Fluorescence ; Indoles ; Microscopy, Fluorescence ; Oxidation-Reduction ; Tetrazolium Salts/metabolism ; }, }
@article {pmid11394782, year = {2001}, author = {Dewettinck, T and Van Hege, K and Verstraete, W}, title = {The electronic nose as a rapid sensor for volatile compounds in treated domestic wastewater.}, journal = {Water research}, volume = {35}, number = {10}, pages = {2475-2483}, doi = {10.1016/s0043-1354(00)00530-3}, pmid = {11394782}, issn = {0043-1354}, mesh = {Adsorption ; Belgium ; *Biosensing Techniques ; Electronics ; Hot Temperature ; Metals/analysis ; Models, Chemical ; Models, Statistical ; Odorants/analysis ; Organic Chemicals/*analysis ; Oxides/analysis ; Reference Standards ; Reproducibility of Results ; Volatilization ; Waste Disposal, Fluid/instrumentation/*methods ; Water Pollutants, Chemical/*analysis ; Water Pollution/prevention &amp; control ; }, abstract = {An electronic nose consisting of 12 metal oxide sensors was used to monitor volatile compounds in effluent of a domestic wastewater treatment plant. Effluent and reference (deionized water) samples were heated to 60 and 90 degrees C to promote the volatilization and to increase the sensitivity. An effluent measuring campaign of 12 weeks was conducted and the repeatability and reproducibility of the procedure and the apparatus were determined. Processing the obtained fingerprints with principal component analysis (PCA) allowed interpretation and differentiation of the samples in terms of origin and quality, relative to the reference. To minimize the variance due to sensitivity fluctuations of the apparatus and to detect effluents with deviating qualities, two new concepts were defined, i.e. the relative sensorial odour perception (in short: rSOP) and the relative fingerprint. Correlations between the relative overall electronic nose output, expressed as rSOP, and selected routine parameters were weak except for the parameter "volatile suspended solids" (VSS), indicating adsorption of volatile organic compounds (VOCs) onto the organic particles. The results clearly demonstrate the possibility to use the electronic nose as a rapid alarm generator towards volatile compounds, e.g. in specific advanced treatment processes to produce reclaimed water from effluent of the domestic wastewater treatment plant under scrutiny.}, }
@article {pmid11392745, year = {2001}, author = {Yang, CK and Yang, SS}, title = {Microbial ecology of soils surrounding nuclear and thermal power plants in Taiwan.}, journal = {Environment international}, volume = {26}, number = {5-6}, pages = {315-322}, doi = {10.1016/s0160-4120(01)00006-x}, pmid = {11392745}, issn = {0160-4120}, mesh = {Environmental Monitoring ; Nitrogen Fixation ; Phosphates/metabolism ; Population Dynamics ; *Power Plants ; Seasons ; *Soil Microbiology ; Taiwan ; }, abstract = {This paper reports a study of the effect of three nuclear and one thermal power plants on the microbial ecology of soils. Populations of bacteria, actinomycetes, fungi, cellulolytic microbes, phosphate-solubilizing microbes and nitrogen-fixing microbes in the soil in the vicinity of each plant were studied. Soils were acidic at three sites, and moisture contents of the power plant soils were lower than those of the surrounding areas. Microbial populations of the topsoils (0-20 cm deep) were higher than the subsoils (21-40 cm deep), and only 10-15% of them showed significant difference (P < .05). Thirty-three percent of the samples from the surrounding areas had higher microbial population than those from the power plant areas, but 19% was the reverse. Populations of cellulolytic, phosphate-solubilizing and nitrogen-fixing microbes varied with sampling locations, season and environmental conditions. Ratios of cellulolytic, phosphate-solubilizing and nitrogen-fixing microbes to total viable counts in some samples of the surrounding areas were significantly higher than in the power plant areas. Although the microbial populations of power plant soil and its surrounding area were somewhat different, it cannot be attributed as an effect of power plant operation, as the differences were not consistent.}, }
@article {pmid11391466, year = {2001}, author = {Holguin, G and Glick, BR}, title = {Expression of the ACC Deaminase Gene fromEnterobacter cloacae UW4 in Azospirillum brasilense.}, journal = {Microbial ecology}, volume = {41}, number = {3}, pages = {281-288}, doi = {10.1007/s002480000040}, pmid = {11391466}, issn = {1432-184X}, abstract = {The ACC deaminase structural gene (acdS) from Enterobacter cloacae UW4 was cloned in the broad host range plasmid pRK415 under the control of the lac promoter and transferred into Azospirillum brasilense Cd and Sp245. A. brasilenseCd and Sp245 transformants showed high ACC deaminase activity, similar to that observed in Enterobacter cloacae UW4. The expression of ACC deaminase improved the existing growth promoting activity of Azospirillum. The roots of tomato and canola seedlings were significantly longer in plants inoculated with A. brasilense Cd transformants than those in plants inoculated with the nontransformed strains of the same bacterium. In the case of wheat seedlings, inoculation with A. brasilense Cd transformants did not promote root growth. The difference in plant response (canola and tomato versus wheat) is attributed to the greater sensitivity of canola and tomato plants to ethylene as compared to wheat plants.}, }
@article {pmid11391465, year = {2001}, author = {Eiland, F and Klamer, M and Lind, AM and Leth, M and Bååth, E}, title = {Influence of Initial C/N Ratio on Chemical and Microbial Composition during Long Term Composting of Straw.}, journal = {Microbial ecology}, volume = {41}, number = {3}, pages = {272-280}, doi = {10.1007/s002480000071}, pmid = {11391465}, issn = {1432-184X}, abstract = {Shredded straw of Miscanthus was composted in 800-L boxes with different amounts of pig slurry added as nitrogen source. The impact of the different initial C/N ratios (11, 35, 47, 50, and 54) on the composting process and the end product was evaluated by examining chemical and microbiological parameters during 12 months of composting. Low initial C/N ratios caused a fast degradation of fibers during the first three months of composting (hemicellulose: 50-80%, cellulose: 40-60%), while high initial C/N ratios resulted in 10-20% degradation of both hemicellulose and cellulose. These differences were reflected in the microbial biomass and respiration, which initially were higher in low C/N treatments than in high C/N treatments. After 12 months of composting, this situation was reversed. Composts with high initial C/N ratios had high microbial biomass (15-20 mg ATP g-1 OM) and respiration rates (200 mg CO2 h-1 g-1 OM) compared to treatments with low initial C/N ratios (less than 10 mg ATP g-1 OM and 25 mg CO2 h-1 g-1 OM). This could be explained by the microorganisms being nitrogen limited in the high C/N ratio treatments. In the low C/N ratio treatments, without nitrogen limitation, the high activity in the beginning decreased with time because of exhaustion of easily available carbon. Different nitrogen availability was also seen in the nitrification patterns, since nitrate was only measured in significant amounts in the treatments with initial C/N ratios of 11 and 35. The microbial community structure (measured as phospholipid fatty acid, PLFA, profile) was also affected by the initial C/N ratios, with lower fungal/bacterial ratios in the low compared to the high C/N treatments after 12 months of composting. However, in the low C/N treatments higher levels of PLFAs indicative of thermophilic gram-positive bacteria were found compared to the high C/N treatments. This was caused by the initial heating phase being longer in the low than in the high C/N treatments. The different fungal/bacterial ratios could also be explained by the initial heating phase, since a significant correlation between this ratio and heat generated during the initial composting phase was found.}, }
@article {pmid11391464, year = {2001}, author = {Ishigaki, T and Sleigh, MA}, title = {Grazing Characteristics and Growth Efficiencies at Two Different Temperatures for Three Nanoflagellates Fed with Vibrio Bacteria at Three Different Concentrations.}, journal = {Microbial ecology}, volume = {41}, number = {3}, pages = {264-271}, doi = {10.1007/s002480000060}, pmid = {11391464}, issn = {1432-184X}, abstract = {Small inocula of one of the flagellates Paraphysomonas imperforata, Pteridomonas danica, and Cafeteria roenbergensis were added to suspensions of the bacterium Vibrio natriegens at each of three concentrations between 107 and 108 cells ml-1 and incubated at each of the temperatures 10 degrees C and 25 degrees C. Samples were taken at intervals for counting the flagellates and bacteria to determine the timing of the maximum of flagellate numbers and the concentrations at that time. Measurements of the protein concentration of the suspensions during incubation were used to determine the gross growth efficiency (GGE) or yield of flagellate grazing in each experiment. The most effective grazer was Pteridomonas, followed by Paraphysomonas, with Cafeteria being least effective, as judged by the threshold bacterial concentrations at which flagellate multiplication ceased, which were about 2 x 105, 2 x 106, and 2 x 107, respectively, and by the finding that Pteridomonas consumed 99%, Paraphysomonas about 95%, and Cafeteria only 60-70% of the available bacteria in the experiments. Peak concentrations of flagellates were reached later at the lower temperature, but the numbers of flagellates produced and of bacteria eaten were of a similar order at the two temperatures and the GGE was only slightly higher at the lower temperature. The time taken to reach peak flagellate numbers changed little with a threefold increase in bacterial concentrations, but the GGE increased and the numbers of bacteria eaten to produce one flagellate decreased when the bacterial concentration was increased. The three flagellates show clear evidence of niche specialization in differences in thresholds of bacterial prey concentration.}, }
@article {pmid11391463, year = {2001}, author = {Chelius, MK and Triplett, EW}, title = {The Diversity of Archaea and Bacteria in Association with the Roots of Zea mays L.}, journal = {Microbial ecology}, volume = {41}, number = {3}, pages = {252-263}, doi = {10.1007/s002480000087}, pmid = {11391463}, issn = {1432-184X}, abstract = {The diversity of bacteria and archaea associating on the surface and interior of maize roots (Zea mays L.) was investigated. A bacterial 16S rDNA primer was designed to amplify bacterial sequences directly from maize roots by PCR to the exclusion of eukaryotic and chloroplast DNA. The mitochondrial sequence from maize was easily separated from the PCR-amplified bacterial sequences by size fractionation. The culturable component of the bacterial community was also assessed, reflecting a community composition different from that of the clone library. The phylogenetic overlap between organisms obtained by cultivation and those identified by direct PCR amplification of 16S rDNA was 48%. Only 4 bacterial divisions were found in the culture collection, which represented 27 phylotypes, whereas 6 divisions were identified in the clonal analysis, comprising 74 phylotypes, including a member of the OP10 candidate division originally described as a novel division level lineage in a Yellowstone hot spring. The predominant group in the culture collection was the actinobacteria and within the clone library, the a-proteobacteria predominated. The population of maize-associated proteobacteria resembled the proteobacterial population of a typical soil community within which resided a subset of specific plant-associated bacteria, such as Rhizobium- and Herbaspirillum-related phylotypes. The representation of phylotypes within other divisions (OP10 and Acidobacterium) suggests that maize roots support a distinct bacterial community. The diversity within the archaeal domain was low. Of the 50 clones screened, 6 unique sequence types were identified, and 5 of these were highly related to each other (sharing 98% sequence identity). The archaeal sequences clustered with good bootstrap support near Marine group I (crenarchaea) and with Marine group II (euryarchaea) uncultured archaea. The results suggest that maize supports a diverse root-associated microbial community composed of species that for the first time have been described as inhabitants of a plant-root environment.}, }
@article {pmid11391462, year = {2001}, author = {Fryar, SC and Yuen, TK and Hyde, KD and Hodgkiss, IJ}, title = {The Influence of Competition between Tropical Fungi on wood colonization in Streams.}, journal = {Microbial ecology}, volume = {41}, number = {3}, pages = {245-251}, doi = {10.1007/s002480000075}, pmid = {11391462}, issn = {1432-184X}, abstract = {Wood blocks inoculated with fungi were placed in a stream in order to investigate their interactions with the native mycota. Wood blocks were inoculated with single or paired isolates of tropical fungi, whereas no fungi were inoculated onto controls. After 3 months, the wood blocks were collected and the number of newly colonizing fungi were identified. More fungi were found on uninoculated than on wood blocks pre-inoculated with Chaetosphaeria sp. Neither Nais aquatica or Annulatascus velatisporus inhibited colonization when inoculated singly. However, in combination, they inhibited colonization by other fungi, indicating an interaction between the two species. Inoculated wood blocks were generally first colonized by hyphomycetes, with a low occurrence of ascomycetes. The study also showed that autoclaving wood for use in experiments affects the outcome of the experiments, i.e., affects the structure of the fungal community.}, }
@article {pmid11391461, year = {2001}, author = {Radajewski, S and Duxbury, T}, title = {Motility Responses and Desiccation Survival of Zoospores from the Actinomycete Kineosporia sp. Strain SR11.}, journal = {Microbial ecology}, volume = {41}, number = {3}, pages = {233-244}, doi = {10.1007/s002480000112}, pmid = {11391461}, issn = {1432-184X}, abstract = {During investigations into the effects of water availability on the ecology of leaf litter actinomycetes, a motile-spored strain (SR11) was isolated and identified as a Kineosporia sp. Observations of spore motility revealed they could achieve speeds up to 160 mm s?1. Chemotaxis was not observed toward several organic compounds, although K, Mg, and Ca salts of phosphate, sulfate, and halides elicited a positive response. The inability of all the corresponding Na salts, and KNO3, to act as attractants suggested that chemoattraction of SR11 spores toward inorganic compounds may be dependent on specific cations and anions. An unusual motility response to CO2 was also observed and a laminar-flow microchamber was designed and constructed to investigate this phenomenon. Increasing the CO2 concentration by as little as 0.3% (v/v) caused a rapid, synchronous arrest of spore motility. A 1% (v/v) decrease in CO2 concentration caused a similar response, although the duration of the pause was much longer. The survival responses of strain SR11 spores were observed following desiccation at various water potentials. At the highest water potential tested (-9 MPa), spore viability declined minimally during the first 24 hr but continued to decrease over 10 days. In contrast, desiccation at -87 MPa and below resulted in a 50% loss in viability within 2 hr and subsequent survival at this level of viability. Continued desiccation at -302 MPa indicated that spores were capable of long-term survival at low water potentials. Many of these responses are likely to be significant in determining the ecology of these motile-spored actinomycetes in leaf litter.}, }
@article {pmid11391460, year = {2001}, author = {Fuxa, JR and Matter, MM and Abdel-Rahman, A and Micinski, S and Richter, AR and Flexner, JL}, title = {Persistence and Distribution of Wild-Type and Recombinant Nucleopolyhedroviruses in Soil.}, journal = {Microbial ecology}, volume = {41}, number = {3}, pages = {222-231}, doi = {10.1007/s002480000088}, pmid = {11391460}, issn = {1432-184X}, abstract = {Persistence of recombinant and wild-type nucleopolyhedroviruses (NPV) was compared in field and laboratory microcosm experiments. Horizontal and vertical distribution of the viruses also was monitored in the field agricultural soil. Mixed populations of the bollworm, Helicoverpa zea, and tobacco budworm, Heliothis virescens, in cotton were sprayed five times during a growing season with wild-type H. zea NPV (HzSNPV.WT) or with a genetically modified H. zea NPV expressing an insect-specific neurotoxin (HzSNPV.LqhIT2). HzNPV.WT accumulated 2.3 times as many occlusion bodies (OB) as HzSNPV.LqhIT2 in soil by the end of the growing season in October 1997. Both NPVs were detected at all soil depths down to 26-35 cm. Both NPVs were randomly distributed among 0-2 cm soil samples throughout the plots according to analysis with Taylor's power law. By 4 August 1998, soil concentration of HzSNPV.WT was only 11-13 OB/g at depths from 0 to 14 cm, and the wild-type virus was not detected below 14 cm. HzSNPV.LqhIT2 was detected only in trace amounts at 0-2 cm at this time. Neither NPV was detected in bioassays of cotton leaves nor in insects sampled from the plots in 1998. Viral persistence also was monitored in laboratory soil microcosms. Three viruses-wild-type Autographa californica NPV (AcNPV.WT), A. californica NPV expressing a scorpion toxin (AcNPV.AaIT), and A. californica NPV expressing juvenile hormone esterase (AcNPV.JHE-S201G)-were introduced into soil microcosms by each of two methods, in water suspension or in host cadavers, for a total of six treatments plus controls. After 17 months, the number of viable OB remaining did not differ among the treatments. The results indicate that the only differences in soil populations of wild-type versus recombinant NPVs are due to the greater amounts of the wild-type viruses that accumulate, probably because they have a greater capacity to replicate in the host insect population.}, }
@article {pmid11391459, year = {2001}, author = {Ballyk, MM and Jones, DA and Smith, HL}, title = {Microbial Competition in Reactors with Wall Attachment.}, journal = {Microbial ecology}, volume = {41}, number = {3}, pages = {210-221}, doi = {10.1007/s002480000005}, pmid = {11391459}, issn = {1432-184X}, abstract = {Competition for nutrient and the ability of bacteria to colonize the gut wall are factors believed to play a role in the observed stability of the indigenous microbiota of the mammalian large intestine. These factors were incorporated into the two-strain continuous-stirred tank reactor (CSTR) model formulated and numerically investigated by Freter et al. In their model simulations, the reactor is parameterized using data for the mouse intestine. An invading bacterial strain is introduced into a CSTR that has already been colonized by a resident strain. The two strains compete for a single growth-limiting nutrient and for limited adhesion sites on the wall of the reactor. The mathematical model described in this paper is motivated in part by the CSTR model, but is based on the plug flow reactor (PFR). Parameter values and initial conditions are chosen so that the numerical performance of the PFR can be compared to that of the CSTR. In simulations bearing a remarkable qualitative and quantitative resemblance to those of the CSTR it is found that the invader is virtually eliminated, despite the fact that it has uptake rate and affinity for the wall identical to those of the resident. The PFR model is then parametrized using data for the human large intestine, and the two-strain simulations are repeated. Though obvious quantitative differences are noted, the more important qualitative outcome is preserved. It is also found that when three strains compete for a single nutrient and for adhesion sites there exists a steady-state solution characterized by the segregation of the bacterial strains into separate nonoverlapping segments along the wall of the reactor.}, }
@article {pmid11391458, year = {2001}, author = {Werker, AG and Hall, ER}, title = {Quantifying Population Dynamics Based on Community Structure Fingerprints Extracted from Biosolids Samples.}, journal = {Microbial ecology}, volume = {41}, number = {3}, pages = {195-209}, doi = {10.1007/s002480000024}, pmid = {11391458}, issn = {1432-184X}, abstract = {This paper presents a standardized metric for quantifying the rate change in community structure of complex mixed microbial cultures such as those maintained in biological wastewater treatment systems. Quantifying the stability of microbial community structures is a first step toward more aggressive monitoring and control of biological systems for greater reliability in contaminant removal. Statistical analysis of compositions that uniquely specify the balance of populations of species in a mixed culture sample can be used to specify a biosolids community state as a unique position in an orthogonal coordinate system. Changes in biosolids state are observable as a trajectory within this coordinate space, and the rate of passage along this trajectory relates to the population dynamics. The geometric interpretation and the statistical analysis methods necessary for the proposed calculation methodology are introduced by way of simulated case studies with a simple model system. With the example of this model system, concepts of changing microbial community shape and size are contrasted. The rate change in community structure is defined geometrically in terms of a rate change in relative proportions of the characteristic community shape at constant biomass. A change in biomass is defined as the rate change in the quantity of biosolids at constant shape. The method robustness with respect to random measurement error was also demonstrated using the model system. The potential applications of the approach are presented with experimental data of microbial fatty acid compositions extracted from samples during the operation of bench-scale bioreactors degrading contaminants found in pulp mill wastewater. Scaling the level of population dynamics with a metric that is independent of chemotypic content presents a standard for direct comparisons of community responses between distinct cultures and experiments.}, }
@article {pmid11391457, year = {2001}, author = {Liu, J and Dazzo, FB and Glagoleva, O and Yu, B and Jain, AK}, title = {CMEIAS: A Computer-Aided System for the Image Analysis of Bacterial Morphotypes in Microbial Communities.}, journal = {Microbial ecology}, volume = {41}, number = {3}, pages = {173-194}, doi = {10.1007/s002480000004}, pmid = {11391457}, issn = {1432-184X}, abstract = {A major challenge in microbial ecology is to develop reliable and facile methods of computer-assisted microscopy that can analyze digital images of complex microbial communities at single cell resolution, and compute useful quantitative characteristics of their organization and structure without cultivation. Here we describe a computer-aided interactive system to analyze the high degree of morphological diversity in growing microbial communities revealed by phase-contrast microscopy. The system, called "CMEIAS" (Center for Microbial Ecology Image Analysis System) consists of several custom plug-ins for UTHSCSA ImageTool, a free downloadable image analysis program operating on a personal computer in a Windows NT environment. CMEIAS uses various measurement features and two object classifiers to extract size and shape measurements of segmented, digital images of microorganisms and classify them into their appropriate morphotype. The first object classifier uses a single measurement feature to analyze relatively simple communities containing only a few morphotypes (e.g., regular rods, cocci, filaments). A second new hierarchical tree classifier uses an optimized subset of multiple measurement features to analyze significantly more complex communities containing greater morphological diversity than ever before possible. This CMEIAS shape classifier automatically categorizes each cell into one of 11 predominant bacterial morphotypes, including cocci, spirals, curved rods, U-shaped rods, regular straight rods, unbranched filaments, ellipsoids, clubs, rods with extended prostheca, rudimentary branched rods, and branched filaments. The training and testing images for development and evaluation of the CMEIAS classifier were obtained from 1,937 phase-contrast grayscale digital images of various diverse communities. The CMEIAS shape classifier had an accuracy of 96.0% on a training set of 1,471 cells and 97.0% on a test set of 4,270 cells representing all 11 bacterial morphotype classes, indicating that accurate classification of rich morphological diversity in microbial communities is now possible. An interactive edit feature was added to address the main sources of error in automatic shape classification, enabling the operator to inspect the assigned morphotype of each bacterium based on visual recognition of its distinctive pseudocolor, reassign it to another morphotype class if necessary, and add up to five other morphotypes to the classification scheme. The shape classifier reports on the number and types of different morphotypes present and the abundance among each of them, thus providing the data needed to compute the morphological diversity within the microbial community. An example of how CMEIAS can augment the analysis of microbial community structure is illustrated by studies of morphological diversity as an indicator of dynamic ecological succession following a nutrient shift-up perturbation in two continuously fed, anaerobic bioreactors with morphologically distinct start communities. Various steps to minimize the limitations of computer-assisted microscopy to classify bacterial morphotypes using CMEIAS are described. In summary, CMEIAS is an accurate, robust, flexible semiautomatic computing tool that can significantly enhance the ability to quantitate bacterial morphotype diversity and should serve as a useful adjunct to the analysis of microbial community structure. This first version of CMEIAS will be released as free, downloadable plug-ins so it can provide wide application in studies of microbial ecology.}, }
@article {pmid11386714, year = {2001}, author = {Forney, LJ and Liu, WT and Guckert, JB and Kumagai, Y and Namkung, E and Nishihara, T and Larson, RJ}, title = {Structure of microbial communities in activated sludge: potential implications for assessing the biodegradability of chemicals.}, journal = {Ecotoxicology and environmental safety}, volume = {49}, number = {1}, pages = {40-53}, doi = {10.1006/eesa.2001.2034}, pmid = {11386714}, issn = {0147-6513}, mesh = {*Bacteria ; Biodegradation, Environmental ; Biomass ; DNA, Bacterial/analysis ; Environmental Monitoring/methods ; Environmental Pollutants/*metabolism ; Fatty Acids/analysis ; Glucose/metabolism ; Phospholipids/analysis ; Polymerase Chain Reaction ; Population Dynamics ; RNA, Ribosomal, 16S/analysis ; Sewage/*microbiology ; Waste Disposal, Fluid/*methods ; }, abstract = {Various methods used to assess the biodegradability of chemicals often employ activated sludge as an inoculum since chemicals that ultimately enter the environment are often discharged through wastewater. Differences in the structure and function of activated sludge microbial communities that may complicate interpretation of biodegradation tests could arise from differences in wastewater composition, wastewater treatment plant (WWTP) operation, or manipulations done after collection of the activated sludge. In this study, various methods were used to characterize the structure of microbial communities found in freshly collected activated sludge from WWTPs in Japan, Europe, and the United States, as well as sludge that had been continuously fed either sewage or a glucose-peptone mixture for several weeks after collection. Comparisons of biomass levels, whole-community substrate utilization (determined using Biolog GN and GP plates), and phospholipid fatty acid (PLFA) profiles indicated there were both geographical and temporal differences among freshly collected activated sludge samples. Moreover, marked shifts in the structure of activated sludge microbial communities occurred upon continuous cultivation in the laboratory for 5 weeks using a glucose-peptone feed. These shifts were evident from whole-community substrate utilization and PLFA profiles as well as differences in the profiles of 16S rDNA genes from numerically dominant populations obtained by denaturing gradient gel electrophoresis and terminal restriction fragment analyses. Further studies are needed to better define the variability within and between activated sludge from wastewater treatment plants and laboratory reactors and to assess the impact of such differences on the outcome of biodegradability tests.}, }
@article {pmid11382013, year = {2000}, author = {Silvey, P and Pullammanappallil, PC and Blackall, L and Nichols, P}, title = {Microbial ecology of the leach bed anaerobic digestion of unsorted municipal solid waste.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {41}, number = {3}, pages = {9-16}, pmid = {11382013}, issn = {0273-1223}, mesh = {Archaea/metabolism ; Bacteria, Anaerobic/*metabolism ; Biodegradation, Environmental ; Biomass ; Bioreactors/*microbiology ; DNA, Archaeal/chemistry ; DNA, Bacterial/chemistry ; Ethers/analysis ; Fatty Acids/analysis ; Hydrogen-Ion Concentration ; Methane/analysis ; Polymerase Chain Reaction ; Refuse Disposal/*methods ; }, abstract = {The microbial ecology of the sequential, leach-bed, mesophilic anaerobic digestion of unsorted, coarse municipal solid waste (MSW) was examined over 80 days. The methane yield was approximately 75% of the ultimate biochemical methane potential (BMP) of the waste loaded into the digesters. The operational strategy involved a sequence of two digesters containing fresh and anaerobically stabilised MSW respectively. Cell wall phospholipid fatty acid (PLFA) and ether lipid (PLEL) analysis was used to monitor changes in microbial biomass. Both Bacterial and Archaeal biomass were heavily influenced by pH during the two-week start up period. Archaeal biomass peaked just before the methane production rate reached a maximum whereas Bacterial biomass peaked at a later stage. Changes in the phylogenetic diversity of the population were monitored by denaturing gradient gel electrophoresis (DGGE). An analysis of the changes in DGGE banding patterns suggested that rapid start-up of a new reactor was effected by inoculation as well as the provision of buffering capacity from the mature reactor leachate.}, }
@article {pmid11381993, year = {2000}, author = {Hammes, F and Kalogo, Y and Verstraete, W}, title = {Anaerobic digestion technologies for closing the domestic water, carbon and nutrient cycles.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {41}, number = {3}, pages = {203-211}, pmid = {11381993}, issn = {0273-1223}, mesh = {Bacteria, Anaerobic/*metabolism ; Biodegradation, Environmental ; Biomass ; Conservation of Natural Resources ; Ecology ; Humans ; *Life Support Systems ; Sewage ; Toilet Facilities ; Waste Disposal, Fluid/economics/*methods ; Waste Management ; Water Purification/economics/*methods ; }, abstract = {Sustainable wastewater treatment requires that household wastewater is collected and treated separately from industrial wastewater and rainwater run-offs. This separate treatment is, however, still inadequate, as more than 70% of the nutrients and much of the chemical oxygen demand (COD) and potential pathogens of a domestic sewage system are confined to the few litres of black water (faeces, urine and toilet water). Whilst grey water can easily be filter treated and re-used for secondary household purposes, black water requires more intensive treatment due to its high COD and microbial (pathogens) content. Recently developed vacuum/dry toilets produce a nutrient rich semi-solid waste stream, which, with proper treatment, offers the possibility of nutrient, carbon, water and energy recovery. This study investigates the terrestrial applicability of Life Support System (LSS) concepts as a framework for future domestic waste management. The possibilities of treating black water together with other types of human-generated solid waste (biowastes/mixed wastes) in an anaerobic reactor system at thermophilic conditions, as well as some post treatment alternatives for product recovery and re-use, are considered. Energy can partially be recovered in the form of biogas produced during anaerobic digestion. The system is investigated in the form of theoretical mass balances, together with an assessment of the current feasibility of this technology and other post-treatment alternatives.}, }
@article {pmid11381937, year = {2001}, author = {Daims, H and Purkhold, U and Bjerrum, L and Arnold, E and Wilderer, PA and Wagner, M}, title = {Nitrification in sequencing biofilm batch reactors: lessons from molecular approaches.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {43}, number = {3}, pages = {9-18}, pmid = {11381937}, issn = {0273-1223}, mesh = {Ammonia/metabolism ; Bacteria/genetics/metabolism ; Base Sequence ; *Biofilms ; Bioreactors/*microbiology ; DNA Primers/genetics ; Genes, Bacterial ; In Situ Hybridization, Fluorescence ; Nitrogen/*metabolism ; Oxidation-Reduction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; Waste Disposal, Fluid ; }, abstract = {The nitrifying microbial diversity and population structure of a sequencing biofilm batch reactor receiving sewage with high ammonia and salt concentrations (SBBR 1) was analyzed by the full-cycle rRNA approach. The diversity of ammonia-oxidizers in this reactor was additionally investigated using comparative sequence analysis of a gene fragment of the ammonia monooxygenase (amoA), which represents a key enzyme of all ammonia-oxidizers. Despite the "extreme" conditions in the reactor, a surprisingly high diversity of ammonia- and nitrite-oxidizers was observed to occur within the biofilm. In addition, molecular evidence for the existence of novel ammonia-oxidizers is presented. Quantification of ammonia- and nitrite-oxidizers in the biofilm by Fluorescent In situ Hybridization (FISH) and digital image analysis revealed that ammonia-oxidizers occurred in higher cell numbers and occupied a considerably larger share of the total biovolume than nitrite-oxidizing bacteria. In addition, ammonia oxidation rates per cell were calculated for different WWTPs following the quantification of ammonia-oxidizers by competitive PCR of an amoA gene fragment. The morphology of nitrite-oxidizing, unculturable Nitrospira-like bacteria was studied using FISH, confocal laser scanning microscopy (CLSM) and three-dimensional visualization. Thereby, a complex network of microchannels and cavities was detected within microcolonies of Nitrospira-like bacteria. Microautoradiography combined with FISH was applied to investigate the ability of these organisms to use CO2 as carbon source and to take up other organic substrates under varying conditions. Implications of the obtained results for fundamental understanding of the microbial ecology of nitrifiers as well as for future improvement of nutrient removal in wastewater treatment plants (WWTPs) are discussed.}, }
@article {pmid11378481, year = {2001}, author = {DeLong, EF}, title = {Microbial seascapes revisited.}, journal = {Current opinion in microbiology}, volume = {4}, number = {3}, pages = {290-295}, doi = {10.1016/s1369-5274(00)00205-8}, pmid = {11378481}, issn = {1369-5274}, mesh = {Animals ; Ecology ; Genomics ; Humans ; Marine Biology/*trends ; Oceans and Seas ; Phylogeny ; Plankton ; *Water Microbiology ; }, abstract = {A remarkable array of new discoveries is emerging from studies of naturally occurring marine microbes. These discoveries originate from novel applications of evolving technologies, ranging from molecular phylogenetics to stable isotope analyses, to advanced microscopic techniques, to genomics. As a consequence, new perspectives on the natural history of marine microbes, the inseparable nature of the geological and biological worlds, and a plethora of unexpected new genotypes, phenotypes and physiologies are now being revealed. As our observations of naturally occurring microbes become increasingly more sophisticated, so will theory, technical applications and predictive capabilities in microbial ecology.}, }
@article {pmid11368089, year = {2001}, author = {Chauhan, S and Lindsay, D and Rey, ME and van Holy, A}, title = {Microbial ecology of muffins baked from cassava and other nonwheat flours.}, journal = {Microbios}, volume = {105}, number = {410}, pages = {15-27}, pmid = {11368089}, issn = {0026-2633}, mesh = {Bacillus/*isolation &amp; purification ; Bread/*microbiology ; Colony Count, Microbial ; Flour/microbiology ; Food Handling ; Food Microbiology ; Food Preservation ; Fungi/*isolation &amp; purification ; Manihot/*microbiology ; }, abstract = {Cassava flour was evaluated as a partial substitute for wheat flour in gluten-free muffins. Four replicate test bakes were carried out to evaluate the microbial ecology of two muffin mixes, made with different combinations of cassava, soya, sorghum, sago, and potato flour. The muffins were baked at 180 degrees C for 25 min, stored at 30 degrees C and analysed microbiologically for up to 10 days post-baking. Raw materials were similarly analysed microbiologically on the day of baking. Characterization of predominant bacterial and mould isolates from the raw materials and the muffins was carried out. The rope-free and minimum mould-free shelf life of both muffin types were approximately 1 day and approximately 3 days, respectively. The predominant bacterial isolates from the raw materials and muffins were Bacillus species (83 and 99%, respectively). The moulds predominating in the raw materials were Gloeosporium (42%), Penicillium (13%) and Mucorales (13%), and from muffins Penicillium (37%) and Aspergillus (37%).}, }
@article {pmid11355190, year = {2001}, author = {Vandevivere, PC and Saveyn, H and Verstraete, W and Feijtel, TC and Schowanek, DR}, title = {Biodegradation of metal-[S,S]-EDDS complexes.}, journal = {Environmental science &amp; technology}, volume = {35}, number = {9}, pages = {1765-1770}, doi = {10.1021/es0001153}, pmid = {11355190}, issn = {0013-936X}, mesh = {Biodegradation, Environmental ; Bioreactors ; Chelating Agents/chemistry/*metabolism ; Computer Simulation ; Ethylenediamines/chemistry/*metabolism ; Metals/*metabolism ; Sewage ; Stereoisomerism ; Succinates/chemistry/*metabolism ; }, abstract = {The [S,S]-stereoisomer of ethylenediaminedisuccinic acid (EDDS), a biodegradable strong metal chelant, has substituted traditional chelants in a number of consumer products. However biodegradability of metal-EDDS complexes has remained largely undocumented. In the present study, activated sludge fed with EDDS as sole C and N source, was shown to readily biodegrade 1 mM pulses of Ca-, Cr(III)-, Fe(III)-, Pb-, Al-, Cd-, Mg-, Na-, or ZnEDDS (the latter only after extensive lag phase). On the other hand, the Cu-, Ni-, Co-, and Hg-complexes remained essentially undegraded. Only in the case of HgEDDS was lack of biodegradation due to metal toxicity. Speciation analysis revealed free HEDDS3- concentration was higher than 10(-5.4) M for all readily biodegradable metal-EDDS complexes and smaller than 10(-9.0) M for all recalcitrant complexes at pseudo-steady-state (i.e. after initial rise of aquo metal concentration at onset of biodegradation). The rate of metal-EDDS degradation may be modeled with a Monod expression with HEDDS3- as substrate (half-saturation constant ca. 10(-6) M). This model explains the drastic effect of additional metal ligands, e.g. phosphate or iron, on biodegradation rate of several recalcitrant metal-EDDS complexes. Continuously fed aerated biofilters removed 10 mM Pb- or ZnEDDS at a rate of ca. 0.4 mM h-1.}, }
@article {pmid11352069, year = {2001}, author = {Russell, JB and Rychlik, JL}, title = {Factors that alter rumen microbial ecology.}, journal = {Science (New York, N.Y.)}, volume = {292}, number = {5519}, pages = {1119-1122}, doi = {10.1126/science.1058830}, pmid = {11352069}, issn = {0036-8075}, mesh = {Animals ; Animals, Domestic/anatomy &amp; histology/microbiology/parasitology/physiology ; Bacteria/metabolism/pathogenicity ; Digestive System/anatomy &amp; histology/*microbiology/parasitology/physiopathology ; *Digestive System Physiological Phenomena ; Drug Resistance, Microbial ; *Ecology ; Eukaryota/metabolism ; Fermentation ; Homeostasis ; Host-Parasite Interactions ; Humans ; Hydrogen-Ion Concentration ; Ruminants/anatomy &amp; histology/*microbiology/parasitology/*physiology ; Symbiosis/physiology ; }, abstract = {Ruminant animals and ruminal microorganisms have a symbiotic relationship that facilitates fiber digestion, but domestic ruminants in developed countries are often fed an abundance of grain and little fiber. When ruminants are fed fiber-deficient rations, physiological mechanisms of homeostasis are disrupted, ruminal pH declines, microbial ecology is altered, and the animal becomes more susceptible to metabolic disorders and, in some cases, infectious disease. Some disorders can be counteracted by feed additives (for example, antibiotics and buffers), but these additives can alter the composition of the ruminal ecosystem even further.}, }
@article {pmid11349275, year = {2001}, author = {Rodrigues, JL and Maltseva, OV and Tsoi, TV and Helton, RR and Quensen, JF and Fukuda, M and Tiedje, JM}, title = {Development of a Rhodococcus recombinant strain for degradation of products from anaerobic dechlorination of PCBs.}, journal = {Environmental science &amp; technology}, volume = {35}, number = {4}, pages = {663-668}, doi = {10.1021/es001308t}, pmid = {11349275}, issn = {0013-936X}, support = {ESO 4911/ES/NIEHS NIH HHS/United States ; }, mesh = {Biodegradation, Environmental ; Chlorobenzoates/metabolism ; DNA, Bacterial/genetics ; Environmental Pollutants/*metabolism ; Genetic Engineering ; Operon ; Plasmids ; Polychlorinated Biphenyls/*metabolism ; Rhodococcus/*genetics/*physiology ; }, abstract = {The Gram-positive bacterium Rhodococcus sp. strain RHA1, naturally containing the biphenyl pathway, was electroporated with a broad host range plasmid containing the 4-chlorobenzoate (4-CBA) degradation operon (fcb) isolated from Arthrobacter globiformis strain KZT1. The recombinant strain grew in medium containing 4-CBA and 4-chlorobiphenyl (4-CB) as the only source of carbon, with stoichiometric release of chloride and a molar growth yield on 4-CB that suggested utilization of both biphenyl rings. In resting cell assays, similar rates of degradation were observed for wild-type and recombinant strains for the most common eight congeners from the anaerobic dechlorination of Aroclor 1242, but the recombinant strain accumulated lower amounts of chlorinated meta-cleavage products and no 4-CBA. Recombinant cells inoculated at 10(4) cells/g into nonsterile soil amended with 4-CB grew to 6-10(5) cells/g, a density consistent with the 4-CB consumed. 4-CB was removed only in the inoculated soil, and the recombinant strain did not grow in the same soil when it was not amended with 4-CB. The fcb operon remained stable in the recombinant strain reisolated from soil after 60 days. This work provides proof of concept that a Rhodococcus strain constructed to grow on a PCB would grow in nonsterile soil if the appropriate chlorobiphenyl is available.}, }
@article {pmid11345527, year = {2001}, author = {Podmore, M and Ebersole, JL and Kinane, DF}, title = {Immunodominant antigens in periodontal disease: a real or illusive concept?.}, journal = {Critical reviews in oral biology and medicine : an official publication of the American Association of Oral Biologists}, volume = {12}, number = {2}, pages = {179-185}, doi = {10.1177/10454411010120020701}, pmid = {11345527}, issn = {1045-4411}, mesh = {Aggregatibacter actinomycetemcomitans/immunology ; Animals ; Antigens, Bacterial/*immunology ; Bacterial Outer Membrane Proteins/immunology ; Exotoxins/immunology ; Fimbriae, Bacterial/immunology ; Humans ; *Immunodominant Epitopes ; Lipopolysaccharides/immunology ; Periodontitis/*immunology/*microbiology ; Porphyromonas gingivalis/immunology ; Virulence ; }, abstract = {The humoral arm of the immune system provides protection from many medically significant pathogens. The antigenic epitopes of the pathogens which induce these responses, and the subsequent characteristics of the host response, have been extensively documented in the medical literature, and in many cases have resulted in the development and implementation of effective vaccines or diagnostic tests. There is a substantial body of literature on the humoral immune response in periodontal disease, which is targeted at micro-organisms present within periodontal pockets. However, the significance and specificity of the immune response in periodontal disease have proved difficult to elucidate, due to the large number of potential pathogens in the plaque biofilm and the apparent commensal nature of many of these opportunistic pathogens. This review addresses our current knowledge of the approaches and strategies which have been used to elucidate and examine the concept of immunodominant antigens in medical infections and, more recently, periodontal disease. An identification/understanding of the immunodominant antigens would be informative with respect to: (i) the relative importance of the implicated pathogens, (ii) new approaches to immunological diagnosis, (iii) specific bacterial virulence determinants, (iv) natural protective responses, and (v) the selection of potential vaccine candidate antigens. We conclude that immunodominance of antigens in periodontal disease may be relevant to our understanding of periodontal disease pathogenesis, but due to the complexity and diversity of the 'pathogenic microbial ecology', it is currently an enigmatic topic requiring a multidisciplinary approach linking clinical, microbiological, and immunological investigations. We also conclude, after assessing the literature available on the topic of immunodominance, that it is a term that, if used, must be clearly defined and understood, since it is often used loosely, leading to a general misinterpretation by readers of oral and medical literature.}, }
@article {pmid11320140, year = {2001}, author = {Hansen, MC and Palmer, RJ and Udsen, C and White, DC and Molin, S}, title = {Assessment of GFP fluorescence in cells of Streptococcus gordonii under conditions of low pH and low oxygen concentration.}, journal = {Microbiology (Reading, England)}, volume = {147}, number = {Pt 5}, pages = {1383-1391}, doi = {10.1099/00221287-147-5-1383}, pmid = {11320140}, issn = {1350-0872}, mesh = {Anaerobiosis ; Biofilms ; Fluorescence ; Green Fluorescent Proteins ; Hydrogen-Ion Concentration ; Luminescent Proteins/genetics/*metabolism ; Microscopy, Confocal ; Microscopy, Fluorescence ; Oxygen/*metabolism ; Plasmids ; Streptococcus/*metabolism/physiology ; }, abstract = {Use of green fluorescent protein (GFP) as a molecular reporter is restricted by several environmental factors, such as its requirement for oxygen in the development of the fluorophore, and its poor fluorescence at low pH. There are conflicting data on these limitations, however, and systematic studies to assess the importance of these factors for growing bacterial cultures are lacking. In the present study, homogeneous expression of the gfpmut3* gene directed by a synthetic constitutive lactococcal promoter was demonstrated in batch cultures and in biofilms of Streptococcus gordonii DL1. A lower limit of oxygen concentration for maturation of the GFP fluorophore was determined: fluorescence was emitted at 0.1 p.p.m. dissolved oxygen (in conventionally prepared anaerobic media lacking reducing agents), whereas no fluorescence was detected in the presence of 0.025 p.p.m. dissolved oxygen (obtained by addition of L-cysteine as reducing agent). When an anaerobically grown (non-fluorescent) >50 microm thick biofilm was shifted to aerobic conditions, fluorescence could be detected within 4 min, reaching a maximum over the next 16 min. It was not possible to detect any fluorescence gradients (lateral or vertical) within the >50 microm thick biofilm, and fluorescence development after the shift to aerobic conditions occurred throughout the biofilm (even at the substratum). This suggests that oxygen gradients, which might result in reduced GFP fluorescence, did not exist in the >50 microm thick biofilm of this organism. Production of lactic acid and the subsequent acidification in batch cultures of S. gordonii DL1 led to a decrease in fluorescence intensity. However, severe pH reduction was prevented when the bacterium was grown as a biofilm in a flowcell, and a homogeneous distribution of a strong fluorescence signal was observed. These findings show that GFP can be applied to studies of oxygen-tolerant anaerobic bacteria, that densely packed, flowcell-grown biofilms of S. gordonii do not develop oxygen gradients inhibitory to GFP fluorescence development, and that the often transient nature of GFP fluorescence in acid-producing bacteria can be overcome in flowcells, probably by the elimination of metabolic by-product accumulation.}, }
@article {pmid11319073, year = {2001}, author = {Röling, WF and Kerler, J and Braster, M and Apriyantono, A and Stam, H and van Verseveld, HW}, title = {Microorganisms with a taste for vanilla: microbial ecology of traditional Indonesian vanilla curing.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {5}, pages = {1995-2003}, pmid = {11319073}, issn = {0099-2240}, mesh = {Bacillus/classification/genetics/*isolation &amp; purification ; Benzaldehydes/*chemistry/metabolism ; DNA, Ribosomal/analysis ; *Ecosystem ; Electrophoresis/methods ; Flavoring Agents/chemistry/microbiology ; Fungi/classification/genetics/*isolation &amp; purification ; Indonesia ; Magnoliopsida/*chemistry/*microbiology ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/genetics ; }, abstract = {The microbial ecology of traditional postharvesting processing of vanilla beans (curing) was examined using a polyphasic approach consisting of conventional cultivation, substrate utilization-based and molecular identification of isolates, and cultivation-independent community profiling by 16S ribosomal DNA based PCR-denaturing gradient gel electrophoresis. At two different locations, a batch of curing beans was monitored. In both batches a major shift in microbial communities occurred after short-term scalding of the beans in hot water. Fungi and yeast disappeared, although regrowth of fungi occurred in one batch during a period in which process conditions were temporarily not optimal. Conventional plating showed that microbial communities consisting of thermophilic and thermotolerant bacilli (mainly closely related to Bacillus subtilis, B. licheniformis, and B. smithii) developed under the high temperatures (up to 65 degrees C) that were maintained for over a week after scalding. Only small changes in the communities of culturable bacteria occurred after this period. Molecular analysis revealed that a proportion of the microbial communities could not be cultured on conventional agar medium, especially during the high-temperature period. Large differences between both batches were observed in the numbers of microorganisms, in species composition, and in the enzymatic abilities of isolated bacteria. These large differences indicate that the effects of microbial activities on the development of vanilla flavor could be different for each batch of cured vanilla beans.}, }
@article {pmid11317884, year = {2001}, author = {Damgaard, LR and Nielsen, LP and Revsbech, NP}, title = {Methane microprofiles in a sewage biofilm determined with a microscale biosensor.}, journal = {Water research}, volume = {35}, number = {6}, pages = {1379-1386}, doi = {10.1016/s0043-1354(00)00412-7}, pmid = {11317884}, issn = {0043-1354}, mesh = {Bacteria/metabolism ; Biofilms ; *Biosensing Techniques ; Calibration ; Diffusion ; Methane/*analysis ; Sewage/*chemistry/microbiology ; }, abstract = {Microprofiles of the methane concentration in a 3.5-mm-thick sewage outlet biofilm were measured at high spatial and temporal resolution using a microscale biosensor for methane. In the freshly collected biofilm, methane was building up to a concentration of 175 mumol l-1 at 3 mm depth with a total methanogenesis of 0.14 mumol m-2 s-1, as compared to an aerobic respiration (including methane oxidation) of 0.80 mumol m-2 s-1. A model biofilm was established by homogenisation of an in situ biofilm and 12 days of incubation with surplus sodium acetate. The homogenised biofilm was able to maintain 50% of the methanogenic activity in the absence of external electron donor. Oxygen had only a minor effect on the methane production, but aerobic respiration consumed a substantial part of the produced methane and was thus an important control on methane export from the biofilm. A concentration of 2 mmol l-1 nitrate was shown to inhibit methanogenesis only in the upper layer of the biofilm, whereas a further addition of 2 mmol l-1 sulphate inhibited methanogenesis in the entire biofilm. The study demonstrated the power of the methane microsensor in the study of microhabitats with concurrent production and consumption of methane.}, }
@article {pmid11313127, year = {2001}, author = {Apoga, D and Ek, B and Tunlid, A}, title = {Analysis of proteins in the extracellular matrix of the plant pathogenic fungus Bipolaris sorokiniana using 2-D gel electrophoresis and MS/MS.}, journal = {FEMS microbiology letters}, volume = {197}, number = {2}, pages = {145-150}, doi = {10.1111/j.1574-6968.2001.tb10596.x}, pmid = {11313127}, issn = {0378-1097}, mesh = {Amino Acid Sequence ; Edible Grain/microbiology ; Electrophoresis, Gel, Two-Dimensional ; Extracellular Matrix Proteins/genetics/*isolation &amp; purification ; Fungal Proteins/genetics/*isolation &amp; purification ; Fungi/*chemistry ; Glycine ; Hydrochloric Acid ; Mass Spectrometry/methods ; Molecular Sequence Data ; Plant Diseases/microbiology ; Streptavidin ; }, abstract = {A method was developed for isolating and sequencing proteins present in the extracellular matrix (ECM) of germlings and hyphae of filamentous fungi. Surface proteins of the cereal pathogen Bipolaris sorokiniana were labelled with a membrane impermeable biotinylating agent and extracted using a glycine-HCl buffer. Extracted proteins were purified by affinity binding to streptavidin-conjugated magnetic beads or by two-dimensional gel electrophoresis. Four of the biotinylated proteins from the ECM of B. sorokiniana were isolated, in gel digested with trypsin and partly sequenced by tandem mass spectrometry. No significant sequence similarities to proteins in databases were obtained.}, }
@article {pmid11309062, year = {2001}, author = {Xu, J and Xu, X and Verstraete, W}, title = {The bactericidal effect and chemical reactions of acidified nitrite under conditions simulating the stomach.}, journal = {Journal of applied microbiology}, volume = {90}, number = {4}, pages = {523-529}, doi = {10.1046/j.1365-2672.2001.01278.x}, pmid = {11309062}, issn = {1364-5072}, mesh = {Anti-Bacterial Agents/*pharmacology ; Escherichia coli/*drug effects ; Gastric Acid/chemistry ; Lactobacillus/drug effects ; Microbial Sensitivity Tests ; Models, Biological ; Nitric Oxide/pharmacology ; Nitrites/chemistry/*pharmacology ; Nitrogen Dioxide/pharmacology ; Nitrous Acid/*pharmacology ; Stomach/chemistry ; }, abstract = {AIMS: To examine the hypothesis of non-immune defence mechanisms based on nitrite.<br><br>METHODS AND RESULTS: The acidified media (nutrient broth or citrate-phosphate buffer) under aerobic conditions with additions of physiological levels of nitrite, L-ascorbic acid, iodide and thiocyanate were used to simulate gastric juice. The bactericidal effects of acidified nitrite on Escherichia coli and lactobacilli were investigated using bacterial plate counts. Conversion of acidified nitrite to nitric oxide, nitrogen dioxide and nitrate was also studied. Nitrite significantly increased the bactericidal effects on E. coli and lactobacilli. The bactericidal effects were enhanced by thiocyanate but not by L-ascorbic acid and iodide. L-Ascorbic acid and thiocyanate, but not iodide, enhanced the decomposition of acidified nitrite in nutrient broth. Acidified nitrite was converted to both nitric oxide and nitrate, but a portion of the acidified nitrite in nutrient broth may have been converted to other unidentified nitrogen compounds. Nitrogen dioxide was not detected in any of the samples.<br><br>CONCLUSION: The bactericidal effects of nitrite appeared to be primarily related to nitrous acid, and possibly to other unidentified nitrogenous metabolites, but not to nitric oxide and nitrogen dioxide.<br><br>The potential role of nitrite as an antimicrobial substance in the stomach may be of some importance in the ecology of the gastrointestinal tract and in host physiology.}, }
@article {pmid11295486, year = {2001}, author = {Xu, J and Xu, X and Verstraete, W}, title = {Quantitative measurement of the nitrate reductase activity in the human oral cavity.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {39}, number = {4}, pages = {393-400}, doi = {10.1016/s0278-6915(00)00150-2}, pmid = {11295486}, issn = {0278-6915}, mesh = {Adult ; Female ; Humans ; Hydrogen-Ion Concentration ; Kinetics ; Male ; Mouth/*enzymology ; Mouthwashes/pharmacology ; Nitrate Reductase ; Nitrate Reductases/*analysis ; Nitrates/*metabolism ; Nitrites/*metabolism ; Saliva ; Seasons ; }, abstract = {To quantitatively characterise the nitrate reductase activity in the human oral cavity, a new assay based on holding 20 ml of 10 mg nitrate-N/L solution in the mouth was developed. The mouth assay appeared to relate primarily to the oral cavity surface rather than to the saliva. Nitrite formation in the assay was 50-100 times higher compared to in vitro incubation. In the proposed assay, the nitrite formation linearly increased over a period of 3 min. The average nitrate reductase activity in the oral cavity of 20 subjects was 2.39+/-1.52 microg nitrite-N formed/person x min. The nitrate reductase activity measured for two subjects at different hours varied about 15% for the same subject. The average nitrate reductase activity measured in June for 10 subjects (3.43+/-1.75 microg-N/person x min) was significantly higher than that measured in November for 10 other subjects (1.54+/-0.46 microg-N/person x min). Therefore, the nitrate reductase activity in the oral cavity appears to be influenced by the seasonal conditions. Although the amounts of nitrite formed in the mouth assay increased with increasing levels of nitrate, the rate of nitrate to nitrite reduction decreased with increasing levels of nitrate. The nitrite formation was also affected by the pH, with an optimal pH about 8. The nitrite formation was not influenced by uptake in the mouth of glucose, L-ascorbic acid and L-arginine.}, }
@article {pmid11292803, year = {2001}, author = {Cooper, VS and Schneider, D and Blot, M and Lenski, RE}, title = {Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of Escherichia coli B.}, journal = {Journal of bacteriology}, volume = {183}, number = {9}, pages = {2834-2841}, pmid = {11292803}, issn = {0021-9193}, mesh = {Adaptation, Physiological ; DNA Transposable Elements/genetics ; Escherichia coli/*genetics/metabolism ; Evolution, Molecular ; Gene Deletion ; Mutation ; Operon ; Phenotype ; Ribose/*metabolism ; }, abstract = {Twelve populations of Escherichia coli B all lost D-ribose catabolic function during 2,000 generations of evolution in glucose minimal medium. We sought to identify the population genetic processes and molecular genetic events that caused these rapid and parallel losses. Seven independent Rbs(-) mutants were isolated, and their competitive fitnesses were measured relative to that of their Rbs(+) progenitor. These Rbs(-) mutants were all about 1 to 2% more fit than the progenitor. A fluctuation test revealed an unusually high rate, about 5 x 10(-5) per cell generation, of mutation from Rbs(+) to Rbs(-), which contributed to rapid fixation. At the molecular level, the loss of ribose catabolic function involved the deletion of part or all of the ribose operon (rbs genes). The physical extent of the deletion varied between mutants, but each deletion was associated with an IS150 element located immediately upstream of the rbs operon. The deletions apparently involved transposition into various locations within the rbs operon; recombination between the new IS150 copy and the one upstream of the rbs operon then led to the deletion of the intervening sequence. To confirm that the beneficial fitness effect was caused by deletion of the rbs operon (and not some undetected mutation elsewhere), we used P1 transduction to restore the functional rbs operon to two Rbs(-) mutants, and we constructed another Rbs(-) strain by gene replacement with a deletion not involving IS150. All three of these new constructs confirmed that Rbs(-) mutants have a competitive advantage relative to their Rbs(+) counterparts in glucose minimal medium. The rapid and parallel evolutionary losses of ribose catabolic function thus involved both (i) an unusually high mutation rate, such that Rbs(-) mutants appeared repeatedly in all populations, and (ii) a selective advantage in glucose minimal medium that drove these mutants to fixation.}, }
@article {pmid11287155, year = {2001}, author = {Lavire, C and Louis, D and Perrière, G and Briolay, J and Normand, P and Cournoyer, B}, title = {Analysis of pFQ31, a 8551-bp cryptic plasmid from the symbiotic nitrogen-fixing actinomycete Frankia.}, journal = {FEMS microbiology letters}, volume = {197}, number = {1}, pages = {111-116}, doi = {10.1111/j.1574-6968.2001.tb10591.x}, pmid = {11287155}, issn = {0378-1097}, mesh = {Actinomycetales/*genetics/growth &amp; development ; Codon/genetics ; DNA Replication ; Molecular Sequence Data ; *Nitrogen Fixation ; Open Reading Frames/genetics ; Plasmids/*genetics ; Replication Origin ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {The actinomycete Frankia has never been transformed genetically. To favour the development of Frankia cloning vectors, we have fully sequenced the Frankia alni pFQ31 cryptic plasmid and performed analyses to characterise its coding and non-coding regions. This plasmid is 8551 bp-long and contains 72% G+C. Computer-assisted analyses identified 18 open reading frames (ORFs). These ORFs show a synonymous codon usage different from the one of Frankia chromosomal genes, suggesting an evolutionary bias linked to the nature of the replicon or a horizontal transfer. Three ORFs were found to encode genes likely to be involved in plasmid replication and stability: parFA (partition protein), ptrFA (transcriptional repressor of the GntR family) and repFA (initiation of replication). DNA signatures of a replication origin were identified in the ptrFA-repFA intergenic region. These structural motifs are similar to those observed among origins of iteron-containing plasmids replicating via a &amp;theta; mode.}, }
@article {pmid11282647, year = {2001}, author = {Braker, G and Ayala-del-Río, HL and Devol, AH and Fesefeldt, A and Tiedje, JM}, title = {Community structure of denitrifiers, bacteria, and archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {4}, pages = {1893-1901}, pmid = {11282647}, issn = {0099-2240}, mesh = {Archaea/enzymology/*genetics ; Bacteria/enzymology/*genetics ; Ecosystem ; Genes, Archaeal ; Genes, Bacterial ; Genes, rRNA ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Nitrates/metabolism ; Nitrite Reductases/*genetics ; Nitrites/metabolism ; Oxidation-Reduction ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Washington ; }, abstract = {Steep vertical gradients of oxidants (O(2) and NO(3)(-)) in Puget Sound and Washington continental margin sediments indicate that aerobic respiration and denitrification occur within the top few millimeters to centimeters. To systematically explore the underlying communities of denitrifiers, Bacteria, and Archaea along redox gradients at distant geographic locations, nitrite reductase (nirS) genes and bacterial and archaeal 16S rRNA genes (rDNAs) were PCR amplified and analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis. The suitablility of T-RFLP analysis for investigating communities of nirS-containing denitrifiers was established by the correspondence of dominant terminal restriction fragments (T-RFs) of nirS to computer-simulated T-RFs of nirS clones. These clones belonged to clusters II, III, and IV from the same cores and were analyzed in a previous study (G. Braker, J. Zhou, L. Wu, A. H. Devol, and J. M. Tiedje, Appl. Environ. Microbiol. 66:2096-2104, 2000). T-RFLP analysis of nirS and bacterial rDNA revealed a high level of functional and phylogenetic diversity, whereas the level of diversity of Archaea was lower. A comparison of T-RFLPs based on the presence or absence of T-RFs and correspondence analysis based on the frequencies and heights of T-RFs allowed us to group sediment samples according to the sampling location and thus clearly distinguish Puget Sound and the Washington margin populations. However, changes in community structure within sediment core sections during the transition from aerobic to anaerobic conditions were minor. Thus, within the top layers of marine sediments, redox gradients seem to result from the differential metabolic activities of populations of similar communities, probably through mixing by marine invertebrates rather than from the development of distinct communities.}, }
@article {pmid11282640, year = {2001}, author = {Aldén, L and Demoling, F and Bååth, E}, title = {Rapid method of determining factors limiting bacterial growth in soil.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {4}, pages = {1830-1838}, pmid = {11282640}, issn = {0099-2240}, mesh = {Agriculture ; Bacteria/*growth &amp; development ; Carbon/metabolism ; Hydrogen-Ion Concentration ; Leucine/*metabolism ; Nitrogen/metabolism ; Phosphorus/metabolism ; *Soil Microbiology ; Thymidine/*metabolism ; Trees ; }, abstract = {A technique to determine which nutrients limit bacterial growth in soil was developed. The method was based on measuring the thymidine incorporation rate of bacteria after the addition of C, N, and P in different combinations to soil samples. First, the thymidine incorporation method was tested in two different soils: an agricultural soil and a forest humus soil. Carbon (as glucose) was found to be the limiting substance for bacterial growth in both of these soils. The effect of adding different amounts of nutrients was studied, and tests were performed to determine whether the additions affected the soil pH and subsequent bacterial activity. The incubation time required to detect bacterial growth after adding substrate to the soil was also evaluated. Second, the method was used in experiments in which three different size fractions of straw (1 to 2, 0.25 to 1, and <0.25 mm) were mixed into the agricultural soil in order to induce N limitation for bacterial growth. When the straw fraction was small enough (<0.25 mm), N became the limiting nutrient for bacterial growth after about 3 weeks. After the addition of the larger straw fractions (1 to 2 and 0.25 to 1 mm), the soil bacteria were C limited throughout the incubation period (10 weeks), although an increase in the thymidine incorporation rate after the addition of C and N together compared with adding them separately was seen in the sample containing the size fraction from 0.25 to 1 mm. Third, soils from high-pH, limestone-rich areas were examined. P limitation was observed in one of these soils, while tendencies toward P limitation were seen in some of the other soils.}, }
@article {pmid11282617, year = {2001}, author = {Thomsen, TR and Finster, K and Ramsing, NB}, title = {Biogeochemical and molecular signatures of anaerobic methane oxidation in a marine sediment.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {4}, pages = {1646-1656}, pmid = {11282617}, issn = {0099-2240}, mesh = {Anaerobiosis ; Archaea/genetics/isolation &amp; purification/*metabolism ; DNA, Archaeal/analysis/isolation &amp; purification ; DNA, Bacterial/analysis/isolation &amp; purification ; Denmark ; Genes, rRNA/genetics ; Geologic Sediments/chemistry/*microbiology ; Methane/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases Acting on Sulfur Group Donors/genetics ; Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; Sulfur/metabolism ; Sulfur-Reducing Bacteria/genetics/isolation &amp; purification/*metabolism ; }, abstract = {Anaerobic methane oxidation was investigated in 6-m-long cores of marine sediment from Aarhus Bay, Denmark. Measured concentration profiles for methane and sulfate, as well as in situ rates determined with isotope tracers, indicated that there was a narrow zone of anaerobic methane oxidation about 150 cm below the sediment surface. Methane could account for 52% of the electron donor requirement for the peak sulfate reduction rate detected in the sulfate-methane transition zone. Molecular signatures of organisms present in the transition zone were detected by using selective PCR primers for sulfate-reducing bacteria and for Archaea. One primer pair amplified the dissimilatory sulfite reductase (DSR) gene of sulfate-reducing bacteria, whereas another primer (ANME) was designed to amplify archaeal sequences found in a recent study of sediments from the Eel River Basin, as these bacteria have been suggested to be anaerobic methane oxidizers (K. U. Hinrichs, J. M. Hayes, S. P. Sylva, P. G. Brewer, and E. F. DeLong, Nature 398:802-805, 1999). Amplification with the primer pairs produced more amplificate of both target genes with samples from the sulfate-methane transition zone than with samples from the surrounding sediment. Phylogenetic analysis of the DSR gene sequences retrieved from the transition zone revealed that they all belonged to a novel deeply branching lineage of diverse DSR gene sequences not related to any previously described DSR gene sequence. In contrast, DSR gene sequences found in the top sediment were related to environmental sequences from other estuarine sediments and to sequences of members of the genera Desulfonema, Desulfococcus, and Desulfosarcina. Phylogenetic analysis of 16S rRNA sequences obtained with the primers targeting the archaeal group of possible anaerobic methane oxidizers revealed two clusters of ANME sequences, both of which were affiliated with sequences from the Eel River Basin.}, }
@article {pmid11269408, year = {1999}, author = {Höfle, MG and Abraham, WR}, title = {Eighth International Symposium on Microbial Ecology (ISME-8)--microbial ecology on the doorstep of the 21st century.}, journal = {Environmental microbiology}, volume = {1}, number = {1}, pages = {107-108}, doi = {10.1046/j.1462-2920.1999.00017.x}, pmid = {11269408}, issn = {1462-2912}, mesh = {*Archaea/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; Biofilms/growth &amp; development ; Canada ; *Ecology ; *Environmental Microbiology ; Eukaryotic Cells/classification ; }, }
@article {pmid11265786, year = {2001}, author = {Andersson, BE and Tornberg, K and Henrysson, T and Olsson, S}, title = {Three-dimensional outgrowth of a wood-rotting fungus added to a contaminated soil from a former gasworks site.}, journal = {Bioresource technology}, volume = {78}, number = {1}, pages = {37-45}, doi = {10.1016/s0960-8524(00)00164-4}, pmid = {11265786}, issn = {0960-8524}, mesh = {Benomyl ; Biodegradation, Environmental ; Culture Media ; Ecosystem ; *Environmental Pollution ; Fungicides, Industrial ; Polyporales/*growth &amp; development/isolation &amp; purification/metabolism ; *Soil Microbiology ; Soil Pollutants/metabolism ; }, abstract = {The capability of wood-rotting fungi (WRF) to colonise contaminated soil is an important fungal characteristic in the development of WRF-based soil bioremediation, it is also important to have methods that monitor the presence of the WRF in the soil. In this lab-scale study, it was shown that it was possible to re-capture, localise and identify a brown-rot fungus, Antrodia vaillantii, after it has been inoculated into, and grown in, a contaminated soil from a former gasworks site. The three-dimensional outgrowth of A. vaillantii was monitored by allowing it to grow into fungicide-treated wood baits, temporarily placed in the soil. After two weeks, the baits were withdrawn from the soil and surface sterilised with hydrogen peroxide to favour fungi growing inside baits, i.e., A. vaillantii. After subsequent plating of baits on selective agar medium the presence of A. vaillantii was confirmed with PCR/RFLP. A. vaillantii was found to be viable throughout the 54 days long study and exhibited a surface growth pattern similar to other well-known cord-forming basidiomycetes. Firstly, the upper part of the soil closest to the place of inoculation was colonised, however, over a period of time, the area of colonisation spread deeper into the soil. The detection method employed in the current study gave a conservative estimate of the fungal proliferation and did not require extensive sampling. Its use could be applicable in both applied research, such as soil bioremediation, and in pure microbial ecology studies.}, }
@article {pmid11260599, year = {2001}, author = {Bernard, L and Courties, C and Duperray, C and Schäfer, H and Muyzer, G and Lebaron, P}, title = {A new approach to determine the genetic diversity of viable and active bacteria in aquatic ecosystems.}, journal = {Cytometry}, volume = {43}, number = {4}, pages = {314-321}, pmid = {11260599}, issn = {0196-4763}, mesh = {Bacteria/classification/*genetics ; Bacterial Physiological Phenomena ; Colony Count, Microbial/methods ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; *Ecosystem ; Electrophoresis, Agar Gel/methods ; Flow Cytometry/methods ; Polymerase Chain Reaction ; Reproducibility of Results ; Seawater/microbiology ; Stem Cells ; *Water Microbiology ; }, abstract = {BACKGROUND: Discrimination among viable, active, and inactive cells in aquatic ecosystems is of great importance to understand which species participate in microbial processes. In this study, a new approach combining flow cytometry (FCM), cell sorting, and molecular analyses was developed to compare the diversity of viable cells determined by different methods with the diversity of total cells and active cells.<br><br>METHODS: Total bacteria were determined by SYBR-II staining. Viable bacteria were determined in water samples from different sites by plate count techniques and by the direct viable count (DVC) method. Substrate-responsive cells (i.e., DVC(+) cells) were distinguished from nonresponsive cells (i.e., DVC(-) cells) by FCM and sorted. The genetic diversity of the sorted cell fraction was compared with the diversity of the total microbial community and with that of the culturable cell fraction by denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rDNA fragments. The same approach was applied to a seawater sample enriched with nutrients. In this case, actively respiring cells (CTC+) were also enumerated by FCM, sorted, and analyzed by DGGE.<br><br>RESULTS: The diversity of viable cells varied depending on the methods (traditional culture or DVC) used for viability assessment. Some phylotypes detected in the fraction of viable cells were not detectable at the community level (from total DNA). Similar results were found for actively respiring cells. Inversely, some phylotypes found at the community level were not found in viable and active cell-sorted fractions. It suggests that diversity determined at the community level includes nonactive and nonviable cells.<br><br>CONCLUSION: This new approach allows investigation of the genetic diversity of viable and active cells in aquatic ecosystems. The diversity determined from sorted cells provides relevant ecological information and uncultured organisms can also be detected. New investigations in the field of microbial ecology such as the identification of species able to maintain cellular activity under environmental changes or in the presence of toxic compounds are now possible.}, }
@article {pmid11256177, year = {2000}, author = {Battaglia, F and Scambia, G and Distefano, M and Ronca, S and Plotti, F and Plotti, G and Mancuso, S}, title = {[Quaternary ammonium salts in gynecology and obstetrics].}, journal = {Minerva ginecologica}, volume = {52}, number = {11}, pages = {471-484}, pmid = {11256177}, issn = {0026-4784}, mesh = {Anti-Infective Agents, Local/*therapeutic use ; Benzalkonium Compounds/*therapeutic use ; Female ; Humans ; Pregnancy ; Pregnancy Complications, Infectious/drug therapy ; Puerperal Disorders/drug therapy ; Quaternary Ammonium Compounds/*therapeutic use ; Recurrence ; Vaginosis, Bacterial/*drug therapy ; }, abstract = {We have summarized chemical, physical, and microbiological characteristics of Quaternary Ammonium Salts: particularly, benzalchromium chloride and didecyl-dimethyl-ammonium chloride characteristics were analyzed. These compounds may act as antimicrobial agents in different way: 1) they are surface-active agents and will denature protein or cause dissociation of an enzyme from its prosthetic group; 2) they may alter the cell permeability of bacteria and yeasts; 3) they may stimulate the glycolysis reaction and 4) may inhibit oxidation of lactate. These latest activities may play a role in maintenance of physiologic microbial ecology of vagina or in the re-establishment of the vaginal ecosystem after vaginitis or vaginosis. We have also summarized the physiologic variation of vaginal ecosystem during the different phases of women's life and the microbiology of vagina during vaginitis and vaginosis. The results of more recent studies about the therapeutic role of quaternary ammonium compounds in vulvo-vaginal infections an in vaginosis are synthetically reported. We concluded that quarternary ammonium compounds are efficacious, handy and safe, in obstetrics and gynecology. A very good compliance and low costs of these compounds suggest that they may be used alone as well in association with specific antimicrobial agents in the treatment of most of gynecological infections, and particularly in bacterial vaginosis.}, }
@article {pmid11252901, year = {2001}, author = {Legrand, JC and Struelens, M}, title = {[For rational use of antibiotics in the hospital].}, journal = {Revue medicale de Bruxelles}, volume = {22}, number = {1}, pages = {15-25}, pmid = {11252901}, issn = {0035-3639}, mesh = {Cross Infection/microbiology/prevention &amp; control ; *Drug Resistance, Microbial ; Drug Utilization/*standards ; Guideline Adherence/*standards ; *Hospitals ; Humans ; Organizational Policy ; Patient Selection ; *Practice Guidelines as Topic ; Practice Patterns, Physicians'/*standards ; }, abstract = {Being faced with the risks of emergence and spread of antibiotic multiresistant bacterial strains in the hospital, it is a joint responsibility of all medical specialities and hospital management to promote the protection of the microbial ecology. Strategies to optimize antimicrobial use and practical approaches are discussed here. The need of mobilization of the entire hospital community and implementation of infectious diseases consultants is emphasized, as recommended by the "Groupement pour le Dépistage, l'Etude et la Prévention des Infections Hospitalières" (GDEPIH).}, }
@article {pmid11252165, year = {2001}, author = {Kerner, M and Spitzy, A}, title = {Nitrate Regeneration Coupled to Degradation of Different Size Fractions of DON by the Picoplankton in the Elbe Estuary.}, journal = {Microbial ecology}, volume = {41}, number = {1}, pages = {69-81}, doi = {10.1007/s002480000031}, pmid = {11252165}, issn = {1432-184X}, abstract = {Bacterial conversion of high (HMW > 3,000 Da) and low (LMW < 3,000 Da) molecular weight DON (dissolved organic nitrogen) was studied along the freshwater section of the Elbe estuary during the summer of 1997. Indigenous populations of picoplankton were incubated in a flow-through chamber that allowed a constant exchange of sterile, filtered Elbe water as the culture medium for the microorganisms, which remained within the chamber. Nitrogen conversion was followed by changes in the concentrations of total and low molecular weight DON and dissolved inorganic nitrogen compounds, the uptake of O2, and bacterial growth. Along the Elbe estuary, total DON concentrations varied between 0.69 and 1.1 mg N L-1, of which between 64 and 79% was LMW-DON. Ammonium was a minor nutrient present in the Elbe at concentrations below 0.26 mg N L-1. During incubation in the laboratory between 27 and 64% of the LMW-DON was consumed at rates ranging from 24 to 51 µg N L-1 h-1. HMW-DON was used only when the degradable LMW-DON pool became exhausted and accounted for between 60 and 100% of the HMW-DON. This produced an increase in the DON consumption rate between 43 and 79 µg N L-1 h-1. Nitrification rates were independent of the external ammonium concentration until it decreased to below 1 µg N-NH4 L-1. Most of the N in the nitrification process originated as NH4 regenerated from DON. Between 75 and 100% of the LMW-DON and ammonium consumed was rapidly converted to nitrate. This amount decreased to between 65 and 85% when HMW-DON was consumed in addition to the LMW-DON. DON and ammonium consumption supported nitrification rates up to 71 µg N L-1 h-1. The amount of DOC (dissolved organic carbon) degraded was not equivalent to the C:N ratio of the total dissolved organic matter. Calculations based on oxygen consumption for respiration and ammonium regeneration revealed that the substrates used during the incubations contained C:N at ratios of about 3:1. These results suggest that the nitrogen-rich compounds had been removed from the dissolved organic matter and subsequently consumed by bacteria, while the carbon skeleton remained mostly unaffected by the degradation processes.}, }
@article {pmid11252164, year = {2001}, author = {Chatila, K and Demers, S and Mostajir, B and Gosselin, M and Chanut, JP and Monfort, P and Bird, D}, title = {The Responses of a Natural Bacterioplankton Community to Different Levels of Ultraviolet-B Radiation: A Food Web Perspective.}, journal = {Microbial ecology}, volume = {41}, number = {1}, pages = {56-68}, doi = {10.1007/s002480000042}, pmid = {11252164}, issn = {1432-184X}, abstract = {With the continuing increase of ultraviolet-B radiation (UVBR: 280-320 nm) fluxes toward the Earth's surface, there is concern regarding a possible negative impact on heterotrophic bacterioplankton. The effects of enhanced UVBR on a natural bacterioplankton community were studied during a 7-day experiment conducted in mesocosms (1500 L). Four light regimes were tested: natural light, 280 to 313 nm excluded UVBR, and two levels of UVBR enhancement. During the first 3 days of the experiment characterized by high inorganic nutrient concentrations (nitrates > 1 µmol L-1 and ammonium > 0.1 µmol L-l), UVBR had no effect on both bacterial abundances and activities. From day 4 to the end of the experiment, nitrate concentrations remained low (}, }
@article {pmid11252163, year = {2001}, author = {Sanford, A and Morgan, J and Evans, D and Ducklow, H}, title = {Bacterioplankton Dynamics in Estuarine Mesocosms: Effects of Tank Shape and Size.}, journal = {Microbial ecology}, volume = {41}, number = {1}, pages = {45-55}, doi = {10.1007/s002480000048}, pmid = {11252163}, issn = {1432-184X}, abstract = {Mesocosms provide a powerful tool for investigating bacterial dynamics at small scales; however, even these controlled studies are not exempt from spatial influences. Differences in mesocosm shape and size may have profound effects on the enclosed community since these features may influence the behavior of the system. Studies were conducted in mesocosms of varying dimensions (narrow, deep and wide, shallow tanks) and volumes (0.1, 1, and 10 m3) in an attempt to decipher effects attributable to changes in container size and shape. Both mesocosm volume and shape affected the course of bacterial growth following containment. Bacterial abundance and production were high in both groups of 0.1 m3 tanks and in the large, wide, shallow tanks with the greatest light supply at depth. Differences in bacterial growth between differently shaped tanks (i.e., differing wall area to volume ratios) were observed among equal volume enclosures, with faster growth in the wide/shallow tanks. Light availability, phytoplankton growth, and primary production differed among tanks, and bacterial growth and production were correlated with these properties. During high nutrient conditions, mesocosm volume and shape influenced bacterial growth, possibly because of periphyton growth on walls in small tanks and elevated light levels in wide/shallow tanks. These results suggest the importance of considering container dimensions when designing and interpreting mesocosm experiments and may allow deeper understanding of the fundamental processes underlying patterns observed in the real world.}, }
@article {pmid11252162, year = {2001}, author = {Steppe, TF and Pinckney, JL and Dyble, J and Paerl, HW}, title = {Diazotrophy in Modern Marine Bahamian Stromatolites.}, journal = {Microbial ecology}, volume = {41}, number = {1}, pages = {36-44}, doi = {10.1007/s002480000066}, pmid = {11252162}, issn = {1432-184X}, abstract = {N2 fixation (nitrogenase activity), primary production, and diazotrophic community composition of stromatolite mats from Highborne Cay, Exuma, Bahamas, were examined over a 2-year period (1997-1998). The purpose of the study was to characterize the ecophysiology of N2 fixation in modern marine stromatolites. Microbial mats are an integral surface component of these stromatolites and are hypothesized to have a major role in stromatolite formation and growth. The stromatolite mats contained active photosynthetic and diazotrophic assemblages that exhibited temporal separation of nitrogenase activity (NA) and photosynthesis. Maximal NA was detected at night. Seasonal differences in NA and net O2 production were observed. Photosynthetic activity and the availability of reduced organic carbon appear to be the key determinants of NA. Additions of the de novo protein synthesis inhibitor chloramphenicol did not inhibit NA in March 1998, but greatly inhibited NA in August 1998. Partial sequence analysis of the nifH gene indicates that a broad diversity of diazotrophs may be responsible for NA in the stromatolites.}, }
@article {pmid11252161, year = {2001}, author = {López-Archilla, AI and Marin, I and Amils, R}, title = {Microbial Community Composition and Ecology of an Acidic Aquatic Environment: The Tinto River, Spain.}, journal = {Microbial ecology}, volume = {41}, number = {1}, pages = {20-35}, doi = {10.1007/s002480000044}, pmid = {11252161}, issn = {1432-184X}, abstract = {We studied the correlation between physicochemical and biological characteristics of an acidic river, the Tinto River, in Southwestern Spain. The Tinto River is an extreme environment characterized by its low pH (mean of 2.2) and high concentrations of heavy metals (Fe 2.3 g/L, Zn 0.22 g/L, Cu 0.11 g/L). These extreme conditions are the product of the metabolic activity of chemolithotrophic microorganisms, including iron- and sulfur-oxidizing bacteria, that can be found in high concentrations in its waters. The food chain in the river is very constrained and exclusively microbial. Primary productivity in the Tinto River is the sum of photosynthetic and chemolithotrophic activity. Heterotrophic bacteria and fungi are the major decomposers and protists are the major predators. A correlation analysis including the physicochemical and biological variables suggested a close relationship between the acidic pH values and abundance of both chemolithotrophic bacteria and filamentous fungi. Chemolithotrophic bacteria correlated with the heavy metals found in the river. A principal component analysis of the biotic and abiotic variables suggested that the Tinto River ecosystem can be described as a function of three main groups of variables: pH values, metal concentrations, and biological productivity.}, }
@article {pmid11252160, year = {2001}, author = {Benlloch, S and Acinas, SG and Antón, J and López-López, A and Luz, SP and Rodríguez-Valera, F}, title = {Archaeal Biodiversity in Crystallizer Ponds from a Solar Saltern: Culture versus PCR.}, journal = {Microbial ecology}, volume = {41}, number = {1}, pages = {12-19}, doi = {10.1007/s002480000069}, pmid = {11252160}, issn = {1432-184X}, abstract = {The culturable haloarchaeal diversity in a crystallizer pond from a solar saltern has been analyzed and compared with the biodiversity directly retrieved by analysis of rRNA genes amplified from the environment. Two different sets of culture conditions have been assayed: solid medium with yeast extract as carbon source and liquid media with either yeast extract or a mixture of fishmeal, Spirulina sp., and Artemia salina. Seventeen colonies grown on plates with yeast extract incubated at 30 degrees C were analyzed by 16S rDNA partial sequencing. Sixteen were closely related to haloarchaea of the genus Halorubrum; 13 of them to Halorubrum coriense, a haloarchaeon isolated from a solar saltern pond in Australia, which had not been previously isolated from the pond analyzed in this study; and one to Haloarcula marismortui. Liquid cultures were analyzed by ribosomal internal spacer analysis (RISA) and partial sequencing of the 16SrRNA genes. A total of 18 sequences were analyzed, 15 corresponding to RISA bands obtained from cultures, and 3 from the environmental sample used as inoculum. Thirteen sequences obtained from cultures were related to several Halorubrum species, and 2 to Haloarcula. One of the clones obtained directly from the environmental sample was distantly related to a Natronobacterium, whereas two were related to SPhT, the phylotype most frequently retrieved from this environment by culture independent techniques. Our results show an extremely low diversity for the haloarchaea retrieved by cultivation even when modifications to the standard technique are introduced.}, }
@article {pmid11252159, year = {2001}, author = {Brandt, KK and Vester, F and Jensen, AN and Ingvorsen, K}, title = {Sulfate Reduction Dynamics and Enumeration of Sulfate-Reducing Bacteria in Hypersaline Sediments of the Great Salt Lake (Utah, USA).}, journal = {Microbial ecology}, volume = {41}, number = {1}, pages = {1-11}, doi = {10.1007/s002480000059}, pmid = {11252159}, issn = {1432-184X}, abstract = {Bacterial sulfate reduction activity (SRA) was measured in surface sediments and slurries from three sites in the Great Salt Lake (Utah, USA) using radiolabeled 35S-sulfate. High rates of sulfate reduction (363 +/- 103 and 6,131 +/- 835 nmol cm-3 d-1) were measured at two sites in the moderately hypersaline southern arm of the lake, whereas significantly lower rates (32 +/- 9 nmol cm-3 d-1) were measured in the extremely hypersaline northern arm. Bacterial sulfate reduction was strongly affected by salinity and showed an optimum around 5-6% NaCl in the southern arm and an optimum of around 12% NaCl in the more hypersaline northern arm of the lake. High densities of sulfate-reducing bacteria (SRB) ranging from 2.2 x 107 to 6.7 x 108 cells cm-3 were determined by a newly developed tracer MPN-technique (T-MPN) employing sediment media and 35S-sulfate. Calculation of specific sulfate reduction rates yielded values comparable to those obtained in pure cultures of SRB. However, when using a conventional MPN technique with synthetic media containing high amounts of Fe(II), the numbers of SRB were underestimated by 1-4 orders of magnitude as compared to the T-MPN method. Our results suggest that high densities of slightly to moderately halophilic and extremely halotolerant SRB are responsible for the high rates of sulfate reduction measured in Great Salt Lake sediments.}, }
@article {pmid11248395, year = {2001}, author = {Buckley, DH and Schmidt, TM}, title = {Environmental factors influencing the distribution of rRNA from Verrucomicrobia in soil.}, journal = {FEMS microbiology ecology}, volume = {35}, number = {1}, pages = {105-112}, doi = {10.1111/j.1574-6941.2001.tb00793.x}, pmid = {11248395}, issn = {1574-6941}, abstract = {The Verrucomicrobia constitute a newly discovered division of the Bacteria identified as a numerically abundant component of soil microbial communities in numerous sites around the world. The relative abundance of rRNA from Verrucomicrobia was investigated in the soil to examine the influence of specific environmental factors on the distribution of Verrucomicrobia and to better understand the distribution of this group in terrestrial ecosystems. The abundance of the verrucomicrobial rRNA was determined by using a novel oligonucleotide probe that is specific for verrucomicrobial 16S rRNA. The abundance of verrucomicrobial 16S rRNA in soil microbial communities was determined in relation to plant community composition and soil management history over a period of 2 years. Additional samples were analyzed to determine if verrucomicrobial rRNA relative abundance changes in relation to either soil depth or soil moisture content. The Verrucomicrobia composed 1.9+/-0.2% of the microbial community rRNA present in the 85 soil samples examined. The distribution of verrucomicrobial rRNA in the soil reveals that Verrucomicrobia are significantly affected by environmental characteristics that change in relation to time, soil history, and soil depth, and reveals that a statistically significant amount of the variation in verrucomicrobial rRNA abundance can be explained by changes in soil moisture content.}, }
@article {pmid11243262, year = {2000}, author = {Bossier, P and Top, EM and Huys, G and Kersters, K and Boonaert, CJ and Rouxhet, PG and Verstraete, W}, title = {Modification of the aggregation behaviour of the environmental Ralstonia eutropha-like strain AE815 is reflected by both surface hydrophobicity and amplified fragment length polymorphism (AFLP) patterns.}, journal = {Environmental microbiology}, volume = {2}, number = {1}, pages = {51-58}, doi = {10.1046/j.1462-2920.2000.00082.x}, pmid = {11243262}, issn = {1462-2912}, mesh = {Adaptation, Physiological ; Bacterial Adhesion ; Cell Wall/chemistry ; Congo Red ; Cupriavidus necator/cytology/genetics/*isolation &amp; purification ; DNA Fingerprinting ; Phenotype ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Polymorphism, Restriction Fragment Length ; Sewage/*microbiology ; }, abstract = {After inoculation of the plasmid-free non-aggregative Ralstonia eutropha-like strain AE815 in activated sludge, followed by reisolation on a selective medium, a mutant strain A3 was obtained, which was characterized by an autoaggregative behaviour. Strain A3 had also acquired an IncP1 plasmid, pLME1, co-aggregated with yeast cells when co-cultured, and stained better with Congo red than did the AE815 strain. Contact angle measurements showed that the mutant strain was considerably more hydrophobic than the parent strain AE815, and scanning electron microscopy (SEM) revealed the production of an extracellular substance. A similar hydrophobic mutant (AE176R) could be isolated from the AE815-isogenic R. eutropha-like strain AE176. With the DNA fingerprinting technique repetitive extragenic palindromic-polymerase chain reaction (REP-PCR), no differences between these four strains, AE815, A3, AE176 and AE176R, could be revealed. However, using the amplified fragment length polymorphism (AFLP) DNA fingerprinting technique with three different primer combinations, small but clear reproducible differences between the banding patterns of the autoaggregative mutants and their non-autoaggregative parent strains were observed for each primer set. These studies demonstrate that, upon introduction of a strain in an activated sludge microbial community, minor genetic changes readily occur, which can nevertheless have major consequences for the phenotype of the strain and its aggregation behaviour.}, }
@article {pmid11229904, year = {2001}, author = {Thirup, L and Johnsen, K and Winding, A}, title = {Succession of indigenous Pseudomonas spp. and actinomycetes on barley roots affected by the antagonistic strain Pseudomonas fluorescens DR54 and the fungicide imazalil.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {3}, pages = {1147-1153}, pmid = {11229904}, issn = {0099-2240}, mesh = {Actinomycetales/genetics/*growth &amp; development ; Antibiosis ; Colony Count, Microbial/methods ; DNA, Bacterial/analysis ; Ecosystem ; Fungicides, Industrial/pharmacology ; Hordeum/*microbiology ; Imidazoles/pharmacology ; Plant Roots/*microbiology ; Polymerase Chain Reaction ; Pseudomonas/genetics/*growth &amp; development ; Pseudomonas fluorescens/growth &amp; development ; Soil Microbiology ; }, abstract = {In recent years, the interest in the use of bacteria for biological control of plant-pathogenic fungi has increased. We studied the possible side effects of coating barley seeds with the antagonistic strain Pseudomonas fluorescens DR54 or a commercial fungicide, imazalil. This was done by monitoring the number of indigenous Pseudomonas organisms and actinomycetes on barley roots during growth in soil, harvest after 50 days, and subsequent decomposition. Bacteria were enumerated by traditional plate spreading on Gould's S1 agar (Pseudomonas) and as filamentous colonies on Winogradsky agar (actinomycetes) and by two quantitative competitive PCR assays. For this we developed an assay targeting Streptomyces and closely related genera. DR54 constituted more than 75% of the Pseudomonas population at the root base during the first 21 days but decreased to less than 10% at day 50. DR54 was not successful in colonizing root tips. Initially, DR54 affected the number of indigenous Pseudomonas organisms negatively, whereas imazalil affected Pseudomonas numbers positively, but the effects were transient. Although plate counts were considerably lower than the number of DNA copies, the two methods correlated well for Pseudomonas during plant growth, but after plant harvest Pseudomonas-specific DNA copy numbers decreased while plate counts were in the same magnitude as before. Hence, Pseudomonas was 10-fold more culturable in a decomposition environment than in the rhizosphere. The abundance of actinomycetes was unaffected by DR54 or imazalil amendments, and CFU and quantitative PCR results correlated throughout the experiment. The abundance of actinomycetes increased gradually, mostly in numbers of DNA copies, confirming their role in colonizing old roots.}, }
@article {pmid11229899, year = {2001}, author = {Boon, N and Goris, J and De Vos, P and Verstraete, W and Top, EM}, title = {Genetic diversity among 3-chloroaniline- and aniline-degrading strains of the Comamonadaceae.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {3}, pages = {1107-1115}, pmid = {11229899}, issn = {0099-2240}, mesh = {Aniline Compounds/*metabolism ; Bacterial Proteins/genetics/metabolism ; Betaproteobacteria/*classification/*genetics/metabolism ; Biodegradation, Environmental ; Blotting, Southern ; Conjugation, Genetic ; DNA Transposable Elements ; DNA, Bacterial/genetics ; Electrophoresis, Polyacrylamide Gel/methods ; Gene Transfer, Horizontal ; *Genetic Variation ; Glutamate-Ammonia Ligase/genetics/metabolism ; Molecular Sequence Data ; Plasmids/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Transaminases/*genetics/metabolism ; }, abstract = {We examined the diversity of the plasmids and of the gene tdnQ, involved in the oxidative deamination of aniline, in five bacterial strains that are able to metabolize both aniline and 3-chloroaniline (3-CA). Three strains have been described and identified previously, i.e., Comamonas testosteroni I2 and Delftia acidovorans CA28 and BN3.1. Strains LME1 and B8c were isolated in this study from linuron-treated soil and from a wastewater treatment plant, respectively, and were both identified as D. acidovorans. Both Delftia and Comamonas belong to the family Comamonadaceae. All five strains possess a large plasmid of ca. 100 kb, but the plasmids from only four strains could be transferred to a recipient strain by selection on aniline or 3-CA as a sole source of carbon and/or nitrogen. Plasmid transfer experiments and Southern hybridization revealed that the plasmid of strain I2 was responsible for total aniline but not 3-CA degradation, while the plasmids of strains LME1 and B8c were responsible only for the oxidative deamination of aniline. Several transconjugant clones that had received the plasmid from strain CA28 showed different degradative capacities: all transconjugants could use aniline as a nitrogen source, while only some of the transconjugants could deaminate 3-CA. For all four plasmids, the IS1071 insertion sequence of Tn5271 was found to be located on a 1.4-kb restriction fragment, which also hybridized with the tdnQ probe. This result suggests the involvement of this insertion sequence element in the dissemination of aniline degradation genes in the environment. By use of specific primers for the tdnQ gene from Pseudomonas putida UCC22, the diversity of the PCR-amplified fragments in the five strains was examined by denaturing gradient gel electrophoresis (DGGE). With DGGE, three different clusters of the tdnQ fragment could be distinguished. Sequencing data showed that the tdnQ sequences of I2, LME1, B8c, and CA28 were very closely related, while the tdnQ sequences of BN3.1 and P. putida UCC22 were only about 83% identical to the other sequences. Northern hybridization revealed that the tdnQ gene is transcribed only in the presence of aniline and not when only 3-CA is present.}, }
@article {pmid11227338, year = {2001}, author = {Midtvedt, T}, title = {Establishment of intestinal microbial functions at birth: bilirubin and bacteria.}, journal = {Acta paediatrica (Oslo, Norway : 1992)}, volume = {90}, number = {1}, pages = {7-8}, doi = {10.1080/080352501750064806}, pmid = {11227338}, issn = {0803-5253}, mesh = {Bilirubin/*metabolism ; Humans ; Infant, Newborn/*physiology ; Intestines/*microbiology ; }, abstract = {UNLABELLED: At birth, several "cross-talks" are rapidly established between the child and its developing microflora. Bile pigments and bile acids represent host-derived compounds that are acted upon by this microflora, thereby creating possibilities for several cross-talks of both physiological and pathophysiological importance. The major aim of this article was to characterize and quantitate individually the bilirubin pigments by newly developed methods. The results clearly demonstrate that quantitative and qualitative alterations in bilirubin metabolism occur shortly after birth.<br><br>CONCLUSION: It is hoped that the methodological improvements will create new interest in bilirubin and its metabolism in early infancy.}, }
@article {pmid11225724, year = {2001}, author = {Nielsen, LB and Finster, K and Welsh, DT and Donelly, A and Herbert, RA and de Wit, R and Lomstein, BA}, title = {Sulphate reduction and nitrogen fixation rates associated with roots, rhizomes and sediments from Zostera noltii and Spartina maritima meadows.}, journal = {Environmental microbiology}, volume = {3}, number = {1}, pages = {63-71}, doi = {10.1046/j.1462-2920.2001.00160.x}, pmid = {11225724}, issn = {1462-2912}, mesh = {Acetylene/metabolism ; Bacteria/*growth &amp; development/isolation &amp; purification/ultrastructure ; Geologic Sediments/*microbiology ; Microscopy, Electron, Scanning ; *Nitrogen Fixation ; Oxidation-Reduction ; Plant Roots/*microbiology ; Poaceae/*microbiology ; Seawater/*microbiology ; Sucrose/metabolism ; Sulfates/*metabolism ; }, abstract = {Sulphate reduction rates (SRR) and nitrogen fixation rates (NFR) associated with isolated roots, rhizomes and sediment from the rhizosphere of the marine macrophytes Zostera noltii and Spartina maritima, and the presence and distribution of Bacteria on the roots and rhizomes, were investigated. Between 1% and 3% of the surface area of the roots and rhizomes of both macrophytes were colonized by Bacteria. Bacteria on the surfaces of S. maritima roots and rhizomes were evenly distributed, while the distribution of Bacteria on Z. noltii roots and rhizomes was patchy. Root- and rhizome-associated SRR and NFR were always higher than rates in the bulk sediment. In particular, nitrogen fixation associated with the roots and rhizomes was 41-650-fold higher than in the bulk sediment. Despite the fact that sulphate reduction was elevated on roots and rhizomes compared with bulk sediment, the contribution of plant-associated sulphate reduction to overall sulphate reduction was small (< or =11%). In contrast, nitrogen fixation associated with the roots and rhizomes accounted for 31% and 91% of the nitrogen fixed in the rhizosphere of Z. noltii and S. maritima respectively. In addition, plant-associated nitrogen fixation could supply 37-1,613% of the nitrogen needed by the sulphate-reducing community. Sucrose stimulated nitrogen fixation and sulphate reduction significantly in the root and rhizome compartments of both macrophytes, but not in the bulk sediment.}, }
@article {pmid11220303, year = {2000}, author = {Li, YH and Chen, YY and Burne, RA}, title = {Regulation of urease gene expression by Streptococcus salivarius growing in biofilms.}, journal = {Environmental microbiology}, volume = {2}, number = {2}, pages = {169-177}, doi = {10.1046/j.1462-2920.2000.00088.x}, pmid = {11220303}, issn = {1462-2912}, support = {R01 DE010362/DE/NIDCR NIH HHS/United States ; DE12236/DE/NIDCR NIH HHS/United States ; DE10362/DE/NIDCR NIH HHS/United States ; }, mesh = {Artificial Gene Fusion ; Biofilms/*growth &amp; development ; Chloramphenicol O-Acetyltransferase/genetics/metabolism ; Gene Deletion ; Gene Expression Regulation ; Glucose ; Hydrogen-Ion Concentration ; Promoter Regions, Genetic ; Streptococcus/enzymology/genetics/*physiology ; Urease/genetics/*metabolism ; }, abstract = {The metabolism of urea by urease enzymes of oral bacteria profoundly influences oral biofilm pH homeostasis and oral microbial ecology. The purpose of this study was to gain insight into the regulation of expression of the low pH-inducible urease genes in populations of Streptococcus salivarius growing in vitro in biofilms and to explore whether urease regulation or the levels of urease expression in biofilm cells differed significantly from planktonic cells. Two strains of S. salivarius harbouring urease promoter fusions to a chloramphenicol acetyltransferase (cat) gene were used: PurelCAT, containing a fusion to the full-length, pH-sensitive promoter; or Pureldelta100CAT, a constitutively derepressed deletion derivative of the urease gene promoter. The strains were grown in a Rototorque biofilm reactor in a tryptone-yeast extract-sucrose medium with or without pH control. Both CAT and urease activities in biofilms were measured at 'quasi-steady state' and after a 25mM glucose pulse. The results showed that CAT expression in PurelCAT was repressed at relatively neutral pH values, and that expression could be induced by acidic pH after carbohydrate challenge. Biofilms of PurelCAT grown at low pH, without buffering, had about 20-fold higher CAT levels, and only a modest further induction could be elicited with carbohydrate pulsing. The levels of CAT in biofilms of PurelCAT grown in buffered medium were slightly higher than those reported for planktonic cells cultured at pH 7.0, and the levels of CAT in Purel-CAT growing at low pH or after induction were similar to those reported for fully induced planktonic cells. CAT activity in Pureldelta100CAT was constitutively high, regardless of growth conditions. Interestingly, urease activity detected in biofilms of the parent strain, S. salivarius 57.1, could be as much as 130-fold higher than that reported for fluid chemostat cultures grown under similar conditions. The higher level of urease activity in biofilms was probably caused by the accumulation of the stable urease enzyme within biofilm cells, low pH microenvironments and the growth phase of populations of cells in the biofilm. The ability of S. salivarius biofilm cells to upregulate urease expression in response to pH gradients and to accumulate greater quantities of urease enzyme when growing in biofilms may have a significant impact on oral biofilm pH homeostasis and microbial ecology in vivo. Additionally, S. salivarius carrying the pH-sensitive urease gene promoter fused to an appropriate reporter gene may be a useful biological probe for sensing biofilm pH in situ.}, }
@article {pmid11214796, year = {2000}, author = {Ziemer, CJ and Sharp, R and Stern, MD and Cotta, MA and Whitehead, TR and Stahl, DA}, title = {Comparison of microbial populations in model and natural rumens using 16S ribosomal RNA-targeted probes.}, journal = {Environmental microbiology}, volume = {2}, number = {6}, pages = {632-643}, doi = {10.1046/j.1462-2920.2000.00146.x}, pmid = {11214796}, issn = {1462-2912}, mesh = {Animals ; Archaea/classification/*growth &amp; development ; Bioreactors ; Cattle ; Culture Media ; Eubacterium/classification/*growth &amp; development ; Female ; RNA, Bacterial/analysis ; RNA, Ribosomal, 16S/*analysis ; Rumen/*microbiology ; }, abstract = {A model rumen system, dual-flow continuous culture fermenters, was evaluated by two comparative criteria in two experiments using ribosomal (r)RNA-targeted DNA probes to compare key microbial groups in samples. The initial experiment measured temporal changes in population structure during adaptation of ruminal microbial populations in fermenters over 240 h. The fermenter inoculum contained 34.9% Bacteria, 60.1% Eukarya and 6.8% Archaea measured as a fraction of total small subunit (SSU) rRNA quantified using a universal probe. The cellulolytic bacterial genus Fibrobacter comprised 9.5% of total SSU rRNA in the inoculum. After 240 h of fermenter operation, the average abundance was 80.9% Bacteria, 6.1% Eukarya, 5.1% Archaea and Fibrobacter genus accounted for 6.6% of the total SSU rRNA. Divergence between ruminal and fermenter population structure was evaluated in the second experiment and samples were classified as ruminal, inoculum or fermenter (96, 120, 144 and 168 h of fermenter operation). Fermenter samples had higher relative abundances of Bacteria (84.5%) and Archaea (2.1%) and lower relative abundances of Eukarya (1.8%) than ruminal samples (average 48.0% Bacteria, 1.3% Archaea and 61.5% Eukarya). The relative abundance of Fibrobacter was similar in all samples, averaging 2.5%. The ruminal and fermenter samples had similar proportions of F. succinogenes and F. succinogenes subgroup 3 (as a percentage of Fibrobacter SSU rRNA). Fibrobacter succinogenes subgroup 1 and F. intestinalis proportions of Fibrobacter were lower in fermenter samples (8.2% and 0.7% respectively) than in ruminal samples (28.4% and 2.2% respectively). Fermenters were able to maintain a core prokaryotic community structure similar to the native microbial community in the rumen. Although protozoa populations were lost, maintenance of Fibrobacter and archaeal populations indicated that the model system supported a functional community structure similar to the rumen. This model rumen system may serve as a suitable tool for studying aspects of ruminal microbial ecology and may resolve some of the relationships between microbial community structure and function by providing control of experimental conditions.}, }
@article {pmid11207776, year = {1999}, author = {Wackett, LP}, title = {Web alert. Microbial ecology.}, journal = {Environmental microbiology}, volume = {1}, number = {6}, pages = {549}, doi = {10.1046/j.1462-2920.1999.00087.x}, pmid = {11207776}, issn = {1462-2912}, mesh = {*Ecology ; *Environmental Microbiology ; Internet ; }, }
@article {pmid11207760, year = {1999}, author = {Meckenstock, RU and Morasch, B and Warthmann, R and Schink, B and Annweiler, E and Michaelis, W and Richnow, HH}, title = {13C/12C isotope fractionation of aromatic hydrocarbons during microbial degradation.}, journal = {Environmental microbiology}, volume = {1}, number = {5}, pages = {409-414}, doi = {10.1046/j.1462-2920.1999.00050.x}, pmid = {11207760}, issn = {1462-2912}, mesh = {Carbon Isotopes/*analysis ; Deltaproteobacteria/growth &amp; development/metabolism ; Gram-Negative Bacteria/growth &amp; development/*metabolism ; Iron/metabolism ; Oxidation-Reduction ; Pseudomonas putida/growth &amp; development/metabolism ; Soil Microbiology ; Sulfates/metabolism ; Thauera/growth &amp; development/metabolism ; Toluene/*metabolism ; }, abstract = {The influence of microbial degradation on the 13C/12C isotope composition of aromatic hydrocarbons is presented using toluene as a model compound. Four different toluene-degrading bacterial strains grown in batch culture with oxygen, nitrate, ferric iron or sulphate as electron acceptors were studied as representatives of different environmental redox conditions potentially prevailing in contaminated aquifers. The biological degradation induced isotope shifts in the residual, non-degraded toluene fraction and the kinetic isotope fractionation factors alphaC for toluene degradation by Pseudomonas putida (1.0026 +/- 0.00017), Thauera aromatica (1.0017 +/- 0.00015), Geobacter metallireducens (1.0018 +/- 0.00029) and the sulphate-reducing strain TRM1 (1.0017 +/- 0.00016) were in the same range for all four species, although they use at least two different degradation pathways. A similar 13C/12C isotope fractionation factor (alphaC = 1.0015 +/- 0.00015) was observed in situ in a non-sterile soil column in which toluene was degraded under sulphate-reducing conditions. No carbon isotope shifts resulting from soil-hydrocarbon interactions were observed in a non-degrading soil column control with aquifer material under the same conditions. The results imply that microbial degradation of toluene can produce a 13C/12C isotope fractionation in the residual hydrocarbon fraction under different environmental conditions.}, }
@article {pmid11207751, year = {1999}, author = {Lilburn, TG and Schmidt, TM and Breznak, JA}, title = {Phylogenetic diversity of termite gut spirochaetes.}, journal = {Environmental microbiology}, volume = {1}, number = {4}, pages = {331-345}, doi = {10.1046/j.1462-2920.1999.00043.x}, pmid = {11207751}, issn = {1462-2912}, mesh = {Animals ; Cattle ; Cloning, Molecular ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal/analysis/genetics ; Genes, rRNA ; Genetic Variation ; Humans ; Isoptera/classification/*microbiology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Stomach/microbiology ; Treponema/classification/*genetics ; }, abstract = {A molecular phylogenetic analysis was done of not-yet-cultured spirochaetes inhabiting the gut of the termite, Reticulitermes flavipes (Kollar). Ninety-eight clones of near-full-length spirochaetal 16S rDNA genes were classified by ARDRA pattern and by partial sequencing. All clones grouped within the genus Treponema, and at least 21 new species of Treponema were recognized within R. flavipes alone. Analysis of 190 additional clones from guts of Coptotermes formosanus Shiraki and Zootermopsis angusticollis (Hagen), as well as published data on clones from Cryptotermes domesticus (Haviland), Mastotermes darwiniensis Froggatt, Nasutitermes lujae (Wasmann) and Reticulitermes speratus(Kolbe), revealed a similar level of novel treponemal phylogenetic diversity in these representatives of five of the seven termite families. None of the clones was closely related (i.e. all bore < or = 91% sequence similarity) to any previously recognized treponeme. The data also revealed the existence of two major phylogenetic groups of treponemes: one containing all of the currently known isolates of Treponema and a large number of phylotypes from the human gingival crevice, but only a minority of the termite gut spirochaete clones; another containing the majority of termite spirochaete clones and two Spirochaeta (S. caldaria and S. stenostrepta), which, although free living, group within the genus Treponema on the basis of 16S rRNA sequence. Signature nucleotides that almost perfectly distinguished the latter group, herein referred to as the 'termite cluster', occurred at the following (E. coli numbering) positions: 289-G x C-311; A at 812; and an inserted nucleotide at 1273. The emerging picture is that the long-recognized and striking morphological diversity of termite gut spirochaetes is paralleled by their phylogenetic diversity and may reflect substantial physiological diversity as well.}, }
@article {pmid11200428, year = {2000}, author = {Ellis, RJ and Timms-Wilson, TM and Bailey, MJ}, title = {Identification of conserved traits in fluorescent pseudomonads with antifungal activity.}, journal = {Environmental microbiology}, volume = {2}, number = {3}, pages = {274-284}, doi = {10.1046/j.1462-2920.2000.00102.x}, pmid = {11200428}, issn = {1462-2912}, mesh = {Cyclopropanes/metabolism ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Fatty Acids/metabolism ; Fluorescence ; Genotype ; Hydrogen Cyanide/metabolism ; Pisum sativum/*microbiology ; Phenotype ; Polymorphism, Restriction Fragment Length ; Pseudomonadaceae/growth &amp; development/isolation &amp; purification/*metabolism ; Pythium/*growth &amp; development/pathogenicity ; Ribotyping ; }, abstract = {A collection of 29 fluorescent pseudomonads, some with known biological control activity against a range of phytopathogenic fungi, were characterized phenotypically and genotypically by comparing carbon source utilization patterns, suppression of Pythium ultimum both in planta and in vitro and the potential to produce known secondary metabolites. Fatty acid profiling and restriction fragment length polymorphism (RFLP) analysis of the ribosomal DNA operon (ribotyping) were used to determine the diversity of isolates. A small group of genetically related Pseudomonas spp. with similar properties was identified; each isolate produced a diffusible bioactive product in vitro and was active against Pythium ultimum in planta. However, other isolates that were able to suppress damping off disease but did not inhibit hyphal extension in vitro clustered outside this group. Phenotypic analyses revealed that the accumulation of C17:0 cyclopropane fatty acid (17CFA) and the production of hydrogen cyanide correlated significantly with biological control activity and with the antagonism of fungal development. The potential of 17CFA as a marker for the selection of fluorescent pseudomonads with biocontrol agent (BCA) potential was demonstrated by the isolation of a novel active strain. This was selected after the screening of 13 clonal groups of fluorescent pseudomonads identified from 500 isolates from the phytosphere of sugar beet. Levels of 17CFA synthesis possibly reflect the efficacy of the rpoS allele in particular strains.}, }
@article {pmid11197172, year = {2001}, author = {Biyani, M and Nishigaki, K}, title = {Hundredfold productivity of genome analysis by introduction of microtemperature-gradient gel electrophoresis.}, journal = {Electrophoresis}, volume = {22}, number = {1}, pages = {23-28}, doi = {10.1002/1522-2683(200101)22:1&lt;23::AID-ELPS23&gt;3.0.CO;2-Z}, pmid = {11197172}, issn = {0173-0835}, mesh = {Bacillus/genetics ; Bacillus subtilis/genetics ; DNA, Bacterial/*analysis ; DNA, Fungal/*analysis ; Electrophoresis, Polyacrylamide Gel/*methods ; Escherichia coli/genetics ; Genome, Bacterial ; Genome, Fungal ; Saccharomyces cerevisiae/genetics ; Staining and Labeling/methods ; Temperature ; }, abstract = {Genome profiling, which employs temperature-gradient gel electrophoresis (TGGE) for DNA analysis, has recently been developed in identifying species by genotype. However, the performance of this technology like the general applications of TGGE was, though highly informative, limited in its ability due to methodological reasons. This study demonstrates that minimization of the gel for TGGE, to around one-tenth of its conventional size (approximately 2 cm), can be successfully introduced, resulting in a hundredfold higher performance (total evaluation of time, cost, and degree of parallel operations) than that of the conventional. Reproducibility was evaluated from the measures of the pattern similarity scores (PaSS) between band patterns (genome profiles) obtained with the conventional TGGE, and that with micro-TGGE (microTGGE) developed here, after extracting a set of featuring points from genome profiles. Size minimization, which leads to the reduction of the amount of samples required (cost-saving), is another great advantage, enhancing the employment of multicolor fluorescence technology. Since the further development of microbe-related fields such as epidemiology and microbial ecology inevitably require knowledge based on the identification of a great number of species and strains, microbe-related fields will receive the most optimal benefits from the technological improvements attained here.}, }
@article {pmid11194969, year = {2000}, author = {Tanghe, T and Dhooge, W and Verstraete, W}, title = {Formation of the metabolic intermediate 2,4,4-trimethyl-2-pentanol during incubation of a Sphingomonas sp. strain with the xeno-estrogenic octylphenol.}, journal = {Biodegradation}, volume = {11}, number = {1}, pages = {11-19}, doi = {10.1023/a:1026518727690}, pmid = {11194969}, issn = {0923-9820}, mesh = {Biodegradation, Environmental ; Pentanols/*metabolism ; Phenols/*metabolism ; Sodium Acetate/metabolism ; Sphingomonas/drug effects/*metabolism ; }, abstract = {Degradation of branched octylphenol was studied in a bacterial culture of a Sphingomonas sp. strain. Octylphenol is considered to be the most stable degradation intermediate formed from the corresponding nonionic octylphenol polyethoxylates surfactants during biological wastewater treatment. Since octylphenol can exert estrogenic effects in wildlife, a detailed study of its biodegradation is warranted. The aerobic microbiological transformation of octylphenol was examined with and without the addition of the easily assimilable sodium acetate. In both cases the formation of the metabolite 2,4,4-trimethyl-2-pentanol, representing the intact alkyl chain as a tertiary alcohol, was observed. Since the octylphenol degradation rate was not affected by the presence of acetate, this strain did not show any diauxic metabolic behaviour when incubated with octylphenol and sodium acetate as the sources of carbon and energy. As a result of the biotransformation of octylphenol, its estrogenic potency was removed because it is the phenolic moiety that interacts with the estrogen receptors. This feature opens perspectives for the use of this strain in the framework of an adequate treatment of wastewater with high levels of alkylphenol polyethoxylates.}, }
@article {pmid11172988, year = {2001}, author = {Crivelli, C and Demarta, A and Peduzzi, R}, title = {Intestinal secretory immunoglobulin A (sIgA) response to Aeromonas exoproteins in patients with naturally acquired Aeromonas diarrhea.}, journal = {FEMS immunology and medical microbiology}, volume = {30}, number = {1}, pages = {31-35}, doi = {10.1111/j.1574-695X.2001.tb01546.x}, pmid = {11172988}, issn = {0928-8244}, mesh = {Adult ; Aeromonas/*immunology ; Aged ; Aged, 80 and over ; Bacterial Proteins/metabolism ; Blotting, Western ; Child, Preschool ; Diarrhea/*immunology/microbiology ; Electrophoresis, Polyacrylamide Gel ; Feces/microbiology ; Female ; Gram-Negative Bacterial Infections/*immunology/microbiology ; Humans ; Immunoglobulin A, Secretory/analysis ; Infant ; Lectins ; Male ; Middle Aged ; *Plant Lectins ; }, abstract = {The secretory immunoglobulin A (sIgA) response at the intestinal mucosa is one of the primary defense mechanisms protecting against enteric infections and may therefore be used as an indicator of bacterial enteropathogenicity. In order to understand the role played by Aeromonas strains as gastrointestinal infectious agents, the sIgA response in fecal specimens obtained from patients with naturally acquired Aeromonas diarrhea was examined. Our results demonstrated a specific sIgA response which was directed against the exoproteins produced by Aeromonas strains. The specific Aeromonas sIgA reacted with extracellular products showing molecular masses similar to those of the Aeromonas hemolytic toxins such as aerolysin and AHH1. Some reactions were directed against other proteins that are known to be important factors in the pathogenicity of Aeromonas. The specific responses highlighted are in support of the view that one should consider at least certain biotypes of Aeromonas enteropathogenic.}, }
@article {pmid11168733, year = {2001}, author = {Ringø, E and Lødemel, JB and Myklebust, R and Kaino, T and Mayhew, TM and Olsen, RE}, title = {Epithelium-associated bacteria in the gastrointestinal tract of Arctic charr (Salvelinus alpinus L.). An electron microscopical study.}, journal = {Journal of applied microbiology}, volume = {90}, number = {2}, pages = {294-300}, doi = {10.1046/j.1365-2672.2001.01246.x}, pmid = {11168733}, issn = {1364-5072}, mesh = {Animals ; Bacteria/*ultrastructure ; Digestive System/cytology/*microbiology/ultrastructure ; Endocytosis ; Enterocytes/*microbiology/*ultrastructure ; Microscopy, Electron ; Microscopy, Electron, Scanning ; Salmoniformes/*microbiology ; }, abstract = {AIMS: The primary aim was to use transmission electron microscopy (TEM) and scanning electron microscopy (SEM) to define the location of epithelium-associated bacteria in the digestive tract of the salmonid fish, Arctic charr (Salvelinus alpinus).<br><br>METHODS AND RESULTS: TEM and SEM examination of the gastrointestinal tract demonstrated substantial numbers of ovoid and rod-shaped bacterial cells associated with the microvillous brush borders of enterocytes. Bacteria were found at the tips of microvilli as well as between adjacent microvilli. Endocytosis of bacteria by epithelial cells was observed in two regions (pyloric caeca and midgut).<br><br>CONCLUSION: Electron microscope examination of the gut is an important tool for evaluating the microbial ecology of the fish digestive tract ecosystem.<br><br>The results of the current study clearly demonstrate that the intestine is involved in bacterial endocytosis.}, }
@article {pmid11166102, year = {2001}, author = {Whiteley, AS and Wiles, S and Lilley, AK and Philp, J and Bailey, MJ}, title = {Ecological and physiological analyses of Pseudomonad species within a phenol remediation system.}, journal = {Journal of microbiological methods}, volume = {44}, number = {1}, pages = {79-88}, doi = {10.1016/s0167-7012(00)00231-1}, pmid = {11166102}, issn = {0167-7012}, mesh = {Biodegradation, Environmental ; Bioreactors ; Biosensing Techniques ; Ecology ; Genotype ; Phenol/*metabolism ; Phylogeny ; Polymerase Chain Reaction ; Pseudomonadaceae/classification/*isolation &amp; purification/physiology ; *Soil Microbiology ; }, abstract = {A diverse collection of 700 bacteria obtained from an operational phenolic remediating industrial treatment plant was made to select potential strains as microbial biosensors. Pseudomonads were the most abundant group, of which 48 selected from the liquor or suspended solids were assessed for their physiological response to phenolic pollutant loading and niche specialisation. By FAME-MIS identification the Pseudomonads were clustered into six major species groups. Those isolates able to utilise phenol as a sole carbon source predominantly belonged to a non-clonal Pseudomonas pseudoalcaligenes cluster determined by REP-PCR genotyping. Rapid microtitre based respiration assays were developed to contrast activity in response to increasing concentrations of phenol. A considerable range in response for both phenol degrader and non-degrader strains was observed. This natural phenotypic and physiological heterogeneity could facilitate the selection of isolates for the development of a suite of ecologically relevant, custom designed sensors with predictable toxicity susceptibilities to monitor process efficacy.}, }
@article {pmid11158339, year = {2001}, author = {Spiers, AJ and Field, D and Bailey, M and Rainey, PB}, title = {Notes on designing a partial genomic database: The PfSBW25 Encyclopaedia, a sequence database for Pseudomonas fluorescens SBW25.}, journal = {Microbiology (Reading, England)}, volume = {147}, number = {Pt 2}, pages = {247-249}, doi = {10.1099/00221287-147-2-247}, pmid = {11158339}, issn = {1350-0872}, mesh = {Base Sequence ; *Databases, Factual ; *Genome, Bacterial ; Information Storage and Retrieval ; Internet ; Plasmids/genetics ; *Programming Languages ; Pseudomonas fluorescens/*genetics ; *Software Design ; }, }
@article {pmid11157350, year = {2001}, author = {Tannock, GW}, title = {Molecular assessment of intestinal microflora.}, journal = {The American journal of clinical nutrition}, volume = {73}, number = {2 Suppl}, pages = {410S-414S}, doi = {10.1093/ajcn/73.2.410s}, pmid = {11157350}, issn = {0002-9165}, mesh = {Animals ; Bifidobacterium/classification/genetics/*isolation &amp; purification ; Colon/microbiology ; DNA Fingerprinting ; DNA, Bacterial/*analysis ; Ecosystem ; Electrophoresis, Gel, Pulsed-Field ; Enterobacteriaceae/classification/genetics/*isolation &amp; purification ; Feces/microbiology ; Humans ; Intestines/*microbiology ; Lactobacillus/classification/genetics/*isolation &amp; purification ; Polymerase Chain Reaction ; Probiotics/pharmacology ; Ribotyping ; Swine/microbiology ; }, abstract = {The application of molecular methodologies to intestinal microflora analysis should enable the development of a detailed knowledge of the microbial ecology of the human colon. This knowledge is essential to derive scientifically valid probiotics. Molecular typing (genetic fingerprinting) methods, eg, ribotyping and pulsed field gel electrophoresis of DNA digests, provide a means of distinguishing bacterial strains inhabiting the intestinal tract. Analysis of lactobacillus, bifidobacterial, and enterobacterial populations with the use of these methods has shown that human and porcine subjects harbor a characteristic collection of bacterial strains. Additionally, perturbations and transitions that occur in these populations and are caused by antibiotic administration or by autogenic or allogenic factors can be detected by molecular analysis of the intestinal microflora. In future studies, molecular typing methods could be used to analyze the composition of bacterial populations before, during, and after the administration of the probiotic product. This experimental approach would provide information on the effect of the probiotic on indigenous strains inhabiting the intestinal tract of humans and other animals.}, }
@article {pmid11157234, year = {2001}, author = {Franklin, RB and Garland, JL and Bolster, CH and Mills, AL}, title = {Impact of dilution on microbial community structure and functional potential: comparison of numerical simulations and batch culture experiments.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {2}, pages = {702-712}, pmid = {11157234}, issn = {0099-2240}, mesh = {Bacteria/genetics/*growth &amp; development ; Carbon/metabolism ; Colony Count, Microbial ; Culture Media ; *Ecosystem ; *Models, Biological ; Polymorphism, Restriction Fragment Length ; Sewage/*microbiology ; }, abstract = {A series of microcosm experiments was performed using serial dilutions of a sewage microbial community to inoculate a set of batch cultures in sterile sewage. After inoculation, the dilution-defined communities were allowed to regrow for several days and a number of community attributes were measured in the regrown assemblages. Based upon a set of numerical simulations, community structure was expected to differ along the dilution gradient; the greatest differences in structure were anticipated between the undiluted-low-dilution communities and the communities regrown from the very dilute (more than 10(-4)) inocula. Furthermore, some differences were expected among the lower-dilution treatments (e.g., between undiluted and 10(-1)) depending upon the evenness of the original community. In general, each of the procedures used to examine the experimental community structures separated the communities into at least two, often three, distinct groups. The groupings were consistent with the simulated dilution of a mixture of organisms with a very uneven distribution. Significant differences in community structure were detected with genetic (amplified fragment length polymorphism and terminal restriction fragment length polymorphism), physiological (community level physiological profiling), and culture-based (colony morphology on R2A agar) measurements. Along with differences in community structure, differences in community size (acridine orange direct counting), composition (ratio of sewage medium counts to R2A counts, monitoring of each colony morphology across the treatments), and metabolic redundancy (i.e., generalist versus specialist) were also observed, suggesting that the differences in structure and diversity of communities maintained in the same environment can be manifested as differences in community organization and function.}, }
@article {pmid11156267, year = {2000}, author = {Ross, T and Dalgaard, P and Tienungoon, S}, title = {Predictive modelling of the growth and survival of Listeria in fishery products.}, journal = {International journal of food microbiology}, volume = {62}, number = {3}, pages = {231-245}, doi = {10.1016/s0168-1605(00)00340-8}, pmid = {11156267}, issn = {0168-1605}, mesh = {Animals ; Fish Products/*microbiology ; Food Contamination ; Food Handling/*methods/standards ; Food Microbiology ; *Forecasting ; Humans ; Listeria monocytogenes/*growth &amp; development ; Listeriosis/*prevention &amp; control ; *Models, Biological ; Risk Assessment ; Temperature ; }, abstract = {Predictive microbiology provides a powerful tool to aid the exposure assessment phase of 'quantitative microbial risk assessment'. Using predictive models changes in microbial populations on foods between the point of production/harvest and the point of eating can be estimated from changes in product parameters (temperature, storage atmosphere, pH, salt/water activity, etc.). Thus, it is possible to infer exposure to Listeria monocytogenes at the time of consumption from the initial microbiological condition of the food and its history from production to consumption. Predictive microbiology models have immediate practical application to improve microbial food safety and quality, and are leading to development of a quantitative understanding of the microbial ecology of foods. While models are very useful decision-support tools it must be remembered that models are, at best, only a simplified representation of reality. As such, application of model predictions should be tempered by previous experience, and used with cognisance of other microbial ecology principles that may not be included in the model. Nonetheless, it is concluded that predictive models, successfully validated in agreement with defined performance criteria, will be an essential element of exposure assessment within formal quantitative risk assessment. Sources of data and models relevant to assessment of the human health risk of L. monocytogenes in seafoods are identified. Limitations of the current generation of predictive microbiology models are also discussed. These limitations, and their consequences, must be recognised and overtly considered so that the risk assessment process remains transparent. Furthermore, there is a need to characterise and incorporate into models the extent of variability in microbial responses. The integration of models for microbial growth, growth limits or inactivation into models that can predict both increases and decreases in microbial populations over time will also improve the utility of predictive models for exposure assessment. All of these issues are the subject of ongoing research.}, }
@article {pmid11144394, year = {2000}, author = {Pichichero, ME}, title = {Evaluating the need, timing and best choice of antibiotic therapy for acute otitis media and tonsillopharyngitis infections in children.}, journal = {The Pediatric infectious disease journal}, volume = {19}, number = {12 Suppl}, pages = {S131-40}, doi = {10.1097/00006454-200012001-00001}, pmid = {11144394}, issn = {0891-3668}, mesh = {Acute Disease ; Anti-Bacterial Agents/*therapeutic use ; Child ; Child, Preschool ; Humans ; Infant ; Infant, Newborn ; Otitis Media/diagnosis/*drug therapy ; Pharyngitis/diagnosis/drug therapy ; Time Factors ; Tonsillitis/diagnosis/drug therapy ; }, abstract = {Deciding whether an antibiotic is necessary, when to begin therapy and selecting an optimal drug is an everyday challenge in clinical practice. In vitro susceptibility testing which determines the minimum concentration necessary for a particular antibiotic to inhibit or kill most strains of a bacterial species and pharmacodynamic modeling are useful but have limitations. The need for antibiotic therapy for acute otitis media (AOM) has been recently questioned. However, explanations for uniformly positive results with many antibiotic and placebo comparative trials include overdiagnosis of AOM at study entry, inclusion of patients with mild or uncomplicated AOM and broad criteria for the definition of clinical success. Recurrent and persistent AOM does not have as favorable a natural history as uncomplicated AOM; children below 2 years of age benefit most from antibiotic therapy. Selecting the best choice among the many antibiotics that can be used to treat AOM has become more complex over the last decade due to escalating antibiotic resistance among the pathogens that cause this infection. Broader spectrum antibiotics such as cefdinir, the newly introduced third generation cephalosporin, have their most prominent use in the treatment of persistent and recurrent AOM. In the early 1950s and 1960s penicillin clearly was the best available agent for the treatment of group A streptococcal (GAS) infections. In the 1970s the situation began to change as cephalosporin antibiotics became available. Superior eradication rates with cephalosporins such as cefdinir have now been well-documented. The leading hypothesis to explain the widening gap in efficacy between penicillin and cephalosporins relates to two major concepts: the presence of copathogens and differential alteration of the normal microbial ecology in the throat as a consequence of the selected therapy. There are positive and negative consequences to early initiation of antibiotic therapy for GAS tonsillopharyngitis. Penicillin has persisting good efficacy in patients older than the age of 12 years and in those who have been ill for >2 days. Shortening therapy for GAS tonsillopharyngitis offers a therapeutic advantage. Cefpodoxime proxetil and cefdinir have a 5-day indication for the treatment of GAS tonsillopharyngitis. Antibiotics with lower side effect profile, infrequent dosing, good palatability in suspension formulation and efficacy with short duration of treatment may lead to better outcomes because noncompliance often results in failed therapy, persistence of infection and morbidity.}, }
@article {pmid11137605, year = {2001}, author = {Lebaron, P and Servais, P and Troussellier, M and Courties, C and Muyzer, G and Bernard, L and Schäfer, H and Pukall, R and Stackebrandt, E and Guindulain, T and Vives-Rego, J}, title = {Microbial community dynamics in Mediterranean nutrient-enriched seawater mesocosms: changes in abundances, activity and composition.}, journal = {FEMS microbiology ecology}, volume = {34}, number = {3}, pages = {255-266}, doi = {10.1111/j.1574-6941.2001.tb00776.x}, pmid = {11137605}, issn = {1574-6941}, abstract = {Quantitative and qualitative changes in bacterial communities from the Mediterranean Sea were compared in duplicate batch mesocosms with or without addition of inorganic nutrients. Methods including traditional microbial ecology techniques, molecular biology and flow cytometry were combined to determine abundances, production, cell size, activity, culturability and taxonomic diversity of bacterial cells. Addition of nutrients and confinement resulted in an increase of bacterial densities which were rapidly controlled by protozoan grazing. Changes in bacterial activity and morphology were observed during the growth phase of bacteria and under grazing pressure. The proportion of medium-size and culturable cells increased during the growth phase. These cells were preferentially consumed by grazers resulting in a strong limitation of bacterial production. As a consequence of the grazing pressure, large cells were produced and contributed to the remaining bacterial productivity after grazing. Grazing had an effect on the taxonomic composition of bacterial communities by preferentially eliminating gamma-Proteobacteria, alpha-Proteobacteria were preserved. It seems that some species from the genera Ruegeria and Cytophaga may have developed defence strategies to escape predation.}, }
@article {pmid11136328, year = {2001}, author = {Bothin, C and Okada, M and Midtvedt, T and Perbeck, L}, title = {The intestinal flora influences adhesion formation around surgical anastomoses.}, journal = {The British journal of surgery}, volume = {88}, number = {1}, pages = {143-145}, doi = {10.1046/j.1365-2168.2001.01613.x}, pmid = {11136328}, issn = {0007-1323}, mesh = {Anastomosis, Surgical ; Animals ; Escherichia coli/physiology ; Intestines/*microbiology ; Lactobacillus acidophilus/physiology ; Rats ; Rats, Inbred Strains ; Tissue Adhesions/*microbiology ; }, abstract = {BACKGROUND: Postsurgical adhesion formation is still a cause of postoperative morbidity because no satisfactory treatment or prophylaxis has yet been developed. The present study was designed to investigate the influence of the gastrointestinal flora on adhesion formation around surgical anastomoses.<br><br>METHODS: Anastomoses were constructed in germfree, conventional, ex-germfree and mono- contaminated rats (Escherichia coli X7 and Lactobacillus acidophilus La5), and adhesion formation was recorded.<br><br>RESULTS: The germfree group had a significantly lower adhesion score than all other groups (P < 0.05) apart from the lactobacillus group, which had a significantly lower score than the conventional group (P < 0.05).<br><br>CONCLUSION: The bacterial flora of the gastrointestinal tract enhances adhesion formation around surgical anastomoses.}, }
@article {pmid11133444, year = {2001}, author = {Hansen, BM and Hendriksen, NB}, title = {Detection of enterotoxic Bacillus cereus and Bacillus thuringiensis strains by PCR analysis.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {1}, pages = {185-189}, pmid = {11133444}, issn = {0099-2240}, mesh = {Bacillus cereus/*classification/genetics/isolation &amp; purification/metabolism ; Bacillus thuringiensis/*classification/genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/*genetics/metabolism ; Blotting, Southern ; DNA, Bacterial/analysis/genetics ; Diarrhea/microbiology ; Enterotoxins/*genetics/metabolism ; Gram-Positive Bacterial Infections/microbiology ; Hemolysin Proteins ; Humans ; Polymerase Chain Reaction/*methods ; }, abstract = {Many strains of Bacillus cereus cause gastrointestinal diseases, and the closely related insect pathogen B. thuringiensis has also been involved in outbreaks of diarrhea. The diarrheal types of diseases are attributed to enterotoxins. Two different enterotoxic protein complexes, hemolysin BL (HBL) and nonhemolytic enterotoxin (NHE), and an enterotoxic protein, enterotoxin T, have been characterized, and the genes have been sequenced. PCR primers for the detection of these genes were deduced and used to detect the genes in 22 B. cereus and 41 B. thuringiensis strains. At least one gene of each of the two protein complexes HBL and NHE was detected in all of the B. thuringiensis strains, while six B. cereus strains were devoid of all three HBL genes, three lacked at least two of the three NHE genes, and one lacked all three. Five different sets of primers were used for detection of the gene (bceT) encoding enterotoxin T. The results obtained with these primer sets indicate that bceT is widely distributed among B. cereus and B. thuringiensis strains and that the gene varies in sequence among different strains. PCR with the two primer sets BCET1-BCET3 and BCET1-BCET4 unambiguously detected the bceT gene, as confirmed by Southern analysis. The occurrence of the genes within the two complexes is significantly associated, while neither the occurrence of the two complexes nor the occurrence of the bceT gene is significantly associated in the 63 strains. We suggest an approach for detection of enterotoxin-encoding genes in B. cereus and B. thuringiensis based on PCR analysis with the six primer sets for the detection of genes in the HBL and NHE operons and with the BCET1, BCET3, and BCET4 primers for the detection of bceT. PCR analysis of the 16S-23S rRNA gene internal transcribed spacer region revealed identical patterns for all strains studied.}, }
@article {pmid11133429, year = {2001}, author = {Mougel, C and Cournoyer, B and Nesme, X}, title = {Novel tellurite-amended media and specific chromosomal and Ti plasmid probes for direct analysis of soil populations of Agrobacterium biovars 1 and 2.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {1}, pages = {65-74}, pmid = {11133429}, issn = {0099-2240}, mesh = {Colony Count, Microbial ; Culture Media/chemistry ; DNA Probes ; DNA, Bacterial/analysis ; Drug Resistance, Microbial ; Ecosystem ; Microbial Sensitivity Tests ; Nucleic Acid Hybridization ; Oxidation-Reduction ; Plant Tumors/microbiology ; *Plasmids ; Rhizobium/*classification/genetics/*isolation &amp; purification/physiology ; Sodium Selenite/metabolism/pharmacology ; *Soil Microbiology ; Tellurium/metabolism/*pharmacology ; }, abstract = {Ecology and biodiversity studies of Agrobacterium spp. require tools such as selective media and DNA probes. Tellurite was tested as a selective agent and a supplement of previously described media for agrobacteria. The known biodiversity within the genus was taken into account when the selectivity of K(2)TeO(3) was analyzed and its potential for isolating Agrobacterium spp. directly from soil was evaluated. A K(2)TeO(3) concentration of 60 ppm was found to favor the growth of agrobacteria and restrict the development of other bacteria. Morphotypic analyses were used to define agrobacterial colony types, which were readily distinguished from other colonies. The typical agrobacterial morphotype allowed direct determination of the densities of agrobacterial populations from various environments on K(2)TeO(3)-amended medium. The bona fide agrobacterium colonies growing on media amended with K(2)TeO(3) were confirmed to be Agrobacterium colonies by using 16S ribosomal DNA (rDNA) probes. Specific 16S rDNA probes were designed for Agrobacterium biovar 1 and related species (Agrobacterium rubi and Agrobacterium fici) and for Agrobacterium biovar 2. Specific pathogenic probes from different Ti plasmid regions were used to determine the pathogenic status of agrobacterial colonies. Various morphotype colonies from bulk soil suspensions were characterized by colony blot hybridization with 16S rDNA and pathogenic probes. All the Agrobacterium-like colonies obtained from soil suspensions on amended media were found to be bona fide agrobacteria. Direct colony counting of agrobacterial populations could be done. We found 10(3) to 10(4) agrobacteria. g of dry soil(-1) in a silt loam bulk soil cultivated with maize. All of the strains isolated were nonpathogenic bona fide Agrobacterium biovar 1 strains.}, }
@article {pmid11131786, year = {2000}, author = {Mårdh, PA}, title = {Bacterial vaginosis: a threat to reproductive health? Historical perspectives, current knowledge, controversies and research demands.}, journal = {The European journal of contraception &amp; reproductive health care : the official journal of the European Society of Contraception}, volume = {5}, number = {3}, pages = {208-219}, doi = {10.1080/13625180008500398}, pmid = {11131786}, issn = {1362-5187}, mesh = {Female ; Health Behavior ; *Health Status ; Humans ; Pregnancy ; Pregnancy Outcome ; Research Design ; Vagina/microbiology ; *Vaginosis, Bacterial/epidemiology/etiology ; *Women's Health ; }, abstract = {Bacterial vaginosis is a change in flora, the cause of which is still unknown in the vast majority of instances. Bacterial vaginosis has generally been used to represent any change in vaginal flora resulting in an assumed loss of lactobacilli. However, whether such a flora represents the genetically normal state of some women is poorly defined. The present 'crude' diagnosis of bacterial vaginosis ought to be refined. The proposed impact of bacterial vaginosis on adverse pregnancy outcome is contradicted by therapeutic studies involving pregnant women that result in a change in flora to a lactobacillus-dominated vaginal flora, but have no influence on the course ofpregnancy. Most therapies recommended for bacterial vaginosis in non-pregnant women are often successful in the short term, but usually unsuccessful if the follow-up period after finishing therapy is prolonged. Although bacterial vaginosis is generally believed to be an endogenous condition, a number of behavioral factors are involved, such as the use of contraceptive and intimate hygiene products and smoking habits. Although bacterial vaginosis is not considered a true sexually transmitted infection, it is correlated to sexual activities. The current review elaborates on these matters and on the vaginal microbial ecology.}, }
@article {pmid11125082, year = {2001}, author = {Maidak, BL and Cole, JR and Lilburn, TG and Parker, CT and Saxman, PR and Farris, RJ and Garrity, GM and Olsen, GJ and Schmidt, TM and Tiedje, JM}, title = {The RDP-II (Ribosomal Database Project).}, journal = {Nucleic acids research}, volume = {29}, number = {1}, pages = {173-174}, pmid = {11125082}, issn = {1362-4962}, mesh = {*Databases, Factual ; Information Services ; Internet ; Phylogeny ; RNA, Ribosomal/*genetics ; Ribosomes/*metabolism ; Sequence Alignment ; }, abstract = {The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [Nucleic Acids Res. (2000), 28, 173-174], continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 8.0 (June 1, 2000) consisted of 16 277 aligned prokaryotic small subunit (SSU) rRNA sequences while the number of eukaryotic and mitochondrial SSU rRNA sequences in aligned form remained at 2055 and 1503, respectively. The number of prokaryotic SSU rRNA sequences more than doubled from the previous release 14 months earlier, and approximately 75% are longer than 899 bp. An RDP-II mirror site in Japan is now available (http://wdcm.nig.ac.jp/RDP/html/index.h tml). RDP-II provides aligned and annotated rRNA sequences, derived phylogenetic trees and taxonomic hierarchies, and analysis services through its WWW server (http://rdp.cme.msu.edu/). Analysis services include rRNA probe checking, approximate phylogenetic placement of user sequences, screening user sequences for possible chimeric rRNA sequences, automated alignment, production of similarity matrices and services to plan and analyze terminal restriction fragment polymorphism experiments. The RDP-II email address for questions and comments has been changed from curator@cme.msu.edu to rdpstaff@msu.edu.}, }
@article {pmid10943373, year = {1998}, author = {Lenski, RE}, title = {Bacterial evolution and the cost of antibiotic resistance.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {1}, number = {4}, pages = {265-270}, pmid = {10943373}, issn = {1139-6709}, mesh = {*Bacteria/genetics ; *Biological Evolution ; Chromosomes, Bacterial ; Drug Resistance, Microbial/genetics ; Models, Biological ; Mutagenesis ; Plasmids ; }, abstract = {Bacteria clearly benefit from the possession of an antibiotic resistance gene when the corresponding antibiotic is present. But do resistant bacteria suffer a cost of resistance (i.e., a reduction in fitness) when the antibiotic is absent? If so, then one strategy to control the spread of resistance would be to suspend the use of a particular antibiotic until resistant genotypes declined to low frequency. Numerous studies have indeed shown that resistant genotypes are less fit than their sensitive counterparts in the absence of antibiotic, indicating a cost of resistance. But there is an important caveat: these studies have put resistance genes into naive bacteria, which have no evolutionary history of association with the resistance genes. An important question, therefore, is whether bacteria can overcome the cost of resistance by evolving adaptations that counteract the harmful side-effects of resistance genes. In fact, several experiments (in vitro and in vivo) show that the cost of antibiotic resistance can be substantially diminished, even eliminated, by evolutionary changes in bacteria over rather short periods of time. As a consequence, it becomes increasingly difficult to eliminate resistant genotypes simply by suspending the use of antibiotics.}, }
@article {pmid11106021, year = {2000}, author = {Timms-Wilson, TM and Ellis, RJ and Renwick, A and Rhodes, DJ and Mavrodi, DV and Weller, DM and Thomashow, LS and Bailey, MJ}, title = {Chromosomal insertion of phenazine-1-carboxylic acid biosynthetic pathway enhances efficacy of damping-off disease control by Pseudomonas fluorescens.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {13}, number = {12}, pages = {1293-1300}, doi = {10.1094/MPMI.2000.13.12.1293}, pmid = {11106021}, issn = {0894-0282}, mesh = {DNA Transposable Elements ; Multigene Family ; Mutagenesis, Insertional ; Pisum sativum/growth &amp; development/*physiology ; Phenazines/*metabolism ; *Plant Diseases ; Pseudomonas fluorescens/*genetics ; Pythium/genetics/*pathogenicity ; Soil Microbiology ; Virulence ; }, abstract = {A disarmed Tn5 vector (pUT::Ptac-phzABCDEFG) was used to introduce a single copy of the genes responsible for phenazine-1-carboxylic acid (PCA) biosynthesis into the chromosome of a plant-growth-promoting rhizobacterium Pseudomonas fluorescens. The PCA gene cluster was modified for expression under a constitutive Ptac promoter and lacked the phzIR regulators. PCA-producing variants significantly improved the ability of the wild-type P. fluorescens to reduce damping-off disease of pea seedlings caused by Pythium ultimum, even under conditions of heavy soil infestation. Under conditions of oxygen limitation that are typical of the rhizosphere, PCA production per cell in vitro was greater than that recorded in fast-growing, nutrient-rich cultures. Similarly, when the in vitro nutrient supply was limited, P fluorescens::phz variants that produced the most PCA effectively competed against P. ultimum by suppressing mycelial development. Soil-based bioassays confirmed that the level of PCA biosynthesis correlated directly with the efficacy of biological control and the persistence of inocula in soil microcosms. They also showed that soil pretreatment with bacteria provides a suitable method for plant protection by reducing infection, effectively decontaminating the soil. These data demonstrate that the insertion of a single chromosomal copy of the genes for a novel antifungal compound, PCA, enhances the ecological fitness of a natural isolate already adapted to the rhizosphere and capable of suppressing fungal disease.}, }
@article {pmid11104813, year = {2000}, author = {Verschuere, L and Rombaut, G and Sorgeloos, P and Verstraete, W}, title = {Probiotic bacteria as biological control agents in aquaculture.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {64}, number = {4}, pages = {655-671}, pmid = {11104813}, issn = {1092-2172}, mesh = {Animals ; Aquaculture/*methods ; *Bacteria ; Crustacea ; Fishes ; Mollusca ; Pest Control, Biological/*methods ; *Probiotics ; }, abstract = {There is an urgent need in aquaculture to develop microbial control strategies, since disease outbreaks are recognized as important constraints to aquaculture production and trade and since the development of antibiotic resistance has become a matter of growing concern. One of the alternatives to antimicrobials in disease control could be the use of probiotic bacteria as microbial control agents. This review describes the state of the art of probiotic research in the culture of fish, crustaceans, mollusks, and live food, with an evaluation of the results obtained so far. A new definition of probiotics, also applicable to aquatic environments, is proposed, and a detailed description is given of their possible modes of action, i.e., production of compounds that are inhibitory toward pathogens, competition with harmful microorganisms for nutrients and energy, competition with deleterious species for adhesion sites, enhancement of the immune response of the animal, improvement of water quality, and interaction with phytoplankton. A rationale is proposed for the multistep and multidisciplinary process required for the development of effective and safe probiotics for commercial application in aquaculture. Finally, directions for further research are discussed.}, }
@article {pmid11098820, year = {2000}, author = {Tsekova, K and Galabova, D and Todorova, K}, title = {Copper accumulation and phosphatase activities of Aspergillus and Rhizopus.}, journal = {Zeitschrift fur Naturforschung. C, Journal of biosciences}, volume = {55}, number = {9-10}, pages = {708-712}, doi = {10.1515/znc-2000-9-1007}, pmid = {11098820}, issn = {0939-5075}, mesh = {Acid Phosphatase/*metabolism ; Aspergillus/drug effects/growth &amp; development/*metabolism ; Aspergillus niger/drug effects/growth &amp; development/metabolism ; Biological Transport ; Copper/*metabolism/pharmacology ; Drug Resistance, Microbial ; Kinetics ; Rhizopus/drug effects/growth &amp; development/*metabolism ; }, abstract = {Copper accumulation and phosphatase activities of three Aspergillus species resistant to copper were compared to three copper-sensitive Rhizopus species. High level of acid phosphatases and decreased Cu2+-uptake were found with resistant in contrast to sensitive strains. The presence of copper(II) ions in the medium increased the production of acid phosphatases in the resistant A. niger and decreased their activity in the sensitive R. delemar. Copper ions inhibited the activity of A. niger cellular acid phosphatase with a Ki of 8.9x10(-4) M and slightly activated the R. delemar enzyme.}, }
@article {pmid11097934, year = {2000}, author = {Griffiths, RI and Whiteley, AS and O'Donnell, AG and Bailey, MJ}, title = {Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {12}, pages = {5488-5491}, pmid = {11097934}, issn = {0099-2240}, mesh = {Bacteria/genetics/isolation &amp; purification ; DNA Fingerprinting ; DNA, Bacterial/*genetics/*isolation &amp; purification ; DNA, Ribosomal/*genetics/*isolation &amp; purification ; Ecosystem ; Electrophoresis, Agar Gel ; *Environmental Microbiology ; Polymerase Chain Reaction ; RNA, Bacterial/*genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/*genetics/*isolation &amp; purification ; Soil Microbiology ; }, abstract = {A rapid protocol for the extraction of total nucleic acids from environmental samples is described. The method facilitates concomitant assessment of microbial 16S rRNA diversity by PCR and reverse transcription-PCR amplification from a single extraction. Denaturing gradient gel electrophoresis microbial community analysis differentiated the active component (rRNA derived) from the total bacterial diversity (ribosomal DNA derived) down the horizons of an established grassland soil.}, }
@article {pmid11097926, year = {2000}, author = {Cho, JC and Tiedje, JM}, title = {Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {12}, pages = {5448-5456}, pmid = {11097926}, issn = {0099-2240}, mesh = {DNA Fingerprinting ; Ecosystem ; Fluorescence ; Genotype ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Pseudomonas/classification/genetics/*isolation &amp; purification ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Fluorescent Pseudomonas strains were isolated from 38 undisturbed pristine soil samples from 10 sites on four continents. A total of 248 isolates were confirmed as Pseudomonas sensu stricto by fluorescent pigment production and group-specific 16S ribosomal DNA (rDNA) primers. These isolates were analyzed by three molecular typing methods with different levels of resolution: 16S rDNA restriction analysis (ARDRA), 16S-23S rDNA intergenic spacer-restriction fragment length polymorphism (ITS-RFLP) analysis, and repetitive extragenic palindromic PCR genomic fingerprinting with a BOX primer set (BOX-PCR). All isolates showed very similar ARDRA patterns, as expected. Some ITS-RFLP types were also found at every geographic scale, although some ITS-RFLP types were unique to the site of origin, indicating weak endemicity at this level of resolution. Using a similarity value of 0.8 or more after cluster analysis of BOX-PCR fingerprinting patterns to define the same genotypes, we identified 85 unique fluorescent Pseudomonas genotypes in our collection. There were no overlapping genotypes between sites as well as continental regions, indicating strict site endemism. The genetic distance between isolates as determined by degree of dissimilarity in BOX-PCR patterns was meaningfully correlated to the geographic distance between the isolates' sites of origin. Also, a significant positive spatial autocorrelation of the distribution of the genotypes was observed among distances of <197 km, and significant negative autocorrelation was observed between regions. Hence, strong endemicity of fluorescent Pseudomonas genotypes was observed, suggesting that these heterotrophic soil bacteria are not globally mixed.}, }
@article {pmid11097914, year = {2000}, author = {Davey, ME and de Bruijn, FJ}, title = {A homologue of the tryptophan-rich sensory protein TspO and FixL regulate a novel nutrient deprivation-induced Sinorhizobium meliloti locus.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {12}, pages = {5353-5359}, pmid = {11097914}, issn = {0099-2240}, mesh = {Artificial Gene Fusion ; Bacterial Proteins/*genetics ; Base Sequence ; Carbon/metabolism ; DNA Transposable Elements/genetics ; DNA, Bacterial/genetics ; *Genes, Bacterial ; Genes, Reporter ; Hemeproteins/*genetics ; Histidine Kinase ; Mutagenesis, Insertional ; Nitrogen/metabolism ; Open Reading Frames ; Osmotic Pressure ; Oxygen/metabolism ; Phenotype ; Sinorhizobium meliloti/*genetics/growth &amp; development/*metabolism ; }, abstract = {A nutrient deprivation-induced locus in Sinorhizobium meliloti strain 1021 was identified by use of a Tn5-luxAB reporter gene transposon. The tagged locus is comprised of two open reading frames (ORFs) designated ndiA and ndiB for nutrient deprivation-induced genes A and B. Comparison of the deduced amino acid sequences of both ndiA and ndiB to the protein databases failed to reveal similarity to any known genes. The expression of the ndi locus was found to be induced by carbon and nitrogen deprivation, osmotic stress, and oxygen limitation and during entry into stationary phase. To identify regulatory components involved in the control of ndi gene expression, a second round of mutagenesis was performed on the primary ndiB::Tn5-luxAB-tagged strain (C22) with transposon Tn1721. A double-mutant strain was obtained that lacked ndi locus transcriptional activity under all of the inducing conditions tested. The Tn1721-tagged gene showed a high degree of similarity to tryptophan-rich sensory protein TspO from Rhodobacter sphaeroides, as well as to mitochondrial benzodiazepine receptor pK18 from mammals. Induction of the ndi::Tn5-luxAB reporter gene fusion was restored under all inducing conditions by introducing the tspO coding region, from either S. meliloti or R. sphaeroides, in trans. Furthermore, it was found that, in addition to tspO, fixL, which encodes the sensor protein of an oxygen-sensing two-component system, is required for full expression of the ndi locus, but only under low oxygen tension.}, }
@article {pmid11097876, year = {2000}, author = {El-Fantroussi, S and Verstraete, W and Top, EM}, title = {Enrichment and molecular characterization of a bacterial culture that degrades methoxy-methyl urea herbicides and their aniline derivatives.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {12}, pages = {5110-5115}, pmid = {11097876}, issn = {0099-2240}, mesh = {Aniline Compounds/metabolism ; Bacteria/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Herbicides/*metabolism ; Linuron/metabolism ; Phenylurea Compounds/metabolism ; Soil Microbiology ; Soil Pollutants/metabolism ; }, abstract = {Soil treated with linuron for more than 10 years showed high biodegradation activity towards methoxy-methyl urea herbicides. Untreated control soil samples taken from the same location did not express any linuron degradation activity, even after 40 days of incubation. Hence, the occurrence in the field of a microbiota having the capacity to degrade a specific herbicide was related to the long-term treatment of the soil. The enrichment culture isolated from treated soil showed specific degradation activity towards methoxy-methyl urea herbicides, such as linuron and metobromuron, while dimethyl urea herbicides, such as diuron, chlorotoluron, and isoproturon, were not transformed. The putative metabolic intermediates of linuron and metobromuron, the aniline derivatives 3, 4-dichloroaniline and 4-bromoaniline, were also degraded. The temperature of incubation drastically affected degradation of the aniline derivatives. Whereas linuron was transformed at 28 and 37 degrees C, 3,4-dichloroaniline was transformed only at 28 degrees C. Monitoring the enrichment process by reverse transcription-PCR and denaturing gradient gel electrophoresis (DGGE) showed that a mixture of bacterial species under adequate physiological conditions was required to completely transform linuron. This research indicates that for biodegradation of linuron, several years of adaptation have led to selection of a bacterial consortium capable of completely transforming linuron. Moreover, several of the putative species appear to be difficult to culture since they were detectable by DGGE but were not culturable on agar plates.}, }
@article {pmid11080383, year = {2000}, author = {Zelenev, VV and van Bruggen AH,  and Semenov, AM}, title = {"BACWAVE," a Spatial-Temporal Model for Traveling Waves of Bacterial Populations in Response to a Moving Carbon Source in Soil.}, journal = {Microbial ecology}, volume = {40}, number = {3}, pages = {260-272}, doi = {10.1007/s002480000029}, pmid = {11080383}, issn = {1432-184X}, abstract = {Previously, we discovered the phenomenon of wavelike spatial distributions of bacterial populations and total organic carbon (TOC) along wheat roots. We hypothesized that the principal mechanism underlying this phenomenon is a cycle of growth, death, autolysis, and regrowth of bacteria in response to a moving substrate source (root tip). The aims of this research were (i) to create a simulation model describing wavelike patterns of microbial populations in the rhizosphere, and (ii) to investigate by simulation the conditions leading to these patterns. After transformation of observed spatial data to presumed temporal data based on root growth rates, a simulation model was constructed with the Runge-Kutta integration method to simulate the dynamics of colony-forming bacterial biomass, with growth and death rates depending on substrate content so that the rate curves crossed over at a substrate concentration within the range of substrate availability in the model. This model was named "BACWAVE," standing for "bacterial waves." Cyclic dynamics of bacteria were generated by the model that were translated into traveling spatial waves along a moving nutrient source. Parameter values were estimated from calculated initial substrate concentrations and observed microbial distributions along wheat roots by an iterative optimization method. The kinetic parameter estimates fell in the range of values reported in the literature. Calculated microbial biomass values produced spatial fluctuations similar to those obtained for experimental biomass data derived from colony forming units. Concentrations of readily utilizable substrate calculated from biomass dynamics did not mimic measured concentrations of TOC, which consist not only of substrate but also various polymers and humic acids. In conclusion, a moving pulse of nutrients resulting in cycles of growth and death of microorganisms can indeed explain the observed phenomenon of moving microbial waves along roots. This is the first report of wavelike dynamics of microorganisms in soil along a root resulting from the interaction of a single organism group with its substrate.}, }
@article {pmid11080382, year = {2000}, author = {van Bruggen AH,  and Semenov, AM and Zelenev, VV}, title = {Wavelike Distributions of Microbial Populations along an Artificial Root Moving through Soil.}, journal = {Microbial ecology}, volume = {40}, number = {3}, pages = {250-259}, doi = {10.1007/s002480000030}, pmid = {11080382}, issn = {1432-184X}, abstract = {In a previous paper, we described wavelike distributions of bacterial populations along roots of wheat, and hypothesized that one mechanism underlying these distributions might be growth and death cycles of microorganisms in response to a moving nutrient source, the root tip. Similar wavelike distributions in microbial biomass were obtained using a simulation model for growth and death of bacteria in relation to their substrate (BACWAVE). The model was parameterized with data from one experiment on rhizosphere bacterial populations along wheat roots, and compared against a similar but independent experiment. In experiments described in this paper, similar wavelike distributions in bacterial populations were observed in response to a single artificial exudate moving linearly through a soil that had been air-dry for almost 2 years. The period of the spatial waves was longer when the tip of the artificial exudate moved at a speed of 4.2 cm/day compared to a tip moving at 1.1 cm/day, but after transformation into the temporal domain, the periods of the waves were similar for both moving speeds. The observed distributions were simulated using the BACWAVE model with similar parameter values as derived from the experiment with wheat roots mentioned above. The results presented in this paper confirm our hypothesis that wavelike distributions of bacterial population along plant roots can arise from "exudates" released primarily from the root tip, without the need for additional exudation points.}, }
@article {pmid11080381, year = {2000}, author = {Küsel, K and Dorsch, T}, title = {Effect of Supplemental Electron Donors on the Microbial Reduction of Fe(III), Sulfate, and CO(2) in Coal Mining-Impacted Freshwater Lake Sediments.}, journal = {Microbial ecology}, volume = {40}, number = {3}, pages = {238-249}, doi = {10.1007/s002480000065}, pmid = {11080381}, issn = {1432-184X}, abstract = {In acidic mining-impacted lake sediments, the microbial reduction of Fe(III) is the dominant electron-accepting process, whereas the reduction of sulfate seems to be restricted to a narrow sediment zone of elevated pH and lower amounts of total and reactive iron. To evaluate the microbial heterogeneity and the commensal interactions of the microbial community, the flow of supplemental carbon and reductant was evaluated in four different zones of the sediment in anoxic microcosms at the in situ temperature of 12 degrees C. Substrate consumption, product formation, and the potential to reduce Fe(III) and sulfate were similar with both upper and lower sediment zones. In the upper acidic iron-rich sediment zone, the rate of Fe(II) formation 204 nmol ml(-1) d(-1) was enhanced to 833 nmol ml(-1) d(-1) and 462 nmol ml(-1) d(-1) by supplemental glucose and H(2), respectively. Supplemental lactate and acetate were not consumed under acidic conditions and decreased the rate of Fe(II) formation to 130 nmol ml(-1) d(-1) and 52 nmol ml(-1) d(-1), respectively. When the pH of the upper sediment increased above pH 5, acetate-dependent reduction of sulfate was initiated even though the pool of Fe(III) was not depleted. In deeper sediment zones with elevated pH, the rapid consumption of acetate was always coincident to a decrease in the concentration of sulfate and soluble Fe(II), indicating the formation of Fe(II) sulfides. Although the reduction of Fe(III) was still an ongoing process in deeper sediment zones, the formation of Fe(II) was only slightly enhanced by the consumption of glucose or cellobiose, but not by H(2) or acetate. H(2)-utilizing acetogens seemed to be involved in the consumption of H(2). These collective results indicated (i) that the reduction of Fe(III) predominated over the reduction of sulfate as long as the sediment remained acidic and carbon-limited, and (ii) that the sulfate-reducing microbiota in this heterogeneous sediment were better adapted to the geochemical gradients present than were other neutrophilic dissimilatory Fe(III) reducers.}, }
@article {pmid11080380, year = {2000}, author = {Yao, H and He, Z and Wilson, MJ and Campbell, CD}, title = {Microbial Biomass and Community Structure in a Sequence of Soils with Increasing Fertility and Changing Land Use.}, journal = {Microbial ecology}, volume = {40}, number = {3}, pages = {223-237}, doi = {10.1007/s002480000053}, pmid = {11080380}, issn = {1432-184X}, abstract = {The microbial biomass and community structure of eight Chinese red soils with different fertility and land use history was investigated. Two community based microbiological measurements, namely, community level physiological profiling (CLPP) using Biolog sole C source utilization tests and phospholipid fatty acid (PLFA) profiles, were used to investigate the microbial ecology of these soils and to determine how land use alters microbial community structure. Microbial biomass-C and total PLFAs were closely correlated to organic carbon and total nitrogen, indicating that these soil microbial measures are potentially good indices of soil fertility in these highly weathered soils. Metabolic quotients and C source utilization were not correlated with organic carbon or microbial biomass. Multivariate analysis of sole carbon source utilization patterns and PLFAs demonstrated that land use history and plant cover type had a significant impact on microbial community structure. PLFAs showed these differences more than CLPP methods. Consequently, PLFA analysis was a better method for assessing broad-spectrum community differences and at the same time attempting to correlate changes with soil fertility. Soils from tea orchards were particularly distinctive in their CLPP. A modified CLPP method, using absorbance readings at 405 nm and different culture media at pH values of 4.7 and 7.0, showed that the discrimination obtained can be influenced by the culture conditions. This method was used to show that the distinctive microbial community structure in tea orchard soils was not, however, due to differences in pH alone.}, }
@article {pmid11080379, year = {2000}, author = {Wörner, U and Zimmerman-Timm, H and Kausch, H}, title = {Succession of Protists on Estuarine Aggregates.}, journal = {Microbial ecology}, volume = {40}, number = {3}, pages = {209-222}, doi = {10.1007/s002480000051}, pmid = {11080379}, issn = {1432-184X}, abstract = {Colonization by and succession of bacteria and bacterivorous protists on laboratory-made aggregates were determined over a period of 14 days during winter and spring in 1997. Aggregates were generated from natural water from the limnetic zone of the Elbe Estuary using a tilting tube roller system. Within 1 h after the beginning of the experiments, macroaggregates started to form. Aggregates reached a maximum size of 1 mm with a tendency toward large sizes at the end of the experiment after the 10th day. On the first day, high bacterial densities of more than 10(9) cells ml(-1) were detected within the aggregates. The abundances of flagellates and ciliates within aggregates were also two or three orders of magnitude higher than in the surrounding water. Densities of aggregate associated organisms are comparable to those occuring in sediments. The first protistan colonizers on the aggregates were small heterotrophic flagellates, such as choanoflagellates and small euglenids. Later, beginning on the 4th day, small sarcodines and ciliates became abundant. The most abundant ciliates associated with aggregates were small species of the Hypotrichia, Cyrtophorida, and Hymenostomata. After 9 days, large omnivorous and carnivorous ciliates, such as large members of the Hypotrichia and the Pleurostomatida, occurred. In spring, large heterotrophic flagellates and amebae also appeared at this time. These findings indicated the existence of a succession of protists on newly formed aggregates and a microbial food net within the aggregates based on bacterial production. Additionally, most of the species observed during this study were adapted for living on surfaces. In natural environments they are more common in benthic than in pelagic environments. For them, aggregates are havens in the water column comparable to sediment communities.}, }
@article {pmid11080378, year = {2000}, author = {Anesio, AM and Theil-Nielsen, J and Granéli, W}, title = {Bacterial Growth on Photochemically Transformed Leachates from Aquatic and Terrestrial Primary Producers.}, journal = {Microbial ecology}, volume = {40}, number = {3}, pages = {200-208}, doi = {10.1007/s002480000045}, pmid = {11080378}, issn = {1432-184X}, abstract = {We measured bacterial growth on phototransformed dissolved organic matter (DOM) leached from eight different primary producers. Leachates (10 mg C liter(-1)) were exposed to artificial UVA + UVB radiation, or kept in darkness, for 20 h. DOM solutions were subsequently inoculated with lake water bacteria. Photoproduction of dissolved inorganic carbon (DIC), ranging from 3 to 16 µg C liter(-1) h(-1), and changes in the absorptive characteristics of the DOM were observed for all leachates upon UV irradiation. The effects of irradiation exposure on DOM bioavailability varied greatly, depending on leachate and type of bacterial growth criterion. Bacterial carbon utilization (biomass production plus respiration) over the entire incubation period (120 h) was enhanced by UV radiation of leachate from the terrestrial leaves, relative to carbon utilization in non-irradiated leachates. Conversely, carbon utilization was reduced by radiation of the leachates from aquatic macrophytes. In a separate experiment, the stable C and N isotope composition of bacteria grown on irradiated and non-irradiated DOM was estimated. Bacterial growth on UV-irradiated DOM was enriched in (13)C relative to the bacteria in the non-irradiated treatments; this result may be explained by selective assimilation of photochemically produced, isotopically enriched labile compounds.}, }
@article {pmid11080377, year = {2000}, author = {Snyder, RA and Millward, JD and Steffensen, WS}, title = {Aquifer Protist Response and the Potential for TCE Bioremediation with Burkholderia cepacia G4 PR1.}, journal = {Microbial ecology}, volume = {40}, number = {3}, pages = {189-199}, doi = {10.1007/s002480000037}, pmid = {11080377}, issn = {1432-184X}, abstract = {Bacterivorous protists have been recovered from pristine and contaminated aquifer environments, but the ecological role of these organisms in bioremediation strategies has not been well defined. Burkholderia cepacia G4 PR1 constitutively expresses a toluene ortho-monooxygenase (tom) due to a secondary transposition of a Tn5 transposable element in a trichloroethylene (TCE) degradative plasmid (TOM). Groundwater and sediment from a potential site for a TCE bioremediation field demonstration were used in laboratory microcosms to test the survival of this organism. In nonsterile aquifer sediment slurries, the bacterium was eliminated in a logrithmic decay concomitant with an increase in bacterivorous protists. A half-life for the organism calculated from extinction coefficients increased logarithmically with increasing inoculation density above 1 x 10(6) PR1 ml(-1). For inoculation densities below this level, the half-life of PR1 increased exponentially with decreasing inoculation density. The lowest half-lives corresponded to densities of bacteria that stimulate response of bacterivores. In a column system designed to incorporate aquifer flow, repeated addition of PR1 resulted in a buildup of bacterivore populations and reduced half-life of the bacterium. Addition of TCE and growth substrate in the eluent resulted in prolonged survival of PR1 and apparent mineralization of TCE. The results indicate significant but predictable losses due to native bacterivores would occur within and beyond a treatment zone where PR1 would be added to the aquifer, and mineralization of TCE in contaminated groundwater might be possible with repeated inoculation and addition of nutrients.}, }
@article {pmid11080376, year = {2000}, author = {Röling, WF and van Breukelen BM,  and Braster, M and Goeltom, MT and Groen, J and van Verseveld HW, }, title = {Analysis of Microbial Communities in a Landfill Leachate Polluted Aquifer using a New Method for Anaerobic Physiological Profiling and 16S rDNA Based Fingerprinting.}, journal = {Microbial ecology}, volume = {40}, number = {3}, pages = {177-188}, doi = {10.1007/s002480000033}, pmid = {11080376}, issn = {1432-184X}, abstract = {Databases containing information regarding presence and activity of microbial communities will be very useful for determination of the potential for intrinsic bioremediation in landfill leachate polluted aquifers. Simple analyses such as community-level physiological profiling (CLPP) and denaturing gradient gel electrophoresis (DGGE) of 16S rDNA fragments yield large sets of data for inclusion into such databases. In this study we describe the development of a method for anaerobic CLPP, using commercially available Biolog plates. Incubation at the in situ temperature of the aquifer (10 degrees C) for 28 days was optimal for obtaining a specific, reproducible physiological profile. Anaerobic incubation was essential for profiling anaerobic communities. The anaerobic cultivation-dependent CLPP method and cultivation-independent DGGE were applied to groundwater and sediment samples from the aquifer near the Coupépolder landfill in The Netherlands. A combination of computer-assisted CLPP and DGGE analysis of both groundwater and sediment samples yielded the best separating power for characterizing microbial communities in the aquifer. Communities in groundwater were significantly different from those in the corresponding sediment. Microbial communities present in subsamples from sediment cores usually were similar for the various sampling locations. Variation was observed for the heterogeneous sediment beneath the landfill. Both anaerobic CLPP and DGGE analysis clearly separated microbial communities from the polluted aquifer underneath the landfill from those in the less or not polluted aquifer downstream and upstream of the landfill.}, }
@article {pmid11080375, year = {2000}, author = {Tabacchioni, S and Chiarini, L and Bevivino, A and Cantale, C and Dalmastri, C}, title = {Bias Caused by Using Different Isolation Media for Assessing the Genetic Diversity of a Natural Microbial Population.}, journal = {Microbial ecology}, volume = {40}, number = {3}, pages = {169-176}, doi = {10.1007/s002480000015}, pmid = {11080375}, issn = {1432-184X}, abstract = {The influence of isolation medium on the biodiversity of Burkholderia cepacia strains recovered from the rhizosphere of Zea mays was evaluated by comparing the genetic diversity of isolates obtained by plating serial dilutions of root macerates on the two selective media TB-T and PCAT. From each medium, 50 randomly chosen colonies were isolated. On the basis of the restriction patterns of DNA coding for 16S rRNA (16S rDNA) amplified by means of PCR (ARDRA), all strains isolated from TB-T medium were assigned to the B. cepacia species, whereas among PCAT isolates only 74% were assigned to the B. cepacia species. Genetic diversity among the PCAT and TB-T isolates was evaluated by the random amplified polymorphic DNA (RAPD) technique. The analysis of molecular variance (AMOVA) method was applied to determine the variance component for RAPD patterns. Most of the genetic diversity (90.59%) was found within the two groups of isolates, but an appreciable amount (9.41%) still separated the two groups (P < 0.001). Mean genetic distances among PCAT isolates (10.39) and TB-T isolates (9.36) were significantly different (P < 0.0001). The results indicate that the two different isolation media select for B. cepacia populations with a different degree of genetic diversity. Moreover, a higher degree of genetic diversity was observed among strains isolated from PCAT medium than among those isolated from TB-T medium.}, }
@article {pmid11077159, year = {2000}, author = {Brune, A and Frenzel, P and Cypionka, H}, title = {Life at the oxic-anoxic interface: microbial activities and adaptations.}, journal = {FEMS microbiology reviews}, volume = {24}, number = {5}, pages = {691-710}, doi = {10.1111/j.1574-6976.2000.tb00567.x}, pmid = {11077159}, issn = {0168-6445}, mesh = {*Adaptation, Physiological ; Aerobiosis/physiology ; Anaerobiosis/physiology ; Animals ; Bacteria/*growth &amp; development/*metabolism ; Intestines/microbiology ; Isoptera/microbiology ; *Oxygen/metabolism ; Water Microbiology ; }, abstract = {Molecular oxygen is one of the most important reactants in biogeochemical cycles. Due to its low solubility in water, the consumption of oxygen leads to the development of oxic-anoxic interfaces, which separate aerobic from anaerobic processes in virtually all environments, ranging in scale from oceanic sediments to the fecal pellets of a small soil invertebrate. Three case studies were selected to illustrate the basic situation and the specific characteristics of oxic-anoxic interfaces: sediments, the rhizosphere of aquatic plants, and the intestinal tract of insects. Each system is governed by the same general principles, but striking differences arise from, e.g., the nature of the major microbial activities and the mechanisms controlling metabolite fluxes. Also scale and dimensional differences as well as the consequences of temporal fluctuations are of fundamental importance. Recent developments in microbial ecology, which often combine traditional and modern approaches, have significantly furthered our understanding of the specific microniches and the metabolic and behavioral adaptations of microorganisms to life at the oxic-anoxic interface. New concepts help to define the targets of future studies: the spatial organization of microbial populations, their microenvironments and in situ activities, and the functional interactions within structured microbial communities.}, }
@article {pmid11077155, year = {2000}, author = {Liesack, W and Schnell, S and Revsbech, NP}, title = {Microbiology of flooded rice paddies.}, journal = {FEMS microbiology reviews}, volume = {24}, number = {5}, pages = {625-645}, doi = {10.1111/j.1574-6976.2000.tb00563.x}, pmid = {11077155}, issn = {0168-6445}, mesh = {*Archaea/classification/growth &amp; development/isolation &amp; purification/metabolism ; *Bacteria/classification/growth &amp; development/isolation &amp; purification/metabolism ; *Ecosystem ; *Oryza ; Oxidation-Reduction ; *Soil Microbiology ; }, abstract = {Flooded rice paddies are one of the major biogenic sources of atmospheric methane. Apart from this contribution to the 'greenhouse' effect, rice paddy soil represents a suitable model system to study fundamental aspects of microbial ecology, such as diversity, structure, and dynamics of microbial communities as well as structure-function relationships between microbial groups. Flooded rice paddy soil can be considered as a system with three compartments (oxic surface soil, anoxic bulk soil, and rhizosphere) characterized by different physio-chemical conditions. After flooding, oxygen is rapidly depleted in the bulk soil. Anaerobic microorganisms, such as fermentative bacteria and methanogenic archaea, predominate within the microbial community, and thus methane is the final product of anaerobic degradation of organic matter. In the surface soil and the rhizosphere well-defined microscale chemical gradients can be measured. The oxygen profile seems to govern gradients of other electron acceptors (e.g., nitrate, iron(III), and sulfate) and reduced compounds (e.g., ammonium, iron(II), and sulfide). These gradients provide information about the activity and spatial distribution of functional groups of microorganisms. This review presents the current knowledge about the highly complex microbiology of flooded rice paddies. In Section 2 we describe the predominant microbial groups and their function with particular regard to bacterial populations utilizing polysaccharides and simple sugars, and to the methanogenic archaea. Section 3 describes the spatial and temporal development of microscale chemical gradients measured in experimentally defined model systems, including gradients of oxygen and dissolved and solid-phase iron(III) and iron(II). In Section 4, the results of measurements of microscale gradients of oxygen, pH, nitrate-nitrite, and methane in natural rice fields and natural rice soil cores taken to the laboratory will be presented. Finally, perspectives of future research are discussed (Section 5).}, }
@article {pmid11077152, year = {2000}, author = {Overmann, J and van Gemerden, H}, title = {Microbial interactions involving sulfur bacteria: implications for the ecology and evolution of bacterial communities.}, journal = {FEMS microbiology reviews}, volume = {24}, number = {5}, pages = {591-599}, doi = {10.1111/j.1574-6976.2000.tb00560.x}, pmid = {11077152}, issn = {0168-6445}, mesh = {Bacteria/genetics/growth &amp; development/metabolism ; *Bacterial Physiological Phenomena ; Biological Evolution ; *Ecosystem ; Oxidation-Reduction ; Sulfur/*metabolism ; Sulfur-Reducing Bacteria/genetics/growth &amp; development/metabolism/*physiology ; }, abstract = {A major goal of microbial ecology is the identification and characterization of those microorganisms which govern transformations in natural ecosystems. This review summarizes our present knowledge of microbial interactions in the natural sulfur cycle. Central to the discussion is the recent progress made in understanding the co-occurrence in natural ecosystems of sulfur bacteria with contrasting nutritional requirements and of the spatially very close associations of bacteria, the so-called phototrophic consortia (e.g. 'Chlorochromatium aggregatum' or 'Pelochromatium roseum'). In a similar way, microbial interactions may also be significant during microbial transformations other than the sulfur cycle in natural ecosystems, and could also explain the low culturability of bacteria from natural samples.}, }
@article {pmid11077149, year = {2000}, author = {Amann, R and Ludwig, W}, title = {Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology.}, journal = {FEMS microbiology reviews}, volume = {24}, number = {5}, pages = {555-565}, doi = {10.1111/j.1574-6976.2000.tb00557.x}, pmid = {11077149}, issn = {0168-6445}, mesh = {Bacteria/*classification/*genetics/growth &amp; development ; Bacterial Typing Techniques ; *Bacteriological Techniques ; *Ecosystem ; History, 20th Century ; *Molecular Probe Techniques ; Oligonucleotide Probes ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal/*genetics ; }, abstract = {With readily applicable hybridization assays, mainly based on rRNA-targeted nucleic acid probes, and direct, cultivation-independent sequence retrieval, microbiologists can for the first time determine the true composition of microbial communities. Phylogenetic identification and exact spatiotemporal quantification of microorganisms will in the future become prerequisites for high quality studies in microbial ecology just as good taxonomy and solid quantification have always been for macroecology. This review is intended to give a short history of the development of rRNA-targeted nucleic acid probes and probe technologies, as well as of their application in microbial ecology. The current state of the art is described, and we will try to look into the future. Over the last decade, rRNA-targeted probes have become a handy tool for microbial ecologists. In order to speed up the transformation of microbial ecology from a mostly descriptive to a hypothesis-driven, experimental science more intense use must be made of the taxonomic precision and quantitativeness of rRNA-targeted probes.}, }
@article {pmid11077148, year = {2000}, author = {Schink, B}, title = {Microbial ecology--a late developing field in science.}, journal = {FEMS microbiology reviews}, volume = {24}, number = {5}, pages = {553}, doi = {10.1016/s0168-6445(00)00043-7}, pmid = {11077148}, issn = {0168-6445}, mesh = {*Bacteria ; Bacteriological Techniques/history ; Ecosystem ; History, 20th Century ; Microbiological Techniques/*history ; }, }
@article {pmid11068828, year = {1999}, author = {Vincke, E and Verstichel, S and Monteny, J and Verstraete, W}, title = {A new test procedure for biogenic sulfuric acid corrosion of concrete.}, journal = {Biodegradation}, volume = {10}, number = {6}, pages = {421-428}, doi = {10.1023/A:1008309320957}, pmid = {11068828}, issn = {1572-9729}, abstract = {A new test method is described for biogenic sulfuric acid corrosion of concrete, more specifically in sewer conditions. The aim of the new test method is the development of an accelerated and reproducible procedure for monitoring the resistance of different types of concrete with regard to biogenic sulfuric acid corrosion. This experimental procedure reflects worst case conditions by providing besides H2S, also an enrichment of thiobacilli and biologically produced sulfur. By simulating the cyclic processes occurring in sewer pipes, significant differences between concrete mixtures could be detected after 51 days. Concrete modified by a styrene-acrylic ester polymer demonstrated a higher resistance against biogenic sulfuric acid attack.}, }
@article {pmid11065378, year = {2000}, author = {Ulrich, A and Zaspel, I}, title = {Phylogenetic diversity of rhizobial strains nodulating Robinia pseudoacacia L.}, journal = {Microbiology (Reading, England)}, volume = {146 (Pt 11)}, number = {}, pages = {2997-3005}, doi = {10.1099/00221287-146-11-2997}, pmid = {11065378}, issn = {1350-0872}, mesh = {DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rhizobium/classification/*genetics/isolation &amp; purification ; Trees/*microbiology ; }, abstract = {Lack of knowledge exists regarding the diversity of rhizobial strains nodulating black locust (Robinia pseudoacacia L.), which is a neophytic tree species widely distributed in Europe. Seventeen rhizobial strains isolated from nodules of black locust at a German location were examined by phenotypic characterization and 16S rDNA analysis. The isolates were classified in nine 16S rDNA genotypes using a set of seven endonucleases. Based on RFLP analysis and sequencing, the strains were shown to belong to the genera Mesorhizobium (76%) and Rhizobium (24%). Five genotypes were identical to the species Mesorhizobium amorphae, Mesorhizobium loti, Mesorhizobium huakuii, Rhizobium leguminosarum and Rhizobium tropici. A strong similarity between the 16S rDNA sequence of another two genotypes and M. amorphae (99.9%) as well as the Mesorhizobium strain R88b (99.8%) was found. The two remaining genotypes were classified in the genus Rhizobium, without a significant relationship at the species level. Comparing isolates nodulating Rob. pseudoacacia and Amorpha fruticosa, a parallel picture of phylogenetic diversity was detected with a range of phylogenetically different rhizobia and M. amorphae dominating. For this study, 18 rhizobial strains which had originally been isolated from a forest in Maryland where black locust is native were additionally analysed. Results revealed seven genotypes all belonging to the genus Mesorhizobium, with four genotypes identical to the isolates from the German sampling location. Whereas the genotype identical to M. amorphae dominated within the strains obtained from the German location, the dominance of a genotype identical to M. huakuii was found among the strains from the native location. Summarizing data from both locations, Rob. pseudoacacia was nodulated with various genomic species, most of which belonged to the genus Mesorhizobium. Concerning phenotypic features such as growth rate, pH tolerance or use of certain carbohydrates, most isolates corresponded to described species and genera. However, there were differences in salt tolerance between these isolates and the corresponding reference strains. Overall, the results demonstrated a high phenotypic and phylogenetic diversity of rhizobial strains nodulating Rob. pseudoacacia. This may be a characteristic of neophytic and other widely spread legumes and may contribute to the success of black locust as a pioneer tree species for the temperate zone.}, }
@article {pmid11053394, year = {2000}, author = {Tolker-Nielsen, T and Brinch, UC and Ragas, PC and Andersen, JB and Jacobsen, CS and Molin, S}, title = {Development and dynamics of Pseudomonas sp. biofilms.}, journal = {Journal of bacteriology}, volume = {182}, number = {22}, pages = {6482-6489}, pmid = {11053394}, issn = {0021-9193}, mesh = {Biofilms/*growth &amp; development ; DNA Transposable Elements/genetics ; Green Fluorescent Proteins ; Luminescent Proteins/genetics ; Microscopy, Confocal ; Molecular Sequence Data ; Pseudomonas/genetics/*physiology/ultrastructure ; Pseudomonas putida/physiology/ultrastructure ; Red Fluorescent Protein ; }, abstract = {Pseudomonas sp. strain B13 and Pseudomonas putida OUS82 were genetically tagged with the green fluorescent protein and the Discosoma sp. red fluorescent protein, and the development and dynamics occurring in flow chamber-grown two-colored monospecies or mixed-species biofilms were investigated by the use of confocal scanning laser microscopy. Separate red or green fluorescent microcolonies were formed initially, suggesting that the initial small microcolonies were formed simply by growth of substratum attached cells and not by cell aggregation. Red fluorescent microcolonies containing a few green fluorescent cells and green fluorescent microcolonies containing a few red fluorescent cells were frequently observed in both monospecies and two-species biofilms, suggesting that the bacteria moved between the microcolonies. Rapid movement of P. putida OUS82 bacteria inside microcolonies was observed before a transition from compact microcolonies to loose irregularly shaped protruding structures occurred. Experiments involving a nonflagellated P. putida OUS82 mutant suggested that the movements between and inside microcolonies were flagellum driven. The results are discussed in relation to the prevailing hypothesis that biofilm bacteria are in a physiological state different from planktonic bacteria.}, }
@article {pmid11051362, year = {2000}, author = {Florin, TH and Zhu, G and Kirk, KM and Martin, NG}, title = {Shared and unique environmental factors determine the ecology of methanogens in humans and rats.}, journal = {The American journal of gastroenterology}, volume = {95}, number = {10}, pages = {2872-2879}, doi = {10.1111/j.1572-0241.2000.02319.x}, pmid = {11051362}, issn = {0002-9270}, mesh = {Adolescent ; Animals ; Breath Tests ; Colon/*microbiology ; Euryarchaeota/*physiology ; Feces/chemistry ; Female ; *Genotype ; Humans ; Male ; Methane/analysis ; Rats ; Rats, Inbred Strains ; *Social Environment ; Weaning ; }, abstract = {OBJECTIVE: This study ascertains the relative contributions of genetics and environment in determining methane emission in humans and rats. There is considerable interest in the factors determining the microbial species that inhabit the colon. Methanogens. which are archaebacteria, are an easily detected colonic luminal bacteria because they respire methane. They are present in some but not all human colons and lower animal hindguts. Opinion varies on the nature of the factors influencing this ecology with some studies proposing the existence of host genetic influences.<br><br>METHODS: Methane emission was measured in human twin pairs by gas chromatography, and structural equation modeling was used to determine the proportion of genetic and environmental determinants. The importance of the timing of environmental effects and rat strain on the trait of methane emission were ascertained by experiments with cohabiting methanogenic and nonmethanogenic rats.<br><br>RESULTS: Analysis of breath samples from 274 adolescent twin pairs and their families indicated that the major influences on the trait of methane emission are the result of shared (53%, 95% confidence interval 39-61) and unique environmental (47%, 95% confidence interval 38-56) effects. No significant autosomal genetic effects were detected, but as observed in other studies, men (37%) were less likely to excrete methane in their breath than women (63%). Investigation of methane emission in rats indicated that environmental effects in this animal are most potent during the weaning period, with stable gut microbial ecology thereafter for some but not all rat strains.<br><br>CONCLUSIONS: These results are consistent with shared and unique environmental factors being the main determinants of the ecology of this colonic microbe.}, }
@article {pmid11048718, year = {2000}, author = {Cooper, VS and Lenski, RE}, title = {The population genetics of ecological specialization in evolving Escherichia coli populations.}, journal = {Nature}, volume = {407}, number = {6805}, pages = {736-739}, doi = {10.1038/35037572}, pmid = {11048718}, issn = {0028-0836}, mesh = {Adaptation, Physiological ; Ecology ; Escherichia coli/*genetics/metabolism ; *Evolution, Molecular ; Genes, Bacterial ; Glucose/metabolism ; Models, Biological ; Mutation ; }, abstract = {When organisms adapt genetically to one environment, they may lose fitness in other environments. Two distinct population genetic processes can produce ecological specialization-mutation accumulation and antagonistic pleiotropy. In mutation accumulation, mutations become fixed by genetic drift in genes that are not maintained by selection; adaptation to one environment and loss of adaptation to another are caused by different mutations. Antagonistic pleiotropy arises from trade-offs, such that the same mutations that are beneficial in one environment are detrimental in another. In general, it is difficult to distinguish between these processes. We analysed the decay of unused catabolic functions in 12 lines of Escherichia coli propagated on glucose for 20,000 generations. During that time, several lines evolved high mutation rates. If mutation accumulation is important, their unused functions should decay more than the other lines, but no significant difference was observed. Moreover, most catabolic losses occurred early in the experiment when beneficial mutations were being rapidly fixed, a pattern predicted by antagonistic pleiotropy. Thus, antagonistic pleiotropy appears more important than mutation accumulation for the decay of unused catabolic functions in these populations.}, }
@article {pmid11045126, year = {2000}, author = {Bussy Malgrange, V and Blanc-Vincent, MP and Escande, MC and Fuhrmann, C and Béal, J and Boineau, F and Biron, P and Crokaert, F and Lesimple, T and Pottecher, B and Raveneau, J and Senet, JM and Viot, M}, title = {[Standards, options and recommendations for good practice in hemoculture in cancerology].}, journal = {Presse medicale (Paris, France : 1983)}, volume = {29}, number = {27}, pages = {1532-1534}, pmid = {11045126}, issn = {0755-4982}, mesh = {Bacteriological Techniques/*standards ; France ; Humans ; Neoplasms/*microbiology ; Practice Guidelines as Topic ; Sepsis/diagnosis/*microbiology ; Systemic Inflammatory Response Syndrome/diagnosis/*microbiology ; }, abstract = {Excepting emergency and aplasia: two to three blood samples should be draw for culture an hour apart within a 24 period (standard). For emergency or aplasia: two to three blood samples should be drawn for culture before initiating early antibiotic therapy. The delay between samples drawn from different sites should be less than one hour (standard). For patients on antibiotics: four to six blood samples should be drawn for culture within 48 hours, outside ongoing antibiotic administration. If the patient is given corticosteroids, it is recommended to draw two or three blood samples in case of deterioration (agreement of the experts). Rigorous aseptic techniques must be used (standard). Culture media are chosen according to the institution's microbial ecology (standard). The volume of blood drawn should be adapted to the system used (standard). Culture positivity is determined at 24 to 48 hours.}, }
@article {pmid11029084, year = {2000}, author = {Delille, D}, title = {Response of Antarctic Soil Bacterial Assemblages to Contamination by Diesel Fuel and Crude Oil.}, journal = {Microbial ecology}, volume = {40}, number = {2}, pages = {159-168}, doi = {10.1007/s002480000027}, pmid = {11029084}, issn = {1432-184X}, abstract = {The effects of diesel fuel and "Arabian light" crude oil addition on Antarctic bacterial assemblages were studied in four contaminated soils during 1 year in the Terre Adelie land area. Monthly sampling allowed a regular survey of the bacterial changes occurring in the contaminated soils. All samples were analyzed for total bacteria, heterotrophic culturable microbiota, and hydrocarbon-utilizing microbiota. Crude oil contamination induced an initial increase of all bacterial parameters in all contaminated soils. Diesel oil contamination had a more complex effect. Hydrocarbon degrading bacterial abundance increases occurred after diesel oil addition. In contrast, general heterotrophic bacterial abundance could significantly decrease in the same conditions. In all cases the stimulatory effects of oil addition disappeared after several months of contamination.}, }
@article {pmid11029083, year = {2000}, author = {Bernard, L and Courties, C and Servais, P and Troussellier, M and Petit, M and Lebaron, P}, title = {Relationships among Bacterial Cell Size, Productivity, and Genetic Diversity in Aquatic Environments using Cell Sorting and Flow Cytometry.}, journal = {Microbial ecology}, volume = {40}, number = {2}, pages = {148-158}, doi = {10.1007/s002480000046}, pmid = {11029083}, issn = {1432-184X}, abstract = {The study of relationships between cell size and productivity is of key importance in microbial ecology to understand which members of natural aquatic communities are responsible for the overall activity and/or productivity. Flow sorting of microorganisms from different environmental samples was used to analyze the activity of bacterial cells depending on their biovolume. Bacterial cells from five different natural samples taken along the Mediterranean coast including fresh- and seawaters were incubated with tritiated leucine, then stained with SYTO 13 and sorted by flow cytometry according to their average side-angle-scattered (SSC) light. In all samples, a bell-shaped relationship was found between cell biovolume and activity, whereas activity of a given cell-size class varied between samples. In contrast, an inverse relationship was found between biovolumes and abundances. These results suggest that medium-sized cells with highest growth rates are probably submitted to intense grazing. For one sample, bacteria within five different size classes were sorted and the genetic diversity of cells within each sorted size class and that of the whole community were analyzed by the denaturing gradient gel electrophoresis (DGGE) method. The genetic diversity, as determined at the community level was highly represented into the pool of small cells, whereas only few species were present into larger cell subpopulations. The results suggest that only a few genotypes may be dominant within the largest and most productive cells. Furthermore, cell size polymorphism as well as heterogeneous cellular activities were found within some species.}, }
@article {pmid11029082, year = {2000}, author = {Olson, JB and Lord, CC and McCarthy, PJ}, title = {Improved Recoverability of Microbial Colonies from Marine Sponge Samples.}, journal = {Microbial ecology}, volume = {40}, number = {2}, pages = {139-147}, doi = {10.1007/s002480000058}, pmid = {11029082}, issn = {1432-184X}, abstract = {The growth of microorganisms from marine sponge samples was studied on various low to high nutrient solid media using media supplements. The supplements utilized were catalase, sodium pyruvate, and a combination of the two. Medium composition was found to influence the growth response on the supplemented media. Microorganisms on low nutrient media responded more favorably to the media additions than on high nutrient media. Thirty-five percent of the supplemented media demonstrated colony forming unit (CFU) recoveries that were 50% or greater than those of the unamended control plates. Twenty-one percent showed recoveries of more than 100% of the control values, with sodium pyruvate additions providing for the greatest overall increase in recovery, whether alone or in conjunction with catalase. These findings suggest that addition of catalase or sodium pyruvate to solid growth and isolation media may improve recoverability of microorganisms from natural samples.}, }
@article {pmid11029081, year = {2000}, author = {Fisher, MM and Klug, JL and Lauster, G and Newton, M and Triplett, EW}, title = {Effects of Resources and Trophic Interactions on Freshwater Bacterioplankton Diversity.}, journal = {Microbial ecology}, volume = {40}, number = {2}, pages = {125-138}, doi = {10.1007/s002480000049}, pmid = {11029081}, issn = {1432-184X}, abstract = {In a study of bacterioplankton in an oligotrophic lake in northern Wisconsin, a community fingerprinting technique, automated ribosomal intergenic spacer analysis (ARISA), was used to determine the effect of resources and trophic interactions on bacterioplankton diversity. Inorganic nitrogen and phosphorus (NP), carbon in the form of glucose (G) or dissolved organic matter extracted from peat (DOM), and carbon and NP in combination were added to two types of experimental systems. Ten-liter mesocosms contained all components of the original aquatic community except for large zooplankton. One-liter dilution cultures were prepared so that the effects of grazers and phytoplankton were removed. During a 3-day incubation, bacterial production showed the greatest response to the carbon plus NP treatment in both experimental systems, but bacterial diversity was strikingly different between them. In the mesocosms, the number of ARISA-PCR fragments averaged 41 per profile, whereas the dilution culture communities were highly reduced in complexity, dominated in most cases by a single PCR fragment. Further analysis of the mesocosm data suggested that whereas the NPDOM addition caused the greatest aggregate bacterial growth response, the addition of NP alone caused the largest shifts in community composition. These results suggest that the measurement of aggregate responses, such as bacterial production, alone in studies of freshwater bacterial communities may mask the effects of resources on bacterioplankton.}, }
@article {pmid11029080, year = {2000}, author = {Middelboe, M}, title = {Bacterial Growth Rate and Marine Virus-Host Dynamics.}, journal = {Microbial ecology}, volume = {40}, number = {2}, pages = {114-124}, doi = {10.1007/s002480000050}, pmid = {11029080}, issn = {1432-184X}, abstract = {The dynamics of a marine virus-host system were investigated at different steady state growth rates in chemostat cultures and the data were analyzed using a simple model. The virus-host interactions showed strong dependence on host cell growth rate. The duration of the infection cycle and the virus burst size were found to depend on bacterial growth rate, and the rate of cell lysis and virus production were positively correlated with steady state growth rate in the cultures (r(2) > 0.96, p < 0.05). At bacterial growth rates of 0.02 to 0.10 h(-1) in the chemostats the virus burst size increased from 12 +/- 4 to 56 +/- 4, and the latent period decreased from 2.0 to 1.7 h. Resistant clones of the host strain were present in the cultures from the beginning of the experiment and replaced the sensitive host cells following viral lysis in the cultures. Regrowth of resistant cells correlated significantly (r(2) = 1.000, p < 0.02) with the lysis rate of sensitive cells, indicating that release of viral lysates stimulated growth of the non-infected, resistant cells. The constructed model was suitable for simulating the observed dynamics of the sensitive host cells, viruses and resistant clones in the cultures. The model was therefore used in an attempt to predict the dynamics of this virus-host interaction in a natural marine environment during a certain set of growth conditions. The simulation indicated that a steady state relationship between the specific viruses and sensitive and resistant bacterial clones may occur at densities that are reasonable to assume for natural environments. The study demonstrates that basic characterization and modeling of specific virus-host interactions may improve our understanding of the behavior of bacteria and viruses in natural systems.}, }
@article {pmid11029079, year = {2000}, author = {Lindström, ES}, title = {Bacterioplankton Community Composition in Five Lakes Differing in Trophic Status and Humic Content.}, journal = {Microbial ecology}, volume = {40}, number = {2}, pages = {104-113}, doi = {10.1007/s002480000036}, pmid = {11029079}, issn = {1432-184X}, abstract = {To investigate the relation between lake type and bacterioplankton community composition, five Swedish lakes, which differed from each other in nutrient content and water color, were studied. Denaturing gradient gel electrophoresis (DGGE) of 16S rDNA was used to examine community composition. The DGGE-patterns of the different samples were analyzed in relation to physical, chemical, and biological data from the lakes by canonical correspondence analysis (CCA). The three variables found to most strongly correlate with the DGGE patterns were biomasses of microzooplankton, cryptophytes, and chrysophytes, suggesting that these biota had an impact on bacterioplankton community structure. Two of the three factors were, in turn, significantly correlated to parameters associated with the trophic status of the lakes, indicating that the nutrient content of the lakes, at least indirectly, influenced the structure of the bacterioplankton community. The relation to water color was less pronounced.}, }
@article {pmid11029078, year = {2000}, author = {Kühl, M and Fenchel, T}, title = {Bio-optical Characteristics and the Vertical Distribution of Photosynthetic Pigments and Photosynthesis in an Artificial Cyanobacterial Mat.}, journal = {Microbial ecology}, volume = {40}, number = {2}, pages = {94-103}, doi = {10.1007/s002480000061}, pmid = {11029078}, issn = {1432-184X}, abstract = {Zonations of photosynthesis and photopigments in artificial cyanobacterial mats were studied with (i) oxygen and pH microsensors, (ii) fiber-optic microprobes for field radiance, scalar irradiance, and PSII fluorescence, and (iii) a light microscope equipped with a spectrometer for spectral absorbance and fluorescence measurements. Our analysis revealed the presence of several distinct 1-2 mm thick cyanobacterial layers mixed with patches of anoxygenic photosynthetic bacteria. Strong attenuation of visible light confined the euphotic zone to the uppermost 3 mm of the mat, where oxygen levels of 3-4 times air saturation and a pH peak of up to pH 8.8 were observed under saturating irradiance (413 µmol photon m(-2) s(-1)). Oxygen penetration was 5 mm in light and decreased to 1 mm in darkness. Volumetric oxygen consumption in the photic and aphotic zones of illuminated mat was 5.5 and 2.9 times higher, respectively, than oxygen consumption in dark incubated mats. Scalar irradiance reached 100-150% of incident irradiance in the upper 0.5 mm of the mat due to intense scattering in the matrix of cells, exopolymers, and carbonate precipitates. In deeper mat layers scalar irradiance decreased nearly exponentially, and highest attenuation coefficients of 6-7 mm(-1) were found in cyanobacterial layers, where photosynthesis and photopigment fluorescence also peaked. Visible light was attenuated >100 times more strongly than near infrared light. Microscope spectrometry on thin sections of mats allowed detailed spectral absorbance and fluorescence measurements at defined positions relative to the mat surface. Besides strong spectral signals of cyanobacterial photopigments (Chl a and phycobiliproteins), the presence of both green and purple photosynthetic bacteria was evident from spectral signals of Bchl a and Bchl c. Microprofiles of photopigment absorbance correlated well with microdistributions of phototrophs determined in an accompanying study.}, }
@article {pmid11029077, year = {2000}, author = {Fenchel, T and Kühl, M}, title = {Artificial Cyanobacterial Mats: Growth, Structure, and Vertical Zonation Patterns.}, journal = {Microbial ecology}, volume = {40}, number = {2}, pages = {85-93}, doi = {10.1007/s002480000062}, pmid = {11029077}, issn = {1432-184X}, abstract = {The formation of cyanobacterial mats (originally induced by incubation of sediment cores in which metazoans and most other eukaryotes had been removed) was followed over approximately 2.6 years. The thickness of the mats increased at a rate of 2-3 mm per year because of accumulation of empty cyanobacterial sheaths and as a result of carbonate deposition; the fraction of living biomass remained relatively constant over at least 2 years, but there was a slow accumulation of nonliving organic C (approximately 1 mmol yr(-1)). Biota composition (dominated by five types of filamentous cyanobacteria, unicellular cyanobacteria, diatoms, anoxygenic phototrophs, and heterotrophic bacteria) and vertical zonation patterns in the upper 2-3 mm of the mats were also almost constant over time. Using transmission electron microscopy and stereological analysis it was possible to quantify the vertical distribution of major groups of organisms.}, }
@article {pmid11029076, year = {2000}, author = {Tolker-Nielsen, T and Molin, S}, title = {Spatial Organization of Microbial Biofilm Communities.}, journal = {Microbial ecology}, volume = {40}, number = {2}, pages = {75-84}, doi = {10.1007/s002480000057}, pmid = {11029076}, issn = {1432-184X}, abstract = {The application of advanced microscopy and molecular and electrochemical high-resolution methods has provided insights into the structural organization and function of biofilm communities. It appears that cellular properties such as growth differentiation, chemotaxis, and cell-to-cell signaling enable biofilm communities to organize structurally in response to the external conditions and the activities of the different biofilm members. Thereby resource utilization becomes optimized, and processes which require syntrophic relationships or special micro-environments become facilitated.}, }
@article {pmid11022327, year = {2000}, author = {Münchmeyer, U and Russow, R and Augustin, J}, title = {Net and gross nitrogen mineralization in drained and reflooded fen soils.}, journal = {Isotopes in environmental and health studies}, volume = {36}, number = {1}, pages = {79-98}, doi = {10.1080/10256010008032934}, pmid = {11022327}, issn = {1025-6016}, mesh = {*Environmental Pollution ; Fresh Water ; Humans ; Nitrogen/*chemistry ; Nitrogen Isotopes ; Soil/*analysis ; Water Movements ; }, abstract = {One purpose of new land use concepts for degraded fens (organic soils with high N content) is the reduction of the mineralization process due to very high groundwater levels. However, knowledge of nitrogen mineralization process (net and gross) in degraded fen soils affected by reflooding is very small. Therefore, the objectives of our study were (a) to evaluate the suitability of 15N pool dilution method for measurements of gross mineralization rates in degraded fen soils and (b) to investigate how the reflooding of a degraded fen affects the net and gross nitrogen mineralization in a short-term incubation experiment. The usability of the 15N pool dilution method was diminished by the low recovery of the applied 15NH4+ at time zero. The recovery of the added 15NH4+ in the extractable soil NH4+ pool was only 13.5% for the drained soil and 59.6% for the reflooded soil. However, the gross mineralization rates were similar for both soils and exceeded always the net rates substantially. The cumulative net mineralization rate was higher for the reflooded soil (1.58 micrograms N*cm-3*d-1) than for the drained soil (-0.67 microgram N*cm-3*d-1). Differences between the two soils were also found in the nitrification intensity and the loss of 15N. This was probably one reason for the higher net mineralization rate in the reflooded soil.}, }
@article {pmid11021917, year = {2000}, author = {Heydorn, A and Ersbøll, BK and Hentzer, M and Parsek, MR and Givskov, M and Molin, S}, title = {Experimental reproducibility in flow-chamber biofilms.}, journal = {Microbiology (Reading, England)}, volume = {146 (Pt 10)}, number = {}, pages = {2409-2415}, doi = {10.1099/00221287-146-10-2409}, pmid = {11021917}, issn = {1350-0872}, mesh = {Analysis of Variance ; Bacterial Proteins/genetics/metabolism ; *Biofilms/growth &amp; development ; Culture Media ; Green Fluorescent Proteins ; Image Processing, Computer-Assisted/*methods ; Luminescent Proteins/genetics/metabolism ; Pseudomonas aeruginosa/genetics/*growth &amp; development ; Reproducibility of Results ; Sigma Factor/genetics/metabolism ; *Software ; }, abstract = {The structural organization of microbial communities is influenced by many factors, e.g. nutrient composition, shear stress and temperature. This paper presents a general method for quantitative comparison of biofilm structures and assessment of experimental reproducibility between independent biofilm experiments. By using a novel computer program, COMSTAT, biofilm structures of Pseudomonas aeruginosa and an isogenic rpoS mutant were quantified. The strains were tagged with the green fluorescent protein (GFP) and grown in flow chambers with a defined minimal medium as substrate. Three independent rounds of biofilm experiments were performed and in each round, each of the two variants was grown in two separate channels. Nine image stacks were acquired in each channel 146 h after inoculation. An analysis of variance model incorporating the factors experiment round, bacterial strain, channel number and image stack number was used to analyse the data calculated by COMSTAT. Experimental reproducibility was verified by estimating the magnitude of the variance of the effects round (sigma(2)R) and the interaction between bacterial strain and round (sigma(2)BR). Mean thickness of the wild-type and rpoS mutant biofilms was estimated at 6.31 microm (SE 0.81 microm) and 16.85 microm (SE 0.87 microm), respectively.}, }
@article {pmid11021916, year = {2000}, author = {Heydorn, A and Nielsen, AT and Hentzer, M and Sternberg, C and Givskov, M and Ersbøll, BK and Molin, S}, title = {Quantification of biofilm structures by the novel computer program COMSTAT.}, journal = {Microbiology (Reading, England)}, volume = {146 (Pt 10)}, number = {}, pages = {2395-2407}, doi = {10.1099/00221287-146-10-2395}, pmid = {11021916}, issn = {1350-0872}, mesh = {*Biofilms/growth &amp; development ; Culture Media/chemistry ; Green Fluorescent Proteins ; Image Processing, Computer-Assisted/*methods ; Luminescent Proteins/genetics/metabolism ; Microscopy, Confocal/methods ; Phylogeny ; Pseudomonas/genetics/*growth &amp; development ; *Software ; }, abstract = {The structural organization of four microbial communities was analysed by a novel computer program, COMSTAT, which comprises ten features for quantifying three-dimensional biofilm image stacks. Monospecies biofilms of each of the four bacteria, Pseudomonas: putida, P. aureofaciens, P. fluorescens and P. aeruginosa, tagged with the green fluorescent protein (GFP) were grown in flow chambers with a defined minimal medium as substrate. Analysis by the COMSTAT program of four variables describing biofilm structure - mean thickness, roughness, substratum coverage and surface to volume ratio - showed that the four Pseudomonas: strains represent different modes of biofilm growth. P. putida had a unique developmental pattern starting with single cells on the substratum growing into micro-colonies, which were eventually succeeded by long filaments and elongated cell clusters. P. aeruginosa colonized the entire substratum, and formed flat, uniform biofilms. P. aureofaciens resembled P. aeruginosa, but had a stronger tendency to form micro-colonies. Finally, the biofilm structures of P. fluorescens had a phenotype intermediate between those of P. putida and P. aureofaciens. Analysis of biofilms of P. aureofaciens growing on 0.03 mM, 0.1 mM or 0.5 mM citrate minimal media showed that mean biofilm thickness increased with increasing citrate concentration. Moreover, biofilm roughness increased with lower citrate concentrations, whereas surface to volume ratio increased with higher citrate concentrations.}, }
@article {pmid11018125, year = {2000}, author = {Szewzyk, U and Szewzyk, R and Manz, W and Schleifer, KH}, title = {Microbiological safety of drinking water.}, journal = {Annual review of microbiology}, volume = {54}, number = {}, pages = {81-127}, doi = {10.1146/annurev.micro.54.1.81}, pmid = {11018125}, issn = {0066-4227}, mesh = {Biofilms ; Drinking ; Ecology ; Feces/microbiology/parasitology ; Risk Assessment ; *Safety ; *Sanitation ; Water/*parasitology ; *Water Microbiology ; *Water Supply ; }, abstract = {Emerging pathogens in drinking water have become increasingly important during the decade. These include newly-recognized pathogens from fecal sources such as Cryptosporidium parvum, Campylobacter spp., and rotavirus, as well as pathogens that are able to grow in water distribution systems, like Legionella spp., mycobacteria, and aeromonads. To perform a risk analysis for the pathogens in drinking water, it is necessary to understand the ecology of these organisms. The ecology of the drinking-water distribution system has to be evaluated in detail, especially the diversity and physiological properties of water bacteria. The interactions between water bacteria and (potential) pathogens in such diverse habitats as free water and biofilms are essential for the survival or growth of hygienically relevant organisms in drinking water. Results of epidemiological studies together with ecological data are the basis for effective resource protection, water treatment, and risk assessment.}, }
@article {pmid11015496, year = {2000}, author = {De Boever, P and Deplancke, B and Verstraete, W}, title = {Fermentation by gut microbiota cultured in a simulator of the human intestinal microbial ecosystem is improved by supplementing a soygerm powder.}, journal = {The Journal of nutrition}, volume = {130}, number = {10}, pages = {2599-2606}, doi = {10.1093/jn/130.10.2599}, pmid = {11015496}, issn = {0022-3166}, mesh = {Bioreactors ; Clostridium/growth &amp; development/metabolism ; Colon/microbiology ; Ecosystem ; Electric Impedance ; Enterobacteriaceae/growth &amp; development/metabolism ; Escherichia coli/growth &amp; development/metabolism ; Estrogens, Non-Steroidal/metabolism ; Feces/microbiology ; *Fermentation ; Humans ; Intestines/*microbiology ; Isoflavones/analysis/metabolism ; Lactobacillus/growth &amp; development/metabolism ; *Models, Biological ; Phytoestrogens ; Plant Preparations ; *Glycine max ; Staphylococcus/growth &amp; development/metabolism ; }, abstract = {An in vitro model, designated the Simulator of the Human Intestinal Microbial Ecosystem (SHIME), was used to study the effect of a soygerm powder rich in beta-glycosidic phytoestrogenic isoflavones on the fermentation pattern of the colon microbiota and to determine to what extent the latter metabolize the conjugated phytoestrogens. Initially, an inoculum prepared from human feces was introduced into the reactor vessels and stabilized over 3 wk using a culture medium. This stabilization period was followed by a 2-wk control period during which the microbiota were monitored. The microbiota were then subjected to a 2-wk treatment period by adding 2.5 g/d soygerm powder to the culture medium. The addition resulted into an overall increase of bacterial marker populations (Enterobacteriaceae:, coliforms, Lactobacillus: sp., Staphylococcus: sp. and Clostridium: sp.), with a significant increase of the Lactobacillus: sp. population. The short-chain fatty acid (SCFA) concentration increased approximately 30% during the supplementation period; this was due mainly to a significant increase of acetic and propionic acids. Gas analysis revealed that the methane concentration increased significantly. Ammonium and sulfide concentrations were not influenced by soygerm supplementation. Use of an electronic nose apparatus indicated that odor concentrations decreased significantly during the treatment period. The beta-glycosidic bonds of the phytoestrogenic isoflavones were cleaved under the conditions prevailing in the large intestine. The increased bacterial fermentation after addition of the soygerm powder was paralleled by substantial metabolism of the free isoflavones (genistein, daidzein and glycitein), resulting in recovery of only 12-17% of the supplemented isoflavones.}, }
@article {pmid11010975, year = {2000}, author = {Putsep, K and Axelsson, LG and Boman, A and Midtvedt, T and Normark, S and Boman, HG and Andersson, M}, title = {Germ-free and colonized mice generate the same products from enteric prodefensins.}, journal = {The Journal of biological chemistry}, volume = {275}, number = {51}, pages = {40478-40482}, doi = {10.1074/jbc.M007816200}, pmid = {11010975}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; Anti-Bacterial Agents/chemistry/metabolism ; Chromatography, High Pressure Liquid ; Defensins/chemistry/*metabolism ; Germ-Free Life ; Intestine, Small/*metabolism/microbiology ; Mice ; Peptide Fragments/chemistry/metabolism ; Protein Precursors/chemistry/*metabolism ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {The use of germ-free mice offers the possibility to study antibacterial components in a gut uncolonized by bacteria. We have developed a method to extract and high pressure liquid chromatography-fractionate the antibacterial factors present in the small intestine of a single mouse. By mass spectrometry and sequence analyses of fractions exhibiting antimicrobial activity, we identified and characterized the defensin region in germ-free mice as well as in colonized mice. Defensins made up around 15% of the total antibacterial activity both in germ-free and colonized mice. The intestine of germ-free mice exhibited the same set of mature enteric defensins (defensins 1, 2, 3, 4, and 6) as mice colonized by a normal microflora. Mature defensins are generated through processing of larger precursors by enzymatic removal of a signal peptide and a propiece. We found that all prodefensins were cleaved at a Ser/Ala-Leu bond, giving 34-residue propiece peptides and only trace amounts of the predicted 39-residue peptide. This first step must be followed by the removal of a residual peptide to render the mature defensins, indicating that the processing is more complex than previously anticipated. The same propieces were found in both germ-free and colonized mice, suggesting that the same processing operates independent of bacterial presence in the intestine.}, }
@article {pmid11010911, year = {2000}, author = {Nold, SC and Zhou, J and Devol, AH and Tiedje, JM}, title = {Pacific Northwest marine sediments contain ammonia-oxidizing bacteria in the beta subdivision of the Proteobacteria.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {10}, pages = {4532-4535}, pmid = {11010911}, issn = {0099-2240}, mesh = {Ammonia/*metabolism ; Base Sequence ; Betaproteobacteria/*classification/genetics/isolation &amp; purification ; DNA Primers ; Gammaproteobacteria/classification/genetics ; Geologic Sediments/*microbiology ; Molecular Sequence Data ; Northwestern United States ; Oxidation-Reduction ; Oxidoreductases/genetics ; Oxygenases/genetics ; Pacific Ocean ; *Phylogeny ; Polymerase Chain Reaction ; Seawater/*microbiology ; }, abstract = {The diversity of ammonia-oxidizing bacteria in aquatic sediments was studied by retrieving ammonia monooxygenase and methane monooxygenase gene sequences. Methanotrophs dominated freshwater sediments, while beta-proteobacterial ammonia oxidizers dominated marine sediments. These results suggest that gamma-proteobacteria such as Nitrosococcus oceani are minor members of marine sediment ammonia-oxidizing communities.}, }
@article {pmid11010903, year = {2000}, author = {Fuller, ME and Streger, SH and Rothmel, RK and Mailloux, BJ and Hall, JA and Onstott, TC and Fredrickson, JK and Balkwill, DL and DeFlaun, MF}, title = {Development of a vital fluorescent staining method for monitoring bacterial transport in subsurface environments.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {10}, pages = {4486-4496}, pmid = {11010903}, issn = {0099-2240}, mesh = {Comamonas/cytology/isolation &amp; purification/*physiology ; Fluoresceins ; Fluorescent Dyes ; Gram-Negative Bacteria/cytology ; Gram-Positive Bacteria/cytology ; Microscopy, Fluorescence/methods ; Succinimides ; Water Microbiology ; }, abstract = {Previous bacterial transport studies have utilized fluorophores which have been shown to adversely affect the physiology of stained cells. This research was undertaken to identify alternative fluorescent stains that do not adversely affect the transport or viability of bacteria. Initial work was performed with a groundwater isolate, Comamonas sp. strain DA001. Potential compounds were first screened to determine staining efficiencies and adverse side effects. 5-(And 6-)-carboxyfluorescein diacetate, succinimidyl ester (CFDA/SE) efficiently stained DA001 without causing undesirable effects on cell adhesion or viability. Members of many other gram-negative and gram-positive bacterial genera were also effectively stained with CFDA/SE. More than 95% of CFDA/SE-stained Comamonas sp. strain DA001 cells incubated in artificial groundwater (under no-growth conditions) remained fluorescent for at least 28 days as determined by epifluorescent microscopy and flow cytometry. No differences in the survival and culturability of CFDA/SE-stained and unstained DA001 cells in groundwater or saturated sediment microcosms were detected. The bright, yellow-green cells were readily distinguished from autofluorescing sediment particles by epifluorescence microscopy. A high throughput method using microplate spectrofluorometry was developed, which had a detection limit of mid-10(5) CFDA-stained cells/ml; the detection limit for flow cytometry was on the order of 1,000 cells/ml. The results of laboratory-scale bacterial transport experiments performed with intact sediment cores and nondividing DA001 cells revealed good agreement between the aqueous cell concentrations determined by the microplate assay and those determined by other enumeration methods. This research indicates that CFDA/SE is very efficient for labeling cells for bacterial transport experiments and that it may be useful for other microbial ecology research as well.}, }
@article {pmid11010885, year = {2000}, author = {Normander, B and Prosser, JI}, title = {Bacterial origin and community composition in the barley phytosphere as a function of habitat and presowing conditions.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {10}, pages = {4372-4377}, pmid = {11010885}, issn = {0099-2240}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Cluster Analysis ; DNA, Bacterial/genetics/isolation &amp; purification ; DNA, Ribosomal/genetics/isolation &amp; purification ; Electrophoresis, Polyacrylamide Gel/methods ; Hordeum/*microbiology ; Molecular Sequence Data ; Polymerase Chain Reaction/methods ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {An understanding of the factors influencing colonization of the rhizosphere is essential for improved establishment of biocontrol agents. The aim of this study was to determine the origin and composition of bacterial communities in the developing barley (Hordeum vulgare) phytosphere, using denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes amplified from extracted DNA. Discrete community compositions were identified in the endorhizosphere, rhizoplane, and rhizosphere soil of plants grown in an agricultural soil for up to 36 days. Cluster analysis revealed that DGGE profiles of the rhizoplane more closely resembled those in the soil than the profiles found in the root tissue or on the seed, suggesting that rhizoplane bacteria primarily originated from the surrounding soil. No change in bacterial community composition was observed in relation to plant age. Pregermination of the seeds for up to 6 days improved the survival of seed-associated bacteria on roots grown in soil, but only in the upper, nongrowing part of the rhizoplane. The potential occurrence of skewed PCR amplification was examined, and only minor cases of PCR bias for mixtures of two different DNA samples were observed, even when one of the samples contained plant DNA. The results demonstrate the application of culture-independent, molecular techniques in assessment of rhizosphere bacterial populations and the importance of the indigenous soil population in colonization of the rhizosphere.}, }
@article {pmid11005926, year = {2000}, author = {Rogers, JB and DuTeau, NM and Reardon, KF}, title = {Use of 16S-rRNA to investigate microbial population dynamics during biodegradation of toluene and phenol by a binary culture.}, journal = {Biotechnology and bioengineering}, volume = {70}, number = {4}, pages = {436-445}, pmid = {11005926}, issn = {0006-3592}, support = {5P42ES05949-05/ES/NIEHS NIH HHS/United States ; }, mesh = {Biodegradation, Environmental ; Biotechnology/*methods ; Burkholderia/*genetics/metabolism ; In Situ Hybridization, Fluorescence ; Models, Theoretical ; Phenol/*metabolism ; Pseudomonas putida/*genetics/metabolism ; *RNA, Ribosomal, 16S ; Toluene/*metabolism ; }, abstract = {Interspecies interactions and changes in the rate and extent of biodegradation in mixed culture-mixed substrate studies were investigated. A binary mixed culture of Pseudomonas putida F1 and Burkholderia sp. JS150 degraded toluene, phenol, and their mixture. Both toluene and phenol can serve as sole sources of carbon and energy for both P. putida F1 and strain JS150. To investigate the population dynamics of this system, a fluorescent in-situ hybridization method was chosen because of its ability to produce quantitative data, its low standard error, and the ease of use of this method. When the binary mixed culture was grown on toluene or phenol alone, significant interactions between the species were observed. These interactions could not be explained by a pure-and-simple competition model and were substrate dependent. Strain JS150 growth was slightly inhibited when grown with P. putida F1 on phenol, and P. putida F1 grew more rapidly than expected. Conversely, when the two species were grown together on toluene alone, P. putida F1 was inhibited while strain JS150 was unaffected. During growth of the mixed culture on a combination of toluene and phenol, the interactions were similar to that observed during growth on phenol alone; P. putida F1 growth was enhanced while strain JS150 was unaffected. Because of the observed interspecies interactions, monoculture kinetic parameters were not sufficient to describe the mixed culture kinetics in any experiment. This is one of the first reports of microbial population dynamics in which molecular microbial ecology and mathematical modeling have been combined. The use of the 16S-rRNA-based method allowed for observation and understanding of interspecies interactions that were not observable with standard culture-based methods. These results suggest the need for more investigations that account for both substrate and microbial interactions when predicting the fate of organic pollutants in real systems.}, }
@article {pmid11000433, year = {2000}, author = {Porter, J and Pickup, RW}, title = {Nucleic acid-based fluorescent probes in microbial ecology: application of flow cytometry.}, journal = {Journal of microbiological methods}, volume = {42}, number = {1}, pages = {75-79}, doi = {10.1016/s0167-7012(00)00178-0}, pmid = {11000433}, issn = {0167-7012}, mesh = {Bacteria/genetics/growth &amp; development/*isolation &amp; purification ; Ecosystem ; *Environmental Microbiology ; Flow Cytometry/*methods ; *Fluorescent Dyes ; *Nucleic Acid Probes ; }, abstract = {Microorganisms in natural environments have often been treated as 'black box' systems. Researchers have measured the inputs and outputs of the box, and have made bulk measurements on cell behaviour. However, unravelling the details of the diversity and interactions that exist within these microbial populations has proven exceptionally difficult. The information gained from the black box approach has been invaluable, and has allowed models of global foodwebs to be generated and tested. However, there is still little information about the interactions of individual microbial cells within natural populations. Such studies are essential to fully understand the integrated functioning of ecosystems. To achieve this goal, researchers need to be able to identify individual cells within a population, enumerate them, estimate both viability and activity, and monitor changes in response to relevant parameters. Due to the diversity, heterogeneity and numbers of cells that make up these populations, these measurements require automation and speed. At present, the use of flow cytometry in conjunction with nucleic acid probes provides an excellent method with which to pursue such studies.}, }
@article {pmid10997832, year = {2000}, author = {Demarta, A and Tonolla, M and Caminada, A and Beretta, M and Peduzzi, R}, title = {Epidemiological relationships between Aeromonas strains isolated from symptomatic children and household environments as determined by ribotyping.}, journal = {European journal of epidemiology}, volume = {16}, number = {5}, pages = {447-453}, pmid = {10997832}, issn = {0393-2990}, mesh = {Aeromonas/classification/genetics/*isolation &amp; purification ; Aeromonas hydrophila/isolation &amp; purification ; Age Factors ; Child ; Child, Preschool ; DNA, Bacterial/analysis ; Diarrhea/epidemiology/etiology/microbiology ; Diarrhea, Infantile/epidemiology/etiology/microbiology ; Electrophoresis, Agar Gel ; Enteritis/epidemiology/etiology/microbiology ; Feces/microbiology ; Female ; Gastroenteritis/epidemiology/etiology/microbiology ; Gastrointestinal Diseases/*epidemiology/etiology/microbiology ; Gram-Negative Bacterial Infections/*epidemiology ; Humans ; Infant ; Male ; RNA, Bacterial/analysis ; *Ribotyping ; Sex Factors ; }, abstract = {Ribotyping was used to study the epidemiology of Aeromonas associated gastro-enteritis in young children. Ribotyping patterns of 29 Aeromonas strains (16 Aeromonas caviae, 8 Aeromonas hydrophila, 3 Aeromonas eucrenophila, 1 Aeromonas veronii, and 1 Aeromonas encheleia) isolated from primary stool cultures of sick children were compared using the GelCompare software with patterns of 104 strains (39 Aeromonas eucrenophila, 29 Aeromonas caviae, 11 Aeromonas encheleia, 10 Aeromonas hydrophila, 6 Aeromonas bestiarum, 3 Aeromonas veronii, 3 Aeromonas popoffii and 3 Aeromonas media) isolated from their household environment in order to investigate the route of transmission of these bacteria. Fifteen strains (approximately 47%) isolated from stool cultures of patients showed the same riboprofile as strains found in contacts or environment. In particular, three strains isolated from patients shared the same riboprofile with strains found in their domestic environment. The wide diffusion of potentially pathogenic Aeromonas strains in our household samples, and the high rate of asymptomatic carriers among family members, suggested that predisposing factors of the host could make children prone to an Aeromonas-related intestinal disease.}, }
@article {pmid10983878, year = {2000}, author = {Hung, SL and Chen, YL and Wan, HC and Liu, TY and Chen, YT and Ling, LJ}, title = {Effects of areca nut extracts on the functions of human neutrophils in vitro.}, journal = {Journal of periodontal research}, volume = {35}, number = {4}, pages = {186-193}, doi = {10.1034/j.1600-0765.2000.035004186.x}, pmid = {10983878}, issn = {0022-3484}, mesh = {Aggregatibacter actinomycetemcomitans/drug effects ; *Areca ; Blood Bactericidal Activity/drug effects ; Cell Survival/drug effects ; Cells, Cultured ; Humans ; Neutrophils/*drug effects/immunology/metabolism ; *Nuts ; Plant Extracts/isolation &amp; purification/pharmacology ; *Plants, Medicinal ; Streptococcus mutans/drug effects ; Superoxides/metabolism ; }, abstract = {Aqueous extracts of ripe areca nut without husk (ripe ANE) and fresh and tender areca nut with husk (tender ANE) were examined for their effects on the defensive functions of human neutrophils. Exposure of peripheral blood neutrophils to ripe ANE and tender ANE inhibited their bactericidal activity against oral pathogens, including Actinobacillus actinomycetemcomitans and Streptococcus mutans, in a dose-dependent manner. At the concentrations tested, ripe and tender ANEs did not significantly affect the viability of neutrophils as verified by their ability to exclude trypan blue dye. However, both ANEs inhibited the production of bactericidal superoxide anion by neutrophils as measured by cytochrome c reduction. Moreover, the ripe ANE inhibited neutrophils more effectively than did tender ANE. Arecoline, a major alkaloid of areca nut, only exhibited an inhibitory effect on the functions of neutrophils when high concentrations were used. Therefore, arecoline could not be used to explain the inhibitory effects observed for ANEs. In conclusion, our results demonstrated that ripe and tender ANEs reduced the antibacterial activity and the superoxide anion production of neutrophils. This effect may contribute to a less efficient elimination of bacteria from the periodontal environment. Inhibition of the antimicrobial functions of neutrophils may alter the microbial ecology of the oral cavity, and this may be one possible mechanism by which areca nut compromises the oral health of users of areca nut products.}, }
@article {pmid10978545, year = {2000}, author = {Vives-Rego, J and Lebaron, P and Nebe-von Caron, G}, title = {Current and future applications of flow cytometry in aquatic microbiology.}, journal = {FEMS microbiology reviews}, volume = {24}, number = {4}, pages = {429-448}, doi = {10.1111/j.1574-6976.2000.tb00549.x}, pmid = {10978545}, issn = {0168-6445}, mesh = {Animals ; Bacteria/isolation &amp; purification ; Bacterial Physiological Phenomena ; Biodegradation, Environmental ; Esterases/metabolism ; Eukaryota/isolation &amp; purification ; Flow Cytometry/*trends ; Image Cytometry ; Membrane Potentials ; Nucleic Acid Probes ; Oxidoreductases/metabolism ; Phytoplankton/isolation &amp; purification ; Viruses/isolation &amp; purification ; *Water Microbiology ; }, abstract = {Flow cytometry has become a valuable tool in aquatic and environmental microbiology that combines direct and rapid assays to determine numbers, cell size distribution and additional biochemical and physiological characteristics of individual cells, revealing the heterogeneity present in a population or community. Flow cytometry exhibits three unique technical properties of high potential to study the microbiology of aquatic systems: (i) its tremendous velocity to obtain and process data; (ii) the sorting capacity of some cytometers, which allows the transfer of specific populations or even single cells to a determined location, thus allowing further physical, chemical, biological or molecular analysis; and (iii) high-speed multiparametric data acquisition and multivariate data analysis. Flow cytometry is now commonly used in aquatic microbiology, although the application of cell sorting to microbial ecology and quantification of heterotrophic nanoflagellates and viruses is still under development. The recent development of laser scanning cytometry also provides a new way to further analyse sorted cells or cells recovered on filter membranes or slides. The main infrastructure limitations of flow cytometry are: cost, need for skilled and well-trained operators, and adequate refrigeration systems for high-powered lasers and cell sorters. The selection and obtaining of the optimal fluorochromes, control microorganisms and validations for a specific application may sometimes be difficult to accomplish.}, }
@article {pmid10977878, year = {2000}, author = {Casamatta, DA and Wickstrom, CE}, title = {Sensitivity of Two Disjunct Bacterioplankton Communities to Exudates from the Cyanobacterium Microcystis aeruginosa Kützing.}, journal = {Microbial ecology}, volume = {40}, number = {1}, pages = {64-73}, doi = {10.1007/s002480000035}, pmid = {10977878}, issn = {0095-3628}, abstract = {Microcystis aeruginosa Kützing releases a variety of bioactive compounds during growth. This study determined whether bacteria from communities co-occurring (M+) or not (M-) with this cosmopolitan cyanobacterium respond similarly to its products. Fifty M+ bacteria from a M. aeruginosa bloom site (Western Basin of Lake Erie) and 50 M- bacteria from a Microcystis-free site (East Twin Lake, Portage Co., OH) were isolated and grown on Standard Methods Agar. Three levels of testing were performed: chemotaxis, antibiotic response, and 48-h cell abundance. Chemotaxis was compared using capillary tubes placed in contact with bacterial, Standard Methods Broth (SMB) suspensions. The capillary choices were conditioned SMB, M. aeruginosa exudate, and BG-11. M+ bacteria showed significantly greater (Tukey's test, p < 0.005) positive chemotaxis to M. aeruginosa exudate compared to control conditions and to M-strains. The latter showed a negative chemotactic response to M. aeruginosa exudate compared to control conditions. Antibiotic response was tested by sensitivity disk assays, first using M. aeruginosa exudates, whole cells, and homogenized cells, and then placing the disks on bacterial lawns of each strain. M+ bacteria were significantly more resistant to inhibition than M- bacteria (chi-square test, p < 0.01). M. aeruginosa exudate, BG-11 algal medium, SMB, and distilled water effects on 48-h abundance of the strains were compared. The M- community bacteria exhibited significantly lower growth yields (Tukey's comparison of means test, p < 0.005) in M. aeruginosa exudate than did the M+ strains. It is evident that those bacteria co-occurring with M. aeruginosa are more likely to be attracted to it, able to withstand exposure to it, and able to utilize its products without inhibition than are bacteria from communities without previous exposure to this cyanobacterium.}, }
@article {pmid10977877, year = {2000}, author = {Pearce, DA and Bazin, MJ and Lynch, JM}, title = {Substrate Concentration and Plasmid Transfer Frequency between Bacteria in a Model Rhizosphere.}, journal = {Microbial ecology}, volume = {40}, number = {1}, pages = {57-63}, doi = {10.1007/s00248000043}, pmid = {10977877}, issn = {0095-3628}, abstract = {The influence of substrate concentration on plasmid transfer frequency in the rhizosphere was investigated using a physical model employing a hollow fiber membrane instead of a real root. The absolute number of transconjugants produced increased with increasing substrate (glucose) concentration, but the plasmid transfer frequency decreased exponentially with increasing substrate concentration from 4.4 × 10(-3) at 90 μg ml(-1) glucose to 1.35 × 10(-5) at 3600 μg ml(-1) glucose. These results were found to be heavily dependant on donor to recipient ratio and distribution of strains, but independent of initial donor and recipient inoculum density and regime. These observations also show that plasmid transfer frequency is reduced at high substrate concentrations, which suggests that plasmid transfer is either stimulated when growth limiting nutrient is scarce or inhibited when it is abundant.}, }
@article {pmid10977876, year = {2000}, author = {Miethling, R and Wieland, G and Backhaus, H and Tebbe, CC}, title = {Variation of Microbial Rhizosphere Communities in Response to Crop Species, Soil Origin, and Inoculation with Sinorhizobium meliloti L33.}, journal = {Microbial ecology}, volume = {40}, number = {1}, pages = {43-56}, doi = {10.1007/s002480000021}, pmid = {10977876}, issn = {0095-3628}, abstract = {A greenhouse study with soil-plant microcosms was conducted in order to compare the effect of crop species, soil origin, and a bacterial inoculant on the establishment of microbial communities colonizing plant roots. Two crop species, alfalfa (Medicago sativa) and rye (Secale cereale), were grown separately in two soils collected from agricultural fields at different locations and with differing histories of leguminous crop rotation. A subset of microcosms was inoculated at 10(6) cfu g(-1) soil with the luciferase marker gene-tagged Sinorhizobium meliloti strain L33, a symbiotic partner of M. sativa. Microbial consortia were collected from the rhizospheres of alfalfa after 10 weeks of incubation and from rye after 11 weeks. S. meliloti L33 populations were one to two orders of magnitude higher in the rhizospheres of alfalfa than of rye. In soil with previous alfalfa cultivation, 80% of the alfalfa nodules were colonized by indigenous bacteria, while in the other soil alfalfa was colonized almost exclusively (>90%) with S. meliloti L33. Three community-level targeting approaches were used to characterize the variation of the extracted microbial rhizosphere consortia: (1) Community level physiological profiles (CLPP), (2) fatty acid methyl ester analysis (FAME), and (3) diversity of PCR amplified 16S rRNA target sequences from directly extracted ribosomes, determined by temperature gradient gel electrophoresis (TGGE). All approaches identified the crop species as the major determinant of microbial community characteristics. Consistently, the influence of soil was of minor importance, while a modification of the alfalfa-associated microbial community structure after inoculation with S. meliloti L33 was only consistently observed by using TGGE.}, }
@article {pmid10977875, year = {2000}, author = {Knoll, D and Schreiber, L}, title = {Plant-Microbe Interactions: Wetting of Ivy (Hedera helix L.) Leaf Surfaces in Relation to Colonization by Epiphytic Microorganisms.}, journal = {Microbial ecology}, volume = {40}, number = {1}, pages = {33-42}, doi = {10.1007/s002480000012}, pmid = {10977875}, issn = {0095-3628}, abstract = {Leaf wettability, cuticular wax composition, and microbial colonization of upper and lower leaf surfaces of ivy (Hedera helix L.) was investigated for young and old leaves sampled in June and September. Contact angles of aqueous buffered solutions measured on young leaf surfaces ranged between 76° and 86° and were not dependent on the pH value of the applied droplets. Contact angles measured on old leaf surfaces were up to 32°, significantly lower than on young leaf surfaces. Furthermore, contact angles were significantly lower using aqueous solutions of pH 9.0 compared to pH 3.0, indicating the influence of ionizable functional groups on leaf surface wetting properties. Observed changes in leaf wetting properties did not correlate with different levels of alkanoic acids in cuticular waxes. However, microscopic examination of the leaf surfaces indicated the influence of epiphytic microorganisms on wetting properties of old leaves, since their surfaces were always colonized by epiphytic microorganisms (filamentous fungi, yeasts, and bacteria), whereas surfaces of young leaves were basically clean. In order to analyze the effect of epiphytic microorganisms on leaf surface wetting, surfaces of young and clean ivy leaves were artificially colonized with Pseudomonas fluorescens. This resulted in a significant increase and a pH dependence of leaf surface wetting in the same way as it was observed on old ivy leaf surfaces. From these results it can be deduced that the native wetting properties of leaf surfaces can be significantly masked by the presence of epiphytic microorganisms. The ecological implications of altered wetting properties for microorganisms using the leaf/atmosphere interface as habitat are discussed.}, }
@article {pmid10977874, year = {2000}, author = {Wang, ET and Martínez-Romero, E}, title = {Sesbania herbacea-Rhizobium huautlense Nodulation in Flooded Soils and Comparative Characterization of S. herbacea-Nodulating Rhizobia in Different Environments.}, journal = {Microbial ecology}, volume = {40}, number = {1}, pages = {25-32}, doi = {10.1007/s002480000010}, pmid = {10977874}, issn = {0095-3628}, abstract = {The nodulation of S. herbacea was compared under flooded and non-flooded conditions in two different soils. One soil was from a flooded field in Sierra de Huautla, the native habitat of this legume, while the other soil was from a well-drained field in Cuernavaca, where rhizobia were found to nodulate the introduced S. herbacea plants. Nodulation of the plants was completely eliminated by flooding in the Cuernavaca soil, whereas nodules were obtained in the same soil under non-flooded conditions. In contrast, nodules were formed in Huautla soil under both flooded and non-flooded conditions. Most isolates, except isolate HS2, from Huautla soil and water were identified as R. huautlense by colony morphology, growth rate, PCR-RFLP of 16S rRNA genes, MLEE, cellular plasmid contents, and RFLP of nifH and nodDAB genes. Isolate HS2 was identified as Mesorhizobium sp. Isolates from Cuernavaca soil were different from R. huautlense in many aspects and were classified into five rDNA types within the genera Mesorhizobium, Rhizobium, and Sinorhizobium by PCR-RFLP of 16S rRNA genes. R. huautlense is a water Rhizobium species. Growth by denitrification under oxygen limitation or with ethanol was observed for R. huautlense bacteria but not for the isolates from Cuernavaca. In an interstrain nodulation competitive assay under both flooded and non-flooded conditions, R. huautlense strain S02 completely inhibited the nodulation of Mesorhizobium sp. Sn2, an isolate from Cuernavaca. From these results, we conclude that R. huautlense has the unique ability to nodulate S. herbacea not only in flooded soils, but in non-flooded soils as well.}, }
@article {pmid10977873, year = {2000}, author = {Romaní, AM and Sabater, S}, title = {Influence of algal biomass on extracellular enzyme activity in river biofilms.}, journal = {Microbial ecology}, volume = {40}, number = {1}, pages = {16-24}, doi = {10.1007/s002480000041}, pmid = {10977873}, issn = {0095-3628}, abstract = {Relationships between biofilm structural components (algal and bacterial biomass) and the activities of some extracellular enzymes that contribute to the ability to degrade organic matter) were explored for six Atlantic and three Mediterranean streams and rivers. The biofilms in these fluvial systems accounted for a wide range of bacterial and algal biomass and colonized the most common benthic habitats. Ratio of bacteria/algae biomass was lower in Atlantic than in Mediterranean streams, but enzymatic activities (β-glucosidase, β-xylosidase, phosphatase) were in general greater in the Mediterranean stream biofilms. Climatic characteristics (especially temperature) may explain the differences in enzymatic activities between biofilms of similar structure but different flow regime. The ratio β-xylosidase: β-glucosidase was similar (around 0.5) for all streams and substrata considered, showing that there is a general higher utilization of cellobiosic than xylobiosic molecules in fluvial systems. In general, highly heterotrophic biofilms showed lower extracellular enzymatic activities than more autotrophic biofilms. Maximum enzymatic activity is achieved when the algal biomass is two- to threefold higher than the bacterial biomass. The relevance of algal biomass on the heterotrophic ability of biofilms may be related to the physical proximity between the two, but also to the high proportion of polymeric carbohydrates included in algal exudates and lysis products, whose use is enzyme-mediated.}, }
@article {pmid10977872, year = {2000}, author = {Rice, AR and Hamilton, MA and Camper, AK}, title = {Apparent surface associated lag time in growth of primary biofilm cells.}, journal = {Microbial ecology}, volume = {40}, number = {1}, pages = {8-15}, doi = {10.1007/s002480000011}, pmid = {10977872}, issn = {0095-3628}, abstract = {The ability of microorganisms to form biofilms has been well documented. Bacterial cells make a transition from a planktonic state to a sessile state, replicate, and subsequently populate a surface. In this study, organisms that initially colonize a ``clean'' surface are referred to as ``primary'' biofilm cells. The progeny of the first generation of sessile cells are known as ``secondary'' biofilm cells. This study examined the growth of planktonic, primary, and secondary biofilm cells of a green fluorescent protein producing (GFP+) Pseudomonas aeruginosa PA01. Biofilm experiments were performed in a parallel plate flow cell reactor with a glass substratum. Individual cells were tracked over time using a confocal scanning laser microscope (CSLM). Primary cells experience a lag in their growth that may be attributed to adapting to a sessile environment or undergoing a phenotypic change. This is referred to as a surface associated lag time. Planktonic and secondary biofilm cells both grew at a faster rate than the primary biofilm cells under the same nutrient conditions.}, }
@article {pmid10977871, year = {2000}, author = {Dolfing, J}, title = {Energetics of anaerobic degradation pathways of chlorinated aliphatic compounds.}, journal = {Microbial ecology}, volume = {40}, number = {1}, pages = {2-7}, doi = {10.1007/s002480000039}, pmid = {10977871}, issn = {0095-3628}, abstract = {This minireview explores the energetics of the (anaerobic) oxidative and fermentative degradation of halogenated ethenes and ethanes. It is shown that these pathways are viable alternatives to the traditional routes that start with one or more reductive dechlorination steps. In contrast to reductive dehalogenation, oxidative and fermentative degradation pathways do not require an external source of reducing equivalents. This suggests that organisms that use these pathways are most likely to be found at high redox potentials, i.e, under conditions where competition for reducing equivalents is great.}, }
@article {pmid10977870, year = {2000}, author = {Fredrickson, JK}, title = {Microbial ecology update.}, journal = {Microbial ecology}, volume = {40}, number = {1}, pages = {1}, doi = {10.1007/s002480000052}, pmid = {10977870}, issn = {0095-3628}, }
@article {pmid10972741, year = {2000}, author = {Kalogo, Y and Rosillon, F and Hammes, F and Verstraete, W}, title = {Effect of a water extract of Moringa oleifera seeds on the hydrolytic microbial species diversity of a UASB reactor treating domestic wastewater.}, journal = {Letters in applied microbiology}, volume = {31}, number = {3}, pages = {259-264}, doi = {10.1046/j.1365-2672.2000.00814.x}, pmid = {10972741}, issn = {0266-8254}, mesh = {Bacteria/classification/*growth &amp; development/isolation &amp; purification/metabolism ; *Bioreactors ; Colony Count, Microbial ; Culture Media ; Hydrolysis ; Plant Extracts/*pharmacology ; *Plants, Medicinal ; *Rosales ; *Seeds ; Sewage/microbiology ; Waste Disposal, Fluid ; }, abstract = {The effect of a continuous supply of a water extract of Moringa oleifera seeds (WEMOS) on the hydrolytic microbial population of biomass grown in mesophilic upflow anaerobic sludge blanket reactors treating domestic wastewater was investigated. The WEMOS-treated sludge had seemingly a wider diversity, with enterobacter and klebsiella as dominant hydrolytic bacteria, compared with the control sludge. Additional tests indicated that various hydrolytic bacteria could degrade WEMOS. It appeared that a continuous supply of WEMOS to an anaerobic digester, treating domestic wastewater, increased the diversity of hydrolytic bacteria and therefore enhanced the biological start-up of the reactor.}, }
@article {pmid10971763, year = {2000}, author = {Wikström, P and Andersson, AC and Nygren, Y and Sjöström, J and Forsman, M}, title = {Influence of TNT transformation on microbial community structure in four different lake microcosms.}, journal = {Journal of applied microbiology}, volume = {89}, number = {2}, pages = {302-308}, doi = {10.1046/j.1365-2672.2000.01111.x}, pmid = {10971763}, issn = {1364-5072}, mesh = {Bacteria/genetics/*growth &amp; development/metabolism ; *Ecosystem ; Fresh Water/*microbiology ; Random Amplified Polymorphic DNA Technique ; Trinitrotoluene/*metabolism ; Water Pollutants, Chemical/*metabolism ; }, abstract = {After World War II, large amounts of obsolete ammunition were dumped in various lakes in Sweden. Trinitrotoluene, TNT, was one of the main components of the dumped explosives. In this study, four different lake microcosms originating from lakes where relatively large amounts of ammunition were dumped were used to mimic the effect of TNT release on the natural microbial community. Increased microbial growth was found in lake microcosms amended with TNT. However, negligible mineralization of TNT was detected, suggesting that TNT was not utilized as a carbon source, but as a nitrogen source. Random amplified polymorphic DNA (RAPD) analysis indicated that the TNT induced no significant differences in microbial community composition and therefore, no major changes in natural selection, despite the increased microbial growth in the presence of the compound. More than 95% of the added TNT bound irreversibly to the sediments, possibly as a result of microbial transformation to reactive metabolites that subsequently bound covalently to components of the sediment. The results, taken together, suggest that no permanent change in the microbial ecology occurred as a result of the TNT amendment. This was probably due partly to the transient exposure of the microbial communities to the TNT before it became irreversibly bound to the sediment, and partly to the fact that TNT was not a primary growth substrate that strongly affects natural selection.}, }
@article {pmid10967208, year = {2000}, author = {Turley, C}, title = {Bacteria in the cold deep-sea benthic boundary layer and sediment-water interface of the NE Atlantic.}, journal = {FEMS microbiology ecology}, volume = {33}, number = {2}, pages = {89-99}, doi = {10.1111/j.1574-6941.2000.tb00731.x}, pmid = {10967208}, issn = {1574-6941}, abstract = {This is a short review of the current understanding of the role of microorganisms in the biogeochemistry in the deep-sea benthic boundary layer (BBL) and sediment-water interface (SWI) of the NE Atlantic, the gaps in our knowledge and some suggestions of future directions. The BBL is the layer of water, often tens of meters thick, adjacent to the sea bed and with homogenous properties of temperature and salinity, which sometimes contains resuspended detrital particles. The SWI is the bioreactive interface between the water column and the upper 1 cm of sediment and can include a large layer of detrital material composed of aggregates that have sedimented from the upper mixed layer of the ocean. This material is biologically transformed, over a wide range of time scales, eventually forming the sedimentary record. To understand the microbial ecology of deep-sea bacteria, we need to appreciate the food supply in the upper ocean, its packaging, passage and transformation during the delivery to the sea bed, the seasonality of variability of the supply and the environmental conditions under which the deep-sea bacteria grow. We also need to put into a microbial context recent geochemical findings of vast reservoirs of intrinsically labile organic material sorped onto sediments. These may well become desorped, and once again available to microorganisms, during resuspension events caused by deep ocean currents. As biotechnologists apply their tools in the deep oceans in search of unique bacteria, an increasing knowledge and understanding of the natural processes undertaken and environmental conditions experienced by deep-sea bacteria will facilitate this exploitation.}, }
@article {pmid10966429, year = {2000}, author = {Fernandez, AS and Hashsham, SA and Dollhopf, SL and Raskin, L and Glagoleva, O and Dazzo, FB and Hickey, RF and Criddle, CS and Tiedje, JM}, title = {Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {9}, pages = {4058-4067}, pmid = {10966429}, issn = {0099-2240}, mesh = {Anaerobiosis ; *Bioreactors ; DNA, Archaeal/analysis/genetics ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal/analysis/genetics ; *Ecosystem ; Euryarchaeota/classification/*growth &amp; development/metabolism/ultrastructure ; Glucose/*metabolism ; Image Processing, Computer-Assisted ; Methane/*metabolism ; Methanosarcina/classification/genetics/metabolism ; Molecular Sequence Data ; Oligonucleotide Probes ; RNA, Ribosomal/genetics ; Restriction Mapping ; Sequence Analysis, DNA ; Spirochaetales/classification/genetics/metabolism ; Streptococcus/classification/genetics/metabolism ; }, abstract = {Methanogenic bioreactor communities were used as model ecosystems to evaluate the relationship between functional stability and community structure. Replicated methanogenic bioreactor communities with two different community structures were established. The effect of a substrate loading shock on population dynamics in each microbial community was examined by using morphological analysis, small-subunit (SSU) rRNA oligonucleotide probes, amplified ribosomal DNA (rDNA) restriction analysis (ARDRA), and partial sequencing of SSU rDNA clones. One set of replicated communities, designated the high-spirochete (HS) set, was characterized by good replicability, a high proportion of spiral and short thin rod morphotypes, a dominance of spirochete-related SSU rDNA genes, and a high percentage of Methanosarcina-related SSU rRNA. The second set of communities, designated the low-spirochete (LS) set, was characterized by incomplete replicability, higher morphotype diversity dominated by cocci, a predominance of Streptococcus-related and deeply branching Spirochaetales-related SSU rDNA genes, and a high percentage of Methanosaeta-related SSU rRNA. In the HS communities, glucose perturbation caused a dramatic shift in the relative abundance of fermentative bacteria, with temporary displacement of spirochete-related ribotypes by Eubacterium-related ribotypes, followed by a return to the preperturbation community structure. The LS communities were less perturbed, with Streptococcus-related organisms remaining prevalent after the glucose shock, although changes in the relative abundance of minor members were detected by morphotype analysis. A companion paper demonstrates that the more stable LS communities were less functionally stable than the HS communities (S. A. Hashsham, A. S. Fernandez, S. L. Dollhopf, F. B. Dazzo, R. F. Hickey, J. M. Tiedje, and C. S. Criddle, Appl. Environ. Microbiol. 66:4050-4057, 2000).}, }
@article {pmid10941781, year = {1999}, author = {Rice, SA and Givskov, M and Steinberg, P and Kjelleberg, S}, title = {Bacterial signals and antagonists: the interaction between bacteria and higher organisms.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {1}, number = {1}, pages = {23-31}, pmid = {10941781}, issn = {1464-1801}, mesh = {4-Butyrolactone/analogs &amp; derivatives/metabolism ; *Bacterial Physiological Phenomena ; Rhodophyta/metabolism/microbiology ; *Signal Transduction ; }, abstract = {It is now well established that bacteria communicate through the secretion and uptake of small diffusable molecules. These chemical cues, or signals, are often used by bacteria to coordinate phenotypic expression and this mechanism of regulation presumably provides them with a competitive advantage in their natural environment. Examples of coordinated behaviors of marine bacteria which are regulated by signals include swarming and exoprotease production, which are important for niche colonisation or nutrient acquisition (e.g. protease breakdown of substrate). While the current focus on bacterial signalling centers on N-Acylated homoserine lactones, the quorum sensing signals of gram-negative bacteria, these are not the only types of signals used by bacteria. Indeed, there appears to be many other types of signals produced by bacteria and it also appears that a bacterium may use multiple classes of signals for phenotypic regulation. Recent work in the area of marine microbial ecology has led to the observation that some marine eukaryotes secrete their own signals which compete with the bacterial signals and thus inhibit the expression of bacterial signalling phenotypes. This type of molecular mimicry has been well characterised for the interaction of marine prokaryotes with the red alga, Delisea pulchra.}, }
@article {pmid10919828, year = {2000}, author = {Marsh, TL and Saxman, P and Cole, J and Tiedje, J}, title = {Terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {8}, pages = {3616-3620}, pmid = {10919828}, issn = {0099-2240}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal/analysis/genetics ; *Databases, Factual ; *Ecosystem ; *Internet ; Phylogeny ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/*genetics ; Sewage/microbiology ; Software ; Soil Microbiology ; }, abstract = {Rapid analysis of microbial communities has proven to be a difficult task. This is due, in part, to both the tremendous diversity of the microbial world and the high complexity of many microbial communities. Several techniques for community analysis have emerged over the past decade, and most take advantage of the molecular phylogeny derived from 16S rRNA comparative sequence analysis. We describe a web-based research tool located at the Ribosomal Database Project web site (http://www.cme.msu.edu/RDP/html/analyses. html) that facilitates microbial community analysis using terminal restriction fragment length polymorphism of 16S ribosomal DNA. The analysis function (designated TAP T-RFLP) permits the user to perform in silico restriction digestions of the entire 16S sequence database and derive terminal restriction fragment sizes, measured in base pairs, from the 5' terminus of the user-specified primer to the 3' terminus of the restriction endonuclease target site. The output can be sorted and viewed either phylogenetically or by size. It is anticipated that the site will guide experimental design as well as provide insight into interpreting results of community analysis with terminal restriction fragment length polymorphisms.}, }
@article {pmid10919811, year = {2000}, author = {Johnsen, AR and Hausner, M and Schnell, A and Wuertz, S}, title = {Evaluation of fluorescently labeled lectins for noninvasive localization of extracellular polymeric substances in Sphingomonas biofilms.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {8}, pages = {3487-3491}, pmid = {10919811}, issn = {0099-2240}, mesh = {*Biofilms/growth &amp; development ; Concanavalin A ; Evaluation Studies as Topic ; Fluorescent Dyes/*metabolism ; Lectins/*metabolism ; Microscopy, Confocal ; Polymers/*analysis/metabolism ; Polysaccharides, Bacterial/analysis/metabolism ; Sphingomonas/*chemistry/*growth &amp; development/metabolism ; }, abstract = {Three strains of Sphingomonas were grown as biofilms and tested for binding of five fluorescently labeled lectins (Con A-type IV-TRITC or -Cy5, Pha-E-TRITC, PNA-TRITC, UEA 1-TRITC, and WGA-Texas red). Only ConA and WGA were significantly bound by the biofilms. Binding of the five lectins to artificial biofilms made of the commercially available Sphingomonas extracellular polysaccharides was similar to binding to living biofilms. Staining of the living and artificial biofilms by ConA might be explained as binding of the lectin to the terminal mannosyl and terminal glucosyl residues in the polysaccharides secreted by Sphingomonas as well as to the terminal mannosyl residue in glycosphingolipids. Staining of the biofilms by WGA could only be explained as binding to the Sphingomonas glycosphingolipid membrane, binding to the cell wall, or nonspecific binding. Glycoconjugation of ConA and WGA with the target sugars glucose and N-acetylglucosamine, respectively, was used as a method for evaluation of the specificity of the lectins towards Sphingomonas biofilms and Sphingomonas polysaccharides. Our results show that the binding of lectins to biofilms does not necessarily prove the presence of specific target sugars in the extracellular polymeric substances (EPS) in biofilms. The lectins may bind to non-EPS targets or adhere nonspecifically to components of the biofilm matrix.}, }
@article {pmid10919784, year = {2000}, author = {Dejonghe, W and Goris, J and El Fantroussi, S and Höfte, M and De Vos, P and Verstraete, W and Top, EM}, title = {Effect of dissemination of 2,4-dichlorophenoxyacetic acid (2,4-D) degradation plasmids on 2,4-D degradation and on bacterial community structure in two different soil horizons.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {8}, pages = {3297-3304}, pmid = {10919784}, issn = {0099-2240}, mesh = {2,4-Dichlorophenoxyacetic Acid/*metabolism ; Bacteria/*genetics/metabolism ; Biodegradation, Environmental ; *Conjugation, Genetic ; Ecosystem ; Electrophoresis, Polyacrylamide Gel/methods ; *Gene Transfer Techniques ; Genes, rRNA ; Molecular Sequence Data ; Plasmids/*genetics ; Pseudomonas putida/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Soil Pollutants/metabolism ; }, abstract = {Transfer of the 2,4-dichlorophenoxyacetic acid (2,4-D) degradation plasmids pEMT1 and pJP4 from an introduced donor strain, Pseudomonas putida UWC3, to the indigenous bacteria of two different horizons (A horizon, depth of 0 to 30 cm; B horizon, depth of 30 to 60 cm) of a 2,4-D-contaminated soil was investigated as a means of bioaugmentation. When the soil was amended with nutrients, plasmid transfer and enhanced degradation of 2,4-D were observed. These findings were most striking in the B horizon, where the indigenous bacteria were unable to degrade any of the 2,4-D (100 mg/kg of soil) during at least 22 days but where inoculation with either of the two plasmid donors resulted in complete 2,4-D degradation within 14 days. In contrast, in soils not amended with nutrients, inoculation of donors in the A horizon and subsequent formation of transconjugants (10(5) CFU/g of soil) could not increase the 2,4-D degradation rate compared to that of the noninoculated soil. However, donor inoculation in the nonamended B-horizon soil resulted in complete degradation of 2,4-D within 19 days, while no degradation at all was observed in noninoculated soil during 89 days. With plasmid pEMT1, this enhanced degradation seemed to be due only to transconjugants (10(5) CFU/g of soil), since the donor was already undetectable when degradation started. Denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes showed that inoculation of the donors was followed by a shift in the microbial community structure of the nonamended B-horizon soils. The new 16S rRNA gene fragments in the DGGE profile corresponded with the 16S rRNA genes of 2,4-D-degrading transconjugant colonies isolated on agar plates. This result indicates that the observed change in the community was due to proliferation of transconjugants formed in soil. Overall, this work clearly demonstrates that bioaugmentation can constitute an effective strategy for cleanup of soils which are poor in nutrients and microbial activity, such as those of the B horizon.}, }
@article {pmid10919337, year = {2000}, author = {Boon, N and Marlé, C and Top, EM and Verstraete, W}, title = {Comparison of the spatial homogeneity of physico-chemical parameters and bacterial 16S rRNA genes in sediment samples from a dumping site for dredging sludge.}, journal = {Applied microbiology and biotechnology}, volume = {53}, number = {6}, pages = {742-747}, doi = {10.1007/s002530000325}, pmid = {10919337}, issn = {0175-7598}, mesh = {Belgium ; DNA, Ribosomal/isolation &amp; purification ; Electrophoresis, Polyacrylamide Gel ; Environmental Microbiology ; Environmental Monitoring/*methods ; Environmental Pollutants ; Fresh Water ; Geological Phenomena ; Geology ; Nucleic Acid Denaturation ; RNA, Ribosomal, 16S/isolation &amp; purification ; *Ribotyping ; Waste Management/*methods ; }, abstract = {The homogeneity of the microbial community structure of a sediment landfill was examined by a culture-independent method and compared with physico-chemical parameters, i.e. organic matter, CaCO3 content, pH, and texture. Total genomic DNA was extracted from samples derived from different places and depths. After amplification with two different primer sets of partial bacterial 16S rRNA genes, the products were separated by denaturing gradient gel electrophoresis (DGGE). The DGGE fingerprints of different sediment samples taken in regular patterns at the same depth were similar, which indicates a spatial homogeneity in the numerically dominant bacterial populations in a landfill over 10,000 m2 in size. In a vertical column of approx. 10 m, only some differences in a few bands of the bacterial community structure were observed between samples taken from different depths. This DNA homogeneity coincided with a similar homogeneity of the physico-chemical parameters in the landfill at this site. Nevertheless, the DGGE technique revealed small differences in less prominent bacteria and was capable of separating the upper and lower samples of one column into two clusters. It therefore seems more sensitive than the physico-chemical approach for characterising the homogeneity of an environmental habitat.}, }
@article {pmid10919331, year = {2000}, author = {De Boever, P and Wouters, R and Verschaeve, L and Berckmans, P and Schoeters, G and Verstraete, W}, title = {Protective effect of the bile salt hydrolase-active Lactobacillus reuteri against bile salt cytotoxicity.}, journal = {Applied microbiology and biotechnology}, volume = {53}, number = {6}, pages = {709-714}, doi = {10.1007/s002530000330}, pmid = {10919331}, issn = {0175-7598}, mesh = {Amidohydrolases/*pharmacology ; Bile Acids and Salts/*toxicity ; Biodegradation, Environmental ; Bioreactors ; Ecosystem ; Fermentation ; Hemolysis ; Intestines/microbiology ; Lactobacillus/*enzymology ; Mutagenicity Tests ; Mutagens/*toxicity ; *Probiotics ; }, abstract = {Bacterial bile salt hydrolysis is considered a risk factor for the development of colon cancer because of the risk of forming harmful secondary bile salts after an initial deconjugation step. In this study, the influence of enhanced bacterial bile salt transformation by the bile salt hydrolase-active Lactobacillus reuteri was studied in batch culture using the microbial suspension of the Simulator of the Human Intestinal Microbial Ecosystem; (SHIME), which was supplemented with oxgall at 5 g/l or 30 g/l. Changes in the fermentative capacity of the microbial ecosystem and the (geno)toxic properties of the SHIME supernatants were investigated. Increasing concentrations of oxgall inhibited the fermentation. Transient cell toxicity was observed for samples supplemented with 5 g oxgall/l, while samples with 30 g oxgall/l exhibited toxicity. The results of the haemolysis test suggest that the detrimental effects were probably due to the membrane-damaging effects of bile salts. In all cases, the adverse effects could be counteracted by the addition of 7.5 +/- 0.5 log10 CFU L. reuteri/ml. Plausible mechanisms for the protective properties of L. reuteri could involve a precipitation of the deconjugated bile salts and a physical binding of bile salts by the bacterium, thereby making the harmful bile salts less bioavailable.}, }
@article {pmid10922501, year = {2000}, author = {Saxena, D and Stotzky, G}, title = {Insecticidal toxin from Bacillus thuringiensis is released from roots of transgenic Bt corn in vitro and in situ.}, journal = {FEMS microbiology ecology}, volume = {33}, number = {1}, pages = {35-39}, doi = {10.1111/j.1574-6941.2000.tb00724.x}, pmid = {10922501}, issn = {1574-6941}, abstract = {The insecticidal toxin encoded by the cry1Ab gene from Bacillus thuringiensis was released in root exudates from transgenic Bt corn during 40 days of growth in soil amended to 0, 3, 6, 9, or 12% (v/v) with montmorillonite or kaolinite in a plant growth room and from plants grown to maturity in the field. The presence of the toxin in rhizosphere soil was determined by immunological and larvicidal assays. No toxin was detected in any soils from isogenic non-Bt corn or without plants. Persistence of the toxin was apparently the result of its binding on surface-active particles in the soils, which reduced the biodegradation of the toxin. The release of the toxin could enhance the control of insect pests or constitute a hazard to nontarget organisms, including the microbiota of soil, and increase the selection of toxin-resistant target insects.}, }
@article {pmid10916359, year = {2000}, author = {Simmonds, RS and Tompkins, GR and George, RJ}, title = {Dental caries and the microbial ecology of dental plaque: a review of recent advances.}, journal = {The New Zealand dental journal}, volume = {96}, number = {424}, pages = {44-49}, pmid = {10916359}, issn = {0028-8047}, mesh = {Adaptation, Biological ; Animals ; Bacterial Adhesion ; Bacterial Vaccines ; Bacteriocins/biosynthesis ; Dental Caries/*microbiology ; Dental Plaque/*microbiology ; Ecosystem ; *Genes, Bacterial ; Glucosyltransferases/metabolism ; Humans ; Immunoglobulin A, Secretory/immunology ; Salivary Proteins and Peptides/immunology ; Streptococcus/genetics/metabolism/*pathogenicity ; }, abstract = {Our understanding of the microbial ecology of dental plaque has rapidly grown with recent developments in the techniques of molecular biology. In particular, knowledge of the mechanisms underlying the acquisition, establishment, pathogenicity, and evolution of the group of organisms responsible for dental caries--the mutans streptococci--has expanded to the point that we can now contemplate new opportunities for caries prevention. These advances reinforce developing concepts of dental plaque as an interdependent, interacting community of specialised organisms with an ability to rapidly adapt conferred by gene structures that facilitate the expeditious modular rearrangement of protein components.}, }
@article {pmid10909936, year = {2000}, author = {Bates, MN and Maas, E and Martin, T and Harte, D and Grubner, M and Margolin, T}, title = {Investigation of the prevalence of Legionella species in domestic hot water systems.}, journal = {The New Zealand medical journal}, volume = {113}, number = {1111}, pages = {218-220}, pmid = {10909936}, issn = {0028-8446}, mesh = {Humans ; Legionella/*isolation &amp; purification ; New Zealand ; Polymerase Chain Reaction ; Sensitivity and Specificity ; *Water Microbiology ; *Water Supply ; }, abstract = {AIMS: To investigate the prevalence of Legionella spp. in the hot water systems of a representative sample of Wellington domestic residences with electrically heated hot water systems, and to investigate risk factors (eg water temperature, plumbing materials) for such contamination.<br><br>METHOD: 100 households with electrically heated hot water systems in the Wellington area were investigated. Samples of hot water from several hot water outlets were collected, and characteristics of the plumbing system were recorded. Water samples and swabs were cultured and further examined by polymerase chain reaction (PCR) and direct fluorescence antibody (DFA) testing to identify Legionella spp. and serogroups.<br><br>RESULTS: No Legionella spp. were isolated by culture. PCR tested positive for Legionella in specimens from twelve residences. Six of these were also positive by DFA testing. The only environmental factor found to be associated with the presence of Legionella was recent plumbing work on the hot water system. Five of the twelve PCR-positive residences, and four of the six DFA-confirmed residences had hot water delivery temperatures in excess of 60 degrees C.<br><br>CONCLUSIONS: The results suggest that either Legionellae colonise domestic hot water reticulation systems and/or that the organisms are killed during passage through the hot water tank. Both possibilities may be correct. Further work to characterise the microbial ecology of Legionella-positive hot water distribution systems would be useful, as would the development of improved methods for culturing the organisms from potable water.}, }
@article {pmid10882437, year = {2000}, author = {Mary, P and Defives, C and Hornez, JP}, title = {Occurrence and Multiple Antibiotic Resistance Profiles of Non-fermentative Gram-Negative Microflora in Five Brands of Non-carbonated French Bottled Spring Water.}, journal = {Microbial ecology}, volume = {39}, number = {4}, pages = {322-329}, pmid = {10882437}, issn = {1432-184X}, abstract = {Five brands of French bottled mineral water were analyzed by heterotrophic plate counts (HPC) and for the presence of multiple antibiotic resistant bacteria. HPC at 22 degrees C were around 10(4) colony forming units ml(-1) on R2A medium. Enumeration on PCA/10, MH, and especially PCA and King B media was less efficient. At 37 degrees C, HPC were two to three orders of magnitude less than at 22 degrees C. Moreover, phenotypic diversity (7 to 15 phenotypes) was optimal on R2A incubated at 22 degrees C. All isolates were identified as non-fermentative Gram-negative rods and 75% were non-identifiable with the API 20NE system. Stenotrophomonas maltophilia and fluorescent Pseudomonas were isolated on VIA and CFC selective agar media, respectively. Burkholderia cepacia strains were not isolated on BCSA medium. The species S. maltophilia was found in 33%, 28%, and 11% of sample from springs A, D, and E, respectively. Independent of brand, isolates from HPC media were less efficient to achieve confluent growth in 18 h on MH at 30 or 37 degrees C (0 to 40%) than isolates from selective media (28 to 63%). Seventy percent of the total isolates from dominant microflora (1-5 x 10(3) CFU ml(-1) on HPC media) were resistant against two or four antibiotics. The antibiotics concerned were principally aztreonam, ampicillin, and nalidixic acid. The remaining dominant bacteria showed a 6-9 multiple antibiotic resistant (MAR) pattern. All isolates were susceptible to newer antimicrobial agents. Owing to their low nutrient and temperature requirements, these isolates are unlikely to cause concern to public heath. Fifty percent of strains isolated from selective media (non-dominant microflora, 4-40 CFU l(-1)) showed a 10-18 MAR pattern and 33%, identified as S. maltophilia, a 20-27 MAR pattern. However, minocycline was effective against all isolates. Owing to its low concentration, colonization of human intestine by MAR S. maltophilia is unlikely.}, }
@article {pmid10882436, year = {2000}, author = {Lighthart, B and Prier, K and Loper, GM and Bromenshenk, J}, title = {Bees Scavenge Airborne Bacteria.}, journal = {Microbial ecology}, volume = {39}, number = {4}, pages = {314-321}, pmid = {10882436}, issn = {1432-184X}, abstract = {An air conditioned wind tunnel system was designed, fabricated, and tested to determine whether tethered bees scavenge microbeads or Bacillus subtilis var. niger spores from aerosols. Tests showed that microbeads and spores were scavenged by bumblebees and honeybees, respectively. Five independent variables and their interactions were used in a stepwise multiple regression. Two of them, the cube root of the electrostatic charge on the honeybee and the dose of the spore aerosol, accounted for most of the statistically significant fit to the model's two dependent variables: the percentage of the dose adsorbed by honeybees and the number of spores adsorbed by the same bees. Both dependent variables increased directly so that an increase in electrostatic charge on the bee (i.e., cube root 32 pC) resulted in an increase (i.e., approximately 1%) in the spore dose adsorbed and the number of spores adsorbed by the bees. It was theorized that the spores were in an adsorption/desorption equilibrium that responded to the concentration "pressure" of the spore aerosol. Further, the charge on the bee affected the adsorption force on the bee's surface, as well as increasing the effective aerosol volume accessible for the bee's scavenging. In short, relating these findings to bees scavenging bacteria from the ambient atmosphere, it appears that the spore exposure (where exposure means the product of the ambient concentration, the time the bee is exposed, and air volume through which the bee flies) controls the number of spores adsorbed by a bee, and the static charge on the bee controls the adsorption/desorption equilibrium and presumably the scavenging volume.}, }
@article {pmid10882435, year = {2000}, author = {Lee, Y and Fuxa, JR}, title = {Transport of Wild-Type and Recombinant Nucleopolyhedroviruses by Scavenging and Predatory Arthropods.}, journal = {Microbial ecology}, volume = {39}, number = {4}, pages = {301-313}, pmid = {10882435}, issn = {1432-184X}, abstract = {Wild-type and recombinant nucleopolyhedroviruses (NPVs) were compared in their capability to be transported over limited distances by the predator Podisus maculiventris (Say) and scavengers Sarcophaga bullata (Parker) and Acheta domesticus (Linnaeus) in Trichoplusia ni (Hübner) larvae infesting collards in a greenhouse microcosm. Viruses tested were variants of Autographa californica (Speyer) NPV (AcNPV): wild-type virus (AcNPV.WT), AcNPV expressing a scorpion toxin (AcNPV.AaIT), and AcNPV expressing juvenile hormone esterase (AcJHE.SG). Podisus maculiventris transported AcNPV.WT and S. bullata transported AcNPV.WT and AcNPV.AaIT. Prevalence and transport of AcNPV.WT were greater than those of AcNPV.AaIT and AcJHE.SG, regardless of whether the nontarget organism carriers were present or absent. Podisus maculiventris and S. bullata transported recombinant and wild-type NPVs at a rate of up to 62.5 cm/day, and A. domesticus transported wild-type NPV at 125 cm/day. The infected host insects, T. ni, undoubtedly contributed to viral transport in the current research. In every experiment, both the wild-type and recombinant virus spread to some degree in the plots without predators or scavengers. The relative amounts of NPVs that accumulated in soil, as indicated by bioassay mortality percentages, generally exhibited spatial patterns similar to those of T. ni mortality due to NPV on the collards plants. Thus, the predator and scavengers in the current research demonstrated some capacity to transport wild-type as well as recombinant viruses at significant rates in a greenhouse microcosm.}, }
@article {pmid10882434, year = {2000}, author = {Mitchell, EA and Borcard, D and Buttler, AJ and Grosvernier, P and Gilbert, D and Gobat, J}, title = {Horizontal Distribution Patterns of Testate Amoebae (Protozoa) in a Sphagnum magellanicum Carpet.}, journal = {Microbial ecology}, volume = {39}, number = {4}, pages = {290-300}, pmid = {10882434}, issn = {1432-184X}, abstract = {The distribution of soil microorganisms is generally believed to be patchy and to reflect habitat heterogeneity. Despite this general rule, the amount of existing data on species distribution patterns is scarce. Testate amoebae (Protozoa; Rhizopoda) are an important component of soil microbial communities and are increasingly used in ecological and paleoecological studies of Sphagnum-dominated peatlands, but data on the spatial structure of communities are completely lacking. This is an important aspect since quantitative models used for paleoecological reconstruction and monitoring are based on species assemblages. We explored the distribution patterns of testate amoebae distribution in a macroscopically homogeneous Sphagnum carpet, down to a scale of several centimeters. Distributions maps of the species and spatially constrained sample groups were produced. Multivariate and individual spatial autocorrelations were calculated. The importance of spatial structure was quantified by canonical correspondence analysis. Our ultimate goal is to find the finest resolution of environmental monitoring using testate amoebae. The distribution patterns differed among species, resulting in a complex spatial structure of the species assemblage in a whole. Spatial structure accounted for 36% of the total variation of species abundance in a canonical correspondence analysis constrained by spatial variables. This structure was partly correlated to altitude (microtopography) at a very fine scale. These results confirmed the existence of significant broad- and fine-scale spatial structures within testate amoebae communities that could in part be interpreted as effects of ecological gradients. This shows that, on a surface area of 0.25 m(2), ecological conditions which look uniform from a macroscopic point of view are not perceived as such by Sphagnum-inhabiting organisms. Therefore, testate amoebae could prove very useful to monitor fine-scale ecological processes or disturbances. Studies of the species' spatial distribution patterns in combination with autoecological studies are needed and should be included in the toolbox of biomonitoring itself.}, }
@article {pmid10882433, year = {2000}, author = {Jensen, S and Holmes, AJ and Olsen, RA and Murrell, JC}, title = {Detection of Methane Oxidizing Bacteria in Forest Soil by Monooxygenase PCR Amplification.}, journal = {Microbial ecology}, volume = {39}, number = {4}, pages = {282-289}, pmid = {10882433}, issn = {1432-184X}, abstract = {Atmospheric methane oxidation by a spruce forest soil from Norway at 15 degrees C was found to be maximal at a depth of ca 7 cm. Examination of the kinetics of this methane oxidation revealed an apparent K(m) of 403.1 nM and a V(max) of 2.2 nmol g(-1) dry weight soil h(-1). The low apparent K(m) suggested the presence of active methane oxidizing bacteria with a high affinity for methane. DNA was extracted from the 5-10 cm horizon, purified, and subjected to PCR amplification with primers directed toward the monooxygenase genes pmoA and amoA, which are essential for methane oxidation. Hybridization analysis of the clone library subsequently constructed revealed that 49% of the 76 cloned PCR fragments were putative methanotroph pmoA sequences and 16% were putative ammonium oxidizing nitrifier amoA sequences. Sequencing of 28 clones identified three major groups showing homology to pmoA from Methylococcus capsulatus, beta-subdivision ammonia-oxidizers (amoA), and a new group of monooxygenase pmoA/amoA sequences.}, }
@article {pmid10882432, year = {2000}, author = {Bai, Q and Gattinger, A and Zelles, L}, title = {Characterization of Microbial Consortia in Paddy Rice Soil by Phospholipid Analysis.}, journal = {Microbial ecology}, volume = {39}, number = {4}, pages = {273-281}, pmid = {10882432}, issn = {1432-184X}, abstract = {Microbial biomass and community structure in paddy rice soil during the vegetation period of rice were estimated by analysis of their phospholipid fatty acids (PLFA), hydroxy fatty acids of lipopolysaccharides (LPS-HYFA), and phospholipid ether lipids (PLEL) directly extracted from the soil. A clear change in the composition of the community structure at different sampling periods was observed, indicated by the principal component analysis of the PLFA. A dramatic decline of ester-linked PLFA was observed in the soil samples taken at the second sampling time. In contrast to the ester-linked PLFA, the non-ester-linked PLFA composition did not change. The hydroxy fatty acids of lipopolysaccharides as well as ether lipids decreased consecutively during the observation period. Total microbial abundance was estimated to be (4.1-7.3) x 10(9) cells g(-1) soil (dry weight). About 44% account for aerobic and 32% for facultative anaerobic bacteria, and 24% for archaea, on average. According to the profile and patterns of PLFA in the soil sample, it may be suggested that the paddy soil at the August sampling period contained more abundant facultative anaerobic bacteria (ca. 36%) and archaea (ca. 37%), but the total microbial biomass was significantly lower than in the remaining sampling periods. As the plant approached maturity, the microbial community structure in the soil changed to contain more abundant Gram-negative bacteria and methanotrophs.}, }
@article {pmid10882431, year = {2000}, author = {Ranjard, L and Poly, F and Combrisson, J and Richaume, A and Gourbière, F and Thioulouse, J and Nazaret, S}, title = {Heterogeneous Cell Density and Genetic Structure of Bacterial Pools Associated with Various Soil Microenvironments as Determined by Enumeration and DNA Fingerprinting Approach (RISA).}, journal = {Microbial ecology}, volume = {39}, number = {4}, pages = {263-272}, pmid = {10882431}, issn = {1432-184X}, abstract = {The cell density and the genetic structure of bacterial subcommunities (further named pools) present in the various microenvironments of a silt loam soil were investigated. The microenvironments were isolated first using a procedure of soil washes that separated bacteria located outside aggregates (outer part) from those located inside aggregates (inner part). A nondestructive physical fractionation was then applied to the inner part in order to separate bacteria located inside stable aggregates of different size (size fractions, i.e., two macroaggregate fractions, two microaggregate fractions, and the dispersible day fraction). Bacterial densities measured by acridine orange direct counts (AODC) and viable heterotrophic (VH) cell enumerations showed the heterogeneous quantitative distribution of cells in soil. Bacteria were preferentially located in the inner part with 87.6% and 95.4% of the whole AODC and VH bacteria, respectively, and in the microaggregate and dispersible clay fractions of this part with more than 70% and 80% of the whole AODC and VH bacteria, respectively. The rRNA intergenic spacer analysis (RISA) was used to study the genetic structure of the bacterial pools. Different fingerprints and consequently different genetic structures were observed between the unfractionated soil and the microenvironments, and also among the various microenvironments, giving evidence that some populations were specific to a given location in addition to the common populations of all the microenvironments. Cluster and multivariate analysis of RISA profiles showed the weak contribution of the pools located in the macroaggregate fractions to the whole soil community structure, as well as the clear distinction between the pool associated to the macroaggregate fractions and the pools associated to the microaggregate ones. Furthermore, these statistical analyses allowed us to ascertain the influence of the clay and organic matter content of microenvironments on the genetic structure relatedness between pools.}, }
@article {pmid10879561, year = {2000}, author = {Vishnivetskaya, T and Kathariou, S and McGrath, J and Gilichinsky, D and Tiedje, JM}, title = {Low-temperature recovery strategies for the isolation of bacteria from ancient permafrost sediments.}, journal = {Extremophiles : life under extreme conditions}, volume = {4}, number = {3}, pages = {165-173}, doi = {10.1007/s007920070031}, pmid = {10879561}, issn = {1431-0651}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Cold Temperature ; Ecosystem ; Genotype ; Geologic Sediments/*microbiology ; Ice ; Phylogeny ; Polymerase Chain Reaction ; Siberia ; }, abstract = {Permafrost represents a unique ecosystem that has allowed the prolonged survival of certain bacterial lineages at subzero temperatures. To better understand the permafrost microbial community, it is important to identify isolation protocols that optimize the recovery of genetically diverse bacterial lineages. We have investigated the impact of different low-temperature isolation protocols on recovery of aerobic bacteria from northeast Siberian permafrost of variable geologic origin and frozen for 5000 to 3 million years. Low-nutrient media enhanced the quantitative recovery of bacteria, whereas the isolation of diverse morphotypes was maximized on rich media. Cold enrichments done directly in natural, undisturbed permafrost led not only to recovery of increased numbers of bacteria but also to isolation of genotypes not recovered by means of liquid low-temperature enrichments. On the other hand, direct plating and growth at 4 degrees C also led to recovery of diverse genotypes, some of which were not recovered following enrichment. Strains recovered from different permafrost samples were predominantly oligotrophic and non-spore-forming but were otherwise variable from each other in terms of a number of bacteriological characteristics. Our data suggest that a combination of isolation protocols from different permafrost samples should be used to establish a culture-based survey of the different bacterial lineages in permafrost.}, }
@article {pmid10877785, year = {2000}, author = {Boon, N and Goris, J and De Vos, P and Verstraete, W and Top, EM}, title = {Bioaugmentation of activated sludge by an indigenous 3-chloroaniline-degrading Comamonas testosteroni strain, I2gfp.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {7}, pages = {2906-2913}, pmid = {10877785}, issn = {0099-2240}, mesh = {Aniline Compounds/*metabolism ; Bacteria/genetics/isolation &amp; purification ; Biodegradation, Environmental ; Bioreactors ; Comamonas testosteroni/genetics/growth &amp; development/*metabolism ; Culture Media ; Ecosystem ; Electrophoresis, Polyacrylamide Gel/methods ; Genes, rRNA ; Green Fluorescent Proteins ; Luminescent Proteins/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; Water Purification ; }, abstract = {A strain identified as Comamonas testosteroni I2 was isolated from activated sludge and found to be able to mineralize 3-chloroaniline (3-CA). During the mineralization, a yellow intermediate accumulated temporarily, due to the distal meta-cleavage of chlorocatechol. This strain was tested for its ability to clean wastewater containing 3-CA upon inoculation into activated sludge. To monitor its survival, the strain was chromosomally marked with the gfp gene and designated I2gfp. After inoculation into a lab-scale semicontinuous activated-sludge (SCAS) system, the inoculated strain maintained itself in the sludge for at least 45 days and was present in the sludge flocs. After an initial adaptation period of 6 days, complete degradation of 3-CA was obtained during 2 weeks, while no degradation at all occurred in the noninoculated control reactor. Upon further operation of the SCAS system, only 50% 3-CA removal was observed. Denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes revealed a dynamic change in the microbial community structure of the activated sludge. The DGGE patterns of the noninoculated and the inoculated reactors evolved after 7 days to different clusters, which suggests an effect of strain inoculation on the microbial community structure. The results indicate that bioaugmentation, even with a strain originating from that ecosystem and able to effectively grow on a selective substrate, is not permanent and will probably require regular resupplementation.}, }
@article {pmid10877783, year = {2000}, author = {Thamdrup, B and Rosselló-Mora, R and Amann, R}, title = {Microbial manganese and sulfate reduction in Black Sea shelf sediments.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {7}, pages = {2888-2897}, pmid = {10877783}, issn = {0099-2240}, mesh = {Bacteria/genetics/isolation &amp; purification/*metabolism ; Bacteria, Anaerobic/classification/genetics/isolation &amp; purification ; Carbon Dioxide/metabolism ; Carbonates/chemistry ; Chemical Precipitation ; Colony Count, Microbial ; DNA, Ribosomal/genetics ; Geologic Sediments/*microbiology ; Iron/metabolism ; Manganese/*metabolism ; Molecular Sequence Data ; Nitrates/metabolism ; Oxidation-Reduction ; Phylogeny ; Quaternary Ammonium Compounds/metabolism ; RNA, Ribosomal, 16S/genetics ; Romania ; Seawater/*microbiology ; Sulfates/*metabolism ; }, abstract = {The microbial ecology of anaerobic carbon oxidation processes was investigated in Black Sea shelf sediments from mid-shelf with well-oxygenated bottom water to the oxic-anoxic chemocline at the shelf-break. At all stations, organic carbon (C(org)) oxidation rates were rapidly attenuated with depth in anoxically incubated sediment. Dissimilatory Mn reduction was the most important terminal electron-accepting process in the active surface layer to a depth of approximately 1 cm, while SO(4)(2-) reduction accounted for the entire C(org) oxidation below. Manganese reduction was supported by moderately high Mn oxide concentrations. A contribution from microbial Fe reduction could not be discerned, and the process was not stimulated by addition of ferrihydrite. Manganese reduction resulted in carbonate precipitation, which complicated the quantification of C(org) oxidation rates. The relative contribution of Mn reduction to C(org) oxidation in the anaerobic incubations was 25 to 73% at the stations with oxic bottom water. In situ, where Mn reduction must compete with oxygen respiration, the contribution of the process will vary in response to fluctuations in bottom water oxygen concentrations. Total bacterial numbers as well as the detection frequency of bacteria with fluorescent in situ hybridization scaled to the mineralization rates. Most-probable-number enumerations yielded up to 10(5) cells of acetate-oxidizing Mn-reducing bacteria (MnRB) cm(-3), while counts of Fe reducers were <10(2) cm(-3). At two stations, organisms affiliated with Arcobacter were the only types identified from 16S rRNA clone libraries from the highest positive MPN dilutions for MnRB. At the third station, a clone type affiliated with Pelobacter was also observed. Our results delineate a niche for dissimilatory Mn-reducing bacteria in sediments with Mn oxide concentrations greater than approximately 10 micromol cm(-3) and indicate that bacteria that are specialized in Mn reduction, rather than known Mn and Fe reducers, are important in this niche.}, }
@article {pmid10876164, year = {2000}, author = {Nishigaki, K and Naimuddin, M and Hamano, K}, title = {Genome profiling: a realistic solution for genotype-based identification of species.}, journal = {Journal of biochemistry}, volume = {128}, number = {1}, pages = {107-112}, doi = {10.1093/oxfordjournals.jbchem.a022719}, pmid = {10876164}, issn = {0021-924X}, mesh = {Animals ; Electrophoresis, Polyacrylamide Gel/methods ; Escherichia coli/genetics/isolation &amp; purification ; *Genetic Techniques ; Genome ; Mice ; Polymerase Chain Reaction ; Rats ; *Species Specificity ; Yeasts/genetics ; }, abstract = {Species identification is the basis of Biology and has been carried out based on phenotype. Although some genes, such as that for 16S rRNA, have been used for species confirmation, identification of species based only on genotype has never been done before, although recent whole genome sequencing studies have demonstrated it to be possible in principle. However, it is evidently unrealistic for routine experiments of species identification. This paper clarifies that a very limited amount of information derived from a genome sequence is sufficient for identifying the species. It also proves that Genome Profiling [Nishigaki, K., Amano, N., and Takasawa, T. (1991) Chem. Lett. 1097-1100], TGGE analysis of random PCR products, can not only fulfill such requirements, but also serve as a universal method to analyze species. Thus, this compact technology can be used in many fields of biology, especially in microbe-related disciplines such as microbial ecology and epidemiology where exact knowledge about all members of a population is essential but previously difficult to obtain. This is the first demonstration that genotype-based identification of species is possible using a simple and uniform protocol for all organisms.}, }
@article {pmid10874076, year = {2000}, author = {Yadav, JS and Bethea, C and Reddy, CA}, title = {Mineralization of trichloroethylene (TCE) by the white rot fungus Phanerochaete chrysosporium.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {65}, number = {1}, pages = {28-34}, doi = {10.1007/s0012800090}, pmid = {10874076}, issn = {0007-4861}, mesh = {Biodegradation, Environmental ; Environmental Pollutants/metabolism ; Phanerochaete/*physiology ; Solvents/*metabolism ; Trichloroethylene/*metabolism ; }, }
@article {pmid10870552, year = {1999}, author = {Maltseva, OV and Tsoi, TV and Quensen, JF and Fukuda, M and Tiedje, JM}, title = {Degradation of anaerobic reductive dechlorination products of Aroclor 1242 by four aerobic bacteria.}, journal = {Biodegradation}, volume = {10}, number = {5}, pages = {363-371}, doi = {10.1023/a:1008319306757}, pmid = {10870552}, issn = {0923-9820}, support = {P42ES04911/ES/NIEHS NIH HHS/United States ; }, mesh = {Anaerobiosis ; Aroclors/*metabolism ; Bacteria, Aerobic/*metabolism ; Biodegradation, Environmental ; Biphenyl Compounds/metabolism ; Burkholderia/metabolism ; Chlorine/*metabolism ; Comamonas/metabolism ; Environmental Pollutants/metabolism ; Fatty Acids, Unsaturated/metabolism ; Oxidation-Reduction ; Polychlorinated Biphenyls/chemistry/metabolism ; Rhodococcus/metabolism ; }, abstract = {We studied the aerobic degradation of eight PCB congeners which comprise from 70 to 85% of the anaerobic dechlorination products from Aroclor 1242, including 2-, 4-, 2,4-, 2,6-, 2,2'-, 2,4'-, 2,2', 4-, and 2,4,4'-chlorobiphenyl (CB), and the biodegradation of their mixtures designed to simulate anaerobic dechlorination profiles M and C. Strains Comamonas testosteroni VP44 and Rhodococcus erythreus NY05 preferentially oxidized a para-substituted ring, while Rhodococcus sp. RHA1, similar to well known strain Burkholderia sp. LB400, preferably attacked an ortho-chlorinated ring. Strains with ortho-directed attack extensively degraded 2,4'- and 2,4,4'-CB into 4-chlorobenzoate, while bacteria with para-directed attack transformed these congeners mostly into potentially problematic meta-cleavage products. The strains that preferentially oxidized an ortho-substituted ring readily degraded seven of the eight congeners supplied individually; only 2,6-CB was poorly degraded. Degradation of 2,2'- and 2,4,4'-CB was reduced when present in mixtures M and C. Higher efficiencies of degradation of the individual congeners and defined PCB mixtures M and C and greater production of chlorobenzoates were observed with bacteria that preferentially attack an ortho-substituted ring. PCB congeners 2,4'-, 2,2',4-, and 2,4,4'-CB can be used to easily identify bacteria with ortho-directed attack which are advantageous for use in the aerobic stage of the two-phase (anaerobic/aerobic) PCB bioremediation scheme.}, }
@article {pmid10865943, year = {2000}, author = {Ranjard, L and Poly, F and Nazaret, S}, title = {Monitoring complex bacterial communities using culture-independent molecular techniques: application to soil environment.}, journal = {Research in microbiology}, volume = {151}, number = {3}, pages = {167-177}, doi = {10.1016/s0923-2508(00)00136-4}, pmid = {10865943}, issn = {0923-2508}, mesh = {Bacteria/*genetics/growth &amp; development ; DNA, Bacterial/*analysis ; *Ecosystem ; Molecular Biology/methods ; *Soil Microbiology ; }, abstract = {Over the last decade, important advances in molecular biology led to the development of culture-independent approaches to describing bacterial communities. These new strategies, based on the analysis of DNA directly extracted from environmental samples, circumvent the steps of isolation and culturing of bacteria, which are known for their selectivity leading to a non-representative view of the extent of bacterial diversity. This review provides an overview of the potentials and limitations of some molecular approaches currently used in microbial ecology. Examples of applications to the study of indigenous soil microbial community illustrate the feasibility and the power of such approaches.}, }
@article {pmid10865198, year = {2000}, author = {Burne, RA and Chen, YY}, title = {Bacterial ureases in infectious diseases.}, journal = {Microbes and infection}, volume = {2}, number = {5}, pages = {533-542}, doi = {10.1016/s1286-4579(00)00312-9}, pmid = {10865198}, issn = {1286-4579}, support = {R01 DE010362/DE/NIDCR NIH HHS/United States ; DE10362/DE/NIDCR NIH HHS/United States ; }, mesh = {Animals ; Antibody Formation ; Bacteria/*enzymology/genetics ; *Gene Expression Regulation, Enzymologic ; Genes, Bacterial ; Helicobacter/enzymology ; Helicobacter Infections/immunology/microbiology ; Humans ; Hydrogen-Ion Concentration ; Immunity, Cellular ; Mouth/microbiology ; Urea/metabolism ; Urease/*genetics/immunology/metabolism ; Urinary Tract Infections/microbiology ; Virulence ; }, abstract = {Ureases are multi-subunit, nickel-containing enzymes that catalyze the hydrolysis of urea to carbon dioxide and ammonia. This brief review discusses the biochemistry and genetics of bacterial ureases and outlines the roles of urea metabolism in microbial ecology and pathogenesis of some of the principle ureolytic species affecting human health.}, }
@article {pmid10856780, year = {2000}, author = {Timms-Wilson, TM and Ellis, RJ and Bailey, MJ}, title = {Immuno-capture differential display method (IDDM) for the detection of environmentally induced promoters in rhizobacteria.}, journal = {Journal of microbiological methods}, volume = {41}, number = {1}, pages = {77-84}, doi = {10.1016/s0167-7012(00)00139-1}, pmid = {10856780}, issn = {0167-7012}, mesh = {DNA Transposable Elements ; Escherichia coli/genetics ; *Escherichia coli Proteins ; Fluorescent Antibody Technique ; *Genes, Bacterial ; Immune Sera ; Membrane Transport Proteins/genetics/immunology ; Microscopy, Phase-Contrast ; *Monosaccharide Transport Proteins ; Mutagenesis, Insertional ; *Promoter Regions, Genetic ; Pseudomonas fluorescens/*genetics ; Pythium/genetics/metabolism ; Recombinant Fusion Proteins/genetics/metabolism ; Seeds/genetics/metabolism ; *Symporters ; beta-Galactosidase/genetics ; }, abstract = {A rapid immunological method for trapping and selection of functionally regulated prokaryotic promoters is described. The method is based on application of a novel mini-Tn5 derived promoter probe (pUTTKZY-promoterless lacZY as a reporter and kanamycin resistance) to mutagenise a plant growth promoting fluorescent pseudomonad, Pseudomonas fluorescens 54/96. The transposon allows selection of operon fusion mutants (lacZY(+)) directly on media containing lactose as a sole carbon source as well as selection for kanamycin and lacZ (beta-galactosidase) expression on X-gal indicator media. We have extended the technique to target the surface expression of the induced lactose permease gene (lacY) from mutagenised libraries and the immuno-capture of bacteria with magnetic beads and anti-LacY monospecifc antisera. The benefits of the lacZY reporter are that a library can be rapidly generated and screened in vitro to isolate non-expressed mutants for further in situ screening. Here we demonstrate the development and utility of the technique and its potential as a differential display method for the isolation of promoters that direct regulated gene expression in the phytosphere, or under other imposed conditions.}, }
@article {pmid10856774, year = {2000}, author = {Xu, J and Xu, X and Verstraete, W}, title = {Adaptation of E. coli cell method for micro-scale nitrate measurement with the Griess reaction in culture media.}, journal = {Journal of microbiological methods}, volume = {41}, number = {1}, pages = {23-33}, doi = {10.1016/s0167-7012(00)00141-x}, pmid = {10856774}, issn = {0167-7012}, mesh = {Culture Media ; Diazonium Compounds ; Escherichia coli/*chemistry ; Hydrogen-Ion Concentration ; Indicators and Reagents ; Meat/analysis ; Nitrates/*analysis ; Nitrites/*analysis ; Oxidation-Reduction ; }, abstract = {The E. coli cell method for nitrate measurement consists of two-steps: nitrate reduction by the E. coli cell usually under anaerobic conditions and subsequently nitrite measurement with the Griess reaction. It was found that the E. coli DSM 498k wildtype cell can reduce nitrate to nitrite under aerobic conditions. Therefore, the E. coli method for nitrate measurement was adapted to be performed under aerobic conditions in a microtiter plate. The adapted method is simpler than the original E. coli method and other nitrate methods such as those with inorganic reductants and with purified enzymes. Furthermore, it was found that for the Griess reaction the pH values of samples after addition of the Griess reagent A should be lower than 1.8 for a stable absorbance at 540 nm to be reached. It is important to add the two Griess reagents separately and to read the absorbance twice consecutively in a microtiter plate. The adapted E. coli method was successfully applied to measure the traces of nitrate in MRS and other medium components by measuring the standard curve of a dilution of each individual medium component. It was found that many organic medium components contain traces of nitrate, while none of them contain detectable nitrite. Among these, the extract of meat and yeast extract contain relatively high amounts of nitrate: 217 mg N/kg and 99 mg N/kg respectively. MRS broth contains nitrate from 0.3 to 0.6 mg N/l depending on the batch numbers of the product. The adapted E. coli can also be used for nitrate measurement in other matrices.}, }
@article {pmid10842795, year = {2000}, author = {Kümmerer, K}, title = {Drugs, diagnostic agents and disinfectants in wastewater and water--a review.}, journal = {Schriftenreihe des Vereins fur Wasser-, Boden- und Lufthygiene}, volume = {105}, number = {}, pages = {59-71}, pmid = {10842795}, issn = {0300-8665}, mesh = {Anti-Bacterial Agents/analysis ; Contrast Media/*analysis ; Disinfectants/*analysis ; Germany ; Humans ; *Medical Waste Disposal ; Pharmaceutical Preparations/*analysis ; Sewage/chemistry ; Water Pollutants, Chemical/*analysis ; Water Purification ; Water Supply/*analysis ; }, abstract = {After administration pharmaceuticals are excreted by the patients into the aquatic environment via wastewater. Unused medications are sometimes disposed of in drains. The drugs may enter the aquatic environment and eventually reach drinking water, if they are not biodegraded or eliminated during sewage treatment. Additionally, antibiotics and disinfectants are assumed to disturb the wastewater treatment process and the microbial ecology in surface waters. Furthermore, resistant bacteria may be selected in the aeration tanks of sewage treatment plants by the antibiotic substances present. Since the 1980s, data on the occurrence of pharmaceuticals in natural surface waters and the effluents of sewage treatment plants have been reported. More recently, pharmaceuticals have been detected in ground and drinking water. However, only little is known about the risk imposed on humans by pharmaceuticals and their metabolites in surface and drinking water. An overview of input, occurrence, elimination (e.g. biodegradability) and possible effects of different pharmaceutical groups such as anti-tumour drugs, antibiotics and contrast media as well as AOX resulting from hospitals effluent input into sewage water and surface water is presented.}, }
@article {pmid10833229, year = {2000}, author = {Liu, Y}, title = {Reduced Growth Yield of Activated Sludge in Organic Protonophore-Containing Batch Culture.}, journal = {Microbial ecology}, volume = {39}, number = {2}, pages = {168-173}, doi = {10.1007/s002489900189}, pmid = {10833229}, issn = {1432-184X}, abstract = {The effects of organic protonophores 2,4-dinitrophenol (dNP) and para-nitrophenol (pNP) on the observed growth yield (Y(obs)) was studied using batch cultures of activated sludge microorganisms. A growth yield model was proposed in relation to the ratio of initial protonophore concentration (C(u)) to initial biomass concentration (X(0)) and was verified with experimental data. It was found that Y(obs) decreased with the increase of the C(u)/X(0) ratio, while the specific rate of glucose consumption was increased. Results showed that the C(u)/X(0) ratio could more reasonably reflect the real strength of organic protonophore exerted to activated sludge than using C(u) only. Based on the concept of growth yield, a model describing the uncoupling degree between energy generated via electron transport system and energy used for growth was further developed for protonophore-containing batch culture. It was shown that more than 60% of glucose was consumed through a futile cycle of energy rather than for growth at higher C(u)/X(0) ratios. This research usefully shows that the dissipation of energy via uncoupling biochemical processes can reduce excessive production of activated sludge markedly.}, }
@article {pmid10833228, year = {2000}, author = {Snoeyenbos-West, OL and Nevin, KP and Anderson, RT and Lovley, DR}, title = {Enrichment of Geobacter Species in Response to Stimulation of Fe(III) Reduction in Sandy Aquifer Sediments.}, journal = {Microbial ecology}, volume = {39}, number = {2}, pages = {153-167}, doi = {10.1007/s002480000018}, pmid = {10833228}, issn = {1432-184X}, abstract = {Engineered stimulation of Fe(III) has been proposed as a strategy to enhance the immobilization of radioactive and toxic metals in metal-contaminated subsurface environments. Therefore, laboratory and field studies were conducted to determine which microbial populations would respond to stimulation of Fe(III) reduction in the sediments of sandy aquifers. In laboratory studies, the addition of either various organic electron donors or electron shuttle compounds stimulated Fe(III) reduction and resulted in Geobacter sequences becoming important constituents of the Bacterial 16S rDNA sequences that could be detected with PCR amplification and denaturing gradient gel electrophoresis (DGGE). Quantification of Geobacteraceae sequences with a PCR most-probable-number technique indicated that the extent to which numbers of Geobacter increased was related to the degree of stimulation of Fe(III) reduction. Geothrix species were also enriched in some instances, but were orders of magnitude less numerous than Geobacter species. Shewanella species were not detected, even when organic compounds known to be electron donors for Shewanella species were used to stimulate Fe(III) reduction in the sediments. Geobacter species were also enriched in two field experiments in which Fe(III) reduction was stimulated with the addition of benzoate or aromatic hydrocarbons. The apparent growth of Geobacter species concurrent with increased Fe(III) reduction suggests that Geobacter species were responsible for much of the Fe(III) reduction in all of the stimulation approaches evaluated in three geographically distinct aquifers. Therefore, strategies for subsurface remediation that involve enhancing the activity of indigenous Fe(III)-reducing populations in aquifers should consider the physiological properties of Geobacter species in their treatment design.}, }
@article {pmid10833227, year = {2000}, author = {Patureau, D and Zumstein, E and Delgenes, JP and Moletta, R}, title = {Aerobic Denitrifiers Isolated from Diverse Natural and Managed Ecosystems.}, journal = {Microbial ecology}, volume = {39}, number = {2}, pages = {145-152}, doi = {10.1007/s002480000009}, pmid = {10833227}, issn = {1432-184X}, abstract = {Twenty-eight bacterial strains were isolated from an ecosystem adapted to fluctuating oxic-anoxic conditions. This ecosystem comprised a mixture of different natural and wastewater treatment environments. Among the 28 strains isolated, 10 exhibited aerobic denitrifying activity, i.e., co-respiration of oxygen and nitrate and simultaneous production of nitrite by 4 of them and of nitrogen gas by the remaining 6. Comparisons between the 16S rDNA sequences of the 10 strains showed that 3 of them were identical to M. aerodenitrificans, whereas RAPD profiles showed that the 3 strains were identical to each other but that they were different from M. aerodenitrificans. This implies that alternating aerobic-anoxic conditions allowed the isolation of a new strain of this aerobic denitrifier. Moreover, other denitrifying bacteria belonging to the genera Paracoccus, Thiobacillus, Enterobacter, Comamonas, and Sphingomonas were isolated in this way. These data imply that a wide variety of bacteria are able to carry out this type of metabolism. M. aerodenitrificans was also detected in methanogenic, denitrifying, nitrifying, phosphate removal, and activated sludge ecosystems by two-step PCR amplification. After 4 months of acclimation to oxic-anoxic phases, the strain was also detected in a canal and in a pond. This suggests that there is no specific natural ecological niche for aerobic denitrifiers but, as soon as selective pressure such as alternating aeration conditions is applied, this metabolism is amplified.}, }
@article {pmid10833226, year = {2000}, author = {Ruiz-Lozano, JM and Bonfante, P}, title = {A Burkholderia Strain Living Inside the Arbuscular Mycorrhizal Fungus Gigaspora margarita Possesses the vacB Gene, Which Is Involved in Host Cell Colonization by Bacteria.}, journal = {Microbial ecology}, volume = {39}, number = {2}, pages = {137-144}, doi = {10.1007/s002480000008}, pmid = {10833226}, issn = {1432-184X}, abstract = {The arbuscular mycorrhizal (AM) fungus Gigaspora margarita harbors a resident population of endosymbiontic Burkholderia in its cytoplasm. Nothing is known about the acquisition of such bacteria and about the molecular bases which allow colonization of the fungus. We wondered whether the intracellular Burkholderia strain possesses genetic determinants involved in colonization of a eukaryotic cell. Using degenerated oligonucleotide primers for vacB, a gene involved in host cell colonization by pathogenic bacteria, an 842 bp DNA fragment was cloned, sequenced, and identified as a part of the vacB gene in Burkholderia sp. The insert was used as a probe to screen a fungal library that, because of the presence of intracellular Burkholderia cells, was also representative of the bacterial genome. The complete nucleotide sequence of vacB and flanking genes was determined. The bacterial origin of this genomic region was established by PCR, using specific vacB primers on DNA from Gigasporaceae that did or did not contain cytoplasmic Burkholderia, as well as on DNA from other bacteria, including free-living Burkholderia. We hypothesize that the vacB gene is part of a new genetic region acquired by a rhizospheric Burkholderia strain, which became able to establish a symbiotic interaction with the AM fungus G. margarita.}, }
@article {pmid10833225, year = {2000}, author = {Bagwell, CE and Lovell, CR}, title = {Microdiversity of Culturable Diazotrophs from the Rhizoplanes of the Salt Marsh Grasses Spartina alterniflora and Juncus roemerianus.}, journal = {Microbial ecology}, volume = {39}, number = {2}, pages = {128-136}, doi = {10.1007/s002480000017}, pmid = {10833225}, issn = {1432-184X}, abstract = {Salt marshes dominated by Spartina alterniflora (smooth cordgrass) are among the most productive ecosystems known, despite nitrogen limitation. Rhizoplane/rhizosphere diazotrophy (nitrogen fixation) serves as a significant source of combined nitrogen in these systems. Several recent studies have demonstrated remarkable physiological and phylogenetic macro- and microdiversity within this important functional group of organisms. However, the ecological significance of this diversity is presently unknown. The physiological characteristics of the culturable, oxygen-utilizing fraction of the rhizoplane diazotroph assemblages from Spartina alterniflora and from another salt marsh grass, the black needle rush Juncus roemerianus, were examined in combination with an assessment of the phylogenetic relatedness by whole genome DNA-DNA hybridization. Analysis of substrate utilization data permitted quantitative evaluation of fully cross-hybridizing strain groups and physiological clusters. Phylogenetically related strains, defined by DNA homology >/=90% relative to the positive control, displayed extensive physiological diversity. Seven bootstrap-supported physiological clusters, composed largely of phylogenetically dissimilar strains, showed similar utilization patterns for at least one class of ecologically relevant substrates (carbohydrates, carboxylic acids, or amino acids). These diazotrophs appear to be physiologically adapted for utilization of specific substrates or classes of substrates, lending support to diazotrophic functional redundancy. Microenvironmental heterogeneity is credited for promoting this diversity by selecting for physiologically specialized diazotroph populations to occupy defined niches in situ. One outcome of this physiological diversity is maintenance of a crucial environmental function (nitrogen fixation) over a broad range of environmental conditions.}, }
@article {pmid10833224, year = {2000}, author = {Yallop, ML and Paterson, DM and Wellsbury, P}, title = {Interrelationships between Rates of Microbial Production, Exopolymer Production, Microbial Biomass, and Sediment Stability in Biofilms of Intertidal Sediments.}, journal = {Microbial ecology}, volume = {39}, number = {2}, pages = {116-127}, doi = {10.1007/s002489900186}, pmid = {10833224}, issn = {1432-184X}, abstract = {The upper few millimeters of intertidal sediment supports a varied biomass of microbial consortia and microphytobenthos. Many of these organisms release extracellular polymers into the surrounding sediment matrix that can result in sediment cohesion and the increased stability of the sediment. The relationship between the heterotrophic and autotrophic components of these biofilms is not well understood. A combination of mesocosm and field investigations were used to investigate the relationship between microbial production rate (algae and bacteria), the extracellular carbohydrates, biomass, and stability in conjunction with a variety of environmental factors. An inverse relationship was found between rates of algal production and sediment stability both in the field and in laboratory mesocosms, though the relationship was significant only in the field (P < 0.001). Stability of sediments increased with increasing bacterial production rate (P < 0.001). Positive correlations were found between sediment stability and a range of other variables, including algal biomass (P < 0.001), colloidal-S EPS (P < 0.001), colloidal-S carbohydrate (P < 0.01), colloidal-S EDTA (P < 0.01), and sediment water content (P < 0.001). Using the data acquired, a preliminary model was developed to predict changes in sediment stability. Chlorophyll a, water content, and colloidal-S EPS were found to be the most important predictors of stability in intact cores incubated under laboratory conditions. Differences observed in patterns of the surface (0-2 mm) distribution of colloidal-S carbohydrate and chlorophyll a when expressed on a dry weight or areal basis were attributed to effects of dewatering and concomitant changes in wet bulk density. The polymeric carbohydrate (colloidal-S EPS) component of the biofilms was not found to be a constant fraction of the colloidal-S carbohydrate extract, varying from 16 to 58%, and the percentage of polymer decreased logarithmically as chlorophyll a concentrations increased and the biofilms matured (P < 0.001). Changes in the relationships between these variables over the period of biofilm development and maturation highlight the difficulties in their use to predict sediment stability. Exopolymer concentrations were more closely correlated with algal biomass than with bacterial numbers. Rates of algal carbon fixation were considerably greater than those for bacteria, suggesting that the algae have a much greater potential for exopolymer production. It is suggested that the microphytobenthos secretions make a more important contribution to sediment stability.}, }
@article {pmid10833223, year = {2000}, author = {Bergström, A and Jansson, M}, title = {Bacterioplankton Production in Humic Lake Örträsket in Relation to Input of Bacterial Cells and Input of Allochthonous Organic Carbon.}, journal = {Microbial ecology}, volume = {39}, number = {2}, pages = {101-115}, doi = {10.1007/s002480000007}, pmid = {10833223}, issn = {1432-184X}, abstract = {In order to compare riverine bacteria input with lake water bacterial production and grazing loss with output loss, a bacterial cell budget was constructed for humic Lake Örträsket in northern Sweden. The riverine input of bacterial cells in 1997 represented 29% of the number of bacterial cells produced within the layer of the lake affected by inlet water. A large share of the in situ lake bacterial production was consumed by grazers, mainly flagellates, which stresses the importance of bacteria as energy mobilizers for the pelagic food web in the lake. The bacterial production in Lake Örträsket, which is almost entirely dependent on humic material as an energy source, was clearly stimulated by high flow episodes which brought high amounts of little degraded material into the lake. During base flow condition the bacterial production in the inlet rivers was high, which led to an input of more degraded material to the lake. This material did not stimulate the lake bacterial production. Internal factors that determined the utilization of the allochthonous DOC in the lake were the retention time and the exposure to light and high temperatures. Thus, the potential for in situ production of bacteria in Lake Örträsket was to a large extent a function of how precipitation and runoff conditions affected terrestrial losses and river transport of humic material.}, }
@article {pmid10832637, year = {2000}, author = {Liu, WT and Linning, KD and Nakamura, K and Mino, T and Matsuo, T and Forney, LJ}, title = {Microbial community changes in biological phosphate-removal systems on altering sludge phosphorus content.}, journal = {Microbiology (Reading, England)}, volume = {146 (Pt 5)}, number = {}, pages = {1099-1107}, doi = {10.1099/00221287-146-5-1099}, pmid = {10832637}, issn = {1350-0872}, mesh = {Actinobacteria/isolation &amp; purification/metabolism ; Bacteria/genetics/*isolation &amp; purification/metabolism ; Biodegradation, Environmental ; Biomarkers/analysis ; Caulobacter/isolation &amp; purification/metabolism ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; *Environmental Microbiology ; Fatty Acids/analysis ; Molecular Sequence Data ; Phosphates/*analysis/metabolism ; Phosphorus/*analysis/metabolism ; Phylogeny ; Polymerase Chain Reaction ; Proteobacteria/isolation &amp; purification/metabolism ; Quinones/analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/analysis/*microbiology ; }, abstract = {Biomarkers (respiratory quinones and cellular fatty acids) and denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA genes were used to characterize the microbial community structure of lab-scale enhanced biological phosphate-removal (EBPR) systems in response to altering sludge phosphorus (P) content. All the data suggest that the microbial community structures of sludge samples with a P content between 8 and 12.3% (sludge dry weight) (i.e. good EBPR activity) were very similar, but differed from those with 2% P content (i.e. no EBPR activity). For all samples analysed, ubiquinones Q-8 and Q-10, menaquinone MK-8(H4), and fatty acids C16:0, C16:1 omega9c and C18:1, omega11c were the major components. The dominance of Q-8, Q-10 and MK-8(H4) suggested that large numbers of organisms belonging to the beta and alpha subclasses of the Proteobacteria and the Actinobacteria from the high G+C Gram-positive bacteria, respectively, were present. DGGE analysis revealed at least 7-9 predominant DNA bands and numerous other fragments in each sample. Five major DGGE fragments from each of the 2% and 12% P-containing sludge samples, respectively, were successfully isolated and sequenced. Phylogenetic analysis of the sequences indicated that both 2% and 12% P-containing sludge samples shared three common phylotypes that were separately affiliated with a novel bacterial group from the gamma subclass of the Proteobacteria, two MK-8(H4)-containing actinobacteria previously isolated from the 2% P-containing sludge, and a Caulobacter spp. in the alpha subclass of the Proteobacteria. The phylogenetic analysis also revealed phylotypes unique to both sludge samples. Changes in sludge P content therefore had an effect on the composition and abundance of the predominant microbial populations, though specific phylotypes could not be unequivocally associated with EBPR.}, }
@article {pmid10831436, year = {2000}, author = {Rondon, MR and August, PR and Bettermann, AD and Brady, SF and Grossman, TH and Liles, MR and Loiacono, KA and Lynch, BA and MacNeil, IA and Minor, C and Tiong, CL and Gilman, M and Osburne, MS and Clardy, J and Handelsman, J and Goodman, RM}, title = {Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {6}, pages = {2541-2547}, pmid = {10831436}, issn = {0099-2240}, support = {F32 GM018871/GM/NIGMS NIH HHS/United States ; R01 CA024487/CA/NCI NIH HHS/United States ; 1 F32 GM18871-01A1/GM/NIGMS NIH HHS/United States ; 1RO3 AI42786-01/AI/NIAID NIH HHS/United States ; CA24487/CA/NCI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Amylases/metabolism ; Bacteria/*classification/*genetics/metabolism ; Chromosomes, Bacterial ; Cloning, Molecular ; DNA, Bacterial/analysis/genetics ; Deoxyribonucleases/metabolism ; *Ecosystem ; Genes, rRNA ; *Genome, Bacterial ; Genomic Library ; Hemolysis ; Lipase/metabolism ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Recent progress in molecular microbial ecology has revealed that traditional culturing methods fail to represent the scope of microbial diversity in nature, since only a small proportion of viable microorganisms in a sample are recovered by culturing techniques. To develop methods to investigate the full extent of microbial diversity, we used a bacterial artificial chromosome (BAC) vector to construct libraries of genomic DNA isolated directly from soil (termed metagenomic libraries). To date, we have constructed two such libraries, which contain more than 1 Gbp of DNA. Phylogenetic analysis of 16S rRNA gene sequences recovered from one of the libraries indicates that the BAC libraries contain DNA from a wide diversity of microbial phyla, including sequences from diverse taxa such as the low-G+C, gram-positive Acidobacterium, Cytophagales, and Proteobacteria. Initial screening of the libraries in Escherichia coli identified several clones that express heterologous genes from the inserts, confirming that the BAC vector can be used to maintain, express, and analyze environmental DNA. The phenotypes expressed by these clones include antibacterial, lipase, amylase, nuclease, and hemolytic activities. Metagenomic libraries are a powerful tool for exploring soil microbial diversity, providing access to the genetic information of uncultured soil microorganisms. Such libraries will be the basis of new initiatives to conduct genomic studies that link phylogenetic and functional information about the microbiota of environments dominated by microorganisms that are refractory to cultivation.}, }
@article {pmid10831418, year = {2000}, author = {Sun, B and Cole, JR and Sanford, RA and Tiedje, JM}, title = {Isolation and characterization of Desulfovibrio dechloracetivorans sp. nov., a marine dechlorinating bacterium growing by coupling the oxidation of acetate to the reductive dechlorination of 2-chlorophenol.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {6}, pages = {2408-2413}, pmid = {10831418}, issn = {0099-2240}, mesh = {Acetates/*metabolism ; Bacterial Proteins/metabolism ; Chlorophenols/*metabolism ; Culture Media ; DNA Fingerprinting ; Desulfovibrio/classification/genetics/*isolation &amp; purification/*physiology ; Genes, rRNA ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater ; *Water Microbiology ; }, abstract = {Strain SF3, a gram-negative, anaerobic, motile, short curved rod that grows by coupling the reductive dechlorination of 2-chlorophenol (2-CP) to the oxidation of acetate, was isolated from San Francisco Bay sediment. Strain SF3 grew at concentrations of NaCl ranging from 0.16 to 2.5%, but concentrations of KCl above 0. 32% inhibited growth. The isolate used acetate, fumarate, lactate, propionate, pyruvate, alanine, and ethanol as electron donors for growth coupled to reductive dechlorination. Among the halogenated aromatic compounds tested, only the ortho position of chlorophenols was reductively dechlorinated, and additional chlorines at other positions blocked ortho dechlorination. Sulfate, sulfite, thiosulfate, and nitrate were also used as electron acceptors for growth. The optimal temperature for growth was 30 degrees C, and no growth or dechlorination activity was observed at 37 degrees C. Growth by reductive dechlorination was revealed by a growth yield of about 1 g of protein per mol of 2-CP dechlorinated, and about 2.7 g of protein per mole of 2,6-dichlorophenol dechlorinated. The physiological features and 16S ribosomal DNA sequence suggest that the organism is a novel species of the genus Desulfovibrio and which we have designated Desulfovibrio dechloracetivorans. The unusual physiological feature of this strain is that it uses acetate as an electron donor and carbon source for growth with 2-CP but not with sulfate.}, }
@article {pmid10831417, year = {2000}, author = {Whiteley, AS and Bailey, MJ}, title = {Bacterial community structure and physiological state within an industrial phenol bioremediation system.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {6}, pages = {2400-2407}, pmid = {10831417}, issn = {0099-2240}, mesh = {Aged ; Colony Count, Microbial ; DNA Fingerprinting ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal/analysis/genetics ; Electrophoresis, Polyacrylamide Gel/methods ; Gram-Negative Bacteria/classification/genetics/isolation &amp; purification/*physiology ; Humans ; In Situ Hybridization, Fluorescence ; Phenols/*metabolism ; Proteobacteria/classification/genetics/isolation &amp; purification/*physiology ; RNA, Ribosomal, 16S/genetics ; *Waste Management ; *Water Microbiology ; }, abstract = {The structure of bacterial populations in specific compartments of an operational industrial phenol remediation system was assessed to examine bacterial community diversity, distribution, and physiological state with respect to the remediation of phenolic polluted wastewater. Rapid community fingerprinting by PCR-based denaturing gradient gel electrophoresis (DGGE) of 16S rDNA indicated highly structured bacterial communities residing in all nine compartments of the treatment plant and not exclusively within the Vitox biological reactor. Whole-cell targeting by fluorescent in situ hybridization with specific oligonucleotides (directed to the alpha, beta and gamma subclasses of the class Proteobacteria [alpha-, beta-, and gamma-Proteobacteria, respectively], the Cytophaga-Flavobacterium group, and the Pseudomonas group) tended to mirror gross changes in bacterial community composition when compared with DGGE community fingerprinting. At the whole-cell level, the treatment compartments were numerically dominated by cells assigned to the Cytophaga-Flavobacterium group and to the gamma-Proteobacteria. The alpha subclass Proteobacteria were of low relative abundance throughout the treatment system whilst the beta subclass of the Proteobacteria exhibited local dominance in several of the processing compartments. Quantitative image analyses of cellular fluorescence was used as an indicator of physiological state within the populations probed with rDNA. For cells hybridized with EUB338, the mean fluorescence per cell decreased with increasing phenolic concentration, indicating the strong influence of the primary pollutant upon cellular rRNA content. The gamma subclass of the Proteobacteria had a ribosome content which correlated positively with total phenolics and thiocyanate. While members of the Cytophaga-Flavobacterium group were numerically dominant in the processing system, their abundance and ribosome content data for individual populations did not correlate with any of the measured chemical parameters. The potential importance of the gamma-Proteobacteria and the Cytophaga-Flavobacteria during this bioremediation process was highlighted.}, }
@article {pmid10831402, year = {2000}, author = {De Wever, H and Cole, JR and Fettig, MR and Hogan, DA and Tiedje, JM}, title = {Reductive dehalogenation of trichloroacetic acid by Trichlorobacter thiogenes gen. nov., sp. nov.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {6}, pages = {2297-2301}, pmid = {10831402}, issn = {0099-2240}, support = {DRR-00480/RR/NCRR NIH HHS/United States ; }, mesh = {Acetates/metabolism ; Anaerobiosis ; Biodegradation, Environmental ; Culture Media ; Deltaproteobacteria/*classification/genetics/growth &amp; development/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Trichloroacetic Acid/*metabolism ; }, abstract = {A bacterium able to grow via reductive dechlorination of trichloroacetate was isolated from anaerobic soil enrichments. The isolate, designated strain K1, is a member of the delta proteobacteria and is related to other known sulfur and ferric iron reducers. In anaerobic mineral media supplemented with acetate and trichloroacetate, its doubling time was 6 h. Alternative electron donor and acceptors were acetoin and sulfur or fumarate, respectively. Trichloroacetate dehalogenation activity was constitutively present, and the dechlorination product was dichloroacetate and chloride. Trichloroacetate conversion seemed to be coupled to a novel sulfur-sulfide redox cycle, which shuttled electrons from acetate oxidation to trichloroacetate reduction. In view of its unique physiological characteristics, the name Trichlorobacter thiogenes is suggested for strain K1.}, }
@article {pmid10817862, year = {2000}, author = {Lowit, MB and Blum, LK and Mills, AL}, title = {Determining replication for discrimination among microbial communities in environmental samples using community-level physiological profiles.}, journal = {FEMS microbiology ecology}, volume = {32}, number = {2}, pages = {97-102}, doi = {10.1111/j.1574-6941.2000.tb00703.x}, pmid = {10817862}, issn = {1574-6941}, abstract = {A statistical approach was employed to assess microbial community variability within a single 4-l water sample and among 10 independent 4-l water samples from a single location using community-level physiological profiles. Power calculations demonstrated that duplicate analyses could distinguish between two different locations at two times during the year. Variability associated with replicates from a single container or from different containers was nearly the same for the two sites examined. Duplicate assays (one from each of two independent samples) were sufficient to resolve the between-site differences at alpha=0.05 with power exceeding 0.95 at both times of the year. Similar methods are recommended to determine the appropriate number of replicates for environments of interest.}, }
@article {pmid10817861, year = {2000}, author = {Hodge, A}, title = {Microbial ecology of the arbuscular mycorrhiza.}, journal = {FEMS microbiology ecology}, volume = {32}, number = {2}, pages = {91-96}, doi = {10.1111/j.1574-6941.2000.tb00702.x}, pmid = {10817861}, issn = {1574-6941}, support = {JF13140/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Arbuscular mycorrhizal (AM) fungi interact with a wide variety of organisms during all stages of their life. Some of these interactions such as grazing of the external mycelium are detrimental, while others including interactions with plant growth promoting rhizobacteria (PG PR) promote mycorrhizal functioning. Following mycorrhizal colonisation the functions of the root become modified, with consequences for the rhizosphere community which is extended into the mycorrhizosphere due to the presence of the AM external mycelium. However, we still know relatively little of the ecology of AM fungi and, in particular, the mycelium network under natural conditions. This area merits attention in the future with emphasis on the fungal partner in the association rather than the plant which has been the focus in the past.}, }
@article {pmid10790522, year = {2000}, author = {Navarrete, A and Peacock, A and Macnaughton, SJ and Urmeneta, J and Mas-Castellà, J and White, DC and Guerrero, R}, title = {Physiological Status and Community Composition of Microbial Mats of the Ebro Delta, Spain, by Signature Lipid Biomarkers.}, journal = {Microbial ecology}, volume = {39}, number = {1}, pages = {92-99}, doi = {10.1007/s002489900185}, pmid = {10790522}, issn = {1432-184X}, abstract = {Physiological status of microbial mats of the Ebro Delta (Tarragona, Spain) based on the extraction of lipids considered "signature lipid biomarkers" (SLB) from the cell membranes and walls of microorganisms has been analyzed. Data from a day-night cycle show significant differences in viable cells countings (PLFA cells counts) ranging from 1.5 x 10(10) to 5.0 x 10(10) cells g(-1) of sediment. Minimum values were observed at 18:00 and 6:00, when physicochemical conditions change drastically. The diversity of the microbial community was assessed by GC/MS analysis of phospholipid fatty acids (PLFA). The ratio of PLFA, representative of Gram-negative bacteria, comprises 47.8% of the total PLFA of the microbial mat community. The remaining PLFA was representative of Gram-positive (10.0%), anaerobic (5.7%), and eukaryotic microorganisms (5.7%), and other common lipids. Two different approaches were used as a comparative study to assess the physiological status of the microbial mats. Two parameters (cyclopropane fatty acids/omega7c monoenoic fatty acids, and measurement of the trans/cis monoenoic PLFA ratio) showed a minimum at midnight, suggesting the highest microbial activity. Higher values were observed at 18:00 and 6:00, coinciding with lower PLFA cell counts. </hea}, }
@article {pmid10790521, year = {2000}, author = {Banerjee, M and Whitton, BA and Wynn-Williams, DD}, title = {Phosphatase Activities of Endolithic Communities in Rocks of the Antarctic Dry Valleys.}, journal = {Microbial ecology}, volume = {39}, number = {1}, pages = {80-91}, doi = {10.1007/s002489900188}, pmid = {10790521}, issn = {1432-184X}, abstract = {Phosphorus is scarce in Beacon Sandstone of the McMurdo Dry Valleys, Antarctica, and any input from precipitation is minimal. In endolithic microbial communities recycling of P by the action of phosphatases may therefore be important. The phosphatase activities of three different types of endolithic communities in the McMurdo Dry Valley, Antarctica, were studied in the laboratory. The dominant phototrophs were Chroococcidiopsis, mixed Gloeocapsa and Trebouxia, and Trebouxia. Bacteria were also visually conspicuous in the latter two communities, and the Trebouxia in both cases formed a lichenized association with fungal hyphae. In each case marked phosphomonoesterase (PMEase) activity was found in assays with 4-methylumbelliferyl phosphate (MUP) or p-nitrophenyl phosphate as substrate, and phosphodiesterase activity with bis-p-nitrophenyl phosphate as substrate. The pH optimum of PMEase (assayed at 0.5 pH intervals) of the Chroococcidiopsis, Gloeocapsa-Trebouxia, and Trebouxia communities was 9.5, 5.5, and 8.0, respectively. These values are similar for aqueous extracts of the respective rocks (pH 9.2, 6.2, 7.5). All three communities showed significantly higher PMEase activity at 5 degrees than 1 degrees C, and the first two also showed much higher activity at 5 degrees than 10 degrees C. All three communities also showed slightly lower activity in the light (7 µmol photon m(-2) s(-1)) than the dark; this was found with all substrates and substrate concentrations. Prior exposure of a moistened sample to light for 2 h led to a reduction in activity even when the subsequent assay was done in the dark. The rate of PMEase activity (using 100 µM MUP) in the Gloeocapsa-Trebouxia and Trebouxia communities was approximately linear with time up to 24 h, whereas the Chroococcidiopsis community showed a marked decrease after 6 h. At least part of this was due to retention of the 4-methylumbelliferone (MU) hydrolysis product. In spite of the assays being conducted on a whole community, the activity-substrate relationship in each case quite closely resembled a typical Michaelis-Menten relationship. Estimates were made of the apparent half-saturation value and the concentration of MUP required to support half-maximal rates. The apparent K (m) values were: Chroococcidiopis, 230 µM; Gloeocapsa-Trebouxia 169 µM; Trebouxia, 135 µM. The respective values for apparent V (max) were 0.053, 0.55, and 0.35 µmol MU g(-1) h(-1). In view of the greater dependence of these communities on the rock for their sole supply of P than for C and probably N, it is suggested that the cycling of P within the communities is a key factor influencing their overall metabolic activity when moisture permits their activation. </hea}, }
@article {pmid10790520, year = {2000}, author = {Yang, Y and Yao, J and Hu, S and Qi, Y}, title = {Effects of Agricultural Chemicals on DNA Sequence Diversity of Soil Microbial Community: A Study with RAPD Marker.}, journal = {Microbial ecology}, volume = {39}, number = {1}, pages = {72-79}, doi = {10.1007/s002489900180}, pmid = {10790520}, issn = {1432-184X}, abstract = {The DNA sequence diversities for microbial communities in four soils affected by agricultural chemicals (mainly triadimefon and ammonium bicarbonate and their intermediates) were evaluated by Random Amplified Polymorphic DNA (RAPD) analysis. Fourteen random primers were used to amplify RAPDs from four soil microbial community DNAs. The products of 12 primers were separated in gel and generated 155 reliable fragments, of which 134 were polymorphic. The richness, modified richness, Shannon-Weaver index, and a similarity coefficient of DNA were calculated to quantify the diversity to access DNA sequence diversities for four soil microbial communities. The results showed that agricultural chemicals affected soil microbial community diversity at the DNA level. The four soil microbial communities were distinguishable in terms of DNA sequence richness, modified richness, Shannon-Weaver index, and coefficient of DNA similarity. Analysis also showed that the amounts of organic C and microbial biomass C were low in the soil polluted by pesticide (mainly triadimefon and its intermediates), but high in the soil polluted by chemical fertilizer (mainly ammonium bicarbonate and its intermediates). The above results combined may indicate that pesticide pollution caused a decrease in the soil microbial biomass but kept high diversity at DNA level, compared with the control without chemical pollution. In contrast, chemical fertilizer pollution caused an increase in the soil biomass but decrease in the DNA diversity. The RAPD marker technique combined with analysis of soil microbial biomass appears to be an effective approach for studying the diversity of soil microbial communities, although the effects of PCR bias on community composition, such as dominating and rare populations in soils, on the diversity needed to be addressed further. </hea}, }
@article {pmid10790519, year = {2000}, author = {Muela, A and García-Bringas, JM and Arana, I and Barcina, I}, title = {The Effect of Simulated Solar Radiation on Escherichia coli: The Relative Roles of UV-B, UV-A, and Photosynthetically Active Radiation.}, journal = {Microbial ecology}, volume = {39}, number = {1}, pages = {65-71}, doi = {10.1007/s002489900181}, pmid = {10790519}, issn = {1432-184X}, abstract = {The relative role of components of solar radiation (UV-B, UV-A, and photosynthetically active radiation) as well as the effect of simulated sunlight upon the physiological state of Escherichia coli in fresh water were evaluated. Simulated solar radiation had a sublethal effect on E. coli populations in a short-time exposure by provoking loss of culturability and the formation of viable but nonculturable cells. Prolonged exposure increased the damage to cells but cellular integrity was never affected. However, important differences between the way the sunlight components acted were detected. After photosynthetically active radiation (PAR) exposure, cells remained metabolically active but only 10% of the cells were culturable. When cells were exposed to UV-A, the culturable fraction was similar to the one obtained after PAR irradiation, although formation of viable but nonculturable cells was not observed. For UV-B radiation short-time exposures (6 h) were enough to provoke loss of culturability and a reduction in activity similar to that of simulated sunlight exposed cells. The effect of simulated solar radiation on E. coli cells was mainly attributable to shorter wavelengths, but a synergistic interaction of the UV-B, UV-A and PAR components was detected. </hea}, }
@article {pmid10790518, year = {2000}, author = {Griffin, DW and Stokes, R and Rose, JB and Paul, JH}, title = {Bacterial Indicator Occurrence and the Use of an F(+) Specific RNA Coliphage Assay to Identify Fecal Sources in Homosassa Springs, Florida.}, journal = {Microbial ecology}, volume = {39}, number = {1}, pages = {56-64}, doi = {10.1007/s002489900193}, pmid = {10790518}, issn = {1432-184X}, abstract = {A microbiological water quality study of Homosassa Springs State Wildlife Park (HSSWP) and surrounding areas was undertaken. Samples were collected in November of 1997 (seven sites) and again in November of 1998 (nine sites). Fecal bacterial concentrations (total and fecal coliforms, Clostridium perfringens, and enterococci) were measured as relative indicators of fecal contamination. F(+)-specific coliphage genotyping was performed to determine the source of fecal contamination at the study sites. Bacterial levels were considerably higher at most sites in the 1997 sampling compared to the 1998 sampling, probably because of the greater rainfall that year. In November of 1997, 2 of the 7 sites were in violation of all indicator standards and guidance levels. In November of 1998, 1 of 9 sites was in violation of all indicator standard and guidance levels. The highest concentrations of all fecal indicators were found at a station downstream of the animal holding pens in HSSWP. The lowest levels of indicators were found at the Homosassa Main Spring vent. Levels of fecal indicators downstream of HSSWP (near the point of confluence with the river) were equivalent to those found in the Southeastern Fork and areas upstream of the park influences. F(+) specific RNA coliphage analysis indicated that fecal contamination at all sites that tested positive was from animal sources (mammals and birds). These results suggest that animal (indigenous and those in HSSWP) and not human sources influenced microbial water quality in the area of Homosassa River covered by this study. </hea}, }
@article {pmid10790517, year = {2000}, author = {Tapia-Hernández, A and Bustillos-Cristales, MR and Jiménez-Salgado, T and Caballero-Mellado, J and Fuentes-Ramírez, LE}, title = {Natural Endophytic Occurrence of Acetobacter diazotrophicus in Pineapple Plants.}, journal = {Microbial ecology}, volume = {39}, number = {1}, pages = {49-55}, doi = {10.1007/s002489900190}, pmid = {10790517}, issn = {1432-184X}, abstract = {The presence of endophytic Acetobacter diazotrophicus was tested for pineapple plants (Ananas comosus [L.] Merr.) grown in the field. Diazotrophic bacteria were isolated from the inner tissues of surface sterilized roots, stems, and leaves of pineapple plants. Phenotypic tests permitted the selection of presumptive nitrogen-fixing A. diazotrophicus isolates. Restriction fragment length polymorphisms (RFLPs) of small subunit (SSU) rDNA using total DNA digested with endonuclease SphI and with endonuclease NcoI, hybridizations of RNA with an A. diazotrophicus large subunit (LSU) rRNA specific probe, as well as patterns in denaturing protein electrophoresis (SDS-PAGE) and multilocus enzyme tests allowed the identification of A. diazotrophicus isolates. High frequencies of isolation were obtained from propagative buds that had not been nitrogen-fertilized, and lower frequencies from 3-month-old plants that had been nitrogen-fertilized. No isolates were recovered from 5- to 7-month-old nitrogen-fertilized plants. All the A. diazotrophicus isolates recovered from pineapple plants belonged to the multilocus genotype which shows the most extensive distribution among all host species previously analyzed. </hea}, }
@article {pmid10790516, year = {2000}, author = {Piceno, YM and Lovell, CR}, title = {Stability in Natural Bacterial Communities: II. Plant Resource Allocation Effects on Rhizosphere Diazotroph Assemblage Composition.}, journal = {Microbial ecology}, volume = {39}, number = {1}, pages = {41-48}, doi = {10.1007/s002489900191}, pmid = {10790516}, issn = {1432-184X}, abstract = {Plant rhizospheres are dynamic environments in which microbes compete for resources, particularly plant-derived organic carbon/energy sources. Altering plant productivity changes the availability of carbon/energy resources to rhizosphere microbiota. This limitation is expected to intensify competition for the remaining carbon supply and could cause the loss of poor competitors from the assemblage. We clipped or shaded plots of the salt marsh cord grass, Spartina alterniflora, to shift plant carbon resource allocation from the rhizosphere to the aboveground shoots. We then examined key porewater parameters (pH, salinity, H(2)S, NH(+)(4)), diazotrophic activity (by acetylene reduction assay), and diazotroph assemblage composition after 2 weeks or 8 weeks of treatment. The diazotroph assemblage composition was monitored via the polymerase chain reaction using nifH specific primers followed by denaturing gradient gel electrophoresis (DGGE) analysis. Porewater parameters and acetylene reduction rates did not differ significantly among treatments. The DGGE profiles also were very similar across the control and experimental treatments, indicating that no detectable diazotroph species were displaced from the assemblage. This implies that rhizosphere diazotrophs are able to compete successfully against nondiazotrophs, in spite of the high energy requirements of nitrogen fixation. These results show that the species composition of the diazotroph assemblage in the S. alterniflora rhizosphere is stable in the face of short-duration but potentially high-impact variations in carbon resource availability. </hea}, }
@article {pmid10790515, year = {2000}, author = {Piceno, YM and Lovell, CR}, title = {Stability in Natural Bacterial Communities: I. Nutrient Addition Effects on Rhizosphere Diazotroph Assemblage Composition.}, journal = {Microbial ecology}, volume = {39}, number = {1}, pages = {32-40}, doi = {10.1007/s002489900192}, pmid = {10790515}, issn = {1432-184X}, abstract = {The ability of rhizosphere diazotrophs to remain competitive during increased nitrogen availability in situ was tested in a salt marsh grass stand. Nitrogen (16.3 g m(-2)) or nitrogen (16.3 g m(-2)) and phosphorus (18.0 g m(-2)) were added to plots of short form Spartina alterniflora for either 2 weeks or 8 weeks. The diazotroph assemblage composition was monitored via the polymerase chain reaction using nifH specific primers followed by denaturing gradient gel electrophoresis (DGGE) analysis. DGGE profiles from the short-term experiments (2 and 8 weeks) were compared to profiles from control (no additions) and from long-term (>10 y) nutrient addition plots. Nitrogen fixation activity was assayed in each short-term treatment and control plot using an acetylene reduction technique. The control and nutrient addition DGGE profiles were very similar throughout the short-term experiments. One DGGE band that was prominent in the control plots was not found in the long-term nutrient addition plots. Diazotrophy may provide a competitive advantage for some species in this system, as indicated by results from the long-term nutrient amended plots. However, the rhizosphere environment in situ appears to limit the immediate impacts of increased nutrient availability on the diazotroph assemblage composition. Results from the short-term nutrient amended plots showed no measurable effect on the diazotroph assemblage. These results indicate substantial short-term stability of the diazotroph assemblage composition, but the potential for change in the face of long-term changes in nutrient availability. </hea}, }
@article {pmid10790514, year = {2000}, author = {Weidner, S and Arnold, W and Stackebrandt, E and Pühler, A}, title = {Phylogenetic Analysis of Bacterial Communities Associated with Leaves of the Seagrass Halophila stipulacea by a Culture-Independent Small-Subunit rRNA Gene Approach.}, journal = {Microbial ecology}, volume = {39}, number = {1}, pages = {22-31}, doi = {10.1007/s002489900194}, pmid = {10790514}, issn = {1432-184X}, abstract = {The phylogenetic diversity of the bacterial community associated with leaves of the marine plant Halophila stipulacea in the northern Gulf of Elat was examined by 16S rRNA gene (rDNA) sequence analyses of a clone library. For 59 clones corresponding to 51 ARDRA (amplified rDNA restriction analysis) groups, the sequence of approximately 1 kb was determined, and the fraction of the corresponding ARDRA groups of the leaf library was calculated. The class Proteobacteria was represented by 62.6% of the clone sequences. Most sequences originated from members of the gamma-subclass (27.3%), affiliated with members of the genera Pseudomonas, Vibrio, Marinomonas, Oceanospirillum, and other marine groups. Affiliation to the alpha-subclass was determined for 24.2% of the sequences. They were related to the genera Hyphomonas, Roseobacter, Ruegeria, and Rhizobiaceae. Several alpha-proteobacterial sequences were distantly related to known sequences. Only 4% of the clone sequences were related to beta-Proteobacteria. Additionally, 7.1% of the sequences possibly belonged to the class Proteobacteria, but branched deeply from known subclasses. Several sequences were affiliated to members of the orders Verrucomicrobiales and Planctomycetales, the Holophaga/Acidobacterium phylum, and chloroplasts of marine diatoms. </hea}, }
@article {pmid10790513, year = {2000}, author = {Shaffer, BT and Widmer, F and Porteous, LA and Seidler, RJ}, title = {Temporal and Spatial Distribution of the nifH Gene of N(2) Fixing Bacteria in Forests and Clearcuts in Western Oregon.}, journal = {Microbial ecology}, volume = {39}, number = {1}, pages = {12-21}, doi = {10.1007/s002489900183}, pmid = {10790513}, issn = {1432-184X}, abstract = {Decomposition of plant litter is a primary mechanism of nutrient recycling and redistribution in most terrestrial ecosystems. Previously we demonstrated by a nested PCR protocol that 20 distinctive nifH (the gene encoding nitrogenase reductase) HaeIII restriction fragment length polymorphism (RFLP) patterns were derived from bulk DNA associated with samples of plant litter and soil collected at one Douglas Fir (DF) forest [33]. Five of the nifH DNA patterns (II-VI) were dominant types in DF litter with characteristic fragments of 237-303 bp length, whereas samples from soil contained primarily seven other patterns 131-188 bp length (IX-XV). Here we report that the 237-303 bp fragments characteristic for forest litter could generally not be detected in plant litter or soil samples collected in clearcuts that adjoin the forest sites. The same fragments (237-303 bp) were also found in the litter at this DF forest site over 16 months and were consistently found in litter at 12 other DF forest or recent (<2 yrs) clearcut sites. However, trace to none of these fragments were detected in 6 clearcut (5-10 yrs) or different forest types (oak, alder) collected over a 200 km east-west direction in western Oregon, USA. Data suggest that the logging practice in DF forests that creates a clearcut removes a unique gene pool of nitrogen-fixing microorganisms. These organisms could potentially contribute more to nitrogen fixation in forest litter than litter from natural or invasive plants that grow in clearcuts [26]. </hea}, }
@article {pmid10790512, year = {2000}, author = {Kinkel, LL and Wilson, M and Lindow, SE}, title = {Plant Species and Plant Incubation Conditions Influence Variability in Epiphytic Bacterial Population Size.}, journal = {Microbial ecology}, volume = {39}, number = {1}, pages = {1-11}, doi = {10.1007/s002489900182}, pmid = {10790512}, issn = {1432-184X}, abstract = {The influences of plant species and plant incubation conditions on the variability in bacterial population sizes among leaves were investigated in field and growth chamber studies. Pseudomonas syringae strains TLP2 and Cit7 were inoculated onto plants and population sizes were measured at intervals after inoculation. Total bacterial population sizes were also assessed in field studies. Levels of leaf-to-leaf variability in both P. syringae population size and bacterial community size differed significantly among plant species. For all plant species, variability among leaves in population sizes of inoculated bacteria was consistently greater than the leaf-to-leaf variability in numbers of total bacteria. Considering levels of variability in population size immediately prior to and following incubation under either wet or dry physical conditions, leaf-to-leaf variability in the population sizes of inoculated P. syringae strains increased significantly following incubation under dry, but not under wet, conditions. Measurements of leaf-to-leaf variability immediately prior to and following incubation were positively correlated regardless of whether the incubation was under wet or dry conditions, though the correlation was greater following dry incubation. These data provide insight into the biological and physical factors that may be important in generating variability in bacterial population sizes among leaves, and they have important implications for the design of appropriate strategies for sampling leaf surface microbial populations. </hea}, }
@article {pmid10788387, year = {2000}, author = {Braker, G and Zhou, J and Wu, L and Devol, AH and Tiedje, JM}, title = {Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in pacific northwest marine sediment communities.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {5}, pages = {2096-2104}, pmid = {10788387}, issn = {0099-2240}, mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Cloning, Molecular ; Genetic Markers ; *Genetic Variation ; Geologic Sediments/*microbiology ; Nitrite Reductases/*genetics ; Pacific Ocean ; *Phylogeny ; Polymerase Chain Reaction/methods ; Polymorphism, Restriction Fragment Length ; Seawater/*microbiology ; Washington ; }, abstract = {Genetic heterogeneity of denitrifying bacteria in sediment samples from Puget Sound and two sites on the Washington continental margin was studied by PCR approaches amplifying nirK and nirS genes. These structurally different but functionally equivalent single-copy genes coding for nitrite reductases, a key enzyme of the denitrification process, were used as a molecular marker for denitrifying bacteria. nirS sequences could be amplified from samples of both sampling sites, whereas nirK sequences were detected only in samples from the Washington margin. To assess the underlying nir gene structure, PCR products of both genes were cloned and screened by restriction fragment length polymorphism (RFLP). Rarefraction analysis revealed a high level of diversity especially for nirS clones from Puget Sound and a slightly lower level of diversity for nirK and nirS clones from the Washington margin. One group dominated within nirK clones, but no dominance and only a few redundant clones were seen between sediment samples for nirS clones in both habitats. Hybridization and sequencing confirmed that all but one of the 228 putative nirS clones were nirS with levels of nucleotide identities as low as 45.3%. Phylogenetic analysis grouped nirS clones into three distinct subclusters within the nirS gene tree which corresponded to the two habitats from which they were obtained. These sequences had little relationship to any strain with known nirS sequences or to isolates (mostly close relatives of Pseudomonas stutzeri) from the Washington margin sediment samples. nirK clones were more closely related to each other than were the nirS clones, with 78.6% and higher nucleotide identities; clones showing only weak hybridization signals were not related to known nirK sequences. All nirK clones were also grouped into a distinct cluster which could not be placed with any strain with known nirK sequences. These findings show a very high diversity of nir sequences within small samples and that these novel nir clusters, some very divergent from known sequences, are not known in cultivated denitrifiers.}, }
@article {pmid10777523, year = {2000}, author = {Hogan, DA and Smith, SR and Saari, EA and McCracken, J and Hausinger, RP}, title = {Site-directed mutagenesis of 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase. Identification of residues involved in metallocenter formation and substrate binding.}, journal = {The Journal of biological chemistry}, volume = {275}, number = {17}, pages = {12400-12409}, doi = {10.1074/jbc.275.17.12400}, pmid = {10777523}, issn = {0021-9258}, support = {GM 54065/GM/NIGMS NIH HHS/United States ; T32-GM08350/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Binding Sites ; Chromatography, Gel ; Electron Spin Resonance Spectroscopy ; Histidine/chemistry ; Kinetics ; Ligands ; Mixed Function Oxygenases/*chemistry/*genetics ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Plasmids ; Protein Binding ; Recombinant Proteins/chemistry ; Sequence Homology, Amino Acid ; }, abstract = {2,4-dichlorophenoxyacetic acid (2,4-D)/alpha-ketoglutarate (alpha-KG) dioxygenase (TfdA) is an Fe(II)-dependent enzyme that catalyzes the first step in degradation of the herbicide 2,4-D. The active site structures of a small number of enzymes within the alpha-KG-dependent dioxygenase superfamily have been characterized and shown to have a similar HXDX(50-70)HX(10)RXS arrangement of residues that make up the binding sites for Fe(II) and alpha-KG. TfdA does not have obvious homology to the dioxygenases containing the above motif but is related in sequence to eight other enzymes in the superfamily that form a distinct consensus sequence (HX(D/E)X(138-207) HX(10)R/K). Variants of TfdA were created to examine the roles of putative metal-binding residues and the functions of the other seven histidines in this protein. The H167A, H200A, H213A, H245A, and H262A forms of TfdA formed inclusion bodies when overproduced in Escherichia coli DH5alpha; however, these proteins were soluble when fused to the maltose-binding protein (MBP). MBP-TfdA exhibited kinetic parameters similar to the native enzyme. The H8A and H235A variants were catalytically similar to wild-type TfdA. MBP-H213A and H216A TfdA have elevated K(m) values for 2,4-D, and the former showed a decreased k(cat), suggesting these residues may affect substrate binding or catalysis. The H113A, D115A, MBP-H167A, MBP-H200A, MBP-H245A and MBP-H262A variants of TfdA were inactive. Gel filtration analysis revealed that the latter two proteins were highly aggregated. The remaining four inactive variants were examined in their Cu(II)-substituted forms by EPR and electron spin-echo envelope modulation (ESEEM) spectroscopic methods. Changes in EPR spectra upon addition of substrates indicated that copper was present at the active site in the H113A and D115A variants. ESEEM analysis revealed that two histidines are bound equatorially to the copper in the D115A and MBP-H167A TfdA variants. The experimental data and sequence analysis lead us to conclude that His-113, Asp-115, and His-262 are likely metal ligands in TfdA and that His-213 may aid in catalysis or binding of 2,4-D.}, }
@article {pmid10768510, year = {2000}, author = {Adamsson, I and Edlund, C and Nord, CE}, title = {Microbial ecology and treatment of Helicobacter pylori infections: review.}, journal = {Journal of chemotherapy (Florence, Italy)}, volume = {12}, number = {1}, pages = {5-16}, doi = {10.1179/joc.2000.12.1.5}, pmid = {10768510}, issn = {1120-009X}, mesh = {Adenocarcinoma/drug therapy/microbiology ; Adult ; Aged ; Amoxicillin/adverse effects/pharmacology ; Anti-Bacterial Agents/adverse effects/*pharmacology ; Anti-Ulcer Agents/adverse effects/*pharmacology ; Clarithromycin/adverse effects/pharmacology ; Drug Resistance, Microbial ; Female ; Gastric Mucosa/drug effects/microbiology ; Gastritis/drug therapy/microbiology ; *Genetic Variation ; Helicobacter Infections/*drug therapy/genetics ; Helicobacter pylori/genetics/*pathogenicity ; Humans ; Hydrogen-Ion Concentration ; Male ; Metronidazole/adverse effects/pharmacology ; Middle Aged ; Omeprazole/adverse effects/pharmacology ; Penicillins/adverse effects/pharmacology ; Peptic Ulcer/drug therapy/microbiology ; Stomach Neoplasms/drug therapy/microbiology ; }, abstract = {The aims of the present study were to investigate the ecological disturbances caused by four different anti-H. pylori regimens, to compare different methods for diagnosing H. pylori, and to study the genetic variability of H. pylori. The patients included in the study were all treated at the Center of Gastroenterology, Huddinge University Hospital, Karolinska Institute. All patients were H. pylori-positive before entering the study, confirmed by rapid urease test, histology, culture and urea breath test or PCR. Treatment regimens included in the study were omeprazole alone (OP), in combination with amoxicillin (OA), in combination with amoxicillin and metronidazole (OAM) and in combination with clarithromycin and metronidazole (OCM). Samples from the mouth (saliva and dental plaque), stomach (biopsies from the gastric mucosa in the corpus and in the antrum) and the intestine (feces) were collected before, during and after treatment. The oral microflora was challenged by the three treatment regimens including antimicrobial agents, with the emergence of resistant streptococci and staphylococci in the OCM group. Bacterial strains in the gastric mucosa increased in numbers during treatment in all treatment groups, probably due to the pH rise, which provides a better environment for the commensal microflora. This overgrowth was especially pronounced during treatment with omeprazole alone (OP), possibly due to the fact that a concomitant suppression exerted by the antimicrobial agents occurred in the other treatment groups. H. pylori was, on the other hand, suppressed during treatment in all treatment groups, possibly due to a direct effect of omeprazole and to the colonization resistance expressed by the normal microflora. An emergence of resistant commensal strains in the gastric mucosa was seen in the OCM and the OAM groups. The intestinal microflora was most altered in the OAM and the OCM groups, with persistent disturbances in the OCM group 4 weeks after treatment. The frequency of resistant Enterococcus spp. (OCM), Enterobacteriaceae spp. (OA and OAM) and Bacteroides spp. (OCM) was increased during and after treatment. Different detection methods for H. pylori were compared and PCR was shown to have higher sensitivity than other routine diagnostic tests. The patients in the present study seemed to be colonized with a single strain of H. pylori. Treatment failures in patients treated with OAM were caused by recrudescence. These four patients with relapsing H. pylori infection, were shown to be reinfected with the original H. pylori strain, indicating that H. pylori escapes treatment by a thus far unknown mechanism.}, }
@article {pmid10759417, year = {1999}, author = {Yeung, MK}, title = {Molecular and genetic analyses of Actinomyces spp.}, journal = {Critical reviews in oral biology and medicine : an official publication of the American Association of Oral Biologists}, volume = {10}, number = {2}, pages = {120-138}, doi = {10.1177/10454411990100020101}, pmid = {10759417}, issn = {1045-4411}, support = {DE11102/DE/NIDCR NIH HHS/United States ; }, mesh = {Actinomyces/enzymology/genetics/*physiology ; Actinomycosis ; Alleles ; Bacterial Adhesion/genetics/physiology ; Chromosome Mapping ; Dental Plaque/microbiology ; Ecology ; Fimbriae, Bacterial/genetics/physiology ; Gene Transfer Techniques ; Humans ; Molecular Biology ; Mouth/microbiology ; Mouth Mucosa/microbiology ; Mutation/genetics ; Neuraminidase/physiology ; Sucrose/metabolism ; Tooth/microbiology ; Urea/metabolism ; }, abstract = {Members of the genus Actinomyces are predominant primary colonizers of the oral cavity and play an important role in initiating plaque development. These bacteria have evolved unique mechanisms that favor colonization and persistence in this micro-environment. The expression of cell-surface fimbriae is correlated with the ability of these bacteria to adhere to specific receptors on the tooth and mucosal surfaces, and to interact with other plaque bacteria. The elaboration of sialidase is thought to enhance fimbriae-mediated adherence by unmasking the fimbrial receptors on mammalian cells. The presence of certain cell-associated or extracellular enzymes, including those involved in sucrose or urea metabolism, may provide the means for these bacteria to thrive under conditions when other growth nutrients are not available. Moreover, these enzyme activities may influence the distribution of other plaque bacteria and promote selection for Actinomyces spp. in certain ecological niches. The recent development of a genetic transfer system for Actinomyces spp. has allowed for studies the results of which demonstrate the existence of multiple genes involved in fimbriae synthesis and function, and facilitated the construction of allelic replacement mutants at each gene locus. Analyses of these mutants have revealed a direct correlation between the synthesis of assembled fimbriae and the observed adherence properties. Further genetic analysis of the various enzyme activities detected from strains of Actinomyces should allow for an assessment of the role of these components in microbial ecology, and their contribution to the overall success of Actinomyces spp. as a primary colonizer and a key player in oral health and disease.}, }
@article {pmid10758185, year = {1999}, author = {Brimecombe, MJ and De Leij FA,  and Lynch, JM}, title = {Effect of Introduced Pseudomonas fluorescens Strains on Soil Nematode and Protozoan Populations in the Rhizosphere of Wheat and Pea.}, journal = {Microbial ecology}, volume = {38}, number = {4}, pages = {387-397}, doi = {10.1007/s002489901004}, pmid = {10758185}, issn = {1432-184X}, abstract = {Previous studies have shown that inoculation of pea seeds with Pseudomonas fluorescens strains F113lacZY or F113G22 increased mineralization of organic nitrogen in the rhizosphere. In contrast, inoculation of the same strains onto wheat seeds reduced mineralization of N from organic residues incorporated into soil. In the present study, we report on a likely explanation of this phenomenon, which appears to be governed by the effect of plant-microbe interactions on bacterial-feeding nematodes and protozoa. In soil microcosm tests, inoculation of pea seeds with Pseudomonas fluorescens strains F113lacZY or F113G22 resulted in an increase in the number of nematodes and protozoa in the rhizosphere as compared to noninoculated controls. This trend was repeated using a model sand system into which the bacteriophagous nematode Caenorhabditis elegans was introduced. It was subsequently found that non-inoculated germinating pea seeds exerted a nematicidal effect on C. elegans, which was remedied by inoculation with either strain F113lacZY or F113G22. This suggests that nematicidal compounds released by the germinating pea seeds were metabolized by the microbial inoculants before they affected nematode populations in the spermosphere or rhizosphere of pea. In contrast, inoculation of wheat plants resulted in significantly lower nematode populations in the rhizosphere, whereas protozoan numbers were unaffected. No nematicidal effects of inoculated or noninoculated wheat seeds could be found, suggesting that microfaunal populations were affected at a later stage during plant growth. Because of their key roles in accelerating the turnover of microbially immobilized N and organic matter, plants that support a larger microfaunal population are likely to benefit from a higher availability of inorganic nitrogen. Therefore, an understanding of plant-microbe interactions and their effects on soil microfaunal populations is essential in order to assess the effects of microbial inocula on plant mineral nutrition.}, }
@article {pmid10758184, year = {1999}, author = {Franklin, RB and Taylor, DR and Mills, AL}, title = {The Distribution of Microbial Communities in Anaerobic and Aerobic Zones of a Shallow Coastal Plain Aquifer.}, journal = {Microbial ecology}, volume = {38}, number = {4}, pages = {377-386}, doi = {10.1007/s002489900179}, pmid = {10758184}, issn = {1432-184X}, abstract = {Randomly amplified polymorphic DNA (RAPD) fingerprinting was used to determine the genetic similarity of whole-community DNA extracts from unattached microorganisms in several groundwater wells. The study site was a shallow coastal plain aquifer on the Eastern Shore of Virginia that contains distinct regions of anaerobic and aerobic groundwater. Several wells in each region were sampled, and principal component and cluster analyses showed a clear separation of the microbial communities from the two chemical zones of the aquifer. Within these zones, there was no relationship between the genetic relatedness of a pair of communities and their spatial separation. Two additional sets of samples were taken at later times, and the same clear separation between communities in the different zones of the aquifer was observed. The specific relationships between wells within each zone changed over time, however, and the magnitude and direction of these changes corresponded to concurrent changes in the groundwater chemistry at each well. Together, these results suggest that local variation in groundwater chemistry can support genetically distinct microbial communities, and that the composition of the microbial communities can follow seasonal fluctuations in groundwater chemistry.}, }
@article {pmid10758183, year = {1999}, author = {Krause, DO and Smith, WJ and Ryan, FM and Mackie, RI and McSweeney, CS}, title = {Use of 16S-rRNA Based Techniques to Investigate the Ecological Succession of Microbial Populations in the Immature Lamb Rumen: Tracking of a Specific Strain of Inoculated Ruminococcus and Interactions with Other Microbial Populations in Vivo.}, journal = {Microbial ecology}, volume = {38}, number = {4}, pages = {365-376}, doi = {10.1007/s002489901006}, pmid = {10758183}, issn = {1432-184X}, abstract = {The establishment of microorganisms in the rumen is a critical step if rumen manipulation is to be accomplished by use of microbial inoculants. Microbial populations in the maturing rumen undergo successional changes and, while in a state of flux, provide a possible opportunity for the introduction of specific strains of bacteria. While the rumen of the young lamb was maturing, we measured changes in several microbial populations with 16S-rRNA specific oligonucleotides: Rumincoccus, Fibrobacter, eukaryotes, Gram-positive bacteria, the Bacteroides-Porphromonas-Prevotella group, and anaerobic rumen fungi. In this study we repeatedly dosed 15 lambs with approximately 3.4 x 10(8) to 0.8 x 10(9) Ruminococcus cells dose(-1), twice a week, for 7 wk from 23 d to 63 d of age. Of the five Ruminococcus strains dosed (R. albus SY3 and AR67, and R. flavefaciens Y1, LP9155, and AR72) the most specific primers (based on 16S rDNA) were obtained for strain SY3. There was an increase in the eukaryotic population during dosing, and it was hypothesized that protozoal predation contributed to the disappearance of strain SY3. At the end of dosing PCR amplification showed that SY3 were approximately 10(9) cells ml(-1), but decreased to below the detection limit of the PCR system (8.6 x 10(4) ml(-1)) within 28 d postdosing. These experiments showed that fibrolytic populations increased significantly (P < 0.1) above the controls during the dosing period and were elevated for several days postdosing. This suggests that dosing of highly fibrolytic bacteria makes more of the fiber available to other organisms able to degrade fiber, and in so doing increases the overall fibrolytic activity of the rumen. Examination of the succession of gram-positive bacteria and the Bacteroides-Porphromonas-Prevotella group showed a decline in relative abundance as the lambs matured.}, }
@article {pmid10758182, year = {1999}, author = {Roane, TM and Pepper, IL}, title = {Microbial Responses to Environmentally Toxic Cadmium.}, journal = {Microbial ecology}, volume = {38}, number = {4}, pages = {358-364}, doi = {10.1007/s002489901001}, pmid = {10758182}, issn = {1432-184X}, abstract = {We analyzed the soil microbial communities from one uncontaminated and two metal-impacted soils and found that while cadmium adversely affected the numbers of culturable bacteria in all soils, cadmium-resistant isolates were found from each of the soils. With exposure to 24 and 48 µg ml(-1) soluble cadmium, the metal-contaminated soil communities were more resistant than the uncontaminated soil community. In addition, in one metal-stressed soil, the resistant population became more resistant with increased cadmium levels. Ribosomal 16S DNA sequencing identified the isolates as Arthrobacter, Bacillus, or Pseudomonas spp. Further characterization demonstrated that two of the isolates were highly resistant to soluble cadmium with maximum resistance at 275 µg ml(-1) cadmium. These isolates were also resistant to a variety of antibiotics, namely ampicillin, gentamicin, penicillin, and streptomycin, but no overall correlation was found between enhanced antibiotic resistance and cadmium resistance. One Pseudomonas isolate H1 did become more resistant with increasing cadmium levels, suggesting a different resistance mechanism at high cadmium concentrations.}, }
@article {pmid10758181, year = {1999}, author = {Muttray, AF and Mohn, WW}, title = {Quantitation of the Population Size and Metabolic Activity of a Resin Acid Degrading Bacterium in Activated Sludge Using Slot-Blot Hybridization to Measure the rRNA:rDNA Ratio.}, journal = {Microbial ecology}, volume = {38}, number = {4}, pages = {348-357}, doi = {10.1007/s002489901005}, pmid = {10758181}, issn = {1432-184X}, abstract = {The 16S rRNA:rDNA ratio is a useful parameter for measuring metabolic activity of a selected member of a complex microbial community, as in pulp effluent activated sludge systems. The RNA:DNA ratio of Sphingomonas sp. DhA-33, previously isolated from a sequencing batch reactor treating pulp mill effluent, is positively correlated with its growth rate (µ) under steady-state conditions. DhA-33 was grown in a chemostat with growth rates ranging from 0.04 to 0.15 cell divisions per hour. DhA-33 was also able to degrade dehydroabietic acid in bleached kraft mill effluent (BKME) plus mineral medium in batch culture. Slot-blot hybridization with radioactively labeled species-specific oligonucleotide probes for 16S rRNA and 16S rDNA was used to measure rRNA, rDNA, and the RNA:DNA ratio of this strain when in a mixed sludge community. An increase in DhA-33 rDNA indicated growth of DhA-33 within the community. The RNA:DNA ratio of DhA-33 increased sharply during exponential growth and declined as cells entered stationary phase. The RNA:DNA ratio decreased earlier and faster in DhA- 33/sludge co-cultures than in DhA-33 pure cultures, presumably due to an earlier depletion of nutrients. The species-specific quantification of the RNA:DNA ratio makes it possible to estimate the metabolic activity of selected members of a microbial community in situ.}, }
@article {pmid10758180, year = {1999}, author = {Ellis, BD and Butterfield, P and Jones, WL and McFeters, GA and Camper, AK}, title = {Effects of Carbon Source, Carbon Concentration, and Chlorination on Growth Related Parameters of Heterotrophic Biofilm Bacteria.}, journal = {Microbial ecology}, volume = {38}, number = {4}, pages = {330-347}, doi = {10.1007/s002489901003}, pmid = {10758180}, issn = {1432-184X}, abstract = {To investigate growth of heterotrophic biofilm bacteria, a model biofilm reactor was developed to simulate a drinking water distribution system. Controlled addition of three different carbon sources (amino acids, carbohydrates, and humics) at three different concentrations (500, 1,000, and 2,000 ppb carbon) in the presence and absence of chlorine were used in separate experiments. An additional experiment was run with a 1:1:2 mixture of the above carbon sources. Biofilm and effluent total and culturable cells in addition to total and dissolved organic carbon were measured in order to estimate specific growth rates (SGRs), observed yields, population densities, and bacterial carbon production rates. Bacterial carbon production rates (µg C/L day) were extremely high in the control biofilm communities (range = 295-1,738). Both growth rate and yield decreased with increasing carbon concentrations. Therefore, biofilm growth rates were zero-order with respect to the carbon concentrations used in these experiments. There was no correlation between growth rate and carbon concentration, but there was a significant negative correlation between growth rate and biofilm cell density (r = -0.637, p = 0.001 control and r = -0.57, p = 0.021 chlorinated biofilms). Growth efficiency was highest at the lowest carbon concentration (range = 12-4.5%, amino acids and humics respectively). Doubling times ranged from 2.3-15.4 days in the control biofilms and 1-12.3 days in the chlorinated biofilms. Growth rates were significantly higher in the presence of chlorine for the carbohydrates, humics, and mixed carbon sources (p = 0.004, < 0.0005, 0.013, respectively). The concept of r/K selection theory was used to explain the results with respect to specific growth rates and yields. Humic removal by the biofilm bacteria (78% and 56% for the control and chlorinated biofilms, respectively) was higher than previously reported literature values for planktonic bacteria. A number of control experiments indicated that filtration of drinking water was as effective as chlorination in controlling bacterial biofilm growth.}, }
@article {pmid10758179, year = {1999}, author = {Konopka, A}, title = {Theoretical Analysis of the Starvation Response under Substrate Pulses.}, journal = {Microbial ecology}, volume = {38}, number = {4}, pages = {321-329}, doi = {10.1007/s002489900178}, pmid = {10758179}, issn = {1432-184X}, abstract = {A simulation model was constructed in which two model bacteria competed with each other in a closed system to which periodic substrate additions were made. One bacterium responded to starvation by entering into a dormant state characterized by a decreased death rate; the other bacterium did not make this transition. The periodicity of substrate addition was varied, and the magnitude of selection for one bacterial type was calculated. For model parameters typical of those measured in Escherichia coli, positive selection for the bacterium capable of the starvation response only occurred if the time interval of substrate addition exceeded 54 times the minimum doubling time of the bacterium. The magnitude of the selection coefficient was most sensitive to two model parameters: the time constant for conversion of dormant cells back to actively growing ones, and the magnitude of the death rate of cells which did not undergo the starvation response.}, }
@article {pmid10758178, year = {1999}, author = {Morita, RY}, title = {Is H(2) the Universal Energy Source for Long-Term Survival?.}, journal = {Microbial ecology}, volume = {38}, number = {4}, pages = {307-320}, doi = {10.1007/s002489901002}, pmid = {10758178}, issn = {1432-184X}, abstract = {This review revisits anabiosis (cryptobiosis or latent life); but more specifically with the discrepancy (time factor) between the finding of viable bacteria in ancient material and the racemization of amino acids and depurination of DNA that would have contributed to their death. The omnipresence of H(2) in the biosphere since life began, its ability to penetrate the microbial cell, its low energy of activation, its ability to form protons and electrons in the presence of Fe(II), and its (including electrons and protons) role in many biochemical reactions make H(2) the best candidate as the energy of survival for microbial cells. Although the concentration of H(2) in most environments is below the threshold level for microbial growth, the surviving cells have a long period of time to carry out the necessary metabolism to offset the racemization and depurination processes. This paper explores a hypothesis that explains this discrepancy.}, }
@article {pmid10742213, year = {2000}, author = {Löffler, FE and Sun, Q and Li, J and Tiedje, JM}, title = {16S rRNA gene-based detection of tetrachloroethene-dechlorinating Desulfuromonas and Dehalococcoides species.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {4}, pages = {1369-1374}, pmid = {10742213}, issn = {0099-2240}, mesh = {DNA Primers ; Deltaproteobacteria/classification/genetics/*isolation &amp; purification/metabolism ; Fresh Water ; *Genes, rRNA ; Polymerase Chain Reaction/*methods ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/*genetics ; Sensitivity and Specificity ; Sulfur-Reducing Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Tetrachloroethylene/*metabolism ; Water Microbiology ; Water Pollutants, Chemical/metabolism ; }, abstract = {Members of the genera Desulfuromonas and Dehalococcoides reductively dechlorinate tetrachloroethene (PCE) and trichloroethene. Two primer pairs specific to hypervariable regions of the 16S rRNA genes of the Dehalococcoides group (comprising Dehalococcoides ethenogenes and Dehalococcoides sp. strain FL2) and the acetate-oxidizing, PCE-dechlorinating Desulfuromonas group (comprising Desulfuromonas sp. strain BB1 and Desulfuromonas chloroethenica) were designed. The detection threshold of a nested PCR approach using universal bacterial primers followed by a second PCR with the Desulfuromonas dechlorinator-targeted primer pair was 1 x 10(3) BB1 cells added per gram (wet weight) of sandy aquifer material. Total community DNA isolated from sediments of three Michigan rivers and six different chloroethene-contaminated aquifer samples was used as template in nested PCR. All river sediment samples yielded positive signals with the BB1- and the Dehalococcoides-targeted primers. One chloroethene-contaminated aquifer tested positive with the Dehalococcoides-targeted primers, and another contaminated aquifer tested positive with the Desulfuromonas dechlorinator-targeted primer pair. Restriction fragment analysis of the amplicons could discriminate strain BB1 from other known Desulfuromonas species. Microcosm studies confirmed the presence of PCE-dechlorinating, acetate-oxidizing Desulfuromonas and hydrogenotrophic Dehalococcoides species in samples yielding positive PCR signals with the specific primers.}, }
@article {pmid10742207, year = {2000}, author = {Klappenbach, JA and Dunbar, JM and Schmidt, TM}, title = {rRNA operon copy number reflects ecological strategies of bacteria.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {4}, pages = {1328-1333}, pmid = {10742207}, issn = {0099-2240}, mesh = {2,4-Dichlorophenoxyacetic Acid/metabolism ; Bacteria/*genetics/*growth &amp; development/isolation &amp; purification/metabolism ; *Ecosystem ; *Gene Dosage ; Genes, rRNA/genetics ; Herbicides/metabolism ; Molecular Sequence Data ; Phylogeny ; *Soil Microbiology ; rRNA Operon/*genetics ; }, abstract = {Although natural selection appears to favor the elimination of gene redundancy in prokaryotes, multiple copies of each rRNA-encoding gene are common on bacterial chromosomes. Despite this conspicuous deviation from single-copy genes, no phenotype has been consistently associated with rRNA gene copy number. We found that the number of rRNA genes correlates with the rate at which phylogenetically diverse bacteria respond to resource availability. Soil bacteria that formed colonies rapidly upon exposure to a nutritionally complex medium contained an average of 5.5 copies of the small subunit rRNA gene, whereas bacteria that responded slowly contained an average of 1.4 copies. In soil microcosms pulsed with the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D), indigenous populations of 2,4-D-degrading bacteria with multiple rRNA genes (= 5.4) became dominant, whereas populations with fewer rRNA genes (= 2.7) were favored in unamended controls. These findings demonstrate phenotypic effects associated with rRNA gene copy number that are indicative of ecological strategies influencing the structure of natural microbial communities.}, }
@article {pmid10741838, year = {2000}, author = {Reysenbach, AL and Ehringer, M and Hershberger, K}, title = {Microbial diversity at 83 degrees C in Calcite Springs, Yellowstone National Park: another environment where the Aquificales and "Korarchaeota" coexist.}, journal = {Extremophiles : life under extreme conditions}, volume = {4}, number = {1}, pages = {61-67}, doi = {10.1007/s007920050008}, pmid = {10741838}, issn = {1431-0651}, mesh = {Archaea/*classification/genetics ; Biological Evolution ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; In Situ Hybridization ; Korarchaeota/*classification/genetics ; Microscopy, Fluorescence ; Mutation ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Temperature ; Wyoming ; }, abstract = {The use of molecular phylogenetic approaches in microbial ecology has revolutionized our view of microbial diversity at high temperatures and led to the proposal of a new kingdom within the Archaea, namely, the "Korarchaeota." We report here the occurrence of another member of this archaeal group and a deeply rooted bacterial sequence from a thermal spring in Yellowstone National Park (USA). The DNA of a mixed community growing at 83 degrees C, pH 7.6, was extracted and the small subunit ribosomal RNA gene (16S rDNA) sequences were obtained using the polymerase chain reaction. The products were cloned and five different phylogenetic types ("phylotypes") were identified: four archaeal phylotypes, designated pBA1, pBA2, pBA3, and pBA5, and only one bacterial phylotype, designated pBB. pBA5 is very closely related to the korarchaeotal phylotype, pJP27, from Obsidian Pool in Yellowstone National Park. The pBB phylotype is a lineage within the Aquificales and, based on 16S rRNA sequence, is different enough from the members of the Aquificales to constitute a different genus. In situ hybridization with bacterial-specific and Aquificales-specific fluorescent oligonucleotide probes indicated the bacterial population dominated the community and most likely contributed significantly to biogeochemical cycling within the community.}, }
@article {pmid10737410, year = {2000}, author = {Moore, FB and Rozen, DE and Lenski, RE}, title = {Pervasive compensatory adaptation in Escherichia coli.}, journal = {Proceedings. Biological sciences}, volume = {267}, number = {1442}, pages = {515-522}, pmid = {10737410}, issn = {0962-8452}, mesh = {*Adaptation, Physiological ; Culture Media ; Epistasis, Genetic ; Escherichia coli/*genetics/*physiology ; Evolution, Molecular ; Genotype ; *Mutation ; Selection, Genetic ; }, abstract = {To investigate compensatory adaptation (CA), we used genotypes of Escherichia coli which were identical except for one or two deleterious mutations. We compared CA for (i) deleterious mutations with large versus small effects, (ii) genotypes carrying one versus two mutations, and (iii) pairs of deleterious mutations which interact in a multiplicative versus synergistic fashion. In all, we studied 14 different genotypes, plus a control strain which was not mutated. Most genotypes showed CA during 200 generations of experimental evolution, where we define CA as a fitness increase which is disproportionately large relative to that in evolving control lines, coupled with retention of the original deleterious mutation(s). We observed greater CA for mutations of large effect than for those of small effect, which can be explained by the greater benefit to recovery in severely handicapped genotypes given the dynamics of selection. The rates of CA were similar for double and single mutants whose initial fitnesses were approximately equal. CA was faster for synergistic than for multiplicative pairs, presumably because the marginal gain which results from CA for one of the component mutations is greater in that case. The most surprising result in our view, is that compensation should be so readily achieved in an organism which is haploid and has little genetic redundancy This finding suggests a degree of versatility in the E. coil genome which demands further study from both genetic and physiological perspectives.}, }
@article {pmid10733245, year = {1999}, author = {}, title = {Microbiological safety evaluations and recommendations on sprouted seeds. National Advisory Committee on Microbiological Criteria for Foods.}, journal = {International journal of food microbiology}, volume = {52}, number = {3}, pages = {123-153}, doi = {10.1016/s0168-1605(99)00135-x}, pmid = {10733245}, issn = {0168-1605}, mesh = {Disease Outbreaks ; Escherichia coli Infections/prevention &amp; control ; Escherichia coli O157/growth &amp; development ; Food Handling/*standards ; *Food Microbiology ; Food-Processing Industry/standards ; Foodborne Diseases/*prevention &amp; control ; Humans ; Public Health ; Salmonella/growth &amp; development ; Salmonella Food Poisoning/prevention &amp; control ; Seeds/*microbiology ; }, abstract = {In 1997, the National Advisory Committee on Microbiological Criteria for Foods (NACMCF/the Committee) was asked to review the current literature on sprout-associated outbreaks: identify the organisms and production practices of greatest public health concern: prioritize research needs: and provide recommendations on intervention and prevention strategies. In response to this charge, the Fresh Produce Work Group (FPWG) documented the relevant epidemiology and microbial ecology of sprout-associated outbreaks and reviewed current industry practices and initiatives related to the growing of seed and the production of sprouts. Sprouts have been identified as a special problem because of the potential for pathogen growth during the sprouting process. If pathogens are present on or in the seed, sprouting conditions may favor their proliferation. There is no inherent step in the production of raw sprouts to reduce or eliminate pathogens. Contaminated seed is the likely source for most reported sprout-associated outbreaks. Research has been initiated on methods to reduce or eliminate pathogenic bacteria on seeds and sprouts and some treatments show promise. However, to date, no single treatment has been shown to completely eliminate pathogens under experimental conditions used. Finally, the Committee found that, at the time of the charge, there was a lack of fundamental food safety knowledge along the continuum from seed production through sprout consumption. More recently, many have become aware of the potential for this food to be a vehicle for foodborne illness and the need for appropriate controls: however, such awareness is not universal. Although seed appears to be the most likely source of contamination in sprout associated outbreaks, practices and conditions at the sprouting facility may also impact on the safety of the finished product. In recent sprout-associated outbreak investigations, facilities associated with outbreaks did not consistently apply seed disinfection treatments prior to sprouting. Conversely, facilities that used seed from the same lot as an implicated facility, but had not been associated with reported illnesses, appear to have been consistently using seed disinfection treatments, such as 20,000 ppm calcium hypochlorite, to disinfect seed prior to sprouting. The Committee has developed a number of specific recommendations, including: 1. The knowledge of all interested parties pertaining to the microbiological safety of sprouted seeds must be enhanced; government and industry should develop education programs for seed and sprout producers on basic principles for microbiological food safety, good agricultural practices, good manufacturing practices, and hazard analysis and critical control point (HACCP) systems. 2. Good agricultural practices should be systematically implemented to reduce the potential for microbial contamination of seeds for sprout production. 3. Seed cleaning, storage, and handling practices that minimize the potential for microbial contamination should be developed and implemented. 4. Seeds should be treated with one or more treatments that have been shown to reduce pathogenic bacteria that may be present. Intervention strategies that deliver less than a given reduction (at this time, 5-log) in levels of Salmonella spp. and enterohemorrhagic Escherichia coli O157 should be coupled with a microbiological testing program. 5. Establish good manufacturing practices and food safety systems, including regulatory oversight, microbial testing, adoption of HACCP, and improved traceback, that systematically look for means to prevent seeds from serving as the vehicle for foodborne disease, and 6. Conduct research related to the microbiological safety of sprouted seeds, particularly in the areas of pathogen reduction or elimination, sources of contamination and its prevention, and preventing or retarding pathogen growth during sprouting.}, }
@article {pmid10709985, year = {2000}, author = {Gmeiner, M and Kneifel, W and Kulbe, KD and Wouters, R and De Boever, P and Nollet, L and Verstraete, W}, title = {Influence of a synbiotic mixture consisting of Lactobacillus acidophilus 74-2 and a fructooligosaccharide preparation on the microbial ecology sustained in a simulation of the human intestinal microbial ecosystem (SHIME reactor).}, journal = {Applied microbiology and biotechnology}, volume = {53}, number = {2}, pages = {219-223}, doi = {10.1007/s002530050011}, pmid = {10709985}, issn = {0175-7598}, mesh = {Animals ; Bifidobacterium/growth &amp; development ; Bioreactors/*microbiology ; Butyric Acid/metabolism ; Colony Count, Microbial ; Culture Media ; Digestive System/microbiology ; Fatty Acids, Volatile/analysis ; Glucuronidase/metabolism ; Humans ; Lactobacillus acidophilus/genetics/*metabolism ; Milk/metabolism ; Oligosaccharides/*metabolism ; Propionates/metabolism ; Time Factors ; beta-Galactosidase/metabolism ; }, abstract = {Lactobacillus acidophilus 74-2, which is used in probiotic products, was administered, with fructo-oligosaccharide in a milk-based product, to the second vessel (duodenum/jejunum) of the SHIME reactor, an in vitro simulation of the human intestinal microbial ecology. The main focus of this study was to monitor the changes of the population density of selected bacterial species in the intestine and the changes of metabolic activities during the supplementation of L. acidophilus and fructooligosaccharide in the SHIME reactor. Interestingly, the addition of L. acidophilus 74-2 with fructooligosaccharide gave rise to an increase of bifidobacteria. Moreover, major positive changes occurred in the production of volatile fatty acids: a strong upward trend was observed especially in the case of butyric acid and propionic acid. Furthermore a noticeable increase of beta-galactosidase activity was monitored, while the activity of beta-glucuronidase, generally considered undesirable, declined.}, }
@article {pmid10705910, year = {2000}, author = {Bosch, JA and de Geus, EJ and Ligtenberg, TJ and Nazmi, K and Veerman, EC and Hoogstraten, J and Amerongen, AV}, title = {Salivary MUC5B-mediated adherence (ex vivo) of Helicobacter pylori during acute stress.}, journal = {Psychosomatic medicine}, volume = {62}, number = {1}, pages = {40-49}, doi = {10.1097/00006842-200001000-00006}, pmid = {10705910}, issn = {0033-3174}, mesh = {Acute-Phase Reaction/*microbiology ; Adolescent ; Adult ; Anxiety/immunology/*metabolism/psychology ; Bacterial Adhesion/*physiology ; Blood Pressure/physiology ; Cell Adhesion Molecules/metabolism ; Enzyme-Linked Immunosorbent Assay ; Female ; Glycosylation ; Helicobacter pylori/*metabolism ; Humans ; Immunoglobulin A, Secretory/immunology ; Inflammation Mediators/*metabolism ; Male ; Mucins/analysis/*metabolism ; Pilot Projects ; Saliva/chemistry/*metabolism/microbiology ; Salivary Proteins and Peptides/*metabolism ; Stress, Psychological/psychology ; Surveys and Questionnaires ; }, abstract = {OBJECTIVE: Biochemical host defenses at mucosal sites, such as the oral cavity, play a key role in the regulation of microbial ecology and the prevention of infectious disease. These biochemical factors have distinct features, some of which benefit the host and some that benefit bacteria. We investigated the effects of acute stress on the salivary levels of the carbohydrate structure sulfo-Lewis (sulfo-Le), which is linked to the mucosal glycoprotein MUC5B. Sulfo-Le was recently identified as an adhesion molecule for Helicobacter pylori; therefore, we also measured saliva-mediated adherence (ex vivo) of H. pylori. The oral cavity is suspected to be involved in the transmission of H. pylori.<br><br>METHODS: Saliva was collected from 17 undergraduates before (baseline), during (stress), and after (recovery) exposure to a video showing surgical procedures. In addition, blood pressure, an impedance cardiogram, and an electrocardiogram were recorded.<br><br>RESULTS: During stressor exposure, participants reported increased state anxiety. In addition, stroke volume increased and heart rate decreased. The stressor induced a strong increase in salivary sulfo-Le concentration (U/ml), sulfo-Le output (U/min), sulfo-Le/total protein ratio (U/mg protein), and saliva-mediated adherence (ex vivo) of H. pylori. As expected, sulfo-Le concentration correlated with the adherence of H. pylori (r = 0.72, p < .05). It was demonstrated that the observed adherence was induced by MUC5B and that the carbohydrate structure sulfo-Le contributed to this process.<br><br>CONCLUSIONS: Our study demonstrated a direct link between stress-mediated biochemical changes and altered host-microbe interactions in humans. Increased bacterial adherence may be a contributing factor in the observed relationship between stress and susceptibility to infectious disease.}, }
@article {pmid10702791, year = {2000}, author = {Cappelli, D and Holt, SC and Singer, RE and Pickrum, HM and Ebersole, JL}, title = {Effects of 0.12% chlorhexidine gluconate on experimental gingivitis in non-human primates: clinical and microbiological alterations.}, journal = {Oral diseases}, volume = {6}, number = {2}, pages = {124-131}, doi = {10.1111/j.1601-0825.2000.tb00113.x}, pmid = {10702791}, issn = {1354-523X}, mesh = {Actinomyces/classification/drug effects ; Animals ; Anti-Infective Agents, Local/*therapeutic use ; Bacteria/drug effects ; Chi-Square Distribution ; Chlorhexidine/*analogs &amp; derivatives/*therapeutic use ; Colony Count, Microbial ; Confidence Intervals ; Dental Plaque/microbiology ; Dental Plaque Index ; Disease Models, Animal ; Ecology ; Female ; Gingival Hemorrhage/microbiology/prevention &amp; control ; Gingivitis/microbiology/*prevention &amp; control ; Gram-Positive Bacteria/drug effects/growth &amp; development ; Macaca fascicularis ; Mouthwashes/*therapeutic use ; Odds Ratio ; Oral Hygiene ; Periodontal Attachment Loss/microbiology/prevention &amp; control ; Periodontal Pocket/microbiology/prevention &amp; control ; Placebos ; }, abstract = {OBJECTIVE: This study examined the efficacy of 0.12% chlorhexidine gluconate (Peridex) to reduce gingival inflammation in the absence of mechanical hygiene and its effect on the oral microbial ecology in a non-human primate (NhP) model of gingivitis.<br><br>DESIGN: Twelve NhP were stratified based on existing inflammation into two groups of six NhP per group. Oral hygiene was performed on both groups so as to reach a level of gingival health (BOP < or = 0.3) at the conclusion of the hygiene phase. One group received 30 ml of 0.12% chlorhexidine gluconate twice daily 7 days/week, and a second group received 30 ml of placebo (distilled water colored to match the active) using the same regimen for 10 weeks. MEASUREMENT OUTCOMES: Clinical parameters including plaque (PLI), pocket depth (PD), attachment level (AL), and bleeding on probing (BOP) were evaluated at 2-week intervals. Subgingival plaque samples were collected by paper point at 2-week intervals and cultured for predominant cultivable bacteria.<br><br>RESULTS: By week 2, there was a difference in BOP between the groups, which reached statistical significance by week 4. This difference in BOP was maintained throughout the course of the study. Chlorhexidine gluconate (0.12%) had no significant effect on PLI, PD, or AL; although PD was greater in the placebo group after week 2 and throughout the study. Microbiologically, at week 4, the treatment group had a reduction in total bacterial counts, as well as Gram positive bacteria, and total black pigmented bacteria, compared to the placebo group. However, only the differences in Actinomyces spp. reached significance. Interestingly, when both groups received only one treatment/day on the weekends (i.e., day 6 and 7), an associated loss of statistically significant differences between the two groups was observed. Additional experiments dosing the non-human primates once daily, 5 days/week yielded no significant differences in clinical parameters, including bleeding, when compared with the placebo group.<br><br>CONCLUSION: Non-human primates provided a model system of gingivitis for testing antimicrobial agent effects on the subgingival ecology and accompanying inflammatory responses. Chlorhexidine gluconate (0.12%), even in the absence of mechanical hygiene, was effective in inhibiting clinical signs of inflammation, associated with alterations in the subgingival microbial ecology, most notably Actinomyces spp.}, }
@article {pmid10699669, year = {2000}, author = {Cassidy, MB and Leung, KT and Lee, H and Trevors, JT}, title = {A comparison of enumeration methods for culturable Pseudomonas fluorescens cells marked with green fluorescent protein.}, journal = {Journal of microbiological methods}, volume = {40}, number = {2}, pages = {135-145}, doi = {10.1016/s0167-7012(99)00131-1}, pmid = {10699669}, issn = {0167-7012}, mesh = {Bacteriological Techniques ; Colony Count, Microbial ; Green Fluorescent Proteins ; Luminescent Proteins/chemistry ; Microscopy, Fluorescence ; Plant Roots/microbiology ; Pseudomonas fluorescens/*growth &amp; development/isolation &amp; purification ; Seeds/microbiology ; Soil Microbiology ; Triticum/microbiology ; }, abstract = {The detection of bacteria in environmental samples using genetic markers is valuable in microbial ecology. The green fluorescent protein (GFP) reporter gene was studied under nutrient starvation conditions at 4 degrees C, 23 degrees C and 30 degrees C in Pseudomonas fluorescens R2fG1 cells tagged with a red-shifted gfp. Fluorescence intensity was not significantly different in cells maintained in a buffer for at least 48 days at all the tested temperatures. gfp-Tagged R2fG1 cells were introduced into bulk soil microcosms and soil microcosms with wheat seedlings. GFP-marked cells were enumerated immediately after inoculation into soil and again in soil and root samples after 10 days. Counts of culturable colonies were obtained from drop plates using 5-microl aliquots of serial dilutions viewed with an epifluorescent microscope. Traditional spread plates (using 100-microl aliquots) and the most-probable-number (MPN) method using a spectrofluorometer were also used to enumerate the GFP-marked Pseudomonas cells in soil, rhizosphere and rhizoplane samples. Microcolonies were visualized on root surfaces under the epifluorescent microscope after immobilizing in agar and incubation for 24 h. Counts from traditional spread plates were significantly higher (P<0.05) than the population estimates of the MPN method for all treatments at any sampling time. Counts using the drop plate method, however, were not significantly different (P<0.05) except in one treatment, and provided similar estimates in half the time of spread plates and at an estimated third of the cost.}, }
@article {pmid10699667, year = {2000}, author = {Brüggemann, J and Stephen, JR and Chang, YJ and Macnaughton, SJ and Kowalchuk, GA and Kline, E and White, DC}, title = {Competitive PCR-DGGE analysis of bacterial mixtures: an internal standard and an appraisal of template enumeration accuracy.}, journal = {Journal of microbiological methods}, volume = {40}, number = {2}, pages = {111-123}, doi = {10.1016/s0167-7012(99)00126-8}, pmid = {10699667}, issn = {0167-7012}, mesh = {Alcaligenes/genetics ; DNA Primers ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Desulfovibrio vulgaris/genetics ; Electrophoresis, Polyacrylamide Gel/methods ; Molecular Sequence Data ; Polymerase Chain Reaction/methods ; Proteobacteria/*genetics ; RNA, Ribosomal, 16S/analysis ; Sensitivity and Specificity ; Shewanella putrefaciens/genetics ; }, abstract = {Analysis of polymerase chain reaction (PCR) amplified 16S rDNA fragments from environmental samples by denaturing gradients of chemicals or heat [denaturing gradient gel electrophoresis (DGGE) and thermal gradient gel electrophoresis (TGGE)] within polyacrylamide gels is a popular tool in microbial ecology. Difficulties in acceptance of the technique and interpretation of the results remain, due to its qualitative nature. In this study we have addressed this problem by the construction and evaluation of a quantitative standard for incorporation into test DNA samples. The standard was based on a naturally occurring 16S rRNA gene carried by the X-endosymbiont of the psyllid Anomoneura mori, a gamma-proteobacterium. This sequence is the most AT-rich 16S rDNA gene recovered from any cultured organism or environmental sample described to date, and a specifically amplified rDNA fragment denatured under exceptionally low stringency denaturing conditions. The native sequence was modified to incorporate perfect matches to the PCR primers used. The efficiency of amplification of this standard in comparison to a range of 16S rDNA sequences and the errors involved in enumerating template molecules under a range of PCR conditions are demonstrated and quantified. Tests indicated that highly accurate counts of released target molecules from a range of bacterial cells could be achieved in both laboratory mixtures and compost.}, }
@article {pmid10698783, year = {2000}, author = {Verschuere, L and Heang, H and Criel, G and Sorgeloos, P and Verstraete, W}, title = {Selected bacterial strains protect Artemia spp. from the pathogenic effects of Vibrio proteolyticus CW8T2.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {3}, pages = {1139-1146}, pmid = {10698783}, issn = {0099-2240}, mesh = {Alcaligenes/physiology ; Animals ; *Antibiosis ; Artemia/*microbiology ; Bacteriolysis ; Digestive System/microbiology/pathology ; Epithelial Cells/microbiology/pathology ; Gram-Negative Bacteria/*physiology ; Gram-Positive Asporogenous Rods, Regular/*physiology ; Moraxella/physiology ; Vibrio/*pathogenicity ; Vibrionaceae/physiology ; }, abstract = {In this study Vibrio proteolyticus CW8T2 has been identified as a virulent pathogen for Artemia spp. Its infection route has been visualized with transmission electron microscopy. The pathogen affected microvilli and gut epithelial cells, disrupted epithelial cell junctions, and reached the body cavity, where it devastated cells and tissues. In vivo antagonism tests showed that preemptive colonization of the culture water with nine selected bacterial strains protected Artemia juveniles against the pathogenic effects. Two categories of the selected strains could be distinguished: (i) strains providing total protection, as no mortality occurred 2 days after the experimental infection with V. proteolyticus CW8T2, with strain LVS8 as a representative, and (ii) strains providing partial protection, as significant but not total mortality was observed, with strain LVS2 as a representative. The growth of V. proteolyticus CW8T2 in the culture medium was slowed down in the presence of strains LVS2 and LVS8, but growth suppression was distinctly higher with LVS8 than with LVS2. It was striking that the strains that gave only partial protection against the pathogen in the in vivo antagonism test showed also a restricted capability to colonize the Artemia compared to the strains providing total protection. The in vivo antagonism tests and the filtrate experiments showed that probably no extracellular bacterial compounds were involved in the protective action but that the living cells were required to protect Artemia against V. proteolyticus CW8T2.}, }
@article {pmid10698769, year = {2000}, author = {Ramsing, NB and Ferris, MJ and Ward, DM}, title = {Highly ordered vertical structure of Synechococcus populations within the one-millimeter-thick photic zone of a hot spring cyanobacterial mat.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {3}, pages = {1038-1049}, pmid = {10698769}, issn = {0099-2240}, mesh = {Circadian Rhythm ; Cyanobacteria/*cytology/genetics/radiation effects ; *Ecosystem ; Fresh Water ; *Hot Temperature ; Image Processing, Computer-Assisted ; Light ; Oxygen/analysis ; Photoperiod ; *Water Microbiology ; }, abstract = {A variety of contemporary techniques were used to investigate the vertical distribution of thermophilic unicellular cyanobacteria, Synechococcus spp., and their activity within the upper 1-mm-thick photic zone of the mat community found in an alkaline siliceous hot spring in Yellowstone National Park in Wyoming. Detailed measurements were made over a diel cycle at a 61 degrees C site. Net oxygenic photosynthesis measured with oxygen microelectrodes was highest within the uppermost 100- to 200-microm-thick layer until midmorning, but as the day progressed, the peak of net activity shifted to deeper layers, stabilizing at a depth of 300 microm from midday throughout the afternoon. Examination of vertical thin sections by bright-field and autofluorescence microscopy revealed the existence of different populations of Synechococcus which form discrete bands at different vertical positions. Denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA gene segments from horizontal cryosections obtained at 100-microm-thick vertical intervals also suggested vertical stratification of cyanobacterial, green sulfur bacterium-like, and green nonsulfur bacterium-like populations. There was no evidence of diel migration. However, image analysis of vertical thin sections revealed the presence of a narrow band of rod-shaped Synechococcus cells in which the cells assumed an upright position. These upright cells, located 400 to 800 microm below the surface, were observed only in mat samples obtained around noon. In mat samples obtained at other time points, the cells were randomly oriented throughout the mat. These combined observations reveal the existence of a highly ordered structure within the very thin photic zone of this hot spring microbial mat, consisting of morphologically similar Synechococcus populations that are likely to be differentially adapted, some co-occurring with green sulfur bacterium-like populations, and all overlying green nonsulfur bacterium-like populations.}, }
@article {pmid10688198, year = {2000}, author = {Radajewski, S and Ineson, P and Parekh, NR and Murrell, JC}, title = {Stable-isotope probing as a tool in microbial ecology.}, journal = {Nature}, volume = {403}, number = {6770}, pages = {646-649}, doi = {10.1038/35001054}, pmid = {10688198}, issn = {0028-0836}, mesh = {Alphaproteobacteria/classification/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Carbon Isotopes ; Centrifugation, Density Gradient ; DNA, Complementary/*isolation &amp; purification ; Ecology ; Methanol/metabolism ; Molecular Probes ; Molecular Sequence Data ; Phylogeny ; *Soil Microbiology ; }, abstract = {Microorganisms are responsible for driving the biogeochemical cycling of elements on Earth. Despite their importance and vast diversity, the taxonomic identity of the microorganisms involved in any specific process has usually been confined to that small fraction of the microbiota that has been isolated and cultivated. The recent coupling of molecular biological methods with stable-isotope abundance in biomarkers has provided a cultivation-independent means of linking the identity of bacteria with their function in the environment. Here we show that 13C-DNA, produced during the growth of metabolically distinct microbial groups on a 13C-enriched carbon source, can be resolved from 12C-DNA by density-gradient centrifugation. DNA isolated from the target group of microorganisms can be characterized taxonomically and functionally by gene probing and sequence analysis. Application of this technique to investigate methanol-utilizing microorganisms in soil demonstrated the involvement of members of two phylogenetically distinct groups of eubacteria; the alpha-proteobacterial and Acidobacterium lineages. Stable-isotope probing thus offers a powerful new technique for identifying microorganisms that are actively involved in specific metabolic processes under conditions which approach those occurring in situ.}, }
@article {pmid10653757, year = {2000}, author = {Tonolla, M and Demarta, A and Peduzzi, S and Hahn, D and Peduzzi, R}, title = {In situ analysis of sulfate-reducing bacteria related to Desulfocapsa thiozymogenes in the chemocline of meromictic Lake Cadagno (Switzerland).}, journal = {Applied and environmental microbiology}, volume = {66}, number = {2}, pages = {820-824}, pmid = {10653757}, issn = {0099-2240}, mesh = {DNA Probes ; Deltaproteobacteria/classification/*genetics/physiology ; Fresh Water/*microbiology ; Gene Library ; Genes, rRNA ; In Situ Hybridization ; Microscopy, Fluorescence ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfur-Reducing Bacteria/classification/*genetics/*physiology ; Switzerland ; Water Microbiology ; }, abstract = {Comparative sequence analysis of a 16S rRNA gene clone library from the chemocline of the meromictic Lake Cadagno (Switzerland) retrieved two clusters of sequences resembling sulfate-reducing bacteria within the family Desulfovibrionaceae. In situ hybridization showed that, similar to sulfate-reducing bacteria of the family Desulfobacteriaceae, bacteria of one cluster with similarity values to the closest cultured relatives of between 92.6 and 93.1% resembled free cells or cells loosely attached to other cells or debris. Bacteria of the second cluster closely related to Desulfocapsa thiozymogenes DSM7269 with similarity values between 97. 9 and 98.4% were generally associated with aggregates of different small-celled phototrophic sulfur bacteria, suggesting a potential interaction between the two groups of bacteria.}, }
@article {pmid10650492, year = {1999}, author = {Yang, SS and Yang, CK and Chang, EH and Wei, CB}, title = {[The effect of thermal power plant on microbial ecology and environmental quality].}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {32}, number = {4}, pages = {269-277}, pmid = {10650492}, issn = {1684-1182}, mesh = {Actinomycetales/isolation &amp; purification ; Bacteria/*isolation &amp; purification ; Ecology ; Fungi/*isolation &amp; purification ; Hot Temperature ; Hydrogen-Ion Concentration ; *Power Plants ; *Soil Microbiology ; }, abstract = {To investigate the effect of thermal power plant on the microbial ecology and the environmental quality, the Hsieh-Ho Thermal Power Plant was chosen and the populations of microbes including bacteria, actinomycetes, fungi, and cellulolytic, phosphate-solubilizing and nitrogen-fixing microbes were selected as the parameters of microbial ecology. The pH values of the soil sample collected from inside and outside of the plant were 5.2-6.2 and 4.0-5.3, respectively. Moisture content in plant area was lower than that in the surrounding area. Microbial populations of the topsoils were higher than those of the subsoils. Each gram of soil contained 3.64 x 10(4)-5.16 x 10(7) colonies of bacteria, 1.75 x 10(3)-1.10 x 10(6) colonies of actinomycetes and 6.72 x 10(3)-8.78 x 10(6) colonies of fungi in the plant area; while they were 5.52 x 10(4)-2.14 x 10(7), 8.26 x 10(3)-7.25 x 10(5) and 3.49 x 10(3)-2.74 x 10(6) colonies of bacteria, actinomycetes and fungi, respectively, in the surrounding area. The effect of seasonal change on microbial populations was not significant. The ratio of cellulolytic, phosphate-solubilizing and nitrogen-fixing microbes to the total count in the plant area was also higher than that in the surrounding area, and some of them had significant differences. From the statistical analysis, the effect of thermal power generator on the population and distribution of microbes was significantly different.}, }
@article {pmid10643278, year = {1999}, author = {Fedorovskaia, EA and Nemirovskaia, LN}, title = {[The interrelation of microbial ecosystems and human immunity].}, journal = {Mikrobiolohichnyi zhurnal (Kiev, Ukraine : 1993)}, volume = {61}, number = {5}, pages = {85-96}, pmid = {10643278}, issn = {1028-0987}, mesh = {Bacteria/immunology/*pathogenicity ; Bacterial Infections/immunology/microbiology ; *Ecosystem ; Humans ; Immune System/immunology/microbiology ; *Immunity ; Phagocytosis/immunology ; Reference Values ; }, abstract = {An analytical survey of literature on the problem of the study of interrelations between the immune status of the organism and microbial ecology of a man is presented. The criteria which characterize normal flora of human organism varying in the process of evolutionary adaptation, interaction with microorganism and response of the immune system, its participation in formation of protective functions of the organism are considered. It is shown that the proceeding character and the finite result of different infectious processes depend on the state of the organism immune system. A possibility of correction of certain immunological indices with the help of representatives of normal microflora has been considered. A conclusion has been made on the necessity to solve the problem of infectious diseases and complications in a complex of microbiological and immunological investigations.}, }
@article {pmid10640669, year = {2000}, author = {Jonkers, HM and van Bergeijk SA,  and van Gemerden H, }, title = {Microbial production and consumption of dimethyl sulfide (DMS) in a sea grass (Zostera noltii)-dominated marine intertidal sediment ecosystem (Bassin d'Arcachon, France).}, journal = {FEMS microbiology ecology}, volume = {31}, number = {2}, pages = {163-172}, doi = {10.1111/j.1574-6941.2000.tb00681.x}, pmid = {10640669}, issn = {1574-6941}, abstract = {The relation between net dimethyl sulfide (DMS) production and changes in near surface (0-5 mm) oxygen concentrations in a sea grass (Zostera noltii Hornem)-covered intertidal sediment ecosystem was examined during a diel cycle. Sediment covered with Zostera was found to be more oxygenated than uncovered sediment during the period of photosynthesis. This phenomenon was probably caused by radial oxygen loss of the Zostera root-rhizome system. The population sizes of the three functional groups of microbes mainly responsible for the concentration of DMS, the dimethylsulfoniopropionate (DMSP)-demethylating, DMSP-cleaving and DMS-oxidizing bacteria, were quantified by most probable number (MPN) methodologies. Sediments with Zostera supported substantially higher populations of both aerobic (149x10(6) cm(-3) DMSP-utilizing and 0.4x10(6) cm(-3) DMS-oxidizing) and anaerobic (43x10(6) cm(-3) DMSP-utilizing and 0.4x10(6) cm(-3) DMS-oxidizing) microorganisms than sediments without Zostera (DMSP-utilizing aerobes and anaerobes both 2x10(6) cm(-3) and DMS-oxidizing aerobes and anaerobes both 0.2x10(6) cm(-3)). Experiments conducted with sediment cores and sediment slurries suggested that the net production of DMS in these sediments was significantly lower during oxic periods than during anoxic periods. Intact sediment cores with and without Zostera produced DMS when incubated under anoxic/dark conditions (97.0 and 53.6 nmol DMS m(-2) h(-1), respectively), while oxic/light-incubated cores did not produce detectable amounts of DMS. In addition, kinetic parameter values (V(max) and K(m)) for DMSP degradation in cell suspensions of isolated DMSP-demethylating and DMSP-cleaving bacteria were measured and compared to documented values for other strains. Both V(max) and K(m) values for DMSP-demethylating organisms were found to be relatively low (14.4-20.1 nmol DMSP mg protein(-1) min(-1) and 4.1-15.5 µM, respectively) while these parameter values varied widely in the group of the DMSP-cleaving organisms (6.7-1000 nmol DMSP mg protein(-1) min(-1) and 2-2000 µM, respectively). It was hypothesized that a diel rhythm in DMS emission occurred, with a relatively low net production during the day and a high net production during the night. Environmental changes which result in increased anoxic conditions in coastal sediments, such as an increase in eutrophication, may therefore result in increased atmospheric DMS emission rates.}, }
@article {pmid10640663, year = {2000}, author = {Gasol, JM and Duarte, CM}, title = {Comparative analyses in aquatic microbial ecology: how far do they go?.}, journal = {FEMS microbiology ecology}, volume = {31}, number = {2}, pages = {99-106}, doi = {10.1111/j.1574-6941.2000.tb00675.x}, pmid = {10640663}, issn = {1574-6941}, abstract = {Methodological developments in recent years have led to an increase in empirical databases on the abundance and functions of aquatic microbes, now allowing synthesis studies. Most of these studies have adopted a comparative approach, such that comparative analyses are now available for most aspects of aquatic microbial food webs (more than 50 papers published in the last 15 years). Some of these analyses apparently yield conflicting results, introducing confusion and unnecessary disputes in the field. We briefly review the comparative analyses so far produced and we highlight generalities, show that some of the perceived discrepancies largely derive from partial analyses of a general underlying trend and formulate predictions based on these general trends that provide new avenues for research.}, }
@article {pmid10630395, year = {1999}, author = {Okada, M and Bothin, C and Blomhoff, R and Kanazawa, K and Midtvedt, T}, title = {Vitamin A deficiency impairs colonic healing but not adhesion formation in germ-free and conventional rats.}, journal = {Journal of investigative surgery : the official journal of the Academy of Surgical Research}, volume = {12}, number = {6}, pages = {319-325}, doi = {10.1080/089419399272304}, pmid = {10630395}, issn = {0894-1939}, mesh = {Animals ; Body Weight ; Colon/*pathology/*surgery ; Female ; Germ-Free Life ; Hydroxyproline/analysis ; Intestines/*microbiology ; Male ; Postoperative Complications ; Rats ; Tissue Adhesions ; Vitamin A Deficiency/*physiopathology ; Wound Healing/physiology ; }, abstract = {Vitamin A is well recognized as a factor of major importance in epithelial and connective tissue repair mechanisms. Recently it was shown that vitamin A deficiency caused overgrowth and translocation of intestinal bacteria in rats. The aim of this study was to investigate the healing of colonic anastomoses and formation of postsurgical adhesions in vitamin A-deficient germ-free and conventional rats. Fourteen germ-free and 10 conventional rats were allocated to four groups: germ-free rats not given vitamin A, germ-free rats given vitamin A, conventional rats not given vitamin A, and conventional rats given vitamin A. All rats underwent surgery for colonic anastomosis. Seven days afterward, they were euthanized, and the bursting pressure of colonic anastomosis and formation of peritoneal adhesions were evaluated. The bursting pressures in groups not given vitamin A were lower than in groups given vitamin A. The adhesion scores in germ-free groups were lower than in conventional groups. These findings demonstrated that vitamin A had an important role in healing of colonic anastomoses whether in the presence or absence of intestinal flora, and that intestinal bacteria had a greater effect than vitamin A on formation of postsurgical adhesions. This may suggest that the mechanism of healing of colonic anastomoses differs from that of postsurgical adhesion formation.}, }
@article {pmid11125085, year = {2001}, author = {Klappenbach, JA and Saxman, PR and Cole, JR and Schmidt, TM}, title = {rrndb: the Ribosomal RNA Operon Copy Number Database.}, journal = {Nucleic acids research}, volume = {29}, number = {1}, pages = {181-184}, pmid = {11125085}, issn = {1362-4962}, mesh = {*Databases, Factual ; *Gene Dosage ; Genes, rRNA/genetics ; Internet ; Phylogeny ; rRNA Operon/*genetics ; }, abstract = {The Ribosomal RNA Operon Copy Number Database (rrndb) is an Internet-accessible database containing annotated information on rRNA operon copy number among prokaryotes. Gene redundancy is uncommon in prokaryotic genomes, yet the rRNA genes can vary from one to as many as 15 copies. Despite the widespread use of 16S rRNA gene sequences for identification of prokaryotes, information on the number and sequence of individual rRNA genes in a genome is not readily accessible. In an attempt to understand the evolutionary implications of rRNA operon redundancy, we have created a phylogenetically arranged report on rRNA gene copy number for a diverse collection of prokaryotic microorganisms. Each entry (organism) in the rrndb contains detailed information linked directly to external websites including the Ribosomal Database Project, GenBank, PubMed and several culture collections. Data contained in the rrndb will be valuable to researchers investigating microbial ecology and evolution using 16S rRNA gene sequences. The rrndb web site is directly accessible on the WWW at http://rrndb.cme. msu.edu.}, }
@article {pmid10627031, year = {1999}, author = {Szpirer, C and Top, E and Couturier, M and Mergeay, M}, title = {Retrotransfer or gene capture: a feature of conjugative plasmids, with ecological and evolutionary significance.}, journal = {Microbiology (Reading, England)}, volume = {145 (Pt 12)}, number = {}, pages = {3321-3329}, doi = {10.1099/00221287-145-12-3321}, pmid = {10627031}, issn = {1350-0872}, mesh = {Biological Evolution ; Chromosomes, Bacterial/genetics ; *Conjugation, Genetic ; Ecology ; *Gene Transfer Techniques ; Plasmids/*genetics ; }, }
@article {pmid10620718, year = {2000}, author = {Persson, C and Olsson, S and Jansson, H}, title = {Growth of Arthrobotrys superba from a birch wood resource base into soil determined by radioactive tracing.}, journal = {FEMS microbiology ecology}, volume = {31}, number = {1}, pages = {47-51}, doi = {10.1111/j.1574-6941.2000.tb00670.x}, pmid = {10620718}, issn = {1574-6941}, abstract = {The ability of a nematode-trapping fungus to establish in field soil is an important characteristic when considering its use as a biological control agent. The outgrowth of the nematode-trapping fungus Arthrobotrys superba from wood was recorded by labelling the fungus with [(14)C]3-O-methylglucose and [(32)P]orthophosphoric acid and by using the soil sprinkling method. The fungus reached a distance of 7-8 cm during 25 days in heat-treated (60 degrees C) soil, detected by either radioactive tracing or the soil sprinkling technique. The two labelled compounds were co-distributed at all sampling times (r(2)=0.946) which indicates that the glucose pool (as methylglucose) and phosphorus content were correlated throughout the mycelium. In natural, non-heat-treated soil the fungus reached a distance of 1.5 cm from one disc of birch wood after 30 days, while it reached 3.2 cm during the same period when the food base was a pile of five inoculated discs. The experiments showed, for the first time, that a nematophagous fungus, A. superba, can grow out into soil from a piece of wood and supported by nutrients translocated from the resource base to the edge of the mycelium.}, }
@article {pmid10618254, year = {2000}, author = {O'Connell, KP and Gustafson, AM and Lehmann, MD and Thomashow, MF}, title = {Identification of cold shock gene loci in Sinorhizobium meliloti by using a luxAB reporter transposon.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {1}, pages = {401-405}, pmid = {10618254}, issn = {0099-2240}, mesh = {Bacterial Proteins/*genetics/metabolism ; Cold Temperature ; *DNA Transposable Elements ; Genes, Reporter/*genetics ; Luciferases/*genetics/metabolism ; Mutagenesis, Insertional ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Sinorhizobium meliloti/*genetics/growth &amp; development ; }, abstract = {Using a luxAB reporter transposon, seven mutants of Sinorhizobium meliloti were identified as containing insertions in four cold shock loci. LuxAB activity was strongly induced (25- to 160-fold) after a temperature shift from 30 to 15 degrees C. The transposon and flanking host DNA from each mutant was cloned, and the nucleic acid sequence of the insertion site was determined. Unexpectedly, five of the seven luxAB mutants contained transposon insertions in the 16S and 23S rRNA genes of two of the three rrn operons of S. meliloti. Directed insertion of luxAB genes into each of the three rrn operons revealed that all three operons were similarly affected by cold shock. Two other insertions were found to be located downstream of a homolog of the major Escherichia coli cold shock gene, cspA. Although the cold shock loci were highly induced in response to a shift to low temperature, none of the insertions resulted in a statistically significant decrease in growth rate at 15 degrees C.}, }
@article {pmid10618253, year = {2000}, author = {O'Connell, KP and Thomashow, MF}, title = {Transcriptional organization and regulation of a polycistronic cold shock operon in Sinorhizobium meliloti RM1021 encoding homologs of the Escherichia coli major cold shock gene cspA and ribosomal protein gene rpsU.}, journal = {Applied and environmental microbiology}, volume = {66}, number = {1}, pages = {392-400}, pmid = {10618253}, issn = {0099-2240}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; Base Sequence ; Blotting, Northern ; Blotting, Southern ; *Gene Expression Regulation, Bacterial ; Luciferases/genetics/metabolism ; Molecular Sequence Data ; Operon ; Promoter Regions, Genetic ; Recombinant Fusion Proteins ; Ribosomal Proteins/*genetics/metabolism ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sinorhizobium meliloti/*genetics/metabolism ; *Transcription, Genetic ; }, abstract = {A homolog of the major eubacterial cold shock gene cspA was identified in Sinorhizobium meliloti RM1021 by luxAB reporter transposon mutagenesis. Here we further characterize the organization and regulation of this locus. DNA sequence analysis indicated that the locus includes three open reading frames (ORFs) encoding homologs corresponding to CspA, a novel 10.6-kDa polypeptide designated ORF2, and a homolog of the Escherichia coli ribosomal protein S21. Transcription analysis indicated that this locus produced two different-sized cspA-hybridizing transcripts upon cold shock, a 400-nucleotide (nt) RNA encoding cspA alone and a 1, 000-nt transcript encoding cspA-ORF2-rpsU. The sizes of the transcripts agreed with the location of the transcription start site determined by primer extension and the locations of two putative transcriptional terminators. The promoter of the cspA-ORF2-rpsU locus had -10 and -35 elements similar to the E. coli sigma(70) consensus promoter and, like the cspA locus of E. coli, included an AT-rich region upstream of the -35 hexamer. The promoter of the S. meliloti cspA locus was found to impart cold shock-induced mRNA accumulation. In addition, the 5'-untranslated region (5' UTR) was found to increase the fold induction of cspA transcripts after cold shock and depressed the level of luxAB mRNA prior to cold shock, another feature similar to cspA regulation in E. coli. No "cold box" was identified upstream of the S. meliloti cspA gene, however, and there was no other obvious sequence identity between the S. meliloti 5' UTR and that of E. coli. DNA hybridization analysis indicated that outside the cspA-ORF2-rpsU cold shock locus there are several additional cspA-like genes and a second rpsU homolog.}, }
@article {pmid10541791, year = {1999}, author = {Kelley, CA and Pakulski, JD and Sandvik, SL and Coffin, RB and Downer, RC and Aas, P and Lyons, MM and Jeffrey, WH}, title = {Phytoplanktonic and Bacterial Carbon Pools and Productivities in the Gerlache Strait, Antarctica, during Early Austral Spring.}, journal = {Microbial ecology}, volume = {38}, number = {3}, pages = {296-305}, doi = {10.1007/pl00021037}, pmid = {10541791}, issn = {1432-184X}, abstract = {Abstract Phytoplankton and bacterial biomass and productivities were investigated at four depths in the upper 500 m of the water column in the Gerlache Strait, Antarctica, during the prebloom period of early austral spring, from October 13 to November 4, 1995. The concentrations of all carbon pools were low, with the total particulate organic carbon (POC) concentration averaging 1.9 +/- 0.9 µM. Bacterial, protozoan, and phytoplankton carbon accounted for 21% of the total POC, indicating that detritus or unenumerated organisms comprised the bulk of the POC during this period. Larger zooplankton or protozoa, such as ciliates, may account for this difference, since microzooplankton can represent a significant fraction of the total microbial biomass. Primary and bacterial secondary production rates were also low, less than 300 and 30 ng C L(-1) h(-1), respectively. However, when production was normalized to either chlorophyll or bacterial cell number, rates were similar to those recorded during the spring bloom periods. This indicates that the cells were metabolically active during the prebloom period. Chlorophyll specific primary production averaged over the upper 80 m of the water column was 1.28 +/- 0.84 µg C µg chl(-1) h(-1), whereas the mean bacterial specific growth rate over the same depth interval was 0.34 +/- 0.24 d(-1). The overall production rates were low only because of the low abundance of cells during the prebloom period. When the site was reoccupied the following year, all measures of biomass and productivity were higher [36], emphasizing the large interannual variability in the Gerlache Strait.http://link.springer-ny.com/link/service/journals/00248/bibs/38n3p296.html</hea}, }
@article {pmid10541790, year = {1999}, author = {Gayte, X and Fontvieille, D and Wilkinson, KJ}, title = {Bacterial Stimulation in Mixed Cultures of Bacteria and Organic Carbon from River and Lake Waters.}, journal = {Microbial ecology}, volume = {38}, number = {3}, pages = {285-295}, doi = {10.1007/pl00021036}, pmid = {10541790}, issn = {1432-184X}, abstract = {Abstract Interactions between natural bacterial assemblages and dissolved organic carbon (DOC) were investigated in two complementary batch experiments. In the first, a positive relationship was found between the proportion of electron transport system (ETS) active bacteria and the diversity of DOC in microcosms enriched with an increasing number of organic substrates. In a second experiment, bacterial and nutrient dynamics were measured in microcosms with natural bacterial populations and organic matter from rivers and lakes of different trophic levels. The interactions between the bacterial assemblages and DOC from different sources was investigated using source systems (rivers or lakes) and blended (different proportions of river and lake water) batch cultures. In each experiment, the number of total and ETS-active bacteria, the fluorescein diacetate (FDA)-hydrolytic activity, and the total (DOC), biodegradable (BDOC) and refractory (RDOC) dissolved organic carbon were measured four times during 5 days. The results suggested that the temperature, more than trophic level, controlled planktonic bacterial production. Furthermore, bacterial activity was stimulated in micrososms where river and lake waters were mixed. For the oligotrophic microcosms, this observation can be explained by a greater diversity of the organic nutrients ("qualitative" stimulation of bacteria), whereas for the meso-eutrophic microcosms, the production of new pools of dissolved organic carbon (both biodegradable and total) could account for the observed "quantitative" stimulation of the bacteria. These experiments suggest that the mixing of bacteria and organic matter from two different systems can give rise to novel nutrient and bacterial dynamics that are likely similar to those that occur in river-lake ecotones.http://link.springer-ny.com/link/service/journals/00248/bibs/38n3p285.html</hea}, }
@article {pmid10541789, year = {1999}, author = {Dalmastri, C and Chiarini, L and Cantale, C and Bevivino, A and Tabacchioni, S}, title = {Soil Type and Maize Cultivar Affect the Genetic Diversity of Maize Root-Associated Burkholderia cepacia Populations.}, journal = {Microbial ecology}, volume = {38}, number = {3}, pages = {273-284}, doi = {10.1007/s002489900177}, pmid = {10541789}, issn = {1432-184X}, abstract = {Abstract Burkholderia cepacia populations associated with the Zea mays root system were investigated to assess the influence of soil type, maize cultivar, and root localization on the degree of their genetic diversity. A total of 180 B. cepacia isolates were identified by restriction analysis of the amplified 16S rDNA (ARDRA technique). The genetic diversity among B. cepacia isolates was analyzed by the random amplified polymorphic DNA (RAPD) technique, using the 10-mer primer AP5. The analysis of molecular variance (AMOVA) method was applied to estimate the variance components for the RAPD patterns. The results indicated that, among the factors studied, the soil was clearly the dominant one in affecting the genetic diversity of maize root-associated B. cepacia populations. In fact, the percentage of variation among populations was significantly higher between B. cepacia populations recovered from maize planted in different soils than between B. cepacia populations isolated from different maize cultivars and from distinct root compartments such as rhizoplane and rhizosphere. The analysis of the genetic relationships among B. cepacia isolates resulted in dendrograms showing bacterial populations with frequent recombinations and a nonclonal genetic structure. The dendrograms were also in agreement with the AMOVA results. We were able to group strains obtained from distinct soils on the basis of their origin, confirming that soil type had the major effect on the degree of genetic diversity of the maize root-associated B. cepacia populations analyzed. On the other hand, strains isolated from distinct root compartments exhibited a random distribution which confirmed that the rhizosphere and rhizoplane populations analyzed did not significantly differ in their genetic structure.http://link.springer-ny.com/link/service/journals/00248/bibs/38n3p273.html</hea}, }
@article {pmid10541788, year = {1999}, author = {Stepanauskas, R and Edling, H and Tranvik, LJ}, title = {Differential Dissolved Organic Nitrogen Availability and Bacterial Aminopeptidase Activity in Limnic and Marine Waters.}, journal = {Microbial ecology}, volume = {38}, number = {3}, pages = {264-272}, doi = {10.1007/s002489900176}, pmid = {10541788}, issn = {1432-184X}, abstract = {Abstract Nitrogen often limits primary production in marine ecosystems and its loading from terrestrial sources is the major cause of enhanced coastal eutrophication worldwide. About 70% of nitrogen transported by rivers globally is dissolved organic nitrogen (DON). Therefore, terrestrial DON is potentially an important component of the N dynamics in aquatic ecosystems, but the bioavailability of this organic nitrogen is poorly known. Bacterial extracellular hydrolysis of polymers is a bottleneck in the utilization of natural dissolved organic matter, mostly consisting of high molecular weight compounds. To study the bacterial utilization and extracellular enzymatic hydrolysis of DON, we developed a bioassay employing natural DON as the only N source, and N as the limiting nutrient. Bacterial cell density and activity of an unspecific aminopeptidase (AMPase) were followed in the cultures. Natural DON stimulated the cell-specific AMPase activity. Furthermore, refractory and humus-rich DOM caused a stronger stimulation than labile DOM. We propose that the previously reported inhibitory effect of humic substances on enzyme activity was outweighed by the induction of enzyme synthesis caused by refractory substrates. AMPase activity and the estimated DON bioavailability were more than twofold higher in seawater than in freshwater with identical substrate additions. This indicates that hydrolysis and turnover of land-derived DON is enhanced when it enters coastal marine waters, enabling it to support elevated bacterioplankton and phytoplankton growth.http://link.springer-ny.com/link/service/journals/00248/bibs/38n3p264.html</hea}, }
@article {pmid10541787, year = {1999}, author = {Kahn, WE and Wetzel, RG}, title = {Effects of Microscale Water Level Fluctuations and Altered Ultraviolet Radiation on Periphytic Microbiota.}, journal = {Microbial ecology}, volume = {38}, number = {3}, pages = {253-263}, doi = {10.1007/s002489900175}, pmid = {10541787}, issn = {1432-184X}, abstract = {Abstract Microscale fluctuations in water level (1-20 mm) are common on a diurnal basis in shallow (<5-10 cm) wetlands, coupled to evapotranspiration losses during the daytime in excess of groundwater resupply. These depth variations alter the intensity of UV irradiance reaching attached periphytic algal and bacterial microbial communities. Effects of alterations of UV irradiance by micro-changes in water level on periphytic microbiota were examined experimentally. Attached microbial communities, grown on glass fiber filters in situ in a natural wetland, were exposed experimentally to near-natural levels of UV irradiance of differing spectral quality. UV intensity was altered by varying the distance of the communities from the light source, changes in UV-attenuating natural dissolved organic matter (DOM), and small changes in water level (2 or 4 mm). Algal productivity and photosynthetic oxygen production were significantly reduced by small enhancements of UV-B radiation, by decreased water levels of only 2 mm, and by reductions in concentrations of DOM. UV-B had only small short-term effects on chlorophyll a, although small increases in water depth and DOM concentration reduced pigment damage. Experimental removal of UV-B during in situ growth indicated that algae could adapt to UV radiation during growth in natural environments. Microbial oxygen consumption and bacterial productivity and biomass were also lowered significantly by UV-B exposure, and damage decreased with small (2 mm) increases in water depth or in DOM concentration. Selective inhibitors of algal photosynthesis and production of released extracellular organic substrates caused a concomitant reduction in bacterial productivity and a significant increase in magnitude of UV-B damage to bacterial biomass. These effects suggested that metabolic interactions between the periphytic autotrophs and heterotrophs altered community responses to UV-B radiation. Microscale water level reductions, common on a diurnal basis in shallow wetlands, and associated increased UV intensity can result in rapid alterations in periphytic metabolism.http://link.springer-ny.com/link/service/journals/00248/bibs/38n3p253.html</hea}, }
@article {pmid10541786, year = {1999}, author = {Albertano, P and Urzì, C}, title = {Structural Interactions among Epilithic Cyanobacteria and Heterotrophic Microorganisms in Roman Hypogea.}, journal = {Microbial ecology}, volume = {38}, number = {3}, pages = {244-252}, doi = {10.1007/s002489900174}, pmid = {10541786}, issn = {1432-184X}, abstract = {Abstract Phototrophic microbial communities present in the Roman Catacombs were characterized and different species of terrestrial epilithic cyanobacteria were found to occur as dominant organisms. Eucapsis, Leptolyngbya, Scytonema, and Fischerella were the most frequently encountered cyanobacterial taxa, while a few species of green algae and the diatom Diadesmis gallica occurred in minor amounts. Streptomyces strains, a few genera of eubacteria, and to a lesser extent fungi were always present in the same microhabitats and contributed to the deterioration of stone surfaces. The combined use of light and electron microscopy evidenced the structural relationships among rod-shaped or filamentous bacteria and cyanobacterial cells, as well as the presence of polysaccharide capsules and sheaths, and of mineral precipitates on S. julianum filaments. The significance of the intimate association among the microorganisms was discussed in relation to the damage caused by the growth of biological patinas on stone surfaces.http://link.springer-ny.com/link/service/journals/00248/bibs/38n3p244.html</hea}, }
@article {pmid10541785, year = {1999}, author = {Lemke, MJ and Leff, LG}, title = {Bacterial Populations in an Anthropogenically Disturbed Stream: Comparison of Different Seasons.}, journal = {Microbial ecology}, volume = {38}, number = {3}, pages = {234-243}, doi = {10.1007/s002489900173}, pmid = {10541785}, issn = {1432-184X}, abstract = {Abstract To determine the effects of environmental changes on stream bacterial populations, assemblage- and population-level measurements were compared between an anthropogenically disturbed stream and an undisturbed reference stream during different seasons. Physical and chemical variables monitored at two disturbed sites from a stream affected by multiple environmental perturbations confirmed discernibly different water quality from three reference sites: two from an adjacent, undisturbed watershed and one from the headwaters of the polluted stream. Assemblage-level variables, including total number of bacteria, colony forming units, and number of Bacteria from in situ hybridization revealed only one statistically significant difference between disturbed and undisturbed sites. Population-level changes of three bacterial species, Burkholderia cepacia, Pseudomonas putida, and Acinetobacter calcoaceticus, were determined by colony hybridization with rDNA probes. Abundance of culturable A. calcoaceticus was higher at disturbed sites in November and February; B. cepacia and P. putida did not exhibit pollution-associated responses. In contrast, in situ hybridization indicated that there was more A. calcoaceticus at the reference sites in November and April, suggesting that culturability of the species increased at disturbed sites. To determine if differences among sites were attributable to changes in water quality among the streams, three bacterial strains isolated from the disturbed stream were grown for 64 h in flasks in water from disturbed and reference sites. As observed in the stream, A. calcoaceticus numbers increased in polluted stream water after an initial lag period of approximately 24 h. Our results indicate that although assemblage-level measurements of bacterial communities did not reflect environmental differences among sites, A. calcoaceticus population sizes differed between disturbed and reference sites, suggesting that anthropogenic disturbance can alter some bacterial populations and not others.http://link.springer-ny.com/link/service/journals/00248/bibs/38n3p234.html</hea}, }
@article {pmid10541784, year = {1999}, author = {McDonald, IR and Upton, M and Hall, G and Pickup, RW and Edwards, C and Saunders, JR and Ritchie, DA and Murrell, JC}, title = {Molecular Ecological Analysis of Methanogens and Methanotrophs in Blanket Bog Peat.}, journal = {Microbial ecology}, volume = {38}, number = {3}, pages = {225-233}, doi = {10.1007/s002489900172}, pmid = {10541784}, issn = {1432-184X}, abstract = {Abstract Methane production and methane oxidation potential were measured in a 30 cm peat core from the Moorhouse Nature Reserve, UK. The distribution of known groups of methanogens and methane oxidizing bacteria throughout this peat core was assessed. Using 16S rRNA gene retrieval and functional gene probing with genes encoding key proteins in methane oxidation and methanogenesis, several major groups of microorganisms were detected. Methane production and oxidation was detected in all depths of the peat core. PCR amplification and oligonucleotide probing experiments using DNA isolated from all sections of the peat core detected methanotrophs from the groups Methylosinus and Methylococcus and methanogens from the groups Methanosarcinaceae, Methanococcaceae, and Methanobacteriaceae. 16S rDNA sequences amplified with the Methylosinus-specific primer were shown to have a high degree of identity with 16S rDNA sequences previously detected in acidic environments. However, no methanogen sequences were detected by the probes available in this study in the sections of the peat core (above 7 cm) where the majority of methanogenesis occurred, either because of low methanogen numbers or because of the presence of novel methanogen sequences.http://link.springer-ny.com/link/service/journals/00248/bibs/38n3p225.html</hea}, }
@article {pmid10541783, year = {1999}, author = {Karthikeyan, S and Wolfaardt, GM and Korber, DR and Caldwell, DE}, title = {Functional and Structural Responses of a Degradative Microbial Community to Substrates with Varying Degrees of Complexity in Chemical Structure.}, journal = {Microbial ecology}, volume = {38}, number = {3}, pages = {215-224}, doi = {10.1007/s002489900171}, pmid = {10541783}, issn = {1432-184X}, abstract = {Abstract The objective of the present study was to determine whether cultivation of a degradative community on substrates with varying degrees of chlorination and complexity in chemical structure, as well as cultivation in batch and flow cell culture, would alter the community's functional capability. The community was isolated from oil-contaminated soil and maintained in the laboratory on 2,4,6-trichlorobenzoic acid for 5 months before its ability to grow on 15 different chemicals as sole carbon source was evaluated in batch and flow cell systems. While the community could grow and develop biofilms in flow cells on all the substrates, only 11 of the 15 substrates could support growth in batch culture. Although biofilm development was less extensive on chemicals such as pentachlorophenol (2.09% average area covered by biofilm; average biofilm depth = 3 µm) than on 2,4,6-trichlorobenzoic acid (50.84% area covered; biofilm depth = 6.4 µm), no correlation was observed between the degree of chlorination, or number of rings, and the number of planktonic cells or biofilm biomass. In contrast, physicochemical characteristics such as the octanol/water partition coefficient had a significant effect on the development of biofilm biomass. In the case of planktonic communities, the degree of chlorination and ring number also had no effect on the BIOLOG carbon utilization profiles of the resulting communities. Although the sessile communities generally clustered separately from their planktonic counterparts, principal component analysis of carbon utilization profiles of the sessile communities showed different grouping between growth on chlorinated and nonchlorinated substrates. Analysis of the degradative community maintained on 2,4,6-trichlorobenzoic acid over an extended period further showed that adaptation to a new chemical environment is a rather slow process, since the substrate utilization profiles did not stabilize even after 12 months. These results demonstrate the flexibility in metabolic ability and community structure found in microbial communities.http://link.springer-ny.com/link/service/journals/00248/bibs/38n3p215.html</hea}, }
@article {pmid10541782, year = {1999}, author = {Van Ommen Kloeke F,  and Geesey, GG}, title = {Localization and Identification of Populations of Phosphatase-Active Bacterial Cells Associated with Activated Sludge Flocs.}, journal = {Microbial ecology}, volume = {38}, number = {3}, pages = {201-214}, doi = {10.1007/s002489900170}, pmid = {10541782}, issn = {1432-184X}, abstract = {Abstract The majority of phosphatase (PO(4)ase) activity detected in fresh aerobic activated sludge from a municipal wastewater treatment plant was associated with suspended floc material. PO(4)ase activity appeared to be localized in discrete bacteria-containing areas of the floc matrix based on the distribution of nucleic acid-stained cells and precipitated fluorescent crystals produced as a result of reaction of the enzyme(s) with the artificial substrate ELFtrade mark-PO(4). Of the total floc-associated bacterial cells that stained positive with the nucleic acid-binding fluorochrome acridine orange (AO), 8.8 +/- 1.2% displayed PO(4)ase activity based on the proximity of AO-stained cells to precipitated ELF crystals. Using a 16S rRNA oligonucleotide probe specific for the cytophaga-flavobacteria group, it was determined that 17-20% of the floc-associated bacteria that probed positive also displayed PO(4)ase activity. Furthermore, 35-45% of the ELF fluorescence was associated with bacterial cells that probed positive for the cytophaga-flavobacteria group. The results suggest that the cytophaga-flavobacteria, as a group, is important in mediating the liberation of inorganic orthophosphate (P(i)) from phosphomonoesters of detrital organic phosphate (organic-P) in the aerobic activated sludge process of wastewater treatment.http://link.springer-ny.com/link/service/journals/00248/bibs/38n3p201.html</hea}, }
@article {pmid10541781, year = {1999}, author = {Velicer, GJ and Schmidt, TM and Lenski, RE}, title = {Application of Traditional and Phylogenetically Based Comparative Methods to Test for a Trade-off in Bacterial Growth Rate at Low versus High Substrate Concentration.}, journal = {Microbial ecology}, volume = {38}, number = {3}, pages = {191-200}, doi = {10.1007/s002489900169}, pmid = {10541781}, issn = {1432-184X}, abstract = {Abstract It is often hypothesized that those organisms that are superior competitors for sparse resources fare poorly in competition for abundant resources, and vice versa. If there is indeed such a systematic trade-off, then this has important implications for the choice of bacterial strains in bioremediation and other applications. We studied seven bacterial strains that can grow on either 2,4-dichlorophenoxyacetate (2,4-D) or succinate as a sole source of carbon. Growth rates were measured on each substrate at both low (5 µg/ml) and high (500 µg/ml) concentrations. We used two different methods to test the significance of correlations among growth rates, a traditional method that treats each strain as an independent observation and a newer method that takes into account phylogenetic relationships between strains, thereby avoiding spurious correlations caused by a lack of statistical independence of strains. In both 2,4-D and succinate, we observed significant positive correlations between growth rates measured at high and low substrate concentrations by the traditional comparative method. No significant correlations were detected after adjusting for the phylogenetic relationships among the strains. In neither case did we observe the negative correlation expected from a trade-off between growth rates at high and low substrate levels.http://link.springer-ny.com/link/service/journals/00248/bibs/38n3p191.html</hea}, }
@article {pmid10592216, year = {2000}, author = {Maidak, BL and Cole, JR and Lilburn, TG and Parker, CT and Saxman, PR and Stredwick, JM and Garrity, GM and Li, B and Olsen, GJ and Pramanik, S and Schmidt, TM and Tiedje, JM}, title = {The RDP (Ribosomal Database Project) continues.}, journal = {Nucleic acids research}, volume = {28}, number = {1}, pages = {173-174}, pmid = {10592216}, issn = {0305-1048}, mesh = {*Databases, Factual ; RNA, Ribosomal/*genetics ; Ribosomes/*metabolism ; }, abstract = {The Ribosomal Database Project (RDP-II), previously described by Maidak et al., continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 7.1 (September 17, 1999) included more than 10 700 small subunit rRNA sequences. More than 850 type strain sequences were identified and added to the prokaryotic alignment, bringing the total number of type sequences to 3324 representing 2460 different species. Availability of an RDP-II mirror site in Japan is also near completion. RDP-II provides aligned and annotated rRNA sequences, derived phylogenetic trees and taxonomic hierarchies, and analysis services through its WWW server (http://rdp.cme.msu.edu/). Analysis services include rRNA probe checking, approx-i-mate phylogenetic placement of user sequences, screening user sequences for possible chimeric rRNA sequences, automated alignment, production of similarity matrices and services to plan and analyze terminal restriction fragment length polymorphism (T-RFLP) experiments.}, }
@article {pmid10583981, year = {1999}, author = {D'Souza, TM and Merritt, CS and Reddy, CA}, title = {Lignin-modifying enzymes of the white rot basidiomycete Ganoderma lucidum.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {12}, pages = {5307-5313}, pmid = {10583981}, issn = {0099-2240}, mesh = {Basidiomycota/drug effects/*enzymology/growth &amp; development ; Gallic Acid/analogs &amp; derivatives/pharmacology ; Kinetics ; Laccase ; Lignin/*metabolism ; Oxidoreductases/biosynthesis/genetics/*metabolism ; Peroxidases/biosynthesis/*metabolism ; Species Specificity ; Trees/microbiology ; }, abstract = {Ganoderma lucidum, a white rot basidiomycete widely distributed worldwide, was studied for the production of the lignin-modifying enzymes laccase, manganese-dependent peroxidase (MnP), and lignin peroxidase (LiP). Laccase levels observed in high-nitrogen (HN; 24 mM N) shaken cultures were much greater than those seen in low-nitrogen (2.4 mM N), malt extract, or wood-grown cultures and those reported for most other white rot fungi to date. Laccase production was readily seen in cultures grown with pine or poplar (100-mesh-size ground wood) as the sole carbon and energy source. Cultures containing both pine and poplar showed 5- to 10-fold-higher levels of laccase than cultures containing pine or poplar alone. Since syringyl units are structural components important in poplar lignin and other hardwoods but much less so in pine lignin and other softwoods, pine cultures were supplemented with syringic acid, and this resulted in laccase levels comparable to those seen in pine-plus-poplar cultures. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of concentrated extracellular culture fluid from HN cultures showed two laccase activity bands (M(r) of 40,000 and 66, 000), whereas isoelectric focusing revealed five major laccase activity bands with estimated pIs of 3.0, 4.25, 4.5, 4.8, and 5.1. Low levels of MnP activity (approximately 100 U/liter) were detected in poplar-grown cultures but not in cultures grown with pine, with pine plus syringic acid, or in HN medium. No LiP activity was seen in any of the media tested; however, probing the genomic DNA with the LiP cDNA (CLG4) from the white rot fungus Phanerochaete chrysosporium showed distinct hybridization bands suggesting the presence of lip-like sequences in G. lucidum.}, }
@article {pmid10577191, year = {1999}, author = {Lloyd, D}, title = {Microbial ecology. How to avoid oxygen.}, journal = {Science (New York, N.Y.)}, volume = {286}, number = {5438}, pages = {249}, doi = {10.1126/science.286.5438.249}, pmid = {10577191}, issn = {0036-8075}, mesh = {Anaerobiosis ; Ecosystem ; Electron Transport ; Hot Temperature ; Hydrogen Peroxide/metabolism ; NADP/metabolism ; Oxidation-Reduction ; Oxidoreductases/*metabolism ; Oxygen/metabolism ; Pyrococcus/*enzymology/growth &amp; development/metabolism ; Rubredoxins/metabolism ; Superoxides/*metabolism ; Water/metabolism ; }, }
@article {pmid10555370, year = {1999}, author = {Strömpl, C and Tindall, BJ and Jarvis, GN and Lünsdorf, H and Moore, ER and Hippe, H}, title = {A re-evaluation of the taxonomy of the genus Anaerovibrio, with the reclassification of Anaerovibrio glycerini as Anaerosinus glycerini gen. nov., comb. nov., and Anaerovibrio burkinabensis as Anaeroarcus burkinensis [corrig.] gen. nov., comb. nov.}, journal = {International journal of systematic bacteriology}, volume = {49 Pt 4}, number = {}, pages = {1861-1872}, doi = {10.1099/00207713-49-4-1861}, pmid = {10555370}, issn = {0020-7713}, mesh = {Bacterial Typing Techniques ; Base Composition ; Benzoquinones/analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Fatty Acids/analysis ; Genes, rRNA ; Gram-Negative Anaerobic Bacteria/chemistry/*classification/physiology ; Lipids/analysis ; Microscopy, Electron ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Chemotaxonomic, electron microscopic and 16S rRNA gene sequence analyses of the three described species of the genus Anaerovibrio demonstrated only remote similarities to each other. The 16S rRNA gene sequence similarities between Anaerovibrio lipolytica, Anaerovibrio glycerini and Anaerovibrio burkinabensis and the derived phylogenetic relationships of the three species studied fell below genus level. All three species clustered within the Sporomusa-Pectinatus-Selenomonas phyletic group. Each species showed a distinct phospholipid pattern and whole-cell fatty acid distribution. Several isoprenologues of the lipoquinone 'lipid F' were found to differ in their quantitative distribution in the Anaerovibrio species. On the basis of these results, the new genera Anaerosinus gen. nov. and Anaeroarcus gen. nov. are proposed. The type species of Anaerosinus is Anaerosinus glycerini comb. nov., and the type species of Anaeroarcus is Anaeroarcus burkinensis [corrig.] comb. nov. The genus Anaerovibrio is consequently restricted to a single species, namely Anaerovibrio lipolyticus [corrig.]}, }
@article {pmid10543797, year = {1999}, author = {Hahn, MW and Höfle, MG}, title = {Flagellate predation on a bacterial model community: interplay of size-selective grazing, specific bacterial cell size, and bacterial community composition.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {11}, pages = {4863-4872}, pmid = {10543797}, issn = {0099-2240}, mesh = {Aeromonas/cytology/genetics/*physiology ; Comamonas/cytology/genetics/*physiology ; Eukaryota/cytology/genetics/*microbiology/*physiology ; Fluorescent Antibody Technique ; Fluorescent Dyes ; In Situ Hybridization, Fluorescence ; Indoles ; Pseudomonas/cytology/genetics/*physiology ; }, abstract = {The influence of grazing by the bacterivorous nanoflagellate Ochromonas sp. strain DS on the taxonomic and morphological structures of a complex bacterial community was studied in one-stage chemostat experiments. A bacterial community, consisting of at least 30 different strains, was fed with a complex carbon source under conditions of low growth rate (0.5 day(-1) when nongrazed) and low substrate concentration (9 mg liter(-1)). Before and after the introduction of the predator, the bacterial community composition was studied by in situ techniques (immunofluorescence microscopy and fluorescent in situ hybridization), as well as by cultivation on agar media. The cell sizes of nonspecifically stained and immunofluorescently labeled bacteria were measured by image analysis. Grazing by the flagellate caused a bidirectional change in the morphological structure of the community. Medium-size bacterial cells, which dominated the nongrazed community, were largely replaced by smaller cells, as well as by cells contained in large multicellular flocs. Cell morphological changes were combined with community taxonomic changes. After introduction of the flagellate, the dominating strains with medium-size cells were largely replaced by single-celled strains with smaller cells on the one hand and, on the other hand, by Pseudomonas sp. strain MWH1, which formed the large, floc-like forms. We assume that size-selective grazing was the major force controlling both the morphological and the taxonomic structures of the model community.}, }
@article {pmid10508639, year = {1999}, author = {Kuipers, OP}, title = {Genomics for food biotechnology: prospects of the use of high-throughput technologies for the improvement of food microorganisms.}, journal = {Current opinion in biotechnology}, volume = {10}, number = {5}, pages = {511-516}, doi = {10.1016/s0958-1669(99)00019-1}, pmid = {10508639}, issn = {0958-1669}, mesh = {Bacillus subtilis/genetics/metabolism ; Computational Biology ; *Food Microbiology ; Food Technology/*methods/trends ; Forecasting ; Gene Expression Regulation, Bacterial ; *Genetic Techniques ; Lactic Acid/metabolism ; Lactococcus/genetics/metabolism ; Proteins/chemistry/genetics ; Saccharomyces cerevisiae/genetics/metabolism ; Structure-Activity Relationship ; }, abstract = {Functional genomics is currently the most effective approach for increasing the knowledge at the molecular level of metabolic and adaptive processes in whole cells. High-throughput technologies, such as DNA microarrays, and improved two-dimensional electrophoresis methods combined with tandem mass-spectroscopy, supported by bioinformatics, are useful tools for food biotechnology, which depends on detailed knowledge of the properties of food microbes (and pathogens) in their industrial, food and consumer environments. Genomics of food microbes, based on rapidly emerging genome sequence information, generates valuable knowledge that can be used for metabolic engineering, improving cell factories and development of novel preservation methods. Furthermore, pre- and probiotic studies, characterization of stress responses, studies of microbial ecology and, last but not least, development of novel risk assessment procedures will be facilitated.}, }
@article {pmid10508086, year = {1999}, author = {Hashsham, SA and Freedman, DL}, title = {Enhanced biotransformation of carbon tetrachloride by Acetobacterium woodii upon addition of hydroxocobalamin and fructose.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {10}, pages = {4537-4542}, pmid = {10508086}, issn = {0099-2240}, mesh = {Bacteria, Anaerobic/*metabolism ; Biotransformation ; Carbon Tetrachloride/*pharmacokinetics ; Fructose/*pharmacology ; Hydroxocobalamin/*pharmacology ; }, abstract = {The objective of this study was to evaluate the effect of hydroxocobalamin (OH-Cbl) on transformation of high concentrations of carbon tetrachloride (CT) by Acetobacterium woodii (ATCC 29683). Complete transformation of 470 microM (72 mg/liter [aqueous]) CT was achieved by A. woodii within 2.5 days, when 10 microM OH-Cbl was added along with 25.2 mM fructose. This was approximately 30 times faster than A. woodii cultures (live or autoclaved) and medium that did not receive OH-Cbl and 5 times faster than those controls that did receive OH-Cbl, but either live A. woodii or fructose was missing. CT transformation in treatments with only OH-Cbl was indicative of the important contribution of nonenzymatic reactions. Besides increasing the rate of CT transformation, addition of fructose and OH-Cbl to live cultures increased the percentage of [(14)C]CT transformed to (14)CO(2) (up to 31%) and (14)C-labeled soluble materials (principally L-lactate and acetate), while decreasing the percentage of CT reduced to chloroform and abiotically transformed to carbon disulfide. (14)CS(2) represented more than 35% of the [(14)C]CT in the presence of reduced medium and OH-Cbl. Conversion of CT to CO was a predominant pathway in formation of CO(2) in the presence of live cells and added fructose and OH-Cbl. These results indicate that the rate and distribution of products during cometabolic transformation of CT by A. woodii can be improved by the addition of fructose and OH-Cbl.}, }
@article {pmid10482536, year = {1999}, author = {Hogan, DA and Auchtung, TA and Hausinger, RP}, title = {Cloning and characterization of a sulfonate/alpha-ketoglutarate dioxygenase from Saccharomyces cerevisiae.}, journal = {Journal of bacteriology}, volume = {181}, number = {18}, pages = {5876-5879}, pmid = {10482536}, issn = {0021-9193}, support = {T32-GM08350/GM/NIGMS NIH HHS/United States ; }, mesh = {Chromosomes, Fungal/genetics ; Cloning, Molecular ; Cupriavidus necator/genetics ; Dioxygenases ; Escherichia coli/genetics ; Kinetics ; Mixed Function Oxygenases/genetics/isolation &amp; purification/*metabolism ; Mutagenesis ; Open Reading Frames ; Recombinant Proteins/isolation &amp; purification/metabolism ; Saccharomyces cerevisiae/*enzymology/*genetics ; *Saccharomyces cerevisiae Proteins ; Sequence Deletion ; Substrate Specificity ; }, abstract = {The Saccharomyces cerevisiae open reading frame YLL057c is predicted to encode a gene product with 31.5% amino acid sequence identity to Escherichia coli taurine/alpha-ketoglutarate dioxygenase and 27% identity to Ralstonia eutropha TfdA, a herbicide-degrading enzyme. Purified recombinant yeast protein is shown to be an Fe(II)-dependent sulfonate/alpha-ketoglutarate dioxygenase. Although taurine is a poor substrate, a variety of other sulfonates are utilized, with the best natural substrates being isethionate and taurocholate. Disruption of the gene encoding this enzyme negatively affects the use of isethionate and taurine as sulfur sources by S. cerevisiae, providing strong evidence that YLL057c plays a role in sulfonate catabolism.}, }
@article {pmid10481172, year = {1999}, author = {Rondon, MR and Goodman, RM and Handelsman, J}, title = {The Earth's bounty: assessing and accessing soil microbial diversity.}, journal = {Trends in biotechnology}, volume = {17}, number = {10}, pages = {403-409}, doi = {10.1016/s0167-7799(99)01352-9}, pmid = {10481172}, issn = {0167-7799}, support = {1F32GM1887101A1/GM/NIGMS NIH HHS/United States ; 1RO3AI42786-01/AI/NIAID NIH HHS/United States ; }, mesh = {Cloning, Molecular ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; *Earth, Planet ; *Soil Microbiology ; Species Specificity ; }, abstract = {The study of microbial diversity represents a major opportunity for advances in biology and biotechnology. Recent progress in molecular microbial ecology shows that the extent of microbial diversity in nature is far greater than previously thought. Here, we discuss methods to analyse microorganisms from natural environments without culturing them and new approaches for gaining access to the genetic and chemical resources of these microorganisms.}, }
@article {pmid10473415, year = {1999}, author = {Löffler, FE and Tiedje, JM and Sanford, RA}, title = {Fraction of electrons consumed in electron acceptor reduction and hydrogen thresholds as indicators of halorespiratory physiology.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {9}, pages = {4049-4056}, pmid = {10473415}, issn = {0099-2240}, mesh = {Chlorobenzoates/metabolism ; Chlorophenols/metabolism ; Electron Transport ; Gram-Negative Anaerobic Bacteria/growth &amp; development/*metabolism ; Hydrocarbons, Chlorinated/*metabolism ; Hydrogen/*metabolism ; Hydroxybenzoates/metabolism ; Oxidation-Reduction ; Propane/analogs &amp; derivatives/metabolism ; Tetrachloroethylene/metabolism ; Vinyl Chloride/metabolism ; }, abstract = {Measurements of the hydrogen consumption threshold and the tracking of electrons transferred to the chlorinated electron acceptor (f(e)) reliably detected chlororespiratory physiology in both mixed cultures and pure cultures capable of using tetrachloroethene, cis-1, 2-dichloroethene, vinyl chloride, 2-chlorophenol, 3-chlorobenzoate, 3-chloro-4-hydroxybenzoate, or 1,2-dichloropropane as an electron acceptor. Hydrogen was consumed to significantly lower threshold concentrations of less than 0.4 ppmv compared with the values obtained for the same cultures without a chlorinated compound as an electron acceptor. The f(e) values ranged from 0.63 to 0.7, values which are in good agreement with theoretical calculations based on the thermodynamics of reductive dechlorination as the terminal electron-accepting process. In contrast, a mixed methanogenic culture that cometabolized 3-chlorophenol exhibited a significantly lower f(e) value, 0.012.}, }
@article {pmid10462633, year = {1999}, author = {Hosein, IK and Hill, DW and Hatfield, RH}, title = {Controversies in the prevention of neurosurgical infection.}, journal = {The Journal of hospital infection}, volume = {43}, number = {1}, pages = {5-11}, doi = {10.1053/jhin.1999.0606}, pmid = {10462633}, issn = {0195-6701}, mesh = {Antibiotic Prophylaxis ; Cross Infection/*prevention &amp; control ; Hospitals ; Humans ; Infection Control/*methods ; *Neurosurgical Procedures ; Risk Factors ; Surgical Wound Infection/*prevention &amp; control ; United Kingdom ; }, abstract = {Amongst post-operative infections, those associated with neurosurgery are of particular significance in view of their proximity to, or location within, the central nervous system. Superficial surgical site infections may be complicated by osteomyelitis of the calvarium and deeper extension to the meninges and cerebral parenchyma. The prevention, diagnosis and management of infections associated with implant devices provide similar challenges to those faced in orthopaedic and cardiac surgery. Whilst some consensus exists regarding the need for antimicrobial prophylaxis in the latter two disciplines, its place in neurosurgery remains controversial. When prophylaxis is considered, choice of antimicrobial agents should take account of up-to-date local information in relation to the relevant microbial ecology in hospitals and in the community setting. The potential for spread of blood-borne virus infections and transmissible spongiform encephalopathies in relation to neurosurgery must also be considered and it should be ensured that appropriate preventive strategies are in place.}, }
@article {pmid10461377, year = {1999}, author = {Gomez, F and Amils, R and Marin, I}, title = {Bioremoval of organic and inorganic sulphur from coal samples.}, journal = {Applied microbiology and biotechnology}, volume = {52}, number = {1}, pages = {118-121}, doi = {10.1007/s002530051497}, pmid = {10461377}, issn = {1432-0614}, abstract = {The microbial ecology of different Spanish coal samples has been studied. Several bacteria have been isolated from enrichment cultures and characterised and their biodesulphurization abilities evaluated. Using morphological and physiological properties, different isolates have been related to species of the Xanthomonas, Pseudomonas, Chryseomonas and Moraxella genera. Some of the isolates, B(30)15 and T(30)10, gave important levels of organic desulphurization, close to 70%. Other isolates, B(30)7 and B(30)8, were able to remove inorganic sulphur with high efficiencies, over 67%. One of the isolates, B(30)10, metabolically related to Xanthomonas maltophila, was able to remove both organic and inorganic sulphur at neutral pH, with efficiencies of 69% and 68% respectively. The results obtained underline the potential use of some of these strains for industrial coal desulphurization processes.}, }
@article {pmid10460885, year = {1999}, author = {Jonkers, HM and Jansen, M and Van der Maarel MJ,  and Van Gemerden H, }, title = {Aerobic turnover of dimethyl sulfide by the anoxygenic phototrophic bacterium thiocapsa roseopersicina.}, journal = {Archives of microbiology}, volume = {172}, number = {3}, pages = {150-156}, doi = {10.1007/s002030050754}, pmid = {10460885}, issn = {1432-072X}, abstract = {This is the first report describing the complete oxidation of dimethyl sulfide (DMS) to sulfate by an anoxygenic, phototrophic purple sulfur bacterium. Complete DMS oxidation was observed in cultures of Thiocapsa roseopersicina M11 incubated under oxic/light conditions, resulting in a yield of 30.1 mg protein mmol(-1). No oxidation of DMS occurred under anoxic/light conditions. Chloroform, methyl butyl ether, and 3-amino-1,2,4-triazole, which are specific inhibitors of aerobic DMS oxidation in thiobacilli and hyphomicrobia, did not affect DMS oxidation in strain M11. This could be due to limited transport of the inhibitors through the cell membrane. The growth yield on sulfide as sole electron donor was 22.2 mg protein mmol(-1) under anoxic/light conditions. Since aerobic respiration of sulfide would have resulted in yields lower than 22 mg protein mmol(-1), the higher yield on DMS under oxic/light conditions suggests that the methyl groups of DMS have served as an additional carbon source or as an electron donor in addition to the sulfide moiety. The kinetic parameters V(max) and K(m) for DMS oxidation under oxic/light conditions were 12.4 +/- 1.3 nmol (mg protein)(-1) min(-1) and 2 &amp;mgr;M, respectively. T. roseopersicina M11 also produced DMS by cleavage of dimethylsulfoniopropionate (DMSP). Specific DMSP cleavage rates increased with increasing initial substrate concentrations, suggesting that DMSP lyase was only partly induced at lower initial DMSP concentrations. A comparison of T. roseopersicina strains revealed that only strain M11 was able to oxidize DMS and cleave DMSP. Both strain M11 and strain 5811 accumulated DMSP intracellularly during growth, while strain 1711 showed neither of these characteristics. Phylogenetic comparison based on 16S rRNA gene sequence revealed a similarity of 99.0% between strain M11 and strain 5811, and 97.6% between strain M11 and strain 1711. DMS and DMSP utilization thus appear to be strain-specific.}, }
@article {pmid10458160, year = {1999}, author = {Lenski, RE and Ofria, C and Collier, TC and Adami, C}, title = {Genome complexity, robustness and genetic interactions in digital organisms.}, journal = {Nature}, volume = {400}, number = {6745}, pages = {661-664}, doi = {10.1038/23245}, pmid = {10458160}, issn = {0028-0836}, mesh = {Biological Evolution ; *Computer Simulation ; *Genome ; *Models, Genetic ; Mutation ; Reproduction ; *Software ; }, abstract = {Digital organisms are computer programs that self-replicate, mutate and adapt by natural selection. They offer an opportunity to test generalizations about living systems that may extend beyond the organic life that biologists usually study. Here we have generated two classes of digital organism: simple programs selected solely for rapid replication, and complex programs selected to perform mathematical operations that accelerate replication through a set of defined 'metabolic' rewards. To examine the differences in their genetic architecture, we introduced millions of single and multiple mutations into each organism and measured the effects on the organism's fitness. The complex organisms are more robust than the simple ones with respect to the average effects of single mutations. Interactions among mutations are common and usually yield higher fitness than predicted from the component mutations assuming multiplicative effects; such interactions are especially important in the complex organisms. Frequent interactions among mutations have also been seen in bacteria, fungi and fruitflies. Our findings support the view that interactions are a general feature of genetic systems.}, }
@article {pmid10441710, year = {1999}, author = {Servais, P and Courties, C and Lebaron, P and Troussellier, M}, title = {Coupling Bacterial Activity Measurements with Cell Sorting by Flow Cytometry.}, journal = {Microbial ecology}, volume = {38}, number = {2}, pages = {180-189}, doi = {10.1007/s002489900160}, pmid = {10441710}, issn = {1432-184X}, abstract = {> Abstract A new procedure to investigate the relationship between bacterial cell size and activity at the cellular level has been developed; it is based on the coupling of radioactive labeling of bacterial cells and cell sorting by flow cytometry after SYTO 13 staining. Before sorting, bacterial cells were incubated in the presence of tritiated leucine using a procedure similar to that used for measuring bacterial production by leucine incorporation and then stained with SYTO 13. Subpopulations of bacterial cells were sorted according to their average right-angle light scatter (RALS) and fluorescence. Average RALS was shown to be significantly related to the average biovolume. Experiments were performed on samples collected at different times in a Mediterranean seawater mesocosm enriched with nitrogen and phosphorus. At four sampling times, bacteria were sorted in two subpopulations (cells smaller and larger than 0.25 µm(3)). The results indicate that, at each sampling time, the growth rate of larger cells was higher than that of smaller cells. In order to confirm this tendency, cell sorting was performed on six subpopulations differing in average biovolume during the mesocosm follow-up. A clear increase of the bacterial growth rates was observed with increasing cell size for the conditions met in this enriched mesocosm.http://link.springer-ny.com/link/service/journals/00248/bibs/38n2p180.html}, }
@article {pmid10441709, year = {1999}, author = {Pennanen, T and Liski, J and Bååth, E and Kitunen, V and Uotila, J and Westman, CJ and Fritze, H}, title = {Structure of the Microbial Communities in Coniferous Forest Soils in Relation to Site Fertility and Stand Development Stage.}, journal = {Microbial ecology}, volume = {38}, number = {2}, pages = {168-179}, doi = {10.1007/s002489900161}, pmid = {10441709}, issn = {1432-184X}, abstract = {> Abstract The structure, biomass, and activity of the microbial community in the humus layer of boreal coniferous forest stands of different fertility were studied. The Scots pine dominated CT (Calluna vulgaris type) represented the lowest fertility, while VT (Vaccinium vitis-idaéa type), MT (Vaccinium myrtillus type), and OMT (Oxalis acetocella-Vaccinium myrtillus type) following this order, were more fertile types. The microbial community was studied more closely by sampling a succession gradient (from a treeless area to a 180-years-old Norway spruce stand) at the MT type site. The phospholipid fatty acid (PLFA) analysis revealed a gradual shift in the structure of the microbial community along the fertility gradient even though the total microbial biomass and respiration rate remained unchanged. The relative abundance of fungi decreased and that of bacteria increased with increasing fertility. The structure of the bacterial community also changed along the fertility gradient. Irrespective of a decrease in fungal biomass and change in bacterial community structure after clear-cutting, the PLFA analysis did not show strong differences in the microbial communities in the stands of different age growing on the MT type site. The spatial variation in the structure of the microbial community was studied at a MT type site. Semivariograms indicated that the bacterial biomass, the ratio between the fungal and bacterial biomasses, and the relative amount of PLFA 16:1omega5 were spatially autocorrelated within distances around 3 to 4 m. The total microbial and fungal biomasses were autocorrelated only up to 1 m. The spatial distribution of the humus microbial community was correlated mainly with the location of the trees, and consequently, with the forest floor vegetation.http://link.springer-ny.com/link/service/journals/00248/bibs/38n2p168.html}, }
@article {pmid10441708, year = {1999}, author = {Piceno, YM and Noble, PA and Lovell, CR}, title = {Spatial and Temporal Assessment of Diazotroph Assemblage Composition in Vegetated Salt Marsh Sediments Using Denaturing Gradient Gel Electrophoresis Analysis.}, journal = {Microbial ecology}, volume = {38}, number = {2}, pages = {157-167}, doi = {10.1007/s002489900164}, pmid = {10441708}, issn = {1432-184X}, abstract = {> Abstract Diazotroph assemblage compositions were assessed in rhizosphere sediments from the tall and short form Spartina alterniflora growth zones over an annual cycle. Sediment cores were collected for DNA extraction and nitrogenase (acetylene reduction) activity assays, and porewater samples were analyzed for several chemical parameters in March, June, September, and December 1997. These data were collected to determine if within- or between-zone differences in the diazotroph assemblage composition correlated with differences in key environmental variables or acetylene reduction activity. Acetylene reduction rates differed between zones and within a zone over an annual period. Soluble sulfide concentrations were higher in the short form S. alterniflora zone on all dates except those in June and differed within both zones on different sample dates. nifH sequences were recovered from rhizosphere sediment DNA by PCR amplification using nifH specific primers. These amplimers were analyzed using denaturing gradient gel electrophoresis (DGGE), and the resulting patterns were compared by neural network and linear discriminant analyses. Ten prominent amplimers, four of which were apparent heteroduplexes, were observed. DGGE banding profiles showed minor differences among sampling dates and between sample zones, but the overall banding pattern was remarkably consistent. This reflects overall similarity between the amplifiable diazotroph assemblages in the tall and short S. alterniflora growth zones and substantial seasonal stability in assemblage composition.http://link.springer-ny.com/link/service/journals/00248/bibs/38n2p157.html}, }
@article {pmid10441707, year = {1999}, author = {López-Archilla, AI and Amils, R}, title = {A Comparative Ecological Study of Two Acidic Rivers in Southwestern Spain.}, journal = {Microbial ecology}, volume = {38}, number = {2}, pages = {146-156}, doi = {10.1007/s002489900165}, pmid = {10441707}, issn = {1432-184X}, abstract = {> Abstract We have analyzed select physicochemical and biological characteristics of two acidic rivers, the Tinto and the Odiel, located in the Pyritic Belt of Southwestern Spain. Despite a common geography and geochemistry, they exhibit important differences. Most of the measured physicochemical parameters, especially pH and those related to conductivity (heavy metal concentrations), showed more extreme values in the Tinto than in the Odiel. However, it was at the microbiological level (fungal and bacterial populations) where both rivers showed the most important differences according to the statistical analysis of principal components. Lithoautotrophic bacteria were more abundant in the more acidic Tinto River and fungal diversity varied significantly from one river to the other.http://link.springer-ny.com/link/service/journals/00248/bibs/38n2p146.html}, }
@article {pmid10441706, year = {1999}, author = {Gurung, TB and Urabe, J}, title = {Temporal and Vertical Difference in Factors Limiting Growth Rate of Heterotrophic Bacteria in Lake Biwa.}, journal = {Microbial ecology}, volume = {38}, number = {2}, pages = {136-145}, doi = {10.1007/s002489900167}, pmid = {10441706}, issn = {1432-184X}, abstract = {> Abstract Dilution bioassays were performed to examine the seasonal and vertical difference in the relative importance of factors limiting growth of heterotrophic bacteria in Lake Biwa. The lake water diluted by 0.2 µm lake filtrate (1:6.6) was enriched either with glucose (C), inorganic phosphorus (P), ammonium nitrogen (N), amino acids (AA), or a combination of these, and incubated for 2 days at the depths where lake water was collected (2.5, 20 and 30 m depths). Experiments showed that at 2.5 m, P was the most deficient resource for bacterial growth, but the magnitude of P limitation depended on water temperature. Among others, amino acids showed a slight but significant stimulation of bacterial growth rates during the fall. At 20 and 30 m, however, growth stimulation by resource addition was rarely detected. Vertically reciprocal translocation experiments revealed that the growth rate was limited by low temperature rather than resource supply at the greater depths. The results support a simple view that bacterial growth rate is basically regulated by water temperature, but high growth rate is not realized in summer because of resource depletion. The present study suggests that both temperature and P supply play a crucial role in biogeochemical cycling of organic matter in Lake Biwa through the bacterial growth rate.http://link.springer-ny.com/link/service/journals/00248/bibs/38n2p136.html}, }
@article {pmid10441705, year = {1999}, author = {Konopka, A and Bercot, T and Nakatsu, C}, title = {Bacterioplankton Community Diversity in a Series of Thermally Stratified Lakes.}, journal = {Microbial ecology}, volume = {38}, number = {2}, pages = {126-135}, doi = {10.1007/s002489900166}, pmid = {10441705}, issn = {1432-184X}, abstract = {> Abstract The dominant members of the bacterioplankton community in a set of 10 small, thermally stratified lakes in northeastern Indiana were determined by denaturing gradient gel electrophoresis (DGGE) of a polymerase chain reaction amplified fragment of 16S rDNA. The variability in community composition was analyzed as function of vertical stratification (epilimnion vs metalimnion), time (July vs August samples), and geographical location. In 58 discrete samples, a range of 8-23 bands were detected (mean = 14, s.d. = 4). For all variables, sample pairs shared about 40-70% of bands. In comparisons between depth strata, pairs of oxic samples shared more bands than an oxic-anoxic pair. There was no obvious relationship between the geographical location of lakes (or their physical connection) and band sharing.http://link.springer-ny.com/link/service/journals/00248/bibs/38n2p126.html}, }
@article {pmid10441704, year = {1999}, author = {Yu, Z and Martin, VJ and Mohn, WW}, title = {Occurrence of Two Resin Acid-Degrading Bacteria and a Gene Encoding Resin Acid Biodegradation in Pulp and Paper Mill Effluent Biotreatment Systems Assayed by PCR.}, journal = {Microbial ecology}, volume = {38}, number = {2}, pages = {114-125}, doi = {10.1007/s002489900163}, pmid = {10441704}, issn = {1432-184X}, abstract = {> Abstract We examined the distribution of two dehydroabietic acid-degrading bacteria, Pseudomonas abietaniphila BKME-9 and Zoogloea resiniphila DhA-35, in biotreatment systems for pulp and paper mill effluents (PPMEs) using PCR assays. These two bacteria were first isolated from two PPME biotreatment systems and can degrade both dehydroabietic acid (DhA) and other abietane resin acids. We also examined the distribution of a catabolic gene, ditA1, encoding the alpha subunit of an aromatic ring-hydroxylating dioxygenase involved in DhA degradation by BKME-9. PCR primers specific for the 16S rDNA of BKME-9 and of DhA-35 and specific for ditA1 were used. Among 3 laboratory- and 17 full-scale PPME biotreatment systems, 10 contained phylotype BKME-9, 3 contained phylotype DhA-35, and 11 contained ditA1, indicating the wider distribution of phylotype BKME-9 than of phylotype DhA-35. Both phylotype BKME-9 and ditA1 were detected in the biotreatment system from which BKME-9 was originally isolated in 1994, suggesting the persistance of BKME-9 in that biotreatment system. The detection limit of the PCR assay was one cell per PCR reaction, which corresponds to one BKME-9 cell per 6 x 10(7) total sludge bacteria. A competitive PCR assay indicated that ditA1 ranged from 51 to 250 copies/mg of dry biomass. BKME-9 appears to contribute to the biodegration of resin acids in some PPME biotreatment systems. Using degenerate PCR primers and touchdown PCR, we obtained from our DhA-degrading strain collection six DNA sequences putatively homologous to that of ditA1. Cluster analysis of these DNA sequences suggests that ditA1 encodes a representative of a novel class of dioxygenase enzymes.http://link.springer-ny.com/link/service/journals/00248/bibs/38n2p114.html}, }
@article {pmid10441703, year = {1999}, author = {Fogel, GB and Collins, CR and Li, J and Brunk, CF}, title = {Prokaryotic Genome Size and SSU rDNA Copy Number: Estimation of Microbial Relative Abundance from a Mixed Population.}, journal = {Microbial ecology}, volume = {38}, number = {2}, pages = {93-113}, doi = {10.1007/s002489900162}, pmid = {10441703}, issn = {1432-184X}, abstract = {> Abstract Determination of the relative abundance of a specific prokaryote in an environmental sample is of major interest in applied and environmental microbiology. Relative abundance can be calculated using knowledge of SSU rDNA copy number, amount of SSU rDNA in the sample, and a weighted average estimate of the genome sizes for organisms in the original sample. By surveying the literature, we provide estimates of genome size and SSU rDNA copy number for 303 and 101 prokaryotes, respectively. This compilation can be used to make reasonable estimates for a wide range of organisms in the calculation of relative abundance. A statistical analysis suggests that no correlation exists between genome size and SSU rDNA copy number. A phylogenetic analysis is used to offer insights into the evolution of both genome size and SSU rDNA copy number.http://link.springer-ny.com/link/service/journals/00248/bibs/38n2p93.html}, }
@article {pmid10427068, year = {1999}, author = {Fernández, A and Huang, S and Seston, S and Xing, J and Hickey, R and Criddle, C and Tiedje, J}, title = {How stable is stable? Function versus community composition.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {8}, pages = {3697-3704}, pmid = {10427068}, issn = {0099-2240}, mesh = {Bacteria/genetics/isolation &amp; purification/metabolism ; Base Sequence ; *Bioreactors ; DNA Primers/genetics ; DNA, Archaeal/genetics/isolation &amp; purification ; DNA, Bacterial/genetics/isolation &amp; purification ; Ecosystem ; Methanobacterium/genetics/isolation &amp; purification/metabolism ; Methanosarcina/genetics/isolation &amp; purification/metabolism ; Molecular Sequence Data ; Phylogeny ; }, abstract = {The microbial community dynamics of a functionally stable, well-mixed, methanogenic reactor fed with glucose were analyzed over a 605-day period. The reactor maintained constant pH and chemical oxygen demand removal during this period. Thirty-six rrn clones from each of seven sampling events were analyzed by amplified ribosomal DNA restriction analysis (ARDRA) for the Bacteria and Archaea domains and by sequence analysis of dominant members of the community. Operational taxonomic units (OTUs), distinguished as unique ARDRA patterns, showed reproducible distribution for three sample replicates. The highest diversity was observed in the Bacteria domain. The 16S ribosomal DNA Bacteria clone library contained 75 OTUs, with the dominant OTU accounting for 13% of the total clones, but just 21 Archaea OTUs were found, and the most prominent OTU represented 50% of the clones from the respective library. Succession in methanogenic populations was observed, and two periods were distinguished: in the first, Methanobacterium formicicum was dominant, and in the second, Methanosarcina mazei and a Methanobacterium bryantii-related organism were dominant. Higher variability in Bacteria populations was detected, and the temporal OTU distribution suggested a chaotic pattern. Although dominant OTUs were constantly replaced from one sampling point to the next, phylogenetic analysis indicated that inferred physiologic changes in the community were not as dramatic as were genetic changes. Seven of eight dominant OTUs during the first period clustered with the spirochete group, although a cyclic pattern of substitution occurred among members within this order. A more flexible community structure characterized the second period, since a sequential replacement of a Eubacterium-related organism by an unrelated deep-branched organism and finally by a Propionibacterium-like species was observed. Metabolic differences among the dominant fermenters detected suggest that changes in carbon and electron flow occurred during the stable performance and indicate that an extremely dynamic community can maintain a stable ecosystem function.}, }
@article {pmid10427058, year = {1999}, author = {Nüsslein, K and Tiedje, JM}, title = {Soil bacterial community shift correlated with change from forest to pasture vegetation in a tropical soil.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {8}, pages = {3622-3626}, pmid = {10427058}, issn = {0099-2240}, mesh = {Agriculture ; Bacteria/classification/genetics/*isolation &amp; purification ; Base Composition ; DNA, Bacterial/chemistry/genetics/isolation &amp; purification ; Ecosystem ; Molecular Sequence Data ; *Soil Microbiology ; Trees ; Tropical Climate ; }, abstract = {The change in vegetative cover of a Hawaiian soil from forest to pasture led to significant changes in the composition of the soil bacterial community. DNAs were extracted from both soil habitats and compared for the abundance of guanine-plus-cytosine (G+C) content, by analysis of abundance of phylotypes of small-subunit ribosomal DNA (SSU rDNA) amplified from fractions with 63 and 35% G+C contents, and by phylogenetic analysis of the dominant rDNA clones in the 63% G+C content fraction. All three methods showed differences between the forest and pasture habitats, providing evidence that vegetation had a strong influence on microbial community composition at three levels of taxon resolution. The forest soil DNA had a peak in G+C content of 61%, while the DNA of the pasture soil had a peak in G+C content of 67%. None of the dominant phylotypes found in the forest soil were detected in the pasture soil. For the 63% G+C fraction SSU rDNA sequence analysis of the three most dominant members revealed that their phyla changed from Fibrobacter and Syntrophomonas assemblages in the forest soil to Burkholderia and Rhizobium-Agrobacterium assemblages in the pasture soil.}, }
@article {pmid10418014, year = {1999}, author = {Honderlick, P and Saheb, F and Cahen, P}, title = {Emergence of multidrug-resistant Enterobacter cloacae: nosocomial outbreak or change of microbial ecology?.}, journal = {Pathologie-biologie}, volume = {47}, number = {5}, pages = {437-439}, pmid = {10418014}, issn = {0369-8114}, mesh = {Cephalosporin Resistance ; Cephalosporins/therapeutic use ; Cross Infection/drug therapy/*microbiology ; *Drug Resistance, Multiple ; Enterobacter cloacae/classification/*drug effects/isolation &amp; purification ; Enterobacteriaceae Infections/drug therapy/*microbiology/*transmission ; Humans ; Retrospective Studies ; }, abstract = {Frequent selection of mutants resistant to extended and broad spectrum cephalosporins in Enterobacter cloacae is observed in hospital. As we noticed an unusual number of isolates of these strains and to answer the question arose whether these Enterobacter had a common source, we retrospectivally studied 56 strains collected in 11 wards of the hospital. Using PFGE with Spe 1 restriction analysis we identified a prevalent clone (11 patients) dispatched in 8 wards. We also obviously proved cross-contamination patients to patients with other clones. PFGE allow us to point out that clonal Enterobacter cloacae has taken place in our hospital, even if there is no real outbreak. A reinforcement of basic hygienic measures and a control of antibiotics prescription seemed very important to jugulate the sudden increase of multiresistant Enterobacter cloacae prevalence.}, }
@article {pmid10417574, year = {1999}, author = {Okada, M and Bothin, C and Kanazawa, K and Midtvedt, T}, title = {Experimental study of the influence of intestinal flora on the healing of intestinal anastomoses.}, journal = {The British journal of surgery}, volume = {86}, number = {7}, pages = {961-965}, doi = {10.1046/j.1365-2168.1999.01161.x}, pmid = {10417574}, issn = {0007-1323}, mesh = {*Anastomosis, Surgical ; Animals ; Body Weight ; *Escherichia coli ; Female ; Hydroxyproline/analysis ; Intestines/*microbiology/surgery ; *Lactobacillus acidophilus ; Male ; Pressure ; Rats ; Specific Pathogen-Free Organisms ; Survival Analysis ; Wound Healing/*physiology ; }, abstract = {BACKGROUND: The beneficial effects of the normal intestinal flora on wound healing in the skin have already been confirmed, and this study attempted to elucidate the influence of the intestinal flora on the healing process in intestinal anastomoses.<br><br>METHODS: Five groups of rats were studied: germ-free, conventional, monocontaminated with Lactobacillus acidophilus La5 or Escherichia coli X7 and ex-germ-free (conventionalized). All animals underwent ileal and colonic resections followed by anastomoses. Seven days later they were killed and the bursting pressure and hydroxyproline concentration of the anastomoses were measured. The microbiological status of the animals was confirmed weekly.<br><br>RESULTS: No bacteria were detected in the germ-free rats and no other bacteria were found in the monocontaminated animals. Conventional rats had a significantly higher anastomotic bursting pressure both in the ileum compared with rats monocontaminated with L. acidophilus, and in the colon compared with germ-free rats. The ex-germ-free rats also showed a significantly higher bursting pressure than germ-free animals and rats monocontaminated with either L. acidophilus or E. coli in the ileum and colon.<br><br>CONCLUSION: The presence of the intestinal flora enhanced the healing of intestinal anastomoses. The data suggest that this effect depends on differences in the types of bacteria in the intestine.}, }
@article {pmid10395460, year = {1999}, author = {Konopka, A and Zakharova, T}, title = {Quantification of bacterial lead resistance via activity assays.}, journal = {Journal of microbiological methods}, volume = {37}, number = {1}, pages = {17-22}, doi = {10.1016/s0167-7012(99)00032-9}, pmid = {10395460}, issn = {0167-7012}, mesh = {Arthrobacter/growth &amp; development/metabolism ; Bacteria/growth &amp; development/*metabolism ; Culture Media/chemistry ; Escherichia coli/growth &amp; development/metabolism ; Lead/*metabolism/toxicity ; Microbial Sensitivity Tests ; Pseudomonas putida/growth &amp; development/metabolism ; }, abstract = {The level of microbial resistance to heavy metals is an important issue for the microbial ecology of heavy metal-contaminated habitats. However, assays based upon growth in nutrient media will overestimate the resistance level due to metal ion interactions with inorganic and organic components. The analysis of Pb-resistant bacteria isolated from soils containing up to 38 mmol total Pb x kg(-1) indicated that PYT80B medium which did not contain inorganic salts, contained low amounts of organic matter, and was buffered with a molecule that did not interact with metal ions (2-N-morpholinoethanesulfonic acid (MES)) provided the lowest estimates of lead resistance. However, better results were obtained by assaying metabolic activity (aerobic respiration) of resting cells suspended in 10 mM MES. By this criterion, 50% inhibition of Arthrobacter JS7 was found at 37 microM Pb(NO3)2. The effects of Pb+2 concentrations upon respiration of resting cells and growth rate in PYT80B medium were similar. The activity assay also showed that metal resistance was induced to higher levels when Arthrobacter JS7 was grown in the presence of Pb.}, }
@article {pmid10388718, year = {1999}, author = {Höfle, MG and Haas, H and Dominik, K}, title = {Seasonal dynamics of bacterioplankton community structure in a eutrophic lake as determined by 5S rRNA analysis.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {7}, pages = {3164-3174}, pmid = {10388718}, issn = {0099-2240}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; *Ecosystem ; Fresh Water/*microbiology ; Molecular Sequence Data ; Phylogeny ; Plankton ; RNA, Ribosomal, 5S/*analysis/chemistry/genetics ; *Seasons ; Water Microbiology ; }, abstract = {Community structure of bacterioplankton was studied during the major growth season for phytoplankton (April to October) in the epilimnion of a temperate eutrophic lake (Lake Plusssee, northern Germany) by using comparative 5S rRNA analysis. Estimates of the relative abundances of single taxonomic groups were made on the basis of the amounts of single 5S rRNA bands obtained after high-resolution electrophoresis of RNA directly from the bacterioplankton. Full-sequence analysis of single environmental 5S rRNAs enabled the identification of single taxonomic groups of bacteria. Comparison of partial 5S rRNA sequences allowed the detection of changes of single taxa over time. Overall, the whole bacterioplankton community showed two to eight abundant (>4% of the total 5S rRNA) taxa. A distinctive seasonal succession was observed in the taxonomic structure of this pelagic community. A rather-stable community structure, with seven to eight different taxonomic units, was observed beginning in April during the spring phytoplankton bloom. A strong reduction in this diversity occurred at the beginning of the clear-water phase (early May), when only two to four abundant taxa were observed, with one taxon dominating (up to 72% of the total 5S rRNA). The community structure during summer stagnation (June and July) was characterized by frequent changes of different dominating taxa. During late summer, a dinoflagellate bloom (Ceratium hirudinella) occurred, with Comamonas acidovorans (beta-subclass of the class Proteobacteria) becoming the dominant bacterial species (average abundance of 43% of the total 5S rRNA). Finally, the seasonal dynamics of the community structure of bacterioplankton were compared with the abundances of other major groups of the aquatic food web, such as phyto- and zooplankton, revealing that strong grazing pressure by zooplankton can reduce microbial diversity substantially in pelagic environments.}, }
@article {pmid10388694, year = {1999}, author = {Bruns, MA and Stephen, JR and Kowalchuk, GA and Prosser, JI and Paul, EA}, title = {Comparative diversity of ammonia oxidizer 16S rRNA gene sequences in native, tilled, and successional soils.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {7}, pages = {2994-3000}, pmid = {10388694}, issn = {0099-2240}, mesh = {Ammonia/*metabolism ; Cloning, Molecular ; Colony Count, Microbial ; DNA, Bacterial/genetics/isolation &amp; purification ; DNA, Ribosomal/analysis ; Ecosystem ; Electrophoresis/methods ; *Genes, rRNA ; *Genetic Variation ; Gram-Negative Chemolithotrophic Bacteria/*genetics/*isolation &amp; purification ; Molecular Sequence Data ; Nitrosomonas/genetics/isolation &amp; purification ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Autotrophic ammonia oxidizer (AAO) populations in soils from native, tilled, and successional treatments at the Kellogg Biological Station Long-Term Ecological Research site in southwestern Michigan were compared to assess effects of disturbance on these bacteria. N fertilization effects on AAO populations were also evaluated with soils from fertilized microplots within the successional treatments. Population structures were characterized by PCR amplification of microbial community DNA with group-specific 16S rRNA gene (rDNA) primers, cloning of PCR products and clone hybridizations with group-specific probes, phylogenetic analysis of partial 16S rDNA sequences, and denaturing gradient gel electrophoresis (DGGE) analysis. Population sizes were estimated by using most-probable-number (MPN) media containing varied concentrations of ammonium sulfate. Tilled soils contained higher numbers than did native soils of culturable AAOs that were less sensitive to different ammonium concentrations in MPN media. Compared to sequences from native soils, partial 16S rDNA sequences from tilled soils were less diverse and grouped exclusively within Nitrosospira cluster 3. Native soils yielded sequences representing three different AAO clusters. Probes for Nitrosospira cluster 3 hybridized with DGGE blots from tilled and fertilized successional soils but not with blots from native or unfertilized successional soils. Hybridization results thus suggested a positive association between the Nitrosospira cluster 3 subgroup and soils amended with inorganic N. DGGE patterns for soils sampled from replicated plots of each treatment were nearly identical for tilled and native soils in both sampling years, indicating spatial and temporal reproducibility based on treatment.}, }
@article {pmid10388669, year = {1999}, author = {Watanabe, K and Teramoto, M and Harayama, S}, title = {An outbreak of nonflocculating catabolic populations caused the breakdown of a phenol-digesting activated-sludge process.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {7}, pages = {2813-2819}, pmid = {10388669}, issn = {0099-2240}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; DNA Gyrase ; DNA Topoisomerases, Type II/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Ecosystem ; Electrophoresis, Agar Gel/methods ; Molecular Sequence Data ; Phenol/*metabolism ; Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; }, abstract = {Activated sludge was fed phenol as the sole carbon source, and the phenol-loading rate was increased stepwise from 0.5 to 1.0 g liter-1 day-1 and then to 1.5 g liter-1 day-1. After the loading rate was increased to 1.5 g liter-1 day-1, nonflocculating bacteria outgrew the sludge, and the activated-sludge process broke down within 1 week. The bacterial population structure of the activated sludge was analyzed by temperature gradient gel electrophoresis (TGGE) of PCR-amplified 16S ribosomal DNA (rDNA) fragments. We found that the population diversity decreased as the phenol-loading rate increased and that two populations (designated populations R6 and R10) predominated in the sludge during the last several days before breakdown. The R6 population was present under the low-phenol-loading-rate conditions, while the R10 population was present only after the loading rate was increased to 1.5 g liter-1 day-1. A total of 41 bacterial strains with different repetitive extragenic palindromic sequence PCR patterns were isolated from the activated sludge under different phenol-loading conditions, and the 16S rDNA and gyrB fragments of these strains were PCR amplified and sequenced. Some bacterial isolates could be associated with major TGGE bands by comparing the 16S rDNA sequences. All of the bacterial strains affiliated with the R6 population had almost identical 16S rDNA sequences, while the gyrB phylogenetic analysis divided these strains into two physiologically divergent groups; both of these groups of strains could grow on phenol, while one group (designated the R6F group) flocculated in laboratory media and the other group (the R6T group) did not. A competitive PCR analysis in which specific gyrB sequences were used as the primers showed that a population shift from R6F to R6T occurred following the increase in the phenol-loading rate to 1.5 g liter-1 day-1. The R10 population corresponded to nonflocculating phenol-degrading bacteria. Our results suggest that an outbreak of nonflocculating catabolic populations caused the breakdown of the activated-sludge process. This study also demonstrated the usefulness of gyrB-targeted fine population analyses in microbial ecology.}, }
@article {pmid10384012, year = {1999}, author = {Herrera, J and Kramer, CL and Reichman, OJ}, title = {Microfungal Community Changes in Rodent Food Stores over Space and Time.}, journal = {Microbial ecology}, volume = {38}, number = {1}, pages = {79-91}, doi = {10.1007/s002489900156}, pmid = {10384012}, issn = {1432-184X}, abstract = {> Abstract This paper reports the changes over time in the microfungal communities that inhabit three rodent species' food stores at two climatically different locations. Results reveal that microfungal diversity values calculated from above-ground food stores are highest in the more commonly disturbed portions of the rodent dens. Interactions among food-inhabiting microbes and between the rodents and food-inhabiting microbes also appear to influence the microfungal communities within the rodent dens. For example, our data suggest that transport by animal vectors, and not by air currents, is more effective at dispersing microbial propagules. Furthermore, although fungal communities inhabiting food stores within dens varied in composition and diversity over time, standardized substrates (sorghum seeds) simultaneously placed within the food stores converged in microfungal composition the longer they were left within the dens. We hypothesize that animal vectors, including rodents, make neighboring fungal communities more alike by introducing similar communities of microbes, which in turn initiate a cascade of biological interactions that, over time, result in similar microfungal communities inhabiting newly stored food items.http://link.springer-ny.com/link/service/journals/00248/bibs/38n1p79.html}, }
@article {pmid10384011, year = {1999}, author = {Piehler, MF and Swistak, JG and Pinckney, JL and Paerl, HW}, title = {Stimulation of Diesel Fuel Biodegradation by Indigenous Nitrogen Fixing Bacterial Consortia.}, journal = {Microbial ecology}, volume = {38}, number = {1}, pages = {69-78}, doi = {10.1007/s002489900157}, pmid = {10384011}, issn = {1432-184X}, abstract = {> Abstract Successful stimulation of N2 fixation and petroleum hydrocarbon degradation in indigenous microbial consortia may decrease exogenous N requirements and reduce environmental impacts of bioremediation following petroleum pollution. This study explored the biodegradation of petroleum pollution by indigenous N2 fixing marine microbial consortia. Particulate organic carbon (POC) in the form of ground, sterile corn-slash (post-harvest leaves and stems) was added to diesel fuel amended coastal water samples to stimulate biodegradation of petroleum hydrocarbons by native microorganisms capable of supplying a portion of their own N. It was hypothesized that addition of POC to petroleum amended water samples from N-limited coastal waters would promote the growth of N2 fixing consortia and enhance biodegradation of petroleum. Manipulative experiments were conducted using samples from coastal waters (marinas and less polluted control site) to determine the effects of POC amendment on biodegradation of petroleum pollution by native microbial consortia. Structure and function of the microbial consortia were determined by measurement of N2 fixation (acetylene reduction), hydrocarbon biodegradation (14C hexadecane mineralization), bacterial biomass (AODC), number of hydrocarbon degrading bacteria (MPN), and bacterial productivity (3H-thymidine incorporation). Throughout this study there was a consistent enhancement of petroleum hydrocarbon degradation in response to the addition of POC. Stimulation of diesel fuel biodegradation following the addition of POC was likely attributable to increases in bacterial N2 fixation, diesel fuel bioavailability, bacterial biomass, and metabolic activity. Toxicity of the bulk phase water did not appear to be a factor affecting biodegradation of diesel fuel following POC addition. These results indicate that the addition of POC to diesel-fuel-polluted systems stimulated indigenous N2 fixing microbial consortia to degrade petroleum hydrocarbons.http://link.springer-ny.com/link/service/journals/00248/bibs/38n1p69.html}, }
@article {pmid10384010, year = {1999}, author = {Greenblatt, CL and Davis, A and Clement, BG and Kitts, CL and Cox, T and Cano, RJ}, title = {Diversity of Microorganisms Isolated from Amber.}, journal = {Microbial ecology}, volume = {38}, number = {1}, pages = {58-68}, doi = {10.1007/s002489900153}, pmid = {10384010}, issn = {1432-184X}, abstract = {> Abstract Claims that organisms can be cultured from amber, if substantiated, would be significant contributions to our understanding of the evolution, tenacity, and potential spread of life. Three reports on the isolation of organisms from amber have been published. Cano and Borucki recently reported the isolation of Bacillus sphaericus and Lambert et al. have described a new species designated Staphylococcus succinus from 25-40 million year old Dominican amber. These characterized organisms were phylogenetically distant from extant relatives and the Staphylococcus sp. sufficiently far removed from other extant staphylococci to be considered a new species. Here we report the culture of bacteria from Dominican and previously untested 120 million year old Israeli (Lebanese lode) amber. Twenty-seven isolates from the amber matrix have been characterized by fatty-acid profiles (FAME) and/or 16S rRNA sequencing. We also performed a terminal restriction fragment pattern (TRF) analysis of the original amber before prolonged culture by consensus primer amplification of the 16S rRNA followed by restriction enzyme digestion of the amplicons. Sample TRFs were consistent with a sparse bacterial assemblage and included at least five of the isolated organisms. Finally, we microscopically mapped the internal topography of an amber slice.http://link.springer-ny.com/link/service/journals/00248/bibs/38n1p58.html}, }
@article {pmid10384009, year = {1999}, author = {Kuehn, KA and Gessner, MO and Wetzel, RG and Suberkropp, K}, title = {Decomposition and CO2 Evolution from Standing Litter of the Emergent Macrophyte Erianthus giganteus.}, journal = {Microbial ecology}, volume = {38}, number = {1}, pages = {50-57}, doi = {10.1007/s002489900154}, pmid = {10384009}, issn = {1432-184X}, abstract = {> Abstract Decomposition of standing litter of the emergent macrophyte Erianthus giganteus (plumegrass) was quantified in a small freshwater wetland in Alabama, USA. Living green shoots of E. giganteus were tagged and periodically retrieved for determination of leaf and culm mass loss, litter-associated fungal biomass (ergosterol), and nitrogen and phosphorus concentrations. Laboratory studies were also conducted to examine the effects of plant litter moisture content and temperature on rates of CO2 evolution from plant litter. Culm and leaf material lost 25 and 32% AFDM, respectively, during plant senescence and early litter decay. Fungal biomass, as determined by ergosterol concentrations, increased significantly in both leaf and culm litter during decomposition, with maximum biomass accounting for 3.7 and 6.7% of the total detrital weight in culm and leaf litter, respectively. Spatial differences in fungal biomass were observed along the culm axis, with upper regions of the culm accumulating significantly greater amounts of fungal mass than basal regions (p < 0.01, ANOVA). Rates of CO2 evolution from both leaf and culm litter increased rapidly after wetting (0 to 76 µg CO2-C g-1 AFDM h-1 within 5 min). In addition, rates of CO2 evolution from water saturated culms increased exponentially as the temperature was increased from 10 to 30 degrees C. These results provide evidence that considerable microbial colonization and mineralization of standing emergent macrophyte litter can occur before collapse of senescent shoot material to the water and sediment surface.http://link.springer-ny.com/link/service/journals/00248/bibs/38n1p50.html}, }
@article {pmid10384008, year = {1999}, author = {Marilley, L and Hartwig, UA and Aragno, M}, title = {Influence of an Elevated Atmospheric CO2 Content on Soil and Rhizosphere Bacterial Communities Beneath Lolium perenne and Trifolium repens under Field Conditions.}, journal = {Microbial ecology}, volume = {38}, number = {1}, pages = {39-49}, doi = {10.1007/s002489900155}, pmid = {10384008}, issn = {1432-184X}, abstract = {> Abstract The increase in atmospheric CO2 content alters C3 plant photosynthetic rate, leading to changes in rhizodeposition and other root activities. This may influence the activity, the biomass, and the structure of soil and rhizosphere microbial communities and therefore the nutrient cycling rates and the plant growth. The present paper focuses on bacterial numbers and on community structure. The rhizospheres of two grassland plants, Lolium perenne (ryegrass) and Trifolium repens (white clover), were divided into three fractions: the bulk soil, the rhizospheric soil, and the rhizoplane-endorhizosphere. The elevated atmospheric CO2 content increased the most probable numbers of heterotrophic bacteria in the rhizosphere of L. perenne. However, this effect lasted only at the beginning of the vegetation period for T. repens. Community structure was assessed after isolation of DNA, PCR amplification, and construction of cloned 16S rDNA libraries. Amplified ribosomal DNA restriction analysis (ARDRA) and colony hybridization with an oligonucleotide probe designed to detect Pseudomonas spp. showed under elevated atmospheric CO2 content an increased dominance of pseudomonads in the rhizosphere of L. perenne and a decreased dominance in the rhizosphere of T. repens. This work provides evidence for a CO2-induced alteration in the structure of the rhizosphere bacterial populations, suggesting a possible alteration of the plant-growth-promoting-rhizobacterial (PGPR) effect.http://link.springer-ny.com/link/service/journals/00248/bibs/38n1p39.html}, }
@article {pmid10384007, year = {1999}, author = {Sundin, GW and Jacobs, JL}, title = {Ultraviolet Radiation (UVR) Sensitivity Analysis and UVR Survival Strategies of a Bacterial Community from the Phyllosphere of Field-Grown Peanut (Arachis hypogeae L.).}, journal = {Microbial ecology}, volume = {38}, number = {1}, pages = {27-38}, doi = {10.1007/s002489900152}, pmid = {10384007}, issn = {1432-184X}, abstract = {> Abstract The short-term population dynamics of the culturable bacterial community from field-grown peanut (Arachis hypogeae L.) was analyzed over three 2-day periods. As in other phyllosphere studies, significant numbers of pigmented organisms were detected, suggesting the importance of pigmentation in the colonization of this habitat. Isolates were grouped according to pigmentation (orange, pink, yellow, nonpigmented), and the sensitivity of each isolate in the collection (n = 617) to ultraviolet radiation (UVR) was determined as the minimal inhibitory dose (MIDC) of UVR that resulted in an inhibition of growth compared to an unirradiated control. The majority of isolates recovered (56.1%) had an MIDC equal to or exceeding that of Pseudomonas syringae 8B48, a known UV-tolerant strain. Among pigmentation groups, the mean MIDC of pink- and orange-pigmented isolates was significantly greater than that of yellow- or nonpigmented isolates at each sampling time of day. Identification of 213 of the isolates using fatty acid methyl ester analysis indicated that a large proportion of the isolates were gram-positive, with Bacillus spp. alone accounting for 35.7% of the total. The genus Curtobacterium contained the largest percentage of highly UVR-tolerant strains. Nonpigmented mutants of four Curtobacterium strains were selected following ethyl methane sulfonate mutagenesis; these nonpigmented mutants were significantly altered in survival following irradiation with UV-A wavelengths. The strategy of avoidance of UVR through colonization of the abaxial leaf surface was evaluated on three separate occasions by leaf imprint sampling. Only 3 of 120 leaves (2.5%) contained larger bacterial populations on the adaxial surface, indicating that colonization of the abaxial leaf surface is important to phyllosphere survival. Our results indicate that tolerance to UVR is a common phenotype among phyllosphere bacteria, suggesting that solar radiation has a strong influence on the microbial ecology of the phyllosphere.http://link.springer-ny.com/link/service/journals/00248/bibs/38n1p27.html}, }
@article {pmid10384006, year = {1999}, author = {Hansen, GH and Olafsen, JA}, title = {Bacterial Interactions in Early Life Stages of Marine Cold Water Fish.}, journal = {Microbial ecology}, volume = {38}, number = {1}, pages = {1-26}, doi = {10.1007/s002489900158}, pmid = {10384006}, issn = {1432-184X}, abstract = {> Abstract The intensive rearing of various fish species in aquaculture has revealed intimate relationships between fish and bacteria that eventually may affect establishment of a "normal" mucosal microflora or result in disease epizootics. Interactions between bacteria and mucosal surfaces play important roles both at the egg and larval stages of marine fish. Bacterial adhesion and colonization of the egg surface occur within hours after fertilization. The diverse flora which eventually develops on the egg appears to reflect the bacterial composition and load of the ambient water, but species-specific adhesion at the egg surface may also play a role in development of the egg epiflora. Proteolytic enzymes produced by members of the adherent epiflora may cause serious damage to the developing egg and may also affect further adhesion of the epiflora. Ingestion of bacteria at the yolk sac stage results in establishment of a primary intestinal microflora which seems to persist beyond first feeding. Establishment of a gut microflora is likely to undergo several stages, resulting in an "adult" microflora weeks to months after first feeding. Ingested bacteria may serve as an exogenous supply of nutrients or essential factors at an early life stage. Early exposure to high bacterial densities is probably important for immune tolerance, and thus for the establishment of a protective intestinal microflora. Successful rearing of early life stages of several marine fish species depends on knowledge of the complex interactions among the cultured organisms and the bacterial communities which develop at the mucosal surfaces and in the ambient water and rearing systems. The routine use of antibiotics during rearing of fish larvae is not advisable, since it may increase the risk of promoting antibiotic resistance and adversely affect the indigenous microflora of the larvae. The use of probiotics has proven advantageous in domestic animal production, and the search for effective probiotics may have a great potential in aquaculture of marine organisms. Bacteria with antagonistic effects against fish pathogens have been successfully administered to several fish species, resulting in decreased mortality or increased growth rate.http://link.springer-ny.com/link/service/journals/00248/bibs/38n1p1.html}, }
@article {pmid10383868, year = {1999}, author = {Muyzer, G}, title = {DGGE/TGGE a method for identifying genes from natural ecosystems.}, journal = {Current opinion in microbiology}, volume = {2}, number = {3}, pages = {317-322}, doi = {10.1016/S1369-5274(99)80055-1}, pmid = {10383868}, issn = {1369-5274}, mesh = {*Ecosystem ; Electrophoresis, Polyacrylamide Gel/*methods ; Environmental Microbiology ; Genes/*genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Five years after the introduction of denaturing gradient gel electrophoresis(DGGE) and temperature gradient gel electrophoresis (TGGE) in environmental microbiology these techniques are now routinely used in many microbiological laboratories worldwide as molecular tools to compare the diversity of microbial communities and to monitor population dynamics. Recent advances in these techniques have demonstrated their importance in microbial ecology.}, }
@article {pmid10383864, year = {1999}, author = {Marsh, TL}, title = {Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products.}, journal = {Current opinion in microbiology}, volume = {2}, number = {3}, pages = {323-327}, doi = {10.1016/S1369-5274(99)80056-3}, pmid = {10383864}, issn = {1369-5274}, mesh = {Ecosystem ; Genetic Variation ; Polymerase Chain Reaction ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/classification/*genetics ; }, abstract = {Terminal restriction fragment length polymorphism is a recent molecular approach that can assess subtle genetic differences between strains as well as provide insight into the structure and function of microbial communities. The technique has both high sensitivity and throughput making it ideal for comparative analyses.}, }
@article {pmid10349723, year = {1999}, author = {Inglis, GD and Yanke, LJ and Kawchuk, LM and McAllister, TA}, title = {The influence of bacterial inoculants on the microbial ecology of aerobic spoilage of barley silage.}, journal = {Canadian journal of microbiology}, volume = {45}, number = {1}, pages = {77-87}, pmid = {10349723}, issn = {0008-4166}, mesh = {Aerobiosis ; Animal Nutritional Physiological Phenomena ; Animals ; Bacteria/classification/isolation &amp; purification ; Colony Count, Microbial ; Enterococcus faecium/*physiology ; Fungi/classification/isolation &amp; purification ; Hordeum/*metabolism/*microbiology ; Hydrogen-Ion Concentration ; Lactobacillus/*physiology ; Silage/*microbiology ; Yeasts/classification/isolation &amp; purification ; }, abstract = {The aerobic decomposition of barley silage treated with two inoculants (LacA and LacB) containing mixtures of Lactobacillus plantarum and Enterococcus faecium was investigated over a 28-day period. Initially, yeast and bacterial populations were larger in silage inoculated with LacA than in silage treated with LacB or water alone (control). Differences in the succession of yeasts in silage treated with LacA were observed relative to the other two treatments. From silage treatment with LacA, Issatchenkia orientalis was the most prevalent yeast taxon over all of the sample times, and the filamentous fungus Microascus brevicaulis was also frequently isolated at later sample dates (> or = 14 days). In contrast, Saccharomyces exiguus was the most prominent yeast recovered from silage treated with LacB and water alone on days 2 and 4, although it was supplanted by I. orientalis at later sample times. Successional trends of bacteria were similar for all three treatments. Lactobacillus spp. were initially the most prevalent bacteria isolated, followed by Bacillus spp. (primarily Bacillus pumilus). However, the onset of Bacillus spp. prominence was faster in LacA silage, and Klebsiella planticola was frequently recovered at later sample times (> or = 14 days). More filamentous fungi were recovered from LacA silage on media containing carboxylmethylcellulose, pectin, or xylan. The most commonly isolated taxa were Absidia sp., Aspergillus flavus, Aspergillus fumigatus, Byssochlamys nivea, Monascus ruber, Penicillium brevicompactum, Pseudoallescheria boydii, and M. brevicaulis. The results of this study indicated that the two bacterial inoculants incorporated into barley at the time of ensilage affected the microbial ecology of silage decomposition following exposure to air. However, neither of the microbial inoculants effectively delayed aerobic spoilage of barley silage, and the rate of decomposition of silage treated with one of the inoculants (LacA) was actually enhanced.}, }
@article {pmid10347038, year = {1999}, author = {Verschuere, L and Rombaut, G and Huys, G and Dhont, J and Sorgeloos, P and Verstraete, W}, title = {Microbial control of the culture of Artemia juveniles through preemptive colonization by selected bacterial strains.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {6}, pages = {2527-2533}, pmid = {10347038}, issn = {0099-2240}, mesh = {Animals ; Artemia/*growth &amp; development/*microbiology ; Bacteria/*growth &amp; development/isolation &amp; purification ; Biomass ; Colony Count, Microbial ; Culture Media ; Ecosystem ; Pseudomonas fluorescens/growth &amp; development/isolation &amp; purification ; Seawater ; Vibrio/growth &amp; development/isolation &amp; purification ; }, abstract = {The use of juvenile Artemia as feed in aquaculture and in the pet shop industry has been getting more attention during the last decade. In this study, the use of selected bacterial strains to improve the nutritional value of dry food for Artemia juveniles and to obtain control of the associated microbial community was examined. Nine bacterial strains were selected based on their positive effects on survival and/or growth of Artemia juveniles under monoxenic culture conditions, while other strains caused no significant effect, significantly lower rates of survival and/or growth, or even total mortality of the Artemia. The nine selected strains were used to preemptively colonize the culture water of Artemia juveniles. Xenic culture of Artemia under suboptimal conditions yielded better survival and/or growth rates when they were grown in the preemptively colonized culture medium than when grown in autoclaved seawater. The preemptive colonization of the culture water had a drastic influence on the microbial communities that developed in the culture water or that were associated with the Artemia, as determined with Biolog GN community-level physiological profiles. Chemotaxonomical characterization based on fatty acid methyl ester analysis of bacterial isolates recovered from the culture tanks was performed, and a comparison with the initially introduced strains was made. Finally, several modes of action for the beneficial effect of the bacterial strains are proposed.}, }
@article {pmid10347030, year = {1999}, author = {van Hannen, EJ and Mooij, W and van Agterveld, MP and Gons, HJ and Laanbroek, HJ}, title = {Detritus-dependent development of the microbial community in an experimental system: qualitative analysis by denaturing gradient gel electrophoresis.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {6}, pages = {2478-2484}, pmid = {10347030}, issn = {0099-2240}, mesh = {Animals ; Bacteria/genetics/growth &amp; development/*isolation &amp; purification ; Chlorophyta/*microbiology ; Cyanobacteria/*physiology ; DNA, Bacterial/genetics ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; *Ecosystem ; Electrophoresis/*methods ; Eukaryota/genetics/growth &amp; development/*isolation &amp; purification ; Models, Biological ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Correlations between the biomass of phytoplankton and the biomass of bacteria and between the biomass of bacteria and the biomass of protozoans suggest that there is coupling between these compartments of the "microbial loop." To investigate this coupling on the species level, bacteria and protozoans from untreated lake water inocula were allowed to grow on detritus of the green alga Ankistrodesmus falcatus or the cyanobacterium Oscillatoria limnetica in continuous-flow systems for 1 month. Denaturing gradient gel electrophoresis (DGGE) of the 16S and 18S rRNA genes was used to monitor the development of the bacterial community structure and the eukaryotic community structure, respectively. Nonmetric multidimensional scaling of the DGGE profiles revealed the changes in the microbial community structure. This analysis showed that significantly different bacterial communities developed on the green algal detritus and on the cyanobacterial detritus. Although similar results were obtained for the eukaryotic communities, the differences were not significant. Hence, our findings indicate that the origin of detritus can affect the structure of at least the bacterial community. A phylogenetic analysis of 20 18S ribosomal DNA clones that were isolated from the continuous cultures revealed that many sequences were related to the sequences of bacterivorous protozoans (members of the Ciliophora, Rhizopoda, Amoeba, and Kinetoplastida). One clone grouped in a recently established clade whose previously described members are all parasites. The affiliations of about 20% of the clones could not be determined.}, }
@article {pmid10341057, year = {1999}, author = {Pelegrí, SP and Christaki, U and Dolan, J and Rassoulzadegan, F}, title = {Particulate and Dissolved Organic Carbon Production by the Heterotrophic Nanoflagellate Pteridomonas danica Patterson and Fenchel.}, journal = {Microbial ecology}, volume = {37}, number = {4}, pages = {276-284}, doi = {10.1007/s002489900150}, pmid = {10341057}, issn = {1432-184X}, abstract = {> Abstract We established a budget of organic carbon utilization of a starved heterotrophic nanoflagellate, Pteridomonas danica, incubated in batch cultures with Escherichia coli as model prey. The cultures were sampled periodically for biomass determinations and total organic carbon dynamics: total organic carbon, total organic carbon <1 µm, and dissolved organic carbon (DOC, <0.2 µm). During the 22 h incubation period, P. danica underwent biovolume variations of 3.2-fold. Gross growth efficiency was 22% and net growth efficiency 40%. P. danica respired 33% and egested 44% of the ingested E. coli carbon during lag and exponential growth phases. The form of the organic carbon egested varied. Of the total ingested carbon, 9% was egested in the form of DOC and occurred mainly during the exponential growth phase; 35% was egested in the form of particulate organic carbon (POC), ranging in size from 0.2 to 1 µm, and took place during the lag phase. P. danica could have reingested as much of 58% of this previously produced POC during the exponential growth phase as food scarcity increased. We concluded that POC egestion by flagellates could represent a significant source of submicrometric particles and colloidal organic matter. In addition, flagellate reingestion of egested POC could play a nonnegligible role in the microbial food web. Finally, the methodology reported in this study has proved to be a useful tool in the study of carbon metabolism in aquatic microorganisms.http://link.springer-ny.com/link/service/journals/00248/bibs/37n4p276.html}, }
@article {pmid10341056, year = {1999}, author = {Bekins, BA and Godsy, EM and Warren, E}, title = {Distribution of Microbial Physiologic Types in an Aquifer Contaminated by Crude Oil.}, journal = {Microbial ecology}, volume = {37}, number = {4}, pages = {263-275}, doi = {10.1007/s002489900149}, pmid = {10341056}, issn = {1432-184X}, abstract = {> Abstract We conducted a plume-scale study of the microbial ecology in the anaerobic portion of an aquifer contaminated by crude-oil compounds. The data provide insight into the patterns of ecological succession, microbial nutrient demands, and the relative importance of free-living versus attached microbial populations. The most probable number (MPN) method was used to characterize the spatial distribution of six physiologic types: aerobes, denitrifiers, iron-reducers, heterotrophic fermenters, sulfate-reducers, and methanogens. Both free-living and attached numbers were determined over a broad cross-section of the aquifer extending horizontally from the source of the plume at a nonaqueous oil body to 66 m downgradient, and vertically from above the water table to the base of the plume below the water table. Point samples from widely spaced locations were combined with three closely spaced vertical profiles to create a map of physiologic zones for a cross-section of the plume. Although some estimates suggest that less than 1% of the subsurface microbial population can be grown in laboratory cultures, the MPN results presented here provide a comprehensive qualitative picture of the microbial ecology at the plume scale. Areas in the plume that are evolving from iron-reducing to methanogenic conditions are clearly delineated and generally occupy 25-50% of the plume thickness. Lower microbial numbers below the water table compared to the unsaturated zone suggest that nutrient limitations may be important in limiting growth in the saturated zone. Finally, the data indicate that an average of 15% of the total population is suspended.http://link.springer-ny.com/link/service/journals/00248/bibs/37n4p263.html}, }
@article {pmid10341055, year = {1999}, author = {Yuen, TK and Hyde, KD and Hodgkiss, IJ}, title = {Interspecific Interactions among Tropical and Subtropical Freshwater Fungi.}, journal = {Microbial ecology}, volume = {37}, number = {4}, pages = {257-262}, doi = {10.1007/s002489900151}, pmid = {10341055}, issn = {1432-184X}, abstract = {> Abstract Twenty-seven species of tropical and subtropical fungi isolated from freshwater were examined for evidence of interspecific interactions, which are important in determining the ecological roles of fungi. Evidence for interspecific interactions was examined by inoculating paired fungi 25 mm apart on the surface of agar plates. The antagonistic activities were different among different isolates and even between isolates of the same species, for example, Ophioceras dolichostomum isolated from different origins. Pseudohalonectria longirostrum and Kirschsteiniothelia elaterascus, which produced pigment in culture, were strongly inhibitory species. Several aquatic hyphomycetes seems to be less competitive and less likely to produce antagonistic substances. Competitive abilities were also influenced by the range of enzymes that a fungus produced. For example, Verticillium sp. and Diaporthe sp., which produced only one or two kinds of enzyme, were found to exhibit weak competitive abilities and were easily replaced. The results of competition experiments also showed that slow-extending fungi (e.g., Pseudohalonectria longirostrum and Kirschsteiniothelia elaterascus) were more competitive than early fast-extending fungi (e.g., Ophioceras dolichostomum and Nectria haematococca).http://link.springer-ny.com/link/service/journals/00248/bibs/37n4p257.html}, }
@article {pmid10341054, year = {1999}, author = {Naseby, DC and Lynch, JM}, title = {Effects of Pseudomonas fluorescens F113 on Ecological Functions in the Pea Rhizosphere Are Dependent on pH.}, journal = {Microbial ecology}, volume = {37}, number = {4}, pages = {248-256}, doi = {10.1007/s002489900147}, pmid = {10341054}, issn = {1432-184X}, abstract = {> Abstract The aim of this microcosm study was to determine influence of the antibiotic 2,4-diacetylphloroglucinol (DAPG) on the effect of wild-type and functionally modified Pseudomonas fluorescens F113 strains in a sandy loam soil of pH 5.4 planted with pea (Pisum sativum var Montana). The functional modification of strain F113 was a repressed production of DAPG, useful in plant disease control, creating the DAPG negative strain F113 G22; both were marked with a lacZY gene cassette. Lowering the soil pH to 4.4 significantly reduced the plant shoot and root weights and the root length, whereas the bacterial inocula had no significant effect. Both inocula significantly reduced the shoot/root ratio at pH 5.4, but this effect was not evident at the lowered or elevated (6.4) pH levels. The decrease in pH significantly increased the fungal and yeast colony-forming units from the rhizosphere (root extract), but did not affect the total bacterial c.f.u.'s. Inoculatioin with strain F113 in the pH 4.4 soil resulted in a significantly greater total bacterial population. The fungal and yeast c.f.u.'s were not significantly affected by the inocula at any pH studied. Increasing the pH significantly increased the indigenous Pseudomonas population in comparison to the reduced pH treatment and significantly increased both the introduced and total Pseudomonas populations. The antibiotic producing strain significantly reduced the total bacterial population and the NAGase activity (related to fungal activity) at pH 6.4 where the inocula population was the greatest. Alkaline phosphatase, phosphodiesterase, aryl sulfatase, beta-glucosidase, alkaline beta-galactosidase, and NAGase activities significantly increased with increasing in pH. The F113 inocula reduced the acid phosphatase activity at pH 5.4 and increased the acid beta-galactosidase activity over all the pH treatments. The results presented illustrate the variation in impact with soil pH, with implications for variability in efficacy of Pseudomonas fluorescens biocontrol agents with soil pH.http://link.springer-ny.com/link/service/journals/00248/bibs/37n4p248.html}, }
@article {pmid10341053, year = {1999}, author = {Ulrich, A and Wirth, S}, title = {Phylogenetic Diversity and Population Densities of Culturable Cellulolytic Soil Bacteria across an Agricultural Encatchment.}, journal = {Microbial ecology}, volume = {37}, number = {4}, pages = {238-247}, doi = {10.1007/s002489900146}, pmid = {10341053}, issn = {1432-184X}, abstract = {> Abstract A typical, small encatchment (catena Bölkendorf) in the moraine, northeast German agricultural landscape Schorfheide-Chorin was studied with respect to summit, midslope, and foot-slope positions at northern and southern slope exposure, respectively, including a central noncultivated kettle hole position (pot hole). Across the sequence of seven distinct sampling positions, soil organic carbon and total nitrogen contents, soil gravimetric water content, and soil microbial biomass displayed maxima at the kettle hole position. Soil pH revealed a decreasing trend at the northern exposed slope and a minimum at the kettle hole position. Against this background, the population density of total culturable bacteria clearly displayed a minimum at the kettle hole position, whereas the population density of carboxymethylcellulose decomposing bacteria was not clearly differentiated in relation to sampling positions. To study the phylogenetic diversity of culturable cellulolytic bacteria, 311 isolates were obtained from the sampling positions across the entire encatchment and examined by restriction analysis of PCR-amplified 16S rDNA. Using the restriction enzyme ScrFI, isolates were classified into 31 pattern groups. Although the ratio of actinomycetes within total isolates ranged from 0.73 to 0.94, only 16 pattern groups originated from actinomycetes, but 15 from other bacteria. At all sampling positions, a dominant pattern group was identified, containing 38 to 65% of total isolates. Two site-specific pattern groups could be identified, representing significant parts of the total population, which were highly specific for the kettle hole (19% of total isolates) and for foot- and midslope positions (15-18% of total isolates), respectively. In general, the composition of cellulolytic isolates across the encatchment displayed differences with respect to slope positions, but was not significantly affected by soil properties. Based on 16S rDNA sequence analysis, isolates of the dominant as well as the specific pattern groups could be assigned to the genus Streptomyces. Furthermore, sequencing of 16S rDNA of isolates of another three pattern groups revealed a high phylogenetic diversity among these isolates, including cellulomonads and bacilli.http://link.springer-ny.com/link/service/journals/00248/bibs/37n4p238.html}, }
@article {pmid10341052, year = {1999}, author = {Manz, W and Wendt-Potthoff, K and Neu, TR and Szewzyk, U and Lawrence, JR}, title = {Phylogenetic Composition, Spatial Structure, and Dynamics of Lotic Bacterial Biofilms Investigated by Fluorescent in Situ Hybridization and Confocal Laser Scanning Microscopy.}, journal = {Microbial ecology}, volume = {37}, number = {4}, pages = {225-237}, doi = {10.1007/s002489900148}, pmid = {10341052}, issn = {1432-184X}, abstract = {> Abstract The phylogenetic composition, three-dimensional structure and dynamics of bacterial communities in river biofilms generated in a rotating annular reactor system were studied by fluorescent in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM). Biofilms grew on independently removable polycarbonate slides exposed in the reactor system with natural river water as inoculum and sole nutrient and carbon source. The microbial biofilm community developed from attached single cells and distinct microcolonies via a more confluent structure characterized by various filamentous bacteria to a mature biofilm rich in polymeric material with fewer cells on a per-area basis after 56 days. During the different stages of biofilm development, characteristic microcolonies and cell morphotypes could be identified as typical features of the investigated lotic biofilms. In situ analysis using a comprehensive suite of rRNA-targeted probes visualized individual cells within the alpha-, beta-, and gamma-Proteobacteria as well as the Cytophaga-Flavobacterium group as major parts of the attached community. The relative abundance of these major groups was determined by using digital image analysis to measure specific cell numbers as well as specific cell area after in situ probing. Within the lotic biofilm community, 87% of the whole bacterial cell area and 79% of the total cell counts hybridized with a Bacteria specific probe. During initial biofilm development, beta-Proteobacteria dominated the bacterial population. This was followed by a rapid increase of alpha-Proteobacteria and bacteria affiliated to the Cytophaga-Flavobacterium group. In mature biofilms, alpha-Proteobacteria and Cytophaga-Flavobacteria continued to be the prevalent bacterial groups. Beta-Proteobacteria constituted the morphologically most diverse group within the biofilm communities, and more narrow phylogenetic staining revealed the importance of distinct phylotypes within the beta1-Proteobacteria for the composition of the microbial community. The presence of sulfate-reducing bacteria affiliated to the Desulfovibrionaceae and Desulfobacteriaceae confirmed the range of metabolic potential within the lotic biofilms.http://link.springer-ny.com/link/service/journals/00248/bibs/37n4p225.html}, }
@article {pmid10319511, year = {1999}, author = {Nielsen, JT and Liesack, W and Finster, K}, title = {Desulfovibrio zosterae sp. nov., a new sulfate reducer isolated from surface-sterilized roots of the seagrass Zostera marina.}, journal = {International journal of systematic bacteriology}, volume = {49 Pt 2}, number = {}, pages = {859-865}, doi = {10.1099/00207713-49-2-859}, pmid = {10319511}, issn = {0020-7713}, mesh = {Base Composition ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Desulfovibrio/*classification/genetics/isolation &amp; purification/physiology ; Fatty Acids/analysis ; Fructose/metabolism ; Genes, rRNA ; Molecular Sequence Data ; Oxidation-Reduction ; Phenotype ; Phylogeny ; Pigments, Biological/analysis ; Plant Roots/*microbiology ; *Poaceae ; RNA, Ribosomal, 16S/genetics ; Sulfates/*metabolism ; }, abstract = {A sulfate-reducing bacterium, designated strain lacT, was isolated from surface-sterilized roots of the benthic macrophyte Zostera marina. Cells were motile by means of a single polar flagellum. Strain lacT utilized lactate, pyruvate, malate, ethanol, L-alanine, fumarate, choline and fructose with sulfate as electron acceptor. In addition, fumarate, pyruvate and fructose were also degraded without an external electron acceptor. Sulfate could be substituted with thiosulfate, sulfite and elemental sulfur. Optimal growth was observed between 32.5 and 34.5 degrees C, at an NaCl concentration of 0.2 M and in a pH range between 6.8 and 7.3. The G + C content of the DNA was 42.7 +/- 0.2 mol%. Desulfoviridin and catalase were present. Strain lacT contained c-type cytochromes. Comparative 16S rRNA gene sequence analysis and the fatty acid pattern grouped this isolate into the genus Desulfovibrio. However, strain lacT differs from all other described Desulfovibrio species on the bases of its 16S rRNA gene sequence, the G + C content, its cellular lipid pattern and the utilization pattern of substrates. These characteristics establish strain lacT (= DSM 11974T) as a novel species of the genus Desulfovibrio, for which the name Desulfovibrio zosterae sp. nov. is proposed.}, }
@article {pmid10319508, year = {1999}, author = {Wainø, M and Tindall, BJ and Schumann, P and Ingvorsen, K}, title = {Gracilibacillus gen. nov., with description of Gracilibacillus halotolerans gen. nov., sp. nov.; transfer of Bacillus dipsosauri to Gracilibacillus dipsosauri comb. nov., and Bacillus salexigens to the genus Salibacillus gen. nov., as Salibacillus salexigens comb. nov.}, journal = {International journal of systematic bacteriology}, volume = {49 Pt 2}, number = {}, pages = {821-831}, doi = {10.1099/00207713-49-2-821}, pmid = {10319508}, issn = {0020-7713}, mesh = {Bacillus/chemistry/*classification/genetics/physiology ; Bacterial Typing Techniques ; Base Composition ; Cell Wall/chemistry ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Gram-Positive Endospore-Forming Rods/chemistry/*classification/genetics/physiology ; Lipids/analysis ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sodium Chloride/metabolism ; Spores, Bacterial/physiology ; Utah ; *Water Microbiology ; }, abstract = {A Gram-positive, extremely halotolerant bacterium was isolated from the Great Salt Lake, Utah, USA. The strain, designated NNT (= DSM 11805T), was strictly aerobic, rod-shaped, motile by peritrichous flagella and spore-forming. Strain NNT grew at salinities of 0-20% (w/v) NaCl. A distinctive feature of strain NNT was its optimal growth in salt-free medium. The polar lipid pattern of strain NNT consisted of phosphatidyl glycerol, diphosphatidyl glycerol and two phospholipids of unknown structure. The G + C content of its DNA was 38 mol%. The morphological, physiological and, particularly, the 16S rDNA sequence data, showed that strain NNT was associated with 'Bacillus group 1'. However, the organisms showing the greatest degree of sequence similarity to strain NNT were members of the genus Halobacillus and the species Marinococcus albus, Virgibacillus pantothenticus, Bacillus salexigens and Bacillus dipsosauri. On the basis of chemotaxonomic data, strain NNT was shown to be chemically most similar to B. salexigens and B. dipsosauri, with the greatest degree of similarity being shown to the latter organism. This was consistent with the 16S rDNA sequence data. Members of the genus Halobacillus comprise a chemically distinct group and can easily be distinguished from all other organisms of 'Bacillus group 1'. On the basis of the 16S rDNA data, chemotaxonomy and the physiology of strain NNT, it is proposed that this organism is a member of a new species, within a new genus, for which the name Gracilibacillus halotolerans is proposed. It is also proposed that B. dipsosauri be transferred to this genus as Gracilibacillus dipsosauri comb. nov. and that B. salexigens be transferred to the genus Salibacillus gen. nov., as Salibacillus salexigens comb. nov. Finally, additional data is provided to support the transfer of Bacillus pantothenticus to the genus Virgibacillus, as Virgibacillus pantothenticus Heyndrickx et al. (1998).}, }
@article {pmid10232648, year = {1999}, author = {Collins, MD and Gibson, GR}, title = {Probiotics, prebiotics, and synbiotics: approaches for modulating the microbial ecology of the gut.}, journal = {The American journal of clinical nutrition}, volume = {69}, number = {5}, pages = {1052S-1057S}, doi = {10.1093/ajcn/69.5.1052s}, pmid = {10232648}, issn = {0002-9165}, mesh = {Dietary Supplements ; Humans ; Infant, Newborn/*immunology ; Intestines/immunology/*microbiology ; Nutritional Status ; *Probiotics ; }, abstract = {The microbiota of the human large intestine influences health and well-being. Whereas it has long been accepted that gut bacteria play a role in host pathogenesis, current opinion is that certain microflora components can have beneficial effects on gastroenteritis resistance, blood lipids, antitumor properties, lactose tolerance, and gastrointestinal immunity. It is postulated that in the infant gut an elevated bifidobacterial count may be associated with health advantages that breast-fed infants may have over formula-fed infants. Whereas beneficial aspects of the human gut flora still need definitive confirmation and mechanistic explanations, there is now interest in modulating the composition of gut flora such that a potentially more remedial community exists. This may be achieved through the targeted use of dietary supplementation. This article provides an overview of how probiotics, prebiotics, and synbiotics may contribute toward nutritional modulation of the gut microecology, with emphasis on the neonatal intestine where appropriate. The use of modern molecular methods, as an essential step forward for assessing the validity and accuracy of the modulatory approach, is also discussed.}, }
@article {pmid10232646, year = {1999}, author = {Mackie, RI and Sghir, A and Gaskins, HR}, title = {Developmental microbial ecology of the neonatal gastrointestinal tract.}, journal = {The American journal of clinical nutrition}, volume = {69}, number = {5}, pages = {1035S-1045S}, doi = {10.1093/ajcn/69.5.1035s}, pmid = {10232646}, issn = {0002-9165}, mesh = {Animals ; Bacteria/classification/genetics ; Breast Feeding ; Digestive System/growth &amp; development/*microbiology ; Ecology ; Humans ; Infant, Newborn/*growth &amp; development ; }, abstract = {The gastrointestinal tract of a normal fetus is sterile. During the birth process and rapidly thereafter, microbes from the mother and surrounding environment colonize the gastrointestinal tract of the infant until a dense, complex microbiota develops. The succession of microbes colonizing the intestinal tract is most marked in early development, during which the feeding mode shifts from breast-feeding to formula feeding to weaning to the introduction of solid food. Dynamic balances exist between the gastrointestinal microbiota, host physiology, and diet that directly influence the initial acquisition, developmental succession, and eventual stability of the gut ecosystem. In this review, the development of the intestinal microbiota is discussed in terms of initial acquisition and subsequent succession of bacteria in human infants. Intrinsic and extrinsic factors influencing succession and their health significance are discussed. The advantages of modern molecular ecology techniques that provide sensitive and specific, culture-independent evaluation of the gastrointestinal ecosystem are introduced and discussed briefly. Further advances in our understanding of developmental microbial ecology in the neonatal gastrointestinal tract are dependent on the application of these modern molecular techniques.}, }
@article {pmid10227879, year = {1999}, author = {Roane, TM}, title = {Lead Resistance in Two Bacterial Isolates from Heavy Metal-Contaminated Soils.}, journal = {Microbial ecology}, volume = {37}, number = {3}, pages = {218-224}, doi = {10.1007/s002489900145}, pmid = {10227879}, issn = {1432-184X}, abstract = {> Abstract Microorganisms have developed mechanisms of coping with a variety of toxic metals; however, few studies have explored microbial resistance to lead. In this study, the overall mechanisms of a lead-resistant Pseudomonas marginalis and a lead-resistant Bacillus megaterium isolated from two different metal-contaminated soils were investigated. The P.marginalis had a higher lead resistance level at 2.5mM total lead as compared to 0.6 mM for B. megaterium. Resistance to soluble lead was much lower, 0.3 and 0.1 mM, respectively. The degree of lead resistance and the mechanism of lead resistance for these two isolates corresponded with their environmental lead exposure. When viewed with transmission electron microscopy, P.marginalis, isolated from a soil contaminated with high total but undetectable soluble lead, showed extracellular lead exclusion. B.megaterium, from a soil with both high total and soluble lead levels, was less resistant with an intracellular cytoplasmic accumulation of lead as observed with TEM. Polarization microscopy indicated that while P.marginalis produced a high amount of an extracellular polymer implicated in the organism's mechanism of lead resistance, B.megaterium produced no discernable extracellular polymeric substances. The study of these two organisms demonstrated differences in how soil microorganisms respond to environmental lead exposure, including the novel mechanism of intracellular sequestration of lead.}, }
@article {pmid10227878, year = {1999}, author = {Féray, C and Volat, B and Degrange, V and Clays-Josserand, A and Montuelle, B}, title = {Assessment of Three Methods for Detection and Quantification of Nitrite-Oxidizing Bacteria and Nitrobacter in Freshwater Sediments (MPN-PCR, MPN-Griess, Immunofluorescence).}, journal = {Microbial ecology}, volume = {37}, number = {3}, pages = {208-217}, doi = {10.1007/s002489900144}, pmid = {10227878}, issn = {1432-184X}, abstract = {> Abstract Nitrification in freshwater, a key process in the nitrogen cycle, is now well known to take place predominantly on suspended particles and in sediment. Nitrobacter is the most commonly isolated nitrite oxidizing bacteria from water environments. Three methods for counting nitrite oxidizing communities (especially Nitrobacter) in sediment were investigated: MPN-Griess, fluorescent antibodies (immunofluorescence), and a more recent molecular method coupling specific DNA amplification by PCR and statistical MPN quantification. After preliminary adjustments of the MPN-PCR technique, the detection level and the yield of each method were determined by inoculating a sediment with a pure Nitrobacter culture. The best recovery yield was obtained with the immunofluorescence technique (21.3%) and the lowest detection level was reached with the MPN-Griess method (10(3) Nitrobacter/g dry weight sediment). The MPN-PCR method resulted in the lowest recovery yields and needs further adaptation to become a reliable and precise tool for investigations of nitrifying bacteria in sediment.}, }
@article {pmid10227877, year = {1999}, author = {Ludvigsen, L and Albrechtsen, H and Ringelberg, DB and Ekelund, F and Christensen, TH}, title = {Distribution and Composition of Microbial Populations in a Landfill Leachate Contaminated Aquifer (Grindsted, Denmark).}, journal = {Microbial ecology}, volume = {37}, number = {3}, pages = {197-207}, doi = {10.1007/s002489900143}, pmid = {10227877}, issn = {1432-184X}, abstract = {> Abstract To investigate whether landfill leachates affected the microbial biomass and/or community composition of the extant microbiota, 37 samples were collected along a 305-m transect of a shallow landfill-leachate polluted aquifer. The samples were analyzed for total numbers of bacteria by use of the acridine orange direct count method (AODC). Numbers of dominant, specific groups of bacteria and total numbers of protozoa were measured by use of the most probable number method (MPN). Viable biomass estimates were obtained from measures of ATP and ester-linked phospholipid fatty acid (PLFA) concentrations. The estimated numbers of total bacteria by direct counts were relatively constant throughout the aquifer, ranging from a low of 4.8 x 10(6) cells/g dry weight (dw) to a high of 5.3 x 10(7) cells/g dw. Viable biomass estimates based on PLFA concentrations were one to three orders of magnitude lower with the greatest concentrations (up to 4 x 10(5) cells/g dw) occurring at the border of the landfill and in samples collected from thin lenses of clay and silt with sand streaks. Cell number estimates based on ATP concentrations were also found to be lower than the direct count measurements (<2.2 x 10(6) cells/g dw), and with the greatest concentrations close to the landfill. Methanogens (Archaea) and reducers of sulfate, iron, manganese, and nitrate were all observed in the aquifer. Methanogens were found to be restricted to the most polluted and reduced part of the aquifer at a maximum cell number of 5.4 x 10(4) cells/g dw. Populations of sulfate reducers decreased with an increase in horizontal distance from the landfill ranging from a high of 9.0 x 10(3) cells/g dw to a low of 6 cells/g dw. Iron, manganese, and nitrate reducers were detected throughout the leachate plume all at maximum cell numbers of 10(6) cells/g dw. Changes in PLFA profiles indicated that a shift in microbial community composition occurred with increasing horizontal distance from the landfill. The types and patterns of lipid biomarkers suggested that increased proportions of sulfate- and iron-reducing bacteria as well as certain microeukaryotes existed at the border of the landfill. The presence of these lipid biomarkers correlated with the MPN results. There was, however, no significant correlation between the abundances of the specific PLFA biomarkers and quantitative measurements of redox processes. The application of AODC, MPN, PLFA, and ATP analyses in the characterization of the extant microbiota within the Grindsted aquifer revealed that as distance increased from the leachate source, viable biomass decreased and community composition shifted. These results led to the conclusion that the landfill leachate induced an increase in microbial cell numbers by altering the subsurface aquifer so that it was conducive to the growth of methanogens and of iron-and sulfate-reducing bacteria and fungi.}, }
@article {pmid10227876, year = {1999}, author = {Battin, TJ and Sengschmitt, D}, title = {Linking Sediment Biofilms, Hydrodynamics, and River Bed Clogging: Evidence from a Large River.}, journal = {Microbial ecology}, volume = {37}, number = {3}, pages = {185-196}, doi = {10.1007/s002489900142}, pmid = {10227876}, issn = {1432-184X}, abstract = {> Abstract We investigated possible effects of the hydrodynamics at the water/sediment interface on river bed biofilms within the reservoir Freudenau (Vienna, Austria) of the Danube River during the period 1996/97. Two study sites (OBB and SSF) that differed in the magnitude of surface/subsurface water exchange were selected and intersite comparisons revealed higher organic matter, bacterial cell numbers, and esterase activity in SSF with lower horizontal outflow. Concentrations of colloidal carbohydrates and uronic acids were unaffected by hydrodynamics. The relative contribution of uronic acids to bulk colloidal carbohydrates was higher in the low-flow site SSF. The distribution patterns of this relative contribution generally matched the subsurface flow pattern. Shortly after impoundment in March 1996 and along with decreased surface flow velocity, maximal biofilm carbohydrate exopolymers concurred with minimal esterase activity in OBB. We hypothesize that this inverse relationship is due to increased diffusional resistance within the exopolymer biofilm matrix that reduces mass transfer and hydrolytic activity. These results, to our knowledge, are the first evidence for microbial participation in the clogging of a large river bed. Biofilm-associated organic carbon increased significantly by a factor of approximately 3.3 to 4.4 with progressive clogging as determined by the sediment leakage coefficient, which increased approximately 3.8 times. Concomitantly, with ongoing clogging, esterase activity exhibited increasingly higher values at the interface relatively to deeper sediment layers, which translates into steeper depth gradients. Furthermore, minimal inflow from the surface water into the river bed along with steepest esterase gradients concurred with a senescent benthic algal bloom. This suggests an important role for algae in clogging. Either algae obstruct voids mechanically, or their exudates fuel heterotrophic bacteria that in turn are involved in clogging processes. However, our data do not allow unequivocal differentiation between biogenic and physical clogging mechanisms.}, }
@article {pmid10227875, year = {1999}, author = {Pringault, O and de Wit R,  and Kühl, M}, title = {A Microsensor Study of the Interaction between Purple Sulfur and Green Sulfur Bacteria in Experimental Benthic Gradients.}, journal = {Microbial ecology}, volume = {37}, number = {3}, pages = {173-184}, doi = {10.1007/s002489900141}, pmid = {10227875}, issn = {1432-184X}, abstract = {> Abstract The interaction between the purple sulfur bacterium Thiocapsa roseopersicina and the green sulfur bacterium Prosthecochloris aestuarii was studied in a gradient chamber under a 16-hours light-8-hours dark regime. The effects of interaction were inferred by comparing the final outcome of a mixed culture experiment with those of the respective axenic cultures using the same inoculation densities and experimental conditions. Densities of bacteria were deduced from radiance microprofiles, and the chemical microenvironment was investigated with O2, H2S, and pH microelectrodes. P. aestuarii always formed a biofilm below the maximal oxygen penetration depth and its metabolism was strictly phototrophic. In contrast, T. roseopersicina formed a bilayer in both the mixed and the axenic culture. The top layer formed by the latter organism was exposed to oxygen, and chemotrophic sulfide oxidation took place during the dark periods, while the bottom layer grew phototrophically during the light periods only. In the mixed culture, the relative density of P. aestuarii was lower than in the axenic culture, which reflects the effects of the competition for sulfide. However, the relative density of T. roseopersicina was actually higher in the mixed culture than in the corresponding axenic culture, indicating a higher growth yield on sulfide in the mixed culture experiment. Several hypotheses are proposed to explain the effects of the interaction.}, }
@article {pmid10227874, year = {1999}, author = {Canhoto, C and Graça, MA}, title = {Leaf Barriers to Fungal Colonization and Shredders (Tipula lateralis) Consumption of Decomposing Eucalyptus globulus.}, journal = {Microbial ecology}, volume = {37}, number = {3}, pages = {163-172}, doi = {10.1007/s002489900140}, pmid = {10227874}, issn = {1432-184X}, abstract = {> Abstract Herein we assess the importance of leaf cuticle, polyphenolic, and essential oils contents of Eucalyptus globulus leaves to hyphomycete colonization and shredder consumption. Optical and electron microscopy revealed that, at least during the first 5 weeks of conditioning, the cuticle remains virtually intact. Stomata provide the main access for hyphae to internal leaf tissues and, eventually, for spore release. We suggest that in E. globulus leaves, fungal decomposition progresses predominantly in and from the eucalyptus leaf mesophyll to the outside. Malt extract agar media supplemented with either eucalyptus essential oils or tannic acid completely inhibited (Articulospora tetracladia, Lemonniera aquatica, and Tricladium gracile) or depressed (Heliscus lugdunensis, Lunulospora curvula, and Tricladium angulatum) aquatic hyphomycetes growth. The transference of both secondary compounds to alder leaves induced similar and significant reduction in Tipula lateralis larval consumption. Results consistently indicate that eucalyptus oils are stronger deterrents than polyphenols. The waxy cuticle of E. globulus appears to be a key physical factor delaying fungal colonization during decomposition. We hypothesize that the relative influence of leaf phenols and essential oils to aquatic hyphomycetes and shredders may be related to three main factors: (a) initial distribution of such compounds in the leaves; (b) possibility of their decrease through decomposition; and (c) consumption strategies of detritivores.}, }
@article {pmid10224015, year = {1999}, author = {Hrywna, Y and Tsoi, TV and Maltseva, OV and Quensen, JF and Tiedje, JM}, title = {Construction and characterization of two recombinant bacteria that grow on ortho- and para-substituted chlorobiphenyls.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {5}, pages = {2163-2169}, pmid = {10224015}, issn = {0099-2240}, mesh = {Arthrobacter/enzymology/genetics ; Biodegradation, Environmental ; Chlorobenzoates/metabolism ; Cloning, Molecular ; Genes, Bacterial ; Gram-Negative Aerobic Rods and Cocci/*genetics/growth &amp; development/*metabolism ; Molecular Sequence Data ; Oxygenases/genetics/metabolism ; Polychlorinated Biphenyls/*metabolism ; Pseudomonas aeruginosa/enzymology/genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Recombination, Genetic ; Transformation, Genetic ; }, abstract = {Cloning and expression of the aromatic ring dehalogenation genes in biphenyl-growing, polychlorinated biphenyl (PCB)-cometabolizing Comamonas testosteroni VP44 resulted in recombinant pathways allowing growth on ortho- and para-chlorobiphenyls (CBs) as a sole carbon source. The recombinant variants were constructed by transformation of strain VP44 with plasmids carrying specific genes for dehalogenation of chlorobenzoates (CBAs). Plasmid pE43 carries the Pseudomonas aeruginosa 142 ohb genes coding for the terminal oxygenase (ISPOHB) of the ortho-halobenzoate 1,2-dioxygenase, whereas plasmid pPC3 contains the Arthrobacter globiformis KZT1 fcb genes, which catalyze the hydrolytic para-dechlorination of 4-CBA. The parental strain, VP44, grew only on low concentrations of 2- and 4-CB by using the products from the fission of the nonchlorinated ring of the CBs (pentadiene) and accumulated stoichiometric amounts of the corresponding CBAs. The recombinant strains VP44(pPC3) and VP44(pE43) grew on, and completely dechlorinated high concentrations (up to 10 mM), of 4-CBA and 4-CB and 2-CBA and 2-CB, respectively. Cell protein yield corresponded to complete oxidation of both biphenyl rings, thus confirming mineralization of the CBs. Hence, the use of CBA dehalogenase genes appears to be an effective strategy for construction of organisms that will grow on at least some congeners important for remediation of PCBs.}, }
@article {pmid10224014, year = {1999}, author = {Tsoi, TV and Plotnikova, EG and Cole, JR and Guerin, WF and Bagdasarian, M and Tiedje, JM}, title = {Cloning, expression, and nucleotide sequence of the Pseudomonas aeruginosa 142 ohb genes coding for oxygenolytic ortho dehalogenation of halobenzoates.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {5}, pages = {2151-2162}, pmid = {10224014}, issn = {0099-2240}, mesh = {Amino Acid Sequence ; Base Sequence ; Biodegradation, Environmental ; Chlorobenzoates/*metabolism ; Cloning, Molecular ; DNA Transposable Elements/genetics ; DNA, Bacterial/genetics ; Escherichia coli/genetics/growth &amp; development/metabolism ; Gene Expression ; *Genes, Bacterial ; Molecular Sequence Data ; Open Reading Frames ; Oxygenases/*genetics/*metabolism ; Phylogeny ; Physical Chromosome Mapping ; Pseudomonas aeruginosa/*genetics/growth &amp; development/*metabolism ; Recombinant Proteins/genetics/metabolism ; }, abstract = {We have cloned and characterized novel oxygenolytic ortho-dehalogenation (ohb) genes from 2-chlorobenzoate (2-CBA)- and 2,4-dichlorobenzoate (2,4-dCBA)-degrading Pseudomonas aeruginosa 142. Among 3,700 Escherichia coli recombinants, two clones, DH5alphaF'(pOD22) and DH5alphaF'(pOD33), converted 2-CBA to catechol and 2,4-dCBA and 2,5-dCBA to 4-chlorocatechol. A subclone of pOD33, plasmid pE43, containing the 3,687-bp minimized ohb DNA region conferred to P. putida PB2440 the ability to grow on 2-CBA as a sole carbon source. Strain PB2440(pE43) also oxidized but did not grow on 2,4-dCBA, 2,5-dCBA, or 2,6-dCBA. Terminal oxidoreductase ISPOHB structural genes ohbA and ohbB, which encode polypeptides with molecular masses of 20,253 Da (beta-ISP) and 48,243 Da (alpha-ISP), respectively, were identified; these proteins are in accord with the 22- and 48-kDa (as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis) polypeptides synthesized in E. coli and P. aeruginosa parental strain 142. The ortho-halobenzoate 1,2-dioxygenase activity was manifested in the absence of ferredoxin and reductase genes, suggesting that the ISPOHB utilized electron transfer components provided by the heterologous hosts. ISPOHB formed a new phylogenetic cluster that includes aromatic oxygenases featuring atypical structural-functional organization and is distant from the other members of the family of primary aromatic oxygenases. A putative IclR-type regulatory gene (ohbR) was located upstream of the ohbAB genes. An open reading frame (ohbC) of unknown function that overlaps lengthwise with ohbB but is transcribed in the opposite direction was found. The ohbC gene codes for a 48,969-Da polypeptide, in accord with the 49-kDa protein detected in E. coli. The ohb genes are flanked by an IS1396-like sequence containing a putative gene for a 39,715-Da transposase A (tnpA) at positions 4731 to 5747 and a putative gene for a 45,247-Da DNA topoisomerase I/III (top) at positions 346 to 1563. The ohb DNA region is bordered by 14-bp imperfect inverted repeats at positions 56 to 69 and 5984 to 5997.}, }
@article {pmid10224007, year = {1999}, author = {Raghukumar, C and D'Souza, TM and Thorn, RG and Reddy, CA}, title = {Lignin-modifying enzymes of flavodon flavus, a basidiomycete isolated from a coastal marine environment.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {5}, pages = {2103-2111}, pmid = {10224007}, issn = {1098-5336}, abstract = {A basidiomycetous fungus Flavodon flavus (Klotzsch) Ryvarden (strain 312), isolated from decaying sea grass from a coral lagoon off the west coast of India, mineralized nearly 24% of 14C-labeled synthetic lignin to 14CO2 in 24 days. When grown in low-nitrogen medium (2.4 mM N) this fungus produced three major classes of extracellular lignin-modifying enzymes (LMEs): manganese-dependent peroxidase (MNP), lignin peroxidase (LIP), and laccase. Low MNP and laccase activities were seen in high-nitrogen medium (24 mM N), but no LIP activity was seen. In media containing lignocellulosic substrates such as pine, poplar, or sugarcane bagasse as the sole source of carbon and nitrogen, relatively high MNP and moderate levels of laccases were seen, but LIP production either was not seen or was minimal. LME production was also seen in media prepared with artificial seawater. Fast protein liquid chromatography and isoelectric focusing resolved LMEs into four isozymes each of MNP and LIP, while laccase isozymes were resolved into two groups, one group containing seven isozymes (pIs 4 to 6) and the other group containing at least three isozymes (pIs < 3). The molecular masses of the different isozymes were 43 to 99 kDa for MNP, 40 and 41.5 kDa for LIP, and 43 and 99 kDa for laccase. F. flavus showed effective degradation of various dye pollutants in media prepared with or without artificial seawater. This is the first report on the production of all three major classes of LMEs by F. flavus and points to the bioremediation potential of this organism in terrestrial as well as marine environments.}, }
@article {pmid10220894, year = {1999}, author = {van der Maarel, MJ and Sprenger, W and Haanstra, R and Forney, LJ}, title = {Detection of methanogenic archaea in seawater particles and the digestive tract of a marine fish species.}, journal = {FEMS microbiology letters}, volume = {173}, number = {1}, pages = {189-194}, doi = {10.1111/j.1574-6968.1999.tb13501.x}, pmid = {10220894}, issn = {0378-1097}, mesh = {Animals ; DNA, Archaeal/analysis ; DNA, Ribosomal/analysis ; Euryarchaeota/genetics/*isolation &amp; purification ; Feces/microbiology ; Flounder/*microbiology ; Intestines/*microbiology ; Methanosarcinaceae/genetics ; Phylogeny ; Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; *Water Microbiology ; }, abstract = {A methanogen-specific nested PCR approach was used to detect methanogenic archaea in seawater particles of the North Sea and the feces and the digestive tract of flounder (Platichthys flesus), a fish found in the North Sea. A number of 16S rDNA sequences with 97.6-99.5% similarity to Methanococcoides methylutens were found in the seawater particles as well as the digestive tract and fecal samples.}, }
@article {pmid10220888, year = {1999}, author = {Tunlid, A and Ahman, J and Oliver, RP}, title = {Transformation of the nematode-trapping fungus Arthrobotrys oligospora.}, journal = {FEMS microbiology letters}, volume = {173}, number = {1}, pages = {111-116}, doi = {10.1111/j.1574-6968.1999.tb13491.x}, pmid = {10220888}, issn = {0378-1097}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; DNA Restriction Enzymes ; Drug Resistance, Microbial/genetics ; Genes, Fungal ; Genes, Reporter ; Genetic Vectors ; Glucuronidase ; Hygromycin B/pharmacology ; Mitosis ; Mitosporic Fungi/drug effects/*genetics ; Nematoda/*microbiology ; *Transformation, Genetic ; }, abstract = {The nematode-trapping fungus Arthrobotrys oligospora was transformed to hygromycin resistance using the hygromycin-B phosphotransferase gene from Escherichia coli under the control of various heterologous fungal promoters. Plasmid DNA was introduced into fungal protoplasts by polyethylene glycol/CaCl2 treatment. Transformation frequencies varied between 1-6 transformants per microgram DNA. Seven out of 13 integration events analyzed from transformants were single copy integrations, whereas the remaining were multiple and more complex integrations. The addition of restriction enzymes during transformations increased the frequency of single copy integrations. Co-transformation, using the E. coli uidA gene encoding the beta-glucuronidase reporter gene under the control of an Aspergillus nidulans promoter, occurred at frequencies of up to 63%.}, }
@article {pmid10220173, year = {1999}, author = {Milcamps, A and de Bruijn, FJ}, title = {Identification of a novel nutrient-deprivation-induced Sinorhizobium meliloti gene (hmgA) involved in the degradation of tyrosine.}, journal = {Microbiology (Reading, England)}, volume = {145 (Pt 4)}, number = {}, pages = {935-947}, doi = {10.1099/13500872-145-4-935}, pmid = {10220173}, issn = {1350-0872}, mesh = {Amino Acid Sequence ; DNA Transposable Elements/genetics ; *Dioxygenases ; *Genes, Bacterial ; Homogentisate 1,2-Dioxygenase ; Homogentisic Acid/metabolism ; Humans ; Luciferases/genetics/metabolism ; Molecular Sequence Data ; Multigene Family ; Mutagenesis ; Oxygenases/chemistry/*genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sinorhizobium meliloti/*genetics/growth &amp; development/metabolism ; Tyrosine/*metabolism ; cis-trans-Isomerases/chemistry/genetics/metabolism ; }, abstract = {Sinorhizobium meliloti strain N4 carries a Tn5luxAB insertion in a gene which is induced by nitrogen and carbon deprivation as well as in the presence of tyrosine. The Tn5luxAB-tagged locus was found to share significant similarity with the human hmgA gene and the corresponding Aspergillus nidulans gene, encoding the enzyme homogentisate dioxygenase, which is involved in the degradation of tyrosine. Extended DNA sequence analysis of the tagged locus revealed the presence of several ORFs, including one encoding a polypeptide sharing a high degree of similarity with human and fungal maleylacetoacetate isomerases. Strain N4 was found to be unable to use tyrosine as carbon source, to lack homogentisate dioxygenase activity, to produce a melanin-like pigment and to be affected in stationary-phase survival. This is believed to be the first report of a hmgA-homologous gene in bacteria.}, }
@article {pmid10203753, year = {1999}, author = {López-Garćia, P and Moreira, D}, title = {Metabolic symbiosis at the origin of eukaryotes.}, journal = {Trends in biochemical sciences}, volume = {24}, number = {3}, pages = {88-93}, doi = {10.1016/s0968-0004(98)01342-5}, pmid = {10203753}, issn = {0968-0004}, mesh = {Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Biological Evolution ; Eukaryotic Cells ; Hydrogen/metabolism ; Mitochondria/metabolism ; *Models, Biological ; Symbiosis/*physiology ; }, abstract = {Thirty years after Margulis revived the endosymbiosis theory for the origin of mitochondria and chloroplasts, two novel symbiosis hypotheses for the origin of eukaryotes have been put forward. Both propose that eukaryotes arose through metabolic symbiosis (syntrophy) between eubacteria and methanogenic Archaea. They also propose that this was mediated by interspecies hydrogen transfer and that, initially, mitochondria were anaerobic. These hypotheses explain the mosaic character of eukaryotes (i.e. an archaeal-like genetic machinery and a eubacterial-like metabolism), as well as distinct eukaryotic characteristics (which are proposed to be products of symbiosis). Combined data from comparative genomics, microbial ecology and the fossil record should help to test their validity.}, }
@article {pmid10103265, year = {1999}, author = {Dunbar, J and Takala, S and Barns, SM and Davis, JA and Kuske, CR}, title = {Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {4}, pages = {1662-1669}, pmid = {10103265}, issn = {0099-2240}, mesh = {Bacteria/genetics/*growth &amp; development/*isolation &amp; purification ; Culture Media ; DNA, Ribosomal/analysis ; Ecosystem ; *Genes, rRNA ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Techniques based on amplification of 16S rRNA genes for comparing bacterial communities are now widely used in microbial ecology, but calibration of these techniques with traditional tools, such as cultivation, has been conspicuously absent. In this study, we compared levels of bacterial community diversity in two pinyon rhizosphere soil samples and two between-tree (interspace) soil samples by analyzing 179 cultivated bacterial isolates and 801 16S rRNA genes amplified from extracted soil DNA. Phylotypes were defined by performing a restriction fragment length polymorphism analysis of 16S rRNA gene sequences with the enzymes RsaI and BstUI. The average level of 16S rRNA gene sequence similarity of members of a phylotype was 86.6% based on an analysis of partial sequences. A total of 498 phylotypes were identified among the 16S ribosomal DNA (rDNA) clones, while 34 phylotypes occurred among the cultivated isolates. Analysis of sequences from a subset of the phylotypes showed that at least seven bacterial divisions were represented in the clone libraries, whereas the isolates represented only three. The phylotype richness, frequency distribution (evenness), and composition of the four culture collections and the four clone libraries were investigated by using a variety of diversity indices. Although cultivation and 16S rRNA cloning analyses gave contradictory descriptions of the relative phylotype richness for one of the four environments, the two methods identified qualitatively consistent relationships when levels of evenness were compared. The levels of phylotype similarity between communities were uniformly low (15 to 31%). Both methods consistently indicated that one environment was distinct from the other three. Our data illustrate that while 16S rDNA cloning and cultivation generally describe similar relationships between soil microbial communities, significant discrepancies can occur.}, }
@article {pmid10103249, year = {1999}, author = {Wielinga, B and Lucy, JK and Moore, JN and Seastone, OF and Gannon, JE}, title = {Microbiological and geochemical characterization of fluvially deposited sulfidic mine tailings.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {4}, pages = {1548-1555}, pmid = {10103249}, issn = {1098-5336}, abstract = {The fluvial deposition of mine tailings generated from historic mining operations near Butte, Montana, has resulted in substantial surface and shallow groundwater contamination along Silver Bow Creek. Biogeochemical processes in the sediment and underlying hyporheic zone were studied in an attempt to characterize interactions consequential to heavy-metal contamination of shallow groundwater. Sediment cores were extracted and fractionated based on sediment stratification. Subsamples of each fraction were assayed for culturable heterotrophic microbiota, specific microbial guilds involved in metal redox transformations, and both aqueous- and solid-phase geochemistry. Populations of cultivable Fe(III)-reducing bacteria were most prominent in the anoxic, circumneutral pH regions associated with a ferricrete layer or in an oxic zone high in organic carbon and soluble iron. Sulfur- and iron-oxidizing bacteria were distributed in discrete zones throughout the tailings and were often recovered from sections at and below the anoxic groundwater interface. Sulfate-reducing bacteria were also widely distributed in the cores and often occurred in zones overlapping iron and sulfur oxidizers. Sulfate-reducing bacteria were consistently recovered from oxic zones that contained high concentrations of metals in the oxidizable fraction. Altogether, these results suggest a highly varied and complex microbial ecology within a very heterogeneous geochemical environment. Such physical and biological heterogeneity has often been overlooked when remediation strategies for metal contaminated environments are formulated.}, }
@article {pmid10099394, year = {1998}, author = {Noguera, DR and Brusseau, GA and Rittmann, BE and Stahl, DA}, title = {A unified model describing the role of hydrogen in the growth of desulfovibrio vulgaris under different environmental conditions.}, journal = {Biotechnology and bioengineering}, volume = {59}, number = {6}, pages = {732-746}, doi = {10.1002/(sici)1097-0290(19980920)59:6&lt;732::aid-bit10&gt;3.0.co;2-7}, pmid = {10099394}, issn = {1097-0290}, abstract = {A unified model for the growth of Desulfovibrio vulgaris under different environmental conditions is presented. The model assumes the existence of two electron transport mechanisms functioning simultaneously. One mechanism results in the evolution and consumption of hydrogen, as in the hydrogen-cycling model. The second mechanism assumes a direct transport of electrons from the donor to the acceptor, without the participation of H2. A combination of kinetic and thermodynamic conditions control the flow of electrons through each pathway. The model was calibrated using batch experiments with D. vulgaris grown on lactate, in the presence and absence of sulfate, and was verified using additional batch experiments under different conditions. The model captured the general trends of consumption of substrates and accumulation of products, including the transient accumulation and consumption of H2. Furthermore, the model estimated that 48% of the electrons transported from lactate to sulfate involved H2 production, indicating that hydrogen cycling is a fundamental process in D. vulgaris. The presence of simultaneous electron transport mechanisms might provide D. vulgaris with important ecological advantages, because it facilitates a rapid response to changes in environmental conditions. This model increases our ability to study the microbial ecology of anaerobic environments and the role of Desulfovibrio species in a variety of environments. Copyright 1998 John Wiley &amp; Sons, Inc.}, }
@article {pmid10093232, year = {1998}, author = {Volz, PA and Parent, SL}, title = {Space flight micro-fungi after 27 years storage in water and in continuous culture.}, journal = {Microbios}, volume = {96}, number = {384}, pages = {111-125}, pmid = {10093232}, issn = {0026-2633}, mesh = {Chaetomium/*growth &amp; development ; Rhodotorula/*growth &amp; development ; Saccharomyces cerevisiae/*growth &amp; development ; *Space Flight ; Time Factors ; Trichophyton/*growth &amp; development ; Water ; }, abstract = {Four species of micro-fungi were selected for study in the National Aeronautics and Space Administration (NASA) Apollo Microbial Ecology Evaluation Device (MEED) mycology experiments. Trichophyton terrestre, Rhodotorula rubra, Saccharomyces cerevisiae and Chaetomium globosum were selected from a series of preflight test fungi for the MEED mycology studies during the 2 years prior to the actual flight (Volz, 1971a, 1972b). Conidia of T. terrestre, ascospores of C. globosum and yeast cells of R. rubra and S. cerevisiae were suspended in sterile distilled water and loaded into wet and dry cuvettes for exposure to specific space flight parameters according to the filters built into the space flight hardware (Volz, 1971b). Living cells were found in the original inocula and phenotype water storage after 27 years. Colony cells were also examined after 27 years of continuous culture.}, }
@article {pmid10049902, year = {1999}, author = {Tonolla, M and Demarta, A and Peduzzi, R and Hahn, D}, title = {In situ analysis of phototrophic sulfur bacteria in the chemocline of meromictic Lake Cadagno (Switzerland).}, journal = {Applied and environmental microbiology}, volume = {65}, number = {3}, pages = {1325-1330}, pmid = {10049902}, issn = {0099-2240}, mesh = {Bacteria/*classification/*genetics ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal/analysis ; *Fresh Water ; Genes, rRNA ; *In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Oligonucleotide Probes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Switzerland ; *Water Microbiology ; }, abstract = {Comparative sequence analysis of a 16S rRNA gene clone library from the chemocline of the meromictic Lake Cadagno (Switzerland) revealed the presence of a diverse number of phototrophic sulfur bacteria. Sequences resembled those of rRNA of type strains Chromatium okenii DSM169 and Amoebobacter purpureus DSM4197, as well as those of four bacteria forming a tight cluster with A. purpureus DSM4197 and Lamprocystis roseopersicina DSM229. In situ hybridization with fluorescent (Cy3 labeled) oligonucleotide probes indicated that all large-celled phototrophic sulfur bacteria in the chemocline of Lake Cadagno were represented by C. okenii DSM169, while small-celled phototrophic sulfur bacteria consisted of four major populations with different distribution profiles in the chemocline indicating different ecophysiological adaptations.}, }
@article {pmid10049895, year = {1999}, author = {Lee, N and Nielsen, PH and Andreasen, KH and Juretschko, S and Nielsen, JL and Schleifer, KH and Wagner, M}, title = {Combination of fluorescent in situ hybridization and microautoradiography-a new tool for structure-function analyses in microbial ecology.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {3}, pages = {1289-1297}, pmid = {10049895}, issn = {0099-2240}, mesh = {Aerobiosis ; Anaerobiosis ; Autoradiography/*methods ; Chlorobi/growth &amp; development/metabolism ; Culture Media ; Ecosystem ; Escherichia coli/growth &amp; development/metabolism ; Evaluation Studies as Topic ; Glucose/metabolism ; In Situ Hybridization, Fluorescence/*methods ; Microscopy, Confocal ; Oligonucleotide Probes/genetics ; Organic Chemicals/metabolism ; Phosphorus/metabolism ; RNA, Ribosomal/genetics ; Sewage/*microbiology ; Structure-Activity Relationship ; }, abstract = {A new microscopic method for simultaneously determining in situ the identities, activities, and specific substrate uptake profiles of individual bacterial cells within complex microbial communities was developed by combining fluorescent in situ hybridization (FISH) performed with rRNA-targeted oligonucleotide probes and microautoradiography. This method was evaluated by using defined artificial mixtures of Escherichia coli and Herpetosiphon aurantiacus under aerobic incubation conditions with added [3H]glucose. Subsequently, we were able to demonstrate the potential of this method by visualizing the uptake of organic and inorganic radiolabeled substrates ([14C]acetate, [14C]butyrate, [14C]bicarbonate, and 33Pi) in probe-defined populations from complex activated sludge microbial communities by using aerobic incubation conditions and anaerobic incubation conditions (with and without nitrate). For both defined cell mixtures and activated sludge, the method proved to be useful for simultaneous identification and analysis of the uptake of labeled substrates under the different experimental conditions used. Optimal results were obtained when fluorescently labeled oligonucleotides were applied prior to the microautoradiographic developing procedure. For single-cell resolution of FISH and microautoradiographic signals within activated sludge flocs, cryosectioned sample material was examined with a confocal laser scanning microscope. The combination of in situ rRNA hybridization techniques, cryosectioning, microautoradiography, and confocal laser scanning microscopy provides a unique opportunity for obtaining cultivation-independent insights into the structure and function of bacterial communities.}, }
@article {pmid10049851, year = {1999}, author = {el Fantroussi, S and Verschuere, L and Verstraete, W and Top, EM}, title = {Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {3}, pages = {982-988}, pmid = {10049851}, issn = {0099-2240}, mesh = {Bacteria/*drug effects/*genetics/growth &amp; development/metabolism ; Biodegradation, Environmental ; Cluster Analysis ; Colony Count, Microbial ; Culture Media ; DNA Fingerprinting ; DNA, Bacterial/analysis ; Diuron/metabolism/pharmacology ; Ecosystem ; Electrophoresis, Polyacrylamide Gel/methods ; Genes, Bacterial ; *Genes, rRNA ; Herbicides/metabolism/*pharmacology ; Linuron/metabolism/pharmacology ; Molecular Sequence Data ; Phenylurea Compounds/metabolism/pharmacology ; RNA, Ribosomal, 16S/*genetics ; *Soil Microbiology ; }, abstract = {The effect of three phenyl urea herbicides (diuron, linuron, and chlorotoluron) on soil microbial communities was studied by using soil samples with a 10-year history of treatment. Denaturing gradient gel electrophoresis (DGGE) was used for the analysis of 16S rRNA genes (16S rDNA). The degree of similarity between the 16S rDNA profiles of the communities was quantified by numerically analysing the DGGE band patterns. Similarity dendrograms showed that the microbial community structures of the herbicide-treated and nontreated soils were significantly different. Moreover, the bacterial diversity seemed to decrease in soils treated with urea herbicides, and sequence determination of several DGGE fragments showed that the most affected species in the soils treated with diuron and linuron belonged to an uncultivated bacterial group. As well as the 16S rDNA fingerprints, the substrate utilization patterns of the microbial communities were compared. Principal-component analysis performed on BIOLOG data showed that the functional abilities of the soil microbial communities were altered by the application of the herbicides. In addition, enrichment cultures of the different soils in medium with the urea herbicides as the sole carbon and nitrogen source showed that there was no difference between treated and nontreated soil in the rate of transformation of diuron and chlorotoluron but that there was a strong difference in the case of linuron. In the enrichment cultures with linuron-treated soil, linuron disappeared completely after 1 week whereas no significant transformation was observed in cultures inoculated with nontreated soil even after 4 weeks. In conclusion, this study showed that both the structure and metabolic potential of soil microbial communities were clearly affected by a long-term application of urea herbicides.}, }
@article {pmid10028275, year = {1999}, author = {Behrendt, U and Ulrich, A and Schumann, P and Erler, W and Burghardt, J and Seyfarth, W}, title = {A taxonomic study of bacteria isolated from grasses: a proposed new species Pseudomonas graminis sp. nov.}, journal = {International journal of systematic bacteriology}, volume = {49 Pt 1}, number = {}, pages = {297-308}, doi = {10.1099/00207713-49-1-297}, pmid = {10028275}, issn = {0020-7713}, mesh = {Base Sequence ; DNA, Bacterial/analysis ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phylogeny ; Poaceae/*microbiology ; Pseudomonas/*classification/cytology/physiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The taxonomic position of a yellow-pigmented group of bacteria, isolated from the phyllosphere of grasses was investigated. Results obtained from restriction analysis of amplified 16S rDNA with seven endonucleases (CfoI, HaeIII, AluI, HinfI, MspI, Sau3A and ScrFI) showed identical restriction patterns for each enzyme of all isolates studied, which suggests that all strains belong to the same species. The grass isolates displayed the characteristics of the genus Pseudomonas. They were Gram-negative, aerobic and rod-shaped with polar flagella. Isolates were catalase-positive and oxidase-negative, and unable to oxidize or ferment glucose with the production of acid. The isolates did not reduce nitrate to nitrite but were able to utilize a wide range of compounds individually as a sole carbon source, with preference being given to the utilization of monosaccharides. The disaccharides tested were not utilized as substrates. The DNA base compositions of the tested strains ranged from 60 to 61 mol% G+C. The major isoprenoid quinone of each was ubiquinone Q-9 and hydroxy fatty acids were represented by 3-hydroxydodecanoic acid and 2-hydroxydodecanoic acid. Comparison of 16S rDNA sequences showed that the bacteria were members of the genus Pseudomonas, with similarity values between 91.5 and 97.7%. DNA-DNA hybridization studies with closely related neighbours revealed a low level of homology (< 27%), indicating that the isolates represent an individual species. On the basis of phenotypic and phylogenetic analyses a new species, Pseudomonas graminis sp. nov. (type strain DSM 11363T), is proposed.}, }
@article {pmid10028263, year = {1999}, author = {Brandt, KK and Patel, BK and Ingvorsen, K}, title = {Desulfocella halophila gen. nov., sp. nov., a halophilic, fatty-acid-oxidizing, sulfate-reducing bacterium isolated from sediments of the Great Salt Lake.}, journal = {International journal of systematic bacteriology}, volume = {49 Pt 1}, number = {}, pages = {193-200}, doi = {10.1099/00207713-49-1-193}, pmid = {10028263}, issn = {0020-7713}, mesh = {Bacteria/*classification/metabolism ; Base Sequence ; Fatty Acids/*metabolism ; *Geologic Sediments ; Molecular Sequence Data ; Sulfates/*metabolism ; *Water Microbiology ; }, abstract = {A new halophilic sulfate-reducing bacterium, strain GSL-But2T, was isolated from surface sediment of the Southern arm of the Great Salt Lake, UT, USA. The organism grew with a number of straight-chain fatty acids (C4-C16), 2-methylbutyrate, L-alanine and pyruvate as electron donors. Butyrate was oxidized incompletely to acetate. Sulfate, but not sulfite or thiosulfate, served as an electron acceptor. Growth was observed between 2 and 19% (w/v) NaCl with an optimum at 4-5% (w/v) NaCl. The optimal temperature and pH for growth were around 34 degrees C and pH 6.5-7.3, respectively. The generation time under optimal conditions in defined medium was around 28 h, compared to 20 h in complex medium containing yeast extract. The G+C content was 35.0 mol%. 16S rRNA gene sequence analysis revealed that strain GSL-But2T belongs to the family Desulfobacteriaceae within the delta-subclass of the Proteobacteria and suggested that strain GSL-But2T represents a member of a new genus. The name Desulfocella halophila gen. nov., sp. nov. is proposed for this organism. The type strain of D. halophila is strain GSL-But2T (= DSM 11763T = ATCC 700426T).}, }
@article {pmid10022061, year = {1998}, author = {Santegoeds, CM and Schramm, A and de Beer, D}, title = {Microsensors as a tool to determine chemical microgradients and bacterial activity in wastewater biofilms and flocs.}, journal = {Biodegradation}, volume = {9}, number = {3-4}, pages = {159-167}, doi = {10.1023/a:1008302622946}, pmid = {10022061}, issn = {0923-9820}, mesh = {Bacteria/*chemistry ; *Biofilms ; Electrochemistry ; Nitrogen/analysis ; Oxygen/analysis ; Sewage/*microbiology ; *Water Microbiology ; }, abstract = {Microsensors used in microbial ecology are reviewed with emphasis on new sensor developments (NO3-, NO2-, NH4+, CO2, H2, H2S and CH4 microsensors as well as fiberoptical microsensors for O2, temperature and pH). Examples of microsensor applications in biofilms and activated sludge flocs are presented, in which sulfate reduction and denitrification were studied.}, }
@article {pmid9929403, year = {1999}, author = {Nyman, JA}, title = {Effect of Crude Oil and Chemical Additives on Metabolic Activity of Mixed Microbial Populations in Fresh Marsh Soils.}, journal = {Microbial ecology}, volume = {37}, number = {2}, pages = {152-162}, doi = {10.1007/s002489900139}, pmid = {9929403}, issn = {1432-184X}, abstract = {> Abstract Hydrocarbons increase abundance of hydrocarbon-degrading microorganisms, but also decrease microbial diversity. This could disrupt ecosystem dynamics by altering soil organic matter mineralization and resultant nutrient remineralization rates. Crude oil, which is known to contain toxins and reduce microbial diversity, was hypothesized to reduce gross metabolic activity of mixed microbial populations in wetland soils. Soil respiration and Eh were compared, for 6 months, among microcosms containing marsh soils that differed in soil organic matter (Panicum hemitomon Shult. or Sagittaria lancifolia L. dominated marshes), crude oil (Arabian crude, Louisiana crude, or no oil), and additives (a cleaner, a dispersant, fertilizer, or no additive). No treatment slowed activity; instead, Louisiana plus fertilizer and all Arabian treatments temporarily accelerated activity. Additional C respired from oiled microcosms exceeded C added as crude oil by 1.4 to 3.5 times. Thus, much additional C originated from soil organic matter rather than crude oil. Crude oils temporarily lowered soil Eh, which is consistent with accelerated metabolism and demand for electron acceptors. The lack of inhibition observed at the community level does not necessarily indicate an absence of toxicity. Instead, tolerant species with metabolic versatility probably maintained activity. Stimulation probably resulted from removal of micronutrient limitation, rather than removal of grazing pressure or macronutrient limitation. Regardless, accelerated soil organic matter mineralization surely accelerated nutrient remineralization. This might explain some reports of crude oil stimulating plant growth. These results are not inconsistent with theoretical and experimental conclusions regarding effects of biodiversity on ecosystem stability and productivity, nor are they inconsistent with conclusions that crude oils contain components that are toxic to microbes, vegetation, and fauna. However, these data do indicate that crude oils also contain components that temporarily stimulate metabolic activity of surviving microbes.}, }
@article {pmid9929402, year = {1999}, author = {Gramss, G and Ziegenhagen, D and Sorge, S}, title = {Degradation of Soil Humic Extract by Wood- and Soil-Associated Fungi, Bacteria, and Commercial Enzymes.}, journal = {Microbial ecology}, volume = {37}, number = {2}, pages = {140-151}, doi = {10.1007/s002489900138}, pmid = {9929402}, issn = {1432-184X}, abstract = {> Abstract An alkaline humic extract (HE) of a black calcareous forest mull was exposed to 36 fungal and 9 eubacterial isolates in liquid standing culture. At 21 d in fungi, and 4 d in bacteria, the groups of wood-degrading basidiomycetes, terricolous basidiomycetes, ectomycorrhizal fungi, soil-borne microfungi, and eubacteria had reduced the absorbance (A340) of HE media by 57, 28, 19, 26 and 5%, respectively. Gel permeation chromatography revealed that the large humic acid molecules were more readily degraded than the smaller fulvic acid molecules and served as a sole source of carbon and energy. The more active HE degraders reduced the overall molecular weight of humic and fulvic acids by 0.25 to 0.47 kDa. They also reduced the chemical reactivity of HE to tetrazotized o-dianisidine, indicating the degradation of hydroxylated aromatic molecules (which are responsible for this reaction). Decreases in absorbance, molecular weight, and reactivity were caused by fungal manganese peroxidase, horseradish peroxidase, beta-glucosidase, and abiotic oxidants such as H2O2 and Mn(III) acetate. It is concluded that fungi, some of which are propagated in contaminated soils to control xenobiotics, metabolize HE compounds enzymatically. They use enzymes which are also involved in the degradation of soil xenobiotics. Because of reductions in the molecular weight of HE, which is a potential carrier of heavy metal ions and xenobiotics, solubility and motility of humic substances in soil and surface waters are increased.}, }
@article {pmid9929401, year = {1999}, author = {Di Giovanni GD,  and Watrud, LS and Seidler, RJ and Widmer, F}, title = {Comparison of Parental and Transgenic Alfalfa Rhizosphere Bacterial Communities Using Biolog GN Metabolic Fingerprinting and Enterobacterial Repetitive Intergenic Consensus Sequence-PCR (ERIC-PCR).}, journal = {Microbial ecology}, volume = {37}, number = {2}, pages = {129-139}, doi = {10.1007/s002489900137}, pmid = {9929401}, issn = {1432-184X}, abstract = {> Abstract Rhizosphere bacterial communities of parental and two transgenic alfalfa (Medicago sativa L.) of isogenic background were compared based on metabolic fingerprinting using Biolog GN microplates and DNA fingerprinting of bacterial communities present in Biolog GN substrate wells by enterobacterial repetitive intergenic consensus sequence-PCR (ERIC-PCR). The two transgenic alfalfa expressed either bacterial (Bacillus licheniformis) genes for alpha-amylase or fungal (Phanerochaete chrysosporium) genes for Mn-dependent lignin peroxidase (Austin S, Bingham ET, Matthews DE, Shahan MN, Will J, Burgess RR, Euphytica 85:381-393). Cluster analysis and principal components analysis (PCA) of the Biolog GN metabolic fingerprints indicated consistent differences in substrate utilization between the parental and lignin peroxidase transgenic alfalfa rhizosphere bacterial communities. Cluster analysis of ERIC-PCR fingerprints of the bacterial communities in Biolog GN substrate wells revealed consistent differences in the types of bacteria (substrate-specific populations) enriched from the rhizospheres of each alfalfa genotype. Comparison of ERIC-PCR fingerprints of bacterial strains obtained from substrate wells to substrate community ERIC-PCR fingerprints suggested that a limited number of populations were responsible for substrate oxidation in these wells. Results of this study suggest that transgenic plant genotype may affect rhizosphere microorganisms and that the methodology used in this study may prove a useful approach for the comparison of bacterial communities.}, }
@article {pmid9929400, year = {1999}, author = {Semenov, AM and van Bruggen AHC,  and Zelenev, VV}, title = {Moving Waves of Bacterial Populations and Total Organic Carbon along Roots of Wheat.}, journal = {Microbial ecology}, volume = {37}, number = {2}, pages = {116-128}, doi = {10.1007/s002489900136}, pmid = {9929400}, issn = {1432-184X}, abstract = {> Abstract To determine if spatial variation in soluble carbon sources along the root coincides with different trophic groups of bacteria, copiotrophic and oligotrophic bacteria were enumerated from bulk soil and rhizosphere samples at 2 cm intervals along wheat roots 2, 3, and 4 weeks after planting. There was a moderate rhizosphere effect in one experiment with soil rich in fresh plant debris, and a very pronounced rhizosphere effect in the second experiment with soil low in organic matter. We obtained wavelike patterns of both trophic groups of bacteria as well as water-soluble total organic carbon (TOC) along the whole root length (60 or 90 cm). TOC concentrations were maximal at the root tip and base and minimal in the middle part of the roots. Oscillations in populations of copiotrophic and oligotrophic bacteria had two maxima close to the root tip and at the root base, or three maxima close to the tip, in the middle section, and at the root base. The location and pattern of the waves in bacterial populations changed progressively from week to week and was not consistently correlated with TOC concentrations or the location of lateral root formation. Thus, the traditional view that patterns in bacterial numbers along the root directly reflect patterns in exudation and rhizodeposition from several fixed sources along the root may not be true. We attributed the observed wavelike patterns in bacterial populations to bacterial growth and death cycles (due to autolysis or grazing by predators). Considering the root tip as a moving nutrient source, temporal oscillations in bacterial populations at any location where the root tip passed would result in moving waves along the root. This change in concept about bacterial populations in the rhizosphere could have significant implications for plant growth promotion and bioremediation.}, }
@article {pmid9929399, year = {1999}, author = {Zubkov, MV and Sleigh, MA}, title = {Growth of Amoebae and Flagellates on Bacteria Deposited on Filters.}, journal = {Microbial ecology}, volume = {37}, number = {2}, pages = {107-115}, doi = {10.1007/s002489900135}, pmid = {9929399}, issn = {1432-184X}, abstract = {> Abstract Artificial bacterial biofilms were formed by making microwave-irradiated, dual-radioisotope-labelled Vibrio bacteria adhere to 0.4 µm pore size filters with albumin. The rate of release of 3H from thymidine label in these bacteria into the surrounding seawater when protozoa were incubated with the biofilm indicated the predator's grazing rate, and the rate of accumulation of 14C in the predators from leucine label in the bacteria indicated the assimilation rate of the protozoa. The amoeba Vanella septentrionalis consumed about 60% of the available bacteria between the 5th and 15th days of incubation with a gross growth efficiency of 22 +/- 6%, compared with about 75% consumption at 29 +/- 8% efficiency for the surface-feeding flagellate Caecitellus parvulus, and about 55% consumption at 16 +/- 5% efficiency for the suspension-feeding flagellate Pteridomonas danica. As a result of their grazing and metabolism these protozoa regenerated about 70-85% of the nutrients present in their food and released these nutrients in the immediate vicinity of the bacterial biofilm. The biomass of the amoeba Vanella was calculated to be 166 pg protein cell-1 during maximum growth and 93 pg protein cell-1 in the stationary phase.}, }
@article {pmid9929398, year = {1999}, author = {Sime-Ngando, T and Demers, S and Juniper, SK}, title = {Protozoan Bacterivory in the Ice and the Water Column of a Cold Temperate Lagoon.}, journal = {Microbial ecology}, volume = {37}, number = {2}, pages = {95-106}, doi = {10.1007/s002489900134}, pmid = {9929398}, issn = {1432-184X}, abstract = {> Abstract Bacterial abundance and bacterivorous protist abundance and activity were examined in ice-brine and water column communities of a cold temperate Japanese lagoon (Saroma-Ko Lagoon, Hokkaido, 44 degreesN, 144 degreesE), during the late winter phase of ice community development (February-March 1992). Bacterial abundance averaged 6 and 1 x 10(5) cells ml-1 in the ice-brine and plankton samples, respectively, and generally decreased during the sampling period. Bacterivorous protists, identified based on direct observation of short-term (<1 h) ingested fluorescently labeled bacteria (FLB) in their food vacuoles, were largely dominated by flagellates, mainly cryothecomonad-type and chrysomonad-like cells and small dinoflagellates of the genus Gymnodinium. Bacterivorous ciliates included mainly the prostomatid Urotricha sp., the scuticociliates Uronema and Cyclidium, the choreotrichs Lohmaniella oviformis and Strobilidium, and the hypotrich Euplotes sp. Protist abundance averaged 4 x 10(3) and 8.1 cells ml-1 in the ice-brine and 0.3 x 10(3) and 1.2 cells ml-1 in the plankton, for flagellates and ciliates, respectively. In contrast to bacteria, the abundance of protists generally increased throughout the sampling period, indicating predator-prey interactions. Protistan bacterivory, measured from the rate of FLB disappearance over 24 h, averaged 36% (ice) and 24% (plankton) of bacterial standing stock and exhibited the same seasonal pattern as for protist abundance. The calculated specific clearance (range, 2-67 nl protozoa-1 h-1) and ingestion (<1-26 particles protozoa-1 h-1) rates were likely to be minimal estimates and grazing impact may have been higher on occasion. Indications for the dependence of "bacterivorous protists" on nonbacterial food items were also provided. Although alternative sources of bacterial loss are likely to be of importance, this study provides evidence for the potential of protozoan assemblages as bacterial grazers in both sea ice-brine biota and water column at the southern limit of sea ice in the northern hemisphere.}, }
@article {pmid9929397, year = {1999}, author = {Vetter, YA and Deming, JW}, title = {Growth Rates of Marine Bacterial Isolates on Particulate Organic Substrates Solubilized by Freely Released Extracellular Enzymes.}, journal = {Microbial ecology}, volume = {37}, number = {2}, pages = {86-94}, doi = {10.1007/s002489900133}, pmid = {9929397}, issn = {1432-184X}, abstract = {> Abstract Growth rates of marine bacterial isolates on particulate organic substrates were measured using a novel apparatus which restricts bacterial cells to the uptake of hydrolysate produced from particulate substrates only by enzymes that are actively released from the bacterium into the culture medium. Significant, varying growth rates were measured for four different marine bacteria, using three different, ecologically significant particulate organic substrates (preparations of amylopectin, chitin, and animal hide). Growth rates sometimes approached but were usually lower than rates that have been reported in laboratory experiments using dissolved organic growth substrates. These results are consistent with recent model predictions and have important implications for microbial ecology and material cycling in diverse liquid-bathed environments.}, }
@article {pmid9929396, year = {1999}, author = {Giuliano, L and De Domenico M,  and De Domenico E,  and Höfle, MG and Yakimov, MM}, title = {Identification of Culturable Oligotrophic Bacteria within Naturally Occurring Bacterioplankton Communities of the Ligurian Sea by 16S rRNA Sequencing and Probing.}, journal = {Microbial ecology}, volume = {37}, number = {2}, pages = {77-85}, doi = {10.1007/s002489900132}, pmid = {9929396}, issn = {1432-184X}, abstract = {> Abstract Typical marine bacteria (i.e., obligately oligotrophic) that were numerically dominant members of naturally occurring marine communities were identified by cloning and sequencing the amplified 16S rRNA genes obtained from dilution cultures of the original samples. The data reported here refer to two different habitats of a marine pelagic environment (28 miles offshore, in the northwestern Mediterranean Sea). The samples were taken from the water column at two representative layers, i.e., the 30-m depth, corresponding to the chlorophyll maximum layer, and the 1800-m depth, representative of a deep, oligotrophic environment. Three major lineages were found in the 16S rDNA clone libraries prepared from the two samples, two of which could be assigned to the Vibrio and the Rhodobacter groups. The third lineage was a distant relative of the genus Flavobacterium, but it was not closely related to any marine isolate. Six oligonucleotide probes, either complementary to the conserved sequence domains or selectively hybridizing to the clone sequences, were designed for use as hybridization group-specific and strain-specific probes. A single-mismatch discrimination between certain probes and nontarget sequences was demonstrated by detecting the probes' specificity at different hybridization and washing conditions. The screening of the clone libraries with the obtained probes revealed that neither the 30-m sample higher dilution nor the 1800-m one were pure cultures. While some representatives of the Vibrio group were found in both the surface and the deep sample, the members of the Flavobacterium and Rhodobacter lineages were detected only in the deep and the euphotic layers, respectively. We suggest an approach for analyzing autochthonous marine bacteria able to grow in unamended seawater.}, }
@article {pmid9928617, year = {1998}, author = {Weimer, PJ}, title = {Manipulating ruminal fermentation: a microbial ecological perspective.}, journal = {Journal of animal science}, volume = {76}, number = {12}, pages = {3114-3122}, doi = {10.2527/1998.76123114x}, pmid = {9928617}, issn = {0021-8812}, mesh = {Animals ; Bacteria/*metabolism ; Dietary Fiber/metabolism ; Dietary Proteins/metabolism ; Fermentation ; Methane/metabolism ; Plants/chemistry ; Rumen/metabolism/*microbiology ; Ruminants/*metabolism ; Toxins, Biological/metabolism ; }, abstract = {The essential role of ruminal microflora in ruminant nutrition provides the potential for improvement in animal production via altering the numbers or activities of specific classes of microorganisms. Successful alterations will be facilitated by an understanding of the microbial ecology of the rumen based on its mechanistic underpinnings. Demonstrated improvements in ruminal fermentation can be traced to their consonance with well-established principles of microbial ecology (niche occupancy, selective pressure, adaptation, and interactions) and the thermodynamics and kinetics of substrate utilization. Application of these principles to several proposed alterations of the ruminal bacterial population allows a prediction of their relative feasibility. Improving fiber digestion, decreasing protein degradation, and detoxifying feed components that are present in low concentrations will be difficult to achieve in the rumen and are best approached by altering the feed, either genetically or with postharvest treatment. By contrast, the detoxification of feed components present in high concentration, and redirection of electron disposal away from methanogenesis, are more productive targets for microbiological research.}, }
@article {pmid9925618, year = {1999}, author = {van Hannen, EJ and Zwart, G and van Agterveld, MP and Gons, HJ and Ebert, J and Laanbroek, HJ}, title = {Changes in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {2}, pages = {795-801}, pmid = {9925618}, issn = {0099-2240}, mesh = {Animals ; Bacteria/genetics/*growth &amp; development ; *Bacteriolysis ; Bacteriophages/*physiology ; Cyanobacteria/physiology/*virology ; DNA, Ribosomal/chemistry/genetics ; Ecosystem ; Electrophoresis, Agar Gel ; Eukaryota/growth &amp; development ; Fungi/growth &amp; development ; Invertebrates/*growth &amp; development ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Rotifera/growth &amp; development ; Water Microbiology ; }, abstract = {During an experiment in two laboratory-scale enclosures filled with lake water (130 liters each) we noticed the almost-complete lysis of the cyanobacterial population. Based on electron microscopic observations of viral particles inside cyanobacterial filaments and counts of virus-like particles, we concluded that a viral lysis of the filamentous cyanobacteria had taken place. Denaturing gradient gel electrophoresis (DGGE) of 16S ribosomal DNA fragments qualitatively monitored the removal of the cyanobacterial species from the community and the appearance of newly emerging bacterial species. The majority of these bacteria were related to the Cytophagales and actinomycetes, bacterial divisions known to contain species capable of degrading complex organic molecules. A few days after the cyanobacteria started to lyse, a rotifer species became dominant in the DGGE profile of the eukaryotic community. Since rotifers play an important role in the carbon transfer between the microbial loop and higher trophic levels, these observations confirm the role of viruses in channeling carbon through food webs. Multidimensional scaling analysis of the DGGE profiles showed large changes in the structures of both the bacterial and eukaryotic communities at the time of lysis. These changes were remarkably similar in the two enclosures, indicating that such community structure changes are not random but occur according to a fixed pattern. Our findings strongly support the idea that viruses can structure microbial communities.}, }
@article {pmid9925611, year = {1999}, author = {Tanghe, T and Dhooge, W and Verstraete, W}, title = {Isolation of a bacterial strain able to degrade branched nonylphenol.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {2}, pages = {746-751}, pmid = {9925611}, issn = {0099-2240}, mesh = {Alcaligenes/classification/isolation &amp; purification ; Biodegradation, Environmental ; Chromatography, High Pressure Liquid ; Culture Media ; Gas Chromatography-Mass Spectrometry ; Gram-Negative Bacteria/growth &amp; development/*isolation &amp; purification/*metabolism ; Phenols/chemistry/*metabolism ; Pseudomonas putida/classification/isolation &amp; purification ; Sewage/*microbiology ; }, abstract = {Conventional enrichment of microorganisms on branched nonylphenol (NP) as only carbon and energy source yielded mixed cultures able to grow on the organic compound. However, plating yielded no single colonies capable, alone or in combination with other isolates, of degrading the NP in liquid culture. Therefore, a special approach was used, referred to as "serial dilution-plate resuspension," to reduce culture complexity. In this way, one isolate, TTNP3, tentatively identified as a Sphingomonas sp., was found to be able to grow on NP in liquid culture. Remarkably, this isolate was able to be filtered through a 0.45-micrometer-pore-diameter filter. Moreover, isolate TTNP3 did not form visible colonies on mineral medium with NP, and it formed visible colonies on R2A agar only after a prolonged incubation of 1 week. High-performance liquid chromatography and gas chromatography-mass spectroscopy analysis of the culture media indicated that the strain starts the degradation of NP with a fission of the phenol ring and preferably uses the para isomer of NP and not the ortho isomer. No distinct accumulation of an intermediary product could be observed.}, }
@article {pmid9924028, year = {1999}, author = {Leadbetter, JR and Schmidt, TM and Graber, JR and Breznak, JA}, title = {Acetogenesis from H2 plus CO2 by spirochetes from termite guts.}, journal = {Science (New York, N.Y.)}, volume = {283}, number = {5402}, pages = {686-689}, doi = {10.1126/science.283.5402.686}, pmid = {9924028}, issn = {0036-8075}, mesh = {Acetates/*metabolism ; Anaerobiosis ; Animals ; Carbon Dioxide/metabolism ; Culture Media ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Digestive System/microbiology ; Hydrogen/metabolism ; Isoptera/*microbiology ; Molecular Sequence Data ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Spirochaetaceae/classification/isolation &amp; purification/metabolism/physiology ; Treponema/classification/isolation &amp; purification/*metabolism/physiology ; }, abstract = {Pure cultures of termite gut spirochetes were obtained and were shown to catalyze the synthesis of acetate from H2 plus CO2. The 16S ribosomal DNA sequences of two strains were 98 percent similar and were affiliated with those of the genus Treponema. However, neither was closely related to any known treponeme. These findings imply an important role for spirochetes in termite nutrition, help to reconcile the dominance of acetogenesis over methanogenesis as an H2 sink in termite hindguts, suggest that the motility of termite gut protozoa by means of attached spirochetes may be based on interspecies H2 transfer, and underscore the importance of termites as a rich reservoir of novel microbial diversity.}, }
@article {pmid9888858, year = {1999}, author = {Arjan, JA and Visser, M and Zeyl, CW and Gerrish, PJ and Blanchard, JL and Lenski, RE}, title = {Diminishing returns from mutation supply rate in asexual populations.}, journal = {Science (New York, N.Y.)}, volume = {283}, number = {5400}, pages = {404-406}, doi = {10.1126/science.283.5400.404}, pmid = {9888858}, issn = {0036-8075}, mesh = {Adaptation, Physiological ; *Biological Evolution ; Escherichia coli/*genetics/physiology ; Genetics, Population ; Genotype ; Linear Models ; *Models, Biological ; *Mutation ; }, abstract = {Mutator genotypes with increased mutation rates may be especially important in microbial evolution if genetic adaptation is generally limited by the supply of mutations. In experimental populations of the bacterium Escherichia coli, the rate of evolutionary adaptation was proportional to the mutation supply rate only in particular circumstances of small or initially well-adapted populations. These experiments also demonstrate a "speed limit" on adaptive evolution in asexual populations, one that is independent of the mutation supply rate.}, }
@article {pmid9872788, year = {1999}, author = {Velicer, GJ}, title = {Pleiotropic effects of adaptation to a single carbon source for growth on alternative substrates.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {1}, pages = {264-269}, pmid = {9872788}, issn = {1098-5336}, abstract = {It is frequently assumed that populations of genetically modified microorganisms will perform their intended function and then disappear from the environment due to inherent fitness disadvantages resulting from their genetic alteration. However, modified organisms used in bioremediation can be expected to adapt evolutionarily to growth on the anthropogenic substrate that they are intended to degrade. If such adaptation results in improved competitiveness for alternative, naturally occurring substrates, then this will increase the likelihood that the modified organisms will persist in the environment. In this study, bacteria capable of degrading the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) were used to test the effects of evolutionary adaptation to one substrate on fitness during growth on an alternative substrate. Twenty lineages of bacteria were allowed to evolve under abundant resource conditions on either 2,4-D or succinate as their sole carbon source. The competitiveness of each evolved line was then measured relative to that of its ancestor for growth on both substrates. Only three derived lines showed a clear drop in fitness on the alternative substrate after demonstrable adaptation to their selective substrate, while five derived lines showed significant simultaneous increases in fitness on both their selective and alternative substrates. These data demonstrate that adaptation to an anthropogenic substrate can pleiotropically increase competitiveness for an alternative natural substrate and therefore increase the likelihood that a genetically modified organism will persist in the environment.}, }
@article {pmid9872755, year = {1999}, author = {Hahn, MW and Moore, ER and Höfle, MG}, title = {Bacterial filament formation, a defense mechanism against flagellate grazing, is growth rate controlled in bacteria of different phyla.}, journal = {Applied and environmental microbiology}, volume = {65}, number = {1}, pages = {25-35}, pmid = {9872755}, issn = {0099-2240}, mesh = {Animals ; Bacteroides/genetics/growth &amp; development/ultrastructure ; Cytophaga/genetics/growth &amp; development/ultrastructure ; Eukaryota/physiology ; Flavobacterium/genetics/growth &amp; development/ultrastructure ; Genes, Bacterial ; Gram-Negative Aerobic Rods and Cocci/genetics/growth &amp; development/ultrastructure ; Gram-Negative Bacteria/genetics/*growth &amp; development/*ultrastructure ; Molecular Sequence Data ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; }, abstract = {A facultatively filamentous bacterium was isolated from eutrophic lake water and was identified as Flectobacillus sp. strain MWH38 (a member of the Cytophaga-Flavobacterium-Bacteroides phylum) by comparative 16S rRNA gene sequence analysis. Filament formation by Flectobacillus sp. strain MWH38 and filament formation by Flectobacillus major, the closest known relative of strain MWH38, were studied in chemostat cultures under grazing pressure by the bacterivorous flagellate Ochromonas sp. strain DS and without predation at several growth rates. The results clearly demonstrated that filament formation by the two flectobacilli is growth rate controlled and thus independent of the presence of a predator. However, flagellate grazing positively influenced bacterial growth rates by decreasing bacterial biomass and thus indirectly stimulated filament formation. The results of investigations of cell elongation and filament formation by Comamonas acidovorans PX54 (a member of the beta subclass of the class Proteobacteria) supported the recent proposal that in this species the mechanism of filament formation is growth rate controlled. The finding that the grazing defense mechanism consisting of filament formation is growth rate controlled in the flectobacilli investigated and C. acidovorans PX54 (i.e., in bacteria belonging to divergent evolutionary phyla) may indicate that this mechanism is a phylogenetically widely distributed defense strategy against grazing.}, }
@article {pmid9871975, year = {1998}, author = {Peteu, SF and Widman, MT and Worden, RM}, title = {In situ mapping of community-level cellular response with catalytic microbiosensors.}, journal = {Biosensors &amp; bioelectronics}, volume = {13}, number = {11}, pages = {1197-1203}, doi = {10.1016/s0956-5663(98)00070-0}, pmid = {9871975}, issn = {0956-5663}, mesh = {*Biosensing Techniques ; Calibration ; *Chemotaxis ; }, abstract = {Chemotaxis, the migration of cells in the direction of a spatial chemical gradient, is important in disease progression, microbial ecology, and bioremediation. The ability to map chemoattractant gradients and the corresponding cellular growth and motility patterns is essential to the study of chemotaxis. Microelectrodes and microbiosensors have the potential to measure chemoattractant gradients with high spatial resolution. In this study, Clark-type amperometric microelectrodes and microbiosensors were used to measure solute concentrations gradients generated by a chemotactic band of Escherichia coli in a semi-solid gel. A computerized image analysis system was used to simultaneously measure the cellular concentration profile across the chemotactic band. The experimental results compared favorably with a mathematical model of solute and cell transport in the gel. Scanning electron micrographs (SEM) of micro(bio)sensor tips taken after 6 months of use showed evidence of degradation, including adhesion of foreign particles to the glass body, the adhesion of a small gel capsule to the sensor tip, and separation of the bio-interface from the tip. A needle-type microbiosensor was constructed to better protect the tip and hence increase the ruggedness of the microbiosensors.}, }
@article {pmid9852524, year = {1999}, author = {Berthe-Corti, L and Bruns, A}, title = {The Impact of Oxygen Tension on Cell Density and Metabolic Diversity of Microbial Communities in Alkane Degrading Continuous-Flow Cultures.}, journal = {Microbial ecology}, volume = {37}, number = {1}, pages = {70-77}, doi = {10.1007/s002489900131}, pmid = {9852524}, issn = {1432-184X}, abstract = {Abstract The impact of the dissolved O2 tension (DOT) and the dilution rate on the metabolic diversity of an autochthonous hexadecane-degrading community in continuous-flow cultures containing hexadecane-coated intertidal sediment was determined in a set of experiments. The DOT was kept constant within each culture at values of 80% (168 µmol O2L-1) or 0.4% (0.84 µmol O2 L-1). The dilution rate was increased from D = 0.012 h-1 to D = 0.06 h-1. To determine the culture activity, we analyzed the hexadecane degradation rate, the protein production rate, and the oxygen consumption rate. The cell concentration of different metabolic groups was determined by colony forming units (CFU), and by most probable number (MPN). The metabolic diversity was determined by the substrate utilization spectrum in Biolog GN microtiter plates. The substrate utilization pattern of the cultures decreased considerably as D increased. This effect was more pronounced at 0.4% of DOT than at 80% of DOT. The MPN and CFU revealed that as D increased, only minor changes occurred in the community structure. The hexadecane degradation rate, the protein production rate, and the oxygen consumption rate increased parallel to D independently of the DOT. This means that the biocenosis at 0.4% of DOT was different from the biocenosis at 80% of DOT, although the metabolic activity of the cultures was unaffected by a 200-factor difference in the oxygen tension and revealed a considerable buffer capacity with respect to changes in DOT.}, }
@article {pmid9852523, year = {1999}, author = {Muela, A and Arana, I and Justo, JI and Seco, C and Barcina, I}, title = {Changes in DNA Content and Cellular Death during a Starvation-Survival Process of Escherichia coli in River Water.}, journal = {Microbial ecology}, volume = {37}, number = {1}, pages = {62-69}, doi = {10.1007/s002489900130}, pmid = {9852523}, issn = {1432-184X}, abstract = {Abstract Four nucleoid staining procedures were compared during the starvation-survival process of Escherichia coli in river water. Only the method performed as a modification of the standard acridine orange direct procedure allowed us to visualize nucleoids during the 95 days of experimentation. Moreover, with this method the total number of cells and nucleoid-containing cells can be simultaneously enumerated. The decrease of the chromosomal DNA content of population and of the nucleoid-containing cells indicates that ghosts form and cellular death occurs throughout the starvation-survival process. A long time (<30 days) is needed for non-nucleoid-containing cells to appear in river water; plasmid DNA is also negatively affected by environmental stress. After 4 days of storage in river water, the need to increase the volume of lysed cells used for the plasmid band visualization as well as the decrease in the plasmid band intensity would indicate a decrease in the plasmid DNA content during the starvation-survival process. According to our results, both chromosomal and plasmid DNA content decrease during the starvation-survival process of E. coli in river water.}, }
@article {pmid9852522, year = {1999}, author = {Friedrich, U and Schallenberg, M and Holliger, C}, title = {Pelagic Bacteria-Particle Interactions and Community-Specific Growth Rates in Four Lakes along a Trophic Gradient.}, journal = {Microbial ecology}, volume = {37}, number = {1}, pages = {49-61}, doi = {10.1007/s002489900129}, pmid = {9852522}, issn = {1432-184X}, abstract = {Abstract The relationships between bacterial concentration, bacterial production, and cell-specific activity of both free and attached bacteria and environmental factors such as suspended solids, nutrients, and temperature were examined in four lakes, two in New Zealand and two in Switzerland. Estimates of cell-specific production were obtained by microautoradiographic counts of [3H]thymidine-labeled cells. Bacteria attached to particles accounted for only 1.3 to 11.6% of the total bacterial abundance, but showed overall 20-fold higher specific growth rates and were relatively more active than their free counterparts. On average, 80 to 100% of epibacteria were attached to organic particles. The abundance and production of free and attached bacteria were positively correlated; however, relationships between these fractions and some environmental variables differed. Cell-specific activities of active bacteria were not equivalent to mean cellular activities of the entire bacterial community and differed in their relationship to trophic state. [3H]Thymidine-positive bacteria were more tightly linked to chlorophyll a than were total bacteria. Our findings indicate that production by attached bacteria, fueled by phytoplankton carbon, supplies "new" free bacteria to the bacterial community. Our results support the idea that particulate organic matter acts as a source of dissolved nutrients to free bacteria. Bottom-up control of bacterial biomass, as shown by regressions of biomass vs production, appeared to be stronger in two ultraoligotrophic lakes than in two more eutrophic ones.}, }
@article {pmid9852521, year = {1999}, author = {Unanue, M and Ayo, B and Agis, M and Slezak, D and Herndl, GJ and Iriberri, J}, title = {Ectoenzymatic Activity and Uptake of Monomers in Marine Bacterioplankton Described by a Biphasic Kinetic Model.}, journal = {Microbial ecology}, volume = {37}, number = {1}, pages = {36-48}, doi = {10.1007/s002489900128}, pmid = {9852521}, issn = {1432-184X}, abstract = {Abstract The kinetics of bacterial hydrolytic ectoenzymatic activity and the uptake of monomeric compounds were investigated in the Northwestern Mediterranean Sea. Aminopeptidase and alpha- and beta-glucosidase activities were analyzed by using fluorogenic substrates at 15-22 concentrations ranging from 1 nM to 500 µM. Radiolabeled glucose and a mixture of amino acids were chosen as representatives of monomeric compounds, and the bacterial uptake rates (assimilation plus respiration) were determined over a wide range of substrate concentrations (from 0.2 nM to 3 µM). We found biphasic kinetics both for hydrolytic enzymes and uptake systems: high affinity enzymes at low concentrations of substrates (Km values ranged from 48 nM to 2.7 µM for ectoenzymes and from 1.4 nM to 42 nM for uptake systems), and low affinity enzymes at high concentrations of substrates (Km values ranged from 18 µM to 142 µM for ectoenzymes and from 0.1 µM to 1.3 µM for uptake systems). Transition between high and low affinity enzymes was observed at 10 µM for aminopeptidase and from 1 µM to 25 µM for glucosidases, and it was more variable and less pronounced for the uptake of glucose (40 nM-0.28 µM) and amino acids (10 nM-0.16 µM). Results showed that the potential rates of hydrolysis and uptake are tightly coupled only if the high affinity hydrolytic ectoenzymes and the low affinity uptake systems are operating simultaneously.}, }
@article {pmid9852520, year = {1999}, author = {Wehr, JD and Petersen, J and Findlay, S}, title = {Influence of Three Contrasting Detrital Carbon Sources on Planktonic Bacterial Metabolism in a Mesotrophic Lake.}, journal = {Microbial ecology}, volume = {37}, number = {1}, pages = {23-35}, doi = {10.1007/s002489900127}, pmid = {9852520}, issn = {1432-184X}, abstract = {Abstract Lakes receive organic carbon from a diversity of sources which vary in their contribution to planktonic microbial food webs. We conducted a mesocosm study to test the effects of three different detrital carbon sources (algae, aquatic macrophytes, terrestrial leaves) on several measures of microbial metabolism in a small meso-eutrophic lake (DOC approximately 5 mg/L). Small DOC additions (DeltaC < 1 mg/L) affected bacterial numbers, growth, and pathways of carbon acquisition. Macrophyte and leaf detritus significantly increased TDP and color, but bacterial densities initially (+12 h) were unaffected. After 168 h, densities in systems amended with terrestrial detritus were 60% less than in controls, while production rates in mesocosms with macrophyte detritus were 4-fold greater. Detritus treatments resulted in greater per-cell production rates either through stable cell numbers and greater growth rates (macrophyte-C) or lower densities with stable production rates (terrestrial-C). After only 12 h, rates of leucine aminopeptidase (LAPase) activity were 2.5x greater in macrophyte-C systems than in controls, but LAPase and beta-N-acetylglucosamindase activities in systems amended with terrestrial-C were only 50% of rates in controls. After 168 h, beta-xylosidase rates were significantly greater in communities with terrestrial and phytoplankton detritus. Microbial utilization of >20% of 102 carbon sources tested were affected by at least one detritus addition. Macrophyte-C had positive (6% of substrates) and negative (14%) effects on substrate use; terrestrial detritus had mainly positive effects. An ordination based on carbon-use profiles (+12 h) revealed a cluster of macrophyte-amended communities with greater use of psicose, lactulose, and succinamic acid; controls and algal-detritus systems were more effective in metabolizing two common sugars and cellobiose. After 168 h, communities receiving terrestrial detritus were most tightly clustered, exhibiting greater use of raffinose, pyroglutamic acid, and sebacic acid. Results suggest that pelagic bacterial communities respond to changes in organic carbon source rapidly and by different routes, including shifts in per-cell production rates and variations in degradation of a variety of compounds comprising the DOC pool.}, }
@article {pmid9852519, year = {1999}, author = {Dini, F and Nyberg, D}, title = {Growth Rates of Marine Ciliates on Diverse Organisms Reveal Ecological Specializations within Morphospecies.}, journal = {Microbial ecology}, volume = {37}, number = {1}, pages = {13-22}, doi = {10.1007/s002489900126}, pmid = {9852519}, issn = {1432-184X}, abstract = {Abstract The growth rate of 31 stocks of Euplotes, a cosmopolitan, marine, unicellular protist, on six food species representing two different food types, microalgae and bacteria, has been determined. The 31 stocks represented nine reproductively isolated groups (biological species?) based on breeding relationships. Three morphospecies, E. vannus, E. crassus, and E. minuta, each with both autogamous and cross-breeding breeding groups, were included. The mean number of fissions completed in 5 days of a breeding group growing on one of the six food species varied from zero to 17.06. There is a strong interaction between morphospecies and food type. The largest morphospecies, E. vannus, translates the nutritional content of algae into growth better than it translates that of bacteria, while the reverse is true for E. minuta, the smallest morphospecies. Autogamous breeding groups grow more rapidly on algae than on bacteria when compared to cross-breeding groups in the same morphospecies. Two breeding groups cannot grow on Escherichia coli. ANOVA of fissions completed in 5 days revealed significant main effects and interactions between many hierarchical levels of stocks and food species. These significant interactions indicate that genetically determined ecologically important information is present at all taxonomic levels-morphospecies, breeding system, breeding group, and stock. As all these levels are biologically meaningful, measuring biodiversity in the E. vannus-crassus-minuta complex solely on morphospecies will inadequately represent the ecological diversity present in the organisms and their environment.}, }
@article {pmid9852518, year = {1999}, author = {Tso, SF and Taghon, GL}, title = {Factors Affecting Predation by Cyclidium sp. and Euplotes sp. on PAH-Degrading and Nondegrading Bacteria.}, journal = {Microbial ecology}, volume = {37}, number = {1}, pages = {3-12}, doi = {10.1007/s002489900125}, pmid = {9852518}, issn = {1432-184X}, abstract = {Abstract If predators select for or against contaminant-degrading bacteria, it will affect bacterial survival and has important implications for bioremediation. Protozoa are important predators of bacteria. In order to determine whether protozoa preyed differentially on bacteria with different degradation abilities, two ciliates (Euplotes sp. and Cyclidium sp.) and three strains of PAH-degrading bacteria (Vibrio spp., degrading naphthalene, anthracene, or phenanthrene) were isolated from sediment from New York/New Jersey Harbor. By manipulating growth conditions, bacterial strains with different PAH-degradation abilities and different cell properties were produced. Stepwise regression models were used to analyze how clearance rates on suspended bacteria and grazing rates on bacteria attached to particles were affected by bacterial size, hydrophobicity, C:N ratio, protein content, and PAH-degradation ability. Clearance rates ranged from 0 to 49 nl ciliate-1 h-1 for Euplotes sp. and from 0 to 1.7 nl ciliate-1 h-1 for Cyclidium sp. Clearance rates of both ciliates were positively correlated with bacterial size, hydrophobicity, and protein content, and negatively correlated with C:N ratio. PAH degradation ability had no (for Euplotes sp.) or small (for Cyclidium sp.) effects on clearance rates. The models accounted for 63-75% of the variation in clearance rates on different bacteria. Only Euplotes sp. grazed on attached bacteria, at rates from 3 to 176 bacteria ciliate-1 h-1. A regression model with only C:N ratio and protein content explained 45% of the variation in grazing rates. These models indicate that multiple properties of bacteria affect their susceptibility to predation by ciliates, but PAH-degradation ability per se has little effect.}, }
@article {pmid9852517, year = {1999}, author = {Fredrickson, JK and Tiedje, JM}, title = {Microbial Ecology Becomes the Official Journal of the International Society for Microbial Ecology.}, journal = {Microbial ecology}, volume = {37}, number = {1}, pages = {1-2}, doi = {10.1007/s002489900124}, pmid = {9852517}, issn = {1432-184X}, }
@article {pmid9852516, year = {1998}, author = {Wells, JM and Harris, MJ and Boddy, L}, title = {Encounter with New Resources Causes Polarized Growth of the Cord-Forming Basidiomycete Phanerochaete velutina on Soil.}, journal = {Microbial ecology}, volume = {36}, number = {3}, pages = {372-382}, doi = {10.1007/s002489900123}, pmid = {9852516}, issn = {1432-184X}, abstract = {Abstract The development and physiology of cord-forming saprotrophic basidiomycetes, which form extensive and persistent mycelial networks in woodland ecosystems, can be conveniently studied on non-sterile soil in laboratory microcosms mimicking field conditions. Morphological responses of Phanerochaete velutina mycelial systems to resource encounters, and decay partitioning following encounters, varied according to whether simulated woody litter was unsterile or autoclaved and on whether encounter took place at the mycelial foraging front or behind the margin (simulating litter fall onto established systems in the field). Results show that encounter of discrete resources by P. velutina is rapidly communicated to the entire mycelial system; that resource capture takes high priority at the expense of continued system extension and decay-derived carbon reallocation; and that polarized growth toward newly encountered resources, previously considered to occur infrequently with this species, may be readily detected using image analysis techniques. Potential advantages of polarized development of P. velutina are discussed.}, }
@article {pmid9852515, year = {1998}, author = {McMahon, KD and Stahl, DA and Raskin, L}, title = {A Comparison of the Use of In Vitro-Transcribed and Native rRNA for the Quantification of Microorganisms in the Environment.}, journal = {Microbial ecology}, volume = {36}, number = {3}, pages = {362-371}, doi = {10.1007/s002489900122}, pmid = {9852515}, issn = {1432-184X}, abstract = {Abstract Nearly full-length, small subunit (SSU) rRNA was transcribed in vitro from clones of SSU rDNA genes. Comparing the use of in vitro-transcribed and native rRNA indicated that, when in vitro-transcribed rRNA was used as a standard for quantitative hybridizations with oligonucleotide probes, the population was consistently underestimated. The population abundance was expressed as a percentage of specific target SSU rRNA (determined with a specific oligonucleotide probe), relative to the total SSU rRNA (measured with a universal probe). Differences in hybridization signals could be related to specific probe target locations and rRNA denaturation conditions, suggesting that higher order structure is important in quantitative membrane hybridizations. Therefore, in vitro-transcribed rRNA cannot always be used for the absolute quantification of microbial populations, but can be employed as a standard to quantify shifts in population abundance over time, and to compare community structure in various environments.}, }
@article {pmid9852514, year = {1998}, author = {Stapleton, RD and Sayler, GS}, title = {Assessment of the Microbiological Potential for the Natural Attenuation of Petroleum Hydrocarbons in a Shallow Aquifer System.}, journal = {Microbial ecology}, volume = {36}, number = {3}, pages = {349-361}, doi = {10.1007/s002489900121}, pmid = {9852514}, issn = {1432-184X}, abstract = {Abstract A multidisciplinary field study investigating the fate and transport of petroleum hydrocarbons commonly associated with jet-fuel contamination is currently underway at Columbus Air Force Base (AFB), Mississippi. Sixty sediment cores from 12 boreholes were recovered from the study aquifer. The goal of this initial sampling was to characterize the potential microbial activity using 14C-labeled substrates, as well as the presence, abundance, and distribution of specific hydrocarbon degrading genotypes using DNA:DNA hybridization. Enumeration of total microbial abundance using a 16S rDNA universal oligonucleotide probe was compared to traditional enumeration methods. Total culturable populations determined by spread plate analysis ranged from a low of 10(4) to more than 10(6) organisms per gram sediment. Microbial abundance estimated by DNA hybridization studies with 16S rDNA genes ranged from 10(7) to 10(8) organisms per gram sediment. Molecular analysis of aquifer samples using DNA probes targeting genes encoding the degradative enzymes alkane hydroxylase (alkB), catechol 2,3-dioxygenase (nahH), naphthalene dioxygenase (nahA), toluene dioxygenase (todC1C2), toluene monooxygenase (tomA), and xylene monooxygenase (xylA), as well as two probes measuring methanogenic microorganisms, codh (carbon monoxide dehydrogenase) and mcr (methyl coenzyme reductase), revealed that each target gene sequence was present in nearly all 60 samples. The presence of organisms demonstrating the phenotype to degrade BTEX and naphthalene was further supported using mineralization assays with 14C-labeled benzene, toluene, naphthalene, and phenanthrene. Minimal activity occurred during the first 24 hours. After a period of 5-7 days, greater than 40% of the target compounds were mineralized in aquifer sediments.}, }
@article {pmid9852513, year = {1998}, author = {Kieft, TL and Murphy, EM and Haldeman, DL and Amy, PS and Bjornstad, BN and McDonald, EV and Ringelberg, DB and White, DC and Stair, J and Griffiths, RP and Gsell, TC and Holben, WE and Boone, DR}, title = {Microbial Transport, Survival, and Succession in a Sequence of Buried Sediments.}, journal = {Microbial ecology}, volume = {36}, number = {3}, pages = {336-348}, doi = {10.1007/s002489900120}, pmid = {9852513}, issn = {1432-184X}, abstract = {Abstract Two chronosequences of unsaturated, buried loess sediments, ranging in age from <10,000 years to >1 million years, were investigated to reconstruct patterns of microbial ecological succession that have occurred since sediment burial. The relative importance of microbial transport and survival to succession was inferred from sediment ages, porewater ages, patterns of abundance (measured by direct counts, counts of culturable cells, and total phospholipid fatty acids), activities (measured by radiotracer and enzyme assays), and community composition (measured by phospholipid fatty acid patterns and Biolog substrate usage). Core samples were collected at two sites 40 km apart in the Palouse region of eastern Washington State, near the towns of Washtucna and Winona. The Washtucna site was flooded multiple times during the Pleistocene by glacial outburst floods; the Winona site elevation is above flood stage. Sediments at the Washtucna site were collected from near surface to 14.9 m depth, where the sediment age was approximately 250 ka and the porewater age was 3700 years; sample intervals at the Winona site ranged from near surface to 38 m (sediment age: approximately 1 Ma; porewater age: 1200 years). Microbial abundance and activities declined with depth at both sites; however, even the deepest, oldest sediments showed evidence of viable microorganisms. Same-age sediments had equal quantities of microorganisms, but different community types. Differences in community makeup between the two sites can be attributed to differences in groundwater recharge and paleoflooding. Estimates of the microbial community age can be constrained by porewater and sediment ages. In the shallower sediments (<9 m at Washtucna, <12 m at Winona), the microbial communities are likely similar in age to the groundwater; thus, microbial succession has been influenced by recent transport of microorganisms from the surface. In the deeper sediments, the populations may be considerably older than the porewater ages, since microbial transport is severely restricted in unsaturated sediments. This is particularly true at the Winona site, which was never flooded.}, }
@article {pmid9852512, year = {1998}, author = {Ohtonen, R and Väre, H}, title = {Vegetation Composition Determines Microbial Activities in a Boreal Forest Soil.}, journal = {Microbial ecology}, volume = {36}, number = {3}, pages = {328-335}, doi = {10.1007/s002489900119}, pmid = {9852512}, issn = {1432-184X}, abstract = {Abstract Forest soil ecology was studied in Fennoscandinavian dry Scots pine forests grazed by reindeer to varying extents (ungrazed, lichen-dominated-sites; grazed sites; and bryophyte-dominated sites). We hypothesized that the productivity parameters of the site (i.e., tree growth and soil nutrient concentrations), the vegetation composition, and the microbial activities are directly correlated. Since the productivity of the lichen-dominated ecosystem is low, microbial activities are assumed to be naturally low. Grazing was expected to decrease both the amount of Scots pine fine roots and the soil microbial activities. Several variables on the characteristics of the soil microbial community, Scots pine fine roots, soil nutrients, and tree growth were studied in relation to vegetation composition by using non-metric multidimensional scaling (NMDS). Basal respiration (Bas), metabolic quotient of the microbial community (qCO2), and pine fine root parameters increased toward the ungrazed, nutrient-poor, lichen-dominated sites, which were grouped at one end of the first axis in the NMDS ordination. Soil nutrient and tree growth parameters and thickness of the humus layer increased toward bryophyte-dominated sites, which were grouped at the other end of the first axis in the ordination. The grazed sites fell between them. These were characterized by lower Bas and qCO2 values and longer lag, compared to ungrazed lichen- or bryophyte-dominated sites, probably due to decreased carbon input and microclimatic change (the soil without lichen carpet is exposed to direct sunlight and wind). Microbial biomass (Cmic), fungal biomass (ergosterol concentration), and the specific growth rate (µCO2) were not related to vegetation ordination. The high fine root production is the most plausible explanation for the high microbial activities at nutrient-poor, lichen-dominated sites, which produce qualitatively poor and slowly decomposing litter, as fine roots secrete considerable amounts of organic substances. At bryophyte-dominated sites, the higher soil nutrient concentrations and the higher production of easily decomposable substrates are likely to maintain the microbial activities.}, }
@article {pmid9852511, year = {1998}, author = {Bååth, E}, title = {Growth Rates of Bacterial Communities in Soils at Varying pH: A Comparison of the Thymidine and Leucine Incorporation Techniques.}, journal = {Microbial ecology}, volume = {36}, number = {3}, pages = {316-327}, doi = {10.1007/s002489900118}, pmid = {9852511}, issn = {1432-184X}, abstract = {Abstract The growth rate of bacteria in 19 soils with pH values ranging from 4 to 8 was determined using the thymidine (TdR) and leucine (Leu) incorporation techniques. The variation in isotope dilution and unspecific incorporation was also studied. The mean Leu incorporation into protein was 45% of the incorporation into total macromolecules, and was not affected by soil pH. TdR incorporation into DNA varied between 5 and 20% of that into total macromolecules, with the lowest values in the low-pH soils. Isotope dilution plots for Leu incorporation were linear. This was not the case for TdR incorporation, indicating non-Michaelis-Menten kinetics. The degree of participation (DP) of the added labeled compound in Leu incorporation varied between 0.4 (in low-pH soils) and 0.7 and was directly affected by pH. DP for TdR incorporation varied more (from 0.1 to 1), with the lowest values in the low-pH soils. The variation in DP in TdR incorporation was, however, not directly affected by pH. Calculated bacterial turnover times at 20 degreesC varied between 2.3 and 33 days (mean 9.3 days) using TdR incorporation data, and between 2.1 and 13.1 days (mean 5.9 days) using Leu incorporation data. Turnover times were longer for bacteria in low-pH soils, calculated using the Leu incroporation data, while no effect from pH was found using the TdR incorporation data. Comparing data from aquatic habitats indicated that bacterial growth rates in soil were lower.}, }
@article {pmid9852510, year = {1998}, author = {Øvreås, L and Torsvik, V}, title = {Microbial Diversity and Community Structure in Two Different Agricultural Soil Communities.}, journal = {Microbial ecology}, volume = {36}, number = {3}, pages = {303-315}, doi = {10.1007/s002489900117}, pmid = {9852510}, issn = {1432-184X}, abstract = {Abstract In this study, two different agricultural soils were investigated: one organic soil and one sandy soil, from Stend (south of Bergen), Norway. The sandy soil was a field frequently tilled and subjected to crop rotations. The organic soil was permanent grazing land, infrequently tilled. Our objective was to compare the diversity of the cultivable bacteria with the diversity of the total bacterial population in soil. About 200 bacteria, randomly isolated by standard procedures, were investigated. The diversity of the cultivable bacteria was described at phenotypic, phylogenetic, and genetic levels by applying phenotypical testing (Biolog) and molecular methods, such as amplified rDNA restriction analysis (ARDRA); hybridization to oligonucleotide probes; and REP-PCR. The total bacterial diversity was determined by reassociation analysis of DNA isolated from the bacterial fraction of environmental samples, combined with ARDRA and DGGE analysis. The relationship between the diversity of cultivated bacteria and the total bacteria was elucidated. Organic soil exhibited a higher diversity for all analyses performed than the sandy soil. Analysis of cultivable bacteria resulted in different resolution levels and revealed a high biodiversity within the population of cultured isolates. The difference between the two agricultural soils was significantly higher when the total bacterial population was analyzed than when the cultivable population was. Thus, analysis of microbial diversity must ultimately embrace the entire microbial community DNA, rather than DNA from cultivable bacteria.}, }
@article {pmid9852509, year = {1998}, author = {Bruns, MA and Fries, MR and Tiedje, JM and Paul, EA}, title = {Functional Gene Hybridization Patterns of Terrestrial Ammonia-Oxidizing Bacteria.}, journal = {Microbial ecology}, volume = {36}, number = {3}, pages = {293-302}, doi = {10.1007/s002489900116}, pmid = {9852509}, issn = {1432-184X}, abstract = {Abstract The biochemical pathway and genetics of autotrophic ammonia oxidation have been studied almost exclusively in Nitrosomonas europaea. Terrestrial autotrophic ammonia-oxidizing bacteria (AAOs), however, comprise two distinct phylogenetic groups in the beta-Proteobacteria, the Nitrosomonas and Nitrosospira groups. Hybridization patterns were used to assess the potential of functional probes in non-PCR-based molecular analysis of natural AAO populations and their activity. The objective of this study was to obtain an overview of functional gene homologies by hybridizing probes derived from N. europaea gene sequences ranging in size from 0.45 to 4.5 kb, and labeled with 32P to Southern blots containing genomic DNA from four Nitrosospira representatives. Probes were specific for genes encoding ammonia monooxygenase (amoA and amoB), hydroxylamine oxidoreductase (hao), and cytochrome c-554 (hcy). These probes produced hybridization signals, at low stringency (30 degreesC), with DNA from each of the four representatives; signals at higher stringency (42 degreesC) were greatly reduced or absent. The hybridization signals at low stringency ranged from 20 to 76% of the total signal obtained with N. europaea DNA. These results indicate that all four functional genes in the ammonia oxidation pathway have diverged between the Nitrosomonas and Nitrosospira groups. The hao probe produced the most consistent hybridization intensities among the Nitrosospira representatives, suggesting that hao sequences would provide the best probes for non-PCR-based molecular analysis of terrestrial AAOs. Since N. europaea can also denitrify, an additional objective was to hybridize genomic DNA from AAOs with probes for Pseudomonas genes involved in denitrification. These probes were specific for genes encoding heme-type dissimilatory nitrite reductase (dNir), Cu-type dNir, and nitrous oxide reductase (nosz). No hybridization signals were observed from probes for the heme-type dNir or nosz, but Nitrosospira sp. NpAV and Nitrosolobus sp. 24-C hybridized, under low-stringency conditions, with the Cu-type dNir probe. These results indicate that AAOs may also differ in their mechanisms and capacities for denitrification.}, }
@article {pmid9852508, year = {1998}, author = {Garza, DR and Suttle, CA}, title = {The Effect of Cyanophages on the Mortality of Synechococcus spp. and Selection for UV Resistant Viral Communities.}, journal = {Microbial ecology}, volume = {36}, number = {3}, pages = {281-292}, doi = {10.1007/s002489900115}, pmid = {9852508}, issn = {1432-184X}, abstract = {Abstract Viruses that cause lysis of Synechococcus spp. are present throughout the year in the western Gulf of Mexico. The effect of sunlight on loss rates of cyanophage infectivity was determined by incubating natural cyanophage communities and cyanophage isolates (strains S-PWM1 and S-PWM3) in UV-transparent bags at the surface, and at depth, on several occasions throughout the year. Decay rates of infectivity of natural cyanophage communities at the surface, at Port Aransas, Texas, USA, ranged from undetectable to 0.335 h-1, with the highest rates occurring during the summer. During the spring and winter, decay rates of cyanophage isolates and natural cyanophage communities were generally similar, but during summer, decay rates of isolates were as much as twofold higher than the natural communities. In situ incubations at two offshore stations during a bloom of Synechococcus spp. produced decay rates of 0.53 and 0.75 d-1, integrated over the mixed layer and averaged over 24 h. Based on a burst size of 81 viruses produced per lysed cell (measured for natural cyanobacterial communities in the Gulf of Mexico), cyanophages imposed mortality rates of 1 and 8%, respectively, on Synechococcus spp. In contrast, in nearshore incubations in the winter and spring, cyanophages were responsible for removing <1% of the Synechococcus cells on a daily basis. Only an estimated 2 to 3% of contacts led to viral infections (based on theoretical contact rates between host cells and cyanophages, and estimates of cyanophage mortality), regardless of the time of year or concentrations of viruses and hosts. These results indicate that natural cyanophage communities tolerate damage by solar radiation better in summer than in winter. Moreover, net decay rates of cyanophage infectivity in sunlight were similar, whether host cells were present or not, indicating that detectable cyanophage production did not occur during daytime in situ incubations.}, }
@article {pmid9852507, year = {1998}, author = {Reche, I and Pace, ML and Cole, JJ}, title = {Interactions of Photobleaching and Inorganic Nutrients in Determining Bacterial Growth on Colored Dissolved Organic Carbon.}, journal = {Microbial ecology}, volume = {36}, number = {3}, pages = {270-280}, doi = {10.1007/s002489900114}, pmid = {9852507}, issn = {1432-184X}, abstract = {Abstract Bacteria are key organisms in the processing of dissolved organic carbon (DOC) in aquatic ecosystems. Their growth depends on both organic substrates and inorganic nutrients. The importance of allochthonous DOC, usually highly colored, as bacterial substrate can be modified by photobleaching. In this study, we examined how colored DOC (CDOC) photobleaching, and phosphorus (P) and nitrogen (N) availability, affect bacterial growth. Five experiments were conducted, manipulating nutrients (P and N) and sunlight exposure. In almost every case, nutrient additions had a significant, positive effect on bacterial abundance, production, and growth efficiency. Sunlight exposure (CDOC photobleaching) had a significant, positive effect on bacterial abundance and growth efficiency. We also found a significant, positive interaction between these two factors. Thus, bacterial use of CDOC was accelerated under sunlight exposure and enhanced P and N concentrations. In addition, the accumulation of cells in sunlight treatments was dependent on nutrient availability. More photobleached substrate was converted into bacterial cells in P- and N-enriched treatments. These results suggest nutrient availability may affect the biologically-mediated fate (new biomass vs respiration) of CDOC.}, }
@article {pmid9852506, year = {1998}, author = {Fisher, MM and Graham, JM and Graham, LE}, title = {Bacterial Abundance and Activity across Sites within Two Northern Wisconsin Sphagnum Bogs.}, journal = {Microbial ecology}, volume = {36}, number = {3}, pages = {259-269}, doi = {10.1007/s002489900113}, pmid = {9852506}, issn = {1432-184X}, abstract = {Abstract Bacterial abundance, temperature, pH, and dissolved organic carbon (DOC) concentration were compared across surface sites within and between two northern Wisconsin Sphagnum peatlands over the summer seasons in 1995 and 1996. Sites of interest were the Sphagnum mat surface, the water-filled moat (lagg) at the bog margin, and the bog lake littoral zone. Significant differences in both bacterial populations and water chemistry were observed between sites. pH was highest in the lake and lowest in the mat at both bogs; the opposite was true for DOC. Large populations of bacteria were present in surface interstitial water from the mat; abundance in this site was consistently higher than in the moat or lake. Bacterial abundance also increased across sites of increasing DOC concentration and declining pH. Bacterial activities (rates of [3H]leucine incorporation) and growth in dilution cultures (with grazers removed) were also assessed in lake, moat, and mat sites. Results using these measures generally supported the trends observed in abundance, although high rates of [3H]leucine incorporation were recorded in the moat at one of the bogs. Our results indicate that bacterial populations in Sphagnum peatlands are not adversely affected by acidity, and that DOC may be more important than pH in determining bacterial abundance in these environments.}, }
@article {pmid9852505, year = {1998}, author = {Nausch, M and Pollehne, F and Kerstan, E}, title = {Extracellular Enzyme Activities in Relation to Hydrodynamics in the Pomeranian Bight (Southern Baltic Sea).}, journal = {Microbial ecology}, volume = {36}, number = {3}, pages = {251-258}, doi = {10.1007/s002489900112}, pmid = {9852505}, issn = {1432-184X}, abstract = {Abstract The Pomeranian Bight in the southern Baltic Sea is characterized by a huge input of nutrients from the Oder river. This input shows seasonal variation. In winter, the nutrients are introduced in inorganic form. Particulate organic material is dominant in the growth season (summer/autumn). From 1993 to 1996, extracellular enzyme activities (alkaline phosphatase, peptidase, alpha-, beta-glucosidase, and chitinase) were investigated to describe microbial reaction to the input of organic material and the modification of introduced material. The distribution patterns of extracellular enzyme activities in salinity gradients were studied, in response to the nutrient load. These activities were distinctly lower in winter than in summer and autumn. A close relationship to other biological parameters (Chl a, POC, PON) was observed during the growth season, but not in winter. Changes in peptidase and phosphatase activities between summer and autumn were also observed. The peptidase activity was 9 to 72 times higher in autumn than in summer. In contrast, the alkaline phosphatase activity was 5 to 30 times higher in summer than in autumn. The organic compound turnover rate/hydrolysis rate (To/Hr) ratio is a relative index which describes the coupling of enzymatic hydrolysis and utilization of monomers from investigated substrates (carbohydrates and proteins). In summer, after dilution, the raised To/Hr quotients of glucose indicated limited importance for hydrolysis products in bacterial turnover. The increased demand for glucose resulted in a parallel decrease in monosaccharides. In autumn, the relationship between the turnover of glucose and amino acids and the supply of these substances by enzymatic degradation remained at the same level.}, }
@article {pmid9852504, year = {1998}, author = {Takacs, CD and Priscu, JC}, title = {Bacterioplankton Dynamics in the McMurdo Dry Valley Lakes, Antarctica: Production and Biomass Loss over Four Seasons.}, journal = {Microbial ecology}, volume = {36}, number = {3}, pages = {239-250}, doi = {10.1007/s002489900111}, pmid = {9852504}, issn = {1432-184X}, abstract = {Abstract Research of the microbial ecology of McMurdo Dry Valley lakes has concentrated primarily on phototrophs; relatively little is known about the heterotrophic bacterioplankton. Bacteria represent a substantial proportion of water column biomass in these lakes, comprising 30 to 60% of total microplankton biomass. Bacterial production and cell numbers were measured 3 to 5 times, within four Antarctic seasons (October to January), in Lakes Fryxell, Hoare, and Bonney. The winter-spring transition (September to October) was included during one year. Lake Fryxell was the most productive, but variable, lake, followed by Lakes Bonney and Hoare. Bacterial production ranged from 0 to 0.009 µg C ml-1 d-1; bacterial populations ranged from 3.2 x 10(4) to 4.4 x 10(7) cells ml-1. Bacterial production was always greatest just below the ice cover at the beginning of the season. A second maximum developed just above the chemocline of all the lakes, as the season progressed. Total bacterioplankton biomass in the lakes decreased as much as 88% between successive sampling dates in the summer, as evidenced by areal integration of bacterial populations; the largest decreases in biomass typically occurred in mid-December. A forward difference model of bacterial loss in the trophogenic zone and the entire water column of these lakes showed that loss rates in the summer reached 6.3 x 10(14) cells m-2 d-1 and 4.16 x 10(12) cells m-2 d-1, respectively. These results imply that bacteria may be a source of carbon to higher trophic levels in these lakes, through grazing.}, }
@article {pmid9852503, year = {1998}, author = {Olson, JB and Steppe, TF and Litaker, RW and Paerl, HW}, title = {N2-Fixing Microbial Consortia Associated with the Ice Cover of Lake Bonney, Antarctica.}, journal = {Microbial ecology}, volume = {36}, number = {3}, pages = {231-238}, doi = {10.1007/s002489900110}, pmid = {9852503}, issn = {1432-184X}, abstract = {Abstract Nitrogen (N) availability is a key nutritional factor controlling microbial production in Antarctic freshwater and soil habitats. Since there are no significant sources of biologically available N entering these ecosystems, nitrogen fixation may be a major source of "new" N supporting primary and secondary production. The role of N2 fixation was examined in cyanobacteria-dominated microbial aggregates embedded in the permanent ice cover of Lake Bonney, McMurdo Dry Valley (Victoria Land) lakes area, and in cyanobacterial mats found in soils adjacent to the ice edge. Nitrogenase activity was extremely low compared to temperate and tropical systems, but N2 fixation was found at all study sites. N2 fixation occurred under both dark and light conditions, indicating the potential involvement of both phototrophic and heterotrophic diazotrophs. Nitrogenase activity measurements (acetylene reduction assay) and molecular characterization (PCR amplification of nifH fragments) demonstrated a diverse and periodically active (when liquid water is present) diazotrophic community in this arid, nutrient-limited environment. As a result of the close proximity to other microorganisms and the nutritional constraints of this environment, these diazotrophs may be involved in mutually beneficial consortial relationships that enhance their growth when water is available.}, }
@article {pmid9852502, year = {1998}, author = {Paerl, HW and Priscu, JC}, title = {Microbial Phototrophic, Heterotrophic, and Diazotrophic Activities Associated with Aggregates in the Permanent Ice Cover of Lake Bonney, Antarctica.}, journal = {Microbial ecology}, volume = {36}, number = {3}, pages = {221-230}, doi = {10.1007/s002489900109}, pmid = {9852502}, issn = {1432-184X}, abstract = {Abstract The McMurdo Dry Valley lakes, Antarctica, one of the Earth's southernmost ecosystems containing liquid water, harbor some of the most environmentally extreme (cold, nutrient-deprived) conditions on the planet. Lake Bonney has a permanent ice cover that supports a unique microbial habitat, provided by soil particles blown onto the lake surface from the surrounding, ice-free valley floor. During continuous sunlight summers (Nov.-Feb.), the dark soil particles are heated by solar radiation and melt their way into the ice matrix. Layers and patches of aggregates and liquid water are formed. Aggregates contain a complex cyanobacterial-bacterial community, concurrently conducting photosynthesis (CO2 fixation), nitrogen (N2) fixation, decomposition, and biogeochemical zonation needed to complete essential nutrient cycles. Aggregate-associated CO2- and N2-fixation rates were low and confined to liquid water (i.e., no detectable activities in the ice phase). CO2 fixation was mediated by cyanobacteria; both cyanobacteria and eubacteria appeared responsible for N2 fixation. CO2 fixation was stimulated primarily by nitrogen (NO3-), but also by phosphorus (PO43-). PO43- and iron (FeCl3 + EDTA) enrichment stimulated of N2 fixation. Microautoradiographic and physiological studies indicate a morphologically and metabolically diverse microbial community, exhibiting different cell-specific photosynthetic and heterotrophic activities. The microbial community is involved in physical (particle aggregation) and chemical (establishing redox gradients) modification of a nutrient- and organic matter-enriched microbial "oasis," embedded in the desertlike (i.e., nutrient depleted) lake ice cover. Aggregate-associated production and nutrient cycling represent microbial self-sustenance in a microenvironment supporting "life at the edge," as it is known on Earth.}, }
@article {pmid9541558, year = {1998}, author = {Morelli, L and Cesena, C and de Haën C,  and Gozzini, L}, title = {Taxonomic Lactobacillus Composition of Feces from Human Newborns during the First Few Days.}, journal = {Microbial ecology}, volume = {35}, number = {2}, pages = {205-212}, doi = {10.1007/s002489900076}, pmid = {9541558}, issn = {1432-184X}, }
@article {pmid9541557, year = {1998}, author = {Bermingham, S and Fisher, PJ and Martin, A and Marriott, M and Lappin-Scott, H}, title = {The Effect of the Herbicide Mecoprop on Heliscus lugdunensis and Its Influence on the Preferential Feeding of Gammarus Pseudolimnaeus.}, journal = {Microbial ecology}, volume = {35}, number = {2}, pages = {199-204}, doi = {10.1007/s002489900075}, pmid = {9541557}, issn = {0095-3628}, support = {//Wellcome Trust/United Kingdom ; }, }
@article {pmid9541556, year = {1998}, author = {Lupi, FM and Fernandes, HML and Sá-Correia, I}, title = {Increase of Copper Toxicity to Growth of Chlorella vulgaris with Increase of Light Intensity.}, journal = {Microbial ecology}, volume = {35}, number = {2}, pages = {193-198}, doi = {10.1007/s002489900074}, pmid = {9541556}, issn = {1432-184X}, }
@article {pmid9541555, year = {1998}, author = {Sainz, JC and Maeda-Martínez, AN and Ascencio, F}, title = {Experimental Vibriosis Induction with Vibrio alginolyticus of Larvae of the Catarina Scallop (Argopecten ventricosus =circularis) (Sowerby II, 1842).}, journal = {Microbial ecology}, volume = {35}, number = {2}, pages = {188-192}, doi = {10.1007/s002489900073}, pmid = {9541555}, issn = {1432-184X}, }
@article {pmid9541554, year = {1998}, author = {Macfarlane, GT and Macfarlane, S and Gibson, GR}, title = {Validation of a Three-Stage Compound Continuous Culture System for Investigating the Effect of Retention Time on the Ecology and Metabolism of Bacteria in the Human Colon.}, journal = {Microbial ecology}, volume = {35}, number = {2}, pages = {180-187}, doi = {10.1007/s002489900072}, pmid = {9541554}, issn = {1432-184X}, }
@article {pmid9541553, year = {1998}, author = {Zhang, Q and Zak, JC}, title = {Potential Physiological Activities of Fungi and Bacteria in Relation to Plant Litter Decomposition along a Gap Size Gradient in a Natural Subtropical Forest.}, journal = {Microbial ecology}, volume = {35}, number = {2}, pages = {172-179}, doi = {10.1007/s002489900071}, pmid = {9541553}, issn = {1432-184X}, }
@article {pmid9541552, year = {1998}, author = {Balkwill, DL and Murphy, EM and Fair, DM and Ringelberg, DB and White, DC}, title = {Microbial Communities in High and Low Recharge Environments: Implications for Microbial Transport in the Vadose Zone.}, journal = {Microbial ecology}, volume = {35}, number = {2}, pages = {156-171}, doi = {10.1007/s002489900070}, pmid = {9541552}, issn = {1432-184X}, }
@article {pmid9541551, year = {1998}, author = {Quesada, A and Nieva, M and Leganés, F and Ucha, A and Martín, M and Prosperi, C and Fernández-Valiente, E}, title = {Acclimation of Cyanobacterial Communities in Rice Fields and Response of Nitrogenase Activity to Light Regime.}, journal = {Microbial ecology}, volume = {35}, number = {2}, pages = {147-155}, doi = {10.1007/s002489900069}, pmid = {9541551}, issn = {1432-184X}, }
@article {pmid9541550, year = {1998}, author = {Unanue, M and Azúa, I and Arrieta, JM and Labirua-Iturburu, A and Egea, L and Iriberri, J}, title = {Bacterial Colonization and Ectoenzymatic Activity in Phytoplankton-Derived Model Particles: Cleavage of Peptides and Uptake of Amino Acids.}, journal = {Microbial ecology}, volume = {35}, number = {2}, pages = {136-146}, doi = {10.1007/s002489900068}, pmid = {9541550}, issn = {1432-184X}, }
@article {pmid9541549, year = {1998}, author = {Vezie, C and Brient, L and Sivonen, K and Bertru, G and Lefeuvre, J and Salkinoja-Salonen, M}, title = {Variation of Microcystin Content of Cyanobacterial Blooms and Isolated Strains in Lake Grand-Lieu (France).}, journal = {Microbial ecology}, volume = {35}, number = {2}, pages = {126-135}, doi = {10.1007/s002489900067}, pmid = {9541549}, issn = {1432-184X}, }
@article {pmid9541548, year = {1998}, author = {Underwood, GJC and Smith, DJ}, title = {Predicting Epipelic Diatom Exopolymer Concentrations in Intertidal Sediments from Sediment Chlorophyll a.}, journal = {Microbial ecology}, volume = {35}, number = {2}, pages = {116-125}, doi = {10.1007/s002489900066}, pmid = {9541548}, issn = {1432-184X}, }
@article {pmid9541547, year = {1998}, author = {Konopka, A and Oliver, L and Turco, RF}, title = {The Use of Carbon Substrate Utilization Patterns in Environmental and Ecological Microbiology.}, journal = {Microbial ecology}, volume = {35}, number = {2}, pages = {103-115}, doi = {10.1007/s002489900065}, pmid = {9541547}, issn = {1432-184X}, }
@article {pmid9847171, year = {1999}, author = {Maidak, BL and Cole, JR and Parker, CT and Garrity, GM and Larsen, N and Li, B and Lilburn, TG and McCaughey, MJ and Olsen, GJ and Overbeek, R and Pramanik, S and Schmidt, TM and Tiedje, JM and Woese, CR}, title = {A new version of the RDP (Ribosomal Database Project).}, journal = {Nucleic acids research}, volume = {27}, number = {1}, pages = {171-173}, doi = {10.1093/nar/27.1.171}, pmid = {9847171}, issn = {0305-1048}, mesh = {Base Sequence ; *Databases, Factual/trends ; Information Storage and Retrieval ; Internet ; Michigan ; Phylogeny ; *RNA, Ribosomal/chemistry/genetics ; Ribosomes/*genetics ; Sequence Alignment ; Universities ; }, abstract = {The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [ Nucleic Acids Res. (1997), 25, 109-111], is now hosted by the Center for Microbial Ecology at Michigan State University. RDP-II is a curated database that offers ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, analysis services, and associated computer programs. During the past two years, data alignments have been updated and now include >9700 small subunit rRNA sequences. The recent development of an ObjectStore database will provide more rapid updating of data, better data accuracy and increased user access. RDP-II includes phylogenetically ordered alignments of rRNA sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software programs for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (ftp.cme.msu. edu) and WWW (http://www.cme.msu.edu/RDP). The WWW server provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree. Additional utilities also exist at RDP-II, including distance matrix, T-RFLP, and a Java-based viewer of the phylogenetic trees that can be used to create subtrees.}, }
@article {pmid9846756, year = {1998}, author = {Milcamps, A and Ragatz, DM and Lim, P and Berger, KA and de Bruijin, FJ}, title = {Isolation of carbon- and nitrogen-deprivation-induced loci of Sinorhizobium meliloti 1021 by Tn5-luxAB mutagenesis.}, journal = {Microbiology (Reading, England)}, volume = {144 (Pt 11)}, number = {}, pages = {3205-3218}, doi = {10.1099/00221287-144-11-3205}, pmid = {9846756}, issn = {1350-0872}, mesh = {Amino Acid Sequence ; Carbon/*metabolism ; DNA Transposable Elements/genetics ; Gene Expression Regulation, Bacterial ; *Genes, Bacterial ; Luciferases ; Luminescent Measurements ; Molecular Sequence Data ; Mutagenesis, Insertional/genetics ; Nitrogen/*metabolism ; Recombinant Fusion Proteins ; Rhizobiaceae/*genetics/growth &amp; development/*metabolism ; Sequence Analysis, DNA ; }, abstract = {Soil bacteria, such as Sinorhizobium meliloti, are subject to variation in environmental conditions, including carbon- and nitrogen-deprivation. The ability of bacteria to sense changes in their environment and respond accordingly is of vital importance to their survival and persistence in the soil and rhizosphere. A derivative of Tn5 which creates transcriptional fusions to the promoterless luxAB genes was used to mutagenize S. meliloti 1021 and 5000 insertion mutants were subsequently screened for gene fusions induced by selected environmental stresses. The isolation of 21 gene fusions induced by nitrogen-deprivation and 12 induced by carbon-deprivation is described. Cloning and partial DNA sequence analysis of the transposon-tagged loci revealed a variety of novel genes, as well as S. meliloti genes with significant similarity to known bacterial loci. In addition, nodule occupancy studies were carried out with selected Tn5-luxAB insertion mutants to examine the role of the tagged genes in competition.}, }
@article {pmid9835595, year = {1998}, author = {Weinbauer, MG and Beckmann, C and Höfle, MG}, title = {Utility of green fluorescent nucleic acid dyes and aluminum oxide membrane filters for rapid epifluorescence enumeration of soil and sediment bacteria.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {12}, pages = {5000-5003}, pmid = {9835595}, issn = {0099-2240}, mesh = {Aluminum Oxide ; Antarctic Regions ; Bacteria/*classification/*isolation &amp; purification ; Escherichia coli/classification/isolation &amp; purification ; Fluorescent Dyes ; Germany ; Indoles ; *Organic Chemicals ; Pseudomonas/classification/isolation &amp; purification ; *Soil Microbiology ; *Water Microbiology ; }, abstract = {High background fluorescence and unspecific staining hampered the epifluorescence enumeration of bacteria in 45% of the tested soil and sediment samples with 4',6-diamidino-2-phenylindole (DAPI) and polycarbonate membrane filters. These problems of the determination of total cell counts can be circumvented by using green fluorescent high-affinity nucleic acid dyes and aluminum oxide membrane filters. Due to the bright staining of cells, we recommend SYBR Green II as dye.}, }
@article {pmid9825224, year = {1998}, author = {Stashenko, P and Teles, R and D'Souza, R}, title = {Periapical inflammatory responses and their modulation.}, journal = {Critical reviews in oral biology and medicine : an official publication of the American Association of Oral Biologists}, volume = {9}, number = {4}, pages = {498-521}, doi = {10.1177/10454411980090040701}, pmid = {9825224}, issn = {1045-4411}, support = {DE-09018/DE/NIDCR NIH HHS/United States ; DE-10517/DE/NIDCR NIH HHS/United States ; DE-11664/DE/NIDCR NIH HHS/United States ; }, mesh = {Cytokines/immunology ; Dental Pulp Exposure/complications/microbiology ; Humans ; Immunocompromised Host ; Inflammation Mediators ; Kinins/immunology ; Lymphocytes/immunology ; Neurogenic Inflammation ; Neuropeptides/immunology ; Periapical Periodontitis/etiology/*immunology ; Prostaglandins/immunology ; }, abstract = {Periapical inflammatory responses occur as a consequence of bacterial infection of the dental pulp, as a result of caries, trauma, or iatrogenic insult. Periapical inflammation stimulates the formation of granulomas and cysts, with the destruction of bone. These inflammatory responses are complex and consist of diverse elements. Immediate-type responses--including vasodilatation, increased vascular permeability, and leukocyte extravasation--are mediated by endogenous mediators, including prostanoids, kinins, and neuropeptides. Non-specific immune responses--including polymorphonuclear leukocyte and monocyte migration and activation, and cytokine production--are elicited in response to bacteria and their products. Interleukin-1 and prostaglandins in particular have been implicated as central mediators of periapical bone resorption. Chronic periapical inflammation further involves specific T- and B-cell-mediated anti-bacterial responses, and activates a network of regulatory cytokines which are produced by Th1- and Th2-type T-lymphocytes. Various naturally occurring and genetically engineered models of immunodeficiency are beginning to help elucidate those components of the immune system which protect the pulpal/periapical complex. Both specific and non-specific responses interface with and are regulated by the neural system. The modulation of these responses by immune response modifies, cytokine antagonists, and other novel therapeutic agents is discussed. As an experimental model, periapical inflammation has many advantages which permit it to be used in studies of microbial ecology and pathogenesis, host response, neuroimmunology, and bone resorption and regeneration.}, }
@article {pmid9807803, year = {1998}, author = {Gu, JD and Mitton, DB and Ford, TE and Mitchell, R}, title = {Microbial degradation of polymeric coatings measured by electrochemical impedance spectroscopy.}, journal = {Biodegradation}, volume = {9}, number = {1}, pages = {39-45}, doi = {10.1023/a:1008252301377}, pmid = {9807803}, issn = {0923-9820}, mesh = {Aspergillus/metabolism ; *Biodegradation, Environmental ; Cladosporium/metabolism ; Electric Impedance ; Electrochemistry/*methods ; Fungi/classification/metabolism ; Polymers/*metabolism ; Sensitivity and Specificity ; Spectrum Analysis/*methods ; }, abstract = {This paper reports results of biodegradation studies of polyimide coatings exposed to a mixed fungal culture using electrochemical impedance spectroscopy (EIS). The fungal consortium was originally isolated from degraded polyimides and identified species include Aspergillus versicolor, Cladosporium cladosporioides, and a Chaetomium species. Actively growing fungi on polyimides yield distinctive EIS spectra through time, indicative of failure of the polymer integrity compared to the uninoculated controls. An initial decline in coating resistance was related to the partial ingress of water molecules and ionic species into the polymeric matrices. This was followed by further degradation of the polymers by activity of the fungi. The relationship between the changes in impedance spectra and microbial degradation of the coatings was further supported by scanning electron microscopy, showing extensive colonization of the polyimide surfaces by the fungi. Our data indicate that EIS can be a sensitive and informative technique for evaluating the biosusceptibility of polymers and coatings.}, }
@article {pmid9802033, year = {1998}, author = {Galbraith, MP and Feng, SF and Borneman, J and Triplett, EW and de Bruijn, FJ and Rossbachl, S}, title = {A functional myo-inositol catabolism pathway is essential for rhizopine utilization by Sinorhizobium meliloti.}, journal = {Microbiology (Reading, England)}, volume = {144 (Pt 10)}, number = {}, pages = {2915-2924}, doi = {10.1099/00221287-144-10-2915}, pmid = {9802033}, issn = {1350-0872}, mesh = {Amino Acid Sequence ; Cloning, Molecular ; Conjugation, Genetic ; Genetic Complementation Test ; Inositol/*analogs &amp; derivatives/*metabolism ; Medicago sativa/microbiology ; Molecular Sequence Data ; Mutagenesis, Insertional ; NAD/metabolism ; Nitrogen Fixation/genetics ; Open Reading Frames/genetics ; Phenotype ; Restriction Mapping ; Rhizobiaceae/chemistry/genetics/*metabolism ; Sequence Homology, Amino Acid ; Sugar Alcohol Dehydrogenases/chemistry/*genetics/metabolism ; }, abstract = {Rhizopine (L-3-O-methyl-scyllo-inosamine) is a symbiosis-specific compound found in alfalfa nodules induced by specific Sinorhizobium meliloti strains. It has been postulated that rhizobial strains able to synthesize and catabolize rhizopine gain a competitive advantage in the rhizosphere. The pathway of rhizopine degradation is analysed here. Since rhizopine is an inositol derivative, it was tested whether inositol catabolism is involved in rhizopine utilization. A genetic locus required for the catabolism of inositol as sole carbon source was cloned from S. meliloti. This locus was delimited by transposon Tn5 mutagenesis and its DNA sequence was determined. Based on DNA similarity studies and enzyme assays, this genetic region was shown to encode an S. meliloti myo-inositol dehydrogenase. Strains that harboured a mutation in the myo-inositol dehydrogenase gene (idhA) did not display myo-inositol dehydrogenase activity, were unable to utilize myo-inositol as sole carbon/energy source, and were unable to catabolize rhizopine. Thus, myo-inositol dehydrogenase activity is essential for rhizopine utilization in S. meliloti.}, }
@article {pmid9797314, year = {1998}, author = {Kuai, L and Verstraete, W}, title = {Ammonium removal by the oxygen-limited autotrophic nitrification-denitrification system.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {11}, pages = {4500-4506}, pmid = {9797314}, issn = {1098-5336}, abstract = {The present lab-scale research reveals the potential of implementation of an oxygen-limited autotrophic nitrification-denitrification (OLAND) system with normal nitrifying sludge as the biocatalyst for the removal of nitrogen from nitrogen-rich wastewater in one step. In a sequential batch reactor, synthetic wastewater containing 1 g of NH4+-N liter-1 and minerals was treated. Oxygen supply to the reactor was double-controlled with a pH controller and a timer. At a volumetric loading rate (Bv) of 0. 13 g of NH4+-N liter-1 day-1, about 22% of the fed NH4+-N was converted to NO2--N or NO3--N, 38% remained as NH4+-N, and the other 40% was removed mainly as N2. The specific removal rate of nitrogen was on the order of 50 mg of N liter-1 day-1, corresponding to 16 mg of N g of volatile suspended solids-1 day-1. The microorganisms which catalyzed the OLAND process are assumed to be normal nitrifiers dominated by ammonium oxidizers. The loss of nitrogen in the OLAND system is presumed to occur via the oxidation of NH4+ to N2 with NO2- as the electron acceptor. Hydroxylamine stimulated the removal of NH4+ and NO2-. Hydroxylamine oxidoreductase (HAO) or an HAO-related enzyme might be responsible for the loss of nitrogen.}, }
@article {pmid9797286, year = {1998}, author = {Buckley, DH and Graber, JR and Schmidt, TM}, title = {Phylogenetic analysis of nonthermophilic members of the kingdom crenarchaeota and their diversity and abundance in soils.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {11}, pages = {4333-4339}, pmid = {9797286}, issn = {1098-5336}, abstract = {Within the last several years, molecular techniques have uncovered numerous 16S rRNA gene (rDNA) sequences which represent a unique and globally distributed lineage of the kingdom Crenarchaeota that is phylogenetically distinct from currently characterized crenarchaeotal species. rDNA sequences of members of this novel crenarchaeotal group have been recovered from low- to moderate-temperature environments (-1.5 to 32 degreesC), in contrast to the high-temperature environments (temperature, >80 degreesC) required for growth of the currently recognized crenarchaeotal species. We determined the diversity and abundance of the nonthermophilic members of the Crenarchaeota in soil samples taken from cultivated and uncultivated fields located at the Kellogg Biological Station's Long-Term Ecological Research site (Hickory Corners, Mich.). Clones were generated from 16S rDNA that was amplified by using broad-specificity archaeal PCR primers. Twelve crenarchaeotal sequences were identified, and the phylogenetic relationships between these sequences and previously described crenarchaeotal 16S rDNA sequences were determined. Phylogenetic analyses included nonthermophilic crenarchaeotal sequences found in public databases and revealed that the nonthermophilic Crenarchaeota group is composed of at least four distinct phylogenetic clusters. A 16S rRNA-targeted oligonucleotide probe specific for all known nonthermophilic crenarchaeotal sequences was designed and used to determine their abundance in soil samples. The nonthermophilic Crenarchaeota accounted for as much as 1.42% +/- 0.42% of the 16S rRNA in the soils analyzed.}, }
@article {pmid9758850, year = {1998}, author = {McGowan, C and Fulthorpe, R and Wright, A and Tiedje, JM}, title = {Evidence for interspecies gene transfer in the evolution of 2,4-dichlorophenoxyacetic acid degraders.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {10}, pages = {4089-4092}, pmid = {9758850}, issn = {0099-2240}, mesh = {2,4-Dichlorophenoxyacetic Acid/*metabolism ; Alcaligenes/classification/genetics/metabolism ; Bacteria/*classification/*genetics/metabolism ; Base Sequence ; Burkholderia/classification/genetics/metabolism ; *Gene Transfer Techniques ; Genes, Bacterial ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Rhodopseudomonas/classification/genetics/metabolism ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {Small-subunit ribosomal DNA (SSU rDNA) from 20 phenotypically distinct strains of 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacteria was partially sequenced, yielding 18 unique strains belonging to members of the alpha, beta, and gamma subgroups of the class Proteobacteria. To understand the origin of 2,4-D degradation in this diverse collection, the first gene in the 2,4-D pathway, tfdA, was sequenced. The sequences fell into three unique classes found in various members of the beta and gamma subgroups of Proteobacteria. None of the alpha-Proteobacteria yielded tfdA PCR products. A comparison of the dendrogram of the tfdA genes with that of the SSU rDNA genes demonstrated incongruency in phylogenies, and hence 2,4-D degradation must have originated from gene transfer between species. Only those strains with tfdA sequences highly similar to the tfdA sequence of strain JMP134 (tfdA class I) transferred all the 2,4-D genes and conferred the 2,4-D degradation phenotype to a Burkholderia cepacia recipient.}, }
@article {pmid9758837, year = {1998}, author = {Xu, KD and Stewart, PS and Xia, F and Huang, CT and McFeters, GA}, title = {Spatial physiological heterogeneity in Pseudomonas aeruginosa biofilm is determined by oxygen availability.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {10}, pages = {4035-4039}, pmid = {9758837}, issn = {0099-2240}, mesh = {Adenosine Triphosphatases/metabolism ; Animals ; *Biofilms ; Fungal Proteins/metabolism ; Industrial Waste ; *Oxygen Consumption ; Plankton ; Polymerase Chain Reaction ; Pseudomonas aeruginosa/genetics/isolation &amp; purification/*physiology ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; }, abstract = {The role of oxygen availability in determining the local physiological activity of Pseudomonas aeruginosa growing in biofilms was investigated. Biofilms grown in an ambient-air environment expressed approximately 1/15th the alkaline phosphatase specific activity of planktonic bacteria subjected to the same phosphate limitation treatment. Biofilms grown in a gaseous environment of pure oxygen exhibited 1.9 times the amount of alkaline phosphatase specific activity of air-grown biofilms, whereas biofilms grown in an environment in which the air was replaced with pure nitrogen prior to the inducing treatment did not develop alkaline phosphatase activity. Frozen cross sections of biofilms stained for alkaline phosphatase activity with a fluorogenic stain demonstrated that alkaline phosphatase activity was concentrated in distinct bands adjacent to the gaseous interfaces. These bands were approximately 30 micron thick with biofilms grown in air, 2 micron thick with biofilms grown in pure nitrogen, and 46 micron thick with biofilms grown in pure oxygen. Overall biofilm thickness ranged from approximately 117 to approximately 151 micron. Measurements with an oxygen microelectrode indicated that oxygen was depleted locally within the biofilm and that the oxygen-replete zone was of a dimension similar to that of the biologically active zone, as indicated by alkaline phosphatase induction. These experiments revealed marked spatial physiological heterogeneity within P. aeruginosa biofilms in which active protein synthesis was restricted by oxygen availability to the upper 30 micron of the biofilm. Such physiological heterogeneity has implications for microbial ecology and for understanding the reduced susceptibilities of biofilms to antimicrobial agents.}, }
@article {pmid9758801, year = {1998}, author = {Bratina, BJ and Stevenson, BS and Green, WJ and Schmidt, TM}, title = {Manganese reduction by microbes from oxic regions of the lake vanda (Antarctica) water column.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {10}, pages = {3791-3797}, pmid = {9758801}, issn = {1098-5336}, abstract = {Depth profiles of metals in Lake Vanda, a permanently ice-covered, stratified Antarctic lake, suggest the importance of particulate manganese oxides in the scavenging, transport, and release of metals. Since manganese oxides can be solubilized by manganese-reducing bacteria, microbially mediated manganese reduction was investigated in Lake Vanda. Microbes concentrated from oxic regions of the water column, encompassing a peak of soluble manganese [Mn(II)], reduced synthetic manganese oxides (MnO2) when incubated aerobically. Pure cultures of manganese-reducing bacteria were readily isolated from waters collected near the oxic Mn(II) peak. Based on phylogenetic analysis of the 16S rRNA gene sequence, most of the isolated manganese reducers belong to the genus Carnobacterium. Cultures of a phylogenetically representative strain of Carnobacterium reduced synthetic MnO2 in the presence of sodium azide, as was seen in field assays. Unlike anaerobes that utilize manganese oxides as terminal electron acceptors in respiration, isolates of the genus Carnobacterium reduced Mn(IV) via a diffusible compound under oxic conditions. The release of adsorbed trace metals accompanying the solubilization of manganese oxides may provide populations of Carnobacterium with a source of nutrients in this extremely oligotrophic environment.}, }
@article {pmid9758799, year = {1998}, author = {Weinbauer, MG and Hofle, MG}, title = {Distribution and life strategies of two bacterial populations in a eutrophic lake.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {10}, pages = {3776-3783}, pmid = {9758799}, issn = {1098-5336}, abstract = {Monoclonal antibodies and epifluorescence microscopy were used to determine the depth distribution of two indigenous bacterial populations in the stratified Lake Plusssee and characterize their life strategies. Populations of Comamonas acidovorans PX54 showed a depth distribution with maximum abundances in the oxic epilimnion, whereas Aeromonas hydrophila PU7718 showed a depth distribution with maximum abundances in the anoxic thermocline layer (metalimnion), i. e., in the water layer with the highest microbial activity. Resistance of PX54 to protist grazing and high metabolic versatility and growth rate of PU7718 were the most important life strategy traits for explaining the depth distribution of the two bacterial populations. Maximum abundance of PX54 was 16,000 cells per ml, and maximum abundance of PU7718 was 20,000 cells per ml. Determination of bacterial productivity in dilution cultures with different-size fractions of dissolved organic matter (DOM) from lake water indicates that low-molecular-weight (LMW) DOM is less bioreactive than total DOM (TDOM). The abundance and growth rate of PU7718 were highest in the TDOM fractions, whereas those of PX54 were highest in the LMW DOM fraction, demonstrating that PX54 can grow well on the less bioreactive DOM fraction. We estimated that 13 to 24% of the entire bacterial community and 14% of PU7718 were removed by viral lysis, whereas no significant effect of viral lysis on PX54 could be detected. Growth rates of PX54 (0.11 to 0.13 h-1) were higher than those of the entire bacterial community (0.04 to 0.08 h-1) but lower than those of PU7718 (0.26 to 0.31 h-1). In undiluted cultures, the growth rates were significantly lower, pointing to density effects such as resource limitation or antibiosis, and the effects were stronger for PU7718 and the entire bacterial community than for PX54. Life strategy characterizations based on data from literature and this study revealed that the fast-growing and metabolically versatile A. hydrophila PU7718 is an r-strategist or opportunistic population in Lake Plusssee, whereas the grazing-resistant C. acidovorans PX54 is rather a K-strategist or equilibrium population.}, }
@article {pmid9726869, year = {1998}, author = {Lorenzen, J and Larsen, LH and Kjaer, T and Revsbech, NP}, title = {Biosensor determination of the microscale distribution of nitrate, nitrate assimilation, nitrification, and denitrification in a diatom-inhabited freshwater sediment.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {9}, pages = {3264-3269}, pmid = {9726869}, issn = {1098-5336}, abstract = {High-resolution NO3- profiles in freshwater sediment covered with benthic diatoms were obtained with a new microscale NO3- biosensor characterized by absence of interference from chemical species other than NO2- and N2O. Analysis of the microprofiles obtained indicated no nitrification during darkness, high rates of nitrification and a tight coupling between nitrification and denitrification during illumination, and substantial rates of NO3- assimilation during illumination. Nitrification during darkness could be induced by purging the bulk water with O2 gas, indicating that the stimulatory effect on nitrification by illumination was caused by algal production of O2. NH4+ addition did not stimulate nitrification during darkness when O2 was restricted to the upper 1-mm layer, and there was thus a low nitrification potential in the permanently oxic top 1 mm of the sediment.}, }
@article {pmid9721265, year = {1998}, author = {Nakatsu, CH and Korona, R and Lenski, RE and de Bruijn, FJ and Marsh, TL and Forney, LJ}, title = {Parallel and divergent genotypic evolution in experimental populations of Ralstonia sp.}, journal = {Journal of bacteriology}, volume = {180}, number = {17}, pages = {4325-4331}, pmid = {9721265}, issn = {0021-9193}, mesh = {Chlorophenols/metabolism ; Cloning, Molecular ; DNA Fingerprinting ; *Evolution, Molecular ; Genome, Bacterial ; Genotype ; Gram-Negative Aerobic Rods and Cocci/*genetics/metabolism ; Plasmids ; Polymerase Chain Reaction ; Sequence Homology, Nucleic Acid ; }, abstract = {Genetic rearrangements within a population of bacteria were analyzed to understand the degree of divergence occurring after experimental evolution. We used 18 replicate populations founded from Ralstonia sp. strain TFD41 that had been propagated for 1,000 generations with 2,4-dichlorophenoxyacetic acid (2,4-D) as the carbon source. Genetic divergence was examined by restriction fragment length polymorphism analysis of the incumbent plasmid that carries the 2,4-D catabolic genes and by amplification of random regions of the genome via PCR. In 18 evolved clones examined, we observed duplication within the plasmid, including the tfdA gene, which encodes a 2,4-D dioxygenase that catalyzes the first step in the 2,4-D catabolic pathway. In 71 of 72 evolved clones, a common 2.4-kb PCR product was lost when genomic fingerprints produced by PCR amplification using degenerate primers based on repetitive extragenic palindromic (REP) sequences (REP-PCR) were compared. The nucleotide sequence of the 2.4-kb PCR product has homology to the TRAP (tripartite ATP-independent periplasmic) solute transporter gene family. Hybridization of the 2. 4-kb REP-PCR product from the ancestor to genomic DNA from the evolved populations showed that the loss of the PCR product resulted from deletions in the genome. Deletions in the plasmid and presence and/or absence of other REP-PCR products were also found in these clones but at much lower frequencies. The common and uncommon genetic changes observed show that both parallel and divergent genotypic evolution occurred in replicate populations of this bacterium.}, }
@article {pmid9720287, year = {1998}, author = {Elena, SF and Ekunwe, L and Hajela, N and Oden, SA and Lenski, RE}, title = {Distribution of fitness effects caused by random insertion mutations in Escherichia coli.}, journal = {Genetica}, volume = {102-103}, number = {1-6}, pages = {349-358}, pmid = {9720287}, issn = {0016-6707}, mesh = {Biological Evolution ; DNA Transposable Elements ; Directed Molecular Evolution ; Escherichia coli/*genetics ; Genetic Vectors ; Genotype ; Models, Genetic ; *Mutagenesis, Insertional ; Selection, Genetic ; }, abstract = {Very little is known about the distribution of mutational effects on organismal fitness, despite the fundamental importance of this information for the study of evolution. This lack of information reflects the fact that it is generally difficult to quantify the dynamic effects of mutation and natural selection using only static distributions of allele frequencies. In this study, we took a direct approach to measuring the effects of mutations on fitness. We used transposon-mutagenesis to create 226 mutant clones of Escherichia coli. Each mutant clone carried a single random insertion of a derivative of Tn10. All 226 mutants were independently derived from the same progenitor clone, which was obtained from a population that had evolved in a constant laboratory environment for 10,000 generations. We then performed competition experiments to measure the effect of each mutation on fitness relative to a common competitor. At least 80% of the mutations had a significant negative effect on fitness, whereas none of the mutations had a significant positive effect. The mutations reduced fitness by about 3%, on average, but the distribution of fitness effects was highly skewed and had a long, flat tail. A compound distribution, which includes both gamma and uniform components, provided an excellent fit to the observed fitness values.}, }
@article {pmid9720276, year = {1998}, author = {Gerrish, PJ and Lenski, RE}, title = {The fate of competing beneficial mutations in an asexual population.}, journal = {Genetica}, volume = {102-103}, number = {1-6}, pages = {127-144}, pmid = {9720276}, issn = {0016-6707}, mesh = {Computer Simulation ; Escherichia coli/*genetics ; Gene Frequency ; *Models, Genetic ; Models, Statistical ; *Mutation ; Polymorphism, Genetic ; Probability ; }, abstract = {In sexual populations, beneficial mutations that occur in different lineages may be recombined into a single lineage. In asexual populations, however, clones that carry such alternative beneficial mutations compete with one another and, thereby, interfere with the expected progression of a given mutation to fixation. From theoretical exploration of such 'clonal interference', we have derived (1) a fixation probability for beneficial mutations, (2) an expected substitution rate, (3) an expected coefficient of selection for realized substitutions, (4) an expected rate of fitness increase, (5) the probability that a beneficial mutation transiently achieves polymorphic frequency (> or = 1%), and (6) the probability that a beneficial mutation transiently achieves majority status. Based on (2) and (3), we were able to estimate the beneficial mutation rate and the distribution of mutational effects from changes in mean fitness in an evolving E. coli population.}, }
@article {pmid9711838, year = {1998}, author = {Heinfling, A and Martínez, MJ and Martínez, AT and Bergbauer, M and Szewzyk, U}, title = {Purification and characterization of peroxidases from the dye-decolorizing fungus Bjerkandera adusta.}, journal = {FEMS microbiology letters}, volume = {165}, number = {1}, pages = {43-50}, doi = {10.1111/j.1574-6968.1998.tb13125.x}, pmid = {9711838}, issn = {0378-1097}, mesh = {Amino Acid Sequence ; Chromatography, Ion Exchange ; Electrophoresis, Polyacrylamide Gel ; Fungal Proteins/chemistry/*isolation &amp; purification/metabolism ; Fungi/*enzymology/growth &amp; development ; Isoenzymes/chemistry/isolation &amp; purification/metabolism ; Manganese/metabolism ; Molecular Sequence Data ; Peroxidases/chemistry/*isolation &amp; purification/metabolism ; Sequence Analysis ; }, abstract = {A peroxidase oxidizing Mn2+ (MnP) is described for the first time in Bjerkandera adusta, a fungus efficiently degrading xenobiotic compounds. The MnP appeared as two isoenzymes, which were purified to homogeneity together with two lignin peroxidases (LiP). Their N-terminal sequences were identical, but the MnP isoenzymes showed more basic isoelectric points and differences in amino acid composition and catalytic properties. The B. adusta LiP is similar to LiP from Phanerochaete chrysoporium. However, the interest of the MnP described here is related to its ability to catalyze Mn(2+)-mediated as well as Mn(2+)-independent reactions on aromatic compounds, which may be of use for applications in biotechnology and environmental technology.}, }
@article {pmid9704117, year = {1998}, author = {Speksnijder, AG and Kowalchuk, GA and Roest, K and Laanbroek, HJ}, title = {Recovery of a Nitrosomonas-like 16S rDNA sequence group from freshwater habitats.}, journal = {Systematic and applied microbiology}, volume = {21}, number = {2}, pages = {321-330}, doi = {10.1016/S0723-2020(98)80040-4}, pmid = {9704117}, issn = {0723-2020}, mesh = {Base Sequence ; Cloning, Molecular ; DNA Primers ; DNA, Bacterial/chemistry ; DNA, Ribosomal/*chemistry ; Electrophoresis, Agar Gel ; Fresh Water/chemistry/*microbiology ; Gene Library ; Geologic Sediments/chemistry/*microbiology ; Molecular Sequence Data ; Netherlands ; Nitrosomonas/classification/*genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; *Water Microbiology ; }, abstract = {In order to study the diversity of ammonia-oxidising bacteria in freshwater habitats, including sediments, a molecular approach focused on the sequencing of 16S rDNA was adopted. 16S rDNA sequences showing affinity with the beta-subgroup of ammonia-oxidising bacteria were recovered by specific PCR of directly isolated DNA from freshwater samples, and samples from brackish water and Glyceria maxima rhizosphere were included in the analysis for comparison. The ammonia oxidiser-like sequences recovered from several locations, which exhibit differences in the composition of their total microbial communities as indicated by denaturing gradient gel electrophoresis, formed a strong monophyletic cluster including Nitrosomonas ureae. This is the first report presenting sequences from an apparently dominant group of Nitrosomonas-like organisms among the beta-subdivision of ammonia-oxidising bacteria in freshwater environments. This group of sequences extends the known diversity within the beta-subgroup of ammonia-oxidisers. The new sequences related to Nitrosomonas ureae do not match with some published primers and probes designed for the detection of Nitrosomonas species, which may explain why these sequences have not previously been detected in freshwater habitats. The sequence diversity detected within this group of sequences was minimal across the environments examined, and no patterns of distribution were indicated with respect to environmental factors such as sediment depth or location.}, }
@article {pmid9688783, year = {1998}, author = {Marshall, WA}, title = {Aerial Transport of Keratinaceous Substrate and Distribution of the Fungus Geomyces pannorum in Antarctic Soils.}, journal = {Microbial ecology}, volume = {36}, number = {2}, pages = {212-219}, doi = {10.1007/s002489900108}, pmid = {9688783}, issn = {1432-184X}, abstract = {> Abstract Aerobiological sampling was conducted year-round at three sites on Signy Island, maritime Antarctic, between December 1992 and January 1994, and during the summer at a fourth coastal site. The concentrations of keratinaceous particles were monitored. Feather fragments were the most abundant of all particle types trapped. Seal hairs were also common, particularly on the coast. Numbers of both particle types were most common in the air in summer. The Antarctic soil fungus Geomyces pannorum, which is able to utilize keratin-based substrates, was also present in aerobiological samples on Signy Island. G. pannorum was only found during early winter on the year-round sampling sites. It was more abundant during summer in the air at the coastal site, which was more heavily influenced by seals, birds and humans. Skuas were swabbed when they returned to the island early in summer. G. pannorum was recovered in culture, suggesting that these birds may act as vectors for the transport of microorganisms between Antarctica and more northern landmasses. Organic material deposited on snow was concentrated on the soil at the edge of the ice cap by melt wash, making additional keratin and other organic substrates available to soil microorganisms.}, }
@article {pmid9688782, year = {1998}, author = {Leff, LG and McArthur, JV and Shimkets, LJ}, title = {Persistence and Dissemination of Introduced Bacteria in Freshwater Microcosms.}, journal = {Microbial ecology}, volume = {36}, number = {2}, pages = {202-211}, doi = {10.1007/s002489900107}, pmid = {9688782}, issn = {1432-184X}, }
@article {pmid9688781, year = {1998}, author = {Han, SO and New, PB}, title = {Variation in Nitrogen Fixing Ability among Natural Isolates of Azospirillum.}, journal = {Microbial ecology}, volume = {36}, number = {2}, pages = {193-201}, doi = {10.1007/s002489900106}, pmid = {9688781}, issn = {1432-184X}, }
@article {pmid9688780, year = {1998}, author = {Rapala, J and Sivonen, K}, title = {Assessment of Environmental Conditions That Favor Hepatotoxic and Neurotoxic Anabaena spp. Strains Cultured under Light Limitation at Different Temperatures.}, journal = {Microbial ecology}, volume = {36}, number = {2}, pages = {181-192}, doi = {10.1007/s002489900105}, pmid = {9688780}, issn = {1432-184X}, }
@article {pmid9688779, year = {1998}, author = {Belitz, LA and Waller, DA}, title = {Effect of Temperature and Termite Starvation on Phagocytosis by Protozoan Symbionts of the Eastern Subterranean Termite Reticulitermes flavipes Kollar.}, journal = {Microbial ecology}, volume = {36}, number = {2}, pages = {175-180}, doi = {10.1007/s002489900104}, pmid = {9688779}, issn = {1432-184X}, }
@article {pmid9688778, year = {1998}, author = {Wilks, SA and Sleigh, MA}, title = {Grazing Rates in Euplotes mutabilis: Relationship between Particle Size and Concentration.}, journal = {Microbial ecology}, volume = {36}, number = {2}, pages = {165-174}, doi = {10.1007/s002489900103}, pmid = {9688778}, issn = {1432-184X}, }
@article {pmid9688777, year = {1998}, author = {Brockman, FJ and Li, SW and Fredrickson, JK and Ringelberg, DB and Kieft, TL and Spadoni, CM and White, DC and McKinley, JP}, title = {Post-Sampling Changes in Microbial Community Composition and Activity in a Subsurface Paleosol.}, journal = {Microbial ecology}, volume = {36}, number = {2}, pages = {152-164}, doi = {10.1007/s002489900102}, pmid = {9688777}, issn = {1432-184X}, }
@article {pmid9688776, year = {1998}, author = {Ulrich, GA and Martino, D and Burger, K and Routh, J and Grossman, EL and Ammerman, JW and Suflita, JM}, title = {Sulfur Cycling in the Terrestrial Subsurface: Commensal Interactions, Spatial Scales, and Microbial Heterogeneity.}, journal = {Microbial ecology}, volume = {36}, number = {2}, pages = {141-151}, doi = {10.1007/s002489900101}, pmid = {9688776}, issn = {1432-184X}, }
@article {pmid9688775, year = {1998}, author = {Findlay, S and Pace, ML and Fischer, DT}, title = {Response of Heterotrophic Planktonic Bacteria to the Zebra Mussel Invasion of the Tidal Freshwater Hudson River.}, journal = {Microbial ecology}, volume = {36}, number = {2}, pages = {131-140}, doi = {10.1007/s002489900100}, pmid = {9688775}, issn = {1432-184X}, }
@article {pmid9688774, year = {1998}, author = {Mohamed, MN and Lawrence, JR and Robarts, RD}, title = {Phosphorus Limitation of Heterotrophic Biofilms from the Fraser River, British Columbia, and the Effect of Pulp Mill Effluent.}, journal = {Microbial ecology}, volume = {36}, number = {2}, pages = {121-130}, doi = {10.1007/s002489900099}, pmid = {9688774}, issn = {1432-184X}, }
@article {pmid9688773, year = {1998}, author = {Pollard, PC}, title = {Estimating the Growth Rate of a Bacterial Species in a Complex Mixture by Hybridization of Genomic DNA.}, journal = {Microbial ecology}, volume = {36}, number = {2}, pages = {111-120}, doi = {10.1007/s002489900098}, pmid = {9688773}, issn = {1432-184X}, abstract = {> Abstract Advances in molecular techniques have enabled new approaches to identifying bacteria. However, once identified, there is no quantitative information on the in situ growth rate of the species, mainly because the technology has not been available. The quantitative incorporation of [methyl-3H]thymidine into dividing bacteria is coupled with a molecular (hybridization) method, to determine the growth rate of bacterial species in situ. The basis of this molecular method is a reverse gene probe-natural populations are labeled in situ with [methyl-3H]thymidine. The probe (3H-Tdr-DNA) is captured, using a hybridization procedure, on a positively charged nylon membrane on which is attached non-labeled target DNA. Two bacterial species, Bacillus cereus and Zoogloea ramigera, were used to demonstrate the principle in laboratory cultures and in a municipal activate sludge treatment process. The DNA of the dividing bacteria in activated sludge was radioactively labeled with [methyl-3H]thymidine, and the DNA of Z. ramigera was recovered using a DNA hybridization method. The recovered radioactively-labeled DNA was used to estimate the growth rate (0.03 x 10(9) cells . ml-1 . h-1) of Z. ramigera in situ. Simultaneously applying these two powerful molecular-based methods could potentially be used to study bacterial population dynamics in situ.}, }
@article {pmid9687447, year = {1998}, author = {van der Maarel, MJ and Artz, RR and Haanstra, R and Forney, LJ}, title = {Association of marine archaea with the digestive tracts of two marine fish species.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {8}, pages = {2894-2898}, pmid = {9687447}, issn = {0099-2240}, mesh = {Animals ; Archaea/classification/genetics/*isolation &amp; purification ; Base Sequence ; DNA Fingerprinting ; DNA, Archaeal/analysis ; DNA, Ribosomal/analysis ; Digestive System/*microbiology ; Feces/microbiology ; Flounder/*microbiology ; Molecular Sequence Data ; Netherlands ; North Sea ; Nucleic Acid Hybridization ; Perciformes/*microbiology ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Water Microbiology ; }, abstract = {Recent studies have shown that archaea which were always thought to live under strict anoxic or extreme environmental conditions are also present in cold, oxygenated seawater, soils, the digestive tract of a holothurian deep-sea-deposit feeder, and a marine sponge. In this study, we show, by using PCR-mediated screening in other marine eukaryotes, that marine archaea are also present in the digestive tracts of flounder and grey mullet, two fish species common in the North Sea, in fecal samples of flounder, and in suspended particulate matter of the North Sea water column. No marine archaea could be detected in the digestive tracts of mussels or the fecal pellets of a copepod species. The archaeal 16S ribosomal DNA clone libraries of feces of flounder and the contents of the digestive tracts of grey mullet and flounder were dominated by group II marine archaea. The marine archaeal clones derived from flounder and grey mullet digestive tracts and feces formed a distinct cluster within the group II marine archaea, with 76.7 to 89. 8% similarity to previously described group II clones. Fingerprinting of the archaeal community of flounder digestive tract contents and feces by terminal restriction fragment length polymorphism of archaeal 16S rRNA genes after restriction with HhaI showed a dominant fragment at 249 bp, which is likely to be derived from group II marine archaea. Clones of marine archaea that were closely related to the fish-associated marine archaea clones were obtained from suspended particulate matter of the water column at two stations in the North Sea. Terminal restriction fragment length polymorphism fingerprinting of the archaeal community present in suspended particulate matter showed the same fragment pattern as was found for the archaeal community of the flounder digestive tract contents and feces. These data demonstrate that marine archaea are present in the digestive tracts and feces of very common marine fish. It is possible that the marine archaea associated with the digestive tracts of marine fish are liberated into the water column through the feces and subsequently contribute to the marine archaeal community of suspended particulate matter.}, }
@article {pmid9687435, year = {1998}, author = {Engelen, B and Meinken, K and von Wintzingerode, F and Heuer, H and Malkomes, HP and Backhaus, H}, title = {Monitoring impact of a pesticide treatment on bacterial soil communities by metabolic and genetic fingerprinting in addition to conventional testing procedures.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {8}, pages = {2814-2821}, pmid = {9687435}, issn = {0099-2240}, mesh = {Bacteria/*drug effects/genetics/isolation &amp; purification/*metabolism ; Bacteriological Techniques ; Biomass ; *DNA Fingerprinting ; DNA, Bacterial/chemistry ; DNA, Ribosomal/chemistry ; Dinitrophenols/toxicity ; Ecology ; Electrophoresis, Polyacrylamide Gel ; Herbicides/*toxicity ; Nitrogen/metabolism ; Oxidoreductases/metabolism ; Oxygen Consumption ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Triazines/toxicity ; }, abstract = {Herbogil (dinoterb), a reference herbicide, the mineral oil Oleo (paraffin oil used as an additive to herbicides), and Goltix (metamitron) were taken as model compounds for the study of impacts on microbial soil communities. After the treatment of soil samples, effects on metabolic sum parameters were determined by monitoring substrate-induced respiration (SIR) and dehydrogenase activity, as well as carbon and nitrogen mineralization. These conventional ecotoxicological testing procedures are used in pesticide registration. Inhibition of biomass-related activities and stimulation of nitrogen mineralization were the most significant effects caused by the application of Herbogil. Even though Goltix and Oleo were used at a higher dosage (10 times higher), the application of Goltix resulted in smaller effects and the additive Oleo was the least-active compound, with minor stimulation of test parameters at later observation times. The results served as a background for investigation of the power of "fingerprinting" methods in microbial ecology. Changes in catabolic activities induced by treatments were analyzed by using the 95 carbon sources provided by the BIOLOG system. Variations in the complex metabolic fingerprints demonstrated inhibition of many catabolic pathways after the application of Herbogil. Again, the effects of the other compounds were expressed at much lower levels and comprised stimulations as well as inhibitions. Testing for significance by a multivariate t test indicated that the sensitivity of this method was similar to the sensitivities of the conventional testing procedures. The variation of sensitive carbon sources, as determined by factor weights at different observation times, indicated the dynamics of the community shift induced by the Herbogil treatment in more detail. DNA extractions from soil resulted in a collection of molecules representing the genetic composition of total bacterial communities. Distinct and highly reproducible community patterns, or genetic fingerprints, resulting from application of the different herbicides were obtained by the sequence-specific separation of partial 16S rDNA amplification products in temperature gradient gel electrophoresis. Significant pattern variations were quantified. For detailed analysis, application-responsive bands from the Herbogil and Oleo treatments were sequenced and their tentative phylogenetic positions were identified. Data interpretation and the potentials and biases of the additional observation windows on microbial communities are discussed.}, }
@article {pmid9687431, year = {1998}, author = {Heinfling, A and Martínez, MJ and Martínez, AT and Bergbauer, M and Szewzyk, U}, title = {Transformation of industrial dyes by manganese peroxidases from Bjerkandera adusta and Pleurotus eryngii in a manganese-independent reaction.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {8}, pages = {2788-2793}, pmid = {9687431}, issn = {0099-2240}, mesh = {Azo Compounds/metabolism ; Basidiomycota/*enzymology/growth &amp; development ; Biodegradation, Environmental ; Coloring Agents/*metabolism ; Indoles/metabolism ; Isoindoles ; Kinetics ; Lignin/metabolism ; Manganese/metabolism ; Oxidation-Reduction ; Peroxidases/*metabolism ; }, abstract = {We investigated the transformation of six industrial azo and phthalocyanine dyes by ligninolytic peroxidases from Bjerkandera adusta and other white rot fungi. The dyes were not oxidized or were oxidized very little by Phanerochaete chrysosporium manganese peroxidase (MnP) or by a chemically generated Mn3+-lactate complex. Lignin peroxidase (LiP) from B. adusta also showed low activity with most of the dyes, but the specific activities increased 8- to 100-fold when veratryl alcohol was included in the reaction mixture, reaching levels of 3.9 to 9.6 U/mg. The B. adusta and Pleurotus eryngii MnP isoenzymes are unusual because of their ability to oxidize aromatic compounds like 2,6-dimethoxyphenol and veratryl alcohol in the absence of Mn2+. These MnP isoenzymes also decolorized the azo dyes and the phthalocyanine complexes in an Mn2+-independent manner. The reactions with the dyes were characterized by apparent Km values ranging from 4 to 16 microM and specific activities ranging from 3.2 to 10.9 U/mg. Dye oxidation by these peroxidases was not increased by adding veratryl alcohol as it was in LiP reactions. Moreover, the reaction was inhibited by the presence of Mn2+, which in the case of Reactive Black 5, an azo dye which is not oxidized by the Mn3+-lactate complex, was found to act as a noncompetitive inhibitor of dye oxidation by B. adusta MnP1.}, }
@article {pmid9654123, year = {1998}, author = {Heinfling, A and Ruiz-Dueñas, FJ and Martínez, MJ and Bergbauer, M and Szewzyk, U and Martínez, AT}, title = {A study on reducing substrates of manganese-oxidizing peroxidases from Pleurotus eryngii and Bjerkandera adusta.}, journal = {FEBS letters}, volume = {428}, number = {3}, pages = {141-146}, doi = {10.1016/s0014-5793(98)00512-2}, pmid = {9654123}, issn = {0014-5793}, mesh = {Basidiomycota/*enzymology ; Binding Sites ; Chromatography, Ion Exchange ; Heme ; Hydrocarbons, Aromatic/metabolism ; Kinetics ; Manganese/metabolism ; Models, Molecular ; Peroxidases/chemistry/isolation &amp; purification/*metabolism ; Polyporaceae/*enzymology ; Protein Conformation ; Substrate Specificity ; }, abstract = {A novel peroxidase, oxidizing Mn2+ and different aromatic compounds, was isolated. Hydroquinones, substituted phenols, dyes, other aromatic compounds and Mn2+ were compared as reducing substrates, and conclusions presented in the light of a molecular model built by homology modeling. The enzymes showed the fastest reaction rates with Mn2+, but the highest affinity corresponded to hydroquinones and dyes. Oxidation of Reactive Black 5 (an azo-dye not oxidized by Mn3+) was non-competitively inhibited by Mn2+. These findings, together with identification of putative Mn-binding site (involving Glu36, Glu40, Asp175 and inner heme propionate) and long-range electron transfer pathways, indicate that different sites are involved in substrate oxidation.}, }
@article {pmid9633643, year = {1998}, author = {Ulrich, A and Müller, T}, title = {Heterogeneity of plant-associated streptococci as characterized by phenotypic features and restriction analysis of PCR-amplified 16S rDNA.}, journal = {Journal of applied microbiology}, volume = {84}, number = {2}, pages = {293-303}, doi = {10.1046/j.1365-2672.1998.00343.x}, pmid = {9633643}, issn = {1364-5072}, mesh = {Bacterial Typing Techniques ; DNA, Ribosomal/genetics ; Enterococcus faecalis/classification/genetics ; Enterococcus faecium/classification/genetics ; Lactococcus/classification/genetics ; Phenotype ; Poaceae/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Streptococcaceae/*classification/genetics ; }, abstract = {Thirty-five strains of streptococci isolated from forage grasses were examined by restriction analysis of PCR-amplified 16S rDNA. Using a set of seven endonucleases, five 16S rDNA genotypes were obtained. The isolates could be identified as belonging to the species Enterococcus faecium, Ent. mundtii, Ent. faecalis, Ent. casseliflavus and Lactococcus lactis ssp. lactis, respectively. To assign the isolates to one of these species, digestion with the endonuclease HinfI was sufficient. Data obtained from whole-cell protein analysis were in accordance with the species identification. Additionally, three of the five species found were subdivided into two related subgroups. Both methods are suitable for a rapid and unequivocal identification of plant-associated streptococci. The phenotypic characters showed a high diversity and were in some cases contrary to the expected features usually given in genus and species descriptions. The results demonstrated the close relatedness of the determined species in contrast to their high phenotypic heterogeneity.}, }
@article {pmid9622569, year = {1998}, author = {Hood, MA and van Dijk KV,  and Nelson, EB}, title = {Factors Affecting Attachment of Enterobacter cloacae to Germinating Cotton Seed.}, journal = {Microbial ecology}, volume = {36}, number = {1}, pages = {101-110}, doi = {10.1007/s002489900097}, pmid = {9622569}, issn = {1432-184X}, }
@article {pmid9622568, year = {1998}, author = {Jonkers, HM and Koopmans, GF and van Gemerden H, }, title = {Dynamics of Dimethyl Sulfide in a Marine Microbial Mat.}, journal = {Microbial ecology}, volume = {36}, number = {1}, pages = {93-100}, doi = {10.1007/s002489900096}, pmid = {9622568}, issn = {1432-184X}, }
@article {pmid9622567, year = {1998}, author = {Vetter, YA and Deming, JW and Jumars, PA and Krieger-Brockett, BB}, title = {A Predictive Model of Bacterial Foraging by Means of Freely Released Extracellular Enzymes.}, journal = {Microbial ecology}, volume = {36}, number = {1}, pages = {75-92}, doi = {10.1007/s002489900095}, pmid = {9622567}, issn = {1432-184X}, }
@article {pmid9622566, year = {1998}, author = {Agis, M and Unanue, M and Iriberri, J and Herndl, GJ}, title = {Bacterial Colonization and Ectoenzymatic Activity in Phytoplankton-Derived Model Particles. Part II. Cleavage and Uptake of Carbohydrates.}, journal = {Microbial ecology}, volume = {36}, number = {1}, pages = {66-74}, doi = {10.1007/s002489900094}, pmid = {9622566}, issn = {1432-184X}, }
@article {pmid9622565, year = {1998}, author = {Latham, BP}, title = {Yeast Community Persistence in a Spatially Structured Environment.}, journal = {Microbial ecology}, volume = {36}, number = {1}, pages = {60-65}, doi = {10.1007/s002489900093}, pmid = {9622565}, issn = {1432-184X}, }
@article {pmid9622564, year = {1998}, author = {McDonald, IR and Riley, PW and Sharp, RJ and McCarthy, AJ}, title = {Survival of Plasmid-Containing Bacillus subtilis Released into Mushroom Compost.}, journal = {Microbial ecology}, volume = {36}, number = {1}, pages = {51-59}, doi = {10.1007/s002489900092}, pmid = {9622564}, issn = {1432-184X}, }
@article {pmid9622563, year = {1998}, author = {Chandler, DP and Brockman, FJ and Bailey, TJ and Fredrickson, JK}, title = {Phylogenetic Diversity of Archaea and Bacteria in a Deep Subsurface Paleosol.}, journal = {Microbial ecology}, volume = {36}, number = {1}, pages = {37-50}, doi = {10.1007/s002489900091}, pmid = {9622563}, issn = {1432-184X}, }
@article {pmid9622562, year = {1998}, author = {Felske, A and Akkermans, ADL}, title = {Spatial Homogeneity of Abundant Bacterial 16S rRNA Molecules in Grassland Soils.}, journal = {Microbial ecology}, volume = {36}, number = {1}, pages = {31-36}, doi = {10.1007/s002489900090}, pmid = {9622562}, issn = {1432-184X}, }
@article {pmid9622561, year = {1998}, author = {Findlay, RH and Watling, L}, title = {Seasonal Variation in the Structure of a Marine Benthic Microbial Community.}, journal = {Microbial ecology}, volume = {36}, number = {1}, pages = {23-30}, doi = {10.1007/s002489900089}, pmid = {9622561}, issn = {1432-184X}, }
@article {pmid9622560, year = {1998}, author = {Gugliandolo, C and Maugeri, TL}, title = {Temporal Variations in Heterotrophic Mesophilic Bacteria from a Marine Shallow Hydrothermal Vent off the Island of Vulcano (Eolian Islands, Italy).}, journal = {Microbial ecology}, volume = {36}, number = {1}, pages = {13-22}, doi = {10.1007/s002489900088}, pmid = {9622560}, issn = {1432-184X}, }
@article {pmid9622559, year = {1998}, author = {Bossio, DA and Scow, KM and Gunapala, N and Graham, KJ}, title = {Determinants of Soil Microbial Communities: Effects of Agricultural Management, Season, and Soil Type on Phospholipid Fatty Acid Profiles.}, journal = {Microbial ecology}, volume = {36}, number = {1}, pages = {1-12}, doi = {10.1007/s002489900087}, pmid = {9622559}, issn = {1432-184X}, }
@article {pmid9616664, year = {1997}, author = {Bernstein, JM and Reddy, MS and Scannapieco, FA and Faden, HS and Ballow, M}, title = {The microbial ecology and immunology of the adenoid: implications for otitis media.}, journal = {Annals of the New York Academy of Sciences}, volume = {830}, number = {}, pages = {19-31}, doi = {10.1111/j.1749-6632.1997.tb51876.x}, pmid = {9616664}, issn = {0077-8923}, mesh = {Adenoids/*immunology/microbiology ; Animals ; Bacteria/*growth &amp; development ; Cytokines/physiology ; Humans ; Immunoglobulin A, Secretory/physiology ; Mucins/physiology ; Nasopharynx/immunology/microbiology ; Otitis Media/*immunology ; }, abstract = {The nasopharyngeal tonsil, or adenoid, is a major inductive site for the synthesis of J-chain-positive B cells that may migrate to other areas of the upper respiratory tract, such as the nasal mucosa, the parotid gland, the lacrimal gland, and the middle ear during inflammation. The production of secretory IgA by both the nasopharyngeal tonsil and the nasal mucosa plays a major role in local immune protection against bacteria and viruses. The release of cytokines from Th1 and Th2 lymphocytes must be appropriate for B cells to produce IgA. The factors or mechanisms responsible for this are not, at present, known, but it appears that there is a difference in the profiles of cytokine secretion by Th1 and Th2 lymphocytes in the adenoids in both otitis-prone, as well as nonotitis-prone children. We have suggested that if this specific immune system does not protect the host from invasion by potential pathogens, there are other modalities of therapy to protect the nasopharynx from colonization with pathogenic bacteria or viruses. These include the production of specific antibodies against bacterial surface proteins that have been identified as mucin-binding proteins. Alteration of the microbial flora with commensal organisms such as viridans streptococci can be utilized. These alpha-hemolytic streptococci probably function by producing an acid environment that prevents colonization of organisms such as nontypeable H. influenzae. Finally, the induction of specific SIgA by conserved outer membrane protein antigens of potential pathogens may be another strategy in the prevention of colonization of potential bacterial pathogens in the nasopharynx.}, }
@article {pmid9531629, year = {1998}, author = {Leadbetter, JR and Crosby, LD and Breznak, JA}, title = {Methanobrevibacter filiformis sp. nov., A filamentous methanogen from termite hindguts.}, journal = {Archives of microbiology}, volume = {169}, number = {4}, pages = {287-292}, doi = {10.1007/s002030050574}, pmid = {9531629}, issn = {0302-8933}, mesh = {Animals ; Euryarchaeota/genetics/*isolation &amp; purification/ultrastructure ; Insecta/*microbiology ; Intestines/*microbiology ; Methanobacteriaceae/genetics/*isolation &amp; purification/ultrastructure ; Phylogeny ; RNA, Archaeal/analysis/genetics ; RNA, Ribosomal/analysis/genetics ; }, abstract = {A morphologically distinct, filamentous methanogen was isolated from hindguts of the subterranean termite, Reticulitermes flavipes (Kollar) (Rhinotermitidae), wherein it was part of the microbiota colonizing the hindgut wall. Individual filaments of strain RFM-3 were 0.23-0.28 micron in diameter and usually > 50 micron in length and aggregated into flocs that were often >/= 0.1 mm in diameter. Optimal growth of strain RFM-3 was obtained at pH 7.0-7.2 and 30 degrees C with a yeast-extract-supplemented, dithiothreitol-reduced medium in which cells produced stoichiometric amounts of methane from H2 + CO2. The morphology and gram-positive staining reaction of strain RFM-3, as well as its resistance to cell lysis by various chemical agents and its restriction to H2 + CO2 as an energy source, suggested that it was a member of the Methanobacteriaceae. The nucleotide sequence of the SSU-rRNA-encoding gene of strain RFM-3 confirmed this affiliation and also supported its recognition as a new species of Methanobrevibacter, for which the epithet filiformis is herewith proposed. Although M. filiformis was one of the dominant methanogens in R. flavipes collected from Woods Hole (Mass., USA), cells of similar morphology were not consistently observed in R. flavipes collected from different geographical locations.}, }
@article {pmid9602286, year = {1998}, author = {Muyzer, G and Smalla, K}, title = {Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology.}, journal = {Antonie van Leeuwenhoek}, volume = {73}, number = {1}, pages = {127-141}, doi = {10.1023/a:1000669317571}, pmid = {9602286}, issn = {0003-6072}, mesh = {Bacteria/genetics ; *Bacterial Physiological Phenomena ; *Bacteriological Techniques ; DNA Fingerprinting ; DNA, Bacterial/analysis ; *Ecosystem ; Electrophoresis, Agar Gel/*methods ; }, abstract = {Here, the state of the art of the application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology will be presented. Furthermore, the potentials and limitations of these techniques will be discussed, and it will be indicated why their use in ecological studies has become so important.}, }
@article {pmid9602277, year = {1998}, author = {Lenski, RE and Mongold, JA and Sniegowski, PD and Travisano, M and Vasi, F and Gerrish, PJ and Schmidt, TM}, title = {Evolution of competitive fitness in experimental populations of E. coli: what makes one genotype a better competitor than another?.}, journal = {Antonie van Leeuwenhoek}, volume = {73}, number = {1}, pages = {35-47}, doi = {10.1023/a:1000675521611}, pmid = {9602277}, issn = {0003-6072}, mesh = {Adaptation, Physiological/genetics ; *Biological Evolution ; Escherichia coli/*genetics/growth &amp; development/*physiology ; Genotype ; Glucose/metabolism ; Mutation ; Time Factors ; }, abstract = {An important problem in microbial ecology is to identify those phenotypic attributes that are responsible for competitive fitness in a particular environment. Thousands of papers have been published on the physiology, biochemistry, and molecular genetics of Escherichia coli and other bacterial models. Nonetheless, little is known about what makes one genotype a better competitor than another even in such well studied systems. Here, we review experiments to identify the phenotypic bases of improved competitive fitness in twelve E. coli populations that evolved for thousands of generations in a defined environment, in which glucose was the limiting substrate. After 10,000 generations, the average fitness of the derived genotypes had increased by approximately 50% relative to the ancestor, based on competition experiments using marked strains in the same environment. The growth kinetics of the ancestral and derived genotypes showed that the latter have a shorter lag phase upon transfer into fresh medium and a higher maximum growth rate. Competition experiments were also performed in environments where other substrates were substituted for glucose. The derived genotypes are generally more fit in competition for those substrates that use the same mechanism of transport as glucose, which suggests that enhanced transport was an important target of natural selection in the evolutionary environment. All of the derived genotypes produce much larger cells than does the ancestor, even when both types are forced to grow at the same rate. Some but not all, of the derived genotypes also have greatly elevated mutation rates. Efforts are now underway to identify the genetic changes that underlie those phenotypic changes, especially substrate specificity and elevated mutation rate for which there are good candidate loci. Identification and subsequent manipulation of these genes may provide new insights into the reproducibility of adaptive evolution, the importance of co-adapted gene complexes, and the extent to which distinct phenotypes (e.g., substrate specificity and cell size) are affected by the same mutations.}, }
@article {pmid9584906, year = {1998}, author = {Smith, VH and Pippin, DJ}, title = {Implications of resource-ratio theory for oral microbial ecology.}, journal = {European journal of oral sciences}, volume = {106}, number = {2 Pt 1}, pages = {605-615}, doi = {10.1046/j.0909-8836..t01-4-.x}, pmid = {9584906}, issn = {0909-8836}, mesh = {Bacteria/growth &amp; development/metabolism ; Dental Plaque/*microbiology ; *Ecosystem ; Humans ; Models, Biological ; }, abstract = {The ability to compete for the limited nutrients available to the microorganisms of dental plaque is a strong ecological determinant of the structure of the subgingival ecosystem. This paper introduces a new concept from the field of ecology, resource-ratio theory, and applies it to the dynamics of microbial dental plaque with emphasis on the putative periodontal pathogens. Resource-ratio theory is a mechanistic theory of resource competition that utilizes pairs of growth-limiting nutrients in a stoichiometric fashion to predict zones of competitive dominance, exclusion, and coexistence for organisms competing for these resources. Once these resource pairs are identified for plaque organisms, resource-ratio theory may provide predictions of changes in the microbial community structure of plaque based on directional changes in their resource supply ratios.}, }
@article {pmid9577446, year = {1998}, author = {Paterson, DL and Playford, EG}, title = {Should third-generation cephalosporins be the empirical treatment of choice for severe community-acquired pneumonia in adults?.}, journal = {The Medical journal of Australia}, volume = {168}, number = {7}, pages = {344-348}, doi = {10.5694/j.1326-5377.1998.tb138964.x}, pmid = {9577446}, issn = {0025-729X}, mesh = {Adult ; Australia ; Cephalosporins/*therapeutic use ; Community-Acquired Infections/*drug therapy/microbiology ; Drug Resistance, Microbial ; Drug Therapy, Combination/*therapeutic use ; Drug Utilization ; Emergency Treatment ; Evidence-Based Medicine ; Humans ; *Patient Selection ; Pneumonia/*drug therapy/microbiology ; Practice Patterns, Physicians' ; Severity of Illness Index ; }, abstract = {The choice of empirical treatment for community-acquired pneumonia (CAP) is highly controversial. Our survey of 42 Australian emergency department doctors showed that monotherapy with a third-generation cephalosporin was the preferred regimen for severe CAP (14/42; 33%). We argue that cheaper regimens with a narrower spectrum are likely to be just as effective as third-generation cephalosporins and will have fewer adverse effects on the microbial ecology of hospitals. We suggest penicillin or ampicillin (to cover pneumococci--even if penicillin "resistant"--and Haemophilus influenzae), plus a macrolide (e.g., azithromycin or erythromycin; to cover Legionella and other "atypical" pathogens), plus a single large dose of an aminoglycoside (e.g., gentamicin; to cover gram-negative bacilli such as Klebsiella pneumoniae) as empirical therapy for severe CAP.}, }
@article {pmid9572971, year = {1998}, author = {Hahn, MW and Höfle, MG}, title = {Grazing Pressure by a Bacterivorous Flagellate Reverses the Relative Abundance of Comamonas acidovorans PX54 and Vibrio Strain CB5 in Chemostat Cocultures.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {5}, pages = {1910-1918}, pmid = {9572971}, issn = {1098-5336}, abstract = {The response of the bacterial strains Comamonas acidovorans PX54 (beta subclass of the class Proteobacteria) and Vibrio strain CB5 (gamma subclass of the class Proteobacteria) to grazing by the bacterivorous flagellate Ochromonas sp. was examined in one-stage chemostat experiments under conditions of low growth rates with a complex carbon source. The two bacterial strains were cultured together; they were cultured without flagellates in the first phase of the experiments and in the presence of the flagellates in the second phase. Monoclonal and polyclonal antibodies were used to determine the numbers and sizes of C. acidovorans PX54 and Vibrio strain CB5 cells. The flagellates caused strong changes in total bacterial cell numbers, in the relative abundances of the individual bacterial strains, and in bacterial cell size distribution. Vibrio strain CB5 dominated the total bacterial cell numbers during the flagellate-free phase of the experiments with a relative abundance of 93%, but this declined to 33% after inoculation with the flagellate. In contrast to Vibrio strain CB5, C. acidovorans PX54 responded to grazing with a strong expansion of cell length distribution toward large, filamentous cells. These changes in cell morphology resulted in a high percentage of inedible cells in the C. acidovorans PX54 population but not in the Vibrio strain CB5 population, which caused the observed change in the relative abundances of the strains. Batch culture experiments without the flagellate demonstrated that the elongation of C. acidovorans PX54 cells was dependent on their growth rate. This indicates that the occurrence of filamentous C. acidovorans PX54 cells is not a direct response to chemical stimuli released by the flagellates but rather a response to increased growth rates due to flagellate grazing.}, }
@article {pmid9572939, year = {1998}, author = {Vester, F and Ingvorsen, K}, title = {Improved Most-Probable-Number Method To Detect Sulfate-Reducing Bacteria with Natural Media and a Radiotracer.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {5}, pages = {1700-1707}, pmid = {9572939}, issn = {1098-5336}, abstract = {A greatly improved most-probable-number (MPN) method for selective enumeration of sulfate-reducing bacteria (SRB) is described. The method is based on the use of natural media and radiolabeled sulfate (35SO42-). The natural media used consisted of anaerobically prepared sterilized sludge or sediment slurries obtained from sampling sites. The densities of SRB in sediment samples from Kysing Fjord (Denmark) and activated sludge were determined by using a normal MPN (N-MPN) method with synthetic cultivation media and a tracer MPN (T-MPN) method with natural media. The T-MPN method with natural media always yielded significantly higher (100- to 1,000-fold-higher) MPN values than the N-MPN method with synthetic media. The recovery of SRB from environmental samples was investigated by simultaneously measuring sulfate reduction rates (by a 35S-radiotracer method) and bacterial counts by using the T-MPN and N-MPN methods, respectively. When bacterial numbers estimated by the T-MPN method with natural media were used, specific sulfate reduction rates (qSO42-) of 10(-14) to 10(-13) mol of SO42- cell-1 day-1 were calculated, which is within the range of qSO42- values previously reported for pure cultures of SRB (10(-15) to 10(-14) mol of SO42- cell-1 day-1). qSO42- values calculated from N-MPN values obtained with synthetic media were several orders of magnitude higher (2 x 10(-10) to 7 x 10(-10) mol of SO42- cell-1 day-1), showing that viable counts of SRB were seriously underestimated when standard enumeration media were used. Our results demonstrate that the use of natural media results in significant improvements in estimates of the true numbers of SRB in environmental samples.}, }
@article {pmid9569288, year = {1998}, author = {Stoeck, T and Schmidt, HJ}, title = {Fast and Accurate Identification of European Species of the Paramecium aurelia Complex by RAPD-Fingerprints.}, journal = {Microbial ecology}, volume = {35}, number = {3}, pages = {311-317}, doi = {10.1007/s002489900086}, pmid = {9569288}, issn = {1432-184X}, }
@article {pmid9569287, year = {1998}, author = {Sharma, S and Rangger, A and Insam, H}, title = {Effects of Decomposing Maize Litter on Community Level Physiological Profiles of Soil Bacteria.}, journal = {Microbial ecology}, volume = {35}, number = {3}, pages = {301-310}, doi = {10.1007/s002489900085}, pmid = {9569287}, issn = {1432-184X}, }
@article {pmid9569286, year = {1998}, author = {Amon, RMW and Benner, R}, title = {Seasonal Patterns of Bacterial Abundance and Production in the Mississippi River Plume and Their Importance for the Fate of Enhanced Primary Production.}, journal = {Microbial ecology}, volume = {35}, number = {3}, pages = {289-300}, doi = {10.1007/s002489900084}, pmid = {9569286}, issn = {1432-184X}, }
@article {pmid9569285, year = {1998}, author = {Blumenroth, P and Wagner-Döbler, I}, title = {Survival of Inoculants in Polluted Sediments: Effect of Strain Origin and Carbon Source Competition.}, journal = {Microbial ecology}, volume = {35}, number = {3}, pages = {279-288}, doi = {10.1007/s002489900083}, pmid = {9569285}, issn = {1432-184X}, }
@article {pmid9569284, year = {1998}, author = {Bossio, DA and Scow, KM}, title = {Impacts of Carbon and Flooding on Soil Microbial Communities: Phospholipid Fatty Acid Profiles and Substrate Utilization Patterns.}, journal = {Microbial ecology}, volume = {35}, number = {3}, pages = {265-278}, doi = {10.1007/s002489900082}, pmid = {9569284}, issn = {1432-184X}, }
@article {pmid9569283, year = {1998}, author = {Rice, TD and Williams, HN and Turng, BF}, title = {Susceptibility of Bacteria in Estuarine Environments to Autochthonous Bdellovibrios.}, journal = {Microbial ecology}, volume = {35}, number = {3}, pages = {256-264}, doi = {10.1007/s002489900081}, pmid = {9569283}, issn = {1432-184X}, }
@article {pmid9569282, year = {1998}, author = {Danovaro, R and Marrale, D and Della Croce N,  and Dell'Anno, A and Fabiano, M}, title = {Heterotrophic Nanoflagellates, Bacteria, and Labile Organic Compounds in Continental Shelf and Deep-Sea Sediments of the Eastern Mediterranean.}, journal = {Microbial ecology}, volume = {35}, number = {3}, pages = {244-255}, doi = {10.1007/s002489900080}, pmid = {9569282}, issn = {1432-184X}, }
@article {pmid9569281, year = {1998}, author = {Jiang, SC and Paul, JH}, title = {Significance of Lysogeny in the Marine Environment: Studies with Isolates and a Model of Lysogenic Phage Production.}, journal = {Microbial ecology}, volume = {35}, number = {3}, pages = {235-243}, doi = {10.1007/s002489900079}, pmid = {9569281}, issn = {1432-184X}, }
@article {pmid9569280, year = {1998}, author = {Martino, DP and Grossman, EL and Ulrich, GA and Burger, KC and Schlichenmeyer, JL and Suflita, JM and Ammerman, JW}, title = {Microbial Abundance and Activity in a Low-Conductivity Aquifer System in East-Central Texas.}, journal = {Microbial ecology}, volume = {35}, number = {3}, pages = {224-234}, doi = {10.1007/s002489900078}, pmid = {9569280}, issn = {1432-184X}, }
@article {pmid9569279, year = {1998}, author = {Wolfaardt, GM and Lawrence, JR and Robarts, RD and Caldwell, DE}, title = {In situ Characterization of Biofilm Exopolymers Involved in the Accumulation of Chlorinated Organics.}, journal = {Microbial ecology}, volume = {35}, number = {3}, pages = {213-223}, doi = {10.1007/s002489900077}, pmid = {9569279}, issn = {1432-184X}, }
@article {pmid9562883, year = {1998}, author = {Leroi, F and Joffraud, JJ and Chevalier, F and Cardinal, M}, title = {Study of the microbial ecology of cold-smoked salmon during storage at 8 degrees C.}, journal = {International journal of food microbiology}, volume = {39}, number = {1-2}, pages = {111-121}, doi = {10.1016/s0168-1605(97)00126-8}, pmid = {9562883}, issn = {0168-1605}, mesh = {Animals ; *Environmental Microbiology ; Fish Products/microbiology ; *Food Packaging ; Food Preservation ; Gram-Negative Bacteria/growth &amp; development ; Gram-Positive Bacteria/growth &amp; development ; Refrigeration/methods ; Salmon/*microbiology ; Time Factors ; }, abstract = {Microbiological, chemical and sensory changes in cold-smoked salmon were studied during 5 weeks of vacuum storage at 8 degrees C. The aerobic 20 degrees C viable count reached its maximum level after 6 days (3 x 10(6) cfu g-1) however, the shelf-life of the product was estimated to be 2 or 3 weeks by the panellists, confirming that there is no correlation between those two factors. Acid, pungent, sour and rancid odours and flavours and pasty texture were the main spoilage characteristics. Trimethylamine did not play a major role in the spoilage mechanisms as only small amounts were produced. Two-hundred and seventy strains were collected over the storage period, purified and characterized. During the first 2 weeks, Gram-negative bacteria were dominant, mainly represented by S. putrefaciens immediately after the smoking process and then P. phosphoreum. Aeromonas spp. were present throughout the storage but in smaller amounts. Gram-negative bacteria then progressively decreased while Gram-positive bacteria, dominated by lactic acid bacteria (LAB), became by far the most common variety found. Carnobacterium piscicola was widely represented (97/155 LAB isolates). A diversification was observed at the end of the storage, with the appearance of L. farciminis, L. sake and L. alimentarius. Occurrence of yeasts and moulds was quite rare. Spoilage potential of the strains was tested on a sterile smoked salmon extract juice. Shewanella putrefaciens, Aeromonas spp. and Brachothrix spp. produced strong off-odours while most of the LAB and P. phosphoreum seemed not to be involved in spoilage.}, }
@article {pmid9546163, year = {1998}, author = {Nüsslein, K and Tiedje, JM}, title = {Characterization of the dominant and rare members of a young Hawaiian soil bacterial community with small-subunit ribosomal DNA amplified from DNA fractionated on the basis of its guanine and cytosine composition.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {4}, pages = {1283-1289}, pmid = {9546163}, issn = {0099-2240}, mesh = {Base Composition ; Clostridium/chemistry/genetics/isolation &amp; purification ; DNA, Bacterial/chemistry/genetics/*isolation &amp; purification ; DNA, Ribosomal/chemistry/genetics/*isolation &amp; purification ; Ecosystem ; Genetic Variation ; Hawaii ; Phylogeny ; Pseudomonas/chemistry/genetics/isolation &amp; purification ; Rhizobium/chemistry/genetics/isolation &amp; purification ; Rhodospirillum/chemistry/genetics/isolation &amp; purification ; *Soil Microbiology ; }, abstract = {The small-subunit ribosomal DNA (rDNA) diversity was found to be very high in a Hawaiian soil community that might be expected to have lower diversity than the communities in continental soils because the Hawaiian soil is geographically isolated and only 200 years old, is subjected to a constant climate, and harbors low plant diversity. Since an underlying community structure could not be revealed by analyzing the total eubacterial rDNA, we first fractionated the DNA on the basis of guanine-plus-cytosine (G + C) content by using bisbenzimidazole and equilibrium centrifugation and then analyzed the bacterial rDNA amplified from a fraction with a high biomass (63% G + C fraction) and a fraction with a low biomass (35% G + C fraction). The rDNA clone libraries were screened by amplified rDNA restriction analysis to determine phylotype distribution. The dominant biomass reflected by the 63% G + C fraction contained several dominant phylotypes, while the community members that were less successful (35% G + C fraction) did not show dominance but there was a very high diversity of phylotypes. Nucleotide sequence analysis revealed taxa belonging to the groups expected for the G + C contents used. The dominant phylotypes in the 63% G + C fraction were members of the Pseudomonas, Rhizobium-Agrobacterium, and Rhodospirillum assemblages, while all of the clones sequenced from the 35% G + C fraction were affiliated with several Clostridium assemblages. The two-step rDNA analysis used here uncovered more diversity than can be detected by direct rDNA analysis of total community DNA. The G + C separation step is also a way to detect some of the less dominant organisms in a community.}, }
@article {pmid9537403, year = {1998}, author = {Stevenson, BS and Schmidt, TM}, title = {Growth rate-dependent accumulation of RNA from plasmid-borne rRNA operons in Escherichia coli.}, journal = {Journal of bacteriology}, volume = {180}, number = {7}, pages = {1970-1972}, pmid = {9537403}, issn = {0021-9193}, mesh = {Escherichia coli/*genetics/growth &amp; development ; *Operon ; *Plasmids ; RNA, Bacterial/*metabolism ; RNA, Ribosomal/*genetics ; Transformation, Bacterial ; }, abstract = {Inadequate regulation of the expression of additional plasmid-borne rRNA operons in Escherichia coli was exaggerated at slow growth rates, resulting in increases of approximately 100% for RNA concentration and 33% for doubling time. These observations are consistent with the hypothesis that multiple rRNA operons constitute a metabolic burden at slow growth rates.}, }
@article {pmid9536863, year = {1998}, author = {De Smet, I and De Boever, P and Verstraete, W}, title = {Cholesterol lowering in pigs through enhanced bacterial bile salt hydrolase activity.}, journal = {The British journal of nutrition}, volume = {79}, number = {2}, pages = {185-194}, doi = {10.1079/bjn19980030}, pmid = {9536863}, issn = {0007-1145}, mesh = {Amidohydrolases/*metabolism ; Analysis of Variance ; Animals ; Cholesterol/*blood ; Cholesterol, LDL/blood ; *Diet ; Feces/chemistry/microbiology ; Female ; Hydrogen-Ion Concentration ; Lactobacillus/*enzymology ; Male ; Swine/growth &amp; development/*metabolism ; }, abstract = {The effect of feeding live Lactobacillus reuteri cells containing active bile salt hydrolase (BSH) on plasma cholesterol levels was studied in pigs. During an experiment lasting 13 weeks, twenty pigs were fed on a high-fat, high-cholesterol, low-fibre for the first 10 weeks, and a regular pig diet for the last 3 weeks. One group of animals received, twice daily, 11.25 (SD 0.16) log10 colony forming units of the potential probiotic bacteria for 4 weeks (from week 3 until week 7). From week 8 onwards, the treated group was again fed on the same diet as the control group without additions. The total faecal Lactobacillus counts were only significantly higher in the treated pigs during the first 2 weeks of L reuteri feeding. Based on limited data, it was suggested that the administered Lactobacillus species had caused a temporary shift within the indigenous Lactobacillus population rather than permanently colonizing the intestinal tract. The probiotic feeding brought about significant lowering (P < or = 0.05) of total and LDL-cholesterol concentrations in the treated pigs compared with the control pigs, while no change in HDL-cholesterol concentration was observed. The data for faecal output of neutral sterols and bile salts were highly variable between the animals of each group, yet they indicated an increased output in the treated pigs. Although the blood cholesterol levels went up in both groups during the 3 weeks following the Lactobacillus administration period, significantly lower serum total and LDL-cholesterol levels were observed in the treated pigs. During the final 3 weeks of normalization to the regular diet, cholesterol concentrations significantly decreased in both animal groups and the differences in total and LDL-cholesterol concentrations between the groups largely disappeared.}, }
@article {pmid9534232, year = {1998}, author = {Bogdanova, ES and Bass, IA and Minakhin, LS and Petrova, MA and Mindlin, SZ and Volodin, AA and Kalyaeva, ES and Tiedje, JM and Hobman, JL and Brown, NL and Nikiforov, VG}, title = {Horizontal spread of mer operons among gram-positive bacteria in natural environments.}, journal = {Microbiology (Reading, England)}, volume = {144 (Pt 3)}, number = {}, pages = {609-620}, doi = {10.1099/00221287-144-3-609}, pmid = {9534232}, issn = {1350-0872}, support = {TW00396-02/TW/FIC NIH HHS/United States ; }, mesh = {Bacillus/drug effects/*genetics ; *DNA Transposable Elements ; Drug Resistance, Microbial/*genetics ; Genetic Variation ; Gram-Positive Bacteria/drug effects/*genetics ; Mercury/*pharmacology ; Molecular Sequence Data ; Operon/*genetics ; Organomercury Compounds/pharmacology ; Oxidoreductases/genetics ; Phylogeny ; Plasmids ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Restriction Mapping ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Horizontal dissemination of the genes responsible for resistance to toxic pollutants may play a key role in the adaptation of bacterial populations to environmental contaminants. However, the frequency and extent of gene dissemination in natural environments is not known. A natural horizontal spread of two distinct mercury resistance (mer) operon variants, which occurred amongst diverse Bacillus and related species over wide geographical areas, is reported. One mer variant encodes a mercuric reductase with a single N-terminal domain, whilst the other encodes a reductase with a duplicated N-terminal domain. The strains containing the former mer operon types are sensitive to organomercurials, and are most common in the terrestrial mercury-resistant Bacillus populations studied in this work. The strains containing the latter operon types are resistant to organomercurials, and dominate in a Minamata Bay mercury-resistant Bacillus population, previously described in the literature. At least three distinct transposons (related to a class II vancomycin-resistance transposon, Tn1546, from a clinical Enterococcus strain) and conjugative plasmids are implicated as mediators of the spread of these mer operons.}, }
@article {pmid9485456, year = {1998}, author = {Saari, RE and Hausinger, RP}, title = {Ascorbic acid-dependent turnover and reactivation of 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase using thiophenoxyacetic acid.}, journal = {Biochemistry}, volume = {37}, number = {9}, pages = {3035-3042}, doi = {10.1021/bi972388p}, pmid = {9485456}, issn = {0006-2960}, mesh = {2,4-Dichlorophenoxyacetic Acid/*metabolism ; Alcaligenes/*enzymology ; Animals ; Ascorbic Acid/*metabolism ; Cattle ; Chromatography, High Pressure Liquid ; Glycolates/*metabolism ; Ketoglutarate Dehydrogenase Complex/*metabolism ; Ketoglutaric Acids/metabolism ; Kinetics ; Models, Chemical ; }, abstract = {The first step in catabolism of the broadleaf herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) is catalyzed by 2,4-D/alpha-ketoglutarate (alpha-KG)-dioxygenase (TfdA) in Ralstonia eutropha (formerly Alcaligenes eutrophus) JMP134. This oxygen- and ferrous-ion-dependent enzyme couples the oxidative decarboxylation of alpha-KG (yielding CO2 and succinate) with the oxidation of 2,4-D to produce 2,4-dichlorophenol and glyoxylate. TfdA was shown to utilize thiophenoxyacetic acid (TPAA) to produce thiophenol, allowing the development of a continuous spectrophotometric assay for the enzyme using the thiol-reactive reagent 4,4'-dithiodipyridine. In contrast to the reaction with 2,4-D, however, the kinetics of TPAA oxidation were nonlinear and ascorbic acid was found to be required for and consumed during TPAA oxidation. The ascorbic acid was needed to reduce a reversibly oxidized inactive state that was formed by reaction of the ferrous enzyme with oxygen, either in the absence of substrate or in the presence of TPAA. The dependency on this reductant was not due to an uncoupling of alpha-KG decarboxylation from substrate hydroxylation, as has been reported for several other alpha-KG-dependent hydroxylases. Significantly, the rate of formation of this reversibly oxidized species was much lower when the enzyme was turning over 2,4-D. Evidence also was obtained for the generation of an inactive enzyme species that could not be reversed by ascorbate. The latter species, not associated with protein fragmentation, arose from an oxidative reaction that is likely to involve hydroxyl radical reactions. On the basis of initial rate studies, the kcat and Km values for TPAA were estimated to be 20-fold lower and 80-fold higher than the corresponding values for 2,4-D. The results are incorporated into a model of TfdA reactivity involving both catalytic and inactivating events.}, }
@article {pmid9529888, year = {1998}, author = {Marcotte, H and Lavoie, MC}, title = {Oral microbial ecology and the role of salivary immunoglobulin A.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {62}, number = {1}, pages = {71-109}, pmid = {9529888}, issn = {1092-2172}, mesh = {Animals ; Bacteria/*immunology ; Ecosystem ; Humans ; Immunoglobulin A, Secretory/*immunology ; Mouth/*microbiology ; Mouth Diseases ; Saliva ; }, abstract = {In the oral cavity, indigenous bacteria are often associated with two major oral diseases, caries and periodontal diseases. These diseases seem to appear following an imbalance in the oral resident microbiota, leading to the emergence of potentially pathogenic bacteria. To define the process involved in caries and periodontal diseases, it is necessary to understand the ecology of the oral cavity and to identify the factors responsible for the transition of the oral microbiota from a commensal to a pathogenic relationship with the host. The regulatory forces influencing the oral ecosystem can be divided into three major categories: host related, microbe related, and external factors. Among host factors, secretory immunoglobulin A (SIgA) constitutes the main specific immune defense mechanism in saliva and may play an important role in the homeostasis of the oral microbiota. Naturally occurring SIgA antibodies that are reactive against a variety of indigenous bacteria are detectable in saliva. These antibodies may control the oral microbiota by reducing the adherence of bacteria to the oral mucosa and teeth. It is thought that protection against bacterial etiologic agents of caries and periodontal diseases could be conferred by the induction of SIgA antibodies via the stimulation of the mucosal immune system. However, elucidation of the role of the SIgA immune system in controlling the oral indigenous microbiota is a prerequisite for the development of effective vaccines against these diseases. The role of SIgA antibodies in the acquisition and the regulation of the indigenous microbiota is still controversial. Our review discusses the importance of SIgA among the multiple factors that control the oral microbiota. It describes the oral ecosystems, the principal factors that may control the oral microbiota, a basic knowledge of the secretory immune system, the biological functions of SIgA, and, finally, experiments related to the role of SIgA in oral microbial ecology.}, }
@article {pmid9495027, year = {1998}, author = {Wagner, M and Schmid, M and Juretschko, S and Trebesius, KH and Bubert, A and Goebel, W and Schleifer, KH}, title = {In situ detection of a virulence factor mRNA and 16S rRNA in Listeria monocytogenes.}, journal = {FEMS microbiology letters}, volume = {160}, number = {1}, pages = {159-168}, doi = {10.1111/j.1574-6968.1998.tb12906.x}, pmid = {9495027}, issn = {0378-1097}, mesh = {Bacterial Proteins/*genetics ; Blotting, Northern ; In Situ Hybridization, Fluorescence/methods ; Listeria monocytogenes/*genetics/*pathogenicity ; Oligonucleotide Probes ; RNA, Bacterial/analysis ; RNA, Messenger/analysis ; RNA, Ribosomal, 16S/*analysis ; Virulence ; }, abstract = {Simultaneous in situ analysis of the structure and function of bacterial cells present within complex communities is a key for improving our understanding of microbial ecology. A protocol for the in situ identification of Listeria spp. using fluorescently tagged, rRNA-targeted oligonucleotide probes was developed. Ethanol fixation and enzymatic pretreatment with lysozyme and proteinase K were used to optimize whole cell hybridization of exponential phase and stationary phase Listeria spp. cells. In parallel, transcript probes carrying multiple digoxigenin molecules were combined with anti-digoxigenin Fab antibody fragments labeled with horseradish peroxidase to detect, via the catalytic deposition of fluorescein-tyramide, the iap-mRNA in single Listeria monocytogenes cells. The iap gene encodes the associated virulence factor p60. Application of the new signal amplification technique resulted in strong signals comparable in intensity to those obtained with fluorescently labeled rRNA-targeted oligonucleotide probes.}, }
@article {pmid9465391, year = {1998}, author = {Ahrén, D and Ursing, BM and Tunlid, A}, title = {Phylogeny of nematode-trapping fungi based on 18S rDNA sequences.}, journal = {FEMS microbiology letters}, volume = {158}, number = {2}, pages = {179-184}, doi = {10.1111/j.1574-6968.1998.tb12817.x}, pmid = {9465391}, issn = {0378-1097}, mesh = {Animals ; Classification ; DNA, Fungal/analysis ; Mitosporic Fungi/*genetics ; Nematoda/*microbiology ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; }, abstract = {The small subunit (SSU) ribosomal DNA (18S rDNA) from 15 species of nematode-trapping fungi and closely related non-parasitic species were sequenced. Phylogenetic analysis indicated that species within the genera of Arthrobotrys, Dactylaria, Dactylella, Monacrosporium and Duddingtonia formed a monophyletic and isolated clade among an unresolved cluster of apothecial ascomycetes. The phylogenetic patterns within this clade were not concordant with the morphology of the conidia nor the conidiophores, but rather with that of the infection structures. The results from the different methods of tree reconstruction supported three lineages; the species having constricting rings, the non-parasitic species and the species having various adhesive structures (nets, hyphae, knobs and non-constricting rings) to infect nematodes.}, }
@article {pmid9464403, year = {1998}, author = {Rhodes, AN and Urbance, JW and Youga, H and Corlew-Newman, H and Reddy, CA and Klug, MJ and Tiedje, JM and Fisher, DC}, title = {Identification of bacterial isolates obtained from intestinal contents associated with 12,000-year-old mastodon remains.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {2}, pages = {651-658}, pmid = {9464403}, issn = {0099-2240}, mesh = {Animals ; *Archaeology ; Bacteria/*isolation &amp; purification ; DNA, Ribosomal/chemistry ; Intestines/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Mastodon (Mammut americanum) remains unearthed during excavation of ancient sediments usually consist only of skeletal material, due to postmortem decomposition of soft tissues by microorganisms. Two recent excavations of skeletal remains in anoxic sediments in Ohio and Michigan, however, have uncovered organic masses which appear to be remnants of the small and large intestines, respectively. Macrobotanical examinations of the composition of these masses revealed assemblages of plant material radiocarbon dated to approximately 11,500 years before the present and thought to be incompletely digested food remains from this extinct mammal. We attempted to cultivate and identify bacteria from the intestinal contents, bone-associated sediments, and sediments not in proximity to the remains using a variety of general and selective media. In all, 295 isolates were cultivated, and 38 individual taxa were identified by fatty acid-methyl ester (FAME) profiles and biochemical characteristics (API-20E). The taxonomic positions of selected enteric and obligately anaerobic bacteria were confirmed by 16S ribosomal DNA (rDNA) sequencing. Results indicate that the intestinal and bone-associated samples contained the greatest diversity of bacterial taxa and that members of the family Enterobacteriaceae represented 41% of all isolates and were predominant in the intestinal masses and sediments in proximity to the skeleton but were uncommon in the background sediments. Enterobacter cloacae was the most commonly identified isolate, and partial rDNA sequencing revealed that Rahnella aquatilis was the correct identity of strains suggested by FAME profiles to be Yersinia enterocolitica. No Bacteroides spp. or expected intestinal anaerobes were recovered. The only obligate anaerobes recovered were clostridia, and these were not recovered from the small intestinal masses. Microbiological evidence from this study supports other, macrobotanical data indicating the intestinal origin of these masses. Whether these organisms are direct descendants of the original intestinal microbiota, however, cannot be established.}, }
@article {pmid9459662, year = {1998}, author = {Wang, JG and Bakken, LR}, title = {Screening of Soil Bacteria for Poly-beta-Hydroxybutyric Acid Production and Its Role in the Survival of Starvation.}, journal = {Microbial ecology}, volume = {35}, number = {1}, pages = {94-101}, doi = {10.1007/s002489900063}, pmid = {9459662}, issn = {1432-184X}, }
@article {pmid9459661, year = {1998}, author = {Gilbert, D and Amblard, C and Bourdier, G and Francez, A}, title = {The Microbial Loop at the Surface of a Peatland:Structure, Function, and Impact of Nutrient Input.}, journal = {Microbial ecology}, volume = {35}, number = {1}, pages = {83-93}, doi = {10.1007/s002489900062}, pmid = {9459661}, issn = {1432-184X}, }
@article {pmid9459660, year = {1998}, author = {Hogan, ME and Ward, BB}, title = {Response of a Marine Sediment Microbial Community Exposed to 2,4-Dichlorophenoxyacetic Acid.}, journal = {Microbial ecology}, volume = {35}, number = {1}, pages = {72-82}, doi = {10.1007/s002489900061}, pmid = {9459660}, issn = {1432-184X}, }
@article {pmid9459659, year = {1998}, author = {Mattison, RG and Abbiati, M and Dando, PR and Fitzsimons, MF and Pratt, SM and Southward, AJ and Southward, EC}, title = {Chemoautotrophic Microbial Mats in Submarine Caves with Hydrothermal Sulphidic Springs at Cape Palinuro, Italy.}, journal = {Microbial ecology}, volume = {35}, number = {1}, pages = {58-71}, doi = {10.1007/s002489900060}, pmid = {9459659}, issn = {1432-184X}, }
@article {pmid9459658, year = {1998}, author = {Ferrier-Pages, C and Gattuso, J}, title = {Biomass, Production and Grazing Rates of Pico- and Nanoplankton in Coral Reef Waters (Miyako Island, Japan).}, journal = {Microbial ecology}, volume = {35}, number = {1}, pages = {46-57}, doi = {10.1007/s002489900059}, pmid = {9459658}, issn = {1432-184X}, }
@article {pmid9459657, year = {1998}, author = {Currin, CA and Paerl, HW}, title = {Environmental and Physiological Controls on Diel Patterns of N2 Fixation in Epiphytic Cyanobacterial Communities.}, journal = {Microbial ecology}, volume = {35}, number = {1}, pages = {34-45}, doi = {10.1007/s002489900058}, pmid = {9459657}, issn = {1432-184X}, }
@article {pmid9459656, year = {1998}, author = {Bennasar, A and Guasp, C and Lalucat, J}, title = {Molecular Methods for the Detection and Identification of Pseudomonas stutzeri in Pure Culture and Environmental Samples.}, journal = {Microbial ecology}, volume = {35}, number = {1}, pages = {22-33}, doi = {10.1007/s002489900057}, pmid = {9459656}, issn = {1432-184X}, }
@article {pmid9459655, year = {1998}, author = {Head, IM and Saunders, JR and Pickup, RW}, title = {Microbial Evolution, Diversity, and Ecology: A Decade of Ribosomal RNA Analysis of Uncultivated Microorganisms.}, journal = {Microbial ecology}, volume = {35}, number = {1}, pages = {1-21}, doi = {10.1007/s002489900056}, pmid = {9459655}, issn = {1432-184X}, }
@article {pmid9435068, year = {1998}, author = {Finster, K and Liesack, W and Thamdrup, B}, title = {Elemental sulfur and thiosulfate disproportionation by Desulfocapsa sulfoexigens sp. nov., a new anaerobic bacterium isolated from marine surface sediment.}, journal = {Applied and environmental microbiology}, volume = {64}, number = {1}, pages = {119-125}, pmid = {9435068}, issn = {0099-2240}, mesh = {Base Composition ; DNA, Bacterial/analysis/genetics ; Ferric Compounds ; Ferritins/metabolism ; Formates/metabolism ; Geologic Sediments/*microbiology ; Gram-Negative Anaerobic Bacteria/classification/genetics/*metabolism ; Hydrogen Sulfide/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sulfates/metabolism ; Sulfides/metabolism ; Sulfites/metabolism ; Sulfur/*metabolism ; Thiosulfates/*metabolism ; }, abstract = {A mesophilic, anaerobic, gram-negative bacterium, strain SB164P1, was enriched and isolated from oxidized marine surface sediment with elemental sulfur as the sole energy substrate in the presence of ferrihydrite. Elemental sulfur was disproportionated to hydrogen sulfide and sulfate. Growth was observed exclusively in the presence of a hydrogen sulfide scavenger, e.g., ferrihydrite. In the absence of a scavenger, sulfide and sulfate production were observed but no growth occurred. Strain SB164P1 grew also by disproportionation of thiosulfate and sulfite. With thiosulfate, the growth efficiency was higher in ferrihydrite-supplemented media than in media without ferrihydrite. Growth coupled to sulfate reduction was not observed. However, a slight sulfide production occurred in cultures incubated with formate and sulfate. Strain SB164P1 is the first bacterium described that grows chemolithoautotrophically exclusively by the disproportionation of inorganic sulfur compounds. Comparative 16S rDNA sequencing analysis placed strain SB164P1 into the delta subclass of the class Proteobacteria. Its closest relative is Desulfocapsa thiozymogenes, and slightly more distantly related are Desulfofustis glycolicus and Desulforhopalus vacuolatus. This phylogenetic cluster of organisms, together with members of the genus Desulfobulbus, forms one of the main lines of descent within the delta subclass of the Proteobacteria. Due to the common phenotypic characteristics and the phylogenetic relatedness to Desulfocapsa thiozymogenes, we propose that strain SB164P1 be designated the type strain of Desulfocapsa sulfoexigens sp. nov.}, }
@article {pmid9421915, year = {1997}, author = {Zhou, J and Davey, ME and Figueras, JB and Rivkina, E and Gilichinsky, D and Tiedje, JM}, title = {Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA.}, journal = {Microbiology (Reading, England)}, volume = {143 (Pt 12)}, number = {}, pages = {3913-3919}, doi = {10.1099/00221287-143-12-3913}, pmid = {9421915}, issn = {1350-0872}, mesh = {Arctic Regions ; Bacteria/*classification/genetics/isolation &amp; purification ; Base Sequence ; Cloning, Molecular ; Cold Climate ; DNA Primers ; DNA, Ribosomal/genetics ; Genetic Variation ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Bacterial/genetics ; Siberia ; *Soil Microbiology ; }, abstract = {Genomic DNA was isolated from the active layer of tundra soil collected from the Kolyma lowland, Northeast Eurasia, near the Arctic Ocean coast. The SSU (small subunit) rRNA genes were amplified with eubacterial primers from the bulk genomic community DNA and cloned into plasmid vectors. Forty-three SSU rDNA clones were obtained, and all of them had different RFLP patterns. Phylogenetic analysis based on partial sequences (about 300 bp) established with the maximum likelihood method revealed the presence of three major and several minor groups that fell into 11 of the established lines of bacteria, and one sequence that could not be assigned to any of the described groups. Most of the clones belonged to the alpha (20.9%) and delta (25.6%) subdivisions of the Proteobacteria, with lesser proportions in the beta (9.3%) and gamma (4.7%) subdivisions, groups typically isolated from soil by culture methods. Fewer than 12% of the clones belonged to Gram-positive bacteria, and 16% of the clones were related to Fibrobacter. The majority of the clones (70%) had sequences that were 5-15% different from those in the current databases, and 7% of the clones had sequences that differed by more than 20% from those in the database. The results suggest that these tundra-derived clones are very diverse in phylogeny, and that many probably reflect new genera or families. Hence, most of the tundra soil bacterial community has never been isolated and thus the physiology and function of its dominant members appears to be unknown.}, }
@article {pmid9395116, year = {1997}, author = {Gaffar, A and Afflitto, J and Nabi, N}, title = {Chemical agents for the control of plaque and plaque microflora: an overview.}, journal = {European journal of oral sciences}, volume = {105}, number = {5 Pt 2}, pages = {502-507}, doi = {10.1111/j.1600-0722.1997.tb00237.x}, pmid = {9395116}, issn = {0909-8836}, mesh = {Anti-Infective Agents, Local/*therapeutic use ; Bacteria/*drug effects ; Bacterial Adhesion/drug effects ; Cariostatic Agents/administration &amp; dosage/therapeutic use ; Cations ; Chemoprevention ; Dental Calculus/prevention &amp; control ; Dental Caries/etiology/prevention &amp; control ; Dental Plaque/microbiology/*prevention &amp; control ; Dentin Sensitivity/prevention &amp; control ; Gels ; Gingiva/microbiology ; Gingivitis/etiology/prevention &amp; control ; Humans ; Longitudinal Studies ; Organophosphonates/therapeutic use ; Oxidants/therapeutic use ; Polyvinyls/therapeutic use ; Sodium Fluoride/therapeutic use ; Tin Fluorides/administration &amp; dosage/therapeutic use ; Tooth/microbiology ; Tooth Discoloration/prevention &amp; control ; Toothpastes ; Triclosan/therapeutic use ; }, abstract = {This presentation provides an overview of the technologies available for the chemical control of plaque. It is generally accepted that the formation of dental plaque at the interfaces of tooth/gingiva is one of the major causes of gingival inflammation and dental caries. Several therapeutic approaches have been used to control dental plaque and supragingival infections. These include fluoride preparations such as stannous fluoride, oxygenating agents, anti-attachment agents, and cationic and non-cationic antibacterial agents. Among the fluoride preparations, stable stannous fluoride pastes and gels have been shown to reduce supragingival plaque, gingivitis, hypersensitivity and caries. The effect of the oxygenating agents on the supragingival plaque has been equivocal, but recent data indicate that a stable agent which provides sustained active oxygen release is effective in controlling plaque. A polymer, PVPA, which reduced attachment of bacteria to teeth was shown to significantly reduce plaque formation in humans. A new generation of antibacterials includes non-ionics such as triclosan, which in combination with a special polymer delivery system, has been shown to reduce plaque, gingivitis, supragingival calculus and dental caries in long-term studies conducted around the world. Unlike the first generation of agents, the triclosan/copolymer/sodium fluoride system is effective in long-term clinicals and does not cause staining of teeth, increase in calculus, or disturbance in the oral microbial ecology.}, }
@article {pmid9389477, year = {1997}, author = {Elena, SF and Lenski, RE}, title = {Test of synergistic interactions among deleterious mutations in bacteria.}, journal = {Nature}, volume = {390}, number = {6658}, pages = {395-398}, doi = {10.1038/37108}, pmid = {9389477}, issn = {0028-0836}, mesh = {Directed Molecular Evolution ; Escherichia coli/*genetics/growth &amp; development ; *Genes, Bacterial ; Genotype ; Models, Genetic ; Mutagenesis, Insertional ; *Mutation ; Recombination, Genetic ; Sex ; }, abstract = {Identifying the forces responsible for the origin and maintenance of sexuality remains one of the greatest unsolved problems in biology. The mutational deterministic hypothesis postulates that sex is an adaptation that allows deleterious mutations to be purged from the genome; it requires synergistic interactions, which means that two mutations would be more harmful together than expected from their separate effects. We generated 225 genotypes of Escherichia coli carrying one, two or three successive mutations and measured their fitness relative to an unmutated competitor. The relationship between mutation number and average fitness is nearly log-linear. We also constructed 27 recombinant genotypes having pairs of mutations whose separate and combined effects on fitness were determined. Several pairs exhibit significant interactions for fitness, but they are antagonistic as often as they are synergistic. These results do not support the mutational deterministic hypothesis for the evolution of sex.}, }
@article {pmid9328648, year = {1998}, author = {Russell, JB and Diez-Gonzalez, F}, title = {The effects of fermentation acids on bacterial growth.}, journal = {Advances in microbial physiology}, volume = {39}, number = {}, pages = {205-234}, doi = {10.1016/s0065-2911(08)60017-x}, pmid = {9328648}, issn = {0065-2911}, mesh = {Acetic Acid/metabolism ; Acids/*metabolism ; Animals ; Bacteria/*growth &amp; development/*metabolism ; Biological Transport ; Fermentation ; Food Microbiology ; Hydrogen-Ion Concentration ; Intestinal Diseases/microbiology ; Rumen/metabolism ; Silage/microbiology ; Soil Microbiology ; Solvents/metabolism ; }, abstract = {Anaerobic habitats often have low pH and high concentrations of fermentation acids, and these conditions can inhibit the growth of many bacteria. The toxicity of fermentation acids at low pH was traditionally explained by an uncoupling mechanism. Undissociated fermentation acids can pass across the cell membrane and dissociate in the more alkaline interior, but there is little evidence that they can act in a cyclic manner to dissipate protonmotive force. Fermentation acid dissociation in the more alkaline interior causes an accumulation of the anionic species, and this accumulation is dependent on the pH gradient (delta pH) across the membrane. Fermentation acid-resistant bacteria have low delta pH and are able to generate ATP and grow with a low intracellular pH. Escherichia coli O157:H7 is able to decrease its intracellular pH to 6.1 before growth ceases, but this modest decrease in delta pH can only partially counteract the toxic effect of fermentation anion accumulation. Fermentation acid-resistant bacteria are in most cases Gram-positive bacteria with a high intracellular potassium concentration, and even acid-sensitive bacteria like E. coli K-12 have increased potassium levels when fermentation acids are present. Intracellular potassium provides a counteraction for fermentation acid anions, and allows bacteria to tolerate even greater amounts of fermentation anions. The delta pH-mediated anion accumulation provides a mechanistic explanation for the effect of fermentation acids on microbial ecology and metabolism.}, }
@article {pmid9337421, year = {1997}, author = {Nijburg, JW and Laanbroek, HJ}, title = {The Fate of 15N-Nitrate in Healthy and Declining Phragmites australis Stands.}, journal = {Microbial ecology}, volume = {34}, number = {3}, pages = {254-262}, doi = {10.1007/s002489900055}, pmid = {9337421}, issn = {1432-184X}, }
@article {pmid9337420, year = {1997}, author = {Fuller, ME and Scow, KM}, title = {Lack of Capsular Exopolymer Effects on the Biodegradation of Organic Compounds by Pseudomonas sp. Strains JS1 and JS150.}, journal = {Microbial ecology}, volume = {34}, number = {3}, pages = {248-253}, doi = {10.1007/s002489900054}, pmid = {9337420}, issn = {1432-184X}, }
@article {pmid9337419, year = {1997}, author = {Cook, KL and Garland, JL}, title = {The Relationship Between Electron Transport Activity as Measured by CTC Reduction and CO2 Production in Mixed Microbial Communities.}, journal = {Microbial ecology}, volume = {34}, number = {3}, pages = {237-247}, doi = {10.1007/s002489900053}, pmid = {9337419}, issn = {1432-184X}, }
@article {pmid9337418, year = {1997}, author = {Lewin, RA}, title = {Saprospira grandis: A Flexibacterium That Can Catch Bacterial Prey by "Ixotrophy".}, journal = {Microbial ecology}, volume = {34}, number = {3}, pages = {232-236}, doi = {10.1007/s002489900052}, pmid = {9337418}, issn = {1432-184X}, }
@article {pmid9337417, year = {1997}, author = {Lemke, MJ and Brown, BJ and Leff, LG}, title = {The Response of Three Bacterial Populations to Pollution in a Stream.}, journal = {Microbial ecology}, volume = {34}, number = {3}, pages = {224-231}, doi = {10.1007/s002489900051}, pmid = {9337417}, issn = {1432-184X}, }
@article {pmid9337416, year = {1997}, author = {Mahaffee, WF and Kloepper, JW}, title = {Temporal Changes in the Bacterial Communities of Soil, Rhizosphere, and Endorhiza Associated with Field-Grown Cucumber (Cucumis sativus L.).}, journal = {Microbial ecology}, volume = {34}, number = {3}, pages = {210-223}, doi = {10.1007/s002489900050}, pmid = {9337416}, issn = {1432-184X}, }
@article {pmid9337415, year = {1997}, author = {Epstein, SS}, title = {Microbial Food Webs in Marine Sediments. II. Seasonal Changes in Trophic Interactions in a Sandy Tidal Flat Community.}, journal = {Microbial ecology}, volume = {34}, number = {3}, pages = {199-209}, doi = {10.1007/s002489900049}, pmid = {9337415}, issn = {1432-184X}, abstract = {>AbstractThe role of grazing by marine sediment flagellates, ciliates, and meiobenthic animals in controlling production of their bacterial and diatom prey was investigated. At six selected time points, over the year, bacterial production and diatom standing stock were compared to grazing pressure exercised by proto- and micrometazoan consumers. The intensity of prey-predator relations showed pronounced yearly dynamics in which two stages could be distinguished. During the first phase, from the end of winter to mid-summer, the consumption of diatoms gradually increased, with possible overgrazing at the end of the period. This was followed by a collapse of diatom abundance, to the winter level. During the first stage, no appreciable bacterial consumption was observed in spite of the high abundance and production of bacteria. The second stage started in mid-summer and continued through the fall. During this period, the grazing on bacteria increased and reached the year's maximum. For at least a brief period (October), micrograzers removed the majority of bacterial production. In contrast, herbivory stayed at the year's lowest level, and diatoms appeared to be controlled by factors other than grazing. The observed ingestion rates seem to support the apparent energy requirements of flagellates and some ciliates (scuticociliates and hypotrichids). Other ciliates (pleurostomatids and karyorelictids) could not subsist on the observed diet and might have to complement it with other energy sources, possibly via dissolved organic matter absorption.}, }
@article {pmid9337414, year = {1997}, author = {Epstein, SS}, title = {Microbial Food Webs in Marine Sediments. I. Trophic Interactions and Grazing Rates in Two Tidal Flat Communities.}, journal = {Microbial ecology}, volume = {34}, number = {3}, pages = {188-198}, doi = {10.1007/s002489900048}, pmid = {9337414}, issn = {1432-184X}, }
@article {pmid9337413, year = {1997}, author = {Guo, C and Sun, W and Harsh, JB and Ogram, A}, title = {Hybridization Analysis of Microbial DNA from Fuel Oil-Contaminated and Noncontaminated Soil.}, journal = {Microbial ecology}, volume = {34}, number = {3}, pages = {178-187}, doi = {10.1007/s002489900047}, pmid = {9337413}, issn = {1432-184X}, }
@article {pmid9337412, year = {1997}, author = {Shaffer, BT and Lighthart, B}, title = {Survey of Culturable Airborne Bacteria at Four Diverse Locations in Oregon: Urban, Rural, Forest, and Coastal.}, journal = {Microbial ecology}, volume = {34}, number = {3}, pages = {167-177}, doi = {10.1007/s002489900046}, pmid = {9337412}, issn = {1432-184X}, }
@article {pmid9336931, year = {1997}, author = {Finster, K and Liesack, W and Tindall, BJ}, title = {Sulfurospirillum arcachonense sp. nov., a new microaerophilic sulfur-reducing bacterium.}, journal = {International journal of systematic bacteriology}, volume = {47}, number = {4}, pages = {1212-1217}, doi = {10.1099/00207713-47-4-1212}, pmid = {9336931}, issn = {0020-7713}, mesh = {Base Composition ; DNA, Bacterial/analysis ; Fatty Acids/analysis ; Gram-Negative Bacteria/chemistry/*classification/genetics/growth &amp; development/isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; Quinones/metabolism ; RNA, Ribosomal, 16S/analysis ; Sulfur-Reducing Bacteria/chemistry/*classification/genetics/growth &amp; development/isolation &amp; purification ; }, abstract = {The isolation of a new motile, gram-negative, heterotrophic, sulfur-reducing, microaerophilic, vibrioid bacterium, strain F1F6, from oxidized marine surface sediment (Arcachon Bay, French Atlantic coast) is described. Hydrogen (with acetate as the carbon source), formate (with acetate as the carbon source), pyruvate, lactate, alpha-ketoglutarate, glutarate, glutamate, and yeast extract supported growth with elemental sulfur under anaerobic conditions. Apart from H2 and formate, the oxidation of the substrates was incomplete. Microaerophilic growth was supported with hydrogen (acetate as the carbon source), formate (acetate as the carbon source), acetate, propionate, pyruvate, lactate, alpha-ketoglutarate, glutamate, yeast extract, fumarate, succinate, malate, citrate, and alanine. The isolate grew fermentatively with fumarate, succinate being the only organic product. Elemental sulfur and oxygen were the only electron acceptors used. Vitamins or amino acids were not required. The isolate was oxidase, catalase, and urease positive. Comparative 16S rDNA sequence analysis revealed a tight cluster consisting of the validly described species Sulfurospirillum deleyianum and the strains SES-3 and CCUG 13942 as the closest relatives of strain F1F6 (level of sequence similarity, 91.7 to 92.4%). Together with strain F1F6, these organisms form a novel lineage within the epsilon subclass of proteobacteria clearly separated from the described species of the genera Arcobacter, Campylobacter, Wolinella, and Helicobacter. Due to the phenotypic characteristics shared by strain F1F6 and S. deleyianum and considering their phylogenetic relationship, we propose the inclusion of strain F1F6 in the genus Sulfurospirillum, namely, as S. arcachonense sp. nov. Based on the results of this study, an emended description of the genus Sulfurospirillum is given.}, }
@article {pmid9378932, year = {1997}, author = {Stapleton, A and Stamm, WE}, title = {Prevention of urinary tract infection.}, journal = {Infectious disease clinics of North America}, volume = {11}, number = {3}, pages = {719-733}, doi = {10.1016/s0891-5520(05)70382-2}, pmid = {9378932}, issn = {0891-5520}, support = {AI-01115/AI/NIAID NIH HHS/United States ; DE 950144/DE/NIDCR NIH HHS/United States ; DK-40045/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Aged ; Anti-Bacterial Agents/administration &amp; dosage/*therapeutic use ; Child ; Child, Preschool ; Female ; Gram-Negative Bacteria/drug effects/pathogenicity ; Gram-Negative Bacterial Infections/diagnosis/drug therapy/microbiology ; Host-Parasite Interactions ; Humans ; Male ; Middle Aged ; Postmenopause ; Pregnancy ; Pregnancy Complications, Infectious/drug therapy/microbiology ; Premenopause ; Recurrence ; Risk-Taking ; Urinary Tract Infections/*drug therapy/epidemiology/*prevention &amp; control ; }, abstract = {Recurrent UTI remains an exceedingly common clinical problem among women of all ages. Among otherwise healthy premenopausal and postmenopausal women, increased susceptibility to recurrences seems to be conferred by intrinsic host factors, such as nonsecretor genotype or estrogen status, and by exogenous exposures or behaviors, such as use of a diaphragm with spermicide, antimicrobial use, and sexual behavior. The natural history of recurrent UTIs is notable for a temporal clustering phenomenon, the tendency of women to revert to a baseline infection pattern after the cessation of preventive interventions, and repeated serial reinfections of the urinary tract from the fecal reservoir, often by genetically identical organisms. Low-dose antimicrobial regimens given daily, three times weekly, or postcoitally are effective in preventing recurrences in most women with a predisposition to frequent infection. Intermittent patient-initiated self-treatment is an appropriate and effective option in some patients with lower recurrence rates. In postmenopausal women, estrogen replacement therapy, particularly vaginally applied estriol creams, may also significantly reduce the rate of recurrent UTI. Ongoing investigations in the areas of microbial ecology of the vaginal flora, the molecular basis for host-parasite interactions within the urinary tract, and vaccine development may eventually lead to improved means to prevent recurrent urinary tract infections more effectively.}, }
@article {pmid9230103, year = {1997}, author = {Strauss, EA and Dodds, WK}, title = {Influence of Protozoa and Nutrient Availability on Nitrification Rates in Subsurface Sediments.}, journal = {Microbial ecology}, volume = {34}, number = {2}, pages = {155-165}, doi = {10.1007/s002489900045}, pmid = {9230103}, issn = {1432-184X}, }
@article {pmid9230102, year = {1997}, author = {del Giorgio PA,  and Prairie, YT and Bird, DF}, title = {Coupling Between Rates of Bacterial Production and the Abundance of Metabolically Active Bacteria in Lakes, Enumerated Using CTC Reduction and Flow Cytometry.}, journal = {Microbial ecology}, volume = {34}, number = {2}, pages = {144-154}, doi = {10.1007/s002489900044}, pmid = {9230102}, issn = {1432-184X}, }
@article {pmid9230101, year = {1997}, author = {Goedkoop, W and Gullberg, KR and Johnson, RK and Ahlgren, I}, title = {Microbial Response of a Freshwater Benthic Community to a Simulated Diatom Sedimentation Event: Interactive Effects of Benthic Fauna.}, journal = {Microbial ecology}, volume = {34}, number = {2}, pages = {131-143}, doi = {10.1007/s002489900043}, pmid = {9230101}, issn = {1432-184X}, }
@article {pmid9230100, year = {1997}, author = {Staddon, WJ and Duchesne, LC and Trevors, JT}, title = {Microbial Diversity and Community Structure of Postdisturbance Forest Soils as Determined by Sole-Carbon-Source Utilization Patterns.}, journal = {Microbial ecology}, volume = {34}, number = {2}, pages = {125-130}, doi = {10.1007/s002489900042}, pmid = {9230100}, issn = {1432-184X}, }
@article {pmid9230099, year = {1997}, author = {May, R and V&amp;ouml;lksch, B and Kampmann, G}, title = {Antagonistic Activities of Epiphytic Bacteria from Soybean Leaves against Pseudomonas syringae pv. glycinea in vitro and in planta.}, journal = {Microbial ecology}, volume = {34}, number = {2}, pages = {118-124}, doi = {10.1007/s002489900041}, pmid = {9230099}, issn = {1432-184X}, }
@article {pmid9230098, year = {1997}, author = {Maloney, PE and van Bruggen AHC,  and Hu, S}, title = {Bacterial Community Structure in Relation to the Carbon Environments in Lettuce and Tomato Rhizospheres and in Bulk Soil.}, journal = {Microbial ecology}, volume = {34}, number = {2}, pages = {109-117}, doi = {10.1007/s002489900040}, pmid = {9230098}, issn = {1432-184X}, }
@article {pmid9230097, year = {1997}, author = {Ross, JL and Boon, PI and Ford, P and Hart, BT}, title = {Detection and Quantification with 16S rRNA Probes of Planktonic Methylotrophic Bacteria in a Floodplain Lake.}, journal = {Microbial ecology}, volume = {34}, number = {2}, pages = {97-108}, doi = {10.1007/s002489900039}, pmid = {9230097}, issn = {1432-184X}, }
@article {pmid9230096, year = {1997}, author = {Hogan, DA and Buckley, DH and Nakatsu, CH and Schmidt, TM and Hausinger, RP}, title = {Distribution of the tfdA Gene in Soil Bacteria That Do Not Degrade 2,4-Dichlorophenoxyacetic Acid (2,4-D).}, journal = {Microbial ecology}, volume = {34}, number = {2}, pages = {90-96}, doi = {10.1007/s002489900038}, pmid = {9230096}, issn = {1432-184X}, }
@article {pmid9230095, year = {1997}, author = {Hosein, SG and Millette, D and Butler, BJ and Greer, CW}, title = {Catabolic Gene Probe Analysis of an Aquifer Microbial Community Degrading Creosote-Related Polycyclic Aromatic and Heterocyclic Compounds.}, journal = {Microbial ecology}, volume = {34}, number = {2}, pages = {81-89}, doi = {10.1007/s002489900037}, pmid = {9230095}, issn = {1432-184X}, }
@article {pmid9379321, year = {1997}, author = {Müller, HP and Heinecke, A and Borneff, M and Knopf, A and Kiencke, C and Pohl, S}, title = {Microbial ecology of Actinobacillus actinomycetemcomitans, Eikenella corrodens and Capnocytophaga spp. in adult periodontitis.}, journal = {Journal of periodontal research}, volume = {32}, number = {6}, pages = {530-542}, doi = {10.1111/j.1600-0765.1997.tb00569.x}, pmid = {9379321}, issn = {0022-3484}, mesh = {Adult ; Aggregatibacter actinomycetemcomitans/*physiology ; Capnocytophaga/*physiology ; Cheek/microbiology ; Dental Plaque/microbiology ; Ecology ; Ecosystem ; Eikenella corrodens/*physiology ; Female ; Gingiva/microbiology ; Gingival Hemorrhage/microbiology ; Humans ; Likelihood Functions ; Male ; Middle Aged ; Molar/microbiology ; Mouth Mucosa/microbiology ; Multivariate Analysis ; Odds Ratio ; Palate/microbiology ; Palatine Tonsil/microbiology ; Periodontal Attachment Loss/microbiology ; Periodontal Pocket/microbiology ; Periodontitis/*microbiology ; Saliva/microbiology ; Tongue/microbiology ; }, abstract = {Information on intraoral distribution of putative periodontal pathogens might be essential for controlling different forms of periodontal disease. Colonization may be either promoted or impeded by other bacteria competing in the subgingival ecosystem. In recent investigations microbial associations between dental organisms have been determined in a multitude of subgingival plaque samples within multiple patients and described by odds ratios, in most circumstances without taking into account the correlated structure of the observations within a single individual. The present investigation had 3 major objectives: (i) to describe the intraoral distribution of some facultatively anaerobic, Gram-negative rods, i.e. Actinobacillus actinomycetemcomitans, Eikenella corrodens-like organisms and Capnocytophaga spp., in a multitude of subgingival and extracrevicular samples of 10 adult subjects with A. actinomycetemcomitans-associated periodontitis; (ii) to analyse possible inconsistencies of microbial associations between these periodontal organisms; and (iii) to determine factors increasing the likelihood of isolating these bacteria in a given subgingival site by employing Generalized Estimation Equation (GEE) methods. Clinical examinations were carried out at 6 sites of every tooth present. In each subject, 13 extracrevicular (2 cheek mucosa, 3 tongue, 4 gingival, 2 tonsillar samples, 1 palatinal, 1 saliva sample) and between 22 and 44 subgingival samples from deepest sites of every tooth present (n = 296) were selectively cultivated for A. actinomycetemcomitans, E. corrodens and Capnocytophaga spp. In extracrevicular material, A. actinomycetemcomitans, Capnocytophaga spp. and E. corrodens were isolated in 9, 10 and 6 patients, and from 65, 82 and 15% samples, respectively. The organisms were recovered from 51, 62 and 27% subgingival plaque samples, respectively. Heterogeneity tests did not reveal significant inconsistencies of microbial associations between bacteria in subgingival plaque. Mantel-Haenszel's odds ratios ranged between 2.0 for A. actinomycetemcomitans and Capnocytophaga spp. and 18.7 for Capnocytophaga spp. and E. corrodens. An exchangeable working dependence structure was employed in the GEE approach. The odds of isolating A. actinomycetemcomitans was increased by factor 3.7 in 4-6 mm deep pockets, and 9.5 in > or = 7 mm deep pockets. The odds of presence of E. corrodens was increased by factor 10.8 in the case of presence of Capnocytophaga spp. and 2.1 in the case of presence of A. actinomycetemcomitans. Capnocytophaga spp. were associated with bleeding on probing and molar sites. Presence of E. corrodens was associated with clinical attachment loss but not periodontal probing depth. Results of the present study indicated an association of A. actinomycetemcomitans with periodontal pathology. Whereas this organism and Capnocytophagae were widely distributed in extracrevicular ecosystems of the mouth, E. corrodens only occasionally appeared in saliva or on mucous membranes of the oral cavity. In general, GEE methods seem to allow to determine factors associated with the presence of periodontal organisms in a multivariate approach and considering the correlated structure of the data.}, }
@article {pmid9234799, year = {1997}, author = {Gordon, VM and Rehemtulla, A and Leppla, SH}, title = {A role for PACE4 in the proteolytic activation of anthrax toxin protective antigen.}, journal = {Infection and immunity}, volume = {65}, number = {8}, pages = {3370-3375}, pmid = {9234799}, issn = {0019-9567}, mesh = {Animals ; *Antigens, Bacterial ; Bacterial Toxins/*metabolism ; CHO Cells ; Cricetinae ; Furin ; Serine Endopeptidases/*physiology ; Subtilisins/physiology ; Transfection ; }, abstract = {Several bacterial protein toxins require activation by eukaryotic proteases. Previous studies have shown that anthrax toxin protective antigen (PA), Pseudomonas exotoxin A (PE), and diphtheria toxin (DT) are cleaved by furin C-terminal to the sequences RKKR, RQPR, and RVRR, respectively. Because furin-deficient cells retain some sensitivity to PA and DT, it is evident that other cellular proteases can activate these toxins. Whereas furin has been shown to require arginine residues at positions -1 and -4 for substrate recognition, another protease with an activity which could substitute for furin in toxin activation, the furin-related protease PACE4, requires basic residues in the -1, -2, and -4 positions of the substrate sequence. To examine the relative roles of furin and PACE4 in toxin activation, we used furin-deficient CHO cells (FD11 cells) transfected with either the furin (FD11/furin cells) or PACE4 (FD11/PACE4 cells) gene. Mutant PA proteins containing the cleavage sequence RAAR or KR were cytotoxic toward cells expressing only PACE4. In vitro cleavage data demonstrated that PACE4 can recognize RAAR and, to a much lesser extent, KR and RR. When extracts from PACE4-transfected cells were used as a source of proteases, PACE4 had minimal activity, indicating that it had been partially inactivated or did not remain associated with the cell membranes. Cleavage of iodinated PA containing the sequence RKKR or RAAR was detected on the surface of all cell types tested, but cleavage of a dibasic sequence was detected only intracellularly and only in cells that expressed furin or PACE4. The data provide evidence that PACE4 is present at the exterior of cells, that it plays a role in the proteolytic activation of anthrax toxin PA, and that PACE4 can activate substrates at the sequence RAAR or KR.}, }
@article {pmid9216880, year = {1997}, author = {Fuller, ME and Manning, JF}, title = {Aerobic gram-positive and gram-negative bacteria exhibit differential sensitivity to and transformation of 2,4,6-trinitrotoluene (TNT).}, journal = {Current microbiology}, volume = {35}, number = {2}, pages = {77-83}, doi = {10.1007/s002849900216}, pmid = {9216880}, issn = {0343-8651}, mesh = {Culture Media/metabolism ; Gram-Negative Bacteria/*growth &amp; development/*metabolism ; Gram-Positive Bacteria/*growth &amp; development/*metabolism ; Molasses ; Trinitrotoluene/*metabolism ; }, abstract = {A systematic evaluation of the ability of different bacterial genera to transform 2,4,6-trinitrotoluene (TNT), and grow in its presence, was conducted. Aerobic Gram-negative organisms degraded TNT and evidenced net consumption of reduced metabolites when cultured in molasses medium. Some Gram-negative isolates transformed all the initial TNT to undetectable metabolites, with no adsorption of TNT or metabolites to cells. Growth and TNT transformation capacity of Gram-positive bacteria both exhibited 50% reductions in the presence of approximately 10 microg TNT ml-1. Most non-sporeforming Gram-positive organisms incubated in molasses media amended with 80 microg TNT ml-1 became unculturable, whereas all strains tested remained culturable when incubated in mineral media amended with 98 microg TNT ml-1, indicating that TNT sensitivity is linked to metabolic activity. These results indicate that the microbial ecology of soil may be severely impacted by TNT contamination.}, }
@article {pmid9242403, year = {1997}, author = {Zeyl, C and Bell, G}, title = {The advantage of sex in evolving yeast populations.}, journal = {Nature}, volume = {388}, number = {6641}, pages = {465-468}, doi = {10.1038/41312}, pmid = {9242403}, issn = {0028-0836}, mesh = {Adaptation, Physiological ; *Biological Evolution ; Diploidy ; Directed Molecular Evolution ; Galactose/metabolism ; Genes, Fungal ; Glucose/metabolism ; Haploidy ; Mutation ; Saccharomyces cerevisiae/genetics/growth &amp; development/metabolism/*physiology ; Selection, Genetic ; *Sex ; }, abstract = {Sex is a general feature of the life cycle of eukaryotes. It is not universal, however, as many organisms seem to lack sex entirely. The widespread occurrence of sex is puzzling, both because meiotic recombination can disrupt co-adapted combinations of genes, and because it halves the potential rate of reproduction in organisms with strongly differentiated male and female gametes. Most attempts to explain the maintenance of sexuality invoke differences between parents and sexual offspring. These differences may be advantageous in novel or changing environments if new gene combinations are favoured from time to time. Sex would then serve to concentrate beneficial mutations that have arisen independently into the same line of descent. But in a stable environment sex might serve to concentrate deleterious mutations, so that they will be more effectively purged from the population by selection. We have studied the effect of sex on mean fitness in experimental populations of the budding yeast Saccharomyces cerevisiae. Our results show that sex increases mean fitness in an environment to which the populations were well adapted, but not in an environment to which new adaptation occurred, supporting the hypothesis that the advantage of sexuality lay in the removal of deleterious mutations.}, }
@article {pmid9296260, year = {1997}, author = {Hattori, T and Mitsui, H and Haga, H and Wakao, N and Shikano, S and Gorlach, K and Kasahara, Y and el-Beltagy, A and Hattori, R}, title = {Advances in soil microbial ecology and the biodiversity.}, journal = {Antonie van Leeuwenhoek}, volume = {72}, number = {1}, pages = {21-28}, doi = {10.1023/a:1000201017238}, pmid = {9296260}, issn = {0003-6072}, mesh = {Bacteria/chemistry/cytology/genetics/*isolation &amp; purification ; Base Composition ; Colony Count, Microbial ; DNA, Bacterial/chemistry ; *Ecosystem ; Phylogeny ; Quinones/analysis ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; }, abstract = {Recent studies on the colony formation of soil bacteria opened the way to categorize soil bacteria into colony forming curve (CFC) groups of different growth rates. A bacterial culture collection comprising organisms from every CFC group is called an ecocollection (EC). Outlines of ECs of paddy soil 1992 and grassland soil 1987 and 1992 were described. Phylogenetic studies by 16S rDNA sequencing showed a great diversity of culture strains of the ecocollections. A set of alternative concepts was proposed; the active and the quiescent forms of bacterial cells in soil. The former is able to be cultivated and thus counted by the plate method, while the latter is not unless it transforms into the former. Based on the results several points required for extensive cataloguing of soil bacteria were noted.}, }
@article {pmid9274052, year = {1997}, author = {Nollet, L and Vande Velde, I and Verstraete, W}, title = {Effect of the addition of Peptostreptococcus productus ATCC35244 on the gastro-intestinal microbiota and its activity, as simulated in an in vitro simulator of the human gastro-intestinal tract.}, journal = {Applied microbiology and biotechnology}, volume = {48}, number = {1}, pages = {99-104}, doi = {10.1007/s002530051022}, pmid = {9274052}, issn = {0175-7598}, mesh = {Acetic Acid/metabolism ; Bioreactors ; Carbon Dioxide/metabolism ; Digestive System/*microbiology ; Gram-Positive Cocci/*metabolism ; Humans ; Methane/metabolism ; Models, Biological ; Oxidation-Reduction ; }, abstract = {Peptostreptococcus productus ATCC35244, a reductive acetogenic strain, was added daily over 9 successive days to the fourth vessel (ascending colon) of the SHIME, a six-stage reactor system simulating the in vivo continuous culture conditions of the human gastro-intestinal tract. Final numbers of organisms (cfu)/ml reactor contents (c) were attained such that log10c = 6.9 +/- 0.1. The addition caused the CH4 production to decrease below the detection limit while total gas and CO2 production in the fifth (transverse colon) and sixth reactor (descending colon) were lowered and the acetic acid concentration was augmented. Ending the supplementation caused CH4 production to re-establish within 4 days, while CO2 production increased much more slowly. The concentration of acetic acid only started to decrease after 7 days. The results indicate that P. productus, upon regular administration, is able to compete with methanogens for H2 in the gastro-intestinal microbial ecosystem because of its reductive acetogenic character.}, }
@article {pmid9249932, year = {1997}, author = {Rodriguez-Zaragoza, S and Magana-Becerra, A}, title = {Prevalence of pathogenic Acanthamoeba (Protozoa:Amoebidae) in the atmosphere of the city of San Luis Potosi, Mexico.}, journal = {Toxicology and industrial health}, volume = {13}, number = {4}, pages = {519-526}, doi = {10.1177/074823379701300404}, pmid = {9249932}, issn = {0748-2337}, mesh = {Acanthamoeba/*isolation &amp; purification/pathogenicity ; *Air Pollutants ; Animals ; Humans ; Mexico/epidemiology ; Mice ; Prevalence ; Suburban Health ; Urban Health ; }, abstract = {Several species of pathogenic Acanthamoeba cause infections to humans, but amoebic keratitis is more frequently found than any other due to the increasing number of contact lens wearers in the world. Cysts and trophozoites of these amebas are airborne and may pollute water from the air. We investigated the proportion of pathogenic Acanthamoeba from the atmosphere of the city of San Luis Potosi. Samples were taken by the impinger method, every month during one year. We isolated 23 strains of Acanthamoeba, 61% of them were non-pathogenic, 31% were non-pathogenic with invasive capacity and 8% were pathogenic to mice. Almost 40% of these strains represent danger of infections to humans. The isolations were more abundant during the dry season in the south (urban) and west (suburban) stations, which means that the sanitary conditions around stands may enhance the proportion of pathogenic strains in the surroundings.}, }
@article {pmid9226908, year = {1997}, author = {Finster, K and Coates, JD and Liesack, W and Pfennig, N}, title = {Desulfuromonas thiophila sp. nov., a new obligately sulfur-reducing bacterium from anoxic freshwater sediment.}, journal = {International journal of systematic bacteriology}, volume = {47}, number = {3}, pages = {754-758}, doi = {10.1099/00207713-47-3-754}, pmid = {9226908}, issn = {0020-7713}, mesh = {Anaerobiosis ; Carbon/metabolism ; Cell Division ; DNA, Bacterial/analysis ; Energy Metabolism/physiology ; Fresh Water/*microbiology ; Genotype ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Phenotype ; Phylogeny ; Sulfur-Reducing Bacteria/*classification/genetics/*metabolism ; Temperature ; }, abstract = {A mesophilic, acetate-oxidizing, sulfur-reducing bacterium, strain NZ27T, was isolated from anoxic mud from a freshwater sulfur spring. The cells were ovoid, motile, and gram negative. In addition to acetate, the strain oxidized pyruvate, succinate, and fumarate. Sulfur flower could be replaced by polysulfide as an electron acceptor. Ferric nitrilotriacetic acid was reduced in the presence of pyruvate; however, this reduction did not sustain growth. These phenotypic characteristics suggested that strain NZ27T is affiliated with the genus Desulfuromonas. A phylogenetic analysis based on the results of comparative 16S ribosomal DNA sequencing confirmed that strain NZ27T belongs to the Desulfuromonas cluster in the recently proposed family "Geobacteracea" in the delta subgroup of the Proteobacteria. In addition, the results of DNA-DNA hybridization studies confirmed that strain NZ27T represents a novel species. Desulfuromonas thiophila, a name tentatively used in previous publication, is the name proposed for strain NZ27T in this paper.}, }
@article {pmid9212434, year = {1997}, author = {Matheson, VG and Munakata-Marr, J and Hopkins, GD and McCarty, PL and Tiedje, JM and Forney, LJ}, title = {A novel means to develop strain-specific DNA probes for detecting bacteria in the environment.}, journal = {Applied and environmental microbiology}, volume = {63}, number = {7}, pages = {2863-2869}, pmid = {9212434}, issn = {0099-2240}, mesh = {Bacteria/*genetics/*isolation &amp; purification ; Burkholderia cepacia/genetics ; Cloning, Molecular ; DNA Probes/*genetics ; DNA, Bacterial/genetics ; *Environmental Microbiology ; False Positive Reactions ; Nucleic Acid Hybridization ; Polymerase Chain Reaction/*methods ; Repetitive Sequences, Nucleic Acid ; Sensitivity and Specificity ; Species Specificity ; Water Microbiology ; }, abstract = {A simple means to develop strain-specific DNA probes for use in monitoring the movement and survival of bacteria in natural and laboratory ecosystems was developed. The method employed amplification of genomic DNA via repetitive sequence-based PCR (rep-PCR) using primers specific for repetitive extragenic palindromic (REP) elements, followed by cloning of the amplified fragments. The cloned fragments were screened to identify those which were strain specific, and these were used as probes for total genomic DNA isolated from microbial communities and subjected to rep-PCR. To evaluate the utility of the approach, we developed probes specific for Burkholderia cepacia G4 and used them to determine the persistence of the strain in aquifer sediment microcosms following bioaugmentation. Two of four probes tested were found to specifically hybridize to DNA fragments of the expected sizes in the rep-PCR fingerprint of B. cepacia G4 but not to 64 genetically distinct bacteria previously isolated from the aquifer. One of these probes, a 650-bp fragment, produced a hybridization signal when as few as 10 CFU of B. cepacia G4 were present in a mixture with 10(6) CFU nontarget strains, indicating that the sensitivity of these probes was comparable to those of other PCR-based detection methods. The probes were used to discriminate groundwater and microcosm samples that contained B. cepacia G4 from those which did not. False-positive results were obtained with a few samples, but these were readily identified by using hybridization to the second probe as a confirmation step. The general applicability of the method was demonstrated by constructing probes specific to three other environmental isolates.}, }
@article {pmid9178608, year = {1997}, author = {Hassan Dar G,  and Zargar, MY and Beigh, GM}, title = {Biocontrol of Fusarium Root Rot in the Common Bean (Phaseolus vulgaris L.) by using Symbiotic Glomus mosseae and Rhizobium leguminosarum.}, journal = {Microbial ecology}, volume = {34}, number = {1}, pages = {74-80}, doi = {10.1007/s002489900036}, pmid = {9178608}, issn = {1432-184X}, }
@article {pmid9178607, year = {1997}, author = {Anesio, AM and Abreu, PC and de Assis Esteves F, }, title = {Influence of the Hydrological Cycle on the Bacterioplankton of an Impacted Clear Water Amazonian Lake.}, journal = {Microbial ecology}, volume = {34}, number = {1}, pages = {66-73}, doi = {10.1007/s002489900035}, pmid = {9178607}, issn = {1432-184X}, }
@article {pmid9178606, year = {1997}, author = {Llarch, A and Logan, NA and Castellvi, J and Prieto, MJ and Guinea, J}, title = {Isolation and Characterization of Thermophilic Bacillus spp. from Geothermal Environments on Deception Island, South Shetland Archipelago.}, journal = {Microbial ecology}, volume = {34}, number = {1}, pages = {58-65}, doi = {10.1007/s002489900034}, pmid = {9178606}, issn = {1432-184X}, }
@article {pmid9178605, year = {1997}, author = {Claret, C and Fontvieille, D}, title = {Characteristics of Biofilm Assemblages in Two Contrasted Hydrodynamic and Trophic Contexts.}, journal = {Microbial ecology}, volume = {34}, number = {1}, pages = {49-57}, doi = {10.1007/s002489900033}, pmid = {9178605}, issn = {1432-184X}, }
@article {pmid9178604, year = {1997}, author = {Quesada, A and Leganes, F and Fernandez-Valiente, E}, title = {Environmental Factors Controlling N2 Fixation in Mediterranean Rice Fields.}, journal = {Microbial ecology}, volume = {34}, number = {1}, pages = {39-48}, doi = {10.1007/s002489900032}, pmid = {9178604}, issn = {1432-184X}, }
@article {pmid9178603, year = {1997}, author = {Kirschner, AKT and Velimirov, B}, title = {A Seasonal Study of Bacterial Community Succession in a Temperate Backwater System, Indicated by Variation in Morphotype Numbers, Biomass, and Secondary Production.}, journal = {Microbial ecology}, volume = {34}, number = {1}, pages = {27-38}, doi = {10.1007/s002489900031}, pmid = {9178603}, issn = {1432-184X}, }
@article {pmid9178602, year = {1997}, author = {Jeppesen, E and Erlandsen, M and Sondergaard, M}, title = {Can Simple Empirical Equations Describe the Seasonal Dynamics of Bacterioplankton in Lakes: An Eight-Year Study in Shallow Hypertrophic and Biologically Highly Dynamic Lake Sobygard, Denmark.}, journal = {Microbial ecology}, volume = {34}, number = {1}, pages = {11-26}, doi = {10.1007/s002489900030}, pmid = {9178602}, issn = {1432-184X}, }
@article {pmid9178601, year = {1997}, author = {Lang, E and Eller, G and Zadrazil, F}, title = {Lignocellulose Decomposition and Production of Ligninolytic Enzymes During Interaction of White Rot Fungi with Soil Microorganisms.}, journal = {Microbial ecology}, volume = {34}, number = {1}, pages = {1-10}, doi = {10.1007/s002489900029}, pmid = {9178601}, issn = {1432-184X}, }
@article {pmid9248067, year = {1997}, author = {Gu, JD and Lu, C and Thorp, K and Crasto, A and Mitchell, R}, title = {Fiber-reinforced polymeric composites are susceptible to microbial degradation.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {18}, number = {6}, pages = {364-369}, doi = {10.1038/sj.jim.2900401}, pmid = {9248067}, issn = {1367-5435}, mesh = {Biodegradation, Environmental ; Composite Resins/*metabolism ; Polymers/*metabolism ; }, abstract = {A mixed culture of fungi, enriched from degraded polymeric materials, formed biofilms on coupons of fiber-reinforced polymeric composites (FRPCs). They grew actively in aqueous extracts of the composites under ambient conditions. The data indicate that the fungi utilized the resins or fiber chemical sizing as carbon and energy sources. A progressive decline in impedance from above 10(7) Ohms to below 10(8) Ohms was detected in the inoculated FRPC panels by electrochemical impedance spectroscopy (EIS) after 179 days of incubation, but not on the sterile controls. The degradation proceeds through an initial ingress of water into the resins, followed by degradation of bonding between fiber surfaces and resins and finally separation of fibers from the resins. At the end of EIS study, the extent of disbonding in the inoculated composite was greater than the control observed by scanning electron microscopy. These results suggest that the composite materials are susceptible to microbial attack by providing nutrients for growth.}, }
@article {pmid9210390, year = {1997}, author = {Tiedje, JM}, title = {Environmental biotechnology.}, journal = {Current opinion in biotechnology}, volume = {8}, number = {3}, pages = {267}, doi = {10.1016/s0958-1669(97)80001-8}, pmid = {9210390}, issn = {1879-0429}, }
@article {pmid9177998, year = {1997}, author = {Travisano, M}, title = {Long-term experimental evolution in Escherichia coli. VI. Environmental constraints on adaptation and divergence.}, journal = {Genetics}, volume = {146}, number = {2}, pages = {471-479}, pmid = {9177998}, issn = {0016-6731}, mesh = {Adaptation, Physiological/*genetics ; Analysis of Variance ; Arabinose/metabolism ; *Biological Evolution ; Culture Media ; Escherichia coli/*genetics/physiology ; Genetic Markers ; *Genetic Variation ; Glucose/metabolism ; Maltose/metabolism ; Selection, Genetic ; Time Factors ; }, abstract = {The effect of environment on adaptation and divergence was examined in two sets of populations of Escherichia coli selected for 1000 generations in either maltose-or glucose-limited media. Twelve replicate populations selected in maltose-limited medium improved in fitness in the selected environment, by an average of 22.5%. Statistically significant among-population genetic variation for fitness was observed during the course of the propagation, but this variation was small relative to the fitness improvement. Mean fitness in a novel nutrient environment, glucose-limited medium, improved to the same extent as in the selected environment, with no statistically significant among-population genetic variation. In contrast, 12 replicate populations previously selected for 1000 generations in glucose-limited medium showed no improvement, as a group, in fitness in maltose-limited medium and substantial genetic variation. This asymmetric pattern of correlated responses suggests that small changes in the environment can have profound effects on adaptation and divergence.}, }
@article {pmid9172359, year = {1997}, author = {Zhou, J and Palumbo, AV and Tiedje, JM}, title = {Sensitive detection of a novel class of toluene-degrading denitrifiers, Azoarcus tolulyticus, with small-subunit rRNA primers and probes.}, journal = {Applied and environmental microbiology}, volume = {63}, number = {6}, pages = {2384-2390}, pmid = {9172359}, issn = {0099-2240}, support = {ES-04911/ES/NIEHS NIH HHS/United States ; }, mesh = {Base Sequence ; Benzene/metabolism ; Benzene Derivatives/metabolism ; Biodegradation, Environmental ; Gram-Negative Facultatively Anaerobic Rods/classification/*genetics/*metabolism ; Molecular Sequence Data ; Polymerase Chain Reaction/statistics &amp; numerical data ; RNA ; RNA Probes ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; Sequence Homology, Nucleic Acid ; Species Specificity ; Toluene/*metabolism ; Water Microbiology ; Water Pollutants, Chemical/*metabolism ; Xylenes/metabolism ; }, abstract = {Azoarcus tolulyticus is a new class of widely distributed toluene-degrading denitrifiers of potential importance in remediating benzene, toluene, ethylbenzene, and xylene (BTEX)-contaminated environments. To detect these organisms in the environment, 16S rRNA gene-based phylogenetic probes were developed. Two sets of specific PCR amplification primers and two oligonucleotide hybridization probes were designed and tested against both closely and distantly related environmental isolates. All of these primers and probes were specific to the species A. tolulyticus. The sensitivity of the PCR amplification primer sets was evaluated with DNA isolated from A. tolulyticus Tol-4 pure culture and from sterile soils seeded with a known number of Tol-4 and Escherichia coli cells. These primer sets were able to detect 1 fg to 1 pg of template DNA from the pure culture and 1.11 x 10(2) to 1.1 x 10(8) Tol-4 cells per g of soil in the presence of 1.56 x 10(10) E. coli cells. These two PCR amplification primers were also successfully tested at two field sites. The primers identified the A. tolulyticus strains among the toluene-degrading bacteria isolated from a low-O2-high-NO(3)- aquifer at Moffett Field, Calif. Also, the presence of A. tolulyticus was detected in the groundwater samples from a BTEX-contaminated aquifer at an industrial site in Detroit, Mich., which showed anaerobic toluene degradation.}, }
@article {pmid9172346, year = {1997}, author = {Kamagata, Y and Fulthorpe, RR and Tamura, K and Takami, H and Forney, LJ and Tiedje, JM}, title = {Pristine environments harbor a new group of oligotrophic 2,4-dichlorophenoxyacetic acid-degrading bacteria.}, journal = {Applied and environmental microbiology}, volume = {63}, number = {6}, pages = {2266-2272}, pmid = {9172346}, issn = {0099-2240}, mesh = {2,4-Dichlorophenoxyacetic Acid/*metabolism ; Alcaligenes/genetics/metabolism ; Bacteria/genetics/isolation &amp; purification/*metabolism ; Base Sequence ; Biodegradation, Environmental ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Environmental Microbiology ; Gene Transfer Techniques ; Genes, Bacterial ; Herbicides/*metabolism ; Molecular Sequence Data ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {2,4-Dichlorophenoxyacetic acid (2,4-D)-degrading bacteria were isolated from pristine environments which had no history of 2,4-D exposure. By using 2,4-D dye indicator medium or 14C-labeled 2,4-D medium, six strains were isolated from eight enrichment cultures capable of degrading 2,4-D. Phylogenetic analyses based on 16S ribosomal DNA (rDNA) sequencing and physiological properties revealed that one isolate from Hawaiian volcanic soil could be classified in the genus Variovorax (a member of the beta subdivision of the class Proteobacteria) and that the other five isolates from Hawaiian volcanic soils, Saskatchewan forest soil, and Chilean forest soil have 16S rDNAs with high degrees of similarity to those of the Bradyrhizobium group (a member of the alpha subdivision of the class Proteobacteria). All the isolates grow slowly on either nutrient media (0.1 x Bacto Peptone-tryptone-yeast extract-glucose [PTYG] or 0.1 x Luria broth [LB] medium) or 2,4-D medium, with mean generation times of 16 to 30 h, which are significantly slower than previously known 2,4-D degraders. Nutrient-rich media such as full-strength PTYG and LB medium did not allow their growth. PCR amplification using internal consensus sequences of tfdA (a gene encoding an enzyme for the first step of 2,4-D mineralization, found in pJP4 of Alcaligenes eutrophus JMP134 and some other 2,4-D-degrading bacteria) as primers and Southern hybridization with pJP4-tfdA as a probe revealed that the isolate belonging to the genus Variovorax carried the tfdA gene. This gene was transmissible to A. eutrophus JMP228 carrying a plasmid with a mutant tfdA gene. The other five isolates did not appear to carry tfdA, and 2,4-D-specific alpha-ketoglutarate-dependent dioxygenase activity could not be detected in cell lysates. These results indicate that 2,4-D-degrading bacteria in pristine environments are slow-growing bacteria and that most of their phylogenies and catabolic genes differ from those of 2,4-D degraders typically isolated from agricultural soils or contaminated environments.}, }
@article {pmid9172342, year = {1997}, author = {Frostegård, A and Petersen, SO and Bååth, E and Nielsen, TH}, title = {Dynamics of a microbial community associated with manure hot spots as revealed by phospholipid fatty acid analyses.}, journal = {Applied and environmental microbiology}, volume = {63}, number = {6}, pages = {2224-2231}, pmid = {9172342}, issn = {0099-2240}, mesh = {Animals ; Biomass ; Cattle/*microbiology ; Ecosystem ; Fatty Acids/*analysis ; Feces/chemistry/*microbiology ; Phospholipids/*analysis ; Soil/analysis ; Soil Microbiology ; Time Factors ; }, abstract = {Microbial community dynamics associated with manure hot spots were studied by using a model system consisting of a gel-stabilized mixture of soil and manure, placed between layers of soil, during a 3-week incubation period. The microbial biomass, measured as the total amount of phospholipid fatty acids (PLFA), had doubled within a 2-mm distance from the soil-manure interface after 3 days. Principal-component analyses demonstrated that this increase was accompanied by reproducible changes in the composition of PLFA, indicating changes in the microbial community structure. The effect of the manure was strongest in the 2-mm-thick soil layer closest to the interface, in which the PLFA composition was statistically significantly different (P < 0.05) from that of the unaffected soil layers throughout the incubation period. An effect was also observed in the soil layer 2 to 4 mm from the interface. The changes in microbial biomass and community structure were mainly attributed to the diffusion of dissolved organic carbon from the manure. During the initial period of microbial growth, PLFA, which were already more abundant in the manure than in the soil, increased in the manure core and in the 2-mm soil layer closest to the interface. After day 3, the PLFA composition of these layers gradually became more similar to that of the soil. The dynamics of individual PLFA suggested that both taxonomic and physiological changes occurred during growth. Examples of the latter were decreases in the ratios of 16:1 omega 7t to 16:1 omega 7c and of cyclopropyl fatty acids to their respective precursors, indicating a more active bacterial community. An inverse relationship between bacterial PLFA and the eucaryotic 20:4 PLFA (arachidonic acid) suggested that grazing was important.}, }
@article {pmid9129866, year = {1997}, author = {de Lalla, F}, title = {Antibiotic treatment of febrile episodes in neutropenic cancer patients. Clinical and economic considerations.}, journal = {Drugs}, volume = {53}, number = {5}, pages = {789-804}, pmid = {9129866}, issn = {0012-6667}, mesh = {Anti-Bacterial Agents/economics/*therapeutic use ; Antineoplastic Agents/*adverse effects/therapeutic use ; Bacterial Infections/complications/*drug therapy/economics ; Cost Control ; Fever/complications/*drug therapy/economics ; Humans ; Mycoses/complications/*drug therapy/economics ; Neoplasms/*drug therapy ; Neutropenia/chemically induced/complications/*drug therapy ; }, abstract = {The increased frequency of infections caused by Gram-positive microorganisms, and the expansion of resistant pathogens resulting from institutional therapeutic practices, represent some of the emerging issues of empirical drug treatment of cancer patients with febrile neutropenia. However, the therapeutic strategies for the treatment of these patients have progressed remarkably over the last decade. Individual therapy in the light of the principal clinical features (in particular, the degree and estimated duration of neutropenia, as well the presence of other potential factors favouring infection such as long-standing intravascular catheters) and local microbial ecology have emerged as the leading concepts. Empirical drug monotherapy has been recognised as a feasible alternative to combination therapy, at least in selected low-risk patients. The indiscriminate use of empirical glycopeptides should be discouraged to prevent the emergence of resistant bacteria, especially in centres where methicillin-resistant staphylococci have not yet become a major issue. Empirical antifungal therapy with amphotericin B is still essential for a successful outcome in case of fever persistence or recurrence. Finally, selected febrile neutropenic patients who exhibit a better prognosis can be handled on an outpatient basis. The prophylactic use of haemopoietic growth factors has been shown to augment cost savings substantially in the management of neutropenic patients via a reduction in the duration and severity of the neutropenia, as well as infectious complications. Although data from economic analyses are not yet available, some cost-containment strategies such as outpatient treatment, monotherapy, and use of more convenient antibiotic combinations may lead to a reduction of therapy expenditures for febrile episodes in these patients.}, }
@article {pmid9524453, year = {1997}, author = {Cisar, JO and Takahashi, Y and Ruhl, S and Donkersloot, JA and Sandberg, AL}, title = {Specific inhibitors of bacterial adhesion: observations from the study of gram-positive bacteria that initiate biofilm formation on the tooth surface.}, journal = {Advances in dental research}, volume = {11}, number = {1}, pages = {168-175}, doi = {10.1177/08959374970110010801}, pmid = {9524453}, issn = {0895-9374}, mesh = {Actinomyces/immunology/physiology ; Adhesins, Bacterial/physiology ; Antibodies, Bacterial ; Bacterial Adhesion/*physiology ; Bacterial Proteins/physiology ; Biofilms/*growth &amp; development ; Dental Plaque/metabolism/*microbiology ; Ecosystem ; Fimbriae, Bacterial/immunology/*physiology ; Gram-Positive Bacteria/immunology/*physiology ; Humans ; Lectins/metabolism ; Molecular Mimicry ; Peptides/metabolism ; Polysaccharides, Bacterial/metabolism ; Proline-Rich Protein Domains ; Receptors, Cell Surface/physiology ; Saliva/immunology ; Streptococcus/immunology/physiology ; }, abstract = {Oral surfaces are bathed in secretory antibodies and other salivary macromolecules that are potential inhibitors of specific microbial adhesion. Indigenous Gram-positive bacteria that colonize teeth, including viridans streptococci and actinomyces, may avoid inhibition of adhesion by host secretory molecules through various strategies that involve the structural design and binding properties of bacterial adhesins and receptors. Further studies to define the interactions of these molecules within the host environment may suggest novel approaches for the control of oral biofilm formation.}, }
@article {pmid9115189, year = {1997}, author = {Susarla, S and Masunaga, S and Yonezawa, Y}, title = {Redox Potential as a Parameter To Predict the Reductive Dechlorination Pathway of Chloroanilines in Anaerobic Environments.}, journal = {Microbial ecology}, volume = {33}, number = {3}, pages = {252-256}, doi = {10.1007/s002489900028}, pmid = {9115189}, issn = {1432-184X}, }
@article {pmid9115188, year = {1997}, author = {Colwell, FS and Lehman, RM}, title = {Carbon Source Utilization Profiles for Microbial Communities from Hydrologically Distinct Zones in a Basalt Aquifer.}, journal = {Microbial ecology}, volume = {33}, number = {3}, pages = {240-251}, doi = {10.1007/s002489900027}, pmid = {9115188}, issn = {1432-184X}, }
@article {pmid9115187, year = {1997}, author = {Pickup, RW and Mallinson, HEH and Rhodes, G and Chatfield, LK}, title = {A Novel Nickel Resistance Determinant Found in Sewage-Associated Bacteria.}, journal = {Microbial ecology}, volume = {33}, number = {3}, pages = {230-239}, doi = {10.1007/s002489900026}, pmid = {9115187}, issn = {1432-184X}, }
@article {pmid9115186, year = {1997}, author = {Bermingham, S and Maltby, L and Dewey, FM}, title = {Use of Immunoassays for the Study of Natural Assemblages of Aquatic Hyphomycetes.}, journal = {Microbial ecology}, volume = {33}, number = {3}, pages = {223-229}, doi = {10.1007/s002489900025}, pmid = {9115186}, issn = {1432-184X}, }
@article {pmid9115185, year = {1997}, author = {Hyun, J and Bennison, BW and LaRock, PA}, title = {The Formation of Large Bacterial Aggregates at Depth Within the Louisiana Hydrocarbon Seep Zone.}, journal = {Microbial ecology}, volume = {33}, number = {3}, pages = {216-222}, doi = {10.1007/s002489900024}, pmid = {9115185}, issn = {1432-184X}, }
@article {pmid9115184, year = {1997}, author = {Phelps, CD and Young, LY}, title = {Microbial Metabolism of the Plant Phenolic Compounds Ferulic and Syringic Acids under Three Anaerobic Conditions.}, journal = {Microbial ecology}, volume = {33}, number = {3}, pages = {206-215}, doi = {10.1007/s002489900023}, pmid = {9115184}, issn = {1432-184X}, }
@article {pmid9115183, year = {1997}, author = {Steward, CC and Lovell, CR}, title = {Respiration and Assimilation of 4-Bromophenol by Estuarine Sediment Bacteria.}, journal = {Microbial ecology}, volume = {33}, number = {3}, pages = {198-205}, doi = {10.1007/s002489900022}, pmid = {9115183}, issn = {1432-184X}, }
@article {pmid9115182, year = {1997}, author = {Cazemier, AE and Hackstein, JHP and Op den Camp HJM,  and Rosenberg, J and van der Drift C, }, title = {Bacteria in the Intestinal Tract of Different Species of Arthropods.}, journal = {Microbial ecology}, volume = {33}, number = {3}, pages = {189-197}, doi = {10.1007/s002489900021}, pmid = {9115182}, issn = {1432-184X}, }
@article {pmid9115181, year = {1997}, author = {Smith, EA and Macfarlane, GT}, title = {Formation of Phenolic and Indolic Compounds by Anaerobic Bacteria in the Human Large Intestine.}, journal = {Microbial ecology}, volume = {33}, number = {3}, pages = {180-188}, doi = {10.1007/s002489900020}, pmid = {9115181}, issn = {1432-184X}, }
@article {pmid9115180, year = {1997}, author = {Shi, T and Reeves, RH and Gilichinsky, DA and Friedmann, EI}, title = {Characterization of viable bacteria from Siberian permafrost by 16S rDNA sequencing.}, journal = {Microbial ecology}, volume = {33}, number = {3}, pages = {169-179}, doi = {10.1007/s002489900019}, pmid = {9115180}, issn = {0095-3628}, support = {DE-FG05-91ER61159/DE/NIDCR NIH HHS/United States ; }, mesh = {Arctic Regions ; Base Sequence ; Cold Climate ; *DNA, Bacterial ; *DNA, Ribosomal ; Geologic Sediments/*microbiology ; Gram-Positive Bacteria/*classification/genetics/*isolation &amp; purification ; Ice ; Phylogeny ; Siberia ; *Soil Microbiology ; }, abstract = {Viable bacteria were found in permafrost core samples from the Kolyma-Indigirka lowland of northeast Siberia. The samples were obtained at different depths; the deepest was about 3 million years old. The average temperature of the permafrost is -10 degrees C. Twenty-nine bacterial isolates were characterized by 16S rDNA sequencing and phylogenetic analysis, cell morphology, Gram staining, endospore formation, and growth at 30 degrees C. The majority of the bacterial isolates were rod shaped and grew well at 30 degrees C; but two of them did not grow at or above 28 degrees C, and had optimum growth temperatures around 20 degrees C. Thirty percent of the isolates could form endospores. Phylogenetic analysis revealed that the isolates fell into four categories: high-GC Gram-positive bacteria, beta-proteobacteria, gamma-proteobacteria, and low-GC Gram-positive bacteria. Most high-GC Gram-positive bacteria and beta-proteobacteria, and all gamma-proteobacteria, came from samples with an estimated age of 1.8-3.0 million years (Olyor suite). Most low-GC Gram-positive bacteria came from samples with an estimated age of 5,000-8,000 years (Alas suite).}, }
@article {pmid9103803, year = {1997}, author = {Slavkin, HC}, title = {Biofilms, microbial ecology and Antoni van Leeuwenhoek.}, journal = {Journal of the American Dental Association (1939)}, volume = {128}, number = {4}, pages = {492-495}, doi = {10.14219/jada.archive.1997.0238}, pmid = {9103803}, issn = {0002-8177}, mesh = {*Biofilms ; Dental Plaque/*microbiology ; Ecosystem ; History, 17th Century ; Humans ; Microscopy/history ; }, }
@article {pmid9084167, year = {1997}, author = {Klier, CM and Kolenbrander, PE and Roble, AG and Marco, ML and Cross, S and Handley, PS}, title = {Identification of a 95 kDa putative adhesin from Actinomyces serovar WVA963 strain PK1259 that is distinct from type 2 fimbrial subunits.}, journal = {Microbiology (Reading, England)}, volume = {143 (Pt 3)}, number = {}, pages = {835-846}, doi = {10.1099/00221287-143-3-835}, pmid = {9084167}, issn = {1350-0872}, mesh = {Actinomyces/*metabolism ; Adhesins, Bacterial/chemistry/genetics/*isolation &amp; purification ; Fimbriae, Bacterial/chemistry/genetics ; Humans ; Mutation ; }, abstract = {The species Actinomyces serovar WVA963 is among the 20 bacteria most frequently isolated from human subgingival plaque. The interactions of this species with streptococci are inhibited by lactose, a function associated with type 2 fimbrial surface structures in Actinomyces naeslundii. Type 1 fimbriae mediate binding of cells to salivary proline-rich proteins. Specific polyclonal antisera against type 1 and type 2 fimbriae of A. naeslundii T14V revealed both types of fimbriae on Actinomyces serovar WVA963 strain PK1259. To investigate the role of type 2 fimbriae of strain PK1259 in Actinomyces-Streptococcus lactose-inhibitable coaggregations, spontaneous coaggregation-defective (Cog-) mutants that failed to coaggregate with streptococci were isolated; three were chosen for study. All three mutant strains synthesized type 1 fimbriae and a 59 kDa protein; mutant strains PK2415 and PK3092 synthesized type 2 fimbriae and a 57 kDa protein. In contrast, the Cog- strain PK2407 did not agglutinate with anti-type 2 antibodies or show the 57 kDa band, suggesting that the 57 kDa protein was the type 2 fimbrial subunit. Polyclonal antiserum raised against the Actinomyces serovar WVA963 strain PK2399, an antibiotic-resistant derivative of wild-type PK1259, blocked coaggregation between this strain and streptococci. Anti-PK2399 serum absorbed with mutant strain PK3092 bearing type 2 fimbriae retained its blocking ability. Surface sonicates of the parent and mutant strains were adsorbed to streptococcal cells and to lactose-agarose beads. Lactose eluates from both the streptococcal cells and the affinity beads were characterized by SDS-PAGE and corresponding immunoblots using anti-PK2399 serum absorbed with Cog- mutant PK3092. These blots revealed a 95 kDa putative adhesin in the parent strain PK2399 that was absent in the Cog- mutant strain PK3092. These results suggest the presence of a putative 95 kDa actinomyces adhesin distinct from the 57 kDa type 2 fimbrial subunit and that this adhesin mediates lactose-inhibitable coaggregation with streptococci.}, }
@article {pmid9055429, year = {1997}, author = {Schofield, P and Pell, AN and Krause, DO}, title = {Molecular beacons: trial of a fluorescence-based solution hybridization technique for ecological studies with ruminal bacteria.}, journal = {Applied and environmental microbiology}, volume = {63}, number = {3}, pages = {1143-1147}, pmid = {9055429}, issn = {0099-2240}, mesh = {Animals ; Bacteria/*genetics ; Ecology ; *Fluorescent Dyes ; *Nucleic Acid Hybridization ; RNA, Ribosomal, 16S/genetics ; Rumen/*microbiology ; Sensitivity and Specificity ; }, abstract = {Molecular beacons are fluorescent probes developed for solution rather than membrane hybridization. We have investigated the utility of these probes to study rumen microbial ecology. Two cellulolytic species, Ruminococcus albus and Fibrobacter succinogenes, were tested. Membrane and solution hybridizations gave similar results in competition experiments with cocultures of R. albus 8 and F. succinogenes S85.}, }
@article {pmid9052650, year = {1997}, author = {Tannock, GW and Bateup, JM and Jenkinson, HF}, title = {Effect of Sodium Taurocholate on the In Vitro Growth of Lactobacilli.}, journal = {Microbial ecology}, volume = {33}, number = {2}, pages = {163-167}, doi = {10.1007/s002489900018}, pmid = {9052650}, issn = {1432-184X}, }
@article {pmid9052649, year = {1997}, author = {Johnson, MD and Ward, AK}, title = {Influence of Phagotrophic Protistan Bacterivory in Determining the Fate of Dissolved Organic Matter (DOM) in a Wetland Microbial Food Web.}, journal = {Microbial ecology}, volume = {33}, number = {2}, pages = {149-162}, doi = {10.1007/s002489900017}, pmid = {9052649}, issn = {1432-184X}, }
@article {pmid9052648, year = {1997}, author = {Tso, SF and Taghon, GL}, title = {Enumeration of Protozoa and Bacteria in Muddy Sediment.}, journal = {Microbial ecology}, volume = {33}, number = {2}, pages = {144-148}, doi = {10.1007/s002489900016}, pmid = {9052648}, issn = {1432-184X}, }
@article {pmid9052647, year = {1997}, author = {Hu, S and van Bruggen AHC, }, title = {Microbial Dynamics Associated with Multiphasic Decomposition of 14C-Labeled Cellulose in Soil.}, journal = {Microbial ecology}, volume = {33}, number = {2}, pages = {134-143}, doi = {10.1007/s002489900015}, pmid = {9052647}, issn = {1432-184X}, }
@article {pmid9052646, year = {1997}, author = {Wand, H and Laht, T and Peters, M and Becker, PM and Stottmeister, U and Heinaru, A}, title = {Monitoring of Biodegradative Pseudomonas putida Strains in Aquatic Environments Using Molecular Techniques.}, journal = {Microbial ecology}, volume = {33}, number = {2}, pages = {124-133}, doi = {10.1007/s002489900014}, pmid = {9052646}, issn = {1432-184X}, }
@article {pmid9052645, year = {1997}, author = {Harris, JM and Tibbles, BJ}, title = {Factors Affecting Bacterial Productivity in Soils on Isolated Inland Nunataks in Continental Antarctica.}, journal = {Microbial ecology}, volume = {33}, number = {2}, pages = {106-123}, doi = {10.1007/s002489900013}, pmid = {9052645}, issn = {1432-184X}, }
@article {pmid9052644, year = {1997}, author = {Delille, D and Basseres, A and Dessommes, A}, title = {Seasonal Variation of Bacteria in Sea Ice Contaminated by Diesel Fuel and Dispersed Crude Oil.}, journal = {Microbial ecology}, volume = {33}, number = {2}, pages = {97-105}, doi = {10.1007/s002489900012}, pmid = {9052644}, issn = {1432-184X}, }
@article {pmid9052643, year = {1997}, author = {Ward, BB and Voytek, MA and Witzel, K}, title = {Phylogenetic Diversity of Natural Populations of Ammonia Oxidizers Investigated by Specific PCR Amplification.}, journal = {Microbial ecology}, volume = {33}, number = {2}, pages = {87-96}, doi = {10.1007/s002489900011}, pmid = {9052643}, issn = {1432-184X}, }
@article {pmid9045824, year = {1997}, author = {Thompson, J and Robrish, SA and Bouma, CL and Freedberg, DI and Folk, JE}, title = {Phospho-beta-glucosidase from Fusobacterium mortiferum: purification, cloning, and inactivation by 6-phosphoglucono-delta-lactone.}, journal = {Journal of bacteriology}, volume = {179}, number = {5}, pages = {1636-1645}, pmid = {9045824}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Binding Sites ; Cloning, Molecular ; Fusobacterium/*enzymology/genetics ; Gluconates/metabolism/*pharmacology ; Glucosephosphate Dehydrogenase/*metabolism ; Glucosidases/antagonists &amp; inhibitors/*genetics/*isolation &amp; purification/metabolism ; Glucosides/metabolism ; Kinetics ; Lactones/metabolism/*pharmacology ; Molecular Sequence Data ; Molecular Weight ; Sequence Alignment ; Substrate Specificity ; }, abstract = {6-Phosphoryl-beta-D-glucopyranosyl:6-phosphoglucohydrolase (P-beta-glucosidase, EC 3.2.1.86) has been purified from Fusobacterium mortiferum. Assays for enzyme activity and results from Western immunoblots showed that P-beta-glucosidase (Mr, 53,000; pI, 4.5) was induced by growth of F. mortiferum on beta-glucosides. The novel chromogenic and fluorogenic substrates, p-nitrophenyl-beta-D-glucopyranoside-6-phosphate (pNPbetaGlc6P) and 4-methylumbelliferyl-beta-D-glucopyranoside-6-phosphate (4MUbetaGlc6P), respectively, were used for the assay of P-beta-glucosidase activity. The enzyme hydrolyzed several P-beta-glucosides, including the isomeric disaccharide phosphates cellobiose-6-phosphate, gentiobiose-6-phosphate, sophorose-6-phosphate, and laminaribiose-6-phosphate, to yield glucose-6-phosphate and appropriate aglycons. The kinetic parameters for each substrate are reported. P-beta-glucosidase from F. mortiferum was inactivated by 6-phosphoglucono-delta-lactone (P-glucono-delta-lactone) derived via oxidation of glucose 6-phosphate. The pbgA gene that encodes P-beta-glucosidase from F. mortiferum has been cloned and sequenced. The first 42 residues deduced from the nucleotide sequence matched those determined for the N terminus by automated Edman degradation of the purified enzyme. From the predicted sequence of 466 amino acids, two catalytically important glutamyl residues have been identified. Comparative alignment of the amino acid sequences of P-beta-glucosidase from Escherichia coli and F. mortiferum indicates potential binding sites for the inhibitory P-glucono-delta-lactone to the enzyme from F. mortiferum.}, }
@article {pmid11542575, year = {1997}, author = {Greene, C and Bubenheim, DL and Wignarajah, K}, title = {Significance of rhizosphere microorganisms in reclaiming water in a CELSS.}, journal = {Advances in space research : the official journal of the Committee on Space Research (COSPAR)}, volume = {20}, number = {10}, pages = {1949-1958}, doi = {10.1016/s0273-1177(97)00860-0}, pmid = {11542575}, issn = {0273-1177}, mesh = {Biodegradation, Environmental ; Conservation of Natural Resources ; Culture Media/chemistry ; Detergents/analysis/metabolism ; *Ecological Systems, Closed ; Gram-Positive Bacteria/isolation &amp; purification ; Hydroponics ; Lactuca/*growth &amp; development/microbiology ; Life Support Systems ; Plant Roots/growth &amp; development/*microbiology ; Surface-Active Agents/analysis/*metabolism ; *Water Microbiology ; Water Purification/*methods ; }, abstract = {Plant-microbe interactions, such as those of the rhizosphere, may be ideally suited for recycling water in a Controlled Ecological Life Support System (CELSS). The primary contaminant of waste hygiene water will be surfactants or soaps. We identified changes in the microbial ecology in the rhizosphere of hydroponical1y grown lettuce during exposure to surfactant. Six week old lettuce plants were transferred into a chamber with a recirculating hydroponic system. Microbial density and population composition were determined for the nutrient solution prior to introduction of plants and then again with plants prior to surfactant addition. The surfactant Igepon was added to the recirculating nutrient solution to a final concentration of 1.0 g L-1. Bacteria density and species diversity of the solution were monitored over a 72-h period following introduction of Igepon. Nine distinct bacterial types were identified in the rhisosphere; three species accounted for 87% of the normal rhizosphere population. Microbial cell number increased in the presence of Igepon, however species diversity declined. At the point when Igepon was degraded from solution, diversity was reduced to only two species. Igepon was found to be degraded directly by only one species found in the rhizosphere. Since surfactants are degraded from the waste hygiene water within 24 h, the potential for using rhizosphere bacteria as a waste processor in a CELSS is promising.}, }
@article {pmid11540055, year = {1997}, author = {Pitulle, C and Dsouza, L and Fox, GE}, title = {A low molecular weight artificial RNA of unique size with multiple probe target regions.}, journal = {Systematic and applied microbiology}, volume = {20}, number = {1}, pages = {133-136}, doi = {10.1016/S0723-2020(97)80057-4}, pmid = {11540055}, issn = {0723-2020}, mesh = {Base Sequence ; Biomarkers ; *DNA, Plant ; Environmental Microbiology ; Escherichia coli/*genetics/growth &amp; development ; Genes, Synthetic ; Genetic Engineering ; Molecular Sequence Data ; Molecular Weight ; Nucleic Acid Conformation ; Nucleic Acid Hybridization ; Plasmids/genetics ; Poaceae/*genetics ; RNA Probes/*chemistry/genetics ; RNA, Bacterial/*genetics ; RNA, Ribosomal/chemistry/*genetics ; }, abstract = {Artificial RNAs (aRNAs) containing novel sequence segments embedded in a deletion mutant of Vibrio proteolyticus 5S rRNA have previously been shown to be expressed from a plasmid borne growth rate regulated promoter in E. coli. These aRNAs accumulate to high levels and their detection is a promising tool for studies in molecular microbial ecology and in environmental monitoring. Herein a new construct is described which illustrates the versatility of detection that is possible with aRNAs. This 3xPen aRNA construct carries a 72 nucleotide insert with three copies of a unique 17 base probe target sequence. This aRNA is 160 nucleotides in length and again accumulates to high levels in the E. coli cytoplasm without incorporating into ribosomes. The 3xPen aRNA illustrates two improvements in detection. First, by appropriate selection of insert size, we obtained an aRNA which provides a unique and hence, easily quantifiable peak, on a high resolution gel profile of low molecular weight RNAs. Second, the existence of multiple probe targets results in a nearly commensurate increase in signal when detection is by hybridization. These aRNAs are naturally amplified and carry sequence segments that are not found in known rRNA sequences. It thus may be possible to detect them directly. An experimental step involving RT-PCR or PCR amplification of the gene could therefore be avoided.}, }
@article {pmid9440284, year = {1997}, author = {Viljoen, CR and von Holy, A}, title = {Microbial populations associated with commercial bread production.}, journal = {Journal of basic microbiology}, volume = {37}, number = {6}, pages = {439-444}, doi = {10.1002/jobm.3620370612}, pmid = {9440284}, issn = {0233-111X}, mesh = {Bacteria/*isolation &amp; purification ; Bread/*microbiology ; }, abstract = {The microbial ecology of a commercial bread production line was assessed by plate counts and characterization of microbial populations of raw materials, dough, equipment surfaces, air inside the bakery and baked bread. Aerobic plate counts for raw materials were higher than mould counts. Dough samples had high aerobic plate counts, but low mould counts. Mould counts on pre-baking equipment surfaces were lower than those on post-baking equipment surfaces, while aerobic plate counts on equipment surfaces varied. Counts of bacteria and moulds on bread increased during storage at 30 degrees C and moulds predominated over bacteria on air settle plates. Of the 316 bacterial isolates, 50% were Bacillus and 31.6% Micrococcus. Of the 97 mould isolates, 37.1% were Penicillium, 18.6% Aspergillus and 13.4% Cladosporium. Bacillus, Aspergillus and Penicillium were isolated predominantly from baked bread.}, }
@article {pmid9412408, year = {1997}, author = {Shenderov, BA}, title = {[Antimicrobial effects of medicines which are not antibiotics].}, journal = {Antibiotiki i khimioterapiia = Antibiotics and chemoterapy [sic]}, volume = {42}, number = {8}, pages = {26-30}, pmid = {9412408}, issn = {0235-2990}, mesh = {Anti-Bacterial Agents/*pharmacology ; Drug Resistance ; Drug Resistance, Microbial ; Enterobacter/*drug effects/genetics ; Humans ; Intestines/microbiology ; Plasmids ; Species Specificity ; Structure-Activity Relationship ; }, abstract = {The data on antimicrobial activity of 69 different drugs not belonging to the class of typical antibiotics were examined. It was shown that many of them had antimicrobial activity against enterobacteria susceptible and resistant to antibiotics. Some of such drugs were able to eliminate the property of resistance to antibiotics and in particular that to chloramphenicol and tetracyclines. The data are indicative of the fact that many of the so called nonantibiotics have the capacity of active interference with the human microbial ecology.}, }
@article {pmid9189639, year = {1997}, author = {Lenski, RE}, title = {The cost of antibiotic resistance--from the perspective of a bacterium.}, journal = {Ciba Foundation symposium}, volume = {207}, number = {}, pages = {131-40; discussion 141-51}, doi = {10.1002/9780470515358.ch9}, pmid = {9189639}, issn = {0300-5208}, mesh = {Bacteria/drug effects/*genetics ; Biological Evolution ; Drug Resistance, Microbial/*genetics ; Gene Expression Regulation, Bacterial ; Gene Frequency ; }, abstract = {The possession of an antibiotic resistance gene clearly benefits a bacterium when the corresponding antibiotic is present. But does the resistant bacterium suffer a cost of resistance (i.e. a reduction in fitness) when the antibiotic is absent? If so, then one strategy to control the spread of resistance would be to suspend the use of a particular antibiotic until resistant genotypes declined to low frequency. Numerous studies have indeed shown that resistant genotypes are less fit than their sensitive counterparts in the absence of antibiotic, indicating a cost of resistance. But there is an important caveat: these studies have put antibiotic resistance genes into naïve bacteria, which have no evolutionary history of association with the resistance genes. An important question, therefore, is whether bacteria can overcome the cost of resistance by evolving adaptations that counteract the harmful side-effects of resistance genes. In fact, several experiments have shown that the cost of antibiotic resistance may be substantially diminished, even eliminated, by evolutionary changes in bacteria over rather short periods of time. As a consequence of this adaptation of bacteria to their resistance genes, it becomes increasingly difficult to eliminate resistant genotypes simply by suspending the use of antibiotics.}, }
@article {pmid9145442, year = {1997}, author = {Midtvedt, T}, title = {Germ-free and conventional animal models for intestinal carbohydrate disposition.}, journal = {Scandinavian journal of gastroenterology. Supplement}, volume = {222}, number = {}, pages = {25-27}, doi = {10.1080/00365521.1997.11720713}, pmid = {9145442}, issn = {0085-5928}, mesh = {Animals ; Bacteria/*metabolism ; Dietary Carbohydrates/*metabolism ; Digestive System/metabolism/*microbiology ; Disease Models, Animal ; Ecosystem ; Fatty Acids, Volatile/metabolism ; Fermentation ; *Germ-Free Life ; Humans ; }, abstract = {Under conventional (CONV) conditions, the microbial flora is capable of breaking down most dietary derived carbohydrates as well as complex carbohydrates (glycolipids, glycoproteins, etc.) from the host. The major end products of these processes are short-chain fatty acids (SCFAs). In non-ruminants, most of the fermentation takes place in the large bowel. In ruminants, however, most acids are formed more proximal in the gastrointestinal (GI) tract. These microbial derived products may influence upon many host related functions, locally in the GI tract as well as elsewhere in the body. In germ-free (GF) animals, neglectable amounts of SCFAs are found in faeces. Parallel studies in GF and CONV animals given a standardized diet and ex-GF animals, receiving the same diet and mono/poly-associated with known microbial species, represent excellent models for answering such questions as (i) what can the microbes do? and (ii) what have the microbes done? These models allow detailed studies of the complex interplay between the host, his diet and his GI flora.}, }
@article {pmid9039768, year = {1997}, author = {Herrmann, RF and Shann, JF}, title = {Microbial Community Changes During the Composting of Municipal Solid Waste.}, journal = {Microbial ecology}, volume = {33}, number = {1}, pages = {78-85}, doi = {10.1007/s002489900010}, pmid = {9039768}, issn = {1432-184X}, }
@article {pmid9039767, year = {1997}, author = {Rothfuss, F and Bender, M and Conrad, R}, title = {Survival and Activity of Bacteria in a Deep, Aged Lake Sediment (Lake Constance).}, journal = {Microbial ecology}, volume = {33}, number = {1}, pages = {69-77}, doi = {10.1007/s002489900009}, pmid = {9039767}, issn = {1432-184X}, }
@article {pmid9039766, year = {1997}, author = {Peel, MC and Wyndham, RC}, title = {The Impact of Industrial Contamination on Microbial Chlorobenzoate Degradation in the Niagara Watershed.}, journal = {Microbial ecology}, volume = {33}, number = {1}, pages = {59-68}, doi = {10.1007/s002489900008}, pmid = {9039766}, issn = {1432-184X}, }
@article {pmid9039765, year = {1997}, author = {Xing, J and Criddle, C and Hickey, R}, title = {Long-Term Adaptive Shifts in Anaerobic Community Structure in Response to a Sustained Cyclic Substrate Perturbation.}, journal = {Microbial ecology}, volume = {33}, number = {1}, pages = {50-58}, doi = {10.1007/s002489900007}, pmid = {9039765}, issn = {1432-184X}, }
@article {pmid9039764, year = {1997}, author = {Arana, I and Justo, JI and Muela, A and Pocino, M and Iriberri, J and Barcina, I}, title = {Influence of a Survival Process in a Freshwater System upon Plasmid Transfer Between Escherichia coli Strains.}, journal = {Microbial ecology}, volume = {33}, number = {1}, pages = {41-49}, doi = {10.1007/s002489900006}, pmid = {9039764}, issn = {1432-184X}, }
@article {pmid9039763, year = {1997}, author = {Assmus, B and Schloter, M and Kirchhof, G and Hutzler, P and Hartmann, A}, title = {Improved In Situ Tracking of Rhizosphere Bacteria Using Dual Staining with Fluorescence-Labeled Antibodies and rRNA-Targeted Oligonucleotides.}, journal = {Microbial ecology}, volume = {33}, number = {1}, pages = {32-40}, doi = {10.1007/s002489900005}, pmid = {9039763}, issn = {1432-184X}, }
@article {pmid9039762, year = {1997}, author = {Miguez, CB and Bourque, D and Sealy, JA and Greer, CW and Groleau, D}, title = {Detection and Isolation of Methanotrophic Bacteria Possessing Soluble Methane Monooxygenase (sMMO) Genes Using the Polymerase Chain Reaction (PCR).}, journal = {Microbial ecology}, volume = {33}, number = {1}, pages = {21-31}, doi = {10.1007/s002489900004}, pmid = {9039762}, issn = {1432-184X}, }
@article {pmid9039761, year = {1997}, author = {Kirchman, DL and Rich, JH}, title = {Regulation of Bacterial Growth Rates by Dissolved Organic Carbon and Temperature in the Equatorial Pacific Ocean.}, journal = {Microbial ecology}, volume = {33}, number = {1}, pages = {11-20}, doi = {10.1007/s002489900003}, pmid = {9039761}, issn = {1432-184X}, }
@article {pmid9039760, year = {1997}, author = {Stewart, PS and Camper, AK and Handran, SD and Huang, C and Warnecke, M}, title = {Spatial Distribution and Coexistence of Klebsiella pneumoniae and Pseudomonas aeruginosa in Biofilms.}, journal = {Microbial ecology}, volume = {33}, number = {1}, pages = {2-10}, doi = {10.1007/s002489900002}, pmid = {9039760}, issn = {1432-184X}, }
@article {pmid9039759, year = {1997}, author = {Fredrickson, JK}, title = {A New Era for Microbial Ecology.}, journal = {Microbial ecology}, volume = {33}, number = {1}, pages = {1}, doi = {10.1007/s002489900001}, pmid = {9039759}, issn = {1432-184X}, }
@article {pmid9008698, year = {1997}, author = {Pichichero, ME}, title = {Sore throat after sore throat after sore throat. Are you asking the critical questions?.}, journal = {Postgraduate medicine}, volume = {101}, number = {1}, pages = {205-6, 209-12, 215-8, passim}, doi = {10.3810/pgm.1997.01.150}, pmid = {9008698}, issn = {0032-5481}, mesh = {Adult ; Anti-Bacterial Agents/therapeutic use ; Carrier State/diagnosis/microbiology ; Child ; Humans ; Patient Compliance ; Pharyngitis/drug therapy/*etiology ; Recurrence ; Streptococcal Infections/diagnosis/drug therapy/*etiology ; *Streptococcus pyogenes ; Tonsillitis/drug therapy/*etiology ; Treatment Failure ; }, abstract = {In this discussion of recurrent group A streptococcal tonsillopharyngitis, the author notes that even at the peak of the streptococcal infection season, not more than 30% to 40% of children with sore throats actually have group A streptococci as the cause. Thus, it is vital to confirm clinical diagnosis of group A streptococcal tonsillopharyngitis with laboratory tests. When patients have recurrent infections with group A streptococci, possible causes include noncompliance, bacterial resistance, repeated exposure, alteration of the throat's microbial ecology, suppression of antibody response due to previous antibiotic therapy, and treatment failure. When noncompliance is an issue, an injection of penicillin G benzathine may be appropriate. In other circumstances, pharmacologic options for treatment of recurrent group A streptococcal tonsillopharyngitis include macrolides, clindamycin hydrochloride, rifampin (in combination with a second agent), and oral cephalosporins. If a patient has six or seven recurrences over 1 or 2 years despite antibiotic treatment, tonsillectomy should be considered.}, }
@article {pmid8979355, year = {1997}, author = {Massol-Deyá, A and Weller, R and Ríos-Hernández, L and Zhou, JZ and Hickey, RF and Tiedje, JM}, title = {Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater.}, journal = {Applied and environmental microbiology}, volume = {63}, number = {1}, pages = {270-276}, pmid = {8979355}, issn = {0099-2240}, support = {ES-04911/ES/NIEHS NIH HHS/United States ; GM14047-04/GM/NIGMS NIH HHS/United States ; }, mesh = {Biodegradation, Environmental ; Biofilms ; *Bioreactors ; Burkholderia/genetics/metabolism ; Burkholderia cepacia/genetics/metabolism ; DNA Fingerprinting ; DNA, Bacterial/genetics/isolation &amp; purification ; Ecosystem ; Hydrocarbons/*metabolism ; Kinetics ; Phylogeny ; Pseudomonas putida/genetics/metabolism ; Water Microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Community composition, succession, and performance were compared in three fluidized bed reactors (FBR) operated to test preemptive colonization and the influence of toluene compared with a mixture of benzene, toluene, and p-xylene (BTX) as feeds. One reactor was inoculated with toluene-degrading strains Pseudomonas putida PaW1, Burkholderia cepacia G4, and B. pickettii PKO1. PaW1 outcompeted the other two strains. When groundwater strains were allowed to challenge the steady-state biofilm developed by inoculated strains, they readily displaced the inoculated strains and further reduced the toluene effluent concentration from 0.140 to 0.063 mg/liter for 98% removal. Amplified ribosomal DNA restriction analysis (ARDRA) of reactor community DNA showed a succession of populations to a pattern that was stable for at least 4 months of operation. Parallel reactors fed toluene and BTX but inoculated directly from groundwater had the same treatment performance and the same ARDRA profiles as each other and as the seeded reactor once the groundwater community took over. Convergence and stability of populations were confirmed by genotype analysis of 120 isolates taken from all reactors and at several times. Ninety percent of the isolates were of 4 of the 12 genotypes found, and their ARDRA patterns accounted for most of the community ARDRA patterns. Estimates of the maximum specific growth rates (mu max), half-saturation constants (K(m)), and maximum substrate utilization rates (Vmax) of the 12 genotypes isolated revealed a rather high diversity of toluene use kinetics even though the toluene in the feed was constant. The climax populations, however, generally showed kinetic parameters indicative of greater competitiveness than the inocula. rRNA sequence analysis of three codominant strains showed them to be members of the alpha, beta, and gamma subdivisions of the Proteobacteria. Two were similar to Comamonas and Pseudomonas putida, but the member of the alpha group was somewhat distant from any organism in the rRNA database. The convergence of communities to the same composition from three different starting conditions and their constancy over several months suggests that a rather stable community was selected.}, }
@article {pmid8979351, year = {1997}, author = {Nollet, L and Demeyer, D and Verstraete, W}, title = {Effect of 2-bromoethanesulfonic acid and Peptostreptococcus productus ATCC 35244 addition on stimulation of reductive acetogenesis in the ruminal ecosystem by selective inhibition of methanogenesis.}, journal = {Applied and environmental microbiology}, volume = {63}, number = {1}, pages = {194-200}, pmid = {8979351}, issn = {0099-2240}, mesh = {Acetic Acid/*metabolism ; Alkanesulfonic Acids/*pharmacology ; Animals ; Ecosystem ; Fermentation/drug effects ; Hydrogen/metabolism ; Male ; Methane/*metabolism ; Oxidation-Reduction ; Peptostreptococcus/*metabolism ; Rumen/drug effects/*metabolism/*microbiology ; Sheep ; }, abstract = {Evidence is provided that reductive acetogenesis can be stimulated in ruminal samples during short-term (24-h) incubations when methanogenesis is inhibited selectively. While addition of the reductive acetogen Peptostreptococcus productus ATCC 35244 alone had no significant influence on CH4 and volatile fatty acid (VFA) production in ruminal samples, the addition of this strain together with 2-bromoethanesulfonic acid (BES) (final concentration, 0.01 or 0.03 mM) resulted in stimulation of acetic acid production and H2 consumption. Since acetate production exceeded amounts that could be attributed to reductive acetogenesis, as measured by H2 consumption, it was found that P. productus also fermented C6 units (glucose and fructose) heterotrophically to mainly acetate (> 99% of the total VFA). Using 14CH3COOH, we concluded that addition of BES and BES plus P. productus did not alter the consumption of acetate in ruminal samples. The addition of P. productus to BES-treated ruminal samples caused supplemental inhibition of CH4 production and stimulation of VFA production, representing a possible energy gain of about 13 to 15%.}, }
@article {pmid8979340, year = {1997}, author = {Field, KG and Gordon, D and Wright, T and Rappé, M and Urback, E and Vergin, K and Giovannoni, SJ}, title = {Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria.}, journal = {Applied and environmental microbiology}, volume = {63}, number = {1}, pages = {63-70}, pmid = {8979340}, issn = {0099-2240}, mesh = {Animals ; Bacteria/classification/*genetics ; Base Sequence ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; *Genes, Bacterial ; Genetic Variation ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Plankton/classification/*genetics ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; }, abstract = {Small-subunit (SSU) ribosomal DNA (rDNA) gene clusters are phylogenetically related sets of SSU rRNA genes, commonly encountered in genes amplified from natural populations. Genetic variability in gene clusters could result from artifacts (polymerase error or PCR chimera formation), microevolution (variation among rrn copies within strains), or macroevolution (genetic divergence correlated with long-term evolutionary divergence). To better understand gene clusters this study assessed genetic diversity and distribution of a single environmental SSU rDNA gene cluster, the SAR11 cluster. SAR11 cluster genes, from an uncultured group of the alpha subclass of the class Proteobacteria, have been recovered from coastal and midoceanic waters of the North Atlantic and Pacific. We cloned and bidirectionally sequenced 23 new SAR11 cluster 16S rRNA genes, from 80 and 250 m in the Sargasso Sea and from surface coastal waters of the Atlantic and Pacific, and analyzed them with previously published sequences. Two SAR11 genes were obviously PCR chimeras, but the biological (nonchimeric) origins of most subgroups within the cluster were confirmed by independent recovery from separate gene libraries. Using group-specific oligonucleotide probes, we analyzed depth profiles of nucleic acids, targeting both amplified rDNAs and bulk RNAs. Two subgroups within the SAR11 cluster showed different highly depth-specific distributions. We conclude that some of the genetic diversity within the SAR11 gene cluster represents macroevolutionary divergence correlated with niche specialization. Furthermore, we demonstrate the utility for marine microbial ecology of oligonucleotide probes based on gene sequences amplified from natural populations and show that a detailed knowledge of sequence variability may be needed to effectively design these probes.}, }
@article {pmid8953731, year = {1996}, author = {Pearson, AD and Greenwood, MH and Feltham, RK and Healing, TD and Donaldson, J and Jones, DM and Colwell, RR}, title = {Microbial ecology of Campylobacter jejuni in a United Kingdom chicken supply chain: intermittent common source, vertical transmission, and amplification by flock propagation.}, journal = {Applied and environmental microbiology}, volume = {62}, number = {12}, pages = {4614-4620}, pmid = {8953731}, issn = {0099-2240}, mesh = {Animals ; Campylobacter Infections/transmission/*veterinary ; Campylobacter jejuni/*isolation &amp; purification ; Chickens/*microbiology ; *Infectious Disease Transmission, Vertical ; Poultry Diseases/*transmission ; }, abstract = {A study of Campylobacter jejuni on a broiler chicken farm between 1989 and 1994 gave an estimated isolation rate of 27% (3,304 of 12,233) from a 0.9% sample of 1.44 million broiler chickens from six to eight sheds over 32 consecutive rearing flocks comprising 251 broiler shed flocks. During the study, C. jejuni was found in 35.5% of the 251 shed flocks but only 9.2% (23 of 251) had Campylobacter isolates in successive flocks, with 9 of those 23 sheds having the same serotype between consecutive flocks, indicating a low level of transmission between flocks. Analysis of a systematic sample of 484 of 3,304 (14.6%) C. jejuni isolates showed that 85% were of 10 serotype complexes but 58% were of 3 serotype complexes, indicating a high degree of strain similarity throughout the entire study. The three commonest types were detected in 8 of 32 flocks during the 5-year study period, suggesting an intermittent common external Campylobacter source. This hypothesis was tested by a retrospective cohort analysis of C. jejuni rates and types by reference to hatchery supplier of the 1-day-old chicks. Isolation rates of C. jejuni and frequency distribution of types were determined in 6-week-old broiler chickens identified by the hatchery supplying the original chicks. The isolation rate of C. jejuni in broilers, supplied by hatchery A, was 17.6%, compared to 42.9% (P < 0.0001) for broilers reared from chicks supplied by hatchery B. In two instances, when both hatcheries were used to stock the same farm flock, Campylobacter isolates were found only in those sheds with chicks supplied by hatchery B. Thus, the frequency distribution of Campylobacter types for chickens supplied by the two hatcheries over the 5-year period showed marked dissimilarity. These findings suggest that the isolation rate and type of Campylobacter isolates in broiler chickens was associated with the hatchery supplying chicks. The lack of diversity of types and the intermittent high positivity of sheds is evidence for a common source of C. jejuni introduced by vertical transmission rather than contamination at the hatchery or during transportation.}, }
@article {pmid8953722, year = {1996}, author = {Zheng, D and Alm, EW and Stahl, DA and Raskin, L}, title = {Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies.}, journal = {Applied and environmental microbiology}, volume = {62}, number = {12}, pages = {4504-4513}, pmid = {8953722}, issn = {0099-2240}, mesh = {Archaea/*isolation &amp; purification ; Bacteria/*isolation &amp; purification ; *Oligonucleotide Probes ; RNA, Ribosomal/*genetics ; Saccharomyces cerevisiae/*isolation &amp; purification ; }, abstract = {Universal oligonucleotide hybridization probes targeting the small-subunit rRNA are commonly used to quantify total microbial representation in environmental samples. Universal probes also serve to normalize results obtained with probes targeting specific phylogenetic groups of microorganisms. In this study, six universal probes were evaluated for stability of probe-target duplexes by using rRNA from nine organisms representing the three domains of Bacteria, Archaea, and Eucarya. Domain-specific variations in dissociation temperatures were observed for all probes. This could lead to a significant bias when these probes are used to quantify microbial populations in environmental samples. We suggest lowering the posthybridization wash stringency for two of the universal probes (S-*-Univ-1390-a-A-18 and S-*-Univ-1392-a-A-15) examined. These two probes were evaluated with traditional and modified hybridization conditions to characterize defined mixtures of rRNAs extracted from pure cultures and rRNA samples obtained from anaerobic digester samples. Probe S-*-Univ-1390-a-A-18 provided excellent estimations of domain-level community composition of these samples and is recommended for future use in microbial ecology studies.}, }
@article {pmid8945600, year = {1996}, author = {Ruhl, S and Sandberg, AL and Cole, MF and Cisar, JO}, title = {Recognition of immunoglobulin A1 by oral actinomyces and streptococcal lectins.}, journal = {Infection and immunity}, volume = {64}, number = {12}, pages = {5421-5424}, pmid = {8945600}, issn = {0019-9567}, support = {DE08178/DE/NIDCR NIH HHS/United States ; }, mesh = {Actinomyces/*immunology ; Humans ; Immunoglobulin A/*immunology ; Lectins/*immunology ; Mouth/microbiology ; Myeloma Proteins/*immunology ; Streptococcus/*immunology ; }, abstract = {Actinomyces naeslundii and Streptococcus gordonii, oral bacteria that possess Gal/GalNAc- and sialic acid-reactive lectins, respectively, were adherent to immobilized secretory immunoglobulin A (IgA) and two IgA1 myeloma proteins but not to two IgA2 myeloma proteins. Apparently, O-linked oligosaccharides at the hinge region of the IgA1 heavy chain are receptors for lectin-mediated adhesion of these bacteria.}, }
@article {pmid8913810, year = {1996}, author = {McMeekin, TA and Ross, T}, title = {Shelf life prediction: status and future possibilities.}, journal = {International journal of food microbiology}, volume = {33}, number = {1}, pages = {65-83}, doi = {10.1016/0168-1605(96)01138-5}, pmid = {8913810}, issn = {0168-1605}, mesh = {*Food Microbiology ; Hydrogen-Ion Concentration ; Pseudomonas/growth &amp; development ; Temperature ; }, abstract = {Although there is rapid progress in the field of chemical detection technology, little of this technology appears to have found application in estimation of the remaining shelf life of foods and early detection of spoilage. Predictive microbiology aims to summarise the probable behaviour of specific spoilage organisms and the progression of spoilage processes in foods. The quantitative knowledge generated in the field of predictive microbiology provides a sound basis for the rational development of devices with which to monitor loss of product shelf life during storage, distribution and retail sale. To predict remaining shelf life accurately it is necessary, however, to consider the microbial ecology of the food system. Aspects of microbial ecology and physiology relevant to the spoilage of foods are briefly reviewed and the potential benefits of the use of predictive microbiology in shelf life estimation are described. These points are exemplified by reference to a modelling program undertaken to develop, validate and 'package' in an easily useable from, models of the effect of temperature, water activity and pH on the growth rate of psychrotrophic spoilage pseudomonads. Necessary properties of devices to monitor loss of shelf life are discussed. 'Bioindicators' are identified as potential monitors of spoilage and suggestions made for their development based on the concept of 'upper limiting bacterial growth' rates, for which preliminary evidence is presented.}, }
@article {pmid8849426, year = {1996}, author = {Richardson, LL}, title = {Horizontal and Vertical Migration Patterns of Phormidium corallyticum and Beggiatoa spp. Associated with Black-Band Disease of Corals.}, journal = {Microbial ecology}, volume = {32}, number = {3}, pages = {323-335}, pmid = {8849426}, issn = {1432-184X}, abstract = {An in situ field study of the motility patterns exhibited by Phormidium corallyticum and Beggiatoa spp. in black-band disease of corals was conducted over a 5-day period. Measurements were made at a spatial resolution of 50 &amp;mgr;m to document the horizontal migration of black-band across living coral tissue, while vertical migrations within the band were documented by observation and macrophotography of the black-band surface. It was determined that horizontal migration occurred both day and night, with the fastest movements by the front of the band during the day and the back of the band at night. Beggiatoa would rise to the band surface at night, and would often remain above the cyanobacterial population during extended periods of illumination the following day. The migration patterns are discussed in terms of motility cues and microbial physiology.}, }
@article {pmid8849425, year = {1996}, author = {McCarthy, CM and Murray, L}, title = {Viability and Metabolic Features of Bacteria Indigenous to a Contaminated Deep Aquifer.}, journal = {Microbial ecology}, volume = {32}, number = {3}, pages = {305-321}, pmid = {8849425}, issn = {1432-184X}, abstract = {The quantitation and characterization of indigenous bacteria of a deep aquifer, located in the southwestern United States and contaminated with halogenated aliphatic compounds, was undertaken. Water samples were obtained aseptically from depths of 45 to 151 m from four sites that ranged from 260 to 1,800 m in distance from the location of contaminant release. Sediment samples were also obtained from the proximal and distal sites for analyses. Results for aerobic and anaerobic colony-forming units were obtained on four agar media that were used to retrieve heterotrophs, oligotrophs, and pseudomonads. Most probable number estimates were obtained from a liquid medium favorable for oligotrophs. Representative isolates were tested against Biolog plates (Biolog, Inc., Hayward, Calif.) for patterns of carbon source utilization. Of 103 Gram-negative (GN) isolates, 48 could not be identified and the others were only tentatively identified via the Biolog database, and none of the 35 Gram-positive (GP) isolates were identifiable. However, the metabolic patterns were subjected to average cluster linkage analyses; the GN and GP bacteria were separable into eight and four groups, respectively. The oligotroph group comprised one-third of the GN and one-half of the GP isolates. The consensus carbon source utilization pattern for each group was determined and will be useful in future characterization of additional aquifer bacterial isolates. Although predominantly aerobic and oligotrophic, the microbial community of this aquifer was highly diverse with discernible viability and metabolic features of the microbiota distinctive to each of the four water and two sediment samples.}, }
@article {pmid8849424, year = {1996}, author = {Jeffrey, WH and Nazaret, S and Barkay, T}, title = {Detection of the merA gene and its expression in the environment.}, journal = {Microbial ecology}, volume = {32}, number = {3}, pages = {293-303}, pmid = {8849424}, issn = {1432-184X}, abstract = {Bacterial transformation of mercury in the environment has received much attention owing to the toxicity of both the ionic form and organomercurial compounds. Bacterial resistance to mercury and the role of bacteria in mercury cycling have been widely studied. The genes specifying the required functions for resistance to mercury are organized on the mer operon. Gene probing methodologies have been used for several years to detect specific gene sequences in the environment that are homologous to cloned mer genes. While mer genes have been detected in a wide variety of environments, less is known about the expression of these genes under environmental conditions. We combined new methodologies for recovering specific gene mRNA transcripts and mercury detection with a previously described method for determining biological potential for mercury volatilization to examine the effect of mercury concentrations and nutrient availability on rates of mercury volatilization and merA transcription. Levels of merA-specific transcripts and Hg(II) volatilization were influenced more by microbial activity (as manipulated by nutrient additions) than by the concentration of total mercury. The detection of merA-specific transcripts in some samples that did not reduce Hg(II) suggests that rates of mercury volatilization in the environment may not always be proportional to merA transcription.}, }
@article {pmid8849423, year = {1996}, author = {Devereux, R and Hines, ME and Stahl, DA}, title = {S Cycling: Characterization of Natural Communities of Sulfate-Reducing Bacteria by 16S rRNA Sequence Comparisons.}, journal = {Microbial ecology}, volume = {32}, number = {3}, pages = {283-292}, pmid = {8849423}, issn = {1432-184X}, abstract = {Past studies of microbial communities responsible for geochemical transformations have been limited by an inability to representatively cultivate, and then identify, the constituent members. Ribosomal RNA sequences, particularly 16S-like rRNAs, provide a measure of phylogenetic relationship that can now be used to examine the structure and diversity of microbial communities. Sulfate-reducing bacteria (SRB) play an important role in the sulfur cycle and the terminal mineralization of organic matter in estuarine and marine environments. Because the Gram-negative mesophilic SRB comprise a phylogenetically coherent assemblage, their communities are well suited to explorations through rRNA sequence-based methodologies. In this study we related molecular biological methods using rRNA probes to geochemical measurements at two different sites. At an unvegetated site in northwest Florida, rates of sulfate reduction were low and SRB rRNA comprised about 5% of the total rRNA extracted from the sediment. The other site, a salt marsh in New Hampshire, had higher rates of sulfate-reduction with SRB rRNA accounting for up to 30% of the total rRNA extracted from the sediment. SRB community structure differed dramatically between the two sites with Desulfobulbus rRNA much less abundant in the unvegetated site than in the salt marsh. The differences in these SRB communities reflect differences in the ecology of their habitats.}, }
@article {pmid8849422, year = {1996}, author = {Zehr, JP and Capone, DG}, title = {Problems and Promises of Assaying the Genetic Potential for Nitrogen Fixation in the Marine Environment.}, journal = {Microbial ecology}, volume = {32}, number = {3}, pages = {263-281}, pmid = {8849422}, issn = {1432-184X}, abstract = {Nitrogen fixation in the sea has attracted the attention of ecologists for decades. Much is known about the habitats in which it occurs and some of the factors that limit N2 fixation activity in different environments, but we still know little about the organisms that fix nitrogen, and what limits the growth and distribution of these organisms in marine environments. Molecular biology technological developments have provided tools for detecting and characterizing N2-fixing organisms in the environment. These techniques hold great promise for unraveling the mysteries and paradoxes of N2 fixation in the sea. In this review, we address the theoretical basis for the use of a molecular approach to N2 fixation, highlight the strengths and weaknesses of the approach, and provide case studies that demonstrate the potential contribution of molecular biology approaches to studies of N2 fixation in the sea.}, }
@article {pmid8849421, year = {1996}, author = {Ward, BB}, title = {Nitrification and Denitrification: Probing the Nitrogen Cycle in Aquatic Environments.}, journal = {Microbial ecology}, volume = {32}, number = {3}, pages = {247-261}, pmid = {8849421}, issn = {1432-184X}, abstract = {Methods designed to detect microorganisms involved in the biogeochemistry of nitrogen in the marine environment are rapidly being developed and deployed in ecological investigations. Probes based on phylogenetic sequences (usually rRNA) and those based on the sequences of functional genes or proteins have both been demonstrated in the nitrogen cycle. The most progress has been made for ammonia oxidizers; several sets of PCR primers have been described and their specificity may be optimized to allow detection of genetically and ecologically meaningful groups. For denitrifying bacteria, functional probes based on nitrite reductase show most promise. These approaches should complement the more familiar, but no less sophisticated, methods that focus on quantification of in situ transformation rates. Both approaches in combination will be useful in understanding regulation and environmental control of biogeochemical processes.}, }
@article {pmid8849420, year = {1996}, author = {Paul, JH}, title = {Carbon Cycling: Molecular Regulation of Photosynthetic Carbon Fixation.}, journal = {Microbial ecology}, volume = {32}, number = {3}, pages = {231-245}, pmid = {8849420}, issn = {1432-184X}, abstract = {Photosynthetic carbon fixation by phytoplankton is a key component of the global carbon cycle. Our understanding of the types of picoplankton and ultraphytoplankton involved in this process is evolving. However, mechanisms of regulation of photosynthetic carbon fixation in the oceans are poorly understood. All phytoplankton fix CO2 by reductive carboxylation employing the enzyme ribulose bisphosphate carboxylase (RuBPCase). The sequence of the gene encoding the large subunit of the enzyme (rbcL) has been relatively conserved, with two major evolutionary groups among oxygenic photoautrotrophs: the cyanobacteria/green algae/higher plants and the chromophytic algae. Gene probes made from representative members of these groups have been used to study the transcriptional regulation of RuBPCase in natural phytoplankton populations. Levels of rbcL mRNA correlated with rates of photosynthetic carbon fixation. A diel pattern in both carbon fixation and levels of rbcL mRNA was observed, with greatest values for both during daylight hours. This data supports transcriptional regulation as a major mechanism for regulation of carbon fixation in the oceans. This approach can be used to measure expression of conserved genes encoding other important geochemical functions.}, }
@article {pmid8849419, year = {1996}, author = {Capone, DG and Zehr, JP}, title = {Preface to Special Section.}, journal = {Microbial ecology}, volume = {32}, number = {3}, pages = {229-230}, doi = {10.1007/BF00183059}, pmid = {8849419}, issn = {1432-184X}, }
@article {pmid8926080, year = {1996}, author = {Whittaker, CJ and Clemans, DL and Kolenbrander, PE}, title = {Insertional inactivation of an intrageneric coaggregation-relevant adhesin locus from Streptococcus gordonii DL1 (Challis).}, journal = {Infection and immunity}, volume = {64}, number = {10}, pages = {4137-4142}, pmid = {8926080}, issn = {0019-9567}, mesh = {Adhesins, Bacterial/*genetics ; Amino Acid Sequence ; Antigens, Surface/analysis ; Base Sequence ; Chromosome Mapping ; DNA Transposable Elements ; Immunoblotting ; Molecular Sequence Data ; Molecular Weight ; *Mutagenesis, Insertional ; Streptococcus/*genetics ; }, abstract = {Transposon Tn916 was used to insertionally inactivate a coaggregation-relevant locus of Streptococcus gordonii DL1 (Challis). One mutant (F11) was isolated that lost the ability to coaggregate with the streptococcal partners of DL1 but retained the ability to coaggregate with partners belonging to other genera. A probe specific for the region flanking the Tn916 insertion was used to isolate a locus-specific fragment from a chromosomal lambda library. Southern analysis of the resulting phagemids revealed that a 0.5-kb EcoRI fragment hybridized with the F11 probe. Cloning of the 0.5-kb EcoRI fragment into the E. coli-streptococcal insertion vector p(omega) yielded pCW4, which was used to insertionally inactivate the putative coaggregation-relevant gene in DL1. Insertion mutants showed altered coaggregation with streptococci but retained wild-type coaggregation properties with other genera of bacteria. Comparison of immunoblots of cell surface proteins showed a 100-kDa protein in DL1 which was not detected in the Tn916 and pCW4 insertion mutants. These results indicate that the 0.5-kb EcoRI fragment is part of an adhesin-relevant locus that is involved in the production of a 100-kDa protein at the cell surface.}, }
@article {pmid8890483, year = {1996}, author = {Frischer, ME and Floriani, PJ and Nierzwicki-Bauer, SA}, title = {Differential sensitivity of 16S rRNA targeted oligonucleotide probes used for fluorescence in situ hybridization is a result of ribosomal higher order structure.}, journal = {Canadian journal of microbiology}, volume = {42}, number = {10}, pages = {1061-1071}, doi = {10.1139/m96-136}, pmid = {8890483}, issn = {0008-4166}, mesh = {Cell Wall/chemistry ; Electronic Data Processing ; Fluorescent Dyes/analysis ; Gram-Negative Bacteria/cytology ; Gram-Positive Bacteria/cytology ; In Situ Hybridization, Fluorescence/*methods ; Molecular Structure ; Oligonucleotide Probes/*analysis ; RNA/isolation &amp; purification ; RNA, Ribosomal, 16S/*chemistry/*ultrastructure ; Sensitivity and Specificity ; }, abstract = {The use of 16S rRNA targeted gene probes for the direct analysis of microbial communities has revolutionized the field of microbial ecology, yet a comprehensive approach for the design of such probes does not exist. The development of 16S rRNA targeted oligonucleotide probes for use with fluorescence in situ hybridization (FISH) procedures has been especially difficult as a result of the complex nature of the rRNA target molecule. In this study a systematic comparison of 16S rRNA targeted oligonucleotide gene probes was conducted to determine if target location influences the hybridization efficiency of oligonucleotide probes when used with in situ hybridization protocols for the detection of whole microbial cells. Five unique universal 12-mer oligonucleotide sequences, located at different regions of the 16S rRNA molecule, were identified by a computer-aided sequence analysis of over 1000 partial and complete 16S rRNA sequences. The complements of these oligomeric sequences were chemically synthesized for use as probes and end labeled with either [gamma-32P]ATP or the fluorescent molecule tetramethylrhodamine-5/-6. Hybridization sensitivity for each of the probes was determined by hybridization to heat-denatured RNA immobilized on blots or to formaldehyde fixed whole cells. All of the probes hybridized with equal efficiency to denatured RNA. However, the probes exhibited a wide range of sensitivity (from none to very strong) when hybridized with whole cells using a previously developed FISH procedure. Differential hybridization efficiencies against whole cells could not be attributed to cell wall type, since the relative probe efficiency was preserved when either Gram-negative or -positive cells were used. These studies represent one of the first attempts to systematically define criteria for 16S rRNA targeted probe design for use against whole cells and establish target site location as a critical parameter in probe design.}, }
@article {pmid8837437, year = {1996}, author = {Sanford, RA and Cole, JR and Löffler, FE and Tiedje, JM}, title = {Characterization of Desulfitobacterium chlororespirans sp. nov., which grows by coupling the oxidation of lactate to the reductive dechlorination of 3-chloro-4-hydroxybenzoate.}, journal = {Applied and environmental microbiology}, volume = {62}, number = {10}, pages = {3800-3808}, pmid = {8837437}, issn = {0099-2240}, mesh = {Anaerobiosis ; Bacteria, Anaerobic/genetics/growth &amp; development/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Chlorine/*metabolism ; Chlorobenzoates ; Hydrogen-Ion Concentration ; Hydroxybenzoates/*metabolism ; Lactic Acid/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Pyruvic Acid/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Homology, Nucleic Acid ; *Soil Microbiology ; Spores, Bacterial/isolation &amp; purification ; Substrate Specificity ; Temperature ; }, abstract = {Strain Co23, an anaerobic spore-forming microorganism, was enriched and isolated from a compost soil on the basis of its ability to grow with 2,3-dichlorophenol (DCP) as its electron acceptor, ortho chlorines were removed from polysubstituted phenols but not from monohalophenols. Growth by chlororespiration was indicated by a growth yield of 3.24 g of cells per mol of reducing equivalents (as 2[H]) from lactate oxidation to acetate in the presence of 3-chloro-4-hydroxybenzoate but no growth in the absence of the halogenated electron acceptor. Other indicators of chlororespiration were the fraction of electrons from the electron donor used for dechlorination (0.67) and the H2 threshold concentration of < 1.0 ppm. Additional electron donors utilized for reductive dehalogenation were pyruvate, formate, butyrate, crotonate, and H2. Pyruvate supported homoacetogenic growth in the absence of an electron acceptor. Strain Co23 also used sulfite, thiosulfate, and sulfur as electron acceptors for growth, but it did not use sulfate, nitrate or fumarate. The temperature optimum for growth was 37 degrees C; however, the rates of dechlorination were optimum at 45 degrees C and activity persisted to temperatures as high as 55 degrees C. The 16S rRNA sequence was determined, and strain Co23 was found to be related to Desulfitobacterium dehalogenans JW/IU DC1 and Desulfitobacterium strain PCE1, with sequence similarities of 97.2 and 96.8%, respectively. The phylogenetic and physiological properties exhibited by strain Co23 place it into a new species designated Desulfitobacterium chlororespirans.}, }
@article {pmid8837418, year = {1996}, author = {Coleman, ME and Dreesen, DW and Wiegert, RG}, title = {A simulation of microbial competition in the human colonic ecosystem.}, journal = {Applied and environmental microbiology}, volume = {62}, number = {10}, pages = {3632-3639}, pmid = {8837418}, issn = {0099-2240}, mesh = {Carbohydrates ; Colon/*microbiology ; *Computer Simulation ; *Ecosystem ; Gram-Negative Bacteria/*physiology ; Humans ; Serine ; }, abstract = {Many investigations of the interactions of microbial competitors in the gastrointestinal tract used continuous-flow anaerobic cultures. The simulation reported here was a deterministic 11-compartment model coded by using the C programming language and based on parameters from published in vitro studies and assumptions were data were unavailable. The resource compartments were glucose, lactose and sucrose, starch, sorbose, and serine. Six microbial competitors included indigenous nonpathogenic colonizers of the human gastrointestinal tract (Escherichia coli, Enterobacter aerogenes, Bacteroids ovatus, Fusobacterium varium, and Enterococcus faecalis) and the potential human enteropathogen Salmonella typhimurium. Flows of carbon from the resources to the microbes were modified by resource and space controls. Partitioning of resources to the competitors that could utilize them was calculated at each iteration on the basis of availability of all resources by feeding preference functions. Resources did not accumulate during iterations of the model. The results of the computer simulation of microbial competition model and for various modifications of the model. The results were based on few measured parameters but may be useful in the design of user-friendly software to aid researchers in defining and manipulating the microbial ecology of colonic ecosystems as relates to food-borne disease.}, }
@article {pmid8824638, year = {1996}, author = {Lunsford, RD and London, J}, title = {Natural genetic transformation in Streptococcus gordonii: comX imparts spontaneous competence on strain wicky.}, journal = {Journal of bacteriology}, volume = {178}, number = {19}, pages = {5831-5835}, pmid = {8824638}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics/metabolism ; Base Sequence ; Culture Media, Conditioned ; Genetic Complementation Test ; Genomic Library ; Molecular Sequence Data ; Phenotype ; Proteins/metabolism ; Sequence Analysis, DNA ; Species Specificity ; Streptococcus/classification/*genetics ; *Transformation, Bacterial ; }, abstract = {Streptococcus gordonii Wicky becomes competent only after stimulation with conditioned medium from strain Challis as a source of competence factor (CF). A 3.2-kbp genomic fragment from Challis was found to impart spontaneous competence on Wicky by a complementation assay. Wicky clones containing the fragment secreted a heat-sensitive activity that induced competence in Wicky and in a comA insertion mutant of Challis. Activity was localized to a putative open reading frame, comX, with the potential to encode a 52-amino-acid peptide. comX had no similarity to known sequences, and a comX::ermAM insertion mutant of Challis transformed normally and secreted CF. These data suggest that a CF-independent pathway for competence induction exists in S. gordonii.}, }
@article {pmid8897415, year = {1996}, author = {Caldwell, DE and Costerton, JW}, title = {Are bacterial biofilms constrained to Darwin's concept of evolution through natural selection?.}, journal = {Microbiologia (Madrid, Spain)}, volume = {12}, number = {3}, pages = {347-358}, pmid = {8897415}, issn = {0213-4101}, mesh = {Bacteria/*genetics ; *Biofilms ; *Biological Evolution ; Ecology ; *Models, Biological ; *Selection, Genetic ; }, abstract = {Numerous antimicrobial agents have been developed which act at the molecular, cellular, and organismal levels. However, few have been developed which act at the community-level. This results largely from the failure of Darwinian selection theory to envision communities as units of proliferation and evolution. It is thus difficult to conceive of microbial communities as causative agents and to develop antimicrobials which are effective against them. Consequently, we find it necessary to consider a more comprehensive biological paradigm which envisions biofilm communities and other microbial associations (e.g. mixed infections, food spoilage, tooth decay) as units of existence, activity, ecology, proliferation, survival, and evolution. These communities exist in the same sense that organisms exist as units of ecological activity. This is a simpler, more comprehensive, and more unifying theory of ecology. It is simpler in that it no longer requires convoluted explanations of altruistic behavior in terms of individual selection. It is more comprehensive by not constraining evolution to the selection of any single level of biological organization (genes, races, lineages, or groups). It unifies in that it bridges the boundaries between microbial ecology, evolutionary ecology and ecosystem ecology. The basis for this theory lies in recognizing that life consists of various forms of information (order) which evolve not only through genetic recombination and mutation, but also through the recombination of organisms within communities (as well as other mechanisms, some of which are considered beyond the realm of biology). It also involves setting aside the concept of evolution through selection and competition, in favor of evolution through proliferation and association.}, }
@article {pmid8795217, year = {1996}, author = {Kersters, I and Verstraete, W}, title = {Inactivation of Aeromonas hydrophila by Fe(II)-related-radical generation in oxidizing groundwaters.}, journal = {Applied and environmental microbiology}, volume = {62}, number = {9}, pages = {3277-3283}, pmid = {8795217}, issn = {0099-2240}, mesh = {2,2'-Dipyridyl/pharmacology ; Aeromonas hydrophila/*physiology ; Free Radical Scavengers/pharmacology ; Free Radicals ; Iron/*pharmacology ; Oxidation-Reduction ; *Water Microbiology ; Water Supply ; }, abstract = {The survival of Aeromonas hydrophila AWWX1 in filter-sterilized phreatic groundwaters was studied by using viable counts. Aeromonas counts rapidly decreased 2 to 3 log units in oxidizing raw groundwaters from Snellegem and Beernem, Belgium (Snellegem-raw and Beernem-raw, respectively), containing high concentrations of Fe2+ (460 to 1,070 microM). The rapid decline in viable counts of Aeromonas cells in the oxidizing raw groundwater of Snellegem was prevented by the addition of an Fe2+ chelator (2,2'-dipyridyl) or compounds (i.e., ascorbic acid and catalase) that act on toxic oxygen species. The results suggest that free radicals, generated spontaneously in oxidizing Fe2+-containing groundwaters, caused the inactivation of A. hydrophila AWWX1. Evidence that free radicals are generated under the given conditions was provided by the observation that propylphosphonic acid, a compound which is very susceptible to radicals, was degraded upon addition to these waters. A. hydrophila PWBS, Pseudomonas fluorescens P17, Spirillum strain NOX, and heterotrophs showed decreases in culturability in filter-sterilized Snellegem-raw water similar to that shown by A. hydrophila AWWX1. These findings indicate that free radicals generated in Fe2+-containing groundwaters upon aeration are capable of inactivating various bacterial species.}, }
@article {pmid8752359, year = {1996}, author = {Mongold, JA and Lenski, RE}, title = {Experimental rejection of a nonadaptive explanation for increased cell size in Escherichia coli.}, journal = {Journal of bacteriology}, volume = {178}, number = {17}, pages = {5333-5334}, pmid = {8752359}, issn = {0021-9193}, mesh = {Adaptation, Physiological ; Biological Evolution ; Escherichia coli/genetics/*growth &amp; development ; }, abstract = {Populations of Escherichia coli that have been serially propagated for thousands of generations in glucose minimal medium show heritable increases in both cell size and growth rate. We sought to test the hypothesis that the increased cell size of the derived genotypes could be explained solely by their faster growth. The regression of cell size on growth rate differed significantly between populations having ancestral and derived genotypes, with the latter producing larger cells over almost the entire range of growth rates. Thus, the physiological coupling between cell size and growth rate has been evolutionarily altered.}, }
@article {pmid8702287, year = {1996}, author = {Hauschild, JE and Masai, E and Sugiyama, K and Hatta, T and Kimbara, K and Fukuda, M and Yano, K}, title = {Identification of an alternative 2,3-dihydroxybiphenyl 1,2-dioxygenase in Rhodococcus sp. strain RHA1 and cloning of the gene.}, journal = {Applied and environmental microbiology}, volume = {62}, number = {8}, pages = {2940-2946}, pmid = {8702287}, issn = {0099-2240}, mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; *Dioxygenases ; Molecular Sequence Data ; Oxygenases/genetics/*isolation &amp; purification/metabolism ; Rhodococcus/*enzymology ; Substrate Specificity ; }, abstract = {Gram-positive Rhodococcus sp. strain RHA1 possesses strong polychlorinated biphenyl-degrading capabilities. An RHA1 bphC gene mutant, strain RDC1, had been previously constructed (E. Masai, A. Yamada, J. M. Healy, T. Hatta, K. Kimbara, M. Fukuda, and K. Yano, Appl. Environ. Microbiol. 61:2079-2085, 1995). An alternative 2,3-dihydroxybiphenyl 1,2-dioxygenase (2,3-DHBD), designated EtbC, was identified in RDC1 cells grown on ethylbenzene. EtbC contained the broadest substrate specificity of any meta cleavage dioxygenase identified in a Rhodococcus strain to date, including RHA1 BphC. EtbC was purified to near homogeneity from RDC1 cells grown on ethylbenzene, and a 58-amino-acid NH2-terminal sequence was determined. The NH2-terminal amino acid sequence was used for the identification of the etbC gene from an RDC1 chromosomal DNA 2,3-DHBD expression library. The etbC gene was successfully cloned, and we report here the determination of its nucleotide sequence. The substrate specificity patterns of cell extract and native nondenaturing polyacrylamide gel electrophoresis analysis identified the coexpression of two 2,3-DHBDs (BphC and EtbC) in RHA1 cells grown on either biphenyl or ethylbenzene. The possible implication of coexpressed BphC extradiol dioxygenases in the strong polychlorinated-biphenyl degradation activity of RHA1 was suggested.}, }
@article {pmid8702260, year = {1996}, author = {Bossier, P and Verstraete, W}, title = {Comamonas testosteroni colony phenotype influences exopolysaccharide production and coaggregation with yeast cells.}, journal = {Applied and environmental microbiology}, volume = {62}, number = {8}, pages = {2687-2691}, pmid = {8702260}, issn = {0099-2240}, mesh = {Gram-Negative Aerobic Bacteria/isolation &amp; purification/*physiology ; Phenotype ; Polysaccharides, Bacterial/*biosynthesis ; Saccharomyces cerevisiae/*physiology ; *Sewage ; *Water Microbiology ; }, abstract = {A Comamonas testosteroni strain was isolated from activated sludge on the basis of its ability to coaggregate with yeast cells. On agar plates the following two types of colonies were formed: colonies with a mucoid appearance and colonies with a nonmucoid appearance. On plates this strain alternated between the two forms, making sectored colonies. In liquid medium with constant agitation no such change was observed. In the absence of agitation and in contact with a glass surface a culture with predominantly nonmucoid-colony-forming cells very rapidly shifted to a culture dominated by mucoid-colony-forming cells. In liquid medium the reverse was observed under stress conditions imposed by hydrogen peroxide, sodium dodecyl sulfate, or starvation. Nonmucoid cells formed very rapidly settling flocs with yeast cells, while coaggregation of mucoid cells with yeast cells did not occur. These findings may be relevant to the behavior of activated sludge microbial communities.}, }
@article {pmid8779586, year = {1996}, author = {Top, EM and Maltseva, OV and Forney, LJ}, title = {Capture of a catabolic plasmid that encodes only 2,4-dichlorophenoxyacetic acid:alpha-ketoglutaric acid dioxygenase (TfdA) by genetic complementation.}, journal = {Applied and environmental microbiology}, volume = {62}, number = {7}, pages = {2470-2476}, pmid = {8779586}, issn = {0099-2240}, mesh = {2,4-Dichlorophenoxyacetic Acid/metabolism ; Alcaligenes/enzymology/genetics/growth &amp; development ; DNA, Bacterial/genetics/isolation &amp; purification ; Genes, Bacterial ; Genetic Complementation Test ; Mixed Function Oxygenases/*genetics ; Plasmids/*genetics/isolation &amp; purification ; *Soil Microbiology ; }, abstract = {The modular pathway for the metabolism of 2,4-dichlorophenoxyacetic acid (2,4-D) encoded on plasmid pJP4 of Alcaligenes eutrophus JMP134 appears to be an example in which two genes, tfdA and tfdB, have been recruited during the evolution of a catabolic pathway. The products of these genes act to convert 2,4-D to a chloro-substituted catechol that can be further metabolized by enzymes of a modified ortho-cleavage pathway encoded by tfdCDEF. Given that modified ortho-cleavage pathways are comparatively common and widely distributed among bacteria, we sought to determine if microbial populations in soil carry tfdA on plasmid vectors that lack tfdCDEF or tfdB. To capture such plasmids from soil populations, we used a recipient strain of A. eutrophus that was rifampin resistant and carried a derivative of plasmid pJP4 (called pBH501aE) in which the tfdA had been deleted. Upon mating with mixed bacterial populations from soil treated with 2,4-D, transconjugants that were resistant to rifampin yet able to grow on 2,4-D were obtained. Among the transconjugants obtained were clones that contained a ca. 75-kb plasmid, pEMT8. Bacterial hosts that carried this plasmid in addition to pBH501aE metabolized 2,4-D, whereas strains with only pEMT8 did not. Southern hybridization showed that pEMT8 encoded a gene with a low level of similarity to the tfdA gene from plasmid pJP4. Using oligonucleotide primers based on known tfdA sequences, we amplified a 330-bp fragment of the gene and determined that it was 77% similar to the tfdA gene of plasmid pJP4 and 94% similar to tfdA from Burkholderia sp. strain RASC. Plasmid pEMT8 lacked genes that exhibited significant levels of homology to tfdB and tfdCDEF. Moreover, cell extracts from A. eutrophus(pEMT8) cultures did not exhibit TfdB, TfdC, TfdD, and TfdE activities, whereas cell extracts from A. eutrophus(pEMT8)(pBH501aE) cultures did. These data suggest that pEMT8 encodes only tfdA and that this gene can effectively complement the tfdA deletion mutation of pBH501aE.}, }
@article {pmid8779585, year = {1996}, author = {Suwa, Y and Wright, AD and Fukimori, F and Nummy, KA and Hausinger, RP and Holben, WE and Forney, LJ}, title = {Characterization of a chromosomally encoded 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase from Burkholderia sp. strain RASC.}, journal = {Applied and environmental microbiology}, volume = {62}, number = {7}, pages = {2464-2469}, pmid = {8779585}, issn = {0099-2240}, mesh = {2,4-Dichlorophenoxyacetic Acid/metabolism ; Alcaligenes/enzymology/genetics ; Amino Acid Sequence ; Base Sequence ; Burkholderia/*enzymology/*genetics ; Chromosomes, Bacterial/*genetics ; Cloning, Molecular ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; Evolution, Molecular ; Genes, Bacterial ; Mixed Function Oxygenases/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Mutagenesis, Insertional ; Plasmids/genetics ; Restriction Mapping ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; }, abstract = {The findings of previous studies indicate that the genes required for metabolism of the pesticide 2,4-dichlorophenoxyacetic acid (2,4-D) are typically encoded on broad-host-range plasmids. However, characterization of plasmid-cured strains of Burkholderia sp. strain RASC, as well as mutants obtained by transposon mutagenesis, suggested that the 2,4-D catabolic genes were located on the chromosome of this strain. Mutants of Burkholderia strain RASC unable to degrade 2,4-D (2,4-D- strains) were obtained by insertional inactivation with Tn5. One such mutant (d1) was shown to have Tn5 inserted in tfdARASC, which encodes 2,4-D/alpha-ketoglutarate dioxygenase. This is the first reported example of a chromosomally encoded tfdA. The tfdARASC gene was cloned from a library of wild-type Burkholderia strain RASC DNA and shown to express 2,4-D/alpha-ketoglutarate dioxygenase activity in Escherichia coli. The DNA sequence of the gene was determined and shown to be similar, although not identical, to those of isofunctional genes from other bacteria. Moreover, the gene product (TfdARASC) was purified and shown to be similar in molecular weight, amino-terminal sequence, and reaction mechanism to the canonical TfdA of Alcaligenes eutrophus JMP134. The data presented here indicate that tfdA genes can be found on the chromosome of some bacterial species and suggest that these catabolic genes are rather mobile and may be transferred by means other than conjugation.}, }
@article {pmid8757725, year = {1996}, author = {Ahman, J and Ek, B and Rask, L and Tunlid, A}, title = {Sequence analysis and regulation of a gene encoding a cuticle-degrading serine protease from the nematophagous fungus Arthrobotrys oligospora.}, journal = {Microbiology (Reading, England)}, volume = {142 (Pt 7)}, number = {}, pages = {1605-1616}, doi = {10.1099/13500872-142-7-1605}, pmid = {8757725}, issn = {1350-0872}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA Primers/genetics ; DNA, Fungal/genetics ; Gene Expression Regulation, Fungal ; *Genes, Fungal ; Mitosporic Fungi/*enzymology/*genetics/pathogenicity ; Molecular Sequence Data ; Nematoda/microbiology ; RNA, Messenger/biosynthesis/genetics ; Sequence Homology, Amino Acid ; Serine Endopeptidases/*genetics ; }, abstract = {The nematode trapping fungus Arthrobotrys oligospora produces an extracellular serine protease (designated PII) that immobilizes free-living nematodes in bioassays and hydrolyses proteins of the nematode cuticle. Peptides were isolated from PII and partly sequenced. Three internal peptide sequences were used to design synthetic oligonucleotides, which allowed the subsequent isolation of the gene encoding PII from a genomic library. The deduced amino acid sequence indicated that PII is synthesized as a preproenzyme containing the mature enzyme, a signal sequence and a propeptide that are removed before the enzyme is secreted into the medium. The primary sequence of PII displayed a high degree of similarity with several other serine proteases of ascomycetes belonging to the subtilisin family. Northern analysis demonstrated that PII was expressed when the fungus was starved of nitrogen and carbon and that the expression was significantly stimulated by the addition to the medium of various soluble and insoluble proteins, including fragments of nematode cuticle. The levels of the mRNA as well as the proteolytic activity of PII were repressed in the presence of more easily metabolized forms of nitrogen (including ammonia, nitrate and amino acids) or glucose. The activity of the enzyme was almost completely inhibited by the peptide Phe-Val, as well as by the amino acid Phe, without a corresponding decrease in mRNA level. Notably, peptides with similar structures are known to be secreted by the host (nematode) and to stimulate the production of infection structures (traps) of the fungus.}, }
@article {pmid8688009, year = {1996}, author = {Fliermans, CB}, title = {Ecology of Legionella: From Data to Knowledge with a Little Wisdom.}, journal = {Microbial ecology}, volume = {32}, number = {2}, pages = {203-228}, pmid = {8688009}, issn = {1432-184X}, abstract = {The respiratory diseases produced by the Legionella genus of bacteria are collectively called Legionellosis. Presently more than 34 species of Legionella have been identified, 20 of which have been isolated from both environmental and clinical sources. The diseases produced by Legionella include the pneumonic form, Legionnaires' disease, and the flu-like form, Pontiac fever. Because the vast majority of Legionellosis is caused by the L. pneumophila species, this bacterium is the thrust of the discussion.Legionella is a global bacterium. The relationship of the bacterium to its environment has told us many things about infectious diseases. Not until Legionellosis and the discovery of its etiologic agent, Legionella, has such a successful modern-day marriage been consummated between the agent and its environment. Nearly two decades have passed since the term Legionellosis found its way into the vocabulary of the scientific journals, the popular press, and courtroom proceedings. Too often the scientific development, engineering implementation, and societal acceptance are disconnected. The focus of scientific research sometimes does not reflect engineering or societal needs and thus contributes little to the solution of immediate and important problems. At other times, scientific knowledge that could contribute to solutions is overlooked because of poor communication between the problem holders, the scientific community, regulatory agencies, the problem makers, and the public. The scope of this paper provides insights on the ecological niche of Legionella, describes the organism's ecological relationships in the natural world, and provides wisdom for effective control of the bacterium for the industrial and user communities.}, }
@article {pmid8688008, year = {1996}, author = {Torr&amp;eacute;ton, J and Dufour, P}, title = {Bacterioplankton Production Determined by DNA Synthesis, Protein Synthesis, and Frequency of Dividing Cells in Tuamotu Atoll Lagoons and Surrounding Ocean.}, journal = {Microbial ecology}, volume = {32}, number = {2}, pages = {185-202}, pmid = {8688008}, issn = {1432-184X}, abstract = {This study compares three independent methods used for estimating bacterioplankton production in waters from the lagoon (mesotrophic) and the surrounding ocean (oligotrophic) of two atolls from the Tuamotu archipelago (French Polynesia).Thymidine and leucine incorporation were calibrated in dilution cultures and gave consistent results when the first was calibrated against cell multiplication and the second against protein synthesis. This study demonstrates that determining conversion factors strongly depends on the selected calculation method (modified derivative, integrative, and cumulative). These different estimates are reconciled when the very low proportion of active cells is accounted for.Frequency of dividing-divided cells (FDDC) calibrated using the same dilution cultures led to unrealistically high estimates of bacterial production. However, highly significant correlations between FDDC and either thymidine- or leucine-specific incorporation per cell were found in lagoon waters in situ. These correlations became more positive when oceanic data were added. This suggests that the FDDC method is also potentially valid to determine bacterioplankton growth rates after cross calibration with thymidine or leucine methods. If recommended precautions are observed, the three methods tested in the present study would give reliable production estimates.}, }
@article {pmid8688007, year = {1996}, author = {Fuller, ME and Scow, KM}, title = {Effects of Toluene on Microbially-Mediated Processes Involved in the Soil Nitrogen Cycle.}, journal = {Microbial ecology}, volume = {32}, number = {2}, pages = {171-184}, pmid = {8688007}, issn = {1432-184X}, abstract = {The effects of toluene on indigenous microbial populations involved in the soil nitrogen cycle were examined. Ammonia oxidation potential (AOP) and nitrite oxidation potential (NOP) were both reduced after incubation with high toluene concentrations for 45 days, with the former activity showing greater sensitivity. KCl-extractable ammonium (NH4+ext) levels increased dramatically in soil exposed to high toluene levels, and arginine ammonification was not significantly affected. Alfalfa-amended soil incubated in the presence of 200 &amp;mgr;g toluene ml-1 showed progressive accumulation of NH4+ext over 37 days, indicating that mineralization of plant-associated nitrogen was not hindered by toluene. AOP in treated soil was much less than in control soil on days 7 and 37, but the MPN of ammonia oxidizers in control and exposed soil were not significantly different. Soil incubated with 100 &amp;mgr;g toluene ml-1for 28 days, vented and allowed to incubate for an additional 7 to 30 days, exhibited only slight increases in AOP and NOP, while NH4+ext returned to control levels within a week. Soil exposed to 200 &amp;mgr;g toluene ml-1 and treated in the same manner showed no increases in either AOP or NOP, and NH4+extremained elevated for the duration of the experiment, indicating more long-term effects on soil nitrogen cycling had occurred. Ammonia oxidizer levels in control soil and soil incubated with 100 &amp;mgr;g toluene ml-1 were not appreciably different, whereas levels of ammonia oxidizers were very low in soil exposed to 200 &amp;mgr;g toluene ml-1 and increased only slightly by 30 days post vent. Experiments to determine how toluene affects the AOP of soil indicated a competitive inhibition mechanism, with an effective concentration causing 50% reduction in activity (EC50) of 11 &amp;mgr;M toluene, and a competitive inhibition constant (Ki) of 0.1± 0.05 &amp;mgr;M toluene. These results indicate the potential for toluene to adversely impact nitrogen cycling in the terrestrial ecosystem by affecting indigenous soil nitrifiers, which are sensitive to lower levels of toluene than has been previously reported.}, }
@article {pmid8688006, year = {1996}, author = {De Troch P,  and Vanderleyden, J}, title = {Surface Properties and Motility of Rhizobium and Azospirillum in Relation to Plant Root Attachment.}, journal = {Microbial ecology}, volume = {32}, number = {2}, pages = {149-169}, pmid = {8688006}, issn = {1432-184X}, abstract = {Plant growth promotion by rhizobacteria is a widely spread phenomenon. However only a few rhizobacteria have been studied thoroughly. Rhizobium is the best-studied rhizobacterium. It forms a symbiosis with a restricted host range. Azospirillum is another plant-growth-promoting rhizobacterium which forms rhizocoenoses with a wide range of plants. In both bacteria, the interaction with the plant involves the attraction toward the host plant and the attachment to the surface of the root. Both bacteria are attracted to plant roots, but differ in specificity. Attachment to plant roots occurs in two steps for both bacteria: a quick, reversible adsorption, and a slow, irreversible anchoring to the plant root surface. However, for the two systems under study, the bacterial surface molecules involved in plant root attachment are not necessarily the same.}, }
@article {pmid8688005, year = {1996}, author = {Gilbert, GS and Clayton, MK and Handelsman, J and Parke, JL}, title = {Use of Cluster and Discriminant Analyses to Compare Rhizosphere Bacterial Communities Following Biological Perturbation.}, journal = {Microbial ecology}, volume = {32}, number = {2}, pages = {123-147}, pmid = {8688005}, issn = {1432-184X}, abstract = {We present an approach to comparing the diversity and composition of bacterial communities from different habitats and for identifying which members of a community are most affected by an introduced bacterium. We use this method to explore both previously published and new data from field and growth chamber experiments in which we isolated heterotrophic bacteria from samples of root-free soil, roots of nontreated soybean seedlings, and from the roots of soybean seedlings grown from Bacillus cereus UW85n1-treated seeds. We characterize bacterial isolates for 40 physiological attributes, and grouped the isolates hierarchically using two-stage density-linkage cluster analysis. Multivariate analysis of variance and discriminant analysis of the relative frequencies of the clusters in the soil and rhizosphere habitats were then used to determine whether there were differences among the bacterial communities from the various habitats, and which of the clusters were most useful in discriminating among the communities. We used rarefied estimates of richness as a measure of community diversity in the various habitats. Introduction of UW85n1 affected the composition and/or diversity of rhizosphere communities in three of four experiments.}, }
@article {pmid8688004, year = {1996}, author = {Kampfer, P and Erhart, R and Beimfohr, C and Bohringer, J and Wagner, M and Amann, R}, title = {Characterization of Bacterial Communities from Activated Sludge: Culture-Dependent Numerical Identification Versus In Situ Identification Using Group- and Genus-Specific rRNA-Targeted Oligonucleotide Probes.}, journal = {Microbial ecology}, volume = {32}, number = {2}, pages = {101-121}, pmid = {8688004}, issn = {1432-184X}, abstract = {The structures of bacterial communities were studied in activated sludge samples obtained from the aerobic and anaerobic zones of a wastewater treatment plant showing enhanced phosphorous removal. Samples were analyzed by in situ hybridization with oligonucleotide probes complementary to selected regions of the 16S and 23S ribosomal RNA (rRNA) characteristic for defined phylogenetic entities (genera and larger groups). The microbial community structures revealed by molecular techniques were compared with the compositions of culturable bacterial communities, obtained from the characterization of 255 isolates from tryptone-soy (TS) agar and R2A agar. These isolates were characterized by 89 physiological tests and their cellular fatty acid patterns, and identified. Culture-dependent techniques indicated the following distribution: different Aeromonas spp. (2.7-8.3% on R2A agar; 45.0-63.7% on TS agar), Acinetobacter spp. (5.4-9.0% on R2A agar; 5.0-9.1% on TS agar), Pseudomonas spp. (up to 10% on R2A agar) and Shewanella putrefaciens (up to 3.0% on R2A agar), all members of the gamma subclass of Proteobacteria, were isolated most frequently. The relatively rare isolates of the beta subclass were identified as Acidovorax spp., Alcaligenes spp., and Comamonas spp.. The Gram-positive bacteria (high DNA G+C) were assigned mainly to Arthrobacter spp., Microbacterium spp., and Mycobacterium phlei. In order to assess the in situ abundance of the most frequently isolated genus, Aeromonas, two rRNA-targeted oligonucleotide probes were developed. The two gamma proteobacterial genera Aeromonas and Acinetobacter constituted less than 5% of all bacteria. In situ, Proteobacteria belonging to the beta subclass and high G+C Gram-positive bacteria were dominant. From filamentous bacteria, Sphaerotilus spp. and Leptothrix spp. could be detected occasionally. In addition, one sample contained a high proportion of the morphologically distinct filaments of Microthrix parvicella.}, }
@article {pmid8661544, year = {1996}, author = {Vrba, J and Simek, K and Pernthaler, J and Psenner, R}, title = {Evaluation of Extracellular, High-affinity beta-N-acetylglucosaminidase Measurements from Freshwater Lakes: An Enzyme Assay to Estimate Protistan Grazing on Bacteria and Picocyanobacteria.}, journal = {Microbial ecology}, volume = {32}, number = {1}, pages = {81-99}, pmid = {8661544}, issn = {1432-184X}, abstract = {Protistan community grazing rates upon both bacterioplankton and autotrophic picoplankton were estimated using fluorescently-labeled prey and by measurement of extracellular hydrolysis of 4-methylumbelliferyl (MUF) beta-N-acetylglucosaminide in a eutrophic reservoir and an oligo-mesotrophic lake during phytoplankton blooms. In addition, enzyme methods were optimized in bacterivorous flagellate cultures by two enzyme assays, based on fluorometric detection of protistan digestive activity, which were compared and calibrated independently against flagellate bacterivory. Enzymatic hydrolyses of MUF beta-N,N',N''-triacetylchitotriose and MUF beta-N-acetylglucosaminide were measured in cell-free (sonicated) and whole-cell (unsonicated) samples. The hydrolysis of both substrates, using the whole-cell enzyme assay at in situ pH, was correlated significantly with total grazing rate of Bodo saltans. Thus the whole-cell enzyme assay with MUF beta-N-acetylglucosaminide was used for freshwater samples. High-affinity (Km < 1 μmol l-1) and low-affinity (Km > 100μmol l-1) enzymes were distinguished kinetically in most samples from both systems studied. Activities (Vmax) of the high-affinity enzyme varied from 0.24 to 1.43 nmol l-1 h-1. Protistan community grazing on bacterioplankton was in the range of 0.15-1.36 μg C l-1 h-1 both for lake and reservoir, the differences being observed in grazing on picocyanobacteria (lake, 0.03-0.22 μg C l-1 h-1; reservoir, 0.35-1.56 μg C l-1 h-1). The enzyme activities were correlated significantly with the protistan grazing both on bacterioplakton (rs=0.62, P<0.001) and total procaryotic picoplankton (the sum of organic carbon grazed from bacteria and picocyanobacteria, rs=0.73, P<0.001) in the eutrophic reservoir. Weaker relationships (rs=0.42) with a lower slope were found for the oligo-mesotrophic lake. Ingestion rate studies are time-consuming and the digestive enzyme assay with MUF beta-N-acetylglucosaminide presents a rapid alternative for estimating total protistan prokaryotic picoplanktivory in freshwaters.}, }
@article {pmid8661543, year = {1996}, author = {Rajashekhar, M and Kaveriappa, KM}, title = {Studies on the Aquatic Hyphomycetes of a Sulfur Spring in the Western Ghats, India.}, journal = {Microbial ecology}, volume = {32}, number = {1}, pages = {73-80}, doi = {10.1007/BF00170108}, pmid = {8661543}, issn = {1432-184X}, abstract = {Studies on the occurrence of aquatic hyphomycetes were carried out in Panekal sulfur spring in the Western Ghats, India by incubation of leaf litter and analysis of natural foam and of induced foam. Sampling was done once every three months over a period of two years from September 1989 to June 1991. The temperature, pH, dissolved oxygen, and sulfide content of water were also measured. No fungi were observed within the spring, whereas 16 species belonging to 13 genera were isolated from two outflow sites of the stream. The percent frequency of Triscelophorus monosporus was high (24.0%). The temperature of water in the spring ranged between 30.0 and 38.5&amp;deg;C and the sulfide content between 3.2 and 4.3 mg 1(-1). Studies showed that sulfide water (4.0 mg 1(-1)) from the spring inhibited the growth of the colonies of Dactylella aquatica, Phalangispora constricta, Tetracladium setigerum, Vermispora cauveriana, and Wiesneriomyces laurinus. When the leaves colonized by aquatic hyphomycetes were incubated at different temperatures in sulfur-spring water and stream water separately, sporulation was not observed in any of the fungi at and above 35&amp;deg;C except Phalangispora constricta, which could sporulate at 35&amp;deg;C. At lower temperatures (15-30&amp;deg;C) relatively fewer species were found to sporulate in sulfur-spring water than in stream water.}, }
@article {pmid8661542, year = {1996}, author = {Couteaudier, Y and Viaud, M and Riba, G}, title = {Genetic Nature, Stability, and Improved Virulence of Hybrids from Protoplast Fusion in Beauveria.}, journal = {Microbial ecology}, volume = {32}, number = {1}, pages = {1-10}, pmid = {8661542}, issn = {1432-184X}, abstract = {Genetic improvement of two different strains of the entomopathogenic fungus Beauveria bassiana for more effective control of Ostrinia nubilalis and Leptinotarsa decemlineata was obtained by crosses with the insecticidal toxin-producing strain Beauveria sulfurescens. Protoplast fusion between diauxotrophic mutants resulted in the recovery of some stable prototrophic fusion products. The low levels of virulence of the wild type strain B. bassiana 28 isolated originally from L. decemlineata were enhanced both on L. decemlineata and O. nubilalis for one of the hybrids obtained (FP 8) from the cross B. bassiana 28xB. sulfurescens 2. Fusion product 25 obtained from the cross between B. sulfurescens and the highly pathogenic strain B. bassiana 147 showed a three-day reduction in the LT50 towards O. nubilalis. Southern blot hybridization with nine probe-enzyme combinations were conducted on genomic DNAs from the original wild strains, parental mutant strains, and fusion products. Additive banding patterns or unique banding pattern of either parental strain was observed in five hybrids, indicating their status as recombinant and/or partially diploid. Combination of RFLP markers indicative of both parental genomes was never observed with fusion product FP 25. The stability of the virulence following passage through insect-host and stability of molecular structure for the fusion products FP 8 and FP 25 suggest that asexual genetic recombination by protoplast fusion may provide an attractive method for the genetic improvement of biocontrol efficiency in entomopathogenic fungi.}, }
@article {pmid8661541, year = {1996}, author = {Kern, J and Darwich, A and Furch, K and Junk, WJ}, title = {Seasonal Denitrification in Flooded and Exposed Sediments from the Amazon Floodplain at Lago Camaleao.}, journal = {Microbial ecology}, volume = {32}, number = {1}, pages = {47-57}, pmid = {8661541}, issn = {1432-184X}, abstract = {Denitrification processes were measured by the acetylene-blockage technique under changing flood conditions along the aquatic/terrestrial transition zone on the Amazon floodplain at Lago Camaleao, near Manaus, Brazil. In flooded sediments, denitrification was recorded after the amendment with NO3- (100 μmol liter-1) throughout the whole study period from August 1992 to February 1993. It ranged from 192.3 to 640.7 μmol N m-2 h-1 in the 0- to 5-cm sediment layer. Without substrate amendment, denitrification was detected only during low water in November and December 1992, when it occurred at a rate of up to 12.2 μmol N m-2 h-1. Higher rates of denitrification at an average rate of 73.3 μmol N m-2 h-1 were measured in sediments from the shallow lake basin that were exposed to air at low water. N2O evolution was never detected in flooded sediments, but in exposed sediments, it was detected at an average rate of 28.3 μmol N m-2 h-1 during the low-water period. The results indicate that under natural conditions there is denitrification and hence a loss in nitrogen from the Amazon floodplain to the atmosphere. Rates of denitrification in flooded sediments were one to two orders of magnitude smaller than in temperate regions. However, the nitrogen removal of exposed sediments exceeded that of undisturbed wetland soils of temperate regions, indicating a considerable impact of the flood pulse on the gaseous turnover of nitrogen in the Amazon floodplain.}, }
@article {pmid8661540, year = {1996}, author = {Schoeffield, AJ and Williams, HN and Turng, B and Fackler, WA}, title = {A Comparison of the Survival of Intraperiplasmic and Attack Phase Bdellovibrios with Reduced Oxygen.}, journal = {Microbial ecology}, volume = {32}, number = {1}, pages = {35-46}, pmid = {8661540}, issn = {1432-184X}, abstract = {The ability of intraperiplasmic and attack phase bdellovibrios to survive and/or grow under anoxic and microaerobic conditions was examined. Both halotolerant and nonhalotolerant bdellovibrio strains were examined. In all instances, the bdellovibrio strains were unable to grow under anoxic conditions, but were able to survive for periods of time in both the extracellular and intraperiplasmic forms. However, the intraperiplasmic organisms were observed to survive longer. Increased temperature hastened the loss of viability of both forms of the predatory bacteria in oxic and anoxic environments. Under microaerobic conditions, halotolerant bdellovibrios were observed to grow, although at a slightly reduced rate than in atmospheric oxygen, while two nonhalotolerant isolates survived but did not grow. The ability of attack phase bdellovibrios to survive in an anoxic environment for up to nine days and their growth or survival under microaerobic conditions greatly expands the possible ecological niches in which the predators may be active members of the microbial community.}, }
@article {pmid8661539, year = {1996}, author = {Becker, K}, title = {Exopolysaccharide Production and Attachment Strength of Bacteria and Diatoms on Substrates with Different Surface Tensions.}, journal = {Microbial ecology}, volume = {32}, number = {1}, pages = {23-33}, pmid = {8661539}, issn = {1432-184X}, abstract = {Attachment strength and exopolysaccharide (EPS) production of Pseudomonas sp. (bacteria) and the diatom Amphora coffaeformis were studied on six different substrata with surface tensions between 19 and 64.5 mN m-1. Test panels of the materials were exposed to bacterial cultures between 3 and 120 hours, and to diatom cultures between 48 and 72 hours. Exopolysaccharide production by surface-associated cells was measured using the phenol sulfuric acid method. Attachment studies were run by exposing test panels to laminar flow pressure using a radial flow chamber. Highest EPS production by bacteria and diatoms was recorded on substrata with surface tensions above 30 mN m-1. Lowest EPS production occurred on substrata between 20 and 25 mN m-1. Highest EPS production and strongest adhesion was found on polycarbonate (33.5 mN m-1). Both test organisms improved their attachment strength with exposure time on most materials. However, amounts of produced EPS and improvement of attachment indicated that mechanisms other than polysaccharide production are more important on substrata with low surface tensions (<25 mN m-1). Simply producing more polysaccharides is not sufficient to overcome weak attachment on materials with low surface tensions. For example, adhesion of Pseudomonas sp. and A. coffaeformis on polytetrafluorethylene/perfluor-copolymer (PFA; 22 mN m-1) and glass (64.5 mN m-1) was equally strong although EPS production was much higher on glass than on PFA. This is somewhat surprising for A. coffaeformis because polysaccharide production has been considered the most important attachment mechanism of A. coffaeformis.}, }
@article {pmid8661538, year = {1996}, author = {Nelson, SM and Attwell, RW and Dawson, MM and Smith, CA}, title = {The Effect of Temperature on Viability of Carbon- and Nitrogen-Starved Escherichia coli.}, journal = {Microbial ecology}, volume = {32}, number = {1}, pages = {11-21}, pmid = {8661538}, issn = {1432-184X}, abstract = {Escherichia coli was grown in a defined medium at optimum temperature and then transferred to each of five different starvation regimes at 5&amp;deg;C, 20&amp;deg;C, or 37&amp;deg;C, for 1000 hours. Cells were maintained with growth-limiting amounts of carbon or nitrogen, or without either or both nutrients. Bacterial cell viability was assessed by dilution plating, the reduction of 2-(p-indophenyl)-3-(p-nitrophenyl)-5-phenyl tetrazolium chloride (INT), direct viable counts (DVC), and microcolony development. The recoverability of cells on solid medium declined most rapidly, and to the greatest extent in most cases, in cultures maintained at 37&amp;deg;C. Only nitrogen-starved cells maintained at 5&amp;deg;C became completely nonculturable. The reduction of INT consistently indicated higher numbers of viable cells compared to the other methods in all cultures. The viabilities of carbon- and nitrogen-limited cells, assessed by all methods, were similar to one another at each of the temperatures. Viability was lowest at 37&amp;deg;C. Nutrient-downshifted cells also followed a temperature-dependent pattern of survival with viability lowest at 37&amp;deg;C. Morphological differences were noted at different temperatures but were most obvious for nitrogen-starved cells at 37&amp;deg;C, which increased in length.}, }
@article {pmid8661537, year = {1996}, author = {Quesada, A and Valiente, EF}, title = {Relationship Between Abundance of N2-fixing Cyanobacteria and Environmental Features of Spanish Rice Fields.}, journal = {Microbial ecology}, volume = {32}, number = {1}, pages = {59-71}, pmid = {8661537}, issn = {1432-184X}, abstract = {In order to estimate the potential utilization of N2-fixing (heterocystous) cyanobacteria as natural biofertilizers in the Valencian rice fields (Spain), the distribution and seasonal variation of these microorganisms in water and sediment samples were evaluated, and the relationships among cyanobacterial abundance and physical and chemical characteristics of soil and water were investigated. N2-fixing cyanobacteria were present in all the samples analyzed (25 sampling points sampled three times per year during two years). The relative cyanobacterial abundance in soil and water followed contrasting patterns, maximum presence in soil coincided with minimum abundance in water. Correlation analysis showed that cyanobacterial abundance in the two phases (water and sediment) was influenced more by water than by soil properties. Salinity,mineralization variables, and soluble reactive phosphate (SRP) correlated positively with heterocystous cyanobacteria presence. Furthermore, dissolved inorganic nitrogen (DIN) and the ratio DIN:SRP correlated negatively with cyanobacterial abundance. However DIN:SRP ratio better described the cyanobacterial distribution, with a threshold effect: below the Redfield ratio value (7.2 in mass units) cyanobacterial abundance was clearly higher.}, }
@article {pmid8650581, year = {1996}, author = {Elena, SF and Cooper, VS and Lenski, RE}, title = {Punctuated evolution caused by selection of rare beneficial mutations.}, journal = {Science (New York, N.Y.)}, volume = {272}, number = {5269}, pages = {1802-1804}, doi = {10.1126/science.272.5269.1802}, pmid = {8650581}, issn = {0036-8075}, mesh = {Alleles ; Analysis of Variance ; *Biological Evolution ; Culture Media ; Escherichia coli/cytology/*genetics/growth &amp; development ; Models, Statistical ; *Mutation ; *Selection, Genetic ; }, abstract = {For more than two decades there has been intense debate over the hypothesis that most morphological evolution occurs during relatively brief episodes of rapid change that punctuate much longer periods of stasis. A clear and unambiguous case of punctuated evolution is presented for cell size in a population of Escherichia coli evolving for 3000 generations in a constant environment. The punctuation is caused by natural selection as rare, beneficial mutations sweep successively through the population. This experiment shows that the most elementary processes in population genetics can give rise to punctuated evolution dynamics.}, }
@article {pmid8706687, year = {1996}, author = {Rosén, S and Bergström, J and Karlsson, KA and Tunlid, A}, title = {A multispecific saline-soluble lectin from the parasitic fungus Arthrobotrys oligospora. Similarities in the binding specificities compared with a lectin from the mushroom agaricus bisporus.}, journal = {European journal of biochemistry}, volume = {238}, number = {3}, pages = {830-837}, doi = {10.1111/j.1432-1033.1996.0830w.x}, pmid = {8706687}, issn = {0014-2956}, mesh = {Agaricus/*chemistry ; Carbohydrate Sequence ; Detergents/pharmacology ; Electrophoresis, Polyacrylamide Gel/methods ; Gels ; Glycolipids/metabolism ; Haptens/metabolism ; Hydrogen-Ion Concentration ; Lectins/drug effects/*metabolism ; Mitosporic Fungi/*chemistry ; Molecular Sequence Data ; Mucins/metabolism ; Osmolar Concentration ; Phosphatidic Acids/metabolism ; Phosphatidylglycerols/metabolism ; Polysaccharides/metabolism ; Substrate Specificity ; Sulfoglycosphingolipids/metabolism ; alpha-Fetoproteins/metabolism ; }, abstract = {Several fungi can express high levels of saline-soluble and low-molecular-mass lectins that bind to glycoproteins such as fetuin and different mucins but not bind to any monosaccharides. In this paper, we report the binding specificities of such a lectin (designated AOL) isolated from the nematophagous fungus Arthrobotrys oligospora. The results show that AOL is a multispecific lectin that interacts with the following ligands: (a) Several sulfated glycoconjugates including sulfatide, dextran sulfate, and fucoidan. The specificity of this binding was indicated by experiments showing that none of the tested neutral- and sialic-acid-containing glycolipids, chondroitin sulfates B and C, heparin, and polyvinyl sulfate bound to AOL; (b) Phosphatidic acid and phospatidylglycerol, two out of several tested phospholipids. (c) N-linked and O-linked sugar chains bound to intact fetuin. The involvement of such sugar structures was demonstrated by analyzing the binding of AOL to chemically deglycosylated (trifluoromethanesulfonic acid) fetuin. Treating fetuin with O-glycosidase and N-glycosidase indicated that AOL bound to Gal beta GaLNAc alpha-Ser/Thr and to some N-linked complex sugars, respectively. Further assays demonstrated that AOL could interact with several other glycoproteins containing O-linked and/or N-linked sugar chains. The observations that AOL did not bind to free N-linked sugars isolated from fetuin, or to fetuin treated with trypsin or pronase, or to any of the tested neoglycoproteins and glycolipids with neutral- or sialic acid-containing sugars, indicated that the sugar chains need to be bound to an intact peptide backbone to interact with AOL. We have recently shown that the deduced primary structure of AOL has a high similarity to the sequence of a saline-soluble lectin isolated from the mushroom Agaricus bisporus (ABL) (Rosén, S., Kata, M., Persson, Y., Lipniunas, P. H., Wikström, M., van den Hondel, C. A. M. J. J., van den Brink, J. M., Rask, L., Hedén L.-O. and Tunlid, A., see companion paper). It is well known that ABL binds to Gal beta 3GaLNAc alpha-Ser/Thr, and in this paper we demonstrate that ABL binds to sulfatide, phosphatidic acid, phospatidylglycerol, and possibly also to the same N-linked complex sugars as AOL. The above data indicate that AOL and ABL are members of a novel family of fungal lectins sharing similar primary structure and binding properties.}, }
@article {pmid8706686, year = {1996}, author = {Rosén, S and Kata, M and Persson, Y and Lipniunas, PH and Wikström, M and Van Den Hondel, MJ and Van Den Brink, J and Rask, L and Hedén, LO and Tunlid, A}, title = {Molecular characterization of a saline-soluble lectin from a parasitic fungus. Extensive sequence similarities between fungal lectins.}, journal = {European journal of biochemistry}, volume = {238}, number = {3}, pages = {822-829}, doi = {10.1111/j.1432-1033.1996.0822w.x}, pmid = {8706686}, issn = {0014-2956}, mesh = {Agaricus/chemistry ; Amino Acid Sequence ; Antibody Specificity ; Base Sequence ; Blotting, Southern ; Carbohydrate Sequence ; Circular Dichroism ; Fungal Proteins/*chemistry/*genetics/immunology ; Genes, Fungal ; Glycosylation ; Isoenzymes ; Lectins/*chemistry/*genetics/immunology ; Mass Spectrometry/methods ; Mitosporic Fungi/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Sequence Homology, Amino Acid ; Sodium Chloride ; Solubility ; }, abstract = {It has been proposed that the interactions between several parasitic and pathogenic fungi and their hosts are mediated by soluble lectins present in the fungus. We have cloned and analyzed a gene encoding such a lectin (AOL) from the nematophagous fungus Arthrobotrys oligospora (deuteromycete). The deduced primary structure of the AOL gene displayed an extensive similarity (identity 46.3%) to that of a gene encoding a lectin (ABL) recently isolated from the mushroom Agaricus bisporus (basidiomycete), but not to any other fungal, microbial, plant or animal lectins. The similarities between AOL and ABL were further demonstrated by the observation that an antibody specific for AOL cross-reacted with ABL. Together with data showing that AOL has a binding specificity that is similar to that of ABL [Rosen, S., Bergström, J., Karlsson, K.-A. &amp; Tunlid, A. (1996) Eur. J. Biochem. 238, 830-837], these results indicate that AOL and ABL are members of a novel family of saline soluble lectins present in fungi. Southern blots indicated that there is only one AOL gene in the genome encoding a subunit (monomer) of the lectin. The primary structure of AOL did not show the presence of a typical N-terminal signal sequence. Comparison of the deduced primary structure with the molecular mass of AOL as determined by electrospray mass spectrometry (16153 Da), indicated that AOL has an acetylated N-terminal but no other post-translational modifications, and that a minor isoform is formed by deamidation. Circular dichroism (CD) spectroscopy suggested that the secondary structure of AOL contains 34% beta-sheets, 21% alpha-helix, and 45% turns and coils.}, }
@article {pmid8787402, year = {1996}, author = {Pellizari, VH and Bezborodnikov, S and Quensen, JF and Tiedje, JM}, title = {Evaluation of strains isolated by growth on naphthalene and biphenyl for hybridization of genes to dioxygenase probes and polychlorinated biphenyl-degrading ability.}, journal = {Applied and environmental microbiology}, volume = {62}, number = {6}, pages = {2053-2058}, pmid = {8787402}, issn = {0099-2240}, mesh = {Bacteria/classification/genetics/*metabolism ; Biodegradation, Environmental ; Biphenyl Compounds/metabolism ; DNA Probes ; Genes, Bacterial ; Iron-Sulfur Proteins/genetics ; Naphthalenes/metabolism ; Nucleic Acid Hybridization ; Oxygenases/genetics ; Polychlorinated Biphenyls/*metabolism ; Polymerase Chain Reaction ; *Soil Microbiology ; Soil Pollutants/*metabolism ; }, abstract = {Approximately equal numbers of bacteria were isolated from primarily tropical soils by growth on biphenyl and naphthalene to compare their competence in polychlorinated biphenyl (PCB) degradation. The strains isolated by growth on biphenyl catalyzed more extensive PCB degradation than the strains isolated by growth on naphthalene, suggesting that naphthalene cocontamination may be only partially effective in stimulating the cometabolism of lower chlorinated PCBs. Probes were made from the bph, nah, and tod genes encoding the large iron iron sulfur protein of the dioxygenase complex and hybridized to 19 different strains. The hybridization patterns did not correlate well with the substrates of isolation, suggesting that there is considerable diversity in these genes in nature and that probe hybridization is not a reliable indication of catabolic capacity. The strains with the most extensive PCB degradation capacity did strongly hybridize to the bph probe, but a few strains that exhibited strong hybridization had poor PCB-degrading ability. Of the 19 strains studied, 5 hybridized to more than one probe and 2, including one strong PCB degrader, hybridized to all three probes. Southern blots showed that the bph and nah probes hybridized to separate bands, suggesting that multiple dioxygenases were present. Multiple dioxygenases may be an important feature of competitive decomposers in nature and hence may not be rare. Most of the isolates identified were members of the beta subgroup of the Proteobacteria, a few were gram positive, and none were true Pseudomonas species.}, }
@article {pmid8725215, year = {1996}, author = {Korona, R}, title = {Genetic divergence and fitness convergence under uniform selection in experimental populations of bacteria.}, journal = {Genetics}, volume = {143}, number = {2}, pages = {637-644}, pmid = {8725215}, issn = {0016-6731}, mesh = {Bacteria/*genetics/growth &amp; development ; *Genetic Variation ; *Selection, Genetic ; }, abstract = {Replicate populations of bacteria were propagated for 1000 generations in the laboratory. The growth substrate was periodically renewed, so that during most generations (cell doublings) it was not limiting. The final clones demonstrated about a 40% fitness increase when competed against their common ancestor. This increase was uniform both among and within populations despite extensive differentiation in correlated traits: cell size, resistance to starvation and dry mass of culture. It is suggested that genetic diversity developed because selection promoted any changes directing cell activity toward a higher maximum growth rate. Evolution of this trait halted at a similar level when some basic constraints on bacterial metabolism were met. The selective values of emerging mutations must have depended on the genetic background. They would be beneficial early in evolution but ineffective near the limit of adaptation. This hypothesis was tested for one mutation that affected both fitness and colony morphology. In some clones it was the first adaptive mutation and provided a third of the total fitness increase, but it was not assimilated by the clones that reached the adaptive ceiling in some other way. Near the limit of adaptation, epistasis levels off the fitnesses of genetically variable clones.}, }
@article {pmid8722758, year = {1996}, author = {Travisano, M and Lenski, RE}, title = {Long-term experimental evolution in Escherichia coli. IV. Targets of selection and the specificity of adaptation.}, journal = {Genetics}, volume = {143}, number = {1}, pages = {15-26}, pmid = {8722758}, issn = {0016-6731}, mesh = {Adaptation, Physiological/*genetics ; Bacterial Outer Membrane Proteins/*metabolism ; *Biological Evolution ; Biological Transport ; Cell Membrane/metabolism ; Culture Media ; Escherichia coli/*genetics/growth &amp; development ; Genetic Variation ; Genotype ; Mathematics ; Models, Biological ; Models, Genetic ; Porins/metabolism ; Receptors, Virus/metabolism ; *Selection, Genetic ; }, abstract = {This study investigates the physiological manifestation of adaptive evolutionary change in 12 replicate populations of Escherichia coli that were propagated for 2000 generations in a glucose-limited environment. Representative genotypes from each population were assayed for fitness relative to their common ancestor in the experimental glucose environment and in 11 novel single-nutrient environments. After 2000 generations, the 12 derived genotypes had diverged into at least six distinct phenotypic classes. The nutrients were classified into four groups based upon their uptake physiology. All 12 derived genotypes improved in fitness by similar amounts in the glucose environment, and this pattern of parallel fitness gains was also seen in those novel environments where the limiting nutrient shared uptake mechanisms with glucose. Fitness showed little or no consistent improvement, but much greater genetic variation, in novel environments where the limiting nutrient differed from glucose in its uptake mechanisms. This pattern of fitness variation in the novel nutrient environments suggests that the independently derived genotypes adapted to the glucose environment by similar, but not identical, changes in the physiological mechanisms for moving glucose across both the inner and outer membranes.}, }
@article {pmid8704953, year = {1996}, author = {Maltseva, O and McGowan, C and Fulthorpe, R and Oriel, P}, title = {Degradation of 2,4-dichlorophenoxyacetic acid by haloalkaliphilic bacteria.}, journal = {Microbiology (Reading, England)}, volume = {142 (Pt 5)}, number = {}, pages = {1115-1122}, doi = {10.1099/13500872-142-5-1115}, pmid = {8704953}, issn = {1350-0872}, mesh = {2,4-Dichlorophenoxyacetic Acid/*metabolism ; Base Sequence ; Biodegradation, Environmental ; Citric Acid Cycle ; Evolution, Molecular ; Gram-Negative Aerobic Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sodium/analysis ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Three 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterial isolates were obtained from the highly saline and alkaline Alkali Lake site in southwestern Oregon contaminated with 2,4-D production wastes. While similar in most respects, the three isolates differed significantly in 2,4-D degradation rates, with the most active strain, I-18, demonstrating an ability to degrade up to 3000 mg 2,4-D I-1 in 3 d. This strain was well adapted to the extreme environment from which it was isolated, growing optimally on 2,4-D at pH 8.4-9.4 and at sodium ion concentrations of 0.6-1.0 M. According to its optimum salt concentration and pH for growth, this isolate was a moderately halophilic, alkaliphilic bacterium. The 16S RNA gene sequence (303 nt) was identical for all three isolates and most closely resembled those of the moderately halophilic eubacteria of the family Halomonadaceae (91% identity). Biochemical and genetic examination revealed strain I-18 utilizes the same 2,4-D degradation pathway as most of the 2,4-D-degrading bacteria from non-extreme environments. Hybridization data and comparison of the partial sequences of the tfdA gene from the Alkali Lake isolates with those of bacteria from non-extreme environments suggested a common genetic origin of the 2,4-D degradation pathway in the two groups of micro-organisms.}, }
@article {pmid8661536, year = {1996}, author = {de Souza MP,  and Yoch, DC}, title = {Differential Metabolism of Dimethylsulfoniopropionate and Acrylate in Saline and Brackish Intertidal Sediments.}, journal = {Microbial ecology}, volume = {31}, number = {3}, pages = {319-330}, pmid = {8661536}, issn = {1432-184X}, abstract = {In anoxic Spartina alterniflora-dominated sediments along a naturally occuring salinity gradient (the Cooper River estuary, South Carolina, U.S.A.), dimethylsulfoniopropionate (DMSP) was metabolized to dimethyl sulfide (DMS) and acrylate by sediment microbes. The rate of DMSP degradation and acrylate mineralization by sediment microbes was similar at all sites along this 25-km transect. However, sediments amended with acrylate (or DMSP) showed significantly higher rates of N2 fixation (measured as acetylene reduction activity) (ARA) in the saline sediments downstream than brackish sediments. These results are consistent with the fact that acrylate stimulated the rates of both denitrification and CO2 production in the saline sediments at the mouth of the river more than tenfold over rates in brackish sediments. Enrichment experiments indicate that microbes capable of using DMSP or acrylate were not present in upstream sediments despite the fact that microbial biomass, percent organic matter, and both glucose-stimulated ARA and denitrification were highest upstream. It appears that acrylate utilizing, N2 fixing, and denitrifying populations are insignificant in the lower salinity sediments of the estuary. These results may reflect the availability of DMSP, which averaged 10.3 nmol g wet wt-1 of saline sediments and levels less than our detection limit (1 &amp;mgr;M) in brackish sediments.}, }
@article {pmid8661535, year = {1996}, author = {Shuttlesworth, KL and Cerniglia, CE}, title = {Bacterial Degradation of Low Concentrations of Phenanthrene and Inhibition by Naphthalene.}, journal = {Microbial ecology}, volume = {31}, number = {3}, pages = {305-317}, pmid = {8661535}, issn = {1432-184X}, abstract = {Phenanthrene-degrading bacteria were isolated from enrichment cultures of soils contaminated with creosote and jet fuel. The isolates from the creosote enrichments were classified by fatty acid methyl ester profiles as Acidovorax delafieldii and Sphingomonas paucimobilis; the bacterium from the jet fuel-contaminated soil was not identified and was designated strain JFD11. All three isolates used phenanthrene as a sole carbon and energy source, and two of the isolates used fluoranthene as a sole carbon and energy source. Anthracene and fluorene were cometabolized by all three strains, but pyrene was not transformed. Naphthalene inhibited all of the strains, and 28-h cultures of A. delafieldii were inhibited by naphthalene concentrations as low as 5 ppm. Short-term degradation experiments were undertaken with center-well flasks and concentrations of phenanthrene ranging from 1.2 to 12.0 &amp;mgr;M. Since initial degradation rates were not a function of phenanthrene concentration, it was inferred that the half-saturation constants were less than the lowest phenanthrene concentration tested.}, }
@article {pmid8661534, year = {1996}, author = {Paerl, HW and Pinckney, JL}, title = {A Mini-review of Microbial Consortia: Their Roles in Aquatic Production and Biogeochemical Cycling.}, journal = {Microbial ecology}, volume = {31}, number = {3}, pages = {225-247}, pmid = {8661534}, issn = {1432-184X}, abstract = {Molecular oxygen (O2) is a potent inhibitor of key microbial processes, including photosynthesis, N2 fixation, denitrification, sulfate reduction, methanogenesis, iron, and metal reduction reactions. Prokaryote survival and proliferation in aquatic environments is often controlled by the ability to tolerate exposure to oxic conditions. Many prokaryotes do not have subcellular organelles for isolating O2-producing from O2-consuming processes and have developed consortial associations with other prokaryotes and eukaryotes that alleviate metabolic constraints of high O2. Nutrient transformations often rely on appropriate cellular and microenvironmental, or microzonal, redox conditions. The spatial and temporal requirements for microenvironmental overlap among microbial groups involved in nutrient transformations necessitates close proximity and diffusional exchange with other biogeochemically distinct, yet complementary, microbial groups. Microbial consortia exist at different levels of community and metabolic complexity, as shown for detrital, microbial mat, biofilm, and planktonic microalgal-bacterial assemblages. To assess the macroscale impacts of consortial interactions, studies should focus on the range of relevant temporal (minutes to hours) and spatial (microns to centimeters) scales controlling microbial production, nutrient exchange, and cycling. In this review, we discuss the utility and application of techniques suitable for determining microscale consortial activity, production, community composition, and interactions in the context of larger scale aquatic ecosystem structure and function.}, }
@article {pmid8661533, year = {1996}, author = {Hood, MA and Schmidt, JM}, title = {The Examination of Seliberia stellata Exopolymers Using Lectin Assays.}, journal = {Microbial ecology}, volume = {31}, number = {3}, pages = {281-290}, pmid = {8661533}, issn = {1432-184X}, abstract = {Holdfast exopolymers of the dimorphic oligotrophic bacterium Seliberia stellata were examined using fluorescent lectins under light microscopy and colloidal gold lectins using transmission electron microscopy. Examination using fluorescent-labeled lectins revealed that lectins specific for polysaccharides and monosaccharides such as glucose and/or mannose, galactose, N-acetylgalactosamine, and N-acetylglucosamine (and its dimer) adhered to holdfast structure. Colloidal gold-labeled lectin assays also suggested the presence of these sugars. Both the holdfast that mediates swarmer cell adhesion and the holdfast that facilitates rosette formation gave similar results, suggesting the structures may be the same. Another exopolymer produced later in the growth cycle was observed using transmission electron microscopy. It appeared as an amorphous glycocalyx-like material very different from holdfast exo-polymers. Retention of the gold lectin (Wheat Germ Agglutinin (WGA), suggested the presence of N-acetylglucosamine, but fluorescent analyses were unsuccessful. The data suggest that S. stellata produces at least two different exopolymers: (a) the exopolymer of the swarmer cell and rosette holdfast whose function is adhesion and whose composition is (but may not be limited to) polysaccharides and (b) a slime-like exopolymer whose composition and function remain unknown.}, }
@article {pmid8661532, year = {1996}, author = {Griffiths, BS and Ritz, K and Glover, LA}, title = {Broad-Scale Approaches to the Determination of Soil Microbial Community Structure: Application of the Community DNA Hybridization Technique.}, journal = {Microbial ecology}, volume = {31}, number = {3}, pages = {269-280}, pmid = {8661532}, issn = {1432-184X}, abstract = {Broad-scale approaches seek to integrate information on whole microbial communities. It is widely recognized that culture techniques are too selective and unrepresentative to allow a realistic assessment of the overall structure of microbial communities. Techniques based on fatty acid or metabolic profiles determine the phenotypic composition of the community. Complementary information about the genotypic structure of soil microbial communities necessitates analysis of community DNA. To determine broad-scale differences in soil microbial community structure (i.e., differences at the whole community level, rather than specific differences in species composition), we have applied a community hybridization technique to determine the similarity and relative diversity of two samples by cross hybridization. In previous studies this assay failed with whole-soil community DNA. Usable hybridization signals were obtained using whole-soil DNA, in this study, by digesting the DNA with restriction enzymes before the labeling with a random-primer reaction. The community hybridization technique was tested using a graded series of microbial fractions, increasing in complexity, all isolated from the same soil sample. This demonstrated that single bacterial species and a mixture of cultivable bacteria were less complex and only 5% similar to whole-community DNA or bacteria directly extracted from the soil. Extracted bacterial and whole-community DNA were 75% similar to each other and equally complex. When DNA was extracted from four different agricultural soils, their similarities ranged from 35 to 75%. The potential usefulness of community hybridization applied to soil microbial communities is discussed.}, }
@article {pmid8661531, year = {1996}, author = {Carrias, J and Amblard, C and Bourdier, G}, title = {Protistan Bacterivory in an Oligomesotrophic Lake: Importance of Attached Ciliates and Flagellates.}, journal = {Microbial ecology}, volume = {31}, number = {3}, pages = {249-268}, pmid = {8661531}, issn = {1432-184X}, abstract = {Seasonal and depth variations of the abundance, biomass, and bacterivory of protozoa (heterotrophic and mixotrophic flagellates and ciliates) were determined during thermal stratification in an oligomesotrophic lake (Lake Pavin, France). Maximal densities of heterotrophic flagellates (1.9x10(3) cells ml-1) and ciliates (6.1 cells ml-1) were found in the metalimnion. Pigmented flagellates dominated the flagellate biomass in the euphotic zone. Community composition of ciliated protists varied greatly with depth, and both the abundance and biomass of ciliates was dominated by oligotrichs. Heterotrophic flagellates dominated grazing, accounting for 84% of total protistan bacterivory. Maximal grazing impact of heterotrophic flagellates was 18.9x10(6) bacteria 1(-1)h-1. On average, 62% of nonpigmented flagellates were found to ingest particles. Ciliates and mixotrophic flagellates averaged 13% and 3% of protistan bacterivory, respectively. Attached protozoa (ciliates and flagellates) were found to colonize the diatom Asterionella formosa. Attached bacterivores had higher ingestion rates than free bacterivorous protozoa and may account for 66% of total protozoa bacterivory. Our results indicated that even in low numbers, epibiotic protozoa may have a major grazing impact on free bacteria.}, }
@article {pmid8661530, year = {1996}, author = {Ogunseitan, OA}, title = {Protein Profile Variation in Cultivated and Native Freshwater Microorganisms Exposed to Chemical Environmental Pollutants.}, journal = {Microbial ecology}, volume = {31}, number = {3}, pages = {291-304}, pmid = {8661530}, issn = {1432-184X}, abstract = {Assimilation of 35S-precursors into microbial proteins was used to investigate toxicity and adaptational responses that occur in nutrient enriched and natural freshwater samples experimentally contaminated with benzene, toluene, trichloroethylene (TCE), or xylene. Experiments were conducted to analyze (1) the potential of using microbial community protein profiles for responsive identification of chemical pollutant exposure, (2) the inhibition of microbial productivity through reduction in rate of protein synthesis caused by specific chemical pollutants, and (3) whether selection of subpopulations in freshwater microbial communities challenged with chemical pollutants leads to adaptive strategies mediated by production of particular polypeptides. The results show that distinct banding patterns of polypeptides in the range of 30 to 100 kilodaltons that were obtained following collective cultivation of freshwater microorganisms differ with each chemical pollutant. Protein yield and radioisotope incorporation were reduced within ten minutes of micro-bial exposure to chemical pollutants in the following order: xylene < toluene < benzene < TCE. Adaptation of the freshwater microbial community to chemical pollutants prior to radioisotope incorporation produced differences in polypeptide profiles, in the banding patterns of radioactive polypeptides, and in the rate of radioisotope incorporation. The rate of radioisotope incorporation by freshwater microorganisms pre-adapted to chemical pollutants was lowest with xylene (88.1% reduction), followed by TCE (84.0% reduction),toluene (67.3% reduction), and benzene (43.5% reduction). In long-term radioisotope incorporation experiments, protein yield and polypeptide radioactivity was higher in the presence of chemical pollutants than in uncontaminated control samples, suggesting increased metabolic productivity attributable to the chemical pollutants.}, }
@article {pmid8626335, year = {1996}, author = {Romanov, V and Hausinger, RP}, title = {NADPH-dependent reductive ortho dehalogenation of 2,4-dichlorobenzoic acid in Corynebacterium sepedonicum KZ-4 and Coryneform bacterium strainNTB-1 via 2,4-dichlorobenzoyl coenzyme A.}, journal = {Journal of bacteriology}, volume = {178}, number = {9}, pages = {2656-2661}, pmid = {8626335}, issn = {0021-9193}, mesh = {Alcaligenes/*enzymology ; *Benzoates/metabolism ; Biodegradation, Environmental ; Chlorine/metabolism ; Chlorobenzoates/*metabolism ; Coenzyme A/*metabolism ; Coenzyme A Ligases/metabolism ; Corynebacterium/*enzymology ; Hydrolases/metabolism ; Mixed Function Oxygenases/metabolism ; NADP/metabolism ; Oxygenases/metabolism ; Thiolester Hydrolases/metabolism ; }, abstract = {Corynebacterium sepedonicum KZ-4, described earlier as a strain capable of growth on 2,4-dichlorobenzoate (G.M. Zaitsev and Y.N. Karasevich, Mikrobiologiya 54:356-369, 1985), is known to metabolize this substrate via 4-hydroxybenzoate and protocatechuate, and evidence consistent with an initial reductive dechlorination step to form 4-chlorobenzoate was found in another coryneform bacterium, strain NTB-1 (W.J.J. van den Tweel, J.B. Kok, and J.A.M. de Bont, Appl. Environ. Microbiol. 53:810-815, 1987). 2-Chloro-4-fluorobenzoate was found to be converted stoichiometrically to 4-fluorobenzoate by resting cells of strain KZ-4, compatible with a reductive process. Experiments with cell extracts demonstrated that Mg - ATP and coenzyme A (CoA) were required to stimulate reductive dehalogenation, consistent with the intermediacy of 2-chloro-4-fluoro-benzoyl-CoA and 2,4-dichlorobenzoyl-CoA thioesters. 2,4-Dichlorobenzoyl-CoA was shown to be converted to 4-chlorobenzoyl-CoA in a novel NADPH-dependent reaction in extracts of both KZ-4 and NTB-1. In addition to the ligase and reductive dehalogenase activities, hydrolytic 4-chlorobenzoyl-CoA dehalogenase and thioesterase activities, 4-hydroxybenzoate 3-monooxygenase, and protocatechuate 3,4-dioxygenase activities were demonstrated to be present in the soluble fraction of KZ-4 extracts following ultracentrifugation. We propose that the pathway for 2,4-dichlorobenzoate catabolism in strains KZ-4 and NTB-1 involves formation of 2,4-dichlorobenzoyl-CoA, NADPH-dependent ortho dehalogenation yielding 4-chlorobenzoyl-CoA, hydrolytic removal of chlorine from the para position to generate 4-hydroxybenzoyl-CoA, hydrolysis to form 4-hydroxybenzoate, oxidation to yield protocatechuate, and oxidative ring cleavage.}, }
@article {pmid8934928, year = {1996}, author = {Hillman, JD}, title = {Principles of microbial ecology and their application to xerostomia-associated opportunistic infections of the oral cavity.}, journal = {Advances in dental research}, volume = {10}, number = {1}, pages = {66-68}, doi = {10.1177/08959374960100011301}, pmid = {8934928}, issn = {0895-9374}, support = {DE0-4529/DE/NIDCR NIH HHS/United States ; }, mesh = {Dental Plaque/microbiology ; Ecosystem ; Humans ; Mouth/*microbiology ; Opportunistic Infections/*etiology/therapy ; Xerostomia/*complications ; }, abstract = {The human oral flora is normally composed of hundreds of different types of bacteria. This high degree of complexity is largely responsible for the observation that a state of health is the predominant condition of the oral cavity: Myriad bacterial interactions between innocuous and potentially pathogenic species prevent the latter from attaining sufficient numbers to initiate clinically observable diseases. However, protracted or profound perturbations of the oral environment may lead to ecological upsets fundamentally characterized by extreme simplification of the resident flora. Radiation- or autoimmune-induced xerostomia is a striking example of such a perturbation. During the period of floral simplification, as the bacterial interactions diminish, impediments to the outgrowth of pathogens are lost, ultimately leading to the onset of disease. In the absence of methods to reverse the conditions responsible for the ecological upset, as is currently the case in many forms of xerostomia, the possibility of restoring a complex, balanced flora is not imminently practical. However, as our understanding of microbial ecology and pathogenesis develops, application of a replacement therapy approach may become plausible to prevent or retard particular diseases prevalent in xerostomia patients.}, }
@article {pmid8934905, year = {1996}, author = {Roberts, MS and Nakamura, LK and Cohan, FM}, title = {Bacillus vallismortis sp. nov., a close relative of Bacillus subtilis, isolated from soil in Death Valley, California.}, journal = {International journal of systematic bacteriology}, volume = {46}, number = {2}, pages = {470-475}, doi = {10.1099/00207713-46-2-470}, pmid = {8934905}, issn = {0020-7713}, support = {GM39501/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacillus subtilis/*classification/enzymology/genetics ; Bacterial Proteins/genetics ; California ; DNA Gyrase ; DNA Polymerase III/genetics ; DNA Topoisomerases, Type II/genetics ; DNA, Bacterial/analysis ; DNA-Directed RNA Polymerases/genetics ; F Factor ; Phenotype ; Phylogeny ; Restriction Mapping ; *Soil Microbiology ; }, abstract = {Five Bacillus strains isolated from Death Valley soil were shown to belong to a previously unidentified species, for which we propose the name Bacillus vallismortis. The type strain is strain DV1-F-3 (= NRRL B-14890). On the basis of previously published restriction digestion data, B. vallismortis is most closely related to Bacillus subtilis. At this time B. vallismortis can be distinguished from B. subtilis only by differences in whole-cell fatty acid compositions, DNA sequences, and levels of reassociation of genomic DNA.}, }
@article {pmid8919776, year = {1996}, author = {Fulthorpe, RR and Rhodes, AN and Tiedje, JM}, title = {Pristine soils mineralize 3-chlorobenzoate and 2,4-dichlorophenoxyacetate via different microbial populations.}, journal = {Applied and environmental microbiology}, volume = {62}, number = {4}, pages = {1159-1166}, pmid = {8919776}, issn = {0099-2240}, mesh = {2,4-Dichlorophenoxyacetic Acid/*metabolism ; Bacteria/isolation &amp; purification/metabolism ; Biodegradation, Environmental ; Chlorobenzoates/*metabolism ; Ecosystem ; Environmental Pollutants/*metabolism ; Minerals/metabolism ; *Soil Microbiology ; }, abstract = {Biodegradation of two chlorinated aromatic compounds was found to be a common capability of the microorganisms found in the soils of undisturbed, pristine ecosystems. We used 2,4-dichlorophenoxyacetate (2,4-D) and 3-chlorobenzoate (3CBA) as enrichment substrates to compare populations of degrading bacteria from six different regions making up two ecosystems. We collected soil samples from four Mediterranean (California, central Chile, the Cape region of South Africa, and southwestern Australia) and two boreal (northern Saskatchewan and northwestern Russia) ecosystems that had no direct exposure to pesticides or to human disturbance. Between 96 and 120 samples from each of the six regions were incubated with 50 ppm of [U-14C]2,4-D or [U-14C]3CBA. Soils from all regions samples mineralized both 2,4-D and 3CBA, but 3CBA was mineralized without a lag period, while 2,4-D was generally not mineralized until the second week. 3CBA degradative capabilities were more evenly distributed spatially than those for 2,4-D. The degradative capabilities of the soils were readily transferred to fresh liquid medium. 3CBA degraders were easily isolated from most soils. We recovered 610 strains that could release carbon dioxide from ring-labeled 3CBA. Of these, 144 strains released chloride and degraded over 80% of 1 mM 3CBA in 3 weeks or less. In contrast, only five 2,4-D degraders could be isolated, although a variety of methods were used in an attempt to culture the degraders. The differences in the distribution and culturability of the bacteria responsible for 3CBA and 2,4-D degradation in these ecosystems suggest that the two substrates are degraded by different populations. We also describe a 14C-based microtiter plate method that allows efficient screening of a large number of samples for biodegradation activity.}, }
@article {pmid8737943, year = {1996}, author = {Araneo, BA and Cebra, JJ and Beuth, J and Fuller, R and Heidt, PJ and Midvedt, T and Nord, CE and Nieuwenhuis, P and Manson, WL and Pulverer, G and Rusch, VC and Tanaka, R and van der Waaij, D and Walker, RI and Wells, CL}, title = {Problems and priorities for controlling opportunistic pathogens with new antimicrobial strategies; an overview of current literature.}, journal = {Zentralblatt fur Bakteriologie : international journal of medical microbiology}, volume = {283}, number = {4}, pages = {431-465}, doi = {10.1016/s0934-8840(96)80122-8}, pmid = {8737943}, issn = {0934-8840}, mesh = {Adjuvants, Immunologic/therapeutic use ; Antibodies/immunology ; Humans ; Immunization, Passive ; Intestines/immunology/microbiology ; Macrophages/immunology ; Nutritional Physiological Phenomena ; Opportunistic Infections/*prevention &amp; control ; }, abstract = {An International Study Group on New Antimicrobial Strategies (ISGNAS) has been formed in response to the recognition that development of microbial resistance to antibiotics is becoming a serious, world-wide problem. The group met in 1993 for the first time to discuss the feasibility of developing rational alternatives to the use of antibiotics and prepared, as a result, a comprehensive overview of normal (physiological) mechanisms involved in the control of potentially pathogenic (oppotunistic) microorganisms. One objective of ISGNAS is to understand the conditions which allow opportunistic microbes present among the symbionts to cause an infection. There is a need for more coherent information concerning the habitat, growth requirements and host and pathogen properties which allow opportunistic pathogens to cause life-threatening infections. In particular, information is urgently being sought to understand the complexity of the interactions between the vast number of microbial species, and the interactions between the microbes and their host. Another goal is to inspire and enable basic and clinical research that will lead to the development of new therapies for regulating colonization, translocation and infection by opportunistic micro-organisms in patients during periods of decreased resistance. With a sufficient amount of knowledge of how healthy individuals keep opportunistic micro-organisms under control, it may become feasible for physicians to maintain host resistance and inter-microbial factors involved in the containment of opportunistic microbes. Therapies aimed at boostering natural resistance mechanisms will be of critical importance to individuals whose resistance has been compromised as a result of another clinical condition.}, }
@article {pmid9161281, year = {1996}, author = {Brägger, U and Lang, NP}, title = {The significance of bone in periodontal disease.}, journal = {Seminars in orthodontics}, volume = {2}, number = {1}, pages = {31-38}, doi = {10.1016/s1073-8746(96)80037-5}, pmid = {9161281}, issn = {1073-8746}, mesh = {Alveolar Bone Loss/*etiology/physiopathology ; Bone Remodeling ; Disease Progression ; Female ; Humans ; Male ; Periodontitis/*complications/*immunology/microbiology ; Risk Factors ; }, abstract = {Although the connective tissue attachment represents the key issue in periodontal health or disease and in periodontal therapy, the assessment of alveolar bone changes renders valuable indirect evidence for periodontal stability, progression of disease, or repair mechanisms. In periodontal disease bacterial products trigger host cells to release mediators, which may imbalance the steady state between resorption of bone and apposition of osteoid. Modulation of the hosts prostaglandin or interleukin-I synthesis by drug therapy could support the antimicrobial concept of periodontal therapy. Cross-sectional and long-term assessments of alveolar bone have been used to estimate the progression rate of periodontal disease. Inherent limitations of bone assessments in radiographs have to be considered when drawing conclusions from measurements that represent remodeling in periodontal lesions after therapy. Both bone quantity and quality seem to be of secondary importance with respect to the progression of disease, as well as response to therapy. Other risk factors that affect the microbial ecology and/or the hosts immune system seem to be the primary determinants for the periodontal health status.}, }
@article {pmid8868446, year = {1996}, author = {Little, SF and Novak, JM and Lowe, JR and Leppla, SH and Singh, Y and Klimpel, KR and Lidgerding, BC and Friedlander, AM}, title = {Characterization of lethal factor binding and cell receptor binding domains of protective antigen of Bacillus anthracis using monoclonal antibodies.}, journal = {Microbiology (Reading, England)}, volume = {142 (Pt 3)}, number = {}, pages = {707-715}, doi = {10.1099/13500872-142-3-707}, pmid = {8868446}, issn = {1350-0872}, mesh = {Antibodies, Monoclonal/immunology ; *Antigens, Bacterial ; Bacillus anthracis/*immunology ; Bacterial Toxins/*immunology ; Base Sequence ; Binding Sites/immunology ; Epitope Mapping ; Molecular Sequence Data ; }, abstract = {Lethal toxin from Bacillus anthracis is composed of protective antigen (PA) and lethal factor (LF). Anti-PA mAbs that neutralized lethal toxin activity, either in vivo or in vitro, identified three non-overlapping antigenic regions on PA. Two distinct antigenic regions were recognized by the four mAbs that neutralized lethal toxin activity by inhibiting the binding of 125I-LF to cell-bound PA. Mapping showed that one mAb, 1G3PA63, recognized an epitope on a 17 kDa fragment located between amino acid residues Ser-168 and Phe-314. The three other mAbs, 2D3PA, 2D5PA and 10D2PA, recognized an epitope between amino acids Ile-581 and Asn-601. A single antigenic region was recognized by the three mAbs, 3B6PA, 14B7PA and 10E10PA63, that inhibited binding of 125I-PA to cells. This region was located between amino acids Asp-671 and Ile-721. These results confirm previously defined functional domains of PA and suggest that LF may interact with two different sites on PA to form lethal toxin.}, }
@article {pmid8857267, year = {1996}, author = {Friman, E}, title = {Influence of phosphate on development of the nematode-trapping fungus Arthrobotrys oligospora.}, journal = {Microbiological research}, volume = {151}, number = {1}, pages = {77-80}, doi = {10.1016/S0944-5013(96)80059-0}, pmid = {8857267}, issn = {0944-5013}, mesh = {Animals ; Culture Media ; Mitosporic Fungi/*physiology ; *Nematoda ; Phosphates/*pharmacology ; }, abstract = {Arthrobotrys oligospora captures and digests nematodes by means of adhesive networks. These traps are formed in the presence of nematodes but can also be induced by low nutrient media containing amino acids. Influence of phosphate on growth and development of A. oligospora was studied in a liquid culture system known to allow heavy trap formation. Substrate-induced but not nematode-induced trap, formation was inhibited by phosphate at concentrations above 30 mu M. High numbers of chlamydospores were formed in aging cultures irrespective of phosphate concentration.}, }
@article {pmid8801090, year = {1996}, author = {Perdreau-Remington, F and Stefanik, D and Peters, G and Ludwig, C and Rütt, J and Wenzel, R and Pulverer, G}, title = {A four-year prospective study on microbial ecology of explanted prosthetic hips in 52 patients with "aseptic" prosthetic joint loosening.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {15}, number = {2}, pages = {160-165}, pmid = {8801090}, issn = {0934-9723}, mesh = {Aged ; Aged, 80 and over ; Colony Count, Microbial ; Corynebacterium/growth &amp; development/isolation &amp; purification ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli/growth &amp; development/isolation &amp; purification ; Female ; Gram-Positive Bacteria/growth &amp; development/*isolation &amp; purification ; Hip Prosthesis/*microbiology ; Humans ; Male ; Middle Aged ; Prospective Studies ; Prosthesis Failure ; Reoperation ; Staphylococcus/growth &amp; development/isolation &amp; purification ; }, abstract = {The bacteriology of explanted prosthetic hips and surrounding soft tissue was studied in 52 patients undergoing surgical revision for joint loosening. In a prospective four-year study, positive bacterial cultures were recorded in 34 (76%) patients. Coagulase-negative staphylococci were the predominant isolates, and 11 patients (33%) had more than three organisms isolated, 7 (20%) had two only, and 11 (33%) had one species. Among the 23 patients from whom specimens from all 11 predetermined anatomic sites were cultured, the highest frequency of positive cultures (52% and 47%) came from the shaft and capsular tissue, respectively. Organisms were less frequently recovered from the cement and acetabulum (13% and 4%, respectively). Using molecular typing in eight patients with paired isolates of the same species, clonal identity was found in four. An additional patient underwent a second revision for loosening 17 months after the first revision and the same clone of Staphylococcus epidermidis was isolated on both occasions.}, }
@article {pmid9027284, year = {1996}, author = {Shenderov, BA}, title = {[Medical microbial ecology: current status and outlook].}, journal = {Antibiotiki i khimioterapiia = Antibiotics and chemoterapy [sic]}, volume = {41}, number = {10}, pages = {10-12}, pmid = {9027284}, issn = {0235-2990}, mesh = {Anti-Bacterial Agents/history/*therapeutic use ; Bacterial Infections/*drug therapy/prevention &amp; control ; *Ecosystem ; Forecasting ; History, 20th Century ; Humans ; Russia ; }, }
@article {pmid8905090, year = {1996}, author = {Whittaker, CJ and Klier, CM and Kolenbrander, PE}, title = {Mechanisms of adhesion by oral bacteria.}, journal = {Annual review of microbiology}, volume = {50}, number = {}, pages = {513-552}, doi = {10.1146/annurev.micro.50.1.513}, pmid = {8905090}, issn = {0066-4227}, mesh = {Adhesins, Bacterial ; Bacterial Adhesion/*physiology ; Carbohydrate Sequence ; Dental Plaque/microbiology ; Humans ; Molecular Sequence Data ; Mouth/*microbiology ; Mouth Mucosa/microbiology ; Receptors, Immunologic ; Tooth/microbiology ; }, abstract = {Adherence to a surface is a key element for colonization of the human oral cavity by the more than 500 bacterial taxa recorded from oral samples. Three surfaces are available: teeth, epithelial mucosa, and the nascent surface created as each new bacterial cell binds to existing dental plaque. Oral bacteria exhibit specificity for their respective colonization sites. Such specificity is directed by adhesin-receptor cognate pairs on genetically distinct cells. Colonization is successful when adherent cells grow and metabolically participate in the oral bacterial community. The potential roles of adherence-relevant molecules are discussed in the context of the dynamic nature of the oral econiche.}, }
@article {pmid8875032, year = {1996}, author = {Liljemark, WF and Bloomquist, C}, title = {Human oral microbial ecology and dental caries and periodontal diseases.}, journal = {Critical reviews in oral biology and medicine : an official publication of the American Association of Oral Biologists}, volume = {7}, number = {2}, pages = {180-198}, doi = {10.1177/10454411960070020601}, pmid = {8875032}, issn = {1045-4411}, mesh = {Bacteria/growth &amp; development/metabolism/pathogenicity ; Bacterial Adhesion ; *Bacterial Physiological Phenomena ; Colony Count, Microbial ; Dental Caries/*microbiology ; Dental Deposits/microbiology/physiopathology ; Dental Pellicle ; Dental Plaque/microbiology ; Dietary Sucrose/metabolism ; Ecology ; Gingival Crevicular Fluid/microbiology ; Growth Substances/physiology ; Humans ; Mouth/*microbiology ; Periodontal Diseases/*microbiology ; Saliva/physiology ; Tooth/microbiology ; Virulence ; }, abstract = {In the human oral cavity, which is an open growth system, bacteria must first adhere to a surface in order to be able to colonize. Ability to colonize a non-shedding tooth surface is necessary prior to any odontopathic or periodontopathic process. Complex microbe-host relationships occur and must be studied before the commensal-to-pathogenic nature of the human indigenous oral flora can be understood. Medical pathogens, if present in the appropriate host, always produce specific disease. Caries and periodontal diseases are conditional diseases, requiring numbers of certain indigenous species at various sites, particularly the tooth surface. In the case of caries, the condition is related to sugar consumption. Periodontal disease/s may require certain host and environmental conditions, such as local environment or nutritional factors in gingival crevicular fluids. Nonetheless, critical numbers of certain indigenous species must be present in order for these diseases to occur. The aim of this review is to understand the acquisition of the indigenous oral flora and the development of human dental plaque. The role of the salivary pellicle and adherence of indigenous bacteria to it are critical first steps in plaque development. Bacterial interactions with saliva, nutritional factors, growth factors, and microbial physiologic processes are all involved in the overall process of microbial colonization.}, }
@article {pmid8683417, year = {1995}, author = {Pabst, MJ and Pabst, KM and Collier, JA and Coleman, TC and Lemons-Prince, ML and Godat, MS and Waring, MB and Babu, JP}, title = {Inhibition of neutrophil and monocyte defensive functions by nicotine.}, journal = {Journal of periodontology}, volume = {66}, number = {12}, pages = {1047-1055}, doi = {10.1902/jop.1995.66.12.1047}, pmid = {8683417}, issn = {0022-3492}, support = {DE05494/DE/NIDCR NIH HHS/United States ; DE08030/DE/NIDCR NIH HHS/United States ; DE11125/DE/NIDCR NIH HHS/United States ; }, mesh = {Actinomyces/immunology/metabolism ; Aggregatibacter actinomycetemcomitans/immunology/metabolism ; Analysis of Variance ; Blood Bactericidal Activity/*drug effects ; Cells, Cultured ; Cytochrome c Group/metabolism ; Dose-Response Relationship, Drug ; Fusobacterium nucleatum/immunology/metabolism ; Humans ; Hydrogen Peroxide/metabolism ; Immunosuppressive Agents/*pharmacology ; Interleukin-1/antagonists &amp; inhibitors/biosynthesis ; Monocytes/drug effects/metabolism ; Neutrophils/*drug effects/metabolism ; Nicotine/*toxicity ; Oxygen Consumption/drug effects ; Phagocytosis/drug effects ; *Plants, Toxic ; Reactive Oxygen Species/*metabolism ; Superoxides/metabolism ; Tobacco, Smokeless/*toxicity ; }, abstract = {To learn more about the effects of smokeless tobacco on the defensive functions of neutrophils, we studied the influence of nicotine on these cells in vitro, looking at their bactericidal activity against oral pathogens, and at their ability to produce microbicidal reactive oxygen species (oxygen radicals). Exposure of human blood neutrophils to nicotine (0.01% to 0.1%) inhibited their ability to kill Actinomyces naeslundii, Actinobacillus actinomycetemcomitans, and Fusobacterium nucleatum. Although these concentrations of nicotine are high, such concentrations are relevant to phagocytes in the gingival sulcus, because smokeless tobacco contains 0.5% to 3.5% nicotine by dry weight. Nicotine had no such inhibitory effect when the killing assay was performed in an anaerobic environment, implying that nicotine preferentially affected oxygen-dependent killing mechanisms. To further investigate the effects of nicotine on production of oxygen radicals, neutrophils were primed with lipopolysaccharide and triggered with f-met-leu-phe or phorbol ester in the presence of nicotine. Nicotine inhibited production of superoxide anion (measured by reduction of cytochrome c) and hydrogen peroxide (measured by oxidation of phenol red). Nicotine inhibition of superoxide production was reversible by washing away the nicotine. By observing that nicotine inhibited the reduction of cytochrome c by reagent potassium superoxide, we determined that nicotine directly absorbed superoxide. In addition, by examining nicotine inhibition of the uptake of oxygen by neutrophils, we determined that nicotine also interfered with the production of oxygen radicals by these cells. Nicotine also inhibited production of superoxide and interleukin-1 beta by monocytes. Nicotine did not affect the viability of neutrophils and monocytes, as determined by their ability to exclude trypan blue dye. Inhibition of the aerobic antimicrobial functions of neutrophils and monocytes by nicotine may alter the microbial ecology of the oral cavity, and this might be one mechanism by which nicotine compromises the oral health of users of tobacco products.}, }
@article {pmid8608267, year = {1995}, author = {Cisar, JO and Sandberg, AL and Abeygunawardana, C and Reddy, GP and Bush, CA}, title = {Lectin recognition of host-like saccharide motifs in streptococcal cell wall polysaccharides.}, journal = {Glycobiology}, volume = {5}, number = {7}, pages = {655-662}, doi = {10.1093/glycob/5.7.655}, pmid = {8608267}, issn = {0959-6658}, support = {DE-09445/DE/NIDCR NIH HHS/United States ; }, mesh = {Actinomyces/physiology ; Bacterial Adhesion/physiology ; Binding Sites ; Carbohydrate Conformation ; Carbohydrate Sequence ; Humans ; *Lectins ; Molecular Sequence Data ; Polysaccharides, Bacterial/*chemistry ; Streptococcus/*chemistry/pathogenicity/physiology ; Tooth/microbiology ; }, abstract = {Viridans streptococci that participate in the microbial colonization of teeth have cell wall polysaccharides composed of linear phosphodiester-linked hexa- or heptasaccharide repeating units, each containing a host-like disaccharide motif, either Gal beta 1-->3GalNAc or GalNAc beta 1-->3Gal. Whereas strains with GalNAc beta 1-->3Gal-containing polysaccharides co-aggregated with streptococci that possess GalNAc-sensitive lectins, strains with either host-like motif co-aggregated with Actinomyces spp. The latter interactions reflected the specificity of Actinomyces spp. lectins for common features of Gal beta 1-->3GalNAc and GalNAc beta 1-->3Gal. Thus, alpha-linked glycosides of both disaccharides were much more potent inhibitors of co-aggregation than Gal or GalNAc. Six non-bacterial lectins also reacted with the streptococcal polysaccharides. In general, precipitation of each lectin with each polysaccharide involved binding of Gal or GalNAc within the host-like motifs, but not saccharides outside these regions. The lectins of Ricinus communis, Abrus precatorius, Codium fragile and Agaricus bisporus were most reactive with the Gal beta 1-->3GalNAc-containing polysaccharides, the Wisteria floribunda lectin with the GalNAc beta 1-->3Gal-containing polysaccharides and the Bauhinia purpurea lectin with polysaccharides containing either disaccharide. Thus, lectin recognition of the streptococcal cell wall polysaccharides involved either the common or specific sides of the Gal beta 1-->3GalNAc and GalNAc beta 1-->3Gal motifs present within these molecules.}, }
@article {pmid11538433, year = {1995}, author = {Horneck, G}, title = {Exobiology, the study of the origin, evolution and distribution of life within the context of cosmic evolution: a review.}, journal = {Planetary and space science}, volume = {43}, number = {1-2}, pages = {189-217}, doi = {10.1016/0032-0633(94)00190-3}, pmid = {11538433}, issn = {0032-0633}, mesh = {Astronomical Phenomena ; Astronomy ; *Biological Evolution ; Earth, Planet ; *Exobiology ; *Extraterrestrial Environment ; Models, Chemical ; *Origin of Life ; Solar System ; Space Flight ; }, abstract = {The primary goal of exobiological research is to reach a better understanding of the processes leading to the origin, evolution and distribution of life on Earth or elsewhere in the universe. In this endeavour, scientists from a wide variety of disciplines are involved, such as astronomy, planetary research, organic chemistry, palaeontology and the various subdisciplines of biology including microbial ecology and molecular biology. Space technology plays an important part by offering the opportunity for exploring our solar system, for collecting extraterrestrial samples, and for utilizing the peculiar environment of space as a tool. Exobiological activities include comparison of the overall pattern of chemical evolution of potential precursors of life, in the interstellar medium, and on the planets and small bodies of our solar system; tracing the history of life on Earth back to its roots; deciphering the environments of the planets in our solar system and of their satellites, throughout their history, with regard to their habitability; searching for other planetary systems in our Galaxy and for signals of extraterrestrial civilizations; testing the impact of space environment on survivability of resistant life forms. This evolutionary approach towards understanding the phenomenon of life in the context of cosmic evolution may eventually contribute to a better understanding of the processes regulating the interactions of life with its environment on Earth.}, }
@article {pmid9127986, year = {1995}, author = {Pace, NR}, title = {Opening the door onto the natural microbial world: molecular microbial ecology.}, journal = {Harvey lectures}, volume = {91}, number = {}, pages = {59-78}, pmid = {9127986}, issn = {0073-0874}, mesh = {Biological Evolution ; *Ecosystem ; Genetic Variation ; Genome ; *Microbiology ; Phylogeny ; RNA, Ribosomal/genetics ; }, }
@article {pmid8664423, year = {1995}, author = {Rudney, JD}, title = {Does variability in salivary protein concentrations influence oral microbial ecology and oral health?.}, journal = {Critical reviews in oral biology and medicine : an official publication of the American Association of Oral Biologists}, volume = {6}, number = {4}, pages = {343-367}, doi = {10.1177/10454411950060040501}, pmid = {8664423}, issn = {1045-4411}, support = {DE 07233/DE/NIDCR NIH HHS/United States ; }, mesh = {Aging ; Bacterial Infections/physiopathology ; *Bacterial Physiological Phenomena ; Circadian Rhythm ; Disease ; Drug Therapy ; Ecology ; Female ; Humans ; Menstruation ; Mouth Diseases/etiology/physiopathology ; *Oral Health ; Pregnancy ; Research Design ; Saliva/chemistry/metabolism/*microbiology ; Salivary Proteins and Peptides/*analysis/physiology ; Secretory Rate ; }, abstract = {Salivary protein interactions with oral microbes in vitro include aggregation, adherence, cell-killing, inhibition of metabolism, and nutrition. Such interactions might be expected to influence oral ecology. However, inconsistent results have been obtained from in vivo tests of the hypothesis that quantitative variation in salivary protein concentrations will affect oral disease prevalence. Results may have been influenced by choices made during study design, including saliva source, stimulation status, control for flow rate, and assay methods. Salivary protein concentrations also may be subject to circadian variation. Values for saliva collected at the same time of day tend to remain consistent within subjects, but events such as stress, inflammation, infection, menstruation, or pregnancy may induce short-term changes. Long-term factors such as aging, systemic disease, or medication likewise may influence salivary protein concentrations. Such sources of variation may increase the sample size needed to find statistically significant differences. Clinical studies also must consider factors such as human population variation, strain and species differences in protein-microbe interactions, protein polymorphism, and synergistic or antagonistic interaction between proteins. Salivary proteins may form heterotypic complexes with unique effects, and different proteins may exert redundant effects. Patterns of protein-microbe interaction also may differ between oral sites. Future clinical studies must take those factors into account. Promising approaches might involve meta-analysis or multi-center studies, retrospective and prospective longitudinal designs, short-term measurement of salivary protein effects, and consideration of individual variation in multiple protein effects such as aggregation, adherence, and cell-killing.}, }
@article {pmid11540206, year = {1994}, author = {Strayer, RF}, title = {Dynamics of microorganism populations in recirculating nutrient solutions.}, journal = {Advances in space research : the official journal of the Committee on Space Research (COSPAR)}, volume = {14}, number = {11}, pages = {357-366}, doi = {10.1016/0273-1177(94)90322-0}, pmid = {11540206}, issn = {0273-1177}, mesh = {Bacteria ; Biofilms ; Crops, Agricultural/growth &amp; development/*microbiology ; Culture Media/*analysis ; *Ecological Systems, Closed ; Environment, Controlled ; Hydrogen-Ion Concentration ; *Hydroponics ; Nitrogen/metabolism ; Plant Roots/growth &amp; development/*microbiology ; Seeds/microbiology ; *Water Microbiology ; }, abstract = {This overview covers the basic microbial ecology of recirculating hydroponic solutions. Examples from NASA and Soviet CELSS tests and the commercial hydroponic industry will be used. The sources of microorganisms in nutrient solutions include air, water, seeds, plant containers and plumbing, biological vectors, and personnel. Microbial fates include growth, death, and emigration. Important microbial habitats within nutrient delivery systems are root surfaces, hardware surfaces (biofilms), and solution suspension. Numbers of bacteria on root surfaces usually exceed those from the other habitats by several orders of magnitude. Gram negative bacteria dominate the microflora with fungal counts usually much lower. Trends typically show a decrease in counts with increasing time unless stressed plants increase root exudates. Important microbial activities include carbon mineralization and nitrogen transformations. Important detrimental interactions include competition with plants, and human and plant pathogenesis.}, }
@article {pmid11537155, year = {1993}, author = {Friedmann, EI and Kappen, L and Meyer, MA and Nienow, JA}, title = {Long-term productivity in the cryptoendolithic microbial community of the Ross Desert, Antarctica.}, journal = {Microbial ecology}, volume = {25}, number = {1}, pages = {51-69}, pmid = {11537155}, issn = {0095-3628}, support = {DPP-83-14180/DP/NCCDPHP CDC HHS/United States ; NSG 7337/NS/NINDS NIH HHS/United States ; }, mesh = {Antarctic Regions ; *Biomass ; Carbon Dioxide/*metabolism ; Computer Simulation ; Cyanobacteria ; Ecosystem ; Eukaryota ; Fungi ; Lichens/*metabolism/physiology ; Oxygen Consumption/physiology ; Photosynthesis/*physiology ; Temperature ; Time Factors ; Yeasts ; }, abstract = {Annual gross productivity of the lichen-dominated cryptoendolithic community was calculated from a computer analysis of photosynthetic response based on laboratory measurements of CO2 exchange and three years (1985-1988) of field nanoclimate data. Photosynthetic optimum increased from -3 to 2 degrees C between irradiance levels of 100 and 1500 micromoles photons m-2 s-1, while the upper compensation point rose from 1 to 17 degrees C. The mean yearly total time available for metabolic activity (temperature above -10 degrees C and moisture present) was 771.3 h for horizontal rock, 421.5 h for northeast-oriented sloped rock, and 1042.2 h for a small depression in horizontal rock (the characteristic site of occasional lichen apothecia). The calculated mean gross productivity value for a horizontal rock was 1215 mg C m-2 y-1, and net photosynthetic gain was 606 mg C m-2 y-1. Net ecosystem productivity (annual accretion of cellular biomass) estimated from long-term events amounted to only about 3 mg C m-2 y-1. The difference between these two values may represent the long-term metabolic costs of the frequent dehydration-rehydration and freezing-thawing cycles or of overwintering, and may account for the leaching of organic substances to the rock. The yearly gross productivity of the cryptoendolithic microbial community of the entire Ross Desert area was estimated at approximately 120,000-180,000 kg C. Of this, 600-900 kg C is in microbial biomass, and much of the rest is soluble compounds that leach into the rocks and possibly percolate to the valleys, providing a source of organic matter for lakes, rivers, and soils.}, }
@article {pmid11539823, year = {1992}, author = {Boston, PJ and Ivanov, MV and McKay, CP}, title = {On the possibility of chemosynthetic ecosystems in subsurface habitats on Mars.}, journal = {Icarus}, volume = {95}, number = {}, pages = {300-308}, doi = {10.1016/0019-1035(92)90045-9}, pmid = {11539823}, issn = {0019-1035}, mesh = {Carbon Dioxide ; *Ecosystem ; *Environmental Microbiology ; Exobiology ; *Extraterrestrial Environment ; Geological Phenomena ; *Geology ; *Mars ; Solar System ; Temperature ; Volcanic Eruptions ; }, abstract = {We have reexamined the question of extant microbial life on Mars in light of the most recent information about the planet and recently discovered nonphotosynthetic microbial ecosystems on Earth--deep sea hydrothermal vent communities and deep subsurface aquifer communities. On Mars, protected subsurface niches associated with hydrothermal activity could have continued to support life even after surface conditions became inhospitable. Geochemical evidence from the SNC meteorites and geomorphological evidence for recent volcanism suggest that such habitats could persist to the present time. There are also extensive geological features that attest to the ubiquitous nature of volcano-ground ice interactions on Mars. We suggest a possible deep subsurface microbial ecology similar to those discovered to depths of several kilometers below the surface of the Earth. We focus on anaerobic systems utilizing CO2 as the primary source of carbon. Liquid water could be provided by the heat of geothermal or volcanic activity melting permafrost or other subsurface water sources. Gases from volcanic activity deep in the planet could provide reducing power (as CH4, H2, or H2S) percolating up from below and enabling the development of a microbial community based upon chemolithoautotrophy. We suggest a methanogen (or acetogen) and sulfur-based microbial ecology as one possible basis for microbial primary production. Our hypothetical ecosystem is neither supported, nor excluded, by current observations of Mars. Tests for such a subsurface system involve locating active geothermal areas associated with ground ice or detecting trace quantities of reduced atmospheric gases that would leak from such a system.}, }
@article {pmid11536484, year = {1991}, author = {Ford, T and Sacco, E and Black, J and Kelley, T and Goodacre, R and Berkeley, RC and Mitchell, R}, title = {Characterization of exopolymers of aquatic bacteria by pyrolysis-mass spectrometry.}, journal = {Applied and environmental microbiology}, volume = {57}, number = {6}, pages = {1595-1601}, pmid = {11536484}, issn = {0099-2240}, mesh = {Carbohydrates/analysis ; Gram-Negative Aerobic Bacteria/*chemistry/isolation &amp; purification ; Mass Spectrometry ; Polysaccharides, Bacterial/analysis/*chemistry ; Proteins/analysis ; Thermus/*chemistry/isolation &amp; purification ; *Water Microbiology ; }, abstract = {Exopolymers from a diverse collection of marine and freshwater bacteria were characterized by pyrolysis-mass spectrometry (Py-MS). Py-MS provides spectra of pyrolysis fragments that are characteristic of the original material. Analysis of the spectra by multivariate statistical techniques (principal component and canonical variate analysis) separated these exopolymers into distinct groups. Py-MS clearly distinguished characteristic fragments, which may be derived from components responsible for functional differences between polymers. The importance of these distinctions and the relevance of pyrolysis information to exopolysaccharide function in aquatic bacteria is discussed.}, }
@article {pmid11537120, year = {1991}, author = {Lizko, NN}, title = {Problems of microbial ecology in man space mission.}, journal = {Acta astronautica}, volume = {23}, number = {}, pages = {163-169}, doi = {10.1016/0094-5765(91)90115-l}, pmid = {11537120}, issn = {0094-5765}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Clostridium ; Enterobacteriaceae ; *Environmental Microbiology ; Humans ; Intestines/immunology/*microbiology ; Lactobacillaceae ; Macaca mulatta ; Mice ; Rats ; *Space Flight ; Stress, Physiological/physiopathology ; *Weightlessness ; }, abstract = {The state of microflora should be considered as one of the important links in chain of the specific functional disorders involving the spaceflight factors effects. At the same time, there occurs an establishment of nonspecific disbiotic response of the human microflora in the space flights of various duration characterized by a decrease up to a reduction of the "defense" group of microorganisms; by an appearance of unusual microorganisms in various biotypes, by accumulation of the potential of pathogenic species of automicroflora with their succeeding colonization and long term persistence. In experimental animal models to simulate dysbacteriosis and with the use of SPF-rats and primates flow aboard Cosmos biosatellites, the significance of indigenous microflora for preserving microecological homeostasis. Theoretically based and experimentally proven need for increasing the colonization resistance is confirmed by the practical use of the measures to stabilize microflora of the cosmonauts during space flights.}, }
@article {pmid11538696, year = {1990}, author = {Palmer, RJ and Friedmann, EI}, title = {Water relations and photosynthesis in the cryptoendolithic microbial habitat of hot and cold deserts.}, journal = {Microbial ecology}, volume = {19}, number = {}, pages = {111-118}, pmid = {11538696}, issn = {0095-3628}, support = {DPP 83-1410/DP/NCCDPHP CDC HHS/United States ; NSG 7337/NS/NINDS NIH HHS/United States ; }, mesh = {Antarctic Regions ; Carbon Dioxide/metabolism ; Cyanobacteria/metabolism/*physiology ; *Desert Climate ; Ecosystem ; Geological Phenomena ; Geology ; *Humidity ; Israel ; Lichens/metabolism/*physiology ; Photosynthesis/*physiology ; Temperature ; *Water ; }, abstract = {Two cryptoendolithic microbial communities, lichens in the Ross Desert of Antarctica and cyanobacteria in the Negev Desert, inhabit porous sandstone rocks of similar physical structure. Both rock types adsorb water vapor by physical mechanisms unrelated to biological processes. Yet the two microbial communities respond differently to water stress: cryptoendolithic lichens begin to photosynthesize at a matric water potential of -46.4 megaPascals (MPa) [70% relative humidity (RH) at 8 degrees C], resembling thallose desert lichens. Cryptoendolithic cyanobacteria, like other prokaryotes, photosynthesize only at very high matric water potentials [> -6.9 MPa, 90% RH at 20 degrees C].}, }
@article {pmid11542183, year = {1989}, author = {Vestal, JR and White, DC}, title = {Lipid analysis in microbial ecology: quantitative approaches to the study of microbial communities.}, journal = {Bioscience}, volume = {39}, number = {8}, pages = {535-541}, pmid = {11542183}, issn = {0006-3568}, mesh = {Acetates/metabolism ; Animals ; Archaea ; Bacteria ; *Biomass ; Chemistry Techniques, Analytical ; Cyanobacteria ; *Ecosystem ; *Environmental Microbiology ; Eukaryota ; Geologic Sediments/chemistry/microbiology ; Lipid Metabolism ; Lipids/*analysis ; Viruses ; }, }
@article {pmid11540085, year = {1989}, author = {Knoll, AH and Bauld, J}, title = {The evolution of ecological tolerance in prokaryotes.}, journal = {Transactions of the Royal Society of Edinburgh: earth sciences}, volume = {80}, number = {}, pages = {209-223}, doi = {10.1017/s0263593300028650}, pmid = {11540085}, mesh = {Adaptation, Biological ; Archaea/genetics/*physiology ; *Biological Evolution ; Cyanobacteria/genetics/*physiology ; Earth, Planet ; *Environmental Microbiology ; Eukaryotic Cells/physiology ; Geological Phenomena ; Geology ; Hydrogen Sulfide/analysis ; Hydrogen-Ion Concentration ; Oxygen/analysis ; Paleontology ; Phylogeny ; Prokaryotic Cells/*physiology ; Temperature ; Ultraviolet Rays ; }, abstract = {The ecological ranges of Archaeobacteria and Eubacteria are constrained by a requirement for liquid water and the physico-chemical stability limits of biomolecules, but within this broad envelope, prokaryotes have evolved adaptations that permit them to tolerate a remarkable spectrum of habitats. Laboratory experiments indicate that prokaryotes can adapt rapidly to novel environmental conditions, yet geological studies suggest early diversification and long-term stasis within the prokaryotic kingdoms. These apparently contradictory perspectives can be reconciled by understanding that, in general, rates and patterns of prokaryotic evolution reflect the developmental history of the Earth's surface environments. Our understanding of modern microbial ecology provides a lens through which our accumulating knowledge of physiology, molecular phylogeny and the Earth's history can be integrated and focussed on the phenomenon of prokaryotic evolution.}, }
@article {pmid11538334, year = {1988}, author = {Nienow, JA and McKay, CP and Friedmann, EI}, title = {The cryptoendolithic microbial environment in the Ross Desert of Antarctica: light in the photosynthetically active region.}, journal = {Microbial ecology}, volume = {16}, number = {}, pages = {271-289}, pmid = {11538334}, issn = {0095-3628}, support = {DPP 80-17581/DP/NCCDPHP CDC HHS/United States ; DPP 83-14180/DP/NCCDPHP CDC HHS/United States ; NSG 7337/NS/NINDS NIH HHS/United States ; }, mesh = {Antarctic Regions ; Carbon/analysis/metabolism ; Chlorophyta/chemistry/metabolism/*physiology ; *Ecosystem ; Fungi/chemistry/metabolism/*physiology ; Geological Phenomena ; Geology ; *Light ; *Models, Theoretical ; Photons ; Photosynthesis/*physiology ; Quartz/analysis/chemistry ; Temperature ; }, abstract = {The vertical zonation of the Antarctic cryptoendolithic community appears to form in response to the light regime in the habitat. However, because of the structure of the habitat, the light regime is difficult to study directly. Therefore, a mathematical model of the light regime was constructed, which was used to estimate the total photon flux in different zones of the community. Maximum fluxes range from about 150 micrometers photons m-2 s-1 at the upper boundary of the community to about 0.1 micrometer photons m-2 s-1. Estimates of the annual productivity in the community indicate that the lowest zone of the community is light limited, with the maximal annual carbon uptake equivalent to less than the carbon content of one algal (Hemichloris) cell.}, }
@article {pmid11538333, year = {1988}, author = {Nienow, JA and McKay, CP and Friedmann, EI}, title = {The cryptoendolithic microbial environment in the Ross Desert of Antarctica: mathematical models of the thermal regime.}, journal = {Microbial ecology}, volume = {16}, number = {}, pages = {253-270}, pmid = {11538333}, issn = {0095-3628}, support = {DPP 80-17581/DP/NCCDPHP CDC HHS/United States ; DPP 83-14180/DP/NCCDPHP CDC HHS/United States ; NSG 7337/NS/NINDS NIH HHS/United States ; }, mesh = {Algorithms ; Antarctic Regions ; *Climate ; Computer Simulation ; *Ecosystem ; Geological Phenomena ; Geology ; *Hot Temperature ; *Models, Biological ; *Models, Theoretical ; Radiation ; Temperature ; }, abstract = {Microbial activity in the Antarctic cryptoendolithic habitat is regulated primarily by temperature. Previous field studies have provided some information on the thermal regime in this habitat, but this type of information is limited by the remoteness of the site and the harsh climatic conditions. Therefore, a mathematical model of the endolithic thermal regime was constructed to augment the field data. This model enabled the parameters affecting the horizontal and altitudinal distribution of the community to be examined. The model predicts that colonization should be possible on surfaces with zenith angle less than 15 degrees. At greater zenith angles, colonization should be restricted to surfaces with azimuth angles less than 135 degrees or greater than 225 degrees. The upper elevational limit of the community should be less than 2,500 m. The thermal regime probably does not influence the zonation of the community within a rock.}, }
@article {pmid11538303, year = {1988}, author = {Davies, DG and McFeters, GA}, title = {Growth and comparative physiology of Klebsiella oxytoca attached to granular activated carbon particles and in liquid media.}, journal = {Microbial ecology}, volume = {15}, number = {2}, pages = {165-175}, pmid = {11538303}, issn = {0095-3628}, mesh = {Adsorption ; *Charcoal ; Culture Media ; DNA, Bacterial/biosynthesis ; Filtration ; Glucose ; Glutamates ; Klebsiella/*growth &amp; development/*physiology ; RNA, Bacterial/metabolism ; Thymidine ; Uridine ; Water Microbiology ; }, abstract = {Experiments were performed to evaluate the comparative growth and physiology of Klebsiella oxytoca grown attached to granular activated carbon particles (GAC) and in liquid medium. Laboratory studies showed that when this organism attached to GAC, the growth rate was enhanced more than 10 times in the presence of glutamate, a substrate that adsorbed to the surface. No differences were observed if the substrate was glucose, which did not adsorb to GAC. Cellular [3H]thymidine uptake was used to estimate DNA biosynthesis. Attached bacteria grown in a minimal nutrient medium containing 20.0 mg/liter glutamate took up 5 times more [3H]thymidine than cells grown in suspension. [3H]uridine was used as a measure of RNA turnover. Attached cells were shown to assimilate 11 times more [3H]uridine than cells in liquid media. Cell size measurements were performed by differential filtration. Cells grown in a minimal medium with 20.0 mg/liter glutamate decreased in size over time, with 62% of the total number passing through a 1.0 micron filter after 9 days incubation. In the same period, 39% of a cell population that was grown on GAC passed through a 1.0 micron filter. These studies indicate that GAC provides an interfacial environment for the enhanced growth of K. oxytoca when glutamate is the substrate.}, }
@article {pmid11039044, year = {1988}, author = {Jones, CL and Ritchie, JA and Marsh, PD and Van der Ouderaa, F}, title = {The effect of long-term use of a dentifrice containing zinc citrate and a non-ionic agent on the oral flora.}, journal = {Journal of dental research}, volume = {67}, number = {1}, pages = {46-50}, doi = {10.1177/00220345880670010901}, pmid = {11039044}, issn = {0022-0345}, mesh = {Adult ; Anti-Infective Agents, Local/pharmacology/therapeutic use ; Candida/*drug effects ; Cariostatic Agents/pharmacology/therapeutic use ; Colony Count, Microbial ; Dental Plaque/drug therapy/microbiology ; Dentifrices/chemistry/*pharmacology/therapeutic use ; Detergents/*pharmacology/therapeutic use ; Female ; Fluorides/pharmacology/therapeutic use ; Humans ; Microbial Sensitivity Tests ; Middle Aged ; Phosphates/pharmacology/therapeutic use ; Saliva/microbiology ; Streptococcus mutans/*drug effects ; Treatment Failure ; Triclosan/pharmacology/therapeutic use ; Zinc Compounds/*pharmacology/therapeutic use ; }, abstract = {The effect on the oral ecology of daily use, for seven months, of a dentifrice containing 0.5% (w/w) zinc citrate and a non-ionic agent, i.e., 0.2% (w/w) Triclosan (2,4,4'-trichloro-2'-hydroxydiphenyl ether), has been monitored on 13 adult volunteers. Plaque and saliva were sampled monthly and the bacterial flora analyzed. Twenty-six volunteers used a placebo dentifrice as part of their normal oral hygiene for four months to establish the baseline microbial flora. The volunteers were then split into two equal groups: One group continued to use the placebo dentifrice; the other used the dentifrice containing zinc citrate and Triclosan. There was no evidence that seven months' use of a dentifrice containing 0.5% zinc citrate and 0.2% Triclosan caused shifts in the oral microbial ecology, nor was there any evidence of developing bacterial resistance to Triclosan.}, }
@article {pmid11539050, year = {1985}, author = {Nichols, PD and Henson, JM and Guckert, JB and Nivens, DE and White, DC}, title = {Fourier transform-infrared spectroscopic methods for microbial ecology: analysis of bacteria, bacteria-polymer mixtures and biofilms.}, journal = {Journal of microbiological methods}, volume = {4}, number = {}, pages = {79-94}, doi = {10.1016/0167-7012(85)90023-5}, pmid = {11539050}, issn = {0167-7012}, support = {NCA2-IR235-401/CA/NCI NIH HHS/United States ; }, mesh = {*Bacterial Physiological Phenomena ; Biofilms/*growth &amp; development ; Caseins/analysis ; *Environmental Microbiology ; Evaluation Studies as Topic ; Gum Arabic/analysis ; Hydroxybutyrates/analysis ; Peptide Fragments/analysis ; Peptones/analysis ; Polyesters/analysis ; Polymers/*analysis ; Spectroscopy, Fourier Transform Infrared/methods ; }, abstract = {Fourier transform-infrared (FT-IR) spectroscopy has been used to rapidly and nondestructively analyze bacteria, bacteria-polymer mixtures, digester samples and microbial biofilms. Diffuse reflectance FT-IR (DRIFT) analysis of freeze-dried, powdered samples offered a means of obtaining structural information. The bacteria examined were divided into two groups. The first group was characterized by a dominant amide I band and the second group of organisms displayed an additional strong carbonyl stretch at approximately 1740 cm-1. The differences illustrated by the subtraction spectra obtained for microbes of the two groups suggest that FT-IR spectroscopy can be utilized to recognize differences in microbial community structure. Calculation of specific band ratios has enabled the composition of bacteria and extracellular or intracellular storage product polymer mixtures to be determined for bacteria-gum arabic (amide I/carbohydrate C-O approximately 1150 cm-1) and bacteria-poly-beta-hydroxybutyrate (amide I/carbonyl approximately 1740 cm-1). The key band ratios correlate with the compositions of the material and provide useful information for the application of FT-IR spectroscopy to environmental biofilm samples and for distinguishing bacteria grown under differing nutrient conditions. DRIFT spectra have been obtained for biofilms produced by Vibrio natriegens on stainless steel disks. Between 48 and 144 h, an increase in bands at approximately 1440 and 1090 cm-1 was seen in FT-IR spectra of the V. natriegens biofilm. DRIFT spectra of mixed culture effluents of anaerobic digesters show differences induced by shifts in input feedstocks. The use of flow-through attenuated total reflectance has permitted in situ real-time changes in biofilm formation to be monitored and provides a powerful tool for understanding the interactions within adherent microbial consortia.}, }
@article {pmid8574134, year = {1996}, author = {Lunsford, RD and Nguyen, N and London, J}, title = {DNA-binding activities in Streptococcus gordonii: identification of a receptor-nickase and a histonelike protein.}, journal = {Current microbiology}, volume = {32}, number = {2}, pages = {95-100}, doi = {10.1007/s002849900017}, pmid = {8574134}, issn = {0343-8651}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics/isolation &amp; purification/*metabolism ; DNA, Bacterial/*metabolism ; DNA-Binding Proteins/genetics/isolation &amp; purification/*metabolism ; Deoxyribonuclease I/genetics/isolation &amp; purification/*metabolism ; Histones/genetics/isolation &amp; purification/*metabolism ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; Streptococcus/genetics/*metabolism ; }, abstract = {Extraction of Streptococcus gordonii cells with the mild chaotropic agent, LiCl, drastically decreased DNA transforming ability, had little effect on viability, and released both DNA nicking and binding activities. Both activities were Mg2+ and Ca2+ independent and were not competence specific. Southwestern blot analysis of the extract identified putative surface proteins of 56 kDa and 68 kDa in strain Challis and Wicky, respectively. Extracts also contained a 10-kDa DNA-binding protein, designated HSgo, that belongs to the eubacterial histonelike class of proteins.}, }
@article {pmid8550211, year = {1996}, author = {Chen, YY and Clancy, KA and Burne, RA}, title = {Streptococcus salivarius urease: genetic and biochemical characterization and expression in a dental plaque streptococcus.}, journal = {Infection and immunity}, volume = {64}, number = {2}, pages = {585-592}, pmid = {8550211}, issn = {0019-9567}, support = {DE10362/DE/NIDCR NIH HHS/United States ; }, mesh = {Base Sequence ; Dental Plaque/*microbiology ; Escherichia coli/genetics ; Glycolysis ; Humans ; Molecular Sequence Data ; Multigene Family ; Recombinant Proteins/metabolism ; Streptococcus/*enzymology/genetics ; Urease/genetics/*metabolism ; }, abstract = {The hydrolysis of urea by urease enzyme of oral bacteria is believed to have a major impact on oral microbial ecology and to be intimately involved in oral health and diseases. To begin to understand the biochemistry and genetics of oral ureolysis, a study of the urease of Streptococcus salivarius, a highly ureolytic organism which is present in large numbers on the soft tissues of the oral cavity, has been initiated. By using as a probe a 0.6-kpb internal fragment of the S. salivarius 57.I ureC gene, two clones from subgenomic libraries of S. salivarius 57.I in an Escherichia coli plasmid vector were identified. Nucleotide sequence analysis revealed the presence of one partial and six complete open reading frames which were most homologous to ureIAB-CEFGD of other ureolytic bacteria. Plasmid clones were generated to construct a complete gene cluster and used to transform E. coli and Streptococcus gordonii DL1, a nonureolytic, dental plaque microorganism. The recombinant organisms expressed high levels of urease activity when the growth medium was supplemented with NiCl2. The urease enzyme was purified from E. coli, and its biochemical properties were compared with those of the urease produced by S. salivarius and those of the urease produced by S. gordonii carrying the plasmid-borne ure genes. In all cases, the enzyme had a Km of 3.5 to 4.1 mM, a pH optimum near 7.0, and a temperature optimum near 60 degrees C. S. gordonii carrying the urease genes was then demonstrated to have a significant capacity to temper glycolytic acidification in vitro in the presence of concentrations of urea commonly found in the oral cavity. The ability to genetically engineer plaque bacteria that can modulate environmental pH through ureolysis will open the way to using recombinant ureolytic organisms to test hypotheses regarding the role of oral ureolysis in dental caries, calculus formation, and periodontal diseases. Such recombinant organisms may eventually prove useful for controlling dental caries by replacement therapy.}, }
@article {pmid8550202, year = {1996}, author = {Gu, M and Gordon, VM and Fitzgerald, DJ and Leppla, SH}, title = {Furin regulates both the activation of Pseudomonas exotoxin A and the Quantity of the toxin receptor expressed on target cells.}, journal = {Infection and immunity}, volume = {64}, number = {2}, pages = {524-527}, pmid = {8550202}, issn = {0019-9567}, mesh = {*ADP Ribose Transferases ; Animals ; Bacterial Toxins/*metabolism ; CHO Cells ; *Carrier Proteins ; Cricetinae ; Exotoxins/*metabolism ; Furin ; Mice ; Pseudomonas aeruginosa/*pathogenicity ; Receptors, Cell Surface/*analysis ; Subtilisins/genetics/*physiology ; Transfection ; *Virulence Factors ; Pseudomonas aeruginosa Exotoxin A ; }, abstract = {Pseudomonas exotoxin A (PE) binds and enters mammalian cells via the alpha 2-macroglobulin receptor/low density lipoprotein receptor-related protein (LRP). The toxin then requires proteolytic cleavage to generate an enzymatically active fragment with translocates to the cell cytosol and inhibits protein synthesis. To assess the role of furin in determining toxin susceptibility, CHO cells were transfected with a mouse furin gene (CHO+fur cells) and maintained under neomycin selection. Cells expressing the transfected gene were about two- to threefold more sensitive to PE than were cells expressing only a neomycin resistance gene (CHO+neo cells). Possible reasons for the increased toxin sensitivity include the cleavage of a greater number of PE molecules and/or the conversion of more single-chain LRP to the processed, two-chain form. Processing of LRP appears to be necessary to allow the surface display of this receptor. Results of ligand binding studies indicated that the CHO+fur cells displayed about twofold more surface-expressed LRP than did CHO+neo cells. In addition, the in vitro cleavage of PE by recombinant furin enhanced toxin potency about threefold for CHO+neo cells but enhanced it very little for CHO+fur cells. This suggested that CHO+fur cells were processing PE at close to the maximum usable rate. Together these findings suggest that furin is involved in at least two separate protein processing pathways that each contribute to the sensitivity of cells to PE.}, }
@article {pmid8542551, year = {1995}, author = {Shooner, F and Tyagi, RD}, title = {Microbial ecology of simultaneous thermophilic microbial leaching and digestion of sewage sludge.}, journal = {Canadian journal of microbiology}, volume = {41}, number = {12}, pages = {1071-1080}, doi = {10.1139/m95-150}, pmid = {8542551}, issn = {0008-4166}, mesh = {Bacteria/*enzymology/*growth &amp; development ; Endopeptidases/*metabolism ; Hot Temperature ; Hydrogen-Ion Concentration ; Oxidation-Reduction ; Sewage/chemistry/*microbiology ; Sulfur/metabolism ; Thiobacillus/growth &amp; development ; Waste Management/methods ; }, abstract = {The microbial population encountered during a simultaneous thermophilic microbial leaching and digestion process at 50 degrees C, based on microbial sulfur oxidation, was investigated. The cell count of the sulfuric acid producer Thiobacillus thermosulfatus increased, followed by a decrease. In the absence of sulfur (control: conventional thermophilic digestion), Thiobacillus thermosulfatus population decreased under the detection limit. Acidophilic and neutrophilic heterotrophic populations increased during the leaching process, and the final acidophilic population count was higher than the neutrophilic population. During the thermophilic digestion (control), the final neutrophilic population count was higher than the acidophilic. Six heterotrophic bacterial strains were isolated and partially characterized. Bacillus was the most predominant genus. The type of bacterial populations in thermophilic microbial leaching and digestion, as well as the thermophilic digestion process (control), were the same, while only the relative concentrations changed. In both processes, the bacterial indicators decreased under the detection limit after 12 h. Mesophilic heterotrophic population was more affected by the thermophilic microbial leaching process than by thermophilic digestion. Sludge mineralization was probably more influenced by the final cell concentration rather than the presence of an individual species or mixed population.}, }
@article {pmid7591151, year = {1995}, author = {Clemans, DL and Kolenbrander, PE}, title = {Identification of a 100-kilodalton putative coaggregation-mediating adhesin of Streptococcus gordonii DL1 (Challis).}, journal = {Infection and immunity}, volume = {63}, number = {12}, pages = {4890-4893}, pmid = {7591151}, issn = {0019-9567}, mesh = {Adhesins, Bacterial/*analysis/chemistry/physiology ; Animals ; *Bacterial Adhesion ; Female ; Immunoblotting ; Molecular Weight ; Rabbits ; Streptococcus/chemistry/*physiology ; }, abstract = {Streptococcus gordonii DL1 (Challis) bears coaggregation-relevant surface proteins which mediate lactose-inhibitable coaggregations with other streptococci. Six spontaneously occurring coaggregation-defective (Cog-) mutants of wild-type strain S. gordonii DL1 unable to coaggregate with wild-type streptococcal partners were characterized. Antiserum raised against wild-type cells and absorbed with Cog- cells specifically blocked lactose-inhibitable coaggregations between S. gordonii DL1 and its streptococcal partner strains; it did not block lactose-noninhibitable coaggregations with actinomyces partners. Surface proteins were released from the cells by mild sonication treatment and separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. A 100-kDa surface protein from S. gordonii DL1 was identified by immunoblot analysis with the mutant-absorbed antiserum. Each of the six Cog- mutants lacked the 100-kDa protein. Several other oral viridans streptococci that exhibit intrageneric lactose-inhibitable coaggregations expressed an immunoreactive protein with about the same size as the 100-kDa putative adhesin. It is proposed that the 100-kDa protein is the adhesin which mediates coaggregation between S. gordonii DL1 and its streptococcal partners. The role of this putative adhesin in accretion of streptococci in early colonization of the tooth surface is discussed.}, }
@article {pmid7591109, year = {1995}, author = {Kolenbrander, PE and Parrish, KD and Andersen, RN and Greenberg, EP}, title = {Intergeneric coaggregation of oral Treponema spp. with Fusobacterium spp. and intrageneric coaggregation among Fusobacterium spp.}, journal = {Infection and immunity}, volume = {63}, number = {12}, pages = {4584-4588}, pmid = {7591109}, issn = {0019-9567}, support = {DE00175/DE/NIDCR NIH HHS/United States ; R01-DE10730/DE/NIDCR NIH HHS/United States ; }, mesh = {Endopeptidase K ; Fusobacterium/*physiology ; Hot Temperature ; Humans ; Serine Endopeptidases/pharmacology ; Treponema/*physiology ; }, abstract = {A total of 22 strains of Treponema spp. including members of all four named human oral species were tested for coaggregation with 7 strains of oral fusobacteria, 2 strains of nonoral fusobacteria, and 45 strains of other oral bacteria, which included actinobacilli, actinomyces, capnocytophagae, eubacteria, porphyromonads, prevotellae, selenomonads, streptococci, and veillonellae. None of the treponemes coaggregated with any of the latter 45 oral strains or with the two nonoral fusobacteria. All treponemes, eight Treponema denticola strains, eight T. socranskii strains, four oral pectinolytic treponemes, one T. pectinovorum strain, and one T. vincentii strain coaggregated with at least one strain of the fusobacteria tested as partners. The partners consisted of one strain of Fusobacterium periodonticum, five F. nucleatum strains including all four subspecies of F. nucleatum, and a strain of F. simiae obtained from the dental plaque of a monkey. In the more than 100 coaggregations observed, the fusobacterial partner was heat inactivated (85 degrees C for 30 min), while the treponemes were unaffected by the heat treatment. Furthermore, the fusobacteria were usually inactivated by proteinase K treatment, and the treponemes were not affected. Only the T. denticola coaggregations were inhibited by lactose and D-galactosamine. None were inhibited by any of 23 other different sugars or L-arginine. Intragenic coaggregations were seen among the subspecies of F. nucleatum and with F. periodonticum, and none were inhibited by any of the sugars tested or by L-arginine. No intrageneric coaggregations were observed among the treponemes. These data indicate that the human oral treponemes show a specificity for oral fusobacteria as coaggregation partners. Such cell-to cell contact may facilitate efficient metabolic communication and enhance the proliferation of each cell in the progressively more severe stages of periodontal disease.}, }
@article {pmid8544102, year = {1995}, author = {Tang-Larsen, J and Claesson, R and Edlund, MB and Carlsson, J}, title = {Competition for peptides and amino acids among periodontal bacteria.}, journal = {Journal of periodontal research}, volume = {30}, number = {6}, pages = {390-395}, doi = {10.1111/j.1600-0765.1995.tb01292.x}, pmid = {8544102}, issn = {0022-3484}, mesh = {Amino Acids, Sulfur/*metabolism ; Bacteria, Anaerobic/*metabolism ; Biological Transport ; Carbon-Sulfur Lyases/metabolism ; Cystathionine gamma-Lyase/metabolism ; Cysteine/metabolism ; Dipeptides/metabolism ; Ecosystem ; Fusobacterium nucleatum/metabolism ; Hydrogen Sulfide/metabolism ; Methionine/metabolism ; Oligopeptides/*metabolism ; Peptostreptococcus/metabolism ; Periodontal Pocket/*microbiology ; Porphyromonas gingivalis/metabolism ; Sulfhydryl Compounds/metabolism ; }, abstract = {We recently studied the utilization of glutathione (L-gamma-glutamyl-L-cysteinylglycine), L-cysteinylglycine and L-cysteine by anaerobic bacteria. The rate of hydrogen sulfide formation from these compounds was determined and it was concluded that Peptostreptococcus micros and Fusobacterium nucleatum subsp. nucleatum had an active transport of small peptides. In the present study it is shown that methyl mercaptan formation from L-methionine and L-methionyl-containing peptides can also be used to study peptide utilization. There were differences among the periodontal bacteria P. micros, F. nucleatum subsp. nucleatum, and Porphyromonas gingivalis in their capacity to use L-cysteine and L-methionine and peptides containing these amino acids. The peptides were used more efficiently by P. micros and F. nucleatum subsp. nucleatum than by P. gingivalis. All three species used the peptides more efficiently than the free amino acids. The efficiency in utilizing various amino acids and peptides may be among the key determinants of the periodontal microbial ecology.}, }
@article {pmid8526521, year = {1995}, author = {Hodson, RE and Dustman, WA and Garg, RP and Moran, MA}, title = {In situ PCR for visualization of microscale distribution of specific genes and gene products in prokaryotic communities.}, journal = {Applied and environmental microbiology}, volume = {61}, number = {11}, pages = {4074-4082}, pmid = {8526521}, issn = {0099-2240}, mesh = {Base Sequence ; Cell Membrane Permeability ; DNA Primers/genetics ; DNA, Bacterial/genetics ; *Ecosystem ; Escherichia coli/genetics ; *Genes, Bacterial ; Marine Biology ; Models, Biological ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; *Prokaryotic Cells ; Pseudomonas aeruginosa/genetics ; Pseudomonas putida/genetics ; }, abstract = {Obtaining information on the genetic capabilities and phylogenetic affinities of individual prokaryotic cells within natural communities is a high priority in the fields of microbial ecology, microbial biogeochemistry, and applied microbiology, among others. A method for prokaryotic in situ PCR (PI-PCR), a technique which will allow single cells within complex mixtures to be identified and characterized genetically, is presented here. The method involves amplification of specific nuclei acid sequences inside intact prokaryotic cells followed by color or fluorescence detection of the localized PCR product via bright-field or epifluorescence microscopy. Prokaryotic DNA and mRNA were both used successfully as targets for PI-PCR. We demonstrate the use of PI-PCR to identify nahA-positive cells in mixtures of bacterial isolates and in model marine bacterial communities.}, }
@article {pmid7582170, year = {1995}, author = {Holben, WE and Harris, D}, title = {DNA-based monitoring of total bacterial community structure in environmental samples.}, journal = {Molecular ecology}, volume = {4}, number = {5}, pages = {627-631}, doi = {10.1111/j.1365-294x.1995.tb00263.x}, pmid = {7582170}, issn = {0962-1083}, mesh = {Base Composition ; Benzimidazoles ; Clostridium perfringens/genetics/growth &amp; development/isolation &amp; purification ; Coloring Agents ; DNA, Bacterial/*analysis/chemistry/genetics ; Environmental Monitoring/*methods ; Escherichia coli/genetics/growth &amp; development/isolation &amp; purification ; Micrococcus/genetics/growth &amp; development/isolation &amp; purification ; Mutation ; }, abstract = {Determining the structure of bacterial communities and their response to stimuli is key to understanding community function and the interactions that occur between micro-organisms and the environment. However, bacterial communities often comprise complex assemblages of large numbers of different bacterial populations. An approach is presented which allows bacterial community structure to be determined by fractionation of the complex mixture of total bacterial community DNA using the DNA-binding dye bisbenzimidazole which imposes G+C-dependent changes in the buoyant density of DNA. Bacterial community structure presented as percentage of total DNA vs. percentage G+C content of DNA is an indication of the relative abundance of phylogenetic groups of bacteria. Changes in the composition of a soil bacterial community in response to perturbations in the form of carbon amendment and altered water status were monitored.}, }
@article {pmid7582169, year = {1995}, author = {Zhou, JZ and Tiedje, JM}, title = {Gene transfer from a bacterium injected into an aquifer to an indigenous bacterium.}, journal = {Molecular ecology}, volume = {4}, number = {5}, pages = {613-618}, doi = {10.1111/j.1365-294x.1995.tb00261.x}, pmid = {7582169}, issn = {0962-1083}, support = {ES-04911/ES/NIEHS NIH HHS/United States ; }, mesh = {Base Sequence ; Biodegradation, Environmental ; Carboxylic Ester Hydrolases/genetics ; Chlorobenzoates/metabolism ; DNA Primers ; *Gene Transfer Techniques ; *Genes, Bacterial ; Gram-Negative Aerobic Bacteria/*genetics ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Probability ; Pseudomonas/classification/*genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Two novel 3-chlorobenzoate-degrading bacteria were previously isolated from an aquifer in which no such bacteria could be enriched prior to the introduction of the 3-chlorobenzoate-degrading strain, Pseudomonas sp. B13. To understand the origin of 3-chlorobenzoate-degrading genes in the two novel isolates, the 16S ribosomal RNA, clcD (dienelactone hydrolase) and clcA (chlorocatechol oxygenase) genes from these bacteria were amplified and sequenced. The partial 16S rRNA gene sequences and REP-PCR patterns showed that these two novel isolates were identical but differed from strain B13. Phylogenetic analyses revealed that the novel isolates were closely related to Alcaligenes eutrophus in the beta subclass of the Proteobacteria, whereas strain B13 was related to Pseudomonas aeruginosa and P. mendocina in the gamma subclass of the Proteobacteria. In contrast, the clcD and clcA gene sequences were identical on strain B13 and these two isolates, indicating that the 3-chlorobenzoate-degrading genes were transferred from strain B13 to these isolates. What cannot be established is when this transfer occurred.}, }
@article {pmid8519477, year = {1995}, author = {Clemans, DL and Kolenbrander, PE}, title = {Isolation and characterization of coaggregation-defective (Cog-) mutants of Streptococcus gordonii DL1 (Challis).}, journal = {Journal of industrial microbiology}, volume = {15}, number = {3}, pages = {193-197}, pmid = {8519477}, issn = {0169-4146}, mesh = {Adhesins, Bacterial/genetics/metabolism ; Bacterial Adhesion/*genetics/physiology ; Biofilms/*growth &amp; development ; Humans ; Models, Biological ; *Mutation ; Polysaccharides, Bacterial/metabolism ; Streptococcus/*genetics/isolation &amp; purification/*physiology ; }, abstract = {Streptococcus gordonii DL1 (Challis) bears coaggregation-mediating surface adhesins which recognize galactoside-containing surface polysaccharides on Streptococcus oralis 34, Streptococcus oralis C104, and Streptococcus SM PK509. Fifty-nine spontaneously-occurring coaggregation-defective (Cog-) mutants of S. gordonii DL1 unable to coaggregate with partner streptococci were isolated. Six representative Cog- mutants were characterized by their coaggregation properties with four Actinomyces naeslundii strains (T14V, PK947, PK606, PK984), Veillonella atypica PK1910, and Propionibacterium acnes PK93. The six representative Cog- mutants showed altered coaggregation with their streptococcal partners, A. naeslundii PK947, and P. acnes PK93. Based on the coaggregation phenotypes of these mutants, a model for the lactose-inhibitable coaggregation between S. gordonii DL1 and its partner bacteria is proposed. The potential use of these mutants in studies of oral biofilms is discussed.}, }
@article {pmid7592123, year = {1995}, author = {De Smet, I and Van Hoorde, L and Vande Woestyne, M and Christiaens, H and Verstraete, W}, title = {Significance of bile salt hydrolytic activities of lactobacilli.}, journal = {The Journal of applied bacteriology}, volume = {79}, number = {3}, pages = {292-301}, doi = {10.1111/j.1365-2672.1995.tb03140.x}, pmid = {7592123}, issn = {0021-8847}, mesh = {Animals ; Bacterial Typing Techniques ; Cell Division/physiology ; Cricetinae ; Culture Media ; Detergents/pharmacology ; Dose-Response Relationship, Drug ; Hydrogen-Ion Concentration ; Lactobacillus/classification/*enzymology/growth &amp; development ; }, abstract = {Bile salt hydrolase (BSH) activity was shown to be constitutive and substrate-specific: the BSH isogenic Lactobacillus plantarum wild type (LP80 WT) and BSH overproducing LP80 (pCBH1) strains preferentially hydrolysed glycodeoxycholic acid (GDCA), whereas the hamster Lact. animalis isolates H362 and H364 showed a higher affinity for taurodeoxycholic acid (TDCA). In viability studies in the presence of nutrients, it was demonstrated that GDCA exerted a higher toxicity than TDCA in a pH-dependent manner. This toxicity was inversely proportionate to the BSH activity level of the strains tested, indicating that BSH activity contributed towards bile salt resistance when appropriate nutrients were available. The high toxicity of GDCA relative to TDCA was suggested to be caused by their weak and strong acid properties respectively. It was therefore hypothesized that the protonated form of bile salts exhibited toxicity as it imported protons in the cell. This puts an energy-burden on BSH- lactobacilli which undergo intracellular acidification. BSH+ cells primarily protect themselves through the formation of the weaker DCA compound, which can help negate the pH-drop by recapturing and exporting the co-transported proton. However, since DCA is more toxic than its conjugated counterparts, an additional energy-dependent detoxification of DCA is suggested.}, }
@article {pmid7574638, year = {1995}, author = {Fulthorpe, RR and McGowan, C and Maltseva, OV and Holben, WE and Tiedje, JM}, title = {2,4-Dichlorophenoxyacetic acid-degrading bacteria contain mosaics of catabolic genes.}, journal = {Applied and environmental microbiology}, volume = {61}, number = {9}, pages = {3274-3281}, pmid = {7574638}, issn = {0099-2240}, mesh = {2,4-Dichlorophenoxyacetic Acid/*metabolism ; Alcaligenes/genetics/metabolism ; Bacteria/classification/*genetics/*metabolism ; Biodegradation, Environmental ; Biological Evolution ; DNA Fingerprinting ; DNA Probes ; DNA, Bacterial/genetics ; *Genes, Bacterial ; Mosaicism ; Nucleic Acid Hybridization ; Recombination, Genetic ; }, abstract = {DNA from 32 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacteria from diverse locations was probed with the first three genes of the well-known 2,4-D degradation pathway found in Alcaligenes eutrophus JMP134(pJP4). The majority of strains did not show high levels of homology to the first three genes of the 2,4-D degradation pathway, tfdA, -B, and -C. Most strains showed combinations of tfdA-, B-, and C-like elements that exhibited various degrees of homology to the gene probes. Strains having the same genomic fingerprints (as determined by repetitive extragenic palindromic PCR) exhibited the same hybridization pattern regardless of the geographic origin of the strain, with the exception of a strain isolated from Puerto Rico. This strain had the same genomic fingerprint as that of numerous other strains in the collection but differed in its hybridization against the tfdA gene probe. Members of the beta subdivision of the Proteobacteria class, specifically Alcaligenes, Burkholderia, and Rhodoferax species, carried DNA fragments with 60% or more sequence similarity to tfdA of pJP4, and most carried fragments showing at least 60% homology to tfdB. However, many strains did not hybridize with tfdC, although they exhibited chlorocatechol dioxygenase activity. Members of the alpha subdivision of the Proteobacteria class, mostly of the genus Sphingomonas, did not hybridize to either tfdA or tfdC, but some hybridized at low stringency to tfdB. The data suggest that extensive interspecies transfer of a variety of homologous degradative genes has been involved in the evolution of 2,4-D-degrading bacteria.}, }
@article {pmid8589411, year = {1995}, author = {Rossbach, S and Rasul, G and Schneider, M and Eardly, B and de Bruijn, FJ}, title = {Structural and functional conservation of the rhizopine catabolism (moc) locus is limited to selected Rhizobium meliloti strains and unrelated to their geographical origin.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {8}, number = {4}, pages = {549-559}, doi = {10.1094/mpmi-8-0549}, pmid = {8589411}, issn = {0894-0282}, mesh = {Base Sequence ; Conserved Sequence ; DNA Fingerprinting ; DNA Primers/genetics ; DNA, Bacterial/genetics ; *Genes, Bacterial ; Inositol/*analogs &amp; derivatives/metabolism ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sinorhizobium meliloti/classification/*genetics/*metabolism ; Species Specificity ; }, abstract = {Rhizopine (L-3-O-methyl-scyllo-inosamine; 3-O-MSI) synthesis (mos) and catabolism (moc) genes were originally isolated from Rhizobium meliloti strain L5-30 (Murphy et al., Proc. Natl. Acad. Sci. U.S.A., 84:493, 1987). These genes have been postulated to give a competitive advantage to this strain in the rhizosphere, since the ability to utilize the unusual nutritional mediator rhizopine as nitrogen and carbon source appears to be correlated with the ability of Moc+ bacteria to efficiently infect alfalfa plants. This study examines the distribution of rhizopine catabolism (moc) genes among different soil bacteria. By using oligonucleotide primers homologous to the moc genes and the polymerase chain reaction (PCR), moc genes were shown to be absent from a random collection of 100 different soil isolates. However, screening 50 different electrophoretic type strains of a worldwide R. meliloti collection (Eardly et al., Appl. Environ. Microbiol. 56:187, 1990) revealed the presence of moc genes in three additional strains, S33, 102F51, and 74B3. These three strains were found to be able to synthesize rhizopine in planta (Mos+) and to catabolize it (Moc+). To determine the relatedness of the Mos+/Moc+ strains to each other and to other R. meliloti strains, we used the rep-PCR method to generate genomic fingerprints, and to create a phylogenetic tree with the help of an optical imaging system and data analysis program (AMBIS). Because of the apparent infrequent occurrence of moc genes among soil bacteria, we suggest that the use of moc genes as a selectable marker trait for tracking genetically manipulated organisms is feasible.}, }
@article {pmid8543492, year = {1995}, author = {Boogaerts, MA}, title = {Anti-infective strategies in neutropenia.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {36 Suppl A}, number = {}, pages = {167-178}, doi = {10.1093/jac/36.suppl_a.167}, pmid = {8543492}, issn = {0305-7453}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Bacterial Infections/complications/*drug therapy ; Humans ; Neutropenia/*complications/microbiology ; }, abstract = {Anti-infective strategies in febrile neutropenic patients have evolved continuously over the past decade. The changing spectrum of not only the infecting organisms but also of the underlying disease have necessitated different approaches. While the duration and degree of neutropenia have remained the most important risk factors for the development of invasive infections, other factors such as the presence of catheters, cytotoxic chemotherapy, mucositis, infection history, microbial colonisation and the concomitant immune dysfunction, also play a major role in the design of the anti-infective strategy. Individualisation of treatment strategy and the need for flexibility in response to local microbial ecology have also become key concepts. Controversy still surrounds the optimal prophylactic and empirical therapeutic regimens. Selective suppression of the endogenous microbial flora, particularly of the alimentary tract and other mucosal surfaces is recommended for high risk patients, such as those with anticipated profound and prolonged neutropenia, severe post chemotherapy mucositis and the presence of long-term intravenous catheters. For all other risk categories, cost benefit ratios must be carefully weighed against potential clinical benefit. Empirical monotherapy with broad-spectrum cephalosporins or a carbapenem is accepted as a cost-effective and usually well tolerated alternative to combination therapy. However, close monitoring of the patient's response is essential. Early empirical antifungal therapy also remains one of the prerequisites for a successful outcome in the management of neutropenic fever. Safer and more effective antifungal agents are urgently needed. In the future haematopoietic growth factors and other new techniques, such as peripheral blood progenitor cell transplantations, are likely to play a role in the early prophylaxis and management of severe neutropenic infective episodes. Future anti-infective strategies in the neutropenic host may not only lie with antibiotics, but also encompass successful modulation of host defences.}, }
@article {pmid7790078, year = {1995}, author = {Sandberg, AL and Ruhl, S and Joralmon, RA and Brennan, MJ and Sutphin, MJ and Cisar, JO}, title = {Putative glycoprotein and glycolipid polymorphonuclear leukocyte receptors for the Actinomyces naeslundii WVU45 fimbrial lectin.}, journal = {Infection and immunity}, volume = {63}, number = {7}, pages = {2625-2631}, pmid = {7790078}, issn = {0019-9567}, mesh = {Actinomyces/*immunology ; Bacterial Adhesion ; Binding, Competitive ; Fimbriae, Bacterial/*metabolism ; Gangliosides/*metabolism ; Glycolipids/*metabolism ; Glycoproteins/*metabolism ; Humans ; Lectins/*metabolism ; Neutrophils/*immunology ; Receptors, Cell Surface/*metabolism ; }, abstract = {Recognition of receptors on sialidase-treated polymorphonuclear leukocytes (PMNs) by the Gal/GalNAc lectin associated with the type 2 fimbriae of certain strains of actinomyces results in activation of the PMNs, phagocytosis, and destruction of the bacteria. In the present study, plant lectins were utilized as probes to identify putative PMN receptors for the actinomyces lectin. The Gal-reactive lectin from Ricinus communis (RCAI), the Gal/GalNAc-reactive lectins from R. communis (RCAII) and Bauhinia purpurea (BPA), as well as the Gal beta 1-3GalNAc-specific lectins from Arachis hypogaea (PNA) and Agaricus bisporus (ABA) inhibited killing of Actinomyces naeslundii WVU45 by sialidase-treated PMNs. These five lectins detected a 130-kDa surface-labeled glycoprotein on nitrocellulose transfers of PMN extracts separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. This glycoprotein was revealed only after treatment of the transfers with sialidase, a condition analogous to the sialidase dependence of the lectin-mediated biological responses of the PMNs to the actinomyces. The mannose-reactive lectin concanavalin A did not inhibit killing of the actinomyces and failed to detect the 130-kDa glycoprotein but did block PMN-dependent killing of Escherichia coli B, a bacterium that possesses mannose-sensitive fimbriae. Therefore, the PMN glycoprotein receptor for A. naeslundii is clearly distinct from those recognized by E. coli. Two major putative glycolipid receptors were also identified by actinomyces and RCAI overlays on sialidase-treated thin-layer chromatograms of PMN gangliosides. Thus, both a 130-kDa glycoprotein and certain gangliosides are implicated in the attachment of the actinomyces to PMNs.}, }
@article {pmid7551018, year = {1995}, author = {Fuerst, JA}, title = {The planctomycetes: emerging models for microbial ecology, evolution and cell biology.}, journal = {Microbiology (Reading, England)}, volume = {141 (Pt 7)}, number = {}, pages = {1493-1506}, doi = {10.1099/13500872-141-7-1493}, pmid = {7551018}, issn = {1350-0872}, mesh = {Bacteria/classification/cytology/*genetics ; Base Sequence ; *Biological Evolution ; DNA, Ribosomal/genetics ; *Ecology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 5S/genetics ; Terminology as Topic ; Water Microbiology ; }, }
@article {pmid8565898, year = {1995}, author = {Tiedje, JM and Thiem, SM and Massol-Deyá, A and Ka, JO and Fries, MR}, title = {Tracking microbial populations effective in reducing exposure.}, journal = {Environmental health perspectives}, volume = {103 Suppl 5}, number = {Suppl 5}, pages = {117-120}, pmid = {8565898}, issn = {0091-6765}, support = {ESO4911/ES/NIEHS NIH HHS/United States ; }, mesh = {Biodegradation, Environmental ; *Environmental Exposure ; *Environmental Microbiology ; *Environmental Monitoring ; Environmental Pollutants/metabolism/*toxicity ; }, abstract = {Microbial ecology provides the link between basic biochemical and molecular studies on toxicity reduction by microbial metabolism and environmental studies that determine exposure. This link provides the ability to determine which microorganisms are responsible for the actual transformations in nature, thereby establishing how predictive the laboratory pathway, kinetic, regulatory, and enzyme mechanistic information is for nature. This information can be important to the rate of toxicant removal, the type and concentration of intermediate product(s), and the identification of conditions that limit effective toxicant removal. Nucleic acid-based methods now provide the main means to track important biodegrading populations. Examples of these methods are given that illustrate tracking a biodegrading microbe injected into an aquifer, following community succession in a toluene-degrading fluidized bed reactor, aiding the isolation from nature of novel biodegrading organisms, and rapidly characterizing the extent of microbial diversity in an aquifer stimulated to co-metabolize trichloroethene.}, }
@article {pmid7774724, year = {1995}, author = {Gu, M and Rappaport, J and Leppla, SH}, title = {Furin is important but not essential for the proteolytic maturation of gp160 of HIV-1.}, journal = {FEBS letters}, volume = {365}, number = {1}, pages = {95-97}, doi = {10.1016/0014-5793(95)00447-h}, pmid = {7774724}, issn = {0014-5793}, mesh = {Amino Acid Sequence ; Animals ; CHO Cells ; Cricetinae ; Furin ; Gene Products, env/*metabolism ; HIV Core Protein p24/analysis ; HIV Envelope Protein gp160 ; HIV-1/*metabolism ; Humans ; Mice ; Molecular Sequence Data ; Polymerase Chain Reaction ; Protein Precursors/*metabolism ; *Protein Processing, Post-Translational ; Recombinant Proteins/metabolism ; Subtilisins/genetics/*metabolism ; }, abstract = {The envelope glycoproteins of HIV are required for viral infectivity. Proteolysis of the precursor envelope glycoprotein gp160 results in the formation of gp120 and gp41. Cleavage occurs after the sequence Arg-Glu-Lys-Arg. This sequence is expected to be a substrate for the cellular protease furin. We examined whether furin is responsible for cleavage of gp160 by using a furin-deficient CHO cell line and the same cell line transfected with furin cDNA. Data obtained from viral transmission assays suggested that furin increased viral infectivity but was not essential for the maturation of gp160, implying that other proprotein processing enzymes also recognize this putative furin cleavage site.}, }
@article {pmid7744873, year = {1995}, author = {Donkersloot, JA and Thompson, J}, title = {Cloning, expression, sequence analysis, and site-directed mutagenesis of the Tn5306-encoded N5-(carboxyethyl)ornithine synthase from Lactococcus lactis K1.}, journal = {The Journal of biological chemistry}, volume = {270}, number = {20}, pages = {12226-12234}, doi = {10.1074/jbc.270.20.12226}, pmid = {7744873}, issn = {0021-9258}, mesh = {Alanine Dehydrogenase ; Amino Acid Oxidoreductases/biosynthesis/chemistry/*genetics ; Amino Acid Sequence ; Bacterial Proteins/biosynthesis/*genetics ; Base Sequence ; Cloning, Molecular ; DNA Transposable Elements/genetics ; Escherichia coli/genetics ; Genes, Bacterial ; Genetic Vectors/genetics ; Glutamate Dehydrogenase/chemistry ; Lactococcus lactis/*genetics ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Oxidation-Reduction ; Saccharopine Dehydrogenases/chemistry ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {The gene (ceo) encoding N5-(carboxyethyl)ornithine synthase (EC 1.5.1.24) has been isolated from the sucrose-nisin transposon Tn5306 of Lactococcus lactis K1, sequenced, and expressed at high level in Escherichia coli. The cloned enzyme has allowed the synthesis of the novel N omega-carboxypropyl amino acids N5-(1-carboxypropyl)-L-ornithine and N6-(1-carboxypropyl)-L-lysine. Comparison of the deduced amino acid sequence of N5-(1-carboxyethyl)-L-ornithine synthase (M(r) = 35,323) to the functionally analogous octopine and nopaline synthases from crown gall tumors showed surprisingly little similarity. However, N5-(1-carboxyethyl)-L-ornithine synthase and yeast saccharopine dehydrogenase exhibit homology at their N and C termini, which suggests that these two proteins constitute a distinct branch of the amino acid dehydrogenase superfamily. A centrally located 9-amino acid segment (GSGNVAQGA) in N5-(1-carboxyethyl)-L-ornithine synthase is virtually identical with a sequence present in the beta alpha beta-fold of the nucleotide binding domain of several microbial NADPH-dependent glutamate dehydrogenases. A much longer sequence of approximately 80 residues has significant similarity to alanine dehydrogenase. Substitution of arginine 15 of N5-(1-carboxyethyl)-L-ornithine synthase by lysine resulted in loss of enzyme activity.}, }
@article {pmid7646006, year = {1995}, author = {Top, EM and Holben, WE and Forney, LJ}, title = {Characterization of diverse 2,4-dichlorophenoxyacetic acid-degradative plasmids isolated from soil by complementation.}, journal = {Applied and environmental microbiology}, volume = {61}, number = {5}, pages = {1691-1698}, pmid = {7646006}, issn = {0099-2240}, mesh = {2,4-Dichlorophenoxyacetic Acid/*metabolism ; Alcaligenes/genetics/*metabolism ; Biodegradation, Environmental ; *Conjugation, Genetic ; Genes, Bacterial ; Genetic Complementation Test ; Nucleic Acid Hybridization ; Plasmids/genetics/isolation &amp; purification/*metabolism ; Sequence Homology, Nucleic Acid ; *Soil Microbiology ; }, abstract = {The diversity of 2,4-dichlorophenoxyacetic acid (2,4-D)-degradative plasmids in the microbial community of an agricultural soil was examined by complementation. This technique involved mixing a suitable Alcaligenes eutrophus (Rifr) recipient strain with the indigenous microbial populations extracted from soil. After incubation of this mixture, Rifr recipient strains which grow with 2,4-D as the only C source were selected. Two A. eutrophus strains were used as recipients: JMP228 (2,4-D-), which was previously derived from A. eutrophus JMP134 by curing of the 2,4-D-degradative plasmid pJP4, and JMP228 carrying pBH501aE (a plasmid derived from pJP4 by deletion of a large part of the tfdA gene which encodes the first step in the mineralization of 2,4-D). By using agricultural soil that had been treated with 2,4-D for several years, transconjugants were obtained with both recipients. However, when untreated control soil was used, no transconjugants were isolated. The various transconjugants had plasmids with seven different EcoRI restriction patterns. The corresponding plasmids are designated pEMT1 to pEMT7. Unlike pJP4, pEMT1 appeared not to be an IncP1 plasmid, but all the others (pEMT2 to pEMT7) belong to the IncP1 group. Hybridization with individual probes for the tfdA to tfdF genes of pJP4 demonstrated that all plasmids showed high degrees of homology to the tfdA gene. Only pEMT1 showed a high degree of homology to tfdB, tfdC, tfdD, tfdE, and tfdF, while the others showed only moderate degrees of homology to tfdB and low degrees of homology to tfdC.(ABSTRACT TRUNCATED AT 250 WORDS)}, }
@article {pmid7706318, year = {1995}, author = {Gentry-Weeks, CR and Spokes, J and Thompson, J}, title = {beta-Cystathionase from Bordetella avium. Role(s) of lysine 214 and cysteine residues in activity and cytotoxicity.}, journal = {The Journal of biological chemistry}, volume = {270}, number = {13}, pages = {7695-7702}, doi = {10.1074/jbc.270.13.7695}, pmid = {7706318}, issn = {0021-9258}, mesh = {3T3 Cells ; Amino Acid Sequence ; Animals ; Base Sequence ; Bordetella/*enzymology ; Cell Survival/*drug effects ; Chymotrypsin ; DNA Primers ; DNA, Bacterial/metabolism ; Escherichia coli/enzymology ; Ethylmaleimide/pharmacology ; Kinetics ; Lyases/*chemistry/*metabolism/toxicity ; Mice ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Osteoblasts/cytology/drug effects ; Peptide Mapping ; Point Mutation ; Polymerase Chain Reaction ; Protein Biosynthesis ; Recombinant Proteins/chemistry/metabolism/toxicity ; Salmonella typhimurium/enzymology ; Sequence Homology, Amino Acid ; Spectrophotometry ; }, abstract = {beta-Cystathionase (EC 4.4.1.8) from Bordetella avium is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the hydrolysis of L-cystine to yield pyruvic acid, NH3, and thiocysteine. The latter compound is highly toxic toward MC3T3-E1 osteogenic cells, rat osteosarcoma cells, and other cell lines maintained in tissue culture (Gentry-Weeks, C. R., Keith, J. M., and Thompson, J. (1993) J. Biol. Chem. 268, 7298-7314). Site-directed mutagenesis has established that lysine 214 of the sequence TKYVGGHSD, is primarily responsible for internal aldimine binding of PLP in the holoenzyme. Translation of the DNA sequence of the beta-cystathionase gene (metC) from B. avium, reveals 4 cysteine residues/enzyme subunit (M(r) = 42,600), and spectrophotometric analysis with 4,4'-dithiodipyridine showed that there were no disulfide linkages in the native protein. beta-Cystathionase is inhibited by sulfhydryl-reactive agents, including N-ethylmaleimide (NEM). To elucidate the mechanism of NEM inhibition, each of the 4 cysteine residues at positions 88, 117, 279, and 309 was individually replaced by alanine or glycine. The mutant proteins C88A, C117G, C279G, and C309A were purified to homogeneity, and each was assayed for enzyme activity, PLP-binding, NEM sensitivity, and susceptibility to chymotrypsin digestion. The activities of mutant proteins C88A and C279G were comparable with that of the native enzyme, and since both forms were inhibited by NEM, neither cysteine 88 nor 279 are prerequisite for enzyme activity. By elimination, cysteine residues 117 and 309 must be the targets for alkylation, and resultant inactivation of beta-cystathionase, by the -SH reactive agent. Substitution of cysteine 117 and 309 with glycine and alanine, respectively, yielded the inactive proteins C117G and C309A. PLP was not detectable in these proteins, and their absorption spectra lacked the peak (at 420 nm) that is characteristic of internal PLP-Schiff base formation. Edman degradation revealed that C117G (M(r) approximately 36,000) also lacked the first 63 amino acids comprising the N terminus of the native protein. The beta-cystathionase mutants C117G and C309A showed enhanced susceptibility to chymotrypsin digestion. Cysteine residues 117 and 309 may reside in conformationally sensitive environments, and in the native enzyme these amino acids most probably serve a structural function. Toxicity assays performed with the various mutant proteins obtained by site-directed mutagenesis established that only catalytically active forms of beta-cystathionase were were cytotoxic for tissue culture cells.}, }
@article {pmid7864482, year = {1995}, author = {Pichichero, ME}, title = {Group A streptococcal tonsillopharyngitis: cost-effective diagnosis and treatment.}, journal = {Annals of emergency medicine}, volume = {25}, number = {3}, pages = {390-403}, doi = {10.1016/s0196-0644(95)70300-4}, pmid = {7864482}, issn = {0196-0644}, mesh = {Adolescent ; Adult ; Cephalosporins/therapeutic use ; Child ; Child, Preschool ; Cost-Benefit Analysis ; Drug Administration Schedule ; Erythromycin/therapeutic use ; Humans ; Penicillin Resistance ; Penicillins/therapeutic use ; Pharyngitis/diagnosis/*drug therapy/microbiology ; Pharynx/microbiology ; Recurrence ; Streptococcal Infections/complications/diagnosis/*drug therapy ; *Streptococcus pyogenes/isolation &amp; purification ; Tonsillitis/diagnosis/*drug therapy/microbiology ; Treatment Failure ; }, abstract = {Most patients who seek medical attention for sore throat are concerned about streptococcal tonsillopharyngitis, but fewer than 10% of adults and 30% of children actually have a streptococcal infection. Group A beta-hemolytic streptococci (GAS) are most often responsible for bacterial tonsillopharyngitis, although Neisseria gonorrhea, Arcanobacterium haemolyticum (formerly Corynebacterium haemolyticum), Chlamydia pneumoniae (TWAR agent), and Mycoplasma pneumoniae have also been suggested as possible, infrequent, sporadic pathogens. Viruses or idiopathic causes account for the remainder of sore throat complaints. Reliance on clinical impression to diagnose GAS tonsillopharyngitis is problematic; an overestimation of 80% to 95% by experienced clinicians typically occurs for adult patients. Overtreatment promotes bacterial resistance, disturbs natural microbial ecology, and may produce unnecessary side effects. Existing data suggest that rapid GAS antigen testing as an aid to clinical diagnosis can be very useful. When used appropriately, it is sensitive (79% to 88%) in detecting GAS-infected patients and is specific (90% to 96%) and cost-effective. Penicillin has been the treatment of choice for GAS tonsillopharyngitis since the 1950s; 10 days of treatment are necessary for bacterial eradication. A single IM injection of benzathine penicillin is effective and obviates compliance issues. Until the early 1970s, the bacteriologic failure rate for the treatment of GAS tonsillopharyngitis ranged from 2% to 10% and was attributed to chronic GAS carriers. Since the late 1970s, the penicillin failure rate has frequently exceeded 20% in published reports. Explanations for recurrent GAS tonsillopharyngitis include poor patient compliance; reacquisition from a family member or peer, copathogenic colonization by Staphylococcus aureus, Haemophilus influenzae, Moraxella catarrhalis, anaerobes that inactivate penicillin with beta-lactamase, or all these organisms; suppression of natural immune response by too-early administration of antibiotics; GAS tolerance to penicillin; antibiotic eradication of normal pharyngeal flora that normally act as natural host defenses; and establishment of a true carrier state. When therapy fails, milder symptoms may occur during the relapse. Several antimicrobials have demonstrated superior efficacy compared with penicillin in eradicating GAS and are administered less frequently to enhance patient compliance. In previously untreated GAS throat infections, cephalosporins produce a 5% to 22% higher bacteriologic cure rate; after a penicillin treatment failure, these differences are greater. Amoxicillin/clavulanate and the extended-spectrum macrolides clarithromycin and azithromycin may also produce enhanced bacteriologic eradication in comparison to penicillin.(ABSTRACT TRUNCATED AT 400 WORDS)}, }
@article {pmid7597109, year = {1995}, author = {Lunsford, RD}, title = {A Tn4001 delivery system for Streptococcus gordonii (Challis).}, journal = {Plasmid}, volume = {33}, number = {2}, pages = {153-157}, doi = {10.1006/plas.1995.1016}, pmid = {7597109}, issn = {0147-619X}, mesh = {Cloning, Molecular/*methods ; *DNA Transposable Elements ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; Streptococcus/*genetics ; Transformation, Bacterial ; }, abstract = {The Staphylococcus aureus transposon Tn4001 was found to transpose in Streptococcus gordonii. Transposition sites appeared to be randomly distributed, and the element was stable in the absence of antibiotic selection. An increase in transposition frequency was noted when the delivery plasmid was propagated in a Dam- Dcm- Escherichia coli host strain. The utility of Tn4001 was demonstrated by the generation of lactose-negative mutants. Small size, clonal stability, random transposition, and known nucleotide sequence make Tn4001 a useful addition to the repertoire of tools available to the streptococcal geneticist.}, }
@article {pmid7860594, year = {1995}, author = {Sniegowski, PD}, title = {A test of the directed mutation hypothesis in Escherichia coli MCS2 using replica plating.}, journal = {Journal of bacteriology}, volume = {177}, number = {4}, pages = {1119-1120}, pmid = {7860594}, issn = {0021-9193}, mesh = {Arabinose/biosynthesis ; Bacteriophage mu/genetics ; Escherichia coli/*genetics ; Genes, Bacterial/*genetics ; Lac Operon/genetics ; Models, Genetic ; Mutagenesis/*genetics ; Operon/*genetics ; Proviruses/genetics ; Virus Activation ; }, abstract = {Excision of phage Mu from Escherichia coli MCS2 was originally put forth as a clear example of directed mutation. This claim was considerably weakened, however, by subsequent evidence that Mu excision occurs during starvation regardless of fitness consequences. Here, I use the classical replica-plating technique to examine Mu excision during starvation of MCS2. The results support the conclusion that Mu excision is not directed but is, instead, nonspecifically induced by starvation.}, }
@article {pmid7743184, year = {1995}, author = {Lenski, RE and Sniegowski, PD}, title = {Evolutionary genetics. Directed mutations slip-sliding away?.}, journal = {Current biology : CB}, volume = {5}, number = {2}, pages = {97-99}, doi = {10.1016/s0960-9822(95)00023-6}, pmid = {7743184}, issn = {0960-9822}, mesh = {Adaptation, Physiological ; *Biological Evolution ; Escherichia coli/genetics ; *Mutation ; Selection, Genetic ; beta-Galactosidase/genetics ; }, abstract = {Adaptive frameshift mutations in the lacZ gene of Escherichia coli are, unusually, nearly all short deletions, perhaps caused by slipped-strand mispairings in mononucleotide runs. But are they directed?}, }
@article {pmid7574613, year = {1995}, author = {Massol-Deyá, AA and Whallon, J and Hickey, RF and Tiedje, JM}, title = {Channel structures in aerobic biofilms of fixed-film reactors treating contaminated groundwater.}, journal = {Applied and environmental microbiology}, volume = {61}, number = {2}, pages = {769-777}, pmid = {7574613}, issn = {0099-2240}, support = {GM14047-04/GM/NIGMS NIH HHS/United States ; }, mesh = {Aerobiosis ; Biodegradation, Environmental ; *Biofilms ; Diffusion ; Fatty Acids/metabolism ; Microbiological Techniques ; Microscopy, Confocal ; Microscopy, Electron, Scanning ; Time Factors ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Scanning electron microscopy, confocal scanning laser microscopy, and fatty acid methyl ester profiles were used to study the development, organization, and structure of aerobic multispecies biofilm communities in granular activated-carbon (GAC) fluidized-bed reactors treating petroleum-contaminated groundwaters. The sequential development of biofilm structure was studied in a laboratory reactor fed toluene-amended groundwater and colonized by the indigenous aquifer populations. During the early stages of colonization, microcolonies were observed primarily in crevices and other regions sheltered from hydraulic shear forces. Eventually, these microcolonies grew over the entire surface of the GAC. This growth led to the development of discrete discontinuous multilayer biofilm structures. Cell-free channel-like structures of variable sizes were observed to interconnect the surface film with the deep inner layers. These interconnections appeared to increase the biological surface area per unit volume ratio, which may facilitate transport of substrates into and waste products out of deep regions of the biofilm at rates greater than possible by diffusion alone. These architectural features were also observed in biofilms from four field-scale GAC reactors that were in commercial operation treating petroleum-contaminated groundwaters. These shared features suggest that formation of cell-free channel structures and their maintenance may be a general microbial strategy to deal with the problem of limiting diffusive transport in thick biofilms typical of fluidized-bed reactors.}, }
@article {pmid7530902, year = {1995}, author = {Enwonwu, CO}, title = {Interface of malnutrition and periodontal diseases.}, journal = {The American journal of clinical nutrition}, volume = {61}, number = {2}, pages = {430S-436S}, doi = {10.1093/ajcn/61.2.430S}, pmid = {7530902}, issn = {0002-9165}, support = {DE-09653/DE/NIDCR NIH HHS/United States ; }, mesh = {Acute-Phase Proteins/physiology ; Cytokines/physiology ; Humans ; Neutrophils/physiology ; Periodontal Diseases/*etiology/microbiology ; Protein-Energy Malnutrition/*complications ; }, abstract = {In response to periodontal pathogens neutrophils release oxidants, proteinases, and other destructive factors. The balance between these factors, the antioxidants, and endogenously synthesized antiproteinases determine the extent of periodontal damage. Malnutrition, particularly protein-energy malnutrition involving concomitant deficiencies of antioxidant nutrients, is characterized by impairment in production and cellular actions of the cytokines, diminished acute-phase protein response (APR) to infections, endocrinopathies, defective metabolism of drugs, and impaired response to stress. The APR plays a central role in promoting healing. Additionally, malnutrition elicits adverse alterations in the oral microbial ecology as well as in the volume and the antibacterial and physicochemical properties of saliva. Good dietary practices and optimal nutritional status are therefore important in mitigating the severity of inflammatory periodontal lesions but are likely of limited value if the stimuli from dental plaque are not removed.}, }
@article {pmid7828926, year = {1995}, author = {Michel, LO and Sandkvist, M and Bagdasarian, M}, title = {Specificity of the protein secretory apparatus: secretion of the heat-labile enterotoxin B subunit pentamers by different species of gram- bacteria.}, journal = {Gene}, volume = {152}, number = {1}, pages = {41-45}, doi = {10.1016/0378-1119(94)00691-k}, pmid = {7828926}, issn = {0378-1119}, mesh = {Bacterial Toxins/genetics ; Biological Transport ; Cell Membrane/metabolism ; Enterotoxins/genetics/*metabolism ; Escherichia coli/genetics ; *Escherichia coli Proteins ; Genetic Vectors ; Gram-Negative Bacteria/genetics/*metabolism ; Protein Conformation ; Recombinant Proteins/metabolism ; Species Specificity ; }, abstract = {The B-subunit pentamer(s) (EtxBp) of Escherichia coli heat-labile enterotoxin (LT) are secreted from Vibrio cholerae via the general secretion pathway (GSP), but remain periplasmic in E. coli. In order to determine if other Gram- bacteria were also able to secrete the ExtBp, the etxB gene, which encodes EtxB was introduced into different bacteria. Of the bacteria examined, most species of Vibrio and Aeromonas were able to secrete this protein through the outer membrane; other Gram- genera, including Erwinia, Klebsiella and Xanthomonas were not, even though they encode GSP genes homologous to those of V. cholerae. Thus, the ability to recognize the EtxBp as a secretable protein is confined to bacteria that were identified as being closely related to V. cholerae by examination of their 5S rRNA [MacDonell and Colwell, Syst. Appl. Microbiol. 6 (1985) 171-182].}, }
@article {pmid7809610, year = {1995}, author = {Travisano, M and Mongold, JA and Bennett, AF and Lenski, RE}, title = {Experimental tests of the roles of adaptation, chance, and history in evolution.}, journal = {Science (New York, N.Y.)}, volume = {267}, number = {5194}, pages = {87-90}, doi = {10.1126/science.7809610}, pmid = {7809610}, issn = {0036-8075}, mesh = {*Adaptation, Physiological ; *Biological Evolution ; Escherichia coli/cytology/genetics/*physiology ; *Gene Frequency ; Genotype ; Glucose/metabolism ; Maltose/metabolism ; *Mutation ; Phenotype ; Temperature ; }, abstract = {The contributions of adaptation, chance, and history to the evolution of fitness and cell size were measured in two separate experiments using bacteria. In both experiments, populations propagated in identical environments achieved similar fitnesses, regardless of prior history or subsequent chance events. In contrast, the evolution of cell size, a trait weakly correlated with fitness, was more strongly influenced by history and chance.}, }
@article {pmid8561455, year = {1995}, author = {Brock, TD}, title = {The road to Yellowstone--and beyond.}, journal = {Annual review of microbiology}, volume = {49}, number = {}, pages = {1-28}, doi = {10.1146/annurev.mi.49.100195.000245}, pmid = {8561455}, issn = {0066-4227}, mesh = {Bacteria/isolation &amp; purification ; Ecology ; Fresh Water ; History, 20th Century ; Microbiology/*history ; Oceans and Seas ; Thermus/isolation &amp; purification ; *Water Microbiology ; }, abstract = {This memoir describes the professional life and times of Thomas D. Brock, with an emphasis on those aspects of his career relating to research in microbial ecology, and how this work led to field research in Yellowstone. The first discovery of extremely thermophilic bacteria is described, followed by a discussion of some of the consequences of this discovery for biotechnology and microbiology. Also covered briefly in this memoir are Brock's activities in textbook writing, publishing, computers, and the history of science.}, }
@article {pmid7806387, year = {1995}, author = {Gordon, VM and Klimpel, KR and Arora, N and Henderson, MA and Leppla, SH}, title = {Proteolytic activation of bacterial toxins by eukaryotic cells is performed by furin and by additional cellular proteases.}, journal = {Infection and immunity}, volume = {63}, number = {1}, pages = {82-87}, pmid = {7806387}, issn = {0019-9567}, mesh = {*ADP Ribose Transferases ; Amino Acid Sequence ; Animals ; *Antigens, Bacterial ; Bacterial Toxins/genetics/*metabolism/*toxicity ; CHO Cells ; Cathepsin B/metabolism ; Cricetinae ; Diphtheria Toxin/metabolism/toxicity ; Dose-Response Relationship, Drug ; Endopeptidases/deficiency/genetics/*metabolism ; Exotoxins/genetics/metabolism/toxicity ; Furin ; Leupeptins/pharmacology ; Molecular Sequence Data ; Peptide Fragments/*toxicity ; Substrate Specificity ; Subtilisins/deficiency/genetics/*metabolism ; *Virulence Factors ; Pseudomonas aeruginosa Exotoxin A ; }, abstract = {Before intoxication can occur, anthrax toxin protective antigen (PA), Pseudomonas exotoxin A (PE), and diphtheria toxin (DT) must be activated by proteolytic cleavage at specific amino acid sequences. Previously, it was shown that PA and DT can be activated by furin. In Chinese hamster ovary (CHO) cells, wild-type (RKKR) and cleavage site mutants of PA, each administered with a modified form of anthrax toxin lethal factor (the N terminus of lethal factor fused to PE domain III), had the following potencies: RKKR (wild type) (concentration causing 50% cell death [EC50] = 12 ng/ml) > or = RAAR (EC50 = 18 ng/ml) > FTKR (EC50 = 24 ng/ml) > STRR (EC50 = 49 ng/ml). In vitro cleavage of PA and cleavage site mutants of PA by furin demonstrated that native PA (RKKR) and PA with the cleavage sequence RAAR are substrates for furin. To characterize eukaryotic proteases that play a role in activating bacterial toxins, furin-deficient CHO cells were selected after chemical mutagenesis. Furin-deficient cells were resistant to PE, whose cleavage site, RQPR, constitutes a furin recognition site and to all PA cleavage site mutants, but were sensitive to DT (EC50 = 2.9 ng/ml) and PA (EC50 = 23 ng/ml), whose respective cleavage sites, RKKR and RVRR, contain additional basic residues. Furin-deficient cells that were transfected with the furin gene regained sensitivity to PE and PA cleavage site mutants. These studies provide evidence that furin can activate the three toxins and that one or more additional proteases contribute to the activation of DT and PA.}, }
@article {pmid7534052, year = {1995}, author = {Kuritz, T and Wolk, CP}, title = {Use of filamentous cyanobacteria for biodegradation of organic pollutants.}, journal = {Applied and environmental microbiology}, volume = {61}, number = {1}, pages = {234-238}, pmid = {7534052}, issn = {0099-2240}, support = {DRR-00480/RR/NCRR NIH HHS/United States ; }, mesh = {Biodegradation, Environmental ; Cyanobacteria/*metabolism ; Environmental Microbiology ; Hexachlorocyclohexane/*metabolism ; }, abstract = {Biodegradation is increasingly being considered as a less expensive alternative to physical and chemical means of decomposing organic pollutants. Pathways of biodegradation have been characterized for a number of heterotrophic microorganisms, mostly soil isolates, some of which have been used for remediation of water. Because cyanobacteria are photoautotrophic and some can fix atmospheric nitrogen, their use for bioremediation of surface waters would circumvent the need to supply biodegradative heterotrophs with organic nutrients. This paper demonstrates that two filamentous cyanobacteria have a natural ability to degrade a highly chlorinated aliphatic pesticide, lindane (gamma-hexachlorocyclohexane); presents quantitative evidence that this ability can be enhanced by genetic engineering; and provides qualitative evidence that those two strains can be genetically engineered to degrade another chlorinated pollutant, 4-chlorobenzoate.}, }
@article {pmid7476403, year = {1995}, author = {London, J}, title = {Identifying and isolating fimbrial-associated adhesins of oral gram-negative bacteria.}, journal = {Methods in enzymology}, volume = {253}, number = {}, pages = {397-403}, doi = {10.1016/s0076-6879(95)53034-7}, pmid = {7476403}, issn = {0076-6879}, mesh = {Actinomyces/chemistry/immunology ; Adhesins, Bacterial/immunology/*isolation &amp; purification/metabolism ; Animals ; Antibodies, Monoclonal/isolation &amp; purification ; Antigens, Bacterial/isolation &amp; purification ; Bacteriological Techniques ; Chromatography, Affinity/methods ; Fimbriae, Bacterial/*chemistry/immunology ; Galactosides/metabolism ; Gram-Negative Bacteria/*chemistry/immunology ; Humans ; Mice ; Mouth/*microbiology ; Prevotella/chemistry/immunology ; Streptococcus/chemistry/immunology ; }, }
@article {pmid7476402, year = {1995}, author = {Kolenbrander, PE}, title = {Coaggregations among oral bacteria.}, journal = {Methods in enzymology}, volume = {253}, number = {}, pages = {385-397}, doi = {10.1016/s0076-6879(95)53033-9}, pmid = {7476402}, issn = {0076-6879}, mesh = {Bacteria/genetics/metabolism ; *Bacterial Adhesion/genetics ; Bacteriological Techniques ; Ecosystem ; Humans ; In Vitro Techniques ; Mouth/*microbiology ; Mutation ; Nephelometry and Turbidimetry ; Species Specificity ; }, abstract = {The oral bacterial community appears to use coaggregation as a major mechanism for interbacterial adhesion and colonization of the host. Methods for measuring and evaluating the specificity of adhesion vary from the visual observation of the phenomenon to quantitative analyses. Not only is aggregation specificity reflected in the choice of partners but also in the fact that many are inhibited by galactosides and sialic acid. Each coaggregation between any two partners within a multigeneric coaggregate is independent of the others and can be shown to be distinct by using the radioactivity-based assay. By using the visual assay, it has been shown that members of the 17 genera of most frequently isolated oral bacteria exhibit coaggregation. With the exception of oral streptococci and a few oral actinomyces, the 17 genera do not exhibit intrageneric coaggregation. As a dynamic population, oral bacteria are in a constant flux of accretion and detachment, which are coupled to growth and death. This ecological community is amenable to intensive study, and the coaggregation assays described here are particularly suited to enhance progress in this study.}, }
@article {pmid7703012, year = {1994}, author = {Harty, DW and Oakey, HJ and Patrikakis, M and Hume, EB and Knox, KW}, title = {Pathogenic potential of lactobacilli.}, journal = {International journal of food microbiology}, volume = {24}, number = {1-2}, pages = {179-189}, doi = {10.1016/0168-1605(94)90117-1}, pmid = {7703012}, issn = {0168-1605}, mesh = {Animals ; Bacterial Adhesion ; Collagen/metabolism ; Endocarditis, Bacterial/etiology/microbiology ; Fibrinogen/metabolism ; Fibronectins/metabolism ; *Food Microbiology ; Gram-Positive Bacterial Infections/etiology/microbiology ; Humans ; In Vitro Techniques ; Lactobacillus/isolation &amp; purification/*pathogenicity/physiology ; Platelet Aggregation ; Species Specificity ; }, abstract = {Lactobacilli are often considered to be commensal or beneficial participants in human microbial ecology and considerable research is being carried out into the effects of the use of lactobacilli as additives in both human and animal diets. However, lactobacilli also cause some human diseases (e.g. dental caries, rheumatic vascular disease, septicaemia and infective endocarditis (IE)), and have recently been identified as potential emerging pathogens in elderly and immunocompromised patients, particularly those receiving broad spectrum antibiotic therapy. The identification of potential pathogenic traits amongst lactobacilli will therefore facilitate the use of the organisms for probiotic purposes. The ability to aggregate human platelets is considered to be a possible pathogenic trait in the progression of IE. A comparison of bacterial cell surface properties amongst L. rhamnosus strains showed that platelets were aggregated by 5/5 IE strains and 8/16 laboratory strains. For the L. paracasei subsp. paracasei strains the respective numbers were 2/5 and 2/9. However two strains, morphological mutants of a non-aggregating strain, which had been re-isolated after passaging through rats were found to aggregate platelets. No loss of aggregating function occurred on extensive subculturing of IE strains. Aggregation also occurred with 11/14 strains for five other species, namely, Lactobacillus acidophilus, Lactobacillus fermentum, Lactobacillus oris, Lactobacillus plantarum and Lactobacillus salvivarius, with each species being represented indicating that the property is not uncommon in the genus. A comparison of IE and oral isolates of L. rhamnosus and L. paracasei subsp. paracasei and seven other Lactobacillus species, has shown that the binding of both fibronectin and fibrinogen by lactobacilli is greatly increased, up to 50 fold, when the pH is reduced from 7.0 to 5.0. Re-exposing the lactobacilli to a neutral pH environment releases most of the bound proteins, but the amount still remaining bound to the cell is several times more than is bound at neutral pH. Lactobacilli will also bind to the proteins that make up the extracellular matrix of endothelial cells. Lactobacilli bound significantly better to collagen types I and V than to types III and IV (p < 0.01). Further, strains isolated from IE cases, particularly L. rhamnosus strains, bound significantly better to types I and V than did 'normal' strains (p < 0.02). Type V collagen has been demonstrated at the sites of endothelial damage. Thus the binding of lactobacilli, particularly L. rhamnosus to these collagen types may be of importance in the early stages of colonization of the damaged heart valve.(ABSTRACT TRUNCATED AT 400 WORDS)}, }
@article {pmid7927776, year = {1994}, author = {Arora, N and Leppla, SH}, title = {Fusions of anthrax toxin lethal factor with shiga toxin and diphtheria toxin enzymatic domains are toxic to mammalian cells.}, journal = {Infection and immunity}, volume = {62}, number = {11}, pages = {4955-4961}, pmid = {7927776}, issn = {0019-9567}, mesh = {Amino Acid Sequence ; Animals ; *Antigens, Bacterial ; Bacterial Toxins/*chemistry/*toxicity ; Biological Transport ; CHO Cells/drug effects ; Cricetinae ; Diphtheria Toxin/*chemistry/toxicity ; In Vitro Techniques ; Molecular Sequence Data ; Recombinant Fusion Proteins ; Shiga Toxins ; Structure-Activity Relationship ; }, abstract = {To investigate the ability of anthrax toxin lethal factor (LF) to translocate foreign proteins into the cytosol of eukaryotic cells and to characterize the structural requirements of this process, fusion proteins containing a portion of LF and the catalytic domains of either diphtheria toxin or Shiga toxin were constructed. Previous work showed that residues 1 to 254 of anthrax toxin lethal factor (LF1-254) are sufficient for binding to the protective antigen component of the toxin and that portions of Pseudomonas exotoxin A fused to LF1-254 are efficiently translocated to the cytosol of eukaryotic cells (N. Arora and S. H. Leppla, J. Biol. Chem. 268:3334-3341, 1993). In this study, it was found that fusion proteins containing the ADP-ribosylation domain of diphtheria toxin fused at either the amino end or the carboxyl end of LF1-254 are highly toxic to Chinese hamster ovary (CHO) cells, indicating that translocation does not strictly require that the amino terminus of LF be free. A fusion protein containing the ribosome-inactivating A1 subunit of Shiga toxin fused to the carboxyl terminus of LF1-254 was also highly toxic for CHO cells. All fusion proteins were toxic only when administered with the anthrax toxin protective antigen component. The data show that the combination of protective antigen and LF fusion proteins can efficiently import polypeptides from diverse bacterial sources to the cytosol of eukaryotic cells and that LF fusion proteins may have the passenger polypeptides fused at either the amino terminus or the carboxyl terminus of LF1-254. These LF fusion proteins could potentially be used as components of a therapeutic agent when the destruction of certain types of cells is desired (e.g., in treating cancer).}, }
@article {pmid7879503, year = {1994}, author = {Mitrokhin, SD and Amerkhanova, AM and Lapchinskaia, AV and Chankov, SV and Tulupov, VP and Ivanov, AA}, title = {[The development of rapid methods for monitoring the microbial ecology of people in contact with xenobiotics].}, journal = {Zhurnal mikrobiologii, epidemiologii i immunobiologii}, volume = {}, number = {6}, pages = {116-117}, pmid = {7879503}, issn = {0372-9311}, mesh = {Bacterial Infections/diagnosis ; Child, Preschool ; Environmental Exposure/*adverse effects ; Environmental Monitoring/*methods ; Feces/chemistry/microbiology ; Humans ; Intestinal Diseases/diagnosis ; Intestinal Mucosa/metabolism ; Intestines/*microbiology ; Xenobiotics/*adverse effects ; }, }
@article {pmid7873329, year = {1994}, author = {Ross, T and McMeekin, TA}, title = {Predictive microbiology.}, journal = {International journal of food microbiology}, volume = {23}, number = {3-4}, pages = {241-264}, doi = {10.1016/0168-1605(94)90155-4}, pmid = {7873329}, issn = {0168-1605}, mesh = {Bacteria/*growth &amp; development ; Environment ; *Food Microbiology ; *Models, Theoretical ; }, abstract = {Predictive microbiology is based upon the premise that the responses of populations of microorganisms to environmental factors are reproducible, and that by considering environments in terms of identifiable dominating constraints it is possible, from past observations, to predict the responses of those microorganisms. Proponents claim that predictive microbiology offers many benefits to the practice of food microbiology, and there is growing interest internationally. This review considers the origins, benefits and approaches to predictive microbiology and critically considers limitations and potential solutions. It is suggested that the traditional delineation between kinetic and probabilistic models is artificial, and that the two approaches represent the opposite ends of a spectrum of modelling needs. It is concluded: that despite the complexity of many food systems predictive modelling can be successfully applied; that strategies based on predictive models can simplify problems and allow useful predictions and analyses to be made; that the full potential of the technique has not yet been realised; and that "predictive microbiology" may be seen as providing a rational framework for understanding the microbial ecology of food.}, }
@article {pmid7823039, year = {1994}, author = {Padan, E and Schuldiner, S}, title = {Molecular physiology of the Na+/H+ antiporter in Escherichia coli.}, journal = {The Journal of experimental biology}, volume = {196}, number = {}, pages = {443-456}, doi = {10.1242/jeb.196.1.443}, pmid = {7823039}, issn = {0022-0949}, mesh = {Amino Acid Sequence ; Escherichia coli/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; *Genes, Bacterial ; Homeostasis ; Models, Biological ; Molecular Sequence Data ; Protein Structure, Secondary ; Sodium-Hydrogen Exchangers/chemistry/genetics/*physiology ; Transcription, Genetic ; }, abstract = {All living cells maintain an inwardly directed Na+ gradient and a constant intracellular pH. Na+/H+ antiporters have been assigned an essential role in these homeostatic mechanisms in all cells. In Escherichia coli, two Na+/H+ antiporter genes, nhaA and nhaB, have been cloned. Deletion of either one or both showed that NhaA is essential for adaptation to high salinity, for growth at alkaline pH in the presence of Na+ and for challenging Li+ toxicity. NhaB confers tolerance to low levels of Na+ and becomes essential when the activity of NhaA limits growth. The adaptive response to Na+ is mediated by the positive regulator nhaR, which transduces the signal (intracellular Na+) to expression of the nhaA gene. We have identified Glu-134 of NhaR as part of the 'Na+ sensor' of NhaA. In agreement with the role of NhaA in pH homeostasis, its Na(+)-dependent expression is enhanced at alkaline pH. Reconstitution of pure NhaA and NhaB in proteoliposomes demonstrates that, whereas both are electrogenic (the H+/Na+ stoichiometry of NhaA is 2), only NhaA is pH-dependent, increasing its activity 1000-fold between pH 7 and 8.5. Mutating all the histidines of NhaA shows that His-226 is part of the 'pH sensor' of NhaA.}, }
@article {pmid7723660, year = {1994}, author = {Vadheim, KL and Singh, Y and Keith, JM}, title = {Expression and mutagenesis of recombinant cholera toxin A subunit.}, journal = {Microbial pathogenesis}, volume = {17}, number = {5}, pages = {339-346}, doi = {10.1006/mpat.1994.1079}, pmid = {7723660}, issn = {0882-4010}, mesh = {Adenosine Diphosphate Ribose/metabolism ; Amino Acid Sequence ; Base Sequence ; Cholera Toxin/biosynthesis/*genetics/metabolism ; DNA Mutational Analysis ; Molecular Sequence Data ; Recombinant Proteins/biosynthesis ; Structure-Activity Relationship ; }, abstract = {ADP-ribosylating protein exotoxins from Vibrio cholerae (CT) and Escherichia coli (LT-I) share two short regions of sequence similarity with Bordetella pertussis toxin (PT). Previous studies have indicated that substitution of arginine for lysine 7 within the first region of CT drastically decreases ADP ribosyltransferase activity. We have more closely defined the role of other amino acids in this region by generating modified proteins in which arginine 7 was replaced with lysine (R7K), aspartate 9 was replaced with arginine (D9R), glycine was substituted for proline 12 (P12G), amino acids 6 to 13 were deleted (delta 613) or the C-terminal KDEL sequence was changed to NEDL. The modified proteins R7K, D9R and delta 613 exhibited undetectable ADP ribosyltransferase activity. Comparison of the tryptic digest of R7K with native CT suggested that changes in protein conformation may be responsible for the loss of ADP-ribosylation activity.}, }
@article {pmid7929330, year = {1994}, author = {Arora, N and Williamson, LC and Leppla, SH and Halpern, JL}, title = {Cytotoxic effects of a chimeric protein consisting of tetanus toxin light chain and anthrax toxin lethal factor in non-neuronal cells.}, journal = {The Journal of biological chemistry}, volume = {269}, number = {42}, pages = {26165-26171}, pmid = {7929330}, issn = {0021-9258}, mesh = {Animals ; *Antigens, Bacterial ; Bacterial Toxins/*toxicity ; Base Sequence ; CHO Cells ; Cells, Cultured ; Cricetinae ; Mice ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Neurons/drug effects ; Rats ; Recombinant Fusion Proteins/*toxicity ; Tetanus Toxin/*toxicity ; Zinc/metabolism ; }, abstract = {The light chain of tetanus toxin is a zinc endoprotease that inhibits neurotransmitter release by selective proteolysis of the synaptic vesicle-associated protein synaptobrevin/vesicle-associated membrane protein. Cellubrevin is a homologue of synaptobrevin that is found in most cell types and is also a substrate for tetanus toxin. The lack of receptors for tetanus toxin on most cell types has made studies of tetanus toxin action in non-neuronal cells difficult. To characterize tetanus toxin effects in non-neuronal cells, a fusion protein consisting of the 254 amino-terminal amino acids of lethal factor (LF) of anthrax toxin and tetanus toxin light chain (LC) was prepared. This protein (LF-LC) inhibited evoked glycine release from primary spinal cord neurons at concentrations between 1.0 and 100 ng/ml. LF-LC was cytotoxic to RAW 264.7, ANA-1 cells (mouse macrophage cell lines), and Chinese hamster ovary cells in a dose-dependent manner. These effects required the presence of protective antigen, the receptor binding component of anthrax toxin. In contrast, LF-LC was not cytotoxic to RBL-2H3, Vero, or mouse hybridoma cell lines. Mutagenesis of conserved amino acids (His237 and Glu234) in the zinc-binding motif of LC resulted in fusion proteins having no biological activity. LF-LC did not inhibit regulated secretion of serotonin in RBL-2H3 cells or constitutive secretion in any non-neuronal cell lines as measured in several different assays. We suggest that the cytotoxic effects of LF-LC result from inhibition of a specific intracellular membrane fusion event mediated by cellubrevin.}, }
@article {pmid7935810, year = {1994}, author = {Olsen, GJ}, title = {Microbial ecology. Archaea, Archaea, everywhere.}, journal = {Nature}, volume = {371}, number = {6499}, pages = {657-658}, doi = {10.1038/371657a0}, pmid = {7935810}, issn = {0028-0836}, mesh = {Animals ; Archaea/classification/*isolation &amp; purification ; Phylogeny ; Plankton ; }, }
@article {pmid7845353, year = {1994}, author = {Rossbach, S and Kulpa, DA and Rossbach, U and de Bruijn, FJ}, title = {Molecular and genetic characterization of the rhizopine catabolism (mocABRC) genes of Rhizobium meliloti L5-30.}, journal = {Molecular &amp; general genetics : MGG}, volume = {245}, number = {1}, pages = {11-24}, pmid = {7845353}, issn = {0026-8925}, mesh = {Amino Acid Sequence ; *Bacterial Proteins ; Base Sequence ; DNA, Plant ; *Genes, Bacterial ; Inositol/*analogs &amp; derivatives/metabolism ; Medicago sativa/microbiology ; Molecular Sequence Data ; Multigene Family ; *Periplasmic Proteins ; Plant Proteins/*genetics/metabolism ; Protein Binding ; Sequence Deletion ; Sequence Homology, Amino Acid ; Sinorhizobium meliloti/*genetics/metabolism ; }, abstract = {Rhizopine (L-3-O-methyl-scyllo-inosamine, 3-O-MSI) is a symbiosis-specific compound, which is synthesized in nitrogen-fixing nodules of Medicago sativa induced by Rhizobium meliloti strain L5-30. 3-O-MSI is thought to function as an unusual growth substrate for R. meliloti L5-30, which carries a locus (mos) responsible for its synthesis closely linked to a locus (moc) responsible for its degradation. Here, the essential moc genes were delimited by Tn5 mutagenesis and shown to be organized into two regions, separated by 3 kb of DNA. The DNA sequence of a 9-kb fragment spanning the two moc regions was determined, and four genes were identified that play an essential role in rhizopine catabolism (mocABC and mocR). The analysis of the DNA sequence and the amino acid sequence of the deduced protein products revealed that MocA resembles NADH-dependent dehydrogenases. MocB exhibits characteristic features of periplasmic-binding proteins that are components of high-affinity transport systems. MocC does not share significant homology with any protein in the database. MocR shows homology with the GntR class of bacterial regulator proteins. These results suggest that the mocABC genes are involved in the uptake and subsequent degradation of rhizopine, whereas mocR is likely to play a regulatory role.}, }
@article {pmid7927711, year = {1994}, author = {Kolenbrander, PE and Andersen, RN and Ganeshkumar, N}, title = {Nucleotide sequence of the Streptococcus gordonii PK488 coaggregation adhesin gene, scaA, and ATP-binding cassette.}, journal = {Infection and immunity}, volume = {62}, number = {10}, pages = {4469-4480}, pmid = {7927711}, issn = {0019-9567}, mesh = {Adenosine Triphosphate/*metabolism ; Amino Acid Sequence ; *Bacterial Adhesion ; Bacterial Proteins/*genetics ; Base Sequence ; Carrier Proteins/*genetics ; DNA, Bacterial/chemistry ; *Genes, Bacterial ; Membrane Proteins/analysis ; Molecular Sequence Data ; Open Reading Frames ; Restriction Mapping ; Streptococcus/*genetics ; Zinc/metabolism ; }, abstract = {Human oral viridans group streptococci that coaggregate with Actinomyces naeslundii PK606 express surface proteins related to ScaA, the coaggregation-mediating adhesin of Streptococcus gordonii PK488 (R. N. Andersen, N. Ganeshkumar, and P. E. Kolenbrander, Infect. Immun. 61:981-987, 1993). The nucleotide sequence of the 6,125-bp EcoRI insert of pRA1, containing scaA, the gene encoding ScaA, was determined. Six open reading frames (ORFs) were identified. The orientation of four ORFs, two upstream (ORF 1 and ORF 2) and one downstream (ORF 4) of scaA (ORF 3), indicated transcription in one direction, whereas ORF 5 and ORF 6 were transcribed divergently. Computer analysis of the deduced amino acid sequences identified a consensus binding site for ATP (GxxGxGKS) in the putative 28,054-Da protein encoded by ORF 1. ORF 2 potentially encoded a hydrophobic protein of 29,705 Da with six potential membrane-spanning regions. ScaA was 310 amino acids, 34,787 Da, and contained the lipoprotein consensus sequence LxxC, also reported for the ScaA-related proteins SsaB, FimA, and PsaA from Streptococcus sanguis 12, Streptococcus parasanguis FW213, and Streptococcus pneumoniae R36A, respectively. ORF 4 potentially encoded a 163-amino-acid protein of 17,912 Da, which was nearly identical to the downstream adjacent gene products of ssaB, fimA, and psaA. No significant homology with other proteins was found with the putative ORF 5 gene product, a 229-amino-acid protein of 25,107 Da. ORF 6 was incomplete and encoded a protein larger than 564 amino acids. This putative protein had a consensus Zn2+ binding motif, HExxH, found among bacterial thermolysins and mammalian neutral endopeptidases and was 40% identical to a homologous 210-amino-acid region of human enkephalinase. The genetic organization of ORFs 1, 2, and 3 was similar to those of the bacterial periplasmic-binding protein-dependent transport systems of gram-negative bacteria and binding-lipoprotein-dependent transport systems of gram-positive bacteria, and these genes appeared to encode ABC (ATP-binding cassette) proteins. This report describes a cell-to-cell adherence function associated with an ATP-binding cassette.}, }
@article {pmid8090765, year = {1994}, author = {Korona, R and Nakatsu, CH and Forney, LJ and Lenski, RE}, title = {Evidence for multiple adaptive peaks from populations of bacteria evolving in a structured habitat.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {91}, number = {19}, pages = {9037-9041}, pmid = {8090765}, issn = {0027-8424}, mesh = {Adaptation, Biological ; Bacteria/*growth &amp; development ; Genetic Variation ; Genetics, Population ; Soil Microbiology ; }, abstract = {Natural selection tends to promote the divergence of populations living in different environments. Even in identical environments, however, replicate populations may diverge if they find alternative adaptive solutions. We describe the evolution of 18 bacterial populations (Comamonas sp.) founded from a single progenitor genotype and propagated separately for 1000 generations in two distinct environments, one physically unstructured (mass-action liquid) and the other structured (agar surfaces). Phenotypic diversity, as reflected in colony morphology, was greater in the structured habitat than in the unstructured habitat. More importantly, the trajectories for mean fitness, as measured by competition against the common ancestor, were more divergent for populations in the structured habitat than those in the unstructured habitat. Structured environments may accelerate evolutionary diversification by promoting genetic polymorphisms within populations, thereby increasing the complexity of genetic constraints that allow divergence among replicate populations.}, }
@article {pmid8071203, year = {1994}, author = {Ka, JO and Tiedje, JM}, title = {Integration and excision of a 2,4-dichlorophenoxyacetic acid-degradative plasmid in Alcaligenes paradoxus and evidence of its natural intergeneric transfer.}, journal = {Journal of bacteriology}, volume = {176}, number = {17}, pages = {5284-5289}, pmid = {8071203}, issn = {0021-9193}, mesh = {2,4-Dichlorophenoxyacetic Acid/*metabolism ; Alcaligenes/*genetics/growth &amp; development/*metabolism ; Blotting, Southern ; Conjugation, Genetic ; Electrophoresis, Agar Gel ; Endodeoxyribonucleases ; Genes, Bacterial ; *Introns ; Plasmids/isolation &amp; purification/*metabolism ; Restriction Mapping ; }, abstract = {A self-transmissible 2,4-dichlorophenoxyacetic acid (2,4-D)-degradative plasmid, pKA2, has been identified in a new 2,4-D-degrading strain, Alcaligenes paradoxus 2811P, isolated from agricultural soil. pKA2 occurred as a 42.9-kb plasmid in strain 2811P. A derivative strain, 2811C, was isolated from a stock culture in which the entire pKA2 plasmid was apparently integrated into the host chromosome without loss of the 2,4-D+ phenotype. This interpretation is based on the disappearance of a free plasmid DNA band, a shift in the tfdA-hybridizing band to the chromosome, loss of transmissibility of the 2,4-D+ trait, and appropriate shifts in Southern hybridization bands of plasmid DNA compared with whole-cell DNA. The integrated plasmid of strain 2811C was excised either precisely or imprecisely after continued transfer on 2,4-D-containing medium. This suggests that a chromosome-free plasmid cycle may occur to optimize fitness under conditions of specific resource fluctuation. Another new 2,4-D-degrading strain, Pseudomonas pickettii 712, which was isolated from the same field plot but at a different time, was found to carry a plasmid that is nearly identical to pKA2. The plasmid of this strain, pKA4, is 40.9 kb long and has features in common with pKA2, such as high self-transmissibility, hybridization only to the tfdA gene among the 2,4-D-metabolic genes of 2,4-D-degradative plasmid pJP4, and similar restriction endonuclease-generated fragments. Furthermore, the genetic homology between the two plasmids was high since all fragments of pKA2 hybridized to pKA4. These results suggest that these two plasmids are closely related and thus their occurrence in two genera in nature is the result of natural horizontal gene transfer.}, }
@article {pmid8058228, year = {1994}, author = {McDonald, HM and O'Loughlin, JA and Vigneswaran, R and Jolley, PT and McDonald, PJ}, title = {Bacterial vaginosis in pregnancy and efficacy of short-course oral metronidazole treatment: a randomized controlled trial.}, journal = {Obstetrics and gynecology}, volume = {84}, number = {3}, pages = {343-348}, pmid = {8058228}, issn = {0029-7844}, mesh = {Administration, Oral ; Adult ; Double-Blind Method ; Drug Administration Schedule ; Female ; Follow-Up Studies ; *Gardnerella vaginalis ; Humans ; Metronidazole/*administration &amp; dosage/therapeutic use ; Pregnancy ; Pregnancy Complications, Infectious/*drug therapy/epidemiology/microbiology ; Time Factors ; Vaginosis, Bacterial/*drug therapy/epidemiology/microbiology ; }, abstract = {OBJECTIVE: To characterize the natural history of bacterial vaginosis in pregnancy and to assess the efficacy of short courses of oral metronidazole therapy for long-term suppression of bacterial vaginosis flora.<br><br>METHODS: This was a randomized, double-blind, placebo-controlled study of two 2-day courses of metronidazole (400 mg twice daily) in pregnant women with bacterial vaginosis (by Gram stain) and/or heavy growth of Gardnerella vaginalis. The first course was given at 24 weeks' gestation and a second course at 29 weeks if the follow-up vaginal swab grew G vaginalis. Follow-up swabs were performed at 28, 32, and 36 weeks' gestation.<br><br>RESULTS: On the basis of their G vaginalis colonization, 196 women were enrolled, and 137 were evaluable for efficacy, including 66 with bacterial vaginosis. The microbial ecology of bacterial vaginosis in 36 women in the placebo group was relatively stable, with 72% persistence at 28 weeks and 57% at 32 weeks' gestation. Metronidazole effectively suppressed bacterial vaginosis for 4 weeks after the first course in 76%, compared with 28% in the placebo group, and had a cumulative efficacy of 87% compared to 44% 4 weeks after the second course (odds ratio 0.12, 95% confidence interval 0.03-0.5).<br><br>CONCLUSIONS: The microbial ecology of bacterial vaginosis in pregnant women is relatively stable. Long-term suppression of bacterial vaginosis flora for 2-3 months can be achieved by short courses of metronidazole therapy in 87% of women in mid-pregnancy. Because bacterial vaginosis has been associated with an increased risk of preterm labor, these findings provide the foundation for an intervention study of women with bacterial vaginosis in pregnancy.}, }
@article {pmid7854123, year = {1994}, author = {Klimpel, KR and Arora, N and Leppla, SH}, title = {Anthrax toxin lethal factor contains a zinc metalloprotease consensus sequence which is required for lethal toxin activity.}, journal = {Molecular microbiology}, volume = {13}, number = {6}, pages = {1093-1100}, doi = {10.1111/j.1365-2958.1994.tb00500.x}, pmid = {7854123}, issn = {0950-382X}, mesh = {Amino Acid Sequence ; Animals ; *Antigens, Bacterial ; Bacillus anthracis/*enzymology/genetics/pathogenicity ; Bacterial Toxins/antagonists &amp; inhibitors/*chemistry/genetics/toxicity ; Cations, Divalent/metabolism ; Cell Line ; Consensus Sequence ; Macrophages/drug effects ; Metalloendopeptidases/*chemistry ; Mice ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Protease Inhibitors/pharmacology ; Recombinant Fusion Proteins/toxicity ; Sequence Alignment ; Sequence Homology, Amino Acid ; Structure-Activity Relationship ; Virulence ; Zinc/*metabolism ; }, abstract = {Comparison of the anthrax toxin lethal factor (LF) amino acid sequence with sequences in the Swiss protein database revealed short regions of similarity with the consensus zinc-binding site, HEXXH, that is characteristic of metalloproteases. Several protease inhibitors, including bestatin and captopril, prevented intoxication of macrophages by lethal toxin. LF was fully inactivated by site-directed mutagenesis that substituted Ala for either of the residues (H-686 and H-690) implicated in zinc binding. Similarly, LF was inactivated by substitution of Cys for E-687, which is thought to be an essential part of the catalytic site. In contrast, replacement of E-720 and E-721 with Ala had no effect on LF activity. LF bound 65Zn both in solution and on protein blots. The 65Zn binding was reduced for several of the LF mutants. These data suggest that anthrax toxin LF is a zinc metallopeptidase, the catalytic function of which is responsible for the lethal activity observed in cultured cells and in animals.}, }
@article {pmid7967617, year = {1994}, author = {Lenski, RE and May, RM}, title = {The evolution of virulence in parasites and pathogens: reconciliation between two competing hypotheses.}, journal = {Journal of theoretical biology}, volume = {169}, number = {3}, pages = {253-265}, doi = {10.1006/jtbi.1994.1146}, pmid = {7967617}, issn = {0022-5193}, mesh = {Animals ; *Biological Evolution ; Host-Parasite Interactions ; Humans ; Mathematics ; *Models, Genetic ; Parasites/*pathogenicity/physiology ; Parasitic Diseases/immunology ; Virulence/*genetics ; }, abstract = {According to conventional wisdom, parasites and pathogens should evolve reduced virulence to their hosts, because more virulent parasites and pathogens are more likely to drive their hosts, and themselves, to extinction. But this view has been criticized for its reliance on group selection. According to an alternative perspective, selection will favor whatever level of virulence maximizes the rate of increase of the parasite or pathogen. This optimum virulence depends on the functional relationship between a parasite or pathogen's transmissibility and its effect on host mortality, with selection often favoring an intermediate degree of virulence. The thesis of this paper is that models in which intermediate levels of virulence are favored lead quite naturally to the further conclusion that parasites and pathogens should-up to a point-become less virulent over time, once the feedbacks between ecological and evolutionary processes are incorporated into the analysis. As a consequence of successive adaptations by the parasite or pathogen, the density of susceptible hosts is reduced, thereby altering the balance between selective forces so as to favor reduced virulence. However, the evolutionarily stable strategy that is achieved is bounded away from complete avirulence. We conclude that models in which intermediate virulence is favored do not necessarily contradict the conventional wisdom in the long run; in fact, these models provide a simple mechanistic explanation for the evolution of reduced virulence.}, }
@article {pmid8082830, year = {1994}, author = {Chalot, M and Brun, A and Finlay, RD and Söderström, B}, title = {Respiration of [14C]alanine by the ectomycorrhizal fungus Paxillus involutus.}, journal = {FEMS microbiology letters}, volume = {121}, number = {1}, pages = {87-91}, doi = {10.1111/j.1574-6968.1994.tb07080.x}, pmid = {8082830}, issn = {0378-1097}, mesh = {Agaricales/*metabolism ; Alanine/*metabolism ; Oxygen Consumption ; Symbiosis ; }, abstract = {The ectomycorrhizal fungus Paxillus involutus efficiently took up exogenously supplied [14C]alanine and rapidly converted it to pyruvate, citrate, succinate, fumarate and to CO2, thus providing direct evidence for the utilisation of alanine as a respiratory substrate. [14C]alanine was further actively metabolised to glutamate, glutamine and aspartate. Exposure to aminooxyacetate completely suppressed 14CO2 evolution and greatly reduced the flow of carbon from [14C]alanine to tricarboxylic acid cycle intermediates and amino acids, suggesting that alanine aminotransferase plays a pivotal role in alanine metabolism in Paxillus involutus.}, }
@article {pmid7963470, year = {1994}, author = {Loulergue, J and Audurier, A and DeLarbre, JM and De Gialluly, C}, title = {Changes in microbial ecology and use of cloxacillin.}, journal = {The Journal of hospital infection}, volume = {27}, number = {4}, pages = {275-283}, doi = {10.1016/0195-6701(94)90115-5}, pmid = {7963470}, issn = {0195-6701}, mesh = {Carrier State/drug therapy/epidemiology ; Cloxacillin/*pharmacology/therapeutic use ; Disease Outbreaks/statistics &amp; numerical data ; Drug Utilization ; France/epidemiology ; Hospital Units/statistics &amp; numerical data ; Humans ; Incidence ; Infection Control ; *Methicillin Resistance ; Orthopedics ; Staphylococcal Infections/drug therapy/epidemiology/*prevention &amp; control ; Staphylococcus aureus/*drug effects ; Trauma Centers/*statistics &amp; numerical data ; }, abstract = {There is generally a positive correlation between antibiotic consumption and incidence of resistance to antibiotics used either for prophylaxis or therapy in human infections. This was not the case for two surgical wards in our hospital. A 15-year study showed that the incidence of methicillin-resistant Staphylococcus aureus (MRSA) was unrelated to cloxacillin consumption, and in fact fell after introduction into the two wards of an antibiotic policy based on cloxacillin. The two wards, a 90-bed orthopaedic unit and a 60-bed trauma unit, had an incidence of MRSA that has remained below the hospital average (23% in 1989, 32% in 1992). Before introduction of the policy the incidence of MRSA in 1977-1979 in the orthopaedic ward was 31%, and in the trauma ward 33%. In 1989 an investigation revealed no MRSA carriers in staff of either ward. In contrast, seven MRSA carriers were found among staff and patients of three other surgical units selected, because the percentage of MRSA isolated was above the average in our hospital. However, a different type of patient is found in these units, the treatment techniques differ and broader-spectrum antibiotics are used. In addition to the usual precautions regarding nursing care and isolation techniques, the best means of reducing MRSA epidemics is to reduce the reservoir of carriers. The fall in the MRSA infection rate in orthopaedic and traumatology wards can be explained by antibiotic policy but also by other infection control measures.}, }
@article {pmid8041701, year = {1994}, author = {Lenski, RE and Travisano, M}, title = {Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {91}, number = {15}, pages = {6808-6814}, pmid = {8041701}, issn = {0027-8424}, mesh = {*Adaptation, Physiological ; *Biological Evolution ; Escherichia coli/genetics/*physiology ; Fossils ; *Genetic Variation ; Selection, Genetic ; }, abstract = {We followed evolutionary change in 12 populations of Escherichia coli propagated for 10,000 generations in identical environments. Both morphology (cell size) and fitness (measured in competition with the ancestor) evolved rapidly for the first 2000 generations or so after the populations were introduced into the experimental environment, but both were nearly static for the last 5000 generations. Although evolving in identical environments, the replicate populations diverged significantly from one another in both morphology and mean fitness. The divergence in mean fitness was sustained and implies that the populations have approached different fitness peaks of unequal height in the adaptive landscape. Although the experimental time scale and environment were microevolutionary in scope, our experiments were designed to address questions concerning the origin as well as the fate of genetic and phenotypic novelties, the repeatability of adaptation, the diversification of lineages, and thus the causes and consequences of the uniqueness of evolutionary history. In fact, we observed several hallmarks of macroevolutionary dynamics, including periods of rapid evolution and stasis, altered functional relationships between traits, and concordance of anagenetic and cladogenetic trends. Our results support a Wrightian interpretation, in which chance events (mutation and drift) play an important role in adaptive evolution, as do the complex genetic interactions that underlie the structure of organisms.}, }
@article {pmid8075805, year = {1994}, author = {Tunlid, A and Rosén, S and Ek, B and Rask, L}, title = {Purification and characterization of an extracellular serine protease from the nematode-trapping fungus Arthrobotrys oligospora.}, journal = {Microbiology (Reading, England)}, volume = {140 (Pt 7)}, number = {}, pages = {1687-1695}, doi = {10.1099/13500872-140-7-1687}, pmid = {8075805}, issn = {1350-0872}, mesh = {Amino Acid Sequence ; Animals ; Glycosylation ; Helminth Proteins/*metabolism ; Isoelectric Point ; Mitosporic Fungi/*enzymology ; Molecular Sequence Data ; Molecular Weight ; Rhabditida/*drug effects ; Sequence Homology, Amino Acid ; Serine Endopeptidases/isolation &amp; purification/*metabolism ; Substrate Specificity ; }, abstract = {When grown in liquid cultures allowing the formation of nematode traps, the fungus Arthrobotrys oligospora produced two extracellular proteases hydrolysing the chromogenic substrate Azocoll. The protease activity was separated into two fractions (FI and FII) using anion-exchange chromatography. In bioassays, protease(s) present in FII immobilized the free-living nematode Panagrellus redivivus indicating that the enzyme(s) might be involved in the infection of nematodes. A protease designated PII was purified from FII to apparent homogeneity by hydrophobic interaction and size-exclusion chromatography, resulting in an approximately 15-fold increase in specific activity. The purified enzyme was glycosylated, had a molecular mass of approximately 35 kDa (gel filtration) and an isoelectric point of pH 4.6. PII immobilized P. redivivus in bioassays and hydrolysed proteins of the purified cuticle. The enzyme hydrolysed several protein substrates including casein, bovine serum albumin and gelatin, but not native collagen. Examination of substrate specificity with synthetic peptides showed that PII readily hydrolysed tripeptides with aromatic or basic amino acids including N-benzoyl-L-phenylalanyl-L-valyl-L-arginine-4-nitroanilide (Bz-Phe-Val-Arg-NA) and succinyl-glycyl-glycyl-L-phenylalanine-4-nitroanilide (Suc-Gly-Gly-Phe-NA). Mono-peptides were hydrolysed at considerably slower rates. PII had an optimum activity between pH 7 and 9 and was susceptible to autodegradation. PII was inhibited by several serine protease inhibitors including phenylmethylsulfonyl fluoride (PMSF), chymostatin and antipain. The protease was N-terminally blocked, but the sequence of one internal peptide showed a high homology with a region containing the active site histidine residue of the subtilisin family of serine proteases.}, }
@article {pmid7936830, year = {1994}, author = {Panigrahi, P and Gupta, S and Gewolb, IH and Morris, JG}, title = {Occurrence of necrotizing enterocolitis may be dependent on patterns of bacterial adherence and intestinal colonization: studies in Caco-2 tissue culture and weanling rabbit models.}, journal = {Pediatric research}, volume = {36}, number = {1 Pt 1}, pages = {115-121}, doi = {10.1203/00006450-199407001-00021}, pmid = {7936830}, issn = {0031-3998}, support = {HD 29735/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Bacterial Adhesion/*physiology ; Cell Line ; Colony Count, Microbial ; Disease Models, Animal ; Enterocolitis, Pseudomembranous/*microbiology ; Gram-Positive Bacteria/isolation &amp; purification/physiology ; Humans ; Infant, Newborn ; Intestines/*microbiology ; Rabbits ; Virulence ; Weaning ; }, abstract = {Necrotizing enterocolitis (NEC) is one of the leading causes of death in neonatal intensive care units. The underlying pathophysiology of NEC is poorly defined, although there is a suggestion that bacterial agents play an important role in the process. In this study, we evaluated bacterial isolates from 17 NEC cases and matched asymptomatic control infants. Isolates from NEC patients were no more likely than control isolates to be adherent to enterocytes, as assessed by a Caco-2 cell tissue culture model. Adherent Escherichia coli isolates, from both NEC cases and controls, were able to cause pathologic changes typical of NEC in a weanling rabbit ileal loop model. Adherence of E. coli strains to Caco-2 cells, and subsequent production of disease in weanling rabbits, could be blocked by coinfection with Gram-positive isolates from control children. In contrast, in three of four instances, adherent E. coli from NEC cases retained their adherence and caused illness in rabbits when coinfected with Gram-positive isolates from the homologous child. Our data suggest that patterns of intestinal adherence, as influenced by the underlying intestinal microbial ecology, play a role in the pathophysiology of NEC.}, }
@article {pmid7865085, year = {1994}, author = {Marsh, PD}, title = {Microbial ecology of dental plaque and its significance in health and disease.}, journal = {Advances in dental research}, volume = {8}, number = {2}, pages = {263-271}, doi = {10.1177/08959374940080022001}, pmid = {7865085}, issn = {0895-9374}, mesh = {Bacteria, Anaerobic/metabolism/pathogenicity ; Dental Caries/microbiology/prevention &amp; control ; Dental Plaque/*microbiology ; Ecosystem ; Gram-Negative Anaerobic Bacteria/metabolism/pathogenicity ; Gram-Positive Bacteria/metabolism/pathogenicity ; Homeostasis/physiology ; Humans ; Periodontal Diseases/microbiology/prevention &amp; control ; }, abstract = {Dental plaque forms naturally on teeth and is of benefit to the host by helping to prevent colonization by exogenous species. The bacterial composition of plaque remains relatively stable despite regular exposure to minor environmental perturbations. This stability (microbial homeostasis) is due in part to a dynamic balance of both synergistic and antagonistic microbial interactions. However, homeostasis can break down, leading to shifts in the balance of the microflora, thereby predisposing sites to disease. For example, the frequent exposure of plaque to low pH leads to inhibition of acid-sensitive species and the selection of organisms with an aciduric physiology, such as mutans streptococci and lactobacilli. Similarly, plaque accumulation around the gingival margin leads to an inflammatory host response and an increased flow of gingival crevicular fluid. The subgingival microflora shifts from being mainly Gram-positive to being comprised of increased levels of obligately anaerobic, asaccharolytic Gram-negative organisms. It is proposed that disease can be prevented or treated not only by targeting the putative pathogens but also by interfering with the processes that drive the breakdown in homeostasis. Thus, the rate of acid production following sugar intake could be reduced by fluoride, alternative sweeteners, and low concentrations of antimicrobial agents, while oxygenating or redox agents could raise the Eh of periodontal pockets and prevent the growth and metabolism of obligately anaerobic species. These views have been incorporated into a modified hypothesis (the "ecological plaque hypothesis") to explain the relationship between the plaque microflora and the host in health and disease, and to identify new strategies for disease prevention.}, }
@article {pmid8195080, year = {1994}, author = {Robrish, SA and Fales, HM and Gentry-Weeks, C and Thompson, J}, title = {Phosphoenolpyruvate-dependent maltose:phosphotransferase activity in Fusobacterium mortiferum ATCC 25557: specificity, inducibility, and product analysis.}, journal = {Journal of bacteriology}, volume = {176}, number = {11}, pages = {3250-3256}, pmid = {8195080}, issn = {0021-9193}, mesh = {Aerobiosis ; Anaerobiosis ; Carbohydrate Sequence ; Cell Membrane Permeability ; Enzyme Induction ; Fusobacterium/*enzymology ; Glucosides/metabolism ; Hydrolysis ; Maltose/*metabolism ; Molecular Sequence Data ; Phosphoenolpyruvate Sugar Phosphotransferase System/*metabolism ; Phosphorylation ; Stereoisomerism ; Sugar Phosphates/*isolation &amp; purification/metabolism ; }, abstract = {Phosphoenolypyruvate-dependent maltose:phosphotransferase activity was induced in cells of Fusobacterium mortiferum ATCC 25557 during growth on maltose. The disaccharide was rapidly metabolized by washed cells maintained under anaerobic conditions, but fermentation ceased immediately upon exposure of the cell suspension to air. Coincidentally, high levels of a phosphorylated derivative accumulated within the cells. Chemical and enzymatic analyses, in conjunction with data from 1H, 13C, and 31P nuclear magnetic resonance spectroscopy, established the structure of the purified compound as 6-O-phosphoryl-alpha-D-glucopyranosyl-(1-4)-D-glucose (maltose 6-phosphate). A method for the preparation of substrate amounts of this commercially unavailable disaccharide phosphate is described. Permeabilized cells of F. mortiferum catalyzed the phosphoenolpyruvate-dependent phosphorylation of maltose under aerobic conditions. However, the hydrolysis of maltose 6-phosphate (to glucose 6-phosphate and glucose) by permeabilized cells or cell-free preparations required either an anaerobic environment or addition of dithiothreitol to aerobic reaction mixtures. The first step in dissimilation of the phosphorylated disaccharide appears to be catalyzed by an oxygen-sensitive maltose 6-phosphate hydrolase. Cells of F. mortiferum, grown previously on maltose, fermented a variety of alpha-linked glucosides, including maltose, turanose, palatinose, maltitol, alpha-methylglucoside, trehalose, and isomaltose. Conversely, cells grown on the separate alpha-glucosides also metabolized maltose. For this anaerobic pathogen, we suggest that the maltose:phosphotransferase and maltose 6-phosphate hydrolase catalyze the phosphorylative translocation and cleavage not only of maltose but also of structurally analogous alpha-linked glucosides.}, }
@article {pmid8195066, year = {1994}, author = {Lenski, RE and Simpson, SC and Nguyen, TT}, title = {Genetic analysis of a plasmid-encoded, host genotype-specific enhancement of bacterial fitness.}, journal = {Journal of bacteriology}, volume = {176}, number = {11}, pages = {3140-3147}, pmid = {8195066}, issn = {0021-9193}, mesh = {Biological Evolution ; Chloramphenicol/pharmacology ; Chloramphenicol Resistance/genetics ; Escherichia coli/drug effects/*physiology ; Genotype ; Plasmids/*genetics ; Promoter Regions, Genetic/genetics ; *Selection, Genetic ; Sequence Deletion ; Tetracycline/pharmacology ; Tetracycline Resistance/*genetics ; }, abstract = {In the absence of antibiotics, carriage of pACYC184 reduces the competitive fitness of an Escherichia coli B genotype that was not previously selected for plasmid carriage, relative to that of an isogenic plasmid-free competitor. However, a host genotype propagated with the plasmid for 500 generations evolved an unexpected competitive advantage from plasmid carriage, relative to its own isogenic plasmid-free segregant. We manipulated the pACYC184 genome in order to identify the plasmid-encoded function that was required for the enhancement of the coevolved host genotype's competitive fitness. Inactivation of the plasmid-encoded tetracycline resistance gene, by deletion of either the promoter region or the entire gene, eliminated the beneficial effect of plasmid carriage for the coevolved host. This beneficial effect for the coevolved host was also manifest with pBR322, which contains a tetracycline resistance gene identical to that of pACYC184 but is otherwise heterologous.}, }
@article {pmid8075833, year = {1994}, author = {Smith, JJ and Scott-Craig, JS and Leadbetter, JR and Bush, GL and Roberts, DL and Fulbright, DW}, title = {Characterization of random amplified polymorphic DNA (RAPD) products from Xanthomonas campestris and some comments on the use of RAPD products in phylogenetic analysis.}, journal = {Molecular phylogenetics and evolution}, volume = {3}, number = {2}, pages = {135-145}, doi = {10.1006/mpev.1994.1016}, pmid = {8075833}, issn = {1055-7903}, mesh = {Blotting, Southern ; DNA, Bacterial/genetics ; Genetic Variation/genetics ; *Phylogeny ; *Polymerase Chain Reaction ; Polymorphism, Genetic/genetics ; Xanthomonas campestris/*genetics ; }, abstract = {As part of our research to determine phylogenetic relationships of organisms within the phytobacterial species Xanthomonas campestris, we have examined the use of the random amplified polymorphic DNA (RAPD) technique. The objective of this aspect of our research was to determine if a valid cladistic character analysis could be carried out by direct comparison of RAPD products separated on ethidium bromide-stained agarose gels. RAPD products were amplified from 47 Xanthomonas campestris DNA templates using a single oligonucleotide primer. These RAPD products were compared and variation was characterized by Southern analysis of both RAPD products and genomic DNA of the 47 bacterial strains using two cloned RAPD products as probes. Analysis of the data set revealed that the RAPD products were not necessarily homologous or independent, crucial prerequisites for characters to be analyzed in a cladistic phylogenetic analysis. It has been commonly assumed that RAPD variation occurs due to insertion/deletion events or alterations in the primer binding site. Within our data set, we demonstrate absence phenotypes arising from the apparent absence of corresponding loci and also due to the preferred synthesis of alternative RAPD products from unrelated loci. These different types of variation are a reflection of different types of genotypic variation, and direct examination of RAPD products did not allow us to distinguish by which mechanism a particular absence phenotype arose. Although this may not be important for phenetic analyses, for analyses of homologous characters using a cladistic approach it is critical. We also detected unrelated, co-migrating RAPD products and multiple related RAPD products within reaction mixtures. These could both contribute to errors in estimates of similarity, important in any phylogenetic analysis. All of these characteristics of RAPD products should be taken into consideration when RAPD products are used for phylogenetic comparisons.}, }
@article {pmid8174436, year = {1994}, author = {Husebye, E and Hellström, PM and Midtvedt, T}, title = {Intestinal microflora stimulates myoelectric activity of rat small intestine by promoting cyclic initiation and aboral propagation of migrating myoelectric complex.}, journal = {Digestive diseases and sciences}, volume = {39}, number = {5}, pages = {946-956}, pmid = {8174436}, issn = {0163-2116}, mesh = {Action Potentials ; Animals ; Bacteria/growth &amp; development ; Eating ; Gastrointestinal Transit ; Germ-Free Life ; Intestine, Small/innervation/*microbiology/physiology ; Male ; *Myoelectric Complex, Migrating ; Rats ; Rats, Sprague-Dawley ; }, abstract = {Microbial modulation of myoelectric activity in small intestine was studied. Germ-free male Sprague-Dawley rats were equipped with bipolar electrodes from the duodenojejunal junction to the midpoint of small intestine. Prior to and one week after introduction of conventional intestinal microflora, 32 +/- 5% and 61 +/- 5% (mean +/- SE), respectively, of activity fronts of the migrating myoelectric complex reached the midpoint (P < 0.05), and the interval between activity fronts in proximal jejunum was reduced from 31.2 +/- 2.0 min to 17.5 +/- 0.8 min, respectively (P < 0.01). The pattern of propagation was more regular after conventionalization. Slow-wave frequency in proximal jejunum was 38.5 +/- 1.2/min in germ-free rats and 43.0 +/- 0.8/min in conventional rats (P < 0.01), but introduction of microflora failed to increase the frequency in germ-free rats. The frequency of spike potentials succeeding jejunal infusion of 5 ml of 12.5% glucose remained unchanged after conventionalization. Statistical analyses showed that the interval between activity fronts varied mainly within rats, whereas the propagation velocity showed statistically significant variability between rats (P < 0.01), regardless of intestinal microflora. Luminal control by the resident microflora is important for physiological cycling and aboral propagation of the migrating myoelectric complex, but seems to be of no major consequence for postprandial myoelectric response.}, }
@article {pmid8144461, year = {1994}, author = {Manch-Citron, JN and London, J}, title = {Expression of the Prevotella loescheii adhesin gene (plaA) is mediated by a programmed frameshifting hop.}, journal = {Journal of bacteriology}, volume = {176}, number = {7}, pages = {1944-1948}, pmid = {8144461}, issn = {0021-9193}, support = {5F32DEO5554/DE/NIDCR NIH HHS/United States ; }, mesh = {*Adhesins, Bacterial ; Amino Acid Sequence ; Bacteria/*genetics ; Bacterial Adhesion/genetics ; Bacterial Proteins/biosynthesis/*genetics ; Base Sequence ; *Gene Expression Regulation, Bacterial ; Genes, Bacterial/*genetics ; Genes, Reporter ; Lac Operon ; Lectins/biosynthesis/*genetics ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Conformation ; Reading Frames/*genetics ; Recombinant Fusion Proteins/biosynthesis ; }, abstract = {The 2.4-kb plaA gene, which encodes a Prevotella loescheii galactoside-specific adhesin, contains a programmed frameshifting hop. The frameshift region consists of two UAA termination codons, two repeats of four identical bases between the terminators, and a stem-loop structure that has the potential to form a pseudoknot located downstream from the second UAA. The stem-loop and pseudoknot are features found in a number of retroviruses where frameshifting is a more common occurrence. The terminators, sequence repeats, and secondary structures were identified in both the P. loescheii plaA gene and the mRNA transcript. An in-frame fusion of the entire plaA frameshift region between codons 9 and 10 of the lacZ gene permitted relatively efficient expression (4 to 25% of that of the control) of beta-galactosidase in Escherichia coli.}, }
@article {pmid8057215, year = {1994}, author = {Midtvedt, AC and Carlstedt-Duke, B and Midtvedt, T}, title = {Establishment of a mucin-degrading intestinal microflora during the first two years of human life.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {18}, number = {3}, pages = {321-326}, doi = {10.1097/00005176-199404000-00012}, pmid = {8057215}, issn = {0277-2116}, mesh = {Anti-Bacterial Agents/pharmacology ; Breast Feeding ; Child Development/physiology ; Child, Preschool ; Diarrhea, Infantile/physiopathology ; Female ; Humans ; Infant ; Infant, Newborn ; Intestines/*microbiology ; Male ; Mucins/*metabolism ; }, abstract = {The establishment of a mucin-degrading intestinal microflora was followed in 30 healthy Swedish children by agar gel electrophoresis of fecal samples taken at 0, 1, 3, 6, 9, 12, 15, 18, 21, and 24 months of age. At 3 months, 18 children showed a limited degree of mucin degradation, while 12 children showed no degradation. In children exclusively breast-fed for at least 4 months, mucin degradation was initiated significantly later than in children who received formula, with or without breast milk, by 1 month of age. Complete degradation of mucin was seen in 21 children after 1 year of age and in all children at 2 years. A positive correlation between increasing age and increased degradation of mucin was found between birth and 1 month and between 6 and 9 months, after standardization for the period of exposure to foods other than breast milk.}, }
@article {pmid8019689, year = {1994}, author = {Lenski, RE and Souza, V and Duong, LP and Phan, QG and Nguyen, TN and Bertrand, KP}, title = {Epistatic effects of promoter and repressor functions of the Tn10 tetracycline-resistance operon of the fitness of Escherichia coli.}, journal = {Molecular ecology}, volume = {3}, number = {2}, pages = {127-135}, doi = {10.1111/j.1365-294x.1994.tb00113.x}, pmid = {8019689}, issn = {0962-1083}, mesh = {*Epistasis, Genetic ; Escherichia coli/*genetics/growth &amp; development ; Genotype ; *Operon ; Plasmids ; *Promoter Regions, Genetic ; Repressor Proteins/*metabolism ; Tetracycline Resistance/*genetics ; }, abstract = {We have been studying the effects of expression of plasmid-borne, Tn10-encoded, tetracycline resistance on the fitness of Escherichia coli K12. We previously demonstrated large reductions in fitness resulting from induced or constitutive expression of the resistance protein; however, any residual expression by the repressed operon was so slight that possession of an inducible resistance function imposed essentially no burden in the absence of antibiotic. Here, we demonstrate two distinct disadvantages for inducible genotypes relative to isogenic constitutive constructs. During the transition from antibiotic-free to antibiotic-containing media, the inducible genotype experiences a longer lag phase prior to growth. In the sustained presence of antibiotic, full induction of the resistance function in the inducible genotype is prevented by the continued action of its repressor. However, these disadvantages may be reduced by increasing the strength of the promoter for the resistance gene in the inducible genotype. Simultaneous consideration of the mode of gene regulation (i.e. constitutive or inducible) and the strength of the resistance-gene promoter (i.e. maximum level of expression) indicates an adaptive landscape with very strong epistasis and, perhaps, multiple fitness peaks.}, }
@article {pmid7912498, year = {1994}, author = {Thiem, SM and Krumme, ML and Smith, RL and Tiedje, JM}, title = {Use of molecular techniques to evaluate the survival of a microorganism injected into an aquifer.}, journal = {Applied and environmental microbiology}, volume = {60}, number = {4}, pages = {1059-1067}, pmid = {7912498}, issn = {0099-2240}, mesh = {Base Sequence ; Biodegradation, Environmental ; Chlorobenzoates/metabolism ; DNA Probes ; DNA, Bacterial/analysis ; Massachusetts ; Molecular Sequence Data ; Oxidation-Reduction ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Pseudomonas/genetics/isolation &amp; purification/*physiology ; *Water Microbiology ; }, abstract = {A PCR primer set and an internal probe that are specific for Pseudomonas sp. strain B13, a 3-chlorobenzoate-metabolizing strain, were developed. Using this primer set and probe, we were able to detect Pseudomonas sp. strain B13 DNA sequences in DNA extracted from aquifer samples 14.5 months after Pseudomonas sp. strain B13 had been injected into a sand and gravel aquifer. This primer set and probe were also used to analyze isolates from 3-chlorobenzoate enrichments of the aquifer samples by Southern blot analysis. Hybridization of Southern blots with the Pseudomonas sp. strain B13-specific probe and a catabolic probe in conjunction with restriction fragment length polymorphism (RFLP) analysis of ribosome genes was used to determine that viable Pseudomonas sp. strain B13 persisted in this environment. We isolated a new 3-chlorobenzoate-degrading strain from one of these enrichment cultures. The B13-specific probe does not hybridize to DNA from this isolate. The new strain could be the result of gene exchange between Pseudomonas sp. strain B13 and an indigenous bacterium. This speculation is based on an RFLP pattern of ribosome genes that differs from that of Pseudomonas sp. strain B13, the fact that identically sized restriction fragments hybridized to the catabolic gene probe, and the absence of any enrichable 3-chlorobenzoate-degrading strains in the aquifer prior to inoculation.}, }
@article {pmid8300195, year = {1994}, author = {Gordon, VM and Leppla, SH}, title = {Proteolytic activation of bacterial toxins: role of bacterial and host cell proteases.}, journal = {Infection and immunity}, volume = {62}, number = {2}, pages = {333-340}, pmid = {8300195}, issn = {0019-9567}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Toxins/genetics/*metabolism ; Binding Sites ; Endopeptidases/*metabolism ; Eukaryotic Cells/metabolism ; Furin ; Humans ; Immunotoxins/metabolism ; Molecular Sequence Data ; Substrate Specificity ; Subtilisins/metabolism ; }, }
@article {pmid8162189, year = {1994}, author = {Kokjohn, TA and Miller, RV}, title = {IncN plasmids mediate UV resistance and error-prone repair in Pseudomonas aeruginosa PAO.}, journal = {Microbiology (Reading, England)}, volume = {140 (Pt 1)}, number = {}, pages = {43-48}, doi = {10.1099/13500872-140-1-43}, pmid = {8162189}, issn = {1350-0872}, mesh = {DNA Repair/genetics ; Escherichia coli/genetics ; Gene Expression ; Mutagenesis ; Phenotype ; Plasmids/*genetics ; Pseudomonas aeruginosa/*genetics/metabolism/radiation effects ; Radiation Tolerance/genetics ; Ultraviolet Rays ; }, abstract = {While it seems likely that the ability to induce the expression of recA-controlled genes is nearly universal among the eubacteria, the expression of plasmid-borne ultraviolet (UV-resistance and mutagenesis genes seems to be species-dependent in a complex fashion. Some plasmids encoding UV-resistance and mutagenesis functions only express these phenotypes in a select number of bacterial species. Several UV-resistance plasmids that express these functions in Escherichia coli are either unstable or simply do not express the UV-resistance-mutagenesis phenotype in Pseudomonas aeruginosa. In order to clarify the role of these plasmids in microbial ecology, we have undertaken a study of the ability of the well-characterized UV-resistance IncN plasmids pKM101 and R46 to express the UV-resistance phenotype in P. aeruginosa. In addition, we have examined the IncP plasmids RP4 and R68.45, observed to confer a UV-resistant phenotype upon Myxococcus xanthus, for the ability to express this phenotype in P. aeruginosa. Our experiments reveal that while pKM101 and R46 transfer to P. aeruginosa at a very low frequency, these plasmids, once transferred, are maintained and clearly support the expression of the UV-resistance and mutagenesis phenotype observed in E. coli. Studies of plasmids R68.45 and RP4 in P. aeruginosa revealed that they do not express UV-resistance functions in this species. UV-resistance plasmids may play an important role in the natural ecology of bacterial habitats exposed to solar radiation or to various DNA-damaging natural and man-made chemicals.}, }
@article {pmid8123562, year = {1994}, author = {Rainey, PB and Thompson, IP and Palleroni, NJ}, title = {Genome and fatty acid analysis of Pseudomonas stutzeri.}, journal = {International journal of systematic bacteriology}, volume = {44}, number = {1}, pages = {54-61}, doi = {10.1099/00207713-44-1-54}, pmid = {8123562}, issn = {0020-7713}, mesh = {Fatty Acids/*analysis ; *Genes, Bacterial ; Pseudomonas/chemistry/*classification/genetics ; Restriction Mapping ; }, abstract = {A genome and fatty acid analysis of 16 Pseudomonas stutzeri reference strains having DNA compositions ranging from 62.2 to 65.5 mol% G+C was performed by pulsed-field gel electrophoresis of XbaI and SpeI macrorestriction fragments and gas chromatography of total cellular fatty acids. Macrorestriction fragment patterns were evaluated by using previously described algorithms (D. Grothues and B. Tümmler, Mol. Microbiol. 5:2763-2776, 1991), and the results allowed us to subdivide the species into two groups which correlated with G+C content. Two examples of recent strain divergence were observed among clinical isolates, but in general a marked degree of heterogeneity was observed in the macrorestriction fragment patterns, and even phenotypically similar strains produced divergent patterns. While the differences were not sufficiently great to exclude any strain from P. stutzeri, they suggest that recombination and niche-specific selection may be significant factors responsible for generating and maintaining the heterogeneity inherent in the species. Genome sizes were estimated from the sums of SpeI restriction fragment sizes and ranged from 3.4 to 4.3 Mbp; the genome sizes of the low-G+C-content strains (G+C contents, approximately 62 mol%) were confined to a narrow range between 3.9 and 4.1 Mbp. An examination of the distributions of macrorestriction fragments resulting from digestion with XbaI and SpeI showed that both distributions differed significantly from the expected (random) distribution, suggesting that there is a supragenic level of chromosomal organization. An analysis of fatty acid methyl ester data by using Microbial Identification System software revealed a similar correlation between phenotype and G+C content, indicating that division of the species is possible by the method used in this study.(ABSTRACT TRUNCATED AT 250 WORDS)}, }
@article {pmid7826008, year = {1994}, author = {Burlage, RS and Kuo, CT}, title = {Living biosensors for the management and manipulation of microbial consortia.}, journal = {Annual review of microbiology}, volume = {48}, number = {}, pages = {291-309}, doi = {10.1146/annurev.mi.48.100194.001451}, pmid = {7826008}, issn = {0066-4227}, mesh = {Bacteria/genetics ; *Bacterial Physiological Phenomena ; Ecology ; *Genes, Reporter ; Luciferases/genetics ; Luminescent Measurements ; }, abstract = {The increasing interest in microbial ecology has resulted in the creation of new tools for the study of complex microbial interactions. Bioreporter genes are particularly useful because they provide a means of determining gene activity. Most bioreporter genes utilize a biochemical assay requiring destructive sampling of the microbial consortium, but lux bioreporter genes produce visible light when active. The measurement of light is rapid, sensitive, and quantifiable, and background signal is usually absent. The usefulness of lux bioreporters is shown in several examples that demonstrate the unique attributes of this bioreporter. Despite some limitations, bioluminescence has proved to be a useful bioreporter under both laboratory and field conditions. Technological developments are discussed that have the potential to increase the number of bioreporter genes.}, }
@article {pmid7802958, year = {1994}, author = {Rodríguez-Zaragoza, S}, title = {Ecology of free-living amoebae.}, journal = {Critical reviews in microbiology}, volume = {20}, number = {3}, pages = {225-241}, doi = {10.3109/10408419409114556}, pmid = {7802958}, issn = {1040-841X}, mesh = {Amoeba/isolation &amp; purification/*physiology ; Animals ; Ecology ; }, abstract = {Small free-living amoebae (FLA) are the main predators controlling bacterial populations in soils. They are distributed in the rhizospheric zone and the surrounding bulk soil; however, they may spread deeper, reaching the vadose zone of groundwater systems, especially where bacterial populations get to high densities. Soil texture is the physical factor controlling the distribution of FLA because it determines the mean bore pore of soil aggregates and other important physical factors. FLA help maintain the high bacterial mineralization rate of organic matter through predation. As attachment onto a surface is necessary for feeding, the quantity of available surfaces is very important for developing this activity. However, the role of protozoa on plant growth promotion is still unclear because they may increase this effect by feeding on both fungi and bacteria. Small FLA are found in soils or sediments, as well as attached to suspended particulate matter in water columns, in the first 30 microns of water surface, or on the bodies of submerged animals and plants. These microorganisms do not distinguish between terrestrial or aquatic environments because they live in the interfaces between them. However, their importance in aquatic systems has been considered as negligible because they are outcompeted by free swimmers. The water conditions affecting amoebae survival are pH, temperature, concentration of sulfhydric acid and salinity. These factors have a strong influence on the structure of amoebae communities in aquatic environments. FLA are considered cosmopolitan as a group, and they live inside vertebrates, in soils, freshwater, marine waters, and on the aerial parts of plants and animals. These microbes, are spread by wind and water currents. Once in the air, cysts and trophozoites behave like any other suspended particulate matter. Therefore, suspension transportation, and removal depend on atmospheric dynamics rather than on their own mechanisms. Ultraviolet light and drought are the main causes of losing viability, but much needs to be learned about the effects of air contaminants on amoebal survival. Naked amoebae also live in the phyllosphere as part of phylloplane community, but their importance and participation in this environment remain unknown. Some species belonging to the genera Acanthamoebae, Naegleria, and Balamuthia cause fatal diseases in humans and are carriers of other pathogens such as Legionella pneumophilia. However, FLA communities can be of some utility in sewage treatment works based in soil filters. FLA's predatory activity in the root zone method may be of greater importance than previously thought, because this is their natural or more favorable environment.(ABSTRACT TRUNCATED AT 400 WORDS)}, }
@article {pmid7778812, year = {1994}, author = {Blech, MF}, title = {[Impact of antibiotic prophylaxis on microbial ecology].}, journal = {Annales francaises d'anesthesie et de reanimation}, volume = {13}, number = {5 Suppl}, pages = {S45-50}, doi = {10.1016/s0750-7658(05)81775-7}, pmid = {7778812}, issn = {0750-7658}, mesh = {Anti-Bacterial Agents/administration &amp; dosage/*therapeutic use ; Bacteria/*drug effects ; Bacterial Physiological Phenomena ; Cross Infection ; Drug Resistance, Microbial ; Ecology ; Humans ; Personnel, Hospital ; Surgical Wound Infection/*prevention &amp; control ; }, abstract = {This review of the literature analysed the impact of prophylactic antibiotics on patients, nurses, the ecosystem of the wards, the hospital and the general environment. After prophylactic antibiotics a qualitative and quantitative modification of the cutaneous and digestive flora of the patient can occur, as well as modification of susceptibility to antibiotics. Several factors may modulate their action on the bacterial flora: the breadth of the spectrum, the administered dose, the duration of treatment, the form of development of resistance and the type of antibiotics. Numerous studies have demonstrated the role of the nursing staff as a reservoir of multi-resistant micro-organisms. Staff of intensive care units is apparently the most affected. Prophylactic antibiotics can also induce changes in the quantitative and qualitative features both in the ward and hospital flora. An increase in the bacterial resistance to antibiotics in the general environment can occur; a long duration of oral prophylactic antibiotic administration is undoubtedly associated with this phenomenon. Thus, the benefit associated with prophylactic antibiotic in the prevention of postoperative infections, unquestionable in some indications, must be balanced with the possible selection of resistant micro-organisms and their consequences on the environment.}, }
@article {pmid7703323, year = {1994}, author = {Scannapieco, FA}, title = {Saliva-bacterium interactions in oral microbial ecology.}, journal = {Critical reviews in oral biology and medicine : an official publication of the American Association of Oral Biologists}, volume = {5}, number = {3-4}, pages = {203-248}, doi = {10.1177/10454411940050030201}, pmid = {7703323}, issn = {1045-4411}, support = {DE-09838/DE/NIDCR NIH HHS/United States ; }, mesh = {Actinomyces/physiology ; Bacterial Adhesion ; *Bacterial Physiological Phenomena ; Dental Deposits/microbiology ; Dental Plaque/microbiology/prevention &amp; control ; Ecology ; Humans ; Saliva/chemistry/*microbiology/*physiology ; Salivary Proteins and Peptides/physiology ; Streptococcus/physiology ; }, abstract = {Saliva is thought to have a significant impact on the colonization of microorganisms in the oral cavity. Salivary components may participate in this process by one of four general mechanisms: binding to microorganisms to facilitate their clearance from the oral cavity, serving as receptors in oral pellicles for microbial adhesion to host surfaces, inhibiting microbial growth or mediating microbial killing, and serving as microbial nutritional substrates. This article reviews information pertinent to the molecular interaction of salivary components with bacteria (primarily the oral streptococci and Actinomyces) and explores the implications of these interactions for oral bacterial colonization and dental plaque formation. Knowledge of the molecular mechanisms controlling bacterial colonization of the oral cavity may suggest methods to prevent not only dental plaque formation but also serious medical infections that may follow microbial colonization of the oral cavity.}, }
@article {pmid8226980, year = {1993}, author = {Fukumori, F and Hausinger, RP}, title = {Purification and characterization of 2,4-dichlorophenoxyacetate/alpha-ketoglutarate dioxygenase.}, journal = {The Journal of biological chemistry}, volume = {268}, number = {32}, pages = {24311-24317}, pmid = {8226980}, issn = {0021-9258}, mesh = {Alcaligenes/*enzymology ; Amino Acid Sequence ; Catalysis ; Cloning, Molecular ; Electrophoresis, Polyacrylamide Gel ; Enzyme Activation ; Enzyme Stability ; Escherichia coli/genetics ; Hydrogen-Ion Concentration ; Kinetics ; Mixed Function Oxygenases/genetics/*isolation &amp; purification/metabolism ; Molecular Sequence Data ; Substrate Specificity ; }, abstract = {The Alcaligenes eutrophus 2,4-dichlorophenoxyacetate/alpha-ketoglutarate dioxygenase, encoded by the tfdA gene of plasmid pJP4, is an Fe(II)-dependent enzyme that catalyzes the conversion of 2,4-dichlorophenoxyacetate to 2,4-dichlorophenol and glyoxylate concomitant with the decomposition of alpha-ketoglutarate to form succinate and carbon dioxide (Fukumori, F., and Hausinger, R. P. (1993) J. Bacteriol. 175, 2083-2086). Using recombinant Escherichia coli cells that overexpress the tfdA gene, the thermolabile enzyme (stable only up to 30 degrees C) was purified to apparent homogeneity (specific activity of 16.9 mumol of substrate converted min-1 mg of protein-1) by a simple two-step procedure. The native protein has an apparent M(r) of 50,000 +/- 2,500, consistent with a homodimeric structure. Ferrous ion is absolutely required for activity and cannot be replaced by several other divalent cations tested. Ascorbic acid stimulates dioxygenase activity and reduces the rate of enzyme inactivation by a metal ion-mediated process. The enzyme exhibits maximum activity at pH 6.5-7, however, it is stable over a pH range of 6.5-11. Although capable of hydroxylating a wide range of phenoxyacetates and related compounds, the enzyme exhibits the greatest affinity (Km 17.5 +/- 1.0 microM) and highest catalytic efficiency for 2,4-dichlorophenoxyacetate. Similarly, alpha-ketoglutarate is the preferred co-substrate (Km 3.20 +/- 0.54 microM) for the enzyme, but it can utilize a range of other alpha-ketoacids with lower efficiency. Results from chemical modification studies are consistent with the presence of multiple essential histidine residues in the enzyme.}, }
@article {pmid7506896, year = {1993}, author = {Ramsing, NB and Kühl, M and Jørgensen, BB}, title = {Distribution of sulfate-reducing bacteria, O2, and H2S in photosynthetic biofilms determined by oligonucleotide probes and microelectrodes.}, journal = {Applied and environmental microbiology}, volume = {59}, number = {11}, pages = {3840-3849}, pmid = {7506896}, issn = {0099-2240}, mesh = {Bacteria/isolation &amp; purification/*metabolism ; Base Sequence ; Ecology ; Hydrogen Sulfide/metabolism ; In Situ Hybridization, Fluorescence ; Microelectrodes ; Molecular Sequence Data ; Oligonucleotide Probes ; Oxidation-Reduction ; Oxygen/metabolism ; Photosynthesis ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sulfates/*metabolism ; }, abstract = {The vertical distribution of sulfate-reducing bacteria (SRB) in photosynthetic biofilms from the trickling filter of a sewage treatment plant was investigated with oligonucleotide probes binding to 16S rRNA. To demonstrate the effect of daylight and photosynthesis and thereby of increased oxygen penetration, we incubated two 4-mm-thick biofilm samples in darkness or exposed to light at natural intensity. Gradients of O2, H2S, and pH were examined with microelectrodes during incubation. The samples were subsequently frozen with liquid nitrogen and sliced on a cryomicrotome in 20-microns vertical slices. Fluorescent-dye-conjugated oligonucleotides were used as "phylogenetic" probes to identify single cells in the slices. Oligonucleotide sequences were selected which were complementary to short sequence elements (16 to 20 nucleotides) within the 16S rRNA of sulfate-reducing bacteria. The probes were labeled with fluorescein or rhodamine derivatives for subsequent visualization by epifluorescence microscopy. Five probes were synthesized for eukaryotes, eubacteria, SRB (including most species of the delta group of purple bacteria), Desulfobacter spp., and a nonhybridizing control. The SRB were unevenly distributed in the biofilm, being present in all states from single scattered cells to dense clusters of several thousand cells. To quantify the vertical distribution of SRB, we counted cells along vertical transects through the biofilm. This was done in a blind experiment to ascertain the reliability of the staining. A negative correlation between the vertical distribution of positively stained SRB cells and the measured O2 profiles was found. The distribution differed in light- and dark-incubated samples presumably because of the different extensions of the oxic surface layer. In both cases the SRB were largely restricted to anoxic layers.}, }
@article {pmid7903444, year = {1993}, author = {Cavedon, K and London, J}, title = {Adhesin degradation: a possible function for a Prevotella loescheii protease?.}, journal = {Oral microbiology and immunology}, volume = {8}, number = {5}, pages = {283-287}, doi = {10.1111/j.1399-302x.1993.tb00575.x}, pmid = {7903444}, issn = {0902-0055}, mesh = {*Adhesins, Bacterial ; *Bacterial Adhesion ; Bacterial Proteins/*metabolism ; Bacteroides/*enzymology ; Dental Plaque/microbiology ; Electrophoresis, Polyacrylamide Gel ; Fimbriae, Bacterial ; Isoelectric Focusing ; Peptide Hydrolases/metabolism ; }, abstract = {Prevotella loescheii PK1295 produces at least 3 proteases that are separable by isoelectric focusing. One of these proteases, an enzyme with an isoelectric point at 8.5 and an M(r) of 36,000, hydrolyzes the fimbria-associated adhesin on P. loescheii responsible for coaggregation with Streptococcus oralis 34, as well as gelatin, casein and fibrin. The action of this protease may contribute to the detachment of P. loescheii from its streptococcal coaggregation partner and provide a mechanism for bacterial relocation in dental plaque.}, }
@article {pmid8366021, year = {1993}, author = {Uchida, I and Hornung, JM and Thorne, CB and Klimpel, KR and Leppla, SH}, title = {Cloning and characterization of a gene whose product is a trans-activator of anthrax toxin synthesis.}, journal = {Journal of bacteriology}, volume = {175}, number = {17}, pages = {5329-5338}, pmid = {8366021}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; *Antigens, Bacterial ; Bacillus anthracis/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Bacterial Toxins/*genetics/metabolism ; Base Sequence ; Bicarbonates/pharmacology ; Cloning, Molecular ; DNA, Bacterial ; Genes, Bacterial ; *Genes, Regulator ; Genetic Complementation Test ; Molecular Sequence Data ; Mutagenesis, Insertional ; Open Reading Frames ; Promoter Regions, Genetic ; Restriction Mapping ; Trans-Activators/*genetics/metabolism ; Transcription, Genetic ; }, abstract = {The 184-kb Bacillus anthracis plasmid pXO1, which is required for virulence, contains three genes encoding the protein components of anthrax toxin, cya (edema factor gene), lef (lethal factor gene), and pag (protective antigen gene). Expression of the three proteins is induced by bicarbonate or serum. Using a pag-lacZ transcriptional construct to measure pag promoter activity, we cloned in Bacillus subtilis a gene (atxA) whose product acts in trans to stimulate anthrax toxin expression. Deletion analysis located atxA on a 2.0-kb fragment between cya and pag. DNA sequencing identified one open reading frame encoding 476 amino acids with a predicted M(r) of 55,673, in good agreement with the value of 53 kDa obtained by in vitro transcription-translation analysis. The cloned atxA gene complemented previously characterized Tn917 insertion mutants UM23 tp29 and UM23 tp32 (J. M. Hornung and C. B. Thorne, Abstr. 91st Gen. Meet. Am. Soc. Microbiol. 1991, abstr. D-121, p. 98), which are deficient in synthesis of all three toxin proteins. These results demonstrate that the atxA product activates not only transcription of pag but also that of cya and lef. beta-Galactosidase synthesis from the pag-lacZ transcriptional fusion construct introduced into an insertion mutant (UM23 tp62) which does not require bicarbonate for toxin synthesis indicated that additional regulatory genes other than atxA play a role in the induction of anthrax toxin gene expression by bicarbonate.}, }
@article {pmid8282422, year = {1993}, author = {Marsh, PD and Bradshaw, DJ}, title = {Microbiological effects of new agents in dentifrices for plaque control.}, journal = {International dental journal}, volume = {43}, number = {4 Suppl 1}, pages = {399-406}, pmid = {8282422}, issn = {0020-6539}, mesh = {Bacteria/*drug effects ; Dental Plaque/*microbiology/*prevention &amp; control ; *Dentifrices ; Drug Combinations ; Humans ; Triclosan/administration &amp; dosage/*therapeutic use ; }, abstract = {The incorporation of antimicrobial agents in dental products has been proposed for many years as a possible valuable adjunct to mechanical plaque control. Out of the diverse collection of potential agents, relatively few can be formulated into dentifrices. Several products have been developed based on Triclosan, a broad spectrum antimicrobial agent. By itself, Triclosan has only moderate antiplaque activities; consequently, it has been combined with other molecules in attempts to boost its clinical efficacy. The combination of Triclosan with a copolymer (polyvinyl methyl ether maleic acid) has been shown to increase the retention of Triclosan to surfaces, and to raise its antiplaque and antimicrobial activity in a range of laboratory tests. Other studies, however, have found greater inhibitory effects on both liquid and biofilm mixed cultures when Triclosan was combined with either pyrophosphate or zinc citrate. Both of these combinations were selectively inhibitory to those species implicated in gingivitis and advanced periodontal diseases. There is little microbiological data on the clinical efficacy of a combination of Triclosan with pyrophosphate, but as pyrophosphate has only a bacteriostatic mode of action and is lost rapidly from the mouth, this may limit the significance of any of its potential antimicrobial effects in vivo. In contrast, zinc citrate is a proven inhibitor of bacterial metabolism and growth, and is retained in the mouth for prolonged periods. Several clinical studies have confirmed an additive, complementary and selective inhibitory antimicrobial effect on dental plaque of a dentifrice containing Triclosan and zinc citrate, without any adverse effects on the natural microbial ecology of the mouth.}, }
@article {pmid8229543, year = {1993}, author = {Midtvedt, AC and Midtvedt, T}, title = {Conversion of cholesterol to coprostanol by the intestinal microflora during the first two years of human life.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {17}, number = {2}, pages = {161-168}, doi = {10.1097/00005176-199308000-00006}, pmid = {8229543}, issn = {0277-2116}, mesh = {Age Factors ; Anti-Bacterial Agents/pharmacology ; Bacteria/*metabolism ; Breast Feeding ; Cholestanol/analysis/*biosynthesis ; Cholesterol/*metabolism ; Feces/chemistry ; Female ; Humans ; Infant ; Infant, Newborn ; Intestines/*microbiology ; Longitudinal Studies ; Male ; Meconium/chemistry ; Prospective Studies ; Sex Factors ; }, abstract = {The establishment of the conversion of cholesterol to coprostanol by the intestinal microflora was followed in 25 healthy Swedish children by gas-chromatographic analysis of fecal samples taken at 0, 1, 3, 6, 9, 12, 15, 18, 21, and 24 months of age. In 15 children, the microbial conversion of cholesterol to coprostanol started during the second half of the first year of life. During the second year of life, a sequestered distribution of the conversion rate could be distinguished. At the end of the study, 13 of the children were stable high converters, 3 were stable low converters, and 6 were unstable converters while the conversion pattern of three children could not be determined. The initiation of the establishment of conversion was delayed by breast-feeding, and only one child had coprostanol in feces while still being breast-fed. Those children exclusively breast-fed for more than 4 months or weaned after 6 months of age had significantly lower conversion rates at 12 months of age than did the other children (p < 0.05). Once conversion started, previous breast-feeding tended to result in a stable, later high rate of conversion of cholesterol. Between 6 and 15 months of age, the conversion rate increased with age, but after standardization for the period of exposure to foods other than breast milk, no age factor could be identified.}, }
@article {pmid8167854, year = {1993}, author = {Fani, R and Damiani, G and Di Serio, C and Gallori, E and Grifoni, A and Bazzicalupo, M}, title = {Use of random amplified polymorphic DNA (RAPD) for generating specific DNA probes for microorganisms.}, journal = {Molecular ecology}, volume = {2}, number = {4}, pages = {243-250}, doi = {10.1111/j.1365-294x.1993.tb00014.x}, pmid = {8167854}, issn = {0962-1083}, mesh = {Ampicillin Resistance/genetics ; Azospirillum/*classification/*genetics ; Azospirillum brasilense/genetics ; Bacillus subtilis/genetics ; Base Sequence ; DNA Fingerprinting ; DNA Primers ; *DNA Probes ; DNA, Bacterial/analysis/*genetics ; Escherichia coli/genetics ; *Gene Amplification ; Genes, Bacterial ; Molecular Sequence Data ; Plasmids ; *Polymorphism, Genetic ; Streptomyces/genetics ; beta-Galactosidase/genetics ; }, abstract = {We report the rapid generation of DNA probes for several Azospirillum strains. This method does not require any knowledge of the genetics and/or the molecular biology of the organism (genome) to be investigated. The procedure is based on the generation of random amplified polymorphic DNA (RAPD) fingerprints using primers with an embedded restriction site. The amplification product(s) peculiar to one strain or common to two or more strains can be purified, cloned, sequenced and used as molecular probes in hybridization experiments for the detection and identification of microorganisms. We have tested this methodology in the nitrogen-fixing bacterium Azospirillum by amplyfing the total DNA extracted from several Azospirillum strains. We have used amplification bands with different specificity as molecular probes in hybridization experiments performed on amplified DNA. Results obtained have demonstrated the usefulness of this methodology for Azospirillum. Its use in microbial ecology studies as a general strategy to generate specific DNA probes is also discussed.}, }
@article {pmid8501028, year = {1993}, author = {Kolenbrander, PE and London, J}, title = {Adhere today, here tomorrow: oral bacterial adherence.}, journal = {Journal of bacteriology}, volume = {175}, number = {11}, pages = {3247-3252}, pmid = {8501028}, issn = {0021-9193}, mesh = {*Bacterial Adhesion ; Bacterial Proteins/*metabolism ; Cell Adhesion Molecules/*metabolism ; Dental Plaque/*microbiology ; Humans ; Mouth/microbiology ; Tooth/*microbiology ; }, }
@article {pmid8506269, year = {1993}, author = {Lenski, RE}, title = {Assessing the genetic structure of microbial populations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {90}, number = {10}, pages = {4334-4336}, pmid = {8506269}, issn = {0027-8424}, mesh = {Animals ; Bacteria/*genetics ; Clone Cells ; Eukaryota/*genetics ; Genetics, Population ; Recombination, Genetic ; }, }
@article {pmid7763732, year = {1993}, author = {Molly, K and Vande Woestyne, M and Verstraete, W}, title = {Development of a 5-step multi-chamber reactor as a simulation of the human intestinal microbial ecosystem.}, journal = {Applied microbiology and biotechnology}, volume = {39}, number = {2}, pages = {254-258}, pmid = {7763732}, issn = {0175-7598}, mesh = {Ammonia/metabolism ; Bacteria/enzymology/growth &amp; development/metabolism ; Bacterial Proteins/metabolism ; Bacteriological Techniques/*instrumentation ; Carbohydrate Metabolism ; Culture Media ; Ecology ; Energy Metabolism ; Equipment Design ; Fatty Acids, Volatile/biosynthesis ; Gases ; Humans ; Intestines/*microbiology ; }, abstract = {A five-stage reactor was developed to simulate the gastro-intestinal microbial ecosystem of humans. The small intestine was simulated by a two-step "fill and draw" system, the large intestine by a three-step reactor. A representative supply medium was developed to support a microbial community resembling that of the human gastro-intestinal tract. The entire system was validated by monitoring fermentation fluxes and products, i.e. indicator bacterial groups, volatile fatty acids, enzymatic activities and headspace gases. The simulator was operated with varying concentrations and combinations of arabinogalactan, xylan, pectin, dextrins and starch. The resulting patterns of microbial diversity and activity were analysed and compared with data for in-vivo gastro-intestinal microbial communities as described in the literature and found to be representative.}, }
@article {pmid8463265, year = {1993}, author = {Gentry-Weeks, CR and Keith, JM and Thompson, J}, title = {Toxicity of Bordetella avium beta-cystathionase toward MC3T3-E1 osteogenic cells.}, journal = {The Journal of biological chemistry}, volume = {268}, number = {10}, pages = {7298-7314}, pmid = {8463265}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Toxins/antagonists &amp; inhibitors/genetics/isolation &amp; purification/*toxicity ; Base Sequence ; Blotting, Western ; Bordetella/*enzymology ; Cattle ; Cell Death ; Cell Line ; Cells, Cultured ; Cloning, Molecular ; DNA, Bacterial ; Electrophoresis, Polyacrylamide Gel ; Guinea Pigs ; Isoelectric Point ; Kinetics ; Lyases/antagonists &amp; inhibitors/genetics/isolation &amp; purification/*toxicity ; Molecular Sequence Data ; Osteoblasts/*drug effects ; Rabbits ; Rats ; Restriction Mapping ; Sequence Homology, Amino Acid ; Spectrum Analysis ; Substrate Specificity ; Swine ; *Transglutaminases ; Turkeys ; *Virulence Factors, Bordetella ; }, abstract = {Bordetella avium is the etiological agent of an upper respiratory disease in birds which, symptomatically and pathologically, resembles bordetellosis in humans. Studies of the virulence of this organism revealed a novel cytotoxic protein, designated osteotoxin, that was lethal for MC3T3-E1 osteogenic cells, fetal bovine trabecular cells, UMR106-01(BSP) rat osteosarcoma cells, and embryonic bovine tracheal cells. The osteotoxin lacked dermonecrotic toxin activity, exhibited no cross-reactivity with antibody against B. avium dermonecrotic toxin, and was non-proteolytic. Osteotoxin (M(r) approximately 80,000 by gel filtration, pI 5.4) was purified to electrophoretic homogeneity from B. avium 197. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and spectrophotometric analyses showed that the native protein was a homodimer and that each of the non-covalently linked subunits (M(r) approximately 41,000) contained one molecule of pyridoxal 5'-phosphate. Microsequencing of the first 32 amino acids from the NH2 terminus allowed the synthesis of two oligonucleotide probes, which, together with polyclonal antibody to the purified protein, facilitated cloning, sequencing, and expression of the osteotoxin gene product in Escherichia coli. The open reading frame encodes a polypeptide of 396 amino acid residues (M(r) = 42,606, calculated pI 5.9), whose sequence exhibits approximately 38% identity (approximately 60% similarity) to pyridoxal 5'-phosphate-dependent beta-cystathionase(s) from E. coli, Salmonella typhimurium, and rat liver. The characteristic motif, TKYXXGHSD, associated with binding the cofactor in these enzymes is also present in osteotoxin. Physicochemical and enzymatic analyses established the coidentity of osteotoxin with beta-cystathionase. The region upstream of the beta-cystathionase (metC) gene in B. avium 197 lacked regulatory sequences ("Met boxes") described for metC in enteric species, and enzyme production was not repressed by methionine. Incubation of MC3T3-E1 osteogenic cells in medium containing L-[35S]cystine and purified beta-cystathionase resulted in 35S-labeling of the enzyme and at least one major MC3T3-E1 cell protein (M(r) approximately 50,000). cytotoxicity can be attributed to: 1) beta-cystathionase-catalyzed cleavage of L-cystine in the medium and formation of reactive sulfane-containing derivative(s), and 2) transfer of sulfane sulfur to metabolically sensitive or structurally important proteins in the osteogenic cells.}, }
@article {pmid8458850, year = {1993}, author = {Fukumori, F and Hausinger, RP}, title = {Alcaligenes eutrophus JMP134 "2,4-dichlorophenoxyacetate monooxygenase" is an alpha-ketoglutarate-dependent dioxygenase.}, journal = {Journal of bacteriology}, volume = {175}, number = {7}, pages = {2083-2086}, pmid = {8458850}, issn = {0021-9193}, mesh = {2,4-Dichlorophenoxyacetic Acid/*metabolism ; Alcaligenes/*enzymology/genetics ; Bacterial Proteins/drug effects/genetics/isolation &amp; purification/*metabolism ; Carbon Dioxide/metabolism ; Escherichia coli/genetics ; Ketoglutaric Acids/metabolism/*pharmacology ; Oxygenases/drug effects/genetics/isolation &amp; purification/*metabolism ; Recombinant Proteins/biosynthesis ; Succinates/analysis ; }, abstract = {The Alcaligenes eutrophus JMP134 tfdA gene, encoding the enzyme responsible for the first step in 2,4-dichlorophenoxyacetic acid (2,4-D) biodegradation, was overexpressed in Escherichia coli, and several enzymatic properties of the partially purified gene product were examined. Although the tfdA-encoded enzyme is typically referred to as 2,4-D monooxygenase, we were unable to observe any reductant-dependent activity. Rather, we demonstrate that this enzyme is a ferrous ion-dependent dioxygenase that uses alpha-ketoglutarate as a cosubstrate. The alpha-ketoglutarate is converted to succinate concomitant with 2,4-D conversion to 2,4-dichlorophenol. By using [1-14C]alpha-ketoglutarate, we established that carbon dioxide is the second product derived from alpha-ketoglutarate. Finally, we verified the proposal that glyoxylate is the second product derived from 2,4-D.}, }
@article {pmid7763570, year = {1993}, author = {Bryers, JD}, title = {Bacterial biofilms.}, journal = {Current opinion in biotechnology}, volume = {4}, number = {2}, pages = {197-204}, doi = {10.1016/0958-1669(93)90125-g}, pmid = {7763570}, issn = {0958-1669}, mesh = {*Bacterial Physiological Phenomena ; Biotechnology ; Ecology ; Environmental Microbiology ; }, abstract = {Over the review period, a significant amount of literature has been published documenting the impact of biofilms on engineered and biomedical systems. Reactor systems and analytical techniques have evolved to study the molecular chemistry and microbial ecology within biofilm layers only tens of micrometers thick, and various protocols have been developed to control cell adhesion and biofilm formation.}, }
@article {pmid8458406, year = {1993}, author = {Lenski, RE}, title = {Evaluating the fate of genetically modified microorganisms in the environment: are they inherently less fit?.}, journal = {Experientia}, volume = {49}, number = {3}, pages = {201-209}, pmid = {8458406}, issn = {0014-4754}, mesh = {Bacteria/genetics ; Containment of Biohazards ; *Environment ; *Genetic Engineering ; Risk Factors ; }, abstract = {Genetically modified microorganisms hold great promise for environmental applications. Nonetheless, some may have unintended adverse effects. Of particular concern for risk assessment is the simple fact that microorganisms are self-replicating entities, so that it may be impossible to control an adverse effect simply by discontinuing further releases of the organism. It has been suggested, however, that genetically modified microorganisms will be poor competitors and therefore unable to persist in the wild due to energetic inefficiency, disruption of genomic coadaptation, or domestication. Many studies support the hypothesis that genetically modified microorganisms are less fit than their progenitors, but there are a few noteworthy counter-examples in which genetic modifications unexpectedly enhance competitive fitness. Furthermore, subsequent evolution may eliminate the maladaptive effects of some genes, increasing the likelihood that a modified organism or its engineered genes will persist. Evaluating the likelihood that a genetically modified microorganism or its engineered genes will persist is a complex ecological and evolutionary problem. Therefore, an efficient regulatory framework would require such evaluations only when there are plausible scenarios for significant adverse environmental effects.}, }
@article {pmid8466808, year = {1993}, author = {McMullen, LM and Stiles, ME}, title = {Microbial ecology of fresh pork stored under modified atmosphere at -1, 4.4 and 10 degrees C.}, journal = {International journal of food microbiology}, volume = {18}, number = {1}, pages = {1-14}, doi = {10.1016/0168-1605(93)90002-x}, pmid = {8466808}, issn = {0168-1605}, mesh = {Animals ; Bacteria/classification/*isolation &amp; purification ; Carbon Dioxide ; Ecology ; *Food Microbiology ; Food Preservation ; Lactobacillaceae/classification/isolation &amp; purification ; Meat/*microbiology ; Refrigeration ; Swine ; }, abstract = {The prevalent bacteria on fresh pork packaged in modified atmosphere with elevated CO2 were determined by selection of representative colonies from the greatest dilution of meat samples. The pork samples were stored in two packaging films of different oxygen permeability at three storage temperatures. Strains were classified and those identified as lactic acid bacteria were screened for production of inhibitory substances. The types of bacteria isolated from samples stored in the two packaging films were similar. Storage temperature influenced the type of bacteria that dominated the microbial population. At 10 degrees C the prevalent microflora consisted of aeromonads, Enterobacteriaceae and lactic acid bacteria but at 4.4 and -1 degrees C, aeromonads, Brochothrix thermosphacta and lactic acid bacteria dominated. Listeriae were detected as part of the prevalent microflora on samples stored at -1 degree C, but not on samples stored at 4.4 or 10 degrees C. Species of lactic acid bacteria dominating the microflora were influenced by growth medium. The majority of isolates taken from Plate Count agar were carnobacteria whereas those from Lactobacilli MRS agar were homofermentative lactic acid bacteria. Of the 538 lactic acid bacteria isolates screened for production of inhibitory substances, 162 strains showed deferred inhibition toward a range of lactic acid bacteria and nonlactic acid bacteria indicator strains.}, }
@article {pmid8462782, year = {1993}, author = {Kolenbrander, PE and Ganeshkumar, N and Cassels, FJ and Hughes, CV}, title = {Coaggregation: specific adherence among human oral plaque bacteria.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {7}, number = {5}, pages = {406-413}, doi = {10.1096/fasebj.7.5.8462782}, pmid = {8462782}, issn = {0892-6638}, mesh = {*Bacterial Adhesion ; Carbohydrate Sequence ; Dental Plaque/*microbiology ; Humans ; Molecular Sequence Data ; }, abstract = {Nearly all human oral bacteria exhibit coaggregation, cell-to-cell recognition of genetically distinct cell types. Clumps or coaggregates composed of the two kinds of cells are formed immediately upon mixing two partner cell types. Members of all 18 genera tested exhibit lactose-reversible coaggregation. Many of these interactions appear to be mediated by a lectin on one cell type that interacts with a complementary carbohydrate receptor on the other cell type. A lactose-sensitive adhesin has been isolated from Prevotella loescheii PK1295, and it exhibits the adherence properties observed with whole cells. Other adhesins have been identified and the genes for some of them have been cloned and sequenced. One Streptococcus sanguis adhesin is a lipoprotein that appears to have a dual function of recognizing both a bacterial carbohydrate receptor and a receptor in human saliva. Carbohydrate receptors for some adhesins have been purified from five oral streptococci, and they specifically block the coaggregations with the streptococcal partners that express the complementary adhesins. Coaggregation offers an explanation for the temporally related accretion of dental plaque and bacterial recognition of mucosal surfaces. Early colonizers of the tooth surface coaggregate with each other and late colonizers of the tooth surface coaggregate with each other, but with few exceptions, early colonizers do not recognize late colonizers. Furthermore, bacteria that colonize mucosal surfaces coaggregate with each other, indicating the high degree of specificity of coaggregation in the oral bacterial population.}, }
@article {pmid8432618, year = {1993}, author = {Andersen, RN and Ganeshkumar, N and Kolenbrander, PE}, title = {Cloning of the Streptococcus gordonii PK488 gene, encoding an adhesin which mediates coaggregation with Actinomyces naeslundii PK606.}, journal = {Infection and immunity}, volume = {61}, number = {3}, pages = {981-987}, pmid = {8432618}, issn = {0019-9567}, mesh = {Actinomyces/cytology ; *Bacterial Adhesion ; Bacterial Proteins/*genetics ; Base Sequence ; Cloning, Molecular ; DNA, Bacterial/genetics ; Genes, Bacterial ; *Membrane Proteins ; Oligodeoxyribonucleotides/chemistry ; Restriction Mapping ; Streptococcus/cytology/*genetics ; }, abstract = {Coaggregation between Streptococcus gordonii PK488 and Actinomyces naeslundii PK606 is mediated by a 38-kDa streptococcal protein, designated ScaA. The gene, scaA, which encodes this protein has been cloned into Escherichia coli. A genomic S. gordonii PK488 library (in Lambda ZAP II) was screened with anti-S. gordonii immunoglobulin G absorbed with S. gordonii PK1804, an isogenic coaggregation-defective mutant of strain PK488. A positive recombinant phage was isolated, and a phagemid designated pRA1 was obtained which contained a 6.6-kb insert. Expression of scaA from pRA1 and from a subcloned internal 2.1-kb fragment was observed. The absorbed antiserum cross-reacted with a 34.7-kDa protein, SsaB, from S. sanguis 12, also a coaggregation partner of A. naeslundii PK606. Absorbed antiserum to S. gordonii PK488 and antiserum to SsaB both reacted with 38-kDa proteins in supernatants from mildly sonicated preparations from 11 other coaggregation partners of A. naeslundii PK606. Putative adhesin genes were identified in each of these coaggregation partners by Southern analysis of their genomic DNA with the cloned 2.1-kb fragment as a probe. A 30-base oligonucleotide probe based on the sequence of ssaB of S. sanguis 12 hybridized in an identical manner. These data extend the notion that most of the viridans streptococci that coaggregate with actinomyces are capable of expressing ScaA-related proteins.}, }
@article {pmid7686071, year = {1993}, author = {Gersdorf, H and Pelz, K and Göbel, UB}, title = {Fluorescence in situ hybridization for direct visualization of gram-negative anaerobes in subgingival plaque samples.}, journal = {FEMS immunology and medical microbiology}, volume = {6}, number = {2-3}, pages = {109-114}, doi = {10.1111/j.1574-695X.1993.tb00312.x}, pmid = {7686071}, issn = {0928-8244}, mesh = {Bacteroidaceae/classification/*isolation &amp; purification ; Bacteroidaceae Infections/*microbiology ; Bacteroides/isolation &amp; purification ; Base Sequence ; DNA Probes ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Dental Plaque/*microbiology ; Humans ; *In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Periodontitis/*microbiology ; Porphyromonas gingivalis/isolation &amp; purification ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Fluorescent oligonucleotide probes complementary to variable regions of Porphyromonas gingivalis and Bacteroides forsythus 16S ribosomal RNA were used to identify these organisms in smears of formaldehyde-fixed subgingival plaque samples from patients suffering from periodontitis. Fluorescence in situ hybridization represents a useful method for assessing the microbial ecology of the periodontal flora.}, }
@article {pmid8429009, year = {1993}, author = {Arora, N and Leppla, SH}, title = {Residues 1-254 of anthrax toxin lethal factor are sufficient to cause cellular uptake of fused polypeptides.}, journal = {The Journal of biological chemistry}, volume = {268}, number = {5}, pages = {3334-3341}, pmid = {8429009}, issn = {0021-9258}, mesh = {*ADP Ribose Transferases ; Animals ; *Antigens, Bacterial ; Bacillus anthracis/genetics ; Bacterial Toxins/genetics/*metabolism/pharmacology ; Binding, Competitive ; Biological Transport ; CHO Cells ; Cell Line ; Cell Membrane/metabolism ; Cell Survival/drug effects ; Cloning, Molecular ; Cricetinae ; Escherichia coli/genetics ; Exotoxins/genetics/metabolism ; Kinetics ; Macrophages ; Peptide Fragments/*metabolism/pharmacology ; Plasmids ; Polymerase Chain Reaction/methods ; Recombinant Fusion Proteins/metabolism/pharmacology ; Repetitive Sequences, Nucleic Acid ; Restriction Mapping ; Sequence Deletion ; *Virulence Factors ; Pseudomonas aeruginosa Exotoxin A ; }, abstract = {Anthrax lethal toxin is a complex of protective antigen (PA, 735 amino acids) and lethal factor (LF, 776 amino acids) that lyses certain eukaryotic cells. LF interacts with PA to gain access to the cytosol to assert its toxicity. The internalization of LF requires that PA bind to a specific membrane receptor and be cleaved by a cell-surface protease (probably furin), so as to expose a site on PA to which LF binds with high affinity. To localize LF functional domains, amino, carboxyl, and internal deletions of LF were made. Toxicity was eliminated by deletion of 40 and 47 residues from the amino and carboxyl termini, respectively. Similarly, deleting the first of the four imperfect repeats of 19 amino acids located at residues 308-383 made LF non-toxic, showing that this region is also essential for activity. To identify the minimum region of LF which is required for binding to PA, varying amino-terminal portions of LF were fused to the ADP-ribosylation domain of Pseudomonas exotoxin A. Fusion proteins containing residues 1-254 of LF were toxic when administered with PA, while those having only residues 1-198 of LF were inactive, showing that the PA-binding domain of LF lies within residues 1-254.}, }
@article {pmid8434915, year = {1993}, author = {Crawford, DL and Doyle, JD and Wang, Z and Hendricks, CW and Bentjen, SA and Bolton, H and Fredrickson, JK and Bleakley, BH}, title = {Effects of a lignin peroxidase-expressing recombinant, Streptomyces lividans TK23.1, on biogeochemical cycling and the numbers and activities of microorganisms in soil.}, journal = {Applied and environmental microbiology}, volume = {59}, number = {2}, pages = {508-518}, pmid = {8434915}, issn = {0099-2240}, mesh = {Acid Phosphatase/*metabolism ; Alkaline Phosphatase/*metabolism ; Arylsulfatases/*metabolism ; Biodegradation, Environmental ; Carbon Dioxide/*metabolism ; Cellulose/*metabolism ; Hydrogen-Ion Concentration ; Lignin/*metabolism ; Peroxidases/genetics ; Recombination, Genetic ; *Soil Microbiology ; Streptomyces/enzymology/genetics/*metabolism ; }, abstract = {A recombinant actinomycete, Streptomyces lividans TK23.1, expressing a pIJ702-encoded extracellular lignin peroxidase gene cloned from the chromosome of Streptomyces viridosporus T7A, was released into soil in flask- and microcosm-scale studies to determine its effects on humification and elemental cycling and on the numbers, types, and activities of microorganisms native to the soil. Strain TK23.1 had been shown previously to transiently increase the rate of organic carbon mineralization in soil via an effect that was recombinant specific and particularly significant in nonsterile soils already possessing an active microflora. The results of this study confirmed the previous findings and showed that additional effects were measurable upon release of the recombinant strain TK23.1 into unamended soil and into soil amended with lignocellulose. In addition to a transient enhancement of carbon mineralization, the recombinant affected soil pH, the rate of incorporation of carbon into soil humus fractions, nitrogen cycling, the relative populations of some microbial groups, and also certain soil enzyme activities. Whereas the survival or persistence in soil of the recombinant TK23.1 strain and that of its parent, TK23, were similar, the observed effects on microbial numbers, types, and activities were recombinant specific and did not occur when the parental strain was released into soil. All of the measured effects were transient, generally lasting for only a few days. While the effects were statistically significant, their ecological significance appears to be minimal. This is the first report showing that a recombinant actinomycete can affect the microbial ecology of soil in ways that can be readily monitored by using a battery of microbiological, enzymological, and chemical assays.}, }
@article {pmid7678468, year = {1993}, author = {Lenski, RE and Mittler, JE}, title = {The directed mutation controversy and neo-Darwinism.}, journal = {Science (New York, N.Y.)}, volume = {259}, number = {5092}, pages = {188-194}, doi = {10.1126/science.7678468}, pmid = {7678468}, issn = {0036-8075}, mesh = {Bacteria/genetics ; Bacterial Outer Membrane Proteins/genetics ; Bacteriophages/genetics ; DNA Damage ; DNA Repair ; DNA, Bacterial/genetics ; *Models, Genetic ; *Mutation ; Phenotype ; RNA, Bacterial/genetics ; RNA, Messenger/genetics ; *Selection, Genetic ; }, abstract = {According to neo-Darwinian theory, random mutation produces genetic differences among organisms whereas natural selection tends to increase the frequency of advantageous alleles. However, several recent papers claim that certain mutations in bacteria and yeast occur at much higher rates specifically when the mutant phenotypes are advantageous. Various molecular models have been proposed that might explain these directed mutations, but the models have not been confirmed. Critics contend that studies purporting to demonstrate directed mutation lack certain controls and fail to account adequately for population dynamics. Further experiments that address these criticisms do not support the existence of directed mutations.}, }
@article {pmid8499087, year = {1993}, author = {Kong, Z and Vanrolleghem, PA and Verstraete, W}, title = {An activated sludge-based biosensor for rapid IC50 estimation and on-line toxicity monitoring.}, journal = {Biosensors &amp; bioelectronics}, volume = {8}, number = {1}, pages = {49-58}, doi = {10.1016/0956-5663(93)80043-o}, pmid = {8499087}, issn = {0956-5663}, mesh = {*Biosensing Techniques ; Environmental Monitoring/*instrumentation ; *Online Systems ; Oxygen Consumption/*drug effects ; Reproducibility of Results ; Sensitivity and Specificity ; *Sewage ; Time Factors ; Water Microbiology ; Water Pollutants, Chemical/*toxicity ; }, abstract = {The RODTOX (Rapid Oxygen Demand and TOXicity tester), an activated sludge-based respirographic biosensor, is a device for on-line monitoring of the short-term biochemical oxygen demand (stBOD) and potential toxicity of incoming wastewater on the basis of on-line interpretation of respirograms resulting from pulse additions of either calibration substrate or sample. The principle of toxicity detection is based on the comparison of calibration respirograms before and after receiving a potential toxicant. In this paper, the results of the RODTOX as an on-line toxicity monitor are presented. In addition, a simple and fast procedure to estimate the IC50 of a toxicant has been developed, and its validity and good repeatability demonstrated. The performance of this procedure is compared with that of the Microtox test.}, }
@article {pmid8419308, year = {1993}, author = {Ganeshkumar, N and Arora, N and Kolenbrander, PE}, title = {Saliva-binding protein (SsaB) from Streptococcus sanguis 12 is a lipoprotein.}, journal = {Journal of bacteriology}, volume = {175}, number = {2}, pages = {572-574}, pmid = {8419308}, issn = {0021-9193}, mesh = {*Adhesins, Bacterial ; Amino Acid Sequence ; Bacterial Proteins/*genetics/isolation &amp; purification ; Base Sequence ; Blotting, Western ; Cloning, Molecular ; Escherichia coli/genetics ; Humans ; Lipoproteins/*genetics/isolation &amp; purification ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Palmitic Acid ; Palmitic Acids/metabolism ; Polymerase Chain Reaction ; Protein Sorting Signals/genetics ; Recombinant Proteins/isolation &amp; purification ; Restriction Mapping ; Saliva ; Streptococcus sanguis/*genetics/metabolism ; }, abstract = {Two lipoprotein consensus sequences (Leu-X-X-Cys) are found in the presumptive signal peptide region (positions 12 to 15 and 17 to 20) of saliva-binding protein (SsaB) from Streptococcus sanguis 12. Three analogs of SsaB containing Cys-->Gly mutations were constructed by site-directed mutagenesis of pSA2, the recombinant plasmid expressing SsaB. [3H]palmitate was incorporated into SsaB only when the native Cys-20 residue was present. These data show that SsaB is a lipoprotein and that Cys-20 is the critical site for acylation.}, }
@article {pmid8349536, year = {1993}, author = {Kolenbrander, PE}, title = {Coaggregation of human oral bacteria: potential role in the accretion of dental plaque.}, journal = {The Journal of applied bacteriology}, volume = {74 Suppl}, number = {}, pages = {79S-86S}, doi = {10.1111/j.1365-2672.1993.tb04344.x}, pmid = {8349536}, issn = {0021-8847}, mesh = {Bacterial Adhesion/*physiology ; *Bacterial Physiological Phenomena ; Dental Plaque/*microbiology ; Humans ; Mouth/*microbiology ; }, }
@article {pmid8317620, year = {1993}, author = {Litiaeva, LA}, title = {[The effect of a combination of immune and bacterial preparations on the microbial ecology of pregnant women in a risk group].}, journal = {Akusherstvo i ginekologiia}, volume = {}, number = {1}, pages = {19-22}, pmid = {8317620}, issn = {0300-9092}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Bacterial Infections/epidemiology/microbiology/*therapy ; Bacteriocins/*therapeutic use ; Biological Products/*therapeutic use ; Combined Modality Therapy ; Ecology ; Female ; Humans ; *Immunization, Passive ; Intestines/microbiology ; *Lactobacillus ; Pregnancy ; Pregnancy Complications, Infectious/epidemiology/microbiology/*therapy ; Risk Factors ; Vagina/microbiology ; }, abstract = {Clinical and microbiologic examinations of 200 pregnant women with perinatal risk factors helped single out a group at high risk of intestinal dysbacteriosis (abnormal microflora) in their babies. The preparation of these women to labor included correction of the bacterial ecology of the vagina and intestine with a complex of immunologic and bacterial drugs. Administration of this drug complex favorably influenced the course of pregnancy, labor and the postpartum period, as well as the bacterial ecologic status of the mother and child, resulting in a reduced incidence of infectious complications in the newborns.}, }
@article {pmid8266899, year = {1993}, author = {Hök, K}, title = {Morbidity, mortality and coronavirus antigen in previously coronavirus free kittens placed in two catteries with feline infectious peritonitis.}, journal = {Acta veterinaria Scandinavica}, volume = {34}, number = {2}, pages = {203-210}, pmid = {8266899}, issn = {0044-605X}, mesh = {Animals ; Antigens, Viral/*immunology ; Cats ; Coronavirus, Feline/*immunology ; Feline Infectious Peritonitis/immunology/*mortality ; Female ; Male ; Morbidity ; Survival Rate ; }, abstract = {Serologically coronavirus free kittens were placed in 2 catteries with a history of feline infectious peritonitis (FIP), each cattery representing 1 of the 2 different predominant clinical characteristics of FIP--effusive and granulomatous. The kittens were clinically observed for 100 days. A 100% morbidity and a 90% mortality was observed. The first signs were observed after 14 and 27 days respectively. The clinical pattern of the disease was similar in all kittens and showed a pattern of recurrent periods of conjunctivitis, upper respiratory and gastrointestinal signs. Once developed, wasting and signs of CNS disturbances were consistent. The "effusive strain" had a 2 weeks earlier onset of signs and death, and a 40% outcome of effusive FIP. Mean survival times during the observation period were 57 +/- 26 and 57 +/- 16 (mean +/- SD in days), respectively. The death rates were similar in both groups. Feline coronavirus (FCoV) antigen was immunohistochemically detected using indirect immunofluorescence and was present in all kittens and in 93% of the 5 investigated organs (lung, liver, spleen, kidney, and mesenteric lymph node).}, }
@article {pmid8220231, year = {1993}, author = {Fouchet, P and Jayat, C and Héchard, Y and Ratinaud, MH and Frelat, G}, title = {Recent advances of flow cytometry in fundamental and applied microbiology.}, journal = {Biology of the cell}, volume = {78}, number = {1-2}, pages = {95-109}, doi = {10.1016/0248-4900(93)90120-4}, pmid = {8220231}, issn = {0248-4900}, mesh = {Biotechnology/methods ; Eukaryotic Cells/chemistry/drug effects/physiology ; Flow Cytometry/*methods/trends ; Fluorescent Dyes ; Infections/drug therapy ; *Microbiological Techniques/trends ; Nucleic Acids/analysis ; Parasitology/*methods/trends ; Prokaryotic Cells/chemistry/drug effects/physiology ; Proteins/analysis ; Scattering, Radiation ; Water Microbiology ; }, abstract = {This review focuses on the recent applications of flow cytometry (FCM) in microbiological research (1987-mid 1992). It tries to give a scope of the important breakthroughs which occurred in this field during this period. The technical difficulties of microorganism analysis by flow cytometry is briefly appraised. The significance and the limits of the different microbial cell parameters attainable by flow analyses are systematically evaluated: light scatter for cell size and structure, fluorescence measurements for quantification of cellular components, microbial antigen detection and cell physiological activity estimation. Emphasis is given on the new technological advances which appeared in the last two years. The second part of the review is devoted to the analysis of the usefulness of flow cytometric approach in the different fields of microbiology: fundamental studies in microbial physiology, differentiation, microbial ecology and aquatic sciences, medical microbiology, parasitology, microbial pharmacology and biotechnology.}, }
@article {pmid8220221, year = {1993}, author = {Troussellier, M and Courties, C and Vaquer, A}, title = {Recent applications of flow cytometry in aquatic microbial ecology.}, journal = {Biology of the cell}, volume = {78}, number = {1-2}, pages = {111-121}, doi = {10.1016/0248-4900(93)90121-t}, pmid = {8220221}, issn = {0248-4900}, mesh = {Bacteria/classification/isolation &amp; purification ; DNA, Bacterial/analysis ; Ecology ; Flow Cytometry/*methods ; Fluorescent Dyes ; France ; Greece ; Indonesia ; Marine Biology/*methods ; Mediterranean Sea ; Phytoplankton/classification/isolation &amp; purification ; Salmonella typhimurium/chemistry/cytology/isolation &amp; purification ; Species Specificity ; Tunisia ; *Water Microbiology ; Water Pollution/analysis ; }, abstract = {Microorganisms (unicellular algae, bacteria) constitute fundamental compartments of aquatic ecosystems because of their high concentrations and activities. The evaluation and understanding of their behavior and role raise different problems for which traditional methodologies are often inadequate, whether they refer to global or classical microscopic analyses. Flow cytometry (FCM) has been recently used to study microorganisms in aquatic environments. Although this technology is still applied on a limited scale in our field, a large number of works has been done showing that FCM seems to be a promising tool for aquatic microbial ecology. This paper summarizes, from the literature produced during the last decade and with original data obtained in our laboratory, the main questions related to the cell identification, the evaluation of cell viability, biomasses and productions and the measurements of bacterial and phytoplanktonic activities. The representatives of sampling and observation scales is also discussed within the framework of the FCM measurements.}, }
@article {pmid8147286, year = {1993}, author = {Hök, K}, title = {Development of clinical signs and occurrence of feline corona virus antigen in naturally infected barrier reared cats and their offspring.}, journal = {Acta veterinaria Scandinavica}, volume = {34}, number = {4}, pages = {345-356}, pmid = {8147286}, issn = {0044-605X}, mesh = {Animals ; Animals, Newborn/microbiology ; Antigens, Viral/*analysis ; Cats ; Conjunctivitis/microbiology/veterinary ; Coronavirus/*immunology/isolation &amp; purification ; Feline Infectious Peritonitis/immunology/*transmission ; Female ; Male ; Nictitating Membrane/microbiology ; Pregnancy ; Respiratory Tract Infections/microbiology/veterinary ; }, abstract = {The onset and pattern of the clinical signs of feline corona virus (FCoV) infection in cats were studied in a setting behind an isolation barrier. Two FCoV-seropositive cats were the source of the infection, and 3 barrier reared cats - initially FCoV-seronegative - were the recipients. The first clinical sign in the recipients appeared 11 days after contact with the source of infection. After 2 years 1 male and 1 female of the recipients started to breed. Their offspring developed clinical signs of disease at an age of 4-5 weeks. A pattern of recurring upper respiratory tract signs and conjunctivitis at intervals of about 4 months was observed in both the recipients and their offspring, while CNS dependent signs and wasting remained or got worse, once developed. Once demonstrated, FCoV antigen persisted in membrana nictitans throughout the investigation, and was found in all cats but 4 (90%). The offspring died during 2 periods, around the first week of life (9/37), and at 3-5 months of age (5/25). For comparison 3 offspring were euthanized at an age of 1 day and 16 offspring at an age of 3-6 months. FCoV antigen was demonstrated in all organs investigated (100%) from offspring dying during the first period, and in 97% from those dying during the second period. For the offspring euthanized during the same 2 periods the corresponding findings were 95% and 85%. Offspring euthanized between 9 and 17 months (4 kittens) had antigen in 67% of all investigated organs. The incidence of FCoV antigen in almost every organ in the investigated newborn kittens suggests an intrauterine infection. The demonstration of FCoV antigen in all euthanised cats, suggests a persistent infection. Virus was cultivated from membrana nictitans, that was FCoV antigen positive in the M3 test.}, }
@article {pmid7764920, year = {1993}, author = {Tiedje, JM and Quensen, JF and Chee-Sanford, J and Schimel, JP and Boyd, SA}, title = {Microbial reductive dechlorination of PCBs.}, journal = {Biodegradation}, volume = {4}, number = {4}, pages = {231-240}, pmid = {7764920}, issn = {0923-9820}, mesh = {Bacteria, Anaerobic/*metabolism ; Biodegradation, Environmental ; Environmental Pollutants/metabolism ; Oxidation-Reduction ; Polychlorinated Biphenyls/*metabolism ; Soil Microbiology ; }, abstract = {Reductive dechlorination is an advantageous process to microorganisms under anaerobic conditions because it is an electron sink, thereby allowing reoxidation of metabolic intermediates. In some organisms this has been demonstrated to support growth. Many chlorinated compounds have now been shown to be reductively dechlorinated under anaerobic conditions, including many of the congeners in commercial PCB mixtures. Anaerobic microbial communities in sediments dechlorinate Aroclor at rates of 3 micrograms Cl/g sediment x week. PCB dechlorination occurs at 12 degrees C, a temperature relevant for remediation at temperate sites, and at concentrations of 100 to 1000 ppm. The positions dechlorinated are usually meta > para > ortho. The biphenyl rings, and the mono-ortho- and diorthochlorobiphenyls were not degraded after a one year incubation. Hence subsequent aerobic treatment may be necessary to meet regulatory standards. Reductive dechlorination of Aroclors does reduce their dioxin-like toxicity as measured by bioassay and by analysis of the co-planar congeners. The most important limitation to using PCB dechlorination as a remediation technology is the slower than desired dechlorination rates and no means yet discovered to substantially enhance these rates. Long term enrichments using PCBs as the only electron acceptor resulted in an initial enhancement in dechlorination rate. This rate was sustained but did not increase in serial transfers. Bioremediation of soil contaminated with Aroclor 1254 from a transformer spill was dechlorinated by greater than 50% following mixing of the soil with dechlorinating organisms and river sediment.(ABSTRACT TRUNCATED AT 250 WORDS)}, }
@article {pmid1487732, year = {1992}, author = {Rosén, S and Ek, B and Rask, L and Tunlid, A}, title = {Purification and characterization of a surface lectin from the nematode-trapping fungus Arthrobotrys oligospora.}, journal = {Journal of general microbiology}, volume = {138}, number = {12}, pages = {2663-2672}, doi = {10.1099/00221287-138-12-2663}, pmid = {1487732}, issn = {0022-1287}, mesh = {Amino Acid Sequence ; Animals ; Fungal Proteins/chemistry/*isolation &amp; purification ; Glycosylation ; Hemagglutination Tests ; Isoelectric Point ; Lectins/chemistry/*isolation &amp; purification ; Membrane Glycoproteins/chemistry/*isolation &amp; purification ; Mitosporic Fungi/*chemistry ; Molecular Sequence Data ; Molecular Weight ; Nematoda/microbiology ; }, abstract = {Several studies have indicated that the capture of nematodes by the nematophagous fungus Arthrobotrys oligospora is mediated by a lectin on the fungal surface. One of the major surface proteins of this fungus showed haemagglutinating activity and was isolated by affinity chromatography using a mucin Sepharose column. Biochemical analysis showed that the protein was a dimeric glycoprotein with a molecular mass of 36 kDa and an isoelectric point of pH 6.5, and contained no sulphur amino acids. The protein was N-terminally blocked; four internal peptides were sequenced, and showed no significant similarity to sequences in the Swiss-Prot or PIR databases. The haemagglutinating activity of the isolated protein was not inhibited by any of the mono- or disaccharides tested, but it was inhibited by the glycoproteins fetuin and mucin. The haemagglutinating activity changed after incubating the protein in buffers of different pH, with maximal activity at pH 11.0 and no activity at pH 2.8. The lectin was tested for different enzymic activities but none were detected. Analysis of the haemagglutinating activity in various cell fractions indicated that the protein was associated with extracellular polymer layers and with the cell wall of the fungus. About the same amount of the haemagglutinating protein was recovered from samples of vegetative mycelium and of mycelium containing nematode-trapping cells.}, }
@article {pmid1476437, year = {1992}, author = {Holben, WE and Schroeter, BM and Calabrese, VG and Olsen, RH and Kukor, JK and Biederbeck, VO and Smith, AE and Tiedje, JM}, title = {Gene probe analysis of soil microbial populations selected by amendment with 2,4-dichlorophenoxyacetic acid.}, journal = {Applied and environmental microbiology}, volume = {58}, number = {12}, pages = {3941-3948}, pmid = {1476437}, issn = {0099-2240}, mesh = {2,4-Dichlorophenoxyacetic Acid/*metabolism ; Bacteria/*genetics/isolation &amp; purification/*metabolism ; Base Sequence ; Biodegradation, Environmental ; DNA Probes ; DNA, Bacterial/genetics ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Soil Microbiology ; }, abstract = {Soils with a history of 2,4-dichlorophenoxyacetic acid (2,4-D) treatment at field application rates and control soils with no prior exposure to 2,4-D were amended with 2,4-D in the laboratory. Before and during these treatments, the populations of 2,4-D-degrading bacteria were monitored by most-probable-number (MPN) enumeration and hybridization analyses, using probes for the tfd genes of plasmid pJP4, which encode enzymes for 2,4-D degradation. Data obtained by these alternate methods were compared. Several months after the most recent field application of 2,4-D (approximately 1 ppm), soils with a 42-year history of 2,4-D treatment did not have significantly higher numbers of 2,4-D-degrading organisms than did control soils with no prior history of treatment. In response to laboratory amendments with 2,4-D, both the previously treated soils and those with no prior history of exposure exhibited a dramatic increase in the number of 2,4-D-metabolizing organisms. The MPN data indicate a 4- to 5-log population increase after one amendment with 250 ppm of 2,4-D and ultimately a 6- to 7-log increase after four additional amendments, each with 400 ppm of 2,4-D. Similarly, when total bacterial DNA from the soil microbial community of these samples was analyzed by using a probe for the tfdA gene (2,4-D monoxygenase) or the tfdB gene (2,4-dichlorophenol hydroxylase) a dramatic increase in the level of hybridization was observed in both soils.(ABSTRACT TRUNCATED AT 250 WORDS)}, }
@article {pmid1476424, year = {1992}, author = {Christiaens, H and Leer, RJ and Pouwels, PH and Verstraete, W}, title = {Cloning and expression of a conjugated bile acid hydrolase gene from Lactobacillus plantarum by using a direct plate assay.}, journal = {Applied and environmental microbiology}, volume = {58}, number = {12}, pages = {3792-3798}, pmid = {1476424}, issn = {0099-2240}, mesh = {Amidohydrolases/biosynthesis/*genetics ; Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; Gene Expression ; Genes, Bacterial ; Genetic Techniques ; Lactobacillus/*enzymology/*genetics ; Molecular Sequence Data ; Plasmids ; Restriction Mapping ; Sequence Homology, Amino Acid ; }, abstract = {The conjugated bile acid hydrolase gene from the silage isolate Lactobacillus plantarum 80 was cloned and expressed in Escherichia coli MC1061. For the screening of this hydrolase gene within the gene bank, a direct plate assay developed by Dashkevicz and Feighner (M. P. Dashkevicz and S. D. Feighner, Appl. Environ. Microbiol. 53:331-336, 1989) was adapted to the growth requirements of E. coli. Because of hydrolysis and medium acidification, hydrolase-active colonies were surrounded with big halos of precipitated, free bile acids. This phenomenon was also obtained when the gene was cloned into a multicopy shuttle vector and subsequently reintroduced into the parental Lactobacillus strain. The cbh gene and surrounding regions were characterized by nucleotide sequence analysis. The deduced amino acid sequence was shown to have 52% similarity with a penicillin V amidase from Bacillus sphaericus. Preliminary characterization of the gene product showed that it is a cholylglycine hydrolase (EC 3.5.1.24) with only slight activity against taurine conjugates. The optimum pH was between 4.7 and 5.5. Optimum temperature ranged from 30 to 45 degrees C. Southern blot analysis indicated that the cloned gene has similarity with genomic DNA of bile acid hydrolase-active Lactobacillus spp. of intestinal origin.}, }
@article {pmid1447140, year = {1992}, author = {Gentry-Weeks, CR and Hultsch, AL and Kelly, SM and Keith, JM and Curtiss, R}, title = {Cloning and sequencing of a gene encoding a 21-kilodalton outer membrane protein from Bordetella avium and expression of the gene in Salmonella typhimurium.}, journal = {Journal of bacteriology}, volume = {174}, number = {23}, pages = {7729-7742}, pmid = {1447140}, issn = {0021-9193}, support = {1-F32-AI-07628/AI/NIAID NIH HHS/United States ; AI-28487/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Bacterial Outer Membrane Proteins/*biosynthesis/*genetics/immunology ; Base Sequence ; Bordetella/*genetics/immunology ; Cell Compartmentation ; Cloning, Molecular ; Escherichia coli/genetics ; Genes, Bacterial/*genetics ; Immunotherapy, Active ; Molecular Sequence Data ; Salmonella typhimurium/genetics ; Sequence Homology, Amino Acid ; Transcription, Genetic ; Turkeys ; }, abstract = {Three gene libraries of Bordetella avium 197 DNA were prepared in Escherichia coli LE392 by using the cosmid vectors pCP13 and pYA2329, a derivative of pCP13 specifying spectinomycin resistance. The cosmid libraries were screened with convalescent-phase anti-B. avium turkey sera and polyclonal rabbit antisera against B. avium 197 outer membrane proteins. One E. coli recombinant clone produced a 56-kDa protein which reacted with convalescent-phase serum from a turkey infected with B. avium 197. In addition, five E. coli recombinant clones were identified which produced B. avium outer membrane proteins with molecular masses of 21, 38, 40, 43, and 48 kDa. At least one of these E. coli clones, which encoded the 21-kDa protein, reacted with both convalescent-phase turkey sera and antibody against B. avium 197 outer membrane proteins. The gene for the 21-kDa outer membrane protein was localized by Tn5seq1 mutagenesis, and the nucleotide sequence was determined by dideoxy sequencing. DNA sequence analysis of the 21-kDa protein revealed an open reading frame of 582 bases that resulted in a predicted protein of 194 amino acids. Comparison of the predicted amino acid sequence of the gene encoding the 21-kDa outer membrane protein with protein sequences in the National Biomedical Research Foundation protein sequence data base indicated significant homology to the OmpA proteins of Shigella dysenteriae, Enterobacter aerogenes, E. coli, and Salmonella typhimurium and to Neisseria gonorrhoeae outer membrane protein III, Haemophilus influenzae protein P6, and Pseudomonas aeruginosa porin protein F. The gene (ompA) encoding the B. avium 21-kDa protein hybridized with 4.1-kb DNA fragments from EcoRI-digested, chromosomal DNA of Bordetella pertussis and Bordetella bronchiseptica and with 6.0- and 3.2-kb DNA fragments from EcoRI-digested, chromosomal DNA of B. avium and B. avium-like DNA, respectively. A 6.75-kb DNA fragment encoding the B. avium 21-kDa protein was subcloned into the Asd+ vector pYA292, and the construct was introduced into the avirulent delta cya delta crp delta asd S. typhimurium chi 3987 for oral immunization of birds. The gene encoding the 21-kDa protein was expressed equivalently in B. avium 197, delta asd E. coli chi 6097, and S. typhimurium chi 3987 and was localized primarily in the cytoplasmic membrane and outer membrane. In preliminary studies on oral inoculation of turkey poults with S. typhimurium chi 3987 expressing the gene encoding the B. avium 21-kDa protein, it was determined that a single dose of the recombinant Salmonella vaccine failed to elicit serum antibodies against the 21-kDa protein and challenge with wild-type B. avium 197 resulted in colonization of the trachea and thymus with B. avium 197.}, }
@article {pmid1429455, year = {1992}, author = {Manch-Citron, JN and Allen, J and Moos, M and London, J}, title = {The gene encoding a Prevotella loescheii lectin-like adhesin contains an interrupted sequence which causes a frameshift.}, journal = {Journal of bacteriology}, volume = {174}, number = {22}, pages = {7328-7336}, pmid = {1429455}, issn = {0021-9193}, support = {5F32DEO5554/DE/NIDCR NIH HHS/United States ; }, mesh = {*Adhesins, Bacterial ; Amino Acid Sequence ; Bacterial Adhesion/genetics ; Bacterial Proteins/*genetics ; Bacteroides/*genetics ; Base Sequence ; Blotting, Southern ; Calorimetry ; Cloning, Molecular ; Codon ; DNA, Bacterial/genetics/isolation &amp; purification ; Escherichia coli/genetics ; *Frameshift Mutation ; *Genes, Bacterial ; Genomic Library ; Lectins/*genetics ; Molecular Sequence Data ; Molecular Weight ; Oligonucleotide Probes ; *Open Reading Frames ; Plasmids ; Protein Conformation ; Restriction Mapping ; Sequence Homology, Amino Acid ; Terminator Regions, Genetic ; }, abstract = {We cloned and sequenced the Prevotella loescheii gene plaA, which encodes a lectin-like adhesin that mediates the coaggregation of P. loescheii 1295 with Streptococcus oralis 34. A probe derived from the N-terminal amino acid sequence of the purified adhesin was used to identify the plaA gene from a P. loescheii genomic library constructed in lambda GEM-11. Sequence analysis of plaA indicates that the initial translation product contains a 22-amino-acid leader. The reading frame of the plaA gene is interrupted after amino acid 28 of the mature protein by a TAA termination codon. Amplification of the P. loescheii genomic DNA in the region surrounding this codon by the polymerase chain reaction followed by DNA sequencing of the cloned DNA fragment established that this stop codon was not an experimental artifact. A frameshift beginning 29 bp downstream of the ochre terminator was required to access the only large open reading frame in the gene. Amino acid sequences of six purified peptides derived by limited proteolysis of adhesin with endoproteinase Lys-C matched the downstream amino acid sequence derived by translation of the large open reading frame. The gene coding sequence of 2.4 kb contains sufficient information for the synthesis of an 89-kDa protein. A putative rho-independent terminator (delta G = -25.5 kcal/mol [ca. -107 kJ/mol]) was detected 38 bp downstream from the plaA stop codon.}, }
@article {pmid1469519, year = {1992}, author = {Midtvedt, AC and Midtvedt, T}, title = {Production of short chain fatty acids by the intestinal microflora during the first 2 years of human life.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {15}, number = {4}, pages = {395-403}, doi = {10.1097/00005176-199211000-00005}, pmid = {1469519}, issn = {0277-2116}, mesh = {Age Factors ; Anti-Bacterial Agents/pharmacology ; Enterococcus faecium/metabolism ; Escherichia coli/metabolism ; Fatty Acids/analysis/*biosynthesis ; Feces/chemistry ; Fermentation ; Humans ; Infant ; Infant Food ; Infant, Newborn ; Intestines/*microbiology ; Milk, Human ; }, abstract = {We have followed the establishment of one group of intestinal microflora-associated characteristics, namely, the production of short chain fatty acids (SCFAs), in 30 healthy children, by gas chromatography analysis of fecal samples taken at 0, 1, 3, 6, 9, 12, 15, 18, 21, and 24 months of age. Acetic and propionic acids were the principal SCFAs at 1 and 3 months. Successively, the production of iso- and n-butyric, valeric, and caproic acids was established. At 2 years, the absolute amounts of all SCFAs with the exception of n-valeric acid had reached adult values. However, not all children had achieved a typically adult range of stool SCFAs by the end of the study. Both absolute and relative amounts of SCFAs were influenced by exposure to foods other than breast milk and exposure to antibiotic therapy. After standardization for exposure to foods other than breast milk, a positive age factor could be seen between 0 and 1 month of age for total amounts produced of SCFAs, acetic, propionic, and n-butyric acids. After this time, however, no clear age factor could be distinguished.}, }
@article {pmid1438214, year = {1992}, author = {Klimpel, KR and Molloy, SS and Thomas, G and Leppla, SH}, title = {Anthrax toxin protective antigen is activated by a cell surface protease with the sequence specificity and catalytic properties of furin.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {89}, number = {21}, pages = {10277-10281}, pmid = {1438214}, issn = {0027-8424}, support = {DK08703/DK/NIDDK NIH HHS/United States ; DK37274/DK/NIDDK NIH HHS/United States ; DK44629/DK/NIDDK NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; *Antigens, Bacterial ; Bacillus anthracis/*enzymology/genetics ; Bacterial Toxins/genetics/*metabolism/*pharmacology ; Base Sequence ; Cell Line ; Cell Membrane/*enzymology ; Cell Survival/*drug effects ; Endopeptidases/*metabolism ; Escherichia coli/genetics ; Furin ; Kinetics ; Molecular Sequence Data ; *Mutagenesis, Insertional ; Oligodeoxyribonucleotides ; Substrate Specificity ; Subtilisins/*metabolism ; }, abstract = {Proteolytic cleavage of the protective antigen (PA) protein of anthrax toxin at residues 164-167 is necessary for toxic activity. Cleavage by a cellular protease at this sequence, Arg-Lys-Lys-Arg, normally follows binding of PA to a cell surface receptor. We attempted to identify this protease by determining its sequence specificity and catalytic properties. Semi-random cassette mutagenesis was used to generate mutants with replacements of residues 164-167 by Arg, Lys, Ser, or Asn. Analysis of 19 mutant proteins suggested that lethal factor-dependent toxicity required the sequence Arg-Xaa-Xaa-Arg. Based on these data, three additional mutants were constructed with the sequences Ala-Lys-Lys-Arg, Arg-Lys-Lys-Ala, and Arg-Ala-Ala-Arg. Of these mutant proteins, Arg-Ala-Ala-Arg was toxic, confirming that the cellular protease can recognize the sequence Arg-Xaa-Xaa-Arg. The mutant containing the sequence Ala-Lys-Lys-Arg was also toxic but required > 13 times more protein to produce equivalent toxicity. This sequence specificity is similar to that of the ubiquitous subtilisin-like protease furin, which is involved in processing of precursors of certain receptors and growth factors. Therefore we tested whether a recombinant soluble furin would cleave PA. This furin derivative efficiently cleaved native PA and the Arg-Ala-Ala-Arg mutant but not the nontoxic PA mutants. In addition, previously identified inhibitors of furin blocked cleavage of receptor-bound PA. These data imply that furin is the cellular protease that activates PA, and that nearly all cell types contain at least a small amount of furin exposed on their cell surface.}, }
@article {pmid1300939, year = {1992}, author = {Shenderov, BA and Manvelova, MA and Stelanchuk, IuB}, title = {[Microbial ecology in man and animals and cholesterol metabolism. 2. Hypocholesterolemic effect of microorganisms].}, journal = {Antibiotiki i khimioterapiia = Antibiotics and chemoterapy [sic]}, volume = {37}, number = {11}, pages = {50-54}, pmid = {1300939}, issn = {0235-2990}, mesh = {Animals ; Arteriosclerosis/prevention &amp; control ; Bacteria, Aerobic/*enzymology ; Cholesterol/blood/*metabolism ; Humans ; Hypercholesterolemia/prevention &amp; control ; }, }
@article {pmid1300938, year = {1992}, author = {Shenderov, BA and Manvelova, MA}, title = {[Microbial ecology of humans and animals and cholesterol metabolism. 1. Evidence and mechanisms of host microflora participation].}, journal = {Antibiotiki i khimioterapiia = Antibiotics and chemoterapy [sic]}, volume = {37}, number = {11}, pages = {46-50}, pmid = {1300938}, issn = {0235-2990}, mesh = {Animals ; Cholesterol/*metabolism ; Humans ; Hypercholesterolemia/*microbiology ; }, }
@article {pmid1438073, year = {1992}, author = {Achi, OK}, title = {Microorganisms associated with natural fermentation of Prosopis africana seeds for the production of okpiye.}, journal = {Plant foods for human nutrition (Dordrecht, Netherlands)}, volume = {42}, number = {4}, pages = {297-304}, pmid = {1438073}, issn = {0921-9668}, mesh = {Bacillus/growth &amp; development/isolation &amp; purification ; Colony Count, Microbial ; Condiments/*microbiology ; Enterobacter cloacae/growth &amp; development/isolation &amp; purification ; Fabaceae/*microbiology ; *Fermentation ; *Food Microbiology ; Klebsiella pneumoniae/growth &amp; development/isolation &amp; purification ; Lactobacillus/growth &amp; development/isolation &amp; purification ; Micrococcus/growth &amp; development/isolation &amp; purification ; *Plants, Medicinal ; Proteus/growth &amp; development/isolation &amp; purification ; Pseudomonas/growth &amp; development/isolation &amp; purification ; Seeds/*microbiology ; Staphylococcus epidermidis/growth &amp; development/isolation &amp; purification ; }, abstract = {Okpiye is a food condiment prepared by the fermentation of Prosopis africana seeds. The traditional process for the production and microbiological characteristics of the condiment were investigated. During laboratory fermentation that lasted 96 h, the mesquite seeds underwent a natural fermentation that was characterised by the growth of microorganisms to 10(6)-10(8) cfu/g. Several species of bacteria especially B. subtilis, B. licheniformis, B. megaterium, Staphylococcus epidermidis and Micrococcus spp were found to be the most actively involved organisms. However, significant contributions to the microbial ecology were made by Enterobacter cloacae and Klebsiella pneumoniae. Lactobacillus spp were present in low numbers towards the end of the fermentation. The presence of Proteus and Pseudomonas spp in traditional fermented samples demonstrate the variability which may exist in the microflora of individual fermented samples. Variations in the important microbial groups show that Bacillus spp were the most prevalent species and occurred until the end of fermentation. Temperature, pH and titratable acidity varied with time and were influenced by the metabolic activities of the microorganisms.}, }
@article {pmid1522069, year = {1992}, author = {Top, E and Vanrolleghem, P and Mergeay, M and Verstraete, W}, title = {Determination of the mechanism of retrotransfer by mechanistic mathematical modeling.}, journal = {Journal of bacteriology}, volume = {174}, number = {18}, pages = {5953-5960}, pmid = {1522069}, issn = {0021-9193}, mesh = {Conjugation, Genetic/*genetics ; Escherichia coli/*genetics ; Genetic Markers/genetics ; Mathematics ; *Models, Genetic ; Plasmids/*genetics ; }, abstract = {Two mathematical models to elucidate the mechanism of retromobilization (or retrotransfer), that is, the ability of conjugative plasmids to mobilize genes into the cell containing the conjugative plasmid, were developed. This study deals with retromobilization of nonconjugative plasmids (Tra-Mob+). Plasmid transfer was modeled by two mass action models. The first is based on the hypothesis that retromobilization of the Tra-Mob+ vector occurs in one step, by means of the pilus formed by the Tra+ plasmid in the original host. In the second model, retromobilization is considered to be a two-step process involving two transfer events. The first step involves the transfer of the Tra+ plasmid from the recipient cell to the donor of the nonconjugative vector, and during the second encounter the nonconjugative vector is mobilized toward the recipient. Since the relationships between the number of transconjugants and the number of recipients for the two models are different, filter matings were performed for short time periods with different initial densities of the recipient population. Comparison of the numbers of transconjugants with the results of the mathematical equations confirmed the hypothesis that retromobilization is a one-step conjugation process.}, }
@article {pmid1639793, year = {1992}, author = {Arora, N and Klimpel, KR and Singh, Y and Leppla, SH}, title = {Fusions of anthrax toxin lethal factor to the ADP-ribosylation domain of Pseudomonas exotoxin A are potent cytotoxins which are translocated to the cytosol of mammalian cells.}, journal = {The Journal of biological chemistry}, volume = {267}, number = {22}, pages = {15542-15548}, pmid = {1639793}, issn = {0021-9258}, mesh = {*ADP Ribose Transferases ; Adenosine Diphosphate Ribose/metabolism ; Animals ; *Antigens, Bacterial ; Bacillus anthracis/genetics ; Bacterial Toxins/genetics/metabolism/*pharmacology ; Binding Sites ; CHO Cells ; Cell Survival/*drug effects ; Cloning, Molecular ; Cricetinae ; Cytosol/metabolism ; Dose-Response Relationship, Drug ; Escherichia coli/genetics ; Exotoxins/genetics/metabolism/*pharmacology ; Genes, Bacterial ; Kinetics ; Macrophages/*cytology/drug effects ; Mice ; Plasmids ; Protein Synthesis Inhibitors/*pharmacology ; Pseudomonas aeruginosa/genetics ; Recombinant Fusion Proteins/metabolism/pharmacology ; Restriction Mapping ; *Virulence Factors ; Pseudomonas aeruginosa Exotoxin A ; }, abstract = {The lethal factor (LF) and edema factor (EF) components of anthrax toxin are toxic to animal cells only if internalized by interaction with the protective antigen (PA) component. PA binds to a cell surface receptor and is proteolytically cleaved to expose a binding site for LF and EF. To study how LF and EF are internalized and trafficked within cells, LF was fused to the translocation and ADP-ribosylation domains (domains II and III, respectively) of Pseudomonas exotoxin A. LF fusion proteins containing Pseudomonas exotoxin A domains II and III were less toxic than those containing only domain III. Fusion proteins with a functional endoplasmic reticulum retention sequence, REDLK, at the carboxyl terminus of domain III were less toxic than those with a nonfunctional sequence, LDER. The most potent fusion protein, FP33, had an EC50 = 2 pM on Chinese hamster ovary cells, exceeding that of native Pseudomonas exotoxin A (EC50 = 420 pM). Toxicity of all the fusion proteins required the presence of PA and was blocked by monensin. These data suggest that LF and LF fusion proteins are efficiently translocated from acidified endosomes directly to the cytosol without trafficking through other organelles, as is required for Pseudomonas exotoxin A. This system provides a potential vehicle for importing diverse proteins into the cytosol of mammalian cells.}, }
@article {pmid1456826, year = {1992}, author = {Shenderov, BA and Glukhova, EV and Viadro, MM}, title = {[Microbial ecology of laboratory animals as a model in evaluation of the immunomodulating and antimicrobial agents].}, journal = {Antibiotiki i khimioterapiia = Antibiotics and chemoterapy [sic]}, volume = {37}, number = {8}, pages = {39-43}, pmid = {1456826}, issn = {0235-2990}, mesh = {Adjuvants, Immunologic ; Animals ; *Bacillus ; Bacterial Adhesion/drug effects/*physiology ; Bacterial Infections/etiology/immunology/microbiology/*prevention &amp; control ; Colitis/etiology/immunology/microbiology/*prevention &amp; control ; Colon/drug effects/immunology/*microbiology ; *Cyclophosphamide ; *Disease Models, Animal ; *Models, Biological ; Neutropenia/chemically induced/*immunology ; Pefloxacin/*administration &amp; dosage ; Polysaccharides, Bacterial/*administration &amp; dosage ; Rats ; Rats, Wistar ; }, abstract = {Rats with altered microbial ecology and decreased colonization resistance due to neutropenia induced by cyclophosphamide were used as a model for estimating the effect of bacterial polysaccharides (lactulose and exopolysaccharide from Bacillus polymyxa) and fluoroquinolones (pefloxacin). Monotherapy with pefloxacin had a favourable effect both on normalization on the intestinal microflora in the rats and their hemopoiesis (decreased neutropenia). The highest correcting effect with respect to the lowered colonization resistance was observed when pefloxacin was used in combination with exopolysaccharide.}, }
@article {pmid1629464, year = {1992}, author = {Van Dyke, TE}, title = {New agents in the chemical control of plaque and gingivitis--reaction paper.}, journal = {Journal of dental research}, volume = {71}, number = {7}, pages = {1457-1458}, doi = {10.1177/00220345920710071901}, pmid = {1629464}, issn = {0022-0345}, mesh = {Anti-Infective Agents, Local/*therapeutic use ; Dental Plaque/*prevention &amp; control ; Gingivitis/*prevention &amp; control ; Humans ; }, abstract = {The papers of Drs. Christersson, Marsh, Cummins, and Ciancio focus on the issues and problems associated with the efficacious delivery of chemical agents intended to control plaque and gingivitis. The infectious nature of periodontal disease, the importance of oral microbial ecology, the success of triclosan formulations, and the review of our current knowledge based upon clinical trials are emphasized.}, }
@article {pmid1350298, year = {1992}, author = {Forney, LJ and Gilsdorf, JR and Marrs, CF and McCrea, K and Bektesh, S}, title = {Comparison of the alpha-pilins of Haemophilus influenzae type b strains Eagan (p+), M43 (p+), and 770235bof+.}, journal = {The Journal of infectious diseases}, volume = {165 Suppl 1}, number = {}, pages = {S106-7}, doi = {10.1093/infdis/165-supplement_1-s106}, pmid = {1350298}, issn = {0022-1899}, mesh = {Amino Acid Sequence ; Bacterial Outer Membrane Proteins/*chemistry/genetics ; Base Sequence ; DNA, Bacterial/chemistry ; Fimbriae Proteins ; Fimbriae, Bacterial/*chemistry ; Gene Expression Regulation, Bacterial ; Haemophilus influenzae/genetics/*physiology ; Humans ; }, }
@article {pmid1622229, year = {1992}, author = {Collins, YE and Stotzky, G}, title = {Heavy metals alter the electrokinetic properties of bacteria, yeasts, and clay minerals.}, journal = {Applied and environmental microbiology}, volume = {58}, number = {5}, pages = {1592-1600}, pmid = {1622229}, issn = {0099-2240}, mesh = {Bacteria/drug effects/growth &amp; development/*metabolism ; Cell Movement/*drug effects ; Electrophoresis ; Hydrogen-Ion Concentration ; Isoelectric Point ; Kinetics ; Metals/*pharmacology ; Minerals/pharmacology ; *Soil Microbiology ; Yeasts/drug effects/growth &amp; development/*metabolism ; }, abstract = {The electrokinetic patterns of four bacterial species (Bacillus subtilis, Bacillus megaterium, Pseudomonas aeruginosa, and Agrobacterium radiobacter), two yeasts (Saccharomyces cerevisiae and Candida albicans), and two clay minerals (montmorillonite and kaolinite) in the presence of the chloride salts of the heavy metals, Cd, Cr, Cu, Hg, Ni, Pb, and Zn, and of Na and Mg were determined by microelectrophoresis. The cells and kaolinite were net negatively charged at pH values above their isoelectric points (pI) in the presence of Na, Mg, Hg, and Pb at an ionic strength (mu) of 3 x 10(-4); montmorillonite has no pI and was net negatively charged at all pH values in the presence of these metals. However, the charge of some bacteria, S. cerevisiae, and kaolinite changed to a net positive charge (charge reversal) in the presence of Cd, Cr, Cu, Ni, and Zn at pH values above 5.0 (the pH at which charge reversal occurred differed with the metal) and then, at higher pH values, again became negative. The charge of the bacteria and S. cerevisiae also reversed in solutions of Cu and Ni with a mu of greater than 3 x 10(-4), whereas there was no reversal in solutions with a mu of less than 3 x 10(-4). The clays became net positively charged when the mu of Cu was greater than 3 x 10(-4) and that of Ni was greater than 1.5 x 10(-4). The charge of the cells and clays also reversed in solutions containing both Mg and Ni or both Cu and Ni (except montmorillonite) but not in solutions containing both Mg and Cu (except kaolinite) (mu = 3 x 10(-4)). The pIs of the cells in the presence of the heavy metals were at either higher or lower pH values than in the presence of Na and Mg. Exposure of the cells to the various metals at pH values from 2 to 9 for the short times (ca. 10 min) required to measure the electrophoretic mobility did not affect their viability. The specific adsorption on the cells and clays of the hydrolyzed species of some of the heavy metals that formed at higher pH values was probably responsible for the charge reversal. These results suggest that the toxicity of some heavy metals to microorganisms varies with pH because the hydrolyzed speciation forms of these metals, which occur at higher pH values, bind on the cell surface and alter the net charge of the cell.(ABSTRACT TRUNCATED AT 400 WORDS)}, }
@article {pmid1533618, year = {1992}, author = {Thompson, J and Nguyen, NY and Robrish, SA}, title = {Sucrose fermentation by Fusobacterium mortiferum ATCC 25557: transport, catabolism, and products.}, journal = {Journal of bacteriology}, volume = {174}, number = {10}, pages = {3227-3235}, pmid = {1533618}, issn = {0021-9193}, mesh = {Acetates/metabolism ; Acetic Acid ; Amino Acid Sequence ; Biological Transport, Active ; Butyrates/metabolism ; Enzyme Induction ; Fusobacterium/*metabolism ; Glycoside Hydrolases/isolation &amp; purification/metabolism ; Lactates/metabolism ; Lactic Acid ; Molecular Sequence Data ; Phosphoenolpyruvate Sugar Phosphotransferase System/metabolism ; Phosphofructokinase-1/isolation &amp; purification/metabolism ; Substrate Specificity ; Sucrose/*metabolism ; beta-Fructofuranosidase ; }, abstract = {Studies of sucrose utilization by Fusobacterium mortiferum ATCC 25557 have provided the first definitive evidence for phosphoenolpyruvate-dependent sugar:phosphotransferase activity in the family Bacteroidaceae. The phosphoenolpyruvate-dependent sucrose:phosphotransferase system and the two enzymes required for the dissimilation of sucrose 6-phosphate are induced specifically by growth of F. mortiferum on the disaccharide. Monomeric sucrose 6-phosphate hydrolase (M(r), 52,000) and a dimeric ATP-dependent fructokinase (subunit M(r), 32,000) have been purified to electrophoretic homogeneity. The physicochemical and catalytic properties of these enzymes have been examined, and the N-terminal amino acid sequences for both proteins are reported. The characteristics of sucrose 6-phosphate hydrolase and fructokinase from F. mortiferum are compared with the same enzymes from both gram-positive and gram-negative species. Butyric, acetic, and D-lactic acids are the end products of sucrose fermentation by F. mortiferum. A pathway is proposed for the translocation, phosphorylation, and metabolism of sucrose by this anaerobic pathogen.}, }
@article {pmid1599245, year = {1992}, author = {Pipke, R and Wagner-Döbler, I and Timmis, KN and Dwyer, DF}, title = {Survival and function of a genetically engineered Pseudomonad in aquatic sediment microcosms.}, journal = {Applied and environmental microbiology}, volume = {58}, number = {4}, pages = {1259-1265}, pmid = {1599245}, issn = {0099-2240}, mesh = {Biodegradation, Environmental ; Chromatography, High Pressure Liquid ; Environmental Pollutants ; *Genetic Engineering ; Pseudomonas/*genetics/metabolism ; *Soil Microbiology ; *Water Microbiology ; }, abstract = {Pseudomonas sp. strain B13 FR1(pFRC20P) is a genetically engineered microorganism (GEM) which is able to degrade chloro- and methylaromatics through a constructed ortho cleavage pathway. The fate of the GEM and its ability to degrade substituted aromatic compounds in two different aquatic sediments was investigated by using a microcosm system which consisted of intact layered sediment cores with an overlying water column. The GEM survived in Lake Plussee and in Rhine river sediments at densities of approximately 10(5) bacteria per g (dry weight) (1 to 5% of the total CFU) throughout a 4-week period of investigation. According to several criteria, the microcosm system was stable and healthy throughout the experiment and the addition of the GEM did not affect the total number of extractable CFU (I. Wagner-Döbler, R. Pipke, K. N. Timmis, and D. F. Dwyer, Appl. Environ. Microbiol. 58:1249-1258, 1992). When compared with uninoculated controls, the presence of the GEM enhanced the rate of degradation of a mixture of 3-chlorobenzoate and 4-methylbenzoate (25 microns each) which had been added to the water column of the sediment cores.}, }
@article {pmid1599244, year = {1992}, author = {Wagner-Döbler, I and Pipke, R and Timmis, KN and Dwyer, DF}, title = {Evaluation of aquatic sediment microcosms and their use in assessing possible effects of introduced microorganisms on ecosystem parameters.}, journal = {Applied and environmental microbiology}, volume = {58}, number = {4}, pages = {1249-1258}, pmid = {1599244}, issn = {0099-2240}, mesh = {Bacteria/isolation &amp; purification/metabolism ; Biodegradation, Environmental ; Chlorophyll/metabolism ; Chlorophyll A ; *Containment of Biohazards ; DNA, Recombinant ; Ecology ; Environmental Pollutants/metabolism ; Evaluation Studies as Topic ; Hydrocarbons/metabolism ; *Models, Biological ; Pseudomonas/genetics/metabolism ; *Soil Microbiology ; }, abstract = {In this paper we describe a sediment microcosm system consisting of 20 undisturbed, layered sediment cores with overlying site water which are incubated under identical conditions of temperature, light, stirring rate of overlying water, and water exchange rate. Ecosystem parameters (nutrient level, photosynthetic potential, community structure of heterotrophic bacteria, thymidine incorporation rate, and oxygen microgradients) of the laboratory microcosms and the source ecosystem were compared and shown to be indistinguishable for the first 2 weeks. In weeks 3 and 4, small differences were detectable in the nutrient level, community structure of heterotrophic bacteria, and thymidine incorporation rate. However, the photosynthetic potential, depth profiles of heterotrophic bacterial community structure, and oxygen microgradients were maintained throughout the incubation period and did not differ between laboratory microcosms and the source ecosystem. The microcosm system described here would thus appear to be a valid model of aquatic sediments for up to 4 weeks; the actual period would depend on the sediment source and incubation temperature. The validated systems were used with Rhine river sediment to assess possible effects on ecosystem parameters of Pseudomonas sp. strain B13 FR1(pFRC20P), a genetically engineered microorganism (GEM) that had been constructed to degrade mixtures of halo- and alkylbenzoates and -phenols. The GEM survived in the surface sediment at densities of 5 x 10(4) to 5 x 10(5)/g (dry weight) for 4 weeks and degraded added chloro- and methylaromatics. The GEM did not measurably influence ecosystem parameters such as photosynthesis, densities of selected heterotrophic bacteria, thymidine incorporation rate, and oxygen microgradients. Thus, the microcosm system described here would seem to be useful for the study of the ecology of biodegradation and the fate and effect of microorganisms introduced into the environment.}, }
@article {pmid1583595, year = {1992}, author = {Riley, C and London, JP and Burmeister, JA}, title = {Periodontal health in 200 HIV-positive patients.}, journal = {Journal of oral pathology &amp; medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology}, volume = {21}, number = {3}, pages = {124-127}, doi = {10.1111/j.1600-0714.1992.tb00995.x}, pmid = {1583595}, issn = {0904-2512}, support = {5F35-DE05587-02/DE/NIDCR NIH HHS/United States ; }, mesh = {Acquired Immunodeficiency Syndrome/*complications ; Adult ; Chronic Disease ; Female ; Gingiva/anatomy &amp; histology ; Gingivitis/complications/pathology ; Gingivitis, Necrotizing Ulcerative/complications/pathology ; HIV Infections/*complications ; *HIV Seropositivity ; Humans ; Male ; Middle Aged ; Necrosis ; Periodontal Pocket/complications/pathology ; Periodontitis/classification/*complications/pathology ; Ulcer ; }, abstract = {Two hundred HIV-positive subjects were surveyed to determine their periodontal health status. Particular attention was given to the occurrence of a severe and rapidly progressing form of periodontal disease designated "HIV-associated periodontitis", which has been reported as being unique to AIDS patients. Among the subjects comprising the cohort, 85 subjects had good gingival health, 59 subjects exhibited gingivitis, 49 cases of adult periodontitis were observed, 5 subjects presented with advance adult periodontitis, and 2 cases of necrotizing ulcerative periodontitis (NUP) were found within the group. The periodontitis of the patients in this survey did not have unique or pathognomonic characteristics which could set their periodontal disease apart from the periodontal disease seen in HIV negative population.}, }
@article {pmid1568947, year = {1992}, author = {Vandevoorde, L and Christiaens, H and Verstraete, W}, title = {Prevalence of coaggregation reactions among chicken lactobacilli.}, journal = {The Journal of applied bacteriology}, volume = {72}, number = {3}, pages = {214-219}, doi = {10.1111/j.1365-2672.1992.tb01826.x}, pmid = {1568947}, issn = {0021-8847}, mesh = {Animals ; *Bacterial Adhesion ; Chickens/*microbiology ; Digestive System/*microbiology ; Flocculation ; Lactobacillus/*metabolism ; }, abstract = {Interbacterial adherence was frequently encountered among chicken lactobacilli. Fourteen of 45 combinations involving nine adhering strains were shown to be coaggregative. The coadherence mechanism was mediated by complementary heat- and sonication-sensitive cell surface structures. It was shown that intrageneric adherence enabled lactobacilli to maintain higher numbers in fed-batch reactors simulating the gastrointestinal tract. The mechanism of coaggregation can substantially increase the colonization potential of lactobacilli in environments with short residence times.}, }
@article {pmid1541534, year = {1992}, author = {Hughes, CV and Andersen, RN and Kolenbrander, PE}, title = {Characterization of Veillonella atypica PK1910 adhesin-mediated coaggregation with oral Streptococcus spp.}, journal = {Infection and immunity}, volume = {60}, number = {3}, pages = {1178-1186}, pmid = {1541534}, issn = {0019-9567}, mesh = {Animals ; *Bacterial Adhesion ; Bacterial Proteins/*analysis ; Electrophoresis, Polyacrylamide Gel ; Female ; Immune Sera/immunology ; Immunoblotting ; Microscopy, Electron ; Mouth/*microbiology ; Rabbits ; Streptococcus/*physiology ; Veillonella/*physiology ; }, abstract = {The gram-negative human oral bacterium Veillonella atypica PK1910 exhibits both lactose-inhibitable and lactose-noninhibitable coaggregations with certain human oral streptococci. A mild sonication procedure was used to obtain a veillonella surface protein preparation against which antisera were prepared. To characterize the lactose-inhibitable coaggregation, coaggregation-defective (COG-) mutants unable to exhibit this kind of coaggregation (class 1 mutants) were used to absorb the antisera. Only the lactose-inhibitable coaggregations were blocked by these absorbed antisera. The absorbed antiserum also reacted with a 45-kDa protein found in the parent and in class 2 COG- mutants that exhibited lactose-inhibitable coaggregation. This protein was not detected in surface protein preparations of class 1 COG- mutants. Two affinity protocols, involving agarose-lactose beads and the streptococcal coaggregation partner cells, were used to bind surface proteins from V. atypica PK1910. In each protocol, the 45-kDa protein was eluted by a solution containing 100 mM lactose. Antiserum was prepared against agarose-lactose beads with bound 45-kDa protein. When absorbed with class 1 COG- mutants, the antiserum blocked lactose-inhibitable coaggregation and reacted with the 45-kDa protein in immunoblots. When the same antiserum was absorbed with class 2 COG- mutant cells, it lost both properties, suggesting that the 45-kDa protein is an adhesin that mediates coaggregation with streptococci. The proposed adhesin does not seem to be the structural subunit of veillonella fimbriae, since no differences in fimbriae were observed by electron microscopy of the parent and all three classes of mutants.}, }
@article {pmid1324548, year = {1992}, author = {Trapezov, EV and Leont'eva, NI and Bondarenko, VM and Gracheva, NM and Solov'eva, AI and Damdingiĭn, R}, title = {[Microbial ecology of the digestive tract in patients with acute intestinal infections].}, journal = {Zhurnal mikrobiologii, epidemiologii i immunobiologii}, volume = {}, number = {3}, pages = {25-29}, pmid = {1324548}, issn = {0372-9311}, mesh = {Acute Disease ; Adolescent ; Adult ; Aged ; Bacterial Infections/*microbiology ; Campylobacter/isolation &amp; purification ; Digestive System/*microbiology/pathology ; Humans ; Klebsiella/isolation &amp; purification ; Male ; Middle Aged ; Proteus/isolation &amp; purification ; Rotavirus/isolation &amp; purification ; Salmonella/isolation &amp; purification ; Shigella/isolation &amp; purification ; Staphylococcus/isolation &amp; purification ; }, }
@article {pmid1441808, year = {1992}, author = {Belokrysenko, SS and Shestopalov, NV and Geras'kina, VP and Parfeniuk, RF}, title = {[Microbial ecology and a retrospective assessment of the possibility of predicting an outbreak of suppurative meningitis caused by a Serratia marcescens strain in a hospital for the nursing care of premature infants].}, journal = {Zhurnal mikrobiologii, epidemiologii i immunobiologii}, volume = {}, number = {2}, pages = {28-31}, pmid = {1441808}, issn = {0372-9311}, mesh = {Cross Infection/*epidemiology/microbiology ; *Disease Outbreaks/statistics &amp; numerical data ; Drug Resistance, Microbial ; Ecology ; Feces/microbiology ; *Hospitals, Maternity/statistics &amp; numerical data ; Humans ; Infant, Newborn ; Infant, Premature ; Meningitis, Bacterial/*epidemiology/microbiology ; Prognosis ; Retrospective Studies ; Serotyping ; Serratia Infections/*epidemiology/microbiology ; *Serratia marcescens/classification/isolation &amp; purification ; }, abstract = {An outbreak of purulent meningitides in a hospital ward for preterm babies, caused by Serratia marcescens strain of serovar 05/13 with multiple resistance, is described. Data on the results of the long-term observation of the ward showed that during three months preceding the outbreak the consecutive spread of the infective strain and its colonization of the intestine of children occurred. At the moment of the outbreak S. marcescens 05/13 was the dominating intestinal microflora in 37% of children in the ward and constituted 30% of the total aerobic flora in the intestine of the examined children. No S. marcescens strains were isolated from the feces and urine of the medical personnel and mothers. The importance of the observation of microflora colonizing newborn infants in the ward for the evaluation and prognostication of the epidemiological situation is discussed.}, }
@article {pmid1410788, year = {1992}, author = {Thompson, J and Donkersloot, JA}, title = {Biosynthesis and distribution of N-carboxyalkyl amino acids (opines) in bacteria.}, journal = {Research in microbiology}, volume = {143}, number = {2}, pages = {127-131}, doi = {10.1016/0923-2508(92)90001-5}, pmid = {1410788}, issn = {0923-2508}, mesh = {Amino Acids/biosynthesis/*metabolism ; Arginine/analogs &amp; derivatives/biosynthesis/chemistry ; Arthrobacter/metabolism ; Bacteria/*metabolism ; In Vitro Techniques ; Lactococcus lactis/metabolism ; Rhizobium/metabolism ; }, }
@article {pmid1728090, year = {1992}, author = {Pichichero, ME}, title = {Culture and antigen detection tests for streptococcal tonsillopharyngitis.}, journal = {American family physician}, volume = {45}, number = {1}, pages = {199-205}, pmid = {1728090}, issn = {0002-838X}, mesh = {Bacteriological Techniques/*standards ; Clinical Protocols/standards ; Diagnosis, Differential ; False Negative Reactions ; False Positive Reactions ; Family Practice/*methods ; Humans ; Immunoenzyme Techniques/*standards ; Latex Fixation Tests/*standards ; *Office Visits ; Penicillins/therapeutic use ; Pharyngitis/*diagnosis/drug therapy/microbiology ; Streptococcal Infections/*diagnosis/drug therapy/microbiology ; *Streptococcus pyogenes ; Tonsillitis/*diagnosis/drug therapy/microbiology ; }, abstract = {A throat culture is necessary for accurate diagnosis of group A beta-hemolytic streptococcal tonsillopharyngitis. The use of penicillin therapy in every patient with sore throat results in overtreatment of 85 percent of children and 95 percent of adults presenting to family physicians with the complaint of sore throat. Indiscriminate use of penicillin also increases the risk of drug side effects and subjects some patients to unnecessary alterations of microbial ecology. The signs and symptoms of group A beta-hemolytic streptococcal tonsillopharyngitis are nonspecific, and reliable clinical diagnosis is difficult. Throat culture is cost-effective and, if properly obtained and processed, more than 95 percent accurate. Antigen detection tests (rapid strep tests) are a viable laboratory alternative to throat cultures if these tests are properly performed and if negative test results are confirmed with traditional throat culture.}, }
@article {pmid1622749, year = {1992}, author = {McMeekin, TA and Ross, T and Olley, J}, title = {Application of predictive microbiology to assure the quality and safety of fish and fish products.}, journal = {International journal of food microbiology}, volume = {15}, number = {1-2}, pages = {13-32}, doi = {10.1016/0168-1605(92)90132-m}, pmid = {1622749}, issn = {0168-1605}, mesh = {Animals ; Fish Products/*microbiology ; Fishes/*microbiology ; Food Handling ; Food Inspection ; *Food Microbiology ; Food Preservation ; *Models, Biological ; Shellfish/*microbiology ; Temperature ; }, abstract = {Predictive microbiology offers an alternative to traditional microbiological assessment of food quality and safety. The concept is that a detailed knowledge of the microbial ecology of a food product can be expressed as a mathematical model to enable objective evaluation of the effect of processing, storage and distribution operations on microbial development. Experience to date indicates the need initially to derive a mathematical model in laboratory studies, to validate the model in food products and to incorporate the information into monitoring devices. These may be chemical or physical indicators or electronic integrators or loggers. To enable a correct decision on quality or safety, it is essential that the response of the monitoring device to environmental changes mimics exactly that of the organism of concern. Most monitoring devices currently available record temperature history, but not other environmental factors that influence growth and that, in some circumstances, change during storage. The next generation of monitoring devices may be required to monitor several parameters to take full advantage of increasingly accurate and sophisticated models.}, }
@article {pmid1541599, year = {1992}, author = {Vande Woestyne, M and Bruyneel, B and Verstraete, W}, title = {Physicochemical characterization of the microbial Fe2+ chelator proferrorosamine from Pseudomonas roseus fluorescens.}, journal = {The Journal of applied bacteriology}, volume = {72}, number = {1}, pages = {44-50}, doi = {10.1111/j.1365-2672.1992.tb04880.x}, pmid = {1541599}, issn = {0021-8847}, mesh = {2,2'-Dipyridyl/pharmacology ; Corrosion ; Iron Chelating Agents/*chemistry ; *Pseudomonas ; Pyrroles/*chemistry ; Solubility ; Spectrophotometry ; Stainless Steel/chemistry ; }, abstract = {The microbial chelating compound proferrorosamine A, produced by Pseudomonas roseus fluorescens, formed a complex with Fe2+ of which the apparent stability constant was found to be 10(23). The following order of increasing stability constants of metal complexes with proferrorosamine was established as: Ba2+, Ca2+, Mg2+, Mn2+ less than Hg2+ less than Zn2+ less than Pb2+ less than Co2+ less than Cu2+ congruent to Fe2+ less than Ni2+. Only Ni(2+)-proferrorosamine had a stability constant which was established as: Ba2+, Ca2+, Mg2+, Mn2+ less than Hg2+ less than Zn2+ less than Pb2+ less than Co2+ less than Cu2+ congruent to Fe2+ less than Ni2+. Only Ni(2+)-proferrorosamine had a stability constant which was ca 32 times higher than Fe(2+)-proferrorosamine. Because of the production of proferrorosamine the growth of Ps. roseus fluorescens was not inhibited in iron limiting media by the addition of 0.15 mmol/l of the weaker chemical Fe2+ chelator 2,2'-dipyridyl. This contrasted with the proferrorosamine-negative mutant K2 and Ps. stutzeri, which only produces Fe(3+)-chelating siderophores. Furthermore, it was found that proferrorosamine was able to dissolve Fe2+ from stainless steel. These results show that proferrorosamine is a strong and selective Fe2+ chelator which could be used as an alternative for the toxic 2,2'-dipyridyl to control lactic acid fermentations.}, }
@article {pmid1502595, year = {1992}, author = {Mossel, DA and Struijk, CB}, title = {The contribution of microbial ecology to management and monitoring of the safety, quality and acceptability (SQA) of foods.}, journal = {Society for Applied Bacteriology symposium series}, volume = {21}, number = {}, pages = {1S-22S}, doi = {10.1111/j.1365-2672.1992.tb03621.x}, pmid = {1502595}, issn = {0300-9610}, mesh = {Food/*standards ; Food Handling/*standards ; *Food Inspection ; *Food Microbiology ; Foodborne Diseases/*prevention &amp; control ; }, }
@article {pmid1497319, year = {1992}, author = {Thompson, J and Donkersloot, JA}, title = {N-(carboxyalkyl)amino acids: occurrence, synthesis, and functions.}, journal = {Annual review of biochemistry}, volume = {61}, number = {}, pages = {517-557}, doi = {10.1146/annurev.bi.61.070192.002505}, pmid = {1497319}, issn = {0066-4154}, mesh = {Amino Acid Sequence ; Amino Acids/biosynthesis/chemistry/*metabolism ; Animals ; Bacteria/metabolism ; Invertebrates/metabolism ; Molecular Sequence Data ; Molecular Structure ; Oxidoreductases/chemistry ; Plants/metabolism ; Yeasts/metabolism ; }, }
@article {pmid1444262, year = {1992}, author = {Triplett, EW and Sadowsky, MJ}, title = {Genetics of competition for nodulation of legumes.}, journal = {Annual review of microbiology}, volume = {46}, number = {}, pages = {399-428}, doi = {10.1146/annurev.mi.46.100192.002151}, pmid = {1444262}, issn = {0066-4227}, mesh = {Fabaceae/*genetics/*microbiology ; Nitrogen Fixation/*genetics ; *Plants, Medicinal ; }, abstract = {An economically important problem in microbial ecology concerns the efficacy of rhizobial inoculants for the formation of nitrogen-fixing root nodules on legume crop plants such as soybean, alfalfa, and clover. Some strains of rhizobia can increase symbiotic nitrogen fixation under controlled conditions. However, attempts to improve nitrogen fixation under agricultural conditions with such strains often fail, usually as a result of the presence of indigenous rhizobia limiting nodulation by the inoculum strains. This problem is referred to as the Rhizobium competition problem, and molecular genetics is being used to address the problem from two perspectives. First, the host specificity of rhizobia is being characterized with the long term goal of developing strains that can nodulate a very strain-specific host-legume genotype. Second, the genetic basis of competitiveness in several strains is being examined. Genetic determinants of nodulation competitiveness have been isolated and mechanisms for their stable integration into the genome of superior nitrogen-fixing strains have been developed. Several phenotypes have been identified as playing an important role in nodulation competitiveness including antibiosis, motility, speed of nodulation, cell-surface characteristics, and nodulation efficiency. Several solutions to this problem are likely to result from these strategies and will be useful for certain legumes in specific locations.}, }
@article {pmid1444255, year = {1992}, author = {Bull, AT and Goodfellow, M and Slater, JH}, title = {Biodiversity as a source of innovation in biotechnology.}, journal = {Annual review of microbiology}, volume = {46}, number = {}, pages = {219-252}, doi = {10.1146/annurev.mi.46.100192.001251}, pmid = {1444255}, issn = {0066-4227}, mesh = {Biotechnology/*methods/*trends ; *Genetic Variation ; Microbiology/*trends ; }, abstract = {The object of this article is to draw attention to the significance of microbial diversity as a major resource for biotechnological products and processes. The topic is approached from two complementary standpoints. First, an attempt is made to assess the extent of biodiversity, particularly microbial diversity. In this context, the application of the modern techniques of molecular biology is enabling the detection of hitherto completely unknown groups of microbes and, also, is revealing the extent of genetic diversity within microbial taxa. The case is made for the establishment of sound microbial taxonomies both on the basis of satisfying fundamental scientific needs, and for designing effective isolation strategies. The impact of an ecological approach to search and discovery of novel organisms and properties also is emphasized and illustrated. Second, the question of screening a collection of appropriate microorganisms for the desired attributes is considered. The focus here is placed on modern intelligent or targeted screening, and on the power of molecular biology to extend the range of screening options. Discussions of microbial ecology or diversity only rarely touch upon questions of gene pool conservation. The point made here is that loss of biodiversity should be as ominous for microbiologists and biotechnologists as it is to conservationists. The article concludes with thoughts on some means of conserving microbial diversity.}, }
@article {pmid1345176, year = {1992}, author = {Molin, S}, title = {Designing microbes for release into the environment.}, journal = {Science progress}, volume = {76}, number = {300 Pt 2}, pages = {139-148}, pmid = {1345176}, issn = {0036-8504}, mesh = {Bacteria/*genetics ; Containment of Biohazards ; Ecology ; *Genetic Engineering ; }, abstract = {After 20 years in which gene technology has become an important part of modern biotechnology we have seen very beneficial applications of the new techniques in the pharmaceutical industry. We are now entering a second phase involving the deliberate release of genetically engineered organisms into the environment. This next step causes concern because of a low level of predictability of their possible effects. While the risk assessment of microbial release is far from easy, the strain designers also face problems concerning optimization of performance of the organisms. The two groups of actors in this new development--the risk assessors and the strain designers--need the same platform of understanding from the field of microbial ecology, and a number of specific areas which may now be approached by modern technology deserve particular attention. An increased understanding of the activities of microbes in the environment will also allow construction of more predictable, and therefore safer, strains. Biological containment and molecular microbial ecology are two sides of the same coin in the context of release of genetically engineered microorganisms.}, }
@article {pmid1317153, year = {1992}, author = {Pinner, E and Carmel, O and Bercovier, H and Sela, S and Padan, E and Schuldiner, S}, title = {Cloning, sequencing and expression of the nhaA and nhaR genes from Salmonella enteritidis.}, journal = {Archives of microbiology}, volume = {157}, number = {4}, pages = {323-328}, pmid = {1317153}, issn = {0302-8933}, mesh = {Amino Acid Sequence ; Base Sequence ; Carrier Proteins/*genetics ; Cloning, Molecular ; Escherichia coli/genetics ; Genes, Bacterial ; Genes, Regulator ; Genetic Complementation Test ; Hydrogen-Ion Concentration ; Lithium/pharmacology ; Molecular Sequence Data ; Protein Conformation ; Salmonella enteritidis/*genetics ; Sequence Homology, Nucleic Acid ; Sodium/pharmacology ; Sodium-Hydrogen Exchangers ; }, abstract = {Na+/H+ antiporter activity is wide-spread and plays essential physiological roles. We found that several Enterobacteriaceae share conserved sequences with nhaA, the gene coding for an E. coli antiporter. A delta nhaA strain, which is sensitive to Na+ and Li+, was used to clone by complementation a DNA fragment from Salmonella enteritidis which confers resistance to the ions. The cloned fragment increased Na+/H+ antiport activity in membranes isolated from strains carrying the respective hybrid plasmid. DNA sequence analysis of the insert revealed two open reading frames. Both encode putative polypeptides which are closely homologous to the nhaA and nhaR gene products from Escherichia coli. The antiporter activity displays properties very similar to that of the E. coli NhaA, namely, it is activated by alkaline pH and recognizes Li+ with high affinity.}, }
@article {pmid1937813, year = {1991}, author = {Robrish, SA and Oliver, C and Thompson, J}, title = {Sugar metabolism by fusobacteria: regulation of transport, phosphorylation, and polymer formation by Fusobacterium mortiferum ATCC 25557.}, journal = {Infection and immunity}, volume = {59}, number = {12}, pages = {4547-4554}, pmid = {1937813}, issn = {0019-9567}, mesh = {Biological Transport ; *Carbohydrate Metabolism ; Fusobacterium/growth &amp; development/*metabolism ; Glucose/metabolism ; Glycogen/metabolism ; Phosphorylation ; Polysaccharides/*metabolism ; }, abstract = {Strains of eight Fusobacterium species differed in the ability to use sugars as energy sources for growth. For Fusobacterium russii ATCC 25533, F. gonidiaformans ATCC 25563, and F. nucleatum ATCC 10953 (except for fructose), growth was marginal to poor on all of the sugars tested. Other species displayed reasonable growth on glucose, fructose, mannose, and galactose, and two strains of F. mortiferum (ATCC 25557 and ATCC 9817) grew well on six of the sugars tested, including sucrose and maltose. Glucose transport by resting cells of most of the species was dependent upon (or markedly stimulated by) the presence of a fermentable amino acid. By contrast, F. mortiferum cells rapidly accumulated glucose and other sugars in the absence of amino acids. Although these cells were constitutive for glucose uptake, accumulation of other sugars was specifically induced by growth of F. mortiferum on the appropriate sugar. Spectrophotometric analyses and in situ staining of anionic polyacrylamide gels showed that glucose and fructose (mannose) are phosphorylated by separate ATP-dependent kinases. Fructokinase was stable in air at 4 degrees C, but under these conditions, greater than 70% of the glucokinase activity was lost. After overnight dialysis of the extract, no glucokinase activity was detectable; however, 65% of the initial enzyme activity was retained by inclusion of 1 mM dithiothreitol in the dialysis buffer. Thin-section electron microscopy showed that cells of F. mortiferum produced various amounts of intracellular glycogen during growth on the following sugars (in decreasing order of formation): galactose greater than sucrose greater than glucose greater than mannose greater than fructose. Mechanisms for sugar transport regulation, phosphorylation, and polymer synthesis by F. mortiferum cells are proposed.}, }
@article {pmid1724265, year = {1991}, author = {Zarda, B and Amann, R and Wallner, G and Schleifer, KH}, title = {Identification of single bacterial cells using digoxigenin-labelled, rRNA-targeted oligonucleotides.}, journal = {Journal of general microbiology}, volume = {137}, number = {12}, pages = {2823-2830}, doi = {10.1099/00221287-137-12-2823}, pmid = {1724265}, issn = {0022-1287}, mesh = {Antibodies, Bacterial/immunology ; Bacteria/genetics/immunology/*isolation &amp; purification ; Base Sequence ; DNA, Bacterial ; Digoxigenin/chemistry/immunology ; Flow Cytometry ; Forecasting ; Microscopy, Fluorescence ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Oligonucleotide Probes/chemistry ; RNA, Bacterial/*analysis ; RNA, Ribosomal/*analysis ; }, abstract = {Oligonucleotides were end-labelled with digoxigenin (DIG), chemically at the 5'-end or enzymically at the 3'-end. Following specific in situ hybridization of these probes to intracellular rRNA molecules, the hybrids were detected with anti-DIG Fab fragments labelled with fluorescent dyes. The antibody fragments penetrated through the bacterial cell periphery and specifically bound to their antigens. Probe-conferred and non-specific fluorescence per cell were quantified by flow cytometry and compared to values obtained with end-labelled fluorescent probes. The DIG reporter molecules could also be detected in whole fixed cells by antibodies labelled with either alkaline phosphatase or horseradish peroxidase. The penetration of the large antibody-enzyme complexes into the cells required lysozyme/EDTA treatment prior to the hybridization and has so far only been achieved for Gram-negative bacteria. This technique has the potential for significant signal amplification as compared to the fluorescently end-labelled oligonucleotides hitherto used for single cell identification in microbial ecology. Moreover, it can be used instead of fluorescent assays in natural samples showing autofluorescence.}, }
@article {pmid1664710, year = {1991}, author = {Turner, JT and Lampel, JS and Stearman, RS and Sundin, GW and Gunyuzlu, P and Anderson, JJ}, title = {Stability of the delta-endotoxin gene from Bacillus thuringiensis subsp. kurstaki in a recombinant strain of Clavibacter xyli subsp. cynodontis.}, journal = {Applied and environmental microbiology}, volume = {57}, number = {12}, pages = {3522-3528}, pmid = {1664710}, issn = {0099-2240}, mesh = {Bacillus thuringiensis/*genetics ; Bacillus thuringiensis Toxins ; *Bacterial Proteins ; *Bacterial Toxins ; Blotting, Southern ; Containment of Biohazards ; *DNA, Recombinant ; Endotoxins/*genetics ; Gram-Positive Bacteria/*genetics/growth &amp; development ; Hemolysin Proteins ; Kanamycin Resistance/genetics ; Kinetics ; Phenotype ; Plants/microbiology ; Plasmids ; Tetracycline Resistance/genetics ; Transformation, Bacterial ; }, abstract = {Deletion of chromosomally inserted gene sequences from Clavibacter xyli subsp. cynodontis, a xylem-inhabiting endophyte, was studied in vitro and in planta. We found that nonreplicating plasmid pCG610, which conferred resistance to kanamycin and tetracycline and contained segments of C. xyli subsp. cynodontis genomic DNA, integrated into a homologous sequence in the bacterial chromosome. In addition, pCG610 contains two copies of the gene encoding the CryIA(c) insecticidal protein of Bacillus thuringiensis subsp. kurstaki HD73. Using drug resistance phenotypes and specific DNA probes, we found that the loss of all three genes arose both in vitro under nonselective conditions and in planta. The resulting segregants are probably formed by recombination between the repeated DNA sequences flanking pCG610 that resulted from the integration event into the chromosome. Eventually, segregants predominated in the bacterial population. The loss of the integrated plasmid from C. xyli subsp. cynodontis revealed a possible approach for decreasing the environmental consequences of recombinant bacteria for agricultural use.}, }
@article {pmid1658003, year = {1991}, author = {Thompson, J and Sackett, DL and Donkersloot, JA}, title = {Purification and properties of fructokinase I from Lactococcus lactis. Localization of scrK on the sucrose-nisin transposon Tn5306.}, journal = {The Journal of biological chemistry}, volume = {266}, number = {33}, pages = {22626-22633}, pmid = {1658003}, issn = {0021-9258}, mesh = {Carbohydrate Metabolism ; Chromatography, Affinity ; Chromatography, Gel ; Chromatography, Ion Exchange ; *DNA Transposable Elements ; Electrophoresis, Polyacrylamide Gel ; Fructokinases/*genetics/*isolation &amp; purification/metabolism ; *Genes, Bacterial ; Isoenzymes/*genetics/*isolation &amp; purification/metabolism ; Kinetics ; Lactococcus lactis/*enzymology/genetics/growth &amp; development ; Macromolecular Substances ; Molecular Weight ; Protein Conformation ; Restriction Mapping ; Sucrose/metabolism ; }, abstract = {Two electrophoretically distinct proteins with fructokinase (ATP:fructose-6-phosphotransferase) activity were detected in Lactococcus lactis subsp. lactis K1. Whereas fructokinase I was induced specifically by growth of the organism on sucrose, fructokinase II was derepressed during growth on ribose, galactose, maltose, and lactulose. Fructokinase I was purified about 1000-fold to electrophoretic homogeneity (specific activity 112 units/mg). The amino acid composition, N-terminal sequence, nucleoside triphosphate, and metal requirement(s) of the enzyme are reported. Ultracentrifugal analysis showed that the enzyme was primarily dimeric with subunits of 33.5 kDa (+/- 5%). When completely reduced, fructokinase I migrated as a single protein (Mr = 32,000) by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, but in the absence of reducing agent two polypeptides (apparent Mr = 29,000 and 31,000) were detected. Isoelectric focusing also revealed two polypeptides (pI 5.6 and 5.8), and both species catalyzed the phosphorylation of fructose and mannose. Hybridization studies showed that: (i) a sucrose-negative mutant lacking the fructokinase I gene (scrK) retained fructokinase II activity and (ii) scrK is closely linked to scrA and scrB which encode Enzyme IIScr and sucrose-6-phosphate hydrolase, respectively. In L. lactis K1, these genes and the N5-(1-carboxyethyl)-L-ornithine synthase gene (ceo) are encoded on the sucrose-nisin transposon Tn5306 in the order ceo-scrKAB.}, }
@article {pmid1939073, year = {1991}, author = {Quinn, CP and Singh, Y and Klimpel, KR and Leppla, SH}, title = {Functional mapping of anthrax toxin lethal factor by in-frame insertion mutagenesis.}, journal = {The Journal of biological chemistry}, volume = {266}, number = {30}, pages = {20124-20130}, pmid = {1939073}, issn = {0021-9258}, mesh = {*Antigens, Bacterial ; Bacterial Toxins/*genetics ; Base Sequence ; Binding, Competitive ; Genes, Bacterial ; Molecular Sequence Data ; *Mutagenesis, Insertional ; Phenotype ; Plasmids ; Restriction Mapping ; }, abstract = {Linker insertion mutagenesis was employed to create structural disruptions of the lethal factor (LF) protein of anthrax toxin to map functional domains. A dodecameric linker was inserted at 17 blunt end restriction enzyme sites throughout the gene. Paired MluI restriction sites within the linker allowed the inserts to be reduced from four to two amino acids. Shuttle vectors containing the mutated genes were transformed into the avirulent Bacillus anthracis UM23C1-1 for expression and secretion of the gene products. Mutations at five sites in the central one-third of the sequence made the protein unstable, and purified protein could not be obtained. Mutated LF proteins with insertions at the other sites were purified and assessed for toxic activity in a macrophage lysis assay and for their ability to bind to the protective antigen (PA) component of anthrax toxin, the receptor binding moiety. Most insertions located in the NH2-terminal one-third of the LF protein eliminated both toxicity and binding to PA, while all four insertions in the COOH-terminal one-third of the protein eliminated toxicity without affecting binding to PA. These data support the hypothesis that the NH2-terminal domain contains the structures required for binding to PA and the COOH-terminal domain contains the putative catalytic domain of LF.}, }
@article {pmid1955415, year = {1991}, author = {Van Renterghem, B and Huysman, F and Rygole, R and Verstraete, W}, title = {Detection and prevalence of Listeria monocytogenes in the agricultural ecosystem.}, journal = {The Journal of applied bacteriology}, volume = {71}, number = {3}, pages = {211-217}, doi = {10.1111/j.1365-2672.1991.tb04450.x}, pmid = {1955415}, issn = {0021-8847}, mesh = {Animals ; Cattle ; Enterococcus faecalis/growth &amp; development ; Feces/*microbiology ; Food Microbiology ; Fresh Water ; Listeria monocytogenes/growth &amp; development/*isolation &amp; purification ; *Manure ; *Soil Microbiology ; Swine ; Vegetables ; Water Microbiology ; }, abstract = {The sensitivity of four different enrichment procedures to detect Listeria monocytogenes in the presence of high levels of Streptococcus faecalis was investigated. Defined mixed cultures of Strep. faecalis and L. monocytogenes gave better results with one-stage enrichment techniques. For manure samples, however, two-stage enrichment techniques gave the best performance. The so-called cold enrichment techniques were found to be unsatisfactory for samples from natural environments. The following materials were examined for the presence of L. monocytogenes: fresh pig faeces (16% positive), fresh cattle faeces (20% positive), stored liquid manure (0% positive), manured soil samples (0% positive) and ground water samples (5% positive). After 3 weeks of storage L. monocytogenes could be detected in only one of the initially nine positive fresh faeces samples. Two months after inoculation of stored liquid pig manure, stored liquid cattle manure and soil with L. monocytogenes, this bacterium could not be traced in any of these materials. Radishes (Raphanus sativus) and carrots (Daucus carota), sown in soil inoculated with L. monocytogenes, were gathered after 3 months and examined for the presence of L. monocytogenes. Three of six radish samples were found to be positive. Remarkably, however, all carrot samples (six) were free of L. monocytogenes.}, }
@article {pmid1832455, year = {1991}, author = {Smith, RN and Andersen, RN and Kolenbrander, PE}, title = {Inhibition of intergeneric coaggregation among oral bacteria by cetylpyridinium chloride, chlorhexidine digluconate and octenidine dihydrochloride.}, journal = {Journal of periodontal research}, volume = {26}, number = {5}, pages = {422-428}, doi = {10.1111/j.1600-0765.1991.tb01732.x}, pmid = {1832455}, issn = {0022-3484}, mesh = {Actinomyces/drug effects ; Anti-Infective Agents, Local/*pharmacology ; Bacterial Adhesion/drug effects ; Cetylpyridinium/*pharmacology ; Chlorhexidine/*analogs &amp; derivatives/pharmacology ; Dental Plaque/*microbiology/prevention &amp; control ; Gram-Negative Bacteria/*drug effects ; Humans ; Imines ; Pyridines/*pharmacology ; Species Specificity ; Streptococcus/drug effects ; }, abstract = {The potential inhibitory effect of chlorhexidine digluconate on the intergeneric coaggregation of 11 pairs of Gram-positive organisms was compared to its ability to inhibit coaggregations of 14 pairs comprised of both a Gram-positive and a Gram-negative cell type. Dramatic differences in the inhibitory effectiveness of the antimicrobial compound on the two kinds of coaggregation pairs were found. Gram-positive pairs were not inhibited at a concentration of 0.25%, whereas the coaggregations involving a Gram-negative partner were usually completely blocked at concentrations as low as 0.01%. Similar effects to chlorhexidine digluconate were found with octenidine dihydrochloride and cetylpyridinium chloride, while sodium dodecylsulfate was inhibitory only at 10- to 50-fold higher concentrations. These results suggest that chlorhexidine digluconate, octenidine dihydrochloride, and cetylpyridinium chloride may be effective inhibitors of later microbial colonizers of dental plaque but may not disturb a normal healthy indigenous flora.}, }
@article {pmid1681155, year = {1991}, author = {Wilkowske, CJ}, title = {General principles of antimicrobial therapy.}, journal = {Mayo Clinic proceedings}, volume = {66}, number = {9}, pages = {931-941}, doi = {10.1016/s0025-6196(12)61582-1}, pmid = {1681155}, issn = {0025-6196}, mesh = {Anti-Bacterial Agents/administration &amp; dosage/adverse effects/*therapeutic use ; Bacterial Infections/*drug therapy ; Drug Therapy, Combination/administration &amp; dosage/adverse effects/therapeutic use ; Humans ; Mycoses/drug therapy ; Virus Diseases/drug therapy ; }, abstract = {Treatment with antimicrobial agents must be tailored to the individual patient, the site of infection, and the etiologic organism involved. Effectiveness, toxicity, and cost are the basic considerations in choosing a drug. Because initiation of therapy often cannot be delayed until microbiologic studies have been performed, empiric treatment should be sufficiently broad to cover the most likely pathogens, based on the site of infection and the type of host. Definitive therapy may differ from initial therapy and should be instituted as soon as specific laboratory and clinical data are available. Information about allergic reactions to drugs should be elicited; because of the numerous families of antimicrobial agents currently available, most infections in patients with drug allergies can be treated with adequate substitutes. Cautious conservatism is advocated in the use of new antimicrobial agents. The effects of new agents on the microbial ecology and the hospital environment should be considered.}, }
@article {pmid1651334, year = {1991}, author = {Singh, Y and Klimpel, KR and Quinn, CP and Chaudhary, VK and Leppla, SH}, title = {The carboxyl-terminal end of protective antigen is required for receptor binding and anthrax toxin activity.}, journal = {The Journal of biological chemistry}, volume = {266}, number = {23}, pages = {15493-15497}, pmid = {1651334}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; *Antigens, Bacterial ; Bacillus subtilis/metabolism ; Bacterial Toxins/*genetics/metabolism ; Base Sequence ; Cell Survival ; Cricetinae ; Cricetulus ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/metabolism ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Plasmids ; Receptors, Cell Surface/*metabolism ; *Receptors, Peptide ; }, abstract = {Anthrax toxin consists of three separate proteins produced by Bacillus anthracis: protective antigen (PA), lethal factor (LF), and edema factor (EF). Previous work showed that the process by which these proteins damage eukaryotic cells begins with binding of PA (83 kDa) to cell surface receptors. PA is then cleaved by a cell surface protease so as to expose a high-affinity binding site for LF or EF on the COOH-terminal, receptor-bound, 63-kilodalton fragment. In this report we more closely define a region of PA involved in receptor binding. The gene encoding PA was mutagenized so as to delete 3, 5, 7, 12, or 14 amino acids from the carboxyl terminus of the protein, and the truncated PA variants were purified from Bacillus subtilis or Escherichia coli. Deletion of 3, 5, or 7 amino acids reduced the binding of PA to cells and the subsequent toxicity of the PA.LF complex to J774A.1 cells and also the ability to cause EF binding to cells. Deletion of 12 or 14 amino acids completely eliminated all these activities. These results show that the carboxy terminus comprises or is part of the receptor-binding domain of PA.}, }
@article {pmid1650362, year = {1991}, author = {Thompson, J and Nguyen, NY and Sackett, DL and Donkersloot, JA}, title = {Transposon-encoded sucrose metabolism in Lactococcus lactis. Purification of sucrose-6-phosphate hydrolase and genetic linkage to N5-(L-1-carboxyethyl)-L-ornithine synthase in strain K1.}, journal = {The Journal of biological chemistry}, volume = {266}, number = {22}, pages = {14573-14579}, pmid = {1650362}, issn = {0021-9258}, mesh = {Amino Acid Oxidoreductases/*genetics/metabolism ; Amino Acid Sequence ; Base Sequence ; Chromatography, Gel ; DNA ; *DNA Transposable Elements ; Electrophoresis, Polyacrylamide Gel ; Genes, Bacterial ; Genetic Linkage ; Glycoside Hydrolases/genetics/*isolation &amp; purification ; Hydrolysis ; Isoelectric Focusing ; Lactococcus lactis/genetics/*metabolism ; Molecular Sequence Data ; Molecular Weight ; Oligonucleotide Probes ; Restriction Mapping ; Sucrose/genetics/*metabolism ; beta-Fructofuranosidase ; }, abstract = {Sucrose-6-phosphate hydrolase from Lactococcus lactis subsp. lactis K1-23 (formerly Streptococcus lactis K1-23) has been purified 600-fold to electrophoretic homogeneity. Purification of the enzyme was achieved by DEAE-Sephacel, phosphocellulose P-11, and gel exclusion (Ultrogel AcA 54) chromatography. The purified enzyme (specific activity 31 units/mg) catalyzed the hydrolysis of both 6-O-phosphoryl-alpha-D-glucopyranosyl-1,2-beta-D-fructofuranoside (sucrose 6-phosphate) and sucrose (Km = 0.1 and 100 mM, respectively). Ultracentrifugal analysis of sucrose-6-phosphate hydrolase indicated an Mr = 52,200. The purified enzyme migrated as a single protein during sodium dodecyl sulfate-polyacrylamide gel electrophoresis (Mr = 52,000). However, four distinct polypeptides were detected by analytical electrofocusing, and all four species hydrolyzed sucrose and sucrose 6-phosphate. The amino acid composition of sucrose-6-phosphate hydrolase, and the sequence of the first 12 amino acids from the NH2 terminus, have been determined. Hybridization studies with oligonucleotide probes show that the genes for sucrose-6-phosphate hydrolase (scrB), Enzyme IIScr of the phosphoenolypyruvate-dependent sucrose:phosphotransferase system (scrA), and N5-(carboxyethyl)ornithine synthase (ceo) are encoded by the same approximately 20-kilobase EcoRI fragment. This fragment is part of a large transposon Tn5306 that also encodes the nisin precursor gene, spaN, and IS904. In L. lactis ATCC 11454, spaN, IS904, scrA, and scrB (but not ceo) are encoded on a related transposon, Tn5307.}, }
@article {pmid1912705, year = {1991}, author = {Bååth, E and Arnebrant, K and Nordgren, A}, title = {Microbial biomass and ATP in smelter-polluted forest humus.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {47}, number = {2}, pages = {278-282}, pmid = {1912705}, issn = {0007-4861}, mesh = {Adenosine Triphosphate/*analysis ; Chromatography, Gas ; *Copper/analysis ; Ecology ; Environmental Pollution/*analysis ; *Industry ; Soil/*analysis ; *Soil Microbiology ; Trees ; Zinc/analysis ; }, }
@article {pmid1880828, year = {1991}, author = {Mathew, M and Mathan, MM and Mani, K and George, R and Jebakumar, K and Dharamsi, R and Kirubakaran, C and Pereira, S and Mathan, VI}, title = {The relationship of microbial pathogens to acute infectious diarrhoea of childhood.}, journal = {The Journal of tropical medicine and hygiene}, volume = {94}, number = {4}, pages = {253-260}, pmid = {1880828}, issn = {0022-5304}, mesh = {Acute Disease ; Child, Preschool ; Cryptosporidiosis/epidemiology/etiology ; Diarrhea, Infantile/epidemiology/*etiology ; Enterobacteriaceae Infections/epidemiology/*etiology ; Female ; Humans ; India ; Infant ; Male ; Rotavirus Infections/epidemiology/*etiology ; Socioeconomic Factors ; }, abstract = {Bacterial, viral and parasitic enteric pathogens were detected in 692 of 916 children below 36 months of age with acute diarrhoea and in 289 of 587 matched controls. The rates of identification of only four groups of pathogens, rotavirus, Shigellae, Salmonella typhimurium and enterotoxigenic E. coli, were significantly higher in the patients. The prevalence of a variety of other enteric pathogens was similar in controls of patients. Shigellosis had a characteristic clinical profile but none of the other agents could be suspected on clinical grounds. The high prevalence of pathogens in controls suggested that the population may be partially protected against a variety of enteric pathogens and that final common pathways leading to diarrhoea may be activated by changes in the microbial ecology of the gut lumen.}, }
@article {pmid1683401, year = {1991}, author = {Cisar, JO and Barsumian, EL and Siraganian, RP and Clark, WB and Yeung, MK and Hsu, SD and Curl, SH and Vatter, AE and Sandberg, AL}, title = {Immunochemical and functional studies of Actinomyces viscosus T14V type 1 fimbriae with monoclonal and polyclonal antibodies directed against the fimbrial subunit.}, journal = {Journal of general microbiology}, volume = {137}, number = {8}, pages = {1971-1979}, doi = {10.1099/00221287-137-8-1971}, pmid = {1683401}, issn = {0022-1287}, mesh = {Actinomyces viscosus/immunology/*metabolism ; Agglutination Tests ; Antibodies, Monoclonal/metabolism ; Bacterial Adhesion/*physiology ; Bacterial Proteins/*immunology/metabolism ; Binding Sites/physiology ; Durapatite ; Electrophoresis, Polyacrylamide Gel ; Fimbriae, Bacterial/chemistry/*immunology/metabolism ; Hydroxyapatites/metabolism ; Immunoglobulin Fab Fragments/metabolism ; Immunoglobulin G/metabolism ; Microscopy, Electron ; Saliva/metabolism ; }, abstract = {Each of five monoclonal antibodies (mAbs) prepared against the type 1 fimbriae of Actinomyces viscosus T14V reacted with a 54 kDa cloned protein previously identified as a fimbrial subunit. This purified protein completely inhibited the reaction of a specific anti-type-1-fimbria rabbit antibody with A. viscosus whole cells. Maximum values for the number of antibody molecules bound per bacterial cell ranged from 7 x 10(3) to 1.2 x 10(4) for the different 125I-labelled mAbs and was approximately 7 x 10(4) for 125I-labelled rabbit IgG or Fab against either type 1 fimbriae or the 54 kDa cloned protein. Although the different mAbs, either individually or as a mixture, failed to inhibit the type-1-fimbria-mediated adherence of A. viscosus T14V to saliva-treated hydroxyapatite, each rabbit antibody gave 50% inhibition of adherence when approximately 5 x 10(4) molecules of IgG were bound per cell. However, binding of each corresponding rabbit Fab had no significant effect on bacterial attachment unless much higher concentrations were used. These findings suggest that antibodies directed solely against the 54 kDa fimbrial subunit do not react with the putative receptor binding sites of A. viscosus T14V type 1 fimbriae. Instead, inhibition of attachment by the polyclonal antibodies may depend on an indirect effect of antibody binding that prevents the fimbria-receptor interaction.}, }
@article {pmid1893273, year = {1991}, author = {Hoover, WH and Miller, TK}, title = {Rumen digestive physiology and microbial ecology.}, journal = {The Veterinary clinics of North America. Food animal practice}, volume = {7}, number = {2}, pages = {311-325}, doi = {10.1016/s0749-0720(15)30801-x}, pmid = {1893273}, issn = {0749-0720}, mesh = {Animals ; Bacterial Physiological Phenomena ; Cattle/*physiology ; Dietary Carbohydrates/metabolism ; Dietary Fats/metabolism ; Dietary Proteins/metabolism ; *Digestion ; Eukaryota/physiology ; Fungi/physiology ; Rumen/microbiology/parasitology/*physiology ; }, abstract = {The rumen is a dynamic, continuous fermentation compartment that provides a suitable environment for a variety of species of anaerobic bacteria, protozoa, and fungi. These microorganisms have a complex series of interactions with the feeds supplied to the host, with some using particulate matter as both sources of nutrients and sites of sequestration to avoid being washed from the rumen by the rapid flow of fluids. Because of the ability to use soluble nutrients and to reproduce rapidly, other microbes associate primarily with the liquid phase of the rumen contents. Due to the metabolic activity of all microbial populations, feeds are converted to microbial matter and fermentation end products, which serve as nutrients for the ruminant. Optimum feed utilization by ruminants is dependent on achieving maximum rumen fermentation and flow of microbial protein to the duodenum. At this time, it is clear that the major nutrients required by the microbial populations include both fibrous and nonfibrous sources of carbohydrates and nitrogen in the form of ammonia, amino acids, and peptides. In spite of five decades of research, the exact quantities and sources of these nutrients that will result in optimum rumen fermentation rates and microbial yields are only partially known.}, }
@article {pmid1892737, year = {1991}, author = {Mossel, DA and Struijk, CB}, title = {Public health implication of refrigerated pasteurized ('sous-vide') foods.}, journal = {International journal of food microbiology}, volume = {13}, number = {3}, pages = {187-206}, doi = {10.1016/0168-1605(91)90003-8}, pmid = {1892737}, issn = {0168-1605}, mesh = {Bacteria/*growth &amp; development ; Consumer Product Safety ; Food Handling ; *Food Microbiology ; *Food Preservation ; *Refrigeration ; }, abstract = {Food that upon pasteurization is stored in hermetically sealed containers at food temperatures not exceeding 3 degrees C could be designated by the generic term Refrigerated Pasteurized Foods of Extended Durability, REPFEDs. If not properly processed or protected against recontamination, or if temperature-abused, REPFEDs may present serious health risks. However, control is readily available. Sound microbial ecology, supported by expert risk assessment, allows the design and introduction of longitudinally integrated manufacture, distribution, handling by outlets and consumers and culinary preparation, which result in the assurance of the wholesomeness of the commodity as eaten. Recent progress, including intrinsic preservation by the incorporation of starter cultures, bacteriocins or particular enzymes, opens vistas for attractive future developments. Once microbiological safety has been built into the REPFED-line, monitoring can be limited to (i) real-time tests particularly applied to the factory environment; and (ii) rapid, simple examination for marker organisms of freshly manufactured products versus those approaching expiration dates. Such audits will allow rapid retrieval of incidental process failure and its rectification. It also serves to substantiate measurements of food temperature and spot checks on intrinsic inhibitory attributes. The application of scientific knowledge and technological expertise should primarily be entrusted to the industry itself, heeding Lord Plumb's strategy of "partnership along the food production chain from farm to fork." It should be supported and validated by Public Health Authorities. At all stages safety communication with the public should be ensured.}, }
@article {pmid1909546, year = {1991}, author = {Aryanta, RW and Fleet, GH and Buckle, KA}, title = {The occurrence and growth of microorganisms during the fermentation of fish sausage.}, journal = {International journal of food microbiology}, volume = {13}, number = {2}, pages = {143-155}, doi = {10.1016/0168-1605(91)90056-u}, pmid = {1909546}, issn = {0168-1605}, mesh = {Animals ; Bacillus cereus/growth &amp; development ; Bacteria/*growth &amp; development ; Clostridium perfringens/growth &amp; development ; Colony Count, Microbial ; Escherichia coli/growth &amp; development ; Fermentation ; *Fish Products ; *Food Microbiology ; Fungi/growth &amp; development ; Hydrogen-Ion Concentration ; Lactobacillus/growth &amp; development ; Micrococcus/growth &amp; development ; Pediococcus/growth &amp; development ; Salmonella/growth &amp; development ; Staphylococcus/growth &amp; development ; Staphylococcus aureus/growth &amp; development ; Vibrio parahaemolyticus/growth &amp; development ; }, abstract = {Minced fish (mullet) sausage mixes containing added sugar, salt, nitrate, nitrite and spices were fermented (48 h, 30 degrees C) by indigenous flora or by a starter culture (Pediococcus acidilactici) and the microbial ecology and behaviour of various bacteria was monitored. Pediococcus pentosaceus and Lactobacillus plantarum dominated the indigenous fermentation, achieving populations of 10(7)-10(8) cfu/g by 48 h, and decreasing the pH of the mix to 4.5-4.7. Significant growth (10(5)-10(7) cfu/g) of Staphylococcus warneri, Staphylococcus aureus, Staphylococcus epidermidis. Micrococcus varians and Micrococcus luteus also occurred during this fermentation. Less growth was exhibited by Bacillus megaterium and yeasts. Pediococcus acidilactici dominated the fermentation when it was inoculated as a starter culture, but indigenous lactic acid bacteria (P. pentosaceus and L. plantarum) also grew to 10(7)-10(8) cfu/g. The growth of other bacteria and yeasts was restricted during fermentation with starter culture. Inoculated Escherichia coli, Salmonella typhimurium, Salmonella sofia, and Staphylococcus aureus grew to 10(6)-10(7) cfu/g in the sausage mix during indigenous fermentation. Lesser growth occurred for Bacillus cereus, Clostridium perfringens and Vibrio parahaemolyticus. Growth of these bacteria was significantly inhibited in sausage mix fermented with P. acidilactici.}, }
@article {pmid1872614, year = {1991}, author = {Norin, KE and Persson, AK and Saxerholt, H and Midtvedt, T}, title = {Establishment of Lactobacillus and Bifidobacterium species in germfree mice and their influence on some microflora-associated characteristics.}, journal = {Applied and environmental microbiology}, volume = {57}, number = {6}, pages = {1850-1852}, pmid = {1872614}, issn = {0099-2240}, mesh = {Actinomycetales Infections/metabolism/*microbiology ; Aging ; Animals ; Bacterial Infections/metabolism/*microbiology ; Bifidobacterium/*physiology ; Bilirubin/metabolism ; Cecum/metabolism/microbiology ; Colon/metabolism/microbiology ; Colony Count, Microbial ; Dipeptides/metabolism ; Germ-Free Life ; Lactobacillus/*physiology ; Mice ; Trypsin/metabolism ; }, abstract = {Germfree mice were inoculated with both Lactobacillus acidophilus A10 and Bifidobacterium bifidum B11. Both strains were established and present in more than 10(8) cells per g of cecum and colon contents. Furthermore, L. acidophilus A10 was established in high numbers in stomach and small intestine. Contents from different parts of the intestine were investigated with regard to the following microflora-associated characteristics: degradation of mucin, beta-aspartylglycine and tryptic activity, conversion of cholesterol to coprostanol and bilirubin to urobilinogen, deconjugation of bilirubin glucuronides, and reduction of the cecum size. In spite of being established, the microbes were not able to mediate any alterations of the parameters investigated. All animals retained values as found in their germfree counterparts.}, }
@article {pmid1999556, year = {1991}, author = {Hojo, S and Takahashi, N and Yamada, T}, title = {Acid profile in carious dentin.}, journal = {Journal of dental research}, volume = {70}, number = {3}, pages = {182-186}, doi = {10.1177/00220345910700030501}, pmid = {1999556}, issn = {0022-0345}, mesh = {Acetates/analysis ; Actinomyces ; Adolescent ; Adult ; Aged ; Carboxylic Acids/*analysis ; Child ; Dental Caries/*metabolism/microbiology ; Dentin/chemistry/*metabolism/microbiology ; Humans ; Lactates/analysis ; Lactobacillus ; Middle Aged ; Propionates/analysis ; Streptococcus ; }, abstract = {Organic acids in carious dentin from 69 permanent teeth were analyzed by gas chromatography. Lactate, acetate, propionate, and butyrate were detected in most samples, and limited amounts of isobutyrate, valerate, isovalerate, caproate, and isocaproate were occasionally detected. Lactate, acetate, and propionate were major acids and altogether accounted for about 90% of total acid in most samples of carious dentin. However, the proportion of these three acids varied among the samples. Some samples contained over 85% lactate, while others contained mainly acetate and propionate. A high percentage of acetate was usually accompanied by an appreciable amount of propionate. All seven samples in carious dentin under fillings or restorations had little lactate, but a high percentage of acetate plus propionate. The differences in acid profiles of carious dentin may reflect differences in the microbial ecology of carious dentin, and a stage of progress of dentin caries or a type of dentin caries.}, }
@article {pmid1901673, year = {1991}, author = {Huis in 't Veld, JH}, title = {[Gastrointestinal flora and health in man and animal].}, journal = {Tijdschrift voor diergeneeskunde}, volume = {116}, number = {5}, pages = {232-239}, pmid = {1901673}, issn = {0040-7453}, mesh = {Animal Nutritional Physiological Phenomena ; Animals ; Digestive System/*microbiology ; Digestive System Physiological Phenomena ; Ecology ; Humans ; Immunity ; Infection Control ; Nutritional Physiological Phenomena ; }, abstract = {A balanced and stable gastro-intestinal microflora is of vital importance for the optimum function of the gastro-intestinal tract and consequently for the health of man and animals. The gastro-intestinal microflora is a very complex ecosystem, the current knowledge of which is still very limited. It is obvious that the intestinal flora has a protective function (prevention of infection). In addition it has a positive effect on nutrition (digestion, effects on physiology, production of vitamins). Changes in diet, stress, the use of antibiotics and excessive hygiene all bring about changes in the micro-biological ecosystem and consequently changes in health conditions. Knowledge about the microbial ecology of the intestine is also of importance in the prevention of zoonoses. Recently, increasing attention is being paid to the development of methods to influence the composition of the gastro-intestinal microflora in man and animals by probiotics (dried cells or fermented food). These concepts will be dealt with in the present paper and, in addition some of the possible uses will be discussed.}, }
@article {pmid1671870, year = {1991}, author = {Krichevsky, MI}, title = {Draft results of a workshop to develop guidelines for studies involving microbial incidence or populations in the oral cavity.}, journal = {Journal of dental research}, volume = {70}, number = {3}, pages = {226-232}, doi = {10.1177/00220345910700031401}, pmid = {1671870}, issn = {0022-0345}, mesh = {DNA, Bacterial/analysis ; Data Collection ; Epidemiologic Methods ; Humans ; Immunologic Techniques ; Interinstitutional Relations ; *Microbiological Techniques ; Mouth/*microbiology ; Nucleic Acid Probes ; Research Design ; }, abstract = {The following five outlines are the results to date of the Workshop held in Rockville, Maryland, in January, 1990. The topics considered in these outlines are: (1) validation of immunological and/or nucleic acid identification probes, (2) cross-calibration of methods and/or laboratories for multi-laboratory cooperative studies, (3) choosing methods for identifying or describing microbial populations appropriate to the scientific question asked, (4) microbial ecology methods (e.g., population dynamics) for the oral cavity studies, and (5) epidemiological methods (e.g., incidence, risk factor analysis) for oral microbial studies. Each topic was considered by two independent groups of participants and later rationalized into one. These outlines are meant to be working outlines for evolution of a set of guidelines to advise on designing studies with microbial incidence and/or population components. We are publishing this preliminary version to elicit comment and criticism from people who did not attend the Workshop. (Attendance at the Workshop was necessarily limited by both space and funds). Some of the topic outlines have been condensed to save Journal space. The full document is available on request. The next stage will be an open forum to gather and discuss further amplification of the "Guidelines", planned for April 17, 1991, Acapulco, Mexico, in conjunction with the IADR/AADR Meeting. Written comments and requests for further information should be sent to the Workshop organizer (MIK) at the above address.(ABSTRACT TRUNCATED AT 250 WORDS)}, }
@article {pmid1671775, year = {1991}, author = {Ganeshkumar, N and Hannam, PM and Kolenbrander, PE and McBride, BC}, title = {Nucleotide sequence of a gene coding for a saliva-binding protein (SsaB) from Streptococcus sanguis 12 and possible role of the protein in coaggregation with actinomyces.}, journal = {Infection and immunity}, volume = {59}, number = {3}, pages = {1093-1099}, pmid = {1671775}, issn = {0019-9567}, mesh = {Actinomyces/*metabolism ; *Adhesins, Bacterial ; Amino Acid Sequence ; Animals ; Antibodies, Bacterial/immunology ; Bacterial Adhesion ; Bacterial Proteins/*genetics/immunology/metabolism ; Base Sequence ; Cross Reactions/immunology ; DNA, Bacterial/genetics ; Fimbriae, Bacterial/metabolism ; *Genes, Bacterial ; *Lipoproteins ; Molecular Sequence Data ; Open Reading Frames ; Rabbits ; Saliva/*metabolism/microbiology ; Sequence Homology, Nucleic Acid ; Streptococcus sanguis/*genetics/metabolism ; }, abstract = {The nucleotide sequence of a 2.9-kb streptococcal DNA fragment which codes for two proteins with MrS of 36,000 (Streptococcus sanguis adhesin B [SsaB]) and 20,000 has been determined. The ssaB gene is 927 bp and codes for a 34,684-Da protein. The open reading frame coding for the 20-kDa protein is 489 bp and codes for a protein of 17,885 Da. The SsaB protein has a putative hydrophobic 19-amino-acid signal sequence resulting in a 32,620-Mr secreted protein, whereas the 20-kDa protein has no signal sequence. Both proteins are hydrophilic, and neither appears to have a hydrophobic membrane anchor sequence in the carboxy-terminal region. A DNA sequence homology of 73% exists between the cloned fragment containing the ssaB gene from S. sanguis 12 and the cloned fragment containing the type 1 fimbrial gene of S. sanguis FW213 (J.C. Fenno, D.J. LeBlanc, and P. Fives-Taylor, Infect. Immun. 57:3527-3533, 1989). Amino acid comparisons of the SsaB and type 1 fimbrial proteins show 87% homology, indicating a close similarity of the two proteins. Antiserum raised against the cloned SsaB protein cross-reacts with a 38-kDa protein identified from Streptococcus gordonii (S. sanguis) PK488 which was proposed to mediate coaggregation with Actinomyces naeslundii PK606 (P.E. Kolenbrander and R.N. Andersen, Infect. Immun. 58:3064-3072, 1990). The SsaB adhesion may play a role in oral colonization by binding either to a receptor on saliva or to a receptor on actinomyces.}, }
@article {pmid1987035, year = {1991}, author = {Kurashima, C and Sandberg, AL and Cisar, JO and Mudrick, LL}, title = {Cooperative complement- and bacterial lectin-initiated bactericidal activity of polymorphonuclear leukocytes.}, journal = {Infection and immunity}, volume = {59}, number = {1}, pages = {216-221}, pmid = {1987035}, issn = {0019-9567}, mesh = {Actinomyces/immunology ; *Blood Bactericidal Activity ; Complement C3/*immunology ; Humans ; Immunoglobulin M/immunology ; Lactose/pharmacology ; Lectins/*immunology ; Neutrophils/*immunology ; Phagocytosis ; }, abstract = {The recognition of glycoconjugate receptors on sialidase-treated polymorphonuclear leukocytes (PMNs) by the Gal/GalNAc-reactive fimbrial lectin of Actinomyces viscosus T14V has previously been shown to initiate lactose-inhibitable phagocytosis and subsequent killing of the bacteria. Although a mutant lacking fimbriae, A. viscosus 147, was not destroyed by this mechanism, the present studies demonstrate that the deposition of C3 fragments on this bacterium by anti-A. viscosus 147 immunoglobulin M (IgM) prior to incubation with either untreated or sialidase-treated PMNs correlated with a reduction in viability of approximately 2 log10. This bactericidal activity was unaffected by lactose. A similar decrease in viability was observed following the addition of untreated PMNs to A. viscosus T14V preincubated with anti-A. viscosus 147 IgM and complement, conditions favorable for C3- but not lectin-mediated bactericidal activity. Neither IgM nor complement alone was opsonic for either strain, and individually they did not alter killing of A. viscosus T14V by sialidase-treated PMNs or inhibition of this bactericidal activity by lactose. The number of viable A. viscosus T14V cells was decreased by approximately 3.5 log10 when the bacteria were incubated with IgM and complement prior to the addition of sialidase-treated PMNs, and lactose only partially inhibited this response. Thus, the PMN-dependent bactericidal activity initiated by the participation of both the actinomyces lectin and complement was significantly greater than that achieved by either ligand alone.}, }
@article {pmid1905094, year = {1991}, author = {Thompson, J and Miller, SP}, title = {N5-(1-carboxyethyl)ornithine and related [N-carboxyalkyl]-amino acids: structure, biosynthesis, and function.}, journal = {Advances in enzymology and related areas of molecular biology}, volume = {64}, number = {}, pages = {317-399}, doi = {10.1002/9780470123102.ch7}, pmid = {1905094}, issn = {0065-258X}, mesh = {Amino Acid Oxidoreductases/*metabolism ; Amino Acids/chemistry/*metabolism ; Animals ; Biological Evolution ; Kinetics ; Lactococcus lactis/metabolism ; Ornithine/*analogs &amp; derivatives/chemistry/metabolism ; Plants/enzymology ; Species Specificity ; }, }
@article {pmid1842852, year = {1991}, author = {Morgan, JA}, title = {Molecular biology: new tools for studying microbial ecology.}, journal = {Science progress}, volume = {75}, number = {298 Pt 3-4}, pages = {265-277}, pmid = {1842852}, issn = {0036-8504}, mesh = {Bacteria/*genetics/isolation &amp; purification ; *Cloning, Molecular ; *Ecology ; Genetic Engineering ; Genotype ; *Molecular Biology ; Molecular Probe Techniques ; Phenotype ; }, abstract = {The general aim of studies in microbial ecology is to determine the activities of particular groups of organisms in the natural environment. Current developments in molecular biology are providing methods that can be adopted for investigations in microbial ecology. Presently, molecular techniques are being used to determine population and community structures in samples. Following on from this, methods are needed to determine the activities of these organisms in their natural state. This review describes the application of molecular techniques to the study of micro-organisms in environmental samples.}, }
@article {pmid1824279, year = {1991}, author = {Nickel, JC}, title = {Catheter-associated urinary tract infection: new perspectives on old problems.}, journal = {The Canadian journal of infection control : the official journal of the Community &amp; Hospital Infection Control Association-Canada = Revue canadienne de prevention des infections}, volume = {6}, number = {2}, pages = {38-42}, pmid = {1824279}, issn = {1183-5702}, mesh = {Bacterial Adhesion ; Cross Infection/*etiology/prevention &amp; control ; Humans ; Infection Control/*methods ; Urinary Catheterization/*adverse effects ; Urinary Tract Infections/*etiology/prevention &amp; control ; }, abstract = {Foley catheterization remains the most common cause of nosocomial infection in medical practice. A new awareness of microbial ecology in various infectious diseases has led to a new understanding of the pathogenesis of this common infection control problem. Colonization of the catheter and its sequelae, including cystitis, result from a creeping adherent biofilm of bacteria ascending the luminal and external surfaces of the catheter and drainage system from a contaminated drainage spigot or from the urethral meatus. With further disruption of bladder defence mechanisms by selected bacteria colonizing the catheter, bacterial adherence to the bladder surface occurs and clinical cystitis becomes evident. An appreciation of bacterial strategies in catheter-associated infections will allow rational adaptation of infection control practices in this high risk patient population.}, }
@article {pmid1778335, year = {1991}, author = {Brown, DR and Keith, JM and Sato, H and Sato, Y}, title = {Construction and characterization of genetically inactivated pertussis toxin.}, journal = {Developments in biological standardization}, volume = {73}, number = {}, pages = {63-73}, pmid = {1778335}, issn = {0301-5149}, mesh = {Animals ; Bordetella pertussis/genetics/immunology/pathogenicity ; Female ; Genes, Bacterial ; Genetic Engineering ; Mice ; *Pertussis Toxin ; Pertussis Vaccine/isolation &amp; purification ; Vaccines, Inactivated/isolation &amp; purification ; Vaccines, Synthetic/isolation &amp; purification ; Virulence/genetics ; Virulence Factors, Bordetella/antagonists &amp; inhibitors/*genetics ; Whooping Cough/prevention &amp; control ; }, abstract = {Pertussis toxin has been shown to be an important virulence factor and an antigen which will probably be essential to a pertussis vaccine. Inactivation of the pertussis toxin was required due to the pharmacological properties associated with this toxin. However, chemical inactivation has the potential of altering important epitopes or of failing to inactivate the toxin. Cloning and sequencing of the pertussis toxin operon has permitted the introduction of specific mutations in the S1 gene which have been shown to have a profound effect on the subsequent enzyme activity. Various mutations were constructed, re-assembled into the pertussis toxin operon and returned to the Bordetella pertussis chromosome for expression. Pertussis toxin, with lysine substituted for arginine at position 9 in the S1 subunit (PTA-K9) was assembled and expressed to wild type levels. Substitution of codons for aspartic acid, glycine and glutamine, for that of glutamic acid at position 129 were incorporated into the PTA-K9 construction. Virulence of these constructed B. pertussis strains and ADP-ribosylation by their toxoids were greatly reduced relative to that found with the wild type. Additionally, PTA-K9 was found to have reduced leukocytosis promotion and histamine sensitization activities. Finally, PTA-K9 was shown to be a protective immunogen in both intracerebral and aeorosol challenge assays.}, }
@article {pmid1666490, year = {1991}, author = {Hök, K}, title = {A comparison between immunofluorescence staining on smears from Membrana nictitans (M3 test), immunohistopathology and routine pathology in cats with suspected feline infectious peritonitis (FIP).}, journal = {Acta veterinaria Scandinavica}, volume = {32}, number = {2}, pages = {171-176}, pmid = {1666490}, issn = {0044-605X}, mesh = {Animals ; Antigens, Viral/*analysis ; Cats ; Coronavirus, Feline/*immunology ; Feline Infectious Peritonitis/*diagnosis/pathology ; *Fluorescent Antibody Technique ; Nictitating Membrane/*microbiology ; Predictive Value of Tests ; }, abstract = {An indirect immunofluorescence method using smears from membrana nictitans (M3 test) to diagnose feline corona virus (FCV) infection was compared with immunohistopathology (using indirect immunofluorescence assay (IFFA) performed on organs (IFO], and routine pathology (RP) in cats with suspected feline infectious peritonitis (FIP). A close correlation between the 2 immunofluorescence methods (IFO and M3) was observed. Although the M3 test requires samples from only 1 organ per animal, both the sensitivity and specificity were high (80%), when compared to IFO (using samples from an average of 5 organs per animal). In 21% of the cats with suspected FIP typical pathological lesions were found. As the M3 test is relatively easy to perform, it could reduce work-load of pathology laboratories and provide valuable data for clinical and epidemiological use.}, }
@article {pmid2125053, year = {1990}, author = {Alpert, CA and Chassy, BM}, title = {Molecular cloning and DNA sequence of lacE, the gene encoding the lactose-specific enzyme II of the phosphotransferase system of Lactobacillus casei. Evidence that a cysteine residue is essential for sugar phosphorylation.}, journal = {The Journal of biological chemistry}, volume = {265}, number = {36}, pages = {22561-22568}, pmid = {2125053}, issn = {0021-9258}, mesh = {Base Sequence ; Binding Sites ; Cloning, Molecular/methods ; *Cysteine ; DNA, Bacterial/*genetics ; Escherichia coli/genetics ; *Genes, Bacterial ; Lacticaseibacillus casei/enzymology/*genetics ; Lactococcus lactis/genetics ; Molecular Sequence Data ; Oligonucleotide Probes ; Phosphoenolpyruvate Sugar Phosphotransferase System/*genetics/metabolism ; Phosphorylation ; Protein Conformation ; Restriction Mapping ; Sequence Homology, Nucleic Acid ; Staphylococcus aureus/enzymology ; }, abstract = {The gene coding for the lactose-specific Enzyme II of the Lactobacillus casei phosphoenolpyruvate-dependent phosphotransferase system, lacE, has been isolated by molecular cloning and expressed in Escherichia coli. The DNA sequence of the lacE gene and the deduced amino acid sequence are presented. The putative translation product comprises a hydrophobic protein of 577 amino acids with a calculated molecular mass of 62,350 Da. The deduced polypeptide has a high degree of sequence similarity with the corresponding lactose-specific enzymes II of Staphylococcus aureus and Lactococcus lactis. The sequence surrounding cysteine 483 was strongly conserved in the three proteins. The identity of the lacE product as the Enzyme IIlacL.casei was demonstrated by in vitro lactose phosphorylation assays using the protein expressed in E. coli. Single replacement of each of the histidine and cysteine residues by site-directed mutagenesis pointed to cysteine 483 as an amino acid residue essential for the phosphoryl group transfer reaction.}, }
@article {pmid2082831, year = {1990}, author = {Kolenbrander, PE and Andersen, RN and Moore, LV}, title = {Intrageneric coaggregation among strains of human oral bacteria: potential role in primary colonization of the tooth surface.}, journal = {Applied and environmental microbiology}, volume = {56}, number = {12}, pages = {3890-3894}, pmid = {2082831}, issn = {0099-2240}, support = {DE-05054/DE/NIDCR NIH HHS/United States ; DE-05139/DE/NIDCR NIH HHS/United States ; DE-08972/DE/NIDCR NIH HHS/United States ; }, mesh = {Actinomyces/*physiology ; *Bacterial Adhesion ; Bacterial Physiological Phenomena ; Humans ; Mouth/*microbiology ; Streptococcus/*physiology ; Tooth/*microbiology ; }, abstract = {Of the 122 human oral bacterial strains tested from 11 genera, only streptococci and a few actinomyces exhibited coaggregation among the strains within their respective genera. Eight of the ten streptococci showed multiple intrageneric coaggregations, all of which were inhibited by galactosides. The widespread intrageneric coaggregation among the streptococci and the less extensive coaggregation among the actinomyces offers an explanation for their accretion on cleaned tooth surfaces and their dominance as primary colonizers.}, }
@article {pmid2211506, year = {1990}, author = {Robrish, SA and Thompson, J}, title = {Regulation of fructose metabolism and polymer synthesis by Fusobacterium nucleatum ATCC 10953.}, journal = {Journal of bacteriology}, volume = {172}, number = {10}, pages = {5714-5723}, pmid = {2211506}, issn = {0021-9193}, mesh = {Cytoplasmic Granules/metabolism/ultrastructure ; Fructose/*metabolism ; Fusobacterium/growth &amp; development/*metabolism/ultrastructure ; Galactose/metabolism ; Glucose/metabolism ; Glutamates/metabolism ; Kinetics ; Magnetic Resonance Spectroscopy ; Microscopy, Electron ; Phosphorus ; Phosphorylation ; Polysaccharides, Bacterial/*biosynthesis ; }, abstract = {Energy for the anaerobic growth of Fusobacterium nucleatum ATCC 10953 can be derived from the fermentation of sugar (fructose) or amino acid (glutamate). During growth on fructose, the cells formed large intracellular granules which after extraction yielded glucose by either acid or enzymatic hydrolysis. The endogenous polymer was subsequently metabolized, and after overnight incubation of the cells in buffer, the glucan granules were no longer detectable by electron microscopy. Anaerobically, washed cells grown previously on fructose fermented this sugar to a mixture of lactic, acetic, and butyric acids, and little intracellular glucan was formed. Aerobically, the cells slowly metabolized fructose to acetate. Provision of glutamic acid as an additional energy (ATP) source elicited rapid synthesis of polymer by glycolyzing cells. Intracellular granules were not present in glutamate-grown cells, and under anaerobic conditions, the resting cells failed to metabolize [14C] fructose. However, the addition of glutamic acid to the suspension resulted in the rapid accumulation of sugar by the cells. Approximately 15% of the 14C-labeled material was extractable with boiling water, and by 31P nuclear magnetic resonance spectroscopy, this phosphorylated derivative was identified as [14C]fructose-1-phosphate. The nonextractable material represented [14C]glucan polymer. Fructose-1-phosphate kinase activity in fructose-grown cells was fivefold greater than that in glutamate-grown cells. We suggest that the activity of fructose-1-phosphate kinase and the availability of ATP regulate the flow of fructose into either the glycolytic or polymer-synthesizing pathway in F. nucleatum.}, }
@article {pmid2178174, year = {1990}, author = {Mackie, RI and White, BA}, title = {Recent advances in rumen microbial ecology and metabolism: potential impact on nutrient output.}, journal = {Journal of dairy science}, volume = {73}, number = {10}, pages = {2971-2995}, doi = {10.3168/jds.S0022-0302(90)78986-2}, pmid = {2178174}, issn = {0022-0302}, mesh = {Animal Feed ; *Animal Nutritional Physiological Phenomena ; Animals ; Bacteria/*metabolism ; Dietary Fiber/metabolism ; Dietary Proteins/metabolism ; Fermentation ; Mycotoxins/metabolism ; Nitrogen/metabolism ; Rumen/metabolism/*microbiology ; Ruminants/*physiology ; Toxins, Biological/metabolism ; }, abstract = {Feedstuffs consumed by ruminants are all initially exposed to fermentative activity in the rumen prior to gastric and intestinal digestion. The extent and type of transformation of feedstuffs thus determines the productive performance of the host. Research on rumen microbial ecology and metabolism is essentially a study of the interactions between the host, microorganisms present, substrates available, and end products of digestion. Furthermore, the interactions of the normal microbial flora with the host can be manipulated to improve the efficiency of nutrient utilization in ruminant animals. Three important areas of ruminal fermentation will be reviewed, N metabolism, fiber degradation, and biotransformation of toxic compounds. The extent of protein degradation and the rate of uptake of resultant peptides and ammonia are extremely important factors in determining the efficiency of N utilization by rumen bacteria and, therefore, the relative amounts of microbial or bypass protein available to the host. Strategies aimed at identifying and characterizing rate-limiting enzymes of cellulolytic bacteria are essential in elucidating mechanisms involved in ruminal fiber degradation. Results obtained with ruminococci will be described. The detoxification of phytotoxins by passage through the gastrointestinal tract of ruminants is a process deserving special attention and several examples will be presented. Opportunities for manipulation of rumen fermentation are good. However, successful manipulation and full exploitation depend on a through understanding of the mechanisms involved.}, }
@article {pmid2387635, year = {1990}, author = {Kolenbrander, PE and Andersen, RN}, title = {Characterization of Streptococcus gordonii (S. sanguis) PK488 adhesin-mediated coaggregation with Actinomyces naeslundii PK606.}, journal = {Infection and immunity}, volume = {58}, number = {9}, pages = {3064-3072}, pmid = {2387635}, issn = {0019-9567}, mesh = {Actinomyces/*physiology ; *Adhesins, Bacterial ; *Bacterial Adhesion ; Bacterial Proteins/*metabolism ; Binding, Competitive ; Humans ; Immunoglobulin G/immunology ; Molecular Weight ; Receptor Aggregation ; Streptococcus sanguis/*physiology ; }, abstract = {Intergeneric coaggregation of Streptococcus gordonii (S. sanguis) PK488 and Actinomyces naeslundii PK606 was studied by using coaggregation-defective (Cog-) mutants of both strains. A streptococcal protein of 38 kilodaltons was identified with anti-S. gordonii serum absorbed with Cog- cells of the streptococcus. Absorbed immunoglobulin G specifically blocked coaggregation of the streptococcus-actinomyces pair but did not affect the coaggregation of the streptococcus with other coaggregation partners. The 38-kilodalton protein was found in the supernatant of mild sonicated cell suspensions and was extracted from whole cells with sodium barbital or with 3-[(3-cholamidopropyl)-dimethylammonio]-1-propanesulfonate (CHAPS). An immunoreactive protein of the same size was found in sonicated cell supernatants of several other oral streptococci that also coaggregated with A. naeslundii PK606. Inhibition of S. gordonii PK488-A. naeslundii PK606 coaggregation was not observed with any of 16 different sugars tested. We propose that a functionally similar adhesin that mediates coaggregations with A. naeslundii PK606 is expressed by several species of the genus Streptococcus.}, }
@article {pmid2271221, year = {1990}, author = {London, J}, title = {Uncommon pathways of metabolism among lactic acid bacteria.}, journal = {FEMS microbiology reviews}, volume = {7}, number = {1-2}, pages = {103-111}, doi = {10.1111/j.1574-6968.1990.tb04882.x}, pmid = {2271221}, issn = {0168-6445}, mesh = {Amino Acids/metabolism ; Biological Transport ; *Carbohydrate Metabolism ; Lactobacillus/*metabolism ; }, abstract = {A small number of lactic acid bacteria possess the ability to derive energy from organic molecules not utilized by the vast majority of representatives of this large group of microorganisms. Thus, strains of Lactobacillus casei and enterococci readily grow at the expense of substrates such as gluconate, malate and pentitols. Transport of gluconate and pentitols is catalysed by phosphotransferase systems unique to these bacteria. Similarly, the initial steps in pentitol dissimilation are mediated by enzymes found only in Lb. casei and Streptococcus avium.}, }
@article {pmid2237261, year = {1990}, author = {Saxerholt, H and Skar, V and Midtvedt, T}, title = {HPLC separation and quantification of bilirubin and its glucuronide conjugates in faeces and intestinal contents of germ-free rats.}, journal = {Scandinavian journal of clinical and laboratory investigation}, volume = {50}, number = {5}, pages = {487-495}, doi = {10.1080/00365519009089163}, pmid = {2237261}, issn = {0036-5513}, mesh = {Animals ; Bilirubin/analogs &amp; derivatives/*analysis/isolation &amp; purification ; Chromatography, High Pressure Liquid/methods ; Feces/*chemistry ; Female ; Germ-Free Life ; Glucuronidase/analysis ; Intestines/*chemistry ; Rats ; }, abstract = {We describe an accurate reverse-phase high-performance liquid chromatography (HPLC) method for the separation and quantification of unconjugated bilirubin (UCB) and its monoglucuronide (BMG) and diglucuronide (BDG) conjugates in faeces and intestinal contents from germ-free (GF) rats. We demonstrated that female GF rats excreted predominantly BMG and that the percentage of this conjugate was at most 71.7% of the total bilirubin excreted with the faeces. The highest percentages for BDG and the UCB were 27.9% and 6.0%, respectively. The bile pigment composition in duodenal contents was 59.8% BDG and 40.2% BMG (median percentage) and was 47.7% BDG, 50.1% BMG and 2.2% UCB in ileal contents. Deconjugation of BDG to BMG was profound in caecal contents with 26.0% BDG, 67.4% BMG and 6.6% UCB. Endogenous (mammalian) beta-glucuronidase activity was present in intestinal contents throughout the entire length of the intestine and in faeces of the GF rats. The results indicated that it is very likely that endogenous beta-glucuronidase plays a role in the deconjugation of bilirubin glucuronides as well as of other glucuronides in the intestine of the GF rat.}, }
@article {pmid2223037, year = {1990}, author = {Midtvedt, T and Lingaas, E and Carlstedt-Duke, B and Höverstad, T and Midtvedt, AC and Saxerholt, H and Steinbakk, M and Norin, KE}, title = {Intestinal microbial conversion of cholesterol to coprostanol in man. Influence of antibiotics.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {98}, number = {9}, pages = {839-844}, doi = {10.1111/j.1699-0463.1990.tb05004.x}, pmid = {2223037}, issn = {0903-4641}, mesh = {Adult ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*metabolism ; Cholestanol/*metabolism ; Cholesterol/*metabolism ; Female ; Humans ; Intestines/*microbiology ; Male ; }, abstract = {The intestinal microbial conversion of cholesterol to coprostanol has been measured in groups of healthy subjects before, during and after they received the antibiotics ampicillin, bacitracin, clindamycin, co-trimoxazole, doxycycline, erythromycin, metronidazole, nalidixic acid, ofloxacin or vancomycin orally for 6 days. Before they received antibiotics, the subjects demonstrated two distinct patterns of cholesterol conversion. One pattern was characterised by extensive conversion of cholesterol, the other by little or no conversion. Intake of bacitracin, clindamycin, erythromycin, metronidazole and vancomycin significantly reduced the conversion to coprostanol. In the groups receiving ampicillin or doxycycline, marked reductions were found in most of the subjects. No alterations were found in the groups receiving co-trimoxazole, nalidixic acid or ofloxacin. In 6 subjects no conversion of cholesterol to coprostanol was found up to 5 weeks after the end of the antibiotic intake. We conclude that orally given antibiotics may cause alterations in the intestinal conversion of cholesterol, reflecting changes in the anaerobic, Gram-positive component of the gut flora.}, }
@article {pmid2212083, year = {1990}, author = {Newman, HN}, title = {Plaque and chronic inflammatory periodontal disease. A question of ecology.}, journal = {Journal of clinical periodontology}, volume = {17}, number = {8}, pages = {533-541}, pmid = {2212083}, issn = {0303-6979}, mesh = {*Bacterial Physiological Phenomena ; Chronic Disease ; Dental Plaque/complications/*microbiology ; Ecology ; Humans ; Periodontitis/*etiology/microbiology ; }, abstract = {The nature of the relationship between dental plaque and chronic inflammatory periodontal disease (CIPD) remains unclear, although there is no doubt that plaque is the direct cause. Non-specific, specific and exogenous hypotheses have been proposed to explain plaque-host relationships. Current evidence indicates that plaque is part of the natural human microflora, one of many such in nature, and that disruption of oral microbial ecology, due primarily to diet texture changes, leads to gingivitis and periodontitis. These result in increased plaque accumulation, and particularly in increased interdental effective plaque thickness. The latter leads to alterations in plaque ecology, particularly increasing anaerobiosis, with resultant shifts in proportions of its constituent species. These shifts are responsible for the increased counts of, for example, Bacteroides gingivalis, Actinobacillus actinomycetemcomitans, Fusobacterium nucleatum, Wolinella recta, spirochaetes and others, associated with chronic periodontitis in its various forms. Measures to prevent or control chronic periodontitis should aim, not to eliminate plaque, which ignores ecology and would compromise host defence, but to restore the species distribution in plaque to that compatible with health.}, }
@article {pmid2146241, year = {1990}, author = {van Ogtrop, ML and Mattie, H and Guiot, HF and van Furth, R}, title = {Relation between the therapeutic efficacy of imipenem in an experimental infection in granulocytopenic mice and its effect on murine intestinal microbial ecology.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {26}, number = {3}, pages = {399-409}, doi = {10.1093/jac/26.3.399}, pmid = {2146241}, issn = {0305-7453}, mesh = {Animals ; Cilastatin/*pharmacology/therapeutic use ; Cilastatin, Imipenem Drug Combination ; Colony Count, Microbial ; Drug Combinations ; Escherichia coli Infections/*drug therapy ; Imipenem/*pharmacology/therapeutic use ; Injections, Subcutaneous ; Intestines/*microbiology ; Male ; Mice ; Muscular Diseases/drug therapy/microbiology ; Specific Pathogen-Free Organisms ; Thigh ; }, abstract = {A study was performed to assess the effect of parenteral administration of imipenem on the intestinal microbial ecology of mice in relation to the therapeutic efficacy of the drug. The therapeutic effect of imipenem was assessed in a short-term experimental thigh muscle infection with Escherichia coli in irradiated mice. The maximum antibacterial effect of imipenem was approached at a single dose of 80 mg/kg. At this dose of imipenem the number of viable E. coli in the thigh muscle decreased from 9 x 10(6) to 4 x 10(5), whereas in untreated controls this number increased from 9 x 10(6) to 2 x 10(8). Daily administration of a dose of 80 mg/kg imipenem caused significant changes in the intestinal flora of conventional mice, despite the low concentrations of the drug (about 1 mg/kg) found in the caecum 30 min after infection of this dose. These changes consisted of an increase in the number of E. coli and enterococci and a decrease in the number of Staphylococcus aureus in the faeces. Furthermore, at this dose of imipenem, the number of Candida albicans recovered from the faeces after oral contamination with this organism was increased. We conclude from these animal experiments that the use of imipenem in high doses causes ecological changes in the intestinal bacterial flora with the potential to promote colonization by candida.}, }
@article {pmid2391384, year = {1990}, author = {Midtvedt, T}, title = {Ecosystems: development, functions and consequences of disturbances, with special reference to the oral cavity.}, journal = {Journal of clinical periodontology}, volume = {17}, number = {7 (Pt 2)}, pages = {474-478}, doi = {10.1111/j.1365-2710.1992.tb01219.x}, pmid = {2391384}, issn = {0303-6979}, mesh = {Animals ; *Bacterial Physiological Phenomena ; Ecology ; Mouth/*microbiology ; }, abstract = {Some general rules for the development and maintenance of microbial ecosystems are outlined. Studies on germ-free animals have given valuable baselines concerning structures and functions in the host per se. The oral cavity represents several consortia of micro-organisms, governed by factors deriving from the host, the diet and/or the micro-organisms. Alterations in these factors, as well as intake of antibiotics, etc., may give disturbances, which can be analyzed according to general guidelines.}, }
@article {pmid2206101, year = {1990}, author = {Top, E and Mergeay, M and Springael, D and Verstraete, W}, title = {Gene escape model: transfer of heavy metal resistance genes from Escherichia coli to Alcaligenes eutrophus on agar plates and in soil samples.}, journal = {Applied and environmental microbiology}, volume = {56}, number = {8}, pages = {2471-2479}, pmid = {2206101}, issn = {0099-2240}, mesh = {Alcaligenes/drug effects/*genetics ; Drug Resistance, Microbial/genetics ; Escherichia coli/drug effects/*genetics ; Genetic Engineering ; Metals/pharmacology ; Plasmids ; Soil Microbiology ; *Transfection ; }, abstract = {Conjugal transfer from Escherichia coli to Alcaligenes eutrophus of the A. eutrophus genes coding for plasmid-borne resistance to cadmium, cobalt, and zinc (czc genes) was investigated on agar plates and in soil samples. This czc fragment is not expressed in the donor strain, E. coli, but it is expressed in the recipient strain, A. eutrophus. Hence, expression of heavy metal resistance by cells plated on a medium containing heavy metals represents escape of the czc genes. The two plasmids into which this DNA fragment has been cloned previously and which were used in these experiments are the nonconjugative, mobilizable plasmid pDN705 and the nonconjugative, nonmobilizable plasmid pMOL149. In plate matings at 28 to 30 degrees C, the direct mobilization of pDN705 occurred at a frequency of 2.4 x 10(-2) per recipient, and the mobilization of the same plasmid by means of the IncP1 conjugative plasmids RP4 or pULB113 (present either in a third cell [triparental cross] or in the recipient strain itself [retromobilization]) occurred at average frequencies of 8 x 10(-4) and 2 x 10(-5) per recipient, respectively. The czc genes cloned into the Tra- Mob- plasmid pMOL149 were transferred at a frequency of 10(-7) to 10(-8) and only by means of plasmid pULB113. The direct mobilization of pDN705 was further investigated in sandy, sandy-loam, and clay soils. In sterile soils, transfer frequencies at 20 degrees C were highest in the sandy-loam soil (10(-5) per recipient) and were enhanced in all soils by the addition of easily metabolizable nutrients.(ABSTRACT TRUNCATED AT 250 WORDS)}, }
@article {pmid1698258, year = {1990}, author = {Sandberg, AL and Cisar, JO and Siraganian, RP and Mudrick, LL and Armstrong, MW}, title = {Complement activation by individual and combinations of monoclonal antibodies to Actinomyces viscosus T14V fimbriae: a probe for epitope distribution on these polymeric proteins.}, journal = {Molecular immunology}, volume = {27}, number = {8}, pages = {787-794}, doi = {10.1016/0161-5890(90)90088-h}, pmid = {1698258}, issn = {0161-5890}, mesh = {Actinomyces/*immunology ; Animals ; Antibodies, Monoclonal ; Binding, Competitive ; Biopolymers ; Complement Activation/*immunology ; Complement System Proteins/metabolism ; Epitopes/immunology ; Fimbriae, Bacterial/*immunology ; Immunoglobulin Fab Fragments ; Mice ; }, abstract = {The spatial requirements for IgG activation of the classical complement pathway has provided a basis for utilizing complement consumption by individual and pairs of monoclonal antibodies (mAbs) to compare the repeating epitope patterns of the type 1 and type 2 fimbriae of Actinomyces viscosus T14V and to examine the co-operative effects of mAbs against these polymeric proteins. Three of five mAbs specific for the type 1 fimbriae consumed complement when assayed individually. Four patterns of complement consumption were detected with pairs of these mAbs: inhibition, addition, enhancement or synergy. Inhibition occurred when both members of a pair reacted with the same epitope but only one consumed complement. A strictly additive effect was observed if both mAbs consumed complement and, in addition, recognized the same epitope. Complement consumption by mAbs against certain epitopes was enhanced by non-complement consuming mAbs that reacted with different epitopes. Synergy was observed with extremely low concentrations of two mAbs each of which reacted with a different epitope and consumed complement. In contrast to the anti-type 1 mAbs, only one of seven mAbs against the type 2 fimbriae consumed more than 20% of the available complement. Pairs of anti-type 2 mAbs exhibited only inhibition or synergy. The latter effect was particularly striking as pairs containing mAbs that reacted with different epitopes and failed to consume complement or were minimally active when assayed individually were extremely efficient. These data indicated that the spatial arrangements of individual mAbs bound to repeating epitopes in the type 1, but not the type 2, fimbriae were appropriate for activation of complement. Thus, the repeating epitope patterns of the two types of fimbriae apparently differ.}, }
@article {pmid1370008, year = {1990}, author = {Takami, H and Akiba, T and Horikoshi, K}, title = {Characterization of an alkaline protease from Bacillus sp. no. AH-101.}, journal = {Applied microbiology and biotechnology}, volume = {33}, number = {5}, pages = {519-523}, pmid = {1370008}, issn = {0175-7598}, mesh = {Amino Acid Sequence ; Bacillus/*enzymology ; Elastin/metabolism ; Hydrogen-Ion Concentration ; Keratins/metabolism ; Molecular Sequence Data ; Protease Inhibitors/metabolism ; Serine Endopeptidases/chemistry/isolation &amp; purification/*metabolism ; }, abstract = {The Bacillus sp. no. AH-101 alkaline protease showed higher hydrolysing activity against insoluble fibrous natural proteins such as elastin and keratin in comparison with subtilisins and Proteinase K. The optimum pH of the enzyme toward elastin and keratin was pH 10.5 and pH 11.0-12.0 respectively. The specific activity toward elastin and keratin was 10,600 units/mg protein and 3970 units/mg protein, respectively. The enzymatic activity was not inhibited by p-chloromercuribenzoic acid and iodoacetic acid. Carbobenzoxy-glycyl-glycyl-L-phenylalanyl chloromethyl ketone completely inhibited the caseinolytic activity, but 36% elastolytic activity remained. No inhibitory effect on caseinolytic and elastolytic activity was shown by tosyl-L-phenylalanyl-chloromethyl ketone, tosyl-L-lysine chloromethyl ketone, carbobenzoxy-L-phenylalanyl chloromethyl ketone, and elastatinal. The amino acid composition and amino terminal sequence of the enzyme were determined. The no. AH-101 alkaline protease was compared with subtilisin BPN', subtilisin Carlsberg, no. 221, and Ya-B alkaline proteases. Extensive sequence homology existed among these enzymes.}, }
@article {pmid2398031, year = {1990}, author = {Bruyneel, B and Vande Woestyne, M and Verstraete, W}, title = {Iron complexation as a tool to direct mixed clostridia-lactobacilli fermentations.}, journal = {The Journal of applied bacteriology}, volume = {69}, number = {1}, pages = {80-85}, doi = {10.1111/j.1365-2672.1990.tb02914.x}, pmid = {2398031}, issn = {0021-8847}, mesh = {2,2'-Dipyridyl/*pharmacology ; Clostridium/*growth &amp; development/metabolism ; Colony Count, Microbial ; Culture Media ; Fermentation ; Lactobacillus/*growth &amp; development/metabolism ; Pyridines/*pharmacology ; }, abstract = {Iron complexation was investigated as a possible tool to give lactobacilli a competitive advantage over clostridia. The iron complexing substance tested, i.e. 2,2'-dipyridyl, was not toxic itself for clostridia, but its addition to a mixed culture of lactobacilli and clostridia resulted in a strong ecological advantage of the lactobacilli.}, }
@article {pmid2168724, year = {1990}, author = {Hök, K}, title = {Demonstration of feline corona virus (FCV) antigen in organs of cats suspected of feline infectious peritonitis (FIP) disease.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {98}, number = {7}, pages = {659-664}, doi = {10.1111/j.1699-0463.1990.tb04985.x}, pmid = {2168724}, issn = {0903-4641}, mesh = {Animals ; Antigens, Viral/*analysis ; *Cat Diseases ; Cats ; Coronaviridae/*isolation &amp; purification ; Coronaviridae Infections/diagnosis/pathology/*veterinary ; Female ; Fluorescent Antibody Technique ; Male ; Organ Specificity ; Peritonitis/microbiology/*pathology/*veterinary ; }, abstract = {Cryosections of organs and smears from membrana nicitians from cats suspected of having spontaneous infection with feline infectious peritonitis virus (FIPV), were investigated using an indirect immunofluorescence assay (IIFA) in order to detect the presence of feline corona virus (FCV). In 113 cats, from each of which six organs were screened, virus antigen was found most often in membrana nicitians and lung. Out of these animals an additional six organs from a group of 30 cats were screened. In these cats membrana nicitians, parotid gland, thymus and apex of caecum had the highest incidence of virus antigen (90%). The lowest incidence of virus antigen was found in the spleen (60%). There was a clear demonstration of a higher incidence of antigen present in more than half of the total number of screened organs per cat (P less than 0.0005). No statistical difference was observed between sexes when comparing the incidence of virus antigen in different organs. Virus antigen was present in less organs in cats with no lesions suggestive of FIP disease compared to cats with such lesions (P less than 0.001). A similar distribution of the incidence of FCV antigen in the investigated organs was observed in these two groups.}, }
@article {pmid2163399, year = {1990}, author = {Donkersloot, JA and Thompson, J}, title = {Simultaneous loss of N5-(carboxyethyl)ornithine synthase, nisin production, and sucrose-fermenting ability by Lactococcus lactis K1.}, journal = {Journal of bacteriology}, volume = {172}, number = {7}, pages = {4122-4126}, pmid = {2163399}, issn = {0021-9193}, mesh = {Amino Acid Oxidoreductases/*genetics/isolation &amp; purification ; Base Sequence ; DNA Transposable Elements ; DNA, Bacterial/genetics/isolation &amp; purification ; Fermentation ; Genes, Bacterial ; Lactococcus lactis/*genetics/metabolism ; Molecular Sequence Data ; Molecular Weight ; Mutation ; Nisin/*biosynthesis ; Oligonucleotide Probes ; Sucrose/*metabolism ; }, abstract = {A spontaneous derivative of Lactococcus lactis subsp. lactis K1 (formerly Streptococcus lactis K1) lacking N5-(carboxyethyl)ornithine synthase (EC 1.5.1.24) was isolated. This mutant had also lost the abilities to ferment sucrose and to produce the antibiotic nisin. Hybridization studies indicate that these linked traits are encoded on the chromosome of L. lactis K1 and that they may be located on a conjugative transposon.}, }
@article {pmid2114037, year = {1990}, author = {Lenoir, G and de Montalembert, M}, title = {[Colonization by pyocyanic bacillus and its treatment in cystic fibrosis].}, journal = {La Revue du praticien}, volume = {40}, number = {17}, pages = {1559-1565}, pmid = {2114037}, issn = {0035-2640}, mesh = {Adolescent ; Anti-Bacterial Agents/therapeutic use ; Child ; Child, Preschool ; Colony Count, Microbial ; Cystic Fibrosis/*complications/microbiology ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Pseudomonas Infections/complications/*drug therapy/physiopathology ; Pseudomonas aeruginosa/*growth &amp; development ; }, abstract = {In cystic fibrosis infection is localized to the bronchi and self-perpetuated by a disorder of mucociliary clearance. At a certain stage of the disease infection is caused by Pseudomonas aeruginosa (PA), and the patient cannot get rid of it as cystic fibrosis reduces his defence mechanisms against this organism, a naturally weak pathogen. The presence and significance of persistent bronchial PA infection result from complex phenomena which have been summarized as "an opportunistic organism in a host whose defences have been very peculiarly compromised". The toxicity of PA and the inappropriate inflammatory response of the host concur to create permanent alveolar lesions which are gradually spreading out. The effectiveness of antibiotics depends on the organism and its resistance, on pharmacokinetic factors bringing the drug in situ and on local conditions of redox, physico-chemical environment and nutrition. Other factors intervene more roughly, including patient's age, liver impairment, lung anatomy (excluded areas), general malnutrition and vitamin deficiencies. Thus, the part played by other treatments in the antibiotic therapy of cystic fibrosis can no longer be ignored, just as it is no longer sensible to limit the use of antibiotics to obvious infections. To evaluate the effectiveness of antibiotics is not easy, but it can be demonstrated beyond any doubt when the above mentioned factors are taken into account. The use of antibiotics creates practical problems relating to their cost, their dosage, their side-effects, the adequacy of therapeutic infrastructures and, above all, it raises the question of short- and long-term changes in microbial ecology.}, }
@article {pmid2166470, year = {1990}, author = {Barkay, T and Gillman, M and Liebert, C}, title = {Genes encoding mercuric reductases from selected gram-negative aquatic bacteria have a low degree of homology with merA of transposon Tn501.}, journal = {Applied and environmental microbiology}, volume = {56}, number = {6}, pages = {1695-1701}, pmid = {2166470}, issn = {0099-2240}, mesh = {*Base Sequence ; *DNA Transposable Elements ; Drug Resistance, Microbial ; Genes, Bacterial ; Mercury/pharmacology ; Oxidoreductases/biosynthesis/*genetics ; Pseudomonas/*genetics/growth &amp; development ; *Sequence Homology, Nucleic Acid ; *Water Microbiology ; }, abstract = {An investigation of the Hg2+ resistance mechanism of four freshwater and four coastal marine bacteria that did not hybridize with a mer operonic probe was conducted (T. Barkay, C. Liebert, and M. Gillman, Appl. Environ. Microbiol. 55:1196-1202, 1989). Hybridization with a merA probe, the gene encoding the mercuric reductase polypeptide, at a stringency of hybridization permitting hybrid formation between evolutionarily distant merA genes (as exists between gram-positive and -negative bacteria), detected merA sequences in the genomes of all tested strains. Inducible Hg2+ volatilization was demonstrated for all eight organisms, and NADPH-dependent mercuric reductase activities were detected in crude cell extracts of six of the strains. Because these strains represented random selections of bacteria from three aquatic environments, it is concluded that merA encodes a common molecular mechanism for Hg2+ resistance and volatilization in aerobic heterotrophic aquatic communities.}, }
@article {pmid1691826, year = {1990}, author = {Olsen, GJ}, title = {Microbial ecology. Variation among the masses.}, journal = {Nature}, volume = {345}, number = {6270}, pages = {20}, doi = {10.1038/345020a0}, pmid = {1691826}, issn = {0028-0836}, mesh = {Bacteria/*genetics ; Cloning, Molecular ; Cyanobacteria/*genetics ; *Ecology ; *Genetic Variation ; Polymerase Chain Reaction ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, }
@article {pmid2204405, year = {1990}, author = {Baker, DA and Genigeorgis, C and Glover, J and Razavilar, V}, title = {Growth and toxigenesis of C. botulinum type E in fishes packaged under modified atmospheres.}, journal = {International journal of food microbiology}, volume = {10}, number = {3-4}, pages = {269-289}, doi = {10.1016/0168-1605(90)90075-g}, pmid = {2204405}, issn = {0168-1605}, mesh = {Animals ; Botulinum Toxins/*biosynthesis ; Clostridium botulinum/*growth &amp; development/metabolism ; Colony Count, Microbial ; Culture Media ; Fishes/*microbiology ; Flatfishes/microbiology ; *Food Microbiology ; *Food Preservation ; Hydrogen-Ion Concentration ; Models, Biological ; Probability ; Regression Analysis ; Salmon/microbiology ; Spores, Bacterial ; Temperature ; }, abstract = {Modified atmosphere packaging of fresh fish is used to market high quality products in some European countries. The potential risk of C. botulinum growth in these extended shelf-life foods is still a concern; especially since toxigenesis may precede organoleptic spoilage. This paper will present toxigenic data from rockfish, salmon and sole muscle tissues which were inoculated with a pool of non-proteolytic C. botulinum type E at seven levels (10(-2)-10(4) spores/sample), and stored under vacuum and 100% CO2, at incubation temperatures between 30 and 4 degrees C, for up to 60 days. Factorial experimental design allowed predictive formulae to be developed able to describe the lag time prior to C. botulinum toxigenesis and the probability of one spore to initiate toxigenesis based upon the storage conditions. Accurate characterization of the microbial ecology of C. botulinum in modified atmosphere-packaged fish, will support safe exploitation of these packaging systems in the market place, and identify critical control points for potential product or process abuses.}, }
@article {pmid2191747, year = {1990}, author = {Saadia, R and Schein, M and MacFarlane, C and Boffard, KD}, title = {Gut barrier function and the surgeon.}, journal = {The British journal of surgery}, volume = {77}, number = {5}, pages = {487-492}, doi = {10.1002/bjs.1800770505}, pmid = {2191747}, issn = {0007-1323}, mesh = {Animals ; Endotoxins/blood ; Humans ; Intestinal Mucosa/*physiopathology ; Intestines/microbiology ; Postoperative Complications/therapy ; Sepsis/*etiology/therapy ; Shock, Hemorrhagic/etiology ; }, abstract = {There is accumulating evidence that multiple organ failure is not always the result of an established septic focus. Increasing attention has centred on the gut as a reservoir of bacteria (and bacterial endotoxins) that can traverse the intestinal mucosal barrier (a process called 'bacterial translocation') and initiate the septic state. Although the link between haemorrhagic shock and sepsis was recognized decades ago, the full experimental demonstration of this phenomenon is more recent. It was shown to occur in three main settings: physical disruption of the gut mucosa, impaired defence mechanisms and altered gut microbial ecology. Conditions such as haemorrhagic shock, burns, protein malnutrition and sepsis are seen in the severely ill surgical patient or the multiply injured, and are known to cause various combinations of circumstances favourable to bacterial translocation and endotoxin absorption. These may play an important role in the mortality of the critically ill.}, }
@article {pmid1970562, year = {1990}, author = {London, J and Allen, J}, title = {Purification and characterization of a Bacteroides loeschei adhesin that interacts with procaryotic and eucaryotic cells.}, journal = {Journal of bacteriology}, volume = {172}, number = {5}, pages = {2527-2534}, pmid = {1970562}, issn = {0021-9193}, mesh = {*Adhesins, Bacterial ; Adhesins, Escherichia coli ; Amino Acid Sequence ; Animals ; Antibodies ; Antibodies, Monoclonal ; *Bacterial Adhesion ; Bacterial Outer Membrane Proteins ; Bacterial Proteins/*isolation &amp; purification/pharmacology ; Bacteroides/*physiology ; Cell Aggregation/drug effects ; Electrophoresis, Polyacrylamide Gel ; Hemagglutination ; Isoelectric Focusing ; Macromolecular Substances ; Molecular Sequence Data ; Molecular Weight ; Neuraminidase ; Sequence Homology, Nucleic Acid ; Sheep ; Streptococcus sanguis/physiology ; }, abstract = {The adhesin of Bacteroides loeschei PK1295 that mediates coaggregation with Streptococcus sanguis 34 and hemagglutination of erythrocytes was purified to electrophoretic homogeneity. The lectinlike protein has an estimated native Mr of 450,000 and consists of six subunits of identical molecular weight (Mr 75,000). The purified adhesin appears to be a basic protein with a pI between 7.4 and 8.0. Amino acid and N-terminal sequence analyses were carried out with the purified protein. These indicated that the protein contains a large number of Asx and Glx residues as well as basic amino acid residues. The binding site of the pure adhesin retained its native configuration during purification. When preincubated with streptococcal partner cells at pH 4.6, the adhesin prevented B. loeschei cells from coaggregating with the streptococci. An adhesin preparation adjusted to a pH of 6.8 rapidly agglutinated both streptococci and neuraminidase-treated erythrocytes. Galactosides inhibited the agglutination reactions.}, }
@article {pmid1970561, year = {1990}, author = {Yeung, MK and Cisar, JO}, title = {Sequence homology between the subunits of two immunologically and functionally distinct types of fimbriae of Actinomyces spp.}, journal = {Journal of bacteriology}, volume = {172}, number = {5}, pages = {2462-2468}, pmid = {1970561}, issn = {0021-9193}, mesh = {Actinomyces/*genetics ; Amino Acid Sequence ; Bacterial Outer Membrane Proteins/*genetics ; Base Sequence ; Fimbriae Proteins ; Fimbriae, Bacterial/immunology/*physiology ; *Genes, Bacterial ; Macromolecular Substances ; Molecular Sequence Data ; Protein Conformation ; Restriction Mapping ; Sequence Homology, Nucleic Acid ; }, abstract = {Nucleotide sequencing of the type 1 fimbrial subunit gene of Actinomyces viscosus T14V revealed a consensus ribosome-binding site followed by an open reading frame of 1,599 nucleotides. The encoded protein of 533 amino acids (Mr = 56,899) was predominantly hydrophilic except for an amino-terminal signal peptide and a carboxy-terminal region identified as a potential membrane-spanning segment. Edman degradation of the cloned protein expressed in Escherichia coli and the type 1 fimbriae of A. viscosus T14V showed that both began with alanine at position 31 of the deduced amino acid sequence. The amino acid compositions of the cloned protein and fimbriae also were comparable and in close agreement with the composition of the deduced protein. The amino acid sequence of the A. viscosus T14V type 1 fimbrial subunit showed no significant global homology with various other proteins, including the pilins of gram-negative bacteria. However, 34% amino acid sequence identity was noted between the type 1 fimbrial subunit of strain T14V and the type 2 fimbrial subunit of Actinomyces naeslundii WVU45 (M. K. Yeung and J. O. Cisar, J. Bacteriol. 170:3803-3809, 1988). This homology included several different conserved sequences of up to eight identical amino acids that were distributed in both the amino- and carboxy-terminal thirds of each Actinomyces fimbrial subunit. These findings indicate that the different types of fimbriae on these gram-positive bacteria share a common ancestry.}, }
@article {pmid2186479, year = {1990}, author = {Rambaud, JC and Flourié, B and Florent, C}, title = {[Colonic fermentation: physiological review and role in digestive pathology].}, journal = {Schweizerische medizinische Wochenschrift}, volume = {120}, number = {14}, pages = {489-495}, pmid = {2186479}, issn = {0036-7672}, mesh = {Carbohydrate Metabolism ; Colitis/metabolism ; Colonic Diseases/*metabolism ; Colonic Diseases, Functional/metabolism ; Diarrhea/etiology/*metabolism ; Fermentation/*physiology ; Humans ; Malabsorption Syndromes/metabolism ; Osmosis ; Polysaccharides/metabolism ; }, abstract = {Diarrhea "with" bacterial fermentation is characterized by acidic liquid stools containing high amounts of organic acids. Disaccharide malabsorption is the main cause. The mechanism of diarrhea is osmotic, and colonic fermentations reduce diarrhea. It is unlikely that starch malabsorption induces significant diarrhea, whereas a high-fiber diet is responsible for "physiologic" diarrhea. Colonic fermentations increase diarrhea due to organic colitis and the "motor diarrheas". They may be responsible for some intestinal symptoms in patients with irritable bowel syndrome. This does not imply a "hyperfermentative" process due to a hypothetical disturbance of colonic microbial ecology.}, }
@article {pmid2339877, year = {1990}, author = {Schowanek, D and Verstraete, W}, title = {Phosphonate utilization by bacterial cultures and enrichments from environmental samples.}, journal = {Applied and environmental microbiology}, volume = {56}, number = {4}, pages = {895-903}, pmid = {2339877}, issn = {0099-2240}, mesh = {Bacteria/isolation &amp; purification/*metabolism ; Biodegradation, Environmental ; Environmental Microbiology ; Nitrogen/metabolism ; Organophosphonates/*metabolism ; }, abstract = {A selection of axenic microbial strains and a variety of environmental samples were investigated with respect to the utilization of a series of natural and xenobiotic phosphonates as the sole phosphorus source for growth. Phosphonate degradation was observed only with bacteria and not with eucaryotic microorganisms. All representatives of the phosphonates examined supported bacterial growth, with the exception of methylphosphonate diethylester. Yet, distinctly different phosphonate utilization patterns were noted between phosphonate-positive strains. C-P bond cleavage by a photosynthetic bacterium is reported for the first time; growing photoheterotrophically, Rhodobacter capsulatus ATCC 23782 was able to utilize 2-aminoethylphosphonate and alkylphosphonates. Bacteria with the potential to utilize at least one of the phosphonate moieties from the xenobiotic phosphonates Dequest 2010, Dequest 2041, and Dequest 2060 were detected in all environments, with only two exceptions for Dequest 2010. Phosphonate P utilization to an extent of 94 and 97%, for Dequest 2010 and Dequest 2041, respectively, provided evidence that a complete breakdown of these compounds with respect to the C-P bond cleavage can be achieved by some bacteria. The results suggest that phosphonate-utilizing bacteria are ubiquitous, and that selected strains can degrade phosphonates that are more complex than those described previously.}, }
@article {pmid2319017, year = {1990}, author = {Kates, SG and Nordstrom, KM and McGinley, KJ and Leyden, JJ}, title = {Microbial ecology of interdigital infections of toe web spaces.}, journal = {Journal of the American Academy of Dermatology}, volume = {22}, number = {4}, pages = {578-582}, doi = {10.1016/0190-9622(90)70075-s}, pmid = {2319017}, issn = {0190-9622}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/drug effects/isolation &amp; purification ; Dermatomycoses/microbiology ; Drug Resistance, Microbial ; Foot Dermatoses/*microbiology ; Humans ; Male ; Middle Aged ; Skin Diseases, Infectious/*microbiology ; Toes ; }, abstract = {The microbial flora of normal and macerated interdigital toe web spaces was qualitatively and quantitatively identified in 77 patients. Dermatophyte fungi were recovered from 11% of normal patients compared with a 31% recovery from patients with macerated interspaces. Macerated interspaces were characterized by a greater recovery of organisms with pathogenic potential, with Staphylococcus aureus recovered from 36% of patients, Micrococcus sedentarius in 37%, Brevibacterium epidermidis in 54%, Corynebacterium minutissimum in 69%, and Pseudomonas species in 26%. The bacterial flora of macerated interspaces showed a significantly higher incidence of resistance to multiple antibiotics, and the recovery of antibiotic-resistant bacteria correlated with the recovery of dermatophytes that produce penicillin-like substances. The results of this study support the hypothesis that overgrowth of the resident bacterial population determines the severity of interdigital toe-web infections.}, }
@article {pmid2140254, year = {1990}, author = {Höfte, M and Mergeay, M and Verstraete, W}, title = {Marking the rhizopseudomonas strain 7NSK2 with a Mu d(lac) element for ecological studies.}, journal = {Applied and environmental microbiology}, volume = {56}, number = {4}, pages = {1046-1052}, pmid = {2140254}, issn = {0099-2240}, mesh = {Ecology ; Genes, Bacterial ; Genetic Markers ; Iron Chelating Agents/metabolism ; Kanamycin Resistance/genetics ; Lac Operon ; Plant Development ; Plants/microbiology ; Plasmids ; Pseudomonas aeruginosa/*genetics/growth &amp; development/physiology ; Siderophores ; Soil Microbiology ; Temperature ; }, abstract = {The mini Mu element Mu dII1681, which contains the lac operon genes and a kanamycin resistance gene, was inserted in the chromosome of plant growth-beneficial Pseudomonas aeruginosa 7NSK2 to construct a marked strain (MPB1). In MPB1, beta-galactosidase is permanently expressed under the culture conditions used. The MPB1 strain could be recovered with an efficiency of about 100% from a sandy loam soil on 5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside medium containing sebacic acid and kanamycin. The limit of detection is about 10 CFU/g of soil. A detailed comparison was made between the wild-type strain 7NSK2 and the Mu dII1681-containing MPB1 strain. The results showed that no genes essential for growth, siderophore production, survival in sterile and nonsterile conditions, plant growth stimulation, or root colonization had been damaged in the MPB1 strain, which means that MPB1 can reliably be used for ecological studies in soil. MPB1 survived well at 4 or 28 degrees C but died off relatively rapidly in air-dried soil or at subzero temperatures. In these conditions, however, the MPB1 strain did not completely disappear from the soil but survived at a very low level of about 100 CFU/g of soil for more than 3 months. This observation stresses the need for very sensitive counting methods for ecological studies and for the evaluation of released microorganisms. Maize was inoculated with MPB1 via seed inoculation or soil inoculation. Upon seed inoculation, only the upper root parts were effectively colonized, while soil inoculation resulted in a complete colonization of the root system.}, }
@article {pmid2321928, year = {1990}, author = {Bruyneel, B and Vande Woestyne, M and Verstraete, W}, title = {Manganese as a controlling factor in mixed cultures of Lactobacillus plantarum and Enterobacteriaceae.}, journal = {Antonie van Leeuwenhoek}, volume = {57}, number = {2}, pages = {119-122}, pmid = {2321928}, issn = {0003-6072}, mesh = {Acetates/metabolism ; Ammonia/metabolism ; Culture Media ; Enterobacteriaceae/drug effects/*growth &amp; development/metabolism ; Fermentation ; Lactates/biosynthesis ; Lactobacillus/drug effects/*growth &amp; development/metabolism ; Manganese/*pharmacology ; }, abstract = {Addition of manganese, at levels of 50 ppm, to a liquid growth medium simulating adverse silage conditions had no effect on the growth or on the fermentation pattern of Enterobacter cloacae and Proteus vulgaris. Yet, the manganese strongly enhanced the growth of Lactobacillus plantarum. Co-cultures of L. plantarum and E. cloacae or P. vulgaris were, by addition of manganese ions, significantly altered in the favour of the former. This finding can be of use in mixed cultures where Enterobacteriaceae act as spoiler microorganisms.}, }
@article {pmid2179326, year = {1990}, author = {Bowden, GH}, title = {Effects of fluoride on the microbial ecology of dental plaque.}, journal = {Journal of dental research}, volume = {69 Spec No}, number = {}, pages = {653-9; discussion 682-3}, doi = {10.1177/00220345900690S127}, pmid = {2179326}, issn = {0022-0345}, mesh = {Adaptation, Physiological ; Bacteria/*drug effects/growth &amp; development ; Dental Plaque/*microbiology ; Ecology ; Fluorides/*pharmacology ; }, abstract = {In order to survive in a community such as dental plaque, bacteria must be able to resist changes in the environment. These changes may be the result of differences in the host or the activities of the bacteria within the community. Bacteria which cannot resist these environmental pressures may cease metabolism but survive, or be eliminated from the community. Fluoride is only one of numerous environmental pressures which impact on oral bacterial communities, yet its beneficial effect on caries is such that it could be proposed that in addition to its effects on enamel and remineralization, fluoride would affect the bacteria. It has been shown on many occasions that fluoride can affect bacterial carbohydrate fermentation; however, are there other effects of fluoride on the bacteriology of dental plaque? Although very high levels of fluoride (0.16-0.3 mol/L) will kill bacteria, there is little evidence that fluoride causes dramatic changes in the number of species found in plaque or their relative concentrations. The survival of the populations in the plaque community in the presence of fluoride could result from: (1) the fact that all the organisms are unaffected, (2) selection of mutant strains resistant to fluoride, or (3) adaptation of strains to fluoride resistance. Examples of these phenomena can be found among members of the oral flora. Some species are unaffected (Veillonella), but Streptococcus can be mutated to fluoride resistance and also adapt phenotypically to increasing levels of fluoride in the environment. Which of these mechanisms operates in vivo, and does resistance, mutation, or phenotypic adaptation of these bacteria reduce the effectiveness of fluoride, in controlling caries?(ABSTRACT TRUNCATED AT 250 WORDS)}, }
@article {pmid2218426, year = {1990}, author = {Midtvedt, T}, title = {Resistance situation of oral antibiotics in the Scandinavian countries with special reference to the fluoro-quinolones.}, journal = {Scandinavian journal of infectious diseases. Supplementum}, volume = {68}, number = {}, pages = {7-13}, pmid = {2218426}, issn = {0300-8878}, mesh = {4-Quinolones ; Anti-Bacterial Agents/*therapeutic use ; Anti-Infective Agents/*therapeutic use ; *Attitude of Health Personnel ; Drug Resistance, Microbial ; Drug Utilization ; Humans ; Respiratory Tract Infections/drug therapy/etiology ; Scandinavian and Nordic Countries ; Urinary Tract Infections/*drug therapy/etiology ; }, abstract = {In general, the Scandinavian countries have a rather conservative attitude towards new antimicrobial agents. Our antibiotic policies are based upon many years of clinical and laboratory experiences. It is generally believed, although not always satisfactorily proven, that our relatively restrictive attitude to the use of new as well as of older antimicrobial drugs by one mechanism or another, is a matter of some importance when explaining the relatively low antibiotic resistance profile (ARP) existing in most places in Scandinavia. When a new group of drugs, such as the quinolones, is going to be introduced in the therapeutic armamentarium, the existing ARPs of the microbes actually involved have to be taken into consideration.}, }
@article {pmid2218416, year = {1990}, author = {Midtvedt, T}, title = {The influence of quinolones on the faecal flora.}, journal = {Scandinavian journal of infectious diseases. Supplementum}, volume = {68}, number = {}, pages = {14-18}, pmid = {2218416}, issn = {0300-8878}, mesh = {Anti-Infective Agents/*pharmacology ; Ciprofloxacin/pharmacology ; Enterobacteriaceae/*drug effects ; Feces/*microbiology ; Humans ; Intestines/*microbiology/physiology ; Norfloxacin/pharmacology ; Ofloxacin/pharmacology ; Pefloxacin/pharmacology ; }, abstract = {Ingestion of antimicrobial agents may in several ways influence the indigenous flora of the human digestive tract. The influence can be evaluated by following qualitative and/or quantitative alterations in the composition of the flora and of its antibiotic resistance profile (ARP). Another approach is to follow alterations in physiological and/or biochemical intestinal characteristics which depend on the intestinal flora. In a Norwegian-Swedish collaborative study, the influence of 10 orally given antimicrobial drugs on seven to nine various biochemical microflora-associated characteristics in groups of healthy volunteers was followed. In contrast to most of the other drugs given, ofloxacin exerted almost no influence upon the characteristics investigated. The result of this study are reviewed, as well as the results of other studies dealing with the influence of the quinolones on the faecal flora.}, }
@article {pmid2088215, year = {1990}, author = {Hughes, CV and Roseberry, CA and Kolenbrander, PE}, title = {Isolation and characterization of coaggregation-defective mutants of Veillonella atypica.}, journal = {Archives of oral biology}, volume = {35 Suppl}, number = {}, pages = {123S-125S}, doi = {10.1016/0003-9969(90)90141-v}, pmid = {2088215}, issn = {0003-9969}, mesh = {Bacterial Adhesion/drug effects/genetics/*physiology ; Dental Plaque/microbiology ; Humans ; Lactose/pharmacology ; *Mutation ; Streptococcus/classification/*physiology ; Streptococcus sanguis/physiology ; Veillonella/genetics/isolation &amp; purification/*physiology ; }, abstract = {Spontaneously occurring coaggregation-defective mutants of Veillonella atypica PK1910 were isolated and used to study the interactions of veillonella with Streptococcus sanguis, Strep. gordonii and Strep. SM. Three classes of mutants were isolated. The first class failed to participate in lactose-inhibitable coaggregations with streptococcal cells. The second class of mutants failed to coaggregate by the lactose-non-inhibitable interactions. The third group, isolated from the first group, failed to coaggregate with any of the oral streptococci. Based on the coaggregation phenotypes of these mutants, a model for veillonella-streptococcal coaggregations is proposed, in which two distinct surface molecules mediate three types of interactions with the oral streptococci.}, }
@article {pmid1368141, year = {1990}, author = {Schowanek, D and Verstraete, W}, title = {Phosphonate utilization by bacteria in the presence of alternative phosphorus sources.}, journal = {Biodegradation}, volume = {1}, number = {1}, pages = {43-53}, pmid = {1368141}, issn = {0923-9820}, mesh = {Biodegradation, Environmental ; Biological Transport, Active ; Kinetics ; Organophosphonates/*metabolism ; Phosphates/metabolism ; Phosphorus/metabolism ; Pseudomonas/growth &amp; development/*metabolism ; }, abstract = {Batch and continuous culture experiments were carried out to investigate the effect of orthophosphate and p-nitrophenylphosphate on the utilization of various phosphonates as a P source by bacteria. Detailed tests with methylphosphonate as a model phosphonate and the phosphonate-degrading Pseudomonas paucimobilis strain MMM101a revealed that, in contrast with the majority of literature data, the phosphates did not suppress phosphonate utilization. Under conditions of P stress, strain MMM101a simultaneously took up both P-sources, with a preference for the phosphate-P. Study of the kinetic parameters for strain MMM101a, growing on the different P sources revealed similar, rather low, maximum growth rates (ca. 0.15 h-1). However, the affinity for orthophosphate (Ks:0.17 microM), was more than two orders of magnitude higher than for methylphosphonate (Ks: 66 microM), which might account for the preferential uptake of orthophosphate. Cellular phosphorus yields in continuous cultures varied considerably with the conditions applied. The results suggest that phosphonate degradation can occur also in environments with substantial backgrounds of phosphate.}, }
@article {pmid2602891, year = {1989}, author = {Rambaud, JC and Flourié, B and Florent, C}, title = {[What is the status of fermentation diarrhea?].}, journal = {La Revue du praticien}, volume = {39}, number = {29}, pages = {2598-2602}, pmid = {2602891}, issn = {0035-2640}, mesh = {Colonic Diseases, Functional/metabolism ; Diarrhea/metabolism/*physiopathology ; *Fermentation ; Gastrointestinal Motility ; Humans ; Intestinal Diseases/metabolism/physiopathology ; Intestinal Mucosa/metabolism ; }, abstract = {Diarrhoea "whith" bacterial fermentation is characterized by acidic liquid stools containing high amounts of organic acids. Carbohydrate malabsorption is the main cause; the mechanism of diarrhoea is an osmotic one, and colonic fermentation does reduce the diarrhoea. It is unlikely that starch malabsorption induces significant diarrhoea, whereas the consumption of high amounts of fibers is responsible for a "physiologic" diarrhoea. Colonic fermentations increase diarrhoea due to organic colitis and the "diarrhées motrices". They can be responsible for some intestinal symptoms in patients with the irritable bowel syndrome. This does not imply a "hyperfermentative" process due to a hypothetical disturbance of colonic microbial ecology.}, }
@article {pmid2572563, year = {1989}, author = {London, J and Hand, AR and Weiss, EI and Allen, J}, title = {Bacteroides loeschei PK1295 cells express two distinct adhesins simultaneously.}, journal = {Infection and immunity}, volume = {57}, number = {12}, pages = {3940-3944}, pmid = {2572563}, issn = {0019-9567}, mesh = {Antibodies, Monoclonal/immunology ; *Bacterial Adhesion ; Bacteroides/immunology/*pathogenicity/ultrastructure ; Fimbriae, Bacterial/*immunology ; Immunohistochemistry ; }, abstract = {Bacteroides loeschei synthesizes two distinct adhesins that mediate its coaggregation with Streptococcus sanguis 34 and Actinomyces israeli PK14. Streptococcal adhesin-specific and actinomyces adhesin-specific monoclonal antibodies were used to prepare antibody-coated 5- or 10-nm gold particles. These were used in immunoelectron microscopic studies to establish that essentially all bacteroides cells in a population express both adhesins. In general, the two sizes of gold particles representing each type of adhesin appeared to be spatially separated on neighboring fimbriae of B. loeschei. Deposition of antibody-coated gold particles, representing both types of adhesin, at or near the same fimbria was observed less frequently.}, }
@article {pmid2641491, year = {1989}, author = {Ardhana, MM and Fleet, GH}, title = {The microbial ecology of tape ketan fermentation.}, journal = {International journal of food microbiology}, volume = {9}, number = {3}, pages = {157-165}, doi = {10.1016/0168-1605(89)90086-x}, pmid = {2641491}, issn = {0168-1605}, mesh = {Bacteria/*growth &amp; development ; Fermentation ; *Food Microbiology ; Fungi/*growth &amp; development ; Indonesia ; Oryza/*microbiology ; }, abstract = {The growth of fungi, yeasts and bacteria was followed during the fermentation of tape ketan. The tape was prepared using samples of Indonesian ragi as inoculum. Fermentation was characterized by the dominant growth of Amylomyces rouxii and Candida pelliculosa (10(5)-10(7) cfu/g), and a lesser contribution from Saccharomyces cerevisiae. Hansenula anomala grew to a limited extent during some fermentations. Bacteria of the genera Bacillus and Acetobacter contributed also to the fermentation, producing populations up to 10(5) cfu/g. Ragi was the main source of microorganisms involved in the fermentation. Tape fermented by inoculating pure cultures of Amylomyces rouxii and the yeasts, either individually or as mixtures, was not of typical quality, indicating the importance of bacteria in the overall fermentation.}, }
@article {pmid2572552, year = {1989}, author = {Tempro, P and Cassels, F and Siraganian, R and Hand, AR and London, J}, title = {Use of adhesin-specific monoclonal antibodies to identify and localize an adhesin on the surface of Capnocytophaga gingivalis DR2001.}, journal = {Infection and immunity}, volume = {57}, number = {11}, pages = {3418-3424}, pmid = {2572552}, issn = {0019-9567}, mesh = {Actinomyces/immunology ; Antibodies, Monoclonal/*immunology ; Antibody Affinity ; Antigens, Bacterial/*immunology ; Antigens, Surface/immunology ; *Bacterial Adhesion ; Bacterial Outer Membrane Proteins/*immunology ; Capnocytophaga/*immunology/ultrastructure ; Cytophagaceae/*immunology ; Fimbriae, Bacterial/immunology ; Microscopy, Electron ; }, abstract = {Monoclonal antibodies capable of inhibiting coaggregation between Capnocytophaga gingivalis DR2001 and Actinomyces israelii PK16 were used to identify the adhesin on C. gingivalis that mediates the interaction. The monoclonal antibodies were used to demonstrate that a 140-kilodalton polypeptide found in the outer membrane of C. gingivalis was the adhesin responsible for coaggregation. A coaggregation-defective mutant that was unable to coaggregate with A. israelii lacked this large polypeptide. The monoclonal antibodies were also used to estimate the number of binding sites on the surfaces of individual cells and show how the adhesin molecules were arranged on the outer membrane. Values of between 220 and 280 were obtained for the number of adhesin molecules per cell. Immunoelectron microscopy performed with the monoclonal antibodies revealed that the adhesin molecules were arranged nonuniformly on the bacterial surface and occurred singly, in pairs, and in small clusters.}, }
@article {pmid2777379, year = {1989}, author = {Kolenbrander, PE and Andersen, RN}, title = {Inhibition of coaggregation between Fusobacterium nucleatum and Porphyromonas (Bacteroides) gingivalis by lactose and related sugars.}, journal = {Infection and immunity}, volume = {57}, number = {10}, pages = {3204-3209}, pmid = {2777379}, issn = {0019-9567}, mesh = {Acetylgalactosamine/pharmacology ; Bacterial Adhesion/*drug effects ; Bacteroides/drug effects/*physiology ; Fusobacterium/drug effects/*physiology ; Galactose/pharmacology ; Kinetics ; Lactose/*pharmacology ; }, abstract = {The coaggregation of Fusobacterium nucleatum PK1594 and Porphyromonas (Bacteroides) gingivalis PK1924 was inhibited equally well by lactose, N-acetyl-D-galactosamine, and D-galactose, which caused 50% inhibition of coaggregation at 2 mM sugar concentration. Other sugars such as D-galactosamine, D-fucose (6-deoxy-D-galactose), and alpha-methyl- and beta-methyl-D-galactosides also inhibited coaggregation. Sugar specificity was apparent, since neither L-fucose, L-rhamnose, N-acetyl-D-glucosamine, nor N-acetylneuraminic acid was an inhibitor. Protease treatment of the fusobacterium completely abolished coaggregation, whereas it had no effect on the coaggregating activity of the porphyromonad. Although numerous lactose-inhibitable coaggregating pairs are known to occur among gram-positive bacteria, this report and the accompanying survey (P. E. Kolenbrander, R. N. Andersen, and L. V. H. Moore, Infect. Immun. 57:3194-3203, 1989) are the first studies demonstrating the extensive nature of this type of interaction between gram-negative human oral bacteria. The significance of galactoside-inhibitable coaggregations between these two potential periodontal pathogens is discussed.}, }
@article {pmid2777378, year = {1989}, author = {Kolenbrander, PE and Andersen, RN and Moore, LV}, title = {Coaggregation of Fusobacterium nucleatum, Selenomonas flueggei, Selenomonas infelix, Selenomonas noxia, and Selenomonas sputigena with strains from 11 genera of oral bacteria.}, journal = {Infection and immunity}, volume = {57}, number = {10}, pages = {3194-3203}, pmid = {2777378}, issn = {0019-9567}, support = {DE-05054/DE/NIDCR NIH HHS/United States ; DE-05139/DE/NIDCR NIH HHS/United States ; }, mesh = {Actinomyces/drug effects/physiology ; *Bacterial Adhesion/drug effects ; Fusobacterium/drug effects/*physiology ; Hot Temperature ; Lactose/pharmacology ; Mouth/*microbiology ; Streptococcus/drug effects/physiology ; Veillonella/drug effects/physiology ; }, abstract = {Twenty-eight strains of Fusobacterium nucleatum and 41 Selenomonas strains, including S. sputigena (24 strains), S. flueggei (10 strains), S. infelix (5 strains), and S. noxia (2 strains), were tested for their ability to coaggregate with each other and with 49 other strains of oral bacteria representing Actinobacillus, Actinomyces, Bacteroides, Capnocytophaga, Gemella, Peptostreptococcus, Porphyromonas, Propionibacterium, Rothia, Streptococcus, and Veillonella species. Selenomonads coaggregated with fusobacteria and with Actinomyces naeslundii PK984 but not with any of the other bacteria, including other selenomonads. In contrast, fusobacteria coaggregated with members of all genera, although not with all strains of each species tested. Each fusobacterium strain appeared to have its own set of partners and coaggregation properties, unlike their partners, whose coaggregation properties in earlier surveys delineated distinct coaggregation groups. Coaggregations of fusobacteria with the 63 gram-negative strains were usually inhibited by EDTA, whereas those with the 27 gram-positive strains were usually not inhibited. Likewise, lactose-inhibitable coaggregations were common among some strains of fusobacteria and some strains from each of the genera containing gram-negative partners but were rarely observed with gram-positive partners. Heating the fusobacteria at 85 degrees C for 30 min completely prevented coaggregation with most partners, suggesting the involvement of a protein on the fusobacteria. Heat treatment of many of the gram-negative partners not only enhanced their coaggregation with the fusobacteria but also changed lactose-sensitive coaggregations to lactose-insensitive coaggregations. Although fusobacteria coaggregated with a broader variety of oral partner strains than any other group of oral bacteria tested to date, each fusobacterium exhibited coaggregation with only a certain set of partner strains, and none of the fusobacteria adhered to other strains of fusobacteria, indicating that recognition of partner cell surfaces is selective. The strains of F. nucleatum are heterogeneous and cannot be clustered into distinct coaggregation groups. Collectively, these results indicate that coaggregation between fusobacteria and many gram-negative partners is significantly different from their coaggregation with gram-positive partners. The contrasting variety of partners for fusobacteria and selenomonads supports the concept of coaggregation partner specificity that has been observed with every genus of oral bacteria so far examined.}, }
@article {pmid2802606, year = {1989}, author = {Armstrong, JL and Porteous, LA and Wood, ND}, title = {The cutworm Peridroma saucia (Lepidoptera: Noctuidae) supports growth and transport of pBR322-bearing bacteria.}, journal = {Applied and environmental microbiology}, volume = {55}, number = {9}, pages = {2200-2205}, pmid = {2802606}, issn = {0099-2240}, mesh = {Animals ; Colony Count, Microbial ; Enterobacteriaceae/*growth &amp; development ; Fabaceae/*microbiology ; Feces/microbiology ; Insect Vectors/microbiology ; Intestines/microbiology ; Kinetics ; Larva/growth &amp; development/microbiology ; Lepidoptera/growth &amp; development/*microbiology ; *Plants, Medicinal ; Plasmids ; Soil Microbiology ; }, abstract = {Variegated cutworms were exposed to bean plants in microcosms sprayed with pBR322-carrying strains of Enterobacter cloacae, Klebsiella planticola, and Erwinia herbicola. The three bacterial species exhibited differential survival on leaves, in soil, and in guts and fecal pellets (frass) of the insects. High numbers of Enterobacter cloacae(pBR322) were detected in all samples, while the other species were unable to establish residence in the insect. To assess the impact of this colonization on site-to-site transport of microorganisms, larvae were fed plants that had been sprayed with the bacteria and then were transferred to uninoculated plants. Cutworms were efficient carriers of Enterobacter cloacae(pBR322), as indicated by its rapid appearance on uninoculated leaves and continued persistence in the insects for 3 days after transfer. Few Erwinia herbicola(pBR322) and K. planticola(pBR322) were obtained from larvae after transfer, although up to 10(3) CFU/g were detected in soil and on plants. Differences in bacterial survival and growth were confirmed by incubating frass overnight and observing the change in population numbers. The proportion of total samples showing at least a 25-fold increase during incubation was 68% for Enterobacter cloacae(pBR322), 39% for K. planticola(pBR322), and 0% for Erwinia herbicola(pBR322). Our results emphasize the role that cutworms and possibly other insects have in persistence and growth of microorganisms in the environment.}, }
@article {pmid2551353, year = {1989}, author = {Hök, K}, title = {Demonstration of feline infectious peritonitis virus in conjunctival epithelial cells from cats. A simple and reliable method for clinical veterinary virology screening.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {97}, number = {9}, pages = {820-824}, doi = {10.1111/j.1699-0463.1989.tb00483.x}, pmid = {2551353}, issn = {0903-4641}, mesh = {Animals ; Antigens, Viral/analysis ; Cat Diseases/*diagnosis ; Cats ; Coronaviridae/immunology ; Coronaviridae Infections/diagnosis/*veterinary ; Epithelium/microbiology ; Fluorescent Antibody Technique ; Nictitating Membrane/*microbiology ; Peritonitis/diagnosis/*veterinary ; }, abstract = {A simple technique demonstrating the presence of feline infectious peritonitis virus (FIPV) in cats is described. Smears from the third eyelid (membrana nictitans) were dried on microscope slides, fixed in aetone, and stained using an indirect immunofluorescence method with rabbit-anti-FIPV serum. By this method FIPV-antigen could be demonstrated in the cytoplasma of epithelial cells. The results obtained with this method (M3) were compared with serological and immunohistopathological methods for confirming FIPV-infection in cats. The results obtained by the M3 test were up to 85% in concordance with these other tests. Furthermore, the M3 test was easier and quicker to perform and should be well suited for clinical practice.}, }
@article {pmid2767771, year = {1989}, author = {Bernhardt, H and Knoke, M}, title = {Recent studies on the microbial ecology of the upper gastrointestinal tract.}, journal = {Infection}, volume = {17}, number = {4}, pages = {259-263}, doi = {10.1007/BF01639536}, pmid = {2767771}, issn = {0300-8126}, mesh = {Bacteria/isolation &amp; purification ; Bacteria, Anaerobic/isolation &amp; purification/physiology ; Bacterial Infections/microbiology ; *Bacterial Physiological Phenomena ; Bacteroides/isolation &amp; purification/physiology ; Duodenum/microbiology ; Ecology ; Gastrointestinal Diseases/microbiology ; Humans ; Intestinal Secretions/microbiology ; Intestine, Small/*microbiology ; Propionibacterium/isolation &amp; purification/physiology ; }, abstract = {Microecological problems have escalated recently in clinical medicine. We studied the microecology of the upper small bowel. Duodenal flora was examined, displaying microbial growth in 90.8% of the 400 patients examined. The microflora was classified according to germ quality into definite types of colonization. Frequency of microbial colonization is normally 36.7% and 63.3% by overgrowth, indicating differing dysbioses. Simulation of microbial overgrowth in the duodenum is possible with a continuous-flow culture, demonstrating a biocenosis of several groups of micro-organisms with great metabolic activity. Continuous culture technique suggests possibilities for future studies of human gastrointestinal microecology.}, }
@article {pmid2767769, year = {1989}, author = {}, title = {The impact of microbial ecology on clinical problems. International symposium Weitenburg/Tübingen, June 1988.}, journal = {Infection}, volume = {17}, number = {4}, pages = {255-271}, pmid = {2767769}, issn = {0300-8126}, mesh = {*Bacterial Physiological Phenomena ; Humans ; }, }
@article {pmid2661543, year = {1989}, author = {Cassels, FJ and London, J}, title = {Isolation of a coaggregation-inhibiting cell wall polysaccharide from Streptococcus sanguis H1.}, journal = {Journal of bacteriology}, volume = {171}, number = {7}, pages = {4019-4025}, pmid = {2661543}, issn = {0021-9193}, mesh = {*Adhesins, Bacterial ; *Bacterial Adhesion/drug effects ; Cell Wall/analysis/physiology ; Chromatography, Gas ; Endopeptidases ; Hydrofluoric Acid ; Hydrolysis ; Monosaccharides/pharmacology ; Mutation ; Oligosaccharides/isolation &amp; purification/metabolism ; Polysaccharides, Bacterial/*isolation &amp; purification/metabolism/physiology ; Streptococcus sanguis/analysis/genetics/*physiology ; }, abstract = {Coaggregation between Streptococcus sanguis H1 and Capnocytophaga ochracea ATCC 33596 cells is mediated by a carbohydrate receptor on the former and an adhesin on the latter. Two methods were used to release the carbohydrate receptor from the gram-positive streptococcus, autoclaving and mutanolysin treatment. The polysaccharide released from the streptococcal cell wall by either treatment was purified by ion-exchange chromatography; this polysaccharide inhibited coaggregation when preincubated with the gram-negative capnocytophaga partner. After hydrolysis of the polysaccharide by hydrofluoric acid (HF), the major oligosaccharide of the polysaccharide was purified by high-performance liquid chromatography. By analysis of the HF hydrolysis of the polysaccharide and the purified oligosaccharide, this major oligosaccharide appeared to be the repeating unit of the polysaccharide, with minor components resulting from internal hydrolysis of the major oligosaccharide. Gas chromatography results showed that the oligomer was a hexasaccharide, consisting of rhamnose, galactose, and glucose, in the ratio of 2:3:1, respectively. By weight, the purified hexasaccharide was a fourfold-more-potent inhibitor of coaggregation than the native polysaccharide. Resistance to hydrolysis by sulfuric acid alone and susceptibility to hydrolysis by HF suggested that oligosaccharide chains of the polysaccharide are linked by phosphodiester bonds. Studies with a coaggregation-defective mutant of S. sanguis H1 revealed that the cell walls of the mutant contained neither the polysaccharide nor the hexasaccharide repeating unit. The purification of both a polysaccharide and its constituent hexasaccharide repeating unit, which both inhibited coaggregation, and the absence of this polysaccharide or hexasaccharide on a coaggregation-defective mutant strongly suggest that the hexasaccharide derived from the polysaccharide functions as the receptor for the adhesin from C. ochracea ATCC 33596.}, }
@article {pmid2498334, year = {1989}, author = {Thompson, J}, title = {N5-(L-1-carboxyethyl)-L-ornithine:NADP+ oxidoreductase from Streptococcus lactis. Purification and partial characterization.}, journal = {The Journal of biological chemistry}, volume = {264}, number = {16}, pages = {9592-9601}, pmid = {2498334}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Catalysis ; Enzyme Activation ; Enzyme Stability ; Isoelectric Point ; Kinetics ; Lactococcus lactis/*enzymology ; Molecular Sequence Data ; Molecular Weight ; NADH, NADPH Oxidoreductases/*isolation &amp; purification/metabolism ; Ornithine/*analogs &amp; derivatives/isolation &amp; purification/metabolism ; Stereoisomerism ; Substrate Specificity ; }, abstract = {N5-(L-1-Carboxyethyl)-L-ornithine:NADP+ oxidoreductase (EC 1.5.1.-) from Streptococcus lactis K1 has been purified 8,000-fold to homogeneity. The NADPH-dependent enzyme mediates the reductive condensation between pyruvic acid and the delta- or epsilon-amino groups of L-ornithine and L-lysine to form N5-(L-1-carboxyethyl)-L-ornithine and N6-(L-1-carboxyethyl)-L-lysine, respectively. The five-step purification procedure involves ion-exchange (DE52 and phosphocellulose P-11), gel filtration (Ultrogel AcA 44), and affinity chromatography (2',5'-ADP-Sepharose 4B). Approximately 100-200 micrograms of purified enzyme of specific activity 40 units/mg were obtained from 60 g of cells, wet weight. Anionic polyacrylamide gel electrophoresis revealed a single enzymatically active protein band, whereas three species (pI 4.8-5.1) were detected by analytical electrofocusing. The purified enzyme is active over a broad pH range of 6.5-9.0 and is stable to heating at 50 degrees C for 10 min. Substrate Km values were determined to be: NADPH, 6.6 microM; pyruvate, 150 microM; ornithine, 3.3 mM; and lysine, 18.2 mM. The oxidoreductase has a relative molecular mass (Mr = 150,000) as estimated by high pressure liquid chromatography exclusion chromatography and by polyacrylamide gradient gel electrophoresis. Conventional gel filtration indicated an Mr = 78,000, and a single protein band of Mr = 38,000 was revealed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The enzyme is composed of identical subunits of Mr = 38,000, which may associate to yield both dimeric and tetrameric forms. Polyclonal antibody to the purified protein inhibited enzyme activity. The amino acid composition of the enzyme is reported, and the sequence of the first 37 amino acids from the NH2 terminus has been determined by stepwise Edman degradation.}, }
@article {pmid2802880, year = {1989}, author = {Goncharova, GI and Dorofeĭchuk, VG and Smolianskaia, AZ and Sokolova, KIa}, title = {[Microbial ecology of the intestines in health and in pathology].}, journal = {Antibiotiki i khimioterapiia = Antibiotics and chemoterapy [sic]}, volume = {34}, number = {6}, pages = {462-466}, pmid = {2802880}, issn = {0235-2990}, mesh = {Adult ; Age Factors ; Bifidobacterium/growth &amp; development ; Colony Count, Microbial ; Humans ; Infant ; Intestines/*microbiology ; Lactobacillus/growth &amp; development ; }, abstract = {Bifidoflora constitute 85--95 per cent of the large intestine microbiocenosis in children under 1 year of age. Bacteroides are not specific of children under 6 months of age. Lactobacilli, lactic acid streptococci, colon bacilli, enterococci and staphylococci (saprophytic, epidermal) constitute not more than 15 per cent. The predominating group peculiar of eubiosis in adults includes bifidobacteria and bacteroides. Changes in human autoflora are often induced by such factors as impaired ecology, stress, uncontrolled use of antibacterial drugs, radio- and chemotherapy, etc. Dysbacteriosis (first of all lower quantitative contents of bifidoflora) has an unfavourable effect on the intestine secretory function, absorption and certain indices of protein, lipid and mineral metabolism, vitamin synthesizing and fermentative functions and leads to disfunction of the gastrointestinal tract. It is a cause of persisting and relapsing infections in children and adults. High and optimal levels of bifidoflora in the intestine usually prevent the pathogenic action of pathogens. Lysozyme of digestive secretion and secretory immunity with immunoglobulin A prevalence also play an important role in the complicated mechanism of the protective barrier. The use of bacterial preparations such as bifidumbacterin, lactobacterin or bifilact for stabilization and recovery of high bifidoflora levels is indicated in all the cases with impaired microbiocenosis of the intestine.}, }
@article {pmid2802879, year = {1989}, author = {Anufrieva, RG and Zaslavskaia, PL and Shenderov, BA}, title = {[Changes in the microbial ecology and morphology of large intestine biofilm in albino rats under the influence of rifampicin].}, journal = {Antibiotiki i khimioterapiia = Antibiotics and chemoterapy [sic]}, volume = {34}, number = {6}, pages = {457-462}, pmid = {2802879}, issn = {0235-2990}, mesh = {Animals ; Colony Count, Microbial ; Escherichia/drug effects ; Feces/microbiology ; Female ; Intestine, Large/drug effects/*microbiology/ultrastructure ; Lactobacillus/drug effects ; Microscopy, Electron, Scanning ; Rats ; Rats, Inbred Strains ; Rifampin/*adverse effects/pharmacokinetics ; }, abstract = {After oral administration in single doses of 40 and 160 mg/kg to Wistar rats rifampicin was detected in 3 hours in the contents of the large intestine The maximum rifampicin concentrations in the feces (120 and 300 micrograms/g) were detected in 24 hours. The antibiotic was present in the animal feces for 6-7 days. The antibiotic administration led to marked changes in microbiocenosis of the large intestine: disappearance of coccal flora, lower quantities of Escherichia and Lactobacillus and lower total quantities of anaerobic bacteria. It was also accompanied by changes in the structure of the typhlon biofilm. By the 28th day after discontinuation of the antibiotic administration (the end of the observation period) the large intestine microflora did not recover completely.}, }
@article {pmid2802878, year = {1989}, author = {Amanov, N and Garib, FIu and Umarov, IaA}, title = {[Intestinal microbial ecology and its modulation under the influence of immunodepressants].}, journal = {Antibiotiki i khimioterapiia = Antibiotics and chemoterapy [sic]}, volume = {34}, number = {6}, pages = {453-457}, pmid = {2802878}, issn = {0235-2990}, mesh = {Animals ; Azathioprine/adverse effects ; Bifidobacterium/drug effects ; Colony Count, Microbial ; *Gossypol/*analogs &amp; derivatives ; Immunosuppressive Agents/*adverse effects ; Intestines/*microbiology ; Lactobacillus/drug effects ; Rats ; }, abstract = {Oral administration of immunodepressants such as imuran (purine analog) and batriden (gossypol derivative) for 3 months led to development of dysbacterioses in various sections of the rat gastrointestinal tract. The dysbacterioses differed in their levels and the pattern of the recovery process. As compared to batriden, imuran in a dose of 30 mg/kg body weight administered at the early observation periods (days 7, 14 and 30) induced more marked disorders in the intestine microecology. The imuran-induced dysbacteriosis was characterized by lower quantities of lactobacilli and bifidobacteria in the rat intestine. After the use of batriden the quantities of bifidobacteria, lactobacilli and bacteroides decreased. After the batriden use at the late observation periods (days 60 to 90) the ratio of anaerobes and lactobacilli to aerobes recovered at the background of increased quantities of Candida in all the intestine sections while the ratio of bacteroides recovered in the stomach. When immunity was suppressed by imuran the recovery period was characterized by normalization of the microflora composition in the distal sections and preservation of the contamination symptom in the proximal section which was evident from predominance of aerobes over anaerobes.}, }
@article {pmid2802877, year = {1989}, author = {Mitrokhin, SD and Shenderov, BA}, title = {[Microbiological and biochemical indices of changes in microbial ecology of rat large intestine under the effect of rifampicin].}, journal = {Antibiotiki i khimioterapiia = Antibiotics and chemoterapy [sic]}, volume = {34}, number = {6}, pages = {448-452}, pmid = {2802877}, issn = {0235-2990}, mesh = {Animals ; Colony Count, Microbial ; Feces/microbiology ; Gram-Negative Bacteria/drug effects ; Gram-Positive Bacteria/drug effects ; Intestine, Large/*microbiology ; Lactobacillus/drug effects ; Male ; Rats ; Rats, Inbred Strains ; Rifampin/*adverse effects ; }, abstract = {Intragastric administration of rifampicin to rats in a dose of 40 mg/kg resulted in decreasing of the contents of grampositive cocci and lactobacilli and increasing of the number of gramnegative aerobic potentially pathogenic bacteria in feces of the experimental animals. It was noted that along with changes in the composition of the fecal microflora after the exposure to the antibiotic there were disorders in feces excretion of ammonia and amino acids such as alanine and glutamic acid as well as lactic, amber, butyric, valeric and alpha-ketoglutaric acids. Reduction of the changed biochemical indices was shown to be slower than that of the routine microbiological indices.}, }
@article {pmid2802876, year = {1989}, author = {Liz'ko, NN}, title = {[New experimental models in microbial ecology].}, journal = {Antibiotiki i khimioterapiia = Antibiotics and chemoterapy [sic]}, volume = {34}, number = {6}, pages = {443-448}, pmid = {2802876}, issn = {0235-2990}, mesh = {Animals ; Anti-Bacterial Agents/*adverse effects ; Bifidobacterium/drug effects ; Intestines/*drug effects/microbiology ; Lactobacillus/drug effects ; *Models, Biological ; Primates ; Rats ; Space Flight ; Stress, Psychological ; }, abstract = {Peculiar features of dysbiosis development in persons under extreme conditions were studied. It was shown that a number of extreme factors participated in formation of dysbiotic disorders in intestinal microflora. Of paramount importance was the neuro-emotional stress. Lability of bifido- and lactoflora was considered as the starting mechanism in dysbacteriosis under the extreme conditions. In the experimental models with rats SPF and Primates during flights of biosatellites of the Kosmos series the role of indigenous++ microflora in maintaining the microecological homeostasis, as well as the need for development of artificial and controlled intestinal microflora promising in prophylaxis of dysbacteriosis under extreme conditions was shown. The theoretical and experimentally grounded necessity of maintaining constant intestine microbiocenosis was confirmed by the practice of using the system of measures for recovery, stabilization and optimization of microflora in persons under extreme conditions.}, }
@article {pmid2802872, year = {1989}, author = {Pruzhniak, OV and Kolotilova, LV}, title = {[Microbial ecology of the upper respiratory tracts and antibiotics].}, journal = {Antibiotiki i khimioterapiia = Antibiotics and chemoterapy [sic]}, volume = {34}, number = {6}, pages = {415-419}, pmid = {2802872}, issn = {0235-2990}, mesh = {Anti-Bacterial Agents/*adverse effects ; Bacteria/*drug effects ; Humans ; Respiratory System/*microbiology ; }, }
@article {pmid2764567, year = {1989}, author = {Barkay, T and Liebert, C and Gillman, M}, title = {Hybridization of DNA probes with whole-community genome for detection of genes that encode microbial responses to pollutants: mer genes and Hg2+ resistance.}, journal = {Applied and environmental microbiology}, volume = {55}, number = {6}, pages = {1574-1577}, pmid = {2764567}, issn = {0099-2240}, mesh = {Adaptation, Physiological ; Bacteria/drug effects/*genetics ; DNA Probes ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Mercury/*pharmacology ; Nucleic Acid Hybridization ; Operon ; Water Microbiology ; Water Pollutants/*pharmacology ; }, abstract = {Nucleic acids extracted from microbial biomass without prior culturing were hybridized with probes representing four mer operons to detect genes encoding adaptation to Hg2+ in whole-community genomes. A 29-fold enrichment in sequences similar to the mer genes of transposon Tn501 occurred during adaptation in a freshwater community. In an estuarine community, all four mer genes were only slightly enriched (by three- to fivefold), suggesting that additional, yet uncharacterized, mer genes encoded adaptation to Hg2+.}, }
@article {pmid2517398, year = {1989}, author = {Chassy, BM and Alpert, CA}, title = {Molecular characterization of the plasmid-encoded lactose-PTS of Lactobacillus casei.}, journal = {FEMS microbiology reviews}, volume = {5}, number = {1-2}, pages = {157-165}, doi = {10.1016/0168-6445(89)90020-x}, pmid = {2517398}, issn = {0168-6445}, mesh = {Cloning, Molecular ; DNA/genetics ; Genes, Bacterial ; Lacticaseibacillus casei/enzymology/*genetics ; Lactose/*metabolism ; Operon ; Phosphoenolpyruvate Sugar Phosphotransferase System/*genetics/metabolism ; *Plasmids ; Sequence Homology, Nucleic Acid ; }, }
@article {pmid2547336, year = {1989}, author = {Barkay, T and Liebert, C and Gillman, M}, title = {Environmental significance of the potential for mer(Tn21)-mediated reduction of Hg2+ to Hg0 in natural waters.}, journal = {Applied and environmental microbiology}, volume = {55}, number = {5}, pages = {1196-1202}, pmid = {2547336}, issn = {0099-2240}, mesh = {Animals ; Bacteria/drug effects/genetics/*metabolism ; Biotransformation ; *DNA Transposable Elements ; Drug Resistance, Microbial ; Eukaryota/drug effects/metabolism ; Fresh Water ; Genes, Bacterial ; Mercury/*metabolism/pharmacology ; Oxidation-Reduction ; Seawater ; Volatilization ; *Water Microbiology ; Water Pollutants, Chemical ; }, abstract = {The role of mer(Tn21) in the adaptation of aquatic microbial communities to Hg2+ was investigated. Elemental mercury was the sole product of Hg2+ volatilization by freshwater and saline water microbial communities. Bacterial activity was responsible for biotransformation because most microeucaryotes did not survive the exposure conditions, and removal of larger microbes (greater than 1 micromole) from adapted communities did not significantly (P greater than 0.01) reduce Hg2+ volatilization rates. DNA sequences homologous to mer(Tn21) were found in 50% of Hg2+-resistant bacterial strains representing two freshwater communities, but in only 12% of strains representing two saline communities (the difference was highly significant; P less than 0.001). Thus, mer(Tn21) played a significant role in Hg2+ resistance among strains isolated from fresh waters, in which microbial activity had a limited role in Hg2+ volatilization. In saline water environments in which microbially mediated volatilization was the major mechanism of Hg2+ loss, other bacterial genes coded for this biotransformation.}, }
@article {pmid2729586, year = {1989}, author = {Boots, S}, title = {Microelectrodes in microbial ecology.}, journal = {Analytical chemistry}, volume = {61}, number = {6}, pages = {425A-427A}, doi = {10.1021/ac00181a002}, pmid = {2729586}, issn = {0003-2700}, mesh = {*Bacterial Physiological Phenomena ; *Ecology ; *Microelectrodes ; Oxidation-Reduction ; Photosynthesis ; }, }
@article {pmid2757366, year = {1989}, author = {Nordbring-Hertz, B and Friman, E and Veenhuis, M}, title = {Hyphal fusion during initial stages of trap formation in Arthrobotrys oligospora.}, journal = {Antonie van Leeuwenhoek}, volume = {55}, number = {3}, pages = {237-244}, pmid = {2757366}, issn = {0003-6072}, mesh = {Cell Wall/physiology/ultrastructure ; Cytoplasm/physiology/ultrastructure ; *Membrane Fusion ; Mitosporic Fungi/*physiology/ultrastructure ; Video Recording ; }, abstract = {Hyphal fusion during initial stages of trap formation by Arthrobotrys oligospora was studied by video-enhanced contrast and electron microscopy. Trap initials grew perpendicularly to the parent hypha, then curved around and anastomosed with a peg that developed on the hypha. Trap initials usually developed 40-140 microns apart while the anastomosis occurred 20-25 microns from the initial. Vigorous cytoplasmic movements in trap initials and developed traps corresponded to intense staining with fluorescein diacetate (FDA) of these cells. In addition, bundles of microfilaments were seen in developing loops of traps. On fusion organelle migration took place from the tip cell of the trap into the peg. Later on a septum was formed at the site of fusion.}, }
@article {pmid2518226, year = {1989}, author = {Mulyowidarso, RK and Fleet, GH and Buckle, KA}, title = {The microbial ecology of soybean soaking for tempe production.}, journal = {International journal of food microbiology}, volume = {8}, number = {1}, pages = {35-46}, doi = {10.1016/0168-1605(89)90078-0}, pmid = {2518226}, issn = {0168-1605}, mesh = {Bacteria/growth &amp; development/*metabolism ; Enterobacteriaceae/growth &amp; development/metabolism ; Fermentation ; *Food Handling ; *Food Microbiology ; Hydrogen-Ion Concentration ; Lacticaseibacillus casei/growth &amp; development/metabolism ; *Glycine max ; Staphylococcus epidermidis/growth &amp; development/metabolism ; Streptococcus/growth &amp; development/metabolism ; Temperature ; Yeasts/growth &amp; development/*metabolism ; }, abstract = {Soybeans soaked in tap water for 24 to 36 h at 20, 30 or 37 degrees C underwent a natural fermentation that was characterized by the growth of microorganisms to 10(8)-10(10) cfu/ml (depending on temperature) and a reduction of pH from 6.5 to 4.5. Lactobacillus casei, Streptococcus faecium, Staphylococcus epidermidis and Streptococcus dysgalactiae dominated the fermentation but, significant contributions were also made by Klebsiella pneumoniae, Klebsiella ozaenae, Enterobacter cloacae, Enterobacter agglomerans, Citrobacter diversus and Bacillus brevis, and the yeasts Pichia burtonii, Candida didensiae and Rhodotorula rubra. Fermentation of surface-decontaminated beans in sterile water with pure cultures of these isolates showed L. casei, Strep. faecium and Staph. epidermidis to be the main species responsible for the pH reduction. Soybeans were the main source of microorganisms for the fermentation. Boiled beans did not undergo an acid fermentation.}, }
@article {pmid2675207, year = {1989}, author = {MacRae, IC}, title = {Microbial metabolism of pesticides and structurally related compounds.}, journal = {Reviews of environmental contamination and toxicology}, volume = {109}, number = {}, pages = {1-87}, doi = {10.1007/978-1-4684-7086-4_1}, pmid = {2675207}, issn = {0179-5953}, mesh = {*Biodegradation, Environmental ; Environmental Pollutants/*metabolism ; Pesticides/*metabolism ; Soil Microbiology ; Water Microbiology ; }, abstract = {This chapter provides a review concerning the microbial metabolism of pesticides and substances that are either major metabolites from pesticides or have structural similarity to certain pesticides, and covers the period 1981 to 1987. While reference has only been made to work published during this period, it should be realized that in some instances the results cited may confirm or expand upon earlier findings rather than being entirely novel. Therefore, the reader is referred to earlier reviews. The metabolism of pesticides in natural environments, water and wastewater, mixed microbial cultures, and pure cultures has been discussed. Attention has been drawn to the meager amount of information concerning the biodegradation of pesticides in anaerobic and marine environments. Issues such as the importance of cometabolism of pesticides in natural environments and a clear understanding of enhanced degradation of pesticides in soil still remain unresolved. Separate sections have been devoted to methodology in biodegradation studies, bound residues and removal of pesticides from soil and water. While pure culture studies have an important place in investigations into microbial metabolism of pesticides, increasing emphasis has been placed on the use of microbial consortia, either natural or artificial and microcosms to provide an understanding of pesticide biodegradation in natural environments. Another dimension in bound residue formation, one of physical entrapment in humic materials has been described. Various questions regarding the bioavailability of bound residues and whether they pose an environmental problem have not been answered fully. The microbiological removal of pesticides from soil and water by selected or genetically-engineered strains is discussed. It has been emphasized that the future success of such methods for the decontamination of soil and water depends very heavily on an improved knowledge of microbial ecology.}, }
@article {pmid2561802, year = {1989}, author = {Raibaud, P}, title = {Experimental models for studying the microbial ecology in the intestinal tract.}, journal = {Acta gastroenterologica Latinoamericana}, volume = {19}, number = {4}, pages = {219-226}, pmid = {2561802}, issn = {0300-9033}, mesh = {Animals ; Bacteroides/*physiology ; Cecum/*microbiology ; Clostridium perfringens/*physiology ; Ecology ; Feces/microbiology ; Fusobacterium/*physiology ; In Vitro Techniques ; Intestine, Small/*microbiology ; Mice ; Mice, Inbred C3H ; Models, Biological ; Rats ; Rats, Inbred F344 ; }, }
@article {pmid3223764, year = {1988}, author = {Newbold, CJ and Wallace, RJ}, title = {Effects of the ionophores monensin and tetronasin on simulated development of ruminal lactic acidosis in vitro.}, journal = {Applied and environmental microbiology}, volume = {54}, number = {12}, pages = {2981-2985}, pmid = {3223764}, issn = {0099-2240}, mesh = {Acidosis, Lactic/metabolism/microbiology/*prevention &amp; control ; Animals ; Cattle ; Furans/pharmacology ; Glucose/metabolism ; Hydrogen-Ion Concentration ; In Vitro Techniques ; Lactates/metabolism ; Lactic Acid ; Monensin/*pharmacology ; Rumen/drug effects/metabolism/*microbiology ; Sheep ; }, abstract = {A continuous coculture of four ruminal bacteria, Megasphaera elsdenii, Selenomonas ruminantium, Streptococcus bovis, and Lactobacillus sp. strain LB17, was used to study the effects of the ionophores monensin and tetronasin on the changes in ruminal microbial ecology that occur during the onset of lactic acidosis. In control incubations, the system simulated the development of lactic acidosis in vivo, with an initial overgrowth of S. bovis when an excess of glucose was added to the fermentor. Lactobacillus sp. strain LB17 subsequently became dominant as pH fell and lactate concentration rose. Both ionophores were able to prevent the accumulation of lactic acid and maintain a healthy non-lactate-producing bacterial population when added at the same time as an excess of glucose. Tetronasin was more potent in this respect than monensin. When tetronasin was added to the culture 24 h after glucose, the proliferation of lactobacilli was reversed and a non-lactate-producing bacterial population developed, with an associated drop in lactate concentration in the fermentor. Rises in culture pH and volatile fatty acid concentrations accompanied these changes. Monensin was unable to suppress the growth of lactobacilli; therefore, in contrast to tetronasin, monensin added 24 h after the addition of glucose failed to reverse the acidosis. Numbers of lactobacilli and lactate concentrations remained high, whereas pH and volatile fatty acid concentrations were low.}, }
@article {pmid3066292, year = {1988}, author = {Boizet, B and Flickinger, JL and Chassy, BM}, title = {Transfection of Lactobacillus bulgaricus protoplasts by bacteriophage DNA.}, journal = {Applied and environmental microbiology}, volume = {54}, number = {12}, pages = {3014-3018}, pmid = {3066292}, issn = {0099-2240}, mesh = {Bacteriophages/*genetics ; Calcium/pharmacology ; DNA, Viral/*genetics ; Endopeptidases/pharmacology ; Lactobacillus/drug effects/*genetics ; Polyethylene Glycols ; Protoplasts/drug effects ; Raffinose/pharmacology ; *Transfection/drug effects ; }, abstract = {A protoplast transfection system has been developed for Lactobacillus bulgaricus. The procedure involves a polyethylene glycol-mediated fusion of bacteriophage DNA encapsulated in liposomes into mutanolysin-treated cells. With L. bulgaricus B004 and DNA isolated from the phage phi c5004, transfection reached a maximum when at least 95% of the cells were osmotically fragile. The incorporation of phage DNA into liposomes was essential; no transfectants were detected in the absence of liposomes. The largest number of transfectants was observed after longer periods (20 min) of fusion of mutanolysin-treated cells and liposomes with polyethylene glycol. The maximum efficiency of 5 x 10(7) PFU/microgram of DNA was reached after a 24-h incubation in growth media prior to plating transfected cells in an agar overlay to detect the appearance of plaques. A minimum of 4 h of incubation in growth medium after fusion was required to detect the production and release of virions. The possibility that the high frequencies observed were due to bursting of transfected cells and subsequent infection of additional cells was found not to be a factor. The number of transfectants observed was directly proportional to the quantity of DNA added. These results define conditions appropriate for the introduction of DNA into L. bulgaricus.}, }
@article {pmid2902012, year = {1988}, author = {Cisar, JO and Vatter, AE and Clark, WB and Curl, SH and Hurst-Calderone, S and Sandberg, AL}, title = {Mutants of Actinomyces viscosus T14V lacking type 1, type 2, or both types of fimbriae.}, journal = {Infection and immunity}, volume = {56}, number = {11}, pages = {2984-2989}, pmid = {2902012}, issn = {0019-9567}, support = {DE 00115/DE/NIDCR NIH HHS/United States ; DE 05429/DE/NIDCR NIH HHS/United States ; }, mesh = {Actinomyces/*genetics ; Antibodies, Bacterial/immunology ; Antibodies, Monoclonal/immunology ; Antigens, Bacterial/genetics ; Fimbriae, Bacterial/*physiology ; Microscopy, Electron ; Mutation ; Saliva/immunology/microbiology ; }, abstract = {Mutants of Actinomyces viscosus T14V lacking type 1 or type 2 fimbriae or both were selected by their failure to react with rabbit antibodies against either or both fimbrial antigens. Immunospecific double labeling with iron dextran and ferritin-conjugated antibodies showed two types of fimbriae on individual cells of the parent organism, a single type on mutant strains with type 1+2- and type 1-2+ fimbriae and no labeled or unlabeled fimbriae on a type 1-2- fimbria-deficient strain. The mutational loss of one fimbrial antigen did not appear to affect expression of the other, since bacteria with one or two types of fimbriae bound similar amounts of a monoclonal antibody directed against the fimbrial antigen present on both bacterial phenotypes. The strong adsorption of strains with type 1+2+ or 1+2- fimbriae to saliva-treated hydroxyapatite and weak adsorption of those with type 1-2+ or no fimbriae was consistent with the known involvement of type 1 fimbriae in this attachment process. Similarly, the A. viscosus lectin was clearly associated with the expression of type 2 fimbriae, since only the strains with type 1+2+ or 1-2+ fimbriae participated in lactose-sensitive coaggregations with Streptococcus sanguis 34. Further studies using the fimbria-deficient mutant strains showed that aggregation of A. viscosus T14V in the presence of sialidase-treated human saliva involved both types of fimbriae, whereas neither type was required for the lactose-resistant coaggregation of the organism with certain streptococcal strains.}, }
@article {pmid3178207, year = {1988}, author = {Hughes, CV and Kolenbrander, PE and Andersen, RN and Moore, LV}, title = {Coaggregation properties of human oral Veillonella spp.: relationship to colonization site and oral ecology.}, journal = {Applied and environmental microbiology}, volume = {54}, number = {8}, pages = {1957-1963}, pmid = {3178207}, issn = {0099-2240}, support = {DE-05054/DE/NIDCR NIH HHS/United States ; DE-05139/DE/NIDCR NIH HHS/United States ; }, mesh = {Actinomyces/metabolism ; Dental Plaque/microbiology ; Humans ; Mouth/*microbiology ; Mouth Mucosa/microbiology ; Saliva/microbiology ; Streptococcus sanguis/metabolism ; Tongue/microbiology ; Veillonella/growth &amp; development/*physiology ; }, abstract = {The primary habitats of oral veillonellae are the tongue, dental plaque, and the buccal mucosa. Isolates were obtained from each habitat and tested for coaggregation with a battery of other oral bacterial strains. All 59 tongue isolates tested for coaggregation were Veillonella atypica or Veillonella dispar. All but one of them coaggregated with strains of Streptococcus salivarius, a predominant inhabitant of the tongue surface but not subgingival dental plaque. These tongue isolates were unable to coaggregate with most normal members of the subgingival flora such as Actinomyces viscosus, Actinomyces naeslundii, Actinomyces israelii, and Streptococcus sanguis. In contrast, 24 of 29 Veillonella isolates, of which 20 were Veillonella parvula from subgingival dental plaque samples, coaggregated strongly with the three species of Actinomyces, S. sanguis, and other bacteria usually present in subgingival plaque, but they did not coaggregate with S. salivarius. The majority of isolates from the buccal mucosa (42 of 55) has coaggregation properties like those from the tongue. These results indicate that the three human oral Veillonella species are distributed on oral surfaces that are also occupied by their coaggregation partners and thus provide strong evidence that coaggregation plays a critical role in the bacterial ecology of the oral cavity.}, }
@article {pmid3145135, year = {1988}, author = {McGroarty, JA and Reid, G}, title = {Detection of a Lactobacillus substance that inhibits Escherichia coli.}, journal = {Canadian journal of microbiology}, volume = {34}, number = {8}, pages = {974-978}, doi = {10.1139/m88-171}, pmid = {3145135}, issn = {0008-4166}, mesh = {Antibiosis ; Bacterial Adhesion ; Culture Media ; Escherichia coli/*growth &amp; development ; Humans ; Hydrogen-Ion Concentration ; Lactobacillus/growth &amp; development/*metabolism ; Lactobacillus acidophilus/growth &amp; development/metabolism ; Lacticaseibacillus casei/growth &amp; development/metabolism ; Urine/microbiology ; }, abstract = {Recent studies have shown that certain lactobacilli strains have the ability to interfere with the adherence and growth of uropathogenic bacteria. This interaction is believed to be important in the maintenance of a normal urogenital flora and in the prevention of infection in females. In the present study, Lactobacillus casei ssp. rhamnosus GR-1 and Lactobacillus acidophilus 76 were found to exert an inhibitory effect on pyelonephritogenic mutant Escherichia coli Hu 734 and E. coli ATCC 25922. The bioactivity of the inhibitor produced by strain GR-1 was retained under pH buffered conditions and was bactericidal. The bioactive substance was heat labile, not precipitated by up to 80% ammonium sulphate, and extractable in chloroform. The data indicated that the inhibitor is not lactic acid or hydrogen peroxide and has a molecular weight greater than 12,000-14,000. Human urine supported production of the inhibitor and reduced and delayed outgrowth of the E. coli. The ability of L. casei GR-1 and possibly other lactobacilli strains to produce inhibitors of uropathogenic bacteria may have clinical importance and significance in the microbial ecology of the urogenital tract.}, }
@article {pmid2839489, year = {1988}, author = {Karpel, R and Olami, Y and Taglicht, D and Schuldiner, S and Padan, E}, title = {Sequencing of the gene ant which affects the Na+/H+ antiporter activity in Escherichia coli.}, journal = {The Journal of biological chemistry}, volume = {263}, number = {21}, pages = {10408-10414}, pmid = {2839489}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Base Sequence ; Carrier Proteins/*genetics/metabolism ; Cloning, Molecular ; DNA Restriction Enzymes ; Escherichia coli/*genetics/metabolism ; *Genes ; *Genes, Bacterial ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Promoter Regions, Genetic ; Protein Conformation ; RNA, Messenger/genetics ; Sodium-Hydrogen Exchangers ; }, abstract = {By introduction of deletions and/or insertions, we have defined a small DNA fragment (1.58 kilobase pairs) which contains the ant gene. Thus, transformants of all plasmid constructs containing this segment exhibit Antup phenotype, i.e. growth is Li+-resistant and Na+/H+ antiporter activity is increased in isolated everted membrane vesicles. Utilizing the T7 promoter expression system, we also found that this fragment encodes for a single protein of 35 kDa. The DNA fragment has been sequenced and found to contain an open reading frame of 1085 base pairs. Analysis of the sequence of the predicted protein suggests the presence of 10 putative transmembrane segments in the protein.}, }
@article {pmid3135382, year = {1988}, author = {Midtvedt, AC and Carlstedt-Duke, B and Norin, KE and Saxerholt, H and Midtvedt, T}, title = {Development of five metabolic activities associated with the intestinal microflora of healthy infants.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {7}, number = {4}, pages = {559-567}, doi = {10.1097/00005176-198807000-00014}, pmid = {3135382}, issn = {0277-2116}, mesh = {Bilirubin/metabolism ; Cholestanol/metabolism ; Cholesterol/metabolism ; Fatty Acids, Volatile/biosynthesis ; Feces/analysis ; Female ; Follow-Up Studies ; Humans ; Infant ; Infant, Newborn/*metabolism ; Intestines/*microbiology ; Longitudinal Studies ; Male ; Mucins/metabolism ; Trypsin/metabolism ; Urobilinogen/biosynthesis ; }, abstract = {The establishment of a functionally active intestinal flora was followed in 17 healthy Swedish children from birth up to 6 months of age. Utilizing gas chromatography, spectrophotometry, and gel electrophoresis, feces were analyzed on certain biochemical markers that reflect the action of the intestinal flora in vivo. The establishment of the following five flora-related functions was investigated: production of short chain fatty acids (SCFAs), degradation of mucin, conversion of bilirubin to urobilinogen and of cholesterol to coprostanol, and inactivation of fecal tryptic activity (FTA). Production of SCFAs was the first function to be established, followed by bilirubin conversion and mucin degradation. No child showed conversion of cholesterol. The values of FTA were lower than in adults. This study indicates that the establishment of a functionally active flora is a slow process and that some functions are almost fully established before other functions have started to develop. Environmental factors, such as the diet, seem to be of importance. In general, the functions seem to develop slower in those children receiving breast milk exclusively than in those receiving formula supplements.}, }
@article {pmid3389805, year = {1988}, author = {Stahl, DA and Flesher, B and Mansfield, HR and Montgomery, L}, title = {Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology.}, journal = {Applied and environmental microbiology}, volume = {54}, number = {5}, pages = {1079-1084}, pmid = {3389805}, issn = {0099-2240}, mesh = {Animals ; Bacteroides/drug effects/genetics/*growth &amp; development ; Cattle ; Ecology ; Female ; Monensin/pharmacology ; *Nucleic Acid Hybridization/drug effects ; *Phylogeny ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/*genetics ; Rumen/metabolism/*microbiology ; }, abstract = {To address the long-standing need for more precise descriptions of natural microbial ecosystems, 16S rRNAs were used to track certain species and phylogenetically coherent groups of microorganisms in their natural setting without culturing. Species- and group-specific 16S rRNA-targeted oligonucleotide hybridization probes were developed to enumerate various strains of Bacteroides succinogenes and Lachnospira multiparus-like organisms in the bovine rumen before, during, and after perturbation of that ecosystem by the addition of the ionophore antibiotic monensin. Based on probe hybridization, relative numbers of L. multiparus-like organisms were depressed about 2-fold during monensin addition and demonstrated a transient 5- to 10-fold increase immediately after removal of the antibiotic from the diet. The most pronounced population changes were observed among different strains of B. succinogenes, as evaluated by three hybridization probes. One probe hybridized to all strains, whereas the other two identified genetically distinct groups represented by strains isolated from the rumen and from the ceca of nonruminants. The rumen-type strains predominated on most days (ca. 0.2 to 0.8% of total ribosome numbers). Their proportion transiently increased about fivefold immediately after the addition of monensin to the feed and then transiently fell below the average premonensin level. During this time (ca. 2 weeks after monensin addition) the cecal type predominated (ca. 0.1 to 0.2%). Cultural enumeration of B. succinogenes on nonselective agar and by observing clearings in cellulose agar media were largely unsuccessful due to the low number of organisms present and the predominance of other cellulolytic species.(ABSTRACT TRUNCATED AT 250 WORDS)}, }
@article {pmid3357191, year = {1988}, author = {Elhag, KM and Bahar, AM and Mubarak, AA}, title = {The effect of a copper intra-uterine contraceptive device on the microbial ecology of the female genital tract.}, journal = {Journal of medical microbiology}, volume = {25}, number = {4}, pages = {245-251}, doi = {10.1099/00222615-25-4-245}, pmid = {3357191}, issn = {0022-2615}, mesh = {Actinomyces/isolation &amp; purification ; Actinomycetaceae/isolation &amp; purification ; Actinomycetales Infections/*etiology/microbiology ; Adult ; Bacteroides/isolation &amp; purification ; Candida/isolation &amp; purification ; Female ; Genitalia, Female/*microbiology ; Humans ; Intrauterine Devices, Copper/*adverse effects ; Lactobacillus/isolation &amp; purification ; Pelvic Inflammatory Disease/*etiology/microbiology ; Staphylococcus/isolation &amp; purification ; Streptococcus/isolation &amp; purification ; }, abstract = {Bacteria isolated from 108 intra-uterine contraceptive devices (IUCD) removed from patients with pelvic inflammatory disease (PID), haemorrhage, pregnancy and from asymptomatic women, and from the genital tracts of 66 healthy controls not wearing an IUCD, were studied. No significant differences were found in the types of micro-organisms or isolation rates from IUCDs removed from women in the various clinical groups. The isolation rate of anaerobic bacteria from IUCDs removed from asymptomatic wearers was significantly lower than that from controls, with the exception of the isolation rate of actinomyces which was significantly higher in IUCD wearers and A. israelii was recovered only from IUCDs. The isolation rates of the different bacterial species varied with the duration of the device in utero. The presence of a copper IUCD altered the bacterial flora of the female genital tract. The insertion of such a device and the ecological changes that follow play a crucial role in the development of PID.}, }
@article {pmid3223247, year = {1988}, author = {Ozawa, A and Sawamura, S}, title = {Microbial ecology and tonsillar infection.}, journal = {Acta oto-laryngologica. Supplementum}, volume = {454}, number = {}, pages = {178-184}, doi = {10.3109/00016488809125023}, pmid = {3223247}, issn = {0365-5237}, mesh = {Adult ; Bacteria/*isolation &amp; purification ; Chronic Disease ; Female ; Humans ; Male ; Middle Aged ; Palatine Tonsil/*microbiology ; Tonsillitis/*microbiology ; }, abstract = {The results of quantitative and qualitative analyses of tonsillar bacterial flora in chronic tonsillitis patients and healthy subjects are reported. Based on these results, the pathogenesis of tonsillar infections is discussed from the standpoint of bacterial ecology.}, }
@article {pmid3144238, year = {1988}, author = {Roth, RR and James, WD}, title = {Microbial ecology of the skin.}, journal = {Annual review of microbiology}, volume = {42}, number = {}, pages = {441-464}, doi = {10.1146/annurev.mi.42.100188.002301}, pmid = {3144238}, issn = {0066-4227}, mesh = {Actinomycetales/isolation &amp; purification ; Bacteria/*isolation &amp; purification/pathogenicity ; Bacterial Infections/*microbiology ; Fungi/isolation &amp; purification ; Humans ; Micrococcaceae/isolation &amp; purification ; Propionibacterium/isolation &amp; purification/pathogenicity ; Skin/*microbiology ; Skin Diseases, Infectious/*microbiology ; Staphylococcus/pathogenicity ; }, abstract = {Humans exist in an environment replete with microorganisms, yet only a few of these microorganisms become residents on the skin surface. These resident flora and the skin constitute a complex ecosystem in which organisms adapt to changes in the microenvironment and to coactions among microorganisms. The skin possesses an assortment of protective mechanisms to limit colonization, and the survival of organisms on the surface lies in part in the ability of the organisms to resist these mechanisms. Microbial colonization on the skin adds to the skin's defense against potentially pathogenic organisms. Although microbes normally live in synergy with their hosts, at times colonization can lead to clinical infection. Common infections consist of superficial infections of the stratum corneum or appendages, which can respond dramatically to therapy but commonly relapse. In rare circumstances these infections can be severe, particularly in immunocompromised patients or hospitalized patients with indwelling foreign devices.}, }
@article {pmid3060002, year = {1988}, author = {Kolenbrander, PE}, title = {Intergeneric coaggregation among human oral bacteria and ecology of dental plaque.}, journal = {Annual review of microbiology}, volume = {42}, number = {}, pages = {627-656}, doi = {10.1146/annurev.mi.42.100188.003211}, pmid = {3060002}, issn = {0066-4227}, mesh = {*Bacterial Adhesion ; Dental Plaque/*microbiology ; Humans ; Mouth/*microbiology ; }, }
@article {pmid3059463, year = {1988}, author = {Midtvedt, T}, title = {Fundamentals in the prophylaxis of septic surgical complications.}, journal = {Scandinavian journal of gastroenterology. Supplement}, volume = {149}, number = {}, pages = {93-101}, doi = {10.3109/00365528809096963}, pmid = {3059463}, issn = {0085-5928}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Colorectal Neoplasms/*surgery ; Humans ; Intestines/microbiology ; *Premedication ; Risk Factors ; Surgical Wound Infection/*prevention &amp; control ; }, abstract = {An operation in which the colonic/rectal wall is opened represents a destruction of a complicated balance between the patient and his intestinal micro-flora, giving way for infective micro-organisms to become established. The surgeon should try to minimize the number of organisms reaching the operation field and reduce their possibilities of establishment. Some strategical and tactical guide-lines for achieving these goals are given.}, }
@article {pmid3041739, year = {1988}, author = {Ghiorse, WC and Wilson, JT}, title = {Microbial ecology of the terrestrial subsurface.}, journal = {Advances in applied microbiology}, volume = {33}, number = {}, pages = {107-172}, doi = {10.1016/s0065-2164(08)70206-5}, pmid = {3041739}, issn = {0065-2164}, mesh = {Bacteria/*growth &amp; development/metabolism ; Biodegradation, Environmental ; *Environmental Pollutants ; Fresh Water ; *Soil Microbiology ; *Water Microbiology ; }, abstract = {We have presented a current view of the microbial ecology of the terrestrial subsurface by considering primarily the ecology of shallow aquifer sediments. The properties of the aquifer sediments and groundwater determine their ability to support microbial life and control the abundance and activities of microorganisms. Pore size, nutrient limitations, availability of electron acceptors, and large surface area for attachment all may have major effects on microbial abundance and activities in aquifer material. Microorganisms are the predominant forms of life in the subsurface. They will be found wherever enough space, nutrients, and water are available for them to live. Environmental factors such as pH, temperature, hydrostatic pressure, and dissolved salts also may influence subsurface microbial populations, but these factors do not exhibit great extremes in shallow water table aquifers, and thus only in very deep formations might they limit diversity or preclude the existence of microorganisms. Although the presence and activity of microorganisms in most subsurface environments are predictable, only recently have subsurface microbial populations in shallow subsurface zones been characterized. Aseptic sampling methods have been employed and microbiological and biochemical methods have been adapted to determine the types, abundance, and metabolic activities of microorganisms in subsurface material. Bacteria dominate, but eukaryotic microorganisms also are present. Vertical profile studies of a shallow aquifer in Oklahoma showed that active microbial biomass declined with depth to the unsaturated zone, but was variable in saturated sediments. Such a distribution of active biomass may be common in shallow aquifers. Studies on the lateral distribution of microorganisms in shallow and deep aquifers suggest that microorganisms are transported or migrate over fairly long distances in aquifer sediments. Surficial aquifers may be colonized by vertical or lateral transport and migration of surface microorganisms from recharge areas, but microorganisms could also have colonized when sediments were originally deposited. The biological and physical mechanisms controlling the migration of microorganisms in aquifers are not well understood. The function of shallow aquifers was considered with regard to nutritional ecology. Most pristine aquifers are oligotrophic. Heterotrophic life in these unique ecosystems is supported by secondary organic compounds that filter down from the soil above. The quantity and quality of organic nutrients depend on the age of water and rate of recharge of the aquifer.(ABSTRACT TRUNCATED AT 400 WORDS)}, }
@article {pmid3124742, year = {1987}, author = {Midtvedt, T and Carlstedt-Duke, B and Höverstad, T and Midtvedt, AC and Norin, KE and Saxerholt, H}, title = {Establishment of a biochemically active intestinal ecosystem in ex-germfree rats.}, journal = {Applied and environmental microbiology}, volume = {53}, number = {12}, pages = {2866-2871}, pmid = {3124742}, issn = {0099-2240}, mesh = {Animals ; Bacteria/*metabolism ; Bilirubin/metabolism ; Cholestanol/metabolism ; Cholesterol/metabolism ; Dipeptides/metabolism ; Fatty Acids, Volatile/biosynthesis ; Feces/analysis ; Female ; Germ-Free Life ; Intestines/*microbiology ; Male ; Mucins/metabolism ; Oxidation-Reduction ; Rats ; Trypsin/metabolism ; Urobilinogen/metabolism ; }, abstract = {A time course study for the establishment of some biochemical microbial intestinal functions was undertaken in ex-germfree rats conventionalized, i.e., colonized with conventional flora, in three different ways: untreated (group 1); contact with visitor rats (group 2); inoculated with intestinal contents from conventional rats (group 3). The first two groups of rats were inoculated with the intestinal contents from conventional rats after being out of the germfree isolators for 4 weeks. The biochemical parameters studied were degradation of mucin, inactivation of tryptic activity, conversion of cholesterol to coprostanol and of bilirubin to urobilinogen, degradation of beta-aspartylglycine, and formation of short-chain fatty acids. The results showed that the way in which the microbes were introduced and the microbial biochemical functions themselves were of importance. In several cases, social contacts, i.e., contact with visitor rats, were just as effective for the functionally adequate establishment of microbial intestinal functions as was inoculation with intestinal contents from conventional rats. Some of the biochemical parameters studied were established after a few days, whereas the establishment of others was markedly delayed. When inoculated after 4 weeks, all rats in the first two groups were colonized with conventional flora within 1 week. The results indicate that the model system described is suitable when studying buildup mechanisms in intestinal ecosystem(s).}, }
@article {pmid3116104, year = {1987}, author = {Tison, DL}, title = {Microbial ecology of Legionella.}, journal = {The Journal of infectious diseases}, volume = {156}, number = {5}, pages = {852}, doi = {10.1093/infdis/156.5.852}, pmid = {3116104}, issn = {0022-1899}, mesh = {Cyanobacteria/growth &amp; development ; Ecology ; Legionella/*growth &amp; development ; Temperature ; }, }
@article {pmid3626628, year = {1987}, author = {Wilkowske, CJ and Hermans, PE}, title = {General principles of antimicrobial therapy.}, journal = {Mayo Clinic proceedings}, volume = {62}, number = {9}, pages = {789-798}, doi = {10.1016/s0025-6196(12)62333-7}, pmid = {3626628}, issn = {0025-6196}, mesh = {Anti-Bacterial Agents/administration &amp; dosage/adverse effects/*therapeutic use ; Drug Hypersensitivity/etiology ; Humans ; }, abstract = {Use of antimicrobial agents must be tailored to the individual patient, site of infection, and etiologic organism. The choice of drug should be based on efficacy, safety, low toxicity, and acceptable cost. Empiric therapy should be broad enough to cover the pathogens that are suspected of causing the infection, based on the site of infection and the type of host. Definitive therapy may differ from initial therapy and should be started as soon as specific laboratory and clinical data are available. Cautious conservatism is advocated with regard to the use of new antimicrobial agents. The effects of the agents on the microbial ecology and hospital environment should be considered. Judicious use is necessary to prevent antimicrobial pollution.}, }
@article {pmid3310885, year = {1987}, author = {Valdes-Collazo, L and Schultz, AJ and Hazen, TC}, title = {Survival of Candida albicans in tropical marine and fresh waters.}, journal = {Applied and environmental microbiology}, volume = {53}, number = {8}, pages = {1762-1767}, pmid = {3310885}, issn = {0099-2240}, support = {RR-2657/RR/NCRR NIH HHS/United States ; RR-8102/RR/NCRR NIH HHS/United States ; }, mesh = {Candida albicans/*growth &amp; development ; Enterobacteriaceae/growth &amp; development ; Escherichia coli/growth &amp; development ; Fresh Water ; Puerto Rico ; Seawater ; Tropical Climate ; *Water Microbiology ; }, abstract = {A survey of Candida albicans indicated that the organism was present at all sites sampled in a rain forest stream and in near-shore coastal waters of Puerto Rico. In the rain forest watershed no relationship existed between densities of fecal coliforms and densities of C. albicans. At two pristine sites in the rain forest watershed both C. albicans and Escherichia coli survived in diffusion chambers for extended periods of time. In near-shore coastal waters C. albicans and E. coli survival times in diffusion chambers were enhanced by effluent from a rum distillery. The rum distillery effluent had a greater effect on E. coli than on C. albicans survival in the diffusion chambers. These studies show that neither E. coli nor C. albicans organisms are good indicators of recent fecal contamination in tropical waters. It further demonstrates that pristine freshwater environments and marine waters receiving organic loading in the tropics can support densities of C. albicans which may be a health hazard.}, }
@article {pmid3559287, year = {1987}, author = {Spriggs, DR}, title = {Legionella, microbial ecology, and inconspicuous consumption.}, journal = {The Journal of infectious diseases}, volume = {155}, number = {5}, pages = {1086-1087}, doi = {10.1093/infdis/155.5.1086}, pmid = {3559287}, issn = {0022-1899}, mesh = {Animals ; Ecology ; Eukaryota/microbiology/physiology ; Legionella/*physiology ; *Water Microbiology ; }, }
@article {pmid3549568, year = {1987}, author = {Voravuthikunchai, SP and Lee, A}, title = {Cecectomy causes long-term reduction of colonization resistance in the mouse gastrointestinal tract.}, journal = {Infection and immunity}, volume = {55}, number = {4}, pages = {995-999}, pmid = {3549568}, issn = {0019-9567}, mesh = {Animals ; Body Weight ; Cecum/*physiology ; Colon/metabolism/*microbiology ; Fatty Acids/metabolism ; Female ; Mice ; Salmonella Infections, Animal/immunology ; Salmonella enteritidis/growth &amp; development ; }, abstract = {Removal of the cecum from normal mice caused a major perturbation of the microbial ecology of the gastrointestinal tract. There was a permanent reduction in colonization resistance resulting in a 1,000-fold increase in the concentration of facultatively anaerobic coliform bacteria. The animals were significantly more susceptible to peroral challenge by the intestinal pathogen Salmonella enteritidis. Coincident with this increase in coliform counts and susceptibility to salmonellae was a decrease in the numbers of strictly anaerobic fusiform bacteria that dominate the rodent intestinal tract, resulting in reduced levels of acetic, propionic, and butyric acids. Cecectomized mice are likely to be a useful model for study of the interaction between intestinal pathogens and the normal microbiota and for studies of translocation of bacteria into host tissues after loss of colonization resistance.}, }
@article {pmid3543153, year = {1987}, author = {Neu, HC}, title = {New antibiotics: areas of appropriate use.}, journal = {The Journal of infectious diseases}, volume = {155}, number = {3}, pages = {403-417}, doi = {10.1093/infdis/155.3.403}, pmid = {3543153}, issn = {0022-1899}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Aztreonam/therapeutic use ; Bacterial Infections/*drug therapy ; Cephalosporins/therapeutic use ; Ciprofloxacin/therapeutic use ; Enoxacin ; Humans ; Imipenem ; Naphthyridines/therapeutic use ; Norfloxacin/therapeutic use ; Ofloxacin ; Oxazines/therapeutic use ; Thienamycins/therapeutic use ; beta-Lactamase Inhibitors ; }, abstract = {This has been an analysis of a number of agents whose clinical use has been approved in the past five years and of several agents that will undoubtedly be available within the next year. By the very nature of time alotted, the analysis had to be superficial. I believe that it is important to view all the agents because they cross each other in uses. I believe that areas of appropriate use exist for all of the compounds that I have discussed, and I also believe that cost and convenience will play increasingly important roles in the selection of what agent is most fitting, the definition of appropriate. In many infections it will not be possible to show a significant difference among drugs in a class, unless extremely large studies are undertaken. From my review of the literature in preparation for this meeting, I doubt these studies will be mounted. The infectious disease clinician must be familiar with all of the agents so that he or she can make judgments about which agent(s) make(s) the most sense for his/her hospital. I believe that it is fitting and proper for the infectious disease physician to appropriate the correct selection, methods of administration, and dose of antibiotic in many clinical situations, particularly ones in which parenteral agents are used. I hope the IDSA will have an impact on the proper use of the quinolones, monobactams, penems, and carbapenems. Our goal in the use of antimicrobial agents should be the selection of agents for prophylaxis, empiric therapy, and therapy for defined infections in a manner that results in cure, with reasonable cost and minimal damage to the microbial ecology.}, }
@article {pmid3153173, year = {1987}, author = {Jain, RK and Sayler, GS}, title = {Problems and potential for in situ treatment of environmental pollutants by engineered microorganisms.}, journal = {Microbiological sciences}, volume = {4}, number = {2}, pages = {59-63}, pmid = {3153173}, issn = {0265-1351}, mesh = {Bacteria/genetics/metabolism ; *Biodegradation, Environmental ; *Environmental Pollutants ; Genetic Engineering ; }, abstract = {Molecular microbial ecology could provide tools for studying the structure and function of biodegradative microbial communities useful for in situ removal of environmental pollutants. Detection and monitoring of released organisms in the environment is required and DNA:DNA colony hybridization seems to be one of the highly sensitive and accurate technologies available for achieving this goal. A realistic and pragmatic view is required for analysis of the risks of environmental release of genetically-modified or engineered organisms.}, }
@article {pmid3106299, year = {1987}, author = {Marshall, J and Leeming, JP and Holland, KT}, title = {The cutaneous microbiology of normal human feet.}, journal = {The Journal of applied bacteriology}, volume = {62}, number = {2}, pages = {139-146}, doi = {10.1111/j.1365-2672.1987.tb02391.x}, pmid = {3106299}, issn = {0021-8847}, mesh = {Actinomycetales/growth &amp; development/isolation &amp; purification ; Adult ; Bacteria/growth &amp; development/*isolation &amp; purification ; Female ; Foot/*microbiology ; Fungi/growth &amp; development/*isolation &amp; purification ; Gram-Negative Bacteria/growth &amp; development/isolation &amp; purification ; Humans ; Hydrogen-Ion Concentration ; Male ; Micrococcaceae/growth &amp; development/isolation &amp; purification ; Middle Aged ; Skin/*microbiology ; Staphylococcus/growth &amp; development/isolation &amp; purification ; }, abstract = {A survey has been made of the bacterial and fungal populations carried at three different sites on the feet of 60 individuals. The bacteria found at the three sites were quantitatively similar and Micrococcaceae and aerobic coryneform bacteria predominated. The carriage of other bacterial groups was generally low. There was a quantitative variation between sites--mean total counts were 1.04 X 10(7) cfu/cm2 skin in the fourth toe cleft, 4.08 X 10(5) cfu/cm2 skin on the sole and 1.21 X 10(3) cfu/cm2 skin on the dorsal surface. Staphylococci were most often dominant on the sole and dorsal surface whereas aerobic coryneforms predominated in the majority of fourth toe clefts. The higher the total count at a given site the more likely it was that aerobic coryneform bacteria predominated. The skin surface pH was significantly higher on the sole (mean value 6.25) than on the dorsal surface (mean value 5.23). Factors controlling the microbial ecology of the foot are discussed.}, }
@article {pmid3828684, year = {1987}, author = {Nickel, JC and Olson, M and McLean, RJ and Grant, SK and Costerton, JW}, title = {An ecological study of infected urinary stone genesis in an animal model.}, journal = {British journal of urology}, volume = {59}, number = {1}, pages = {21-30}, doi = {10.1111/j.1464-410x.1987.tb04573.x}, pmid = {3828684}, issn = {0007-1331}, mesh = {Animals ; Disease Models, Animal ; Ecology ; Male ; Microscopy, Electron ; Rats ; Rats, Inbred Strains ; Urinary Calculi/etiology/*microbiology/pathology ; Urinary Tract Infections/complications/*microbiology/pathology ; }, abstract = {Direct molecular and morphological techniques of modern microbiology were used to monitor the sequential development of bacterial microcolonies and biofilms in a rat model of urinary infection and to demonstrate that the urease activity of the infecting organisms sets in course a series of reactions in which struvite and apatite crystals develop within the matrix of the enlarging bacterial aggregate. This forms multiple stone nidi on the uroepithelial surface upon which succeeding bacterial biofilms develop and with the incorporation of other urine components, such as urinary mucroproteins, establishes a matrix skeleton that becomes mineralised, thus allowing for the growth of the stone in concentric layers. To arrive at this hypothesis, we studied infection stone genesis using a newly developed model for infection-induced bladder stone formation in the rat. We examined in detail the sequential events in the evolving microbial ecology of progressive struvite calculogenesis, using conventional microbiological techniques, direct ultrastructural observation, newly developed ultrastructural cytochemical localisation techniques and immunological procedures for stabilisation of the biofilm glycocalix and stone matrix in the rat model. It was concluded that the organic glycocalix material secreted by the associated bacteria comprises a substantial and aetiologically important part of the infection stone calculogenesis and matrix production.}, }
@article {pmid3481316, year = {1987}, author = {Midtvedt, T}, title = {Influence of ofloxacin on the faecal flora.}, journal = {Drugs}, volume = {34 Suppl 1}, number = {}, pages = {154-158}, pmid = {3481316}, issn = {0012-6667}, mesh = {Adult ; Anti-Infective Agents/adverse effects/*pharmacology ; Feces/*microbiology ; Humans ; Ofloxacin ; Oxazines/adverse effects/*pharmacology ; }, abstract = {In a continuing, Norwegian-Swedish collaborative study, the effects of several antimicrobials upon intestinal biochemical microflora-associated characteristics are being investigated. In the present study, 7 healthy volunteers were given ofloxacin 200mg bid for 6 days. Faecal sampling was performed twice before, on days 3 and 6 during treatment, and weekly to monthly afterwards. Blood sampling was performed on day 6 during treatment. The concentrations of ofloxacin were measured in faeces and serum on day 6. Additionally, the following microflora-associated characteristics were studied in all the faecal samples: presence of short chain fatty acids, absence of beta-aspartylglycine, production of coprostanol, formation of urobilinogen, inactivation of tryptic activity and breakdown of mucin. The mean concentrations of ofloxacin in faeces and serum were 44.0 mg/kg and 2.1 mg/L, respectively. In contrast to most of the other antimicrobials so far tested, ofloxacin exerted almost no influence upon the microflora-associated characteristics investigated.}, }
@article {pmid3324856, year = {1987}, author = {Kennedy, MJ}, title = {Role of motility, chemotaxis, and adhesion in microbial ecology.}, journal = {Annals of the New York Academy of Sciences}, volume = {506}, number = {}, pages = {260-273}, doi = {10.1111/j.1749-6632.1987.tb23825.x}, pmid = {3324856}, issn = {0077-8923}, mesh = {Animals ; *Bacterial Physiological Phenomena ; Candida albicans/physiology ; Cell Adhesion ; Cell Movement ; *Chemotaxis ; Ecology ; Humans ; Intestinal Mucosa/microbiology ; Nitrogen/metabolism ; Yeasts/*physiology ; }, abstract = {This review emphasized the implications of recent data pertaining to the role that motility, chemotaxis, and adhesion play in microbial ecology. Some of these processes appear to promote colonization by allowing certain organisms to selectively "seek out" nutrients or sites of colonization. For example, chemotaxis to NO3- and NO2- may provide pseudomonads with such a strong competitive mechanism that it allows this group of bacteria to outcompete other members of the soil microbiota for these chemicals. Likewise, chemotaxis also allows other bacteria to enter and colonize the mucus gel lining the intestinal epithelium and thereby resist physical removal from the gut. On the other hand, the understanding of such mechanisms offers important new possibilities for the deliberate control of microorganisms for the benefit of man. To that end, much remains to be done before a thorough understanding of the ecology of the microflora of any ecosystem can be accomplished. It is hoped that this review will stimulate further work in this area, as well as to lead to collaboration between engineers and microbiologists, which should lead to fruitful and exciting research in the future.}, }
@article {pmid3324304, year = {1987}, author = {Midtvedt, T}, title = {Intestinal bacteria and rheumatic disease.}, journal = {Scandinavian journal of rheumatology. Supplement}, volume = {64}, number = {}, pages = {49-54}, doi = {10.3109/03009748709096721}, pmid = {3324304}, issn = {0301-3847}, mesh = {Animals ; Arthritis, Experimental/etiology ; Arthritis, Rheumatoid/*etiology ; *Bacterial Infections ; Germ-Free Life ; Humans ; Intestines/*microbiology ; Phagocytosis ; Rats ; Synovial Membrane/physiology ; }, abstract = {The striking clinical and pathological similarities between certain naturally occurring infectious diseases in animal species and those of some human rheumatic diseases, such as rheumatoid arthritis (RA), have stimulated the search for a microbial etiology of the latter syndrome. A long series of microbial species, including aerobic and anaerobic intestinal bacteria, mycoplasma and several viruses have been put into focus. Most often, however, an initially positive report has been followed by several reports denying an etiological role of the microbial species in focus. However, the concept of a microbial trigger in the etiology and symptomatology of RA is still a subject of intense debate. Recent results have indicated a reversed effect of gram-positive vs. gram-negative intestinal bacteria on adjuvant-induced arthritis in germfree rats and microbial peptidoglycans have been shown to play a major role in this experimental model. It has been shown that the intestinal flora may include bacteria containing antigenic determinant(s) cross-reacting with some markers within the HLA-system. The intestinal flora may also influence upon several digestive and absorptive functions and thereby acting upon parameters of importance in the development of rheumatic disease.}, }
@article {pmid3318681, year = {1987}, author = {Cruden, DL and Markovetz, AJ}, title = {Microbial ecology of the cockroach gut.}, journal = {Annual review of microbiology}, volume = {41}, number = {}, pages = {617-643}, doi = {10.1146/annurev.mi.41.100187.003153}, pmid = {3318681}, issn = {0066-4227}, support = {AI-13990/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*metabolism ; Cockroaches/*microbiology ; Ecology ; Periplaneta/*microbiology ; }, }
@article {pmid3533778, year = {1986}, author = {Wilson, KH and Freter, R}, title = {Interaction of Clostridium difficile and Escherichia coli with microfloras in continuous-flow cultures and gnotobiotic mice.}, journal = {Infection and immunity}, volume = {54}, number = {2}, pages = {354-358}, pmid = {3533778}, issn = {0019-9567}, support = {R01-AM33967/AM/NIADDK NIH HHS/United States ; }, mesh = {Animals ; Cecum/*microbiology ; Clostridium/*growth &amp; development/physiology ; Cricetinae ; Escherichia coli/*growth &amp; development/physiology ; *Germ-Free Life ; Mesocricetus ; Mice ; Mice, Inbred BALB C ; }, abstract = {We studied the interactions between the entire cecal flora of hamsters and the pathogens Clostridium difficile and Escherichia coli in gnotobiotic mice and in a continuous-flow (CF) culture system in which the growth medium consisted of an extract of fecal pellets from germfree mice. CF cultures and germfree mice were colonized first with C. difficile and E. coli and then with the cecal flora of hamsters. Both in vivo and in vitro hamster flora markedly suppressed the potential pathogens. Contents of CF cultures inoculated with hamster flora were introduced into gnotobiotic mice previously colonized with C. difficile and E. coli. These mice were compared with mice given homogenates of hamster ceca. In both groups, the C. difficile population decreased by a factor of more than 10(6) and the E. coli population decreased by a factor of 10(4) to 10(5). CF culture contents also reduced the size of the dilated germfree mouse cecum to normal. When veal infusion broth was used as a medium, contents of CF cultures colonized with hamster flora failed to eliminate C. difficile from mice. Thus, the extract of fecal pellets appeared to contain a substance important for sustained colonization by important components of the cecal flora. We also studied the ability of collections of isolates to suppress the potential pathogens in both gnotobiotic mice and CF cultures. A total of 150 isolates obtained from predominant hamster flora at the ecologic climax stage (C flora) suppressed C. difficile and E. coli to 10 and 1 to 3%, respectively, of the population sizes attained in monoassociated mice. A total of 67 isolates obtained during ecologic succession combined with a C flora consisting of 100 isolates suppressed the potential pathogens to 0.3 and 0.03% of their original levels, respectively. Similar degrees of suppression occurred in CF cultures, further indicating that anaerobic CF cultures are promising models for investigation of the microbial ecology of C. difficile.}, }
@article {pmid3096204, year = {1986}, author = {Wang, MY and Ogrydziak, DM}, title = {Residual effect of storage in an elevated carbon dioxide atmosphere on the microbial flora of rock cod (Sebastes spp.).}, journal = {Applied and environmental microbiology}, volume = {52}, number = {4}, pages = {727-732}, pmid = {3096204}, issn = {0099-2240}, mesh = {Acinetobacter/growth &amp; development ; Animals ; Bacteria/*growth &amp; development ; Carbon Dioxide/analysis/*pharmacology ; Fishes/*microbiology ; *Food Microbiology ; *Food Preservation ; Gram-Negative Aerobic Bacteria/growth &amp; development ; Hydrogen-Ion Concentration ; Lactobacillus/growth &amp; development ; Micrococcus/growth &amp; development ; Pseudomonas/growth &amp; development ; }, abstract = {A residual inhibitory effect on microbial growth due to modified-atmosphere (MA) storage (MA, 80% CO2-20% air) was demonstrated for rock cod fillets stored in MA and transferred to air at 4 degrees C. Results of measurements of CO2 concentrations of the fillets suggested that the residual effect after transfer from MA to air was not due to retention of CO2 at the surface of the fillets but was probably due to the microbial ecology of the system. Lactobacillus spp. and tan Alteromonas spp. (TAN) predominated after 7 and 14 days of storage in MA. During storage in MA, Pseudomonas spp. were inhibited or killed. Following transfer from MA to air, the percentage of the total flora represented by Lactobacillus spp. and TAN bacteria decreased, and 6 days after transfer Pseudomonas spp. were again dominant.}, }
@article {pmid3763418, year = {1986}, author = {Bennet, R and Eriksson, M and Nord, CE and Zetterström, R}, title = {Fecal bacterial microflora of newborn infants during intensive care management and treatment with five antibiotic regimens.}, journal = {Pediatric infectious disease}, volume = {5}, number = {5}, pages = {533-539}, doi = {10.1097/00006454-198609000-00009}, pmid = {3763418}, issn = {0277-9730}, mesh = {Anti-Bacterial Agents/*therapeutic use ; Bacteria, Aerobic/drug effects/*isolation &amp; purification ; Bacteria, Anaerobic/drug effects/*isolation &amp; purification ; Cephalosporins/therapeutic use ; Cesarean Section ; Clostridium/drug effects/isolation &amp; purification ; Drug Therapy, Combination ; Enterobacteriaceae/drug effects/isolation &amp; purification ; Feces/*microbiology ; Female ; Gentamicins/pharmacology ; Gram-Negative Aerobic Bacteria/drug effects/isolation &amp; purification ; Humans ; Infant, Newborn/*microbiology ; Infant, Premature/*microbiology ; Intensive Care Units, Neonatal ; Penicillins/therapeutic use ; Pregnancy ; }, abstract = {Aerobic and anaerobic fecal bacterial flora of normal newborn infants, of preterm newborn infants without other health problems and of five groups of newborn infants treated with combinations of benzylpenicillin, cloxacillin, flucloxacillin, ampicillin, cefuroxime, cefoxitin and gentamicin were compared. Preterm birth alone was associated with growth of Klebsiella which could be attributed to a higher rate of cesarean section in preterm than in term infants. All antibiotic regimens led to a pronounced suppression of anaerobic flora and overgrowth of Klebsiella but not with other gram-negative aerobic bacteria. A slight colonization with Clostridium difficile and Clostridium perfringens occurred. Disturbances of the intestinal microbial ecology can be expected in newborn infants after preterm birth by cesarean section and/or treatment with antibiotics, including some penicillins that are usually regarded as relatively harmless in this respect in adults.}, }
@article {pmid3577111, year = {1986}, author = {Zhao, YW and Cai, MY and Qian, B and Wang, DS}, title = {[A preliminary study on the microbial ecology of the river in the city].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {26}, number = {3}, pages = {200-205}, pmid = {3577111}, issn = {0001-6209}, mesh = {Aspergillus/isolation &amp; purification ; Bacillus/isolation &amp; purification ; China ; Enterobacteriaceae/isolation &amp; purification ; Fresh Water/*analysis ; Geotrichum/isolation &amp; purification ; Penicillium/isolation &amp; purification ; Pseudomonas/isolation &amp; purification ; Seasons ; Water/*analysis ; *Water Microbiology ; Water Pollution/*analysis ; }, }
@article {pmid3016049, year = {1986}, author = {Babu, JP and Dabbous, MK}, title = {Interaction of salivary fibronectin with oral streptococci.}, journal = {Journal of dental research}, volume = {65}, number = {8}, pages = {1094-1100}, doi = {10.1177/00220345860650081001}, pmid = {3016049}, issn = {0022-0345}, support = {DE-07313/DE/NIDCR NIH HHS/United States ; }, mesh = {Adhesiveness ; Animals ; Carrier Proteins/metabolism ; Cell Membrane/metabolism ; Durapatite ; Electrophoresis, Polyacrylamide Gel ; Enzyme-Linked Immunosorbent Assay ; Fibronectins/analysis/metabolism/*physiology ; Humans ; Hydroxyapatites ; Protein Binding ; Rats ; Salivary Proteins and Peptides/analysis/metabolism/*physiology ; Sodium Dodecyl Sulfate ; Streptococcus/*physiology/ultrastructure ; Surface Properties ; }, abstract = {Immunoreactive Fibronectin (Fn) has been demonstrated in stimulated human parotid saliva by western blot analysis and also found to be a component of the artificial tooth pellicles derived from hydroxyapatite (HA) beads coated with parotid saliva. Saliva depleted of gelatin-binding components showed a significantly lower degree of reactivity with anti-Fn antibodies than did the control saliva when tested by and enzyme-linked immunosorbent assay (ELISA). Depletion of gelatin-binding components from saliva was also found to affect the degree of saliva-mediated aggregation of four of the seven oral streptococci tested [Streptococcus mutans strains GS-5 and OMZ 176, S. sobrinus, and S. rattus]. Similarly, the adherence of the same four micro-organisms to the artificial tooth pellicles (derived form saliva which had previously been depleted of gelatin-binding component) was significantly inhibited (37-53%) when compared with the control saliva-coated HA beads. Pre-treatment of streptococci with 100 micrograms of soluble Fn also caused a 34-57% inhibition of adherence of the same oral streptococci to saliva-treated HA beads. Quantitation of Fn in human parotid saliva showed that the amounts of immunoreactive Fn varied form 2 to 6 micrograms/mL of parotid saliva. Furthermore, the Fn from parotid saliva was found to be adsorbed onto the bacterial surfaces, as demonstrated by immunofluorescence and ELISA. The presence of Fn in parotid saliva and its ability to bind to HA beads (artificial pellicles), in conjunction with the ability of soluble Fn to inhibit the adherence of streptococcal strains to the artificial tooth pellicles, suggest that the microbial ecology of the oral cavity may, in part, be influenced by the interactions mediated by salivary fibronectin.}, }
@article {pmid3739462, year = {1986}, author = {Hamada, S and Imanishi, H and Ooshima, T}, title = {Isolation and mode of action of a cell-free bacteriocin (mutacin) from serotype g Streptococcus mutans MT3791.}, journal = {Zentralblatt fur Bakteriologie, Mikrobiologie, und Hygiene. Series A, Medical microbiology, infectious diseases, virology, parasitology}, volume = {261}, number = {3}, pages = {287-298}, doi = {10.1016/s0176-6724(86)80046-3}, pmid = {3739462}, issn = {0176-6724}, mesh = {Bacteriocins/analysis/*isolation &amp; purification/pharmacology ; Child ; Chromatography, Gel ; Humans ; Streptococcus mutans/growth &amp; development/*metabolism ; Temperature ; }, abstract = {A bacteriocin, mutacin MT3791, was isolated from the culture supernatant of a dialysate medium of Tryptose phosphate broth cultures of Streptococcus mutans MT3791 (serotype g), a clinical isolate from a carious lesion of a Japanese child. The mutacin was found to inhibit the growth of most indicator strains of S. mutans and S. salivarius by the drop assay method. The mutacin was purified 1,450 fold from culture supernatant of S. mutans MT3791 by 60% saturated ammonium sulfate precipitation, followed by ultracentrifugation at 300,000 X g for 18 h. Gel filtration studies using Sepharose 4B indicated that the mutacin was highly aggregated, but could be dissociated by addition of 1% (final concentration) Tween 80 or 6M urea. The mutacin was heat stable, but the activity was destroyed after autoclaving at 120 degrees C for 60 min. It was susceptible to the enzymatic action of papain and pronase, but not trypsin, lipase or nucleases. The mutacin was adsorbed to whole cells of most strains of S. mutans. Mutacin MT3791 was bactericidal for an indicator strain, S. mutans MT703R (serotype e). The mutacin inhibited the incorporation of isotope-labelled precursors of protein, DNA, and RNA. Furthermore, mutacin MT3791 selectively and markedly suppressed the growth of S. mutans present in the dental plaque obtained from active carious lesions in the teeth of children. Possible role of mutacin in vivo was discussed with special reference to oral microbial ecology.}, }
@article {pmid3512730, year = {1986}, author = {Wilson, KH and Sheagren, JN and Freter, R and Weatherbee, L and Lyerly, D}, title = {Gnotobiotic models for study of the microbial ecology of Clostridium difficile and Escherichia coli.}, journal = {The Journal of infectious diseases}, volume = {153}, number = {3}, pages = {547-551}, doi = {10.1093/infdis/153.3.547}, pmid = {3512730}, issn = {0022-1899}, support = {R01-AM 33967/AM/NIADDK NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/adverse effects ; Cecum/microbiology ; Cefoxitin/adverse effects ; *Clostridium ; Colitis/chemically induced/microbiology ; Cricetinae ; Enzyme-Linked Immunosorbent Assay ; *Escherichia coli ; *Germ-Free Life ; Male ; Mesocricetus/microbiology ; Mice ; }, abstract = {Hamster flora introduced into germfree mice reduced the cecum to conventional size, suppressed populations of Escherichia coli and Clostridium difficile to the same degree that mouse flora did, and corrected the hypocellularity that is characteristic of the small bowel of germfree mice. A highly toxigenic strain of C. difficile readily induced cecitis in germfree and antibiotic-treated conventional mice, and histological examination frequently revealed pseudomembranes. Toxins A and B were both detected in ceca of animals with colitis. Gnotobiotic mice provide a model in which to study the role of the indigenous microflora in protecting against antibiotic-associated colitis.}, }
@article {pmid3944854, year = {1986}, author = {Månsson, W and Colleen, S and Mårdh, PA}, title = {The microbial flora of the continent cecal urinary reservoir, its stoma and the peristomal skin.}, journal = {The Journal of urology}, volume = {135}, number = {2}, pages = {247-250}, doi = {10.1016/s0022-5347(17)45599-6}, pmid = {3944854}, issn = {0022-5347}, mesh = {Adult ; Antibiosis ; Bacteria/isolation &amp; purification ; Bacteriuria/microbiology ; Cecum/*microbiology/surgery ; Female ; Humans ; Male ; Middle Aged ; Postoperative Period ; Skin/*microbiology ; Time Factors ; *Urinary Diversion ; }, abstract = {The bacteria occurring in reservoir urine, on the cutaneous stoma and on the abdominal skin were studied in 9 patients who had undergone urinary diversion via a continent cecal reservoir. Aerobic and/or facultatively anaerobic bacteria were isolated persistently from reservoir urine in 3 patients but only occasionally in the remainder. These organisms were isolated in pure culture. Anaerobic bacteria also were found, although infrequently and only in conjunction with facultative anaerobes. Most stomal cultures showed heavy growth of Staphylococcus epidermidis, while fewer microbes were isolated in the abdominal skin cultures. Propionibacterium acnes, present in most skin cultures, was absent or scantily represented on the stoma. Microbial antibiosis was demonstrated in vitro between stomal and urinary reservoir bacteria in 6 patients. However, bacteria from stomal isolates had no antagonistic effect against bacteria belonging to the family of Enterobacteriacae or against anaerobic species isolated from urine. Antibiosis may influence the microbial ecology of the urine reservoir and cutaneous stoma.}, }
@article {pmid3547617, year = {1986}, author = {Bauernfeind, A and Hörl, G and Mönch, V}, title = {Changes in microbial ecology by therapeutic use of aminoglycosides.}, journal = {Scandinavian journal of infectious diseases. Supplementum}, volume = {49}, number = {}, pages = {106-114}, pmid = {3547617}, issn = {0300-8878}, mesh = {Aminoglycosides/pharmacology/therapeutic use ; Animals ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; Bacteria/*drug effects/enzymology ; Bacterial Infections/*drug therapy ; Drug Resistance, Microbial ; Humans ; }, abstract = {Alterations in microbial ecology caused by the usage of aminoglycosides for therapy of human infections are due to their selective pressure favouring insensitive or resistant species or strains. There is a positive correlation between aminoglycoside consumption and the incidence of resistance to aminoglycosides. This correlation is, however, modified by measures of infection control. At the present time, the overall incidence of resistance to aminoglycosides does not show major changes. The ecological impacts of aminoglycoside consumption appear to be less significant as compared to other antibiotics due to factors specific for the aminoglycoside group.}, }
@article {pmid2430518, year = {1986}, author = {Olsen, GJ and Lane, DJ and Giovannoni, SJ and Pace, NR and Stahl, DA}, title = {Microbial ecology and evolution: a ribosomal RNA approach.}, journal = {Annual review of microbiology}, volume = {40}, number = {}, pages = {337-365}, doi = {10.1146/annurev.mi.40.100186.002005}, pmid = {2430518}, issn = {0066-4227}, support = {GM34527/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*classification/genetics ; Base Sequence ; Chromosome Mapping ; DNA, Recombinant ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Bacterial/*analysis ; RNA, Ribosomal/*analysis ; }, }
@article {pmid4096503, year = {1985}, author = {Bergogne-Berezin, E}, title = {[Microbial ecology of the colon].}, journal = {Annales de gastroenterologie et d'hepatologie}, volume = {21}, number = {6}, pages = {383-388}, pmid = {4096503}, issn = {0066-2070}, mesh = {Colon/*microbiology ; Humans ; }, abstract = {It has been known for a long time that the human gastrointestinal tract contains 10(14) micro-organisms, which are predominantly anaerobic. Recent research has provided a better understanding of the functions and the equilibrium of the intestinal ecosystem in which the intestinal mucosa and the microbial flora which it supports interact. Any modification in one or other of the constituents of this ecosystem is likely to disturb the normal ecological equilibrium, resulting in a variety of gastro-intestinal diseases. Today, the intestinal ecosystem can be considered to be a system of defence and equilibrium or, conversely, as a reservoir of infection, which is confirmed by the study of certain faecal bacterial profiles with a high risk of infection. In gastrointestinal surgery and paediatrics, the correlation between antibiotic therapy, intestinal microbial proliferation and the development of septicaemia confers a fundamental role of the defence barriers of the gastrointestinal tract in the control or potentially pathogenic endogenous micro-organisms.}, }
@article {pmid3903626, year = {1985}, author = {Cattoen, C and Colombel, JF and Leclerc, H}, title = {[Value of spiral automatic plating in quantitative bacteriology].}, journal = {Pathologie-biologie}, volume = {33}, number = {8}, pages = {858-860}, pmid = {3903626}, issn = {0369-8114}, mesh = {*Bacteriological Techniques ; }, abstract = {The Spiral plate count method, semi-automated plating technique, presents some advantages: saving of time and materials, fast and easy counting. This method appears well adapted for studies of microbial ecology.}, }
@article {pmid3917196, year = {1985}, author = {Guerrero, R and Pedrós-Alió, C and Schmidt, TM and Mas, J}, title = {A survey of buoyant density of microorganisms in pure cultures and natural samples.}, journal = {Microbiologia (Madrid, Spain)}, volume = {1}, number = {1-2}, pages = {53-65}, pmid = {3917196}, issn = {0213-4101}, mesh = {*Bacteria/ultrastructure ; *Centrifugation, Density Gradient ; Culture Media ; Water Microbiology ; }, abstract = {Values of buoyant density of microorganisms reported in literature are widely divergent because of techniques used. Many of these involve centrifugation in density gradients formed by substances with high osmolarity which dehydrate the cells. In order to better understand the ranges of variation of density of microbial cells several approaches were taken. Firstly, samples from several natural aquatic habitats were taken and the densities of the microorganisms present determined. Secondly, experiments were performed with selected microorganisms to maximize density changes by forcing them to accumulate intracytoplasmic inclusions of dense materials or to loose their capsules. Finally, the relevant literature was reviewed. It could be demonstrated that most microorganisms have a density around 1.080 pg microns-3 when measured in low osmolarity media such as Percoll. However, many species are able to modify their density by as much as 7% (for instance, from 1.097 to 1.022 pg microns-3 in Thiocapsa roseopersicina, and similar variations in other bacteria), by incorporating substances into inclusions (sulfur, carbon, phosphorous storage materials, etc.), or by making capsules and/or gas vesicles. The relevance of buoyant density determinations for several aspects of microbial ecology and physiology is discussed.}, }
@article {pmid4026292, year = {1985}, author = {Banwell, JG and Howard, R and Cooper, D and Costerton, JW}, title = {Intestinal microbial flora after feeding phytohemagglutinin lectins (Phaseolus vulgaris) to rats.}, journal = {Applied and environmental microbiology}, volume = {50}, number = {1}, pages = {68-80}, pmid = {4026292}, issn = {0099-2240}, support = {AM 31093/AM/NIADDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*growth &amp; development ; Cecum/ultrastructure ; Diet ; Disaccharides/analysis ; Eukaryota/*growth &amp; development ; Feces/drug effects/metabolism/microbiology ; Giardia/cytology ; Gram-Negative Bacteria/growth &amp; development/ultrastructure ; Gram-Positive Bacteria/growth &amp; development/ultrastructure ; Ileum/microbiology/ultrastructure ; Intestinal Mucosa/microbiology/ultrastructure ; Intestine, Small/*microbiology ; Jejunum/microbiology/ultrastructure ; Male ; Microscopy, Electron ; Microvilli/ultrastructure ; Phytohemagglutinins/*pharmacology ; Rats ; Rats, Inbred Strains ; Vitamin B 12/analysis ; }, abstract = {Incorporation of purified phytohemagglutinin (PHA) lectins derived from red kidney beans (Phaseolus vulgaris) in the diet of weanling rats will cause growth failure, malabsorption of nutrients, and bacterial overgrowth in the small intestine. These effects are not caused by feeding a similar quantity of PHA to germfree rats. To define the morphological and bacterial changes on the mucosal surfaces of the jejunum, ileum, and cecum in greater detail, we pair fed two groups of weanling rats isocaloric, isonitrogenous diets with or without 0.5% PHA protein. On the jejunal surfaces of control rats, the mucous layer was a confluent covering with sparsely scattered bacteria and protozoa. In PHA-treated rats, the mucous layer was thin and discontinuous, and the microvillous surface of the tissue was extensively populated by bacterial cells of two distinct morphotypes--a gram-negative rod and a gram-positive coccobacillus. In all PHA-treated animals, these bacteria formed adherent monospecific or mixed adherent microcolonies on the tissue surface. Tissue damage was observed in PHA-exposed jejunal tissue as evidenced by vesiculation of the microvillous plasma membrane and by damage to the brush border membrane. On the ileal surfaces of control rats, there was a thick mucous layer within which small numbers of bacteria and protozoa were seen. Segmented filamentous bacteria were anchored in the tissue surface. In PHA-treated rats, the ileal surface was only incompletely covered by a mucous layer, and the overlying mucosal surface was extensively covered by large numbers of protozoan cells (predominantly Hexamita muris). Most of the ileal surfaces not covered by the mucous layer were occupied and virtually occluded by an overgrowth of these protozoan cells with occasional cells of Giardia muris and the tissue-associated segmented bacillus. In the ceca of control rats, the mucosa was incompletely covered by a discontinuous mucous layer and colonized by an unnamed Spirillum sp., other bacteria, and occasional protozoa. The cecal surfaces of PHA-treated rats retained most of their incomplete overlying mucous layer, which was heavily colonized by the same type of Spirillum sp. seen in untreated animals; intestinal crypts were colonized. These descriptive morphological studies demonstrate that exposure to purified PHA in the diet caused characteristic changes in the microbial ecology of the small intestine. The changes in microbial flora contributed to the malabsorption of nutrients in the small intestines of PHA-fed animals.}, }
@article {pmid4008044, year = {1985}, author = {Tylenda, CA and Calvert, C and Kolenbrander, PE and Tylenda, A}, title = {Isolation of Actinomyces bacteriophage from human dental plaque.}, journal = {Infection and immunity}, volume = {49}, number = {1}, pages = {1-6}, pmid = {4008044}, issn = {0019-9567}, mesh = {Actinomyces/*genetics/pathogenicity ; Adhesiveness ; Bacteriophages/*isolation &amp; purification/ultrastructure ; Dental Plaque/*microbiology ; Humans ; Microscopy, Electron ; Sewage ; Species Specificity ; Virus Replication ; }, abstract = {Human dental plaque samples were screened for the presence of bacteriophage for Actinomyces viscosus and Streptococcus sanguis. None of the 336 samples yielded phage for S. sanguis, but 10 contained virulent actinomyces phage. A high host cell specificity was observed in that one phage isolate infected only A. viscosus T14V, eight phage isolates infected only A. viscosus MG-1, and one infected both strains. None was capable of productively infecting various other actinomyces strains that represented the six actinomyces coaggregation groups. Because phage-containing samples occurred randomly in this survey, no correlation between the individual collecting the samples, dental clinic, or type of patient and the presence of phage in the sample was noted. Examination of one of the samples that yielded phage for the presence of a natural host strain for that particular phage resulted in the isolation of two strains which were identified as A. viscosus serotype II and Actinomyces naeslundii serotype I. This is the first report of an A. naeslundii host strain and actinomyces bacteriophage of human dental plaque origin. The finding of both phage and host strains in the same dental plaque sample along with the observation of high host cell specificity by these phage provide indicators that support an active role for actinomyces bacteriophage in oral microbial ecology. The use of these freshly isolated phage as probes to study actinomyces coaggregation properties is discussed.}, }
@article {pmid3988345, year = {1985}, author = {Isogai, E and Isogai, H and Sawada, H and Kaneko, H and Ito, N}, title = {Microbial ecology of plaque in rats with naturally occurring gingivitis.}, journal = {Infection and immunity}, volume = {48}, number = {2}, pages = {520-527}, pmid = {3988345}, issn = {0019-9567}, mesh = {Animals ; Bacteroidaceae/*isolation &amp; purification ; Dental Plaque/*microbiology ; Disease Susceptibility ; Enterobacteriaceae/isolation &amp; purification ; Gingivitis/etiology/*microbiology/pathology ; Lactobacillus/isolation &amp; purification ; Neisseria/isolation &amp; purification ; Rats ; Rats, Inbred Strains ; Streptococcus/*isolation &amp; purification ; Time Factors ; Veillonella/isolation &amp; purification ; }, abstract = {The microbial ecology of adherent plaque was investigated in relation to the pathological findings of gingivitis in plaque-susceptible rats. Plaque developed in the gingiva of the lower incisor in plaque-susceptible rats, but not in plaque-resistant rats, after they were fed a commercial powder diet. With increase in plaque volume, the total counts of bacteria increased 10(9) to 10(11)/g. In the first 3 months, Bacteroides species increased and became the predominant population. Streptococcus species also increased at the same time. After 9 months, Fusobacterium species and oral Treponema species were recognized in increasing numbers. The anaerobic bacteria increased in proportion with the progression of plaque development. Bacteroides intermedius, Fusobacterium nucleatum, Streptococcus salivarius, and other species were isolated. Acute gingivitis was observed within 3 months, and subacute-chronic gingivitis was observed between 2 and 12 months. These findings suggest that proportional changes in the gingival plaque flora may uniquely contribute to the development of gingival inflammation in this experimental model.}, }
@article {pmid3981713, year = {1985}, author = {Nickel, JC and Emtage, J and Costerton, JW}, title = {Ultrastructural microbial ecology of infection-induced urinary stones.}, journal = {The Journal of urology}, volume = {133}, number = {4}, pages = {622-627}, doi = {10.1016/s0022-5347(17)49116-6}, pmid = {3981713}, issn = {0022-5347}, mesh = {Bacterial Infections/complications/*pathology ; Crystallization ; Glycoproteins/analysis ; Humans ; Magnesium ; *Magnesium Compounds ; Microscopy, Electron ; Microscopy, Electron, Scanning ; Phosphates ; Polysaccharides/analysis ; Struvite ; Urinary Calculi/etiology/*microbiology/pathology ; Urinary Tract Infections/complications/*pathology ; }, abstract = {With advanced techniques of scanning and transmission electron microscopy we studied the ultrastructural ecology of bacteria associated with struvite calculi on catheter surfaces, and in the bladder, ureter and renal pelvis. These detailed morphological data indicate that the interstices, core and external surface of such struvite aggregates contain large numbers of bacterial cells that grow as microcolonies and thick biofilms within extensive fibrous organic matrices. These bacterial cells and their secreted products (glycocalyx or biofilm matrix) appear to provide initial foci for crystal development and aggregation of crystals to form macroscopic struvite stones. The protective glycocalyx-enclosed microcolonial mode of bacterial growth also may explain the relative resistance to antibiotics observed in bacteria associated with infection stones.}, }
@article {pmid4051125, year = {1985}, author = {Ducluzeau, R and Raibaud, P}, title = {[Microbial ecology of the digestive system].}, journal = {Agressologie: revue internationale de physio-biologie et de pharmacologie appliquees aux effets de l'agression}, volume = {26}, number = {2}, pages = {161-163}, pmid = {4051125}, issn = {0002-1148}, mesh = {Animals ; *Bacterial Physiological Phenomena ; Digestive System/*microbiology ; Digestive System Physiological Phenomena ; Ecology ; Germ-Free Life ; Humans ; }, }
@article {pmid6393195, year = {1984}, author = {Renner, RP and Gomes, BC and McNamara, TF and Shakun, ML and Baer, PN and Hackett, D}, title = {Periodontal health, prosthodontic factors and microbial ecology of patients treated with overdentures--a 2 1/2-year report.}, journal = {Quintessence international, dental digest}, volume = {15}, number = {6}, pages = {645-652}, pmid = {6393195}, mesh = {Adult ; Aged ; *Bacterial Physiological Phenomena ; *Dental Abutments ; *Denture, Overlay ; Ecology ; Humans ; Middle Aged ; Periodontal Diseases/diagnosis/*etiology ; Periodontium/*microbiology/physiology ; Tooth Root/microbiology ; }, }
@article {pmid6234376, year = {1984}, author = {Leeming, JP and Holland, KT and Cunliffe, WJ}, title = {The microbial ecology of pilosebaceous units isolated from human skin.}, journal = {Journal of general microbiology}, volume = {130}, number = {4}, pages = {803-807}, doi = {10.1099/00221287-130-4-803}, pmid = {6234376}, issn = {0022-1287}, mesh = {Acne Vulgaris/microbiology ; Adolescent ; Adult ; Biopsy ; Ecology ; Humans ; Propionibacterium/isolation &amp; purification ; Propionibacterium acnes/isolation &amp; purification ; Sebaceous Glands/*microbiology ; Skin/*microbiology ; Staphylococcus/isolation &amp; purification ; }, abstract = {A method allowing isolation and microbiological analysis of individual pilosebaceous units (follicles) was used to study biopsies of back skin obtained from volunteer acne vulgaris patients. The main microbial groups isolated were members of the genera Propionibacterium, Staphylococcus and Pityrosporum. The incidence (and mean density) of these organisms in 140 normal follicles was 12% (2.6 X 10(5) per follicle), 4% (5.5 X 10(3) per follicle) and 13% (10(2) per follicle) respectively. Colonized follicles were not distributed evenly amongst the subjects studied. The results are analysed and discussed from an ecological standpoint.}, }
@article {pmid6583240, year = {1984}, author = {Gibbons, RJ}, title = {Adherent interactions which may affect microbial ecology in the mouth.}, journal = {Journal of dental research}, volume = {63}, number = {3}, pages = {378-385}, doi = {10.1177/00220345840630030401}, pmid = {6583240}, issn = {0022-0345}, support = {DE-02847/DE/NIDCR NIH HHS/United States ; }, mesh = {Adhesiveness ; Adsorption ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/*cytology ; Bacterial Proteins/physiology ; Bacteroides/cytology ; Binding Sites ; Cell Wall/physiology ; Dental Deposits/physiopathology ; Ecology ; Humans ; Lectins/physiology ; Ligands/metabolism ; Mouth/*microbiology ; Saliva/physiology ; Species Specificity ; Streptococcus mutans/cytology/metabolism ; Sucrose/metabolism ; Tooth/microbiology ; }, abstract = {Bacteria attach to teeth and oral mucosal surfaces in a surprisingly selective manner, and attachment appears to be the first step in the colonization process. Attachment is thought to involve lectin-like and/or hydrophobic ligands, called adhesins, often present in bacterial surface appendages which interact with receptors on oral tissues. A variety of factors can influence bacterial attachment, and therefore have the potential to affect host-parasite interactions in the mouth. Factors discussed include salivary components, dietary lectins, and sublethal concentrations of antibiotics.}, }
@article {pmid6324219, year = {1984}, author = {Van Soest, PJ}, title = {Some physical characteristics of dietary fibres and their influence on the microbial ecology of the human colon.}, journal = {The Proceedings of the Nutrition Society}, volume = {43}, number = {1}, pages = {25-33}, doi = {10.1079/pns19840024}, pmid = {6324219}, issn = {0029-6651}, mesh = {Body Weight ; Colon/metabolism/*microbiology ; Dietary Fiber/*analysis/pharmacology ; Energy Intake ; Feces/analysis ; Humans ; Models, Biological ; }, }
@article {pmid6871389, year = {1983}, author = {Takano, CT and Folsome, CE and Karl, DM}, title = {ATP as a biomass indicator for closed ecosystems.}, journal = {Bio Systems}, volume = {16}, number = {1}, pages = {75-78}, doi = {10.1016/0303-2647(83)90027-8}, pmid = {6871389}, issn = {0303-2647}, mesh = {Adenosine Triphosphate/*analysis ; Cell Count ; *Ecology ; Microbiology ; Oxygen/analysis ; Time Factors ; }, abstract = {Nucleotide measurements have been used as biomass indicators in microbial ecology. We report the use of this metric in materially closed, energetically open microbial ecosystems. Our results indicate that: (i) both ATP concentrations and pO2 show an increase from time of closure; (ii) ATP concentrations (0.2 1.2 ng/ml) are approximately 2 3 times higher than open ocean water; (iii) there is an apparent oscillation of ATP concentrations on the order of 50 days; and (iv) within experimental limitations the ratios of ATP concentrations to observed total cell counts is constant.}, }
@article {pmid6359443, year = {1983}, author = {Mossel, DA}, title = {Essentials and perspectives of the microbial ecology of foods.}, journal = {Society for Applied Bacteriology symposium series}, volume = {11}, number = {}, pages = {1-45}, pmid = {6359443}, issn = {0300-9610}, mesh = {Bacteria/metabolism ; *Ecology ; Food/standards ; Food Handling/*standards ; *Food Microbiology ; Food Preservation/standards ; Foodborne Diseases/prevention &amp; control ; Fungi/metabolism ; Gram-Negative Bacteria/metabolism ; Gram-Positive Bacteria/metabolism ; Humans ; Prospective Studies ; Retrospective Studies ; }, }
@article {pmid6820968, year = {1982}, author = {Sklavounou, AD}, title = {[Basic principles of oral microbial ecology].}, journal = {Odontostomatologike proodos}, volume = {36}, number = {5}, pages = {209-218}, pmid = {6820968}, issn = {0029-8506}, mesh = {Adhesiveness ; Bacteria/cytology ; *Bacterial Physiological Phenomena ; Ecology ; Epithelial Cells ; Humans ; Mouth/*microbiology ; Saliva/physiology ; }, }
@article {pmid7143428, year = {1982}, author = {Stark, PL and Lee, A}, title = {The microbial ecology of the large bowel of breast-fed and formula-fed infants during the first year of life.}, journal = {Journal of medical microbiology}, volume = {15}, number = {2}, pages = {189-203}, doi = {10.1099/00222615-15-2-189}, pmid = {7143428}, issn = {0022-2615}, mesh = {Actinomycetaceae/isolation &amp; purification ; Aerobiosis ; Aging ; Anaerobiosis ; Bacteroides/isolation &amp; purification ; *Bottle Feeding ; *Breast Feeding ; Clostridium/isolation &amp; purification ; Enterobacteriaceae/isolation &amp; purification ; Feces/microbiology ; Humans ; Infant ; Infant, Newborn ; Intestine, Large/*microbiology ; Prospective Studies ; }, abstract = {The succession of bacterial populations in the large bowel of seven breast-fed and seven formula-fed infants was examined during the first year of life. The composition of the intestinal microflora varied according to the infant's diet. During the first week of life breast-fed and formula-fed infants were colonised by enterobacteria and enterococci followed by bifidobacteria, Bacteroides spp., clostridia and anaerobic streptococci. From week 4 until solid foods were given, breast-fed babies had a simple flora consisting of bifidobacteria and relatively few enterobacteria and enterococci. Formula-fed babies during the corresponding period were more often colonised by other anaerobes in addition to bifidobacteria and had higher counts of facultatively anaerobic bacteria. The introduction of solid food to the breast-fed infants caused a major disturbance in the microbial ecology of the large bowel as counts of enterobacteria and enterococci rose sharply and colonisation by Bacteroides spp., clostridia and anaerobic streptococci occurred. This was not observed when formula-fed infants began to take solids; instead, counts of facultative anaerobes remained high while colonisation by anaerobes other than bifidobacteria continued. At 12 months, the anaerobic bacterial populations of the large bowel of breast-fed and formula-fed infants were beginning to resemble those of adults in number and composition and there was a corresponding decrease in the number of facultative anaerobes. These changes are discussed in relation to changes in susceptibility to gastro-intestinal infection.}, }
@article {pmid7049577, year = {1982}, author = {Hobson, PN and Wallace, RJ}, title = {Microbial ecology and activities in the rumen: Part II.}, journal = {Critical reviews in microbiology}, volume = {9}, number = {4}, pages = {253-320}, doi = {10.3109/10408418209104492}, pmid = {7049577}, issn = {1040-841X}, mesh = {Amino Acids/metabolism ; Anaerobiosis ; Animals ; Bacteria/growth &amp; development/metabolism ; Cattle ; Cell Wall/metabolism ; Energy Metabolism ; Fermentation ; Lipid Metabolism ; Methane/metabolism ; Nitrogen/metabolism ; Oxalates/metabolism ; Oxidative Phosphorylation ; Peptides/metabolism ; Proteins/metabolism ; Rumen/*microbiology ; Urea/metabolism ; }, }
@article {pmid6286253, year = {1982}, author = {Hobson, PN and Wallace, RJ}, title = {Microbial ecology and activities in the rumen: part 1.}, journal = {Critical reviews in microbiology}, volume = {9}, number = {3}, pages = {165-225}, doi = {10.3109/10408418209104490}, pmid = {6286253}, issn = {1040-841X}, mesh = {Amino Acids/analysis ; Aminoethylphosphonic Acid/analysis ; Animals ; Bacteria/isolation &amp; purification/metabolism ; Carbohydrate Metabolism ; Cattle/growth &amp; development/metabolism/*microbiology ; Diaminopimelic Acid/analysis ; Dietary Fiber/metabolism ; Eukaryota/isolation &amp; purification/metabolism ; Fermentation ; Microbiological Techniques ; Rumen/*microbiology ; Sheep/growth &amp; development/metabolism/*microbiology ; }, abstract = {This review describes the progress which has been made during the last 10 to 15 years in the field of rumen microbiology. It is basically an account of new discoveries in the bacteriology, protozoology, biochemistry, and ecology of the rumen microbial population. As such it covers a wide range of subjects including the isolation and properties of methanogenic bacteria, the role of rumen phycomycete fungi, anaerobic energy conservation, and general metabolic aspects of rumen microorganisms. It also attempts, however, to describe and develop new concepts in rumen microbiology. These consist principally of interactions of the microbemicrobe, microbe-food and microbe-host types, and represent the main areas of recent advance in our understanding of the rumen ecosystem. The development of experimental techniques such as chemostat culture and scanning electron microscopy are shown to have been instrumental in progress in these areas. The paper is concluded with an assessment of our present knowledge of the rumen fermentation, based on the degree of success of experiments with gnotobiotic ruminants inoculated with defined flora and in mathematical modeling of the fermentation. The efficacy of chemical manipulation of the fermentation in ruminant is also discussed in this light.}, }
@article {pmid7068220, year = {1982}, author = {Stark, PL and Lee, A and Parsonage, BD}, title = {Colonization of the large bowel by Clostridium difficile in healthy infants: quantitative study.}, journal = {Infection and immunity}, volume = {35}, number = {3}, pages = {895-899}, pmid = {7068220}, issn = {0019-9567}, mesh = {Bacterial Toxins/biosynthesis ; Clostridium/*growth &amp; development/isolation &amp; purification/metabolism ; Cytotoxins/biosynthesis ; Feces/microbiology ; Humans ; Infant ; Infant, Newborn ; Intestine, Large/*microbiology ; Prospective Studies ; Time Factors ; }, abstract = {Colonization of the large bowel of healthy infants by Clostridium difficile was studied. Feces were collected from five breast-fed aand five formula-fed infants throughout the first year of life, and levels of C. difficile were quantitated. Three breast-fed and five formula-fed infants were colonized for periods of between 8 and 42 weeks, and another infant harbored the organism only during week 1. Colonization of breast-fed infants commenced before or during weaning, with levels reaching 10(3) to 10(5) organisms per g of wet feces. Colonization of formula-fed infants commenced before solid foods were given, with levels of 10(3) to 10(7) organisms per g of wet feces. Isolates from eight of the babies were shown to produce cytotoxin in vitro. Single fecal specimens from 60 more children aged up to 4 years were also examined, and it was found that the carriage rate of C. difficile fell sharply after 1 year of age, although in the second year it was still higher than in adults. These findings are discussed in relation to the microbial ecology of the large bowel and the paradox that levels of C. difficile in the large bowel of healthy infants are similar to those causing pseudomembranous colitis in patients.}, }
@article {pmid7195685, year = {1981}, author = {Kleyn, JG and Johnson, WM and Wetzler, TF}, title = {Microbial aerosols and actinomycetes in etiological considerations of mushroom workers' lungs.}, journal = {Applied and environmental microbiology}, volume = {41}, number = {6}, pages = {1454-1460}, pmid = {7195685}, issn = {0099-2240}, mesh = {Actinomycetales/*isolation &amp; purification ; *Air Microbiology ; Alveolitis, Extrinsic Allergic/*etiology ; Bacteria/*isolation &amp; purification ; *Basidiomycota ; Dust ; Humans ; Hydrogen-Ion Concentration ; Water ; }, abstract = {Spent steamed compost, phase II compost, and dust emanating from spent compost during dumping of stationary-bed mushroom houses were examined bacteriologically. The total count for spent compost was 16 X 10(8) microorganisms per g. The total count for dust was 333 microorganisms per liter of air. Actinomycetes belonging to the genus Streptomyces often constituted 90% or more of isolates from dust, whereas mold spores constituted approximately 5%. Dust weight averaged 3.4 mg/liter of air and contained approximately 33% inanimate and 67% animate (microbial) particles. Spent compost and casing contained approximately 60% moisture; the average pH of compost was 6.93, and that of casing was 7.70. Ouchterlony precipitin results with antisera from workers afflicted with either farmer's or mushroom worker's lung were positive for Bacillus licheniformis, Micropolyspora faeni, Thermoactinomyces vulgaris, Aspergillus fumigatus, Humicola grisea var. thermoidea, spent compost, and phase II compost. Their usefulness in determining the etiology of this and related forms of allergic alveolitis is questioned and discussed. The relationship of dust particle size; microbial species, prevalence and antigenicity; and compost antigenicity to the etiology of mushroom worker's lung is discussed. The microbial ecology of mushroom compost and moldy hay associated with farmer's lung is compared.}, }
@article {pmid7231153, year = {1981}, author = {Shlaes, DM and Lerner, PI and Wolinsky, E and Gopalakrishna, KV}, title = {Infections due to Lancefield group F and related Streptococci (S. milleri, S. anginosus).}, journal = {Medicine}, volume = {60}, number = {3}, pages = {197-207}, doi = {10.1097/00005792-198105000-00003}, pmid = {7231153}, issn = {0025-7974}, mesh = {Abdomen ; Abscess/diagnosis ; Adolescent ; Adult ; Aged ; Anti-Bacterial Agents/therapeutic use ; Brain Abscess/diagnosis ; Child ; Female ; Humans ; Lung Diseases/diagnosis ; Male ; Middle Aged ; Mouth Diseases/diagnosis ; Osteomyelitis/diagnosis ; Sepsis/diagnosis ; Streptococcal Infections/*diagnosis/drug therapy/etiology ; Streptococcus/classification/metabolism ; }, abstract = {We can no longer accept classification of streptococci solely on the basis of hemolytic reactions or Lancefield agglutinations. While the "viridans" streptococci cannot be serologically differentiated, physiological separation of the species offers a satisfactory method of classifying human isolates. We review the microbiology of Lancefield group F and related streptococci (S. milleri, S. anginosus), emphasizing microbial ecology and current taxonomic considerations. A series of 28 patients infected with these organisms is presented. There was a striking male predominance in the series (6:1) as well as an obvious association with underlying diseases and/or antecedent trauma. The most remarkable feature of these pathogens is their predilection for abscess formation, confirming their overdue recognition as the most common "viridans" streptococcus recovered from abscesses within internal organs. We observed purulent disease of the nervous and skeletal systems, oral cavity, lung and pleural space, abdomen and subcutaneous tissues. Microbial synergy (i.e. polymicrobic infection) was not a requisite for abscess formation. Four of the five deaths in this series occurred in patients 60 years of age of older. Some degree of variability in antimicrobial susceptibility was noted, so speciation alone may not always provide sufficient information on which to base a therapeutic decision.}, }
@article {pmid7010116, year = {1980}, author = {Karl, DM}, title = {Cellular nucleotide measurements and applications in microbial ecology.}, journal = {Microbiological reviews}, volume = {44}, number = {4}, pages = {739-796}, pmid = {7010116}, issn = {0146-0749}, mesh = {Adenosine Triphosphate/metabolism ; *Bacterial Physiological Phenomena ; Cell Cycle ; Ecology ; Energy Metabolism ; Eukaryota/*physiology ; Fungi/*physiology ; Microbiological Techniques ; NAD/metabolism ; NADP/metabolism ; Nucleotides/*metabolism ; Soil Microbiology ; Water Microbiology ; }, }
@article {pmid7387158, year = {1980}, author = {Russell, JB and Dombrowski, DB}, title = {Effect of pH on the efficiency of growth by pure cultures of rumen bacteria in continuous culture.}, journal = {Applied and environmental microbiology}, volume = {39}, number = {3}, pages = {604-610}, pmid = {7387158}, issn = {0099-2240}, mesh = {Animals ; Bacteria/*growth &amp; development ; Cellobiose/metabolism ; Culture Media ; Glucose/metabolism ; Hydrogen-Ion Concentration ; Rumen/microbiology ; Species Specificity ; }, abstract = {A total of 10 strains of rumen bacteria, Selenomonas ruminantium HD4, Megasphaera elsdenii B159, Butyrivibrio fibrisolvens A38, Streptococcus bovis JB1, Lactobacillus vitulinus GA1, Bacteroides ruminicola B14, B. ruminicola GA33, Ruminococcus albus 7, Ruminococcus flavefaciens C94, and Bacteroides succinogenes S85, were grown in energy-limiteH of the medium reservoir was lowered approximately 0.3 pH units, and the energy source concentration remaining in the culture vessel, optical density, cell mass, and pH were determined. A low pH appeared to have a detrimental effect on cell yields. Large variations were seen among strains in both the magnitude of yield depressions at lower pH values and in the pH at which the culture washed out. Lactate analysis indicated ta are discussed in relation to the effect of pH on the efficiency of protein synthesis in the rumen and rumen microbial ecology.}, }
@article {pmid528050, year = {1979}, author = {Liljemark, WF and Bloomquist, CG and Ofstehage, JC}, title = {Aggregation and adherence of Streptococcus sanguis: role of human salivary immunoglobulin A.}, journal = {Infection and immunity}, volume = {26}, number = {3}, pages = {1104-1110}, pmid = {528050}, issn = {0019-9567}, mesh = {Adhesiveness ; Adult ; Colostrum/immunology ; Female ; Humans ; Hydroxyapatites ; Immunoglobulin A/*physiology ; Male ; Movement ; Saliva/*immunology ; Streptococcus sanguis/*physiology ; }, abstract = {Fourteen freshly isolated strains of Streptococcus sanguis were obtained from the dental plaque of five healthy adults. Whole saliva was collected concomitant with the plaque isolates from the five subjects, and a second whole saliva sample was collected 10 weeks later. All possible combinations of the first five saliva samples, the second five saliva samples, and 14 strains of bacteria were tested for aggregation. Of the 140 combinations examined, 108 of 140 (77%) of the strains aggregated with the first saliva samples and 95 of 140 (68%) aggregated with the second saliva samples. Overall, 72% of the strains aggregated with both the first and second saliva samples. Removal of immunoglobulin A (IgA) from these same salivas resulted in 38 of 108 (35%) of the aggregates decreasing in intensity with the first saliva samples and 27 of 95 (29%) of the aggregates decreasing in intensity with the second saliva samples. No aggregates increased in intensity with saliva samples when IgA had been removed. Removal of IgA from saliva also resulted in a mean decrease of 46% in adherence of S. sanguis to hydroxyapatite coated with the IgA-deficient saliva. Several strains of S. sanguis were shown to aggregate strongly with human salivary and colostral IgA. In addition, S. sanguis strain S7 showed a 31% stimulation of adherence to hydroxyapatite precoated with human salivary IgA over the uncoated controls. Stepwise removal of IgA from saliva resulted in a decrease in aggregation intensity from strong (4+) to weak (1+ to 2+). Similarly, the adherence of S. sanguis to hydroxyapatite coated with these saliva samples decreased linearly as the salivary IgA was depleted. Alternatively, the addition of a small quantity of salivary IgA (20 mug/ml) to progressively diluted saliva maintained a high level of adherence and strong aggregation until the saliva dilutions reached between 1:8 in the adherence experiments and 1:32 for the aggregations. These data indicate that salivary IgA may play an important role in the microbial ecology of human dental plaque formation.}, }
@article {pmid453841, year = {1979}, author = {Torrella, F and Morita, RY}, title = {Evidence by electron micrographs for a high incidence of bacteriophage particles in the waters of Yaquina Bay, oregon: ecological and taxonomical implications.}, journal = {Applied and environmental microbiology}, volume = {37}, number = {4}, pages = {774-778}, pmid = {453841}, issn = {0099-2240}, mesh = {Bacteriophages/*isolation &amp; purification/ultrastructure ; Ecology ; Oregon ; Seawater ; *Water Microbiology ; }, abstract = {A variety of viral particles, the majority of them clearly identifiable as bacteriophages, were found in the seawater of Yaquina Bay, Oregon. These phages were obtained as free particles from the seawater without employing specific hosts for enrichments or further purification in the laboratory. A variety of electron micrographs showing different morphologies of phages as well as phage-bacterium interactions found in the seawater are presented. In the area where the bay received organic enrichment from seafood processing plants, a minimum of 10(4) phage particles per ml was estimated. Since the technique used was designed to concentrate particles 0.2 micrometer in diameter or larger it is assumed that the actual number of phage particles is higher than 10(4) particles per ml. The implications of the presence of such phage concentrations in bays and estuaries with a certain level of eutrophication are of obvious importance in considering the microbial ecology of these environments.}, }
@article {pmid429798, year = {1979}, author = {Leyden, JJ and Stewart, R and Kligman, AM}, title = {Updated in vivo methods for evaluating topical antimicrobial agents on human skin.}, journal = {The Journal of investigative dermatology}, volume = {72}, number = {4}, pages = {165-170}, doi = {10.1111/1523-1747.ep12676347}, pmid = {429798}, issn = {0022-202X}, mesh = {Adult ; Anti-Bacterial Agents/*pharmacology ; Anti-Infective Agents, Local/*pharmacology ; Dermatologic Agents/pharmacology ; Drug Evaluation ; Humans ; Microbial Sensitivity Tests/*methods ; Skin/drug effects ; }, abstract = {Updated and expanded in vivo quantitative testing procedures to determine the efficacy of topical antimicrobial agents are presented. The occlusion test measures the ability of an agent to prevent the expansion of the resident microflora which occurs when an impermeable dressing is applied to the forearm. Measurements are made at 24 and 48 hr. The expanded flora test measures the ability of an agent to suppress a dense population of micro-organisms produced by expansion of the resident flora of the forearm by prior application of an impermeable occlusive dressing. Measurements are made at 6, 24 and 48 hr or after 10 min in the case for agents designed for immediate degerming. The persistence test measures the ability of an agent to establish a reservoir in skin and exert an antimicrobial effect up to 3 days after the last application of the test material. The ecological shift test determines any major alteration in cutaneous microbial ecology following several applications of the material under occlusive dressings. The serum inactivation test determines whether the presence of serum proteins interferes with antimicrobial activity.}, }
@article {pmid890603, year = {1977}, author = {Bibel, DJ and Greenberg, JH and Cook, JL}, title = {Staphylococcus aureus and the microbial ecology of atopic dermatitis.}, journal = {Canadian journal of microbiology}, volume = {23}, number = {8}, pages = {1062-1068}, doi = {10.1139/m77-159}, pmid = {890603}, issn = {0008-4166}, mesh = {Adolescent ; Adult ; Aerobiosis ; Aged ; Bacteria/isolation &amp; purification ; Child ; Child, Preschool ; Dermatitis, Atopic/*microbiology ; Ecology ; Female ; Humans ; Male ; Micrococcus/isolation &amp; purification ; Middle Aged ; Skin/microbiology ; Staphylococcus/isolation &amp; purification ; Staphylococcus aureus/growth &amp; development/*isolation &amp; purification ; }, abstract = {Two surveys were conducted to ascertain the effect which Staphylococcus aureus has on resident flora and on skin of patients with eczema. Forty paired sites, normal and lesions, were sampled from 32 patients with chronic lichenified atopic dermatitis, and 162 sites covering the entire body of a patient with an acute flare of chronic atopic dermatitis were examined. In the first study, 34 lesions (85%) carried S. aureus, and 85% of these positive samples supported greater than 10(4) colony-forming units (CFU) of total aerobic bacteria/cm2. About 55% of normal sites carried S. aureus with 18% of such samples supporting greater than 10(4) CFU/cm2 total aerobic bacteria. Normal sites carried fewer but more diverse flora than lesions. The composition of flora on lesion sites was mainly S. aureus or S. epidermidis biotype 1, or both. At densities greater than 10(7) CFU/cm2, S. aureus constituted almost 100% of the total aerobic bacterial flora. The total body survey of the single eczema patient yielded similar results. Evidence supports the hypotheses that (1) S. aureus is able to exploit the environment of eczematous lesions and to influence the composition of cohabiting aerobic skin bacteria, and (2) its inhabitation of normal appearing sites is transitory.}, }
@article {pmid405025, year = {1977}, author = {Meloni, GA and Busolo, F and Conventi, L and Bertoloni, G}, title = {[Research on the vaginal microbial ecology in the fertile age].}, journal = {Bollettino dell'Istituto sieroterapico milanese}, volume = {56}, number = {1}, pages = {7-14}, pmid = {405025}, issn = {0021-2547}, mesh = {Adolescent ; Adult ; Age Factors ; *Bacteria/isolation &amp; purification ; *Candida/isolation &amp; purification ; Female ; Fertility ; Humans ; *Lactobacillus acidophilus/isolation &amp; purification ; Mycoplasma/isolation &amp; purification ; Ureaplasma/isolation &amp; purification ; Vagina/*microbiology ; Vaginal Diseases/*microbiology ; }, }
@article {pmid334036, year = {1977}, author = {Savage, DC}, title = {Microbial ecology of the gastrointestinal tract.}, journal = {Annual review of microbiology}, volume = {31}, number = {}, pages = {107-133}, doi = {10.1146/annurev.mi.31.100177.000543}, pmid = {334036}, issn = {0066-4227}, mesh = {Animals ; Antigens, Bacterial ; Bacteria/*growth &amp; development/metabolism ; Bile Acids and Salts ; Diet ; Ecology ; Fatty Acids/metabolism ; Feces/microbiology ; Fermentation ; Humans ; Infant ; Intestine, Large/*microbiology ; Intestine, Small/*microbiology ; Mammals/*microbiology ; Microbiological Techniques ; Mucins/metabolism ; Peristalsis ; Phagocytosis ; Stomach/*microbiology ; Temperature ; Yeasts/*growth &amp; development/metabolism ; }, }
@article {pmid1064573, year = {1976}, author = {Morhart, RE and Fitzgerald, RJ}, title = {Nutritional determinants of the ecology of the oral flora.}, journal = {Dental clinics of North America}, volume = {20}, number = {3}, pages = {473-489}, pmid = {1064573}, issn = {0011-8532}, mesh = {Adhesiveness ; Antibiosis ; Bacteria/cytology/metabolism ; Dental Deposits/metabolism ; Dental Plaque/metabolism/microbiology ; Dietary Carbohydrates ; Dietary Fats ; Dietary Proteins ; Ecology ; Humans ; Mouth/*microbiology ; *Nutritional Physiological Phenomena ; Oxidation-Reduction ; Polysaccharides, Bacterial/physiology ; Saliva/microbiology ; Streptococcus/isolation &amp; purification ; Tongue/microbiology ; Tooth/anatomy &amp; histology ; }, abstract = {Consideration of nutritional factors as determinants of oral microbial ecology leads to the conclusion that endogenous factors play a dominant role. It is the interactions between specific microorganisms and nutritional and other factors provided by the host that selectively determine the kinds of microorganisms which willinitially reside in the oral cavity and the sites which they will colonize. The persistence of these original "colonists" in their respective ecologic niches will depend in part on the accessibility of endogenous nutrients variously provided by saliva, tissue exudates, crevicular fluids, or degenerating host cells. It will also depend on their response to and interaction with microorganisms which immigrate to that site subsequently. The microbial ecology of a given site is therefore rarely uncomplicated, the notable exception occurring at the most microscopic level where one may encounter microcolonies of individual species within more heterogenous populations of microorganisms. The extent of this heterogeneity quantitatively and qualitatively is a reflection of the degree to which the interactions between the resident flora and the new arrivals, plus the local environmental changes which they both generate, serve to promote or to discourage the survival and growth of the individual species. This element of heterogeneity in a dynamic system with its inherent potential for variation makes it possible for relatively minor changes in local environmental conditions to result in significant differences in the microflora between one site and another even though they may be in close proximity to each other. Once this concept is appreciated it becomes easy to understand how disease processes such as dental caries may affect specific areas of a tooth while nearby areas are unaffected. The effects of exogenous nutrients on the ecology of the oral microbiota, nevertheless cannot be ignored. The diet may modulate such endogenous factors as the salivary secretions and the local resistance of the gingival tissues to infections. Although at our present state of knowledge the direct influence of dietary proteins and fats on the oral microbiota is thought to be of relatively minor consequence, dietary carbohydrates are of major ecological significance. Dietary sugars provide readily available substrates for the oral microorganisms, most of which depend on carbohydrates for energy sources. The metabolism of dietary sucrose by S. sanguis and S. mutans with the productions of acids and intracellular and extracellular polysaccharides has specific influence on the microbial composition, metabolic activities, and mass of coronal plaque. The ready availability of dietary carbohydrates undoubtedly influences the microflora of other parts of the oral cavity as well, eic species or indirectly through the interactions of other organisms with them...}, }
@article {pmid938030, year = {1976}, author = {Van Dijck, P and van de Voorde, H}, title = {Sensitivity of environmental microorganisms to antimicrobial agents.}, journal = {Applied and environmental microbiology}, volume = {31}, number = {3}, pages = {332-336}, pmid = {938030}, issn = {0099-2240}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/growth &amp; development ; Chlorella/drug effects/growth &amp; development ; Drug Resistance, Microbial ; Ecology ; Eukaryota/drug effects/growth &amp; development ; *Soil Microbiology ; Species Specificity ; *Water Microbiology ; }, abstract = {The sensitivity of different microorganisms, considered as typical representatives of the microflora of soil and water, was established to evaluate the influence of the nonmedical use of antimicrobial agents on bacterial ecology. Only seven strains, six chemoorganotrophs and one chemolithotroph, could be considered as relatively sensitive to the 21 antimicrobial compounds tested. The other 29 microorganisms may be regarded as resistant to most antimicrobial agents. Streptomyces were sensitive to high concentrations of active substances. Broad-spectrum antibiotics showed an effect on environmental bacteria similar to that on human pathogens. Cephalothin stimulated the growth of a Chlorella sp. From these experiments, it appears that spilled antimicrobial agents have little chance of causing an alteration in the microbial ecology.}, }
@article {pmid775978, year = {1976}, author = {Dickman, MD and Chappelka, AR and Schaedler, RW}, title = {The Microbial ecology of the upper small bowel.}, journal = {The American journal of gastroenterology}, volume = {65}, number = {1}, pages = {57-62}, pmid = {775978}, issn = {0002-9270}, mesh = {Adolescent ; Adult ; Bacteriological Techniques ; Humans ; Intestine, Small/*microbiology ; Intubation, Gastrointestinal ; Lactobacillus/isolation &amp; purification ; Male ; Streptococcus/isolation &amp; purification ; Veillonella/isolation &amp; purification ; Yeasts/isolation &amp; purification ; }, }
@article {pmid1147604, year = {1975}, author = {Sawyer, RT and Deskins, DC and Volz, PA}, title = {Phosphoglycerides of Trichophyton terrestre and one phenotype selected from the Apollo 16 microbial ecology evaluation device.}, journal = {Applied microbiology}, volume = {29}, number = {5}, pages = {658-662}, pmid = {1147604}, issn = {0003-6919}, mesh = {Cardiolipins/analysis ; Chromatography, Paper ; Chromatography, Thin Layer ; Diglycerides/analysis ; Genetic Variation ; Lipids/analysis ; Phenotype ; Phosphatidic Acids/analysis ; Phosphatidylcholines/analysis ; Phosphatidylethanolamines/analysis ; Phosphatidylinositols/analysis ; Phosphatidylserines/analysis ; Phospholipids/*analysis ; Radiation Effects ; *Space Flight ; Trichophyton/*chemistry/cytology/radiation effects ; Ultraviolet Rays ; }, abstract = {Total lipid extracted from wild-type Trichophyton terrestre CDC-X285 was found to be 2.0 percent of the dry cell weight. The total lipid contained the following phospholipid components identified by silicic acid-impregnated thin-layer and paper chromatography: phosphatidyl inositol, phosphatidyl choline, phosphatidyl serine, and phosphatidic acid. The total lipid extracted from the phenotype T. terrestre 7048-1 isolated from the Apollo 16 Microbial Ecology Evaluation Device (MEED) was found to vary according to the time at which the phospholipids were extracted. The Trichophyton phenotype was selected from a cuvette housed in the MEED exposed to specific space parameters including ultraviolet light of known wavelengths and energy levels in deep space. The phospholipid components, identified in the phenotype were phosphatidyl ethanolamine and cardiolipin. The major lipid fraction was composed of digalactosyl diglyceride and monogalactosyl diglyceride. An unusual lipid was detected in the phenotype, which appeared to be sterol glycoside.}, }
@article {pmid1180512, year = {1975}, author = {Gibbons, RJ and Houte, JV}, title = {Bacterial adherence in oral microbial ecology.}, journal = {Annual review of microbiology}, volume = {29}, number = {}, pages = {19-44}, doi = {10.1146/annurev.mi.29.100175.000315}, pmid = {1180512}, issn = {0066-4227}, mesh = {Animals ; Antibodies, Bacterial ; Bacteria/drug effects/*growth &amp; development ; Cell Adhesion/drug effects ; Dental Plaque/microbiology ; Diet ; Ecology ; Glycoproteins/pharmacology ; Humans ; Mouth/*microbiology ; Mouth Mucosa/microbiology ; Saliva/immunology ; Tongue/microbiology ; Tooth/microbiology ; }, }
@article {pmid1124348, year = {1975}, author = {Philipson, B and Brandberg A,  and Jagenburg, R and Kock, NG and Lager, I and Ahrén, C}, title = {Mucosal morphology, bacteriology, and absorption in intra-abdominal ileostomy reservoir.}, journal = {Scandinavian journal of gastroenterology}, volume = {10}, number = {2}, pages = {145-153}, pmid = {1124348}, issn = {0036-5521}, mesh = {Biopsy ; Colectomy ; Colitis, Ulcerative/metabolism/pathology ; Female ; Follow-Up Studies ; Humans ; *Ileostomy ; Ileum/metabolism/microbiology/ultrastructure ; *Intestinal Absorption ; Intestinal Mucosa/metabolism/microbiology/*ultrastructure ; Male ; Microscopy, Electron ; Phenylalanine/metabolism ; Xylose/metabolism ; }, abstract = {Six patients who had undergone proctocolectomy and been provided with intra-abdominal ileostomy reservoirs were studied in intervals during the 24 postoperative months. The studies included the mucosal morphology, bacteriology, and the local absorption in the reservoir. The results showed that the mucous membrane of the terminal ileal segment used for construction of the reservoir underwent morphological changes characterized by an increased cell turnover and a shortening of the villi. These changes in morphological structure took place rather promptly after construction of the reservoir. No indications for a continuously progressing process could be found. The brushborder was intact and no cellular lesions were discovered. Soon after construction the reservoir was inhabited by a microbial flora which held an intermediate position between the flora of effluent from conventional ileostomies and normal faeces. The flora remained rather stable in the reservoir. In spite of the new microbial ecology and the morphological changes, the reservoir mucous membrane did retain absorptive capacity for D-xylose and phenylalanine.}, }
@article {pmid4612361, year = {1974}, author = {Volz, PA and Hsu, YC and Hiser, JL and Veselenak, JM and Jerger, DE}, title = {The Microbial Ecology Evaluation Device Mycology spaceflight studies of Apollo 16.}, journal = {Mycopathologia et mycologia applicata}, volume = {54}, number = {2}, pages = {221-233}, pmid = {4612361}, issn = {0027-5530}, mesh = {*Ascomycota ; Cell Count ; Cell Survival ; Culture Media ; Environment, Controlled ; Equipment and Supplies ; Light ; *Mitosporic Fungi ; Phenotype ; *Saccharomyces cerevisiae ; *Space Flight ; *Trichophyton ; United States ; }, }
@article {pmid4851133, year = {1974}, author = {Oliver, JD and Colwell, RR}, title = {Computer program designed to follow fluctuations in microbial populations and its application in a study of Chesapeake Bay microflora.}, journal = {Applied microbiology}, volume = {28}, number = {2}, pages = {185-192}, pmid = {4851133}, issn = {0003-6919}, mesh = {Bacteria/*classification/isolation &amp; purification ; *Computers ; District of Columbia ; Ecology ; Seasons ; Temperature ; Washington ; *Water Microbiology ; }, abstract = {A computer program has been developed which performs cluster analysis of microorganisms using methods of numerical taxonomy. The program is designed to group related strains, identify the groups by reference to known strains, and calculate a hypothetical median organism (HMO) for each group. The HMO serves to condense taxonomic information and provides a tag for each strain cluster. Every strain in a group is compared with the HMO established for that group. A representative strain for the group is obtained by selection of the strain showing highest similarity to the HMO. New data sets can be compared with data sets of previous analyses. Hence, the occurrence of the same taxonomic groups within separate data sets can be determined. Quantitative or qualitative differences in distribution of taxonomic groups within or between data sets can be measured. The output from the computer is a graphical display, using an on-line plotter; thus, the investigator is provided with visual comparison of data sets. Results obtained from a study applying the computer program in an analysis of taxonomic data obtained for 43 bacterial strains isolated from Chesapeake Bay indicate the usefulness of this method of taxonomic analysis in microbial ecology.}, }
@article {pmid4601860, year = {1974}, author = {Vilain, R and Avril, JL}, title = {[Microbial ecology and ethology. Between the sabre and the swab].}, journal = {La Nouvelle presse medicale}, volume = {3}, number = {22}, pages = {1445-1446}, pmid = {4601860}, issn = {0301-1518}, mesh = {Anti-Infective Agents ; Antisepsis ; Bacteriological Techniques ; *Cross Infection ; Ecology ; Equipment and Supplies, Hospital ; Ethology ; Humans ; Microbial Sensitivity Tests ; Serotyping ; *Surgical Procedures, Operative ; *Surgical Wound Infection ; }, }
@article {pmid4583789, year = {1973}, author = {Kotrajaras, R and Udihitanonda, M}, title = {Study of microbial ecology of Thai women with dermatophytosis.}, journal = {International journal of dermatology}, volume = {12}, number = {5}, pages = {318-321}, doi = {10.1111/j.1365-4362.1973.tb00063.x}, pmid = {4583789}, issn = {0011-9059}, mesh = {Candida albicans/isolation &amp; purification ; Candidiasis, Cutaneous/microbiology ; Dermatitis/microbiology ; Dermatomycoses/*microbiology ; Ear Canal/microbiology ; Female ; Hand/microbiology ; Humans ; Micrococcus/isolation &amp; purification ; Perineum/microbiology ; Staphylococcus/isolation &amp; purification ; Thailand ; Tinea/microbiology ; Trichophyton/isolation &amp; purification ; }, }
@article {pmid4567976, year = {1972}, author = {Greaves, H}, title = {Microbial ecology of untreated and copper-chrome-arsenic treated stakes exposed in a tropical soil. 1. The initial invaders.}, journal = {Canadian journal of microbiology}, volume = {18}, number = {12}, pages = {1923-1931}, doi = {10.1139/m72-298}, pmid = {4567976}, issn = {0008-4166}, mesh = {Arsenic/pharmacology ; Bacteria/drug effects/enzymology/growth &amp; development/isolation &amp; purification ; Cellulose ; Chromium/pharmacology ; Copper/pharmacology ; Culture Media ; Ecology ; Fungi/drug effects/enzymology/growth &amp; development/isolation &amp; purification ; Glycoside Hydrolases/biosynthesis ; Microbial Sensitivity Tests ; Microscopy, Interference ; Microscopy, Phase-Contrast ; *Soil Microbiology ; Species Specificity ; Time Factors ; Tropical Climate ; *Wood ; }, }
@article {pmid5077031, year = {1972}, author = {Chiang, C and Sinnaeve, J and Dubuisson, G}, title = {[Microbial ecology of Moroccari soils. I. Seasonal fluctuations].}, journal = {Annales de l'Institut Pasteur}, volume = {122}, number = {6}, pages = {1171-1182}, pmid = {5077031}, issn = {0020-2444}, mesh = {Actinomycetales/growth &amp; development ; Ammonia/analysis ; Bacteria/growth &amp; development ; Culture Media ; Ecology ; Fungi/growth &amp; development ; Humidity ; Morocco ; Nitrates/analysis ; Nitrobacter/growth &amp; development ; Nitrogen/analysis ; Nitrogen Fixation ; Nitrosomonas/growth &amp; development ; Seasons ; Soil/analysis ; *Soil Microbiology ; Weather ; }, }
@article {pmid4504259, year = {1972}, author = {van der Hoeven, JS and Mikx, FH and Plasschaert, AJ and König, KG}, title = {Methodological aspects of gnotobiotic caries experimentation. Preliminary investigations into the microbial ecology of dental plaque.}, journal = {Caries research}, volume = {6}, number = {3}, pages = {203-210}, doi = {10.1159/000259800}, pmid = {4504259}, issn = {0008-6568}, mesh = {Animals ; Dental Caries/epidemiology/*microbiology ; Dental Plaque/*microbiology ; Disease Models, Animal ; *Germ-Free Life ; Polysaccharides, Bacterial/metabolism ; Rats ; Streptococcus/metabolism/pathogenicity ; }, }
@article {pmid4398536, year = {1971}, author = {DiSalvo, LH}, title = {Regenerative functions and microbial ecology of coral reefs. II. Oxygen metabolism in the regenerative system.}, journal = {Canadian journal of microbiology}, volume = {17}, number = {8}, pages = {1091-1100}, doi = {10.1139/m71-172}, pmid = {4398536}, issn = {0008-4166}, mesh = {Aerobiosis ; Azides ; Bacteria/drug effects/isolation &amp; purification/*metabolism ; Bacteriological Techniques ; Circadian Rhythm ; Cnidaria ; Ecology ; Filtration ; Hawaii ; Indicators and Reagents ; Micronesia ; Oxygen/analysis ; *Oxygen Consumption/drug effects ; Polymyxins/pharmacology ; Seawater ; *Soil Microbiology ; Tetracycline/pharmacology ; Water/analysis ; *Water Microbiology ; }, }
@article {pmid4398535, year = {1971}, author = {DiSalvo, L and Gundersen, K}, title = {Regenerative functions and microbial ecology of coral reefs. I. Assays for microbial population.}, journal = {Canadian journal of microbiology}, volume = {17}, number = {8}, pages = {1081-1089}, doi = {10.1139/m71-171}, pmid = {4398535}, issn = {0008-4166}, mesh = {Bacteria/growth &amp; development/*isolation &amp; purification/metabolism ; Bacteriological Techniques ; Chitin/metabolism ; Cnidaria ; Culture Media ; Ecology ; Eukaryota ; Filtration ; Fungi/metabolism ; Hawaii ; Micronesia ; Polysaccharides/metabolism ; Seawater ; *Soil Microbiology ; *Water Microbiology ; }, }
@article {pmid4347114, year = {1971}, author = {Pike, EB and Curds, CR}, title = {The microbial ecology of the activated sludge process.}, journal = {Society for Applied Bacteriology symposium series}, volume = {1}, number = {}, pages = {123-147}, doi = {10.1016/b978-0-12-648050-4.50012-2}, pmid = {4347114}, issn = {0300-9610}, mesh = {Bacteria/isolation &amp; purification ; Ciliophora/isolation &amp; purification ; Ecology ; Enterovirus/isolation &amp; purification ; Escherichia coli/isolation &amp; purification ; Eukaryota/isolation &amp; purification ; Flocculation ; Fungi/isolation &amp; purification ; Gram-Negative Aerobic Bacteria/metabolism ; Mathematics ; Models, Biological ; Nitrobacter/isolation &amp; purification ; Nitrosomonas/isolation &amp; purification ; *Sewage ; *Water Microbiology ; }, }
@article {pmid5510605, year = {1970}, author = {Gundermann, KO}, title = {[Modification of microbial ecology of skin upper layers].}, journal = {Cosmetologica}, volume = {19}, number = {8}, pages = {281-288}, pmid = {5510605}, issn = {0070-055X}, mesh = {Bacteria/drug effects/isolation &amp; purification ; Deodorants/pharmacology ; Detergents/pharmacology ; Humans ; Hydrogen-Ion Concentration ; Skin/*microbiology ; Sterilization ; }, }
@article {pmid4978925, year = {1969}, author = {Pearson, HA}, title = {Rumen microbial ecology in mule deer.}, journal = {Applied microbiology}, volume = {17}, number = {6}, pages = {819-824}, pmid = {4978925}, issn = {0003-6919}, mesh = {Animal Feed ; Animals ; Bacteria/isolation &amp; purification ; Ciliophora/isolation &amp; purification ; *Deer ; Ecology ; Rumen/*microbiology ; Sodium Chloride/pharmacology ; }, abstract = {Mule deer rumen microbial populations from animals in the natural habitat in Utah and from captive deer fed various rations were studied. The microorganisms were characterized on the basis of morphology and Gram reaction. Rumen samples contained 13 identifiable types of bacteria and one genus of ciliate protozoa (Entodinium). Highest rumen bacterial populations were produced on rations containing barley. No differences in proportions of ruminal bacteria in the various morphological groups could be detected when animals were fed either natural browse plants or alfalfa hay. The total numbers of bacteria were similar for animals feeding on controlled diets of browse or hay and those in the natural habitat. Numbers of some bacterial types were directly related to ciliate protozoal numbers, whereas others were inversely related. Highest rumen ciliate protozoal populations were observed on rations containing barley. No differences in protozoal populations were noted between diets containing only browse or hay. Seasonal variations were noted in ciliate protozoal numbers from deer feeding in the natural habitat. The total number of ciliate protozoa decreased in the fall and winter and remained low until spring. There were indications that salt in the deer diet favorably affected rumen ciliate protozoa. Rather than revealing direct deer management applications, this study serves to stimulate and illuminate new approaches to research in range and wildlife nutrition.}, }
@article {pmid5248838, year = {1968}, author = {Loesche, WJ}, title = {Importance of nutrition in gingival crevice microbial ecology.}, journal = {Periodontics}, volume = {6}, number = {6}, pages = {245-249}, pmid = {5248838}, issn = {0553-6685}, mesh = {Amino Acids/metabolism ; Bacteria/*metabolism ; Bacteroides/metabolism ; Butyrates/metabolism ; Carbohydrate Metabolism ; Ecology ; Fusobacterium/metabolism ; Gingiva/*microbiology ; Humans ; Mouth/*microbiology ; Spermine/metabolism ; Symbiosis ; Treponema/metabolism ; Vibrio/metabolism ; }, }
@article {pmid5664122, year = {1968}, author = {Idziak, ES and Incze, K}, title = {Radiation treatment of foods. I. Radurization of fresh eviscerated poultry.}, journal = {Applied microbiology}, volume = {16}, number = {7}, pages = {1061-1066}, pmid = {5664122}, issn = {0003-6919}, mesh = {*Food Irradiation ; Food Microbiology ; *Poultry Products ; Radiation Genetics ; Radiometry ; Salmonella/radiation effects ; Staphylococcus/radiation effects ; }, abstract = {Radurization processing of fresh eviscerated poultry has been microbiologically studied. The recommended dose of 0.5 Mrads extended the shelf life at 5 C by approximately 14 days. This treatment also effected a 10 and 11 log reduction in the number of viable Salmonella species and Staphylococcus aureus strains, respectively. Recycling these organisms at sublethal doses of irradiation resulted in strains possessing increased irradiation resistance. Shifts in the microbial ecology after irradiation and storage resulted, in some instances, in the isolation of organisms tentatively identified as Moraxella sp. and Herellea vaginicola.}, }
@article {pmid4385122, year = {1968}, author = {Gorbach, SL and Nahas, L and Plaut, AG and Weinstein, L and Patterson, JF and Levitan, R}, title = {Studies of intestinal microflora. V. Fecal microbial ecology in ulcerative colitis and regional enteritis: relationship to severity of disease and chemotherapy.}, journal = {Gastroenterology}, volume = {54}, number = {4}, pages = {575-587}, pmid = {4385122}, issn = {0016-5085}, mesh = {Adolescent ; Adult ; Bacteriological Techniques ; Clinical Trials as Topic ; Colitis, Ulcerative/drug therapy/etiology/*microbiology ; Crohn Disease/drug therapy/etiology/*microbiology ; Feces/*microbiology ; Glucocorticoids/*therapeutic use ; Humans ; Intestines/*microbiology ; Male ; Placebos ; Sulfasalazine/*therapeutic use ; }, }
@article {pmid4868864, year = {1968}, author = {Harris, RF and Sommers, LE}, title = {Plate-dilution frequency technique for assay of microbial ecology.}, journal = {Applied microbiology}, volume = {16}, number = {2}, pages = {330-334}, pmid = {4868864}, issn = {0003-6919}, mesh = {Bacteria/*isolation &amp; purification ; *Bacteriological Techniques ; Culture Media ; Fungi/*isolation &amp; purification ; Methods ; Statistics as Topic ; }, abstract = {The plate-dilution frequency technique described facilitates simultaneous enumeration of a wide range of physiologically different microorganisms in complex systems with a precision comparable to dilution tube (most probable number) methods. Replicate microsamples are inoculated from each member of a dilution series onto areas delineated on plates of prepoured solid media; the plates are incubated, and the occurrence of growth or specific biochemical transformation is recorded for each inoculated area. Microbial enumeration is accomplished by reference to appropriate tables. Details of the experimental procedures are described, and tables are presented from which microbial numbers with 95% confidence limits can be obtained and compared for significant difference directly for 10-fold and 4-fold dilution series. Results of experiments in which microbial populations were estimated simultaneously by the plate-dilution frequency and conventional plate count methods are compared. The potential of the technique for broad-spectrum microbial assay is also discussed.}, }
@article {pmid4863723, year = {1967}, author = {Gorbach, SL and Nahas, L and Weinstein, L and Levitan, R and Patterson, JF}, title = {Studies of intestinal microflora. IV. The microflora of ileostomy effluent: a unique microbial ecology.}, journal = {Gastroenterology}, volume = {53}, number = {6}, pages = {874-880}, pmid = {4863723}, issn = {0016-5085}, mesh = {*Adult ; Escherichia coli/*isolation &amp; purification ; Feces/*microbiology ; Fungi/*isolation &amp; purification ; Humans ; *Ileostomy ; Intestine, Small/*microbiology ; Lactobacillus/*isolation &amp; purification ; Staphylococcus/*isolation &amp; purification ; Streptococcus/*isolation &amp; purification ; }, }
@article {pmid5243611, year = {1967}, author = {Stotzky, G}, title = {Clay minerals and microbial ecology.}, journal = {Transactions of the New York Academy of Sciences}, volume = {30}, number = {1}, pages = {11-21}, doi = {10.1111/j.2164-0947.1967.tb02449.x}, pmid = {5243611}, issn = {0028-7113}, mesh = {*Ecology ; *Soil Microbiology ; }, }
@article {pmid6039197, year = {1967}, author = {Tribe, HT and Williams, PA}, title = {Investigations into the basis of microbial ecology in soil, illustrated with reference to growth of soil diphtheroids and Azotobacter in a model system.}, journal = {Canadian journal of microbiology}, volume = {13}, number = {5}, pages = {467-480}, doi = {10.1139/m67-062}, pmid = {6039197}, issn = {0008-4166}, mesh = {Arthrobacter/*growth &amp; development ; Azotobacter/*growth &amp; development ; Bacteria/*growth &amp; development ; *Ecology ; *Soil Microbiology ; }, }
@article {pmid5922142, year = {1966}, author = {Brock, TD and Brock, ML}, title = {Autoradiography as a tool in microbial ecology.}, journal = {Nature}, volume = {209}, number = {5024}, pages = {734-736}, doi = {10.1038/209734a0}, pmid = {5922142}, issn = {0028-0836}, mesh = {*Autoradiography ; *Bacteria ; Carbon Isotopes ; Eukaryota ; Glutamates/*metabolism ; Thymidine/*metabolism ; Tritium ; }, }
@article {pmid5973679, year = {1966}, author = {Brock, TD}, title = {Microbial ecology and applied microbiology.}, journal = {Advances in applied microbiology}, volume = {8}, number = {}, pages = {61-75}, doi = {10.1016/s0065-2164(08)70492-1}, pmid = {5973679}, issn = {0065-2164}, mesh = {Actinomycetales/metabolism ; *Anti-Bacterial Agents/biosynthesis/pharmacology ; Bacteria/drug effects ; *Ecology ; *Microbiology ; Research ; }, }
@article {pmid5221713, year = {1966}, author = {de Araujo, WC}, title = {[Disturbances of the microbial ecology due to the use of antibiotics].}, journal = {Arquivos do Centro de Estudos da Faculdade de Odontologia da U. F. M. G}, volume = {3}, number = {1}, pages = {83-100}, pmid = {5221713}, issn = {0004-2838}, mesh = {Anti-Bacterial Agents/pharmacology ; Dentistry ; Mouth/drug effects ; Saliva ; }, }
@article {pmid5318989, year = {1965}, author = {Jannasch, HW}, title = {Continuous culture in microbial ecology.}, journal = {Laboratory practice}, volume = {14}, number = {10}, pages = {1162-1167}, pmid = {5318989}, issn = {0023-6853}, mesh = {Bacteria/*isolation &amp; purification ; *Bacteriological Techniques ; *Culture Media ; Ecology ; In Vitro Techniques ; }, }